# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Halogeometricum_borinquense_DSM_11551_uid54919/all.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Halogeometricum_borinquense_DSM_11551_uid54919/all.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Halogeometricum_borinquense_DSM_11551_uid54919/all.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|313124789|ref|YP_004035053.1|  [L=347]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-12   46.0   0.0    1.3e-11   44.7   0.0    1.7  1  Rep_fac_C        Replication factor C C-terminal domain
    7.1e-12   45.9   0.0    1.6e-11   44.7   0.0    1.6  1  AAA              ATPase family associated with various cellul
    1.7e-10   41.0   0.0    2.9e-10   40.2   0.0    1.4  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
    3.5e-08   33.8   0.0    1.3e-07   32.0   0.0    1.9  2  AAA_22           AAA domain
      3e-06   27.7   1.3    8.3e-06   26.3   0.0    2.2  2  AAA_16           AAA ATPase domain
    7.5e-05   22.8   0.0     0.0002   21.4   0.0    1.7  1  AAA_14           AAA domain
    0.00014   21.6   0.0     0.0037   17.0   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
    0.00015   22.1   0.8      0.014   15.7   0.0    2.3  2  AAA_19           AAA domain
    0.00019   21.5   0.5     0.0012   18.9   0.1    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00051   20.6   0.0     0.0012   19.3   0.0    1.7  1  AAA_18           AAA domain
      0.001   18.9   0.0     0.0015   18.3   0.0    1.4  1  AAA_11           AAA domain
     0.0019   18.1   0.0      0.008   16.1   0.0    2.0  1  NACHT            NACHT domain
     0.0019   17.9   0.0      0.003   17.3   0.0    1.3  1  AAA_24           AAA domain
     0.0026   17.5   0.0     0.0099   15.6   0.0    1.9  2  IstB_IS21        IstB-like ATP binding protein
      0.007   15.8   0.0      0.013   14.9   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0092   15.9   0.0        3.3    7.6   0.0    2.9  3  NTPase_1         NTPase
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.049   13.4   0.0    1.7  1  AAA_30           AAA domain
      0.035   14.0   0.0      0.064   13.2   0.0    1.4  1  Rad17            Rad17 P-loop domain
      0.042   14.4   0.0       0.12   12.9   0.0    1.9  1  ABC_tran         ABC transporter
      0.061   13.7   0.0       0.26   11.7   0.0    2.0  2  RNA_helicase     RNA helicase
      0.066   12.5   0.0       0.28   10.4   0.0    1.9  2  Zeta_toxin       Zeta toxin
      0.073   13.2   0.1       0.14   12.3   0.1    1.6  1  AAA_33           AAA domain
      0.076   13.3   0.1       0.27   11.4   0.1    2.1  1  AAA_28           AAA domain
      0.079   13.1   0.0       0.19   11.8   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.083   12.9   0.0       0.23   11.4   0.0    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.087   12.7   0.0         20    4.9   0.1    2.6  2  Bac_DnaA         Bacterial dnaA  protein
       0.14   12.5   1.2       0.47   10.8   0.9    2.0  1  AAA_assoc_2      AAA C-terminal domain
       0.15   11.6   0.0       0.27   10.7   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.18   11.5   0.0        0.6    9.9   0.0    1.8  2  DNA_pol3_delta   DNA polymerase III, delta subunit


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   2.1e-14   1.3e-11       2      87 ..     246     332 ..     245     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.1e-14
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS...S-HHHHHHHHHHHHHHHHHHHCTH- CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeq.eelpeaqkleilellgeiekrlveGas 77 
                                       h+++++eile+++ng++++a+k++++ll ++Gy ++++l+ l  +  +  ee+ ea  +++  l+g ++  l+eG +
  gi|313124789|ref|YP_004035053.1| 246 HDDKLKEILETARNGEIRDARKTITTLLDDEGYDGQELLRDLLAIADKYpEEFGEADVMRLHRLAGAVDLDLTEGLD 322
                                       8899*********************999999***************999999***********9************* PP

                                       HHHHHHHHHH CS
                         Rep_fac_C  78 ehlqlsalla 87 
                                       ++l+l+ ll+
  gi|313124789|ref|YP_004035053.1| 323 DRLHLTHLLS 332
                                       *******997 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   2.6e-14   1.6e-11       2     124 ..      37     170 ..      36     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.6e-14
                                       EEESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCSSS..............STTHHHHHHHHHHHHH.HHTS.. CS
                               AAA   2 llyGppGtGKTllakavakelg....vefleisgsellsk..............yvgesekkirelfkea.keka.. 57 
                                       +l GppG+GKT++++a+a++++     +++ei++++++s               + g s +  r++++++ ke+a  
  gi|313124789|ref|YP_004035053.1|  37 VLQGPPGVGKTAAVRALARKSHedpeNDLVEINVADFFSRtkkqirtdprfeqfLTGRSRMAKRDMISRVlKESAgy 113
                                       799*****************95444488**********8889************99999999999999962666699 PP

                                       .....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTS CS
                               AAA  58 .....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRf 124
                                            + + +++D+++ +            e+ +++L +++++  +   ++ ++++t +p kl p+++ +R+
  gi|313124789|ref|YP_004035053.1| 114 apvsgDYKTILLDNAEHIR-----------EDFQQALRRVMEQHHR---TTQFVITTRQPTKLIPPIR-SRC 170
                                       9**96569**********3...........356***********99...477999*************.998 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   4.7e-13   2.9e-10      24     160 ..      38     176 ..      33     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 4.7e-13
                   DNA_pol3_delta2  24 feGdegigkkelalnlakallceeknetkpcgecksckkieqgkhpDviviet.eekersikldqir.elieelsrk 98 
                                       ++G+ g+gk ++  +la++   + +n+  + +  +   + +++   D  + +   +++r  k d i   l+e++   
  gi|313124789|ref|YP_004035053.1|  38 LQGPPGVGKTAAVRALARKSHEDPENDLVEINVADFFSRTKKQIRTDPRFEQFlTGRSRMAKRDMISrVLKESAGYA 114
                                       6778888888888888888777777777766666666666666666665553334444688889997367888999* PP

                   DNA_pol3_delta2  99 preskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfs 160
                                       p+ + +k i++++ae++++  + al +++E  ++ + f+++t++++kl+++irSRc  + ++
  gi|313124789|ref|YP_004035053.1| 115 PVSGDYKTILLDNAEHIREDFQQALRRVMEQHHRTTQFVITTRQPTKLIPPIRSRCFPVPVR 176
                                       ********************************************************998766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.1e-10   1.3e-07       7     126 ..      35     153 ..      30     162 .. 0.81
   2 ?   -2.2   0.0       7.3   4.5e+03      52      70 ..     261     279 ..     229     303 .. 0.56

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.1e-10
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelkaerlsseellea 81 
                                        lv+ G++G+GKT  +r l+++ +e+     ++ ++v+++++     + k+++++   +  l + + r  +++++++
  gi|313124789|ref|YP_004035053.1|  35 NLVLQGPPGVGKTAAVRALARKSHED-----PENDLVEINVADFFsrTKKQIRTDPRFEQFLTGRS-RMAKRDMISR 105
                                       58999*****************9655.....69999999999999999999966544444444444.56999999** PP

                            AAA_22  82 leqalrarav....ielliiDEaqhlrseealeeLrsllnlsrkgvqli 126
                                       + + +  +a      + +++D+a+h+ +e+  + Lr+ ++ ++  +q++
  gi|313124789|ref|YP_004035053.1| 106 VLKESAGYAPvsgdYKTILLDNAEHI-REDFQQALRRVMEQHHRTTQFV 153
                                       ********99****************.8888888888888544444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.3
                            AAA_22  52 sskdllrellralglelka 70 
                                       + +d ++ +   l++e+ +
  gi|313124789|ref|YP_004035053.1| 261 EIRDARKTITTLLDDEGYD 279
                                       4455555555555544443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.3e-08   8.3e-06      12     135 ..      22     148 ..      16     157 .. 0.55
   2 ?   -0.8   0.4       2.8   1.7e+03     118     118 ..     249     249 ..     180     297 .. 0.48

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.3e-08
                            AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslvrellralekd...ggiflrgkcdqlesaipysalaqalareellrql 85 
                                       +++ l+r+  ++p +++l G++GvGK++ vr+l+r   +d   +  +++ +  ++     +s   +++ ++  ++q 
  gi|313124789|ref|YP_004035053.1|  22 VRDRLGRTV-DEPMNLVLQGPPGVGKTAAVRALARKSHEDpenD--LVEINVADF-----FSRTKKQIRTDPRFEQF 90 
                                       566666665.457999******************9988884321..333333333.....34456666666666666 PP

                            AAA_16  86 lde.aesaeleawrekleealaavpelagaea.......srllellkrll.allsrder 135
                                       l+  ++ a+++  ++ l+e+++  ++++g+ +       ++++e ++++l + +++++r
  gi|313124789|ref|YP_004035053.1|  91 LTGrSRMAKRDMISRVLKESAG-YAPVSGDYKtilldnaEHIREDFQQALrRVMEQHHR 148
                                       6662222233333333333333.333444333555666666666666666444444333 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.8
                            AAA_16 118 r 118
                                        
  gi|313124789|ref|YP_004035053.1| 249 K 249
                                       1 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.2e-07    0.0002       5      98 ..      36     155 ..      32     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.2e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikell.vkkesilyinldderd...........kkladpe............kllelil 57 
                                       lv++G+  vGKT  ++ l++++   ++++ ++in+ d                    e            +      
  gi|313124789|ref|YP_004035053.1|  36 LVLQGPPGVGKTAAVRALARKSHeDPENDLVEINVADFFSrtkkqirtdprF-----EqfltgrsrmakrD------ 101
                                       79*******************9998889999999998544333333333330.....13333333333333...... PP

                            AAA_14  58 eklke...............ekktylflDEiqev.pewekalkslvdeg.knldvivt 98 
                                                            + + ++lD + ++ +++++al+++++++ +  ++++t
  gi|313124789|ref|YP_004035053.1| 102 ----MisrvlkesagyapvsGDYKTILLDNAEHIrEDFQQALRRVMEQHhRTTQFVIT 155
                                       ....033333334456778755566********9456**********88677899988 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     6e-06    0.0037      10      61 ..      21      73 ..      15      81 .. 0.87
   2 ?    2.1   0.0      0.22   1.4e+02      95     121 ..     121     147 ..     109     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6e-06
                                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTT.TS-EEEEETTTS CS
                   Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrk.ekpfvavncaai 61
                                      e+++++ ++++ +++++++G  G+GK+   ra+ ++s+++ e+ +v++n+a++
  gi|313124789|ref|YP_004035053.1| 21 EVRDRLGRTVDEPMNLVLQGPPGVGKTAAVRALARKSHEDpENDLVEINVADF 73
                                      6778889999************************9988753789******986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.22
                                       SEEEEETGGGS-HHHHHHHHHHHHHSE CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqege 121
                                        t++LD+ +++  ++Q+ L rv+++++
  gi|313124789|ref|YP_004035053.1| 121 KTILLDNAEHIREDFQQALRRVMEQHH 147
                                       5899*******************9875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-05     0.014      12     130 ..      35     147 ..      28     155 .. 0.81
   2 ?    4.5   0.4     0.066        41      28     122 ..     184     288 ..     179     297 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddllteal 88 
                                       +l++ ++pG GKT  +++  +   e  + ++ ei ++ f +r  k++r+      ++  T  +   ++  d +    
  gi|313124789|ref|YP_004035053.1|  35 NLVLQGPPGVGKTAAVRALARKSHEDPENDLVEINVADFFSRTKKQIRTDP--RFEQFLTGRSR--MAKRDMI---S 104
                                       67899******************************************9876..55666776655..4555555...5 PP

                            AAA_19  89 elleeaeeekklqeee.llivDEfqdvdelqyrLlkallgekk 130
                                        +l+e++   ++   + +++ D +  + e  ++ l++++++++
  gi|313124789|ref|YP_004035053.1| 105 RVLKESAGYAPVSGDYkTILLDNAEHIREDFQQALRRVMEQHH 147
                                       6778888889997777899999999999888888888886665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.066
                            AAA_19  28 khivallvelggvkpeeillvaftgrAakelrerlaalgae............atTiHrlalldfddlltealelle 92 
                                       ++i++ + e+++v+ +e++l   +++A  +lre++ a++ +            a+T    ++++ dd+l+e le  +
  gi|313124789|ref|YP_004035053.1| 184 EAILSDIAEAEDVAYDEMALNIIASKADGNLREAILAAQSAavegddeitmesAQTAL--SEVGHDDKLKEILETAR 258
                                       56666777888888899999999**********9955555599999999988777755..55999999977777744 PP

                            AAA_19  93 eaeeekklqeee.llivDEfqdvdelqyrLl 122
                                       +  e ++ +++  +l+ DE  d +el   Ll
  gi|313124789|ref|YP_004035053.1| 259 N-GEIRDARKTItTLLDDEGYDGQELLRDLL 288
                                       2.22233333344777777777666666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.9e-06    0.0012       1      95 [.      35     149 ..      35     164 .. 0.78
   2 ?   -1.1   0.0       2.9   1.8e+03      60      80 ..     218     238 ..     191     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
                                       EEEEE--SSSSHHHHHHHGGGGB....S--EEEEE--TT--HHHHH--B--...................------- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal....nreveyvqltrdtteedlkgrreik..........ngttslvdsplvraa 63 
                                       +++L+GppG+gK+  ++ la+      ++ +++++  ++ ++++ + r++++          + ++ +   +l+++a
  gi|313124789|ref|YP_004035053.1|  35 NLVLQGPPGVGKTAAVRALARKShedpENDLVEINVADFFSRTKKQIRTDPRfeqfltgrsrMAKRDMISRVLKESA 111
                                       689*******************9999977788888888777776666666666677744444555555555555555 PP

                                       -......G-SEEEEESGGG--HHHHHHHHHHHHSSEEE CS
                             AAA_5  64 r......egeilvlDEveraesevlnsLlslleerrll 95 
                                                ++++lD  e+++ + +++L +++e+ ++ 
  gi|313124789|ref|YP_004035053.1| 112 GyapvsgDYKTILLDNAEHIREDFQQALRRVMEQHHRT 149
                                       59999888899999999999999999999999998876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.9
                                       -----G-SEEEEESGGG--HH CS
                             AAA_5  60 vraaregeilvlDEveraese 80 
                                         aa+++++  +DE+++ + +
  gi|313124789|ref|YP_004035053.1| 218 ILAAQSAAVEGDDEITMESAQ 238
                                       235668888888888864433 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     2e-06    0.0012       3      81 ..      38     127 ..      36     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpe....aldeskrldedkldklldaleen 67 
                                       l G+pGvGKt   ++L+++            +n+ d ++     +  dp      + +s+ +++d+  ++l++  + 
  gi|313124789|ref|YP_004035053.1|  38 LQGPPGVGKTAAVRALARKS-HedpendlvEINVADFFSRTKKQIRTDPRfeqfLTGRSRMAKRDMISRVLKESAGY 113
                                       78**************9993.24567777866666666666666666666655577777777777777777777776 PP

                            AAA_18  68 ssaleegknlvidg 81 
                                       +  +++ k++++d 
  gi|313124789|ref|YP_004035053.1| 114 APVSGDYKTILLDN 127
                                       66888888888885 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.5e-06    0.0015      10     108 ..      26     139 ..      19     277 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.5e-06
                            AAA_11  10 iksalseseitliqGPPGtgKTktivellsqllsr................rkseeeksakpriLvCapSNaAvDel 70 
                                       + +++ e+   ++qGPPG gKT ++ +l ++ ++                 +k++ + ++  +  +++ S  A  ++
  gi|313124789|ref|YP_004035053.1|  26 LGRTVDEPMNLVLQGPPGVGKTAAVRALARKSHEDpendlveinvadffsrTKKQIRTDPRFEQFLTGRSRMAKRDM 102
                                       5667777888899*******************933444555555555554344566666666778899999999999 PP

                            AAA_11  71 lerllrglldsegekykpkivRvgneeeriseavksvs 108
                                       ++r+l++       + + k++ + n+e +i+e+ ++  
  gi|313124789|ref|YP_004035053.1| 103 ISRVLKESAGYAPVSGDYKTILLDNAE-HIREDFQQAL 139
                                       999999555555556666777777777.5666666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-05     0.008       3     128 ..      36     157 ..      35     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCS CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllel 79 
                                       ++lqG++G+GKT+ ++ la++  e+  +      v  +++r+ +++ + +++ ++l+      +++       ++  
  gi|313124789|ref|YP_004035053.1|  36 LVLQGPPGVGKTAAVRALARKSHEDPENDLVEINVADFFSRTKKQIRTDPRFEQFLTGRSRMAKRDMIS----RVLK 108
                                       689*****************9888776665433344444555555554479999998765443333322....3444 PP

                                       CCCEE.........EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEE CS
                             NACHT  80 perlL.........lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvr 128
                                       +             ++lD ++ +++d++q         L++ +++ + +++ +++t+r
  gi|313124789|ref|YP_004035053.1| 109 ESAGYapvsgdyktILLDNAEHIREDFQQ--------ALRRVMEQ-HHRTTQFVITTR 157
                                       44444568889999999999999999999........77777777.555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.9e-06     0.003       3      90 ..      34     144 ..      32     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-06
                            AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel.................... 59 
                                       +++++ Gp+g+GKT  ++ l  +    d e+ l ++++++f         ++++ ++                    
  gi|313124789|ref|YP_004035053.1|  34 MNLVLQGPPGVGKTAAVRAL-ARKSHEDPENDLVEINVADFF-----SRTKKQIRTDprfeqfltgrsrmakrdmis 104
                                       6899****************.777777777777666666664.....333333333333334444444445556666 PP

                            AAA_24  60 .........aaeladyktlviDtideleelclaevirqne 90 
                                                a    dykt+ +D+++++ e   + ++r  e
  gi|313124789|ref|YP_004035053.1| 105 rvlkesagyAPVSGDYKTILLDNAEHIREDFQQALRRVME 144
                                       67777888899999*************9988887776555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05    0.0099      44     104 ..      30      92 ..      17     134 .. 0.70
   2 ?   -1.2   0.0       2.3   1.5e+03     121     150 ..     130     159 ..     117     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavr.aglsvlfvrvedLveelkra.rrdgklaralk 104
                                       +++  n+vl Gp+GvGK+    al+++  +  +   + + v+d++++ k++ r+d ++++ l+
  gi|313124789|ref|YP_004035053.1|  30 VDEPMNLVLQGPPGVGKTAAVRALARKSHEdPENDLVEINVADFFSRTKKQiRTDPRFEQFLT 92 
                                       67788*********************9998445566667788877665543266666666654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.3
                         IstB_IS21 121 pldqaeaellfeviekryerrsiiitsnlp 150
                                       ++ ++ ++ l +v+e+   ++  +it+ +p
  gi|313124789|ref|YP_004035053.1| 130 HIREDFQQALRRVMEQHHRTTQFVITTRQP 159
                                       456677788999999999999999999887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.1e-05     0.013      24     134 ..      35     147 ..      19     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasvag.kkeeekllkrrpfraphhsaskaalvGggskpkp 99 
                                       nl+l GppG GKt   ++l+    +  e++ +e++     ++ kk+ ++  +   f + +  ++k  ++    k   
  gi|313124789|ref|YP_004035053.1|  35 NLVLQGPPGVGKTAAVRALARKSHEDPENDLVEINVADFFSRtKKQIRTDPRFEQFLTGRSRMAKRDMISRVLKESA 111
                                       89*****************9999999999999988777666633444555566678888888889999999888888 PP

                      Mg_chelatase 100 Geisla.hnGvLfLDElpefkrkvlevLRePledge 134
                                       G    +     ++LD + +++++  ++LR+ +e+++
  gi|313124789|ref|YP_004035053.1| 112 GYAPVSgDYKTILLDNAEHIREDFQQALRRVMEQHH 147
                                       86544313445679****************999875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0054       3.3       2      22 ..      36      56 ..      35      62 .. 0.85
   2 ?   -1.0   0.0       2.3   1.4e+03       3      22 ..      90     109 ..      88     120 .. 0.85
   3 ?    4.7   0.0     0.042        26     108     147 ..     129     169 ..     127     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0054
                                      EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlel 22
                                      +++ GppGvGKt  v+ ++++
  gi|313124789|ref|YP_004035053.1| 36 LVLQGPPGVGKTAAVRALARK 56
                                      7899*********99988876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                                       EEE--TTSSHHHHHHHHHHH CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlel 22 
                                       f+TG++ + K  ++++vl++
  gi|313124789|ref|YP_004035053.1|  90 FLTGRSRMAKRDMISRVLKE 109
                                       89*************99976 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.042
                                       GGG-HHHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT- CS
                          NTPase_1 108 ElkskkfkeaveevLk.sekpvlavihrrkdlalveeirer 147
                                       E   + f++a+++v++ +++   +vi  r++ +l+  ir+r
  gi|313124789|ref|YP_004035053.1| 129 EHIREDFQQALRRVMEqHHRTTQFVITTRQPTKLIPPIRSR 169
                                       556789**********8888889999999999999999987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.9e-05     0.049      21      45 ..      36      60 ..      25     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-05
                            AAA_30 21 avltGpAGtGKttalkalreaweaa 45
                                       vl+Gp+G GKt a++al++  +++
  gi|313124789|ref|YP_004035053.1| 36 LVLQGPPGVGKTAAVRALARKSHED 60
                                      689***************6554444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.064      48     157 ..      36     144 ..      13     160 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakylklqk 124
                                       L++ GP+G gk+ +v+ L+++   + ++ l  ++       + df + t+k+ r  ++ e f     + ak  ++++
  gi|313124789|ref|YP_004035053.1|  36 LVLQGPPGVGKTAAVRALARKSHEDPENDLVEIN-------VADFFSRTKKQIRTDPRFEQFLTGRSRMAKRDMISR 105
                                       889****************987766666555555.......334444444443333333333333333333333332 PP

                             Rad17 125 lGdd......lrtdkklilvedlPnkfyrds.dalrevir 157
                                         ++      + +d k il+++       d  +alr v+ 
  gi|313124789|ref|YP_004035053.1| 106 VLKEsagyapVSGDYKTILLDNAEH-IREDFqQALRRVME 144
                                       2222111111567888888876542.22232244555544 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00019      0.12      10      67 ..      32      87 ..      24     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                                      TTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 10 egekvaivGenGaGKStLlkllagllkp..teGeilldgkdlkeqeleslrkeigvlpqe 67
                                      e   +++ G+ G GK+  +++la++++   +++ ++++ +d+ +    +++k+i++ p  
  gi|313124789|ref|YP_004035053.1| 32 EPMNLVLQGPPGVGKTAAVRALARKSHEdpENDLVEINVADFFS----RTKKQIRTDPRF 87
                                      55678999***************987653388888888777766....444444443333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00043      0.26       2      25 ..      37      60 ..      36      83 .. 0.74
   2 ?   -1.7   0.0         6   3.7e+03      10      60 ..      93     137 ..      92     165 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00043
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkk 25
                                      +l+Gp+g+GK+ +++ La++  ++
  gi|313124789|ref|YP_004035053.1| 37 VLQGPPGVGKTAAVRALARKSHED 60
                                      799*************99887633 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6
                      RNA_helicase  10 GKStlake.LakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgq 60 
                                       G S++ak+ +++++lk+      +  y  +++ d+     +++ ++ +Df q
  gi|313124789|ref|YP_004035053.1|  93 GRSRMAKRdMISRVLKE------SAGY-APVSGDYKTILLDNAEHIREDFQQ 137
                                       66777776333333322......2222.244444444445555555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00045      0.28      13      52 ..      30      71 ..      20      80 .. 0.83
   2 ?   -1.1   0.0       1.5   9.4e+02     152     184 ..     121     154 ..      90     164 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                        Zeta_toxin 13 qerPklillgGqpGAGKselaellkdele..rqgnvvrldpD 52
                                       ++P  ++l G pG GK+++ ++l+++ +  ++++ v+++  
  gi|313124789|ref|YP_004035053.1| 30 VDEPMNLVLQGPPGVGKTAAVRALARKSHedPENDLVEINVA 71
                                      478999****************99998876788888888865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                        Zeta_toxin 152 Rlvpkeehdeafeglresvealeeek.qldrvki 184
                                         +  ++ + + e ++++++++ e++ ++ + +i
  gi|313124789|ref|YP_004035053.1| 121 KTILLDNAEHIREDFQQALRRVMEQHhRTTQFVI 154
                                       4444445555555555555555444434444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00022      0.14       3      40 ..      37      80 ..      36     193 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                            AAA_33  3 llvGlpGsGKstlaerllkklg......avllssdtlrrrlfgt 40
                                      +l G+pG+GK+  ++ l++k +       v ++  ++++r +++
  gi|313124789|ref|YP_004035053.1| 37 VLQGPPGVGKTAAVRALARKSHedpendLVEINVADFFSRTKKQ 80
                                      678***************99887777655556666655555553 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00044      0.27       2      24 ..      36      58 ..      35     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                            AAA_28  2 ivitGgestGKTtlleaLaargy 24
                                       v+ G+++ GKT  ++aLa++ +
  gi|313124789|ref|YP_004035053.1| 36 LVLQGPPGVGKTAAVRALARKSH 58
                                      5899***************7633 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00031      0.19       4     105 ..      34     145 ..      31     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                                       --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.......... CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.......... 70 
                                       +++ l gp gvGkt + +ala+  + + e+ l+ ++  ++      ++ +  +   +++ +g+              
  gi|313124789|ref|YP_004035053.1|  34 MNLVLQGPPGVGKTAAVRALARKSHEDPENDLVEINVADFFS--RTKKQIRTDPRFEQFLTGRSRMAkrdmisrvlk 108
                                       68899*******************986666777777666666..555556555555555555555555556666666 PP

                                       .............EEEEETGGG-------------HHHHHHHHHHHH- CS
                             AAA_2  71 .............ivllDEidKihpkessgadvSregVqrdLLqileg 105
                                                     +llD+ + i +           + q++L +++e+
  gi|313124789|ref|YP_004035053.1| 109 esagyapvsgdykTILLDNAEHIRE-----------DFQQALRRVMEQ 145
                                       6666666666668999999999988...........888888888886 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00038      0.23       9      43 ..      25      57 ..      17      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                                      HHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  9 algkklakalgdvilLeGdLGaGKTtlvrglakal 43
                                      +lg+++ +     ++L+G+ G+GKT+ vr+la++ 
  gi|313124789|ref|YP_004035053.1| 25 RLGRTVDE--PMNLVLQGPPGVGKTAAVRALARKS 57
                                      34444433..4569*****************9975 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.034        21      37      90 ..      36      89 ..      22     106 .. 0.73
   2 ?    4.9   0.1     0.032        20     114     204 ..     130     216 ..     120     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.034
                                      EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHT.T-HHH CS
                          Bac_DnaA 37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrd.kkaee 90
                                      l++ g+ G+Gkt  ++a++ +  e+ ++  v  ++  +F ++  k +r+  + e+
  gi|313124789|ref|YP_004035053.1| 36 LVLQGPPGVGKTAAVRALARKSHEDPENDLV-EINVADFFSRTKKQIRTdPRFEQ 89
                                      678899*************998877665555.55655666666666665244555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHTTT-...EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT---- CS
                          Bac_DnaA 114 ktqeelfhtfnalleegk...qvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklevp 187
                                       +++e++ + +  ++e+++   q v+++ r+P++l      +rsr    + v +  p ++   ail   +eae++   
  gi|313124789|ref|YP_004035053.1| 130 HIREDFQQALRRVMEQHHrttQFVITT-RQPTKLI---PPIRSR---CFPVPVRAPSTDETEAILSDIAEAEDVAYD 199
                                       555555555555555443111445544.4444332...334444...356788899999999*************** PP

                                       TTHHHHHHHH--S-HHH CS
                          Bac_DnaA 188 eevlefiaervtdnvRe 204
                                       e +l+ ia++ + n+Re
  gi|313124789|ref|YP_004035053.1| 200 EMALNIIASKADGNLRE 216
                                       ****************8 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9   0.00076      0.47       3      56 ..     194     242 ..     192     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00076
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledleealq 56 
                                       +++++++ al+ +a+ adG  R a+ + + aa        + eit e +++al+
  gi|313124789|ref|YP_004035053.1| 194 EDVAYDEMALNIIASKADGNLREAILAAQSAAVEG-----DDEITMESAQTALS 242
                                       57899*******************98888666554.....56777777777764 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00043      0.27      30      68 ..      30      69 ..      23      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                             AAA_7 30 lknkkpvllvGptGtGKtviikdllkkld.kekylsltin 68
                                      +++ ++++l Gp G+GKt+ ++ l +k + + +   + in
  gi|313124789|ref|YP_004035053.1| 30 VDEPMNLVLQGPPGVGKTAAVRALARKSHeDPENDLVEIN 69
                                      56678899***************77766513344444444 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00097       0.6      55     164 ..     117     216 ..      98     221 .. 0.91
   2 ?   -2.6   0.0       6.5     4e+03       5      24 ..     228     247 ..     226     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00097
                                       SSSEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTH CS
                    DNA_pol3_delta  55 fsdkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeel 131
                                        +d ++++l+n+     e    e+ +++L +++++ + +t ++++++    + +kl+  + ++   v +  ++++e+
  gi|313124789|ref|YP_004035053.1| 117 SGDYKTILLDNA-----EH-IREDFQQALRRVMEQHHRTTQFVITTR----QPTKLIPPIRSRCFPVPVRAPSTDET 183
                                       578899999999.....44.89999*********************9....566899999999999*********** PP

                                       HHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHH CS
                    DNA_pol3_delta 132 kkwiqkraqelglkiekealelLlelvennlsa 164
                                          ++++a+++ +  ++ al+ ++++  +nl+ 
  gi|313124789|ref|YP_004035053.1| 184 EAILSDIAEAEDVAYDEMALNIIASKADGNLRE 216
                                       ******************************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.5
                                       ES-HHHHHHHHHHHHHHHHT CS
                    DNA_pol3_delta   5 Gedellleeskdqilkqalk 24 
                                       G+de ++e++++++ ++  +
  gi|313124789|ref|YP_004035053.1| 228 GDDEITMESAQTALSEVGHD 247
                                       99999999999999877444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.66u 0.38s 00:00:01.04 Elapsed: 00:00:00.66
# Mc/sec: 1588.89
//
Query:       gi|313124790|ref|YP_004035054.1|  [L=216]
Description: phosphatidylserine decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-25   89.3   0.0    2.1e-20   73.2   0.0    2.0  2  PS_Dcarbxylase  Phosphatidylserine decarboxylase


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   9.7e-07     0.017       4      35 ..      53      82 ..      51      88 .. 0.80
   2 !   73.2   0.0   1.1e-24   2.1e-20      71     199 ..      88     211 ..      82     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.7e-07
                    PS_Dcarbxylase  4 ffvrklkdgaRpidddpgaivsPaDgrilqig 35
                                      f+ ++++d++R + + +g i+sPaDgr++ ++
  gi|313124790|ref|YP_004035054.1| 53 FVLWFFRDPERRP-SAQG-IISPADGRVSVVR 82
                                      899******8777.3444.*********9884 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 1.1e-24
                    PS_Dcarbxylase  71 yfvviyLspgdyHryhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlview.kGkvavvpvGatnvgs 146
                                       + + ++++++d+H+++aP + +ve+++h  G+    +p++ ke+     +neRv + +++ +G   +  ++++++++
  gi|313124790|ref|YP_004035054.1|  88 IRIGVFMNVTDVHVNRAPFDATVERVTHRSGA---HRPAFSKES----ERNERVDVALQTpEGPAELSLIAGAFARR 157
                                       67899***************************...788888888....889********658*************** PP

                    PS_Dcarbxylase 147 ivlnvlkgdelkkGeelGyFqfGStvvlvfeag.kfieslvekgqkvkmGeklg 199
                                       i+ ++ ++del +Ge++G++ fGS+ ++++++  +  + lve+g+ +++Ge+++
  gi|313124790|ref|YP_004035054.1| 158 IHPYIAENDELARGERIGHIDFGSRADVLLPPCyDRSDLLVEEGDTLRAGESVV 211
                                       *******************************887778899***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1536.82
//
Query:       gi|313124791|ref|YP_004035055.1|  [L=73]
Description: hypothetical protein Hbor_00030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.081   13.0   0.5      0.081   13.0   0.5    1.9  2  MitoNEET_N  Iron-containing outer mitochondrial membrane prot
       0.13   11.6   0.0       0.14   11.4   0.0    1.0  1  Fumerase_C  Fumarase C-terminus


Domain annotation for each model (and alignments):
>> MitoNEET_N  Iron-containing outer mitochondrial membrane protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5     9e-06     0.081      39      58 ..      22      41 ..      16      46 .. 0.89
   2 ?   -0.1   0.2      0.11   9.5e+02      43      50 ..      45      52 ..      40      68 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9e-06
                        MitoNEET_N 39 lvpfaavtaalgYlaykafl 58
                                      lv+++a  +algYl+y  +l
  gi|313124791|ref|YP_004035055.1| 22 LVVLLACCGALGYLTYESLL 41
                                      9***************9876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                        MitoNEET_N 43 aavtaalg 50
                                      +a++aa+g
  gi|313124791|ref|YP_004035055.1| 45 TAFLAAVG 52
                                      55555554 PP

>> Fumerase_C  Fumarase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.6e-05      0.14     114     164 ..      10      62 ..       5      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.6e-05
                        Fumerase_C 114 dkyvekllkktgllimlaK.gnrskkvleaikkhggvYLgaiGG.aAilakka 164
                                       d++ +  l+ + l++ la  g  +  + e++ ++ +++L a+GG aA +++  
  gi|313124791|ref|YP_004035055.1|  10 DTFLKGALNLETLVVLLACcGALGYLTYESLLSTTTAFLAAVGGgAAGIVATV 62 
                                       7788888888888888875267899999****************888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 537.30
//
Query:       gi|313124792|ref|YP_004035056.1|  [L=129]
Description: hypothetical protein Hbor_00040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.48   10.1   4.4       0.46   10.2   1.5    1.9  2  Orai-1    Mediator of CRAC channel activity


Domain annotation for each model (and alignments):
>> Orai-1  Mediator of CRAC channel activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5   2.6e-05      0.46      22      74 ..      19      73 ..      16      80 .. 0.81
   2 ?    0.7   0.1      0.02   3.6e+02      66      84 ..      96     114 ..      88     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.6e-05
                            Orai-1 22 tsALlsgFamvamvelqlkeseekeee..isealliafsvvtavlvavhllalli 74
                                      ++ALls Fa+  ++ l+++ s e+++   i + ll  f+ +  + va+++l  li
  gi|313124792|ref|YP_004035056.1| 19 LTALLSRFAVHRFIKLSTSGSGESDSVaaIASFLLSSFADLVGLSVALFVLVCLI 73
                                      68***************98776554433499999*********999998765444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.02
                            Orai-1  66 avhllallistliLpniea 84 
                                       +vhl+ ++ +tl+ +++ a
  gi|313124792|ref|YP_004035056.1|  96 VVHLVGTMFTTLLVVSVPA 114
                                       6899999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 922.68
//
Query:       gi|313124793|ref|YP_004035057.1|  [L=374]
Description: n2-methylguanosine tRNA methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-19   70.7   0.1    1.1e-18   67.7   0.1    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    1.5e-06   28.8   0.1    3.3e-06   27.7   0.1    1.6  1  Methyltransf_25  Methyltransferase domain
    2.7e-05   24.3   0.0    4.3e-05   23.6   0.0    1.3  1  THUMP            THUMP domain
    0.00016   22.2   0.0    0.00037   21.1   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
      0.003   17.2   0.0     0.0046   16.6   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.046   13.5   0.0      0.069   12.9   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
       0.26   10.8   0.0       0.36   10.4   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.1   4.3e-22   1.1e-18       3     154 ..     200     328 ..     198     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 4.3e-22
                                       SS-SS---SS-HHHHHHHHHHTT-..-TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH- CS
                           UPF0020   3 yRefngpapLketLAaalvrlagw..kpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearael 77 
                                        R+f++p+++ +  A+a v+la     p+ + +DPmCG+G+ilIEa+l+ga+ +                       
  gi|313124793|ref|YP_004035057.1| 200 DRPFFQPGSMDPLDARAYVNLAAGpdLPDATVVDPMCGTGGILIEAGLVGARGV----------------------- 253
                                       69*******************8642258*************************9....................... PP

                                       -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHHHH CS
                           UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflrelk 153
                                          g D ++++ +gareN+ ++  + +++++  da++L+l ++  d++v + PYG+  + ++    +L    l e++
  gi|313124793|ref|YP_004035057.1| 254 ---GNDAQSKMARGARENLTAYLPDAEWDVVRGDATSLPLCDDAADAVVFDAPYGRQSKIARHElSDLVGGALAEAA 327
                                       ...************************************99999***********9866554332555544444444 PP

                                       H CS
                           UPF0020 154 r 154
                                       r
  gi|313124793|ref|YP_004035057.1| 328 R 328
                                       4 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   1.3e-09   3.3e-06       1      70 [.     231     300 ..     231     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.3e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvs 70 
                                       v+d  cGtG +++++    g a+ +g D +++m + are++ +  +  ++++v+gda++lp+ d+  D+vv 
  gi|313124793|ref|YP_004035057.1| 231 VVDPMCGTGGILIEAGLV-G-ARGVGNDAQSKMARGARENLTAYLPdaEWDVVRGDATSLPLCDDAADAVVF 300
                                       78999*********9865.6.********************98555558889******************97 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.7e-08   4.3e-05      62     141 ..     106     183 ..      53     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.7e-08
                                       SSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEE CS
                             THUMP  62 adledileaakeivkkkfeeeketFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdka 138
                                       ++  d++ a+  +    f  e+ + aVr + +++   +++   +r++G+ +v+++  +Vdl++Pd v+r+ + +d++
  gi|313124793|ref|YP_004035057.1| 106 RTDADVESAVALLSAASFDREG-SVAVRGRDVRSSSGVSASAAERALGGVLVDRGF-EVDLDDPDHVLRALFADDTC 180
                                       5556666666666666666655.***********99********************.******************99 PP

                                       EEE CS
                             THUMP 139 yis 141
                                       +++
  gi|313124793|ref|YP_004035057.1| 181 LLG 183
                                       987 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.5e-07   0.00037       2      87 ..     233     329 ..     232     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES....... CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvsse....... 69 
                                       d  cGtG ++ +    gar vg D   +m + a+e+     +  + ++v++da++lp+ d+  D+vv          
  gi|313124793|ref|YP_004035057.1| 233 DPMCGTGGILIEAGLVGARGVGNDAQSKMARGARENLTAYLPdaEWDVVRGDATSLPLCDDAADAVVFDApygrqsk 309
                                       556**********9999*****************99998777887899******************98765555555 PP

                                       .-CCC-.CCHHHHHHHHHHH CS
                   Methyltransf_11  70 .vlhhv.edpekalkeiaRv 87 
                                        + h + + +  al+e+aRv
  gi|313124793|ref|YP_004035057.1| 310 iARHELsDLVGGALAEAARV 329
                                       44444445555566666665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-06    0.0046      38     129 ..     224     310 ..     215     350 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                                       CCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EE CS
                     Cons_hypoth95  38 aeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeef 114
                                       +++ +a+v+D  +G+G++ +EA   ga + v  + ++++++  +enl +   ++e+++++ da++  l         
  gi|313124793|ref|YP_004035057.1| 224 PDLPDATVVDPMCGTGGILIEAGLVGA-RGVGNDAQSKMARGARENLTAYLPDAEWDVVRGDATSLPLCD----DAA 295
                                       568999****************99996.567789999999999*****999888*********9998777....457 PP

                                       EEEEE--SSSTTCH. CS
                     Cons_hypoth95 115 divflDPPyakelli 129
                                       d v +D Py ++  i
  gi|313124793|ref|YP_004035057.1| 296 DAVVFDAPYGRQSKI 310
                                       99*******998763 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.7e-05     0.069       5      84 ..     229     304 ..     226     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                        +v+D+ CGtG +++e+  ++g  a+ vG D + ++ + Aren+     d +  + +gd+++l+  l+d+  D ++ 
  gi|313124793|ref|YP_004035057.1| 229 ATVVDPMCGTGGILIEAG-LVG--ARGVGNDAQSKMARGARENLTAYLPDaEWDVVRGDATSLP--LCDDAADAVVF 300
                                       689**************9.775..7889***************99888888999999*******..9********99 PP

                   Methyltransf_31  81 nevl 84 
                                       +++ 
  gi|313124793|ref|YP_004035057.1| 301 DAPY 304
                                       9665 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00014      0.36       3      61 ..     230     288 ..     228     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfel 61 
                                       +++D+++G+GG  i+  lv+ + ++ + + +    a +N  +Y  + + ++v gd ++l
  gi|313124793|ref|YP_004035057.1| 230 TVVDPMCGTGGILIEAGLVGARGVGNDAQSKMARGARENLTAYLPDAEWDVVRGDATSL 288
                                       689****************************************8899999999998773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2578.87
//
Query:       gi|313124794|ref|YP_004035058.1|  [L=119]
Description: hypothetical protein Hbor_00060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.6   0.1      0.092   12.8   0.0    1.5  1  DUF2784   Protein of Unknown function (DUF2784)


Domain annotation for each model (and alignments):
>> DUF2784  Protein of Unknown function (DUF2784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.1e-06     0.092      36     107 ..      18      84 ..       4      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.1e-06
                           DUF2784  36 laaialvaasellglaCplTdlenqlreaageaaleegFiehylekllyldlpeelttavqlllallvlllw 107
                                       l a+++v+a+ ++g+   +T++  + r  a e++    F+ ++ +++    +p+  ++a++++++++ ++ +
  gi|313124794|ref|YP_004035058.1|  18 LDAVLWVIAVIFYGIGDYVTTIAATSRPGARERN---PFVRRLFDGIPV--PPSMTFAAAKVTAFAFFVVGY 84 
                                       6799************************999996...9*********99..888899999998888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 803.33
//
Query:       gi|313124795|ref|YP_004035059.1|  [L=187]
Description: tata binding protein of transcription factor tfiid [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-56  186.8   0.0    1.5e-27   95.3   0.0    2.0  2  TBP         Transcription factor TFIID (or TATA-binding prote
    0.00024   21.2   0.0       0.43   10.7   0.0    2.2  2  DUF3378     Domain of unknown function (DUF3378)
    0.00039   20.7   0.0       0.04   14.2   0.0    2.2  2  T4bSS_IcmS  Type IVb secretion, IcmS, effector-recruitment
  ------ inclusion threshold ------
      0.034   14.4   0.0        2.3    8.5   0.0    2.4  2  PucR        Purine catabolism regulatory protein-like family
      0.089   12.8   0.0        0.7    9.9   0.0    2.0  2  DUF218      DUF218 domain


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   0.0   4.3e-31   1.5e-27       2      84 ..       8      88 ..       7      89 .. 0.97
   2 !   89.9   0.0   2.2e-29   7.7e-26       1      84 [.      98     181 ..      98     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 4.3e-31
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++i+Nvvas+ +g+eldL+ +a+++  ++a Y+pe+fpglvyr +epk +aliF+sGk+v+tGaks+++++e ++ +++
  gi|313124795|ref|YP_004035059.1|  8 INIENVVASTGIGQELDLQSVAMDL--EGADYDPEQFPGLVYRTQEPKSAALIFRSGKIVCTGAKSTDDVHESLNLVFD 84
                                      79********************998..***************************************************9 PP

                                      HHHH CS
                               TBP 81 ilkk 84
                                      +l+ 
  gi|313124795|ref|YP_004035059.1| 85 KLRA 88
                                      9985 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 2.2e-29
                                       EEEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHH CS
                               TBP   1 dfkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakk 77 
                                       d+++qN+v sa+lg +l+L+++a  +  +n+eYepe+fpglvyrl++p v+al+F sGk+vitG k +++++ a+++
  gi|313124795|ref|YP_004035059.1|  98 DITVQNIVTSADLGRNLNLNAIAIGLGLENIEYEPEQFPGLVYRLDSPDVVALLFGSGKLVITGGKHPSDAEGAVDE 174
                                       689********************99779************************************************* PP

                                       HHHHHHH CS
                               TBP  78 iapilkk 84 
                                       i+  l++
  gi|313124795|ref|YP_004035059.1| 175 IVSRLSD 181
                                       **99875 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00065       2.3      24      56 ..      39      71 ..      25      77 .. 0.87
   2 !   10.7   0.0   0.00012      0.43      24      60 ..     132     168 ..     127     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00065
                           DUF3378 24 skkppyavfaakkndttItaYtSgKVlFQGkna 56
                                       ++ p+ v++ ++++    +++SgK++  G++ 
  gi|313124795|ref|YP_004035059.1| 39 PEQFPGLVYRTQEPKSAALIFRSGKIVCTGAKS 71
                                      5689***********************999875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeaeA 60 
                                        ++ p+ v++ +++d++  ++ SgK+++ G +  ++A
  gi|313124795|ref|YP_004035059.1| 132 PEQFPGLVYRLDSPDVVALLFGSGKLVITGGKHPSDA 168
                                       5789************************998876666 PP

>> T4bSS_IcmS  Type IVb secretion, IcmS, effector-recruitment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.1e-05      0.04      12      68 ..      17      73 ..       5      92 .. 0.77
   2 ?    4.6   0.0     0.011        40      12      59 ..     108     157 ..      97     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                        T4bSS_IcmS 12 eeadddfdddasaisaeeveedtglleqliraadqlaSlaLffglkatvekaevall 68
                                        ++++ d++  a+  e  + d ++ ++l+ ++++ +S+aL f+ ++ v     ++ 
  gi|313124795|ref|YP_004035059.1| 17 TGIGQELDLQSVAMDLEGADYDPEQFPGLVYRTQEPKSAALIFRSGKIVCTGAKSTD 73
                                      44788888899999999999************************9988765555543 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                        T4bSS_IcmS  12 eeadddfdddasai..saeeveedtglleqliraadqlaSlaLffglkat 59 
                                       ++++ + +++a ai    e++e + ++ ++l+ + d    +aL fg ++ 
  gi|313124795|ref|YP_004035059.1| 108 ADLGRNLNLNAIAIglGLENIEYEPEQFPGLVYRLDSPDVVALLFGSGKL 157
                                       5566666667666522579***************************9875 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.015        55      53      80 ..      36      63 ..       2      92 .. 0.75
   2 ?    8.5   0.0   0.00064       2.3      27      71 ..     139     184 ..     103     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                              PucR 53 kddpealaelvrelaeagvaaLviklgr 80
                                      + dpe++  lv + +e + aaL++  g+
  gi|313124795|ref|YP_004035059.1| 36 DYDPEQFPGLVYRTQEPKSAALIFRSGK 63
                                      4599*******************99983 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00064
                              PucR  27 vhvlevpdiaell.rggeLllttglalkddpealaelvrelaeagv 71 
                                       v+ l+ pd+++ll   g L++t g + +d + a+ e+v +l++ g+
  gi|313124795|ref|YP_004035059.1| 139 VYRLDSPDVVALLfGSGKLVITGGKHPSDAEGAVDEIVSRLSDLGL 184
                                       56689999965553788899999999999999*********99887 PP

>> DUF218  DUF218 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0002       0.7      19      79 ..      54     110 ..      32     122 .. 0.82
   2 ?    0.9   0.0      0.12   4.4e+02      21      44 ..     149     169 ..     118     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0002
                            DUF218  19 eaaelyragkiivsGg.gadedvseaeamaeylrelgvpeeailledrsrnTeenarfskel 79 
                                        aa ++r gki+++G  ++d+ ++  +++ + lr+l++p     ++d+   T +n++ s++l
  gi|313124795|ref|YP_004035059.1|  54 SAALIFRSGKIVCTGAkSTDDVHESLNLVFDKLRALQIP-----VDDEPDITVQNIVTSADL 110
                                       6888999*********5444555567889999*******.....799999999999999887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                            DUF218  21 aelyragkiivsGggadedvseae 44 
                                       a l+  gk++++Gg+   ++s+ae
  gi|313124795|ref|YP_004035059.1| 149 ALLFGSGKLVITGGK---HPSDAE 169
                                       456667799****94...344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1300.46
//
Query:       gi|313124796|ref|YP_004035060.1|  [L=127]
Description: hypothetical protein Hbor_00080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 887.10
//
Query:       gi|313124797|ref|YP_004035061.1|  [L=316]
Description: caax amino terminal protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-09   36.7  25.7    8.2e-08   32.5  22.0    3.5  2  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
        0.6    9.9   7.7      0.073   12.9   2.1    2.1  2  Amastin   Amastin surface glycoprotein
        2.1    8.1   5.0       0.68    9.7   1.5    2.1  2  DUF3094   Protein of unknown function (DUF3094)


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5  22.0   1.4e-11   8.2e-08       7      91 ..     140     236 ..       5     237 .. 0.92
   2 ?    0.4   0.1      0.14   8.4e+02      60      78 ..     280     300 ..     245     307 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.4e-11
                                       HHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-........HHHHHHHHHHHHHCSGGG....HHHHHHHHHHHHHHHH CS
                              CPBP   7 vfllalllapllEEllfRglllqllqergss........tlailissilFglaHlpn....gpsvllaalaGlvlgy 71 
                                       ++ + +l +++ EE++ Rg+ll+ ++e  s          +a+l+ss++Fg+aHl n     +s++ ++laG++l++
  gi|313124797|ref|YP_004035061.1| 140 LLTIQFLAVGVSEEIVSRGYLLTNVAEGLSGyttrfvaaSTAVLFSSVVFGAAHLQNpnatLVSTVGISLAGIFLAI 216
                                       45558999***************98888444457788889*****************99877779************ PP

                                       HHHHTT-HHHHHHHHHHHHH CS
                              CPBP  72 lylktgsllaaillHallnl 91 
                                        y+ t +l+++i lH+ +nl
  gi|313124797|ref|YP_004035061.1| 217 GYVLTDELAIPIGLHITWNL 236
                                       *******************8 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.14
                                       HHHHHHH..HHHHHHHHHTT- CS
                              CPBP  60 llaalaG..lvlgylylktgs 78 
                                       ++a+++G  l++gy+++++g+
  gi|313124797|ref|YP_004035061.1| 280 VFAIILGtfLIIGYVRWRYGE 300
                                       566666622556899999884 PP

>> Amastin  Amastin surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.1   1.2e-05     0.073      68     155 .]      26     116 ..       5     116 .. 0.86
   2 ?   -0.6   0.3      0.18   1.1e+03      69      89 ..     176     196 ..     167     222 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                           Amastin  68 fsiisilvlaaalllsvllllccsslkwvclllnivsvvtllivwalmvavyykrfCd...alksttakygaGFgLl 141
                                       +++++++v+++ l l + l++    +  + + l++v++++  +  +  ++v   r         ++++  + GFgL+
  gi|313124797|ref|YP_004035061.1|  26 LAVVALIVSVLLLGLFLSLFFTTTPITSASFGLSFVAILFPGVLAVGLAVVVDRRTIAdlgFGFDRDWWIDLGFGLF 102
                                       78999999999999999999999****************99999998888888666642556669999********* PP

                           Amastin 142 vvawlldlinivvL 155
                                       + a l++ i +v L
  gi|313124797|ref|YP_004035061.1| 103 LGAALMTAIFLVAL 116
                                       ******99988765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.18
                           Amastin  69 siisilvlaaalllsvllllc 89 
                                          s +vl+++++++ + l +
  gi|313124797|ref|YP_004035061.1| 176 VAASTAVLFSSVVFGAAHLQN 196
                                       456777777777777776666 PP

>> DUF3094  Protein of unknown function (DUF3094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.5   0.00011      0.68      24      52 ..      15      43 ..      11      46 .. 0.91
   2 ?   -3.3   0.1       1.3   7.7e+03      33      49 ..     141     157 ..     139     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                           DUF3094 24 ERqPFrpWlllvvvlavvigLGllsRlLs 52
                                      ER+P  p +l+++v+a ++++ ll  +Ls
  gi|313124797|ref|YP_004035061.1| 15 ERRPPAPVRLMLAVVALIVSVLLLGLFLS 43
                                      9******************9999988887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                           DUF3094  33 llvvvlavvigLGllsR 49 
                                       l +  lav ++  ++sR
  gi|313124797|ref|YP_004035061.1| 141 LTIQFLAVGVSEEIVSR 157
                                       55667899988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2024.63
//
Query:       gi|313124798|ref|YP_004035062.1|  [L=281]
Description: ATP phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-48  164.9   0.1    2.1e-48  164.3   0.1    1.3  1  HisG      ATP phosphoribosyltransferase
      2e-29  101.6   0.4    1.7e-28   98.6   0.1    2.2  2  HisG_C    HisG, C-terminal domain
      0.002   18.1   0.1      0.054   13.4   0.1    2.1  2  NMT1      NMT1/THI5 like


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.3   0.1   3.5e-52   2.1e-48       1     159 [.      49     201 ..      49     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 164.3 bits;  conditional E-value: 3.5e-52
                                       -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT-.EEEEES-HHH CS
                              HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlvedkgkriaTsypnl 77 
                                       raadip+yV++ga+ +GitG D+++Es+  +++eel+dL+fg+c+lv+a+pe+ +++s++d    +gk +aT++p++
  gi|313124798|ref|YP_004035062.1|  49 RAADIPEYVRDGAAAVGITGLDQMRESG--HDLEELVDLQFGSCRLVLAAPEDGDIESVEDV---AGKIVATEFPTI 120
                                       89************************85..47*************************99987...6889******** PP

                                       HHHHHHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHSHHHHHHH CS
                              HisG  78 akkyfeekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkkkekieel 154
                                       a++yf+e+g++++++++sG++E++p++++aDaI+D+++tG+TLr n+L +++++l+ss +L+a+++  + + k+++l
  gi|313124798|ref|YP_004035062.1| 121 ARNYFDEQGVEADVVEVSGATELTPHVEMADAIIDITSTGTTLRVNRLAIVDEVLSSSVRLFARPDVVD-DPKVDQL 196
                                       ***************************************************************999997.6799999 PP

                                       HHHHH CS
                              HisG 155 lerlr 159
                                       ++ ++
  gi|313124798|ref|YP_004035062.1| 197 VTAFQ 201
                                       98775 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.095   5.7e+02      14      41 ..     103     131 ..      99     156 .. 0.74
   2 !   98.6   0.1   2.8e-32   1.7e-28       1      73 []     206     278 ..     206     278 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.095
                                       GGHHHHHHH---SSS-EEEE-..SS-EEE CS
                            HisG_C  14 esleevlkilPGlrsPTvspla.degwva 41 
                                       es+e+v+  + + + PT+++ + de+ v+
  gi|313124798|ref|YP_004035062.1| 103 ESVEDVAGKIVATEFPTIARNYfDEQGVE 131
                                       678999999999999***99877444333 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 2.8e-32
                                       TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                            HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspladegwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                       A++++++m+nvp+e+l++v ++lPGl +PTv+++a +++vaV+avv+e+ v+ev+++Lk++GAs+Ilv++ie+
  gi|313124798|ref|YP_004035062.1| 206 AEDKRYVMMNVPQERLDDVREVLPGLGGPTVMDVAGDDMVAVHAVVDERHVFEVVNDLKSVGASGILVTEIER 278
                                       899********************************************************************96 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   9.1e-06     0.054      23     134 ..      43     145 ..      40     158 .. 0.78
   2 !    5.8   0.0    0.0019        12      12      54 ..     121     163 ..     116     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-06
                                       EEEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEECCC-.-SSGGGGTTSEEEE CS
                              NMT1  23 Veivepadpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlkdsg.ikspkDLkGkrigy 98 
                                       V+++     +d +e+v  g+a +g++  +++    ++g ++  +  l   +   +++  ++g i+s++D +Gk +++
  gi|313124798|ref|YP_004035062.1|  43 VTVLFA-RAADIPEYVRDGAAAVGITGLDQMR---ESGHDLEELVDLQFGSCRLVLAAPEDGdIESVEDVAGKIVAT 115
                                       555554.348999**************99985...99*********99999998888888888***********998 PP

                                       -S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHH CS
                              NMT1  99 vgspfekallkallakdggdpsdvtlvnvggtslak 134
                                              ++ +    ++g++++ v++   g t+l++
  gi|313124798|ref|YP_004035062.1| 116 EF----PTIARNYFDEQGVEADVVEV--SGATELTP 145
                                       77....67888888888887777777..44666654 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0019
                                       HTTHHHHTTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHH CS
                              NMT1  12 ekGYFkeeGldVeivepadpsdatelvasgkadfgvsyqesll 54 
                                       ++ YF e+G++ ++ve ++ ++ t++v+  +a + ++++ ++l
  gi|313124798|ref|YP_004035062.1| 121 ARNYFDEQGVEADVVEVSGATELTPHVEMADAIIDITSTGTTL 163
                                       689*****************99999999888877777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1904.16
//
Query:       gi|313124799|ref|YP_004035063.1|  [L=173]
Description: hypothetical protein Hbor_00110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-12   45.8   0.0    6.4e-07   28.8   0.0    2.2  2  HTH_24           Winged helix-turn-helix DNA-binding
    1.6e-07   31.1   0.0    0.00035   20.4   0.0    2.3  2  HTH_5            Bacterial regulatory protein, arsR family
    2.4e-07   30.7   4.7      9e-06   25.7   1.2    2.6  3  HTH_20           Helix-turn-helix domain
    7.8e-06   25.7   0.1    0.00039   20.3   0.0    2.4  2  MarR             MarR family
    0.00011   22.0   2.9      0.022   14.6   0.3    2.5  3  MarR_2           MarR family
    0.00038   20.3   0.0     0.0014   18.4   0.0    1.9  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00087   19.4   0.0       0.01   16.0   0.0    2.1  2  HTH_34           Winged helix DNA-binding domain
      0.002   17.9   0.4      0.016   15.0   0.2    2.4  2  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.063   13.5   0.0    1.9  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.015   15.3   0.2      0.044   13.8   0.2    1.8  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.045   13.7   0.3       0.35   10.9   0.1    2.3  2  BLACT_WH         Beta-lactamase associated winged helix domai
      0.065   13.0   0.1       0.52   10.1   0.0    2.4  3  HTH_10           HTH DNA binding domain
       0.14   12.5   0.0        7.8    6.9   0.0    2.2  2  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   9.8e-06     0.014       2      44 ..       2      44 ..       1      47 [. 0.89
   2 !   28.8   0.0   4.7e-10   6.4e-07       3      48 .]      77     122 ..      75     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.8e-06
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeee 44
                                       +t+++I  ++  +p+i  + L + l+l p+ v  +++rL+++
  gi|313124799|ref|YP_004035063.1|  2 TDTRIQIRTYVDSHPGIHFNGLVRSLDLAPGQVQHHVRRLIDS 44
                                      5677777788999***************************996 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 4.7e-10
                            HTH_24   3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       et r+IL +L +      + LAe lg+ +st+ +++  LeeeG+++
  gi|313124799|ref|YP_004035063.1|  77 ETARNILTTLLDAEEARPASLAEDLGVARSTLEWHVGHLEEEGIVR 122
                                       789*****************************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0012       1.6      19      42 ..      21      44 ..       3      48 .. 0.88
   2 !   20.4   0.0   2.5e-07   0.00035       2      47 .]      77     123 ..      76     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                                      HHHHHHHTS-HHHHHHHHHHHHHT CS
                             HTH_5 19 celaeelglsqstvShHLkkLrea 42
                                        l++ l+l ++ v hH ++L ++
  gi|313124799|ref|YP_004035063.1| 21 NGLVRSLDLAPGQVQHHVRRLIDS 44
                                      6799****************9875 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.5e-07
                                       HHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   2 ptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                       +t + IL  L + +e+    lae+lg+ +st+  H   L+e+G+V+k
  gi|313124799|ref|YP_004035063.1|  77 ETARNILTTLLDaEEARPASLAEDLGVARSTLEWHVGHLEEEGIVRK 123
                                       68899*******888******************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.011        15      32      54 ..      25      48 ..      13      54 .. 0.83
   2 !   25.7   1.2   6.5e-09     9e-06       6      59 ..      72     126 ..      67     128 .. 0.93
   3 ?   -1.6   0.0       2.2     3e+03      16      35 ..     132     149 ..     126     156 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                                      HHHTS-HHHHHHHHHHHHH.CTTE CS
                            HTH_20 32 erldlskntlsyHLrvLee.agLv 54
                                      + ldl++ ++ +H+r L +   Lv
  gi|313124799|ref|YP_004035063.1| 25 RSLDLAPGQVQHHVRRLIDsDRLV 48
                                      6789*************9944455 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 6.5e-09
                                       HHS-.HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20   6 ALah.PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                       AL h ++ r il  L +ae++ ++ lae l+++++tl  H+  Lee g+v+ +r 
  gi|313124799|ref|YP_004035063.1|  72 ALYHrETARNILTTLLDAEEARPASLAEDLGVARSTLEWHVGHLEEEGIVRKERD 126
                                       788999*********************************************9986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.2
                                       HHHHSTCTTB-HHHHHHHHT CS
                            HTH_20  16 lraLaraegltaselaerld 35 
                                          L  ++++  ++l +rld
  gi|313124799|ref|YP_004035063.1| 132 TLVL--ERPAATAALLARLD 149
                                       5556..66666666666664 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.065        90      12      45 ..      12      45 ..       1      51 [. 0.83
   2 !   20.3   0.0   2.8e-07   0.00039       8      56 ..      82     130 ..      77     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.065
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkG 45
                                      +++++++    L + l + ++ v   ++rL++ +
  gi|313124799|ref|YP_004035063.1| 12 VDSHPGIHFNGLVRSLDLAPGQVQHHVRRLIDSD 45
                                      6789999999********************9876 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.8e-07
                                       HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTST CS
                              MarR   8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDr 56 
                                       iL++l + ++++ + La+ lgv +st+   + +Le++G ++++++ ++r
  gi|313124799|ref|YP_004035063.1|  82 ILTTLLDAEEARPASLAEDLGVARSTLEWHVGHLEEEGIVRKERDIRNR 130
                                       9******************************************997765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0028       3.9      14      47 ..      12      43 ..       1      51 [. 0.84
   2 !   14.6   0.3   1.6e-05     0.022       8      56 ..      80     126 ..      75     130 .. 0.92
   3 ?   -3.3   0.0       6.2   8.6e+03      18      26 ..     138     144 ..     133     148 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0028
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLva 47
                                      +  +pg  +  + l+r l+l ++ v+ +++rL +
  gi|313124799|ref|YP_004035063.1| 12 VDSHPG--IHFNGLVRSLDLAPGQVQHHVRRLID 43
                                      566888..89999*******************86 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2   8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                       + +L  L ++++   +++ la+ lg+ +s++  ++  L++ G v+++++
  gi|313124799|ref|YP_004035063.1|  80 RNILTTLLDAEE--ARPASLAEDLGVARSTLEWHVGHLEEEGIVRKERD 126
                                       678999999999..9*******************************987 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.2
                                       TTSEEEHHH CS
                            MarR_2  18 pgrdltvge 26 
                                       p    t++ 
  gi|313124799|ref|YP_004035063.1| 138 PA--ATAAL 144
                                       22..33333 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.5   2.1e+03      33      56 ..      28      51 ..      20      61 .. 0.65
   2 !   18.4   0.0     1e-06    0.0014      13      58 ..      82     127 ..      77     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.5
                                      TSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 33 gvprskvYevLrsLedkGlVerek 56
                                      ++   +v+  +r+L+d +   re+
  gi|313124799|ref|YP_004035063.1| 28 DLAPGQVQHHVRRLIDSDRLVREE 51
                                      555567888999998877555554 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1e-06
                                       HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       + ++Ll  ++a+   +ae+lgv rs+    +  Le+ G+V++e+  
  gi|313124799|ref|YP_004035063.1|  82 ILTTLLDAEEARPASLAEDLGVARSTLEWHVGHLEEEGIVRKERDI 127
                                       5789**************************************9865 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.27   3.7e+02       2      45 ..       5      48 ..       4      72 .. 0.83
   2 !   16.0   0.0   7.5e-06      0.01       5      53 ..      82     130 ..      80     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.27
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      R+++ +y  s   + f+ l  +l +  g+   h++ L + + ++
  gi|313124799|ref|YP_004035063.1|  5 RIQIRTYVDSHPGIHFNGLVRSLDLAPGQVQHHVRRLIDSDRLV 48
                                      566667777788899999999**************998877665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.5e-06
                            HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53 
                                       +l++L++++ea +++l e l++  + L  h+  Le+ g +  + + +++
  gi|313124799|ref|YP_004035063.1|  82 ILTTLLDAEEARPASLAEDLGVARSTLEWHVGHLEEEGIVRKERDIRNR 130
                                       899***********************************99988888777 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.6   8.2e+02      23      43 ..      22      42 ..      13      50 .. 0.80
   2 !   15.0   0.2   1.1e-05     0.016       8      51 ..      82     124 ..      79     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.6
                                      HHHHHHTS-HHHHHHHHHHHH CS
                          HTH_IclR 23 elArrtglpkStvhRlLqtLv 43
                                       l r ++l++  v ++++ L+
  gi|313124799|ref|YP_004035063.1| 22 GLVRSLDLAPGQVQHHVRRLI 42
                                      588999999999999998886 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.1e-05
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       iL  l  a ++ + + lA+ +g+++St   ++  L+e+G+v+++
  gi|313124799|ref|YP_004035063.1|  82 ILTTLLDAEEA-RPASLAEDLGVARSTLEWHVGHLEEEGIVRKE 124
                                       67777777776.999**************************986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   1.9e+03      30      47 ..      25      42 ..      11      53 .. 0.80
   2 ?   13.5   0.0   4.6e-05     0.063      17      55 ..      86     124 ..      77     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                                      HHHTS-HHHHHHHHHHHH CS
                    Fe_dep_repress 30 erLnvspssVsemlkkLe 47
                                      + L+ +p  V+  +++L 
  gi|313124799|ref|YP_004035063.1| 25 RSLDLAPGQVQHHVRRLI 42
                                      678889999999999984 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.6e-05
                                       HHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress  17 seekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55 
                                         + + ++++ lae L+v+ s+    +  Le++G v  e
  gi|313124799|ref|YP_004035063.1|  86 LLDAEEARPASLAEDLGVARSTLEWHVGHLEEEGIVRKE 124
                                       334556899*************************99765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.3   4.6e+03      34      45 ..      75      86 ..      67      91 .. 0.76
   2 ?   13.8   0.2   3.2e-05     0.044      26      58 ..      96     128 ..      73     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.3
                                      SHHHHHHHHHHH CS
                         HTH_Crp_2 34 tretvsrilseL 45
                                      +ret   il+ L
  gi|313124799|ref|YP_004035063.1| 75 HRETARNILTTL 86
                                      688888888877 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.2e-05
                                       HHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEE CS
                         HTH_Crp_2  26 elAsmlGltretvsrilseLkreglisrgrrir 58 
                                        lA+ lG+ r+t+    ++L++eg+++++r+ir
  gi|313124799|ref|YP_004035063.1|  96 SLAEDLGVARSTLEWHVGHLEEEGIVRKERDIR 128
                                       69*************************754343 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.73     1e+03      21      41 ..      30      50 ..      25      52 .. 0.80
   2 ?   10.9   0.1   0.00025      0.35      20      43 ..     103     126 ..      98     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.73
                          BLACT_WH 21 AergvlahLeKLeeeGkVkre 41
                                      A  +v++h ++L + ++ +re
  gi|313124799|ref|YP_004035063.1| 30 APGQVQHHVRRLIDSDRLVRE 50
                                      677899999999888887776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00025
                          BLACT_WH  20 aAergvlahLeKLeeeGkVkregd 43 
                                        A+ ++  h  +LeeeG V++e d
  gi|313124799|ref|YP_004035063.1| 103 VARSTLEWHVGHLEEEGIVRKERD 126
                                       69999999*************987 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   2.1e+03      31      46 ..      25      40 ..      17      43 .. 0.80
   2 ?   -1.6   0.0       1.7   2.4e+03       1      10 [.      63      72 ..      63      73 .. 0.84
   3 ?   10.1   0.0   0.00038      0.52      27      44 ..      95     112 ..      90     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                            HTH_10 31 kelGIskstlsehLrk 46
                                        l++++  ++ h+r+
  gi|313124799|ref|YP_004035063.1| 25 RSLDLAPGQVQHHVRR 40
                                      5788999999999998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                            HTH_10  1 LTdkqlevlk 10
                                      LT++++++++
  gi|313124799|ref|YP_004035063.1| 63 LTEWERATVA 72
                                      9****99875 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00038
                            HTH_10  27 keLAkelGIskstlsehL 44 
                                       ++LA++lG+++stl+ h+
  gi|313124799|ref|YP_004035063.1|  95 ASLAEDLGVARSTLEWHV 112
                                       68************9987 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.046        63      29      70 ..      25      67 ..      18      92 .. 0.79
   2 ?    6.9   0.0    0.0056       7.8      26      59 ..      96     129 ..      77     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.046
                                      GGG---HHHHHHHHHHHHHTTS-EEEEE.TTEEEEE----XXX CS
                   Penicillinase_R 29 eekelaysTVktllrrLvkKgllsreke.grafiYsplvseee 70
                                      +  +la+  V+  +rrL + + l re+  gr++ Y p ++e e
  gi|313124799|ref|YP_004035063.1| 25 RSLDLAPGQVQHHVRRLIDSDRLVREEFyGRTHYYPPGLTEWE 67
                                      55677888899999999999877777766****9999877654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0056
                                       T--GGG---HHHHHHHHHHHHHTTS-EEEEETTE CS
                   Penicillinase_R  26 eleeekelaysTVktllrrLvkKgllsrekegra 59 
                                        l+e+  +a+sT    +++L++ g++++e++ r 
  gi|313124799|ref|YP_004035063.1|  96 SLAEDLGVARSTLEWHVGHLEEEGIVRKERDIRN 129
                                       478888999*********************9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1229.42
//
Query:       gi|313124800|ref|YP_004035064.1|  [L=433]
Description: cytosine deaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-67  226.5   3.9    6.5e-67  226.3   3.9    1.1  1  Amidohydro_1  Amidohydrolase family
    3.1e-27   96.2  17.7    2.6e-21   76.7  11.0    2.5  2  Amidohydro_3  Amidohydrolase family
    0.00087   18.7   0.0     0.0019   17.6   0.0    1.5  1  A_deaminase   Adenosine/AMP deaminase
  ------ inclusion threshold ------
      0.039   13.3   0.0      0.055   12.8   0.0    1.4  1  TatD_DNase    TatD related DNase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.3   3.9   1.4e-70   6.5e-67       1     343 [.      55     402 ..      55     403 .. 0.93

  Alignments for each domain:
  == domain 1  score: 226.3 bits;  conditional E-value: 1.4e-70
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       +v+PGl++aH+H+ ++llrg     +l++wl          + pe++++++e g+ ++++sGttt+adm++     +
  gi|313124800|ref|YP_004035064.1|  55 LVMPGLVNAHTHVAMTLLRGYaddkPLDSWLrediwpaeaeLEPEDVRAGTELGLIEMIRSGTTTFADMYF----EV 127
                                       59*********************************************************************....9* PP

                                       HHHHHHHHTSSSEEEEEEESSEGGS....GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHH CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldr....gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelke 136
                                       + ++ a+e+   g+r+ +g ++++      +a t++++  ++++++     g adg++ +a++ph+ +++ +  l+e
  gi|313124800|ref|YP_004035064.1| 128 PEIAAAVEAS--GMRARLGHGIVTVakddAEAATDIEEGLRVAREF----DGAADGRIHTAFMPHSLTTVDEKFLRE 198
                                       *********9..****999999998977666667777777776666....99************************* PP

                                       HHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHH CS
                      Amidohydro_1 137 alkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkea 213
                                        +  a++  +p+++Ha et+ ev  ++++ +   ++  +l +a++lg+  e    lahgvh++++e+ell+er  ++
  gi|313124800|ref|YP_004035064.1| 199 SVATARENEIPLHFHANETTDEVDPIVEERD---QR--PLAYADELGMVSE-EDFLAHGVHVDAAEIELLAER--GT 267
                                       **********************977777777...66..*******999999.999******************..** PP

                                       CEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHT CS
                      Amidohydro_1 214 gvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaT 290
                                       gv hcp+sn++l+sg++++ ++ld+Gv vg+gtDgaas+n l++++elr+a++l +  l  d++  ++++ a+++aT
  gi|313124800|ref|YP_004035064.1| 268 GVIHCPASNMKLASGIAPVQQMLDAGVTVGIGTDGAASNNDLDMFDELRDAAMLGK--LGADDASAVPAEAAITAAT 342
                                       ****************************************************5555..33366778*********** PP

                                       HHHHHHTT-TTTSSSS-TTSB--EEEECC...CT......CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 291 ingAkalglddkvGsievGkdADlvvvdl...di......laafvglkkdgnvkkvivkGkl 343
                                        + A+a+gl    G+ie+G  AD++vvdl   ++       +++++  +   v+++i++G++
  gi|313124800|ref|YP_004035064.1| 343 AGSADAIGL--PGGRIEEGGVADIAVVDLdapHLapahdvVSHLAYAVRGSDVRHTICDGQI 402
                                       *********..8*****************85522678888********************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.5     1e-08   4.5e-05       1      25 [.      47      71 ..      47      83 .. 0.81
   2 !   76.7  11.0   5.7e-25   2.6e-21     154     472 ..      97     403 ..      81     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1e-08
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlaggg 25
                                      e+ Da+G+lv+PG+v +HtH+a + 
  gi|313124800|ref|YP_004035064.1| 47 ETLDADGCLVMPGLVNAHTHVAMTL 71
                                      689*****************77665 PP

  == domain 2  score: 76.7 bits;  conditional E-value: 5.7e-25
                      Amidohydro_3 154 areaeaaavaaalaalasyGitsveagggnvsslddleplfeltaeeklplrvi......ikelldaaerlglplsp 224
                                       ++e+ +a ++ +l ++ + G t+    +++     +   ++++ ++ ++  r+        k+ ++aa  +++ l  
  gi|313124800|ref|YP_004035064.1|  97 EPEDVRAGTELGLIEMIRSGTTTF---ADMYFEVPE---IAAAVEASGMRARLGhgivtvAKDDAEAATDIEEGLR- 166
                                       555555555555555556665555...333222222...2222222223333333334444444444444444444. PP

                      Amidohydro_3 225 gseeltigavklfadgvlgsrtalltepyftgwpdfedealaelvaaadergldvaihaigdaavd.dvldafeaa. 299
                                             ++ ++ +ad  ++++ta + +    + ++++++ l+e va a+e+++++++ha+++++    ++++ +++ 
  gi|313124800|ref|YP_004035064.1| 167 -----VAREFDGAAD--GRIHTAFMPH----SLTTVDEKFLRESVATARENEIPLHFHANETTDEVdPIVEERDQRp 232
                                       .....4555566666..4777777777....567888777********************99988779999999989 PP

                      Amidohydro_3 300 ...aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkval 372
                                          a+++g+   +  l+h+  v++++ie +a+ +     +p++n            + a+g++pv+ +l+agv+v  
  gi|313124800|ref|YP_004035064.1| 233 layADELGMVSEEdFLAHGVHVDAAEIELLAERGTGVIHCPASNM-----------KLASGIAPVQQMLDAGVTVGI 298
                                       9888999999888999999999*********************99...........899****************** PP

                      Amidohydro_3 373 gsD..apvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvlda 447
                                       g+D  a  + +d + ++++a m+ +      +++   ++ e+a+ + T+g+A a+gl+   G++e+G  AD++v d 
  gi|313124800|ref|YP_004035064.1| 299 GTDgaASNNDLDMFDELRDAAMLGKL----GADDASAVPAEAAITAATAGSADAIGLPG--GRIEEGGVADIAVVDL 369
                                       *************************6....558**************************..***************9 PP

                      Amidohydro_3 448 dpldvdppelaear.........vrltvvdGrvv 472
                                       d+ ++ p++++            vr+t++dG+++
  gi|313124800|ref|YP_004035064.1| 370 DAPHLAPAHDVVSHlayavrgsdVRHTICDGQIL 403
                                       9999999977777799****************96 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.2e-07    0.0019     218     303 ..     248     328 ..     241     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.2e-07
                                       ECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCC.T-SHHHHHHHH CS
                       A_deaminase 218 igHGvrlrkdpvLqyllalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqf.gttLieeYaia 293
                                       ++HGv++  ++   +lla++ +++  cP+SN++l    +    P+++ l++g+ v ++tD  +   ++++ +e   a
  gi|313124800|ref|YP_004035064.1| 248 LAHGVHVDAAE--IELLAERGTGVIHCPASNMKL----ASGIAPVQQMLDAGVTVGIGTDGAASNnDLDMFDELRDA 318
                                       78999986554..6899*****************....77789*****************87654155688888877 PP

                                       HHHHT--HHH CS
                       A_deaminase 294 aqvfklseed 303
                                       a   kl++ d
  gi|313124800|ref|YP_004035064.1| 319 AMLGKLGADD 328
                                       7777777666 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.2e-05     0.055     102     161 ..     185     277 ..      64     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                                       CCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHH..................................HH CS
                        TatD_DNase 102 eestkeaqeevFeeqlrlAkelklplviHlrkaeedlleil..................................ke 144
                                        +s   + e++++e ++ A+e + pl  H+ ++ +++  i+                                  + 
  gi|313124800|ref|YP_004035064.1| 185 PHSLTTVDEKFLRESVATARENEIPLHFHANETTDEVDPIVeerdqrplayadelgmvseedflahgvhvdaaeiEL 261
                                       567778899******************************99777777777777777777777777777776655444 PP

                                       CGGCCSEEEETT--S-H CS
                        TatD_DNase 145 aaeakakvvlHsfsgsa 161
                                       +ae++ ++v+H+  +++
  gi|313124800|ref|YP_004035064.1| 262 LAERG-TGVIHCPASNM 277
                                       44444.77777743333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2838.22
//
Query:       gi|313124801|ref|YP_004035065.1|  [L=427]
Description: adenosylhomocysteinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-51  175.3   0.0    4.7e-26   91.6   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    2.7e-48  164.1   1.0      4e-48  163.5   0.6    1.5  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
      2e-10   40.3   0.2    3.5e-10   39.5   0.2    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.5e-06   27.9   1.3    2.9e-06   27.0   0.2    2.0  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0067   16.5   0.1      0.012   15.7   0.1    1.5  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.025   14.8   0.1      0.057   13.7   0.1    1.6  1  TrkA_N         TrkA-N domain


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0     4e-27   1.2e-23       9     138 ..      17     142 ..      10     145 .. 0.93
   2 !   91.6   0.0   1.6e-29   4.7e-26     171     289 ..     142     424 ..     139     427 .] 0.98

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 4e-27
                                       GHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   9 laefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqdeaaa 85 
                                         e+Gr++++ a + mp l +lr+++++ekpl+g  i  ++h+ ++ta L+e L   Gaev  + Cn  st d+++a
  gi|313124801|ref|YP_004035065.1|  17 AREAGRRKMDWALQHMPILNELRDQFEAEKPLDGEVIGMAMHVEAKTANLVELLALGGAEVAITGCNPLSTHDDVSA 93 
                                       4579************************************************************************* PP

                                       HHCCT.TEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  86 aiaea.gvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                       a+ ++ +++ +a++g   +ey + ie+++++     ep + +DdG D+   +h+
  gi|313124801|ref|YP_004035065.1|  94 ALDANdNITSYAVRGVGDDEYYEAIESVISH-----EPTITVDDGMDMVFAIHE 142
                                       **7766***********************55.....79*************998 PP

  == domain 2  score: 91.6 bits;  conditional E-value: 1.6e-29
                                       THHCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                         AdoHcyase 171 kkytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD........................... 220
                                       ++y+el+++i G +eetttGvhrL  + ++g+L+ p + vnd+  k  fD                           
  gi|313124801|ref|YP_004035065.1| 142 EEYPELIDTIVGGAEETTTGVHRLRAMDDDGELKYPVFAVNDTPMKRLFDnihgtgesslaniamttnvsfasknvv 218
                                       78*************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|313124801|ref|YP_004035065.1| 219 vagygycgkgvakkaagqnanvivaeveprraleahmegydvmpmneaakvgdifvtttgnrdiiteedfevmkdga 295
                                       ***************************************************************************** PP

                                       ............................................................S-HHHHHHHHHHHHHHH CS
                                       ............................................................xxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 ............................................................hpsfvmsasftnqvlaq 237
                                                                                                   hp  vm++sf  q++  
  gi|313124801|ref|YP_004035065.1| 296 ilsnaghfdieidldalsdlavdeyeardgvqayemedgrrlnvlaegrlvnlaspialgHPIEVMDQSFGVQAVCV 372
                                       ***************************************************************************** PP

                                       HHHHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCTSXT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 238 ielfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyigvev 289
                                        el ++ ++y+ +v+ +p +lD +va+++l++ g+++++lt+eq ey+g   
  gi|313124801|ref|YP_004035065.1| 373 RELVENGDDYDAGVHDVPDELDKEVAEIKLDAEGVEIDTLTDEQREYMGSWS 424
                                       ******9*****************************************9655 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       4.6   1.4e+04      46      58 ..      74      86 ..      69      95 .. 0.75
   2 !  163.5   0.6   1.4e-51     4e-48       1     159 [.     192     350 ..     192     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.6
                                      T-EEEEE-S-HHH CS
                     AdoHcyase_NAD 46 GarvivtevdPic 58
                                      Ga v +t  +P++
  gi|313124801|ref|YP_004035065.1| 74 GAEVAITGCNPLS 86
                                      7888888888875 PP

  == domain 2  score: 163.5 bits;  conditional E-value: 1.4e-51
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n++g+ es +  i  +t+v +a k++vvaGyG  GkG a+   g+ a viv+ev+P  al a meG++v+ ++e++k
  gi|313124801|ref|YP_004035065.1| 192 NIHGTGESSLANIAMTTNVSFASKNVVVAGYGYCGKGVAKKAAGQNANVIVAEVEPRRALEAHMEGYDVMPMNEAAK 268
                                       788999999******************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        +di+vtttGn+diit e+++ mkd ai++n Ghfd eid++al+  a++  e +  v+ ++++dg+++ +laeGrl
  gi|313124801|ref|YP_004035065.1| 269 VGDIFVTTTGNRDIITEEDFEVMKDGAILSNAGHFDIEIDLDALSDLAVDEYEARDGVQAYEMEDGRRLNVLAEGRL 345
                                       ***************************************************************************** PP

                                       CHHHT CS
                     AdoHcyase_NAD 155 lnlgc 159
                                       +nl++
  gi|313124801|ref|YP_004035065.1| 346 VNLAS 350
                                       ***85 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.2   1.2e-13   3.5e-10      33     128 ..     211     302 ..     194     340 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.2e-13
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSB CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhli 109
                                       + + k v + G+G  G+ vak++++ +++vi+ ++ +++  e++ +g++++ ++e+ +  Di +     t  +r++i
  gi|313124801|ref|YP_004035065.1| 211 SFASKNVVVAGYGYCGKGVAKKAAGQNANVIVAEVEPRRALEAHMEGYDVMPMNEAAKVGDIFVT----TTGNRDII 283
                                       67899*********************************99999999****************997....5569**** PP

                                       SHHHHHCSTTTEEEEESS- CS
                      2-Hacid_dh_C 110 naeelakmkkgailiNtaR 128
                                       ++e ++ mk+gail N++ 
  gi|313124801|ref|YP_004035065.1| 284 TEEDFEVMKDGAILSNAGH 302
                                       ****************996 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   9.7e-10   2.9e-06       3     101 ..     213     307 ..     211     316 .. 0.90
   2 ?   -2.1   0.1      0.85   2.6e+03      52      80 ..     370     401 ..     361     405 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 9.7e-10
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHH CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyee 79 
                                        +k+++v GyG  G+  a++   +  +v+v+  e +  + +A+ eg++v+ ++ea+k  d+ ++ +    ++++++e
  gi|313124801|ref|YP_004035065.1| 213 ASKNVVVAGYGYCGKGVAKKAAGQNANVIVAEVEPR-RALEAHMEGYDVMPMNEAAKVGDIFVTTT---GNRDIITE 285
                                       689****************************99998.67789******************877665...56789999 PP

                                       HTGGG--TT-EEEESSSHHHHT CS
                              IlvN  80 eiepnlkegkalafahGfnihf 101
                                       e  + +k+g++l+ a  f+i  
  gi|313124801|ref|YP_004035065.1| 286 EDFEVMKDGAILSNAGHFDIEI 307
                                       99999*********99999976 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.85
                                       EEHHHHHHT-...SEEEE-S-HHHHHHHHHHH CS
                              IlvN  52 ltvaeavkka...dvvmiliPDelqkevyeee 80 
                                       + v+e+v++    d  +  +PDel kev e +
  gi|313124801|ref|YP_004035065.1| 370 VCVRELVENGddyDAGVHDVPDELDKEVAEIK 401
                                       45555555441114556779999999998655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   4.1e-06     0.012       9      99 ..     211     292 ..     201     333 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.1e-06
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSS CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatas 85 
                                       s+++k+v++ G G  ++ vak+ + ++++ v+va  + +ra     +++g+   +++   ++e+ +  d+ ++ t+ 
  gi|313124801|ref|YP_004035065.1| 211 SFASKNVVVAGYGYCGKGVAKKAAGQNAN-VIVAEVEPRRAL--EAHMEGY--DVMP---MNEAAKVGDIFVTTTGN 279
                                       7899********************99998.999988888775..4566555..4555...55666889999888877 PP

                                       SS-SB-HHHHHCCH CS
                      Shikimate_DH  86 eepilekeeveeal 99 
                                       ++ i+++e++e ++
  gi|313124801|ref|YP_004035065.1| 280 RD-IITEEDFEVMK 292
                                       65.66777777555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.9e-05     0.057       1      45 [.     217     261 ..     217     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevv 45 
                                       ++++G+G  G+ +a++   ++ +v+v + +++r+ e+  eg++v+
  gi|313124801|ref|YP_004035065.1| 217 VVVAGYGYCGKGVAKKAAGQNANVIVAEVEPRRALEAHMEGYDVM 261
                                       79*****************7667*****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2894.54
//
Query:       gi|313124802|ref|YP_004035066.1|  [L=53]
Description: hypothetical protein Hbor_00140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 349.49
//
Query:       gi|313124803|ref|YP_004035067.1|  [L=151]
Description: holliday junction resolvase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-30  105.5   0.0    1.3e-30  105.2   0.0    1.1  1  Hjc       Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.26   11.4   0.0    1.5  1  NHL       NHL repeat


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.0   1.5e-34   1.3e-30       2      91 ..      10     100 ..       9     102 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 1.5e-34
                                       HHHHHHHHHHHTT-EEEEBSCSSSSSS.SS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEE CS
                               Hjc   2 yERelvkiLrergfavvRsagSggatk.plpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelll 77 
                                        ERelv+ L++ gfav+R+++Sg+at+ +lpDv+A++g+++++iE K s++++iyl+ e+ve l+ fa+++g++  +
  gi|313124803|ref|YP_004035067.1|  10 RERELVNKLDDAGFAVMRAPASGSATErELPDVLAGNGEMFYAIEAKASSGRPIYLQGEEVEALIYFAQNFGAKSRI 86 
                                       7************************999************************************************* PP

                                       EEEETTTEEEEEEG CS
                               Hjc  78 avklqgkewkllvv 91 
                                       av++++++w+++++
  gi|313124803|ref|YP_004035067.1|  87 AVRFDREDWYFFHP 100
                                       ************97 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05      0.26      13      27 ..     101     115 ..     101     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                                       TEEEEEECCCTEEEE CS
                               NHL  13 GdiyVaDsenhrvqv 27 
                                       Gd+yV+D +n rv++
  gi|313124803|ref|YP_004035067.1| 101 GDLYVTDGGNYRVKK 115
                                       89***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1033.37
//
Query:       gi|313124804|ref|YP_004035068.1|  [L=62]
Description: hypothetical protein Hbor_00160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0024   17.2   1.4       0.54    9.7   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.8   1.8        1.8    8.8   0.1    2.0  2  Yippee-Mis18     Yippee zinc-binding/DNA-binding /Mis18, cent
      0.013   15.7   0.7      0.016   15.3   0.7    1.1  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
      0.021   14.6   1.1       0.34   10.8   0.1    2.2  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
       0.05   14.0   2.2       0.95    9.9   2.2    2.0  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.078   13.0   2.0       0.12   12.4   2.0    1.4  1  DZR              Double zinc ribbon
      0.078   13.0   1.0       0.38   10.8   1.0    1.8  1  CpXC             CpXC protein
      0.082   12.6   2.0       0.12   12.1   0.3    1.9  2  Zn_Tnp_IS1       InsA N-terminal domain
      0.083   12.9   0.1      0.083   12.9   0.1    1.8  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.13   11.6   1.1       0.36   10.2   0.1    1.9  2  zf-TFIIB         Transcription factor zinc-finger
       0.17   11.5   1.1        2.5    7.8   0.2    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.18   11.9   3.0       0.41   10.8   0.3    2.1  2  UPF0547          Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00036      0.54       2      14 ..       1      13 [.       1      18 [. 0.71
   2 !    6.9   0.2    0.0028       4.1      18      24 ..      39      45 ..      37      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                       zf-ribbon_3  2 tvrCPnCGa.plss 14
                                      +v+CP+C + + ss
  gi|313124804|ref|YP_004035068.1|  1 MVHCPECQStL-SS 13
                                      79999998855.43 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C++CG+
  gi|313124804|ref|YP_004035068.1| 39 NCASCGM 45
                                      8*****7 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0012       1.8       3      30 ..       2      29 ..       1      34 [. 0.80
   2 ?    7.3   0.2    0.0035       5.2      52      67 ..      34      49 ..      29      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                                      EEETTTS-EEEECCCEEEEECCCEEEES CS
                      Yippee-Mis18  3 fqCkkCktilgdslqlvsegralnivvl 30
                                      ++C +C++ l+ s ++  e++++++ ++
  gi|313124804|ref|YP_004035068.1|  2 VHCPECQSTLSSSEDIAFEETEARTGFV 29
                                      79**************998877665554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0035
                                      EEEEEEETTT--EEEE CS
                      Yippee-Mis18 52 tystlsCkgCnsvlGw 67
                                       ++t +C++C+ ++G 
  gi|313124804|ref|YP_004035068.1| 34 RFYTANCASCGMTIGS 49
                                      57899*********96 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.7   1.1e-05     0.016       1      44 [.       3      46 ..       3      47 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                    zinc_ribbon_13  1 kCpKCgnteaevkevaatGsglskifdvqnkkfitvsCknCgYt 44
                                      +Cp C++t  +++++a   +     f   +k+f+t  C +Cg t
  gi|313124804|ref|YP_004035068.1|  3 HCPECQSTLSSSEDIAFEETEARTGFVRASKRFYTANCASCGMT 46
                                      6****************************************975 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.066        99      15      20 ..       3       8 ..       1      19 [. 0.74
   2 ?   10.8   0.1   0.00023      0.34       9      22 ..      33      46 ..      30      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.066
                         zf-C2H2_3 15 qCkeCg 20
                                      +C+eC+
  gi|313124804|ref|YP_004035068.1|  3 HCPECQ 8 
                                      5****7 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                         zf-C2H2_3  9 ksfgasqCkeCgMv 22
                                      k f +  C+ CgM+
  gi|313124804|ref|YP_004035068.1| 33 KRFYTANCASCGMT 46
                                      7788889******7 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.2   0.00064      0.95       6      43 ..       4      47 ..       1      59 [. 0.63

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00064
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigq.............cvyCadCgastpwfki 43
                                      CP C +   l  s++ + e  +             + +Ca Cg+     +i
  gi|313124804|ref|YP_004035068.1|  4 CPECQST--LSSSEDIAFEETEartgfvraskrfyTANCASCGM-----TI 47
                                      7777654..44444444443335678888888888999******.....22 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.0   8.3e-05      0.12      14      36 ..       3      45 ..       1      52 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                               DZR 14 fCseCgtklkavaa....................edrCpsCge 36
                                       C+eC+++l++ ++                      +C sCg 
  gi|313124804|ref|YP_004035068.1|  3 HCPECQSTLSSSEDiafeeteartgfvraskrfyTANCASCGM 45
                                      6********97777***************************96 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.0   0.00026      0.38       1      46 [.       2      46 ..       2      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                              CpXC  1 ltCpaCgkefeaeiwtsidadedpelkekl.ldgslfeatCpkCgat 46
                                      ++Cp+C+++      + i+ +e++     +  ++++ +a C +Cg t
  gi|313124804|ref|YP_004035068.1|  2 VHCPECQST--LSSSEDIAFEETEARTGFVrASKRFYTANCASCGMT 46
                                      689999765..556788888888888888844678999999999987 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   8.2e-05      0.12       6      14 ..       2      10 ..       1      11 [. 0.92
   2 ?   -0.3   0.1      0.61   9.1e+02       7      11 ..      39      43 ..      31      46 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                        Zn_Tnp_IS1  6 ihCPrCsst 14
                                      +hCP C+st
  gi|313124804|ref|YP_004035068.1|  2 VHCPECQST 10
                                      9*******7 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.61
                        Zn_Tnp_IS1  7 hCPrC 11
                                       C +C
  gi|313124804|ref|YP_004035068.1| 39 NCASC 43
                                      34444 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.6e-05     0.083       1      14 [.       3      16 ..       3      26 .. 0.79
   2 ?   -1.7   0.1       2.1   3.2e+03       2       6 ..      40      44 ..      39      47 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                    DNA_ligase_ZBD  1 hCPvCGsavvReeg 14
                                      hCP+C s +   e+
  gi|313124804|ref|YP_004035068.1|  3 HCPECQSTLSSSED 16
                                      9******9987775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                    DNA_ligase_ZBD  2 CPvCG 6 
                                      C +CG
  gi|313124804|ref|YP_004035068.1| 40 CASCG 44
                                      55787 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00024      0.36       1      13 [.       3      15 ..       3      26 .. 0.83
   2 ?    0.2   0.1      0.33     5e+02       1       7 [.      39      45 ..      39      49 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                          zf-TFIIB  1 kCPkCqdeleese 13
                                      +CP Cq++l  se
  gi|313124804|ref|YP_004035068.1|  3 HCPECQSTLSSSE 15
                                      7*******98654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.33
                          zf-TFIIB  1 kCPkCqd 7 
                                      +C +C+ 
  gi|313124804|ref|YP_004035068.1| 39 NCASCGM 45
                                      5788876 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0017       2.5       4      16 ..       3      15 ..       1      18 [. 0.85
   2 ?    2.8   0.1     0.061        91       4      12 ..      39      47 ..      37      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                            zf_UBZ  4 lCerCgkeipese 16
                                       C++C++++++se
  gi|313124804|ref|YP_004035068.1|  3 HCPECQSTLSSSE 15
                                      6*******99985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.061
                            zf_UBZ  4 lCerCgkei 12
                                       C+ Cg +i
  gi|313124804|ref|YP_004035068.1| 39 NCASCGMTI 47
                                      6*****998 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00027      0.41       2      11 ..       3      12 ..       3      14 .. 0.87
   2 ?    1.5   0.2      0.23   3.4e+02      17      21 ..      40      44 ..      37      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                           UPF0547  2 vCPeCeakvP 11
                                      +CPeC+++++
  gi|313124804|ref|YP_004035068.1|  3 HCPECQSTLS 12
                                      7*****9987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.23
                           UPF0547 17 CphCG 21
                                      C+ CG
  gi|313124804|ref|YP_004035068.1| 40 CASCG 44
                                      99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 443.68
//
Query:       gi|313124805|ref|YP_004035069.1|  [L=55]
Description: hypothetical protein Hbor_00170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0031   16.9   1.6       0.62    9.6   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.7   0.3        3.2    7.7   0.1    2.1  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.049   14.0   0.0      0.057   13.8   0.0    1.2  1  DUF3280          Protein of unknown function (DUF2380)
      0.054   13.7   0.2      0.076   13.2   0.2    1.3  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
      0.055   13.8   0.1        2.1    8.7   0.0    2.1  2  Arc_trans_TRASH  Archaeal TRASH domain
      0.092   12.8   3.9       0.11   12.6   0.4    2.1  2  UPF0547          Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00021      0.62       2      11 ..       1      11 [.       1      17 [. 0.67
   2 !    7.1   0.2    0.0012       3.7       5      15 ..      40      50 ..      38      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00021
                       zf-ribbon_3  2 tvrCPnCGa.p 11
                                      +v+CP+C + +
  gi|313124805|ref|YP_004035069.1|  1 MVHCPECETeL 11
                                      67888886544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0012
                       zf-ribbon_3  5 CPnCGa.plssd 15
                                      C++CGa +  s+
  gi|313124805|ref|YP_004035069.1| 40 CNECGAaI-GSG 50
                                      ******55.776 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0011       3.2       6      19 ..       3      16 ..       1      19 [. 0.63
   2 ?    6.6   0.0    0.0025       7.4      20      28 ..      37      45 ..      29      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                       Prok-RING_1  6 kCpvCgkelkeedD 19
                                      +Cp C+ el+ + D
  gi|313124805|ref|YP_004035069.1|  3 HCPECETELAGQGD 16
                                      56666666666666 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0025
                       Prok-RING_1 20 iVvCpeCgt 28
                                      iV C eCg+
  gi|313124805|ref|YP_004035069.1| 37 IVGCNECGA 45
                                      99******8 PP

>> DUF3280  Protein of unknown function (DUF2380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05     0.057      35      76 ..       7      50 ..       2      55 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                           DUF3280 35 lreaLaesgryevvdlapaaaeie..kesnlrkCngceadiArk 76
                                       +++La +g++e+vdl +++   +  k+  +  Cn+c a i+  
  gi|313124805|ref|YP_004035069.1|  7 CETELAGQGDVEFVDLGAETGFFKasKRFYIVGCNECGAAIGSG 50
                                      5789****************9988545555999*******9864 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   2.5e-05     0.076       1      42 [.       3      44 ..       3      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                    zinc_ribbon_13  1 kCpKCgnteaevkevaatGsglskifdvqnkkfitvsCknCg 42
                                      +Cp C+ + a +++v+    g    f   +k+f++v C++Cg
  gi|313124805|ref|YP_004035069.1|  3 HCPECETELAGQGDVEFVDLGAETGFFKASKRFYIVGCNECG 44
                                      699999999999999999988888888899***********8 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.03        90      26      33 ..       4      11 ..       1      14 [. 0.86
   2 ?    8.7   0.0   0.00072       2.1      15      30 ..      29      44 ..      23      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.03
                   Arc_trans_TRASH 26 CktCksel 33
                                      C+ C++el
  gi|313124805|ref|YP_004035069.1|  4 CPECETEL 11
                                      ******98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00072
                   Arc_trans_TRASH 15 yklknkvYyvCCktCk 30
                                      +k  ++ Y v C+ C 
  gi|313124805|ref|YP_004035069.1| 29 FKASKRFYIVGCNECG 44
                                      6889***********5 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   3.7e-05      0.11       2      11 ..       3      12 ..       3      13 .. 0.90
   2 ?    1.5   0.2      0.11   3.1e+02      17      21 ..      40      44 ..      38      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                           UPF0547  2 vCPeCeakvP 11
                                      +CPeCe++++
  gi|313124805|ref|YP_004035069.1|  3 HCPECETELA 12
                                      7******986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                           UPF0547 17 CphCG 21
                                      C +CG
  gi|313124805|ref|YP_004035069.1| 40 CNECG 44
                                      77777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 367.61
//
Query:       gi|313124806|ref|YP_004035070.1|  [L=244]
Description: swim zinc finger-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-05   22.1   0.0    0.00016   21.3   0.0    1.4  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   8.7e-09   0.00016      11      37 ..      65      91 ..      50      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.7e-09
                              SWIM 11 rlnkatCsCpefqkngipCkHalAvll 37
                                      +++  tC+Cp+ ++ +  CkH+  v++
  gi|313124806|ref|YP_004035070.1| 65 DVEAGTCTCPDSSIRHVRCKHLRRVAI 91
                                      57789*****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1707.22
//
Query:       gi|313124807|ref|YP_004035071.1|  [L=309]
Description: hypothetical protein Hbor_00190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.023   14.7   0.1       0.37   10.8   0.1    2.2  2  PapC_N        PapC N-terminal domain
      0.041   14.1   2.7      0.099   12.9   2.7    1.7  1  ABC_tran_CTD  ABC transporter C-terminal domain
      0.082   12.7   0.1       0.13   12.1   0.1    1.3  1  MukB          MukB N-terminal
        1.1    9.8   4.7       0.39   11.2   1.8    1.8  2  FadA          Adhesion protein FadA


Domain annotation for each model (and alignments):
>> PapC_N  PapC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.053   2.4e+02      93     127 ..      61      95 ..      34     100 .. 0.77
   2 ?   10.8   0.1   8.3e-05      0.37       3     100 ..     101     199 ..      99     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.053
                                       HHSTT-EEEEETTTTEEEEE--GGGBSTTSTTSSX CS
                            PapC_N  93 alipgasvkfdlakqrLdlsiPqaalknsargyvs 127
                                        ++++a++  ++++ ++ + + qaa ++ + + v 
  gi|313124807|ref|YP_004035071.1|  61 LAVQDAEIAREVETRTFGIRVAQAATDEAKADVVA 95 
                                       4689999999***************9977776665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.3e-05
                                       XCCCCTTXTTHHHHHHHHHTT-SS-SEEEEEEEEETTEEEEEEEEEEEECCTCCCEEEE-BHHHHHHTTB-GGGSCC CS
                            PapC_N   3 npdfLegssasnvdlsrFskgnavlpGeYrvdvyvNgkeigrqevefkaekkkkklepcltrelleqlgvkleklpe 79 
                                       n++ L + +++++ l+  ++++++  GeY+  +   +   ++++v+ + ++++ +++  l +elleq gv++ ++ +
  gi|313124807|ref|YP_004035071.1| 101 NEARLAELEQRKARLEAARENGSISKGEYNTRMA--RVAAETETVK-ELTNRSATASERLPNELLEQRGVNTTAIRT 174
                                       566677778899999999999********98765..6667777777.333489999***************999999 PP

                                       GHHTSTT....SC--HHHHSTT-EE CS
                            PapC_N  80 lakaqee....eCvdlsalipgasv 100
                                       la ++e+    e+ ++++ i g+ +
  gi|313124807|ref|YP_004035071.1| 175 LATRAEDltgpEVSEIARQIAGSAT 199
                                       9998887888888888888877665 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.7   2.2e-05     0.099      10      56 ..      98     146 ..      84     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                      ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsaeleeleae 56 
                                       l   ea++++LE+++a lea+ ++ ++    + +++a++ ae e++++ 
  gi|313124807|ref|YP_004035071.1|  98 LNSNEARLAELEQRKARLEAARENGSISkGEYnTRMARVAAETETVKEL 146
                                       66679***************99999988444467777777776666553 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.8e-05      0.13      95     163 ..      52     119 ..      43     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                                       TS-EEEEEEEEEE-SSTTT-EEEEEEEEE..S--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT-E CS
                              MukB  95 reqrllvgvrleqvagrdkkvdikpfalq..gleedvkltdvlleklddkkarvrelnelkekleelegvr 163
                                       +   ll gv   q a+  + v+ ++f ++  + ++d +  dv+ e+l+ ++ar+ el++ k++le+   +r
  gi|313124807|ref|YP_004035071.1|  52 QSGELLSGVLAVQDAEIAREVETRTFGIRvaQAATDEAKADVVAERLNSNEARLAELEQRKARLEA---AR 119
                                       445789999999**************9862266788999**********99998888777776655...33 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.8   8.7e-05      0.39      22      72 ..      86     137 ..      80     162 .. 0.80
   2 ?   -3.8   0.1         4   1.8e+04      23      35 ..     233     245 ..     228     249 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.7e-05
                              FadA  22 kekakaeaaaaklakkkelkakieeklaklea.dsevrfykdeYkellkeyk 72 
                                         +aka+  a++l+ +++  a++e++ a+lea  ++ ++ k eY++ + ++ 
  gi|313124807|ref|YP_004035071.1|  86 TDEAKADVVAERLNSNEARLAELEQRKARLEAaRENGSISKGEYNTRMARVA 137
                                       6799***************************977888999999987666554 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4
                              FadA  23 ekakaeaaaakla 35 
                                       +++++e+a+ + a
  gi|313124807|ref|YP_004035071.1| 233 QRETLENATTENA 245
                                       5667777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2062.56
//
Query:       gi|313124808|ref|YP_004035072.1|  [L=236]
Description: hypothetical protein Hbor_00200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.8e-07   28.9   5.6    7.8e-07   28.9   5.6    2.4  3  PGF-CTERM  PGF-CTERM motif
    8.2e-06   25.7   0.0    1.1e-05   25.3   0.0    1.2  1  DUF4897    Domain of unknown function (DUF4897)


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   2.1       1.7   1.5e+04      20      20 ..      19      19 ..      12      29 .. 0.52
   2 ?   -3.4   0.3       1.2   1.1e+04       4       9 ..     188     193 ..     188     193 .. 0.93
   3 !   28.9   5.6   8.7e-11   7.8e-07       1      22 [.     213     234 ..     213     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.7
                         PGF-CTERM 20 a 20
                                      a
  gi|313124808|ref|YP_004035072.1| 19 A 19
                                      2 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.2
                         PGF-CTERM   4 FGavlA 9  
                                       F++ +A
  gi|313124808|ref|YP_004035072.1| 188 FEVTFA 193
                                       9**998 PP

  == domain 3  score: 28.9 bits;  conditional E-value: 8.7e-11
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRR 22 
                                       tPGFG+v+A ++LL+aalLaR 
  gi|313124808|ref|YP_004035072.1| 213 TPGFGIVIASVALLGAALLARL 234
                                       9*******************95 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.3e-09   1.1e-05      13     150 ..      43     186 ..      37     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.3e-09
                           DUF4897  13 dysgsavlttkaelkfkdekkeeeyieqYqkasee...tfekylsqls....eevgreikvvslessateregilev 82 
                                       d s +++l t+ +l   +e +    + + + a e+   ++++ +s+++     e+gr+++v++    + ++ ++  v
  gi|313124808|ref|YP_004035072.1|  43 DGSATVTLRTTYDLASDEEARAFTDLREDDDAREKlveKYKDRMSRVAataaTETGRTMQVTNERIELSTSGDVGVV 119
                                       5566777777778877777665444444455555445577777887753233699***********99999999999 PP

                           DUF4897  83 eEkavlkglvkvengvvetslgdiklnlagdselvvslPkdaklisvePtPtkivenellWkgeseie 150
                                          ++ +gl++   g + +       +  +d +l+++ P+  ++  ++P P +++en l W+   e+ 
  gi|313124808|ref|YP_004035072.1| 120 ALSVQWEGLAATDTGRLVVT-RPFAGDFESDHSLTLVGPHGYDVTATNPSPDSQTENRLTWQSGTELN 186
                                       9999*****99998877665.567778888999*****************************966554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1673.04
//
Query:       gi|313124809|ref|YP_004035073.1|  [L=89]
Description: hypothetical protein Hbor_00210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 709.43
//
Query:       gi|313124810|ref|YP_004035074.1|  [L=65]
Description: hypothetical protein Hbor_00220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.023   15.1   0.9      0.023   15.1   0.9    1.8  2  DUF5455      Family of unknown function (DUF5455)
        0.2   10.3   0.6        0.2   10.3   0.6    1.0  1  Tmemb_161AB  Predicted transmembrane protein 161AB
        6.6    5.4   5.3        6.6    5.4   5.3    1.0  1  DUF2207      Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF5455  Family of unknown function (DUF5455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.9   3.8e-06     0.023      23      49 ..       8      34 ..       2      44 .. 0.88
   2 ?   -0.3   0.3      0.24   1.4e+03      38      49 ..      46      57 ..      40      64 .. 0.47

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-06
                           DUF5455 23 tkklAvaivalgliialivgllvvlla 49
                                       +k+ v +va+g++i+livg+ v++ +
  gi|313124810|ref|YP_004035074.1|  8 RRKILVSVVAVGFFISLIVGVGVTYNN 34
                                      6788999***************99987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.24
                           DUF5455 38 alivgllvvlla 49
                                        +++l+++ ++
  gi|313124810|ref|YP_004035074.1| 46 VGTIALFILAMG 57
                                      334444433333 PP

>> Tmemb_161AB  Predicted transmembrane protein 161AB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   3.3e-05       0.2     132     186 ..       5      59 ..       1      64 [. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.3e-05
                       Tmemb_161AB 132 kevnlsllwcllvvlFalkvllsltsvYfkseeggErslllvfgflflvlamlvl 186
                                        e+  ++l +++ v F +++++ +  +Y +s  gg   l+lv +++ ++lam v+
  gi|313124810|ref|YP_004035074.1|   5 AEMRRKILVSVVAVGFFISLIVGVGVTYNNSGLGGTGGLILVGTIALFILAMGVI 59 
                                       577778999*******************************************986 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   5.3    0.0011       6.6     377     431 ..       9      56 ..       2      65 .] 0.35

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0011
                           DUF2207 377 kkklkklsalglgliilglilillallllvll..lvfllilllillliaiivlllfs 431
                                       +k+l ++ a+g+++ +++ +++++ + +l+++  l         +l+  i++++l+ 
  gi|313124810|ref|YP_004035074.1|   9 RKILVSVVAVGFFISLIVGVGVTYNNSGLGGTggL---------ILVGTIALFILAM 56 
                                       33333333333333333333333333333332222.........2222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 493.27
//
Query:       gi|313124811|ref|YP_004035075.1|  [L=375]
Description: DNA primase, large subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-17   62.9   0.0    6.5e-17   61.8   0.0    1.5  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
  ------ inclusion threshold ------
        1.4    9.2   7.6       0.25   11.6   3.1    2.2  2  DUF2267          Uncharacterized conserved protein (DUF2267)


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0   7.3e-21   6.5e-17      17     232 ..     172     365 ..     152     372 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 7.3e-21
                                       G....GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHCT--.......... CS
                   DNA_primase_lrg  17 r....rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleellealsesyvaedvqe 89 
                                       r    ++ l  G + ++ +el +ll+e++ +r++++l +  +  ++  +ei +  ++++ ++ + l+          
  gi|313124811|ref|YP_004035075.1| 172 RwrlvNRELATGAVRVTTDELHRLLEEAVHRRVADGLPFEVRG-SSAGDEIADALEDEVASIRDLLN---------- 237
                                       15555666889****************************5555.55668888999989999999999.......... PP

                                       ...TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST..HHHHHHHT CS
                   DNA_primase_lrg  90 eedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftrteekFdkey 166
                                        ++++ ++ ++++++  +fPpCm++l+++ +++++l+ ++ ++l++Fl  +g++  e+  l         ++ ++++
  gi|313124811|ref|YP_004035075.1| 238 -DHDAAGRTDVEAVVPALFPPCMKALVQRAREGESLPAHSEFSLVSFLVALGMDATEVTTLLDVT-----DETASRI 308
                                       .8889999999**********************************************99999887.....4444455 PP

                                       HCHCHHHCC-STT--------HHHHHHS....TT---S.-HHHH..HHHHHHHHHHTT..HHHHHHHH CS
                   DNA_primase_lrg 167 rynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cpfrh.dpdklktlLqeyglseediedil 232
                                       +  +++  +   ++ ++ p+sC+ +         +++g C+ ++ + + +++ L++y ++ +d  d++
  gi|313124811|ref|YP_004035075.1| 309 ATRVEYLTD--AGGSQFAPPSCASM---------QSYGdCVNKDeRCETISHPLSYYTSAVRDAGDVR 365
                                       555555555..66899*********.........******9888888888888988887766666665 PP

>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.47   4.2e+03      53      74 ..      46      67 ..      28     128 .. 0.60
   2 ?   11.6   3.1   2.7e-05      0.25      10      99 ..     171     254 ..     167     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.47
                                      HHHHTT--TTS-----SHHHHH CS
                           DUF2267 53 gllrdgwppvepgkrfdreefl 74
                                      +l++ +   +ep++  dree+l
  gi|313124811|ref|YP_004035075.1| 46 ALMEGTVAAEEPHRWSDREELL 67
                                      4444444444444444444443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.7e-05
                                       HHHT---HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHHHHTS..... CS
                           DUF2267  10 erlgledreeAeratravLrtLrdrlteeeaadlaaqLPeelrgllrdgwppvepgkrfdreeflervaeelgvdpe 86 
                                       er +l +re A  a+r++   L+++l+e   +++a+ LP e+rg    ++ +         e+ ++ +++ l+ +++
  gi|313124811|ref|YP_004035075.1| 171 ERWRLVNRELATGAVRVTTDELHRLLEEAVHRRVADGLPFEVRGSSAGDE-I-----ADALEDEVASIRDLLNDHDA 241
                                       6778999************************************9986664.3.....34577778888888888888 PP

                                       EHHHHHHHHHHHH CS
                           DUF2267  87 daeqaaraVfaal 99 
                                       + ++ ++aV+ al
  gi|313124811|ref|YP_004035075.1| 242 AGRTDVEAVVPAL 254
                                       8888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2684.72
//
Query:       gi|313124812|ref|YP_004035076.1|  [L=243]
Description: hypothetical protein Hbor_00240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1631.91
//
Query:       gi|313124813|ref|YP_004035077.1|  [L=197]
Description: hypothetical protein Hbor_00250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0034   17.0   5.3     0.0034   17.0   5.3    1.8  2  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0     0.037   6.6e+02      92     110 ..       8      26 ..       3      58 .. 0.70
   2 !   17.0   5.3   1.9e-07    0.0034      93     159 ..     114     173 ..      99     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.037
                              TauE  92 lkllfgvlllllallmllr 110
                                       ++ll+g+ll+++ l++l  
  gi|313124813|ref|YP_004035077.1|   8 FTLLIGILLVASPLYILPH 26 
                                       6677777777777777653 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.9e-07
                              TauE  93 kllfgvlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvpllllllg 159
                                       ++ fgv+l  ++  +l+ ++    +   rr ++++ +++ g+++++++++G+G+G+  v ll+++  
  gi|313124813|ref|YP_004035077.1| 114 LVTFGVVLCCSVGVTLRDST----D---RRIGPPIGFAVVGFGAVITAVTGVGTGAGAVLLLTVVIA 173
                                       46788888888888887553....3...45555556666699**************99999987653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1398.13
//
Query:       gi|313124814|ref|YP_004035078.1|  [L=247]
Description: monomeric archaeal DNA polymerase sliding clamp [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-10   39.1   2.5    8.5e-10   38.4   0.6    2.0  2  PCNA_N           Proliferating cell nuclear antigen, N-termin
    6.5e-09   36.0   0.0    2.8e-07   30.8   0.0    2.5  2  PCNA_C           Proliferating cell nuclear antigen, C-termin
  ------ inclusion threshold ------
       0.12   12.2   1.3       0.51   10.2   0.3    2.2  2  DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal 
       0.16   11.4   0.0       0.23   10.9   0.0    1.3  1  Rad9             Rad9


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.6   1.9e-13   8.5e-10       6     102 ..       5     100 ..       1     108 [. 0.93
   2 ?    0.0   0.0      0.14   6.5e+02      87     101 ..     151     165 ..     134     190 .. 0.53

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.9e-13
                                       ESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTS CS
                            PCNA_N   6 leqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkca 82 
                                       ++ as l+  l+++  lv+e  +  +++ +s++a+D + v +v l+l + +fe+y  D   ++gvnl+ l   + +a
  gi|313124814|ref|YP_004035078.1|   5 IVSASTLRDALDSVSVLVDECKIRLNEDNLSIRAVDPANVGMVDLTLDAASFESYEADGG-VIGVNLSKLEDFVGMA 80 
                                       568999****************************************************87.59************** PP

                                       TTTSEEEEEEETTSSEEEEE CS
                            PCNA_N  83 nnedsvtlkaedeadtlalv 102
                                       n ++ v l+ ++e+ +l++ 
  gi|313124814|ref|YP_004035078.1|  81 NSDQLVELELDEETRKLNIR 100
                                       *********99999888765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.14
                                       EEEEEEETTSSEEEE CS
                            PCNA_N  87 svtlkaedeadtlal 101
                                        v l+ +d+a+++ +
  gi|313124814|ref|YP_004035078.1| 151 HVRLRVDDTAEAFHI 165
                                       444444444443322 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.034   1.5e+02      47      76 ..      64      93 ..      52     100 .. 0.84
   2 !   30.8   0.0   6.2e-11   2.8e-07       2     127 ..     122     242 ..     121     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.034
                                      ETTEEEEEEE--BEESSSGGGCBEEEESS- CS
                            PCNA_C 47 GdiGsasivlkqvkdvdkeeeavklelkep 76
                                      G iG    +l++++ ++++++ v+lel+e 
  gi|313124814|ref|YP_004035078.1| 64 GVIGVNLSKLEDFVGMANSDQLVELELDEE 93
                                      457888889*****************9985 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 6.2e-11
                                       ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEE..ETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS- CS
                            PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisv..tkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkep 76 
                                       ipd++  a + l  ++  r ++    +sd v + v  t e+ + +a+Gd               + e+ + l    +
  gi|313124814|ref|YP_004035078.1| 122 IPDLDLPAEIVLEGAQLDRGIKAADMVSDHVRLRVddTAEAFHIQAQGDTDDV-------DFQLDTEDLIDLTS-GT 190
                                       88888888888888888888888888888887766336677777788876555.......33345677777754.56 PP

                                       EEEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTC.EEEEEEE-B CS
                            PCNA_C  77 vtltfalkYlaeftkatsLservtlslssevPlvveykikdv.gllayllak 127
                                        +  f+l+Yl ++ ka +   +vt +l +e P++++y+i+++ g+++y+la+
  gi|313124814|ref|YP_004035078.1| 191 ADSLFSLDYLKDMNKAIPKDAEVTAELGEEFPVKLHYQIAEGqGHVTYMLAP 242
                                       6788***********************************9864899999998 PP

>> DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00011      0.51      12     105 ..       4      99 ..       2     111 .. 0.76
   2 ?    0.4   0.0      0.12   5.5e+02      23      50 ..     142     167 ..     127     231 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                                       EEEEHHHHHHHHHHHHTTSSTSTGEEEEEEETTEEEEEEEETT.SEEEEEEEEEBEE....SS-EEEEEEHHHHHHH CS
                   DNA_pol3_beta_3  12 vtvdlkelkealkRvalladeknrkvrLsleegqlklsaense.vgeaeEevdvnye....GeeleiafNvsYllda 83 
                                       ++v+   l++al+ v++l+d    + ++ l+e++l + a ++  vg +   +d++       +   i+ N s l d 
  gi|313124814|ref|YP_004035078.1|   4 AIVSASTLRDALDSVSVLVD----ECKIRLNEDNLSIRAVDPAnVGMVDLTLDAASFesyeADGGVIGVNLSKLEDF 76 
                                       789999*************8....67888899999999988751565555777643223337777899999999999 PP

                                       HHHH-SSE.EEEEESSTTS-EEE CS
                   DNA_pol3_beta_3  84 lkaletee.velqltdstkpvll 105
                                       ++  ++++ vel+l + t+ + +
  gi|313124814|ref|YP_004035078.1|  77 VGMANSDQlVELELDEETRKLNI 99 
                                       98888877678888888776665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                                       HHHHHTTSSTSTGEEEEEEE..TTEEEEEE CS
                   DNA_pol3_beta_3  23 lkRvalladeknrkvrLsle..egqlklsa 50 
                                       +k +++++d     vrL ++  ++  +++a
  gi|313124814|ref|YP_004035078.1| 142 IKAADMVSD----HVRLRVDdtAEAFHIQA 167
                                       555555554....55555542223333333 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.2e-05      0.23       4      52 ..      14      62 ..      11     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.2e-05
                              Rad9  4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyeke 52
                                      al ++s + de  +  +ed l++r+v+ ++ + + +tl  + F++ye +
  gi|313124814|ref|YP_004035078.1| 14 ALDSVSVLVDECKIRLNEDNLSIRAVDPANVGMVDLTLDAASFESYEAD 62
                                      688999999*************************************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1730.78
//
Query:       gi|313124815|ref|YP_004035079.1|  [L=150]
Description: hypothetical protein Hbor_00270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1041.22
//
Query:       gi|313124816|ref|YP_004035080.1|  [L=83]
Description: hypothetical protein Hbor_00280 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 631.61
//
Query:       gi|313124817|ref|YP_004035081.1|  [L=75]
Description: hypothetical protein Hbor_00290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 548.64
//
Query:       gi|313124818|ref|YP_004035082.1|  [L=73]
Description: hypothetical protein Hbor_00300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 546.23
//
Query:       gi|313124819|ref|YP_004035083.1|  [L=75]
Description: hypothetical protein Hbor_00310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 590.89
//
Query:       gi|313124820|ref|YP_004035084.1|  [L=74]
Description: hypothetical protein Hbor_00320 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.5    9.9   3.8       0.66    9.5   3.8    1.2  1  DUF4044   Protein of unknown function (DUF4044)


Domain annotation for each model (and alignments):
>> DUF4044  Protein of unknown function (DUF4044)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.8   3.7e-05      0.66      11      32 ..       1      22 [.       1      23 [. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 3.7e-05
                           DUF4044 11 iTkvvvwlMliaTVGSvllgal 32
                                      +T v v+ Ml++T +S  ++al
  gi|313124820|ref|YP_004035084.1|  1 MTGVLVVAMLVLTAFSGGAAAL 22
                                      799*************877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 514.34
//
Query:       gi|313124821|ref|YP_004035085.1|  [L=556]
Description: hypothetical protein Hbor_00330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-19   70.6   0.0    2.9e-12   47.1   0.0    2.1  2  TraB      TraB family
  ------ inclusion threshold ------
       0.15   12.1   2.3       0.86    9.7   2.3    2.3  1  DUF1290   Protein of unknown function (DUF1290)
        2.6    8.2   5.9       0.69   10.0   0.5    2.7  3  bPH_6     Bacterial PH domain


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   4.8e-16   2.9e-12      10     155 ..       8     141 ..       2     150 .. 0.89
   2 !   21.4   0.0   3.3e-08    0.0002     160     251 ..     279     352 ..     268     356 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.8e-16
                              TraB  10 ttsyLfGTiHvskksvyplspeveealeksdtvvvEldlsddtdeatqkelaklkllpdgktlsdllseelyarlqk 86 
                                        t+ ++GT+Hvs +sv ++++++++  e++d+v+vEld+ ++   +  ++ ++   l + +t   l+ +  ++ +q+
  gi|313124821|ref|YP_004035085.1|   8 GTIRIVGTAHVSADSVREVESVIRD--EHPDVVAVELDEGRYRRLTGDTDDPDPEALLESTTSVRLILHWVLSYVQA 82 
                                       3479*********************..9**************888888888888777779***************** PP

                              TraB  87 alakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlsll 155
                                        l + ++++      +P  +++ll + e a  + g d++lvDr+++ t +r + ++   E++++  +ll
  gi|313124821|ref|YP_004035085.1|  83 QLGD-QFDI------EP--GSELLKAVETA-DEIGTDIALVDRDIRVTVQRFWSQMTIREKLRLAGGLL 141
                                       ****.9***......**..99999999975.66799999***********************9988887 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3.3e-08
                              TraB 160 deeqlealeetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieallkepgsvf 236
                                        +e +e+++++l    +++d ++++++              e++e  p+  ++l+deR+++ a ++ al +++  v+
  gi|313124821|ref|YP_004035085.1| 279 IDEADEFVAADL----TDTDVVQTMLT--------------EFRELCPNGARALIDERDAYIAYQLVALRDSGLDVV 337
                                       444455554444....23445555555..............888999999*****************988999**** PP

                              TraB 237 vaVGagHlaGedgvl 251
                                       ++ GagH  G + +l
  gi|313124821|ref|YP_004035085.1| 338 AVLGAGHRGGVEQYL 352
                                       *******99987665 PP

>> DUF1290  Protein of unknown function (DUF1290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.3   0.00014      0.86      11      54 ..     385     425 ..     376     443 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00014
                           DUF1290  11 vailaaldsvfGgiraslekkFdekvfisgffsnvllAalLvyl 54 
                                       v   a + s++    a +++ +  +vf+  f++n ++Aa ++yl
  gi|313124821|ref|YP_004035085.1| 385 V---AFVASFVLLAMAGVDDAYLLEVFVAWFLVNGVFAAGMAYL 425
                                       3...44445555567899*************************8 PP

>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00011      0.69      16      71 ..      12      70 ..      10      71 .. 0.81
   2 ?   -1.3   0.0       0.4   2.4e+03      28      47 ..     275     294 ..     260     320 .. 0.79
   3 ?   -2.1   0.1      0.72   4.3e+03       4      18 ..     327     341 ..     327     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                             bPH_6 16 lfrtrrlpWsaiagvrfpegrrl...arldlrdgelvplpavqlgddpelvadalrrlr 71
                                      +++t ++  +++++v+   +      + ++l++g++++l++ +++ dpe+ +++ + +r
  gi|313124821|ref|YP_004035085.1| 12 IVGTAHVSADSVREVESVIRDEHpdvVAVELDEGRYRRLTGDTDDPDPEALLESTTSVR 70
                                      56888888888888885555555667999********************9999877666 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.4
                             bPH_6  28 agvrfpegrrlarldlrdge 47 
                                        g++++e+  ++ +dl+d +
  gi|313124821|ref|YP_004035085.1| 275 SGIDIDEADEFVAADLTDTD 294
                                       57899999999999999943 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.72
                             bPH_6   4 vrvdpdGvevrnlfr 18 
                                       v++ ++G++v+ +++
  gi|313124821|ref|YP_004035085.1| 327 VALRDSGLDVVAVLG 341
                                       677899*****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 3452.01
//
Query:       gi|313124822|ref|YP_004035086.1|  [L=183]
Description: hypothetical protein Hbor_00340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00091   19.2   0.0     0.0089   16.1   0.0    2.1  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     5e-07    0.0089       2      59 ..      29     105 ..      28     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5e-07
                                       HHHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHH.....T.............S-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20   2 qiaeALahPvRrrilraL.araegltaselaerl.....d.............lskntlsyHLrvLeeagLvevvre 59 
                                       +++e+L+++ Rr il +L a +e ++++ lae++     d             +  +    HL +Le ag++e  r+
  gi|313124822|ref|YP_004035086.1|  29 ELFEVLGNRRRRYILYYLyAIDESVSCGSLAEQVtawenDtlvddislrqyqsVYNSFYQTHLPTLENAGFIEYDRS 105
                                       789*******************************6665516666777555542333334569999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 974.42
//
Query:       gi|313124823|ref|YP_004035087.1|  [L=256]
Description: 23S rRNA um-2552 2'-o-methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-56  189.3   0.0      1e-55  188.6   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
    2.4e-12   46.7   0.8    6.2e-12   45.3   0.8    1.8  1  TRAM             TRAM domain
      1e-05   25.4   0.0    6.3e-05   22.8   0.0    1.9  1  Methyltransf_31  Methyltransferase domain
    0.00062   19.6   0.0     0.0024   17.7   0.0    1.8  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.026   15.2   0.3       0.13   13.0   0.3    2.3  2  Methyltransf_25  Methyltransferase domain
       0.12   12.7   0.5       0.25   11.6   0.5    1.5  1  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.6   0.0   3.4e-59     1e-55       1     176 [.      15     192 ..      15     193 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 3.4e-59
                                       CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH..TTEEEECS-CCCSSH CS
                              FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl..pgvttiqgditdpet 75 
                                       yr+RsayKL ++de+ +lf pg+tvvDlgaaPGgw qv+++++  +g vv+vDlq ++ +  ++v+ti+gd td+et
  gi|313124823|ref|YP_004035087.1|  15 YRTRSAYKLKQLDEETGLFGPGNTVVDLGAAPGGWLQVAAEEVSDHGTVVGVDLQRIRDIdaDNVETIRGDMTDEET 91 
                                       9******************************************999***********999889************** PP

                                       HHHHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCE CS
                              FtsJ  76 iekikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfF 152
                                       +e ++e ++e+++d+v+sD+ap+++g  +ld++++++L+++a+e+al+ll  gg f +k+f+g++ +++ +++++ F
  gi|313124823|ref|YP_004035087.1|  92 KESLRERIGEEGADVVISDMAPNMTGEYSLDHARSIHLARQAFEVALDLLPAGGDFAVKVFDGQDLADFRADVEEEF 168
                                       ***************************************************************************** PP

                                       EEEEEEE-SS--CCG-EEEEEEEE CS
                              FtsJ 153 ekvsvvkPkssrsesseeflvcrg 176
                                       ++v+ ++P +sr esse +lv + 
  gi|313124823|ref|YP_004035087.1| 169 QYVRSIRPDASRDESSEQYLVGKH 192
                                       *********************975 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.8   2.1e-15   6.2e-12       5      62 .]     201     254 ..     197     254 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.1e-15
                                       XXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   5 GstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                       G +++V + +++ seg+gi+++d g+++fv+ ++   Gd+V V++t+ k+++ ++e++
  gi|313124823|ref|YP_004035087.1| 201 GDELDVVIDDVG-SEGDGIAKVD-GYTLFVSETET--GDEVHVRVTDIKPNFGFAEVI 254
                                       99**********.**********.***********..*******************85 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.1e-08   6.3e-05       4     132 ..      36     174 ..      34     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.1e-08
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled.......e 73 
                                       g++v+DlG++ G  + ++aee+ ++++vvG+D          ++ ++   dnve  +gd+++ e++ e        e
  gi|313124823|ref|YP_004035087.1|  36 GNTVVDLGAAPGGWLQVAAEEVSDHGTVVGVDL---------QRIRDIDADNVETIRGDMTDEETK-ESlrerigeE 102
                                       789*****************************6.........455566789***********7754.223569**9* PP

                   Methyltransf_31  74 kfDlilsnevl...........naladpdkileeiervlkpggilliedpr..llaelpakveeeskayevv 132
                                         D+++s+ +              +    +++e + ++l  gg +++  ++   la+++a veee ++ +++
  gi|313124823|ref|YP_004035087.1| 103 GADVVISDMAPnmtgeysldhaRSIHLARQAFEVALDLLPAGGDFAVKVFDgqDLADFRADVEEEFQYVRSI 174
                                       ********5555555555566677888889999999999999999999998555666669999999876443 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.1e-07    0.0024      21      78 ..      34      94 ..      15     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.1e-07
                   Methyltransf_23 21 raggrvLdiGcGtGillevlrengf...svtgvDlspeaveiaekakkaqkdqfdeqeaae 78
                                       +g+ v+d+G++ G +l+v++e++    +v+gvDl ++    a +  + + d++de+  + 
  gi|313124823|ref|YP_004035087.1| 34 GPGNTVVDLGAAPGGWLQVAAEEVSdhgTVVGVDLQRIRDIDADNVETIRGDMTDEETKES 94
                                      57889*****************9877799******98877666688888888887665444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   4.4e-05      0.13       1      31 [.      39      70 ..      39     145 .. 0.75
   2 ?    0.1   0.0      0.47   1.4e+03      22      36 ..     104     118 ..      90     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.4e-05
                                      EEEET-TTSHHHHHHHCTS.TSSEEEEEESSH CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrl.gkakvtgvDise 31
                                      v+dlG+ +G +++ +a+++  +++v+gvD++ 
  gi|313124823|ref|YP_004035087.1| 39 VVDLGAAPGGWLQVAAEEVsDHGTVVGVDLQR 70
                                      89*****************548*******863 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.47
                                       SEEEEEESSHHHHHH CS
                   Methyltransf_25  22 akvtgvDiseemlea 36 
                                       a+v+  D++++m  +
  gi|313124823|ref|YP_004035087.1| 104 ADVVISDMAPNMTGE 118
                                       677777777777533 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   8.4e-05      0.25      13      69 ..      53     110 ..      49     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                                       HHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHH....HTTGGGESEEEE- CS
                            TrkA_N  13 laeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLe....eagiekadaviaa 69 
                                        aee+s++g  vv++d   +r++ + ++++e++ gd tdee+ e    ++g e ad+vi  
  gi|313124823|ref|YP_004035087.1|  53 AAEEVSDHGT-VVGVDL--QRIRDIDADNVETIRGDMTDEETKEslreRIGEEGADVVISD 110
                                       6788888774.899988..79******************9985411114566667766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1719.27
//
Query:       gi|313124824|ref|YP_004035088.1|  [L=418]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-23   81.1   1.8      8e-23   80.2   1.8    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    2.2e-21   76.3   0.1    6.7e-21   74.7   0.0    1.8  2  OrfB_IS605       Probable transposase
     0.0039   17.5   1.6       0.01   16.2   1.6    1.7  1  C1_2             C1 domain
  ------ inclusion threshold ------
        0.1   12.6   3.8       0.23   11.5   3.8    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.28   11.3   4.3      0.096   12.8   0.7    2.1  3  Ribosomal_L37ae  Ribosomal L37ae protein family


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   1.8   2.2e-26     8e-23       1      69 []     309     378 ..     309     378 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 2.2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++ + leyka+e+Gi v  v++++TSktCs+Cg++ +  ++++ +++C++C +++++Dvn+a+Ni ++
  gi|313124824|ref|YP_004035088.1| 309 FDRFARLLEYKAEEHGILVDRVDEENTSKTCSCCGKIRDSnRVERGLYVCSSCETTMNADVNGAVNIRRK 378
                                       789************************************9999************************985 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.4   5.2e+03      58      73 ..      54      69 ..      52      85 .. 0.61
   2 !   74.7   0.0   1.9e-24   6.7e-21       3     119 ..     176     285 ..     169     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                        OrfB_IS605 58 aelqsklkksknykka 73
                                      ael s lk++k+y   
  gi|313124824|ref|YP_004035088.1| 54 AELKSELKDHKRYSDL 69
                                      6777777777766443 PP

  == domain 2  score: 74.7 bits;  conditional E-value: 1.9e-24
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       +++ e + + ++gn++agiDlGi+n ++   edg+++ly g+ lk+d+ y+++e  + +            s++ ++
  gi|313124824|ref|YP_004035088.1| 176 VCKTEIPVEDAPGNNTAGIDLGISNYLAIDYEDGESELYPGNVLKEDKHYFTREEYQTEGENGP-------SKRARK 245
                                       56666678899******************************************99888777544.......567888 PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                         +k+srr +h+lh l++h+++++ e+gve++ vg+++di
  gi|313124824|ref|YP_004035088.1| 246 ARQKLSRRKDHFLHTLSKHIVERCVEEGVEKIAVGDLSDI 285
                                       88999********************************987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.6   2.8e-06      0.01      13      42 ..     331     365 ..     319     368 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-06
                              C1_2  13 edssesfnCsaCgrk..idgff.....YsCseCdfsl 42 
                                       ++++ s++Cs+Cg+   +  ++     Y Cs C+ ++
  gi|313124824|ref|YP_004035088.1| 331 DEENTSKTCSCCGKIrdS--NRverglYVCSSCETTM 365
                                       467788*********554..4455999******9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.8   6.4e-05      0.23      19      45 ..     337     363 ..     333     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                        +C  Cg+   + r+++ gl+ C++C +
  gi|313124824|ref|YP_004035088.1| 337 KTCSCCGKIrDSNRVER-GLYVCSSCET 363
                                       57*****9999999997.********86 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.1   1.1e+04      20      47 ..       6      33 ..       4      37 .. 0.65
   2 ?   -2.9   0.1       2.1   7.7e+03      31      50 ..     261     280 ..     245     280 .. 0.75
   3 ?   12.8   0.7   2.7e-05     0.096      31      62 ..     334     366 ..     326     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.1
                                      HHHHHHHHHHHHS-BEESSSSSSEEEEE CS
                   Ribosomal_L37ae 20 rkrvkkieisqhakytCpfcgktkvkRk 47
                                      r  v++i  +q+ +    +cg ++ k +
  gi|313124824|ref|YP_004035088.1|  6 RTYVARITNHQQVRDDLDQCGFSASKLW 33
                                      6667777777777777777776666555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                                       HS-BEESSSSSSEEEEEETT CS
                   Ribosomal_L37ae  31 hakytCpfcgktkvkRkavg 50 
                                        +k+  ++c ++ v++ avg
  gi|313124824|ref|YP_004035088.1| 261 LSKHIVERCVEEGVEKIAVG 280
                                       56788888888888888886 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 2.7e-05
                                       HS-BEESSSSSS.EEEEEETTEEEETTTTEEEE CS
                   Ribosomal_L37ae  31 hakytCpfcgkt.kvkRkavgiwkCkkcgktva 62 
                                       +++ tC+ cgk  + +R+  g++ C++c+ t+ 
  gi|313124824|ref|YP_004035088.1| 334 NTSKTCSCCGKIrDSNRVERGLYVCSSCETTMN 366
                                       44569******9899**************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2659.36
//
Query:       gi|313124825|ref|YP_004035089.1|  [L=239]
Description: hypothetical protein Hbor_00370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-49  166.9   6.2    3.7e-49  166.9   6.2    1.4  2  Vut_1     Putative vitamin uptake transporter
  ------ inclusion threshold ------
       0.76   10.1  10.6      0.048   13.9   2.2    2.9  3  DUF2568   Protein of unknown function (DUF2568)


Domain annotation for each model (and alignments):
>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2         1     9e+03      41      46 ..      17      22 ..       8      36 .. 0.45
   2 !  166.9   6.2   4.1e-53   3.7e-49       2     150 .]      54     221 ..      53     221 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                             Vut_1 41 lillll 46
                                      +i+ l 
  gi|313124825|ref|YP_004035089.1| 17 FIMALT 22
                                      222222 PP

  == domain 2  score: 166.9 bits;  conditional E-value: 4.1e-53
                             Vut_1   2 aGvllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa......ealesvfgltprivlaslia 72 
                                       +++l+++ltf+++d++se+yG++ a+ +v++gf++n+++l+l++ ++ +pa       ++ +v+   ++i+++sl+a
  gi|313124825|ref|YP_004035089.1|  54 GAALAYALTFFASDCYSELYGRRPAQLMVNVGFAMNFILLALVWGTIFAPAanpefaGQFRTVLASGTNIIAGSLLA 130
                                       789***********************************************999999889****************** PP

                             Vut_1  73 ylvsqlldvyvfhrlkkltkgkklwlrnigStlvsqlvdtlifvtiaflg.............eqlleiilsqylik 136
                                       ylvsq++dv +fh +++lt++++lwlrni+St++sq++dt+ifv++af++             + +l ++++qyl+k
  gi|313124825|ref|YP_004035089.1| 131 YLVSQNWDVVAFHSIRELTGSSHLWLRNIASTATSQAIDTFIFVSVAFALaprffgigealpeNIILGLMIGQYLLK 207
                                       ************************************************88************9999*********** PP

                             Vut_1 137 llialldtplvylv 150
                                       llial+dtp+vylv
  gi|313124825|ref|YP_004035089.1| 208 LLIALVDTPFVYLV 221
                                       ************96 PP

>> DUF2568  Protein of unknown function (DUF2568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.08   7.2e+02       9      33 ..      11      34 ..       4      43 .. 0.60
   2 ?   13.9   2.2   5.4e-06     0.048      31      85 ..      82     139 ..      50     144 .. 0.81
   3 ?   -1.6   0.1      0.39   3.5e+03      60      76 ..     165     181 ..     157     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.08
                           DUF2568  9 aalaalgvwGfrlgkgallkivlav 33
                                      +al+al +++ ++++  +++ +la+
  gi|313124825|ref|YP_004035089.1| 11 VALLALFIMALTTAQL-TASKLLAI 34
                                      5666666666666655.44444444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.4e-06
                           DUF2568  31 lavllp...llaavlWglfaaPkarvrlpgpvrlllellvfalaalalavaghptlal 85 
                                       + v+     +l a++Wg+  aP a+ ++ g +r +l     ++a+ +la + ++ + +
  gi|313124825|ref|YP_004035089.1|  82 VNVGFAmnfILLALVWGTIFAPAANPEFAGQFRTVLASGTNIIAGSLLAYLVSQNWDV 139
                                       4444333348999**************************9999999999888888765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.39
                           DUF2568  60 rlllellvfalaalala 76 
                                         ++  ++f+ +a+ala
  gi|313124825|ref|YP_004035089.1| 165 SQAIDTFIFVSVAFALA 181
                                       55677888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1554.41
//
Query:       gi|313124826|ref|YP_004035090.1|  [L=57]
Description: hypothetical protein Hbor_00380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-05   22.7   2.2    9.4e-05   22.2   0.5    2.0  2  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.014   15.6   0.1      0.014   15.6   0.1    1.1  1  RHH_8     Ribbon-Helix-Helix transcriptional regulator family
       0.12   12.5   0.2       0.12   12.4   0.2    1.1  1  DUF1515   Protein of unknown function (DUF1515)


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.5   1.6e-08   9.4e-05       2      37 ..       4      41 ..       3      42 .. 0.92
   2 ?    0.8   0.1     0.089   5.3e+02      10      20 ..      40      50 ..      38      56 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.6e-08
                                      EEEEEEHHHHHHHHHHHHHHT..SSHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg..rSrSelIReAlreyl 37
                                      +s+ +++ell+ +de++ + +  ++rS++IR+ +r  l
  gi|313124826|ref|YP_004035090.1|  4 ISVEIPDELLADIDEHVGDDKkfVNRSDAIRASIRKTL 41
                                      8****************998889***********9755 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.089
                                      HHHHHHHHHHH CS
                             RHH_1 10 llerLdelarr 20
                                      +l+ Lde+ +r
  gi|313124826|ref|YP_004035090.1| 40 TLDVLDEIDAR 50
                                      66667776655 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   2.4e-06     0.014       5      47 ..       3      46 ..       1      54 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                             RHH_8  5 kvtinlgvvDLgqiDlLv.eeGfYsnRtDlirtairaqLakhdd 47
                                      k+++ +    L+ iD  v ++  + nR+D ir++ir+ L+  d+
  gi|313124826|ref|YP_004035090.1|  3 KISVEIPDELLADIDEHVgDDKKFVNRSDAIRASIRKTLDVLDE 46
                                      788888888899999888456789***************98765 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2     2e-05      0.12      11      47 ..      10      46 ..       3      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                           DUF1515 11 gtllaevkelredlkrsedrsdasrakmyrkmdelve 47
                                      ++lla++ e   d k+  +rsda+ra++ + +d l e
  gi|313124826|ref|YP_004035090.1| 10 DELLADIDEHVGDDKKFVNRSDAIRASIRKTLDVLDE 46
                                      57999****9999****************99998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 380.67
//
Query:       gi|313124827|ref|YP_004035091.1|  [L=729]
Description: twin arginine targeting (tat) protein translocase tatc [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-71  238.0  41.1    8.6e-41  140.0  13.4    2.3  2  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0  13.4   4.8e-45   8.6e-41       3     207 .]      24     242 ..      22     242 .. 0.87
   2 !  103.7  19.7   6.3e-34   1.1e-29       4     207 .]     484     699 ..     482     699 .. 0.81

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 4.8e-45
                                       HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHH..HCCHHHHC.C.....TTS-EE--SSS-HHHHHHHHHHHHHHHHS CS
                              TatC   3 LeeLrkrlirallavaiafiitfvfaeelia..fllepleeae.....eevelivlspleafllklkvslvaglvla 72 
                                       L+  +k l +++++++++f+ tf +a +l+   fl    +++      ++ e+i+ +p++++ll+ k++lv+gl++a
  gi|313124827|ref|YP_004035091.1|  24 LRAAQKDLQKVFIVFLVGFLGTF-YALRLYVwgFLESVTRRNMnqvinQDLEIIAQTPFDVVLLQAKIGLVTGLIIA 99 
                                       66778999**************7.444544434333332222123333568999*********************** PP

                                       HHHHHHHHHCCCTTTTS--........-STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHTTTTS....STTEEH CS
                              TatC  73 sPvilyqlwafvapgLykh........errlvlvfliaslllfllGaafayfvvlplvlkfllseev....epllsl 137
                                       +Pv++y    f + +L+++         r ++  + +  ++lf lG+a++y++++p++++fl++++v    +p++s+
  gi|313124827|ref|YP_004035091.1| 100 APVFIY----FSRDALRERdlwpsapvPRWQLALIGTGMVVLFSLGVAYGYLFFFPITFEFLAQNTVnigfSPKYSI 172
                                       ******....*********899888888899999999999***********************55555566778*** PP

                                       HHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S.SHHHHHHHHHH CS
                              TatC 138 seylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltPpdvisqlllavP 207
                                        ++ +f++ll++ fg+a +lPlv+++l+++++v +et+r+++rya+++++ ++a++tPpd+++q+l+avP
  gi|313124827|ref|YP_004035091.1| 173 VKWAQFMFLLTVSFGLASQLPLVMTILSYAEIVPYETFRDQWRYAVLGVFAAGALFTPPDPFTQILWAVP 242
                                       *********************************************************************9 PP

  == domain 2  score: 103.7 bits;  conditional E-value: 6.3e-34
                                       HHHHHHHHHHHHHHHHHHHHHHHT.HHHHHH.HCCHHHHC..C......TTS-EE--SSS-HHHHHHHHHHHHHHHH CS
                              TatC   4 eeLrkrlirallavaiafiitfvf.aeelia.fllepleea.e......eevelivlspleafllklkvslvaglvl 71 
                                       e + ++ +r++++++ a++ tf++ ++  ++ ++++   +  +      e  ++++l+p+ea+l+++k s ++++++
  gi|313124827|ref|YP_004035091.1| 484 ETITSKTFRIVAVFMAALAGTFTWlYTVGFKaVFQQF-LNRlPaevrpnEVLNVVTLHPMEALLFEVKFSTLVAIIV 559
                                       6678899999999999999999752333333233333.33323333333237899********************** PP

                                       SHHHHHHHHHCCCTTTTS--.....-STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHTTTTSSTT....EEHHH CS
                              TatC  72 asPvilyqlwafvapgLykh.....errlvlvfliaslllfllGaafayfvvlplvlkfllseevepl....lslse 139
                                       ++P+++y  w     +L+++     +r  ++ +  + ++  l+G++++yf+++p+v+++l+++ v+++    +++++
  gi|313124827|ref|YP_004035091.1| 560 TLPLVAYYAWP----ALRERnivrrRRSTIFLWTGSLVVGLLGGLVLGYFYIAPAVISWLVNDAVQANmiisYRVTD 632
                                       *******6665....555444443377888888888889999*******************55554433444***** PP

                                       HHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S.SHHHHHHHHHH CS
                              TatC 140 ylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltPpdvisqlllavP 207
                                       +++++++++ ++g++  +P+++vll+  g+ +++ lr+++r + v+il +aa++tP+ ++s++l+++P
  gi|313124827|ref|YP_004035091.1| 633 FFWLIFFTTAGIGLLADVPILMVLLNGSGI-TYQVLRSRWREVTVGILTFAALFTPAGIVSMFLVTIP 699
                                       *****************************8.9**********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (729 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 4653.45
//
Query:       gi|313124828|ref|YP_004035092.1|  [L=469]
Description: sec-independent protein secretion pathway component tatc [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-37  127.4  14.5    7.9e-37  127.1  14.5    1.0  1  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1  14.5   4.4e-41   7.9e-37       1     205 [.     225     450 ..     225     451 .. 0.83

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 4.4e-41
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHT..............HHHHHHHCCHHHHC.C......TTS-EE--SSS-HH CS
                              TatC   1 ehLeeLrkrlirallavaiafiitfvf..............aeeliafllepleeae......eevelivlspleaf 57 
                                       +h+ee+ +rl  ++++ +i+++i++                ++++i+fl++     +      +e++  v+ ple +
  gi|313124828|ref|YP_004035092.1| 225 DHIEEMVRRLAVVFAIGGIITLILYPGadlansalhlnltsSTDVINFLWNKH---IpgapeiAERRPRVYGPLELV 298
                                       7**********999999999999975422222222222222222455555432...1233333234455******** PP

                                       HHHHHHHHHHHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT...TTTS CS
                              TatC  58 llklkvslvaglvlasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll...seev 131
                                       l++lkv+ +aglv+ +Pv++y+++ f++pgL ++err++l ++++sl+l ++G+afa+fvvlp+++k+++   + ++
  gi|313124828|ref|YP_004035092.1| 299 LTELKVAGLAGLVIGLPVFVYETYLFMRPGLFPKERRYYLAAVPTSLILAFIGIAFAHFVVLPTLIKYFTsytQGTA 375
                                       **********************************************************************7753333 PP

                                       STTEEHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S..SHHHHHHHH CS
                              TatC 132 epllslseylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltP.pdvisqllla 205
                                         ++ l+e ++++l+l+    i+F++Pl+++l+++++lv++++l ++r +++  +l +a++++P p+ +  +++a
  gi|313124828|ref|YP_004035092.1| 376 VIAFGLKETFNLILILMGYNAIIFQIPLFIMLAIMMNLVTRQWLVARRLIFWASFLGLAFFVSPdPTGMAPIIIA 450
                                       447*************************************************************99999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.86u 0.35s 00:00:01.21 Elapsed: 00:00:00.54
# Mc/sec: 2631.84
//
Query:       gi|313124829|ref|YP_004035093.1|  [L=302]
Description: hypothetical protein Hbor_00410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-10   40.2   0.1    5.3e-10   39.5   0.1    1.3  1  Asn_synthase     Asparagine synthase
    1.5e-09   37.1   0.0    2.1e-06   26.8   0.0    2.3  2  tRNA_Me_trans    tRNA methyl transferase
    1.2e-08   34.4   0.0    2.1e-08   33.6   0.0    1.3  1  NAD_synthase     NAD synthase
    1.5e-05   24.6   0.0    0.00021   20.8   0.0    2.2  2  QueC             Queuosine biosynthesis protein QueC
    0.00056   19.3   0.0     0.0015   17.9   0.0    1.6  2  Arginosuc_synth  Arginosuccinate synthase
     0.0037   17.0   0.0      0.023   14.5   0.0    2.1  2  ATP_bind_3       PP-loop family
  ------ inclusion threshold ------
      0.011   15.9   0.1       0.03   14.4   0.0    1.7  2  QueH             Epoxyqueuosine reductase QueH


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.1   2.1e-13   5.3e-10      13      83 ..      24      94 ..      15     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.1e-13
                      Asn_synthase 13 rlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteee 83
                                       l+ +  v + +SGG+DSS++aala   +  ++ + +++ e+   +e++ a++va+++g++h  ++++e +
  gi|313124829|ref|YP_004035093.1| 24 SLEERDGVLIAFSGGVDSSVVAALAHDALGDDAIACTAKSETLPTEELDDARRVADEIGIRHEIVEFSELD 94
                                      556666678889****************************99********************999998754 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0     8e-10   2.1e-06       3      72 ..      31      92 ..      29     100 .. 0.81
   2 !    8.2   0.0   0.00037      0.95     169     191 ..     161     183 ..     150     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 8e-10
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq.gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                      v++a+SgGVDSsv+aal +++ g + i+++ k          e   +e+l da+rva+++gi++e+v+f++
  gi|313124829|ref|YP_004035093.1| 31 VLIAFSGGVDSSVVAALAHDAlGDDAIACTAKS---------ETLPTEELDDARRVADEIGIRHEIVEFSE 92
                                      89***************9987245666555432.........23346899******************986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00037
                     tRNA_Me_trans 169 geltKeevrkiAkeaglavaekk 191
                                       +++ Keevr+iA ++gl+va+k+
  gi|313124829|ref|YP_004035093.1| 161 HDISKEEVRAIADSYGLSVADKP 183
                                       6899*****************98 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   8.1e-12   2.1e-08      19      83 ..      29      92 ..      17     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 8.1e-12
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83
                                      +gv++  SGGvDSs+vaala +alg++ ++a    s++ + e++ da+ +a+++gi+ + ++ ++
  gi|313124829|ref|YP_004035093.1| 29 DGVLIAFSGGVDSSVVAALAHDALGDD-AIACTAKSETLPTEELDDARRVADEIGIRHEIVEFSE 92
                                      68999*******************766.56777779999******************99998766 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   8.3e-08   0.00021       3      64 ..      32      93 ..      30      99 .. 0.90
   2 ?    1.1   0.0      0.09   2.3e+02     150     185 ..     150     189 ..     141     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.3e-08
                                      EEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGG CS
                              QueC  3 vvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgveehkildldll 64
                                      ++ +SGG+DS++v+ala+++ g+  +a t + +   ++el+ a+++a+e+g+ +h+i++ + l
  gi|313124829|ref|YP_004035093.1| 32 LIAFSGGVDSSVVAALAHDAlGDDAIACTAKSETLPTEELDDARRVADEIGI-RHEIVEFSEL 93
                                      788**************98735999999***9999*****************.****998765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.09
                                       S--EEE-TTT..T--HHHHHHHHHHTT..HHHHH-B-STT CS
                              QueC 150 kkieieaPli..dlsKaeivklgkelg..vpleetlsCYe 185
                                       +++e+  Pl+  d+sK+e+ ++++++g  v  + +++C +
  gi|313124829|ref|YP_004035093.1| 150 EELEVLSPLLthDISKEEVRAIADSYGlsVADKPSMACLS 189
                                       678999999734689**********996666677888866 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.8e-07    0.0015       2      58 ..      33      89 ..      32     101 .. 0.85
   2 ?   -2.3   0.0      0.82   2.1e+03     133     163 ..     151     181 ..     142     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.8e-07
                   Arginosuc_synth  2 LaysGGlDtsviikllkeklgeeviavavdvGq.eeedldevkekalklgavksvvvD 58
                                      +a+sGG+D sv+ +l ++ lg++ ia+++     + e+ld +++ a ++g  ++ +v+
  gi|313124829|ref|YP_004035093.1| 33 IAFSGGVDSSVVAALAHDALGDDAIACTAKSETlPTEELDDARRVADEIGI-RHEIVE 89
                                      79*************************998654389**************8.555554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.82
                   Arginosuc_synth 133 dlkviaPvReleltReeeieyakekgipvev 163
                                       +l+v++P+   ++++ee  + a++ g+ v+ 
  gi|313124829|ref|YP_004035093.1| 151 ELEVLSPLLTHDISKEEVRAIADSYGLSVAD 181
                                       899******9999999999999999998876 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   8.9e-06     0.023       2     108 ..      31     137 ..      30     143 .. 0.67
   2 ?   -0.4   0.0      0.33   8.4e+02     135     163 ..     149     179 ..     140     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.9e-06
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......HHCT CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv......akkk 72 
                                       vl+A+SgG+DS +   l+++   +   +++a++   ++     ee +  ++++++++i++ei +++          +
  gi|313124829|ref|YP_004035093.1|  31 VLIAFSGGVDSSVVAALAHDALGD---DAIACTAKSETL--PTEELDDARRVADEIGIRHEIVEFSEldnpdfV-AN 101
                                       79************9999988554...555555544444..334444456667777777777777766556532.23 PP

                                       TSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHH CS
                        ATP_bind_3  73 gknleeaARelRYevlkealkkegievlllAhhadD 108
                                               R++R   +  a+++ gie ++ + +a D
  gi|313124829|ref|YP_004035093.1| 102 DGDRCYHCRTMRLGRMYDAARERGIETVCDGTNASD 137
                                       344445788888888888888888888887777666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.33
                                       ETTCCEE-CCC..T--HHHHHHHHHHTT--- CS
                        ATP_bind_3 135 iasirlvRPlL..kvskeeleeylkekkikw 163
                                       +++ +++ PlL  ++skee++++++  +++ 
  gi|313124829|ref|YP_004035093.1| 149 VEELEVLSPLLthDISKEEVRAIADSYGLSV 179
                                       5678899999966689*****9999888765 PP

>> QueH  Epoxyqueuosine reductase QueH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05      0.03      79     110 ..     100     131 ..      79     140 .. 0.87
   2 ?   -2.3   0.0       1.6   4.2e+03      34      56 ..     196     218 ..     193     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                              QueH  79 kekgeRCekCyelrLektaelAkengfdaftt 110
                                       ++ g+RC +C ++rL +  + A+e+g+++++ 
  gi|313124829|ref|YP_004035093.1| 100 ANDGDRCYHCRTMRLGRMYDAARERGIETVCD 131
                                       5689***********************99985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                              QueH  34 ihpeeEyekRleelkrlieelki 56 
                                       i+ +eE  +R+e+ +r+++++++
  gi|313124829|ref|YP_004035093.1| 196 IEVTEERLSRVEKAERVVRQWGF 218
                                       56677888888888888887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1670.10
//
Query:       gi|313124830|ref|YP_004035094.1|  [L=662]
Description: DNA mismatch repair protein, muts family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-08   34.0   0.1    6.2e-08   32.9   0.0    1.6  2  MutS_V    MutS domain V
    2.2e-05   25.0   2.8    8.1e-05   23.2   0.6    2.8  2  HHH_5     Helix-hairpin-helix domain
    0.00072   19.3   0.9      0.007   16.2   0.0    2.8  2  HHH       Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.14   12.0   0.1       0.31   10.8   0.1    1.6  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.6   1.2e+04      84     108 ..     270     294 ..     254     304 .. 0.73
   2 !   32.9   0.0   1.4e-11   6.2e-08       2     136 ..     482     613 ..     481     649 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.6
                                       ESTS-SS-HHHHHHHHHHHHHHHHH CS
                            MutS_V  84 DElGRGtstydGlaialavaeylle 108
                                       +El R t+++d +  a + ae +++
  gi|313124830|ref|YP_004035094.1| 270 EELDRLTNAVDDVDAAVSTAESVAN 294
                                       3688888888888888888877765 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 1.4e-11
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TT CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatek 78 
                                       l+ G n +Gk + l  val+v+laq+G  vpae++e++ + +++    ++ +l  g  +F   + +  ++++   ++
  gi|313124830|ref|YP_004035094.1| 482 LLSGVNSGGKTSTLDLVALVVVLAQMGLPVPAERVELERFSELHYYAKSQGTLDAG--AFESTLRDFRELVDG-ESN 555
                                       789*****************************************998777777665..799999999987765.678 PP

                                       SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-G.GGGGHHHHSTTEEEE CS
                            MutS_V  79 slvilDElGRGtstydGlaialavaeyllekikaktlfatHyh.eltklaekleevknl 136
                                        lv++DEl   t       i   ++e l + + a+++f  H   e+ + a  + +v  +
  gi|313124830|ref|YP_004035094.1| 556 RLVLVDELESITEPGASAKIIAGILEALDD-QAATAVFVSHLAdEIREAAGFTVAVDGI 613
                                       8*******99999999999999*****998.6788888888751565555555555554 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.6   1.8e-08   8.1e-05       6      51 ..       5      49 ..       2      53 .. 0.91
   2 ?    0.2   0.1      0.27   1.2e+03      34      57 .]     560     585 ..     533     585 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.8e-08
                                      TSTT--HHHHHHHHTTT--SHH.HHHHS-HHHHHTSTTS-HHHHHHH CS
                             HHH_5  6 svsGiGpktAlallsaGiesve.dlaaadveeLakipGiGkktAeri 51
                                       ++G+G+ktA al +   +  e +la+ dv++La++pG+ + +A  i
  gi|313124830|ref|YP_004035094.1|  5 AIPGVGEKTAEALSEL--DDAErALADGDVAALARAPGLTEGRAAAI 49
                                      79*************9..*99879***************99888877 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.27
                                       HHHHHTS..TTS-HHHHHHHHHHHHH CS
                             HHH_5  34 veeLaki..pGiGkktAeriilelkd 57 
                                       v+eL +i  pG ++k    i+++l d
  gi|313124830|ref|YP_004035094.1| 560 VDELESItePGASAKIIAGILEALDD 585
                                       78888889999999999999999976 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.6e-06     0.007      12      27 ..       2      17 ..       2      19 .. 0.90
   2 ?   -0.1   0.2      0.22     1e+03       9      28 ..      31      50 ..      25      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-06
                                      HHHTSTT-SHHHHHHH CS
                               HHH 12 eLlalPGVGpktAeaI 27
                                      e +a+PGVG+ktAea 
  gi|313124830|ref|YP_004035094.1|  2 EFEAIPGVGEKTAEAL 17
                                      6799**********95 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.22
                                      SHHHHHTSTT-SHHHHHHHH CS
                               HHH  9 sreeLlalPGVGpktAeaIl 28
                                      +++ L+  PG  + +A aI+
  gi|313124830|ref|YP_004035094.1| 31 DVAALARAPGLTEGRAAAIA 50
                                      66778999**********96 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1     7e-05      0.31      13      47 ..     468     503 ..     465     508 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7e-05
                            AAA_29  13 dg.htieidlkgatlltGpsGsGKSTllDAiqalLv 47 
                                       +  + ++  ++g+tll+G +  GK++ lD ++ + v
  gi|313124830|ref|YP_004035094.1| 468 EAaEPVDYGVSGVTLLSGVNSGGKTSTLDLVALVVV 503
                                       555667888899*****************7777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4551.80
//
Query:       gi|313124831|ref|YP_004035095.1|  [L=132]
Description: hypothetical protein Hbor_00430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1086  (0.0605723); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 770.46
//
Query:       gi|313124832|ref|YP_004035096.1|  [L=366]
Description: orc complex protein cdc6/orc1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-12   46.9   1.9    7.3e-11   42.7   0.3    2.9  2  AAA_16           AAA ATPase domain
      4e-09   36.9   0.0    7.8e-09   35.9   0.0    1.4  1  AAA_22           AAA domain
    3.6e-05   23.6   0.1    0.00014   21.7   0.0    2.1  1  Cdc6_C           CDC6, C terminal winged helix domain
    9.3e-05   22.9   0.0    0.00026   21.4   0.0    1.8  1  AAA              ATPase family associated with various cellul
    0.00077   19.6   0.0     0.0013   18.9   0.0    1.6  1  AAA_33           AAA domain
     0.0011   18.7   0.1     0.0066   16.2   0.0    2.0  2  AAA_30           AAA domain
     0.0014   18.5   0.0     0.0023   17.8   0.0    1.3  1  AAA_11           AAA domain
     0.0053   16.7   0.0     0.0092   15.9   0.0    1.4  1  NACHT            NACHT domain
     0.0081   15.2   0.0      0.014   14.4   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
     0.0099   15.8   0.2      0.019   14.9   0.2    1.5  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.064   12.8   0.0    2.0  2  AAA_7            P-loop containing dynein motor region
      0.013   15.6   0.0      0.033   14.3   0.0    1.7  1  TIP49_C          TIP49 AAA-lid domain
      0.016   14.2   0.0      0.027   13.5   0.0    1.3  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.017   15.1   0.0      0.065   13.1   0.0    2.1  2  Rad17            Rad17 P-loop domain
      0.021   14.9   0.0       0.12   12.4   0.0    2.1  1  AAA_14           AAA domain
      0.027   14.2   0.0      0.054   13.2   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.029   13.6   0.0       0.05   12.9   0.0    1.3  1  Zeta_toxin       Zeta toxin
       0.03   14.7   0.0      0.046   14.0   0.0    1.4  1  AAA_19           AAA domain
      0.035   14.7   0.0      0.074   13.6   0.0    1.7  1  AAA_18           AAA domain
      0.048   12.5   0.0       0.63    8.8   0.0    2.1  2  AAA_35           AAA-like domain
      0.075   13.0   0.1       0.18   11.8   0.1    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
       0.08   12.7   0.0       0.13   12.0   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.093   12.5   0.5        1.5    8.5   0.5    2.3  1  IstB_IS21        IstB-like ATP binding protein
       0.11   12.9   0.0       0.22   11.9   0.0    1.5  1  RNA_helicase     RNA helicase
       0.13   12.0   0.0        0.5   10.1   0.0    1.9  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.15   12.6   0.0       0.37   11.3   0.0    1.7  2  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.3   1.1e-13   7.3e-11       4      91 ..      26     111 ..      23     171 .. 0.77
   2 ?    0.0   0.1       1.4   9.7e+02     138     165 ..     262     290 ..     204     356 .. 0.64

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.1e-13
                            AAA_16   4 GReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd.ggiflrgkcdqlesaipysalaqalar 78 
                                        Re +l+ L+ al+ +vr +rp +++++G++G+GK++ v++l+ +l ++ g+ ++r +c+    +++y+++ +++ +
  gi|313124832|ref|YP_004035096.1|  26 HRETQLQSLKYALRpAVRGSRPLNTIVRGPPGTGKTTAVQKLYGELGTQsGVRTVRVNCQVD--STRYAVFSRIF-E 99 
                                       5*************66666666*************************9955888********..88898899999.5 PP

                            AAA_16  79 eellrqlldeaes 91 
                                        ++++ +   +  
  gi|313124832|ref|YP_004035096.1| 100 -HIFEYEPPSSGI 111
                                       .898887766443 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.4
                            AAA_16 138 vlvlDdlqwadeaslql.laaLlrllesk 165
                                        ++l+d++ a + s  + l+  lr l+++
  gi|313124832|ref|YP_004035096.1| 262 SVTLEDVEAAYDKSKYVhLSRCLRGLSDS 290
                                       44444444444444433333333333332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   1.1e-11   7.8e-09       7     125 ..      49     168 ..      43     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.1e-11
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.erlsseelleal 82 
                                        ++v G++GtGKTt +++l  +l  +      ++++v+v++++++++  +++++++ + +     ++ s + l+ ++
  gi|313124832|ref|YP_004035096.1|  49 NTIVRGPPGTGKTTAVQKLYGELGTQ-----SGVRTVRVNCQVDSTRYAVFSRIFEHIFEYEPPsSGISFKKLFGQI 120
                                       57899*****************9755.....6**********************99887644445899********* PP

                            AAA_22  83 eqalraravielliiDEaqhlr.seealeeLrsllnl....srkgvql 125
                                       ++ l + + + ++ +D++ +l+ ++ea  +L sll      s   + +
  gi|313124832|ref|YP_004035096.1| 121 TDRLVEEDEVLAVALDDVNYLFyENEASDTLYSLLRAhethSGARIGV 168
                                       *******999***********998888888888888665454555554 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.1e-07   0.00014      35      83 ..     317     364 ..     309     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-07
                                       ----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHHH CS
                            Cdc6_C  35 dpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvle 83 
                                       + l  +++s++ ++L+ lgi+++e   + +++gr+r  sL +dp+ vl+
  gi|313124832|ref|YP_004035096.1| 317 TDLGYTRYSEITNKLDQLGIIDTEYA-EIEGRGRSRSLSLAYDPEAVLD 364
                                       56889*******************76.66666*************9985 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.8e-07   0.00026       3     127 ..      52     190 ..      50     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.8e-07
                                       EESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTS CS
                               AAA   3 lyGppGtGKTllakavakelg....vefleisgsellsk..................yvgesekkirelfkeakeka 57 
                                       + GppGtGKT++++ +  elg    v+ +++++                             +k + ++ +++ e+ 
  gi|313124832|ref|YP_004035096.1|  52 VRGPPGTGKTTAVQKLYGELGtqsgVRTVRVNCQVDSTRyavfsrifehifeyeppsSGISFKKLFGQITDRLVEED 128
                                       67*****************9544447777777754443355666666666666555322222333333333333333 PP

                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.GGGSTHHHHSTTSSEE CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr.pdkldpallrgRfdrk 127
                                       +   + +D++  l+ ++      e+++++  Ll++ +  +   +++ vi+++ +   ++ ++l  gR++++
  gi|313124832|ref|YP_004035096.1| 129 EVLAVALDDVNYLFYEN------EASDTLYSLLRAHETHSG--ARIGVIIVSSDlALDVIEELD-GRVQSV 190
                                       34667788888888777......566666666666666666..355555555554555555555.666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.9e-06    0.0013       3      33 ..      51      93 ..      50     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
                            AAA_33  3 llvGlpGsGKstlaerllkklg......avllssdt......l 33
                                      ++ G+pG+GK+t +++l+ +lg      +v+++  +      +
  gi|313124832|ref|YP_004035096.1| 51 IVRGPPGTGKTTAVQKLYGELGtqsgvrTVRVNCQVdstryaV 93
                                      789*******************888766666654444455551 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.6e-06    0.0066      15      48 ..      44      78 ..      31      87 .. 0.77
   2 ?   -0.5   0.0       1.3   8.8e+02     144     182 ..     273     311 ..     259     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.6e-06
                            AAA_30 15 tsgdrvavltGpAGtGKttalkal.reaweaaggr 48
                                      +s+ + +++ Gp+GtGKtta+++l  e+ +++g r
  gi|313124832|ref|YP_004035096.1| 44 GSRPLNTIVRGPPGTGKTTAVQKLyGELGTQSGVR 78
                                      556667899************99956666666744 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                            AAA_30 144 agigtaeLtevvRqkeseeraaalalregdaeealeala 182
                                       ++ + ++L+   R  +++era+++ ++e d e+a   ++
  gi|313124832|ref|YP_004035096.1| 273 DKSKYVHLSRCLRGLSDSERALVRVIAEYDGEQAGTVYE 311
                                       456889999999999999999999999888776655554 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.3e-06    0.0023       9      42 ..      37      72 ..      26      94 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                            AAA_11  9 aiksalsese..itliqGPPGtgKTktivellsqll 42
                                      a++ a++ s    t++ GPPGtgKT+++ +l+ +l 
  gi|313124832|ref|YP_004035096.1| 37 ALRPAVRGSRplNTIVRGPPGTGKTTAVQKLYGELG 72
                                      34444444447789****************999983 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-05    0.0092       3     115 ..      50     157 ..      48     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C.....CHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse.....vwa 74 
                                        i++G++G GKTt +qkl  ++ ++   +  ++ v + ++ + +r   + ++ +++f+  p++++ + +     +  
  gi|313124832|ref|YP_004035096.1|  50 TIVRGPPGTGKTTAVQKLYGELGTQS--G--VRTVRVNCQVDSTRYAVFSRIFEHIFEYEPPSSGISFKklfgqITD 122
                                       589*****************998777..4..4566666666666655557778888877777766665555554444 PP

                                       HHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                             NACHT  75 vllelperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                        l+e  e l   lD++++l  ++++       + L +l+r+
  gi|313124832|ref|YP_004035096.1| 123 RLVEEDEVLAVALDDVNYLFYENEA------SDTLYSLLRA 157
                                       4444444444888888888887766......6666666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.1e-05     0.014     106     156 ..      22      74 ..       3      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                             T2SSE 106 ddlgaeealkekiaevlrkavr..erglilvsGgTgsGKttllyallkeinks 156
                                       +++  +e++ + ++ +lr avr  +  + +v G+ g+GKtt +  l  e+ ++
  gi|313124832|ref|YP_004035096.1|  22 ETFNHRETQLQSLKYALRPAVRgsRPLNTIVRGPPGTGKTTAVQKLYGELGTQ 74 
                                       566778899999********973356899**************9999998877 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   2.8e-05     0.019       3      37 ..      51      81 ..      49      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                                      EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfytee 37
                                      ++ GppG+GKtT v+k++ +l  +    +G+ t +
  gi|313124832|ref|YP_004035096.1| 51 IVRGPPGTGKTTAVQKLYGELGTQ----SGVRTVR 81
                                      788****************99443....5555554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.3e-05     0.064      35      75 ..      49      88 ..      30     103 .. 0.73
   2 ?   -0.6   0.0       1.2   8.3e+02     102     133 ..     131     162 ..     126     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-05
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsa 75
                                      ++++ Gp GtGKt+ +++l  +l  ++  + t+ ++ q ++
  gi|313124832|ref|YP_004035096.1| 49 NTIVRGPPGTGKTTAVQKLYGELG-TQSGVRTVRVNCQVDS 88
                                      57899*************999998.4444445555444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                             AAA_7 102 lvvFvDDlnmpakekygaqppiellRqlldyg 133
                                       l v +DD+n    e+  + +   llR +  ++
  gi|313124832|ref|YP_004035096.1| 131 LAVALDDVNYLFYENEASDTLYSLLRAHETHS 162
                                       56789********************9987776 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.8e-05     0.033      18      61 ..     228     272 ..     209     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-05
                           TIP49_C  18 ldlLakigtetS.LRYaiqLltpasilakkrkkkevevedveeve 61 
                                       ld+ a++  e++ LR  i Ll  a + a++r +++v++edve ++
  gi|313124832|ref|YP_004035096.1| 228 LDRVAELTAESGdLRVGIDLLRRAGLNAEMRASRSVTLEDVEAAY 272
                                       6667776666544*****************************998 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.9e-05     0.027      34      80 ..      49     100 ..      37     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                             AAA_6  34 ggapaGpagtGKtEtvkdLakalakq....vvvfncs.dqldykslgkifkG 80 
                                        + + Gp gtGKt +v++L  +l++q    +v +nc+ d+  y   ++if+ 
  gi|313124832|ref|YP_004035096.1|  49 NTIVRGPPGTGKTTAVQKLYGELGTQsgvrTVRVNCQvDSTRYAVFSRIFEH 100
                                       56789************88777766522226778997578889999999975 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.5     1e+03     138     169 ..      17      51 ..      10      53 .. 0.70
   2 ?   13.1   0.0   9.5e-05     0.065      49      74 ..      51      76 ..      19     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.5
                             Rad17 138 vedlPnkfyrds...dalrevirkylrssealpli 169
                                       ++ +P+ f+      ++l+  +r ++r s++l  i
  gi|313124832|ref|YP_004035096.1|  17 IDYVPETFNHREtqlQSLKYALRPAVRGSRPLNTI 51 
                                       78899999765413366677799999999998554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.5e-05
                             Rad17 49 LisGPsGCgkstvvkvLskelgiklr 74
                                      ++ GP+G gk+t+v+ L  elg++  
  gi|313124832|ref|YP_004035096.1| 51 IVRGPPGTGKTTAVQKLYGELGTQSG 76
                                      578******************99854 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018      0.12       5      86 ..      50     154 ..      47     191 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                            AAA_14   5 lvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelileklke.................. 62 
                                        +++G+  +GKTt +++l+ el   +  +++ +n++ ++++ +a ++++ e i+e   +                  
  gi|313124832|ref|YP_004035096.1|  50 TIVRGPPGTGKTTAVQKLYGELGtQSGVRTVRVNCQVDSTR-YAVFSRIFEHIFEYE-Ppssgisfkklfgqitdrl 124
                                       589****************9999866678888888877663.343433444444421.1122333333333333334 PP

                            AAA_14  63 ...ekktylflDEiqev...pewekalksl 86 
                                          ++   + lD + ++   +e++++l sl
  gi|313124832|ref|YP_004035096.1| 125 veeDEVLAVALDDVNYLfyeNEASDTLYSL 154
                                       432444446677766666664444444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.8e-05     0.054      20      71 ..      45      98 ..      25     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                                      TSSS-EEEECSTTSSHHHHHHHHHH.HSTTTTS-EEEEETT.TS-TTCHHHHHH CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKellaraihe.askrkekpfvavnca.aipeelleseLF 71
                                      + +l+++++G  GtGK++  ++++    +++  + v+vnc  + ++  + s++F
  gi|313124832|ref|YP_004035096.1| 45 SRPLNTIVRGPPGTGKTTAVQKLYGeLGTQSGVRTVRVNCQvDSTRYAVFSRIF 98
                                      34599******************983556677799*****84445555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.2e-05      0.05      11      88 ..      42     125 ..      33     128 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-05
                        Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdelerqgnv..vrl....dpDdlRelhPeyeeilkadpkkaseltqkdas 81 
                                       ++++rP   ++ G pG GK+++ ++l  el++q++v  vr+    d +++  + + +e i++ +p +  + ++k  +
  gi|313124832|ref|YP_004035096.1|  42 VRGSRPLNTIVRGPPGTGKTTAVQKLYGELGTQSGVrtVRVncqvDSTRYAVFSRIFEHIFEYEPPSSGISFKKLFG 118
                                       5779**************************95554422544111144555555666666666666666666666666 PP

                        Zeta_toxin  82 elvekll 88 
                                       +++++l+
  gi|313124832|ref|YP_004035096.1| 119 QITDRLV 125
                                       6666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.7e-05     0.046       5      44 ..      42      81 ..      39     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.7e-05
                            AAA_19  5 vealkekvllvtaGpGtGKTrvlkhivallvelggvkpee 44
                                      v+ ++  + +v ++pGtGKT+ +++   +l  + gv   +
  gi|313124832|ref|YP_004035096.1| 42 VRGSRPLNTIVRGPPGTGKTTAVQKLYGELGTQSGVRTVR 81
                                      5556666789**************9999998888776544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00011     0.074       2      32 ..      51      84 ..      51     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf...gvnlrdva 32
                                      ++ G+pG+GKtt  + L  +lg    ++ +r ++
  gi|313124832|ref|YP_004035096.1| 51 IVRGPPGTGKTTAVQKLYGELGTqsgVRTVRVNC 84
                                      578**************77765556644444444 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.19   1.3e+02      36      70 ..      52      87 ..      45     100 .. 0.82
   2 ?    8.8   0.0   0.00091      0.63     124     157 ..     126     159 ..     112     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.19
                            AAA_35 36 ikapkkmGKtSLlarilaka.kqqgyktvsldlqla 70
                                      +++p  +GKt  ++++  +  +q+g++tv +++q  
  gi|313124832|ref|YP_004035096.1| 52 VRGPPGTGKTTAVQKLYGELgTQSGVRTVRVNCQVD 87
                                      689999*********9977615669*******9864 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00091
                            AAA_35 124 eidkplvLaldevdrlfeypeiakdflslLRswh 157
                                       e d+ l +ald+v+ lf ++e ++ + slLR+  
  gi|313124832|ref|YP_004035096.1| 126 EEDEVLAVALDDVNYLFYENEASDTLYSLLRAHE 159
                                       5578999************************865 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00026      0.18       2      37 ..      50      89 ..      49     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                                      EEEE--SSSSHHHHHHHGGGGB....S--EEEEE--TT-- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal....nreveyvqltrdtt 37
                                       ++ GppGtgK++ +++l   l    + +++ v+++ d t
  gi|313124832|ref|YP_004035096.1| 50 TIVRGPPGTGKTTAVQKLYGELgtqsGVRTVRVNCQVDST 89
                                      5788*************99988774444455555555555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.13       1      21 [.      50      70 ..      50     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllrt 21
                                      ++v G pG GK+t+++kl+ +
  gi|313124832|ref|YP_004035096.1| 50 TIVRGPPGTGKTTAVQKLYGE 70
                                      5899**************988 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.5    0.0022       1.5      49     140 ..      49     161 ..      16     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0022
                         IstB_IS21  49 nivllGpsGvGKsh........laialgveavraglsv...lfvrvedLveel..........krarrdgklaralk 104
                                       n ++ Gp+G+GK+         l +  gv++vr + +v   ++   ++++e++          + ++  g+++ +l 
  gi|313124832|ref|YP_004035096.1|  49 NTIVRGPPGTGKTTavqklygeLGTQSGVRTVRVNCQVdstRYAVFSRIFEHIfeyeppssgiSFKKLFGQITDRLV 125
                                       78899999999985222222224444466667766655333666677777775222111111133444556666666 PP

                         IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfeviekryer 140
                                       +  +v  + lDd+ +l  +++++ +l+ ++ +   +
  gi|313124832|ref|YP_004035096.1| 126 EEDEVLAVALDDVNYLFYENEASDTLYSLLRAHETH 161
                                       666666778999999999999999999999776554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00031      0.22       2      26 ..      51      75 ..      50      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      ++ Gp+g+GK+t++++L  +l +++
  gi|313124832|ref|YP_004035096.1| 51 IVRGPPGTGKTTAVQKLYGELGTQS 75
                                      589*************999998776 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00072       0.5       1      43 [.      52      93 ..      52     105 .. 0.76
   2 ?   -1.7   0.0       2.9     2e+03     126     185 ..     262     318 ..     251     334 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00072
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYea 43
                                      v Gp+G GKtt v++l+  l ++   v++v     ++++ Y++
  gi|313124832|ref|YP_004035096.1| 52 VRGPPGTGKTTAVQKLYGELGTQ-SGVRTVRVNCQVDSTRYAV 93
                                      67**************9877766.6677776666677777766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.9
                        ATP_bind_1 126 vvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkeklekeleffedvea 185
                                       +v L D++ + d +k+++    +l+ +   e   v v+ + D+ +  +    e f+d  +
  gi|313124832|ref|YP_004035096.1| 262 SVTLEDVEAAYDKSKYVHL-SRCLRGLSDSERALVRVIAEYDGEQ--AGTVYEAFHDETD 318
                                       6777788888888888765.6667777777777788888888755..5555555555544 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00054      0.37      16      74 ..      52     111 ..      47     165 .. 0.70
   2 ?   -2.3   0.0       8.4   5.8e+03      31      31 ..     298     298 ..     247     353 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00054
                                       EEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  16 ivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpel 74 
                                       + G+ G+GK+t ++ l+g+l  ++G  +++ + ++++++  ++++ ++ +++ +   +++
  gi|313124832|ref|YP_004035096.1|  52 VRGPPGTGKTTAVQKLYGELGTQSGVRTVRvNCQVDSTRYAVFSRIFEHIFEYEPPSSGI 111
                                       67*********************9977666666666666666666666666665555555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.4
                                       H CS
                                       x RF
                          ABC_tran  31 l 31 
                                       +
  gi|313124832|ref|YP_004035096.1| 298 I 298
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2102.57
//
Query:       gi|313124833|ref|YP_004035097.1|  [L=228]
Description: ribose-5-phosphate isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-65  220.1   0.1    1.7e-65  219.8   0.1    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    2.3e-07   30.9   0.8    2.9e-05   24.1   0.1    2.2  2  DeoRC           DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.8   0.1   1.9e-69   1.7e-65       2     173 .]      55     223 ..      54     223 .. 0.97

  Alignments for each domain:
  == domain 1  score: 219.8 bits;  conditional E-value: 1.9e-69
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       gvptS++++ela+e gipl+ +deve+id+aiDGaD+ d dlnliKGgG+a+ rEKiv+a+a++f+v+ad sK++e+
  gi|313124833|ref|YP_004035097.1|  55 GVPTSFASRELAREEGIPLVAVDEVETIDVAIDGADQLDGDLNLIKGGGAAHAREKIVDAMADRFVVVADPSKVTET 131
                                       8**************************************************************************** PP

                                       TTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEE CS
                    Rib_5-P_isom_A  79 lgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVve 155
                                       l+  +vP+eVlp a++a a ++++l  g+++lR+a++kdgpvvTdngnl+lD++f+ +i+dpe+l+++l+++pGVve
  gi|313124833|ref|YP_004035097.1| 132 LE-RAVPLEVLPDARTAAAARVSEL-DGEATLRRAERKDGPVVTDNGNLVLDCEFG-QISDPESLAADLSATPGVVE 205
                                       *6.9******************975.9****************************6.566***************** PP

                                       ESEE-S--SEEEEEETTC CS
                    Rib_5-P_isom_A 156 tGlFlgladkvlvgkedg 173
                                       +GlF+glad++++g++dg
  gi|313124833|ref|YP_004035097.1| 206 HGLFVGLADEAYIGTDDG 223
                                       ***************997 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   3.2e-09   2.9e-05       4      40 ..       9      45 ..       7      76 .. 0.91
   2 !    5.6   0.0    0.0016        14      93     141 ..      82     130 ..      75     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.2e-09
                             DeoRC  4 eeKrrIAkaAaeliedgdtifldaGtTtlelaraLae 40
                                      ++Krr A++Aa+l+e g+t+ l++G+T+++ +raL +
  gi|313124833|ref|YP_004035097.1|  9 DQKRRAAERAADLVETGATVGLGTGSTAAFAIRALGR 45
                                      79*******************************9976 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0016
                             DeoRC  93 vdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKfgk 141
                                       +d+a+ ga+ +d + +l++   +  + ++ + ++a+r +++aD sK+ +
  gi|313124833|ref|YP_004035097.1|  82 IDVAIDGADQLDGDLNLIKGGGAAHAREKIVDAMADRFVVVADPSKVTE 130
                                       5667777777777777777777666777777789************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1462.88
//
Query:       gi|313124834|ref|YP_004035098.1|  [L=270]
Description: hypothetical protein Hbor_00460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0065   16.2   0.0      0.011   15.4   0.0    1.4  1  YcxB      YcxB-like protein
  ------ inclusion threshold ------
        2.5    8.7   4.3        2.2    8.8   0.1    2.4  2  DUF4179   Domain of unknown function (DUF4179)


Domain annotation for each model (and alignments):
>> YcxB  YcxB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-06     0.011       2      35 ..     205     238 ..     204     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-06
                              YcxB   2 tedgievdsgggesiipWdsiekvkEtkdyfyLf 35 
                                       +e+g+ v++gg ++ + Wd+i+ +  t+d  +L 
  gi|313124834|ref|YP_004035098.1| 205 YENGVAVEQGGVTAFYGWDQITAIDRTDDAVVLR 238
                                       699**9************************9996 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.2      0.12   1.1e+03      10      31 ..      14      35 ..       2      61 .. 0.62
   2 ?    8.8   0.1   0.00024       2.2       7      69 ..     149     211 ..     145     218 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.12
                                      XXXXXXXXXXXXXXXXXXXXXX CS
                           DUF4179 10 aaaaaalvllllssrllspalA 31
                                       +aaa+++ ++++ + ++ +l 
  gi|313124834|ref|YP_004035098.1| 14 FVAAAVVTPVAVGLIAADVSLV 35
                                      3455555555455555554444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00024
                                       XXXXXXXXXXXXX...XXXXXXXXXXXXXXX.--SS-HHHHT--SS-HHHHSEEEEEEEEETTEEE CS
                           DUF4179   7 kkvaaaaaalvll...llssrllspalAsalnpvigslfeklsdskgeqeyvkpvnksaednGitv 69 
                                       k+ +++a  l++l    + + ++ p l+s l p +g+lf  + +s   ++++++    a +nG+ v
  gi|313124834|ref|YP_004035098.1| 149 KSSVVVASGLTALivsTVAAFTVAPWLSSLL-PFVGGLFGGMLGS--ISQLKQSRSYLAYENGVAV 211
                                       4455556566666455667788888899999.*******999888..5666666555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1706.38
//
Query:       gi|313124835|ref|YP_004035099.1|  [L=55]
Description: hypothetical protein Hbor_00470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-05   23.5   1.2      5e-05   23.4   1.2    1.1  1  DUF1931        Domain of unknown function (DUF1931)
    0.00042   20.6   0.1     0.0006   20.0   0.1    1.4  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
  ------ inclusion threshold ------
      0.014   14.7   0.1      0.015   14.7   0.1    1.1  1  DctP           Bacterial extracellular solute-binding protein
      0.023   15.0   0.1      0.023   15.0   0.1    1.2  1  Histone        Core histone H2A/H2B/H3/H4
      0.085   12.7   0.1      0.092   12.6   0.1    1.1  1  Peptidase_M41  Peptidase family M41


Domain annotation for each model (and alignments):
>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.2   1.4e-08     5e-05      14      53 ..      16      55 .]       2      55 .] 0.91

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.4e-08
                                      -HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS CS
                           DUF1931 14 dkedlkrisdfVekklydLllvaeenAkangrdviepaDL 53
                                      dk+ ++++ d +++++++Ll+ a ++A++n r++++p+DL
  gi|313124835|ref|YP_004035099.1| 16 DKNVASDFYDALDEEVKELLEDAARRAEENDRKTVQPRDL 55
                                      69999**********************************8 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.7e-07    0.0006      29      61 ..      23      55 .]       2      55 .] 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.7e-07
                                      HHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHH CS
                     CBFD_NFYB_HMF 29 iaecveefieelaseAaeickkekrKtikaehi 61
                                      +++++ e ++el++ Aa+++++++rKt+++ ++
  gi|313124835|ref|YP_004035099.1| 23 FYDALDEEVKELLEDAARRAEENDRKTVQPRDL 55
                                      67889999**********************997 PP

>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   4.2e-06     0.015     212     243 ..      20      51 ..       8      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-06
                                       EHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHH CS
                              DctP 212 nkktwdsLpedlqaileeaakeatelqrklve 243
                                        ++++d L e++++ le+aa++a+e  rk v+
  gi|313124835|ref|YP_004035099.1|  20 ASDFYDALDEEVKELLEDAARRAEENDRKTVQ 51 
                                       579**********************9999876 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   6.5e-06     0.023     100     124 ..      31      55 .]       5      55 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.5e-06
                                       HHHHHHHHHHHHHHTTXSEEXHHHH CS
                           Histone 100 lvelfeeAnllakhaKRvTitpkDi 124
                                         el+e+A++ a+++ R+T++p+D+
  gi|313124835|ref|YP_004035099.1|  31 VKELLEDAARRAEENDRKTVQPRDL 55 
                                       569*********************6 PP

>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.6e-05     0.092     128     161 ..      11      44 ..       4      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                                       .------SS-HHHHHHHHHHHHHHHHHHHHHHHH CS
                     Peptidase_M41 128 kelkkekelseetaeeideevkelveeayerake 161
                                       ke  ++k+++++  +++deevkel+e+a +ra+e
  gi|313124835|ref|YP_004035099.1|  11 KEALNDKNVASDFYDALDEEVKELLEDAARRAEE 44 
                                       556678999**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1224  (0.0682693); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 396.92
//
Query:       gi|313124836|ref|YP_004035100.1|  [L=257]
Description: ncair mutase-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-15   55.4   3.8    4.9e-15   55.4   3.8    2.0  2  AIRC      AIR carboxylase


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1     0.029   5.2e+02     104     135 ..      41      73 ..      25      83 .. 0.71
   2 !   55.4   3.8   2.7e-19   4.9e-15       2     127 ..     119     247 ..     118     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.029
                                       TTS--EE-SST.HHHHHHHHHHHHHTTT-HHHH CS
                              AIRC 104 sgvpvatvaig.kaknAallAaqilalkdeela 135
                                       +gvp a +a g  ++ Aa lAa  +  + +++ 
  gi|313124836|ref|YP_004035100.1|  41 RGVPEAILADGkTPDEAATLAAAAVKSTGRAIL 73 
                                       678877777666678888888876665555554 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 2.7e-19
                                       EEEEESSGGGHHHHHHHHHHHHHTT-EE..EEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHS CS
                              AIRC   2 VgiimGSdsDlevmkkaaeilkelgvey..evrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslt 76 
                                       Vgi++G +sD e + +a  il+e+g ++    +v  ah    ++++ +++ ++   +v++++AG++ +Lp vva+l+
  gi|313124836|ref|YP_004035100.1| 119 VGIVTGGTSDAEAAGEASVILEEMGATVtrVEDVGVAH--LGRVIDHLDTLRA--ADVLVVAAGREGALPTVVAGLV 191
                                       9**********************987663245677777..4577777787765..79******************** PP

                                       SS-EEEEEE--...STTCCHHHHHHHHT--TTS--EE-SST..HHHHHHHHHHHHH CS
                              AIRC  77 tlPVigvPvks...kalkgldsllSivqmPsgvpvatvaig..kaknAallAaqil 127
                                       ++PVig Pv++   +  +g  +l  ++q ++ ++v+++++g   +++A+l+A  i 
  gi|313124836|ref|YP_004035100.1| 192 DTPVIGLPVSTgygHGGSGKAALEGMLQSCTVISVVNIDAGfvAGAQAGLIARAIS 247
                                       **********8443468899*********************999999****98885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1610.56
//
Query:       gi|313124837|ref|YP_004035101.1|  [L=49]
Description: hypothetical protein Hbor_00490 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0011   19.1   2.0        0.6   10.4   0.1    2.2  2  zf-RING_7        C4-type zinc ribbon domain
     0.0044   17.0   0.3     0.0056   16.7   0.3    1.2  1  DZR              Double zinc ribbon
     0.0064   16.4   0.4       0.02   14.8   0.4    1.7  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0081   16.5   0.4     0.0093   16.3   0.4    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.017   14.5   3.3       0.53    9.8   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.019   15.3   0.1       0.02   15.2   0.1    1.1  1  DUF3268          zinc-finger-containing domain
      0.019   15.3   0.4        6.3    7.3   0.0    2.2  2  zf-IS66          zinc-finger binding domain of transposase IS
      0.021   14.7   0.4      0.027   14.4   0.4    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.031   14.4   3.3       0.24   11.5   3.3    2.0  1  Zn-ribbon_8      Zinc ribbon domain
      0.032   14.1   0.2      0.046   13.6   0.2    1.3  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.041   13.8   0.3        1.3    9.0   0.0    2.1  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.045   13.5   0.2        2.6    7.9   0.0    2.2  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.079   13.7   0.6      0.085   13.6   0.6    1.1  1  ATPase-cat_bd    Putative metal-binding domain of cation tran
      0.093   12.3   0.4       0.99    9.1   0.1    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.32   11.0   2.4        1.9    8.5   0.1    2.1  2  zinc_ribbon_4    zinc-ribbon domain
       0.53   10.3   4.0        7.3    6.7   3.9    2.0  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.77    9.8   5.2        3.9    7.5   0.7    2.1  2  Ogr_Delta        Ogr/Delta-like zinc finger


Domain annotation for each model (and alignments):
>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.3    0.0021       2.2      24      30 ..       2       8 ..       1       9 [. 0.87
   2 !   10.4   0.1   0.00056       0.6      12      30 ..      13      33 ..      12      34 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                                      EE-TTT- CS
                         zf-RING_7 24 vtCpeCG 30
                                      +tC++CG
  gi|313124837|ref|YP_004035101.1|  2 PTCDHCG 8 
                                      8*****9 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00056
                                      CHHHHHCCS..TB-EE-TTT- CS
                         zf-RING_7 12 qvlselrag..devvtCpeCG 30
                                      ++++++ a   + +  Cp+C+
  gi|313124837|ref|YP_004035101.1| 13 ERFARVFADveGRILACPNCS 33
                                      6677776666688*******7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   5.3e-06    0.0056      14      37 ..       3      35 ..       1      41 [. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.3e-06
                               DZR 14 fCseCgtklkavaa.........edrCpsCgek 37
                                      +C++Cg+++++  a           +Cp+C++ 
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVSERFArvfadvegrILACPNCSAN 35
                                      7********977779*******999*****986 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.4   1.9e-05      0.02       2      26 ..       1      33 [.       1      35 [. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                    PhnA_Zn_Ribbon  2 lpkCplCaSeytY........edgallvCpeCa 26
                                      +p C +C+S ++         ++g +l Cp+C+
  gi|313124837|ref|YP_004035101.1|  1 MPTCDHCGSHVSErfarvfadVEGRILACPNCS 33
                                      799******998889*****************7 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   8.8e-06    0.0093       5      38 ..       3      36 ..       1      49 [] 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.8e-06
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCgast 38
                                       C++Cg+     ++   +   g   +C +C a+ 
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVSERFARVFADVEGRILACPNCSANA 36
                                      7******9999999665555555*********22 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0005      0.53       4      14 ..       3      13 ..       1      14 [. 0.64
   2 ?    5.6   0.5      0.01        11       5       8 ..      29      32 ..      27      37 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0005
                       zf-ribbon_3  4 rCPnCGaplss 14
                                      +C +CG+++s+
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVSE 13
                                      57777776665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                       zf-ribbon_3  5 CPnC 8 
                                      CPnC
  gi|313124837|ref|YP_004035101.1| 29 CPNC 32
                                      7777 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   1.9e-05      0.02       4      44 ..       3      40 ..       1      48 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                           DUF3268  4 rCpyCGekvilvsaseiYkerskgkllylCpkCdayvgvhk 44
                                      +C++CG++v  + a+ ++   + +  +  Cp+C a  g+ +
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVSERFAR-VF--ADVEGRILACPNCSANAGIAE 40
                                      7*******9988775.66..355567889******999865 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0099        10       3      15 ..       3      12 ..       2      23 .. 0.69
   2 ?    7.3   0.0     0.006       6.3       3      22 ..      28      45 ..      27      48 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0099
                           zf-IS66  3 tCpcCGgllkpig 15
                                      tC++CG+    + 
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSH---VS 12
                                      8*****84...33 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.006
                           zf-IS66  3 tCpcCGg.llkpigedrvree 22
                                      +Cp+C + +   i+e+  r++
  gi|313124837|ref|YP_004035101.1| 28 ACPNCSAnA--GIAEV-ARQR 45
                                      6****9944..77777.6665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   2.6e-05     0.027      30      55 ..       3      35 ..       2      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke.......alsgrtfkCpnCgfe 55
                                      tC +Cgs ++e       +++gr + CpnC + 
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVSErfarvfaDVEGRILACPNCSAN 35
                                      8********999******************875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.3   0.00023      0.24       8      35 ..       4      35 ..       1      37 [. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                       Zn-ribbon_8  8 CeeCghefe.vlqsis...dapltaCPeCgse 35
                                      C+ Cg+    ++++++   +    aCP+C ++
  gi|313124837|ref|YP_004035101.1|  4 CDHCGSHVSeRFARVFadvEGRILACPNCSAN 35
                                      9999966655555555413444566****875 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   4.4e-05     0.046      13      37 ..       3      35 ..       1      36 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-05
                                      B-TTT-SB-.......-S.SSS-EEEETTT--E CS
                              C1_1 13 fCkhCgefl.......wg.kekqglkCswCkll 37
                                      +C+hCg+++       +   e ++l+C +C+ +
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVserfarvFAdVEGRILACPNCSAN 35
                                      6**********999997779999*******875 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.081        85      24      30 ..       4      10 ..       2      13 .. 0.75
   2 ?    9.0   0.0    0.0012       1.3      16      29 ..      21      34 ..      18      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.081
                                      ESSSS-E CS
                    RNA_POL_M_15KD 24 CrqCgYe 30
                                      C+ Cg++
  gi|313124837|ref|YP_004035101.1|  4 CDHCGSH 10
                                      7777765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0012
                                      CSCCCEEEESSSS- CS
                    RNA_POL_M_15KD 16 dkegknfeCrqCgY 29
                                      d+eg++++C +C++
  gi|313124837|ref|YP_004035101.1| 21 DVEGRILACPNCSA 34
                                      89**99******97 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0024       2.6       3      15 ..       3      15 ..       2      18 .. 0.85
   2 ?    4.2   0.0     0.036        38       4       9 ..      29      34 ..      26      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0024
                                      E-SSS--EEEEEE CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkr 15
                                      +C+ Cg+++ ++ 
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVSERF 15
                                      7*******99886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.036
                                      -SSS-- CS
                    zf-C4_Topoisom  4 CPkCgg 9 
                                      CP C +
  gi|313124837|ref|YP_004035101.1| 29 CPNCSA 34
                                      ****86 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6     8e-05     0.085       1      35 [.       3      36 ..       3      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8e-05
                     ATPase-cat_bd  1 aCyHCglpveesaklkaeiegeerefCCkGCqava 35
                                      +C HCg++v+e    ++  + e r + C+ C a a
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVSER-FARVFADVEGRILACPNCSANA 36
                                      6********885.34444555668999****9855 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00094      0.99       4      14 ..       3      13 ..       1      17 [. 0.89
   2 ?    1.9   0.0      0.16   1.7e+02       4      10 ..      28      34 ..      27      42 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00094
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C+ Cg++++e
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVSE 13
                                      8*******997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                            zf_UBZ  4 lCerCgk 10
                                       C+ C +
  gi|313124837|ref|YP_004035101.1| 28 ACPNCSA 34
                                      5****86 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.5      0.13   1.3e+02       4       9 ..       3       8 ..       2      10 .. 0.63
   2 ?    8.5   0.1    0.0018       1.9       3      11 ..      27      35 ..      23      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                     zinc_ribbon_4 4 tCpsCk 9
                                     tC +C+
  gi|313124837|ref|YP_004035101.1| 3 TCDHCG 8
                                     566665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0018
                     zinc_ribbon_4  3 itCpsCkak 11
                                        Cp+C+a 
  gi|313124837|ref|YP_004035101.1| 27 LACPNCSAN 35
                                      579999886 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.9    0.0069       7.3      19      45 ..       2      34 ..       1      35 [. 0.80
   2 ?    5.8   0.2     0.013        14      20      28 ..      28      37 ..      18      48 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0069
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt......rglfqCkeCrk 45
                                      ++C hCgs  + r+++       + + C  C++
  gi|313124837|ref|YP_004035101.1|  2 PTCDHCGSHVSERFARvfadveGRILACPNCSA 34
                                      79*****99777777777788878889998875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                     Zn_Tnp_IS1595 20 vCPhCgsr.k 28
                                       CP+C     
  gi|313124837|ref|YP_004035101.1| 28 ACPNCSANaG 37
                                      5****86554 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.2    0.0044       4.7       1      41 [.       3      40 ..       3      44 .. 0.75
   2 ?    7.5   0.7    0.0037       3.9       2      13 ..      29      40 ..      28      49 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0044
                         Ogr_Delta  1 rCPhCgapaaartsrnlskdvreryyqCsnfeCgatfvaae 41
                                      +C hCg++   r  r   +dv  r+  C n  C+a+   ae
  gi|313124837|ref|YP_004035101.1|  3 TCDHCGSHVSERFARV-FADVEGRILACPN--CSANAGIAE 40
                                      5889999888877664.5678889999999..999866655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0037
                         Ogr_Delta  2 CPhCgapaaart 13
                                      CP+C a+a +  
  gi|313124837|ref|YP_004035101.1| 29 CPNCSANAGIAE 40
                                      ******997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 327.17
//
Query:       gi|313124838|ref|YP_004035102.1|  [L=278]
Description: 5''/3''-nucleotidase sure [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-45  153.2   0.0    8.8e-45  152.9   0.0    1.1  1  SurE      Survival protein SurE


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.9   0.0   4.9e-49   8.8e-45       1     179 [.       7     179 ..       7     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 4.9e-49
                                       EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHH CS
                              SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvkla 77 
                                       iLltNDDGi+apgi +l e+l++ g +v+v+aPd +rSg+g+  + +  +r       e+   ya+sGtPadcv ++
  gi|313124838|ref|YP_004035102.1|   7 ILLTNDDGIDAPGIATLREELTSLG-DVTVIAPDGNRSGVGRTRNHTAVVR-------EHPWGYALSGTPADCVAYG 75 
                                       8*********************888.****************993333333.......45789************** PP

                                       HHTTTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSS....SS-SSS---HHHHHHHH CS
                              SurE  78 leellkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskk....eeekkeedtfeaaakva 149
                                       l++l  +   d+VvSG+N G+N+g+ v   SGTvgA +eaa+ g pa+AvS+ +++    ++   ee +f++ a+va
  gi|313124838|ref|YP_004035102.1|  76 LRGLDTD--FDVVVSGVNDGPNAGNYVvGRSGTVGAGIEAAFLGTPALAVSAFHTTdfflSPP--EEYDFSRPARVA 148
                                       *888865..5*****************99***********************98889985333..4556******** PP

                                       HHHHTTETTS-...SS-EEEEEEE.SS.GCG CS
                              SurE 150 aklveklieklllekvellnvNvP.eleeee 179
                                       + lve+ +++ + ++v+llnvN P ++++  
  gi|313124838|ref|YP_004035102.1| 149 VGLVERALDSGVYDDVDLLNVNAPvDSPNPP 179
                                       ************************5444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1990.30
//
Query:       gi|313124839|ref|YP_004035103.1|  [L=82]
Description: endonuclease containing a uri domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-18   65.3   0.0    5.1e-18   65.1   0.0    1.0  1  GIY-YIG   GIY-YIG catalytic domain
  ------ inclusion threshold ------
      0.013   16.0   0.1      0.015   15.8   0.1    1.2  1  T5orf172  T5orf172 domain


Domain annotation for each model (and alignments):
>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   5.6e-22   5.1e-18       2      76 ..       4      75 ..       3      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 5.6e-22
                                      -EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-HS.STEEEEEEEE----HHHHHHHHHHHHHHTTSS CS
                           GIY-YIG  2 ggvYiirskenkliYvGstknlekRlkqHnagkkakytrkkgkkpfeliileifptksealelEkklikkyksnk 76
                                      ++vY++r+ +++l Y+G+t+++++R  +H ag++akytr+  ++p+el++ e f+++s a+++E+++++ ++++k
  gi|313124839|ref|YP_004035103.1|  4 HYVYVLRCSDDSL-YTGYTTDVDRRVAEHDAGEGAKYTRG--RTPVELVHTEAFDSRSTAMSREYEIKQLSRRQK 75
                                      8***********7.*************************8..****************************99854 PP

>> T5orf172  T5orf172 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.1   1.7e-06     0.015       2      66 ..       5      68 ..       4      82 .] 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-06
                          T5orf172  2 yvYiltnessegetillKIGrtsnvqrRlkelsk....yptkppselevvaekevrkvpnahrvErlih 66
                                      yvY+l+ ++++        G+t++v+rR++e+      ++t   +++e+v++++  ++  a+  E +i+
  gi|313124839|ref|YP_004035103.1|  5 YVYVLRCSDDSLY-----TGYTTDVDRRVAEHDAgegaKYTRGRTPVELVHTEAFDSRSTAMSREYEIK 68
                                      7888855555444.....7**************999996666666666666644444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.31s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 529.39
//
Query:       gi|313124840|ref|YP_004035104.1|  [L=186]
Description: flavoprotein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-32  111.8   0.0    3.1e-32  111.5   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    2.3e-08   34.0   0.0    4.3e-08   33.1   0.0    1.6  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.032   14.5   0.0    1.5  2  Flavodoxin_5  Flavodoxin domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.0   5.2e-36   3.1e-32       1     151 [.       2     140 ..       2     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 5.2e-36
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEE CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadali 77 
                                       ++i++i+GS r+gs+trk +e +++a++ agae++++dl+d +lp  l++ d++    ++ + ++l++ +++ad++i
  gi|313124840|ref|YP_004035104.1|   2 TRIVAICGSRREGSYTRKSLEIVLDAARDAGAETTMVDLGDVDLP--LFHPDKD----EQGESERLTRLVRKADGVI 72 
                                       69*******************************************..9998884....79999************** PP

                                       EEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEET CS
                           FMN_red  78 ivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavg 151
                                       i++P+Y+gsys+ + n+ D++s    k+e ++ +v+lva++gg + g +a e++r+  + ++ +vvp+ +v v+
  gi|313124840|ref|YP_004035104.1|  73 IGSPVYHGSYSSTFRNFHDYCS----KDEYEDTAVGLVATAGGGSYG-GALEHMRSTIRGVHGHVVPE-QVGVR 140
                                       *********************9....***************995555.89999******9*******9.87765 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   7.2e-12   4.3e-08       2     137 ..       3     112 ..       2     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 7.2e-12
                                       EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTTCHHHHHHH.HHHHHC CS
                      Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeekpadveseq.ieklla 77 
                                       +i+ i ++ r+ +s +++ ++ +++a+++ag +e t +dL +  lp + +          +k    ese+    ++ 
  gi|313124840|ref|YP_004035104.1|   3 RIVAICGSRRE-GSYTRKSLEIVLDAARDAG-AETTMVDLGDVDLPLFHP----------DKDEQGESERlTRLVRK 67 
                                       78889999998.7******************.9*********98888875..........323678999999***** PP

                                       SSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS- CS
                      Flavodoxin_2  78 adaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgp 137
                                       ad +++++P++  ++++ + ++ D+     +               ++  + +++t+Gg 
  gi|313124840|ref|YP_004035104.1|  68 ADGVIIGSPVYHGSYSSTFRNFHDYCSKDEY---------------EDTAVGLVATAGGG 112
                                       ************************9633322...............34455555555555 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.5   9.2e+03      11      33 ..      17      39 ..      10      47 .. 0.54
   2 ?   14.5   0.0   5.4e-06     0.032      42      67 ..      66      91 ..      55     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.5
                      Flavodoxin_5 11 Tkkiaeriaeelreegelvdved 33
                                      T+k  e + ++ r++g+++++ d
  gi|313124840|ref|YP_004035104.1| 17 TRKSLEIVLDAARDAGAETTMVD 39
                                      45555555555555555444444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.4e-06
                      Flavodoxin_5 42 esydavvigasvyygkllpelakFve 67
                                       ++d v+ig++vy+g+ ++++++F +
  gi|313124840|ref|YP_004035104.1| 66 RKADGVIIGSPVYHGSYSSTFRNFHD 91
                                      67899*******************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1149.48
//
Query:       gi|313124841|ref|YP_004035105.1|  [L=457]
Description: phosphomannomutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-37  126.8   0.0    8.1e-37  126.0   0.0    1.4  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.8e-26   92.7   0.1    3.6e-26   91.8   0.1    1.5  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.6e-24   83.9   0.1    1.6e-23   83.1   0.1    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
      9e-13   48.2   0.1    2.8e-12   46.6   0.1    1.9  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.0   1.8e-40   8.1e-37       3     133 ..       5     134 ..       3     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 1.8e-40
                                       GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEE.EB- CS
                         PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillg.llp 78 
                                       +fgt+G+R      ++t+e v+ +gqa+a+yl+ e+ +++v+vG+D+R +s  +ae+la++la nG++v+l +  +p
  gi|313124841|ref|YP_004035105.1|   5 SFGTDGWRATLD--TFTDERVRIVGQAVADYLSDEGYEAPVFVGYDARDTSLGFAESLAEVLAGNGFDVLLPDrDRP 79 
                                       7********998..79************************************************************* PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCC CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiek 133
                                       tP v++ai + ++++++m+taSHnppeyng+K+++++G+p+ p v+e+I +++++
  gi|313124841|ref|YP_004035105.1|  80 TPLVAHAIVERNLAGALMVTASHNPPEYNGVKFIPADGAPALPYVTEAIVERLAE 134
                                       *************************************************999876 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.1   8.1e-30   3.6e-26       3     102 ..     155     250 ..     153     252 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 8.1e-30
                                       HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGG CS
                        PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvk 79 
                                       ++e+ +e vd      sgl+vv+d++hG+g+++++ ll+++g++vv++++e+d df+++ p+p + e+l+ l+e+v+
  gi|313124841|ref|YP_004035105.1| 155 HFEHARELVD---ADLSGLTVVHDAMHGSGRGVTSALLESAGAEVVSIRDERDSDFGGTPPEPSA-ENLEPLVEAVE 227
                                       5677888888...56789***********************************************.*********** PP

                                       GGG-SEEEEE-TTS-BEEEEETT CS
                        PGM_PMM_II  80 kegadlglafDgDaDRlgvvder 102
                                       +++adlg+a+DgDaDR+++v+++
  gi|313124841|ref|YP_004035105.1| 228 EHDADLGVANDGDADRVAFVTPE 250
                                       ********************864 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.1   3.5e-27   1.6e-23       5     108 ..     259     357 ..     255     363 .. 0.86

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 3.5e-27
                                       HHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBS CS
                       PGM_PMM_III   5 llallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeat 81 
                                        +a + +yll+e  + g   ++tv+t+ +++r+a+++g +++et+vG+k+v+++mke++a++GgEeSg+++++ +++
  gi|313124841|ref|YP_004035105.1| 259 FFAAAYDYLLAE--ESGP-AIRTVSTTFLIDRIAEAHGQEVFETAVGFKWVADAMKEHDALMGGEESGGFSIRGHVR 332
                                       567788899885..4455.8********************************************************* PP

                                       S--HHHHHHHHHHHHHHHTS-HHHHHH CS
                       PGM_PMM_III  82 tkDGilaallvleilaetgkslselle 108
                                       +kDG+l+ ll ++++a++  +++e ++
  gi|313124841|ref|YP_004035105.1| 333 EKDGVLMGLLGAAATADE--PMDERVD 357
                                       **********99999976..4555443 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   6.2e-16   2.8e-12      16      68 ..     400     448 ..     371     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 6.2e-16
                                       CCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHH CS
                        PGM_PMM_IV  16 laallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaee 68 
                                       ++++     + +g k lledG++l  RpSGTep+ rvy+Ea+s++ + +l e+
  gi|313124841|ref|YP_004035105.1| 400 IEKV----VTLDGFKLLLEDGSWLLARPSGTEPKMRVYAEASSEDDVRELLEA 448
                                       2222....489************************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3184.62
//
Query:       gi|313124842|ref|YP_004035106.1|  [L=133]
Description: acetyltransferase (gnat) family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-11   42.1   0.0    8.6e-11   41.9   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.2e-10   41.7   0.0    1.6e-10   41.3   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      1e-08   35.4   0.0    1.3e-08   35.1   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.8e-07   29.2   0.3    7.5e-06   26.1   0.3    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    8.3e-06   25.6   2.4    1.1e-05   25.2   2.4    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
  ------ inclusion threshold ------
      0.027   14.6   0.0       0.05   13.7   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.029   14.3   0.1      0.053   13.5   0.1    1.4  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
      0.055   13.3   0.6      0.065   13.0   0.6    1.1  1  Amidohydro_2     Amidohydrolase
      0.061   13.3   0.1       0.13   12.2   0.1    1.6  2  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   4.3e-14   8.6e-11      17     109 ..      23     111 ..       5     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 4.3e-14
                   Acetyltransf_10  17 ispealrerieegealllvaeeggkivGviel.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgiklelt 90 
                                       ++ +++r+rie+g++  lva+ +g++vGv+ l r+++   i+ ++V+++ r +Gig++L+e++ ++   dg    +t
  gi|313124842|ref|YP_004035106.1|  23 VESDRVRRRIEDGDV--LVADANGRVVGVCVLvRRDDatAITQIAVHRSRRARGIGRRLVETAASRT--DG---PVT 92 
                                       46689999*977666..9************887777789************************9997..43...799 PP

                   Acetyltransf_10  91 vnaspyavpfYeklGFkav 109
                                       +   ++ +pfYe l F+ +
  gi|313124842|ref|YP_004035106.1|  93 ATFRRQVRPFYEALEFEIT 111
                                       9999************987 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   7.9e-14   1.6e-10       2      75 ..      34     109 ..      33     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 7.9e-14
                                       TEEEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHHTT...SE.EEEEEEEETHH.HHHHHHHH CS
                    Acetyltransf_7   2 kgevfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLleaae...kg.iileqlelnae.kaikfYek 71 
                                       +g v+Va+ +g++vG ++l+++d  + it +aV+ + r +GiGr+L+e a+    g ++     +  + + ++fYe 
  gi|313124842|ref|YP_004035106.1|  34 DGDVLVADANGRVVGVCVLVRRDdaTAITQIAVHRSRRARGIGRRLVETAAsrtDGpVT----ATF-RrQVRPFYEA 105
                                       6889****************9999999999******************63333444221....111.123466**** PP

                                       TTEE CS
                    Acetyltransf_7  72 lGFe 75 
                                       l Fe
  gi|313124842|ref|YP_004035106.1| 106 LEFE 109
                                       *998 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   6.5e-12   1.3e-08      23      90 ..      28      88 ..       4     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.5e-12
                                      HHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHH CS
                    Acetyltransf_1 23 efeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerar 90
                                      ++    ++e++  lva  +g+++G + l  ++d     ++i ++aV++++r +G+G++L+e+++ r  
  gi|313124842|ref|YP_004035106.1| 28 VR---RRIEDGDVLVADANGRVVGVCVLVRRDD----ATAITQIAVHRSRRARGIGRRLVETAASRTD 88
                                      22...4447779999******************....89999********************997655 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.3   3.7e-09   7.5e-06       3     103 ..       2      88 ..       1     111 [. 0.84

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.7e-09
                                       EEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEE CS
                    Acetyltransf_9   3 relteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgV 79 
                                       r ++++d  +++ell++a  + es++      +r+++e+++vl+a  ng++vg++ l++++        +a ++t +
  gi|313124842|ref|YP_004035106.1|   2 RLARSDDRAACVELLDAAMLEVESDR------VRRRIEDGDVLVADANGRVVGVCVLVRRD--------DATAITQI 64 
                                       8899********************94......799***********************988........7889**** PP

                                       EE-CCGTTS-HHHHHHHHHHHHHH CS
                    Acetyltransf_9  80 avapehrgrgvlskLlaraleemr 103
                                       av+   r rg+ ++L+++a  + +
  gi|313124842|ref|YP_004035106.1|  65 AVHRSRRARGIGRRLVETAASRTD 88 
                                       *****************9987766 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   2.4   5.3e-09   1.1e-05      36      89 ..      33      86 ..      16     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.3e-09
                              PanZ 36 eegalfaarFNdRlLgAvkveledkeaelsdlcVRevTRrRGVgsyLleearrq 89
                                      e+g +++a  N R  g + + ++d++ +++++ V +  R RG+g++L+e a  +
  gi|313124842|ref|YP_004035106.1| 33 EDGDVLVADANGRVVGVCVLVRRDDATAITQIAVHRSRRARGIGRRLVETAASR 86
                                      5677889999**************************************987654 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-05      0.05       9      51 ..      44      85 ..      37      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                   Acetyltransf_CG  9 geevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaald 51
                                      g  v+++    r+++  ++t + V+ + r +Gi+++Lv++a  
  gi|313124842|ref|YP_004035106.1| 44 GRVVGVCVLV-RRDDATAITQIAVHRSRRARGIGRRLVETAAS 85
                                      5667777776.88889***********************9976 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.7e-05     0.053       6      32 ..      60      86 ..      58      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                   Acetyltransf_13  6 GisriWvssshRrkgiAtkLldaaren 32
                                       i +i v++s R +gi ++L+++a+++
  gi|313124842|ref|YP_004035106.1| 60 AITQIAVHRSRRARGIGRRLVETAASR 86
                                      58999******************9986 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6   3.3e-05     0.065      68     139 ..      30     107 ..       6     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH.......HHHHHH CS
                      Amidohydro_2  68 gannrvlaeaakrpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrld.......rpifea 137
                                       +  ++   ++a++++r+vg  ++v++d+++a+ ++  +  +++++G+   +     ++++ +         rp++ea
  gi|313124842|ref|YP_004035106.1|  30 RRIEDGDVLVADANGRVVGVCVLVRRDDATAITQIAVHR-SRRARGIGRRLVETAASRTDGPVTatfrrqvRPFYEA 105
                                       5555556688999**************************.******9988888888888888888999999*****9 PP

                                       HH CS
                      Amidohydro_2 138 le 139
                                       le
  gi|313124842|ref|YP_004035106.1| 106 LE 107
                                       97 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.7e-05      0.13      17      47 ..      53      84 ..      38      89 .. 0.81
   2 ?   -2.5   0.0       2.5     5e+03      69      78 ..     100     109 ..      91     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                                      EE-TT.SSEEEEEE-GGG-SSSHHHHHHHHHH CS
                              FR47 17 lrkdg.gelgalqvlpehrrrGlgsrlvkala 47
                                      +r+d+ +++  + v+ + r rG g+rlv+  a
  gi|313124842|ref|YP_004035106.1| 53 VRRDDaTAITQIAVHRSRRARGIGRRLVETAA 84
                                      455555**********************8755 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.5
                                       HHHHHHHT-E CS
                              FR47  69 irlyeklGfe 78 
                                       + +ye+l fe
  gi|313124842|ref|YP_004035106.1| 100 RPFYEALEFE 109
                                       5689999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 897.46
//
Query:       gi|313124843|ref|YP_004035107.1|  [L=159]
Description: peroxiredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-17   64.0   0.0    1.4e-17   63.7   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    4.3e-07   29.7   0.0    5.4e-07   29.4   0.0    1.1  1  Redoxin        Redoxin
  ------ inclusion threshold ------
      0.041   14.0   0.0      0.086   13.0   0.0    1.4  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
       0.11   12.8   0.1       0.12   12.7   0.1    1.3  1  Thioredoxin_8  Thioredoxin-like


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   3.2e-21   1.4e-17       5     100 ..       6     104 ..       3     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 3.2e-21
                                       --.--EEESTTC..EEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHH CS
                          AhpC-TSA   5 ap.dfelknadg..etvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfie 78 
                                       ap dfel+n     +t+s +d   +++vl+  +   c+ C++++++ +++y+ef+++++ev+ v +++ ++ kk++ 
  gi|313124843|ref|YP_004035107.1|   6 APlDFELPNVGAgpDTFSPADADAEYLVLLLQRDYYCKKCRRQVQSAKRRYDEFQDANAEVVSVLPEPTDRTKKWQT 82 
                                       5548****87652377999999999**************************************************** PP

                                       H-H.SSEEEE-TTSHHHHHTT- CS
                          AhpC-TSA  79 keslnfpllsDeegkvakaygv 100
                                        ++l+fpll+De ++v +a + 
  gi|313124843|ref|YP_004035107.1|  83 SYDLPFPLLADEGKEVGDAMDQ 104
                                       ****************988765 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.2e-10   5.4e-07       5     147 .]       5     153 ..       1     153 [. 0.86

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.2e-10
                                       BB-.--ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHH CS
                           Redoxin   5 kaP.dftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefw 80 
                                       +aP df+lp++  ++ ++s ++     +v+   +   c  C++++   +  ++++ + + +vv v     +  k++ 
  gi|313124843|ref|YP_004035107.1|   5 TAPlDFELPNVGAGPDTFSPADADAEYLVLLLQRDYYCKKCRRQVQSAKRRYDEFQDANAEVVSVLPEPTDRTKKWQ 81 
                                       5777999***************99999999999999**********777777888********************** PP

                                       HHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG......EEE-EEEEEE.ETTEEEEEEESSSCHTSTTSHHHHH CS
                           Redoxin  81 gkeglkfpvlsDgsaaftkalGlrleedaseg......lrtpryavid.edgkvvylevepepeteesnaeavl 147
                                       ++++l+fp+l+D+++++  a++ + +     g       r+p   v+d e g v   + +++p +++++++++l
  gi|313124843|ref|YP_004035107.1|  82 TSYDLPFPLLADEGKEVGDAMDQPERFG-VLGslhdlvGRMPEALVLDvETGEVLFDHAGDSP-GDRPDIDELL 153
                                       *********************9663322.2236788888999888886377899999999999.5699999876 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.9e-05     0.086       4      51 ..      54     102 ..      52     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                        AhpC-TSA_2   4 rdkpeldaagvklvaigigdps.akkFvkltgfpfelyvDpsaklyqal 51 
                                       r+ +e+++a+ ++v +  +  +  kk++   + pf+l++D+ +++ +a+
  gi|313124843|ref|YP_004035107.1|  54 RRYDEFQDANAEVVSVLPEPTDrTKKWQTSYDLPFPLLADEGKEVGDAM 102
                                       56799****************55*******************9999887 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.7e-05      0.12       3      43 ..      32      71 ..      30     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                                      EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE- CS
                     Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl 43
                                      +vlL   +++c++c++ +++ k+ y++++ + + e+v+v  
  gi|313124843|ref|YP_004035107.1| 32 LVLLLQRDYYCKKCRRQVQSAKRRYDEFQ-DANAEVVSVLP 71
                                      58889999********************9.69999998855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1171.30
//
Query:       gi|313124844|ref|YP_004035108.1|  [L=68]
Description: hypothetical protein Hbor_00560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 574.97
//
Query:       gi|313124845|ref|YP_004035109.1|  [L=328]
Description: replication factor c small subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-24   85.9   0.1    8.1e-24   83.8   0.0    2.1  2  Rep_fac_C        Replication factor C C-terminal domain
    5.7e-18   65.2   0.0    3.4e-12   46.4   0.0    2.2  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    5.8e-18   65.6   0.0    4.8e-16   59.4   0.0    2.2  2  AAA              ATPase family associated with various cellul
      1e-08   35.7   1.1    6.2e-06   26.7   0.0    2.9  3  AAA_16           AAA ATPase domain
    5.3e-08   32.8   0.0    1.6e-06   27.9   0.0    2.5  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.7e-07   30.1   0.0    9.5e-07   28.8   0.0    1.7  2  DNA_pol3_delta   DNA polymerase III, delta subunit
    2.8e-06   27.6   0.2    8.7e-06   26.0   0.2    1.9  1  AAA_assoc_2      AAA C-terminal domain
    3.4e-05   23.8   0.0    7.6e-05   22.7   0.0    1.6  1  Rad17            Rad17 P-loop domain
    0.00019   21.5   0.0    0.00036   20.6   0.0    1.5  1  AAA_14           AAA domain
     0.0003   21.1   0.2       0.86    9.9   0.1    2.6  2  AAA_22           AAA domain
    0.00084   19.4   0.0     0.0049   16.9   0.0    2.1  1  ResIII           Type III restriction enzyme, res subunit
      0.001   18.7   0.0     0.0028   17.2   0.0    1.7  1  AAA_25           AAA domain
     0.0013   18.6   0.0     0.0023   17.8   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
     0.0021   18.0   0.0      0.025   14.6   0.0    2.4  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0034   17.1   0.0        0.2   11.3   0.0    2.3  1  Sigma54_activat  Sigma-54 interaction domain
     0.0035   16.8   0.0       0.43    9.9   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0035   17.1   0.0      0.016   15.0   0.0    1.9  2  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.047   14.2   0.0    2.0  2  AAA_18           AAA domain
      0.016   15.7   0.1      0.032   14.7   0.1    1.7  1  AAA_23           AAA domain
      0.016   14.9   0.0      0.031   14.0   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.028   14.3   0.0        1.3    8.9   0.0    2.4  2  NACHT            NACHT domain
      0.055   13.0   0.0       0.14   11.7   0.0    1.7  2  AAA_7            P-loop containing dynein motor region
      0.073   12.7   0.0       0.13   11.8   0.0    1.4  1  DDE_Tnp_1        Transposase DDE domain
      0.074   12.7   0.1       0.36   10.4   0.0    2.1  3  SRP54            SRP54-type protein, GTPase domain
       0.12   11.8   0.0        2.1    7.7   0.0    2.4  2  PhoH             PhoH-like protein
       0.14   12.6   0.0        0.3   11.5   0.0    1.5  1  RNA_helicase     RNA helicase
       0.32   10.8   1.0        6.6    6.5   0.0    2.7  3  DEAD             DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         8   5.3e+03      34      54 ..      30      49 ..      20      52 .. 0.78
   2 !   83.8   0.0   1.2e-26   8.1e-24       2      88 .]     236     321 ..     235     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8
                                      --HHHHHHHHHHHGCCS..S- CS
                         Rep_fac_C 34 ysaediltqlhrvvkeqeelp 54
                                      y  edi++ l  ++ + ++lp
  gi|313124845|ref|YP_004035109.1| 30 YGQEDIVERLRSYIEQ-DDLP 49
                                      6678999999999887.4576 PP

  == domain 2  score: 83.8 bits;  conditional E-value: 1.2e-26
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-H CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGase 78 
                                       +p++iee+++++  g+f +a++kl++llv+ G+++ di+ qlhr v +  +l+e++ ++++e++ge+++r++eGa+e
  gi|313124845|ref|YP_004035109.1| 236 RPEDIEEMVQSAIDGEFLTARSKLETLLVDTGMAGGDIIDQLHRSVWDF-DLDERTTVRLMERIGEADYRITEGANE 311
                                       79**********99**********************************8.6************************** PP

                                       HHHHHHHHHH CS
                         Rep_fac_C  79 hlqlsallar 88 
                                       ++ql+alla+
  gi|313124845|ref|YP_004035109.1| 312 QVQLEALLAS 321
                                       ********96 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.4e-06    0.0042       1      46 [.      31      75 ..      31      85 .. 0.92
   2 !   46.4   0.0   5.1e-15   3.4e-12      84     162 ..      91     170 ..      79     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.4e-06
                   DNA_pol3_delta2  1 gqeealkilskalksgrlahayLfeGdegigkkelalnlakallce 46
                                      gqe++++ l++ ++++ l h +Lf+G++g+gk ++a+++a+a+  +
  gi|313124845|ref|YP_004035109.1| 31 GQEDIVERLRSYIEQDDLPH-LLFAGPAGVGKTTSATAIARAIYGD 75
                                      69999**************9.8*******************99765 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 5.1e-15
                   DNA_pol3_delta2  84 kldqirelieelsrkpres.kkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkf 159
                                        +d +r+ i+++ r+++ +  ++ii +++a+ +t+ A+ al +t+E  s+n+ fiL  + ++k++++i+SRc +++f
  gi|313124845|ref|YP_004035109.1|  91 GIDVVRDRIKNFARSSFGGfDYRIIFLDEADSLTSDAQSALRRTMEQFSDNTRFILSCNYSSKIIDPIQSRCAVFRF 167
                                       7999************99548******************************************************** PP

                   DNA_pol3_delta2 160 spl 162
                                       spl
  gi|313124845|ref|YP_004035109.1| 168 SPL 170
                                       *97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   7.2e-19   4.8e-16       1     129 [.      51     167 ..      51     170 .. 0.85
   2 ?    4.2   0.1     0.083        55      67     127 ..     195     251 ..     173     256 .. 0.74

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 7.2e-19
                                       EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHH CS
                               AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidala 71 
                                       +l+ Gp G+GKT+ a a+a+ +       +fle+++s+ +   +    ++i+++ ++      +  i+f+DE+d+l+
  gi|313124845|ref|YP_004035109.1|  51 LLFAGPAGVGKTTSATAIARAIygddwRGNFLELNASDER--GIDVVRDRIKNFARSSFG-GfDYRIIFLDEADSLT 124
                                       699******************844433599**********..777777777777766443.2577***********9 PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                       ++            +++L + ++++++   ++ +i+ +n+ +k+ +++  +R+ +  +
  gi|313124845|ref|YP_004035109.1| 125 SDA-----------QSALRRTMEQFSD---NTRFILSCNYSSKIIDPIQ-SRCAVFRF 167
                                       999...........*************...699****************.9**98766 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.083
                                       GGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                               AAA  67 idalaksrsgseseeeervvnqLlteldgvkkk.eskvivigatnrpdkldpallrgRfdrk 127
                                       +dal+ +      ++ +r++n L ++    +   e+ v +i+ t rp+++++ +  + +d +
  gi|313124845|ref|YP_004035109.1| 195 LDALVYAA----GGDMRRAINSLQAAATTGEIVdEEAVYLITSTARPEDIEEMVQ-SAIDGE 251
                                       56666665....56777888888776655554447779*************9988.777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   9.3e-09   6.2e-06       2      53 ..      29      77 ..      28      91 .. 0.86
   2 ?    6.3   0.0     0.017        11     119     164 ..      95     140 ..      80     146 .. 0.70
   3 ?   -0.1   0.2       1.6   1.1e+03      72     149 ..     231     303 ..     173     326 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.3e-09
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdgg 53
                                      ++G e+ +e+L+s++e   +++ + +l+ G++GvGK++ +++++ra+ +d++
  gi|313124845|ref|YP_004035109.1| 29 VYGQEDIVERLRSYIE---QDDLPHLLFAGPAGVGKTTSATAIARAIYGDDW 77
                                      69*************9...66779*********************9998853 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.017
                            AAA_16 119 llellkrllallsrderplvlvlDdlqwadeaslqllaaLlrlles 164
                                       +++ +k++++ +  + +  +++lD+++ + ++ +++l+ +++  ++
  gi|313124845|ref|YP_004035109.1|  95 VRDRIKNFARSSFGGFDYRIIFLDEADSLTSDAQSALRRTMEQFSD 140
                                       4555666663333334569******************999887555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.6
                            AAA_16  72 laqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwa 147
                                       +++++ r e ++++ + a + e+  +r kle+ l     ++g +  ++ ++l r + ++    er++v +++ +  a
  gi|313124845|ref|YP_004035109.1| 231 ITSTA-RPEDIEEMVQSAIDGEFLTARSKLETLLV----DTGMAGGDIIDQLHRSVwDFDLD-ERTTVRLMERIGEA 301
                                       34444.55777777777777788888888887777....44444455555555555333333.55555555555555 PP

                            AAA_16 148 de 149
                                       d 
  gi|313124845|ref|YP_004035109.1| 302 DY 303
                                       55 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   2.4e-09   1.6e-06       2      57 ..      22      72 ..      21      78 .. 0.93
   2 ?    1.7   0.0      0.29   1.9e+02      86     112 ..     113     139 ..     107     147 .. 0.92
   3 ?   -2.7   0.1       6.4   4.3e+03      97     141 ..     192     236 ..     178     249 .. 0.55

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.4e-09
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                                      rP++l++  gqe++ e+l+ +ie     ++ l h+l++Gp G+Gktt a+ ia+ +
  gi|313124845|ref|YP_004035109.1| 22 RPQTLDDVYGQEDIVERLRSYIE-----QDDLPHLLFAGPAGVGKTTSATAIARAI 72
                                      9******************9998.....6889********************9865 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.29
                            RuvB_N  86 dvlfideihrlsraveevlysamedfr 112
                                        ++f+de   l++ ++  l  +me f+
  gi|313124845|ref|YP_004035109.1| 113 RIIFLDEADSLTSDAQSALRRTMEQFS 139
                                       589*********************985 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.4
                            RuvB_N  97 sraveevlysamedfrldivigkGpsarsikldlpkftlvgattr 141
                                       +  ++ ++y+a  d+r  i   + ++++   +d +   l+++t+r
  gi|313124845|ref|YP_004035109.1| 192 EDGLDALVYAAGGDMRRAINSLQAAATTGEIVDEEAVYLITSTAR 236
                                       555555666666665555554444444444455555555555554 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.4e-09   9.5e-07      55     170 ..     109     214 ..      78     217 .. 0.92
   2 ?   -3.3   0.0       9.7   6.4e+03      18      39 ..     231     252 ..     225     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.4e-09
                                       SSSEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTH CS
                    DNA_pol3_delta  55 fsdkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeel 131
                                       ++d ri++l+ +      ++l+ + + +L +++++ +++t +il ++       k+++ ++++  v+++++l  + +
  gi|313124845|ref|YP_004035109.1| 109 GFDYRIIFLDEA------DSLTSDAQSALRRTMEQFSDNTRFILSCN----YSSKIIDPIQSRCAVFRFSPLGDDAV 175
                                       57999*****99......5599999**********************....5578********************** PP

                                       HHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta 132 kkwiqkraqelglkiekealelLlelvennlsaikqele 170
                                       +++++++a+++ ++++++ l+ L+++ +++++++ ++l+
  gi|313124845|ref|YP_004035109.1| 176 REQVKDIAETEEIELTEDGLDALVYAAGGDMRRAINSLQ 214
                                       ************************************998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.7
                                       HHHHHHTTTEEEEEEEE-STTS CS
                    DNA_pol3_delta  18 ilkqalkqgfedlnyikfdlne 39 
                                       i ++a  +++e++ ++ +d++ 
  gi|313124845|ref|YP_004035109.1| 231 ITSTARPEDIEEMVQSAIDGEF 252
                                       5666666778888888888775 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.2   1.3e-08   8.7e-06       3      42 ..     186     225 ..     184     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.3e-08
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeakeg 42 
                                       ++++l++d l+al+ +a+GD+R+a+n L++aa++ e  ++
  gi|313124845|ref|YP_004035109.1| 186 EEIELTEDGLDALVYAAGGDMRRAINSLQAAATTGEIVDE 225
                                       689****************************998875532 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.1e-07   7.6e-05       5      67 ..      13      70 ..       9     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.1e-07
                             Rad17  5 enelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                      + e W+eky+P++++++      +e ++ +++ d L++     LL +GP+G gk+t    +++
  gi|313124845|ref|YP_004035109.1| 13 GREIWIEKYRPQTLDDVYGQEDIVERLRSYIEQDDLPH-----LLFAGPAGVGKTTSATAIAR 70
                                      6799**************99999999999999999987.....6************9887776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.5e-07   0.00036       6      99 ..      52     148 ..      49     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.5e-07
                            AAA_14   6 vitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelileklkeekktylflDEiqev.pew 79 
                                       +  G+  vGKTt +  +++  +    + ++l++n  der  +     ++ ++ ++++ + + +++flDE+  + +++
  gi|313124845|ref|YP_004035109.1|  52 LFAGPAGVGKTTSATAIARAIYgdDWRGNFLELNASDERGIDVVRD-RIKNFARSSFGGFDYRIIFLDEADSLtSDA 127
                                       667999************9999887789999999999999765533.46677777665667789******987368* PP

                            AAA_14  80 ekalkslvdeg.knldvivtG 99 
                                       ++al++ +++  +n ++i++ 
  gi|313124845|ref|YP_004035109.1| 128 QSALRRTMEQFsDNTRFILSC 148
                                       *********887889999864 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0013      0.86       7      27 ..      50      70 ..      44      76 .. 0.87
   2 !    8.7   0.0     0.003         2      79     128 ..      96     147 ..      78     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                            AAA_22  7 ilvvtGesGtGKTtllrrlle 27
                                      +l+  G++G+GKTt++  +++
  gi|313124845|ref|YP_004035109.1| 50 HLLFAGPAGVGKTTSATAIAR 70
                                      67889**********988765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.003
                            AAA_22  79 lealeqalrarav...ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                       ++++ + +r+ +     +++ +DEa+ l + +a + Lr+ ++  ++++++iL 
  gi|313124845|ref|YP_004035109.1|  96 RDRIKNFARSSFGgfdYRIIFLDEADSL-TSDAQSALRRTMEQFSDNTRFILS 147
                                       4666666666666777899*********.999999999999988999999986 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.4e-06    0.0049       6      60 ..      30      84 ..      26     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.4e-06
                                      HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60
                                      + Qe+++e+l++ +++++  ++l++ + G+GKT  a++++++++   ++ +fl l
  gi|313124845|ref|YP_004035109.1| 30 YGQEDIVERLRSYIEQDDLPHLLFAGPAGVGKTTSATAIARAIYGDDWRGNFLEL 84
                                      68************988888**********************9999998888855 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.3e-06    0.0028      37     153 ..      52     160 ..      36     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-06
                            AAA_25  37 llaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds..edelrrRlravgeal..rddarllvldla 109
                                       l+aG+ g+GKtt a+ +a a+  G+ w g       + l ++a d    d +r R++   +     +d r  +ld a
  gi|313124845|ref|YP_004035109.1|  52 LFAGPAGVGKTTSATAIARAIY-GDDWRG-------NFLELNASDErgIDVVRDRIKNFARSSfgGFDYRIIFLDEA 120
                                       789*******************.787977.......55666665541267888999886655567778888888877 PP

                            AAA_25 110 gveslpLfakdrggtl.ltadvdaleaaieevegvrlvviDplsr 153
                                       ++    L+++ +   + + +++ +  + i + +++   +iDp+++
  gi|313124845|ref|YP_004035109.1| 121 DS----LTSDAQSALRrTMEQFSDNTRFILS-CNYSSKIIDPIQS 160
                                       65....5444444444556667777777777.5577777777776 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.5e-06    0.0023       1      88 [.      50     137 ..      50     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-06
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkk.Gpvfanllladeinrapp 76 
                                       h+l+ g  G++kt+ + a+a+a+  +  r  f  +l  sd  G++v++++ k+f  ++ G     +++ de +  ++
  gi|313124845|ref|YP_004035109.1|  50 HLLFAGPAGVGKTTSATAIARAIYGDDWRGNFL-ELNASDERGIDVVRDRIKNFARSSfGGFDYRIIFLDEADSLTS 125
                                       9999**************************996.79***************99976543888899************ PP

                             AAA_3  77 ktqsalleamee 88 
                                        +qsal  +me+
  gi|313124845|ref|YP_004035109.1| 126 DAQSALRRTMEQ 137
                                       *******99985 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.8e-05     0.025       1      90 [.      50     136 ..      50     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-05
                                       EEEEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlD 72 
                                       ++l  Gp G+gK++ a  +a+a+     + ++++ + ++    + ++ r+      + +  s++   +   +i++lD
  gi|313124845|ref|YP_004035109.1|  50 HLLFAGPAGVGKTTSATAIARAIygddwRGNFLELNASDERGIDVVRDRI------KNFARSSFG--GFDYRIIFLD 118
                                       68999*******************88544444444444443334344433......467777776..6688999999 PP

                                       SGGG--HHHHHHHHHHHH CS
                             AAA_5  73 EveraesevlnsLlslle 90 
                                       E + + s+++++L + +e
  gi|313124845|ref|YP_004035109.1| 119 EADSLTSDAQSALRRTME 136
                                       999999999998876665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0    0.0003       0.2      11     117 ..      35     135 ..      30     141 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                                       HHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETTTS.-TTCHHHHHHEBSSSSSTTTS CS
                   Sigma54_activat  11 lleqikkvaktd..lsvlitGesGtGKellaraihe..askrkekpfvavncaai.peelleseLFGhekGaFtGAe 82 
                                       ++e++++++++d   ++l  G  G+GK++ a+ai +    +  +++f+++n ++    ++++ ++   ++ +F G +
  gi|313124845|ref|YP_004035109.1|  35 IVERLRSYIEQDdlPHLLFAGPAGVGKTTSATAIARaiYGDDWRGNFLELNASDErGIDVVRDRIKNFARSSFGGFD 111
                                       66777777777666688999***********9999955567778899999988652456666666666666666544 PP

                                       S-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHH CS
                   Sigma54_activat  83 kekkGlfekadgGtlfLDeigelplelQekLlrvl 117
                                                    ++fLDe  +l+ ++Q+ L r +
  gi|313124845|ref|YP_004035109.1| 112 Y-----------RIIFLDEADSLTSDAQSALRRTM 135
                                       3...........35666666666666666666655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00065      0.43       4      43 ..      28      69 ..      25      88 .. 0.71
   2 ?    4.7   0.0     0.026        18     109     133 ..     114     138 ..     111     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00065
                      Mg_chelatase  4 dvkGqeeakrale..iaaaGgHnlllvGppGsGKtmlakrlp 43
                                      dv Gqe+  + l+  i      +ll++Gp+G GKt  a++++
  gi|313124845|ref|YP_004035109.1| 28 DVYGQEDIVERLRsyIEQDDLPHLLFAGPAGVGKTTSATAIA 69
                                      56666655555542244444569*************999886 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.026
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledg 133
                                       ++fLDE+  +++++  +LR+ +e+ 
  gi|313124845|ref|YP_004035109.1| 114 IIFLDEADSLTSDAQSALRRTMEQF 138
                                       79********************985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-05     0.016       6      95 ..      52     141 ..      49     147 .. 0.75
   2 ?   -1.1   0.0       1.9   1.3e+03      31      73 ..     191     266 ..     188     276 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                            AAA_24   6 liyGpsgiGKTtlakelgpkplfidtekG.lksldadkfpdieswedfldevvel...aaeladyktlviDtidele 78 
                                       l  Gp+g+GKTt+a+ +  ++++ d  +G + +l+a +     +++ ++d ++ +   +    dy+++++D +d l 
  gi|313124845|ref|YP_004035109.1|  52 LFAGPAGVGKTTSATAI-ARAIYGDDWRGnFLELNASDER---GIDVVRDRIKNFarsSFGGFDYRIIFLDEADSLT 124
                                       678**************.8888876555315555555544...55555555555544488999************** PP

                            AAA_24  79 elclaevirqnekaesk 95 
                                       + +   ++r  e ++++
  gi|313124845|ref|YP_004035109.1| 125 SDAQSALRRTMEQFSDN 141
                                       *9999998888887776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                            AAA_24  31 tekGlksldadkfpdieswedfldevvel.................................aaeladyktlviDt 73 
                                       te+Gl++l  + + d++  ++ l+++++                                   ++ ++++tl +Dt
  gi|313124845|ref|YP_004035109.1| 191 TEDGLDALVYAAGGDMRRAINSLQAAATTgeivdeeavylitstarpedieemvqsaidgefLTARSKLETLLVDT 266
                                       5667777666666655522222222222234444444445555555555555566666667777778888888887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     7e-05     0.047       3      57 ..      53     100 ..      51     156 .. 0.60
   2 ?   -1.1   0.0         4   2.7e+03      45      70 ..     233     265 ..     176     294 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkl 57 
                                        +G++GvGKtt a ++++       ++d ++ n l+l   +e  +  +++++   
  gi|313124845|ref|YP_004035109.1|  53 FAGPAGVGKTTSATAIARAI-----YGDDWRGNFLELNASDE--RGIDVVRDRIK 100
                                       79**************9994.....45544444444444444..33333333333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4
                            AAA_18  45 aldeskrldedkldklldaleenss.......a 70 
                                        + + + ++e+++ ++  ++  ++s       +
  gi|313124845|ref|YP_004035109.1| 233 STARPEDIEEMVQSAIDGEFLTARSkletllvD 265
                                       444455556666666666666655544444443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   4.8e-05     0.032      22      84 ..      51     121 ..      40     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.8e-05
                            AAA_23  22 tlItGpNGaGKTTildAiklaLygetprlsrks.........grgfeksdveiesegkvkay.veltfenkdg 84 
                                        l+ Gp G GKTT   Ai  a yg+    +++          g + +++ ++ + + +  ++ +++ f ++ +
  gi|313124845|ref|YP_004035109.1|  51 LLFAGPAGVGKTTSATAIARAIYGDD--WRGNFlelnasderGIDVVRDRIKNFARSSFGGFdYRIIFLDEAD 121
                                       5899********************75..333333355566555555566666444444444445555444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.7e-05     0.031      43      85 ..      42      86 ..      30     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                         IstB_IS21 43 fiekke..nivllGpsGvGKshlaialgveavraglsvlfvrved 85
                                      +ie+ +   +++ Gp+GvGK+  a+a++++   ++++  f+ +++
  gi|313124845|ref|YP_004035109.1| 42 YIEQDDlpHLLFAGPAGVGKTTSATAIARAIYGDDWRGNFLELNA 86
                                      5555442268999****************9999999999987765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.002       1.3       4      25 ..      52      73 ..      50      82 .. 0.84
   2 ?    2.5   0.0      0.18   1.2e+02      86     142 ..     191     247 ..     170     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                                      EEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  4 ilqGeaGsGKTtLlqklalawa 25
                                      +  G+aG+GKTt +  +a+a+ 
  gi|313124845|ref|YP_004035109.1| 52 LFAGPAGVGKTTSATAIARAIY 73
                                      678**************99875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.18
                                       EEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE CS
                             NACHT  86 ilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleea 142
                                       + DglD lv   g + +++++ l +   +++++ e  + l++++ + +d+ee++++a
  gi|313124845|ref|YP_004035109.1| 191 TEDGLDALVYAAGGDMRRAINSLQAAATTGEIVDEEAVYLITSTARPEDIEEMVQSA 247
                                       55999999999999889999999999999999********************99987 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.1   2.7e+03     115     132 ..      28      45 ..      26      48 .. 0.88
   2 ?   11.7   0.0   0.00021      0.14      35      72 ..      50      87 ..      39     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.1
                             AAA_7 115 ekygaqppiellRqlldy 132
                                       + yg+   +e lR ++++
  gi|313124845|ref|YP_004035109.1|  28 DVYGQEDIVERLRSYIEQ 45 
                                       89***********99997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00021
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                      ++l+ Gp+G+GKt+ ++ + +++  +++  ++++++a+
  gi|313124845|ref|YP_004035109.1| 50 HLLFAGPAGVGKTTSATAIARAIYGDDWRGNFLELNAS 87
                                      789******************99999999999999875 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.13      52     102 ..     229     284 ..     217     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                         DDE_Tnp_1  52 vvit.pgnvhdskglkq.lldelrpr...kgklvlaDaGYasaelldtleekgvdy 102
                                       + it +++  d++ + q  +d+   +   k  ++l+D G+a+ +++d+l+ + +d+
  gi|313124845|ref|YP_004035109.1| 229 YLITsTARPEDIEEMVQsAIDGEFLTarsKLETLLVDTGMAGGDIIDQLHRSVWDF 284
                                       56666999999**9999888887777999*********************888876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00055      0.36       4      25 ..      51      72 ..      49      88 .. 0.88
   2 ?   -1.8   0.1         3     2e+03      79     123 ..     190     234 ..     174     255 .. 0.58
   3 ?   -2.0   0.0       3.6   2.4e+03      78      91 ..     253     266 ..     199     276 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00055
                                      EEEEESTTSSHHHHHHHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaall 25
                                      +l++G+ G+GKTt+++ +a+ +
  gi|313124845|ref|YP_004035109.1| 51 LLFAGPAGVGKTTSATAIARAI 72
                                      699*************999865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEET CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvlda 123
                                         e++ d+++    G ++   + ++  +++ ++v+++ v+l+ ++
  gi|313124845|ref|YP_004035109.1| 190 LTEDGLDALVYAAGGDMRRAINSLQAAATTGEIVDEEAVYLITST 234
                                       444455555555555555555556666666666655555555544 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.6
                                       HHHHTTSSEEEEEE CS
                             SRP54  78 kakeekidvvlvDT 91 
                                          ++k +++lvDT
  gi|313124845|ref|YP_004035109.1| 253 LTARSKLETLLVDT 266
                                       23344566666666 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0032       2.1       9      41 ..      32      70 ..      28      78 .. 0.70
   2 ?    1.2   0.0      0.31   2.1e+02     119     151 ..     111     146 ..     108     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                                      HHHHHHHHH....H-S..EEEEE--TTSSTTHHHHHHHH CS
                              PhoH  9 Qkeylealk....knd..ivfaiGpaGtGKtylavalav 41
                                      Q++++e l+    + d   +  +GpaG GKt  a+a+a 
  gi|313124845|ref|YP_004035109.1| 32 QEDIVERLRsyieQDDlpHLLFAGPAGVGKTTSATAIAR 70
                                      55566655544434444446779*********9999885 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.31
                                       -SEEEEE-SGGG--HHH...HHHHHTTB-TT-EEEE CS
                              PhoH 119 ndafvilDEAQnttkeq...mkmfltRlGenskvvv 151
                                       +  +++lDEA ++t+     ++  +  +  n+++++
  gi|313124845|ref|YP_004035109.1| 111 DYRIIFLDEADSLTSDAqsaLRRTMEQFSDNTRFIL 146
                                       667899999999987541113334444555666665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00045       0.3       2      34 ..      52      81 ..      51      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00045
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsv 34
                                      ++ Gp+g+GK+t a+ +a+a+    ++++++++
  gi|313124845|ref|YP_004035109.1| 52 LFAGPAGVGKTTSATAIARAIY---GDDWRGNF 81
                                      689****************998...55555555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.31     2e+02      17      33 ..      51      67 ..      30      80 .. 0.80
   2 ?    6.5   0.0      0.01       6.6     122     153 ..     112     142 ..      84     155 .. 0.82
   3 ?   -1.0   0.0         2   1.3e+03     110     157 ..     197     221 ..     148     249 .. 0.49

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.31
                                      EEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                              DEAD 17 vlvaaeTGsGKTlafli 33
                                      +l a++ G GKT+ +  
  gi|313124845|ref|YP_004035109.1| 51 LLFAGPAGVGKTTSATA 67
                                      67899*******98654 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.01
                                       EEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 122 vrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                        r++ lDEad l ++  +  ++r ++q+++ t
  gi|313124845|ref|YP_004035109.1| 112 YRIIFLDEADSLTSD-AQSALRRTMEQFSDNT 142
                                       57899*********8.8999999999996554 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2
                                       HHH......HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTST CS
                                       xxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 110 dll......stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgk 157
                                        l+                                    +r +n+l+ + ++g+
  gi|313124845|ref|YP_004035109.1| 197 ALVyaaggdM-----------------------------RRAINSLQAAATTGE 221
                                       3333333331.............................333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 2096.20
//
Query:       gi|313124846|ref|YP_004035110.1|  [L=743]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-23   83.3   2.9    9.4e-11   42.2   0.1    3.0  2  GAF_2      GAF domain
    5.2e-13   49.5   0.0    1.2e-12   48.3   0.0    1.7  1  HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like A
    5.5e-12   45.5   1.4    2.7e-11   43.3   1.4    2.2  1  HisKA      His Kinase A (phospho-acceptor) domain
    3.3e-08   34.2   0.1     0.0017   19.0   0.0    2.8  3  GAF        GAF domain
    1.5e-05   25.2   1.9    6.1e-05   23.2   0.1    2.9  3  PAS_4      PAS fold
    0.00012   22.0   0.0    0.00055   19.9   0.0    2.2  1  PAS_8      PAS domain
    0.00016   22.0   0.1     0.0041   17.5   0.1    2.6  2  GAF_3      GAF domain
     0.0006   19.8   0.0     0.0016   18.5   0.0    1.7  1  PAS        PAS fold
     0.0013   18.9   0.0     0.0052   17.0   0.0    2.1  2  PAS_9      PAS domain
  ------ inclusion threshold ------
      0.078   13.1   1.1       0.18   11.9   0.2    2.0  2  DivIVA     DivIVA protein
        4.6    8.0   5.8          9    7.1   0.9    3.7  5  PMC2NT     PMC2NT (NUC016) domain


Domain annotation for each model (and alignments):
>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   5.8e-14   9.4e-11       2     134 ..     121     243 ..     120     245 .. 0.84
   2 !   40.3   0.3   2.2e-13   3.5e-10       2     135 ..     276     402 ..     275     405 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 5.8e-14
                                       HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG- CS
                             GAF_2   2 adleelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleed 77 
                                        + +el+++++d + ++  ++ + i + d ++g+r+++ +++ +e++     p ++gl+ge +rtg++ ++nd+++d
  gi|313124846|ref|YP_004035110.1| 121 ETTDELFERTIDIADRIlAFDNSSISI-DVGDGFRIRSTRGDFDEDDRI---PYDAGLLGETYRTGESRLINDIRTD 193
                                       5789************65899999988.545567766666555555444...57899*******************8 PP

                                       S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHH CS
                             GAF_2  78 pdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqia 134
                                       +   ++   ++ +rs ++vP+   g  +Gv+   +++ +afde d +l+e+l + +a
  gi|313124846|ref|YP_004035110.1| 194 ETAAPH---DPEYRSVISVPV---G-DIGVFQAISTEVGAFDEMDHHLAELLVSYVA 243
                                       876665...6***********...9.9******9******************99988 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 2.2e-13
                                       HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEE.EEEES-TTSTT-S-B.---TT.HHHHHHHHTS-EEES-G CS
                             GAF_2   2 adleelldlvldelvel.gaalgyillvdddgglrla.awgeaeeefgaaldr.plgeg.lvgealrtgrpvilndl 74 
                                       +dl el+d+++  + e+  ++++yi++v   +g  l  ++++  ++  + +++ ++++g +++++++tg+  +++d+
  gi|313124846|ref|YP_004035110.1| 276 TDLGELFDRTVAVADEIlSFDMSYIGVVK--DG--LIvPAAMSKRFPEDGAEPlSVEDGsVAADVYQTGKTRLVEDM 348
                                       699*************659********88..66..441333333333333333377***99***************7 PP

                                       GG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiai 135
                                       +e +d    +  + ++rs+l+v +   g  ++v+  +a  p+afde+d el e+l++++a+
  gi|313124846|ref|YP_004035110.1| 349 DEADDA---NPVKDAYRSGLSVAI---G-DFAVFQAAAYTPRAFDEADAELTELLMAHVAV 402
                                       774444...44679**********...9.9*****************************97 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   7.3e-16   1.2e-12       2     108 ..     643     742 ..     642     743 .] 0.89

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 7.3e-16
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGl 78 
                                       d +rL +++ nl  N+v++  ++g+  v++++   d  + veD+G Gi  + ++ +fe+  +     +g  g G+Gl
  gi|313124846|ref|YP_004035110.1| 643 DTERLAELFGNLFRNSVEH--NDGDAGVTVRVGPLDDGFYVEDDGSGIAADRREVVFEPGET-----TGDDGIGYGL 712
                                       789***************9..6666666666645578899******************8888.....6779****** PP

                                       HHHHHHHHHTTTEEEEEEETTTEEEEEEEE CS
                         HATPase_c  79 sivkklvelmgGeiwvesepgrGttftftl 108
                                       +iv +++e +g ++ v+++  +G +f f++
  gi|313124846|ref|YP_004035110.1| 713 AIVSRIAEAHGWSVAVTESAAGGARFEFRV 742
                                       ****************9999*******986 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   1.4   1.7e-14   2.7e-11       2      65 ..     546     604 ..     545     605 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.7e-14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l++f+  v+H+Lr+PL++ +g +e+ ++      + +e ++ + +  +++++l++dlL l+r +
  gi|313124846|ref|YP_004035110.1| 546 LEEFANIVSHDLRNPLAVAQGHLELARE-----VNREESFDAVADALDQMEELIDDLLSLARQG 604
                                       789**********************999.....99**************************976 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     1e-06    0.0017       3     127 ..     124     240 ..     122     248 .. 0.75
   2 !   12.2   0.0   0.00013      0.21       1     131 [.     277     402 ..     277     404 .. 0.73
   3 ?   -3.4   0.0       8.8   1.4e+04      12      31 ..     606     625 ..     605     651 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC.....EEEETTSHHHHHHHHHSSSEEESTGGTSTTHH CS
                               GAF   3 eelldtvveelrellgadrvalylpdydGlhydipqasrw.....lfmkngrgicgqvlatgqplvipdstpdprfa 74 
                                       +el++++++ + ++l+ d+ ++ ++  dG  +    + r       +++ + g+ g++++tg++ +i+d+++d+  a
  gi|313124846|ref|YP_004035110.1| 124 DELFERTIDIADRILAFDNSSISIDVGDG--F-RIRSTRGdfdedDRIPYDAGLLGETYRTGESRLINDIRTDETAA 197
                                       89********************9944555..3.22222222444444455777888*************99999988 PP

                                       TTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHH CS
                               GAF  75 qynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvlad 127
                                       +       + +++rs+++vP+ +    +G+++++++    f++ + +l++ l +
  gi|313124846|ref|YP_004035110.1| 198 P-------HDPEYRSVISVPVGD----IGVFQAISTEVgAFDEMDHHLAELLVS 240
                                       8.......6799**********9....9******97668776666555555444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                                       SHHHHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECCEEEET........TSHHHHHHHHHSSSEEESTGGT CS
                               GAF   1 dleelldtvveelrellgadrvalylpdydGlhydipqasrwlfmkn........grgicgqvlatgqplvipdstp 69 
                                       dl el+d++v+ + e+l  d   +     dGl +  p+a +  f+++        + ++++ v++tg++ +++d ++
  gi|313124846|ref|YP_004035110.1| 277 DLGELFDRTVAVADEILSFDMSYIGV-VKDGLIV--PAAMSKRFPEDgaeplsveDGSVAADVYQTGKTRLVEDMDE 350
                                       7899*****************99966.4788644..44444433333212111212225669***********9554 PP

                                       STTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHH CS
                               GAF  70 dprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvav 131
                                        ++ ++           +rs l+v++ +    ++++++   +p  f++++ el + l ++vav
  gi|313124846|ref|YP_004035110.1| 351 ADDANP-------VKDAYRSGLSVAIGD----FAVFQAAAYTPrAFDEADAELTELLMAHVAV 402
                                       444444.......23577788*****99....9*******55556***************998 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 8.8
                                       HHHHHHTESEEEEEEEEETT CS
                               GAF  12 elrellgadrvalylpdydG 31 
                                        ++e++++d +a+ +  +d 
  gi|313124846|ref|YP_004035110.1| 606 VVGETTAVDVGAIARRAWDT 625
                                       67899999999997733333 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.99   1.6e+03      45      77 ..     386     420 ..     375     441 .. 0.78
   2 !   23.2   0.1   3.7e-08   6.1e-05      17     110 .]     445     534 ..     424     534 .. 0.83
   3 ?   -2.1   0.0       2.8   4.6e+03      42      71 ..     605     634 ..     586     657 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.99
                             PAS_4  45 peedaarleralrrvlegeepiefleelll..pge 77 
                                        e da+  e  +++v+ + e+i+ +e l+   +++
  gi|313124846|ref|YP_004035110.1| 386 DEADAELTELLMAHVAVTAERIRAEENLREerDRS 420
                                       45577778889999999999999999988844444 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 3.7e-08
                             PAS_4  17 vlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrdes 92 
                                       ++ +N+a++e fg+++ +++G  l  e++p+      +++ + +++ +e+++++  +l +g++r + l+++Pl d++
  gi|313124846|ref|YP_004035110.1| 445 IQSVNNAFEEQFGRRDIDIIGDDLLaEIVPD----SERDPPELCVADGERHRSEVQRLADGQTREFILNVVPL-DPN 516
                                       6789*****************9998899997....5555555666666777777777778*************.888 PP

                             PAS_4  93 GevigvlvisrDiTerrr 110
                                             +++ +DiTer++
  gi|313124846|ref|YP_004035110.1| 517 AADGVGYALYTDITERKQ 534
                                       8878889999******85 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.8
                             PAS_4  42 ellpeedaarleralrrvlegeepieflee 71 
                                       e++ e  a ++ ++ rr++++ e+++ +  
  gi|313124846|ref|YP_004035110.1| 605 EVVGETTAVDVGAIARRAWDTVETADGTLK 634
                                       666666777788888888888888777665 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.4e-07   0.00055       4      53 ..     421     477 ..     418     494 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.4e-07
                             PAS_8   4 ralfesspdgiav..vdlgd...rivd.vNqaalellGys.adlkgellg.qllpvlr 53 
                                        alfe+++d+ +   vd ++    +++ vN+a++e +G +  d++g++l  +++p+++
  gi|313124846|ref|YP_004035110.1| 421 TALFEHVSDAAVAyeVD-DEsgvACIQsVNNAFEEQFGRRdIDIIGDDLLaEIVPDSE 477
                                       68*******77764544.2334455555**********77888888888775555544 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.18   2.9e+02       2     125 ..     123     244 ..     122     248 .. 0.76
   2 !   17.5   0.1   2.5e-06    0.0041       1     128 [.     277     405 ..     277     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.18
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvsepsfae..ed 76 
                                        del+e +++ + ++l ++ +++ +  +dg +++ ++g + +++    ++ d  l  +++ +ge    ++ +   + 
  gi|313124846|ref|YP_004035110.1| 123 TDELFERTIDIADRILAFDNSSISIDVGDGFRIRSTRGDFDEDD---RIPYDAGLLGETYRTGESRLINDIRTdeTA 196
                                       58999999999999999999999998889888888888866665...578999999999999997666555331133 PP

                             GAF_3  77 glpd...raalavPLvagrqviGvlalastkprafdaedlelleslArqiat 125
                                       + +d   r+++ vP+ +    iGv  + st+ +afd+ d +l e l +++a 
  gi|313124846|ref|YP_004035110.1| 197 APHDpeyRSVISVPVGD----IGVFQAISTEVGAFDEMDHHLAELLVSYVAE 244
                                       33334446667777777....9999999999999999999999999888886 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.5e-06
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagw.dgkpalsesld.edsalarralssgevvsepsfaee 75 
                                       +l el++ ++  + ++l+++ + ++++  dg  + +a+++ ++++   e l  ed ++a+ ++++g    + +++e+
  gi|313124846|ref|YP_004035110.1| 277 DLGELFDRTVAVADEILSFDMSYIGVVK-DGLIVPAAMSKrFPEDGA-EPLSvEDGSVAADVYQTGKTRLVEDMDEA 351
                                       6889********************9999.889998888886888877.6887799************9999999998 PP

                             GAF_3  76 dglpd.raalavPLvagr.qviGvlalastkprafdaedlelleslArqiataie 128
                                       d  +    a+   L +   + + v  +a + prafd++d+el e l++++a   e
  gi|313124846|ref|YP_004035110.1| 352 DDANPvKDAYRSGLSV-AiGDFAVFQAAAYTPRAFDEADAELTELLMAHVAVTAE 405
                                       7775424443344555.3366******999********************97766 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.5e-07    0.0016      22      96 ..     444     513 ..     430     549 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.5e-07
                                       BEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEE CS
                               PAS  22 rilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspv 96 
                                       +i  vN a+ee++G +  +++g  ll +i++++    ++  e + ++ge+ r+ e+ +   dg ++++ ++++p+
  gi|313124846|ref|YP_004035110.1| 444 CIQSVNNAFEEQFGRRDIDIIGDDLLAEIVPDS---ERDPPELCVADGERHRS-EVQRLA-DGQTREFILNVVPL 513
                                       7999***************************96...56666666666665555.776777.99999999999986 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.2e-06    0.0052       5     104 .]     435     531 ..     429     531 .. 0.79
   2 ?   -3.3   0.0       6.7   1.1e+04      41      73 ..     574     604 ..     551     611 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.2e-06
                             PAS_9   5 lidnpdg..rilyaNeaalrllGyspeevlgks.itdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                        +d+++g   i ++N+a+++ +G    +++g + + +++  ++++++  + ++ +g+   r++  v +  +g+t  +
  gi|313124846|ref|YP_004035110.1| 435 EVDDESGvaCIQSVNNAFEEQFGRRDIDIIGDDlLAEIV--PDSERDPPELCVADGE---RHRSEVQRLADGQTREF 506
                                       467788887788*******************88777777..6666666666666666...77777777777889999 PP

                             PAS_9  79 lltaspv.kdddgelvgiivilrDite 104
                                        l+++p+  ++ +++    ++ +Dite
  gi|313124846|ref|YP_004035110.1| 507 ILNVVPLdPNAADGVGY--ALYTDITE 531
                                       9******7777888888..9*****98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.7
                             PAS_9  41 vtdpeanerlraaleqgrkkerevevvlirkng 73 
                                       v+ +e+ + +++al+q++  e  +++    + g
  gi|313124846|ref|YP_004035110.1| 574 VNREESFDAVADALDQME--ELIDDLLSLARQG 604
                                       566777778888888888..5555555444444 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.3   3.8e+03      93     113 ..     246     266 ..     220     277 .. 0.58
   2 ?   11.9   0.2   0.00011      0.18      38     104 ..     529     596 ..     521     625 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
                                       XXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  93 eAekkaekiveeaeeeakkia 113
                                       +A+ ++ek ++e++++++ ++
  gi|313124846|ref|YP_004035110.1| 246 AARIESEKALRESRSRVEALH 266
                                       344455555555555555554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHCCCCTXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  38 lkeneelkekvkeleeklkeykel.eetLkktlvvaqetaeevkanakkeaeliikeAekkaekivee 104
                                       + e+++ ++++++++++l+e++++   +L++ l vaq   e +++  ++e+   +++A ++ e+++++
  gi|313124846|ref|YP_004035110.1| 529 ITERKQRESELERQNQRLEEFANIvSHDLRNPLAVAQGHLELAREVNREESFDAVADALDQMEELIDD 596
                                       5789999**************9973678************************************9996 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.9   3.1e+03      60      79 ..     121     137 ..      93     150 .. 0.62
   2 ?   -2.2   0.0       4.2   6.8e+03      58      79 ..     271     292 ..     204     293 .. 0.51
   3 ?   -1.4   0.0       2.5     4e+03      24      75 ..     380     430 ..     360     431 .. 0.69
   4 ?    7.1   0.9    0.0055         9      27      87 ..     537     598 ..     529     602 .. 0.70
   5 ?   -0.9   0.0       1.7   2.8e+03      26      51 ..     637     662 ..     632     677 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                            PMC2NT  60 ededdveekfksvvdvvDsl 79 
                                       e+ d+    f+  +d+ D +
  gi|313124846|ref|YP_004035110.1| 121 ETTDE---LFERTIDIADRI 137
                                       33333...666666666665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.2
                            PMC2NT  58 klededdveekfksvvdvvDsl 79 
                                       +l  + d+ e f+  v v D++
  gi|313124846|ref|YP_004035110.1| 271 DLAAVTDLGELFDRTVAVADEI 292
                                       2223333444666666666666 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.5
                            PMC2NT  24 efaksldeqserllslinsllklaaskseisassklededdveekfksvvdv 75 
                                        + ++ de  ++l +l+ + +  +a++ +++++  +e+ d  ++ f+ v+d+
  gi|313124846|ref|YP_004035110.1| 380 YTPRAFDEADAELTELLMAHVAVTAERIRAEEN-LREERDRSTALFEHVSDA 430
                                       555677788888888888888888888887664.556666656688888875 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0055
                            PMC2NT  27 ksldeqserllslinsllklaaskseisas....sklededdveekfksvvdvvDsllEkadtcL 87 
                                       ++l++q++rl + +n + + + +   + +      ++ + ++   +f++v d++D++ E +d +L
  gi|313124846|ref|YP_004035110.1| 537 SELERQNQRLEEFANIVSHDLRNPLAVAQGhlelAREVNREE---SFDAVADALDQMEELIDDLL 598
                                       578888888888888885544444444333543344444444...***********999999877 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 1.7
                            PMC2NT  26 aksldeqserllslinsllklaasks 51 
                                       ++ +d+++erl +l  +l ++  + +
  gi|313124846|ref|YP_004035110.1| 637 SATMDADTERLAELFGNLFRNSVEHN 662
                                       56899*********999988766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (743 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 4968.06
//
Query:       gi|313124847|ref|YP_004035111.1|  [L=162]
Description: tryptophan-rich sensory protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-43  147.1  17.7    3.5e-43  146.9  17.7    1.0  1  TspO_MBR  TspO/MBR family
  ------ inclusion threshold ------
       0.27   11.5  13.7       0.35   11.1  13.7    1.1  1  TctB      Tripartite tricarboxylate transporter TctB family


Domain annotation for each model (and alignments):
>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9  17.7   3.9e-47   3.5e-43       2     134 ..      18     159 ..      17     160 .. 0.97

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 3.9e-47
                                       HHHHHHHHHHHHHHHHHCCH.HHHHHS---TTS--HHHHTTHHHHHHHHHHHHHHHHHHH........HHHHHHHHH CS
                          TspO_MBR   2 alalpllvgllgglftksee.ewykslrkPpwaPpdwvfppvWtvlyilmgvaaylvwka........lalyavqlv 69 
                                       +++l+ l+gl+gg++t+s++ +wy++l +P++aPpdwvf+pvWt+ly+lmg aa+lv ++        l +++ +lv
  gi|313124847|ref|YP_004035111.1|  18 WVLLSELAGLIGGVATASAVeTWYTTLAQPSFAPPDWVFGPVWTTLYALMGTAAFLVSRSddsrtrpaLYAFVGHLV 94 
                                       5789999**********8888*********************************************99779999*** PP

                                       HHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHCHHHHHHHHHHHHHHHHH CS
                          TspO_MBR  70 lnllwsplffglkspvlalvdivallglvvalilafskvdklaallllpyllWllfatylnasiw 134
                                       ln++ws++ffgl+sp+ +lv+iv ll+++va+++ f +vd+ aa+l+lpyl+W++fat+ln+++w
  gi|313124847|ref|YP_004035111.1|  95 LNVSWSLAFFGLQSPLYGLVVIVPLLVAIVAVTALFGRVDRRAAALMLPYLVWVAFATALNYQFW 159
                                       ***************************************************************99 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  13.7   3.9e-05      0.35      12     134 ..      29     158 ..      13     158 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.9e-05
                              TctB  12 g.va..favgald.tgarvgpgffP..lll....gvllallg.llllvaadgekeekearedwrkllklvlallaal 77 
                                       g va  +av+++  t    +p+f P  ++     + l al+g +++lv  +++++++++++    +  lvl +  +l
  gi|313124847|ref|YP_004035111.1|  29 GgVAtaSAVETWYtT--LAQPSFAPpdWVFgpvwTTLYALMGtAAFLV--SRSDDSRTRPALYAFVGHLVLNVSWSL 101
                                       222111223322232..3346655543221333488888888445555..667777777778888888888888899 PP

                              TctB  78 llyallleplGfilatalflllll....greerkwlkalilavvlallvyllFtklLgvpL 134
                                       ++++l  +  G+++ ++l++++++    + +  + +   + a+ l+ lv+++F+++L+ ++
  gi|313124847|ref|YP_004035111.1| 102 AFFGLQSPLYGLVVIVPLLVAIVAvtalF-G--R-VDRRAAALMLPYLVWVAFATALNYQF 158
                                       9999999999**99999888666677643.2..3.555688999999**********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1095.89
//
Query:       gi|313124848|ref|YP_004035112.1|  [L=922]
Description: alanyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     1e-117  394.0   0.1   1.4e-117  393.6   0.1    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
    4.5e-18   66.0   1.0    1.1e-17   64.7   1.0    1.8  1  DHHA1         DHHA1 domain
    2.4e-14   53.1   1.5    4.8e-14   52.2   1.5    1.5  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
       0.14   12.6   0.0       0.38   11.2   0.0    1.6  1  RXLR          RXLR phytopathogen effector protein, Avirulence
       0.47    9.7   1.8       0.61    9.3   0.5    1.8  2  tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.6   0.1  3.8e-121  1.4e-117       1     549 [.      64     603 ..      64     606 .. 0.92

  Alignments for each domain:
  == domain 1  score: 393.6 bits;  conditional E-value: 3.8e-121
                                       HHHHHHHHHHHCTT-EEE----SS-S.SSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpe.ndptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenV 76 
                                       e+re+Fl+fFe+++H++++ ++v ++ +++++l+++A++++f+p+++++++ p+++++++sQ+ciR++    D++nV
  gi|313124848|ref|YP_004035112.1|  64 EMREEFLSFFEEHDHERIEPYPVAANrWRDDVLLTQASIYDFQPLVTSGQTPPPANPLTISQPCIRMQ----DIDNV 136
                                       89**********************988*****************************************....***** PP

                                       TTSSS--SEEEEEEEEESS..............SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHH CS
                      tRNA-synt_2c  77 GktarHhTfFeMlGnfsfg..............dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiwe 137
                                       Gkt+rH   FeM+++++f+               Y+k+ ++e++ e++  ++g d e++++++ ++ +  +a++++e
  gi|313124848|ref|YP_004035112.1| 137 GKTGRHTMAFEMMAHHAFNareevddqyaysgeVYWKDRTVELCDEFFE-HMGADLEEITYIEDPWVGggNAGPAFE 212
                                       ************************************************9.****************9999******* PP

                                       HTTTTEGGGEEEE-HH.....HHEE.ESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEE CS
                      tRNA-synt_2c 138 klvgvpeerilrfgek.....dnfw.emgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnr 208
                                        l+++ e ++l+f +       +++ + g+ +  ++++++++++g e++++ ++++ +++++ + ++++ ++++++ 
  gi|313124848|ref|YP_004035112.1| 213 VLYQGAELATLVFMSMeqdpeGEYEmKDGNRYSPMDTYIVDTGYGLERWAWVSQGTATVYEAVYPDMIQFLKENAGI 289
                                       ***********99433233333454455777*********************************************9 PP

                                       STTSHEEEE.EEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_2c 209 eedgtlkpL.pkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralaf 284
                                       +   ++++L  + ++  G  ++  v ++ e+r   +++l+v   e++e +++          e++++iaDH+r+la+
  gi|313124848|ref|YP_004035112.1| 290 SLTAEEEELvHRAAKLSGYLDIDEVDDVYEARVDIADELGVDADELAELLRP---------LEDIYAIADHCRTLAY 357
                                       9877766661566789************************************.........799************* PP

                                       HHHTT--SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCC CS
                      tRNA-synt_2c 285 aladGvvpsnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakT 361
                                       + +dG+vpsn+g gY++R++lRr+ r+++ +g++++ l++lv++++e l+       ++++++++i+++Ee ++++T
  gi|313124848|ref|YP_004035112.1| 358 MFGDGIVPSNVGTGYLARMVLRRTKRLVDSVGVDAP-LDELVDMQAERLE------YQNRDTIRDIVRTEERKYRET 427
                                       ************************************.************9......5789***************** PP

                                       HHHHHHHHHHHHHHCCC.CSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSX CS
                      tRNA-synt_2c 362 lerGlklleelikklkk.kkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekkl 437
                                       lerG++ ++ l+ + ++ ++ ++  ++++Lyd++G+ +d++++iaee+g++vd++++++++++ r++ + ++++   
  gi|313124848|ref|YP_004035112.1| 428 LERGTRKVQSLADDYADrEESIPVTELIELYDSHGIQPDMVADIAEERGATVDVPDNFYSLVADRHEGEGATEAA-- 502
                                       *************9998899***********************************************96555554.. PP

                                       XXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEE CS
                      tRNA-synt_2c 438 ikkdvealkelkkteeflgyeeleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegae 514
                                        ++  e l++l++te+ l+y++ + ++++          + +e+ e   vvLd+T+fY+e+GGq +D+G+i++++++
  gi|313124848|ref|YP_004035112.1| 503 -EEREERLADLPDTEK-LYYDD-QERTEFE-----AVVLDVIEREEGYDVVLDQTMFYPEGGGQPADHGTISTDDKT 571
                                       .5999**********9.99999.4444444.....33455666667777**************************** PP

                                       EEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEX CS
                      tRNA-synt_2c 515 frvkdvqkakgvvlhkgkleegklkvgdkvkaevd 549
                                       ++v+dvq ++gvvlh+++       +g+ v++++d
  gi|313124848|ref|YP_004035112.1| 572 VQVSDVQIRDGVVLHRTDED---PGKGEFVRGQLD 603
                                       ***************99875...556777776666 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   1.0   3.2e-21   1.1e-17       2     134 ..     784     912 ..     783     916 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 3.2e-21
                                       HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC..TCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEE CS
                             DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevk..gvkvlvaevgeewdagalgiaadklksklkkpvivfva 76 
                                       e++  e+ke  k +++lk +la++ a++     ee++  g++ +v+++  + da+ l+  a+ + +  + +v+v+ +
  gi|313124848|ref|YP_004035112.1| 784 ERFFTEWKERGKTIDRLKSELAEARAAAET---EEIDvsGTPAVVQRL--DGDADELRATANAIVD--EGKVAVLGS 853
                                       56789******************9876554...344455*********..889999**********..779999999 PP

                                       EEECTEEEEEEEESSH.SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHH CS
                             DHHA1  77 keegdkvkvsarskkd.gvdagelakeaaaklgggGGGH.dlAaGagipaekleealeal 134
                                       + +g  + +++++ ++ g++age++ ++aa +gggGGG  d+A+G+g + ekl+e l+++
  gi|313124848|ref|YP_004035112.1| 854 AAGG-SAQFVVGVPDNvGINAGEVVGQLAASVGGGGGGPpDFAQGGGPNVEKLDETLDEA 912
                                       9999.*********99***************************************99986 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   1.5   1.3e-17   4.8e-14       1      44 []     705     747 ..     705     747 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.3e-17
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +rv+++Gd +v++CgGtHv++Tg+Ig +kil  e +++g+ RI+
  gi|313124848|ref|YP_004035112.1| 705 IRVITVGD-DVQACGGTHVKRTGDIGSIKILTTEPVQDGIERIV 747
                                       7******9.**********************************7 PP

>> RXLR  RXLR phytopathogen effector protein, Avirulence activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.38      92     120 ..     781     809 ..     776     814 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                              RXLR  92 kyakklFreWkanGftlkdieseLkqsea 120
                                       ++a++ F eWk++G+t ++ +seL+++ a
  gi|313124848|ref|YP_004035112.1| 781 DTAERFFTEWKERGKTIDRLKSELAEARA 809
                                       689*********************98765 PP

>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5   0.00017      0.61     104     183 ..     192     282 ..     176     306 .. 0.73
   2 ?   -3.6   0.0       1.4   5.1e+03     166     205 ..     407     446 ..     403     456 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00017
                                       S-EEEEEEEEEEGGGTEEEEEEEEEETTCEEEEEEEE..EE..ETTEE-S.........S--EEEEEEHHHHHHHHC CS
                      tRNA-synt_2e 104 hdirfveDdWesptlGawGlGwevwldGmeitqftYf..qq..vgglelk.........pvsveityGleRlamylq 167
                                       ++i ++eD W     G  G  +ev  +G e++ + ++  +q   g +e+k         +  v+  yGleR a + q
  gi|313124848|ref|YP_004035112.1| 192 EEITYIEDPWV--GGGNAGPAFEVLYQGAELATLVFMsmEQdpEGEYEMKdgnryspmdTYIVDTGYGLERWAWVSQ 266
                                       57999999996..56999999999999999999888733222234444331111111114567889*********** PP

                                       T-SSGGG-ECCTTEEH CS
                      tRNA-synt_2e 168 evdnvydlewnekvty 183
                                       ++ +vy+ ++ + +++
  gi|313124848|ref|YP_004035112.1| 267 GTATVYEAVYPDMIQF 282
                                       **********998776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.4
                                       HCT-SSGGG-ECCTTEEHHHHHHHHHHHHHHHHHCTS-HH CS
                      tRNA-synt_2e 166 lqevdnvydlewnekvtygdvflqneveqsaynfeeadve 205
                                        q+ d++ d++ +e+ +y++  ++  +++ +   ++ad e
  gi|313124848|ref|YP_004035112.1| 407 YQNRDTIRDIVRTEERKYRETLERGTRKVQSLADDYADRE 446
                                       5888899999999999998888877777666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (922 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.48
# Mc/sec: 5793.10
//
Query:       gi|313124849|ref|YP_004035113.1|  [L=197]
Description: hypothetical protein Hbor_00610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0023   17.7   0.0     0.0032   17.2   0.0    1.2  1  DUF835    Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.8e-07    0.0032      57     136 .]      96     179 ..      87     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-07
                            DUF835  57 sPtnlekltetivkflkeaekg....vvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekel 129
                                       +P++++ +  +  k+l++ e+     vv +D+l +++ + + e+ ++fl+ l  ++ + ++t ++++d++a ++k +
  gi|313124849|ref|YP_004035113.1|  96 NPADVTGIGMQATKYLNSWEEDdatvVVALDSLTLMLQYVSLETLYRFLHVLTRRLDVLGATGLFFLDPSAQDQKTV 172
                                       67788888888888888777666778999************************************************ PP

                            DUF835 130 alLkref 136
                                       + Lk  f
  gi|313124849|ref|YP_004035113.1| 173 NTLKTLF 179
                                       ***9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1546.01
//
Query:       gi|313124850|ref|YP_004035114.1|  [L=254]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-16   59.0   0.2    1.3e-08   34.8   0.1    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold
    1.3e-14   55.4   9.7    1.5e-14   55.1   9.7    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    2.2e-12   46.8   0.2    5.7e-12   45.4   0.2    1.6  1  Hydrolase_4    Serine aminopeptidase, S33
      1e-06   28.8   0.0    1.7e-06   28.1   0.0    1.4  1  Abhydrolase_4  TAP-like protein
     0.0054   16.4   0.0     0.0076   15.9   0.0    1.3  1  FSH1           Serine hydrolase (FSH1)
     0.0074   15.8   0.0      0.012   15.1   0.0    1.3  1  Peptidase_S9   Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.041   13.7   0.0        4.3    7.1   0.0    2.2  2  Abhydrolase_5  Alpha/beta hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.1   5.1e-12   1.3e-08      30     135 ..      44     141 ..      22     160 .. 0.88
   2 !   21.9   0.0   4.3e-08   0.00011     209     255 ..     191     237 ..     158     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 5.1e-12
                                       SEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                     Abhydrolase_1  30 fdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllga 106
                                       ++ +++D+rG g+S+++p +    y++a++  dl  +l   g ++ ++vG  +GG ++l++a     rV++lv+lg+
  gi|313124850|ref|YP_004035114.1|  44 YESVVTDVRGAGRSDAPPGP----YSIADLVTDLTSVLSDAGFRSAAVVGAGLGGIVGLEAART-TARVDRLVCLGS 115
                                       7789**************75....************************************9987.999********* PP

                                       CSSCCHHHHHHHHHHHHHHCHHCHHHHHH CS
                     Abhydrolase_1 107 idpaaslieaqrqqaksfpdffdgyaadc 135
                                          aa  +++++ +++ +p+  dg  +  
  gi|313124850|ref|YP_004035114.1| 116 ---AATGDQLDLESLYAPPNDRDGLKQSL 141
                                       ...*****************999987765 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 4.3e-08
                                       HHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHH CS
                     Abhydrolase_1 209 nvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafle 255
                                       +v+ ptlv++gt+D + p + +++la+ lp+ +  +++dagHla++e
  gi|313124850|ref|YP_004035114.1| 191 EVTTPTLVVHGTDDAVWPVERGRELAESLPRGEFAAVEDAGHLAHIE 237
                                       5899*****************************************98 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   9.7     6e-18   1.5e-14       1     219 [.      20     244 ..      20     245 .. 0.64

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 6e-18
                                       EEEE--GC.....G..CHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT....TTSEEEEEET CS
                     Abhydrolase_6   1 vlllHGagssassW..lvapLaallaagvhvlapDlpGhGrsdpppldledladlaalldelaa..gggpvvlvGHS 73 
                                       v+++  ag++a++W  +    +a+ a+ ++ +++D +G Grsd pp  ++  adl+  l+++ +  g + + +vG  
  gi|313124850|ref|YP_004035114.1|  20 VVFVGDAGYGAWQWgwQ----HAAVAGPYESVVTDVRGAGRSDAPPGPYSI-ADLVTDLTSVLSdaGFRSAAVVGAG 91 
                                       57774467888889333....555588899999*******99888877766.7776666666554568888****** PP

                                       CHHHHHHHHHHCC...EE.EEES-..----TTT.......S----TTHHHHHHTT-CCCCHCCH.S-HSCCCC...H CS
                     Abhydrolase_6  74 lGGalalaaapla.lvvg.vlldppptalpagl.......laaalelllallallrllawlsre.plprlfla...d 137
                                       lGG+++l+aa+ + +v + v l +  t++   l       ++  +  l++ l+++ +++++ +  ++ ++++a   +
  gi|313124850|ref|YP_004035114.1|  92 LGGIVGLEAARTTaRVDRlVCLGSAATGDQ--LdleslyaPPNDRDGLKQSLKAAFSDRFVEEQpDAIQQMIAwrsE 166
                                       ********7777764444555555223333..234444554444444445555555567775555444455552224 PP

                                       HHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEECTT-CHHHHCHHCCCH....STTEEETCE...SSS-HH CS
                     Abhydrolase_6 138 edadaawrarlarlaallaglgllpaaawadlpvpllvlggeDplvprllerlla....qagarlpvvlpgaGHlph 210
                                       ed  a+ ra+ a  aa +++      aa++ ++++l+v+g++D+++p  +er       +++ ++   +++aGHl h
  gi|313124850|ref|YP_004035114.1| 167 ED--ASPRAWEAQIAAIRDYAL---DAAYEVTTPTLVVHGTDDAVWP--VERGRElaesLPRGEF-AAVEDAGHLAH 235
                                       44..444444444444444333...8899999999966689999999..7766663356566666.99********* PP

                                       HHSHHHHHH CS
                     Abhydrolase_6 211 leepdevae 219
                                       +e+ ++v++
  gi|313124850|ref|YP_004035114.1| 236 IEQSKRVND 244
                                       *77699886 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.2   2.2e-15   5.7e-12      32     238 ..      44     238 ..      38     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.2e-15
                       Hydrolase_4  32 favyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsa 108
                                       ++ +  D rG Grs+   g   s+ d+v+Dl ++++ +      +   ++G  +GG++ l+++ + ++ v++l++ +
  gi|313124850|ref|YP_004035114.1|  44 YESVVTDVRGAGRSDAPPG-PYSIADLVTDLTSVLSDAG----FRSAAVVGAGLGGIVGLEAARTTAR-VDRLVCLG 114
                                       677889*********9999.889********99987776....555799**************99999.******** PP

                       Hydrolase_4 109 Palkikaklkappllklllkllgkllpklqvsnnlkadslsrdpevvaayeadplvhgkitvrlllelldamkrlee 185
                                       +a   ++      l  l +    +   k ++++    +++ ++p+ ++++ a     ++    + +++  + +++++
  gi|313124850|ref|YP_004035114.1| 115 SAATGDQ----LDLESLYAPPNDRDGLKQSLKAAFSDRFVEEQPDAIQQMIAWRSEEDASPRAWEAQIAAIRDYALD 187
                                       **88874....345555555555555555556688899999999999999998888777777888899999999*** PP

                       Hydrolase_4 186 raakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                        a ++t+P+l++hG++D v + e  rel+e+l+  + +++  + + H  + E+
  gi|313124850|ref|YP_004035114.1| 188 AAYEVTTPTLVVHGTDDAVWPVERGRELAESLP--RGEFAAVEDAGHLAHIEQ 238
                                       *********************************..699999999999988886 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   6.7e-10   1.7e-06      18      93 ..     174     252 ..     162     254 .] 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 6.7e-10
                     Abhydrolase_4  18 wpvspqrprdestakg...aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYL 91 
                                       w+++ ++ rd + ++    ++p+L++ ++ D++ P e +++la+ l++++   ve++GH a +++++ v++ + a+L
  gi|313124850|ref|YP_004035114.1| 174 WEAQIAAIRDYALDAAyevTTPTLVVHGTDDAVWPVERGRELAESLPRGEFAAVEDAGHLAHIEQSKRVNDELLAFL 250
                                       655555555555543233389*******************************************************9 PP

                     Abhydrolase_4  92 lt 93 
                                       ++
  gi|313124850|ref|YP_004035114.1| 251 AD 252
                                       86 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.9e-06    0.0076     156     189 ..     188     221 ..     138     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.9e-06
                              FSH1 156 eedkiqtptLhvlGelDtvvdeerseaLaeafkn 189
                                         ++++tptL v+G++D+v + er ++Lae+  +
  gi|313124850|ref|YP_004035114.1| 188 AAYEVTTPTLVVHGTDDAVWPVERGRELAESLPR 221
                                       45689************************98766 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.6e-06     0.012     113     205 ..     163     250 ..     148     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.6e-06
                                       HHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTT CS
                      Peptidase_S9 113 eeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvg 189
                                       ++ +e   p+  e++  ++  y+  +++++++p+L++hG+ D   p++ + +l++ L +     ++    d+gH + 
  gi|313124850|ref|YP_004035114.1| 163 WRSEEDASPRAWEAQIAAIRDYALDAAYEVTTPTLVVHGTDDAVWPVERGRELAESLPR----GEFAAVEDAGHLA- 234
                                       45556666655666677777787777778****************************98....5788899999944. PP

                                       SSHHHHHHHHHHHHHH CS
                      Peptidase_S9 190 kprakveelarllaFl 205
                                         +++++   +llaFl
  gi|313124850|ref|YP_004035114.1| 235 HIEQSKRVNDELLAFL 250
                                       4555556667777776 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0017       4.3      56      98 ..      82     124 ..      61     155 .. 0.83
   2 ?    4.5   0.0      0.01        26      94     129 ..     187     222 ..     177     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0017
                     Abhydrolase_5  56 lekfvvgGhslGGvvasrfaaeeekiegvvflasYPekdelse 98 
                                        +   v G  lGG+v  + a+   +++ +v l+s  + d+l  
  gi|313124850|ref|YP_004035114.1|  82 FRSAAVVGAGLGGIVGLEAARTTARVDRLVCLGSAATGDQLDL 124
                                       455678899*************************999887765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                     Abhydrolase_5  94 delselskkvlsivgteDgvlnvkslekakkflpkd 129
                                       d   e ++++l + gt+D+v +v++ ++ ++ lp+ 
  gi|313124850|ref|YP_004035114.1| 187 DAAYEVTTPTLVVHGTDDAVWPVERGRELAESLPRG 222
                                       555678899***********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1879.64
//
Query:       gi|313124851|ref|YP_004035115.1|  [L=234]
Description: GMP synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-23   83.5   0.0      2e-23   83.1   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    5.4e-12   45.9   0.4    3.8e-11   43.2   0.5    2.2  2  Peptidase_C26  Peptidase C26
    2.7e-05   23.2   0.0    3.5e-05   22.9   0.0    1.1  1  HTS            Homoserine O-succinyltransferase
  ------ inclusion threshold ------
      0.048   13.3   0.0      0.072   12.7   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      0.077   12.8   0.0       0.13   12.0   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.0   5.7e-27     2e-23      25     177 ..      33     181 ..      16     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 5.7e-27
                                       EEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEE CS
                            GATase  25 evvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgrkvvkek 96 
                                       ++ ++da+  e      ++dg++v g   s++     +    e +  a+e+++PiLG+C+G+Qlla ++g++v  + 
  gi|313124851|ref|YP_004035115.1|  33 DLAEFDATEGELP-SHFDFDGVVVTGSRASVYwdekwIPPLAEYVADAAEHDMPILGVCYGHQLLATALGGHVQDMG 108
                                       4444444433332.47899***********99988888888999999999*************************** PP

                                       CEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTS CS
                            GATase  97 ekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEs 173
                                       e+e    +   ++ e +l++g ++++++   H+++v +   +p+g e +a++e +  ++++++ +  ++gvQFHPE+
  gi|313124851|ref|YP_004035115.1| 109 EYEIGYREVSQTA-EDELFEGIDETFTVFTTHSDAVAE---LPEGAELIAENEYG--VHAFRKGH--AWGVQFHPEY 177
                                       7666666666665.67**********************...***********998..77777777..6********9 PP

                                       TTST CS
                            GATase 174 tstp 177
                                        + +
  gi|313124851|ref|YP_004035115.1| 178 DPDT 181
                                       8765 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.68   2.4e+03      59      75 ..      50      63 ..      49      69 .. 0.75
   2 !   43.2   0.5   1.1e-14   3.8e-11      98     216 .]      76     176 ..      72     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.68
                     Peptidase_C26 59 ldgllltGgqdvePsly 75
                                      +dg+++tG++    s+y
  gi|313124851|ref|YP_004035115.1| 50 FDGVVVTGSRA---SVY 63
                                      69******984...455 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 1.1e-14
                     Peptidase_C26  98 iraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkve.kgsllaellgseeievnsl 173
                                       ++ a e+++Pilg+C G+qll+ alGG++  d+ e   +            ++v+ + ++ l++ +   e++ v + 
  gi|313124851|ref|YP_004035115.1|  76 VADAAEHDMPILGVCYGHQLLATALGGHVQ-DMGE--YEI---------GYREVSQTaEDELFEGI-D-ETFTVFTT 138
                                       678999*********************864.4443..122.........23344444066666655.4.69****** PP

                     Peptidase_C26 174 HhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       H+ a+ el e+ + +A  e gv  a++       ++gvQ+HPE
  gi|313124851|ref|YP_004035115.1| 139 HSDAVAELPEGAELIAENEYGV-HAFRK----GHAWGVQFHPE 176
                                       *******************996.55544....458*******9 PP

>> HTS  Homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   9.8e-09   3.5e-05      96     242 ..      47     182 ..      15     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.8e-09
                                       T--EEEEEE---S-TTS-GGGSTTHHHHHHHHHHHHHHEEEEEEETHHHHHHHHHHH----EEEEEEEEEEEEEEES CS
                               HTS  96 dekfDgliiTGApveqlefeevkYWeelteildwakenvtstlfiCwaaqaalyylygvekkklpeKlfGvfehkvl 172
                                       +  fDg+++TG+      + ++k+   l+e +  a e+ +  l +C++ q  l+   g + +++ e  +G ++  ++
  gi|313124851|ref|YP_004035115.1|  47 HFDFDGVVVTGSRA--SVYWDEKWIPPLAEYVADAAEHDMPILGVCYGHQL-LATALGGHVQDMGEYEIG-YREVSQ 119
                                       568********975..5699****************************997.777778888899999999.777779 PP

                                       .S--GGGTT--SEEEEEEEEEEE--HHHHTT-TTEEEEEEETTTEEEEEEESSSSEEEE-S-TT--TTHH CS
                               HTS 173 kekspllrgfddeflvphsRytevkeedieekkelevLaeseeaGvsllaskdkrevfvlgHpEYdaetL 242
                                       + +++l++g+d++f+v         +  ++e +e   L+  +e Gv+ +  ++++   v+ HpEYd +t 
  gi|313124851|ref|YP_004035115.1| 120 TAEDELFEGIDETFTVFTTHS----D-AVAELPEGAELIAENEYGVHAF--RKGHAWGVQFHPEYDPDTA 182
                                       99999*********9965433....3.33334444446667899***99..5566777899*****9985 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05     0.072      41      92 ..      50     100 ..      26     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                          GATase_3  41 adlvilpGgkdtiq.dlallresgldeaikeaaeaggpvlgiCGGlqmLGeei 92 
                                        d v++ G++  +  d ++     l+e +++aae ++p+lg+C G q+L + +
  gi|313124851|ref|YP_004035115.1|  50 FDGVVVTGSRASVYwDEKWIPP--LAEYVADAAEHDMPILGVCYGHQLLATAL 100
                                       6667777776544314445444..88999********************9876 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.7e-05      0.13      59     110 ..      46      99 ..      23     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                                       CC.G-SEEEE--BHHHHHHHHTS..HHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                         DJ-1_PfpI  59 aa.eyDalvlpGGragperlren..ekvvelvkefaekgklvaaICagpqlLaaa 110
                                       +  ++D +v+ G ra + +  e+  + + e v ++ae + ++  +C g qlLa a
  gi|313124851|ref|YP_004035115.1|  46 SHfDFDGVVVTGSRA-SVYWDEKwiPPLAEYVADAAEHDMPILGVCYGHQLLATA 99 
                                       55589********99.777666533599************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1696.35
//
Query:       gi|313124852|ref|YP_004035116.1|  [L=96]
Description: hypothetical protein Hbor_00640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.021   14.6   0.0    1.0  1  DUF2785   Protein of unknown function (DUF2785)


Domain annotation for each model (and alignments):
>> DUF2785  Protein of unknown function (DUF2785)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.2e-06     0.021     104     165 ..      29      90 ..       9      96 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-06
                           DUF2785 104 trtqsvlaadEdeRlatailalleknkleeetllawleelrqelakkeplksrapfylrtNa 165
                                       ++ + v a +++++l++ ++++ e++++e ++l++ +e lr  ++ ++p+++r+p  + +N 
  gi|313124852|ref|YP_004035116.1|  29 SIEDAVEAGEDPDELVSFLTRVEENADFECDELASLVEVLRSYVNGQAPSRDRRPARNAINN 90 
                                       334555666778********************************999999999887766664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 671.63
//
Query:       gi|313124853|ref|YP_004035117.1|  [L=106]
Description: ferredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-12   47.8  21.2    2.7e-07   31.1   7.4    2.0  3  Fer4_7    4Fe-4S dicluster domain
    7.3e-12   44.6  12.5      3e-07   30.0   4.0    2.3  2  Fer4      4Fe-4S binding domain
    4.6e-09   36.0  13.8    3.6e-05   23.6   5.2    2.4  2  Fer4_6    4Fe-4S binding domain
    7.8e-08   32.4   5.1      2e-07   31.0   5.4    1.5  2  Fer4_9    4Fe-4S dicluster domain
    4.4e-07   29.9  10.8    3.6e-06   27.0  10.9    2.0  2  Fer4_21   4Fe-4S dicluster domain
    9.1e-07   28.9  17.9    4.7e-05   23.4   7.9    2.1  2  Fer4_10   4Fe-4S dicluster domain
    1.1e-05   26.2   5.1    0.00088   20.2   1.4    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    3.6e-05   23.6   9.5       0.02   15.0   2.4    2.5  2  Fer4_2    4Fe-4S binding domain
    0.00019   21.9   2.3       0.11   13.0   0.7    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00039   20.8   6.6       0.16   12.5   2.5    2.1  2  Fer4_8    4Fe-4S dicluster domain
    0.00056   20.2   2.5    0.00056   20.2   2.5    2.3  2  Fer4_4    4Fe-4S binding domain
     0.0006   20.6  11.1     0.0058   17.5   3.0    2.3  2  Fer4_3    4Fe-4S binding domain
     0.0008   19.9  13.9      0.027   15.0  13.9    2.4  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.014   15.5   4.0      0.014   15.5   4.0    2.0  2  Fer4_18   4Fe-4S dicluster domain
       0.08   13.1   0.7      0.099   12.8   0.7    1.1  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
        1.8    9.4  15.1         30    5.5  15.1    2.8  1  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.2e-05     0.014      29      52 .]      37      60 ..       6      60 .. 0.73
   2 !   31.1   7.4   2.4e-10   2.7e-07       6      52 .]      50      98 ..      45      98 .. 0.80
   3 !   20.5   1.8   4.8e-07   0.00054       1      21 [.      83     103 ..      83     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                            Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                       +v++d++ Cl  gaC + CP+++
  gi|313124853|ref|YP_004035117.1| 37 THVAVDYDICLADGACLENCPVDV 60
                                      7889*****************986 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.4e-10
                            Fer4_7  6 gaCvaaCpvkaieldeeenek.gtekve.idpekClgCgaCvavCPtga 52
                                      gaC ++Cpv+++++ +  +++   +kve  ++++C++C  Cv+ CP++a
  gi|313124853|ref|YP_004035117.1| 50 GACLENCPVDVFTWVDTPDHPvSEQKVEpTREDQCIDCMLCVDICPVDA 98
                                      8*************9987776433555525799**************97 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 4.8e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaielde 21 
                                       +Ci C  Cv+ Cpv+ai++d 
  gi|313124853|ref|YP_004035117.1|  83 QCIDCMLCVDICPVDAIDVDA 103
                                       6****************9875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.3   4.3e-07   0.00048       2      23 ..      40      61 ..      39      62 .. 0.91
   2 !   30.0   4.0   2.6e-10     3e-07       5      24 .]      81     100 ..      78     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.3e-07
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       +d++ C + GaC e CPv++ 
  gi|313124853|ref|YP_004035117.1| 40 AVDYDICLADGACLENCPVDVF 61
                                      69*****************986 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 2.6e-10
                                       TTTSSS-THHHHHSTTTEEE CS
                              Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                       e+ Ci C++Cv++CPv+AI+
  gi|313124853|ref|YP_004035117.1|  81 EDQCIDCMLCVDICPVDAID 100
                                       899***************95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.3   3.1e-06    0.0035       2      23 ..      39      60 ..      38      61 .. 0.92
   2 !   23.6   5.2   3.2e-08   3.6e-05       6      24 .]      81      99 ..      80      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.1e-06
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      v++d+d C+  g+C  +CP ++
  gi|313124853|ref|YP_004035117.1| 39 VAVDYDICLADGACLENCPVDV 60
                                      89*****************976 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 3.2e-08
                            Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                      +d Ci+C+ Cv++CP +ai
  gi|313124853|ref|YP_004035117.1| 81 EDQCIDCMLCVDICPVDAI 99
                                      699*************998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.2    0.0059       6.6      35      49 ..      45      59 ..      16      61 .. 0.77
   2 !   31.0   5.4   1.8e-10     2e-07       6      51 .]      50      99 ..      44      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0059
                            Fer4_9 35 aCigCgaCveaCpkg 49
                                       C+  gaC+e Cp +
  gi|313124853|ref|YP_004035117.1| 45 ICLADGACLENCPVD 59
                                      477778899999976 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.8e-10
                            Fer4_9  6 gaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51
                                      gaC e Cp +v++  + +     +++ e    ++Ci+C+ Cv++Cp +ai
  gi|313124853|ref|YP_004035117.1| 50 GACLENCPVDVFTWVDTPDHPVSEQKVEptreDQCIDCMLCVDICPVDAI 99
                                      78******9999887777777666655567779**************987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.6   0.00098       1.1      32      55 ..      37      59 ..      32      64 .. 0.85
   2 !   27.0  10.9   3.2e-09   3.6e-06       3      58 ..      41     100 ..      39     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00098
                           Fer4_21 32 tvlkvvedeCvGCnlCssvCPved 55
                                      t+++v  d C +   C++ CPv d
  gi|313124853|ref|YP_004035117.1| 37 THVAVDYDICLADGACLENCPV-D 59
                                      67889999*************9.4 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 3.2e-09
                           Fer4_21   3 idedkCigCgkCliaCedtshqai.....eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +d d C+  g Cl  C+    + +      +++++v +++ed+C+ C lC+++CPv d+i+
  gi|313124853|ref|YP_004035117.1|  41 VDYDICLADGACLENCPVDVFTWVdtpdhPVSEQKVEPTREDQCIDCMLCVDICPV-DAID 100
                                       78999************99999996665446677888999***************9.8886 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   7.9   4.2e-08   4.7e-05       1      56 []      38      95 ..      38      95 .. 0.79
   2 !   17.0   2.3   4.1e-06    0.0046       6      26 ..      81     101 ..      78     106 .] 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.2e-08
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +v +d d C+  g+C + CP+d+  + +      se++++ +  ++C++c  Cv++CP
  gi|313124853|ref|YP_004035117.1| 38 HVAVDYDICLADGACLENCPVDVftWVDTPDHPVSEQKVEPTREDQCIDCMLCVDICP 95
                                      67889*****************99644444444555555555779************9 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.1e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadltsv 26 
                                       +d+Ci C  Cv+ CP+d+  v
  gi|313124853|ref|YP_004035117.1|  81 EDQCIDCMLCVDICPVDAIDV 101
                                       689*************66554 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0055       6.1       2      18 ..      46      62 ..      45      82 .. 0.73
   2 !   20.2   1.4   7.8e-07   0.00088       1      20 [.      83     102 ..      83     106 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0055
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C   g+C+e CP+++++
  gi|313124853|ref|YP_004035117.1| 46 CLADGACLENCPVDVFT 62
                                      555689*******9987 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 7.8e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++C  C+++CP++ai+ +
  gi|313124853|ref|YP_004035117.1|  83 QCIDCMLCVDICPVDAIDVD 102
                                       6****************987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.7   0.00011      0.12       2      21 ..      38      57 ..      37      58 .. 0.91
   2 !   15.0   2.4   1.7e-05      0.02       7      21 ..      81      95 ..      80      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      +v+vd d+C++ gaC+ +CP
  gi|313124853|ref|YP_004035117.1| 38 HVAVDYDICLADGACLENCP 57
                                      799******988******** PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.7e-05
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                      +d Ci C  Cv+ CP
  gi|313124853|ref|YP_004035117.1| 81 EDQCIDCMLCVDICP 95
                                      588************ PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0021       2.4      44      60 ..      44      60 ..      24      61 .. 0.86
   2 !   13.0   0.7    0.0001      0.11      42      58 ..      80      96 ..      65      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0021
                           Fer4_17 44 slCieCgeCerkCPqgl 60
                                      + C+  g C + CP ++
  gi|313124853|ref|YP_004035117.1| 44 DICLADGACLENCPVDV 60
                                      67************875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0001
                           Fer4_17 42 kaslCieCgeCerkCPq 58
                                      + ++Ci C +C+  CP 
  gi|313124853|ref|YP_004035117.1| 80 REDQCIDCMLCVDICPV 96
                                      55789999999999985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00076      0.85      48      65 .]      43      60 ..       7      60 .. 0.79
   2 !   12.5   2.5   0.00014      0.16       4      17 ..      83      96 ..      80     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00076
                            Fer4_8 48 lwsCttcgaCtevCpvgi 65
                                       + C++ gaC e+Cpv++
  gi|313124853|ref|YP_004035117.1| 43 YDICLADGACLENCPVDV 60
                                      567999999999999975 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                            Fer4_8  4 kCieCgaCqsaCpv 17
                                      +Ci C++C + Cpv
  gi|313124853|ref|YP_004035117.1| 83 QCIDCMLCVDICPV 96
                                      68888888888876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.35   3.9e+02       8      16 ..      50      58 ..      43      64 .. 0.76
   2 !   20.2   2.5     5e-07   0.00056       4      16 ..      84      96 ..      78      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.35
                            Fer4_4  8 gsCvaaCPq 16
                                      g+C   CP+
  gi|313124853|ref|YP_004035117.1| 50 GACLENCPV 58
                                      788888996 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5e-07
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      Ci+C+ Cv++CP+
  gi|313124853|ref|YP_004035117.1| 84 CIDCMLCVDICPV 96
                                      ************7 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   1.2    0.0057       6.4       5      14 ..      50      59 ..      46      60 .. 0.78
   2 !   17.5   3.0   5.2e-06    0.0058       1      15 []      84      98 ..      84      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0057
                            Fer4_3  5 gaCvevCPvg 14
                                      gaC+e CPv+
  gi|313124853|ref|YP_004035117.1| 50 GACLENCPVD 59
                                      79******97 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.2e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C++Cv+ CPv+A
  gi|313124853|ref|YP_004035117.1| 84 CIDCMLCVDICPVDA 98
                                      9************98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0  13.9   2.4e-05     0.027       1      58 []      41     101 ..      41     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                           Fer4_13   1 VDrdtCiacgaCvelaP.dvFeeddeggasvvaeqpts...eeekadaeeAadaCPvesIgv 58 
                                       VD d C a+gaC e +P dvF   d    + v eq++    e++  d++  +d CPv++I v
  gi|313124853|ref|YP_004035117.1|  41 VDYDICLADGACLENCPvDVFTWVDT-PDHPVSEQKVEptrEDQCIDCMLCVDICPVDAIDV 101
                                       89999************99***9997.56778887665333777777888899*******86 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4      0.24   2.6e+02      60      75 ..      45      60 ..      30      65 .. 0.81
   2 ?   15.5   4.0   1.3e-05     0.014      52      77 ..      75     101 ..      62     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.24
                           Fer4_18 60 dcidcescvkvcPtgi 75
                                       c++ ++c++ cP+++
  gi|313124853|ref|YP_004035117.1| 45 ICLADGACLENCPVDV 60
                                      5888899999999876 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.3e-05
                           Fer4_18  52 erkekgagdcidcescvkvcPtg.idi 77 
                                       + + + + +cidc  cv++cP++ id+
  gi|313124853|ref|YP_004035117.1|  75 KVEPTREDQCIDCMLCVDICPVDaIDV 101
                                       344567789************853665 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   8.8e-05     0.099      25      90 ..      31      99 ..      26     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.8e-05
                                      SEEESSTTHHHHTHHHHHS-THHHH-TTS-EEEEETTT..TSSEEEE.E-CCC--S--HHHHH-TT--E CS
                            ETF_QO 25 hLklkdaevavkvnlekyagpeqryCPagvyeivedee..akekklq.inaqnCvhCktCdikdpsqni 90
                                       L ++ ++vav+  +   +g +   CP  v+ +v++ +   +e+k++     +C+ C  C    p + i
  gi|313124853|ref|YP_004035117.1| 31 KLGIHGTHVAVDYDICLADGACLENCPVDVFTWVDTPDhpVSEQKVEpTREDQCIDCMLCVDICPVDAI 99
                                      566777777788888888999999**********9875224445554245679******9665666666 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  15.1     0.026        30       1      66 []      39     101 ..      39     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                           Fer4_15   1 VvvDrdaCigcglCvaeap.evfeldedglasvllddgeiaegevpddeee...aaqeAaraCPvdAIrv 66 
                                       V vD d C  +g+C++++p +vf+    + +++ +     +e+ v++++e+   +    ++ CPvdAI v
  gi|313124853|ref|YP_004035117.1|  39 VAVDYDICLADGACLENCPvDVFTWV--DTPDHPV-----SEQKVEPTREDqciDCMLCVDICPVDAIDV 101
                                       88****************82444444..4443334.....456666666651115556789*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 748.80
//
Query:       gi|313124854|ref|YP_004035118.1|  [L=151]
Description: ferritin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-23   83.8   0.8    1.2e-23   83.6   0.8    1.0  1  Ferritin       Ferritin-like domain
    7.8e-07   29.6   0.1    9.4e-07   29.3   0.1    1.1  1  Rubrerythrin   Rubrerythrin
    0.00084   19.3   0.0    0.00089   19.2   0.0    1.2  1  Ferritin-like  Ferritin-like
     0.0014   18.7   2.6     0.0048   16.9   2.6    1.9  1  DUF892         Domain of unknown function (DUF892)
     0.0018   18.4   0.1     0.0025   18.0   0.1    1.3  1  Ferritin_2     Ferritin-like domain
     0.0032   16.5   0.2     0.0093   15.0   0.1    1.6  2  Mn_catalase    Manganese containing catalase


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.8     4e-27   1.2e-23       2     135 ..       8     144 ..       7     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 4e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH....C-S CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee....iea 74 
                                       ++L ++ +del+  + yl  + +++g+  e+++  ++  ++ee++ha+ l +r+++l+++p+++   +e+    +++
  gi|313124854|ref|YP_004035118.1|   8 DLLKKAYQDELETVMNYLTNSIVLDGVRAEEIKGSLQADIQEELNHAELLGNRLKQLDEKPPGSAE-FEAnqmnLQP 83 
                                       6899***********************************************************986.4444574555 PP

                                       SSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  75 pkefgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleal 135
                                       p + ++v++v+e +l++e+++++++r+li+ aee++Dp+t+d++  +l+++e h  e++ +
  gi|313124854|ref|YP_004035118.1|  84 PADSTDVLSVIEGVLTAEEDAISTYRDLIAAAEEANDPVTEDLAVTVLADEEAHRTEFRGF 144
                                       55555***************************************************99876 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   3.1e-10   9.4e-07       1     134 [.       8     142 ..       8     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.1e-10
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS------ CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaeak 75 
                                       ++L+kA+  E +  + Y   +  ++  + ++i+  +++ ++eE  Ha++l + l++l+++       e +   ++++
  gi|313124854|ref|YP_004035118.1|   8 DLLKKAYQDELETVMNYLTNSIVLDgVRAEEIKGSLQADIQEELNHAELLGNRLKQLDEKPPgSAEFEANQMNLQPP 84 
                                       78********************************************************9999666666666667777 PP

                                       -TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  76 pkflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlr 134
                                       ++  t   +++e +  a++  +  yr +  +ae++ ++ +++l  ++  +E+ H   +r
  gi|313124854|ref|YP_004035118.1|  85 ADS-TDVLSVIEGVLTAEEDAISTYRDLIAAAEEANDPVTEDLAVTVLADEEAHRTEFR 142
                                       666.333455556666666666677888899***********************99998 PP

>> Ferritin-like  Ferritin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     3e-07   0.00089       1      64 [.      10      73 ..      10     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3e-07
                                      HHHHHHHHHHHHHHHHHHHHHBS-TTSH.HHHHHHHHHHHHHHHHHHHHHHHHHTT------.. CS
                     Ferritin-like  1 LqqAielEhstippYLtalySikdgtneeaealilevvkeEMlHltlvaNllnalGgsPvleap 64
                                      L++A + E+ t++ YLt +  ++  ++ee++  +++ ++eE  H+ l  N l+ l+++P  +a+
  gi|313124854|ref|YP_004035118.1| 10 LKKAYQDELETVMNYLTNSIVLDGVRAEEIKGSLQADIQEELNHAELLGNRLKQLDEKPPGSAE 73
                                      78999****************************************************9765533 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.6   1.6e-06    0.0048      31     143 ..      34     138 ..       7     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                                       -SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------.-HHHHTTT----.-------THHHHHHH...HHHHHH CS
                            DUF892  31 aespeLkaaleqHleeTegqierLeqvferlgesasekkcdamegliaegqe.lieeaaedeslkdaaliaaaqave 106
                                       ++ +e+k  l+ +++e  +++e L + +++l+e++ +           e ++  ++ ++  +s+  + +i    + e
  gi|313124854|ref|YP_004035118.1|  34 VRAEEIKGSLQADIQEELNHAELLGNRLKQLDEKPPGSA---------EFEAnQMNLQPPADSTDVLSVIEGVLTAE 101
                                       566899999999999999*******99999999999988.........33333555556667777777889****** PP

                                       HHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHH CS
                            DUF892 107 hyEiAsYgtLialAeqlgekeaaklLeqtleeekatd 143
                                          i++Y+ Lia+Ae++ ++ + +l  + l+ e+a  
  gi|313124854|ref|YP_004035118.1| 102 EDAISTYRDLIAAAEEANDPVTEDLAVTVLADEEAHR 138
                                       *******************************999865 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   8.2e-07    0.0025      38     134 ..      38     145 ..       5     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.2e-07
                        Ferritin_2  38 evrevaeeiakheeaHveflkaale.......Gaaavakptfdf.afdpfadeksflalaavlEdvgvsAY...lga 103
                                       e++  ++   ++e +H+e+l + l+       G+a +++ ++++ +  + +d  s++++  + E+ ++s Y   + a
  gi|313124854|ref|YP_004035118.1|  38 EIKGSLQADIQEELNHAELLGNRLKqldekppGSAEFEANQMNLqPPADSTDVLSVIEGVLTAEEDAISTYrdlIAA 114
                                       45556666678999**********999888888888888888987677777888999999999********333345 PP

                        Ferritin_2 104 apllsnkelltaaasIlsvEArHaavirtll 134
                                       a+  +++    +a+ +l++E  H + +r  +
  gi|313124854|ref|YP_004035118.1| 115 AEEANDPVTEDLAVTVLADEEAHRTEFRGFR 145
                                       55777899****************9999765 PP

>> Mn_catalase  Manganese containing catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.1e-06    0.0093      34      94 ..      16      78 ..       8      89 .. 0.81
   2 ?   -1.0   0.0      0.22   6.7e+02     147     188 ..      98     142 ..      87     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-06
                       Mn_catalase 34 GElsvalrYlfQgf...nirdkekyk.dLlmdiatEElgHvEliatmiarllegatleqqedvee 94
                                       El ++++Yl+ +    ++r++e+ k  L +di  EEl H El+++ +++l e  + + + ++++
  gi|313124854|ref|YP_004035118.1| 16 DELETVMNYLTNSIvldGVRAEEI-KgSLQADI-QEELNHAELLGNRLKQLDEKPPGSAEFEANQ 78
                                      699*********984445677777.63777777.6****************99988877766655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.22
                       Mn_catalase 147 laaEakarlqverlyel...tddpgvrdmlsfLlaRelvHqlafe 188
                                       l+aE+ a  ++  l++    ++dp+  d     la e +H  +f+
  gi|313124854|ref|YP_004035118.1|  98 LTAEEDAISTYRDLIAAaeeANDPVTEDLAVTVLADEEAHRTEFR 142
                                       567777777777777551114678888887778888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1138.95
//
Query:       gi|313124855|ref|YP_004035119.1|  [L=705]
Description: Fe-S oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-18   66.9   0.0    4.1e-13   49.4   0.1    2.4  2  CCG       Cysteine-rich domain
    4.8e-10   39.4   9.9    1.7e-08   34.5   9.6    2.9  3  Fer4_10   4Fe-4S dicluster domain
    2.1e-09   37.7   4.1    2.1e-09   37.7   4.1    1.9  1  Fer4_8    4Fe-4S dicluster domain
    3.3e-09   36.2  14.0     0.0001   21.9   2.5    2.6  2  Fer4      4Fe-4S binding domain
    1.2e-08   34.9   5.2    1.2e-08   34.9   5.2    2.2  2  Fer4_9    4Fe-4S dicluster domain
    1.8e-07   30.8  13.5    7.6e-05   22.6   2.3    2.7  2  Fer4_2    4Fe-4S binding domain
    1.6e-05   25.4  15.2    2.1e-05   25.0  12.5    2.5  3  Fer4_7    4Fe-4S dicluster domain
    2.8e-05   24.2  10.3     0.0083   16.2   0.4    2.8  3  Fer4_21   4Fe-4S dicluster domain
     0.0001   22.8   9.2     0.0001   22.8   9.2    2.5  2  Fer4_17   4Fe-4S dicluster domain
    0.00062   19.9   1.2       0.89    9.8   0.2    2.5  2  Fer4_18   4Fe-4S dicluster domain
     0.0015   18.9  17.6     0.0041   17.5   0.8    2.8  2  Fer4_4    4Fe-4S binding domain
     0.0017   18.4   3.6     0.0017   18.4   3.6    2.8  2  Fer4_6    4Fe-4S binding domain
     0.0053   17.7  14.6      0.096   13.6  13.4    2.7  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0072   17.1   7.1      0.087   13.7   0.5    2.8  2  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
        6.3    8.0  26.4       0.79   10.8   5.6    2.9  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05     0.021      10      79 ..     452     522 ..     443     527 .. 0.92
   2 !   49.4   0.1   3.4e-16   4.1e-13       1      83 [.     569     659 ..     569     661 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                               CCG  10 lraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpg 79 
                                       ++ +++ v ++l++l+e +gv + +l e+e+  G+  +r g+e l e l++ n++++ + + d+iv ++p+
  gi|313124855|ref|YP_004035119.1| 452 YDERNRRVARSLARLFELTGVSYGILyEDEQHDGNDVRRVGEEGLYEMLVEDNADAIHDCEFDKIVCTDPH 522
                                       6778999***********************************************************99998 PP

  == domain 2  score: 49.4 bits;  conditional E-value: 3.4e-16
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaee.tg... 69 
                                       v+y+d+Chl+r++  y+++r+++++  +a+++e++++ +++ CCG ggg  ++e  +  +  ++++++a e t+   
  gi|313124855|ref|YP_004035119.1| 569 VTYHDPCHLGRYNdeYEAPRELVRAT-GATLAEMPRNrSDSFCCGGGGGGLWMELeEETKPSEERLREALEdTDaga 644
                                       89************888888866666.**************************996555888888888777523445 PP

                               CCG  70 .adaivtacpgCllq 83 
                                        +++ v+acp C ++
  gi|313124855|ref|YP_004035119.1| 645 aVEKFVVACPMCATM 659
                                       59**********987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   9.6   1.4e-11   1.7e-08       3      56 .]     295     374 ..     293     374 .. 0.92
   2 !   18.8   1.5   1.1e-06    0.0013       6      24 ..     360     391 ..     354     411 .. 0.71
   3 ?   -0.1   0.0      0.89   1.1e+03      18      23 ..     652     657 ..     635     678 .. 0.65

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.4e-11
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.........................tsvgakgeaseeeavrk.kvekCtgcgaCve 53 
                                       ++d+d C++Cg+C ++CPa+                          t+   + ++ + ++++   +e+C++c aC++
  gi|313124855|ref|YP_004035119.1| 295 ILDTDACTKCGRCSSVCPAKEsgrpldprdvildlkqyredldagrTEEIDIVADGGTSVIDSsTMESCMACMACMD 371
                                       789****************99************************97777778888888877779************ PP

                           Fer4_10  54 aCP 56 
                                       aCP
  gi|313124855|ref|YP_004035119.1| 372 ACP 374
                                       **9 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.1e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadl.............t 24 
                                        ++C+ C +C++aCP+d+             t
  gi|313124855|ref|YP_004035119.1| 360 MESCMACMACMDACPVDIehlshftemnrrlT 391
                                       689*************8877777654443331 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.89
                           Fer4_10  18 aCPadl 23 
                                       aCP+++
  gi|313124855|ref|YP_004035119.1| 652 ACPMCA 657
                                       455544 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   4.1   1.8e-12   2.1e-09       2      65 .]     298     377 ..     297     377 .. 0.63

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.8e-12
                            Fer4_8   2 lekCieCgaCqsaCp............vlrrtkkhlldargeaaedvqeeqvlee...............eealwsC 51 
                                        ++C++Cg+C s Cp            v+ + k+ + d   ++           +                 +++sC
  gi|313124855|ref|YP_004035119.1| 298 TDACTKCGRCSSVCPakesgrpldprdVILDLKQYREDLDAGR-----------TeeidivadggtsvidSSTMESC 363
                                       579***********95555555555553333332222222222...........1333344444455688999**** PP

                            Fer4_8  52 ttcgaCtevCpvgi 65 
                                       ++c+aC ++Cpv+i
  gi|313124855|ref|YP_004035119.1| 364 MACMACMDACPVDI 377
                                       ***********987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   2.5   8.6e-08    0.0001       3      20 ..     296     313 ..     295     314 .. 0.92
   2 !   19.1   3.9     7e-07   0.00084       6      21 ..     361     376 ..     359     377 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.6e-08
                                       EETTTSSS-THHHHHSTT CS
                              Fer4   3 ideekCigCGaCvevCPv 20 
                                        d++ C++CG+C +vCP 
  gi|313124855|ref|YP_004035119.1| 296 LDTDACTKCGRCSSVCPA 313
                                       69***************6 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 7e-07
                                       TTSSS-THHHHHSTTT CS
                              Fer4   6 ekCigCGaCvevCPvg 21 
                                       e C++C+aC+++CPv+
  gi|313124855|ref|YP_004035119.1| 361 ESCMACMACMDACPVD 376
                                       89*************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   5.2     1e-11   1.2e-08       1      49 [.     300     376 ..     300     378 .. 0.96
   2 ?   -0.2   0.0      0.96   1.1e+03      10      27 ..     651     668 ..     650     673 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase............................eaCigCgaCveaCpkg 49 
                                       +Ct+Cg+C ++Cpa+   +   +r + l+ +++                            e+C+ C+aC++aCp +
  gi|313124855|ref|YP_004035119.1| 300 ACTKCGRCSSVCPAKESGRPLDPRDVILDLKQYredldagrteeidivadggtsvidsstmESCMACMACMDACPVD 376
                                       6************************9999888899****************************************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.96
                            Fer4_9  10 eaCpagvvvedaaerkar 27 
                                        aCp++++++++++++  
  gi|313124855|ref|YP_004035119.1| 651 VACPMCATMYEDGRKTGD 668
                                       589999999999887765 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   2.3   6.4e-08   7.6e-05       3      22 .]     294     313 ..     292     313 .. 0.90
   2 !   13.0   3.7     7e-05     0.083       8      21 ..     361     374 ..     358     375 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.4e-08
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                          dtd+C+ Cg C s+CPa
  gi|313124855|ref|YP_004035119.1| 294 QILDTDACTKCGRCSSVCPA 313
                                       568****************8 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7e-05
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       ++C++C aC +aCP
  gi|313124855|ref|YP_004035119.1| 361 ESCMACMACMDACP 374
                                       78************ PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   3.4   4.1e-05     0.049      33      50 ..     296     313 ..     258     315 .. 0.79
   2 !   25.0  12.5   1.7e-08   2.1e-05       1      52 []     300     377 ..     300     377 .. 0.60
   3 ?   -2.8   0.1       8.7     1e+04      10      18 ..     651     659 ..     650     671 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
                            Fer4_7  33 idpekClgCgaCvavCPt 50 
                                       +d + C+ Cg+C +vCP+
  gi|313124855|ref|YP_004035119.1| 296 LDTDACTKCGRCSSVCPA 313
                                       477889999999999996 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.7e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaie..ldeeenek.......................gtekveid.pekClgCgaCvavCPtg 51 
                                       +C++Cg+C ++Cp+k     ld++++                         gt  ++ + +e+C+ C aC+++CP++
  gi|313124855|ref|YP_004035119.1| 300 ACTKCGRCSSVCPAKESGrpLDPRDVILdlkqyredldagrteeidivadgGTSVIDSStMESCMACMACMDACPVD 376
                                       5***********955444114432222133333344555544444444444444445433999************98 PP

                            Fer4_7  52 a 52 
                                       +
  gi|313124855|ref|YP_004035119.1| 377 I 377
                                       5 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.7
                            Fer4_7  10 aaCpvkaie 18 
                                       +aCp+ a +
  gi|313124855|ref|YP_004035119.1| 651 VACPMCATM 659
                                       677766555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4     7e-06    0.0083      36      54 ..     296     314 ..     275     316 .. 0.75
   2 !   13.6   0.9   4.6e-05     0.055      37      54 ..     359     376 ..     339     379 .. 0.76
   3 ?   -2.9   0.1       6.8   8.1e+03      41      48 ..     650     657 ..     640     659 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7e-06
                           Fer4_21  36 vvedeCvGCnlCssvCPve 54 
                                       + +d C+ C  CssvCP +
  gi|313124855|ref|YP_004035119.1| 296 LDTDACTKCGRCSSVCPAK 314
                                       3589*************75 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.6e-05
                           Fer4_21  37 vedeCvGCnlCssvCPve 54 
                                       + ++C++C  C++ CPv+
  gi|313124855|ref|YP_004035119.1| 359 TMESCMACMACMDACPVD 376
                                       4699************94 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.8
                           Fer4_21  41 CvGCnlCs 48 
                                        v+C +C+
  gi|313124855|ref|YP_004035119.1| 650 VVACPMCA 657
                                       46666665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   2.7    0.0002      0.24      43      58 ..     298     313 ..     281     316 .. 0.81
   2 !   22.8   9.2   8.5e-08    0.0001       1      60 [.     300     377 ..     300     378 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                           Fer4_17  43 aslCieCgeCerkCPq 58 
                                        + C++Cg+C+++CP+
  gi|313124855|ref|YP_004035119.1| 298 TDACTKCGRCSSVCPA 313
                                       689***********97 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 8.5e-08
                           Fer4_17   1 rCiqCgyClpeCpsyea.ydnepk.......kllraaklgllee..........aekeekaslCieCgeCerkCPqg 59 
                                       +C++Cg C  +Cp  e  ++ +p+       ++++++ +g++ee          +++++++++C+ C  C  +CP +
  gi|313124855|ref|YP_004035119.1| 300 ACTKCGRCSSVCPAKESgRPLDPRdvildlkQYREDLDAGRTEEidivadggtsVIDSSTMESCMACMACMDACPVD 376
                                       6************9888755555512222215666666655555444444444466669****************88 PP

                           Fer4_17  60 l 60 
                                       +
  gi|313124855|ref|YP_004035119.1| 377 I 377
                                       7 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0018       2.2      54      73 ..     294     313 ..     244     319 .. 0.82
   2 !    9.8   0.2   0.00074      0.89      55      76 ..     357     378 ..     320     385 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                           Fer4_18  54 kekgagdcidcescvkvcPt 73 
                                       +  ++  c++c+ c +vcP 
  gi|313124855|ref|YP_004035119.1| 294 QILDTDACTKCGRCSSVCPA 313
                                       4556778************7 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00074
                           Fer4_18  55 ekgagdcidcescvkvcPtgid 76 
                                       ++++  c++c +c++ cP++i+
  gi|313124855|ref|YP_004035119.1| 357 SSTMESCMACMACMDACPVDIE 378
                                       4556677777777777777664 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   3.8    0.0004      0.48       2      16 ..     299     313 ..     298     319 .. 0.92
   2 !   17.5   0.8   3.4e-06    0.0041       2      16 ..     361     375 ..     360     385 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C+ Cg+C ++CP 
  gi|313124855|ref|YP_004035119.1| 299 DACTKCGRCSSVCPA 313
                                       89************6 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.4e-06
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+C  C++C++aCP+
  gi|313124855|ref|YP_004035119.1| 361 ESCMACMACMDACPV 375
                                       89************7 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   3.6   1.4e-06    0.0017       5      21 ..     297     313 ..     297     317 .. 0.93
   2 !   11.5   4.8   0.00021      0.25       7      22 ..     361     376 ..     359     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                            Fer4_6   5 dpdkCigCgdCvrvCPe 21 
                                       d d+C+ Cg+C +vCP+
  gi|313124855|ref|YP_004035119.1| 297 DTDACTKCGRCSSVCPA 313
                                       789*************8 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00021
                            Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                       ++C  C++C+++CP +
  gi|313124855|ref|YP_004035119.1| 361 ESCMACMACMDACPVD 376
                                       79************75 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6  13.4     8e-05     0.096       2      66 ..     301     375 ..     300     376 .. 0.57
   2 !   11.0   2.1   0.00053      0.63       2      20 ..     363     381 ..     362     410 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek..kekeiearecisy...........ntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                       C++Cg+C +vCP++    +   + +i   + ++y            ++  ++ +  + + +  e ++ C +C+d+CP
  gi|313124855|ref|YP_004035119.1| 301 CTKCGRCSSVCPAKESGRPldPRDVI--LDLKQYredldagrteeIDIVADGGTSVIDSST-MESCMACMACMDACP 374
                                       **************987773222222..222222223444433322333333333333333.478************ PP

                           Fer4_16  66 a 66 
                                       +
  gi|313124855|ref|YP_004035119.1| 375 V 375
                                       7 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00053
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C  C +C+++CP++  +  
  gi|313124855|ref|YP_004035119.1| 363 CMACMACMDACPVDIEHLS 381
                                       99**********9865444 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.5   7.3e-05     0.087      73      94 ..     292     313 ..     283     315 .. 0.86
   2 !    6.8   0.1    0.0099        12      77      96 .]     358     377 ..     347     422 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-05
                           Fer4_22  73 fkekfgesgCvGCgRCieacpv 94 
                                       +k+  ++ +C+ CgRC+++cp+
  gi|313124855|ref|YP_004035119.1| 292 WKQILDTDACTKCGRCSSVCPA 313
                                       67778999************97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0099
                           Fer4_22  77 fgesgCvGCgRCieacpvki 96 
                                         +++C+ C  C++acpv+i
  gi|313124855|ref|YP_004035119.1| 358 STMESCMACMACMDACPVDI 377
                                       55667777777777777665 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.2   0.00081      0.96       1      12 [.     301     312 ..     301     315 .. 0.93
   2 ?   10.8   5.6   0.00066      0.79       1      14 [.     363     376 ..     363     377 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00081
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       Ct Cg+C  vCP
  gi|313124855|ref|YP_004035119.1| 301 CTKCGRCSSVCP 312
                                       ************ PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00066
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ C+aC+++CPv+
  gi|313124855|ref|YP_004035119.1| 363 CMACMACMDACPVD 376
                                       988*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (705 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4910.84
//
Query:       gi|313124856|ref|YP_004035120.1|  [L=235]
Description: cobalt ABC transporter permease cbiq [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.1e-15   55.7   3.0    6.7e-15   55.3   3.0    1.1  1  CbiQ        Cobalt transport protein
  ------ inclusion threshold ------
       0.26   11.4   2.2        5.3    7.2   2.8    2.5  2  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   3.0   7.5e-19   6.7e-15       3     210 ..      10     205 ..       8     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 7.5e-19
                                       CCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE...... CS
                              CbiQ   3 svlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilprvlaqalilpllflllgllillfqlitte 79 
                                       s  hrldpr+kl++  ++ la++  +++ +l   +++++++ ++ +  rv  + +i +++ + l +l+++  l+   
  gi|313124856|ref|YP_004035120.1|  10 SLAHRLDPRTKLFVQAAFALAIFAHTTPRGL---AVFTVVTGGILAAGRVSPADPI-RGFAPALPFLLIAP-LV--- 78 
                                       789****************************...7778888888888899999999.89999999999988.34... PP

                                       .EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--H...HHHHHHHHHHHHHHHH CS
                              CbiQ  80 gefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPl...elalillLayRfiflL 153
                                        ++ ++++g   i     +  +l + R+l +l++   ++ TT++ +  +++erl+  +    + + ++L++Rf+++L
  gi|313124856|ref|YP_004035120.1|  79 RTVSLSPLG---IDPAAAVEPALASYRVLLVLVVSGVYLRTTSVRDSRAAVERLLPGRigrFFGVGVALVFRFFPVL 152
                                       478888888...8889999**********99999999****************974448889*************** PP

                                       HHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTS-S CS
                              CbiQ 154 leevqrikqAqklRlgdsklgirrslrslgkliaalflr.alkraervalAmeaRGYt 210
                                       l  ++r ++A k+Rlg+      rsl++  + i+++ +r a+ r++r+ lA+ aR++ 
  gi|313124856|ref|YP_004035120.1| 153 LADLRRVREASKARLGNE-----RSLSERMRIIGTAGVRrAFARSDRLSLALRARCFA 205
                                       *****************9.....44555555555555555****************96 PP

>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.06   5.4e+02      15      36 ..      12      33 ..       2      33 .. 0.82
   2 ?    7.2   2.8   0.00059       5.3      22      36 ..     221     235 .]     220     235 .] 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.06
                                      SS-B-THHHHHHHHHHHHHHHH CS
                        Sec61_beta 15 gikidPkvVlvlsvafiasVil 36
                                      + ++dP + l++ +af+ ++++
  gi|313124856|ref|YP_004035120.1| 12 AHRLDPRTKLFVQAAFALAIFA 33
                                      6689***999999999999985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00059
                                       HHHHHHHHHHHHHHH CS
                        Sec61_beta  22 vVlvlsvafiasVil 36 
                                        Vlv++vaf+asV++
  gi|313124856|ref|YP_004035120.1| 221 PVLVVGVAFVASVFV 235
                                       69***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1457.64
//
Query:       gi|313124857|ref|YP_004035121.1|  [L=234]
Description: cobalt ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-30  104.0   0.0    1.4e-29  103.4   0.0    1.3  1  ABC_tran      ABC transporter
    4.2e-11   43.2   0.0    2.2e-05   24.4   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.5e-06   26.2   0.0    3.2e-05   23.5   0.0    1.9  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00024   20.8   0.0    0.00046   19.9   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00038   20.9   0.1    0.00055   20.3   0.1    1.5  1  AAA_16        AAA ATPase domain
    0.00061   20.0   0.1     0.0099   16.1   0.1    2.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0077   15.8   0.7      0.028   14.0   0.0    2.1  2  AAA_25        AAA domain
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.018   14.9   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.011   15.7   0.0      0.019   14.9   0.0    1.4  1  NACHT         NACHT domain
      0.012   15.7   0.2      0.055   13.6   0.2    2.0  1  AAA_33        AAA domain
      0.021   14.8   0.0      0.036   14.1   0.0    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.022   14.4   0.1      0.073   12.7   0.0    1.8  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.024   15.2   0.0      0.035   14.6   0.0    1.2  1  AAA_23        AAA domain
      0.025   14.3   0.0      0.035   13.8   0.0    1.3  1  AAA_15        AAA ATPase domain
      0.025   14.8   0.0      0.058   13.6   0.0    1.7  1  AAA_28        AAA domain
      0.035   14.1   0.0       0.12   12.3   0.0    1.9  2  AAA_5         AAA domain (dynein-related subfamily)
      0.038   13.7   0.2       0.11   12.2   0.0    1.9  2  AAA_30        AAA domain
       0.04   13.2   0.0        1.3    8.3   0.0    2.1  2  DnaB_C        DnaB-like helicase C terminal domain
      0.046   13.3   0.2      0.079   12.6   0.2    1.4  1  FlbD          Flagellar and Swarming motility proteins
      0.047   13.0   0.1       0.11   11.8   0.0    1.6  2  Zeta_toxin    Zeta toxin
      0.047   14.2   0.1       0.43   11.1   0.0    2.2  2  AAA_18        AAA domain
      0.052   12.9   0.0      0.088   12.2   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.053   13.8   0.0       0.12   12.6   0.0    1.6  1  AAA_22        AAA domain
      0.077   11.6   0.0       0.14   10.8   0.0    1.3  1  AAA_13        AAA domain
      0.093   13.1   0.2       0.38   11.1   0.0    2.1  2  AAA_19        AAA domain
      0.096   12.4   0.0       0.17   11.6   0.0    1.4  1  AAA_24        AAA domain
       0.12   12.3   0.0       0.33   10.8   0.0    1.6  2  ATPase_2      ATPase domain predominantly from Archaea
       0.19    9.2   0.0       0.26    8.8   0.0    1.1  1  DUF3584       Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.0   2.2e-32   1.4e-29       2     136 ..      19     162 ..      18     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 2.2e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       ++vsl++++ge v++ G nG+GK+tL++ + gll+p+ G+i ++g++++e +   +r  +g+++q+    f   tv+
  gi|313124857|ref|YP_004035121.1|  19 DEVSLEIEAGEFVVLAGANGSGKTTLVRHFNGLLEPDTGDIAVNGQPVSE-NPVAARTAVGMVFQDpRDQFVAATVG 94 
                                       78************************************************.88899**********65556666788 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                      e d+++++al+ ++l + +++++     +LSgG+++rva+a al+ +p+ l+lDEp+
  gi|313124857|ref|YP_004035121.1|  95 ADvafgpenlglpraEIDDRVADALDAVNLRGRRNERI----DELSGGEQERVAIAGALAMHPDHLVLDEPF 162
                                       889***********************************....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.7e-06    0.0043       1      23 [.      30      52 ..      30      75 .. 0.79
   2 !   24.4   0.0   3.5e-08   2.2e-05     192     299 ..     108     194 ..      90     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.7e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + vl G+NgsGK++L + + +l 
  gi|313124857|ref|YP_004035121.1| 30 FVVLAGANGSGKTTLVRHFNGLL 52
                                      689************99998874 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 3.5e-08
                            AAA_21 192 lklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEn 268
                                       + ++++++ d +++++l  +++er                  ++elS G ++  a++ al+  +   + l++DEp +
  gi|313124857|ref|YP_004035121.1| 108 RAEIDDRVADALDAVNLRGRRNER------------------IDELSGGEQERVAIAGALAMHP---DHLVLDEPFT 163
                                       556666777777777777766666..................677****************988...77******** PP

                            AAA_21 269 gLHPkllrrllellkelsrngaQviltTHSp 299
                                       gL+  +   +++ l +l+ ng+ ++++TH+ 
  gi|313124857|ref|YP_004035121.1| 164 GLDAPARNAVMDRLTALHGNGTSIVVVTHDL 194
                                       *****************************95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0     5e-08   3.2e-05      25     204 ..      29     199 ..      17     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5e-08
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk...skekasvkkaeveitfdnedkklkiekeevs 98 
                                       +f ++ G+NGSGK+ l+     +L           ++ d+  +    +e++ + +  v ++f+++ ++++  +    
  gi|313124857|ref|YP_004035121.1|  29 EFVVLAGANGSGKTTLVRHFNGLLE---------PDTGDIAVNgqpVSENPVAARTAVGMVFQDPRDQFVAATVGAD 96 
                                       6999************987744444.........344444444455677899999*************999999999 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                       +    ++ g  + +i+++ +   +  +l  + +  +++LSgGe+  va+a  +A++  +     +lDe    LD+  
  gi|313124857|ref|YP_004035121.1|  97 VAFGPENLGLPRAEIDDRVADALDAVNLRGRRNERIDELSGGEQERVAIAGALAMHPDH----LVLDEPFTGLDAPA 169
                                       9999999999*****************************************99998544....589*********** PP

                                       HHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkekskn.aQfivislreemlek 204
                                       +++v ++l + + n + ++v++++ + ++ 
  gi|313124857|ref|YP_004035121.1| 170 RNAVMDRLTALHGNgTSIVVVTHDLRDVQT 199
                                       *********877765888899998665554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   7.1e-07   0.00046      13      55 ..      19      62 ..      16      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.1e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      d+ ++ei+  ++++l+G++GsGK+Tl+  ++ lL p++ +++ N
  gi|313124857|ref|YP_004035121.1| 19 DEVSLEIEAGEFVVLAGANGSGKTTLVRHFNGLLEPDTgDIAVN 62
                                      567788986669***************99999999988666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   8.7e-07   0.00055      24      63 ..      28      68 ..      16     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.7e-07
                            AAA_16 24 pelvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                      +e v+l G+ G+GK++lvr++   le d g i+++g+ ++ 
  gi|313124857|ref|YP_004035121.1| 28 GEFVVLAGANGSGKTTLVRHFNGLLEPDtGDIAVNGQPVSE 68
                                      489*******************9888885233344444444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.5e-05    0.0099      24      88 ..     126     177 ..     110     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                           SbcCD_C  24 kelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       ++ ++++ +lSGGe+     +a+a ala++ ++          ++LDE F +lD+  ++++++ l
  gi|313124857|ref|YP_004035121.1| 126 GRRNERIDELSGGEQ---ERVAIAGALAMHPDH----------LVLDEPFTGLDAPARNAVMDRL 177
                                       556889999******...456777777766665..........9***************999866 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   4.3e-05     0.028      30      50 ..      25      45 ..      21      49 .. 0.91
   2 ?   -0.6   0.2       1.3   8.4e+02     148     149 ..     158     159 ..     103     214 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-05
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + age+++laGa g+GKttl+
  gi|313124857|ref|YP_004035121.1| 25 IEAGEFVVLAGANGSGKTTLV 45
                                      579****************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                            AAA_25 148 iD 149
                                       +D
  gi|313124857|ref|YP_004035121.1| 158 LD 159
                                       22 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.9e-05     0.018      88     131 ..      16      60 ..       2      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                        +++e++ +++  +++vl+G  G GK+tL+ ++++ le  tg++ 
  gi|313124857|ref|YP_004035121.1|  16 VAIDEVSLEIEAgEFVVLAGANGSGKTTLVRHFNGLLEPDTGDIA 60 
                                       56777777777779*******************999999999885 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.9e-05     0.019       3      21 ..      31      49 ..      29      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      v+l G++GsGKTtL++++ 
  gi|313124857|ref|YP_004035121.1| 31 VVLAGANGSGKTTLVRHFN 49
                                      89**************985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   8.6e-05     0.055       2      19 ..      31      48 ..      30     228 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.6e-05
                            AAA_33  2 vllvGlpGsGKstlaerl 19
                                      v+l G++GsGK+tl+++ 
  gi|313124857|ref|YP_004035121.1| 31 VVLAGANGSGKTTLVRHF 48
                                      7899***********985 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.7e-05     0.036      18      40 ..      25      49 ..       4      59 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                                      H..TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrgla 40
                                      +  g++++L G  G+GKTtlvr++ 
  gi|313124857|ref|YP_004035121.1| 25 IeaGEFVVLAGANGSGKTTLVRHFN 49
                                      133788****************985 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.073       3      21 ..      31      49 ..      29      68 .. 0.79
   2 ?   -1.0   0.0       1.7   1.1e+03     103     120 ..     191     209 ..     139     230 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                      +vl+G  GsGKTtL++h  
  gi|313124857|ref|YP_004035121.1| 31 VVLAGANGSGKTTLVRHFN 49
                                      799*************975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                                       SHHHHH.CCCECEEEEEEE CS
                              cobW 103 eeelks.dltldavvavvD 120
                                       +++l++ ++ +d vv++ D
  gi|313124857|ref|YP_004035121.1| 191 THDLRDvQTLADRVVVLSD 209
                                       2333332333333333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.5e-05     0.035      21      39 ..      30      48 ..      17      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-05
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                      ++++ G NG+GKTT+++ +
  gi|313124857|ref|YP_004035121.1| 30 FVVLAGANGSGKTTLVRHF 48
                                      67999**********9876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.5e-05     0.035      17      48 ..      23      53 ..      17      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-05
                            AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFln 48
                                       ei+  e + vl G+N+sGK+++++ ++ +l+
  gi|313124857|ref|YP_004035121.1| 23 LEIEAGE-FVVLAGANGSGKTTLVRHFNGLLE 53
                                      4666677.***************998877766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.1e-05     0.058       2      20 ..      31      49 ..      30      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.1e-05
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      +v+ G+ ++GKTtl+++++
  gi|313124857|ref|YP_004035121.1| 31 VVLAGANGSGKTTLVRHFN 49
                                      89*************9976 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00019      0.12       2      24 ..      31      54 ..      30      83 .. 0.85
   2 ?   -1.8   0.0       4.3   2.8e+03      11      38 ..     169     196 ..     163     223 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                      EEEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                      v+L G+ G+gK++l++++  +l  
  gi|313124857|ref|YP_004035121.1| 31 VVLAGANGSGKTTLVRHFNGLLeP 54
                                      79****************998853 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.3
                                       SHHHHHHHGGGGBS--EEEEE--TT--H CS
                             AAA_5  11 gKselaerlaaalnreveyvqltrdtte 38 
                                       +++ +++rl a+ ++ + +v  t d++ 
  gi|313124857|ref|YP_004035121.1| 169 ARNAVMDRLTALHGNGTSIVVVTHDLRD 196
                                       5666777777777555555555555443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.11      19      48 ..      29      58 ..      14      93 .. 0.85
   2 ?   -1.4   0.1       2.5   1.6e+03      81      97 ..     195     217 ..     165     228 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggr 48
                                       ++vl G+ G+GKtt++++ + ++e + g+
  gi|313124857|ref|YP_004035121.1| 29 EFVVLAGANGSGKTTLVRHFNGLLEPDTGD 58
                                      4899***************99999877444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                            AAA_30  81 k......grarlepgtllivDEa 97 
                                       +      +r+ + ++  ++vDE+
  gi|313124857|ref|YP_004035121.1| 195 RdvqtlaDRVVVLSDGRVVVDET 217
                                       23334443344444456677776 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0021       1.3       9      38 ..      18      47 ..      14      75 .. 0.88
   2 ?    3.0   0.0     0.085        54      64     119 ..     174     227 ..     148     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                                      HHHHCTSBXTTXEEEEEEXTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  9 LDkltsGlqkgdliiiAarpsmGktalaln 38
                                      +D++   ++ g+++++A+  + Gkt+l+ +
  gi|313124857|ref|YP_004035121.1| 18 IDEVSLEIEAGEFVVLAGANGSGKTTLVRH 47
                                      6888888999****************9865 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.085
                                       HHHHHHHHHTXXHHHHHHTTSXHHHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  64 vqRllsseaeidskklrtgklkeedweklteaieelseaklfiddtpaltvseirs 119
                                       ++Rl + +++ +s  + t +l+  d+++l++++  ls+ ++++d+tp+  v+++++
  gi|313124857|ref|YP_004035121.1| 174 MDRLTALHGNGTSIVVVTHDLR--DVQTLADRVVVLSDGRVVVDETPEQAVEQVEQ 227
                                       5555555555555555555554..69999*******************99999865 PP

>> FlbD  Flagellar and Swarming motility proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00012     0.079       8      55 ..     183     229 ..     174     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                              FlbD   8 ngeefvlNadlIetieetPDTvItLtnGkkyvVkEsvdeviervieyr 55 
                                       ng+ +v+  +  + ++   D v++L +G ++vV E+ ++ +e+v +y 
  gi|313124857|ref|YP_004035121.1| 183 NGTSIVVVTHDLRDVQTLADRVVVLSDG-RVVVDETPEQAVEQVEQYD 229
                                       567888888999999***********99.59**************996 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.11      18      41 ..      30      53 ..      17      64 .. 0.81
   2 ?   -2.9   0.0       5.2   3.3e+03     137     165 ..     197     224 ..     182     227 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                        Zeta_toxin 18 lillgGqpGAGKselaellkdele 41
                                       ++l+G+ G+GK++l + ++  le
  gi|313124857|ref|YP_004035121.1| 30 FVVLAGANGSGKTTLVRHFNGLLE 53
                                      699*************99987776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.2
                        Zeta_toxin 137 rlgvldRyeeevaegRlvpkeehdeafeg 165
                                       ++ ++dR+      gR+v  e+ ++a+e+
  gi|313124857|ref|YP_004035121.1| 197 VQTLADRVVVL-SDGRVVVDETPEQAVEQ 224
                                       44455555554.33566655555555554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00067      0.43       1      20 [.      31      50 ..      31      76 .. 0.80
   2 ?    0.9   0.0         1   6.5e+02      51     101 ..     164     216 ..     109     231 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00067
                            AAA_18  1 IlltGtpGvGKttlakeLsk 20
                                      ++l+G+ G+GKttl ++ + 
  gi|313124857|ref|YP_004035121.1| 31 VVLAGANGSGKTTLVRHFNG 50
                                      789***********998755 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1
                            AAA_18  51 rldedkldklldaleenssaleegknlvidghlaeleseaakdikk.....vvLta 101
                                        ld + +++++d l +     ++g ++v+  h    +++ a + +      vv++ 
  gi|313124857|ref|YP_004035121.1| 164 GLDAPARNAVMDRLTAL---HGNGTSIVVVTHDLRDVQTLADRVVVlsdgrVVVDE 216
                                       45556666666666665...356777777777766666665554445555555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014     0.088      22      51 ..      28      57 ..       9     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                      Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllpplse 51
                                      g  ++l+G+ GsGKt l + +++ll p + 
  gi|313124857|ref|YP_004035121.1| 28 GEFVVLAGANGSGKTTLVRHFNGLLEPDTG 57
                                      445899*******************88665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00019      0.12       5      29 ..      28      52 ..      24      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                        ++v+ G  G+GKTtl+r +   l
  gi|313124857|ref|YP_004035121.1| 28 GEFVVLAGANGSGKTTLVRHFNGLL 52
                                      56899**************998766 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.14      23      44 ..      35      56 ..      26      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                            AAA_13 23 GwNGaGKTtLSrllrslelget 44
                                      G+NG+GKTtL r ++ l +  t
  gi|313124857|ref|YP_004035121.1| 35 GANGSGKTTLVRHFNGLLEPDT 56
                                      9*************99855444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0006      0.38       8      34 ..      25      52 ..       9      96 .. 0.84
   2 ?   -0.2   0.1       1.8   1.2e+03      45      50 ..     187     192 ..     109     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0006
                            AAA_19  8 lkekvllvtaGp.GtGKTrvlkhivall 34
                                      ++++ ++v+aG+ G+GKT++++h   ll
  gi|313124857|ref|YP_004035121.1| 25 IEAGEFVVLAGAnGSGKTTLVRHFNGLL 52
                                      5555566666655*********986665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
                            AAA_19  45 illvaf 50 
                                       i++v+ 
  gi|313124857|ref|YP_004035121.1| 187 IVVVTH 192
                                       333333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00027      0.17       5      30 ..      31      55 ..      28     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplfid 30
                                      +++ G +g+GKTtl++++ +  l  d
  gi|313124857|ref|YP_004035121.1| 31 VVLAGANGSGKTTLVRHF-NGLLEPD 55
                                      789***************.5555544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00052      0.33      15      41 ..      23      49 ..      16      62 .. 0.84
   2 ?   -1.8   0.0       3.8   2.5e+03      57     131 ..     124     198 ..     118     218 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00052
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeii 41
                                      le e  e++++ G  gsGKt+L++++ 
  gi|313124857|ref|YP_004035121.1| 23 LEIEAGEFVVLAGANGSGKTTLVRHFN 49
                                      66778999****************985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.8
                          ATPase_2  57 lreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                       lr+++++++de  + e+e+  ++ al+       l+e +    + + +a+ + l ++  +g+ i+++  +l  + 
  gi|313124857|ref|YP_004035121.1| 124 LRGRRNERIDELSGGEQERVAIAGALAMHPDHLVLDEPFTGLDAPARNAVMDRLTALHGNGTSIVVVTHDLRDVQ 198
                                       555555555555444455555555555555555555555555566666777777777777777777777666554 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00041      0.26      13      35 ..      24      46 ..      20      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00041
                           DUF3584 13 eldldghtnieGtNaaGKTtLlr 35
                                      e++  + + + G+N++GKTtL r
  gi|313124857|ref|YP_004035121.1| 24 EIEAGEFVVLAGANGSGKTTLVR 46
                                      66667778899**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1682.60
//
Query:       gi|313124858|ref|YP_004035122.1|  [L=202]
Description: hypothetical protein Hbor_00700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-33  115.9  20.7      2e-33  115.3  20.7    1.2  1  BioY        BioY family
  ------ inclusion threshold ------
        1.6    8.7   8.7        2.9    7.8   8.8    1.6  1  ATP-synt_A  ATP synthase A chain
        2.7    7.8  23.5          7    6.4  23.5    1.6  1  CbiM        Cobalt uptake substrate-specific transmembrane re


Domain annotation for each model (and alignments):
>> BioY  BioY family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3  20.7   3.4e-37     2e-33       2     131 ..      42     195 ..      41     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 3.4e-37
                              BioY   2 gpvpitlqtlavllaglllgprrgalavllYlllGalglPvfagg.gGlavllgptgGYllGFlvaalvvgll.... 73 
                                       +p p++lq+l+v+lag++lgp +g ++++lYl +Ga+g+P+fagg +Gl+ llg t+GYl+++++aa+++gll    
  gi|313124858|ref|YP_004035122.1|  42 SPHPVSLQVLGVFLAGIFLGPVWGGASMVLYLTAGAAGAPIFAGGsAGLGSLLGLTAGYLWSYPPAAALIGLLvhgv 118
                                       799*****************************************66******************************* PP

                              BioY  74 ......kk..laelllallagllviyalGvlwlalv.....ls......laaalaagvlpfipgdlvkavlaallak 131
                                             ++  +a+l+ a++ag++viy++G++++a+v     ls      l++a++++ l f+p ++vk+++a+ +++
  gi|313124858|ref|YP_004035122.1| 119 sglvdpEHvpVARLVGAMVAGTVVIYVFGTVGFAIVqtggiLSafapnvLWDAFVVSALAFVPFEAVKIAAAVGIIR 195
                                       **9986224699***********************65555522555666999********************99875 PP

>> ATP-synt_A  ATP synthase A chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.8   0.00049       2.9     146     191 ..     130     173 ..       5     182 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHHHHHHHHHHHHHCCCTGCCCTTCHHH.HHHHHHHHHHH CS
                        ATP-synt_A 146 lRLfgNifAGelllallagllllllllavllsvli.lllavllllle 191
                                        RL+g ++AG++++ ++ ++ ++++ +    ++l+ ++ +vl+ ++ 
  gi|313124858|ref|YP_004035122.1| 130 ARLVGAMVAGTVVIYVFGTVGFAIVQT---GGILSaFAPNVLWDAFV 173
                                       4****************7554333333...33444344566666654 PP

>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  23.5    0.0012         7      38     201 ..      21     195 ..      13     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0012
                              CbiM  38 rvpllallaafifaaqminipipggtslHllgavlaaiLlGpwaaflavavvlllqal...lfgdG..Gita.LGaN 108
                                       r++l+a+l+ ++  +++ n   p ++sl  lg+ la+i+lGp  +  ++++ l+  a+   +f+ G  G+ + LG+ 
  gi|313124858|ref|YP_004035122.1|  21 RAALFAALTGAFAYVSFQNPLSPHPVSLQVLGVFLAGIFLGPVWGGASMVLYLTAGAAgapIFAGGsaGLGSlLGLT 97 
                                       3444555555555555555555588******************9999999999887653336765533775427999 PP

                              CbiM 109 ilnmavigvllaylvyrllsrla..sskkrvalaafl.aallsvvlaallvalelalsgleas...lsltaalaaml 179
                                       +  +   ++++a +    +++       ++v +a ++ a ++++v+ +++ ++ +a+ ++ +    ++  +++ a++
  gi|313124858|ref|YP_004035122.1|  98 AGYLWSYPPAAALIGLL-VHGVSglVDPEHVPVARLVgAMVAGTVVIYVFGTVGFAIVQTGGIlsaFAPNVLWDAFV 173
                                       99999999988884444.333334433455555555534444455555555555555544322444999999***** PP

                              CbiM 180 lvhlpvgilEgviTaaivkalk 201
                                       +  l+ +  E+v  aa+v +++
  gi|313124858|ref|YP_004035122.1| 174 VSALAFVPFEAVKIAAAVGIIR 195
                                       *****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1424.91
//
Query:       gi|313124859|ref|YP_004035123.1|  [L=217]
Description: hypothetical protein Hbor_00710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.57
# Mc/sec: 1151.68
//
Query:       gi|313124860|ref|YP_004035124.1|  [L=1818]
Description: replication control ARTPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-79  266.4   0.1    7.1e-34  116.9   0.0    3.3  3  MCM              MCM P-loop domain
    1.3e-55  185.6   2.1    8.4e-17   61.3   0.1    4.9  4  LAGLIDADG_3      LAGLIDADG-like domain
    2.1e-47  160.5   0.0      8e-23   80.9   0.0    3.6  3  Intein_splicing  Intein splicing domain
    6.1e-35  119.8   0.6    1.1e-34  119.0   0.6    1.4  1  MCM_OB           MCM OB domain
    4.9e-28   97.4   1.3    6.4e-27   93.8   0.2    2.7  2  MCM_lid          MCM AAA-lid domain
    7.3e-10   38.8   0.0    0.00021   21.3   0.0    3.7  3  HTH_3            Helix-turn-helix
    2.4e-09   37.4   1.1       0.03   14.5   0.0    3.9  3  Hom_end          Homing endonuclease
    3.9e-07   30.3   4.5     0.0066   16.8   0.1    4.9  4  HTH_31           Helix-turn-helix domain
    4.4e-07   30.4   3.1    1.1e-06   29.2   1.4    2.6  1  MCM_N            MCM N-terminal domain
    4.8e-05   23.0   0.0     0.0046   16.5   0.0    3.6  3  Hint             Hint module
    0.00011   21.6   0.1     0.0003   20.1   0.1    1.8  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
     0.0003   20.4   0.0    0.00062   19.4   0.0    1.5  1  HTH_Tnp_4        Helix-turn-helix of DDE superfamily endonucl
     0.0099   15.3   0.1        4.9    6.5   0.0    3.1  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.014   15.2   0.0       0.11   12.3   0.0    2.6  1  HTH_23           Homeodomain-like domain
      0.021   15.2   0.0        1.5    9.3   0.0    2.8  2  HTH_26           Cro/C1-type HTH DNA-binding domain
      0.022   14.5   0.0      0.079   12.7   0.0    2.0  1  HTH_38           Helix-turn-helix domain
      0.031   14.4   0.0      0.085   13.0   0.0    1.7  1  HTH_Tnp_1_2      Helix-turn-helix of insertion element transp
      0.036   14.2   0.1       0.55   10.4   0.0    2.8  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
      0.063   11.6   0.4        0.1   10.9   0.4    1.2  1  MAD              Mitotic checkpoint protein
      0.064   13.2   0.0          2    8.4   0.0    3.2  3  MarR_2           MarR family
       0.11   12.2   0.0        0.3   10.8   0.0    1.8  1  CENP-B_N         CENP-B N-terminal DNA-binding domain
       0.12   12.3   0.2        1.7    8.6   0.0    3.0  3  YdaS_antitoxin   Putative antitoxin of bacterial toxin-antito
       0.13   12.7   1.4       0.55   10.7   0.5    2.7  1  DUF4072          Domain of unknown function (DUF4072)
       0.14   12.1   0.0       0.52   10.3   0.0    2.0  1  HTH_36           Helix-turn-helix domain
       0.15   11.9   0.1       0.55   10.1   0.1    2.0  1  LacI             Bacterial regulatory proteins, lacI family
        1.5    8.4   4.0        1.4    8.4   1.8    2.1  2  Snf7             Snf7


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   2.5e-21   1.8e-18       2      71 ..     268     337 ..     267     339 .. 0.97
   2 !   79.0   0.0   3.9e-25   2.7e-22      66     136 ..     800     872 ..     787     885 .. 0.86
   3 !  116.9   0.0     1e-36   7.1e-34     134     223 ..    1516    1605 ..    1512    1606 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 2.5e-21
                                       HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHH CS
                               MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKs 71 
                                       v+ei el++++di++k++ s+apsiyg+e+ k a++lqlf+gv+k+l+d++++rgd ++ll+gdpgt+K 
  gi|313124860|ref|YP_004035124.1| 268 VAEIVELSNDPDIYQKMIGSVAPSIYGYEQEKLAMILQLFSGVTKHLPDGSRIRGDLHMLLIGDPGTGKC 337
                                       68999***************************************************************95 PP

  == domain 2  score: 79.0 bits;  conditional E-value: 3.9e-25
                                       STSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSEEEEES..SSSSEEEEETHHHHTTTSEEEEESGGGSTCH CS
                               MCM  66 pgtaKsqlLkyveklapravytsgkgssaagLtaavvrde..etgefvleaGalvladkGvcciDefdkmkee 136
                                       +    sq+L+y+ ++apr+vytsgkgss+agLtaa vrd+  + ++++leaGalvladkG++++De+dkm+  
  gi|313124860|ref|YP_004035124.1| 800 VVSHNSQMLQYIRNIAPRSVYTSGKGSSSAGLTAAAVRDDfgDGQQWTLEAGALVLADKGIAAVDELDKMRCV 872
                                       55668**********************************8334567************************865 PP

  == domain 3  score: 116.9 bits;  conditional E-value: 1e-36
                                        TCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SST CS
                               MCM  134 keedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkv 208 
                                        ++edrsa+hE +Eqq+is++KaGi+atL++r+s+l Aanpk+gr+d+ +s+ e+i+l++al+srFDlif++ D++
  gi|313124860|ref|YP_004035124.1| 1516 NSEDRSAMHEGLEQQQISVSKAGINATLKSRCSLLGAANPKYGRFDQYESIGEQIDLEPALISRFDLIFTVTDDP 1590
                                        6789*********************************************************************** PP

                                        THHHHHHHHHHHHHH CS
                               MCM  209 deekDeelaehivsl 223 
                                        d e+D+elaehi+++
  gi|313124860|ref|YP_004035124.1| 1591 DPESDAELAEHIINT 1605
                                        ************986 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   7.4e-15   5.1e-12       4      82 ..     486     561 ..     483     562 .. 0.91
   2 !   56.9   0.0   2.8e-18   1.9e-15       2      83 .]     585     658 ..     584     658 .. 0.97
   3 !   17.2   0.0   6.7e-06    0.0046       7      42 ..    1025    1061 ..    1020    1064 .. 0.92
   4 !   61.3   0.1   1.2e-19   8.4e-17       2      83 .]    1123    1201 ..    1122    1201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 7.4e-15
                                       HHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGGT CS
                       LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFle 80 
                                       +a L G+ +a+G+v+ +  ++  +s+t+s++e+l+dv+  L +lG+ +t + +  ++ +++ r+li+s+++l  +le
  gi|313124860|ref|YP_004035124.1| 486 LARLLGYVAAEGYVERRDSGSAFVSITNSDREILDDVADALDELGLRATERST--HDDKTT-RELICSSSELVSLLE 559
                                       689***************98777******************************..555555.6************** PP

                                       TT CS
                       LAGLIDADG_3  81 ki 82 
                                       ki
  gi|313124860|ref|YP_004035124.1| 560 KI 561
                                       99 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 2.8e-18
                                       HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGG CS
                       LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrF 78 
                                       vk++fLr++ da+G+vs s++    ++++s+s+++le+v+ lLl +GI s++++k     +g++ +l++sg+++ r+
  gi|313124860|ref|YP_004035124.1| 585 VKRGFLRAFVDAEGTVSPSQRE---VTVSSTSRDVLEGVRSLLLAFGISSQLRTK----ADGSF-RLRVSGDDFARY 653
                                       79*******************9...******************************....88888.9*********** PP

                                       GTTTX CS
                       LAGLIDADG_3  79 lekig 83 
                                         +ig
  gi|313124860|ref|YP_004035124.1| 654 TAQIG 658
                                       ***98 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 6.7e-06
                                        HHHHHHHCCECCECSTTTTS.EEEEES-HHHHHHHHH CS
                       LAGLIDADG_3    7 LrGlfdaDGsvskskkkgvs.isltssskelledvqr 42  
                                          G+ ++DG v  +++ gv+ i++t++++ell d+ r
  gi|313124860|ref|YP_004035124.1| 1025 VLGYLSGDGNVYYDREEGVYgIRFTNKEEELLADFER 1061
                                        57******************************99876 PP

  == domain 4  score: 61.3 bits;  conditional E-value: 1.2e-19
                                        HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTC CS
                       LAGLIDADG_3    2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlk 76  
                                        +kaaf r++ d++Gsv++++++   ++++sss+el+ +++ lLl++ I+++i+++ ++++r++y l ++  e+l+
  gi|313124860|ref|YP_004035124.1| 1123 TKAAFVRAMADSEGSVDTDSGN---VKISSSSYELVLGIKSLLLEFDITTQIQHRERSGKRDLYVLAVTAAESLQ 1194
                                        689******************9...************************************************** PP

                                        GGGTTTX CS
                       LAGLIDADG_3   77 rFlekig 83  
                                        rF ++ig
  gi|313124860|ref|YP_004035124.1| 1195 RFNRHIG 1201
                                        ******8 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.0   1.2e-25     8e-23       4     134 .]     347     804 ..     344     804 .. 0.94
   2 !   43.3   0.0   4.7e-14   3.3e-11      17     112 ..     894    1382 ..     878    1386 .. 0.95
   3 !   32.0   0.0   1.4e-10   9.9e-08     104     134 .]    1487    1516 ..    1470    1516 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 1.2e-25
                                       CTTCEEEEHHHHCC...............ECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEET CS
                                       xxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                   Intein_splicing   4 edgeekvkieelve...............kegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTp 64 
                                       +d + +v+i++lve               + ++ev s+  +d ++   + +k++k +    +yei++++g+++ +Tp
  gi|313124860|ref|YP_004035124.1| 347 AD-GSEVPIRKLVEqnldepkpvddgvwdAVDFEVPSMA-HDGSITTRRATKVWKREAPdRMYEIRTAAGHELTVTP 421
                                       55.556699999998887777665555544445555444.44555555589999988877***************** PP

                                       T-EEEECCTTEEEEEECCC--TT-EEEEE................................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................ RF
                   Intein_splicing  65 eHkllvvrdegivEkradeLkegdliavp................................................ 93 
                                        H+l+v  d+g+  + ad+L++g+++avp                                                
  gi|313124860|ref|YP_004035124.1| 422 SHPLFVGCDGGTEAVVADNLEAGQFVAVPrslptdgdnsldvsirrsqsnnavrldlpdrltpslarllgyvaaegy 498
                                       *******99999789************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|313124860|ref|YP_004035124.1| 499 verrdsgsafvsitnsdreilddvadaldelglratersthddkttrelicssselvsllekiepalldgsseqrvp 575
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|313124860|ref|YP_004035124.1| 576 apilrakspvkrgflrafvdaegtvspsqrevtvsstsrdvlegvrslllafgissqlrtkadgsfrlrvsgddfar 652
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|313124860|ref|YP_004035124.1| 653 ytaqiglvterkrraaeavvdvdgntnrdvipgvgdtlcdlreslgleqddcglprstyqhyergdrnpsrdslqtv 729
                                       ***************************************************************************** PP

                                       .................................HSCEEEEEEEEEEE.EECEEEEEEEEETTT-EEEECTTEEE- CS
                                       .................................xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  94 .................................dadvvwdkvksiev.edeeeyVYdltvednhNFvangiivHN 134
                                                                        d+d++wd+++si+  e ++e VYdl++e++hNF+ n+++ HN
  gi|313124860|ref|YP_004035124.1| 730 vqtfseaaadglaadgdggasverclaslralaDGDIAWDRIESIDPvEPDDEWVYDLEIEGTHNFLTNNVVSHN 804
                                       *********************************************961567999********************9 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 4.7e-14
                                        C..................ECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECC CS
                                        x..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing   17 e..................kegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvr 72  
                                                           + + ev+s+  +d kl    v+++ +++   el +++l+sg+++ a  +H++++++
  gi|313124860|ref|YP_004035124.1|  894 HdaaregsteelangrtirNFDAEVWSMT-DDGKLVSRPVTAIHEYDAPdELTRVTLQSGERLTAIHDHPFITFD 967 
                                        44554444444444666656677888776.888888888******99989************************9 PP

                                        TTEEEEEECCC--TT-EEEEE...................................................... CS
                                        xxxxxxxxxxxxxxxxxxxxx...................................................... RF
                   Intein_splicing   73 degivEkradeLkegdliavp...................................................... 93  
                                        d++ vEk a ++++gd + vp                                                      
  gi|313124860|ref|YP_004035124.1|  968 DGESVEKPAANVSPGDWVFVPrrladratdggvrtadsiaggtvtatenelspafgavlgylsgdgnvyydreeg 1042
                                        9************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Intein_splicing   94 ........................................................................... 93  
                                                                                                                   
  gi|313124860|ref|YP_004035124.1| 1043 vygirftnkeeelladferacrdacdaeairppseqrddgvetvrlsgkefadvvldagmnlevydgkafptais 1117
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Intein_splicing   94 ........................................................................... 93  
                                                                                                                   
  gi|313124860|ref|YP_004035124.1| 1118 aasratkaafvramadsegsvdtdsgnvkissssyelvlgikslllefdittqiqhrersgkrdlyvlavtaaes 1192
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Intein_splicing   94 ........................................................................... 93  
                                                                                                                   
  gi|313124860|ref|YP_004035124.1| 1193 lqrfnrhigftldrkqsaldevcesvsgdrtildviphcgellsslreslrlyvsecglvdatdcnfenkdanvs 1267
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Intein_splicing   94 ........................................................................... 93  
                                                                                                                   
  gi|313124860|ref|YP_004035124.1| 1268 iscartildafesrtqeaesdaeqltepcdweilsdikeryhvsqselatgtpysqqqisllwgaddelravtrn 1342
                                        *************************************************************************** PP

                                        .....................HSCEEEEEEEEEEEEECEE CS
                                        .....................xxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing   94 .....................dadvvwdkvksievedeee 112 
                                                             ++dv w +vks+e+ de +
  gi|313124860|ref|YP_004035124.1| 1343 rlreivesvvntdiepfrhlvRGDVKWRRVKSVETVDESD 1382
                                        ***********************************99876 PP

  == domain 3  score: 32.0 bits;  conditional E-value: 1.4e-10
                                        EEEEEECEEEEEEEEETTT-EEEECTTEEE- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  104 sievedeeeyVYdltvednhNFvangiivHN 134 
                                         ie ++ ++ VYdltve++hNFvang++vHN
  gi|313124860|ref|YP_004035124.1| 1487 TIESRSTPK-VYDLTVEGTHNFVANGMVVHN 1516
                                        678888888.********************9 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.0   0.6   1.6e-37   1.1e-34       5     124 ..     107     229 ..     101     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 1.6e-37
                                       --GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSEEEE CS
                            MCM_OB   5 lrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkletekskfvd 76 
                                       ++ +hig++v+v+Giv +a++v+pk+++a+fec++cg+++ +      ++eP++C  + Ce+++pf+++ ++s+fvd
  gi|313124860|ref|YP_004035124.1| 107 VHDDHIGRMVSVQGIVRKATDVRPKITEAAFECQRCGTMTYIpqtdsGFQEPHEC--QGCERQGPFHVDFDQSEFVD 181
                                       45789********************************98888888877888****..99****************** PP

                                       EEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                            MCM_OB  77 fqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                        qkl++QEspe +  Ge+P+s+++ +edd++ +v++Gd+v+vtG++++
  gi|313124860|ref|YP_004035124.1| 182 SQKLRVQESPEGLRGGETPQSIDIDIEDDVTGEVTAGDHVTVTGVLHI 229
                                       *********************************************987 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.57     4e+02      64      85 ..    1371    1392 ..    1369    1394 .. 0.90
   2 !   93.8   0.2   9.3e-30   6.4e-27       1      86 [.    1642    1726 ..    1642    1727 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.57
                                        HHHTSSSE-HHHHHHHHHHHHH CS
                           MCM_lid   64 klrlsevvteedveeairllke 85  
                                        +++  e+v+e+dv++ irllk+
  gi|313124860|ref|YP_004035124.1| 1371 RVKSVETVDESDVDDQIRLLKH 1392
                                        788899*************987 PP

  == domain 2  score: 93.8 bits;  conditional E-value: 9.3e-30
                                        HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHH CS
                           MCM_lid    1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteed 75  
                                        ellrkYiaya++++ P++++eake ++++Yv++R + +d+ ++ +p+t+R+Le+l+RL+eA+A++rls++vte+d
  gi|313124860|ref|YP_004035124.1| 1642 ELLRKYIAYAKRNCYPTMTDEAKEVIRDFYVNFRAKGADE-DSPVPVTARKLEALVRLAEASARVRLSDTVTEDD 1715
                                        68*********************************99766.99******************************** PP

                                        HHHHHHHHHHH CS
                           MCM_lid   76 veeairllkes 86  
                                        + +++++++++
  gi|313124860|ref|YP_004035124.1| 1716 AVRVTNIVESC 1726
                                        *******9987 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     3e-07   0.00021       4      46 ..     693     731 ..     692     734 .. 0.89
   2 ?   -1.4   0.1       3.6   2.5e+03       9      27 ..    1309    1327 ..    1303    1328 .. 0.85
   3 !   12.4   0.0   0.00018      0.12      13      34 ..    1437    1458 ..    1424    1463 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3e-07
                                       HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHH CS
                             HTH_3   4 lRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklak 46 
                                       lR+ lgl q    + +G++rst++++E+G+rnPs + l+ + +
  gi|313124860|ref|YP_004035124.1| 693 LRESLGLEQ----DDCGLPRSTYQHYERGDRNPSRDSLQTVVQ 731
                                       799999999....9********************999987655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                                        THHHHHHHHHHTSSHHHHH CS
                             HTH_3    9 glsqeeLAeklGvsrstis 27  
                                          sq eLA  +  s+++is
  gi|313124860|ref|YP_004035124.1| 1309 HVSQSELATGTPYSQQQIS 1327
                                        679*****99999999998 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00018
                                        HHHHHHHTSSHHHHHHHHTTSS CS
                             HTH_3   13 eeLAeklGvsrstisriEnGer 34  
                                        +++A+ lGv  st+sr++nG  
  gi|313124860|ref|YP_004035124.1| 1437 ADIARDLGVADSTVSRWFNGVV 1458
                                        899*****************54 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.4e-05      0.03      18      68 ..     489     541 ..     486     559 .. 0.83
   2 !   11.9   0.0   0.00028       0.2      12      65 ..     584     636 ..     573     650 .. 0.85
   3 !    7.0   0.1    0.0094       6.5      13      85 ..    1123    1188 ..    1112    1209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.4e-05
                           Hom_end  18 laGLvdsdgyvkkeked..satvktedksvmegivklarsLGikasvktkeek 68 
                                       l+G v ++gyv++++++   ++++ +d+++++++    + LG++a+  + +  
  gi|313124860|ref|YP_004035124.1| 489 LLGYVAAEGYVERRDSGsaFVSITNSDREILDDVADALDELGLRATERSTHDD 541
                                       89************99988899999*******************987664222 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00028
                           Hom_end  12 evREaFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktk 65 
                                        v+  Fl  +vd++g+v+   ++++tv+++++ v+eg+ +l    Gi+ +  tk
  gi|313124860|ref|YP_004035124.1| 584 PVKRGFLRAFVDAEGTVSPS-QREVTVSSTSRDVLEGVRSLLLAFGISSQLRTK 636
                                       455589999*********99.77******************9999999998876 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0094
                           Hom_end   13 vREaFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktkeekidakgvkhqfcyaitls 85  
                                        ++ aF+  + ds+g+v+++ ++ + +++++ +++ gi +l    +i+++++ +e +    g++    y + ++
  gi|313124860|ref|YP_004035124.1| 1123 TKAAFVRAMADSEGSVDTD-SGNVKISSSSYELVLGIKSLLLEFDITTQIQHRERS----GKRD--LYVLAVT 1188
                                        5567888899*********.669999999999999998777777777777666444....3332..3555555 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.7   4.6e+03      36      62 ..     580     606 ..     578     607 .. 0.81
   2 ?   -2.1   0.1       7.5   5.2e+03      23      59 ..     642     677 ..     641     680 .. 0.85
   3 !   16.8   0.1   9.6e-06    0.0066       3      58 ..     687     745 ..     686     749 .. 0.84
   4 !   11.0   0.0   0.00059      0.41      11      42 ..    1430    1461 ..    1423    1471 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.7
                            HTH_31  36 qGrrgrpspavlealaralgl.dpaera 62 
                                       +++ + +++++l+a+++a g+ +p++r+
  gi|313124860|ref|YP_004035124.1| 580 RAKSP-VKRGFLRAFVDAEGTvSPSQRE 606
                                       67776.99**********9976888875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.5
                            HTH_31  23 rlgvsestlsrlEqGrrgrpspavlealaralgldpa 59 
                                       rl+vs +   r+      +++++  +a+  ++++d++
  gi|313124860|ref|YP_004035124.1| 642 RLRVSGDDFARYTAQIG-LVTERKRRAAEAVVDVDGN 677
                                       78999999999999888.8999999999888888875 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 9.6e-06
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspa........vlealaralgldp 58 
                                       G++L +lRe  GL q++    +g+ +st+ ++E+G r +ps++        + ea+a++l +d+
  gi|313124860|ref|YP_004035124.1| 687 GDTLCDLRESLGLEQDD----CGLPRSTYQHYERGDR-NPSRDslqtvvqtFSEAAADGLAADG 745
                                       889999***********....9***************.6*999666666667777777777766 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00059
                            HTH_31   11 eraGLsqeevAerlgvsestlsrlEqGrrgrp 42  
                                        +r+++s ++ A+ lgv  st+sr+ +G     
  gi|313124860|ref|YP_004035124.1| 1430 NRHNVSFADIARDLGVADSTVSRWFNGVVETD 1461
                                        7999***********************87544 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   1.4   1.6e-09   1.1e-06       6      73 ..      15      76 ..      11      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.6e-09
                             MCM_N  6 dFLeefkddsededgekkYrdqlqemaer...ekttLevdlddLaafdeeLaeailenpkeylplleealk 73
                                      +F++ +         +k+Y d + ++a+r   e+++L++d+ddL  fde+Lae  +++p ++ ++ eeal+
  gi|313124860|ref|YP_004035124.1| 15 RFIQFY---------RKYYSDDIGRLAQRypnEQRSLYIDYDDLFRFDEDLAEDYRKKPDQIREYAEEALR 76
                                      566655.........788**********99999************************************96 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.7e-06    0.0046      10     117 ..     335     452 ..     332     473 .. 0.69
   2 ?   -0.3   0.0      0.94   6.5e+02       7      32 ..     866     892 ..     861     894 .. 0.79
   3 ?   -0.7   0.0       1.2   8.3e+02      38     115 ..     918     988 ..     913    1003 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.7e-06
                                       XXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXX.XXXXXXXXXXXXXXXXXX............XXXXXXXXXXX CS
                              Hint  10 ggCFpgestvtvedgeqkslseL..epGdkVlavd.esgevvfsevllfldrds............eqraefveiet 71 
                                       g C  g+ +vtv+dg+++++++L  +  d+   vd +  + v  ev +  +  s            e+  +++ei+t
  gi|313124860|ref|YP_004035124.1| 335 GKCVAGDTRVTVADGSEVPIRKLveQNLDEPKPVDdGVWDAVDFEVPSMAHDGSittrratkvwkrEAPDRMYEIRT 411
                                       67777777777777777777777433345555555233344555555555555555666666666688999****** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..X CS
                              Hint  72 engekltlTpaHLvfvsenekssseeeeavfaskvregdyvlvedt 117
                                         g++lt+Tp+H +fv          +eav+a++ ++g++v v+++
  gi|313124860|ref|YP_004035124.1| 412 AAGHELTVTPSHPLFVGCDGG-----TEAVVADNLEAGQFVAVPRS 452
                                       ****************75543.....3679***********99443 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.94
                                       HHXXXXXXXXXXXXXXX.XXXXXXXXX CS
                              Hint   7 akkggCFpgestvtved.geqkslseL 32 
                                       + k+ C +g+s+v+++d g+ k+++++
  gi|313124860|ref|YP_004035124.1| 866 LDKMRCVTGDSLVHLADdGGIKRIRDI 892
                                       56899*********9752678888876 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint  38 VlavdesgevvfsevllfldrdseqraefveietengekltlTpaHLvfvsenekssseeeeavfaskvregdyvlv 114
                                       V ++ ++g++v  +v +  + d  +  e   +++++ge+lt  + H   + +  +s +       a++v +gd v+v
  gi|313124860|ref|YP_004035124.1| 918 VWSMTDDGKLVSRPVTAIHEYD--APDELTRVTLQSGERLTAIHDHPFITFDDGESVE-----KPAANVSPGDWVFV 987
                                       7788888888888887764444..4566777888888888888888544444443333.....47888888888888 PP

                                       . CS
                              Hint 115 e 115
                                       +
  gi|313124860|ref|YP_004035124.1| 988 P 988
                                       3 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   4.4e-07    0.0003      25      49 ..    1431    1455 ..    1421    1458 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.4e-07
                      HTH_Tnp_ISL3   25 lesrsvkavArqlgvSwtTVwrild 49  
                                        +++ s++++Ar+lgv ++TV r+++
  gi|313124860|ref|YP_004035124.1| 1431 RHNVSFADIARDLGVADSTVSRWFN 1455
                                        5678********************7 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     9e-07   0.00062      17      45 ..    1431    1459 ..    1430    1460 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9e-07
                         HTH_Tnp_4   17 RlnltyqdLayrFgvsestvsrifhkwvd 45  
                                        R+n+++ d+a   gv  stvsr+f+ +v+
  gi|313124860|ref|YP_004035124.1| 1431 RHNVSFADIARDLGVADSTVSRWFNGVVE 1459
                                        9***********************99886 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.037        26      21      37 ..     322     338 ..     319     346 .. 0.86
   2 ?   -0.2   0.0      0.81   5.6e+02      96     126 ..     847     877 ..     837     893 .. 0.79
   3 !    6.5   0.0    0.0071       4.9     125     159 ..    1522    1556 ..    1513    1582 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.037
                      Mg_chelatase  21 GgHnlllvGppGsGKtm 37 
                                       G  ++ll+G pG+GK +
  gi|313124860|ref|YP_004035124.1| 322 GDLHMLLIGDPGTGKCV 338
                                       7889***********86 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.81
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevL 126
                                       + + G++ la +G+  +DEl +++  + ++L
  gi|313124860|ref|YP_004035124.1| 847 TLEAGALVLADKGIAAVDELDKMRCVTGDSL 877
                                       7789****************98876666655 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0071
                      Mg_chelatase  125 vLRePledgevtisrakakvefparfqlvaamNpc 159 
                                        ++ e le++++++s+a  +++  +r+ l+ a+Np 
  gi|313124860|ref|YP_004035124.1| 1522 AMHEGLEQQQISVSKAGINATLKSRCSLLGAANPK 1556
                                        67899****************************94 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.11      19      39 ..    1435    1455 ..    1427    1461 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                            HTH_23   19 svreIAreLgvsrrTvyrwlk 39  
                                        s ++IAr Lgv  +Tv+rw +
  gi|313124860|ref|YP_004035124.1| 1435 SFADIARDLGVADSTVSRWFN 1455
                                        6689***************75 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.27   1.9e+02      10      32 ..    1309    1331 ..    1301    1347 .. 0.80
   2 ?    9.3   0.0    0.0022       1.5       2      36 ..    1425    1459 ..    1424    1466 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.27
                            HTH_26   10 gitkseLargtgisaatlsrlvk 32  
                                        ++++seLa gt  s++++s l+ 
  gi|313124860|ref|YP_004035124.1| 1309 HVSQSELATGTPYSQQQISLLWG 1331
                                        569******************96 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0022
                            HTH_26    2 LrelmadrgitkseLargtgisaatlsrlvkgkpe 36  
                                        Lr+ +  ++++ ++ ar++g+  +t+sr+++g +e
  gi|313124860|ref|YP_004035124.1| 1425 LRVELNRHNVSFADIARDLGVADSTVSRWFNGVVE 1459
                                        899999*************************9665 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.079      20      39 ..    1433    1452 ..    1428    1453 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                            HTH_38   20 GlslreIArrLgrspsTIsR 39  
                                        + s+++IAr Lg++ sT+sR
  gi|313124860|ref|YP_004035124.1| 1433 NVSFADIARDLGVADSTVSR 1452
                                        689****************9 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.085      18      75 ..    1425    1485 ..    1421    1529 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                        HHHHHHH--S-HHHHHHHHTS-HHHHHHHH....H-HHHHHHHHHHHHHHHHTTHHHHHHHH CS
                       HTH_Tnp_1_2   18 llvendyekltldeiaeevgvsrsTlykWk....kkkeFieyvnelaeefleeeraevykaL 75  
                                        l ve + +++++++ia+++gv+ sT  +W     +   F++  n   ++f e  ra v + L
  gi|313124860|ref|YP_004035124.1| 1425 LRVELNRHNVSFADIARDLGVADSTVSRWFngvvETDRFVDVANAARDRFAE-IRADVRRYL 1485
                                        556667799********************733345789******99999864.556665555 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0008      0.55      27      78 ..     502     562 ..     480     610 .. 0.83
   2 ?   -0.1   0.1       1.5     1e+03       3      29 ..     672     696 ..     670     817 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0008
                                       HHTT-EEEEEE---SS-HHHHHHHHHHTT----GG.........GEEEHHHHHHHHHHHHS CS
                       Hydrolase_6  27 raagkpvvllTNnsskseeeyakkleklgvditee.........qvvtsataaaeylkkrk 78 
                                       r++g  +v +TN+ ++  +++a+ l +lg+ +te          ++++s++ ++ +l+k++
  gi|313124860|ref|YP_004035124.1| 502 RDSGSAFVSITNSDREILDDVADALDELGLRATERsthddkttrELICSSSELVSLLEKIE 562
                                       66779**************************955434444455599999999999999865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                                       EESTTTSEETTEE-TTHHHHHHHHHHT CS
                       Hydrolase_6   3 fDidGvLwrgdkaipgaaealnalraa 29 
                                       +D+dG+   ++++ipg+ ++l  lr++
  gi|313124860|ref|YP_004035124.1| 672 VDVDGN--TNRDVIPGVGDTLCDLRES 696
                                       566665..4556677777777666665 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00015       0.1     364     436 ..    1738    1810 ..    1731    1817 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                               MAD  364 syDkelteseaspklleRieeaedlvqkvqahneeveaqlevaeeevggykqqastlerelqalrqqeslada 436 
                                         +D ++ e+ +s+++  Ri+++++l+ +++   ee     ev  +  +  +   s  e+e++ lr++ +  ++
  gi|313124860|ref|YP_004035124.1| 1738 EFDADIVETGTSKNQRDRIKNLKQLISDIEDEYEEGAPVDEVISRATTELNLDESKAEQEIENLRRKGEVYEP 1810
                                        79****************************99999888788999999*******************9988776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.2   8.5e+02      37      56 ..     485     504 ..     483     507 .. 0.81
   2 ?   -2.3   0.0       6.2   4.3e+03       9      39 ..    1299    1327 ..    1293    1327 .. 0.73
   3 ?    8.4   0.0    0.0029         2      14      40 ..    1429    1452 ..    1416    1459 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHTTSEEEEES CS
                            MarR_2  37 avsrilkrLvaaGLverrpg 56 
                                       ++ r+l    a G+verr++
  gi|313124860|ref|YP_004035124.1| 485 SLARLLGYVAAEGYVERRDS 504
                                       66788888899******976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.2
                                        HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHH CS
                            MarR_2    9 rvLaaLgrrpgrdltvgelarrlglsksavs 39  
                                         +L  +  r    ++++ela  + +s++ +s
  gi|313124860|ref|YP_004035124.1| 1299 EILSDIKERYH--VSQSELATGTPYSQQQIS 1327
                                        55556666655..899999999888888776 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0029
                                        HHCTTTSEEEHHHHHHHHTSSHHHHHH CS
                            MarR_2   14 Lgrrpgrdltvgelarrlglsksavsr 40  
                                        L r+    ++ +++ar lg+  s+vsr
  gi|313124860|ref|YP_004035124.1| 1429 LNRHN---VSFADIARDLGVADSTVSR 1452
                                        66666...9*****************9 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00043       0.3      23      44 ..    1433    1455 ..    1426    1456 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                                        T.-HHHHHHHHT--CCHHHHHHH CS
                          CENP-B_N   23 e.Skaelarrfnvpestlsdilk 44  
                                        + S a++ar+++v  st+s++ +
  gi|313124860|ref|YP_004035124.1| 1433 NvSFADIARDLGVADSTVSRWFN 1455
                                        45899****************76 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         9   6.2e+03      35      50 ..     221     236 ..     215     236 .. 0.82
   2 ?   -1.9   0.0       4.5   3.1e+03      10      44 ..    1311    1348 ..    1309    1355 .. 0.72
   3 ?    8.6   0.0    0.0024       1.7      13      32 ..    1438    1457 ..    1435    1482 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9
                    YdaS_antitoxin  35 vpaervpeIekatnGe 50 
                                       v++  v+ Ie+ t+G+
  gi|313124860|ref|YP_004035124.1| 221 VTVTGVLHIEQQTSGQ 236
                                       6667799*******97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.5
                    YdaS_antitoxin   10 gqkaLAealgvsqqaVsqWlkgkkq....vpaervpeIe 44  
                                        +q++LA     sqq++s +  g       v+ +r +eI+
  gi|313124860|ref|YP_004035124.1| 1311 SQSELATGTPYSQQQISLLW-GADDelraVTRNRLREIV 1348
                                        79999999999999999763.433335566666666666 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0024
                    YdaS_antitoxin   13 aLAealgvsqqaVsqWlkgk 32  
                                          A+ lgv+ ++Vs+W +g 
  gi|313124860|ref|YP_004035124.1| 1438 DIARDLGVADSTVSRWFNGV 1457
                                        57**************9874 PP

>> DUF4072  Domain of unknown function (DUF4072)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   0.00079      0.55       5      33 ..    1683    1711 ..    1683    1720 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00079
                           DUF4072    5 spaPLsaahletLaaLagAsrieridaqA 33  
                                        sp P+ a  le+L++La+As+ +r++++ 
  gi|313124860|ref|YP_004035124.1| 1683 SPVPVTARKLEALVRLAEASARVRLSDTV 1711
                                        799*********************99886 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00076      0.52      25      50 ..    1433    1458 ..    1430    1461 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00076
                            HTH_36   25 fpsqetlakrlglsknTvsraikeLe 50  
                                        + s++++a++lg+ ++Tvsr+ +  +
  gi|313124860|ref|YP_004035124.1| 1433 NVSFADIARDLGVADSTVSRWFNGVV 1458
                                        5799*****************98655 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00079      0.55       3      22 ..    1437    1456 ..    1435    1477 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00079
                                        HHHHHHCTS-HHHHHHHCTT CS
                              LacI    3 kDVArlAGVSkaTVSrvLnn 22  
                                         D+Ar  GV  +TVSr  n+
  gi|313124860|ref|YP_004035124.1| 1437 ADIARDLGVADSTVSRWFNG 1456
                                        6***************9997 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.5   3.8e+03     135     156 ..    1621    1642 ..    1613    1653 .. 0.76
   2 ?    8.4   1.8    0.0021       1.4     102     150 ..    1755    1802 ..    1748    1809 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.5
                                        GGTTHHHHHHHHHHHHHHHHHC CS
                              Snf7  135 deedEeeleaeLdaLeqelgde 156 
                                        +e+ E+e++ + ++++ e+ +e
  gi|313124860|ref|YP_004035124.1| 1621 SEFTEAEVNSVTEEVAPEIDAE 1642
                                        7788888888888888887665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0021
                                        CCHHHHHHHHHHHHHHHHHTCHHHHHHHHHTT-GGTTHHHHHHHHHHHH CS
                              Snf7  102 didkidklmdeiedqmekaeeisEalsrslddadeedEeeleaeLdaLe 150 
                                        +i ++++l  +ied+ e+   ++E++sr+ +   + dE   e+e+++L 
  gi|313124860|ref|YP_004035124.1| 1755 RIKNLKQLISDIEDEYEEGAPVDEVISRATTE-LNLDESKAEQEIENLR 1802
                                        68899*************************76.999*********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1818 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 1.13u 0.31s 00:00:01.44 Elapsed: 00:00:00.51
# Mc/sec: 10638.53
//
Query:       gi|313124861|ref|YP_004035125.1|  [L=94]
Description: hypothetical protein Hbor_00730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.052   13.4   0.0       0.06   13.2   0.0    1.2  1  Tir_receptor_N  Translocated intimin receptor (Tir) N-terminu
      0.055   13.8   0.1      0.088   13.1   0.1    1.5  1  GARS_C          Phosphoribosylglycinamide synthetase, C domai


Domain annotation for each model (and alignments):
>> Tir_receptor_N  Translocated intimin receptor (Tir) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.7e-06      0.06     144     187 ..      39      83 ..      18      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.7e-06
                    Tir_receptor_N 144 aidpegkdkfv.ftggrggaghamvtvasdiaearqrildklepk 187
                                       a d eg++ +  +  +  g  h +v va   a+ar+ri d+l+ +
  gi|313124861|ref|YP_004035125.1|  39 ATDFEGEEGLApYQATGEGRAHGLVVVAESSADARDRIYDLLDEE 83 
                                       667788877762444445899*********************965 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.8e-06     0.088      35      65 ..      52      82 ..       5      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.8e-06
                                      EEE-SSEEEEEEEEESSHHHHHHHHHHHHTT CS
                            GARS_C 35 lvtsGGRvlavvavgetleeArakayeavkk 65
                                        t +GR  ++v v+e+ ++Ar+++y+ +++
  gi|313124861|ref|YP_004035125.1| 52 QATGEGRAHGLVVVAESSADARDRIYDLLDE 82
                                      46889*********************99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 677.88
//
Query:       gi|313124862|ref|YP_004035126.1|  [L=112]
Description: hypothetical protein Hbor_00740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 689.05
//
Query:       gi|313124863|ref|YP_004035127.1|  [L=291]
Description: hypothetical protein Hbor_00750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.086   13.0   0.9        7.1    6.9   0.4    2.4  2  DUF5446   Family of unknown function (DUF5446)
       0.34    9.8   1.5       0.53    9.1   1.5    1.3  1  Spc7      Spc7 kinetochore protein


Domain annotation for each model (and alignments):
>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0066        59      41      57 ..      88     104 ..      77     106 .. 0.82
   2 ?    6.9   0.4   0.00079       7.1      19      51 ..     148     182 ..     142     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0066
                           DUF5446  41 ekeeerldllekElkdL 57 
                                       + ee  l+++e+El+d 
  gi|313124863|ref|YP_004035127.1|  88 VPEERTLERVESELADV 104
                                       568999********995 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00079
                           DUF5446  19 eeltevEkelseavneteaek..eekeeerldlle 51 
                                        +++++E el e + ++   +  +++  +rl+ le
  gi|313124863|ref|YP_004035127.1| 148 GDIDAAEAELAETMTRLSEVAteRVAARQRLEMLE 182
                                       589************99877611567789999998 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.5   5.9e-05      0.53     186     261 ..      97     171 ..      76     212 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 5.9e-05
                              Spc7 186 lqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                        +++ ++++  ++ +L+ +r++ a++ ae e+++++ a  + ++e+++e+  ++++  +el e + +  +v  e +
  gi|313124863|ref|YP_004035127.1|  97 VESELADVTPPEPGDLADARRRAAAAGAETERLQERAAMIRGRVEAVREAGGDIDAAEAELAETMTRLSEVATE-R 171
                                       33333333334566677777777777777777777766666666666666666665555555555555554442.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1700.51
//
Query:       gi|313124864|ref|YP_004035128.1|  [L=278]
Description: hypothetical protein Hbor_00760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1704.29
//
Query:       gi|313124865|ref|YP_004035129.1|  [L=221]
Description: chromosome partitioning ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-10   41.5   0.7    4.5e-05   23.0   0.3    3.0  2  ParA         NUBPL iron-transfer P-loop NTPase
    7.8e-08   32.4   0.1      0.011   15.6   0.0    2.1  2  AAA_31       AAA domain
    1.3e-07   31.7   0.0    1.8e-07   31.2   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00076   19.0   0.4        1.4    8.3   0.4    2.9  3  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0031   17.3   0.0     0.0043   16.8   0.0    1.2  1  AAA_24       AAA domain
  ------ inclusion threshold ------
       0.03   13.8   0.2        6.1    6.2   0.1    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.052   12.8   0.7       0.25   10.6   0.7    1.9  1  MipZ         ATPase MipZ
      0.056   12.6   0.2      0.079   12.1   0.2    1.3  1  ArsA_ATPase  Anion-transporting ATPase
        0.1   12.8   0.0       0.16   12.1   0.0    1.6  1  AAA_33       AAA domain
        0.1   12.2   3.2        0.7    9.4   3.2    2.3  1  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.3   2.5e-08   4.5e-05       5      37 ..       2      36 ..       1      68 [. 0.77
   2 !   12.5   0.0   4.2e-05     0.075     116     243 ..     102     213 ..      95     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.5e-08
                              ParA  5 viavlSgKGGVGKStvavnlAlaLa..kkglkvgl 37
                                      ++av+ gKGGVGKSt+a +l +a+     +++ g+
  gi|313124865|ref|YP_004035129.1|  2 ILAVTGGKGGVGKSTLAFELGAAMDavVVDADLGM 36
                                      789******************99972223344444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.2e-05
                              ParA 116 iiDlPPGt.gDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgk 191
                                       ++D+P G  +D+ + +a     +++viV++p+  alad+ ++ e+++++++ +++v  N ++   p+     ++f++
  gi|313124865|ref|YP_004035129.1| 102 VVDCPAGMkADAGVPLA---VADACVIVASPRPYALADAVRTRELARELDAGLVAVAVNRAVEDPPE-----AVFEE 170
                                       66666664244443333...24678**************************9999999877665553.....44533 PP

                              ParA 192 gggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiae 243
                                         g        +p   ++p dp++++++++g+p++  +p+s+a +a++++a+
  gi|313124865|ref|YP_004035129.1| 171 VLG--------AP-AVTVPADPRMARTVETGRPVCRIAPSSRAGQAISSLAR 213
                                       322........22.23566677777777777776666666666666666666 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.4   1.3e-05     0.023       3      27 ..       2      26 ..       1      37 [. 0.88
   2 !   15.6   0.0   6.2e-06     0.011     104     155 ..      84     135 ..      46     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                            AAA_31  3 vIaianqKGGvGKTTtsvnlaaala 27
                                      ++a++  KGGvGK+T +++l+aa+ 
  gi|313124865|ref|YP_004035129.1|  2 ILAVTGGKGGVGKSTLAFELGAAMD 26
                                      6799999**************9985 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.2e-06
                            AAA_31 104 eeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayale 155
                                        ++l + l++v+  Y  +++Dcp  ++  +   L+++d ++i+  +++yal 
  gi|313124865|ref|YP_004035129.1|  84 VRRLGDSLRAVERAYGDVVVDCPAGMKADAGVPLAVADACVIVASPRPYALA 135
                                       4568899*******************************************96 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0     1e-10   1.8e-07       1      84 [.       3     159 ..       3     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1e-10
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       +a++++kGGvGK+tla  L++a+       ++vDaD  +  l    g  +d++                        
  gi|313124865|ref|YP_004035129.1|   3 LAVTGGKGGVGKSTLAFELGAAMDA-----VVVDADLGMADLP--TGPGPDLHDvlagradaveavredgpvrllpc 72 
                                       68**********************9.....*********9999..77777777778888888999999999999999 PP

                                       ...............................................................CCHCCCHHHHHHCH CS
                                       ...............................................................xxxxxxxxxxxxxx RF
                              CbiA  55 ...............................................................dlkrllellealgk 68 
                                                                                                      d+ r  el+++l+ 
  gi|313124865|ref|YP_004035129.1|  73 grslsgaraadvrrlgdslraveraygdvvvdcpagmkadagvplavadacvivasprpyalaDAVRTRELARELDA 149
                                       99999999997777777777777777777777777777777777777777777777777777777777777777776 PP

                                       CHHHH..EEEEEEEEE CS
                                       xxxxxxxxxxxxxxxx RF
                              CbiA  69 kkalllkiagvvlnrv 84 
                                       +      ++ v +nr 
  gi|313124865|ref|YP_004035129.1| 150 G------LVAVAVNRA 159
                                       5......445555554 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.4    0.0008       1.4       3      28 ..       2      27 ..       1      34 [. 0.91
   2 !    6.0   0.0    0.0041       7.3     100     147 ..      82     129 ..      58     145 .. 0.85
   3 ?    1.0   0.0      0.14   2.5e+02     197     231 ..     179     213 ..     172     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0008
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhe 28
                                      +la++G +GGvG+++l+  L+ a+++
  gi|313124865|ref|YP_004035129.1|  2 ILAVTGGKGGVGKSTLAFELGAAMDA 27
                                      799*******************9986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0041
                          CBP_BcsQ 100 ekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvep 147
                                       ++  +l + l+++++ y  +++D+pag++a +   la+ad  + v++p
  gi|313124865|ref|YP_004035129.1|  82 ADVRRLGDSLRAVERAYGDVVVDCPAGMKADAGVPLAVADACVIVASP 129
                                       55667788899999******************************9988 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.14
                          CBP_BcsQ 197 ihrDealaEalaakqPlgeyrpdslaaeevktLan 231
                                       +  D  +a ++ +  P+ + +p s a +++++La 
  gi|313124865|ref|YP_004035129.1| 179 VPADPRMARTVETGRPVCRIAPSSRAGQAISSLAR 213
                                       566777888888999******************96 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.4e-06    0.0043       9      59 ..       8      64 ..       3     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                            AAA_24  9 GpsgiGKTtlakel..gpkplfidtekGlksldadkfpdie....swedfldevvel 59
                                      G+ g+GK+tla el    +++++d + G+++l    +pd++    + +d +++v e+
  gi|313124865|ref|YP_004035129.1|  8 GKGGVGKSTLAFELgaAMDAVVVDADLGMADLPTGPGPDLHdvlaGRADAVEAVRED 64
                                      899***********999******************9999996555333444433333 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0034       6.1       7      25 ..       8      26 ..       1      30 [. 0.83
   2 ?    6.0   0.0    0.0038       6.8     133     245 ..     114     216 ..      47     221 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0034
                         Fer4_NifH  7 GkGGiGksttsqnlsaala 25
                                      GkGG+Gkst +  l aa+ 
  gi|313124865|ref|YP_004035129.1|  8 GKGGVGKSTLAFELGAAMD 26
                                      8********9999999886 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0038
                         Fer4_NifH 133 alPiredkaqevyivtsgelmalyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvP 209
                                       ++P++   a+ ++iv+s    al  a +     ++ a++ + +l  + +n r v+d  e +  f e lg + + +vP
  gi|313124865|ref|YP_004035129.1| 114 GVPLA--VADACVIVASPRPYALADAVR----TRELARELDAGLVAVAVN-RAVEDPPEAV--FEEVLGAPAV-TVP 180
                                       46776..899999999999999866655....467788888888888899.9899888876..7778888877.69* PP

                         Fer4_NifH 210 rdeivrkaelrkktvieyapeseqakeyrelarkil 245
                                       +d  + ++    + v   ap+s+ ++    lar+++
  gi|313124865|ref|YP_004035129.1| 181 ADPRMARTVETGRPVCRIAPSSRAGQAISSLARAVQ 216
                                       *******9999*********************9997 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   0.00014      0.25       4     126 ..       4     124 ..       1     129 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                                       EE--SSTTSSHHHHHHHHHHHH..HTTT--EEEEE--TTT.-HHHHHHHHHHHHHHHHT------EEE-SSS-HHHH CS
                              MipZ   4 vlgnekGGsGksttavhvavaL..lkkGarvaaidldlrq.rtlarylenraataerkglsLplpealalseaeeae 77 
                                        ++  kGG Gkst a  +  a+  +   a  +  dl +     l+  l  ra+ +e    + p+     l+ +   +
  gi|313124865|ref|YP_004035129.1|   4 AVTGGKGGVGKSTLAFELGAAMdaVVVDADLGMADLPTGPgPDLHDVLAGRADAVEAVREDGPVRL---LPCG--RS 75 
                                       56778**********999888722345677888899876415789999999998887766655544...4554..45 PP

                                       TTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEE CS
                              MipZ  78 veeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtlv 126
                                       +++   a+v++l + ++++e+ +  +v+d+P   +a + +  ++ad+ v
  gi|313124865|ref|YP_004035129.1|  76 LSGARAADVRRLGDSLRAVERAYGDVVVDCPAGMKADAGVPLAVADACV 124
                                       66777777789************99******999999999999999876 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.4e-05     0.079       5      25 ..       5      25 ..       1      60 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                                      EEEESTTSSHHHHHHHHHHHH CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatavkl 25
                                      + gGKGGVGK+t++  +++ +
  gi|313124865|ref|YP_004035129.1|  5 VTGGKGGVGKSTLAFELGAAM 25
                                      579*********987666554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     9e-05      0.16       2      33 ..       4      47 ..       3     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt............l 33
                                       ++ G  G+GKstla +l ++ +av+++ d             l
  gi|313124865|ref|YP_004035129.1|  4 AVTGGKGGVGKSTLAFELGAAMDAVVVDADLgmadlptgpgpdL 47
                                      578899*************9********9975444444444441 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.2   0.00039       0.7      35      57 ..       3      25 ..       1     111 [. 0.95

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00039
                            AAA_25 35 lallaGapgtGKttlaldlalav 57
                                      la+  G +g+GK+tla +l++a+
  gi|313124865|ref|YP_004035129.1|  3 LAVTGGKGGVGKSTLAFELGAAM 25
                                      68899**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1310.32
//
Query:       gi|313124866|ref|YP_004035130.1|  [L=296]
Description: transcription initiation factor iib (tfiib) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-34  117.9   1.5    1.1e-16   60.6   0.7    2.3  2  TFIIB         Transcription factor TFIIB repeat
    2.9e-10   39.5   2.4      6e-10   38.5   2.3    1.6  1  TF_Zn_Ribbon  TFIIB zinc-binding
    0.00015   21.8   0.0    0.00026   21.0   0.0    1.3  1  RB_B          Retinoblastoma-associated protein B domain
     0.0086   15.4   0.9      0.015   14.7   0.9    1.4  1  zf-ribbon_3   zinc-ribbon domain
  ------ inclusion threshold ------
      0.046   13.7   0.6      0.096   12.7   0.6    1.4  1  DZR           Double zinc ribbon
        1.7    8.8   4.4        2.3    8.4   0.6    2.4  2  Zn-ribbon_8   Zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.7   3.6e-20   1.1e-16       1      68 [.     121     188 ..     121     190 .. 0.95
   2 !   55.8   0.0   1.2e-18   3.4e-15       1      71 []     215     285 ..     215     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 3.6e-20
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--S CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVse 68 
                                       i r+ +al Lpe ++d A  l+k a +e++l Grs +g aAAc+y Acr ++v rt  e+++ ++ +e
  gi|313124866|ref|YP_004035130.1| 121 IRRLTSALSLPERIRDHACSLFKSAQNEDLLRGRSLEGFAAACVYAACRVANVSRTVGEVVAEAKATE 188
                                       7899*********************************************************9988776 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 1.2e-18
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rfa++l+L+  V+++A e a +a+e+++  Gr p g+aA cly A+r   v+ tq+e ++v+ V+ +t+
  gi|313124866|ref|YP_004035130.1| 215 VPRFASRLDLSRDVERRAREYAAEAAEQGLSVGRNPSGVAAGCLYTAARDLDVEVTQTEAADVADVTPVTL 285
                                       689****************************************************************9986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   2.3     2e-13     6e-10       2      43 .]      15      53 ..      14      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2e-13
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+C ++   + +e  e+vC+dCGlV+ +  id+gpewr f
  gi|313124866|ref|YP_004035130.1| 15 TCPECDGR---LHAEGQETVCGDCGLVVSEYTIDHGPEWRSF 53
                                      7******8...788999***********************87 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   8.7e-08   0.00026      12      93 ..     116     195 ..     109     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.7e-08
                              RB_B  12 laavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqa 88 
                                       +a + +r+L++ L+l +++r+++ +lf+ +  ++++ll+ R l+ +  ++vY+ ++v + +++  e+++  +  + +
  gi|313124866|ref|YP_004035130.1| 116 YAFTEIRRLTSALSLPERIRDHACSLFKSA--QNEDLLRGRSLEGFAAACVYAACRVANVSRTVGEVVAEAKATEAE 190
                                       577899*********************985..899********************************9998887777 PP

                              RB_B  89 sskvy 93 
                                       +s  y
  gi|313124866|ref|YP_004035130.1| 191 QSAAY 195
                                       77666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.9     5e-06     0.015       2      25 ..      13      38 ..      12      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5e-06
                       zf-ribbon_3  2 tvrCPnCGa.p.lssddnvCpyCGtk 25
                                      t++CP+C+  + ++ + +vC  CG +
  gi|313124866|ref|YP_004035130.1| 13 TTTCPECDGrLhAEGQETVCGDCGLV 38
                                      789****99988************85 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   3.2e-05     0.096      14      39 ..      15      40 ..       4      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                               DZR 14 fCseCgtklkavaaedrCpsCgekvd 39
                                      +C+eC  +l a+ +e++C  Cg  v+
  gi|313124866|ref|YP_004035130.1| 15 TCPECDGRLHAEGQETVCGDCGLVVS 40
                                      899******999999***99997776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.6   0.00078       2.3      21      36 ..       7      23 ..       2      26 .. 0.76
   2 ?    1.7   0.2     0.093   2.8e+02      23      33 ..      26      36 ..      22      41 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00078
                       Zn-ribbon_8 21 isdaplta.CPeCgsev 36
                                       +da lt+ CPeC +++
  gi|313124866|ref|YP_004035130.1|  7 PDDATLTTtCPECDGRL 23
                                      458889999****9865 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.093
                       Zn-ribbon_8 23 dapltaCPeCg 33
                                      +  +t+C +Cg
  gi|313124866|ref|YP_004035130.1| 26 EGQETVCGDCG 36
                                      56678899998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1808.71
//
Query:       gi|313124867|ref|YP_004035131.1|  [L=174]
Description: hypothetical protein Hbor_00790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   13.5   0.6         28    4.7   0.0    3.7  4  HTH_23    Homeodomain-like domain
       0.13   12.4   0.6        3.7    7.7   0.1    3.3  4  HTH_28    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0031        28      21      33 ..       4      16 ..       2      16 .. 0.88
   2 ?    4.0   0.0    0.0052        47       9      48 ..      52      88 ..      46      93 .. 0.81
   3 ?   -0.2   0.0       0.1   9.1e+02      32      46 ..      94     108 ..      93     112 .. 0.77
   4 ?   -1.4   0.0      0.26   2.3e+03      18      28 ..     142     152 ..     133     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0031
                            HTH_23 21 reIAreLgvsrrT 33
                                      ++IA+eLgv+  T
  gi|313124867|ref|YP_004035131.1|  4 ADIADELGVTTTT 16
                                      69*******9877 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0052
                            HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkryreeGleg 48
                                       +l  +a G+sv ++A++  v + T  ++l+r    G+eg
  gi|313124867|ref|YP_004035131.1| 52 TVLERHAAGDSVGDAAEAAIVAPVTAAKVLHR---AGIEG 88
                                      57778888**********99999999999999...45554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.1
                            HTH_23  32 rTvyrwlkryreeGl 46 
                                        T +++l+ + +++l
  gi|313124867|ref|YP_004035131.1|  94 PTARQILRDWLAGQL 108
                                       599999999965555 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.26
                            HTH_23  18 lsvreIAreLg 28 
                                       +++r++A+ Lg
  gi|313124867|ref|YP_004035131.1| 142 ATRRDAAASLG 152
                                       79999999887 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.34   3.1e+03      15      28 ..       3      16 ..       1      16 [. 0.80
   2 ?    7.7   0.1   0.00042       3.7       4      47 ..      52      95 ..      51      99 .. 0.89
   3 ?    0.4   0.0     0.084   7.6e+02       4      23 ..      98     118 ..      97     121 .. 0.80
   4 ?   -0.5   0.0      0.16   1.4e+03       5      19 ..     125     140 ..     124     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.34
                            HTH_28 15 vreaArelgisrrt 28
                                       +++A elg++ +t
  gi|313124867|ref|YP_004035131.1|  3 LADIADELGVTTTT 16
                                      578999***98765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00042
                            HTH_28  4 eiikllaaGhsvreaArelgisrrtvyrWikryeegGiagLvpr 47
                                      +++++ aaG+sv +aA++  + + t  + ++r   +G+  L+p 
  gi|313124867|ref|YP_004035131.1| 52 TVLERHAAGDSVGDAAEAAIVAPVTAAKVLHRAGIEGVTPLAPT 95
                                      78999**************9999999999999999999988885 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.084
                            HTH_28   4 eiikllaaGh.svreaArelg 23 
                                       +i++ ++aG  s+++a ++ g
  gi|313124867|ref|YP_004035131.1|  98 QILRDWLAGQlSRADALELTG 118
                                       789999999999999877655 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.16
                            HTH_28   5 iikllaaGh.svreaA 19 
                                       ++ ++++ h +v+e+A
  gi|313124867|ref|YP_004035131.1| 125 ALAAYIETHdPVPELA 140
                                       5677888877888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1146.70
//
Query:       gi|313124868|ref|YP_004035132.1|  [L=260]
Description: cobq/cobb/mind/para nucleotide binding domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-08   34.5   0.0    2.8e-08   33.9   0.0    1.3  1  AAA_31          AAA domain
    1.1e-06   28.3   0.1      2e-06   27.4   0.1    1.4  1  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
    5.6e-06   26.0   0.5      0.018   14.5   0.1    2.1  2  ParA            NUBPL iron-transfer P-loop NTPase
    0.00034   20.0   1.6       0.38   10.0   0.1    2.4  3  MipZ            ATPase MipZ
     0.0096   16.0   0.1      0.018   15.1   0.1    1.5  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.27   11.2   0.0    1.5  1  Glyco_transf_4  Glycosyltransferase Family 4
       0.16   11.3   2.3       0.45    9.8   1.7    1.9  2  VirC1           VirC1 protein


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.1e-11   2.8e-08       3     167 ..      19     184 ..      17     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.1e-11
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgie.kneiektlyevli..eeknikeaiikt 76 
                                       + a++   GG G T  ++++a ala  g  v + D+     at+gl  +   +ie +l+ +l+   ++ ++e +++ 
  gi|313124868|ref|YP_004035132.1|  19 IAAFVGATGGAGTTRCTLEVATALAADGADVGVFDAA---FATQGLAAHiPGQIEPDLTALLTeeADAPLSEGLTTL 92 
                                       67899999*************************9984...4555555432678999999999733566789999989 PP

                            AAA_31  77 kvenldlipssidLaeaeielve.lekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeay 152
                                       +ve+   +  s  +a +e      + +  +++++ l++  d++Dy+++D+pP  +  ++ a+ ++d+ i++   + +
  gi|313124868|ref|YP_004035132.1|  93 DVETAGRVAVSPAFAPFERFARAkTPDAAQRFETRLSAAADRFDYVLVDVPPVASNQAIAAVNVADQSIVVAPGTTR 169
                                       99988555555667777765544044557789****************************************99999 PP

                            AAA_31 153 aleGleqllktieev 167
                                         + ++q+ +++++v
  gi|313124868|ref|YP_004035132.1| 170 GADAVQQMRTRLTHV 184
                                       999999998887766 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   7.9e-10     2e-06       4     168 ..      20     192 ..      17     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.9e-10
                          CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspd.nlLrlhFnvdieqregwaraeldgapwrqaaleyapgl 79 
                                        a+ G  GG+Gtt  +   a+al + g  v v D++ + + L+ h   +ie + +   +e ++ap+++  + +    
  gi|313124868|ref|YP_004035132.1|  20 AAFVGATGGAGTTRCTLEVATALAADGADVGVFDAAFAtQGLAAHIPGQIEPDLTALLTEEADAPLSEGLTTLDV-- 94 
                                       578899****************************9865166************9999999999999987654332.. PP

                          CBP_BcsQ  80 dllPfGelnve......ekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvve.... 146
                                            G+++v+      e+ + +++ ++a+++ ++l++ + +++++l+D+p  as+++ +++++ad+++ v+     
  gi|313124868|ref|YP_004035132.1|  95 --ETAGRVAVSpafapfERFARAKTPDAAQRFETRLSAAADRFDYVLVDVPPVASNQAIAAVNVADQSIVVAPgttr 169
                                       ..22333333310000034434445567888899999999*****************************99842222 PP

                          CBP_BcsQ 147 .pdanchvrLhqqalpaaellLi 168
                                        +da  ++r +  ++ ++++l +
  gi|313124868|ref|YP_004035132.1| 170 gADAVQQMRTRLTHVGSEATLVV 192
                                       24555555555555555555555 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1     7e-06     0.018       7      40 ..      21      54 ..      16      77 .. 0.90
   2 !   10.0   0.0   0.00016      0.42     110     151 ..     133     172 ..     116     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7e-06
                              ParA  7 avlSgKGGVGKStvavnlAlaLakkglkvgllDa 40
                                      a + + GG G + ++ ++A+aLa+ g++vg++Da
  gi|313124868|ref|YP_004035132.1| 21 AFVGATGGAGTTRCTLEVATALAADGADVGVFDA 54
                                      556778***************************8 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00016
                              ParA 110 gelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevala 151
                                       +  Dy+++D+PP  +  +++ ++  +  + ++V+   +  ++
  gi|313124868|ref|YP_004035132.1| 133 DRFDYVLVDVPPVASNQAIAAVNVAD--QSIVVAPGTTRGAD 172
                                       578****************9998874..55666544433333 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1   0.00015      0.38       9      41 ..      26      58 ..      19      72 .. 0.84
   2 ?   -2.5   0.0      0.98   2.5e+03     225     237 ..      87      99 ..      85     108 .. 0.78
   3 !    8.9   0.1   0.00033      0.85      85     125 ..     120     160 ..      90     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                                      STTSSHHHHHHHHHHHHHTTT--EEEEE--TTT CS
                              MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldlrq 41
                                       GG+G +  ++ va+aL++ Ga v++ d     
  gi|313124868|ref|YP_004035132.1| 26 TGGAGTTRCTLEVATALAADGADVGVFDAAFAT 58
                                      69************************9976655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.98
                                       GT--GGGSSSS-- CS
                              MipZ 225 sGltlldlkelgl 237
                                       +Glt ld++++g+
  gi|313124868|ref|YP_004035132.1|  87 EGLTTLDVETAGR 99 
                                       79******99984 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00033
                                       HHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEE CS
                              MipZ  85 evaeleelvadleaeldfividtPGsdsalsrlahsladtl 125
                                         +++e+ +++++ ++d++++d+P   s+ +  a ++ad  
  gi|313124868|ref|YP_004035132.1| 120 AAQRFETRLSAAADRFDYVLVDVPPVASNQAIAAVNVADQS 160
                                       34699***********************9999999999964 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     7e-06     0.018       2      44 ..      21      65 ..      20     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7e-06
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE..EEESSCCCCH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                              CbiA  2 aiastkGGvGKTtlaanLaralarrglrVllvD..aDpqannlai 44
                                      a+++ +GG+G T  ++  a+ala +g +V ++D  + +q+ +++i
  gi|313124868|ref|YP_004035132.1| 21 AFVGATGGAGTTRCTLEVATALAADGADVGVFDaaFATQGLAAHI 65
                                      67899****************************444556666664 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001      0.27       3      38 ..      30      96 ..      28     162 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                    Glyco_transf_4  3 GverhvleLaraLarrGheVtvv..tpgddgpleeev.............................e 38
                                      G  r +le+a aLa++G +V v+  +++++g ++  +                              
  gi|313124868|ref|YP_004035132.1| 30 GTTRCTLEVATALAADGADVGVFdaAFATQGLAAHIPgqiepdltallteeadaplseglttldveT 96
                                      899********************98444444333333444666666677666666666667666663 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.7   0.00018      0.45       5      38 ..      21      54 ..      17      62 .. 0.89
   2 ?   -0.8   0.0      0.31   7.9e+02      79     114 ..     130     167 ..     119     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                             VirC1  5 tfcslkGGaGkttalmglcsalasdgkrvalfea 38
                                      +f+   GGaG t + + + +ala+dg  v++f+a
  gi|313124868|ref|YP_004035132.1| 21 AFVGATGGAGTTRCTLEVATALAADGADVGVFDA 54
                                      4666789*************************98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.31
                             VirC1  79 aegeGfdyaladtrgGsse..lnntiiassdllliPtm 114
                                       a+++ fdy+l+d    +s+  + ++ +a   +++ P  
  gi|313124868|ref|YP_004035132.1| 130 AAADRFDYVLVDVPPVASNqaIAAVNVADQSIVVAPGT 167
                                       56678999999998776652256666777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1621.98
//
Query:       gi|313124869|ref|YP_004035133.1|  [L=757]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-21   74.9   0.0    2.8e-20   72.6   0.0    2.3  2  Response_reg     Response regulator receiver domain
    7.1e-21   74.3   0.1    5.6e-09   36.0   0.0    2.9  2  PAS              PAS fold
    2.9e-17   62.8   0.1    2.6e-08   34.1   0.0    3.1  3  PAS_9            PAS domain
    8.3e-17   61.7   0.1    1.8e-16   60.7   0.1    1.5  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    1.9e-15   57.1   2.7    9.2e-08   32.3   0.1    3.3  3  PAS_4            PAS fold
    7.1e-15   54.8   2.1    3.2e-13   49.5   0.2    3.3  2  HisKA            His Kinase A (phospho-acceptor) domain
      3e-14   52.6   0.6    3.2e-07   30.2   0.1    2.8  2  PAS_8            PAS domain
    1.3e-05   25.4   0.0     0.0068   16.7   0.0    3.0  3  PAS_3            PAS fold
      0.001   19.4   0.0     0.0033   17.8   0.0    1.9  1  GAF_3            GAF domain
  ------ inclusion threshold ------
      0.024   15.2   0.1        4.9    7.8   0.0    2.8  2  PAS_10           PAS domain
      0.028   14.2   0.0       0.11   12.3   0.0    2.0  2  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
      0.031   14.0   0.0      0.077   12.7   0.0    1.7  1  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
      0.044   14.3   0.0       0.29   11.7   0.0    2.5  2  Chitin_bind_4    Insect cuticle protein
      0.064   14.3   0.2       0.92   10.6   0.1    2.9  2  Methyltransf_24  Methyltransferase domain
        8.3    6.6   8.4        4.3    7.5   0.0    4.0  5  PAS_7            PAS fold


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   2.3e-23   2.8e-20       1     106 [.      10     116 ..      10     122 .. 0.95
   2 ?   -1.7   0.0       2.7   3.2e+03      72      86 ..     199     213 ..     180     238 .. 0.52

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 2.3e-23
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl+vdD+p  ++l++ +le  ++ + +v++a++ +  l+ l e ++d+i+ D +mpg+dGl +l+ +r + p+lp i
  gi|313124869|ref|YP_004035133.1|  10 VLCVDDEPGSADLTAAYLErhDDRL-TVTTATSVQGGLNALTETDFDCIVSDYDMPGLDGLAFLEAVRVDRPKLPFI 85 
                                       89*****************855666.*************************************************** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpee 106
                                       ++t++++e++a ea++ag++d+++K+   ++
  gi|313124869|ref|YP_004035133.1|  86 LFTGKGSEAVASEAISAGVSDYVQKESGTDQ 116
                                       *************************988776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.7
                                       SEEEEEESSTSHHHH CS
                      Response_reg  72 lpviiltahseeeda 86 
                                       ++ +i  a+++e+++
  gi|313124869|ref|YP_004035133.1| 199 VKAVIAHAQDDEKVI 213
                                       333333333333333 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   6.7e-12     8e-09       4     113 .]     145     252 ..     142     252 .. 0.92
   2 !   36.0   0.0   4.7e-12   5.6e-09       1      91 [.     263     349 ..     263     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 6.7e-12
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsr.eevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       ++ile++pd+i+v     +++++N++a +l+  +  +++lg++ll lih +d + +++ +  +  + +  ++ +++ 
  gi|313124869|ref|YP_004035133.1| 145 KSILENSPDAIVVS-VGDEFVFANTSAVSLFEADDaDDLLGRNLLSLIHKQDTEAVKAVIAHAQDDEKVISQTQRTM 220
                                       78*********999.888999*************99*************9999999999999999999999999999 PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       k+ dg ++ +e++++ +++ g+   g + +lrd+
  gi|313124869|ref|YP_004035133.1| 221 KTLDGMTFSAEMTVRAITWNGES--GHVAILRDV 252
                                       99******************998..999999986 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 4.7e-12
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++ a ++ + d+i+v D d +++ vN +a+el+Gl+ree+lg++l+++ ++ +     + ++   ++  e++++  
  gi|313124869|ref|YP_004035133.1| 263 ERYAAAFSRAMDAIIVADDDDEFIDVNGSAAELFGLPREELLGRNLSEFTPNGS---EIDDMWADFQSLGENHGVLS 336
                                       57889999999*************************************999987...78888888888888888888 PP

                                       EEECTTSSEEEEEE CS
                               PAS  78 sfklrdgrpihlev 91 
                                        ++  dg+ + +e 
  gi|313124869|ref|YP_004035133.1| 337 LIRP-DGERRVVEY 349
                                       8888.888877765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.3e-08   1.6e-05       1     103 [.     152     253 ..     152     254 .. 0.79
   2 !   34.1   0.0   2.2e-11   2.6e-08       2      82 ..     274     351 ..     273     368 .. 0.87
   3 ?   -1.7   0.0       2.9   3.5e+03      41      73 ..     577     607 ..     550     622 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.3e-08
                             PAS_9   1 pdgili.dnpdgrilyaNeaalrllG.yspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirkn 72 
                                       pd+i++ +  d   ++aN++a  l+   +++++lg+++  l+  ++++ e ++a++   ++      + + ++ + +
  gi|313124869|ref|YP_004035133.1| 152 PDAIVVsV-GDE-FVFANTSAVSLFEaDDADDLLGRNLLSLI--HKQDTEAVKAVIAHAQDdekVISQTQRTMKTLD 224
                                       67888834.444.7************777*************..44444444444444444466688999999999* PP

                             PAS_9  73 getfwvlltaspvkdddgelvgiivilrDit 103
                                       g tf +++t++++ +++    g+++ilrD+t
  gi|313124869|ref|YP_004035133.1| 225 GMTFSAEMTVRAITWNG--ESGHVAILRDVT 253
                                       *************9986..44568******9 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 2.2e-11
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       d+i++ ++d + +++N +a++l+G  +ee+lg++++++  ++ ++ ++++a ++++   e ++ + lir++ge+  v
  gi|313124869|ref|YP_004035133.1| 274 DAIIVADDDDEFIDVNGSAAELFGLPREELLGRNLSEFT-PNGSEIDDMWADFQSLG--ENHGVLSLIRPDGERRVV 347
                                       68899778888****************************.*****************..**************9998 PP

                             PAS_9  79 llta 82 
                                       +  a
  gi|313124869|ref|YP_004035133.1| 348 EYAA 351
                                       7554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.9
                             PAS_9  41 vtdpeanerlraaleqgrkkerevevvlirkng 73 
                                       ++dpe  +r+++al +++     +++ +  +++
  gi|313124869|ref|YP_004035133.1| 577 DGDPEQFDRIEDALSRME--RIIGDLLYLAREN 607
                                       678899999999999999..4444444433333 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.1   1.5e-19   1.8e-16       2     106 ..     650     745 ..     649     751 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.5e-19
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlG 77 
                                       d+ rL q++ nl  Na+++   +++++v++   + d  + veD+G+Gip+++++++fe  +++      +  gtG+G
  gi|313124869|ref|YP_004035133.1| 650 DQNRLCQLLENLFRNAIDH--VGTDVRVRVG--SLDDGFYVEDDGPGIPESERDNVFEqGYTT------RNDGTGFG 716
                                       899***************9..8999****99..4478899*****************977777......668***** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftf 106
                                       lsiv ++ve +g +i v++ + +G +f +
  gi|313124869|ref|YP_004035133.1| 717 LSIVTEIVEGHGWSIAVTEGELGGARFEI 745
                                       *****************999999999986 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   5.7e-08   6.9e-05       1     109 [.     148     256 ..     148     257 .. 0.88
   2 !   32.3   0.1   7.7e-11   9.2e-08       3     108 ..     271     370 ..     269     372 .. 0.89
   3 ?   -0.9   0.0       1.6     2e+03      50      80 ..     616     646 ..     595     656 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.7e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaae.lfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.. 74 
                                       l+++pda++v      +++aN++a +   + ++++llG+ l +l  ++d +++ + ++++ + e++i++++ +    
  gi|313124869|ref|YP_004035133.1| 148 LENSPDAIVVS-VGDEFVFANTSAVSlFEADDADDLLGRNLLSLIHKQDTEAVKAVIAHAQDDEKVISQTQRTMKtl 223
                                       78999999994.44567889999889556677899************************************999999 PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +g +   e++++ +   +Ge  g+++i+rD+T+++
  gi|313124869|ref|YP_004035133.1| 224 DGMTFSAEMTVRAI-TWNGE-SGHVAILRDVTNQE 256
                                       99999999999999.57899.***********986 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 7.7e-11
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                       +  da++v d+d  ++++N +aaelfg+p+eellG+ l e+ p   + ++++ ++   + +e +  l   +++ge+r
  gi|313124869|ref|YP_004035133.1| 271 RAMDAIIVADDDDEFIDVNGSAAELFGLPREELLGRNLSEFTPN--GSEIDDMWADFQSLGENHGVLSLIRPDGERR 345
                                       6789************************************9996..9*********************9999***** PP

                             PAS_4  80 hyelrllPlrdesGevigvlvisrDiTer 108
                                       ++e  +++ +   Ge   +l ++rD+T r
  gi|313124869|ref|YP_004035133.1| 346 VVEYAATR-DVVPGE---HLSVLRDVTGR 370
                                       *9988877.456666...77777887776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.6
                             PAS_4  50 arleralrrvlegeepiefleelll.pgeerh 80 
                                        +le+a++r++++ +  + + +l   +g+  +
  gi|313124869|ref|YP_004035133.1| 616 VELESAVERAWQTVDETTHEATL-SvDGDIGT 646
                                       45666666666663333333222.23555555 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.018        21      22      52 ..     520     550 ..     519     551 .. 0.94
   2 !   49.5   0.2   2.7e-16   3.2e-13       2      65 ..     549     607 ..     548     609 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.018
                                       HHHHHHHC..T-HSSCHHHHHHHHHHHHHHH CS
                             HisKA  22 gnaeaLkregklteelkeyletiesearrld 52 
                                       +++e+L r++++ +e +++ + ++s+++rl+
  gi|313124869|ref|YP_004035133.1| 520 AFVELLARWVSYEQEHRRNNRELQSQTERLE 550
                                       699**************************97 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 2.7e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l++f+++v H+Lr+PLs+ +g++e+ ++     +   e++++ie+   r+++++ dlL l+r+ 
  gi|313124869|ref|YP_004035133.1| 549 LEEFASMVTHDLRNPLSVASGYLELARE-----DGDPEQFDRIEDALSRMERIIGDLLYLAREN 607
                                       789**********************999.....8999************************986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     5e-07    0.0006       3      48 ..     144     187 ..     142     201 .. 0.80
   2 !   30.2   0.1   2.6e-10   3.2e-07       1      57 [.     263     316 ..     263     328 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5e-07
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGysadlkgellg.ql 48 
                                        ++++e+spd+i+v  +++ +v++N +a  l+   ad+ ++llg +l
  gi|313124869|ref|YP_004035133.1| 144 AKSILENSPDAIVVSVGDE-FVFANTSAVSLFE--ADDADDLLGrNL 187
                                       589**********866778.************9..667777776444 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 2.6e-10
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpvlrplle 57 
                                       er+ a+f  + d+i+v+d++d ++dvN +a+el+G++   ++ellg+ l +++p+  
  gi|313124869|ref|YP_004035133.1| 263 ERYAAAFSRAMDAIIVADDDDEFIDVNGSAAELFGLP---REELLGRNLSEFTPNGS 316
                                       799999999*******996667*************99...44555566666666655 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.7e-06    0.0068      16      83 ..     179     244 ..     163     249 .. 0.84
   2 ?    5.4   0.0     0.019        23       2      30 ..     286     312 ..     285     352 .. 0.73
   3 ?   -2.8   0.0       6.8   8.1e+03      33      70 ..     393     433 ..     384     435 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.7e-06
                             PAS_3  16 peellgkveswldlvhpeDrervrealqealkkgepyegeyRirrk.dGeyrwveararvirdengkpv 83 
                                       +++llg+  ++l+l+h +D e v++ +++a ++ +++++  R ++  dG ++  e ++r+i  +ng+  
  gi|313124869|ref|YP_004035133.1| 179 ADDLLGR--NLLSLIHKQDTEAVKAVIAHAQDDEKVISQTQRTMKTlDGMTFSAEMTVRAI-TWNGESG 244
                                       4599***..*******************9999999*****9999998**999999999999.8888765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                             PAS_3   2 iyvserveeilGyspeellgkveswldlv 30 
                                       i v+++  e++G+ +eellg+  ++ ++ 
  gi|313124869|ref|YP_004035133.1| 286 IDVNGSAAELFGLPREELLGR--NLSEFT 312
                                       889*****************9..766665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.8
                             PAS_3  33 eDrervrealqealkkgepy.egeyRirrk..dGeyrwvea 70 
                                       +  + ++e++ ++l+ g++y ++ y ++++  dG+ + +e+
  gi|313124869|ref|YP_004035133.1| 393 DREAAFEEKVSALLELGADYlDVPYGFLTRiqDGTQTIIES 433
                                       33455667777888888877788888888776787777766 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.8e-06    0.0033       3     124 ..     399     530 ..     397     532 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.8e-06
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvsepsfae..... 74 
                                       +e +++ll+l+++ l++ +g+l   +++ +++    g ++  ++ e+ +   a +r ++ ++e vs++ +++     
  gi|313124869|ref|YP_004035133.1| 399 EEKVSALLELGADYLDVPYGFLTRIQDGTQTIIESVGDHELLQPGETGPLSKAYCRKTVIEDELVSVQNSEAegwed 475
                                       7889999999999999999999777766555544444444455566778999999************6664412211 PP

                             GAF_3  75 ...edglpdraalavPLvagrqviGvlalastkpra..fdaedlelleslArqia 124
                                           +++++++++ + +++ + ++G+l++a t  r+  f+  +++++e lAr+++
  gi|313124869|ref|YP_004035133.1| 476 dpaYERYELGCYIGAKVIVNEDLFGTLCFAGTASRKqaFSHGEEAFVELLARWVS 530
                                       222566888999999999999********988766556***************97 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.05        59      32      76 ..     174     223 ..     155     253 .. 0.74
   2 ?    7.8   0.0    0.0041       4.9      11      65 ..     275     331 ..     268     355 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.05
                            PAS_10  32 fklipad..vGrpladihpkkavknveeviealrtgekdevevvvp...k 76 
                                       f+  +ad  +Gr+l ++ +k+  + v+ vi   ++ ek+ ++++++    
  gi|313124869|ref|YP_004035133.1| 174 FEADDADdlLGRNLLSLIHKQDTEAVKAVIAHAQDDEKVISQTQRTmktL 223
                                       5555444448***********************99999888887763334 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0041
                            PAS_10  11 eltflDdnlqirrFtpaakklfklipad.vGrpladihpk.kavknveeviealrtg 65 
                                       +++ +Dd+++++  + +a++lf l +++ +Gr+l++++p+ ++++++  ++++l ++
  gi|313124869|ref|YP_004035133.1| 275 AIIVADDDDEFIDVNGSAAELFGLPREElLGRNLSEFTPNgSEIDDMWADFQSLGEN 331
                                       68999*******************988737*********988888888888777655 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1         3   3.6e+03      82     115 ..     226     259 ..     195     272 .. 0.64
   2 ?   12.3   0.0   9.6e-05      0.11       9      61 ..     660     709 ..     655     718 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3
                       HATPase_c_3  82 lslgkkltvitkke.gesstltldvdkidkenekv 115
                                       + +++++tv   +  ges ++ + +d++++e+ ++
  gi|313124869|ref|YP_004035133.1| 226 MTFSAEMTVRAITWnGESGHVAILRDVTNQEE-QD 259
                                       55667777777554155556666666665544.33 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.6e-05
                       HATPase_c_3   9 elvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatssk 61 
                                        l +N++d   + v + v   +   + + +eDdG G++e+e +n+++ + +++
  gi|313124869|ref|YP_004035133.1| 660 NLFRNAIDHVGTDVRVRVGSLD---DGFYVEDDGPGIPESERDNVFEQGYTTR 709
                                       5789**************9976...79*****************998776665 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.4e-05     0.077       6      59 ..     543     596 ..     538     598 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.4e-05
                            SPOB_a   6 ikelkeliklLrsqRHDflNhLQvIsGylqLgkydkaeeyieevvkelkeeski 59 
                                       +++++ l +  ++  HD  N L v sGyl+L + d   e+ +++ ++l ++++i
  gi|313124869|ref|YP_004035133.1| 543 QSQTERLEEFASMVTHDLRNPLSVASGYLELAREDGDPEQFDRIEDALSRMERI 596
                                       56778888888999*********************9888888888888887776 PP

>> Chitin_bind_4  Insect cuticle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00024      0.29      28      48 ..     331     351 ..     324     354 .. 0.89
   2 ?   -2.8   0.0       7.9   9.4e+03      14      38 ..     625     650 ..     617     652 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                     Chitin_bind_4  28 vqGsYsyvdpdGktrtVkYtA 48 
                                        +G  s++ pdG++r+V+Y A
  gi|313124869|ref|YP_004035133.1| 331 NHGVLSLIRPDGERRVVEYAA 351
                                       58999**************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.9
                     Chitin_bind_4  14 eeegr.tgtedeglvvqGsYsyvdpd 38 
                                        ++++ + t+++ l+v G    +++d
  gi|313124869|ref|YP_004035133.1| 625 AWQTVdETTHEATLSVDGDIGTIEAD 650
                                       45555667788889999987777666 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00077      0.92      19      87 ..       3      71 ..       1      81 [. 0.77
   2 ?   -0.5   0.0       2.2   2.6e+03      26      87 ..     528     588 ..     499     597 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00077
                   Methyltransf_24 19 rrngagrlvavdhdpgaee.aaalareaglddrvrlikadsee.alaslaagsiDllfiDgghaaeavled 87
                                      r++++ ++++vd +pg+++ +aa++++   ddr+++  a+s +  l  l + ++D+++ D +  + + l++
  gi|313124869|ref|YP_004035133.1|  3 RDAETVTVLCVDDEPGSADlTAAYLER--HDDRLTVTTATSVQgGLNALTETDFDCIVSDYDMPGLDGLAF 71
                                      67777899*******855536666665..9**********9553788888999******988766555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.2
                   Methyltransf_24  26 lvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiDllfiDgghaaeavled 87 
                                        v+ + +++ ++ +   +++ l++++ ++  d+++ l+  + g   l+  Dg++++ +++ed
  gi|313124869|ref|YP_004035133.1| 528 WVSYEQEHRRNNRELQSQTERLEEFASMVTHDLRNPLSVAS-GYLELAREDGDPEQFDRIED 588
                                       44445544333334444458888888888888888887666.88888888888777665555 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.24   2.9e+02      17     113 ..     163     258 ..     148     260 .. 0.46
   2 ?    7.5   0.0    0.0036       4.3       6      43 ..     274     310 ..     269     322 .. 0.86
   3 ?   -2.8   0.1       5.8     7e+03      46      72 ..     366     392 ..     346     404 .. 0.49
   4 ?   -2.1   0.1       3.5   4.2e+03      74     104 ..     528     558 ..     507     559 .. 0.64
   5 ?   -2.0   0.0       3.3     4e+03      44      93 ..     600     652 ..     587     655 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.24
                             PAS_7  17 LvawNrrylelldlpeelvqvgvpleellrynaergefg....agdveaeverrlaaaragkphsfererpdgrvie 89 
                                        v+ N   ++l++  +     g++l +l++ + ++   +    a+d e+ + ++ + +++ +  +f  e        
  gi|313124869|ref|YP_004035133.1| 163 FVFANTSAVSLFEADDADDLLGRNLLSLIHKQDTEAVKAviahAQDDEKVISQTQRTMKTLDGMTFSAE-------- 231
                                       555666666666665555555655555554442222222222222233333333333333333332222........ PP

                             PAS_7  90 vrgnpl...pdgGfVttytDiTerrra 113
                                       ++ +++    + G V++  D+T++ ++
  gi|313124869|ref|YP_004035133.1| 232 MTVRAItwnGESGHVAILRDVTNQEEQ 258
                                       111222222357889999999888765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0036
                             PAS_7   6 qGisvfDadlrLvawNrrylelldlpeelvqvgvplee 43 
                                       ++i+v D d++ + +N    el++lp+e +  g++l+e
  gi|313124869|ref|YP_004035133.1| 274 DAIIVADDDDEFIDVNGSAAELFGLPREEL-LGRNLSE 310
                                       689***********************9987.6766665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.8
                             PAS_7  46 rynaergefgagdveaeverrlaaara 72 
                                       +++ ++   +++++++e+ +r+ +++a
  gi|313124869|ref|YP_004035133.1| 366 DVTGRTRLERQRQADHEALERMYRITA 392
                                       333222222233344444444444444 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.5
                             PAS_7  74 kphsfererpdgrvievrgnplpdgGfVtty 104
                                         ++ + +r+++r ++ ++++l++   ++t+
  gi|313124869|ref|YP_004035133.1| 528 WVSYEQEHRRNNRELQSQTERLEEFASMVTH 558
                                       4445566677777888888777776666665 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 3.3
                             PAS_7  44 llrynaergefg...agdveaeverrlaaaragkphsfererpdgrvievrgn 93 
                                       ll   +e+++++   + + e++ver  + + + +++++     d  +ie  +n
  gi|313124869|ref|YP_004035133.1| 600 LLYLARENEQIRetePVELESAVERAWQTVDETTHEATLSVDGDIGTIEADQN 652
                                       55555555555522266688889988888888777777776666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 4340.01
//
Query:       gi|313124870|ref|YP_004035134.1|  [L=162]
Description: hypothetical protein Hbor_00820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 998.75
//
Query:       gi|313124871|ref|YP_004035135.1|  [L=121]
Description: hypothetical protein Hbor_00830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        2.5    8.4  10.2        8.1    6.7   4.0    2.1  2  TrbC         TrbC/VIRB2 family
        3.5    5.8   9.9        4.3    5.5   9.9    1.0  1  DUF2070      Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.0   0.00091       8.1      47      93 ..       7      53 ..       3      58 .. 0.86
   2 ?    5.6   0.4    0.0021        19      36      68 ..      69     101 ..      60     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00091
                              TrbC 47 dfltgplakviatiaiivaGimlafgrlswrtlvmvviGiviifgAs 93
                                      d ++ p   + +++++i+a++++ + r+   + v + + ++i+fgAs
  gi|313124871|ref|YP_004035135.1|  7 DRISLPRLVIFVVLGVIAAAFVVTTDRAITVEYVSLTVLVAIFFGAS 53
                                      556666678899***************999999*************8 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0021
                              TrbC  36 dpvetvlqnivdfltgplakviatiaiivaGim 68 
                                       +  + +l  +++ + gp ++++a+ +++v+G++
  gi|313124871|ref|YP_004035135.1|  69 AVYTALLFGLLTIIWGPNVFILALTGLAVVGVA 101
                                       5567777889999******************86 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   9.9   0.00048       4.3      82     171 ..      14     105 ..       5     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.00048
                           DUF2070  82 vviisllaillsall....qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesf 154
                                       +vi+++l+++++a++     a+++ ++ l++ +++++   ++ av ++ l++ +  ++++++l++ ll+++ +p+ f
  gi|313124871|ref|YP_004035135.1|  14 LVIFVVLGVIAAAFVvttdRAITVEYVSLTVLVAIFFGASIFDAVREHPLFNLA--SAVYTALLFGLLTIIWGPNVF 88 
                                       455555555555555556777777777777788888888888888887777655..888888888888888899999 PP

                           DUF2070 155 llllllslifalavylf 171
                                       +l+l  ++++++av l+
  gi|313124871|ref|YP_004035135.1|  89 ILALTGLAVVGVAVELY 105
                                       99999999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 848.45
//
Query:       gi|313124872|ref|YP_004035136.1|  [L=139]
Description: hit family hydrolase, diadenosine tetraphosphate hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-26   92.2   0.0    3.2e-26   91.9   0.0    1.1  1  HIT            HIT domain
      1e-11   45.3   0.0    1.4e-11   44.9   0.0    1.1  1  DcpS_C         Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
      0.056   13.2   0.0      0.076   12.7   0.0    1.1  1  GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-te
        0.2   11.5   0.0       0.31   10.9   0.0    1.3  1  CwfJ_C_1       Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   7.1e-30   3.2e-26       3      96 ..      14     107 ..      12     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 7.1e-30
                                       CC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESG CS
                               HIT   3 eipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinnga 79 
                                        ip+++vye+d vlafld +p apgh+Lv+pk+  ++l dl+++  ++l++av+++   +++ + +++l+v +n+g+
  gi|313124872|ref|YP_004035136.1|  14 DIPARIVYETDTVLAFLDANPLAPGHTLVVPKEAHERLRDLPDDVATDLWAAVDELTPRVEDAVDADALTVGVNDGE 90 
                                       699************************************************************************** PP

                                       GGT-SSSS-EEEEEEC- CS
                               HIT  80 hagqsvahlHiHviprr 96 
                                       +agq+v+h+H+H++pr+
  gi|313124872|ref|YP_004035136.1|  91 AAGQEVPHVHVHLVPRF 107
                                       ***************97 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   3.1e-15   1.4e-11       3     103 ..       6     106 ..       4     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 3.1e-15
                                       HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.-E CS
                            DcpS_C   3 vfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.vd 78 
                                       +f+++a g +p+r+vye+++++++ D++p a+ h lv+pk+  + lrdL ++    l + ++++   +e+   +   
  gi|313124872|ref|YP_004035136.1|   6 IFEQIAAGDIPARIVYETDTVLAFLDANPLAPGHTLVVPKEAHERLRDLPDDVATDLWAAVDELTPRVEDAVDAdAL 82 
                                       899**********************************************6555555555554444444443311112 PP

                                       EEEE--SCCCT--S-S--EEEEE.. CS
                            DcpS_C  79 aeelrvgvhyqPsvyhlHlHvisld 103
                                          ++ g  + + v h+H+H++  +
  gi|313124872|ref|YP_004035136.1|  83 TVGVNDGEAAGQEVPHVHVHLVP-R 106
                                       344555667899********986.5 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05     0.076      32     119 ..      19     104 ..      13     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                                       EEEE-SSEEEE--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHHHHCTS---EEEEEE---SCCC CS
                     GalP_UDP_tr_C  32 vvelkdsflavvpylakWPfevlllrkaevkslaeladeekedlaailkklarkydnlfetsfeysmGlhqaplnae 108
                                       +v ++d  la        P ++l+++k+  ++l +l d   +dl a++ +l+ + ++  ++++   +G+ +   +++
  gi|313124872|ref|YP_004035136.1|  19 IVYETDTVLAFLDANPLAPGHTLVVPKEAHERLRDLPDDVATDLWAAVDELTPRVEDAVDADA-LTVGVNDGEAAGQ 94 
                                       555666333333333344678************************************999886.6789844443333 PP

                                       TTTT--EEEEE CS
                     GalP_UDP_tr_C 109 ednswlHaHfe 119
                                       e    +H+H+ 
  gi|313124872|ref|YP_004035136.1|  95 EV-PHVHVHLV 104
                                       33.23677765 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.9e-05      0.31      38     108 ..      29     105 ..      17     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.9e-05
                                       E---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHH.HHHHHTT--EEEEEE-.....SSS-----EEEEE CS
                          CwfJ_C_1  38 alpkgpLssgHvliipieHisallsldeevldeirkfrkalv.kmykkqdkdavvfEis.....sersvHlaiqvip 108
                                        l  +pL+ gH l++p e  + l+ l+++v  ++ +    l+ ++ ++ d da++  ++      ++ +H++++++p
  gi|313124872|ref|YP_004035136.1|  29 FLDANPLAPGHTLVVPKEAHERLRDLPDDVATDLWAAVDELTpRVEDAVDADALTVGVNdgeaaGQEVPHVHVHLVP 105
                                       45569***********************9999998877777735678889999987555554548999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 961.02
//
Query:       gi|313124873|ref|YP_004035137.1|  [L=331]
Description: tyrosyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-48  164.4   0.0    4.7e-48  164.0   0.0    1.1  1  tRNA-synt_1b   tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.034   13.1   0.0        1.7    7.5   0.0    2.2  2  tRNA-synt_1f   tRNA synthetases class I (K)
      0.053   13.9   0.1       0.11   12.9   0.1    1.4  1  Chordopox_E11  Chordopoxvirus E11 protein


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.0   0.0   7.9e-52   4.7e-48       7     292 ..      31     319 ..      28     320 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.0 bits;  conditional E-value: 7.9e-52
                                       EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTT CS
                      tRNA-synt_1b   7 rvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpe 83 
                                       r+y+G +P+g lH+G+++  +kl+elq+ag ev++l+aD+hA+++d+   +  ++++ +++++++    +a gl+ +
  gi|313124873|ref|YP_004035137.1|  31 RAYVGYEPSGVLHIGHMLTANKLIELQEAGFEVVVLLADVHAYLNDKG--TFDEIQETATRMQEQ---FVAYGLEED 102
                                       79*********************************************9..999************...********* PP

                                       TEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGG CS
                      tRNA-synt_1b  84 kaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQ 160
                                       ++e+vl+se +   +++ +l  l   +sl+r  ++ +   ++++g+ +++++  Ypl+qa+Di++l++dl +gG+ Q
  gi|313124873|ref|YP_004035137.1| 103 QTEFVLGSEFQLDDDYTLDLHALELETSLSRAERAMA---EIKSGDTVTVAQAVYPLMQALDIVYLDVDLAIGGMEQ 176
                                       **********************999888888877777...9999889****************************** PP

                                       HHHHHHHHHHHHHHHHHSTTSS-EEEEET.-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTCSHHHH CS
                      tRNA-synt_1b 161 kqnielgrdlarrfnkkevfkkpegltvp.lltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsdeevekl 236
                                       ++   l+rd ++++        p +l +p + ++++G  KmS+S+g   I ++d++e+ ++k++ka++ + ++   +
  gi|313124873|ref|YP_004035137.1| 177 RKVHMLARDTLPSIDAD----APTCLHTPlISDLSTGVGKMSSSSGV-SISMEDSEEELREKVNKAFCPPSRDPDPD 248
                                       **************999....********5566789999********.********************999955555 PP

                                       HHHHHTHHH...............CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 237 lklktelsn...............elierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                         ++   ++                ++er e+++g+ ++ ++e l+++   +++h+ d+k ala+ lnel 
  gi|313124873|ref|YP_004035137.1| 249 DDGNERDNPvlqifeyhvfprfgeVVVERPEQYGGNLTYDDYESLAEDLDAGELHPADAKGALANYLNELV 319
                                       55554444455555569999***999***************************************999985 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00029       1.7       8      42 ..      11      47 ..       7      69 .. 0.75
   2 ?    3.3   0.0    0.0053        32     278     297 ..     209     228 ..     189     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00029
                      tRNA-synt_1f  8 aeklieerkkk.ka.ekdevvvesGispSGliHiGnl 42
                                      a+++++e + +  a + d      G+ pSG +HiG +
  gi|313124873|ref|YP_004035137.1| 11 AAEVVTEDEARsLAdDPDGKRAYVGYEPSGVLHIGHM 47
                                      445554444330345788899999***********87 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0053
                      tRNA-synt_1f 278 ggekmssSkGnvltledwle 297
                                       g +kmssS+G+ +++ed  e
  gi|313124873|ref|YP_004035137.1| 209 GVGKMSSSSGVSISMEDSEE 228
                                       445************99765 PP

>> Chordopox_E11  Chordopoxvirus E11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.8e-05      0.11      41     108 ..      51     120 ..      43     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                     Chordopox_E11  41 kkyikveestFylvvkdkdiFyykcdkGrvspvenefyvfdeellfv..kdvseeevtgveFvvtddmev 108
                                       +k i+++e+ F++vv   d+  y  dkG    ++++   ++e++ ++  ++ + e v g eF + dd  +
  gi|313124873|ref|YP_004035137.1|  51 NKLIELQEAGFEVVVLLADVHAYLNDKGTFDEIQETATRMQEQFVAYglEEDQTEFVLGSEFQLDDDYTL 120
                                       799*********************************9999999987622333345677777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2086.66
//
Query:       gi|313124874|ref|YP_004035138.1|  [L=67]
Description: hypothetical protein Hbor_00860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.69    8.8   6.1        0.7    8.8   6.1    1.0  1  DUF726    Protein of unknown function (DUF726)
        4.5    6.9   6.1        5.1    6.7   6.1    1.0  1  RTX       N-terminal domain in RTX protein


Domain annotation for each model (and alignments):
>> DUF726  Protein of unknown function (DUF726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.1   7.8e-05       0.7       9      53 ..      13      59 ..       7      67 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 7.8e-05
                            DUF726  9 iglAglaGgaligltggLaa...PlvaagigallaglGltgsaafLas 53
                                      +g  g+aG +l+    g++a   P+vaagi+ ++aglGl +s   + s
  gi|313124874|ref|YP_004035138.1| 13 LGTKGIAGVVLLVAGIGIVAyqePIVAAGIALVVAGLGLVASGL-VQS 59
                                      67778889888877777766666***************987765.444 PP

>> RTX  N-terminal domain in RTX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.1   0.00057       5.1      78     122 ..      16      60 ..      11      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00057
                               RTX  78 taistvldvvsavvsaaaaasgVGaPvallvalitglisgileas 122
                                        +i  v+  v++++  a    +V+a +al+va+++ + sg+++ +
  gi|313124874|ref|YP_004035138.1|  16 KGIAGVVLLVAGIGIVAYQEPIVAAGIALVVAGLGLVASGLVQSV 60 
                                       578899999*************************99999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 456.89
//
Query:       gi|313124875|ref|YP_004035139.1|  [L=96]
Description: translation initiation factor 1a (aeif-1a) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-24   84.2   0.5      5e-24   83.9   0.5    1.1  1  eIF-1a         Translation initiation factor 1A / IF-1
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.024   14.3   0.0    1.1  1  Sclerostin     Sclerostin (SOST)
      0.027   14.2   0.0      0.049   13.4   0.0    1.4  1  zinc_ribbon_5  zinc-ribbon domain
       0.12   12.6   0.0       0.19   11.9   0.0    1.4  1  ChapFlgA_N     FlgA N-terminal domain


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.5   1.1e-27     5e-24       2      64 .]      19      80 ..      18      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 1.1e-27
                                      EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      e  ++V  +lg n+++V+++d g+e++a+ipg++ ++iwi++Gd+VlVe+++ +++k+++++r
  gi|313124875|ref|YP_004035139.1| 19 EEFAVVQDMLGANRVKVRCAD-GVERTARIPGRMQKRIWIREGDVVLVEPWDWQDEKADVTWR 80
                                      789****************96.***************************************98 PP

>> Sclerostin  Sclerostin (SOST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.4e-06     0.024     116     147 ..      16      47 ..       5      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.4e-06
                                       SS------EEEEEEEEEEEEB-TTSSSEEEEE CS
                        Sclerostin 116 rssqefrcvndktrtqriqlqcedGatrtykv 147
                                        + +ef  v+d   ++r++++c dG  rt ++
  gi|313124875|ref|YP_004035139.1|  16 DDDEEFAVVQDMLGANRVKVRCADGVERTARI 47 
                                       56789************************987 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05     0.049       6      29 ..      15      38 ..      12      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                     zinc_ribbon_5  6 pdCdtkFklvdsklKksgkkVrCa 29
                                      pd d  F +v++ l  + +kVrCa
  gi|313124875|ref|YP_004035139.1| 15 PDDDEEFAVVQDMLGANRVKVRCA 38
                                      566778*****************9 PP

>> ChapFlgA_N  FlgA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.2e-05      0.19      29      73 ..      10      49 ..       4      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
                        ChapFlgA_N 29 prlrlpacdeaLevelpsgsrplGrtsvkvrcngpeppwtvyvpv 73
                                      ++lr+p+ de+ +v+     ++lG ++vkvrc+ +    t ++p+
  gi|313124875|ref|YP_004035139.1| 10 RDLRMPDDDEEFAVV----QDMLGANRVKVRCADGVE-RTARIPG 49
                                      778888888888888....899***********9886.5777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 687.72
//
Query:       gi|313124876|ref|YP_004035140.1|  [L=302]
Description: serine/threonine protein kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-61  205.5   0.7      1e-60  204.6   0.0    1.6  2  RIO1            RIO1 family
    6.4e-07   29.5   2.1      7e-05   22.9   0.0    2.6  3  APH             Phosphotransferase enzyme family
    9.6e-07   28.4   0.1    2.1e-06   27.2   0.1    1.6  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00032   20.1   0.0    0.00064   19.2   0.0    1.4  2  Pkinase         Protein kinase domain
    0.00038   19.3   0.0    0.00048   19.0   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.041   13.5   0.0      0.069   12.8   0.0    1.4  1  WaaY            Lipopolysaccharide core biosynthesis protein 
      0.091   12.3   0.1        0.2   11.2   0.1    1.6  1  VQ              VQ motif


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.64   1.6e+03      17      43 ..      35      61 ..      26      71 .. 0.78
   2 !  204.6   0.0   3.9e-64     1e-60       1     182 [.      94     271 ..      94     277 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.64
                                      EE-S---SS-HHHHCTTTSTTSTCG-- CS
                              RIO1 17 iyktstteFkkrkkyvsgekrfkdrks 43
                                      i +   ++F++ +k+ ++  +fk ++s
  gi|313124876|ref|YP_004035140.1| 35 IARKRDRKFDEFRKRLKDADQFKVEQS 61
                                      667777899999999999999987765 PP

  == domain 2  score: 204.6 bits;  conditional E-value: 3.9e-64
                                       EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       nVy+a   ++++va Kiy++++++F++++ y +g++rf+      +++++v +w++kEf+nL+r+++agv+vP+pi+
  gi|313124876|ref|YP_004035140.1|  94 NVYEALGPEDTDVATKIYRINASNFRHMRDYLEGDPRFEGI--GNDKKRVVLAWTQKEFANLERARQAGVRVPEPIA 168
                                       7**************************************77..79999***************************** PP

                                       EETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEE CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQave 154
                                       ++r+vlvme++g  + +a +l +v+  e+ +++ye v e+mr+ly  aglvH+DLSeyN++++++++viID++Qav+
  gi|313124876|ref|YP_004035140.1| 169 VERNVLVMELVGLVEDRARRLAEVS-VENPQTAYEVVREYMRRLY-SAGLVHGDLSEYNMIIHDGELVIIDLGQAVT 243
                                       *************************.66777788888889*****.******************************* PP

                                       TTSTTHHHHHHHHHHHHHHHHHTTC--- CS
                              RIO1 155 ldhpnalefLerDveniikfFrrkgvek 182
                                       ++hpna efL+rD++n++kfF+r+g+++
  gi|313124876|ref|YP_004035140.1| 244 VHHPNADEFLRRDCRNVAKFFSRQGTDT 271
                                       ************************9984 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.4   6.1e+03     123     148 ..      28      53 ..      17      66 .. 0.53
   2 !    6.6   0.2    0.0026       6.6      37      72 ..     146     177 ..      86     205 .. 0.70
   3 !   22.9   0.0   2.8e-08     7e-05     151     198 ..     191     243 ..     177     246 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.4
                                       CCHHHHHHCHHHCCCGCCTCCHHHHH CS
                               APH 123 lellrqlesatarllaselldlleel 148
                                        + ++++ +++++++  e++++l ++
  gi|313124876|ref|YP_004035140.1|  28 TDTEADRIARKRDRKFDEFRKRLKDA 53 
                                       44455555554444444444433333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEE CS
                               APH  37 irrevallrlLakagvpvPevlagdtddeeigllfa 72 
                                       +++e+a l   ++agv+vPe++a     e + l+++
  gi|313124876|ref|YP_004035140.1| 146 TQKEFANLERARQAGVRVPEPIAV----ERNVLVME 177
                                       6788999****************5....33333344 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 2.8e-08
                                       H...........HHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                               APH 151 q...........vlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                       +           v ++  ++l    +++l+HgDl+  N++++ d+  v  +iD++ a++
  gi|313124876|ref|YP_004035140.1| 191 EvsvenpqtayeVVREYMRRLY---SAGLVHGDLSEYNMIIH-DGELV--IIDLGQAVT 243
                                       2333334442224444444444...7****************.55555..****99976 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   8.2e-10   2.1e-06      59     171 ..     147     243 ..     140     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 8.2e-10
                               Kdo  59 vrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrliaklh 135
                                        +Ef++l+r ++agv+vp+p+a +        r +l++e +  ++d +  la+   +++e  ++ ++ v   +++l 
  gi|313124876|ref|YP_004035140.1| 147 QKEFANLERARQAGVRVPEPIAVE--------RNVLVMELVGLVEDRARRLAE---VSVENPQTAYEVVREYMRRLY 212
                                       58*******************986........679***********9999997...9******************** PP

                               Kdo 136 ragvnHadlyaknillqqeeeeeaeiwliDldkarl 171
                                       +ag+ H+dl   n+ ++ +e     +++iDl +a +
  gi|313124876|ref|YP_004035140.1| 213 SAGLVHGDLSEYNMIIHDGE-----LVIIDLGQAVT 243
                                       *****************997.....9****988866 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.5   6.4e+03       9      33 ..      89     112 ..      86     117 .. 0.76
   2 !   19.2   0.0   2.5e-07   0.00064      74     152 ..     173     248 ..     162     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.5
                                       EESSEEEEEEEETTTTEEEEEEEEE CS
                           Pkinase   9 eGsfGkVykaveketgkivAvKkik 33 
                                       +G+ ++Vy+a+   ++  vA K+ +
  gi|313124876|ref|YP_004035140.1|  89 TGKEANVYEAL-GPEDTDVATKIYR 112
                                       68899999999.5777788888765 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.5e-07
                                       EEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSS CS
                           Pkinase  74 ylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakeles 150
                                       +lv+e+v    ++d+ +r   +s e+ +   + + e ++ l+s+g++H Dl   N++i+ +gel i+D+G a  +++
  gi|313124876|ref|YP_004035140.1| 173 VLVMELVG--LVEDRARRLAEVSVENPQTAYEVVREYMRRLYSAGLVHGDLSEYNMIIH-DGELVIIDLGQAVTVHH 246
                                       57777776..44666665555777777777777788999********************.************99988 PP

                                       SC CS
                           Pkinase 151 ss 152
                                        +
  gi|313124876|ref|YP_004035140.1| 247 PN 248
                                       66 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.9e-07   0.00048     319     369 ..     208     251 ..     131     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-07
                    Pkinase_fungal 319 hrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddsses 369
                                        r+L+  ag++H D Se+N++i       + + ++iDL  a++++++++++
  gi|313124876|ref|YP_004035140.1| 208 MRRLY-SAGLVHGDLSEYNMIIH------DGELVIIDLGQAVTVHHPNADE 251
                                       48999.*****************......8899**********99988776 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.7e-05     0.069     142     181 ..     202     241 ..     144     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                              WaaY 142 akikqsieklhqlgmvsgdphrgnfivkkdevriidlsgk 181
                                       + +++ +++l++ g+v gd    n+i++++e+ iidl   
  gi|313124876|ref|YP_004035140.1| 202 EVVREYMRRLYSAGLVHGDLSEYNMIIHDGELVIIDLGQA 241
                                       4578899*****************************9654 PP

>> VQ  VQ motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   7.9e-05       0.2       3      16 ..     107     120 ..     106     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.9e-05
                                VQ   3 pPtvvhtdasnFRa 16 
                                        +++++++asnFR 
  gi|313124876|ref|YP_004035140.1| 107 ATKIYRINASNFRH 120
                                       69***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1591.95
//
Query:       gi|313124877|ref|YP_004035141.1|  [L=180]
Description: universal archaeal kh domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-12   45.7   5.1    8.3e-07   28.8   0.2    2.2  2  KH_1      KH domain
     0.0008   19.2   3.3      0.028   14.2   0.2    2.4  2  KH_2      KH domain
     0.0056   16.5   1.3        1.3    9.0   0.2    2.7  2  KH_4      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.2   1.4e-10   8.3e-07       3      41 ..       3      40 ..       1      64 [. 0.86
   2 !   18.8   0.9   1.7e-07     0.001       9      61 ..     100     144 ..      98     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.4e-10
                                      EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT. CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksede 41
                                       ++vP++ +g +IG gG++ +eI+++  ++ +++ se++
  gi|313124877|ref|YP_004035141.1|  3 HVKVPQDRIGVLIGEGGETMREIERRAEVRLDID-SESG 40
                                      689**********************88*****87.5543 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.7e-07
                                       GHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHH CS
                              KH_1   9 slvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAk 61 
                                       ++ gr+IG +G++   ++e tga +++  +       +++ i+G pe ve+ +
  gi|313124877|ref|YP_004035141.1| 100 RQKGRLIGENGRTRELMEELTGAEVVIR-G-------TTLGIIGQPEEVEAVR 144
                                       788**********99888989*****75.4.......58*****777799876 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   4.8e-06     0.028      33      59 ..       8      34 ..       3      51 .. 0.76
   2 !    5.4   0.4    0.0028        16      35      58 ..     101     124 ..      97     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.8e-06
                                      ESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2 33 esqpgivIGkgGsnikkigkelrkdie 59
                                        + g++IG gG+++++i+  ++ +++
  gi|313124877|ref|YP_004035141.1|  8 QDRIGVLIGEGGETMREIERRAEVRLD 34
                                      5689***************99988875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0028
                                       CHHHHHTGGGHHHHHHHHHHHHHH CS
                              KH_2  35 qpgivIGkgGsnikkigkelrkdi 58 
                                       q+g++IG +G++ + +++  + ++
  gi|313124877|ref|YP_004035141.1| 101 QKGRLIGENGRTRELMEELTGAEV 124
                                       9*********99877777777666 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2   0.00021       1.3      33      51 ..       4      22 ..       2      27 .. 0.90
   2 !    5.7   0.0    0.0023        14      39      50 ..     101     112 ..      95     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00021
                              KH_4 33 lnvegedlGrvIGkrGrtl 51
                                      ++v ++ +G++IG  G+t+
  gi|313124877|ref|YP_004035141.1|  4 VKVPQDRIGVLIGEGGETM 22
                                      88999************97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0023
                              KH_4  39 dlGrvIGkrGrt 50 
                                       ++Gr+IG +Grt
  gi|313124877|ref|YP_004035141.1| 101 QKGRLIGENGRT 112
                                       68*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1108.65
//
Query:       gi|313124878|ref|YP_004035142.1|  [L=69]
Description: hypothetical protein Hbor_00910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 386.17
//
Query:       gi|313124879|ref|YP_004035143.1|  [L=559]
Description: thermosome subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.3e-180  599.5  12.8   4.9e-180  599.4  12.8    1.0  1  Cpn60_TCP1       TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.06   13.9   0.3         10    6.8   0.0    3.0  2  PepSY            Peptidase propeptide and YPEB domain
       0.13   12.7   0.8       0.61   10.5   0.8    2.2  1  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  599.4  12.8  8.2e-184  4.9e-180       1     489 [.      37     522 ..      37     524 .. 0.99

  Alignments for each domain:
  == domain 1  score: 599.4 bits;  conditional E-value: 8.2e-184
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v+ttlGPkGmdKmlv++ g+vvvTnDG+tilke++i+hPaa+++ve++e+q++evGDGTtt+v++ageLl++a
  gi|313124879|ref|YP_004035143.1|  37 VAEAVRTTLGPKGMDKMLVDNSGEVVVTNDGVTILKEMDIDHPAANMIVEVSETQEDEVGDGTTTAVVIAGELLDQA 113
                                       689************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+li+++vh tti +g+++a+eka e L+    +i+++e+dre+L+k+a+t++++k  ++ ++ l++lvvd+v+++ 
  gi|313124879|ref|YP_004035143.1| 114 EDLIEQDVHATTIAQGFRQAAEKAKEVLEGD--AIDVSEDDRETLVKIASTAMTGKGAESAKDLLAELVVDSVLAVA 188
                                       ****************************988..7777788*********************************7776 PP

                                       CCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHH CS
                        Cpn60_TCP1 155 enekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeele 231
                                       ++   +d +++ ++k+ ggs+++selveG+++dk+ ++++mp ++e+a+v+l+d  Le  +te++++v+++d+++l+
  gi|313124879|ref|YP_004035143.1| 189 DD-DGIDTDNVSIEKVVGGSIDNSELVEGVIVDKERVHENMPYMVEDANVALFDGALEVRETEIDAEVNVTDPDQLQ 264
                                       66.48************************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC CS
                        Cpn60_TCP1 232 klekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpee 308
                                       +++++eekql+e+++++++ g++vv++ +gidd+a+h+lak+gila+rr+k +dl+rla+atG+++v sl+d++ ++
  gi|313124879|ref|YP_004035143.1| 265 QFLDQEEKQLKEMVDQLVDVGADVVFVGDGIDDMAQHYLAKEGILAVRRAKSSDLKRLARATGGSVVGSLDDIEADD 341
                                       ***************************************************************************** PP

                                       -EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHH CS
                        Cpn60_TCP1 309 lGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelak 385
                                       lG a++v +++ig ++ +++e+v+++k++t++lrg td+v+de+erai+d+l vv+ ++ed+kv+pGGG+ e+el+ 
  gi|313124879|ref|YP_004035143.1| 342 LGFAGSVGQKDIGGDERIFVEDVEEAKSVTLILRGGTDHVVDEVERAIDDSLGVVRTTLEDGKVLPGGGSPETELSL 418
                                       ***************************************************************************** PP

                                       HHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEE CS
                        Cpn60_TCP1 386 klkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDp 462
                                       +l+e+a+sv g+eqla+eafa+AL vip+tLaeNaGldpi+ l +lra+h+ ge+ +g+d+ +ge+id+ e+gvv+p
  gi|313124879|ref|YP_004035143.1| 419 QLREFADSVGGREQLAVEAFAEALDVIPRTLAENAGLDPIDSLVDLRARHDGGEFGAGLDAYTGEVIDMEEEGVVEP 495
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 463 lkvkrqalksAteaastiLrideiika 489
                                       l+vk+qa++sAteaa +iLrid++i a
  gi|313124879|ref|YP_004035143.1| 496 LRVKTQAIESATEAAVMILRIDDVIAA 522
                                       *************************97 PP

>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.013        80       6      28 ..     132     154 ..     129     169 .. 0.81
   2 ?    6.8   0.0    0.0017        10      52      62 ..     477     487 ..     461     488 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.013
                                       HHHHHHHHHSTTEEEEEEEEEEE CS
                             PepSY   6 qAlaiAlaavpgkiieieleded 28 
                                       qA ++A++ ++g++i++  +d++
  gi|313124879|ref|YP_004035143.1| 132 QAAEKAKEVLEGDAIDVSEDDRE 154
                                       89999999999999999999876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0017
                                       EETTT--EEEE CS
                             PepSY  52 iDAkTGkvlkk 62 
                                        DA+TG+v+++
  gi|313124879|ref|YP_004035143.1| 477 LDAYTGEVIDM 487
                                       6********97 PP

>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.8    0.0001      0.61      39      99 ..     104     164 ..      93     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                   Phage_holin_6_1  39 kiaei.aknaVkaveqvakedakgeeKkeeAleklkellkekgisitddeleglIEaaVkel 99 
                                        ia+   ++a  + eq     +++++ +++A ek+ke l+   i++++d+ e+l++ a +++
  gi|313124879|ref|YP_004035143.1| 104 VIAGElLDQAEDLIEQDVHA-TTIAQGFRQAAEKAKEVLEGDAIDVSEDDRETLVKIASTAM 164
                                       55554478888899999888.99*********************************998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.40s 00:00:01.12 Elapsed: 00:00:00.57
# Mc/sec: 2966.16
//
Query:       gi|313124880|ref|YP_004035144.1|  [L=136]
Description: hypothetical protein Hbor_00940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-09   38.0  23.3    9.6e-06   26.2   7.7    2.1  2  YccF        Inner membrane component domain
  ------ inclusion threshold ------
        6.8    6.8   9.5        1.9    8.5   3.3    2.1  2  COPI_assoc  COPI associated protein


Domain annotation for each model (and alignments):
>> YccF  Inner membrane component domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   7.7   3.7e-07    0.0033       5      46 ..      22      63 ..      18      64 .. 0.93
   2 !   26.2   7.7   1.1e-09   9.6e-06       5      44 ..      88     127 ..      84     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-07
                              YccF  5 lWlllfGwwlaliyllaglllfitiigipygrvlfklakyll 46
                                      lW++++Gww   i + ++ +l  tii +p g+ l++l   +l
  gi|313124880|ref|YP_004035144.1| 22 LWFVFVGWWATPIVINVAWALNATIILLPLGIKLINLVPTVL 63
                                      9***********************************987665 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.1e-09
                              YccF   5 lWlllfGwwlaliyllaglllfitiigipygrvlfklaky 44 
                                       ++++++Gwwl+ +++ +++ll++tiig+p++  +f+   y
  gi|313124880|ref|YP_004035144.1|  88 VYFVFVGWWLSFLWANIAALLAVTIIGLPVAYWMFNRLPY 127
                                       89*****************************999986666 PP

>> COPI_assoc  COPI associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.4     0.021   1.9e+02      66      98 ..      16      47 ..      12      80 .. 0.66
   2 ?    8.5   3.3   0.00022       1.9      66     105 ..      82     122 ..      80     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.021
                        COPI_assoc 66 sylGRGlfyillgllvsyggvlsilialllflv 98
                                      s l+R+l ++++g    +  v+++ +al   ++
  gi|313124880|ref|YP_004035144.1| 16 SLLVRALWFVFVGWWATPI-VINVAWALNATII 47
                                      7788999999999888777.7777766633222 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00022
                        COPI_assoc  66 sylGRGlfyillgllvsyggvlsilialllflvGLv..yill 105
                                       s l+R+++++++g  +s+  + +i + l + ++GL   y ++
  gi|313124880|ref|YP_004035144.1|  82 SLLVRAVYFVFVGWWLSFL-WANIAALLAVTIIGLPvaYWMF 122
                                       789**************99.9999999999999994225555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 747.44
//
Query:       gi|313124881|ref|YP_004035145.1|  [L=195]
Description: dephospho-CoA kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-21   75.7   0.1    7.1e-21   75.1   0.1    1.3  1  AAA_17         AAA domain
    8.3e-13   49.0   0.1    1.3e-12   48.4   0.1    1.3  1  AAA_18         AAA domain
    6.1e-06   26.5   0.0    1.1e-05   25.7   0.0    1.4  1  AAA_33         AAA domain
    0.00038   20.6   0.1    0.00075   19.6   0.1    1.5  1  ADK            Adenylate kinase
  ------ inclusion threshold ------
      0.032   13.9   0.7        7.4    6.2   0.1    2.3  2  CoaE           Dephospho-CoA kinase
      0.055   13.2   0.3       0.13   12.0   0.3    1.7  1  PEP-utilizers  PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.1   2.4e-24   7.1e-21       1     136 []       7     138 ..       7     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2.4e-24
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC.TSHHHHHHHHHHHHHHHH....HHHHHSS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr.klpleekkelqkeaaeki....aeeakkk 72 
                                       +G+PGsGKg+++  ++++ g++++++Gd++r+e++++gl++a+++ r    l+e++ l+++aa+++    ae ++++
  gi|313124881|ref|YP_004035145.1|   7 VGLPGSGKGEAA-SVAREAGVPVVTMGDVIRNECRERGLDPAEHHGRiAKALREEEGLDAIAARSLplieAELEDSD 82 
                                       7***********.**************************99999999445788888999999998777544445888 PP

                                       EEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HH.HHHHHHHHHTTST-TS-SHHHHH CS
                            AAA_17  73 gvlvdghprikeqagfldglpkevleelkpdaiilleadpe.eilerrlkdrtrgrdddneesik 136
                                        vlvdg  +          ++ + +e+++ d ++l+++++  +++++rl dr+r+++d + e +k
  gi|313124881|ref|YP_004035145.1|  83 VVLVDGLRSE---------YELDRFEDAFGDDFVLVSIEAPfDLRAERLLDRGRDDSDVDREALK 138
                                       99****9863.........334446688888888888887779*************999999886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.1   4.3e-16   1.3e-12       1     121 [.       4     133 ..       4     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 4.3e-16
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I+  G pG+GK + a   ++  g+     g+++r  ++e+gl   + +  + + +r++e+ ++ + + l  + + le
  gi|313124881|ref|YP_004035145.1|   4 IGTVGLPGSGKGEAASVAREA-GVpvvtmGDVIRNECRERGLDPAEHHGRIAKALREEEGLDAIAARSLPLIEAELE 79 
                                       6678**************999.5666999*************99999999*******************99999*** PP

                            AAA_18  73 egknlvidghlaeleseaakdikk.....vvLtaspeelleRlekRgyeeakik 121
                                       + +++++dg+++e+e +++ d+ +     v ++a+ + ++eRl +Rg+ + +  
  gi|313124881|ref|YP_004035145.1|  80 DSDVVLVDGLRSEYELDRFEDAFGddfvlVSIEAPFDLRAERLLDRGRDDSDVD 133
                                       ***********************************************8887766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   3.5e-09   1.1e-05       1     137 [.       3     141 ..       3     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.5e-09
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.avllssdtlrrrlfgtdqqskt.........dytrvldrlyqilnelarkal 67 
                                       ++ +vGlpGsGK   a  ++++ g  v+   d++r+ +++++ ++ +         +  + ld + ++   l+ +a 
  gi|313124881|ref|YP_004035145.1|   3 VIGTVGLPGSGKGEAAS-VAREAGvPVVTMGDVIRNECRERGLDPAEhhgriakalREEEGLDAIAARSLPLI-EAE 77 
                                       5679********99776.8999996666677888889998555555545555555544556677777777999.567 PP

                            AAA_33  68 sagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeealdrqk 137
                                        +  +v+l  +++s+ e +rf  ++   +  + +v +e++ ++ +eRl  R ++   +s+v++eal++  
  gi|313124881|ref|YP_004035145.1|  78 LEDSDVVLVDGLRSEYELDRFEDAFG--D-DFVLVSIEAPFDLRAERLLDRGRD---DSDVDREALKERE 141
                                       777899*******************8..5.899********************5...678*****99865 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.5e-07   0.00075       2     134 ..       7     175 ..       6     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.5e-07
                                       EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT.....-HHHHHHHHHHHTTSS--.HHHHHHHHHHHHHCHG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                               ADK   2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevksg.....telGkeakevmdkgelvp.devvvklvkeeleked 72 
                                       +G Pg+GKG  a++++++ g++ ++ Gd++R+e ++       + G+ ak++ ++  l +     + l++ ele++ 
  gi|313124881|ref|YP_004035145.1|   7 VGLPGSGKGE-AASVAREAGVPVVTMGDVIRNECRERgldpaEHHGRIAKALREEEGLDAiAARSLPLIEAELEDS- 81 
                                       79*******6.66799*****************9875222224678888888877766331334567888888876. PP

                                       TTTEEEEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                               ADK  73 kkkgfllDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg........................... 122
                                         +  l+DG  R+  + +++e+    +  +  +++++++p ++  eRl++                           
  gi|313124881|ref|YP_004035145.1|  82 --DVVLVDGL-RSEYELDRFED----AFGDDFVLVSIEAPFDLRAERLLDrgrddsdvdrealkereerelgfgmgt 151
                                       ..78899997.44444555555....344444456778888888888877777788887777777777777777777 PP

                                       ............GSHHHHHHHHHH CS
                                       ............xxxxxxxxxxxx RF
                               ADK 123 ............DneetvkkRlet 134
                                                   D+ e  ++R++t
  gi|313124881|ref|YP_004035145.1| 152 vmdradvviqntDSLERFRERIQT 175
                                       776666666666666666666655 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0025       7.4       2      39 ..       3      41 ..       2      56 .. 0.82
   2 ?    6.1   0.0    0.0027         8     125     176 ..     108     165 ..      98     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0025
                                      EEEEEESTTSSHHHHHHHHHHTT-EEEE.HHHHHHHTTC CS
                              CoaE  2 ivgltGgiasGKstvanlfadlgvpivD.aDlvArqvve 39
                                      ++g  G  +sGK  +a++ ++ gvp+v   D++  + +e
  gi|313124881|ref|YP_004035145.1|  3 VIGTVGLPGSGKGEAASVAREAGVPVVTmGDVIRNECRE 41
                                      688888889*****************9724666655555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0027
                                       EEEEE--HHHHHHHHHHC....CTSTHHHHHHHHHHS--..HHHHHHH-SEEEE-.SS CS
                              CoaE 125 vlvvdvelelqveRlvar....dgvseeevkaiiaaQls..eeerlaladvvldNdss 176
                                        ++++++++l+ eRl++r    ++v++e +k++ +  l       + +advv++N  s
  gi|313124881|ref|YP_004035145.1| 108 LVSIEAPFDLRAERLLDRgrddSDVDREALKEREERELGfgMGTVMDRADVVIQNTDS 165
                                       46799999999999999854434899999999999887522678899********766 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   4.4e-05      0.13      32      70 ..      11      88 ..       2      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                                      -TTHHHHHHHHHHTT--EEE--SSHH........................................HH--TEEEEEET CS
                     PEP-utilizers 32 GGmtSHaAivArelgiPaVvgvgeati.......................................elkegdlitvDg 70
                                      G+    aA vAre g+P+V   + ++                                        el++ d++ vDg
  gi|313124881|ref|YP_004035145.1| 11 GSGKGEAASVAREAGVPVVTMGDVIRNecrergldpaehhgriakalreeegldaiaarslplieaELEDSDVVLVDG 88
                                      677788***********9988777777888888888888888888888888888888888888887777778888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1124.62
//
Query:       gi|313124882|ref|YP_004035146.1|  [L=139]
Description: hypothetical protein Hbor_00960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-09   37.4   2.7    4.9e-08   33.3   2.7    2.1  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   2.7   2.7e-12   4.9e-08       3     112 ..       8     104 ..       6     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.7e-12
                                       EEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.HHHHH CS
                       RNA_binding   3 evrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.keLlk 78 
                                       ++ + v+ TE  ++V++a++n++p+ e           ++ +   + +e       ++l+++ e+l e++i +  ++
  gi|313124882|ref|YP_004035146.1|   8 RIVVPVRDTEVTDRVEDAVRNIFPNVE-----------FEREAGQIVGE------THSLEEFSEKLHEQAIlDTARR 67 
                                       67789*******************886...........45444444444......4568888888888888777888 PP

                                       CCHCCB-TTSEEEEEEEHHHHHTT---BESSSS....E CS
                       RNA_binding  79 eleervdekgklylrldKQaaylgklslvegdd....v 112
                                       e+++r d+++ + + l KQaa++++++++ g       
  gi|313124882|ref|YP_004035146.1|  68 EFSKR-DDESGFSFALKKQAAFKDVVNFSVGNPdelgD 104
                                       88886.669*******************8765455552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 808.47
//
Query:       gi|313124883|ref|YP_004035147.1|  [L=348]
Description: hypothetical protein Hbor_00970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1916.11
//
Query:       gi|313124884|ref|YP_004035148.1|  [L=185]
Description: cation transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-21   76.0  10.8    3.1e-21   76.0  10.8    1.4  2  MgtE      Divalent cation transporter
  ------ inclusion threshold ------
        1.8    8.2   8.2        2.9    7.6   1.5    2.3  2  DUF697    Domain of unknown function (DUF697)


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         1     9e+03      79      83 ..      18      22 ..       6      39 .. 0.49
   2 !   76.0  10.8   3.4e-25   3.1e-21       1     123 [.      49     178 ..      49     179 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1
                                      HHHHH CS
                              MgtE 79 llaaa 83
                                      lla +
  gi|313124884|ref|YP_004035148.1| 18 LLALT 22
                                      22222 PP

  == domain 2  score: 76.0 bits;  conditional E-value: 3.4e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-......CTSHHHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekk.lkkvllkelrvvlllgvilgllifllalllgw.....slllalvv 71 
                                       +Pv +g++Gnlg++la+r+sta+hlg+l+ + +++ l+ ++++ + l+v+++ l+++ a+ l++      l +++v+
  gi|313124884|ref|YP_004035148.1|  49 VPVTIGTAGNLGSILAARLSTAFHLGTLSFDpTDEELVGNAIATVALSVTVFPLVGVGAWGLTSllggtRLSVWTVL 125
                                       69************************99888889**********************999977778888889999999 PP

                                       HHHHHHHHHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  72 glalvlvllaaall.ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       +++l+  +++a+l+ +++ + ++++++++lDPd ++iPl+t   D+lg+++l+
  gi|313124884|ref|YP_004035148.1| 126 SVSLASGVVLAVLAvVVTLAATYAAYQFELDPDDVVIPLVTNSCDVLGVVVLF 178
                                       99**999999999999999999******************************9 PP

>> DUF697  Domain of unknown function (DUF697)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.7    0.0023        21      69     109 ..       2      42 ..       1      77 [. 0.74
   2 ?    7.6   1.5   0.00033       2.9      88     132 ..     103     147 ..      82     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0023
                            DUF697  69 lgyegaqrLarsvlknlaglGlvelgtdllkqllslnlatk 109
                                       ++++  + ++r +l  l++l+lvelg+ l+ + ++++l+++
  gi|313124884|ref|YP_004035148.1|   2 PTEWTVRAITRAMLPVLLALTLVELGSGLVLGSFEAQLLQY 42 
                                       58899999*********************777777744433 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00033
                            DUF697  88 lGlvelgtdllkqllslnlatklsaraaQGvvagllTarvGlsai 132
                                       +G+ ++g   l + + l+++t+ls+ +a Gvv ++l  +v l+a 
  gi|313124884|ref|YP_004035148.1| 103 VGVGAWGLTSLLGGTRLSVWTVLSVSLASGVVLAVLAVVVTLAAT 147
                                       4555555555555555688******************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1142.16
//
Query:       gi|313124885|ref|YP_004035149.1|  [L=193]
Description: cation transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-20   74.0   8.9    1.6e-20   73.7   7.0    1.8  2  MgtE      Divalent cation transporter
  ------ inclusion threshold ------
        5.7    5.7   5.3        8.7    5.0   5.3    1.3  1  DUF4781   Domain of unknown function (DUF4781)
        5.9    6.0  17.0        8.9    5.4  17.0    1.4  1  CitMHS    Citrate transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.19   1.1e+03      35      53 ..      17      35 ..       2      46 .. 0.64
   2 !   73.7   7.0   2.7e-24   1.6e-20       1     123 [.      49     180 ..      49     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.19
                                      HHHHHHHHHHHHHHHHHHH CS
                              MgtE 35 vllkelrvvlllgvilgll 53
                                       l+ +l+ +l+ g++lg +
  gi|313124885|ref|YP_004035149.1| 17 ALVASLVGGLIAGIVLGGM 35
                                      4445555566666666554 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 2.7e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-......CTSHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekk...lkkvllkelrvvlllgvilgllifllalllgw.....slllal 69 
                                       +P++l+++Gn++  l +ri talh+g++e++    ++ l+  ++++l +g++ ++++++ ++l+ +      + l +
  gi|313124885|ref|YP_004035149.1|  49 VPALLATRGNVYGSLGARIATALHQGLIEPRvtaGDRRLRAAAAAALGNGLLASAFAAVAVFLVLSalgnrVAPLPV 125
                                       69**************************9998644999999999999999999999998888766666666666666 PP

                                       HHHHHHHHHHHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  70 vvglalvlvllaaall.ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       +vg+a+++ ll+ a+l  + v+++++ +++g +Pd+ ++P++t+ gD++g+l+l+
  gi|313124885|ref|YP_004035149.1| 126 LVGIAVLAGLLSGAVLiAVVVTVVFAGYRRGRNPDTLVGPIVTTTGDVFGILFLL 180
                                       7***************86666777999*************************997 PP

>> DUF4781  Domain of unknown function (DUF4781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   5.3    0.0015       8.7      94     142 ..     114     163 ..      91     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0015
                           DUF4781  94 stvvglva..avpvgaaalatPvaapvllaalvvgvgsavYstgRsiqrLv 142
                                       s++++ va   v vg+a la  +++ vl+a +vv+v+ a+Y  gR+  +Lv
  gi|313124885|ref|YP_004035149.1| 114 SALGNRVAplPVLVGIAVLAGLLSGAVLIA-VVVTVVFAGYRRGRNPDTLV 163
                                       5666666644566788889999*******9.99************988886 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  17.0    0.0015       8.9      38     123 ..      57     169 ..       7     192 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0015
                                       x.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  38 i.............................llllgamiigaaleetGlfdrlaakllrlaggkrdllvllvlltall 85 
                                                                     l  ++a  +g++l  + ++  +a +l+  a g+r  ++++ ++ a+l
  gi|313124885|ref|YP_004035149.1|  57 GnvygslgariatalhqglieprvtagdrrLRAAAAAALGNGLLASAFAA-VAVFLVLSALGNRVAPLPVLVGIAVL 132
                                       03333333344466666666777777777777889999999999665555.55555555555555799999999999 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  86 safvsndgvvlimipivlslakrlkklppllliplala 123
                                       ++++s  + +++++ +v++ ++r +++p  l+ p+++ 
  gi|313124885|ref|YP_004035149.1| 133 AGLLSGAVLIAVVVTVVFAGYRR-GRNPDTLVGPIVTT 169
                                       99999999**************9.99999998887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1149.52
//
Query:       gi|313124886|ref|YP_004035150.1|  [L=464]
Description: signal recognition particle subunit ffh/srp54 (srp54) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-63  211.4   0.4    1.8e-62  210.5   0.1    1.6  2  SRP54            SRP54-type protein, GTPase domain
    6.8e-29  100.4   3.4    6.8e-29  100.4   3.4    2.6  3  SRP_SPB          Signal peptide binding domain
    1.8e-19   69.7   3.1    3.1e-19   69.0   0.3    2.7  2  SRP54_N          SRP54-type protein, helical bundle domain
    0.00012   21.5   0.0    0.00032   20.1   0.0    1.7  1  Zeta_toxin       Zeta toxin
    0.00013   22.1   0.0     0.0003   20.8   0.0    1.7  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0029   17.5   0.0     0.0068   16.3   0.0    1.6  1  APS_kinase       Adenylylsulphate kinase
     0.0045   16.4   0.0     0.0074   15.7   0.0    1.3  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0053   17.0   0.1      0.039   14.2   0.0    2.3  3  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.043   13.9   0.0    1.7  1  DCX              Doublecortin
      0.016   14.8   0.5       0.18   11.4   0.5    2.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.019   15.1   0.0      0.047   13.9   0.0    1.7  1  AAA_33           AAA domain
      0.023   15.1   0.0      0.058   13.8   0.0    1.6  1  AAA_16           AAA ATPase domain
      0.031   13.4   0.0      0.031   13.4   0.0    2.6  3  ArsA_ATPase      Anion-transporting ATPase
      0.031   14.0   0.1        0.1   12.3   0.0    2.0  2  AAA_24           AAA domain
      0.049   14.1   0.2       0.12   12.8   0.2    2.0  1  AAA_23           AAA domain
      0.051   14.1   0.1       0.26   11.9   0.0    2.3  2  AAA_18           AAA domain
      0.076   12.9   0.0       0.17   11.8   0.0    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.083   11.8   0.0       0.15   11.0   0.0    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.085   12.3   0.0       0.17   11.3   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
      0.089   12.5   0.2       0.25   11.1   0.2    1.7  1  E3_UbLigase_EDD  E3 ubiquitin ligase EDD
      0.095   12.4   0.0       0.21   11.3   0.0    1.6  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.097   12.6   0.0       0.26   11.2   0.0    1.6  1  AAA_31           AAA domain
       0.13   11.9   0.4       0.71    9.5   0.0    2.3  2  Thymidylate_kin  Thymidylate kinase
       0.14   11.5   0.1       0.39   10.0   0.1    1.7  1  DUF1611          Domain of unknown function (DUF1611_C) P-loo
       0.16   11.9   0.0       0.39   10.7   0.0    1.7  1  ResIII           Type III restriction enzyme, res subunit
        3.6    7.1   5.6       0.83    9.2   1.0    2.3  3  AAA_25           AAA domain
        4.2    7.9   7.1       0.34   11.4   0.2    2.5  2  Spectrin         Spectrin repeat


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.5   0.1   2.7e-65   1.8e-62       2     196 .]      98     290 ..      97     290 .. 0.98
   2 ?   -3.2   0.0       8.2   5.4e+03      45      75 ..     294     324 ..     292     333 .. 0.63

  Alignments for each domain:
  == domain 1  score: 210.5 bits;  conditional E-value: 2.7e-65
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                       + ill+GlqG+GKTtt+aK+a +++++g +++++ +DtfR++A++Q k++ e+++v++++   e+dp+++a++++e+
  gi|313124886|ref|YP_004035150.1|  98 QTILLAGLQGSGKTTTAAKMAWWFSTKGLRAAVIQTDTFRPGAYDQAKQMCERAEVEFYGDPDEEDPVKIARDGLEA 174
                                       689*************************************************************************9 PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                        ++  +d+ +vDTaGr++ +++l++e+++i ++v+pd++llvlda++gq a  qa++F++++gi+gv +tklDg+ak
  gi|313124886|ref|YP_004035150.1| 175 TED--ADIHIVDTAGRHALEDALIDEIEDIDSAVNPDRSLLVLDAAIGQGAKDQARQFDDSIGIDGVAITKLDGTAK 249
                                       887..89********************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       gG+al++++e+++ i f+g+Ge+++d+e+f+p+ ++srllg
  gi|313124886|ref|YP_004035150.1| 250 GGGALTAVNETDSSIGFLGTGETVQDIERFEPNGFISRLLG 290
                                       ***************************************95 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.2
                                       HHHHHHHHHHTTEEEEESSTTSCHHHHHHHH CS
                             SRP54  45 veQLktlaeklgvpvikkkeeadpaavakea 75 
                                       ++QL++  e++ ++  +++ + dp +++k +
  gi|313124886|ref|YP_004035150.1| 294 LKQLSERVERAMAETQEEEDDWDPEDIMKGS 324
                                       4566666666666655555555888887765 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.7   2.5e+03      13      35 ..     287     309 ..     283     321 .. 0.70
   2 !  100.4   3.4     1e-31   6.8e-29       2      98 ..     325     426 ..     324     427 .. 0.91
   3 ?   -1.8   0.1       7.6   5.1e+03      11      27 ..     427     445 ..     424     451 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.7
                                       HHHCCCCCCHHHHCCC.....H. CS
                           SRP_SPB  13 qikkmGplskllsmiPgmsaeak 35 
                                       ++  mG+l++l + +   +ae++
  gi|313124886|ref|YP_004035150.1| 287 RLLGMGDLKQLSERVERAMAETQ 309
                                       66789999999999887665532 PP

  == domain 2  score: 100.4 bits;  conditional E-value: 1e-31
                                       SCTHHHHHHHHHHHCCCCCCHHHHCCC...........H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHH CS
                           SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsae......akaeeeaekklkrieaiidSMTkeErdspekllkesRkr 72 
                                       ftl+d+++q++ +++mGpl+++l+miPg++         +a++ ++++++ + +i+dSMT++E+++p+ ++ +sR+r
  gi|313124886|ref|YP_004035150.1| 325 FTLKDMQKQMEAMNRMGPLDQVLDMIPGLGGGfkdqlpDDAMDVTQDRMRSFDVIMDSMTEAELENPR-TIGASRVR 400
                                       9***************************998876655544448999**********************.6669**** PP

                                       HHHHHTTS-HHHHHHHHHHHHHHHHH CS
                           SRP_SPB  73 RiArGsGtsvqevnellkqfeqmkkm 98 
                                       RiArGsG + + v+ell+q+++m+++
  gi|313124886|ref|YP_004035150.1| 401 RIARGSGKDEETVQELLEQHKMMERT 426
                                       ***********************975 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 7.6
                                       HHHHHCCC..CCCHHHHCC CS
                           SRP_SPB  11 lqqikkmG..plskllsmi 27 
                                       ++q + mG  +++++++++
  gi|313124886|ref|YP_004035150.1| 427 IKQFQGMGdgDMQRMMKKL 445
                                       5666666422577777776 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.3   4.7e-22   3.1e-19       1      75 []       6      83 ..       6      83 .. 0.97
   2 ?   -0.5   0.0       2.2   1.4e+03      13      28 ..     403     418 ..     396     422 .. 0.65

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 4.7e-22
                                      HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                      Lg++l++ l kl+gks++de+d+ee+++e++++Ll+aDV v++v++l +++k++a++e+    ++ +++v kiv++eL
  gi|313124886|ref|YP_004035150.1|  6 LGSSLRGSLDKLQGKSRLDEDDVEEIVREIQRSLLSADVDVNLVMDLSSSIKERALNEEPpggTSARDHVLKIVYEEL 83
                                      899**************************************************9999666*****************8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.2
                                       CCSSCGHHHHHHHHHH CS
                           SRP54_N  13 sgkskideedleealk 28 
                                        ++s  dee+++e+l+
  gi|313124886|ref|YP_004035150.1| 403 ARGSGKDEETVQELLE 418
                                       3334449999999776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.8e-07   0.00032      15      56 ..      96     138 ..      88     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.8e-07
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                       +P  ill+G +G+GK+++a++++  +  ++ ++ ++++D++R+
  gi|313124886|ref|YP_004035150.1|  96 EPQTILLAGLQGSGKTTTAAKMAWWFStKGLRAAVIQTDTFRP 138
                                       799********************99987899**********96 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.6e-07    0.0003       9      64 ..     107     302 ..     100     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.6e-07
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt+aa++a  ++ +glr +++ +D+ ++ +        d+++                               
  gi|313124886|ref|YP_004035150.1| 107 GSGKTTTAAKMAWWFSTKGLRAAVIQTDTFRPGAY-------DQAKqmceraevefygdpdeedpvkiardgleate 176
                                       9***************************9988866.......22222233455667777777777888888888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|313124886|ref|YP_004035150.1| 177 dadihivdtagrhaledalideiedidsavnpdrsllvldaaigqgakdqarqfddsigidgvaitkldgtakggga 253
                                       88888888888888888888888888888888888888888888888888888888888888888888887777777 PP

                                       .......................................CCHCCCHHHH CS
                                       .......................................xxxxxxxxxx RF
                              CbiA  55 .......................................dlkrllelle 64 
                                                                              dlk+l+e +e
  gi|313124886|ref|YP_004035150.1| 254 ltavnetdssigflgtgetvqdierfepngfisrllgmgDLKQLSERVE 302
                                       7777777777777777777777777777777777777774444444443 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     1e-05    0.0068       2      44 ..      97     139 ..      96     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg 44 
                                       + +++l+Gl gsGK+t a +++    +kg ++ +++ d+ R g
  gi|313124886|ref|YP_004035150.1|  97 PQTILLAGLQGSGKTTTAAKMAWWFSTKGLRAAVIQTDTFRPG 139
                                       679***********************************99976 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05    0.0074       5      89 ..      78     162 ..      74     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                       EEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--....BTTCSSTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                             SMC_N   5 leienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk....skekasvkka 77 
                                       ++ e+   + g+++++p++++   + G  GSGK+     + + ++   +k lr++ ++   ++     ++k+  ++a
  gi|313124886|ref|YP_004035150.1|  78 IVYEELVGLIGESTDIPLEPQTILLAGLQGSGKTTTAAKMAWWFS---TKGLRAAVIQTDTFRpgayDQAKQMCERA 151
                                       55666666778999*******************************...56899999988887778877889999999 PP

                                       EEEEEEEETTEE CS
                                       xxxxxxxxxxxx RF
                             SMC_N  78 eveitfdnedkk 89 
                                       eve +  ++d++
  gi|313124886|ref|YP_004035150.1| 152 EVEFY-GDPDEE 162
                                       99985.444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.8   3.9e+03      70      91 ..      16      44 ..       2      55 .. 0.56
   2 !   14.2   0.0   5.9e-05     0.039       7      98 ..      99     216 ..      96     218 .. 0.80
   3 ?   -1.9   0.0       5.7   3.8e+03      40      81 ..     376     419 ..     360     431 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.8
                            AAA_22 70 a.......erlsseellealeqalrarav 91
                                      +        +++ ee+++ +++ l +++v
  gi|313124886|ref|YP_004035150.1| 16 KlqgksrlDEDDVEEIVREIQRSLLSADV 44
                                      23333334456666666777776666655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.9e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee...................erpevvfvtlpsstsskdllrellral 64 
                                        +++ G  G+GKTt++++++ ++      +                    er+ev f+  p ++++ +++r+ l+a+
  gi|313124886|ref|YP_004035150.1|  99 TILLAGLQGSGKTTTAAKMAWWFSTKGLRAAviqtdtfrpgaydqakqmcERAEVEFYGDPDEEDPVKIARDGLEAT 175
                                       58999******************876666668889999999999998888888888988888889999999988888 PP

                            AAA_22  65 glelka..erlsseellealeqalrarav.....ielliiD 98 
                                       ++   +   ++ +++l +al + +++ +      ++ll++D
  gi|313124886|ref|YP_004035150.1| 176 EDADIHivDTAGRHALEDALIDEIEDIDSavnpdRSLLVLD 216
                                       87776688777777777777777777776677777777777 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.7
                            AAA_22  40 pevv..fvtlpsstsskdl.lrellralglelkaerlsseellea 81 
                                        +v+  ++t +++++++++ ++++ r+   ++k+ + + +elle+
  gi|313124886|ref|YP_004035150.1| 376 FDVImdSMTEAELENPRTIgASRVRRIARGSGKD-EETVQELLEQ 419
                                       5556667777777888888666666666666666.6666666633 PP

>> DCX  Doublecortin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.4e-05     0.043       2      48 ..     368     419 ..     368     422 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-05
                               DCX   2 lnkrrfrsfealLdeltek.....vklpfg...VrklytldGrkvvssldeLedg 48 
                                       ++++r+rsf+ ++d +te+        + g   Vr++ + +G+++ + ++eL ++
  gi|313124886|ref|YP_004035150.1| 368 VTQDRMRSFDVIMDSMTEAelenpR--TIGasrVRRIARGSGKDEET-VQELLEQ 419
                                       6899***************976541..333346*********99999.9999765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00028      0.18       3     151 ..     100     245 ..      98     264 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleale 77 
                                       ++l+G  GsGKTt   ++     ++gl+ avi  +    +   +  + +  e  e+e  + +    ed +k +++ +
  gi|313124886|ref|YP_004035150.1| 100 ILLAGLQGSGKTTTAAKMAwwFSTKGLRAAVIQTDTFRPGAYDQAKQMC--ERAEVEFYGDPDE--EDPVKIARDGL 172
                                       7899**************9998899********9987643333332222..2345555455544..55555555544 PP

                                       HHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                              cobW  78 ereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                       e  e+ d+ ++ t G  a    ++ + e++ s+++ d  + v+Da ++ +  ++++++++d +   d + ++K D
  gi|313124886|ref|YP_004035150.1| 173 EATEDADIHIVDTAGrHALEDALIDEIEDIDSAVNPDRSLLVLDA-AIGQGAKDQARQFDDSIGI-DGVAITKLD 245
                                       444477777777777655555554456777777777777777777.5556666666666666654.555566666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     7e-05     0.047       2      39 ..     100     142 ..     100     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7e-05
                            AAA_33   2 vllvGlpGsGKstlaerl.....lkklgavllssdtlrrrlfg 39 
                                       +ll Gl+GsGK+t a ++      k l a ++ +dt+r   + 
  gi|313124886|ref|YP_004035150.1| 100 ILLAGLQGSGKTTTAAKMawwfsTKGLRAAVIQTDTFRPGAYD 142
                                       6899*************97775445555999999997765554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.7e-05     0.058      24     142 ..      97     216 ..      88     230 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p+ +ll G +G+GK++ + + +  ++++g  ++  ++d + +  +y++  q+++r   ++  +d++e++ +  +r+ 
  gi|313124886|ref|YP_004035150.1|  97 PQTILLAGLQGSGKTTTAAKMAWWFSTKGLRAAVIQTDTF-RPGAYDQAKQMCER-AEVEFYGDPDEEDPVKIARDG 171
                                       689****************999888888655555555555.33678999999955.999999999888777777777 PP

                            AAA_16 101 leeala.avpelagaeasrllellkrll...allsrderplvlvlD 142
                                       le++   ++  ++ a++++l ++l + +   + + +++r  +lvlD
  gi|313124886|ref|YP_004035150.1| 172 LEATEDaDIHIVDTAGRHALEDALIDEIediDSAVNPDR-SLLVLD 216
                                       666655633333333334554444444421122222233.555555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.7e-05     0.031       3      38 ..      99     134 ..      97     138 .. 0.95
   2 ?   -2.9   0.1       4.6     3e+03     152     181 ..     330     359 ..     319     386 .. 0.51
   3 ?    0.1   0.5      0.54   3.6e+02     151     189 ..     412     447 ..     406     449 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                        il++G  G GKtt +a +a + s kg +  +i tD
  gi|313124886|ref|YP_004035150.1|  99 TILLAGLQGSGKTTTAAKMAWWFSTKGLRAAVIQTD 134
                                       6999*******************************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHHHHHHHHHCCCSHCHHHHHH CS
                       ArsA_ATPase 152 leklvklkeklsplakqlvkllglggvsie 181
                                       ++k ++  + ++pl + l  + glgg   +
  gi|313124886|ref|YP_004035150.1| 330 MQKQMEAMNRMGPLDQVLDMIPGLGGGFKD 359
                                       455555555555555555444444444333 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHH CS
                       ArsA_ATPase 151 lleklvklkeklsplakqlvkllglggvsieealeelee 189
                                       ++++l++ +++++  +kq+    g+g+ ++++++++l++
  gi|313124886|ref|YP_004035150.1| 412 TVQELLEQHKMMERTIKQF---QGMGDGDMQRMMKKLQN 447
                                       5566777777777777777...56799999999999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015       0.1       3      33 ..      98     135 ..      96     217 .. 0.74
   2 ?   -2.8   0.1       6.7   4.5e+03     129     162 ..     306     339 ..     304     350 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtek 33 
                                       + il+ G +g+GKTt+a+++       g ++++i+t+ 
  gi|313124886|ref|YP_004035150.1|  98 QTILLAGLQGSGKTTTAAKMawwfstkGLRAAVIQTDT 135
                                       689*****************888888877777877775 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.7
                            AAA_24 129 ahektrkdedpegeakytrlepklgkktanelke 162
                                       a++++++d+ ++++ ++ ++++k  +k +++++ 
  gi|313124886|ref|YP_004035150.1| 306 AETQEEEDDWDPEDIMKGSFTLKDMQKQMEAMNR 339
                                       7888888888889988888888888888777764 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00019      0.12      12      78 ..      90     168 ..      78     448 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00019
                            AAA_23  12 dqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks............grgfeksdveiesegkvkayve 76 
                                        ++i +++   l+ G  G+GKTT    + + +  +  r                 ++ +e+++ve+  + + +  v+
  gi|313124886|ref|YP_004035150.1|  90 STDIPLEPQTILLAGLQGSGKTTTAAKMAWWFSTKGLRAAVIQtdtfrpgaydqaKQMCERAEVEFYGDPDEEDPVK 166
                                       467999******************99999999775333333224555555555556666666666666655555566 PP

                            AAA_23  77 lt 78 
                                       + 
  gi|313124886|ref|YP_004035150.1| 167 IA 168
                                       55 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00038      0.26       1      44 [.     100     160 ..     100     217 .. 0.63
   2 ?   -2.2   0.0       8.7   5.7e+03      40      61 ..     314     337 ..     293     389 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00038
                            AAA_18   1 IlltGtpGvGKttlakeL....skrlgf..............gvnlrdvakenglllevdpe 44 
                                       Ill+G +G+GKtt a       s + g+               ++ ++++   + +++ dp+
  gi|313124886|ref|YP_004035150.1| 100 ILLAGLQGSGKTTTAAKMawwfSTK-GLraaviqtdtfrpgaYDQAKQMCERAEVEFYGDPD 160
                                       99***********998774444222.123344555555555555555555555555555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.7
                            AAA_18  40 evdpe..aldeskrldedkldkll 61 
                                       ++dpe  +  ++   d++k+++++
  gi|313124886|ref|YP_004035150.1| 314 DWDPEdiMKGSFTLKDMQKQMEAM 337
                                       333333322222222333333333 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.17       2      35 ..     100     133 ..      99     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiKh 35 
                                       + ++g +gsGKTt   k+  +++ +glr ++i  
  gi|313124886|ref|YP_004035150.1| 100 ILLAGLQGSGKTTTAAKMAWWFSTKGLRAAVIQT 133
                                       6789***************************976 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00022      0.15      13      51 ..      95     133 ..      88     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                     TrwB_AAD_bind  13 retqhilivGttGsGKtqalekllrairargdraivlDl 51 
                                        e q il++G +GsGKt+++ k+  +   +g ra v+ +
  gi|313124886|ref|YP_004035150.1|  95 LEPQTILLAGLQGSGKTTTAAKMAWWFSTKGLRAAVIQT 133
                                       58899*************************999988755 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.17       4      41 ..     100     137 ..      98     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                       ++l Gl  sGK+t a+++a  ++ ++ +  vi++++++
  gi|313124886|ref|YP_004035150.1| 100 ILLAGLQGSGKTTTAAKMAWWFSTKGLRAAVIQTDTFR 137
                                       899*******************************9998 PP

>> E3_UbLigase_EDD  E3 ubiquitin ligase EDD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00038      0.25      19      43 ..      17      47 ..      14      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                   E3_UbLigase_EDD 19 LqgKSR......qvIiRELQrtnLdVNlAVN 43
                                      LqgKSR      + I+RE+Qr+ L   + VN
  gi|313124886|ref|YP_004035150.1| 17 LQGKSRldeddvEEIVREIQRSLLSADVDVN 47
                                      89999977775556********998888887 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.21       2      39 ..     100     137 ..      99     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                               PRK   2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsfl 39 
                                       I +ag  G+Gktt+a+k+   f  ++++aa+i+ d f 
  gi|313124886|ref|YP_004035150.1| 100 ILLAGLQGSGKTTTAAKMAWWFSTKGLRAAVIQTDTFR 137
                                       6689999************************9988774 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00039      0.26      12      40 ..     107     135 ..     100     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                       G GKTTt+ ++a +++++g +  ++  D+
  gi|313124886|ref|YP_004035150.1| 107 GSGKTTTAAKMAWWFSTKGLRAAVIQTDT 135
                                       99***********************9996 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0011      0.71       3      28 ..     104     130 ..     102     140 .. 0.88
   2 ?   -0.9   0.1       1.7   1.1e+03     132     162 ..     399     429 ..     395     441 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                       ESTTSSHHHHHHHHHHHHHHTTE..EE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.vv 28 
                                       Gl G+GKtt a++++ +++++g++ +v
  gi|313124886|ref|YP_004035150.1| 104 GLQGSGKTTTAAKMAWWFSTKGLRaAV 130
                                       99*******************998655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                                       HTSCCTTSSTT.TSHHHHHHHHHHHHHHHHHH CS
                   Thymidylate_kin 132 lkRlakrdeld.eeeeeqldflrkvrerylel 162
                                       ++R+a+++ +d e+++e l+ ++k++er  + 
  gi|313124886|ref|YP_004035150.1| 399 VRRIARGSGKDeETVQELLE-QHKMMERTIKQ 429
                                       56666666655155555555.55666555554 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00059      0.39      24      51 ..     108     135 ..      95     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00059
                           DUF1611  24 vGKrttaleleealeerGlkaafvaTgq 51 
                                        GK tta +++  +  +Gl+aa++ T+ 
  gi|313124886|ref|YP_004035150.1| 108 SGKTTTAAKMAWWFSTKGLRAAVIQTDT 135
                                       7*************************96 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00059      0.39      25      53 ..      98     126 ..      58     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                                       SEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgk 53 
                                       + +l++   G+GKT +aak+++ +++kg 
  gi|313124886|ref|YP_004035150.1|  98 QTILLAGLQGSGKTTTAAKMAWWFSTKGL 126
                                       578899999*************9998865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.2   4.1e+03      80     139 ..      25      81 ..      24      87 .. 0.55
   2 ?    9.2   1.0    0.0013      0.83      35     134 ..      99     200 ..      95     219 .. 0.58
   3 ?   -2.4   0.0       4.4   2.9e+03      85     138 ..     296     348 ..     292     354 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.2
                            AAA_25  80 EdsedelrrRlravgealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaiee 139
                                       Ed+ +e+ r +++ +  ++ d +l v+dl ++ +++ L ++  g    t++ d++ + + e
  gi|313124886|ref|YP_004035150.1|  25 EDDVEEIVREIQRSLLSADVDVNL-VMDLSSSiKERALNEEPPG---GTSARDHVLKIVYE 81 
                                       677777777777777776555555.6666666566555333222...34445555555555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0013
                            AAA_25  35 lallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.....rddarllvl 106
                                       ++llaG +g+GKtt a  +a   +t          +  +  +++++  + +    +++++e +      d+++++ +
  gi|313124886|ref|YP_004035150.1|  99 TILLAGLQGSGKTTTAAKMAWWFST----------KGLRAAVIQTDTFRPGAYDQAKQMCERAevefyGDPDEEDPV 165
                                       689***********99888865553..........455677777777777777777777766666666333333333 PP

                            AAA_25 107 d......lagv.eslpLfakdrggtlltadvdale 134
                                       +       a++  +++++++  +++l +a +d++e
  gi|313124886|ref|YP_004035150.1| 166 KiardglEATEdADIHIVDTAGRHALEDALIDEIE 200
                                       33334433444455666655555555455555544 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.4
                            AAA_25  85 elrrRlravgeal.rddarllvldlagveslpLfakdrggtlltadvdaleaaie 138
                                       +l +R+++++++  ++ ++++  d+++ +s +L ++++++++ ++ +  l+++++
  gi|313124886|ref|YP_004035150.1| 296 QLSERVERAMAETqEEEDDWDPEDIMK-GSFTLKDMQKQMEAMNR-MGPLDQVLD 348
                                       577788877744435566666666644.57777777776666443.345555555 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4       3.6   2.4e+03      10      52 ..     294     336 ..     291     341 .. 0.54
   2 ?   11.4   0.2   0.00052      0.34      30      54 ..     407     431 ..     400     448 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  10 adeleeWieekeellssedlgkdleevqallkkhkaleaelaa 52 
                                       +++l e  e ++++ ++e+   d+e++ +   ++k+++++++a
  gi|313124886|ref|YP_004035150.1| 294 LKQLSERVERAMAETQEEEDDWDPEDIMKGSFTLKDMQKQMEA 336
                                       4455555555555555555555555555555555555555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00052
                                       SSSHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  30 gkdleevqallkkhkaleaelaaqq 54 
                                       gkd e+vq+ll++hk +e+++++ q
  gi|313124886|ref|YP_004035150.1| 407 GKDEETVQELLEQHKMMERTIKQFQ 431
                                       89*******************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.73u 0.41s 00:00:01.13 Elapsed: 00:00:00.74
# Mc/sec: 1904.35
//
Query:       gi|313124887|ref|YP_004035151.1|  [L=318]
Description: phosphoglycerate dehydrogenase-like oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-50  169.8   0.0    5.1e-50  169.3   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.2e-16   60.5   0.0    1.4e-16   60.4   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
  ------ inclusion threshold ------
      0.054   13.7   0.1       0.19   11.9   0.0    1.8  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
       0.16   11.3   0.0       0.25   10.6   0.0    1.2  1  ThiF           ThiF family


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.3   0.0   1.1e-53   5.1e-50       2     178 .]     109     282 ..     108     282 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 1.1e-53
                                       HHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                      2-Hacid_dh_C   2 alllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                       + ll+l+r l e+ ++++++ew  ++     el+g+tv ++GlG+IGqa+ +rl +fg++ i++  +++k     ++
  gi|313124887|ref|YP_004035151.1| 109 GWLLMLARSLDEGIRRQQRREW--RQFQAFGELQGSTVTVVGLGAIGQAIGERLDPFGVETIGVRYTPEKGG-PTDE 182
                                       6789******************..77777779********************************99999777.6666 PP

                                       TCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--S CS
                      2-Hacid_dh_C  79 gvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfe 155
                                        + ++++e +l ++D+++l++plt+ t +li+a++l++++ +a l+N++RGg+vd++aL++ +++ ++++aalDv++
  gi|313124887|ref|YP_004035151.1| 183 VIGFDEIESALVQTDYLVLACPLTETTAGLIDADALKSLPTDAALVNVGRGGVVDTDALVRTIRRDRLRAAALDVTD 259
                                       7899************************************************************************* PP

                                       SSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 156 eeplpedspllelpnviltPHia 178
                                       +eplp+d+pl++++nv+ltPH++
  gi|313124887|ref|YP_004035151.1| 260 PEPLPHDHPLWDFENVLLTPHVS 282
                                       *********************95 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   3.1e-20   1.4e-16      12     128 ..      21     308 ..       4     314 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 3.1e-20
                                       HHHHHHTTE.EEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh  12 lellkeegv.evevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilV 87 
                                          l+e ++ e +v +  +te ++e+a+da ++  +    + ++vlea+ +L++ a a++G+D++ ld ++erG++V
  gi|313124887|ref|YP_004035151.1|  21 D-ELRE-RLpETTVIHRETTEATVEAAADAAVI--TGIH-LPDDVLEAAAELRLFAAASAGYDHLPLDRLRERGVTV 92 
                                       3.3333.57788888899999999977665555..5544.78*********************************** PP

                                       EE-TTTTHHHHHHHH.............................................................. CS
                                       xxxxxxxxxxxxxxx.............................................................. RF
                        2-Hacid_dh  88 tnvpgystesvAElt.............................................................. 102
                                       tn+ g++   +AE++                                                              
  gi|313124887|ref|YP_004035151.1|  93 TNASGVHGPNIAEHVigwllmlarsldegirrqqrrewrqfqafgelqgstvtvvglgaigqaigerldpfgvetig 169
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|313124887|ref|YP_004035151.1| 170 vrytpekggptdevigfdeiesalvqtdylvlacpltettaglidadalkslptdaalvnvgrggvvdtdalvrtir 246
                                       ***************************************************************************** PP

                                       ....................................T-BHHHHHHHHHHHHHHHHHHHTTCC CS
                                       ....................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ....................................aaTeeaqeniaeeaaenlvaflkges 128
                                                                           ++T +   + a++ a n++ ++++++
  gi|313124887|ref|YP_004035151.1| 247 rdrlraaaldvtdpeplphdhplwdfenvlltphvsGYTPQYWTRRADILARNIEHIFETGE 308
                                       *******************************************************9998865 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.4   1.8e+03      41      75 ..      30      66 ..      15      77 .. 0.56
   2 ?   11.9   0.0   4.3e-05      0.19       2     108 ..     144     249 ..     143     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.4
                                      TTEEE-SSHHHHHHHC..SEEEE-SSSHHHHHHHHHS CS
                     NAD_binding_2 41 egakaaesieelvasl..dvvitmvkagkavdevieg 75
                                      + +   e+ e+ v+++   +vit ++  ++v e   +
  gi|313124887|ref|YP_004035151.1| 30 TTVIHRETTEATVEAAadAAVITGIHLPDDVLEAAAE 66
                                      3444445555555555555566666665555555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.3e-05
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       + ++GlG +G+ + ++l   g +++++  t+ek      +++ ++++ie+++ + d  ++  + ++ +  +i+   l
  gi|313124887|ref|YP_004035151.1| 144 VTVVGLGAIGQAIGERLDPFGVETIGVRYTPEKGGPT--DEVIGFDEIESALVQTDYLVLACPLTETTAGLIDAdAL 218
                                       789***************************9987765..5789******************************9999 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHHTT CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelkekg 108
                                       ++l  ++ l++++   + dt  l + +++  
  gi|313124887|ref|YP_004035151.1| 219 KSLPTDAALVNVGRGGVVDTDALVRTIRRDR 249
                                       ***********99999999988887776665 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.7e-05      0.25      15      47 ..     138     170 ..     123     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.7e-05
                                       HHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  15 kLrdskvllvGaGglGsellknLalsGvgkltl 47 
                                       +L+ s+v +vG+G++G+ + + L   Gv+ + +
  gi|313124887|ref|YP_004035151.1| 138 ELQGSTVTVVGLGAIGQAIGERLDPFGVETIGV 170
                                       6899***************99999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1914.27
//
Query:       gi|313124888|ref|YP_004035152.1|  [L=205]
Description: threonine efflux protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-30  106.3   9.5    1.6e-30  106.0   9.5    1.1  1  LysE      LysE type translocator
  ------ inclusion threshold ------
      0.057   13.1   0.1      0.057   13.1   0.1    1.7  2  TerC      Integral membrane protein TerC family


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   9.5   1.8e-34   1.6e-30       2     191 ..      22     204 ..      21     205 .] 0.88

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 1.8e-34
                              LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlal 78 
                                       +l+l+pGp++++vl++g  +g+ +g+  alg+ +g +v+  +++lGla+Ll+aap + ++++++G++yL++lg++al
  gi|313124888|ref|YP_004035152.1|  22 ALILTPGPDTMYVLARG-MQGRSAGVRSALGISTGVLVHTAAAALGLAALLRAAPTAYRLVKYAGALYLIYLGLSAL 97 
                                       789**************.6777******************************************************* PP

                              LysE  79 rdakekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfslla 155
                                       rd      ++ ++       +f++g++++ +NPk+ lf+l++++++++  +      +++l  +  v + +++s +a
  gi|313124888|ref|YP_004035152.1|  98 RDDEFDPTVQTDAE-----GSFRRGVFVNALNPKVALFFLAFLPGFAGS-GSGAELRMFLLGGTYAVLTALYLSGVA 168
                                       *9876664333333.....58***************************5.44444455555556667788******* PP

                              LysE 156 flaarlsrrlsskkvlriinvvvgvlligfavklll 191
                                       f +  + + l+s++ +  +n + g ++++++v +++
  gi|313124888|ref|YP_004035152.1| 169 FASGQMGSMLASSRFSSGLNWLGGGVMVALGVGVAV 204
                                       **************99***************98765 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.3e-06     0.057      37      82 ..      51     101 ..      32     135 .. 0.69
   2 ?   -2.6   0.1      0.41   3.7e+03      58      58 ..     161     161 ..     138     200 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.3e-06
                              TerC  37 GilgAlvlRilli.llavallel....fdlilligglfLlytavkellekr 82 
                                       Gi   +++  ++  l  +all++    + l++++g+l+L+y++++ l++++
  gi|313124888|ref|YP_004035152.1|  51 GISTGVLVHTAAAaLGLAALLRAaptaYRLVKYAGALYLIYLGLSALRDDE 101
                                       5544444444433044455555555555*******************9876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.41
                              TerC  58 l 58 
                                       +
  gi|313124888|ref|YP_004035152.1| 161 A 161
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1307.77
//
Query:       gi|313124889|ref|YP_004035153.1|  [L=446]
Description: signal recognition particle-docking protein ftsy [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-70  235.6   0.4    5.9e-70  234.9   0.4    1.3  1  SRP54            SRP54-type protein, GTPase domain
    1.4e-15   57.2   0.5    1.4e-15   57.2   0.5    1.9  2  SRP54_N          SRP54-type protein, helical bundle domain
    4.3e-05   22.9   0.7    0.00025   20.4   0.2    2.1  2  Zeta_toxin       Zeta toxin
    5.2e-05   23.3   0.0    0.00014   22.0   0.0    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00015   21.5   0.1      0.015   15.0   0.0    2.7  2  Thymidylate_kin  Thymidylate kinase
    0.00015   21.7   0.0    0.00027   20.9   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
    0.00053   20.4   0.0    0.00053   20.4   0.0    2.8  1  AAA_16           AAA ATPase domain
    0.00066   19.3   0.2     0.0016   18.1   0.2    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0086   16.2   0.1      0.052   13.7   0.0    2.3  2  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.027   14.4   0.1    1.6  1  NTPase_1         NTPase
      0.012   16.1   0.1      0.012   16.1   0.1    2.8  3  AAA_17           AAA domain
      0.016   14.7   0.0      0.029   13.8   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
      0.027   14.8   0.1       0.14   12.4   0.0    2.1  2  AAA_22           AAA domain
       0.03   13.8   0.2       0.17   11.4   0.1    2.1  2  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.042   13.7   0.1       0.14   12.1   0.0    1.8  2  AAA_31           AAA domain
      0.068   13.2   0.0       0.15   12.1   0.0    1.7  1  AAA_14           AAA domain
      0.092   12.5   0.0       0.18   11.5   0.0    1.6  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.14   12.5   2.1       0.22   11.9   0.1    2.1  2  AAA_19           AAA domain
       0.21   11.5   9.8        0.3   10.9   9.8    1.2  1  SPX              SPX domain
       0.29   11.6   2.9       0.53   10.7   0.1    2.8  3  AAA              ATPase family associated with various cellul
       0.37   11.3   1.9        0.9   10.0   0.1    2.5  3  ABC_tran         ABC transporter
       0.48    8.9   4.4       0.67    8.4   4.4    1.2  1  Macoilin         Macoilin family


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.9   0.4   7.2e-73   5.9e-70       3     196 .]     250     443 ..     248     443 .. 0.99

  Alignments for each domain:
  == domain 1  score: 234.9 bits;  conditional E-value: 7.2e-73
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeaveka 79 
                                        +++ G++G+GKTt++aK+a++++k+g +v+l+  Dt+Ra+A eQ++ +ae+l+ ++i+++++ dpaav+++ave a
  gi|313124889|ref|YP_004035153.1| 250 TLIFTGVNGVGKTTSIAKMARYFEKQGLSVVLANGDTYRAGANEQIRKHAENLDTKIISHEQGGDPAAVIYDAVEYA 326
                                       6799************************************************************************* PP

                                       HHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSST CS
                             SRP54  80 keekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakg 156
                                       ++++idvvl DTaGrl++ ++lm++l+ki +vv+pd +l+v +a++gq+av+ ak+F+ea++i+g++ltk D+d++g
  gi|313124889|ref|YP_004035153.1| 327 EAHDIDVVLGDTAGRLHTSNDLMAQLEKIDRVVEPDLTLFVDEAVAGQDAVERAKQFNEAAEIDGAVLTKADADSNG 403
                                       ***************************************************************************** PP

                                       THHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 157 GaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       Gaa+sia+ +++Pi f+gvG+ ++d+e+fdper+v+rllg
  gi|313124889|ref|YP_004035153.1| 404 GAAISIAYVTGKPILFLGVGQGYDDIEQFDPERMVERLLG 443
                                       **************************************95 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       9.7   7.9e+03      46      55 ..      11      20 ..       5      32 .. 0.57
   2 !   57.2   0.5   1.8e-18   1.4e-15       3      75 .]     152     227 ..     151     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.7
                                      HHHHHHHHHH CS
                           SRP54_N 46 klienvkkka 55
                                      +++env+++a
  gi|313124889|ref|YP_004035153.1| 11 SFRENVEDTA 20
                                      4566665533 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 1.8e-18
                                       HHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N   3 kklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75 
                                       ++l++a +  +gk  i eedle+ l+ele+aLle+DV + v++++++ +++k vge +    + +q v+++++d+L
  gi|313124889|ref|YP_004035153.1| 152 GRLKRAAAFATGKVIIEEEDLEDPLWELEMALLESDVEMHVAEEILDTIREKMVGETRrqvETMGQLVQEALHDAL 227
                                       578888888899999****************************************777887669**********97 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.47   3.8e+02      61      99 ..     193     231 ..     189     237 .. 0.88
   2 !   20.4   0.2   3.1e-07   0.00025      10     145 ..     242     381 ..     235     392 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.47
                        Zeta_toxin  61 yeeilkadpkkaseltqkdaselvekllqeaiengynii 99 
                                       +eeil+   +k++  t++++ ++++ + ++++++ y++i
  gi|313124889|ref|YP_004035153.1| 193 AEEILDTIREKMVGETRRQVETMGQLVQEALHDALYDVI 231
                                       57888888899999*******************999998 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.1e-07
                        Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelh.Peyeeilka.dpkkaseltqkdasel 83 
                                       + + ++P+ ++  G  G GK++ ++++++++e ++ +vv  ++D++R+    + +++ ++ d k  s     d   +
  gi|313124889|ref|YP_004035153.1| 242 IAEADKPVTLIFTGVNGVGKTTSIAKMARYFEkQGLSVVLANGDTYRAGAnEQIRKHAENlDTKIISHEQGGDPAAV 318
                                       44679***************************44556677799****754033344333437777788888888999 PP

                        Zeta_toxin  84 vekllqeaiengyniivegtlrspdvvkklaealkkaGYevev.vvvavkkelSrlgvldRye 145
                                          ++++a  + +++++  t    ++ ++l+ +l+k  + ve  + + v+++++ +++ +R +
  gi|313124889|ref|YP_004035153.1| 319 IYDAVEYAEAHDIDVVLGDTAGRLHTSNDLMAQLEKIDRVVEPdLTLFVDEAVAGQDAVERAK 381
                                       999999999999999999999999999999999988777776424566666666666666665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.7e-07   0.00014       6      55 ..     255     372 ..     250     418 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.7e-07
                                       SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                              CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................ 54 
                                       +  GvGKTt  a++ar++ ++gl V+l   D+ +  ++      ++i++                            
  gi|313124889|ref|YP_004035153.1| 255 GVNGVGKTTSIAKMARYFEKQGLSVVLANGDTYRAGAN------EQIRKhaenldtkiisheqggdpaaviydavey 325
                                       5569************************9998855544......222222333555777777788888888888888 PP

                                       ..............................................C CS
                                       ..............................................x RF
                              CbiA  55 ..............................................d 55 
                                                                                      
  gi|313124889|ref|YP_004035153.1| 326 aeahdidvvlgdtagrlhtsndlmaqlekidrvvepdltlfvdeavA 372
                                       88888888888777777766655555555555555544444444331 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.8e-05     0.015       2      30 ..     254     282 ..     253     324 .. 0.84
   2 ?    3.7   0.0     0.052        42     103     140 ..     347     385 ..     341     396 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                                       EESTTSSHHHHHHHHHHHHHHTTE.EEEE CS
                   Thymidylate_kin   2 EGlDGaGKttqaellkerlkeegikvvlt 30 
                                        G++G+GKtt +++++++++++g++vvl 
  gi|313124889|ref|YP_004035153.1| 254 TGVNGVGKTTSIAKMARYFEKQGLSVVLA 282
                                       59***********************7664 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.052
                                       TCHHHHHHGGGTTSE-SEEEEEE..SSHHHHHTSCCTTSS CS
                   Thymidylate_kin 103 dldlvlslnedvllkPdltflld..vdpevalkRlakrde 140
                                       dl + l++ + v+ +Pdlt+++d  v  + a++R+++ +e
  gi|313124889|ref|YP_004035153.1| 347 DLMAQLEKIDRVV-EPDLTLFVDeaVAGQDAVERAKQFNE 385
                                       5555556666777.********966777788888777666 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   3.3e-07   0.00027       2      55 ..     248     301 ..     247     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.3e-07
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHH CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseed 55 
                                       +v++ +tG+ g GK+t   +++++ +++g sv+l +Gd+ R g n+++  ++e+
  gi|313124889|ref|YP_004035153.1| 248 PVTLIFTGVNGVGKTTSIAKMARYFEKQGLSVVLANGDTYRAGANEQIRKHAEN 301
                                       799*************999************************99988766655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   6.4e-07   0.00053      21      91 ..     245     304 ..     235     401 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.4e-07
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaes 91 
                                       ++ p  ++++G  GvGK++ + + +r++ek+g  ++ ++ d ++++             e +r+ ++++++
  gi|313124889|ref|YP_004035153.1| 245 ADKPVTLIFTGVNGVGKTTSIAKMARYFEKQGLSVVLANGDTYRAG-----AN------EQIRKHAENLDT 304
                                       56678999***********************999999999999222.....22......333333333222 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   1.9e-06    0.0016       3     152 ..     251     399 ..     248     410 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.9e-06
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT....EEEETTTTECCHCTT-HHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve...ivelenGciCctlredllkele 74 
                                       +++tG  G GKTt + ++    +++gl++ +  ++ +  + ++++ +++++    i++ e+G+ + ++  d++    
  gi|313124889|ref|YP_004035153.1| 251 LIFTGVNGVGKTTSIAKMAryFEKQGLSVVLANGDTYRAGANEQIRKHAENLdtkIISHEQGGDPAAVIYDAV---- 323
                                       689****************665667777777779999999988887666333455999999999999555555.... PP

                                       HHHHHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-H CS
                              cobW  75 aleereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKt 150
                                       +++e + ++dv+l  t G l + + ++ + e++ + ++ d +++v +a +   ++  ++ k  ++ a  d  vl+K+
  gi|313124889|ref|YP_004035153.1| 324 EYAEAH-DIDVVLGDTAGrLHTSNDLMAQLEKIDRVVEPDLTLFVDEAVA--GQDAVERAKQFNEAAEIDGAVLTKA 397
                                       556666.8**********88888888999999999999999999888833..2333333344445555577888888 PP

                                       HH CS
                              cobW 151 Dl 152
                                       D 
  gi|313124889|ref|YP_004035153.1| 398 DA 399
                                       86 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.5   3.6e+03      31      47 ..     198     215 ..     176     233 .. 0.56
   2 !   13.7   0.0   6.3e-05     0.052       3     134 ..     252     395 ..     251     400 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.5
                            AAA_33  31 dtlrrrlfg.tdqqsktd 47 
                                       dt+r++++g t +q +t 
  gi|313124889|ref|YP_004035153.1| 198 DTIREKMVGeTRRQVETM 215
                                       558888888433333333 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.3e-05
                            AAA_33   3 llvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgtdqqskt......dytrvldr.....lyqilnela 63 
                                       ++ G++G+GK+t + ++    +k+g  +vl + dt+r    ++ +++ +            ++       + + + +
  gi|313124889|ref|YP_004035153.1| 252 IFTGVNGVGKTTSIAKMaryFEKQGlsVVLANGDTYRAGANEQIRKHAEnldtkiI-----SHeqggdPAAVIYDAV 323
                                       899**********9988443566669777788888777666533333332222221.....2212222344666888 PP

                            AAA_33  64 rkalsagrnvildatnlsrrerarflklarrlgvpvri.vvvetdeetlkeRlakRaangddrsevpeeald 134
                                       + a ++ ++v+l  t  + ++  ++++ +++++  v+  +++ +de+++ +   +Ra++ ++++e + ++l 
  gi|313124889|ref|YP_004035153.1| 324 EYAEAHDIDVVLGDTAGRLHTSNDLMAQLEKIDRVVEPdLTLFVDEAVAGQDAVERAKQFNEAAEIDGAVLT 395
                                       888899999999888777777777777777666444445788889999999999999988888888888876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.3e-05     0.027       2      30 ..     251     279 ..     250     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                       ++ TG  GvGKtT + k+++  +++g++v
  gi|313124889|ref|YP_004035153.1| 251 LIFTGVNGVGKTTSIAKMARYFEKQGLSV 279
                                       678**********************9987 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4       5.4   4.4e+03      42      68 ..      12      37 ..       3      45 .. 0.56
   2 ?   -1.5   0.1       3.7     3e+03      26      68 ..     162     203 ..     157     229 .. 0.60
   3 ?   16.1   0.1   1.4e-05     0.012       1     109 [.     254     368 ..     254     388 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.4
                                      SHHHHCTSHHHHHHHHHHHHHHHHHHH CS
                            AAA_17 42 ardemrklpleekkelqkeaaekiaee 68
                                       r+++ +   eek e q+eaae+ a++
  gi|313124889|ref|YP_004035153.1| 12 FRENV-EDTAEEKAEAQAEAAEAAADT 37
                                      33333.334566666777777777665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHH CS
                            AAA_17  26 aGdllreeakrgglakardemrklpleekkelqkeaaekiaee 68 
                                       +G +++ee   +     + em+ l+ +++ ++ +e+ ++i+e+
  gi|313124889|ref|YP_004035153.1| 162 TGKVIIEEEDLEDP-LWELEMALLESDVEMHVAEEILDTIREK 203
                                       56666655333322.2344566666666666666666666665 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.4e-05
                                       EE-TTSSHHHHHHHHH...HHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHHHHH..HHHHHHHHHH..HHHH CS
                            AAA_17   1 lGgPGsGKgtqceklv...ekygfthlsa.Gdllreeakrgglakardemrklpleekk..elqkeaaeki..aeea 69 
                                       +G+ G+GK+t ++k++   ek g++++ a Gd  r+ a+++   k+ +++++  +++++  +  + + +++  ae+ 
  gi|313124889|ref|YP_004035153.1| 254 TGVNGVGKTTSIAKMAryfEKQGLSVVLAnGDTYRAGANEQIR-KHAENLDTKIISHEQggDPAAVIYDAVeyAEAH 329
                                       69*************944445588876445******9987754.566666644333333113333333333213444 PP

                                       HSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                            AAA_17  70 kkkgvlvdghprikeqagfldglpkevleelkpdaiille 109
                                       + + vl d+  r+ ++++++++l+k + + ++pd+ ++++
  gi|313124889|ref|YP_004035153.1| 330 DIDVVLGDTAGRLHTSNDLMAQLEK-IDRVVEPDLTLFVD 368
                                       5677999999999999999999885.89999999999887 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.6e-05     0.029       4      52 ..     251     299 ..     249     328 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGG CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsak 52 
                                       +++tG+  +GK+t  +++a+++e+++ svv+ + ++++   ++   +++
  gi|313124889|ref|YP_004035153.1| 251 LIFTGVNGVGKTTSIAKMARYFEKQGLSVVLANGDTYRAGANEQIRKHA 299
                                       589*********************************9966555333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.4     2e+03      59      95 ..     195     231 ..     181     239 .. 0.65
   2 ?   12.4   0.0   0.00018      0.14       8     110 ..     251     353 ..     245     374 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.4
                            AAA_22  59 ellralglelka.erlsseellealeqalraraviell 95 
                                       e+l  + ++  +  r + e + +++++al+++    ++
  gi|313124889|ref|YP_004035153.1| 195 EILDTIREKMVGeTRRQVETMGQLVQEALHDALY-DVI 231
                                       3333333333333344777888999999998765.555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00018
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlsseel 78 
                                       l+ tG  G+GKTt+++++++ ++         ++ ++v l+++ + +  ++e  r+  ++l++      ++++  ++
  gi|313124889|ref|YP_004035153.1| 251 LIFTGVNGVGKTTSIAKMARYFE---------KQGLSVVLANGDTYRAGANEQIRKHAENLDTkiisheQGGDPAAV 318
                                       6889****************994.........444444444444333332222222222222234445555666666 PP

                            AAA_22  79 lealeqalraravielliiDEaqhlr.s...eeale 110
                                       +    ++++a++   +++ D a +l  s   +++le
  gi|313124889|ref|YP_004035153.1| 319 IYDAVEYAEAHDI-DVVLGDTAGRLHtSndlMAQLE 353
                                       6555556666666.6777777777754333444444 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0002      0.17       7      65 ..     252     309 ..     248     313 .. 0.83
   2 ?   -1.9   0.0       2.3   1.9e+03      29      59 ..     327     356 ..     312     368 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                              KdpD   7 iflGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkevey 65 
                                       if+G ++GvGkt ++ + a+  +++g  vv++  +t +    e+  ++ e +++k +++
  gi|313124889|ref|YP_004035153.1| 252 IFTG-VNGVGKTTSIAKMARYFEKQGLSVVLANGDTYRAGANEQIRKHAENLDTKIISH 309
                                       4555.68*************************999998888888888888887777666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.3
                              KdpD  29 keegvdvviglvethgrkete.alleglevip 59 
                                       +++ +dvv+g  +t gr +t+ +l+++le i+
  gi|313124889|ref|YP_004035153.1| 327 EAHDIDVVLG--DTAGRLHTSnDLMAQLEKID 356
                                       3344444444..34444443313445555544 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.5   2.1e+03      64     104 ..     167     209 ..     144     233 .. 0.57
   2 ?   12.1   0.0   0.00017      0.14      12      62 ..     258     309 ..     252     360 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.5
                            AAA_31  64 ieeknikeaiiktkvenldlipssidLaeaeielvelekk.....e 104
                                       iee+++++ +      ++ l+ s++++  ae  l ++++k     +
  gi|313124889|ref|YP_004035153.1| 167 IEEEDLEDPLW---ELEMALLESDVEMHVAEEILDTIREKmvgetR 209
                                       45555555555...23356677777776666666666555444441 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00017
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyev 62 
                                       GvGKTT+  ++a  + k+g  v l + D+  + ++ +++ + +++++++++ 
  gi|313124889|ref|YP_004035153.1| 258 GVGKTTSIAKMARYFEKQGLSVVLANGDTYRAGANeQIRKHAENLDTKIISH 309
                                       9*************************99876544413343455566666554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.15       5      60 ..     251     310 ..     247     390 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd...kkladpe....kllelilekl 60 
                                       l+ tG+  vGKTt + ++++    +  s++  n d+ r    +   + +    +l++ i ++ 
  gi|313124889|ref|YP_004035153.1| 251 LIFTGVNGVGKTTSIAKMARYFEKQGLSVVLANGDTYRAganE---QIRkhaeNLDTKIISHE 310
                                       688***************9877766677777777777764331...22111224555555553 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.18       2      34 ..     254     286 ..     253     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDP 34 
                                       +G+ G+GKtt + +++ ++e++g sv + N D+
  gi|313124889|ref|YP_004035153.1| 254 TGVNGVGKTTSIAKMARYFEKQGLSVVLANGDT 286
                                       799*********************999998775 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.62     5e+02      89     142 ..     182     242 ..      23     246 .. 0.67
   2 ?   11.9   0.1   0.00027      0.22       4     111 ..     242     370 ..     239     383 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.62
                            AAA_19  89 elle...eaeeekklqeee.llivDEfqdvdelqyrLlkallgek.kklllvG..DpdQli 142
                                       +lle   e +  +++ ++    +v E+    e++ +L+++ l+++  +++ vG  D dQ i
  gi|313124889|ref|YP_004035153.1| 182 ALLEsdvEMHVAEEILDTIrEKMVGETRRQVETMGQLVQEALHDAlYDVISVGqfDFDQRI 242
                                       3333444222223333444466777887777888899988888887779999877777776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00027
                            AAA_19   4 avealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgr..Aakelrerlaalgae.......... 68 
                                       ++ea k  +l+ t+  G GKT+ + ++ ++++++g +    +l+   t r  A +++r+  ++l+ +          
  gi|313124889|ref|YP_004035153.1| 242 IAEADKPVTLIFTGVNGVGKTTSIAKMARYFEKQG-L--SVVLANGDTYRagANEQIRKHAENLDTKiisheqggdp 315
                                       4424444455667889*********9999999988.4..45666655655115678888887777777777777777 PP

                            AAA_19  69 ....................atTiHrlalldfddlltealelleeaeeekklqeee.llivDEf 111
                                                            +T  rl   + +dl+        + e+ + + e + +l+vDE+
  gi|313124889|ref|YP_004035153.1| 316 aaviydaveyaeahdidvvlGDTAGRL--HTSNDLM-------AQLEKIDRVVEPDlTLFVDEA 370
                                       666666555555444333333333333..3333333.......233333334466669999996 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   9.8   0.00037       0.3      24     173 ..       4     147 ..       2     188 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                               SPX  24 qLKKlIkkvqrele.slgleaetlrellnrpedskkksse........rtepstsaaadesgnsaadasssepkdea 91 
                                       +LKK+++  +   e +   +ae   e  + + d++++++e        +       a+++++   +++  ++++d+a
  gi|313124889|ref|YP_004035153.1|   4 GLKKKLNSFRENVEdTAEEKAEAQAEAAEAAADTTDADTEtetpdaetH------DADATEAVGGENEPTETTADSA 74 
                                       79*********88855555556666666666666666555542222221......2222222222222222222222 PP

                               SPX  92 e.slprrsplsrssrssssygglvssppsansssssddssesnpadssssssssesesssssspsllrrlfs..ese 165
                                       + s  + ++++++ ++  +  +  ++++ ++++++s+d  +             ++  + +++ s+ +rl+s  ++e
  gi|313124889|ref|YP_004035153.1|  75 TvSDADDTTSETEAETADAQASPAPDSETPETGDESGDTAD------------DSAADEADEAASSRERLASdaANE 139
                                       22111111111111111111111111111111111111111............222222222333333333332222 PP

                               SPX 166 sreekser 173
                                         e+ +++
  gi|313124889|ref|YP_004035153.1| 140 ALESGQKE 147
                                       22222222 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       7.7   6.3e+03      65      84 ..     120     139 ..     119     146 .. 0.71
   2 ?   -0.4   0.0       1.7   1.4e+03      32      55 ..     198     221 ..     181     232 .. 0.76
   3 ?   10.7   0.1   0.00066      0.53       2      48 ..     252     297 ..     251     441 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.7
                                       ETGGGHHHHHTTCCCHHHHH CS
                               AAA  65 DEidalaksrsgseseeeer 84 
                                       DE+d+ a+sr++ +s+ +++
  gi|313124889|ref|YP_004035153.1| 120 DEADEAASSRERLASDAANE 139
                                       99999999995555554444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                                       TTCSSSSTTHHHHHHHHHHHHHHH CS
                               AAA  32 sellskyvgesekkirelfkeake 55 
                                        ++++k+vge+ ++++ + + ++e
  gi|313124889|ref|YP_004035153.1| 198 DTIREKMVGETRRQVETMGQLVQE 221
                                       467789999999999988777655 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00066
                                       EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSSSTTHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakel...gvefleisgsellskyvgesekkire 48 
                                       +++G  G+GKT+ +  +a+ +   g +++  +g + +      ++++ir+
  gi|313124889|ref|YP_004035153.1| 252 IFTGVNGVGKTTSIAKMARYFekqGLSVVLANGDTYR----AGANEQIRK 297
                                       899***************9973333555555555555....222222332 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.7     3e+03      35      35 ..      64      64 ..       6     157 .. 0.57
   2 ?   -0.9   0.0       2.7   2.2e+03      38      84 ..     161     211 ..     151     245 .. 0.55
   3 ?   10.0   0.1    0.0011       0.9      14      60 ..     251     298 ..     242     360 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.7
                                      S CS
                                      x RF
                          ABC_tran 35 l 35
                                       
  gi|313124889|ref|YP_004035153.1| 64 N 64
                                      1 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.7
                                       SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.......HHHTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx RF
                          ABC_tran  38 teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.......esdee 84 
                                       + G++ ++++dl++   + ++ e++ l+ + ++    ++ ++       e +++
  gi|313124889|ref|YP_004035153.1| 161 ATGKVIIEEEDLED---PLWELEMALLESDVEMHVAEEILDTirekmvgETRRQ 211
                                       56888888888888...5555555555555333333333333222244322222 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0011
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrke 60 
                                       + ++G nG GK+t ++ +a+  +++  ++ l + d+ +    e+ rk+
  gi|313124889|ref|YP_004035153.1| 251 LIFTGVNGVGKTTSIAKMARYFEKQGLSVVLANGDTYRaGANEQIRKH 298
                                       6789****************9999888887775555544444444444 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.4   0.00082      0.67     242     386 ..      15     165 ..       3     239 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00082
                          Macoilin 242 nkkdsslklpeleyrekkksakssrsdskkkhehnesvdsklqekeymenkskskrlsksessgsesel..lveesv 316
                                       n +d++++ +e + +  + +a  +++d++ +  ++e++d++++e+   en+ +++   + + s+   ++  +  e +
  gi|313124889|ref|YP_004035153.1|  15 NVEDTAEEKAEAQAEAAEAAADTTDADTETETPDAETHDADATEAVGGENEPTETTADSATVSDADDTTseTEAETA 91 
                                       33445555555555555444444445555555555777777777777777665555444433332222200233444 PP

                          Macoilin 317 kskssssssssnknskkasagsagssnssskkhsessksvtsss....ssknskkqklpaGkssaalkdaaens 386
                                       ++++s++  s+++++ ++s+++a+ s +  ++  +ss+++  s     + ++ +k++ +aG+ ++a   a+ ++
  gi|313124889|ref|YP_004035153.1|  92 DAQASPAPDSETPETGDESGDTADDSAADEADEAASSRERLASDaaneALESGQKESSGAGRLKRAAAFATGKV 165
                                       45555555555566666666555555555555555555444444333233344666777777766554444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1536  (0.0856713); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); expected 17.9 (0.001)
Passed Fwd filter:                        46  (0.00256568); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.86u 0.38s 00:00:01.24 Elapsed: 00:00:00.53
# Mc/sec: 2548.03
//
Query:       gi|313124890|ref|YP_004035154.1|  [L=153]
Description: prefoldin subunit alpha/subunit 5 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-22   78.5  11.1    3.7e-22   78.5  11.1    2.1  1  Prefoldin        Prefoldin subunit
    2.1e-06   27.6  19.4    6.5e-05   22.8   4.8    3.6  2  Prefoldin_2      Prefoldin subunit
    5.7e-06   25.4  20.8    0.00091   18.2   4.0    2.0  2  Spc7             Spc7 kinetochore protein
    3.7e-05   23.2  14.8     0.0085   15.5   0.6    2.1  2  GAS              Growth-arrest specific micro-tubule binding
    0.00027   20.7  16.6      0.044   13.6   0.6    2.3  2  SKA2             Spindle and kinetochore-associated protein 2
    0.00038   21.0  27.9      0.034   14.7   7.6    2.1  2  APG6_N           Apg6 coiled-coil region
     0.0008   19.1  13.1      0.035   13.8   0.8    2.2  2  Syntaxin         Syntaxin
     0.0019   18.3  23.4      0.024   14.8   4.5    2.2  2  Tropomyosin_1    Tropomyosin like
     0.0023   18.0  23.1      0.068   13.2  11.6    2.2  2  DHR10            Designed helical repeat protein 10 domain
     0.0027   17.4   2.8        0.4   10.4   1.7    2.2  2  DUF3287          Protein of unknown function (DUF3287)
     0.0029   17.9  20.9     0.0086   16.4   4.9    2.5  2  DUF5082          Domain of unknown function (DUF5082)
     0.0033   16.8  15.9      0.017   14.5   5.2    2.0  2  Dynamitin        Dynamitin
     0.0039   17.2   9.1      0.096   12.7   0.1    2.2  2  Laminin_II       Laminin Domain II
      0.004   17.8  13.9       0.12   13.0   0.1    2.1  2  YabA             Initiation control protein YabA
     0.0044   16.8   6.0     0.0044   16.8   6.0    3.2  2  DivIC            Septum formation initiator
     0.0048   15.8  22.2      0.089   11.7   3.5    2.0  2  DUF812           Protein of unknown function (DUF812)
     0.0056   17.1  31.1       0.24   11.8  16.1    2.3  2  ZapB             Cell division protein ZapB
     0.0068   15.7  26.3      0.083   12.2   5.4    2.1  2  DUF3450          Protein of unknown function (DUF3450)
     0.0069   16.8   6.5        1.1    9.7   3.8    2.1  2  HCMV_UL139       Human Cytomegalovirus UL139 protein
     0.0071   15.1  12.7      0.069   11.8   1.9    2.0  2  AAA_13           AAA domain
     0.0077   16.7  17.2      0.042   14.3   2.7    2.5  2  NPV_P10          Nucleopolyhedrovirus P10 protein
     0.0078   16.3  21.8      0.036   14.2  10.1    2.1  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
     0.0085   16.3  15.2       0.17   12.1   0.8    2.3  2  Fib_alpha        Fibrinogen alpha/beta chain family
  ------ inclusion threshold ------
      0.012   15.9  20.4      0.028   14.7   4.5    2.7  3  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.013   15.5   9.3       0.37   10.8   0.5    2.2  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.015   15.6   4.9      0.015   15.6   4.9    3.1  2  TSC22            TSC-22/dip/bun family
      0.017   15.0  19.9        0.4   10.6   2.0    2.2  2  Ax_dynein_light  Axonemal dynein light chain
      0.018   14.5  17.1       0.15   11.5   1.4    2.3  2  DUF4618          Domain of unknown function (DUF4618)
      0.018   15.1  13.4       0.25   11.5   7.5    2.1  2  DUF4337          Domain of unknown function (DUF4337)
      0.019   15.4  16.0        0.2   12.1   0.4    2.2  2  CENP-H           Centromere protein H (CENP-H)
      0.021   14.9  11.6      0.061   13.4   0.2    2.3  2  COG2             COG (conserved oligomeric Golgi) complex com
      0.021   15.0  12.3        0.4   10.9   2.2    2.4  2  XhlA             Haemolysin XhlA
      0.025   14.9  29.8      0.076   13.3   1.1    2.1  2  OmpH             Outer membrane protein (OmpH-like)
      0.026   14.2   7.3        0.2   11.3   0.5    2.4  2  DUF4988          Domain of unknown function
      0.029   12.7  18.2       0.14   10.5   8.7    2.0  2  MAD              Mitotic checkpoint protein
       0.03   13.7  14.0      0.047   13.0  14.0    1.3  1  DUF4407          Domain of unknown function (DUF4407)
      0.031   13.9  17.0       0.42   10.1   2.3    2.1  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
      0.034   14.2  23.2      0.038   14.0   3.3    2.2  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.035   14.5   2.4      0.035   14.5   2.4    2.6  1  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
      0.036   14.1  10.2       0.29   11.2   0.9    2.6  3  DUF1515          Protein of unknown function (DUF1515)
      0.048   13.9  23.7       0.25   11.6   5.1    2.4  2  Spc24            Spc24 subunit of Ndc80
       0.05   13.8   2.5       0.05   13.8   2.5    2.8  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
      0.052   13.8  20.5      0.091   13.0   8.5    2.2  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.059   13.0  14.7       0.24   11.0   1.4    2.2  2  DUF4795          Domain of unknown function (DUF4795)
      0.061   14.5   0.9      0.061   14.5   0.9    2.6  2  SOGA             Protein SOGA
      0.077   12.6  10.7        1.8    8.1   6.0    2.0  2  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
      0.094   12.5  15.0       0.94    9.3   1.6    2.1  2  SKA1             Spindle and kinetochore-associated protein 1
        0.1   12.7  13.5       0.92    9.6   1.2    2.3  2  ORF6C            ORF6C domain
        0.1   13.3  14.1       0.49   11.2   1.0    2.3  2  Occludin_ELL     Occludin homology domain
       0.11   11.9  24.3       0.23   10.9  13.0    2.0  2  Golgin_A5        Golgin subfamily A member 5
       0.11   12.5  19.3       0.28   11.2   2.8    2.7  2  DUF1664          Protein of unknown function (DUF1664)
       0.12   12.6  20.4      0.095   12.9   1.8    2.1  2  ATG16            Autophagy protein 16 (ATG16)
       0.12   12.5  11.3        1.3    9.2   0.7    2.9  2  Vps51            Vps51/Vps67
       0.13   10.9  14.7       0.53    8.8   2.0    2.0  2  FapA             Flagellar Assembly Protein A
       0.15   12.3   9.5       0.62   10.4   0.6    2.2  2  DUF948           Bacterial protein of unknown function (DUF94
       0.17   12.4  17.7       0.88   10.0   5.4    2.1  2  AAA_23           AAA domain
       0.17   11.1  12.7          2    7.6   0.1    2.0  2  TMPIT            TMPIT-like protein
       0.18   11.4  16.5       0.18   11.3   0.8    2.1  2  Paralemmin       Paralemmin
       0.19   12.2  19.4       0.53   10.8   2.8    2.3  2  Spectrin         Spectrin repeat
       0.19   11.1  15.9       0.42   10.0   6.3    2.0  2  Cluap1           Clusterin-associated protein-1
       0.21    9.9   4.5       0.75    8.1   0.1    2.0  2  Hemagglutinin    Haemagglutinin
       0.24   11.8  30.4       0.65   10.4  14.2    2.7  2  YlqD             YlqD protein
       0.29   10.0  19.6      0.048   12.6   2.6    2.1  2  IFT57            Intra-flagellar transport protein 57
       0.38    8.6  10.9       0.74    7.7   0.5    2.0  2  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.38    9.5  18.9       0.76    8.5   3.8    2.3  2  Tektin           Tektin family
       0.41   10.5  16.7       0.14   12.1   2.3    2.1  2  Sec34            Sec34-like family
        0.5   10.5   9.9        1.3    9.1   0.9    2.9  2  DUF2730          Protein of unknown function (DUF2730)
       0.52   10.7  21.0       0.12   12.8   3.6    3.3  3  FlaC_arch        Flagella accessory protein C (FlaC)
       0.58   10.5  23.0        2.6    8.4  11.3    2.6  2  Tup_N            Tup N-terminal
       0.59   10.2  17.7       0.68   10.0   6.3    2.1  2  ADIP             Afadin- and alpha -actinin-Binding
       0.59   10.3  12.2        3.4    7.8   2.7    2.6  2  bZIP_1           bZIP transcription factor
        0.6   10.2  17.9        1.6    8.8   2.6    2.2  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.66    9.0  19.4        8.1    5.4  19.4    1.9  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.69    9.3  12.4        1.1    8.6   6.9    2.1  2  FliD_C           Flagellar hook-associated protein 2 C-termin
       0.73    9.7   3.1         10    6.0   0.1    2.7  2  MtrG             Tetrahydromethanopterin S-methyltransferase,
       0.84    9.4  20.1       0.77    9.6   1.9    2.1  2  DUF724           Protein of unknown function (DUF724)
       0.98    9.4  15.4        2.1    8.3   7.0    2.4  2  AAA_lid_9        AAA lid domain
        1.2    9.4   9.1        2.8    8.1   3.9    2.2  2  PHM7_cyt         Cytosolic domain of 10TM putative phosphate 
        1.3    9.4  19.3       0.85   10.0   1.1    2.2  2  Muted            Organelle biogenesis, Muted-like protein
        1.3    8.9  18.2        2.3    8.1   8.5    2.2  2  DASH_Spc19       Spc19
        1.4    8.2  26.8        2.1    7.5   6.4    2.1  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
        1.4    8.9   6.1         31    4.6   0.0    3.0  3  Borealin         Cell division cycle-associated protein 8
        1.5    8.0  20.7       0.29   10.4   1.1    2.2  2  DUF4763          Domain of unknown function (DUF4763)
        1.6    8.8  29.1        1.2    9.2   8.9    2.9  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        1.7    9.1  18.5        2.6    8.5   8.7    2.4  2  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
        1.8    8.4  12.6        0.2   11.5   4.7    2.4  2  Synaptobrevin    Synaptobrevin
        1.9    8.3  24.9          2    8.2   4.1    2.6  3  DUF4515          Domain of unknown function (DUF4515)
        2.1    6.4  20.7       0.39    8.8   3.3    2.1  2  EzrA             Septation ring formation regulator, EzrA
        2.1    8.4  21.9        1.5    8.9   4.0    2.7  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        2.2    8.1  23.1       0.92    9.4  12.3    2.1  2  DUF2570          Protein of unknown function (DUF2570)
        2.5    8.5  19.8        1.2    9.5   2.8    2.9  3  Lzipper-MIP1     Leucine-zipper of ternary complex factor MIP
        2.7    7.1  10.5        1.3    8.2   2.9    2.0  2  Tho2             Transcription factor/nuclear export subunit 
        2.8    7.8  13.6        5.7    6.8   0.5    3.6  2  DASH_Dam1        DASH complex subunit Dam1
        3.1    7.7  10.6        6.9    6.5   5.2    2.2  2  CLP_protease     Clp protease
        3.2    7.4  19.3        3.4    7.3   2.3    2.3  2  Med4             Vitamin-D-receptor interacting Mediator subu
        3.4    7.4  15.7       0.79    9.4   8.4    2.0  2  TEX13            Testis-expressed sequence 13 protein family
        3.4    7.6  11.5        6.7    6.7   0.5    2.2  2  DUF4446          Protein of unknown function (DUF4446)
        4.4    5.7   6.5        6.9    5.1   6.5    1.2  1  FUSC             Fusaric acid resistance protein family
        4.6    6.6  13.2       0.23   10.9   1.4    2.1  2  HNOBA            Heme NO binding associated
        4.6    7.0  12.1        3.7    7.3   0.2    2.3  2  USP8_interact    USP8 interacting
        4.6    6.9   8.9        6.6    6.4   0.1    2.1  2  DUF932           Domain of unknown function (DUF932)
        4.8    7.0  19.8        3.8    7.3   3.4    2.4  2  Nsp1_C           Nsp1-like C-terminal region
        4.8    7.6  19.5        7.7    6.9   9.7    2.5  2  CLZ              C-terminal leucine zipper domain of cyclic n
        4.9    6.0  12.9        6.3    5.6   5.4    2.1  2  Vps53_N          Vps53-like, N-terminal
        4.9    7.4  12.8          5    7.4   1.6    2.1  2  zf-C4H2          Zinc finger-containing protein
        5.1    7.6  20.7        2.4    8.7   9.2    2.2  2  GPS2_interact    G-protein pathway suppressor 2-interacting d
        5.2    7.6  20.4        7.1    7.2   7.8    2.2  2  DUF16            Protein of unknown function DUF16
        5.9    6.9   9.2        1.2    9.1   4.1    2.0  2  FAD-SLDH         Membrane bound FAD containing D-sorbitol deh
        6.4    7.7  17.1        2.7    9.0   1.0    2.3  2  PRKG1_interact   cGMP-dependent protein kinase interacting do
        6.4    7.3  18.9       0.98    9.9   4.2    2.4  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
        6.6    6.8   8.4         14    5.8   2.4    2.2  2  Cauli_DNA-bind   Caulimovirus DNA-binding protein
        6.7    5.8  15.9        3.2    6.9   2.2    2.1  2  DLP_helical      Dynamin-like helical domain
        6.8    6.3  19.6        3.5    7.3   2.5    2.2  2  GrpE             GrpE
        6.9    6.8  35.5       0.14   12.2   6.2    2.6  2  TolA_bind_tri    TolA binding protein trimerisation
          7    5.4   7.4         15    4.3   7.4    1.4  1  LMBR1            LMBR1-like membrane protein
        8.3    5.7  18.1         64    2.8  18.1    2.0  1  CASP_C           CASP C terminal
        8.8    6.1  26.9        1.6    8.5   3.2    2.1  2  ERM              Ezrin/radixin/moesin family
        8.9    6.5  17.3        8.2    6.6   3.3    2.5  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
        9.9    5.6   8.3       0.71    9.3   0.9    2.2  2  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5  11.1   2.5e-24   3.7e-22       1     120 []      19     135 ..      19     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 2.5e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHH CS
                         Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyvekslee 77 
                                       +++e+e+l+ +++ l+++++e+++++e+++tl++   g +v+vplg+g+y++a+v+d d+v+v lG +y++e + ++
  gi|313124890|ref|YP_004035154.1|  19 IEQEIEELEGDVSDLQQEKSEIDEAIEAIETLET---GSTVQVPLGGGAYLRADVQDIDEVIVGLGGDYAAEQEQDD 92 
                                       689*******************************...**************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittleanlaqlyqk 120
                                       Aie l  k +++++ +  ++ e+ +l d+  +le++++q +q+
  gi|313124890|ref|YP_004035154.1|  93 AIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQ 135
                                       *****99999999999999999999999999999999999986 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   6.7   2.6e-05    0.0039       1      52 [.      10      61 ..       5      76 .. 0.80
   2 !   22.8   4.8   4.3e-07   6.5e-05      52     105 ..      82     135 ..      72     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEET CS
                       Prefoldin_2  1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvG 52
                                      q+l  ++q ++q++++l+ ++ +l+++++e+++++e++e+l+   +v+   G
  gi|313124890|ref|YP_004035154.1| 10 QQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETGSTVQVPLG 61
                                      6778888999999999999999999****************99987765444 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 4.3e-07
                                       TTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  52 GdvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklqq 105
                                       Gd   +q++++++e L  ++++++++i++++ ++++le e +el+++ q+++qq
  gi|313124890|ref|YP_004035154.1|  82 GDYAAEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQ 135
                                       677789**********************************************97 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   4.0     6e-06   0.00091     198     241 ..       6      49 ..       4      57 .. 0.91
   2 !   13.4   8.9   0.00017     0.026     194     257 ..      87     148 ..      66     153 .] 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6e-06
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelke 241
                                       +++L++l +el+++++eiee++ ++++lq+++ e++e+ie++++
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIET 49 
                                       6899***********************************99986 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00017
                              Spc7 194 esidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervl 257
                                       e+ + + +e+lr + +++++ i++ + e+++l+++  ele++ +++++q+++   ++++ ++++
  gi|313124890|ref|YP_004035154.1|  87 EQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQ--QMQQMQQMQ 148
                                       6678999***************************************9999864..444445544 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   5.6e-05    0.0085      53      98 ..       6      51 ..       2      55 .. 0.73
   2 !   12.4   7.7   0.00048     0.072      95     156 ..      88     149 ..      65     153 .] 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.6e-05
                               GAS 53 sqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkele 98
                                      +q+ ++l+++L++ e+e+eeL+ ++ + +++k++++++ + +++le
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLE 51
                                      6777788888888888888888888888888887777666666555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00048
                               GAS  95 kelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqe 156
                                       +e+++ +++l++++++  +r+++v+ e+ +l+++  +  q++qq  +  +    ++++++qe
  gi|313124890|ref|YP_004035154.1|  88 QEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       67888899999999999999999999999999888887766666544444444444444444 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.6   0.00029     0.044      41      76 ..      10      45 ..       3      57 .. 0.86
   2 !   11.4   9.7    0.0014      0.21      45      88 ..     106     149 ..      85     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00029
                              SKA2 41 vkLlerlkkvkeelqaLkeqceellaekkelidkir 76
                                       +L ++l+++ +e+++L+ ++ +l++ek e+ ++i+
  gi|313124890|ref|YP_004035154.1| 10 QQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIE 45
                                      6899*************************8877765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0014
                              SKA2  45 erlkkvkeelqaLkeqceellaekkelidkirttlvanrellqq 88 
                                       er+++v+ e++ L+++  el ++ +++ ++++++ +++++ +q+
  gi|313124890|ref|YP_004035154.1| 106 ERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       89******************************999777777764 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   7.6   0.00022     0.034      47      89 ..       7      49 ..       4      55 .. 0.78
   2 !   12.5  12.3    0.0011      0.16      45     104 ..      90     149 ..      71     153 .] 0.59

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00022
                            APG6_N 47 eeleeleeeleklekeeeelleeLkelekereeleaelaalee 89
                                      ++l++l +el+++e+e eel+    +l++e++e++++++a+e 
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIET 49
                                      4677888888888888888888888888888888888888775 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0011
                            APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwre 104
                                       qd+ +e+l+ + + +++  ++ + e+ +le+e +ele++ ++ +++ ++ + ++ + ++e
  gi|313124890|ref|YP_004035154.1|  90 QDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       345555555555555555555555555555555555555555555555555555555554 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.8   0.00023     0.035       1      40 [.       9      48 ..       9      58 .. 0.89
   2 !   10.3   5.5    0.0028      0.42       6      50 ..     106     150 ..     102     153 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00023
                          Syntaxin  1 leeffkeveeikkeiekleeevkklkkqneesktstraks 40
                                      l+++ +e ++i++eie+le +v++l+++++e+ ++ +a +
  gi|313124890|ref|YP_004035154.1|  9 LQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48
                                      578889*************************998887765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0028
                          Syntaxin   6 keveeikkeiekleeevkklkkqneesktstraksvklkkrmesd 50 
                                       + + +++ ei++le+e ++l++q +++ +++++++++  ++m++d
  gi|313124890|ref|YP_004035154.1| 106 ERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQED 150
                                       6799********************************955566654 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   4.5   0.00016     0.024      35      78 ..       7      50 ..       4      54 .. 0.87
   2 !    9.5  10.9    0.0067         1       2      53 ..      94     146 ..      93     153 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 0.00016
                     Tropomyosin_1 35 qeiksLtkknqqleeevekleeklkeakekaeesekkktnneal 78
                                      q++++L++ +q++e+e+e+le ++++ +++++e +++    e+l
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETL 50
                                      89999*********************999999988877777766 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0067
                     Tropomyosin_1   2 lnsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqle.eevek 53 
                                       +++L+l +++  e+  +++ ++ +le+e+ e eq+ +++++++qq + +++ +
  gi|313124890|ref|YP_004035154.1|  94 IEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQmQQMQQ 146
                                       689**************************************999866233444 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   3.6    0.0027       0.4      28      70 ..       9      51 ..       3      55 .. 0.54
   2 !   13.2  11.6   0.00045     0.068      43      99 ..      92     149 ..      74     153 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0027
                             DHR10 28 lqvvekdlrsciklleeieaelakleeakkklkelrdaleeke 70
                                      lq++ ++l+++ + +ee+e ++  l+++k++++e+ +a+e++e
  gi|313124890|ref|YP_004035154.1|  9 LQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLE 51
                                      4555555555555555555555555555555555555555544 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00045
                             DHR10  43 eeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenae.eklerlre 99 
                                       + iea   k+++ ++++++ + +++++e e++ele++ +++q+q ++ + +++++++e
  gi|313124890|ref|YP_004035154.1|  92 DAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQmQQMQQMQE 149
                                       66888888999999******************************99776244444444 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.051       7.6      64     101 ..       9      46 ..       6      73 .. 0.50
   2 !   10.4   1.7    0.0027       0.4      69     120 ..      92     143 ..      85     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.051
                           DUF3287  64 HrrlcderqklgkkrqtleaRiarveRklreleseprd 101
                                        ++l++e q + + ++ le  +  ++ +  e++     
  gi|313124890|ref|YP_004035154.1|   9 LQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEA 46 
                                       34444444444444444444444444444444444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0027
                           DUF3287  69 derqklgkkrqtleaRiarveRklreleseprdWeeleldevariPdsllvy 120
                                       d  + l++k +++  Ria+v+ ++  le e  + e+   + ++++ +  ++ 
  gi|313124890|ref|YP_004035154.1|  92 DAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQ 143
                                       666789***********************99999998888888777666655 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   4.9   5.7e-05    0.0086       9      56 ..       6      53 ..       5      57 .. 0.92
   2 ?    8.2   6.7     0.019       2.8      82     120 ..     100     138 ..      82     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.7e-05
                           DUF5082  9 qaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplns 56
                                      q+q  +l++e++a+e+ Ie+L+   + l++ek++++++++++e+ +  
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETG 53
                                      8999**************************************998765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.019
                           DUF5082  82 yvdkldelidaieeEIerLenqiseaqgvldtlqsqlns 120
                                        +d +de i+a++ EI++Le + se+++  ++ q+q+++
  gi|313124890|ref|YP_004035154.1| 100 KQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQ 138
                                       589999999999999999999999999999999999875 PP

>> Dynamitin  Dynamitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   3.0    0.0084       1.3      94     139 ..       6      51 ..       4      59 .. 0.68
   2 !   14.5   5.2   0.00011     0.017      72     139 ..      83     148 ..      63     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0084
                         Dynamitin  94 eqklqRLqrEveeleeEvekakeaakeseeeeldpvelaeqleslq 139
                                       +q lq L  E++ +e+E+e+ + + ++ ++e+++  e +e +e+l+
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLE 51 
                                       5667777777777777777777777666666666666666666664 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.00011
                         Dynamitin  72 gykasssreyeladegeeketleqklqRLqrEveeleeEvekakeaakeseeeeldpvelaeqleslq 139
                                        y+a+++++  +     +++++ ++++  q E++ le+E ++ +++a++ +++   +++ ++q++++q
  gi|313124890|ref|YP_004035154.1|  83 DYAAEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQM--QQQQMQQMQQMQ 148
                                       57777555555554444*************************999998763333..333456666655 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   0.00064     0.096      16      64 ..       6      50 ..       3      78 .. 0.60
   2 ?    6.7   5.1     0.046       6.9      36      82 ..      97     143 ..      85     151 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00064
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkL 64
                                      ++ql++lsq+l+ ++++++e++++v     ++++ +  i++A +++ +L
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVS----DLQQEKSEIDEAIEAIETL 50
                                      45555555555555555555555533....3333334444444444444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.046
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II  36 inrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       ++ + + ++e + + +  i d ++++++Le++a+q+ +++++ ++++
  gi|313124890|ref|YP_004035154.1|  97 LRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQ 143
                                       55555566666666666666666666666666666666655544433 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   0.00078      0.12      15      54 ..       7      46 ..       3      65 .. 0.69
   2 ?    7.1   9.5     0.054       8.2       8      65 ..      92     149 ..      86     153 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00078
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXX CS
                              YabA 15 eqleelleeleelkeelaelleenaeLeleneklrerlee 54
                                      +ql++l++el+++++e++el  + ++L+ e++++ e +e 
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEA 46
                                      6777777777777777777777777777777777666643 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkke 65 
                                       d++e+l  + +++ e++++++ e+++l +e +eLe + +++++++++++ ++ ++ +e
  gi|313124890|ref|YP_004035154.1|  92 DAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       67888888889999999*************************9997666666655544 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   6.0   2.9e-05    0.0044      23      59 ..       6      42 ..       4      45 .. 0.95
   2 !    9.6   6.7     0.005      0.76      14      62 ..      82     130 ..      76     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                             DivIC 23 kqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59
                                      +q++++l +el+++ +e+eeLe  v+dL+++++ i+e
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDE 42
                                      69*******************************9998 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.005
                                       XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXX CS
                             DivIC  14 kgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerAR 62 
                                       + + a ++++  i+al  + +++ +++++ + e++dL+++ + +e++A 
  gi|313124890|ref|YP_004035154.1|  82 GDYAAEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQ 130
                                       567778999****************************99999****996 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   3.5   0.00059     0.089     329     374 ..       6      51 ..       4      60 .. 0.87
   2 !   10.2  10.8    0.0016      0.24     325     381 ..      87     143 ..      71     151 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00059
                            DUF812 329 eeeleelqeqieeleskieeleeeikklessikqveeeleeekeen 374
                                       +++l++l+++++++e++ieele ++++l+++ ++++e++e+ ++  
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLE 51 
                                       68899***************************99999999877655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0016
                            DUF812 325 kkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekev 381
                                       ++++++ +e+l+ + ++++++i++++ ei++le++ +++e+++++++++ ++++ + 
  gi|313124890|ref|YP_004035154.1|  87 EQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQ 143
                                       455666666666666666677777766666666666666666666666666555443 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   7.0     0.003      0.45      24      64 ..       6      46 ..       6      58 .. 0.69
   2 !   11.8  16.1    0.0016      0.24       7      59 ..      95     147 ..      86     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.003
                              ZapB 24 qmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64
                                      q+++++L +e ++ ++e++ele  ++ l++e++++ e +++
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEA 46
                                      55666777777777777777777777777777766666654 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0016
                              ZapB   7 eqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawq 59 
                                       e L  k ++  ++i++ q ei++L+ e++el++++++++++ +q + ++ +++
  gi|313124890|ref|YP_004035154.1|  95 EALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQM 147
                                       6777888888899**************************99999998887775 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   5.4   0.00055     0.083      50      97 ..       6      53 ..       4      58 .. 0.94
   2 !    9.8  13.0    0.0029      0.44      15      71 ..      91     147 ..      71     153 .] 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00055
                           DUF3450 50 laeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeiere 97
                                      ++++++l++el+++e + e+le  v++++qe ++++e ie ie +e++
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETG 53
                                      799****************************************99876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0029
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqle 71 
                                       ++++++++ ++ ++ +  a++q +i++l+de++el+++ ++++++ ++ ++++ q+ 
  gi|313124890|ref|YP_004035154.1|  91 DDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQM 147
                                       445555555566666666666666666666666666666666666666666555543 PP

>> HCMV_UL139  Human Cytomegalovirus UL139 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0      0.03       4.6      53     116 ..       9      73 ..       6      77 .. 0.76
   2 !    9.7   3.8     0.007       1.1      53      99 ..      94     140 ..      89     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.03
                        HCMV_UL139  53 idaldakyvaisrdlrslkgeveeaerkeeereryyea.krkemeeflpmgetfesearpqvgsl 116
                                       +++l    +ai +++ +l g+v+++++ + e +   ea + +e   + +    + ++ r  v+++
  gi|313124890|ref|YP_004035154.1|   9 LQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAiETLETGSTVQVPLGGGAYLRADVQDI 73 
                                       677888899****************9988887765555156677777777777778888777765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.007
                        HCMV_UL139  53 idaldakyvaisrdlrslkgeveeaerkeeereryyeakrkemeefl 99 
                                       i+al+ k+++i + +  ++ge++++e    e e+  ++ +++m++ +
  gi|313124890|ref|YP_004035154.1|  94 IEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQ 140
                                       88999999999999999999999888888887777666666665433 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.9   0.00046     0.069     422     465 ..       6      49 ..       2      57 .. 0.87
   2 !    9.1   3.5    0.0029      0.44     420     469 ..      89     138 ..      64     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00046
                            AAA_13 422 ekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeink 465
                                       ++++++l +el+++e+e+++le+++++L+++ +++ +a+e i++
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIET 49 
                                       57889999999999999999999999999999999999999876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0029
                            AAA_13 420 klekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                       + ++aie l  +++ + ++++++++ei++Le + ++ ++ a+++ +++++
  gi|313124890|ref|YP_004035154.1|  89 EQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQ 138
                                       34567777777777777777777777777777777777777777777765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.7   0.00028     0.042      12      64 ..       8      76 ..       6      79 .. 0.85
   2 ?    7.3   6.9     0.044       6.6      12      54 ..      93     135 ..      90     151 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00028
                           NPV_P10 12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet................kvenIqdi 64
                                        +++++ ++a++q++++++ ++ d+++ ++++d+  +++++let                 v++I+++
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETgstvqvplgggaylraDVQDIDEV 76
                                      678899999999999999999999999999999999999999999888888888888888888888776 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.044
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLael 54 
                                       +i+a+  k d+++++++ vq ++ d+++ +++L++q++q+++ 
  gi|313124890|ref|YP_004035154.1|  93 AIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQ 135
                                       5566666666666666666666666666666666666666542 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.8     0.016       2.4      96     157 ..       7      46 ..       4      56 .. 0.45
   2 !   14.2  10.1   0.00024     0.036      85     146 ..      88     149 ..      67     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.016
                           UPF0242  96 eeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqet 157
                                       ++ ++L +el+a e+e+e+l+ +   Lq                      +++  ++e  e 
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQ----------------------QEKSEIDEAIEA 46 
                                       3333444444444444444444444444......................333334433333 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00024
                           UPF0242  85 ktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLae 146
                                       +++++a+e l+ +++   e+++a + e+  l+ e  +L+++++++++++++++ +  +q++e
  gi|313124890|ref|YP_004035154.1|  88 QEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       56778******************************************999988887777765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.8    0.0011      0.17      26      64 ..      12      50 ..       6      61 .. 0.79
   2 ?    8.4   7.5     0.015       2.3      26      74 ..      97     145 ..      93     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0011
                                      CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHH CS
                         Fib_alpha 26 llkyekdvkkdlekleneleeisnstkeaeelvkeikds 64
                                      l++  + +++++e+le ++++++++++e++e +++i++ 
  gi|313124890|ref|YP_004035154.1| 12 LSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETL 50
                                      566677888999999999999999999999999988876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.015
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkd 74 
                                       l  ++ +++++++ ++ e+++++++++e e+  ++++++++++q ++ +
  gi|313124890|ref|YP_004035154.1|  97 LRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQ 145
                                       55678899*********************************99998875 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   4.5   0.00019     0.028      51      92 ..       7      48 ..       3      51 .. 0.90
   2 ?    8.9   1.1     0.012       1.9      36      94 ..      70     128 ..      67     130 .. 0.89
   3 ?    6.9   6.3     0.051       7.7      35      66 ..     107     138 ..      99     150 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00019
                           BLOC1_2 51 eklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92
                                      ++l+++++elq   q+i+++e +v++L++  se+De + ++E
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48
                                      689999999999999999999999999999999999999888 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.012
                           BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                       ++++++v+ +l  +  + +e++++++ +  + d i+++++  +  +s L+  s+eLE++
  gi|313124890|ref|YP_004035154.1|  70 VQDIDEVIVGLGGDYAAEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQ 128
                                       6788899999999999999999999999999999***************9999999987 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.051
                           BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqq 66 
                                       ++++++ ++++le+++++l+++ +++q+++qq
  gi|313124890|ref|YP_004035154.1| 107 RIAAVQGEISDLEDESSELEQQAQQMQQQMQQ 138
                                       44555555555555555555555555555543 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5    0.0025      0.37      34      79 ..      10      47 ..       5      61 .. 0.45
   2 ?    8.8   2.9      0.01       1.6      28      82 ..      90     143 ..      65     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0025
                      Baculo_PEP_C 34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnal 79
                                       ql++ l+aie+++++l+ d+++        l++  +++++a+ a+
  gi|313124890|ref|YP_004035154.1| 10 QQLSQELQAIEQEIEELEGDVSD--------LQQEKSEIDEAIEAI 47
                                      34444444444444444444444........333333333333333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.01
                      Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq.dt 82 
                                       q   i  +l    d+i++++ a++ ++++ l++ +++l+++++++++++++ q ++
  gi|313124890|ref|YP_004035154.1|  90 QDDAI-EALRLKQDSIDERIAAVQGEISD-LEDESSELEQQAQQMQQQMQQQQmQQ 143
                                       55555.78888899999999999999999.66677888888888888888766433 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.5      0.22        33      20      38 ..      20      38 ..      13      56 .. 0.78
   2 ?   15.6   4.9    0.0001     0.015      20      56 ..     112     148 ..     103     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.22
                             TSC22 20 kekIkeLeernseleeENs 38
                                       ++I eLe ++s l++E s
  gi|313124890|ref|YP_004035154.1| 20 EQEIEELEGDVSDLQQEKS 38
                                      5789999999999999865 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 0.0001
                             TSC22  20 kekIkeLeernseleeENslLkalaspeqleqlsakl 56 
                                       + +I +Le++ sele++ +++++++ ++q++q+++++
  gi|313124890|ref|YP_004035154.1| 112 QGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQ 148
                                       668*******************************976 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.0    0.0027       0.4     114     154 ..       8      49 ..       4      58 .. 0.65
   2 ?   10.1  10.2    0.0037      0.56     119     164 ..     106     151 ..      85     153 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0027
                   Ax_dynein_light 114 al.qaeqgkselekkikeLeeekeelekqvaelkaklealek 154
                                       +l q  q+ + +e++i+eLe ++++l+++ +e+++ +ea+e 
  gi|313124890|ref|YP_004035154.1|   8 QLqQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIET 49 
                                       442334666677777777777777777777777777777665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0037
                   Ax_dynein_light 119 qgkselekkikeLeeekeelekqvaelkaklealekrekerrqeee 164
                                       ++ + ++ +i++Le+e +ele+q +++++++++++ ++ +++qe++
  gi|313124890|ref|YP_004035154.1| 106 ERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQEDD 151
                                       4455667778888888888888888888888888888888888765 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.4   0.00099      0.15      63     230 ..       7      44 ..       3      55 .. 0.51
   2 ?    8.4   7.9    0.0083       1.3     176     226 ..      89     139 ..      82     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00099
                           DUF4618  63 kqleqakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLstYkDkeYpvkavqIanlvrqlqqlkdsqqde 139
                                       +ql+q+ +eLq +e+                                                              
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQ-------------------------------------------------------------- 21 
                                       555555555555554.............................................................. PP

                           DUF4618 140 ldeleelikevleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaev 216
                                                                                                           ei+eL+ +v
  gi|313124890|ref|YP_004035154.1|  22 --------------------------------------------------------------------EIEELEGDV 30 
                                       ....................................................................444444444 PP

                           DUF4618 217 eqLqaqaeeprevi 230
                                        +Lq++  e+ e i
  gi|313124890|ref|YP_004035154.1|  31 SDLQQEKSEIDEAI 44 
                                       44444444443333 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0083
                           DUF4618 176 atqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeep 226
                                       +  +a+++  l++ ++ + i+ ++ +i++le e +eL+++ +q+q+q+++ 
  gi|313124890|ref|YP_004035154.1|  89 EQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQ 139
                                       456788889999999*******************************99964 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3     0.028       4.2      66     104 ..      11      48 ..       3      59 .. 0.68
   2 ?   11.5   7.5    0.0016      0.25      70     114 ..      99     143 ..      82     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.028
                           DUF4337  66 akaeelaaavdkkiakykkkiarykkekkeikkkAkele 104
                                       + ++el+ a++++i++++ ++   ++ek+ei +  +++e
  gi|313124890|ref|YP_004035154.1|  11 QLSQELQ-AIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48 
                                       2244555.4667888888888888888888887766666 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0016
                           DUF4337  70 elaaavdkkiakykkkiarykkekkeikkkAkeleaerdeaneas 114
                                        +++ +d++ia+++ +i   ++e++e++++A++++++ +++++++
  gi|313124890|ref|YP_004035154.1|  99 LKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQ 143
                                       4678899*******************************9999876 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4    0.0013       0.2      14      50 ..       8      44 ..       6      74 .. 0.67
   2 ?    7.4   9.7     0.038       5.7       8      56 ..     101     150 ..      85     153 .] 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0013
                            CENP-H 14 ellklsqelrelqeeltevekenlrlkrknrelaael 50
                                      +l++lsqel+++++e++e+e +  +l++++ e+ + +
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAI 44
                                      4555666666666666666666666665555554444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.038
                            CENP-H   8 rdelssellklsqelrelqeeltevekenlrlkrk.nrelaaellelake 56 
                                       +d + +++++ + e+++l++e +e+e+++ +++++ +++ ++++++ +++
  gi|313124890|ref|YP_004035154.1| 101 QDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQmQQQQMQQMQQMQED 150
                                       45555666666666666666666666666666655234456666444443 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2    0.0004     0.061      66     107 ..       4      48 ..       2      80 .. 0.65
   2 ?    4.3   6.6      0.26        40      68     112 ..     105     145 ..      85     151 .. 0.41

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0004
                              COG2  66 glqeeleevesplaaarkkvesvreklseree...eveskleeak 107
                                       g q++l++++++l+a+ +++e+++  +s+ ++   e+++ +e+ +
  gi|313124890|ref|YP_004035154.1|   4 GGQQQLQQLSQELQAIEQEIEELEGDVSDLQQeksEIDEAIEAIE 48 
                                       667777777777777777777766555444430003444444433 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.26
                              COG2  68 qeeleevesplaaarkkvesvreklsereeeveskleeakeleek 112
                                       +e++  v    +   +++e+  ++l+++ +++++++++++  +++
  gi|313124890|ref|YP_004035154.1| 105 DERIAAV----QGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQ 145
                                       2222222....2222233333333333333333333333333333 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.2    0.0027       0.4       3      37 ..      13      47 ..      11      50 .. 0.91
   2 ?    9.3   2.7    0.0087       1.3       2      35 ..     104     137 ..      91     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0027
                              XhlA  3 kerlerietkldnleervdkleekaaeaeekiknl 37
                                       ++l+ ie+++++le +v++l++ ++e +e i+ +
  gi|313124890|ref|YP_004035154.1| 13 SQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAI 47
                                      6899*************************999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0087
                              XhlA   2 ikerlerietkldnleervdkleekaaeaeekik 35 
                                       i+er++ +++++ +le++ ++le+ a  ++++ +
  gi|313124890|ref|YP_004035154.1| 104 IDERIAAVQGEISDLEDESSELEQQAQQMQQQMQ 137
                                       7778888888888888877778888777777765 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.1   0.00051     0.076      63     105 ..       7      47 ..       4      80 .. 0.60
   2 ?    7.0  21.5     0.045       6.9      25      88 ..      87     149 ..      81     153 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  63 qelqkkeqelqqkqqqkaqelqkkqqellkpildkinkaikev 105
                                       q+lq++ qelq+  +q+ +el+    +l+++   +i++ai+++
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQA-IEQEIEELEGDVSDLQQE-KSEIDEAIEAI 47 
                                       444444444444.444444444444444442.34444444443 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHH CS
                              OmpH  25 ekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka.qelqkkqq 88 
                                       e+++ +  ++l+ k++++++ +++ q + ++   e++  el+++ q++qq++qq++ q++q+ q+
  gi|313124890|ref|YP_004035154.1|  87 EQEQDDAIEALRLKQDSIDERIAAVQGEISD--LEDESSELEQQAQQMQQQMQQQQmQQMQQMQE 149
                                       4566666777888888899999999866655..56777778788788777777777777777775 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5    0.0014       0.2       1      35 [.      19      53 ..       6      66 .. 0.74
   2 ?    6.7   0.9     0.035       5.3       3      33 ..     106     136 ..      97     152 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0014
                           DUF4988  1 leddvndlkdrvaaleeqvkelndniealkkllee 35
                                      +e+++++l+  v+ l+++ +e+++ iea+++l ++
  gi|313124890|ref|YP_004035154.1| 19 IEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETG 53
                                      56778888888888888888888888888777633 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.035
                           DUF4988   3 ddvndlkdrvaaleeqvkelndniealkkll 33 
                                       +++ +++ +++ le + +el+++ +++++ +
  gi|313124890|ref|YP_004035154.1| 106 ERIAAVQGEISDLEDESSELEQQAQQMQQQM 136
                                       3444444444444444444444444444444 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.0    0.0049      0.74     132     177 ..       7      52 ..       3      59 .. 0.63
   2 ?   10.5   8.7   0.00095      0.14     420     483 ..      90     148 ..      66     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0049
                               MAD 132 seleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLef 177
                                       ++l++l ++l+  +++++ele  +++l+++++e  ea + i +Le 
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLET 52 
                                       4556666666666666666666666666666666666666666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00095
                               MAD 420 lerelqalr.qqesladassskeevdslkkkleeLelerqrLreqkeelElelerreLqgdydlk 483
                                        +  ++alr +q s ++       + +++ ++ +Le e ++L++q +++  +++++++q++ +++
  gi|313124890|ref|YP_004035154.1|  90 QDDAIEALRlKQDSIDE------RIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQ 148
                                       44557777744444444......4899********************************998876 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  14.0   0.00031     0.047     132     240 ..       6     150 ..       4     153 .] 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00031
                           DUF4407 132 taelaeleaqiaalqaeidaaearldalraeaqkeldgtk........gtgttgvaGkgpaake............. 187
                                       +++l++l ++++a+++ei+++e ++++l++e   e+d +         g++ +   G g++ ++             
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKS-EIDEAIeaietletGSTVQVPLGGGAYLRAdvqdidevivglg 81 
                                       467777777777777777777777777777765.6666667777777777777788888888889999999999999 PP

                           DUF4407 188 ...............kkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqaaaaad 240
                                                       + + d +++++a+++++++  +++ ++l+++++++++++++++ ++ ++ ++d
  gi|313124890|ref|YP_004035154.1|  82 gdyaaeqeqddaieaLRLKQDSIDERIAAVQGEISdLEDESSELEQQAQQMQQQMQQQQMQQMQQMQED 150
                                       998877777777777444444444444444444445444444444444444444444444444444443 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.3    0.0028      0.42      63      98 ..       6      41 ..       2      55 .. 0.75
   2 ?    9.6   7.0    0.0041      0.62      65     115 ..     100     150 ..      71     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0028
                      HAUS-augmin3 63 qedvellevileeeeesleaLeqelqeLqkekalkl 98
                                      q++ ++l+++l+++e+ +e+Le  +++Lq+ek  + 
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEID 41
                                      567788888888888888888888888888887655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0041
                      HAUS-augmin3  65 dvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqel 115
                                       +++++++ +++ +  + +Le+e +eL+++ +  ++++++ q+q +++ qe+
  gi|313124890|ref|YP_004035154.1| 100 KQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQED 150
                                       335555666667777777777777777777777777777777777777765 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.3   0.00026     0.038      67     102 ..       8      43 ..       4      55 .. 0.39
   2 ?    5.9  12.1     0.078        12      74     132 ..      93     148 ..      84     153 .] 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00026
                    CENP-F_leu_zip  67 elreleldLvalrsekeeLekelqkkqervseLesl 102
                                       +l++l+++L+a+ +e eeLe ++ + q++ se +++
  gi|313124890|ref|YP_004035154.1|   8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEA 43 
                                       344444444444444444433222222222222222 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.078
                    CENP-F_leu_zip  74 dLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLq 132
                                        ++alr  ++++++ +   q ++s+Le   s+le++ ++    + qm++++ ++++++q
  gi|313124890|ref|YP_004035154.1|  93 AIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQ---MQQQMQQQQMQQMQQMQ 148
                                       466777777777777777777777777777777755443...34455555555555555 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.4   0.00023     0.035      13      59 ..       6      52 ..       2      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00023
                            CC2-LZ 13 keeieeLkaqlqaaeealaakqeeidelkeeikkkeeeletisvlka 59
                                      ++++++L+++lqa e+ +++ + ++ +l++e ++ +e +e i+ l +
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLET 52
                                      5799**************************************99976 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9    0.0019      0.29       2      55 ..       1      53 [.       1      61 [. 0.76
   2 ?    8.8   0.6     0.011       1.6      13      72 ..      66     131 ..      59     137 .. 0.77
   3 ?   -0.4   0.4       7.5   1.1e+03       7      20 ..     126     139 ..     122     151 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0019
                           DUF1515  2 idagvlqqlgtllaevkelredlkrse.drsdasrakmyrkmdelvervtalegs 55
                                      + +g +qql++l +e++ + +++ + e d sd ++   +  +de +e +++le+ 
  gi|313124890|ref|YP_004035154.1|  1 MMGGGQQQLQQLSQELQAIEQEIEELEgDVSDLQQ--EKSEIDEAIEAIETLETG 53
                                      457779*****************987723444443..34679**********963 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.011
                           DUF1515  13 llaevkelredlk......rsedrsdasrakmyrkmdelvervtalegsvvklkaditsvkevted 72 
                                       l a+v+++ e +        +e+  d +   +  k d + er++a++g ++ l+++ +++ + +++
  gi|313124890|ref|YP_004035154.1|  66 LRADVQDIDEVIVglggdyAAEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQ 131
                                       556666666666677777766777666667788999******************999988776655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 7.5
                           DUF1515   7 lqqlgtllaevkel 20 
                                        qq +++++++++ 
  gi|313124890|ref|YP_004035154.1| 126 EQQAQQMQQQMQQQ 139
                                       45555555554432 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.1    0.0016      0.25       4      43 ..       7      46 ..       5     100 .. 0.72
   2 ?    8.5  10.5     0.015       2.3       3      48 ..     105     147 ..     103     153 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0016
                             Spc24  4 nekfriakelsdleselesleselaelkeeleeleeesee 43
                                      ++++++++el+ +e+e+e+le   ++l++e  e++e  e+
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEA 46
                                      5677777777777777777777777777777777776665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.015
                             Spc24   3 dnekfriakelsdleselesleselaelkeeleeleeeseekeser 48 
                                       d++  +++ e+sdle+e ++le++ +++++++++ ++++ +   ++
  gi|313124890|ref|YP_004035154.1| 105 DERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQ---QM 147
                                       55666778899***********************9999988...22 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.5   0.00033      0.05      11      49 ..       6      44 ..       2      57 .. 0.73
   2 ?    2.7  11.0      0.92   1.4e+02      43      85 ..     102     145 ..      87     153 .] 0.43

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00033
                       TMF_TATA_bd 11 vqlverlsseirrlEgElaslkeelerleaerdeareei 49
                                      +q +++ls+e++  E E+++l+ +++ l++e++e+ e i
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAI 44
                                      567788888888888888888888888888888876655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.92
                       TMF_TATA_bd  43 deareeivklmkeneelkelkkeleelekelee.lqeryetlLe 85 
                                       d++ e i+++  e  +l+++++ele++ +++++ +q+++ + ++
  gi|313124890|ref|YP_004035154.1| 102 DSIDERIAAVQGEISDLEDESSELEQQAQQMQQqMQQQQMQQMQ 145
                                       44444444444444444444444444444443212222222222 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.1     0.046       6.9      38      71 ..       9      42 ..       5      57 .. 0.47
   2 ?   13.0   8.5   0.00061     0.091      66     133 ..      84     150 ..      65     153 .] 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.046
                     Jnk-SapK_ap_N 38 LeslasrneeeeaeleelreeleqLeteyereke 71
                                      L +l ++ ++ e+e+eel+ ++++L++e+++  e
  gi|313124890|ref|YP_004035154.1|  9 LQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDE 42
                                      4444444444444444444444444444433322 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00061
                     Jnk-SapK_ap_N  66 yerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkey 133
                                       y  e+e+  +  e l ++ d+++e+  ++q ++++le+e  ele++a+++++q+++ + ++ ++++e+
  gi|313124890|ref|YP_004035154.1|  84 YAAEQEQDDAI-EALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQED 150
                                       55555444444.5899999*************************999999999999888888877765 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.4    0.0016      0.24       7      47 ..       7      47 ..       3      53 .. 0.61
   2 ?    7.5   6.1     0.019       2.8      14     111 ..     106     144 ..      66     153 .] 0.46

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0016
                           DUF4795  7 ellkklqeaieklqeelekleekvkelekrledkekkleal 47
                                      + l++l ++++ +++e+e+le+ v++l++++++ ++ +ea+
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAI 47
                                      44566666666666666666666666666666666666554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.019
                           DUF4795  14 eaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDeak 90 
                                       e i  +q e+++                                                            ++   
  gi|313124890|ref|YP_004035154.1| 106 ERIAAVQGEISD------------------------------------------------------------LEDES 122
                                       222222222222............................................................33333 PP

                           DUF4795  91 keLekmleellekleeqe.eal 111
                                       +eLe++++++ +++++q+ +++
  gi|313124890|ref|YP_004035154.1| 123 SELEQQAQQMQQQMQQQQmQQM 144
                                       3333333333333332221222 PP

>> SOGA  Protein SOGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.9    0.0004     0.061      61      92 ..       6      37 ..       2      40 .. 0.89
   2 ?    4.1   5.6      0.69     1e+02      22      54 ..     114     146 ..      97     153 .] 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.0004
                              SOGA 61 sskeaelkeeLklarlqineLsgkvvkLqven 92
                                      +++ ++l +eL++ +++i+eL+g v  Lq e+
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEK 37
                                      4567899**********************997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.69
                              SOGA  22 slseleeenkqlteeLnkyksklgeeessleee 54 
                                       ++s+le+e+ +l+++ ++++ ++++++ ++ ++
  gi|313124890|ref|YP_004035154.1| 114 EISDLEDESSELEQQAQQMQQQMQQQQMQQMQQ 146
                                       466777777777777777777666666555443 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1     0.019       2.8     212     252 ..       8      48 ..       2      70 .. 0.52
   2 ?    8.1   6.0     0.012       1.8     198     258 ..      89     146 ..      73     152 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.019
                         Phage_GPO 212 elsekveallaleaelaalkkeveklkaeleaLkekLsktd 252
                                       +l++  ++l+a e+e+++l+ +v++l++e +++ e +++ +
  gi|313124890|ref|YP_004035154.1|   8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48 
                                       23333333335555555555555555555555555544433 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.012
                         Phage_GPO 198 dveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekLsktdakekqr 258
                                       +  +a+e++  ++ +++e+++   a + e+++l++e ++l+++++++++++++++ ++ q+
  gi|313124890|ref|YP_004035154.1|  89 EQDDAIEALRLKQDSIDERIA---AVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQ 146
                                       445566666666666666666...7777788888888888888888888887777754443 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.6    0.0062      0.94      18      57 ..       9      48 ..       4      58 .. 0.66
   2 ?    8.8   6.0    0.0085       1.3      13      58 ..     103     148 ..      93     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0062
                                      ......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1 18 pallkedlskieaevsaleellnklkkelqeeeeaikklk 57
                                       + l++ l++ie+e+++le  +++l++e  e  eai+ ++
  gi|313124890|ref|YP_004035154.1|  9 LQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48
                                      3344677777777777777777777777777777666665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0085
                                       ...........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  13 ainqdpallkedlskieaevsaleellnklkkelqeeeeaikklkk 58 
                                       +i++  a+ +  +s++e+e s+le++ +++++++q++++++ ++++
  gi|313124890|ref|YP_004035154.1| 103 SIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQ 148
                                       5667777888999999999999999999999999999988877765 PP

>> ORF6C  ORF6C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.2    0.0061      0.92       1      30 [.       8      37 ..       7      60 .. 0.72
   2 ?    8.0   5.2     0.019       2.9       7      53 ..      99     145 ..      93     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0061
                             ORF6C  1 alelllealkehdekieeidervkkLeenm 30
                                      +l+ l ++l+ ++++iee++ +v++L++++
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQELQAIEQEIEELEGDVSDLQQEK 37
                                      466677778888888888888888887543 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.019
                             ORF6C   7 ealkehdekieeidervkkLeenmpldesekeeiqkkvkkkvvellg 53 
                                        ++ ++de+i++++ ++++Le++    e++++++q++++++ ++ ++
  gi|313124890|ref|YP_004035154.1|  99 LKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQ 145
                                       567899******************999**********9999887665 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0    0.0032      0.49      24      62 ..       9      47 ..       6      53 .. 0.88
   2 ?    7.1   6.0     0.061       9.2      27      71 ..     104     149 ..      99     153 .] 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0032
                      Occludin_ELL 24 YkelhaeleevskkfseLerelkelkegskeykkieeei 62
                                       ++l +el++++++++eLe ++++l+++++e+++++e i
  gi|313124890|ref|YP_004035154.1|  9 LQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAI 47
                                      67899************************9999999886 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.061
                      Occludin_ELL  27 lhaeleevskkfseLerelkelkegskeykk.ieeeilqeykklkk 71 
                                       + +++++v+ ++s+Le+e +el+++ +++++ ++++ +q+ +++++
  gi|313124890|ref|YP_004035154.1| 104 IDERIAAVQGEISDLEDESSELEQQAQQMQQqMQQQQMQQMQQMQE 149
                                       5688999999999999999999999995555044444555555554 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.5     0.019       2.9      54     100 ..       7      52 ..       4      60 .. 0.62
   2 ?   10.9  13.0    0.0015      0.23      40     105 ..      85     150 ..      66     153 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.019
                         Golgin_A5  54 qerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqelee 100
                                       q+ ++l +elq+ +q+ie+l  ++ dl++++ +e++++ e ++ le+
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEK-SEIDEAIEAIETLET 52 
                                       4445566667777777777777776666544.666666666666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0015
                         Golgin_A5  40 esstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleee 105
                                        +++++ +++++l+ ++d + e +++++++i++l  e  +le+q+q+ ++++++q+ +  +q++e+
  gi|313124890|ref|YP_004035154.1|  85 AAEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQED 150
                                       456778899999********************************9999999998888887777765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.8    0.0018      0.28      73     114 ..       7      48 ..       4      58 .. 0.76
   2 ?    6.4   8.4     0.059       8.8      72     123 ..      91     142 ..      84     150 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0018
                           DUF1664  73 kkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       ++l++ ++  ++i++e++e+++d+s+++++ ++++ea+e +e
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48 
                                       566777777778888888888888888888888888777766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.059
                           DUF1664  72 dkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                                       d+ +++    + +i+e +++v++++s+++++++++++  +++++++++ + +
  gi|313124890|ref|YP_004035154.1|  91 DDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQ 142
                                       4445555555556666666666666666666666666666666665544333 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.8   0.00063     0.095     109     147 ..       7      45 ..       3      57 .. 0.51
   2 ?    5.2  11.1      0.14        21     126     167 ..     102     143 ..      82     152 .. 0.42

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00063
                             ATG16 109 eelqkleeklkedeerlaeleaeraaletklkdreeelr 147
                                       ++lq+l ++l++ e++++ele ++++l+++ ++ +e+++
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIE 45 
                                       344444444444444444444444444444444444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.14
                             ATG16 126 aeleaeraaletklkdreeelrekeklvqdlqDElsaLqlql 167
                                       +++ +++aa++ +++d+e+e  e+e+  q++q  +++ q+q 
  gi|313124890|ref|YP_004035154.1| 102 DSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQ 143
                                       233333444444444444444444444444444444444432 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.7    0.0086       1.3      55      84 ..      18      47 ..       6      49 .. 0.74
   2 ?    7.1   3.8     0.039       5.8      57      86 ..     112     141 ..     106     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0086
                             Vps51 55 sasdtIrkmksemdkldqklselkqaiski 84
                                      ++ ++I+++++++++l+q+ se+++ai+ i
  gi|313124890|ref|YP_004035154.1| 18 AIEQEIEELEGDVSDLQQEKSEIDEAIEAI 47
                                      566788888888888888888888888776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.039
                             Vps51  57 sdtIrkmksemdkldqklselkqaiskiae 86 
                                         +I+++++e ++l+q+ ++++q +++ ++
  gi|313124890|ref|YP_004035154.1| 112 QGEISDLEDESSELEQQAQQMQQQMQQQQM 141
                                       56899999***9999999999999998776 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.0    0.0035      0.53     378     421 ..       7      48 ..       3      68 .. 0.53
   2 ?    7.9   5.1    0.0068         1     321     383 ..      89     147 ..      68     153 .] 0.69

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0035
                              FapA 378 eqlkklletkeklkeeleeleeelkelkeeleskkeeakikvnk 421
                                       +ql++l ++++++++e+eele +  +l++e  +   ++ i++ +
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEI--DEAIEAIE 48 
                                       4455555555555555555555555555554444..22333333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0068
                              FapA 321 gtkteiev.gldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkkl 383
                                       ++   ie+  l++ +++e++++++ e+ +le+e  +l+++ +++++  +++     +++q++++
  gi|313124890|ref|YP_004035154.1|  89 EQDDAIEAlRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQ-----QMQQMQQM 147
                                       455556666888888999999999999999999999999988888833333.....33333333 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6    0.0041      0.62      32      82 ..       6      52 ..       1      57 [. 0.70
   2 ?    6.3   2.7     0.078        12      29      72 ..     102     146 ..      93     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0041
                            DUF948 32 aatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82
                                      ++++++l +++++i +e+e+l   v +    ++++  ++d+ +ea+++l +
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSD----LQQEKSEIDEAIEAIETLET 52
                                      455666666666666666666666655....67799999999999998765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.078
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvne.klekvdp 72 
                                       d++ ++i+ ++ ++  + +e+ +l ++++++++++++ +++++++
  gi|313124890|ref|YP_004035154.1| 102 DSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQqQMQQMQQ 146
                                       677788999999999999999999999999999988745555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.4     0.018       2.8     153     195 ..       7      50 ..       2      55 .. 0.53
   2 ?   10.0   5.4    0.0058      0.88     142     193 ..      91     146 ..      61     151 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.018
                            AAA_23 153 erleelekeleeledekkllekl.eqekekekeleeleeeleei 195
                                       ++l++l++el+ +e+e+++le    ++++++ e++e  e++e++
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDvSDLQQEKSEIDEAIEAIETL 50 
                                       34555555555555555555544444455555555555555554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0058
                            AAA_23 142 r....feefelkdkkerleelekeleeledekkllekleqekekekeleeleeele 193
                                       +    + ++++ +  er+++++ e+ +lede ++le++ q+ +++ + ++ ++ ++
  gi|313124890|ref|YP_004035154.1|  91 DdaieALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQ 146
                                       22222222223445559999999999999999999987655444444443333332 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1     0.013         2      37      82 ..       7      51 ..       4      74 .. 0.49
   2 ?    5.3   9.1     0.064       9.6      18      74 ..      94     150 ..      83     153 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.013
                             TMPIT 37 keikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82
                                      +++++ +++l+++++++++l+ +v+ + ++e +e++e ++ +++  
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVS-DLQQEKSEIDEAIEAIETLE 51
                                      3444444445555555555544443.33333344444444444443 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.064
                             TMPIT  18 akeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkee 74 
                                        + ++ k +++ + + +++ ei+  + + +el+++ +++++++++++ +++++++e+
  gi|313124890|ref|YP_004035154.1|  94 IEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQED 150
                                       455667788889999999999999999999999999999999999999999999986 PP

>> Paralemmin  Paralemmin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8    0.0012      0.18       2      40 ..       7      45 ..       4      73 .. 0.64
   2 ?    5.2   8.9      0.09        14       9      60 ..      99     148 ..      87     153 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0012
                        Paralemmin  2 kqleedeakvrkLEesiqrLekeieeLeseesaisakee 40
                                      +ql++  +  + +E++i+ Le +++ L++e+s+i +  e
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIE 45
                                      456666666666666666666666666666666553333 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.09
                        Paralemmin   9 akvrkLEesiqrLekeieeLeseesaisakeevlaeklketeksvedlqksl 60 
                                        k  +++e i  ++ ei+ Le+e+s+  ++ ++++++++++  +++++q+++
  gi|313124890|ref|YP_004035154.1|  99 LKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQ--QMQQMQQMQ 148
                                       4667899********************98888888776544..444444443 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.8    0.0035      0.53      34      67 ..       7      40 ..       2      57 .. 0.67
   2 ?    7.3   8.8     0.044       6.6      35      80 ..      93     146 ..      66     150 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0035
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin 34 eevqallkkhkaleaelaaqqervkalnelaekl 67
                                      +++q+l ++++a+e+e+++ ++ v +l++ ++++
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEI 40
                                      5667777777777777777777777777666665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHH.HHTTHTTHHHHHH CS
                          Spectrin  35 evqallkkhkaleaelaaqqervkaln.......elaekl.ldeghsaseeiee 80 
                                       +++al  k + + + +aa q+++ +l+       ++a+++ ++ +++++++ ++
  gi|313124890|ref|YP_004035154.1|  93 AIEALRLKQDSIDERIAAVQGEISDLEdesseleQQAQQMqQQMQQQQMQQMQQ 146
                                       445555555555555555555555555111111155555544444444444444 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.0     0.024       3.6     168     203 ..      10      45 ..       5      53 .. 0.67
   2 ?   10.0   6.3    0.0028      0.42     159     220 ..      86     148 ..      68     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.024
                            Cluap1 168 kalkeaikkvkeelektkkalenlesdeanLeakie 203
                                       ++l+++++++++e+e+++ ++++l+++++++++ ie
  gi|313124890|ref|YP_004035154.1|  10 QQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIE 45 
                                       456667777777777777777777777777777665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0028
                            Cluap1 159 rqleleeiekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraq.krLqslq 220
                                       +++e+++  +al+ + ++++e+++ ++ ++++le++ ++Le++ ++ +q+++++q +++q++q
  gi|313124890|ref|YP_004035154.1|  86 AEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQmQQMQQMQ 148
                                       56777788889999999*****************************99999866524555555 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1     0.005      0.75     389     418 ..       7      36 ..       3      58 .. 0.82
   2 ?    3.2   1.1      0.15        23     359     422 ..      81     139 ..      77     150 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.005
                                       TEEEBXSSXXTTTTHHHHHHHHHHHHHHHH CS
                     Hemagglutinin 389 kqleavgkelnelekrieeldkkvddgfld 418
                                       +ql+++++el  +e++ieel+  v d+  +
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQE 36 
                                       79************************9765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                                       EEEEEEXHHHHHHHHHHHHHHHHHHHHHTTTEEEBXSSXXTTTTHHHHHHHHHHHHHHHHHHHH CS
                     Hemagglutinin 359 Gsavaadkkstqeainkitkkvnsliekenkqleavgkelnelekrieeldkkvddgfldvity 422
                                       G  +aa+++   +ai+ +  k +s+ e+    + av +e+ +le++  el+++ +     +   
  gi|313124890|ref|YP_004035154.1|  81 GGDYAAEQEQ-DDAIEALRLKQDSIDER----IAAVQGEISDLEDESSELEQQAQQMQQQMQQQ 139
                                       5567777764.67888888777777665....67788888888888888888777666555444 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.2     0.078        12      42      95 ..       8      56 ..       4      59 .. 0.65
   2 ?   10.4  14.2    0.0043      0.65      20      63 ..     106     149 ..      93     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.078
                              YlqD 42 qakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkLelgsev 95
                                      q+++l +     + q+ie+  e++e   s+++++k+++++ +e +++Le gs v
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQ-----ELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETGSTV 56
                                      2222222.....333455555667778888888888888888888888888877 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0043
                              YlqD  20 elqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqe 63 
                                       e ++ +q +i+ l+ e ++Le+qa+++ +++++q++qq++++qe
  gi|313124890|ref|YP_004035154.1| 106 ERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       55678999********************************9997 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.6   0.00032     0.048     277     318 ..       7      48 ..       4      52 .. 0.92
   2 ?    3.2   9.2      0.23        35     285     326 ..     100     141 ..      83     152 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00032
                             IFT57 277 qeyreaqeelsevkekykqlsegvseltrelaeiseelekvk 318
                                       q+++++++el+++++++++l++ vs+l++e +ei+e +e+++
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48 
                                       789999******************************999875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.23
                             IFT57 285 elsevkekykqlsegvseltrelaeiseelekvkqemeergs 326
                                       + +++ e++  +++++s+l++e +e++++ ++++q+m++++ 
  gi|313124890|ref|YP_004035154.1| 100 KQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQM 141
                                       344566677777777777777777777777777777776643 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.5    0.0049      0.74      68     112 ..       6      50 ..       3      59 .. 0.83
   2 ?    5.5   4.3     0.022       3.4      64     124 ..      87     144 ..      64     153 .] 0.46

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0049
                        V_ATPase_I  68 ekeldeleeelekleeelkelnenleklkkelnelvelkavleka 112
                                       +++l++l++el+ +e+e++el+   ++l++e++e+ e+ + +e+ 
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETL 50 
                                       678999999999999999999999999999999998887777655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.022
                        V_ATPase_I  64 eapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleeeeeeee 124
                                       e+++++ ++ l  + ++++e++  ++ + ++l++e +el+++ + +++  +  + +   + 
  gi|313124890|ref|YP_004035154.1|  87 EQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQ---QM 144
                                       44444555555555555555555555555555555555544443332222211111...11 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.8     0.005      0.76     259     297 ..       8      46 ..       5      51 .. 0.58
   2 ?    6.7   7.2     0.017       2.6      55     276 ..      97     138 ..      83     151 .. 0.41

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.005
                            Tektin 259 aknkleeqlkkvleeiaeleknieeLekairdkeaplkl 297
                                         ++l ++l+ +++ei+ele ++++L+++  + ++++  
  gi|313124890|ref|YP_004035154.1|   8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEA 46 
                                       455666666666666666666666666666655555544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.017
                            Tektin  55 iefwkeeLekeleelkeeieaLeeekrrlekalealeeplhiaqeclelRekRqgidlvhDevekeLlkEveliegv 131
                                       ++  ++ +++ +++++ ei +Le+e  +le++ ++++                                        
  gi|313124890|ref|YP_004035154.1|  97 LRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQ---------------------------------------- 133
                                       3333333333333333333333333333333333333........................................ PP

                            Tektin 132 qellkrtleqaeeqlrllraakhkLekdlsdKkeAleiDeeclslkntsanisykpgaerlpetsstpeeWekftkd 208
                                                                                                                    
  gi|313124890|ref|YP_004035154.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                            Tektin 209 nieraekerqasakLreaidsilkqtandlraqaeavnealrkrieetedaknkleeqlkkvleeiae 276
                                                                                                      +++++
  gi|313124890|ref|YP_004035154.1| 134 ---------------------------------------------------------------QQMQQ 138
                                       ...............................................................33333 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.3    0.0009      0.14      23      65 ..       6      48 ..       4      51 .. 0.89
   2 ?    4.2   6.8      0.25        37      12      52 ..     101     141 ..      86     152 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0009
                             Sec34 23 leqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65
                                      ++qL++l+++ ++++++ ++l+ +  +l +e+++++e  e+ie
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48
                                      5899999999999999999999999999999999999999997 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.25
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlle 52 
                                        d++ e++ +++ ++++le++ ++ +++ ++++++++q   
  gi|313124890|ref|YP_004035154.1| 101 QDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQM 141
                                       23334444444444444444444444444444444444333 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.9    0.0088       1.3      52      90 ..      12      41 ..       4      52 .. 0.47
   2 ?    4.7   2.3      0.21        32      65      93 ..     108     136 ..      88     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0088
                           DUF2730 52 letkvenLPtakdlekLkllladlrgelkaleaevrqls 90
                                      l          ++l++++ ++++l+g++++l++e ++++
  gi|313124890|ref|YP_004035154.1| 12 LS---------QELQAIEQEIEELEGDVSDLQQEKSEID 41
                                      33.........4444445555555555444444433333 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.21
                           DUF2730  65 lekLkllladlrgelkaleaevrqlshqv 93 
                                       +++++ +++dl+ e+++le++ +q+++q+
  gi|313124890|ref|YP_004035154.1| 108 IAAVQGEISDLEDESSELEQQAQQMQQQM 136
                                       56677777777777777777777777765 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.6     0.024       3.6      19      40 ..       5      26 ..       1      26 [. 0.80
   2 ?   12.8   3.6   0.00078      0.12       3      34 ..      17      48 ..      15      50 .. 0.94
   3 ?    6.7   4.5     0.061       9.2       3      38 ..     102     137 ..      94     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.024
                         FlaC_arch 19 vkkeneelsksveelkenVkdl 40
                                       ++++++ls++++ +++++++l
  gi|313124890|ref|YP_004035154.1|  5 GQQQLQQLSQELQAIEQEIEEL 26
                                      5889999999999999999876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00078
                         FlaC_arch  3 delEnklsklsteletvkkeneelsksveelk 34
                                      + +E+++++l+  ++ +++e +e+ + +e ++
  gi|313124890|ref|YP_004035154.1| 17 QAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48
                                      579**************************997 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.061
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVk 38 
                                       d++++++  ++ e++ +++e +el+++ ++++++ +
  gi|313124890|ref|YP_004035154.1| 102 DSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQ 137
                                       778888899999999999999999999999998774 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.8     0.033       4.9       4      32 ..      14      42 ..       6      51 .. 0.56
   2 ?    8.4  11.3     0.017       2.6       2      46 ..     104     149 ..      87     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.033
                             Tup_N  4 elLdavkqEfdalsqeasslkaqkdeyel 32
                                        L+a+ qE+++l+ ++s l+++k e++ 
  gi|313124890|ref|YP_004035154.1| 14 QELQAIEQEIEELEGDVSDLQQEKSEIDE 42
                                      33555555555555555555555555554 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.017
                             Tup_N   2 lnelLdavkqEfdalsqeasslkaqkdeyelk.iqsqiqElqqirq 46 
                                       ++e + av+ E++ l+ e s l++q + + ++  q+q+q +qq+++
  gi|313124890|ref|YP_004035154.1| 104 IDERIAAVQGEISDLEDESSELEQQAQQMQQQmQQQQMQQMQQMQE 149
                                       5677889999999999999999999999999945667899999986 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.5      0.07        11      60      94 ..       7      41 ..       5      52 .. 0.63
   2 ?   10.0   6.3    0.0045      0.68      55      99 ..     101     145 ..      74     152 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.07
                              ADIP 60 etirkleaeierlqskierlktqleqlerelalvq 94
                                      +++++l+ e++  +++ie l+  +++l++e +   
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEID 41
                                      56666666666666666666666666666665444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0045
                              ADIP  55 reslnetirkleaeierlqskierlktqleqlerelalvqakerq 99 
                                       + s  e+i   + ei+ l+ + + l++q +q +++++++q ++ q
  gi|313124890|ref|YP_004035154.1| 101 QDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQ 145
                                       334444444444444444444444444444444444433333222 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.2     0.032       4.7      36      63 ..      10      37 ..       6      52 .. 0.60
   2 ?    7.8   2.7     0.023       3.4      38      63 ..     111     136 ..      95     150 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.032
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 36 kaLekeNksLkseleelkkevekLkskv 63
                                      ++L++e ++  +e+eel+ +v+ L++++
  gi|313124890|ref|YP_004035154.1| 10 QQLSQELQAIEQEIEELEGDVSDLQQEK 37
                                      5555555555556666666666665554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  38 LekeNksLkseleelkkevekLkskv 63 
                                        ++e ++L +e +el+ + ++++++ 
  gi|313124890|ref|YP_004035154.1| 111 VQGEISDLEDESSELEQQAQQMQQQM 136
                                       55555555555555555555554443 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.6     0.011       1.6      54      87 ..       7      40 ..       4      54 .. 0.59
   2 ?    7.1   7.6     0.035       5.3      30      88 ..      89     147 ..      70     152 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.011
                             Mod_r 54 peleelrselqekleelkelekefeekeqeldel 87
                                      ++l++l++elq+  +e++ele  + +++qe +e+
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEI 40
                                      5566666666666666666666666666655544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.035
                             Mod_r  30 qlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell 88 
                                       +++++ e l+ ++ s+ e+  + + e+ +l +e +e  ++++++++++++ + ++ + +
  gi|313124890|ref|YP_004035154.1|  89 EQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQM 147
                                       44555555555555665555555667777777777777777777777777666665544 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  19.4     0.054       8.1      28     138 ..       6     149 ..       3     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.054
                             Atg14  28 rerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrer...................... 82 
                                       +++l++l  e ++++++ie+++   ++ +q++++i+   +++e+l + +  +                         
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETGSTVQVPLgggaylradvqdidevivglgg 82 
                                       67888888888888888888888888777777777766666666666666555558888888888888888888888 PP

                             Atg14  83 ...........lqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqd 138
                                                  ++ l+ k+++ +++i++ + +++ l d+ ++  ++++ +q+++++ + +q++++q+
  gi|313124890|ref|YP_004035154.1|  83 dyaaeqeqddaIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       8888888889999999999999999999999999999999999999999999999999999999885 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.19        29     184     221 ..      12      48 ..       3      53 .. 0.74
   2 ?    8.6   6.9    0.0072       1.1     191     239 ..      96     145 ..      81     149 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.19
                                       HHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHH CS
                            FliD_C 184 yvkssngtlqtasknltkqikdldkkiedldkrletle 221
                                       +++   +++++++++l+ +++dl+++  ++d+++e++e
  gi|313124890|ref|YP_004035154.1|  12 LSQEL-QAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48 
                                       44333.67888888999999999999999998888765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0072
                                       HHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHH.HHHHHHHH CS
                            FliD_C 191 tlqtasknltkqikdldkkiedldkrletleerlkkqfaal.ekavskln 239
                                       +l+ ++++++++i  ++ +i dl++++++le++ ++  +++ ++ +++++
  gi|313124890|ref|YP_004035154.1|  96 ALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMqQQQMQQMQ 145
                                       55566667777777777777777766666666655433333144555555 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.4      0.42        64      10      34 ..       7      31 ..       5      41 .. 0.84
   2 ?    6.0   0.1     0.069        10      11      34 ..      93     116 ..      88     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.42
                              MtrG 10 ddfnevkkrLdeieekvefvnsEia 34
                                      ++ +++ + L+ ie+ +e  +++++
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVS 31
                                      677899999*********9998876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.069
                              MtrG  11 dfnevkkrLdeieekvefvnsEia 34 
                                        ++++  + d i+e++  v++Ei+
  gi|313124890|ref|YP_004035154.1|  93 AIEALRLKQDSIDERIAAVQGEIS 116
                                       567788899*************97 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.9    0.0051      0.77     103     143 ..       8      48 ..       5      83 .. 0.65
   2 ?    5.3  11.0       0.1        16      99     154 ..      96     149 ..      86     153 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0051
                            DUF724 103 eqtklleerkklekkieeeesekrkleeeidelekkilele 143
                                       + ++l +e++++e++iee e + + l++e +e++++i  +e
  gi|313124890|ref|YP_004035154.1|   8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48 
                                       33444555555555555555555555555555555544443 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.1
                            DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekke 154
                                       +l+ +q+++ e++ +++ +i++ e+e+++le++ +++++++++ ++q+++  +++e
  gi|313124890|ref|YP_004035154.1|  96 ALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQ--QMQE 149
                                       46778888899999999999999999999999999999999998888863..2332 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.2     0.071        11      63      89 ..      15      41 ..       5      53 .. 0.49
   2 ?    8.3   7.0     0.014       2.1      54     101 ..      91     138 ..      90     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.071
                         AAA_lid_9 63 kkeskpeeleklekelaklekekeale 89
                                      + ++ ++e+e+le ++++l++ek+++ 
  gi|313124890|ref|YP_004035154.1| 15 ELQAIEQEIEELEGDVSDLQQEKSEID 41
                                      223333444444444444444444443 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.014
                         AAA_lid_9  54 Deaaarvrlkkeskpeeleklekelaklekekealekeeekekaerlk 101
                                       D a  ++rlk++s +e++++++ e+++le+e ++le++ ++ +++  +
  gi|313124890|ref|YP_004035154.1|  91 DDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQ 138
                                       788889999999999999999999999999999998887754443222 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2      0.28        43      95     116 ..      15      36 ..       2      58 .. 0.60
   2 ?    8.1   3.9     0.019       2.8      91     150 ..      89     146 ..      79     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.28
                          PHM7_cyt  95 aidyyrekleeldeeieeerek 116
                                        ++ +++++eel+  +++++++
  gi|313124890|ref|YP_004035154.1|  15 ELQAIEQEIEELEGDVSDLQQE 36 
                                       3444555555555555555553 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.019
                          PHM7_cyt  91 kkvdaidyyrekleeldeeieeerekvkkkplgaaFvtfesersaaavakqakcaaqiqq 150
                                       ++ dai+ +r k +++de+i + + +++  + ++   + + +++ +++  q +++ q+qq
  gi|313124890|ref|YP_004035154.1|  89 EQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQ-QQQMQ-QMQQ 146
                                       6679***********************9999999999999888888884.32332.3333 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.1    0.0056      0.85      60      93 ..       9      42 ..       2      54 .. 0.52
   2 ?    4.5  11.2      0.27        40      51     101 ..      99     149 ..      85     153 .] 0.52

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0056
                             Muted 60 lesmkenLselnkkleaalekverllqkeleeek 93
                                      l++++++L+ +++++e++  +v++l+q+++e ++
  gi|313124890|ref|YP_004035154.1|  9 LQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDE 42
                                      3444555555555555555555555555444332 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.27
                             Muted  51 lkeqllpkclesmkenLselnkkleaalekverllqkeleeekrkseqlqe 101
                                       lk++ +++ +++++ ++s+l+++  ++ +++++++q+ +++++++ +q+qe
  gi|313124890|ref|YP_004035154.1|  99 LKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       444455555555555555555555555555555555555555544444444 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   3.5      0.09        14      74     110 ..       7      43 ..       4     101 .. 0.75
   2 ?    8.1   8.5     0.015       2.3      63     112 ..     102     151 ..      84     153 .] 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT CS
                        DASH_Spc19  74 keleklerreetLkaklelqegrlsnaesskkeeees 110
                                       ++l++l+++ +++++++e +eg +s+ +++k+e +e+
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEA 43 
                                       5677777777777777777777777755555444443 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.015
                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-X CS
                        DASH_Spc19  63 PqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeesee 112
                                        +i+e +  ++ e++ le + ++L++++++ ++ ++++++++ ++ ++++
  gi|313124890|ref|YP_004035154.1| 102 DSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQEDD 151
                                       57999999999999999999999999999999999998777777766654 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.4     0.014       2.1      26      69 ..       5      48 ..       1      58 [. 0.49
   2 ?    6.6  13.1     0.028       4.2      18     103 ..      60     143 ..      54     152 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                              HemX 26 gqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlq 69
                                      gqqq q+l++e ++++q++++le  ++ +++ek++ +e +e+++
  gi|313124890|ref|YP_004035154.1|  5 GQQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48
                                      45555444444444444444444444444444444444444443 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.028
                              HemX  18 vgaglyylgqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqq 94 
                                       +g+g+y  +  q       +  l  + aa ++q +++ea++ +++ + er+++ ++++++le e+++l++q +++qq
  gi|313124890|ref|YP_004035154.1|  60 LGGGAYLRADVQD--IDEVIVGLGGDYAAEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQ 134
                                       5666666555553..44444555566666666666666666666666666666666666666666666666666666 PP

                              HemX  95 qlskvsgae 103
                                       q+++ + ++
  gi|313124890|ref|YP_004035154.1| 135 QMQQQQMQQ 143
                                       666544433 PP

>> Borealin  Cell division cycle-associated protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1         3   4.5e+02     106     119 ..       6      19 ..       1      29 [. 0.85
   2 ?    4.6   0.0      0.21        31      70      93 ..      53      76 ..      42      81 .. 0.85
   3 ?    3.8   2.1      0.36        54      87     114 ..     122     149 ..      95     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 3
                          Borealin 106 lkqlkkLqsnLaki 119
                                        +ql++L+++L++i
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAI 19 
                                       68999999999987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.21
                          Borealin 70 vanvniPvgdGevlslqakeldev 93
                                         v++P+g+G  l+   +++dev
  gi|313124890|ref|YP_004035154.1| 53 GSTVQVPLGGGAYLRADVQDIDEV 76
                                      5689***********999999987 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.36
                          Borealin  87 akeldevdeellekLdeetlkqlkkLqs 114
                                       ++el++  +++ ++++++ ++q++++q+
  gi|313124890|ref|YP_004035154.1| 122 SSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       67888888889999********999886 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.1     0.002      0.29     113     151 ..       6      44 ..       5      58 .. 0.75
   2 ?    2.7  12.4      0.42        64      86     127 ..      99     140 ..      86     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.002
                           DUF4763 113 rqqlaelqqhlkasrkslkelreslcqekkrlrklqkrl 151
                                       +qql++l+q l+a +++++el+ +++ +++   +  + +
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAI 44 
                                       789999999999999999999988887777655555544 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.42
                           DUF4763  86 vdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkasr 127
                                       +++d  +e++  +q ei +L  +++ L qq +++qq++++++
  gi|313124890|ref|YP_004035154.1|  99 LKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQ 140
                                       455666677777999999999999999999999999887654 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.5      0.03       4.5      57      93 ..       7      43 ..       5      54 .. 0.60
   2 ?    9.2   8.9    0.0079       1.2      77     127 ..      87     137 ..      85     139 .. 0.78
   3 ?    8.0  12.1     0.019       2.8       3      42 ..     108     148 ..     106     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.03
                        TPR_MLP1_2 57 kelqalreelnelkaeiaelkaeaesakaeleesees 93
                                      ++lq+l +el+ +++ei+el+ ++ ++++e +e  e+
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEA 43
                                      5666666666666666666666666655554444443 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0079
                        TPR_MLP1_2  77 kaeaesakaeleeseesweeqkeelekelselekriedlneqNklLhdQlE 127
                                       ++e ++a ++l  ++ s++e+  + + e+s+le    +l++q + + +Q++
  gi|313124890|ref|YP_004035154.1|  87 EQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQ 137
                                       677788888888888888888888888888888888888888888888887 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.019
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqa.eiakeaq 42 
                                       +++++ ei++l++e++e+e+++q++q+++++q+ ++++++q
  gi|313124890|ref|YP_004035154.1| 108 IAAVQGEISDLEDESSELEQQAQQMQQQMQQQQmQQMQQMQ 148
                                       78899************************987625566666 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.2       0.1        15       9      44 ..       8      43 ..       2      52 .. 0.53
   2 ?    8.5   8.7     0.018       2.6      10      56 ..     101     147 ..      88     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.1
                       Cep57_MT_bd  9 pkeaLaevlkeLedEfehlklelqelaaqynaldps 44
                                        ++L+  l+++e E+e+l  + ++l+++  + d +
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEA 43
                                      334455555555555555555555555555444443 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.018
                       Cep57_MT_bd  10 keaLaevlkeLedEfehlklelqelaaqynaldpslgkrkRkdLaee 56 
                                       +++  e + + + E++ l  e +el++q +++++ +++++ +++++ 
  gi|313124890|ref|YP_004035154.1| 101 QDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQM 147
                                       6778899*****************************99999988875 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.0       1.6   2.4e+02       5      30 ..       9      37 ..       5      55 .. 0.47
   2 ?   11.5   4.7    0.0013       0.2      25      61 ..     107     143 ..      87     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.6
                                      HHHHHHHHHCCCCHHCC...HHHHCHCCC CS
                     Synaptobrevin  5 lakikaevdevkdimke...Nidkvlerg 30
                                      l+++ +e++ +++ ++e   ++ ++ + +
  gi|313124890|ref|YP_004035154.1|  9 LQQLSQELQAIEQEIEElegDVSDLQQEK 37
                                      55555555555554443211333333333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0013
                                       HCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHHH CS
                     Synaptobrevin  25 kvlergekldeLvdktenLqssaqqFkkqarklkrkm 61 
                                       ++ + + ++++L+d++++L+++aqq ++q ++++ ++
  gi|313124890|ref|YP_004035154.1| 107 RIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQ 143
                                       5566677888888888888888888888877766554 PP

>> DUF4515  Domain of unknown function (DUF4515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.1     0.013         2     169     201 ..       6      38 ..       5      47 .. 0.80
   2 ?    7.9   9.8     0.017       2.5     148     202 ..      84     138 ..      80     144 .. 0.91
   3 ?   -0.8   2.6       7.4   1.1e+03      67      81 ..     138     149 ..     134     153 .] 0.38

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.013
                           DUF4515 169 rkeLlqliketkkLekekskLeeqkqrlkeeqe 201
                                       +++L+ql++e +++e+e ++Le     l++e+ 
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKS 38 
                                       678888888888888888888888888888874 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.017
                           DUF4515 148 laAkkalseftrsvkreNqeLrkeLlqliketkkLekekskLeeqkqrlkeeqey 202
                                        aA +  ++++++++ + + + ++ +  + e+  Le+e+s+Le+q q+++++ + 
  gi|313124890|ref|YP_004035154.1|  84 YAAEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQ 138
                                       689999*******************************************998764 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 7.4
                           DUF4515  67 kkeLqalediaklke 81 
                                       ++++q++   ++++e
  gi|313124890|ref|YP_004035154.1| 138 QQQMQQM---QQMQE 149
                                       3333333...33333 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.3    0.0026      0.39     101     142 ..       7      48 ..       4      53 .. 0.68
   2 ?    3.6   9.6       0.1        15     347     409 ..      88     151 ..      81     153 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHH CS
                              EzrA 101 kklaeleeeldeveekikkileelkelteseeknreeieklk 142
                                       ++l++l +el+ +e++i+++  ++++l++ +++  e+ie+++
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48 
                                       566777777777777777777777777777777776666654 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHH.HHHHHHHHHHHHHHH CS
                              EzrA 347 relekelkelekdyeeleekleekkvaYSelqeeleeleekleeieek.qeeileslkslrkdE 409
                                       +e ++ ++ l+ + ++++e++++ +   S+l++e  ele++ ++++++ q++  ++++++++d+
  gi|313124890|ref|YP_004035154.1|  88 QEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQmQQQQMQQMQQMQEDD 151
                                       5566788899999999999999999999999999999999999998763556678888888886 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.2     0.012       1.8      27      67 ..       8      48 ..       6      54 .. 0.72
   2 ?    8.9   4.0    0.0099       1.5      28      73 ..      87     132 ..      85     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.012
                        TMF_DNA_bd 27 kelklnntikkLrkknkelekeikelkkkleklekeleele 67
                                      + ++l++ +    ++++ele ++++l++++++ ++ +e +e
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIE 48
                                      45667777777788888888888888888887777777766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0099
                        TMF_DNA_bd  28 elklnntikkLrkknkelekeikelkkkleklekeleeleerlkea 73 
                                       e+++  +i  Lr k    ++ i+  + ++++le e +ele+ ++++
  gi|313124890|ref|YP_004035154.1|  87 EQEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQM 132
                                       889999***********************************99886 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.9      0.16        24      45      96 ..       8      59 ..       4      67 .. 0.78
   2 ?    9.4  12.3    0.0061      0.92      10      79 ..      76     149 ..      64     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.16
                           DUF2570 45 anqrLteqLeqerqavekqqkianelkakveeekeevktilkqesCakvalP 96
                                        q+L ++L+   q +e+ +    +l+++ +e  e + +i + e+   v++P
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETGSTVQVP 59
                                      3466777777777777788888889999999999999999888888888887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0061
                           DUF2570  10 iilgLgv...wlwsqsqkidsLraenkaqaqlieeqqkanqrLt.eqLeqerqavekqqkianelkakveeeke 79 
                                       +i+gLg+   +  +q + i++Lr  + + ++ i+  q     L  e+ e e+qa + qq+++++  +++++ +e
  gi|313124890|ref|YP_004035154.1|  76 VIVGLGGdyaAEQEQDDAIEALRLKQDSIDERIAAVQGEISDLEdESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       799999732245678889**********9999998776666666157899*************99999999887 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.8    0.0077       1.2      51      80 ..       7      36 ..       5      40 .. 0.91
   2 ?    7.6   4.7     0.031       4.7      48      84 .]     103     139 ..      87     139 .. 0.81
   3 ?    5.7   4.2      0.12        18       4      25 ..     120     141 ..     117     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0077
                      Lzipper-MIP1 51 kkakellkeiallEeevvkLEqkllsLyrk 80
                                      ++ ++l +e+  +E+e+ +LE  +++L+++
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQE 36
                                      58899**********************975 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.031
                      Lzipper-MIP1  48 llpkkakellkeiallEeevvkLEqkllsLyrklfqe 84 
                                       ++++ ++    ei+ lE e ++LEq+ +++++++ q+
  gi|313124890|ref|YP_004035154.1| 103 SIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQ 139
                                       4777777777899999999999999999999998887 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.12
                      Lzipper-MIP1   4 ekrssLeqeveqLqerLqeeek 25 
                                       ++ s+Leq  +q+q+++q+++ 
  gi|313124890|ref|YP_004035154.1| 120 DESSELEQQAQQMQQQMQQQQM 141
                                       5678999999999999999975 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.9      0.16        23      28      67 ..      13      48 ..       5      58 .. 0.42
   2 ?    8.2   2.9    0.0085       1.3      46      99 ..      94     148 ..      66     153 .] 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.16
                              Tho2 28 ekeieklkseieelakdrsderaaakkkkkekkrlkelie 67
                                       +e++ +++eieel++d sd     +++k e+++  e ie
  gi|313124890|ref|YP_004035154.1| 13 SQELQAIEQEIEELEGDVSD----LQQEKSEIDEAIEAIE 48
                                      23444444444444333333....2333333333333333 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0085
                              Tho2  46 sde.raaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekkswfknde 99 
                                        ++ r ++++ +++++ ++  i+ Le+E +e +++ +++++++++++ + +++ +
  gi|313124890|ref|YP_004035154.1|  94 IEAlRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQ 148
                                       3344777888899999999999999999999999999999999998877666444 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.5     0.038       5.7       2      29 ..      13      40 ..       6      51 .. 0.71
   2 ?    2.1   6.7       1.1   1.7e+02       3      25 ..     113     135 ..     111     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.038
                         DASH_Dam1  2 epafaeLaDsletLdknledLqqihesL 29
                                      +++++ ++ ++e+L+  ++dLqq + ++
  gi|313124890|ref|YP_004035154.1| 13 SQELQAIEQEIEELEGDVSDLQQEKSEI 40
                                      4567777777777777777777765555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 1.1
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqi 25 
                                        ++++L+D+ ++L+++ +++qq 
  gi|313124890|ref|YP_004035154.1| 113 GEISDLEDESSELEQQAQQMQQQ 135
                                       57899**************9974 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2      0.19        29     110     147 ..      18      55 ..       1      59 [. 0.76
   2 ?    6.5   5.2     0.045       6.9     116     158 ..     109     151 ..     101     153 .] 0.92

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.19
                                       EES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      CLP_protease 110 mihqPlggaqgqasdieieaeellkikerlneilakht 147
                                        i q    ++g +sd+++e  e+++  e ++++ + +t
  gi|313124890|ref|YP_004035154.1|  18 AIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETGST 55 
                                       57788888999999999999999988888877666555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.045
                                       EEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHH CS
                      CLP_protease 116 ggaqgqasdieieaeellkikerlneilakhtgqslekiekdl 158
                                        ++qg+ sd+e e  el++  +++++ ++++  q+++++++d 
  gi|313124890|ref|YP_004035154.1| 109 AAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQEDD 151
                                       5789***********************************9985 PP

>> Med4  Vitamin-D-receptor interacting Mediator subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.3     0.023       3.4      29      58 ..       7      36 ..       5      58 .. 0.58
   2 ?    5.7   9.3     0.072        11      25      82 ..      88     143 ..      84     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.023
                              Med4 29 arilqLraeveslDekikeivksLkeyeke 58
                                      ++++qL +e ++ +++i e+++ + ++++e
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQE 36
                                      556666666666666666666555555444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.072
                              Med4  25 qknearilqLraeveslDekikeivksLkeyekeLkavpdqenskldtasiklaekre 82 
                                       q+  + i+ Lr ++ s De i  +++++ ++e e +++ +q+++    +++++++ ++
  gi|313124890|ref|YP_004035154.1|  88 QEQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQ--QQMQQQQMQQ 143
                                       788899999**********999999999999977666554444443..4444444443 PP

>> TEX13  Testis-expressed sequence 13 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.7      0.62        94      86     135 ..       9      43 ..       4      55 .. 0.45
   2 ?    9.4   8.4    0.0053      0.79      70     139 ..      80     148 ..      77     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.62
                             TEX13  86 vqkLqdqveehksaaqaLaselkrlreqqemerkeaasqlqlaqaalaev 135
                                       +q+L + ++  +   + L ++++                lq+ ++++ e+
  gi|313124890|ref|YP_004035154.1|   9 LQQLSQELQAIEQEIEELEGDVS---------------DLQQEKSEIDEA 43 
                                       33333333333333333444444...............444444444444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0053
                             TEX13  70 LgvrvaarqrelqarrvqkL.qdqveehksaaqaLaselkrlreqqemerkeaasqlqlaqaalaevqker 139
                                       Lg   aa q++ +a    +L qd ++e+ +a q  +s+l+   +  e e++  ++q q++q++++++q+ +
  gi|313124890|ref|YP_004035154.1|  80 LGGDYAAEQEQDDAIEALRLkQDSIDERIAAVQGEISDLEDESS--ELEQQAQQMQQQMQQQQMQQMQQMQ 148
                                       6667899999999988888757999**99999999999998877..7777777777777777777776643 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5     0.045       6.7      38      71 ..      14      47 ..       2      58 .. 0.57
   2 ?    5.1   5.0      0.14        21      39      78 ..     100     139 ..      84     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.045
                           DUF4446 38 kdgksleellkekleeveelkeeseelekeieel 71
                                      ++ + +e+ ++e   +v +l++e++e+++ ie++
  gi|313124890|ref|YP_004035154.1| 14 QELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAI 47
                                      2445555555555555566666666655555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.14
                           DUF4446  39 dgksleellkekleeveelkeeseelekeieeleeklkks 78 
                                       +++s++e ++    e+ +l++es+ele++ ++++++++++
  gi|313124890|ref|YP_004035154.1| 100 KQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQ 139
                                       6788999999999999999999999999999999988764 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   6.5     0.046       6.9     181     319 ..       7     141 ..       2     152 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.046
                              FUSC 181 egaeareaararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpela 257
                                       ++ ++ +++++++ ++i +le+ +s +  e+++                                          ++
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSE------------------------------------------ID 41 
                                       333333444444444444444444444444444..........................................55 PP

                              FUSC 258 allaelaal......................................eaaaaaealeaalaalrarlralrralead 296
                                       + ++++++l                                      e+ +a eal+ + +++++r++a++ + ++ 
  gi|313124890|ref|YP_004035154.1|  42 EAIEAIETLetgstvqvplgggaylradvqdidevivglggdyaaeqEQDDAIEALRLKQDSIDERIAAVQGEISDL 118
                                       55555555555555566666666555555555555666665555555445677777777788888888888888888 PP

                              FUSC 297 adtaalllarlaellaelaqlla 319
                                        d + +l ++++++ ++++q + 
  gi|313124890|ref|YP_004035154.1| 119 EDESSELEQQAQQMQQQMQQQQM 141
                                       88888888888888887777433 PP

>> HNOBA  Heme NO binding associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.4    0.0015      0.23     169     207 ..       4      42 ..       1      47 [. 0.92
   2 ?    1.5   4.5       1.2   1.7e+02     180     200 ..     121     141 ..      88     153 .] 0.50

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0015
                             HNOBA 169 agiqqsaelelaldqleeksaeLeesmkeleeekkrtde 207
                                        g+qq+++l+  l+  e++ +eLe   ++l++ek  +de
  gi|313124890|ref|YP_004035154.1|   4 GGQQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDE 42 
                                       689********************************9997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.2
                             HNOBA 180 aldqleeksaeLeesmkelee 200
                                          +le+++++++++m++ + 
  gi|313124890|ref|YP_004035154.1| 121 ESSELEQQAQQMQQQMQQQQM 141
                                       222222222222222222222 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2     0.025       3.7       4      47 ..       7      50 ..       5      78 .. 0.78
   2 ?    3.1   6.7      0.49        74       7      38 ..     109     140 ..      85     152 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.025
                     USP8_interact  4 elvqkqqqkiaelkkevaeqkqqlseqkrelellkeyiralrst 47
                                      +++q+ +q+++ +++e++e +  +s+ ++e + + e+i a+ + 
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETL 50
                                      56788888888888888888888888888888888877777654 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.49
                     USP8_interact   7 qkqqqkiaelkkevaeqkqqlseqkrelellk 38 
                                          q +i++l++e++e +qq ++ ++++++ +
  gi|313124890|ref|YP_004035154.1| 109 AAVQGEISDLEDESSELEQQAQQMQQQMQQQQ 140
                                       44455555555555555554444444443322 PP

>> DUF932  Domain of unknown function (DUF932)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.044       6.6     112     155 ..       6      49 ..       2      70 .. 0.89
   2 ?    2.5   5.3      0.67     1e+02     109     154 ..     102     146 ..      85     153 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.044
                            DUF932 112 dakvieakkaLglvveefeefeeeaealaavklteaeaeafaea 155
                                       ++++++ +++L+ + +e+ee+e  + +l++ k + +ea + +e+
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIET 49 
                                       6899999************************9999999998884 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.67
                            DUF932 109 gnvdakvieakkaLglvveefeefeeeaealaavklteaeaeafae 154
                                       +++d+++++++ ++    +e+ e+e++a+++++ ++++++++++ +
  gi|313124890|ref|YP_004035154.1| 102 DSIDERIAAVQGEISDLEDESSELEQQAQQMQQ-QMQQQQMQQMQQ 146
                                       6789999999*99*****************987.566666666655 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.4     0.025       3.8      74     106 ..      10      42 ..       2      54 .. 0.44
   2 ?    5.4   8.5       0.1        16      68     114 ..      96     142 ..      68     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.025
                            Nsp1_C  74 nkidqeLeyiesqqdeLeslLdnyEkeleells 106
                                       +++ qeL+ ie++ +eLe  + ++ +e +e+ +
  gi|313124890|ref|YP_004035154.1|  10 QQLSQELQAIEQEIEELEGDVSDLQQEKSEIDE 42 
                                       334444444444444444443333333333332 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.1
                            Nsp1_C  68 eaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsklesqksd 114
                                       + + +q  id+++  ++ + ++Le+   ++E++++++++++++q+ +
  gi|313124890|ref|YP_004035154.1|  96 ALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQ 142
                                       44568899999999999999999999999999999998877777654 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   2.2      0.11        17      27      56 ..      10      39 ..       4      52 .. 0.51
   2 ?    6.9   9.7     0.051       7.7      22      63 ..      97     138 ..      87     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.11
                               CLZ 27 keleekverLessLeaLqtrlarLlaeyes 56
                                      ++l + ++ +e+++e L+  +  L +e ++
  gi|313124890|ref|YP_004035154.1| 10 QQLSQELQAIEQEIEELEGDVSDLQQEKSE 39
                                      444455555555555555555555555444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.051
                               CLZ  22 agaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkq 63 
                                        + +q++++e++  +++++  L++    L ++ +++q++++q
  gi|313124890|ref|YP_004035154.1|  97 LRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQ 138
                                       455666666666666666666666666666666666666665 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.8     0.059       8.8      55      87 ..      12      44 ..       3      54 .. 0.46
   2 ?    5.6   5.4     0.042       6.3      21      64 ..     102     146 ..      92     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.059
                           Vps53_N 55 gkealeeaqkaieelfqkikeikdkaekseemv 87
                                        ++l+ +++ ieel+ +++++++   + +e +
  gi|313124890|ref|YP_004035154.1| 12 LSQELQAIEQEIEELEGDVSDLQQEKSEIDEAI 44
                                      233444444444444444444444333333333 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.042
                           Vps53_N  21 anidelikklqeeikklddeiksvvraqanvgekgk.ealeeaqk 64 
                                       + ide i+ +q+ei+ l+de  +++++  ++ ++ + ++++++q+
  gi|313124890|ref|YP_004035154.1| 102 DSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQqQQMQQMQQ 146
                                       579********************9999888887754155666654 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.6     0.033         5      21      57 ..      11      47 ..       4      53 .. 0.52
   2 ?    5.7   3.9      0.11        17       2      56 ..      94     146 ..      66     153 .] 0.52

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.033
                           zf-C4H2 21 kevealekeekcleeykkelelLeqEkmaHveeLrlI 57
                                      +  ++l++ e+ +ee +  ++ L+qEk +  e +  I
  gi|313124890|ref|YP_004035154.1| 11 QLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAI 47
                                      3334444444455555555555555555544444444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.11
                           zf-C4H2   2 ikeirektleleklknklakevealekeekcleeykkelel.LeqEkmaHveeLrl 56 
                                       i+ +r k +++++  + ++ e++ le+e++ le+  +++++ ++q +m+ ++   +
  gi|313124890|ref|YP_004035154.1|  94 IEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQqMQQQQMQQMQ---Q 146
                                       3444444444444444444444444444444444444433212222322222...2 PP

>> GPS2_interact  G-protein pathway suppressor 2-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.7      0.23        35      31      63 ..      11      43 ..       6      58 .. 0.70
   2 ?    8.7   9.2     0.016       2.4      17      80 ..      89     145 ..      82     153 .] 0.53

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.23
                     GPS2_interact 31 eLlqnidkvDREiakveqqiskLkkkqkeleee 63
                                      +L q+++ +  Ei   e ++s L++ + e++e+
  gi|313124890|ref|YP_004035154.1| 11 QLSQELQAIEQEIEELEGDVSDLQQEKSEIDEA 43
                                      566777777777777777777777777777664 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.016
                     GPS2_interact  17 eqeqelvpsrlsKdeLlqnidkvDREiakveqqiskLkkkqkeleeeaakpkeeekpvepssse 80 
                                       eq+++  + rl  d + + i+ v  Ei+  e + s+L ++ ++++++ ++        + ++++
  gi|313124890|ref|YP_004035154.1|  89 EQDDAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQ-------QMQQMQ 145
                                       455555555555555555555555555555555555555555555555444.......333333 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   4.6     0.078        12      49      88 ..       8      47 ..       4      58 .. 0.46
   2 ?    7.2   7.8     0.047       7.1      38      81 ..     103     147 ..      70     152 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.078
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHH CS
                             DUF16 49 qinkleqkvekqgekikelkveqkaqgeelnkvdetleli 88
                                      q+++l q+ ++ +++i+el+ ++   ++e  ++de++e i
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAI 47
                                      4444444444444444444444444444444444443333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.047
                                       HHHHHHH...HHHHHHHHHHHHHHHHHHHHHHH.HHHHHH..... CS
                             DUF16  38 kieakvdklgeqinkleqkvekqgekikelkve.qkaqgeelnkv 81 
                                        i++++++ + +i+ le++ ++++++ ++++++ q++q ++++++
  gi|313124890|ref|YP_004035154.1| 103 SIDERIAAVQGEISDLEDESSELEQQAQQMQQQmQQQQMQQMQQM 147
                                       345555555555555555555555555444333122223333333 PP

>> FAD-SLDH  Membrane bound FAD containing D-sorbitol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2       3.3     5e+02      69      94 ..       9      34 ..       4      53 .. 0.47
   2 ?    9.1   4.1    0.0082       1.2      62      97 ..     115     150 ..      93     153 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 3.3
                          FAD-SLDH 69 daefkaqlaaLaallekqkakdveal 94
                                       ++++++l+a+ + +e+ +++  + +
  gi|313124890|ref|YP_004035154.1|  9 LQQLSQELQAIEQEIEELEGDVSDLQ 34
                                      34444444444444433333322222 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0082
                          FAD-SLDH  62 yaalvaedaefkaqlaaLaallekqkakdveallaa 97 
                                        + l +e +e+++q++++++ +++q+++++++++++
  gi|313124890|ref|YP_004035154.1| 115 ISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQED 150
                                       5679999*************************9987 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.0     0.018       2.7      11      45 ..       7      40 ..       4      57 .. 0.65
   2 ?    3.7   9.0      0.76   1.1e+02      18      69 ..     106     147 ..      84     153 .] 0.34

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.018
                    PRKG1_interact 11 eenerLkreLeelekelselkseleklkqqrqesv 45
                                      ++ ++L +eL+ +e+e++el+  ++ l+q+++e +
  gi|313124890|ref|YP_004035154.1|  7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSE-I 40
                                      556777888888888888888888887755443.2 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.76
                    PRKG1_interact  18 reLeelekelselkseleklkqqrqesvskrssllelekrerrslerkisel 69 
                                       +++  ++ e+s+l+ e ++l+qq            +++++ ++++ ++++++
  gi|313124890|ref|YP_004035154.1| 106 ERIAAVQGEISDLEDESSELEQQ----------AQQMQQQMQQQQMQQMQQM 147
                                       33333333333333333333222..........1112222222222222222 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.2    0.0065      0.98      37      71 ..       6      40 ..       5      48 .. 0.90
   2 ?    3.3   6.3      0.75   1.1e+02      37      68 ..     112     143 ..     105     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0065
                       Fungal_TACC 37 qkkldklelenkslkqeieqLkkqleaerkEKqeL 71
                                      q++l++l++e ++ +qeie+L+  ++  ++EK+e+
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEI 40
                                      789**********************9999999987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.75
                       Fungal_TACC  37 qkkldklelenkslkqeieqLkkqleaerkEK 68 
                                       q +++ le e ++l+q+ +q+++q++ +++  
  gi|313124890|ref|YP_004035154.1| 112 QGEISDLEDESSELEQQAQQMQQQMQQQQMQQ 143
                                       789999999999**********9999887754 PP

>> Cauli_DNA-bind  Caulimovirus DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4      0.21        31      10      43 ..      11      44 ..       3      56 .. 0.57
   2 ?    5.8   2.4     0.092        14       7      52 ..      93     138 ..      87     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.21
                                      HHHHHHHHHHHHHHHHHHHHHTS--HHHHHHHHH CS
                    Cauli_DNA-bind 10 evlsdqkkieaeikaileklgstkpekesleeva 43
                                      ++ ++++ ie+ei+++   ++  ++ek++++e+ 
  gi|313124890|ref|YP_004035154.1| 11 QLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAI 44
                                      5555555555555555555555555555555443 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHH CS
                    Cauli_DNA-bind   7 eieevlsdqkkieaeikaileklgstkpekesleevaakiikdltk 52 
                                        ie +  +q +i++ i a+   ++  ++e+++le+ a ++ + + +
  gi|313124890|ref|YP_004035154.1|  93 AIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQ 138
                                       58888999999***********************999988777654 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.2     0.021       3.2      74     112 ..       7      45 ..       5      53 .. 0.69
   2 ?    4.8   6.1     0.092        14      48     117 ..      75     142 ..      69     151 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.021
                       DLP_helical  74 rqlpeaeerleelekevekleesakriekelaelkkeie 112
                                       +ql++  ++l+++e+e+e+le +++++++e +e+ + ie
  gi|313124890|ref|YP_004035154.1|   7 QQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIE 45 
                                       677777777777777777777777777777776666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.092
                       DLP_helical  48 ekikknggelalieetkksvirdvlerqlpeaeerleelekevekleesakriekelaelkkeieearie 117
                                       e+i   gg     e+ +++ i + l  +   + er+ +++ e+ +le++++++e++ +++++++++ +++
  gi|313124890|ref|YP_004035154.1|  75 EVIVGLGGD-YAAEQEQDDAIEA-LRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQ 142
                                       555666666.4555555555533.3333455555555555555555555555555555555555555544 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.5     0.023       3.5      11      47 ..       6      42 ..       4      52 .. 0.65
   2 ?    4.8   9.4      0.13        20      13      58 ..     100     145 ..      86     152 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.023
                                      HHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHH CS
                              GrpE 11 edeeeeleeeleelekevkelkekllrllaefenlrk 47
                                      ++++++l +el+++e+e++el+ ++  l++e  ++ +
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDE 42
                                      4667777777777777777777666666665555444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.13
                                       HHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHH CS
                              GrpE  13 eeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakk 58 
                                       ++++ +e++++ + e+ +l+++  +l+++++++++++++++ +  +
  gi|313124890|ref|YP_004035154.1| 100 KQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQ 145
                                       4444555555555555555555555555555555555555444433 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.2   0.00094      0.14      24      56 ..       6      38 ..       2      54 .. 0.63
   2 ?    0.1  21.3       5.8   8.7e+02      16      62 ..     104     150 ..      89     153 .] 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00094
                     TolA_bind_tri 24 qqqlealqqelreLRGqiEelqyqleqleerQr 56
                                      qqql++l+qel+ +  +iEel+ ++++l++   
  gi|313124890|ref|YP_004035154.1|  6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKS 38
                                      566666666666666666666666666655443 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 5.8
                     TolA_bind_tri  16 rsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldl 62 
                                        ++ +  +q ++++l+ e +eL  q +++q q++q + +Q ++ ++ 
  gi|313124890|ref|YP_004035154.1| 104 IDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQED 150
                                       45667778888888888888888888888888888888888888775 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   7.4     0.099        15     206     308 ..       6     145 ..       4     152 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.099
                             LMBR1 206 yfeaaklntekeeaereledllkevkklrksisesdplrkyleeilk.............................. 252
                                       + ++++l++e++  e+e+e+l  +v+ l++++se d+  + +e++ +                              
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETgstvqvplgggaylradvqdidevivglgg 82 
                                       56778889999999999999999999999999888855555555555777766666666666666666666666666 PP

                             LMBR1 253 .kvPeeiaeklks.......nenkteeslaklekqlikalqkrertekqwkrllekaleledii 308
                                        +  e+ ++++ +       +  +   +++ + ++l  ++++ e++ +q+++ ++++ +++++ 
  gi|313124890|ref|YP_004035154.1|  83 dYAAEQEQDDAIEalrlkqdSIDERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQ-QMQQMQ 145
                                       522222222222234432221111111222222333333444444444444444444.333332 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  18.1      0.42        64       4     127 ..       6     135 ..       5     153 .] 0.67

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.42
                            CASP_C   4 qeelseleaeleeqkeLnekLEndllkvqseasnaskasdassagsevsrkaese.........grk.sptssiisg 70 
                                       q++l++l++el+  ++ +e+LE d++ +q+e+s+  +a +a ++ ++ s+ +              + +   ++i g
  gi|313124890|ref|YP_004035154.1|   6 QQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETLETGSTVQ--VplgggaylrA-DvQDIDEVIVG 79 
                                       799*****************************98766555554444433333..12334455432.22556666666 PP

                            CASP_C  71 aeesesaesssessiLpivtsQRDRFrkrnaeLEeelrkqeetvsslraeiaslqkD 127
                                       +  +  ae+++++ i ++  +Q D   +r+a ++ e+++ e++ s+l ++++++q+ 
  gi|313124890|ref|YP_004035154.1|  80 LGGDYAAEQEQDDAIEALRLKQ-DSIDERIAAVQGEISDLEDESSELEQQAQQMQQQ 135
                                       6666556655555555554444.7777777777777777777777777777777764 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.2     0.011       1.6      34      84 ..       8      44 ..       4      56 .. 0.38
   2 ?    3.4  15.9      0.37        55      20      76 ..      89     149 ..      84     152 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.011
                               ERM 34 taelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerkl 84
                                      + ++L ++++  e+e e+Le + +++++e++++               + +
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQELQAIEQEIEELEGDVSDLQQEKSEI--------------DEAI 44
                                      223333333333333333333333333333333..............2222 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.37
                               ERM  20 eaekaqeaLrese....etaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeee 76 
                                       e + a eaLr ++    e++   + +   +e e+ +Leq+a+++++++q+ +++++++++e
  gi|313124890|ref|YP_004035154.1|  89 EQDDAIEALRLKQdsidERIAAVQGEISDLEDESSELEQQAQQMQQQMQQQQMQQMQQMQE 149
                                       4444555555444111134445666677777777777777777777777777777777666 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   3.3     0.054       8.2       4      32 ..       8      36 ..       6      51 .. 0.52
   2 ?    5.3   6.2      0.14        21       3      46 ..      92     135 ..      90     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.054
                       Cep57_CLD_2  4 evktLqnrLdsltrklqvheeelkrLnkE 32
                                      + ++L  +L  +++++++ e+   +L +E
  gi|313124890|ref|YP_004035154.1|  8 QLQQLSQELQAIEQEIEELEGDVSDLQQE 36
                                      33444444444444444444444444444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.14
                       Cep57_CLD_2   3 aevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyee 46 
                                        ++++L+ + ds+++++++ ++e+ +L  E ++ ++q ++  + 
  gi|313124890|ref|YP_004035154.1|  92 DAIEALRLKQDSIDERIAAVQGEISDLEDESSELEQQAQQMQQQ 135
                                       57899******************************999986555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.9    0.0047      0.71      33      78 ..       5      50 ..       1      77 [. 0.89
   2 ?   -0.2   1.3       3.8   5.7e+02      45      74 ..     102     131 ..      72     145 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0047
                                      CHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short 33 seekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78
                                       +++l+++ +el++ ++++  +++Dv+d ++ +  +++a++ +++l
  gi|313124890|ref|YP_004035154.1|  5 GQQQLQQLSQELQAIEQEIEELEGDVSDLQQEKSEIDEAIEAIETL 50
                                      57899**************************999999998887766 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.8
                                       HHTTSEEEEEE-TTTSHHHHHHHHHHHHHH CS
                         adh_short  45 keegakalaiqvDvtdreevealvekavkk 74 
                                        +  +++ a+q+ ++d e+ +  +e+ +++
  gi|313124890|ref|YP_004035154.1| 102 DSIDERIAAVQGEISDLEDESSELEQQAQQ 131
                                       333556666666665543332222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4648  (0.259245); expected 358.6 (0.02)
Passed bias filter:                     1455  (0.0811534); expected 358.6 (0.02)
Passed Vit filter:                       312  (0.017402); expected 17.9 (0.001)
Passed Fwd filter:                       186  (0.0103743); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             119  [number of targets reported over threshold]
# CPU time: 0.95u 0.40s 00:00:01.35 Elapsed: 00:00:00.54
# Mc/sec: 859.27
//
Query:       gi|313124891|ref|YP_004035155.1|  [L=58]
Description: 50S ribosomal protein Lx [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-10   40.0   0.0    3.8e-10   39.9   0.0    1.0  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   2.1e-14   3.8e-10      68     121 .]       3      56 ..       1      56 [. 0.95

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.1e-14
                                       ...........TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                    Ribosomal_L18A  68 nygiwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                        +++  +++sr+g+ +f   + + +e+ a ++v+s++gs+h +kr++I+I +v+
  gi|313124891|ref|YP_004035155.1|   3 QFTVSGQFQSRDGYSEFQTVVDAPNENVARDRVFSNIGSQHGLKRTQIEITEVS 56 
                                       5888899********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.33s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 362.32
//
Query:       gi|313124892|ref|YP_004035156.1|  [L=221]
Description: translation initiation factor 6 (aeif-6) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-69  233.3   0.1    1.9e-69  233.1   0.1    1.0  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.1   0.1     1e-73   1.9e-69       1     197 []       3     199 ..       3     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.1 bits;  conditional E-value: 1e-73
                                       .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHH CS
                             eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeele 77 
                                       r+s++gs ++Gvfa++t++++lv++++e+++v+a+ +eL+v++v+tt++gs +vG+l++gN+ng+lv+ ++t++e e
  gi|313124892|ref|YP_004035156.1|   3 RASFAGSAYVGVFACVTDHVLLVRPDAEDDVVDAMTAELDVPAVRTTVGGSGTVGALAMGNDNGILVSARATEREKE 79 
                                       689************************************************************************** PP

                                       HHHHHHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE CS
                             eIF-6  78 klkeslkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllv 154
                                       ++++ + ++v++l+ +++A+GNv+laND++A+vhpdls+e+  +++d+L+v+ +rg++a+++t G+aav+tn g+l+
  gi|313124892|ref|YP_004035156.1|  80 TIEDVAGVPVTELPGRINAAGNVVLANDSGAYVHPDLSDEALAVVEDALDVPAERGDLADVRTAGTAAVATNDGVLC 156
                                       ***************************************************************************** PP

                                       -TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 155 hpkateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       hpk++e ele leell+v++++gTvN+G +lvgsglvaN+ g+
  gi|313124892|ref|YP_004035156.1| 157 HPKSREPELEALEELLDVRADIGTVNYGAPLVGSGLVANEFGY 199
                                       ***************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1299.54
//
Query:       gi|313124893|ref|YP_004035157.1|  [L=92]
Description: 50S ribosomal protein L31e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-06   27.5   0.0    3.6e-06   27.1   0.0    1.1  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0     2e-10   3.6e-06      12      78 ..      15      83 ..       8      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2e-10
                    Ribosomal_L31e 12 hkrihgvgfkkraprAlkeikkfamkemg..tpdvridtrLnkavwakgirnvpyrirvrlsrkrnedE 78
                                       + ++ v   +ra rA+k i++  ++++    +dvr+++++n+ +  +g + +p + rvr +r  ++ E
  gi|313124893|ref|YP_004035157.1| 15 LRDVKAVPSYERAGRAMKIIREHLAQHFSvdPEDVRLEPEINEQIGGRGRQTPPSKFRVRAARFDEDGE 83
                                      56788999999***************9985568***************************999666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 586.46
//
Query:       gi|313124894|ref|YP_004035158.1|  [L=50]
Description: 50S ribosomal protein L39e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-21   73.3   7.7    9.8e-21   73.1   7.7    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   7.7   5.5e-25   9.8e-21       1      40 [.       8      47 ..       8      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 5.5e-25
                     Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtk 40
                                      kK+rLaK  +qN++vPaWv++ktd +v++npkrR+WRr++
  gi|313124894|ref|YP_004035158.1|  8 KKKRLAKLERQNSRVPAWVMMKTDMEVTRNPKRRNWRRSD 47
                                      7*************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 323.10
//
Query:       gi|313124895|ref|YP_004035159.1|  [L=313]
Description: dmt(drug/metabolite transporter) superfamily permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-35  122.0  34.5    1.9e-20   73.5  15.9    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
        7.7    6.7  10.0        2.3    8.4   0.4    3.8  4  CrgA      Cell division protein CrgA


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8  10.5   1.2e-18   1.1e-14       6     135 ..       9     139 ..       4     140 .. 0.91
   2 !   73.5  15.9   2.1e-24   1.9e-20       2     135 ..     153     289 ..     152     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 1.2e-18
                              EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllf 82 
                                       +++l+  +w+++fv++k++l++++p  ++++rf ia+++l+ +a+++  +l+  s+++w  ++  g l++ + + ++
  gi|313124895|ref|YP_004035159.1|   9 FVFLS-AIWGTAFVATKVGLASLPPTLFAAMRFDIAAAVLFGFAFIRSDRLRPTSRTEWYPIITGGMLNIGIHHAFL 84 
                                       44455.57*******************************************7777778888899999********** PP

                              EamA  83 fyalkkts.asnaslitslePvftlilsvlll.gekltlkqllgivlillGvlli 135
                                       f+++ +++ a++ ++++ l+Pv+t +l  l    e+l+   ++g+vl++ Gv++i
  gi|313124895|ref|YP_004035159.1|  85 FSGQAYIDnAAVPAVLLGLIPVITPVLTRLTTsSERLSAVGVVGLVLGFTGVVVI 139
                                       *******626677999**************9999*******************98 PP

  == domain 2  score: 73.5 bits;  conditional E-value: 2.1e-24
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllgt 75 
                                       +g+ l+l++a+ +a+++vl+    ++++ +++ ++++li++++l ++++   +     a+++l ++++l++lg++++
  gi|313124895|ref|YP_004035159.1| 153 MGVGLVLASAVAFALGAVLTHGSKSELPFFSIQAWTMLIGAVFLHATSVALPWESfagARWTLDAVISLVYLGVVAG 229
                                       7899****************************************66644444433359******************* PP

                              EamA  76 vlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       + +f+l+f++l ++++ +asl+ +++Pvf++i ++++ g  +   +++g+++i++G ll+
  gi|313124895|ref|YP_004035159.1| 230 AGGFGLYFWLLDHIGPIEASLLEYVIPVFAAIGGWIIRGNAIDTNTVIGFAVIFVGFLLV 289
                                       *********************************************************997 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.22     2e+03      30      48 ..      63      81 ..      55     107 .. 0.75
   2 ?    0.9   0.3     0.055     5e+02      38      79 ..      95     138 ..      86     140 .. 0.73
   3 ?    0.9   0.1     0.055   4.9e+02      56      77 ..     176     196 ..     148     205 .. 0.72
   4 ?    8.4   0.4   0.00025       2.3      68      84 ..     273     289 ..     250     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.22
                              CrgA 30 sprwyvpvmlglmllGllw 48
                                        +wy ++  g++ +G+  
  gi|313124895|ref|YP_004035159.1| 63 RTEWYPIITGGMLNIGIHH 81
                                      5679988888888888865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.055
                              CrgA  38 mlglmllGllwlvvyYlage..eipfmaelgawNlliGfgliiv 79 
                                        +  +llGl+ +++  l++   + + ++++g   l+ Gf+ ++v
  gi|313124895|ref|YP_004035159.1|  95 AVPAVLLGLIPVITPVLTRLttSSERLSAVGVVGLVLGFTGVVV 138
                                       56778889988888877766444556888888888888876664 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.055
                              CrgA  56 geeipfmaelgawNlliGfgli 77 
                                       ++e+p + +++aw +liG  ++
  gi|313124895|ref|YP_004035159.1| 176 KSELP-FFSIQAWTMLIGAVFL 196
                                       34677.5689999999998776 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.00025
                              CrgA  68 wNlliGfgliivGllmt 84 
                                        N +iGf++i vG+l+ 
  gi|313124895|ref|YP_004035159.1| 273 TNTVIGFAVIFVGFLLV 289
                                       69************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1715.60
//
Query:       gi|313124896|ref|YP_004035160.1|  [L=187]
Description: 2'-5' RNA ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-23   82.7   0.0      4e-12   46.2   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
      2e-17   63.5   0.1    2.4e-17   63.2   0.1    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    5.4e-09   36.2   0.0    6.5e-09   36.0   0.0    1.1  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.034   14.3   0.0    1.5  1  Peptidase_S66    LD-carboxypeptidase N-terminal domain


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0     9e-16     4e-12       1      87 []       7      92 ..       7      92 .. 0.92
   2 !   34.7   0.0   3.3e-12   1.5e-08       7      87 .]     100     178 ..      95     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 9e-16
                                      EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHH..HHTSBEEEEEEEEEEEE CS
                        LigT_PEase  1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaei..asgaepfelkvdgvglf 77
                                      +++p++++e +++ +++++    + gl+++ p + H+T +flg++de++++++ eal+ +  a+ + p + +v g+g+f
  gi|313124896|ref|YP_004035160.1|  7 IDLPDSLTESVEAAQERFA---DAEGLRFTDPSQAHVTMKFLGDTDEDRLEDIDEALEAAiaAADVDPYDATVGGFGVF 82
                                      68899999***********...888**************************9999998753366889************ PP

                                      EECCSCCEEE CS
                        LigT_PEase 78 psrlrprviy 87
                                      ps ++  v++
  gi|313124896|ref|YP_004035160.1| 83 PSIEYISVVW 92
                                      ****999998 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 3.3e-12
                                       HHHHHHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC CS
                        LigT_PEase   7 iaeelarlaaeleralaklglkpv.rpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvglfpsrl 81 
                                        a + + la+ +er+  ++g+ p+ + f+pH+T+a+  + + ++ v++++++    +       ++v++v l +s+l
  gi|313124896|ref|YP_004035160.1| 100 GAAKTTTLAEAIERETVERGFDPEdHSFTPHVTIARMDDARgKDHVQRVVREE---DPDLGT--FHVEEVRLKQSTL 171
                                       5677889********************************99888888886544...344444..************* PP

                                       .SCCEEE CS
                        LigT_PEase  82 .rprviy 87 
                                        + ++ y
  gi|313124896|ref|YP_004035160.1| 172 tNDGPRY 178
                                       9999988 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.1   5.4e-21   2.4e-17       2     145 ..      10     166 ..       9     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 5.4e-21
                   2_5_RNA_ligase2   2 ppslaapiealrrslydka....yprwppHitLlypfvededl.adlaellsrlak..etepfevrldgfgvFeh.k 70 
                                       p+sl + +ea+++++ d      +   ++H+t+++++++ded  +d++e+l+++++  + +p +++++gfgvF++ +
  gi|313124896|ref|YP_004035160.1|  10 PDSLTESVEAAQERFADAEglrfTDPSQAHVTMKFLGDTDEDRlEDIDEALEAAIAaaDVDPYDATVGGFGVFPSiE 86 
                                       7888888999995555554454366666************998999999999987755899**************97 PP

                   2_5_RNA_ligase2  71 ks.vvylsv...sdsealqalraallealpeagdkedsgeftPHlTiaqsadstsaaelleklaqalpple.fevde 142
                                          vv++ v    + ++   l +a++++  e g + +++ ftPH+Tia+ +d++  + +++ ++++ p+l  f+v+e
  gi|313124896|ref|YP_004035160.1|  87 YIsVVWAGVrddGGAAKTTTLAEAIERETVERGFDPEDHSFTPHVTIARMDDARGKDHVQRVVREEDPDLGtFHVEE 163
                                       777******999999999**********9999999999*****************99999999888877766****9 PP

                   2_5_RNA_ligase2 143 val 145
                                       v l
  gi|313124896|ref|YP_004035160.1| 164 VRL 166
                                       987 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.4e-12   6.5e-09       4     205 ..       4     184 ..       2     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.4e-12
                                       EEEEE---HHHHHHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS- CS
                         AKAP7_NLS   4 FlsiplnsnklrkklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkp 80 
                                       F+si l + +l++ +e+ qe+ +++    +   f++p++ H+T+  l  ++++++++  e+L+ ++       d  p
  gi|313124896|ref|YP_004035160.1|   4 FVSIDLPD-SLTESVEAAQERFADA----EGLRFTDPSQAHVTMKFLGDTDEDRLEDIDEALEAAI---AA-ADVDP 71 
                                       66666654.4777777777777663....3345899**************************9995...33.3669* PP

                                       -EEEEEEEEEE.....TTTEEEEEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHT CS
                         AKAP7_NLS  81 lslrlkGletfnddpakarVlYakveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqak 157
                                          ++ G ++f  +     V++a+v +++  +k ++la++i ++ +e+g+  e+  + +++H+T++    +++k + 
  gi|313124896|ref|YP_004035160.1|  72 YDATVGGFGVF-PSIEYISVVWAGVRDDGGAAKTTTLAEAIERETVERGFDPEDH-S-FTPHVTIARMDDARGKDHV 145
                                       ***********.577779*******************************988765.4.7**************9998 PP

                                       T--S--GG.GGGGGTT-EEEEEE--EEEEEESSS---TTS--EEEEEE CS
                         AKAP7_NLS 158 skesfdareilkqfkdfefgeekineihLsqlesddesdgyYkviasv 205
                                       ++        + + +d ++g+ +++e+ L q + +++    Y+++ + 
  gi|313124896|ref|YP_004035160.1| 146 QR--------VVREEDPDLGTFHVEEVRLKQSTLTND-GPRYETVRRY 184
                                       88........5567999*************9999988.7778777665 PP

>> Peptidase_S66  LD-carboxypeptidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.6e-06     0.034      16      85 ..      14      88 ..       5      98 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.6e-06
                                      .HHHHHHHHHH.HHCTEEEEEGCTC--TTTTCSS.-HHHHHHHHHHHHC-....TTECEEEES--SS-CHHCHHHH CS
                     Peptidase_S66 16 keeleraievl.eelglevvlgksaaksagylag.tdeeRaadLnealad....peikaiicarGGygaarllpyl 85
                                       e++e+a e++ ++ gl+ + +++a+ ++ ++ g tde+R++d+ eal+      +++   ++ GG g+   ++y+
  gi|313124896|ref|YP_004035160.1| 14 TESVEAAQERFaDAEGLRFTDPSQAHVTM-KFLGdTDEDRLEDIDEALEAaiaaADVDPYDATVGGFGVFPSIEYI 88
                                      458999999995556*****777554444.45555*******9988776522226677777888888887777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1123.49
//
Query:       gi|313124897|ref|YP_004035161.1|  [L=261]
Description: arylamine n-acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-50  170.7   0.0    4.9e-50  170.6   0.0    1.0  1  Acetyltransf_2  N-acetyltransferase


Domain annotation for each model (and alignments):
>> Acetyltransf_2  N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.6   0.0   2.7e-54   4.9e-50       2     234 ..      22     257 ..      21     261 .] 0.94

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 2.7e-54
                                       HHHHHHHHHHHHHHS-EE-HHHHTT.......-----SHHHHHHHHTTST--B-HHHHHHHHHHHHHHTT-EEEEEE CS
                    Acetyltransf_2   2 LetLrellqahlraiPFENldvllg.......eeieldlealfdklVkkkRGGyCyelNgLlarvLkelGFevtlla 71 
                                        ++L++l++ah++++PFE l++  +       e i l++ al++k+V+++RGG+C+elNgL++++L+elGF+vt++a
  gi|313124897|ref|YP_004035161.1|  22 FQALERLQRAHVTSVPFETLSITGDphgardgEGIVLSIPALYEKVVERHRGGFCFELNGLFGWLLTELGFDVTRVA 98 
                                       689******************987777777779******************************************** PP

                                       EEEETTGGSSSSSSCEEEEEEEEETTEEEEE-SSSSCG.-SS-EESSTTCEEEESSEEEEEEEETTC..EEEEEEEE CS
                    Acetyltransf_2  72 grvvvkaeeaastertHllllVtidgetylvDvGFGgstltaplelesgkdqqtthgifrlveeeen..ewvlekkk 146
                                       +r+v   e     + +H  llVt++g++ lvD+G G + l +p++l +  d  +    +r  +++    e++l+  +
  gi|313124897|ref|YP_004035161.1|  99 ARMVSDLEL----PANHHPLLVTLNGDDHLVDAGMGAPMLRRPVPLGESVDRDEAGVAWRTADSDRPdaEYLLQYCE 171
                                       **9987766....899*********************************99999999****87776667******** PP

                                       TTEEEEEEEEEEEEB-HHHHHHHHHHHHHSTT-HHHCS-EEEEEETTEEEEEETTEEEEEETTSEEEEEEE-SHHHH CS
                    Acetyltransf_2 147 reewvklYsftleprqiedfeeandylstspdsvftkkllcslatpdgrltLvgrtlterekdgaleeiklltdeel 223
                                       +++w++ Y f+ + r+ + f +++dyl+++p+s ft + ++ + tpdg++ L  + ++ + + + +++ + ++++e+
  gi|313124897|ref|YP_004035161.1| 172 SDDWQDRYVFDSTRRELDYFAATCDYLQSAPESGFTGDPVVVKPTPDGHAKLKPTVFSRT-RGD-ETDEQSVDEAEY 246
                                       ************************************************************.444.6888899***** PP

                                       HHHHHHTT--- CS
                    Acetyltransf_2 224 eevlkekFgie 234
                                        ++l+e Fgie
  gi|313124897|ref|YP_004035161.1| 247 RRLLRETFGIE 257
                                       **********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1595.10
//
Query:       gi|313124898|ref|YP_004035162.1|  [L=248]
Description: tetratricopeptide hypothetical protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.5e-26   88.9   6.8    2.6e-08   33.3   0.3    5.1  5  TPR_1       Tetratricopeptide repeat
      1e-23   81.5  13.5    7.5e-07   28.8   0.6    5.2  5  TPR_2       Tetratricopeptide repeat
    8.8e-23   78.6   4.2    0.00011   22.1   0.3    5.2  5  TPR_8       Tetratricopeptide repeat
    2.1e-19   69.9  18.4    1.2e-08   35.4   1.8    3.2  3  TPR_16      Tetratricopeptide repeat
    8.2e-16   57.4   6.1    5.9e-05   22.7   0.0    4.7  4  TPR_11      TPR repeat
    9.7e-16   57.8  19.3    2.1e-10   40.8   6.0    3.8  3  TPR_12      Tetratricopeptide repeat
    3.3e-12   46.1  20.4    0.00016   22.2   0.7    5.1  5  TPR_14      Tetratricopeptide repeat
    2.6e-11   43.1   2.9    9.2e-05   22.6   0.0    4.3  4  TPR_17      Tetratricopeptide repeat
    3.3e-11   43.2  10.1     0.0002   21.4   1.4    3.5  3  TPR_9       Tetratricopeptide repeat
    5.7e-08   32.3  13.9    0.00011   22.0   0.4    4.8  5  TPR_7       Tetratricopeptide repeat
    5.1e-07   29.4  20.1    0.00081   19.2   0.3    5.2  5  TPR_10      Tetratricopeptide repeat
    2.1e-06   28.1  19.5    0.00088   19.7   2.7    3.5  3  TPR_19      Tetratricopeptide repeat
    2.3e-05   24.5  12.1      0.093   12.8   0.5    4.2  3  DUF3856     Domain of Unknown Function (DUF3856)
    5.2e-05   23.6   7.0        7.5    7.4   0.1    5.1  5  TPR_6       Tetratricopeptide repeat
    6.2e-05   23.1   0.9       0.36   11.1   0.1    2.6  2  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    0.00029   20.8   5.7        0.3   11.2   0.6    3.5  2  ANAPC5      Anaphase-promoting complex subunit 5
    0.00089   19.7  15.1       0.08   13.6   0.9    5.0  5  TPR_4       Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.011   15.5   0.5      0.011   15.5   0.5    1.7  2  YfiO        Outer membrane lipoprotein
       0.02   15.1   2.9       0.63   10.3   0.1    2.5  2  TPR_5       Tetratrico peptide repeat
       0.03   13.5   1.0      0.039   13.1   1.0    1.1  1  CAF1        CAF1 family ribonuclease
      0.083   13.0   6.5          3    8.0   0.0    3.2  2  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
       0.29   11.5  10.1        0.3   11.4   1.3    3.1  3  TPR_20      Tetratricopeptide repeat
          3    7.7   9.2         15    5.5   0.8    3.1  3  Wzy_C_2     Virulence factor membrane-bound polymerase, C-ter


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   7.4e-05     0.058       8      29 ..      71      92 ..      65      97 .. 0.90
   2 !   33.3   0.3   3.3e-11   2.6e-08       2      33 ..     103     134 ..     103     135 .. 0.95
   3 !   22.5   0.0   9.1e-08   7.1e-05       1      34 []     139     172 ..     139     172 .. 0.94
   4 !   18.0   0.1   2.4e-06    0.0019       1      30 [.     173     202 ..     173     202 .. 0.97
   5 ?    1.6   0.0      0.36   2.8e+02       2      22 ..     208     228 ..     207     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-05
                                      HHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1  8 GnayfklgkydeAleyyekALe 29
                                      G+ y++ ++++eA e +e+A +
  gi|313124898|ref|YP_004035162.1| 71 GLSYMQINRFEEATETFERAAQ 92
                                      99******************76 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 3.3e-11
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       +a+ n+G+a+ +l++ydeA+ +y++AL+++ +
  gi|313124898|ref|YP_004035162.1| 103 EAWVNKGAAHAQLEEYDEAIGAYKEALRIDDD 134
                                       69***************************965 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 9.1e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a  nl++a+ + g+ +eAl + e+A+e++P +
  gi|313124898|ref|YP_004035162.1| 139 ASAETNLAYALWQFGETEEALHHAERAVEIDPRF 172
                                       56889***************************76 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+a+yn+G  +++ g  ++A+ +++ A++l
  gi|313124898|ref|YP_004035162.1| 173 AQAWYNRGFFLQERGLSEDAVNAFDNAIRL 202
                                       79**************************87 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHTT-HHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAle 22 
                                       ++l  ++ a+ +lg+ deA++
  gi|313124898|ref|YP_004035162.1| 208 DVLEEKARALEELGREDEAEQ 228
                                       566678999**********86 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05     0.012       6      31 ..      69      94 ..      64      97 .. 0.86
   2 !   28.8   0.6   9.7e-10   7.5e-07       2      33 ..     103     134 ..     102     135 .. 0.95
   3 !   20.4   0.1   4.7e-07   0.00037       6      33 ..     144     171 ..     139     172 .. 0.93
   4 !   15.2   0.1   2.1e-05     0.017       1      30 [.     173     202 ..     173     206 .. 0.94
   5 !    7.6   0.3    0.0057       4.5       1      27 [.     207     233 ..     207     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                             TPR_2  6 nlGlayyklgdyeeAleafekAleld 31
                                        Gl+y++ +++eeA e fe+A + +
  gi|313124898|ref|YP_004035162.1| 69 DVGLSYMQINRFEEATETFERAAQFA 94
                                      679*******************9876 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 9.7e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       ea+ n G a+++l +y+eA+ a+++Al++d +
  gi|313124898|ref|YP_004035162.1| 103 EAWVNKGAAHAQLEEYDEAIGAYKEALRIDDD 134
                                       89***************************976 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 4.7e-07
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                       nl++a+++ g+ eeAl++ e+A+e+dP+
  gi|313124898|ref|YP_004035162.1| 144 NLAYALWQFGETEEALHHAERAVEIDPR 171
                                       8**************************7 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 2.1e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+a+yn+G  + ++g  e+A++af+ A++l
  gi|313124898|ref|YP_004035162.1| 173 AQAWYNRGFFLQERGLSEDAVNAFDNAIRL 202
                                       78**************************98 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0057
                             TPR_2   1 aealynlGlayyklgdyeeAleafekA 27 
                                       a++l + ++a+++lg+ +eA++  ++A
  gi|313124898|ref|YP_004035162.1| 207 ADVLEEKARALEELGREDEAEQVQQQA 233
                                       6788999*************9988776 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00018      0.14       7      30 ..      70      93 ..      67      97 .. 0.87
   2 !   22.1   0.3   1.4e-07   0.00011       2      33 ..     103     134 ..     102     135 .. 0.95
   3 !   16.2   0.0   1.1e-05    0.0084       6      32 ..     144     170 ..     140     172 .. 0.95
   4 !   10.4   0.0   0.00082      0.64       1      30 [.     173     202 ..     173     202 .. 0.96
   5 !   14.8   0.1   3.2e-05     0.025       2      33 ..     208     239 ..     207     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                                      HHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8  7 lgsiylklgdyeeAkeyyekalel 30
                                       g+ y++ +++eeA e++e+a + 
  gi|313124898|ref|YP_004035162.1| 70 VGLSYMQINRFEEATETFERAAQF 93
                                      5899****************9765 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.4e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ea++n+g ++ +l++y+eA+ +y++al++d d
  gi|313124898|ref|YP_004035162.1| 103 EAWVNKGAAHAQLEEYDEAIGAYKEALRIDDD 134
                                       79***************************975 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldp 32 
                                       nl++++++ g+ eeA    e+a+e+dp
  gi|313124898|ref|YP_004035162.1| 144 NLAYALWQFGETEEALHHAERAVEIDP 170
                                       9*************************9 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00082
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+a+yn g  +++ g  e A+ ++  a++l
  gi|313124898|ref|YP_004035162.1| 173 AQAWYNRGFFLQERGLSEDAVNAFDNAIRL 202
                                       79***********************99986 PP

  == domain 5  score: 14.8 bits;  conditional E-value: 3.2e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++  +++++++lg+ +eA+++ ++a el+++
  gi|313124898|ref|YP_004035162.1| 208 DVLEEKARALEELGREDEAEQVQQQADELRQQ 239
                                       667789*********************99875 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   1.8   1.6e-11   1.2e-08       3      67 ..      70     135 ..      68     136 .. 0.95
   2 !   24.7   0.9   3.5e-08   2.8e-05       2      44 ..     144     183 ..     143     188 .. 0.92
   3 !   20.7   2.4   6.4e-07    0.0005       8      61 ..     184     234 ..     183     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.6e-11
                            TPR_16   3 laraalragdyddAaaal.eaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                        ++++++ +++++A + + +aa  +d +s +a eA+ ++g a++++ +++eA+ +y++alr + d+
  gi|313124898|ref|YP_004035162.1|  70 VGLSYMQINRFEEATETFeRAAQFADEDSLEAQEAWVNKGAAHAQLEEYDEAIGAYKEALRIDDDS 135
                                       5899**************99****************************************999886 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 3.5e-08
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaa 44 
                                       +la+a+++ g+ ++A++ +e+a++ d   P+ a+A++++g  +
  gi|313124898|ref|YP_004035162.1| 144 NLAYALWQFGETEEALHHAERAVEID---PRFAQAWYNRGFFL 183
                                       79************************...***********876 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 6.4e-07
                            TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                        ++g  +dA++a++ a++++    ++a+ l ++++a+ ++gr +eA+++ + a 
  gi|313124898|ref|YP_004035162.1| 184 QERGLSEDAVNAFDNAIRLG---MRNADVLEEKARALEELGREDEAEQVQQQAD 234
                                       578889**************...************************9988875 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0039       3.1       1      22 [.      71      92 ..      71      98 .. 0.91
   2 !   19.0   2.0   1.1e-06   0.00083       2      27 ..     110     135 ..     109     153 .. 0.77
   3 !   22.7   0.0   7.5e-08   5.9e-05       6      39 ..     151     184 ..     146     187 .. 0.87
   4 !    7.6   0.0     0.004       3.1      10      42 .]     189     221 ..     183     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0039
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlk 22
                                      G  y++ +++eeA e +++A +
  gi|313124898|ref|YP_004035162.1| 71 GLSYMQINRFEEATETFERAAQ 92
                                      789*****************87 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.1e-06
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdn 27 
                                        a  ++ +y+eAi aYk+Al++d d+
  gi|313124898|ref|YP_004035162.1| 110 AAHAQLEEYDEAIGAYKEALRIDDDS 135
                                       577899*****************986 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 7.5e-08
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       + G+ eeA+ + ++A+++dP +a a+yn+G+ ++
  gi|313124898|ref|YP_004035162.1| 151 QFGETEEALHHAERAVEIDPRFAQAWYNRGFFLQ 184
                                       5699**************************8665 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.004
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        e+A++a+ +A++l   na+++ + + a+ ++G
  gi|313124898|ref|YP_004035162.1| 189 SEDAVNAFDNAIRLGMRNADVLEEKARALEELG 221
                                       599*****************9999888888877 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   2.2   2.1e-09   1.7e-06       8      74 ..      69     131 ..      67     132 .. 0.93
   2 !   40.8   6.0   2.6e-13   2.1e-10       4      76 ..     103     170 ..     100     171 .. 0.93
   3 !   14.2   2.4     5e-05     0.039       3      74 ..     173     236 ..     171     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.1e-09
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        +++ +++  r++eA e +e+a + a    ++d++++ ++  n g ++ +l++y+eA+ +++eal+i
  gi|313124898|ref|YP_004035162.1|  69 DVGLSYMQINRFEEATETFERAAQFA----DEDSLEAQEAWVNKGAAHAQLEEYDEAIGAYKEALRI 131
                                       57999*****************9999....489999*****************************98 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 2.6e-13
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        a++n +a++++l++ydeA+  +++al+i      +d++ +a++  nL+ +++++g++eeAl + e+a++i++
  gi|313124898|ref|YP_004035162.1| 103 EAWVNKGAAHAQLEEYDEAIGAYKEALRID-----DDSEHAASAETNLAYALWQFGETEEALHHAERAVEIDP 170
                                       6899**************************.....66666******************************975 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5e-05
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a+a++n++ +l+++g  ++A   ++ a+++  r         a +l   +r++++lgr +eA++  ++a ++
  gi|313124898|ref|YP_004035162.1| 173 AQAWYNRGFFLQERGLSEDAVNAFDNAIRLGMR--------NADVLEEKARALEELGREDEAEQVQQQADEL 236
                                       8899***********************666633........4778999****************99999555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2    0.0019       1.5       6      41 ..      69     105 ..      64     107 .. 0.79
   2 !   16.3   1.1   1.7e-05     0.013       2      35 ..     103     136 ..     102     143 .. 0.89
   3 !   22.2   0.7   2.1e-07   0.00016       7      42 ..     145     180 ..     139     183 .. 0.93
   4 !   14.0   0.4   8.9e-05     0.069       2      43 ..     174     215 ..     173     216 .. 0.95
   5 ?    4.6   0.5     0.089        70       7      23 ..     213     229 ..     209     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0019
                            TPR_14   6 alaeallalGdpdeAiallrrala.laPddaeawlll 41 
                                       + +  +++  +++eA + ++ra + ++ d++ea+ ++
  gi|313124898|ref|YP_004035162.1|  69 DVGLSYMQINRFEEATETFERAAQfADEDSLEAQEAW 105
                                       5677899999************994467788988776 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.7e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPdda 35 
                                       ea+   ++a+++l+++deAi ++++al+ + d++
  gi|313124898|ref|YP_004035162.1| 103 EAWVNKGAAHAQLEEYDEAIGAYKEALRIDDDSE 136
                                       67888899********************998876 PP

  == domain 3  score: 22.2 bits;  conditional E-value: 2.1e-07
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawllla 42 
                                       la al++ G+++eA+ +++ra++ +P +a+aw+  +
  gi|313124898|ref|YP_004035162.1| 145 LAYALWQFGETEEALHHAERAVEIDPRFAQAWYNRG 180
                                       89******************************9766 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 8.9e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +a++ ++ +l ++G  ++A+++++ a++l+  +a+++ + a+
  gi|313124898|ref|YP_004035162.1| 174 QAWYNRGFFLQERGLSEDAVNAFDNAIRLGMRNADVLEEKAR 215
                                       79***********************************99998 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.089
                            TPR_14   7 laeallalGdpdeAial 23 
                                        a+al++lG+ deA+++
  gi|313124898|ref|YP_004035162.1| 213 KARALEELGREDEAEQV 229
                                       599***********986 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.081        63      14      33 ..     103     122 ..      86     123 .. 0.88
   2 ?    0.8   0.1         1   8.1e+02       2      32 ..     125     158 ..     124     160 .. 0.67
   3 !   22.6   0.0   1.2e-07   9.2e-05       2      32 ..     162     192 ..     161     194 .. 0.93
   4 !   12.7   0.0   0.00016      0.13       2      34 .]     196     228 ..     195     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.081
                            TPR_17  14 daynnLAelllknGdlmtAr 33 
                                       +a+ n++ +++++ ++++A+
  gi|313124898|ref|YP_004035162.1| 103 EAWVNKGAAHAQLEEYDEAI 122
                                       79****************97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1
                            TPR_17   2 ylkaleldPnn...adaynnLAelllknGdlmtA 32 
                                       y++al++d ++   a a +nLA++l + G++++A
  gi|313124898|ref|YP_004035162.1| 125 YKEALRIDDDSehaASAETNLAYALWQFGETEEA 158
                                       7777777766656666667888887666666666 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 1.2e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                        ++a+e+dP  a a++n++ +l ++G +++A
  gi|313124898|ref|YP_004035162.1| 162 AERAVEIDPRFAQAWYNRGFFLQERGLSEDA 192
                                       69************************99888 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00016
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a++l   nad++ ++A++l+++G+ ++A+q
  gi|313124898|ref|YP_004035162.1| 196 FDNAIRLGMRNADVLEEKARALEELGREDEAEQ 228
                                       7789999999*********************98 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   6.9e-05     0.054      27      62 ..      62      97 ..      54     103 .. 0.87
   2 !   12.5   0.7   0.00016      0.12      30      71 ..     103     144 ..     100     146 .. 0.90
   3 !   21.4   1.4   2.6e-07    0.0002       5      61 ..     149     205 ..     145     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.9e-05
                             TPR_9 27 ddpeerrdRGlllaqlGclsaAladLeaylalapda 62
                                       d+e + d Gl ++q +++++A + +e++++ a+++
  gi|313124898|ref|YP_004035162.1| 62 VDVEQLVDVGLSYMQINRFEEATETFERAAQFADED 97
                                      689999************************988765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                             TPR_9  30 eerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                                       e +   G ++aql+ + +A+ +   +l++++d + a+ ++  
  gi|313124898|ref|YP_004035162.1| 103 EAWVNKGAAHAQLEEYDEAIGAYKEALRIDDDSEHAASAETN 144
                                       67999**************************99999988765 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 2.6e-07
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +++  + e+al  +er + ++P+ ++ ++ RG+ l+++G  + A+++++ +++l   
  gi|313124898|ref|YP_004035162.1| 149 LWQFGETEEALHHAERAVEIDPRFAQAWYNRGFFLQERGLSEDAVNAFDNAIRLGMR 205
                                       56677889******************************************9966543 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0024       1.9       6      32 ..      71      97 ..      67     101 .. 0.85
   2 !   22.0   0.4   1.4e-07   0.00011       1      35 [.     104     138 ..     104     139 .. 0.91
   3 !    7.6   0.1    0.0053       4.1       4      31 ..     144     169 ..     143     174 .. 0.86
   4 ?   -1.2   0.0       3.6   2.8e+03      10      28 ..     184     200 ..     175     207 .. 0.67
   5 ?   -0.1   0.5       1.5   1.2e+03       6      21 ..     214     229 ..     209     243 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0024
                             TPR_7  6 arlysrlGdyeeAielyeqsLaltkdp 32
                                      +  y + +++eeA e +e++ ++++++
  gi|313124898|ref|YP_004035162.1| 71 GLSYMQINRFEEATETFERAAQFADED 97
                                      55799**************98888776 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.4e-07
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a++n + ++ +l +y+eAi+ y+++L++++d e+a
  gi|313124898|ref|YP_004035162.1| 104 AWVNKGAAHAQLEEYDEAIGAYKEALRIDDDSEHA 138
                                       68999*******************99999998775 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0053
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkd 31 
                                       nLa +  + G++eeA+ + e+  a++ d
  gi|313124898|ref|YP_004035162.1| 144 NLAYALWQFGETEEALHHAER--AVEID 169
                                       9*****************999..65544 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 3.6
                             TPR_7  10 srlGdyeeAielyeqsLal 28 
                                       +++G  e+A+  +    a+
  gi|313124898|ref|YP_004035162.1| 184 QERGLSEDAVNAFDN--AI 200
                                       566777777777766..44 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 1.5
                             TPR_7   6 arlysrlGdyeeAiel 21 
                                       ar+ ++lG+ +eA+++
  gi|313124898|ref|YP_004035162.1| 214 ARALEELGREDEAEQV 229
                                       7888888888888765 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.059        46       9      30 ..      71      92 ..      66      96 .. 0.86
   2 !    9.1   0.5    0.0016       1.2       7      31 ..     107     131 ..     106     131 .. 0.92
   3 !   19.2   0.3     1e-06   0.00081       6      31 ..     143     168 ..     139     168 .. 0.94
   4 ?    1.3   0.0      0.44   3.5e+02       7      30 ..     178     201 ..     175     203 .. 0.88
   5 ?    6.0   1.7     0.015        12       9      28 ..     214     233 ..     207     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.059
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      +  + q +r++eA + +e+a +
  gi|313124898|ref|YP_004035162.1| 71 GLSYMQINRFEEATETFERAAQ 92
                                      7889**********99999976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N ++a+ q+ +ydeA   ++eal+i
  gi|313124898|ref|YP_004035162.1| 107 NKGAAHAQLEEYDEAIGAYKEALRI 131
                                       5699*******************86 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1e-06
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       +NLa al+q g+ +eA+ ++e+a++i
  gi|313124898|ref|YP_004035162.1| 143 TNLAYALWQFGETEEALHHAERAVEI 168
                                       7***********************97 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.44
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N +  l++rg  ++A++ ++ a++
  gi|313124898|ref|YP_004035162.1| 178 NRGFFLQERGLSEDAVNAFDNAIR 201
                                       6688999**********9999987 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.015
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       a+al ++gr deAe+ +++a
  gi|313124898|ref|YP_004035162.1| 214 ARALEELGREDEAEQVQQQA 233
                                       899**************999 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.098        77      35      53 ..      74      92 ..      72     103 .. 0.82
   2 !   19.7   2.7   1.1e-06   0.00088       5      61 ..     116     175 ..     110     178 .. 0.82
   3 !   10.8   6.0    0.0007      0.54       4      57 ..     186     239 ..     183     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.098
                            TPR_19 35 llalgqldeAealLdalpe 53
                                      +++ ++++eA ++ +++ +
  gi|313124898|ref|YP_004035162.1| 74 YMQINRFEEATETFERAAQ 92
                                      899999****999998865 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.1e-06
                            TPR_19   5 gdyaeAlalleqalqedpk...naearllLAeallalgqldeAealLdalpeedpddary 61 
                                       + y+eA+ ++++al  d +    a a  +LA al++ g+++eA    +++ e dp  a++
  gi|313124898|ref|YP_004035162.1| 116 EEYDEAIGAYKEALRIDDDsehAASAETNLAYALWQFGETEEALHHAERAVEIDPRFAQA 175
                                       68************6655522266666699**************9999999999987665 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0007
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       +g  ++A++++ +a+     na+++   A+al +lg+ deAe++ +++ e  ++
  gi|313124898|ref|YP_004035162.1| 186 RGLSEDAVNAFDNAIRLGMRNADVLEEKARALEELGREDEAEQVQQQADELRQQ 239
                                       566789**************************************9999988887 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.3     0.011       8.5      23      76 ..      78     130 ..      62     138 .. 0.54
   2 !    8.9   0.3    0.0019       1.5      55     125 ..     139     198 ..     131     207 .. 0.69
   3 !   12.8   0.5   0.00012     0.093     102     137 ..     209     244 ..     203     248 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.011
                                       T-HHHHHHHHHHHHHHHT..TS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           DUF3856  23 gayeeaaasyrkalevsr..tipaeeafdheGfdalchaglsealaklgrydeale 76 
                                       +++eea++ +++a +++   ++ a+ea+  +G    +ha l e    +g y+eal+
  gi|313124898|ref|YP_004035162.1|  78 NRFEEATETFERAAQFADedSLEAQEAWVNKG---AAHAQLEEYDEAIGAYKEALR 130
                                       45555555555555554311444445554444...245555555555555555544 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           DUF3856  55 alchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrm 125
                                       a + + l+ al+++g+ +eal+ a++a++   r           + +a ++r+  l+e G +++a++af  
  gi|313124898|ref|YP_004035162.1| 139 ASAETNLAYALWQFGETEEALHHAERAVEIDPR-----------FAQAWYNRGFFLQERGLSEDAVNAFDN 198
                                       556788999999999999999999988754333...........233345666666666666666666655 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH--S-- CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagemiaerkGel 137
                                       ++ ++a+aleelGr+dea +  ++a+e+ ++++ el
  gi|313124898|ref|YP_004035162.1| 209 VLEEKARALEELGREDEAEQVQQQADELRQQQEQEL 244
                                       56689**********************988887775 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.068        53       7      27 ..      71      91 ..      67      93 .. 0.88
   2 !    7.4   0.1    0.0096       7.5       1      32 [.     103     134 ..     103     135 .. 0.83
   3 ?    4.0   0.0      0.12        95       5      31 ..     144     170 ..     141     171 .. 0.83
   4 ?    6.1   0.0     0.025        20       1      28 [.     174     201 ..     174     202 .. 0.90
   5 ?    1.3   0.1      0.89   6.9e+02       6      20 ..     213     227 ..     208     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.068
                                      HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  7 alsyrklgdtdkAlealerli 27
                                      +lsy + ++ ++A e++er  
  gi|313124898|ref|YP_004035162.1| 71 GLSYMQINRFEEATETFERAA 91
                                      99****88**********975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0096
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       +A  + + ++ +l ++d+A+ a+++ ++   d
  gi|313124898|ref|YP_004035162.1| 103 EAWVNKGAAHAQLEEYDEAIGAYKEALRIDDD 134
                                       57778899999988**********99986655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeYP 31 
                                       +la+++ + g+t++Al   er ++  P
  gi|313124898|ref|YP_004035162.1| 144 NLAYALWQFGETEEALHHAERAVEIDP 170
                                       5888888856*****999999998777 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       +A y+++  +++ g +++A+ a+++ i+
  gi|313124898|ref|YP_004035162.1| 174 QAWYNRGFFLQERGLSEDAVNAFDNAIR 201
                                       699****9999988*********99886 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.89
                                       HHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAl 20 
                                        a+++++lg+ d+A 
  gi|313124898|ref|YP_004035162.1| 213 KARALEELGREDEAE 227
                                       599999999999995 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00046      0.36      37      81 ..      85     127 ..      58     128 .. 0.76
   2 !   10.2   0.0   0.00087      0.68       5      78 ..     155     229 ..     151     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                                       T-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  37 gqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       + ++rA +++++     + +++++ ++ +  +L++y+eAi a+++
  gi|313124898|ref|YP_004035162.1|  85 ETFERAAQFADED--SLEAQEAWVNKGAAHAQLEEYDEAIGAYKE 127
                                       3456666666666..4455599******************99876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00087
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +++A+ +aer+++ +++ +++ y  +  l ++g  + A + +++a +l  ++  ++  +A++l +L++ +eA+++
  gi|313124898|ref|YP_004035162.1| 155 TEEALHHAERAVEIDPRFAQAWYNRGFFLQERGLSEDAVNAFDNAiRLGMRNADVLEEKARALEELGREDEAEQV 229
                                       789*********999***9999999***********************************************986 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.6   0.00038       0.3      33      71 ..      95     132 ..      71     140 .. 0.75
   2 !    6.7   0.6    0.0099       7.7      40      76 ..     172     208 ..     132     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                            ANAPC5  33 essqkksyqyalLnlaslhadfghneeAvkaleeairlA 71 
                                       ++  + + q a +n    ha++++++eA+ a +ea r+ 
  gi|313124898|ref|YP_004035162.1|  95 DED-SLEAQEAWVNKGAAHAQLEEYDEAIGAYKEALRID 132
                                       333.45668999***********************9985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0099
                            ANAPC5  40 yqyalLnlaslhadfghneeAvkaleeairlArenkD 76 
                                       +  a  n   + ++ g  e+Av+a+ +airl   n+D
  gi|313124898|ref|YP_004035162.1| 172 FAQAWYNRGFFLQERGLSEDAVNAFDNAIRLGMRNAD 208
                                       5555556666666667778888888888888877777 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.9   3.9e+03      16      26 .]      79      89 ..      78      89 .. 0.88
   2 ?    1.1   0.1       1.1   8.8e+02       3      20 ..     104     121 ..     102     122 .. 0.84
   3 !   13.6   0.9    0.0001      0.08       3      26 .]     141     164 ..     139     164 .. 0.89
   4 ?    4.3   0.0      0.11        83       1      21 [.     173     193 ..     173     197 .. 0.89
   5 ?    7.0   0.3     0.014        11       8      22 ..     214     228 ..     209     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.9
                             TPR_4 16 dldeAraller 26
                                      +++eA +++er
  gi|313124898|ref|YP_004035162.1| 79 RFEEATETFER 89
                                      89***999997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.1
                             TPR_4   3 allaLArallalGdldeA 20 
                                       a ++ + a+++l ++deA
  gi|313124898|ref|YP_004035162.1| 104 AWVNKGAAHAQLEEYDEA 121
                                       778889999999999998 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.0001
                             TPR_4   3 allaLArallalGdldeAraller 26 
                                       a  +LA al++ G+ +eA+ ++er
  gi|313124898|ref|YP_004035162.1| 141 AETNLAYALWQFGETEEALHHAER 164
                                       6679***************99997 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.11
                             TPR_4   1 arallaLArallalGdldeAr 21 
                                       a+a ++++  l+++G +++A 
  gi|313124898|ref|YP_004035162.1| 173 AQAWYNRGFFLQERGLSEDAV 193
                                       6899**************997 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.014
                             TPR_4   8 ArallalGdldeAra 22 
                                       Aral +lG+ deA++
  gi|313124898|ref|YP_004035162.1| 214 ARALEELGREDEAEQ 228
                                       9************98 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         4   3.1e+03      11      31 ..      70      90 ..      61      96 .. 0.60
   2 ?   15.5   0.5   1.4e-05     0.011      10      80 ..     107     177 ..      97     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4
                                      HHHHHHHHT-HHHHHHHHHHH CS
                              YfiO 11 kgqealqkgdyaeAikkleal 31
                                       g + +q + ++eA + +e +
  gi|313124898|ref|YP_004035162.1| 70 VGLSYMQINRFEEATETFERA 90
                                      555556666666666666654 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHT-HHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-SSSTTHHH CS
                              YfiO  10 ekgqealqkgdyaeAikklealdsryPfspyaeqaqldliyAyykdadyaealasaerFlrlyPthknvdy 80 
                                       +kg    q ++y eAi + +++  +   s++a++a+ +l+yA ++ ++++eal  aer ++  P+  ++ y
  gi|313124898|ref|YP_004035162.1| 107 NKGAAHAQLEEYDEAIGAYKEALRIDDDSEHAASAETNLAYALWQFGETEEALHHAERAVEIDPRFAQAWY 177
                                       6788888999************************************************9998887665444 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00081      0.63       9      59 ..     110     160 ..     102     170 .. 0.85
   2 ?    4.4   0.7     0.052        41       2      64 ..     174     233 ..     173     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00081
                             TPR_5   9 garDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeeala 59 
                                       +a+    + d+a+  Y++aL    +  ++  a   La +L + Ge+eeal+
  gi|313124898|ref|YP_004035162.1| 110 AAHAQLEEYDEAIGAYKEALRIDDDSEHAASAETNLAYALWQFGETEEALH 160
                                       5555666789**************************************987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.052
                             TPR_5   2 vaaFeragarDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLrae 64 
                                       +a ++r+ +    G ++ av+ + +a+  G+++a         a +L  lG+ +ea+++ ++ 
  gi|313124898|ref|YP_004035162.1| 174 QAWYNRGFFLQERGLSEDAVNAFDNAIRLGMRNADVLE---EKARALEELGREDEAEQVQQQA 233
                                       56778888888899999999999999999987765444...4578888999988888765543 PP

>> CAF1  CAF1 family ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.0   5.1e-05     0.039     111     179 ..      58     233 ..      22     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                                       HHTT--HHHHHTT-B-B--HHHHHHHHCH----....-.....---..................-----TTC.HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx..................xxxxxxxxxxxxx RF
                              CAF1 111 akngfdfnkliseGipYlsrkeeekakerleer....keekekske..................nvkivsdedkefv 165
                                       ak + d+++l++ G++Y++ ++ e+a+e +e+     +e++    e                  +            
  gi|313124898|ref|YP_004035162.1|  58 AKDQVDVEQLVDVGLSYMQINRFEEATETFERAaqfaDEDSL---EaqeawvnkgaahaqleeyD------------ 119
                                       78999****************999999999887644322222...24456655555544444440............ PP

                                       HH........................................................................... CS
                                       xx........................................................................... RF
                              CAF1 166 ee........................................................................... 167
                                        e                                                                           
  gi|313124898|ref|YP_004035162.1| 120 -Eaigaykealridddsehaasaetnlayalwqfgeteealhhaeraveidprfaqawynrgfflqerglsedavna 195
                                       .1444445555555555555566677778888888888888888888888999999999999999999999999999 PP

                                       ...........................-S.HHHHHHHHH CS
                                       ...........................xxxxxxxxxxxx RF
                              CAF1 168 ...........................kskeeeelkeee 179
                                                                  + +e e+ +++ 
  gi|313124898|ref|YP_004035162.1| 196 fdnairlgmrnadvleekaraleelgrE-DEAEQVQQQA 233
                                       9999999999998888877777665531.2222222111 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0075       5.8      10      37 ..     111     138 ..     109     140 .. 0.86
   2 ?    8.0   0.0    0.0038         3       7      37 ..     145     175 ..     144     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0075
                                       HHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQa 37 
                                       +h+ l eY+eA    +  L+i+ + + a
  gi|313124898|ref|YP_004035162.1| 111 AHAQLEEYDEAIGAYKEALRIDDDSEHA 138
                                       9*******************99876655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0038
                                       HHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C   7 lAlGhyklgeYseArryvdalLeiEPenrQa 37 
                                       lA++    ge +eA+  +++  ei+P++ Qa
  gi|313124898|ref|YP_004035162.1| 145 LAYALWQFGETEEALHHAERAVEIDPRFAQA 175
                                       899999999*********************8 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.3   0.00038       0.3      12      73 ..      54     124 ..      49     131 .. 0.82
   2 ?    5.0   0.3      0.04        31      22      55 ..     139     172 ..     119     180 .. 0.81
   3 ?    0.6   0.4      0.91   7.1e+02       9      50 ..     160     201 ..     156     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw.........eddaarkqllkifealgs 73 
                                       e+++a++  d++  +d+ l +++ +r eeA e + +  +   ++         +++aa  ql ++ ea+g+
  gi|313124898|ref|YP_004035162.1|  54 ERNIAKDQVDVEQLVDVGLSYMQINRFEEATETFERAAQFADEDsleaqeawvNKGAAHAQLEEYDEAIGA 124
                                       56799*************************99988777766666677777778888888888777777776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.04
                            TPR_20  22 ldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                         a+ +lA al + g+ eeAl +  + ++ d  +
  gi|313124898|ref|YP_004035162.1| 139 ASAETNLAYALWQFGETEEALHHAERAVEIDPRF 172
                                       478899***************9988888887766 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.91
                            TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                          e+a++ +p   +a ++    l ++g  e+A++++ + ++
  gi|313124898|ref|YP_004035162.1| 160 HHAERAVEIDPRFAQAWYNRGFFLQERGLSEDAVNAFDNAIR 201
                                       567788888888888888888888888888888776544443 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       0.4   3.1e+02     151     182 ..      72     102 ..      67     108 .. 0.83
   2 ?    5.1   0.3     0.024        19     147     180 ..     143     176 ..     138     180 .. 0.85
   3 ?    5.5   0.8     0.019        15     145     172 ..     209     236 ..     206     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.4
                           Wzy_C_2 151 lslallGdedeAeqilararalfpeedakwvq 182
                                       ls+++  + +eA+ + +ra  +f++ed   +q
  gi|313124898|ref|YP_004035162.1|  72 LSYMQINRFEEATETFERAA-QFADEDSLEAQ 102
                                       688899999**********9.9*999977655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                           Wzy_C_2 147 erlilslallGdedeAeqilararalfpeedakw 180
                                       ++l+++l++ G ++eA+ + +ra  + p  +++w
  gi|313124898|ref|YP_004035162.1| 143 TNLAYALWQFGETEEALHHAERAVEIDPRFAQAW 176
                                       589*******************987766666666 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.019
                           Wzy_C_2 145 vierlilslallGdedeAeqilararal 172
                                       v+e  + +l  lG+edeAeq+ ++a  l
  gi|313124898|ref|YP_004035162.1| 209 VLEEKARALEELGREDEAEQVQQQADEL 236
                                       77888999999************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1395  (0.0778069); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1472.72
//
Query:       gi|313124899|ref|YP_004035163.1|  [L=100]
Description: hypothetical protein Hbor_01130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-29  100.4   0.0    5.7e-29  100.2   0.0    1.0  1  DUF424    Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   3.2e-33   5.7e-29       2      92 .]       6      99 ..       5      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 3.2e-33
                                      EETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE...-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG CS
                            DUF424  2 rtddllklvavcdkellgktfkegelllnvsegfyggela...seeeaikeLekatiaNivgeeavvlavkaGlvdpds 77
                                      r + ++ lv+vcd+++lg+t+++g+++l+v+e+fygge a   ++++++++L +at+aNivge+av +a++aG+vd+++
  gi|313124899|ref|YP_004035163.1|  6 RETPEGLLVSVCDRDCLGETYEDGQVSLEVTEEFYGGEEAdkvDADAVVDSLTRATVANIVGERAVGVAIDAGIVDEET 84
                                      5678899*******************************997778999******************************** PP

                                      -EEETTEEEEEEEE- CS
                            DUF424 78 Vlvidgvphaqigkl 92
                                      Vl +++++haq+ ++
  gi|313124899|ref|YP_004035163.1| 85 VLDVGETRHAQLLWM 99
                                      ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.34s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 594.87
//
Query:       gi|313124900|ref|YP_004035164.1|  [L=425]
Description: cysteine desulfurase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.5e-150  499.0   0.0   8.5e-150  498.8   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    9.1e-12   45.0   0.2    1.4e-11   44.3   0.2    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.5e-07   31.0   0.0    2.1e-07   30.5   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    1.6e-05   23.7   0.0    2.8e-05   22.8   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00039   19.3   0.0     0.0011   17.8   0.0    1.7  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
  ------ inclusion threshold ------
      0.012   14.6   0.1      0.025   13.6   0.1    1.5  1  SelA             L-seryl-tRNA selenium transferase
      0.096   12.0   0.3          2    7.7   0.1    2.1  2  YPEB             YpeB sporulation


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.8   0.0  3.3e-153  8.5e-150       1     371 []      43     413 ..      43     413 .. 1.00

  Alignments for each domain:
  == domain 1  score: 498.8 bits;  conditional E-value: 3.3e-153
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       +yld+aAttq+p++V+da+ eyy+ yn+nvhr++hhl++ea+ a+e+a+++vae+i+a+ +eei+ft++ttea+nlv
  gi|313124900|ref|YP_004035164.1|  43 VYLDNAATTQTPKQVVDAIVEYYYGYNSNVHRGIHHLSQEASVAYENAHDRVAEFIGASGREEIVFTKNTTEAMNLV 119
                                       7**************************************************************************** PP

                                       HHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTT CS
                       Aminotran_5  78 alslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtG 153
                                       a++++ + l+pgd++v+te+ehha lv+wq++ak+tga v++i++de+g+ld+d++++l++e+tk+v++ h+sn++G
  gi|313124900|ref|YP_004035164.1| 120 AYAWGLEeLEPGDKVVLTEMEHHASLVTWQQIAKKTGASVEYIRVDEDGRLDMDHAADLIDEDTKMVSVVHISNTLG 196
                                       *****99********************************************************************** PP

                                       EB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 154 tiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggem 230
                                       t++pv e++++a+++g +++vD+aq+v+ +p+dv ++++Df+afsghK+lgPtGiGvly+++e+le++ p l+ggem
  gi|313124900|ref|YP_004035164.1| 197 TVNPVSELADMAHEVGSYIFVDGAQSVPTRPVDVTDIDADFFAFSGHKMLGPTGIGVLYGKEEILEEMTPYLYGGEM 273
                                       ***************************************************************************** PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                                       +++v+++++t+++ p+kfeaGTp + + i+l+aa++yl+eig+e++++he++la+y+++rl++ +++++ygp + ++
  gi|313124900|ref|YP_004035164.1| 274 IRRVTYDDSTWEDLPWKFEAGTPVIEQGIALHAAIDYLDEIGMENVQAHEERLAAYAYDRLAEFDDIEIYGP-PGDE 349
                                       ***********************************************************************6.99** PP

                                       CBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 308 rasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       r ++v+fn++gvha+d+ ++L+++++avr+G hc+qpl++ l+++++ RaS+y+ynt +evd+l
  gi|313124900|ref|YP_004035164.1| 350 RGGLVAFNLDGVHAHDLSSILNDHAVAVRAGDHCTQPLHDKLDIAASTRASFYVYNTYDEVDKL 413
                                       **************************************************************97 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.2   5.6e-15   1.4e-11      32     176 ..      97     248 ..      86     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 5.6e-15
                                       HHHHHT-SEEEEESSHHHHHHHHHHHTTTT...TT-EEEEESSS-THHH....HHHHHTT-EEEEE-B-TTTSSB-G CS
                   DegT_DnrJ_EryC1  32 faaylgvkhaiavssGtaAlhlaLralgvg...pgdeVIvpsltFvata....navlelgakpvfvDvdpdtynidp 101
                                       f    g +  + + + t+A+ l+  a g++   pgd+V+ + +   a+     + + ++ga + ++ vd ++  +d 
  gi|313124900|ref|YP_004035164.1|  97 FIGASGREEIVFTKNTTEAMNLVAYAWGLEelePGDKVVLTEMEHHASLvtwqQIAKKTGASVEYIRVD-EDGRLDM 172
                                       333445789999**************8887777*********99999753333678899**********.899**** PP

                                       GGCGGG--TTEEEEEEB-G...GGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS CS
                   DegT_DnrJ_EryC1 102 aaieaaitertkaIlpVhl...yGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnl 175
                                       ++++ +i e tk + +Vh+   +G v+ +++l ++a++ g +++ D A+++ ++  +  v ++ da  f F + K l
  gi|313124900|ref|YP_004035164.1| 173 DHAADLIDEDTKMVSVVHIsntLGTVNPVSELADMAHEVGSYIFVDGAQSVPTRPVD--VTDI-DADFFAFSGHKML 246
                                       ******************744479***************************998766..5555.4777777777777 PP

                                       .- CS
                   DegT_DnrJ_EryC1 176 .t 176
                                         
  gi|313124900|ref|YP_004035164.1| 247 gP 248
                                       33 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   8.3e-11   2.1e-07      32     215 ..      85     261 ..      65     345 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 8.3e-11
                                       HHHHHHHHHHHH...HTT-SEEEEES-HHHH.HHHHH...HHH--TTEEEEEETT.-HHHHSSTTHHHHCC--EEEE CS
                   Beta_elim_lyase  32 ktvnrLedavae...lfgkeaalfvpqGtaA.nsill...killqrgeevivtep.ahihfdetgaiaelagvklrd 100
                                         +++  d+vae   + g e ++f+ + t A n +++      l++g++v++te   h    + ++ia   g+ +  
  gi|313124900|ref|YP_004035164.1|  85 VAYENAHDRVAEfigASGREEIVFTKNTTEAmNLVAYawgLEELEPGDKVVLTEMeHHASLVTWQQIAKKTGASVEY 161
                                       4677788888883334456899*****998846666676655668*****99998577778888************* PP

                                       E-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHH CS
                   Beta_elim_lyase 101 lknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaaks 177
                                       ++ +e+G +d++  +++i+e+    + ++++ + +T      +v   + + e+a++a++ g  +++DgA      +s
  gi|313124900|ref|YP_004035164.1| 162 IRVDEDGRLDMDHAADLIDEDT---KMVSVVHISNTLG----TV---NPVSELADMAHEVGSYIFVDGA------QS 222
                                       ********************33...3666666666665....45...556778899************8......56 PP

                                       HTS-CHHHHTT.SSEEEEESSSTT--SS-.EEEEE-HH.. CS
                   Beta_elim_lyase 178 lgeivkemfsy.vDsvtmslkKdllanvG.gvlafrddel 215
                                       +   + ++++  +D + +s+ K  l + G gvl ++++ l
  gi|313124900|ref|YP_004035164.1| 223 VPTRPVDVTDIdADFFAFSGHKM-LGPTGiGVLYGKEEIL 261
                                       67777777755599999999997.5679999999999833 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.1e-08   2.8e-05      88     200 ..     128     246 ..     112     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-08
                                       S-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHH CS
                   Cys_Met_Meta_PP  88 lkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaikentklvylEtptnpllkvvDieki 159
                                       l+ Gd++v+++  +  +    ++++kk+g +v+++ +      d+++ +  i+e tk+v +  ++n l  v  + ++
  gi|313124900|ref|YP_004035164.1| 128 LEPGDKVVLTEMEHHASLVTWQQIAKKTGASVEYIRVdedgrLDMDHAADLIDEDTKMVSVVHISNTLGTVNPVSEL 204
                                       789************************999999876633444577888999************************** PP

                                       HHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTT CS
                   Cys_Met_Meta_PP 160 aklakkagvlvvvDntfasp.llqrplklgaDivvhSaTKyl 200
                                       a++a+++g  ++vD + + p   +   + +aD    S+ K l
  gi|313124900|ref|YP_004035164.1| 205 ADMAHEVGSYIFVDGAQSVPtRPVDVTDIDADFFAFSGHKML 246
                                       **************9988883334445566777766666655 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.2e-07    0.0011     156     374 ..     146     358 ..     130     359 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEE CS
                     Pyridoxal_deC 156 ssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlH 232
                                       + ++++a+ +g  + +i++de+g+l +++   +i ed +   ++  +  tlGt      + ++el+d+ ++ +  + 
  gi|313124900|ref|YP_004035164.1| 146 VTWQQIAKKTGASVEYIRVDEDGRLDMDHAADLIDEDTKMVSVV-HISNTLGTV-----NPVSELADMAHEVGSYIF 216
                                       56899******************999999999999999995555.888899886.....5799************** PP

                                       EE-TTGGGGGGSGGGGG.GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TT..TTTSEE CS
                     Pyridoxal_deC 233 vDAAyaGsaficpeirh.llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehed..sdvaad 306
                                       vD A           r+  ++ i+ ad +++++hK+l+ + ++++l+ k++ +l++       YL   +    v++d
  gi|313124900|ref|YP_004035164.1| 217 VDGAQSV------PTRPvDVTDID-ADFFAFSGHKMLG-PTGIGVLYGKEE-ILEEMT----PYLYGGEmiRRVTYD 280
                                       **99987......45662556665.9*********765.899999988865.565554....344333335778888 PP

                                       CCCGS.....SSSSG..HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECS...TTBSSEEEEE CS
                     Pyridoxal_deC 307 lgtka.....iplsr..rvrilklwfvlralGveglqnqirksvelakyleklirkderfeiva...evelglVcFr 373
                                         t++      + +     + + l+  +  l   g++n++ +  +la+y ++++++  + ei     ++  glV+F 
  gi|313124900|ref|YP_004035164.1| 281 DSTWEdlpwkFEAGTpvIEQGIALHAAIDYLDEIGMENVQAHEERLAAYAYDRLAEFDDIEIYGppgDERGGLVAFN 357
                                       77763311115555565445566888888888888888888889999999999999999999887888888888887 PP

                                       E CS
                     Pyridoxal_deC 374 l 374
                                       l
  gi|313124900|ref|YP_004035164.1| 358 L 358
                                       6 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.8e-06     0.025     162     234 ..     204     265 ..     150     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.8e-06
                                       HHHHHHHHT--EEEEEES-B-S-GGGGT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHH CS
                              SelA 162 LvelgkekglpvleDlGsGllvdlseyglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklk 234
                                       L+++++e        +Gs ++vd ++  +++ P     +   +d  +fsG k+lG    G++ Gk e++e++ 
  gi|313124900|ref|YP_004035164.1| 204 LADMAHE--------VGSYIFVDGAQ-SVPTRPVDVTDI--DADFFAFSGHKMLGPTGIGVLYGKEEILEEMT 265
                                       4444443........56666666544.455556544444..569*************************9985 PP

>> YPEB  YpeB sporulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00079         2     188     248 ..      67     127 ..      47     158 .. 0.70
   2 ?    2.3   0.0     0.033        83     277     305 ..     294     322 ..     291     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00079
                              YPEB 188 Gpfsdhlekktpkglsg.kevseeeakkiakkflgkkkaekvevvesek.kgkipaYsvevkd 248
                                       G  s+ +  +  ++ls+ ++v  e+a +++++f+g++  e+++ +++++   ++ aY   +++
  gi|313124900|ref|YP_004035164.1|  67 GYNSN-V-HRGIHHLSQeASVAYENAHDRVAEFIGASGREEIVFTKNTTeAMNLVAYAWGLEE 127
                                       44433.3.466677777699*****************77777766665505678888877766 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.033
                              YPEB 277 gepkisleeaaekAkefLeklGyknmept 305
                                       g+p i++  a  +A ++L+++G++n+++ 
  gi|313124900|ref|YP_004035164.1| 294 GTPVIEQGIALHAAIDYLDEIGMENVQAH 322
                                       788999999****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2654.80
//
Query:       gi|313124901|ref|YP_004035165.1|  [L=139]
Description: suf system fes assembly protein, nifu family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-29  100.5   0.1    8.2e-29  100.3   0.1    1.0  1  NifU_N    NifU-like N terminal domain
  ------ inclusion threshold ------
      0.057   13.3   0.0       0.08   12.8   0.0    1.2  1  SufE      Fe-S metabolism associated domain


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.1   9.2e-33   8.2e-29       1     126 [.       5     128 ..       5     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 9.2e-33
                                       CSCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHH CS
                            NifU_N   1 aysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelv 77 
                                       +y++++ldhyknPrn+G +e+      + +  +p cGD++++q+k++++ + ie + F + GC++++As+s+l e +
  gi|313124901|ref|YP_004035165.1|   5 MYRQQILDHYKNPRNKGEMEDPTF---SHTGENPSCGDTITMQVKLEDDDETIEFVAFTGDGCAISQASASMLSERL 78 
                                       59*******************995...77888********************************************* PP

                                       TTSBHHHHCCCCHHHHHHHHTC.SCSSSCHCSCHHHHHHHHHHHHHHHHC CS
                            NifU_N  78 kgktleealkitnkeiaeelgg.lpkeklhcsvlaedalkaavkkYkakk 126
                                       +g tl e +++ ++++ e lg  + + +++c+vla+++++ +++ Y++  
  gi|313124901|ref|YP_004035165.1|  79 QGTTLSELEEMDTDDVTEMLGVdISPMRIKCAVLARQVAQDGAAIYEGDA 128
                                       ********************8559**********************9865 PP

>> SufE  Fe-S metabolism associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.9e-06      0.08      44     108 ..      40     106 ..      28     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-06
                                       EEEEEEEEETTS.....EEEEEEESSHHHHHHHHHHHHHCTTEECCCCTCC-TCHHHHHTTSHHHHCHHH CS
                              SufE  44 qvwlaaeledgk.....lkfeadsdarivkGllalllevlsgktpeeilavdledfleelglsehlspsR 108
                                       ++ ++++led++     + f++d   +i+++ +++l e l+g t +e+ ++d++d+ e lg++  +sp R
  gi|313124901|ref|YP_004035165.1|  40 TITMQVKLEDDDetiefVAFTGD-GCAISQASASMLSERLQGTTLSELEEMDTDDVTEMLGVD--ISPMR 106
                                       55566666664456443444444.3789*************************9999999875..35555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 902.54
//
Query:       gi|313124902|ref|YP_004035166.1|  [L=343]
Description: DNA repair and recombination protein rada [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-72  242.4   0.0    4.4e-71  239.1   0.0    1.9  1  Rad51            Rad51
    1.3e-11   45.0   0.1    1.2e-10   41.8   0.0    2.3  2  HHH_5            Helix-hairpin-helix domain
    9.5e-08   31.8   0.0    0.00043   19.8   0.0    2.1  2  RecA             recA bacterial DNA recombination protein
    1.1e-06   28.2   0.3    0.00021   21.0   0.0    2.9  3  HHH              Helix-hairpin-helix motif
    1.5e-06   28.0   0.0    2.2e-06   27.4   0.0    1.2  1  AAA_25           AAA domain
    2.4e-05   24.3   0.0    7.2e-05   22.8   0.0    1.7  1  HHH_2            Helix-hairpin-helix motif
      7e-05   22.3   0.2    0.00036   20.0   0.2    2.2  1  ATPase           KaiC
    0.00044   20.4   0.0    0.00092   19.4   0.0    1.5  1  Cdd1             Pathogenicity locus
     0.0035   17.1   0.0      0.023   14.5   0.0    2.4  3  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
      0.045   14.1   0.0       0.22   11.9   0.0    2.2  2  IMS_HHH          IMS family HHH motif
       0.14   12.5   0.0         12    6.2   0.0    2.7  2  HHH_3            Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.1   0.0   2.7e-74   4.4e-71       2     252 ..      65     340 ..      64     342 .. 0.91

  Alignments for each domain:
  == domain 1  score: 239.1 bits;  conditional E-value: 2.7e-74
                                       S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEE CS
                             Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyid 78 
                                       gf +++ +le+r+++ +l+ G +++D+lLgGG+et+site++Gef++Gk+q++h+++v vqlp e gG  g ++++d
  gi|313124902|ref|YP_004035166.1|  65 GFETGSAVLERREQIGKLSWGISEVDDLLGGGLETQSITEVYGEFGAGKSQVTHQMAVNVQLPPEHGGLGGSCIFVD 141
                                       899************************************************************************** PP

                                       SSS---GGGGHHHH......................HHTT--H..HHHGGGEEEEE--STTHHHHHHHHTHHH...H CS
                             Rad51  79 tegtfrperlveia......................erykldk..eevlenvayaRaytiehqeellqqaaal...l 128
                                       +e tfrper+ ++                       +   +++  ++ l+++ +a+a++++hq  l ++a +l    
  gi|313124902|ref|YP_004035166.1| 142 SEDTFRPERIDDMVrglddeiiqatmdereiegspdDEAAMEEllNDFLDKIHVAKAFNSNHQILLAEKAKELardH 218
                                       ************9999***********999988887444444333899***************97776544330004 PP

                                       HHS-..EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.---------- CS
                             Rad51 129 aedk..fallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkk 203
                                        ed+  ++ll vDs+ta++R+++ grg+la+Rqqkl+k+l+ L ++ d ++ av++tnqv +++d     + +dp++
  gi|313124902|ref|YP_004035166.1| 219 EEDEfpVRLLCVDSLTAHFRAEYVGRGQLAERQQKLNKHLHDLMRIGDLYNTAVLVTNQVASNPDS----YFGDPTQ 291
                                       455533589********************************************************9....99***** PP

                                       --HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEEEEETTEE CS
                             Rad51 204 PigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavfaigeeGi 252
                                       PigG++l+h+st R++lrk kg++Riv++vd+Pnl++ e ++ +++ G+
  gi|313124902|ref|YP_004035166.1| 292 PIGGNILGHTSTFRIYLRKSKGDKRIVRLVDAPNLADGEGIMRVQDGGL 340
                                       ********************************************99997 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   7.5e-14   1.2e-10       2      57 .]       4      59 ..       3      59 .. 0.97
   2 ?    0.2   0.0      0.74   1.2e+03      19      40 ..      82     105 ..      81     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 7.5e-14
                                      HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                      ++L s++G+Gp+tA +l +aG+es++++a a++ eL+   ++G+ t   ii ++++
  gi|313124902|ref|YP_004035166.1|  4 DDLESLPGVGPATADKLTDAGFESYQAIAVASPSELSNTADVGESTSSDIINAARE 59
                                      69***************************************************996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.74
                                       HTTT--SHHHHHHS..-HHHHHTS CS
                             HHH_5  19 lsaGiesvedlaaa..dveeLaki 40 
                                       ls Gi+ v+dl+    +++ ++++
  gi|313124902|ref|YP_004035166.1|  82 LSWGISEVDDLLGGglETQSITEV 105
                                       789********9753355556665 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.6e-07   0.00043      28     101 ..      76     154 ..      65     173 .. 0.82
   2 !   10.0   0.0   0.00027      0.44     134     223 ..     227     312 ..     208     322 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.6e-07
                                       -----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH......HTT--EEEEESS----HHHH CS
                              RecA  28 klkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq......kkggvaafidaehaldpkya 98 
                                       ++++  +s G   +d  lG GGl    i+e+yG   +Gk+ ++ ++ +++q        gg + f+d+e ++ p+  
  gi|313124902|ref|YP_004035166.1|  76 REQIGKLSWGISEVDDLLG-GGLETQSITEVYGEFGAGKSQVTHQMAVNVQlppehgGLGGSCIFVDSEDTFRPERI 151
                                       568999999**********.***********************9999999944432235889********9998866 PP

                                       HHT CS
                              RecA  99 kkl 101
                                         +
  gi|313124902|ref|YP_004035166.1| 152 DDM 154
                                       555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00027
                                       EEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHH CS
                              RecA 134 livvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralk 210
                                       l+ vds++a   +ae  G     +++ + + + + l  l    +  nt+v+  nq+       fg+p    GG+ l 
  gi|313124902|ref|YP_004035166.1| 227 LLCVDSLTAHF-RAEYVG---RGQLAERQQKLNKHLHDLMRIGDLYNTAVLVTNQVASNPDSYFGDPTQPIGGNILG 299
                                       56666666543.444433...33344444445677777777778889****************************** PP

                                       HH-SEEEEEEEES CS
                              RecA 211 fyasvrldvrrie 223
                                         ++ r+ +r+++
  gi|313124902|ref|YP_004035166.1| 300 HTSTFRIYLRKSK 312
                                       **********986 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.3e-07   0.00021      11      28 ..       4      21 ..       3      23 .. 0.89
   2 ?    4.4   0.0     0.023        37       1      23 [.      27      49 ..      27      56 .. 0.86
   3 ?   -3.2   0.0       5.9   9.7e+03       4      12 ..     161     169 ..     160     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                                      HHHHTSTT-SHHHHHHHH CS
                               HHH 11 eeLlalPGVGpktAeaIl 28
                                      ++L++lPGVGp+tA++  
  gi|313124902|ref|YP_004035166.1|  4 DDLESLPGVGPATADKLT 21
                                      8*************9875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.023
                                      SHHHHHTSSHHHHHTSTT-SHHH CS
                               HHH  1 sleglipasreeLlalPGVGpkt 23
                                      s++++  as+ eL     VG++t
  gi|313124902|ref|YP_004035166.1| 27 SYQAIAVASPSELSNTADVGEST 49
                                      7999**********999999998 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.9
                                       HHHTSSHHH CS
                               HHH   4 glipasree 12 
                                        +i a+++e
  gi|313124902|ref|YP_004035166.1| 161 EIIQATMDE 169
                                       5899**998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.4e-09   2.2e-06      10     187 ..      77     276 ..      70     282 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.4e-09
                            AAA_25  10 vsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedel 86 
                                        ++++l + + ++++l++g l  ++++ ++G  g+GK+ ++ ++a+ v +  p    +    g +++v+ Ed+    
  gi|313124902|ref|YP_004035166.1|  77 EQIGKLSWGISEVDDLLGGGLETQSITEVYGEFGAGKSQVTHQMAVNVQL-PPE---HGGLGGSCIFVDSEDTF--R 147
                                       46788889999*************************************96.222...33479***********8..7 PP

                            AAA_25  87 rrRlravgeal...................rddarllvld..lagv.eslpLfak.drggtl.ltadvdaleaaiee 139
                                       ++R+  + + l                   +    ++++   l ++ ++++++++  +++++ l+++ ++l+++ ee
  gi|313124902|ref|YP_004035166.1| 148 PERIDDMVRGLddeiiqatmdereiegspdD----EAAMEelLNDFlDKIHVAKAfNSNHQIlLAEKAKELARDHEE 220
                                       9**********88899999999999855432....33333445678899999988445555579***********99 PP

                            AAA_25 140 veg..vrlvviDplsralgg.....densnsd..vgalvealeriarrtgaavllvh 187
                                         +  vrl+++D+l++ +++     +  ++++   ++ + +l ri + ++ avl++ 
  gi|313124902|ref|YP_004035166.1| 221 D-EfpVRLLCVDSLTAHFRAeyvgrGQLAERQqkLNKHLHDLMRIGDLYNTAVLVTN 276
                                       5.459**********988874433322222222246666666666666666666665 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   4.4e-08   7.2e-05       8      54 ..       9      56 ..       8      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.4e-08
                             HHH_2  8 IrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivef 54
                                      ++ VG +tA +L  + F+s +a++ as  eL++  d+Ge ++++i++ 
  gi|313124902|ref|YP_004035166.1|  9 LPGVGPATADKLTDAgFESYQAIAVASPSELSNTADVGESTSSDIINA 56
                                      689*********9866***************************99875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   2.2e-07   0.00036       4      42 ..      85     123 ..      82     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.2e-07
                            ATPase   4 gIeglDeilkgGipegrvvlitGepGtGKtifalqFlik 42 
                                       gI + D++l gG+  ++++ ++Ge G+GK+ +  q +++
  gi|313124902|ref|YP_004035166.1|  85 GISEVDDLLGGGLETQSITEVYGEFGAGKSQVTHQMAVN 123
                                       9*****************************999999887 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.7e-07   0.00092       7      44 ..       5      42 ..       3      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.7e-07
                              Cdd1  7 elqdiPniGkalaedlvelGirsveelkgedpeelyek 44
                                      +l+++P++G+a+a++l++ G++s + ++  +p el + 
  gi|313124902|ref|YP_004035166.1|  5 DLESLPGVGPATADKLTDAGFESYQAIAVASPSELSNT 42
                                      799******************************99876 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.4e-05     0.023       8      42 ..      11      46 ..       6      54 .. 0.84
   2 ?   -2.1   0.0       2.2   3.7e+03      21      30 ..      85      94 ..      83     106 .. 0.76
   3 ?   -2.7   0.0       3.5   5.7e+03      34      49 ..     246     261 ..     238     262 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                   DNA_pol_lambd_f  8 GVGpktAkkwyakGirtledlra.krakLtreqqiG 42
                                      GVGp+tA k+ ++G+ + + +    +++L++  ++G
  gi|313124902|ref|YP_004035166.1| 11 GVGPATADKLTDAGFESYQAIAVaSPSELSNTADVG 46
                                      9****************9998876667777776666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                   DNA_pol_lambd_f 21 Girtledlra 30
                                      Gi  ++dl+ 
  gi|313124902|ref|YP_004035166.1| 85 GISEVDDLLG 94
                                      8999999986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.5
                   DNA_pol_lambd_f  34 kLtreqqiGlkyyeDl 49 
                                       +L + qq   k+ +Dl
  gi|313124902|ref|YP_004035166.1| 246 QLAERQQKLNKHLHDL 261
                                       5666666555676665 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.22      12      31 ..       5      24 ..       5      25 .. 0.89
   2 ?   -2.5   0.0       5.1   8.4e+03       8      18 ..      97     107 ..      97     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                           IMS_HHH 12 pitkipGiGgklgekLeklG 31
                                      ++ ++pG+G+ +++kL + G
  gi|313124902|ref|YP_004035166.1|  5 DLESLPGVGPATADKLTDAG 24
                                      5889************9877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.1
                           IMS_HHH   8 LwplpitkipG 18 
                                       L+  +it+++G
  gi|313124902|ref|YP_004035166.1|  97 LETQSITEVYG 107
                                       67789****98 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0075        12      14      30 ..       4      20 ..       2      23 .. 0.85
   2 ?    3.2   0.0     0.066   1.1e+02      10      33 ..      33      56 ..      30      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0075
                             HHH_3 14 eeLqklpGlgpklAknI 30
                                      ++L+ lpG+gp++A+++
  gi|313124902|ref|YP_004035166.1|  4 DDLESLPGVGPATADKL 20
                                      68999*******99987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.066
                             HHH_3 10 tAsaeeLqklpGlgpklAknIvay 33
                                       As +eL+  + +g++++  I+++
  gi|313124902|ref|YP_004035166.1| 33 VASPSELSNTADVGESTSSDIINA 56
                                      59************9999998853 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2241.49
//
Query:       gi|313124903|ref|YP_004035167.1|  [L=221]
Description: hypothetical protein Hbor_01170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1379.85
//
Query:       gi|313124904|ref|YP_004035168.1|  [L=201]
Description: hypothetical protein Hbor_01180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   13.7   0.3      0.095   12.5   0.3    1.6  1  SH3_16    Bacterial dipeptidyl-peptidase Sh3 domain


Domain annotation for each model (and alignments):
>> SH3_16  Bacterial dipeptidyl-peptidase Sh3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   5.3e-06     0.095      16      38 ..      80     102 ..      79     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-06
                                       TT-EEEEEEEEETEEEEEETTT- CS
                            SH3_16  16 aGrhlrvleeadgwawVqlceDg 38 
                                       +G+ +r++e++ gw wV l+ D+
  gi|313124904|ref|YP_004035168.1|  80 TGTDFRLYEDSHGWEWVVLEDDD 102
                                       599*****************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1191.25
//
Query:       gi|313124905|ref|YP_004035169.1|  [L=289]
Description: heat shock protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-44  150.0   0.0      1e-43  149.4   0.0    1.2  1  Peptidase_M48    Peptidase family M48
    1.6e-07   30.9   0.1    4.2e-05   22.9   0.0    2.3  2  Peptidase_M56    BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.089   12.7   0.0       0.12   12.2   0.0    1.2  1  SprT-like        SprT-like family
       0.11   12.6   0.3       0.11   12.6   0.3    2.4  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        2.7    6.7   6.1        3.8    6.2   0.2    2.1  2  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.4   0.0   2.9e-47     1e-43       4     195 ..      72     282 ..      69     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 2.9e-47
                                       SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   4 eaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrh 79 
                                        +el++++++l ++a+l  p++k++vv+s+  NAFa+g+++n+  i +t+gL+ ++l+ +el++Vl+HEl+H+k+r+
  gi|313124905|ref|YP_004035169.1|  72 YPELHATISRLSQQADL--PKPKIAVVDSRVPNAFATGRSQNNaAICVTTGLM-RMLDSDELEGVLAHELAHVKNRD 145
                                       579**************..**********************************.*********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH..TT-SHHHHHTT--S---HHHHHHHHHHTT...HHHHHHHHHHHHHHHHTTT.H CS
                                       xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  80 svvslivsllasillllglall..israeedaagafldalavliglliillfl...alSRkrEyqADeagvellkra 151
                                       ++v++i s l+++++++++  +  ++ +++++ g++++a+av ++ + i++f+   alSR+rEy AD+ ++ ++ ++
  gi|313124905|ref|YP_004035169.1| 146 VMVMTIASFLSTVAFMIVRWGFwfGGGNRDRQGGGIIAAIAVSLV-VWIVSFVlirALSRYREYAADRGAAVITGQP 221
                                       ***********9999998754311444444444445444444332.2233333568********************* PP

                                       HHHHHHHHHHHHHTT--S---HHHH.................HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 152 kdlvraliklakdlerqdvsaslrs.................ellstHPplleRiqalkel 195
                                        +l++al+k++ +++++++++  ++                  ++stHP++++Ri++l++l
  gi|313124905|ref|YP_004035169.1| 222 SALASALMKISGGMDKVPQDDLREQsemnaffiipiksdfigRVFSTHPSTENRIERLRQL 282
                                       *********************99999********************************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.2e-08   4.2e-05     151     225 ..      83     159 ..      23     161 .. 0.68
   2 !    6.0   0.0    0.0017         6       7      35 ..     181     209 ..     178     250 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.2e-08
                     Peptidase_M56 151 keemqlkrnikirlsssidsPavlgllkp..rIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqclf 225
                                       +++  l ++   ++ s + + + +g  ++   I + + +++ l+ +ele +l+HElaH+k++D++v  ++ +l+ + 
  gi|313124905|ref|YP_004035169.1|  83 SQQADLPKPKIAVVDSRVPNAFATGRSQNnaAICVTTGLMRMLDSDELEGVLAHELAHVKNRDVMVMTIASFLSTVA 159
                                       4444444444444455555555555544322588889999999***************************9998775 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0017
                     Peptidase_M56   7 siaaaiavllvlllrrilrrllsaiaaYa 35 
                                       +iaa ++ l+v+++ ++l r ls  ++Ya
  gi|313124905|ref|YP_004035169.1| 181 IIAAIAVSLVVWIVSFVLIRALSRYREYA 209
                                       6899999****************999997 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.4e-05      0.12      42      77 ..     108     143 ..      49     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                         SprT-like  42 tvrhhasIeLseklldsrsedrllntLaHElcHlal 77 
                                       +++++a I   + l++  ++d+l+ +LaHEl+H+ +
  gi|313124905|ref|YP_004035169.1| 108 RSQNNAAICVTTGLMRMLDSDELEGVLAHELAHVKN 143
                                       45677888888889999999*************866 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3     3e-05      0.11      43     110 ..      16      87 ..       9      90 .. 0.66
   2 ?    2.8   2.5     0.033   1.2e+02      41      85 ..     150     200 ..     138     232 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                   Phage_holin_3_6  43 agvlallalllllval.a...lalaa...lwlaalivaavllvlagvlalvglkklkkakp.lpertieelkedva 110
                                       ++ ++l+al +++v++ +       +   + +a ++ a +++   ++l  +g kk+++ +   + +ti+ l + ++
  gi|313124905|ref|YP_004035169.1|  16 TM-FLLFALYIVFVGAlVytdS---FivlPFVAVFLFAQFFFSDKLALYSMGAKKVSEDEYpELHATISRLSQQAD 87 
                                       33.3333333333333132331...23447777777788888888*************99879999**99998776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.033
                   Phage_holin_3_6  41 gaagvlallalllllvalalalaa......lwlaalivaavllvlagvlal 85 
                                        +a +l  +a++++ ++++++ +         +aa+ v +v+ ++  vl++
  gi|313124905|ref|YP_004035169.1| 150 TIASFLSTVAFMIVRWGFWFGGGNrdrqggGIIAAIAVSLVVWIVSFVLIR 200
                                       333444444444444444333321343344445555555555555555544 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.7     0.012        42     392     433 ..      16      56 ..       7      79 .. 0.57
   2 ?    6.2   0.2     0.001       3.8     408     442 ..     173     210 ..     134     243 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.012
                           DUF2207 392 ilglilillallllvlllvfllilllillliaiivlllfsrl 433
                                        ++l+++l+++++ +l ++  ++++l ++ +++++ ++fs  
  gi|313124905|ref|YP_004035169.1|  16 TMFLLFALYIVFVGAL-VYTDSFIVLPFVAVFLFAQFFFSDK 56 
                                       2222222222222222.5566666666666666666666554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.001
                           DUF2207 408 l...lvfllilllillliaiivlllfsrllgrrteeGa 442
                                             +  i ++++ l+++iv +++ r l+r+ e+ a
  gi|313124905|ref|YP_004035169.1| 173 NrdrQGGGIIAAIAVSLVVWIVSFVLIRALSRYREYAA 210
                                       04444555555555555555555555555555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1863.65
//
Query:       gi|313124906|ref|YP_004035170.1|  [L=209]
Description: phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-27   93.4   0.2    1.2e-26   93.1   0.2    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    6.9e-06   25.7   0.2    1.3e-05   24.7   0.1    1.5  2  UPRTase       Uracil phosphoribosyltransferase
     0.0037   16.8   0.1      0.034   13.6   0.0    2.3  2  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.2     2e-30   1.2e-26      14     151 ..       8     186 ..       1     193 [. 0.92

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 2e-30
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE................... CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes........... 79 
                                       a +r +ae+l+e+  +pd+v++i+rgG+p++ ++ad+L+vpl++v ++k+ ++g++e a+g++              
  gi|313124906|ref|YP_004035170.1|   8 AGKR-LAERLQEAAVNPDLVLAIPRGGLPVGRAVADALGVPLDVVVASKVGAPGNPELAIGAVTGEgdlwlndslve 83 
                                       4445.55555555*************************************************9888*********** PP

                                       ..............................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE- CS
                      Pribosyltran  80 ..............................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdk 126
                                                                     ++ +d+ gk+V+iVDD+++tG T la l+ +++ g++++ +av+v+ 
  gi|313124906|ref|YP_004035170.1|  84 qfgigdryiesqrereadvarekvrayrggKPVPDVSGKRVVIVDDGVATGATALACLQQVRSGGAARIVFAVPVAS 160
                                       ***************************************************************************** PP

                                       HHHHHHHHHH-TTS......EEEEEE CS
                      Pribosyltran 127 pateeevdknakrvfsls.pdnfvav 151
                                        at  + +  a+ v+ ++ p+ f av
  gi|313124906|ref|YP_004035170.1| 161 AATIPRLREVADDVVVVEvPETFAAV 186
                                       *************9999988888776 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.51     3e+03      71      89 ..      26      44 ..       8      50 .. 0.77
   2 !   24.7   0.1   2.2e-09   1.3e-05     119     192 ..     119     188 ..      98     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.51
                           UPRTase 71 lVpilRaGegmeealrell 89
                                      + +i R+G++  +a+ ++l
  gi|313124906|ref|YP_004035170.1| 26 VLAIPRGGLPVGRAVADAL 44
                                      5678899999888888765 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.2e-09
                           UPRTase 119 iaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkvvtaavDeeldekgy 192
                                       ++ ++v+++D  +aTG++a a++q++++   g  +I+++  +as++ + rl e   +v vv  +v e+  + gy
  gi|313124906|ref|YP_004035170.1| 119 VSGKRVVIVDDGVATGATALACLQQVRS--GGAARIVFAVPVASAATIPRLREVADDVVVV--EVPETFAAVGY 188
                                       57789***********************..5568*****************9999987654..45555555555 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.065   3.9e+02      34      75 ..       7      44 ..       3     104 .. 0.73
   2 !   13.6   0.0   5.7e-06     0.034     122     147 ..     122     147 ..     117     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.065
                          PRTase_2 34 eagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadal 75
                                      eag++Lae+l+    e++ +p lv+++      +g++vadal
  gi|313124906|ref|YP_004035170.1|  7 EAGKRLAERLQ----EAAVNPDLVLAIPRGGLPVGRAVADAL 44
                                      67888888888....445566667777777777777777665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.7e-06
                          PRTase_2 122 kelvLvDDEistGktalnliralqek 147
                                       k++v+vDD ++tG tal+ ++++++ 
  gi|313124906|ref|YP_004035170.1| 122 KRVVIVDDGVATGATALACLQQVRSG 147
                                       789****************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1316.27
//
Query:       gi|313124907|ref|YP_004035171.1|  [L=376]
Description: nmd protein affecting ribosome stability and mRNA decay [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-63  212.0   0.1    1.1e-62  211.7   0.1    1.1  1  NMD3           NMD3 family
    0.00062   20.0   0.6      0.032   14.5   0.0    2.7  2  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
     0.0023   17.9   4.2       0.11   12.5   2.2    3.1  2  DZR            Double zinc ribbon
      0.009   16.2   0.4      0.021   15.0   0.0    1.8  2  DUF2703        Domain of unknown function (DUF2703)
  ------ inclusion threshold ------
      0.018   15.2   2.2        1.3    9.2   0.5    2.6  2  FYVE           FYVE zinc finger
        0.2   11.6   1.8       0.35   10.8   0.3    2.1  2  eIF-5_eIF-2B   Domain found in IF2B/IF5
       0.27   11.6   3.4         33    4.9   0.0    3.6  3  GFA            Glutathione-dependent formaldehyde-activating 
       0.41   10.1  10.7        3.9    7.0   0.2    4.1  4  zf-ribbon_3    zinc-ribbon domain
        1.8    8.2   4.2        4.9    6.8   0.0    3.1  3  zf_C2H2_13     Zinc finger domain
        1.9    8.2  12.6          1    9.0   0.4    3.0  2  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
        1.9    8.3  12.3       0.75    9.6   0.3    3.6  4  zinc_ribbon_2  zinc-ribbon domain
          3    7.7   5.3         36    4.2   0.1    3.1  3  CxC4           CxC4 like cysteine cluster associated with KDZ
        5.3    6.7  12.7       0.59    9.8   0.2    3.6  4  zf_UBZ         Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.7   0.1   7.8e-66   1.1e-62       1     243 []       7     253 ..       7     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 211.7 bits;  conditional E-value: 7.8e-66
                              NMD3   1 CcrCGkei....eeling...........lCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseella 62 
                                       C+rCG+++    e    +           lC++C+++++d+++++e+iev+vC++Cg+++++++Wv++    +++++
  gi|313124907|ref|YP_004035171.1|   7 CPRCGDPVpereE----PlpgmprdrdavLCDACYFEDFDLVDAPERIEVRVCSQCGAVHKGNRWVDV---GARDYT 76 
                                       ********66550....344566666778************************************666...99**** PP

                              NMD3  63 eclkklvekgLkvseeveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsr 139
                                       +++ ++v+++L v+ ++e+v++  v++e   +++ +++i+++++++g vr+   t ++++v+v+vk++rq+C+rC r
  gi|313124907|ref|YP_004035171.1|  77 DVAIEEVSEALGVHLKAEDVQWG-VEPE---QVD-QNTIRMHCSFSGFVRD---THIEETVTVPVKISRQTCKRCGR 145
                                       ***********************.****...888.999***********66...7799******************* PP

                              NMD3 140 iaggyyeaivQvRqk.relteeehkrtfelleqli....lkhdahafiskikevkeGlDfyfgsksaArklveflks 211
                                       iaggyy +ivQ+R++ r++t+ee +r+ e++e++i    +++d++afis+i++  +G ++++++++ +  +++ + +
  gi|313124907|ref|YP_004035171.1| 146 IAGGYYSSIVQIRAEeRDPTKEEAQRAVEIAESYIeereETGDRNAFISEISNSGDGPNIKISTNQMGSGVAKHVVR 222
                                       *************************************99999*********************************** PP

                              NMD3 212 evggkvkeseklvsedkksgkevyrltysvrl 243
                                       e+gg+v+e ++lv+ed + g+evyr+ty+vrl
  gi|313124907|ref|YP_004035171.1| 223 ELGGNVEEYPTLVTEDGD-GNEVYRVTYAVRL 253
                                       ******************.***********97 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.088   1.2e+02      39      54 ..      46      61 ..      41      71 .. 0.86
   2 !   14.5   0.0   2.4e-05     0.032      20      76 ..     112     168 ..      90     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.088
                                      -SSTCCCTB-TTT--B CS
                              Rpr2 39 lppsvkrtvCkkCgsv 54
                                       p+ ++ +vC++Cg+v
  gi|313124907|ref|YP_004035171.1| 46 APERIEVRVCSQCGAV 61
                                      6788999******987 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.... CS
                              Rpr2  20 lsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkk 76 
                                       ++++++  +r+   ++++ +p +++r++Ck+Cg +     ++ v+++ +++   k++
  gi|313124907|ref|YP_004035171.1| 112 MHCSFSGFVRDTHIEETVTVPVKISRQTCKRCGRIAGGYYSSIVQIRAEERDPTKEE 168
                                       566666677777888999*****************9999999999977665544333 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   2.2   8.3e-05      0.11      14      36 ..       6      60 ..       2      67 .. 0.63
   2 ?    2.2   0.0      0.13   1.8e+02      12      19 ..     137     144 ..     120     148 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.3e-05
                               DZR 14 fCseCgtklkavaa................................edrCpsCge 36
                                      fC++Cg ++++ ++                                 ++C++Cg+
  gi|313124907|ref|YP_004035171.1|  6 FCPRCGDPVPEREEplpgmprdrdavlcdacyfedfdlvdaperieVRVCSQCGA 60
                                      7777777776555577777777775555555555555555555677777888876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                               DZR  12 arfCseCg 19 
                                        ++C++Cg
  gi|313124907|ref|YP_004035171.1| 137 RQTCKRCG 144
                                       34444444 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       6.3   8.7e+03      80      89 ..      50      59 ..      27      64 .. 0.62
   2 !   15.0   0.0   1.5e-05     0.021      20      94 ..      75     149 ..      70     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.3
                           DUF2703 80 vkeelCescg 89
                                       +   C++cg
  gi|313124907|ref|YP_004035171.1| 50 IEVRVCSQCG 59
                                      4455666666 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.5e-05
                           DUF2703  20 eTgktleeavkelkeaLealgievelekvelseeelareflesntilingrpleell..gvevkeelCescgelsGe 94 
                                        T+ ++ee+ + l   L+a +++  +e ++++++ ++  +  s +  + ++ +ee +   v+ + ++C+ cg+++G 
  gi|313124907|ref|YP_004035171.1|  75 YTDVAIEEVSEALGVHLKAEDVQWGVEPEQVDQNTIR--MHCSFSGFVRDTHIEETVtvPVKISRQTCKRCGRIAGG 149
                                       58899********************************..6667777889******995556667899******9985 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.5   0.00093       1.3      34      64 ..      31      60 ..      26      63 .. 0.88
   2 ?    4.9   0.1     0.021        29      23      40 ..     135     152 ..     110     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00093
                                      EE-STTS-EEE.EEGGGTEEEEEEE-HHHHH CS
                              FYVE 34 vvCekCssklvallekeaeeksvrvCkeCla 64
                                      v+C++C  + ++l+ ++ e+ +vrvC++C a
  gi|313124907|ref|YP_004035171.1| 31 VLCDACYFEDFDLV-DAPERIEVRVCSQCGA 60
                                      89*****9999666.999***********76 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.021
                                       S--EE-TTT--EE-STTS CS
                              FYVE  23 rrrhhCrlCGkvvCekCs 40 
                                       + r  C+ CG++     s
  gi|313124907|ref|YP_004035171.1| 135 ISRQTCKRCGRIAGGYYS 152
                                       56899******9875555 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00025      0.35      88     116 ..      31      60 ..      28      61 .. 0.93
   2 ?   -0.8   0.1      0.99   1.4e+03     103     116 ..     132     145 ..     120     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                       TSTSSSTSTCEEECC.SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  88 VlCkeCkspetelek.eerllvlkCkaCga 116
                                       VlC  C   + +l+   er+ v  C++Cga
  gi|313124907|ref|YP_004035171.1|  31 VLCDACYFEDFDLVDaPERIEVRVCSQCGA 60 
                                       9*************967************7 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.99
                                       SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B 103 eerllvlkCkaCga 116
                                         +++  +Ck Cg+
  gi|313124907|ref|YP_004035171.1| 132 PVKISRQTCKRCGR 145
                                       45677789999995 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.024        33      50      66 ..       5      21 ..       1      32 [. 0.82
   2 ?    0.5   0.2      0.55   7.6e+02      42      57 ..      45      60 ..      34      75 .. 0.81
   3 ?    4.4   0.0     0.034        47       4      32 ..     139     167 ..     136     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.024
                               GFA 50 sfCpeCgsplyseesaa 66
                                       fCp+Cg p+  +e++ 
  gi|313124907|ref|YP_004035171.1|  5 DFCPRCGDPVPEREEPL 21
                                      6*********9777665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.55
                               GFA 42 dsgnkvtrsfCpeCgs 57
                                      d  ++++ ++C++Cg+
  gi|313124907|ref|YP_004035171.1| 45 DAPERIEVRVCSQCGA 60
                                      5567788899****97 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.034
                               GFA   4 hCsdCrkasgsaftanavvkaealelleg 32 
                                        C++C +++g+ +++ + ++ae+   +++
  gi|313124907|ref|YP_004035171.1| 139 TCKRCGRIAGGYYSSIVQIRAEERDPTKE 167
                                       6***************9999987665555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0028       3.9       4      14 ..       6      16 ..       3      19 .. 0.77
   2 ?   -1.0   0.2      0.91   1.3e+03      14      22 ..      28      36 ..      26      36 .. 0.85
   3 ?    6.3   0.1    0.0047       6.5       3      11 ..      53      61 ..      51      66 .. 0.77
   4 ?    1.2   0.1      0.19   2.6e+02      11      23 ..     132     144 ..     130     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0028
                       zf-ribbon_3  4 rCPnCGaplss 14
                                      +CP+CG p+ +
  gi|313124907|ref|YP_004035171.1|  6 FCPRCGDPVPE 16
                                      8*****97665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.91
                       zf-ribbon_3 14 sddnvCpyC 22
                                       d++ C  C
  gi|313124907|ref|YP_004035171.1| 28 RDAVLCDAC 36
                                      789999999 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0047
                       zf-ribbon_3  3 vrCPnCGap 11
                                      + C++CGa+
  gi|313124907|ref|YP_004035171.1| 53 RVCSQCGAV 61
                                      5799**995 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.19
                       zf-ribbon_3  11 plssddnvCpyCG 23 
                                       p++ + ++C+ CG
  gi|313124907|ref|YP_004035171.1| 132 PVKISRQTCKRCG 144
                                       5677889999999 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.5      0.55   7.6e+02      20      27 ..       7      14 ..       6      16 .. 0.90
   2 ?    6.8   0.0    0.0036       4.9      15      24 ..      50      59 ..      41      61 .. 0.81
   3 ?   -0.1   0.0      0.52   7.1e+02      19      25 ..     139     145 ..     124     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.55
                        zf_C2H2_13 20 CnkCGkPi 27
                                      C  CG P+
  gi|313124907|ref|YP_004035171.1|  7 CPRCGDPV 14
                                      99*****8 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0036
                        zf_C2H2_13 15 lnYRvCnkCG 24
                                      ++ RvC +CG
  gi|313124907|ref|YP_004035171.1| 50 IEVRVCSQCG 59
                                      789******* PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.52
                        zf_C2H2_13  19 vCnkCGk 25 
                                        C+ CG+
  gi|313124907|ref|YP_004035171.1| 139 TCKRCGR 145
                                       5*****7 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4   0.00076         1       5      12 ..       6      13 ..       5      15 .. 0.91
   2 ?    7.3   0.5    0.0026       3.6      22      31 ..      53      62 ..      52      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00076
                     zf-NADH-PPase  5 FCgrCGap 12
                                      FC+rCG p
  gi|313124907|ref|YP_004035171.1|  6 FCPRCGDP 13
                                      ******98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                     zf-NADH-PPase 22 rvCpaCgleh 31
                                      rvC++Cg+ h
  gi|313124907|ref|YP_004035171.1| 53 RVCSQCGAVH 62
                                      8999999988 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3   0.00054      0.75       1      13 [.       6      18 ..       6      20 .. 0.81
   2 ?   -3.5   0.1         7   9.6e+03      12      19 ..      29      36 ..      28      36 .. 0.83
   3 ?    4.3   0.1     0.025        35      16      21 ..      55      60 ..      51      65 .. 0.65
   4 ?    1.1   0.4      0.25   3.4e+02       2       7 ..     140     145 ..     139     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00054
                     zinc_ribbon_2  1 fCpnCGaelqdna 13
                                      fCp+CG ++++++
  gi|313124907|ref|YP_004035171.1|  6 FCPRCGDPVPERE 18
                                      8999999988865 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7
                     zinc_ribbon_2 12 nakFCpyC 19
                                      +a+ C  C
  gi|313124907|ref|YP_004035171.1| 29 DAVLCDAC 36
                                      58899998 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.025
                     zinc_ribbon_2 16 CpyCGt 21
                                      C++CG+
  gi|313124907|ref|YP_004035171.1| 55 CSQCGA 60
                                      555554 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.25
                     zinc_ribbon_2   2 CpnCGa 7  
                                       C++CG+
  gi|313124907|ref|YP_004035171.1| 140 CKRCGR 145
                                       999996 PP

>> CxC4  CxC4 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.3     0.053        73      45      60 ..      48      63 ..       2      76 .. 0.69
   2 ?    4.2   0.1     0.026        36      39      61 ..     127     146 ..     105     154 .. 0.81
   3 ?   -0.6   0.0      0.82   1.1e+03      83     112 ..     286     315 ..     280     328 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.053
                              CxC4 45 vrielqrCpaCahtrr 60
                                       rie++ C++C ++++
  gi|313124907|ref|YP_004035171.1| 48 ERIEVRVCSQCGAVHK 63
                                      58*********54443 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.026
                              CxC4  39 ltgalevrielqrCpaCahtrrf 61 
                                        t +++v+i  q+C++C    r 
  gi|313124907|ref|YP_004035171.1| 127 ETVTVPVKISRQTCKRCG---RI 146
                                       477899***********4...44 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.82
                              CxC4  83 ellneytsaftasetpfsafvaavsrryee 112
                                       ++ ++y s+f+++etp  + + +v+   e+
  gi|313124907|ref|YP_004035171.1| 286 DSGEQYESQFEEGETPDARRLGTVEDAAET 315
                                       5668999********987777666666555 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00043      0.59       4      17 ..       6      19 ..       3      20 .. 0.86
   2 ?   -3.0   0.2       4.3   5.9e+03       2       8 ..      30      36 ..      29      36 .. 0.81
   3 ?    1.7   0.1      0.14     2e+02       4      10 ..      54      60 ..      51      62 .. 0.86
   4 ?    2.6   0.4     0.075     1e+02       3      10 ..     138     145 ..     136     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00043
                            zf_UBZ  4 lCerCgkeipesel 17
                                      +C+rCg ++pe e 
  gi|313124907|ref|YP_004035171.1|  6 FCPRCGDPVPEREE 19
                                      8*********9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.3
                            zf_UBZ  2 tylCerC 8 
                                       +lC+ C
  gi|313124907|ref|YP_004035171.1| 30 AVLCDAC 36
                                      579**99 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.14
                            zf_UBZ  4 lCerCgk 10
                                      +C++Cg+
  gi|313124907|ref|YP_004035171.1| 54 VCSQCGA 60
                                      8****97 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.075
                            zf_UBZ   3 ylCerCgk 10 
                                       ++C+rCg+
  gi|313124907|ref|YP_004035171.1| 138 QTCKRCGR 145
                                       79****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 2079.38
//
Query:       gi|313124908|ref|YP_004035172.1|  [L=63]
Description: hypothetical protein Hbor_01220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-07   28.8   0.1    8.6e-07   28.6   0.1    1.1  1  UPF0175   Uncharacterised protein family (UPF0175)
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.17   12.0   0.0    1.2  1  AbiEi_4   Transcriptional regulator, AbiEi antitoxin


Domain annotation for each model (and alignments):
>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   9.6e-11   8.6e-07      23      66 ..       7      50 ..       3      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.6e-11
                           UPF0175 23 alAvklYeegrlSlgkAaelaglsrveflelLarrgiplinyde 66
                                       +A+ lY+ g l+l++Aa+ ag s       L+++g+ +++ +e
  gi|313124908|ref|YP_004035172.1|  7 TTAMTLYQSGTLTLSQAATRAGRSEEALVSALHQHGVEVREQEE 50
                                      68************************************876544 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.9e-05      0.17      10      36 ..      14      42 ..       8      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                           AbiEi_4 10 qvGlfttrelea.aGispsa.lrrLvrkG 36
                                      q+G++t ++++  aG+s+ a ++ L+++G
  gi|313124908|ref|YP_004035172.1| 14 QSGTLTLSQAATrAGRSEEAlVSALHQHG 42
                                      459******9888*****99899999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 393.38
//
Query:       gi|313124909|ref|YP_004035173.1|  [L=627]
Description: DNA helicase, rad3 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-24   87.3   0.0    1.9e-24   86.7   0.0    1.3  1  Helicase_C_2  Helicase C-terminal domain
    1.6e-05   24.6   0.0    2.7e-05   23.9   0.0    1.3  1  DEAD_2        DEAD_2
    6.2e-05   23.3   0.1     0.0011   19.3   0.1    2.7  2  AAA_22        AAA domain
    7.8e-05   22.5   0.0       0.11   12.2   0.0    2.5  2  DEAD          DEAD/DEAH box helicase
    0.00023   21.2   0.0        0.1   12.6   0.0    2.3  2  ResIII        Type III restriction enzyme, res subunit
    0.00024   21.5   0.8     0.0039   17.6   0.7    2.6  1  AAA_16        AAA ATPase domain
    0.00089   19.0   0.5       0.69    9.6   0.1    2.3  2  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.022   14.0   0.0        5.1    6.2   0.0    2.3  2  DUF2075       Uncharacterized conserved protein (DUF2075)
      0.023   15.0   0.0      0.048   14.0   0.0    1.5  1  AAA_19        AAA domain
       0.11   13.0   0.1        1.2    9.6   0.1    2.3  1  AAA           ATPase family associated with various cellular 
       0.13   11.7   0.0       0.26   10.7   0.0    1.4  1  PhoH          PhoH-like protein
       0.13   11.6   0.0       0.22   10.9   0.0    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   1.3e-27   1.9e-24       3     170 ..     375     530 ..     373     531 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 1.3e-27
                      Helicase_C_2   3 ellevvp.ggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGi 78 
                                       +l+++ p ++ lv ++Sy++  e+++rl++ +   + +i  + ++++r++ le++k+  ++ga ++ ++  k+ E +
  gi|313124909|ref|YP_004035173.1| 375 RLMAKHPdEKGLVHCHSYAIQSELRKRLAQLGL--GGRIRGH-DKANRDAELETWKA--SSGADVFLSV--KMEEAL 444
                                       66666665789*******************998..5567776.789***********..8888777777..9***** PP

                      Helicase_C_2  79 dfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRf 155
                                       d+++dl+r  +i++ P+ n++d +v+++ e        ++ ++wy ++alr+v Qa+GR++R  dDyga +l D+ +
  gi|313124909|ref|YP_004035173.1| 445 DLKGDLCRWQVICKAPYLNTNDSRVAQRLE--------DGQWSWYRRAALRTVIQACGRVVRAPDDYGATYLADSSL 513
                                       *************************99976........567************************************ PP

                      Helicase_C_2 156 ak..eeireklpkwlre 170
                                        +  +++r+++p+w+ e
  gi|313124909|ref|YP_004035173.1| 514 LQlfDRTRSEMPEWFAE 530
                                       *99999********976 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.8e-08   2.7e-05     107     173 ..     131     193 ..     126     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.8e-08
                                       CT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHHT..GCGCEEEECTCCCHHHHHHHCC-EEEEC CS
                            DEAD_2 107 lklCPYylsrelledadiiilpYqyLldekireslkgislknsivilDEAhNiedvceeaasveise 173
                                        + CPY++ r+++++ +i  +  +y+++    + ++    +  +v++DEAh + + +e  a ++++ 
  gi|313124909|ref|YP_004035173.1| 131 RHRCPYFSDRAIASNRKIAAMTLAYFMQTAGSDVFR----QRDVVVIDEAHGLAEWAEMYATIDLNP 193
                                       578************************999888885....789************999999988875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   7.2e-07    0.0011       7     112 ..      36     189 ..      31     199 .. 0.78
   2 ?   -1.1   0.0       1.4   2.1e+03      70      98 ..     240     278 ..     218     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.2e-07
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelka............ 70 
                                       +++v +++G+GK++l+r ++  +   ++a+ ++++ +++t p+ + ++d+   ell++l   + +            
  gi|313124909|ref|YP_004035173.1|  36 VVLVRAPTGSGKSLLARSIAGAARTTEEAKPAQATDAYYTTPQVSQLDDVaEDELLEDLSIIRGKsnytcilngetd 112
                                       678899*****************9999999988888899999999888885557888888777667889******** PP

                            AAA_22  71 ...............................erlsseell.ealeqalrarav..ielliiDEaqhlrs..eealee 111
                                                                      ++ +  ++  +++ q + +     + +++iDEa+ l    +e++ +
  gi|313124909|ref|YP_004035173.1| 113 tpvdrapcarqkgfdctvrhrcpyfsdraiaSNRKIAAMTlAYFMQTAGSDVFrqRDVVVIDEAHGL-AewAEMYAT 188
                                       ***********************9999987633333333334444433333336889*********9.446777776 PP

                            AAA_22 112 L 112
                                       +
  gi|313124909|ref|YP_004035173.1| 189 I 189
                                       6 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                            AAA_22  70 a.......erlsseellealeqalrarav...ielliiD 98 
                                       +       +r++++el++ l   ++++++   +   ++D
  gi|313124909|ref|YP_004035173.1| 240 EltpeeasRRDRLQELRSELKWFIEDYRDpesPTTWVVD 278
                                       033444557899999999999999988887777777776 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   7.5e-05      0.11      13      43 ..      33      65 ..      17      97 .. 0.67
   2 !    7.6   0.0     0.002         3     118     136 ..     164     182 ..     139     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                                      TTCEEEEEESTTSSHHHHH.HHHHHHHHHHS.T CS
                                      xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.x RF
                              DEAD 13 gggdvlvaaeTGsGKTlaf.lipvlqivyet.k 43
                                      g++ vlv+a+TGsGK+l + +i+  ++ +e+ k
  gi|313124909|ref|YP_004035173.1| 33 GNDVVLVRAPTGSGKSLLArSIAGAARTTEEaK 65
                                      556788**********87525555555544444 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                                       HCTTEEEEEEETHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD 118 nlsqvrflVlDEadrlldq 136
                                        ++q  ++V+DEa++l ++
  gi|313124909|ref|YP_004035173.1| 164 VFRQRDVVVIDEAHGLAEW 182
                                       488999**********998 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   6.8e-05       0.1       5      47 ..      16      57 ..      13      69 .. 0.86
   2 !    6.1   0.0    0.0066       9.8     131     147 ..     166     182 ..     140     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.8e-05
                                      -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHH CS
                            ResIII  5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklier 47
                                      r  Qe+a+ ++++++   ++  +l+ ++TG+GK+l+a +++ +
  gi|313124909|ref|YP_004035173.1| 16 RGAQEQALCDIRDAFA-AGNDVVLVRAPTGSGKSLLARSIAGA 57
                                      678************9.******************99777654 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0066
                                       TT-SEEEEETGGGTTS. CS
                            ResIII 131 drfdviiiDEaHrlgak 147
                                        + dv++iDEaH l++ 
  gi|313124909|ref|YP_004035173.1| 166 RQRDVVVIDEAHGLAEW 182
                                       4678********99884 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.7   2.6e-06    0.0039       4     145 ..      15     177 ..      13     282 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                            AAA_16   4 GReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalaree 80 
                                       +R+++ ++L ++ ++ ++g   +vl++ + G+GKs l+r+++ a++++     ++k  q          ++a  +  
  gi|313124909|ref|YP_004035173.1|  15 YRGAQEQALCDIRDAFAAGN-DVVLVRAPTGSGKSLLARSIAGAARTT----EEAKPAQA---------TDAYYTTP 77 
                                       58888888888877777777.8********************988888....67777776.........44444556 PP

                            AAA_16  81 llrqlldeaesaeleawrekleeala......................................avpelagaeasrl 119
                                        + ql+d ae+ el ++   +++  +                                      a+++ +  +a  l
  gi|313124909|ref|YP_004035173.1|  78 QVSQLDDVAED-ELLEDLSIIRGKSNytcilngetdtpvdrapcarqkgfdctvrhrcpyfsdrAIASNRKIAAMTL 153
                                       66666666555.55555555555555566666666665555555555555566666665555554444444444555 PP

                            AAA_16 120 lellkrll.allsrderplvlvlDdlq 145
                                       ++ ++ +  +  ++ ++  v+v+D+++
  gi|313124909|ref|YP_004035173.1| 154 AYFMQTAGsDVFRQ-RD--VVVIDEAH 177
                                       55555555444444.33..56666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00046      0.69      10      45 ..      26      61 ..      14      90 .. 0.79
   2 !    7.4   0.1    0.0022       3.3      63      98 ..     143     177 ..     138     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                            AAA_30 10 vealltsgdrvavltGpAGtGKttalkalreaweaa 45
                                      ++ + + g+ v+++ +p G+GK+ + ++++ a+++ 
  gi|313124909|ref|YP_004035173.1| 26 IRDAFAAGNDVVLVRAPTGSGKSLLARSIAGAARTT 61
                                      4566677778****************9999887765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0022
                            AAA_30  63 aeelgieastiakllkrlkgrarlepgtllivDEag 98 
                                       a +  i+a+t+a ++++ ++   +++++++++DEa 
  gi|313124909|ref|YP_004035173.1| 143 ASNRKIAAMTLAYFMQTAGS-DVFRQRDVVVIDEAH 177
                                       5567899********66664.578888*******95 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0062       9.3       3      32 ..      36      65 ..      34      98 .. 0.76
   2 ?    6.2   0.0    0.0034       5.1      82     105 ..     161     184 ..     137     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0062
                           DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeer 32
                                      vvlV+  +G+GK++++ +++ +++++ee +
  gi|313124909|ref|YP_004035173.1| 36 VVLVRAPTGSGKSLLARSIAGAARTTEEAK 65
                                      8999999*************9994333333 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0034
                           DUF2075  82 ekkeepkedvvivDEAhrlltksd 105
                                        ++  ++ dvv++DEAh l + ++
  gi|313124909|ref|YP_004035173.1| 161 GSDVFRQRDVVVIDEAHGLAEWAE 184
                                       46667899*********9988544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.2e-05     0.048       4     115 ..      29     180 ..      26     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                            AAA_19   4 avealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.........atT 71 
                                       a  a+ ++v+lv a+ G+GK+ + + i   +  +++ kp++ + + +t   +++l +  +  ++e            
  gi|313124909|ref|YP_004035173.1|  29 AF-AAGNDVVLVRAPTGSGKSLLARSIAGAARTTEEAKPAQATDAYYTTPQVSQLDDVAEDELLEdlsiirgksN-- 102
                                       45.78899*******************************999999999999999999775544445555555552.. PP

                            AAA_19  72 iHrlal.......................................ldfddlltealelleeaeeekklqeeellivD 109
                                                                                      + ++  ++l+++ +++ ++ +++++++++D
  gi|313124909|ref|YP_004035173.1| 103 -----YtcilngetdtpvdrapcarqkgfdctvrhrcpyfsdraiASNRKIAAMTLAYFMQTAGSDVFRQRDVVVID 174
                                       .....0444444566666666667777777777777777877775444444444444444788888887888***** PP

                            AAA_19 110 Efqdvd 115
                                       E+  + 
  gi|313124909|ref|YP_004035173.1| 175 EAHGLA 180
                                       *97765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00079       1.2       1      25 [.      37      61 ..      37     190 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00079
                                      EEEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  1 vllyGppGtGKTllakavakelgve 25
                                      vl+  p G GK+lla+++a  + ++
  gi|313124909|ref|YP_004035173.1| 37 VLVRAPTGSGKSLLARSIAGAARTT 61
                                      577889*************997432 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00017      0.26      17      44 ..      31      59 ..      16      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                                      H.H-SEEEEE--TTSSTTHHHHHHHHHHH CS
                              PhoH 17 k.kndivfaiGpaGtGKtylavalaveal 44
                                         nd+v + +p+G+GK++la ++a +a 
  gi|313124909|ref|YP_004035173.1| 31 AaGNDVVLVRAPTGSGKSLLARSIAGAAR 59
                                      25799****************88875554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.22      19      48 ..      31      60 ..      18      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                      Mg_chelatase 19 aaGgHnlllvGppGsGKtmlakrlpsllpp 48
                                      aaG+  +l+  p GsGK++la+ +++    
  gi|313124909|ref|YP_004035173.1| 31 AAGNDVVLVRAPTGSGKSLLARSIAGAART 60
                                      899999****************99876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 3976.79
//
Query:       gi|313124910|ref|YP_004035174.1|  [L=67]
Description: hypothetical protein Hbor_01240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 499.53
//
Query:       gi|313124911|ref|YP_004035175.1|  [L=303]
Description: hypothetical protein Hbor_01250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-06   26.8   0.9     0.0043   17.7   0.0    2.3  2  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.4   0.00038       6.8       1      17 [.       4      20 ..       4      37 .. 0.81
   2 !   17.7   0.0   2.4e-07    0.0043      42      72 ..     111     143 ..      75     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00038
                          CxxCxxCC  1 eCkeCgaCCkelkvklt 17
                                      +C++C+ CC ++++  +
  gi|313124911|ref|YP_004035175.1|  4 NCEGCAGCCIDWRPVSP 20
                                      6*********8876655 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.4e-07
                          CxxCxxCC  42 adgrCvfldeetklCkiYeeR..pkicrlfpas 72 
                                       + ++Cvfld+et +C+i+ +   p+ cr +p +
  gi|313124911|ref|YP_004035175.1| 111 WLHACVFLDPETLQCRIHGDEmyPSECRDYPGH 143
                                       5679**************97777*******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1628.51
//
Query:       gi|313124912|ref|YP_004035176.1|  [L=351]
Description: nucleoside-diphosphate sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-12   45.9   0.3    8.5e-10   38.5   0.1    2.4  2  Epimerase       NAD dependent epimerase/dehydratase family
    1.6e-11   44.4   0.2    5.7e-09   36.1   0.1    2.3  2  NAD_binding_10  NAD(P)H-binding
    8.3e-08   32.1   0.0    3.5e-07   30.0   0.1    1.8  2  NmrA            NmrA-like family
    1.2e-06   28.2   0.1    2.3e-06   27.3   0.1    1.5  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
    1.1e-05   24.8   0.0    2.1e-05   23.8   0.0    1.5  1  NAD_binding_4   Male sterility protein
    0.00034   19.8   0.0    0.00093   18.4   0.0    1.6  2  RmlD_sub_bind   RmlD substrate binding domain
     0.0014   17.7   0.0      0.014   14.4   0.0    2.0  2  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
  ------ inclusion threshold ------
       0.04   14.0   0.0      0.078   13.1   0.0    1.5  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
      0.067   13.6   0.0       0.18   12.2   0.0    1.8  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
       0.22   11.0   0.0       0.33   10.4   0.0    1.2  1  adh_short       short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.1   4.8e-13   8.5e-10       1      52 [.       3      52 ..       3      58 .. 0.95
   2 !    5.3   0.0    0.0065        12     213     241 .]     204     230 ..     151     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 4.8e-13
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltd 52
                                      +lVtGatGf+Gs lv+all+ g+ev +l r+  asn ++ +d++++e+dl++
  gi|313124912|ref|YP_004035176.1|  3 VLVTGATGFVGSRLVRALLDDGHEVSALVRD--ASNAELPADVHVIEGDLLE 52
                                      79*****************************..9999999999*******97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0065
                                       EEHHHHHHHHHHHHHHHTT-STTEEEEES CS
                         Epimerase 213 lyveDvaeaillvlehvdagdkgeiyniG 241
                                       +yv+Dv+  ++ vl+++++  +ge+y iG
  gi|313124912|ref|YP_004035176.1| 204 IYVDDVVAYLVGVLDAPET--AGETYEIG 230
                                       8***************988..58999998 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   3.2e-12   5.7e-09       1      50 [.       7      52 ..       7      57 .. 0.93
   2 !    6.3   0.0    0.0045       8.1      73     158 ..     104     182 ..      69     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.2e-12
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT- CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtd 50
                                      GAtG vG++lv+ ll++ ghev alvR+++ ++ l+  + ++v+egd+++
  gi|313124912|ref|YP_004035176.1|  7 GATGFVGSRLVRALLDD-GHEVSALVRDASNAE-LP--ADVHVIEGDLLE 52
                                      9****************.5*************9.86..79*******986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0045
                                       C....HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE-C CS
                    NAD_binding_10  73 k....deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTivrpgg 145
                                       +    d+++a++  + + +a v+R+v+++++g ++           + l++ l+  r+ e +l + + d T +r + 
  gi|313124912|ref|YP_004035176.1| 104 DfeerDRRAARHFERGVSAASVERVVYLGGLGEER-----------DHLSPHLRSRREVEYVLGEGDYDLTTLRAAI 169
                                       2344577889999999999********99999773...........4577889999999999999999999999999 PP

                                       EE-ST--SEEEEE CS
                    NAD_binding_10 146 Ltdepttkyrvve 158
                                       +  + +  ++v+ 
  gi|313124912|ref|YP_004035176.1| 170 IIGDGSASFEVIR 182
                                       8877766677664 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1     2e-10   3.5e-07       1      36 [.       3      38 ..       3      71 .. 0.86
   2 ?   -0.4   0.0      0.37   6.7e+02     176     225 ..     200     248 ..     120     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2e-10
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHH CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtksel 36
                                      +lv+GaTG  G+ +vrall++gh+v alvRd ++ +
  gi|313124912|ref|YP_004035176.1|  3 VLVTGATGFVGSRLVRALLDDGHEVSALVRDASNAE 38
                                      79*****************************96544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.37
                                       TS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHH CS
                              NmrA 176 kavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekki 225
                                       +  ++  ++D+ a+ + +l+ p+++   +     ++l++ e+++   + +
  gi|313124912|ref|YP_004035176.1| 200 ECQPI-YVDDVVAYLVGVLDAPETAGETYEIGGPDVLTYGEVLKRVGEHL 248
                                       44455.78999999999999999995555555667888888877666555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   1.3e-09   2.3e-06       1      42 [.       4      45 ..       4      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.3e-09
                                      EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHC CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehl 42
                                      L+TG +Gf+Gs l++ Ll+ g+ev  +vr++s+ ++    h+
  gi|313124912|ref|YP_004035176.1|  4 LVTGATGFVGSRLVRALLDDGHEVSALVRDASNAELPADVHV 45
                                      9*****************************999876554454 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.2e-08   2.1e-05       1      35 [.       5      37 ..       5      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.2e-08
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksge 35
                                      +TGaTGF+G++L++ LL++    ++ +lvR  s++
  gi|313124912|ref|YP_004035176.1|  5 VTGATGFVGSRLVRALLDDGH--EVSALVRDASNA 37
                                      7******************98..8******88775 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.2e-07   0.00093       1      44 [.       1      44 [.       1      51 [. 0.91
   2 ?   -2.2   0.0      0.94   1.7e+03     142     212 ..     161     229 ..     144     261 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.2e-07
                                      EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHH CS
                     RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltreeldltdaeava 44
                                      mk+lvtGa+G +Gs L+++l  +g+ev al r++ + + ++ v+
  gi|313124912|ref|YP_004035176.1|  1 MKVLVTGATGFVGSRLVRALLDDGHEVSALVRDASNAELPADVH 44
                                      89****************************99998888777776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.94
                                       SEEEEEE-SEESSSSS-HHHHHHHHHHH-SEEEEE...SS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE- CS
                     RmlD_sub_bind 142 kalivRtswvygekgknfvktmlrlakereelkvv...aDqlgsPTsardlAevllqllekaaeekelagvyHl 212
                                       + + +R + + g+   +f   ++r +++r ++ v     D   +P +++d+ ++l+ +l++      + ++y +
  gi|313124912|ref|YP_004035176.1| 161 DLTTLRAAIIIGDGSASF--EVIRQLADRLPVMVTprwVDTECQPIYVDDVVAYLVGVLDAPET---AGETYEI 229
                                       556666666666655554..44555555555555422246677888888888888888877665...4455555 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     8e-06     0.014       1      27 [.       4      28 ..       4      55 .. 0.76
   2 ?    0.9   0.0       0.1   1.8e+02     175     223 ..     164     211 ..     153     222 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-06
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevr 27
                                      +vtG++GF+G++lv++L++ ++  ev 
  gi|313124912|ref|YP_004035176.1|  4 LVTGATGFVGSRLVRALLDDGH--EVS 28
                                      69****************9986..443 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.1
                         3Beta_HSD 175 aLRpagiyGegdkllvpllkqlaklglalfkigdeevlsdrvYvgNvaw 223
                                        LR a+i G+g+  ++  ++qla     ++     ++  +++Yv+ v+ 
  gi|313124912|ref|YP_004035176.1| 164 TLRAAIIIGDGSASFEV-IRQLADRLPVMVTPRWVDTECQPIYVDDVVA 211
                                       59*********998765.5555554445544444444458999998875 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.4e-05     0.078       1      36 [.       1      35 [.       1      54 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke 36
                                      +kv+v+Ga+G +G+++v+a+ + +++e++a v   +
  gi|313124912|ref|YP_004035176.1|  1 MKVLVTGATGFVGSRLVRALLD-DGHEVSALVRDAS 35
                                      89******************99.9999999887766 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.18       1      22 [.       2      25 ..       2      47 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                      EEEEETTTSHHHHHHHHHHHC..T CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLee..h 22
                                      kv + GatG vG++l+r L +  h
  gi|313124912|ref|YP_004035176.1|  2 KVLVTGATGFVGSRLVRALLDdgH 25
                                      68999***********99887333 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00018      0.33       3      38 ..       3      38 ..       1      52 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekle 38
                                      vlvtGa++ +G  ++++l+ +G +v ++ r ++++e
  gi|313124912|ref|YP_004035176.1|  3 VLVTGATGFVGSRLVRALLDDGHEVSALVRDASNAE 38
                                      9*************************9888877663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1873.78
//
Query:       gi|313124913|ref|YP_004035177.1|  [L=231]
Description: hypothetical protein Hbor_01270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 1261.08
//
Query:       gi|313124914|ref|YP_004035178.1|  [L=55]
Description: hypothetical protein Hbor_01280 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.063   11.8   0.2      0.065   11.8   0.2    1.0  1  MmgE_PrpD      MmgE/PrpD family
      0.096   12.7   0.0        0.1   12.6   0.0    1.0  1  Peptidase_M16  Insulinase (Peptidase family M16)


Domain annotation for each model (and alignments):
>> MmgE_PrpD  MmgE/PrpD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   7.3e-06     0.065     366     415 ..       8      52 ..       2      55 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-06
                                       HHHHHTTT---EEEEETTS-B---EEESS-TTSGGHHHHHHHHHHHHHHH CS
                         MmgE_PrpD 366 ltadypekrsivvvvlkdggrtleerveypkGhprnplsreeleeKfrrl 415
                                         ++ + k   v  +++d++++++ +v y+ G+     s+e l++Kfr++
  gi|313124914|ref|YP_004035178.1|   8 EHERRERKNGSVDATFDDDRTVYHGEVTYDSGD-----STEALLDKFREM 52 
                                       22223333333*********************8.....899999999976 PP

>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05       0.1      57      94 ..      12      52 ..       3      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                                      HHHTTCEEEEEEESSEEEEEEEEEGGG...HHHHHHHHHHH CS
                     Peptidase_M16 57 leklGgslnAttsrentvYyvevlskd...lekaldvladv 94
                                       e+ +gs++At + ++tvY+ ev+ ++   +e +ld + ++
  gi|313124914|ref|YP_004035178.1| 12 RERKNGSVDATFDDDRTVYHGEVTYDSgdsTEALLDKFREM 52
                                      5889*******************998877888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.55
# Mc/sec: 301.43
//
Query:       gi|313124915|ref|YP_004035179.1|  [L=329]
Description: hypothetical protein Hbor_01290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1730.86
//
Query:       gi|313124916|ref|YP_004035180.1|  [L=94]
Description: hypothetical protein Hbor_01300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 601.37
//
Query:       gi|313124917|ref|YP_004035181.1|  [L=262]
Description: metal-dependent phosphoesterase, php family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-05   24.5   0.0    2.7e-05   24.5   0.0    1.2  1  PHP       PHP domain
     0.0017   18.1   0.1     0.0089   15.8   0.0    2.3  2  PHP_C     PHP-associated


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     3e-09   2.7e-05       1      74 [.       3      96 ..       3     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3e-09
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE.............. CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse...... 73
                                      dlH+Ht+ s  dg+l+i e+ ++a + g + +a+TDh+ ++  +++       +++g+++i G+e+ v+  ++      
  gi|313124917|ref|YP_004035181.1|  3 DLHLHTTAS--DGVLTIAEVPDAAVAGGVEVVAVTDHDRVHPDLDAPVT----ERDGVTMIRGVELRVETPEQrldllg 75
                                      79***9877..677889***********************976655533....45789999999999888777566666 PP

                                      ..................... CS
                                      ....................x RF
                               PHP 74 ....................k 74
                                                          k
  gi|313124917|ref|YP_004035181.1| 76 yavrdtpairevteriqtdrK 96
                                      665555555555555555541 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.31   2.7e+03      11      22 ..     200     211 ..     191     213 .. 0.73
   2 !   15.8   0.0   9.9e-07    0.0089       5      25 ..     218     238 ..     214     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.31
                             PHP_C  11 AeklglpgtgGS 22 
                                       A ++ +p  gGS
  gi|313124917|ref|YP_004035181.1| 200 AVERFYPYGGGS 211
                                       667889999999 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.9e-07
                             PHP_C   5 rrArrfAeklglpgtgGSDAH 25 
                                       + ++r+A++++l  tgGSDAH
  gi|313124917|ref|YP_004035181.1| 218 ELVERIAAANDLLLTGGSDAH 238
                                       6789***************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1541.12
//
Query:       gi|313124918|ref|YP_004035182.1|  [L=54]
Description: hypothetical protein Hbor_01320 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.6   10.1   4.4       0.49   10.3   2.2    1.9  2  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me


Domain annotation for each model (and alignments):
>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.2   2.7e-05      0.49      34      43 ..       1      10 [.       1      14 [. 0.84
   2 ?   -0.3   0.0     0.056     1e+03      39      45 ..      24      30 ..      12      32 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.7e-05
                                      EEETTT--EE CS
                            PyrI_C 34 lkCkYCekei 43
                                      +kC+YCe+  
  gi|313124918|ref|YP_004035182.1|  1 MKCHYCERDA 10
                                      79*****975 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.056
                                      T--EEEH CS
                            PyrI_C 39 Cekeise 45
                                      Ce+ ++e
  gi|313124918|ref|YP_004035182.1| 24 CERHFRE 30
                                      9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 349.92
//
Query:       gi|313124919|ref|YP_004035183.1|  [L=55]
Description: hypothetical protein Hbor_01330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.47
# Mc/sec: 355.32
//
Query:       gi|313124920|ref|YP_004035184.1|  [L=205]
Description: hypothetical protein Hbor_01340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-09   36.6   3.0      1e-08   35.7   2.9    1.5  1  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.22   11.3   0.0    1.3  1  DUF3868      Domain of unknown function, B. Theta Gene descri


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   2.9   1.1e-12     1e-08      15     114 ..      93     194 ..      55     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.1e-12
                       SNARE_assoc  15 glllgtlvtslgallGaslayllgrylgr...kalrrkllsekrvkalerlverygflallllrllpivPrdlvnyv 88 
                                         + ++ +++lga++G    + ++++ gr    + r  ++se ++++++ ++er g +++ ++  l +  r +++++
  gi|313124920|ref|YP_004035184.1|  93 AAVAVIGIAVLGATIGQYALFKVAQRGGReylLQKRWFAVSESKLDRFDGWFERWGPIVVPVSNTLLFT-RGMLTVP 168
                                       2345999**********************877566666789999999********************98.******* PP

                       SNARE_assoc  89 aGltrvsfkrFflatfiGsipwalvy 114
                                       aG +++  ++F++ +++G++   +++
  gi|313124920|ref|YP_004035184.1| 169 AGFAEMDDRQFVALSAVGTLSFEVIL 194
                                       ******************98765555 PP

>> DUF3868  Domain of unknown function, B. Theta Gene description (DUF3868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.5e-05      0.22      60     103 ..      94     137 ..      87     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.5e-05
                           DUF3868  60 ahsveliPvLiseerteeLpkvsikGrkeykaykRklalmsake 103
                                       a +v+ i vL ++ +++ L kv  +G +ey++ kR+ a+++ k 
  gi|313124920|ref|YP_004035184.1|  94 AVAVIGIAVLGATIGQYALFKVAQRGGREYLLQKRWFAVSESKL 137
                                       55678889999*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1177.58
//
Query:       gi|313124921|ref|YP_004035185.1|  [L=326]
Description: porphobilinogen synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.7e-144  479.7   0.6   4.1e-144  479.6   0.6    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.6   0.6  2.3e-148  4.1e-144       2     316 ..       5     324 ..       4     325 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.6 bits;  conditional E-value: 2.3e-148
                                       --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE- CS
                              ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvp 78 
                                        r+rrlr++  +r+lv+et+lsa+dli+p+fv+ +++e+ +i+smpg++r++v+e+v++vee++++g++av+lFg+p
  gi|313124921|ref|YP_004035185.1|   5 DRPRRLRTDG-IRSLVSETNLSATDLIAPVFVDATTDERLPIESMPGHERVPVSEAVARVEEVLETGVEAVMLFGIP 80 
                                       699**99765.****************************************************************** PP

                                       SS-BSS-GGGGSTTSHHHHHHHHHHHH-TTSEEEEEE-STTTBSS-SSSEEESS........EEHHHHHHHHHHHHH CS
                              ALAD  79 eekdeegsealnedglvqrairaikeevpelvvitDvclceytshGhcgileeke.......vdndetlellakvav 148
                                       e+kde+gs+a++edg+vq+a+r++ ee ++ +vitDvc+ceytshGhcgi+e+++       v+ndetl+llak+av
  gi|313124921|ref|YP_004035185.1|  81 ESKDERGSRAWAEDGVVQKATRRVTEE-TDAYVITDVCMCEYTSHGHCGIVEDHAesdptltVKNDETLALLAKTAV 156
                                       *************************99.899********************86656889999*************** PP

                                       HHHHCT-SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHH CS
                              ALAD 149 sqaeaGadivapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansre 225
                                       s+aeaGad+vapS+m Dg+v+aireaLde+g+e+v+i+sY+aKy SafYgPFrdaa+ ap+fgdr++Yqmdpan+re
  gi|313124921|ref|YP_004035185.1| 157 SHAEAGADMVAPSSMTDGMVGAIREALDESGHESVPIMSYAAKYESAFYGPFRDAADGAPAFGDRRHYQMDPANARE 233
                                       ***************************************************************************** PP

                                       HHHHHHHHHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT CS
                              ALAD 226 alreveldleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAG 302
                                       a+rev+ld+e+GAD++mvKPalaylDi+r+v+eefd+pvaay+vSGEYam++aaae+gw+d +++++Esll++kRAG
  gi|313124921|ref|YP_004035185.1| 234 AIREVTLDVEQGADVLMVKPALAYLDIVRAVREEFDHPVAAYNVSGEYAMLHAAAEKGWMDLDETAFESLLAMKRAG 310
                                       ***************************************************************************** PP

                                       -SEEEETTHHHHHH CS
                              ALAD 303 adliltYfakevak 316
                                       adliltYfa+++a+
  gi|313124921|ref|YP_004035185.1| 311 ADLILTYFAEDIAD 324
                                       ***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2118.91
//
Query:       gi|313124922|ref|YP_004035186.1|  [L=457]
Description: ammonium transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-96  321.0  40.7    1.1e-95  320.8  40.7    1.0  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
       0.19   11.7   0.1       0.19   11.7   0.1    2.3  2  PsbY             Photosystem II protein Y (PsbY)


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.8  40.7   1.2e-99   1.1e-95       1     399 []      19     423 ..      19     423 .. 0.93

  Alignments for each domain:
  == domain 1  score: 320.8 bits;  conditional E-value: 1.2e-99
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCB..SSSSSCE-TTTTSC CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgksk..gvsgfignlglsaa 75 
                                       +++l++++l++fmq+gfalleag+vr+knv n+l+kn+ d+++++l+y+++G ++a       + + f+++   + a
  gi|313124922|ref|YP_004035186.1|  19 VWILVVTFLIFFMQPGFALLEAGQVRAKNVGNVLMKNMTDWILGTLIYFVVGAAIATIVGGltSPGPFSIS--AAFA 93 
                                       7****************************************************999664421133333333..3334 PP

                                       CGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--..... CS
                   Ammonium_transp  76 gvqdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvl..... 147
                                        v+d t + g  +lf ++fa+ta+tivsgavaer++f+ay+lf +l++ ++yp+v+ ++wg gg+l++ g+l     
  gi|313124922|ref|YP_004035186.1|  94 YVNDPTAWIG--WLFGAVFAMTAATIVSGAVAERMEFNAYVLFTVLMTAIIYPVVVGFTWG-GGLLSSGGFLgnvlg 167
                                       5555555555..*************************************************.*************** PP

                                       ....-SSSTTTTHHHHHHHHHHHHHHHS-STTTTG..TTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHH CS
                   Ammonium_transp 148 ...iDfAgstvVHlvggvagLaaalvlgkregrfe..gkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankra 219
                                           DfAg tvVH++ggvagL+aa ++g r+gr++  g+++ i+gh++++avlGt++L+fgW+gFN+G+++t+ ++a
  gi|313124922|ref|YP_004035186.1| 168 agyLDFAGATVVHMCGGVAGLVAAKMVGARKGRYDanGESQPIPGHSMLLAVLGTFILAFGWYGFNVGTQATILSVA 244
                                       ************************************9**************************************** PP

                                       HH............HHHHHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHH CS
                   Ammonium_transp 220 ra...........raavtTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAg 285
                                       +            r+a++T+l + ag+ +a+l+s   +gk++ l +anG+lAGlVA+T+a   v+ wg  ++G ++g
  gi|313124922|ref|YP_004035186.1| 245 DDgsltfmgaalgRVALVTTLGMGAGGAMAMLMSARYQGKPDPLWTANGLLAGLVAVTGAVPHVTWWGGALLGGLGG 321
                                       999**********9999999999999999999988888*************************************** PP

                                       HHHHHHHHHHHHHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHH CS
                   Ammonium_transp 286 vlsvlgvkklkeklkidDsldvvavHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayaf 362
                                       +l++ ++ +  ++lk+dD+++v+avHgv+G++G+ +  +fa             +s   +q+  q++g+l+i+a+++
  gi|313124922|ref|YP_004035186.1| 322 FLVLPAFRFTVDTLKVDDVCGVFAVHGVAGAVGTALIPVFAVGG----------FSA--SQFALQILGVLIIAAWTV 386
                                       *****************************************985..........333..579*************** PP

                                       HHHHHHHHHHHHHTTSB--HHHHHHSHHHHHHSSSSB CS
                   Ammonium_transp 363 vvtlilllllklllgLrvseeeeevglDvaehgetay 399
                                       + + i+l++l+l++gLrv e ee +glD+ ehg + y
  gi|313124922|ref|YP_004035186.1| 387 TASGIVLYVLDLTVGLRVGETEEAEGLDLGEHGVSVY 423
                                       ********************************98766 PP

>> PsbY  Photosystem II protein Y (PsbY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.1e-05      0.19       5      27 ..     216     238 ..     216     239 .. 0.94
   2 ?   -3.2   0.5      0.92   8.2e+03       8      16 ..     375     383 ..     373     385 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                              PsbY   5 vLiVLaPillAagWAlfNIgkaA 27 
                                       +L+VL+  +lA gW  fN+g+ A
  gi|313124922|ref|YP_004035186.1| 216 LLAVLGTFILAFGWYGFNVGTQA 238
                                       699*****************988 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.92
                                       HHHHHHHHH CS
                              PsbY   8 VLaPillAa 16 
                                       +L+++++Aa
  gi|313124922|ref|YP_004035186.1| 375 ILGVLIIAA 383
                                       577778775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2898.82
//
Query:       gi|313124923|ref|YP_004035187.1|  [L=118]
Description: nitrogen regulatory protein p-ii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-34  119.1   0.1    1.2e-34  118.9   0.1    1.0  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.1   6.9e-39   1.2e-34       1     102 []      10     111 ..      10     111 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 6.9e-39
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       ++aiirp+kl +vk aL+++g ++ltvt+v+GrG+q  +++  rg+ey+v+l +kvk+e +v d  +++vv+ai +a
  gi|313124923|ref|YP_004035187.1|  10 VMAIIRPDKLADVKRALAEVGAPSLTVTNVSGRGSQPAKKGQWRGEEYTVDLHQKVKIECIVADIPADDVVDAIREA 86 
                                       78*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+tg++GDGk+Fvlpve+++++rtg
  gi|313124923|ref|YP_004035187.1|  87 AHTGDPGDGKVFVLPVESAVQVRTG 111
                                       ************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 753.03
//
Query:       gi|313124924|ref|YP_004035188.1|  [L=237]
Description: caax amino terminal protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-07   29.3   9.2    3.5e-06   27.3   9.2    2.1  1  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   9.2   1.9e-10   3.5e-06       9      91 ..     120     206 ..       6     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.9e-10
                                       HHHHHHHHHHHHHHHTTCHHHHHHHH.S-.HHHHHHHHHHHHHCSGGGHHH...HHHHHHHHHHHHHHHHHTT-HHH CS
                              CPBP   9 llalllapllEEllfRglllqllqergss.tlailissilFglaHlpngps...vllaalaGlvlgylylktgslla 81 
                                       l+++  a+++EE+ + g+ +++l++ ++s  +a +is ++F+l Hl  ++    vl +a   lv ++lyl  +sl a
  gi|313124924|ref|YP_004035188.1| 120 LFVAATAGVTEEIPYHGYAVERLAALTGSlPFAGIISFLAFTLGHLGETWDrqaVLRIAQPALVTTLLYLWFRSLPA 196
                                       669999********************55559*****************666656888888999************** PP

                                       HHHHHHHHHH CS
                              CPBP  82 aillHallnl 91 
                                        i++Hal+++
  gi|313124924|ref|YP_004035188.1| 197 LIAIHALNDA 206
                                       *******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1399.56
//
Query:       gi|313124925|ref|YP_004035189.1|  [L=445]
Description: glutamate-1-semialdehyde 2,1-aminomutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-66  222.4   0.0    1.6e-65  221.3   0.0    1.5  1  Aminotran_3    Aminotransferase class-III
     0.0096   15.1   0.0      0.016   14.4   0.0    1.4  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.3   0.0   1.8e-69   1.6e-65       6     337 ..      28     342 ..      23     445 .] 0.82

  Alignments for each domain:
  == domain 1  score: 221.3 bits;  conditional E-value: 1.8e-69
                                       B--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HH.HHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHH CS
                       Aminotran_3   6 ednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPk.vvkavkeqaaklshvsfgaltnepalklaekllk 81 
                                        ++ +++i++++G+ ++d+dg+rylD v ++ +++ Gh  P+ v +av++ a +    +     +e  +k ae + +
  gi|313124925|ref|YP_004035189.1|  28 TQPYPFFIERGDGAHVVDADGNRYLDYVLGYGPLLYGHDMPEpVRAAVQSHASEG--PM-YGAPTEVEVKHAEFVSR 101
                                       455669***********************************84556667766666..44.445667778999***** PP

                                       HCT-..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEE CS
                       Aminotran_3  82 lapkgldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevv 158
                                       ++p  ++++ ++nsG+eA+ +A++lar+      +t + ki+ ++g++HG    +l  +++      +++p++ +++
  gi|313124925|ref|YP_004035189.1| 102 HVPS-VEMIRFVNSGTEATVSAVRLARA------YTGRDKIVIMQGGYHGAQESTLVEGEP-----GDVHPSTRGIP 166
                                       ***9.***********************......9**********************9999.....66677777777 PP

                                       EE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TT CS
                       Aminotran_3 159 rlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvq 235
                                          ++ ++ +++n+       e+++++ +++ d++aAv++Epi g+ G+v++ +++l++lr+l+++hd+ll++DEv 
  gi|313124925|ref|YP_004035189.1| 167 ESFAEHTIPVPFND------FEAVRDVFETHGDDIAAVLTEPILGNKGIVMPVDGYLEHLRNLTEDHDALLVFDEVI 237
                                       77777777778888......88899999************************************************* PP

                                       TTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHH CS
                       Aminotran_3 236 tGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiie 309
                                       tGf   G   A  ++g++pD++t++K ++gG+p+ a+ ++ e+ ++++p++   +++Tf+G p+  a+  + l+ ++
  gi|313124925|ref|YP_004035189.1| 238 TGFRVGGLQCAQGKFGITPDVTTFGKIIGGGFPVGAIGGKSEIIEQFTPSGnvfQSGTFSGHPVTIAAGYEYLKYAA 314
                                       ***999988889999**********************************999************************* PP

                                       HTTHHHHHHHHHHHHHHHHHHHCTT-TT CS
                       Aminotran_3 310 eekllenaqelgaalkegLeelqkkyev 337
                                       e+++ +++++lg++l+ g +++ +++  
  gi|313124925|ref|YP_004035189.1| 315 ENDVYDHVNRLGEKLRRGITDIVEDQAP 342
                                       *********************9987633 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.8e-06     0.016     129     281 ..     178     325 ..     167     440 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-06
                                       EE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHH CS
                     Aminotran_1_2 129 hldlealeealkeapegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsldavatr 204
                                        +d+ea+ +  ++ + +++    +l+e +  + G v++ +  le l +l++ + +ll++De+  gf  g l+ ++  
  gi|313124925|ref|YP_004035189.1| 178 FNDFEAVRDVFET-HGDDI--AAVLTEPILGNKGIVMPVDGyLEHLRNLTEDHDALLVFDEVITGFRVGGLQCAQGK 251
                                       5788888887777.44444..8999999999999999987536778888********************98765556 PP

                                       GGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH..HHHHHH CS
                     Aminotran_1_2 205 anveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqs..eleemr 278
                                       +++ ++     v++++K  G  G+ vG+i g++++++q +   + f s + ++ +++ aa    l+++   ++ + +
  gi|313124925|ref|YP_004035189.1| 252 FGITPD-----VTTFGKIIG-GGFPVGAIGGKSEIIEQFTPSGNVFQSgTFSGHPVTIAAGYEYLKYAAenDVYDHV 322
                                       666665.....66******9.5999*************999999988887788888888877777776655555555 PP

                                       HHH CS
                     Aminotran_1_2 279 qrl 281
                                        rl
  gi|313124925|ref|YP_004035189.1| 323 NRL 325
                                       555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2543.78
//
Query:       gi|313124926|ref|YP_004035190.1|  [L=183]
Description: hypothetical protein Hbor_01400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1136.27
//
Query:       gi|313124927|ref|YP_004035191.1|  [L=151]
Description: hypothetical protein Hbor_01410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.01   14.9   5.7      0.012   14.6   5.7    1.0  1  PTS_EIIC_2       Phosphotransferase system, EIIC
       0.27   11.7  10.7       0.39   11.2  10.7    1.3  1  MerC             MerC mercury resistance protein
        2.3    7.2  18.6    1.1e+02    1.7  18.6    2.0  1  ABC2_membrane_3  ABC-2 family transporter protein
          6    7.3  12.8          5    7.5   1.4    2.2  2  DUF4149          Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> PTS_EIIC_2  Phosphotransferase system, EIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   5.7   2.7e-06     0.012      30     139 ..      24     132 ..       9     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                        PTS_EIIC_2  30 italllqvgevaqsllgvaiGvlvalalkanplvlfslgaagvigsgavklkeaglllagsGdpinallaailavlv 106
                                        + l l +g++++ l++++ +v va  + + +lv+ + ++++ + ++a + + +++ +  +G ++++l+ a+ a l+
  gi|313124927|ref|YP_004035191.1|  24 LVGLWLAFGTMFTPLSAIVNAVFVAEPFSFGQLVSQIFVLVALVVTNARYPEVSAFWIWATG-LVSMLIFAASAGLA 99 
                                       3477899****************************************999999999999999.************** PP

                        PTS_EIIC_2 107 gklvskkktkldilvvplvtilvgglvglllap 139
                                       g l  +  ++l +++  l+    + ++++ ++ 
  gi|313124927|ref|YP_004035191.1| 100 GVLEPNTSGSLAVIFRLLLFWAGSIMLAVAILN 132
                                       *999999****9999998888888888877765 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  10.7   8.7e-05      0.39      20     115 ..      34     132 ..      20     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.7e-05
                              MerC  20 vllallpllglsflasel.lhqvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflgteaeetl...l 92 
                                       +++ l+++++++f+a++  + q++  ++v+++l+ +   y +   +++++ g++++li+++++ l  ++ e      
  gi|313124927|ref|YP_004035191.1|  34 MFTPLSAIVNAVFVAEPFsFGQLVSQIFVLVALVVTNARYPEVSAFWIWATGLVSMLIFAASAGLA-GVLEPNtsgS 109
                                       56677778888887766669*****************************************99999.5555554453 PP

                              MerC  93 fgslwq.vltvlGaalLaiahvlN 115
                                         ++++  l+++G+++La+  +lN
  gi|313124927|ref|YP_004035191.1| 110 LAVIFRlLLFWAGSIMLAV-AILN 132
                                       3444541467888888888.5555 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7  18.6     0.024   1.1e+02     236     323 ..      19     135 ..       9     143 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.024
                   ABC2_membrane_3 236 gnlglllllfllfglayialgyllsslfkns..etaqilifivil..........................llsgff 284
                                       ++l++l+ l+l fg ++++l++ + ++f  +  + +q++  i+ l                          l+++++
  gi|313124927|ref|YP_004035191.1|  19 SDLFYLVGLWLAFGTMFTPLSAIVNAVFVAEpfSFGQLVSQIFVLvalvvtnarypevsafwiwatglvsmLIFAAS 95 
                                       45666666666666666666666666655554533333333333333344444444444444444444433777777 PP

                   ABC2_membrane_3 285 gglfp..ledlpsalkwifsiiPffapglgllrlitgdplw 323
                                       +gl     ++ +++l++if+++ f+a + +l   i ++ +w
  gi|313124927|ref|YP_004035191.1|  96 AGLAGvlEPNTSGSLAVIFRLLLFWAGSIMLAVAILNY-WW 135
                                       77743334566699***********9999999999888.66 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   4.1    0.0064        29       2      44 ..      24      67 ..      21      71 .. 0.78
   2 ?    7.5   1.4    0.0011         5       3      57 ..      80     134 ..      78     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0064
                           DUF4149  2 slglllGsqlwvtfvvapv.lfrsLprhqfgelqsklFplyfgl 44
                                      ++gl+l   +++t  +a+v + ++ +++ fg+l+s++F l++ +
  gi|313124927|ref|YP_004035191.1| 24 LVGLWLAFGTMFTPLSAIVnAVFVAEPFSFGQLVSQIFVLVALV 67
                                      57888888888888888884445559999*********998766 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                           DUF4149   3 lglllGsqlwvtfvvapvlfrsLprhqfgelqsklFplyfglglalsvlllltev 57 
                                       + +++G + ++ f ++ +l  +L+++++g+l+     l+f+ g++++++++l + 
  gi|313124927|ref|YP_004035191.1|  80 WIWATGLVSMLIFAASAGLAGVLEPNTSGSLAVIFRLLLFWAGSIMLAVAILNYW 134
                                       7888999999999999999999*********99999999*****99999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 906.91
//
Query:       gi|313124928|ref|YP_004035192.1|  [L=398]
Description: hypothetical protein Hbor_01420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-26   91.9  15.3    6.5e-17   61.9   2.4    3.1  3  PQQ_2     PQQ-like domain
    1.2e-17   63.8  29.0      9e-05   22.8   0.2    7.9  7  PQQ_3     PQQ-like domain
    4.6e-14   51.6   8.5     0.0021   17.9   0.1    7.1  8  PQQ       PQQ enzyme repeat


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   1.3e-07   0.00077      58     113 ..      69     127 ..      66     144 .. 0.73
   2 !   34.3   0.9     3e-12   1.8e-08       9     179 ..     151     300 ..     143     301 .. 0.72
   3 !   61.9   2.4   1.1e-20   6.5e-17       5     181 ..     225     396 ..     223     398 .] 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-07
                             PQQ_2  58 vlWettl..egpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepae..lr 113
                                       + Wet++   +  + + +va+g v+v+ +d++l+a++ ++G++ W++   ++ p +  ++
  gi|313124928|ref|YP_004035192.1|  69 LAWETSVpdVAYGHRSLTVADGAVYVA-ADNSLLAVERDTGDVRWRFPGKTQRPWRrrVS 127
                                       68999995333334449*******999.5*****************87777666663433 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 3e-12
                             PQQ_2   9 daatGaelWrvdlarplgggvsravlsggtlfva.tgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvas 84 
                                         ++G++ W+ d  +  ++ +      g+t++   t+g r+v  d +tG ++ +  l+ + v++  + +g + v  +
  gi|313124928|ref|YP_004035192.1| 151 GSNDGQIGWSHDSSP-GDSLF--CR-VGNTVYWQgTDGTRVV--DIETGLERERSPLSTK-VEPFAFRNGLL-VGRG 219
                                       5689*******9844.45555..44.4666666537888888..667*****99999988.67745555555.6666 PP

                             PQQ_2  85 dg..qlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtsel 159
                                       d    l+a++a++G+++Ws+ +  + p +     +p + g  +v+ + sg l+a++++dG+v W+  ++  +     
  gi|313124928|ref|YP_004035192.1| 220 DSpdKLVAVNAQTGRLQWSVTLGVAHPSH----LTPCI-GTDAVFYG-SGPLYAVSLADGDVSWKGDIGTYQ----- 285
                                       7778***************7777743333....44444.45555555.8*****************996523..... PP

                             PQQ_2 160 srvgdisgrpvvaegtVyas 179
                                             s  pv ++++Vya+
  gi|313124928|ref|YP_004035192.1| 286 -----ASIHPVTDGERVYAV 300
                                       .....356788887788876 PP

  == domain 3  score: 61.9 bits;  conditional E-value: 1.1e-20
                             PQQ_2   5 vsaldaatGaelWrvdl.arplgggvsravlsggtlfvatgggrlvaldaatGkvlWettl.egpvvgaplvaegrv 79 
                                       ++a++a tG++ W+v+l     ++ +  +  + + +f   g+g l+a++ a+G v W+ +  + ++   p  +++rv
  gi|313124928|ref|YP_004035192.1| 225 LVAVNAQTGRLQWSVTLgVAHPSHLT--PCIGTDAVFY--GSGPLYAVSLADGDVSWKGDIgTYQASIHPVTDGERV 297
                                       57*************99433466666..9999999999..8********************87777777******** PP

                             PQQ_2  80 vvvasdg.....qlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerela 151
                                       ++va+d+       +ald+e+G+r+W+  ++        +  +pav+g+t+++++ + + v+ld+++G+vl     a
  gi|313124928|ref|YP_004035192.1| 298 YAVAEDEeaettFAVALDTETGDRVWR-RETPLD-----PLCTPAVVGETLYAAT-PAGFVVLDATNGEVLARFDAA 367
                                       ****999776644556***********.555533.....5559************.9999**********9999999 PP

                             PQQ_2 152 aprgtselsrvgdisgrpvvaegtVyassg 181
                                       ++rg+++   v+d +  + ++ +t+ya++g
  gi|313124928|ref|YP_004035192.1| 368 SGRGRARSPAVVDGTVYVGLD-ETLYAVEG 396
                                       999777543333333222222.46666665 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.6   8.4e-08    0.0005       3      40 .]      69     107 ..      68     107 .. 0.91
   2 ?    3.4   0.2      0.02   1.2e+02       1      24 [.     108     140 ..     108     141 .. 0.52
   3 ?    0.3   0.0      0.19   1.1e+03      18      40 .]     209     232 ..     176     232 .. 0.72
   4 !    5.3   0.2     0.005        30       1      31 [.     233     273 ..     233     276 .. 0.74
   5 !   10.1   0.2   0.00015      0.88       1      40 []     273     318 ..     273     318 .. 0.83
   6 !   22.8   0.2   1.5e-08     9e-05       1      39 [.     319     356 ..     319     357 .. 0.88
   7 !   18.0   0.5   4.9e-07    0.0029      13      37 ..     371     395 ..     358     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.4e-08
                             PQQ_3   3 vlWsvqlpg..pvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       + W++++p+  ++++s++v++g vyv+++ ++l A++ +t
  gi|313124928|ref|YP_004035192.1|  69 LAWETSVPDvaYGHRSLTVADGAVYVAAD-NSLLAVERDT 107
                                       57******998999************995.*****99887 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.02
                             PQQ_3   1 GevlWsv..........qlpgpvnssp...avdgglv 24 
                                       G+v+W++          ++       +   a++gg++
  gi|313124928|ref|YP_004035192.1| 108 GDVRWRFpgktqrpwrrRVSFS----AspvAFSGGVL 140
                                       7888888554433222133322....24458888886 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.19
                             PQQ_3  18 avdgglvyvgtg.dGtlyAlDaet 40 
                                       a+ +gl++  ++   +l+A++a+t
  gi|313124928|ref|YP_004035192.1| 209 AFRNGLLVGRGDsPDKLVAVNAQT 232
                                       666677766666788999999987 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.005
                             PQQ_3   1 GevlWsvqlpg..pvnsspavdgglvyvgtg........dG 31 
                                       G+++Wsv+l+   p + +p ++ + v+ g+g        dG
  gi|313124928|ref|YP_004035192.1| 233 GRLQWSVTLGVahPSHLTPCIGTDAVFYGSGplyavslaDG 273
                                       899****9986456666679999999999985555555665 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00015
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtg.....dGtlyAlDaet 40 
                                       G+v W+ +++  ++   p++dg +vy++++         +AlD+et
  gi|313124928|ref|YP_004035192.1| 273 GDVSWKGDIGTyQASIHPVTDGERVYAVAEdeeaeTTFAVALDTET 318
                                       778899999865555567************9999999999998887 PP

  == domain 6  score: 22.8 bits;  conditional E-value: 1.5e-08
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       G+++W++++p +  ++pav+g ++y++t+  +++ lDa+
  gi|313124928|ref|YP_004035192.1| 319 GDRVWRRETPLDPLCTPAVVGETLYAATP-AGFVVLDAT 356
                                       899*******7555***************.888888886 PP

  == domain 7  score: 18.0 bits;  conditional E-value: 4.9e-07
                             PQQ_3  13 vn.sspavdgglvyvgtgdGtlyAlD 37 
                                       +  +spav++g+vyvg  d tlyA++
  gi|313124928|ref|YP_004035192.1| 371 GRaRSPAVVDGTVYVGL-DETLYAVE 395
                                       33389**********99.5*****85 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   3.5e-07    0.0021       1      27 [.      90     115 ..      90     123 .. 0.89
   2 ?   -3.4   0.0       1.9   1.2e+04      17      26 ..     152     161 ..     148     167 .. 0.63
   3 ?   -1.0   0.0      0.35   2.1e+03      13      29 ..     186     202 ..     177     206 .. 0.78
   4 !    5.6   0.0    0.0028        17       8      29 ..     222     242 ..     215     247 .. 0.83
   5 !    5.2   0.1    0.0036        21       3      29 ..     258     282 ..     256     288 .. 0.81
   6 !   14.7   0.0   3.6e-06     0.022      13      37 ..     312     336 ..     309     337 .. 0.91
   7 !    5.9   0.0    0.0023        13       4      28 ..     343     366 ..     341     370 .. 0.75
   8 ?   -1.2   0.0      0.39   2.3e+03       1      15 [.     381     394 ..     381     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.5e-07
                                       TEEEEEETTSEEEEEETTTCCEEEEEE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfk 27 
                                       g vy++ ad+ l+A+ +dTG+v+Wrf+
  gi|313124928|ref|YP_004035192.1|  90 GAVYVA-ADNSLLAVERDTGDVRWRFP 115
                                       568888.899***************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.9
                                       TTTCCEEEEE CS
                               PQQ  17 adTGkvlWrf 26 
                                        ++G++ W++
  gi|313124928|ref|YP_004035192.1| 152 SNDGQIGWSH 161
                                       4666666665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.35
                                       EEEETTTCCEEEEEESS CS
                               PQQ  13 yAlDadTGkvlWrfktg 29 
                                       + +D++TG ++ r +++
  gi|313124928|ref|YP_004035192.1| 186 RVVDIETGLERERSPLS 202
                                       679****9777776665 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0028
                                       TTSEEEEEETTTCCEEEEEESS CS
                               PQQ   8 adGylyAlDadTGkvlWrfktg 29 
                                       +d +l+A++a TG++ W++ +g
  gi|313124928|ref|YP_004035192.1| 222 PD-KLVAVNAQTGRLQWSVTLG 242
                                       45.899***********98775 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.0036
                                       EEEEETTSEEEEEETTTCCEEEEEESS CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWrfktg 29 
                                       v++g   G lyA+ +++G+v W+ ++g
  gi|313124928|ref|YP_004035192.1| 258 VFYG--SGPLYAVSLADGDVSWKGDIG 282
                                       6666..6779************98776 PP

  == domain 6  score: 14.7 bits;  conditional E-value: 3.6e-06
                                       EEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ  13 yAlDadTGkvlWrfktggpvlslpi 37 
                                       +AlD +TG+ +Wr +t+ ++l +p+
  gi|313124928|ref|YP_004035192.1| 312 VALDTETGDRVWRRETPLDPLCTPA 336
                                       69***************99998886 PP

  == domain 7  score: 5.9 bits;  conditional E-value: 0.0023
                                       EEEETTSEEEEEETTTCCEEEEEES CS
                               PQQ   4 ylgsadGylyAlDadTGkvlWrfkt 28 
                                       y++++   ++ lDa++G+vl rf++
  gi|313124928|ref|YP_004035192.1| 343 YAATPA-GFVVLDATNGEVLARFDA 366
                                       555555.4678********988876 PP

  == domain 8  score: -1.2 bits;  conditional E-value: 0.39
                                       TEEEEEETTSEEEEE CS
                               PQQ   1 gvvylgsadGylyAl 15 
                                       g+vy+g  d +lyA+
  gi|313124928|ref|YP_004035192.1| 381 GTVYVG-LDETLYAV 394
                                       789999.88899996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2370.55
//
Query:       gi|313124929|ref|YP_004035193.1|  [L=375]
Description: hydroxymethylbilane synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-66  223.7   0.2    6.3e-51  172.8   0.2    2.1  2  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    1.7e-11   44.3   0.1    4.1e-11   43.1   0.1    1.6  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
  ------ inclusion threshold ------
       0.24   11.9   4.1        3.3    8.2   0.0    3.1  4  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8   0.2   1.1e-54   6.3e-51       1     150 [.       6     158 ..       6     168 .. 0.94
   2 !   48.9   0.0   9.2e-17   5.5e-13     150     202 ..     217     270 ..     207     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 1.1e-54
                    Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLkeeee..veivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlK 75 
                                       +r++tR+S+LAl q+  v+++L++ ++  ve+v+++t+GD+i+d+ L+++g++g+F+++l+e++l++e+d aVhS+K
  gi|313124929|ref|YP_004035193.1|   6 LRLATRGSDLALRQTASVRDTLAD-RRfdVELVEVETRGDQIRDELLHRLGKTGAFVRALDERVLDEEVDAAVHSMK 81 
                                       699*******************65.33348*********************************************** PP

                    Porphobil_deam  76 DlptelpeglelaavlkredprDvlvvks..sleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkld 150
                                       D+pte p++l++a v++r+ ++Dvl++ +   +e+lp+g+vvgTsSlRRkaq+ ++rpdlev++lRGnvdtR++kl 
  gi|313124929|ref|YP_004035193.1|  82 DMPTEHPRDLVVAGVPERAPANDVLLTPDgtAFENLPAGSVVGTSSLRRKAQILSARPDLEVEPLRGNVDTRVEKLL 158
                                       **************************833558*******************************************95 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 9.2e-17
                    Porphobil_deam 150 degeydaiiLAaAGLkRlgleeri.sevlspeellpavgQGalavevrkedeel 202
                                        e+eydai+LA+AGLkR gl +r+  + l+p+e++pa+gQGa+av++r+++e+l
  gi|313124929|ref|YP_004035193.1| 217 VETEYDAIVLAEAGLKRSGLLHRVeYDRLPPTEFVPAPGQGAIAVTARRDHENL 270
                                       3469********************5446*********************98875 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.1   6.8e-15   4.1e-11       4      53 ..     286     332 ..     284     355 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 6.8e-15
                                       HHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEE CS
                   Porphobil_deamC   4 vlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveea 53 
                                        ++ER++l+eL+GGC +PiGv+a+++++  +  ++ vls dg++  +  a
  gi|313124929|ref|YP_004035193.1| 286 TTVERTVLAELGGGCIAPIGVHAKLQGEH-VHVTARVLSTDGEE--EVSA 332
                                       689*********************88655.************77..3333 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00056       3.3      10      76 ..      20      87 ..      17     100 .. 0.82
   2 ?   -2.3   0.0       1.1   6.4e+03      63      81 ..     151     171 ..     134     185 .. 0.60
   3 ?   -2.4   0.1       1.1   6.6e+03      21      43 ..     193     215 ..     188     218 .. 0.82
   4 ?    3.7   0.1     0.014        84       9      35 ..     344     370 ..     342     375 .] 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00056
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S...--------TTHHHHHHHHHHHHHHHH CS
                       GlutR_dimer 10 veefeawlkslevvptIkalrekaeeireeeleralkkla.ldgedreelekltrslvnkllheptar 76
                                      +++  + l  ++++  ++++ ++ ++ir+e l+r+ k  a ++  d+++l++ +++ v+ +   pt++
  gi|313124929|ref|YP_004035193.1| 20 TASVRDTLADRRFDVELVEVETRGDQIRDELLHRLGKTGAfVRALDERVLDEEVDAAVHSMKDMPTEH 87
                                      56677788888899999999****************99999777777778888888888877777766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHSS..- CS
                       GlutR_dimer  63 rslvnkllheptarLkea..e 81 
                                       ++ v kll ++ +r +ea  +
  gi|313124929|ref|YP_004035193.1| 151 DTRVEKLLAPTLQREHEArvD 171
                                       444566666666655555432 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                       GlutR_dimer  21 evvptIkalrekaeeireeeler 43 
                                       +++ tI +  + ++ei ++ ler
  gi|313124929|ref|YP_004035193.1| 193 DFDRTIEEWFDDLSEIERRSLER 215
                                       67788999999999999998887 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       GlutR_dimer   9 eveefeawlkslevvptIkalrekaee 35 
                                       +++ef + l s++++++I++ r+ a +
  gi|313124929|ref|YP_004035193.1| 344 AAAEFAESLASQGAADLISEARDDARD 370
                                       5789******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2339.58
//
Query:       gi|313124930|ref|YP_004035194.1|  [L=267]
Description: uroporphyrinogen-III C-methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-55  188.1   1.3    2.3e-55  187.8   1.3    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
       0.13   12.7   0.1       0.38   11.1   0.1    1.9  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.8   1.3   2.6e-59   2.3e-55       1     212 [.       7     218 ..       7     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 2.6e-59
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       ++ylVG GpGdp+l+Tv+A+r+l+tadvvl d+   +eil+++++e   ++++ gk++  + + +e  +++l+e++r
  gi|313124930|ref|YP_004035194.1|   7 TVYLVGSGPGDPDLMTVKAARLLETADVVLHDKLPGPEILERIPEE---KREDVGKRAGGEWTPQEYTNRRLVELAR 80 
                                       59*******************************7799999766544...45555555555555588899999***** PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglake 149
                                       +gk+Vv+l++GDP+v+g+g+e++e+l+a  a+i++ev+PG++s+ a +  +gip+t+++ ++sv+     ++++++e
  gi|313124930|ref|YP_004035194.1|  81 EGKTVVRLKGGDPFVFGRGGEEMEHLAA--ADIPFEVVPGITSAIAGPGTAGIPVTHRDHASSVSfvtghEDPTKEE 155
                                       ****************************..****************************************888899* PP

                      TP_methylase 150 eereleallangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       ++ +++al+a+g+tlv+l+++ kl++  ++L+ea ++++t pva+vera++++ rv +gtl ++
  gi|313124930|ref|YP_004035194.1| 156 SAVDWDALAATGGTLVVLMGVGKLPDYTAALREAgMDPET-PVALVERATWPEMRVATGTLDTI 218
                                       **********************************888866.********************875 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.3e-05      0.38      27      75 ..      64     128 ..      37     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.................C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................x RF
                       Radical_SAM  27 rslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.................v 75 
                                       +  ++e+  + + el a+ g+ +v l gg+p++  +  e++e+la+ +                  
  gi|313124930|ref|YP_004035194.1|  64 EWTPQEYTNRRLVEL-AREGKTVVRLKGGDPFVFGRGGEEMEHLAAADipfevvpgitsaiagpgT 128
                                       444555555555566.56669*************************98888884444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1696.08
//
Query:       gi|313124931|ref|YP_004035195.1|  [L=247]
Description: uroporphyrinogen-III synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-41  141.6   0.0    2.9e-41  141.4   0.0    1.0  1  HEM4           Uroporphyrinogen-III synthase HemD
  ------ inclusion threshold ------
      0.015   15.1   0.0       0.03   14.2   0.0    1.5  1  DAHP_snth_FXD  DAHP synthase ferredoxin-like domain


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   3.2e-45   2.9e-41       3     230 ..      20     233 ..      18     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 3.2e-45
                                       HHHHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEES CS
                              HEM4   3 laealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaav 79 
                                        +e+l ++Ga+p+  P++ +ep         a+ d    + d++i+tS+++ve l+e          +++  ++a++
  gi|313124931|ref|YP_004035195.1|  20 AVELLDSLGATPIPDPMLAVEP-------TGAMPD----SGDYVILTSKTGVELLAEDGW-------EPNGSTLACI 78 
                                       57899*****************.......666653....67*************666555.......99999***** PP

                                       SHHHHHHHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HH CS
                              HEM4  80 GpaTaraLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYetvpaee 156
                                       GpaTa+a+++ g  vd+vp+ e+t+ gL+e l+ ++a+ +v + r+++++d l +gL+e+ga+++e ++Y+ v++e+
  gi|313124931|ref|YP_004035195.1|  79 GPATADAARDSGWSVDIVPE-EYTSSGLVERLRDDVANATVEVARSDHGSDVLTDGLREAGADLHETVLYRLVRPEG 154
                                       *******************9.***************************************************77766 PP

                                       HHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HH......HHHCTSEEEEESHHHHHHHHHTT---SEEETS--H CS
                              HEM4 157 epeelkealkagevdavvftSpstvrnllellkdeg......delkevkvaaiGptTaealkklglkvdvvaeepta 227
                                       + ++ + ++  +ev++v+f S+ tv+n+l ++ ++g      ++l+++ v +iGp T+e+++++g++vdvv+e+++ 
  gi|313124931|ref|YP_004035195.1| 155 AGQS-TVMVAGDEVEGVCFSSSLTVENFLDAAAERGvreeviEGLNSLVVGVIGPPTRETAESYGINVDVVPENADF 230
                                       5555.6677789**********************99***************************************99 PP

                                       HHH CS
                              HEM4 228 egl 230
                                       e l
  gi|313124931|ref|YP_004035195.1| 231 EEL 233
                                       987 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.3e-06      0.03      14      48 ..     178     212 ..     173     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-06
                     DAHP_snth_FXD  14 ieevierieelGlkvhvskGeertViGviGdtskl 48 
                                       +e+ ++   e G++ +v++G +  V+GviG  ++ 
  gi|313124931|ref|YP_004035195.1| 178 VENFLDAAAERGVREEVIEGLNSLVVGVIGPPTRE 212
                                       778889999*********************75543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1446.23
//
Query:       gi|313124932|ref|YP_004035196.1|  [L=478]
Description: single-stranded DNA-specific exonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-17   64.8   1.5    2.7e-17   63.5   1.5    1.8  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
      0.074   13.3   0.1       0.14   12.4   0.1    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   1.5     3e-21   2.7e-17       4     137 ..     338     472 ..     336     473 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 3e-21
                                       HCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHG...BT.TCEEEEE CS
                             DHHA1   4 lneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklkskl...kk.pvivfva 76 
                                       l++ r  l+++  +l+e l+++k+e++  +     +   ++ +  + ++ +++gi+a++        ++ p+ +f+ 
  gi|313124932|ref|YP_004035196.1| 338 LEQARTLLRNHRRNLSEGLQWVKNEGVTVE-----ENVQWFDAG-TRIRETIVGIIAGMAVGASgirGDiPILAFAE 408
                                       666777777888889999999999999876.....777777777.999**************777678888888888 PP

                                       EEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHH CS
                             DHHA1  77 keegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeea 137
                                       k  + +vkvsar +      g+d++ +++ea++++gg GGGH  AaGa+ipa+  ee++++++++
  gi|313124932|ref|YP_004035196.1| 409 KSAE-EVKVSARGSHVlvrkGLDLSVVMREASRAVGGDGGGHSVAAGATIPAGTREEFVAEADRI 472
                                       8888.*********88********************************************99976 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.6e-05      0.14       7      57 ..      36     123 ..      32     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                                       ECSSSHHHHHH.HHHHHH................................CECS--TCGGCGCCHHCCCSE.EEEEE CS
                                       xxxxxxxxxxx.xxxxxx................................xxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                               DHH   7 hknpDtDsigS.aialan................................llvDhneksqavegeakeeae.dviii 49 
                                         + D+D+++S aia ++                                l  D+++ + + +++ ++ ++ + +i 
  gi|313124932|ref|YP_004035196.1|  36 ASHIDADGLTSaAIASSAleragipfetvfskqldkeevasiaateyetvLFTDFGSGQLDIIADHEAAGDfTPVIA 112
                                       6799*******888888877777777777777777777777777777776699999999999887666655255788 PP

                                       E-S---S...S CS
                                       xxxxxxx...x RF
                               DHH  50 DHHrlge...e 57 
                                       DHH++++   e
  gi|313124932|ref|YP_004035196.1| 113 DHHQPADadtE 123
                                       ****9965541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.88
# Mc/sec: 1643.17
//
Query:       gi|313124933|ref|YP_004035197.1|  [L=569]
Description: hypothetical protein Hbor_01470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0012   18.2   6.4     0.0012   18.2   6.4    2.4  2  ABC2_membrane_2  ABC-2 family transporter protein
     0.0061   16.1   6.1      0.013   15.1   1.2    2.6  2  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.011   15.4   0.5      0.034   13.8   0.1    2.0  2  DUF1345          Protein of unknown function (DUF1345)


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   6.4     2e-07    0.0012       3     282 ..      12     288 ..      10     296 .. 0.66
   2 ?   -4.0   2.6       1.2   7.1e+03     129     159 ..     459     503 ..     451     523 .. 0.39

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-07
                   ABC2_membrane_2   3 iakkEfrdlvrsrrfllltvllplidvala...ylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkv 76 
                                       +a+ +f ++ rsr + ++ ++++ i ++l     +k +++  + +  +++   ++ +y                   
  gi|313124933|ref|YP_004035197.1|  12 VARADFLQRARSRQLAVVLAVIASI-GYLVntgGVKLAYQVRSDGTLQAFHGEPTAAYIGL---------------- 71 
                                       8999*********999988888888.44441112222333333333333344444333322................ PP

                   ABC2_membrane_2  77 vstimavlipvi..aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiila 151
                                        ++ ++++i+++  +  +  +a+ ++++ g   l   +P+s +++l+gK++++la g +++++l+++ ++  a+  +
  gi|313124933|ref|YP_004035197.1|  72 -KAGITGAIVLLfgGFYLMKNALQRDRNHGVAQLVARTPISDRTYLFGKWLSNLAFGGVLILTLGVSSIANHAVHGV 147
                                       .3344444444444666668999*******9999999*******************888888888884443333333 PP

                   ABC2_membrane_2 152 lgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqe 228
                                          +++l +ll+ ++a+ + ++++  ++  +l+S ++    + +   +  f++  ++ +  l +v+++l g  +   
  gi|313124933|ref|YP_004035197.1| 148 --GPTTLTALLIPLLAFAFPVAAL--VSGLALFSETVD-PLNGMFGNICYFLFMPVVLGSTLTPVGDMLPGQLP--L 217
                                       ..3455566666666666555533..566666666666.55555555555555555555556668888887777..8 PP

                   ABC2_membrane_2 229 indflsllsptsayntllneilagsdlna.................lgstatnllilllllavllvlgyvl 282
                                       +   l+l+ +++ y++  +++la +++ a                  g ++   ++   l +vl++l++vl
  gi|313124933|ref|YP_004035197.1| 218 WVKSLDLMGYIAIYTLTASSLLAQQPVYAgglpsvgtleatrafywNGGAWPLWVYPQRLGVVLCGLCIVL 288
                                       9999999*****************99998888888888888777775666666666666666666666554 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.2
                   ABC2_membrane_2 129 aiglaiavallatvll..............alaiilalgivlale 159
                                       ++g+++a+ ++ +v +                ++ la + ++a++
  gi|313124933|ref|YP_004035197.1| 459 LSGIIVAIGVGSGVFAvyiatghtgallgfVSGVLLAPSLATAAG 503
                                       444444444444433322233333333333223333333333333 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.2   2.2e-06     0.013      38     136 ..      75     170 ..      65     239 .. 0.73
   2 ?    2.8   0.3     0.013        76     107     155 ..     445     492 ..     440     525 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-06
                   ABC2_membrane_5  38 lifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgnvtis 114
                                       ++++i+ l+  ++l+ ++l+ D+++++ +++  +P++ +++   K l+ l ++ + il + + +i ++ ++g     
  gi|313124933|ref|YP_004035197.1|  75 ITGAIVLLFGGFYLMKNALQRDRNHGVAQLVARTPISDRTYLFGKWLSNLAFGGVLILTLGVSSIANHAVHGVG--- 148
                                       45666666777887889***********************************9999999888887777777662... PP

                   ABC2_membrane_5 115 evllsiliglvialiflaivlP 136
                                       ++ l++l++ ++a++f +  l+
  gi|313124933|ref|YP_004035197.1| 149 PTTLTALLIPLLAFAFPVAALV 170
                                       3445555555555555444444 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.013
                   ABC2_membrane_5 107 ikgnvtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiif 155
                                       +++++ +++++  +l g+++a+ +++ v+ +y+ +g  +g ++ +++ +
  gi|313124933|ref|YP_004035197.1| 445 LSSRYPLKQLIAEWLSGIIVAIGVGSGVFAVYIATG-HTGALLGFVSGV 492
                                       566678899999999999999999999999999999.455544444433 PP

>> DUF1345  Protein of unknown function (DUF1345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.3   7.9e+03      48      58 ..      26      36 ..      12      56 .. 0.60
   2 ?   13.8   0.1   5.7e-06     0.034      44     121 ..     458     536 ..     438     542 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.3
                           DUF1345 48 llvllaalasl 58
                                      l v+la++as+
  gi|313124933|ref|YP_004035197.1| 26 LAVVLAVIASI 36
                                      33333333333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.7e-06
                           DUF1345  44 vlilllvllaalaslvaivlllasakaekpaekllhlalavatvvlsWllvhtvfalhYahlyy.ekkeeeggldFp 119
                                       +l  ++v + +   ++a+ +++ +++a  +  + + la ++at + sW    t+f l Y  l+y    + ++ +dF 
  gi|313124933|ref|YP_004035197.1| 458 WLSGIIVAIGVGSGVFAVYIATGHTGALLGFVSGVLLAPSLATAAGSWSRSTTLFELSYLTLWYvGPLNGAQPVDFI 534
                                       666677888889999999999999999999999*******************************7666666777776 PP

                           DUF1345 120 gt 121
                                       g 
  gi|313124933|ref|YP_004035197.1| 535 GA 536
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 3490.90
//
Query:       gi|313124934|ref|YP_004035198.1|  [L=290]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-28   97.4   0.0    1.5e-27   96.8   0.0    1.3  1  ABC_tran     ABC transporter
      1e-08   35.4   0.5     0.0013   18.7   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      2e-05   24.3   0.1      4e-05   23.3   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00015   22.3   0.0    0.00027   21.5   0.0    1.3  1  AAA_23       AAA domain
     0.0044   16.5   0.1      0.078   12.4   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0071   16.1   0.0      0.095   12.4   0.0    2.0  2  AAA_15       AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.031   14.1   0.1    1.6  2  MukB         MukB N-terminal
      0.043   13.7   0.1      0.082   12.8   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
      0.043   13.5   0.5       0.19   11.4   0.5    1.9  1  AAA_30       AAA domain
       0.05   13.8   0.1       0.47   10.6   0.1    2.1  1  AAA_33       AAA domain
      0.076   12.6   0.0       0.12   12.0   0.0    1.2  1  AAA_27       AAA domain
       0.21   10.8   0.0       0.32   10.2   0.0    1.2  1  DUF2813      Protein of unknown function (DUF2813)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.0   9.9e-31   1.5e-27       2     136 ..      19     160 ..      18     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 9.9e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++vsl+l eg +++++G+nGaGKStL+ +l+  +kpt+G+  ++g d+ +     +r  +g+lpq+    p+lt+ e
  gi|313124934|ref|YP_004035198.1|  19 RDVSLELDEG-IHGLLGPNGAGKSTLMGILTTVMKPTAGTAYWNGSDIVD-APDAVRPVLGYLPQDFGTYPDLTLSE 93 
                                       6789999888.89*************************************.88999*******************99 PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     +++++i+++++ ++l + +d+++    +++SgG+ qrv +a+all++p+ll++DEpt
  gi|313124934|ref|YP_004035198.1|  94 FleylaalcgldseTASARITELIELVNLADARDRKL----KTFSGGMHQRVGIAQALLNDPELLVVDEPT 160
                                       9**********99999999******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     1e-05     0.016       2      19 ..      30      47 ..      29      67 .. 0.90
   2 !   18.7   0.0   8.4e-07    0.0013     237     297 ..     133     189 ..     107     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       +l GpNg+GKS+L+ +l
  gi|313124934|ref|YP_004035198.1| 30 HGLLGPNGAGKSTLMGIL 47
                                      689************999 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 8.4e-07
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +S G+ +  +++ all ++    ll++DEp  gL+P+   rl   l+++ + +  +il+TH
  gi|313124934|ref|YP_004035198.1| 133 FSGGMHQRVGIAQALLNDP---ELLVVDEPTVGLDPEERVRLRNALSNTGD-DRVIILSTH 189
                                       4666655459999999999...9***********************99988.9999***** PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   2.7e-08     4e-05      15      53 ..      21      59 ..      15      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.7e-08
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvr 53
                                       ++e+d +g++ l Gp+G+GKSTl+  +++++ p+  ++ 
  gi|313124934|ref|YP_004035198.1| 21 VSLELD-EGIHGLLGPNGAGKSTLMGILTTVMKPTAgTAY 59
                                      445666.55899**********************994444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.8e-07   0.00027      11      40 ..      19      48 ..      10      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.8e-07
                            AAA_23 11 rdqeidFskgltlItGpNGaGKTTildAik 40
                                      rd++++++ g+  + GpNGaGK+T++  ++
  gi|313124934|ref|YP_004035198.1| 19 RDVSLELDEGIHGLLGPNGAGKSTLMGILT 48
                                      8999*********************97776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   5.2e-05     0.078      17      42 ..      20      45 ..      15      57 .. 0.86
   2 ?    1.9   0.0     0.087   1.3e+02     160     198 ..     152     190 ..     111     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                                      EEEEETTSSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 17 tvilpfsksftaivGpNGSGKsnlld 42
                                       v+l++++++  ++GpNG+GKs l+ 
  gi|313124934|ref|YP_004035198.1| 20 DVSLELDEGIHGLLGPNGAGKSTLMG 45
                                      6789999***************9986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.087
                                       SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellkeksknaQfivislr 198
                                        l ++De    LD +++ ++ + l ++ ++  +i  ++ 
  gi|313124934|ref|YP_004035198.1| 152 ELLVVDEPTVGLDPEERVRLRNALSNTGDDRVIILSTHI 190
                                       47899*********************9988777777765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   6.4e-05     0.095      14      45 ..      18      49 ..      17      68 .. 0.90
   2 ?    1.5   0.0      0.13     2e+02     322     364 ..     149     189 ..     138     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.4e-05
                            AAA_15 14 lkdveidlseeltvliGkNnsGKSsilealdl 45
                                      ++dv+++l+e +  l G+N++GKS+++ +l  
  gi|313124934|ref|YP_004035198.1| 18 IRDVSLELDEGIHGLLGPNGAGKSTLMGILTT 49
                                      799***********************999865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++ +l+++EP + L p+    l ++l +  +d    +i++TH
  gi|313124934|ref|YP_004035198.1| 149 NDPELLVVDEPTVGLDPEERVRLRNALSNTGDDRV--IILSTH 189
                                       57899**********************99999995..****** PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.1e-05     0.031      21      53 ..      22      54 ..      15      63 .. 0.87
   2 ?   -3.7   0.0       5.5   8.3e+03     144     165 ..     111     131 ..     104     136 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                                      EE-HHHHHHHHHS--SHHHHHHHHHHHHHHS-- CS
                              MukB 21 tfdldelvttlsGgnGaGksttmaafvtaliPd 53
                                        +lde +  l G nGaGkst m  + t++ P 
  gi|313124934|ref|YP_004035198.1| 22 SLELDEGIHGLLGPNGAGKSTLMGILTTVMKPT 54
                                      5789*******************9999998875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.5
                                       -EE--HHHHHHHHHTSTT-EEE CS
                              MukB 144 arvrelnelkekleelegvrlk 165
                                       ar++el el + +++  + +lk
  gi|313124934|ref|YP_004035198.1| 111 ARITELIELVNLADA-RDRKLK 131
                                       455555555444443.233444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   5.5e-05     0.082      88     121 ..      16      49 ..       7      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-05
                                       TTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkdktsvlvGqSGvGKStLinallp 121
                                        g+++++ +l++ +  l+G+ G+GKStL+  l+ 
  gi|313124934|ref|YP_004035198.1|  16 WGIRDVSLELDEGIHGLLGPNGAGKSTLMGILTT 49 
                                       67889999999*****************988876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00013      0.19      20      47 ..      29      62 ..      22     187 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.g.....g 47
                                      ++ l Gp G+GK+t+++ l+ +++   g     g
  gi|313124934|ref|YP_004035198.1| 29 IHGLLGPNGAGKSTLMGILTTVMKPTaGtaywnG 62
                                      67789**************999987745555552 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00032      0.47       5     106 ..      33     188 ..      30     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                            AAA_33   5 vGlpGsGKstlaerl...lkklg..avllssdt...............................lrrrlfgtdqqsk 45 
                                        G++G+GKstl   l   +k+++  a+   sd+                               ++ +l+g d ++ 
  gi|313124934|ref|YP_004035198.1|  33 LGPNGAGKSTLMGILttvMKPTAgtAYWNGSDIvdapdavrpvlgylpqdfgtypdltlsefleYLAALCGLDSETA 109
                                       699*******9866544366666774444444455666999999999999999999999999985555555444433 PP

                            AAA_33  46 t..................dytrvldrlyqilnelarkalsagrnvildat..nlsrrerarflklarrlgvpvriv 102
                                       +                  ++++++  ++q++ ++a+  l     +++d +   l+++er r+++++++ g  +r++
  gi|313124934|ref|YP_004035198.1| 110 SaritelielvnladardrKLKTFSGGMHQRV-GIAQALLNDPELLVVDEPtvGLDPEERVRLRNALSNTG-DDRVI 184
                                       34455555555444444336666777799998.99999999999999999944456999999999999999.78887 PP

                            AAA_33 103 vvet 106
                                       +++t
  gi|313124934|ref|YP_004035198.1| 185 ILST 188
                                       7765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.8e-05      0.12      15      44 ..      19      45 ..       9      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.8e-05
                            AAA_27 15 tdrsldfsaeeadlhliyGpNEAGKstalr 44
                                       d sl+++   +++h ++GpN AGKst++ 
  gi|313124934|ref|YP_004035198.1| 19 RDVSLELD---EGIHGLLGPNGAGKSTLMG 45
                                      56677776...899*************986 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00022      0.32      13      52 ..      17      57 ..      15      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                           DUF2813 13 GinrLSlslee.ntvLiGENaWGKSSLldALslilnvekel 52
                                      Gi+  Sl+l+e    L+G N  GKS L+  L+ ++++++  
  gi|313124934|ref|YP_004035198.1| 17 GIRDVSLELDEgIHGLLGPNGAGKSTLMGILTTVMKPTAGT 57
                                      9********983568*******************9988654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1785.07
//
Query:       gi|313124935|ref|YP_004035199.1|  [L=111]
Description: hth domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-08   32.7   0.0    1.3e-07   31.4   0.0    1.6  1  HTH_11          HTH domain
      1e-07   31.9   0.0    1.8e-07   31.1   0.0    1.5  1  HTH_20          Helix-turn-helix domain
    6.8e-07   29.1   0.0    1.3e-06   28.1   0.0    1.4  1  MarR_2          MarR family
    1.7e-06   27.5   0.0    3.2e-06   26.6   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.3e-06   26.8   0.1    7.8e-06   25.6   0.0    1.6  2  HTH_IclR        IclR helix-turn-helix domain
    2.1e-05   24.5   0.0    3.3e-05   23.8   0.0    1.3  1  HTH_29          Winged helix-turn helix
    2.5e-05   23.9   0.0    4.7e-05   23.1   0.0    1.4  1  HTH_23          Homeodomain-like domain
    2.7e-05   24.0   0.0    5.4e-05   23.0   0.0    1.5  1  MarR            MarR family
    3.4e-05   23.6   0.1    5.5e-05   22.9   0.1    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    4.1e-05   22.9   0.0    8.1e-05   22.0   0.0    1.5  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
    4.4e-05   23.1   0.0    8.5e-05   22.2   0.0    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    6.5e-05   22.8   0.0     0.0001   22.2   0.0    1.3  1  HTH_36          Helix-turn-helix domain
    7.7e-05   22.6   0.0    0.00017   21.5   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00011   22.0   0.0    0.00026   20.7   0.0    1.7  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00015   21.6   0.0    0.00022   21.0   0.0    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00017   21.3   0.0    0.00041   20.0   0.0    1.7  1  HTH_38          Helix-turn-helix domain
    0.00022   21.3   0.0     0.0004   20.4   0.0    1.4  1  HTH_28          Helix-turn-helix domain
     0.0004   20.7   0.0    0.00063   20.0   0.0    1.2  1  Rrf2            Transcriptional regulator
    0.00047   20.1   0.0    0.00071   19.5   0.0    1.3  1  PadR            Transcriptional regulator PadR-like family
    0.00086   19.3   0.0     0.0016   18.5   0.0    1.4  1  HTH_7           Helix-turn-helix domain of resolvase
     0.0023   18.1   0.0     0.0031   17.7   0.0    1.3  1  FUR             Ferric uptake regulator family
     0.0024   17.6   0.0      0.005   16.6   0.0    1.5  1  TetR_N          Bacterial regulatory proteins, tetR family
     0.0024   17.8   0.1     0.0064   16.5   0.0    1.7  1  HTH_6           Helix-turn-helix domain, rpiR family
     0.0033   17.6   0.0     0.0046   17.1   0.0    1.3  1  HTH_17          Helix-turn-helix domain
     0.0034   16.9   0.0     0.0064   16.1   0.0    1.4  1  HTH_50          Helix-turn-helix domain
      0.006   17.1   0.1      0.012   16.1   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
     0.0061   16.2   0.1      0.011   15.4   0.1    1.4  1  Sigma70_r4_2    Sigma-70, region 4
     0.0078   16.3   0.1     0.0084   16.2   0.1    1.1  1  Replic_Relax    Replication-relaxation
     0.0082   15.9   0.0      0.015   15.0   0.0    1.4  1  HTH_psq         helix-turn-helix, Psq domain
     0.0083   15.8   0.0      0.014   15.0   0.0    1.3  1  GntR            Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.012   15.8   0.0       0.02   15.1   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.017   14.6   0.0      0.034   13.7   0.0    1.4  1  Sigma70_r4      Sigma-70, region 4
      0.021   14.7   0.0       0.03   14.2   0.0    1.3  1  HxlR            HxlR-like helix-turn-helix
      0.021   14.9   0.0      0.039   14.0   0.0    1.4  1  HTH_22          HTH domain
      0.022   15.3   0.0      0.053   14.1   0.0    1.6  1  Mga             Mga helix-turn-helix domain
      0.024   14.3   0.0      0.041   13.5   0.0    1.3  1  CENP-B_N        CENP-B N-terminal DNA-binding domain
      0.035   14.2   0.0      0.081   13.0   0.0    1.6  1  HTH_3           Helix-turn-helix
       0.04   14.4   0.0      0.057   13.9   0.0    1.3  1  HTH_40          Helix-turn-helix domain
      0.045   13.5   0.0       0.06   13.0   0.0    1.2  1  DUF4423         Domain of unknown function (DUF4423)
      0.045   13.9   0.0      0.055   13.6   0.0    1.3  1  HTH_Tnp_1_2     Helix-turn-helix of insertion element transpo
      0.057   13.4   0.1      0.073   13.1   0.1    1.2  1  Cdc6_C          CDC6, C terminal winged helix domain
      0.062   13.5   0.0      0.093   13.0   0.0    1.4  1  Rio2_N          Rio2, N-terminal
      0.067   13.0   0.1       0.41   10.4   0.0    2.0  2  MerR            MerR family regulatory protein
      0.071   13.0   0.0        0.1   12.5   0.0    1.3  1  Sigma70_ECF     ECF sigma factor
      0.084   13.2   0.1       0.19   12.1   0.0    1.6  1  HTH_31          Helix-turn-helix domain
      0.092   12.6   0.0       0.16   11.8   0.0    1.4  1  HTH_30          PucR C-terminal helix-turn-helix domain
       0.12   12.6   0.0       0.18   12.0   0.0    1.3  1  DUF1492         Protein of unknown function (DUF1492)
       0.13   12.3   0.1        0.9    9.6   0.0    2.1  2  HTH_46          Winged helix-turn-helix DNA binding


Domain annotation for each model (and alignments):
>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   3.5e-10   1.3e-07       9      51 ..      21      62 ..      19      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3.5e-10
                            HTH_11  9 Lleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                      L +a+++ +s +eLA++ nvS++t++r+++ L+e g  ++se++
  gi|313124935|ref|YP_004035199.1| 21 LVQAHEQyMSVSELADRCNVSESTIYRRLDPLREHG--LISERK 62
                                      77889999**************************99..666666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   4.9e-10   1.8e-07      21      58 ..      25      62 ..       7      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.9e-10
                                      TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                       ++ +++sela+r+ +s +t++++L+ L+e+gL+  ++
  gi|313124935|ref|YP_004035199.1| 25 HEQYMSVSELADRCNVSESTIYRRLDPLREHGLISERK 62
                                      5899******************************9997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.6e-09   1.3e-06      20      59 ..      28      67 ..      20      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.6e-09
                                      SEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS.S CS
                            MarR_2 20 rdltvgelarrlglsksavsrilkrLvaaGLverrpgpe.D 59
                                      + ++v+ela+r+++s s++ r+l+ L ++GL+ +r+ pe D
  gi|313124935|ref|YP_004035199.1| 28 Y-MSVSELADRCNVSESTIYRRLDPLREHGLISERKRPEaD 67
                                      4.79****************************888555525 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   8.5e-09   3.2e-06      15      47 ..      26      58 ..      20      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8.5e-09
                            HTH_24 15 nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +  +s +eLA+r+++S st+ rrl+ L e GlI
  gi|313124935|ref|YP_004035199.1| 26 EQYMSVSELADRCNVSESTIYRRLDPLREHGLI 58
                                      4569***************************99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.1e-08   7.8e-06      13      49 ..      23      59 ..      20      62 .. 0.91
   2 ?   -1.9   0.0       7.9   2.9e+03      19      27 ..     100     110 ..      95     111 .] 0.64

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.1e-08
                                      CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                       ++ q +++selA+r+ ++ St +R L  L e+G++ 
  gi|313124935|ref|YP_004035199.1| 23 QAHEQYMSVSELADRCNVSESTIYRRLDPLREHGLIS 59
                                      578888****************************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.9
                                       -..BHHHHHHH CS
                          HTH_IclR  19 l..tlselArr 27 
                                       +  +l++l ++
  gi|313124935|ref|YP_004035199.1| 100 MaeRLTDLVEK 110
                                       33488888876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   8.8e-08   3.3e-05       4      50 ..      21      64 ..      18      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.8e-08
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrs 50
                                       ++++++ +s vs++A ++++s++t+yr l+  +e+G   l++ r+r+
  gi|313124935|ref|YP_004035199.1| 21 LVQAHEQYMS-VSELADRCNVSESTIYRRLDPLREHG---LISeRKRP 64
                                      6899999998.**************************...78777775 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.3e-07   4.7e-05       8      46 ..      19      57 ..      17      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.3e-07
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      +  ++++ + +sv+e A++++vs++T+yr l   re+Gl
  gi|313124935|ref|YP_004035199.1| 19 CILVQAHEQYMSVSELADRCNVSESTIYRRLDPLREHGL 57
                                      5568888899******************98876666665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.4e-07   5.4e-05      17      54 ..      28      65 ..      20      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.4e-07
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRskspe 54
                                       +svseLa++ +vs st+ r ld L ++Gli+ +k pe
  gi|313124935|ref|YP_004035199.1| 28 YMSVSELADRCNVSESTIYRRLDPLREHGLISERKRPE 65
                                      499****************************9999886 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   1.5e-07   5.5e-05      13      46 ..      26      59 ..      19      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-07
                                      TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 13 egelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      e+ ++v+ela+  ++s+st+ + L  Lre GL++
  gi|313124935|ref|YP_004035199.1| 26 EQYMSVSELADRCNVSESTIYRRLDPLREHGLIS 59
                                      4669****************************97 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.2e-07   8.1e-05      21      50 ..      21      51 ..      20      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.2e-07
                      HTH_Tnp_ISL3 21 lellles.rsvkavArqlgvSwtTVwrildr 50
                                      l +++e  +sv++ A++++vS++T+ r+ld 
  gi|313124935|ref|YP_004035199.1| 21 LVQAHEQyMSVSELADRCNVSESTIYRRLDP 51
                                      567788889*******************995 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.3e-07   8.5e-05      11      44 ..      25      58 ..      21      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.3e-07
                          HTH_DeoR 11 qqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                       ++++sv el+++++vSe Ti R L+ L e gl+
  gi|313124935|ref|YP_004035199.1| 25 HEQYMSVSELADRCNVSESTIYRRLDPLREHGLI 58
                                      5789****************************97 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.7e-07    0.0001      24      55 .]      27      58 ..      20      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.7e-07
                            HTH_36 24 cfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                       + s++ la r+++s++T++r ++ L+++G+i
  gi|313124935|ref|YP_004035199.1| 27 QYMSVSELADRCNVSESTIYRRLDPLREHGLI 58
                                      5889**************************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.7e-07   0.00017      22      55 ..      29      62 ..      17      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.7e-07
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglisrgr 55
                                      ++  elA++++++ +t+ r l  L+++glis ++
  gi|313124935|ref|YP_004035199.1| 29 MSVSELADRCNVSESTIYRRLDPLREHGLISERK 62
                                      7889***************************543 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     7e-07   0.00026      18      41 ..      29      52 ..      22      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7e-07
                     HTH_AsnC-type 18 isyaeLAervGlSestvlrRvrrL 41
                                      +s++eLA+r+++Sest+ rR++ L
  gi|313124935|ref|YP_004035199.1| 29 MSVSELADRCNVSESTIYRRLDPL 52
                                      79******************9866 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     6e-07   0.00022      21      57 ..      27      63 ..      19      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6e-07
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      + ++++e+a + +v++s++Y+ L  L + Gl+  +k+
  gi|313124935|ref|YP_004035199.1| 27 QYMSVSELADRCNVSESTIYRRLDPLREHGLISERKR 63
                                      56899***************************99876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.1e-06   0.00041      17      39 ..      25      47 ..      18      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-06
                            HTH_38 17 laeGlslreIArrLgrspsTIsR 39
                                      +++ +s++e A r+++s sTI+R
  gi|313124935|ref|YP_004035199.1| 25 HEQYMSVSELADRCNVSESTIYR 47
                                      7888******************9 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.1e-06    0.0004       8      51 ..      23      64 ..      18      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.1e-06
                            HTH_28  8 llaaGh.svreaArelgisrrtvyrWikryeegGiagLvprrrrp 51
                                      ++ ++  sv+e+A + ++s++t+yr +  ++e+G+      r+rp
  gi|313124935|ref|YP_004035199.1| 23 QAHEQYmSVSELADRCNVSESTIYRRLDPLREHGL---ISERKRP 64
                                      4445656*************************886...5555554 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.7e-06   0.00063      20      58 ..      23      61 ..      17      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.7e-06
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      +++e+ +s++e+a+r n+s+s + + l  Lr++gl+  +
  gi|313124935|ref|YP_004035199.1| 23 QAHEQYMSVSELADRCNVSESTIYRRLDPLREHGLISER 61
                                      344455******************************865 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.9e-06   0.00071      27      57 ..      38      68 ..      26      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.9e-06
                                      CCTTHHHHHHHHHHHHHTTSEEEEEE-STSS CS
                              PadR 27 lelseGslYpaLkrLekeglveseweesgeg 57
                                       ++se+++Y+ L+ L+++gl++++++++++g
  gi|313124935|ref|YP_004035199.1| 38 CNVSESTIYRRLDPLREHGLISERKRPEADG 68
                                      689**********************998776 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.3e-06    0.0016      18      40 ..      25      47 ..      21      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.3e-06
                                      TTTT--STTTSSSS---SSSS-- CS
                             HTH_7 18 leeGisiskIAkevnisRsTvYR 40
                                      +e+ +s+s++A++ n+s sT+YR
  gi|313124935|ref|YP_004035199.1| 25 HEQYMSVSELADRCNVSESTIYR 47
                                      67779****************** PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.3e-06    0.0031      23      63 ..      28      63 ..       9      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.3e-06
                                      SBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEE CS
                               FUR 23 hlsaeevykelkeedpeislaTVYrtLklleeaglvkelef 63
                                      ++s+ e+      ++ ++s +T+Yr L+ l+e gl++e + 
  gi|313124935|ref|YP_004035199.1| 28 YMSVSEL-----ADRCNVSESTIYRRLDPLREHGLISERKR 63
                                      4444443.....46789*******************98765 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.4e-05     0.005      17      36 ..      29      48 ..      27      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-05
                                      --HHHHHHHHTSSHHHHHHH CS
                            TetR_N 17 ttvreIAkrAGvskgalYry 36
                                      ++v+e+A+r++vs++++Yr+
  gi|313124935|ref|YP_004035199.1| 29 MSVSELADRCNVSESTIYRR 48
                                      599***************95 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.7e-05    0.0064      31      53 ..      26      47 ..      13      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-05
                                      --TT--HHHHHHHTT--HHHHHH CS
                             HTH_6 31 kaielsikalAkaaavSeativr 53
                                      + +++s+++lA  ++vSe+ti r
  gi|313124935|ref|YP_004035199.1| 26 E-QYMSVSELADRCNVSESTIYR 47
                                      4.679****************88 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.2e-05    0.0046       1      20 [.      28      47 ..      28      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-05
                            HTH_17  1 lltveEaAelLgvsrstvyr 20
                                      +++v+E+A+  +vs+st+yr
  gi|313124935|ref|YP_004035199.1| 28 YMSVSELADRCNVSESTIYR 47
                                      8******************8 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.7e-05    0.0064      12      44 ..      17      49 ..      13      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                            HTH_50 12 ErelikkayekYpStRklAkrLGvShtaiankl 44
                                       r ++ +a e+Y S+  lA r  vS ++i ++l
  gi|313124935|ref|YP_004035199.1| 17 SRCILVQAHEQYMSVSELADRCNVSESTIYRRL 49
                                      578999**************************8 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.2e-05     0.012      19      57 ..      29      68 ..      17      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.2e-05
                            HTH_27 19 kkladlcgrlnvedshisyslkkLtekGLv.ertgdeadr 57
                                      ++ ++l++r nv+ s+i   l+ L e+GL+ er++ ead+
  gi|313124935|ref|YP_004035199.1| 29 MSVSELADRCNVSESTIYRRLDPLREHGLIsERKRPEADG 68
                                      6779**************************7777666665 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     3e-05     0.011      16      47 ..      18      49 ..      17      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-05
                                      HHHHHHHHTS---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 16 reifllryleglsykEIAellgisegtVksrl 47
                                      r i++  +++ +s  E A ++++se+t+++rl
  gi|313124935|ref|YP_004035199.1| 18 RCILVQAHEQYMSVSELADRCNVSESTIYRRL 49
                                      67888889999******************997 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.2e-05    0.0084       7      51 ..      26      70 ..      22     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-05
                      Replic_Relax  7 hrvlTtrqiarllfashratarrrLarLrelgllsr.lrkrvggar 51
                                       ++++ + +a  ++ s+++ ++rrL  Lre+gl+s   r++++g++
  gi|313124935|ref|YP_004035199.1| 26 EQYMSVSELADRCNVSEST-IYRRLDPLREHGLISErKRPEADGHH 70
                                      578999999***9999999.****************7777744443 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.1e-05     0.015      14      37 ..      25      49 ..      19      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.1e-05
                           HTH_psq 14 nGk.mSirkAArkYgiPrsTLwrrk 37
                                       ++ mS++++A++ +++ sT++rr+
  gi|313124935|ref|YP_004035199.1| 25 HEQyMSVSELADRCNVSESTIYRRL 49
                                      5788******************996 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.9e-05     0.014      20      58 ..      25      62 ..      22      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-05
                                      TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR 20 pGdkLPsereLaaefgVsrttvReALrrLeaeglverrq 58
                                      +++ + s++eLa++ +Vs +t+ + L+ L + gl+  r+
  gi|313124935|ref|YP_004035199.1| 25 HEQYM-SVSELADRCNVSESTIYRRLDPLREHGLISERK 62
                                      68899.****************************98776 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   5.4e-05      0.02      19      56 ..      25      62 ..      21      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.4e-05
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                       +++ ++++la r nvs s++   l  L++ G++   k
  gi|313124935|ref|YP_004035199.1| 25 HEQYMSVSELADRCNVSESTIYRRLDPLREHGLISERK 62
                                      56899***************************987655 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.2e-05     0.034      10      40 ..      18      48 ..      15      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.2e-05
                                      HHHHHHHHTTT--HHHHHHHHTS-HHHHHHH CS
                        Sigma70_r4 10 revlelrfgeglTleEIgerlgiSrerVrqi 40
                                      r +l++  ++ ++ +E+++r ++S++++ ++
  gi|313124935|ref|YP_004035199.1| 18 RCILVQAHEQYMSVSELADRCNVSESTIYRR 48
                                      56899999*******************9766 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     8e-05      0.03       1      59 [.      11      68 ..      11      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8e-05
                                      HHHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS- CS
                              HxlR  1 liggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPp 59
                                      +i+++ +  ilv+  +  +  sel++++ ++s++++ +rL  L ++gli+ +  pe   
  gi|313124935|ref|YP_004035199.1| 11 VIDDQCSRCILVQAHEQYMSVSELADRC-NVSESTIYRRLDPLREHGLISERKRPEADG 68
                                      577788889*******************.********************9887777655 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0    0.0001     0.039      43      62 ..      30      49 ..      28      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.0001
                            HTH_22 43 avekvAekLgiSraTvYryL 62
                                      +v+++A++ ++S+ T+Yr L
  gi|313124935|ref|YP_004035199.1| 30 SVSELADRCNVSESTIYRRL 49
                                      899***************98 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   0.00014     0.053      27      55 ..      25      53 ..      15      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00014
                                      HHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                               Mga 27 eeeevsieelaqelyiSestlkrkikeln 55
                                      +e+++s+ ela++  +Sest++r ++ l+
  gi|313124935|ref|YP_004035199.1| 25 HEQYMSVSELADRCNVSESTIYRRLDPLR 53
                                      7899*******************998765 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00011     0.041      16      42 ..      22      48 ..      20      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                                      HHHHHCTT-HHHHHHHHT--CCHHHHH CS
                          CENP-B_N 16 IqrleegeSkaelarrfnvpestlsdi 42
                                      +q  e+ +S+ ela r nv est+++ 
  gi|313124935|ref|YP_004035199.1| 22 VQAHEQYMSVSELADRCNVSESTIYRR 48
                                      68889999****************985 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00022     0.081       8      28 ..      27      47 ..      24      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00022
                                      TTHHHHHHHHHHTSSHHHHHH CS
                             HTH_3  8 lglsqeeLAeklGvsrstisr 28
                                      + +s  eLA++++vs sti+r
  gi|313124935|ref|YP_004035199.1| 27 QYMSVSELADRCNVSESTIYR 47
                                      67999**************98 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   0.00015     0.057       7      41 ..      23      64 ..      20     110 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00015
                            HTH_40  7 elleeglsieeIAkerglkesTIegHLaelieeg.......e 41
                                      + +e+ +s+ e A++ +++esTI++ L  l e+g        
  gi|313124935|ref|YP_004035199.1| 23 QAHEQYMSVSELADRCNVSESTIYRRLDPLREHGliserkrP 64
                                      567899*******************99999999844444432 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00016      0.06      29      72 ..      21      62 ..      18      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                           DUF4423 29 llplkdfkadpeelakrlrpkisaeevekalefLlklgllkkde 72
                                      l+++++   +++ela+r++  +s++ + + l+ L + gl+ + +
  gi|313124935|ref|YP_004035199.1| 21 LVQAHEQYMSVSELADRCN--VSESTIYRRLDPLREHGLISERK 62
                                      5777788899*********..*******************9876 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00015     0.055      13      46 ..      17      48 ..       7      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00015
                                      HHHHHHHHHHHH--S-HHHHHHHHTS-HHHHHHH CS
                       HTH_Tnp_1_2 13 kkaaellvendyekltldeiaeevgvsrsTlykW 46
                                       + + + ++++y  ++++e+a+ + vs+sT+y+ 
  gi|313124935|ref|YP_004035199.1| 17 SRCILVQAHEQY--MSVSELADRCNVSESTIYRR 48
                                      566666678888..******************95 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1    0.0002     0.073      18      73 ..      21      75 ..       7      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
                                      HHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEE CS
                            Cdc6_C 18 tgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkis 73
                                      + +++e+Y s+ e  +   ++++++++ l+ L   g+++ +k+ +   +   ++++
  gi|313124935|ref|YP_004035199.1| 21 LVQAHEQYMSVSELADRCNVSESTIYRRLDPLREHGLISERKRPEAD-GHHFTEFR 75
                                      5689***********************************99986655.35555555 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00025     0.093      22      67 ..      26      72 ..      20      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00025
                            Rio2_N 22 hevVptelieeisrlkeeevkkrlsrllkaklisr.ktakydGYkLt 67
                                       +++++++++ +++++e+ + +rl+ l +++lis  k  + dG++ t
  gi|313124935|ref|YP_004035199.1| 26 EQYMSVSELADRCNVSESTIYRRLDPLREHGLISErKRPEADGHHFT 72
                                      468999***************************99788889999887 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0011      0.41       1      17 [.      30      46 ..      30      47 .. 0.90
   2 ?   -0.1   0.1       2.2   8.2e+02      21      32 ..      54      65 ..      52      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                                      EHHHHHHHHTTTHHHHH CS
                              MerR  1 tIgevAeltGvsprtLR 17
                                      +++e+A++++vs +t+ 
  gi|313124935|ref|YP_004035199.1| 30 SVSELADRCNVSESTIY 46
                                      579************95 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.2
                                      HTTSSTSEEETT CS
                              MerR 21 reGLipppeRte 32
                                      + GLi +  R+e
  gi|313124935|ref|YP_004035199.1| 54 EHGLISERKRPE 65
                                      569**8888876 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00028       0.1     152     177 ..      29      54 ..       2      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00028
                       Sigma70_ECF 152 lsveEiAeklgvskrtverrlalaRa 177
                                       +sv E+A++ +vs++t++rrl   R+
  gi|313124935|ref|YP_004035199.1|  29 MSVSELADRCNVSESTIYRRLDPLRE 54 
                                       589******************98886 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00052      0.19      14      33 ..      28      47 ..      20      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00052
                            HTH_31 14 GLsqeevAerlgvsestlsr 33
                                       +s  e+A+r++vsest+ r
  gi|313124935|ref|YP_004035199.1| 28 YMSVSELADRCNVSESTIYR 47
                                      5899*************987 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00042      0.16      12      38 ..      28      54 ..      20      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00042
                                      TT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 12 ggnisatAkaLhvHrnTlryRLrriee 38
                                       +++s+ A++ +v+  T++ RL+ ++e
  gi|313124935|ref|YP_004035199.1| 28 YMSVSELADRCNVSESTIYRRLDPLRE 54
                                      5799******************98877 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00048      0.18      52      92 ..       9      49 ..       2      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00048
                           DUF1492 52 idklensdsrsvLrmvyidkltvwqvidklnisrstyyrll 92
                                         ++++ sr +L   + + ++v ++ d+ n+s+st yr l
  gi|313124935|ref|YP_004035199.1|  9 AGVIDDQCSRCILVQAHEQYMSVSELADRCNVSESTIYRRL 49
                                      45678999******************************976 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0024       0.9      30      54 ..      35      59 ..      22      64 .. 0.87
   2 ?    1.2   0.0         1   3.8e+02      20      41 ..      63      84 ..      56      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0024
                            HTH_46 30 qkrtnLSrSsimkvLseLkkggyIe 54
                                       +r+n+S S+i + L  L++ g I+
  gi|313124935|ref|YP_004035199.1| 35 ADRCNVSESTIYRRLDPLREHGLIS 59
                                      68******************99986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1
                            HTH_46 20 reninvlkyIqkrtnLSrSsim 41
                                      r +    ++ + rtnL r si+
  gi|313124935|ref|YP_004035199.1| 63 RPEADGHHFTEFRTNLDRLSIQ 84
                                      555555789999****998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              48  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 703.85
//
Query:       gi|313124936|ref|YP_004035200.1|  [L=103]
Description: hypothetical protein Hbor_01500 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 695.30
//
Query:       gi|313124937|ref|YP_004035201.1|  [L=145]
Description: ester cyclase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-31  106.4   0.0    9.7e-31  106.2   0.0    1.0  1  SnoaL         SnoaL-like polyketide cyclase
    9.7e-23   80.8   0.1    1.1e-22   80.5   0.1    1.1  1  SnoaL_2       SnoaL-like domain
    0.00066   20.0   0.0    0.00087   19.7   0.0    1.2  1  DUF4440       Domain of unknown function (DUF4440)
  ------ inclusion threshold ------
      0.076   12.5   0.0      0.095   12.2   0.0    1.1  1  Peptidase_A4  Peptidase A4 family
       0.15   12.2   0.0       0.18   11.9   0.0    1.2  1  SnoaL_4       SnoaL-like domain


Domain annotation for each model (and alignments):
>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.0   2.7e-34   9.7e-31       3     126 .]      17     139 ..      15     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 2.7e-34
                                       HHHHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEE CS
                             SnoaL   3 vlrfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftG 79 
                                       ++r  e+v+  g ld l++l+a++ vdhnp  +++ Gle++r+ +e+++ afPD++ +ve+ v+ gd va+++t +G
  gi|313124937|ref|YP_004035201.1|  17 ARRIPEDVFGDGGLDVLGDLYAPNAVDHNP-FGSQEGLEAIRESYESFLSAFPDITQTVERSVVHGDVVALHITSRG 92 
                                       56777899999*****************66.5********************************************* PP

                                       EESSEBTTBE-TT-EEEEEEEEEEEEETTEEEEEEEEECHHHHHHHC CS
                             SnoaL  80 thtgeflGipptGkkvkfeeitllrvedGkIveewdviDllgllrQl 126
                                       th+g + Gi pt k+++++++ ++r+edG I+e+w + D+l+llrQl
  gi|313124937|ref|YP_004035201.1|  93 THSGVLWGIEPTAKEIEVQQMAFVRIEDGLIAERWFLSDNLTLLRQL 139
                                       **********************************************8 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.1   3.2e-26   1.1e-22       6     101 ..      23     125 ..      17     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 3.2e-26
                                       HHHHTTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE...... CS
                           SnoaL_2   6 aalnagdldalaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt...... 76 
                                       +++ +g ld l +l+ap++v ++p+g+++G eair+ +++++ afpd++ ++++ v++gd va+++t +gt      
  gi|313124937|ref|YP_004035201.1|  23 DVFGDGGLDVLGDLYAPNAVDHNPFGSQEGLEAIRESYESFLSAFPDITQTVERSVVHGDVVALHITSRGThsgvlw 99 
                                       4789999********************************************************************** PP

                                       .EETTSSEEEEEEEEEEEEETTEEEE CS
                           SnoaL_2  77 .ipatgrgvtvrgvdvfrvrdGkive 101
                                        i++t ++++v+ +++ r++dG+i+e
  gi|313124937|ref|YP_004035201.1| 100 gIEPTAKEIEVQQMAFVRIEDGLIAE 125
                                       ************************98 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.4e-07   0.00087      13      83 ..      26      96 ..      16     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.4e-07
                                      HCT-HHHHHHCEEEEEEEE-TTS-EEEHHHHHHHHHCCHCEEEEEEEEEEEEEEETTEEEEEEEEEEEECC CS
                           DUF4440 13 vagdaealaallapdavlvgpsgtvldkeellealeagfaagrslelteeevrvlgdlAvvtgrytfegrg 83
                                        g ++ l++l+ap+av  +p+g+  + e++ e++e+  +a+++++ t e+  v gd+++++ + + ++ g
  gi|313124937|ref|YP_004035201.1| 26 GDGGLDVLGDLYAPNAVDHNPFGSQEGLEAIRESYESFLSAFPDITQTVERSVVHGDVVALHITSRGTHSG 96
                                      5677899****************999***********99***********************999998754 PP

>> Peptidase_A4  Peptidase A4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05     0.095      73     114 ..      58      98 ..      48     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                      Peptidase_A4  73 qsydawyewyPayavdfsglavsaGDsvtvtvtatsatsgtv 114
                                        sy+ + + +P+++++++  +v  GD+v +++t+ +++sg++
  gi|313124937|ref|YP_004035201.1|  58 ESYESFLSAFPDITQTVER-SVVHGDVVALHITSRGTHSGVL 98 
                                       699*************997.******************9986 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.1e-05      0.18      26      81 ..      31      83 ..      27     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                                      HHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH-EEEEE---EEEEET CS
                           SnoaL_4 26 eeladlFtedavvdytgvgegvlegrdairaalrealdgfaltqHllsnplieldg 81
                                      + l+dl++++av d++++  g  eg +air+ +++ l +f++++  +   +++ d 
  gi|313124937|ref|YP_004035201.1| 31 DVLGDLYAPNAV-DHNPF--GSQEGLEAIRESYESFLSAFPDITQTVERSVVHGDV 83
                                      5689******98.99988..9*****************999777777666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 976.01
//
Query:       gi|313124938|ref|YP_004035202.1|  [L=211]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-14   53.0   0.1    3.4e-14   52.4   0.1    1.4  1  HTH_10      HTH DNA binding domain
     0.0011   18.7   0.1     0.0071   16.1   0.0    2.2  2  HTH_IclR    IclR helix-turn-helix domain
     0.0073   16.2   0.1      0.019   14.8   0.1    1.7  1  MarR_2      MarR family
  ------ inclusion threshold ------
      0.026   14.6   0.3      0.089   12.9   0.0    1.9  2  HTH_20      Helix-turn-helix domain
      0.037   13.5   0.4       0.33   10.5   0.1    2.4  2  Sigma70_r4  Sigma-70, region 4
       0.15   11.6   0.0       0.23   11.0   0.0    1.2  1  FANCI_S1    FANCI solenoid 1


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1   1.1e-17   3.4e-14       1      53 []     151     203 ..     151     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.1e-17
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT +q++++ +A+e G++d PR +tl eLA +l+I ks++s    +aes+li+
  gi|313124938|ref|YP_004035202.1| 151 LTNRQRQFIETALEEGFYDDPRACTLTELAATLDIHKSAASRLRHRAESRLIT 203
                                       9*****************************************999*****985 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.45   1.4e+03      33      41 ..      26      34 ..      17      43 .. 0.75
   2 !   16.1   0.0   2.4e-06    0.0071      15      38 ..     170     193 ..     166     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.45
                                      HHHHHHHHH CS
                          HTH_IclR 33 StvhRlLqt 41
                                      + v+RlL+t
  gi|313124938|ref|YP_004035202.1| 26 ADVFRLLAT 34
                                      568888877 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.4e-06
                                       TBSS-BHHHHHHHHTS-HHHHHHH CS
                          HTH_IclR  15 apqeltlselArrtglpkStvhRl 38 
                                        p++ tl+elA+ ++++kS+++Rl
  gi|313124938|ref|YP_004035202.1| 170 DPRACTLTELAATLDIHKSAASRL 193
                                       68899******************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   6.4e-06     0.019      18      47 ..     170     199 ..     162     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.4e-06
                                       TTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  18 pgrdltvgelarrlglsksavsrilkrLva 47 
                                       ++r +t +ela++l++ ksa+sr+  r+++
  gi|313124938|ref|YP_004035202.1| 170 DPRACTLTELAATLDIHKSAASRLRHRAES 199
                                       56678******************9888876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.1   6.3e+03      14      20 ..      27      36 ..      20      46 .. 0.58
   2 ?   12.9   0.0     3e-05     0.089       4      43 ..     148     192 ..     145     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.1
                                      HHHHHH...S CS
                            HTH_20 14 rilraL...a 20
                                      +++r+L    
  gi|313124938|ref|YP_004035202.1| 27 DVFRLLatqL 36
                                      5555553332 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3e-05
                                       HHHHS-HHHHHHHHHH.....STCTTB-HHHHHHHHTS-HHHHHH CS
                            HTH_20   4 aeALahPvRrrilraL.....araegltaselaerldlskntlsy 43 
                                       a +L+++ R  i+ aL      ++++ t++ela++ld++k+ +s+
  gi|313124938|ref|YP_004035202.1| 148 ATILTNRQRQFIETALeegfyDDPRACTLTELAATLDIHKSAASR 192
                                       5678899999999999999999*******************9985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.21   6.3e+02      16      26 ..     124     134 ..     122     145 .. 0.85
   2 ?   10.5   0.1   0.00011      0.33       5      47 ..     151     200 ..     150     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.21
                                       HHTTT--HHHH CS
                        Sigma70_r4  16 rfgeglTleEI 26 
                                       +++e+lT +EI
  gi|313124938|ref|YP_004035202.1| 124 SYVEELTAAEI 134
                                       6899***9999 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrk 47 
                                       L+ r+r+ +e           +  Tl E++++l+i +++++++ +rA  +
  gi|313124938|ref|YP_004035202.1| 151 LTNRQRQFIETALeegfyddPRACTLTELAATLDIHKSAASRLRHRAESR 200
                                       677777777777777766555667**********************9665 PP

>> FANCI_S1  FANCI solenoid 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.6e-05      0.23     136     218 ..     122     205 ..     114     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.6e-05
                          FANCI_S1 136 llrslkklklqElPpLvyQlLlLsakgskkviLeglikyFaeqdkk...dresakeeesnsisse...eietvstke 206
                                       l++ +++l+  E+P   yQ+L+Ls++++ ++iL   ++ F e   +       ++ ++ + +++    +i +  ++ 
  gi|313124938|ref|YP_004035202.1| 122 LSSYVEELTAAEIP---YQVLSLSQSHDTATILTNRQRQFIETALEegfY---DDPRACTLTELAatlDIHKSAASR 192
                                       56677888889988...*****************9999998888774432...333333333333345889999999 PP

                          FANCI_S1 207 Lre.vegTvllhi 218
                                       Lr+ +e+  + h+
  gi|313124938|ref|YP_004035202.1| 193 LRHrAESRLITHV 205
                                       9998999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1422.10
//
Query:       gi|313124939|ref|YP_004035203.1|  [L=81]
Description: hypothetical protein Hbor_01530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 527.21
//
Query:       gi|313124940|ref|YP_004035204.1|  [L=67]
Description: hypothetical protein Hbor_01540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 453.43
//
Query:       gi|313124941|ref|YP_004035205.1|  [L=105]
Description: hypothetical protein Hbor_01550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 683.71
//
Query:       gi|313124942|ref|YP_004035206.1|  [L=119]
Description: thioredoxin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-13   50.2   0.2    4.4e-13   49.2   0.2    1.6  2  NifU      NifU-like domain


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.6   0.0    0.0084   1.5e+02      45      63 ..       9      27 ..       5      28 .. 0.86
   2 !   49.2   0.2   2.5e-17   4.4e-13      11      66 ..      25      81 ..      16      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0084
                                      .THHHHHHHHHHHHH-TT- CS
                              NifU 45 tvtlkegiekaLkeevpev 63
                                      +  lke +++ L++++p++
  gi|313124942|ref|YP_004035206.1|  9 DDDLKERVTNFLRRNFPQI 27
                                      5689*************98 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 2.5e-17
                                      GG--GG--EEEE..EEEETTEEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EE CS
                              NifU 11 PaLasdGGdiel..vdvdegvVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeV 66
                                      P+++++GG+  +  +d +eg+V++ l GaCsgC  s +t+ ++i++++ +e+pe+++V
  gi|313124942|ref|YP_004035206.1| 25 PQIQMHGGSAAIqhLDREEGEVTIMLGGACSGCGISPMTI-QAIKSRMVKEIPEIEKV 81
                                      9*******976611555666********************.9**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 755.21
//
Query:       gi|313124943|ref|YP_004035207.1|  [L=513]
Description: arylsulfatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-45  156.4   0.4    1.7e-45  155.8   0.4    1.3  1  Sulfatase     Sulfatase
    9.3e-13   48.5   0.6    2.3e-05   24.2   0.0    2.3  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
  ------ inclusion threshold ------
      0.022   13.8   0.0      0.041   13.0   0.0    1.3  1  DUF1501       Protein of unknown function (DUF1501)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.8   0.4   2.8e-49   1.7e-45       2     309 .]       8     342 ..       7     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 155.8 bits;  conditional E-value: 2.8e-49
                                       EEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHHC CS
                         Sulfatase   2 nvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevggggl 78 
                                       nv+++++d+++ + l+ yg+ ++ttpnl++ aee ++f ++++ ap + p+ a+l+tg+yp ++g+ +      ++ 
  gi|313124943|ref|YP_004035207.1|   8 NVLFVVMDTVRKDRLTPYGYDRPTTPNLESFAEEATVFEQAVAPAPWTLPVHASLFTGMYPSRHGADQE-----NPY 79 
                                       9****************************************************************5555.....566 PP

                                       TTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC........CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC. CS
                         Sulfatase  79 pqteatLpellkeaGYntaaigkwhlgwssrqsvyk........nrgfdrflgfptgsaalkdpekseyngevlrv. 146
                                        +  +tL++ l +aGY+ta++   ++ w+      +        +++f +++      + l++p +  +      + 
  gi|313124943|ref|YP_004035207.1|  80 LEGATTLAQTLSAAGYDTACYS--SNAWITPY---ThltdgftdQDNFFEVMP----GDFLSGPLAKMWK-----Tl 142
                                       789***************7766..55555333...233245556444444332....2222222222222.....11 PP

                                       ..........................TTTTCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGS CS
                         Sulfatase 147 ..........................ppeggysddrlldealefllarndkpfflylatlapHappeapdeyakkya 197
                                                                 +      + ++ d+a +f+  + ++  f ++ ++  H p++ pd++a ++a
  gi|313124943|ref|YP_004035207.1| 143 ndndslrtladklvsignvaheylagSDGADSKTPAVIDRAMTFI--EGSEQSFTFINLMDAHLPYHPPDRFAREFA 217
                                       1223455589999999999*****99999999999*********7..448999************************ PP

                                       TTTTCCCCCCH.................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHH CS
                         Sulfatase 198 tffddgseaar.................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesn 257
                                        + d+++  ++                   ++ y++ ++ +Dd++gr++++L+e+g +d+t+vv+ +Dhg+    + 
  gi|313124943|ref|YP_004035207.1| 218 PGVDSTEICQNskeynsgardideeeweAIRGLYDAEIAHIDDQLGRLFDWLKETGRWDDTMVVVCADHGELH--GE 292
                                       99999888877889999999***************************************************99..56 PP

                                       TTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTTE CS
                         Sulfatase 258 gplrggkganayeggtrvPllvwwpgekaprvseelvshiDlfptildlagi 309
                                       ++l g++    y+  ++vPl+v  p   +  + e  v++iD+++t+ld++++
  gi|313124943|ref|YP_004035207.1| 293 HDLYGHEF-GLYDPLVNVPLMVKHPALEED-RHEDQVELIDMYHTVLDALDV 342
                                       99999999.*********************.999999************985 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.8e-09   2.3e-05       1      62 [.       9      72 ..       9      77 .. 0.89
   2 !   22.4   0.1   1.3e-08   7.6e-05     196     237 ..     224     291 ..     199     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.8e-09
                                      EEEEEETT-BTTHHHHHG.S..TSHHHHHHHHHSEEESEEE-SSS.-SHHHHHHHHHHSS-HHHHS CS
                      Phosphodiest  1 vlvislDGlradlldrla.e..llpnlaaLakegvsapnlrpvfP.tlTfpnhaslvTGlyPgeHG 62
                                      vl++++D +r d l ++  +  ++pnl+++a+e + +++  +v+P + T p hasl TG yP+ HG
  gi|313124943|ref|YP_004035207.1|  9 VLFVVMDTVRKDRLTPYGyDrpTTPNLESFAEEATVFEQ--AVAPaPWTLPVHASLFTGMYPSRHG 72
                                      78999***********988789****************4..4444257*****************9 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.3e-08
                                       H..........................HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEE CS
                      Phosphodiest 196 e..........................vedalrrvDkaigdLlealderglsaetniilvSDHGmadv 237
                                       e                            ++++ +D+ +g+L++ l+e+g +++t +++ +DHG  + 
  gi|313124943|ref|YP_004035207.1| 224 EicqnskeynsgardideeeweairglYDAEIAHIDDQLGRLFDWLKETGRWDDTMVVVCADHGELHG 291
                                       344445555555555555566666666778899*******************************6666 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.8e-06     0.041     269     302 ..     254     287 ..     246     288 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-06
                           DUF1501 269 lakelDqalaaLlkdLkqrGllddTlVvwagEFG 302
                                        ++ +D+ l  L + Lk++G++ddT+Vv++++ G
  gi|313124943|ref|YP_004035207.1| 254 EIAHIDDQLGRLFDWLKETGRWDDTMVVVCADHG 287
                                       56789*************************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3284.44
//
Query:       gi|313124944|ref|YP_004035208.1|  [L=299]
Description: ketopantoate reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-33  114.6   0.2    4.4e-33  114.1   0.2    1.2  1  ApbA_C    Ketopantoate reductase PanE/ApbA C terminal
    2.1e-26   92.4   0.5    3.9e-26   91.5   0.1    1.6  2  ApbA      Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.2   4.9e-37   4.4e-33       4     124 ..     172     291 ..     169     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 4.9e-37
                            ApbA_C   4 larweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaanrsS 80 
                                       ++ weKl++na in++tal+++ ng+l  ++ +++l+ ++++E  +va+aegv+ls  r+e a+ +v+e+t+anrsS
  gi|313124944|ref|YP_004035208.1| 172 RRLWEKLAVNAGINAVTALARVENGALA-DGPGHQLAHRAARETARVARAEGVSLSNRRAERALDEVVEATSANRSS 247
                                       679************************9.777********************************************* PP

                            ApbA_C  81 MlqDveagrktEidyinGavvklAeklgvetPvnellyellkal 124
                                       MlqDv+  r+tE+++i G vv++A+++ +++P+n++l +ll++ 
  gi|313124944|ref|YP_004035208.1| 248 MLQDVDDERRTEVEAIHGVVVARADAHRLSVPTNRTLADLLRTW 291
                                       *****************************************975 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.1   4.4e-30   3.9e-26       1     151 [.       3     143 ..       3     144 .. 0.88
   2 ?   -2.0   0.0      0.29   2.6e+03      35      61 ..     216     243 ..     195     259 .. 0.57

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 4.4e-30
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SS CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsaeekselepidlvivtvK 77 
                                       +++ GaG++G+l++a La+  +dvtl++r++++ +++++G+++++   e +  p++++++    +++ +dl +vtvK
  gi|313124944|ref|YP_004035208.1|   3 VLVFGAGSLGTLVGALLAR-VHDVTLVGRDPHVSHVRERGVTVSGAI-EAQTAPDATTES----DGHRADLAVVTVK 73 
                                       689**************88.9************************99.444444444444....59*********** PP

                                       GGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEEEECS--EEEEEESS CS
                              ApbA  78 ayqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgevhhagkgeikigela 151
                                       +++t  a++++     +  +vl+lqNGl  e+el+++l +++vl+g+ t ga  ++pg+v+ +g g++++g+ +
  gi|313124944|ref|YP_004035208.1|  74 SFDTPTAAAALSTGAFD--AVLSLQNGLT-EDELAARL-DAPVLAGTATYGARLREPGHVECTGIGRVVLGARD 143
                                       ******99998887777..5********7.67788999.77*****************************9865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.29
                                       H.HHHHCEEEEETTCEEEEEECEEECCH CS
                              ApbA  35 a.lkknGlrltseggeeilrppealsae 61 
                                       +  + +G++l+ ++ e+ l + ++++++
  gi|313124944|ref|YP_004035208.1| 216 RvARAEGVSLSNRRAERALDEVVEATSA 243
                                       2245566666666655555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1830.68
//
Query:       gi|313124945|ref|YP_004035209.1|  [L=96]
Description: hypothetical protein Hbor_01590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-05   22.5   3.5    0.00024   20.7   0.0    2.2  2  Rubredoxin_2  Rubredoxin metal binding domain
      0.008   16.2   0.1      0.011   15.8   0.1    1.2  1  PRC           PRC-barrel domain
  ------ inclusion threshold ------
      0.012   15.7   0.7       0.02   15.0   0.7    1.4  1  Zn-ribbon_8   Zinc ribbon domain
      0.028   14.4   0.0      0.031   14.3   0.0    1.2  1  HypA          Hydrogenase/urease nickel incorporation, metall
      0.047   13.6   6.2       0.22   11.4   0.1    3.1  3  HalOD2        Halobacterial output domain 2
       0.52   10.4   4.7        4.9    7.3   1.1    2.4  2  Rubredoxin    Rubredoxin


Domain annotation for each model (and alignments):
>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   8.2e-08   0.00024      10      28 .]      57      75 ..      54      75 .. 0.89
   2 ?    2.0   1.2     0.058   1.7e+02      17      22 ..      80      85 ..      79      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.2e-08
                      Rubredoxin_2 10 sakwfGrCpsCgsWntlke 28
                                       a +++rC +Cg+++tl+e
  gi|313124945|ref|YP_004035209.1| 57 EAELMWRCANCGEMDTLDE 75
                                      6789*************87 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.058
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+C++
  gi|313124945|ref|YP_004035209.1| 80 CPGCNA 85
                                      ****96 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.6e-06     0.011      10      27 ..      10      27 ..       9      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.6e-06
                                      TT-EEEETTSSEEEEEEE CS
                               PRC 10 iGkeVytedGeklGkVkD 27
                                      iG++VytedG++lG+V  
  gi|313124945|ref|YP_004035209.1| 10 IGTTVYTEDGDELGTVRG 27
                                      89**************76 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.7   6.8e-06      0.02       7      35 ..      63      86 ..      61      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.8e-06
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgse 35
                                      rC +Cg e + l +     l++ CP C+++
  gi|313124945|ref|YP_004035209.1| 63 RCANCG-EMDTLDE-----LPDsCPGCNAP 86
                                      8*****.9998864.....8888****985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05     0.031      62      98 ..      53      89 ..      21      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                                      EEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 62 LeieevpvkvrCreCgkefeleekalrCpkCgsadve 98
                                       e+ e ++  rC +Cg+  +l+e   +Cp C++ + e
  gi|313124945|ref|YP_004035209.1| 53 HEFGEAELMWRCANCGEMDTLDELPDSCPGCNAPKEE 89
                                      567788999*******77778863448****998765 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.083   2.5e+02      14      31 ..      16      35 ..       9      42 .. 0.84
   2 ?   11.4   0.1   7.4e-05      0.22      31      40 ..      61      70 ..      51      73 .. 0.88
   3 ?    2.4   0.6      0.05   1.5e+02       1       9 [.      76      84 ..      76      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.083
                            HalOD2 14 trhGdglGe..GyrqLGayv 31
                                      t +Gd lG   G+++ G +v
  gi|313124945|ref|YP_004035209.1| 16 TEDGDELGTvrGFDEDGFFV 35
                                      889**999888999888776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.4e-05
                            HalOD2 31 vWkCtrCGev 40
                                      +W+C++CGe+
  gi|313124945|ref|YP_004035209.1| 61 MWRCANCGEM 70
                                      7*******96 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.05
                            HalOD2  1 rPekCseCs 9 
                                      +P++C+ C+
  gi|313124945|ref|YP_004035209.1| 76 LPDSCPGCN 84
                                      59******7 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.012        34      25      41 ..      52      68 ..      46      73 .. 0.75
   2 ?    7.3   1.1    0.0016       4.9      29      46 ..      74      89 ..      69      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.012
                                      T--GGGS-TT-BBTTTB CS
                        Rubredoxin 25 gTkFedlPddWvCPdCg 41
                                      g +F +    W+C +Cg
  gi|313124945|ref|YP_004035209.1| 52 GHEFGEAELMWRCANCG 68
                                      55666666679999997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                                      GGS-TT-BBTTTB-BGGG CS
                        Rubredoxin 29 edlPddWvCPdCgvekeq 46
                                      ++lPd   CP C+++ke+
  gi|313124945|ref|YP_004035209.1| 74 DELPD--SCPGCNAPKEE 89
                                      57888..5********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 606.73
//
Query:       gi|313124946|ref|YP_004035210.1|  [L=1195]
Description: DNA polymerase type ii, large subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1326.3   0.0          0 1324.6   0.0    1.7  2  PolC_DP2        DNA polymerase II large subunit DP2
    0.00055   19.9  18.0      0.091   12.8   6.4    3.3  3  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.59   10.2  18.0        2.5    8.2   0.2    3.4  3  HypA            Hydrogenase/urease nickel incorporation, meta
        0.6   10.1  16.8         11    6.1   0.1    3.0  2  zinc-ribbons_6  zinc-ribbons
        1.9    7.2   4.4        3.1    6.5   4.4    1.2  1  tRNA-synt_1g    tRNA synthetases class I (M)
        3.3    7.5   7.5        7.6    6.4   7.5    1.5  1  Sigma70_ner     Sigma-70, non-essential region


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1324.6   0.0         0         0       1     864 []       7     945 ..       7     945 .. 0.97
   2 ?   -1.1   0.1       0.1   3.1e+02     617     675 ..    1110    1172 ..    1079    1191 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1324.6 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeia 77 
                                       +Yf ++e++l+ea+++a++a+ +g dp++evEip+Akd+adRve++lgi+gvaer+rele ++sree+al+++++++
  gi|313124946|ref|YP_004035210.1|   7 RYFARIEDRLDEAFDLARAAKGQGRDPQPEVEIPVAKDMADRVENILGIPGVAERVRELEGQMSREEAALELVNDFV 83 
                                       6**************************************************************************** PP

                          PolC_DP2  78 egkvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDy 154
                                       eg+vg+++s++ +v+ avrta+alltegvvaAP+eGi++v+i +nddgte+++vyyaGPiRsaGGtaqalsvLvaDy
  gi|313124946|ref|YP_004035210.1|  84 EGSVGDYDSRAGKVEGAVRTAVALLTEGVVAAPIEGIDRVEILENDDGTEFVNVYYAGPIRSAGGTAQALSVLVADY 160
                                       ***************************************************************************** PP

                          PolC_DP2 155 vrkklgldrykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnrv 231
                                       +r+ lg+++yk+r+ e+eRy+eEi+lY++ ++lqysp+d+e+++i++++p+++dGeat+deevsg+rdlerv+tn++
  gi|313124946|ref|YP_004035210.1| 161 ARSLLGIEEYKARDIEVERYAEEIDLYDKETGLQYSPKDKETKFIAEHMPIMLDGEATGDEEVSGFRDLERVDTNSA 237
                                       ***************************************************************************** PP

                          PolC_DP2 232 RGGmllvlaeGialkakKikkkvkklklegWewleelika.................ekeekkeeeeek........ 283
                                       RGGm+lv+aeGialka+Ki++++++l+  +W+wl++li++                 +          +        
  gi|313124946|ref|YP_004035210.1| 238 RGGMCLVMAEGIALKAPKIQRYTRQLDEVDWPWLQDLIDGtigkddgdkadadddgdD----------Eeadaedde 304
                                       ****************************************999998877655555431..........123345555 PP

                          PolC_DP2 284 ...............kevkpkekylrdliaGRpvlshpsrkGGfRLrYGRsrntglatagihPatmelldeflavGt 345
                                                      ++v+p++kylrdliaGRpv++hps++GGfRLrYGRsrn+g+atag+hPatm+l+d+fla+Gt
  gi|313124946|ref|YP_004035210.1| 305 addgetpdspepagpARVDPATKYLRDLIAGRPVFGHPSEAGGFRLRYGRSRNHGFATAGVHPATMHLVDDFLATGT 381
                                       6689999********************************************************************** PP

                          PolC_DP2 346 qlkverPgKaaavvpvdsiegPtvklknGdvvriddveealeikkeveeildlGeiLvayGeflennhpLvpasyve 422
                                       q+k+erPgKa +v+pvdsiegPtv+l+nGdv+ridd eeale+++ veei+dlGe+Lv++Gef+ennhpL+pasyv+
  gi|313124946|ref|YP_004035210.1| 382 QIKTERPGKAGGVIPVDSIEGPTVRLANGDVRRIDDPEEALEVRNGVEEIIDLGEYLVNFGEFVENNHPLAPASYVY 458
                                       ***************************************************************************** PP

                          PolC_DP2 423 ewwiqelekaaakkeaee........kpsaeealelseeldvpLhPkytylwhdisveelekLaeavaekkkl.... 487
                                       eww+qe+e+a+a  +a e        +p+ e+a+e+++e+d++LhP+ytylwhd+sv e+e+La+av++ +++    
  gi|313124946|ref|YP_004035210.1| 459 EWWVQEFEAAGAPIQALEddpsvdleHPTPERAFEWATEYDCHLHPDYTYLWHDVSVAEFEALADAVSSGRIAdvea 535
                                       ************99999999**************************************************97799** PP

                          PolC_DP2 488 .............eeeklvleleeevkeiLekllvehkvkeekivieealallkslgldleeekleke..eek.... 545
                                                    +++ l l+++e+v ++Le+llveh+++ee++ i e+++l++slgl++e e++ ++    +    
  gi|313124946|ref|YP_004035210.1| 536 dggvvvrptdtdpTDGILELDRTEDVTRTLEQLLVEHTQTEETLRIPEWRPLVRSLGLTEELEQTWDDlsA-Earew 611
                                       ***********998999*****************************************9998877555541.14678 PP

                          PolC_DP2 546 ....dalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavhvLfpigeaggkrrsvkeaakk......kgei 612
                                           +a+++vne+++++vre+aptrig+RmGRPeKs++R+++pavh+Lfpige gg++r+v eaa++      +ge+
  gi|313124946|ref|YP_004035210.1| 612 dggdNAVKAVNEVAPFDVRERAPTRIGNRMGRPEKSESRDLSPAVHTLFPIGEMGGSQRDVGEAARErnergaRGEV 688
                                       8999*************************************************************9558999999** PP

                          PolC_DP2 613 eveiarrkCkkCgketlearCeeCgekteeklvCkkceeeve.eek....cekcekeakavkkkkidlkellekale 684
                                       +v ++ r+C++Cg++t+++ C+eC+++te++++C++c++ ve +e+    ce+ce+e+++ +   id+ ++l++ale
  gi|313124946|ref|YP_004035210.1| 689 NVLVGDRQCPDCGTQTYKNVCPECETHTEPHYECEECGTVVEpDESgrvfCERCEREVESPDWYAIDIGAELRAALE 765
                                       ***************************************9995665999**************************** PP

                          PolC_DP2 685 klgereekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrelGYt 761
                                       +lgere+++  lkgvkglts++k+pEp+eKg+lRakh+vs fkdgtvRyDmtdlp+t++rp+e++v+++++relGY+
  gi|313124946|ref|YP_004035210.1| 766 NLGERESSYPILKGVKGLTSSNKTPEPIEKGVLRAKHGVSSFKDGTVRYDMTDLPVTSVRPAELDVTADHFRELGYE 842
                                       ***************************************************************************** PP

                          PolC_DP2 762 eDieGkplesedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnvekkedLiGklviglaPHtsagv 838
                                       +Di+G+pl+ +dq+velkvqDivls++aae++lk+a+fvDdlL+++ygle+fY+v++++dL+G+lv+g+aPHtsa+v
  gi|313124946|ref|YP_004035210.1| 843 TDINGEPLQFDDQLVELKVQDIVLSDGAAEHMLKTADFVDDLLTEFYGLEPFYEVSERDDLVGELVFGMAPHTSAAV 919
                                       ***************************************************************************** PP

                          PolC_DP2 839 lgRiiGftkasvgyahPyfHaakRRn 864
                                       +gR++Gft+a+vgyahPyfHaakRRn
  gi|313124946|ref|YP_004035210.1| 920 VGRVVGFTSAAVGYAHPYFHAAKRRN 945
                                       *************************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.1
                          PolC_DP2  617 arrkCkkCgket....learCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidl 675 
                                        ++++C +Cg++     l+  C+eCg +++ +++  ++++ ++++     e + + ++k+++++
  gi|313124946|ref|YP_004035210.1| 1110 QETRCLDCGEKYrrmpLTGDCRECGGRVNLTVHQGSVNKYMDTAIQVAEEFDCRPYTKQRLEV 1172
                                        567788888754111145578888888888666666666554443333444444555555543 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3  12.7   8.9e-05      0.27       1      48 [.     697     742 ..     688     743 .. 0.82
   2 !   12.8   6.4   3.1e-05     0.091       1      39 [.     709     747 ..     709     753 .. 0.82
   3 !    6.7   0.3    0.0024       7.2      11      39 ..    1110    1138 ..    1104    1142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.9e-05
                               DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpear...fCpeC 48 
                                       Cp Cg++    +++C+eC t+ ++   ++ C +Cg+ v+p+++   fC  C
  gi|313124946|ref|YP_004035210.1| 697 CPDCGTQ--TYKNVCPECETHTEP---HYECEECGTVVEPDESgrvFCERC 742
                                       8999988..456789999999886...999999999999987644479999 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.1e-05
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa.edrCpsCgekvd 39 
                                       Cp+C++ ++p+ + C+eCgt +++ ++   +C +C+++v+
  gi|313124946|ref|YP_004035210.1| 709 CPECETHTEPHYE-CEECGTVVEPDESgRVFCERCEREVE 747
                                       9999999888765.99999999876668999999999976 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0024
                               DZR   11 darfCseCgtklkavaaedrCpsCgekvd 39  
                                        +   C +Cg+k ++++    C +Cg  v+
  gi|313124946|ref|YP_004035210.1| 1110 QETRCLDCGEKYRRMPLTGDCRECGGRVN 1138
                                        56679999999999999999999998776 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.5     0.011        34      62      95 ..     686     715 ..     674     717 .. 0.73
   2 ?    6.0   2.9    0.0038        11      67      95 ..     716     745 ..     714     750 .. 0.83
   3 ?    8.2   0.2   0.00084       2.5      69     102 ..    1110    1144 ..    1100    1150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                                       EEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  62 LeieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                        e++      +C +Cg+++ ++     Cp+C+++
  gi|313124946|ref|YP_004035210.1| 686 GEVNVLVGDRQCPDCGTQTYKN----VCPECETH 715
                                       56666667789*****877754....7****976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0038
                                       E--EEEETTTS-EEECHHH.HHS-TTTSSS CS
                              HypA  67 vpvkvrCreCgkefeleek.alrCpkCgsa 95 
                                       ++ +++C+eCg+ +e +e+ ++ C++C+++
  gi|313124946|ref|YP_004035210.1| 716 TEPHYECEECGTVVEPDESgRVFCERCERE 745
                                       567899*********98866788****874 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00084
                                        -EEEETTTS-EEECHHHHHS-TTTSSS.-EEEEES CS
                              HypA   69 vkvrCreCgkefeleekalrCpkCgsa.dveivsG 102 
                                         ++rC +Cg++++    +  C +Cg++ ++++ +G
  gi|313124946|ref|YP_004035210.1| 1110 QETRCLDCGEKYRRMPLTGDCRECGGRvNLTVHQG 1144
                                        5789********96644679****99767777777 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  13.1     0.022        66       3      56 ..     697     743 ..     689     750 .. 0.56
   2 ?    6.1   0.1    0.0036        11      14      47 ..    1109    1145 ..    1098    1151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.022
                                       -SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S---EEEETTEEEE--TTTT CS
                    zinc-ribbons_6   3 CpeCqqelekrgeqyhCeaCqedlkkealCpeCeqelevlkaCgavdyfCnkcn 56 
                                       Cp+C +++ k+     C +C+++ + +  C+eC+  +e  +  g    fC++c+
  gi|313124946|ref|YP_004035210.1| 697 CPDCGTQTYKNV----CPECETHTEPHYECEECGTVVEPDES-GR--VFCERCE 743
                                       777776655544....56666666656666666555544332.22..2444443 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0036
                                        SSEEE-TTT--EEEEEEE...-SSS-S---EEEETTE CS
                    zinc-ribbons_6   14 geqyhCeaCqedlkkeal...CpeCeqelevlkaCga 47  
                                         ++++C  C e++++ +l   C eC+ +++     g+
  gi|313124946|ref|YP_004035210.1| 1109 RQETRCLDCGEKYRRMPLtgdCRECGGRVNLTVHQGS 1145
                                        47899*****988876653338888888777666555 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   4.4     0.001       3.1     136     173 ..     706     743 ..     693     753 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.001
                                       EE........-TTS-EE-TTSSB-E............. CS
                      tRNA-synt_1g 136 egtCPkckseeargdqceecgkkleptelinpksaisg 173
                                       +  CP+c++++    +ceecg+ +ep+e     +  ++
  gi|313124946|ref|YP_004035210.1| 706 KNVCPECETHTEPHYECEECGTVVEPDESGRVFCERCE 743
                                       678***********************997777776665 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   7.5    0.0026       7.6      22      61 ..     271     309 ..     267     325 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0026
                       Sigma70_ner  22 LrdiidGflDeeeeeeeeeeeedeeeeeee..edddeeeses 61 
                                       L+d+idG + +  ++ ++++++d+ ++ee+  edd++++  +
  gi|313124946|ref|YP_004035210.1| 271 LQDLIDGTIGK--DDGDKADADDDGDDEEAdaEDDEADDG-E 309
                                       89********4..333322222222222221133332111.1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.95u 0.38s 00:00:01.33 Elapsed: 00:00:00.60
# Mc/sec: 6019.67
//
Query:       gi|313124947|ref|YP_004035211.1|  [L=139]
Description: DNA-binding protein with pd1-like DNA-binding motif [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-19   69.1   0.0    4.1e-19   68.9   0.0    1.0  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   2.3e-23   4.1e-19       2     105 ..      11     121 ..      10     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 2.3e-23
                                       EEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT......EE-S-EEEEEEEEEEEE..TT. CS
                            DUF296   2 phvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee......kllgrfeilslsGtilp..dg. 68 
                                        ++++l++G d+ e+ieefa+ ++i++a++ +a+Gav+++   ++d+++      ++++++e+ +++G+i+   d+ 
  gi|313124947|ref|YP_004035211.1|  11 EFLVSLDNGADWREEIEEFAHLEDIESAWF-NAMGAVQDADvWFYDQDDqayrsvTFDEPLEVAACVGNIALldDEp 86 
                                       68899*************************.**********99999999999999999**************85449 PP

                                       .EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE- CS
                            DUF296  69 .lHlhvslagedgqvvgGhlaegplvaattvevvvaef 105
                                        +H h++l++++gq ++Ghl  + +v  +  ev++  f
  gi|313124947|ref|YP_004035211.1|  87 fAHTHAVLSRPSGQSLAGHLNAA-TV--FAGEVYIRAF 121
                                       9********************44.66..7777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 879.86
//
Query:       gi|313124948|ref|YP_004035212.1|  [L=64]
Description: hypothetical protein Hbor_01620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 511.89
//
Query:       gi|313124949|ref|YP_004035213.1|  [L=166]
Description: hypothetical protein Hbor_01630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1040.05
//
Query:       gi|313124950|ref|YP_004035214.1|  [L=281]
Description: cbs domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-33  112.6  14.2    1.5e-11   44.6   1.0    4.1  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.2   5.9e-12   1.1e-07       1      54 [.       3      61 ..       3      64 .. 0.87
   2 !   44.6   1.0   8.2e-16   1.5e-11       8      56 ..      73     119 ..      67     120 .. 0.92
   3 !   12.5   0.1   8.3e-06      0.15       2      53 ..     130     181 ..     129     184 .. 0.85
   4 !   31.0   0.2   1.4e-11   2.5e-07       1      55 [.     228     281 .]     228     281 .] 0.92

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5.9e-12
                                      HHHHSBS..SCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTB.EEEEEEHHHHHHH CS
                               CBS  1 Vgdimtr..dvvtvppdttleealelmrekgvsrlPVV..dedgk.lvGivtlrDllra 54
                                      V+d mt+  dvvtv    t  ++le + e+g+s++PVV   +dg+ + Givt+ Dl++ 
  gi|313124950|ref|YP_004035214.1|  3 VADAMTPreDVVTVELPGTRDDVLEYLQERGFSSVPVVkrTDDGEaYRGIVTRQDLIEH 61
                                      567766666******************9999*********66775499********985 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 8.2e-16
                                       SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       dv+t + dt++e+++ +m+ek+ +r+PVV  dg l Gi+t +D++ra++
  gi|313124950|ref|YP_004035214.1|  73 DVPTTTADTSVEDVAHMMVEKNARRVPVV--DGTLEGIITVTDVIRAIA 119
                                       789*******************99*****..688*************97 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 8.3e-06
                                       HHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEE.EETTTBEEEEEEHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealel.mrekgvsrlPV.VdedgklvGivtlrDllr 53 
                                       +d+ trdv t +++++l  a ++ +  ++v    V +de g   Gi+t+ D+++
  gi|313124950|ref|YP_004035214.1| 130 ADVATRDVNTTYEEAPLTVAEREiF-YANVPYA-VaLDETGTMSGILTEVDIID 181
                                       6999*****************9978.4448666.767****888********97 PP

  == domain 4  score: 31.0 bits;  conditional E-value: 1.4e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+ +m++d+vtv+  t+  ea++ m+ +++ ++P V +d +l Giv + Dll+al
  gi|313124950|ref|YP_004035214.1| 228 VSTFMSTDLVTVSKRTSAVEAAQAMITNDIEQIPLVGGD-QLTGIVRDVDLLEAL 281
                                       6789********************99888*******555.5***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1650.59
//
Query:       gi|313124951|ref|YP_004035215.1|  [L=596]
Description: glycyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-21   76.0   0.1    5.6e-21   74.5   0.0    1.8  2  HGTP_anticodon  Anticodon binding domain
    1.1e-07   32.0   0.0    1.3e-06   28.6   0.0    2.1  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
     0.0053   16.1   0.3       0.38   10.2   0.0    2.4  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
       0.26   10.8   1.7        2.5    7.7   1.7    2.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.27   11.2   0.3         12    5.9   0.1    2.4  2  zinc_ribbon_4   zinc-ribbon domain
       0.48   10.8   2.0       0.57   10.5   0.3    2.0  2  FRD2            Bacteriophage FRD2 protein
       0.55   10.0   2.8        0.6    9.9   0.2    2.2  2  zinc_ribbon_2   zinc-ribbon domain
        3.7    7.4   9.4          9    6.1   3.0    3.1  3  DUF348          G5-linked-Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.9   8.8e+03      78      93 ..     113     128 ..     109     129 .. 0.79
   2 !   74.5   0.0   2.5e-24   5.6e-21       1      91 [.     481     573 ..     481     575 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                       + e++sl+e++e++ +
  gi|313124951|ref|YP_004035215.1| 113 DAETLSLEEAAEEIAA 128
                                       5689999999999865 PP

  == domain 2  score: 74.5 bits;  conditional E-value: 2.5e-24
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHH...HTEEEEEET CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekele...kgtvtvrdr 74 
                                       +v v pl ++  el ++a+++ ++Lraag++v++d +++sig+++r+ d++g+pf+++v+ + le   + tvtvr+r
  gi|313124951|ref|YP_004035215.1| 481 DVGVFPLVSNVPELVDLADEIVDDLRAAGLSVVYD-DSGSIGRRYRRQDEVGTPFCITVDRDGLEsdgETTVTVRER 556
                                       689***************************99997.79**************************966679******* PP

                                       TTCEEEEEETTHHHHHH CS
                    HGTP_anticodon  75 dtreqervsldelvekl 91 
                                       d+++q+rv+++ l+++l
  gi|313124951|ref|YP_004035215.1| 557 DSGRQIRVPVSALADEL 573
                                       *************9986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   5.6e-10   1.3e-06      12      75 ..     165     229 ..     160     252 .. 0.78
   2 ?    1.1   0.0      0.15   3.3e+02     145     177 ..     423     455 ..     276     457 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.6e-10
                                       EE-SSSHHHH.HHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGG CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  12 iLkPtneetf.velirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeas 75 
                                       +L+P+  +++ ve  r +    +rLP+ ++q+++ yR+E s  + ++R reF+q + + f  +++
  gi|313124951|ref|YP_004035215.1| 165 YLRPETAQGIfVEFPRIKEYARNRLPFGVTQVGRAYRNEISPRKSIVRTREFTQAELEQFIDPER 229
                                       788888887514554433244466****************9777****************99653 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.15
                                       TTEEEECTTSSEEEEEEEEEEEEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 145 lgatvldennreksvimicaaigveRllsaile 177
                                       + ++    n+++ +++++  ++gv R++  +l+
  gi|313124951|ref|YP_004035215.1| 423 FAVEEQTINGEHITPHVVEPSFGVDRTVYTLLA 455
                                       444444457888999999999999999988776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.022        50       3      11 ..      90      99 ..      88     103 .. 0.77
   2 !   10.2   0.0   0.00017      0.38      14      26 .]     128     140 ..     124     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.022
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      v+CP+C + +
  gi|313124951|ref|YP_004035215.1| 90 VECPECAEsH 99
                                      89****8855 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                       zf-ribbon_3  14 sddnvCpyCGtkl 26 
                                       + d vCp+CG++l
  gi|313124951|ref|YP_004035215.1| 128 ALDLVCPNCGAEL 140
                                       5688999999876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.7    0.0011       2.5      13      34 ..     124     145 ..      90     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                                       EETSTTCEEESSSSBEEEECCC CS
                      TF_Zn_Ribbon  13 eDpergelvCtdCGlVlednsi 34 
                                       e+ +  +lvC++CG+ l  +s+
  gi|313124951|ref|YP_004035215.1| 124 EEIAALDLVCPNCGAELAGQSV 145
                                       556778999****998766655 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0053        12       1      11 [.      88      98 ..      88     104 .. 0.86
   2 ?    2.7   0.0     0.053   1.2e+02       4      10 ..     132     138 ..     130     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0053
                     zinc_ribbon_4  1 MkitCpsCkak 11
                                      M ++Cp+C   
  gi|313124951|ref|YP_004035215.1| 88 MLVECPECAES 98
                                      9*******865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.053
                     zinc_ribbon_4   4 tCpsCka 10 
                                       +Cp+C+a
  gi|313124951|ref|YP_004035215.1| 132 VCPNCGA 138
                                       7999987 PP

>> FRD2  Bacteriophage FRD2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1         7   1.6e+04      21      63 ..      82     124 ..      79     132 .. 0.60
   2 ?   10.5   0.3   0.00026      0.57      35      73 ..     330     368 ..     309     377 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 7
                              FRD2  21 ldgfdyvteiicangeiynddgmgddyfelseeefycfreyke 63 
                                       ld fd +       +e +  d + +d  +l + e   + e  e
  gi|313124951|ref|YP_004035215.1|  82 LDTFDDMLVECPECAESHRADHLIEDNSDLEDAETLSLEEAAE 124
                                       5666654433334456666777777777777777666666555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                              FRD2  35 geiynddgmgddyfelseeefycfreykeptseedevkd 73 
                                       g  y  d     + e see++ +fr+y ep + e  v d
  gi|313124951|ref|YP_004035215.1| 330 GFSYRSDYDLSKHAEYSEEDYTVFRQYDEPKTVERAVVD 368
                                       55667777677889****************999888876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.71   1.6e+03       2       5 ..      92      95 ..      91     101 .. 0.69
   2 ?    9.9   0.2   0.00027       0.6       2       9 ..     133     140 ..     132     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.71
                     zinc_ribbon_2  2 CpnC 5 
                                      Cp+C
  gi|313124951|ref|YP_004035215.1| 92 CPEC 95
                                      6666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00027
                     zinc_ribbon_2   2 CpnCGael 9  
                                       CpnCGael
  gi|313124951|ref|YP_004035215.1| 133 CPNCGAEL 140
                                       89999887 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.02        44      15      26 ..     381     392 ..     377     394 .. 0.87
   2 ?    6.1   3.0     0.004         9       1      14 [.     405     418 ..     405     421 .. 0.95
   3 ?   -3.5   0.1       4.1   9.2e+03       6      13 ..     546     554 ..     545     554 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.02
                                       --SSHHHHHHHT CS
                            DUF348  15 aadTVgdlLeea 26 
                                       aa++V+d+Le +
  gi|313124951|ref|YP_004035215.1| 381 AAGDVKDALERL 392
                                       89*******965 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.004
                                       EEEEETTEEEEE-- CS
                            DUF348   1 VtltvDGktvtvrT 14 
                                       Vt+ vDG+t tv T
  gi|313124951|ref|YP_004035215.1| 405 VTVEVDGETHTVET 418
                                       9***********98 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.1
                                       TTE.EEEE- CS
                            DUF348   6 DGk.tvtvr 13 
                                       DG+ tvtvr
  gi|313124951|ref|YP_004035215.1| 546 DGEtTVTVR 554
                                       899677775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3646.32
//
Query:       gi|313124952|ref|YP_004035216.1|  [L=208]
Description: dolichol kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.16   12.2   7.6       0.27   11.5   7.6    1.4  1  EI24       Etoposide-induced protein 2.4 (EI24)


Domain annotation for each model (and alignments):
>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   7.6   1.5e-05      0.27      24     121 ..      44     159 ..      12     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHHH..........-...................TTHHHHHHHHHHHHHHHHHH.HHHHHHHHHHH CS
                              EI24  24 llnlllfllllvlll..........w...................vllasllvllllllplwlfp.lvalllaapfy 70 
                                       +l++++ +      l          w                     + s  ++ l++ p+  +p ++ l+l+ p+ 
  gi|313124952|ref|YP_004035216.1|  44 FLTVVVAV------LeflrlrvgldWaiydeltrsyeqtnlagyaLYIFSMTAVVLVFEPYVAVPgMLMLALGDPVS 114
                                       11111111......13446677778666677777777776666554455677777777778888899********97 PP

                                       HHHHHHHHH.H.HCCTTSHHHHHHHHHHHHHHHHHHHHHHHTTHHH....HH CS
                              EI24  71 gllaekvekrh.lglvkslaeslkslllllllllvllplliPvvglilspll 121
                                       gll +  e+ + +       +  + +++++++l+v+ p+l+Pv g+i ++++
  gi|313124952|ref|YP_004035216.1| 115 GLLGRTREAGEpK-------RLGTLAAMFIVCLAVSVPFLLPVAGTIGVIAA 159
                                       7777777652111.......334677888888889999977****9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1393.13
//
Query:       gi|313124953|ref|YP_004035217.1|  [L=161]
Description: potassium/proton antiporter regulatory subunit, cpa2 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-21   75.5   0.1    6.9e-21   73.9   0.0    1.8  2  TrkA_C    TrkA-C domain
  ------ inclusion threshold ------
      0.072   12.9   0.1       0.13   12.1   0.1    1.5  1  KH_1      KH domain


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.23     2e+03      45      65 ..      17      37 ..      14      41 .. 0.67
   2 !   73.9   0.0   7.7e-25   6.9e-21       2      65 ..      89     154 ..      88     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.23
                                      -B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C 45 tvLeeGDvllvvgspsdlael 65
                                       +L  G +l++v++ s+ +e+
  gi|313124953|ref|YP_004035217.1| 17 VELGDGGRLIIVTHNSGKREV 37
                                      566677788888877766555 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 7.7e-25
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlael 65 
                                        +v+v+++sp++G+tl+e+nlr+  g+ v+ai R+ g+ ++p+gdt++e+GD+l+++g++++ +++
  gi|313124953|ref|YP_004035217.1|  89 EWVEVGPDSPIAGQTLGESNLRQTtGASVIAIERDdGVTVSPGGDTTIEAGDTLVIIGPRQACRDA 154
                                       689*****************************9999************************998775 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.5e-05      0.13      26      62 ..     110     156 ..     107     160 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                                       HHHHT-EEEEESSTT..............T.-EEEEEESHHHHHHHHH CS
                              KH_1  26 reetgakIkvpksedeg...........sderevtisGspeavekAke 62 
                                       r+ tga++  + ++d+g           +  ++++i+G+++a+ +A+ 
  gi|313124953|ref|YP_004035217.1| 110 RQTTGASVIAI-ERDDGvtvspggdttiEAGDTLVIIGPRQACRDALS 156
                                       55445554444.3333334555555569999999999****9*99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1070.47
//
Query:       gi|313124954|ref|YP_004035218.1|  [L=378]
Description: potassium/proton antiporter membrane subunit, cpa2 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-48  165.1  43.0    2.5e-48  164.8  43.0    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8  43.0   1.4e-52   2.5e-48       5     372 ..      12     374 ..       9     378 .] 0.90

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 1.4e-52
                                       HHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS..........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTH CS
                    Na_H_Exchanger   5 illallvgllarrlklpeivgliiaGlllGpsglg.....liepseedlevlselglilllFlaGleldlrelrknl 76 
                                       +++++++g++a r++l++i++++i G+l Gp++ g      +e++ e++++++e+g++lllF +Gle++l++l++ +
  gi|313124954|ref|YP_004035218.1|  12 FVVVAVTGAIALRVGLSVIPLYVIGGVLAGPFVAGrlglpYVENG-EVVTLFAEVGIVLLLFFLGLEFSLDRLLESR 87 
                                       4556677777*************************9998879998.******************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHH CS
                    Na_H_Exchanger  77 ksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDa 153
                                         i+  +++ +++++ + G+ ++l  +lg++++e+ll+g+i+ +++ +++++ l ++g +    +  llg++v++D+
  gi|313124954|ref|YP_004035218.1|  88 TRITRSGVADIAVNLPI-GIGIGL--LLGWSVVESLLLGGIVYISSSAIITKSLIDLGWIADPEAEPLLGTLVFEDL 161
                                       *****************.999997..6889*********************************************** PP

                                       HCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.CTHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 154 vavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft.dddrelevllvlllallaall 229
                                       +  v+lav+ +l+     g+ ++++++ +++v+++++ +l +++ +  rl+ r++    +e +vl +l+++  +a++
  gi|313124954|ref|YP_004035218.1| 162 FIAVYLAVVTSLV----LGGDGIGSIGRSLAVAFGFLGILLVAVQYGNRLFARVLdVSGQEAFVLRTLAVVVPIAGA 234
                                       ************8....7777788888888888888888888888888888888876789999************** PP

                                       HHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTH CS
                    Na_H_Exchanger 230 aellgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillg 306
                                       a +lgvs +++af++G+ ++++++++k+++ l ++r ++f  +fF+ +G+ +d++++         ++l++v+ + +
  gi|313124954|ref|YP_004035218.1| 235 ALALGVSEAVAAFFVGMGFATSGHREKIEHLLTPVR-DVFGAVFFFWIGVGTDPTLI---GAAAVPLVLAVVLTTPA 307
                                       ************************************.9*******************...6777777777777879* PP

                                       HHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHH.XHHHHTT.SSTTTCSTSXHHHHHH CS
                    Na_H_Exchanger 307 rilavflllrllglslrealiigfgglqrgavalalaalgpal.gllarel.yallivvvlftvlvqG 372
                                       ++++++l  r++ ls r +l +g+g+++rg+++l++aal+ +    + re+  a+++++vl++    G
  gi|313124954|ref|YP_004035218.1| 308 KVVSGYLGGRVYDLSKRRSLRVGVGMVPRGEFSLVIAALAASGtTPIMREViPAFAVGYVLVMSA-IG 374
                                       ***********************************999998876555556634455555555444.23 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2518.57
//
Query:       gi|313124955|ref|YP_004035219.1|  [L=631]
Description: hypothetical protein Hbor_01690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.12   12.6   0.0         22    5.3   0.0    3.2  3  CDI        Cyclin-dependent kinase inhibitor


Domain annotation for each model (and alignments):
>> CDI  Cyclin-dependent kinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0013        22      11      35 ..     448     473 ..     447     475 .. 0.81
   2 ?    2.8   0.0    0.0078   1.4e+02      26      35 ..     551     560 ..     529     562 .. 0.72
   3 ?   -0.9   0.0      0.11     2e+03      22      36 ..     591     605 ..     582     610 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0013
                               CDI  11 leeffqralerqqeease.kWNFDFe 35 
                                       +e+++  +++ +++e s+ k+++DF+
  gi|313124955|ref|YP_004035219.1| 448 IEREVPDEERLTRDEISQaKYGYDFA 473
                                       5778888888888887777******7 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0078
                               CDI  26 asekWNFDFe 35 
                                        + k+++DF+
  gi|313124955|ref|YP_004035219.1| 551 SQAKYGYDFA 560
                                       456******7 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.11
                               CDI  22 qqeeasekWNFDFen 36 
                                        +e a+++++ DF n
  gi|313124955|ref|YP_004035219.1| 591 REEIARQRYGADFDN 605
                                       567789999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1775  (0.0990016); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                       169  (0.00942607); expected 17.9 (0.001)
Passed Fwd filter:                        85  (0.00474092); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.64u 0.32s 00:00:01.96 Elapsed: 00:00:00.58
# Mc/sec: 3259.48
//
Query:       gi|313124956|ref|YP_004035220.1|  [L=411]
Description: argininosuccinate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-142  475.6   0.0   1.7e-142  475.3   0.0    1.0  1  Arginosuc_synth  Arginosuccinate synthase
    4.9e-05   22.9   0.0    9.2e-05   22.0   0.0    1.4  1  QueC             Queuosine biosynthesis protein QueC
     0.0025   17.0   0.0     0.0038   16.4   0.0    1.2  1  NAD_synthase     NAD synthase
     0.0032   17.2   0.3     0.0054   16.4   0.3    1.7  1  Asn_synthase     Asparagine synthase
     0.0059   15.5   0.0     0.0088   14.9   0.0    1.3  1  tRNA_Me_trans    tRNA methyl transferase
  ------ inclusion threshold ------
       0.05   12.6   0.1       0.19   10.7   0.0    1.9  2  DUF2156          Uncharacterised conserved protein (DUF2156)


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.3   0.0  5.6e-146  1.7e-142       2     387 ..       6     386 ..       5     387 .. 0.98

  Alignments for each domain:
  == domain 1  score: 475.3 bits;  conditional E-value: 5.6e-146
                   Arginosuc_synth   2 LaysGGlDtsviikllkeklg.eeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanal 77 
                                       La+sGGlDt+v+++ll+e++g +ev+ v+vdvGq+e +++e+ke a + g  +  vvDak+ef+ + +f +++ana+
  gi|313124956|ref|YP_004035220.1|   6 LAFSGGLDTTVCVSLLQEEYGyDEVVGVTVDVGQPESEFEEAKETADAHGL-DIHVVDAKDEFA-ELCFDSVRANAT 80 
                                       9********************899***********************9998.999*********.9*********** PP

                   Arginosuc_synth  78 YedrYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieya 154
                                       Y++ Y+lgtalaRP+ia++++eva++eg++a+ahGctGkGnDq+Rfe++ r+ +  l+viaPvRe+ ltRe+e +ya
  gi|313124956|ref|YP_004035220.1|  81 YQG-YPLGTALARPVIAEAILEVAQEEGCDALAHGCTGKGNDQLRFEAVWRASD--LDVIAPVREMGLTREWEKQYA 154
                                       ***.*********************************************99987..********************* PP

                   Arginosuc_synth 155 kekgipvevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeels 231
                                       +ek++pv++ ++  +siD nl++rs+e+g Le+p  +p+ediye+t++p +++   e +ei fe+G Pvaldgee++
  gi|313124956|ref|YP_004035220.1| 155 DEKNLPVQAGNDGVWSIDTNLWSRSVEGGDLEKPGHVPSEDIYEWTEQPGSET---ECIEITFEEGYPVALDGEEME 228
                                       ************************************************98876...9******************** PP

                   Arginosuc_synth 232 vlelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYk 308
                                       ++elie+lne+ag+ GvGR+D++edR++glk Re+Ye+paa++L++ah+ le l+l+++++ fk++v++++a+  Y+
  gi|313124956|ref|YP_004035220.1| 229 PVELIETLNELAGQYGVGRTDMMEDRMLGLKVRENYEHPAATTLLNAHESLEGLVLTKDERDFKTTVDNEWAQKGYE 305
                                       ***************************************************************************** PP

                   Arginosuc_synth 309 GlwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydee..defdqkeaeGfikihglq 383
                                       Gl+  Pl++ald fie+tq +vtGtv +k+  G+++ +gRese++ Y+e  as+++e  d + q++a+G++k+hg+q
  gi|313124956|ref|YP_004035220.1| 306 GLVEAPLMAALDGFIEQTQTKVTGTVTIKFEGGQARPVGRESEYAAYSESAASFNTEtvDGITQEDATGVAKYHGFQ 382
                                       ******************************************************976336899************** PP

                   Arginosuc_synth 384 akly 387
                                       ++++
  gi|313124956|ref|YP_004035220.1| 383 TRIA 386
                                       9986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.1e-08   9.2e-05       5      62 ..       7      64 ..       3      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.1e-08
                                      E--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC  5 llSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildld 62
                                       +SGGlD t+++ l ++e+  +ev  +t+d gq  ++e e ak+ a+++g+ + +++d +
  gi|313124956|ref|YP_004035220.1|  7 AFSGGLDTTVCVSLLQEEYgyDEVVGVTVDVGQP-ESEFEEAKETADAHGL-DIHVVDAK 64
                                      69************99997669**********97.5799***********9.88888865 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-06    0.0038      20      85 ..       3      67 ..       1      82 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-06
                                      EEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHH CS
                      NAD_synthase 20 gvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpiv 85
                                      +v l  SGG+D ++   l ++  g ++v+++ + ++ ++e++ e+a++ a+  g++++++d k+  
  gi|313124956|ref|YP_004035220.1|  3 SVALAFSGGLDTTVCVSLLQEEYGYDEVVGVTV-DVGQPESEFEEAKETADAHGLDIHVVDAKDEF 67
                                      788999***************************.9999********************99998765 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   1.8e-06    0.0054      20      87 ..       4      70 ..       2     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-06
                      Asn_synthase 20 vGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgtehtelvlteeellda 87
                                      v++ +SGGlD ++ ++l++++    ++  ++++   +  +e + ake+a+++g++  ++v  ++e++++
  gi|313124956|ref|YP_004035220.1|  4 VALAFSGGLDTTVCVSLLQEEYGyDEVVGVTVDV-GQPESEFEEAKETADAHGLDI-HVVDAKDEFAEL 70
                                      78889***************99988999999999.8999****************4.455555566665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.9e-06    0.0088       2      83 ..       3      76 ..       2     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-06
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78
                                       v+ a+SgG D +v + ll+e++   ev+gv++ + +           e+++++a++ a+  g+ ++vvd ++e+ e  
  gi|313124956|ref|YP_004035220.1|  3 SVALAFSGGLDTTVCVSLLQEEYgyDEVVGVTVDVGQP----------ESEFEEAKETADAHGLDIHVVDAKDEFAELC 71
                                      5899****************997546899999876655..........4567789999999999999999999999999 PP

                     tRNA_Me_trans 79 feefl 83
                                      f+++ 
  gi|313124956|ref|YP_004035220.1| 72 FDSVR 76
                                      98765 PP

>> DUF2156  Uncharacterised conserved protein (DUF2156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.084   2.5e+02      60      87 ..      44      71 ..      36      78 .. 0.86
   2 ?   10.7   0.0   6.4e-05      0.19      26      89 ..      62     125 ..      57     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.084
                                      HHHHHHHHHHCTSEEEEEEE-HHHHHHH CS
                           DUF2156 60 ieeflelaaehgwrpafygvseelaell 87
                                      +ee +e+a++hg+++ ++ +++e+ael 
  gi|313124956|ref|YP_004035220.1| 44 FEEAKETADAHGLDIHVVDAKDEFAELC 71
                                      68899*******************9875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.4e-05
                                       EECCTTEEEEEEEECTCEEEECS-EE.CCGHHHHHHHHHHHHHHCTSEEEEEEE-HHHHHHHHH CS
                           DUF2156  26 fspsgdalvayrvkggvalalgdPvGdpeawpeaieeflelaaehgwrpafygvseelaellae 89 
                                        ++++ a +++  +  +a++ g P+G+  a+p ++e++le a+e+g +++  g++ ++ ++l+ 
  gi|313124956|ref|YP_004035220.1|  62 DAKDEFAELCFDSVRANATYQGYPLGTALARPVIAEAILEVAQEEGCDALAHGCTGKGNDQLRF 125
                                       5566667777888889999**************************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2493.53
//
Query:       gi|313124957|ref|YP_004035221.1|  [L=489]
Description: argininosuccinate lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-57  193.4   0.5    1.7e-56  191.9   0.1    1.8  2  Lyase_1        Lyase
    1.1e-15   58.1   2.2    1.1e-15   58.1   2.2    2.7  2  ASL_C2         Argininosuccinate lyase C-terminal
  ------ inclusion threshold ------
       0.25   11.9   1.4        3.6    8.2   0.3    3.1  4  Syntaxin-6_N   Syntaxin 6, N-terminal
       0.36   10.4   0.0       0.36   10.4   0.0    4.1  4  Phage_fiber_2  Phage tail fibre repeat


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.9   0.1   3.9e-60   1.7e-56      40     308 ..      50     295 ..      23     298 .. 0.91
   2 ?   -0.9   0.0      0.19   8.7e+02      35      85 ..     368     412 ..     342     478 .. 0.68

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 3.9e-60
                                       HHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHH CS
                           Lyase_1  40 akanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekvepndkvhtgqSsnDqvp 116
                                       ++ ++    +aa+i++ald+v +eg++       +  e+ + a++ ++ e +g          +k ht++S+nD v+
  gi|313124957|ref|YP_004035221.1|  50 EEQEIVESDVAAEILAALDDVESEGHAA-----LPEGEDVHEAIETAVVEQVG-------PDGGKMHTARSRNDEVA 114
                                       33333336679************99888.....6899****************.......899************** PP

                                       HHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Lyase_1 117 TalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrl 193
                                       T +r+ l++ l + +++    L++al++ a+++ ++v++G+Thlq+A+P+t ++ l +y +a+ rd  rl ++++r+
  gi|313124957|ref|YP_004035221.1| 115 TCIRYRLREDLLDAIEA-TLALREALVDAAEAEVETVMPGYTHLQPAQPTTVAHYLLSYEAAFARDTARLLDAYDRT 190
                                       ***********886655.558******************************************************** PP

                                       TCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           Lyase_1 194 lvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrlls 270
                                       ++++lg+++ +gt++++d+e   + a+ l+ ++g   + +ns++a s+rD+++e ++al++ at Ls +aeDl ++s
  gi|313124957|ref|YP_004035221.1| 191 NQSPLGAAAFAGTPFDIDRE---RTAELLG-FDG---VLRNSMDASSARDFLLESVSALATHATTLSGLAEDLVIFS 260
                                       ********************...99**9*9.***...**************************************** PP

                                       STTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHH CS
                           Lyase_1 271 sgeaglvelslaesepGSSiMPgKvNPvqlElltgvag 308
                                       +   g+vels+ + +  SSiMP+KvNP++lEl++  ag
  gi|313124957|ref|YP_004035221.1| 261 N--KGFVELSDDYAS-TSSIMPQKVNPDTLELVRATAG 295
                                       9..9*********99.9****************99887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.19
                                       HHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHH CS
                           Lyase_1  35 lkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnm 85 
                                       ++ a+a+a+++  + a+++++a+ e +e g  d    l++ + ++   + +
  gi|313124957|ref|YP_004035221.1| 368 VADALAMAGLPF-RTAHEVVAAAAERAE-GTPD----LATLDASAEEVLDA 412
                                       567888888888.777777777777777.5555....44444444444444 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       1.5   6.7e+03      42      63 ..      59      89 ..      43      93 .. 0.46
   2 !   58.1   2.2   2.5e-19   1.1e-15       1      69 []     362     434 ..     362     434 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                                      --HHHHHHH-........TT--.GGGGGGSS CS
                            ASL_C2 42 ltleelkeis........plle.edveeaLd 63
                                      +  e l++++         l e edv+ea++
  gi|313124957|ref|YP_004035221.1| 59 VAAEILAALDdveseghaALPEgEDVHEAIE 89
                                      3333333332222222224455567777665 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 2.5e-19
                                       STTHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-....TT--.GGGGGGSSHHHHTT CS
                            ASL_C2   1 FstATdlADyLvrkGlpFReAHeivgravrlaeekgkeleeltleelkeis....plle.edveeaLdpeasVa 69 
                                       FstAT++AD+L++ GlpFR+AHe+v++a+++ae +  +l++l+ ++ + ++    + ++ +dv++ Ldp +sV+
  gi|313124957|ref|YP_004035221.1| 362 FSTATGVADALAMAGLPFRTAHEVVAAAAERAEGTP-DLATLDASAEEVLDaslfEYVSrADVQQTLDPTHSVE 434
                                       9******************************75542.35544444444333334455999************96 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.84   3.8e+03      78      95 ..     130     147 ..      57     150 .. 0.59
   2 ?    0.4   0.0      0.22     1e+03      14      63 ..     305     357 ..     297     363 .. 0.81
   3 ?   -3.1   0.0       2.7   1.2e+04       2      19 ..     378     395 ..     378     398 .. 0.88
   4 ?    8.2   0.3   0.00081       3.6       7      68 ..     420     487 ..     416     489 .] 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.84
                      Syntaxin-6_N  78 ekelsrrrafveevreev 95 
                                       e++l+ r+a+v++++ ev
  gi|313124957|ref|YP_004035221.1| 130 EATLALREALVDAAEAEV 147
                                       344555555555555555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.22
                      Syntaxin-6_N  14 lnkaeslyrrwe.rlledtss..stseeldetrteLrkalrsiewdledLeet 63 
                                       l ++++l r ++ +l++ t++  +  ++++e++  +  a++s++w  e Le +
  gi|313124957|ref|YP_004035221.1| 305 LTTLKGLPRAYNrDLQRATPHawDAVDSVSEATAVVAGAVSSASWPEETLESA 357
                                       56788888899647777777656589999999999999999999999999876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.7
                      Syntaxin-6_N   2 PFfevkeeVqkslnkaes 19 
                                       PF  + e V  ++++ae+
  gi|313124957|ref|YP_004035221.1| 378 PFRTAHEVVAAAAERAEG 395
                                       899999999999999987 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.00081
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtsss.........tseeldetrteLrkalrsiewdledLeetvrive 68 
                                       +++Vq++l+ ++s+ +r +     ++++          + el+++rteL++  + +e   e L   v+++ 
  gi|313124957|ref|YP_004035221.1| 420 RADVQQTLDPTHSVESRDST---GGPAPaavtaqldeATVELNDHRTELNTRTDALESATEKLAAEVAVIT 487
                                       67777777777777777643...222213344556668899999999999999999999999999998875 PP

>> Phage_fiber_2  Phage tail fibre repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   8.1e-05      0.36       3      19 ..     260     276 ..     258     278 .. 0.91
   2 ?   -2.0   1.4      0.59   2.7e+03      12      24 ..     328     340 ..     328     347 .. 0.75
   3 ?    2.9   0.1     0.018        78      13      36 ..     432     455 ..     430     460 .. 0.88
   4 ?   -1.2   0.3      0.35   1.6e+03      10      23 ..     468     481 ..     465     481 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.1e-05
                     Phage_fiber_2   3 tqkGivqLssatdStse 19 
                                       ++kG+v Ls+ + Sts+
  gi|313124957|ref|YP_004035221.1| 260 SNKGFVELSDDYASTSS 276
                                       68*************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.59
                     Phage_fiber_2  12 satdStsetlAAT 24 
                                       +a+dS se +A  
  gi|313124957|ref|YP_004035221.1| 328 DAVDSVSEATAVV 340
                                       89******99955 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.018
                     Phage_fiber_2  13 atdStsetlAATpkAVKtayDkAn 36 
                                       ++ S ++t  + p AV ++ D+A+
  gi|313124957|ref|YP_004035221.1| 432 SVESRDSTGGPAPAAVTAQLDEAT 455
                                       7899999****************8 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.35
                     Phage_fiber_2  10 LssatdStsetlAA 23 
                                       +++a  S  e+lAA
  gi|313124957|ref|YP_004035221.1| 468 RTDALESATEKLAA 481
                                       68999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3197.48
//
Query:       gi|313124958|ref|YP_004035222.1|  [L=59]
Description: lysine biosynthesis protein lysw [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       173  (0.00964917); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 389.06
//
Query:       gi|313124959|ref|YP_004035223.1|  [L=291]
Description: l-2-aminoadipate n-acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-26   91.7   0.0    5.4e-26   91.3   0.0    1.1  1  RimK         RimK-like ATP-grasp domain
    3.7e-09   36.8   0.0    5.7e-09   36.2   0.0    1.2  1  ATP-grasp_3  ATP-grasp domain
    4.3e-09   36.0   0.0    7.7e-09   35.2   0.0    1.4  1  GSH-S_ATP    Prokaryotic glutathione synthetase, ATP-grasp do
    7.4e-07   28.9   0.1    2.5e-06   27.2   0.0    1.8  2  ATP-grasp    ATP-grasp domain
    7.1e-06   25.7   0.0    1.9e-05   24.3   0.0    1.8  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
    0.00025   20.6   0.0    0.00079   18.9   0.0    2.0  2  ATP-grasp_5  ATP-grasp domain
     0.0025   17.1   0.0      0.038   13.2   0.0    2.2  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0   2.1e-29   5.4e-26       2     188 .]      88     276 ..      87     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 2.1e-29
                                       H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH......G CS
                              RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea......l 72 
                                        dK+k    L +a++++pnt++a   + a k i+k+  + P vvK v gs G  +     + +++ +le        
  gi|313124959|ref|YP_004035223.1|  88 ADKVKNSLALEQAGVPTPNTEVAFTTDSAMKSIKKF--GYPCVVKPVVGSWGRLMAKIDSPAAAEAILEHkatlghY 162
                                       599999999*************************98..6**************999999999******987777663 PP

                                       GG--.EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEE CS
                              RimK  73 keai.lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaG 148
                                       ++++  vqe++++  ++diRvl vd+e +aa+ r s    + +n  +G+ ae ++l++  kel  ka++a++  ++G
  gi|313124959|ref|YP_004035223.1| 163 QHKVfYVQEFVKK-PGRDIRVLAVDGEPIAAMTRSSDH--WLTNAAKGADAEAFELDDRAKELVQKASDAVGGGLLG 236
                                       333359*****85.689*****************9766..************************************* PP

                                       EEEEEETTEEEEEEEESS--SHHHHHHHT--HHHHHHHHH CS
                              RimK 149 vDllrakrgllvlEvnsspglekiektlgidiakklieai 188
                                       vDl+++ +++ v Evn  ++ + +++ ++ d+ + +++++
  gi|313124959|ref|YP_004035223.1| 237 VDLMETGDDYTVHEVNHTVEFKALNNAVEKDVPAAVVDWL 276
                                       ****************************999999999885 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   2.2e-12   5.7e-09       1     155 [.      87     252 ..      87     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.2e-12
                                       HTSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE............. CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...... 64 
                                       ++dK+k   +L++agv++P       t   ++++++  +++vvKp+ G+ g  + +++   +aea++e+++      
  gi|313124959|ref|YP_004035223.1|  87 CADKVKNSLALEQAGVPTPntevaftTDSAMKSIKKFGYPCVVKPVVGSWGRLMAKIDSPAAAEAILEHKAtlghyq 163
                                       89*****************988887666777777777*******************************9999***** PP

                                       ....EEEE---..SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT-- CS
                       ATP-grasp_3  65 ....lvqefie..GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevveklegla 135
                                            vqef++  G+++ v ++  ge +  ++ +  ++ +    ++ +G  +++  el++++ el++++  ++    
  gi|313124959|ref|YP_004035223.1| 164 hkvfYVQEFVKkpGRDIRVLAVD-GEPIAAMTRSSDHWLT----NAAKGADAEAF-ELDDRAKELVQKASDAV--GG 232
                                       **9999****7447777776655.7777777777777755....88999999887.89999999999999999..57 PP

                                       EEEEEEEEESS.SEEEEEEE CS
                       ATP-grasp_3 136 GyvGvDlvlkdeepyviEvN 155
                                       G++GvDl+ + ++  v EvN
  gi|313124959|ref|YP_004035223.1| 233 GLLGVDLMETGDDYTVHEVN 252
                                       9**********999999**9 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0     3e-12   7.7e-09      12     153 ..     104     241 ..      93     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3e-12
                                       S--EEEES-HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-TTHHHHHH...HHTTTTTS-EEEEE--GGGGG- CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgd.vilKPldgkgGegvfrvkksdpnlksile...llteegkepviaqrylpeikeG 84 
                                       +p+t v+  +++ ++ +++ g   ++KP+ g+ G+ + ++++  +  ++ile   +l +++++ + +q+++++  + 
  gi|313124959|ref|YP_004035223.1| 104 TPNTEVAFTTDSAMKSIKKFGYpCVVKPVVGSWGRLMAKIDS-PAAAEAILEhkaTLGHYQHKVFYVQEFVKKPGR- 178
                                       688999988887777777777669***********9999987.45667787733245678889999******9887. PP

                                       EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEET CS
                         GSH-S_ATP  85 DkRillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvig 153
                                       D R+l vdGepi  a++R   ++   +n a g+ aea el++r +e+ ++ ++++   G  + G+D+++
  gi|313124959|ref|YP_004035223.1| 179 DIRVLAVDGEPIA-AMTRS--SDHWLTNAAKGADAEAFELDDRAKELVQKASDAV---GGGLLGVDLME 241
                                       *************.99995..577899********************99877654...44455777664 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.6   6.7e+03     148     162 ..      13      27 ..      11      33 .. 0.84
   2 !   27.2   0.0   9.7e-10   2.5e-06       2     155 ..      98     250 ..      97     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.6
                                       TCTEEEEEEESS--G CS
                         ATP-grasp 148 dgellvnElapRpHn 162
                                       d++ll+ El  R H+
  gi|313124959|ref|YP_004035223.1|  13 DEKLLLTELRERGHE 27 
                                       677999999999997 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 9.7e-10
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC......GTTCEEEEE-- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal......keekvivEefv 72 
                                       e++g+p+p+  ++ +++++ + ++++g+p+vvK +++g+ G+    + s++ +e +le        +++ ++v efv
  gi|313124959|ref|YP_004035223.1|  98 EQAGVPTPNTEVAFTTDSAMKSIKKFGYPCVVK-PVVGSWGRLMAKIDSPAAAEAILEHKatlghyQHKVFYVQEFV 173
                                       799******************************.**********************999999999999999****** PP

                                       --.SEEEEEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                         ATP-grasp  73 pf.ekElsvlvvrsaeGetafypvvetvqedgilrlsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvle 147
                                       +   + + vl+v   +Ge  +     t  +d  l    + a++++     +a+e+++k+ +++gg G+++v l ++ 
  gi|313124959|ref|YP_004035223.1| 174 KKpGRDIRVLAV---DGEPIA---AMTRSSDHWLTNAAKGADAEAFeLDDRAKELVQKASDAVGG-GLLGVDLMET- 242
                                       862467777765...784322...33455555566555555555433778999999999999987.9999999999. PP

                                       TCT.EEEEE CS
                         ATP-grasp 148 dge.llvnE 155
                                        g+   v E
  gi|313124959|ref|YP_004035223.1| 243 -GDdYTVHE 250
                                       .33355555 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.9   7.4e+03      73      94 ..      42      63 ..      37      74 .. 0.76
   2 !   24.3   0.0   7.4e-09   1.9e-05       1      93 [.      89     177 ..      89     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.9
                                      HHHHHHSTS-EEEEE--SSSEE CS
                       CPSase_L_D2 73 eakaafgnkqvlvekslkgpke 94
                                      e +aaf +  + +++ l+  + 
  gi|313124959|ref|YP_004035223.1| 42 EPPAAFEDVDIVLDRCLATSRS 63
                                      5678899999999998887765 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 7.4e-09
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       Dk++ + al++++vp+ + + a   t++ a++  k++gyP+++k+ +g  G+ m  +++ +  ++++++  +     
  gi|313124959|ref|YP_004035223.1|  89 DKVKNSLALEQAGVPTPNTEVA--FTTDSAMKSIKKFGYPCVVKPVVGSWGRLMAKIDSPAAAEAILEHKATLG--H 161
                                       8999999*********999888..99**********************************99999999888888..5 PP

                                       HSTS-EEEEE--SSSE CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpk 93 
                                       + +k  +v++++k+p 
  gi|313124959|ref|YP_004035223.1| 162 YQHKVFYVQEFVKKPG 177
                                       999999*******983 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.71   1.8e+03      16      29 ..      67      80 ..      63      96 .. 0.80
   2 !   18.9   0.0   3.1e-07   0.00079      18      55 ..      96     133 ..      81     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.71
                       ATP-grasp_5 16 kelleaygipvvet 29
                                       + l+ay+ipvv++
  gi|313124959|ref|YP_004035223.1| 67 TRFLDAYDIPVVNS 80
                                      56799*****9986 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 3.1e-07
                       ATP-grasp_5  18 lleaygipvvetrlassaeeaveaaeeigypvvlKivs 55 
                                        le+ g+p+++t +a ++++a++ ++++gyp+v+K v+
  gi|313124959|ref|YP_004035223.1|  96 ALEQAGVPTPNTEVAFTTDSAMKSIKKFGYPCVVKPVV 133
                                       58999******************************765 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   1.5e-05     0.038       8      79 ..      76     143 ..      72     173 .. 0.84
   2 ?    1.4   0.0     0.061   1.6e+02     227     272 ..     218     261 ..     216     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                       ATPgrasp_ST   8 rkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvi 79 
                                       + +N+   + + +dK+k +  +++ag+++p++ + + + + ++++++f   +    v+Kp+ gs+G+ + +i
  gi|313124959|ref|YP_004035223.1|  76 PVVNSADTADVCADKVKNSLALEQAGVPTPNTEVAFTTDSAMKSIKKFGYPC----VVKPVVGSWGRLMAKI 143
                                       568999999***********************99999999999999997666....9*********977666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.061
                       ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpglaivq 272
                                       ++ el+ ka++  +g g+lG+D+  + +    + E+N+++  +  +
  gi|313124959|ref|YP_004035223.1| 218 RAKELVQKASD-AVGGGLLGVDLMETGDD-YTVHEVNHTVEFKALN 261
                                       57899999999.9999******9877777.9999999998776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1919.28
//
Query:       gi|313124960|ref|YP_004035224.1|  [L=352]
Description: n2-acetyl-l-aminoadipate semialdehyde dehydrogenase; n-acetyl-gamma-glutamyl-phosphate reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-27   96.3   0.0    2.9e-27   95.5   0.0    1.5  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.016   14.7   0.0    1.3  1  Epimerase       NAD dependent epimerase/dehydratase family
      0.014   15.5   0.0      0.032   14.4   0.0    1.7  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
       0.02   14.8   0.0      0.045   13.6   0.0    1.6  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   6.6e-31   2.9e-27       2     120 ..      12     144 ..      11     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 6.6e-31
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHH CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagv 78 
                                       +a+vG+tG +G ellrlL +hp++++v ++s+s+ + k++  +++   + +++ ++ +++e+l++vd++f a+p+gv
  gi|313124960|ref|YP_004035224.1|  12 AAVVGGTGFTGGELLRLLYQHPNFDVVQATSRSK-ERKTVGHVHP---NLREMDLRFTSPEDLESVDVLFAATPHGV 84 
                                       69********************************.**********...55555555566****************** PP

                                       HHHHHHHHHHTTSEEEESSSTTTTST..................TSEBE-HHHHGGGGGG CS
                    Semialdhyde_dh  79 skelapklaeagvkviDlssdfRlkd..................davyvlpevnreaikk 120
                                       s+e+ +++ +a  +v+Dls+dfRl++                  +a y lpe+nre+++ 
  gi|313124960|ref|YP_004035224.1|  85 SMEHIDAFQDAADTVVDLSADFRLNTeaqydewydghvcpeyleQAEYALPEINRENLAG 144
                                       ********************************************************9975 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.5e-06     0.016       2      51 ..      13      63 ..      12     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-06
                                      EEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHCEEEE--TT CS
                         Epimerase  2 lVtGatGfiGsalvkallekg.yevigldrlssasntarledlelveldlt 51
                                       V+G+tGf G  l++ l ++   +v+  +++s++++t  + + +l e+dl+
  gi|313124960|ref|YP_004035224.1| 13 AVVGGTGFTGGELLRLLYQHPnFDVVQATSRSKERKTVGHVHPNLREMDLR 63
                                      59******************9899*******99999888888888888885 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.1e-06     0.032       4      87 ..      13      92 ..      10     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.1e-06
                                      EEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHS.SSS--S-BEBSSHHHHHHH-SEEEE-S-HHHHH CS
                            DapB_N  4 avvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagell.glgklgvavtddleevlekadvliDFTtpeavl 81
                                      avvG +G  G e+++++ +++++ +v+a +r++   e k +g++  +l+++++ +t    e le++dvl   T + +++
  gi|313124960|ref|YP_004035224.1| 13 AVVGGTGFTGGELLRLLYQHPNFDVVQATSRSK---ERKTVGHVHpNLREMDLRFT--SPEDLESVDVLFAATPHGVSM 86
                                      89*****************************99...67777765414446666666..344566789999999888888 PP

                                      HHHHHH CS
                            DapB_N 82 enlkla 87
                                      e++++ 
  gi|313124960|ref|YP_004035224.1| 87 EHIDAF 92
                                      888765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     1e-05     0.045       1      68 [.      16      80 ..      16     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                                      TTTSHHHHHHHHHHHHC-T-EE.EEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES- CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghev.talvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal 68
                                      G+tG +G +l++ l ++ +++v  a  R++e+ +    +++l+ +++ +t++edl++    +d+ ++a+
  gi|313124960|ref|YP_004035224.1| 16 GGTGFTGGELLRLLYQHPNFDVvQATSRSKERKTVGHVHPNLREMDLRFTSPEDLES----VDVLFAAT 80
                                      9***********9999998776378899999988555789999999999****9764....56555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2181.23
//
Query:       gi|313124961|ref|YP_004035225.1|  [L=325]
Description: N2-acetyl-L-aminoadipate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-35  122.7   5.0    2.2e-35  122.4   5.0    1.1  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.14   12.0   0.8       0.26   11.1   0.8    1.4  1  Arteri_Gl  Arterivirus GL envelope glycoprotein


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   5.0   2.5e-39   2.2e-35       3     241 .]      37     283 ..      35     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 2.5e-39
                                       EEEEE-TT.CCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC........E..HHHH CS
                         AA_kinase   3 vVvKlGGs.sltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa....glrstleeag 74 
                                       vVvK+GG+ +++++++      ++++a l+ +g+++vvVhGg+  +d  l++  g ++++ ++      r t+e ++
  gi|313124961|ref|YP_004035225.1|  37 VVVKVGGArAVDPAGA------VQDVAHLVANGRDVVVVHGGSTAVDDTLEE-LGEEPTYVETpsgvVGRFTDERTM 106
                                       8*******99998887......88888888888*******************.9999999999999999******** PP

                                       HHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.................HHHTTTCEEECCHHHHHHH CS
                         AA_kinase  75 evatrdalaslgerlvaallaaglpavglsaaaldateagr...............degsdgnvesvdaeaieelle 136
                                       ev ++++ ++l+++lv+ l +ag++a gls+ + ++ ++ r               +  ++g++++v+a+ +e+l++
  gi|313124961|ref|YP_004035225.1| 107 EVFSMVMPGKLNTDLVTTLREAGVDALGLSGVDGGLLTGPRksavrvvedgkkkikRGDHSGRITNVNADLLETLMA 183
                                       ***************************************************************************** PP

                                       TT-EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEE.EHHHCHHCSS CS
                         AA_kinase 137 agvvpvltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpei.svdeaeesas 212
                                       + +vpv+t    l ++g   + ++D++aa++A algA +l++ltdV+GVy ++ ++    +l++ + ++de+e+  +
  gi|313124961|ref|YP_004035225.1| 184 DTYVPVVTVPM-LADDGVAVNADADRAAAAVAGALGA-ELVVLTDVSGVYEDPDDDS---TLIESVtTADEFEA-LE 254
                                       *********87.89999999*****************.99999*******8887777...******76777777.66 PP

                                       S.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 213 elatgGmkvkhpaalaaarrggipvvItn 241
                                         a g m  k+ aa +a+ +g ++v++++
  gi|313124961|ref|YP_004035225.1| 255 SAAEGFMTKKVMAAKEALTGGAMKVIVAD 283
                                       688888899*****************985 PP

>> Arteri_Gl  Arterivirus GL envelope glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.8   2.9e-05      0.26     129     170 ..      26      69 ..      19      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.9e-05
                         Arteri_Gl 129 akGrifrsksqvvvekpgkteVggk.lv.gikkvVlgGrkavkl 170
                                       + G++++ +++vvv+ +g  +V++   v +++++V++Gr +v +
  gi|313124961|ref|YP_004035225.1|  26 DGGTVPADDPPVVVKVGGARAVDPAgAVqDVAHLVANGRDVVVV 69 
                                       7799******************9873679**********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1915.11
//
Query:       gi|313124962|ref|YP_004035226.1|  [L=378]
Description: acetylornithine aminotransferase apoenzyme; n2-acetyl-l-lysine aminotransferase apoenzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.2e-111  370.5   0.1   1.1e-110  370.1   0.1    1.1  1  Aminotran_3      Aminotransferase class-III
  ------ inclusion threshold ------
      0.021   13.4   0.0       0.12   10.8   0.0    1.9  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.1   0.1  1.2e-114  1.1e-110      10     404 ..      10     375 ..       5     377 .. 0.96

  Alignments for each domain:
  == domain 1  score: 370.1 bits;  conditional E-value: 1.2e-114
                                       CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                       Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                       +++i+ +eG+yl+  dg +ylD+ +s+av++lGhahP+v++av++qa+kl++v  + +  +   +l+ekl+++ap g
  gi|313124962|ref|YP_004035226.1|  10 PINIESGEGAYLYGSDGTEYLDFGASYAVAALGHAHPAVTDAVQKQAEKLTYVQ-ASYPVDVRTELYEKLAAVAPDG 85 
                                       599***************************************************.999******************* PP

                                       .SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TT CS
                       Aminotran_3  87 ldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkyp 163
                                       l++v l+nsG+eA+e+A+K+ar+      at ++kiia k +fHGrt+gal++t++ +kyk+ f+p++ +v ++ y 
  gi|313124962|ref|YP_004035226.1|  86 LENVWLCNSGTEANEAAMKFARS------ATDRSKIIATKRGFHGRTMGALAMTWK-DKYKKPFEPLAGDVEFVTYG 155
                                       ***********************......***************************.******************** PP

                                       BGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTT CS
                       Aminotran_3 164 deevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGr 240
                                       de                  +l +++++e+aAv +Ep+qgegG+ +a  e+l+++r+l+++ +++l +DE+qtG+Gr
  gi|313124962|ref|YP_004035226.1| 156 DE-----------------AELAEAIDEETAAVFLEPVQGEGGIHPAGTEYLQTARKLTEEAGAALAFDEIQTGIGR 215
                                       93.................34567899************************************************** PP

                                       TSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHH CS
                       Aminotran_3 241 TGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllena 317
                                       TG+l+A+e agv+pD++t+aK++++Glpl a+l+ + +++    g+hgsTf+G p+ ca+a+a+l++i ee++  +a
  gi|313124962|ref|YP_004035226.1| 216 TGTLWACEGAGVTPDILTSAKGIANGLPLGATLVADWIAENP--GNHGSTFSGGPVVCAAANATLDTIVEEDYPSHA 290
                                       ***************************************987..********************************* PP

                                       HHHHHHHHHHHHHHCTT-.TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HH CS
                       Aminotran_3 318 qelgaalkegLeelqkky.evikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitde 393
                                       +++g++lk++Le++++++   +++vRg+Glm+++ +k  a+   + + + a  + vl l+aG++v+rllppl++t+ 
  gi|313124962|ref|YP_004035226.1| 291 AAVGEYLKAELEAAAEEHdLPVRDVRGQGLMLGVQVKRGAN---RVLKNLAISEQVLALPAGRTVVRLLPPLVVTEG 364
                                       ****************996789************9999888...33556678999********************** PP

                                       HHHHHHHHHHH CS
                       Aminotran_3 394 eidelleilkk 404
                                       ++de++e++++
  gi|313124962|ref|YP_004035226.1| 365 HADEFVESFVE 375
                                       *******9976 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   1.4e-05      0.12      35     145 ..      50     175 ..      33     178 .. 0.70
   2 ?   -0.3   0.0     0.032   2.9e+02     284     321 ..     305     339 ..     297     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.4e-05
                                       HHCTTCSSS-SBTTT--HH..HHHHHHHHHHHH..T-SEEEEESSHHHHHHHHHHTTS-TTEE...EEEESTSS.HH CS
                   Cys_Met_Meta_PP  35 eafageekgyeYsRsgnpt..rsvleeriaaLe..ggeaalavssGmaAiaaailallkaGde...ivvsddlY.gg 103
                                       +a ++++++  Y     p   r+ l e++aa+   g e++ +++sG+ A   a ++++++ ++   i++++  + g 
  gi|313124962|ref|YP_004035226.1|  50 DAVQKQAEKLTYVQASYPVdvRTELYEKLAAVApdGLENVWLCNSGTEAN-EAAMKFARSATDrskIIATKRGFhGR 125
                                       446677777788777777433788889999985225599**********9.67777777754446688887765155 PP

                                       HHHHHHHT........HHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEES CS
                   Cys_Met_Meta_PP 104 tqrllkkv........lkklgievkfvdtsdleelekaikentklvylEt 145
                                       t   l  +        ++ l  +v+fv   d++el++ai+e+t +v+lE 
  gi|313124962|ref|YP_004035226.1| 126 TMGALAMTwkdkykkpFEPLAGDVEFVTYGDEAELAEAIDEETAAVFLEP 175
                                       766655441111111144567799************************95 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.032
                                       STTHHHHHHHSSSG-SEEEEEESSHHHHHHHHHHC-SS CS
                   Cys_Met_Meta_PP 284 hpqhelakkqlkgaggvlsFelkseeekakkfvdnlkl 321
                                        ++h+l  ++++g g +l+ ++k +   a+++++nl +
  gi|313124962|ref|YP_004035226.1| 305 AEEHDLPVRDVRGQGLMLGVQVKRG---ANRVLKNLAI 339
                                       57899******************99...4567776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2456.55
//
Query:       gi|313124963|ref|YP_004035227.1|  [L=357]
Description: acetylornithine deacetylase; n2-acetyl-l-lysine deacetylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-28   98.7   0.4    4.9e-28   98.2   0.4    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    6.8e-06   26.0   0.0    1.2e-05   25.2   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.4   5.5e-32   4.9e-28       1     205 [.      75     352 ..      75     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 5.5e-32
                                       EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgG 77 
                                       ll sH+D+Vp +e      p + +  dG+l+GrG++d +g ++a++ a+    ++g      + ++ +++EE+++ G
  gi|313124963|ref|YP_004035227.1|  75 LLTSHIDTVP-GEV-----PVKIE--DGVLWGRGSVDATGPLAAMAVAAV---ETG------VSFVGVVEEETSSTG 134
                                       689*******.555.....55555..9******************99984...465......99********999** PP

                                       HHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                     Peptidase_M20  78 akallegleerekvdavfelhieepgileagklaigvv....................................... 115
                                       a +lle   +re++da   ++ +ep++++    +i+++                                       
  gi|313124963|ref|YP_004035227.1| 135 AWHLLE---DREEPDA---VINGEPSGWD----GITLGyrgflsgtyvatselghssrpennaiqsavdwwsrvadf 201
                                       ******...799****...55********....556669999*********************************** PP

                                       ...........................................................EEEEEEEEEESHEEEC.C CS
                                       ...........................................................xxxxxxxxxxxxxxxx.x RF
                     Peptidase_M20 116 ...........................................................kvevelleggapvtln.d 132
                                                                                                  + +v+++   +pv+++  
  gi|313124963|ref|YP_004035227.1| 202 feaededgvfdtvttkpvnfeggptedglaveatvdvqfrvpphltiediqevaegelvEGSVHWEKPIPPVMTSpR 278
                                       **********************************************************98999999*********** PP

                                       HHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 133 splvkalaeaaeelfgekvelivsgpggtdarff...agiptvmifgpgs.glaHspnEyvdledlekgikvlarll 205
                                        ++++a++ a++++ g +++l  +  g++d+++f   ++ p +  +gpg+ +l H+pnE++dl+++ ++i+vl+++ 
  gi|313124963|ref|YP_004035227.1| 279 TEVARAFRVAIRNADG-DPRLLRKT-GTSDMNIFaseWNCPMA-TYGPGDsDLDHAPNEHLDLAEYDAAIEVLTNVC 352
                                       *************866.78898888.9*******866666644.59***77**********************9875 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.3e-09   1.2e-05       2     101 ..     162     259 ..     161     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.3e-09
                                       EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEE CS
                         M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaea 78 
                                       g +G+++g+  ++ + gHs+ p++   Ai  +++  ++  d  + + e+  + + t  + ++egG     ++ ea++
  gi|313124963|ref|YP_004035227.1| 162 GYRGFLSGTYVATSELGHSSRPENN--AIQSAVDWWSRVADFFEAEDEDGVFDTVTTKPVNFEGGPTEDGLAVEATV 236
                                       569999**************66554..666666665555555333335678************************** PP

                                       EEEEEHHHHHHHHHHHHHHHHHH CS
                         M20_dimer  79 kidiRllpgedpeevleeieeil 101
                                        + +R++p+ + e+++e  e  l
  gi|313124963|ref|YP_004035227.1| 237 DVQFRVPPHLTIEDIQEVAEGEL 259
                                       ***************99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2248.92
//
Query:       gi|313124964|ref|YP_004035228.1|  [L=299]
Description: ornithine carbamoyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-50  170.9   0.0    2.7e-50  170.2   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    4.7e-50  169.7   0.0    6.6e-50  169.2   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   0.0     3e-54   2.7e-50       2     148 .]       6     141 ..       5     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 3e-54
                                       -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSC CS
                          OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediq 78 
                                       h+l+++dl+++e++++ld+aa++k+ +    +++ l+++tl++lFe+pStRTr+Sfe+++++lGg++++l+ +ediq
  gi|313124964|ref|YP_004035228.1|   6 HFLDIDDLTTTELHHVLDRAAAIKAGK----EDPRLEDQTLGMLFEKPSTRTRISFETGMTQLGGHAIFLG-PEDIQ 77 
                                       9***********************986....59**************************************.88*** PP

                                       TTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  79 lssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       l+     ++E+l+Dt rvlsryvd++++R +++e+l e+a+ya+vpv+N++ +d+ HP+Q+LaDlltire
  gi|313124964|ref|YP_004035228.1|  78 LG-----HGEPLSDTSRVLSRYVDVVMARLFDHEDLVEIADYADVPVVNGL-TDDAHPCQTLADLLTIRE 141
                                       **.....67******************************************.****************98 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   0.0   7.4e-54   6.6e-50       2     155 ..     148     294 ..     147     296 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 7.4e-54
                                       C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE- CS
                            OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytd 78 
                                       +++ a+vGd+ nnv +s + ++a+ g+d+++++P+++  d+evl++a    +++gg+ ti e +++av++aDvvytd
  gi|313124964|ref|YP_004035228.1| 148 DVQAAWVGDG-NNVGQSFVLGCAMAGLDLTVATPEEYGIDEEVLAHA----AEYGGEPTIAETPAQAVADADVVYTD 219
                                       6789******.*********************************665....557*********************** PP

                                       -SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                            OTCace  79 vwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                       vw+smg+e+er+e+++++++yqv+e ll+    da v+HcLPa+rgeE++++V +s+r++v++qaeNrlh++k llv
  gi|313124964|ref|YP_004035228.1| 220 VWISMGQEDERDEKIAAFEGYQVNEGLLAE--TDAEVMHCLPAHRGEEISHDVLESDRALVWDQAENRLHAQKGLLV 294
                                       ***************************995..6889***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1834.60
//
Query:       gi|313124965|ref|YP_004035229.1|  [L=153]
Description: hypothetical protein Hbor_01790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-05   23.1   2.4    7.7e-05   23.1   2.4    1.5  1  DUF1440          Protein of unknown function (DUF1440)
  ------ inclusion threshold ------
      0.024   14.8  11.6      0.024   14.8  11.6    2.7  3  DUF5518          Family of unknown function (DUF5518)
       0.03   14.3   9.3      0.076   12.9   9.3    1.6  1  YqhR             Conserved membrane protein YqhR
      0.069   13.2   0.2      0.069   13.2   0.2    2.9  3  Phage_holin_2_1  Bacteriophage P21 holin S
          4    6.9   9.3        7.7    5.9   0.5    2.1  2  DUF1129          Protein of unknown function (DUF1129)
        4.4    7.0  22.3        1.2    8.9   1.2    2.7  3  CbtA             Probable cobalt transporter subunit (CbtA)
        4.6    8.0  13.8       0.75   10.6   0.2    2.4  3  DUF4282          Domain of unknown function (DUF4282)
        6.3    6.8   9.0       0.36   10.8   1.8    2.1  3  RseC_MucC        Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> DUF1440  Protein of unknown function (DUF1440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   2.4   3.4e-08   7.7e-05      46     131 ..      53     140 ..      36     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.4e-08
                           DUF1440  46 tysgqkvnwvsvlvhilfsivfavlYvvvaev...fpkiklwqGalfGllvtiavHlivlPl.lglvpalkelpl.e 117
                                        +sg    ++++++h+  +++++v+++ va         +l  G+++G++++ ++ ++v+P+ l +v ++++ pl +
  gi|313124965|ref|YP_004035229.1|  53 FFSGG---LAGFTIHVAHGAILGVVFAAVAATrnlSTGQSLGLGVAYGVALWAVLAVFVMPVwLSVVGSPANPPLpN 126
                                       55544...78999**************9998833234456888******************8678999999999835 PP

                           DUF1440 118 ehvsEilghivwlw 131
                                        +v  ++gh+v++ 
  gi|313124965|ref|YP_004035229.1| 127 VNVTSLVGHVVYGG 140
                                       6899*******975 PP

>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8  11.6   1.1e-05     0.024      44     112 ..      12      80 ..       9      82 .. 0.80
   2 ?   -2.1  15.5       1.8   4.1e+03      53     111 ..      56     117 ..      53     120 .. 0.54
   3 ?   -3.6  10.0       5.3   1.2e+04      60      79 ..      96     119 ..      82     150 .. 0.36

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                           DUF5518  44 gdskdgavaGalaGligaipvlvlllvlllglvaaigglagfvallvalllvvllllvvllvilgaiGG 112
                                       ++s d   aG+laG+ig+i+++++++v + ++++ + ++  f+ +++a + + ++  ++l+v+++a+++
  gi|313124965|ref|YP_004035229.1|  12 STSNDDWQAGVLAGIIGGIVMGAMMVVQMRSALEVAIPSMYFFSGGLAGFTIHVAHGAILGVVFAAVAA 80 
                                       667788889************777777777788888888888888888888888888888888888875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                           DUF5518  53 GalaGligaipvlvlllvlll...glvaaigglagfvallvalllvvllllvvllvilgaiG 111
                                       G laG+   +  +++l+v+++   ++ ++ +g ++ + ++++++l ++l+++v+ v l+++G
  gi|313124965|ref|YP_004035229.1|  56 GGLAGFTIHVAHGAILGVVFAavaATRNLSTGQSLGLGVAYGVALWAVLAVFVMPVWLSVVG 117
                                       44555444444422222222222234455555555666666666666788888888888888 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.3
                           DUF5518  60 gaipvlvlllvlll....glvaai 79 
                                        ++ + ++l+v+++    ++v+ +
  gi|313124965|ref|YP_004035229.1|  96 YGVALWAVLAVFVMpvwlSVVGSP 119
                                       333332222222223111222222 PP

>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   9.3   3.4e-05     0.076      22     150 ..      22     146 ..       4     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                              YqhR  22 viiGfvGGvlWsllaylaylfnfsevspnlilepwvlgdWkkkalGtvisivligvvsigvall.yyvllkkikslw 97 
                                       v+ G +GG++ +++  +     +    p++ + +  l        G +i +   +++ +++a +     l   +sl 
  gi|313124965|ref|YP_004035229.1|  22 VLAGIIGGIVMGAMMVVQMRSALEVAIPSMYFFSGGL-------AGFTIHVAHGAILGVVFAAVaATRNLSTGQSLG 91 
                                       5667777777777666665555555556665555444.......455555555555555544431456799999*** PP

                              YqhR  98 agilyGvvlwllvfyvlnPlfPdv..kavaelekntiittlclyilyGvfvGysi 150
                                        g++yGv+lw+++   + P++  v  ++ +    n  +t+l  +++yG  vG + 
  gi|313124965|ref|YP_004035229.1|  92 LGVAYGVALWAVLAVFVMPVWLSVvgSPANPPLPNVNVTSLVGHVVYGGVVGVAY 146
                                       ***********99999999998873334555567899***********9999654 PP

>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   3.1e-05     0.069      21      46 ..       7      31 ..       2      36 .. 0.86
   2 ?   -1.3   1.7         1   2.3e+03      25      25 ..      82      82 ..      50     108 .. 0.61
   3 ?   -0.9   0.2      0.75   1.7e+03       6      11 ..      93      98 ..      82     117 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                   Phage_holin_2_1 21 kqlldklspeeWsaigvlgglvigll 46
                                       q+++  s ++W+a gvl+g++ g++
  gi|313124965|ref|YP_004035229.1|  7 MQTVESTSNDDWQA-GVLAGIIGGIV 31
                                      6999*********9.99999999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                   Phage_holin_2_1 25 d 25
                                       
  gi|313124965|ref|YP_004035229.1| 82 R 82
                                      1 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.75
                   Phage_holin_2_1  6 gvsYga 11
                                      gv+Yg 
  gi|313124965|ref|YP_004035229.1| 93 GVAYGV 98
                                      333333 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.5    0.0034       7.7      99     132 ..       7      41 ..       1      47 [. 0.72
   2 ?    5.3   2.7    0.0053        12     111     192 ..      59     139 ..      44     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0034
                           DUF1129  99 lalfskkkqtas..iGlitlllvalvgGlamvlvyr 132
                                       ++ +++ ++  +  +G+++ ++ ++v+G++mv+ +r
  gi|313124965|ref|YP_004035229.1|   7 MQTVESTSND-DwqAGVLAGIIGGIVMGAMMVVQMR 41 
                                       5555553333.346899*************998776 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0053
                           DUF1129 111 iGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLppl.vliii 186
                                       +G++  +  +++ G+++  v+     + ++ +  +l     ++l ++++ +v+ + ++++ +  Np Lp + v+ ++
  gi|313124965|ref|YP_004035229.1|  59 AGFTIHVAHGAILGVVFAAVAATR--NLSTGQSLGLGVAYGVALWAVLAVFVMPVWLSVVGSPANPPLPNVnVTSLV 133
                                       488888889999999998887654..468999999999999999999999999999999*********987355566 PP

                           DUF1129 187 gviafv 192
                                       g + ++
  gi|313124965|ref|YP_004035229.1| 134 GHVVYG 139
                                       666665 PP

>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.2   0.00053       1.2       7      35 ..      20      48 ..      18      50 .. 0.90
   2 ?    6.0   9.6     0.004         9      77     133 ..      63     123 ..      53     126 .. 0.71
   3 ?   -0.3   0.1      0.33   7.4e+02      79      97 ..     132     150 ..     126     153 .] 0.56

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00053
                              CbtA  7 rgllaGllAGllaflvqrlvvePlilaAe 35
                                      +g+laG+++G+++++++ +++ + ++ A+
  gi|313124965|ref|YP_004035229.1| 20 AGVLAGIIGGIVMGAMMVVQMRSALEVAI 48
                                      89*****************9999888776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.004
                              CbtA  77 anvltgvalglllaavfallegrlgklsaralalllalagflavvlvPf....lklPpepP 133
                                         v +g+ lg+++aav+a +  ++g+  +   a+ +al + lav+++P     ++ P++pP
  gi|313124965|ref|YP_004035229.1|  63 IHVAHGAILGVVFAAVAATRNLSTGQSLGLGVAYGVALWAVLAVFVMPVwlsvVGSPANPP 123
                                       4567788888888888887776666666666777777777788999995333368899998 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.33
                              CbtA  79 vltgvalglllaavfalle 97 
                                       ++  v +g+++++++++++
  gi|313124965|ref|YP_004035229.1| 132 LVGHVVYGGVVGVAYSAVR 150
                                       3334556666666666665 PP

>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00033      0.75      40      74 ..      14      48 ..       1      53 [. 0.78
   2 ?    3.8   5.1     0.045     1e+02      20      65 ..      68     112 ..      57     117 .. 0.72
   3 ?   -3.1   0.1       6.2   1.4e+04      52      58 ..     136     142 ..     126     149 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                           DUF4282 40 seslsagggllllllaviafllmilllRivlEfli 74
                                      s+++   g l +++ ++++  +m++ +R  lE++i
  gi|313124965|ref|YP_004035229.1| 14 SNDDWQAGVLAGIIGGIVMGAMMVVQMRSALEVAI 48
                                      445556678889999*****************987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.045
                           DUF4282  20 givlialvllslivgafaalseslsagggllllllaviafllmill 65 
                                       g++l ++++ ++  + +++  +sl++g++ +  l+av+a+++m ++
  gi|313124965|ref|YP_004035229.1|  68 GAILGVVFAAVAATRNLST-GQSLGLGVAYGVALWAVLAVFVMPVW 112
                                       3444444444444444444.489999999999*******9999876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6.2
                           DUF4282  52 lllavia 58 
                                       ++++ ++
  gi|313124965|ref|YP_004035229.1| 136 VVYGGVV 142
                                       3333222 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.65   1.5e+03      99     111 ..      25      37 ..       9      49 .. 0.54
   2 ?   -0.1   1.5      0.38   8.4e+02      82     102 ..      30      52 ..      20      82 .. 0.45
   3 ?   10.8   1.8   0.00016      0.36      42      88 ..      78     124 ..      73     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.65
                         RseC_MucC  99 gallglvlgfliv 111
                                       g + g+v+g ++v
  gi|313124965|ref|YP_004035229.1|  25 GIIGGIVMGAMMV 37 
                                       2222233333322 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.38
                         RseC_MucC  82 allgsall..gssellaalgall 102
                                       +++g +++  + s l +a+ ++ 
  gi|313124965|ref|YP_004035229.1|  30 IVMGAMMVvqMRSALEVAIPSMY 52 
                                       44444444432222222222222 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00016
                         RseC_MucC  42 veneigakvGdkVevgieeksllkaallvYllPllllilgallgsal 88 
                                       v+ + ++++G++  +g+     l a+l v+++P+ l ++g  +   l
  gi|313124965|ref|YP_004035229.1|  78 VAATRNLSTGQSLGLGVAYGVALWAVLAVFVMPVWLSVVGSPANPPL 124
                                       5677899****************************999997666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 960.40
//
Query:       gi|313124966|ref|YP_004035230.1|  [L=155]
Description: hypothetical protein Hbor_01800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.7   2.4      0.034   14.5   1.8    1.9  1  DUF1440   Protein of unknown function (DUF1440)
       0.13   12.2   3.7       0.45   10.4   3.7    1.9  1  YqhR      Conserved membrane protein YqhR


Domain annotation for each model (and alignments):
>> DUF1440  Protein of unknown function (DUF1440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.8   3.8e-06     0.034      49     132 ..      54     145 ..      31     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-06
                           DUF1440  49 gqkvnwvsvlvhilfsivfavlYvvvaevfpk....i..klwqGalfGllvtiavHlivlPllglvpal...kelpl 116
                                       g +  ++++ +h++ +++++v++v v + +p     +  +   G+++G++++ ++ ++v+Pl            lp 
  gi|313124966|ref|YP_004035230.1|  54 GLSGGMAGMGIHLSHGALLGVVFVAVLRLWPDpgrtVtrAAIAGTAYGVVLWGILAVFVMPLWLSAVGFagaPSLPA 130
                                       55556788999******************99533333224678******************9654433311144555 PP

                           DUF1440 117 eehvsEilghivwlws 132
                                          +s ++gh++++++
  gi|313124966|ref|YP_004035230.1| 131 FDLMS-LVGHVLYGIV 145
                                       55555.8899998876 PP

>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.7   5.1e-05      0.45       2     120 ..       3     118 ..       2     150 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.1e-05
                              YqhR   2 kkekleqnkkekplsllakvviiGfvGGvlWsllaylaylfnfsevspnli.lepwvlgdWkkkalGtvisivligv 77 
                                       ++++ eq +  + +   +  v+ G++G v +s+l  +     ++   p++  l   ++g   +   G      l+gv
  gi|313124966|ref|YP_004035230.1|   3 QQQRDEQSELTTGVERWQAGVVAGLLGAVAFSALLAISAPAALTAAIPSMYgLSGGMAGMGIHLSHGA-----LLGV 74 
                                       55556666666666666777777888888777777777777777777766523444444444444455.....5555 PP

                              YqhR  78 vsigvallyyvllkki.kslwagilyGvvlwllvfyvlnPlfPd 120
                                       v ++v  l+    + + ++  ag +yGvvlw ++   + Pl+  
  gi|313124966|ref|YP_004035230.1|  75 VFVAVLRLWPDPGRTVtRAAIAGTAYGVVLWGILAVFVMPLWLS 118
                                       5555555666665655146789*********9998888888644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 967.34
//
Query:       gi|313124967|ref|YP_004035231.1|  [L=725]
Description: DNA helicase, rad3 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-35  121.9   0.0      8e-35  120.5   0.0    1.7  1  Helicase_C_2  Helicase C-terminal domain
    4.9e-23   81.7   0.4      1e-22   80.6   0.4    1.6  1  DEAD_2        DEAD_2
    3.1e-09   36.9   1.1    5.9e-06   26.2   0.2    3.8  4  DEAD          DEAD/DEAH box helicase
      6e-06   26.4   0.1    0.00074   19.6   0.1    2.4  1  ResIII        Type III restriction enzyme, res subunit
      3e-05   23.4   0.1     0.0044   16.3   0.0    2.3  2  DUF2075       Uncharacterized conserved protein (DUF2075)
    8.2e-05   22.1   0.0    0.00016   21.1   0.0    1.5  1  ATPase        KaiC
    0.00052   19.8   0.6     0.0053   16.5   0.0    2.4  2  HBB           Helical and beta-bridge domain
      0.001   18.7   0.2       0.24   11.0   0.0    2.4  2  Zot           Zonular occludens toxin (Zot)
     0.0016   18.9   0.4       0.87   10.0   0.0    2.9  2  AAA           ATPase family associated with various cellular 
     0.0072   15.8   0.0      0.019   14.4   0.0    1.7  1  PhoH          PhoH-like protein
  ------ inclusion threshold ------
      0.015   15.0   2.4      0.034   13.9   0.2    2.3  2  AAA_30        AAA domain
      0.033   14.6   4.5       0.17   12.2   1.1    3.2  2  AAA_16        AAA ATPase domain
      0.054   12.4   0.0      0.096   11.6   0.0    1.3  1  AAA_34        P-loop containing NTP hydrolase pore-1
       0.09   12.3   3.1       0.66    9.5   0.1    3.4  3  AAA_25        AAA domain
       0.12   12.7   5.6       0.28   11.4   0.9    2.8  2  AAA_22        AAA domain
       0.16   11.8   1.7       0.44   10.3   0.5    2.3  2  AAA_11        AAA domain
        2.1    8.4   7.9       0.19   11.8   2.2    2.2  2  TPR_MLP1_2    TPR/MLP1/MLP2-like protein


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.5   0.0   7.6e-38     8e-35       4     159 ..     522     676 ..     519     683 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 7.6e-38
                      Helicase_C_2   4 llevvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidf 80 
                                        ++ +pg++lvffpSy+  e+ +erl+++++ ++  +++e +   +e++ +++ e  ++ aill ++ G+l EG+ f
  gi|313124967|ref|YP_004035231.1| 522 ASRFTPGNTLVFFPSYAEAERYHERLQARMDVTDRLFLDE-SGTPTEEIRSKFVE--SQSAILLTSLWGTLAEGVSF 595
                                       67889*************************9999999999.999***********..******************** PP

                      Helicase_C_2  81 sddllraviivglPfpnpkdpeveakreyldekgk...knsgkewylpealravnQaiGRliRhkdDygaivllDeR 154
                                        +d +r v++vg+P+p++ ++++ea ++ +d+  +   + +++++ + +++r+ +Qa+GR+iR+ dD+g+ +l D+R
  gi|313124967|ref|YP_004035231.1| 596 DGDDARTVVVVGVPYPHL-SERMEAIQDAYDRVYSsrrEAGWRYAVEIPTIRKTRQALGRVIRSPDDFGVRILADKR 671
                                       *****************9.67889999999985554434557788999***************************** PP

                      Helicase_C_2 155 fakee 159
                                       +++++
  gi|313124967|ref|YP_004035231.1| 672 YTRAS 676
                                       *9876 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.4   9.9e-26     1e-22       5     176 .]      72     285 ..      68     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 9.9e-26
                                       SHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCH........... CS
                            DEAD_2   5 ThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeek........... 70 
                                        h+q++q+v++ + +++++     +++v+ ++++ +C   +v+ ++  +++ ++ ++l++k++ +            
  gi|313124967|ref|YP_004035231.1|  72 VHQQMRQFVEDARAITRTE----PIRAVVFKGKSSMCH-IDVEYQE-CQTLRDTTRSLVEKEQDKAelseqadalvd 142
                                       699************7555....5*************5.4777755.56666677777777766557899******* PP

                                       ................................TTTTTT-SCC..CCHHHHHHHHHHC---CHHHHHHHHHCT--HHH CS
                            DEAD_2  71 ................................eekCsffenl..eelkklkkllleevvdiedlvelgeklklCPYy 113
                                                                        + C+++ n+  e++++  + l++ v + ed++e+  + klC Y 
  gi|313124967|ref|YP_004035231.1| 143 rmrageqgaadartavtdeldtledeledlreGNICEYYYNNltEDTDEFFSWLFDDVRTPEDIYEYADQRKLCGYE 219
                                       ******************************99788**998886788888899************************* PP

                                       HHHHHHCCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTCCCHHHHHHHCC-EEEECHHH CS
                            DEAD_2 114 lsrelledadiiilpYqyLldekireslk...gislknsivilDEAhNiedvceeaasveiseesl 176
                                       l +e +e++d++++ Y+ Lld++ire++    + + ++ i ++DEAhNie+ +++ as  ++e++l
  gi|313124967|ref|YP_004035231.1| 220 LLKEGMEEVDLVVCNYHHLLDPNIREQFFrwlNREPEDVITVFDEAHNIESAARDHASRALTENTL 285
                                       **************************997766667899***********************99876 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   5.6e-09   5.9e-06       4     136 ..      20     168 ..      17     194 .. 0.67
   2 ?    5.1   0.0     0.016        17      96     146 ..     226     280 ..     182     296 .. 0.69
   3 ?    1.0   0.0       0.3   3.2e+02     160     174 ..     453     468 ..     429     469 .. 0.75
   4 ?   -1.3   0.0       1.5   1.6e+03      43      94 ..     523     573 ..     508     594 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.6e-09
                                       HHHHHHHHH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                       xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 Qaeaiplil....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                       Q ea++ i      ++dvlv+++ G+GKTl +l+p+++      +++ + ++i +  ++ ++q +++++ ++ +  +
  gi|313124967|ref|YP_004035231.1|  20 QGEAMDGIAealeAERDVLVEGAPGTGKTLSALVPAVEYA----RQEDKTVVITTNVHQQMRQFVEDARAITRTEPI 92 
                                       5555555554434679*********************887....6777799*******************9996556 PP

                                       EEEEEETT......SSHHHHHHHHHTTCSEEEEEH..........HHHHHHHHCTSSHCTTEEEEEEETHHHHHHT CS
                                       xxxxxxxx......xxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliigg......vaardqlskldngvdivvgtp..........grlddllstgklnlsqvrflVlDEadrlldq 136
                                       r++++ g+      + + ++ ++l+ +++ +v             + l+d ++ g+    + r+ V DE d+l d+
  gi|313124967|ref|YP_004035231.1|  93 RAVVFKGKssmchiDVEYQECQTLRDTTRSLVEKEqdkaelseqaDALVDRMRAGEQGAADARTAVTDELDTLEDE 168
                                       6665555322222222223333333334444444444444442224444444666666899999999999999887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                                       TTCSEEEEEHHHHHH.HHHCTSSH.....CTTEEEEEEETHHHHHHTTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxx.xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  96 ngvdivvgtpgrldd.llstgkln.....lsqvrflVlDEadrlldqgfsdfinril 146
                                       ++vd+vv +   l+d  ++++ ++      ++  + V+DEa+++ +   +d+ +r l
  gi|313124967|ref|YP_004035231.1| 226 EEVDLVVCNYHHLLDpNIREQFFRwlnrePED-VITVFDEAHNIESA-ARDHASRAL 280
                                       44888888888888865544443331121233.379*********98.666666644 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.3
                                       SEEEEEESSBS.HHHH CS
                                       xxxxxxxxxxx.xxxx RF
                              DEAD 160 rqvivlSATlp.kdvk 174
                                       +  i++SATl  +dv+
  gi|313124967|ref|YP_004035231.1| 453 HASILMSATLRpFDVT 468
                                       348*******999986 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.5
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskl 94 
                                        + t   +l+  P+ + ae  +++l+ +++ +d r+ l  +g+++++ +sk+
  gi|313124967|ref|YP_004035231.1| 523 SRFTPGNTLVFFPSYAEAERYHERLQARMDVTD-RLFLDESGTPTEEIRSKF 573
                                       667777899999999999999999999999888.666556677776666666 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1     7e-07   0.00074       4     146 ..      16     270 ..      14     295 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7e-07
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG...... CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef...... 74 
                                       +++ Q ea++ ++e+l  + ++ +l++ a GtGKTl a+  + +++++++  k++++  ++++ +q+++ +      
  gi|313124967|ref|YP_004035231.1|  16 PYPNQGEAMDGIAEAL--EAERDVLVEGAPGTGKTLSALVPAVEYARQED--KTVVI--TTNVHQQMRQFVedarai 86 
                                       5789************..599*****************999999988744..77666..455666666444555677 PP

                                       ............................................................................. CS
                            ResIII  75 ............................................................................. 74 
                                                                                                                    
  gi|313124967|ref|YP_004035231.1|  87 trtepiravvfkgkssmchidveyqecqtlrdttrslvekeqdkaelseqadalvdrmrageqgaadartavtdeld 163
                                       77777777777777777777777777777777777777777777777766666666666666666666666666655 PP

                                       ...................GGGTGG....GEEEESSS-B--...................................- CS
                            ResIII  75 ...................kkflseaykeigkkvsgdkkka............................kekdstnk 104
                                                          +++++++++            +                             ++  ++ 
  gi|313124967|ref|YP_004035231.1| 164 tledeledlregniceyyyNNLTEDTDE------------FfswlfddvrtpediyeyadqrklcgyelLKEGMEEV 228
                                       5555555555444444443222222222............1222222223333333333333555666655666677 PP

                                       SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS CS
                            ResIII 105 kilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlga 146
                                       +++v +++ l  ++ +e+  +  +++ +  + ++DEaH++ +
  gi|313124967|ref|YP_004035231.1| 229 DLVVCNYHHLLDPNIREQFFRWLNREPEDVITVFDEAHNIES 270
                                       777777777776664433333333333333557777777766 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.2e-06    0.0044       4      51 ..      37      83 ..      34     146 .. 0.72
   2 ?    5.0   0.1     0.012        12      66     121 ..     227     290 ..     206     295 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.2e-06
                           DUF2075  4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlreal 51
                                      vlV+G++GtGKt+ +l  ++e+   +e++t+v+ +  h++++   e+ 
  gi|313124967|ref|YP_004035231.1| 37 VLVEGAPGTGKTLSALVPAVEY-ARQEDKTVVITTNVHQQMRQFVEDA 83
                                      79**************999999.5555555555555566555544443 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.012
                           DUF2075  66 klssfinnlsef......kkaeekkeepkedv.vivDEAhrllt.ksdqaekqseenqlkelmk 121
                                       +++ ++ n+++       ++  +  ++++edv +++DEAh + +  +d+a +  +en l++ ++
  gi|313124967|ref|YP_004035231.1| 227 EVDLVVCNYHHLldpnirEQFFRWLNREPEDViTVFDEAHNIESaARDHASRALTENTLEQALN 290
                                       5555555555555555443334444556666526********9965666677777888877665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.5e-07   0.00016      14      70 ..      29      86 ..      21     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                            ATPase 14 gGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa..edlrenaksl 70
                                      + +  +r vl+ G pGtGKt+ al  +++ a++ ++++v +t++ ++  +++ e+a+++
  gi|313124967|ref|YP_004035231.1| 29 EALEAERDVLVEGAPGTGKTLSALVPAVEYARQ-EDKTVVITTNVHQqmRQFVEDARAI 86
                                      56778899**********************999.999*****98776555666655544 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.38     4e+02       6      36 ..     126     156 ..     125     179 .. 0.71
   2 !   16.5   0.0   5.1e-06    0.0053     125     178 ..     439     493 ..     434     498 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.38
                                       CCCCHHCCCCCCCHHHHHHHHHCCCCHHHHS CS
                               HBB   6 ketdepklqdeysrLvegLreaeeereeeyv 36 
                                       ke+d+ +l+++ ++Lv+ +r+ e+ +++ ++
  gi|313124967|ref|YP_004035231.1| 126 KEQDKAELSEQADALVDRMRAGEQGAADART 156
                                       789*****************99996554333 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 5.1e-06
                                       CS-TCCHHHHH.HHCHCCCCCCTS-SSHHHHHHHHT.....EEE.S..S.GGHCCC CS
                               HBB 125 cldPskalrfl.kerlssllmsgtltpleeysdiiGle.aklkkfpspfpkEnliv 178
                                       c+ P+++++ l +e++ s+lms tl p++  +d++Gl  + +  +    p+En+ +
  gi|313124967|ref|YP_004035231.1| 439 CI-PREVTETLfEEVHASILMSATLRPFDVTEDVLGLSdPATMAYGLAYPEENRHT 493
                                       55.47777765489************************9**************976 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00023      0.24       4      53 ..      38      85 ..      37     128 .. 0.72
   2 ?    5.3   0.1     0.013        14      61     103 ..     234     278 ..     217     322 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                               Zot  4 lvtGapGsgKtsgavkkdllpalkegR..kiitnidGlrlerieqvlgekvs 53
                                      lv+GapG+gKt+ a+   +  a +e++  +i tn++    ++++q ++++  
  gi|313124967|ref|YP_004035231.1| 38 LVEGAPGTGKTLSALVPAVEYARQEDKtvVITTNVH----QQMRQFVEDARA 85
                                      89***************9999988654114456999....777775555444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.013
                               Zot  61 d..npegaetlkefakwatid.kgallviDEcqeifpvrakegrkd 103
                                       +  + + + + ++f+ w   + ++ + v+DE+++i ++ + + +++
  gi|313124967|ref|YP_004035231.1| 234 NyhHLLDPNIREQFFRWLNREpEDVITVFDEAHNIESAARDH-ASR 278
                                       3447788899999****99666************98877764.444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00083      0.87       1      39 [.      37      80 ..      37     104 .. 0.71
   2 ?    6.0   0.1     0.014        15      49      99 ..     247     298 ..     221     327 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00083
                                      EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSST CS
                               AAA  1 vllyGppGtGKTllakavakel.....gvefleisgsellskyv 39
                                      vl+ G pGtGKTl a   a e      ++ ++++++++ + ++v
  gi|313124967|ref|YP_004035231.1| 37 VLVEGAPGTGKTLSALVPAVEYarqedKTVVITTNVHQQMRQFV 80
                                      6999*********9988777753333233356666665555544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                                       HHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTTS CS
                               AAA  49 lfkeakekakpsilfiDEidalaksr.sgseseeeervvnqLlteldgvkkk 99 
                                       +f+ + ++ + +i ++DE++++ ++  +++++  +e++++q l+el++ +++
  gi|313124967|ref|YP_004035231.1| 247 FFRWLNREPEDVITVFDEAHNIESAArDHASRALTENTLEQALNELEDTDDS 298
                                       344443333458999*******998866667777888888888888887765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.8e-05     0.019      13      55 ..      28      70 ..      18      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                                      HHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEE CS
                              PhoH 13 lealkkndivfaiGpaGtGKtylavalavealkkkkvkriilt 55
                                      +eal+++  v + G  GtGKt+ a++ ave+ ++++ + +i t
  gi|313124967|ref|YP_004035231.1| 28 AEALEAERDVLVEGAPGTGKTLSALVPAVEYARQEDKTVVITT 70
                                      567778888999*******************999886666654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.2e-05     0.034      12      67 ..      29      84 ..      17     158 .. 0.75
   2 ?    0.3   0.2      0.48     5e+02     135     185 ..     246     296 ..     243     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                            AAA_30 12 alltsgdrvavltGpAGtGKtt.alkalreaweaaggrviglAptgkaAkvLaeelg 67
                                      ++l+ + r ++++G++GtGKt  al  ++e ++++ ++v++ +  +++ ++  e++ 
  gi|313124967|ref|YP_004035231.1| 29 EALEAE-RDVLVEGAPGTGKTLsALVPAVEYARQEDKTVVITTNVHQQMRQFVEDAR 84
                                      334444.46899*********626888899999999999999888887777554443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                            AAA_30 135 gvlrdlveaagigtaeLtevvRqkeseeraaalalregdaeealealadrg 185
                                       + +r+l ++ +   +  +e + +++++  +a++al e++ e+al+ l+d +
  gi|313124967|ref|YP_004035231.1| 246 QFFRWLNREPEDVITVFDEAHNIESAARDHASRALTENTLEQALNELEDTD 296
                                       56888877667777778999999999999**************99999875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1   0.00016      0.17      25     124 ..      35     163 ..      22     178 .. 0.62
   2 ?    1.2   0.1       0.4   4.2e+02     130     156 ..     251     277 ..     235     353 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            AAA_16  25 elvllsGesGvGKsslv..rellralekd..............................ggiflrgkcdqlesaipy 69 
                                       + vl+ G++G+GK+  +   ++  +++++                              ++++++gk   ++ +++y
  gi|313124967|ref|YP_004035231.1|  35 RDVLVEGAPGTGKTLSAlvPAVE-YARQEdktvvittnvhqqmrqfvedaraitrtepiRAVVFKGKSSMCHIDVEY 110
                                       679**********8666224444.44444566777777777777777777777777776677777777777777777 PP

                            AAA_16  70 ...salaqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellk 124
                                          ++l ++  +++l++++ d+   ael++ +++l ++++a+ + a+++++++ ++l 
  gi|313124967|ref|YP_004035231.1| 111 qecQTLRDT--TRSLVEKEQDK---AELSEQADALVDRMRAGEQGAADARTAVTDELD 163
                                       442223333..33777766666...566666666777777555555555544444443 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.4
                            AAA_16 130 lsrderplvlvlDdlqwadeaslqlla 156
                                       l r+ + ++ v+D+++ +++a ++  +
  gi|313124967|ref|YP_004035231.1| 251 LNREPEDVITVFDEAHNIESAARDHAS 277
                                       444333355566666655554443321 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.1e-05     0.096     162     195 ..     245     279 ..     205     297 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-05
                            AAA_34 162 eqlveWlg.edfdGvivfDEchkaknlakseekka 195
                                       eq+ +Wl+ e  d + vfDE+h+++++a ++ ++a
  gi|313124967|ref|YP_004035231.1| 245 EQFFRWLNrEPEDVITVFDEAHNIESAARDHASRA 279
                                       799*****555666679*********998764433 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00063      0.66      36      61 ..      37      62 ..      27     146 .. 0.88
   2 ?   -3.1   0.1       4.8     5e+03     109     142 ..     262     294 ..     243     317 .. 0.64
   3 ?    0.7   0.0      0.32   3.4e+02      49     109 ..     581     643 ..     579     660 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00063
                            AAA_25 36 allaGapgtGKttlaldlalavatGk 61
                                      +l+ GapgtGKt  al  a+++a+ +
  gi|313124967|ref|YP_004035231.1| 37 VLVEGAPGTGKTLSALVPAVEYARQE 62
                                      7889*****************99654 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.8
                            AAA_25 109 agv.eslpLfakdrggtlltadvdaleaaieeveg 142
                                        ++ +++  +a d+ + +lt+ +  le+a++e e+
  gi|313124967|ref|YP_004035231.1| 262 FDEaHNIESAARDHASRALTENT--LEQALNELED 294
                                       34555666666665555566554..5555555544 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.32
                            AAA_25  49 laldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.......rddarllvldla 109
                                       l+++l  ++a+G ++ g+     ++V++v    +   l +R++a+  a+       r+ ++ +++ ++
  gi|313124967|ref|YP_004035231.1| 581 LLTSLWGTLAEGVSFDGD---DARTVVVVGVPYPH--LSERMEAIQDAYdrvyssrREAGWRYAVEIP 643
                                       677888889999999994...78899999977777..********99997777776666666666654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9   0.00027      0.28       9     113 ..      38     173 ..      32     183 .. 0.83
   2 ?    2.5   0.2      0.15   1.6e+02      84     117 ..     249     297 ..     175     311 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............... 70 
                                       +v G +GtGKT+++   + ++ ++      ++++v +t ++    +++ ++   ++  e  +               
  gi|313124967|ref|YP_004035231.1|  38 LVEGAPGTGKTLSALVPAVEYARQ------EDKTVVITTNVHQQMRQFVEDARAITRTEPIRavvfkgkssmchidv 108
                                       789**********98776666444......88889899999999999999999999988888999999999999999 PP

                            AAA_22  71 .................erlsseellealeqalrarav.......ielliiDEaqhlrseealeeLr 113
                                                        +++++ el e+    +++ ++        +  + DE + l  e+ le+Lr
  gi|313124967|ref|YP_004035231.1| 109 eyqecqtlrdttrslveKEQDKAELSEQADALVDRMRAgeqgaadARTAVTDELDTL--EDELEDLR 173
                                       99999999999999999777777777777766666666777777799999*******..88888887 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                            AAA_22  84 qalraravielliiDEaqhlr...s............eealeeLrslln 117
                                       + l++    ++ + DEa+++    +            e+al+eL +  +
  gi|313124967|ref|YP_004035231.1| 249 RWLNREPEDVITVFDEAHNIEsaaRdhasraltentlEQALNELEDTDD 297
                                       44444444567799*****976551455567777777777777766655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5   0.00042      0.44      10      42 ..      27      60 ..      19     177 .. 0.85
   2 ?   -2.2   0.0       2.7   2.8e+03      96     131 ..     264     297 ..     240     393 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                            AAA_11 10 iksalseseitliqGPPGtgKT.ktivellsqll 42
                                      i++al+ +  +l++G PGtgKT +++v  ++++ 
  gi|313124967|ref|YP_004035231.1| 27 IAEALEAERDVLVEGAPGTGKTlSALVPAVEYAR 60
                                      58899999999***********888887777774 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                            AAA_11  96 eeeriseavksvsleekvekrlekeekaqlakeisk 131
                                       e+ +i++a++++  +  +e+ le+    +  +++++
  gi|313124967|ref|YP_004035231.1| 264 EAHNIESAARDHASRALTENTLEQA--LNELEDTDD 297
                                       3333444444444333333333332..111111111 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.2   0.00018      0.19      55     119 ..     112     176 ..     108     178 .. 0.91
   2 ?   -2.3   0.3       4.1   4.3e+03      60      70 ..     283     293 ..     264     316 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                        TPR_MLP1_2  55 dvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqN 119
                                       + ++l+++   l e +++ ael ++a+++   + + e+  +  +++  +el+ le  +edl e N
  gi|313124967|ref|YP_004035231.1| 112 ECQTLRDTTRSLVEKEQDKAELSEQADALVDRMRAGEQGAADARTAVTDELDTLEDELEDLREGN 176
                                       5577777777889999*********************************************9987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.1
                        TPR_MLP1_2  60 qalreelnelk 70 
                                       ++l + lnel+
  gi|313124967|ref|YP_004035231.1| 283 NTLEQALNELE 293
                                       22222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (725 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.49
# Mc/sec: 4461.94
//
Query:       gi|313124968|ref|YP_004035232.1|  [L=452]
Description: cytochrome p450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-90  303.0   0.0    4.3e-90  302.7   0.0    1.0  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.7   0.0   2.4e-94   4.3e-90       1     456 [.       5     441 ..       5     446 .. 0.90

  Alignments for each domain:
  == domain 1  score: 302.7 bits;  conditional E-value: 2.4e-94
                                       --SESEHHCCHCHHHHTTTCCHHHHHHHHHHHH-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHH CS
                              p450   1 Ppgptplplvgnllqlgrkeelhevlrklqkkygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallat 77 
                                       Ppgp+ +pl+gn  +++  + ++ +lr++++ yg+++ + lg+ ++ +l++p ++++vl+ ++   +++ ++ + + 
  gi|313124968|ref|YP_004035232.1|   5 PPGPKGVPLFGNSREYA--KDPFTFLRQVSEAYGDVVYFGLGPLDTYMLTNPADIERVLVSED--AKFH-KPDFQDD 76 
                                       9****************..889999*************************************6..5554.5566667 PP

                                       HHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHH CS
                              p450  78 srkpfkgkgvlfangekwkklRrfltptltsfgklsleelveeeaedlveklrkkagesselditellskaaldvig 154
                                       + ++ +g g+l+++ge+w+k+R +  p++    + +l e++++ a  +ve +++        d++  ++++++ +i 
  gi|313124968|ref|YP_004035232.1|  77 AIGTLLGDGLLLSEGETWRKQRELAQPSFDPRRIAALGETMTDHATAMVEGWNDGEV----RDVQLEMARVTVKIIV 149
                                       7899**************************996669999999999999999986443....579************* PP

                                       HHHHSSHHHTTTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCH CS
                              p450 155 silFgarfdlledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerretl 231
                                       + +Fg++   l de+  + ++  e l + +        l f + ++ pt+ +r++k+   +l++++d ++ er  t 
  gi|313124968|ref|YP_004035232.1| 150 DAMFGSS---LADERVRTVQENLEPLGKRF----EPDPLRFLIPDWAPTRENREYKQSISILEGIIDDVVAERLGTE 219
                                       ******8...66775555555555554444....3333444455788*****************************9 PP

                                       CHC.......SCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHH CS
                              p450 232 dsa.......kksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklre 301
                                       ++        +  ++d+l++ll ak  ++g  + +d++++ +++++l+aG+dTt+ tl++a+y+L ++Pe ++k++ 
  gi|313124968|ref|YP_004035232.1| 220 NDPsaavageDGAPMDLLSVLLRAK--QRG--EQTDQQIRDEMMTMLLAGHDTTALTLTYAFYLLSQHPESEAKVQA 292
                                       9999******889***********8..333..47******************************************* PP

                                       HHHHHCCTTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSS CS
                              p450 302 EidevlgdkreptyddlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfp 378
                                       E+d+v g+ ++pt +d+ +  yl+ v++E++Rl+p+v+  + Re   dv ++gy ip G+ ++++ + +hr+p  ++
  gi|313124968|ref|YP_004035232.1| 293 EVDKVCGG-ETPTVADVRQFDYLERVLQEAMRLYPPVY-VIFREPQVDVRLGGYRIPSGSAIMLPQWVVHRSPRWYD 367
                                       ******98.47***************************.************************************** PP

                                       STTS--GGGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSGGEEESSCSSEEE CS
                              p450 379 nPeeFdpeRFldekgnskrksfaflPFGaGpRnCiGerlArmelklflatlLqnFevelqpetdpppileksglllp 455
                                        P eFdp+R+ +e+ + +r+ f+++PFG GpR CiG+++ +me kl+lat+ q +e+++   +d p +l++ +l+++
  gi|313124968|ref|YP_004035232.1| 368 APTEFDPDRWRPERRA-SRPRFSYFPFGGGPRHCIGKQFSMMEAKLILATVAQAYELDYV--RDRPFSLRG-SLTMH 440
                                       **************95.5****************************************85..466666665.35555 PP

                                       S CS
                              p450 456 p 456
                                       p
  gi|313124968|ref|YP_004035232.1| 441 P 441
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2774.46
//
Query:       gi|313124969|ref|YP_004035233.1|  [L=170]
Description: hypothetical protein Hbor_01830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-19   70.8   0.0    1.3e-19   70.6   0.0    1.2  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    4.5e-10   39.6   0.1    0.00017   21.7   0.0    2.7  2  LigT_PEase       LigT like Phosphoesterase
    3.5e-06   27.1   0.0    4.1e-06   26.8   0.0    1.1  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain


Domain annotation for each model (and alignments):
>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.0   2.2e-23   1.3e-19      37     147 ..      48     157 ..       8     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 2.2e-23
                   2_5_RNA_ligase2  37 dedladlaellsrlaketepfevrldgfgvFeh....kks.vvylsvsdsealqalraallealpeagdkedsgeft 108
                                        ++l++l+e+l++++++ +pfe+r+dg+++Fe+    + + vvyl v  s+ l++l+++l+++++  +  e  +e+t
  gi|313124969|ref|YP_004035233.1|  48 ADSLPRLRERLRETLRSVAPFEARIDGIDYFERptrgD-GpVVYLRV-ESSGLHELHRRLCTEFGTVEGMEG-DEYT 121
                                       3445*******************************955.45******.*******************98875.**** PP

                   2_5_RNA_ligase2 109 PHlTiaqsadstsaaelleklaqalpplefevdevallr 147
                                       PH+T+a+  +  +   + + ++++ ++++++v ev ++ 
  gi|313124969|ref|YP_004035233.1| 122 PHVTLARGGRIDD---AAALAEREIEAVRWTVGEVRVWD 157
                                       *******996666...445555679**********9986 PP

>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.9e-06     0.017      44      85 ..      45      87 ..       4      89 .. 0.90
   2 !   21.7   0.0   2.9e-08   0.00017      11      82 ..      98     161 ..      92     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-06
                                      EESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCCE CS
                        LigT_PEase 44 evdeekvpellealaeiasgaepfelkvdgvglfpsrl.rprv 85
                                      + d++ +p+l e+l+e  + ++pfe ++dg+ +f+ +    ++
  gi|313124969|ref|YP_004035233.1| 45 DPDADSLPRLRERLRETLRSVAPFEARIDGIDYFERPTrGDGP 87
                                      456999****************************988855555 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.9e-08
                                       HHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCS CS
                        LigT_PEase  11 larlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlr 82 
                                       l +l+++l  +++  ++    +++pH+TLa+ g +d+ +     +alae   ++e+++++v +v ++ sr r
  gi|313124969|ref|YP_004035233.1|  98 LHELHRRLCTEFGTVEGMEGDEYTPHVTLARGGRIDD-A-----AALAER--EIEAVRWTVGEVRVWDSRYR 161
                                       6677777777777777755599************974.2.....233444..455667*********99865 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   6.9e-10   4.1e-06      61     147 ..      47     128 ..      34     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 6.9e-10
                                       HHHHHHHHHHHHHHHHTT.S--EEEEEEEEEE.....T..TTEEEEEE--SHHHHHHHHHHHHHHHHHHTTT--B-- CS
                         AKAP7_NLS  61 akevLkevkeeikdaldn.kplslrlkGletfnddpak..arVlYakveeesneekLqeladriikafeeaglvlek 134
                                        ++ L +++e++++ l    p++ r++G+++f+  p++    V+Y++ve    ++ L el++r+ ++f   g v+  
  gi|313124969|ref|YP_004035233.1|  47 DADSLPRLRERLRETLRSvAPFEARIDGIDYFE-RPTRgdGPVVYLRVE----SSGLHELHRRLCTEF---GTVEGM 115
                                       56788999999****9666*************5.66663577*******....889************...666666 PP

                                       SS-.---EEEEEE CS
                         AKAP7_NLS 135 dkkkvklHaTlmn 147
                                       + +++++H+Tl+ 
  gi|313124969|ref|YP_004035233.1| 116 EGDEYTPHVTLAR 128
                                       666699****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 988.65
//
Query:       gi|313124970|ref|YP_004035234.1|  [L=65]
Description: hypothetical protein Hbor_01840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        1.9    8.4   5.3        8.3    6.3   0.6    2.1  2  DUF5337    Family of unknown function (DUF5337)


Domain annotation for each model (and alignments):
>> DUF5337  Family of unknown function (DUF5337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.6   0.00046       8.3      20      39 ..      18      37 ..      16      42 .. 0.87
   2 ?    4.7   0.4    0.0015        26      16      29 ..      49      62 ..      46      65 .] 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00046
                           DUF5337 20 iavtmllwlgaqwigeqlgl 39
                                      i v +++wl+++++g  +g 
  gi|313124970|ref|YP_004035234.1| 18 ILVLVVIWLVLKIVGDVVGF 37
                                      78889**********99986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0015
                           DUF5337 16 valviavtmllwlg 29
                                       ++vi v ++lwl+
  gi|313124970|ref|YP_004035234.1| 49 LGVVILVLIVLWLL 62
                                      79**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 431.33
//
Query:       gi|313124971|ref|YP_004035235.1|  [L=320]
Description: hypothetical protein Hbor_01850 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1893.69
//
Query:       gi|313124972|ref|YP_004035236.1|  [L=177]
Description: hypothetical protein Hbor_01860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.006   17.1   0.2      0.006   17.1   0.2    1.5  2  Spectrin  Spectrin repeat
  ------ inclusion threshold ------
      0.036   14.3   0.1      0.092   13.0   0.1    1.7  1  XhlA      Haemolysin XhlA


Domain annotation for each model (and alignments):
>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   6.7e-07     0.006      28      68 ..      26      66 ..      18      76 .. 0.87
   2 ?   -3.3   0.1       1.4   1.3e+04       3      12 ..     145     154 ..     141     164 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.7e-07
                                      SCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin 28 dlgkdleevqallkkhkaleaelaaqqervkalnelaekll 68
                                      d g  + +v++l+++  ++ + ++++++++k++++ +e+++
  gi|313124972|ref|YP_004035236.1| 26 DDGMLYGAVEDLQQQVSEHDESIETHKTNIKNIEDRQEQMM 66
                                      55666789******************************996 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHHH CS
                          Spectrin   3 lqqfaqdade 12 
                                       l+q++++++e
  gi|313124972|ref|YP_004035236.1| 145 LEQMYYEMAE 154
                                       3333333333 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     1e-05     0.092      20      53 ..      34      67 ..      20      72 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                              XhlA 20 vdkleekaaeaeekiknleedlkklesnqkWlir 53
                                      v++l++  +e++e+i+    ++k++e+ q   ++
  gi|313124972|ref|YP_004035236.1| 34 VEDLQQQVSEHDESIETHKTNIKNIEDRQEQMMG 67
                                      6677777777777777777777777777655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      779  (0.0434492); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1113.23
//
Query:       gi|313124973|ref|YP_004035237.1|  [L=344]
Description: hypothetical protein Hbor_01870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2289.86
//
Query:       gi|313124974|ref|YP_004035238.1|  [L=366]
Description: hypothetical protein Hbor_01880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-31  107.6   1.2    6.8e-31  106.3   1.2    1.8  1  DUF4157        Domain of unknown function (DUF4157)
  ------ inclusion threshold ------
      0.016   15.5   0.4      0.035   14.4   0.2    1.6  1  Peptidase_M91  Effector protein
        1.2    9.3   3.6        5.1    7.2   0.5    3.0  2  PKHD_C         PKHD-type hydroxylase C-terminal domain


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   1.2   1.1e-34   6.8e-31       2      78 ..      98     174 ..      97     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 1.1e-34
                           DUF4157   2 lpeavraemerafgadlsdVrvhtgsaaaraaralgAqAfTlgndivfaageyqpesaagrellaHELtHvvqqreg 78 
                                       l++++++ me ++g++l+dVrvhtg++aa+a+++++A+AfT+gn+i+f++gey+p+sa+g+++laHEL+Hv qq++g
  gi|313124974|ref|YP_004035238.1|  98 LDTSIQRAMEDRMGDNLGDVRVHTGPSAAKACEDINARAFTVGNHIAFNHGEYDPSSAEGQHILAHELAHVRQQTGG 174
                                       899***********************************************************************986 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   5.9e-06     0.035      69     135 ..     136     197 ..      85     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.9e-06
                     Peptidase_M91  69 gegtdaeinynpafsseeegkegrPsavLyHElaHaydalngtlddgeydgkdeedssgvpneErqA 135
                                        ++ +++i +n         +  + +++L+HElaH+++++ g +   +++g+ e d +   + Er+A
  gi|313124974|ref|YP_004035238.1| 136 AFTVGNHIAFNHGEYDP---SSAEGQHILAHELAHVRQQTGGAVSMLPQEGELEIDPDP--RLEREA 197
                                       45555666666553333...45556699**************99888888776666654..555554 PP

>> PKHD_C  PKHD-type hydroxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.5   0.00085       5.1      10      24 ..       4      19 ..       3      24 .. 0.87
   2 ?    1.2   0.2     0.065   3.9e+02       9      21 ..      97     109 ..      96     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00085
                            PKHD_C 10 LDqaIqrlraelg.dd 24
                                      LD++Iqrl++++g d+
  gi|313124974|ref|YP_004035238.1|  4 LDTKIQRLAKKHGaDQ 19
                                      9************554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.065
                            PKHD_C   9 dLDqaIqrlrael 21 
                                       +LD++Iqr  ++ 
  gi|313124974|ref|YP_004035238.1|  97 QLDTSIQRAMEDR 109
                                       69*****987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2146.20
//
Query:       gi|313124975|ref|YP_004035239.1|  [L=367]
Description: spfh domain, band 7 family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-36  124.6   1.3    6.8e-36  123.9   0.8    1.6  1  Band_7    SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.054   13.2   0.1       0.11   12.2   0.1    1.6  1  Band_7_1  SPFH domain-Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.9   0.8   7.6e-40   6.8e-36      12     177 ..      63     222 ..      53     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 7.6e-40
                            Band_7  12 vrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaaveresan 88 
                                       + fG++++ lepGl +i Pf+ +++++++r+qtl+v+  ++++t D+ pvt d++v+ rv +da+k++++v    ++
  gi|313124975|ref|YP_004035239.1|  63 TVFGEYRGLLEPGLNIIPPFVARTYTFDMRTQTLNVPP-QEAITEDNSPVTADAVVYLRV-KDAKKAFLEV----DQ 133
                                       44************************************.*********************.**********....** PP

                            Band_7  89 ldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaaea 165
                                       +++ ++ + + +lr+vi++m+l+e ls ree++ ++ +elne  +++Gvev++v +++++p+++v++a+++   ae+
  gi|313124975|ref|YP_004035239.1| 134 YKTAVSYLSQTSLRAVIGDMELDETLSRREEINRRIHRELNEPTDEWGVEVESVEVSEVKPSADVQSAMEEQSSAER 210
                                       ***************************************************************************** PP

                            Band_7 166 eaqaeiaraeae 177
                                        ++a i +a+++
  gi|313124975|ref|YP_004035239.1| 211 HRRAMILEAQGK 222
                                       **9999888875 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.2e-05      0.11     157     209 ..     156     208 ..      82     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                          Band_7_1 157 ldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                        +  ++ ee+ ++++  l+e  +e G+e+e++e++++    +v+ a+++++s+
  gi|313124975|ref|YP_004035239.1| 156 DETLSRREEINRRIHRELNEPTDEWGVEVESVEVSEVKPSADVQSAMEEQSSA 208
                                       345578999****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2089.30
//
Query:       gi|313124976|ref|YP_004035240.1|  [L=63]
Description: hypothetical protein Hbor_01900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 406.98
//
Query:       gi|313124977|ref|YP_004035241.1|  [L=361]
Description: hypothetical protein Hbor_01910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-29  100.8  23.4    8.7e-29  100.8  23.4    1.6  1  TauE           Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
        1.2    8.9  17.1       0.73    9.6   4.8    3.2  3  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8  23.4   9.7e-33   8.7e-29       4     235 ..      56     352 ..      52     353 .. 0.85

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 9.7e-33
                              TauE   4 agllaG.fvagllGiGggliavPlLll.l..l....ppavavatsllavvatslsgalahrrrgnvdwrlllllllg 72 
                                       ++l +G ++ + +Gi g+ ++vP+L++ +  +    +p ++v + l++ +++  s+a+a+ + g vd rl+l+l+ g
  gi|313124977|ref|YP_004035241.1|  56 VFL-TGaTIVNTVGISGSALFVPFLIFiFpqFaqplSPTTIVKVGLISEAFGLSSSAVAFVQYGLVDRRLALTLVGG 131
                                       445.555********************5565489999999************************************* PP

                              TauE  73 sliGallGallllllpsellkllfgvlllllallmllrkkr.................................... 113
                                       s++ +++Gall+  +p+ +++ l+g++ll++a+l+++                                        
  gi|313124977|ref|YP_004035241.1| 132 SVPFVIAGALLSFIIPEMVFHSLLGLALLASAYLLFRADLGhegagssddseavadggslntdlpndagklgpagvr 208
                                       *********************************99984444678999**********************99999999 PP

                              TauE 114 .............srak....grerrptaillvligglvGllsGllGiGgGfllvpllllllglplkkavatsllli 173
                                                       +    +r  + ++        ++Gl+ Gl G G+G l+++ +l  +++p+++a++t  +++
  gi|313124977|ref|YP_004035241.1| 209 tddngtvtrvdreG--DdytyTRGGYLRRF---GNYSIGGLFQGLAGFGVGELGIISML-GTNVPVRVAIGTNHIVV 279
                                       99998887776430..23222223333333...334569*****************998.59*************** PP

                              TauE 174 lvislagalgyal....agavd..........wpllllllpgallGallGarlarrlsertlrrlfallllvlgvk 235
                                       +++++ + l++++                   w+++++ +p++++G++++ ++++ l + t++ ++++l +v++v 
  gi|313124977|ref|YP_004035241.1| 280 ALTAVLASLVHVFggglV---GghslslattpWNMVVFTVPATVIGGQIAPYVSNALETDTIKNFVGVLFTVISVA 352
                                       ***********7764440...34444455555999999**********************************9986 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.8   8.2e-05      0.73     127     177 ..      11      64 ..       3      73 .. 0.85
   2 ?    1.8   1.3      0.02   1.7e+02     143     180 ..     124     159 ..     109     187 .. 0.79
   3 ?    4.2   0.0    0.0037        33      88     172 ..     228     316 ..     212     335 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 8.2e-05
                     FA_desaturase 127 psksrrrkwrllawlllllawlglwlalllllglall...lwlvplllllflla 177
                                       +s+ r +   +l + ++++++++lw+++ +++gl ++   +wl+p++l +++++
  gi|313124977|ref|YP_004035241.1|  11 KSFLRHQHLFVLIAPVVFVTAVLLWAPTDGAGGLDHWleyWWLFPVFLTGATIV 64 
                                       45556666899999999999*************************999998765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.02
                     FA_desaturase 143 lllawlglwlalllllglalllwlvplllllfllalvl 180
                                       l+l+++g+ ++++ +++l+   +++p +++++ll l l
  gi|313124977|ref|YP_004035241.1| 124 LALTLVGGSVPFVIAGALL--SFIIPEMVFHSLLGLAL 159
                                       4455699999999999998..99999999999998774 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0037
                     FA_desaturase  88 rfeglfryllrlllgllvlg...wllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllllgla 161
                                       +++g+ r++ ++  g l+ g   + ++ ++  ++  l+ +   +  + ++++++a+ ++l++++ ++++ l+ +g++
  gi|313124977|ref|YP_004035241.1| 228 TRGGYLRRFGNYSIGGLFQGlagFGVGELG--IISMLGTNVPVRVAIGTNHIVVALTAVLASLVHVFGGGLV-GGHS 301
                                       445555555666665555553222222222..3333333333333344448888888888885555555554.5666 PP

                     FA_desaturase 162 ll....lwlvpllll 172
                                       l+     w ++++++
  gi|313124977|ref|YP_004035241.1| 302 LSlattPWNMVVFTV 316
                                       665888554444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2279.61
//
Query:       gi|313124978|ref|YP_004035242.1|  [L=38]
Description: hypothetical protein Hbor_01920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 247.51
//
Query:       gi|313124979|ref|YP_004035243.1|  [L=704]
Description: excinuclease ABC subunit b [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-32  111.9   0.0    3.3e-32  110.5   0.0    1.8  1  UvrB_inter  UvrB interaction domain
    4.8e-21   74.3   0.2      1e-20   73.3   0.2    1.6  1  UvrB        Ultra-violet resistance protein B
    1.9e-17   63.6   0.1    5.5e-17   62.1   0.1    1.8  1  Helicase_C  Helicase conserved C-terminal domain
    2.1e-09   37.6   0.1    3.3e-08   33.7   0.0    2.3  2  ResIII      Type III restriction enzyme, res subunit
    7.8e-08   31.8   8.2    7.8e-08   31.8   8.2    3.2  2  UVR         UvrB/uvrC motif
    0.00075   19.3   0.1      0.013   15.3   0.0    2.8  3  DEAD        DEAD/DEAH box helicase
     0.0071   16.3   0.4      0.066   13.2   0.0    2.8  4  UB2H        Bifunctional transglycosylase second domain
     0.0097   16.0   0.5      0.086   12.9   0.0    2.7  3  DUF87       Helicase HerA, central domain
  ------ inclusion threshold ------
      0.016   15.6   0.4        8.2    6.8   0.3    2.7  2  AAA_19      AAA domain
      0.022   15.0   0.3          5    7.4   0.3    2.8  2  AAA_22      AAA domain
      0.039   13.7   0.4       0.37   10.5   0.0    2.5  3  AAA_30      AAA domain
      0.045   13.5   1.9        3.6    7.2   0.1    3.1  3  RPN7        26S proteasome subunit RPN7
      0.091   13.2   0.0        8.4    6.9   0.0    2.6  2  DNA_circ_N  DNA circularisation protein N-terminus
        0.5   10.6   3.0        4.4    7.5   0.1    3.3  4  FlaG        FlaG protein
        7.1    5.9   8.6        5.4    6.3   0.3    3.7  4  CorA        CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0   2.8e-35   3.3e-32       1      91 []     176     265 ..     176     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 2.8e-35
                        UvrB_inter   1 lelkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgksl 77 
                                       l+l+vg+++dr++llr+Lv+l+Yerndv++++GtFrvrGdtve+fp++ +++a+rief+gdei++++++dpl+g ++
  gi|313124979|ref|YP_004035243.1| 176 LRLEVGDRMDRDDLLRRLVDLNYERNDVDFQQGTFRVRGDTVEVFPMY-GRYAVRIEFWGDEIDRMQKLDPLQGAVK 251
                                       789*********************************************.7*************************** PP

                        UvrB_inter  78 ekleeitifPakhf 91 
                                       ++  ++ i Pa+h+
  gi|313124979|ref|YP_004035243.1| 252 STEPAVLIHPAEHY 265
                                       *************9 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.2   8.5e-24     1e-20       1      42 [.     567     608 ..     567     609 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 8.5e-24
                                       EE-SS--HHHHHHHHHHHHHHHHHHHHHHHHT------XXXX CS
                              UvrB   1 lYADkiTdSMkkAideTerRReiQeaYNeehgItPktikKki 42 
                                       lYAD+ TdSM++Ai+eT+rRR+iQ+a+Neehg  P+ti K++
  gi|313124979|ref|YP_004035243.1| 567 LYADETTDSMEAAIEETQRRRAIQQAFNEEHGYEPTTIDKAV 608
                                       8***************************************97 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   4.6e-20   5.5e-17      10     109 ..     454     559 ..     445     561 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 4.6e-20
                                       H.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                        Helicase_C  10 l.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                       + ++ e+++++l+ + t++++e+ +++l e+ g+ va++h e+ + er e +++ + g++dvL+  + + +G+dip+
  gi|313124979|ref|YP_004035243.1| 454 IdTRIERDERTLVTTLTKRMAEDlTEYL-EEAGVDVAYMHDETDTLERHELIRDLRLGHIDVLVGINLLREGLDIPE 529
                                       35567999*************9977777.7779******************************************** PP

                                       ESEEEESSSS.....SSHHHHHHHHTTSSS CS
                        Helicase_C  85 vnlVinfdlp.....rnvtsyiqriGRtgR 109
                                       v+lV ++d++     r++t++iq +GR++R
  gi|313124979|ref|YP_004035243.1| 530 VSLVAILDADqegflRSTTTLIQTMGRAAR 559
                                       **********88888889***********9 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   2.7e-11   3.3e-08       7     128 ..      33     146 ..      28     157 .. 0.74
   2 ?    1.3   0.0      0.26   3.1e+02     101     148 ..     322     370 ..     268     414 .. 0.49

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.7e-11
                                       HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                            ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                        Q eaie+l+  ++  + ++  +   TG+GKT + a ++e+++k      +l+++++k+l  q++eefk+++++++ 
  gi|313124979|ref|YP_004035243.1|  33 DQPEAIEQLARGFE-AGMEKQTLLGVTGSGKTNTVAWTVEEIQK-----PTLVIAHNKTLAAQLYEEFKNLFPDNAV 103
                                       699**********9.9999999999*****************99.....8***********************9874 PP

                                       .GEEEESSS-B--.......-SEEEEEHHHHHHTH........HH CS
                            ResIII  84 eigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseel 128
                                         + +vs   + + e  +++++ ++ +  s+++++++ +   ++ 
  gi|313124979|ref|YP_004035243.1| 104 --EYFVSYYDYYQPEAYIEQTDTYIDKDMSINEEIDRLRHSATRS 146
                                       ..4444433333334444466666666666666654444444444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.26
                                       ...-SEEEEEHHHHHHTH........HHHTTT-S...EEEEETGGGTTS........T CS
                            ResIII 101 stnkkilvttiqsldadseeeeeeseellrdrfd...viiiDEaHrlgak.......k 148
                                       ++n ++++++ +s da+      +  ++     +   + +iDE+H +  +       +
  gi|313124979|ref|YP_004035243.1| 322 IENYSVHMSNRESGDAPY-----TLLDYF----PddfLTVIDESHQTLPQirgqfagD 370
                                       344444444444444444.....333333....24456788****9876555444440 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.6      0.85     1e+03       2      13 ..     274     285 ..     273     288 .. 0.83
   2 !   31.8   8.2   6.5e-11   7.8e-08       2      35 ..     636     669 ..     635     670 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.85
                               UVR   2 klikeLeeemee 13 
                                       + i+e+ee mee
  gi|313124979|ref|YP_004035243.1| 274 QAISEIEELMEE 285
                                       5699******98 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 6.5e-11
                               UVR   2 klikeLeeemeeAaenedFEkAAklRDqinalkk 35 
                                       ++i+ Le+ m+eAa+n++FE+AA +RD+i+ l++
  gi|313124979|ref|YP_004035243.1| 636 EQIEYLEDRMQEAADNLEFELAADIRDRIRDLRR 669
                                       67888*************************9986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05     0.013       4      73 ..      34     100 ..      32     147 .. 0.76
   2 ?    0.1   0.0      0.48   5.8e+02     125     169 ..     351     412 ..     348     418 .. 0.53
   3 ?   -2.3   0.0       2.8   3.3e+03      58      82 ..     468     492 ..     436     519 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHTT.....CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 Qaeaiplilgg.....gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                       Q eai+++ +g     ++  + + TGsGKT   +  v         + ++ +l+++  + La q ++++k+++  
  gi|313124979|ref|YP_004035243.1|  34 QPEAIEQLARGfeagmEKQTLLGVTGSGKTNTVAWTVE--------EIQKPTLVIAHNKTLAAQLYEEFKNLFPD 100
                                       667777777554444456667889*******9776665........334567******************99874 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.48
                                       EEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT.................SEEEEEESSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxx RF
                              DEAD 125 lVlDEadrlldqgfsdfinrilnqlpqitcdgklq.................rqvivlSATl 169
                                        V+DE ++ l q +++f    +++ +  ++  +l                   q++ +SAT+
  gi|313124979|ref|YP_004035243.1| 351 TVIDESHQTLPQIRGQFAGDKARKDSLVENGFRLPtaydnrpltfeefeektDQTLYVSATP 412
                                       68888888888866665554333332222222211344555555555555545566666665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHTTTSTSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  58 eLaeqtlnnlkkfkkyidlrvllii 82 
                                        L++ ++++l+++++++++ v  + 
  gi|313124979|ref|YP_004035243.1| 468 TLTKRMAEDLTEYLEEAGVDVAYMH 492
                                       3444444455555554443443332 PP

>> UB2H  Bifunctional transglycosylase second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.5e-05     0.066       1      42 [.     178     219 ..     178     222 .. 0.95
   2 ?   -2.1   0.0       3.4     4e+03      58      75 ..     227     244 ..     224     247 .. 0.87
   3 ?   -3.3   0.0       8.1   9.7e+03       5      36 ..     391     418 ..     388     422 .. 0.61
   4 ?   -2.3   0.1       3.9   4.6e+03      38      54 ..     662     678 ..     659     680 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.5e-05
                              UB2H   1 LypGaalsaaqleqeLellgYrkvsnvtrpGeyavsgnriel 42 
                                       L+ G+++++++l + L +l+Y +++   ++G+++v+g+++e+
  gi|313124979|ref|YP_004035243.1| 178 LEVGDRMDRDDLLRRLVDLNYERNDVDFQQGTFRVRGDTVEV 219
                                       789*********************9999************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.4
                              UB2H  58 rvrlrfagnrvasiqdld 75 
                                        vr++f g+++ ++q+ld
  gi|313124979|ref|YP_004035243.1| 227 AVRIEFWGDEIDRMQKLD 244
                                       589**********99988 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.1
                              UB2H   5 aalsaaqleqeLellgYrkvsnvtrpGeyavs 36 
                                       ++l+ +++e+  +++ Y +    ++pG+y+++
  gi|313124979|ref|YP_004035243.1| 391 RPLTFEEFEEKTDQTLYVS----ATPGDYERE 418
                                       5666666666666666654....478888776 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 3.9
                              UB2H  38 nriellrRgFdfpdgae 54 
                                       +ri+ lrR+Fd  d++e
  gi|313124979|ref|YP_004035243.1| 662 DRIRDLRREFDLFDEEE 678
                                       5677789****999987 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   7.2e-05     0.086      28      50 ..      54      75 ..      52     150 .. 0.91
   2 ?   -3.0   0.0       5.4   6.5e+03     176     176 ..     435     435 ..     374     501 .. 0.53
   3 ?   -0.5   0.2      0.88   1.1e+03     139     179 ..     634     671 ..     564     687 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-05
                             DUF87 28 ilgsTGsGKSntvavLleellek 50
                                       lg TGsGK+ntva  +ee+  k
  gi|313124979|ref|YP_004035243.1| 54 LLGVTGSGKTNTVAWTVEEIQ-K 75
                                      59************9999997.4 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.4
                             DUF87 176 l 176
                                       +
  gi|313124979|ref|YP_004035243.1| 435 D 435
                                       2 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.88
                             DUF87 139 sdepveklleelkkekeelrklknqaiarlldkledllrkg 179
                                       ++e +e+l++ ++   e +++l  +++a + d+++dl r+ 
  gi|313124979|ref|YP_004035243.1| 634 AREQIEYLEDRMQ---EAADNLEFELAADIRDRIRDLRREF 671
                                       2333333333333...5556666666666666666666555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.012        14      14      57 ..      53      89 ..      41     165 .. 0.66
   2 ?    6.8   0.3    0.0069       8.2      37     113 ..     460     574 ..     431     613 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                            AAA_19 14 lvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAake 57
                                       +++  G+GKT ++   v+++++ +       l++a ++  a +
  gi|313124979|ref|YP_004035243.1| 53 TLLGVTGSGKTNTVAWTVEEIQKPT-------LVIAHNKTLAAQ 89
                                      688999*******999998877644.......455555555555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0069
                            AAA_19  37 lggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal.................................... 77 
                                       +     e+ l+ ++t+r a+ l+e l+++g++   +H  +                                     
  gi|313124979|ref|YP_004035243.1| 460 RD----ERTLVTTLTKRMAEDLTEYLEEAGVDVAYMHDETDtlerhelirdlrlghidvlvginllregldipevsl 532
                                       22....899*****************999999555554322344444577778788888888888887777777777 PP

                            AAA_19  78 .......................ldfddlltealelleeaeeekklqeee.llivDEfqd 113
                                                                                  +++ ++e +l  DE+ d
  gi|313124979|ref|YP_004035243.1| 533 vaildadqegflrstttliqtmgR-----------------AARNV-NGEvILYADETTD 574
                                       777554433332222222222220.................23334.3333555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.035        42      10      66 ..      54     100 ..      52     158 .. 0.63
   2 ?    7.4   0.3    0.0042         5      32     115 ..     421     510 ..     407     523 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.035
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralgl 66 
                                       + G +G+GKT ++++ +e+ +        +p+  +v + ++t  ++l++e+ + + +
  gi|313124979|ref|YP_004035243.1|  54 LLGVTGSGKTNTVAWTVEEIQ--------KPT--LVIAHNKTLAAQLYEEFKNLFPD 100
                                       6799*********99999984........333..33444444455555555555554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0042
                            AAA_22  32 eakaee..erpevv..fvtlpsst.sskdllrellralglelka.erlsseellealeqalraravielliiDEaqh 102
                                       e+ ae+  ++ ++v  +v+l+  t   +dll ++   ++++  +  +  ++++ e l+++l++++v ++ + DE + 
  gi|313124979|ref|YP_004035243.1| 421 EQIAEQivRPTHLVdpKVELADATgQVDDLLDRIDTRIERDERTlVTTLTKRMAEDLTEYLEEAGVDVAYMHDETDT 497
                                       33333377888888999*******999999*********999998788888899999999999999999******** PP

                            AAA_22 103 lrseealeeLrsl 115
                                       l ++e++++Lr  
  gi|313124979|ref|YP_004035243.1| 498 LERHELIRDLRLG 510
                                       *659999999865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00031      0.37       5      67 ..      33      95 ..      30     157 .. 0.75
   2 ?   -0.2   0.1       0.6   7.1e+02      47      80 ..     462     498 ..     449     572 .. 0.65
   3 ?   -1.8   0.1       1.8   2.1e+03      32      77 ..     548     608 ..     546     635 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                            AAA_30  5 eQaaaveallts...gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg 67
                                      +Q +a+e+l+ +   g   ++l G+ G+GKt +++  +e ++   ++ +++A++++ A++L ee+ 
  gi|313124979|ref|YP_004035243.1| 33 DQPEAIEQLARGfeaGMEKQTLLGVTGSGKTNTVAWTVEEIQ---KPTLVIAHNKTLAAQLYEEFK 95
                                      677777777643221556799************999998888...56799**********999876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.6
                            AAA_30  47 grviglAptgkaAkvLae...elgieastiakllkrl 80 
                                       +r ++ + t+++A++L+e   e+g++ + ++  +++l
  gi|313124979|ref|YP_004035243.1| 462 ERTLVTTLTKRMAEDLTEyleEAGVDVAYMHDETDTL 498
                                       4667777888888888852224444444444333333 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.8
                            AAA_30  32 ttalkalreaweaaggrviglAptgkaAkvLa...............eelgieastiakll 77 
                                       tt+++++ +a+++ +g+vi++A + + + + a               ee g e  ti+k +
  gi|313124979|ref|YP_004035243.1| 548 TTLIQTMGRAARNVNGEVILYADETTDSMEAAieetqrrraiqqafnEEHGYEPTTIDKAV 608
                                       5666666666666666777777655444443333333444443333345555555555555 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.6   1.9e+03     146     163 ..     145     162 ..     136     165 .. 0.84
   2 ?    3.7   0.1     0.037        44      33      62 ..     277     306 ..     269     314 .. 0.88
   3 ?    7.2   0.1     0.003       3.6       9      50 ..     444     485 ..     438     487 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
                                       TTT--HHHHHHHHHHHHH CS
                              RPN7 146 kellsyedlavyavlcal 163
                                         ll+ +d++v+a ++a+
  gi|313124979|ref|YP_004035243.1| 145 RSLLTRDDVIVVASVSAI 162
                                       6799**********9997 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  33 eeirrakldlaehYlkigdleeAlkaysri 62 
                                       +ei ++++++ +++ + gdl  A++  +r+
  gi|313124979|ref|YP_004035243.1| 277 SEIEELMEERVRYFERQGDLVAAQRIEERT 306
                                       6899********************988875 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT CS
                              RPN7   9 rkknekeleeLdaelkdakenlgkeeirrakldlaehYlkig 50 
                                       + ++++ l+++d+++++ + +l+ + ++r  +dl e+  ++g
  gi|313124979|ref|YP_004035243.1| 444 TGQVDDLLDRIDTRIERDERTLVTTLTKRMAEDLTEYLEEAG 485
                                       67899********************************99987 PP

>> DNA_circ_N  DNA circularisation protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.007       8.4      47      81 ..     225     261 ..     221     263 .. 0.88
   2 ?    3.4   0.1     0.085     1e+02      36      71 ..     549     584 ..     543     592 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.007
                        DNA_circ_N  47 eirleavlvgdd..ylaqrdaLiealekpgageLvhP 81 
                                       ++ ++  ++gd+   ++++d L  a+++++++ L+hP
  gi|313124979|ref|YP_004035243.1| 225 RYAVRIEFWGDEidRMQKLDPLQGAVKSTEPAVLIHP 261
                                       56788889999866899******************** PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.085
                        DNA_circ_N  36 pdvedlGrkareirleavlvgddylaqrdaLieale 71 
                                         ++ +Gr+ar+++ e++l+ d++ + ++a ie  +
  gi|313124979|ref|YP_004035243.1| 549 TLIQTMGRAARNVNGEVILYADETTDSMEAAIEETQ 584
                                       67899*****************99999888777655 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       0.4   4.7e+02      27      47 ..     265     285 ..     251     291 .. 0.84
   2 ?   -1.2   0.0         2   2.3e+03      31      59 ..     467     495 ..     444     497 .. 0.78
   3 ?   -2.3   0.1       4.3   5.1e+03      34      78 ..     547     591 ..     537     596 .. 0.67
   4 ?    7.5   0.1    0.0036       4.4      16      59 ..     616     659 ..     602     664 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.4
                                       ----HHHHHHHHHHHHHHHTT CS
                              FlaG  27 kevseeeleeaveklnkklss 47 
                                         + e++le+a++++++ +++
  gi|313124979|ref|YP_004035243.1| 265 YSIPEDQLEQAISEIEELMEE 285
                                       5677899**********9987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHTTSS--EEEEEEEE CS
                              FlaG  31 eeeleeaveklnkklsslnteleFsvded 59 
                                           ++++e+l + l++ + ++++  de+
  gi|313124979|ref|YP_004035243.1| 467 TTLTKRMAEDLTEYLEEAGVDVAYMHDET 495
                                       44468899999999999999999998885 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.3
                                       HHHHHHHHHHHHTTSS--EEEEEEEETTEEEEEEEETTT-SEEEE CS
                              FlaG  34 leeaveklnkklsslnteleFsvdedtkrvvVkviDketgevIrq 78 
                                         ++++ + +++ ++n e+    de+t+++   + +++  + I q
  gi|313124979|ref|YP_004035243.1| 547 TTTLIQTMGRAARNVNGEVILYADETTDSMEAAIEETQRRRAIQQ 591
                                       556677777777777777777777777777777777666666655 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0036
                                       S-----SS-------HHHHHHHHHHHHHHHTTSS--EEEEEEEE CS
                              FlaG  16 eeekaekaeeekevseeeleeaveklnkklsslnteleFsvded 59 
                                       +e++a  + +e+ ++e++  e +e l++++++   +leF++  d
  gi|313124979|ref|YP_004035243.1| 616 SETSATRSASEQPTDEDDAREQIEYLEDRMQEAADNLEFELAAD 659
                                       4556666677777777779999*****************98766 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.3   1.6e+03     127     143 ..     269     285 ..     256     302 .. 0.63
   2 ?   -0.9   0.0      0.66   7.9e+02     107     149 ..     333     377 ..     325     386 .. 0.78
   3 ?    1.8   0.7       0.1   1.2e+02     122     174 ..     446     498 ..     395     552 .. 0.72
   4 ?    6.3   0.3    0.0045       5.4     121     162 ..     632     673 ..     631     703 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                              CorA 127 lekleeeldeledeled 143
                                        ++le+ + e+e+ +e+
  gi|313124979|ref|YP_004035243.1| 269 EDQLEQAISEIEELMEE 285
                                       45666666666666633 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.66
                              CorA 107 spgellyrlldeivdrlfellekleeeldeledel..edstkkei 149
                                        +g+  y lld + d++++++++ ++ l ++  ++  ++ +k+++
  gi|313124979|ref|YP_004035243.1| 333 ESGDAPYTLLDYFPDDFLTVIDESHQTLPQIRGQFagDKARKDSL 377
                                       567777999*******************99999998444444443 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.1
                              CorA 122 rlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevl 174
                                       ++++ll+ +++++++ e++l +  +k ++++l+++ ++++    ++++ +++l
  gi|313124979|ref|YP_004035243.1| 446 QVDDLLDRIDTRIERDERTLVTTLTKRMAEDLTEYLEEAGVDVAYMHDETDTL 498
                                       34455555555555555555555555555555555554444444444444444 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0045
                              CorA 121 drlfellekleeeldeledeledstkkeilrelaqlrrrlvk 162
                                       d+ +e++e le++++e+ d+le +  ++i++++ +lrr+   
  gi|313124979|ref|YP_004035243.1| 632 DDAREQIEYLEDRMQEAADNLEFELAADIRDRIRDLRREFDL 673
                                       56789999*****************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 4260.08
//
Query:       gi|313124980|ref|YP_004035244.1|  [L=89]
Description: hypothetical protein Hbor_01940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00015   21.7   9.0    0.00023   21.1   9.0    1.3  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
     0.0034   17.9   4.3       0.03   14.8   4.3    2.1  1  YtxH            YtxH-like protein
     0.0078   16.3   0.7      0.032   14.4   0.3    2.2  2  cwf21           cwf21 domain
      0.008   15.5   1.6       0.01   15.1   1.6    1.1  1  HemX            HemX, putative uroporphyrinogen-III C-methylt
  ------ inclusion threshold ------
      0.014   16.1   0.6       0.04   14.6   0.1    1.8  2  Cytochrom_B562  Cytochrome b562
       0.03   13.9   0.3      0.033   13.7   0.3    1.0  1  Exonuc_VII_L    Exonuclease VII, large subunit
      0.033   14.5   0.7        3.6    8.0   0.0    2.3  2  MT0933_antitox  MT0933-like antitoxin protein
      0.049   13.5   3.1        2.6    7.9   0.4    2.0  2  CdvA            CdvA-like coiled-coil domain
      0.098   12.2   2.9       0.11   12.0   2.9    1.1  1  Lant_dehydr_C   Lantibiotic biosynthesis dehydratase C-term
       0.12   12.5   9.7       0.32   11.1   1.3    2.1  2  ATP-synt_B      ATP synthase B/B' CF(0)
       0.14   12.3   2.1         10    6.4   0.3    2.1  2  T3SS_needle_F   Type III secretion needle MxiH, YscF, SsaG, E
       0.32   11.6   7.3         32    5.2   6.8    2.1  1  DUF883          Bacterial protein of unknown function (DUF883
       0.81    9.7   5.3        6.7    6.7   0.4    2.1  2  T2SSF           Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   9.0   1.7e-07   0.00023      83     166 ..       3      82 ..       1      88 [. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                                       HHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHH CS
                    Apolipoprotein  83 rerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrveel 159
                                       re l+a++eel ++ ++  +elrer+++ ++al a  ++++   + +la+++ +l+e +++++e +eer++s  + +
  gi|313124980|ref|YP_004035244.1|   3 RELLSAASEELSDAADTAEDELRERISDQADALAALAEADRGPDHGRLARHMNALSEIAEQASEDIEERVESARDKV 79 
                                       56688999999999999999999999999999999999888888889999999999999999999886555555555 PP

                                       HHTS-TT CS
                    Apolipoprotein 160 rekleeq 166
                                       +e    +
  gi|313124980|ref|YP_004035244.1|  80 SE----Y 82 
                                       54....3 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   4.3   2.2e-05      0.03      26      74 ..       2      79 ..       1      87 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-05
                              YtxH 26 tRkdlkekaddlkekakelleeakeka.............................kekaedlkekvkekadelkekv 74
                                      tR+ l+ + ++l++ a+ + +e++e+                              +e ae+++e+++e+++++++kv
  gi|313124980|ref|YP_004035244.1|  2 TRELLSAASEELSDAADTAEDELRERIsdqadalaalaeadrgpdhgrlarhmnalSEIAEQASEDIEERVESARDKV 79
                                      78888888888888888888888888888888888888888889999*****99988888888888888888888876 PP

>> cwf21  cwf21 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.3   2.3e-05     0.032      15      40 ..      23      78 ..      10      81 .. 0.89
   2 ?    1.0   0.0      0.35   4.9e+02      12      18 ..      78      84 ..      78      87 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                             cwf21 15 elrdeLEeeg..............................lseeeIeervdelRek 40
                                      elr++  ++                               +  e+Ieerv+  R+k
  gi|313124980|ref|YP_004035244.1| 23 ELRERISDQAdalaalaeadrgpdhgrlarhmnalseiaeQASEDIEERVESARDK 78
                                      78888888867999999999999999999999999999978*************98 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.35
                             cwf21 12 kvlelrd 18
                                      kv+e+r+
  gi|313124980|ref|YP_004035244.1| 78 KVSEYRE 84
                                      6777776 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.6   7.5e-06      0.01     133     219 ..       3      85 ..       2      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.5e-06
                              HemX 133 lalLksADevLaevndpsllavRralaedlkaLravnqvDrdgiilrLeqLanqvdeLpladneldeapsdadnael 209
                                       ++lL++A e L++  d+   ++R+ +++   aL+a+ + Dr     rL++  n + e   ++++++e + +++ + +
  gi|313124980|ref|YP_004035244.1|   3 RELLSAASEELSDAADTAEDELRERISDQADALAALAEADRGPDHGRLARHMNALSE---IAEQASE-DIEERVESA 75 
                                       579**************************************9988777766665555...5555555.555666666 PP

                              HemX 210 sdslsdWkqn 219
                                        d++s++++ 
  gi|313124980|ref|YP_004035244.1|  76 RDKVSEYREG 85 
                                       7777777765 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.54   7.5e+02      63      83 ..      12      32 ..       2      41 .. 0.50
   2 ?   14.6   0.1   2.9e-05      0.04      15      62 ..      40      87 ..      23      89 .] 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.54
                    Cytochrom_B562 63 klidqldkaealakagkleea 83
                                      +l d+ d+ae ++ +   ++a
  gi|313124980|ref|YP_004035244.1| 12 ELSDAADTAEDELRERISDQA 32
                                      344444444444444444443 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.9e-05
                    Cytochrom_B562 15 qvakaddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGld 62
                                      ++ +  d   l+ ++++l ++ae+a+e   + +e  + ++++Y+eG +
  gi|313124980|ref|YP_004035244.1| 40 EADRGPDHGRLARHMNALSEIAEQASEDIEERVESARDKVSEYREGVE 87
                                      344445788899*********************************975 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   2.4e-05     0.033     145     219 ..       9      84 ..       2      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                      Exonuc_VII_L 145 leeqleelerrlekaikrlleekkqrleklasrlkspee.llerkrqrldeleerleralkkqlkkkrerleelke 219
                                         e+l+++++  e+++++++++++  l +la++ + p++ +l+r+ ++l+e++e+ ++ ++++++++r +++e++e
  gi|313124980|ref|YP_004035244.1|   9 ASEELSDAADTAEDELRERISDQADALAALAEADRGPDHgRLARHMNALSEIAEQASEDIEERVESARDKVSEYRE 84 
                                       4678888999999999999999999999999888877777******************************999885 PP

>> MT0933_antitox  MT0933-like antitoxin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.021        29       8      27 ..       6      25 ..       2      37 .. 0.58
   2 ?    8.0   0.0    0.0026       3.6       5      27 ..      58      80 ..      54      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.021
                    MT0933_antitox  8 aekhedkvdqgiDKAgdavd 27
                                      ++ ++++  ++ D A+d   
  gi|313124980|ref|YP_004035244.1|  6 LSAASEELSDAADTAEDELR 25
                                      55555555555555555333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0026
                    MT0933_antitox  5 kdlaekhedkvdqgiDKAgdavd 27
                                       + ae++++ ++  ++ A d+v 
  gi|313124980|ref|YP_004035244.1| 58 SEIAEQASEDIEERVESARDKVS 80
                                      57899999999999999999885 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.4    0.0019       2.6      25      61 ..       4      40 ..       1      42 [. 0.86
   2 ?    6.4   0.1    0.0053       7.3      26      57 ..      49      80 ..      47      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0019
                              CdvA 25 ekleealkklkekakelkeklkkrlkeledqikslek 61
                                      e l+ a+++l + a++  ++l++r+++  d +++l++
  gi|313124980|ref|YP_004035244.1|  4 ELLSAASEELSDAADTAEDELRERISDQADALAALAE 40
                                      66788999******************99999888865 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0053
                              CdvA 26 kleealkklkekakelkeklkkrlkeledqik 57
                                      +l + +++l e a++ +e +++r+++ +d+++
  gi|313124980|ref|YP_004035244.1| 49 RLARHMNALSEIAEQASEDIEERVESARDKVS 80
                                      67888999999999999999999999888776 PP

>> Lant_dehydr_C  Lantibiotic biosynthesis dehydratase C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.9   7.9e-05      0.11     203     268 ..       9      70 ..       2      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                                       HHHHHHHHHHHTHHHHHHHHHHHHHHHH-SSS-SS.....HHHHHHHHHHHHHHHHHHHHHHTTS- CS
                     Lant_dehydr_C 203 lrealdrkyraqrealearlravlaaaaepesegesadlppflaewaerlrelrrrlealeasgel 268
                                       + e+l+++ ++ +++l++r++  ++a+a+ ++    ad+ p  +++a+++++l +++e+++++ e 
  gi|313124980|ref|YP_004035244.1|   9 ASEELSDAADTAEDELRERISDQADALAALAE----ADRGPDHGRLARHMNALSEIAEQASEDIEE 70 
                                       56889999999999******999999997544....55566666***************9555443 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   0.00023      0.32      95     127 ..       4      36 ..       2      39 .. 0.88
   2 ?    5.3   3.3     0.014        19      78     109 ..      53      84 ..      32      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                        ATP-synt_B  95 rlkesAaaeIeqekdralaeLreqvvalavqia 127
                                        l ++A +e++ + d+a++eLre++ ++a + a
  gi|313124980|ref|YP_004035244.1|   4 ELLSAASEELSDAADTAEDELRERISDQADALA 36 
                                       56789***********************97665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
                        ATP-synt_B  78 aeklkeeieaeaeaeaerlkesAaaeIeqekd 109
                                         ++  ei ++a++++e + esA+++++  ++
  gi|313124980|ref|YP_004035244.1|  53 HMNALSEIAEQASEDIEERVESARDKVSEYRE 84 
                                       45667889999999999999999998877665 PP

>> T3SS_needle_F  Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3    0.0076        10       2      28 ..       7      33 ..       6      41 .. 0.83
   2 ?    5.9   0.1     0.011        15       5      30 ..      54      79 ..      50      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0076
                                      HHHHHHHHCCTHHHHHHHHHHHHHHHH CS
                     T3SS_needle_F  2 dsvasalsqkvskaekelqdalealka 28
                                      ++ +++ls+ +++ae el+++++ +++
  gi|313124980|ref|YP_004035244.1|  7 SAASEELSDAADTAEDELRERISDQAD 33
                                      677899***************998843 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                                      HHHHHCCTHHHHHHHHHHHHHHHHST CS
                     T3SS_needle_F  5 asalsqkvskaekelqdalealkadp 30
                                      ++als+ +++a++++++++e+  +++
  gi|313124980|ref|YP_004035244.1| 54 MNALSEIAEQASEDIEERVESARDKV 79
                                      799****************9987766 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.8     0.023        32       3      69 ..      13      79 ..       1      82 [. 0.57

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                            DUF883  3 leaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyV 69
                                      l +  +++ ++l+e ++++ad  +  ae+ R   + rl+r  ++l++ +e++ e ++e +e+a+d V
  gi|313124980|ref|YP_004035244.1| 13 LSDAADTAEDELRERISDQADALAALAEADRGPDHGRLARHMNALSEIAEQASEDIEERVESARDKV 79
                                      3344445555555555555555555555556666666666666666666666666666666666655 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.6     0.011        15      78     106 ..      10      38 ..       4      42 .. 0.51
   2 ?    6.7   0.4    0.0048       6.7      75     101 ..      55      81 ..      47      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTX CS
                             T2SSF  78 aevLerlaeyleeerelrrkllaallepl 106
                                       +e L+++a++ e+e++ r+  +a  l  l
  gi|313124980|ref|YP_004035244.1|  10 SEELSDAADTAEDELRERISDQADALAAL 38 
                                       45555555555555555554444444333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0048
                                       T-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             T2SSF  75 gnLaevLerlaeyleeerelrrkllaa 101
                                         L+e+ e+++e++ee+ e++r++ ++
  gi|313124980|ref|YP_004035244.1|  55 NALSEIAEQASEDIEERVESARDKVSE 81 
                                       6799999*************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1143  (0.0637515); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 583.40
//
Query:       gi|313124981|ref|YP_004035245.1|  [L=205]
Description: hypothetical protein Hbor_01950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   14.1   0.1       0.14   12.5   0.1    1.9  2  DinI      DinI-like family
      0.067   13.6   5.0       0.12   12.8   0.1    2.9  3  HEAT_2    HEAT repeats
       0.15   12.6   0.2       0.15   12.6   0.2    1.9  2  HSCB_C    HSCB C-terminal oligomerisation domain


Domain annotation for each model (and alignments):
>> DinI  DinI-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   6.5e+03      26      42 ..       9      25 ..       5      26 .. 0.80
   2 ?   12.5   0.1   2.4e-05      0.14      32      62 ..     141     172 ..     137     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                                      EEEEESS-EEEEES--H CS
                              DinI 26 rvrkasanglsveGask 42
                                      r+r + ++++s  G sk
  gi|313124981|ref|YP_004035245.1|  9 RIRDDHETAFSRLGSSK 25
                                      78999999999888776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.4e-05
                                       S-EEEEES.--HHHHHHHHHHHHHHHHTHHHH CS
                              DinI  32 anglsveG.askedkeriseiLQetwesADdW 62 
                                       a+++++ + a +++++r+ e+L e+ es DdW
  gi|313124981|ref|YP_004035245.1| 141 ASEFRTLRsAIEDERDRVVETLAEVCESDDDW 172
                                       567777787899******************** PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4      0.08   4.8e+02      57      84 ..      20      45 ..       5      52 .. 0.60
   2 ?    0.5   1.1      0.14   8.2e+02      51      67 ..      39      55 ..      25      84 .. 0.59
   3 ?   12.8   0.1     2e-05      0.12      29      70 ..     155     197 ..     133     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.08
                            HEAT_2 57 aigdpealpaLkellddddddvvReaAa 84
                                      ++g+++al aL+    + + d vR+aAa
  gi|313124981|ref|YP_004035245.1| 20 RLGSSKALYALTG--GEMEADAVRAAAA 45
                                      4455555555554..3344455555554 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.14
                            HEAT_2 51 aaeaLgaigdpealpaL 67
                                      a++a++a + ++a+++L
  gi|313124981|ref|YP_004035245.1| 39 AVRAAAADDQHAAADVL 55
                                      33333333333333333 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 2e-05
                            HEAT_2  29 npealpaLvell.ededpavRraaaeaLgaigdpealpaLkel 70 
                                        ++++++L e++ +d+d++  ++aa+a ++ + ++ ++ L+++
  gi|313124981|ref|YP_004035245.1| 155 RDRVVETLAEVCeSDDDWDAAHEAADAVVEAAYDDYVETLERM 197
                                       458999****9988899**********9999999999988875 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4      0.89   5.3e+03      56      56 ..      59      59 ..      35      85 .. 0.53
   2 ?   12.6   0.2   2.4e-05      0.15      24      62 ..     140     179 ..     133     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.89
                                      H CS
                            HSCB_C 56 e 56
                                      +
  gi|313124981|ref|YP_004035245.1| 59 A 59
                                      1 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.4e-05
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-HHHHHHHH CS
                            HSCB_C  24 dkeeleelkaeveerieeleaeleeafekk.dleaaadll 62 
                                        ++e + l++++e +++  ++ l+e  e + d++aa +++
  gi|313124981|ref|YP_004035245.1| 140 TASEFRTLRSAIEDERDRVVETLAEVCESDdDWDAAHEAA 179
                                       348999*********************5556***666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1207.33
//
Query:       gi|313124982|ref|YP_004035246.1|  [L=481]
Description: hypothetical protein Hbor_01960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-26   92.6   8.2    2.5e-26   92.6   8.2    3.5  2  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -21.3  29.1         1   1.8e+04      77     115 ..     132     170 ..      27     251 .. 0.53
   2 !   92.6   8.2   1.4e-30   2.5e-26       2     156 .]     314     473 ..     313     473 .. 0.87

  Alignments for each domain:
  == domain 1  score: -21.3 bits;  conditional E-value: 1
                            SpoIIM  77 vaalvaefgglllflllilPhgilelpaiiiagaaglrl 115
                                       +++l ++f  +  +++  +P gil l  i +aga+g+  
  gi|313124982|ref|YP_004035246.1| 132 LSFLGVRFLLFGALAVVTVPIGILGLGLIAVAGAVGVVG 170
                                       333333333333333344444444444444444444222 PP

  == domain 2  score: 92.6 bits;  conditional E-value: 1.4e-30
                            SpoIIM   2 lllflvgillgallaa.......snfaeqis...seskensalslflaifanNlrvalllfllGllllgiptilvll 68 
                                       +++f++gi+ g++++a              +   s+     +  +f+++ +nN+ va+ +  +G+ ++g+p+++ l+
  gi|313124982|ref|YP_004035246.1| 314 AVIFGAGIVGGWATTApygpslpV------QgeiSNVFGSLPVGTFVNLAVNNWLVAVDTAYSGV-AVGVPSVVNLV 383
                                       79**************55443320......13356667777889********************7.*********** PP

                            SpoIIM  69 inGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal......rsrrkalkeakrellkllll 139
                                       +nG+++Ga+++++        f +l++Phgi+e+pa++++g++gl lg         ++  + l++a r+ +++ll+
  gi|313124982|ref|YP_004035246.1| 384 FNGVLIGALGGVFDPT----AFTALVAPHGIIEVPALVLGGGLGLWLGGVGyrtargQTDADGLAAALRRTYRVLLG 456
                                       *********9999985....7**************************6666666777777777888*********** PP

                            SpoIIM 140 lvpllliAaliEafvtp 156
                                       lv l+++Aa+iEaf+tp
  gi|313124982|ref|YP_004035246.1| 457 LVTLFVVAAFIEAFLTP 473
                                       ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2786.92
//
Query:       gi|313124983|ref|YP_004035247.1|  [L=286]
Description: rhodanese-related sulfurtransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-36  124.2   0.1    5.1e-18   65.6   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.1   1.4e-19   2.5e-15       1     106 [.      13     127 ..      13     128 .. 0.77
   2 !   65.6   0.0   2.8e-22   5.1e-18       7     105 ..     162     275 ..     157     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.4e-19
                         Rhodanese   1 sakelkellekgkva.....llDvRppee.YekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkk 67 
                                       s+++++++l++ + +     l+ v  + e Y++gh pgA+ ++++t  + + +  ++  + ee+++l    gi++++
  gi|313124983|ref|YP_004035247.1|  13 SPEWVEDHLDEFQSDdpayrLVEVDVDTEaYDEGHAPGAIGFNWET--QLQDQTTRDILTKEEFEDLlgshGISEDS 87 
                                       578888888655555688899999955555************5554..4445555555555555555555******* PP

                         Rhodanese  68 tvvvycdgggr.aaaaaallkklGykn.vsvldGGfkawke 106
                                       tvv+y+d+++  aa +++++k++G+ + v++l+GG + w e
  gi|313124983|ref|YP_004035247.1|  88 TVVLYGDNSNWfAAYTYWQFKYYGH-DdVRLLNGGRDYWLE 127
                                       ***********99999********5.55********99976 PP

  == domain 2  score: 65.6 bits;  conditional E-value: 2.8e-22
                         Rhodanese   7 ellekgkvallDvRppeeY..............ek.ghIpgAvnvskdtlsrakkseapllelpeellelgidnkkt 68 
                                          ++g   l+DvR+pee+              ++ ghIpgA n+s+  + +a+ + ++  el e ++++gid ++t
  gi|313124983|ref|YP_004035247.1| 162 HAVDEGL-PLVDVRSPEEFsgeilappglqetaQRgGHIPGAENISWAATVNADGTFKSAEELEELYADQGIDGNET 237
                                       4444554.3**********999999999999995559**************************************** PP

                         Rhodanese  69 vvvycdgggraaaaaallkk.lGyknvsvldGGfkawk 105
                                        v yc+ g+r++ a+ +l + lGy +v ++dG++++w 
  gi|313124983|ref|YP_004035247.1| 238 TVAYCRIGERSSIAWFALHElLGYDEVVNYDGSWTEWG 275
                                       **********99999888866**888***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1739.17
//
Query:       gi|313124984|ref|YP_004035248.1|  [L=261]
Description: rhodanese-related sulfurtransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-38  132.1   0.0    2.9e-19   69.5   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   8.2e-21   1.5e-16       1     106 [.       8     118 ..       8     119 .. 0.85
   2 !   69.5   0.0   1.6e-23   2.9e-19       6     106 ..     151     252 ..     146     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 8.2e-21
                         Rhodanese   1 sakelkellekgkvallDvRppeeYek.ghIpgAvnv..skdtlsrakkseapllelpeellel.gidnkktvvvyc 73 
                                       s+++++ ++++ +  l+DvR+++e++  gh+pgAvn+     +  ++++ + p ++  e+ll+  gi +++++v y+
  gi|313124984|ref|YP_004035248.1|   8 SPDWVESRRDEIR--LVDVRDAWEFDGiGHVPGAVNIpfDEFRSADGDEGMLPGADVWESLLSAaGIGPDDHLVAYD 82 
                                       6899999997776..**********************554445566677788999999999999************* PP

                         Rhodanese  74 dgggr.aaaaaallkklGy.kn.vsvldGGfkawke 106
                                       d+ g  aa+   +++ +G+ ++ +++ldG ++aw++
  gi|313124984|ref|YP_004035248.1|  83 DTHGVfAARFLVTAELYGHpTErLHLLDGDYSAWNR 118
                                       *****777776666679986557***********97 PP

  == domain 2  score: 69.5 bits;  conditional E-value: 1.6e-23
                         Rhodanese   6 kellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel.gidnkktvvvycdgggraaa 81 
                                        + l++++++++D+R+++e+e+gh+pgAvn+ ++ l + + +  + ++ +e++l++ gi+++++vv+yc+++ r + 
  gi|313124984|ref|YP_004035248.1| 151 LDSLDDEAAVVVDTREAWEFEEGHLPGAVNLDWRELVDDETRGLKPADELEAILDEvGITPDRRVVLYCNTARRISH 227
                                       5667888888****************************************************************888 PP

                         Rhodanese  82 aaallkklGyknvsvldGGfkawke 106
                                       ++  l++lGy+n+ +++G++++w e
  gi|313124984|ref|YP_004035248.1| 228 TYVVLRSLGYENIAFYEGSLTEWEE 252
                                       8999999**999***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1586.09
//
Query:       gi|313124985|ref|YP_004035249.1|  [L=333]
Description: permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-24   86.2  37.1    1.4e-23   83.6  37.1    2.1  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6  37.1   7.8e-28   1.4e-23       4     322 ..      10     317 ..       7     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 7.8e-28
                   AI-2E_transport   4 ilvllllllalypfiselllplliAlvlayllnpvvkfLkkrgvk....rvlavllvlllllvllvllvlllvplli 76 
                                        ++++l ++a+ ++++++l ++++++ +ayll+pv ++  +rg +      la++  +l++l+ l+ l ++++ l  
  gi|313124985|ref|YP_004035249.1|  10 GSLFVLAGVAAAFLLRSVLGTVFFSVTVAYLLWPVRQAVVRRGWSpraaSGLATAGAFLAVLAGLTPLAIVVY-LRF 85 
                                       6899***********************************7776541111567888888888888888888888.999 PP

                   AI-2E_transport  77 aqltqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnsllsllasllglilslvlvlll 153
                                       ++lt lv  lp      +n+  el+ ++  l         +l+++ +  + ++ + ++ ++a ++ l++++ l+++l
  gi|313124985|ref|YP_004035249.1|  86 DSLTTLVGLLP------SNLSFELFGMTYAL---------TLAEVTTFTVAYLRQLATVVAAATPVLLVKVTLFVFL 147
                                       99999999999......77888888888888.........68999999999999999999***************** PP

                   AI-2E_transport 154 lffllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvgl 230
                                       ++ ll++ge   q  l ++p++++  ++a+ +++ +tl +++  q+ +a+ ++vl+  ++ +lg++   +la ++ +
  gi|313124985|ref|YP_004035249.1| 148 VYSLLYHGEDAQQAALAVVPSSYQSAARALNSRARDTLFAIYVLQAATAAGTFVLAVPVFFFLGYDAVVTLATVAAV 224
                                       ***************************************************************************** PP

                   AI-2E_transport 231 anliPyiGavivlipiaiialltgg.ikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGl 306
                                       ++++P++G+++ l+ +a++ l +g  + ++l+v ++ +lv  + + +++P l +++++++  + ++ +++g   +G 
  gi|313124985|ref|YP_004035249.1| 225 LQFVPIVGPTLLLLGLAAYQLALGHtVQALLVVTVGGALVAWLPDVLIRPPLAKQTADIPGSLYFVGFFGGTLTLGA 301
                                       *************************8888888889999*************************************** PP

                   AI-2E_transport 307 vGlilavpltavikai 322
                                       vG+  ++++++++ ++
  gi|313124985|ref|YP_004035249.1| 302 VGIVAGPLVVGLFVEA 317
                                       **********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2203.24
//
Query:       gi|313124986|ref|YP_004035250.1|  [L=388]
Description: ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-21   75.7   0.0    4.7e-21   75.3   0.0    1.1  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    6.3e-19   68.9   0.1    8.3e-19   68.5   0.1    1.2  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.7e-11   44.7   0.1    2.2e-11   44.3   0.1    1.2  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    1.3e-07   31.6   0.0    2.5e-07   30.7   0.0    1.4  1  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.021   14.7   5.5       0.05   13.5   5.5    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   1.3e-24   4.7e-21      45     232 ..     164     356 ..     124     366 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.3e-24
                         SBP_bac_6  45 kdpdgkyypygvgplvlavnkdrlkgrpv.PksWaDLldPeykgkvalpgnngsdlfealllalykdfgedgvkkll 120
                                        dpdg+ +py++g+++l++nk   + +   P++++ Ll+++y++   + ++  s++ +a+ll+  k +g d + +++
  gi|313124986|ref|YP_004035250.1| 164 FDPDGRAVPYDTGYICLVFNKLFGDSEFTaPETFDGLLKEQYADDLLVQNPVSSATGKAFLLHSIKAKGRDSYLDFW 240
                                       478*****************9765555448*********************************************** PP

                         SBP_bac_6 121 rnlkanlhpaq..mvkaagslesgepavsvvpyffadilpekkkgk...nlkvvwPedGalvspifmlvkkg.kkke 191
                                        +lk+n+  +     +++++ ++ge  +++v+ +++d++ + ++g    + ++   +d ++++p+ m++  g  ++e
  gi|313124986|ref|YP_004035250.1| 241 QKLKENGVRVLkdWGTSYDAYSKGE--APMVVSYSTDQVYAHESGEdlaKHQLRFLNDQGYANPEGMALFEGtDQPE 315
                                       **********9888899********..****************9999**88888888889***************** PP

                         SBP_bac_6 192 lakafidfllspevqailakaggvfPvvtnpavlnelpega 232
                                       la+ f+df+l pe+qa +a  + ++P++t +++ +++ ++a
  gi|313124986|ref|YP_004035250.1| 316 LARTFMDFMLRPEIQAEIAVRNVQYPATTTAELPESFGKYA 356
                                       ***************************98888888776665 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.1   2.3e-22   8.3e-19      40     280 ..     129     358 ..      86     360 .. 0.78

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 2.3e-22
                                       EE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-HHHHHTT--TS.----EEEEEEE-EEEEEHHHHHHS...---BHH CS
                         SBP_bac_8  40 idvvwanedalatlaeeglladlsdldnlddltdalaavgydgklygvPyasetpyvliynkdlleka..edpktwd 114
                                       +dv++     +++  ++ ++  ++dl n  d++  l+ ++ dg   +vPy+++   +l+ n +l+ +     p+t+d
  gi|313124986|ref|YP_004035250.1| 129 LDVNMLI--RIDENLDSPMFTSVDDLSNRGDVKESLE-FDPDG--RAVPYDTGY-ICLVFN-KLFGDSefTAPETFD 198
                                       4544444..3555556667777778888888866555.78888..********7.899999.8998855779***** PP

                                       HHHHHHHHHHHH-SEGG---G.GGGGGTHHETTEE---H..HHH.HHHHHHHHHHHHTT-.EE-S..--SSTTTTTS CS
                         SBP_bac_8 115 ellaaakklkgkfglpdpasg.wlqaallakdgksldddggkdglkealellkklkdngk.tydtgadavsefanGe 189
                                       +ll+  +++       +p s+ ++ a+ll  + k +       g + +l++++klk+ng+ +++++ +  +++ +Ge
  gi|313124986|ref|YP_004035250.1| 199 GLLK--EQYADDLLVQNPVSSaTGKAFLLH-SIKAK-------GRDSYLDFWQKLKENGVrVLKDWGTSYDAYSKGE 265
                                       ****..***999999999975488888887.64443.......5689************84669***9********* PP

                                       BSEEEE-TTHHHHHH-TTTSEEEE...--S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---B CS
                         SBP_bac_8 190 vaftingswdiaaaqkagkklgai...vpkqgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyip 263
                                       + +++++s d   a + g++l+     +++++  a+ +g+a + ++++++l A  F+ +++ pe qa+ a      p
  gi|313124986|ref|YP_004035250.1| 266 APMVVSYSTDQVYAHESGEDLAKHqlrFLNDQGYANPEGMALFEGTDQPEL-ARTFMDFMLRPEIQAEIAVRNVQYP 341
                                       *****************998764434478*********************9.*******************777789 PP

                                       S-S-TTTHHHHHH-HHH CS
                         SBP_bac_8 264 vnksaalspevkkdpal 280
                                       ++++a+l++ + k++++
  gi|313124986|ref|YP_004035250.1| 342 ATTTAELPESFGKYAQA 358
                                       99999999999888766 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   6.1e-15   2.2e-11      89     314 ..     156     330 ..      84     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 6.1e-15
                                       TEEEEHHHHTHHHHCEEEESEEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHH CS
                         SBP_bac_1  89 aadklsssvlpkildskvlyvPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgt 164
                                       +  k s +++p+ ++     vP+++ +  l++  +lf +++ ++p+t+d l++     +    +p         s t
  gi|313124986|ref|YP_004035250.1| 156 GDVKESLEFDPDGRA-----VPYDTgYICLVF-NKLFGDSEFTAPETFDGLLKEQYADDLLVQNP-------VSSAT 219
                                       444445567888888.....****77******.99**************9886555555555555.......77888 PP

                                       HHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEE CS
                         SBP_bac_1 165 ayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivg 241
                                       + +f+l+ +k  g                       +++y  ++++k + + +   kd+   +++ ++Gea+m +++
  gi|313124986|ref|YP_004035250.1| 220 GKAFLLHSIKAKG-----------------------RDSY-LDFWQKLKENGVRVLKDWGTSYDAYSKGEAPMVVSY 272
                                       8888888888888.......................5555.999********************************* PP

                                       HHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 242 lwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                       +++  ++   + + ++a+ +  + ++ g+a             +  g+a++ g+++pe A+ F+df+l pe q
  gi|313124986|ref|YP_004035250.1| 273 STD--QVYAHESGEDLAKHQLRFLNDQGYA-------------NPEGMALFEGTDQPELARTFMDFMLRPEIQ 330
                                       *99..3444444456666666666666666.............9**************************988 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0     7e-11   2.5e-07      70     223 ..     160     332 ..     147     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 7e-11
                                       G.......GG-EEEEEEEEEEEESTT-TT....---SHHHHHHSS-..-EEEE--T-TTTTHH.H.HHHGGG--... CS
                        SBP_bac_11  70 a.......esavplassplviavpkgnpk....kikgwadLlkpgl..klavadPttspsGlaal.alleaaga... 129
                                       +       ++avp+ +  ++++ +k   +     + +++ Llk++    l v +P +s++G+a l   ++a g+   
  gi|313124986|ref|YP_004035250.1| 160 EslefdpdGRAVPYDTGYICLVFNKLFGDseftAPETFDGLLKEQYadDLLVQNPVSSATGKAFLlHSIKAKGRdsy 236
                                       4555555677788888888888888886522335678888999999888*************9888999*9999999 PP

                                       HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHH.HHH..HSTTSSEEEE-...-TTT--...EEEEEEEE-T CS
                        SBP_bac_11 130 qellkalekkvvklgessrqlltaveageadagivyes.eakaaengdkleavyl...peglnldpldypaavlkka 202
                                        +++++l+++ v+  ++ ++ ++a   gea ++++y + +++a+e g++l    l    ++ ++   + ++a+  ++
  gi|313124986|ref|YP_004035250.1| 237 LDFWQKLKENGVRVLKDWGTSYDAYSKGEAPMVVSYSTdQVYAHESGEDLAKHQLrflNDQGYA--NPEGMALFEGT 311
                                       99********99999999******************9956777777776665444111566664..5889999**** PP

                                       T--HHHHHHHHHTTSHHHHHH CS
                        SBP_bac_11 203 akreaAraFlafLrspeaqai 223
                                       +++e Ar F++f++ pe qa 
  gi|313124986|ref|YP_004035250.1| 312 DQPELARTFMDFMLRPEIQAE 332
                                       *****************9985 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   5.5   1.4e-05      0.05       4      25 ..      11      31 ..       9      32 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                        TAT_signal  4 RRdFLKgsAAaaAAaalggcaa 25
                                      RR+FL +++A + Aa l+gc++
  gi|313124986|ref|YP_004035250.1| 11 RRSFLTAAGASGVAA-LAGCVG 31
                                      ******888888666.666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2345.14
//
Query:       gi|313124987|ref|YP_004035251.1|  [L=570]
Description: iron ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-28   99.1  47.5    1.8e-15   57.1  21.0    3.6  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.5       0.1   1.9e+03     159     173 ..      18      32 ..       4      43 .. 0.47
   2 !   57.1  21.0     1e-19   1.8e-15       1     166 [.      84     263 ..      80     323 .. 0.83
   3 !   53.4   9.4   1.5e-18   2.6e-14       2     178 ..     378     559 ..     377     565 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.1
                      BPD_transp_1 159 lalviavlllnlvad 173
                                       +a+v a +l++l+++
  gi|313124987|ref|YP_004035251.1|  18 VAAVTAAILIVLFYY 32 
                                       333333333333322 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 1e-19
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.............vilsilghlilp.viilllls 63 
                                       g+++++++  ++ +++++ lr l+i+++ +Ps+ +ai +v+ f              + ++   + lp ++++ +++
  gi|313124987|ref|YP_004035251.1|  84 GLPGAWVLS-RFEFPGRETLRSLTILPFVMPSIMVAIGFVATFgqngtlndvltalGLPKVTLLYSLPaILVAHAFY 159
                                       456666666.9999**************************999************966666777888879******* PP

                      BPD_transp_1  64 aapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.... 136
                                       +ap++++++ aa +s++ + ve+ar+lGas+ + f+ vv+P++lp ++ g+ l+f++ +  + +++ lg   G    
  gi|313124987|ref|YP_004035251.1| 160 NAPLITRVTTAAWESVDASAVETARTLGASPYRAFFDVVVPQLLPAVAVGATLTFIFTFASFPIVLALG---Gtqla 233
                                       *********************************************************************...63346 PP

                      BPD_transp_1 137 .lgtllleailgydyseisnggvlalviavl 166
                                        +  l+ +  ++ d++e++  ++++ +++ l
  gi|313124987|ref|YP_004035251.1| 234 tVEVLIYSGVQNLDFAEAA-SLAVVETVLSL 263
                                       6677777777777777777.33333333332 PP

  == domain 3  score: 53.4 bits;  conditional E-value: 1.5e-18
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.....vilsilg.hlilpviillllsaapyvrl 70 
                                       +++G+++   + r ++++k+++ l+ ++l++  +v+++ l+  +     v+ + ++ +++l+++++ +++a p+v++
  gi|313124987|ref|YP_004035251.1| 378 LPMGVVMSvlTTRDFRGRKIIDALSMAPLTVSGIVVGLGLLRGLvfgveVFGTRVQvTGALAIVAAHAVGAYPFVTR 454
                                       789999999999***********************777655444558897777777689999*************** PP

                      BPD_transp_1  71 irraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailg 147
                                       +++  l  l+ +lve ar+lGasr + +  + lP+++  +++g+++af++++g++  + +l+ ++  ++++  a + 
  gi|313124987|ref|YP_004035251.1| 455 NVAPLLGGLDPQLVESARTLGASRVRALLDIELPLVAAGVVAGAAFAFAISIGEFDSTVILAEGS-ASYTMPVAVQR 530
                                       **************************************************************888.67777777777 PP

                      BPD_transp_1 148 ydyseisnggvlalviavlllnlvadilqrl 178
                                       y     + g++ a+++++ll++ +++++ + 
  gi|313124987|ref|YP_004035251.1| 531 YLGR-RL-GPATAMGCVLLLVTSLSFVVIER 559
                                       7666.44.67777777777777777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3594.45
//
Query:       gi|313124988|ref|YP_004035252.1|  [L=226]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-25   87.4   0.0    1.4e-24   86.5   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    5.2e-21   75.2   0.0    9.3e-21   74.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    5.8e-18   65.1   0.0    8.1e-18   64.7   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    4.9e-13   49.2   0.0    6.4e-13   48.9   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    4.6e-12   46.5   0.0    7.2e-12   45.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.3e-11   44.3   0.0    1.7e-11   43.9   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.5e-06   27.4   0.0      2e-06   27.0   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
    0.00013   21.9   0.0     0.0002   21.4   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
    0.00032   20.3   0.0     0.0007   19.2   0.0    1.5  1  MTS              Methyltransferase small domain
    0.00074   19.3   0.0       0.17   11.5   0.0    2.2  2  N6_N4_Mtase      DNA methylase
    0.00094   18.6   0.0     0.0013   18.1   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.001   18.7   0.0     0.0017   18.0   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
     0.0014   18.0   0.0      0.002   17.5   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
     0.0019   18.1   0.0     0.0072   16.2   0.0    1.8  1  Methyltransf_8   Hypothetical methyltransferase
     0.0021   17.9   0.0     0.0037   17.1   0.0    1.5  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.084   12.5   0.0      0.097   12.2   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.11   11.0   0.0       0.19   10.2   0.0    1.4  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
       0.13   12.2   0.0       0.22   11.4   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
       0.21   11.7   0.0        4.1    7.5   0.0    2.1  2  FtsJ             FtsJ-like methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   1.5e-27   1.4e-24       1      96 []      43     138 ..      43     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.5e-27
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       Ld+GcG+G+  +al ++   +rv+g+D s+em + a++ + +e+  + ++v+d+ +lpf+d+s+D v+s e++ + +
  gi|313124988|ref|YP_004035252.1|  43 LDLGCGSGYAGRALRETKeaGRVYGLDGSPEMARNAQSYTDDEK--IGYLVGDFDELPFADDSIDHVFSMEAFYYAA 117
                                       8**************655669***************99999998..9****************************** PP

                                       CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllvi 96 
                                       dp+++l+e+aRvL+pgG++++
  gi|313124988|ref|YP_004035252.1| 118 DPHHTLSEVARVLRPGGTFFC 138
                                       ******************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   9.8e-24   9.3e-21       1      97 []      42     134 ..      42     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 9.8e-24
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLdlGcG+G   +al +  ++++v+g+D s+em ++a++  ++e  ++ +++gd+++lpf+d+s+D v+s+ a+ + 
  gi|313124988|ref|YP_004035252.1|  42 VLDLGCGSGYAGRALRETKEAGRVYGLDGSPEMARNAQSYTDDE--KIGYLVGDFDELPFADDSIDHVFSMEAFYYA 116
                                       9**************999669********************776..8***********************8889886 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                          d +++l+e+arvL+pgG
  gi|313124988|ref|YP_004035252.1| 117 A--DPHHTLSEVARVLRPGG 134
                                       6..56699***********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   8.6e-21   8.1e-18       4     127 ..      39     157 ..      37     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 8.6e-21
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       + +vlDlGCG+G+ + +l  e  + ++v+G+D s+e+ + A++ +++ ++      +gd+ el+  ++d+++D ++s
  gi|313124988|ref|YP_004035252.1|  39 DDVVLDLGCGSGYAGRALR-ETKEAGRVYGLDGSPEMARNAQSYTDDEKIG---YLVGDFDELP--FADDSIDHVFS 109
                                       568****************.8889999****************99988886...89********..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedprllaelp.akveeesk 127
                                        e++++ adp  +l e+ rvl+pgg + ++    ++++  ++++e+  
  gi|313124988|ref|YP_004035252.1| 110 MEAFYYAADPHHTLSEVARVLRPGGTFFCAVNYYEENVHsHEWQENIS 157
                                       **************************9876555333333333333333 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   6.8e-16   6.4e-13      13     162 ..      31     179 ..      17     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 6.8e-16
                   Methyltransf_23  13 lerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgk 82 
                                       l+r++   +++  vLd+GcG+G+  + lre      v+g D spe+   a+     +++ +    f  +e ++ +++
  gi|313124988|ref|YP_004035252.1|  31 LARMP--VEPDDVVLDLGCGSGYAGRALRETKEagRVYGLDGSPEMARNAQsytddEKIGYLVGDF--DELPFADDS 103
                                       45554..578889***************7765448*********9999876666443333333333..58888999* PP

                   Methyltransf_23  83 fdlIvlrevlehvpdppellrqiatllkpgGylllse..plaslkedrllldwlylvpagrhisffsarslkellee 157
                                       +d + ++e ++   dp+++l+ +a+ l+pgG +++ +  + ++ ++ ++ +++  + ++      ++ ++++e+++e
  gi|313124988|ref|YP_004035252.1| 104 IDHVFSMEAFYYAADPHHTLSEVARVLRPGGTFFCAVnyYEENVHSHEWQENISVEMTR------WTGEEYREAFRE 174
                                       *********************************99995556666666666666666655......999********* PP

                   Methyltransf_23 158 aGlev 162
                                       aGl v
  gi|313124988|ref|YP_004035252.1| 175 AGLFV 179
                                       **966 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   7.6e-15   7.2e-12       1      99 []      43     136 ..      43     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 7.6e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcG+G   ral+e  +  +++g+D sp++  + ++   + e+    + ++++l  +d+    s D v++ +++ 
  gi|313124988|ref|YP_004035252.1|  43 LDLGCGSGYAGRALRETKEAGRVYGLDGSPEMA-RNAQSYTDDEKIGYLVGDFDELPFADD----SIDHVFSMEAFY 114
                                       8********************************.666666666655666666666666554....************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                       + +d++ +l++++++L+pgG +
  gi|313124988|ref|YP_004035252.1| 115 YAADPHHTLSEVARVLRPGGTF 136
                                       ********************75 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.8e-14   1.7e-11      33     151 ..      22     138 ..      19     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.8e-14
                                       HHHHH..HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--T CS
                   Ubie_methyltran  33 rlWkk..fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqana 107
                                       r W++   v  ++ v +   vlD+ +G+g    + +++ +e g+v +lD +++m + ++    +e   +i +l+++ 
  gi|313124988|ref|YP_004035252.1|  22 RHWHTakHVLARMPVEPDDVVLDLGCGSGYAGRA-LRETKEAGRVYGLDGSPEMARNAQSYTDDE---KIGYLVGDF 94 
                                       55665446778888889999********976655.5677999*************9999887776...89******* PP

                                       TT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran 108 eeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                        eLpf dds D v     +   +D +++L e+ rvl+pGG++++
  gi|313124988|ref|YP_004035252.1|  95 DELPFADDSIDHVFSMEAFYYAADPHHTLSEVARVLRPGGTFFC 138
                                       ************9988899999********************99 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   2.1e-09     2e-06     107     216 ..      30     137 ..      16     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.1e-09
                                       HGGGS.--TT-EEEEET-TTSHHHHHHH.HCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.-- CS
                    Methyltransf_9 107 vlphlsdlkgrtildvGcgnGyhlwrmv.gegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.le 181
                                       vl  ++   + ++ld+Gcg+Gy    +  +++a  v G+d s          + +  +d++   l    ++lp   +
  gi|313124988|ref|YP_004035252.1|  30 VLARMPVEPDDVVLDLGCGSGYAGRALReTKEAGRVYGLDGSPEMARN---AQSYT-DDEKIGYLVGDFDELPFaDD 102
                                       444444456889**********864443267899*******9986544...34455.667777776889****8679 PP

                                       -EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEE CS
                    Methyltransf_9 182 afdtvfsmGvlyhrrsPldhllqlkdqlvkgGelv 216
                                       + d vfsm  +y+   P  +l+++   l+ gG++ 
  gi|313124988|ref|YP_004035252.1| 103 SIDHVFSMEAFYYAADPHHTLSEVARVLRPGGTFF 137
                                       ********************************975 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.2e-07    0.0002      25      71 ..      38      82 ..      25     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.2e-07
                   Methyltransf_32 25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekra 71
                                      ++  v+D+G+G gY +++l    ++   +v+g+d + e++++a+   
  gi|313124988|ref|YP_004035252.1| 38 PDDVVLDLGCGSGYAGRALRE--TKEAGRVYGLDGSPEMARNAQSYT 82
                                      567899**************9..44689**********999998654 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.4e-07    0.0007      22     140 ..      29     141 ..      21     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.4e-07
                                       HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-E CS
                               MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkf 98 
                                         l  +p e ++ vlDlGcG G+ g al + ++  +v  +d + +  + a+    ++k+   v   d l  ++++++
  gi|313124988|ref|YP_004035252.1|  29 HVLARMPVEPDDVVLDLGCGSGYAGRALRETKEAGRVYGLDGSPEMARNAQSYTDDEKIGYLVGDFDELP-FADDSI 104
                                       5677899999999*********************9******99998888888887777654444444443.335788 PP

                                       EEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEE CS
                               MTS  99 dlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVan 140
                                       d++ s   f    +      ++ + e +++L++gG++++ +n
  gi|313124988|ref|YP_004035252.1| 105 DHVFSMEAFYYAAD-----PHHTLSEVARVLRPGGTFFCAVN 141
                                       88877777766666.....34445555667777777776655 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00018      0.17     186     227 ..      33      76 ..      26      81 .. 0.79
   2 !    5.9   0.0      0.01       9.4      36      60 ..     120     144 ..     107     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                       HHHS-TT-EEEETT-TTTHHHHHHHHTT-E..EEEEESSHHHHH CS
                       N6_N4_Mtase 186 klstkkgdivlDpFaGSGtTavaakelgrk..fiGieieeeyve 227
                                       ++  +++d+vlD  +GSG+ ++a +e ++    +G + ++e ++
  gi|313124988|ref|YP_004035252.1|  33 RMPVEPDDVVLDLGCGSGYAGRALRETKEAgrVYGLDGSPEMAR 76 
                                       666789******************99886444788877777766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHEEEEEEEEEEE-CCC CS
                       N6_N4_Mtase  36 ekvlkevrrvLkddgsifiniddse 60 
                                       +  l+ev rvL ++g++f+ + + e
  gi|313124988|ref|YP_004035252.1| 120 HHTLSEVARVLRPGGTFFCAVNYYE 144
                                       56799*************9876655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.3e-06    0.0013      47     165 ..      23     139 ..      11     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GG CS
                              CMAS  47 qlaKldlileklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvdeldlerkvevklldye 122
                                         +  +++l ++ ++p + +Ld+GcG G+  r   e  ++ +v gl  S e a+ a+   d++        ++ d+ 
  gi|313124988|ref|YP_004035252.1|  23 HWHTAKHVLARMPVEPDDVVLDLGCGSGYAGRALRETKEAgRVYGLDGSPEMARNAQSYTDDEK----IGYLVGDFD 95 
                                       55667899******************9998766555444439*********9999998887765....566778898 PP

                                       G---...--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEE CS
                              CMAS 123 dlde...kvdrvvsvgafehvgkenydtffkklkkllkedGllllh 165
                                       +l+     +d+v s++af      ++    +++ ++l+++G++   
  gi|313124988|ref|YP_004035252.1|  96 ELPFaddSIDHVFSMEAFYYAADPHH--TLSEVARVLRPGGTFFCA 139
                                       88652237777777777765443333..367899999999998754 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.8e-06    0.0017      11     103 ..      36     131 ..      26     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-06
                              MetW  11 ikpgsrvldlGcGdGellellkeekqv.dgrGleldeegvaecva....kGlsviqgdldkdlenfedksfdyvvls 82 
                                       ++p   vldlGcG G   + l+e+k+  + +Gl+ + e   ++ +      +  + gd d+    f+d+s d v   
  gi|313124988|ref|YP_004035252.1|  36 VEPDDVVLDLGCGSGYAGRALRETKEAgRVYGLDGSPEMARNAQSytddEKIGYLVGDFDE--LPFADDSIDHVFSM 110
                                       89999*******************9974689*99887776665541111445555566554..4699********99 PP

                              MetW  83 qtlqatrnpkevldellrigr 103
                                        ++    +p++ l+e+ r+ r
  gi|313124988|ref|YP_004035252.1| 111 EAFYYAADPHHTLSEVARVLR 131
                                       9*************9999865 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.1e-06     0.002      41     193 ..      17     166 ..       7     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                                       HHHHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE.-HHHHHHHHHHS-----TTEEEE CS
                    Methyltransf_2  41 kglqessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfD.lpeVveaAkehlsageeervefv 116
                                       kg+++    +ak+vl+ + +e+  +++D+G G+G + +a  ++    +v  +D  pe +++A+++   + +e++ + 
  gi|313124988|ref|YP_004035252.1|  17 KGMEDRHWHTAKHVLARMPVEPDDVVLDLGCGSGYAGRALRETKEAGRVYGLDgSPEMARNAQSY---TDDEKIGYL 90 
                                       7899999999******************************9998888888777457888888888...999****** PP

                                       ES-TTTS-----SEEE..EESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHHHHHHHHCSS CS
                    Methyltransf_2 117 gGdffkdslPeaDail..lkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelvdlimlvqte 191
                                        Gdf   +lP aD  +  + ++   +  ++ ++ L +v + l++gG    +    +++ +++  +e +++ m    +
  gi|313124988|ref|YP_004035252.1|  91 VGDFD--ELPFADDSIdhVFSMEAFYYAADPHHTLSEVARVLRPGGTFFCAVNYYEENVHSHEWQENISVEMTRW-T 164
                                       ***86..9**9986541222222234556678899***********99988777888777777777778887766.3 PP

                                       -- CS
                    Methyltransf_2 192 Gk 193
                                       G+
  gi|313124988|ref|YP_004035252.1| 165 GE 166
                                       43 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.7e-06    0.0072      73     157 ..      39     139 ..      27     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                                       TS-EEEES-TT-HHH...HH--S-..EEEEESS-S..........STTE..EES-TTS-S--TT-EEEEEEES--.- CS
                    Methyltransf_8  73 nlvvadlGcGeakia...eavrekekvrsfdlvav..........nerv..vacdlakvPledesvdvavfclsl.m 133
                                       + vv dlGcG         + +e  +v  +d  +           +e++   + d+ ++P +d+s+d +    ++  
  gi|313124988|ref|YP_004035252.1|  39 DDVVLDLGCGSGYAGralRETKEAGRVYGLDGSPEmarnaqsytdDEKIgyLVGDFDELPFADDSIDHVFSMEAFyY 115
                                       5689999999876551124445556788888654211111111112333225789************7655544425 PP

                                       SS-HHHHHHHHHHHEEEEEEEEEE CS
                    Methyltransf_8 134 gtnladflkeanrvlkvGGllkva 157
                                       + + ++ l e+ rvl++GG ++ a
  gi|313124988|ref|YP_004035252.1| 116 AADPHHTLSEVARVLRPGGTFFCA 139
                                       78999**************99876 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.9e-06    0.0037      68     118 ..      33      82 ..      21     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.9e-06
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHH CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnl 118
                                        + +++ + vL++G+GsGy    l +  +e grv +++ ++e++++a+   
  gi|313124988|ref|YP_004035252.1|  33 RMPVEPDDVVLDLGCGSGYAGRALRE-TKEAGRVYGLDGSPEMARNAQSYT 82 
                                       445889999**********9998876.6999*************9998754 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001     0.097       3      61 ..      41     103 ..      39     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                   Methyltransf_15   3 vilDlfsGaG..GnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe......l 61 
                                       v+lDl +G+G  G +    ++  +v++++ ++e    +++Na++Y  ++ki + +gd+ e       
  gi|313124988|ref|YP_004035252.1|  41 VVLDLGCGSGyaGRALRETKEAGRVYGLDGSPE----MARNAQSYTDDEKIGYLVGDFDElpfaddS 103
                                       79******997778888788899******9997....579******************985554441 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002      0.19     175     233 ..      97     151 ..      36     170 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                   Methyltransf_29 175 lpyPsrsfdlihCsrCridwteedgilllevdRvlRpgGyfvlsappvyerkeeelkee 233
                                       lp+   s d +  s     + ++    l ev RvlRpgG f  + +  +e   + +++e
  gi|313124988|ref|YP_004035252.1|  97 LPFADDSIDHVF-SMEAFYYAADPHHTLSEVARVLRPGGTFFCAVNYYEE---NVHSHE 151
                                       666666666554.333455677777899***********99887664332...222222 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.22      12      61 ..      36      85 ..      30      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                   Methyltransf_18 12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakenieka 61
                                      ve++++v+D G+  gy   +l +++ a +v+  D +++  ++a++  +++
  gi|313124988|ref|YP_004035252.1| 36 VEPDDVVLDLGCGSGYAGRALRETKEAGRVYGLDGSPEMARNAQSYTDDE 85
                                      78899*************************************99877665 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0043       4.1      12      57 ..      30      73 ..      20     107 .. 0.76
   2 ?    1.7   0.0      0.25   2.4e+02     122     135 ..     127     140 ..     119     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0043
                                      HHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS CS
                              FtsJ 12 idekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm 57
                                      +++++  ++p++ v+Dlg++ G     l +  +a g+v+++D  p 
  gi|313124988|ref|YP_004035252.1| 30 VLARMP-VEPDDVVLDLGCGSGYAGRALRETKEA-GRVYGLDGSPE 73
                                      555666.678999********9888888888665.*******9664 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.25
                                       CCCCECCCEEEECC CS
                              FtsJ 122 lkllkpggtfvlki 135
                                        ++l+pggtf + +
  gi|313124988|ref|YP_004035252.1| 127 ARVLRPGGTFFCAV 140
                                       579********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1452.62
//
Query:       gi|313124989|ref|YP_004035253.1|  [L=152]
Description: hypothetical protein Hbor_02030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-06   27.6   1.4    3.6e-06   26.5   1.4    1.6  1  DUF2391   Putative integral membrane protein (DUF2391)


Domain annotation for each model (and alignments):
>> DUF2391  Putative integral membrane protein (DUF2391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.4     2e-10   3.6e-06     142     230 ..      10      98 ..       5     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2e-10
                           DUF2391 142 ladlgltliGAlllafniAPTeEvvllaaavspvqllalillsLlisylivfeagftgqekreeqrgifqrflsetv 218
                                       l+d +  ++G  lla +   TeEv  laa++s+vq +  +++ L + y+ +++a+ ++ ++ ++  g+  rf+s  +
  gi|313124989|ref|YP_004035253.1|  10 LSDTAQQIVGGFLLAGPFVVTEEVWSLAASMSAVQGVFTVVIVLTVGYGALYKADDRDPDRERDLLGVPVRFVSLIL 86 
                                       567778899******************************************************************** PP

                           DUF2391 219 vsYlvsLlvsll 230
                                       v+Yl +L+ +l+
  gi|313124989|ref|YP_004035253.1|  87 VAYLSVLILALA 98 
                                       ***999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1044.92
//
Query:       gi|313124990|ref|YP_004035254.1|  [L=192]
Description: hypothetical protein Hbor_02040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   18.3   0.0     0.0015   17.9   0.0    1.1  1  ATPase    KaiC


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   8.3e-08    0.0015      53     188 ..      47     183 ..      37     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.3e-08
                            ATPase  53 fvtveepaedlrenakslGwdlekleeegklaiidasesaeesaee........kdkedleelieelaeaikeika. 120
                                        v++  +a+++ ++ ++ ++d  +       +i+d+ + +++++++        +  +dl+ ++e++++ +++    
  gi|313124990|ref|YP_004035254.1|  47 VVSTRTTAREVEQKLEHYDVDESR------AVILDTLSVDRGYSRRgsnhvhyvSAPDDLDGIVEQVRNFLESHDGk 117
                                       566666677777777777666544......44555555555544444555568899999999999999999998773 PP

                            ATPase 121 krvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLd 188
                                        rv +Ds+t lay+++ + a e  ++l+  l + + + ++    +++ee +   +  e + +gv+ Ld
  gi|313124990|ref|YP_004035254.1| 118 LRVSVDSVTELAYYADVDRAYEATKRLLDLLDEHDAVGLFHLSNEVHEEPT-LERFRE-LFEGVVELD 183
                                       69**************************************88866654433.333444.566776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1339.56
//
Query:       gi|313124991|ref|YP_004035255.1|  [L=273]
Description: hypothetical protein Hbor_02050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1757.88
//
Query:       gi|313124992|ref|YP_004035256.1|  [L=29]
Description: hypothetical protein Hbor_02060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (29 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.31s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 185.48
//
Query:       gi|313124993|ref|YP_004035257.1|  [L=489]
Description: efflux protein, mate family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-57  192.9  25.1    4.1e-30  104.6  11.3    2.4  2  MatE             MatE
    5.9e-12   45.9   3.7    5.9e-12   45.9   3.7    4.8  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
      0.058   13.2   0.3       0.18   11.6   0.3    1.9  1  CAAD             CAAD domains of cyanobacterial aminoacyl-tRN


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6  11.3   6.8e-34   4.1e-30       1     160 [.      40     200 ..      40     201 .. 0.98
   2 !   94.0   5.9   1.2e-30   7.5e-27       1     161 []     266     425 ..     266     425 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 6.8e-34
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P++++  + +ll ++d l+v+   g  a+A++ ++++  ++ f ++l+l +++ ++v++++Ga+++++a +a+ q+l
  gi|313124993|ref|YP_004035257.1|  40 PVMVTGGMRTLLRIADFLMVSIAlGNAAVAGLELGFQYYFIPFGLALALTSGTISVVSRFVGANDYDAADFAVKQSL 116
                                       777888888999*********999***************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisll 153
                                       +l+ll+s++i++++++++++++ l+t+d + ++l++ ylri+ l++ + + +++++++l g+g+t++p+y+ l++l+
  gi|313124993|ref|YP_004035257.1| 117 WLALLISVPISIAGWMYARPLIALLTNDLQTIKLGSAYLRIVMLSVAFRFWSMIAARALAGVGDTRTPMYVRLLTLP 193
                                       ***************************************************************************** PP

                              MatE 154 lniplny 160
                                        ni+ln 
  gi|313124993|ref|YP_004035257.1| 194 TNIILNA 200
                                       *****97 PP

  == domain 2  score: 94.0 bits;  conditional E-value: 1.2e-30
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+a + l  ++  + + +++g lg++ +Aa++i+ ++  l  ++++g sta++tlvgqa+G ++  +a e+  q+l 
  gi|313124993|ref|YP_004035257.1| 266 PLAGTRLSRTFGRFPFLFVLGLLGTNVVAAYAIGRRVMLLALMPAWGYSTAASTLVGQAIGGGDDGEATEYGWQTLR 342
                                       77888888889999999999********************************************************* PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.l 153
                                       ++l+  l+ia+++++ + +i+++f++++  ++l++r++r+ +lg+ +++++ + +g+lrgag+t++ply  l+++ l
  gi|313124993|ref|YP_004035257.1| 343 IALVTQLLIAAAIFVAATPIAQVFGASD--IPLTARFIRVFGLGVAGFSVSRTMRGALRGAGDTRWPLYGGLVGTyL 417
                                       ****************************..9********************************************** PP

                              MatE 154 lniplnyl 161
                                       +++p+++l
  gi|313124993|ref|YP_004035257.1| 418 VRLPIAFL 425
                                       ****9986 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   3.8     0.024   1.4e+02      35     117 ..      65     142 ..      42     152 .. 0.76
   2 !   45.9   3.7   9.9e-16   5.9e-12       1      78 [.     154     237 ..     154     253 .. 0.94
   3 ?   -1.9   3.9      0.54   3.2e+03      45      68 ..     303     325 ..     290     365 .. 0.77
   4 !    6.1   1.1    0.0018        11       2      44 ..     378     420 ..     377     467 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.024
                   Polysacc_synt_C  35 lvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgikl.ellrrllkpllaalvmgivvyllll 110
                                       +++ a + l++++++ip fg     +a +l+  +++v+  +   + +      + ++l+  ll+++ ++i+ ++ ++
  gi|313124993|ref|YP_004035257.1|  65 NAAVAGLELGFQYYFIP-FG-----LALALTSGTISVVSRFVGANDYDAADfAVKQSLWLALLISVPISIAGWMYAR 135
                                       45556689999999998.76.....7777777777778877777777776667799999999999999999776666 PP

                   Polysacc_synt_C 111 lllglll 117
                                        l+ ll+
  gi|313124993|ref|YP_004035257.1| 136 PLIALLT 142
                                       5555554 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 9.9e-16
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvav 71 
                                       +L+i++ls+ f ++s++ +  L g+g +++++++ ++++  ++iln +li      p +g+ Gaa++tv+a +++av
  gi|313124993|ref|YP_004035257.1| 154 YLRIVMLSVAFRFWSMIAARALAGVGDTRTPMYVRLLTLPTNIILNAVLIfglfgaPALGVEGAAWGTVAANTLAAV 230
                                       69************************************************98888888899**************** PP

                   Polysacc_synt_C  72 lnlyalr 78 
                                       + +++l 
  gi|313124993|ref|YP_004035257.1| 231 IFFVLLA 237
                                       9988875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.54
                   Polysacc_synt_C  45 lnllliplfgivGaaiatvlallv 68 
                                       + l l+p +g +  a++t++++++
  gi|313124993|ref|YP_004035257.1| 303 MLLALMPAWG-YSTAASTLVGQAI 325
                                       5677888888.6677788888776 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0018
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvkli 44 
                                       ++++ l++  +s+s+++ + L g g ++++l+  ++g  +  +
  gi|313124993|ref|YP_004035257.1| 378 IRVFGLGVAGFSVSRTMRGALRGAGDTRWPLYGGLVGTYLVRL 420
                                       57889999***************************99865444 PP

>> CAAD  CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   3.1e-05      0.18       7      61 ..     338     392 ..     332     399 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                              CAAD   7 wskyerklkviglilaaivalklalavldaiddiPllpplleLvGlgytgwFvyr 61 
                                       w++ + +l +  li+aai++    +a +    diPl + ++++ Glg++g+ v+r
  gi|313124993|ref|YP_004035257.1| 338 WQTLRIALVTQLLIAAAIFVAATPIAQVFGASDIPLTARFIRVFGLGVAGFSVSR 392
                                       77777788888888888888888888888889****************9976666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3070.74
//
Query:       gi|313124994|ref|YP_004035258.1|  [L=370]
Description: zn-ribbon containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-31  106.8  16.6    6.9e-22   78.1  16.6    3.3  1  DUF2072        Zn-ribbon containing protein
  ------ inclusion threshold ------
      0.036   14.2   2.4      0.086   13.0   2.4    1.6  1  Zn-ribbon_8    Zinc ribbon domain
       0.18   11.4   1.1        8.6    6.0   0.1    2.5  2  TF_Zn_Ribbon   TFIIB zinc-binding
       0.22   11.3   3.0       0.52   10.1   3.0    1.7  1  zinc_ribbon_2  zinc-ribbon domain
       0.27   11.3   0.4       0.41   10.7   0.4    1.3  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.34   10.9   3.9       0.17   11.9   1.1    1.9  2  DUF1451        Zinc-ribbon containing domain
          1    9.4   4.7        4.4    7.4   4.7    2.0  1  DUF1610        Domain of unknown function (DUF1610)


Domain annotation for each model (and alignments):
>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1  16.6   2.7e-25   6.9e-22       1     130 [.       2     362 ..       2     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 2.7e-25
                           DUF2072   1 PHkCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseekeelvaeaeee..................... 56 
                                       PH+Ct+C+kvf dgske+l+GCp+CGg+kF++    + ++d++e++++++++++++                     
  gi|313124994|ref|YP_004035258.1|   2 PHQCTNCGKVFADGSKEMLSGCPNCGGNKFQFSPSGSDSDDAAETTTRQQTSSSGTtpssgsaadattdrepntnre 78 
                                       9*******************************998888888888888666665555688888877777777777777 PP

                           DUF2072  57 .............................ieevldaeeteeeklekk.............................. 74 
                                                                                     +                              
  gi|313124994|ref|YP_004035258.1|  79 sasddtagsttwqraasraadveerrsanQ----------------Tpsgsaddggrsdtrshktqnrsadqtndni 139
                                       776666666666665555555555555550................0455555555555555556666666666667 PP

                           DUF2072  75 ............................................................................. 74 
                                                                                                                    
  gi|313124994|ref|YP_004035258.1| 140 dsarrsektlrewansrgfasevedandettlrenrrrtgdaqrrpserrssssarqsspsdrqssddaqsdssvpt 216
                                       7777777777777888899999999999999999999999999********************************** PP

                           DUF2072  75 ............................................................................. 74 
                                                                                                                    
  gi|313124994|ref|YP_004035258.1| 217 dsssaspettasketktptgtpapsdepapsskqakssaadpsvfgddveddaqasarsdvvspdeiaaaqpddrps 293
                                       ***************************************************************************** PP

                           DUF2072  75 .............ekekaekekeeedrvesvrilepGsYelNlekLlerdelvmalkeegkYvvdlpsv 130
                                                    + +  e ++e +d++es++i+ pG+YelNl++L++r e +++l+e+g+Yv+++p++
  gi|313124994|ref|YP_004035258.1| 294 dadgrviepesddRPDLDELREELNDQFESIKIVAPGEYELNLMELYDRPEYIISLREDGRYVIEVPDT 362
                                       **********9988888999*********************************************9976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.4   3.3e-05     0.086       7      35 ..       4      30 ..       3      32 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.3e-05
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.e 35
                                      +C++Cg++f       ++ l  CP+Cg+ +
  gi|313124994|ref|YP_004035258.1|  4 QCTNCGKVFADGS---KEMLSGCPNCGGnK 30
                                      6*****9999443...333555*****955 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.019        48      22      31 ..       5      14 ..       3      18 .. 0.77
   2 ?    6.0   0.1    0.0034       8.6       3      11 ..      23      31 ..      22      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.019
                                      ESSSSBEEEE CS
                      TF_Zn_Ribbon 22 CtdCGlVled 31
                                      Ct+CG V  d
  gi|313124994|ref|YP_004035258.1|  5 CTNCGKVFAD 14
                                      8888888766 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0034
                                      ETTTTCEEC CS
                      TF_Zn_Ribbon  3 CPnCgstnl 11
                                      CPnCg+ ++
  gi|313124994|ref|YP_004035258.1| 23 CPNCGGNKF 31
                                      *****9764 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.0    0.0002      0.52       2      20 ..       5      27 ..       4      30 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                     zinc_ribbon_2  2 CpnCGaelqdnakF....CpyCG 20
                                      C+nCG+   d++k     Cp+CG
  gi|313124994|ref|YP_004035258.1|  5 CTNCGKVFADGSKEmlsgCPNCG 27
                                      **********************9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00016      0.41      72      99 ..       4      33 ..       1      39 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                      EETTTS-EEECHHH..HHS-TTTSSS-EEE CS
                              HypA 72 rCreCgkefeleek..alrCpkCgsadvei 99
                                      +C++Cgk f   +k     Cp+Cg++++++
  gi|313124994|ref|YP_004035258.1|  4 QCTNCGKVFADGSKemLSGCPNCGGNKFQF 33
                                      7********9665434458******99876 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.1   6.7e-05      0.17     116     144 ..       4      32 ..       3      35 .. 0.95
   2 ?   -2.7   0.1       2.2   5.6e+03       5      30 ..     126     151 ..     123     162 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                           DUF1451 116 vCekCgkelalkkteeippCpkCgateFr 144
                                       +C++Cgk  a  + e ++ Cp+Cg+++F+
  gi|313124994|ref|YP_004035258.1|   4 QCTNCGKVFADGSKEMLSGCPNCGGNKFQ 32 
                                       6***************************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                           DUF1451   5 eaeekseeeleelvekakeklseaee 30 
                                       +++++s+++ ++ +++a++ ++ + e
  gi|313124994|ref|YP_004035258.1| 126 KTQNRSADQTNDNIDSARRSEKTLRE 151
                                       66777777778888888777766655 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.7    0.0017       4.4       1      23 [.       5      27 ..       5      28 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0017
                           DUF1610  1 CtSCGaelaprEravvFpCPNCG 23
                                      Ct CG++ a++ +     CPNCG
  gi|313124994|ref|YP_004035258.1|  5 CTNCGKVFADGSKEMLSGCPNCG 27
                                      9***********99999*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1513  (0.0843884); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 1.11u 0.38s 00:00:01.49 Elapsed: 00:00:00.54
# Mc/sec: 2052.63
//
Query:       gi|313124995|ref|YP_004035259.1|  [L=129]
Description: hypothetical protein Hbor_02090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-46  155.6   0.3    3.8e-46  155.3   0.3    1.1  1  DUF2073   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2073  Uncharacterized protein conserved in archaea (DUF2073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3   0.3   2.1e-50   3.8e-46       1     105 []      24     127 ..      24     127 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 2.1e-50
                           DUF2073   1 lekmtsmekirlildkvkegkivvlEkgLtpeeeakliettmeeikpdeFsGieietypkkekdkgllekllgkkes 77 
                                       ++ ++smekirlild v++g+iv+lE+gL+p+ee+klie+tm+ei+pdeF+Gieie+yp+++  +g+l++l+gk+ +
  gi|313124995|ref|YP_004035259.1|  24 MDGLASMEKIRLILDGVRDGNIVILEEGLSPDEESKLIEVTMTEISPDEFNGIEIESYPQSKGGQGFLGRLMGKE-E 99 
                                       57789*********************************************************************8.9 PP

                           DUF2073  78 eerltvigPanqlktlkkdkdlisalvs 105
                                       +++ltvigPanq++tl+kd++lisalvs
  gi|313124995|ref|YP_004035259.1| 100 TKKLTVIGPANQIQTLHKDENLISALVS 127
                                       9*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.35s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 735.95
//
Query:       gi|313124996|ref|YP_004035260.1|  [L=213]
Description: small GTP-binding protein domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-15   55.3   0.0    8.4e-15   54.9   0.0    1.2  1  MMR_HSR1      50S ribosome-binding GTPase
    2.9e-11   43.3   0.1    0.00025   20.6   0.0    3.4  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    4.1e-07   29.6   0.0    0.00045   19.7   0.0    2.7  3  Arf           ADP-ribosylation factor family
    1.7e-05   24.4   0.4    0.00019   21.0   0.4    2.4  1  FeoB_N        Ferrous iron transport protein B
    0.00012   22.0   0.0       0.32   10.9   0.0    2.3  2  RsgA_GTPase   RsgA GTPase
    0.00013   21.5   0.0      0.067   12.6   0.0    2.2  2  SRPRB         Signal recognition particle receptor beta subun
    0.00013   21.4   0.0    0.00046   19.6   0.0    1.7  2  Septin        Septin
    0.00091   19.8   0.0     0.0041   17.6   0.0    2.2  1  AAA_18        AAA domain
     0.0011   19.0   0.0     0.0019   18.2   0.0    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0011   19.1   0.0     0.0082   16.4   0.0    2.1  2  Roc           Ras of Complex, Roc, domain of DAPkinase
     0.0022   18.3   0.2      0.075   13.3   0.0    2.2  2  AAA_28        AAA domain
      0.004   16.9   0.0     0.0094   15.7   0.0    1.6  2  AAA_24        AAA domain
     0.0047   17.3   0.0     0.0088   16.4   0.0    1.7  1  AAA_16        AAA ATPase domain
     0.0056   17.1   0.0      0.024   15.1   0.0    2.0  2  AAA           ATPase family associated with various cellular 
     0.0065   16.5   0.0        1.1    9.3   0.1    2.6  2  Dynamin_N     Dynamin family
     0.0097   16.3   0.0      0.019   15.3   0.0    1.6  1  RNA_helicase  RNA helicase
  ------ inclusion threshold ------
      0.012   14.8   0.0       0.02   14.1   0.0    1.3  1  NB-ARC        NB-ARC domain
      0.018   15.0   0.0      0.034   14.1   0.0    1.8  1  ATPase_2      ATPase domain predominantly from Archaea
       0.02   14.5   0.1          6    6.4   0.1    2.4  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.024   13.6   0.0        1.5    7.7   0.0    2.8  3  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.04   13.9   0.0      0.081   12.8   0.0    1.5  1  NACHT         NACHT domain
      0.047   14.2   0.0      0.062   13.8   0.0    1.5  1  ABC_tran      ABC transporter
      0.063   12.8   0.1       0.18   11.3   0.1    1.8  1  AAA_25        AAA domain
      0.074   12.8   0.0       0.16   11.7   0.0    1.5  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
       0.11   12.2   0.0       0.11   12.2   0.0    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   1.2e-17   8.4e-15       1     114 []      26     170 ..      26     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.2e-17
                                       EEEEEESTTSSHHHHHHHHHTS.....TEEESSSTTSSSSE.EEEEEE....ETTEEEEEEECGGC........... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.....kaivsdkpgtTrdi.negrvk....lkgkeielvDtpGl........... 56 
                                       +++i+G pN+GK+tL n++ ++     +   s++p  Tr   ++++v+     k+  i +vDtpG+           
  gi|313124996|ref|YP_004035260.1|  26 RIGIYGPPNAGKTTLANRIARDwtgdaVGPESHIPHETRRArRKENVEiernGKKVTIDIVDTPGVttkvdykefld 102
                                       69*****************984444335688********9944445655443223679*******866666666544 PP

                                       ........SS.HHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  57 ........ie.gaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                               +  + +  +g+++a++ l+e +d +++v+d++e+ +++++  l  ++e+++ p+++ +nk
  gi|313124996|ref|YP_004035260.1| 103 hdmekddaVRrSREATEGVAEAMHWLREdVDGVVYVLDSTEDPFTQVNTMLIGIIESQDLPVLIFANK 170
                                       443333322222333336777777777779********888899***999999999999999999997 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.6e-06    0.0018       4      79 ..      25      90 ..      22     107 .. 0.82
   2 !   20.6   0.0   3.6e-07   0.00025      93     188 ..     131     208 ..     118     213 .] 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                                      EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESS CS
                          GTP_EFTU  4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPG 79
                                      r igi g  ++GKtTL  r+  +   ++   e           ++E +r      +++++e+++kk +i ++DtPG
  gi|313124996|ref|YP_004035260.1| 25 RRIGIYGPPNAGKTTLANRIARDWTGDAVGPES--------HIPHETRRAR--RKENVEIERNGKKVTIDIVDTPG 90
                                      889******************988886664443........4677777754..5677777777************9 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.6e-07
                                       T-SEEEEEEETTTBSTHHHHHHH.HHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTE CS
                          GTP_EFTU  93 vlDgavlvvdaveGvepqteevl.rlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekev 168
                                        +Dg+v v+d++e++ +q +++l  ++ ++++p+ +f NK D  ++++++i ++  q+                   
  gi|313124996|ref|YP_004035260.1| 131 DVDGVVYVLDSTEDPFTQVNTMLiGIIESQDLPVLIFANKTDLEESNVQRISNAFPQHE------------------ 189
                                       68***************9998752788999**************999999887766443.................. PP

                                       EEEEEBTTTTBTHHHHHHHH CS
                          GTP_EFTU 169 pvvfgSalkgegvktlleal 188
                                         v+ Sal+g +++++ + +
  gi|313124996|ref|YP_004035260.1| 190 -TVPLSALEGNNMDEVYDKI 208
                                       .4555555555555555555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0037       2.7       3      38 ..      13      48 ..      11      99 .. 0.84
   2 ?   -1.2   0.0       1.7   1.2e+03     160     174 ..     117     131 ..     109     132 .. 0.81
   3 !   19.7   0.0   6.3e-07   0.00045      80     134 ..     130     179 ..     126     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                                      HHHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSS CS
                               Arf  3 silaklklkkkelrilllGLDnaGKtTilkklklee 38
                                      ++++++++     ri + G  naGKtT+ +++  + 
  gi|313124996|ref|YP_004035260.1| 13 RVVDRMFSDAEPRRIGIYGPPNAGKTTLANRIARDW 48
                                      67778888888889999************9998765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                                       TTBTHHHHHHHHHHH CS
                               Arf 160 kgeglkeglewlses 174
                                         eg+ e+++wl e+
  gi|313124996|ref|YP_004035260.1| 117 ATEGVAEAMHWLRED 131
                                       5799********876 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 6.3e-07
                                       TTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HH CS
                               Arf  80 ektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealsee 134
                                       e++d+v++v+Ds++ + +++ ++ L  ++e    ++ ++l++aNK Dl+e+   +
  gi|313124996|ref|YP_004035260.1| 130 EDVDGVVYVLDSTE-DPFTQVNTMLIGIIE---SQDLPVLIFANKTDLEESNV-Q 179
                                       579********986.568888887777775...56779**********98743.3 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.4   2.7e-07   0.00019       3     155 ..      27     207 ..      25     208 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.7e-07
                                       EEEEESTTSSHHHHHHHHHT..TSEEEEESTTSSSE......EEEEEEEETT..EEEEEEE----.....SSS.... CS
                            FeoB_N   3 valvGnpnvGkttlfnaltg..akqkvgNwpGvtve......kkegklklkg..keveivDlPGi.....Ysl.... 60 
                                       + + G pn+Gkttl n+++   +   vg  + +  e      k++++++ +g   +++ivD PG+     Y+     
  gi|313124996|ref|YP_004035260.1|  27 IGIYGPPNAGKTTLANRIARdwTGDAVGPESHIPHEtrrarrKENVEIERNGkkVTIDIVDTPGVttkvdYKEfldh 103
                                       7789**************86223456665554444400011144555555552267899*****9666663326676 PP

                                       .........SSSSHHHHHHHHH.HHCTSSSEEEEEEEGGG..HHHHHHHHHHHHHTT.SSEEEEEETHHHHHHTTEE CS
                            FeoB_N  61 .........sayseeekvardf.lleeepdvvvnvvdatn..lernLyLtlqllelg.vpvvlalnmideaekkgie 124
                                                 +    e va+ +  l+e++d vv v+d+t+  + +  ++++ ++e + +pv++  n++d  e++  +
  gi|313124996|ref|YP_004035260.1| 104 dmekddavrRSREATEGVAEAMhWLREDVDGVVYVLDSTEdpFTQVNTMLIGIIESQdLPVLIFANKTDLEESNVQR 180
                                       667776655333334555554415699***********975556666667777776548999999****99998887 PP

                                       E-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 125 idlkkLsekLgvpvvktsakkkegieellka 155
                                       i ++      + + v++sa ++++++e+ ++
  gi|313124996|ref|YP_004035260.1| 181 ISNAFP----QHETVPLSALEGNNMDEVYDK 207
                                       765433....346778888888888887766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0017       1.2      97     162 ..      22      92 ..       6      97 .. 0.64
   2 !   10.9   0.0   0.00044      0.32      19      97 ..     135     208 ..     116     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                                       CTTSEEEEECSTTSSHHHHHHHHCTT-.----S--------------SEEEEEETTTE.....EEESS-SSS CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpel.elktgevseklgrGkhTTtavellelaegg.....lliDtPGfr 162
                                        + + + + G+  +GK+tL n+++ +    ++g  s+  ++ +   ++ e +e++++g      ++DtPG++
  gi|313124996|ref|YP_004035260.1|  22 AEPRRIGIYGPPNAGKTTLANRIARDWtGDAVGPESHIPHETRR-ARRKENVEIERNGkkvtiDIVDTPGVT 92 
                                       5556677899999**********997313444444444444333.344555666665523322589999986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00044
                                       EEEEEESTTTT--HHHHHHHHH.HHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHH CS
                       RsgA_GTPase  19 llivvslkepelslnlldrfLv.laeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelk 94 
                                       ++ v+  +e+     +++ +L+ ++e+++++++i  nK+Dl e++   +++++++ +   e++ +sa ++++++e+ 
  gi|313124996|ref|YP_004035260.1| 135 VVYVLDSTEDP--FTQVNTMLIgIIESQDLPVLIFANKTDLEESNV--QRISNAFPQH--ETVPLSALEGNNMDEVY 205
                                       44444333233..23455555527899*************977665..8888887777..56666667777777776 PP

                                       HHC CS
                       RsgA_GTPase  95 ell 97 
                                       +++
  gi|313124996|ref|YP_004035260.1| 206 DKI 208
                                       665 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   9.3e-05     0.067       5      59 ..      26      91 ..      22     113 .. 0.67
   2 !    6.8   0.0    0.0057       4.1      73     125 ..     129     174 ..     121     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.3e-05
                                      EEEEE-STTSSHHHHHHHHHHSS---B-..--SS-EEETTG............GGTT-SEEEETT- CS
                             SRPRB  5 avllvGlsdsGKTslftrLttdsvkktv..tSqessaalkv.........ksekgskltliDfPGh 59
                                      ++ + G+ ++GKT+l +r+  d + ++v   S  ++ + +          ++ k+ +++++D PG 
  gi|313124996|ref|YP_004035260.1| 26 RIGIYGPPNAGKTTLANRIARDWTGDAVgpESHIPHETRRArrkenveieRNGKKVTIDIVDTPGV 91
                                      66799*****************555444222333443333333345554567788888999**995 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0057
                                       HGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTST CS
                             SRPRB  73 ksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelf 125
                                       ++ + g+v+v+DSt dp   ++v  +l+ i+       + +++li  nK +l 
  gi|313124996|ref|YP_004035260.1| 129 REDVDGVVYVLDSTEDP--FTQVNTMLIGIIES-----QDLPVLIFANKTDLE 174
                                       56799*********998..56666667666543.....458888888888875 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.4e-07   0.00046       9      80 ..      29      99 ..      26     108 .. 0.79
   2 ?   -1.3   0.0       1.4     1e+03     156     196 ..     143     183 ..     135     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.4e-07
                                      EEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE---BSSSSSHHC CS
                            Septin  9 vvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdavdnsk 80
                                      + G    Gkttl n + ++   ++   +e +  +++    +k++v+ie +g k+++ ++Dtpg   +vd ++
  gi|313124996|ref|YP_004035260.1| 29 IYGPPNAGKTTLANRIARDWTGDAVG-PESHIPHETRRARRKENVEIERNGKKVTIDIVDTPGVTTKVDYKE 99
                                      5688889********98877777643.333344555555668999*******************99999765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHHTT--------SSSS-SCCHHHHHH CS
                            Septin 156 keElkefKkkireeleeeeikiyklpdeeededeeakelse 196
                                       ++  +++ ++++  +e++++++  + ++ + e++++++ s+
  gi|313124996|ref|YP_004035260.1| 143 EDPFTQVNTMLIGIIESQDLPVLIFANKTDLEESNVQRISN 183
                                       55567777888888999999988877766666555544443 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.8e-06    0.0041       1      82 [.      27     142 ..      27     157 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.8e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskr..lgf...........................gvnlrdvakenglllevdpe.... 44 
                                       I++ G+p +GKttla+++++   +                               + +d++   g  + vd +    
  gi|313124996|ref|YP_004035260.1|  27 IGIYGPPNAGKTTLANRIARDwtG-DavgpeshiphetrrarrkenveierngKKVTIDIVDTPGVTTKVDYKefld 102
                                       89****************665220.1334444444445555555545777776444555555555555555554444 PP

                            AAA_18  45 .......aldeskrldedkldklldaleenssaleegknlvidgh 82 
                                              a+++s+++ e++ ++++  l+e      +g ++v+d+ 
  gi|313124996|ref|YP_004035260.1| 103 hdmekddAVRRSREATEGV-AEAMHWLREDV----DGVVYVLDST 142
                                       4444444455555555554.55666666644....4777777765 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.7e-06    0.0019      56     103 ..     162     211 ..     140     213 .] 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.7e-06
                      MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare...pnsvviSaekelnldeLkekiwee 103
                                       +p+l++ NK+Dl ++++++++++    +++v++Sa ++ n+de+ +ki e+
  gi|313124996|ref|YP_004035260.1| 162 LPVLIFANKTDL-EESNVQRISNAfpqHETVPLSALEGNNMDEVYDKIAEY 211
                                       699********9.6777888888544379******************9876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-05    0.0082       2      67 ..      27      92 ..      26     130 .. 0.90
   2 ?    0.8   0.0      0.74   5.3e+02      81     119 ..     133     172 ..     116     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGG CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqe 67
                                      + + G  ++GKt+l++r+ +d   +   +   +   t+++ + ++ve +++ kkv+++i Dt G +
  gi|313124996|ref|YP_004035260.1| 27 IGIYGPPNAGKTTLANRIARDWTGDAVGPESHIPHETRRARRKENVEIERNGKKVTIDIVDTPGVT 92
                                      56789******************99999999999999999999999*9**************9965 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.74
                                       CEEEEEEEGHHH..HCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  81 alailvydsrss..enlkeWlkelkkvagkspvilvgnkiD 119
                                       + +++v+ds+++  +++++ l  + + +++ pv++ +nk+D
  gi|313124996|ref|YP_004035260.1| 133 DGVVYVLDSTEDpfTQVNTMLIGIIE-SQDLPVLIFANKTD 172
                                       56677777665422455544444433.45669999999999 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0    0.0001     0.075       1      30 [.      26      57 ..      26      72 .. 0.78
   2 ?    3.9   0.2     0.079        57      55     109 ..      63     116 ..      49     175 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                            AAA_28  1 kivitGgestGKTtlleaLaar..gypvvpEa 30
                                      +i i G++ +GKTtl++++a++  g  v pE+
  gi|313124996|ref|YP_004035260.1| 26 RIGIYGPPNAGKTTLANRIARDwtGDAVGPES 57
                                      5789****************876554444665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.079
                            AAA_28  55 faervleeqleeeaaaaankvlfcDrglldtla.Yarayggeaeaeleaaarekry 109
                                        ++++ +e +e e++ ++  + ++D+  ++t + Y ++++ + +++ ++a+r++r 
  gi|313124996|ref|YP_004035260.1|  63 TRRARRKENVEIERNGKKVTIDIVDTPGVTTKVdYKEFLDHD-MEK-DDAVRRSRE 116
                                       5667778888889999999999****9999999788888877.333.334443332 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.3e-05    0.0094       3      22 ..      25      44 ..      23      56 .. 0.88
   2 ?   -2.0   0.1       3.5   2.5e+03     171     171 ..     102     102 ..      61     154 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      ++i iyGp+ +GKTtla+++
  gi|313124996|ref|YP_004035260.1| 25 RRIGIYGPPNAGKTTLANRI 44
                                      799**************987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                            AAA_24 171 n 171
                                       +
  gi|313124996|ref|YP_004035260.1| 102 D 102
                                       2 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0088      12      51 ..      11      51 ..       4     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                            AAA_16 12 Llsalervrsgrp.elvllsGesGvGKsslvrellralekd 51
                                      + ++++r  s+ + + + ++G++  GK++l+++++r +++d
  gi|313124996|ref|YP_004035260.1| 11 ISRVVDRMFSDAEpRRIGIYGPPNAGKTTLANRIARDWTGD 51
                                      455566555555559999*******************9999 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.3e-05     0.024       3      22 ..      29      48 ..      27      88 .. 0.85
   2 ?   -0.5   0.0       2.1   1.5e+03      86     116 ..     149     175 ..     105     189 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      +yGpp  GKT+la+ +a+++
  gi|313124996|ref|YP_004035260.1| 29 IYGPPNAGKTTLANRIARDW 48
                                      7****************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                               AAA  86 vnqLlteldgvkkkeskvivigatnrpdkld 116
                                       vn++l  +    + ++++ v++ +n+ d  +
  gi|313124996|ref|YP_004035260.1| 149 VNTMLIGII---E-SQDLPVLIFANKTDLEE 175
                                       222222222...2.23367777777766544 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.037        26       1      20 [.      27      46 ..      27      77 .. 0.81
   2 !    9.3   0.1    0.0015       1.1     100     142 ..      80     145 ..      56     193 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.037
                                      EEEEEBTTTTHHHHHHHHHT CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlg 20
                                      i + G  ++GK++++n + +
  gi|313124996|ref|YP_004035260.1| 27 IGIYGPPNAGKTTLANRIAR 46
                                      6788999**********974 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                                       S-SEEEEE---B-SSSGTTS......................HHHHHHH.STTEEEEEEEETTS-C CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdq......................elvkeyi.kkadiilavtsanhdl 142
                                       + ++ +vD+PG++   + ++                      + +++ + ++ d +++v+++  d 
  gi|313124996|ref|YP_004035260.1|  80 KVTIDIVDTPGVTTKVDYKEfldhdmekddavrrsreategvAEAMHWLrEDVDGVVYVLDSTEDP 145
                                       55789*******997666666888888888888888888888444444445555555555555443 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.7e-05     0.019       3      26 ..      29      52 ..      27     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                      +yGp++ GK+tla+++a++++++ 
  gi|313124996|ref|YP_004035260.1| 29 IYGPPNAGKTTLANRIARDWTGDA 52
                                      8******************98665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-05      0.02       3      43 ..       9      47 ..       7      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                                      HHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  3 ksvekviekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                      +s+ +v ++++   e+    ++++G +  GKttla+ i ++
  gi|313124996|ref|YP_004035260.1|  9 DSISRVVDRMFSDAEPR--RIGIYGPPNAGKTTLANRIARD 47
                                      6789999****889999..9******************988 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.7e-05     0.034      23      44 ..      27      48 ..      13     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                          ATPase_2 23 yfiYGpegsGKtaLlkeiienl 44
                                      + iYGp + GKt+L ++i+   
  gi|313124996|ref|YP_004035260.1| 27 IGIYGPPNAGKTTLANRIARDW 48
                                      459**************98766 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.013       9.4       3      23 ..      27      47 ..      25      54 .. 0.83
   2 ?    6.4   0.1    0.0083         6      92     156 ..     120     177 ..     115     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                                      EEEEESTTCCHHHHHHHHHCT CS
                              cobW  3 tvltGflGsGKTtLlnhllen 23
                                      +++ G++ +GKTtL n++ ++
  gi|313124996|ref|YP_004035260.1| 27 IGIYGPPNAGKTTLANRIARD 47
                                      57899**********999865 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0083
                                       TTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSE...EEEE-HHHHCHC CS
                              cobW  92 GlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadl...lvlnKtDlldee 156
                                       G+ae++ +         +  +d+vv+v+D++  e+  ++ ++ +   ++  dl   +  nKtDl +++
  gi|313124996|ref|YP_004035260.1| 120 GVAEAMHW--------LREDVDGVVYVLDST--EDPFTQVNTMLIGIIESQDLpvlIFANKTDLEESN 177
                                       55555555........36789*********4..46777888888888888886322667****98776 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0021       1.5      20      50 ..      16      45 ..       3      52 .. 0.79
   2 ?   -3.2   0.0       4.4   3.2e+03      52      66 ..      73      87 ..      69      93 .. 0.72
   3 ?    2.8   0.0     0.065        47     163     228 ..     154     211 ..     117     213 .] 0.58

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                                      HHHGGG-S-SEEEEEEE-TTSSHHHHHHHHH CS
                              MeaB 20 erllakaGraqvvGltGvPGaGkstlvealg 50
                                      +r++++a + +++G+ G P aGk tl ++++
  gi|313124996|ref|YP_004035260.1| 16 DRMFSDA-EPRRIGIYGPPNAGKTTLANRIA 45
                                      5555554.5689**************99986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.4
                                      HHHCTT--EEEEEE- CS
                              MeaB 52 elrrrGkrvavlavD 66
                                      e+ r+Gk+v++  vD
  gi|313124996|ref|YP_004035260.1| 73 EIERNGKKVTIDIVD 87
                                      667888888887777 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.065
                                       CCCHHH-SEEEE...E---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHH CS
                              MeaB 163 kGileiaDiivv...nkaDkkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieeh 228
                                        Gi+e  D+ v+   nk+D++e++        ++++++   +  + + +  sa+eg+ +de+ d+i e+
  gi|313124996|ref|YP_004035260.1| 154 IGIIESQDLPVLifaNKTDLEESN--------VQRISN---AFPQHETVPLSALEGNNMDEVYDKIAEY 211
                                       566665555443122444433322........122222...2222334556777777777777777776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.081       2      31 ..      26      55 ..      25      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpq 31
                                       + + G++  GKTtL+ ++a++w  +    
  gi|313124996|ref|YP_004035260.1| 26 RIGIYGPPNAGKTTLANRIARDWTGDAVGP 55
                                      566899999**************8776544 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.7e-05     0.062      12      53 ..      25      70 ..      18     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-05
                                      SEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGGB- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkp....teGeilldgkdlkeqe 53
                                      ++++i G+  aGK+tL++ +a+  +      e +i  + +  +++e
  gi|313124996|ref|YP_004035260.1| 25 RRIGIYGPPNAGKTTLANRIARDWTGdavgPESHIPHETRRARRKE 70
                                      689*****************99854322222333322222222222 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00025      0.18      38      65 ..      29      54 ..      22     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                            AAA_25 38 laGapgtGKttlaldlalavatGkpwlg 65
                                      ++G+p +GKttla  +a +++ +    g
  gi|313124996|ref|YP_004035260.1| 29 IYGPPNAGKTTLANRIARDWTGDA--VG 54
                                      79******************9433..23 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.16      36      57 ..      27      48 ..       9      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                            RuvB_N 36 vllyGpPGlGkttlakiiakel 57
                                      + +yGpP  Gkttla+ ia++ 
  gi|313124996|ref|YP_004035260.1| 27 IGIYGPPNAGKTTLANRIARDW 48
                                      568***************9985 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.11       3      38 ..      13      48 ..      12     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      HHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  3 rvlDalfpivqGqrtlipgafgvGktvisqslskqs 38
                                      rv+D +f+ ++  r++i g  + Gkt++++ +++  
  gi|313124996|ref|YP_004035260.1| 13 RVVDRMFSDAEPRRIGIYGPPNAGKTTLANRIARDW 48
                                      89******************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1149.04
//
Query:       gi|313124997|ref|YP_004035261.1|  [L=576]
Description: orc complex protein cdc6/orc1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-24   83.3   0.0    2.3e-23   81.9   0.0    1.8  1  Cdc6_C           CDC6, C terminal winged helix domain
    8.7e-11   42.5   0.2    3.1e-10   40.7   0.0    1.9  2  AAA_16           AAA ATPase domain
    8.9e-09   35.7   0.2    4.3e-07   30.3   0.2    2.5  1  AAA_22           AAA domain
    4.1e-08   33.7   0.3    1.5e-06   28.7   0.3    2.4  1  AAA              ATPase family associated with various cellul
     0.0013   18.0   0.0     0.0027   17.0   0.0    1.5  1  KAP_NTPase       KAP family P-loop domain
      0.002   18.1   0.1     0.0057   16.6   0.1    1.7  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0022   17.4   0.2      0.015   14.7   0.0    2.2  2  TniB             Bacterial TniB protein
     0.0026   17.5   0.0      0.006   16.3   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
     0.0028   16.8   0.0     0.0057   15.9   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
     0.0039   17.0   0.1       0.01   15.6   0.0    1.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0071   15.4   0.0      0.013   14.6   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
     0.0095   16.1   0.0       0.25   11.5   0.0    2.3  1  AAA_2            AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.017   14.3   0.0      0.028   13.6   0.0    1.3  1  NB-ARC           NB-ARC domain
      0.031   14.8   0.0      0.074   13.6   0.0    1.7  1  ABC_tran         ABC transporter
      0.052   13.3   0.0       0.18   11.5   0.0    1.9  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.056   12.1   0.0      0.084   11.5   0.0    1.2  1  AAA_13           AAA domain
      0.056   12.6   0.0       0.13   11.4   0.0    1.6  1  TIP49            TIP49 P-loop domain
      0.059   12.9   0.0      0.099   12.1   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.072   12.7   0.0        0.2   11.2   0.0    1.7  1  AAA_25           AAA domain
      0.072   13.6   0.0       0.17   12.5   0.0    1.6  1  AAA_18           AAA domain
      0.085   12.2   0.2       0.36   10.1   0.2    2.1  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.099   13.0   0.3       0.32   11.3   0.3    1.8  1  AAA_assoc_2      AAA C-terminal domain
       0.14   12.3   1.4       0.37   11.0   1.4    1.8  1  MutS_III         MutS domain III
       0.15   12.1   0.0       0.27   11.2   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.18   12.2   0.0       0.43   11.0   0.0    1.7  1  RNA_helicase     RNA helicase
       0.18   11.5   0.7        0.5   10.1   0.1    1.9  2  AAA_24           AAA domain
       0.53   10.0   3.7        7.7    6.2   2.1    2.6  1  DEAD             DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   3.5e-26   2.3e-23       1      82 [.     472     551 ..     472     553 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 3.5e-26
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L a++ll++ +g + + tgev++ Yk+lCe+ ++d ltqr+v dl+seL+mlgi+++ ++skGr +grt++isL+v+
  gi|313124997|ref|YP_004035261.1| 472 LFAIILLEK-NGVRNINTGEVFNIYKRLCEEIDADILTQRRVTDLISELDMLGIVNAVVVSKGR-YGRTKEISLSVP 546
                                       7799*9999.*****************************************************9.************ PP

                                       CHHHH CS
                            Cdc6_C  78 pddvl 82 
                                        d+ +
  gi|313124997|ref|YP_004035261.1| 547 IDETE 551
                                       99976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   4.7e-13   3.1e-10       2     161 ..     146     335 ..     145     346 .. 0.61
   2 ?   -1.6   0.1       4.7   3.1e+03      72     100 ..     410     437 ..     369     473 .. 0.46

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4.7e-13
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd........ggiflrgkcdqlesaipy 69 
                                       l+ R e+++q++++l ++ +g++ +++l++G  G+GK++ ++ + ++le +        +  + + +c+    ++ y
  gi|313124997|ref|YP_004035261.1| 146 LPHRTEQINQMATILVSALRGETpSNILIYGKTGTGKTASAKFVSQELESTsqkydvpcE--VEYINCEVT--DTQY 218
                                       789*************99999999**********************99999666554321..244444444..4566 PP

                            AAA_16  70 salaqalareellrqlldeaesaeleawrekleeala.................avpelagaea............. 116
                                        +laq++ + +++++  d  e+ el++  + l+++++                 +        +             
  gi|313124997|ref|YP_004035261.1| 219 RVLAQLA-N-KFIEKNFDVIEN-ELDRLED-LRTRARdtpdlladtsfdsldgvE--------Erieqletdceeme 283
                                       5555555.4.566665555222.3333333.444444233344455344333330........23333333333444 PP

                            AAA_16 117 .........srllellkrllallsrderplvlvlDdlqwadeaslql.laaLlrl 161
                                                 r++ ++ +++++ +r    +v+ lD+++++ e s +  l++L r 
  gi|313124997|ref|YP_004035261.1| 284 tvpmtgwptDRVYSTFFDAVDYNER---VVVIMLDEIDKLVEKSGDDtLYNLSRM 335
                                       4555554445555555555555444...6*********99888777768888776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.7
                            AAA_16  72 laqalareellrqlldeaesaeleawrek 100
                                       +a +    +  r+l+   ++ el++  ++
  gi|313124997|ref|YP_004035261.1| 410 FAAQEHG-DARRALDLLRTAGELAERGQA 437
                                       3333322.333333333233333333332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.2   6.4e-10   4.3e-07       4     115 ..     168     335 ..     165     353 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 6.4e-10
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.......... 70 
                                       t + ++++G +GtGKT +++ + ++l+  ++  + + ev ++++ +  ++  +l +l++++ +++ +          
  gi|313124997|ref|YP_004035261.1| 168 TPSNILIYGKTGTGKTASAKFVSQELESTSQKYDVPCEVEYINCEVTDTQYRVLAQLANKFIEKNFDvieneldrle 244
                                       66789*********************75544444888888**********************99999****999999 PP

                            AAA_22  71 ...........................................erlsseellealeqalraravielliiDEaqhlr 104
                                                                                   +  ++++++++ +a++   +++++++DE+++l 
  gi|313124997|ref|YP_004035261.1| 245 dlrtrardtpdlladtsfdsldgveerieqletdceemetvpmTGWPTDRVYSTFFDAVDYNERVVVIMLDEIDKLV 321
                                       99999999999988888886666666666666666555555544444455555555555544448899999999987 PP

                            AAA_22 105 ..s.eealeeLrsl 115
                                         s ++ l +L+++
  gi|313124997|ref|YP_004035261.1| 322 ekSgDDTLYNLSRM 335
                                       65367777777333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.3   2.2e-09   1.5e-06       1     112 [.     172     356 ..     172     374 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.2e-09
                                       EEEESSTTSSHHHHHHHHHHHHTHE...............................EEEEETTTCSSS......... CS
                               AAA   1 vllyGppGtGKTllakavakelgve...............................fleisgsellsk......... 37 
                                       +l+yG  GtGKT+ ak v +el+++                               f                    
  gi|313124997|ref|YP_004035261.1| 172 ILIYGKTGTGKTASAKFVSQELESTsqkydvpceveyincevtdtqyrvlaqlankF----------Ieknfdvien 238
                                       699******************854433444555555555555555555544444443..........0445555555 PP

                                       ................................................STTHHHHHHHHHHHHHHHTS.TSEEEEEE CS
                               AAA  38 ................................................yvgesekkirelfkeakeka.kpsilfiD 65 
                                                                                       + g   +++  +f +a   + + +++++D
  gi|313124997|ref|YP_004035261.1| 239 eldrledlrtrardtpdlladtsfdsldgveerieqletdceemetvpMTGWPTDRVYSTFFDAVDYNeRVVVIMLD 315
                                       58888888888888888888888888888888888888888888888999999999988888887777566****** PP

                                       TGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...G CS
                               AAA  66 EidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...p 112
                                       Eid+l++++       +++++  L ++ +++++  s++ ++g++n+    
  gi|313124997|ref|YP_004035261.1| 316 EIDKLVEKS-------GDDTLYNLSRMNSELSN--SRISIMGISNDlkfT 356
                                       *******99.......77777777777777777..578899999984444 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.1e-06    0.0027       2     186 ..     150     321 ..     149     334 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.1e-06
                        KAP_NTPase   2 dlyasaladilseptl..atpivvgLygkWGsGKssllnkledelkefa......kpvrflfaefnawsfkggddav 70 
                                       +  ++++a+il++  l  +tp+ + +ygk G+GK++  +++ +el++ +       +v+ + +e+    +    ++ 
  gi|313124997|ref|YP_004035261.1| 150 TEQINQMATILVSA-LrgETPSNILIYGKTGTGKTASAKFVSQELESTSqkydvpCEVEYINCEVTDTQYRVLAQLA 225
                                       56789999999954.6689*****************************99***9989******************** PP

                        KAP_NTPase  71 aellaaLadaleeeygqlatkllrakklkalkikgkiklrkacaiplvlilevalflliegasllavlsraaklkee 147
                                        ++++  +d++e e ++l+    ra+++++l ++ +++  +  ++  ++  +                     ++e 
  gi|313124997|ref|YP_004035261.1| 226 NKFIEKNFDVIENELDRLEDLRTRARDTPDLLADTSFD--SLDGVEERIEQLE------------------TDCEEM 282
                                       *************************************9..5555555533322..................347777 PP

                        KAP_NTPase 148 aplkklqteveelladmektLdalqkrlVvviDdLDrce 186
                                       +++ + +   + +++ ++++ d +++ +V+ +D++D + 
  gi|313124997|ref|YP_004035261.1| 283 ETVPMTGWPTDRVYSTFFDAVDYNERVVVIMLDEIDKLV 321
                                       888888888888899999999999999999999999875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   8.6e-06    0.0057      11     132 ..     160     322 ..     148     347 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.6e-06
                          ATPase_2  11 leeilerepneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldefieeeeekkkleka 81 
                                       l + l+ e+ + ++iYG  g GKta  k + ++le+ ++      +v y++   ++ + ++      +  +k++ek 
  gi|313124997|ref|YP_004035261.1| 160 LVSALRGETPSNILIYGKTGTGKTASAKFVSQELESTSQkydvpcEVEYINCEVTDTQYRVLA----QLANKFIEKN 232
                                       345678899999***************999999977665455665444444333333333322....3333333333 PP

                          ATPase_2  82 l........................................giavpkaeleeilk..eksklvfkaielllekikkk 116
                                       +                                        +    ++  ee+     +    ++  + +++++  +
  gi|313124997|ref|YP_004035261.1| 233 FdvieneldrledlrtrardtpdlladtsfdsldgveerieQ---LETDCEEMETvpMTGWPTDRVYSTFFDAVDYN 306
                                       344445555566666889999999999999999999774331...23333343335567788899999999999999 PP

                          ATPase_2 117 gkkiiiiiDelqklid 132
                                        + ++i++De+ kl++
  gi|313124997|ref|YP_004035261.1| 307 ERVVVIMLDEIDKLVE 322
                                       9999999999999993 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.2e-05     0.015      15      93 ..     149     227 ..     139     249 .. 0.76
   2 ?   -0.6   0.1       1.1   7.5e+02     120     138 ..     309     327 ..     301     352 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                              TniB  15 rakeilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppek.dedaekvpvlvvqappkpdekrlyaai 90 
                                       r ++i ++   L+++ + + ++n+l++G++ +GKt+   kF +++ +++ ++ +  ++v ++++  + ++ r  a++
  gi|313124997|ref|YP_004035261.1| 149 RTEQINQMATILVSALRGETPSNILIYGKTGTGKTAS-AKFVSQELESTsQKYDVPCEVEYINCEVTDTQYRVLAQL 224
                                       4555666666677888888999************986.567777766651566778999999999888887777666 PP

                              TniB  91 Lea 93 
                                        ++
  gi|313124997|ref|YP_004035261.1| 225 ANK 227
                                       555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                              TniB 120 vrvLiiDEihnllagsark 138
                                       v v+++DEi++l++ s ++
  gi|313124997|ref|YP_004035261.1| 309 VVVIMLDEIDKLVEKSGDD 327
                                       67899*****999766554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     9e-06     0.006      16      52 ..     161     199 ..     146     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9e-06
                                       HHHC..TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
                   Sigma54_activat  16 kkva..ktdlsvlitGesGtGKellaraiheaskrkekp 52 
                                        ++   +t++++li G++GtGK+  a+ + ++ + ++++
  gi|313124997|ref|YP_004035261.1| 161 VSALrgETPSNILIYGKTGTGKTASAKFVSQELESTSQK 199
                                       3333225679******************99966555543 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.5e-06    0.0057      35      81 ..     151     197 ..     137     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.5e-06
                            DUF815  35 kqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg 81 
                                       +q +++ +     l+g++ +n+L++G+ GtGK +  k++ +e+++++
  gi|313124997|ref|YP_004035261.1| 151 EQINQMATILVSALRGETPSNILIYGKTGTGKTASAKFVSQELESTS 197
                                       566777777778899*************************9998765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05      0.01      17      63 ..     155     199 ..     137     209 .. 0.77
   2 ?   -3.2   0.0       9.6   6.4e+03      87     105 ..     311     330 ..     306     332 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                            RuvB_N  17 eklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklki 63 
                                       +  +i++  +  r+e+   +l+yG  G Gkt+ ak +++el+++ + 
  gi|313124997|ref|YP_004035261.1| 155 QMATILV--SALRGETPSNILIYGKTGTGKTASAKFVSQELESTSQK 199
                                       3333444..44799***************************987665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.6
                            RuvB_N  87 vlfideihrlsr.aveevly 105
                                       v+++dei +l + + ++ ly
  gi|313124997|ref|YP_004035261.1| 311 VIMLDEIDKLVEkSGDDTLY 330
                                       7899***9986514566666 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     2e-05     0.013     107     158 ..     145     198 ..     130     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                             T2SSE 107 dlgaeealkekiaevlrkavr..erglilvsGgTgsGKttllyallkeinksde 158
                                       +l  + ++ +++a +l +a+r  +  +il+ G Tg+GKt ++  + +e++++++
  gi|313124997|ref|YP_004035261.1| 145 ELPHRTEQINQMATILVSALRgeTPSNILIYGKTGTGKTASAKFVSQELESTSQ 198
                                       55556666678888888887622457**********************998844 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00037      0.25       4      83 ..     170     323 ..     167     336 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                                       --EEEE--TTSSHHHHHHHHHHHTT-................................................... CS
                             AAA_2   4 isilllgptgvGktelakalaellfv...............................................kkek 33 
                                       ++il+ g+tg+Gkt  ak +++ l+                                                    
  gi|313124997|ref|YP_004035261.1| 170 SNILIYGKTGTGKTASAKFVSQELEStsqkydvpceveyincevtdtqyrvlaqlankfieknfdvieneldrL--- 243
                                       68999999999999988888888887677777777777777766633333333333333333333333333221... PP

                                       -EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS........................................ CS
                             AAA_2  34 kliradaselleeeevehlvsrligappgyvgaeegG........................................ 70 
                                                                                                                    
  gi|313124997|ref|YP_004035261.1| 244 ------------------------------------Edlrtrardtpdlladtsfdsldgveerieqletdceemet 284
                                       ....................................02222222223444555555555566666666666677777 PP

                                       ..........................EEEEETGGG---- CS
                             AAA_2  71 ..........................ivllDEidKihpk 83 
                                                                 +++lDEidK  +k
  gi|313124997|ref|YP_004035261.1| 285 vpmtgwptdrvystffdavdynervvVIMLDEIDKLVEK 323
                                       7777799999999999999999999999*******9985 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.2e-05     0.028      18      83 ..     169     235 ..     149     258 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                                       SCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT...EEEEEEEESXXHHHHHHHXXHHHHHCCCTTS CS
                            NB-ARC  18 lqslvvalvGmgGvGKttlakqilnksdevegrFd...svawvvvsktdkseeiletilkeLslseddl 83 
                                       +    + ++G+ G GKt  ak + ++++++ +++d    v ++    td+++++l ++++++ +++ d 
  gi|313124997|ref|YP_004035261.1| 169 PS--NILIYGKTGTGKTASAKFVSQELESTSQKYDvpcEVEYINCEVTDTQYRVLAQLANKFIEKNFDV 235
                                       33..688****************************3333455577778888888888888887765444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00011     0.074      13      80 ..     171     267 ..     164     352 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx....... RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqe..pqlfpeltvren....... 79 
                                        + i G++G+GK+  +k ++++l+ t+ +   d   ++++++ e+++ + +vl q   +++ ++  v en       
  gi|313124997|ref|YP_004035261.1| 171 NILIYGKTGTGKTASAKFVSQELESTSQKY--DvPCEVEYINCEVTDTQYRVLAQLanKFIEKNFDVIENeldrled 245
                                       6789********************999886..556888889999999999999998444444555566666666665 PP

                                       .....................H CS
                                       .....................x RF
                          ABC_tran  80 .....................e 80 
                                                             
  gi|313124997|ref|YP_004035261.1| 246 lrtrardtpdlladtsfdsldG 267
                                       5555555555555544444441 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.18      15      63 ..     165     214 ..     149     347 .. 0.74
   2 ?   -1.5   0.0       2.8   1.9e+03      74     110 ..     443     479 ..     390     489 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                   DNA_pol3_delta2  15 sgrlahayLfeGdegigkkelalnlakallceeknetkpcg.ecksckki 63 
                                       +g+    +L++G++g+gk ++a+ ++++l +++++ + pc+ e  +c+  
  gi|313124997|ref|YP_004035261.1| 165 RGETPSNILIYGKTGTGKTASAKFVSQELESTSQKYDVPCEvEYINCEVT 214
                                       46778889**************************9999997344455544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                   DNA_pol3_delta2  74 ieteekersikldqirelieelsrkpreskkkiiiie 110
                                       ++  +++++i+ld++ e+ ++l  ++ +    ii++e
  gi|313124997|ref|YP_004035261.1| 443 AHVRQAQDKIELDRVVEVVRTLPTQSKIVLFAIILLE 479
                                       2333444489999999988888888777777777666 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013     0.084      20      79 ..     173     238 ..     170     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                            AAA_13  20 liYGwNGaGKTtLSrllrslelgetepkfang.sieitng..eeldirVf...NrdFveenls.eqg 79 
                                       liYG+ G+GKT  +++ ++ el++t++k+  + ++e+ n   +  + rV     ++F+e+n++  ++
  gi|313124997|ref|YP_004035261.1| 173 LIYGKTGTGKTASAKFVSQ-ELESTSQKYDVPcEVEYINCevTDTQYRVLaqlANKFIEKNFDvIEN 238
                                       7*********997777766.89999999975448866666444556666511156899999986444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.13      38      95 ..     159     215 ..     150     248 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX CS
                             TIP49  38 vivelikekklaGravLlaGpsgtGktalaiaiskelg.edvpfvalsgsevyslevkk 95 
                                       ++v+ ++ ++ +   +L+ G++gtGkta a  +s+el  ++ ++ +    e   +ev  
  gi|313124997|ref|YP_004035261.1| 159 ILVSALRGETPS--NILIYGKTGTGKTASAKFVSQELEsTSQKYDVPCEVEYINCEVTD 215
                                       555555555544..89*********************8344445444445555555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015     0.099      33      60 ..     169     196 ..     150     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldke 60 
                                         ++l++G+tGtGKt+ +k + ++l+++
  gi|313124997|ref|YP_004035261.1| 169 PSNILIYGKTGTGKTASAKFVSQELEST 196
                                       5689**************9999999843 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031       0.2      36     143 ..     172     285 ..     165     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal..........rddar 102
                                       +l++G +gtGKt+ a  ++ ++ + ++  +     +  V y+++E +   ++ R+ a++++           ++ +r
  gi|313124997|ref|YP_004035261.1| 172 ILIYGKTGTGKTASAKFVSQELESTSQKYD----VPCEVEYINCEVTD--TQYRVLAQLANKfieknfdvieNELDR 242
                                       689*********998766666664443333....688*********99..666666666555599999999955555 PP

                            AAA_25 103 llvldlagv.eslpLfakdrggtl..ltadvdaleaaieevegv 143
                                       l  l      +  +L+a+++ ++l  +++ +++le ++ee+e v
  gi|313124997|ref|YP_004035261.1| 243 LEDLRTR-ArDTPDLLADTSFDSLdgVEERIEQLETDCEEMETV 285
                                       5444432.2367788888887777799*************9976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00025      0.17       1      49 [.     172     221 ..     172     266 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00025
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpealdes 49 
                                       Il+ G+ G+GKt  ak +s++l++    + + + +   +++ +++++  +  
  gi|313124997|ref|YP_004035261.1| 172 ILIYGKTGTGKTASAKFVSQELEStsqKYDVPCEVEYINCEVTDTQY--RVL 221
                                       99******************997778855555555555555555555..333 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00055      0.36      29      57 ..     158     187 ..     144     313 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00055
                                       -EEEEEGGGS-..SEEEE--TTSSHHHHHH CS
                      FtsK_SpoIIIE  29 nplvldlkkma.shllvaGatgsGKStaln 57 
                                        +lv+ l++ + s++l+ G tg+GK+   +
  gi|313124997|ref|YP_004035261.1| 158 TILVSALRGETpSNILIYGKTGTGKTASAK 187
                                       455666666657*************97554 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00049      0.32      15      56 ..     410     450 ..     397     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00049
                                       XXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                       AAA_assoc_2  15 laeladGDaRkaLnlLElaaeaaeakegkieitledleealq 56 
                                        a+  +GDaR+aL lL +a e ae+  +  +++++++++a +
  gi|313124997|ref|YP_004035261.1| 410 FAAQEHGDARRALDLLRTAGELAER-GQADTVEEAHVRQAQD 450
                                       455558***********99999986.7778888888887754 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.4   0.00056      0.37     151     187 ..     328     522 ..     133     523 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00056
                                       T............................................................................ CS
                                       x............................................................................ RF
                          MutS_III 151 a............................................................................ 151
                                       +                                                                            
  gi|313124997|ref|YP_004035261.1| 328 Tlynlsrmnselsnsrisimgisndlkftdfldprvksslgeeeivfppydanqlrdilqhradvafksgaltedvi 404
                                       03333333333333445555555555555555555555555555555555555555555555555555555555555 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                          MutS_III 152 ............................................................................. 151
                                                                                                                    
  gi|313124997|ref|YP_004035261.1| 405 plcaafaaqehgdarraldllrtagelaergqadtveeahvrqaqdkieldrvvevvrtlptqskivlfaiillekn 481
                                       55555555555555555666666666666666666666666666666667788888888888888888888899999 PP

                                       .....HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHH CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 .....iealeqelfqelleeveealerlrrlaealaeLDvl 187
                                            ++ +  +++++l+ee+++ + + rr++++++eLD+l
  gi|313124997|ref|YP_004035261.1| 482 gvrniNTGEVFNIYKRLCEEIDADILTQRRVTDLISELDML 522
                                       9888666666999********999****************8 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00041      0.27       4      45 ..     150     195 ..     147     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                                       HHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE   4 eeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgv 45 
                                       +e+++++++ l +al     + il++G+ G+GKT+ ++ + ++l+ 
  gi|313124997|ref|YP_004035261.1| 150 TEQINQMATILVSALrgetPSNILIYGKTGTGKTASAKFVSQELES 195
                                       6788899999998888543345****************99999975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00065      0.43       1      26 [.     172     197 ..     172     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i++yG++g+GK+  ak ++++l++++
  gi|313124997|ref|YP_004035261.1| 172 ILIYGKTGTGKTASAKFVSQELESTS 197
                                       789**************999999666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00075       0.5       3      20 ..     170     187 ..     168     198 .. 0.88
   2 ?   -1.6   0.0       2.8   1.9e+03      60      85 ..     303     328 ..     247     342 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00075
                            AAA_24   3 lkiliyGpsgiGKTtlak 20 
                                        +iliyG+ g+GKT +ak
  gi|313124997|ref|YP_004035261.1| 170 SNILIYGKTGTGKTASAK 187
                                       589***********9997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                            AAA_24  60 aaeladyktlviDtideleelclaev 85 
                                        + +++  ++ +D id+l+e   +++
  gi|313124997|ref|YP_004035261.1| 303 VDYNERVVVIMLDEIDKLVEKSGDDT 328
                                       33344566788888888888776665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.1     0.012       7.7      15      42 ..     170     196 ..     151     356 .. 0.46

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyet 42 
                                        ++l+ ++TG+GKT+ + + v q++ +t
  gi|313124997|ref|YP_004035261.1| 170 SNILIYGKTGTGKTASAKF-VSQELEST 196
                                       6899999999999988543.44455444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.50
# Mc/sec: 3441.15
//
Query:       gi|313124998|ref|YP_004035262.1|  [L=262]
Description: hypothetical protein Hbor_02120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0071   16.3   0.1      0.014   15.3   0.1    1.5  1  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
        0.7   10.0   4.2         13    6.0   0.4    2.6  2  O_Spanin_T7    outer-membrane spanin sub-unit


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.6e-06     0.014       2      29 ..      75     106 ..      74     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-06
                                       XXSSTTCCTXXTTXEEEEE.CTS....---TTS CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVd.kfs....epkrGd 29 
                                       v+++SMep +  Gdli++  + +    ++  Gd
  gi|313124998|ref|YP_004035262.1|  75 VESGSMEPHMYRGDLIFITaP-DrftpDYAYGD 106
                                       89***************9852.22446777777 PP

>> O_Spanin_T7  outer-membrane spanin sub-unit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3    0.0037        33       6      16 ..      17      27 ..      13      29 .. 0.93
   2 ?    6.0   0.4    0.0014        13       8      20 ..      70      81 ..      69      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0037
                       O_Spanin_T7  6 PEPPmvsvDss 16
                                      PEP  vsv ss
  gi|313124998|ref|YP_004035262.1| 17 PEPNAVSVKSS 27
                                      9*********9 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0014
                       O_Spanin_T7  8 PPmvsvDssLmvE 20
                                      PPmv+v+s  m E
  gi|313124998|ref|YP_004035262.1| 70 PPMVAVESGSM-E 81
                                      9*******877.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1548.04
//
Query:       gi|313124999|ref|YP_004035263.1|  [L=543]
Description: DNA polymerase ii small subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-14   52.8   0.0    5.3e-14   52.1   0.0    1.3  1  DNA_pol_E_B    DNA polymerase alpha/epsilon subunit B
    1.3e-12   48.2   3.1    3.5e-12   46.8   3.1    1.7  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    1.5e-11   45.2   0.9    2.8e-11   44.3   0.9    1.4  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   8.9e-18   5.3e-14       3     203 ..     292     487 ..     290     491 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 8.9e-18
                                       EEES--S-TT---...-HHHHHHHHHHH.HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTT CS
                       DNA_pol_E_B   3 ivsglnldndnrs...leaLrkiLqgyapeesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsiles 76 
                                       ++s++++ ++++     + + ++L   a  +++++ +++aG +v+      ++ +  + +  +  d  +++++ l++
  gi|313124999|ref|YP_004035263.1| 292 LISDVHVGSQEFMagaWHRFADWLHTDA--AEHVEYILIAGDMVEGVGVYPNQDE--ELDIVDIYDQYEQFSEYLKE 364
                                       7888888877777777788888888888..9999999999999994433333332..23455555555666666666 PP

                                       S-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHH CS
                       DNA_pol_E_B  77 llekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkes 153
                                       +   +++v++Pg  D++   + Pq+ +++  l +i +v   +++++NPs++++++v v+++ +  ++++ +e  +es
  gi|313124999|ref|YP_004035263.1| 365 VPGDIEIVMIPGNHDAVRL-AEPQPGFDEE-LRDIMSVHD-ARITSNPSTVTVEGVNVLMYHGVSLDEVIAELPSES 438
                                       668999************9.*******666.999999866.***********************************9 PP

                                       HHHS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE-- CS
                       DNA_pol_E_B 154 ntdverlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlp 203
                                       + + ++ +k++ ++l+ rh+aP +        +++d lv++++Pd++  +
  gi|313124999|ref|YP_004035263.1| 439 A-SYDEPHKAMYQLLKKRHVAPQYGGHTRLAPEEQDYLVMKEVPDIFHTG 487
                                       9.6*******************************************9766 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   3.1   5.9e-16   3.5e-12       3     150 ..     290     512 ..     288     527 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 5.9e-16
                     Metallophos_2   3 laiiSDlH........snldaleavlealkevgvdaiihaGD.......leeeep............evleellela 52 
                                        a+iSD+H        ++ ++ + +l+  +++ v++i+ aGD       +    p            +  e++ e +
  gi|313124999|ref|YP_004035263.1| 290 AALISDVHvgsqefmaGAWHRFADWLHTDAAEHVEYILIAGDmvegvgvY----PnqdeeldivdiyDQYEQFSEYL 362
                                       689*******99999967777777777777777*********55555541....14455556665553334444333 PP

                     Metallophos_2  53 .......pvlaVrGNnD......eev.veedvlreaaelgtdlp.eeaelelagekvlliHgdpl............ 102
                                              ++++++GN+D      ++  ++e++ +    ++ +++ +  +++++g++vl++Hg  l            
  gi|313124999|ref|YP_004035263.1| 363 kevpgdiEIVMIPGNHDavrlaePQPgFDEELRDIMSVHDARITsNPSTVTVEGVNVLMYHGVSLdeviaelpsesa 439
                                       5556989**********88887634468888888888888888889999999**********988************ PP

                     Metallophos_2 103 ......................gvkdalaellke...aeegsdvvvcGHtHvpevekeggvlvvnPGsvgepr 150
                                                             g++ +la+  ++   ++e+ d++  GH H+ ++ k ++vl vn G  + + 
  gi|313124999|ref|YP_004035263.1| 440 sydephkamyqllkkrhvapqyGGHTRLAPEEQDylvMKEVPDIFHTGHVHKLGWGKYHNVLAVNSGCWQAQT 512
                                       ***************9999999666677666666776779999************************987764 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.9   4.7e-15   2.8e-11       4     203 ..     291     491 ..     289     492 .. 0.63

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4.7e-15
                                       EEEESBTB...TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.................HHHHHHHHHHHHH CS
                       Metallophos   4 lvigDlHl...algggqlddllkllddllreekpdlvllaGDlvdrg.................dlekellellaal 60 
                                       ++i+D+H+   +   g +++++++l ++ + e + ++l+aGD v++                  ++e+ + e     
  gi|313124999|ref|YP_004035263.1| 291 ALISDVHVgsqEFMAGAWHRFADWL-HTDAAEHVEYILIAGDMVEGVgvypnqdeeldivdiydQYEQ-FSE----- 360
                                       689********9999**********.5556669*********99997788888787766654433333.444..... PP

                                       HHH......TSEEEEEC-TTS.........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEES CS
                       Metallophos  61 vky......pipvylllGNHe.........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhG 122
                                         y      +i +++++GNH+         g        ++++ ++ +   +da   +n+  +   +  ++vl +hG
  gi|313124999|ref|YP_004035263.1| 361 --YlkevpgDIEIVMIPGNHDavrlaepqpG--------FDEELRDIMSV-HDARITSNPSTVTVEG--VNVLMYHG 424
                                       ..24445558999********5444333333........33333222222.2233334555555444..59999999 PP

                                       ECEEETHHHHHHHHHHHSCHHHHCC.HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEE CS
                       Metallophos 123 gspellvsldklgslnleleapepg.dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvis 198
                                        s ++   + +l s++   ++p++  +++lk+              H+ +  ++g++   ++  d+l  ++v  +++
  gi|313124999|ref|YP_004035263.1| 425 VSLDE--VIAELPSESASYDEPHKAmYQLLKK-------------RHVAPQ-YGGHTRLAPEEQDYLVMKEVPDIFH 485
                                       94333..3444444444444444448999999.............788888.6666666666666655555555555 PP

                                       .ESSSS CS
                       Metallophos 199 .GHtHv 203
                                        GH+H+
  gi|313124999|ref|YP_004035263.1| 486 tGHVHK 491
                                       5****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 3057.41
//
Query:       gi|313125000|ref|YP_004035264.1|  [L=143]
Description: hypothetical protein Hbor_02140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 893.80
//
Query:       gi|313125001|ref|YP_004035265.1|  [L=392]
Description: aspartate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-46  157.7   4.4    5.5e-46  157.1   4.4    1.3  1  AA_kinase  Amino acid kinase family
    6.6e-17   61.1   0.2    4.2e-08   32.9   0.1    2.9  3  ACT_7      ACT domain
    1.2e-13   50.5   0.3    2.8e-05   23.8   0.1    3.2  2  ACT        ACT domain
    5.5e-07   30.1   0.3      0.067   13.8   0.0    2.9  3  ACT_4      ACT domain
    0.00032   20.6   0.2        1.4    8.9   0.0    2.9  2  ACT_6      ACT domain
  ------ inclusion threshold ------
       0.18   12.8   1.7        1.3   10.0   0.1    2.8  3  LytR_C     LytR cell envelope-related transcriptional attenua


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.1   4.4   1.8e-49   5.5e-46       1     239 [.       1     225 [.       1     227 [. 0.90

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 1.8e-49
                                       TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC....E..HHHHHH CS
                         AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaaglrstleeagev 76 
                                       +rvV K+GG+sl+++++  ++r+a+ iaa++e+g++++vV ++ g++td ll++   ++++  +             
  gi|313125001|ref|YP_004035265.1|   1 MRVVAKFGGTSLGSGDR--INRAADSIAAAVEKGHEIAVVASAmGNTTDDLLDE-IRFDADDRD------------- 61 
                                       79***************..***********************************.666666666............. PP

                                       HHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE......HHHTTTCEEECCHHHHHHHT.T-EEEEESEEE CS
                         AA_kinase  77 atrdalaslgerlvaallaaglpavglsaaaldateagr....degsdgnvesvdaeaieellea.gvvpvltgfig 148
                                         r++++s+ger + ++l+a+l+a+g++a  + + ++++    ++    +ve+ + +a     +  +vvpv+tgf +
  gi|313125001|ref|YP_004035265.1|  62 --RAEIVSMGERTSVRMLKAALAARGVNALFVEPGADQWpviaNDLGEVDVEETKHRAADLAADLdNVVPVITGFLA 136
                                       ..49**************************************9666666666665555555554325********** PP

                                       EETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHC CS
                         AA_kinase 149 ldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvk 222
                                        +++ge   lgrg+sDt+a++l+ +++Ad+++i+tdV+GV++ dp++v+ ar + +i+vde+++    l+  G++v+
  gi|313125001|ref|YP_004035265.1| 137 ENHDGEittLGRGGSDTTAVMLGRYMDADEVVIVTDVEGVMTGDPHVVEGARNVGRITVDELRN----LSFRGAEVV 209
                                       ****************************************************************....********* PP

                                       HHHHHHHHHCTT-EEEE CS
                         AA_kinase 223 hpaalaaarrggipvvI 239
                                        p+al     +   v++
  gi|313125001|ref|YP_004035265.1| 210 APSALSYKDDN-LAVRV 225
                                       ****9887766.66666 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7     5e+03      29      41 ..      79      91 ..      77      92 .. 0.86
   2 !   25.1   0.0   3.8e-09   1.1e-05       3      65 .]     252     314 ..     251     314 .. 0.96
   3 !   32.9   0.1   1.4e-11   4.2e-08       2      64 ..     327     389 ..     326     390 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                                      HHHHTTT---EEE CS
                             ACT_7 29 spLaeagIsifqi 41
                                      ++La+ g++ +++
  gi|313125001|ref|YP_004035265.1| 79 AALAARGVNALFV 91
                                      699*****99986 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 3.8e-09
                                       EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHHH CS
                             ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLhe 65 
                                       ed  ++++v g +++   +Gi+a l+++L e g+++ +++   +++ + V e+ +e+A + Lh+
  gi|313125001|ref|YP_004035265.1| 252 EDPLACVTVAGRSIRN-RPGILADLSQALREKGVNVDAVAsGMDSITFYVGEDRAEEAENLLHS 314
                                       68899*******9999.***********************999*******************96 PP

  == domain 3  score: 32.9 bits;  conditional E-value: 1.4e-11
                                       EEEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7   2 sedgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLh 64 
                                       ++d++++++v g+ lp   +G++  +++p +eagI+i  +  ++++  i+V  +d e+ +++ +
  gi|313125001|ref|YP_004035265.1| 327 VDDDVAVIRVTGGELPN-RPGVILDIVQPISEAGINIHDVItSATSVAIFVAWDDREETLKIVQ 389
                                       689************99.********************9988***************9999865 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.5e-08   4.4e-05       8      36 ..     266     294 ..     264     312 .. 0.79
   2 !   23.8   0.1   9.4e-09   2.8e-05       7      37 ..     341     371 ..     340     389 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.5e-08
                                       ESSTTHHHHHHHHHHHTTSEEEEEEEEEE CS
                               ACT   8 pDrPGlLarvfgaladrgiNidsieqrss 36 
                                       ++rPG+La++++al + g+N+d + ++ +
  gi|313125001|ref|YP_004035265.1| 266 RNRPGILADLSQALREKGVNVDAVASGMD 294
                                       79*********************998755 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 9.4e-09
                                       EESSTTHHHHHHHHHHHTTSEEEEEEEEEES CS
                               ACT   7 vpDrPGlLarvfgaladrgiNidsieqrsse 37 
                                       +p+rPG++ ++ + ++++giNi+ + ++ + 
  gi|313125001|ref|YP_004035265.1| 341 LPNRPGVILDIVQPISEAGINIHDVITSATS 371
                                       79***********************999884 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         5   1.5e+04      24      52 ..      26      55 ..      21      63 .. 0.63
   2 !   13.4   0.0     3e-05      0.09      13      39 ..     265     291 ..     263     299 .. 0.89
   3 !   13.8   0.0   2.2e-05     0.067      14      42 ..     342     370 ..     331     377 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5
                             ACT_4 24 tqvisee.kanivsvnaktrkkdglaeiki 52
                                      ++++++  ++++v+  + ++ +d l ei++
  gi|313125001|ref|YP_004035265.1| 26 AAAVEKGhEIAVVASAMGNTTDDLLDEIRF 55
                                      555555556777777777766565555555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3e-05
                             ACT_4  13 aedrkglLaditqviseekanivsvna 39 
                                        ++r+g+Lad++q++ e+++n+ +v +
  gi|313125001|ref|YP_004035265.1| 265 IRNRPGILADLSQALREKGVNVDAVAS 291
                                       58********************99976 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 2.2e-05
                             ACT_4  14 edrkglLaditqviseekanivsvnaktr 42 
                                        +r+g++ di+q ise+++ni++v ++++
  gi|313125001|ref|YP_004035265.1| 342 PNRPGVILDIVQPISEAGINIHDVITSAT 370
                                       69**********************99885 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00048       1.4      11      30 ..     267     286 ..     258     290 .. 0.89
   2 !    8.5   0.1   0.00065       1.9       4      33 ..     333     365 ..     331     383 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00048
                             ACT_6  11 drpGltasLtsvlaefgvni 30 
                                       +rpG++a+L+++l e gvn+
  gi|313125001|ref|YP_004035265.1| 267 NRPGILADLSQALREKGVNV 286
                                       8****************998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00065
                             ACT_6   4 litvtG...pdrpGltasLtsvlaefgvnilDi 33 
                                       +i+vtG   p+rpG++ ++ + ++e g+ni D+
  gi|313125001|ref|YP_004035265.1| 333 VIRVTGgelPNRPGVILDIVQPISEAGINIHDV 365
                                       68888877789*******************997 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.37   1.1e+03      43      43 ..      72      72 ..      14     133 .. 0.52
   2 ?   -3.4   0.0         6   1.8e+04      20      34 ..     195     209 ..     188     232 .. 0.56
   3 ?   10.0   0.1   0.00044       1.3      12      75 ..     268     323 ..     264     339 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.37
                            LytR_C 43 t 43
                                      t
  gi|313125001|ref|YP_004035265.1| 72 T 72
                                      2 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6
                            LytR_C  20 adaLeerGftvgevg 34 
                                        d+L++  f+ +ev 
  gi|313125001|ref|YP_004035265.1| 195 VDELRNLSFRGAEVV 209
                                       566666666555432 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00044
                            LytR_C  12 vsGlAarvadaLeerGftvgevgnagnadeettivy.reaaaaaakalaaalglgelqedsvkda 75 
                                       ++G+ a++++aL+e+G +v +   +++  + +  +y +e   + a++ +++l+ +   +d+++ +
  gi|313125001|ref|YP_004035265.1| 268 RPGILADLSQALREKGVNVDA---VASGMD-SITFYvGE---DRAEEAENLLHSKV--VDDQSLS 323
                                       7899*************9999...444422.44444533...35556666665444..2222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2510.06
//
Query:       gi|313125002|ref|YP_004035266.1|  [L=167]
Description: acyl-CoA hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-16   59.8   0.3    3.6e-16   59.3   0.3    1.3  1  4HBT             Thioesterase superfamily
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.034   14.1   0.0    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.017   15.6   0.0      0.021   15.3   0.0    1.2  1  4HBT_2           Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.3     6e-20   3.6e-16       4      75 ..      35     105 ..      32     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 6e-20
                                       B-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTS CS
                              4HBT   4 vhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedg 75 
                                         gG++l+++D ++++ +r+  +r ++v+++ +++df++p+ lgd++tv++ v  +grts+ v+v+v++e +
  gi|313125002|ref|YP_004035266.1|  35 ALGGTVLHWMDICGAISARRFSKR-QVVTASMDHVDFKAPIELGDVVTVTGYVFDTGRTSMDVHVDVCAERP 105
                                       569********************9.******************************************99876 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.7e-06     0.034      37      71 ..      65      99 ..      46     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-06
                                      HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEE CS
                   tRNA_anti-codon 37 eeatklaenlkeGdvvrvtGrvkrrpggelelkve 71
                                       +  +++  ++ Gdvv vtG+v+ + +  + ++v+
  gi|313125002|ref|YP_004035266.1| 65 MDHVDFKAPIELGDVVTVTGYVFDTGRTSMDVHVD 99
                                      566889999***************97665666665 PP

>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.5e-06     0.021      42     116 ..      57     133 ..      16     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-06
                            4HBT_2  42 rgiglilssahvryrrplkfpdrltvefrvididaktliiehrfls..nadgkk..aarveerivvmdygkrskkap 114
                                       +++ +  s +hv+++ p+ ++d +tv+  v d  ++++ + + +    +++g k  +a+     v  d +++  +ap
  gi|313125002|ref|YP_004035266.1|  57 KRQVVTASMDHVDFKAPIELGDVVTVTGYVFDTGRTSMDVHVDVCAerPSEGEKreTASSFFSFVALDENET--PAP 131
                                       2455566667********************999888888888888755556666679999999999999886..888 PP

                            4HBT_2 115 vP 116
                                       vP
  gi|313125002|ref|YP_004035266.1| 132 VP 133
                                       88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.81
# Mc/sec: 626.27
//
Query:       gi|313125003|ref|YP_004035267.1|  [L=457]
Description: tryptophanase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-71  241.1   0.0    2.3e-71  240.5   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
       0.12   12.2   0.5       0.36   10.6   0.0    2.0  3  HrpB4            Bacterial type III secretion protein (HrpB4)


Domain annotation for each model (and alignments):
>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.5   0.0   2.6e-75   2.3e-71       1     292 [.      46     414 ..      46     415 .. 0.97

  Alignments for each domain:
  == domain 1  score: 240.5 bits;  conditional E-value: 2.6e-75
                                       E-S-GGG----HHHHHHH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEE CS
                   Beta_elim_lyase   1 DLlSDsvtkgteamsdaq.aaamlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeeviv 76 
                                       DLl+Ds   gt+ ms++q aa+m Gde+Y++++++ +L dav++++g+e++++++qG++A+++ + +l++ g+ v  
  gi|313125003|ref|YP_004035267.1|  46 DLLTDS---GTGTMSADQwAALMRGDEAYAGSRSFSELRDAVRDVMGFEYVVPTHQGRGAENVVYGVLVEEGDVV-- 117
                                       9*****...************************************************************888765.. PP

                                       ETT-HHHHSSTTHHHHCC--EEEEE-EBTT..........TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB CS
                   Beta_elim_lyase  77 tepahihfdetgaiaelagvklrdlknkea..........GkmdlekleaaikevgaheekiklisltvTnntagGq 143
                                         p++ hfd+t+a+++ +g+ ++d++++ a          G++d+++  ++++evg+  + i++++ t+Tnn+++Gq
  gi|313125003|ref|YP_004035267.1| 118 --PNNAHFDTTRAHVANQGADPVDCPHELAhdadadhpfkGNFDIDAGWELVEEVGE--DSIPVVVQTITNNSVAGQ 190
                                       ..99***********************99999*************************..****************** PP

                                       ---HHHHHHHHHHHHHCT-EEEEEETTHHHHH............HHHTS-CHHHHTTSSEEEEESSSTT--SS-EEE CS
                   Beta_elim_lyase 144 vvsleelrevaaiakkygiplhlDgARfanaa............kslgeivkemfsyvDsvtmslkKdllanvGgvl 208
                                       +vs+e+ revaa+a++ + ++++D++Rfa++a            +s++ei++e +sy+D vtms+kKd+++n+Gg+ 
  gi|313125003|ref|YP_004035267.1| 191 PVSVENTREVAAFADEIDATFVIDACRFAENAyfvqqreaefsdASVAEIAREQLSYADAVTMSGKKDAIVNIGGFA 267
                                       ***************************************************************************** PP

                                       EE-HH.........................................HHHHHHHHHHHHT---SSTHHHHH....... CS
                   Beta_elim_lyase 209 afrddel.....................................edylaerveqrkylggglrqagvlaa....... 241
                                       a++d el                                       y+ erveq+  lg  l++ag+++        
  gi|313125003|ref|YP_004035267.1| 268 AMNDPELfelakqrgilyegfptygglagrdvaamavglreavePPYVGERVEQVAELGRLLTDAGIPVYeptggha 344
                                       *****99*************************************9******************************** PP

                                       .............................HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT--EEECCGTTCCEEEEE CS
                   Beta_elim_lyase 242 ...........................leagiraleeglaslerdhktaeqlaeklelvrlaiprrvytqehldyva 291
                                                                  le g+r +e+g          a   +++ +lvrla+prr+y+ ehl++va
  gi|313125003|ref|YP_004035267.1| 345 vyidaeavlphvpkdqfpgqelvcalyLEGGVRGVELG--------GFAFPGTDRPDLVRLALPRRTYSREHLEHVA 413
                                       *******************9888888888888888888........67788888899*****************998 PP

                                       . CS
                   Beta_elim_lyase 292 a 292
                                       +
  gi|313125003|ref|YP_004035267.1| 414 E 414
                                       7 PP

>> HrpB4  Bacterial type III secretion protein (HrpB4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.47   4.2e+03     138     173 ..      38      75 ..      23      83 .. 0.66
   2 ?   -2.9   0.0      0.55   4.9e+03     151     179 ..     214     242 ..     185     256 .. 0.72
   3 ?   10.6   0.0   4.1e-05      0.36     168     201 ..     385     418 ..     358     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.47
                             HrpB4 138 lelkeglapLaarda.aalaleGwrllvr.egawpdsa 173
                                       l+++  +  L   ++  +++++ w  l+r + a + s+
  gi|313125003|ref|YP_004035267.1|  38 LDAEDVFIDLLTDSGtGTMSADQWAALMRgDEAYAGSR 75 
                                       45555666666666656899999998888776666555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.55
                             HrpB4 151 daaalaleGwrllvregawpdsalrrlvr 179
                                       da ++a++ ++  +re+  +d+ ++++ r
  gi|313125003|ref|YP_004035267.1| 214 DACRFAENAYFVQQREAEFSDASVAEIAR 242
                                       55677888888888888877777777766 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 4.1e-05
                             HrpB4 168 awpdsalrrlvrLaLprslaaarwleerasalda 201
                                       a p ++   lvrLaLpr    +++le+ a+ ++a
  gi|313125003|ref|YP_004035267.1| 385 AFPGTDRPDLVRLALPRRTYSREHLEHVAETAAA 418
                                       556778889*****************99998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2884.12
//
Query:       gi|313125004|ref|YP_004035268.1|  [L=359]
Description: hypothetical protein Hbor_02180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.1e-123  411.4   4.6   2.4e-123  411.2   4.6    1.0  1  DUF2891   Protein of unknown function (DUF2891)


Domain annotation for each model (and alignments):
>> DUF2891  Protein of unknown function (DUF2891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.2   4.6  1.3e-127  2.4e-123       2     323 ..      26     345 ..      25     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: 411.2 bits;  conditional E-value: 1.3e-127
                           DUF2891   2 klaelaleciereyPnklahvleseedvkeprelhPvFyGcfDWHSsVhghWllvrllrlfpeleeaeeiravldes 78 
                                       ++++++l+ ie+eyP+ +++v +s++ v++p++ hPvFyGc+DWHS+Vh+hW+l+r lr f+++++++ei++ +d++
  gi|313125004|ref|YP_004035268.1|  26 TFSQHPLDAIETEYPHYVRSV-DSPDGVERPKNNHPVFYGCYDWHSAVHSHWALLRQLRVFESHPAESEIKQRIDAR 101
                                       6999************99988.9****************************************************** PP

                           DUF2891  79 ltaekiaaEvaylkkeekksferpYGwaWllkLaaeleelddpeakewaealeplaeliverlkeflpkltypirvG 155
                                       +t+e+i++E++y+++++  +ferpYGwaWll+La+el+ +dd++a+ew++ +epl+++i + +++ + +++ p+rvG
  gi|313125004|ref|YP_004035268.1| 102 FTPENIEREIEYFEANR--TFERPYGWAWLLHLASELTLWDDDHADEWKSIIEPLEREIIALIESEFLSQEQPLRVG 176
                                       **************998..********************************************************** PP

                           DUF2891 156 tHsntaFalalaldyaraakdeeleelieekakrfyakdkdapaalEPsgddFLSpaLeeadlmrrvlpkeefakwl 232
                                       tH+n+aFal+++ldyar++++e+le++++e+a +f+a+d+++p+++EP g+dFLSp+L+eadlmrrv++++ef++w+
  gi|313125004|ref|YP_004035268.1| 177 THENSAFALHCILDYARTTSNESLESAVVETAIEFFAQDRNYPVEYEPLGWDFLSPTLTEADLMRRVYDEDEFRTWI 253
                                       ***************************************************************************** PP

                           DUF2891 233 eaflpklaek.eatllepaev.sdrtDgkiaHldGLnlsrawclralakalpeddklkaaleeaaeehleaslpkvv 307
                                       + flp++++k  +tllep++  +d++++ ++Hl GLnls+aw l++la++l +++++++a+e++a++h+e++l++++
  gi|313125004|ref|YP_004035268.1| 254 DGFLPDITTKpYDTLLEPVHAeTDPDEEVAIHLVGLNLSKAWSLAGLATTL-DGHRYAEAFERSAKKHAERGLSQAF 329
                                       **********99******9986899999999********************.779********************** PP

                           DUF2891 308 sedYageHWLasFall 323
                                       +++Yag+HWL+sFal+
  gi|313125004|ref|YP_004035268.1| 330 TDNYAGSHWLSSFALY 345
                                       ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2159.91
//
Query:       gi|313125005|ref|YP_004035269.1|  [L=219]
Description: phosphoesterase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-31  109.6   0.4    2.2e-31  109.3   0.4    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    7.4e-13   49.5   1.0    9.2e-12   45.9   1.0    2.0  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.4   2.5e-35   2.2e-31       1     164 [.       1     183 [.       1     184 [. 0.86

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 2.5e-35
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepe.vleellelapvlaVrGNnD............ 62 
                                       M++a+iSD+H+n+ al+avl+++ +v  d i++aGD+  ++  p  +++el++ ++v +V GN+D            
  gi|313125005|ref|YP_004035269.1|   1 MRVAVISDVHANRVALDAVLDDMPDV--DSILCAGDVvgYNPWPAeCVAELRA-RDVPTVMGNHDravasdttfrfn 74 
                                       9*************************..********97766666537777777.5***************9999998 PP

                     Metallophos_2  63 ......eev.veedvlreaaelgtdlp.eeaelelagekvlliHgdpl.....gvkdalaellkeaeegsdvvvcGH 126
                                                 ++e++ + a ++  dlp e+ e++  g +v l+H++p       ++d++++++ +   g+dv+v+GH
  gi|313125005|ref|YP_004035269.1|  75 amaaagV-KhAREKLDDDAMTWLSDLPdERTEFD--G-RVRLTHDHPRiqdkyTYPDEFEADFLD---GEDVLVLGH 144
                                       8766532.25777788888888888874444444..4.8*******98*8888888888888888...999****** PP

                     Metallophos_2 127 tHvpevekeggvlvvnPGsvgeprdgdpe.tyaildtde 164
                                       tHv++ +  ++ +v nPGsvg+prdgdp+  yaild+d+
  gi|313125005|ref|YP_004035269.1| 145 THVQGHRVFDEGIVMNPGSVGQPRDGDPRaAYAILDLDD 183
                                       ****99999999************************986 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   1.0     1e-15   9.2e-12       1     203 [.       1     147 [.       1     148 [. 0.80

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1e-15
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       +r++vi+D+H     ++  +l+++ldd    +++d +l+aGD+v  ++++ e++  l+a         +++GNH+  
  gi|313125005|ref|YP_004035269.1|   1 MRVAVISDVH-----ANRVALDAVLDDM---PDVDSILCAGDVVGYNPWPAECVAELRARDV-----PTVMGNHD-- 62 
                                       89********.....*************...789*****************99998666666.....89******.. PP

                                       HHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH. CS
                       Metallophos  78 eeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkd. 153
                                                      ++  + +  fn++  a+      +  l++                            wl+d 
  gi|313125005|ref|YP_004035269.1|  63 --------------RAVASDTTFRFNAMAAAGVKHA--REKLDDDA------------------------MTWLSDl 99 
                                       ..............3444444777888888884444..55555555........................99***** PP

                                       HHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 154 lekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                        ++r++ d  + l+H  +  +  y+++de  +d+l+    d+ + GHtHv
  gi|313125005|ref|YP_004035269.1| 100 PDERTEFDGRVRLTHDHPRIQDKYTYPDEFEADFLDGE--DVLVLGHTHV 147
                                       99999999999999999995666666666666665555..68888****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1366.19
//
Query:       gi|313125006|ref|YP_004035270.1|  [L=192]
Description: IMP cyclohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-66  221.8   0.0    6.8e-66  221.5   0.0    1.0  1  IMP_cyclohyd  IMP cyclohydrolase-like protein


Domain annotation for each model (and alignments):
>> IMP_cyclohyd  IMP cyclohydrolase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.5   0.0   3.8e-70   6.8e-66       1     189 [.       2     181 ..       2     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 3.8e-70
                                       ---SEEEEEEETTEE.EEEEEEE-SS---EEEEEETTEEEEEE-TGGGGGT-TTSSEEEEEEETTEEEEESSTHHHH CS
                      IMP_cyclohyd   1 YvGRfivvgksedgkavaaYrvssRSfpnrnrvfredkirveptdeeklednpyiiYncvrvlddkavvtNGsqtdt 77 
                                       YvGRfiv+g++     + aYrvssRSfpnr++v+r+++++v+pt+ +  +dnpyi+Yncvr  +d +vv+NGs++d+
  gi|313125006|ref|YP_004035270.1|   2 YVGRFIVIGPD-----FGAYRVSSRSFPNRQVVERDGTLTVAPTPDAPETDNPYISYNCVREGGDSVVVGNGSHVDP 73 
                                       9**********.....*****************************77778*************************** PP

                                       HHHHHHTSB-HHHHHHHHHHHH-S--STT---EEEEEE-SS.EEEEEEETTEEEEEE--..TTS-EEEESSS--S-E CS
                      IMP_cyclohyd  78 iaeklekgltardalalsLlaldyEkDdynTPRiagvvkeeeaalgivksdallvekvelkagegtliatYekgepk 154
                                       iaekl++g++ardala+sLla+dyEkDdy+TPRiagvv ee  ++giv++dallv+ v+   ++++l+atYe+++p+
  gi|313125006|ref|YP_004035270.1|  74 IAEKLDLGYPARDALAESLLAMDYEKDDYDTPRIAGVVGEE-SYIGIVRRDALLVRPVT---ENPMLVATYEEDDPA 146
                                       **************************************985.89*************99...89************* PP

                                       E----.-SSHHHHHHHHHHGGGSS-EEEEEEEEESS CS
                      IMP_cyclohyd 155 evele.aedaeeaaeelweslefenkVslavavide 189
                                        v ++ + +++e+ae ++e +++e++V++a+++ d+
  gi|313125006|ref|YP_004035270.1| 147 VVVFDgDGSPAELAERAYE-MDYEHAVCAAGVTYDD 181
                                       ****624589*********.************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1180.85
//
Query:       gi|313125007|ref|YP_004035271.1|  [L=162]
Description: hypothetical protein Hbor_02220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-10   39.6   0.0      7e-10   39.3   0.0    1.1  1  CGI-121   Kinase binding protein CGI-121


Domain annotation for each model (and alignments):
>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   3.9e-14     7e-10      22     161 ..      30     157 ..      10     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 3.9e-14
                                       T-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS- CS
                           CGI-121  22 dfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvsssea 98 
                                        + + da++++s++hl  Av  a  a +rg+   +    E+l++  + ++I +al  +g+s+ +t +++  v+    
  gi|313125007|ref|YP_004035271.1|  30 TVQVFDARYVVSEKHLRRAVELADRAIERGENVARDRAVEMLLYAAGRRQIDDALA-MGVSEGETPVVAL-VDGG-- 102
                                       46789**************************************************9.******7744433.3333.. PP

                                       -HHHHHHHHHHHS-SEEE--SHHHHHH--HHHHHHHTT--..TT---SSHHHHHHHHHHHHHT CS
                           CGI-121  99 deeevlkslkevvegelvpleeeleeltdwkkikkiYklneleeekeeevkeledlvvsaval 161
                                       de +  ++l ++    ++     l++ +d ++++ ++ ++  ++e ++   +le+lv+++val
  gi|313125007|ref|YP_004035271.1| 103 DEAKAAAQLRDLFTERQT-----LGR-YDDERVRDFFDVT--DAELAAVDGDLESLVCERVAL 157
                                       568888899999886555.....444.899**********..4444455555*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 997.47
//
Query:       gi|313125008|ref|YP_004035272.1|  [L=841]
Description: superfamily ii helicase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-21   75.6   0.0    7.8e-21   74.6   0.0    1.5  1  DEAD             DEAD/DEAH box helicase
    2.9e-07   31.0   0.2    1.6e-06   28.6   0.2    2.4  1  HHH_5            Helix-hairpin-helix domain
    6.1e-06   26.6   0.0    0.00012   22.4   0.0    2.6  2  Helicase_C       Helicase conserved C-terminal domain
    8.5e-05   22.3   0.0     0.0004   20.2   0.0    2.1  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   1.7e-24   7.8e-21       2     170 ..      27     183 ..      26     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.7e-24
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STS CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idl 76 
                                       + Qa a+++ + +g++vl++++T+sGKT ++ +++l++v     ++g kal+++P+r+La +   +++++ ++ id+
  gi|313125008|ref|YP_004035272.1|  27 PPQADAVEAGVtEGESVLASIPTASGKTFIAELAMLSSV-----QRGGKALYIVPLRALASEKKAEFERWEEFgIDV 98 
                                       669999999887999*********************999.....6788***********************965664 PP

                                       EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                        v+  +g  ++++  + l ++ di+v+t +++d+l++++   +++++++V DE++ + d  ++++++  l +l++i+
  gi|313125008|ref|YP_004035272.1|  99 GVS--TG--NYDSSGEWL-ASRDIIVATSEKVDSLIRNNAPWVEDLSCVVSDEVHLVNDGHRGPTLEVTLGKLRKIN 170
                                       433..44..667788888.899**************888878*******************************8876 PP

                                       TTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxx RF
                              DEAD 154 cdgklqrqvivlSATlp 170
                                           lq  v++lSAT+ 
  gi|313125008|ref|YP_004035272.1| 171 PG--LQ--VVALSATVG 183
                                       65..44..*******86 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.2   3.6e-10   1.6e-06       4      56 ..     722     774 ..     718     775 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 3.6e-10
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHH.HHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadvee.LakipGiGkktAeriilelk 56 
                                       L +v G+G+k+A++l +aGie+  dl +ad+   La++     ktAe++++++ 
  gi|313125008|ref|YP_004035272.1| 722 LAGVRGVGRKRARRLFEAGIETRNDLREADKSVvLAAL-RGRRKTAENVLEAAG 774
                                       889****************************9625555.556899999999885 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.2   5.6e+03       9      45 ..      61     100 ..      54     108 .. 0.60
   2 !   22.4   0.0   2.6e-08   0.00012      14     111 .]     244     387 ..     233     387 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                                       HHHHTTTTSEEEEEESSHH.HHHHHHHH..HHHTTSTEEE CS
                        Helicase_C   9 llkleeeggkilifvntid.rlekvkll..lekkgikvav 45 
                                       +l++ ++ggk+l +v+ +    ek   +   e++gi v v
  gi|313125008|ref|YP_004035272.1|  61 MLSSVQRGGKALYIVPLRAlASEKKAEFerWEEFGIDVGV 100
                                       3478899999999999999533333333111334666655 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.6e-08
                                       TTTSEEEEEESSHHHHHH.HHHH............................HHHT.........TSTEEEESTTSTH CS
                        Helicase_C  14 eeggkilifvntidrlek.vkll............................lekk.........gikvavlhgelpq 52 
                                       ee+g +l+fvn+++++e  +k l                               +         +  +a +h+ l +
  gi|313125008|ref|YP_004035272.1| 244 EEDGSSLVFVNSRRNAEAaAKRLkdvtsraltdeersklaelaqeirdvsdA--EtsdtlancvAKGAAFHHAGLAA 318
                                       5666667777777744323111122222222333333333333333333331..02334444567788899999*** PP

                                       HHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE....ESSSS......SSHHHHHHHHTTSSSTT CS
                        Helicase_C  53 nereeileqfnkgesdvLiatdvaerGidipkvnlVi....nfdlp......rnvtsyiqriGRtgRag 111
                                       ++r  + ++f++  ++ + at  ++ G++ p+ ++++    ++d         +v +++q++GR+gR g
  gi|313125008|ref|YP_004035272.1| 319 EHRSLVEDAFRDRLVKTVSATPTLAAGVNTPSRRVIVrdwrRYDGEfggmkpLDVLEVHQMMGRAGRPG 387
                                       *******************************999888777766666655555668************75 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.99   4.4e+03      19      45 ..     286     311 ..     285     313 .. 0.75
   2 !   20.2   0.0   8.9e-08    0.0004       3      30 ..     722     749 ..     721     758 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.99
                   DNA_pol_lambd_f  19 akGirtledlrakrakLtreqqiGlky 45 
                                       a+ ir++ d+ +  ++L + +  G  +
  gi|313125008|ref|YP_004035272.1| 286 AQEIRDVSDAET-SDTLANCVAKGAAF 311
                                       6889*****999.68887777666665 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 8.9e-08
                   DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyakGirtledlra 30 
                                       + +v GVG+k+A++++++Gi t +dlr+
  gi|313125008|ref|YP_004035272.1| 722 LAGVRGVGRKRARRLFEAGIETRNDLRE 749
                                       6799***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (841 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 4826.84
//
Query:       gi|313125009|ref|YP_004035273.1|  [L=80]
Description: ferredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-21   74.9   3.3    7.5e-21   74.6   3.3    1.1  1  Fer4_15   4Fe-4S single cluster domain
    6.5e-05   23.4   2.1     0.0002   21.8   2.1    1.8  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.025   14.4   1.8       0.47   10.4   0.2    2.5  2  Fer4      4Fe-4S binding domain
      0.082   13.0   2.2          3    8.1   0.2    2.3  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   3.3   1.7e-24   7.5e-21       1      65 [.       3      70 ..       3      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.7e-24
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaeg....evpddeeeaaqeAaraCPvdAIr 65
                                      +++Drd+Cig+++Cv+e++++ ++ ++g+a++ ++ +e++e+    evp+dee +a++Aar+CPvdAI+
  gi|313125009|ref|YP_004035273.1|  3 IRYDRDTCIGMFQCVDEWDTFEKNLDAGKADLAGA-EEVEEDifelEVPEDEEFEAEFAARVCPVDAIE 70
                                      789****************9999999****99975.677777999***********************8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   2.1   4.6e-08    0.0002       2      57 ..       6      70 ..       5      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.6e-08
                           Fer4_13  2 DrdtCiacgaCvelaPdvFeeddeggasvvaeqpts..........eeekadaeeAadaCPvesIg 57
                                      DrdtCi+  +Cv+   d+Fe + + g++  a  ++           e+e+ +ae Aa  CPv++I+
  gi|313125009|ref|YP_004035273.1|  6 DRDTCIGMFQCVDEW-DTFEKNLDAGKADLAGAEEVeedifelevpEDEEFEAEFAARVCPVDAIE 70
                                      9************96.9*******9999987543334566667676999****************7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.019        86       2      10 ..       4      12 ..       3      12 .. 0.86
   2 ?   10.4   0.2   0.00011      0.47      15      24 .]      61      70 ..      61      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.019
                                      EEETTTSSS CS
                              Fer4  2 videekCig 10
                                       +d + Cig
  gi|313125009|ref|YP_004035273.1|  4 RYDRDTCIG 12
                                      689*****8 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00011
                                      HHHSTTTEEE CS
                              Fer4 15 vevCPvgAIt 24
                                      + vCPv+AI+
  gi|313125009|ref|YP_004035273.1| 61 ARVCPVDAIE 70
                                      579******6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2   0.00067         3       1      11 [.       2      12 ..       2      19 .. 0.75
   2 ?    4.9   0.1     0.007        31      17      24 .]      62      69 ..      61      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00067
                            Fer4_6  1 vveidpdkCig 11
                                      ++++d+d Cig
  gi|313125009|ref|YP_004035273.1|  2 KIRYDRDTCIG 12
                                      689*******6 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.007
                            Fer4_6 17 rvCPegai 24
                                      rvCP +ai
  gi|313125009|ref|YP_004035273.1| 62 RVCPVDAI 69
                                      8****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.52
# Mc/sec: 463.94
//
Query:       gi|313125010|ref|YP_004035274.1|  [L=56]
Description: hypothetical protein Hbor_02250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.9   0.2      0.036   14.2   0.2    1.4  1  bPH_6     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2     2e-06     0.036      14      58 ..      14      52 ..      12      56 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-06
                             bPH_6 14 rnlfrtrrlpWsaiagvrfpegrrlarldlrdgelvplpavqlgd 58
                                      r   ++r++ W++++g+++p++        +dg++ +lpa++++d
  gi|313125010|ref|YP_004035274.1| 14 RKTHGHRLMEWADLVGASVPDSVA------DDGDEPTLPAWDDAD 52
                                      56669***************9994......889999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 348.60
//
Query:       gi|313125011|ref|YP_004035275.1|  [L=843]
Description: ercc4-like helicase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-24   87.1   0.0    3.2e-24   85.9   0.0    1.7  1  ERCC4          ERCC4 domain
    7.9e-23   80.9   0.0    3.6e-22   78.8   0.0    2.2  3  Helicase_C     Helicase conserved C-terminal domain
    6.6e-16   58.6   0.0    2.4e-15   56.8   0.0    1.9  1  DEAD           DEAD/DEAH box helicase
      1e-13   51.7   0.0    2.2e-13   50.5   0.0    1.6  1  ResIII         Type III restriction enzyme, res subunit
      2e-10   40.6   0.5    1.4e-09   37.9   0.2    2.4  2  HHH_2          Helix-hairpin-helix motif
    3.4e-10   40.4   0.5    1.7e-09   38.1   0.2    2.4  2  HHH_5          Helix-hairpin-helix domain
    7.9e-08   31.8   0.4    2.7e-05   23.8   0.1    3.2  3  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.018   15.2   0.1      0.063   13.4   0.1    1.9  1  Helicase_C_2   Helicase C-terminal domain
      0.021   15.4   0.0      0.092   13.4   0.0    2.1  1  5_3_exonuc     5'-3' exonuclease, C-terminal SAM fold
        4.9    6.4  11.0        5.6    6.2   3.2    2.4  2  DUF4407        Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.0   1.8e-27   3.2e-24       1     153 [.     634     754 ..     634     757 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.8e-27
                                       EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCC..SH CS
                             ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikd..gr 75 
                                       +D+rel s+i + l  + g+e++ etl +gdy ++   +++               v+verks++d+ ++++   ++
  gi|313125011|ref|YP_004035275.1| 634 VDQRELDSNIAKDLSTRDGIETRLETLAVGDY-VL---SDR---------------VAVERKSVSDFLDTLTGgdRS 691
                                       8************555777*************.**...9**...............***************77558* PP

                                       HHHHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHH CS
                             ERCC4  76 leeqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaew 152
                                       l+eq+ +l+r +y +pil++eg+  + ++n              i++ +i +aL++l++df+vs+l+t+++ +tae+
  gi|313125011|ref|YP_004035275.1| 692 LFEQIGDLSR-AYARPILILEGEGLFEERN--------------IHPGAIRGALASLAVDFDVSVLQTRDEDDTAEL 753
                                       **********.******************9..............********************************9 PP

                                       H CS
                             ERCC4 153 l 153
                                       l
  gi|313125011|ref|YP_004035275.1| 754 L 754
                                       8 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.6   6.5e+03      12      58 ..      60     110 ..      51     141 .. 0.70
   2 ?   -3.8   0.0       8.9   1.6e+04      21      56 ..     301     332 ..     293     342 .. 0.69
   3 !   78.8   0.0     2e-25   3.6e-22      12     109 ..     367     471 ..     356     473 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.6
                                       HTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHH CS
                        Helicase_C  12 leeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereei 58 
                                       l+e+ggk+l  ++t+  +++ +++ +e     + +++v++g+   ++r + 
  gi|313125011|ref|YP_004035275.1|  60 LHEVGGKALFLAPTKPLVQQhADFYREALeipDDEIVVFTGDVRPDDRAAL 110
                                       578889999999888877665444433223446777777777777777665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.9
                                       EEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHH CS
                        Helicase_C  21 ifvntidrlekvklllekkgikvavlhgelpqnere 56 
                                       + +++++++   +++  +++ ++a+  g  ++++r+
  gi|313125011|ref|YP_004035275.1| 301 VETQSVESVR--RYF--ERQRNAARSSGASKASQRL 332
                                       5556666775..888..4457888888877777775 PP

  == domain 3  score: 78.8 bits;  conditional E-value: 2e-25
                                       HTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT......STHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
                        Helicase_C  12 leeeggkilifvntidrlek.vklllekkgikvavlhge......lpqnereeileqfnkgesdvLiatdvaerGid 81 
                                         ++g+++++f++++d++e  +++l e+++ +  v +g+      ++q+e++e+l++f++ge+ vL++t+vae+G+d
  gi|313125011|ref|YP_004035275.1| 367 GIQDGERVIVFTESRDTAEAlTDFLSESFDARRFVGQGDkegsdgMTQKEQQETLDEFRNGEFEVLVSTSVAEEGLD 443
                                       55899***********99988899977776666666666999999******************************** PP

                                       STTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       +p+v+lV +f++  +  + iqr+GRtgR
  gi|313125011|ref|YP_004035275.1| 444 VPEVDLVLFFEPVPTAIRSIQRKGRTGR 471
                                       **************************** PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   1.3e-18   2.4e-15      14     147 ..      35     164 ..      25     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.3e-18
                                       TCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardq 90 
                                       + + lv+ +TG GKT++ l+   +++    ++ g kal+++Pt+ L++q+++ +++ ++  d  + ++++g+ + d+
  gi|313125011|ref|YP_004035275.1|  35 DAHTLVCLPTGLGKTTVSLLVTAERL----HEVGGKALFLAPTKPLVQQHADFYREALEIPD-DEIVVFTGDVRPDD 106
                                       56789*********************....56888************************766.67777888888899 PP

                                       HHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                              DEAD  91 lskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinriln 147
                                       +++l  +++iv++tp+ + + l  ++++l++v+ l +DE++r   +  +    +r ++
  gi|313125011|ref|YP_004035275.1| 107 RAALWDDARIVIATPQVVENDLIGNRISLREVTHLTFDECHRGTGDyAYVYIAERYHA 164
                                       9999899************977668899*************97766455555555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   1.3e-16   2.2e-13      22     169 ..      33     178 ..      18     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.3e-16
                                       .TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B CS
                            ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkk 94 
                                        rd + l+ ++TG GKT v+ + ++erl++ g+  k+lfl+p+k l++q  + +++ l+ +++e    +++v+ d +
  gi|313125011|ref|YP_004035275.1|  33 ARDAHTLVCLPTGLGKTTVSlLVTAERLHEVGG--KALFLAPTKPLVQQHADFYREALEIPDDEivvFTGDVRPDDR 107
                                       7899****************7777888888777..************************999887776666777777 PP

                                       --.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---....SEEEEEES CS
                            ResIII  95 kakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfke....avllglTA 167
                                        a     ++++i+++t q + +d+       ++ +  +   + +DE+Hr +++ ++  i+e + +     ++ g++A
  gi|313125011|ref|YP_004035275.1| 108 AA---LWDDARIVIATPQVVENDL-----IGNRISLREVTHLTFDECHRGTGDYAYVYIAERYHAdaerPLVTGMSA 176
                                       66...89*****************.....89999999999************8899998666643344477888888 PP

                                       S- CS
                            ResIII 168 Tp 169
                                        p
  gi|313125011|ref|YP_004035275.1| 177 SP 178
                                       76 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.1     2e+03      45      61 ..     303     319 ..     288     320 .. 0.77
   2 !   37.9   0.2   7.7e-13   1.4e-09       8      53 ..     791     836 ..     787     841 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                             HHH_2  45 eeiAqsivefFeneknr 61 
                                       ++  +s++++Fe ++n 
  gi|313125011|ref|YP_004035275.1| 303 TQSVESVRRYFERQRNA 319
                                       566689******99885 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 7.7e-13
                             HHH_2   8 IrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsive 53 
                                       I ++G  tA+ L ++F++++a ++a +e+Llev +iG ++A+ i++
  gi|313125011|ref|YP_004035275.1| 791 IADIGPVTARSLLEEFGTVEAVMTAREEDLLEVSGIGSVTAERIRD 836
                                       889*****************************************98 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.6     1e+04      39      57 .]     254     272 ..     234     272 .. 0.78
   2 !   38.1   0.2   9.7e-13   1.7e-09       7      52 ..     791     835 ..     787     839 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.6
                                       TSTTS-HHHHHHHHHHHHH CS
                             HHH_5  39 kipGiGkktAeriilelkd 57 
                                       + p++++k+   +  el++
  gi|313125011|ref|YP_004035275.1| 254 TSPDVSQKQLNGMRAELQK 272
                                       4588999999888888875 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 9.7e-13
                                       STT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5   7 vsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAerii 52 
                                       +  iGp+tA++ll+  +++ve+++ a +e+L ++ GiG  tAeri 
  gi|313125011|ref|YP_004035275.1| 791 IADIGPVTARSLLEE-FGTVEAVMTAREEDLLEVSGIGSVTAERIR 835
                                       778************.*****************************7 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.2   1.3e+04      12      19 ..     504     511 ..     503     511 .. 0.90
   2 ?    4.8   0.0     0.016        29      15      29 ..     790     804 ..     789     805 .. 0.87
   3 !   23.8   0.1   1.5e-08   2.7e-05       2      29 ..     809     836 ..     808     837 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.2
                                       HHHTSTT- CS
                               HHH  12 eLlalPGV 19 
                                       eL +l+GV
  gi|313125011|ref|YP_004035275.1| 504 ELRDLKGV 511
                                       999****9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.016
                                       TSTT-SHHHHHHHHH CS
                               HHH  15 alPGVGpktAeaIls 29 
                                       a+  +Gp tA++ l+
  gi|313125011|ref|YP_004035275.1| 790 AIADIGPVTARSLLE 804
                                       6789*******9986 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 1.5e-08
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIls 29 
                                       +e++++a +e+Ll+++G+G  tAe+I++
  gi|313125011|ref|YP_004035275.1| 809 VEAVMTAREEDLLEVSGIGSVTAERIRD 836
                                       6899**********************86 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.5e-05     0.063      10      82 ..     372     446 ..     363     453 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                      Helicase_C_2  10 ggvlvffpSyklleevverlkeeleskkieifvee......keesrekvleeykekkkkgaillavcrGklsEGidf 80 
                                       ++v+vf+ S ++ e ++++l+e+ +++++  +  +      ++++++++l+e+++  ++  +l+++      EG+d+
  gi|313125011|ref|YP_004035275.1| 372 ERVIVFTESRDTAEALTDFLSESFDARRFVGQGDKegsdgmTQKEQQETLDEFRN--GEFEVLVSTS--VAEEGLDV 444
                                       689*******************9976665333333678888999***********..9999999998..999****9 PP

                      Helicase_C_2  81 sd 82 
                                       ++
  gi|313125011|ref|YP_004035275.1| 445 PE 446
                                       85 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.1e-05     0.092      21      49 ..     789     817 ..     784     835 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                        5_3_exonuc  21 pGvpgiGektAakLlkeygsleeilenld 49 
                                         ++ iG+ tA +Ll+e+g++e+++ + +
  gi|313125011|ref|YP_004035275.1| 789 SAIADIGPVTARSLLEEFGTVEAVMTARE 817
                                       56899*******************98654 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.0     0.011        19     122     231 ..     229     341 ..     196     355 .. 0.72
   2 ?    6.2   3.2    0.0031       5.6     130     212 ..     484     622 ..     448     662 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                           DUF4407 122 elkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqae 198
                                       ++++ +++  +++l++l++      +  d  +++l+  rae+qk +++++++g +g+    +++k ++a     ++ 
  gi|313125011|ref|YP_004035275.1| 229 AIRDAVNEVIKDRLEKLKSLGVTNTTSPDVSQKQLNGMRAELQKLMNNDQSEGYKGMSTHAEVMKLRRAVELVETQS 305
                                       455555666888899999999999999999******************99999999888888888888888888888 PP

                           DUF4407 199 laelkakld...atarlaalraelaeleaerakera 231
                                       ++++++  +   ++ar + + +  ++l ae + ++a
  gi|313125011|ref|YP_004035275.1| 306 VESVRRYFErqrNAARSSGASKASQRLVAEPKVREA 341
                                       888888844544444444444444444444433333 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0031
                           DUF4407 130 a.........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.......gtgttgvaGkgpaake... 187
                                       +         ++ + +e+++++++l++  d+ e++ld+ ++ +++   g++       ++   g   +g  a +   
  gi|313125011|ref|YP_004035275.1| 484 NtrdeayfwiSRRREKEMKSELRDLKGVADEVEEELDDSQKGLDAFSGGDSagtddgeSS---GAIANGGTAAAtte 557
                                       1344567777899999****************************8877777877764422...23333433433133 PP

                           DUF4407 188 ........................................kkaqldaaqaelaelkakldatarl 212
                                                                                ++++++a++e +++ ++ d t ++
  gi|313125011|ref|YP_004035275.1| 558 tpdastaeadsgtdggtasgtdatdtnsnddqagldsfsaSDEEIARADEESEAAVEDGDGTVAT 622
                                       44444444444444444444444444444444444444444444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (843 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.50
# Mc/sec: 5068.98
//
Query:       gi|313125012|ref|YP_004035276.1|  [L=71]
Description: hypothetical protein Hbor_02270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       136  (0.00758548); expected 358.6 (0.02)
Passed bias filter:                       87  (0.00485247); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 400.49
//
Query:       gi|313125013|ref|YP_004035277.1|  [L=129]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-22   80.2   1.8    3.2e-22   79.5   1.8    1.3  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   1.8   1.8e-26   3.2e-22       4     140 ..       2     128 ..       1     129 [] 0.93

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 1.8e-26
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       +Il ++Dgse+s +A+e+A+e+a +++a+l+++h++d++++++   + ++    e  +  +e e+           +
  gi|313125013|ref|YP_004035277.1|   2 KILAPIDGSECSIRAAEFAVEFAVRFEADLHVVHFSDAETDATDIVLGRARDIIEGTDLSTEPEL----------SI 68 
                                       9***********************************************************98764..........57 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       ++  vv +++++eeil +++e+d d +V+G++g ++++r++lGS +e v+rh ++  +++
  gi|313125013|ref|YP_004035277.1|  69 IELDVVPGKQVGEEILNLVDERDFDHVVMGHHGDGAIERAILGSAAETVVRHESVAATII 128
                                       7777788999******************************************77766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 782.55
//
Query:       gi|313125014|ref|YP_004035278.1|  [L=223]
Description: hypothetical protein Hbor_02290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-14   54.3   0.6    1.5e-14   53.8   0.6    1.2  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
    0.00066   19.7   2.8     0.0012   18.8   2.8    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.029   14.7   1.4        1.1    9.6   1.4    2.5  1  GFA             Glutathione-dependent formaldehyde-activating
      0.038   13.7   1.3      0.077   12.7   1.3    1.5  1  A2L_zn_ribbon   A2L zinc ribbon domain
       0.04   14.7   1.5      0.075   13.8   1.5    1.4  1  zinc_ribbon_15  zinc-ribbon family
      0.048   13.7   0.9      0.095   12.7   0.9    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.064   13.2   1.3       0.12   12.4   1.3    1.4  1  zinc-ribbons_6  zinc-ribbons
      0.079   13.0   1.3       0.17   11.9   1.3    1.6  1  Zn_Tnp_IS91     Transposase zinc-binding domain
       0.62    9.6   5.0        2.6    7.6   5.0    2.0  1  zf-ribbon_3     zinc-ribbon domain
       0.67    9.9   3.5       0.84    9.6   0.2    2.2  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
        1.8    8.4   5.6        5.9    6.7   5.5    1.8  2  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.6   9.2e-18   1.5e-14       2      40 .]      29      65 ..      28      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 9.2e-18
                     Auto_anti-p27  2 kmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                      +m+elLl+G+tM +++C +Cg+P++r+  +g  +C++C+
  gi|313125014|ref|YP_004035278.1| 29 RMSELLLQGATMSNKHCNECGTPIFRY--QGAEFCPTCQ 65
                                      8*************************5..6788*****6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.8   7.6e-07    0.0012      11      39 ..      41      70 ..      36      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.6e-07
                               DZR 11 darfCseCgtklkavaaedrCpsCgek.vd 39
                                      +++ C+eCgt++ +++ +++Cp C+ k ++
  gi|313125014|ref|YP_004035278.1| 41 SNKHCNECGTPIFRYQGAEFCPTCQDKqAK 70
                                      6899*********9***********98444 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.4    0.0007       1.1      43      62 ..      36      55 ..      17      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0007
                               GFA 43 sgnkvtrsfCpeCgsplyse 62
                                      +g +++++ C+eCg+p++  
  gi|313125014|ref|YP_004035278.1| 36 QGATMSNKHCNECGTPIFRY 55
                                      7899*************964 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   4.7e-05     0.077       1      28 [.      40      65 ..      40      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                     A2L_zn_ribbon  1 snlkvCsvCggngilnseqgylvCieCg 28
                                      +++k+C  Cg++ i+ + qg ++C+ C+
  gi|313125014|ref|YP_004035278.1| 40 MSNKHCNECGTP-IF-RYQGAEFCPTCQ 65
                                      789********9.89.***********8 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.5   4.6e-05     0.075      48      85 ..      18      64 ..       6      65 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                    zinc_ribbon_15 48 easkelgkeiekkesse.............kkeCknCgkev..eeefkyCpkC 85
                                      e+++e  +e+      +             +k+C++Cg+ +   +  ++Cp C
  gi|313125014|ref|YP_004035278.1| 18 EKDTERRQET------QrmselllqgatmsNKHCNECGTPIfrYQGAEFCPTC 64
                                      3333222222......23344668888888*********99333569****** PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9   5.8e-05     0.095      69     107 ..      41      81 ..       7      85 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-05
                                       -EEEETTTS-EEECHHHHHS-TTTSSS..-EEEEESSSEEE CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsa..dveivsGeellv 107
                                        + +C+eCg+ +   + a+ Cp+C+ +  + +  +Ge  +v
  gi|313125014|ref|YP_004035278.1|  41 SNKHCNECGTPIFRYQGAEFCPTCQDKqaKADAEQGEAANV 81 
                                       3468*****98886654556****98822445566766665 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.3   7.1e-05      0.12      15      39 ..      41      68 ..      19      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.1e-05
                                      SEEE-TTT--...EEEEEEE-SSS-S-- CS
                    zinc-ribbons_6 15 eqyhCeaCqe...dlkkealCpeCeqel 39
                                      ++ hC++C +   +++   +Cp+C+++ 
  gi|313125014|ref|YP_004035278.1| 41 SNKHCNECGTpifRYQGAEFCPTCQDKQ 68
                                      6778888888888888888999998764 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.3   0.00011      0.17      35      74 ..      38      75 ..       4      83 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                       Zn_Tnp_IS91 35 lGfaryeCeeCghekivyfsCksrhCpsCqkkateewlek 74
                                        ++  +C+eCg   + y+  +  +Cp+Cq k+++  +e+
  gi|313125014|ref|YP_004035278.1| 38 ATMSNKHCNECGTPIFRYQ--GAEFCPTCQDKQAKADAEQ 75
                                      3456678****97655555..789********99887765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.0    0.0016       2.6       2      23 ..      42      65 ..      41      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0016
                       zf-ribbon_3  2 tvrCPnCGa.p.lssddnvCpyCG 23
                                       ++C++CG+ +    ++ +Cp C+
  gi|313125014|ref|YP_004035278.1| 42 NKHCNECGTpIfRYQGAEFCPTCQ 65
                                      68*******55556899****997 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3       0.3   4.9e+02       4      11 ..      45      52 ..      43      54 .. 0.92
   2 ?    9.6   0.2   0.00051      0.84      20      29 ..      57      66 ..      56      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.3
                                      -TTT--BB CS
                      zf-FPG_IleRS  4 CpRCwryi 11
                                      C  C+++i
  gi|313125014|ref|YP_004035278.1| 45 CNECGTPI 52
                                      999***98 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00051
                                      EEEE-TTTT. CS
                      zf-FPG_IleRS 20 styfCprCqk 29
                                      + +fCp+Cq+
  gi|313125014|ref|YP_004035278.1| 57 GAEFCPTCQD 66
                                      579******6 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.5    0.0045       7.4      13      23 .]      42      52 ..      41      53 .. 0.79
   2 ?    6.7   5.5    0.0036       5.9       2      19 ..      45      64 ..      44      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0045
                     zinc_ribbon_2 13 akFCpyCGtpl 23
                                      +k C +CGtp+
  gi|313125014|ref|YP_004035278.1| 42 NKHCNECGTPI 52
                                      57799999985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0036
                     zinc_ribbon_2  2 CpnCGael.q.dnakFCpyC 19
                                      C +CG+++    +a FCp C
  gi|313125014|ref|YP_004035278.1| 45 CNECGTPIfRyQGAEFCPTC 64
                                      *********98*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1761  (0.0982208); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 1318.65
//
Query:       gi|313125015|ref|YP_004035279.1|  [L=304]
Description: malate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-39  133.5   0.3    8.2e-39  132.9   0.3    1.3  1  Ldh_1_N   lactate/malate dehydrogenase, NAD binding domain
    6.8e-29  100.9   0.0    1.3e-28  100.1   0.0    1.5  2  Ldh_1_C   lactate/malate dehydrogenase, alpha/beta C-terminal


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.3   9.1e-43   8.2e-39       1     141 []       2     143 ..       2     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 9.1e-43
                                       EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHH..HHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEEE CS
                           Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLlDiake..kleGvaldlshistflsvkvkvsekeeealkdadvvvi 75 
                                       +kv+vvGaaG++G++  ++la ++++del+++Di+++  k+ G+a+d++h+ ++  ++++v+++ +e+++++dvvvi
  gi|313125015|ref|YP_004035279.1|   2 TKVSVVGAAGTVGAAAGYNLALRDIVDELVFVDIPDMedKTVGQAADTNHGVAYD-SNTEVYQGGYEDTAGSDVVVI 77 
                                       69********************************98778************9998.99******************* PP

                                       --S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                           Ldh_1_N  76 tagvprkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                       tag+prk+G+tR dL  +Na I+++i++++a+++++ i +  sNPvd+l+++l++a++ ++++vig
  gi|313125015|ref|YP_004035279.1|  78 TAGIPRKEGQTRIDLAGDNAPIMEDIGSSLAEHNDDFISVTTSNPVDLLNRHLYEAGDRDRHKVIG 143
                                       ****************************************************************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.88   7.8e+03      71      94 ..       9      31 ..       5      53 .. 0.69
   2 !  100.1   0.0   1.4e-32   1.3e-28       2     163 ..     147     303 ..     146     304 .] 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.88
                                      HHTTSSSS-HHHHHHHHHHHHHHH CS
                           Ldh_1_C 71 akkGagsatlsmAvAgakfveall 94
                                      a  G   a+++   A+ ++v++l+
  gi|313125015|ref|YP_004035279.1|  9 AA-GTVGAAAGYNLALRDIVDELV 31
                                      44.666666777777777777665 PP

  == domain 2  score: 100.1 bits;  conditional E-value: 1.4e-32
                                       HHHHHHHHHHHHHHHTS-GGGEE--EEBSSSTETTEEHHHHHTTST...TSTHHHHHHHHHHHHHHHHHHHHHHTTS CS
                           Ldh_1_C   2 tLDivRaktflaekagvtprsvkvtViGgHsgvtiipllsqvkell...klsekqleeliervqnggdevvkakkGa 75 
                                       +LD++R++++l+++++v  ++v++t++G+H++ + +p++s v       +++ ++ ee+  + q+ + +v+ +k   
  gi|313125015|ref|YP_004035279.1| 147 RLDSARFRYVLSQRFDVPVKNVEATILGEHGDAQ-VPVFSKVRVDGtdpEFTADEREEILSDLQESAMDVISRK--- 219
                                       7*******************************77.777777665431117889*********************... PP

                                       SSS-HHHHHHHHHHHHHHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHH CS
                           Ldh_1_C  76 gsatlsmAvAgakfveallrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleks 152
                                       g++  + A+ +a +vea++rdt+e+l+ + +ldge+g +d   + f+vPv lg +G+e+v+e   l+d e++ ++++
  gi|313125015|ref|YP_004035279.1| 220 GATQWGPATGVAHMVEAIVRDTGEVLPGSLVLDGEYGYED---TAFGVPVKLGSDGIEEVVE-WDLDDYEQDLMDDA 292
                                       9***************************************...7******************.************** PP

                                       HHHHHHHHHHH CS
                           Ldh_1_C 153 vkeLkkeiekg 163
                                       +++L+++++k+
  gi|313125015|ref|YP_004035279.1| 293 AEKLRDQYDKI 303
                                       *******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1912.58
//
Query:       gi|313125016|ref|YP_004035280.1|  [L=315]
Description: caax amino terminal protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-13   51.5   8.2      1e-13   51.5   8.2    3.1  3  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
      0.067   11.9   0.3       0.11   11.2   0.3    1.2  1  DUF3525   Protein of unknown function (DUF3525)


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   4.2       1.4   1.2e+04       4       4 ..      62      62 ..      16     147 .. 0.58
   2 !   51.5   8.2   1.1e-17     1e-13       5      91 ..     165     269 ..     153     270 .. 0.83
   3 ?   -1.1   0.1      0.27   2.4e+03      57      80 ..     290     314 ..     273     315 .] 0.73

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.4
                                      T CS
                              CPBP  4 l 4 
                                      +
  gi|313125016|ref|YP_004035280.1| 62 S 62
                                      1 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 1.1e-17
                                       HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.......HHHH..............H CS
                              CPBP   5 llvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.......gpsv..............l 60 
                                       l v+ l+  + +++EE+++R++ll++l+  g  + a l+ ++++g++H+p        g  +              +
  gi|313125016|ref|YP_004035280.1| 165 LTVAPLFNAIFAFGEEFGWRAYLLPKLHPLGA-RKAALLVGVVWGVWHWPIlamgynyG--FgytgapwtgflamcV 238
                                       4555667788899*****************54.89***************977766550..155555555666666* PP

                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              CPBP  61 laalaGlvlgylylktgsllaaillHallnl 91 
                                       ++++ G++l++++l+t s+++a++ H+++n+
  gi|313125016|ref|YP_004035280.1| 239 FTVATGVFLAWVTLRTDSVWPAAIGHGAINA 269
                                       ******************************8 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.27
                                       HH.HHHHHHHHHHHHHHHHHTT-HH CS
                              CPBP  57 ps.vllaalaGlvlgylylktgsll 80 
                                       p  v++a+   ++ ++l l++ s++
  gi|313125016|ref|YP_004035280.1| 290 PVgVIAALPWVVLAAWLLLRSDSFA 314
                                       4457888888888899999998876 PP

>> DUF3525  Protein of unknown function (DUF3525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   1.2e-05      0.11     102     158 ..      98     152 ..      89     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.2e-05
                           DUF3525 102 vlgflfayavswavylvlrppqaaatvyqwafperswdksklyqllgfaaggtvpme 158
                                       v g l  ya +w v  vl    + a++y  +fpe+       y +   aaggtvpm+
  gi|313125016|ref|YP_004035280.1|  98 VSGSLRVYAAAWFVPAVLT--LLGAALYFAVFPEQFDPSLSAYAAALQAAGGTVPMD 152
                                       5577889**********97..578889*******97777789999999********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1919.65
//
Query:       gi|313125017|ref|YP_004035281.1|  [L=424]
Description: protein exported by tat pathway [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0024   17.7   6.6     0.0024   17.7   6.6    2.0  2  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   6.6   1.3e-07    0.0024       2      25 ..       6      29 ..       5      30 .. 0.94
   2 ?   -3.9   1.6      0.87   1.6e+04      11      14 ..     127     130 ..     126     132 .. 0.32

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      lSRR++L+g+ Aaa  +al+gc+a
  gi|313125017|ref|YP_004035281.1|  6 LSRRSLLRGGVAAAGITALAGCTA 29
                                      8*********************97 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.87
                        TAT_signal  11 sAAa 14 
                                       +A+a
  gi|313125017|ref|YP_004035281.1| 127 AAVA 130
                                       3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2306.42
//
Query:       gi|313125018|ref|YP_004035282.1|  [L=120]
Description: hypothetical protein Hbor_02330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 702.27
//
Query:       gi|313125019|ref|YP_004035283.1|  [L=435]
Description: hypothetical protein Hbor_02340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-07   31.9  10.3     0.0014   18.8   0.0    4.6  4  NPCBM_assoc     NPCBM-associated, NEW3 domain of alpha-galact
    5.3e-06   26.7   4.4      0.038   14.3   0.1    4.6  3  DUF11           Domain of unknown function DUF11
    6.7e-05   23.1   0.8        1.7    8.8   0.0    3.9  4  FixG_C          IG-like fold at C-terminal of FixG, putative 
    0.00018   21.4   0.0       0.23   11.3   0.0    2.8  2  DUF4832         Domain of unknown function (DUF4832)
    0.00032   21.4   0.3      0.093   13.5   0.0    3.7  4  N_BRCA1_IG      Ig-like domain from next to BRCA1 gene
     0.0027   18.1   0.1        1.6    9.1   0.0    2.7  2  E1_DerP2_DerF2  ML domain
     0.0036   17.1   0.2         12    5.9   0.0    4.0  4  A2M             Alpha-2-macroglobulin family
     0.0037   17.5   0.1        2.8    8.2   0.0    2.8  2  DUF4625         Domain of unknown function (DUF4625)
  ------ inclusion threshold ------
      0.014   15.4   0.1         20    5.3   0.0    4.0  4  DUF916          Bacterial protein of unknown function (DUF916
      0.036   14.3   0.7         23    5.3   0.2    3.3  2  ASH             Abnormal spindle-like microcephaly-assoc'd, A
      0.054   13.3   0.4        0.3   10.9   0.0    2.3  2  DUF824          Salmonella repeat of unknown function (DUF824
      0.081   13.6   4.7        4.2    8.1   0.0    3.8  3  fn3_5           Fn3-like domain
       0.94    8.8   6.1        3.3    7.0   1.6    2.9  4  DUF1616         Protein of unknown function (DUF1616)
        5.2    7.3   7.7         21    5.3   0.0    4.1  4  Cohesin         Cohesin domain


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.6       8.1     1e+04      46      60 ..      26      40 ..      20      48 .. 0.50
   2 !   14.7   0.8   2.2e-05     0.028       2      71 ..      68     140 ..      67     146 .. 0.78
   3 ?   -0.1   0.0       0.9   1.2e+03       1      21 [.     187     207 ..     160     210 .. 0.83
   4 !   18.8   0.0   1.1e-06    0.0014      43      74 ..     237     268 ..     231     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.1
                       NPCBM_assoc 46 slapGetveatvkVt 60
                                      +++ G t+ a ++ t
  gi|313125019|ref|YP_004035283.1| 26 AVDSGNTAAAAAENT 40
                                      455555554444433 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.2e-05
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslP.eGWtvvevspasaa...slapGetveatvkVtppagaaaGdye 71 
                                       +pGet ++t+tv+n+++++++     +++P ++    e++  s++   s+++Get++ tv V +p++ ++ dy+
  gi|313125019|ref|YP_004035283.1|  68 KPGETLEYTVTVKNGEEESVEVNPHLVTTPmSEYP-MEKKWVSIDgpsSIDAGETAKYTVSVEIPEDVETADYR 140
                                       7999********99999888754444555734555.666666666667************************96 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.9
                       NPCBM_assoc   1 vepGetvtltltvtndgtaaa 21 
                                       v++G++ t ++++ n+g++a+
  gi|313125019|ref|YP_004035283.1| 187 VKAGDSFTREVVIENTGDSAV 207
                                       467888888888888887765 PP

  == domain 4  score: 18.8 bits;  conditional E-value: 1.1e-06
                       NPCBM_assoc  43 saaslapGetveatvkVtppagaaaGdyevta 74 
                                       s +++a+Ge++++ v+V+pp++a+ G y+ ++
  gi|313125019|ref|YP_004035283.1| 237 SPSQVAAGEKATVSVTVSPPENADRGRYDTEI 268
                                       5679************************8766 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   2.9e-05     0.038       9      26 ..      66      83 ..      48      98 .. 0.83
   2 ?    2.2   0.0      0.18   2.3e+02       8      22 ..     114     128 ..     104     138 .. 0.87
   3 !    7.7   0.2    0.0034       4.3      61      85 ..     237     262 ..     174     267 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                             DUF11  9 evrpGdtvtytltvtNtg 26
                                      +++pG+t++yt+tv+N  
  gi|313125019|ref|YP_004035283.1| 66 DAKPGETLEYTVTVKNGE 83
                                      799*************65 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                             DUF11   8 sevrpGdtvtytltv 22 
                                       s +++G+t +yt+ v
  gi|313125019|ref|YP_004035283.1| 114 SSIDAGETAKYTVSV 128
                                       57899*******998 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0034
                             DUF11  61 v.gsLeagesatlsftvrvtrtaasg 85 
                                       +  +++age+at+s+tv+++  a++g
  gi|313125019|ref|YP_004035283.1| 237 SpSQVAAGEKATVSVTVSPPENADRG 262
                                       25789*************99998876 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.25   3.2e+02      71     108 ..      67      85 ..      31     103 .. 0.61
   2 !    8.8   0.1    0.0014       1.8      35      99 ..      75     145 ..      70     155 .. 0.65
   3 !    8.8   0.0    0.0014       1.7      67     106 ..     237     276 ..     225     293 .. 0.69
   4 ?   -0.5   0.0       1.1   1.4e+03      82     112 ..     315     347 ..     302     351 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.25
                                       E-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEEEGGGTE CS
                            FixG_C  71 vapgekrkvpvfvrvpaealkkkstpitfkvtdddeke 108
                                        +pge+++++v+v+  +e                   e
  gi|313125019|ref|YP_004035283.1|  67 AKPGETLEYTVTVKNGEE-------------------E 85 
                                       344444444444443333...................2 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0014
                                       EEEEEEE-SSS-EEEEEEEES-S......S-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEE.EEEE CS
                            FixG_C  35 YtlkilNktekprrytlsveglp......glelagraekeitvapgekrkvpvfvrvpaealkkkst.pitf 99 
                                       Yt+++ N +e+  +++  +   p      + ++++  + + ++++ge+ k++v+v++p++ ++++    + f
  gi|313125019|ref|YP_004035283.1|  75 YTVTVKNGEEESVEVNPHLVTTPmseypmEKKWVS-IDGPSSIDAGETAKYTVSVEIPEDVETADYRgRVAF 145
                                       55555555555555555555433333333333323.2478999****************9977766555555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0014
                                       -EEEE-TT-EEEEEEEEEE-GGG-SSSEE.EEEEEEEEGGG CS
                            FixG_C  67 keitvapgekrkvpvfvrvpaealkkkst.pitfkvtddde 106
                                       ++ +va+gek +v v+v+ p++a +     +i++ ++d ++
  gi|313125019|ref|YP_004035283.1| 237 SPSQVAAGEKATVSVTVSPPENADRGRYDtEINLGLKD-PN 276
                                       6789**************99998553333377777763.22 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.1
                                       EEEE-GGG.-SSSEEEEEEEEE.EGGGTEEEEE CS
                            FixG_C  82 fvrvpaea.lkkkstpitfkvt.dddeketver 112
                                       ++++ +e   +  s +++f v+  ++++e+v +
  gi|313125019|ref|YP_004035283.1| 315 SLTLMPERyNADNSDEVSFDVEfVSPDGEVVNA 347
                                       444433330344455999999865676776654 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0036       4.6     158     212 ..     106     160 ..      53     163 .. 0.64
   2 !   11.3   0.0   0.00018      0.23     109     203 ..     178     278 ..     177     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0036
                           DUF4832 158 klkldadprkwlpgttttitiklklpselakGkykvyLnlpdpseglkdrpeysI 212
                                       k ++   p+++  g+t ++t+++++p+++++++y+  ++ +d+  +   rp++ I
  gi|313125019|ref|YP_004035283.1| 106 KWVSIDGPSSIDAGETAKYTVSVEIPEDVETADYRGRVAFTDETVTYPGRPARPI 160
                                       3344455788888999******************999999998888777777776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00018
                           DUF4832 109 lessslskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklk...ldad.prkwlpgttttitiklk 181
                                       l+++ ++ +vkag++++ e+ ++N+G +a+    +v+   r+  g    kl+   +d+d p++++ g++ t++++++
  gi|313125019|ref|YP_004035283.1| 178 LSDTYVNGQVKAGDSFTREVVIENTGDSAVPLSPEVKTERRHCRGHCPNKLNpswIDIDsPSQVAAGEKATVSVTVS 254
                                       6778889999*******************9999999999999999996666566755553788889*********** PP

                           DUF4832 182 lpselakGkyk..vyLnlpdpseg 203
                                        p++   G y+  + L l+dp+++
  gi|313125019|ref|YP_004035283.1| 255 PPENADRGRYDteINLGLKDPNRE 278
                                       ********7751166666776655 PP

>> N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.2   1.5e+03      53      76 ..      63      86 ..      31     112 .. 0.59
   2 ?    1.3   0.0      0.45   5.7e+02      10      75 ..      69     134 ..      65     155 .. 0.56
   3 !   13.5   0.0   7.3e-05     0.093       7      88 ..     186     274 ..     182     290 .. 0.72
   4 ?    1.2   0.0      0.49   6.3e+02      57      94 ..     325     362 ..     291     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                        N_BRCA1_IG 53 svpavapgeevevsvelkaPskpg 76
                                      s+++++pge+ e +v++k  ++++
  gi|313125019|ref|YP_004035283.1| 63 SYRDAKPGETLEYTVTVKNGEEES 86
                                      445566666666666666554444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.45
                        N_BRCA1_IG  10 pgteftktWrlrNtGseaWpagtklvfvgGdkmgs..asaeessvs.vpavapgeevevsvelkaPskp 75 
                                       pg++ + t +++N  +e+ + + +lv++    m++   +++  s+   +++ +ge+++ +v++ +P+  
  gi|313125019|ref|YP_004035283.1|  69 PGETLEYTVTVKNGEEESVEVNPHLVTTP---MSEypMEKKWVSIDgPSSIDAGETAKYTVSVEIPEDV 134
                                       55555555555555444444444444433...3221222223334434568889999999999888654 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 7.3e-05
                        N_BRCA1_IG   7 vvppgteftktWrlrNtGseaWpagtklvfvgGdkmgs.....asaeessvs.vpavapgeevevsvelkaP..skp 75 
                                       +v++g  ft+   ++NtG++a p + ++++   +  g+     ++ +  ++   ++va+ge+++vsv++  P  +  
  gi|313125019|ref|YP_004035283.1| 186 QVKAGDSFTREVVIENTGDSAVPLSPEVKTERRHCRGHcpnklNP-SWIDIDsPSQVAAGEKATVSVTVSPPenADR 261
                                       6899**********************9998885555445655422.2333333677****************54556 PP

                        N_BRCA1_IG  76 gryisywrlated 88 
                                       gry ++  l  +d
  gi|313125019|ref|YP_004035283.1| 262 GRYDTEINLGLKD 274
                                       7787777666555 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.49
                        N_BRCA1_IG  57 vapgeevevsvelkaPskpgryisywrlatedgseFGd 94 
                                       + + +ev++ ve+++P+ +    +  r++++ ++ +Gd
  gi|313125019|ref|YP_004035283.1| 325 ADNSDEVSFDVEFVSPDGEVVNAERVRVTDSGHVDLGD 362
                                       55678899999999999888877888877755555766 PP

>> E1_DerP2_DerF2  ML domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0095        12      87     120 ..     115     148 ..      68     151 .. 0.86
   2 !    9.1   0.0    0.0013       1.6       5      55 ..     218     267 ..     214     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0095
                                       SB-TCEEEEEEEEEES-CCCHSCEEEEEEEEEEC CS
                    E1_DerP2_DerF2  87 Pikageyvtytlslplpselpngkyrvelellde 120
                                        i+age+++yt s+++p+ + + +yr ++  +de
  gi|313125019|ref|YP_004035283.1| 115 SIDAGETAKYTVSVEIPEDVETADYRGRVAFTDE 148
                                       6899**************9999999999888876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                                       EESSTTTSSEEEEEEEEEESSECEECTSEEEEEEEEEECSSBBSSEEEEEE CS
                    E1_DerP2_DerF2   5 edCgankddavtvksveisppcplkrgqnltisadgstsdeissglkaeve 55 
                                       + C+ +  + +++++++i++p ++++g+++t+s+++  ++e+++  + + e
  gi|313125019|ref|YP_004035283.1| 218 RHCRGHCPNKLNPSWIDIDSPSQVAAGEKATVSVTV-SPPENADRGRYDTE 267
                                       567555667799*******888**************.66666665555555 PP

>> A2M  Alpha-2-macroglobulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.025        32      64      89 ..      65      90 ..      31      93 .. 0.71
   2 ?   -0.1   0.0      0.66   8.4e+02      58      78 ..     108     128 ..     101     134 .. 0.85
   3 ?    0.3   0.0      0.48   6.2e+02      65      87 ..     186     208 ..     181     213 .. 0.88
   4 !    5.9   0.0     0.009        12      55      79 ..     230     254 ..     227     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                                      SEEETTSEEEEEEEEEE-SSS-EEEE CS
                               A2M 64 ysvrrgeqveikavvfNyldkeikvr 89
                                      + ++ ge++e +++v N +++ ++v+
  gi|313125019|ref|YP_004035283.1| 65 RDAKPGETLEYTVTVKNGEEESVEVN 90
                                      45899***************999986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.66
                                       EEEE--SEEETTSEEEEEEEE CS
                               A2M  58 vdlnlPysvrrgeqveikavv 78 
                                       v++  P+s+  ge+ + +++v
  gi|313125019|ref|YP_004035283.1| 108 VSIDGPSSIDAGETAKYTVSV 128
                                       788999999999999988876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.48
                                       EEETTSEEEEEEEEEE-SSS-EE CS
                               A2M  65 svrrgeqveikavvfNyldkeik 87 
                                       +v+ g++++ ++v+ N  d+++ 
  gi|313125019|ref|YP_004035283.1| 186 QVKAGDSFTREVVIENTGDSAVP 208
                                       5899************9998765 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.009
                                       SEEEEEE--SEEETTSEEEEEEEEE CS
                               A2M  55 pffvdlnlPysvrrgeqveikavvf 79 
                                       p  +d+  P++v+ ge+ +++++v+
  gi|313125019|ref|YP_004035283.1| 230 PSWIDIDSPSQVAAGEKATVSVTVS 254
                                       667999*****************97 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1     0.008        10      89     119 ..     119     149 ..      71     152 .. 0.78
   2 !    8.2   0.0    0.0022       2.8      87     115 ..     242     270 ..     166     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.008
                           DUF4625  89 kkeyelheeieiPadaeaGdYhlvirvtDas 119
                                        ++++ ++++eiP+d+e+ dY   +  tD++
  gi|313125019|ref|YP_004035283.1| 119 GETAKYTVSVEIPEDVETADYRGRVAFTDET 149
                                       35788999**************999999985 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0022
                           DUF4625  87 gskkeyelheeieiPadaeaGdYhlvirv 115
                                       +  +++++ +++++P++a++G Y+  i +
  gi|313125019|ref|YP_004035283.1| 242 AAGEKATVSVTVSPPENADRGRYDTEINL 270
                                       3345889999**************99875 PP

>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.016        20      23      48 ..      67      92 ..      58     100 .. 0.86
   2 ?    1.7   0.0      0.21   2.6e+02      80     107 ..     107     134 ..      95     146 .. 0.80
   3 ?   -0.3   0.0      0.84   1.1e+03      16      49 ..     180     213 ..     176     216 .. 0.82
   4 ?    2.1   0.0      0.15   1.9e+02      84     110 ..     236     262 ..     230     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                            DUF916 23 vkpgqeqelevkikNssdkeitveit 48
                                      +kpg++ e +v++kN ++++++v+  
  gi|313125019|ref|YP_004035283.1| 67 AKPGETLEYTVTVKNGEEESVEVNPH 92
                                      79******************998765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.21
                            DUF916  80 lvkipkeitlpakesktvklkikmPkee 107
                                        v+i+   ++ a+e+ + ++++++P++ 
  gi|313125019|ref|YP_004035283.1| 107 WVSIDGPSSIDAGETAKYTVSVEIPEDV 134
                                       56677777899**************975 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.84
                            DUF916  16 ksYFdLkvkpgqeqelevkikNssdkeitveitv 49 
                                       ++Y + +vk g + + ev i+N+ d+++ ++ +v
  gi|313125019|ref|YP_004035283.1| 180 DTYVNGQVKAGDSFTREVVIENTGDSAVPLSPEV 213
                                       57888899999999*********99988776655 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.15
                            DUF916  84 pkeitlpakesktvklkikmPkeefdG 110
                                       ++  +++a+e+ tv+++++ P+++ +G
  gi|313125019|ref|YP_004035283.1| 236 DSPSQVAAGEKATVSVTVSPPENADRG 262
                                       5566899*************9998777 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.021        27      18      64 ..      66     112 ..      60     128 .. 0.83
   2 ?    5.3   0.2     0.018        23      17      77 ..     185     256 ..     183     263 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.021
                                       ----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXX CS
                               ASH  18 dvkvGssaerlLtveNpseepaevkvskvpaaekgfsveetelevqp 64 
                                       d k G++ e ++tv+N+ ee++ev+   v  +  ++ +e++++ +++
  gi|313125019|ref|YP_004035283.1|  66 DAKPGETLEYTVTVKNGEEESVEVNPHLVTTPMSEYPMEKKWVSIDG 112
                                       667899999***************99988888888877777766655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
                                       -----EEEEEEE-EEESS-SS--....EEEEEE..EE--XXXXXXXXXX......XXXXXXXXXXXXXXXXXX CS
                               ASH  17 gdvkvGssaerlLtveNpseepa....evkvsk..vpaaekgfsveete......levqpgesvtltvtwtPt 77 
                                       g+vk G s +r++++eN+++ ++    evk+++  +    +  ++++++       +v++ge+ t++vt +P 
  gi|313125019|ref|YP_004035283.1| 185 GQVKAGDSFTREVVIENTGDSAVplspEVKTERrhCR-GHCPNKLNPSWididspSQVAAGEKATVSVTVSPP 256
                                       6789999999999999999876311122222211111.22223333333334447778888888888887775 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023       0.3       8      25 ..      66      83 ..      63      89 .. 0.89
   2 ?   -1.7   0.1       2.1   2.6e+03       8      21 ..     240     253 ..     238     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                            DUF824  8 kaKkGEsipltitvkDas 25
                                      +aK GE++  t+tvk+  
  gi|313125019|ref|YP_004035283.1| 66 DAKPGETLEYTVTVKNGE 83
                                      69**************86 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                            DUF824   8 kaKkGEsipltitv 21 
                                        +  GE  ++ +tv
  gi|313125019|ref|YP_004035283.1| 240 QVAAGEKATVSVTV 253
                                       58899999999998 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.7      0.31     4e+02      23      80 ..      44      91 ..      26     100 .. 0.52
   2 ?    2.4   0.0      0.19   2.4e+02      68     103 ..     116     148 ..     103     154 .. 0.85
   3 ?    8.1   0.0    0.0033       4.2       8      88 ..     191     261 ..     185     281 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.31
                             fn3_5 23 altykvsandvlTdladkeegklilkaaspeike.....aaltfetskvtvpAnssktvtvtl 80
                                      a++ k +a          +++ l+ +a+     +     +  ++ + +vtv+ ++++ v+v+ 
  gi|313125019|ref|YP_004035283.1| 44 AAQEKTKA----------NYTRLFIDAE-----DsyrdaKPGETLEYTVTVKNGEEESVEVNP 91
                                      22222222..........2222222222.....134444566666777777777777777764 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.19
                             fn3_5  68 vpAnssktvtvtldlpsdakkkngyfveGfvtlkds 103
                                       + A+++++ tv + +p+d++      + G v ++d+
  gi|313125019|ref|YP_004035283.1| 116 IDAGETAKYTVSVEIPEDVET---ADYRGRVAFTDE 148
                                       89***************8887...667788888776 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0033
                             fn3_5   8 dkfsftltlkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvtldlps 84 
                                       d+f+ ++ ++Nt++ a+ ++ +   v+T+++    g      ++++  ++ ++ ++++ +v A++++tv+vt+++p+
  gi|313125019|ref|YP_004035283.1| 191 DSFTREVVIENTGDSAVPLSPE---VKTERRH-CRGHCP---NKLN--PSWIDIDSPS-QVAAGEKATVSVTVSPPE 257
                                       5666666666666666654443...3355542.222221...2211..1355666655.7999************99 PP

                             fn3_5  85 dakk 88 
                                       +a++
  gi|313125019|ref|YP_004035283.1| 258 NADR 261
                                       8876 PP

>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.6    0.0025       3.3     157     260 ..      41     133 ..       5     165 .. 0.74
   2 ?    0.7   0.0      0.22   2.8e+02     187     263 ..     237     261 ..     181     266 .. 0.56
   3 ?    2.6   0.0     0.059        75     186     223 ..     236     275 ..     229     332 .. 0.66
   4 ?   -1.3   0.1      0.86   1.1e+03     170     204 ..     303     336 ..     289     430 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                           DUF1616 157 gyavvaPkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqevtdeeevevler 233
                                         a+++ k++ ++T l +  ed+         ++ + ge+ e +v+++N E+e+v+ +  +++      +e  ++++
  gi|313125019|ref|YP_004035283.1|  41 SAAAAQEKTKANYTRLFIDAEDS--------YRDAKPGETLEYTVTVKNGEEESVEVNPHLVTTP---MSEYPMEKK 106
                                       44455556677777777777766........6788999999************998666555554...223333455 PP

                           DUF1616 234 teldrrevtladnetweqelevepeat 260
                                        +    + +++++et + +++ve++++
  gi|313125019|ref|YP_004035283.1| 107 WVSIDGPSSIDAGETAKYTVSVEIPED 133
                                       556667778888888888888887765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.22
                           DUF1616 187 ypteltagesqevivgieNhEheevnYtvvvllqevtdeeevevlerteldrrevtladnetweqelevepeatgen 263
                                                                                            + ++a++e+ + +++v+p+++ ++
  gi|313125019|ref|YP_004035283.1| 237 S----------------------------------------------------PSQVAAGEKATVSVTVSPPENADR 261
                                       3....................................................345666666666666666665555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.059
                           DUF1616 186 nypteltagesqevivgieNhEheev.nYtvvvllqev.t 223
                                       + p++++age+ +v v+++  E+ ++  Y +++ l  +  
  gi|313125019|ref|YP_004035283.1| 236 DSPSQVAAGEKATVSVTVSPPENADRgRYDTEINLGLKdP 275
                                       6799999999999999999999876537888888865442 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.86
                           DUF1616 170 Telyllgedgdelvaenypteltagesqevivgie 204
                                       T +++  e++ +l  + +p++++a++s ev   +e
  gi|313125019|ref|YP_004035283.1| 303 TSFQVSDETD-NLSLTLMPERYNADNSDEVSFDVE 336
                                       6666666665.666666677777777776655443 PP

>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.017        21       9      27 ..      66      84 ..      60      89 .. 0.87
   2 ?    0.5   0.0       0.5   6.4e+02       3      25 ..     108     131 ..     107     140 .. 0.80
   3 ?   -1.4   0.1         2   2.6e+03      10      26 ..     187     203 ..     181     207 .. 0.79
   4 ?    2.6   0.3      0.12   1.5e+02       4      27 ..     234     258 ..     232     356 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                                      EE-TTSEEEEEEEEESECT CS
                           Cohesin  9 sakvGdtvtvpvtvsnvsk 27
                                      +ak+G+t++++vtv+n  +
  gi|313125019|ref|YP_004035283.1| 66 DAKPGETLEYTVTVKNGEE 84
                                      679************9765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.5
                                       EEESEEEE.-TTSEEEEEEEEESE CS
                           Cohesin   3 vkidkvsa.kvGdtvtvpvtvsnv 25 
                                       v+id+ s+  +G+t +++v+v+  
  gi|313125019|ref|YP_004035283.1| 108 VSIDGPSSiDAGETAKYTVSVEIP 131
                                       7899***************99754 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2
                                       E-TTSEEEEEEEEESEC CS
                           Cohesin  10 akvGdtvtvpvtvsnvs 26 
                                       +k+Gd++t  v ++n  
  gi|313125019|ref|YP_004035283.1| 187 VKAGDSFTREVVIENTG 203
                                       499*****999999965 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.12
                                       EESEEEE.-TTSEEEEEEEEESECT CS
                           Cohesin   4 kidkvsa.kvGdtvtvpvtvsnvsk 27 
                                        id+ s  ++G++ tv vtvs   +
  gi|313125019|ref|YP_004035283.1| 234 DIDSPSQvAAGEKATVSVTVSPPEN 258
                                       6889999999********9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 2420.88
//
Query:       gi|313125020|ref|YP_004035284.1|  [L=581]
Description: excinuclease ABC subunit c [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-40  138.8   0.0    2.4e-40  138.0   0.0    1.4  1  UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
    3.1e-12   46.9   0.0    7.6e-12   45.6   0.0    1.7  1  HHH_5       Helix-hairpin-helix domain
    6.8e-11   41.5   0.7      3e-06   26.8   0.1    3.0  3  HHH         Helix-hairpin-helix motif
    8.2e-10   38.6   0.0    2.6e-09   37.0   0.0    1.8  2  HHH_2       Helix-hairpin-helix motif
    4.5e-08   32.6   2.0    1.3e-07   31.1   2.0    1.8  1  UVR         UvrB/uvrC motif
    8.2e-06   26.3   0.1     0.0082   16.7   0.0    2.8  3  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
    7.8e-05   22.8   0.0        0.1   13.0   0.0    2.6  2  IMS_HHH     IMS family HHH motif
    9.4e-05   22.6   0.0     0.0002   21.5   0.0    1.6  1  GIY-YIG     GIY-YIG catalytic domain
     0.0021   18.4   0.3        1.3    9.4   0.0    3.3  3  HHH_8       Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.15   11.9   0.5       0.65    9.9   0.5    2.1  1  PELOTA_1    PELOTA RNA binding domain


Domain annotation for each model (and alignments):
>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.0   0.0   1.3e-43   2.4e-40       2     154 .]     368     513 ..     367     513 .. 0.91

  Alignments for each domain:
  == domain 1  score: 138.0 bits;  conditional E-value: 1.3e-43
                                       HHTT-SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS--HHHHHHHHHHHHHTTS....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                        UvrC_HhH_N   2 ellglkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvkegdDyaamrevlrRrfkrllke..fs 76 
                                       e+l+++ +p+rie++D+Sh qg+++vgs v+f dg+++k +yR+ k+   +++dDy+ mr ++r r +r+ +   ++
  gi|313125020|ref|YP_004035284.1| 368 ERLDIP-RPSRIEGFDVSHAQGKAVVGSDVCFVDGSAEKADYRRKKLP--ERNDDYENMRALIRWRAERAVEGrdDR 441
                                       678888.5****************************************..679*****************9874466 PP

                                       ---SEEEESSSHHHHHHHHHHHHHTT----EEEEES............SSSEEEE--TT-HHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N  77 klPdLiliDGGkgqlnaakevleelglkipvvglaKdkkrktrakaeereeevlelkkssealkllqrirdeaHrfA 153
                                       + PdL+liDGG gql aa+++l+e+g+++p ++laKd++         + + v++ +++ + l++lqr+rdeaHrfA
  gi|313125020|ref|YP_004035284.1| 442 PDPDLLLIDGGDGQLGAARDALTEVGWDVPAIALAKDEEL------VITPDGVYDWPSDAPHLHVLQRVRDEAHRFA 512
                                       778*********************************6543......2233457************************ PP

                                       H CS
                                       x RF
                        UvrC_HhH_N 154 I 154
                                       +
  gi|313125020|ref|YP_004035284.1| 513 V 513
                                       7 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   4.3e-15   7.6e-12       4      55 ..     527     577 ..     524     578 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 4.3e-15
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                                       L +v+G+G+kt +all+  ++sve + aa++++L+++pG+G+ktA  +++ l
  gi|313125020|ref|YP_004035284.1| 527 LDDVPGVGEKTRRALLRR-FGSVENVRAATTADLTDVPGVGEKTATELKQRL 577
                                       789***************.**************************8887765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.3   5.9e+03      12      19 ..     325     332 ..     321     333 .. 0.85
   2 !   11.8   0.0   9.9e-05      0.18      13      28 ..     527     542 ..     526     543 .. 0.89
   3 !   26.8   0.1   1.7e-09     3e-06       1      25 [.     547     571 ..     547     575 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.3
                                       HHHTSTT- CS
                               HHH  12 eLlalPGV 19 
                                       e+l ++GV
  gi|313125020|ref|YP_004035284.1| 325 EWLNVEGV 332
                                       8999***9 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.9e-05
                                       HHTSTT-SHHHHHHHH CS
                               HHH  13 LlalPGVGpktAeaIl 28 
                                       L ++PGVG+kt +a l
  gi|313125020|ref|YP_004035284.1| 527 LDDVPGVGEKTRRALL 542
                                       678*********9987 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 1.7e-09
                                       SHHHHHTSSHHHHHTSTT-SHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAe 25 
                                       s+e++++a+ ++L+++PGVG+ktA 
  gi|313125020|ref|YP_004035284.1| 547 SVENVRAATTADLTDVPGVGEKTAT 571
                                       689*********************6 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.9   1.2e+04      49      58 ..     187     196 ..     187     197 .. 0.82
   2 !   37.0   0.0   1.4e-12   2.6e-09       8      53 ..     530     575 ..     529     578 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.9
                             HHH_2  49 qsivefFene 58 
                                       +siv+fFe e
  gi|313125020|ref|YP_004035284.1| 187 ESIVRFFEGE 196
                                       69*****966 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 1.4e-12
                             HHH_2   8 IrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsive 53 
                                       ++ VGekt ++L +rF+s+++ ++a++ +L+ v+++Ge++A++ ++
  gi|313125020|ref|YP_004035284.1| 530 VPGVGEKTRRALLRRFGSVENVRAATTADLTDVPGVGEKTATELKQ 575
                                       589**************************************98765 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   2.0   7.5e-11   1.3e-07       6      34 ..     203     231 ..     199     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 7.5e-11
                               UVR   6 eLeeemeeAaenedFEkAAklRDqinalk 34 
                                        L++ meeAa++e+FE+AA  RD+++a++
  gi|313125020|ref|YP_004035284.1| 203 PLRRTMEEAAQAENFERAANARDKLEAVE 231
                                       59************************987 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0        10   1.8e+04      55      75 ..     408     428 ..     402     434 .. 0.73
   2 !   16.7   0.0   4.6e-06    0.0082      21      48 ..     528     555 ..     515     561 .. 0.84
   3 !    7.1   0.0    0.0045       8.1      20      34 ..     559     573 ..     554     579 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 10
                        5_3_exonuc  55 klkekLeenkeearlskkLat 75 
                                        +++kL e +++ + ++ L++
  gi|313125020|ref|YP_004035284.1| 408 YRRKKLPERNDDYENMRALIR 428
                                       467888888888887777765 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.6e-06
                        5_3_exonuc  21 pGvpgiGektAakLlkeygsleeilenl 48 
                                         vpg+Gekt  +Ll+++gs+e++ +++
  gi|313125020|ref|YP_004035284.1| 528 DDVPGVGEKTRRALLRRFGSVENVRAAT 555
                                       679*********************9865 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0045
                        5_3_exonuc  20 ipGvpgiGektAakL 34 
                                       +  vpg+GektA++L
  gi|313125020|ref|YP_004035284.1| 559 LTDVPGVGEKTATEL 573
                                       567**********98 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0045       8.1      13      31 ..     527     546 ..     526     546 .. 0.86
   2 !   13.0   0.0   5.6e-05       0.1      12      29 ..     558     575 ..     555     577 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0045
                           IMS_HHH  13 itkipGiGgklgek.LeklG 31 
                                       + ++pG+G k+    L+ +G
  gi|313125020|ref|YP_004035284.1| 527 LDDVPGVGEKTRRAlLRRFG 546
                                       689********999887766 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.6e-05
                           IMS_HHH  12 pitkipGiGgklgekLek 29 
                                       ++t++pG+G k++ +L++
  gi|313125020|ref|YP_004035284.1| 558 DLTDVPGVGEKTATELKQ 575
                                       79*************986 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.1e-07    0.0002       3      78 .]      18      89 ..      16      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                                      EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-HS.STEEEEEEEE----HHHHHHHHHHHHHHTTSSSS CS
                           GIY-YIG  3 gvYiirskenkliYvGstknlekRlkqHnagkkakytrkkgkkpfeliileifptksealelEkklikkyksnkyn 78
                                      gvY++ + +   +YvG++ +++ R +++   ++ ++++   ++    i + + +t+++al lE+ l k++++ +yn
  gi|313125020|ref|YP_004035284.1| 18 GVYQFLDGDTV-LYVGKAVDIRARVRSYADPRGERIRQM--VERAGAIDFAVTDTETQALLLEANLVKRHQP-RYN 89
                                      89999999666.5**********************9986..8999999999*********************.998 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.69   1.2e+03      11      38 ..     200     227 ..     199     238 .. 0.81
   2 ?    4.4   0.0     0.028        50      27      61 ..     508     539 ..     502     543 .. 0.78
   3 !    9.4   0.0   0.00074       1.3      41      65 ..     554     575 ..     546     578 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.69
                                       HHHHHHHCT--CCCHHHHHHHHCCCCC- CS
                             HHH_8  11 ladllelkgedpfrvraYrrAaraieal 38 
                                       lad l ++ e++  + ++ rAa+a ++l
  gi|313125020|ref|YP_004035284.1| 200 LADPLRRTMEEAAQAENFERAANARDKL 227
                                       5677788889999999999999986655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.028
                                       HHHHHHCCCCC-SS-HHHHTTHCTTSTT--HHHHH CS
                             HHH_8  27 aYrrAaraiealpeeitsleeeltklpgiGkkiaa 61 
                                       a+r A++    l +++++    l ++pg+G+k+++
  gi|313125020|ref|YP_004035284.1| 508 AHRFAVQYHQTLRDDVRT---VLDDVPGVGEKTRR 539
                                       666677777778888888...4789*******976 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00074
                                       -HHHHTTHCTTSTT--HHHHHHHHH CS
                             HHH_8  41 eitsleeeltklpgiGkkiaakiee 65 
                                       ++t    +lt++pg+G+k+a ++++
  gi|313125020|ref|YP_004035284.1| 554 ATTA---DLTDVPGVGEKTATELKQ 575
                                       3333...6************98876 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5   0.00036      0.65      24      52 ..     531     560 ..     520     576 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00036
                          PELOTA_1  24 PgigEaT.RvlLRRvPekvlvrdeeepdla 52 
                                       Pg+gE T R+lLRR      vr+++++dl+
  gi|313125020|ref|YP_004035284.1| 531 PGVGEKTrRALLRRFGSVENVRAATTADLT 560
                                       *****99459****9887777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 3333.00
//
Query:       gi|313125021|ref|YP_004035285.1|  [L=156]
Description: hypothetical protein Hbor_02360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.9   2.5        3.8    7.7   1.2    2.3  2  HTH_20    Helix-turn-helix domain
       0.19   10.1   0.0       0.19   10.0   0.0    1.1  1  DUF505    Protein of unknown function (DUF505)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.2   0.00042       3.8       4      40 ..      10      47 ..       7      54 .. 0.86
   2 ?    6.3   0.0    0.0011        10      43      61 .]      69      87 ..      67      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00042
                                      HHHHS-HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHH CS
                            HTH_20  4 aeALahPvRrrilraL.araegltaselaerldlsknt 40
                                       e+L+++ Rr++l  L + +++l   ela+r+ ++++ 
  gi|313125021|ref|YP_004035285.1| 10 YELLSSERRRDVLITLtSAERPLARDELARRIVVRRQR 47
                                      589999**********99*************9766665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0011
                                      HHHHHHHHCTTEEEECTEE CS
                            HTH_20 43 yHLrvLeeagLvevvregr 61
                                       HL +Le  gL+++++ gr
  gi|313125021|ref|YP_004035285.1| 69 VHLPKLENGGLIDQTKDGR 87
                                      59*************9997 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   2.1e-05      0.19     504     542 ..      70     108 ..       9     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 2.1e-05
                            DUF505 504 aleklearglvevlpdgnvvlTeaGelikrAlsgvpegl 542
                                        l kle  gl++  +dg + +T +G+ ++rA  + +++l
  gi|313125021|ref|YP_004035285.1|  70 HLPKLENGGLIDQTKDGRYDVTLLGQDVERAARAFKKAL 108
                                       4789***************************98887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 883.90
//
Query:       gi|313125022|ref|YP_004035286.1|  [L=96]
Description: hypothetical protein Hbor_02370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 632.41
//
Query:       gi|313125023|ref|YP_004035287.1|  [L=134]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-37  127.1   0.0    4.3e-37  126.9   0.0    1.0  1  Y1_Tnp      Transposase IS200 like
  ------ inclusion threshold ------
      0.059   13.3   0.0      0.087   12.8   0.0    1.4  1  IQ_SEC7_PH  PH domain


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   0.0   4.8e-41   4.3e-37       2     121 .]      13     132 ..      12     132 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 4.8e-41
                            Y1_Tnp   2 snlkyhivlvtkyRrkvltgeveerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassrl 78 
                                       ++l+yh++l+tkyRr vlt+e  ++++e+i+++ ++++v+++++++++DHvH+l++++p++++ k++++ kga++r+
  gi|313125023|ref|YP_004035287.1|  13 YSLHYHLILTTKYRRGVLTEERTQFIHEVISGFTDNYGVELTNFDGEDDHVHILFRAKPTTDLVKFINTAKGATARR 89 
                                       789************************************************************************** PP

                            Y1_Tnp  79 inkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIenq 121
                                       i++e+++  k+ l++ s+W+++Y++ ++g++sl+++k+Y+e+q
  gi|313125023|ref|YP_004035287.1|  90 IRNEYADELKTELWGDSFWNDSYCLISTGQVSLDVLKQYVEDQ 132
                                       *****************************************98 PP

>> IQ_SEC7_PH  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.7e-06     0.087      79     117 ..      46      83 ..      10      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-06
                        IQ_SEC7_PH  79 yypygielvsavpgaeskvlitfnakneedrkkfvedlk 117
                                         +yg+el++ ++g++++v i f ak ++d  kf++  k
  gi|313125023|ref|YP_004035287.1|  46 TDNYGVELTN-FDGEDDHVHILFRAKPTTDLVKFINTAK 83 
                                       5579****76.89*********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 874.70
//
Query:       gi|313125024|ref|YP_004035288.1|  [L=413]
Description: transposase, is605 orfb family, central region [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-23   80.9   0.1    1.8e-22   79.8   0.1    1.6  1  OrfB_IS605      Probable transposase
    8.5e-21   73.7   0.2    8.5e-21   73.7   0.2    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.7e-07   29.2   1.1    9.2e-07   28.3   1.1    1.5  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.085   11.9   0.1       0.15   11.1   0.1    1.4  1  Clusterin       Clusterin
       0.11   12.7   0.1       0.28   11.4   0.1    1.7  1  Clr5            Clr5 domain
       0.19   11.8   1.3       0.46   10.5   1.3    1.7  1  DZR             Double zinc ribbon
        3.4    7.9   9.7        1.4    9.1   0.9    2.9  3  Zn-ribbon_8     Zinc ribbon domain
          9    6.5   9.2         11    6.2   2.6    3.2  3  Ribosomal_L37e  Ribosomal protein L37e


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.1   8.2e-26   1.8e-22       4     117 ..     174     283 ..     156     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 8.2e-26
                        OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarl 80 
                                       ++ e+++p+++++k +giD+Gi + a   ++        +  l  +  +l++e+++l++k+++s+ny+k++r++a  
  gi|313125024|ref|YP_004035288.1| 174 MDREPPEPPENPEKCVGIDVGILKYAHDTDGA----AVGSLDLSDERDRLEREQRKLSRKQHGSNNYEKQRRRVAEC 246
                                       4556779********************99999....55667999********************************* PP

                        OrfB_IS605  81 hrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       h+ ++r+r+++lhkl+ + +++++ v+ve+Lnv++m+
  gi|313125024|ref|YP_004035288.1| 247 HADLRRKRRDFLHKLSAYYAREYDLVAVEDLNVKGMM 283
                                       ************************************9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3      0.92   2.1e+03      33      50 ..     230     247 ..     229     257 .. 0.74
   2 !   73.7   0.2   3.8e-24   8.5e-21       1      69 []     297     365 ..     297     365 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.92
                    OrfB_Zn_ribbon  33 eCgsknkealsgrtfkCp 50 
                                       ++gs+n+e++ +r+ +C 
  gi|313125024|ref|YP_004035288.1| 230 QHGSNNYEKQRRRVAECH 247
                                       589999997888888886 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 3.8e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +r++   leyk++++G +++ vnp+ T k+C+ Cg   +++l  r++ Cp+CgfeadrD nAa+Nil r
  gi|313125024|ref|YP_004035288.1| 297 WRTFLSLLEYKCEREGTHFVAVNPRGTTKECASCGVSTDKPLWVREHSCPACGFEADRDANAAWNILSR 365
                                       99****************************************************************976 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   1.1   4.1e-10   9.2e-07       1      43 [.       1      42 [.       1      46 [. 0.88

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4.1e-10
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeaye 43
                                      M   aykyrl+P +  +e+l r+ +++R  YN+ L + +e+  
  gi|313125024|ref|YP_004035288.1|  1 M-YYAYKYRLKPSDANREELDRHRDICRQLYNHTLYRLNEYQD 42
                                      5.569******************************98887654 PP

>> Clusterin  Clusterin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   6.6e-05      0.15     297     348 ..      44      95 ..      16     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.6e-05
                         Clusterin 297 sedCpsvaeLheeleealrlaevstqqYdelLqivqehmedtsslleklneq 348
                                       + + ps + L++el +  + ++ +++ Y ++Lq+v e+++d  + l+kl+e+
  gi|313125024|ref|YP_004035288.1|  44 HRELPSMTSLRSELPDLKEWWDDLSDVYSKVLQTVVERLFDNLKGLSKLKEN 95 
                                       45669********************************************986 PP

>> Clr5  Clr5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.28       2      22 ..      16      33 ..      15      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                              Clr5  2 eedWeahkatIrrLYleenrs 22
                                       e++++h++++r+LY +   +
  gi|313125024|ref|YP_004035288.1| 16 REELDRHRDICRQLYNH---T 33
                                      589************33...3 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.3   0.00021      0.46      13      44 ..     325     358 ..     306     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                               DZR  13 rfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + C  Cg + +++    e+ Cp+Cg ++d +a+ 
  gi|313125024|ref|YP_004035288.1| 325 KECASCGVSTDKPLWvrEHSCPACGFEADRDANA 358
                                       579****99875555789*******999998875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.3   5.1e+03      31      38 ..     245     252 ..     244     253 .. 0.87
   2 ?    9.1   0.9   0.00062       1.4       5      35 ..     305     333 ..     303     338 .. 0.80
   3 ?    4.8   3.6     0.013        30       7      38 ..     326     354 ..     326     355 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.3
                       Zn-ribbon_8  31 eCgsevrr 38 
                                       eC++++rr
  gi|313125024|ref|YP_004035288.1| 245 ECHADLRR 252
                                       7***9999 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00062
                       Zn-ribbon_8   5 eYrCeeCghefevlqsisdaplta.CPeCgse 35 
                                       eY+Ce+ g+ f ++ +      t+ C +Cg  
  gi|313125024|ref|YP_004035288.1| 305 EYKCEREGTHFVAVNPRG---TTKeCASCGVS 333
                                       9*****999999998866...4555****964 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.013
                       Zn-ribbon_8   7 rCeeCghefe..vlqsisdapltaCPeCgsevrr 38 
                                       +C +Cg   +   +++     +  CP+Cg e+ r
  gi|313125024|ref|YP_004035288.1| 326 ECASCGVSTDkpLWVR-----EHSCPACGFEADR 354
                                       6999996666654543.....455****977766 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4      0.26   5.9e+02      23      45 ..     232     254 ..     226     259 .. 0.80
   2 ?    2.6   0.3     0.071   1.6e+02      31      40 ..     324     333 ..     307     338 .. 0.83
   3 ?    6.2   2.6    0.0051        11      19      50 ..     327     361 ..     322     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.26
                    Ribosomal_L37e  23 gkrsyhvqkktCascGypsaklr 45 
                                       g++ y  q+++ a+c    +++r
  gi|313125024|ref|YP_004035288.1| 232 GSNNYEKQRRRVAECHADLRRKR 254
                                       8999***********87555555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.071
                    Ribosomal_L37e  31 kktCascGyp 40 
                                       +k+CascG  
  gi|313125024|ref|YP_004035288.1| 324 TKECASCGVS 333
                                       799****964 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0051
                    Ribosomal_L37e  19 CrrCgkrs...yhvqkktCascGypsaklrkynWs 50 
                                       C  Cg ++     v++++C +cG+ + +  +  W+
  gi|313125024|ref|YP_004035288.1| 327 CASCGVSTdkpLWVREHSCPACGFEADRDANAAWN 361
                                       6666643322266899*********9998888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2375.16
//
Query:       gi|313125025|ref|YP_004035289.1|  [L=365]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-29  101.4   0.0    8.7e-29  100.8   0.0    1.3  1  ABC_tran       ABC transporter
    3.1e-11   43.7   0.0      1e-07   32.1   0.0    2.2  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.3e-07   32.2   0.0    2.9e-07   31.1   0.0    1.7  1  DUF4162        Domain of unknown function (DUF4162)
     0.0051   16.6   4.4        1.2    8.8   0.0    2.8  3  AAA_30         AAA domain
  ------ inclusion threshold ------
      0.015   14.8   0.0       0.21   11.1   0.0    2.2  2  AAA_7          P-loop containing dynein motor region
      0.021   15.3   0.1      0.039   14.5   0.1    1.4  1  AAA_23         AAA domain
      0.027   14.4   0.1       0.05   13.5   0.1    1.4  1  RsgA_GTPase    RsgA GTPase
      0.054   13.2   0.0       0.13   12.1   0.0    1.6  1  AAA_29         P-loop containing region of AAA domain
        3.9    7.4   5.3        4.8    7.1   0.1    3.3  5  DAHP_snth_FXD  DAHP synthase ferredoxin-like domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.0   4.4e-32   8.7e-29       2     136 ..      39     198 ..      38     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 4.4e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++sl+++ege+ +++G+nGaGKSt +++l+  ++pteG+i + g d ++ +   +r++ gvlp+   + ++lt re
  gi|313125025|ref|YP_004035289.1|  39 RDLSLTVEEGEVFGFLGPNGAGKSTTINMLLDFVRPTEGTISVLGFDAND-QSVDVRARTGVLPEGFDVYERLTGRE 114
                                       689**********************************************9.88999********************* PP

                                       H..............................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHH CS
                                       x..............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallk 125
                                       +                                +e+++++l+++gl   +d+++      +S+G++qr+ala+al+ 
  gi|313125025|ref|YP_004035289.1| 115 HvefaasskgvemaaaattesegetmeseesVGEEKVDAVLDRVGLAAAADRKA----GGYSKGMRQRLALAMALIG 187
                                       ****************99999988876654444445************999999....******************* PP

                                       TSSEEEEESTT CS
                                       xxxxxxxxxxx RF
                          ABC_tran 126 kpkllllDEpt 136
                                       +p+ll+lDEp+
  gi|313125025|ref|YP_004035289.1| 188 DPDLLILDEPS 198
                                       **********7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00041      0.81       2      19 ..      51      68 ..      50     108 .. 0.80
   2 !   32.1   0.0   5.2e-11     1e-07     235     297 ..     169     228 ..     155     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00041
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       ++ GpNg+GKS+ +  l
  gi|313125025|ref|YP_004035289.1| 51 FGFLGPNGAGKSTTINML 68
                                      5789*********98766 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 5.2e-11
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                          S G+++ lal+ al+ ++   +ll++DEp +gL+P+  ++  +++ e++++g+ v++++H
  gi|313125025|ref|YP_004035289.1| 169 GGYSKGMRQRLALAMALIGDP---DLLILDEPSSGLDPAGAKEMRDIVVEEAERGTTVFFSSH 228
                                       5579**************999...9*************9999999999777777********* PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.5e-10   2.9e-07       5      81 .]     256     342 ..     253     342 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.5e-10
                                       HHHTTS.-SSEEEEE.......-------..---EEEE-TT..S-EEEEE-------------.----EEEEEEEE- CS
                           DUF4162   5 eiKrsy.gknrieve.......adaeelleepgveeveeeg..gelelkledeeaanellkal.tsgveirsFeeee 70 
                                        ++++  +  +++v+        d +++ +++gv++v+ e+  ++l++ +  ++a+ +++++l ++g+ +  Fe +e
  gi|313125025|ref|YP_004035289.1| 256 SLREKSnADSTLNVRvagdvttVDTDAVTALDGVHSVTVEDgdDKLIVSCA-GDAKTAVIAELeSQGLGVADFETRE 331
                                       5555553444444666666666779999999******99884455666666.57*********77************ PP

                                       --HHHHHHHHH CS
                           DUF4162  71 PsLndIFiekv 81 
                                       +sL+d F+ ++
  gi|313125025|ref|YP_004035289.1| 332 ASLEDLFLSYT 342
                                       *******9875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00061       1.2      16      53 ..      46      83 ..      36     102 .. 0.77
   2 !    6.9   1.7    0.0024       4.8      41     121 ..     119     225 ..     111     237 .. 0.83
   3 ?   -1.6   0.0      0.91   1.8e+03      20      39 ..     299     318 ..     285     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00061
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrviglA 53
                                      ++  v    Gp G+GK+t+++ l + ++  +g++ +l 
  gi|313125025|ref|YP_004035289.1| 46 EEGEVFGFLGPNGAGKSTTINMLLDFVRPTEGTISVLG 83
                                      444588889*************9998888866666654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0024
                            AAA_30  41 aweaaggrviglAptgkaAkvLaeelgieastiakllkrlk......................grarlepgtllivD 95 
                                       a+ ++g +++++A t+   ++++ e  +  + ++ +l+r +                      ++a + + +lli D
  gi|313125025|ref|YP_004035289.1| 119 AASSKGVEMAAAATTESEGETMESEESVGEEKVDAVLDRVGlaaaadrkaggyskgmrqrlalAMALIGDPDLLILD 195
                                       4555699****************9999999999999999999999*****************977788888****** PP

                            AAA_30  96 Eagmv....dtkqlaallkaaekagakvil 121
                                       E +      ++k++++++ + +++g++v +
  gi|313125025|ref|YP_004035289.1| 196 EPSSGldpaGAKEMRDIVVEEAERGTTVFF 225
                                       *98755555888888876555555777765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.91
                            AAA_30  20 vavltGpAGtGKttalkalr 39 
                                        ++++  AG  Kt ++++l+
  gi|313125025|ref|YP_004035289.1| 299 DKLIVSCAGDAKTAVIAELE 318
                                       47889999999999999875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.21      27      77 ..      42      92 ..      37      96 .. 0.86
   2 ?    1.1   0.0      0.12   2.5e+02      13      54 ..     277     318 ..     268     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanq 77
                                      +l ++++  + + Gp G GK+++i+ ll+ + +++ ++ ++ f a+ ++ +
  gi|313125025|ref|YP_004035289.1| 42 SLTVEEGEVFGFLGPNGAGKSTTINMLLDFVRPTEGTISVLGFDANDQSVD 92
                                      566778888889*******************99999999999998877755 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                             AAA_7  13 lVptvdtvrysyllelllknkkpvllvGptGtGKtviikdll 54 
                                       +V t   + ++ + +  ++ +   l+v  +G +Kt++i +l 
  gi|313125025|ref|YP_004035289.1| 277 TVDTDAVTALDGVHSVTVEDGDDKLIVSCAGDAKTAVIAELE 318
                                       45555556666678889999999***************9854 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     2e-05     0.039      20      38 ..      49      67 ..      33      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                            AAA_23 20 gltlItGpNGaGKTTildA 38
                                       ++ + GpNGaGK+T ++ 
  gi|313125025|ref|YP_004035289.1| 49 EVFGFLGPNGAGKSTTINM 67
                                      6899***********9986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.5e-05      0.05      91     122 ..      39      71 ..      29      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       ++l+  +++ ++  ++G+ G+GKSt in+ll  
  gi|313125025|ref|YP_004035289.1|  39 RDLSLTVEEgEVFGFLGPNGAGKSTTINMLLDF 71 
                                       56666666668999***************9875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.4e-05      0.13      18      39 ..      44      65 ..      36      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                            AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                      ++++ +++ + Gp+G+GKST +
  gi|313125025|ref|YP_004035289.1| 44 TVEEGEVFGFLGPNGAGKSTTI 65
                                      4554448889**********87 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.6   9.3e+03      14      27 ..       6      19 ..       5      23 .. 0.76
   2 ?   -3.3   0.0       4.1   8.2e+03       9      20 ..     146     157 ..     143     158 .. 0.75
   3 ?   -3.9   0.0       6.4   1.3e+04      12      21 ..     231     240 ..     230     240 .. 0.81
   4 ?    7.1   0.1    0.0024       4.8      41      63 ..     271     293 ..     261     294 .. 0.91
   5 ?    1.7   0.0      0.12   2.3e+02      30      55 ..     294     319 ..     291     327 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.6
                     DAHP_snth_FXD 14 ieevierieelGlk 27
                                      +++v++r+ee G  
  gi|313125025|ref|YP_004035289.1|  6 LDRVTKRFEEGGRV 19
                                      68999999998855 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.1
                     DAHP_snth_FXD   9 ateeqieevier 20 
                                       + ee++++v++r
  gi|313125025|ref|YP_004035289.1| 146 VGEEKVDAVLDR 157
                                       668999999887 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 6.4
                     DAHP_snth_FXD  12 eqieevieri 21 
                                       eq+e+v++r+
  gi|313125025|ref|YP_004035289.1| 231 EQVEAVCDRV 240
                                       7899999885 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0024
                     DAHP_snth_FXD  41 viGdtskldkeqlealpgVekVv 63 
                                       v Gd++ +d++ + al+gV +V 
  gi|313125025|ref|YP_004035289.1| 271 VAGDVTTVDTDAVTALDGVHSVT 293
                                       78******************995 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.12
                     DAHP_snth_FXD  30 vskGeertViGviGdtskldkeqlea 55 
                                       v  G ++ ++ + Gd +   + +le+
  gi|313125025|ref|YP_004035289.1| 294 VEDGDDKLIVSCAGDAKTAVIAELES 319
                                       66788888888888877665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2337.08
//
Query:       gi|313125026|ref|YP_004035290.1|  [L=306]
Description: multi-copper enzyme maturation ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-67  227.4  12.8    2.4e-67  227.3  12.8    1.0  1  ABC2_membrane_2  ABC-2 family transporter protein
    2.9e-11   43.2   9.9    2.9e-11   43.2   9.9    1.6  2  ABC2_membrane    ABC-2 type transporter
    1.2e-08   34.4  14.1    1.2e-08   34.4  14.1    1.9  3  ABC2_membrane_3  ABC-2 family transporter protein
    2.5e-07   30.8   6.7    2.5e-07   30.8   6.7    1.7  2  ABC2_membrane_4  ABC-2 family transporter protein
    6.9e-07   29.0   5.4    6.9e-07   29.0   5.4    2.2  2  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.79    9.6   8.0      0.038   13.9   1.1    2.3  2  YqhR             Conserved membrane protein YqhR


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.3  12.8   7.9e-71   2.4e-67       2     288 .]       5     306 .]       4     306 .] 0.98

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 7.9e-71
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       a+a+kEf d++rsr++++ tv+++l+ v  a+l+++g   +  +k+++++  ++  + + s s +            
  gi|313125026|ref|YP_004035290.1|   5 AVARKEFDDSIRSRWLHGATVFFVLF-VGGAALLAFGLIYPDRFKDASNLFGFFLDLGIFSLSFPG----------- 69 
                                       79************************.*******************************99986666........... PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                        ++a+++++ia+ +++ +i++E+e gT+kl Ls+P+sR+++++gK++g+ a+   ++valla++l+a++ ++a g+ 
  gi|313125026|ref|YP_004035290.1|  70 -LLALILGFIALSTSYGSITEERETGTMKLSLSLPNSRRDLIVGKLLGRGAV---VIVALLAGFLAAFVAMVATGTG 142
                                       .***************************************************...********************** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp...... 226
                                       +++++++ +++++vll++  +f+++gl++S+va ++rea+++ lgl++++ il++ ++ g+ +ll++ a +      
  gi|313125026|ref|YP_004035290.1| 143 ISYGSFVPMIALTVLLAF--AFVSIGLGISAVADTNREATLATLGLYLIFGILWKPIAEGIPKLLNYVAEQagmgal 217
                                       ******************..78******************************************************* PP

                   ABC2_membrane_2 227 .....qeindflsllsptsayntllneilagsdlna......................lgstatnllilllllavll 276
                                             +i +fl++l+p + y+tl ++++ g+++ +                      ++s a++++ill++++v++
  gi|313125026|ref|YP_004035290.1| 218 envtrVKIGLFLKYLNPLRTYETLSAQVYYGAARGRllgattgetlviepvlkqgippYLSGAAMMAILLAWIVVPV 294
                                       ********************************8888***************************************** PP

                   ABC2_membrane_2 277 vlgyvlFkrkDl 288
                                       v+gy++F+++Dl
  gi|313125026|ref|YP_004035290.1| 295 VVGYYVFQKQDL 306
                                       ***********7 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   9.9   9.8e-15   2.9e-11      14     172 ..      18     190 ..       3     207 .. 0.76
   2 ?   -3.8   0.8       2.4   7.1e+03     112     118 ..     285     291 ..     272     301 .. 0.42

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 9.8e-15
                     ABC2_membrane  14 rwrdpslgllwrliqplllalvfgtvfgn.lgnsedglnr..................pgllffsvlflafsaltsv 71 
                                       rw   ++  ++ l+     +l fg+++ +  +                          pgll+ ++ f+a+s+  ++
  gi|313125026|ref|YP_004035290.1|  18 RWLHGATV-FFVLFVGGAALLAFGLIYPDrFK-------DasnlfgffldlgifslsfPGLLALILGFIALSTSYGS 86 
                                       44444333.55666666778888888885311.......1222344467788888889************7777777 PP

                     ABC2_membrane  72 apvferergvlerelvsplyslsayvlakvlvelpvsllq...alifllivyflvgldls..rfflflllllltala 143
                                        ++ ere g+++  l+ p  s+ + +++k+l+  +v +++   +++  +++ + +g  +s  +f+ +++l++l+a+a
  gi|313125026|ref|YP_004035290.1|  87 -ITEERETGTMKLSLSLPN-SRRDLIVGKLLGRGAVVIVAllaGFLAAFVAMVATGTGISygSFVPMIALTVLLAFA 161
                                       .******************.***********995555544000444444555555666667799************* PP

                     ABC2_membrane 144 asslgllisalapsfedasqlaslvllpl 172
                                       ++s+gl isa+a + + a++ +  ++l++
  gi|313125026|ref|YP_004035290.1| 162 FVSIGLGISAVADTNREATLATLGLYLIF 190
                                       ****************9999888887776 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.4
                     ABC2_membrane 112 aliflli 118
                                       +l+ +++
  gi|313125026|ref|YP_004035290.1| 285 ILLAWIV 291
                                       1111111 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   1.5      0.62   1.8e+03     241     258 ..      25      42 ..      20      68 .. 0.50
   2 !   34.4  14.1   4.1e-12   1.2e-08     163     300 ..      67     208 ..      38     210 .. 0.78
   3 ?   -4.0   0.3       2.1   6.2e+03     169     173 ..     285     289 ..     272     303 .. 0.43

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.62
                   ABC2_membrane_3 241 llllfllfglayialgyl 258
                                       ++++++++g a++a+g+ 
  gi|313125026|ref|YP_004035290.1|  25 VFFVLFVGGAALLAFGLI 42 
                                       344444455555555443 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 4.1e-12
                   ABC2_membrane_3 163 lvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..l....afgl.. 231
                                       + gl+++il fi +s    si eE+e+++++l l+ + s+  ++++k+lg ++v ++ ll  +l  +    a  +  
  gi|313125026|ref|YP_004035290.1|  67 FPGLLALILGFIALSTSYGSITEERETGTMKLSLSLPNSRRDLIVGKLLGRGAVVIVALLAGFLaaFvamvA--Tgt 141
                                       555555555555555556699***********************************9998655523334233..256 PP

                   ABC2_membrane_3 232 gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwi 300
                                       gi++g+++ ++ l +l ++a++++g+ +s++ ++ ++a ++++ + l++++++ ++   e +p+ l+++
  gi|313125026|ref|YP_004035290.1| 142 GISYGSFVPMIALTVLLAFAFVSIGLGISAVADTNREATLATLGLYLIFGILWKPIA--EGIPKLLNYV 208
                                       9*************************************9998888886766655554..6666666665 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 2.1
                   ABC2_membrane_3 169 iilif 173
                                       i+l++
  gi|313125026|ref|YP_004035290.1| 285 ILLAW 289
                                       11111 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   6.7   8.2e-11   2.5e-07      21     177 ..      27     192 ..      17     193 .. 0.64
   2 ?   -1.3   0.1      0.61   1.8e+03     144     156 ..     283     295 ..     258     304 .. 0.56

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 8.2e-11
                   ABC2_membrane_4  21 aallvpllallyfnllgktgldp.....aefysls....vfgftlllllplilgiiasylifrEeqndtlknLltiP 88 
                                        +l+v   all+f l+ ++ +++       f +l     +f+  l l+l +i    +  +i++E++ +t+k  l +P
  gi|313125026|ref|YP_004035290.1|  27 FVLFVGGAALLAFGLIYPDRFKDasnlfGFFLDLGifslSFPGLLALILGFIALSTSYGSITEERETGTMKLSLSLP 103
                                       333333344444443333222221101033333331112444444444444444445558***************** PP

                   ABC2_membrane_4  89 vsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkks. 164
                                        sr+ l+++Kl+    ++++ +l+ fl+++++ ++++++g+s ++++ ++  +++l+   + + l i a++  +++ 
  gi|313125026|ref|YP_004035290.1| 104 NSRRDLIVGKLLGRGAVVIVALLAGFLAAFVA-MVATGTGISYGSFVPMIALTVLLAFAFVSIGLGISAVADTNREa 179
                                       **************999999999988876665.89999***999988887766655555555566677777666641 PP

                   ABC2_membrane_4 165 yvlpliltlvyti 177
                                        +++l+l l+++i
  gi|313125026|ref|YP_004035290.1| 180 TLATLGLYLIFGI 192
                                       5777888888876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.61
                   ABC2_membrane_4 144 lgllvffavlpii 156
                                       +++l++ +v+p++
  gi|313125026|ref|YP_004035290.1| 283 MAILLAWIVVPVV 295
                                       2222222333332 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   5.4   2.3e-10   6.9e-07      36     159 ..      67     191 ..      40     207 .. 0.80
   2 ?   -1.2   0.1      0.43   1.3e+03      84     106 ..     277     299 ..     273     305 .. 0.47

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.3e-10
                   ABC2_membrane_5  36 vllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn.v 111
                                       +  +++++  +i+ ++   ++  ++  +++k+ l+LP +r++++  K l+   ++++a+l ++l++++a++ +g+ +
  gi|313125026|ref|YP_004035290.1|  67 FPGLLALILGFIALSTSYGSITEERETGTMKLSLSLPNSRRDLIVGKLLGRGAVVIVALLAGFLAAFVAMVATGTgI 143
                                       22334445556666667889999****************************************************98 PP

                   ABC2_membrane_5 112 tisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiif 159
                                          +++ +i++ +++a++f++i l +     + +  +++ +  ++i++
  gi|313125026|ref|YP_004035290.1| 144 SYGSFVPMIALTVLLAFAFVSIGLGISAVADTNREATLATLGLYLIFG 191
                                       88999999***********99988777776666666655555555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.43
                   ABC2_membrane_5  84 lfvlililiailitlllliiavl 106
                                       l+++ +++i +  +++ ++++++
  gi|313125026|ref|YP_004035290.1| 277 LSGAAMMAILLAWIVVPVVVGYY 299
                                       44444444444444444444333 PP

>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.1   1.3e-05     0.038      67     144 ..     112     192 ..      67     195 .. 0.76
   2 ?   -1.3   0.9      0.59   1.8e+03     129     148 ..     279     298 ..     216     305 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                              YqhR  67 GtvisivligvvsigvallyyvllkkikslwagilyG.....vvlwllvfyvlnPlfPdvkavaelekntiittlcl 138
                                       G++++   + +v++ + +l    +  + ++ +gi yG     ++l +l+ + +  +  +++ava+ ++++ ++tl l
  gi|313125026|ref|YP_004035290.1| 112 GKLLGRGAVVIVALLAGFLAA--FVAMVATGTGISYGsfvpmIALTVLLAFAFVSIGLGISAVADTNREATLATLGL 186
                                       555554445555555555432..22333344556665333337888999999999********************** PP

                              YqhR 139 yilyGv 144
                                       y+++G+
  gi|313125026|ref|YP_004035290.1| 187 YLIFGI 192
                                       *****8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.59
                              YqhR 129 kntiittlclyilyGvfvGy 148
                                         ++++ l  +i+  v vGy
  gi|313125026|ref|YP_004035290.1| 279 GAAMMAILLAWIVVPVVVGY 298
                                       33333333344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1846.49
//
Query:       gi|313125027|ref|YP_004035291.1|  [L=694]
Description: NAD-dependent DNA ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.6e-106  354.5   0.0     7e-106  353.9   0.0    1.3  1  DNA_ligase_aden  NAD-dependent DNA ligase adenylation domain
    1.9e-29  101.3   3.5    4.4e-29  100.2   3.5    1.6  1  DNA_ligase_OB    NAD-dependent DNA ligase OB-fold domain
    2.7e-24   85.0   0.0      3e-23   81.7   0.0    2.5  2  HHH_2            Helix-hairpin-helix motif
    1.8e-16   60.5   0.2    2.4e-08   34.4   0.0    2.8  2  HHH_5            Helix-hairpin-helix domain
    9.9e-11   40.9   0.5    1.1e-06   28.2   0.0    3.8  3  HHH              Helix-hairpin-helix motif
      1e-09   38.6   0.0      2e-09   37.7   0.0    1.4  1  BRCT             BRCA1 C Terminus (BRCT) domain
    0.00015   21.7   4.5    0.00049   20.1   4.5    2.0  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
     0.0078   16.8   0.0      0.068   13.8   0.0    2.4  2  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.017   15.5   0.1       0.48   10.8   0.0    3.3  3  HHH_8            Helix-hairpin-helix domain
      0.031   14.5   0.0       0.62   10.4   0.0    2.9  3  HHH_3            Helix-hairpin-helix motif
        0.1   12.2   1.8       0.62    9.7   0.0    2.7  3  ThiP_synth       Thiamine-phosphate synthase


Domain annotation for each model (and alignments):
>> DNA_ligase_aden  NAD-dependent DNA ligase adenylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.9   0.0  4.3e-109    7e-106       3     318 .]      35     342 ..      33     342 .. 0.97

  Alignments for each domain:
  == domain 1  score: 353.9 bits;  conditional E-value: 4.3e-109
                                       HHHHHHHHHHHHHHHHHHHHCTT-SSC-HCHHHHHHHHHHHHHHHSGGG--TTSCCG-SSSS--CTS-EEE-SS--- CS
                   DNA_ligase_aden   3 akkeleelrellrkydyeYyvldePlvsDaeyDrllkelkelEekfPelitpdSPtqrvgaeleaefkkveHeapll 79 
                                       a++e++ lre +r++d++Yyv ++Plv D +yD+l+++l+elE++f +l    SPt+rvg e++ e+++veH ap+l
  gi|313125027|ref|YP_004035291.1|  35 AEREARLLREAVREHDHRYYVAADPLVADRTYDALFNRLQELEDAF-DLDDESSPTRRVGGEPLDELDTVEHVAPML 110
                                       6788999*************************************99.9***************************** PP

                                       --EEE-SHHHHHHHHHHHHHHSSS--S-EEEEEEEESSEEEEEEEETTEEEEEEE-TTSSEEEB-HHHHCT-TTS-S CS
                   DNA_ligase_aden  80 SLdnafdedelkaflerieealgnkekvayvvelKiDGlavsllYengvlvraatRGdGttGedvtaNvktiksiPl 156
                                       S+d++ +++++++f++r++ea+g+     yv+e+K DGl+v ++Ye+g  vraatRGdG+ G+dvta v+ti+siPl
  gi|313125027|ref|YP_004035291.1| 111 SIDQSVEAADVRDFDRRVREAVGEVR---YVCEPKFDGLSVEVVYEDGEYVRAATRGDGERGDDVTAQVRTIRSIPL 184
                                       ********************998766...9*********************************************** PP

                                       B-SSSS--SEEEEEEEEE--HHHHHHHHHHHHHCT----SSHHHHHHHHHT-SSHHHHHTS--EEEEEEEEEEESS- CS
                   DNA_ligase_aden 157 klkvdnlpeelevRGEvylrkedFeklNeerleegeklfaNpRNaAaGslRqldpkitakrkLkliayglglvekee 233
                                       +l+ d  p  l vRGEvy+++++F++lN+er+e++e++faNpRNaA G+lRqldp +ta r+L+ ++y++   ++ +
  gi|313125027|ref|YP_004035291.1| 185 RLRGD-YPDFLTVRGEVYMPRDAFQELNRERIEADEEPFANPRNAAVGTLRQLDPSVTADRPLDCFFYDVL--DA-S 257
                                       ****8.****************************************************************9..44.5 PP

                                       --.SBHHHHHHHHHHCT--B-TT-EEECSHHHHHHHHHHHHHHGGGSSS-EEEEEEEESBHHHHHHH-EETSCESSE CS
                   DNA_ligase_aden 234 levktqsealkvlkklglkvseelklvksieevleyieelekkRdeleyeiDGvVvkvdelalqeeLGftakaPrwA 310
                                       + ++tq+++l+ l+++gl++++++++v +i++ ++y +el ++R++l+yeiDG+V+kvd ++++e+LG t+++ rwA
  gi|313125027|ref|YP_004035291.1| 258 DVPETQTATLSRLDSWGLRTNDRVESVADIDGAIAYRDELMAAREDLNYEIDGTVIKVDRRDQREQLGETSRSVRWA 334
                                       6779************************************************************************* PP

                                       EEEE---C CS
                   DNA_ligase_aden 311 iAyKfpae 318
                                        AyKfpa+
  gi|313125027|ref|YP_004035291.1| 335 FAYKFPAR 342
                                       ******96 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   3.5   2.7e-32   4.4e-29       2      76 ..     346     420 ..     345     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 2.7e-32
                                       --XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     DNA_ligase_OB   2 tkledievqVGRtGaltpvAeLepvelaGttVsratLhnedeierkdirigdtVvvekaGdvIPevvgvvlekre 76 
                                       t+++d+ vqVGRtG+ltpvA L+pv+++G+tVsra+Lhn +eier++++igd V +++aGdvIP v +vv+++ e
  gi|313125027|ref|YP_004035291.1| 346 TTMTDVVVQVGRTGRLTPVALLDPVDVGGVTVSRASLHNPEEIERLGVNIGDEVRIKRAGDVIPDVEEVVEKHSE 420
                                       899******************************************************************998765 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.61     1e+03      29      53 ..     493     517 ..     487     525 .. 0.82
   2 !   81.7   0.0   1.8e-26     3e-23       2      64 .]     530     592 ..     529     592 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.61
                             HHH_2  29 LkkasleeLlevddiGeeiAqsive 53 
                                       L + + +eL+e+++ G++ A++ v+
  gi|313125027|ref|YP_004035291.1| 493 LYRLERDELSELEGWGKTSADNLVT 517
                                       5666789***********9998765 PP

  == domain 2  score: 81.7 bits;  conditional E-value: 1.8e-26
                             HHH_2   2 llfaLGIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFeneknreli 64 
                                       +l++LGI++VG +tA++La++F+slda ++as+eeL ev+d+G+++A++i+efF++e+nr+ i
  gi|313125027|ref|YP_004035291.1| 530 FLVGLGIPEVGGSTARNLARAFGSLDAVMDASVEELEEVEDVGPTVAEKIREFFDTESNRKAI 592
                                       899*********************************************************976 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1     5e-08   8.1e-05       5      55 ..     468     519 ..     465     521 .. 0.95
   2 !   34.4   0.0   1.5e-11   2.4e-08       5      53 ..     534     581 ..     530     585 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5e-08
                                       HTSTT--HHHHHHHHTTT.--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   5 lsvsGiGpktAlallsaG.iesvedlaaadveeLakipGiGkktAeriilel 55 
                                       l+++G+G +++  l++ G ie + dl +++++eL+++ G Gk  A++++ e+
  gi|313125027|ref|YP_004035291.1| 468 LDIEGLGGERVEQLVDEGlIEGLPDLYRLERDELSELEGWGKTSADNLVTEI 519
                                       79***************98999**************************9986 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1.5e-11
                                       HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                       l+++ +G +tA++l++a ++s++++++a+veeL ++ ++G+  Ae+i +
  gi|313125027|ref|YP_004035291.1| 534 LGIPEVGGSTARNLARA-FGSLDAVMDASVEELEEVEDVGPTVAEKIRE 581
                                       79***************.*****************************87 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0033       5.5      10      25 ..     498     513 ..     497     516 .. 0.91
   2 ?    0.9   0.0      0.31     5e+02      16      25 ..     536     545 ..     534     549 .. 0.84
   3 !   28.2   0.0   6.6e-10   1.1e-06       1      30 []     553     582 ..     553     582 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0033
                                       HHHHHTSTT-SHHHHH CS
                               HHH  10 reeLlalPGVGpktAe 25 
                                       r+eL +l+G+G+  A+
  gi|313125027|ref|YP_004035291.1| 498 RDELSELEGWGKTSAD 513
                                       79***********998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.31
                                       STT-SHHHHH CS
                               HHH  16 lPGVGpktAe 25 
                                       +P VG +tA+
  gi|313125027|ref|YP_004035291.1| 536 IPEVGGSTAR 545
                                       8********8 PP

  == domain 3  score: 28.2 bits;  conditional E-value: 6.6e-10
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                       sl+++++as+eeL++++ VGp +Ae+I+++
  gi|313125027|ref|YP_004035291.1| 553 SLDAVMDASVEELEEVEDVGPTVAEKIREF 582
                                       7899***********************986 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   1.2e-12     2e-09       6      79 .]     613     684 ..     610     684 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.2e-12
                                       TTTEEEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHHHH CS
                              BRCT   6 fhgckfvitgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivheewlldci 79 
                                       ++g++fv+ ++    tr +++el++ hG+  t++vs +t++lv+g++  +++k   a ++ +p+++e+++ +++
  gi|313125027|ref|YP_004035291.1| 613 LDGLTFVF-TGSLAVTRGDAQELVQAHGANATSSVSGNTDYLVIGDN-PGQSKRDDAAANDVPVLDEDEFAELL 684
                                       79******.999999********************************.*********************99875 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   4.5     3e-07   0.00049       1      27 []     428     453 ..     428     453 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                    DNA_ligase_ZBD   1 hCPvCGsavvReegeaiyRCtn.lsCpA 27 
                                       +CPvCGs+v R  ++  ++Ct+ l C A
  gi|313125027|ref|YP_004035291.1| 428 ECPVCGSPVNR--EGPLAYCTGgLTCEA 453
                                       5********77..569*****77***98 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.8   2.9e+03      18      39 ..     499     520 ..     497     524 .. 0.85
   2 !   13.8   0.0   4.2e-05     0.068      22      76 ..     535     595 ..     534     607 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.8
                        5_3_exonuc  18 DnipGvpgiGektAakLlkeyg 39 
                                       D++   +g+G+  A +L++e++
  gi|313125027|ref|YP_004035291.1| 499 DELSELEGWGKTSADNLVTEIE 520
                                       7888899***********9986 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.2e-05
                        5_3_exonuc  22 GvpgiGektAakLlkeygsleeilenl.delke.....kklkekLeenkeearlskkLati 76 
                                       G+p +G  tA +L + +gsl++++++  +el+e     ++++ek++e  ++    k +a++
  gi|313125027|ref|YP_004035291.1| 535 GIPEVGGSTARNLARAFGSLDAVMDASvEELEEvedvgPTVAEKIREFFDTESNRKAIAEM 595
                                       9***********************9653344445446677999999988887777777776 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.56   9.1e+02      47      63 ..     500     515 ..     487     549 .. 0.64
   2 ?   10.8   0.0   0.00029      0.48      36      67 ..     552     583 ..     544     584 .. 0.69
   3 ?   -3.4   0.0         8   1.3e+04      29      44 ..     589     604 ..     589     615 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.56
                                       THCTTSTT--HHHHHHH CS
                             HHH_8  47 eeltklpgiGkkiaaki 63 
                                       e l++l g Gk  a+ +
  gi|313125027|ref|YP_004035291.1| 500 E-LSELEGWGKTSADNL 515
                                       4.777777777666654 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00029
                                       CC-SS-HHHH.TTHCTTSTT--HHHHHHHHHHH CS
                             HHH_8  36 ealpeeitsl.eeeltklpgiGkkiaakieeil 67 
                                        +l+   +   ee l+++  +G+ +a+ki+e+ 
  gi|313125027|ref|YP_004035291.1| 552 GSLDAVMDASvEE-LEEVEDVGPTVAEKIREFF 583
                                       4444433333355.99***************96 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 8
                                       HHHHCCCCC-SS-HHH CS
                             HHH_8  29 rrAaraiealpeeits 44 
                                       r+A++  ++l+ e ++
  gi|313125027|ref|YP_004035291.1| 589 RKAIAEMRSLGVEPET 604
                                       8999999999887666 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.9   1.1e+04      48      60 ..     469     481 ..     468     483 .. 0.81
   2 ?   -0.1   0.0      0.73   1.2e+03      14      32 ..     499     517 ..     497     523 .. 0.87
   3 ?   10.4   0.0   0.00038      0.62      11      32 ..     560     581 ..     558     598 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.9
                             HHH_3  48 kvkglgpktfeql 60 
                                       +++glg + +eql
  gi|313125027|ref|YP_004035291.1| 469 DIEGLGGERVEQL 481
                                       6899999999998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.73
                             HHH_3  14 eeLqklpGlgpklAknIva 32 
                                       +eL+ l+G g++ A+n+v 
  gi|313125027|ref|YP_004035291.1| 499 DELSELEGWGKTSADNLVT 517
                                       699************9985 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00038
                             HHH_3  11 AsaeeLqklpGlgpklAknIva 32 
                                       As+eeL+ ++ +gp++A++I +
  gi|313125027|ref|YP_004035291.1| 560 ASVEELEEVEDVGPTVAEKIRE 581
                                       6666666666666666666644 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.75   1.2e+03      32      62 ..     114     144 ..     110     148 .. 0.85
   2 ?    9.7   0.0   0.00038      0.62      87     145 ..     291     360 ..     279     371 .. 0.82
   3 ?   -0.3   0.1      0.44   7.1e+02     107     148 ..     562     603 ..     548     605 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.75
                                       T--SGGGEEEETT-EEE-TSSEEE-S-EEET CS
                        ThiP_synth  32 dAksieDvaavpGRIvrvkgrvkvvgepefg 62 
                                       +  + +Dv  ++ R++++ g+v++v ep+f 
  gi|313125027|ref|YP_004035291.1| 114 QSVEAADVRDFDRRVREAVGEVRYVCEPKFD 144
                                       566788999999****************996 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00038
                                       EE--HHHHHHHCCTTSE....EEE--CCCS-CCC...T-HHHHHHHHHHHCC....S-ECEEEE--BCTB CS
                        ThiP_synth  87 irydekilealeelglk....vvefdreeepeev...gstmewgvaeaieel....evpdviydeGgvGk 145
                                       i+y +++++a e+l+++    v+++dr+++ e+     ++++w+ a  +  +    ++ dv+++ G+ G 
  gi|313125027|ref|YP_004035291.1| 291 IAYRDELMAAREDLNYEidgtVIKVDRRDQREQLgetSRSVRWAFAYKFPARsevtTMTDVVVQVGRTGR 360
                                       7899999999999999633337***********98888999999998887777666699*******9996 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.44
                                       --CCCS-CCCT-HHHHHHHHHHHCCS-ECEEEE--BCTB--E CS
                        ThiP_synth 107 fdreeepeevgstmewgvaeaieelevpdviydeGgvGkEpm 148
                                       +++ ee e+vg t++++++e +++++  ++i +    G+Ep 
  gi|313125027|ref|YP_004035291.1| 562 VEELEEVEDVGPTVAEKIREFFDTESNRKAIAEMRSLGVEPE 603
                                       455566666799**********99955799999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.76u 0.36s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 3813.75
//
Query:       gi|313125028|ref|YP_004035292.1|  [L=767]
Description: heat repeat-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-57  190.6  44.1    2.9e-15   56.4   7.7    7.3  7  HEAT_2          HEAT repeats
    3.4e-21   73.5  31.6     0.0015   18.6   0.1   12.0 12  HEAT            HEAT repeat
    4.8e-17   60.8  33.1    0.00034   21.0   0.2    9.8  8  HEAT_PBS        PBS lyase HEAT-like repeat
    9.4e-14   51.6  37.1      0.011   16.2   0.5   10.6 11  HEAT_EZ         HEAT-like repeat
    1.2e-07   31.5   9.5      0.031   14.3   0.1    7.6  9  Arm             Armadillo/beta-catenin-like repeat
      2e-06   27.9   2.7       0.42   10.6   0.1    5.0  5  Cnd1            non-SMC mitotic condensation complex subunit 
     0.0015   18.2   4.3        1.3    8.5   0.1    3.5  2  ERAP1_C         ERAP1-like C-terminal domain
  ------ inclusion threshold ------
      0.052   12.1   0.4         13    4.2   0.0    3.1  3  Adaptin_N       Adaptin N terminal region
      0.089   11.9   0.5        2.8    7.0   0.0    3.4  4  IFRD            Interferon-related developmental regulator (I
      0.089   12.9   1.3          3    8.0   0.1    3.1  2  Unstab_antitox  Putative addiction module component
       0.16   11.5   0.0        7.5    6.0   0.0    2.8  3  Tti2            Tti2 family
       0.18   12.2   0.0         29    5.1   0.0    3.6  4  RasGEF_N_2      Rapamycin-insensitive companion of mTOR RasGE


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2    0.0007         1       8      74 ..     359     391 ..     352     393 .. 0.50
   2 !   56.4   7.7   1.9e-18   2.9e-15       5      87 ..     385     467 ..     381     468 .. 0.95
   3 !   28.9   0.7   7.5e-10   1.1e-06       1      59 [.     444     503 ..     444     508 .. 0.93
   4 !   32.4   0.1   6.2e-11   9.2e-08       6      62 ..     512     568 ..     507     572 .. 0.90
   5 !   21.3   0.2   1.7e-07   0.00026      30      75 ..     583     628 ..     575     629 .. 0.91
   6 !   49.7   3.7   2.5e-16   3.7e-13       6      88 .]     622     702 ..     618     702 .. 0.95
   7 !   50.3   5.3   1.6e-16   2.4e-13       3      87 ..     680     766 ..     678     767 .] 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0007
                            HEAT_2   8 lendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddd 74 
                                       l                                  +dp  R+aaa+ L++ + + a +  +++l++d
  gi|313125028|ref|YP_004035292.1| 359 L----------------------------------SDPSLRAAAATELARRDADGATETITDCLRTD 391
                                       3..................................34555555555555555555555555555544 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 1.9e-18
                            HEAT_2   5 lqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRe 81 
                                          l++dp    rra ++aL  ++++ a+paLve l+d++p+vRraaa aL+ +gdp++l+ L+ ++++++d+ +R+
  gi|313125028|ref|YP_004035292.1| 385 TDCLRTDPPVSDRRALVHALDVLADDVAVPALVERLDDTNPDVRRAAAVALATVGDPDSLDPLLSAVRTEPDAATRR 461
                                       567999*********************************************************************** PP

                            HEAT_2  82 aAaeaL 87 
                                       a+a+a 
  gi|313125028|ref|YP_004035292.1| 462 AIARAA 467
                                       999875 PP

  == domain 3  score: 28.9 bits;  conditional E-value: 7.5e-10
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaig 59 
                                       ld+Ll+a+++ pd ++rra++ra  +i++++al+ + +l+ +d++p+vR+ +++ L+  g
  gi|313125028|ref|YP_004035292.1| 444 LDPLLSAVRTEPDAATRRAIARAARDIDPTSALDHFASLVrTDTEPEVRESVVRVLSGTG 503
                                       689*************************************9999**********998655 PP

  == domain 4  score: 32.4 bits;  conditional E-value: 6.2e-11
                            HEAT_2   6 qalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpe 62 
                                         +++dp+p+v+ +ai a  ++ +++ +  L++ l+d+dp vR aaa+a  ++g  +
  gi|313125028|ref|YP_004035292.1| 512 VEAVDDPNPDVACEAISAVRWFTDERPVGGLLRRLTDDDPGVRVAAADAFIELGARA 568
                                       44459********************************************99998765 PP

  == domain 5  score: 21.3 bits;  conditional E-value: 1.7e-07
                            HEAT_2  30 pealpaLvellededpavRraaaeaLgaigdpealpaLkelldddd 75 
                                       +++++aL++ l+de+  vR++a eaLg  ++pe++  L++++d+d+
  gi|313125028|ref|YP_004035292.1| 583 TRVVRALLDRLDDENVPVRETAMEALGSQAHPESVMPLCAAYDEDE 628
                                       5789************************************999875 PP

  == domain 6  score: 49.7 bits;  conditional E-value: 2.5e-16
                            HEAT_2   6 qalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRea 82 
                                       +a   d+d++ r  ai+aLgri++p+a+p++v +l+d+++ vRr a++a +++g+++ ++ L++l+ +d+   vR +
  gi|313125028|ref|YP_004035292.1| 622 AAY--DEDEACRSSAIDALGRIDDPRAIPTVVAALDDTEASVRRRACRACARLGTSAGVRRLCHLAENDPQLAVRVE 696
                                       544..99********************************************************************** PP

                            HEAT_2  83 AaeaLa 88 
                                       A+ aL+
  gi|313125028|ref|YP_004035292.1| 697 AVDALG 702
                                       ***996 PP

  == domain 7  score: 50.3 bits;  conditional E-value: 1.6e-16
                            HEAT_2   3 aLlqalendpdpevrraairaLgrign..pealpaLvellededpavRraaaeaLgaigdpealpaLkelldddddd 77 
                                        L+ ++endp  +vr +a++aLg  g+  ++++++L  +l+ +d++ R++a++aLg++++p+a  +L++++ dd+d+
  gi|313125028|ref|YP_004035292.1| 680 RLCHLAENDPQLAVRVEAVDALGHVGDgrETVFDTLETALDADDADLRWEAVTALGRLDHPRARFLLRRAAEDDPDE 756
                                       69999******************775432899********************************************* PP

                            HEAT_2  78 vvReaAaeaL 87 
                                        vR +A + L
  gi|313125028|ref|YP_004035292.1| 757 SVRDRARSRL 766
                                       *****98766 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.3     2e+03       9      21 ..     138     150 ..     137     152 .. 0.84
   2 ?   -0.1   0.1         1   1.6e+03       9      22 ..     355     370 ..     352     374 .. 0.77
   3 !   18.6   0.1   9.8e-07    0.0015       2      26 ..     413     437 ..     412     440 .. 0.92
   4 !    8.4   0.0    0.0019       2.8       2      24 ..     476     499 ..     475     501 .. 0.87
   5 ?    2.2   0.1      0.19   2.8e+02       5      24 ..     511     530 ..     509     531 .. 0.84
   6 !   12.1   0.0   0.00013      0.19       5      27 ..     542     564 ..     539     567 .. 0.90
   7 !   11.6   0.0   0.00017      0.26       2      25 ..     586     609 ..     585     610 .. 0.91
   8 ?    6.1   0.1      0.01        15       7      27 ..     622     641 ..     617     642 .. 0.82
   9 !   14.0   0.2   3.1e-05     0.046       2      27 ..     647     672 ..     646     675 .. 0.93
  10 !    7.9   0.0    0.0027       4.1       4      27 ..     680     704 ..     678     707 .. 0.88
  11 ?    3.2   0.1     0.091   1.4e+02       3      27 ..     713     737 ..     711     737 .. 0.90
  12 ?    0.3   0.2       0.8   1.2e+03      10      20 ..     752     762 ..     745     762 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                                       HT-SSHHHHHHHH CS
                              HEAT   9 lsDpspeVReaAa 21 
                                       l D+ +e+Re A 
  gi|313125028|ref|YP_004035292.1| 138 LADEVAEIREQAG 150
                                       67********995 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                                       HT-..SSHHHHHHHHH CS
                              HEAT   9 lsD..pspeVReaAak 22 
                                       l+D  ++p+ R+aAa 
  gi|313125028|ref|YP_004035292.1| 355 LKDalSDPSLRAAAAT 370
                                       6666789999999985 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 9.8e-07
                                       HHHHHHHHT-SSHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLga 26 
                                       +P+l++ l D++p+VR+aAa aL++
  gi|313125028|ref|YP_004035292.1| 413 VPALVERLDDTNPDVRRAAAVALAT 437
                                       79********************987 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0019
                                       HHHHHHHH.T-SSHHHHHHHHHHH CS
                              HEAT   2 lPlllkll.sDpspeVReaAakaL 24 
                                       l+++ +l  +D++peVRe++++ L
  gi|313125028|ref|YP_004035292.1| 476 LDHFASLVrTDTEPEVRESVVRVL 499
                                       6788889889***********988 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.19
                                       HHHHHT-SSHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaL 24 
                                       ++++  Dp+p+V + A+ a+
  gi|313125028|ref|YP_004035292.1| 511 VVEAVDDPNPDVACEAISAV 530
                                       788999******99998875 PP

  == domain 6  score: 12.1 bits;  conditional E-value: 0.00013
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       ll+ l+D++p VR aAa a+ +l
  gi|313125028|ref|YP_004035292.1| 542 LLRRLTDDDPGVRVAAADAFIEL 564
                                       7899***************9887 PP

  == domain 7  score: 11.6 bits;  conditional E-value: 0.00017
                                       HHHHHHHHT-SSHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLg 25 
                                       + +ll  l D++  VRe+A +aLg
  gi|313125028|ref|YP_004035292.1| 586 VRALLDRLDDENVPVRETAMEALG 609
                                       5689999****************9 PP

  == domain 8  score: 6.1 bits;  conditional E-value: 0.01
                                       HHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   7 kllsDpspeVReaAakaLgal 27 
                                        +  D++   R++A+ aLg++
  gi|313125028|ref|YP_004035292.1| 622 AA-YDEDEACRSSAIDALGRI 641
                                       43.69**************98 PP

  == domain 9  score: 14.0 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                       +P+++ +l D++++VR+ A++a+++l
  gi|313125028|ref|YP_004035292.1| 647 IPTVVAALDDTEASVRRRACRACARL 672
                                       799********************998 PP

  == domain 10  score: 7.9 bits;  conditional E-value: 0.0027
                                       HHHHHH.T-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkll.sDpspeVReaAakaLgal 27 
                                        l++l  +Dp   VR  A+ aLg++
  gi|313125028|ref|YP_004035292.1| 680 RLCHLAeNDPQLAVRVEAVDALGHV 704
                                       6899988****************86 PP

  == domain 11  score: 3.2 bits;  conditional E-value: 0.091
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       ++l ++l  ++++ R  A+ aLg+l
  gi|313125028|ref|YP_004035292.1| 713 DTLETALDADDADLRWEAVTALGRL 737
                                       678899999**************97 PP

  == domain 12  score: 0.3 bits;  conditional E-value: 0.8
                                       T-SSHHHHHHH CS
                              HEAT  10 sDpspeVReaA 20 
                                        Dp+ +VR+ A
  gi|313125028|ref|YP_004035292.1| 752 DDPDESVRDRA 762
                                       79******976 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.044        65       2      27 .]     397     422 ..     396     422 .. 0.92
   2 !   21.0   0.2   2.2e-07   0.00034       1      25 [.     427     451 ..     427     453 .. 0.94
   3 ?    3.5   0.4       0.1   1.5e+02       1      22 [.     553     590 ..     553     595 .. 0.67
   4 !    9.9   0.0   0.00087       1.3       1      26 [.     600     625 ..     600     626 .. 0.94
   5 !   17.2   0.0     4e-06     0.006       2      27 .]     631     656 ..     631     656 .. 0.97
   6 ?    4.3   0.6     0.057        85       1      26 [.     661     686 ..     661     687 .. 0.90
   7 !   10.5   0.0   0.00056      0.84       1      26 [.     693     720 ..     693     721 .. 0.94
   8 !    7.4   0.6    0.0056       8.4       1      27 []     726     752 ..     726     752 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                       Rra + aL  l d+ a+paL+e L+d
  gi|313125028|ref|YP_004035292.1| 397 RRALVHALDVLADDVAVPALVERLDD 422
                                       89999999999************998 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       vRraAa aL+++gd++++++Ll a 
  gi|313125028|ref|YP_004035292.1| 427 VRRAAAVALATVGDPDSLDPLLSAV 451
                                       9********************9985 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHCTS................GGGHHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgd................eeaipaLl 22 
                                       vR aAa a  +lg+                ++++ aLl
  gi|313125028|ref|YP_004035292.1| 553 VRVAAADAFIELGAraahyhdgdelsaetrTRVVRALL 590
                                       9************9666665555555555555555555 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00087
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       vR  A++aLg   ++e++ +L++a +
  gi|313125028|ref|YP_004035292.1| 600 VRETAMEALGSQAHPESVMPLCAAYD 625
                                       89********************9965 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 4e-06
                                       HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                       R +A+ aLg++ d++aip+ ++aL+d
  gi|313125028|ref|YP_004035292.1| 631 RSSAIDALGRIDDPRAIPTVVAALDD 656
                                       889*********************98 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.057
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       vRr+A +a ++lg+ + + +L+ + +
  gi|313125028|ref|YP_004035292.1| 661 VRRRACRACARLGTSAGVRRLCHLAE 686
                                       9**************99999998765 PP

  == domain 7  score: 10.5 bits;  conditional E-value: 0.00056
                                       HHHHHHHHHHHCTS..GGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgd..eeaipaLleaLq 26 
                                       vR +A+ aLg +gd  e + ++L  aL+
  gi|313125028|ref|YP_004035292.1| 693 VRVEAVDALGHVGDgrETVFDTLETALD 720
                                       8***************999999999997 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0056
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       +R++A+ aLg+l +++a  +L++a +d
  gi|313125028|ref|YP_004035292.1| 726 LRWEAVTALGRLDHPRARFLLRRAAED 752
                                       59**************98877777765 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.012        17      14      44 ..      44      73 ..      33      74 .. 0.82
   2 ?    1.0   0.2      0.44   6.5e+02       7      52 ..     366     404 ..     362     407 .. 0.84
   3 !   16.2   0.5   7.3e-06     0.011      28      53 ..     411     436 ..     405     438 .. 0.92
   4 ?    4.1   0.1     0.046        69      27      53 ..     473     500 ..     449     500 .. 0.73
   5 !    9.3   0.1    0.0011       1.7      31      53 ..     540     562 ..     539     564 .. 0.88
   6 !   10.8   0.1   0.00037      0.55      27      53 ..     583     609 ..     574     610 .. 0.87
   7 ?    0.3   0.0      0.69     1e+03      40      55 .]     625     641 ..     617     641 .. 0.84
   8 !   13.2   1.6   6.7e-05       0.1      27      55 .]     644     672 ..     628     672 .. 0.73
   9 ?    2.2   0.0      0.18   2.7e+02      36      54 ..     684     703 ..     678     704 .. 0.74
  10 !    8.0   0.4    0.0028       4.1       2      55 .]     692     737 ..     691     737 .. 0.79
  11 ?   -0.0   0.1      0.91   1.4e+03      33      48 ..     746     762 ..     743     762 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                           HEAT_EZ 14 laggepellqplvpeilpaLlalLnddsdeV 44
                                      +a ++++ l+ + +++++aL +lL+ ++++V
  gi|313125028|ref|YP_004035292.1| 44 VA-CGRDGLHWHCTQLVRALEPLLEGEPATV 73
                                      44.78899****************9877766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                           HEAT_EZ   7 AawaLGrlaggepellqplvpeilpaLlalLnddsdeV..RaaAagaL 52 
                                       Aa+a     + ++++  ++ + i ++L       +++V  R a ++aL
  gi|313125028|ref|YP_004035292.1| 366 AAAAT----ELARRDADGATETITDCLR-----TDPPVsdRRALVHAL 404
                                       44455....7789999999*********.....999999999999988 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 7.3e-06
                           HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLg 53 
                                       +++paL+ +L d +++VR aAa aL+
  gi|313125028|ref|YP_004035292.1| 411 VAVPALVERLDDTNPDVRRAAAVALA 436
                                       68**********************97 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.046
                           HEAT_EZ  27 peilpaLlalL.nddsdeVRaaAagaLg 53 
                                       + +l+ +++l  +d ++eVR+ +++ L+
  gi|313125028|ref|YP_004035292.1| 473 TSALDHFASLVrTDTEPEVRESVVRVLS 500
                                       57889999999555666*******9986 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0011
                           HEAT_EZ  31 paLlalLnddsdeVRaaAagaLg 53 
                                         Ll++L+dd++ VR aAa a+ 
  gi|313125028|ref|YP_004035292.1| 540 GGLLRRLTDDDPGVRVAAADAFI 562
                                       5799***************9986 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00037
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLg 53 
                                       +++++aLl +L d++ +VR++A  aLg
  gi|313125028|ref|YP_004035292.1| 583 TRVVRALLDRLDDENVPVRETAMEALG 609
                                       6899*******99999**********9 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 0.69
                           HEAT_EZ  40 dsdeV.RaaAagaLgnl 55 
                                       d+de  R  A+ aLg++
  gi|313125028|ref|YP_004035292.1| 625 DEDEAcRSSAIDALGRI 641
                                       78888899999999997 PP

  == domain 8  score: 13.2 bits;  conditional E-value: 6.7e-05
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       p+++p  +a+L d +++VR  A++a+++l
  gi|313125028|ref|YP_004035292.1| 644 PRAIPTVVAALDDTEASVRRRACRACARL 672
                                       4677777777778888*********9986 PP

  == domain 9  score: 2.2 bits;  conditional E-value: 0.18
                           HEAT_EZ  36 lLnddsd.eVRaaAagaLgn 54 
                                       l ++d++ +VR  A+ aLg 
  gi|313125028|ref|YP_004035292.1| 684 LAENDPQlAVRVEAVDALGH 703
                                       66667777999999999995 PP

  == domain 10  score: 8.0 bits;  conditional E-value: 0.0028
                           HEAT_EZ   2 rvRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       +vR  A+ aL    g+ ++  +     + + L  +L  d+++ R+ A+ aLg+l
  gi|313125028|ref|YP_004035292.1| 692 AVRVEAVDAL----GHVGDGRE----TVFDTLETALDADDADLRWEAVTALGRL 737
                                       6999999999....56666666....677777777777777***********97 PP

  == domain 11  score: -0.0 bits;  conditional E-value: 0.91
                           HEAT_EZ  33 LlalLnddsd.eVRaaA 48 
                                       L ++ +dd+d +VR  A
  gi|313125028|ref|YP_004035292.1| 746 LRRAAEDDPDeSVRDRA 762
                                       55777999999999866 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   2.1e-05     0.031      13      37 ..     412     436 ..     405     438 .. 0.94
   2 ?   -0.4   0.0       0.9   1.4e+03       8      35 ..     438     466 ..     436     468 .. 0.85
   3 ?   -1.3   0.0       1.7   2.6e+03      13      37 ..     475     500 ..     474     500 .. 0.88
   4 ?   -1.6   0.0       2.1   3.1e+03      22      37 ..     516     531 ..     511     531 .. 0.81
   5 ?    1.5   0.0      0.23   3.4e+02      17      35 ..     542     560 ..     539     561 .. 0.88
   6 ?    1.7   0.0       0.2     3e+02      13      37 ..     585     609 ..     583     610 .. 0.89
   7 ?    5.0   0.0     0.017        26      12      35 ..     645     668 ..     641     668 .. 0.92
   8 ?    5.7   0.0     0.011        17      13      38 ..     677     703 ..     675     704 .. 0.95
   9 ?   -2.7   0.1       4.6   6.9e+03      21      39 ..     719     737 ..     713     737 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeAawALs 37 
                                       avp+Lv+ L++++++v+++Aa AL+
  gi|313125028|ref|YP_004035292.1| 412 AVPALVERLDDTNPDVRRAAAVALA 436
                                       8**********************95 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.9
                                       HHHTTHHHHHHHHTT.TSSHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLs.sedeevqeeAawA 35 
                                       v +   ++pL++  +  +d  +++++a+A
  gi|313125028|ref|YP_004035292.1| 438 VGDPDSLDPLLSAVRtEPDAATRRAIARA 466
                                       5566679999999999********99998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHTT.TSSHHHHHHHHHHHH CS
                               Arm  13 avppLvrLLs.sedeevqeeAawALs 37 
                                       a++++ +L + ++ +ev+e +++ Ls
  gi|313125028|ref|YP_004035292.1| 475 ALDHFASLVRtDTEPEVRESVVRVLS 500
                                       7899999999999****999998886 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.1
                                       TTSSHHHHHHHHHHHH CS
                               Arm  22 ssedeevqeeAawALs 37 
                                       ++++++v +eA +A++
  gi|313125028|ref|YP_004035292.1| 516 DDPNPDVACEAISAVR 531
                                       689999****999975 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.23
                                       HHHHTTTSSHHHHHHHHHH CS
                               Arm  17 LvrLLssedeevqeeAawA 35 
                                       L+r L+++d++v+ +Aa A
  gi|313125028|ref|YP_004035292.1| 542 LLRRLTDDDPGVRVAAADA 560
                                       777899***********98 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.2
                                       HHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeAawALs 37 
                                       +v++L++ L++e++ v+e A  AL+
  gi|313125028|ref|YP_004035292.1| 585 VVRALLDRLDDENVPVRETAMEALG 609
                                       799***************9977775 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.017
                                       THHHHHHHHTTTSSHHHHHHHHHH CS
                               Arm  12 GavppLvrLLssedeevqeeAawA 35 
                                        a+p  v+ L+++  +v++ A++A
  gi|313125028|ref|YP_004035292.1| 645 RAIPTVVAALDDTEASVRRRACRA 668
                                       68********************98 PP

  == domain 8  score: 5.7 bits;  conditional E-value: 0.011
                                       HHHHHHHHTT.TSSHHHHHHHHHHHHH CS
                               Arm  13 avppLvrLLs.sedeevqeeAawALsN 38 
                                       +v++L++L + ++   v+ eA+ AL++
  gi|313125028|ref|YP_004035292.1| 677 GVRRLCHLAEnDPQLAVRVEAVDALGH 703
                                       79***********************96 PP

  == domain 9  score: -2.7 bits;  conditional E-value: 4.6
                                       TTTSSHHHHHHHHHHHHHH CS
                               Arm  21 LssedeevqeeAawALsNL 39 
                                       L+ +d +++ eA++AL+ L
  gi|313125028|ref|YP_004035292.1| 719 LDADDADLRWEAVTALGRL 737
                                       6667777888999999865 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.8   2.8e+03      15      34 ..     344     363 ..     336     373 .. 0.81
   2 !   10.6   0.1   0.00028      0.42      23      52 ..     413     442 ..     408     446 .. 0.86
   3 ?   -1.5   0.0       1.5   2.2e+03      60      82 ..     476     499 ..     470     503 .. 0.80
   4 !    9.6   0.0   0.00057      0.85      26      86 ..     542     612 ..     536     621 .. 0.81
   5 ?    2.5   0.1     0.087   1.3e+02      24      49 ..     648     674 ..     629     682 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                              Cnd1  15 vpnlveylvepLrkrLkDed 34 
                                        p++ +   ++L+ +L+D++
  gi|313125028|ref|YP_004035292.1| 344 APSMADRSESHLKDALSDPS 363
                                       67889999999999999986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00028
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilnd 52 
                                       v+ L +rL D++p VR+ aa+++a + ++d
  gi|313125028|ref|YP_004035292.1| 413 VPALVERLDDTNPDVRRAAAVALATVGDPD 442
                                       778999*****************9876665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.5
                              Cnd1  60 lselakll.eDenprVvanalaal 82 
                                       l+++a+l+ +D++p+V+++++ +l
  gi|313125028|ref|YP_004035292.1| 476 LDHFASLVrTDTEPEVRESVVRVL 499
                                       788888888899999999888777 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00057
                              Cnd1  26 LrkrLkDedpyVRktaaivvakL.....ilnd....mvkekg.flselaklleDenprVvanalaalteis 86 
                                       L +rL+D+dp VR  aa ++++L     + +d      + +  ++  l++ l+Den  V++ a  al   +
  gi|313125028|ref|YP_004035292.1| 542 LLRRLTDDDPGVRVAAADAFIELgaraaHYHDgdelSAETRTrVVRALLDRLDDENVPVRETAMEALGSQA 612
                                       7799*******************99988444434543555557999***************9999987665 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.087
                              Cnd1  24 epLrkrLkDedpyVRktaaivvakL.i 49 
                                       + + ++L D+++ VR+ a  ++a+L  
  gi|313125028|ref|YP_004035292.1| 648 PTVVAALDDTEASVRRRACRACARLgT 674
                                       5566899**************999944 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1   0.00084       1.3     161     222 ..     392     453 ..     326     480 .. 0.64
   2 !    7.4   0.2    0.0019       2.8     123     210 ..     626     706 ..     564     727 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00084
                                       S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHC.T CS
                           ERAP1_C 161 ippdlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfv.l 222
                                        p + r a++ al    ++  + al er  d ++p+ ++aa+ ala + dp+ l  ll  v +
  gi|313125028|ref|YP_004035292.1| 392 PPVSDRRALVHALDVLADDVAVPALVERL-DDTNPDVRRAAAVALATVGDPDSLDPLLSAVrT 453
                                       34445555555553345888889999998.666679999999999999999999999988833 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHH.HC-SSHHHH CS
                           ERAP1_C 123 ldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewdallery.kdtsapsek 198
                                        d   rs+++ a+++ +dp+++  + + ++++        +++r ++ +a+a+ g+ a++  l  +  +d++  + +
  gi|313125028|ref|YP_004035292.1| 626 EDEACRSSAIDALGRIDDPRAIPTVVAALDDT-------EASVRRRACRACARLGTSAGVRRLCHLAeNDPQL-AVR 694
                                       56777888888888888888888888888888.......3689999999999999999999999998556777.899 PP

                                       HHHHHHHCC-S- CS
                           ERAP1_C 199 eaalralaatpd 210
                                         a+ al+++ d
  gi|313125028|ref|YP_004035292.1| 695 VEAVDALGHVGD 706
                                       999999999877 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0087        13     121     179 ..     386     438 ..     376     474 .. 0.65
   2 ?   -0.8   0.0      0.28   4.2e+02     160     180 ..     545     570 ..     512     608 .. 0.76
   3 ?    4.0   0.1    0.0099        15      89     141 ..     624     672 ..     621     704 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0087
                                       HHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHH CS
                         Adaptin_N 121 kllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleei 179
                                       ++l+ + p+  + A++ +l+++  d        v+ ++e l+d++p v +aA  +l  +
  gi|313125028|ref|YP_004035292.1| 386 DCLRTDPPVSDRRALVHALDVLADDV------AVPALVERLDDTNPDVRRAAAVALATV 438
                                       55555555555555555554443222......256677777777777777777777776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.28
                                       CTT-SSHHHHHHHHHHHHHH.....H CS
                         Adaptin_N 160 llsdkdpgvvlaAvalleei.....k 180
                                        l+d+dpgv +aA  ++ e+      
  gi|313125028|ref|YP_004035292.1| 545 RLTDDDPGVRVAAADAFIELgaraaH 570
                                       57888889998888888888665443 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0099
                                       CSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHC CS
                         Adaptin_N  89 kdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailkl 141
                                        d ++  r++A+ +L++i +p+      p++ ++l d++++vr+ A  a ++l
  gi|313125028|ref|YP_004035292.1| 624 YDEDEACRSSAIDALGRIDDPRA----IPTVVAALDDTEASVRRRACRACARL 672
                                       5889999*************975....567888999*********98888776 PP

>> IFRD  Interferon-related developmental regulator (IFRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0018       2.8     217     247 ..     408     436 ..     395     441 .. 0.83
   2 ?   -2.7   0.0       1.6   2.5e+03     227     245 ..     542     560 ..     534     597 .. 0.80
   3 ?   -0.2   0.0      0.28   4.2e+02     221     246 ..     583     608 ..     566     610 .. 0.72
   4 ?   -1.6   0.0      0.75   1.1e+03     221     245 ..     644     668 ..     621     672 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0018
                              IFRD 217 eedleealealvelLdssdvevriAAGeaiA 247
                                        +    a++alve Ld+++ +vr AA  a+A
  gi|313125028|ref|YP_004035292.1| 408 AD--DVAVPALVERLDDTNPDVRRAAAVALA 436
                                       34..347*********************999 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.6
                              IFRD 227 lvelLdssdvevriAAGea 245
                                       l   L+++d  vr+AA  a
  gi|313125028|ref|YP_004035292.1| 542 LLRRLTDDDPGVRVAAADA 560
                                       5677899999999999876 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.28
                              IFRD 221 eealealvelLdssdvevriAAGeai 246
                                        ++++al + Ld+++v vr +A ea+
  gi|313125028|ref|YP_004035292.1| 583 TRVVRALLDRLDDENVPVRETAMEAL 608
                                       45788888888888888888888877 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.75
                              IFRD 221 eealealvelLdssdvevriAAGea 245
                                        +a++++v+ Ld+++ +vr  A +a
  gi|313125028|ref|YP_004035292.1| 644 PRAIPTVVAALDDTEASVRRRACRA 668
                                       5789999999999999999877665 PP

>> Unstab_antitox  Putative addiction module component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.13   1.9e+02      22      39 ..     360     377 ..     354     381 .. 0.86
   2 ?    8.0   0.1     0.002         3       2      29 ..     577     603 ..     576     610 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.13
                    Unstab_antitox  22 adpelpaawkaElerRla 39 
                                       +dp+l aa ++El rR a
  gi|313125028|ref|YP_004035292.1| 360 SDPSLRAAAATELARRDA 377
                                       7899************76 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.002
                    Unstab_antitox   2 LppaERleLaedLwdSLdeeadpelpaa 29 
                                       L+ + R +++ +L+d Ld+e++p + + 
  gi|313125028|ref|YP_004035292.1| 577 LSAETRTRVVRALLDRLDDENVP-VRET 603
                                       999****************9998.7765 PP

>> Tti2  Tti2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.17   2.5e+02     124     150 ..     412     438 ..     410     450 .. 0.87
   2 ?   -0.5   0.0      0.47     7e+02     125     148 ..     586     609 ..     575     612 .. 0.88
   3 ?    6.0   0.0     0.005       7.5     123     147 ..     645     669 ..     644     676 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                              Tti2 124 ivPpiLnllDdtdtsvKlrGlklLqtl 150
                                        vP+++  lDdt++ v+  +   L t+
  gi|313125028|ref|YP_004035292.1| 412 AVPALVERLDDTNPDVRRAAAVALATV 438
                                       59***************9999888775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.47
                              Tti2 125 vPpiLnllDdtdtsvKlrGlklLq 148
                                       v ++L  lDd++++v++++++ L 
  gi|313125028|ref|YP_004035292.1| 586 VRALLDRLDDENVPVRETAMEALG 609
                                       6689999***********999985 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.005
                              Tti2 123 livPpiLnllDdtdtsvKlrGlklL 147
                                       + +P +++ lDdt+ sv+ r+++  
  gi|313125028|ref|YP_004035292.1| 645 RAIPTVVAALDDTEASVRRRACRAC 669
                                       569*******************975 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.02        29       6      32 ..     412     438 ..     408     459 .. 0.80
   2 ?   -2.0   0.0       3.2   4.7e+03       9      35 ..     510     536 ..     509     540 .. 0.84
   3 ?    1.9   0.0       0.2   2.9e+02       7      33 ..     586     612 ..     584     643 .. 0.83
   4 ?   -1.4   0.0       2.1   3.1e+03      15      44 ..     624     652 ..     617     688 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.02
                        RasGEF_N_2   6 giellvnqLydqsrevvaaaleiLeea 32 
                                       +++ lv++L d +++v++aa+ +L  +
  gi|313125028|ref|YP_004035292.1| 412 AVPALVERLDDTNPDVRRAAAVALATV 438
                                       57889******************9877 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                        RasGEF_N_2   9 llvnqLydqsrevvaaaleiLeeacdd 35 
                                       l v+ + d++++v+  a++++  ++d+
  gi|313125028|ref|YP_004035292.1| 510 LVVEAVDDPNPDVACEAISAVRWFTDE 536
                                       6788999**********9998777765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.2
                        RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeeac 33 
                                       ++ l+++L d++  v+++a+e+L +  
  gi|313125028|ref|YP_004035292.1| 586 VRALLDRLDDENVPVRETAMEALGSQA 612
                                       67899****************997655 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.1
                        RasGEF_N_2  15 ydqsrevvaaaleiLeeacddkeslevlve 44 
                                       yd++++ ++ a+++L ++ dd++ + ++v 
  gi|313125028|ref|YP_004035292.1| 624 YDEDEACRSSAIDALGRI-DDPRAIPTVVA 652
                                       888888899999998877.66666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.87u 0.34s 00:00:01.21 Elapsed: 00:00:00.55
# Mc/sec: 4198.92
//
Query:       gi|313125029|ref|YP_004035293.1|  [L=440]
Description: oah/oas sulfhydrylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-128  427.9   0.0   2.9e-128  427.6   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    8.3e-05   21.7   0.1    0.00014   21.0   0.1    1.2  1  Aminotran_5      Aminotransferase class-V
     0.0081   15.5   2.1      0.014   14.7   1.1    1.7  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.024   13.9   0.0      0.039   13.2   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.6   0.0  6.5e-132  2.9e-128       2     381 ..       7     419 ..       6     420 .. 0.97

  Alignments for each domain:
  == domain 1  score: 427.6 bits;  conditional E-value: 6.5e-132
                                       HHHHHTTTTCHTTTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESS CS
                   Cys_Met_Meta_PP   2 Tllvhagqekdeqtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalavss 75 
                                       T  +hagqe+d +tg++a+p+y+t++y+f+d+d a    a  ++g +YsR+ npt++vle+r+aaLe g  a+a++s
  gi|313125029|ref|YP_004035293.1|   7 TRSLHAGQEPDAATGSRAPPLYQTTSYVFEDADYAadlYALDAEGDVYSRISNPTTRVLEDRLAALEAGVGAVATAS 83 
                                       8899**************************999988989999999******************************** PP

                                       HHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT- CS
                   Cys_Met_Meta_PP  76 GmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllk 152
                                       GmaA++aa   l++aGd++v+s d+Yggt+ +l+k++++ g+++++v+t d ++ + ai+  t  v++Et++np lk
  gi|313125029|ref|YP_004035293.1|  84 GMAALDAATSLLASAGDNVVASADMYGGTSTYLTKMATRRGVDIRVVETLDYDAYADAIDADTAFVHVETIANPSLK 160
                                       ***************************************************************************** PP

                                       ---HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHH.. CS
                   Cys_Met_Meta_PP 153 vvDiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflq.. 227
                                       ++D+e++a++a++ g+++vvDntfa+p+l+rp+++gaDiv +S+TK+l G +++v+Gv+++ g + +++  +  +  
  gi|313125029|ref|YP_004035293.1| 161 TPDFERLAHVAHEGGAPLVVDNTFATPYLCRPIEHGADIVWESTTKWLHGSGTTVGGVLIDGGTFPWEHADYD-Els 236
                                       ****************************************************************999986553.247 PP

                                       ............................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEE CS
                   Cys_Met_Meta_PP 228 ............................nalGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvekv 276
                                                                   ++lG+  spfdaw++l+G++TL lR+e+h enA +vA fL+ h+ v +v
  gi|313125029|ref|YP_004035293.1| 237 genpafgvdfverfgerafamaarqrslRTLGNQQSPFDAWQTLQGIETLPLRMEQHCENAHEVATFLRDHDDVAWV 313
                                       9**************************************************************************** PP

                                       E-TTSTTSTTHHHHHHHSSS.G-SEEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHH CS
                   Cys_Met_Meta_PP 277 yYpglpshpqhelakkqlkg.aggvlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipkeere 352
                                       +Ypg+++h++h+ a ++l g +gg+++F l ++ ++ak+ ++n+ l+s+++++G++++li++pas+tha+++++e++
  gi|313125029|ref|YP_004035293.1| 314 SYPGFEDHESHDNATEYLDGgFGGMVTFGLADGYAAAKRTCENTALASFLANVGDAKTLIIHPASTTHAQLSADEQR 390
                                       *****************9862567***************************************************** PP

                                       HTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 353 aagvtddliRlsvGiEdvdDliaDlkqal 381
                                       aagv +d++RlsvGiEd+ D++aDl++++
  gi|313125029|ref|YP_004035293.1| 391 AAGVGPDMLRLSVGIEDAADIVADLDESI 419
                                       *************************9986 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   3.1e-08   0.00014      77     210 ..      86     215 ..      76     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.1e-08
                                       HHHHCCCC..-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETT CS
                       Aminotran_5  77 valslars..lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnv 151
                                       +al +a s   ++gd++v ++  + ++     ++a r+g++++v++      ld d+++++++ +t+ v++  + n 
  gi|313125029|ref|YP_004035293.1|  86 AALDAATSllASAGDNVVASADMYGGTSTYLTKMATRRGVDIRVVET-----LDYDAYADAIDADTAFVHVETIANP 157
                                       3333333334799********999999999***************98.....9************************ PP

                                       TTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EE CS
                       Aminotran_5 152 tGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGv 210
                                       +    ++e+++++a++ ga ++vD + a +     + + g+D++  s+ K l  +G++v
  gi|313125029|ref|YP_004035293.1| 158 SLKTPDFERLAHVAHEGGAPLVVDNTFATPYLCRPI-EHGADIVWESTTKWLHGSGTTV 215
                                       ************************987777655444.5688888888888666666665 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.1   3.2e-06     0.014      20     145 ..      57     182 ..      39     191 .. 0.84
   2 ?   -1.4   0.0      0.26   1.1e+03     244     320 ..     253     326 ..     247     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-06
                                       SSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTT CS
                   DegT_DnrJ_EryC1  20 tsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdt 96 
                                       +s+p+++ +E ++aa      a+a++sG aAl  a + l    gd V+  +  + +t    +++ a+   vD+    
  gi|313125029|ref|YP_004035293.1|  57 ISNPTTRVLEDRLAALEAGVGAVATASGMAALDAATSLLASA-GDNVVASADMYGGTSTYLTKM-ATRRGVDIRV-V 130
                                       44999****************************998887665.9*************9998887.5667899995.5 PP

                                       SSB-GGGCGGG--TTEEEEEEB-GGGB--....-HHHHHHHHHHCT-EEEEE- CS
                   DegT_DnrJ_EryC1  97 ynidpaaieaaitertkaIlpVhlyGqva....dmdalkaiaakhglkvieDa 145
                                        ++d +a + ai   t+ +  V++  +++    d+++l  +a++ g +++ D 
  gi|313125029|ref|YP_004035293.1| 131 ETLDYDAYADAIDADTAFV-HVETIANPSlktpDFERLAHVAHEGGAPLVVDN 182
                                       589***********99765.56666666556679**************99996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHH CS
                   DegT_DnrJ_EryC1 244 RreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvyae 320
                                       R  +++  ++ L+ l++ ++ +++ +++ + +  +++++e++ e +  e++++l+++   + v yp  ++ ++  ++
  gi|313125029|ref|YP_004035293.1| 253 RAFAMAARQRSLRTLGN-QQSPFDAWQTLQGIETLPLRMEQHCE-NAHEVATFLRDHDDVAWVSYP-GFEDHESHDN 326
                                       66667777888888885.57788888876788888999997766.889999999988777777774.6666665555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.8e-06     0.039      30     168 ..      58     182 ..      39     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.8e-06
                                       --HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT CS
                   Beta_elim_lyase  30 edktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea 106
                                        ++t+++Led++a+l    +a+ +++G aA   + ++l+  g++v+++  a ++  +   +  +a  + +d++  e 
  gi|313125029|ref|YP_004035293.1|  58 SNPTTRVLEDRLAALEAGVGAVATASGMAALDAATSLLASAGDNVVAS--ADMYGGTSTYLTKMATRRGVDIRVVE- 131
                                       599************9999********************999999865..77888888888888888888999999. PP

                                       TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                   Beta_elim_lyase 107 GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                        ++d ++ ++ai++  +    ++++ +++  n      ++    +++a++a++ g pl++D 
  gi|313125029|ref|YP_004035293.1| 132 -TLDYDAYADAIDA--D----TAFVHVETIANP----SLKTPDFERLAHVAHEGGAPLVVDN 182
                                       .9************..3....778888877774....7889999999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2550.60
//
Query:       gi|313125030|ref|YP_004035294.1|  [L=402]
Description: homoserine o-acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-32  110.9   0.1    9.2e-32  110.7   0.1    1.1  1  Abhydrolase_1  alpha/beta hydrolase fold
    0.00075   20.2  13.9     0.0015   19.2  13.7    1.6  2  Abhydrolase_6  Alpha/beta hydrolase family
     0.0089   15.3   0.0      0.015   14.6   0.0    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.047   13.8   0.0    1.5  1  Abhydrolase_4  TAP-like protein
      0.026   14.2   0.0       0.11   12.2   0.0    1.8  2  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.1   2.6e-35   9.2e-32       1     257 []      38     356 ..      38     356 .. 0.94

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 2.6e-35
                                       SEEEEE-STTTCGGG.............GTTGHHHHHHHHT..TSEEEEEEETTSTTSSSTTTGB........CHHS CS
                     Abhydrolase_1   1 pvlvilhGlpgssdv.............waerglapaLakd..gfdvillDlrGvgySspapacin.......ddyg 55 
                                       ++++++h+l+gs +v             w++  ++p+ a d  ++ v++ +++G++y++++pa+ +       +d++
  gi|313125030|ref|YP_004035294.1|  38 NAVLVCHALTGSQNVagygtetagqaraWWNDIVGPGKAIDtnEYYVVCANVPGSCYGTTGPASESpdgepygTDFP 114
                                       68*********88888888888899999***********999*********************999**********9 PP

                                       HHHHHHHHH...HHHHHCTTSSEE.EEEETHHHHHHHHHHHHHGGGEEEEEEESE....CSSCCHHHHHHHHHHHHH CS
                     Abhydrolase_1  56 tasvaddld...rildalgddklt.lvGhSmGGmialayaaeyperVkalvllga....idpaaslieaqrqqaksf 124
                                        +++ d+ +   r+ld lg+++l+ +vG+S GGm al +  +yp+ V+ l ++++     + + +l+  +r+++ ++
  gi|313125030|ref|YP_004035294.1| 115 PVTIGDWTRaqrRLLDELGVGRLHaVVGGSVGGMNALDWVRRYPDDVRYLLAVATagrlDPQCLALDAIARRSITTD 191
                                       99999999988788********************************************9999*************** PP

                                       HCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHH...............HCHHHCCHHHHHHHCHHHHHHHH CS
                     Abhydrolase_1 125 pdffdgyaadcarnpagplladelaaleqrhrlvdalkf...............pdkskrfpssgsdnasslatgal 186
                                       p+++ g+++d +++ +g+ la++l+++ + ++ + + kf               +d + +f   ++d +s+l+++a 
  gi|313125030|ref|YP_004035294.1| 192 PNWNGGDYYDSEPPDDGLALARQLGHVMYLSKSSMERKFgrraagrdarrdsfpADPAASFFA-YRDVESYLDYQAE 267
                                       **********************************99999**************7777777776.88*********** PP

                                       HHHHHHHHCCHHHHHHHHHC.............THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS.....EEEEEE CS
                     Abhydrolase_1 187 ksieqwpttdsaklllrlre.............lknvlaptlvisgtsDplvppkaledlaqllpk.....krlvvi 245
                                       k++++++++ + +l +  +              + +    +l++s t D+ ++ ++ e la+ +++     + +v++
  gi|313125030|ref|YP_004035294.1| 268 KFVDRFDANSYLYLTRAMDDydlaegyeddadaVAAFEGEALLLSFTGDWHFTTEQAESLAESFRDtsvpvAHHVIE 344
                                       ***********999999888*******999666555555************************9999999899**** PP

                                       ETCSSSHHHHSH CS
                     Abhydrolase_1 246 sdagHlaflegp 257
                                       sd gH+afl++p
  gi|313125030|ref|YP_004035294.1| 345 SDHGHDAFLVEP 356
                                       *********986 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.74   2.6e+03      60      81 ..      34      58 ..      20      87 .. 0.69
   2 !   19.2  13.7   4.2e-07    0.0015      10     217 ..      56     359 ..      40     360 .. 0.48

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.74
                                      TT..TTSEEEEEETCHHH.....HHHH CS
                     Abhydrolase_6 60 laagggpvvlvGHSlGGa.....lala 81
                                      +  +g+++vlv+H l G+     ++++
  gi|313125030|ref|YP_004035294.1| 34 F--DGDNAVLVCHALTGSqnvagYGTE 58
                                      3..588999999998887554444444 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4.2e-07
                                       ..........G.CHHHHHHHHCCT....CEEEEE--TTS..T..............S-GGCS--HHHC.HHHHHHHC CS
                     Abhydrolase_6  10 s......assW.lvapLaallaag....vhvlapDlpGh..G..............rsdpppldledl.adlaalld 58 
                                       +      a++W     ++  + a     + v++   pG   G              ++d pp +  d  +++++lld
  gi|313125030|ref|YP_004035294.1|  56 GtetagqARAWwN--DIVGPGKAIdtneYYVVCANVPGScyGttgpasespdgepyGTDFPPVTIGDWtRAQRRLLD 130
                                       1445555666632..44222222233456779999999999855555553332222224444444443366699999 PP

                                       CTT..TTSE.EEEEETCHHHHHHHHHHCC...EE..EEES-.................................... CS
                     Abhydrolase_6  59 elaagggpv.vlvGHSlGGalalaaapla.lvvg..vlldp..................................pp 97 
                                       el+   g+   +vG S GG+ al +++   ++v+  +++++                                  p 
  gi|313125030|ref|YP_004035294.1| 131 ELG--VGRLhAVVGGSVGGMNALDWVRRYpDDVRylLAVATagrldpqclaldaiarrsittdpnwnggdyydseP- 204
                                       996..7777899********99994444445555543333344555555544445555555443444443333222. PP

                                       ----TTTS----TTHHHHHHTT-CCCCHCCH....S-HSCCCCHHH....CCCCHCHCCCGHH.............. CS
                     Abhydrolase_6  98 talpagllaaalelllallallrllawlsre....plprlfladed....adaawrarlarla.............. 152
                                         ++ + la+ l ++  l ++ +   + +r+    +++++f ad++    a++++  +l+  a              
  gi|313125030|ref|YP_004035294.1| 205 -PDDGLALARQLGHVMYLSKSSMERKFGRRAagrdARRDSFPADPAasffAYRDVESYLDYQAekfvdrfdansyly 280
                                       .2222223444444443333333333332223343333366665553222122222222222233333333333443 PP

                                       HHCCHHCHTTCCHHTT-TTGC.......EEE.CTT-CHHHHCHHCCCH..STTEEET....CE...SSS-HHHHSHH CS
                     Abhydrolase_6 153 allaglgllpaaawadlpvpl.......lvl.ggeDplvprllerlla..qagarlp....vvlpgaGHlphleepd 215
                                        ++a++++  a+ ++d   ++       l+l  ++D +     ++ la   ++  +p    v+  + GH  +l ep+
  gi|313125030|ref|YP_004035294.1| 281 LTRAMDDYDLAEGYEDDADAVaafegeaLLLsFTGDWHFTTEQAESLAesFRDTSVPvahhVIESDHGHDAFLVEPE 357
                                       22224445556677777777777788887775488885443333444445555555556637777****55554887 PP

                                       HH CS
                     Abhydrolase_6 216 ev 217
                                       +v
  gi|313125030|ref|YP_004035294.1| 358 KV 359
                                       76 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.1e-06     0.015      78     117 ..     138     177 ..     126     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.1e-06
                       Hydrolase_4  78 lfllGhSmGGliallyllrypdkvaglilsaPalkikakl 117
                                       + ++G S+GG+ al ++ rypd+v+ l  +a+a +++++ 
  gi|313125030|ref|YP_004035294.1| 138 HAVVGGSVGGMNALDWVRRYPDDVRYLLAVATAGRLDPQC 177
                                       6899*****************************9999875 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.3e-05     0.047      35      95 ..     306     371 ..     289     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                     Abhydrolase_4  35 apvLllqnerDpaTPyegakklakalgg.a....vlvtvegeGHgalaagntCvdkavdaYLltGe 95 
                                        ++Lll+ ++D    +e+a++la+ +++ +    ++v++ + GH+a+  + + v  +v+++L+ G 
  gi|313125030|ref|YP_004035294.1| 306 GEALLLSFTGDWHFTTEQAESLAESFRDtSvpvaHHVIESDHGHDAFLVEPEKVGPPVRDFLDAGV 371
                                       679************************9746666**************8888899*******9885 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.9e-05      0.11     107     169 ..     123     198 ..      97     231 .. 0.75
   2 ?   -0.8   0.0      0.27   9.7e+02     208     240 ..     320     352 ..     308     355 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                                       HHHCSEECCC.....EEEEEETHHHHHHHHHHHCSTT..TCCEEEEES--S-CC....HCHHHC......TTCCHHH CS
                          Esterase 107 danfrtapdg.....ravaGqSmGGlgALilalkhpd..rFgsvssfSpivnps....namWgq......eekeawq 166
                                       +a++r  ++      +av+G S GG+ AL    ++pd  r+  + + ++ ++p     +    +      +++++w+
  gi|313125030|ref|YP_004035294.1| 123 RAQRRLLDELgvgrlHAVVGGSVGGMNALDWVRRYPDdvRYLLAVATAGRLDPQclalD----AiarrsiTTDPNWN 195
                                       5555555555566779*********************4446667777788888755531....22334555556665 PP

                                       CC- CS
                          Esterase 167 end 169
                                        +d
  gi|313125030|ref|YP_004035294.1| 196 GGD 198
                                       555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                                       HHHHHCCHHHHCCCCCCTT-SCCCC--SSHHHH CS
                          Esterase 208 vlarnrelkeqlaargvegedheydGghsweyW 240
                                       +++++++l+e +++ +v+   h+ +++h   ++
  gi|313125030|ref|YP_004035294.1| 320 TTEQAESLAESFRDTSVPVAHHVIESDHGHDAF 352
                                       578899999999999**9999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 2179.86
//
Query:       gi|313125031|ref|YP_004035295.1|  [L=144]
Description: hypothetical protein Hbor_02460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 825.77
//
Query:       gi|313125032|ref|YP_004035296.1|  [L=436]
Description: o-acetylhomoserine sulfhydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.1e-135  449.9   0.0   5.8e-135  449.7   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    2.5e-08   33.5   0.0    3.9e-08   32.9   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    9.6e-06   25.1   0.2    3.1e-05   23.5   0.2    1.7  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0066   15.5   0.0      0.013   14.4   0.0    1.4  1  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.7   0.0  1.3e-138  5.8e-135       2     382 .]      16     432 ..      15     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 449.7 bits;  conditional E-value: 1.3e-138
                                       HHHHHTTTTCHTTTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESS CS
                   Cys_Met_Meta_PP   2 Tllvhagqekdeqtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalavss 75 
                                       T  +hagq++d +tga+a+piy+t++y+f+d+++a   fa e++gy+YsR++npt+ +l+er+a Legg  a a++s
  gi|313125032|ref|YP_004035296.1|  16 TRSLHAGQDPDAATGARAPPIYQTTSYVFDDAEDAagqFALEKEGYIYSRLMNPTVATLQERLASLEGGVGAAATAS 92 
                                       889*****************************999999*************************************** PP

                                       HHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT- CS
                   Cys_Met_Meta_PP  76 GmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllk 152
                                       GmaA ++a + l++aGd+iv+ ++lYggt+ +l++++++ gi++kfvdt d ++  +ai+e t  v++Et++np l 
  gi|313125032|ref|YP_004035296.1|  93 GMAAFDLATFLLASAGDNIVSASSLYGGTYTYLTHTVERRGITTKFVDTLDYDAYDEAIDEDTAFVHVETIGNPALV 169
                                       ***************************************************************************** PP

                                       ---HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHH.. CS
                   Cys_Met_Meta_PP 153 vvDiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflq.. 227
                                       ++D+e++a++a+++gv+++vDntfa+p+l++pl++gaD+v +S+TK++ G +++++G++v+ g++ +++ + + +  
  gi|313125032|ref|YP_004035296.1| 170 TPDFERLADIAHDHGVPLFVDNTFATPYLCQPLEHGADLVWESTTKWIHGAGTTIGGILVDGGSFPWTDYADKYPei 246
                                       *********************************************************************9999889* PP

                                       ..............................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEE CS
                   Cys_Met_Meta_PP 228 ..............................nalGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkve 274
                                                                     ++lG+  spfdaw +l  ++ L +R+erh enA+ vAefLe+h++v+
  gi|313125032|ref|YP_004035296.1| 247 akpnsayhgvnfaerfgdaaftyaaiarglRDLGNQQSPFDAWNTLEKVESLPMRMERHCENAQVVAEFLESHDEVS 323
                                       ***************************************************************************** PP

                                       EEE-TTSTTSTTHHHHHHHSSSG-S.EEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHH CS
                   Cys_Met_Meta_PP 275 kvyYpglpshpqhelakkqlkgagg.vlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipkee 350
                                       +v+Ypgl+sh+ he a k+l g+ g +++F l+ +  +a++ v++++l+sl++++G++++l+++pas+th+++++ee
  gi|313125032|ref|YP_004035296.1| 324 WVNYPGLESHETHEEASKYLDGGYGgMITFGLEAGYDAARETVNHVELASLLANVGDAKTLVIHPASTTHQQLTEEE 400
                                       ********************987555*************************************************** PP

                                       HHHTTS-TTEEEEE--SS-HHHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 351 reaagvtddliRlsvGiEdvdDliaDlkqale 382
                                       + aagvt+d++RlsvG+Ed+dD++aDl+qa+e
  gi|313125032|ref|YP_004035296.1| 401 QVAAGVTPDMVRLSVGVEDADDIVADLQQAIE 432
                                       *****************************985 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   8.6e-12   3.9e-08      46     194 ..      71     197 ..      42     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 8.6e-12
                                       HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEES....S-THHHHHHHHTTSEEE CS
                     Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdp....tyasyknilrlsggevv 118
                                        ++l+e+la++ g          +a  + sG  a + a + l++  +gd+i++ +     ty+  ++ ++ +g++  
  gi|313125032|ref|YP_004035296.1|  71 VATLQERLASLEG--------GVGAAATASGMAAFDLATFLLAS--AGDNIVSASSlyggTYTYLTHTVERRGITTK 137
                                       5678888888888........77789999999988777777776..******99862233667777888999***** PP

                                       EEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCB CS
                     Aminotran_1_2 119 ryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfv 194
                                        +        +ld +a++ea++e       t ++ ve++ NP  + ++ e l ++   a+ +++ lfvD ++a+ +
  gi|313125032|ref|YP_004035296.1| 138 FVD-------TLDYDAYDEAIDE------DTAFVHVETIGNPALVTPDFERLADI---AHDHGVPLFVDNTFATPY 197
                                       ***.......*************......899**********9999999999999...*************99755 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   6.9e-09   3.1e-05      21     145 ..      65     191 ..      46     200 .. 0.84
   2 ?   -1.8   0.0      0.33   1.5e+03     251     318 ..     272     336 ..     267     351 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.9e-09
                                       S..SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THH....HHHHHHTT-EEEEE- CS
                   DegT_DnrJ_EryC1  21 s..gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvat....anavlelgakpvfvD 91 
                                       +  +p+v+ + +++a   g   a a++sG aA  la   l   +gd ++ +s  + +t     ++v + g ++ fvD
  gi|313125032|ref|YP_004035296.1|  65 RlmNPTVATLQERLASLEGGVGAAATASGMAAFDLATFLLAS-AGDNIVSASSLYGGTytylTHTVERRGITTKFVD 140
                                       24599******************************9777655.59****99987777722225788899******** PP

                                       B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB--....-HHHHHHHHHHCT-EEEEE- CS
                   DegT_DnrJ_EryC1  92 vdpdtynidpaaieaaitertkaIlpVhlyGqva....dmdalkaiaakhglkvieDa 145
                                              +d +a  +ai e t+  + V++ G++a    d+++l +ia++hg++++ D 
  gi|313125032|ref|YP_004035296.1| 141 T------LDYDAYDEAIDEDTA-FVHVETIGNPAlvtpDFERLADIAHDHGVPLFVDN 191
                                       6......69***********96.5689*****988889****************9996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.33
                                       HHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCH CS
                   DegT_DnrJ_EryC1 251 ykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvy 318
                                       + ++L++l++ ++ +++ +++ + +  +++++e++ e + + ++e+l+++   + v yp  l+++++ 
  gi|313125032|ref|YP_004035296.1| 272 IARGLRDLGN-QQSPFDAWNTLEKVESLPMRMERHCE-NAQVVAEFLESHDEVSWVNYP-GLESHETH 336
                                       5566666664.45666666654566666666665544.556666666666555555553.55555555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     3e-06     0.013     126     207 ..     141     221 ..      88     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-06
                                       CBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTT CS
                       Aminotran_5 126 eldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKl 202
                                       +ld d+++++++e+t+ v++  + n   +  ++e+++++a+++g+ ++vD + a +     + + g+D++  s+ K 
  gi|313125032|ref|YP_004035296.1| 141 TLDYDAYDEAIDEDTAFVHVETIGNPALVTPDFERLADIAHDHGVPLFVDNTFATPYLCQPL-EHGADLVWESTTKW 216
                                       5999**********************************************988877665554.56888888888884 PP

                                       TSSTT CS
                       Aminotran_5 203 lgPtG 207
                                       +  +G
  gi|313125032|ref|YP_004035296.1| 217 IHGAG 221
                                       44445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2492.25
//
Query:       gi|313125033|ref|YP_004035297.1|  [L=388]
Description: phosphate/sulfate permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.3e-38  130.5  34.1    2.3e-37  128.8  34.1    1.7  1  PHO4       Phosphate transporter family
  ------ inclusion threshold ------
       0.64   10.5   2.8       0.56   10.7   0.2    2.3  2  DUF4713    Domain of unknown function (DUF4713)


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8  34.1   2.6e-41   2.3e-37       1     309 [.      20     306 ..      20     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 2.6e-41
                              PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwl 77 
                                       iG   ++ af+++vgs++++   A +l++if ++G +++G +V+ t+++ ++    +     +++ +++ll  ++ l
  gi|313125033|ref|YP_004035297.1|  20 IGGSNTGVAFGPAVGSRTVSKFGAGVLMGIFALFGGWTVGRRVVTTLGSDLI----IGDPFTVAASVVILLFIGLAL 92 
                                       68889999*******************************************9....32233457888899999**** PP

                              PHO4  78 llatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknal 154
                                       ++ +++g+P+St+++ vGa++G +la+   + +  + +++iv  w+++P+lg+ ++a++   v   i   + +   +
  gi|313125033|ref|YP_004035297.1|  93 FVSNLFGIPASTSMTAVGAVAGYGLAT---DRLAVQLIMEIVSWWLVAPILGFWLSAVVGRYVYDDIA--SVVAIDR 164
                                       **************************5...55666779********************9999988855..3344444 PP

                              PHO4 155 ralpvlvlvtiailalsilfkgeskkddeeteklf.kflqvvsaalvsfahGanDvanaiGpllaalisiykaskev 230
                                          p+++l    ++ +  l        +++ ++l  + l+v  +++++f+ Ga++vana++pl +   s+      +
  gi|313125033|ref|YP_004035297.1| 165 SDGPLVILRRDGVVPVPAL------GAGTTPRELTgSLLVVAIGCFMAFSAGASNVANAVAPL-VGNGSL------S 228
                                       4455443333333333332......344555666669999***********************.433221......2 PP

                              PHO4 231 plwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGla 307
                                           +ll g aia+G l++++r  +t+G+++t+ l  + ++++++++a++v ++s lg+P S+  ++++++vG G+ 
  gi|313125033|ref|YP_004035297.1| 229 MNAGILLAGGAIAIGALTIARRTLETMGNELTE-LPLTAALVVATVSATLVTVLSLLGIPASFVVIATMSTVGLGWG 304
                                       34567788889*********************5.******************************************9 PP

                              PHO4 308 kk 309
                                       ++
  gi|313125033|ref|YP_004035297.1| 305 RE 306
                                       94 PP

>> DUF4713  Domain of unknown function (DUF4713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   6.3e-05      0.56       5      40 ..      57      92 ..      56      95 .. 0.89
   2 ?   -2.7   0.3      0.94   8.5e+03      38      44 ..     279     285 ..     276     295 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.3e-05
                           DUF4713  5 svlqevllkLqslqpfqspwdiaaFvvlllFigtVl 40
                                      +v+ +v++ L s     +p ++aa vv+llFig  l
  gi|313125033|ref|YP_004035297.1| 57 TVGRRVVTTLGSDLIIGDPFTVAASVVILLFIGLAL 92
                                      68889999999999999***************9766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.94
                           DUF4713  38 tVllLll 44 
                                       tVl+Ll 
  gi|313125033|ref|YP_004035297.1| 279 TVLSLLG 285
                                       6666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2191.36
//
Query:       gi|313125034|ref|YP_004035298.1|  [L=385]
Description: phosphate/sulfate permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-43  147.2  21.7    1.3e-42  146.1  21.3    1.8  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.1  21.3     7e-47   1.3e-42       1     337 []      20     376 ..      20     376 .. 0.88

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 7e-47
                              PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselm.lgmlaallgaavw 76 
                                       iG   ++ af+++vgs+ ++   A+ l++ f +lG +++G eV +t++ +iv      +se++ ++ +a+l+  ++ 
  gi|313125034|ref|YP_004035298.1|  20 IGGSSTGVAFGPAVGSGLVSKLLAAGLMTAFALLGGWTAGREVIKTMGGQIV-----PQSEFTlAASVAVLFFVGFA 91 
                                       68889999********************************************.....4555554899********** PP

                              PHO4  77 lllatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklkna 153
                                       ll+ +++g+P+St+++ vGa++G ++a+    +++   +++i+  w+++P++++ + a++   v  + l  +kl  +
  gi|313125034|ref|YP_004035298.1|  92 LLISNTFGVPASTSMTAVGAIAGLGVAT---GTLNEAVMLEIISWWIVAPVIAFWVCAVIGRYVYPY-L-DAKL--E 161
                                       ***************************5...456777799********************9999999.3.3444..4 PP

                              PHO4 154 lralpvlvlvtiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGplla..alisiykask 228
                                       l + p     ++ +  + il k     +++  e + ++l++  a++++++ Ga+++ana++pl+   al        
  gi|313125034|ref|YP_004035298.1| 162 LDSSPGP---LVEFDNAGILPKLRLGPNTTPREAWSTVLVIAIACYMAYSAGASNAANAVAPLVGngAL-------- 227
                                       5555533...4456666666666444555556666799*************************442222........ PP

                              PHO4 229 evplw.vlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGv 304
                                         +l   +llg+ ai+lG +++++r   tvG+++t+ l    ++ +e+++a +++++s++g+P S    +++++vG 
  gi|313125034|ref|YP_004035298.1| 228 --KLNeGILLGAGAIGLGAFTIARRTLDTVGNDLTE-LPILAALIVETVSASLIAFLSYIGIPASLAVSATMCIVGL 301
                                       ..2222789**************************5.**************************************** PP

                              PHO4 305 Glak..........................................kresavnwklvrnivlaWvlTlpvsalls 337
                                       G+ +                                           ++   + ++++++++ W+lT  +sal s
  gi|313125034|ref|YP_004035298.1| 302 GWGRatrtvtlgealggkspemsvnalaaetqeevpamgqetetdlAGSDLFDPGTTGRVIFFWLLTPSLSALAS 376
                                       **********************************************6668*********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2417.10
//
Query:       gi|313125035|ref|YP_004035299.1|  [L=129]
Description: ferredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-15   54.6   0.3    1.1e-14   54.1   0.3    1.3  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.021   14.8   0.2      0.045   13.8   0.2    1.6  1  Fer2_4    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.3   1.3e-18   1.1e-14       9      74 ..      40     104 ..      33     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 1.3e-18
                                       EEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCECTT.SSSSTHHHHHTTEEEEGGG CS
                              Fer2   9 evevadgettlldaaeenggidipysCggggCgtClvevlegevqsd.etelegeeldegklrlaCq 74 
                                       ++ev++ge+ +l+aae + g+d p+sC++g+C+ C++ v+ege+q d ++ l++ee  e+ +rl+C 
  gi|313125035|ref|YP_004035299.1|  40 TLEVNQGEY-ILEAAEAQ-GYDWPFSCRAGACANCAAIVKEGEIQMDmQQILSDEEVSEKNVRLTCI 104
                                       6899*****.******88.*************************6556******************6 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   5.1e-06     0.045      12      58 ..      40      76 ..      32      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-06
                            Fer2_4 12 evtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVev 58
                                      +++v +G+ +++A+ a+g d+p sc            g+C nC   v
  gi|313125035|ref|YP_004035299.1| 40 TLEVNQGEYILEAAEAQGYDWPFSCRA----------GACANCAAIV 76
                                      469**********************98..........5566665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 779.08
//
Query:       gi|313125036|ref|YP_004035300.1|  [L=319]
Description: leader peptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-11   44.8   0.4    8.4e-10   39.0   0.4    2.3  1  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
    1.4e-09   38.3   7.1    3.1e-09   37.2   7.1    1.6  1  Peptidase_A24  Type IV leader peptidase family
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.29   11.1   0.0    1.6  1  CbiN           Cobalt transport protein component CbiN


Domain annotation for each model (and alignments):
>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.4   1.4e-13   8.4e-10       3      92 .]     156     308 ..     154     308 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.4e-13
                       Arc_PepC_II   3 llymligyrvkvkellkkflflleefeekdgk.....ikrkfisvekeld........................... 47 
                                       l +m++g+r+ v +l++ +++l e  +    +       r++++     +                           
  gi|313125036|ref|YP_004035300.1| 156 LPLMFLGRRIPVGSLATAHGRLFETTTGYTRNgldidALRMYLRW----Rgttlselrehpdklrdptsitethept 228
                                       778999999999999999999998766433333333333333333....2445678999999999999999999999 PP

                       Arc_PepC_II  48 .......................................eelrkelkkykkkglieetvWvtygvPflipitaGfii 85 
                                                                              e+lr+ l+ + +++    +vW+++g+Pf++p+++G +i
  gi|313125036|ref|YP_004035300.1| 229 dgavgdgmavdggtvetedpwgaaaflddidstaygttpEKLRDGLQVVASQD----EVWISPGIPFIVPMFVGTVI 301
                                       99999999999999999999999999999999999777777777777777776....9******************* PP

                       Arc_PepC_II  86 alvlGDl 92 
                                       a+ +GD+
  gi|313125036|ref|YP_004035300.1| 302 AFTYGDI 308
                                       ******7 PP

>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   7.1   5.1e-13   3.1e-09       1      91 [.      11     107 ..      11     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 5.1e-13
                     Peptidase_A24   1 lvlltillvlsviDldtrtlpdeltlpllllgvlfa.....qllllglpnlaqavlgalvgalvllli........s 64 
                                       lv++ +l  ++++D++tr++p  +++pl+ lgv++              +la a + +l ++ v +++        +
  gi|313125036|ref|YP_004035300.1|  11 LVIVPVLGWAAWQDIETRRVPSVIWYPLVALGVVLLawdtlP-------HLAFAPEDILYFVRVGISLlfvaplsyI 80 
                                       588999*****************************9555442.......4444444443333333332222333446 PP

                     Peptidase_A24  65 lvdeqamGgGDvklaavlgaflgwerl 91 
                                       +++++++Gg+D+k +++++++++ +  
  gi|313125036|ref|YP_004035300.1|  81 FWRLGGFGGADAKALITISILVPTFPQ 107
                                       88********************95544 PP

>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.8e-05      0.29       6      40 ..      67     103 ..      62     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                              CbiN   6 llvvllavvplflv..kgaeFgGaDdqaeevIeeiap 40 
                                       + + ll+v+pl ++  +   FgGaD +a   I+ + p
  gi|313125036|ref|YP_004035300.1|  67 VGISLLFVAPLSYIfwRLGGFGGADAKALITISILVP 103
                                       67889******999988889********888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1921.89
//
Query:       gi|313125037|ref|YP_004035301.1|  [L=116]
Description: hypothetical protein Hbor_02520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.015   14.9   2.2        4.4    7.0   3.0    2.2  2  Oxidored_q2     NADH-ubiquinone/plastoquinone oxidoreductase 
       0.23   11.2   1.0       0.51   10.1   1.0    1.6  1  Phage_Coat_Gp8  Phage major coat protein, Gp8
       0.38   10.9  11.0      0.072   13.2   6.0    2.0  2  DUF4229         Protein of unknown function (DUF4229)
       0.88    7.4   1.9          1    7.1   1.9    1.1  1  DUF4175         Domain of unknown function (DUF4175)


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0026        12      54      74 ..      45      73 ..       8      81 .. 0.72
   2 ?    7.0   3.0   0.00098       4.4      70      90 ..      90     110 ..      80     116 .] 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0026
                                      ................TTSCGGHHHHHHH CS
                       Oxidored_q2 54 i........tnpatefadplpqalvLtai 74
                                      +        + ++t++ad lp a+vL++ 
  gi|313125037|ref|YP_004035301.1| 45 VryrtewtgDPDRTSAADGLPSAFVLFVG 73
                                      144556666788999***********985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00098
                                       HHHHHHHHHHHHHHHHHHHHH CS
                       Oxidored_q2  70 vLtaivigaaetavgLallvr 90 
                                       +L+++v+ga ++a+gL++l++
  gi|313125037|ref|YP_004035301.1|  90 ALVVLVVGALVAAIGLGILLA 110
                                       799***************976 PP

>> Phage_Coat_Gp8  Phage major coat protein, Gp8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.0   0.00011      0.51      28      41 ..      88     101 ..      85     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHH CS
                    Phage_Coat_Gp8  28 aWavVvvvvvAtlg 41 
                                        Wa+Vv+vv+A ++
  gi|313125037|ref|YP_004035301.1|  88 RWALVVLVVGALVA 101
                                       6*********9664 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.17   7.5e+02       3      28 ..      21      46 ..      19      52 .. 0.73
   2 ?   13.2   6.0   1.6e-05     0.072       8      52 ..      68     112 ..      68     116 .] 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                           DUF4229  3 YtlaRlaLfvvltavillvarliglp 28
                                      Ytl   +L  +++++ ++v+ +++++
  gi|313125037|ref|YP_004035301.1| 21 YTLYADLLLSATAGLCWGVGSALTVR 46
                                      56655567778899999999887765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.6e-05
                           DUF4229   8 laLfvvltavillvarliglpvpllvaallAlvvalplSmvllkk 52 
                                       ++Lfv+l++v +++    gl+  l+v+++ Alv+a  l+++l ++
  gi|313125037|ref|YP_004035301.1|  68 FVLFVGLFGVHAGLPIPDGLRWALVVLVVGALVAAIGLGILLARR 112
                                       68*************999999*******************99776 PP

>> DUF4175  Domain of unknown function (DUF4175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.9   0.00023         1      15      58 ..      67     112 ..      62     116 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00023
                           DUF4175  15 alflalsllglwqll..pdllrlalllafalallaalvlplrrfrw 58 
                                       a++l + l+g++  l  pd lr+al+++++ al+aa+ l+++  r+
  gi|313125037|ref|YP_004035301.1|  67 AFVLFVGLFGVHAGLpiPDGLRWALVVLVVGALVAAIGLGILLARR 112
                                       46677788888877622799*****************999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 798.20
//
Query:       gi|313125038|ref|YP_004035302.1|  [L=121]
Description: phosphoribosyl-amp cyclohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-35  120.4   0.1    3.5e-35  119.7   0.1    1.3  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.1     2e-39   3.5e-35       1      74 []      29     102 ..      29     102 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 2e-39
                                       EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                            PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                                       mlay++ eale+t etg+a+yySrsr++lW KG+tSg++q+v+e+r+DcD+D+ll+ veq+g aCHtg++sCFy
  gi|313125038|ref|YP_004035302.1|  29 MLAYVSPEALERTRETGRAHYYSRSRDELWEKGATSGHTQSVEEVRVDCDADTLLYLVEQTGGACHTGRRSCFY 102
                                       9************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.34s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 719.85
//
Query:       gi|313125039|ref|YP_004035303.1|  [L=379]
Description: hypothetical protein Hbor_02540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.044   13.8   0.3       0.19   11.8   0.3    2.1  1  VHL_C         VHL box domain
      0.082   12.9   3.9        0.2   11.7   0.3    3.0  3  SOAR          STIM1 Orai1-activating region
       0.55   10.3   2.7        7.3    6.7   0.0    3.7  4  Sel_put       Selenoprotein, putative
        6.4    7.4   8.7        2.6    8.7   1.4    3.2  2  Syntaxin-6_N  Syntaxin 6, N-terminal


Domain annotation for each model (and alignments):
>> VHL_C  VHL box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   4.2e-05      0.19      14      41 ..     317     344 ..     316     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHH-XXXXXXXXXXXXXXXXXX CS
                             VHL_C  14 cLqvvRkLVrpedyrrLeIarcLkeeLe 41 
                                       +L+ vR+L r++dy+rL  a   + eL 
  gi|313125039|ref|YP_004035303.1| 317 ALRTVRELTRRDDYDRLRTAARARTELT 344
                                       799**************98877777776 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   4.4e-05       0.2      22      95 ..     127     200 ..     120     205 .. 0.92
   2 ?    0.1   0.1      0.18   7.9e+02      41      61 ..     293     313 ..     290     353 .. 0.63
   3 ?   -0.9   0.1      0.37   1.6e+03      64      85 ..     355     376 ..     345     378 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.4e-05
                              SOAR  22 lnkkkqeaekqlqeAkeeveklkkkrssllgslrlahssslddvdkkileakqaleevtkelkerqeRWqqiek 95 
                                       +  +++e++++l+eA++ ++ l k   s +++l  +      dvd+ + ++++ +++ +++++e+ + ++q e+
  gi|313125039|ref|YP_004035303.1| 127 YLDHRTETKEELTEARRDAKLLLKDTDSRISELERLVELGEADVDAPVEHIRDPIDRYNEAVSEEFQSFKQSES 200
                                       556899***************************9999999999************************9999887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                              SOAR  41 eklkkkrssllgslrlahsss 61 
                                       e l++k + l++ l   +s++
  gi|313125039|ref|YP_004035303.1| 293 ETLRRKANELVSVLDRFASET 313
                                       667777777777665444433 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.37
                              SOAR  64 dvdkkileakqaleevtkelke 85 
                                        v+++++e+++a ++++ +l+e
  gi|313125039|ref|YP_004035303.1| 355 AVETELHELREAHDKLADALSE 376
                                       5677777777777777777766 PP

>> Sel_put  Selenoprotein, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0016       7.3       3      27 ..      48      72 ..      46      76 .. 0.91
   2 ?    0.3   0.1      0.16   7.3e+02      21      33 ..     123     135 ..     118     141 .. 0.78
   3 ?   -1.3   0.0      0.52   2.3e+03      37      53 ..     222     238 ..     220     242 .. 0.81
   4 ?   -1.7   0.0       0.7   3.1e+03      11      24 ..     319     332 ..     315     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0016
                           Sel_put  3 rralrrvrqylrllvGepdYerYve 27
                                      r+a+r +++y ++ vG  d+++Yve
  gi|313125039|ref|YP_004035303.1| 48 RKAIRLLDNYEESAVGTGDFQAYVE 72
                                      8999********************8 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.16
                           Sel_put  21 dYerYvehmrrhH 33 
                                       +Y +Y++h+ ++ 
  gi|313125039|ref|YP_004035303.1| 123 SYVEYLDHRTETK 135
                                       6888999988774 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.52
                           Sel_put  37 ppmsereFfrerqdary 53 
                                       pp   reF re  da +
  gi|313125039|ref|YP_004035303.1| 222 PPRDLREFVRESPDADE 238
                                       777889****9988876 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.7
                           Sel_put  11 qylrllvGepdYer 24 
                                       +++r+l+  +dY+r
  gi|313125039|ref|YP_004035303.1| 319 RTVRELTRRDDYDR 332
                                       56777777777776 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.4   0.00058       2.6      23      70 ..     123     169 ..     112     199 .. 0.77
   2 ?    1.3   0.7      0.11     5e+02      24      42 ..     348     366 ..     291     378 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00058
                      Syntaxin-6_N  23 rwerlledtssstseeldetrteLrkalrsiewdledLeetvrivekn 70 
                                       ++ + l+  + +t+eel e+r++ +  l++ +  +++Le+ v+  e++
  gi|313125039|ref|YP_004035303.1| 123 SYVEYLDHRT-ETKEELTEARRDAKLLLKDTDSRISELERLVELGEAD 169
                                       4444444433.469****************************877664 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                      Syntaxin-6_N  24 werlledtssstseeldet 42 
                                        erl++ + +++ +el+e+
  gi|313125039|ref|YP_004035303.1| 348 LERLRSGAVETELHELREA 366
                                       1222222222233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2335.81
//
Query:       gi|313125040|ref|YP_004035304.1|  [L=93]
Description: hypothetical protein Hbor_02550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.1   1.6       0.14   12.2   0.1    2.2  2  DUF3185   Protein of unknown function (DUF3185)


Domain annotation for each model (and alignments):
>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.013   2.3e+02      46      57 ..       3      14 ..       1      23 [. 0.68
   2 ?   12.2   0.1   7.6e-06      0.14      39      57 ..      73      91 ..      67      93 .] 0.76

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.013
                           DUF3185 46 igGgvaaivGlv 57
                                      + G+ a+++Gl+
  gi|313125040|ref|YP_004035304.1|  3 VVGALALLTGLA 14
                                      556666666665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.6e-06
                           DUF3185 39 dktlllligGgvaaivGlv 57
                                      +++++ll+ G++a ++Gl+
  gi|313125040|ref|YP_004035304.1| 73 ERGVILLVFGAIACLFGLF 91
                                      6788888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 599.24
//
Query:       gi|313125041|ref|YP_004035305.1|  [L=193]
Description: acetyltransferase (gnat) family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-14   53.8   0.0    2.5e-14   53.5   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.1e-09   35.7   0.0    1.2e-08   35.0   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.7e-08   34.7   0.0    2.6e-08   34.2   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.1e-05   23.9   0.0    4.6e-05   23.3   0.0    1.3  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.014   16.1   0.0      0.017   15.8   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.016   15.3   0.0      0.024   14.7   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   8.5e-18   2.5e-14      19     117 .]      49     166 ..      20     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 8.5e-18
                                       HHHHH..HHHHHHSTTCEEEE..EEET...........TEEEEEEEEEEEET.....TSTTEEEEEEEEESGGGTTS CS
                    Acetyltransf_1  19 aseee..feesfsleaegllv..aeed...........geliGfisllkipd.....ekggvayieslaVspeyrgk 75 
                                       +  e    +e +s  +e+++v  a e+           + ++G++++ ++p       + + a+++ l+V+p+++g 
  gi|313125041|ref|YP_004035305.1|  49 RASELkaAYETASAANESHIVavADEEsadtggavtggESIVGYARGVWDPVrtesfAADDDAELRALYVRPDHWGE 125
                                       2222223344467777756663444448888888888566*****************9999**************** PP

                                       SHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1  76 GlGsaLlealeerareegikkivlaveedndaairlYek.lGF 117
                                       G+GsaLl  le  a   g++++ l++++dn+  +++Y +  GF
  gi|313125041|ref|YP_004035305.1| 126 GIGSALLSSLESNAPA-GVDRLALQTFADNEDGCAFY-RtRGF 166
                                       ***********96665.59******************.76999 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   3.9e-12   1.2e-08      49     119 ..     108     179 ..      54     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.9e-12
                   Acetyltransf_10  49 rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgeeqeenGir 119
                                       +d+ ++  l+V+p++ g Gig+aLl  +e++a  +g    +l   a++    +fY++ GF++vge+++e G +
  gi|313125041|ref|YP_004035305.1| 108 DDDAELRALYVRPDHWGEGIGSALLSSLESNA-PAGVDRlALQTFADNeDGCAFYRTRGFEVVGENTYEVGDE 179
                                       4455999************************9.7888888********9*****************9998865 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   8.8e-12   2.6e-08       4      75 ..      68     167 ..      64     168 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8.8e-12
                                       EEEEEEET...........TEEEEEEEEEEES...........TCTEEEEE-GGGTTSSHHHHHHH.HTT....SEE CS
                    Acetyltransf_7   4 evfVaedd...........gkivGfialslld...........aeitrlaVdpeyrgkGiGraLle.aae....kgi 53 
                                        v Va+++           + ivG+++ + +            ae+  l+V+p++ g GiG+aLl  + e     g+
  gi|313125041|ref|YP_004035305.1|  68 IVAVADEEsadtggavtggESIVGYARGVWDPvrtesfaadddAELRALYVRPDHWGEGIGSALLSsL-EsnapAGV 143
                                       455665557777777777777788888777779998888877666666*****************943.22446564 PP

                                       E.EE.EEEETHHHHHHHHHHTTEE CS
                    Acetyltransf_7  54 i.le.qlelnaekaikfYeklGFe 75 
                                         l  q+  ++e   +fY+  GFe
  gi|313125041|ref|YP_004035305.1| 144 DrLAlQTFADNEDGCAFYRTRGFE 167
                                       3323344444446677*******8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.5e-08   4.6e-05      19      82 ..     108     172 ..      90     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.5e-08
                                       -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE.EE CS
                              FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki.ee 82 
                                        d+ el al+v+p+h ++G gs l ++l  +  +  + + l + a+N+  +++y   Gfe+  e+
  gi|313125041|ref|YP_004035305.1| 108 DDDAELRALYVRPDHWGEGIGSALLSSLESNAPAGVDRLALQTFADNEDGCAFYRTRGFEVVgEN 172
                                       4559***************************99999999999*****************998444 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   5.6e-06     0.017      44     137 ..      56     166 ..      10     167 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.6e-06
                    Acetyltransf_3  44 awaeeseeeg.ygwaivl...kdtg........viGsv.glrdleeedee......aelg.ymlapsfwgkGyatea 100
                                       a+++ s+ ++    a+ +    dtg        ++G++ g++d  + + +      ael  ++++p++wg G+++  
  gi|313125041|ref|YP_004035305.1|  56 AYETASAANEsHIVAVADeesADTGgavtggesIVGYArGVWDPVRTE-SfaadddAELRaLYVRPDHWGEGIGSAL 131
                                       322222222213344433333222233333443799996666555444.359999999985678899********** PP

                    Acetyltransf_3 101 vralleyafeelglerlvavidkeNeaSirvleklGf 137
                                       +++l   a    g++rl   + ++Ne   + ++  Gf
  gi|313125041|ref|YP_004035305.1| 132 LSSLESNA--PAGVDRLALQTFADNEDGCAFYRTRGF 166
                                       ****9999..5679***********988777777777 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   8.2e-06     0.024      58     140 ..      87     172 ..      82     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.2e-06
                    Acetyltransf_4  58 drivGyaylg..qfkkr..akdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhk 130
                                       + ivGya+++   ++    a d  ael  + ++ d   eg+g++l+ +le  +   ++ +l  +++++ne   +f+ 
  gi|313125041|ref|YP_004035305.1|  87 ESIVGYARGVwdPVRTEsfAADDDAELRALYVRPDHWGEGIGSALLSSLESNA-PAGVDRLALQTFADNEDGCAFYR 162
                                       6788888877644433335778888887655578999************9877.569******************** PP

                    Acetyltransf_4 131 alGFelvgif 140
                                         GFe+vg+ 
  gi|313125041|ref|YP_004035305.1| 163 TRGFEVVGEN 172
                                       *******974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.35s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1123.30
//
Query:       gi|313125042|ref|YP_004035306.1|  [L=454]
Description: phosphomannomutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-34  116.1   0.0    1.6e-33  115.3   0.0    1.4  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    4.7e-28   97.8   0.2      1e-27   96.7   0.2    1.6  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.7e-16   59.1   0.5    2.1e-15   56.6   0.5    2.3  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
    3.3e-13   49.8   0.0    7.1e-13   48.8   0.0    1.5  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
     0.0013   18.8   0.0      0.003   17.6   0.0    1.5  1  Melibiase_C  Alpha galactosidase C-terminal beta sandwich dom
  ------ inclusion threshold ------
      0.036   14.2   1.1        1.8    8.8   0.2    2.8  2  CinA_KH      Damage-inducible protein CinA KH domain
       0.39   10.8   2.3       0.68   10.0   0.9    2.1  2  Smoothelin   Smoothelin cytoskeleton protein


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   6.3e-37   1.6e-33       2     136 ..       2     130 ..       1     132 [. 0.96

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 6.3e-37
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fg sG Rg+vg g ltpe+v+++++a++++  +     + vv+rDtR++++++++a+ +gla+ Gv+v +lg +p
  gi|313125042|ref|YP_004035306.1|   2 KLFGSSGTRGVVGDG-LTPEFVLRVSKAAGTVWGS----DRAVVARDTRTTGEMFSNAATSGLASVGVDVDVLGAVP 73 
                                       68***********77.9*****************9....6************************************* PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT-E CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekeee 136
                                       tP v  +++  ++ a ++itaSHnppeyngiK++  +G+++s ++ e+Ie+++ +ee+
  gi|313125042|ref|YP_004035306.1|  74 TPGVVRYCEVEEVPA-VVITASHNPPEYNGIKLVGDDGVELSVADLERIEDHVLAEEF 130
                                       *******99988888.************************************998876 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.2     4e-31     1e-27       2     103 .]     150     250 ..     149     250 .. 0.99

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 4e-31
                                       HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHG CS
                        PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielv 78 
                                       +Y+++l++ vd+eai+ ++l+v++dp+hGag  + ++ ++elg++vv++na+pd++fp++ ++p   + l +l++lv
  gi|313125042|ref|YP_004035306.1| 150 DYVDDLLASVDREAIADANLTVALDPGHGAGCLTSPDFFRELGCEVVTVNANPDGHFPGRESEPVG-SKLGDLCRLV 225
                                       7*****************************************************************.********** PP

                                       GGGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  79 kkegadlglafDgDaDRlgvvderG 103
                                       k+++ad+g+a+DgDaDR ++vde+G
  gi|313125042|ref|YP_004035306.1| 226 KASDADVGIAHDGDADRAVFVDENG 250
                                       ***********************98 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.5   8.3e-19   2.1e-15      13      69 ..     390     443 ..     366     448 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 8.3e-19
                                       .EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHH CS
                        PGM_PMM_IV  13 vaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeev 69 
                                        a++a+++ +  + +g + +++d+++l vRpSGTep++rvy+Ea++++++++la+  
  gi|313125042|ref|YP_004035306.1| 390 YAESADATPN--TTDGYRLDYGDAWVL-VRPSGTEPKVRVYAEARDEARAEDLAAGA 443
                                       4555566555..***************.*************************9765 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   2.8e-16   7.1e-13       4     110 ..     258     361 ..     255     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.8e-16
                                       HHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHT...T..ECEEEETTCEEE CS
                       PGM_PMM_III   4 qllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkee...g..avlGgEeSghii 75 
                                       +l+al+a +l e    ++ + v+ v  s+ l +v+++ g++l  t++G  +++ ++++    g  + ++gE +g+i+
  gi|313125042|ref|YP_004035306.1| 258 SLAALAAAQLEE----DD-TAVAAVNVSQRLVDVCNEVGANLELTPIGATNLITRIRDLwaqGetVPIAGEGNGGIF 329
                                       466777776644....35.49************************************99666256************ PP

                                       ETTTBSS--HHHHHHHHHHHHHHHTS-HHHHHHHH CS
                       PGM_PMM_III  76 fldeattkDGilaallvleilaetgkslselleel 110
                                       f+++   +DG+++a+++le+++++   +s+++ + 
  gi|313125042|ref|YP_004035306.1| 330 FPNYRLVRDGAYTAAKFLELITDR--EVSDVV-AP 361
                                       *********************775..788887.54 PP

>> Melibiase_C  Alpha galactosidase C-terminal beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-06     0.003       8      51 ..     264     316 ..     259     329 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                                       EEE-SSS-EEEEEEE.....-E.....EEEE-..GTT--S-..EEEEETTTTEE CS
                       Melibiase_C   8 akpLsdGdvaValfN.....rt...tvtvdws..dlglpgsssysvrDlWtgkd 51 
                                       a++L++ d+aVa +N      +   +v ++++   +g ++    ++rDlW++ +
  gi|313125042|ref|YP_004035306.1| 264 AAQLEEDDTAVAAVNvsqrlVDvcnEVGANLEltPIGATNL-ITRIRDLWAQGE 316
                                       679************97644115566777776559998888.89******9976 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.042   1.1e+02      30      61 ..     360     389 ..     343     394 .. 0.76
   2 ?    8.8   0.2   0.00071       1.8      34      69 ..     418     453 ..     414     454 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.042
                                       EEEEETTEEEEEEE...EEHHHHHHHHH.... CS
                           CinA_KH  30 AiyakegevtvRltakaaneeeaealiapvee 61 
                                       A+y  ++ v vR+    ++e+e ea+++ + e
  gi|313125042|ref|YP_004035306.1| 360 APY--TDYVNVRVNLGYDDEAELEAMLDAARE 389
                                       555..46688999999***********98766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00071
                                       ETTEEEEEEE...EEHHHHHHHHH....HHHHHTTT CS
                           CinA_KH  34 kegevtvRltakaaneeeaealiapveeeirerlgd 69 
                                       +  e +vR+ a+a++e+ ae l+a +++++ ++l d
  gi|313125042|ref|YP_004035306.1| 418 SGTEPKVRVYAEARDEARAEDLAAGAKDALLAALED 453
                                       567889******************999999888865 PP

>> Smoothelin  Smoothelin cytoskeleton protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6   4.1e+03       9      19 ..     113     123 ..     110     126 .. 0.81
   2 ?   10.0   0.9   0.00027      0.68      19      35 ..     376     392 ..     374     393 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                        Smoothelin   9 ltseeLeaIeD 19 
                                       l+  +Le IeD
  gi|313125042|ref|YP_004035306.1| 113 LSVADLERIED 123
                                       67789****99 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00027
                        Smoothelin  19 DeevLdkmLeqasdyEe 35 
                                       De++L+ mL++a +y e
  gi|313125042|ref|YP_004035306.1| 376 DEAELEAMLDAAREYAE 392
                                       9**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2768.89
//
Query:       gi|313125043|ref|YP_004035307.1|  [L=245]
Description: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-75  252.7   6.4    3.1e-75  252.5   6.4    1.0  1  His_biosynth    Histidine biosynthesis protein
    1.7e-11   43.8   0.4    2.4e-05   23.6   0.0    2.1  2  Dus             Dihydrouridine synthase (Dus)
    3.3e-10   39.7   2.0    1.4e-05   24.4   0.5    2.1  2  DHO_dh          Dihydroorotate dehydrogenase
      8e-10   38.4   7.9    4.7e-05   22.8   0.4    2.1  2  ThiG            Thiazole biosynthesis protein ThiG
    3.3e-09   36.6  15.4    9.3e-07   28.5   6.1    2.1  2  NMO             Nitronate monooxygenase
    1.8e-05   24.1   4.6    0.00074   18.9   1.0    2.2  2  TMP-TENI        Thiamine monophosphate synthase
    2.3e-05   23.7   1.5     0.0033   16.6   0.1    2.9  3  IGPS            Indole-3-glycerol phosphate synthase
    0.00013   21.5   3.7       0.15   11.5   0.4    2.2  2  PcrB            PcrB family
    0.00027   20.4   2.5      0.011   15.2   0.4    2.2  2  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
    0.00053   18.9   4.3        0.1   11.4   0.2    2.2  2  Trp_syntA       Tryptophan synthase alpha chain
     0.0051   15.9   6.6       0.11   11.5   1.5    2.1  2  IMPDH           IMP dehydrogenase / GMP reductase domain
     0.0059   15.8   1.6       0.76    8.9   0.2    2.3  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
      0.009   15.1  10.6       0.25   10.3   2.2    2.2  2  FMN_dh          FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.087   12.0   0.1       0.22   10.7   0.1    1.6  2  DUF561          Protein of unknown function (DUF561)
       0.24   10.8   7.1        2.8    7.3   1.2    2.7  3  BtpA            BtpA family
        1.5    8.9   6.5        9.8    6.3   1.4    2.5  2  PA              PA domain
        1.6    8.1   5.1       0.99    8.8   0.5    2.4  3  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.5   6.4     3e-78   3.1e-75       2     229 .]      10     234 ..       9     234 .. 0.98

  Alignments for each domain:
  == domain 1  score: 252.5 bits;  conditional E-value: 3e-78
                                       EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEE CS
                      His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqv 78 
                                       ++pa+D++dG+vV+lv+G+r +e+ry gdpv++a+r+ +egad lh+vDld+a+eg+++n d+ve+++++v++pvq+
  gi|313125043|ref|YP_004035307.1|  10 VVPAVDMQDGEVVQLVQGERGTEKRY-GDPVAAAERWINEGADTLHLVDLDGAFEGERQNADAVEAVVDAVDVPVQL 85 
                                       89******************777666.9************************************************* PP

                                       ESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHH CS
                      His_biosynth  79 GGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakk 155
                                       GGGIr+  d+ +lle+g+++vi+gtaav+np++++e+++++++ +++v++Da++g +v+++gw+e tgld+   a +
  gi|313125043|ref|YP_004035307.1|  86 GGGIRTAADAIDLLERGVERVILGTAAVENPDIVREISDAHPG-SVMVSLDAKDG-EVVVSGWTEGTGLDPAAAAAR 160
                                       *******************************************.***********.********************* PP

                                       HHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS- CS
                      His_biosynth 156 leelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegelt 229
                                       +eelgag+il+td+d +G l+G+   +t+++ +av+ipv+asGGv+sl+d+++lk++g++av+vg+alye  +t
  gi|313125043|ref|YP_004035307.1| 161 YEELGAGAILFTDVDVEGQLEGIQTAVTQRVVDAVTIPVVASGGVASLSDVRALKEAGAAAVVVGTALYEDAFT 234
                                       **********************************************************************9875 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.3e-08   2.4e-05     167     229 ..      63     125 ..      38     139 .. 0.90
   2 !   18.7   0.1   7.2e-07   0.00076     177     227 ..     190     240 ..     180     245 .] 0.83

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.3e-08
                                       -C.G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHHH CS
                               Dus 167 eg.tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaestav 229
                                       eg + + +a+++v +av +pv   G+I++a da + le+ G++ v+ g +a +nP +++e   +
  gi|313125043|ref|YP_004035307.1|  63 EGeRQNADAVEAVVDAVDVPVQLGGGIRTAADAIDLLER-GVERVILGTAAVENPDIVREISDA 125
                                       56688999******************************9.*****************9974344 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 7.2e-07
                                       HHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HH CS
                               Dus 177 evkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.st 227
                                        v +av+ipv+a G++ +++d++a l+e Ga +v++g + +++ + +++ + 
  gi|313125043|ref|YP_004035307.1| 190 RVVDAVTIPVVASGGVASLSDVRA-LKEAGAAAVVVGTALYEDAFTLQAaQD 240
                                       6789999**************987.5666***********998877775454 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.3e-05     0.014     241     289 ..      79     124 ..      67     127 .. 0.86
   2 !   24.4   0.5   1.4e-08   1.4e-05     231     286 ..     185     237 ..     178     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                                       TTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHH CS
                            DHO_dh 241 lkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikk 289
                                       ++  +p+   GGi ++ Da++ +e G   v ++ta   e+p i+++i +
  gi|313125043|ref|YP_004035307.1|  79 VD--VPVQLGGGIRTAADAIDLLERGVERVILGTAA-VENPDIVREISD 124
                                       44..888888*************************9.899***999976 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHH CS
                            DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakk 286
                                       ++v +++ + +   ip++++GG+ s  D+    eaGA++v v+tal +e+ +  + 
  gi|313125043|ref|YP_004035307.1| 185 TAVTQRVVDAVT--IPVVASGGVASLSDVRALKEAGAAAVVVGTAL-YEDAFTLQA 237
                                       555666666666..********************************.999887765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.4   4.5e-08   4.7e-05     162     215 ..      67     120 ..      35     131 .. 0.84
   2 !   19.4   2.0   5.1e-07   0.00054     135     209 ..     156     230 ..     136     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.5e-08
                                       S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 162 lnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                       +n+ a++ +++ ++vPv +  Gi+++ da+  +e G++ v+l ta  e  d+v+
  gi|313125043|ref|YP_004035307.1|  67 QNADAVEAVVDAVDVPVQLGGGIRTAADAIDLLERGVERVILGTAAVENPDIVR 120
                                       67899****************************************999988875 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 5.1e-07
                                       HHHHHHHHTT-SEBEEBSSST.TS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
                              ThiG 135 vlarrleevGcaavmPlaapi.GsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavae 209
                                        +a r ee+G+ a++     + G  +G++++   + +++ +++Pv+   G+ s sd+ +  e Ga av++ ta+ e
  gi|313125043|ref|YP_004035307.1| 156 AAAARYEELGAGAILFTDVDVeGQLEGIQTAV-TQRVVDAVTIPVVASGGVASLSDVRALKEAGAAAVVVGTALYE 230
                                       568899*****999988877747778888765.577899**********************************865 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.9   2.6e-05     0.027     179     224 ..      66     111 ..      39     126 .. 0.87
   2 !   28.5   6.1   8.8e-10   9.3e-07     181     225 ..     184     228 ..     117     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                               NMO 179 kglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                       ++    v+ v+davd+Pv   GGi ++ +    L +G + v +gt+
  gi|313125043|ref|YP_004035307.1|  66 RQNADAVEAVVDAVDVPVQLGGGIRTAADAIDLLERGVERVILGTA 111
                                       455677999************************************8 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 8.8e-10
                               NMO 181 lfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                       ++a+ ++v+dav iPv+A GG+    +v a   +GA++v +gt++
  gi|313125043|ref|YP_004035307.1| 184 QTAVTQRVVDAVTIPVVASGGVASLSDVRALKEAGAAAVVVGTAL 228
                                       578999*************************************97 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1     0.004       4.2     136     177 ..      66     108 ..      62     112 .. 0.84
   2 !   18.9   1.0     7e-07   0.00074     114     180 ..     158     227 ..     147     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.004
                          TMP-TENI 136 plgleglkelaealeiPvvaiGGit.lenvaevleagadgvav 177
                                        ++ + ++++++a+ +Pv   GGi+ ++++ ++le g+++v +
  gi|313125043|ref|YP_004035307.1|  66 RQNADAVEAVVDAVDVPVQLGGGIRtAADAIDLLERGVERVIL 108
                                       67888999****************625789999*****99865 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 7e-07
                          TMP-TENI 114 algadYigvGpifpTdtKkdaeplglegl..kelaealeiPvvaiGGi.tlenvaevleagadgvavvsa 180
                                       a+    +g+G+i  Td   + +  g++++  +++++a++iPvva GG+ +l++v ++ eaga+ v v +a
  gi|313125043|ref|YP_004035307.1| 158 AARYEELGAGAILFTDVDVEGQLEGIQTAvtQRVVDAVTIPVVASGGVaSLSDVRALKEAGAAAVVVGTA 227
                                       455566899*******9999966666654449***************945799***********999776 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.014        14     215     251 ..      86     122 ..      61     124 .. 0.80
   2 ?   -0.9   0.1      0.69   7.2e+02      69      91 ..     153     174 ..     150     189 .. 0.77
   3 !   16.6   0.1   3.1e-06    0.0033     200     245 ..     189     232 ..     178     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                                       ESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHH CS
                              IGPS 215 eSGiktredveklkeegvnafLvGeslmrqedvekai 251
                                         Gi+t++d+ +l e gv+ ++ G++ ++++d  ++i
  gi|313125043|ref|YP_004035307.1|  86 GGGIRTAADAIDLLERGVERVILGTAAVENPDIVREI 122
                                       569************************9999976665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.69
                                       -HHHHHHHHTTT.-SEEEEE--C CS
                              IGPS  69 dpaeiAkkyeeagAsaiSVLtee 91 
                                       dpa+ A  yee gA ai   t+ 
  gi|313125043|ref|YP_004035307.1| 153 DPAAAAARYEELGAGAI-LFTDV 174
                                       789999*******9998.45555 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 3.1e-06
                                       HHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-T CS
                              IGPS 200 eeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqe 245
                                       +++++ v   + +va  G+++  dv++lke+g+ a+ vG++l +++
  gi|313125043|ref|YP_004035307.1| 189 QRVVDAVT--IPVVASGGVASLSDVRALKEAGAAAVVVGTALYEDA 232
                                       44444444..789*****************************8765 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   0.00016      0.17     163     223 ..      64     123 ..      40     126 .. 0.78
   2 !   11.5   0.4   0.00015      0.15     166     216 ..     181     236 ..     150     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                       TSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHHHHH CS
                              PcrB 163 GaledveevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekderkidail 223
                                       G  ++ ++v a++  ++   +  GGGir a +A + +e   + ++ G++  e++ + +++i 
  gi|313125043|ref|YP_004035307.1|  64 GERQNADAVEAVVDAVD-VPVQLGGGIRTAADAIDLLERgVERVILGTAAVENP-DIVREIS 123
                                       44455555555555543.45778****************9********999999.5666665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00015
                                       S-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH...H CS
                              PcrB 166 edv.eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd...e 216
                                       e +  +v + +    ++ ++  GG+ s  + +   ea A ++vvG++++e+    +
  gi|313125043|ref|YP_004035307.1| 181 EGIqTAVTQRVVDAVTIPVVASGGVASLSDVRALKEAgAAAVVVGTALYEDAftlQ 236
                                       4443333333333445567889**************9*************984443 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.013        13     130     167 ..      71     108 ..      67     113 .. 0.87
   2 !   15.2   0.4     1e-05     0.011     125     168 ..     182     225 ..     172     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                                       HHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                      G3P_antiterm 130 vikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                        ++++ +++++p+  GG i+t  d  ++l+ G+  v  
  gi|313125043|ref|YP_004035307.1|  71 AVEAVVDAVDVPVQLGGGIRTAADAIDLLERGVERVIL 108
                                       577888999***********************998865 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1e-05
                                       GGGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 125 glvpkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                       g+   v++++ ++++ip++a+G + + +dv+++ +aGa av ++
  gi|313125043|ref|YP_004035307.1| 182 GIQTAVTQRVVDAVTIPVVASGGVASLSDVRALKEAGAAAVVVG 225
                                       566789999*******************************9865 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.2   9.9e-05       0.1     187     232 ..      69     115 ..      61     133 .. 0.87
   2 !    9.0   0.6   0.00054      0.57     190     232 ..     188     231 ..     175     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.9e-05
                                       HHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 187 delverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                        ++ve++ ++ +vPv +G Gi+t++++  +  ++ + vi G a v++
  gi|313125043|ref|YP_004035307.1|  69 ADAVEAVVDAVDVPVQLGGGIRTAADAIDLLeRGVERVILGTAAVEN 115
                                       6789999999**************999999989**********9974 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00054
                                       HHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 190 verlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                        +r+ ++ + Pv    G+++ ++v+++  ++a++v+vG al ++
  gi|313125043|ref|YP_004035307.1| 188 TQRVVDAVTIPVVASGGVASLSDVRALKeAGAAAVVVGTALYED 231
                                       4678888889**9999************99*********99765 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.3    0.0022       2.3     128     173 ..      64     109 ..      30     114 .. 0.58
   2 !   11.5   1.5    0.0001      0.11     175     239 ..     165     228 ..     157     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0022
                                       SSHHHHHHHHHHHHHTTTSEE.EEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 128 hsekvleavkeikkkveevev.iaGnvataegakaLieagadavkvG 173
                                        +++  +av+++ ++v +v v ++G + ta+ a +L+e g++ v  G
  gi|313125043|ref|YP_004035307.1|  64 GERQNADAVEAVVDAV-DVPVqLGGGIRTAADAIDLLERGVERVILG 109
                                       4445556666666666.333324666777777777777777666555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0001
                                       S-STTBHHHH.HCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 175 GpGsiCttrv.vagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsll 239
                                       G+G+i  t v v g   +  tAv+   ++++   +pv+a GG+ +  d+     aGa av++G  l
  gi|313125043|ref|YP_004035307.1| 165 GAGAILFTDVdVEGQLEGIQTAVT--QRVVDAVTIPVVASGGVASLSDVRALKEAGAAAVVVGTAL 228
                                       666666665435555555555554..357888899********999998766689*****999876 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0055       5.8     137     185 ..      72     121 ..      56     126 .. 0.78
   2 !    8.9   0.2   0.00072      0.76     143     177 ..     195     229 ..     164     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0055
                                       HHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHH CS
                              NanE 137 vkalsea.glkviaeGrintPekakkaieiGvdavvvGsaitrleeiakk 185
                                       v+a+++a ++ v   G i t + a + +e Gv+ v++G+a     +i++ 
  gi|313125043|ref|YP_004035307.1|  72 VEAVVDAvDVPVQLGGGIRTAADAIDLLERGVERVILGTAAVENPDIVRE 121
                                       5555554367788899***********************98877777765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00072
                                       TT--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                              NanE 143 aglkviaeGrintPekakkaieiGvdavvvGsait 177
                                         + v+a G + +    +   e G++avvvG+a+ 
  gi|313125043|ref|YP_004035307.1| 195 VTIPVVASGGVASLSDVRALKEAGAAAVVVGTALY 229
                                       4678*****************************85 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   2.2   0.00024      0.25     251     302 ..      62     111 ..      39     114 .. 0.81
   2 !    9.7   1.5   0.00036      0.38     261     303 ..     188     228 ..     159     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                                       STT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                            FMN_dh 251 ldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                       ++g     d+  ++v+av+  ++v + gGir+ +D++  l  G + v+lG +
  gi|313125043|ref|YP_004035307.1|  62 FEGERQNADAVEAVVDAVD--VPVQLGGGIRTAADAIDLLERGVERVILGTA 111
                                       5666777899999999997..***************************9976 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00036
                                       HHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 261 LpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                        +++v+av   i+v+++gG+ + sDv      GA av++G ++
  gi|313125043|ref|YP_004035307.1| 188 TQRVVDAVT--IPVVASGGVASLSDVRALKEAGAAAVVVGTAL 228
                                       356777775..***************99999*********765 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.6   2.8e+03     177     197 ..      71      91 ..      61     100 .. 0.70
   2 ?   10.7   0.1   0.00021      0.22     176     217 ..     186     228 ..     172     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.6
                            DUF561 177 styeiskkvslPvicasGlsd 197
                                       ++ +++ +v++Pv    G+ +
  gi|313125043|ref|YP_004035307.1|  71 AVEAVVDAVDVPVQLGGGIRT 91 
                                       455677777777777777665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00021
                            DUF561 176 astyeiskkvslPvicasGlsdvtvplals.lgasGiGigsav 217
                                       a t  ++ +v++Pv+++ G+++++   al+ +ga+ + +g a+
  gi|313125043|ref|YP_004035307.1| 186 AVTQRVVDAVTIPVVASGGVASLSDVRALKeAGAAAVVVGTAL 228
                                       67899******************99889864799999998775 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0055       5.8     178     228 ..      58     110 ..      45     137 .. 0.77
   2 ?   -1.0   0.0      0.93   9.8e+02     175     188 ..     140     153 ..     128     169 .. 0.80
   3 ?    7.3   1.2    0.0027       2.8     164     211 ..     183     230 ..     152     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0055
                              BtpA 178 lsGkatGgevdleelklaketvkvkvlvgsGvse..enlekllsiadGvivgt 228
                                       l G   G++ +++ ++++ ++v+v+v  g G+ +  + ++ l +  + vi+gt
  gi|313125043|ref|YP_004035307.1|  58 LDGAFEGERQNADAVEAVVDAVDVPVQLGGGIRTaaDAIDLLERGVERVILGT 110
                                       678999*************************8641144444444555555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.93
                              BtpA 175 avilsGkatGgevd 188
                                        v++sG++ G+  d
  gi|313125043|ref|YP_004035307.1| 140 EVVVSGWTEGTGLD 153
                                       499*****998766 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0027
                              BtpA 164 vkdtvergladavilsGkatGgevdleelklaketvkvkvlvgsGvse 211
                                       ++ +v +  +dav +   a+Gg ++l ++++ ke+    v+vg+   e
  gi|313125043|ref|YP_004035307.1| 183 IQTAVTQRVVDAVTIPVVASGGVASLSDVRALKEAGAAAVVVGTALYE 230
                                       45677788899999999******************9999999997655 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3      0.03        31      37      80 ..     156     201 ..     124     206 .. 0.69
   2 ?    6.3   1.4    0.0093       9.8      39      54 ..     211     226 ..     205     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.03
                                PA  37 eKarnAqaaGAagviiv...ndgelgaatgasgnegepdgitiPavg 80 
                                         a+  ++ GA ++++    ++g + +  +++ +++  d +tiP+v 
  gi|313125043|ref|YP_004035307.1| 156 AAAARYEELGAGAILFTdvdVEG-QLEGIQTAVTQRVVDAVTIPVVA 201
                                       44555567888888888764333.4555556778888999****985 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0093
                                PA  39 arnAqaaGAagviivn 54 
                                       +r+ ++aGAa+v++ +
  gi|313125043|ref|YP_004035307.1| 211 VRALKEAGAAAVVVGT 226
                                       68899*********83 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.3   1.3e+03      21      38 ..      45      62 ..      34      85 .. 0.69
   2 ?    0.6   0.2      0.29   3.1e+02     159     196 ..      75     111 ..      65     113 .. 0.74
   3 ?    8.8   0.5   0.00094      0.99     157     198 .]     187     229 ..     171     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                                      HHHTT-SEEEEEEEBSSS CS
                    Ribul_P_3_epim 21 veeagadllHvDvmDghf 38
                                        ++gad+lH+   Dg f
  gi|313125043|ref|YP_004035307.1| 45 WINEGADTLHLVDLDGAF 62
                                      457888888876667766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.29
                                       HHHHHT---EEEEESS--TT.TCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 159 lidekeldlkievDGGvkld.nieqiaeagadvlVagsa 196
                                       ++d+  +d+ ++  GG++++  +  + e g++ ++ g+a
  gi|313125043|ref|YP_004035307.1|  75 VVDA--VDVPVQLGGGIRTAaDAIDLLERGVERVILGTA 111
                                       4444..88999999***8651567888999999999987 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00094
                                       HHHHHHHT---EEEEESS--.TTTCHHHHHHT--EEEESHHHH CS
                    Ribul_P_3_epim 157 rklidekeldlkievDGGvk.ldnieqiaeagadvlVagsavf 198
                                        +      +++ + + GGv  l  ++++ eaga ++V+g+a++
  gi|313125043|ref|YP_004035307.1| 187 VTQRVVDAVTIPVVASGGVAsLSDVRALKEAGAAAVVVGTALY 229
                                       3333333578889999**962789*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1591.17
//
Query:       gi|313125044|ref|YP_004035308.1|  [L=203]
Description: imidazoleglycerol-phosphate dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-61  206.2   1.7    2.5e-61  206.2   1.7    1.3  2  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.51   9.2e+03      18      31 ..      26      39 ..      12      40 .. 0.55
   2 !  206.2   1.7   1.4e-65   2.5e-61       1     144 []      41     183 ..      41     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.51
                                      T--EEEEEEESSH. CS
                              IGPD 18 gfdlkvkvkgdlev 31
                                      ++ l+++ +gd +v
  gi|313125044|ref|YP_004035308.1| 26 EVTLTIDGDGDATV 39
                                      34444444455555 PP

  == domain 2  score: 206.2 bits;  conditional E-value: 1.4e-65
                                       ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEE CS
                              IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaeval 77 
                                       Tg+gf+dhmL+++akhg fdl+v+++gdle+ddHhtvedv+i++G a++ealgdkrgi R+++  +p+Dea+a v++
  gi|313125044|ref|YP_004035308.1|  41 TGVGFFDHMLEAFAKHGLFDLTVNCDGDLEIDDHHTVEDVAIVIGDAFSEALGDKRGIVRYADRQVPLDEAVAGVVV 117
                                       9**************************************************************************** PP

                                       E--SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                              IGPD  78 dlsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                       d+sgrpy+ +++e+++e+ig+++ ++ ++f  sla++ag+tlh +++ genahh +ealfKa+araL
  gi|313125044|ref|YP_004035308.1| 118 DVSGRPYFDFDGEFSQEQIGDFTSDMARHFGYSLAMHAGLTLHTEIR-GENAHHEAEALFKALARAL 183
                                       ********************************************977.******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1285.84
//
Query:       gi|313125045|ref|YP_004035309.1|  [L=266]
Description: hypothetical protein Hbor_02600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.03   14.7   0.0       0.08   13.3   0.0    1.8  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.27   11.9   0.2       0.27   11.9   0.2    2.3  2  TSP9             Thylakoid soluble phosphoprotein TSP9
        1.4    8.6  10.9        1.8    8.2  10.9    1.2  1  DUF966           Domain of unknown function (DUF966)
        2.2    7.5   9.9          3    7.0   9.9    1.1  1  ORC6             Origin recognition complex subunit 6 (ORC6)
        3.5    6.2   6.3        4.4    5.8   6.3    1.1  1  Hamartin         Hamartin protein
        5.3    5.7  13.0        6.6    5.4  13.0    1.0  1  Mitofilin        Mitochondrial inner membrane protein


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.7e-05      0.08       2      34 ..       3      41 ..       2      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                   Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigq......cvyCadC 34
                                      +L  C+fCgg+a  + + ++++   +      +v C+ C
  gi|313125045|ref|YP_004035309.1|  3 QLRSCDFCGGDAAGIYEVLPAELSPTeseqrrVVLCDGC 41
                                      899*********999988887644447888888888778 PP

>> TSP9  Thylakoid soluble phosphoprotein TSP9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2     9e-05      0.27      33      76 ..      50      94 ..      42      97 .. 0.67
   2 ?   -1.0   1.1      0.94   2.8e+03      31      59 ..     127     161 ..     117     175 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9e-05
                              TSP9 33 dPlLkKVdekegsggrttvrggktsaavkvapkkkeeGgfgGf.g 76
                                      dPlL++    e++ + +  ++++ s++ +++p++ e+G  gG+ g
  gi|313125045|ref|YP_004035309.1| 50 DPLLNRLRAGESGQSVEKDTQRERSSSPNPTPASTESGEHGGVeG 94
                                      9*****987777744443334444444457788889999999843 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.94
                              TSP9  31 ETdPlLkK..Vdekegsggrttvrg....gktsaa 59 
                                       E +P+ +K  Vde++  +++ t ++    + +sa+
  gi|313125045|ref|YP_004035309.1| 127 EAEPVSDKqpVDEEADDATEDTPSAavetSDASAS 161
                                       55555555445555544333333321111222222 PP

>> DUF966  Domain of unknown function (DUF966)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  10.9    0.0006       1.8     115     227 ..      87     205 ..      39     224 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0006
                            DUF966 115 a.......eeasssssssevavse...........assesespesskarrkssssaeleeykvykaeeeeeaaeega 173
                                               + +s ++s                   ++s++++++s++ +++  s +++ + +   a+e + +a+ + 
  gi|313125045|ref|YP_004035309.1|  87 GehggvegSGQSPDTS-------AtaqtpaetlvgEDSSTTTDHSAA-EAEPVSDKQPVDEEADDATEDTPSAAVET 155
                                       1112211122222222.......022223344543333334444433.44456777777888778888889999999 PP

                            DUF966 174 adastqtddkrrrsretkketasrgvstedeeeekeekestelsreeispppss 227
                                        das + dd+   + e ++++ + +  t    ++++ ++ te++++++ p +s+
  gi|313125045|ref|YP_004035309.1| 156 SDASASGDDTAGAADEGEQRESRADDET----TNETDETPTETKETDAEPAESE 205
                                       ********99998888654444433333....3333333444444444333322 PP

>> ORC6  Origin recognition complex subunit 6 (ORC6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   9.9   0.00099         3      89     222 ..      64     232 ..      42     236 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00099
                              ORC6  89 s.......satstPskspsspst.............dpkslrkqlfsTPtKsktlktalsa........sksssplk 137
                                       s       + +s+P+ +p+s+               d         +++t +++  t   +        s+ ++ + 
  gi|313125045|ref|YP_004035309.1|  64 SvekdtqrERSSSPNPTPASTESgehggvegsgqspD---------TSATAQTPAETLVGEdsstttdhSAAEAEPV 131
                                       2444445566777777777777766665555433331.........3333333333332224444454433333333 PP

                              ORC6 138 rrrklaneedgeeeeedapswvstsir.............dsrpeisrtlspskslgdesilfndss.ddekkseqk 200
                                         ++  +e + ++  ed ps    ++              + ++ +sr+++++ +  de + + +++  ++++se +
  gi|313125045|ref|YP_004035309.1| 132 SDKQPVDE-EADDATEDTPSAAVETSDasasgddtagaadEGEQRESRADDETTNETDETPTETKETdAEPAESEPP 207
                                       23333333.33333333333333333345789999999987777778887777777777776666667899999999 PP

                              ORC6 201 sprk...llkkkkdkisdediielc 222
                                        +rk   ll  ++  +  +++ +l+
  gi|313125045|ref|YP_004035309.1| 208 NFRKvmrLLNNREFPVERTEFADLA 232
                                       9999888888888888888887775 PP

>> Hamartin  Hamartin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.3    0.0015       4.4     376     511 ..      76     218 ..      36     246 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0015
                          Hamartin 376 tpetTPakssrkl........ppslsesavvvalpassrksspprkdeksesskpdlskqeev.enekeleeslksk 443
                                       +p+ TPa + +          +++ ++ ++++   +   + s + +d++  +++p +s +++v e+++  +e++   
  gi|313125045|ref|YP_004035309.1|  76 SPNPTPASTESGEhggvegsgQSPDTSATAQTPAETLVGEDSSTTTDHSAAEAEP-VSDKQPVdEEADDATEDT-PS 150
                                       3333333333322333333333333333333333333333333333433333333.333333324444444433.33 PP

                          Hamartin 444 ssvtlseLsdvikelleaesedsvekeeeeaaisqelseiteekketlvsrggldspfsrtleslaks 511
                                        +v++s+ s + +++  a  e  + + + +++ ++e +e+ +e ket     + + p++r++  l ++
  gi|313125045|ref|YP_004035309.1| 151 AAVETSDASASGDDTAGAADEGEQRESRADDETTNETDETPTETKETDAEPAESEPPNFRKVMRLLNN 218
                                       44555555555555555555555555555555555555555555555555555566666655555554 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  13.0    0.0022       6.6      60     210 ..      70     220 ..      44     235 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0022
                         Mitofilin  60 klkeisklqvsavsevtkeskepkeekkkeksekqssassevaeeeaeatkkaaeakaqqpkseqekekaleevlke 136
                                       + +  s+  ++  s+  +e ++++ ++++ + ++  +++ e    e ++t++  +a++++p s ++   ++++ ++e
  gi|313125045|ref|YP_004035309.1|  70 QRERSSSPNPTPASTESGEHGGVEGSGQSPDTSATAQTPAETLVGEDSSTTTDHSAAEAEPVSDKQPVDEEADDATE 146
                                       22222222233333333333344444444333333333333222233333333333324555555555555555555 PP

                         Mitofilin 137 alskaekataaakeakdeakkavkeavdklkeasdteeksrekardtaleaaeaaaekeleklkevielakqse 210
                                          +a+  t +a  + d++  a +e ++ + +a d+++++ +++ +  +e+ ++ ae+e  + ++v++l++++e
  gi|313125045|ref|YP_004035309.1| 147 DTPSAAVETSDASASGDDTAGAADEGEQRESRADDETTNETDETPTETKETDAEPAESEPPNFRKVMRLLNNRE 220
                                       55555666666666667777777777777666666666666666666666677777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 1557.66
//
Query:       gi|313125046|ref|YP_004035310.1|  [L=167]
Description: regulator of amino acid metabolism, contains act domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-05   23.5   0.0    0.00011   21.9   0.0    1.8  2  ACT_7     ACT domain
    3.8e-05   23.4   0.2     0.0002   21.1   0.1    2.4  2  ACT       ACT domain


Domain annotation for each model (and alignments):
>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.4   3.6e+03      11      26 ..      35      50 ..      34      51 .. 0.79
   2 !   21.9   0.0   1.2e-08   0.00011       7      44 ..      94     129 ..      91     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.4
                                      E-S-.---SS--HHHH CS
                             ACT_7 11 vvgsglpfdvtGivak 26
                                      vv++g+ + +tGi+ +
  gi|313125046|ref|YP_004035310.1| 35 VVSGGIEIPNTGIARE 50
                                      7888898899999876 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.2e-08
                                       EEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE-S CS
                             ACT_7   7 iklsvvgsglpfdvtGivaklaspLaeagIsifqiSty 44 
                                       ++l+v+ ++   d++Giva++++ Lae +Isi q+ ++
  gi|313125046|ref|YP_004035310.1|  94 SVLTVEVADA--DAPGIVAEITGRLAERDISIRQTISE 129
                                       6788888866..9*******************998876 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.51   4.6e+03      17      29 ..      18      30 ..      17      31 .. 0.80
   2 !   21.1   0.1   2.2e-08    0.0002       9      64 ..     104     157 ..      94     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.51
                                      HHHHHHHTTSEEE CS
                               ACT 17 vfgaladrgiNid 29
                                      v ++l +rg+++ 
  gi|313125046|ref|YP_004035310.1| 18 VIRLLLERGFSVN 30
                                      7789999999985 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.2e-08
                                       SSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT   9 DrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                       D PG+ a+++g la+r+i+i+   +   e  + +   + +v+d+ ++ ++l++l +
  gi|313125046|ref|YP_004035310.1| 104 DAPGIVAEITGRLAERDISIRQTISEDPE--FTDDPKLYLVTDQPVPGDLLNELSS 157
                                       88*****************9976666664..4788888888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1127.72
//
Query:       gi|313125047|ref|YP_004035311.1|  [L=206]
Description: hypothetical protein Hbor_02620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-27   96.0   0.0    1.9e-27   95.6   0.0    1.2  1  UPF0029   Uncharacterized protein family UPF0029
    1.1e-10   41.2   0.5      3e-10   39.8   0.0    1.9  2  DUF1949   Domain of unknown function (DUF1949)
     0.0037   17.3   0.0     0.0085   16.1   0.0    1.7  1  EFG_C     Elongation factor G C-terminus


Domain annotation for each model (and alignments):
>> UPF0029  Uncharacterized protein family UPF0029
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.0   3.2e-31   1.9e-27       1     104 [.      19     131 ..      19     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 3.2e-31
                                       TTEEEEEEEEE-SSHHHHHHHHHHH--..TTSSEEEEEE....EE......TT......EE-TTSST..SHHHHHHH CS
                           UPF0029   1 kkSrFiavlaaveseeevkaileelkkenkkathniyAyrlrqkvek..vned......sdddgEpa..AGkkllel 67 
                                       + S+Fi+++ ++++ e+++a+++++++++++athn+ Ayr+    ++     +      s+ddgEp+  +Gk+ l++
  gi|313125047|ref|YP_004035311.1|  19 RGSEFIGYVDRANTVEKAEAFIDRIEERHPDATHNVPAYRVPAGGDSggA--NtmlreySSDDGEPSgsSGKPALNV 93 
                                       68*************************************88777655440..3556666****************** PP

                                       HHHTTB-SEEEEEEEE--SS--HHHHH.HHHHHHHHHH CS
                           UPF0029  68 LekeklenvlvvvtRwfGGikLGpgrl.raiseaarea 104
                                       L +++++nv++vvtR++GG++LG g+l ra+s+ ++ea
  gi|313125047|ref|YP_004035311.1|  94 LVQQEIRNVVAVVTRYYGGTNLGVGGLaRAYSRGVKEA 131
                                       *********************************99987 PP

>> DUF1949  Domain of unknown function (DUF1949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.32   1.9e+03      40      51 ..      34      45 ..      32      46 .. 0.81
   2 !   39.8   0.0     5e-14     3e-10       1      56 []     148     202 ..     148     202 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.32
                           DUF1949 40 eeveafkaaLtd 51
                                      e++eaf++++ +
  gi|313125047|ref|YP_004035311.1| 34 EKAEAFIDRIEE 45
                                      7899***99866 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 5e-14
                           DUF1949   1 ltvdYadlgkverlLeqfgativdteYtddVtltlavpeeeveafkaaLtdltsGr 56 
                                       +tv+Y+d g v+ lLe++++   d+ Y +dV + ++vp+ee ++++++L+ +tsGr
  gi|313125047|ref|YP_004035311.1| 148 VTVAYDDSGSVRGLLESADVSF-DAAYEADVSFDVRVPVEEGAELRDRLRSATSGR 202
                                       79********************.********************************8 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-06    0.0085      38      71 ..     168     205 ..     140     206 .] 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-06
                                       E.....TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EE CS
                             EFG_C  38 d....asgrviieaeiPlaeligfateLrslTkGegsf 71 
                                             ++ v    ++P+ e  +++++Lrs+T+G++ +
  gi|313125047|ref|YP_004035311.1| 168 SfdaaYEADVSFDVRVPVEEGAELRDRLRSATSGRADI 205
                                       3333246689999**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1362.28
//
Query:       gi|313125048|ref|YP_004035312.1|  [L=378]
Description: glycine/d-amino acid oxidase, deaminating [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-58  197.7   6.9    4.5e-58  197.5   6.9    1.0  1  DAO              FAD dependent oxidoreductase
    1.1e-07   31.2   0.6     0.0062   15.7   0.7    2.2  2  GIDA             Glucose inhibited division protein A
    2.7e-06   26.9   2.6    2.9e-05   23.5   2.6    2.1  1  FAD_binding_3    FAD binding domain
    4.2e-06   26.2   0.3     0.0027   17.0   0.0    2.2  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    4.4e-06   26.0   4.7    1.3e-05   24.5   4.7    1.7  1  FAD_binding_2    FAD binding domain
      4e-05   23.7   1.0    9.2e-05   22.6   1.0    1.6  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    0.00018   20.5   0.3      0.054   12.3   0.0    2.1  2  Trp_halogenase   Tryptophan halogenase
    0.00044   19.4   0.1       0.22   10.5   0.0    2.1  2  Lycopene_cycl    Lycopene cyclase protein
      0.002   17.8   0.1     0.0032   17.1   0.1    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0028   17.6   1.1     0.0053   16.7   0.4    1.7  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0039   17.2   2.5          2    8.4   0.0    2.9  3  NAD_binding_9    FAD-NAD(P)-binding
     0.0081   16.7   0.9     0.0081   16.7   0.9    2.1  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
      0.015   14.7   0.9      0.027   13.8   0.5    1.5  2  FAD_oxidored     FAD dependent oxidoreductase
      0.017   13.9   0.5        1.3    7.7   0.0    2.1  2  HI0933_like      HI0933-like protein
      0.038   13.2   0.0        1.1    8.5   0.0    2.1  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
       0.09   13.0   0.0       0.16   12.2   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.15   12.5   0.0       0.27   11.7   0.0    1.5  1  NAD_binding_7    Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.5   6.9   4.3e-61   4.5e-58       2     351 ..       7     359 ..       6     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 4.3e-61
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHH.... CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelrele.... 72 
                                        v++GGGi+G+s+Ay+Lar+g  ++l+++  + g  a+ + +g+l++g    ++++  ++++ ea+++++el     
  gi|313125048|ref|YP_004035312.1|   7 AVVVGGGIVGSSVAYHLAREGveTLLVDRT-DDG-RATDAGAGILSPGTT-SRDNEPWVKFAVEAVAYYDELVpvle 80 
                                       69****************************.889.9************96.44444788******988888877777 PP

                                       .HHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHH........HHTTTTEEEEEHHHHHHHSTTSTTTSEEEEETTE CS
                               DAO  73 .eelgididyrrtGllslaadeeelealdkllall........leagldaelldaeevrelepalpgllgalfypdt 140
                                        e+ g+  +y ++G+ls+a d+ee + +d+ l+++        ++    +e lda+e+++++p l+++  a+f+ d+
  gi|313125048|ref|YP_004035312.1|  81 rEQDGP-HGYAKRGVLSVAMDDEEANVCDETLERVrkrqerfgTPEPGTVEELDADEAQAKFPPLAETERAFFSADA 156
                                       533465.7***********977555555555555444443335444445588**********9555999******** PP

                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT.CTTT CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll.keld 214
                                       ++v+ + +  al+ra +++G   +e   v+ l  +dg+v gve   + g + +a+ v++a Gaws+ +  +l  e+ 
  gi|313125048|ref|YP_004035312.1| 157 ARVNGRTFEGALRRAGRTHGLSEREA-SVETLLVDDGGVEGVE--LAgGDQIEAESVIIAGGAWSQSFgSQLgVEI- 229
                                       *************************8.999987889******5..33365545577*********95545554555. PP

                                       SEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHH CS
                               DAO 215 lpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellea 291
                                        p++p rgq+++l+   ++      ++p   ++ ++rg+y++p+ dgrv +G+t ++ sg+ +  ++ e + e+ e+
  gi|313125048|ref|YP_004035312.1| 230 -PVEPQRGQIVHLDVDADT-----DGWP---IVSPFRGHYMVPWDDGRVAAGATRETGSGYAP-HTTIEGLTEVFEQ 296
                                       .************443332.....3444...99*********************955555555.************* PP

                                       HHHHSGGGCG..EEEEEEEEEEE.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                               DAO 292 lrklfPqlgd..vlrkwaGlrpl.pdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                       + ++ P+l+d  ++ +++Glrpl pdglp++g +p v+++yl+tGh+  Gl+l+p +Gkl+a+
  gi|313125048|ref|YP_004035312.1| 297 VLRVAPGLADatLRTARVGLRPLsPDGLPVLGSVPDVSDVYLCTGHGPTGLQLGPYSGKLVAD 359
                                       *******96643667*******769********99999************************8 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.7   5.8e-06    0.0062       3      29 ..       8      34 ..       6      50 .. 0.86
   2 !   13.3   0.0   3.1e-05     0.032     109     154 ..     175     220 ..     134     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.8e-06
                                      EEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA  3 iViGgGhAGceAAlaaarlGakvlLit 29
                                      +V+GgG  G+  A+++ar G+++lL+ 
  gi|313125048|ref|YP_004035312.1|  8 VVVGGGIVGSSVAYHLAREGVETLLVD 34
                                      8************************93 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.1e-05
                                       TTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT- CS
                              GIDA 109 pnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkg 154
                                       + l+ +e++ve l+v+++ v+gv ++ g +i+a++v+ia G+++++
  gi|313125048|ref|YP_004035312.1| 175 HGLSEREASVETLLVDDGGVEGVELAGGDQIEAESVIIAGGAWSQS 220
                                       566778999********************************97664 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   2.6   2.8e-08   2.9e-05       3     213 ..       6     269 ..       4     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.8e-08
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrqlGledrilaegapnelmgealyn 78 
                                       + ++VG+G +G + a  L++ Gv+++lv++ ++   +   a++l++ t    ++  ++  ++a ++  el+  + ++
  gi|313125048|ref|YP_004035312.1|   6 EAVVVGGGIVGSSVAYHLAREGVETLLVDRTDDGRATDaGAGILSPGTTSRDNEPWVKFAVEAVAYYDELVPVLERE 82 
                                       678***************************987655554999******99999999999999999999998888888 PP

                                       E...............................CCCC.......CEEEEEHHCHHCST-CEE--HHHHHHHHHHH..H CS
                     FAD_binding_3  79 e...............................lsdt.......pkaradlelesspervtvypqteleriLveh..a 115
                                       +                                          p++ +  el++   + +  p  e+er+  ++  a
  gi|313125048|ref|YP_004035312.1|  83 QdgphgyakrgvlsvamddeeanvcdetlervR--KrqerfgtPEPGTVEELDADEAQAKFPPLAETERAFFSAdaA 157
                                       8999************99999999988866541..045567765555555578999999999999999998654114 PP

                                       HHHTEEETCSEE....EECCEECCCCCCCEEE.......ECCTTEE....EEEEEEEEEE--GTT-HH.HHHHTGGE CS
                     FAD_binding_3 116 eerglqvrfkte....vesleqdeegvtaevr.......dketgee....etvrakYlvGaDGgrStv.rktlgief 176
                                       +  g +++ + +    +++l + e +v++ +              e     +++a+ ++ a G++S++  ++lg+e+
  gi|313125048|ref|YP_004035312.1| 158 RVNGRTFEGALRragrTHGLSEREASVETLLVddggvegV-----ElaggDQIEAESVIIAGGAWSQSfGSQLGVEI 229
                                       4445544433333333888888888888877755333322.....3555569**************864799****9 PP

                                       EEEEEEEEEEEEEEEEEC-SCCCTTC...CEEEEECCTTE CS
                     FAD_binding_3 177 egeetvyeagvldvlfdadlsdivep...lvlilsaesrg 213
                                       + e +  ++  ldv +d+d   iv+p   +++++ ++ r+
  gi|313125048|ref|YP_004035312.1| 230 PVEPQRGQIVHLDVDADTDGWPIVSPfrgHYMVPWDDGRV 269
                                       9999997777777777763333666666555555555554 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.6e-06    0.0027     145     176 ..       7      38 ..       3     119 .. 0.72
   2 !    7.4   0.0    0.0022       2.3     185     258 ..     164     238 ..     153     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.6e-06
                                       EEEES-SHHHHHHHHHHHHHT-EEEEEESSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardr 176
                                       +vvvGgG +G+ +A +la+ g+e+ lv++ d 
  gi|313125048|ref|YP_004035312.1|   7 AVVVGGGIVGSSVAYHLAREGVETLLVDRTDD 38 
                                       45555555555555555555555555555443 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE...EETTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                       Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvvavGvrpstelleeklglel...dergg 257
                                       ++ al++a + +G   + ++sv+++  ++  +e v+l  g++i+a+ v++a G   ++ +   +lg+e+    +rg+
  gi|313125048|ref|YP_004035312.1| 164 FEGALRRAGRTHGLSER-EASVETLLVDDGGVEgVELAGGDQIEAESVIIAGGAWSQSFG--SQLGVEIpvePQRGQ 237
                                       55566666666777766.778887777777788888888888888888888888777766..677777755555565 PP

                                       E CS
                                       x RF
                       Pyr_redox_2 258 i 258
                                       i
  gi|313125048|ref|YP_004035312.1| 238 I 238
                                       5 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   4.7   1.2e-08   1.3e-05       2     204 ..       7     219 ..       6     241 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.2e-08
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHT..... CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkal..... 73 
                                       ++V+G+G+ G + A+ +a++G ++++v+ ++   g ++ +++gi  ++++   ++   + +++ + ++++       
  gi|313125048|ref|YP_004035312.1|   7 AVVVGGGIVGSSVAYHLAREGVETLLVDRTDD--GRATDAGAGILSPGTTSR-DN---EPWVKFAVEAVAYYdelvp 77 
                                       79*****************************9..999999999999994443.33...2344444444444466678 PP

                                       ....TT-S-HHHHHHHHHTHHHHHHHHHHTT----B..CCTS...............SB-EEE-TT-SSTEEEE-.S CS
                     FAD_binding_2  74 ....deladqplveafveaapeavdeLeelgvpfsr..tedg...............pvdvrelGglsatartlhda 129
                                            +++++ +++ +v  ++   +e   +   + r  ++++                 +++++  l +t r  +  
  gi|313125048|ref|YP_004035312.1|  78 vlerEQDGPHGYAKRGVLSVAMDDEEANVCDETLERvrKRQErfgtpepgtveeldaDEAQAKFPPLAETERAFF-S 153
                                       889555559999998887666665555555444444323333122222223333334444455555555577777.5 PP

                                       TT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 130 adarretlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                       ada   + v+g++   +l ++ r +g+    ++++++L+v+dg+v G++++    g++ +i+a  v++a g++++
  gi|313125048|ref|YP_004035312.1| 154 ADA---ARVNGRTFEGALRRAGRTHGLS-EREASVETLLVDDGGVEGVELA----GGD-QIEAESVIIAGGAWSQ 219
                                       555...4578888888888888888876.46789*****************....443.478***********98 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.0   8.8e-08   9.2e-05       1      30 [.       9      38 ..       9      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.8e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                      +vG+G+ G++ Ay+La++g++ ll+++ d+
  gi|313125048|ref|YP_004035312.1|  9 VVGGGIVGSSVAYHLAREGVETLLVDRTDD 38
                                      8*************************9875 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0032       3.4       3      31 ..       8      33 ..       6      44 .. 0.83
   2 !   12.3   0.0   5.2e-05     0.054     148     215 ..     156     222 ..     111     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0032
                                      EEE--SHHHHHHHHHHHHHTTTSSEEEEE CS
                    Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlv 31
                                      v+vGGG+ G+ +A +la+ +   +e +lv
  gi|313125048|ref|YP_004035312.1|  8 VVVGGGIVGSSVAYHLAREG---VETLLV 33
                                      8*****************98...555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.2e-05
                                       EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIII CS
                    Trp_halogenase 148 AyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllie 215
                                       A +++ + ++  Lrr +  +G+  +e+ v++    +dg ve+++l+ g ++ea+ +i + G  +   +
  gi|313125048|ref|YP_004035312.1| 156 AARVNGRTFEGALRRAGRTHGLSEREASVETLL-VDDGGVEGVELAGGDQIEAESVIIAGGAWSQSFG 222
                                       44667778999****************996665.56788***************99999998776555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0028         3       3      35 ..       8      38 ..       6      43 .. 0.90
   2 !   10.5   0.0   0.00021      0.22      82     163 ..     157     242 ..     144     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0028
                     Lycopene_cycl  3 vviGaGpAglslAarlteakpglkvvlieasps 35
                                      vv+G+G  g s+A +l  a+ g++ +l++  ++
  gi|313125048|ref|YP_004035312.1|  8 VVVGGGIVGSSVAYHL--AREGVETLLVDRTDD 38
                                      8***************..9********998765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00021
                     Lycopene_cycl  82 grvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslkkarrlgl....Qt 154
                                       +rv+ + ++  l +   ++g + +ea ve    ++ g   v l+gg +i+a  v+ a g+ s++ + +lg+      
  gi|313125048|ref|YP_004035312.1| 157 ARVNGRTFEGALRRAGRTHGLSEREASVETLLVDDGGVEGVELAGGDQIEAESVIIAGGAWSQSFGSQLGVeipvEP 233
                                       6888899999999998999****************************************999995555554000045 PP

                     Lycopene_cycl 155 fyGvevevd 163
                                        +G+ v++d
  gi|313125048|ref|YP_004035312.1| 234 QRGQIVHLD 242
                                       667777766 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   3.1e-06    0.0032       2      31 ..       8      37 ..       7      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.1e-06
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr 31
                                      +++G G +Gs +a++La+ g +  l++r++
  gi|313125048|ref|YP_004035312.1|  8 VVVGGGIVGSSVAYHLAREGVETLLVDRTD 37
                                      69**************************98 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4     5e-06    0.0053       3      33 ..       8      38 ..       6      54 .. 0.88
   2 ?   -1.5   0.0       1.9     2e+03      23      76 ..      95     150 ..      89     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                                      EEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdisee 33
                                       v+G G++G+++a+ +a++g+e+ lvd++++
  gi|313125048|ref|YP_004035312.1|  8 VVVGGGIVGSSVAYHLAREGVETLLVDRTDD 38
                                      69*************************9776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                       -EEEEE-S-HHHHHHHHHHHHHHHHCCT..TTTSS-HHHHCCCHHCEEEES-HHHH CS
                           3HCDH_N  23 leVvlvdiseealekalekieksleklv..ekgklkeeeveaalarisfttdleea 76 
                                       l+V + d +++  ++ le+++k+ e++   e g ++e ++++a a+  + +++e+a
  gi|313125048|ref|YP_004035312.1|  95 LSVAMDDEEANVCDETLERVRKRQERFGtpEPGTVEELDADEAQAKFPPLAETERA 150
                                       56778888888888888888887777641156677777777777666655555555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.3    0.0047       4.9       1      35 [.       8      37 ..       8      50 .. 0.79
   2 !    8.4   0.0    0.0019         2     103     154 ..     163     215 ..     157     216 .. 0.92
   3 ?   -0.9   0.0       1.4   1.4e+03     141     155 ..     328     342 ..     290     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0047
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpse 35
                                      ++vG+G+ G +v+ +L+++      +e  l+d++ 
  gi|313125048|ref|YP_004035312.1|  8 VVVGGGIVGSSVAYHLAREG-----VETLLVDRTD 37
                                      69***************995.....5555555554 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0019
                     NAD_binding_9 103 lfeellarlpegvtvevhraevvdleeradgq.avlladgaslaadaVvLAlG 154
                                       +fe +l+r+ +   ++  +a+v+ l  +++g+  v la+g++++a++V++A G
  gi|313125048|ref|YP_004035312.1| 163 TFEGALRRAGRTHGLSEREASVETLLVDDGGVeGVELAGGDQIEAESVIIAGG 215
                                       6889999999999*************99999857*****************87 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.4
                     NAD_binding_9 141 gaslaadaVvLAlGh 155
                                       g+  ++  V L++Gh
  gi|313125048|ref|YP_004035312.1| 328 GSVPDVSDVYLCTGH 342
                                       4556788999****9 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.9   7.6e-06    0.0081       2      33 ..       7      38 ..       6      47 .. 0.90
   2 ?   -1.4   0.1       3.4   3.6e+03       7      16 ..     192     201 ..     181     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.6e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                      +vvvGgG +g  +A  la+ g ++ +v+r d 
  gi|313125048|ref|YP_004035312.1|  7 AVVVGGGIVGSSVAYHLAREGVETLLVDRTDD 38
                                      79***************************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.4
                                       SSHHHHHHHH CS
                         Pyr_redox   7 gGyiglElAg 16 
                                       gG+ g+ElAg
  gi|313125048|ref|YP_004035312.1| 192 GGVEGVELAG 201
                                       6777777775 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   2.6e-05     0.027       3      32 ..       8      37 ..       6      44 .. 0.95
   2 ?   -2.5   0.0       2.4   2.5e+03      84     140 ..     155     211 ..      88     213 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                      FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGakvlLveerg 32
                                      vVvGGg+ G   A+  ar+G ++lLv++++
  gi|313125048|ref|YP_004035312.1|  8 VVVGGGIVGSSVAYHLAREGVETLLVDRTD 37
                                      9**************************985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                      FAD_oxidored  84 fepevakavleemlaeagvtvllntrlvevek...egkriesvtveskegrktirAkvfi 140
                                          +v+ +++e  l++ag t  l +r  +ve+   +++ +e+v+++   g+ +i+A+ +i
  gi|313125048|ref|YP_004035312.1| 155 DAARVNGRTFEGALRRAGRTHGLSEREASVETllvDDGGVEGVELA---GGDQIEAESVI 211
                                       3445556666666666666665555555555433355667777774...56666666655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.011        12       2      32 ..       6      36 ..       5      44 .. 0.92
   2 ?    7.7   0.0    0.0012       1.3     124     172 ..     176     223 ..     146     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      + +v+GgG  G   A ++a++g ++ll++++
  gi|313125048|ref|YP_004035312.1|  6 EAVVVGGGIVGSSVAYHLAREGVETLLVDRT 36
                                      689**************************87 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                                       -EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT- CS
                       HI0933_like 124 vklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGs 172
                                          + e +v+++  +++g+  v++ +++++ea+++++A GG+   + Gs
  gi|313125048|ref|YP_004035312.1| 176 GLSEREASVETLLVDDGGVEGVELAGGDQIEAESVIIA-GGAWSQSFGS 223
                                       45577889999999************************.6665566676 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0     0.001       1.1     164     217 ..       4      56 ..       1      81 [. 0.77
   2 ?    2.7   0.0     0.059        62     115     136 ..     196     218 ..     139     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienr 217
                                        ++ vV+Gg+  +  +A++l+r+g e  +v+r++  ++++      l+p + +r
  gi|313125048|ref|YP_004035312.1|   4 RHEAVVVGGGIVGSSVAYHLAREGVETLLVDRTDDGRATD-AGAGILSPGTTSR 56 
                                       56889*********************99999998655554.3333566666655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.059
                       Pyr_redox_3 115 evetske.tyeAkkviiAtGefd 136
                                        ve   + ++eA++viiA G ++
  gi|313125048|ref|YP_004035312.1| 196 GVELAGGdQIEAESVIIAGGAWS 218
                                       466555449***********986 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.16       2      39 ..       8      42 ..       7      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHH CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklea 39
                                      +++G+G vG++va  lar++    e  ++dr++++ + 
  gi|313125048|ref|YP_004035312.1|  8 VVVGGGIVGSSVAYHLAREGV---ETLLVDRTDDGRAT 42
                                      79****************985...69******999544 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00025      0.27       7      40 ..       4      37 ..       1     114 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                      + + +vvGgG v+ + +++l+++g +  +v+ + 
  gi|313125048|ref|YP_004035312.1|  4 RHEAVVVGGGIVGSSVAYHLAREGVETLLVDRTD 37
                                      56789*********************99999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2417.44
//
Query:       gi|313125049|ref|YP_004035313.1|  [L=719]
Description: dipeptidyl aminopeptidase/acylaminoacyl peptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-57  192.8   1.1    7.7e-57  192.2   1.1    1.2  1  Peptidase_S9   Prolyl oligopeptidase family
    1.8e-15   56.4   0.7    2.2e-06   27.4   0.1    4.7  4  PD40           WD40-like Beta Propeller Repeat
    3.8e-06   25.9   0.1       0.21   10.3   0.0    4.5  4  DPPIV_N        Dipeptidyl peptidase IV (DPP IV) N-terminal re
    3.5e-05   23.5   0.0    6.3e-05   22.6   0.0    1.4  1  DLH            Dienelactone hydrolase family
    0.00015   21.5   0.6      0.028   14.1   0.7    2.3  2  Abhydrolase_1  alpha/beta hydrolase fold
     0.0014   17.4   0.7      0.081   11.6   0.7    2.2  1  AXE1           Acetyl xylan esterase (AXE1)
     0.0026   17.0   0.8       0.71    9.1   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.019   14.1   0.0       0.47    9.6   0.0    2.0  2  DUF2920        Protein of unknown function (DUF2920)
      0.049   13.4   0.0      0.093   12.5   0.0    1.4  1  Abhydrolase_2  Phospholipase/Carboxylesterase


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   1.1   3.8e-60   7.7e-57       5     209 ..     464     669 ..     459     672 .. 0.97

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 3.8e-60
                                       HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHH CS
                      Peptidase_S9   5 selqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaa 81 
                                       +e qlla+rGyvv++ n+rGs+gyGe+f+ a++ ++g+++++D+++++e + +++yvd+e+ ++tGgS+GGy+tg++
  gi|313125049|ref|YP_004035313.1| 464 HEYQLLAARGYVVFWSNPRGSTGYGEEFATAIESDWGDVTMTDVMNGVERVCDRDYVDAENAFVTGGSFGGYMTGWI 540
                                       899************************************************************************** PP

                                       HHH-GGG-SEEEEESE---CCCHHCSTTSTHH.HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS CS
                      Peptidase_S9  82 lnqrpdlFkaavaevpvvdvlrydsdtdllte.eymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrv 157
                                       ++ ++d+F++av +++v+d+ +++ +td+++  e ++ ++p++++e  +e sp++++dn  +++p+L++h+++D rv
  gi|313125049|ref|YP_004035313.1| 541 VG-HTDFFAGAVGQRGVYDLSSFYGSTDAFKLiEGDFDTTPWDDPEFLWEKSPVAYADN--VTTPTLVMHADNDFRV 614
                                       **.**************************99999*************************..**************** PP

                                       -THHHHHHHHHHH--S-SEEEEEETTS-S...STTSSHHHHHHHHHHHHHHHHHC CS
                      Peptidase_S9 158 ppaealklvaaLqkkgknvlllifpdegH...gvgkprakveelarllaFlkeal 209
                                       p++++++++  ++k+g++++++ +p egH   ++g+p + v++l+r++++++ + 
  gi|313125049|ref|YP_004035313.1| 615 PVNNGEMFYLFMKKNGVETRFVRYPREGHelsRSGEPGHVVDRLERTVRWFDGYS 669
                                       *****************************9999999***************9876 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0001       0.2      14      38 .]      18      46 ..      16      46 .. 0.84
   2 !   27.4   0.1   1.1e-09   2.2e-06       3      38 .]      57      94 ..      55      94 .. 0.86
   3 !   11.1   0.0   0.00015      0.29      16      25 ..     117     126 ..     109     127 .. 0.93
   4 ?   -0.1   0.0      0.47   9.4e+02       2      25 ..     190     212 ..     189     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                      EEE-TTSSEEEEEEECT...TCEE..EEE CS
                              PD40 14 PsfSPDGkrlaFsSdRg..sGkpd..Iyv 38
                                      P +SPDG+r aF++  +  + +++  Iyv
  gi|313125049|ref|YP_004035313.1| 18 PQVSPDGTRVAFVRKEPkdDESYEqtIYV 46
                                      668***********999887777788887 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.1e-09
                                      E--SSSS.EEEEEE-TTSSEEEEEEECT...TCEEEEE CS
                              PD40  3 rltntpgnegaPsfSPDGkrlaFsSdRg..sGkpdIyv 38
                                      rlt  +g +  P++SP G rlaF+S+Rg  + +p+++v
  gi|313125049|ref|YP_004035313.1| 57 RLTIAEGVDSQPRWSPSGDRLAFVSTRGadDDRPQLWV 94
                                      55556788999*****************8888888998 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00015
                                       E-TTSSEEEE CS
                              PD40  16 fSPDGkrlaF 25 
                                       +SPDG+r+aF
  gi|313125049|ref|YP_004035313.1| 117 WSPDGTRIAF 126
                                       *********9 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.47
                                       EE--SSSS.EEEEEE-TTSSEEEE CS
                              PD40   2 krltntpgnegaPsfSPDGkrlaF 25 
                                       +r+t ++ +  aP++  D  +l+F
  gi|313125049|ref|YP_004035313.1| 190 ERVTDGELDHVAPAWRDDD-TLYF 212
                                       68888999999****9998.8877 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.013        25      45      62 ..      15      32 ..       3      34 .. 0.88
   2 !   10.3   0.0    0.0001      0.21      18     119 ..      37     128 ..      21     135 .. 0.62
   3 ?   -3.0   0.0       1.1   2.3e+03     256     288 ..     170     204 ..     162     212 .. 0.55
   4 !    4.0   0.0    0.0088        18     161     300 ..     280     421 ..     271     428 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.013
                                      BSEEEEESSTTEEEEEET CS
                           DPPIV_N 45 lqlakwSPagdklafvrn 62
                                      ++++++SP+g+++afvr+
  gi|313125049|ref|YP_004035313.1| 15 VEDPQVSPDGTRVAFVRK 32
                                      6799************97 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0001
                                       SSEETTEEEEEETTT.EECEEEETTTT.BSEEEEESSTTEEEEEETT.......EEEEESTTTSEEEECES-STTTE CS
                           DPPIV_N  18 Rhsytaeyyiydlet.neveelspgeeklqlakwSPagdklafvrnn.......nLyvrelatgkeiqlTsdgsagi 86 
                                        +sy+++ y+++ +   + ++l+  e+  + ++wSP gd+lafv  +        L+v  +  g++ q+T+      
  gi|313125049|ref|YP_004035313.1|  37 DESYEQTIYVVPAAGdSDPRRLTIAEGVDSQPRWSPSGDRLAFVSTRgadddrpQLWVLPMDGGEAEQVTD------ 107
                                       45666666666655447788888888999999999999999999765222222235555555555555554...... PP

                                       EESB--HHHHHHTSSSSBEEEE-TTSSEEEEEE CS
                           DPPIV_N  87 fnGvadWvyeEEvlgsnsavwWspdgsrlaylr 119
                                          v+         g  s++ Wspdg+r+a+ +
  gi|313125049|ref|YP_004035313.1| 108 ---VP---------GGVSGIEWSPDGTRIAFQQ 128
                                       ...33.........4455777888888888765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.1
                                       TTS.SEEEEEEESSS-C.EE..ESS-SSS-EEEEEE CS
                           DPPIV_N 256 kdG.fkHLylfdldgkseik..qlTsGeweVtsila 288
                                       +dG   H+yl  +d     +   +T Ge +   +++
  gi|313125049|ref|YP_004035313.1| 170 RDGtVAHVYLAHVDRDD-DRveRVTDGELDHVAPAW 204
                                       44445666666666655.333466666665544444 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.0088
                                       EEEECTTSCEEECS-HHHHCTTCEEEEEEEECTTSCCEEEEEEETTSTEEEEEEEETTT.CCEEEEE...EEESSS- CS
                           DPPIV_N 161 kvvdlasgktvevqlpdslsekdeyitrvkWtsdeksllvqwlnRsqnrlkvvlvdaet.gravvkl...eetsdgW 233
                                        v+d ++++   v++ + l+ ++ + + ++W +de+ +++ + +  +   + v++d+e  ++a++++   + + +  
  gi|313125049|ref|YP_004035313.1| 280 EVYDPETER--AVVPTETLDRTVDLAAGLSWGPDEEDVYFLTPDGGHYVTRRVSADVEErSSADRETqsdDAEPELL 354
                                       567776666..58889999999*********************************8855233333334445555566 PP

                                       SSS-S-EEE-.TTTSSEEEEEEETTSSEE...EEEEESSS-C.EEESS-SSS-EEEEEEEETTTTEEEEEE CS
                           DPPIV_N 234 velhdevhfl.krdesgflwisekdGfkH...LylfdldgkseikqlTsGeweVtsilavdekrdlvyFta 300
                                       ++  +++ f+ + ++++ + +++k+ ++H   +++f++d++     lT+ + +    + v+e  ++++F++
  gi|313125049|ref|YP_004035313.1| 355 ISDGHTTGFSiGARSDSPVLAVAKSEWDHpgdVFVFESDEER---RLTEVNADYLTEVDVQEP-EEIWFES 421
                                       688888888889999999999999****95555566555555...888888888555555444.6788877 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   3.2e-08   6.3e-05      61     196 ..     490     652 ..     458     669 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.2e-08
                               DLH  61 eaaraldelvskvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG....... 130
                                       e a+a++  + +v++ +v++ +    + +  + +v+ ++  v+G  +GG ++  +  + +++++av+  G       
  gi|313125049|ref|YP_004035313.1| 490 EFATAIESDWGDVTMTDVMNGV----ERVCDRDYVDAENAFVTGGSFGGYMTGWIVGHTDFFAGAVGQRGvydlssf 562
                                       4455554555555444444444....555566667777888888888888888888888888888865555555555 PP

                               DLH 131 ........................lspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYp 183
                                                               l  ++++++a+++ +p l++++++D  +p ++ e +   +k+++v+ +++ Yp
  gi|313125049|ref|YP_004035313.1| 563 ygstdafkliegdfdttpwddpefLWEKSPVAYADNVTTPTLVMHADNDFRVPVNNGEMFYLFMKKNGVETRFVRYP 639
                                       5599999999999999999999988899************************************************* PP

                               DLH 184 gagHaFandsres 196
                                         gH   +  +++
  gi|313125049|ref|YP_004035313.1| 640 REGHELSRSGEPG 652
                                       ****776666554 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.7   1.4e-05     0.028       6      86 ..     448     536 ..     446     543 .. 0.90
   2 !    5.0   0.0     0.008        16     206     234 ..     590     623 ..     549     646 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                       E-STTT.....CGGGGTTGHHHHHHHHTTSEEEEEEETTS.TTSSSTTTGB.CHHSHHHHHHHHH...HH..HHHCT CS
                     Abhydrolase_1   6 lhGlpg.....ssdvwaerglapaLakdgfdvillDlrGv.gySspapacinddygtasvaddld...ri..ldalg 71 
                                       +hG+p      s+ +w+e    + La +g+ v+  ++rG+ gy++   + i +d+g++++ d+++   r+  +d  +
  gi|313125049|ref|YP_004035313.1| 448 IHGGPHamwstSGTMWHE---YQLLAARGYVVFWSNPRGStGYGEEFATAIESDWGDVTMTDVMNgveRVcdRDYVD 521
                                       7*****888877777999...7799999***********7689999999999*************988889****** PP

                                       TSSEEEEEETHHHHH CS
                     Abhydrolase_1  72 ddkltlvGhSmGGmi 86 
                                        ++  + G+S+GG +
  gi|313125049|ref|YP_004035313.1| 522 AENAFVTGGSFGGYM 536
                                       *************76 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.008
                                       C.....THHHHSEEEEEEETTCSSSCHHHHHHHH CS
                     Abhydrolase_1 206 e.....lknvlaptlvisgtsDplvppkaledla 234
                                       +      +nv+ ptlv+++++D  vp +++e + 
  gi|313125049|ref|YP_004035313.1| 590 KspvayADNVTTPTLVMHADNDFRVPVNNGEMFY 623
                                       1555666899****************98887665 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.7     4e-05     0.081      59     131 ..     417     495 ..     391     543 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4e-05
                                       EEEEEGGGEEEEEEEEEES...SSSSEEEEEEEE-.....TT--GGGHHHHHHHHHTT-EEEEEE-TTTS..SSB-S CS
                              AXE1  59 ltfegvrgarikaklvlPk..ekeeklPavvefhG.....YegsrgeihdllnyaaaGyavvvmdvRGqggesedkv 128
                                       + fe+  g +++++++ P   +++e+ P+ ve hG     +++s   +h+    aa Gy+v+  + RG  g+ e+  
  gi|313125049|ref|YP_004035313.1| 417 IWFES-DGVEVQGWVLTPPgcSEDETYPLAVEIHGgphamWSTSGTMWHEYQLLAARGYVVFWSNPRGSTGYGEEFA 492
                                       55554.6789*****99963357899********96655556667889**********************9999855 PP

                                       SCC CS
                              AXE1 129 gsk 131
                                       +  
  gi|313125049|ref|YP_004035313.1| 493 TAI 495
                                       544 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   1.0     0.005        10      11      90 ..     453     537 ..     450     553 .. 0.76
   2 !    9.1   0.0   0.00036      0.71     187     234 ..     596     645 ..     590     650 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.005
                       Hydrolase_4  11 HGlaehsgryaelaeaLaaqGfavyalDhrGhGrse...gkrghvpsfddyvdDlaafvekvkeehpel..plfllG 82 
                                       H + ++sg + +  + Laa+G+ v+  + rG    +       + +  d  ++D+   ve+v+++      + f+ G
  gi|313125049|ref|YP_004035313.1| 453 HAMWSTSGTMWHEYQLLAARGYVVFWSNPRGSTGYGeefATAIESDWGDVTMTDVMNGVERVCDRDYVDaeNAFVTG 529
                                       6677889999999999*************986444434355555555666789**********55554448****** PP

                       Hydrolase_4  83 hSmGGlia 90 
                                        S GG+++
  gi|313125049|ref|YP_004035313.1| 530 GSFGGYMT 537
                                       *****975 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00036
                       Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHel 234
                                       a+++t+P+l++h+++D  v+ ++ + +y  ++++  + ++  yp   Hel
  gi|313125049|ref|YP_004035313.1| 596 ADNVTTPTLVMHADNDFRVPVNNGEMFYLFMKKNgvETRFVRYPREGHEL 645
                                       7899****************999988887777665588888999999997 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00024      0.47     159     196 ..     503     539 ..     497     563 .. 0.85
   2 ?    2.3   0.0     0.037        73     286     318 ..     601     633 ..     589     638 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00024
                           DUF2920 159 aAlDiinalkdlvkrfpkeadlpviliGgsyGGYlalL 196
                                          D++n ++ +  r   +a ++  + Ggs+GGY++  
  gi|313125049|ref|YP_004035313.1| 503 TMTDVMNGVERVCDRDYVDA-ENAFVTGGSFGGYMTGW 539
                                       5689****************.9************9865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.037
                           DUF2920 286 tiyvsyHsekDklapaeeKiqlakilkklgfdv 318
                                       t  +++H+++D  +p+++ ++++  +kk g + 
  gi|313125049|ref|YP_004035313.1| 601 TPTLVMHADNDFRVPVNNGEMFYLFMKKNGVET 633
                                       667899**********************99875 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.7e-05     0.093     154     202 ..     596     646 ..     584     649 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                                       G..GG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS-- CS
                     Abhydrolase_2 154 t..kklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsid 202
                                       +  + +p l +H + D  vp+  g++++ ++kk+  +  ++ y+  +H+ +
  gi|313125049|ref|YP_004035313.1| 596 AdnVTTPTLVMHADNDFRVPVNNGEMFYLFMKKNGVETRFVRYPREGHELS 646
                                       434789******************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4828.40
//
Query:       gi|313125050|ref|YP_004035314.1|  [L=89]
Description: hypothetical protein Hbor_02650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00085   19.0   0.7     0.0017   18.0   0.7    1.5  1  Neurensin     Neurensin
     0.0068   16.2   1.2      0.012   15.4   1.2    1.5  1  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
  ------ inclusion threshold ------
      0.087   13.0   0.7       0.36   11.0   0.0    1.9  2  SdpI          SdpI/YhfL protein family
       0.12   12.2   3.2       0.12   12.1   0.1    1.9  2  DUF2157       Predicted membrane protein (DUF2157)
       0.99    9.2   5.1       0.91    9.4   0.2    2.2  2  DUF2976       Protein of unknown function (DUF2976)
        1.2    9.5   7.6        4.9    7.5   0.2    2.1  2  DUF3040       Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.7   5.8e-07    0.0017      53     114 ..      10      82 ..       5      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.8e-07
                         Neurensin  53 llGvtallvGylvprrlelv........ksegelvvvDkqai...efnnaLdtlklaGavllclGglllalsl 114
                                       +lG+++l+vGy++  r+e+         +  ++  +  + +    ++++   t+ l G+vll++G ll+a+++
  gi|313125050|ref|YP_004035314.1|  10 VLGLACLVVGYVLVFRVETAlavqekyaEAASSTPPSENPEYyeeTHEHRRWTFYLGGMVLLAVGTLLIAAAV 82 
                                       69****************9999***999777788887776543338999999****************99876 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.2   4.1e-06     0.012      66     140 ..       7      81 ..       1      87 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
                      Trp_oprn_chp  66 grrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaaveltawpvlalaggvllllagvllllra 140
                                       +  v+g+ ++++g ++++++ ++l+ +++ a+aa+++    + +  + ++    +   +gg++ll+ g ll+++a
  gi|313125050|ref|YP_004035314.1|   7 APAVLGLACLVVGYVLVFRVETALAVQEKYAEAASSTPPSENPEYYEETHEHRRWTFYLGGMVLLAVGTLLIAAA 81 
                                       557899999999999999999988888888888886644444444555588899999999999999999998765 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4      0.27   8.2e+02      36      44 ..      11      19 ..       2      32 .. 0.56
   2 ?   11.0   0.0   0.00012      0.36      17      55 ..      47      80 ..      46      88 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.27
                              SdpI 36 aGlilllla 44
                                      +Gl++l+++
  gi|313125050|ref|YP_004035314.1| 11 LGLACLVVG 19
                                      344444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                              SdpI 17 kseetWrkahrfagklwiiaGlilllla...lgavvlvllvl 55
                                      ++ e ++ +h    +++ ++G++ll+++   +        ++
  gi|313125050|ref|YP_004035314.1| 47 ENPEYYEETHEHRRWTFYLGGMVLLAVGtllI--------AA 80
                                      69999******888888888888877773221........22 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.7     0.086   2.6e+02      41      82 ..      11      24 ..       2      44 .. 0.56
   2 ?   12.1   0.1   4.1e-05      0.12      20      62 ..      51      87 ..      31      89 .] 0.71

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.086
                           DUF2157 41 lGalllglGlilfvAanWqglsrlvkfllllvllllslllga 82
                                      lG                             ++l++ ++l++
  gi|313125050|ref|YP_004035314.1| 11 LGL----------------------------ACLVVGYVLVF 24
                                      333............................33333333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.1e-05
                           DUF2157 20 ryeaeeresarrrsfleallvlGalllglGlilfvAanWqgls 62
                                      +ye+   +++    ++ ++++ G++ll++G +l+ Aa++ ++s
  gi|313125050|ref|YP_004035314.1| 51 YYEE--THEH----RRWTFYLGGMVLLAVGTLLIAAAVYGTFS 87
                                      3332..2233....478888889999999****9999987765 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5     0.036   1.1e+02      30      54 ..      13      39 ..       3      48 .. 0.57
   2 ?    9.4   0.2   0.00031      0.91      23      52 ..      58      87 ..      41      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.036
                           DUF2976 30 llgLvlaavaflaVaka..alkkfnei 54
                                      l+ Lv++ v ++ V +a  + +k++e+
  gi|313125050|ref|YP_004035314.1| 13 LACLVVGYVLVFRVETAlaVQEKYAEA 39
                                      445555555555554331034556665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00031
                           DUF2976 23 ylkdgvillgLvlaavaflaVakaalkkfn 52
                                      +    + l+g+vl av+ l +a a++++f+
  gi|313125050|ref|YP_004035314.1| 58 HRRWTFYLGGMVLLAVGTLLIAAAVYGTFS 87
                                      55567899******************9995 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.9     0.008        24      46      65 ..       3      23 ..       1      34 [. 0.77
   2 ?    7.5   0.2    0.0016       4.9      38      63 ..      56      82 ..      25      88 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.008
                           DUF3040 46 vlavllfvaGllllvlG.vaa 65
                                      ++ ++ +v+Gl++lv+G v++
  gi|313125050|ref|YP_004035314.1|  3 LQLIAPAVLGLACLVVGyVLV 23
                                      567889999********6654 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0016
                           DUF3040 38 rrslrrlavlavllfva.GllllvlGv 63
                                      + ++r++ +l+ ++++a G ll+ + v
  gi|313125050|ref|YP_004035314.1| 56 HEHRRWTFYLGGMVLLAvGTLLIAAAV 82
                                      444556566655555555666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 554.38
//
Query:       gi|313125051|ref|YP_004035315.1|  [L=172]
Description: hypothetical protein Hbor_02660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.33   11.0   1.8         15    5.7   0.4    2.4  2  DUF1201          Protein of unknown function (DUF1201)
        3.3    6.7  14.6        4.3    6.4  14.6    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> DUF1201  Protein of unknown function (DUF1201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0054        49      11      38 ..      55      82 ..      53      91 .. 0.89
   2 ?    5.7   0.4    0.0017        15      15      31 ..     138     154 ..     132     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0054
                           DUF1201 11 lafGfliclflfclvvfiwfvykqilfr 38
                                      l f f + lf++ lv+   fv   +l+r
  gi|313125051|ref|YP_004035315.1| 55 LGFTFGMGLFFLPLVLPTSFVIGTLLWR 82
                                      7899999**************9999998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0017
                           DUF1201  15 fliclflfclvvfiwfv 31 
                                       +li  f+f lv   wfv
  gi|313125051|ref|YP_004035315.1| 138 LLIPSFVFALVAAGWFV 154
                                       37889***********9 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  14.6   0.00048       4.3     211     311 ..      26     147 ..      22     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00048
                   ABC2_membrane_3 211 lgdflvyllqlllill....lafglgipfgnlglllllfllfglayialgyllsslfkns..........etaqili 273
                                       +++++ +ll ++++++    +a +     g lg+++ + l+f+ ++++ ++++++l  +           +++++++
  gi|313125051|ref|YP_004035315.1|  26 IAMAATGLLATVVWFAgawaIAAK--TGNGTLGFTFGMGLFFLPLVLPTSFVIGTLLWRKlypkenrelyGAVFGAM 100
                                       788889999999999876434555..7777**************************999999999987666666667 PP

                   ABC2_membrane_3 274 fivilllsgffgglfp..ledlp.......salkwifsiiPffapgl 311
                                       +++ +l+ g +g+  +  +++++       +a+  ++ +iP+f ++l
  gi|313125051|ref|YP_004035315.1| 101 TALASLAVGSLGPALFlaISNVNsgampvsEAAGFALLLIPSFVFAL 147
                                       777777777777774458777776666677888889*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1045.44
//
Query:       gi|313125052|ref|YP_004035316.1|  [L=365]
Description: beta-mannanase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-06   27.4   5.1    2.3e-06   27.3   1.8    2.2  3  Glyco_hydro_26  Glycosyl hydrolase family 26


Domain annotation for each model (and alignments):
>> Glyco_hydro_26  Glycosyl hydrolase family 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.18   3.2e+03      30      74 ..      40      83 ..      33     100 .. 0.64
   2 !   27.3   1.8   1.3e-10   2.3e-06     160     231 ..     156     232 ..     149     241 .. 0.80
   3 ?    0.4   0.1      0.02   3.5e+02      39     117 ..     247     323 ..     237     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.18
                                      EECTTTT-SSCHHHHHHHHHSS--SEEEEEEEECCEGGCTCCCGC CS
                    Glyco_hydro_26 30 qglsidrtdlkeasrirnvtgkfpAiygfdlidgwyslsrvedkv 74
                                       g+si+r  +   +r  + tgk  A++ + ++   +s  ++++ v
  gi|313125052|ref|YP_004035316.1| 40 AGVSIQRSPVRSLDRFEQWTGKPHAVV-VQYATLGQSEEEIAQTV 83
                                      567888888888888888899988888.55555333333333333 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.3e-10
                                       STTSSSSTTSTT.STCHHHHHHHHHHHHHHH.HHTTS---SEEEEE--BTTSS-...TCCC---TTT-SEEEEEEEE CS
                    Glyco_hydro_26 160 EaeGeWFWWGak.gqerpelykqLyrllyey.lvdvkgldnliwvyspeasrdv...aeefYPGdeyvDivGlDvYl 231
                                       E++G+W  WGa  g ++p+ y  ++r +  + + +    +n+ w++ p+a+        ++YPGd+ vD  G++ Y 
  gi|313125052|ref|YP_004035316.1| 156 EMNGDWVPWGAPaGDSTPDDYVAMFRHVHRRvMSNGLDSSNIQWIWGPNAGGRGgipIPDYYPGDDVVDWAGVNGYN 232
                                       9*********962569**********998772344455679********985431124689***********99985 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.02
                                       SCHHHHHHHHHSS--SEEEEEEEECCEGGCTCCCGCT-TTHHHHHHHHCTT-EEEEEEE---TTTCSSSTTTTSTCH CS
                    Glyco_hydro_26  39 lkeasrirnvtgkfpAiygfdlidgwyslsrvedkvessivedliayakrgGivqlslHlnnPakqkggfktritsd 115
                                       +k+ ++ir+vt+   Ai  +         s  +++ ++    +l +y +++ +  + +   + ++++ +f     +d
  gi|313125052|ref|YP_004035316.1| 247 GKALKQIRSVTDAPIAITEVGCST--EVDSGNDPERKGAWITELYDYVRTEDVKMVCWFNHTKETDWRVFDSVRGTD 321
                                       577889999999999999777766..556666777777888889999998888888776666666666998776666 PP

                                       HC CS
                    Glyco_hydro_26 116 dv 117
                                       ++
  gi|313125052|ref|YP_004035316.1| 322 EI 323
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2171.08
//
Query:       gi|313125053|ref|YP_004035317.1|  [L=101]
Description: hypothetical protein Hbor_02680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-11   44.6   1.1    1.5e-11   44.3   1.1    1.0  1  TackOD1         Thaumarchaeal output domain 1
    9.5e-07   28.8   2.8      0.058   13.5   0.1    3.2  3  Zn-ribbon_8     Zinc ribbon domain
    0.00011   22.4   9.5      0.013   15.7   0.0    3.3  3  zinc_ribbon_9   zinc-ribbon
     0.0026   17.5   2.7          6    6.7   0.1    3.2  3  Zn_Tnp_IS1      InsA N-terminal domain
     0.0059   16.5   0.8        3.2    7.7   0.0    3.1  3  DUF3797         Domain of unknown function (DUF3797)
      0.007   17.1   1.6        7.4    7.7   0.1    3.3  3  zf-C2H2_4       C2H2-type zinc finger
  ------ inclusion threshold ------
      0.018   15.0   5.5      0.099   12.6   1.5    2.4  2  zinc-ribbons_6  zinc-ribbons
      0.019   15.4   4.6          7    7.3   0.2    3.4  3  zf-C2H2         Zinc finger, C2H2 type
      0.038   13.5   5.5       0.22   11.1   0.1    3.1  3  zf_C2H2_10      C2H2 type zinc-finger
        0.1   12.0  10.8       0.97    8.9   0.2    3.5  3  zf-ribbon_3     zinc-ribbon domain
       0.34   11.4   6.7        3.7    8.2   0.1    3.1  3  zf-H2C2_2       Zinc-finger double domain
       0.34   11.0  14.8        3.9    7.7   0.2    4.1  4  UPF0547         Uncharacterised protein family UPF0547
        0.4   10.3   6.0         10    5.8   0.1    3.2  3  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.45   10.6   9.3        2.9    8.0   0.2    2.7  3  DUF1272         Protein of unknown function (DUF1272)
       0.48   10.5   7.7         13    5.9   8.0    2.3  2  DZR             Double zinc ribbon
       0.55   10.2   9.8        4.3    7.4   0.1    3.0  3  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
       0.62   10.1   5.5        2.4    8.2   1.5    2.3  3  HypA            Hydrogenase/urease nickel incorporation, meta
       0.63    9.7   5.3         18    5.0   0.3    3.1  3  Sgf11           Sgf11 (transcriptional regulation protein)
        1.1    8.7   9.4          3    7.3   0.7    3.1  3  zf-TFIIB        Transcription factor zinc-finger
        1.4    9.2   5.6         13    6.1   5.6    2.1  1  IBR             IBR domain, a half RING-finger domain
        1.8    8.4  10.6         17    5.2   0.5    3.2  3  zinc_ribbon_5   zinc-ribbon domain
          3    7.6   6.8        2.7    7.8   1.4    2.9  2  Ribosomal_S27e  Ribosomal protein S27
        3.2    7.8   9.0         14    5.7   5.2    2.9  3  Prok-RING_1     Prokaryotic RING finger family 1
        3.2    7.7   4.7         20    5.1   0.2    2.6  3  Rad50_zn_hook   Rad50 zinc hook motif
        4.3    7.2   6.3         11    6.0   3.8    2.5  2  Cys_rich_KTR    Cysteine-rich KTR
        4.7    7.6   7.4      1e+02    3.4   7.4    2.4  1  DnaJ_CXXCXGXG   DnaJ central domain


Domain annotation for each model (and alignments):
>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   1.1   2.1e-14   1.5e-11      87     159 ..      15      88 ..       8      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.1e-14
                           TackOD1  87 revCpkCkSidieeqelihhftCgnvgpeeef.lkegkleCpkCktkLrhiGvDYdrplevykCnsCkslfsep 159
                                         +Cp+C   ++++  +++h tCg v++   f   +  l+CpkC+++L++ +     ++ v +C +C++ f++ 
  gi|313125053|ref|YP_004035317.1|  15 DTACPDCDGGRVQRVGMFEHTTCGFVDVAAGFdAADRYLSCPKCDETLTTADDGLTCVAFVLHCPECDRRFDDV 88 
                                       679*****************************767788*********************************986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   8.4e-05     0.058      24      39 ..      13      29 ..       4      29 .. 0.78
   2 ?    6.5   0.1     0.013       9.1      11      36 ..      37      62 ..      32      64 .. 0.66
   3 !    8.0   0.0    0.0046       3.2       6      19 ..      76      89 ..      73      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.4e-05
                       Zn-ribbon_8 24 apltaCPeCgs.evrrv 39
                                      +++taCP+C + +v+rv
  gi|313125053|ref|YP_004035317.1| 13 SADTACPDCDGgRVQRV 29
                                      45777**********97 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                       Zn-ribbon_8 11 Cghefevlqsisdaplta.CPeCgsev 36
                                      Cg   +v + ++ a+    CP+C +++
  gi|313125053|ref|YP_004035317.1| 37 CG-FVDVAAGFDAADRYLsCPKCDETL 62
                                      77.5556666665555557****8755 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0046
                       Zn-ribbon_8  6 YrCeeCghefevlq 19
                                       +C eC+++f+ ++
  gi|313125053|ref|YP_004035317.1| 76 LHCPECDRRFDDVA 89
                                      589*****999654 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.9e-05     0.013      17      33 ..      11      27 ..       4      29 .. 0.79
   2 ?    5.7   0.3     0.026        18      20      29 ..      49      60 ..      36      63 .. 0.62
   3 ?    5.7   1.1     0.026        18      23      31 ..      77      85 ..      60      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                     zinc_ribbon_9 17 dedsdvlCPhCgggFVE 33
                                      d ++d++CP+C+gg V+
  gi|313125053|ref|YP_004035317.1| 11 DASADTACPDCDGGRVQ 27
                                      6678899*******997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.026
                     zinc_ribbon_9 20 sd..vlCPhCgg 29
                                      +d   +CP C+ 
  gi|313125053|ref|YP_004035317.1| 49 ADryLSCPKCDE 60
                                      333347****85 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.026
                     zinc_ribbon_9 23 lCPhCgggF 31
                                       CP+C+  F
  gi|313125053|ref|YP_004035317.1| 77 HCPECDRRF 85
                                      5*****998 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0087         6       2      20 ..      12      30 ..      12      33 .. 0.87
   2 ?    4.4   0.1     0.045        31       6      12 ..      53      59 ..      49      64 .. 0.84
   3 ?    5.1   0.1     0.027        18       6      12 ..      76      82 ..      72      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0087
                        Zn_Tnp_IS1  2 AsVsihCPrCsstdVyRhG 20
                                      As    CP C    V R G
  gi|313125053|ref|YP_004035317.1| 12 ASADTACPDCDGGRVQRVG 30
                                      677889******9999987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.045
                        Zn_Tnp_IS1  6 ihCPrCs 12
                                       +CP+C 
  gi|313125053|ref|YP_004035317.1| 53 LSCPKCD 59
                                      59****7 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.027
                        Zn_Tnp_IS1  6 ihCPrCs 12
                                       hCP C 
  gi|313125053|ref|YP_004035317.1| 76 LHCPECD 82
                                      6*****6 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.06        41      14      25 ..      16      27 ..       9      31 .. 0.84
   2 !    7.7   0.0    0.0046       3.2       7      21 ..      46      60 ..      40      71 .. 0.80
   3 ?    1.7   0.1      0.34   2.4e+02      15      20 ..      77      82 ..      74      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.06
                           DUF3797 14 vqCPeCgNnkvl 25
                                       +CP+C   +v+
  gi|313125053|ref|YP_004035317.1| 16 TACPDCDGGRVQ 27
                                      58****988885 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0046
                           DUF3797  7 vkLdekYvqCPeCgN 21
                                      ++  ++Y  CP+C  
  gi|313125053|ref|YP_004035317.1| 46 FDAADRYLSCPKCDE 60
                                      556789*******75 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.34
                           DUF3797 15 qCPeCg 20
                                       CPeC 
  gi|313125053|ref|YP_004035317.1| 77 HCPECD 82
                                      6****6 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.56   3.9e+02       2       7 ..      17      23 ..      16      35 .. 0.69
   2 ?    4.9   0.0     0.084        58       2      14 ..      54      66 ..      53      70 .. 0.82
   3 ?    7.7   0.1     0.011       7.4       2      12 ..      77      87 ..      76      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.56
                         zf-C2H2_4  2 kCpiC.g 7 
                                       Cp C g
  gi|313125053|ref|YP_004035317.1| 17 ACPDCdG 23
                                      6****44 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.084
                         zf-C2H2_4  2 kCpiCgksFsskk 14
                                       Cp C+++ ++ +
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDETLTTAD 66
                                      6*****9998865 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.011
                         zf-C2H2_4  2 kCpiCgksFss 12
                                       Cp C+++F +
  gi|313125053|ref|YP_004035317.1| 77 HCPECDRRFDD 87
                                      6********76 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   6.8     0.003       2.1       2      56 ..      17      82 ..      16      83 .. 0.74
   2 ?   12.6   1.5   0.00014     0.099       2      30 ..      54      89 ..      53      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.003
                                      --SSS-S--EE-S...SEEE-TTT--.....EEEEEEE-SSS-S---EEE...ETTEEEE--TTTT CS
                    zinc-ribbons_6  2 kCpeCqqelekrg...eqyhCeaCqe.....dlkkealCpeCeqelevlk...aCgavdyfCnkcn 56
                                       Cp+C+   ++r    e+++C   +        ++   Cp+C++ l +      C a    C +c+
  gi|313125053|ref|YP_004035317.1| 17 ACPDCDGGRVQRVgmfEHTTCGFVDVaagfdAADRYLSCPKCDETLTTADdglTCVAFVLHCPECD 82
                                      699999988877745566666655558888778889999999999988763336888888888886 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                                      --SSS-S--EE-S.......SEEE-TTT--EEEEEE CS
                    zinc-ribbons_6  2 kCpeCqqelekrg.......eqyhCeaCqedlkkea 30
                                      +Cp+C++ l++ +         +hC +C+++++ +a
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDETLTTADdgltcvaFVLHCPECDRRFDDVA 89
                                      6********977768888888889999999888765 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.38   2.6e+02       3       7 ..      18      22 ..      16      34 .. 0.87
   2 ?    6.3   0.1     0.021        15       2      14 ..      54      66 ..      53      67 .. 0.85
   3 ?    7.3   0.2      0.01         7       2      11 ..      77      86 ..      76      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.38
                                      ETTTT CS
                           zf-C2H2  3 CpdCg 7 
                                      CpdC+
  gi|313125053|ref|YP_004035317.1| 18 CPDCD 22
                                      ****8 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.021
                                      EETTTTEEESSHH CS
                           zf-C2H2  2 kCpdCgksFkrks 14
                                       Cp+C+++ ++ +
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDETLTTAD 66
                                      6******999876 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.01
                                      EETTTTEEES CS
                           zf-C2H2  2 kCpdCgksFk 11
                                       Cp+C+++F 
  gi|313125053|ref|YP_004035317.1| 77 HCPECDRRFD 86
                                      5*******96 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.23   1.6e+02       4       9 ..      17      22 ..      15      23 .. 0.81
   2 ?   11.1   0.1   0.00032      0.22       4      12 ..      54      62 ..      52      66 .. 0.87
   3 ?    1.5   0.1      0.31   2.1e+02       5      10 ..      78      83 ..      76      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.23
                        zf_C2H2_10  4 sCPKCq 9 
                                      +CP C 
  gi|313125053|ref|YP_004035317.1| 17 ACPDCD 22
                                      8**995 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00032
                        zf_C2H2_10  4 sCPKCqekl 12
                                      sCPKC e l
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDETL 62
                                      9*****986 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.31
                        zf_C2H2_10  5 CPKCqe 10
                                      CP C  
  gi|313125053|ref|YP_004035317.1| 78 CPECDR 83
                                      ****86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.4      0.03        20      16      22 ..      15      21 ..      12      24 .. 0.83
   2 ?    8.9   0.2    0.0014      0.97       4      16 ..      54      67 ..      51      71 .. 0.83
   3 ?    4.5   0.0     0.035        24       4       9 ..      77      82 ..      75      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.03
                       zf-ribbon_3 16 dnvCpyC 22
                                      d++Cp C
  gi|313125053|ref|YP_004035317.1| 15 DTACPDC 21
                                      899**99 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                       zf-ribbon_3  4 rCPnCGa.plssdd 16
                                      +CP+C++ + ++dd
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDEtLTTADD 67
                                      8******9977776 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.035
                       zf-ribbon_3  4 rCPnCG 9 
                                      +CP+C+
  gi|313125053|ref|YP_004035317.1| 77 HCPECD 82
                                      788886 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3       1.3   9.2e+02      17      21 ..      18      22 ..      17      24 .. 0.87
   2 ?    5.0   0.1     0.053        37      16      23 ..      54      61 ..      49      64 .. 0.78
   3 ?    8.2   0.1    0.0053       3.7      15      24 ..      76      85 ..      72      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.3
                         zf-H2C2_2 17 CplCd 21
                                      Cp Cd
  gi|313125053|ref|YP_004035317.1| 18 CPDCD 22
                                      ****8 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.053
                         zf-H2C2_2 16 eCplCdka 23
                                       Cp+Cd +
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDET 61
                                      6****987 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0053
                         zf-H2C2_2 15 yeCplCdkaF 24
                                      ++Cp+Cd +F
  gi|313125053|ref|YP_004035317.1| 76 LHCPECDRRF 85
                                      68******99 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4      0.28   1.9e+02       3       7 ..      18      22 ..      16      23 .. 0.75
   2 ?    1.8   0.0      0.39   2.7e+02      20      25 ..      37      42 ..      35      43 .. 0.83
   3 ?    7.7   0.2    0.0056       3.9       3      13 ..      55      65 ..      54      65 .. 0.83
   4 ?    6.7   1.4     0.011       7.5       2       8 ..      77      83 ..      77      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.28
                           UPF0547  3 CPeCe 7 
                                      CP C+
  gi|313125053|ref|YP_004035317.1| 18 CPDCD 22
                                      78776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.39
                           UPF0547 20 CGyvFq 25
                                      CG+v+ 
  gi|313125053|ref|YP_004035317.1| 37 CGFVDV 42
                                      ****87 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0056
                           UPF0547  3 CPeCeakvPva 13
                                      CP C++++ +a
  gi|313125053|ref|YP_004035317.1| 55 CPKCDETLTTA 65
                                      ******98665 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.011
                           UPF0547  2 vCPeCea 8 
                                      +CPeC++
  gi|313125053|ref|YP_004035317.1| 77 HCPECDR 83
                                      7****97 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3       0.5   3.4e+02       4       9 ..      17      22 ..      14      23 .. 0.84
   2 ?    5.4   0.1      0.02        14       4      13 ..      54      63 ..      51      67 .. 0.80
   3 ?    5.8   0.1     0.015        10       5      16 ..      78      89 ..      76      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.5
                            zf_UBZ  4 lCerCg 9 
                                       C++C+
  gi|313125053|ref|YP_004035317.1| 17 ACPDCD 22
                                      6****6 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.02
                            zf_UBZ  4 lCerCgkeip 13
                                       C++C++++ 
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDETLT 63
                                      7*****9876 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.015
                            zf_UBZ  5 CerCgkeipese 16
                                      C++C++++ + +
  gi|313125053|ref|YP_004035317.1| 78 CPECDRRFDDVA 89
                                      ******998765 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0043       2.9      41      54 ..      15      28 ..       8      31 .. 0.84
   2 ?   -1.5   0.1       4.2   2.9e+03      24      32 ..      29      37 ..      24      39 .. 0.79
   3 ?    7.4   1.5    0.0068       4.7       7      38 ..      54      84 ..      52      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0043
                           DUF1272 41 envCPncgGelvkR 54
                                      +  CP+c G+ v+R
  gi|313125053|ref|YP_004035317.1| 15 DTACPDCDGGRVQR 28
                                      678******99998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.2
                           DUF1272 24 icsyEctFC 32
                                      +  +E+t C
  gi|313125053|ref|YP_004035317.1| 29 VGMFEHTTC 37
                                      667999998 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0068
                           DUF1272  7 nCecCdkdlppdseearicsyEctFCaeCaee 38
                                      +C +Cd++l +++ +   c+    +C eC  +
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDETLTTAD-DGLTCVAFVLHCPECDRR 84
                                      699******9999.888888889999999665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.6      0.27   1.9e+02      28      35 ..      15      22 ..       4      38 .. 0.71
   2 ?    5.9   8.0     0.018        13       9      38 ..      49      85 ..      12      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.27
                               DZR 28 edrCpsCg 35
                                       ++Cp C+
  gi|313125053|ref|YP_004035317.1| 15 DTACPDCD 22
                                      45666664 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.018
                               DZR  9 ppdarfCseCgtklkavaa.......edrCpsCgekv 38
                                       ++   C++C ++l  + +         +Cp+C++  
  gi|313125053|ref|YP_004035317.1| 49 ADRYLSCPKCDETLTTADDgltcvafVLHCPECDRRF 85
                                      556668********866659999999999****9875 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0062       4.3      25      40 ..       8      25 ..       2      29 .. 0.73
   2 ?    6.8   0.3    0.0095       6.6      30      54 ..      52      75 ..      35      77 .. 0.75
   3 ?    2.0   0.5       0.3   2.1e+02      31      37 ..      76      82 ..      73      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0062
                                      E........E-TTTTTSS CS
                         Anti-TRAP 25 e..eprasleCPkCsGkg 40
                                      +  +  a   CP+C G  
  gi|313125053|ref|YP_004035317.1|  8 TglDASADTACPDCDGGR 25
                                      4457788899****9976 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0095
                                      ..E-TTTTTSSEEE-HHHHHHHHHH CS
                         Anti-TRAP 30 sleCPkCsGkglipTaqGqkLldFi 54
                                       l CPkC  + l   ++G + + F+
  gi|313125053|ref|YP_004035317.1| 52 YLSCPKCD-ETLTTADDGLTCVAFV 75
                                      589****7.4566666788888887 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.3
                                      .E-TTTT CS
                         Anti-TRAP 31 leCPkCs 37
                                      l CP+C 
  gi|313125053|ref|YP_004035317.1| 76 LHCPECD 82
                                      7899995 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.11        78      86      99 ..      15      28 ..       3      36 .. 0.73
   2 ?    5.0   2.4     0.033        23      71     102 ..      16      68 ..      11      72 .. 0.60
   3 ?    8.2   1.5    0.0034       2.4      71      95 ..      53      84 ..      45      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                                      HHS-TTTSSS-EEE CS
                              HypA 86 alrCpkCgsadvei 99
                                      ++ Cp+C++ +v+ 
  gi|313125053|ref|YP_004035317.1| 15 DTACPDCDGGRVQR 28
                                      568****9988875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.033
                                       EEETTTS-EEECHHHHH......................S-TTTSSS-EEEEES CS
                              HypA  71 vrCreCgkefeleekal......................rCpkCgsadveivsG 102
                                       + C +C+  +++++  +                      +CpkC+++ ++  +G
  gi|313125053|ref|YP_004035317.1|  16 TACPDCDG-GRVQRVGMfehttcgfvdvaagfdaadrylSCPKCDETLTTADDG 68 
                                       56777762.222221112345666677777777777777999999887776666 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0034
                                      EEETTTS-EEECHHHHH.......S-TTTSSS CS
                              HypA 71 vrCreCgkefeleekal.......rCpkCgsa 95
                                      + C +C+++ +++++ l       +Cp+C+++
  gi|313125053|ref|YP_004035317.1| 53 LSCPKCDETLTTADDGLtcvafvlHCPECDRR 84
                                      78*****999988652235677889****875 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.51   3.5e+02       2      10 ..      13      21 ..      12      22 .. 0.81
   2 ?    4.6   0.1     0.035        24       3      11 ..      51      59 ..      49      64 .. 0.84
   3 ?    5.0   0.3     0.026        18       5      12 ..      76      83 ..      75      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.51
                                      C-EEE-TTT CS
                             Sgf11  2 seyvtCpnC 10
                                      s+++ Cp C
  gi|313125053|ref|YP_004035317.1| 13 SADTACPDC 21
                                      67889**** PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.035
                                      -EEE-TTTS CS
                             Sgf11  3 eyvtCpnCg 11
                                      +y +Cp C+
  gi|313125053|ref|YP_004035317.1| 51 RYLSCPKCD 59
                                      699*****7 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.026
                                      EE-TTTSS CS
                             Sgf11  5 vtCpnCgR 12
                                       +Cp C+R
  gi|313125053|ref|YP_004035317.1| 76 LHCPECDR 83
                                      59*****9 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.6      0.12        83      21      27 ..      17      23 ..      14      24 .. 0.87
   2 ?    7.3   0.7    0.0043         3       2      13 ..      55      66 ..      54      72 .. 0.88
   3 ?    3.1   0.0     0.089        61       1       6 [.      77      82 ..      75      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                          zf-TFIIB 21 yCpqCrG 27
                                       Cp+C G
  gi|313125053|ref|YP_004035317.1| 17 ACPDCDG 23
                                      5999998 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0043
                          zf-TFIIB  2 CPkCqdeleese 13
                                      CPkC  +l++++
  gi|313125053|ref|YP_004035317.1| 55 CPKCDETLTTAD 66
                                      ********9875 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.089
                          zf-TFIIB  1 kCPkCq 6 
                                      +CP C 
  gi|313125053|ref|YP_004035317.1| 77 HCPECD 82
                                      588876 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.6     0.019        13      18      48 ..      52      85 ..       7      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                               IBR 18 lkwCprpdCeaiiekseg...cks..vtCskCgfef 48
                                      +  Cp  +C+  +   ++   c    ++C++C  +f
  gi|313125053|ref|YP_004035317.1| 52 YLSCP--KCDETLTTADDgltCVAfvLHCPECDRRF 85
                                      67899..999888777775653337788****9887 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.5     0.066        46       3       9 ..      16      22 ..      15      24 .. 0.86
   2 ?    5.2   0.5     0.025        17       4      17 ..      54      67 ..      52      71 .. 0.80
   3 ?    5.0   0.2     0.029        20       3      12 ..      76      85 ..      74      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.066
                     zinc_ribbon_5  3 irCpdCd 9 
                                      + CpdCd
  gi|313125053|ref|YP_004035317.1| 16 TACPDCD 22
                                      68****8 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.025
                     zinc_ribbon_5  4 rCpdCdtkFklvds 17
                                      +Cp+Cd +   +d+
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDETLTTADD 67
                                      8*****98777776 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.029
                     zinc_ribbon_5  3 irCpdCdtkF 12
                                        Cp+Cd  F
  gi|313125053|ref|YP_004035317.1| 76 LHCPECDRRF 85
                                      57*****988 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.4    0.0039       2.7      20      38 ..      46      64 ..      14      73 .. 0.90
   2 ?    0.5   0.3      0.73     5e+02       9      14 ..      77      82 ..      72      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0039
                                      ESS-SS-EEESSSTCEEEE CS
                    Ribosomal_S27e 20 FshaatvvkCisCgkvLve 38
                                      F+ a ++  C +C ++L +
  gi|313125053|ref|YP_004035317.1| 46 FDAADRYLSCPKCDETLTT 64
                                      999**********999986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.73
                                      E-TTTS CS
                    Ribosomal_S27e  9 kCpdCe 14
                                       Cp+C 
  gi|313125053|ref|YP_004035317.1| 77 HCPECD 82
                                      799996 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.73   5.1e+02      22      27 ..      17      22 ..       4      25 .. 0.79
   2 ?    5.7   5.2      0.02        14       6      26 ..      54      81 ..      50      85 .. 0.74
   3 ?    2.5   0.2      0.21   1.4e+02       6      15 ..      77      86 ..      73      89 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.73
                       Prok-RING_1 22 vCpeCg 27
                                       Cp+C 
  gi|313125053|ref|YP_004035317.1| 17 ACPDCD 22
                                      488884 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                       Prok-RING_1  6 kCpvCgkelkeedD.......iVvCpeC 26
                                      +Cp C+++l+ +dD       +  CpeC
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDETLTTADDgltcvafVLHCPEC 81
                                      7***********9944444434456666 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.21
                       Prok-RING_1  6 kCpvCgkelk 15
                                      +Cp C+++++
  gi|313125053|ref|YP_004035317.1| 77 HCPECDRRFD 86
                                      5777777665 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       4.6   3.2e+03      17      26 ..      13      22 ..      12      23 .. 0.74
   2 ?    3.9   0.1     0.068        47      21      31 ..      54      64 ..      48      66 .. 0.84
   3 ?    5.1   0.2     0.028        20      22      32 ..      78      88 ..      77      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.6
                                      T-SEE-TTT- CS
                     Rad50_zn_hook 17 eakgcCPlCg 26
                                      +a+  CP C+
  gi|313125053|ref|YP_004035317.1| 13 SADTACPDCD 22
                                      66778**996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.068
                                      E-TTT--EE-H CS
                     Rad50_zn_hook 21 cCPlCgRelde 31
                                      +CP C+ +l++
  gi|313125053|ref|YP_004035317.1| 54 SCPKCDETLTT 64
                                      7*****99987 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.028
                                      -TTT--EE-HH CS
                     Rad50_zn_hook 22 CPlCgReldee 32
                                      CP C+R +d+ 
  gi|313125053|ref|YP_004035317.1| 78 CPECDRRFDDV 88
                                      *********85 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.8   1.2e+03       6      11 ..      18      23 ..      16      35 .. 0.72
   2 ?    6.0   3.8     0.015        11       3      35 ..      52      83 ..      50      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.8
                      Cys_rich_KTR  6 cPvCgn 11
                                      cP C++
  gi|313125053|ref|YP_004035317.1| 18 CPDCDG 23
                                      777764 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                      Cys_rich_KTR  3 WvlcPvCgnkTRlkiredTvLknfpLfCPKCkq 35
                                      ++ cP C+  T +   +      f L+CP C +
  gi|313125053|ref|YP_004035317.1| 52 YLSCPKCDE-TLTTADDGLTCVAFVLHCPECDR 83
                                      688999975.7777777777889*******965 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   7.4      0.15     1e+02      11      50 ..      12      61 ..       6      84 .. 0.48

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.15
                     DnaJ_CXXCXGXG 11 kgkkktCktCkGsG.v.vree..........qktlgp.fv.qqsqstCpeCeGt 50
                                      +++ + C++C+G   + v                ++  f       +Cp+C+ t
  gi|313125053|ref|YP_004035317.1| 12 ASADTACPDCDGGRvQrV--GmfehttcgfvD--VAAgFDaADRYLSCPKCDET 61
                                      455678999999762221..112222222110..11111101222356666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 604.13
//
Query:       gi|313125054|ref|YP_004035318.1|  [L=567]
Description: glycosyl transferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-36  126.4   0.0    2.1e-36  126.0   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    7.3e-35  120.3   0.0    1.1e-34  119.8   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    2.5e-31  109.1   1.3    2.5e-31  109.1   1.3    3.0  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    3.2e-17   62.6   0.0    5.8e-17   61.7   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
    1.3e-15   57.0   1.5    2.1e-09   36.6   0.0    3.1  3  Chitin_synth_2   Chitin synthase
    1.5e-13   50.8   0.0    3.1e-13   49.8   0.0    1.4  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    1.1e-06   27.5   9.6      4e-06   25.6   0.2    2.6  3  Cellulose_synt   Cellulose synthase
     0.0029   18.1   0.0     0.0065   17.0   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.03   13.7   0.0      0.055   12.9   0.0    1.3  1  Tnp_P_element    Transposase protein
        0.1   11.3   0.0       0.15   10.8   0.0    1.1  1  GNT-I            GNT-I family
       0.51   10.3   0.0       0.51   10.3   0.0    3.0  1  Syndecan         Syndecan domain


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.0   1.3e-39   2.1e-36       4     230 .]     204     424 ..     201     424 .. 0.92

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 1.3e-39
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       ++vlVp++ne+ ++g++l+s+la++yp+  +ev+v++d+s+++t ++a +    + + rv+v ++++    +gk  a
  gi|313125054|ref|YP_004035318.1| 204 VSVLVPAYNESNYVGDCLDSILASDYPTdrLEVIVIDDGSTDGTYAEASA----YRNDRVSVFHRSN----GGKHAA 272
                                       89************************5555***************98876....8888***999988....59**** PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrstlvsalgalefaerhl.rflaarr 153
                                       ln +l+  ++d+v+ vD+D+++ P +l+ ++ ++  +p+ gav + v ++n +  v  ++ale+       ++a+++
  gi|313125054|ref|YP_004035318.1| 273 LNLGLSCSRGDVVVAVDADSILAPSALRTAVEQLqSDPRLGAVAGTVVVNNADGIVGSVQALEYVLGINtLRRAFSY 349
                                       **********************************9999************************998776525666667 PP

                   Glyco_tranf_2_3 154 algvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                                        ++v+ + G + ++rre l e +g dp   +t+D++l++rl +ag+r+   + a+v+++ p sl+++ +qr Rw++g
  gi|313125054|ref|YP_004035318.1| 350 LGTVMVIPGCLGVFRREALSEVGGYDP-DTVTEDFDLTVRLLKAGWRVELSE-ALVYTEAPFSLTDLLNQRLRWTRG 424
                                       77788888*******************.********************9765.55*******************986 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8   0.0   6.5e-38   1.1e-34       1     169 [.     205     371 ..     205     372 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 6.5e-38
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       sv +p+yNe++++  +l+s+la  +p +++e+iv+DDgStD+t + + +++  ++rv v++r+ n Gk++aln gl+
  gi|313125054|ref|YP_004035318.1| 205 SVLVPAYNESNYVGDCLDSILASdYPTDRLEVIVIDDGSTDGTYAEASAYR--NDRVSVFHRS-NGGKHAALNLGLS 278
                                       89************************************************8..6*********.55*********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTT CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsf 153
                                        ++gd+++ +DaD++ +p  l+  ve l+ d++ ++++++++ +  ++     +  ++   +++ +r +s+ g++++
  gi|313125054|ref|YP_004035318.1| 279 CSRGDVVVAVDADSILAPSALRTAVEQLQSDPRLGAVAGTVVVNNADGIVGSVQALEYVLGINTLRRAFSYLGTVMV 355
                                       ********************************************999999999999********************* PP

                                       CSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 154 eigsaallrrealeel 169
                                       + g+  ++rreal e+
  gi|313125054|ref|YP_004035318.1| 356 IPGCLGVFRREALSEV 371
                                       *************997 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   1.3   1.6e-34   2.5e-31       1     188 [.     284     492 ..     284     501 .. 0.74

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 1.6e-34
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsg 76 
                                       +++ +DaD+ l p  lr +++ l+ +p+ ++v g v+v+n   ++  ++al++ + ++ +++ +++lg v+ ++G  
  gi|313125054|ref|YP_004035318.1| 284 VVVAVDADSILAPSALRTAVEQLQsDPRLGAVAGTVVVNNADGIVGSVQALEYVLGINTLRRAFSYLGTVMVIPGCL 360
                                       5899********************66*************************************************** PP

                   Glyco_trans_2_3  77 aflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.....elek 148
                                        ++rr+al+evgg+d  +++v+EDfd+ +rl+++G+rv + ++  v+++ p++l + l+Qr Rw++G+     +   
  gi|313125054|ref|YP_004035318.1| 361 GVFRREALSEVGGYD--PDTVTEDFDLTVRLLKAGWRVELSEAL-VYTEAPFSLTDLLNQRLRWTRGNiqtllK--- 431
                                       ***************..***********************9976.**********************7433220... PP

                   Glyco_trans_2_3 149 lillvrll........gylgsllwsalplhlallllfslla...................lalvlll 188
                                             ++        g+l+++++    l++++++ +s++                     a++l++
  gi|313125054|ref|YP_004035318.1| 432 ------HRdvfsepayGFLHRFAFPLSALSILFVPFASIVVttmifvailngaflgvalvAAYFLFV 492
                                       ......2222333322333333322222222333333332222222223344544444433333333 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   3.5e-20   5.8e-17      18     173 .]     269     423 ..     258     423 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 3.5e-20
                   Glyco_transf_21  18 KvnnllqaleaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakglaaaleaafl....ntlag 89 
                                       K  +l+ +l+  + d++v  D+d +++p +L++ +++l++ p+ g V +++v+ +a+g+ + ++a+      ntl +
  gi|313125054|ref|YP_004035318.1| 269 KHAALNLGLSCSRGDVVVAVDADSILAPSALRTAVEQLQSdPRLGAVAGTVVVNNADGIVGSVQALEYvlgiNTLRR 345
                                       777888899999*************************9876****************98888866664345799999 PP

                   Glyco_transf_21  90 vlqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslralla 166
                                       ++++ l+ +  + G   ++rreaL ++GG+ +  d++ eD+ l+ +l +aG++v ls+a  + t++p   sl +ll+
  gi|313125054|ref|YP_004035318.1| 346 AFSY-LGTVMVIPGCLGVFRREALSEVGGYDP--DTVTEDFDLTVRLLKAGWRVELSEAL-VYTEAPF--SLTDLLN 416
                                       9999.9999***********************..************************96.6688885..9****** PP

                   Glyco_transf_21 167 RqlrWar 173
                                       + lrW r
  gi|313125054|ref|YP_004035318.1| 417 QRLRWTR 423
                                       *****86 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0   0.00096       1.6      26      74 ..     203     250 ..     178     260 .. 0.82
   2 !   36.6   0.0   1.3e-12   2.1e-09     196     292 ..     276     371 ..     269     383 .. 0.87
   3 !   10.0   1.1   0.00015      0.24     346     465 ..     397     517 ..     378     529 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00096
                    Chitin_synth_2  26 fticlvtaysegeeglrttldslastdyddkrklllvvcdGlikGsGnd 74 
                                        + +lv+ay e++  +  +lds+ + dy+  r  ++v+ dG   G+  +
  gi|313125054|ref|YP_004035318.1| 203 LVSVLVPAYNESN-YVGDCLDSILASDYPTDRLEVIVIDDGSTDGTYAE 250
                                       455799***9975.689************************98887655 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 1.3e-12
                    Chitin_synth_2 196 GvspdfyeivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvtaiqvfeyyishhlskafesvfG 272
                                       G+s ++ ++v+ vdad+ +ap +l+  v +l++dp++ ++ G t + n+++  v  +q  ey +  ++ +   s +G
  gi|313125054|ref|YP_004035318.1| 276 GLSCSRGDVVVAVDADSILAPSALRTAVEQLQSDPRLGAVAG-TVVVNNADGIVGSVQALEYVLGINTLRRAFSYLG 351
                                       777888899***************************999998.667777899************99987777799** PP

                    Chitin_synth_2 273 svtclPGcfslyrikaakga 292
                                       +v  +PGc+ ++r +a  + 
  gi|313125054|ref|YP_004035318.1| 352 TVMVIPGCLGVFRREALSEV 371
                                       *************9887764 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00015
                    Chitin_synth_2 346 fvpqakcktvaPdtfkvllsqrrrwinstvhnllelvlvrdlcG..tfcfsmrfvvfieligtvvlPvaiaftlyli 420
                                        + +a + t aP + + ll qr rw    +  l   ++ rd+     + f  rf   +  ++ + +P a + +  +i
  gi|313125054|ref|YP_004035318.1| 397 ELSEALVYTEAPFSLTDLLNQRLRWTRGNIQTL---LKHRDVFSepAYGFLHRFAFPLSALSILFVPFASIVVTTMI 470
                                       56789999*****************87766655...5566665422577889*****************99999999 PP

                    Chitin_synth_2 421 vasilkskl..vpviplvllaivlGlpailivltarkleyvawllvy 465
                                         +il+ ++  v +++  +l ++l + a+ + l    + ++a+  ++
  gi|313125054|ref|YP_004035318.1| 471 FVAILNGAFlgVALVAAYFLFVLLFVAAMALDLSDGDWRLLAYAPLH 517
                                       99999966612334555566666666777666666666666665555 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   1.9e-16   3.1e-13       2     221 ..     206     410 ..     205     423 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 1.9e-16
                   Glyco_tranf_2_2   2 vviplraseerhyieerv..lqkakyy.deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNr 75 
                                       v++p ++  e +y+ + +   + a+ y  + +e+iv+ddgS++ +  e s+  + +  v+ + +     ++ aa N+
  gi|313125054|ref|YP_004035318.1| 206 VLVPAYN--ESNYVGDCLdsIL-ASDYpTDRLEVIVIDDGSTDGTYAEASAYRNDRVSVFHRSN----GGKHAALNL 275
                                       5566554..4458999996434.45555999**********************99999974333....5999***** PP

                   Glyco_tranf_2_2  76 GaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsev..lkdvedltassrvledl 150
                                       G s + +d+v+ +DaD   ++  +   ++     +l+  +    v   v  n++d  v  ++  e+ +  ++ l+ +
  gi|313125054|ref|YP_004035318.1| 276 GLSCSRGDVVVAVDADSILAPSALRTAVE-----QLQSDPRLGAVAGTVVVNNADGIVgsVQALEY-VLGINTLRRA 346
                                       ************************99999.....77777776666666666666654321444444.5677888888 PP

                   Glyco_tranf_2_2 151 laakstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykaraks 221
                                       +     l   ++  +   + +r+a++evGGyD       +EDfdl +Rl+ka   + + +  l y +   s
  gi|313125054|ref|YP_004035318.1| 347 FS---YLGTVMVIPGCLGVFRREALSEVGGYDPDT---VTEDFDLTVRLLKAGWRV-ELSEALVYTEAPFS 410
                                       88...45555666788999*************998...89************9999.78888888776555 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.1       1.3   2.1e+03     496     558 ..      90     155 ..      76     173 .. 0.64
   2 !    8.1   0.1    0.0005      0.81      20      48 ..     219     247 ..     203     265 .. 0.80
   3 !   25.6   0.2   2.5e-09     4e-06     420     550 ..     377     501 ..     343     513 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                    Cellulose_synt 496 laylnviiypfts.ifllvycilpalsllsgkfivk..elsnlasiyllllflslivlavlelkws 558
                                       lay +      t  +fl+++c+   +sl  g  + +  +  + +si+l +++ +l++++ + + ws
  gi|313125054|ref|YP_004035318.1|  90 LAYTERYTTEATPfVFLVAFCLPWVVSLTVGGRLRRlaNTRVRLSIWLAIVLSALVLTGGFVFGWS 155
                                       566555444444317888999766777766554433003344567777777777777776666665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0005
                    Cellulose_synt  20 ntvlsilavdypvekvscyvsddGaallt 48 
                                       + + sila dyp +++ + v ddG++  t
  gi|313125054|ref|YP_004035318.1| 219 DCLDSILASDYPTDRLEVIVIDDGSTDGT 247
                                       56779*******************97544 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 2.5e-09
                    Cellulose_synt 420 GsvtedvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnnalfagykkklkllerl 496
                                        +vted     ++ + Gwr        +     ap  l+d l+q lrw+ G ++ ++ ++  +f        +l+r+
  gi|313125054|ref|YP_004035318.1| 377 DTVTEDFDLTVRLLKAGWRVEL---SEALVYTEAPFSLTDLLNQRLRWTRGNIQTLL-KHRDVFSE--PAYGFLHRF 447
                                       579999999999******9643...33445678*********************988.67788877..788889998 PP

                    Cellulose_synt 497 ay....lnviiypftsifllvycilpalsllsgkfivkelsnlasiyllllflslivl 550
                                       a+    l +   pf+si++ +   +  +++l g f+   l +++ + ++llf++ ++l
  gi|313125054|ref|YP_004035318.1| 448 AFplsaLSILFVPFASIVVTT---MIFVAILNGAFLGVALVAAYFL-FVLLFVAAMAL 501
                                       874333566667888887655...4557899999997776554433.34455555444 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     4e-06    0.0065       2      87 ..     212     297 ..     211     306 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4e-06
                   Glyco_tranf_2_4   2 neadiLpeflahhlalgf..dr..ilvydndstDgtrailkelpe..vkllhvdksyederrqvellkallaryaea 72 
                                       ne ++ + +l+ +la ++  dr  ++v+d++stDgt+a  +++ +  v+++h  +  +     +++l+  l + +++
  gi|313125054|ref|YP_004035318.1| 212 NESNYVGDCLDSILASDYptDRleVIVIDDGSTDGTYAEASAYRNdrVSVFHRSNGGK-----HAALNLGL-SCSRG 282
                                       7788888888888777754443449*************99997552377776666544.....45555434.55688 PP

                   Glyco_tranf_2_4  73 dwvlvvDaDEflvvp 87 
                                       d v++vDaD +l+ +
  gi|313125054|ref|YP_004035318.1| 283 DVVVAVDADSILAPS 297
                                       999999999888765 PP

>> Tnp_P_element  Transposase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.4e-05     0.055      50     112 ..     417     478 ..     400     502 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                     Tnp_P_element  50 krvqkWtreeiskalklry.vskrayvylknelnyPlPglstlqrwakslelenGiledvlell 112
                                       +r++ Wtr +i   lk r  +s+ ay +l+ +  +Pl +ls l     s+ + + i+  +l+  
  gi|313125054|ref|YP_004035318.1| 417 QRLR-WTRGNIQTLLKHRDvFSEPAYGFLH-RFAFPLSALSILFVPFASIVVTTMIFVAILNGA 478
                                       4555.*************989********9.9***********999999999999999999865 PP

>> GNT-I  GNT-I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.2e-05      0.15      89     147 ..     198     256 ..     182     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.2e-05
                             GNT-I  89 kqakdviavlvlacsradavrrtvekllkyrpsaekfPlivsqdcsneevkkevlsygd 147
                                       +   + ++vlv a + +++v ++++++l     +++  +iv  d+s + +  e+  y +
  gi|313125054|ref|YP_004035318.1| 198 DDDAPLVSVLVPAYNESNYVGDCLDSILASDYPTDRLEVIVIDDGSTDGTYAEASAYRN 256
                                       45678899***********************99999************99999999965 PP

>> Syndecan  Syndecan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00031      0.51      11      48 ..     163     200 ..     161     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                          Syndecan  11 aviggvvvgllfaillvlflvYRmrKKDEGSYaLdepk 48 
                                       av +g vv+  ++++++ + +  mr + E   +Ld+  
  gi|313125054|ref|YP_004035318.1| 163 AVFAGFVVIAFIVVVVFPLTIVQMRGREESDHTLDDDD 200
                                       899*******************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.52
# Mc/sec: 3274.22
//
Query:       gi|313125055|ref|YP_004035319.1|  [L=67]
Description: hypothetical protein Hbor_02700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0034   17.6   1.8     0.0097   16.1   0.0    2.0  2  zinc_ribbon_9  zinc-ribbon
     0.0085   16.1   0.2      0.011   15.7   0.2    1.3  1  DZR            Double zinc ribbon
     0.0093   15.4   2.2        1.4    8.5   0.1    2.2  2  zf-ribbon_3    zinc-ribbon domain
  ------ inclusion threshold ------
      0.017   14.5   0.3      0.066   12.6   0.0    1.9  2  zf_Rg          Reverse gyrase zinc finger
      0.067   13.3   0.2      0.088   13.0   0.2    1.2  1  FYVE           FYVE zinc finger


Domain annotation for each model (and alignments):
>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4      0.19   6.7e+02      18      29 ..       2      12 ..       1      14 [. 0.80
   2 !   16.1   0.0   2.7e-06    0.0097      10      35 .]      20      48 ..      19      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.19
                     zinc_ribbon_9 18 edsdvlCPhCgg 29
                                      +d d+ C  Cg 
  gi|313125055|ref|YP_004035319.1|  2 SDTDP-CDACGE 12
                                      58899.999986 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.7e-06
                     zinc_ribbon_9 10 rfVsvspdedsd.v..lCPhCgggFVEei 35
                                      r+V+++ d ++  +  lCP+C  g +E++
  gi|313125055|ref|YP_004035319.1| 20 RTVRITVDRSEVdSqrLCPNCFAGWIERY 48
                                      88999888444443459*********975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   3.2e-06     0.011      13      35 ..       5      41 ..       1      49 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.2e-06
                               DZR 13 rfCseCgtklkavaa..............edrCpsCg 35
                                        C++Cg+++  + a              ++ Cp+C 
  gi|313125055|ref|YP_004035319.1|  5 DPCDACGEQVTDALArtvritvdrsevdsQRLCPNCF 41
                                      56********988889********************5 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1   0.00038       1.4       3      13 ..       5      16 ..       4      21 .. 0.72
   2 !    6.6   0.4    0.0015       5.4      15      22 ..      33      40 ..      32      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00038
                       zf-ribbon_3  3 vrCPnCGa.pls 13
                                        C +CG+ + +
  gi|313125055|ref|YP_004035319.1|  5 DPCDACGEqVTD 16
                                      57******5544 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0015
                       zf-ribbon_3 15 ddnvCpyC 22
                                      +++ Cp+C
  gi|313125055|ref|YP_004035319.1| 33 SQRLCPNC 40
                                      78999999 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.21   7.5e+02      27      31 ..       6      10 ..       2      18 .. 0.59
   2 ?   12.6   0.0   1.8e-05     0.066       7      23 ..      34      51 ..      31      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.21
                             zf_Rg 27 pCkrC 31
                                      pC  C
  gi|313125055|ref|YP_004035319.1|  6 PCDAC 10
                                      34444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.8e-05
                             zf_Rg  7 eklCPNC.gGdisdeRle 23
                                      ++lCPNC  G i+ +R e
  gi|313125055|ref|YP_004035319.1| 34 QRLCPNCfAGWIERYRTE 51
                                      68*****7799**99975 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.4e-05     0.088      28      64 ..       7      42 ..       3      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                      -TTT--EE-STTS-EEE.EEGGGTEEEEEEE-HHHHH CS
                              FYVE 28 CrlCGkvvCekCssklvallekeaeeksvrvCkeCla 64
                                      C +CG+ v ++  ++    + +++e++s+r+C +C+a
  gi|313125055|ref|YP_004035319.1|  7 CDACGEQVTDALARTVR-ITVDRSEVDSQRLCPNCFA 42
                                      88899998877655544.56699************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 426.20
//
Query:       gi|313125056|ref|YP_004035320.1|  [L=226]
Description: uracil phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-44  151.4   0.0    2.5e-44  151.2   0.0    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    2.4e-07   30.4   0.1    3.5e-07   29.9   0.1    1.2  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.2   0.0   2.8e-48   2.5e-44       3     207 .]      13     225 ..      11     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 2.8e-48
                           UPRTase   3 shpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysgelldeekialVpilRaGe 79 
                                        h l+k  l  lRd +t++  fr+ + +++r+ ++e++  ++++e vtv+tpl++++ ++++  ++++++ +lRa  
  gi|313125056|ref|YP_004035320.1|  13 THALAKDTLLRLRDVETEQVAFRKGLVKLGRICGYEIIDGVMETEYVTVETPLTETTGEHVKGLDNVVIINVLRAAT 89 
                                       68899999999****************************************************************** PP

                           UPRTase  80 gmeealrellpearvghlglqreeet.......lepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLker.g 148
                                       +++e+l++++p+a+ g +   r+ee            + y kLP+  +++tv++ Dp++aTG++++a++++++++  
  gi|313125056|ref|YP_004035320.1|  90 PFVEGLLKAFPRAKQGVISAGRDEEAgmdddgeFPITIDYVKLPEITEKDTVIVADPMLATGSTMCAVLDHVLSNaA 166
                                       ************************997777775444588******************************99866527 PP

                           UPRTase 149 vgeekIlvlsvlaseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRlFgT 207
                                       ++  + +vls ++++ g+ r+  +fp+ ++ t+++D++ld++gyi+pGlGD+GDR F T
  gi|313125056|ref|YP_004035320.1| 167 AEPTDLFVLSAVSAPDGLLRVGGQFPDADLLTVSIDDHLDDDGYIIPGLGDAGDRAFRT 225
                                       7889*****************************************************98 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   3.9e-11   3.5e-07      28     113 ..      76     165 ..      64     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.9e-11
                                       GGGEEEEEEETTTHHHHHHHHHHS....TT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSS CS
                      Pribosyltran  28 gkpdvvvgiargGvpfakiladeL....evplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtG 100
                                         ++v++ ++r + pf+  l +++     + +   r +    d+ +e++++ +d  +l+e++++ +V++ D +l+tG
  gi|313125056|ref|YP_004035320.1|  76 LDNVVIINVLRAATPFVEGLLKAFprakQGVISAGRDEEAGMDDDGEFPIT-IDYVKLPEITEKDTVIVADPMLATG 151
                                       6789********************655422333333344444455555543.34448******************** PP

                                       HHHHHHHH.HHHCC CS
                      Pribosyltran 101 gTllaale.lLkek 113
                                       +T++a+l+  L ++
  gi|313125056|ref|YP_004035320.1| 152 STMCAVLDhVLSNA 165
                                       ********444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1447.94
//
Query:       gi|313125057|ref|YP_004035321.1|  [L=62]
Description: hypothetical protein Hbor_02720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.057   13.6   3.8      0.069   13.3   3.8    1.1  1  Phage_r1t_holin  Putative lactococcus lactis phage r1t holin


Domain annotation for each model (and alignments):
>> Phage_r1t_holin  Putative lactococcus lactis phage r1t holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.8   3.9e-06     0.069      13      46 ..      20      53 ..      18      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.9e-06
                   Phage_r1t_holin 13 vkTaaqallgllgagatglldvdwaaaasvaala 46
                                      v +++ a++ ++g + +g++++  +++as+a + 
  gi|313125057|ref|YP_004035321.1| 20 VLSSVFAAVVVWGLDFIGMVELTFVNVASLALVL 53
                                      789999************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 407.95
//
Query:       gi|313125058|ref|YP_004035322.1|  [L=98]
Description: hypothetical protein Hbor_02730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 631.37
//
Query:       gi|313125059|ref|YP_004035323.1|  [L=322]
Description: arsenite efflux ATP-binding protein arsa [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-70  235.5   0.0    9.6e-70  235.2   0.0    1.0  1  ArsA_ATPase  Anion-transporting ATPase
    4.2e-11   43.1   0.0      6e-11   42.6   0.0    1.2  1  AAA_31       AAA domain
      5e-08   33.1   0.0    8.8e-08   32.3   0.0    1.7  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    5.6e-05   22.7   0.0     0.0027   17.2   0.0    2.4  2  ParA         NUBPL iron-transfer P-loop NTPase
    0.00037   19.9   0.0    0.00052   19.4   0.0    1.3  1  ATPase       KaiC
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.019   14.4   0.0    1.4  1  PhoH         PhoH-like protein
      0.031   14.4   2.2      0.041   14.0   0.1    2.4  2  AAA_33       AAA domain
      0.048   12.9   0.0      0.099   11.9   0.0    1.5  1  Zeta_toxin   Zeta toxin
      0.056   12.9   0.0      0.093   12.2   0.0    1.3  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.063   12.9   0.2       0.19   11.4   0.1    1.7  2  SRP54        SRP54-type protein, GTPase domain
      0.064   12.4   0.2        0.1   11.7   0.2    1.3  1  NB-ARC       NB-ARC domain
      0.083   12.5   8.4      0.033   13.8   3.9    2.5  2  AAA_25       AAA domain
      0.092   12.5   0.1       0.19   11.4   0.1    1.4  1  IstB_IS21    IstB-like ATP binding protein
        0.1   12.4   0.1        0.3   10.8   0.1    1.7  2  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.16   10.9   0.1       0.37    9.7   0.1    1.6  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.34   11.2   4.6         16    5.7   1.6    3.3  2  AAA_28       AAA domain


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.2   0.0   8.6e-73   9.6e-70       2     294 ..       3     303 ..       2     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 235.2 bits;  conditional E-value: 8.6e-73
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEET..SSEEEEE--HHHHHHHH CS
                       ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvk..eNLsavEidpeveleea 76 
                                       k++++gGKGGVGKtt+++a a+k++++g ++l++stDPAhs sD+fdq++g +p++v+   NL a+E+dp++e+e+ 
  gi|313125059|ref|YP_004035323.1|   3 KFVFFGGKGGVGKTTLASAYALKCAREGLDTLVVSTDPAHSTSDVFDQQFGDDPQAVEgeTNLAAMEVDPDTEVERH 79 
                                       89*********************************************************99**************** PP

                                       HCCHHGGGSCCH...HHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHH.CSSSSEEEEESBSCCHTCGGGGHHHHHH CS
                       ArsA_ATPase  77 kqevqkeeeall...gleeledvlaeelaslPGideilsfeellkyvk.eeeydvvvlDtaPTGhtlrllslpevle 149
                                         e+++++++++   +++e + +++++ ++ PG  e++ ++++++ ++ ++e+d vv+Dt+PTG tlrllslp+ le
  gi|313125059|ref|YP_004035323.1|  80 LMETKRAMGDQVspaMVNEIDRQIEMAHQT-PGAYEAALMDRFIEVMRsADEFDRVVFDTSPTGGTLRLLSLPDLLE 155
                                       *********999666677777889999999.****************96789************************* PP

                                       HHHHHHHHHHHHHHHHHHHHC..CCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHH CS
                       ArsA_ATPase 150 klleklvklkeklsplakqlv..kllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEte 224
                                       +++++lv  +ek  +l ++    +  +   ++ +  l++l+++ke+++ + e+l ++    f+lVv+p++ls++Et+
  gi|313125059|ref|YP_004035323.1| 156 SWIDRLVYKREKSIDLYEKAAigNNEPRRMMDGDPILDRLRTRKERFEFAGETLRENAA--FFLVVNPDELSIRETR 230
                                       ******988887777776653113333334444489******************99876..**************** PP

                                       HHHHHHHHTT-EEEEEEEEEE-TTCSSS....TSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHH CS
                       ArsA_ATPase 225 RaikeLkkygikvdavivNkllpeeeqe....nCeflearkkiqkkylkeieelfedlevvklplleeEvvGle 294
                                       Rai +L++y++++  +  N+l pe e +      +fl+ r ++++++l e++e f+  +v+++    +Ev+G +
  gi|313125059|ref|YP_004035323.1| 231 RAIDDLESYDLTICGLAANRLTPEPEPHeegrGARFLRDRVETERERLRELREDFRYPVVAEVATRVSEVKG-D 303
                                       **********************9987655577789************************************9.4 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   5.4e-14     6e-11       4     133 ..       4     146 ..       1     151 [. 0.79

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 5.4e-14
                            AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne......iektlyevli.eeknikeai 73 
                                        ++   KGGvGKTT + + a   a++g  +L+v  Dp  +++  ++ +  +       e++l  + +  +++++  +
  gi|313125059|ref|YP_004035323.1|   4 FVFFGGKGGVGKTTLASAYALKCAREGLDTLVVSTDPAHSTSDVFDQQFGDdpqaveGETNLAAMEVdPDTEVERHL 80 
                                       567778***********************************996665433345566688899999988899999999 PP

                            AAA_31  74 iktkvenl.dlipssidLaeaeielvelekk..eeil.kellekvk..deYDyiiiDcpPsLgllt 133
                                       ++tk  +  ++ p+ ++ ++ +ie+++ +    e +l ++++e ++  de+D +++D++P+ g+l 
  gi|313125059|ref|YP_004035323.1|  81 METKRAMGdQVSPAMVNEIDRQIEMAHQTPGayEAALmDRFIEVMRsaDEFDRVVFDTSPTGGTLR 146
                                       9888666559*******999999999888765544443777766652267**********987765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   7.8e-11   8.8e-08       2      55 ..       5     137 ..       4     301 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 7.8e-11
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       ++ ++kGGvGKTtla + a   ar+gl++l+v +Dp  + + ++++  +d  +                        
  gi|313125059|ref|YP_004035323.1|   5 VFFGGKGGVGKTTLASAYALKCAREGLDTLVVSTDPAHSTSDVFDQQFGDDPQavegetnlaamevdpdteverhlm 81 
                                       5789*********************************9999974444444444666899999999999999999999 PP

                                       .......................................................C CS
                                       .......................................................x RF
                              CbiA  55 .......................................................d 55 
                                                                                              d
  gi|313125059|ref|YP_004035323.1|  82 etkramgdqvspamvneidrqiemahqtpgayeaalmdrfievmrsadefdrvvfD 137
                                       99999999999999997777777777777777666666666666665555555551 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.4e-06    0.0027       7      41 ..       5      39 ..       1      70 [. 0.89
   2 ?    3.2   0.0     0.046        51     137     173 ..     213     249 ..     205     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                              ParA  7 avlSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                      +   gKGGVGK+t+a+  Al+ a++gl++ ++ +D
  gi|313125059|ref|YP_004035323.1|  5 VFFGGKGGVGKTTLASAYALKCAREGLDTLVVSTD 39
                                      5678**********************999888776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.046
                              ParA 137 agaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                       a+  +V  p e+++ ++++ai+ +++ ++++ G+  N
  gi|313125059|ref|YP_004035323.1| 213 AAFFLVVNPDELSIRETRRAIDDLESYDLTICGLAAN 249
                                       45678999*************************9988 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.6e-07   0.00052      22      96 ..       5      78 ..       1     136 [. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.6e-07
                            ATPase 22 vlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesa 96
                                      v   G+ G GKt++a  +++k a++ g  ++ v+++   +      +++G d +++e e +la +++  ++e + 
  gi|313125059|ref|YP_004035323.1|  5 VFFGGKGGVGKTTLASAYALKCARE-GLDTLVVSTDPAHSTSDVFDQQFGDDPQAVEGETNLAAMEVDPDTEVER 78
                                      5567999***************999.**********888777777789***********9999999888776533 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-05     0.019      20      60 ..       3      43 ..       1      99 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                      SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S-- CS
                              PhoH 20 divfaiGpaGtGKtylavalavealkkkkvkriiltrpave 60
                                      ++vf  G+ G GKt la a+a++  +++  + ++ t pa +
  gi|313125059|ref|YP_004035323.1|  3 KFVFFGGKGGVGKTTLASAYALKCAREGLDTLVVSTDPAHS 43
                                      6899********************99988777777777765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.7e-05     0.041       2      48 ..       5      56 ..       4     141 .. 0.77
   2 ?   -1.4   0.3       2.1   2.3e+03      80      80 ..     267     267 ..     194     315 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqsktdy 48
                                      v++ G  G+GK+tla  ++ k +     + ++s+d ++++  + dqq   d+
  gi|313125059|ref|YP_004035323.1|  5 VFFGGKGGVGKTTLASAYALKCAregldTLVVSTDPAHSTSDVFDQQFGDDP 56
                                      7999**************7666666698999999997775555444433333 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                            AAA_33  80 l 80 
                                       l
  gi|313125059|ref|YP_004035323.1| 267 L 267
                                       0 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.8e-05     0.099      17      83 ..       3      70 ..       2      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.8e-05
                        Zeta_toxin 17 klillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdasel 83
                                      k ++ gG  G GK++la++ + + + ++ + +++++D   +    +++ + +dp+ +   t+ +a e+
  gi|313125059|ref|YP_004035323.1|  3 KFVFFGGKGGVGKTTLASAYALKCArEGLDTLVVSTDPAHSTSDVFDQQFGDDPQAVEGETNLAAMEV 70
                                      5799****************999997788999999999988888888888888888888887777665 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.3e-05     0.093       5      43 ..       7      45 ..       2      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                         Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDst 43
                                      + GkGG+Gk+t ++  +   a+ g   l+v  DP + + 
  gi|313125059|ref|YP_004035323.1|  7 FGGKGGVGKTTLASAYALKCAREGLDTLVVSTDPAHSTS 45
                                      448*******************************87554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00017      0.19       4      38 ..       5      39 ..       2      45 .. 0.89
   2 ?   -1.7   0.0       1.6   1.8e+03      57      92 ..     103     139 ..      95     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      + + G  G+GKTt ++  a ++ +eg ++l+v++D
  gi|313125059|ref|YP_004035323.1|  5 VFFGGKGGVGKTTLASAYALKCAREGLDTLVVSTD 39
                                      56678889*************************99 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                                       EEEEESSTTSCHHHHHHHHHHHHHH.TTSSEEEEEE- CS
                             SRP54  57 vpvikkkeeadpaavakeavekake.ekidvvlvDTa 92 
                                       +++ +++ +a +aa++ + +e +++ +++d v+ DT+
  gi|313125059|ref|YP_004035323.1| 103 IEMAHQTPGAYEAALMDRFIEVMRSaDEFDRVVFDTS 139
                                       5566677777778888888877665156999999997 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   9.3e-05       0.1      21      39 ..       3      21 ..       1      30 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.3e-05
                                      EEEEEEESTTSSHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakq 39
                                       +v++ G+gGvGKttla+ 
  gi|313125059|ref|YP_004035323.1|  3 KFVFFGGKGGVGKTTLASA 21
                                      489*************985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.9   2.9e-05     0.033      34      78 ..       3      37 ..       1     140 [. 0.62
   2 ?   -2.8   0.1       3.4   3.8e+03      85     106 ..     273     294 ..     265     316 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                            AAA_25 34 elallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvs 78
                                      +++ + G +g+GKttla+  al++a +G   l           +vs
  gi|313125059|ref|YP_004035323.1|  3 KFVFFGGKGGVGKTTLASAYALKCArEGLDTL-----------VVS 37
                                      678899*******************6666443...........333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.4
                            AAA_25  85 elrrRlravgealrddarllvl 106
                                       + r+Rlr+++e++r +    v 
  gi|313125059|ref|YP_004035323.1| 273 TERERLRELREDFRYPVVAEVA 294
                                       5567777777776443333333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00017      0.19      51      83 ..       6      38 ..       2      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                         IstB_IS21 51 vllGpsGvGKshlaialgveavraglsvlfvrv 83
                                       + G  GvGK+ la a + + +r+gl +l v++
  gi|313125059|ref|YP_004035323.1|  6 FFGGKGGVGKTTLASAYALKCAREGLDTLVVST 38
                                      4557889******************99887765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00027       0.3       3      37 ..       9      43 ..       7      48 .. 0.93
   2 ?   -2.7   0.0       3.7   4.1e+03     198     237 ..     272     310 ..     258     313 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                        ATP_bind_1  3 GpaGsGKttfvgalseilelrgrsvavvNLDPAae 37
                                      G  G+GKtt+ +a +  +  +g +  vv  DPA +
  gi|313125059|ref|YP_004035323.1|  9 GKGGVGKTTLASAYALKCAREGLDTLVVSTDPAHS 43
                                      788******************************76 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                        ATP_bind_1 198 kklaeaiaelleefalvlrflplssekeesiedllslide 237
                                       ++  e ++el e+f    ++  ++++  e   dll+++ +
  gi|313125059|ref|YP_004035323.1| 272 ETERERLRELREDFRYP-VVAEVATRVSEVKGDLLDAVAH 310
                                       56667778888888877.8888888888888888888876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00033      0.37      34      70 ..       7      43 ..       2      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00033
                                      EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      + G  G+Gk tl +a +l+ +r+G    v++ DP+ +
  gi|313125059|ref|YP_004035323.1|  7 FGGKGGVGKTTLASAYALKCAREGLDTLVVSTDPAHS 43
                                      67999*****************************865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.6     0.014        16       1      27 [.       3      36 ..       3     143 .. 0.77
   2 ?    3.6   0.1     0.064        72      16      40 ..     278     303 ..     273     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
                            AAA_28  1 kivitGgest.GKTtlleaLa...ar...gypvv 27
                                      k+v++Gg ++ GKTtl++a a   ar   ++ vv
  gi|313125059|ref|YP_004035323.1|  3 KFVFFGGKGGvGKTTLASAYAlkcAReglDTLVV 36
                                      67999998644******98775554444434444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.064
                            AAA_28  16 leaLaar.gypvvpEaareileekla 40 
                                       l++L ++  ypvv+E+a+++ e k++
  gi|313125059|ref|YP_004035323.1| 278 LRELREDfRYPVVAEVATRVSEVKGD 303
                                       567888789***********988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2099.50
//
Query:       gi|313125060|ref|YP_004035324.1|  [L=158]
Description: hypothetical protein Hbor_02750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-15   54.5   0.7    1.1e-14   53.9   0.7    1.3  1  Cupin_2       Cupin domain
    0.00013   21.6   0.3    0.00028   20.5   0.3    1.5  1  Cupin_3       Protein of unknown function (DUF861)
     0.0011   18.9   0.1     0.0013   18.6   0.1    1.2  1  AraC_binding  AraC-like ligand binding domain
  ------ inclusion threshold ------
      0.024   14.3   0.0      0.028   14.0   0.0    1.2  1  Cupin_1       Cupin
       0.06   13.3   0.1      0.074   13.0   0.1    1.3  1  Pirin         Pirin
      0.066   12.7   2.1       0.12   11.9   2.1    1.5  1  TF_Zn_Ribbon  TFIIB zinc-binding
       0.15   11.7   0.1       0.24   11.0   0.1    1.3  1  DMSP_lyase    Dimethlysulfonioproprionate lyase
       0.17   12.3   0.0       0.23   11.8   0.0    1.2  1  Pirin_C       Pirin C-terminal cupin domain
       0.18   11.6   0.0       0.27   11.1   0.0    1.3  1  PCuAC         Copper chaperone PCu(A)C
       0.34   11.1   4.3        2.3    8.4   4.3    2.1  1  Zn-ribbon_8   Zinc ribbon domain
       0.72    9.5   0.0       0.72    9.5   0.0    2.5  4  Sgf11         Sgf11 (transcriptional regulation protein)


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.7   6.5e-18   1.1e-14       3      70 ..      39     108 ..      37     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 6.5e-18
                                       EEEETTE.EEE.EECSSSEEEEEEEEESEEEEE.ECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   3 velppGe.sap.shrHpgedeffyVleGegelt.vdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       ++l+pGe s++  h+H +++e+fyVl+G+++++ v+g  ve++++++v f +g  H+  N +d+pa +l +
  gi|313125060|ref|YP_004035324.1|  39 YTLEPGEgSSGgLHTHLDQEEVFYVLSGTVTFQtVEGS-VEVSEDEAVRFAPGDYHHGTNQSDDPATVLAI 108
                                       7899***86667****9999*************88887.*****************************988 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   1.7e-07   0.00028      14      60 ..      46      91 ..      44     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                                      EECEEEEECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 14 ctpGkfrltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgl 60
                                       + G+++++ +++E +y+l+G v++    +  ve+++  +v++ +g 
  gi|313125060|ref|YP_004035324.1| 46 GSSGGLHTHLDQEEVFYVLSGTVTFQTV-EGSVEVSEDEAVRFAPGD 91
                                      67899********************995.444566666666665553 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   8.2e-07    0.0013      19      89 ..      52     123 ..      39     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.2e-07
                                       ETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE---GGGGGGG--- CS
                      AraC_binding  19 hvhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfegelleriledss 89 
                                       h+h  + ++ yv++Gt++++  ++ +++++++ + + pg+ H +   s+d+ +   ++ +g + ++ + + +
  gi|313125060|ref|YP_004035324.1|  52 HTHLdQEEVFYVLSGTVTFQTVEGSVEVSEDEAVRFAPGDYHHGTNQSDDPATVLAIGAPGPQHDWEQIRVP 123
                                       566558999*************************************************99999888777665 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-05     0.028      42      87 ..      45      91 ..      11     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                      TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS..EEEEEEEETTE CS
                           Cupin_1 42 pgglllPhyhpnateiayvlqGegrvgfvvpgng.nrdfhkklreGd 87
                                      +g+   +h+h   +e++yvl G++++++v  + + ++d+  ++ +Gd
  gi|313125060|ref|YP_004035324.1| 45 EGSSGGLHTHLDQEEVFYVLSGTVTFQTVEGSVEvSEDEAVRFAPGD 91
                                      4677889******************6655444323333333355555 PP

>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.5e-05     0.074      40      77 ..      46      83 ..      11     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.5e-05
                                      T-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT CS
                             Pirin 40 gagfpphphrgletvtylleGevehrDslGnkgvirpG 77
                                      g + + h+h + e v y+l+G+v+++  +G+ +v +  
  gi|313125060|ref|YP_004035324.1| 46 GSSGGLHTHLDQEEVFYVLSGTVTFQTVEGSVEVSEDE 83
                                      566678************************98876655 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.1   7.6e-05      0.12       3      27 ..     126     154 ..     124     158 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                                       ETTTTCEE.C...HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   3 CPnCgstn.l...veDpergelvCtdCGl 27 
                                       CP+C   + l    +D  ++ l C++CG 
  gi|313125060|ref|YP_004035324.1| 126 CPDCEDVDaLgirFTDDGETALSCPECGR 154
                                       ******9988*99999999999******6 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00015      0.24     111     160 ..      52     102 ..      50     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                        DMSP_lyase 111 Hhhaa.eelYlvlsggaefrqgeaewlsrgiGevifnepgikhamrsaeeP 160
                                       H h + ee+++vlsg + f+  e+   + +   v f++ + +h +   ++P
  gi|313125060|ref|YP_004035324.1|  52 HTHLDqEEVFYVLSGTVTFQTVEGSVEVSEDEAVRFAPGDYHHGTNQSDDP 102
                                       999988***************999966666666778888888888777777 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.23      16      70 ..      53     109 ..      38     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                       --TT-EEEEEEEES-EEESSTT..EEE-TTEEEEE-SSSEEEEE--S.S-EEEEEEEE CS
                           Pirin_C  16 lpegleaavyvleGelevgger..seieeeqlavlgdgdslvvkaee.kgarvlLlaG 70 
                                       +  + e + yvl+G++++++ +   e++e++ + +++gd  + + ++ ++a+vl + G
  gi|313125060|ref|YP_004035324.1|  53 THLDQEEVFYVLSGTVTFQTVEgsVEVSEDEAVRFAPGDYHHGTNQSdDPATVLAI-G 109
                                       455678899*******776666557***********77777766666367776655.4 PP

>> PCuAC  Copper chaperone PCu(A)C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.27      51      79 ..      65      93 ..      51     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                      TCEEEEEECS.SEEEETTEEEEE-TTSCE CS
                             PCuAC 51 dgvmkmrqveegieipaggqveLkpggfh 79
                                      +g+ + + ve+++e+   + v+++pg +h
  gi|313125060|ref|YP_004035324.1| 65 SGTVTFQTVEGSVEVSEDEAVRFAPGDYH 93
                                      678899**********************9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.3    0.0014       2.3       8      37 ..     126     157 ..     114     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                       Zn-ribbon_8   8 CeeCghefevlqsis.daplta..CPeCgsevr 37 
                                       C +C  + ++l   + d+ +ta  CPeCg +v+
  gi|313125060|ref|YP_004035324.1| 126 CPDCE-DVDALGIRFtDDGETAlsCPECGRDVE 157
                                       99999.888665444455555559*****9875 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.3   5.4e+03      14      19 ..      34      39 ..      33      40 .. 0.81
   2 ?   -1.2   0.0      0.93   1.5e+03      16      21 ..      84      89 ..      83      89 .. 0.85
   3 ?   -3.0   0.4       3.6   5.9e+03       7      10 ..     126     129 ..     124     130 .. 0.81
   4 ?    9.5   0.0   0.00044      0.72       5      14 ..     147     156 ..     144     158 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.3
                                      EEGGGH CS
                             Sgf11 14 iaasRF 19
                                      +a +R+
  gi|313125060|ref|YP_004035324.1| 34 VALNRY 39
                                      899**9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.93
                                      GGGHHH CS
                             Sgf11 16 asRFAp 21
                                      a RFAp
  gi|313125060|ref|YP_004035324.1| 84 AVRFAP 89
                                      78***8 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.6
                                       -TTT CS
                             Sgf11   7 CpnC 10 
                                       Cp C
  gi|313125060|ref|YP_004035324.1| 126 CPDC 129
                                       9999 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00044
                                       EE-TTTSSEE CS
                             Sgf11   5 vtCpnCgRqi 14 
                                        +Cp CgR++
  gi|313125060|ref|YP_004035324.1| 147 LSCPECGRDV 156
                                       69******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1022.47
//
Query:       gi|313125061|ref|YP_004035325.1|  [L=611]
Description: carbon starvation protein, membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-107  360.1  19.0   1.2e-107  360.1  19.0    2.4  2  CstA      Carbon starvation protein CstA
    3.2e-29  101.7   4.6    3.2e-29  101.7   4.6    3.7  4  CstA_5TM  5TM C-terminal transporter carbon starvation CstA
  ------ inclusion threshold ------
        4.4    7.6  22.3      0.098   13.0   6.1    3.3  2  Vut_1     Putative vitamin uptake transporter


Domain annotation for each model (and alignments):
>> CstA  Carbon starvation protein CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.1  19.0    2e-111  1.2e-107       3     353 ..       4     390 ..       2     398 .. 0.91
   2 ?    1.0   2.9     0.027   1.6e+02     121     167 ..     519     571 ..     462     594 .. 0.59

  Alignments for each domain:
  == domain 1  score: 360.1 bits;  conditional E-value: 2e-111
                              CstA   3 avllvvvavvvfviayrfYgkfiakkvlklddkraTPaerledgkdyvptnklvlfghhFasiagagPlvGpvlA.a 78 
                                        ++lv++ +++f  +y  Y++++a+  ++ldd+r+TPa+++edg++yvp++k vl+ghh++siag++P+vGp++A +
  gi|313125061|ref|YP_004035325.1|   4 VIWLVIAVLALFSAGYLGYSRYLAQF-VELDDSRETPAHKYEDGQEYVPAKKPVLLGHHYSSIAGGAPIVGPITAgV 79 
                                       69**********************99.9**********************************************956 PP

                              CstA  79 qfGylPgllWilvGavfagavhDfvvlvasvrrkgkslgelakkelgkvakllallaillililvlavlalvvvkal 155
                                        +G++P+l Wi +G+ ++g vhDfv+l as r++g+s+g ++ +++g+++k ++l +++l++ilv++v+alvv+  +
  gi|313125061|ref|YP_004035325.1|  80 VWGWVPALAWIAIGNPLMGSVHDFVSLSASLRHEGRSIGYIIGEYVGERGKNMLLWFAFLTIILVVGVFALVVAIVF 156
                                       9**************************************************************************** PP

                              CstA 156 aespaavfsviltipialllGvllrklrkgvleasvigvvllllavvvgseveealaell................. 215
                                       ++ p a+++++++i +a+llG +l++l+   +  ++  vv +++ v+vg +   al e+                  
  gi|313125061|ref|YP_004035325.1| 157 NAYPEAATASLIYIGLAVLLGAYLYQLDLPFIPGTIAFVVAMFVGVWVGIQYPLALFEPAsrapaqttvllsgigtw 233
                                       **************************************************995555555579999************ PP

                              CstA 216 ........tlsketlaivlivYvfvAsvlPvwlllaPrdYlstflligtivllalgilv..vapelklpa....... 275
                                                 ++ +++ +++vY+ +As+lPvw+ll+PrdYls+fll++++ +++l+++v  v + l + a       
  gi|313125061|ref|YP_004035325.1| 234 wlpasdslGANTAAWVPIILVYGAFASALPVWVLLQPRDYLSSFLLYTGVGGALLAVIVgtVGGALGISAvtpsqpl 310
                                       ******88888999************************************999997777554556666663343444 PP

                              CstA 276 vtef..vdgegpvfagslfPllfitiACGaiSGFHslvssgttskllekesdarlvgygamllEslvailalvaaav 350
                                       vt++  + g      ++lfPllfitiACG+iSGFHslvssgtt+k+l++esdar++gyg+ml E+l+a +al+++a 
  gi|313125061|ref|YP_004035325.1| 311 VTNLdpFYGFIGRSGAPLFPLLFITIACGTISGFHSLVSSGTTAKQLNRESDARIIGYGGMLGEGLLATVALITVAL 387
                                       44432222222223569**********************************************************98 PP

                              CstA 351 lep 353
                                       + p
  gi|313125061|ref|YP_004035325.1| 388 VAP 390
                                       866 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.027
                              CstA 121 kkelgkvakllallaillililvlavlalvvvkal......aespaavfsvil 167
                                       k+ +++ + ++++++i ++ +l la   +v +k l       ++  +++s+++
  gi|313125061|ref|YP_004035325.1| 519 KQLISTGGPMVVMVFITVMGLLWLALHDNVYAKFLndawmeSATTLSMVSAAV 571
                                       45566666677777777777777777777766666333333222223333333 PP

>> CstA_5TM  5TM C-terminal transporter carbon starvation CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.1      0.55   3.3e+03      29      60 ..     119     150 ..     109     203 .. 0.53
   2 ?   -0.3   0.1      0.22   1.3e+03      79      91 ..     376     388 ..     374     403 .. 0.85
   3 !  101.7   4.6   5.3e-33   3.2e-29       2     115 ..     419     537 ..     418     538 .. 0.90
   4 ?   -1.7   0.4      0.61   3.6e+03      72      90 ..     566     584 ..     547     594 .. 0.51

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.55
                          CstA_5TM  29 yilqellgelkkkaltnkyvatliavalavll 60 
                                       yi+ e++ge  k+ l    + t+i v+ +++l
  gi|313125061|ref|YP_004035325.1| 119 YIIGEYVGERGKNMLLWFAFLTIILVVGVFAL 150
                                       55555555555444222222222222222222 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.22
                          CstA_5TM  79 lLAalaLlvvtvw 91 
                                       lLA++aL++v+++
  gi|313125061|ref|YP_004035325.1| 376 LLATVALITVALV 388
                                       89*******9987 PP

  == domain 3  score: 101.7 bits;  conditional E-value: 5.3e-33
                          CstA_5TM   2 avaytfailfvalfalTtlDtatRlaRyilqellgelk...kkaltnkyvatliavalavllllwggintlWplFGa 75 
                                       ++++ f++l++++f+lT+ Dta+Rl+Ry+++e++g+      + + ++y ++++ ++ a+ll+++g++ tlW+lFG 
  gi|313125061|ref|YP_004035325.1| 419 SFGAPFMALVLVSFLLTSTDTAVRLGRYMMEEIVGTPGsplGSFAVDRYGNAVAQALPAYLLVTSGSWLTLWQLFGG 495
                                       68899******************************9987764456778888888888889999999*********** PP

                          CstA_5TM  76 aNQlLAalaLlvvtvwllktgr..kalvtliPmvfmlvvtlt 115
                                       aNQlLAalaLl++tvwl+++++  +++ t  Pmv+m+++t++
  gi|313125061|ref|YP_004035325.1| 496 ANQLLAALALLTATVWLANWSEskQLISTGGPMVVMVFITVM 537
                                       ******************776666999999*********985 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.61
                          CstA_5TM  72 lFGaaNQlLAalaLlvvtv 90 
                                       + +aa Q++ a++L+ +++
  gi|313125061|ref|YP_004035325.1| 566 MVSAAVQVVVAFVLMYLAL 584
                                       3333334444444444443 PP

>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   6.1   1.6e-05     0.098      13      84 ..     117     181 ..     116     208 .. 0.64
   2 ?   -1.5   8.3      0.47   2.8e+03      35     121 ..     501     582 ..     488     594 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                             Vut_1  13 itdiisevyGkkaarkvvllgflanllalillllalllpaealesvfgltprivlasliaylvsqlldvyvf 84 
                                       i+ ii e+ G++  + + +++fl+ +l++ ++ l++++        f+  p  + asli + ++ ll +y++
  gi|313125061|ref|YP_004035325.1| 117 IGYIIGEYVGERGKNMLLWFAFLTIILVVGVFALVVAIV-------FNAYPEAATASLIYIGLAVLLGAYLY 181
                                       5679************************99999886554.......33344444444443333333333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.47
                             Vut_1  35 lanllalillllalllpaealesvfgltprivlasliaylvsqlldvyvfhrlkkltkgkklwl.rnigStlvsqlv 110
                                       +a +l++++++la + ++++l s+ g+++ +v+  ++ +l   l+d    ++l         w+  ++  ++vs +v
  gi|313125061|ref|YP_004035325.1| 501 AALALLTATVWLANWSESKQLISTGGPMVVMVFITVMGLLWLALHDNVYAKFLN------DAWMeSATTLSMVSAAV 571
                                       445555677777777777889999999999999999999999999999999996......45542455556777777 PP

                             Vut_1 111 dtlifvtiafl 121
                                         ++ +++ +l
  gi|313125061|ref|YP_004035325.1| 572 QVVVAFVLMYL 582
                                       77777777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.53
# Mc/sec: 3498.25
//
Query:       gi|313125062|ref|YP_004035326.1|  [L=212]
Description: hypothetical protein Hbor_02770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1297.49
//
Query:       gi|313125063|ref|YP_004035327.1|  [L=140]
Description: cupin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-12   44.4   0.0    1.5e-11   43.8   0.0    1.3  1  Cupin_2          Cupin domain
    0.00066   19.9   0.0    0.00076   19.7   0.0    1.2  1  Ectoine_synth    Ectoine synthase
     0.0015   18.2   0.0     0.0024   17.5   0.0    1.3  1  Cupin_3          Protein of unknown function (DUF861)
     0.0048   16.5   0.0     0.0071   16.0   0.0    1.2  1  Cupin_1          Cupin
      0.008   16.1   0.0       0.01   15.7   0.0    1.2  1  MannoseP_isomer  Mannose-6-phosphate isomerase
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.031   14.7   0.0    1.4  1  Ppnp             Pyrimidine/purine nucleoside phosphorylase
       0.17   12.1   0.0       0.24   11.6   0.0    1.3  1  CENP-C_C         Mif2/CENP-C like


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   5.9e-15   1.5e-11       3      70 ..      38     109 ..      36     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 5.9e-15
                                       EEEETTEEEE..EECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS..-EEEEEE CS
                           Cupin_2   3 velppGesap..shrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgde..parllvv 70 
                                       ++ +pGe++p   h+H+ ++e fyVl+G+++++   e++e+ +G ++ ++++ p r  N+ ++  ++++l +
  gi|313125063|ref|YP_004035327.1|  38 FRAAPGEQIPlaYHYHETQEEAFYVLSGTMAVETPAETYEVDEGSLFAVEPNSPQRAYNPANAteAVEVLAI 109
                                       6679***999999*******************************************9995544326666665 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     3e-07   0.00076      43     115 ..      41     118 ..      12     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3e-07
                                       -TT--EEEE-TT-...EEEEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEE....EEESS-EEEEEEEES--X CS
                     Ectoine_synth  43 kagtetelkYknH...leavycieGegeveeledgevyeikpgtlYlldkhdkHl....lrakkelrlvcvFnPplt 112
                                         g++  l Y++H    ea y+++G+  ve+    e+ye+ +g+l++++ +         +a++ ++++++  P++t
  gi|313125063|ref|YP_004035327.1|  41 APGEQIPLAYHYHetqEEAFYVLSGTMAVETP--AETYEVDEGSLFAVEPNSPQRaynpANATEAVEVLAIGAPAVT 115
                                       568888888988844459************97..69***********987764431111345669999********* PP

                                       SSS CS
                     Ectoine_synth 113 Gke 115
                                       G+ 
  gi|313125063|ref|YP_004035327.1| 116 GDT 118
                                       975 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   9.3e-07    0.0024      19      60 ..      50      90 ..      37     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.3e-07
                                      EEECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 19 frltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgl 60
                                      ++ + +++E +y+l+G + v+    et+e+++G+l+ +++++
  gi|313125063|ref|YP_004035327.1| 50 YHYHETQEEAFYVLSGTMAVET-PAETYEVDEGSLFAVEPNS 90
                                      66677889999**********9.9*************99987 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.8e-06    0.0071      37     113 ..      37     109 ..      25     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                                       EEEE.TTEEEEE..EEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEES.SSSEEEE CS
                           Cupin_1  37 rvdlepgglllP..hyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsg.depavai 110
                                       r++ +pg ++++  hyh   +e +yvl G++ v++         ++ ++ eG +f+v ++ ++ +yn    ++av++
  gi|313125063|ref|YP_004035327.1|  37 RFRAAPGEQIPLayHYHETQEEAFYVLSGTMAVETP-------AETYEVDEGSLFAVEPNSPQRAYNPAnATEAVEV 106
                                       555566666555228889999***********5443.......35679*******************9856777777 PP

                                       EEE CS
                           Cupin_1 111 vvf 113
                                        ++
  gi|313125063|ref|YP_004035327.1| 107 LAI 109
                                       765 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     4e-06      0.01      63     128 ..      33     100 ..      21     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4e-06
                   MannoseP_isomer  63 yqvkritvkPgeklslqkhhhra..ehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGki 128
                                         + r    Pge++ l  h+h +  e + v++Gt  v++  e++++ e     +  ++  r  np + 
  gi|313125063|ref|YP_004035327.1|  33 VAINRFRAAPGEQIPLAYHYHETqeEAFYVLSGTMAVETPAETYEVDEGSLFAVEPNSPQRAYNPANA 100
                                       56889999************97533889*******************999888888888888888765 PP

>> Ppnp  Pyrimidine/purine nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.2e-05     0.031      32      76 ..      48      90 ..      39      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                      ECEEEEESS-EEEEEEESEEEEEETT-SS-EEEETT-EEEE-TTE CS
                              Ppnp 32 geyeFgtsakEvmevvsGelevklpgeeewktykagesFevpans 76
                                        y+++ +++E   v+sG++ v+ p+e+   ++++g+ F+v+ ns
  gi|313125063|ref|YP_004035327.1| 48 LAYHYHETQEEAFYVLSGTMAVETPAET--YEVDEGSLFAVEPNS 90
                                      569**********************776..999*********997 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.4e-05      0.24      35      67 ..      58      90 ..      41     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.4e-05
                                      EEEEEEESEEEEEETTEEEEEETT-EEEE-TT- CS
                          CENP-C_C 35 lvFyViqGrvevtvsktsfvigkgsvFqvPagn 67
                                       +FyV+ G++ v+   + + + +gs F v   +
  gi|313125063|ref|YP_004035327.1| 58 EAFYVLSGTMAVETPAETYEVDEGSLFAVEPNS 90
                                      57**************************95444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 891.22
//
Query:       gi|313125064|ref|YP_004035328.1|  [L=70]
Description: hypothetical protein Hbor_02790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.55
# Mc/sec: 386.12
//
Query:       gi|313125065|ref|YP_004035329.1|  [L=228]
Description: hypothetical protein Hbor_02800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.76   10.4   5.0       0.23   12.1   2.0    1.7  2  DUF4398   Domain of unknown function (DUF4398)


Domain annotation for each model (and alignments):
>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.0   1.3e-05      0.23       4      69 ..      60     125 ..      57     135 .. 0.76
   2 ?   -3.4   0.1      0.86   1.6e+04      10      16 ..     205     211 ..     199     218 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.3e-05
                           DUF4398   4 adAraaleaAraagaeeyApaeleeAreaLaqAeaamaekdyeeAdhlaylAerdaelAearAkaa 69 
                                       ++A+a++++ + + a +++ ++l+ A e+L +  +++ e+d++ A +   ++  +++ A   A ++
  gi|313125065|ref|YP_004035329.1|  60 TAAQASVSEGQGEKAGKEPNEDLQTAGEKLSESYQKVDEGDNDGAVERWSESIGYVARAADSAGRK 125
                                       579*****************************************6655555555433333333332 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.86
                           DUF4398  10 leaAraa 16 
                                        ++A+aa
  gi|313125065|ref|YP_004035329.1| 205 TTTAEAA 211
                                       3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1292.62
//
Query:       gi|313125066|ref|YP_004035330.1|  [L=360]
Description: zn-dependent protease with chaperone function [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-31  107.5   0.0    7.4e-30  104.2   0.0    2.0  1  Peptidase_M48    Peptidase family M48
    2.2e-07   30.4   0.0    4.2e-07   29.5   0.0    1.4  1  Peptidase_M56    BlaR1 peptidase M56
    0.00024   20.7  13.1      0.028   13.9   2.7    2.2  2  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
     0.0015   18.4   0.0     0.0024   17.7   0.0    1.3  1  SprT-like        SprT-like family
  ------ inclusion threshold ------
      0.035   14.4   0.3       0.17   12.2   0.0    2.2  2  DUF4157          Domain of unknown function (DUF4157)
       0.82    9.9   3.1       0.92    9.7   0.1    2.4  3  DUF4381          Domain of unknown function (DUF4381)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.0   2.5e-33   7.4e-30       2     194 ..     101     353 ..     100     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 2.5e-33
                                       --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhr 78 
                                       ++ ++l++ + +la++++l  ++++++vv+ +  N  a+gg   +++v+++gL+ + ls++el aVl+HEl+H+k+r
  gi|313125066|ref|YP_004035330.1| 101 STHPNLHARITRLAAQFDL--RPPELAVVDTDVPNSLAVGGPRASTVVISRGLI-DDLSDDELDAVLAHELAHVKNR 174
                                       57899**************..*********************999*********.********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                     Peptidase_M48  79 hsvvslivsllasillllglallisraeedaagafldalavliglliillfl......................... 130
                                       +++v+++ s+l+ ++ +  ++      +   a   ++a++  ++       +                         
  gi|313125066|ref|YP_004035330.1| 175 DATVMTLASVLPALANGEYSTSDSVIPSMSGAHYLIGAIGLFVL-------Yvmatprlsgtafggsslgefllvvg 244
                                       **999999999988876665543333333334444444444333.......33344555999*************** PP

                                       ......................HHHHHHHHHHHHHHHHTTT.HHHHHHHHHHHHHHTT--S---HHHH......... CS
                                       ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                     Peptidase_M48 131 ......................alSRkrEyqADeagvellkrakdlvraliklakdlerqdvsaslrs......... 176
                                                              lSR+rE+ AD ag++++ +++++++a+ +la++ ++  +  s+ s         
  gi|313125066|ref|YP_004035330.1| 245 ftlllggvllgllaapavvltrRLSRRRELVADTAGARATGDPAAMASAIRTLADEERTRRDLRSTAStlsglcflp 321
                                       *******************************************************9999555554444555555555 PP

                                       ..............HHS-SS--HHHHHHHHHH CS
                                       ..............xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 177 ..............ellstHPplleRiqalke 194
                                                       ++tHP+ ++R+++l++
  gi|313125066|ref|YP_004035330.1| 322 hgfstdaeddekatIATQTHPSVEDRLENLRT 353
                                       5555555555566699**************97 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   1.4e-10   4.2e-07     142     222 ..     105     186 ..      57     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.4e-10
                     Peptidase_M56 142 elkeaLkeakeemqlkrnikirlsssidsP...avlgllkprIvlPadflkklsdeeleyillHElaHlkrkDllvn 215
                                       +l  ++     +    r++++ + ++ d+P   av g   + +v++  +   lsd+el+ +l+HElaH+k++D+ v 
  gi|313125066|ref|YP_004035330.1| 105 NLHARITRLAAQFD-LRPPELAVVDT-DVPnslAVGGPRASTVVISRGLIDDLSDDELDAVLAHELAHVKNRDATVM 179
                                       44445544444444.35555555443.444111445666778*********************************** PP

                     Peptidase_M56 216 llvavlq 222
                                        l+ vl 
  gi|313125066|ref|YP_004035330.1| 180 TLASVLP 186
                                       **99986 PP

>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.7   9.4e-06     0.028     110     179 ..      27      95 ..      15     138 .. 0.73
   2 !   12.4   2.9   2.9e-05     0.086     118     197 ..     209     287 ..     177     324 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.4e-06
                   LPG_synthase_TM 110 lasvvverlldllalvllgllallllggllaegaavllllalallllavlalllllllrrrla.rlarvlk 179
                                       +a++ +   +d++a++++g l+++++  +l +g  +  +l+++++++av++++ll  lr++++  la+v  
  gi|313125066|ref|YP_004035330.1|  27 AAALALVVTIDVVAVAAFGYLVAPWVEPYLPSG--TPSVLVGGVAIVAVTGVFLLAHLRYARRgVLAAVGA 95 
                                       455555567********************9999..666666666666666666655555544404444544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.9e-05
                   LPG_synthase_TM 118 lldllalvllgllallllggllaegaa....vllllalallllavlalllllllrrrlarlarvlkrlarllarfar 190
                                       l++ ++l++l + a + l+g+     a     l+ ++l++++ ++l+ +ll ll ++++ l r+l+r + l a  a+
  gi|313125066|ref|YP_004035330.1| 209 LIGAIGLFVLYVMATPRLSGT-----AfggsSLGEFLLVVGFTLLLGGVLLGLLAAPAVVLTRRLSRRRELVADTAG 280
                                       444444444444444444444.....25555999999999999999999999999999999999***9999998887 PP

                   LPG_synthase_TM 191 klasakr 197
                                        +a  ++
  gi|313125066|ref|YP_004035330.1| 281 ARATGDP 287
                                       7665444 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.1e-07    0.0024      44      76 ..     140     172 ..      86     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.1e-07
                         SprT-like  44 rhhasIeLseklldsrsedrllntLaHElcHla 76 
                                        +  ++ +s+ l+d+ s+d+l  +LaHEl+H+ 
  gi|313125066|ref|YP_004035330.1| 140 PRASTVVISRGLIDDLSDDELDAVLAHELAHVK 172
                                       5678999************************86 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.6e-05      0.17      58      75 ..     157     174 ..     139     178 .. 0.71
   2 ?   -1.2   0.2      0.81   2.4e+03      27      61 ..     298     331 ..     276     337 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                           DUF4157  58 saagrellaHELtHvvqq 75 
                                         + +++laHEL+Hv  +
  gi|313125066|ref|YP_004035330.1| 157 DDELDAVLAHELAHVKNR 174
                                       4455799********876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.81
                           DUF4157  27 saaaraaralgAqAfTlgndivfaageyqpesaag 61 
                                       ++ +r  r+l+  A Tl    ++ ++ ++ +++++
  gi|313125066|ref|YP_004035330.1| 298 ADEERTRRDLRSTASTLSGLCFL-PHGFSTDAEDD 331
                                       34677778888888888877777.55555555554 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.42   1.2e+03      28      49 ..      68      87 ..      49     115 .. 0.52
   2 ?   -3.7   0.0       4.4   1.3e+04      13      36 ..     198     221 ..     195     224 .. 0.63
   3 ?    9.7   0.1   0.00031      0.92      17      75 ..     241     297 ..     235     322 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.42
                           DUF4381 28 lllllllvlalwllrrrkrnrr 49
                                      ++++++ +++l+++ r+   rr
  gi|313125066|ref|YP_004035330.1| 68 VAIVAVTGVFLLAHLRYA--RR 87
                                      222222222222222332..33 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.4
                           DUF4381  13 swwPpapGwwlllaalllllllvl 36 
                                       s+ P   G   l+ a+ l++l v+
  gi|313125066|ref|YP_004035330.1| 198 SVIPSMSGAHYLIGAIGLFVLYVM 221
                                       667888888888855555444443 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00031
                           DUF4381  17 papGwwlllaalllllllvlalwllrrrkrnrreAlreLaalradeadakellaalsel 75 
                                       + +G  lll ++ll ll++ a++l rr  r rre  +  a +r +  d++++++a+ +l
  gi|313125066|ref|YP_004035330.1| 241 LVVGFTLLLGGVLLGLLAAPAVVLTRRLSR-RRELVADTAGAR-ATGDPAAMASAIRTL 297
                                       678999999888888888888888988888.888888888887.677777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1953.59
//
Query:       gi|313125067|ref|YP_004035331.1|  [L=356]
Description: hypothetical protein Hbor_02820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-11   43.0   3.2    3.9e-11   43.0   3.2    2.1  2  DUF4129   Domain of unknown function (DUF4129)
  ------ inclusion threshold ------
      0.047   14.2   0.2      0.092   13.2   0.2    1.4  1  MGC-24    Multi-glycosylated core protein 24 (MGC-24), sialom
       0.24   11.4   0.7       0.73    9.9   0.0    2.0  3  DUF4366   Domain of unknown function (DUF4366)


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.1   6.3e+03      30      38 ..      60      68 ..      41      80 .. 0.51
   2 !   43.0   3.2   6.6e-15   3.9e-11       4      67 ..     277     340 ..     276     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                           DUF4129 30 riapspaaa 38
                                        +psp +a
  gi|313125067|ref|YP_004035331.1| 60 TPTPSPTEA 68
                                      333333333 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 6.6e-15
                           DUF4129   4 allraLaer.gldrrpgeTprEyarrvriapspaaalaalaelfeearYGgrpasaeeyrrlvea 67 
                                       ++++++aer  +  r ++Tp+Eyar++ +a+ p+ a+++l+++fe++rYGg    ++e+ ++++a
  gi|313125067|ref|YP_004035331.1| 277 EAWAMMAERvPIGNRKAATPGEYARAAVAAGFPESAVQRLTRAFERVRYGGKS-GRDELPSVRDA 340
                                       5789***********************88899*****************6655.45556666665 PP

>> MGC-24  Multi-glycosylated core protein 24 (MGC-24), sialomucin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.5e-05     0.092      61     124 ..      62     124 ..      51     132 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                            MGC-24  61 kptnstaktttkpsstttstsvatsgttnttvtptsqp.arkstFDaAsFiG...GivLvLgvqAviF 124
                                       +p+     +t++  ++   ++ +++gt++ t+tpt+ p +  +t D+ s  G   Gi+L++gv A   
  gi|313125067|ref|YP_004035331.1|  62 TPS-----PTEAAQTADDGQTETATGTPTPTPTPTETPvSDGPTDDGISMDGafaGIMLIIGVCAAGL 124
                                       222.....233333333334444666666677766544135577777776554449*******99755 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.46   2.8e+03     118     133 ..       8      23 ..       2      27 .. 0.66
   2 ?    9.9   0.0   0.00012      0.73      72     138 ..      63     127 ..      55     131 .. 0.65
   3 ?   -3.7   0.2       1.9   1.1e+04      94     108 ..     259     273 ..     251     283 .. 0.46

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.46
                           DUF4366 118 nglllvvlavaliggg 133
                                       + l+l+ ++v+l+gg 
  gi|313125067|ref|YP_004035331.1|   8 AALALLCVVVVLFGGS 23 
                                       4566777777888875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00012
                           DUF4366  72 eeeevcactekcaagkvntdcpveepepekeaepeepeeepekksnnglllvvlavaligggaayyf 138
                                        ++ ++a+    + g+ +t++  ++p+p+++++p +  ++++  s  g+   ++++++++++++ +f
  gi|313125067|ref|YP_004035331.1|  63 PSPTEAAQ--TADDGQTETATGTPTPTPTPTETPVSDGPTDDGISMDGAFAGIMLIIGVCAAGLLVF 127
                                       33333434..345788888888889999999998775555555555788888888888888887777 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.9
                           DUF4366  94 veepepekeaepeep 108
                                        ++++ e+e++p+ +
  gi|313125067|ref|YP_004035331.1| 259 TPTADVEEETDPTPQ 273
                                       333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2027.40
//
Query:       gi|313125068|ref|YP_004035332.1|  [L=284]
Description: hypothetical protein Hbor_02830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   18.0   0.8     0.0032   17.4   0.8    1.3  1  DUF4345   Domain of unknown function (DUF4345)
  ------ inclusion threshold ------
      0.016   15.4   0.4      0.016   15.4   0.4    3.6  4  HemY_N    HemY protein N-terminus
        0.2   11.6   0.5       0.48   10.4   0.5    1.6  1  DUF3437   Domain of unknown function (DUF3437)


Domain annotation for each model (and alignments):
>> DUF4345  Domain of unknown function (DUF4345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.8   5.3e-07    0.0032       2      72 ..       6      76 ..       5      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.3e-07
                           DUF4345  2 lqillalsalvliaiGllgllagaaliagavgvelenatldselRflaglllglGllllwaipriekrraa 72
                                      l+  l ++ +++++iG++ ++ + +l+++ v +++++  + s+l  +a++l+gl  + ++  p+ e++++ 
  gi|313125068|ref|YP_004035332.1|  6 LRRHLQIVFAACALIGAVVVVLPEWLLPSFVVTLASSSLASSSLVLVAAGLVGLYGIRVLVSPDEEETSQT 76
                                      688999***********************77788888999999********99999999999999888765 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.8      0.12   7.2e+02      14      43 ..      10      39 ..       3      48 .. 0.66
   2 ?   -2.0   0.2      0.69   4.1e+03      15      29 ..      48      62 ..      36      67 .. 0.53
   3 ?    7.3   0.2   0.00086       5.1      49      73 ..     112     136 ..      95     166 .. 0.87
   4 ?   15.4   0.4   2.7e-06     0.016      44      95 ..     175     225 ..     170     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                            HemY_N 14 tslvvavlllvllfvllylllrllrlllrl 43
                                      + +v+a+ +l++++v+++  + l +++++l
  gi|313125068|ref|YP_004035332.1| 10 LQIVFAACALIGAVVVVLPEWLLPSFVVTL 39
                                      567777777777777776555555555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.69
                            HemY_N 15 slvvavlllvllfvl 29
                                      slv++++ lv+l+ +
  gi|313125068|ref|YP_004035332.1| 48 SLVLVAAGLVGLYGI 62
                                      444444444444433 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00086
                            HemY_N  49 rwrrrrrerkarealseGlialaeG 73 
                                       +w +rr++r+a+  l+++ ++  ++
  gi|313125068|ref|YP_004035332.1| 112 KWKQRRHRRRAYGTLRTAAVDAIAE 136
                                       8*****************9987665 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 2.7e-06
                            HemY_N  44 parvrrwrrrrrerkarealseGlialaeGdfarAekaaakaaklseaplla 95 
                                        +rvr w +  r ++a + +  +++++  Gd+  A+ ++a+ ++ +++++ a
  gi|313125068|ref|YP_004035332.1| 175 RTRVRDWAAGERTERAVQDTVSAILSIRDGDADVARAELAAIESTASQSV-A 225
                                       689****************************************9998873.3 PP

>> DUF3437  Domain of unknown function (DUF3437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5     8e-05      0.48       3      37 ..       8      43 ..       6      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8e-05
                           DUF3437  3 erhaavlglsAlvlafpydvPkwl.pevleeLaraa 37
                                      + ++ v++ +Al+ a+   +P+wl p+ +++La+ +
  gi|313125068|ref|YP_004035332.1|  8 RHLQIVFAACALIGAVVVVLPEWLlPSFVVTLASSS 43
                                      567889****************97366777798854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1606.96
//
Query:       gi|313125069|ref|YP_004035333.1|  [L=442]
Description: hypothetical protein Hbor_02840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-13   50.9   1.0    4.2e-13   49.4   1.0    1.8  1  DUF58        Protein of unknown function DUF58
    9.4e-11   41.9   0.3    2.4e-10   40.6   0.3    1.6  1  DUF11        Domain of unknown function DUF11
    2.6e-05   24.4   0.1      6e-05   23.2   0.1    1.6  1  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   1.0   7.1e-17   4.2e-13       1      85 [.     210     296 ..     210     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 7.1e-17
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg..dekletavsaaaslar 75 
                                       g++f+ +R+ ++ Dp+rr+dWk +A+tgel + ef +era+tv+ ++d + e++ + ++   +++  + +aa   ++
  gi|313125069|ref|YP_004035333.1| 210 GVEFYATRQHHRTDPMRRVDWKRYAKTGELTTVEFRRERAATVICLVDVRVEAHVARREgePDAVWLSKYAAERAME 286
                                       679*************************************************9988877754444444444444555 PP

                             DUF58  76 qlldegdrvg 85 
                                       +ll++g+r g
  gi|313125069|ref|YP_004035333.1| 287 SLLSTGNRAG 296
                                       5666666665 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.3   3.9e-14   2.4e-10       1      82 [.      78     151 ..      78     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 3.9e-14
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvr 77 
                                       l++t +++ ++pG+tv++tltvtN    + +++++ D +P+ la v +s + g        +sL +ges  l++++r
  gi|313125069|ref|YP_004035333.1|  78 LDRTLSTQSPAPGATVEVTLTVTNETEEPVPDLRLVDGVPERLAVVDGSPRLG--------TSLGPGESESLTYAIR 146
                                       67999999*******************************************33........57************** PP

                             DUF11  78 vtrta 82 
                                       ++r +
  gi|313125069|ref|YP_004035333.1| 147 ARRGS 151
                                       *9865 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1     1e-08     6e-05       3      74 ..      89     160 ..      88     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1e-08
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevta 74 
                                       pG+tv++tltvtn++++++ +++l   +Pe   vv  sp+ ++sl pGe+ + t ++++  g   +d  v+a
  gi|313125069|ref|YP_004035333.1|  89 PGATVEVTLTVTNETEEPVPDLRLVDGVPERLAVVDGSPRLGTSLGPGESESLTYAIRARRGSHSFDECVVA 160
                                       8*****************************************************999998888888866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2464.31
//
Query:       gi|313125070|ref|YP_004035334.1|  [L=506]
Description: hypothetical protein Hbor_02850 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.79u 0.35s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 2774.21
//
Query:       gi|313125071|ref|YP_004035335.1|  [L=79]
Description: hypothetical protein Hbor_02860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.25   11.4   0.0    1.6  2  EF-hand_6  EF-hand domain


Domain annotation for each model (and alignments):
>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.4e-05      0.25      13      28 ..       8      23 ..       6      35 .. 0.87
   2 ?   -3.1   0.0      0.62   1.1e+04      20      27 ..      64      71 ..      63      74 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.4e-05
                         EF-hand_6 13 gdGkidaeElrkalrk 28
                                      ++G+++a+E+ ++lr 
  gi|313125071|ref|YP_004035335.1|  8 KSGELTADEILDILRE 23
                                      79************94 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.62
                         EF-hand_6 20 eElrkalr 27
                                      eE+r+++ 
  gi|313125071|ref|YP_004035335.1| 64 EEMRNCIV 71
                                      68888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.36s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 434.97
//
Query:       gi|313125072|ref|YP_004035336.1|  [L=123]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-13   50.8   0.0    1.5e-13   50.4   0.0    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
    9.1e-06   25.5   0.1    1.3e-05   24.9   0.1    1.2  1  MarR_2           MarR family
      6e-05   22.5   0.1    9.7e-05   21.9   0.1    1.2  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0005   19.9   0.1    0.00079   19.3   0.1    1.3  1  MarR             MarR family
    0.00075   19.2   0.0     0.0029   17.4   0.0    1.9  2  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.016   15.2   0.0    1.3  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.017   14.9   0.0      0.024   14.5   0.0    1.2  1  HTH_5            Bacterial regulatory protein, arsR family
       0.02   14.8   0.1       0.04   13.8   0.1    1.6  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
      0.028   14.5   0.1      0.042   13.9   0.1    1.4  1  HTH_20           Helix-turn-helix domain
      0.044   13.7   0.0       0.21   11.5   0.0    1.9  2  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
       0.14   12.2   0.0       0.19   11.8   0.0    1.3  1  MetJ             Met Apo-repressor, MetJ
       0.22   11.2   0.4        0.4   10.4   0.1    1.6  2  GntR             Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0     1e-16   1.5e-13       1      57 [.      22      79 ..      22      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1e-16
                                      HH.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  1 Lq.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      L+ ++G++e E+++Yl+Ll +  +t+ e+a +l+++rs+v+++L  L++k l +re++
  gi|313125072|ref|YP_004035336.1| 22 LAcVFGIQEHESRTYLTLLDNPGSTVAELADILDRDRSNVNRSLTTLMEKNLADRERR 79
                                      6779***************************************************976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   8.9e-09   1.3e-05      13      55 ..      38      78 ..      27      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 8.9e-09
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                       L ++pg   tv+ela+ l+ ++s+v+r l  L ++ L  r++
  gi|313125072|ref|YP_004035336.1| 38 TLLDNPG--STVAELADILDRDRSNVNRSLTTLMEKNLADRER 78
                                      68899*9..8*****************************9986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   6.5e-08   9.7e-05      11      45 ..      38      72 ..      30      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.5e-08
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeG 45
                                      +L +np+ + +eLA+ l+  +s+vnr l  L+e+ 
  gi|313125072|ref|YP_004035336.1| 38 TLLDNPGSTVAELADILDRDRSNVNRSLTTLMEKN 72
                                      799*****************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   5.3e-07   0.00079      11      52 ..      38      79 ..      33      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.3e-07
                                      HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      +l ++++ +v+eLa+ l  ++s+v r l++L +k+l +R++ 
  gi|313125072|ref|YP_004035336.1| 38 TLLDNPGSTVAELADILDRDRSNVNRSLTTLMEKNLADRERR 79
                                      56678999****************************999985 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.9e-06    0.0029      17      50 ..      43      76 ..      36      78 .. 0.87
   2 ?   -1.0   0.0       1.1   1.6e+03      26      40 ..      89     103 ..      87     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.9e-06
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++ t++elA+ ++  +S+v R L tL+e  +  +
  gi|313125072|ref|YP_004035336.1| 43 PGSTVAELADILDRDRSNVNRSLTTLMEKNLADR 76
                                      4569************************988765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                       HHHTS-HHHHHHHHH CS
                          HTH_IclR  26 rrtglpkStvhRlLq 40 
                                       + tg p + +  +L+
  gi|313125072|ref|YP_004035336.1|  89 QYTGTPLPEAKEMLH 103
                                       67999*999999997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     1e-05     0.016      23      62 ..      46      83 ..      21      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-H CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrgrririldl 62
                                      t +elA++l   r+ v+r l+ L +++l +r+r  r+ld+
  gi|313125072|ref|YP_004035336.1| 46 TVAELADILDRDRSNVNRSLTTLMEKNLADRER--RLLDP 83
                                      678***************************876..56665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.6e-05     0.024      11      45 ..      39      74 ..      37      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                                      HTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5 11 Laege.lcvcelaeelglsqstvShHLkkLreaGLV 45
                                      L +++  +v ela++l+  +s+v + L  L+e +L 
  gi|313125072|ref|YP_004035336.1| 39 LLDNPgSTVAELADILDRDRSNVNRSLTTLMEKNLA 74
                                      56667689************************9996 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.6e-05      0.04       6      36 ..      58      88 ..      51      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                      GGGHHHHHHHHHHTT-B-TTS--EEETTEEE CS
                            Trm5_N  6 kkegEkvRkkLlekglLdrnyKIksdddyly 36
                                      ++++++   +L+ek+l dr++++   ++y+y
  gi|313125072|ref|YP_004035336.1| 58 RSNVNRSLTTLMEKNLADRERRLLDPGGYVY 88
                                      7899999**********************99 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.8e-05     0.042      18      58 ..      39      78 ..      12      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                      HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 18 aLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +  ++ g t++ela+ ld +++++++ L +L e  L +++r
  gi|313125072|ref|YP_004035336.1| 39 L-LDNPGSTVAELADILDRDRSNVNRSLTTLMEKNLADRER 78
                                      3.489999**********************99988877776 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.21      45      84 ..      36      75 ..      27      80 .. 0.88
   2 ?   -0.5   0.0      0.77   1.1e+03      50      73 ..      93     116 ..      80     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                   Phage_rep_org_N 45 elylsenipytaemlalifnreletvrlaLkvlkdlelie 84
                                      +l l +n  +t  +la i++r+ ++v   L++l++++l +
  gi|313125072|ref|YP_004035336.1| 36 YLTLLDNPGSTVAELADILDRDRSNVNRSLTTLMEKNLAD 75
                                      7788889999*************************99865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.77
                   Phage_rep_org_N  50 enipytaemlalifnreletvrla 73 
                                         +p  +eml   +++  e+v+  
  gi|313125072|ref|YP_004035336.1|  93 TPLPEAKEMLHNALDKWAEQVHES 116
                                       456788999999999988888765 PP

>> MetJ  Met Apo-repressor, MetJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.19      59      95 ..      85     121 ..      56     123 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                              MetJ  59 aflhaftgqplpddedlrkdnedkipkevkelleekg 95 
                                        +++ +tg plp+ +++ ++  dk  ++v+e +ee g
  gi|313125072|ref|YP_004035336.1|  85 GYVYQYTGTPLPEAKEMLHNALDKWAEQVHESIEEYG 121
                                       58899**************************999876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00027       0.4      26      59 ..      46      79 ..      42      80 .. 0.92
   2 ?   -3.1   0.0       4.2   6.2e+03      21      29 ..      92     100 ..      91     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 26 sereLaaefgVsrttvReALrrLeaeglverrqg 59
                                      ++ eLa+ ++ +r+ v+++L +L +++l+ r+++
  gi|313125072|ref|YP_004035336.1| 46 TVAELADILDRDRSNVNRSLTTLMEKNLADRERR 79
                                      569*************************999876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.2
                                       TSB---HHH CS
                              GntR  21 GdkLPsere 29 
                                       G++LP+ +e
  gi|313125072|ref|YP_004035336.1|  92 GTPLPEAKE 100
                                       788887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 707.94
//
Query:       gi|313125073|ref|YP_004035337.1|  [L=421]
Description: l-threonine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-74  248.8   0.6    8.5e-74  248.6   0.6    1.0  1  PALP           Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.053   13.7   0.0        2.2    8.5   0.0    2.9  3  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.6   0.6   9.5e-78   8.5e-74       2     294 .]      81     388 ..      80     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 248.6 bits;  conditional E-value: 9.5e-78
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       +l++g+TPl+++prl +++gv+ l +K E++nptgSfKdRg++  +  +ke  g +++++as+GN+ +alAa++a+ 
  gi|313125073|ref|YP_004035337.1|  81 SLPEGDTPLHEAPRLREDIGVNtLRIKHEGMNPTGSFKDRGMTVGVRVAKEL-GVDRLACASTGNTSAALAAYGARG 156
                                       7899************************************************.************************ PP

                                       T-EEEEEEETTS-.HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHH.. CS
                              PALP  78 Glkvtivvpadas.pekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEil.. 151
                                       G++  +++p+++  ++k+a+  l+ a++ ev+g++d+++++++ela++ +++yl+++  np + eg++tiglEil  
  gi|313125073|ref|YP_004035337.1| 157 GMETLVLLPSGKVaAGKIAQAALHDARILEVDGNFDSCLDIVQELAER-GEVYLLNSL-NPFRLEGQKTIGLEILea 231
                                       **********99956*********************************.*********.9**************988 PP

                                       ..HHTTTTEEEEEEE-SSSHHHHHHHHHHHH......HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B...SSS CS
                              PALP 152 ..eqlggkpdavvvpvGgGgliaGiaaglke......rrpd..vrvigvepegsdalarslragrrvtvpvs..dti 216
                                         +++g+ pd +v+pvG++g+ ++++++++e       +p+  +++ gv++eg++++ +++++g ++t      +t 
  gi|313125073|ref|YP_004035337.1| 232 frDDYGRFPDRIVLPVGNAGNTSALYKAFRElvqsgaLDPEqvPKLTGVQAEGAAPMVEAIENGWEDTKRWDevETR 308
                                       889999*************************998777666699******************9999988877777*** PP

                                       .CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEE CS
                              PALP 217 adglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvv 290
                                       a+++++g  +++++a++ ++++ +++v+vsdee+ ea+r la  egi vep+saa++a+l klr+ g ++++++vv+
  gi|313125073|ref|YP_004035337.1| 309 ATAIRIGnpVNAPKALPGIRETDGTAVAVSDEEITEAQRDLA-GEGIGVEPASAASVAGLqKLRHEGVVDPDEDVVC 384
                                       *******99999999***************************.********************************** PP

                                       EE-B CS
                              PALP 291 iltg 294
                                       + tg
  gi|313125073|ref|YP_004035337.1| 385 LTTG 388
                                       9997 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.15   1.3e+03      43      51 ..     140     148 ..     127     153 .. 0.75
   2 ?    8.5   0.0   0.00024       2.2      21      72 ..     226     275 ..     222     282 .. 0.86
   3 ?    0.6   0.0     0.074   6.6e+02      50      78 ..     360     388 ..     358     389 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.15
                                       HHH-B-GGG CS
                     ACP_syn_III_C  43 deyGntsaa 51 
                                       + +Gntsaa
  gi|313125073|ref|YP_004035337.1| 140 ASTGNTSAA 148
                                       689****98 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHT--GGGB--THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EE CS
                     ACP_syn_III_C  21 lriidavakklglpeekvvvnldeyGntsaasiplaLdeaveegklkpgdlv 72 
                                       l+i++a ++  g  ++++v  + + Gntsa  +  a+ e+v++g l+p +  
  gi|313125073|ref|YP_004035337.1| 226 LEILEAFRDDYGRFPDRIVLPVGNAGNTSA--LYKAFRELVQSGALDPEQVP 275
                                       68999************************9..57899999999999988765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.074
                                       GGHHHHHHHHHHHTTSS-TT-EEEEEEEE CS
                     ACP_syn_III_C  50 aasiplaLdeaveegklkpgdlvllvgfG 78 
                                       +a ++  L+++ +eg ++p + v+ +++G
  gi|313125073|ref|YP_004035337.1| 360 SAASVAGLQKLRHEGVVDPDEDVVCLTTG 388
                                       7888999****************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2494.50
//
Query:       gi|313125074|ref|YP_004035338.1|  [L=141]
Description: hypothetical protein Hbor_02890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0032   17.8   0.3     0.0054   17.1   0.3    1.3  1  FlaC_arch       Flagella accessory protein C (FlaC)
     0.0067   16.7   3.3     0.0067   16.7   3.3    1.7  2  Mto2_bdg        Micro-tubular organiser Mto1 C-term Mto2-bind
  ------ inclusion threshold ------
      0.011   14.6   1.7      0.013   14.4   1.7    1.2  1  PV-1            PV-1 protein (PLVAP)
      0.015   14.7   0.8      0.016   14.5   0.8    1.2  1  DUF4407         Domain of unknown function (DUF4407)
      0.015   14.6   1.1      0.019   14.3   1.1    1.1  1  DUF4763         Domain of unknown function (DUF4763)
      0.017   14.4   0.5      0.021   14.2   0.5    1.1  1  GAS             Growth-arrest specific micro-tubule binding
      0.021   14.9   0.2      0.028   14.5   0.2    1.2  1  Herpes_BLRF2    Herpesvirus BLRF2 protein
      0.029   14.5   5.0      0.095   12.8   5.5    1.6  1  Cep57_CLD_2     Centrosome localisation domain of PPC89
      0.044   13.7   0.2      0.055   13.4   0.2    1.1  1  STAT_alpha      STAT protein, all-alpha domain
      0.044   12.4   0.4      0.053   12.2   0.4    1.1  1  Dor1            Dor1-like family
      0.057   13.6   4.2      0.072   13.3   4.2    1.1  1  Jnk-SapK_ap_N   JNK_SAPK-associated protein-1
      0.085   12.5   2.1        0.1   12.3   2.1    1.1  1  GrpE            GrpE
      0.088   10.7   0.3      0.099   10.5   0.3    1.0  1  V_ATPase_I      V-type ATPase 116kDa subunit family
      0.093   13.2   7.4       0.13   12.7   7.4    1.2  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
       0.13   12.6   6.4       0.26   11.6   6.1    1.6  1  THOC7           Tho complex subunit 7
       0.15   12.2   2.0       0.18   11.9   2.0    1.1  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
        0.2   11.8   0.9       0.59   10.3   0.3    2.0  2  NYD-SP28_assoc  Sperm tail C-terminal domain


Domain annotation for each model (and alignments):
>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   5.1e-06    0.0054       6      46 ..      45      85 ..      43      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.1e-06
                         FlaC_arch  6 EnklsklsteletvkkeneelsksveelkenVkdllsLYEv 46
                                      E++ +++s el+ +++eneel+  + e  ++ +d+++ YE 
  gi|313125074|ref|YP_004035338.1| 45 ETESQSVSAELAHLRRENEELRRALSEARQQRQDVIDRYER 85
                                      7788899********************************95 PP

>> Mto2_bdg  Micro-tubular organiser Mto1 C-term Mto2-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.3   6.3e-06    0.0067      22      51 ..      46      75 ..      43      76 .. 0.89
   2 ?   -2.6   0.1       6.6     7e+03      19      27 ..      84      92 ..      81      95 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.3e-06
                          Mto2_bdg 22 ldrsgarerLeelkaeNrlLkaeLerdrsh 51
                                      +  ++++++L+ l++eN++L+++L+  r++
  gi|313125074|ref|YP_004035338.1| 46 TESQSVSAELAHLRRENEELRRALSEARQQ 75
                                      67789*******************998875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                          Mto2_bdg 19 aRlldrsga 27
                                       Rlldr  a
  gi|313125074|ref|YP_004035338.1| 84 ERLLDRAQA 92
                                      577777655 PP

>> PV-1  PV-1 protein (PLVAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.7   1.2e-05     0.013     264     343 ..      25     104 ..      19     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                              PV-1 264 elasirracdelPslmstkveelarslragiervarensdlqrqkleaeqslrasqeakekvekeaqareaklqaec 340
                                       ++ +++racde  +      e  ++s+ a++ ++ ren++l+r   ea q+ +   +  e++   aqa ++   a  
  gi|313125074|ref|YP_004035338.1|  25 DVPRLERACDEPSEAADPTTETESQSVSAELAHLRRENEELRRALSEARQQRQDVIDRYERLLDRAQAEASADSASV 101
                                       788999*****999999999999******************************999999999999999887766666 PP

                              PV-1 341 arq 343
                                       ++q
  gi|313125074|ref|YP_004035338.1| 102 SHQ 104
                                       666 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   1.6e-05     0.016     187     252 ..      31      95 ..       7     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                           DUF4407 187 ekkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarlealdr 252
                                       ++ ++  +a    +e +++ + +a+la+lr+e +el+++++++r++ q+ ++    ll+r +a   
  gi|313125074|ref|YP_004035338.1|  31 RACDEPSEAADPTTETESQ-SVSAELAHLRRENEELRRALSEARQQRQDVIDRYERLLDRAQAEAS 95 
                                       4444444444444444444.4788888888888888888888888888888888888888888654 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.1   1.8e-05     0.019      79     130 ..      32      83 ..      24      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                           DUF4763  79 cPeidecvdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkasrksl 130
                                        ++  +++ +++ +++++s++ e+  L+r+n  Lr  l+e+ q+++   +  
  gi|313125074|ref|YP_004035338.1|  32 ACDEPSEAADPTTETESQSVSAELAHLRRENEELRRALSEARQQRQDVIDRY 83 
                                       5888788888888888888************************999866555 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5     2e-05     0.021      53     137 ..      45      91 ..      34     116 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                               GAS  53 sqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkf 129
                                       ++e ++ + +L ++++e+eeLr++l + ++++q                                      ++ +++
  gi|313125074|ref|YP_004035338.1|  45 ETESQSVSAELAHLRRENEELRRALSEARQQRQ--------------------------------------DVIDRY 83 
                                       445555555555555555555555555555555......................................555555 PP

                               GAS 130 eaaiqevq 137
                                       e+ ++ +q
  gi|313125074|ref|YP_004035338.1|  84 ERLLDRAQ 91 
                                       55544444 PP

>> Herpes_BLRF2  Herpesvirus BLRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   2.7e-05     0.028       6      47 ..      50      98 ..      45     126 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-05
                      Herpes_BLRF2  6 dlaaelakLkvENkaLkkkl......kssvs....pkdeeLTaaekeavlts 47
                                       + aela+L+ EN++L+++l      +   +      ++ L  a+ ea   s
  gi|313125074|ref|YP_004035338.1| 50 SVSAELAHLRRENEELRRALsearqqR---QdvidRYERLLDRAQAEASADS 98
                                      5789****************5554432...0344244556666666665543 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.5     9e-05     0.095      16      57 ..      45      86 ..      43      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                       Cep57_CLD_2 16 trklqvheeelkrLnkERdsalrqLgvAyeelneLkaeveal 57
                                      +++ q+   el++L++E+++  r+L++A++  ++  ++ e+l
  gi|313125074|ref|YP_004035338.1| 45 ETESQSVSAELAHLRRENEELRRALSEARQQRQDVIDRYERL 86
                                      566778889**********************99999999887 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   5.2e-05     0.055      43      87 ..      47      91 ..      24      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                        STAT_alpha 43 eqeraesekkelkkqkellqqmlnaLdqkRkelvdklkellnlle 87
                                      e+++++ e ++l++++e+l++ l++  q+R++++d+ ++ll++++
  gi|313125074|ref|YP_004035338.1| 47 ESQSVSAELAHLRRENEELRRALSEARQQRQDVIDRYERLLDRAQ 91
                                      5678899999*******************************9986 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4     5e-05     0.053       3      51 ..      49      96 ..      47     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-05
                              Dor1  3 elsskpleelekepelLaeeaeeilaqiqdLarknyktlidaaealeai 51
                                      ++ s +l++l++e e+L+    e  +q+qd+ ++ y  l+d a+a  + 
  gi|313125074|ref|YP_004035338.1| 49 QSVSAELAHLRRENEELRRALSEARQQRQDV-IDRYERLLDRAQAEASA 96
                                      677899************************9.799******99886543 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.2   6.8e-05     0.072      43     100 ..      46     103 ..      43     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-05
                     Jnk-SapK_ap_N  43 srneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveq 100
                                       +++++ +ael  lr+e+e+L+  +++ +++r++  +++e++ d  + e+++ ++ v++
  gi|313125074|ref|YP_004035338.1|  46 TESQSVSAELAHLRRENEELRRALSEARQQRQDVIDRYERLLDRAQAEASADSASVSH 103
                                       5789999*************************************99999877766665 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.1   9.5e-05       0.1       9      65 ..      43      99 ..      34     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.5e-05
                                      TTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE  9 eeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfa 65
                                       +e+e ++  +el+ l++e +el  +l +++++ + +  r+e+ ++ a+ +a  + a
  gi|313125074|ref|YP_004035338.1| 43 TTETESQSVSAELAHLRRENEELRRALSEARQQRQDVIDRYERLLDRAQAEASADSA 99
                                      567899999************************************999999887765 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   9.4e-05     0.099      66     139 ..      36     109 ..      18     127 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.4e-05
                        V_ATPase_I  66 peekeldeleeelekleeelkelnenleklkkelnelvel.kavlekakefleeeeeeeeeeeseeeeeekeeee 139
                                       p+e+   + e+e +++ +el +l++++e+l++ l+e+ ++ + v+ + +++l+++++e+++++++ + +++++ +
  gi|313125074|ref|YP_004035338.1|  36 PSEAADPTTETESQSVSAELAHLRRENEELRRALSEARQQrQDVIDRYERLLDRAQAEASADSASVS-HQSADGS 109
                                       44555556789999999***************99998766156999999999987444333332222.2222222 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   7.4   0.00012      0.13      14      88 ..      30     106 ..      23     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  14 EaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaey..eqelaeevarireeararaeaeaqavrkrae 88 
                                       E++ d+  EaA  ++e e +   ae a + re e+  +al ++   +q + +  +r+ ++a+a+a+a++ +v+++++
  gi|313125074|ref|YP_004035338.1|  30 ERACDEPSEAADPTTETESQSVSAELAHLRRENEELRRALSEARqqRQDVIDRYERLLDRAQAEASADSASVSHQSA 106
                                       89999999********************************8765004455578889999999999999999887765 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   6.1   0.00025      0.26      74     109 ..      45      80 ..      42      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                             THOC7  74 eaekeeieseieavreeieelkaqLeearatranrk 109
                                       e+e++ + +e++ +r e+eel+  L+ear++r+++ 
  gi|313125074|ref|YP_004035338.1|  45 ETESQSVSAELAHLRRENEELRRALSEARQQRQDVI 80 
                                       67899999************************9874 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.0   0.00017      0.18     102     161 ..      45     104 ..      28     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                           UPF0242 102 keeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeq 161
                                       + e ++ + el++l++en++L+  l+++ ++ +++   +e  L++ q   +   ++++ q
  gi|313125074|ref|YP_004035338.1|  45 ETESQSVSAELAHLRRENEELRRALSEARQQRQDVIDRYERLLDRAQAEASADSASVSHQ 104
                                       4567788999999*********99999999999999999999999988777766666655 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00056      0.59      37      58 ..      50      71 ..      46      72 .. 0.83
   2 ?   -1.1   0.0         2   2.1e+03      27      40 ..      82      94 ..      75     103 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00056
                    NYD-SP28_assoc 37 klieetesLekqNeeLrnlLkq 58
                                      ++ +e  +L+++NeeLr+ L +
  gi|313125074|ref|YP_004035338.1| 50 SVSAELAHLRRENEELRRALSE 71
                                      5678999***********9965 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                    NYD-SP28_assoc 27 kYhevLteRaklie 40
                                      +Y + L +Ra+  +
  gi|313125074|ref|YP_004035338.1| 82 RYER-LLDRAQAEA 94
                                      4444.556776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1674  (0.0933683); expected 358.6 (0.02)
Passed bias filter:                      912  (0.0508673); expected 358.6 (0.02)
Passed Vit filter:                       152  (0.00847788); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 803.81
//
Query:       gi|313125075|ref|YP_004035339.1|  [L=534]
Description: D-3-phosphoglycerate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-58  197.6   0.0      2e-58  196.6   0.0    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.1e-36  124.5   0.8    6.1e-36  123.0   0.9    1.7  2  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    0.00019   21.1   0.2      0.001   18.8   0.0    2.4  2  ACT             ACT domain
     0.0055   16.9   0.4        0.3   11.2   0.0    3.4  4  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.011   16.1   0.1        0.1   13.0   0.0    2.6  3  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      0.022   15.0   0.0       0.51   10.6   0.1    2.9  2  TrkA_N          TrkA-N domain
       0.29   11.3   1.2        4.8    7.4   0.1    2.7  3  DUF2163         Uncharacterized conserved protein (DUF2163)


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.6   0.0     8e-62     2e-58       1     178 []     109     283 ..     109     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 196.6 bits;  conditional E-value: 8e-62
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       +a+++a +r +++a++++++gew ++ ++lg+el+ kt+Gi+GlGr+Gq+vakrl ++gm+++ayd++  +e+ +e+
  gi|313125075|ref|YP_004035339.1| 109 VAMAFASARSIPQAHARLKTGEW-AKGDYLGTELNAKTLGIVGLGRVGQEVAKRLDGIGMDLVAYDPYIGEER-AER 183
                                       5899*******************.9*******************************************99777.99* PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                       lg++lv++e+ l+++D++++h+pltpet++li+ eel++m  g +l+N+aRGg+vde+aL++a+++g++ gaa+Dvf
  gi|313125075|ref|YP_004035339.1| 184 LGAKLVEFEACLERADFLTVHTPLTPETEDLISTEELELMG-GGYLVNCARGGVVDEDALAAAVEDGTLDGAAIDVF 259
                                       ****************************************8.889******************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                       + ep+++d+pll+++ v++tPH++
  gi|313125075|ref|YP_004035339.1| 260 ADEPVSPDNPLLDVDDVVVTPHLG 283
                                       **********************97 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.9   2.4e-39   6.1e-36       1     134 []       7     315 ..       7     315 .. 0.99
   2 ?   -2.2   0.0       1.2     3e+03      79      92 ..     392     405 ..     390     411 .. 0.80

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 2.4e-39
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       vl+++p+++++le+l+e+g+eve+  + + + ll++++da al+vrs t+vt++v+ea+++L +++rag+GvDn+D+
  gi|313125075|ref|YP_004035339.1|   7 VLVTDPIDDAGLERLREAGHEVETAYDVTGDALLDAVADANALVVRSGTEVTDAVFEAASDLVIVGRAGIGVDNIDI 83 
                                       79***************999********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       daa+ +G++V+n+p+ + +++AE+t                                                    
  gi|313125075|ref|YP_004035339.1|  84 DAATDHGVIVANAPEGNVRAAAEHTvamafasarsipqaharlktgewakgdylgtelnaktlgivglgrvgqevak 160
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|313125075|ref|YP_004035339.1| 161 rldgigmdlvaydpyigeeraerlgaklvefeacleradfltvhtpltpetedlisteelelmgggylvncarggvv 237
                                       ***************************************************************************** PP

                                       ..............................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ..............................................aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                                                     a+Te aqen+a+ +a+++ a+++ge++ na+
  gi|313125075|ref|YP_004035339.1| 238 dedalaaavedgtldgaaidvfadepvspdnplldvddvvvtphlgASTEAAQENVATSIADQIDAAFNGEPVMNAL 314
                                       ************************************************************************99998 PP

                                       S CS
                                       x RF
                        2-Hacid_dh 134 n 134
                                       n
  gi|313125075|ref|YP_004035339.1| 315 N 315
                                       7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                       HHHHTT-EEEE-TT CS
                                       xxxxxxxxxxxxxx RF
                        2-Hacid_dh  79 aakerGilVtnvpg 92 
                                        a+erGi Vt+  +
  gi|313125075|ref|YP_004035339.1| 392 IAEERGIEVTESKT 405
                                       589******98765 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.7   4.3e+03      25      52 ..     397     423 ..     395     427 .. 0.45
   2 !   18.8   0.0     4e-07     0.001       5      65 ..     459     518 ..     456     520 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.7
                                       TSEEEEEEEEEESTTECEEEEEEEEEEH CS
                               ACT  25 giNidsieqrssedkvagivfvvivvde 52 
                                       gi ++   +r  ed + ++v+v++  d+
  gi|313125075|ref|YP_004035339.1| 397 GIEVTESKTRQAED-FQSLVTVTVGNDD 423
                                       44444444444444.4444444444444 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4e-07
                                       EEEESSTTHHHHHHHHHHHTTSEEEEE.EEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   5 vgvpDrPGlLarvfgaladrgiNidsi.eqrssedkvagivfvvivvdeedleevlealkkl 65 
                                        +  D+PG+++ ++++l+++++Ni+ + + r+s d  +g++ +v   d+  +eev e+l + 
  gi|313125075|ref|YP_004035339.1| 459 ARNYDKPGVIGFIGTVLGENDVNIAGMfNARRSAD--GGEALTVYNLDDPIPEEVSEKLLAD 518
                                       5778*********************6537888888..9*******************99775 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.17   4.3e+02      18      82 ..      21      71 ..       5     119 .. 0.61
   2 !   11.2   0.0   0.00012       0.3       2      62 ..     146     204 ..     145     258 .. 0.68
   3 ?   -0.7   0.0      0.56   1.4e+03      38      88 ..     392     444 ..     380     452 .. 0.76
   4 ?   -4.0   0.0         6   1.5e+04      15      34 ..     488     507 ..     482     517 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                                      HHHTT-EE.EEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC--T CS
                     NAD_binding_2 18 llkagykv.avynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llealkk 82
                                      l +ag++v ++y++t +++ ++va                d+  ++v++g++v + +++   + +  
  gi|313125075|ref|YP_004035339.1| 21 LREAGHEVeTAYDVTGDALLDAVA----------------DANALVVRSGTEVTDAVFEaASDLVIV 71
                                      444444443344444444333333................444445555555544444423333344 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-..SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE- CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavyn..rtkekveelvaegakaaesieelvasldvvitm 62 
                                       +g++GlG  G++ a++l   g+++++y+    +e++e+l a+      + e++++++d+  + 
  gi|313125075|ref|YP_004035339.1| 146 LGIVGLGRVGQEVAKRLDGIGMDLVAYDpyIGEERAERLGAKL----VEFEACLERADFLTVH 204
                                       79**************************433345555544432....2344455555555555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.56
                                       HHHT.TEEE-SSHHHHHHHC.SEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE CS
                     NAD_binding_2  38 lvae.gakaaesieelvasl.dvvitmvkagkavdeviegllealkkgdilid 88 
                                       +++e g++++es    +++   +v + v ++++  +v+  l++  ++  + id
  gi|313125075|ref|YP_004035339.1| 392 IAEErGIEVTESKTRQAEDFqSLVTVTVGNDDESLSVCGTLFAGEDPRIVRID 444
                                       444426999999999999998999999*9999999999988887777666666 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 6
                                       HHHHHHTT-EEEEE-SSHHH CS
                     NAD_binding_2  15 alnllkagykvavynrtkek 34 
                                       a++ ++ g  ++vyn++   
  gi|313125075|ref|YP_004035339.1| 488 ARRSADGGEALTVYNLDDPI 507
                                       67778899999999987654 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.2     3e+03      53      72 ..      31      51 ..       6      68 .. 0.70
   2 ?   13.0   0.0     4e-05       0.1      21      75 ..     157     206 ..     155     227 .. 0.89
   3 ?   -2.9   0.0       3.7   9.5e+03      50      74 ..     394     418 ..     378     422 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                                      CCEEES-C.HHHHTT-SEEEE CS
                    UDPG_MGDP_dh_C 53 gvevvdsl.eealkgadaivi 72
                                       + v+ ++  +a+++a+a+v+
  gi|313125075|ref|YP_004035339.1| 31 AYDVTGDAlLDAVADANALVV 51
                                      444444444888999998887 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4e-05
                                       HHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S- CS
                    UDPG_MGDP_dh_C  21 diieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilte 75 
                                       +++++L   g+++++yDP++ ee++e+     g+++v ++e +l+ ad + ++t+
  gi|313125075|ref|YP_004035339.1| 157 EVAKRLDGIGMDLVAYDPYIGEERAER----LGAKLV-EFEACLERADFLTVHTP 206
                                       68999*9******************99....477888.699*******9999986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.7
                                       GBTCCEEES-CHHHHTT-SEEEE-S CS
                    UDPG_MGDP_dh_C  50 eekgvevvdsleealkgadaivilt 74 
                                       ee+g+ev++s ++ +++++ +v +t
  gi|313125075|ref|YP_004035339.1| 394 EERGIEVTESKTRQAEDFQSLVTVT 418
                                       3678888888888888888888777 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0002      0.51       3      28 ..     148     173 ..     146     198 .. 0.73
   2 ?    0.6   0.0      0.25   6.4e+02      65      95 ..     414     442 ..     404     447 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                       EES-SHHHHHHHHHHHH.TTEEEEEEE CS
                            TrkA_N   3 iiGlGrvGrslaeeLse.ggkdvvvid 28 
                                       i+GlGrvG+++a++L   g  d v+ d
  gi|313125075|ref|YP_004035339.1| 148 IVGLGRVGQEVAKRLDGiGM-DLVAYD 173
                                       9**************98555.566555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.25
                                       EEEE-SSSHHHHHHHHHHHHHHTSSSEEEEE CS
                            TrkA_N  65 aviaatgddeanilavllakelnpkkkiiar 95 
                                       +v +++g+d++++ ++ ++    ++ + i+r
  gi|313125075|ref|YP_004035339.1| 414 LVTVTVGNDDESLSVCGTLFA--GEDPRIVR 442
                                       5678899*********99942..33344555 PP

>> DUF2163  Uncharacterized conserved protein (DUF2163)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0019       4.8      60     132 ..      70     145 ..      44     151 .. 0.85
   2 ?    1.3   0.0      0.14   3.5e+02      79     101 ..     238     260 ..     230     288 .. 0.84
   3 ?   -2.2   0.0       1.6   4.1e+03      82     123 ..     361     410 ..     348     433 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0019
                           DUF2163  60 isqssglsvdnleitgalssdaiteedlaaglfdgaevevwrvnwed...peqrvllfrgrlgevrrsggaftael 132
                                       i  ++g+ vdn++i+ a ++  i  ++ + + +  ae +v +++ ++   p+++ +l  g+  + +  g++++a+ 
  gi|313125075|ref|YP_004035339.1|  70 IVGRAGIGVDNIDIDAATDHGVIVANAPEGNVRAAAEHTVAMAFASArsiPQAHARLKTGEWAKGDYLGTELNAKT 145
                                       667889************************************9998888666699999999998888888887765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                           DUF2163  79 sdaiteedlaaglfdgaevevwr 101
                                       ++++  ++++ g +dga ++v+ 
  gi|313125075|ref|YP_004035339.1| 238 DEDALAAAVEDGTLDGAAIDVFA 260
                                       6778889************9985 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.6
                           DUF2163  82 ite......edlaaglfdgaevevwrvnwed..peqrvllfrgrlgevrr 123
                                       + e      +   +g f+  e++v  vn  +  +e  +++ + +  + + 
  gi|313125075|ref|YP_004035339.1| 361 AEEdielvtASALKGVFEPLEWQVNAVNAPRiaEERGIEVTESKTRQAED 410
                                       44444445467777777778888877777443222244444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3313.53
//
Query:       gi|313125076|ref|YP_004035340.1|  [L=216]
Description: phosphoserine phosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-26   93.4   1.7    2.7e-26   93.1   1.7    1.1  1  HAD              haloacid dehalogenase-like hydrolase
    2.3e-16   60.7   6.6      1e-13   52.1   6.6    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.3e-13   50.5   0.1      3e-09   37.0   0.0    3.0  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    3.9e-07   30.3   0.1    9.5e-05   22.5   0.0    2.7  2  HAD_2            Haloacid dehalogenase-like hydrolase
    0.00095   19.6   0.2     0.0015   19.0   0.2    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0016   17.9   0.0      0.053   12.9   0.0    2.0  2  Put_Phosphatase  Putative Phosphatase
     0.0089   15.6   0.0       0.02   14.4   0.0    1.5  1  S6PP             Sucrose-6F-phosphate phosphohydrolase
  ------ inclusion threshold ------
      0.031   13.7   0.0        1.8    8.0   0.0    2.1  2  DUF4392          Domain of unknown function (DUF4392)
       0.05   13.7   0.0       0.26   11.4   0.0    2.1  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   1.7   1.4e-29   2.7e-26       1     188 []       4     173 ..       4     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 1.4e-29
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       + fDfDgTL d+++  ll r  + +     +++++  ++ a+++el++    +  +  +all gl+ e+  +  ++ 
  gi|313125076|ref|YP_004035340.1|   4 VAFDFDGTLSDSEMTVLLGR-QMDV-----ADEMADITERAMNDELSYA---DSLRKRAALLDGLDdEAASEAYGQV 71 
                                       67**********99999999.4444.....7788888888887777777...77888899999***66666666666 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg..adevlatelevdd.rltgelglegkpvr 150
                                                l+pga +l+++ r+aG++v++++gg+++ ve+ l++ g  +d ++a++l v++ rltge  +eg+++ 
  gi|313125076|ref|YP_004035340.1|  72 T--------LRPGAADLIERLRDAGHHVAILTGGFERGVERALEKDGveVDSIVANRLPVEGgRLTGE--VEGPLIE 138
                                       6........88*********************************99999*******************..******* PP

                               HAD 151 gegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                       g  k +al++   a + + dl+++va+GD+ +Dlp+l+
  gi|313125076|ref|YP_004035340.1| 139 G-TKDDALES--LADELDVDLARTVAVGDGANDLPMLE 173
                                       *.999*****..99999*******************96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   6.6   5.1e-17     1e-13       1     210 []       1     176 [.       1     176 [. 0.77

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 5.1e-17
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       +++v+fD+dGTL ++e      +v +                         ++  + +++++     +++  +  + 
  gi|313125076|ref|YP_004035340.1|   1 MRLVAFDFDGTLSDSE-----MTVLL---------------------GRQMDVADEMADITE-----RAMNDELSYA 46 
                                       6789999999999999.....66677.....................444555666789999.....9999999999 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                       ++l               + r + l+  +  a  ++  + +++p+aa+++++L++ag  v++ltg++++ +era+++
  gi|313125076|ref|YP_004035340.1|  47 DSL---------------RKRAALLDGLDDEAASEAYGQVTLRPGAADLIERLRDAGHHVAILTGGFERGVERALEK 108
                                       999...............66666666334444444446666************************************ PP

                                       TT..........GGGESEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xx..........xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lG..........ddyfdaviasdiet..vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        G               + +++++e+  + + + ++++ +++eL ++ +++++VGDg+nD+++l+ Ag
  gi|313125076|ref|YP_004035340.1| 109 DGvevdsivanrLPVEGGRLTGEVEGplIEGTKDDALESLADELDVDLARTVAVGDGANDLPMLEVAG 176
                                       99766555543222224444444444776777*********************************998 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.034        69       1      15 [.       4      18 ..       4      34 .. 0.87
   2 !    6.8   0.0    0.0024       4.8      18      55 ..      75     112 ..      68     124 .. 0.82
   3 !   37.0   0.0   1.5e-12     3e-09     187     226 ..     140     179 ..     137     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.034
                                      EEEEIIIIIS-TTS- CS
                       Hydrolase_3  1 ialDlDGTLlnsdkk 15
                                      +a+D DGTL +s+ +
  gi|313125076|ref|YP_004035340.1|  4 VAFDFDGTLSDSEMT 18
                                      79*******988765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       + +++ i++l+++g++v+i TG   r+v++ le+ g++
  gi|313125076|ref|YP_004035340.1|  75 PGAADLIERLRDAGHHVAILTGGFERGVERALEKDGVE 112
                                       667899****************9999999988877666 PP

  == domain 3  score: 37.0 bits;  conditional E-value: 1.5e-12
                                       SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEE CS
                       Hydrolase_3 187 sKgtalkklakelnisleeviafGDgeNDieMLeaaglgv 226
                                       +K  al+ la el+++l++++a+GDg ND++MLe+agl+v
  gi|313125076|ref|YP_004035340.1| 140 TKDDALESLADELDVDLARTVAVGDGANDLPMLEVAGLSV 179
                                       7999***********************************9 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   4.8e-08   9.5e-05       2     118 ..       5     111 ..       4     117 .. 0.76
   2 ?    4.4   0.0     0.018        36     139     173 ..     143     177 ..     136     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.8e-08
                             HAD_2   2 iFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkev 78 
                                        FD+DgTl d+e +++   +  ++++ + +++e  ++   +ls+ ++lrk +       +++ l ++  +e +  +v
  gi|313125076|ref|YP_004035340.1|   5 AFDFDGTLSDSEMTVLLGRQMDVADE-MADITERAMND--ELSYADSLRKRAA------LLDGLDDEAASEAYG-QV 71 
                                       6**********998876665555444.34454444443..3344444444444......899999999999999.** PP

                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsksreaveekleqlgi 118
                                       ++ +g+ +l+e L++ag++++i T + ++ ve+ le+ g+
  gi|313125076|ref|YP_004035340.1|  72 TLRPGAADLIERLRDAGHHVAILTGGFERGVERALEKDGV 111
                                       **************************99999999988665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.018
                             HAD_2 139 eviekaleklklkkeeviyvGDsptDieaakkagi 173
                                       + +e + ++l+++ ++++ vGD  +D+     ag+
  gi|313125076|ref|YP_004035340.1| 143 DALESLADELDVDLARTVAVGDGANDLPMLEVAGL 177
                                       667888999*****************977766665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   7.7e-07    0.0015       7      51 ..      77     122 ..      74     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.7e-07
                   Glyco_trans_4_4   7 vaelaraLaarGheVtvltpapapg.apeleedgvrvhrlpvprrp 51 
                                       +a+l+++L+++Gh+V +lt +  +g +++le dgv+v ++ + r p
  gi|313125076|ref|YP_004035340.1|  77 AADLIERLRDAGHHVAILTGGFERGvERALEKDGVEVDSIVANRLP 122
                                       589****************987777355699999999976666554 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   2.6e-05     0.053       2     112 ..       3     111 ..       2     122 .. 0.80
   2 ?    3.0   0.0     0.028        55     166     182 ..     153     169 ..     140     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                   Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkg..lwnelmdrvlkelheqgvseadikkvlrsiplspgl 76 
                                       lv+fDFD t+ d++    + +++   ++++++ e   ++   + + + +  + l  +g   +   +++ +++l pg 
  gi|313125076|ref|YP_004035340.1|   3 LVAFDFDGTLSDSEMTVLLGRQMDVADEMADITERAMNDelSYADSLRKRAALL--DGLDDEAASEAYGQVTLRPGA 77 
                                       89************999999*****99999998877654114555555544444..45677778899********** PP

                   Put_Phosphatase  77 velikslakkkleldliiiSDaNsffieeileaagl 112
                                        +li+ l  ++ +  + i+    + ++e +le+ g+
  gi|313125076|ref|YP_004035340.1|  78 ADLIERL--RDAGHHVAILTGGFERGVERALEKDGV 111
                                       *******..567889999999888888888887765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.028
                   Put_Phosphatase 166 gveyerliYvGDganDl 182
                                       +v   r + vGDganDl
  gi|313125076|ref|YP_004035340.1| 153 DVDLARTVAVGDGANDL 169
                                       4677899*********8 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     1e-05      0.02     164     203 ..     139     178 ..     136     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                                       -SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEE CS
                              S6PP 164 askgeAlryLakkleleleqilvcGdsgnDeellignvlg 203
                                       + k++Al+ La+ l+++l +++ +Gd  nD  +l+   l+
  gi|313125076|ref|YP_004035340.1| 139 GTKDDALESLADELDVDLARTVAVGDGANDLPMLEVAGLS 178
                                       689******************************9655555 PP

>> DUF4392  Domain of unknown function (DUF4392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.017        35      59      99 ..      75     115 ..      74     133 .. 0.81
   2 ?    8.0   0.0   0.00089       1.8     170     208 ..     146     184 ..     133     198 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.017
                           DUF4392  59 lGAialaraLqalgkkvvivtdelnekiveaaveq.gvlkte 99 
                                       +GA+ l + L+  g +v i+t    e+ ve+a+e+ gv  ++
  gi|313125076|ref|YP_004035340.1|  75 PGAADLIERLRDAGHHVAILTG-GFERGVERALEKdGVEVDS 115
                                       799****************998.6667777888877888776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00089
                           DUF4392 170 ddlfeaakeig...iptigiGDgGNElGmGkvkeavkkhvpn 208
                                       + l +++       + t+++GDg N+l m +v+     ++p+
  gi|313125076|ref|YP_004035340.1| 146 ESLADEL---DvdlARTVAVGDGANDLPMLEVAGLSVGFLPK 184
                                       4444444...333689*************9998766666665 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.26      12      42 ..      70     100 ..       4     115 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                       TTEE-TTHHHHHHHHHHTT-EEEEEE---SS CS
                       Hydrolase_6  12 gdkaipgaaealnalraagkpvvllTNnssk 42 
                                       + ++ pgaa+++++lr+ag +v++lT +  +
  gi|313125076|ref|YP_004035340.1|  70 QVTLRPGAADLIERLRDAGHHVAILTGGFER 100
                                       45677*********************77655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1359.45
//
Query:       gi|313125077|ref|YP_004035341.1|  [L=234]
Description: hypothetical protein Hbor_02920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1441.97
//
Query:       gi|313125078|ref|YP_004035342.1|  [L=169]
Description: universal stress family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-08   34.6   0.2    3.2e-08   34.2   0.2    1.2  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.2   1.8e-12   3.2e-08       4     141 .]       2     142 ..       1     142 [. 0.93

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.8e-12
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....HHHHHH CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....akaaae 76 
                                       + lV++Dgs  + +Al +A e+ + ++  + ++ vi++r+ +++ +  + + +e+ + e   +++ +     +   +
  gi|313125078|ref|YP_004035342.1|   2 TLLVPFDGSVLAAAALVRATEFGRVFDQNVLAVSVIPDRNAEYARERGWIETDEPFDRETVVSKLHEqvteCCPSSD 78 
                                       68******************************************999999999888888888877778888899999 PP

                                       CTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  77 aggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        ++++v+   + g  a  + ++ae+e+a+++ +Gs   +++    + Sv ++v++    +V++Vr
  gi|313125078|ref|YP_004035342.1|  79 FRHEVVDRYATPGTIANCLRKTAEREQASMVFIGSENAGHIVT-TITSVGSKVAADEAYDVVIVR 142
                                       9999999999***************************888886.78*********9999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1090.62
//
Query:       gi|313125079|ref|YP_004035343.1|  [L=475]
Description: dihydrolipoamide dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-70  237.6   3.4    1.7e-70  237.6   3.4    1.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-37  128.4   3.0    1.8e-37  128.0   1.6    2.0  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.3e-20   72.9   2.6    5.8e-18   65.2   0.2    3.0  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.4e-14   53.3   0.1    1.5e-13   50.6   0.1    1.9  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.3e-11   42.5   4.1      9e-08   31.6   2.1    2.5  2  GIDA            Glucose inhibited division protein A
    5.7e-10   38.8   7.6      6e-07   28.9   0.7    3.8  4  FAD_binding_2   FAD binding domain
    1.6e-09   37.5   6.9    0.00092   18.5   0.3    3.2  3  FAD_binding_3   FAD binding domain
    6.8e-08   31.6   3.1    0.00027   19.8   0.2    3.5  4  HI0933_like     HI0933-like protein
    1.1e-07   31.6   4.3    2.8e-07   30.2   0.4    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
    2.2e-07   31.0   2.0    0.00073   19.7   0.5    2.8  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.4e-07   29.8  15.6      0.052   13.1   1.4    4.5  5  DAO             FAD dependent oxidoreductase
    3.3e-05   23.5   1.4     0.0013   18.4   0.1    2.4  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    0.00033   20.0   5.9       0.14   11.5   0.1    3.3  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00038   20.4   3.9     0.0091   15.9   0.1    2.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    0.00057   20.3   0.3       0.37   11.3   0.1    2.6  2  NAD_binding_7   Putative NAD(P)-binding
     0.0037   17.5   0.8      0.058   13.7   0.1    2.6  2  TrkA_N          TrkA-N domain
      0.004   16.3   1.0       0.72    8.8   0.1    2.4  2  Lycopene_cycl   Lycopene cyclase protein
     0.0043   16.3   5.1      0.057   12.7   0.2    2.8  3  Thi4            Thi4 family
     0.0087   15.2   0.0        2.3    7.3   0.0    2.3  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.009   16.3   0.1       0.22   11.8   0.0    2.7  2  Hydrolase       haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.024   15.5   0.5      0.024   15.5   0.5    2.4  1  MDMPI_C         MDMPI C-terminal domain
      0.054   13.5   2.9        9.8    6.1   0.1    3.4  4  NAD_binding_9   FAD-NAD(P)-binding
      0.057   13.9   0.1        1.1    9.8   0.0    2.6  2  XdhC_C          XdhC Rossmann domain
      0.062   12.7   0.1       0.69    9.3   0.0    2.5  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
        1.7    7.4   4.4       0.38    9.6   0.1    2.1  3  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.6   3.4   2.3e-73   1.7e-70       2     294 .]      11     334 ..      10     334 .. 0.95
   2 ?   -2.6   0.1       3.6   2.6e+03     146     195 ..     413     464 ..     389     473 .. 0.57

  Alignments for each domain:
  == domain 1  score: 237.6 bits;  conditional E-value: 2.3e-73
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.................. 57 
                                       +v+viG+Gp+G+ aa+++aq+g+++tlve    +gtcln+gc++ska+  +++ a++a                   
  gi|313125079|ref|YP_004035343.1|  11 EVLVIGAGPGGYVAAIRAAQNGLDTTLVEkdaYGGTCLNHGCIPSKAFITASSLAHEAGhaeemgihanpavdmsql 87 
                                       69**************************9999***************99999999988899**************** PP

                                       .....HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC.......TCEEEEEESEEEE---EEE-BCTCTTC.TT CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .....evvkklnqgielllgeevvkidpgkkkvklekkke.......gdeekiaydklvlAtGssprdlgipGvaen 122
                                             vv++l+ g+e+l ++++v++++g +++k+   ++       +  e+++++++++AtGs+p     pG  e 
  gi|313125079|ref|YP_004035343.1|  88 rnwkdGVVDQLTGGVEKLCKANGVNLIEGTARFKDDGAVRiehggegQGSETVEFEHCIIATGSRPIQV--PGF-EF 161
                                       ***********************************99998******97779**************9775..999.66 PP

                                       BEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 123 vgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGve 199
                                       + +    + s +al  + +p+++vvvG+GyiG+El+ ++aklg++vt+ve +d +l+++++++++ ++++ e  Gv+
  gi|313125079|ref|YP_004035343.1| 162 ADD--AVWSSRDALAADSVPDDLVVVGAGYIGMELSTTFAKLGANVTVVEMLDDVLPGYEDDVARVVRKHAESLGVK 236
                                       644..59********************************************************************** PP

                                       EEESCEEEEEEETTE..EEEEEETTSCE..EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTE CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 200 vklgtsvkeidgnge..klevvledgee..idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgi 271
                                       +++g+ +    ++ge   +e+++edge   + ad v+vavG++p t++l+ e++gle +e+g++++d+++rt v++i
  gi|313125079|ref|YP_004035343.1| 237 FHFGEGASGWSPDGEdvVVETETEDGEIstYRADKVLVAVGRSPVTDTLDiENAGLEPNENGFLETDDRMRTDVEHI 313
                                       ***************766667777877788*********************************************** PP

                                       EE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 272 yaiGDvaggkggpelaqaAvqqG 294
                                       yaiGDv+   ++p+la++ +++G
  gi|313125079|ref|YP_004035343.1| 314 YAIGDVV--ADSPMLAHVGSKEG 334
                                       *******..9********99987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.6
                                       EEES-SHHHHHHHHHHHHHT-....EEEEEESSSSSSTTS-HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 146 vvvGgGyiGvElAaalaklgk....evtlveardrllraldkelsaaleealek 195
                                        + G+  +G E +   a+l+      +tl + + ++   + + l++a++ea e+
  gi|313125079|ref|YP_004035343.1| 413 FILGAQIVGPEASELVAELALaiemGATLEDVAGTIH--THPTLAEAVMEAAEN 464
                                       5667767777766666555543322456666655554..333444444444443 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   1.6   2.5e-40   1.8e-37       1     109 [.     353     461 ..     353     462 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 2.5e-40
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p++vft+pe+++vG+t++eA++ag   +vgk+pf+a+gral+ ++t+gfv++vad+++g +lGa+ivGp+a+el++
  gi|313125079|ref|YP_004035343.1| 353 VPAAVFTEPEIGTVGMTQAEAEEAGFTPVVGKMPFNASGRALTTGHTDGFVRIVADEDSGFILGAQIVGPEASELVA 429
                                       79*************************************************************************** PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealkea 109
                                       ela+ai++g+t ed+a tih+hPtl+ea+ ea
  gi|313125079|ref|YP_004035343.1| 430 ELALAIEMGATLEDVAGTIHTHPTLAEAVMEA 461
                                       *****************************998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.018        13       2      30 ..      12      40 ..      11      43 .. 0.94
   2 !   65.2   0.2   8.1e-21   5.8e-18       2      76 ..     182     257 ..     181     262 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      v+v+G+G  g  +A  +a+ g ++t+ve 
  gi|313125079|ref|YP_004035343.1| 12 VLVIGAGPGGYVAAIRAAQNGLDTTLVEK 40
                                      89*************************96 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 8.1e-21
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesv 76 
                                       +vvvG+Gyig+El +++a+lg++Vtvve+ d +l++++++++++++++ e +g+++++++ +  +  +++  v + 
  gi|313125079|ref|YP_004035343.1| 182 LVVVGAGYIGMELSTTFAKLGANVTVVEMLDDVLPGYEDDVARVVRKHAESLGVKFHFGEGASGWSPDGEDvVVET 257
                                       79***************************************************************99998844433 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.1   2.2e-16   1.5e-13       1     305 []      13     317 ..      13     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.2e-16
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyryp..kemtfispsftsekleipdlnaiseetspafslke 75 
                                       ++iGaGP G  aai + ++gl d + +Ek++ g +  +     ++ fi+ s   ++ +  +   +  +++pa+ +++
  gi|313125079|ref|YP_004035343.1|  13 LVIGAGPGGYVAAIRAAQNGL-DTTLVEKDAYGGTCLNHGciPSKAFITASSLAHEAGHAE--EMGIHANPAVDMSQ 86 
                                       69*******************.689*******99999985225789999986666555555..56667899999999 PP

                       Pyr_redox_3  76 eklsrkealeYlrevaksfelpiklfeeVesvkk..edegfevetske.....tyeAkkviiAtGefdkPnklnipG 145
                                        +  ++ ++++l+  +++   + +  + +e  ++  +d+  ++e   e     t+e +++iiAtG     +++++++
  gi|313125079|ref|YP_004035343.1|  87 LRNWKDGVVDQLTGGVEKLC-KANGVNLIEGTARfkDDGAVRIEHGGEgqgseTVEFEHCIIATGS-RPIQVPGFEF 161
                                       99999999999988777643.456666666666632344466654332344459***********9.5557899999 PP

                       Pyr_redox_3 146 eeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelv 222
                                       ++  ++ +s +  +++   +++vV+G++  +++  + +++ ga+Vtvv   +            + p +e+ ++++v
  gi|313125079|ref|YP_004035343.1| 162 AD-DAVWSSRDALAADSVPDDLVVVGAGYIGMELSTTFAKLGANVTVVEMLDD-----------VLPGYEDDVARVV 226
                                       99.6777778888889999*****************************99863...........4455555555555 PP

                       Pyr_redox_3 223 ke....ekikvlfnaevkeikekeeeykvk..tedgkkvev.kddvvlatGykpdlsflkk..slfeldedgrpvlt 290
                                       ++      +k++f + +   + + e + v+  tedg+  +   d+v++a+G +p ++ l+   +++e +e+g+ + t
  gi|313125079|ref|YP_004035343.1| 227 RKhaesLGVKFHFGEGASGWSPDGEDVVVEteTEDGEISTYrADKVLVAVGRSPVTDTLDIenAGLEPNENGFLE-T 302
                                       5444322399999999999998877777762266665444457888899*****999966544899998888876.5 PP

                       Pyr_redox_3 291 eeteetnvpglflaG 305
                                       ++ + t v+ ++ +G
  gi|313125079|ref|YP_004035343.1| 303 DDRMRTDVEHIYAIG 317
                                       6789********998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   2.1   1.3e-10     9e-08       2      60 ..      12      72 ..      11     159 .. 0.81
   2 !   10.5   0.0   0.00032      0.23       1      28 [.     181     208 ..     181     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.3e-10
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalg 60
                                      v ViG+G  G+ AA+ aa+ G++++L+      +t+++ +C ps   i ++ l +E  + +
  gi|313125079|ref|YP_004035343.1| 12 VLVIGAGPGGYVAAIRAAQNGLDTTLVekDAYGGTCLNHGCIPSKAFITASSLAHEAGHAE 72
                                      89*************************7777789**************9999999987744 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00032
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi 28 
                                       d++V+G+G  G+e + + a+lGa+v+ +
  gi|313125079|ref|YP_004035343.1| 181 DLVVVGAGYIGMELSTTFAKLGANVTVV 208
                                       689**********************998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.7   8.3e-10     6e-07       2      35 ..      12      44 ..      11      53 .. 0.91
   2 !   10.6   0.2    0.0003      0.22       1      30 [.     181     210 ..     181     214 .. 0.95
   3 ?   -0.4   0.0      0.66   4.7e+02     177     200 ..     253     277 ..     222     284 .. 0.83
   4 ?   -0.2   0.0      0.56     4e+02     376     402 ..     300     320 ..     291     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 8.3e-10
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      v+ViG+G +G++AA++aa++Gl++++vek  + g
  gi|313125079|ref|YP_004035343.1| 12 VLVIGAGPGGYVAAIRAAQNGLDTTLVEKDAY-G 44
                                      9****************************988.3 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0003
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvek 30 
                                       D++V+G+G  G+  +++ a+ G++v+vve 
  gi|313125079|ref|YP_004035343.1| 181 DLVVVGAGYIGMELSTTFAKLGANVTVVEM 210
                                       89**************************95 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.66
                                       EEEEET.TTTCEEEEEESEEEE--- CS
                     FAD_binding_2 177 avvenp.esgrevrirakavvlatg 200
                                       +vve + e+g++ ++ra++v++a g
  gi|313125079|ref|YP_004035343.1| 253 VVVETEtEDGEISTYRADKVLVAVG 277
                                       456655699*************977 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.56
                                       EEBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGeva 402
                                       +etd+++r+       ++  YA+G v 
  gi|313125079|ref|YP_004035343.1| 300 LETDDRMRT------DVEHIYAIGDVV 320
                                       578888888......*********997 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   1.3e-06   0.00092       2      34 ..      10      42 ..       9      49 .. 0.95
   2 !    7.8   0.2    0.0024       1.7       4      34 ..     182     212 ..     180     218 .. 0.90
   3 !   13.7   0.1   3.9e-05     0.028     105     184 ..     220     296 ..     214     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      t+Vl++GaGp G ++a   ++ G +++lvek +
  gi|313125079|ref|YP_004035343.1| 10 TEVLVIGAGPGGYVAAIRAAQNGLDTTLVEKDA 42
                                      89****************************975 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0024
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                        ++VGaG  G+ l++  ++ G +v++ve  +
  gi|313125079|ref|YP_004035343.1| 182 LVVVGAGYIGMELSTTFAKLGANVTVVEMLD 212
                                       579************************9765 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEE CS
                     FAD_binding_3 105 teleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeet 181
                                       +++ r++++hae+ g++++f++   +   d+e v  e    e+ge++t ra+ +  a G rS+v +tl+ie  g e 
  gi|313125079|ref|YP_004035343.1| 220 DDVARVVRKHAESLGVKFHFGEGASGWSPDGEDVVVETET-EDGEISTYRADKVLVAVG-RSPVTDTLDIENAGLEP 294
                                       5789*************************99998877665.58********99999987.899*******9888775 PP

                                       EEE CS
                     FAD_binding_3 182 vye 184
                                         e
  gi|313125079|ref|YP_004035343.1| 295 N-E 296
                                       5.4 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   3.8e-07   0.00027       2      33 ..      11      42 ..      10      49 .. 0.92
   2 ?   -2.8   0.0       2.7   1.9e+03     148     165 ..     135     152 ..     104     155 .. 0.70
   3 !    5.5   0.1    0.0079       5.6       2      31 ..     181     210 ..     180     215 .. 0.92
   4 ?    4.8   0.0     0.014       9.8     110     164 ..     221     278 ..     218     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.8e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +v+viG+G+ G  aAi+aa++g +++l+ek  
  gi|313125079|ref|YP_004035343.1| 11 EVLVIGAGPGGYVAAIRAAQNGLDTTLVEKDA 42
                                      79***************************975 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                       .TTEEEEESEEEE----S CS
                       HI0933_like 148 kseeeleadklvlAtGGl 165
                                       +++e++e ++ ++AtG+ 
  gi|313125079|ref|YP_004035343.1| 135 QGSETVEFEHCIIATGSR 152
                                       47789999******9975 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0079
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllek 31 
                                       d++v+G+G  G+  + + ak g++V+++e 
  gi|313125079|ref|YP_004035343.1| 181 DLVVVGAGYIGMELSTTFAKLGANVTVVEM 210
                                       78*************************996 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.....TTEEEEESEEEE---- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvkt.k...seeeleadklvlAtGG 164
                                       d+ ++  k++++ gvk++  +  ++++ + +  + v+t +   + ++++adk+++A+G 
  gi|313125079|ref|YP_004035343.1| 221 DVARVVRKHAESLGVKFHFGEGASGWSPDGED-VVVETeTedgEISTYRADKVLVAVGR 278
                                       7889999*******************886666.7777732233345889*******995 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.4     4e-10   2.8e-07       1      37 [.      11      46 ..      11      73 .. 0.87
   2 ?    2.7   0.3     0.088        63       1      29 [.     181     209 ..     181     214 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4e-10
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGl 37
                                      +v+V+G+gp+G++AAi Aa++G  + Lve++ + GG+
  gi|313125079|ref|YP_004035343.1| 11 EVLVIGAGPGGYVAAIRAAQNGLDTTLVEKDAY-GGT 46
                                      59***************************9765.554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.088
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLve 29 
                                       D+vVvG+g  G+    + a+ Ga+v +ve
  gi|313125079|ref|YP_004035343.1| 181 DLVVVGAGYIGMELSTTFAKLGANVTVVE 209
                                       99**************************9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.5     1e-06   0.00073       1      34 [.      14      46 ..      14      78 .. 0.88
   2 !    9.7   0.0    0.0013      0.94       1      30 [.     184     213 ..     184     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                      ++GaG +G vaA ++a++g+d +l+ek  + GG 
  gi|313125079|ref|YP_004035343.1| 14 VIGAGPGGYVAAIRAAQNGLDTTLVEKDAY-GGT 46
                                      8**************************755.444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                       +vGaG  G+ +  + ak g++v+++e+ d+
  gi|313125079|ref|YP_004035343.1| 184 VVGAGYIGMELSTTFAKLGANVTVVEMLDD 213
                                       8*************************9887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.4   7.2e-05     0.052       2      37 ..      12      46 ..      11      87 .. 0.83
   2 ?    5.7   0.2     0.013       9.5     147     202 ..      97     151 ..      80     160 .. 0.75
   3 !    8.2   0.1    0.0022       1.6       1      28 [.     181     210 ..     181     217 .. 0.90
   4 !   10.9   0.0   0.00035      0.25     150     201 ..     224     277 ..     219     294 .. 0.76
   5 ?   -2.6   0.0       4.3   3.1e+03     121     159 ..     424     465 ..     385     470 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.2e-05
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGG CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaS 37
                                      v++iG+G  G  +A  +a+ g  +tl+ek+   g   +
  gi|313125079|ref|YP_004035343.1| 12 VLVIGAGPGGYVAAIRAAQNGldTTLVEKD-AYG--GT 46
                                      99****************************.554..44 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEE.EEEEEEEE--GG CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgve..rttpgen.daadavVnaaGa 202
                                       +lt ++ + ++a+Gv+++egt ++ +++ d +++++e   + +g++ ++++++++a+G 
  gi|313125079|ref|YP_004035343.1|  97 QLTGGVEKLCKANGVNLIEGT-AR-FKD-D-GAVRIEhgGEGQGSEtVEFEHCIIATGS 151
                                       678899999***********4.43.533.3.456666763333555457799*****94 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0022
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEES CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllek 28 
                                       d+v++G+G+iG+      a+ g  Vt++e+
  gi|313125079|ref|YP_004035343.1| 181 DLVVVGAGYIGMELSTTFAKLGanVTVVEM 210
                                       89**********999999999999****97 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00035
                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEE..EEEEEEE--G CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttp.gend..aadavVnaaG 201
                                       + +++ ae+lGv++++g+ + g   +dg  + ve++t+ ge++  +ad+v +a G
  gi|313125079|ref|YP_004035343.1| 224 RVVRKHAESLGVKFHFGEGASGW-SPDGEDVVVETETEdGEIStyRADKVLVAVG 277
                                       556788****************9.4566656666566668884245577****99 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 4.3
                                       HHHHSTTST.TTS.EEEEETTEEEEEHHHHHHH.HHHHHHHT CS
                               DAO 121 vrelepalp.gll.galfypdtgqvdpakltaa.laraaeal 159
                                       + el   l+  +  ga +++ +g+++++  +a  +++aae++
  gi|313125079|ref|YP_004035343.1| 424 ASELVAELAlAIEmGATLEDVAGTIHTHPTLAEaVMEAAENA 465
                                       333332211223327777888888866655544044445544 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.053        38       2      42 ..      11      51 ..      10      59 .. 0.85
   2 !   18.4   0.1   1.8e-06    0.0013       3      31 ..     182     210 ..     180     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.053
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTT CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsg 42
                                      ++ viG+G  G v a+  a+ g + ++v +d+     ln+g
  gi|313125079|ref|YP_004035343.1| 11 EVLVIGAGPGGYVAAIRAAQNGLDTTLVEKDAYGGTCLNHG 51
                                      578*************************9998665555555 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.8e-06
                                       EEEE--STTHHHHHHHHHHCTSEEEEE-S CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDi 31 
                                       ++v+G+GY+G+  ++ +a++g +v++v +
  gi|313125079|ref|YP_004035343.1| 182 LVVVGAGYIGMELSTTFAKLGANVTVVEM 210
                                       579**********************9976 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.4    0.0026       1.9      21      60 ..       4      41 ..       1      66 [. 0.87
   2 !   11.5   0.1   0.00019      0.14      30      69 ..     181     220 ..     172     262 .. 0.86
   3 ?    2.1   0.0      0.14     1e+02     127     151 ..     433     456 ..     413     470 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0026
                                      CEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C 21 GgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                      G ++  +  +vlviG+G  G  A+  a++ g ++t+++++
  gi|313125079|ref|YP_004035343.1|  4 GDIS--TGTEVLVIGAGPGGYVAAIRAAQNGLDTTLVEKD 41
                                      6666..6789******************999999998876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00019
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                         +v+G+G  G++   t ++lga+Vtv+++  ++l   e+
  gi|313125079|ref|YP_004035343.1| 181 DLVVVGAGYIGMELSTTFAKLGANVTVVEMLDDVLPGYED 220
                                       679*************************998888776666 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                                       TTGGGT-SBTT--TBBTTSEEEEET CS
                       AlaDh_PNT_C 127 vAidqGGnvetsrltthgepvveek 151
                                       +Ai+ G ++e+++ t h++p++  +
  gi|313125079|ref|YP_004035343.1| 433 LAIEMGATLEDVAGTIHTHPTLA-E 456
                                       799***************99987.3 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.024        17       2      31 ..      12      41 ..      11      48 .. 0.92
   2 !   15.9   0.1   1.3e-05    0.0091       3      51 ..     183     231 ..     181     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                      v viGaG  G   a  +a++gl+++lv+ +
  gi|313125079|ref|YP_004035343.1| 12 VLVIGAGPGGYVAAIRAAQNGLDTTLVEKD 41
                                      78************************9976 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.3e-05
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklve 51 
                                        v+GaG +G ++ + fa+ g +V++v++ ++ l   ++ +++ ++k +e
  gi|313125079|ref|YP_004035343.1| 183 VVVGAGYIGMELSTTFAKLGANVTVVEMLDDVLPGYEDDVARVVRKHAE 231
                                       69**************************999888887777776666555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.013       9.4       6      40 ..       8      42 ..       6      95 .. 0.87
   2 !   11.3   0.1   0.00051      0.37       9      37 ..     181     209 ..     173     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                     NAD_binding_7  6 kgkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                      +g +vlv+G+G+ ++  + + +++g + t+v ++ 
  gi|313125079|ref|YP_004035343.1|  8 TGTEVLVIGAGPGGYVAAIRAAQNGLDTTLVEKDA 42
                                      5789**************************99884 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00051
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvva 37 
                                         +vvG+G ++++   ++++ ga+vtvv 
  gi|313125079|ref|YP_004035343.1| 181 DLVVVGAGYIGMELSTTFAKLGANVTVVE 209
                                       579************************85 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.49   3.5e+02       1      30 [.      12      41 ..      12      43 .. 0.89
   2 !   13.7   0.1   8.1e-05     0.058       2      50 ..     183     231 ..     182     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.49
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkd 30
                                      +++iG+G  G+  a +  ++g d ++++kd
  gi|313125079|ref|YP_004035343.1| 12 VLVIGAGPGGYVAAIRAAQNGLDTTLVEKD 41
                                      68***************9977579***998 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.1e-05
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TT CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdat 50 
                                       +++G+G +G++l  ++ + g  +v+v++  ++++  ++++ ++vv  +a 
  gi|313125079|ref|YP_004035343.1| 183 VVVGAGYIGMELSTTFAKlGA-NVTVVEMLDDVLPGYEDDVARVVRKHAE 231
                                       8*****************777.6***************999999988876 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1    0.0079       5.7       2      32 ..      12      40 ..      11     120 .. 0.87
   2 !    8.8   0.1     0.001      0.72       1      36 [.     181     214 ..     181     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0079
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvliea 32
                                      v+viGaGp g   A r   a+ gl  +l+e 
  gi|313125079|ref|YP_004035343.1| 12 VLVIGAGPGGYVAAIRA--AQNGLDTTLVEK 40
                                      89***************..999999999985 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.001
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       D+vv+GaG  g+ l      ak g +v+++e  +++
  gi|313125079|ref|YP_004035343.1| 181 DLVVVGAGYIGMELSTTF--AKLGANVTVVEMLDDV 214
                                       9*****************..**********988877 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.2   7.9e-05     0.057      18      65 ..      10      55 ..       5     118 .. 0.79
   2 ?    5.2   0.2     0.015        11      16      48 ..     178     209 ..     169     218 .. 0.84
   3 ?   -2.9   0.0       4.5   3.2e+03      65     110 ..     416     461 ..     411     464 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfs 65
                                      ++v+++GaG+ G  aa   a++ +l ++++e+  ++GG     G + s
  gi|313125079|ref|YP_004035343.1| 10 TEVLVIGAGPGGYVAAIRAAQN-GLDTTLVEKD-AYGGTCLNHGCIPS 55
                                      689*******************.********87.67776666555544 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                                       TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4  16 aesDvvivGaGssGLtaayylakkpdlkvaile 48 
                                       +  D+v+vGaG  G+  + ++ak  + +v+++e
  gi|313125079|ref|YP_004035343.1| 178 VPDDLVVVGAGYIGMELSTTFAKL-GANVTVVE 209
                                       5679******************99.77777777 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.5
                                       SEEEEETTTHHHHHHTT---EEESSEEEESEHHHHHHHHHHHHHTS CS
                              Thi4  65 saivvrkpakelLdelgikyedegdyvvvkdaalftstllskvlql 110
                                        a +v  +a+el+ el ++ e   +   v+ ++    tl+ +v++ 
  gi|313125079|ref|YP_004035343.1| 416 GAQIVGPEASELVAELALAIEMGATLEDVAGTIHTHPTLAEAVMEA 461
                                       5667778888888888888877777777777777777777777764 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0032       2.3     132     213 ..     125     201 ..     104     212 .. 0.74
   2 ?    5.5   0.0     0.011         8     108     161 ..     232     281 ..     224     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0032
                       K_oxygenase 132 lltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeife 208
                                       ++++e+  + + +e++e ++ ++++G++p   + +e    ++ v+ s ++l        +++++VvG+G  + e+  
  gi|313125079|ref|YP_004035343.1| 125 AVRIEHGGEGQGSETVEFEHCIIATGSRPIQVPGFEF-A-DDAVWSSRDALAAD---SVPDDLVVVGAGYIGMELST 196
                                       556665554455688999********99964444553.3.47888888888776...7999********99999877 PP

                       K_oxygenase 209 dllrr 213
                                         ++ 
  gi|313125079|ref|YP_004035343.1| 197 TFAKL 201
                                       76655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                       K_oxygenase 108 qleeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepk 161
                                       +l  + +fge     +pd e+    + ve+++++ge ++++a +++++vG +p 
  gi|313125079|ref|YP_004035343.1| 232 SLGVKFHFGEGASGWSPDGED----VVVETETEDGEISTYRADKVLVAVGRSPV 281
                                       555566777777777777764....6788888******************9995 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00031      0.22     164     210 .]     283     330 ..     266     330 .. 0.84
   2 ?    0.9   0.0      0.66   4.7e+02      94     131 ..     374     432 ..     351     463 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                                       EEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 164 iasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       ++ die    +p+ +g++++ ++++ + e++ ++GD v D+++la +g
  gi|313125079|ref|YP_004035343.1| 283 DTLDIENaGLEPNENGFLETDDRMRTDVEHIYAIGDVVADSPMLAHVG 330
                                       555666667799*********************************987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.66
                                       HHHCHHHHHH.......................TTHHHHHHHHHHTHHBHTTHHHHHHHHH CS
                                       xxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  94 qsqgrtvall.......................qaralavftiadplkvkpeaaeavasLk 131
                                       +++g t ++                         ++  + +  a+   v pea e+va+L 
  gi|313125079|ref|YP_004035343.1| 374 EEAGFTPVVGkmpfnasgralttghtdgfvrivADEDSGFILGAQI--VGPEASELVAELA 432
                                       5555555555555555555555555555555555588888888888..9999999999986 PP

>> MDMPI_C  MDMPI C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.5   3.4e-05     0.024       6      82 ..     206     287 ..     203     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.4e-05
                           MDMPI_C   6 gvdellatvvarraaapd.srvvlelegprtvhlhatdggra.rlalwadg.........adatvrGtaadlllllw 71 
                                        v e+l++v++   +  d +rvv    +   v +h ++g+++      +dg          d +++   ad +l++ 
  gi|313125079|ref|YP_004035343.1| 206 TVVEMLDDVLPGYED--DvARVVRKHAESLGVKFHFGEGASGwS----PDGedvvvetetEDGEISTYRADKVLVAV 276
                                       578999999999976..459********************8542....344456778888999************** PP

                           MDMPI_C  72 GRlspddtlev 82 
                                       GR ++ dtl++
  gi|313125079|ref|YP_004035343.1| 277 GRSPVTDTLDI 287
                                       ******99554 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.014       9.8       2      40 ..      14      46 ..      13      59 .. 0.87
   2 ?   -1.7   0.0       3.4   2.5e+03     140     155 ..     136     151 ..     115     152 .. 0.68
   3 ?   -1.4   0.1       2.9   2.1e+03       1      30 [.     183     210 ..     183     225 .. 0.72
   4 ?    5.9   0.0     0.017        12     104     155 ..     222     278 ..     213     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                      ++GaGp G  ++ r +++      l+ tl++++ +g g+
  gi|313125079|ref|YP_004035343.1| 14 VIGAGPGGYVAAIRAAQN-----GLDTTLVEKDAYG-GT 46
                                      8*************9999.....5999999998887.65 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                     NAD_binding_9 140 dgaslaadaVvLAlGh 155
                                       + ++++++++++A+G 
  gi|313125079|ref|YP_004035343.1| 136 GSETVEFEHCIIATGS 151
                                       446799********95 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.9
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitl 30 
                                       ++vGaG  G+ + + +++    ++ + + +
  gi|313125079|ref|YP_004035343.1| 183 VVVGAGYIGMELSTTFAKLG--ANVTVVEM 210
                                       699***99999888888874..44444444 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.017
                     NAD_binding_9 104 feellarlpegvtvevh.raevvdleeradgqavll..adg..aslaadaVvLAlGh 155
                                       +++++++  e++ v++h  + +   +++++ + v +  +dg  ++++ad+V +A+G 
  gi|313125079|ref|YP_004035343.1| 222 VARVVRKHAESLGVKFHfGEGASGWSPDGEDVVVETetEDGeiSTYRADKVLVAVGR 278
                                       5677788888999999956689999999999866553367755579*********96 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.68   4.9e+02       1      31 [.      12      42 ..      12      83 .. 0.87
   2 ?    9.8   0.0    0.0015       1.1       1      31 [.     182     212 ..     182     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.68
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-G CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpre 31
                                      ++++Gag+ +   a  aa+ g+++t+v++++
  gi|313125079|ref|YP_004035343.1| 12 VLVIGAGPGGYVAAIRAAQNGLDTTLVEKDA 42
                                      589************************9886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-G CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpre 31 
                                       lv++Gag ++ +l +  a+lg +vtvv+  +
  gi|313125079|ref|YP_004035343.1| 182 LVVVGAGYIGMELSTTFAKLGANVTVVEMLD 212
                                       79************************98655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         2   1.4e+03      36      64 ..       9      37 ..       4      43 .. 0.82
   2 ?    9.3   0.0   0.00096      0.69      31      67 ..     174     210 ..     159     230 .. 0.78
   3 ?   -1.0   0.0       1.3   9.4e+02     113     139 ..     263     289 ..     259     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                                      TSEEEEES-SHHHHHHHHHHHHTT-EEEE CS
                      2-Hacid_dh_C 36 gktvGiiGlGrIGqavakrlkafgmkvia 64
                                      g +v +iG+G  G  +a r+++ g++ + 
  gi|313125079|ref|YP_004035343.1|  9 GTEVLVIGAGPGGYVAAIRAAQNGLDTTL 37
                                      78899******999999999988877665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00096
                                       BS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                      2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqavakrlkafgmkviaydr 67 
                                         +     + ++G+G IG ++  +++++g++v++++ 
  gi|313125079|ref|YP_004035343.1| 174 AADSVPDDLVVVGAGYIGMELSTTFAKLGANVTVVEM 210
                                       4444556789**********************99876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.3
                                       HHHCSTTTEEEEESS-GGGB-HHHHHH CS
                      2-Hacid_dh_C 113 elakmkkgailiNtaRGglvdeeaLle 139
                                       e++  + + +l+ ++R ++ d+ ++ +
  gi|313125079|ref|YP_004035343.1| 263 EISTYRADKVLVAVGRSPVTDTLDIEN 289
                                       677788899************988765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00053      0.38       2      48 ..      12      55 ..      11      65 .. 0.83
   2 ?   -2.6   0.2       2.5   1.8e+03       2      32 ..     182     209 ..     181     212 .. 0.85
   3 ?   -2.7   0.0       2.7   1.9e+03     156     196 ..     222     263 ..     219     267 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00053
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--TH CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatips 48
                                      ++++G+G+ G++aA+  a+ +   l+ tlve+++ g      + ips
  gi|313125079|ref|YP_004035343.1| 12 VLVIGAGPGGYVAAIRAAQNG---LDTTLVEKDAYGGTCLNHGCIPS 55
                                      89************9877777...9*******998877666666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                       EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlve 32 
                                       +v+vG+G  G    +++ak +   ++vt+ve
  gi|313125079|ref|YP_004035343.1| 182 LVVVGAGYIGMELSTTFAKLG---ANVTVVE 209
                                       799****99999888888888...8899998 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHCT-EEEE--EEEEEE-T.TS-EEEEEETTS- CS
                    Trp_halogenase 156 yakfLrrvaearGvtrvegkvvevqlde.dgrveslrledgr 196
                                       +a++ r++ae+ Gv+   g+ ++    + ++ v + ++edg+
  gi|313125079|ref|YP_004035343.1| 222 VARVVRKHAESLGVKFHFGEGASGWSPDgEDVVVETETEDGE 263
                                       789999********9999888776665547777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2988.58
//
Query:       gi|313125080|ref|YP_004035344.1|  [L=509]
Description: pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-90  302.5   0.0    2.5e-90  302.0   0.0    1.2  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    2.3e-24   85.0   1.6    4.6e-24   84.0   1.6    1.6  1  Biotin_lipoyl    Biotin-requiring enzyme
    3.9e-23   81.5   0.7    3.7e-16   59.2   0.1    2.8  2  E3_binding       e3 binding domain
    7.4e-07   28.9   0.1      0.017   15.0   0.0    3.0  2  Biotin_lipoyl_2  Biotin-lipoyl like
    0.00038   21.1   1.2        0.1   13.3   0.0    2.7  2  HlyD_3           HlyD family secretion protein
     0.0035   17.2   0.2     0.0089   15.9   0.2    1.7  1  GCV_H            Glycine cleavage H-protein
  ------ inclusion threshold ------
      0.068   13.1   0.1       0.19   11.7   0.1    1.8  1  RnfC_N           RnfC Barrel sandwich hybrid domain
        3.4    8.4   6.9        4.3    8.0   5.4    2.0  1  NUDIX-like       NADH pyrophosphatase-like rudimentary NUDIX 


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.0   0.0   1.1e-93   2.5e-90       5     233 .]     281     508 ..     278     508 .. 0.98

  Alignments for each domain:
  == domain 1  score: 302.0 bits;  conditional E-value: 1.1e-93
                                       XXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG CS
                      2-oxoacid_dh   5 ervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPeln 81 
                                       ervp++g+r+ai +++++sk ++ph+t++devdvt+l+elr+elk  +++++ ++lt+++f++kav++AlkefP +n
  gi|313125080|ref|YP_004035344.1| 281 ERVPYRGVRRAIGDQMERSKYTAPHVTHHDEVDVTELVELREELKPLAEEQD-TRLTYMPFVMKAVIAALKEFPFMN 356
                                       89********************************************997655.6*********************** PP

                                       -EE.EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE---- CS
                      2-oxoacid_dh  82 asvdeeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGm 158
                                       +++dee++eiv+++++niGvA+at+ GL+vPv+ +ad k+ll+++++++e +ekare+k++pe+++ggtfti+N+G+
  gi|313125080|ref|YP_004035344.1| 357 SQLDEENEEIVLRDEYNIGVATATDVGLMVPVVDDADGKGLLDLSRDMNEKVEKARERKIAPEEMQGGTFTITNIGG 433
                                       ***************************************************************************** PP

                                       -----------TT-SEEEEE---.B--TTSTT-HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-HHXXXXX CS
                      2-oxoacid_dh 159 lGvtsftPiinppqvaIlgvgrikerpvvkegelvvrkvmtlslsaDHRvidGaeaarFlntlkkllenpeelll 233
                                       +G++++tPiin+p+vaIl++g+ike+p v++g++v+rkv+tlsls+DHR++dGa +arF+n++k++l np++lll
  gi|313125080|ref|YP_004035344.1| 434 IGGEYATPIINYPEVAILALGAIKEKPRVVDGDIVPRKVLTLSLSFDHRIVDGAVGARFTNKVKEYLMNPKLLLL 508
                                       ***********************************************************************9985 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   1.6   2.1e-27   4.6e-24       2      72 ..       5      76 ..       4      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 2.1e-27
                                      EEEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEE CS
                     Biotin_lipoyl  2 eiksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllak 72
                                      e+k+P++Ge v+eg  v+++v +Gd+V+++qv+aeve++K+ +++++p +G+vke+l++eG++v vgd++++
  gi|313125080|ref|YP_004035344.1|  5 EFKLPDVGEGVAEGeLVTWHVTPGDTVEEDQVVAEVETDKALVDVPSPYNGTVKELLAEEGEMVPVGDVIIT 76
                                      89********************************************************************97 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.1   1.7e-19   3.7e-16       1      36 []     115     150 ..     115     150 .. 0.98
   2 !   19.9   0.0   3.1e-07   0.00069       2      24 ..     204     226 ..     203     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.7e-19
                                       SBE-HHHHHHHHHCT--TTTS---CTTTBE-HHHHC CS
                        E3_binding   1 vlAsPaaRklAkelGidLsdvkGtGpgGRItkeDVl 36 
                                       v+AsP++R lA+elG+d+++v+GtGp GR+t+ DV+
  gi|313125080|ref|YP_004035344.1| 115 VFASPSVRQLARELGVDIASVSGTGPSGRVTESDVR 150
                                       89*********************************6 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.1e-07
                                       BE-HHHHHHHHHCT--TTTS--- CS
                        E3_binding   2 lAsPaaRklAkelGidLsdvkGt 24 
                                       lA Pa R+ A+e+G+d+++v+++
  gi|313125080|ref|YP_004035344.1| 204 LAAPATRRVAEEKGVDINNVPAS 226
                                       699*****************987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00013      0.29      10      37 ..      17      44 ..       9      49 .. 0.88
   2 !   15.0   0.0   7.4e-06     0.017       3      34 ..      47      78 ..      41      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                   Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVkaGdvLaelDsra 37
                                       G +++++V+ G+ V++ +v ae ++++
  gi|313125080|ref|YP_004035344.1| 17 EGELVTWHVTPGDTVEEDQVVAEVETDK 44
                                      6999******************998765 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 7.4e-06
                   Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelD 34
                                      v + +p +G+V++l+ ++G  V  Gdv+++ +
  gi|313125080|ref|YP_004035344.1| 47 VDVPSPYNGTVKELLAEEGEMVPVGDVIITFE 78
                                      6677899*********************9975 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2    0.0071        16       8      39 ..      18      48 ..      15      50 .. 0.86
   2 !   13.3   0.0   4.5e-05       0.1       3      30 ..      50      77 ..      48      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0071
                            HlyD_3  8 Gvvvelnveegevvqagdelleiippdtllve 39
                                      G++v ++v++g+ v++ ++++e+  +d++lv+
  gi|313125080|ref|YP_004035344.1| 18 GELVTWHVTPGDTVEEDQVVAEVE-TDKALVD 48
                                      88999******************9.6777766 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.5e-05
                            HlyD_3  3 rApvdGvvvelnveegevvqagdellei 30
                                       +p+ G+v+el +eege+v+ gd++ + 
  gi|313125080|ref|YP_004035344.1| 50 PSPYNGTVKELLAEEGEMVPVGDVIITF 77
                                      59**********************9875 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2     4e-06    0.0089      34      74 ..      21      60 ..       8      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4e-06
                                      EEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                             GCV_H 34 vfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74
                                      v  ++   g++v++++ +a vE+ Ka  +v++p +G+v e 
  gi|313125080|ref|YP_004035344.1| 21 VTWHVT-PGDTVEEDQVVAEVETDKALVDVPSPYNGTVKEL 60
                                      555554.599****************************885 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.6e-05      0.19      42      80 ..      21      60 ..      15      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-05
                            RnfC_N 42 akplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkai 80
                                       +  v  gd+V++ q++ae e+    + v ++  GtVk++
  gi|313125080|ref|YP_004035344.1| 21 VTWHVTPGDTVEEDQVVAEVETdKALVDVPSPYNGTVKEL 60
                                      566799*************98777799**********986 PP

>> NUDIX-like  NADH pyrophosphatase-like rudimentary NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.4    0.0019       4.3      56     100 ..     218     259 ..     144     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0019
                        NUDIX-like  56 vdvsareeeikeaeeeggafvelRavmlalsaedaalaaqArall 100
                                       vd+   ++   +++++g afv++ av++  +a++aa aa A+al 
  gi|313125080|ref|YP_004035344.1| 218 VDINNVPA---SEQRDGQAFVSAEAVHEYAEAQQAAQAADAQALA 259
                                       44555555...7899****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3243.10
//
Query:       gi|313125081|ref|YP_004035345.1|  [L=331]
Description: pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase component subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-51  173.6   0.0    4.4e-51  173.1   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    2.1e-38  131.0   0.5    3.4e-38  130.3   0.2    1.5  2  Transketolase_C  Transketolase, C-terminal domain
    0.00013   22.2   0.0    0.00023   21.4   0.0    1.4  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.1   0.0   7.3e-55   4.4e-51       3     176 ..      10     184 ..       8     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 173.1 bits;  conditional E-value: 7.3e-55
                                       EEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEE CS
                      Transket_pyr   3 iawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviv 77 
                                       ++  +a+++ l +++++d++vv++g+Dv+  gg+f +++gl++++g++rvid++++E++++g+a+G+a+ g +++++
  gi|313125081|ref|YP_004035345.1|  10 LTLVQAVRDGLYTEMQADDRVVVMGEDVGknGGVFRATEGLWEEFGDDRVIDTPLAESGIAGTAIGMAAMG-MRPVA 85 
                                       56779999***************************************************************.8**** PP

                                       EEEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHH CS
                      Transket_pyr  78 eaqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkh 152
                                       e+qF+ F+ +A  qi+ ++a  + +++g++++++v+r+p+g g ++peh+s + eaf+++ +glkvv Ps+p +tk+
  gi|313125081|ref|YP_004035345.1|  86 EMQFSGFMYPAfdQIVSHAARLRTRSRGRYTCPLVVRAPYGGGIRAPEHHSESKEAFYAHEAGLKVVIPSTPHDTKG 162
                                       ***************************************************************************** PP

                                       HHHHHHHSSS.SEEEEEE-SSEEC CS
                      Transket_pyr 153 llrrairredrkPvvlrlpksllr 176
                                       ll  air  d++Pv++++pk  +r
  gi|313125081|ref|YP_004035345.1| 163 LLISAIR--DPDPVIFLEPKLIYR 184
                                       *******..899********9997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.4   8.5e+03      61      76 ..      28      43 ..      20      54 .. 0.65
   2 !  130.3   0.2   5.6e-42   3.4e-38       1     124 []     200     321 ..     200     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                                      HSEEEEEEEEESTTSH CS
                   Transketolase_C 61 tgrlvvveeavkrgGi 76
                                       + +v+ e+  k+gG+
  gi|313125081|ref|YP_004035345.1| 28 DRVVVMGEDVGKNGGV 43
                                      3445566667777776 PP

  == domain 2  score: 130.3 bits;  conditional E-value: 5.6e-42
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       g+a ++reg d+ + +yG+m +  +eAae+Le+egi+aeVvdlrtv+p+Dketi es kktgr  vv+ea k+gG+g
  gi|313125081|ref|YP_004035345.1| 200 GEAAVRREGADISVYTYGAMTRPTIEAAENLEEEGIDAEVVDLRTVSPMDKETIVESFKKTGRAAVVHEAPKTGGLG 276
                                       7999************************************************************************* PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                       +e++++++eea+ + +apv+r++g+dv  p++  +le++++++++++
  gi|313125081|ref|YP_004035345.1| 277 AEITTTIQEEALLHQEAPVERIAGYDV--PYPLYALEDYYLPSVARV 321
                                       ***************************..888889*******99886 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.9e-08   0.00023       1      94 [.     209     300 ..     209     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.9e-08
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A++ + ++G++ + + +a+++l eegi++ ++ lrt+ P  +e + e  kk+ + +v+  + +   +G l+ e+ + 
  gi|313125081|ref|YP_004035345.1| 209 ADISVYTYGAMTRPTIEAAENLEEEGIDAEVVDLRTVSPMDKETIVESFKKTGRAAVVHEAPK---TGGLGAEITTT 282
                                       8999*********************************************99999999988883...58889999998 PP

                                       TGGG.TSEEEEEE--GGG CS
                           PFOR_II  78 lkks.kvkvvnfvaglgG 94 
                                       ++++   +    v++++G
  gi|313125081|ref|YP_004035345.1| 283 IQEEaLLHQEAPVERIAG 300
                                       888753333344445444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1743.39
//
Query:       gi|313125082|ref|YP_004035346.1|  [L=367]
Description: pyruvate dehydrogenase e1 component subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-89  298.3   0.0    5.4e-89  298.1   0.0    1.0  1  E1_dh            Dehydrogenase E1 component
    6.6e-07   28.8   0.0      1e-06   28.2   0.0    1.2  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    4.3e-05   22.6   0.0    8.5e-05   21.7   0.0    1.5  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
     0.0006   19.6   3.0      0.001   18.8   0.3    2.5  2  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
  ------ inclusion threshold ------
      0.035   13.8   0.0      0.077   12.7   0.0    1.5  1  HTH_41           Helix-turn-helix domain
       0.17   11.2   0.0       0.88    8.9   0.0    1.9  2  Mig-14           Mig-14


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.1   0.0   1.8e-92   5.4e-89       2     299 ..      38     330 ..      37     331 .. 0.95

  Alignments for each domain:
  == domain 1  score: 298.1 bits;  conditional E-value: 1.8e-92
                                       HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TT CS
                             E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvk 78 
                                       + + ++r +d ++++++r++r+g+y +  gqe +++g+a+al++eD+++++YRe+g  l rgl+l+  l++++g++ 
  gi|313125082|ref|YP_004035346.1|  38 REMWMARHFDTRAVSLQRQGRMGTYPPLSGQEGAQIGSAFALDEEDWMFPSYREHGAALHRGLPLKRTLLYWMGHE- 113
                                       77999***********************************************************************. PP

                                       TSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EE CS
                             E1_dh  79 gkggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvi 155
                                          ++++     ++ ++i++   ++++q p++ G+a a+k +g+++++++++GDg++++Gd++e+ln+a +++ p i
  gi|313125082|ref|YP_004035346.1| 114 ---KGNR----IPEDANIFPVAVPISTQIPHATGAAWAKKLQGEDSAVLCYFGDGGTSEGDFHEGLNFAGVFNTPNI 183
                                       ...5555....568889************************************************************ PP

                                       EEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHH....TTT--EEEEEEE--SS CS
                             E1_dh 156 fvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaerar....egkgpllielvtYRyg 228
                                       f+++NN+++is+++e+++as ++a++a+++g  g++Vdg+Dplavy+A+++A++ a+     + +p+lie+v YR+g
  gi|313125082|ref|YP_004035346.1| 184 FFCNNNQWAISVPRERQTASATIAQKAKAYGFEGVQVDGMDPLAVYAATRAAVKKAKdpaeDERRPTLIEAVQYRFG 260
                                       **********************************************9887766665422117999************ PP

                                       -SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS----G CS
                             E1_dh 229 gHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkelep 299
                                        H++ Ddp+ yr ++eve++++k dpi rl+++L ++g +++e++++i++ev+ ev ea+k ae+++ +ep
  gi|313125082|ref|YP_004035346.1| 261 AHTTADDPTVYRDSDEVEQWKQK-DPIPRLETFLRDTGRLDDEKVDAIQSEVEDEVAEAIKAAEAEPRPEP 330
                                       *****************998777.*******************************************9987 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   3.4e-10     1e-06     114     177 ..     132     195 ..     125     260 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.4e-10
                    DXP_synthase_N 114 stsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk 177
                                       st i  a+G a a++l+ge++ v++  GDg+ + G  +e+ln +g  ++  +   N+N+++is 
  gi|313125082|ref|YP_004035346.1| 132 STQIPHATGAAWAKKLQGEDSAVLCYFGDGGTSEGDFHEGLNFAGVFNTPNIFFCNNNQWAISV 195
                                       899*********************************************************9986 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.8e-08   8.5e-05     144     241 ..     151     254 ..     139     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.8e-08
                                       ---EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGGG.T--S-HHHHHHHTT-EEEEETTTT-H CS
                   Transketolase_N 144 dhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGetei.sftedvakrfeaygWhvievedgedv 219
                                       d+ + +  gDg   eG  +e  ++ag+ +  + i + ++n+ +i    e  + +  +a++ +ayg++ ++v+ g d 
  gi|313125082|ref|YP_004035346.1| 151 DSAVLCYFGDGGTSEGDFHEGLNFAGVFNTPN-IFFCNNNQWAISVPRERqTASATIAQKAKAYGFEGVQVD-GMDP 225
                                       788999***********************998.679999998888766551556678999*******99964.4444 PP

                                       ....HHHHHHHHHHH...H-TTS-EEEEE CS
                   Transketolase_N 220 ....eaikaaieeak...aekdkPslikl 241
                                           +a +aa+++ak   +++ +P+li+ 
  gi|313125082|ref|YP_004035346.1| 226 lavyAATRAAVKKAKdpaEDERRPTLIEA 254
                                       01113456677777733235679999975 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   3.5e-07     0.001      31     152 ..     132     253 ..     111     257 .. 0.60
   2 ?   -2.3   0.2       1.1   3.4e+03     128     148 ..     310     328 ..     303     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.5e-07
                                       TTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT.GGGHHHHHHT.T-SEEEEEEE-SBCCCHHHH.HHHHTCCTT CS
                      TPP_enzyme_C  31 GyglpaAiGakla....kpdrevvaivGDGgflmi.lqelatavrr.nlpitvvvlnNegygmtggq.qepfggkrk 100
                                         ++p A+Ga+ a     +d+ v ++ GDGg+    ++e  +++   n p ++++ nN++   + ++ q  + +   
  gi|313125082|ref|YP_004035346.1| 132 STQIPHATGAAWAkklqGEDSAVLCYFGDGGTSEGdFHEGLNFAGVfNTPNIFFCNNNQWAISVPRErQ--TAS--- 203
                                       5689*******9633323479**********99999777666555516666666666666544444321..221... PP

                                       TTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH........CSSSEEEEE CS
                      TPP_enzyme_C 101 sgpagkdlkpvdfaklaealGakgarvekadveeleealkeal........ekkgpalie 152
                                                   +a+ a+a+G +g++v+  d+  + +a ++a+        ++++p+lie
  gi|313125082|ref|YP_004035346.1| 204 ----------ATIAQKAKAYGFEGVQVDGMDPLAVYAATRAAVkkakdpaeDERRPTLIE 253
                                       ..........23555566666665555555554443333333322224444455555554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                       SSH.HHHHHHHHHHHHCSSSE CS
                      TPP_enzyme_C 128 ekadveeleealkealekkgp 148
                                       e++  +e++ea+k+a ++ +p
  gi|313125082|ref|YP_004035346.1| 310 EVE--DEVAEAIKAAEAEPRP 328
                                       455..8999999999877665 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.6e-05     0.077      32      47 ..      47      62 ..      46      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                            HTH_41 32 ddkaislerrGrlGtf 47
                                      d +a+sl+r+Gr+Gt+
  gi|313125082|ref|YP_004035346.1| 47 DTRAVSLQRQGRMGTY 62
                                      578************9 PP

>> Mig-14  Mig-14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0003      0.88     118     152 ..      11      45 ..       3      58 .. 0.84
   2 ?   -0.8   0.0      0.27   8.2e+02     128     158 ..     235     265 ..     226     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0003
                            Mig-14 118 elrlleeaGGsvrsvsdfssdelasiyielfrrrf 152
                                        lr l+e G  v +v d+s del  +y e++  r+
  gi|313125082|ref|YP_004035346.1|  11 MLRVLDEDGEPVGEVPDLSDDELVRMYREMWMARH 45 
                                       58999*************************98875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                            Mig-14 128 svrsvsdfssdelasiyielfrrrfGfsatg 158
                                       +v++++d + de     ie  + rfG ++t+
  gi|313125082|ref|YP_004035346.1| 235 AVKKAKDPAEDERRPTLIEAVQYRFGAHTTA 265
                                       799999********************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 1961.63
//
Query:       gi|313125083|ref|YP_004035347.1|  [L=311]
Description: lipoate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-14   53.1   0.0    8.9e-14   52.2   0.0    1.5  1  Radical_SAM  Radical SAM superfamily
    1.3e-10   41.6   0.1    6.1e-10   39.5   0.0    2.0  2  LIAS_N       N-terminal domain of lipoyl synthase of Radical_
  ------ inclusion threshold ------
      0.022   14.8   0.4          3    7.9   0.0    2.9  3  B12-binding  B12 binding domain
      0.025   13.9   0.0      0.036   13.4   0.0    1.2  1  BKACE        beta-keto acid cleavage enzyme
      0.074   12.1   0.0        2.2    7.2   0.0    2.6  3  DUF2090      Uncharacterized protein conserved in bacteria (D


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   2.5e-17   8.9e-14       4     166 ..      63     222 ..      60     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.5e-17
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla....vp 76 
                                       +  C+++C+fC++      +g  + l+++e ++ + ++ ae g ++v+l++ + ++ pd     ++   ++    +p
  gi|313125083|ref|YP_004035347.1|  63 GDRCSRGCNFCDVQ-----TGGMEPLDPDEPANVAAAV-AEIGLDYVVLTSVDRDDLPDQGASHFAQTIREikqrDP 133
                                       568***********.....6999999999999999999.8999**************88888888877777666678 PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET.EEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr.vvdrivg 151
                                        i + v ++ +  dee ++++ ++ +d++++++e++     + +++ r+ ++e+ l +le  ++   +  +++ i++
  gi|313125083|ref|YP_004035347.1| 134 SILVEVLIPDFQGDEEAVRKIIDAKPDVIAHNIETVER--LQWPVRdRRANYEQSLSVLEQVKRE-SDIyTKTSIML 207
                                       88888888888888***********************9..79999999**************998.4556******* PP

                                       BTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeeleellel 166
                                       + Ge d+e+ ++l++
  gi|313125083|ref|YP_004035347.1| 208 GLGEYDHEIYQTLSD 222
                                       *********999976 PP

>> LIAS_N  N-terminal domain of lipoyl synthase of Radical_SAM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   1.7e-13   6.1e-10      72     108 .]       5      41 ..       2      41 .. 0.96
   2 ?   -1.0   0.0      0.65   2.3e+03      60      97 ..     184     223 ..     158     228 .. 0.64

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.7e-13
                            LIAS_N  72 rLPswlktkiPlGknynkikndlreLnLhtvCeeaRC 108
                                       r P+wlk + P G+ ++ ik++lr+ +LhtvCeea C
  gi|313125083|ref|YP_004035347.1|   5 RKPDWLKMRPPSGRRFTDIKQTLRDRDLHTVCEEANC 41 
                                       78**********************************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.65
                            LIAS_N  60 kgnlkrekgerlrLPswlktkiPlGk.ny.nkikndlreL 97 
                                       ++ l+  ++ +     + kt+i lG  +y + i ++l +L
  gi|313125083|ref|YP_004035347.1| 184 EQSLSVLEQVKRESDIYTKTSIMLGLgEYdHEIYQTLSDL 223
                                       4444433333334556889998877423424566666666 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00083         3      40      84 ..      88     137 ..      70     139 .. 0.86
   2 ?    4.2   0.1     0.012        43      36      58 ..     143     165 ..     136     208 .. 0.80
   3 ?   -0.4   0.0      0.31   1.1e+03      45      62 ..     221     238 ..     183     301 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00083
                       B12-binding  40 nedivaairaekpdvvglSal.....ltsqleavkelvellkrirprvkv 84 
                                       +++++aa+++   d v+l+++     + +  ++++++++++k+++p + v
  gi|313125083|ref|YP_004035347.1|  88 PANVAAAVAEIGLDYVVLTSVdrddlPDQGASHFAQTIREIKQRDPSILV 137
                                       38899999999*******99999999********************9877 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.012
                       B12-binding  36 anvenedivaairaekpdvvglS 58 
                                         + +e+ v++i++ kpdv++  
  gi|313125083|ref|YP_004035347.1| 143 DFQGDEEAVRKIIDAKPDVIAHN 165
                                       33445999************975 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.31
                       B12-binding  45 aairaekpdvvglSallt 62 
                                       + +r+ ++dvv l ++l+
  gi|313125083|ref|YP_004035347.1| 221 SDLREADVDVVTLGQYLQ 238
                                       455555555555544422 PP

>> BKACE  beta-keto acid cleavage enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     1e-05     0.036      22     117 ..      82     179 ..      76     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                                       --SHHHHHHHHHHHHHHTESEEEE-EE-TTTS-EE--HHHHHHHHHHHHHHHTTSEEEE-SSTTTTG-HHHHHTHHH CS
                             BKACE  22 PvtpeeiaeeaveaaeaGAaivHlHaRdpedgrpsldpelyrevlarirekepdviinlttggastmsaeerlavle 98 
                                       P+ p+e a+ a++ ae G   v l   d  d+ p + ++++++++++i++++p +++ + +   + + +ee ++ + 
  gi|313125083|ref|YP_004035347.1|  82 PLDPDEPANVAAAVAEIGLDYVVLTSVD-RDDLPDQGASHFAQTIREIKQRDPSILVEVLIP--DFQGDEEAVRKII 155
                                       999******************9999999.78*****************************99..5556788888766 PP

                                       HH--SEEEEE-S-EEEB-.....S CS
                             BKACE  99 alkpemasldlgslnfgl.....k 117
                                         kp++++ ++ ++   +     +
  gi|313125083|ref|YP_004035347.1| 156 DAKPDVIAHNIETVERLQwpvrdR 179
                                       67********99987744444331 PP

>> DUF2090  Uncharacterized protein conserved in bacteria (DUF2090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00062       2.2     209     237 ..       6      34 ..       5      36 .. 0.94
   2 ?    2.0   0.0     0.024        84     221     260 ..     185     224 ..      79     244 .. 0.84
   3 ?   -2.3   0.0      0.48   1.7e+03     144     172 ..     245     273 ..     233     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00062
                           DUF2090 209 kPdWwkleplsaeaweeiealieerdpyc 237
                                       kPdW+k+ p s   +++i++ +++rd ++
  gi|313125083|ref|YP_004035347.1|   6 KPDWLKMRPPSGRRFTDIKQTLRDRDLHT 34 
                                       7************************9875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.024
                           DUF2090 221 eaweeiealieerdpycrGvvlLGldapaeelaagfeaaa 260
                                       ++ + +e++ +e+d y++  ++LGl    +e+ ++++  +
  gi|313125083|ref|YP_004035347.1| 185 QSLSVLEQVKRESDIYTKTSIMLGLGEYDHEIYQTLSDLR 224
                                       45556778888999999*99****9998888888877655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.48
                           DUF2090 144 kclvfyHPddeaelraeqeaklkelyeaa 172
                                        +  ++HPd   + r+  e +l  ly a+
  gi|313125083|ref|YP_004035347.1| 245 DVFEYVHPDAFETWRQVAEDELGFLYCAS 273
                                       56678999999999999999998888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1719.14
//
Query:       gi|313125084|ref|YP_004035348.1|  [L=448]
Description: hypothetical protein Hbor_02990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-30  102.9   1.6    2.3e-29  101.4   1.3    2.0  2  DUF4157        Domain of unknown function (DUF4157)
  ------ inclusion threshold ------
      0.023   15.0   0.1      0.042   14.2   0.1    1.4  1  Peptidase_M91  Effector protein
       0.14   10.6   0.0       0.18   10.2   0.0    1.1  1  Cohesin_load   Cohesin loading factor


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   1.3   3.9e-33   2.3e-29       2      78 ..      71     147 ..      70     148 .. 0.97
   2 ?   -2.2   0.0      0.86   5.1e+03      19      33 ..     292     306 ..     286     310 .. 0.77

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 3.9e-33
                           DUF4157   2 lpeavraemerafgadlsdVrvhtgsaaaraaralgAqAfTlgndivfaageyqpesaagrellaHELtHvvqqreg 78 
                                       l++++++ me+++g++l+dVr+htg+ aa+a+++++A+AfT+gn+i+f++gey+ +sa+g+++laHEL+Hv qq++g
  gi|313125084|ref|YP_004035348.1|  71 LETSIQRTMEERMGDNLGDVRIHTGPLAAKACEEINARAFTVGNHIAFNHGEYDLSSAEGQHVLAHELAHVRQQTGG 147
                                       7899**********************************************************************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.86
                           DUF4157  19 sdVrvhtgsaaaraa 33 
                                       + Vr+ tg++a++  
  gi|313125084|ref|YP_004035348.1| 292 DPVRFMTGEEANEWH 306
                                       679*****9998765 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   7.1e-06     0.042      68     135 ..     108     170 ..      52     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.1e-06
                     Peptidase_M91  68 kgegtdaeinynpafsseeegkegrPsavLyHElaHaydalngtlddgeydgkdeedssgvpneErqA 135
                                       + ++ +++i +n         +  + ++vL+HElaH+++++ g +   +++gk e d ++  + Er+A
  gi|313125084|ref|YP_004035348.1| 108 RAFTVGNHIAFNHGEYDL---SSAEGQHVLAHELAHVRQQTGGAVSLLPQEGKLEIDPDK--RLEREA 170
                                       556667777777775555...6677789***************99988888887777766..555555 PP

>> Cohesin_load  Cohesin loading factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.1e-05      0.18     545     596 ..     231     283 ..     217     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.1e-05
                      Cohesin_load 545 kser.alqlakksidysdglWvlvaetilaqlleqlgerakaeqteesldals 596
                                        s + +++ a  +i+  d lW+++++ti+++  ++++e++  + +e+ ld+++
  gi|313125084|ref|YP_004035348.1| 231 ESFEgNRKKAVEQIRQNDDLWTSLLRTIAMDVIQSSIEANGTNVIEDALDRYH 283
                                       4444599999999*************************999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2573.27
//
Query:       gi|313125085|ref|YP_004035349.1|  [L=112]
Description: hypothetical protein Hbor_03000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.024   14.3   0.0      0.028   14.1   0.0    1.1  1  Carbam_trans_N  Carbamoyltransferase N-terminus


Domain annotation for each model (and alignments):
>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.6e-06     0.028     161     206 ..      49      97 ..      34     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-06
                    Carbam_trans_N 161 prllaveketelkikslvsfse....siGhlYaaateylGfkknsdegKl 206
                                        +lla  ++++   +s+++  +    + G +Y + + ++G+  ns+e+K+
  gi|313125085|ref|YP_004035349.1|  49 RNLLAFDEQGNKLWESEIP-EHserhMFGEIYKENGDIIGWSWNSNEYKI 97 
                                       5677777777777777777.225788***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 629.85
//
Query:       gi|313125086|ref|YP_004035350.1|  [L=35]
Description: hypothetical protein Hbor_03010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 219.04
//
Query:       gi|313125087|ref|YP_004035351.1|  [L=786]
Description: superfamily ii helicase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-25   88.5   0.0    2.2e-24   86.2   0.0    2.0  2  DEAD             DEAD/DEAH box helicase
    6.2e-22   78.0   0.0    8.4e-22   77.6   0.0    1.1  1  Sec63            Sec63 Brl domain
      2e-11   44.2   0.0    3.1e-11   43.6   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit
    1.7e-08   34.8   0.0    1.1e-07   32.2   0.0    2.3  1  Helicase_C       Helicase conserved C-terminal domain
      4e-06   27.3   0.1    2.5e-05   24.8   0.1    2.3  2  HHH_5            Helix-hairpin-helix domain
     0.0052   16.6   0.0      0.018   14.9   0.0    1.8  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.0   7.2e-28   2.2e-24       2     175 ..      21     184 ..      20     185 .. 0.84
   2 ?   -1.0   0.0      0.44   1.3e+03      80     113 ..     406     437 ..     393     449 .. 0.67

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 7.2e-28
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       ++Q+ea p+il ++++v++aa+T+sGKT+ + +++++++     ++   al+++P+r+L+++  +++++f + ++++
  gi|313125087|ref|YP_004035351.1|  21 RMQREAAPAILeRDENVVAAAPTASGKTALAELAICRAL-----RNDGTALFIAPLRALTNEKESEWERFEE-LGYS 91 
                                       68*********5557*********************999.....45568*******************9999.6878 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH....HCTSSH...CTTEEEEEEETHHHHHHTTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddll....stgkln...lsqvrflVlDEadrlldqgfsdfinriln 147
                                       v +++g+ +   + ++  +++di+v+tp++ d+ +    s    +   + +v + V+DE++ l ++ ++  ++  ++
  gi|313125087|ref|YP_004035351.1|  92 VYVVTGERDL--NPRRA-ERADILVMTPEKTDSATrkheSA---RysfITDVDCCVIDEVHLLDSDTRGGVLEVTVS 162
                                       8777775444..44444.67*************88655333...244699*************************** PP

                                       HSHHHCTTSTTTSEEEEEESSBSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 148 qlpqitcdgklqrqvivlSATlpkdvkk 175
                                       +l++i cd +    v++lSAT+p +v++
  gi|313125087|ref|YP_004035351.1| 163 RLRRI-CDPR----VVALSATMP-NVED 184
                                       **655.6655....********9.7765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                                       EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  80 liiggvaardqlskldngvdivvgtpgrlddlls 113
                                         i++  a+d  s+l  +++i +gt g l d++s
  gi|313125087|ref|YP_004035351.1| 406 KEIESRLAEDLDSHL--NAEIAMGTIGDLEDVMS 437
                                       444444445555555..69***********9884 PP

>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.0   2.8e-25   8.4e-22       2     151 ..     488     688 ..     487     741 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 2.8e-25
                                       CHHHHHHHHHT--HHHHHHHHHHS-TT-.-HHHHHHHHHTSGGGGGS---TTHHHHHHHHHHTSSS--SSSTTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             Sec63   2 telGriaShYyisyetiklfneslkpnt.tlkdlLeilssasEFeeipvReeEkkelkkLlekvpikvkediespea 77 
                                       t lGr+aS+Yy++ +t + f + + ++t t++++Le ++ a+EF +++ R+ E + ++++l      v++++e+   
  gi|313125087|ref|YP_004035351.1| 488 TRLGRLASKYYLRLDTARRFASLCDRDTiTDESILETVAGAAEFHDVSARQSEMDAVDSVLTG----VDTTLEDGPR 560
                                       89***********************9999********************************77....67899***** PP

                                       HHHHHHHHHHTT---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHTS-TT......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                             Sec63  78 KvniLlqayisrlklegsdlvsDlkyilqnairilralveillskgwlslalslleLskmveqrlwds......... 145
                                       Kv  +l a +s+++ + sdl sD++ i qn+ r+l+al e++ +   +++a+ + ++   ve+++  +         
  gi|313125087|ref|YP_004035351.1| 561 KVLAILYAGMSNST-P-SDLRSDAWVIRQNGLRLLSALREFVDAFAGPRAANLARRVEARVEHGVSRDavaltavdg 635
                                       ************99.4.7**********************************************9977799999999 PP

                                       ...............................................S--EEE CS
                                       ...............................................xxxxxx RF
                             Sec63 146 ...............................................lPklei 151
                                                                                      +P+++i
  gi|313125087|ref|YP_004035351.1| 636 igpnrasklatgglrsprdvveagtaeltqaglsdgvakqvvqnarnFPDIDI 688
                                       99999999999999999999999999999999999999999999999999998 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0     1e-14   3.1e-11       4     170 ..      19     180 ..      16     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1e-14
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       ++ +Q ea  ++l     +rd++++ +++T +GKT +a ++++++l++ g    +lf++p ++l++  ++e+++f +
  gi|313125087|ref|YP_004035351.1|  19 FNRMQREAAPAIL-----ERDENVVAAAPTASGKTALAeLAICRALRNDG---TALFIAPLRALTNEKESEWERFEE 87 
                                       6788999999998.....89******************888888888864...69********************** PP

                                       G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......T CS
                            ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......s 149
                                         y     +v+g+++ +  ++++ ++ilv+t ++ d++ ++  e       +  d+ +iDE+H l +++       +
  gi|313125087|ref|YP_004035351.1|  88 LGY--SVYVVTGERDLN-PRRAERADILVMTPEKTDSATRK-HESARYSFITDVDCCVIDEVHLLDSDTrggvlevT 160
                                       999..677888888887.789999***************44.4444445556667************7455444444 PP

                                       THHHHHT---SEEEEEESS-S CS
                            ResIII 150 wreilekfkeavllglTATpe 170
                                       + + l+ + +  +++l+AT++
  gi|313125087|ref|YP_004035351.1| 161 VSR-LRRICDPRVVALSATMP 180
                                       444.55566689999999975 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   3.6e-11   1.1e-07       3     111 .]     226     379 ..     224     379 .. 0.65

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 3.6e-11
                                       HHHHHHHH....HHTTTTSEEEEEESSHH.HH...........................HHHHHHHHHT........ CS
                        Helicase_C   3 leallell....kleeeggkilifvntid.rl...........................ekvklllekk........ 39 
                                       +++l++ +    ++ ++gg++l+fv +++ ++                           e +k l   +        
  gi|313125087|ref|YP_004035351.1| 226 YRRLYRAIdlseQHIRDGGQALVFVSSRQdTVraagkardelgkrdipigargdydfhnE-AKEL---Sndslrkav 298
                                       555666655566666778888888888885224455555555555555555554433321.2222...012233335 PP

                                       TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS..........SSHHHHHHHHTT CS
                        Helicase_C  40 gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp..........rnvtsyiqriGR 106
                                          v  +h+ l +++r+++ + f++g++++L +t+ ++ G+++p   +Vi  d +           ++ ++ q+ GR
  gi|313125087|ref|YP_004035351.1| 299 PDGVGFHHAGLAKDDRDKVEAWFKEGKIQLLFSTSTLAWGVNLPARCVVI-RDTKyhdplegevdISPLDILQMLGR 374
                                       5667779999**********************************666666.44443344554444446********* PP

                                       SSSTT CS
                        Helicase_C 107 tgRag 111
                                       +gR g
  gi|313125087|ref|YP_004035351.1| 375 AGRPG 379
                                       ***75 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.2   3.5e+03      11      31 ..     558     580 ..     558     583 .. 0.83
   2 !   24.8   0.1   8.3e-09   2.5e-05       4      56 ..     630     681 ..     627     682 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                                       -HHHHHHHHTTT--..SHHHHHH CS
                             HHH_5  11 GpktAlallsaGie..svedlaa 31 
                                       Gp+ +la+l aG++  ++ dl +
  gi|313125087|ref|YP_004035351.1| 558 GPRKVLAILYAGMSnsTPSDLRS 580
                                       99*******99988667888875 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 8.3e-09
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       L+ v+GiGp +A +l+ +G +s+ d+++a ++eL+++ G++   A+++++ ++
  gi|313125087|ref|YP_004035351.1| 630 LTAVDGIGPNRASKLATGGLRSPRDVVEAGTAELTQA-GLSDGVAKQVVQNAR 681
                                       999*********************************9.998888888887665 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.9e-06     0.018       3      37 ..     630     665 ..     629     668 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.9e-06
                   DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyakGirtledlra.krakLtr 37 
                                       +t v G+Gp +A+k+   G+r+  d+++ ++a+Lt+
  gi|313125087|ref|YP_004035351.1| 630 LTAVDGIGPNRASKLATGGLRSPRDVVEaGTAELTQ 665
                                       68899***********************98899996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (786 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 4819.69
//
Query:       gi|313125088|ref|YP_004035352.1|  [L=216]
Description: haloacid dehalogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-25   90.3   0.0    1.7e-25   90.1   0.0    1.0  1  HAD_2            Haloacid dehalogenase-like hydrolase
    3.4e-14   53.6   0.2    4.8e-13   49.9   0.2    2.0  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.8e-09   36.5   0.1    9.3e-09   35.2   0.1    1.6  1  Hydrolase_like   HAD-hyrolase-like
    3.1e-07   31.0   0.7    4.3e-07   30.5   0.7    1.3  1  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
        0.2   11.5   0.0       0.76    9.6   0.0    1.9  2  INT_SG_DDX_CT_C  INTS6/SAGE1/DDX26B/CT45 C-terminus


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   4.8e-29   1.7e-25       1     177 [.       8     186 ..       8     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 4.8e-29
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkk.. 75 
                                       ++FD+Dg+l+d+e+++ q+   ++    + e  +   +++ g+++re++++l e++ +  + +e++  y ++ +   
  gi|313125088|ref|YP_004035352.1|   8 VLFDMDGVLVDSETYWHQFEDDWVFAAAI-ESGDPSHEEVTGMNYREIYDYLSETYGTTVTKAEFVAAYDDRAQSly 83 
                                       79*********************966655.8999999*********************99999999***99999999 PP

                             HAD_2  76 .kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk.KPdpeviekaleklkl 150
                                        ++v+++dg++ l +++++ g +lgiv+s  ++ +    +++g+ + +d +++++d+ k+ KP+p ++e a e  +l
  gi|313125088|ref|YP_004035352.1|  84 gEQVRLMDGANALFDDIRDDGRQLGIVSSAPQDWIGIVRDRFGL-DPLDLVLSADDIDKPgKPEPHIYEHAAEAVGL 159
                                       9******************************************7.899**********999**************** PP

                             HAD_2 151 kkeeviyvGDsptDieaakkagikvia 177
                                       +++++++v+Ds +++eaa +ag  ++a
  gi|313125088|ref|YP_004035352.1| 160 DPQSCVVVEDSVHGVEAAVRAGAFTVA 186
                                       **********************99887 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.2   1.3e-16   4.8e-13       3     210 .]       7     181 ..       6     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.3e-16
                                       EEEEESBTTTBCHH...HHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHH CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   3 tvvfDkdGTLttge...psvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpew 76 
                                       +v+fD+dG+L+++e   ++ ed +v a                     aa +   ++ ++++         +   ++
  gi|313125088|ref|YP_004035352.1|   7 AVLFDMDGVLVDSEtywHQFEDDWVFA---------------------AAIESGDPSHEEVTG-----MNYREIYDY 57 
                                       89************5555555555555.....................566655666677777.....666666777 PP

                                       HHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  77 ltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraan 153
                                       l +           g+  ++++ va  ++ra  ++  +    ++++a  ++  +++ g +++++++  +     + +
  gi|313125088|ref|YP_004035352.1|  58 LSET---------YGTTVTKAEFVAAYDDRAQSLYGEQVR--LMDGANALFDDIRDDGRQLGIVSSAPQDWIGIVRD 123
                                       7777.........888888888888887777777777766..*******************************9999 PP

                                       HTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 154 qlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       ++G d +d v+++d+    +kp+p ++++a++  + +p+ +++V+D+v +++a+ +Ag
  gi|313125088|ref|YP_004035352.1| 124 RFGLDPLDLVLSADDIDkPGKPEPHIYEHAAEAVGLDPQSCVVVEDSVHGVEAAVRAG 181
                                       9**666755555555444************************************9998 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   2.6e-12   9.3e-09       3      61 ..     143     200 ..     142     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.6e-12
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHH CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleep 61 
                                       gKPep +y+ a+e++g+dp+ ++++ D+  + +++A +aG+ +v++++  +++ dl+++
  gi|313125088|ref|YP_004035352.1| 143 GKPEPHIYEHAAEAVGLDPQSCVVVEDS-VHGVEAAVRAGAFTVAYRSTHNAELDLSRA 200
                                       9***************************.******************999988887744 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.7   1.2e-10   4.3e-07       1     180 [.       8     170 ..       8     211 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.2e-10
                               HAD   1 alfDfDgTLldgdsle.lllrfllrrgaprlwralreklllalfrellrl..draglaelleallaglseelaaele 74 
                                       +lfD+Dg L+d+++++  + + ++   a + ++  +e+     +re+ ++  +  g+    +++ a+++++     +
  gi|313125088|ref|YP_004035352.1|   8 VLFDMDGVLVDSETYWhQFEDDWVFAAAIESGDPSHEEVTGMNYREIYDYlsETYGTTVTKAEFVAAYDDRAQSLYG 84 
                                       79**************9555556655555556666666444444444444001123344444445555544444444 PP

                               HAD  75 rfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg...adevlatelevddrltgelglegkp 148
                                       + v      +l+  ga +l++  r+ G ++ +vS++++ ++ ++ +++g    d vl+      d++++ +++e+++
  gi|313125088|ref|YP_004035352.1|  85 EQV------RLM-DGANALFDDIRDDGRQLGIVSSAPQDWIGIVRDRFGldpLDLVLSA-----DDIDKPGKPEPHI 149
                                       444......255.9***********************************5555555555.....2777774444444 PP

                               HAD 149 vrgegkvaalrewlaaegegidleevvayGDs 180
                                          +      ++       g+d+ ++v++ Ds
  gi|313125088|ref|YP_004035352.1| 150 YEHA-----AEA------VGLDPQSCVVVEDS 170
                                       4433.....333......44444445544444 PP

>> INT_SG_DDX_CT_C  INTS6/SAGE1/DDX26B/CT45 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00021      0.76      18      43 ..      48      73 ..      44      75 .. 0.93
   2 ?   -3.0   0.0       1.8   6.4e+03       9      20 ..      95     106 ..      94     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00021
                   INT_SG_DDX_CT_C 18 grnyekiFklLeevqGslevrkkfve 43
                                      g ny +i++ L+e  G++ ++ +fv 
  gi|313125088|ref|YP_004035352.1| 48 GMNYREIYDYLSETYGTTVTKAEFVA 73
                                      88**********************95 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                   INT_SG_DDX_CT_C   9 qlvkevRrpgrn 20 
                                        l+ ++R  gr+
  gi|313125088|ref|YP_004035352.1|  95 ALFDDIRDDGRQ 106
                                       589999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1289.86
//
Query:       gi|313125089|ref|YP_004035353.1|  [L=245]
Description: nuclease of the recb family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-08   34.4   0.0    1.9e-08   34.0   0.0    1.1  1  NucS             Endonuclease NucS
      5e-07   29.4   1.6    2.9e-06   26.9   0.1    2.4  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
      0.036   14.2   3.2        5.3    7.2   0.1    3.2  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
      0.048   13.6   3.6       0.95    9.5   3.1    2.4  1  zinc-ribbons_6   zinc-ribbons
      0.056   12.9   2.4        1.7    8.1   0.1    3.1  3  zf-ribbon_3      zinc-ribbon domain
      0.083   13.1  15.9       0.13   12.5   0.2    3.7  3  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.11   11.9   0.2       0.11   11.9   0.2    2.6  3  zf-TFIIB         Transcription factor zinc-finger
       0.23   12.0   0.2       0.23   12.0   0.2    2.5  3  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.37   10.4   2.5        2.7    7.7   0.1    2.7  3  zf_UBZ           Ubiquitin-Binding Zinc Finger
        1.4    8.9   8.3        4.4    7.4   0.3    3.6  3  ADK_lid          Adenylate kinase, active site lid
          2    8.6   9.2        1.2    9.3   3.0    3.5  3  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.1e-11   1.9e-08       3      88 ..       4      86 ..       2      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.1e-11
                              NucS  3 avlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeeeLk 81
                                      +++v    C+ ++eG  +sr + g+ ++v+kpd ++lvh    ++Pv W + + slt+e +++ + l  + r  e+ L+
  gi|313125089|ref|YP_004035353.1|  4 TIRVFAGDCTTTFEG-SRSRTQRGRVVVVVKPDRTVLVHDADGYQPVSWLTRPDSLTVETDRSGFGL--VARADEQVLR 79
                                      57888899*******.599**************************************8888777765..6777788888 PP

                              NucS 82 veieeve 88
                                      +  +e  
  gi|313125089|ref|YP_004035353.1| 80 IRSHETS 86
                                      8888766 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.22   3.5e+02       1       8 [.     136     143 ..     136     148 .. 0.82
   2 !   26.9   0.1   1.8e-09   2.9e-06       3      37 ..     179     213 ..     177     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                                       -EE-SSS- CS
                    zf-C4_Topoisom   1 vekCPkCg 8  
                                       +e+C+ Cg
  gi|313125089|ref|YP_004035353.1| 136 DETCDDCG 143
                                       589****9 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.8e-09
                                       E-SSS--EEEE.EE-SSSEEEEESST.T----EEB- CS
                    zf-C4_Topoisom   3 kCPkCggdLvl.krgkkGkFvGCsnYPeCkftkklk 37 
                                       +CP Cg++L + +rg +    GCs YP+C+++ +++
  gi|313125089|ref|YP_004035353.1| 179 TCPDCGSPLSIiRRGGR-LLAGCSAYPDCETAFSIP 213
                                       7*******965155544.99**********998876 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.011        18      15      26 ..     135     146 ..      87     151 .. 0.86
   2 ?    7.2   0.1    0.0032       5.3      16      26 ..     177     187 ..     163     191 .. 0.84
   3 ?    0.1   0.1      0.53   8.6e+02      21      27 ..     222     228 ..     205     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                          zf-Mss51  15 vdfeCpdCGipt 26 
                                       vd +C dCG+p 
  gi|313125089|ref|YP_004035353.1| 135 VDETCDDCGLPK 146
                                       6779******96 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0032
                          zf-Mss51  16 dfeCpdCGipt 26 
                                       + +CpdCG p 
  gi|313125089|ref|YP_004035353.1| 177 EWTCPDCGSPL 187
                                       679*****997 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.53
                          zf-Mss51  21 dCGipty 27 
                                       dCG+p++
  gi|313125089|ref|YP_004035353.1| 222 DCGLPVF 228
                                       9****97 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.1   0.00058      0.95      16      46 ..     160     194 ..     138     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00058
                                       EEE-TTT--....EEEEEEE-SSS-S---EEEETT CS
                    zinc-ribbons_6  16 qyhCeaCqe....dlkkealCpeCeqelevlkaCg 46 
                                          Ce+ ++    +++ e +Cp+C+++l++++  g
  gi|313125089|ref|YP_004035353.1| 160 DRACESLDDavrdRFDDEWTCPDCGSPLSIIRRGG 194
                                       444554444777799**************998765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.034        56      16      25 ..     136     145 ..     133     145 .. 0.86
   2 ?   -2.0   0.0       1.6   2.6e+03      22      25 ..     151     154 ..     149     155 .. 0.54
   3 ?    8.1   0.1    0.0011       1.7      18      26 .]     179     187 ..     175     189 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.034
                       zf-ribbon_3  16 dnvCpyCGtk 25 
                                       d +C  CG +
  gi|313125089|ref|YP_004035353.1| 136 DETCDDCGLP 145
                                       779*****75 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                       zf-ribbon_3  22 CGtk 25 
                                       CG++
  gi|313125089|ref|YP_004035353.1| 151 CGAV 154
                                       6654 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0011
                       zf-ribbon_3  18 vCpyCGtkl 26 
                                       +Cp CG++l
  gi|313125089|ref|YP_004035353.1| 179 TCPDCGSPL 187
                                       466666554 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   7.7e-05      0.13       9      28 ..     130     149 ..     128     160 .. 0.78
   2 ?    6.6   0.6    0.0055       8.9      17      25 ..     179     187 ..     177     195 .. 0.89
   3 ?    2.9   1.4     0.078   1.3e+02      18      36 ..     221     236 ..     218     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.7e-05
                     Auto_anti-p27   9 kGwtMLaetCpvCgvPLmrd 28 
                                        G+t  +etC++Cg P    
  gi|313125089|ref|YP_004035353.1| 130 AGATVVDETCDDCGLPKISA 149
                                       69*************97665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0055
                     Auto_anti-p27  17 tCpvCgvPL 25 
                                       tCp+Cg+PL
  gi|313125089|ref|YP_004035353.1| 179 TCPDCGSPL 187
                                       8*******9 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.078
                     Auto_anti-p27  18 CpvCgvPLmrdrkggkvyC 36 
                                       C+ Cg P +++  +g+  C
  gi|313125089|ref|YP_004035353.1| 221 CD-CGLPVFETA-RGR-RC 236
                                       85.*******96.344.45 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       1.4   2.2e+03      21      26 ..     138     143 ..     134     143 .. 0.82
   2 ?   11.9   0.2   6.7e-05      0.11       2      23 ..     180     201 ..     179     207 .. 0.90
   3 ?   -1.1   0.2      0.72   1.2e+03      15      23 ..     214     222 ..     204     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                          zf-TFIIB  21 yCpqCr 26 
                                       +C++C+
  gi|313125089|ref|YP_004035353.1| 138 TCDDCG 143
                                       799997 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.7e-05
                          zf-TFIIB   2 CPkCqdeleeserggveidyCp 23 
                                       CP C+++l +++rgg ++  C 
  gi|313125089|ref|YP_004035353.1| 180 CPDCGSPLSIIRRGGRLLAGCS 201
                                       ***************9998885 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.72
                          zf-TFIIB  15 ggveidyCp 23 
                                        gv +d C+
  gi|313125089|ref|YP_004035353.1| 214 AGVVVDDCD 222
                                       689999996 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9     3e+03       9      24 ..      10      25 ..       6      33 .. 0.70
   2 ?   -2.8   0.1         6   9.7e+03       8      12 ..     139     143 ..     138     147 .. 0.83
   3 ?   12.0   0.2   0.00014      0.23       8      32 ..     180     203 ..     178     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                   Zn_ribbon_recom  9 geCGspmtrrkrkgkr 24
                                      g+C  ++ +++++ +r
  gi|313125089|ref|YP_004035353.1| 10 GDCTTTFEGSRSRTQR 25
                                      8999999997665333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6
                   Zn_ribbon_recom   8 CgeCG 12 
                                       C +CG
  gi|313125089|ref|YP_004035353.1| 139 CDDCG 143
                                       999*9 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00014
                   Zn_ribbon_recom   8 CgeCGspmtrrkrkgkrhyYrCsty 32 
                                       C +CGsp++  +r g+r    Cs+y
  gi|313125089|ref|YP_004035353.1| 180 CPDCGSPLSIIRR-GGRLLAGCSAY 203
                                       ***********99.78877777777 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.13   2.1e+02       4       9 ..     138     143 ..     136     146 .. 0.87
   2 ?   -3.5   0.0         5   8.2e+03       7      12 ..     150     155 ..     149     156 .. 0.77
   3 ?    7.7   0.1    0.0016       2.7       1      13 [.     176     188 ..     176     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.13
                            zf_UBZ   4 lCerCg 9  
                                       +C++Cg
  gi|313125089|ref|YP_004035353.1| 138 TCDDCG 143
                                       8****9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5
                            zf_UBZ   7 rCgkei 12 
                                       +Cg+ +
  gi|313125089|ref|YP_004035353.1| 150 ECGAVF 155
                                       8*9987 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0016
                            zf_UBZ   1 dtylCerCgkeip 13 
                                       d ++C++Cg++++
  gi|313125089|ref|YP_004035353.1| 176 DEWTCPDCGSPLS 188
                                       679******9876 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2     2e+03      26      33 ..     105     112 ..     104     112 .. 0.84
   2 ?    3.2   2.0     0.054        89      20      29 ..     135     144 ..     126     148 .. 0.84
   3 ?    7.4   0.3    0.0027       4.4      19      31 ..     175     187 ..     146     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                                       TT--.-B- CS
                           ADK_lid  26 kCGepLvq 33 
                                        +GepLv+
  gi|313125089|ref|YP_004035353.1| 105 QTGEPLVR 112
                                       59****95 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.054
                                       STTB-TTT-- CS
                           ADK_lid  20 veglCDkCGe 29 
                                       v+  CD+CG 
  gi|313125089|ref|YP_004035353.1| 135 VDETCDDCGL 144
                                       7899****95 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0027
                                       SSTTB-TTT--.- CS
                           ADK_lid  19 kveglCDkCGepL 31 
                                         e  C +CG+pL
  gi|313125089|ref|YP_004035353.1| 175 DDEWTCPDCGSPL 187
                                       4788899999998 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.7   4.4e+03      10      19 ..      11      20 ..      10      26 .. 0.72
   2 ?    0.4   0.1      0.44   7.1e+02      28      33 ..     138     143 ..     132     147 .. 0.71
   3 ?    9.3   3.0   0.00075       1.2      10      36 ..     150     187 ..     149     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.7
                       Zn-ribbon_8 10 eCghefevlq 19
                                      +C ++fe  +
  gi|313125089|ref|YP_004035353.1| 11 DCTTTFEGSR 20
                                      7999999544 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.44
                       Zn-ribbon_8  28 aCPeCg 33 
                                       +C +Cg
  gi|313125089|ref|YP_004035353.1| 138 TCDDCG 143
                                       577776 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00075
                       Zn-ribbon_8  10 eCghefe.............vlqsisdapltaCPeCgsev 36 
                                       eCg +fe             v+ +++d  + +CP+Cgs++
  gi|313125089|ref|YP_004035353.1| 150 ECGAVFElcvdraceslddaVRDRFDD--EWTCPDCGSPL 187
                                       799999988887666666533333332..566*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1522.87
//
Query:       gi|313125090|ref|YP_004035354.1|  [L=349]
Description: tRNA intron endonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-31  106.0   0.2    3.3e-15   55.5   0.0    2.4  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
    1.9e-30  104.8   0.8      3e-23   81.7   0.0    3.8  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
      0.002   18.3   0.0      0.043   14.0   0.0    2.4  2  tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-t


Domain annotation for each model (and alignments):
>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   5.5e-19   3.3e-15       1      65 [.      10      70 ..      10      72 .. 0.91
   2 !   48.3   0.1   9.5e-17   5.7e-13       3      59 ..     183     241 ..     181     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 5.5e-19
                                      EEEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHH CS
                   tRNA_int_endo_N  1 vegeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfee 65
                                      ++++L +d v v d +a++r+y++++YG+pl++++L+L++vEA++Ll++G+l+     + ++f+e
  gi|313125090|ref|YP_004035354.1| 10 MDATLHDDVVRVGD-DARQRFYDSRGYGRPLDGNRLELAPVEAAHLLSRGDLDDI---DGMEFRE 70
                                      789**********9.*************************************866...5555555 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 9.5e-17
                                       EEEETTEEEESSHHHHHHHHHTTT-SEE.....CCTSSEEEEHHHHHHHHHTTSEEEETTSE CS
                   tRNA_int_endo_N   3 geLsgdrvlvedeeaakrlyekgfYGkp.....lidepLqLslvEAlYLlekGklevvkgge 59 
                                       ++L++drv+    e   ++ye+gfYG++      ++ pLqLsl+E++YL+++G+++v + +e
  gi|313125090|ref|YP_004035354.1| 183 ADLLSDRVVCY--ESPDEVYENGFYGQRlfgrnAEEGPLQLSLIEGAYLARRGVIDVDD-EE 241
                                       789********..999****************9************************94.44 PP

>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   6.5e-07    0.0039       3      56 ..      79     142 ..      77     160 .. 0.75
   2 !   81.7   0.0   5.1e-27     3e-23       1      85 []     254     341 ..     254     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.5e-07
                                       HHHHHHHHHHHTT-EEEEC........GGGTSSEEEE..TSCTTTSSCSEEEEEEETTSEEEHH CS
                     tRNA_int_endo   3 lkyavyrdLrekGyvvrsG........lkFGadFrvY..qrrpslehseylVvvvsedeeldwp 56 
                                       l ++vy+dLr++G+++ +            G dF+vY  +++p  +  ey ++v+ e+e++   
  gi|313125090|ref|YP_004035354.1|  79 LAFVVYKDLRDRGFYLSPAreewpgvsDADGIDFVVYprGKGPTDGDVEYRIRVIGERERVAAA 142
                                       6799***********9975222222222349******99999999999******9999887544 PP

  == domain 2  score: 81.7 bits;  conditional E-value: 5.1e-27
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE...TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY...qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklil 74 
                                       f++++++y++Lr+ G v++sG+kFGadFrvY   ++ +sl+hs  lV+vv  d+++ ++dls +vrla +v+K++++
  gi|313125090|ref|YP_004035354.1| 254 FDRRLKTYAALRDAGSVPKSGFKFGADFRVYtdfETVSSLSHSADLVRVVTPDHAFFPRDLSLDVRLAGGVRKRMVF 330
                                       899************************************************************************** PP

                                       EEETTTSCEEE CS
                     tRNA_int_endo  75 aivdaegdvty 85 
                                       a++da++ +++
  gi|313125090|ref|YP_004035354.1| 331 ALTDANDGIDW 341
                                       ******99988 PP

>> tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   7.1e-06     0.043      24      69 ..      16      61 ..      11      62 .. 0.88
   2 ?    1.6   0.0     0.053   3.2e+02      42      70 ..     210     237 ..     130     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.1e-06
                   tRNA_int_end_N2 24 drvvvvespkarGkhfktmGvsra.rrgrlwLlpeEaLYLvErGsld 69
                                      d vv+v ++ ar  +  + G+ r    +rl+L p Ea +L+ rG ld
  gi|313125090|ref|YP_004035354.1| 16 DDVVRVGDD-ARQRFYDSRGYGRPlDGNRLELAPVEAAHLLSRGDLD 61
                                      678888744.899999999988888*******************997 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.053
                   tRNA_int_end_N2  42 mGvsra.rrgrlwLlpeEaLYLvErGsldi 70 
                                       +G  r+ ++g l L   E  YL+ rG +d+
  gi|313125090|ref|YP_004035354.1| 210 FG--RNaEEGPLQLSLIEGAYLARRGVIDV 237
                                       55..3449999999999999***9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2365.27
//
Query:       gi|313125091|ref|YP_004035355.1|  [L=538]
Description: tryptophanyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-43  146.6   0.0    4.7e-26   91.8   0.0    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   2.6e-30   4.7e-26       4     175 ..      92     254 ..      89     272 .. 0.90
   2 !   52.7   0.0   2.1e-18   3.8e-14     164     293 .]     374     506 ..     372     506 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 2.6e-30
                                       S--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTC CS
                      tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgl 80 
                                       +p++v+sG++PTg++H+G+ +++  +++ q++g +++ liaDl+A   + +  +++++ k+++++  +   +la g+
  gi|313125091|ref|YP_004035355.1|  92 DPFAVLSGFMPTGDPHIGHKLVFDEIIWHQQQGGDAYGLIADLEAHSARGM--TWEEIDKHARDYLLS---LLALGF 163
                                       6899**************8888888888888********************..9**************...****** PP

                                       HTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS.S.C--BHHHHHHHHHHHHHHHHTCHSEEE CS
                      tRNA-synt_1b  81 dpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee.g.egislgeftYplLqaaDilllkadlvp 155
                                       dpe+ e++ qs+  + ++l   l + +++ + + ++ f+s  +++++ +    ++++++Yp+L++      k+++ p
  gi|313125091|ref|YP_004035355.1| 164 DPEEGELYRQSDNRQLQDLSFELGSKANFSEFEAIYGFDS-GTNVSHlQsVVTQMADILYPQLDE-----PKPTVIP 234
                                       ****************************************.666666433346899999999964.....5999*** PP

                                       EEGGGHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 156 gGsDQkqnielgrdlarrfn 175
                                       +G DQ+ +++l+rdla r++
  gi|313125091|ref|YP_004035355.1| 235 VGPDQDPHVRLARDLAARMR 254
                                       *****************985 PP

  == domain 2  score: 52.7 bits;  conditional E-value: 2.1e-18
                                       HHHHHHHHHHHHHH...STTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHH CS
                      tRNA-synt_1b 164 ielgrdlarrfnkk...evfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evek 235
                                       +e++ +lar+++ +     f  p++++++++tgl+G+ KmS+S + s I L+d++e+ + k+++a+t  +e  e ++
  gi|313125091|ref|YP_004035355.1| 374 FEAADELAREVEVEhggYGFVAPSSIYHRFMTGLTGG-KMSSSIPASHISLLDDPEDGYNKVKSATTGGREtaEKQR 449
                                       688999999999999999*******************.********************************9888888 PP

                                       HHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 236 llklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                        l +    ++ ++e + ++++ ++ + a+e++ e+v ++  +g +k+++ae ++++le
  gi|313125091|ref|YP_004035355.1| 450 ELGGEADKCP-VYELYAYLLSGDDDEFAKEVYDECVGGERLCGGCKEQAAELMRAFLE 506
                                       8999999999.*******999999899***************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3511.98
//
Query:       gi|313125092|ref|YP_004035356.1|  [L=322]
Description: ornithine cyclodeaminase, mu-crystallin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-59  200.7   0.2    3.1e-59  200.5   0.2    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
     0.0077   16.3   0.0      0.014   15.4   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.5   0.2   3.4e-63   3.1e-59       5     316 ..       6     313 ..       2     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 3.4e-63
                                       EE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCG.TEEEEEEEEEETTTTEEEEEEEEEETTTCCC CS
                   OCD_Mu_crystall   5 vltaveveeelllddlakaveeafrrlasgkvkkpprvalevkds.rgelevmpaylagrellgvKlvnshpenkks 80 
                                       vl+ ++v ++l+l+dl++ +e af +   g+v++ppr + +v  +  g    mpay  g  ++++Kl  +h++n ++
  gi|313125092|ref|YP_004035356.1|   6 VLSDEQVASLLSLSDLLPEIERAFLKQGRGEVERPPRPHYPVGTEtPGTALTMPAYVHGDPTYATKLAAVHESNAEK 82 
                                       788999********************************999977769************88**************** PP

                                       TSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEE CS
                   OCD_Mu_crystall  81 glptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikev 157
                                       glptv+a +   d etG p a + +t +t+ RT+ ++++aa+ La +   +l+++GaG+qa+ q++a+    ++++v
  gi|313125092|ref|YP_004035356.1|  83 GLPTVNAQIAVTDAETGLPRAYLAGTRVTNARTGCIGGLAARELADAP-VRLGVFGAGAQARWQTRAIASATNLERV 158
                                       ********************************************9875.579************************* PP

                                       EEE-SSHHHHHHHHHHCCS...CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB CS
                   OCD_Mu_crystall 158 riydrdeeaaekfaenlqe..fefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteL 232
                                       riy+ +e+ a+ +a+ l+e   +++vsa++s+  + +g ++vvt+T++++p++    ++pG+++ a+ga  +  +eL
  gi|313125092|ref|YP_004035356.1| 159 RIYAPSESRAQ-CASDLRErlSDVAVSAVESPDPVLDGSNVVVTATTSTEPVFDGARLEPGTLVVAIGAFTESMREL 234
                                       ****9988765.6666666555******************************************************* PP

                                       -HHHHHCC.EEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHH CS
                   OCD_Mu_crystall 233 dddilkra.difvdseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaak 308
                                       d + ++ra ++f d ++   e G+ ++    g   ++   +   +v +   +GR++d+ei++  svG av D ++a 
  gi|313125092|ref|YP_004035356.1| 235 DSETVRRAsRLFADVPEEVAETGDFAY---VG--VDATDLTPFSDVFE-AGTGRENDAEIVVVASVGSAVLDAVTAG 305
                                       *998877626888**************...33..33444555666665.3579************************ PP

                                       HHHHHHCC CS
                   OCD_Mu_crystall 309 lvyeraee 316
                                       + yerae 
  gi|313125092|ref|YP_004035356.1| 306 YLYERAET 313
                                       *****986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.6e-06     0.014      14      96 ..     132     216 ..     121     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                                       EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHH...HHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  14 kvlliGaGemaelvakhLlak.gvkkvvvaNRtlerak...elaeelkgeeiealkleelkellaeadvvisatase 86 
                                       +  + GaG  a+  +++++++ ++++v +   + +ra+   +l+e+l+++   + ++e+ + +l+ ++vv++at s+
  gi|313125092|ref|YP_004035356.1| 132 RLGVFGAGAQARWQTRAIASAtNLERVRIYAPSESRAQcasDLRERLSDV--AVSAVESPDPVLDGSNVVVTATTST 206
                                       56789********99999877699*******9999976444899999777..88888999999************** PP

                                       S-SB-HHHHH CS
                      Shikimate_DH  87 epilekeeve 96 
                                       ep+++ +++e
  gi|313125092|ref|YP_004035356.1| 207 EPVFDGARLE 216
                                       ***9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1905.83
//
Query:       gi|313125093|ref|YP_004035357.1|  [L=384]
Description: glycine/d-amino acid oxidase, deaminating [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-76  258.8   5.6    1.2e-76  258.6   5.6    1.0  1  DAO             FAD dependent oxidoreductase
    8.6e-10   38.2   0.6    1.2e-09   37.8   0.6    1.2  1  FAD_binding_2   FAD binding domain
    1.6e-08   34.1   4.4     0.0018   17.6   2.6    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    8.4e-08   31.8   2.0     0.0028   17.0   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    5.4e-07   29.7   0.6    1.4e-06   28.5   0.6    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.2e-06   28.1   3.2    0.00014   22.4   2.4    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.8e-06   26.3   1.6      0.014   14.1   1.5    2.1  2  HI0933_like     HI0933-like protein
    4.8e-06   26.1   1.6    0.00073   18.9   0.0    2.1  2  Amino_oxidase   Flavin containing amine oxidoreductase
    2.2e-05   24.0   5.0    7.5e-05   22.3   5.0    1.7  1  FAD_oxidored    FAD dependent oxidoreductase
    0.00042   19.6   1.5    0.00065   19.0   1.5    1.2  1  Thi4            Thi4 family
     0.0091   16.4   0.3      0.017   15.5   0.3    1.4  1  NAD_binding_7   Putative NAD(P)-binding
     0.0092   15.3   6.0       0.73    9.0   0.1    2.3  2  FAD_binding_3   FAD binding domain
  ------ inclusion threshold ------
      0.052   12.8   1.2      0.082   12.2   1.2    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.11   12.4   4.9        1.1    9.2   1.4    2.3  2  NAD_binding_9   FAD-NAD(P)-binding
       0.14   11.7   1.0       0.28   10.7   1.0    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.14   11.1   1.4        0.3   10.1   1.4    1.5  1  Lycopene_cycl   Lycopene cyclase protein
       0.24   10.2   2.3       0.31    9.8   1.4    1.6  2  Trp_halogenase  Tryptophan halogenase
        3.9    7.3   5.6        2.1    8.2   2.5    2.1  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
        5.2    6.1   4.6        7.6    5.5   4.6    1.2  1  GIDA            Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.6   5.6   1.3e-79   1.2e-76       1     352 []       2     352 ..       2     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 258.6 bits;  conditional E-value: 1.3e-79
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       ++vi+GGG++Gls+A++La+r   Vt++e+g  +g g++gr++g ++ +++ +p +   ++ls +++  ++ +ee+ 
  gi|313125093|ref|YP_004035357.1|   2 HIVIVGGGVVGLSCAHALAERDanVTVCEAG-TLGGGSTGRAAGGIRMQFS-TPVN---VDLSVASVPVWESFEERF 73 
                                       79******************9889*******.8888**************8.6644...5***************** PP

                                       SSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHHHH CS
                               DAO  76 gididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpaklta 150
                                       g+didyr++G+l+la+++e  ++++ +++++++ g++++ l+++ ++el+p   ++++++a ++p++g++dp+ +++
  gi|313125093|ref|YP_004035357.1|  74 GVDIDYRKNGYLFLAREAETADDFESNVEMQTARGVPSRTLSPADAAELCPElhTEEFVAATYCPEDGVADPHSAVQ 150
                                       ****************99999**********99**********99******96555********************* PP

                                       HHHHHHHHTT-EEEESECEEEEEEEE.TCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT.CTTTSEEEEEEEE CS
                               DAO 151 alaraaealGveilegtevtgleeed.gkvwgverttp.gendaadavVnaaGawsdll.gll.keldlpispvrgq 223
                                       ++ +a+ ++Gv+++++t+vtgl++e+ +  w+v  +tp ++ + ad++VnaaGaw++ + + +    +lpi p+r q
  gi|313125093|ref|YP_004035357.1| 151 GYSQAVTDAGVDVRTNTPVTGLDREEnENRWRV--ETPdETLT-ADYIVNAAGAWARRVgRFAdV--ELPIAPRRRQ 222
                                       **********************77555666***..88866655.5************88344444..55******** PP

                                       EEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHH.........HHHH CS
                               DAO 224 vlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedide.........llea 291
                                         v++p  e     +a  p+  t+d + g y++p ++g+ lvGg+     +d dp+vd++d+ e           e+
  gi|313125093|ref|YP_004035357.1| 223 AAVVEPERE----LDAMHPL--TIDLDSGAYFRPEREGTALVGGHF----ADSDPDVDPDDFSEsadldwtieAVER 289
                                       ****99777....3355555..8999*****************975....444446666644444444444443333 PP

                                       HHHHS....GGGCGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 292 lrklf....PqlgdvlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                       ++++     P+  +v+  waGl++ +pd+  +++e+   +g+++a+G+sghG+++apatG+++ael
  gi|313125093|ref|YP_004035357.1| 290 AADVAgyfgPE-TRVRNGWAGLYAvTPDHHAVVDEV--RPGFVVAAGFSGHGFQHAPATGQCVAEL 352
                                       33333222344.78999*******77*********7..69************************97 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.6   1.3e-12   1.2e-09       2     173 ..       3     178 ..       2     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.3e-12
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SS.GGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeq.kkagikdspelhrtdtlkaldela 77 
                                       ++++G+G+ GL++A+++ae+ ++v+v e +   gg+t  + Ggi +  s++   ++ +   p++  ++ + ++d ++
  gi|313125093|ref|YP_004035357.1|   3 IVIVGGGVVGLSCAHALAERDANVTVCEAGTLGGGSTGRAAGGIRMQFSTPVnVDLSVASVPVWESFEERFGVDIDY 79 
                                       89******************************999*********998766650455555555666666666666555 PP

                                       -HHHHHHHHHTHHHHHHHHHHT.T----BCCTS.......SB-EEE-TT-SSTEEEE-.STT-......HHHHHHHH CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeel.gvpfsrtedg.......pvdvrelGglsatartlhdaadarretlvtghallar 146
                                        ++   +f+++ +e  d +e++  ++  r   g       p d++el    +t + ++ ++ + ++ +++ h  +  
  gi|313125093|ref|YP_004035357.1|  80 -RKNGYLFLAREAETADDFESNvEMQTAR---GvpsrtlsPADAAELCPELHTEEFVAATYCP-EDGVADPHSAVQG 151
                                       .5566667777778889999998666666...4444545599999998888884444433333.2444477777777 PP

                                       HHHHHHTCTEEEEESEEEEEEEECTTE CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgr 173
                                         +++ +agvd++++t+++ L +e+++
  gi|313125093|ref|YP_004035357.1| 152 YSQAVTDAGVDVRTNTPVTGLDREENE 178
                                       777778888************998774 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.6   1.9e-06    0.0018     144     174 ..       2      32 ..       1      49 [. 0.72
   2 !   16.1   0.0   5.5e-06    0.0052     188     252 ..     151     216 ..     142     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlvear 174
                                       +iv+vGgG++G+ +A ala+  ++vt+ ea+
  gi|313125093|ref|YP_004035357.1|   2 HIVIVGGGVVGLSCAHALAERDANVTVCEAG 32 
                                       5677777777777777777777777766664 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.5e-06
                                       HHHHHHHHTTEEEEESCEEEEEEETTEEEE..EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 188 aleealekeGvevklgtsvkeidgngekle..vvledgeeidadlvvvavGvrpstelleeklglel 252
                                        + +a+++ Gv+v+++t v+ +d+++++ +  v++ d++ + ad++v a+G  +++ ++  ++ l++
  gi|313125093|ref|YP_004035357.1| 151 GYSQAVTDAGVDVRTNTPVTGLDREENENRwrVETPDET-LTADYIVNAAGAWARRVGRFADVELPI 216
                                       57889999**************99999444526666665.9**********9999988655555555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.6   4.8e-05     0.045       1      33 [.       4      35 ..       4      38 .. 0.94
   2 !   17.0   0.0   2.9e-06    0.0028      82     135 ..     147     202 ..     123     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      +I+G+G  Gl++a++l + +  ++++ E g++g
  gi|313125093|ref|YP_004035357.1|  4 VIVGGGVVGLSCAHALAERDA-NVTVCEAGTLG 35
                                      7*******************9.79*****9886 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.9e-06
                       Pyr_redox_3  82 ealeYlrevaksfelpiklfeeVesvkk..edegfevetsketyeAkkviiAtGef 135
                                        a++ +++ ++   +++++++ V+ +++  +++  +vet  et++A++++ A+G +
  gi|313125093|ref|YP_004035357.1| 147 SAVQGYSQAVTDAGVDVRTNTPVTGLDReeNENRWRVETPDETLTADYIVNAAGAW 202
                                       4566677777888***************534567********************86 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.6   1.4e-09   1.4e-06       1      44 [.       5      47 ..       5      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.4e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvr 44
                                      IvG+G+ Gl++A++La+++++v++ e++  lGG ++ +  +g+r
  gi|313125093|ref|YP_004035357.1|  5 IVGGGVVGLSCAHALAERDANVTVCEAG-TLGGGSTGRAAGGIR 47
                                      9**************************9.788888877777743 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   2.4   1.5e-07   0.00014       1      31 [.       2      32 ..       2      44 .. 0.94
   2 ?    4.1   0.0     0.075        70      48      72 ..     154     178 ..     145     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.5e-07
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                      ++v+vGgG++gl +A alae  ++Vtv+e++
  gi|313125093|ref|YP_004035357.1|  2 HIVIVGGGVVGLSCAHALAERDANVTVCEAG 32
                                      79**************************975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.075
                                       HHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  48 eklekngievllntkveeiegsedg 72 
                                       + +++ g++v++nt v+ ++ +e++
  gi|313125093|ref|YP_004035357.1| 154 QAVTDAGVDVRTNTPVTGLDREENE 178
                                       567899************9988775 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.5   1.5e-05     0.014       2      33 ..       2      33 ..       1      57 [. 0.88
   2 !   10.2   0.0   0.00023      0.21     112     164 ..     149     201 ..     139     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +++++GgG  Gl +A ++a+r+++V++ e+++
  gi|313125093|ref|YP_004035357.1|  2 HIVIVGGGVVGLSCAHALAERDANVTVCEAGT 33
                                      69***************************985 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHT-EEE-S--EEEEECET.TE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 112 vdallkelkeagvklrletevksvekee.dgkfrvktkseeeleadklvlAtGG 164
                                       v+ + +++++agv++r++t v+++++ee +++ rv+t  +e+l+ad++v A G 
  gi|313125093|ref|YP_004035357.1| 149 VQGYSQAVTDAGVDVRTNTPVTGLDREEnENRWRVET-PDETLTADYIVNAAGA 201
                                       66778999****************7765155789999.9************986 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.5    0.0051       4.8       3      27 ..      12      36 ..      11      40 .. 0.90
   2 !   18.9   0.0   7.7e-07   0.00073     194     266 ..     127     205 ..      50     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0051
                                      HHHHHHHHHHTTEEEEEEESSSSSB CS
                     Amino_oxidase  3 GLaaArqLlsaGfdVtvlEardrvG 27
                                      GL++A+ L+++  +Vtv Ea    G
  gi|313125093|ref|YP_004035357.1| 12 GLSCAHALAERDANVTVCEAGTLGG 36
                                      9*******************86555 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 7.7e-07
                                       HHHHHTSCCCEETTHTHHHHHHHHH.....TTTTEEEETSEEEEEEEEETTCEEEEETTSTEE.EESEEEE-S-HHH CS
                     Amino_oxidase 194 elegfggslllprgGlsqlpealae.....elrgldirlntrVkeikregdgvtvtledgevv.eaDaVvvTvplgv 264
                                       ++e+f + ++ p++G + +  a++      +  g+d+r+nt+V+ ++re+++ + ++e+ +++ +aD++v ++  ++
  gi|313125093|ref|YP_004035357.1| 127 HTEEFVAATYCPEDGVADPHSAVQGysqavTDAGVDVRTNTPVTGLDREENENRWRVETPDETlTADYIVNAAGAWA 203
                                       556666666666777666666666666677889***************9999999999999999******9999887 PP

                                       HH CS
                     Amino_oxidase 265 lk 266
                                        +
  gi|313125093|ref|YP_004035357.1| 204 RR 205
                                       76 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   5.0   7.9e-08   7.5e-05       2     144 ..       3     200 ..       2     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7.9e-08
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee......................... 53 
                                       +v+vGGg+ G+ +A a a+++a+v + e     GG + +++++  +++ ++                          
  gi|313125093|ref|YP_004035357.1|   3 IVIVGGGVVGLSCAHALAERDANVTVCEAGTLGGGSTGRAAGGIRMQFSTPVnvdlsvasvpvwesfeerfgvdidy 79 
                                       8**************************98776666665555565566554447778766663333333344444444 PP

                      FAD_oxidored  54 ........qvvtgiareflerlrqrggarlkkrskwn........................................ 82 
                                               +    +a++f +                n                                        
  gi|313125093|ref|YP_004035357.1|  80 rkngylflAREAETADDFES----------------Nvemqtargvpsrtlspadaaelcpelhteefvaatycped 140
                                       44444444444444444444................1444555555566666667777889999999999******* PP

                      FAD_oxidored  83 .tfepevakavleemlaeagvtvllntrlvevekegkr.iesvtveskegrktirAkvfiDATg 144
                                        + +p+ a + + + +++agv+v +nt +++ ++e+++  + v++     ++t++A++++ A g
  gi|313125093|ref|YP_004035357.1| 141 gVADPHSAVQGYSQAVTDAGVDVRTNTPVTGLDREENEnRWRVETP----DETLTADYIVNAAG 200
                                       **********************************863336777775....79999999999876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.5   6.9e-07   0.00065      19      59 ..       2      40 ..       1      60 [. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.9e-07
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTT CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGawl 59
                                       +vivG+G  GL++a+ la++ d +v++ e+   +GGG+ +
  gi|313125093|ref|YP_004035357.1|  2 HIVIVGGGVVGLSCAHALAER-DANVTVCEAGT-LGGGSTG 40
                                      69*******************.********985.5555433 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   1.8e-05     0.017       9      36 ..       2      29 ..       1      53 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvv 36
                                      ++++vGgG v+++ ++ l+e +a+vtv 
  gi|313125093|ref|YP_004035357.1|  2 HIVIVGGGVVGLSCAHALAERDANVTVC 29
                                      89************************96 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   2.7    0.0024       2.3       4      31 ..       3      30 ..       1      44 [. 0.88
   2 !    9.0   0.1   0.00077      0.73     114     166 ..     155     203 ..     146     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0024
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlve 31
                                      ++IVG+G +Gl+ a+ L+e+  +v++ e
  gi|313125093|ref|YP_004035357.1|  3 IVIVGGGVVGLSCAHALAERDANVTVCE 30
                                      79*****************988888766 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00077
                                       HHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT- CS
                     FAD_binding_3 114 haeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrS 166
                                       + + +g++vr +t v++l ++e++ + +v       +et++a+Y+v a G++ 
  gi|313125093|ref|YP_004035357.1| 155 AVTDAGVDVRTNTPVTGLDREENENRWRVETP----DETLTADYIVNAAGAWA 203
                                       556778**********9988888754444443....468***********987 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.2   8.7e-05     0.082      30      58 ..       2      30 ..       1      59 [. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlD 58
                                      +++++GgGv+Gl+ +++ ++ +a+Vtv++
  gi|313125093|ref|YP_004035357.1|  2 HIVIVGGGVVGLSCAHALAERDANVTVCE 30
                                      689***********************987 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.4    0.0012       1.1       1      39 [.       4      37 ..       4      48 .. 0.85
   2 ?    4.2   0.1     0.041        39     114     154 ..     160     200 ..     148     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgag 39
                                      +ivG+G+ Gl+++ +L++r     + ++t+ +  ++g g
  gi|313125093|ref|YP_004035357.1|  4 VIVGGGVVGLSCAHALAER-----DANVTVCEAGTLGGG 37
                                      7****************99.....588999998888734 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.041
                     NAD_binding_9 114 gvtvevhraevvdleeradgq.avlladgaslaadaVvLAlG 154
                                       gv+v+  ++ v+ l++++++  + +++ +++l+ad++v A G
  gi|313125093|ref|YP_004035357.1| 160 GVDVR-TNTPVTGLDREENENrWRVETPDETLTADYIVNAAG 200
                                       44444.4889****99887752777888899*******9998 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0    0.0003      0.28       1      29 [.       1      29 [.       1      33 [. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigv 29
                                      m+i+++G G vGl +a +lae+  +v+++
  gi|313125093|ref|YP_004035357.1|  1 MHIVIVGGGVVGLSCAHALAERDANVTVC 29
                                      79************************987 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.4   0.00032       0.3       2      33 ..       3      32 ..       2      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00032
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieas 33
                                      +v++G+G  gls A+ l  a+ + +v++ ea+
  gi|313125093|ref|YP_004035357.1|  3 IVIVGGGVVGLSCAHAL--AERDANVTVCEAG 32
                                      89***************..7788888888876 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.4   0.00033      0.31       2      44 ..       3      42 ..       2      57 .. 0.90
   2 ?   -2.5   0.0       1.8   1.7e+03     165     209 ..     157     201 ..     152     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGea 44
                                      ivivGGG  G   A ala+     ++vt+ e+ ++g    G+a
  gi|313125093|ref|YP_004035357.1|  3 IVIVGGGVVGLSCAHALAERD---ANVTVCEAGTLGGGSTGRA 42
                                      9****************9988...89******99998888876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                                       HHCT-EEEE--EEEEEE-T.TS-EEEEEETTS-EEE-SEEEE-SGG CS
                    Trp_halogenase 165 earGvtrvegkvvevqlde.dgrveslrledgreveadlfiDcsGf 209
                                       +++Gv+++  + v+   +e +++  ++++ d+ ++ ad ++ + G 
  gi|313125093|ref|YP_004035357.1| 157 TDAGVDVRTNTPVTGLDREeNENRWRVETPDE-TLTADYIVNAAGA 201
                                       56799888777665544443777677777665.5999999999996 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.5    0.0022       2.1       2      30 ..       3      31 ..       2      47 .. 0.93
   2 ?   -1.4   0.1         2   1.8e+03      72      87 ..     273     288 ..     271     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0022
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      + ++G G++G + a+++a+++ +V++++ 
  gi|313125093|ref|YP_004035357.1|  3 IVIVGGGVVGLSCAHALAERDANVTVCEA 31
                                      789**********************9875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                                       -HHHHHC-SEEEE-S- CS
                           3HCDH_N  72 dleeavdadlviEavv 87 
                                       d++e +d d+ iEav 
  gi|313125093|ref|YP_004035357.1| 273 DFSESADLDWTIEAVE 288
                                       778899********95 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   4.6     0.008       7.6       2      28 ..       3      29 ..       2      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.008
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi 28
                                      ++++GgG  G+ +A a+a++ a+v+ +
  gi|313125093|ref|YP_004035357.1|  3 IVIVGGGVVGLSCAHALAERDANVTVC 29
                                      89**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2417.16
//
Query:       gi|313125094|ref|YP_004035358.1|  [L=503]
Description: phenylalanyl-tRNA synthetase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-79  265.7   0.0    4.5e-79  265.4   0.0    1.1  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    0.00018   20.7   0.3      0.024   13.7   0.1    2.3  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0003   20.6   0.4      0.003   17.4   0.1    2.4  2  MarR_2           MarR family
    0.00093   18.7   0.0     0.0016   18.0   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0034   16.8   0.0       0.26   10.7   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0047   17.1   0.0     0.0094   16.1   0.0    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0053   16.7   0.1        2.1    8.4   0.0    2.3  2  HTH_45           Winged helix-turn-helix
     0.0093   15.9   0.0       0.24   11.3   0.0    2.4  2  MarR             MarR family
  ------ inclusion threshold ------
      0.017   14.9   0.3       0.31   10.8   0.0    2.1  2  DUF4364          Domain of unknown function (DUF4364)
      0.026   14.5   0.0      0.083   12.9   0.0    1.8  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.066   12.9   0.3        1.2    8.9   0.0    2.5  2  GntR             Bacterial regulatory proteins, gntR family
       0.25   11.3   1.5         10    6.1   0.1    3.0  3  TrmB             Sugar-specific transcriptional regulator Trm


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.4   0.0     3e-82   4.5e-79       2     244 ..     222     498 ..     221     499 .. 0.96

  Alignments for each domain:
  == domain 1  score: 265.4 bits;  conditional E-value: 3e-82
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       ++v+++++++++gk+h+l+++++++k++++ +gf+e+egp+ +++f++ d+L++pqdhpaR+++d F l+ p  +  
  gi|313125094|ref|YP_004035358.1| 222 YNVEADAPEVRTGKTHILRQTADRVKDVLVGMGFQEMEGPHADADFWINDCLFMPQDHPARTHWDRFALDVPPIEdv 298
                                       8********************************************************************77766689 PP

                                       ..............................ECESEEE-SSTHHHHHHHH.....TTS-SSEEEEEEEEEEBSST-SS CS
                      tRNA-synt_2d  77 ..............................veekllLRthttavqirtl.....ekkkppikiisigrvfRrdavDa 118
                                                                     +++   LR htt++++r+l      + + p++++s+++v+R+d++D 
  gi|313125094|ref|YP_004035358.1| 299 pedlvdrvedahrngvgpdgdgyhspwsedFARAIALRGHTTSLSMRYLsghevGDLESPQRYFSVEKVYRNDTLDP 375
                                       ******************************999****************8776667779****************** PP

                                       SB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE CS
                      tRNA-synt_2d 119 thlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmv 195
                                       thl eF+q+eg+v+ +++s++dl+g++ee+++++ g + +++f+p+y+p+tePs+e++  + +++++ +E++++Gm+
  gi|313125094|ref|YP_004035358.1| 376 THLLEFYQIEGWVMADDLSVRDLMGTFEEFYEQF-GIT-DIQFKPHYNPYTEPSFELFGRH-PETGELIEIGNSGMF 449
                                       **********************************.**9.**********************.*************** PP

                                       -HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT...HHHHGG CS
                      tRNA-synt_2d 196 rpevleavgideevsgfafGlGveRlamlkygieDiRelven..dlrflrq 244
                                       r+evle++g+  e +++a+Gl++eRl ml+yg++DiR+++ +  dl++lr+
  gi|313125094|ref|YP_004035358.1| 450 RDEVLEPLGV--ECDVMAWGLALERLLMLMYGFDDIRDVHGTmsDLELLRE 498
                                       **********..***************************998779988876 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   1.6e-05     0.024      92     122 ..     359     388 ..     355     410 .. 0.77
   2 !    4.6   0.0    0.0094        14     287     307 ..     466     486 ..     456     488 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                       SEEEEEEEEE--S--BTTB-S-CEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  92 drvfqiaraFRaEdsrtdrhlaEFtqieaem 122
                                       +r+f++ +++R+  ++ ++ l EF+qie  +
  gi|313125094|ref|YP_004035358.1| 359 QRYFSVEKVYRNDTLDPTHLL-EFYQIEGWV 388
                                       79**************99999.*****9544 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0094
                                       EEEEHHHHHHHHCT-SSGGGC CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                       +gl l+Rl+ml+ g ++Irdv
  gi|313125094|ref|YP_004035358.1| 466 WGLALERLLMLMYGFDDIRDV 486
                                       7999****************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     2e-06     0.003       6      55 ..       6      53 ..       2      58 .. 0.88
   2 ?    0.4   0.0      0.41   6.1e+02      41      54 ..     161     174 ..     160     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +q  vL+a  + +    t+g la+++gl++ +v+++  +L + G+v+ ++
  gi|313125094|ref|YP_004035358.1|  6 SQVAVLNAASATDA--TTIGSLAEETGLKPETVTQAAFELRDDGYVTVEE 53
                                      68889999999998..8*****************************8774 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.41
                                       HHHHHHHTTSEEEE CS
                            MarR_2  41 ilkrLvaaGLverr 54 
                                       +l+ Lv++ Lver 
  gi|313125094|ref|YP_004035358.1| 161 TLDQLVSRNLVERH 174
                                       5899*******995 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.1e-06    0.0016       5      48 .]       7      50 ..       3      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + ++L++  +   +++  LAe++gl p tv++   +L ++G+++
  gi|313125094|ref|YP_004035358.1|  7 QVAVLNAASATDATTIGSLAEETGLKPETVTQAAFELRDDGYVT 50
                                      56789999999999****************************96 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.022        33      10      37 ..     233     258 ..     225     259 .. 0.79
   2 !   10.7   0.0   0.00017      0.26      98     209 ..     360     465 ..     355     470 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.022
                   tRNA_synthFbeta  10 ttegelnkeqklrrklrdllagaGlnEv 37 
                                       t+  + +  +++ ++++d+l+g+G++E+
  gi|313125094|ref|YP_004035358.1| 233 TG--KTHILRQTADRVKDVLVGMGFQEM 258
                                       33..346788999*************96 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00017
                   tRNA_synthFbeta  98 rlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehpalh 173
                                       r F + kv+++d  + +   e  ++ + ++ ++            ++ dl g+ e++ e++gi++++f+p  +p+ +
  gi|313125094|ref|YP_004035358.1| 360 RYFSVEKVYRNDtLDPTHLLEFYQIEGWVMADD-----------LSVRDLMGTFEEFYEQFGITDIQFKPHYNPYTE 425
                                       677778888887655566777777777777777...........9999***************************99 PP

                   tRNA_synthFbeta 174 pgrsAeikvdgk......evGvlGelhpevleafdlkqrvyv 209
                                       p      +          e+G  G +  evle ++++  v++
  gi|313125094|ref|YP_004035358.1| 426 PSFELFGRH--PetgeliEIGNSGMFRDEVLEPLGVECDVMA 465
                                       964443333..2447788999999999999999998888776 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.3e-06    0.0094      25      57 ..      22      54 ..       9      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.3e-06
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                         lae+ + +p +V++   +L++dGyv +e +
  gi|313125094|ref|YP_004035358.1| 22 IGSLAEETGLKPETVTQAAFELRDDGYVTVEER 54
                                      5689************************99976 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0014       2.1      42      67 ..      42      70 ..       9      76 .. 0.85
   2 !    5.9   0.0    0.0084        12      40      70 ..     162     195 ..     156     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                            HTH_45 42 mLvekgli...kkskekYvlTekGlelle 67
                                       L + g++   + ++ +Y+lTe+G++++e
  gi|313125094|ref|YP_004035358.1| 42 ELRDDGYVtveEREEVEYELTEEGRQYVE 70
                                      688999988877799**********9987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0084
                            HTH_45  40 LdmLvekgli...kkskekYvlTekGlelleklk 70 
                                       Ld+Lv+++l+   +++  + +lT+ G  ll++  
  gi|313125094|ref|YP_004035358.1| 162 LDQLVSRNLVerhEETVRSVTLTDDGVTLLMEGV 195
                                       99********66555666789********99755 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00016      0.24       2      52 ..       4      54 ..       3      56 .. 0.91
   2 ?    1.8   0.0      0.16   2.4e+02      37      50 ..     161     174 ..     160     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                       ++q+ +L   +  ++ ++  La+  g+++ tvt ++ +L ++G+++ +  
  gi|313125094|ref|YP_004035358.1|  4 PESQVAVLNAASATDATTIGSLAEETGLKPETVTQAAFELRDDGYVTVEER 54
                                      5789999999999*********************************98765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.16
                                       HHHHHHHTTSEEEE CS
                              MarR  37 vldrLekkGlieRs 50 
                                       +ld+L+ ++l+eR 
  gi|313125094|ref|YP_004035358.1| 161 TLDQLVSRNLVERH 174
                                       79**********96 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.31      35      71 ..      35      70 ..      26      75 .. 0.90
   2 ?    1.9   0.0      0.11   1.7e+02      38      70 ..     160     191 ..     158     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                           DUF4364 35 dlqqalseLvesglieeeekenktlykiTekGketle 71
                                      +++qa  eL ++g++++ee +++  y++Te+G++ +e
  gi|313125094|ref|YP_004035358.1| 35 TVTQAAFELRDDGYVTVEE-REEVEYELTEEGRQYVE 70
                                      578999**********965.9999*********9875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                           DUF4364  38 qalseLvesglieeeekenktlykiTekGketl 70 
                                       ++l++Lv+ +l+e + +e+    ++T++G   l
  gi|313125094|ref|YP_004035358.1| 160 ETLDQLVSRNLVERH-EETVRSVTLTDDGVTLL 191
                                       789**********85.58889999999998765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.5e-05     0.083      26      55 ..      24      54 ..      18      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.rgr 55
                                       lA+  Gl +etv+++  eL+++g+++  +r
  gi|313125094|ref|YP_004035358.1| 24 SLAEETGLKPETVTQAAFELRDDGYVTvEER 54
                                      69************************95444 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00077       1.2      28      59 ..      23      54 ..      18      57 .. 0.92
   2 ?    1.0   0.1      0.22   3.3e+02      43      57 ..     160     174 ..     159     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00077
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverrqg 59
                                       +La+e g +  tv +A  +L  +g+v+++ +
  gi|313125094|ref|YP_004035358.1| 23 GSLAEETGLKPETVTQAAFELRDDGYVTVEER 54
                                      68**************************9987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.22
                                       HHHHHHHHTTSEEEE CS
                              GntR  43 eALrrLeaeglverr 57 
                                       e L++L++++lver+
  gi|313125094|ref|YP_004035358.1| 160 ETLDQLVSRNLVERH 174
                                       6799*********97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.007        10      22      64 ..      19      61 ..       5      64 .. 0.89
   2 ?    2.8   0.0     0.072   1.1e+02      41      58 ..     160     177 ..     159     185 .. 0.85
   3 ?   -2.3   0.1       2.9   4.3e+03      16      29 ..     189     202 ..     188     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.007
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                        t+  +aee+g+   +v ++  +L d G+V++e+++   Y+ 
  gi|313125094|ref|YP_004035358.1| 19 ATTIGSLAEETGLKPETVTQAAFELRDDGYVTVEEREEVEYEL 61
                                      5677889****************************99888875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.072
                                       HHHHHHHHCTSEEEESST CS
                              TrmB  41 evLrsLedkGlVerekgr 58 
                                       e+L +L+++ lVer +++
  gi|313125094|ref|YP_004035358.1| 160 ETLDQLVSRNLVERHEET 177
                                       6899**********9987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.9
                                       HHHHHCCCHHCHHC CS
                              TrmB  16 aLlklgpatadeia 29 
                                       +Ll++g  ta+++ 
  gi|313125094|ref|YP_004035358.1| 189 TLLMEGVETAETVD 202
                                       89********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3582.15
//
Query:       gi|313125095|ref|YP_004035359.1|  [L=592]
Description: phenylalanyl-tRNA synthetase subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-42  144.2   0.0    5.1e-42  143.7   0.0    1.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    2.3e-15   56.6   0.1    2.6e-14   53.2   0.1    2.5  2  B5               tRNA synthetase B5 domain
    2.3e-11   43.7   0.0    3.5e-11   43.1   0.0    1.2  1  B3_4             B3/4 domain
    1.9e-10   40.8   0.2    0.00013   22.1   0.0    3.8  3  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
    4.2e-06   26.4   0.0    8.6e-06   25.4   0.0    1.5  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
        0.2   11.8   0.2         32    4.7   0.0    2.9  3  TIP49_C          TIP49 AAA-lid domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.7   0.0   1.7e-45   5.1e-42       2     214 .]     383     588 ..     382     588 .. 0.95

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 1.7e-45
                   tRNA_synthFbeta   2 pstlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldkll......eddderkavelanPlsedqs 72 
                                       +++ P++ t++g ++++ +l++++r+ l+g+G+ +++++ ++se+e+ + +      e     ++ e+  P sed++
  gi|313125095|ref|YP_004035359.1| 383 QPRYPNVGTVGG-RHERSRLEDAARNSLVGLGFEDMLNFHMTSEEEVYDRMgieagsEVLGGGDTAEITGPYSEDYT 458
                                       578899999999.99****************************999877776866544446677************* PP

                   tRNA_synthFbeta  73 vlRtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkg 148
                                       +lRt  lp+l+ vl++N +r  +   l Eig v   d s +++++e+rh+a+vl+ ++           + f+d+k+
  gi|313125095|ref|YP_004035359.1| 459 ILRTWALPSLMMVLENNTHRAYP-QDLAEIGLVAERDdSVNTRVDERRHVAGVLARHD-----------ATFEDAKA 523
                                       ***********************.*************999******************...........******** PP

                   tRNA_synthFbeta 149 ivealleslgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                        +++l++ +g  +++  +++hp++  gr+A+++vdg++vGv+Ge+hp+vl ++dl+ +v++fE+dl
  gi|313125095|ref|YP_004035359.1| 524 RLQSLCRDFGA-ELKTPATDHPSFIDGRAASVVVDGENVGVVGEIHPRVLVEHDLELPVAAFEFDL 588
                                       ***********.****************************************************97 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.28   8.3e+02       2      38 ..       5      42 ..       4     136 .. 0.78
   2 !   53.2   0.1   8.8e-18   2.6e-14       3      67 .]     291     379 ..     289     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.28
                                      EEEHHHHHHHHTS.---HHHHHHHHHHTT-E.EESSTT CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  2 slrvekinkllGi.dlseeeiikiLkrlgceriekdkd 38
                                      +++ ++++ l+G  + s+ee ++ L +lg+e + +++d
  gi|313125095|ref|YP_004035359.1|  5 DVHPDELRDLTGHeEKSDEEFKDDLFALGLEFEGETED 42
                                      67788889999984667789999999999985444433 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 8.8e-18
                                       EEHHHHHHHHTS---HHHHHHHHHHTT-E.........................EESSTTCEEEE--TT-TT--SHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   3 lrvekinkllGidlseeeiikiLkrlgce........................riekdkdlllVtvPswRsDleree 55 
                                       +++++i+ +lG+dl++ e++++++r g++                        + e+d+ +++V +P++R+D++++ 
  gi|313125095|ref|YP_004035359.1| 291 VSHDRIETMLGVDLEPREVVDLFERSGLDadaddgadagdgsdtteaggenatDAESDDLVYEVSIPPYRVDVLHPL 367
                                       789**********************************************99997789999***************** PP

                                       HHHHHHHHHH-G CS
                                       xxxxxxxxxxxx RF
                                B5  56 DliEEvaRlyGY 67 
                                       Dl+++v R+yG+
  gi|313125095|ref|YP_004035359.1| 368 DLVDDVGRAYGF 379
                                       ***********7 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.2e-14   3.5e-11       2     135 ..      98     252 ..      97     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.2e-14
                                       SSEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTB..........T CS
                              B3_4   2 cpryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiq..........g 63 
                                       +p+++++v+rgv+ + +                +++++ ++++++  +g+     +++++Dl  ++          +
  gi|313125095|ref|YP_004035359.1|  98 RPYVTGAVIRGVDLDDDA---------------LDSLIQLQEKLHATMGRkrakgAIGIHDLTMLKgdalsedsdgN 159
                                       799999999999999999...............9*******************************9999999**955 PP

                                       EEE.EEE--TTEEEEBTTS-EEEE-T.....................TSEEEETEEEEEEETTTEEBTTTB--TT-- CS
                              B3_4  64 div.vrlakegeklvtldgkerelde.....................edlviadsekpvslagvmggeeskvsedTk 118
                                       +i+     +eg ++v+ld  + e+++                     +++ i+d+ +  s ++v++g +++v+ d++
  gi|313125095|ref|YP_004035359.1| 160 SITyTGIDPEGDTFVPLD-ADAEMTParvleehptgqtyadlvseyeRYPAIYDELGLFSFPPVINGRRTEVTTDSR 235
                                       9999999***********.668887779**************************99988****************** PP

                                       EEEEEEEE--HHHHHHH CS
                              B3_4 119 nvfleaaafdpvsirkt 135
                                       + ++e ++ d+ +i + 
  gi|313125095|ref|YP_004035359.1| 236 ELLVELTGTDQWTIDRM 252
                                       **********9999875 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   4.3e-08   0.00013       1      78 [.       1      67 [.       1      72 [. 0.91
   2 !   11.9   0.0   6.9e-05       0.2       6      68 ..     291     364 ..     287     373 .. 0.86
   3 ?    2.0   0.0     0.084   2.5e+02      21      36 ..     522     537 ..     513     554 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.3e-08
                         PhetRS_B1  1 MPtisvkkeaLfkalg.kelteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLLcleglaralk 78
                                      MP++ v+ ++L +++g +e ++ee++d lf +GlE+   +e+ +            ++++    r D L++eg+ar l+
  gi|313125095|ref|YP_004035359.1|  1 MPVVDVHPDELRDLTGhEEKSDEEFKDDLFALGLEFEGETEDGA------------FQLEFGPDRLDRLSVEGVARSLR 67
                                      9***************55599***************99888887............9999999**********999997 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.9e-05
                         PhetRS_B1   6 vkkeaLfkalgkelteeeledllfefGlElDeiveeee...........kkkadkkseeviykidipAnryDLL 68 
                                       v+++++ + lg +l+  e+ dl+ + Gl+ D     ++           ++++d +s++ +y + ip  r D+L
  gi|313125095|ref|YP_004035359.1| 291 VSHDRIETMLGVDLEPREVVDLFERSGLDADADDGADAgdgsdtteaggENATDAESDDLVYEVSIPPYRVDVL 364
                                       78899999********************9986554444578888888887899*******************99 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.084
                         PhetRS_B1  21 eeeledllfefGlElD 36 
                                       + +l+ l+ +fG El 
  gi|313125095|ref|YP_004035359.1| 522 KARLQSLCRDFGAELK 537
                                       46799*********96 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.9e-09   8.6e-06      13     214 ..     392     584 ..     385     591 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.9e-09
                                       HSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHH CS
                      tRNA-synt_2d  13 agklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthtta 89 
                                        g++h  +++ +  ++ ++ lgfe + + ++ se  + d + ++    +    dt  ++ p +  e+ ++LRt + +
  gi|313125095|ref|YP_004035359.1| 392 VGGRHERSRLEDAARNSLVGLGFEDMLNFHMTSEEEVYDRMGIEAGSEVLGGGDTAEITGPYS--EDYTILRTWALP 466
                                       588999****************************************************99999..889********* PP

                                       HHHHHH...TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEE CS
                      tRNA-synt_2d  90 vqirtl...ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrp 163
                                         + +l   +++  p+ +  ig v  rd+   t+  e   v g+++ ++ +++d k+ l++l++++ gae  ++   
  gi|313125095|ref|YP_004035359.1| 467 SLMMVLennTHRAYPQDLAEIGLVAERDDSVNTRVDERRHVAGVLARHDATFEDAKARLQSLCRDF-GAE--LKTPA 540
                                       ******76555669************9999************************************.999..55555 PP

                                       CEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEE CS
                      tRNA-synt_2d 164 syfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfaf 214
                                       +  p    +  ++v++    ++   ++ +G ++p+vl + ++  e +++af
  gi|313125095|ref|YP_004035359.1| 541 TDHPSFIDGRAASVVV---DGE--NVGVVGEIHPRVLVEHDL--ELPVAAF 584
                                       5555555555555555...222..245556677777777766..6666665 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.011        32      16      32 ..      52      68 ..      46      70 .. 0.86
   2 ?    3.6   0.0     0.025        75      10      27 ..     108     125 ..     104     126 .. 0.88
   3 ?   -1.7   0.0       1.1   3.4e+03       9      32 ..     397     420 ..     395     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                           TIP49_C 16 eAldlLakigtetSLRY 32
                                      + ld+L+  g+++SLRY
  gi|313125095|ref|YP_004035359.1| 52 DRLDRLSVEGVARSLRY 68
                                      6699************* PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.025
                           TIP49_C  10 gvkldeeAldlLakigte 27 
                                       gv+ld++Ald L +++++
  gi|313125095|ref|YP_004035359.1| 108 GVDLDDDALDSLIQLQEK 125
                                       79**********999876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.1
                           TIP49_C   9 EgvkldeeAldlLakigtetSLRY 32 
                                       E+  l++ A + L+ +g e  L +
  gi|313125095|ref|YP_004035359.1| 397 ERSRLEDAARNSLVGLGFEDMLNF 420
                                       666899**********99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3885.98
//
Query:       gi|313125096|ref|YP_004035360.1|  [L=400]
Description: cystathionine gamma-synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.2e-137  456.0   0.0   8.1e-137  455.8   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.8e-11   43.9   1.8    4.2e-10   39.5   1.8    2.6  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.7e-08   32.2   0.1    4.6e-07   29.4   0.1    2.2  1  Beta_elim_lyase  Beta-eliminating lyase
    4.6e-05   22.8   0.0    6.3e-05   22.3   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    0.00027   20.0   0.0    0.00041   19.4   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    0.00038   19.1   0.0    0.00091   17.8   0.0    1.5  1  Met_gamma_lyase  Methionine gamma-lyase


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.8   0.0  2.7e-140  8.1e-137       1     381 [.       9     397 ..       9     398 .. 0.96

  Alignments for each domain:
  == domain 1  score: 455.8 bits;  conditional E-value: 2.7e-140
                                       HHHHHHTTTTCHT..TTTBSS--B---SBBBESSHHHH.....CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEE CS
                   Cys_Met_Meta_PP   1 eTllvhagqekde..qtgavavpiyltstykfkdvdea.....fageekgyeYsRsgnptrsvleeriaaLeggeaa 70 
                                       eTl+v  g+++++    + vavp++l+st+ + ++d           + +y YsR+ nptr++le+riaaL gg++a
  gi|313125096|ref|YP_004035360.1|   9 ETLAVTHGERQRPaeGVEDVAVPVHLASTFAVPEIDPDaslesLDPDAGEYLYSRLSNPTRNALEHRIAALCGGDHA 85 
                                       5889988888777557889**************99987777744444455*************************** PP

                                       EEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEESS CS
                   Cys_Met_Meta_PP  71 lavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvylEtp 146
                                       la++sG+aAi +ai a ++ Gd+iv+ ddlYggt+++l+ +++  l+++v+ vd  d++ +++a++e+t+lv++Etp
  gi|313125096|ref|YP_004035360.1|  86 LAFASGTAAIVTAISAAVQPGDHIVAFDDLYGGTKSMLSDLFEDrLNVSVSLVDARDTDTVAAAMREETSLVWMETP 162
                                       ***************************************999754******************************** PP

                                       -TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHH CS
                   Cys_Met_Meta_PP 147 tnpllkvvDiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkel 223
                                       tnpll+++Die+ia++a + g++  vDntf+ p +qrpl+lgaD+vvhS+TKyl+Ghsd ++G++++++ e+ ++e+
  gi|313125096|ref|YP_004035360.1| 163 TNPLLRLCDIEAIAAIADEYGATFGVDNTFVGPHFQRPLELGADVVVHSTTKYLNGHSDSIGGALATND-EAYAEEM 238
                                       *********************************************************************.9999999 PP

                                       HHHHH.HHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-S CS
                   Cys_Met_Meta_PP 224 kflqn.alGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgagg 299
                                       +flq+  +G++l pfda+l+lrGlkTL lR+e+h++nA++vAefL+ hp+ve+v Ypgl+shpqh+la +q++g+gg
  gi|313125096|ref|YP_004035360.1| 239 TFLQRvGMGNMLAPFDAYLTLRGLKTLPLRMEKHASNAQAVAEFLADHPAVEAVHYPGLESHPQHDLASRQMSGYGG 315
                                       99987369********************************************************************* PP

                                       EEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHH CS
                   Cys_Met_Meta_PP 300 vlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaD 376
                                       vls el++++  +++fv +l+ f la+slGgveslie+pasmth  +++eer+  g+td+l+RlsvG+E+  Dl++D
  gi|313125096|ref|YP_004035360.1| 316 VLSIELDTDLDGVARFVAALEHFPLAVSLGGVESLIEHPASMTHSPLSQEERDMLGITDSLLRLSVGVEHEADLLSD 392
                                       ***************************************************************************** PP

                                       HHHHH CS
                   Cys_Met_Meta_PP 377 lkqal 381
                                       l++al
  gi|313125096|ref|YP_004035360.1| 393 LSDAL 397
                                       ***99 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   1.8   1.4e-13   4.2e-10      21     228 ..      65     256 ..      55     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.4e-13
                                       SSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTS CS
                   DegT_DnrJ_EryC1  21 sgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdty 97 
                                       s+p+ +++E+++aa +g +ha+a++sGtaA+  a++a  v+pgd ++     + +t ++ + l  +   v v   + 
  gi|313125096|ref|YP_004035360.1|  65 SNPTRNALEHRIAALCGGDHALAFASGTAAIVTAISA-AVQPGDHIVAFDDLYGGTKSMLSDLFEDRLNVSVSLVDA 140
                                       489999*****************************98.699********************9988888888887665 PP

                                       SB-GGGCGGG--TTEEEE...EEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BT CS
                   DegT_DnrJ_EryC1  98 nidpaaieaaitertkaI...lpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyp 171
                                         d ++++aa  e+t+ +   +p + + + +d++a+ aia+++g  +  D    +G +++ +++   +d+ v S   
  gi|313125096|ref|YP_004035360.1| 141 -RDTDTVAAAMREETSLVwmeTPTNPLLRLCDIEAIAAIADEYGATFGVDNT-FVGPHFQ-RPLELGADVVVHST-- 212
                                       .499***********98855568999999******************99975.4676665.57766678888885.. PP

                                       TSSS...-SSS-EEEEESTHHHHHHHHHHHBTTCEC..CTCSSCECCSS---B-B-BHHHHH CS
                   DegT_DnrJ_EryC1 172 tKnl...ttGeGGavvtndeelaekarvlrnhGlkr..kaekryvgevelGynyrlteiqAA 228
                                       tK l   +   GGa+ tnde++ae+++ l+  G+ +  +                   + A 
  gi|313125096|ref|YP_004035360.1| 213 TKYLnghSDSIGGALATNDEAYAEEMTFLQRVGMGNmlA------------------PFDAY 256
                                       66665144555**********************995333..................33333 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.5e-10   4.6e-07      31     276 ..      66     289 ..      57     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.5e-10
                                       -HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSST.THHHHC.C--EEEEE-EBT CS
                   Beta_elim_lyase  31 dktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdet.gaiael.agvklrdlknke 105
                                       ++t n+Le+++a+l+g ++al +++GtaA   ++++ +q+g+ +++       fd   g+ + + ++     l+ + 
  gi|313125096|ref|YP_004035360.1|  66 NPTRNALEHRIAALCGGDHALAFASGTAAIVTAISAAVQPGDHIVA-------FDDLyGGTKSMlSDLFEDRLNVSV 135
                                       7899************************************998854.......555556666664555555555554 PP

                                       T..TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS CS
                   Beta_elim_lyase 106 a..GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslge 180
                                             d + ++aa++e      +++l+ +++ +n      + l  ++++aaia++yg ++ +D +        +g 
  gi|313125096|ref|YP_004035360.1| 136 SlvDARDTDTVAAAMRE------ETSLVWMETPTNP----LLRLCDIEAIAAIADEYGATFGVDNT-------FVGP 195
                                       23355566666666666......799*********5....9*********************9954.......6666 PP

                                       -CHHHH.TTSSEEEEESSS...TT--SS-EEEEE-HH....HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHSS CS
                   Beta_elim_lyase 181 ivkemf.syvDsvtmslkK...dllanvGgvlafrddeledylaerveqrkylggglrqagvlaaleagiraleegl 253
                                       + ++ +  ++D+v+ s +K   + +  +Gg la++d+    y ae +++ +++g g   a + a     +r l+   
  gi|313125096|ref|YP_004035360.1| 196 HFQRPLeLGADVVVHSTTKylnGHSDSIGGALATNDE---AY-AEEMTFLQRVGMGNMLAPFDAY--LTLRGLKTLP 266
                                       7766662569********9663334579********9...66.8888888888877777899999..9999999999 PP

                                       TTHHHHHHHHHHHHHHHHHCT-- CS
                   Beta_elim_lyase 254 aslerdhktaeqlaeklelvrla 276
                                        ++e++  +a+  ae l++++ +
  gi|313125096|ref|YP_004035360.1| 267 LRMEKHASNAQAVAEFLADHPAV 289
                                       99999999999999999998876 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.1e-08   6.3e-05      46     196 ..      69     198 ..      55     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.1e-08
                                       HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEB CS
                     Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvrypl 122
                                         +le+++a + g         + a+ + sG+ a+  a+ ++ +  pgd i+++d  y+  k +l         +++
  gi|313125096|ref|YP_004035360.1|  69 RNALEHRIAALCG--------GDHALAFASGTAAIVTAISAAVQ--PGDHIVAFDDLYGGTKSMLSDLFEDRLNVSV 135
                                       6899*********........7889*******998888888887..************9888877765444444443 PP

                                       EETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSS CS
                     Aminotran_1_2 123 yseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfg 196
                                       +       d + + +a +e      +t +++ e+p NP   +++ e + ++   a++y++   vD ++ g  f+
  gi|313125096|ref|YP_004035360.1| 136 S--LVDARDTDTVAAAMRE------ETSLVWMETPTNPLLRLCDIEAIAAI---ADEYGATFGVDNTFVGPHFQ 198
                                       3..1126688888888888......899**********9888888888888...***********999887776 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.4e-07   0.00041      49     203 ..      73     216 ..      62     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTS CS
                       Aminotran_5  49 rekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeeg 125
                                       + ++a+l + +  + + f sGt+ ai +++ ++   ++pgd+iv  +  + ++     +l  +  ++v v  +d   
  gi|313125096|ref|YP_004035360.1|  73 EHRIAALCGGD--HALAFASGTA-AIVTAISAA---VQPGDHIVAFDDLYGGTKSMLSDLF-EDRLNVSVSLVD--- 139
                                       56677777777..5889999998.777777777...9********9988888776667765.334555544443... PP

                                       CBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTT CS
                       Aminotran_5 126 eldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKl 202
                                         d+d+++++++e+t+lv +    n +  + ++e+i+++a ++ga + vD +   +h +  + +lg+D+++ s+ K+
  gi|313125096|ref|YP_004035360.1| 140 ARDTDTVAAAMREETSLVWMETPTNPLLRLCDIEAIAAIADEYGATFGVDNTFVGPHFQRPL-ELGADVVVHSTTKY 215
                                       3688999*********************************************9999999887.7**********995 PP

                                       T CS
                       Aminotran_5 203 l 203
                                       l
  gi|313125096|ref|YP_004035360.1| 216 L 216
                                       4 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.1e-07   0.00091      56     257 ..      68     248 ..      55     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.1e-07
                   Met_gamma_lyase  56 GrdtldkvyaevfgaeaalvrpqlvsGthaiatalfgvlrpgdellaitGkPydtleeviGlrgegqgslkdfgiky 132
                                        r++l++  a + g+++al    + sGt ai ta+ + ++pgd+++a     +   +++ G +++    l +  ++ 
  gi|313125096|ref|YP_004035360.1|  68 TRNALEHRIAALCGGDHAL---AFASGTAAIVTAISAAVQPGDHIVA-----F---DDLYGGTKSMLSDLFEDRLNV 133
                                       5899999999999999998...599*******************997.....3...455677777777777766664 PP

                   Met_gamma_lyase 133 kevdlleegkvdieavkeaikektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncyGefveekeP 209
                                        +v l++    d+++v++a++e+t l+ +   +     + l++ +ie i ++  e        vdn +    + + P
  gi|313125096|ref|YP_004035360.1| 134 -SVSLVD--ARDTDTVAAAMREETSLVWMETPT----NPLLRLCDIEAIAAIADEY-GA-TFGVDNTFVG-PHFQRP 200
                                       .578888..678999*************99765....6889999998765554444.33.4569**9744.35689* PP

                   Met_gamma_lyase 210 tevGadliaGsliknpGGgiaktGGyiaGkeelveaasyrltaPGiGk 257
                                        e+Gad++  s  k   G   ++GG +a ++e   +    l+  G+G+
  gi|313125096|ref|YP_004035360.1| 201 LELGADVVVHSTTKYLNGHSDSIGGALATNDEAYAEEMTFLQRVGMGN 248
                                       ****************************99876655555577777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2537.69
//
Query:       gi|313125097|ref|YP_004035361.1|  [L=870]
Description: valyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.8e-132  441.0   0.6   1.1e-130  436.8   0.6    2.1  1  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    6.6e-35  120.3   0.2    1.3e-34  119.3   0.2    1.5  1  Anticodon_1     Anticodon-binding domain of tRNA
    5.8e-20   71.4   0.1    2.5e-09   36.4   0.0    3.5  3  tRNA-synt_1g    tRNA synthetases class I (M)
    1.4e-06   27.9   0.0       0.01   15.2   0.0    2.4  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    7.7e-06   25.5   0.0    0.00078   19.0   0.0    2.7  2  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
    6.9e-05   21.9   0.0     0.0015   17.5   0.0    2.6  2  tRNA-synt_1f    tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.032   14.3   3.3       0.53   10.4   0.7    2.9  2  Zn-ribbon_8     Zinc ribbon domain
      0.056   13.5   0.4        4.6    7.3   0.1    2.4  2  DZR             Double zinc ribbon
      0.083   11.2   0.4       0.46    8.7   0.0    1.9  2  SpecificRecomb  Site-specific recombinase
        1.3    9.2   5.1         20    5.4   0.4    2.5  2  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.8   0.6    6e-134  1.1e-130       1     599 [.      14     574 ..      14     577 .. 0.94

  Alignments for each domain:
  == domain 1  score: 436.8 bits;  conditional E-value: 6e-134
                       tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       k++++W +ed++    ++ +    f++  +PP v GslH Gha+  tl+d+v r++rm+Gkev + +G+D  G+a e
  gi|313125097|ref|YP_004035361.1|  14 KWQDRWVDEDTYSYDDSAVDADTAFSIDSPPPTVSGSLHWGHAYGFTLQDFVARFNRMRGKEVFFPFGFDDNGIASE 90 
                                       5899***********89999999****************************************************** PP

                       tRNA-synt_1  78 akvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                          e +l  +++    ++ r ef+e +re  ++y +e ++++++lG+s+D+d+ y T+++e++ a +  f +l+d+g
  gi|313125097|ref|YP_004035361.1|  91 RLTEDELDVRHQ----DYDRREFQEMCREVCEQYEAEFTEKMQNLGISIDWDQTYQTISPEVQRASQLSFIELYDDG 163
                                       *******77775....************************************************************* PP

                       tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitke 231
                                         yr   +  w+++++ta+s++E+e  ++ + + +++f++ d+ee ++vi TT+Pe l++ +av v+p+        
  gi|313125097|ref|YP_004035361.1| 164 REYRQRAPAIWCPECETAISQVETEDDEQGSHFHDIEFEVVDSEE-EFVISTTRPELLPACVAVFVHPD-------- 231
                                       *********************************************.***********************........ PP

                       tRNA-synt_1 232 klilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkk 308
                                                              de+ ++L+g e++ pl ++++pii+d+ vd e+G+G+V +    d+ D e  + 
  gi|313125097|ref|YP_004035361.1| 232 -----------------------DEENQHLVGEEARIPLFGQEVPIIEDERVDLETGSGIVMCCTFGDQTDIEWYQA 285
                                       .......................999*************************************************** PP

                       tRNA-synt_1 309 ynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvk 385
                                       +nl++  ++de+gtlt+ a+e+egl+ ++ar+++v++l++ g+ll +  i+h+v + er ++ +++ +++qW+v++ 
  gi|313125097|ref|YP_004035361.1| 286 HNLDLRIAIDESGTLTDVAGEYEGLSSEEAREAIVSDLDDDGALLDKRAITHTVNVHERCGTGVEFLVKDQWYVELL 362
                                       ***************************************************************************** PP

                       tRNA-synt_1 386 eladaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeae 461
                                       + +d+ l+a +++ ++p++  +ry++w+e  q dW iSRqr  G + p+++ ++ e vvv  e ++l  +       
  gi|313125097|ref|YP_004035361.1| 363 DKTDEYLEAGREMDWYPEKMFTRYKNWIEGLQwDWSISRQRSSGIPFPVWYCDDCEHVVV-AERENLPVDPL----- 433
                                       ******************************988***********************9988.33333333222..... PP

                       tRNA-synt_1 462 kkalekeakdkl.kkekgelekdedvlDvWFsSgswpfstlgypee.dteel....kkffpadmlleGlDiirgWva 532
                                           ++  +d+  +++++e+  ++dv+D+W  S+++p    g+    d+ee+    ++ +p+d+  +G Dii +W+ 
  gi|313125097|ref|YP_004035361.1| 434 ---SDDPPVDTCpECDHDEFVPEDDVFDTWATSSLTPLINAGWDWDeDAEEIvidrEELYPFDVRPQGHDIISFWLF 507
                                       ...223344444578999*******************9888887542455433333899****************** PP

                       tRNA-synt_1 533 rlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdi 599
                                         ++   + tg++Pf +v+++g+v+de+  KmSKs+gNv++p++v++ky +da R++ + s vg d+
  gi|313125097|ref|YP_004035361.1| 508 HTVVKCYEHTGEVPFDSVMINGMVLDENREKMSKSKGNVVSPDEVMSKYPVDAARYWAAGSAVGDDL 574
                                       ***********************************************************99999886 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.2   7.4e-38   1.3e-34       1     150 [.     618     757 ..     618     761 .. 0.89

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 7.4e-38
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       drw+l+ l++ ++ vte++++ +f+ka ++l +ffwn++cd yle++k+r   +++    + a+++l+++ + +l+l
  gi|313125097|ref|YP_004035361.1| 618 DRWLLASLDREIEHVTEKLQNREFSKARDDLRSFFWNTFCDDYLEIAKQRVRESDD----EsAKYTLRTAHRRFLKL 690
                                       9**************************************************76544....4489************* PP

                       Anticodon_1  77 laPfmPfitEelwqreeeelgkkesimlaewpekaeelekeleeeevellkeivkairklrselkikpsselkv 150
                                       +aP++ ++tEelw    +e+ +++s+++a+wpe +  le++   e+ e + ++v a+rk++s+++++ +++++ 
  gi|313125097|ref|YP_004035361.1| 691 FAPILAHVTEELW----REMHEETSVHRASWPE-PLGLEADF--EAGETAMAVVGALRKYKSDNQLSMNAPIDL 757
                                       *************....99999**********5.43344444..578888899****************99765 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.4e-12   2.5e-09       3     131 ..      40     183 ..      38     189 .. 0.80
   2 !    7.0   0.0    0.0012       2.2     172     239 ..     345     415 ..     310     422 .. 0.72
   3 !   23.7   0.0     1e-08   1.8e-05     290     368 ..     499     578 ..     495     594 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.4e-12
                                       EEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.............TS-HHHH CS
                      tRNA-synt_1g   3 vttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.............gvtpeel 66 
                                       + ++ p ++g+lH Gh++     D +aR++r+rg+ev+f  g D  G++ e   e+e             +   +e+
  gi|313125097|ref|YP_004035361.1|  40 IDSPPPTVSGSLHWGHAYGFTLQDFVARFNRMRGKEVFFPFGFDDNGIASERLTEDEldvrhqdydrrefQEMCREV 116
                                       566778899*********99999************************998765543321111111111112235678 PP

                                       HHHHHHHHHHHHHHTT--..-SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE- CS
                      tRNA-synt_1g  67 vekvheeikelfkklnis..fdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflp 131
                                       +e++++e++e +++l+is  +d+ ++t s e ++++q  f +l++ g  y+++   ++cp++e+ ++
  gi|313125097|ref|YP_004035361.1| 117 CEQYEAEFTEKMQNLGISidWDQTYQTISPEVQRASQLSFIELYDDGREYRQRAPAIWCPECETAIS 183
                                       99999999999999877622679999************************************98765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                                       .....EEE.EEEEEE-GGGGHHHHHHHH.HH-TT..SHHHHHHHH.HHHHT----EE-ESS-SSS-EET....T CS
                      tRNA-synt_1g 172 sgskpevketehlffklskfekklkewieeeeke..leenvkkivkewlkegLkdlaisrdldwGipvP....g 239
                                       +g+  e+  +++++ +l + +    e++e  ++    +e++ +  k+w++    d++isr+ + Gip+P    +
  gi|313125097|ref|YP_004035361.1| 345 CGTGVEFLVKDQWYVELLDKT---DEYLEAGREMdwYPEKMFTRYKNWIEGLQWDWSISRQRSSGIPFPvwycD 415
                                       555555556677777765554...455544443344789999999****98556**************966554 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 1e-08
                                       GGGHH...HHHTHHHHHHHHTT----S-EEEE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS CS
                      tRNA-synt_1g 290 kdiik...FHtifwPaillgaelklpkkvvahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekk 362
                                        dii    FHt++  +  +  e+ + ++v+ +++ l  + +K+SkS+g+vv ++e++ ++++d+ RY+ a +    +
  gi|313125097|ref|YP_004035361.1| 499 HDIISfwlFHTVV-KCYEHTGEVPF-DSVMINGMvLDENREKMSKSKGNVVSPDEVMSKYPVDAARYWAAGS-AVGD 572
                                       6666522256665.34444455554.556666651556678**************************97654.4456 PP

                                       -EEE-H CS
                      tRNA-synt_1g 363 Dldfsw 368
                                       Dl +s+
  gi|313125097|ref|YP_004035361.1| 573 DLPYSE 578
                                       666665 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0002      0.36      17      93 ..      45     134 ..      34     168 .. 0.82
   2 !   15.2   0.0   5.8e-06      0.01     242     297 ..     526     582 ..     495     586 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                                       EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-................HHHHHH CS
                      tRNA-synt_1e  17 ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks................vkelae 77 
                                       ptv    h Gha  +   D ++r+ +++g +v f   +    D  i+  r  e +                ++e++e
  gi|313125097|ref|YP_004035361.1|  45 PTVSGSLHWGHAYGFTLQDFVARFNRMRGKEVFFPFGFD---DNGIASERLTEDEldvrhqdydrrefqemCREVCE 118
                                       89*******************************987775...444433332222235788889999999999***** PP

                                       HHHHHHHHHHHHTT-- CS
                      tRNA-synt_1e  78 kfieefkkdleaLnvl 93 
                                       ++++ef++++++L++ 
  gi|313125097|ref|YP_004035361.1| 119 QYEAEFTEKMQNLGIS 134
                                       *************986 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.8e-06
                                       EEE--E.EETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHH CS
                      tRNA-synt_1e 242 lhnghl.kiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelle 297
                                       + ng++   ++ekmsks +n+++  +v+ k+   + R+  +     + l ++e+ l+
  gi|313125097|ref|YP_004035361.1| 526 MINGMVlDENREKMSKSKGNVVSPDEVMSKYPVDAARYWAAGSAVGDDLPYSEKGLR 582
                                       556765145679*****************************9999999999998876 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.02        35      11      45 ..     198     232 ..     193     244 .. 0.82
   2 !   19.0   0.0   4.4e-07   0.00078      86     145 ..     240     299 ..     231     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.02
                     tRNA-synt_1_2  11 eiefkveeseeklevfttrpdtlfGvtfvalapeh 45 
                                       +ief+v +see++ + ttrp+ l     v + p+ 
  gi|313125097|ref|YP_004035361.1| 198 DIEFEVVDSEEEFVISTTRPELLPACVAVFVHPDD 232
                                       79*******************99887777776665 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 4.4e-07
                     tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpede 145
                                       g +a  P+ g+++pi   + v  e g+g vm++   dq D e+ + +nl+++  i ++++
  gi|313125097|ref|YP_004035361.1| 240 GEEARIPLFGQEVPIIEDERVDLETGSGIVMCCTFGDQTDIEWYQAHNLDLRIAIDESGT 299
                                       678999**********************************************99987654 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.092   1.6e+02      33     129 ..      47     138 ..      45     158 .. 0.61
   2 !   17.5   0.0   8.3e-07    0.0015     272     309 ..     529     566 ..     495     577 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.092
                      tRNA-synt_1f  33 pSGliHiGnlrevltadlvaralrkrgeevrlilisDdmD..glRkvpenlpekllekylgkpltsiPdpkgkhesy 107
                                       +SG++H G +      d+var  r rg+ev + +  Dd      R   ++l+ +  ++y ++  ++       + + 
  gi|313125097|ref|YP_004035361.1|  47 VSGSLHWGHAYGFTLQDFVARFNRMRGKEVFFPFGFDDNGiaSERLTEDELDVR-HQDYDRREFQEM------CREV 116
                                       688888888888888888888888888877666666663211234444444444.444444443332......3334 PP

                      tRNA-synt_1f 108 aehfnaelvesLdelgievefi 129
                                        e+++ae+ e +++lgi +++ 
  gi|313125097|ref|YP_004035361.1| 117 CEQYEAEFTEKMQNLGISIDWD 138
                                       4555666666666666666665 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 8.3e-07
                      tRNA-synt_1f 272 elillkggekmssSkGnvltledwlevaepevlrflil 309
                                        ++l++++ekms+SkGnv++++++++ ++ +  r+  +
  gi|313125097|ref|YP_004035361.1| 529 GMVLDENREKMSKSKGNVVSPDEVMSKYPVDAARYWAA 566
                                       58999***********************9999999766 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.059   1.1e+02      23      36 ..     169     182 ..     163     185 .. 0.70
   2 ?   10.4   0.7    0.0003      0.53       8      34 ..     414     447 ..     411     451 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.059
                       Zn-ribbon_8  23 dapltaCPeCgsev 36 
                                       +ap + CPeC  + 
  gi|313125097|ref|YP_004035361.1| 169 RAPAIWCPECETAI 182
                                       456666****8765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0003
                       Zn-ribbon_8   8 CeeCghefe......vlqsisdaplta.CPeCgs 34 
                                       C++C h+        ++ + sd+p+++ CPeC +
  gi|313125097|ref|YP_004035361.1| 414 CDDCEHVVVaerenlPVDPLSDDPPVDtCPECDH 447
                                       999**99999999999999996666666****76 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.036        64      12      27 ..     172     187 ..     163     226 .. 0.81
   2 ?    7.3   0.1    0.0026       4.6      14      37 ..     413     448 ..     408     457 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.036
                               DZR  12 arfCseCgtklkavaa 27 
                                       a+ C+eC t++++v++
  gi|313125097|ref|YP_004035361.1| 172 AIWCPECETAISQVET 187
                                       5678888888876655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                               DZR  14 fCseCgtklkavaa............edrCpsCgek 37 
                                       +C++C + + a+ +             d+Cp+C+++
  gi|313125097|ref|YP_004035361.1| 413 YCDDCEHVVVAEREnlpvdplsddppVDTCPECDHD 448
                                       8*******9877779**********9*******976 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00026      0.46     199     263 ..      97     162 ..      85     179 .. 0.79
   2 ?    0.2   0.1       0.1   1.8e+02      76     142 ..     577     644 ..     563     651 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00026
                    SpecificRecomb 199 edeeeaeedlkhlrvll.dqcreavdrvrkhleenGvsvslvfllerlrqrleRleeLldllleee 263
                                        d +++++d ++++ +  + c+++ +++++++++ G+s++     ++++ +++R+++L  + l ++
  gi|313125097|ref|YP_004035361.1|  97 LDVRHQDYDRREFQEMCrEVCEQYEAEFTEKMQNLGISIDWDQTYQTISPEVQRASQLSFIELYDD 162
                                       45567778888888776267*************************************977655334 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                    SpecificRecomb  76 selaerleekllPeapdeedlsdllsllfpkeeDaewlealddetlarLlell.eeeeeeeeeaaekl 142
                                       se   r +ekll +  + ++l d ls+  p++ D++ l+++d+  la+L + + + +e+ ++++ +k+
  gi|313125097|ref|YP_004035361.1| 577 SEKGLRAGEKLLRKLWNASKLVDSLSEDAPESFDHDDLKQIDRWLLASLDREIeHVTEKLQNREFSKA 644
                                       566679999****************************************9999444444455555555 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.5     0.012        21       3      11 ..     175     183 ..     174     184 .. 0.89
   2 ?    5.4   0.4     0.011        20       2       8 ..     441     447 ..     441     455 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.012
                           UPF0547   3 CPeCeakvP 11 
                                       CPeCe+ ++
  gi|313125097|ref|YP_004035361.1| 175 CPECETAIS 183
                                       *****9886 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                           UPF0547   2 vCPeCea 8  
                                       +CPeC++
  gi|313125097|ref|YP_004035361.1| 441 TCPECDH 447
                                       7****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (870 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.54
# Mc/sec: 4827.56
//
Query:       gi|313125098|ref|YP_004035362.1|  [L=428]
Description: hypothetical protein Hbor_03130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        8.5    6.2   6.4          1    9.1   1.6    1.9  2  PsbH      Photosystem II 10 kDa phosphoprotein


Domain annotation for each model (and alignments):
>> PsbH  Photosystem II 10 kDa phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.6   5.7e-05         1      21      39 ..      29      47 ..      15      51 .. 0.87
   2 ?   -2.9   0.2      0.33   5.9e+03      27      37 ..     173     183 ..     172     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 5.7e-05
                              PsbH 21 GWGttpvmavfilLflvfL 39
                                      GW tt++ +vfi+ ++v L
  gi|313125098|ref|YP_004035362.1| 29 GWSTTVLFGVFIAEIAVVL 47
                                      9************999987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.33
                              PsbH  27 vmavfilLflv 37 
                                       + av+ilLf+ 
  gi|313125098|ref|YP_004035362.1| 173 LFAVAILLFAA 183
                                       56899999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2818.25
//
Query:       gi|313125099|ref|YP_004035363.1|  [L=352]
Description: dihydroorotate oxidase a [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-85  284.3   0.0    1.1e-84  284.1   0.0    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    1.8e-05   24.3   0.3    0.00018   21.1   0.2    2.0  2  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.053   13.0   0.0      0.089   12.2   0.0    1.4  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.1   0.0   1.9e-88   1.1e-84       2     295 .]      51     336 ..      50     336 .. 0.95

  Alignments for each domain:
  == domain 1  score: 284.1 bits;  conditional E-value: 1.9e-88
                                       G-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HH CS
                            DHO_dh   2 latkvlglkfknpiglAaGfdkegeeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGld 78 
                                       l+t+ +g  f np+g+AaGfdk++e  + l  lgfg +e+g vt++pq Gn++Pr+frl+ed +++N++GlnneG+d
  gi|313125099|ref|YP_004035363.1|  51 LHTEAFGCSFDNPVGVAAGFDKNAEVPDVLGSLGFGHVEVGGVTAEPQDGNARPRMFRLPEDGAIINRMGLNNEGAD 127
                                       78999************************************************************************ PP

                                       HHHHHHHHHHHHHHCC.CEEEEEEE-TTS..S.HHHHHHHHHHHHGGGESEEEEES-SCTCCTSCCCGCHHHHHHHH CS
                            DHO_dh  79 avlekllkrrkeqeekkelginlskakkt..enavddyvevvrkigpfadilelNvSsPntpglrdlqekeelkail 153
                                       av ++l++  +  +    +g+nl+ + +t  e+a +dy+++ ++++  ad++++NvS+Pn  g rdlq+ ++l+ail
  gi|313125099|ref|YP_004035363.1| 128 AVGARLAAGPRADI---PVGVNLALSESTdaEDAPADYRYTYEQVADAADYVAVNVSCPNSEGFRDLQNRDSLEAIL 201
                                       *******9998755...6999998888876688999***************************************** PP

                                       HHHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHH CS
                            DHO_dh 154 lkvvkevskvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdia 230
                                          v + +  p+lvKl+Pdl d + +d  dv+ e +ldg+++tNtt+ r+  +l++ +n+   + GGlsG+++ ++a
  gi|313125099|ref|YP_004035363.1| 202 GGLVDAGA-DPLLVKLSPDLPDPAVEDALDVVNEYGLDGVVATNTTTDRP-AELQN-PNRA--ERGGLSGAPIEERA 273
                                       ***99988.89***************************************.77777.3433..48************ PP

                                       HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                            DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                       ++++r +++r++  +p++gvGG+ s+eDa+ ki+aGAslvq+yt+lvfegp++ ++i ++l  lL
  gi|313125099|ref|YP_004035363.1| 274 TEMVRFVAERTD--VPVVGVGGVASAEDAYAKIRAGASLVQLYTGLVFEGPTLTRDINEGLLTLL 336
                                       ************..*********************************************998765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.036   2.1e+02      62      98 ..     140     180 ..     137     197 .. 0.72
   2 !   21.1   0.2   2.9e-08   0.00018     166     226 ..     260     318 ..     257     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.036
                               NMO  62 dkPfgvnlflpkkdaadra....ekykkeleeaalelniee 98 
                                       d P+gvnl l++   a++a     +  +++++aa ++++++
  gi|313125099|ref|YP_004035363.1| 140 DIPVGVNLALSESTDAEDApadyRYTYEQVADAADYVAVNV 180
                                       56*********999999988443334455666666665555 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.9e-08
                               NMO 166 eaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                       e GG  G  +++ +  +++v  v++  d+Pv+  GG+  +++  a +++GAs vq+ t ++
  gi|313125099|ref|YP_004035363.1| 260 ERGGLSG-APIE-ERATEMVRFVAERTDVPVVGVGGVASAEDAYAKIRAGASLVQLYTGLV 318
                                       78*****.6664.78999*************************************998765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.5e-05     0.089      58     112 ..     270     325 ..     264     339 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH.H-THHH CS
                      His_biosynth  58 reanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaav.knpeli 112
                                       +e+ +++v+ +ae++++pv   GG+ s ed+ + ++aga+ v + t  v + p l 
  gi|313125099|ref|YP_004035363.1| 270 EERATEMVRFVAERTDVPVVGVGGVASAEDAYAKIRAGASLVQLYTGLVfEGPTLT 325
                                       57788999999*******999999**************999988776552445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2242.06
//
Query:       gi|313125100|ref|YP_004035364.1|  [L=65]
Description: hypothetical protein Hbor_03150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0022   18.0   0.0     0.0023   17.9   0.0    1.2  1  SymE_toxin      Toxin SymE, type I toxin-antitoxin system
  ------ inclusion threshold ------
      0.016   15.2   0.2      0.024   14.6   0.2    1.3  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> SymE_toxin  Toxin SymE, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.6e-07    0.0023      30      53 ..      31      54 ..       4      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.6e-07
                        SymE_toxin 30 LeqaGFatGqpltisVmegrlvit 53
                                      L  aG ++G ++ ++V++g+++i+
  gi|313125100|ref|YP_004035364.1| 31 LAVAGMEIGDEVFVRVRDGKIIIQ 54
                                      7789*******************7 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   2.6e-06     0.024      20      40 ..      35      55 ..      28      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-06
                                      CEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin 20 gireGdevelevdgdkiilrp 40
                                      g + Gdev ++v ++kii+ +
  gi|313125100|ref|YP_004035364.1| 35 GMEIGDEVFVRVRDGKIIIQK 55
                                      8899***********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 441.03
//
Query:       gi|313125101|ref|YP_004035365.1|  [L=104]
Description: nucleoid protein mc1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-47  158.5   0.3    4.5e-47  158.3   0.3    1.0  1  MC1       Non-histone chromosomal protein MC1


Domain annotation for each model (and alignments):
>> MC1  Non-histone chromosomal protein MC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.3   0.3   2.5e-51   4.5e-47       2      96 .]       7     103 ..       5     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 2.5e-51
                               MC1   2 krnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeake..eeirLrekGtkkvhiyegkaeeeeaPddkpd 76 
                                       krnf+lr+e+G+e+svfsG++PrqaaLkaarrl++ dse++a+e  +eirLrekGt+kvhi++++a+ ++aPddkpd
  gi|313125101|ref|YP_004035365.1|   7 KRNFVLREENGTESSVFSGSMPRQAALKAARRLDPVDSEDKAREqaTEIRLREKGTDKVHIFDAWAWVDDAPDDKPD 83 
                                       9*****************************************98889****************************** PP

                               MC1  77 Wledkitkanvskqgiekle 96 
                                       W+e++itk+nvskqgie+le
  gi|313125101|ref|YP_004035365.1|  84 WMEGDITKGNVSKQGIEHLE 103
                                       ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 568.05
//
Query:       gi|313125102|ref|YP_004035366.1|  [L=285]
Description: hypothetical protein Hbor_03220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.021   14.7   0.2        2.7    7.9   0.0    3.1  4  PTSIIA_gutA  PTS system glucitol/sorbitol-specific IIA compon


Domain annotation for each model (and alignments):
>> PTSIIA_gutA  PTS system glucitol/sorbitol-specific IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00015       2.7      40      72 ..      32      64 ..      19      66 .. 0.87
   2 ?    2.7   0.0    0.0061   1.1e+02      44      74 ..      88     118 ..      78     141 .. 0.84
   3 ?   -0.7   0.0     0.069   1.2e+03      44      71 ..     170     197 ..     145     200 .. 0.84
   4 ?   -3.7   0.0      0.62   1.1e+04      47      62 ..     210     225 ..     204     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00015
                                      EE-T.GG----TT-EEEETTEEEEEEEE-TTHH CS
                       PTSIIA_gutA 40 heveelkeeikkgdtltigeqeykitaVGevan 72
                                      +e+++ + +++ gd++++g+q+y +t++  +++
  gi|313125102|ref|YP_004035366.1| 32 IEFQNPAYDLSSGDSFEVGSQTYSVTEITAEVE 64
                                      567788899*****************9987776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0061
                                       .GG----TT-EEEETTEEEEEEEE-TTHHHH CS
                       PTSIIA_gutA  44 elkeeikkgdtltigeqeykitaVGevankn 74 
                                       + +e+ ++++t+ti+++e+++   Ge+ +++
  gi|313125102|ref|YP_004035366.1|  88 RYTETWENNSTVTIDDTEWTVLVSGEENETE 118
                                       567888999************9999987665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.069
                                       .GG----TT-EEEETTEEEEEEEE-TTH CS
                       PTSIIA_gutA  44 elkeeikkgdtltigeqeykitaVGeva 71 
                                       +++++ ++g+t++ +++e ++ aV ++a
  gi|313125102|ref|YP_004035366.1| 170 PQSQTYSEGNTFEYNGNETTVGAVTTEA 197
                                       5788889999999999999999997666 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 0.62
                                       ----TT-EEEETTEEE CS
                       PTSIIA_gutA  47 eeikkgdtltigeqey 62 
                                        +++++ ++t+geq+y
  gi|313125102|ref|YP_004035366.1| 210 IDVANEGNVTLGEQKY 225
                                       5667777888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1731.90
//
Query:       gi|313125103|ref|YP_004035367.1|  [L=167]
Description: hypothetical protein Hbor_03230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-25   88.0   0.4    5.6e-25   87.5   0.4    1.3  1  Transglut_core3  Transglutaminase-like superfamily
  ------ inclusion threshold ------
       0.72   10.2   8.5       0.44   10.9   6.2    1.8  2  DUF3995          Protein of unknown function (DUF3995)


Domain annotation for each model (and alignments):
>> Transglut_core3  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.4   6.3e-29   5.6e-25       4     115 ..      42     157 ..      39     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 6.3e-29
                   Transglut_core3   4 llpfrlrlarlglarlrarlreaprgarpasaeearrlgravraaarllpgrs....kCLpralalalllrrrgipa 76 
                                       ++++++ + r+ l +l+ +     +g+r+a++ ++ ++gr v+++a+ +p+      +CL+ al++++l+++ g++a
  gi|313125103|ref|YP_004035367.1|  42 AVGWSVERLRRVLSMLAGVFLTVVSGSRTADRTSIPDIGRTVEMTAHAAPWPLagklTCLRVALVAHVLYEQFGVDA 118
                                       5666777777777778889999999***************************99999******************** PP

                   Transglut_core3  77 tlviGvrkeddpfaaHAWvevggrvvtdapeereaftpl 115
                                       ++++Gv+++++ f+aHAWve++g+vvt+++++++a+++l
  gi|313125103|ref|YP_004035367.1| 119 DIRFGVMRKSGVFEAHAWVECDGAVVTGDVSNLDAYAVL 157
                                       *********99*************************997 PP

>> DUF3995  Protein of unknown function (DUF3995)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.2   4.9e-05      0.44      20      81 ..       5      65 ..       1      95 [. 0.74
   2 ?   -0.2   0.1      0.14   1.2e+03      30      50 ..      87     107 ..      66     149 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.9e-05
                           DUF3995 20 eslaeavvgekegsavPsavatlavallllaaAllvlalarllgaplssrllr.laawvvaav 81
                                      + ++  vv ++ g+ vPs   +++v ++ll+ A l la +  ++  + +r+l+ la++++++v
  gi|313125103|ref|YP_004035367.1|  5 RHVGGVVVTRRIGHSVPSQRILAVVSAALLVVAHLGLAVG--WSVERLRRVLSmLAGVFLTVV 65
                                      566788888888877***********************99..544444444330333444444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.14
                           DUF3995  30 kegsavPsavatlavalllla 50 
                                       +++ ++P a+ + +  ++l+a
  gi|313125103|ref|YP_004035367.1|  87 AHAAPWPLAGKLTCLRVALVA 107
                                       333334444444444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 1055.40
//
Query:       gi|313125104|ref|YP_004035368.1|  [L=88]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-09   37.0   0.0    3.6e-09   36.0   0.0    1.5  2  HTH_24         Winged helix-turn-helix DNA-binding
    9.7e-05   22.2   0.0    0.00011   22.0   0.0    1.2  1  MarR_2         MarR family
    0.00021   21.1   0.0     0.0003   20.7   0.0    1.3  1  MarR           MarR family
    0.00025   20.6   0.0    0.00036   20.1   0.0    1.3  1  GntR           Bacterial regulatory proteins, gntR family
    0.00035   20.4   0.1    0.00046   20.0   0.1    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0004   20.3   0.0    0.00047   20.1   0.0    1.2  1  HTH_Crp_2      Crp-like helix-turn-helix domain
     0.0015   18.2   0.1     0.0024   17.6   0.1    1.3  1  HTH_IclR       IclR helix-turn-helix domain
     0.0026   17.7   0.1     0.0034   17.3   0.1    1.2  1  HTH_11         HTH domain
     0.0059   16.5   0.3      0.037   14.0   0.2    2.2  1  HTH_12         Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.021   14.7   0.0    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
      0.017   14.7   0.0      0.017   14.7   0.0    1.0  1  HTH_42         Winged helix DNA-binding domain
      0.018   15.1   0.0      0.024   14.7   0.0    1.2  1  HTH_28         Helix-turn-helix domain
       0.02   15.1   0.0      0.032   14.5   0.0    1.3  1  PaaX           PaaX-like protein
      0.028   13.8   0.0      0.033   13.6   0.0    1.0  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
      0.039   13.9   0.3      0.071   13.1   0.3    1.5  1  PadR           Transcriptional regulator PadR-like family
      0.052   13.4   0.1      0.067   13.0   0.1    1.2  1  HxlR           HxlR-like helix-turn-helix
      0.062   13.3   0.1       0.66   10.0   0.1    2.4  2  BLACT_WH       Beta-lactamase associated winged helix domain
      0.067   13.7   0.2      0.081   13.4   0.2    1.2  1  HTH_27         Winged helix DNA-binding domain
       0.07   13.2   0.0       0.11   12.6   0.0    1.3  1  HTH_20         Helix-turn-helix domain
        0.1   12.4   0.1       0.58   10.0   0.0    1.9  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.15   12.1   0.0       0.19   11.8   0.0    1.2  1  HTH_29         Winged helix-turn helix
       0.16   12.4   0.0       0.24   11.8   0.0    1.3  1  FaeA           FaeA-like protein
       0.17   12.3   0.0       0.25   11.7   0.0    1.2  1  Rrf2           Transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   4.7e-12   3.6e-09       8      48 .]      19      59 ..      14      59 .. 0.94
   2 ?   -2.6   0.0       5.5   4.3e+03      10      20 ..      72      82 ..      71      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 4.7e-12
                            HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++++L+ ++ ++qr+LA+++ l+  tv++ l+rLeeeG++k
  gi|313125104|ref|YP_004035368.1| 19 VYKVLEHDGPLTQRQLADHSLLPTRTVRYALDRLEEEGIVK 59
                                      6789***********************************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.5
                            HTH_24 10 elLqknprisq 20
                                        L ++ r ++
  gi|313125104|ref|YP_004035368.1| 72 YHLSEDERVPN 82
                                      56889999887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.4e-07   0.00011      14      54 ..      23      61 ..      12      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.4e-07
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      L  ++g+ lt+++la++  l+  +v ++l+rL++ G v ++
  gi|313125104|ref|YP_004035368.1| 23 LE-HDGP-LTQRQLADHSLLPTRTVRYALDRLEEEGIVKEK 61
                                      44.5554.******************************876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.8e-07    0.0003      12      48 ..      23      59 ..      17      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.8e-07
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      l++ gpl++ +La+++ + + tv  +ldrLe++G ++
  gi|313125104|ref|YP_004035368.1| 23 LEHDGPLTQRQLADHSLLPTRTVRYALDRLEEEGIVK 59
                                      778899****************************996 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.6e-07   0.00036      13      55 ..      18      59 ..      15      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.6e-07
                                      HHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 13 IlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      ++ ++l++  +L ++r+La+     + tvR AL+rLe+eg+v 
  gi|313125104|ref|YP_004035368.1| 18 LVYKVLEHDGPL-TQRQLADHSLLPTRTVRYALDRLEEEGIVK 59
                                      5567899999**.****************************95 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   5.9e-07   0.00046      13      55 ..      19      61 ..      15      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.9e-07
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      vY++L   gp+t +++a ++ +p  +v  +L +Le+ G+V+ +
  gi|313125104|ref|YP_004035368.1| 19 VYKVLEHDGPLTQRQLADHSLLPTRTVRYALDRLEEEGIVKEK 61
                                      899999**********************************875 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     6e-07   0.00047      21      61 ..      28      66 ..       9      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES- CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririld 61
                                      pltq++lA++  l   tv  +l +L++eg+++ +  + i d
  gi|313125104|ref|YP_004035368.1| 28 PLTQRQLADHSLLPTRTVRYALDRLEEEGIVKEK--LYIQD 66
                                      9******************************954..55555 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   3.1e-06    0.0024      14      49 ..      24      59 ..      22      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.1e-06
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      e++++lt ++lA+++ lp  tv+  L  L+e+G+v+
  gi|313125104|ref|YP_004035368.1| 24 EHDGPLTQRQLADHSLLPTRTVRYALDRLEEEGIVK 59
                                      799*******************************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.4e-06    0.0034       4      44 ..      17      57 ..      15      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.4e-06
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      +++  +le++gp++  +LA++  + +rtvr  +++Lee g+
  gi|313125104|ref|YP_004035368.1| 17 KLVYKVLEHDGPLTQRQLADHSLLPTRTVRYALDRLEEEGI 57
                                      5666677********************************93 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   4.7e-05     0.037      30      53 ..      40      63 ..      19      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                            HTH_12 30 igeravRyrLrkleergltrrvgy 53
                                      + +r+vRy L  lee+g+++ + y
  gi|313125104|ref|YP_004035368.1| 40 LPTRTVRYALDRLEEEGIVKEKLY 63
                                      679***************997766 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.7e-05     0.021       6      46 ..      17      59 ..      15      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                                      HHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      k+++ + e  g+l+  +la++  l+  tv++ L +L+e+G+V+
  gi|313125104|ref|YP_004035368.1| 17 KLVYKVLEhdGPLTQRQLADHSLLPTRTVRYALDRLEEEGIVK 59
                                      7788888889********************************7 PP

>> HTH_42  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.2e-05     0.017     171     234 ..      17      80 ..       4      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                            HTH_42 171 eLvrrylrayGpatvadlaawsgltkarlraalaelvaegelvevrve..rgre.rlfdlpedlael 234
                                       +Lv + l+  Gp t ++la+ s l+ + +r al++l++e  +v  ++   + ++ rl+ l ed+ ++
  gi|313125104|ref|YP_004035368.1|  17 KLVYKVLEHDGPLTQRQLADHSLLPTRTVRYALDRLEEE-GIVKEKLYiqD-ARkRLYHLSEDE-RV 80 
                                       7999999999**************************877.66666666643.344788888853.33 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.1e-05     0.024      14      52 .]      30      70 ..      21      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                            HTH_28 14 svreaArelgisrrtvyrWikryeegGi..agLvprrrrpr 52
                                      ++r++A +  +  rtv+  + r+ee+Gi  + L+ +  r+r
  gi|313125104|ref|YP_004035368.1| 30 TQRQLADHSLLPTRTVRYALDRLEEEGIvkEKLYIQDARKR 70
                                      8999***********************98888888877665 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.1e-05     0.032      38      68 ..      43      76 ..      40      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
                              PaaX 38 slvRaalsRlakaGwlvre...kegrrsfYrLsd 68
                                      ++vR al Rl+++G ++++   +++r+ +Y+Ls+
  gi|313125104|ref|YP_004035368.1| 43 RTVRYALDRLEEEGIVKEKlyiQDARKRLYHLSE 76
                                      79**************9864448999*******8 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.2e-05     0.033      82     148 ..      10      74 ..       7      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                                       HTSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSXEEEES CS
                     RNA_pol_Rpc34  82 tslsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptkkiYll 148
                                        +++ + +lVy++ e  G     +r++     L+   v+  L  Le ++ +k+   ++   k++Y l
  gi|313125104|ref|YP_004035368.1|  10 REMPPSSKLVYKVLEHDGP--LTQRQLADHSLLPTRTVRYALDRLEEEGIVKEKLYIQDARKRLYHL 74 
                                       57999**********9997..89****************************************9966 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   9.1e-05     0.071      37      68 ..      48      77 ..      32      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.1e-05
                                      HHHHHHHTTSEEEEEE-STSSS-EEEEEESHC CS
                              PadR 37 aLkrLekeglveseweesgegpprkyYrlTda 68
                                      aL+rLe+eg+v+++     ++ ++++Y+l ++
  gi|313125104|ref|YP_004035368.1| 48 ALDRLEEEGIVKEKLYI--QDARKRLYHLSED 77
                                      8***********99997..589999***9886 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   8.6e-05     0.067      30      68 ..      39      77 ..      16      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.6e-05
                                      TS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TC CS
                              HxlR 30 kisqkmLaqrLreLeqdglierevypevPpkveYsltek 68
                                       +++++    L +Le++g+++ + y +   k  Y+l+e 
  gi|313125104|ref|YP_004035368.1| 39 LLPTRTVRYALDRLEEEGIVKEKLYIQDARKRLYHLSED 77
                                      5678888999**************************985 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00085      0.66      23      40 ..      43      60 ..      41      69 .. 0.88
   2 ?    0.4   0.0      0.87   6.8e+02      29      39 ..      71      81 ..      65      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00085
                          BLACT_WH 23 rgvlahLeKLeeeGkVkr 40
                                      r+v+  L++LeeeG Vk+
  gi|313125104|ref|YP_004035368.1| 43 RTVRYALDRLEEEGIVKE 60
                                      789999**********98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.87
                          BLACT_WH 29 LeKLeeeGkVk 39
                                      L +L+e+++V 
  gi|313125104|ref|YP_004035368.1| 71 LYHLSEDERVP 81
                                      77999**9996 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2    0.0001     0.081      16      66 ..      26      76 ..      17      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66
                                      +++ ++++l++   +   ++ y+l++L+e G v+++ + +d r +++ l++
  gi|313125104|ref|YP_004035368.1| 26 DGPLTQRQLADHSLLPTRTVRYALDRLEEEGIVKEKLYIQDARKRLYHLSE 76
                                      566666666666666777788*************************99987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014      0.11      15      55 ..      19      59 ..      14      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +++ L  +++lt  +la+   l+  t++y L+ Lee g+v+
  gi|313125104|ref|YP_004035368.1| 19 VYKVLEHDGPLTQRQLADHSLLPTRTVRYALDRLEEEGIVK 59
                                      567788899999999999988******************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00075      0.58      11      42 .]      22      53 ..      20      53 .. 0.95
   2 ?    0.2   0.0       0.9     7e+02       9      21 ..      71      83 ..      68      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00075
                     HTH_AsnC-type 11 aLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                       L++d+ ++ ++LA+   l + tv+  ++rLe
  gi|313125104|ref|YP_004035368.1| 22 VLEHDGPLTQRQLADHSLLPTRTVRYALDRLE 53
                                      699***************************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.9
                     HTH_AsnC-type  9 LeaLqedaRisya 21
                                      L +L ed R +++
  gi|313125104|ref|YP_004035368.1| 71 LYHLSEDERVPNT 83
                                      6689999999986 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.19      14      62 ..      30      79 ..      21      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGlaa....lldrrrsgrprnrlseeqe 62
                                      t +q+A    l  rtv+ +l+r ee+G+ +    ++d r  +r+++ lse+++
  gi|313125104|ref|YP_004035368.1| 30 TQRQLADHSLLPTRTVRYALDRLEEEGIVKeklyIQDAR--KRLYH-LSEDER 79
                                      7778888888889**************888887777733..77888.888776 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00031      0.24      13      46 ..      26      59 ..      16      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                                      S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA 13 kapckTreiAdalglsaYQaRyYLeqLekegkik 46
                                       +p + r++Ad+  l    +Ry L  Le eg +k
  gi|313125104|ref|YP_004035368.1| 26 DGPLTQRQLADHSLLPTRTVRYALDRLEEEGIVK 59
                                      678999*************************998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00033      0.25      21      56 ..      24      59 ..      17      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      e+++p++ +++a++  ++ + ++  l +L+++g+vk
  gi|313125104|ref|YP_004035368.1| 24 EHDGPLTQRQLADHSLLPTRTVRYALDRLEEEGIVK 59
                                      56778******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 480.61
//
Query:       gi|313125105|ref|YP_004035369.1|  [L=117]
Description: hypothetical protein Hbor_03250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.6   0.1       0.06   13.3   0.0    1.7  2  YokU      YokU-like protein, putative antitoxin


Domain annotation for each model (and alignments):
>> YokU  YokU-like protein, putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.4e-06      0.06      23      43 ..       9      29 ..       5      44 .. 0.83
   2 ?   -1.8   0.0      0.18   3.2e+03       2       6 ..      72      76 ..      69     105 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-06
                              YokU 23 dgtkaieiketPsieCseCgl 43
                                      d t++ +i++tPs++Cs+C+ 
  gi|313125105|ref|YP_004035369.1|  9 DQTHSHDIDDTPSVTCSRCDR 29
                                      7788999************85 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.18
                              YokU  2 CewCe 6 
                                      C+ C 
  gi|313125105|ref|YP_004035369.1| 72 CRHCP 76
                                      44443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 678.71
//
Query:       gi|313125106|ref|YP_004035370.1|  [L=95]
Description: translation initiation factor 1a (aeif-1a) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-21   76.4   0.3    1.4e-21   76.1   0.3    1.1  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.3   7.6e-26   1.4e-21       2      64 .]      18      79 ..      17      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 7.6e-26
                                      EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      e  ++V++  g+n++rV++ d gke++++ipg+++ + wi++Gd+VlVe+++ +++k+ I +r
  gi|313125106|ref|YP_004035370.1| 18 ELFAVVTQHNGGNHVRVRCQD-GKERMGRIPGRMKYRTWINEGDVVLVEPWDWQDEKANIEWR 79
                                      789****************85.**************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 551.22
//
Query:       gi|313125107|ref|YP_004035371.1|  [L=225]
Description: methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-12   47.3   0.0    3.9e-12   46.7   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    5.7e-12   46.1   0.0    9.1e-12   45.5   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.3e-07   31.4   0.0    2.3e-07   30.6   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
    1.5e-07   31.4   0.0    2.1e-07   30.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    8.4e-06   26.5   0.1    1.4e-05   25.7   0.1    1.3  1  Methyltransf_12  Methyltransferase domain
    2.8e-05   23.9   0.0    3.6e-05   23.6   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   14.5   0.0      0.016   14.2   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.015   14.7   0.1      0.098   12.1   0.1    1.9  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.8e-15   3.9e-12       1      93 [.      65     157 ..      65     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.8e-15
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGB..SSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedl..pfedgsfDlvvssgalh 75 
                                       +L+lGc +Gr++++l ++ g ++v gv+i++e+ + + e++ e +   +f++  +e++  +fed+ fD+v+s+ +l+
  gi|313125107|ref|YP_004035371.1|  65 ILELGCSSGRHLAHLFDH-GYENVSGVEINAEAFDVMDEEYPELSDAGTFYHDAIESVvrKFEDDAFDVVYSVETLQ 140
                                       8*****************.69********************886669999*99999974469**********999** PP

                                       GSSHHHHHHHHHHHHHHE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvL 93 
                                       hl+ +d+e +++e+ar++
  gi|313125107|ref|YP_004035371.1| 141 HLH-PDAEWVFDELARIT 157
                                       *98.78899******986 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   4.1e-15   9.1e-12       1      88 [.      66     157 ..      66     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 4.1e-15
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT..SS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaekl..pfednsfDlvvssevlhhv 74 
                                       L++Gc +Gr++++l ++g ++v gv++++e+ ++  e+++e     +f +  +e++  +fed+ fD+v+s e+l+h+
  gi|313125107|ref|YP_004035371.1|  66 LELGCSSGRHLAHLFDHGyENVSGVEINAEAFDVMDEEYPELSDAGTFYHDAIESVvrKFEDDAFDVVYSVETLQHL 142
                                       89**************************************9998778999999985467****************** PP

                                       .CCHHHHHHHHHHHE CS
                   Methyltransf_11  75 .edpekalkeiaRvL 88 
                                        +d e +++e+aR+ 
  gi|313125107|ref|YP_004035371.1| 143 hPDAEWVFDELARIT 157
                                       99***********86 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0     1e-10   2.3e-07       6     113 ..      54     168 ..      51     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1e-10
                              MetW   6 liaelikpgsrvldlGcGdGellellkeekqvdgrGleldeeg..vaec....vakGlsviqgdldkdlenfedksf 76 
                                       +i +  +p + +l+lGc  G  l  l ++   +  G+e+++e+  v++     ++   +  ++ +++ + +fed++f
  gi|313125107|ref|YP_004035371.1|  54 TISQHAEPDAAILELGCSSGRHLAHLFDHGYENVSGVEINAEAfdVMDEeypeLSDAGTFYHDAIESVVRKFEDDAF 130
                                       67888999******************999777777777777651144331111233335788999************ PP

                              MetW  77 dyvvlsqtlqatr.npkevldellrigrraivsfPnfG 113
                                       d+v    tlq ++ +++ v+del ri++  +++  n G
  gi|313125107|ref|YP_004035371.1| 131 DVVYSVETLQHLHpDAEWVFDELARITETLLITVENEG 168
                                       ************934567**************998876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   9.3e-11   2.1e-07       1     110 [.      39     158 ..      39     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9.3e-11
                   Methyltransf_23   1 ydaqreeelsdklerll.pklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqe 75 
                                       y+ + ++e s++l+++  +  ++++ +L++Gc +G+ l +l ++g+ +v gv+++ e               fd ++
  gi|313125107|ref|YP_004035371.1|  39 YAYYGPNETSELLKETIsQHAEPDAAILELGCSSGRHLAHLFDHGYeNVSGVEINAE--------------AFDVMD 101
                                       5666777778888665526689*************99999999***7888****975..............233333 PP

                   Methyltransf_23  76 aaepqg.....................kfdlIvlrevlehvp.dppellrqiatllk 110
                                       +++p+                       fd++++ e+l h++ d + +++ +a++++
  gi|313125107|ref|YP_004035371.1| 102 EEYPELsdagtfyhdaiesvvrkfeddAFDVVYSVETLQHLHpDAEWVFDELARITE 158
                                       333222222334444444444444444***************667777777777665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   6.3e-09   1.4e-05       1      91 [.      66     155 ..      66     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.3e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       Le+Gc +G+ l++l ++  + e + gv+i+++a++   e+  + ++   ++++   +++  +++ ++fD+v++ ++l
  gi|313125107|ref|YP_004035371.1|  66 LELGCSSGRHLAHLFDH--GYENVsGVEINAEAFDVMDEEYPELSD-AGTFYHDAIESVVRKFEDDAFDVVYSVETL 139
                                       8****************..777777*********999999999996.6677777777778888889*********** PP

                   Methyltransf_12  77 hhl.kdirevldnirk 91 
                                       +hl +d + v+d++++
  gi|313125107|ref|YP_004035371.1| 140 QHLhPDAEWVFDELAR 155
                                       ***9999999988776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.6e-08   3.6e-05       4      99 ..      62     155 ..      59     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.6e-08
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlil 79 
                                       +  +l+lGC +G+ +  l++  ++  +v G++i++ea  ++ e+  +l +d  +F +  ie+   k +ed+ fD++ 
  gi|313125107|ref|YP_004035371.1|  62 DAAILELGCSSGRHLAHLFDHGYE--NVSGVEINAEAFDVMDEEYPEL-SDAGTFYHDAIESvVRK-FEDDAFDVVY 134
                                       6689***************86555..588**************86644.5679*********5555.********** PP

                   Methyltransf_31  80 snevl.naladpdkileeier 99 
                                       s e+l ++ +d + ++ e+ r
  gi|313125107|ref|YP_004035371.1| 135 SVETLqHLHPDAEWVFDELAR 155
                                       *****7667777777766665 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.1e-06     0.016     116     198 ..      62     145 ..      47     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.1e-06
                                       T-EEEEET-TTSHHHHHHHHCT-SEEEEE---.HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEES- CS
                    Methyltransf_9 116 grtildvGcgnGyhlwrmvgegaklvvGidPs.elfliqfeavrkllgedqrahllplgieqlpeleafdtvfsmGv 191
                                       + +il++Gc++G hl  +  +g + v G++ + e f +  e   +l++  +  h+   ++ +  e +afd+v+s+  
  gi|313125107|ref|YP_004035371.1|  62 DAAILELGCSSGRHLAHLFDHGYENVSGVEINaEAFDVMDEEYPELSDAGTFYHDAIESVVRKFEDDAFDVVYSVET 138
                                       568***************************7625677777888889888887777655555556689********** PP

                                       GGG-S-H CS
                    Methyltransf_9 192 lyhrrsP 198
                                       l h +  
  gi|313125107|ref|YP_004035371.1| 139 LQHLHPD 145
                                       9997654 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.4e-05     0.098      32     166 ..      63     200 ..      47     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                                       -EEEEES-TTSHHHHHHHHTT-.EEEEEES-HHHHHHHHHHH.HH.TT-TTEEEEE--GGG----S-EEEEEEESSG CS
                              TehB  32 gkvldlgcgqgrnslylsllgy.dvtawdknensiafleeik.ek.enlknistalydineaklderydfilstvvl 105
                                       + +l+lgc +gr   +l   gy +v+ ++ n+++   ++e   e  ++ +  + a+  +     d+ +d + s   l
  gi|313125107|ref|YP_004035371.1|  63 AAILELGCSSGRHLAHLFDHGYeNVSGVEINAEAFDVMDEEYpELsDAGTFYHDAIESVVRKFEDDAFDVVYSVETL 139
                                       4689******************55999******99999864312212223334444444444556778888888888 PP

                                       GGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB..--SSS--SS..--S--B-TTHHHHHTTTSEEE CS
                              TehB 106 mfleaeripsiienmqectkvggynlivaam..stddvpctv..pfsftfkegelkeyykdwell 166
                                         l++++   + +++ + t++    li      +  d   t     s  + +ge+  yy+dw+ +
  gi|313125107|ref|YP_004035371.1| 140 QHLHPDA-EWVFDELARITETL---LITVENegEHSDAGGTAddEPSVNYVDGEVPLYYRDWNAV 200
                                       8877764.34444555544432...1211110012222222211335666777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1274.11
//
Query:       gi|313125108|ref|YP_004035372.1|  [L=570]
Description: ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.6e-51  173.1   2.5    5.8e-44  150.6   1.6    2.2  2  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
  ------ inclusion threshold ------
      0.033   14.0   5.9      0.058   13.3   5.9    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.3e-08   0.00011     300     374 ..      71     144 ..      43     147 .. 0.74
   2 !  150.6   1.6   6.4e-48   5.8e-44       6     292 ..     287     564 ..     284     568 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-08
                                       EEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECT.TSTTHHHHHHHHSTTC CS
                         SBP_bac_5 300 tlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgad.ypdpdnflnpflsssg 374
                                       +   +s++p++ ++ +li+ ql++iG++vev +++w  t +  + + ++d +++ w +  ++dp   l++  +ss+
  gi|313125108|ref|YP_004035372.1|  71 VNNSQSYNPPRHDAINLIARQLNDIGLDVEVDVLEW-GTLY-NRVSVEYDYSFSTWHTFfTIDPVLELSSTMHSSN 144
                                       455677899999************************.6664.4556777777777777656777666666656555 PP

  == domain 2  score: 150.6 bits;  conditional E-value: 6.4e-48
                                       SEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEEE CS
                         SBP_bac_5   6 LAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrftl 82 
                                       LA++ w +  D +t ++++R +  ++DG++lt eDv+f+++++++++ + ++ ++++    i+++eavdd tvr+++
  gi|313125108|ref|YP_004035372.1| 287 LATD-W-TRVDETTMEYTIRTDHAWHDGEDLTTEDVAFTYNYIAENEVPLYSVQTQY----IDSAEAVDDSTVRINM 357
                                       99**.3.599******************************************99997....**************** PP

                                       SSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSEEEEEE CS
                         SBP_bac_5  83 kkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldriefkv 159
                                       +++  +f tl+  +++ ++k+++e  ++++  + e+pvg+GP +++ +++g +  l+++ d     ++ +++  +++
  gi|313125108|ref|YP_004035372.1| 358 SQALGPFHTLVGTQIPILPKHKWERRSNPSQANVEEPVGSGPLMFDYWNKGTEFGLKKFADH--FAPVDFEQRYWRI 432
                                       *************************************************************5..69*********** PP

                                       -.SHHHHHHHHHTTSSSEEESTTCCTHCHH.HHHTTEEE..EEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-H CS
                         SBP_bac_5 160 ipdsdaraaalqsGeiddvaepppsdieql.keakglkv..lyespgggvtylafNtkkppfddkrvRqAlsyAiDr 233
                                       ip++++  + l++Ge+  ++ p+     +l ++++++    ++++p +++++++ N +++ +dd+ +R+A   Ai+r
  gi|313125108|ref|YP_004035372.1| 433 IPEASTVWELLKNGEL-NYE-PFGRIDRSLnENQDHE-AigTKFEPATTFWHFTPNERQTGLDDPVLRKAAVNAIPR 506
                                       *6666666666*****.443.3333333331333333.2478*********************************** PP

                                       HHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCE CS
                         SBP_bac_5 234 eeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdgggl 292
                                       + ivk++l    +++  +++p +   + e  + y+    ekA+  LkeaGy ++d+g+l
  gi|313125108|ref|YP_004035372.1| 507 TPIVKQILFDFPQKGFDIVSPAFGPLHTEEVTRYE-ESKEKARSRLKEAGYSWTDDGML 564
                                       ******************99999999999998875.699***************99876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   5.9   6.4e-06     0.058       4      23 ..      10      29 ..       7      34 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-06
                        TAT_signal  4 RRdFLKgsAAaaAAaalggc 23
                                      RR FLK++ A++ A++++ +
  gi|313125108|ref|YP_004035372.1| 10 RRRFLKATTAGGLAGMTALA 29
                                      ********999966665533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 3436.56
//
Query:       gi|313125109|ref|YP_004035373.1|  [L=325]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-42  143.1  11.7    7.9e-42  143.1  11.7    2.0  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       0.5   8.9e+03     164     176 ..      17      29 ..      10      46 .. 0.59
   2 ?    0.2   0.4     0.029   5.3e+02     110     131 ..      93     114 ..      91     116 .. 0.63
   3 !  143.1  11.7   4.4e-46   7.9e-42       1     184 [.     115     323 ..     115     324 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.5
                      BPD_transp_1 164 avlllnlvadilq 176
                                        ++++ +v+++l 
  gi|313125109|ref|YP_004035373.1|  17 TFWAVGTVLFFLF 29 
                                       3333333333333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.029
                      BPD_transp_1 110 iitglilafggllggavllefl 131
                                       i+t l+++++++l+++v+++ +
  gi|313125109|ref|YP_004035373.1|  93 ILTYLPNTLVLMLTAFVIAYAF 114
                                       6666777777777777666655 PP

  == domain 3  score: 143.1 bits;  conditional E-value: 4.4e-46
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..........................vilsilgh 51 
                                       gi+lG+l++ +r++++ +   +   + +s+Psf++++++++vf                             + l+h
  gi|313125109|ref|YP_004035373.1| 115 GITLGVLSGWYRGSRFERSTVITALLARSVPSFWVGLMVLWVFgsmfnlipmagmtspgvehenfltmvLSVDFLKH 191
                                       89******************************************************************97788899* PP

                      BPD_transp_1  52 lilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavll 128
                                       l+ p+++l+ ++++ + +++r+++l++l++d++ + ra+G+++++i++k++ +nal pi+t +++a+g+++gg+vl+
  gi|313125109|ref|YP_004035373.1| 192 LVAPALVLAYYFMGYPLLIMRSSMLEVLSEDFIDVCRAKGLKERTIMFKHAARNALLPIVTAAAIALGYAVGGSVLI 268
                                       ***************************************************************************** PP

                      BPD_transp_1 129 eflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       e++++wpG+g+ +++a l +d++ ++ g++ +l++ ++lln+vad+ + +ldprv+
  gi|313125109|ref|YP_004035373.1| 269 ETVFAWPGIGREMVRAVLRRDFPVAQ-GTFMVLAATIILLNFVADLAYGYLDPRVT 323
                                       **************************.***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2015.67
//
Query:       gi|313125110|ref|YP_004035374.1|  [L=326]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-24   86.1  11.6    2.4e-24   86.1  11.6    2.1  3  BPD_transp_1  Binding-protein-dependent transport system inne
    4.5e-05   23.3   0.3    4.5e-05   23.3   0.3    3.1  3  OppC_N        N-terminal TM domain of oligopeptide transport 
     0.0033   17.1   0.3      0.012   15.3   0.0    1.9  2  TadZ_N        Pilus assembly protein TadZ N-terminal


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4       0.3   1.8e+03     157     170 ..      54      67 ..      31      75 .. 0.55
   2 ?   -3.5   2.4       1.3   7.5e+03     143     153 ..     108     118 ..      58     140 .. 0.51
   3 !   86.1  11.6   4.1e-28   2.4e-24       1     182 [.     141     324 ..     141     326 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.3
                      BPD_transp_1 157 gvlalviavlllnl 170
                                       ++l+++++vl+ +l
  gi|313125110|ref|YP_004035374.1|  54 SMLMVAFFVLVAIL 67 
                                       33333333333333 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.3
                      BPD_transp_1 143 eailgydysei 153
                                       ++ +g+d+ + 
  gi|313125110|ref|YP_004035374.1| 108 TTAQGFDIFSQ 118
                                       22223333222 PP

  == domain 3  score: 86.1 bits;  conditional E-value: 4.1e-28
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g+++G++a+ ++++ +d++l++l+++l+++P +  +i+lv        lg   +  ++++++l++ +++r+ir++al
  gi|313125110|ref|YP_004035374.1| 141 GTMVGLVAG-YYGGAVDDALMRLVDFLYGMPLLPTVIILV------ALLGPNLWNiILAVIILQWRATARVIRSQAL 210
                                       7899*****.******************************......99**8888889******************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG....lgtllleailgyd 149
                                       + +++ +v+aa + Gas+w+i+ +++ Pn+lp+ +    +a+++++   + ++f+g + +     gt+l  a  ++ 
  gi|313125110|ref|YP_004035374.1| 211 SLRERPFVKAAQVAGASDWHIISRHLAPNVLPMSFLYGSFAIAWAILTEAGVSFIGLGDPntvsWGTMLQAARAYSA 287
                                       ********************************************************666677777777777777777 PP

                      BPD_transp_1 150 yseis....nggvlalviavlllnlvadilqrlldpr 182
                                       +s+++    + + + ++++v+   l+ +   ++ +p+
  gi|313125110|ref|YP_004035374.1| 288 LSFGAwwwfVPPGVCIGLLVISGFLIGRGYEEITNPK 324
                                       7777777777777777777777777766666666665 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   0.7         3   1.8e+04       2       9 ..      33      40 ..      33      42 .. 0.85
   2 !   23.3   0.3   7.5e-09   4.5e-05      18      45 ..      53      82 ..      50      91 .. 0.83
   3 ?    1.4   0.5     0.053   3.2e+02      25      36 ..     175     186 ..     173     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 3
                            OppC_N  2 lwqdawrr 9 
                                      lwq++++r
  gi|313125110|ref|YP_004035374.1| 33 LWQETLKR 40
                                      79*99987 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 7.5e-09
                            OppC_N 18 vglvilllllliaifaPliaPydp..qdli 45
                                      +++ ++++++l+ai+aP+iaP++p  +++ 
  gi|313125110|ref|YP_004035374.1| 53 LSMLMVAFFVLVAILAPYIAPNPPleRQYQ 82
                                      5899******************99994443 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.053
                            OppC_N  25 lllliaifaPli 36 
                                       +++l+a+++P +
  gi|313125110|ref|YP_004035374.1| 175 VIILVALLGPNL 186
                                       799999999988 PP

>> TadZ_N  Pilus assembly protein TadZ N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.23   1.3e+03     103     117 ..     119     133 ..     102     141 .. 0.81
   2 !   15.3   0.0     2e-06     0.012       4      68 ..     216     280 ..     213     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.23
                                       EETT-BHHHHHHHHH CS
                            TadZ_N 103 itygaraseltglir 117
                                       + +g+ra+ l gli 
  gi|313125110|ref|YP_004035374.1| 119 LIFGTRAALLVGLIA 133
                                       568999999999996 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2e-06
                                       EEEEE-SSHHHHHHHHHHTTTTEEEEE--ST-HHHHHHHHHHHT-SEEEEEE-TTTHHHHHHHHH CS
                            TadZ_N   4 nfvaltqhpgeldwlqnslasagqvvpagsasleellalldvtaagvlfislgksnlvsqgalve 68 
                                        fv  +q  g  dw   s   a +v+p         +a   +t agv fi lg  n vs g++++
  gi|313125110|ref|YP_004035374.1| 216 PFVKAAQVAGASDWHIISRHLAPNVLPMSFLYGSFAIAWAILTEAGVSFIGLGDPNTVSWGTMLQ 280
                                       699999*********************999888888999999*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2099.72
//
Query:       gi|313125111|ref|YP_004035375.1|  [L=345]
Description: oligopeptide/dipeptide ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-29  103.5   0.0      2e-29  102.9   0.0    1.3  1  ABC_tran         ABC transporter
    6.8e-21   74.6   0.3    1.6e-20   73.4   0.3    1.7  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    6.9e-07   28.9   0.0    1.1e-06   28.3   0.0    1.2  1  SMC_N            RecF/RecN/SMC N terminal domain
    2.9e-06   27.3   0.2      0.054   13.3   0.1    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    6.5e-05   23.2   0.3    0.00045   20.5   0.3    2.0  1  AAA_22           AAA domain
    0.00034   21.0   0.0    0.00067   20.1   0.0    1.7  1  AAA_16           AAA ATPase domain
    0.00039   20.3   0.0    0.00089   19.2   0.0    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
    0.00054   20.4   0.1     0.0021   18.5   0.1    2.0  1  AAA              ATPase family associated with various cellul
    0.00063   19.2   0.0     0.0013   18.1   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0022   16.9   1.0       0.02   13.7   0.1    2.2  2  ABC_ATPase       Predicted ATPase of the ABC class
      0.006   16.7   0.0      0.015   15.4   0.0    1.5  2  tRNA_lig_kinase  tRNA ligase kinase domain
     0.0093   16.5   0.2      0.021   15.4   0.0    1.7  1  AAA_23           AAA domain
     0.0094   15.7   0.0      0.016   15.0   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.032   14.0   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.021   14.6   0.0      0.037   13.8   0.0    1.3  1  AAA_29           P-loop containing region of AAA domain
      0.024   14.6   0.0      0.061   13.2   0.0    1.6  1  NACHT            NACHT domain
      0.029   14.9   0.0      0.055   14.0   0.0    1.5  1  AAA_18           AAA domain
      0.037   14.0   0.0      0.092   12.7   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
      0.044   13.4   0.1      0.066   12.9   0.1    1.4  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.068   12.7   0.0       0.14   11.7   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.076   12.9   0.1       0.17   11.8   0.0    1.6  1  RsgA_GTPase      RsgA GTPase
      0.083   13.0   0.1       0.25   11.5   0.0    1.8  2  MMR_HSR1         50S ribosome-binding GTPase
      0.089   13.2   0.0       0.17   12.3   0.0    1.6  1  RNA_helicase     RNA helicase
       0.11   12.2   0.0       0.22   11.3   0.0    1.4  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.11   12.2   0.0       0.19   11.5   0.0    1.4  1  AAA_24           AAA domain
       0.12   12.6   0.0       0.22   11.8   0.0    1.4  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.29   10.3   3.7       0.22   10.7   0.2    2.2  3  NB-ARC           NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.0     3e-32     2e-29       2     136 ..      24     180 ..      23     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 3e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..x RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....qeleslrkeigvlpqe..p 68 
                                       + vs++l++ge ++ivGe+G+GK+tL+k+l+g l +    ++G+i+++g+dl+e    ++++   +ei+++ q   +
  gi|313125111|ref|YP_004035375.1|  24 DGVSFSLEAGENLGIVGESGCGKTTLAKALIGILPNegyvNAGRIEFKGDDLTEmsdsERRRLKWEEISMIAQSamN 100
                                       78*******************************998888899999********99987777777799*******999 PP

                                       -S-TTSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       +l+p +t+re+             + e  e + + ++l++l+ +++++ p+++SgG++qr ++a+al+ +p+l+l+D
  gi|313125111|ref|YP_004035375.1| 101 SLDPVYTIREQiveaiethrpgtGRVESTEIVTEMFELVGLDPDRADDYPHQFSGGMRQRAMIAMALALEPSLILAD 177
                                       *************998888887644444777778888888888999999**************************** PP

                                       STT CS
                                       xxx RF
                          ABC_tran 134 Ept 136
                                       Ept
  gi|313125111|ref|YP_004035375.1| 178 EPT 180
                                       **9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.3   2.4e-23   1.6e-20       2      65 .]     233     296 ..     232     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2.4e-23
                         oligo_HPY   2 ErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       E+gp++++f++p+HPYT++L r++p ++++ + l +ikg +p+l + ++GC+Fa RCp+a++ C
  gi|313125111|ref|YP_004035375.1| 233 EEGPVEEIFNQPYHPYTIGLKRAFPNIRQPEQDLLSIKGYPPELVDPPTGCRFAARCPMATDRC 296
                                       99*************************************************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.6e-09   1.1e-06      28     212 ..      37     227 ..      26     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.6e-09
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH..CCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrse..klsdlihk.skekasvkkaeveitfdnedkklkiekeevsisr 101
                                        ivG+ G+GK+ l  A+  +L ++ + +  +   k +dl     +e++++k  e++++ +     ++  ++ ++i+ 
  gi|313125111|ref|YP_004035375.1|  37 GIVGESGCGKTTLAKALIGILPNEGYVNAGRIefKGDDLTEMsDSERRRLKWEEISMIAQSA---MNSLDPVYTIRE 110
                                       59***************9999877553332220133566665456888999999*9984444...44589999**** PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                       ++++  e++    g+  + + v+e++e +g++++       ++SgG ++ +++a+ +A++     +l l De   aL
  gi|313125111|ref|YP_004035375.1| 111 QIVEAIETHRPGTGRVESTEIVTEMFELVGLDPDraddyphQFSGGMRQRAMIAMALALE----PSLILADEPTTAL 183
                                       *******999999999999999************9*******************999986....46999******** PP

                                       -HHHHHHHHHHHHHHCTTSE..EEEE-SSHHHCCC-.SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxx RF
                             SMC_N 172 DeknvkkvaellkeksknaQ..fivislreemleka.dklvgvt 212
                                       D     ++ +++ + +++ Q  ++vi+++  ++++  d+++ ++
  gi|313125111|ref|YP_004035375.1| 184 DVIMQDQILKRISQIQDEIQssMLVITHDVSVVAETcDRVLVMY 227
                                       *************9999977558999999888766536665555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00022      0.14       3      62 ..      37      90 ..      36      98 .. 0.85
   2 !   13.3   0.1   8.2e-05     0.054     228     302 ..     144     216 ..     126     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefei 62
                                      +++G  g+GK++L +al      ++ + ++++++ g+ ++++++    +++++ + ++e 
  gi|313125111|ref|YP_004035375.1| 37 GIVGESGCGKTTLAKAL------IGILPNEGYVNAGRIEFKGDDLTEMSDSERRRLKWEE 90
                                      69***************......7778899999999999999888888888888877775 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.2e-05
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell...kelsrngaQviltTHSpll 301
                                       d+ +  ++++S G+++  a++++ l++ +  sl+l DEp + L+  ++  +l+ +    ++    +  ++ TH+ ++
  gi|313125111|ref|YP_004035375.1| 144 DRADDYPHQFSGGMRQR-AMIAMALALEP--SLILADEPTTALDVIMQDQILKRIsqiQDEI--QSSMLVITHDVSV 215
                                       666677899********.99999999887..9*************88888888885432222..3567999998776 PP

                            AAA_21 302 l 302
                                       +
  gi|313125111|ref|YP_004035375.1| 216 V 216
                                       5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   6.8e-07   0.00045      10     127 ..      38     208 ..      31     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.8e-07
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.....................................erpevvfvtlps 49 
                                       ++GesG+GKTtl++ l   l++e + +                                                  
  gi|313125111|ref|YP_004035375.1|  38 IVGESGCGKTTLAKALIGILPNEGYVNAgriefkgddltemsdserrrlkweeismiaqsamnslD----------- 103
                                       89*******************999998899999999999999987777666333333333333330........... PP

                            AAA_22  50 stsskdllrellralglelka...................erlsseellealeqalrarav........ielliiDE 99 
                                            ++++++++a++  + +                    +++ +++ +++   +r+ra+        ++l++ DE
  gi|313125111|ref|YP_004035375.1| 104 --PVYTIREQIVEAIETHRPGtgrvesteivtemfelvglDPDRADDYPHQFSGGMRQRAMiamalalePSLILADE 178
                                       ..555555555555555444466666666666666666665555555556666666666666666666779999999 PP

                            AAA_22 100 aqh.lr...seealeeLrsllnlsrkgvqliL 127
                                           l+   ++++l+ ++++++  + + ++++
  gi|313125111|ref|YP_004035375.1| 179 PTTaLDvimQDQILKRISQIQD--EIQSSMLV 208
                                       8887877777999999999888..77666644 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     1e-06   0.00067      25      70 ..      34      79 ..      21     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggif....lrgkcdqlesaipys 70
                                      e++ ++GesG+GK++l+++l   l  + g++    ++ k d+l   +++s
  gi|313125111|ref|YP_004035375.1| 34 ENLGIVGESGCGKTTLAKALIGILPNE-GYVnagrIEFKGDDL---TEMS 79
                                      78889****************655555.888788899999999...3332 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.3e-06   0.00089       2      28 ..      36      62 ..      35      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                              MobB  2 lgivgksgsGKTtLleklipelkargl 28
                                      lgivg sg+GKTtL + li +l ++g+
  gi|313125111|ref|YP_004035375.1| 36 LGIVGESGCGKTTLAKALIGILPNEGY 62
                                      79**********************998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   3.2e-06    0.0021       3      38 ..      38      86 ..      36     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.2e-06
                                      EESSTTSSHHHHHHHHHHHH......THEEEEEETTTCSSS.......S CS
                               AAA  3 lyGppGtGKTllakavakel......gvefleisgsellsk.......y 38
                                      ++G  G+GKT+laka++  l      ++  +e++g +l+++       +
  gi|313125111|ref|YP_004035375.1| 38 IVGESGCGKTTLAKALIGILpnegyvNAGRIEFKGDDLTEMsdserrrL 86
                                      68*****************866554456678999999885544443330 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     2e-06    0.0013       8      49 ..      19      60 ..      15     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                      Mg_chelatase  8 qeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                        +a   +  +   g nl +vG +G+GKt lak+l ++lp+ 
  gi|313125111|ref|YP_004035375.1| 19 PAQAVDGVSFSLEAGENLGIVGESGCGKTTLAKALIGILPNE 60
                                      556666666777778899**********************85 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.17   1.1e+02     249     264 ..      38      53 ..       9      57 .. 0.88
   2 !   13.7   0.1     3e-05      0.02     323     379 ..     153     208 ..     144     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.17
                                       EEE-TTSSHHHHHHHH CS
                        ABC_ATPase 249 IvGggfhGKsTLLeAl 264
                                       IvG    GK+TL +Al
  gi|313125111|ref|YP_004035375.1|  38 IVGESGCGKTTLAKAL 53 
                                       99*************8 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3e-05
                                       --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHC CS
                        ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdr 379
                                        SG + q a i+ al ++ +l+L DE t+A   +++D+ ++++  + ++ i++ +  
  gi|313125111|ref|YP_004035375.1| 153 FSGGMRQRAMIAMALALEPSLILADEPTTALDVIMQDQILKRIS-QIQDEIQSSMLV 208
                                       59***********************************9999886.555556654444 PP

>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.2e-05     0.015       9      80 ..      43     119 ..      38     130 .. 0.82
   2 ?   -2.9   0.0       9.5   6.3e+03     143     149 ..     192     198 ..     173     218 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                                       TSSHHHHHHHHHHH-TTSEEEEGGGS-TT..-SS-HHHHHHHTTSSTT--EEEEES---...SHHHHHHHHHHHHHH CS
                   tRNA_lig_kinase   9 GCGkttvaltlenlfgeWghvqnDnitgk..dkkklvkealellkkdeskvvlvDrnnh...qkreRkqlfeeidel 80 
                                       GCGktt a++l  + ++ g+v    i+ k  d +++ ++  + lk +e++++     n+     + R+q++e i++ 
  gi|313125111|ref|YP_004035375.1|  43 GCGKTTLAKALIGILPNEGYVNAGRIEFKgdDLTEMSDSERRRLKWEEISMIAQSAMNSldpVYTIREQIVEAIETH 119
                                       9***********************99666547788999999999999999999888887222356788888888765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.5
                                       HHT---- CS
                   tRNA_lig_kinase 143 ikrfqpv 149
                                       +kr  ++
  gi|313125111|ref|YP_004035375.1| 192 LKRISQI 198
                                       2222222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.1e-05     0.021      23      45 ..      37      59 ..      22     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.1e-05
                            AAA_23 23 lItGpNGaGKTTildAiklaLyg 45
                                       I+G+ G+GKTT+  A+  +L +
  gi|313125111|ref|YP_004035375.1| 37 GIVGESGCGKTTLAKALIGILPN 59
                                      5***************9988866 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-05     0.016       3      41 ..      37      78 ..      36     122 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                               PRK  3 gvagsSGaGkttvarklekifgrekvk.aaei..egdsflrl 41
                                      g+ g+SG+Gktt+a++l  i+ +e+   a  i  +gd ++++
  gi|313125111|ref|YP_004035375.1| 37 GIVGESGCGKTTLAKALIGILPNEGYVnAGRIefKGDDLTEM 78
                                      99*******************987755033343333333333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.8e-05     0.032      35      67 ..      20      53 ..       4      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                         IstB_IS21 35 vkeLatlsf.iekkenivllGpsGvGKshlaial 67
                                       +++ + sf +e+ en+ ++G sG GK+ la al
  gi|313125111|ref|YP_004035375.1| 20 AQAVDGVSFsLEAGENLGIVGESGCGKTTLAKAL 53
                                      56666677757899******************98 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.6e-05     0.037      13      46 ..      24      57 ..      21      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      dg +++++  ++  ++G+sG GK+Tl  A++ +L
  gi|313125111|ref|YP_004035375.1| 24 DGVSFSLEAGENLGIVGESGCGKTTLAKALIGIL 57
                                      67778888666999************99998877 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.2e-05     0.061       5      22 ..      38      55 ..      35      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.2e-05
                                      EEC-TTTCHHHHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqklal 22
                                      + Ge+G+GKTtL++ l+ 
  gi|313125111|ref|YP_004035375.1| 38 IVGESGCGKTTLAKALIG 55
                                      89************9985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.2e-05     0.055       3      65 ..      38     100 ..      36     139 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.2e-05
                            AAA_18   3 ltGtpGvGKttlakeL....skrlgf..gvnlrdvakenglllevdpealdeskrldedkldklldale 65 
                                       + G +G+GKttlak+L         +   vn + + ++++ l+e  +   ++ +   e+  + +++a++
  gi|313125111|ref|YP_004035375.1|  38 IVGESGCGKTTLAKALigilP----NegYVNAGRIEFKGDDLTEMSDS--ERRRLKWEEISMIAQSAMN 100
                                       8899************44431....24566666666665555555555..2333333333333333333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014     0.092       4      55 ..      38      89 ..      35     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                      EE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--........ CS
                             AAA_5  4 LvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslv 55
                                      +vG++G+gK++la+ l   l +e  + +++   + +dl+   + + ++ +++
  gi|313125111|ref|YP_004035375.1| 38 IVGESGCGKTTLAKALIGILPNEGYVNAGRIEFKGDDLTEMSDSERRRLKWE 89
                                      79**************999988877777777777777776666555555555 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1    0.0001     0.066       9      36 ..      28      55 ..      20     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                      S-EBTT-EEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  9 fpivqGqrtlipgafgvGktvisqslsk 36
                                      f++  G++++i+g++g+Gkt+++++l+ 
  gi|313125111|ref|YP_004035375.1| 28 FSLEAGENLGIVGESGCGKTTLAKALIG 55
                                      78889******************99875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.14      30      64 ..      30      64 ..      26      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                             AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekyls 64
                                      l+++ ++ +vG++G+GKt+++k l+  l++e y+ 
  gi|313125111|ref|YP_004035375.1| 30 LEAGENLGIVGESGCGKTTLAKALIGILPNEGYVN 64
                                      677888999****************9999998875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00026      0.17      88     121 ..      21      55 ..       5      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       ++++ ++  l+  +   +vG+SG GK+tL +al++
  gi|313125111|ref|YP_004035375.1|  21 QAVDGVSFSLEAgENLGIVGESGCGKTTLAKALIG 55 
                                       566677777777678889*************9986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00037      0.25       2      21 ..      36      55 ..      35      94 .. 0.83
   2 ?   -1.4   0.1       3.7   2.5e+03      51      51 ..     176     176 ..     105     239 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                       +ivG +  GK+tL +al+g
  gi|313125111|ref|YP_004035375.1| 36 LGIVGESGCGKTTLAKALIG 55
                                      69****************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.7
                                       E CS
                          MMR_HSR1  51 v 51 
                                       +
  gi|313125111|ref|YP_004035375.1| 176 A 176
                                       3 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00026      0.17       3      22 ..      38      57 ..      36      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                      RNA_helicase  3 lyGpsgeGKStlakeLakal 22
                                      ++G+sg+GK+tlak L+  l
  gi|313125111|ref|YP_004035375.1| 38 IVGESGCGKTTLAKALIGIL 57
                                      78*************98655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.22       6      23 ..      38      55 ..      34      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                         PduV-EutP  6 liGkvgsGKttLtqalkg 23
                                      ++G++g+GKttL++al g
  gi|313125111|ref|YP_004035375.1| 38 IVGESGCGKTTLAKALIG 55
                                      79************9965 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.19       4      22 ..      35      53 ..      32      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                      ++ i+G+sg GKTtlak l
  gi|313125111|ref|YP_004035375.1| 35 NLGIVGESGCGKTTLAKAL 53
                                      6789************988 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00033      0.22       3      80 ..      37     110 ..      35     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                                       EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCT CS
                               Roc   3 vlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylre 79 
                                        +vG+sg GKt+l+k ++    +e + +   ++f+  ++t+++     ++ +++k +   +  q  ++sl p+y  +
  gi|313125111|ref|YP_004035375.1|  37 GIVGESGCGKTTLAKALIGILPNEGYVNAGRIEFKGDDLTEMSD----SERRRLKWEEISMIAQSAMNSLDPVYTIR 109
                                       58***************998888888888888888877765443....22344555555566677777777776655 PP

                                       S CS
                               Roc  80 a 80 
                                       +
  gi|313125111|ref|YP_004035375.1| 110 E 110
                                       5 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00033      0.22      23      39 ..      36      52 ..      21      56 .. 0.85
   2 ?   -2.7   0.0         4   2.6e+03     118     143 ..      88     113 ..      81     139 .. 0.73
   3 ?   -0.1   0.3      0.66   4.4e+02     109     145 ..     183     217 ..     123     227 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                                      EEEEESTTSSHHHHHHH CS
                            NB-ARC 23 valvGmgGvGKttlakq 39
                                      +++vG  G+GKttlak 
  gi|313125111|ref|YP_004035375.1| 36 LGIVGESGCGKTTLAKA 52
                                      78************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4
                                       H.....HHHHCHTTSEEEEEESBCCC CS
                            NB-ARC 118 wdkigvvlparenrlrvllTTRdeev 143
                                       w++i++  ++  n l  + T R++ v
  gi|313125111|ref|YP_004035375.1|  88 WEEISMIAQSAMNSLDPVYTIREQIV 113
                                       88888887777777777777777655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.66
                                       EEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCC CS
                            NB-ARC 109 lDDVweeedwdkigvvlparenrlrvllTTRdeevan 145
                                       lD + + + +++i++     e ++++l+ T d++v  
  gi|313125111|ref|YP_004035375.1| 183 LDVIMQDQILKRISQIQD--EIQSSMLVITHDVSVVA 217
                                       444555555878877766..88888888888888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1951.87
//
Query:       gi|313125112|ref|YP_004035376.1|  [L=376]
Description: oligopeptide/dipeptide ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-30  106.8   0.0    1.7e-30  106.3   0.0    1.2  1  ABC_tran     ABC transporter
    2.3e-16   60.1   0.0    4.7e-16   59.1   0.0    1.6  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
     0.0064   16.4   0.0      0.011   15.7   0.0    1.3  1  Rad17        Rad17 P-loop domain
  ------ inclusion threshold ------
      0.035   14.4   0.1       0.11   12.8   0.1    1.8  1  AAA_22       AAA domain
      0.052   14.1   0.0      0.096   13.2   0.0    1.5  1  AAA_18       AAA domain
      0.086   12.6   0.0       0.17   11.6   0.0    1.5  1  PRK          Phosphoribulokinase / Uridine kinase family
       0.11   12.1   0.0       0.11   12.1   0.0    1.2  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0   6.7e-34   1.7e-30       2     136 ..      54     203 ..      53     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 6.7e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + vs++l++ge++++ Ge+G+GK+t  + l +l++ t G+i ++gk+l +    el+++r++ ++++q+  ++l+p+
  gi|313125112|ref|YP_004035376.1|  54 DGVSFDLRRGETLGLAGESGCGKTTTGMSLVKLHDATDGDIYYNGKSLGDatdAELKQFRQNAQMIFQDpfESLNPR 130
                                       78**********************************************999999***************9999**** PP

                                       SBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +tv+++           ++++++++al+  +l   +++  ++ p++LSgGq+qrva+aral+ +p+++++DEp 
  gi|313125112|ref|YP_004035376.1| 131 MTVYDTvaeplrihniaNETARVQRALEFAELLP-AEQYFDQYPHELSGGQRQRVAIARALVLDPDFIVADEPV 203
                                       **************99999999999999999998.89999*********************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   1.8e-19   4.7e-16       1      60 [.     255     315 ..     255     321 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.8e-19
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpf 60 
                                       vE+gp+++++++p+HPYT+ L+++vp +++    + ++++ge+ ++ ++++GC+F +RCp 
  gi|313125112|ref|YP_004035376.1| 255 VEKGPTDQIIENPKHPYTQSLINAVPVPEPSVGrERVELQGEVGDVIDIPSGCRFKSRCPE 315
                                       8****************************998889************************96 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.3e-06     0.011      43     166 ..      61     190 ..      50     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.3e-06
                             Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdn.qksdfk..gltekesrf...lsqiesfkel 112
                                       r+ + L ++G sGCgk+t+   L k +       + n+ sl ++   + ++f+  ++++ ++ f    +++ ++  +
  gi|313125112|ref|YP_004035376.1|  61 RRGETLGLAGESGCGKTTTGMSLVKLHDATDgDIYYNGKSLGDATDaELKQFRqnAQMIFQDPFeslNPRMTVYDTV 137
                                       55567889*****************99766515689***99765443666666114455666675557889999888 PP

                             Rad17 113 eLkdakylklqklGddlrtdkklilvedlPnkfyrds..dalrevirkylrsseal 166
                                            +   +    + +r ++ l + e lP + y d   + l    r+ + + +al
  gi|313125112|ref|YP_004035376.1| 138 -AEPLRIHNIA--NETARVQRALEFAELLPAEQYFDQypHELSGGQRQRVAIARAL 190
                                       .3333333333..6778999999999999954444443688888888888888886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.2e-05      0.11      10      71 ..      68     144 ..      61     242 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.....sskdllrellralglelka........... 70 
                                       + GesG+GKTt+   l++ +d+        ++ ++++ +s++     ++k+++++   +++++ ++           
  gi|313125112|ref|YP_004035376.1|  68 LAGESGCGKTTTGMSLVKLHDA-------TDGDIYYNGKSLGdatdaELKQFRQNAQMIFQDPFESlnprmtvydtv 137
                                       67*****************985.......777778887777766666677777777777776665544444444444 PP

                            AAA_22  71 ......e 71 
                                              
  gi|313125112|ref|YP_004035376.1| 138 aeplriH 144
                                       4444440 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.7e-05     0.096       3      69 ..      68     129 ..      66     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                       l+G +G+GKtt +  L k++      +d+ +++ +l + +++   e k+++++ ++  +d +e  + 
  gi|313125112|ref|YP_004035376.1|  68 LAGESGCGKTTTGMSLVKLH--DATDGDIYYNGKSLGDATDA---ELKQFRQNAQMIFQDPFESLNP 129
                                       89*****************9..99999999999999999999...9999999999988888887766 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.5e-05      0.17       2      64 ..      66     127 ..      65     159 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.5e-05
                               PRK   2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsfl 64 
                                       +g+ag+SG+Gktt+   l+k+   +     + +g+s+   + ae +   ++++  ++  ++ l
  gi|313125112|ref|YP_004035376.1|  66 LGLAGESGCGKTTTGMSLVKLHDATDGD-IYYNGKSLGDATDAELKQFRQNAQMIFQDPFESL 127
                                       599***********99999876633333.4445555555555555555555555555555555 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.4e-05      0.11       9      48 ..      58      97 ..      50     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                                      S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  9 fpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg 48
                                      f + +G+++++ g++g+Gkt+   sl+k ++++d  iy  
  gi|313125112|ref|YP_004035376.1| 58 FDLRRGETLGLAGESGCGKTTTGMSLVKLHDATDGDIYYN 97
                                      66789**********************9987776555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2312.85
//
Query:       gi|313125113|ref|YP_004035377.1|  [L=484]
Description: zn-dependent protease-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-25   90.2   2.1    2.5e-25   89.9   2.1    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   2.1   1.4e-29   2.5e-25       2     277 ..      28     310 ..      27     311 .. 0.77

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1.4e-29
                                       EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-... CS
                         PmbA_TldD   2 aevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea... 75 
                                       aev + + + t + + ++  +   s +++g+  rv+ +g+  + +t+++++e+l+++++rav+  ++ ++d++a   
  gi|313125113|ref|YP_004035377.1|  28 AEVGALSQTKTDLVLTENGPRDELSFDETGVWCRVFADGAADYRYTTSLDEETLADVADRAVRGGEFLAQDDSAryd 104
                                       666655555555555555555544555689*********9999666666667*********************9**9 PP

                                       .................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEE CS
                         PmbA_TldD  76 .................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveq 135
                                                        ++v  e k++ le+  +a+++a           +    +++++ + +++ a+++G+ v++
  gi|313125113|ref|YP_004035377.1| 105 rltthqavhdgwasgriDDVALETKRSTLESGLAAVADA-----------VERCWINYDDAHIDSTAATTTGSTVRT 170
                                       999999999888888888888888886655555443333...........33334567888888999********** PP

                                       EEEEEEEEEEEEE..S.TCSET.EEEEEEEE..SSHHHS..SSHHHHHHHHHHCTTT-B-..--SEEEEEEE-HHHH CS
                         PmbA_TldD 136 trtrvslslsvia.dd.ggsgd.gmgggsgy..edleeedleeiaeeaaekalasleakp..lppgkypVvlspeav 205
                                       t  r+++ ++  + d+   + + g  +g     e+l++     + ++aa  ++ + +a+   +p+g+++V l+p+a+
  gi|313125113|ref|YP_004035377.1| 171 TLDRANVTVTLSVrDGpTVRRHaGSTRGA-VflEELAD-----VFADAAADVRTLANAETaaAPTGETTVALTPRAA 241
                                       *****999999994433222222222222.23444444.....77788777777776544459************** PP

                                       HHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-.....-SB-TTSBB---EEEEETTEE- CS
                         PmbA_TldD 206 gsllheavghaleadavlegrSflkdklGekvaselltivddptsgglgsypfDdEGvptqrtvlIenGvLk 277
                                       g+l+ +a    lead  + g S++  ++G++ +++ l++ d  + g+++ +++D+E  pt +++lIe G ++
  gi|313125113|ref|YP_004035377.1| 242 GQLFAFAA-RYLEADTHYMGLSPY--DVGDEFGPDSLSVADTVHAGSWAARAYDAELRPTTPVQLIEGGTVT 310
                                       *****988.8**************..9**************88779***********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2675.28
//
Query:       gi|313125114|ref|YP_004035378.1|  [L=80]
Description: hypothetical protein Hbor_03340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 435.53
//
Query:       gi|313125115|ref|YP_004035379.1|  [L=394]
Description: ferrichrome ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-27   94.7   0.0    1.1e-26   93.9   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.0   6.2e-31   1.1e-26       2     234 ..      77     345 ..      77     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 6.2e-31
                                       EE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT........TS-BSBESSSB-H.........HHHHHH--SEE CS
                      Peripla_BP_2   2 aslspsvteillalGatdkvvgvdtttsdpldadklee......aivevgadgeidv.........EklaalkPDlv 63 
                                       ++++ +++++ +alG td ++g+++++++ +d ++++       +  e++  g++d+           +  ++P ++
  gi|313125115|ref|YP_004035379.1|  77 VAYDGGYADMGVALGKTDGMTGIGGSDRYYTDVYDELPgvsverETLEANDLGDADMskevfyeldNDVHLMDPQML 153
                                       78999*****************************9999999999889999999999999555555555555555555 PP

                                       EE-GGG...GGGHHHHHHHS-EEE----TTS............HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH CS
                      Peripla_BP_2  64 ilskglgltdedeellksgiptvivessntg............eslkeqiralgellgledeaeklvaeidsklaaa 128
                                       +   g+      e   ++++  v   ++n +            + l+e ++ +++l+++e++++++++ +d+ +a++
  gi|313125115|ref|YP_004035379.1| 154 VNWFGW-----SETDVDEIATNVGPFFGNLIfrredkwhdyryYTLYEAFEKVAQLFQEEERFNAFQSLHDEFIAEI 225
                                       555555.....3333334444444444444466666778************************************** PP

                                       HHTS-TT...-EEEEEEEETTE......EEEE-TTSTTTHHHHTS--EESTTT--.....STT-EEE-HHHHHHH-- CS
                      Peripla_BP_2 129 ksaidse..kpkpvlvfggade....ggyvvagsnsyigdlldalgieniaaesk.....kseyeeisaEqilasdp 194
                                       +  ++ +   p  +lv+ g+de    ++y ++ +++ +++  d lg+ ++++  +     + ++++i+ E++l+ dp
  gi|313125115|ref|YP_004035379.1| 226 QRQLPPAdeRPNVLLVYEGSDEpetfSPYRLNDRGTSKKQWRD-LGVSDALSGTGihgisTTDRGRIDYETMLEIDP 301
                                       *******855555555666666999888888888888887766.*********99********************** PP

                                       SEEEEEEH....HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 195 dvifvsgr....aeadnktgleflkenpllaelpAvkngrVyal 234
                                       dvi+ + +    a++++ t+lef+  +p+ +el+Av+ngrVy+ 
  gi|313125115|ref|YP_004035379.1| 302 DVIMLRAHerksATEFRETVLEFMRDHPVGSELTAVQNGRVYRG 345
                                       ******************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2283.92
//
Query:       gi|313125116|ref|YP_004035380.1|  [L=433]
Description: hydrogenobyrinic acid a,c-diamide synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-34  118.8   0.0    3.2e-34  118.3   0.0    1.2  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    3.1e-14   53.1   0.0    4.9e-14   52.5   0.0    1.3  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    3.4e-11   43.3   0.0    5.8e-05   23.0   0.0    2.3  2  AAA_26    AAA domain
  ------ inclusion threshold ------
      0.072   12.9   0.0       0.13   12.1   0.0    1.3  1  SNO       SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.0     7e-38   3.2e-34       1     195 [.     236     425 ..     236     426 .. 0.88

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 7e-38
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       ++av+ + a+ + +   ++ L++++ + v f+p+ +++l +d+d v+lpGg+++++  +l+ +  + ++i++ a++g
  gi|313125116|ref|YP_004035380.1| 236 RVAVASDAAFCFAYpaTIERLRERA-EVVTFSPIAGDNL-PDCDGVYLPGGYPELHGSELEGS-PTLDDIAARAADG 309
                                       699*********999******9977.8899*********.56******************999.55678999999** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel......aaegeevkGyEiHs 146
                                        pv+g+CGGl+ L e+++++eg      ++e+ g+L++++++ + + +   ++e+++      a++g++++G+E+H+
  gi|313125116|ref|YP_004035380.1| 310 LPVIGECGGLMALTESLTTDEG------TYEMAGVLPADVQMCD-RYQALDHVELRAktdtltASQGDRLRGHEFHY 379
                                       ******************9998......5***************.6653333333336699987788********** PP

                          GATase_3 147 Grtilkekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglfdnrn 195
                                       ++   + +a+ +++v++g +++ ++dG+ +     ++lGtY H+++++ +
  gi|313125116|ref|YP_004035380.1| 380 SSADVASDARFAFDVVRGSGIQdSSDGLTEY----RTLGTYCHLHAESGA 425
                                       ***************88666667******77....**********99865 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   1.1e-17   4.9e-14       2     126 ..       5     185 ..       4     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.1e-17
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH........HTTEB-HHHH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxx................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai........leglendiep................ 54 
                                       ++a+tk+GvGKT+ ++++ +al+++g+ V++ +a+p+    ++                 +                
  gi|313125116|ref|YP_004035380.1|   5 VLAGTKSGVGKTVATLAIVQALQDDGYTVQPAKAGPDFIDPSHhervagrpS--------Rtldlwlegddgvrrny 73 
                                       689**********************************888887444333330........3566677777777777* PP

                                       .......................................CCHCCCHHHHHHCHCHHHH.........EEEEEEEEES CS
                                       .......................................xxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx RF
                              CbiA  55 .......................................dlkrllellealgkkkall.......lkiagvvlnrvd 85 
                                                                              d+k + e+++a  ++++         +++ag+++ r  
  gi|313125116|ref|YP_004035380.1|  74 hrgdgdicvvegvmglydgdcsstamvadaldvpvvlvvDAKAGMESVAATAHGFREYashagrdIDVAGIIAQRAH 150
                                       ***************************************88888888888888887777889*************** PP

                                       S...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  86 geneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                       g ++e  +keal +     g+  +g ip ++++ e+p r++
  gi|313125116|ref|YP_004035380.1| 151 GGRHEDGIKEALPD-----GMAYFGRIPPRSNL-EIPDRHL 185
                                       **********9999.....************99.9998875 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     4e-07    0.0018       3      32 ..       4      33 ..       2      38 .. 0.90
   2 !   23.0   0.0   1.3e-08   5.8e-05      97     195 ..      76     179 ..      49     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4e-07
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkv 32
                                      ++++gt  gvGKTv +l++v+al++ g+ v
  gi|313125116|ref|YP_004035380.1|  4 FVLAGTKSGVGKTVATLAIVQALQDDGYTV 33
                                      789********************9988876 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.3e-08
                            AAA_26  97 kdadivvVEGagglgvpiteellnadiaknlgapvilVargglgtinqllltiealr......qknvrvlGvilNkv 167
                                        d di vVEG+ gl ++     ++a +a +l++pv+lV+ ++ g ++ +++t++ +r       +++ v+G+i+ + 
  gi|313125116|ref|YP_004035380.1|  76 GDGDICVVEGVMGLYDGDC--SSTAMVADALDVPVVLVVDAKAG-MESVAATAHGFReyashaGRDIDVAGIIAQRA 149
                                       5789**********99965..578999************99886.344444444444333333589**********8 PP

                            AAA_26 168 rnpenvetlekksg..ipvlGvvPylpdle 195
                                          +  + ++++ +  +  +G++P  ++le
  gi|313125116|ref|YP_004035380.1| 150 HGGRHEDGIKEALPdgMAYFGRIPPRSNLE 179
                                       888999999999886689999999998886 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05      0.13      29      89 ..     271     332 ..     253     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                                       GGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB..S CS
                               SNO  29 edlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene..l 89 
                                       ++l ++d++ +PGG     +  +e    ++d+ + ++++ ++v+G C Gl+ l++ l+++   
  gi|313125116|ref|YP_004035380.1| 271 DNLPDCDGVYLPGGYPELHGSELEGSPTLDDIAARAADG-LPVIGECGGLMALTESLTTDegT 332
                                       7899***********9999999999999**********9.**************999877443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2669.98
//
Query:       gi|313125117|ref|YP_004035381.1|  [L=262]
Description: precorrin-6y c5,15-methyltransferase (decarboxylating), cbie subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-33  117.1   0.2    1.2e-33  116.8   0.2    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   0.2   6.8e-38   1.2e-33       2     212 ..      34     231 ..      33     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 6.8e-38
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal...aea 75 
                                       +y+VG+GpG+ e+lT+r+lra+++advv+g +  + + + d            +++++ l+ +y++ a+al   ae+
  gi|313125117|ref|YP_004035381.1|  34 VYGVGIGPGNLEYLTPRGLRAIQEADVVVGFQ-TVVDFVAD------------ETDADLLTCGYADEADALnefAER 97 
                                       8*******************************.88888854............57889******************* PP

                      TP_methylase  76 lragkdVvllvsGDPlvy..gtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakee 150
                                       +++g++   + +GDP+ +  +  +++ + +++  +   v+ iPG+sslq aa+r+++p+++++ v+ +   +l+++ 
  gi|313125117|ref|YP_004035381.1|  98 VADGERGTAVLMGDPNHSgyQFLGKVQQVVER--P---VKAIPGISSLQIAASRARTPMEDTRFVTLHKSGSLDADL 169
                                       ****************9976778888878888..5...**********************99999999966666666 PP

                      TP_methylase 151 ereleallangdtlvllkapr..klaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       +r+ e + +  ++l++l +p    + ++a+lL+e+  d+ +++ v er++ +de+++r+tl+el
  gi|313125117|ref|YP_004035381.1| 170 DRLTEVVGE--RHLLVLPRPFdwMPGDIAKLLLESGADRSLEALVLERLTHDDEQITRTTLGEL 231
                                       677777666..8999998998555***********555677*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1733.70
//
Query:       gi|313125118|ref|YP_004035382.1|  [L=226]
Description: precorrin-8x methylmutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-51  173.6   1.5    4.2e-51  173.4   1.5    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.4   1.5   2.3e-55   4.2e-51       1     195 [.      19     210 ..      19     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 173.4 bits;  conditional E-value: 2.3e-55
                                       HHHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HH CS
                              CbiC   1 eIeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkk 77 
                                       eI+++S++i++  + +e   + ++++ ++++h+t+d+e+++l+r++++   ag++a+ +++pivtD++m+kaGit +
  gi|313125118|ref|YP_004035382.1|  19 EIAETSMDIVRTFVPDE---TLNDRLRQKAVHSTGDIEFQHLIRCQNNPAVAGARAVLDEQPIVTDITMAKAGITGR 92 
                                       699***********977...88999*************************************************999 PP

                                       HHHTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHH..CTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE- CS
                              CbiC  78 rleklgnevlclladpevaelakekgitrsaaamekaae..elegaivviGnAPtALlellelieegkvkpalvigv 152
                                        ++   ++v+ ++ +   aela+e+g+tr+aa++ ++ +   ++gai v+GnAPt  l+l+++ie+g+ +pa+++++
  gi|313125118|ref|YP_004035382.1|  93 GHD---CPVKKAIGNG--AELAAETGMTRTAASVLELDKqgVYDGAIAVVGNAPTGALALADCIEDGT-RPAAIVAT 163
                                       876...59******98..9*******************9899************************97.******** PP

                                       ---SCCHHHHHHHHHCSS....S-EEEESSS---HHHHHHHHHHHHH CS
                              CbiC 153 PvGFvgaaesKealaese....vpyitveGrkGGsavAaaivnaLle 195
                                       PvGFv+a+es++++++      +p++t+ G++GGs +Aaa++n+L++
  gi|313125118|ref|YP_004035382.1| 164 PVGFVKAEESRKRVRDIAdeydIPAVTNVGKRGGSGLAAALTNELIH 210
                                       ***************7444566***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1403.49
//
Query:       gi|313125119|ref|YP_004035383.1|  [L=1272]
Description: cobaltochelatase cobn subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
          0 1269.7   0.0          0 1269.5   0.0    1.0  1  CobN-Mg_chel   CobN/Magnesium Chelatase
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.34   10.7   0.0    1.8  1  LexA_DNA_bind  LexA DNA binding domain


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1269.5   0.0         0         0       2    1087 ..     110    1244 ..     109    1246 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1269.5 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilf 76  
                                        +Yl+ ggv N++nl+r+la+++ +  +++ve+pv+lp+eg+yhpd++ +     ey+e  +++ +++ ptvg++f
  gi|313125119|ref|YP_004035383.1|  110 EYLERGGVVNIENLCRFLAAEYDD-FDTDVEDPVSLPTEGVYHPDYPGI-----EYEEL-RETFDPDDPTVGVWF 177 
                                        7*********************97.8889****************9873.....34332.456799********* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   77 yrahllagntavidaliraleerglnvlpvfvssl...d..seaqealeelftkegeekvdalinttsfalvkgp 146 
                                        y++h++++nt+++dal+r+le+ g+nvlp+f++ +   +  ++a+  ++++f +++ + vda+++  +f+l++++
  gi|313125119|ref|YP_004035383.1|  178 YESHWTHANTRYVDALVRRLESLGVNVLPAFCNPAtdeEgqENAEWVARNWFSDDDGPIVDAVVSSFMFSLSMSE 252 
                                        **********************************98541447777788899999999****************99 PP

                                        xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                      CobN-Mg_chel  147 aeeeeeeaeeea....lkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfke..ee 215 
                                        ++++++++ ++a    l+el+vPvlqai++++sr+++e s++G+ + +la+svalpE+dG +++ +is+ke  e+
  gi|313125119|ref|YP_004035383.1|  253 RGRDAADEGDDAedvfLTELGVPVLQAITTMRSRSRYEGSDTGVMGFELALSVALPEFDGNVITHPISGKErmED 327 
                                        99998888777799*********************************************************8733 PP

                                        x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  216 e..eetevekyepipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalk 288 
                                        e    ++ +++ pi++r+++va+la +wa+Lr  pn+ekkva++l+nypp+++ +g+a gLd+paS+vnlL++l 
  gi|313125119|ref|YP_004035383.1|  328 EagVGSAPKQHFPIEDRIDHVARLAVNWANLRYLPNDEKKVAVVLHNYPPSDDGIGTAFGLDTPASTVNLLHELD 402 
                                        3477888899***************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  289 eeGYdveelpesgdeLiellleggtndpew...eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppgem 360 
                                        ++GY+v++ p++g+ Li+ l+++ t d +w   e+++  +++ ++ ++Ye+wfe+ +e+ +++++e+Wgepp+  
  gi|313125119|ref|YP_004035383.1|  403 SRGYTVGDPPTDGQSLIDDLTSQLTLDDRWvapEDVRDLSVDVVSPDQYEDWFEATDERFQDHLIEEWGEPPE-- 475 
                                        ******888*********************9998888799*********************************.. PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  361 veeeksgekklvipglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtl 435 
                                                + ++ipg+++ nv+v+vQP+rg+++dpsk+yhd+dl+P+h+YlAfY W+reef+adavvH+G+HG+l
  gi|313125119|ref|YP_004035383.1|  476 --------RPFAIPGVEFENVLVTVQPPRGFGMDPSKVYHDSDLQPPHDYLAFYAWMREEFDADAVVHLGTHGSL 542 
                                        ........79***************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  436 EwlPGKqvglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideY 510 
                                        EwlPGK+vgl +e+ Pd l+gdlP++YpYivnnpgEGtqAKRRsyA i+d+ltP+m +a++y++l++Leel +eY
  gi|313125119|ref|YP_004035383.1|  543 EWLPGKTVGLNAESAPDQLVGDLPNVYPYIVNNPGEGTQAKRRSYAAIVDYLTPVMRTAGTYDDLSDLEELAREY 617 
                                        *************************************************************************** PP

                                        xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  511 eeaesl..dperlkalreqilelveelnldkdlg...leeakeeeeeefeellekldgyleelkeaqirdglhil 580 
                                        +ea      p+r ++lre +le v +l+l  +lg   l++ ++ e++ef+el+e++++yl+++k++qir glh++
  gi|313125119|ref|YP_004035383.1|  618 REAGMDeaRPDRGEHLRELVLEAVDDLDLAVELGfedLDDVHDLETTEFDELVERIHEYLTDVKTTQIRMGLHTM 692 
                                        **9776335779*********************988866678999****************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  581 Geapegeqlvdlvvailrleneegesltealaealgldldeleeksekelrt....agdalealeeeaeelveel 651 
                                         e+p++++lv+++va++rl+n +++sl+e++a  +g+d+d+++++  +  ++     ++a +++ +++ elve+l
  gi|313125119|ref|YP_004035383.1|  693 SEPPADDRLVEYLVALTRLPNADTPSLRESVAGVMGVDYDRMRDEPGAYDEAlgmyLSEAADHVYDQCVELVETL 767 
                                        *****************************************55555444444000055667777999999***** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxx.....................................xxxxxxxxxxxxxx RF
                      CobN-Mg_chel  652 leeeaeeeeaeaeeleeeeeeeee.....................................eteeEitallraLd 689 
                                        +e++++  e+e e+++++e + +                                      ++ +Ei ++ +aLd
  gi|313125119|ref|YP_004035383.1|  768 AEHDFDVPESEVEADADDEVNMNLlvvdidqlgdakakrgahddlrevlaficeeaaprvaAAADEIPQTADALD 842 
                                        ***999988877777777776666************************************8667*********** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  690 GeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeellerylqehgeyPekvglslwgtetm 764 
                                        Gey++pg sG+ptrg  + LPTGrNfy++Dpr++P + Aw+vGk++ae +ler++++h+eyPe+ g++ wgt t+
  gi|313125119|ref|YP_004035383.1|  843 GEYVRPGGSGAPTRGGVDLLPTGRNFYTLDPRKVPAKPAWDVGKRVAEGVLERHYDDHDEYPEEFGVVAWGTPTV 917 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  765 rteGediAqiLallGvrPvwdaagrvvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldE 839 
                                        rt+Ge+iAq+La +Gv+Pvw +agr+ d+e ipl+eLgRPR+DVt r+SG+fRDafp+  +++++av++v +ldE
  gi|313125119|ref|YP_004035383.1|  918 RTRGETIAQVLAFMGVEPVWTDAGRIDDVEPIPLDELGRPRVDVTTRVSGLFRDAFPQAASVINDAVDAVVDLDE 992 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  840 peedNfvrkhvleeeaelee....keeaeeratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaY 910 
                                        p+++N+v+khv+e++aele+    +++ae+ a+ RvF+  pG Ygag ++++++++W+d++dLa++Y++w++ya 
  gi|313125119|ref|YP_004035383.1|  993 PHDMNYVKKHVEEDTAELEDdgvdEGDAEKLAKHRVFTTTPGGYGAGTNKAVDEGEWDDRSDLADVYVQWGGYAL 1067
                                        *******************9777566899********************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  911 gkgaegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvr 985 
                                        g++ +++ea++afe+rL+ v+++v+ +d+ e d +ds+d y+f+GG+  av ++sg++p++y+gdss+p+np++ 
  gi|313125119|ref|YP_004035383.1| 1068 GSRGRVTEAHDAFERRLSGVEATVKIEDTAEQDEFDSSDWYAFHGGFVSAVGEISGSDPASYVGDSSDPDNPQIY 1142
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  986 tlkeeiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevreflee 1060
                                        t +e++++ +r+rvlNP W+++m +hGykGa +l+ tvd ++gwdat++v++d ++e++a++Y++De  +e++++
  gi|313125119|ref|YP_004035383.1| 1143 TNEEKVRKAMRARVLNPDWLDSMEEHGYKGAGDLSTTVDVTLGWDATTGVISDTLWENLADAYAFDESRQEWMRD 1217
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1061 kNpwAlreiaerLlEaarrglWeasee 1087
                                         NpwAl++i++++lEa++rglW+a+++
  gi|313125119|ref|YP_004035383.1| 1218 VNPWALESITATFLEAIDRGLWDADDD 1244
                                        ************************986 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.8e-05      0.34      22      56 ..     373     407 ..     367     413 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.8e-05
                                       HSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                     LexA_DNA_bind  22 tgypPsireiaralglkSpsaveehLkaLerKGyi 56 
                                       + ypPs   i+ a+gl  p++  + L+ L  +Gy 
  gi|313125119|ref|YP_004035383.1| 373 HNYPPSDDGIGTAFGLDTPASTVNLLHELDSRGYT 407
                                       78*******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.87u 0.35s 00:00:01.22 Elapsed: 00:00:00.52
# Mc/sec: 7317.98
//
Query:       gi|313125120|ref|YP_004035384.1|  [L=738]
Description: protoporphyrin ix magnesium-chelatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-22   78.4   5.7    2.9e-22   78.3   2.7    2.6  2  AAA_lid_2        AAA lid domain
    7.6e-12   45.8   0.1    2.1e-11   44.4   0.0    1.8  2  VWA_2            von Willebrand factor type A domain
      9e-12   44.8   0.0    2.8e-08   33.4   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.6e-10   40.8   0.0    4.9e-10   39.9   0.0    1.4  1  VWA              von Willebrand factor type A domain
    5.9e-09   36.1   0.0    1.7e-06   28.1   0.0    2.6  1  AAA_5            AAA domain (dynein-related subfamily)
    2.3e-05   23.6   0.0    0.00061   18.9   0.0    2.4  2  MCM              MCM P-loop domain
     0.0056   16.4   0.0       0.18   11.5   0.0    2.5  3  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.018   15.4   1.8      0.058   13.8   0.2    2.7  2  AAA_16           AAA ATPase domain
      0.041   13.8   0.2      0.075   13.0   0.2    1.4  1  VWA_3            von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   2.7   1.4e-25   2.9e-22       4      72 ..     278     346 ..     276     347 .. 0.96
   2 ?   -1.6   0.1       1.2   2.4e+03      29      45 ..     539     555 ..     535     557 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.4e-25
                         AAA_lid_2   4 rahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeivee 72 
                                       +a+l++ +gv+g+Rad+a++r+Ar+lAal+gr++V+  Dv++aa+l+L+HRlr +p+++  +t++++++
  gi|313125120|ref|YP_004035384.1| 278 IAELCLDAGVEGHRADIAIARTARTLAALDGRTKVIGGDVRDAAELALPHRLRSRPFDDAPDTDDVLDD 346
                                       799*********************************************************999999875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                         AAA_lid_2  29 lAalegrdyVtpeDvke 45 
                                        Aa +gr+++   D+++
  gi|313125120|ref|YP_004035384.1| 539 AAASNGRTQIDRSDLRT 555
                                       5999*****99999985 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         9   1.8e+04      66      91 ..      30      56 ..      26      59 .. 0.63
   2 !   44.4   0.0   1.1e-14   2.1e-11       1     106 [.     566     666 ..     566     667 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 9
                             VWA_2 66 lrnleak.gggtnlaaaLqlarkalkk 91
                                      +++l  + ++gt   +a++ ++++l++
  gi|313125120|ref|YP_004035384.1| 30 IDGLLVRgEKGTAKSTAVRALTDLLPE 56
                                      555555556677777777777777764 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 1.1e-14
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl..pgdrvglvtfsd.gpevlipltkdkakilnalrnleakgg 74 
                                       +vfv+D S+Smr+       +   k  v +ll++   ++d v+ v++++ ++ev++p+t++ +   + l++l a g+
  gi|313125120|ref|YP_004035384.1| 566 IVFVVDASASMRPA------MRETKGTVMSLLEDAyqQRDEVAFVAVAGdEAEVVLPPTDSVSLAARHLKQLPA-GD 635
                                       79***********8......9***********94444699******99978**********************9.6* PP

                             VWA_2  75 gtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                        t l ++L+ a+ ++ +    +++ +v++tDg
  gi|313125120|ref|YP_004035384.1| 636 RTPLPSGLDAAHRLVTRAD-ADSSLVVVVTDG 666
                                       ***************9997.9**********9 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0004      0.79       4      50 ..      10      58 ..       7      64 .. 0.80
   2 !   33.4   0.0   1.4e-11   2.8e-08      89     159 ..     114     184 ..     103     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0004
                      Mg_chelatase  4 dvkGqeeakrale.iaaaGg.HnlllvGppGsGKtmlakrlpsllppls 50
                                       ++Gqee kral  + +  +   ll+ G  G+ K+   ++l+ llp+ +
  gi|313125120|ref|YP_004035384.1| 10 AIVGQEELKRALLaVGVNEQiDGLLVRGEKGTAKSTAVRALTDLLPEQT 58
                                      699*******98514444432469999*******************976 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.4e-11
                      Mg_chelatase  89 alvGggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                         + g ++  pG +++a++G+L++DE+  ++ + ++ L +   +g  +++r   +ve+pa+f+l+ +mNp 
  gi|313125120|ref|YP_004035384.1| 114 DALAGDASFDPGLLARANRGILYVDEVNLLEDHLVDLLLDAAASGVNRVERDGVSVEHPAEFTLIGTMNPE 184
                                       445678899************************************************************95 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   2.4e-13   4.9e-10       2     151 ..     566     708 ..     566     729 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.4e-13
                                       EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGGS CS
                               VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysggg 77 
                                       ivfv+D+S sm +  + ++k  + +l+e+ +  ++++ v++v  +++ ++++ + +d  s + ++++l++l    g+
  gi|313125120|ref|YP_004035384.1| 566 IVFVVDASASM-RPAMRETKGTVMSLLEDAY--QQRDEVAFVAVAGDeAEVVLPPTD--SVSLAARHLKQL--PAGD 635
                                       8**********.999****************..************8879999*****..6689999****7..5555 PP

                                       SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.S.HTHHHHHHHHGC..TEEEEEEEESSSHHHHHHHH CS
                               VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksnd.g.dpkeaaneakeq..gikvfavGvgnadekelLnk 150
                                        t + ++l++a + + ++ a      +++++++tdG+ n  + +p+ a ++a +     +  +v v+  d+ + L++
  gi|313125120|ref|YP_004035384.1| 636 RTPLPSGLDAAHRLVTRADAD-----SSLVVVVTDGRANVaDgSPTAATRSAARHlaTSDASVVLVDAGDDGTGLTD 707
                                       5559*********99999999.....************985467777776665432344445555555555555555 PP

                                       H CS
                               VWA 151 i 151
                                       i
  gi|313125120|ref|YP_004035384.1| 708 I 708
                                       5 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   8.3e-10   1.7e-06       2     138 .]      33     196 ..      32     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 8.3e-10
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.............--------.......... CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik....ngttslvdsplvraar.......... 64 
                                       +l+ G++Gt+Ks+ ++ l  +l  ++++ +++ + +++d + + +      + + + ++ plv+             
  gi|313125120|ref|YP_004035384.1|  33 LLVRGEKGTAKSTAVRALTDLLPEQTVVAACPYGCPPDDPTRQCDSCrerdDYDVETRPVPLVTLPLgatrdrvagt 109
                                       7889*************************************999965877766777777777754447788****** PP

                                       .....................G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEE CS
                             AAA_5  65 .....................egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviata 120
                                                            +  il++DEv+ +e++ ++ Ll        ++e  g  v ++++     f++i+t+
  gi|313125120|ref|YP_004035384.1| 110 lsvsdalagdasfdpgllaraNRGILYVDEVNLLEDHLVDLLLDAAASGVNRVERDGVSVEHPAE-----FTLIGTM 181
                                       *********************99*********************999999998888877777775.....******* PP

                                       SS--.-TT-TTHHHHTT- CS
                             AAA_5 121 npldrslnelspalrsRf 138
                                       np +    +l p+lr+Rf
  gi|313125120|ref|YP_004035384.1| 182 NPEE---GDLRPQLRDRF 196
                                       ***9...77889*****9 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.054   1.1e+02      24      85 ..       9      58 ..       5      63 .. 0.65
   2 !   18.9   0.0   3.1e-07   0.00061     103     179 ..     113     189 ..      99     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.054
                                      TTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEE CS
                               MCM 24 psiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklaprav 85
                                      p+i+g+e+ k+a+l     gv+++ +          +l+ g+ gtaKs+ ++++++l+p+++
  gi|313125120|ref|YP_004035384.1|  9 PAIVGQEELKRALLA---VGVNEQIDG---------LLVRGEKGTAKSTAVRALTDLLPEQT 58
                                      666666666666543...233322222.........56669999999999999988888765 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 3.1e-07
                                       EESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCC CS
                               MCM 103 rdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagryd 179
                                        d   g+  ++ G l  a++G++++De++  +++  + l++a  +    + + G+ +  +a+ +++  +np++g   
  gi|313125120|ref|YP_004035384.1| 113 SDALAGDASFDPGLLARANRGILYVDEVNLLEDHLVDLLLDAAASGVNRVERDGVSVEHPAEFTLIGTMNPEEGDLR 189
                                       4777889999**************************************************************99755 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.083   1.6e+02      24      45 ..      32      53 ..      14      63 .. 0.80
   2 !   11.5   0.0   8.9e-05      0.18      79     142 ..     117     182 ..     111     196 .. 0.81
   3 ?   -3.7   0.0       4.2   8.4e+03      12      34 ..     680     704 ..     675     707 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.083
                                      -EEEECSTTSSHHHHHHHHHHH CS
                   Sigma54_activat 24 svlitGesGtGKellaraihea 45
                                       +l++Ge+Gt K++  ra+ + 
  gi|313125120|ref|YP_004035384.1| 32 GLLVRGEKGTAKSTAVRALTDL 53
                                      479**********999998765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.9e-05
                                       TTTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHS..EEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  79 tGAekekkGlfekadgGtlfLDeigelplelQekLlrvlqeg..evervGsskeikvdvriiaatn 142
                                        G  +   Gl+ +a+ G+l++De++ l+ +l   Ll +  +g  +ver G s e+++++ +i + n
  gi|313125120|ref|YP_004035384.1| 117 AGDASFDPGLLARANRGILYVDEVNLLEDHLVDLLLDAAASGvnRVERDGVSVEHPAEFTLIGTMN 182
                                       56666678**********************999999988775226788888888888888887766 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.2
                                       HHHHHHHCTSSS-EEE..ECSTTSS CS
                   Sigma54_activat  12 leqikkvaktdlsvli..tGesGtG 34 
                                       ++ ++++a++d+sv++   G+ GtG
  gi|313125120|ref|YP_004035384.1| 680 RSAARHLATSDASVVLvdAGDDGTG 704
                                       5677888888887776345999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.9e-05     0.058      12      54 ..      17      60 ..      12     216 .. 0.79
   2 ?   -1.0   0.1         1   2.1e+03     116     142 ..     626     665 ..     541     697 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                            AAA_16 12 Llsalervrsgrp.elvllsGesGvGKsslvrellralekdggi 54
                                      L++al +v  ++    +l++Ge+G+ Ks+ vr+l + l ++ ++
  gi|313125120|ref|YP_004035384.1| 17 LKRALLAVGVNEQiDGLLVRGEKGTAKSTAVRALTDLLPEQTVV 60
                                      5444444444444489*******************988888322 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                            AAA_16 116 a.............srllellkrllallsrderplvlvlD 142
                                       +              + l++  rl+ ++  d++ +v+v D
  gi|313125120|ref|YP_004035384.1| 626 RhlkqlpagdrtplPSGLDAAHRLVTRADADSSLVVVVTD 665
                                       2222222233345555556666666666665554555555 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   3.7e-05     0.075       3     108 ..     566     668 ..     564     712 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                             VWA_3   3 vvivvDvsssmsaen.klvkdaLsvalrqLptndkia.vllfgtkprplfpgsravsaaelqealqkikelelslga 77 
                                       +v+vvD+s+sm+    ++    +s++  + +++d++a v+++g++++ + p  ++vs      a+  +k+l++  + 
  gi|313125120|ref|YP_004035384.1| 566 IVFVVDASASMRPAMrETKGTVMSLLEDAYQQRDEVAfVAVAGDEAEVVLPPTDSVS-----LAARHLKQLPA-GDR 636
                                       8***********877778888899999999999977549999***999999999998.....889999**999.999 PP

                             VWA_3  78 snlegaLkealrqp.akpgevrsvilltDgss 108
                                       ++l + L++a r   +  +  + v+++tDg +
  gi|313125120|ref|YP_004035384.1| 637 TPLPSGLDAAHRLVtRADADSSLVVVVTDGRA 668
                                       ********9999664566778889999**985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 4406.14
//
Query:       gi|313125121|ref|YP_004035385.1|  [L=404]
Description: pqq enzyme repeat-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-17   61.5  12.6    2.2e-08   34.0   2.8    2.2  2  PQQ_2     PQQ-like domain
    1.2e-11   44.8  15.1     0.0071   16.8   0.1    7.7  9  PQQ_3     PQQ-like domain
    3.6e-08   32.9   8.5       0.23   11.4   0.0    6.4  6  PQQ       PQQ enzyme repeat


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   2.8   3.7e-12   2.2e-08      67     157 ..      22     107 ..       7     147 .. 0.65
   2 !   32.5   2.8     1e-11   6.3e-08       3     220 ..     146     381 ..     144     396 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 3.7e-12
                             PQQ_2  67 pvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvges..sgklvaldpkd 141
                                       ++++a   a grv+v ++dgq++a+d++   +lWs + ++       s+ s+a ++d +vvge   ++ l +ldp++
  gi|313125121|ref|YP_004035385.1|  22 WARSAVAAAAGRVFVGTNDGQVSAFDSALDSELWSADGAT-------SVVSMAATDDCLVVGERgeDSSLRVLDPET 91 
                                       4555666677777777777777777777777777733333.......566667667777777766677777777777 PP

                             PQQ_2 142 GkvlWerelaaprgts 157
                                       G+++We++ +++ gt+
  gi|313125121|ref|YP_004035385.1|  92 GERRWEYATTDDIGTA 107
                                       7777777776655444 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 1e-11
                             PQQ_2   3 gvvsaldaatGaelWrvdlarplgggvsravlsggtlfva......tgggrlvaldaatGkvlWettl...egpvvg 70 
                                       +vv  +d+ +Ga+ Wr ++     + ++ +v ++g+++va       + + lv ld +tG  l + ++   e + vg
  gi|313125121|ref|YP_004035385.1| 146 SVVLGFDR-DGAVQWRYRV---GASPIALTV-ENGRVAVAynrcpkPDQDGLVVLDSETGDTLTTWDPdtdEDRRVG 217
                                       56788995.9*******88...667777788.*******976555549999**********9877777558555566 PP

                             PQQ_2  71 aplvaegrv.vvvasdgqlialdaedGkrlWstqqrseepae...lrssaspava.....gdtvvvges........ 130
                                       +  +a+g + v+  +d++ + ld  dG ++W ++++++++ +   +               d v+v+ +        
  gi|313125121|ref|YP_004035385.1| 218 DVAFADGDIaVCCHGDKRGYLLD-SDGHEQWGFDLATKQDIDgetVYAY-----PnhvcvADGVAVFVTgntfaest 288
                                       66666666648888999******.*************888774332222.....13345555555555435677777 PP

                             PQQ_2 131 .......sgklvaldpkdGkvlWerel.aaprgtselsrvgdisgrpvvaegtVyassgqgr..llaldlatgrrlw 197
                                              + + +a+ +++G++lW ++  + +r        ++ +gr ++ + + ++ +  ++  +  +d+++g    
  gi|313125121|ref|YP_004035385.1| 289 rdpdarhPDEHTAFAVENGEQLWTHSNgGFAR------AARSSDGRAIIPSAQNFRRRSAEThgVHTFDAEEGH--V 357
                                       77777777777***************988887......456788999999775555444443335555*****9..5 PP

                             PQQ_2 198 .skeissinglpildgdllyvvsa 220
                                        +++i++i + +++ +d+l vv++
  gi|313125121|ref|YP_004035385.1| 358 eTDSIAGIPTAVAVGDDVLAVVEE 381
                                       256699977779999999999985 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.2e-06    0.0071      13      37 ..      23      47 ..      16      49 .. 0.88
   2 !    9.2   0.1   0.00029       1.7       3      40 .]      53      91 ..      52      91 .. 0.90
   3 !    8.8   0.0   0.00038       2.3       1      28 [.      92     132 ..      92     144 .. 0.83
   4 ?   -2.0   0.0      0.96   5.8e+03       9      19 ..     139     149 ..     133     150 .. 0.68
   5 !    8.0   0.1   0.00069       4.1       1      40 []     155     199 ..     155     199 .. 0.83
   6 ?   -2.3   0.1       1.2   7.3e+03      14      30 ..     216     233 ..     205     241 .. 0.58
   7 ?    2.2   0.0     0.046   2.7e+02      17      30 ..     266     282 ..     245     289 .. 0.75
   8 ?    2.8   0.0     0.031   1.9e+02       1      29 [.     307     334 ..     307     353 .. 0.73
   9 ?   -0.7   0.1      0.37   2.2e+03      12      27 ..     364     379 ..     356     391 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                             PQQ_3 13 vnsspavdgglvyvgtgdGtlyAlD 37
                                      + s++a++ g+v+vgt dG + A+D
  gi|313125121|ref|YP_004035385.1| 23 ARSAVAAAAGRVFVGTNDGQVSAFD 47
                                      56889*******************9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00029
                             PQQ_3  3 vlWsvqlpgpvnsspavdgglvyvgtg..dGtlyAlDaet 40
                                      +lWs +    v  s+a+ ++ ++vg    d +l+ lD+et
  gi|313125121|ref|YP_004035385.1| 53 ELWSADGATSV-VSMAATDDCLVVGERgeDSSLRVLDPET 91
                                      79999988888.57999999**99999***********98 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00038
                             PQQ_3   1 GevlWsvqlpgpvnssp.............avdgglvyvgt 28 
                                       Ge++W++ + +++++++             av +++v +++
  gi|313125121|ref|YP_004035385.1|  92 GERRWEYATTDDIGTATkeslffypyvvdvAVTDDRVIAAA 132
                                       99*****9999998777999999999999988788887776 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.96
                             PQQ_3   9 lpgpvnsspav 19 
                                        +++v+ss+++
  gi|313125121|ref|YP_004035385.1| 139 GDERVWSSVVL 149
                                       34599999986 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.00069
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtg......dGtlyAlDaet 40 
                                       G v+W++++++ p+   ++v +g+v v+        + +l+ lD et
  gi|313125121|ref|YP_004035385.1| 155 GAVQWRYRVGAsPIA--LTVENGRVAVAYNrcpkpdQDGLVVLDSET 199
                                       899*******98884..999999998877788888888888888776 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 1.2
                             PQQ_3  14 nsspavdgg.lvyvgtgd 30 
                                       ++ +a+++g + ++  gd
  gi|313125121|ref|YP_004035385.1| 216 VGDVAFADGdIAVCCHGD 233
                                       366677665144444444 PP

  == domain 7  score: 2.2 bits;  conditional E-value: 0.046
                             PQQ_3  17 p...avdgglvyvgtgd 30 
                                       p    v++g+ +++tg+
  gi|313125121|ref|YP_004035385.1| 266 PnhvCVADGVAVFVTGN 282
                                       34448999999999986 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.031
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg 29 
                                       Ge+lW+++ +g + +++  ++g+  + + 
  gi|313125121|ref|YP_004035385.1| 307 GEQLWTHSNGGFA-RAARSSDGRAIIPSA 334
                                       9******999855.667778888888776 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 0.37
                             PQQ_3  12 pvnsspavdgglvyvg 27 
                                        + +++av+++++ v+
  gi|313125121|ref|YP_004035385.1| 364 GIPTAVAVGDDVLAVV 379
                                       4557789999988765 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00011      0.64       1      17 [.      32      48 ..      32      49 .. 0.92
   2 !   11.4   0.0   3.9e-05      0.23       9      32 ..      81     104 ..      74     108 .. 0.86
   3 !    4.9   0.0    0.0047        28      12      35 ..     148     170 ..     144     173 .. 0.84
   4 ?    1.5   0.2     0.054   3.2e+02      12      24 ..     192     204 ..     190     211 .. 0.84
   5 ?   -0.5   0.0      0.23   1.4e+03      13      29 ..     237     252 ..     228     259 .. 0.82
   6 ?    3.5   0.0     0.013        76      17      31 ..     304     318 ..     300     322 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                                      TEEEEEETTSEEEEEET CS
                               PQQ  1 gvvylgsadGylyAlDa 17
                                      g+v++g++dG++ A+D 
  gi|313125121|ref|YP_004035385.1| 32 GRVFVGTNDGQVSAFDS 48
                                      78**************5 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.9e-05
                                       TSEEEEEETTTCCEEEEEESSSCG CS
                               PQQ   9 dGylyAlDadTGkvlWrfktggpv 32 
                                       d  l+ lD +TG+ +W++ t +++
  gi|313125121|ref|YP_004035385.1|  81 DSSLRVLDPETGERRWEYATTDDI 104
                                       567999*************99887 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0047
                                       EEEEETTTCCEEEEEESSSCGSSE CS
                               PQQ  12 lyAlDadTGkvlWrfktggpvlsl 35 
                                       ++ +D ++G v Wr+++g+ + +l
  gi|313125121|ref|YP_004035385.1| 148 VLGFD-RDGAVQWRYRVGASPIAL 170
                                       67789.9**********9988776 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.054
                                       EEEEETTTCCEEE CS
                               PQQ  12 lyAlDadTGkvlW 24 
                                       l+ lD +TG+ l 
  gi|313125121|ref|YP_004035385.1| 192 LVVLDSETGDTLT 204
                                       678******9986 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.23
                                       EEEETTTCCEEEEEESS CS
                               PQQ  13 yAlDadTGkvlWrfktg 29 
                                       y lD ++G + W f++ 
  gi|313125121|ref|YP_004035385.1| 237 YLLD-SDGHEQWGFDLA 252
                                       5578.999999999876 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.013
                                       TTTCCEEEEEESSSC CS
                               PQQ  17 adTGkvlWrfktggp 31 
                                       +++G+ lW++ +gg 
  gi|313125121|ref|YP_004035385.1| 304 VENGEQLWTHSNGGF 318
                                       689*******99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 2817.55
//
Query:       gi|313125122|ref|YP_004035386.1|  [L=125]
Description: hypothetical protein Hbor_03420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-52  177.7   2.8    1.2e-52  177.5   2.8    1.0  1  DUF3209   Protein of unknown function (DUF3209)


Domain annotation for each model (and alignments):
>> DUF3209  Protein of unknown function (DUF3209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.5   2.8     7e-57   1.2e-52       1     124 []       1     124 [.       1     124 [. 0.99

  Alignments for each domain:
  == domain 1  score: 177.5 bits;  conditional E-value: 7e-57
                                       ---HHHHHHHHHHHHHTT.--GGGCHHHHHHHTTTTTT-HHHHHHHH--SHHHHHHHHHHHHHHHHHHHHH....ST CS
                           DUF3209   1 maCheleaLrlglmnvlgvkdeaerrHaeaEleaeleepgpikalaeAkdlaelerhldaalvdLeeevaktdeddp 77 
                                       maC+eleaLrl+lmn++g+ de  ++HaeaEle++l+epgpi+alaeA++l+e +rhldaalv+Leee+ ++d+ddp
  gi|313125122|ref|YP_004035386.1|   1 MACAELEALRLALMNITGTVDEGVKQHAEAELEGYLDEPGPIQALAEASTLDEAQRHLDAALVELEEEAMQADDDDP 77 
                                       9**************************************************************************** PP

                                       T-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--XX CS
                           DUF3209  78 eldYlRgrlvavrdaeralkrlveeleallddleelHdtlHeifPvd 124
                                       +  YlRgr+vavrda+r+l+rl+ +++++l+dl+e+H+tlHe+fPv+
  gi|313125122|ref|YP_004035386.1|  78 QSGYLRGRVVAVRDAQRTLSRLRGQTDSFLEDLGEAHHTLHETFPVE 124
                                       *********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 762.85
//
Query:       gi|313125123|ref|YP_004035387.1|  [L=404]
Description: hypothetical protein Hbor_03430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-47  159.9   0.0    3.1e-24   85.4   0.0    2.5  2  CbiX             CbiX
    5.2e-10   39.4   0.1    8.8e-10   38.6   0.1    1.3  1  2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
    3.2e-08   33.2   0.0    7.3e-05   22.2   0.0    2.1  2  CbiK             Cobalt chelatase (CbiK)
     0.0002   21.3   0.1    0.00087   19.2   0.1    2.1  2  Suc_Fer-like     Sucrase/ferredoxin-like
    0.00097   18.3   0.0      0.026   13.6   0.0    2.3  2  Ferrochelatase   Ferrochelatase
  ------ inclusion threshold ------
       0.21   11.5   0.8        0.4   10.6   0.8    1.5  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0     1e-27   3.1e-24       1     106 [.      18     120 ..      18     121 .. 0.98
   2 !   72.2   0.0   1.3e-23   3.8e-20       1     106 [.     146     249 ..     146     250 .. 0.99

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 1e-27
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeele 77 
                                       HGSr+++sne+v++la +l+ + + +pv  +++el+eps+e+a+++l +  ++  +v+Pl lfa+ hvk+D+p +++
  gi|313125123|ref|YP_004035387.1|  18 HGSRREKSNEQVRTLAGKLETELS-VPVDAAYIELAEPSIEDAIETL-APTCRTLTVIPLSLFAASHVKNDVPMAVQ 92 
                                       ************************.*******************999.77*************************** PP

                                       --SSSS-TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  78 eaeeahpkdveieytepLGthplvaevlk 106
                                       +a+++++ dv+++++++LG hp+++++l+
  gi|313125123|ref|YP_004035387.1|  93 TARTKYD-DVTFHFGSHLGIHPSIVDLLD 120
                                       *******.******************997 PP

  == domain 2  score: 72.2 bits;  conditional E-value: 1.3e-23
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeele 77 
                                       +GS+dp+sn +v+kl + l e ++f  ve++f+ +++p+le++l ++a+ + + +vvvP++l +Gv++++ I ++ e
  gi|313125123|ref|YP_004035387.1| 146 RGSSDPDSNGDVHKLSRLLYEGREFTRVEPSFIGVTSPRLEDTLHSVAKDRPDAVVVVPYMLGDGVLTQR-IIDTAE 221
                                       7*********************************************************************.****** PP

                                       --SSSS-TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  78 eaeeahpkdveieytepLGthplvaevlk 106
                                       ++++++p  v+   + pLGt++++++vl+
  gi|313125123|ref|YP_004035387.1| 222 TFDDEYP-YVRAGASGPLGTDERLVDVLA 249
                                       *******.*******************97 PP

>> 2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1   2.9e-13   8.8e-10      65     142 ..     313     387 ..     307     389 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 2.9e-13
                                       SEEEEEE-SHHHHTTTHHHHHHHHHHHHT--TT-B-TTSSEEEEEES--S-GGGSSEEEE..SSSSEEES-HHHHHH CS
                   2Fe-2S_thioredx  65 kyviqvCtttpCalrgseeilealekklgikagettadgkftleeveClGaCanaPvvqi..ndevyedltpekvee 139
                                         ++ vCt+ +Ca+ g+ ++le+l+++        ++d  + +++ +ClG+C+ +P+v +  +   y+++tp+++e+
  gi|313125123|ref|YP_004035387.1| 313 AKHVAVCTNQTCAASGAATVLEQLRQHA-----RDSDDCDVHFSRSSCLGQCGDGPIVAVypDSIWYGSVTPDDTER 384
                                       679***********************97.....57899**********************555569**********9 PP

                                       HHH CS
                   2Fe-2S_thioredx 140 ile 142
                                       i++
  gi|313125123|ref|YP_004035387.1| 385 IVS 387
                                       986 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.4e-08   7.3e-05     140     217 ..       9      87 ..       1     104 [. 0.86
   2 !    8.9   0.0   0.00028      0.84     135     211 ..     132     211 ..     109     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.4e-08
                                       TTEEEEEEE---SC.HHHHHHHHHHHHHHHCT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHH CS
                              CbiK 140 kdealvfvgHGteh.esnavyaeldkvlkekdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHak 214
                                        d+a+++vgHG++  +sn+  ++l   l+ +    v  + +e + P++e+ ie+l    +++ ++iPl l A  H+k
  gi|313125123|ref|YP_004035387.1|   9 DDDAILLVGHGSRReKSNEQVRTLAGKLETELSVPVDAAYIElAEPSIEDAIETLAP-TCRTLTVIPLSLFAASHVK 84 
                                       6899*******97526899999**99999999899999***9789*********976.69***************** PP

                                       CCC CS
                              CbiK 215 nDm 217
                                       nD+
  gi|313125123|ref|YP_004035387.1|  85 NDV 87 
                                       **6 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00028
                                       S----TTEEEEEEE---SC.HHHHHHHHHHHHHHH.CT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS CS
                              CbiK 135 ierarkdealvfvgHGteh.esnavyaeldkvlke.kdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlv 208
                                       ++r + d a+v+ + G++   sn+   +l ++l e ++f++v  + +  + P++e+ ++++ k+   +v ++P+ml 
  gi|313125123|ref|YP_004035387.1| 132 VDRDNDDVAVVLCARGSSDpDSNGDVHKLSRLLYEgREFTRVEPSFIGvTSPRLEDTLHSVAKDRPDAVVVVPYMLG 208
                                       4556688999******86526899999*****9998999999877775268************************97 PP

                                       --H CS
                              CbiK 209 AGd 211
                                        G 
  gi|313125123|ref|YP_004035387.1| 209 DGV 211
                                       774 PP

>> Suc_Fer-like  Sucrase/ferredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.34     1e+03      55     107 ..      65     150 ..       7     151 .. 0.48
   2 !   19.2   0.1   2.9e-07   0.00087     135     193 ..     347     400 ..     181     402 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.34
                      Suc_Fer-like  55 eekttvlllPdfklveevtpssveelvkeflkp.................................kvrklpekali 98 
                                        +  t++++P   +  +  +++v+  v++   +                                  v + ++++ +
  gi|313125123|ref|YP_004035387.1|  65 PTCRTLTVIPLSLFAASHVKNDVPMAVQTARTKyddvtfhfgshlgihpsivdllddrirtvesdlGVDRDNDDVAV 141
                                       33334444444433333333333333333333344455555555555555555555555556666644455666677 PP

                      Suc_Fer-like  99 LvCshktrD 107
                                        +C+ ++ D
  gi|313125123|ref|YP_004035387.1| 142 VLCARGSSD 150
                                       777776665 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.9e-07
                      Suc_Fer-like 135 gvrvgfisHvGGHkfAgnviiyrkekagqgiwygrvepedvegiveetilkgkvvkell 193
                                       +v+  + s +G     + v +y+ +     iwyg v+p+d e+iv+++++++++v++l+
  gi|313125123|ref|YP_004035387.1| 347 DVHFSRSSCLGQCGDGPIVAVYPDS-----IWYGSVTPDDTERIVSSHLERDRIVSDLV 400
                                       5555555555555555566677665.....9***********************99875 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   8.5e-06     0.026      71     195 ..      25     150 ..      15     205 .. 0.70
   2 ?    3.5   0.0     0.011        32      98     123 ..     181     206 ..     157     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.5e-06
                                       HHHHHHHHHHHHHHH---EEEEEEE.SSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHHHTT CS
                    Ferrochelatase  71 trkqaealekelaergidvkvylam.rywePsiedaleelkadgvervvvlplyPqysasttgssleeleralkkkr 146
                                       +++q + l+ +l+  + +v+v+ a+ +  ePsieda+e l+   ++ ++v+pl+   ++     +  +++ a++k  
  gi|313125123|ref|YP_004035387.1|  25 SNEQVRTLAGKLET-ELSVPVDAAYiELAEPSIEDAIETLA-PTCRTLTVIPLSLFAASHVKNDVPMAVQTARTK-Y 98 
                                       56677777777754.4689***9973679***********9.68*********9998888888888888888877.4 PP

                                       -SSEEEEE---TT-HHHHHHHHHHHHHHHTTS-...HC..C-EEEEEEE--BH CS
                    Ferrochelatase 147 eapevrvirqfydhpgyiealaesikealeelp...eek.kakllfsaHglPe 195
                                       + +++++ ++   hp  ++ l ++i+    +l    + +  +++++ a g   
  gi|313125123|ref|YP_004035387.1|  99 DDVTFHFGSHLGIHPSIVDLLDDRIRTVESDLGvdrD-NdDVAVVLCARGSSD 150
                                       7789999999999999999999998887666666532.235677776666555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.011
                                       SSSBHHHHHHHHHCTT-SEEEEEES- CS
                    Ferrochelatase  98 wePsiedaleelkadgvervvvlply 123
                                       ++P +ed+l  +++d  + vvv+p +
  gi|313125123|ref|YP_004035387.1| 181 TSPRLEDTLHSVAKDRPDAVVVVPYM 206
                                       68999999999999999999999976 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   0.00013       0.4      14      34 ..     253     274 ..     252     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                       EECSCCCE.EEESSSS-EEESS CS
                    RNA_POL_M_15KD  14 kedkegkn.feCrqCgYeepad 34 
                                       +e+++g++ + C++C+Y+ + +
  gi|313125123|ref|YP_004035387.1| 253 QEARSGSVeMSCDTCKYKVELS 274
                                       68999999*********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2238.28
//
Query:       gi|313125124|ref|YP_004035388.1|  [L=222]
Description: hypothetical protein Hbor_03440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0059   16.9   0.0      0.043   14.1   0.0    2.0  2  LAGLIDADG_3  LAGLIDADG-like domain
  ------ inclusion threshold ------
      0.077   12.8   0.1       0.64    9.8   0.0    2.2  2  Mersacidin   Two-component Enterococcus faecalis cytolysin (E


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.091   8.1e+02      15      59 ..      24      69 ..      20      91 .. 0.73
   2 !   14.1   0.0   4.8e-06     0.043       1      45 [.     115     160 ..     115     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.091
                                      CECCECSTTTTS.EEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EEE CS
                       LAGLIDADG_3 15 Gsvskskkkgvs.isltssskelledvqrlLlrlGIestiyek.kka 59
                                      G+v +s++ +++  +++++++  ++ ++ +     I  + +e+ + a
  gi|313125124|ref|YP_004035388.1| 24 GHVAGSGDIQPGeFTISTNDETCADRLAAIAGGGDIDQRETERpY-A 69
                                      788888888888899999999999999888888888888888833.3 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.8e-06
                                       HHHHHHHHHHHHHCCEC.CECSTTTTSEEEEES-HHHHHHHHHHHH CS
                       LAGLIDADG_3   1 evkaafLrGlfdaDGsv.skskkkgvsisltssskelledvqrlLl 45 
                                       e+++ +LrGl ++ G+v  ks+ ++v+is+   +++lle v  lL 
  gi|313125124|ref|YP_004035388.1| 115 EFQRQLLRGLLESCGTVcFKSSSGTVGISFVHDDRKLLETVDSLLD 160
                                       6899************94455555555*****************97 PP

>> Mersacidin  Two-component Enterococcus faecalis cytolysin (EFC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1     0.088   7.9e+02      26      34 ..      26      34 ..      24      46 .. 0.84
   2 ?    9.8   0.0   7.1e-05      0.64      19      46 ..      46      73 ..      41      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.088
                        Mersacidin 26 iyGagDvqa 34
                                      + G+gD+q+
  gi|313125124|ref|YP_004035388.1| 26 VAGSGDIQP 34
                                      78*****98 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7.1e-05
                        Mersacidin 19 SeeElsaiyGagDvqaetTPicytlksv 46
                                       ++ l ai G+gD++ + T  +y  +++
  gi|313125124|ref|YP_004035388.1| 46 CADRLAAIAGGGDIDQRETERPYAHNTA 73
                                      5799***************999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1232.78
//
Query:       gi|313125125|ref|YP_004035389.1|  [L=83]
Description: hypothetical protein Hbor_03450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-13   49.6   9.5    1.9e-12   47.7   9.5    1.8  1  Fer4_15   4Fe-4S single cluster domain
     0.0074   16.8   3.2      0.013   16.0   3.2    1.7  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   9.5   2.2e-16   1.9e-12       1      66 []       4      78 ..       4      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.2e-16
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvl.........lddgeiaeg.....evpddeeeaaqeAaraCPvdAIr 65
                                      +++Dr+aC+g+++C+a+ + +f++de gla+++         + d+    +        +  +++aq Aa+aCP dAI+
  gi|313125125|ref|YP_004035389.1|  4 IEIDRTACDGIFACLAR-DGRFVEDETGLATIDadaegvievARDD----ErnsvvATVEGNIDDAQLAAQACPPDAIT 77
                                      79***************.58*************8887777653333....1334465557899***************9 PP

                           Fer4_15 66 v 66
                                      v
  gi|313125125|ref|YP_004035389.1| 78 V 78
                                      7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   3.2   1.5e-06     0.013      37      58 .]      47      78 ..       6      78 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-06
                           Fer4_13 37 s..........eeekadaeeAadaCPvesIgv 58
                                      +          e  ++da+ Aa+aCP ++I+v
  gi|313125125|ref|YP_004035389.1| 47 DdernsvvatvEGNIDDAQLAAQACPPDAITV 78
                                      02223455555888****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 472.18
//
Query:       gi|313125126|ref|YP_004035390.1|  [L=320]
Description: precorrin-3 methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-34  118.6   0.5    4.6e-34  118.2   0.5    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2   0.5   2.5e-38   4.6e-34       2     212 ..      68     279 ..      67     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 2.5e-38
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea..yeeiaeal..ae 74 
                                       l+ VG+GpG +  +T  A ++l++a++++g++  + e+l d + e         +e+  +  +  + e++++   ++
  gi|313125126|ref|YP_004035390.1|  68 LVAVGLGPGRASEMTTLAKETLRDAEHIVGYT-TYIELLPDDIVEG--------AEDIYS--TpmCGEVSRTEeaID 133
                                       899*****************************.7777775444332........221112..133555555555599 PP

                      TP_methylase  75 alragkdVvllvsGDPlvy...gtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpgl 146
                                       +  ag dV+++ sGDP+vy   g + e++e   a +  ++++v+ Gv+++q++aarlg+pl+++ ++ s++  l+++
  gi|313125126|ref|YP_004035390.1| 134 RTLAGNDVAIVGSGDPNVYalaGLALEILESKGATASMVDFDVVAGVPAAQSCAARLGAPLVNDTVTISLSdhLTSM 210
                                       999999*************544455555555555555556*******************************997777 PP

                      TP_methylase 147 akeeereleallangdtlvllkapr.k.....laelaelLkealyddttpvavveragtedervvrgtleel 212
                                        ++e r+ +a+ + g t+v++ +p+ +     +++ +e+L+e+ +d++tpv +v+ ag+ede+v  + l++l
  gi|313125126|ref|YP_004035390.1| 211 PTIESRLHSAAKE-GFTIVIY-NPWsRkrrsnYEKCCEILLEH-RDPETPVGIVHGAGREDEEVEIVELQDL 279
                                       7777777777555.5555555.7775457888***********.77788******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 1887.29
//
Query:       gi|313125127|ref|YP_004035391.1|  [L=283]
Description: precorrin-3 methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-41  141.9   0.0    3.2e-41  141.6   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.0   1.8e-45   3.2e-41       1     199 [.      21     219 ..      21     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 1.8e-45
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel....eleapmgkekepleeayeeiaeala 73 
                                       +ly+VG+GpG p+++T+rA ++++t+d+v++++ ++ e l+d    +     e  ++  + ++++ + + e  +  +
  gi|313125127|ref|YP_004035391.1|  21 TLYVVGIGPGLPDHMTQRAKEVIQTSDCVVASN-LYQEFLRD----DGtlppEDSDDGPEVVRSSMGQQVELTREAF 92 
                                       69****************************999.77777754....223443445555555777777788999999* PP

                      TP_methylase  74 ealragkdVvllvsGDPlvygtgselve.alrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpgla 147
                                       e++r+g+dV+++++GDP+vyg  + +++ a ++++ ++++e++PGv+++   aa +g+pl++++++ s++  ++g++
  gi|313125127|ref|YP_004035391.1|  93 ERVRDGEDVAHVSGGDPNVYGKSDLVFTmAESDDATDVPIEIVPGVTAALGGAAMMGAPLSNDFCTISLSdkWRGWD 169
                                       *************************99746777788999************************************** PP

                      TP_methylase 148 keeereleallangdtlvllkapr.klaelaelLkealyddttpvavveragt 199
                                       ++ee++++a+++   ++++l++++ ++ +++++ +e+ ++d+ pv ++++ag+
  gi|313125127|ref|YP_004035391.1| 170 EIEEKLRAAAIS--NFVIVLYNCWrNYTRAIDIVREE-RADDVPVGIFNDAGR 219
                                       *********999..99********77***********.88999*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1589.39
//
Query:       gi|313125128|ref|YP_004035392.1|  [L=320]
Description: cobalamin biosynthesis protein cbig [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-28   97.6   0.0    8.2e-28   96.2   0.0    1.8  1  CbiG_N    Cobalamin synthesis G N-terminal
    8.8e-23   81.1   0.0    2.6e-22   79.6   0.0    1.7  2  CbiG_C    Cobalamin synthesis G C-terminus
  ------ inclusion threshold ------
      0.032   14.9   0.1       0.38   11.4   0.2    2.4  2  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   1.4e-31   8.2e-28       2      82 .]      59     137 ..      58     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.4e-31
                                       .HHHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XX CS
                            CbiG_N   2 llrelfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviT 78 
                                       +++e++ eyd++v ++a+Gi++R  a ll+dK++DpaVvvvde+ +++i+l++Gh +gAn++A ++ + lga p++T
  gi|313125128|ref|YP_004035392.1|  59 VFAEHWGEYDCFVGLMASGIAMRKTAGLLDDKWEDPAVVVVDEELTWAIPLTGGH-HGANQVAYDL-SKLGAVPAMT 133
                                       789****************************************************.**********.678******* PP

                                       XXX. CS
                            CbiG_N  79 tatd 82 
                                       ta++
  gi|313125128|ref|YP_004035392.1| 134 TASE 137
                                       **96 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.68     4e+03      61      88 ..     119     146 ..      88     168 .. 0.67
   2 !   79.6   0.0   4.3e-26   2.6e-22       1     115 [.     202     318 ..     202     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.68
                                       EEE-HHHHHCHH.CSCT-CHHHCCCSSS- CS
                            CbiG_C  61 ktfsaeeLaave.vpnpsefvkkevGvps 88 
                                       ++++ ++L av+ + ++ + ++ + Gv+s
  gi|313125128|ref|YP_004035392.1| 119 VAYDLSKLGAVPaM-TTASEAAGKQGVES 146
                                       55555566666533.33333333334443 PP

  == domain 2  score: 79.6 bits;  conditional E-value: 4.3e-26
                                       EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT- CS
                            CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnps 77 
                                       +v+G G  +g+++e++ +a+e+al++a+++ ++v+ +at ++Kadepg+l++a++++  +++f++e+L ++e p+ps
  gi|313125128|ref|YP_004035392.1| 202 VVLGTGSVSGAKKEQFLTAWERALDDADCDWDDVDFVATGTRKADEPGMLDAAQEIDAGVVYFEKETLTEFEGPTPS 278
                                       69**********************************************************************99998 PP

                                       CHHHCCCSSS-HHHHHHHHHC...EECSCEEEE.TTEEEEE CS
                            CbiG_C  78 efvkkevGvpsVaEaaAllaa..arllvpKqak.ggvTvAi 115
                                          k+ +G p++aEa+A++    ++l+v+Kq++ ++vTvA+
  gi|313125128|ref|YP_004035392.1| 279 R-SKELIGWPGIAEASAIAGGrdHELIVEKQRYdDAVTVAV 318
                                       6.679*************997557******98889*****8 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.19   1.1e+03      52      93 ..      29      78 ..      20      79 .. 0.73
   2 ?   11.4   0.2   6.4e-05      0.38       7      83 ..      97     165 ..      84     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.19
                                      EC....HHHHHHHHHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEE CS
                              AIRS 52 lp....wleevvrglaeaaeelgvplvgGdtsfsne....ptisvtavGl 93
                                      ++    ++ee+ r+la+  +++++ +  Gd+  +      +++ ++a G+
  gi|313125128|ref|YP_004035392.1| 29 FErkleTAEEIKRDLADDYDRIDILTYHGDVFAEHWgeydCFVGLMASGI 78
                                      445566899999******************97653345666666666665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.4e-05
                                       EEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEECHHHHHHHHHHHHHHHTT-EEEEEEEEEESS CS
                              AIRS   7 vttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalpwleevvrglaeaaeelgvplvgGdtsfsne 83 
                                       v +d  ++ +   p ++ G+ ++ +++ Dl   GA P + + s a ++     +g+++ a++l++++v Gd+++ ++
  gi|313125128|ref|YP_004035392.1|  97 VVVD--EELTWAIPLTG-GHHGANQVAYDLSKLGAVPAMTTASEAAGK-----QGVESKAKALDTHVVNGDSTVATN 165
                                       4445..45566678889.********************9999998884.....8*****************998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1915.94
//
Query:       gi|313125129|ref|YP_004035393.1|  [L=281]
Description: precorrin-4 C(11)-methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-42  146.2   0.6    1.5e-42  146.0   0.6    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
     0.0044   17.7   0.0      0.014   16.1   0.0    1.8  2  RraB          Regulator of ribonuclease activity B
  ------ inclusion threshold ------
       0.17   11.2   0.0       0.26   10.6   0.0    1.2  1  DUF5066       Domain of unknown function (DUF5066)


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.0   0.6   2.5e-46   1.5e-42       3     212 ..      20     225 ..      18     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 2.5e-46
                      TP_methylase   3 ylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealrag 79 
                                        +VG+GpGdpellTv+++r++++ad+v+ ++s++ + lld        + + ++++++ +++ ee    +a+a ++g
  gi|313125129|ref|YP_004035393.1|  20 PFVGAGPGDPELLTVAGRRLVEEADLVVHAGSLVNSELLDE-------YCDHAEQVNSVGKDLEELIPLMADAYESG 89 
                                       58*****************************9966666543.......3356788899999999999999******* PP

                      TP_methylase  80 kdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpglakeeer 152
                                       ++Vv+l+sGDP vyg++ e ++al+   +g+++  +PGv+s+ aa a l++ lt ++++ +v+    + ++   ee+
  gi|313125129|ref|YP_004035393.1|  90 ETVVRLHSGDPAVYGAALEQMDALES--EGVPTYLVPGVTSAFAASATLRTQLTLNEVANHVVftrpQGRTLSAEED 164
                                       **************************..9***********************************9886666677888 PP

                      TP_methylase 153 eleallangdtlvllkapr.klaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       ++++++  gdt v ++ +   ++e++++L+++ ++++t pvavv +a+++de v++gt+e++
  gi|313125129|ref|YP_004035393.1| 165 HISDFVGFGDTTVCIYLGThAVEETMDRLLDEgHDPET-PVAVVYHASWPDEDVIEGTIETI 225
                                       888888887766666555538***********888855.********************986 PP

>> RraB  Regulator of ribonuclease activity B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.75   4.5e+03      39      77 ..      81     116 ..      60     121 .. 0.53
   2 !   16.1   0.0   2.4e-06     0.014       5      42 ..     187     228 ..     183     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.75
                              RraB  39 faeeleklgyevedaeedeedgeevycldlskemsldae 77 
                                       +++++ ++g +v ++   +   + vy + l++ ++l+ e
  gi|313125129|ref|YP_004035393.1|  81 LMADAYESGETVVRLHSGD---PAVYGAALEQMDALESE 116
                                       3344444444444433333...46777777777776665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.4e-06
                              RraB   5 revldalledGddldkpreiehhfyfedeedlekfae....e 42 
                                       +e++d+ll++G+d++ p  + +h++ +de+ +e  +e    +
  gi|313125129|ref|YP_004035393.1| 187 EETMDRLLDEGHDPETPVAVVYHASWPDEDVIEGTIEtigqK 228
                                       899***************************999998833334 PP

>> DUF5066  Domain of unknown function (DUF5066)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.3e-05      0.26      62     135 ..      31     104 ..      27     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.3e-05
                           DUF5066  62 lkspygqkvleylvdsideegvilsyspdeeayygsgldiagvdledlmpvwnddprlpaliriahaGdqrifi 135
                                       l++  g++++e     ++   +++s  +de   ++ ++++ g dle+l+p+ +d  +    +   h+Gd +++ 
  gi|313125129|ref|YP_004035393.1|  31 LLTVAGRRLVEEADLVVHAGSLVNSELLDEYCDHAEQVNSVGKDLEELIPLMADAYESGETVVRLHSGDPAVYG 104
                                       55566666677666677777899999*****************************99998888889***99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1566.47
//
Query:       gi|313125130|ref|YP_004035394.1|  [L=242]
Description: precorrin-2 methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-39  134.6   0.5    5.8e-39  134.2   0.5    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   0.5   3.2e-43   5.8e-39       1     210 [.       2     199 ..       2     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 3.2e-43
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel..eleapmgkekepleeayeeiaealaea 75 
                                       ++y+VG+GpGd++l+Tv++ r+l+++dvv+ ++++  + +l++++ee+   l +pm+++ ++l++a++e+a+ +ae+
  gi|313125130|ref|YP_004035394.1|   2 TVYGVGLGPGDADLVTVKGKRILESVDVVYSPGRLSRTVALNHVPEERigDLDFPMTRDPDELRRAWKEAAAEVAER 78 
                                       59*******************************66999999*****99***************************** PP

                      TP_methylase  76 lragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeer 152
                                       +++g dV++++ GDP+vy+t+++l + l a ++ +e ev+PGvs+++a a++lg++++ +g+ ls+        e++
  gi|313125130|ref|YP_004035394.1|  79 AESG-DVAFVTLGDPNVYSTFGHLRRTLDAFHPAVELEVVPGVSAMTAFATALGVEIE-SGTGLSLR-------EAA 146
                                       ***9.8***************************************************9.88888888.......333 PP

                      TP_methylase 153 eleallangdtlvllkaprklaelaelLkealyddttpvavveragte.dervvrgtle 210
                                         +a    +d+++l+k ++ ++ + e L ea  +  ++v +++r+ +e +e++v+++ +
  gi|313125130|ref|YP_004035394.1| 147 NGAA-PTGPDRMILFKVTD-APATYEGLTEA--G--YDVKFGRRLFMEqGETLVTSNPQ 199
                                       3333.34489999998888.99999999999..5..78999999999955988887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1355.23
//
Query:       gi|313125131|ref|YP_004035395.1|  [L=185]
Description: precorrin-6y c5,15-methyltransferase (decarboxylating), cbit subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-06   26.5   0.0      6e-06   26.0   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    4.7e-06   26.3   0.0    8.3e-06   25.4   0.0    1.4  1  MTS              Methyltransferase small domain
      5e-06   27.1   0.1    7.9e-06   26.5   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    8.5e-05   22.4   0.0    9.7e-05   22.2   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    0.00012   21.9   0.0    0.00015   21.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00013   22.5   0.1    0.00021   21.9   0.1    1.4  1  Methyltransf_11  Methyltransferase domain
     0.0018   17.8   0.0     0.0031   17.1   0.0    1.4  1  DOT1             Histone methylation protein DOT1
     0.0018   18.2   0.1     0.0033   17.4   0.1    1.6  1  Methyltransf_18  Methyltransferase domain
     0.0024   17.0   0.0     0.0038   16.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0039   16.5   0.0     0.0057   16.0   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
       0.02   14.5   0.0      0.029   13.9   0.0    1.3  1  GATase_3         CobB/CobQ-like glutamine amidotransferase do
      0.028   13.8   0.1      0.042   13.2   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.069   12.8   0.0        0.1   12.2   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
       0.16   11.5   0.0       0.17   11.4   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   4.7e-09     6e-06      16      96 ..       7      85 ..       2     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.7e-09
                                      TTXXXXXSSSHHHHHHHHHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTE CS
                     Cons_hypoth95 16 legkstRPttdrvrealFnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeeta 94
                                      ++  +  Pt+++vr    + l+ +    +++D+ + +G++++EA+ R  k++++ve++++ +++ ++nl++ + ++ +a
  gi|313125131|ref|YP_004035395.1|  7 PHDAKAGPTKSEVRAVTLDKLDLR-PTDHFVDVGSCTGSVSIEAAQRV-KRVTAVERKAKRLEVTRKNLAANEYDADVA 83
                                      5556778**********9999965.5667*****************97.********************9988776555 PP

                                      EE CS
                     Cons_hypoth95 95 el 96
                                       +
  gi|313125131|ref|YP_004035395.1| 84 LH 85
                                      44 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   6.5e-09   8.3e-06      24      88 ..      24      86 ..      19     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 6.5e-09
                                      HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-S CS
                               MTS 24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasd 88
                                      l++l+ + +++ +D+G+ +G +++++a++ ++  vt+v+ +a+ le++++nl+an+ +++v  ++
  gi|313125131|ref|YP_004035395.1| 24 LDKLDLRPTDHFVDVGSCTGSVSIEAAQRVKR--VTAVERKAKRLEVTRKNLAANEYDADVALHE 86
                                      77888889999*****************9999..9**********************95554333 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   6.2e-09   7.9e-06       2      92 ..      36     130 ..      35     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.2e-09
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE.....EST CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs.....sga 73 
                                       +d+G  tG +++++a+r+  ++vt+v+  ++ le +r++++++++++++  ++ae+     +  D++++     + a
  gi|313125131|ref|YP_004035395.1|  36 VDVGSCTGSVSIEAAQRV--KRVTAVERKAKRLEVTRKNLAANEYDADVALHEAEAPAGLPDDADAMFIggsrnFEA 110
                                       7****************9..9*********************99966666666666544444667777755454444 PP

                                       .GGGSSHHHHHHHHHHHHHH CS
                   Methyltransf_25  74 .lhhlsdedlekalkeiarv 92 
                                        l h  ++++++++ +++rv
  gi|313125131|ref|YP_004035395.1| 111 vLDHAVKSEIDRVVMNVSRV 130
                                       55565556667777666665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   7.5e-08   9.7e-05       6     100 ..      34     130 ..      29     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.5e-08
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklled.......e 73 
                                       +++D+G+ tG  ++e+a+++   ++v+ ++++++ +e+ r+n++ +++d  v ++++++ + l+ + +d       +
  gi|313125131|ref|YP_004035395.1|  34 HFVDVGSCTGSVSIEAAQRV---KRVTAVERKAKRLEVTRKNLAANEYDaDVALHEAEAPAgLPDD-ADamfiggsR 106
                                       689**************987...56************************9**********999964.3367888878 PP

                   Methyltransf_31  74 kfDlilsnevlnaladpdkileeierv 100
                                       +f  +l+++v    ++ d + ++++rv
  gi|313125131|ref|YP_004035395.1| 107 NFEAVLDHAVK---SEIDRVVMNVSRV 130
                                       88888887666...4555555565555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.2e-07   0.00015      60     147 ..      18     101 ..       5     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGG CS
                              PCMT  60 hmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrk 135
                                        + a++l+ l+l++ ++ ++vGs +G  +   a+ v++++   ++er ++  e +++nl +++++ +v++++++   
  gi|313125131|ref|YP_004035395.1|  18 EVRAVTLDKLDLRPTDHFVDVGSCTGSVSIEAAQRVKRVT---AVERKAKRLEVTRKNLAANEYDaDVALHEAEAPA 91 
                                       567999********************98888888887766...********************9989********99 PP

                                       TTGGG-SEEEEE CS
                              PCMT 136 GyeekaPYdaih 147
                                       G ++ a  da++
  gi|313125131|ref|YP_004035395.1|  92 GLPDDA--DAMF 101
                                       999988..5555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.7e-07   0.00021       1      87 [.      36     130 ..      36     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES......- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvsse......v 70 
                                       +dvG++tG+++ + a+r++rv++v+  ++ l++ +++   ++   ++   +ae    ++d   D+ ++        v
  gi|313125131|ref|YP_004035395.1|  36 VDVGSCTGSVSIEAAQRVKRVTAVERKAKRLEVTRKNLAANEYDADVALHEAEAPaGLPD-DADAMFIGGsrnfeaV 111
                                       59************************************9999966666666666337999.8999999885544555 PP

                                       CCC-..CCHHHHHHHHHHH CS
                   Methyltransf_11  71 lhhv..edpekalkeiaRv 87 
                                       l+h    + ++++ ++ Rv
  gi|313125131|ref|YP_004035395.1| 112 LDHAvkSEIDRVVMNVSRV 130
                                       5555555555555555555 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0031      29      74 ..      18      61 ..      11      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE- CS
                              DOT1 29 eflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEi 74
                                      e+ +  ldk++l++ d FvD GS  G v + aa  v+    + vE 
  gi|313125131|ref|YP_004035395.1| 18 EVRAVTLDKLDLRPTDHFVDVGSCTGSVSIEAAQRVKR--VTAVER 61
                                      5556679************************9987653..355555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.6e-06    0.0033      14      90 ..      31     104 ..      27     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.6e-06
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvviaG 90 
                                       ++++++D+G+  g ++i+++  +++k+v+a++ +++ le  ++n++ ++++ ++ ++ ++  + l ++++d++ i G
  gi|313125131|ref|YP_004035395.1|  31 PTDHFVDVGSCTGSVSIEAA--QRVKRVTAVERKAKRLEVTRKNLAANEYDADVALHEAEAPAGL-PDDADAMFIGG 104
                                       56799**************9..68999*************************9999999998888.56689888875 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.9e-06    0.0038      23      73 ..      24      74 ..      16      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.9e-06
                                      HHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT CS
                            RrnaAD 23 ldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls 73
                                      ldkl+l++++  +++g+ +G  + e a+r+k v+++E   + +++++k+l 
  gi|313125131|ref|YP_004035395.1| 24 LDKLDLRPTDHFVDVGSCTGSVSIEAAQRVKRVTAVERKAKRLEVTRKNLA 74
                                      89************************************9999999999775 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.5e-06    0.0057      52     113 ..      21      81 ..      10      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.5e-06
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS- CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerk 113
                                        ++l+kl+l+p ++ +d+G   Gs+ ++a++r   +v ++   +++ ++++k++++ + + +
  gi|313125131|ref|YP_004035395.1|  21 AVTLDKLDLRPTDHFVDVGSCTGSVSIEAAQR-VKRVTAVERKAKRLEVTRKNLAANEYDAD 81 
                                       5789****************************.55677777778888888888888776655 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.3e-05     0.029      15      73 ..      72     129 ..      56     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                          GATase_3  15 dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaae 73 
                                       +l + e+ ++v ++ ++     l++dad+++++G+++ ++ l ++ +s++d+ + + ++
  gi|313125131|ref|YP_004035395.1|  72 NLAANEYDADVALHEAE-APAGLPDDADAMFIGGSRNFEAVLDHAVKSEIDRVVMNVSR 129
                                       67777888888999999.888899**********************9999998887765 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.3e-05     0.042     155     219 ..      24      87 ..      18     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                              PrmA 155 lekl.vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalse 219
                                       l+kl ++++++++DvG  +G  +i aa+   k+v+av      ++v+++N++ N+ +a + ++  +
  gi|313125131|ref|YP_004035395.1|  24 LDKLdLRPTDHFVDVGSCTGSVSIEAAQ-RVKRVTAVERKAKRLEVTRKNLAANEYDADVALHE-A 87 
                                       566535677899************9987.689*************************9997753.3 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.2e-05       0.1       8      74 ..      11      77 ..       7     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                                      ---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHH CS
                           UPF0020  8 gpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeear 74
                                      + +p k+++ a+ +   +++p++ ++D  + +G++ IEaa+ ++++ +   + + le+ ++  ++++
  gi|313125131|ref|YP_004035395.1| 11 KAGPTKSEVRAVTLDKLDLRPTDHFVDVGSCTGSVSIEAAQRVKRVTAVERKAKRLEVTRKNLAANE 77
                                      55666667777777778999*************************9976666666663333333333 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.17       4      48 ..      35      79 ..      32     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                   Methyltransf_15  4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvs 48
                                       +D+ s +G  +i+ a+  ++v a+e + ++l+++ +N  + + +
  gi|313125131|ref|YP_004035395.1| 35 FVDVGSCTGSVSIEAAQRVKRVTAVERKAKRLEVTRKNLAANEYD 79
                                      68999999******************************7654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1058.46
//
Query:       gi|313125132|ref|YP_004035396.1|  [L=220]
Description: cobalamin biosynthesis protein cbim [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-49  168.3  23.6    2.3e-49  168.1  23.6    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.1  23.6   1.3e-53   2.3e-49       1     203 [.       2     208 ..       2     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 168.1 bits;  conditional E-value: 1.3e-53
                              CbiM   1 HipdgiLspavllaayavalallalalrrlrkeld.ear.vpllallaafifaaqminipipggtslHllgavlaai 75 
                                       Hi++g+L+p ++ +++aval+++a++++r  k+++ + +  +l+a+ +af+f+++ +++p  +g+s+H++g++++ +
  gi|313125132|ref|YP_004035396.1|   2 HIMEGFLPPFWAFVWTAVALPFVAYGAKRTIKTMRaDTKmKALIAIGTAFVFVLSALKLPSVTGSSSHPTGTGVMVV 78 
                                       *********************************8844448999********************************** PP

                              CbiM  76 LlGpwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvla 152
                                       L+Gp+++++a+a+vll q+ll+++GG+t+LGaN++ m+++g++++++ yr+++    s+ ++  ++f+aa+l+ + +
  gi|313125132|ref|YP_004035396.1|  79 LFGPAVTAFAAAIVLLYQSLLLAHGGLTTLGANVVAMGIVGPFVGWVAYRAVR----SSLSLEQSTFVAAVLADWTT 151
                                       **************************************************994....45789*************** PP

                              CbiM 153 allvalelalsgleas......lsltaalaamllvhlpvgilEgviTaaivkalkkv 203
                                       +l+++++l+++   +       +s+  ++a+++++++p+gilEgvi aa+v +l++v
  gi|313125132|ref|YP_004035396.1| 152 YLTTSVQLGVAFPGGGgidgilTSVIDFVAVFAITQVPIGILEGVIAAALVGYLARV 208
                                       ***********665458*****9*******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1284.97
//
Query:       gi|313125133|ref|YP_004035397.1|  [L=90]
Description: cobalt ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-13   50.2   0.0    2.5e-13   49.8   0.0    1.2  1  CbiN      Cobalt transport protein component CbiN


Domain annotation for each model (and alignments):
>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   1.4e-17   2.5e-13       6      66 ..       9      67 ..       4      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 1.4e-17
                              CbiN  6 llvvllavvplflvkgaeFgGaDdqaeevIeeiapdyepwfeplweppsGEiESlLFalQA 66
                                      llvv l++++ ++v  +  g +D+qa + I++ +p+y pw+ p+wepp+G  E  LFalQ 
  gi|313125133|ref|YP_004035397.1|  9 LLVVGLVILSTIAV--SGLGATDEQAVATITDKDPNYSPWMGPVWEPPGGYGEMALFALQG 67
                                      44555555555554..679*****************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 508.32
//
Query:       gi|313125134|ref|YP_004035398.1|  [L=243]
Description: cobalt ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-40  138.4   8.9    3.5e-40  138.0   8.9    1.1  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.0   8.9   1.9e-44   3.5e-40      14     211 ..      20     212 ..      12     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.0 bits;  conditional E-value: 1.9e-44
                                       HHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE.......EECTTEEE. CS
                              CbiQ  14 liwlfllllalvlapnlvtlliiiallllllllvilp.rvlaqalilpllflllgllillfqlittegefvfagggq 89 
                                       l ++f  + +l  a++  +++++++++++ +l  +   r++++++++p+ fl+++l +++f    t+g++vf     
  gi|313125134|ref|YP_004035398.1|  20 LKVYFVAVSLLLTATSARLPTFVAVIVVFSVLTTHAVgRAYFRFVRYPFWFLVPSLALITF---VTPGQTVFEYSV- 92 
                                       66777888888888888999999999999999999889***********************...479*****9999. PP

                                       ..E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              CbiQ  90 isitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqrikqAqkl 166
                                       + + +eG+  ++ ++lR++++ls+l++lalTT++++l+s+l rlg P+ ++++llL+yR i++L++e  r+++A kl
  gi|313125134|ref|YP_004035398.1|  93 LHVSEEGVRLAIRTGLRSVASLSVLSFLALTTTVPQLVSALDRLGLPDSIVEMLLLVYRGIQVLIDESIRLYTAAKL 169
                                       99*************************************************************************** PP

                                       TTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 167 RlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                       R+g +  ++r++ r+++ ++ +l+l++l+ ae++ l+m +R+Y+g
  gi|313125134|ref|YP_004035398.1| 170 RGGFT--SRRSTFRTTKHVATSLLLSSLDSAEQLDLSMRSRCYSG 212
                                       *****..*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1345.34
//
Query:       gi|313125135|ref|YP_004035399.1|  [L=231]
Description: cobalt ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.6e-32  110.5   0.0    1.1e-31  110.2   0.0    1.1  1  ABC_tran     ABC transporter
    4.4e-13   49.7   0.0    5.1e-06   26.5   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.5e-08   34.4   0.0      2e-06   27.4   0.0    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    8.5e-06   25.7   0.0    0.00076   19.3   0.0    2.0  2  AAA_15       AAA ATPase domain
    0.00013   21.6   0.0    0.00024   20.8   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00047   20.7   0.0    0.00071   20.1   0.0    1.2  1  AAA_23       AAA domain
    0.00067   20.1   0.0     0.0013   19.2   0.0    1.5  1  AAA_16       AAA ATPase domain
     0.0013   18.7   0.0     0.0021   18.0   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
     0.0019   17.8   0.0      0.003   17.2   0.0    1.2  1  AAA_27       AAA domain
     0.0022   17.3   0.0     0.0035   16.6   0.0    1.3  1  Zeta_toxin   Zeta toxin
     0.0052   16.5   0.0      0.011   15.4   0.0    1.4  2  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.018   15.2   0.1       0.41   10.9   0.1    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.021   15.1   0.0      0.045   14.0   0.0    1.7  1  AAA_22       AAA domain
      0.055   13.4   0.0      0.096   12.6   0.0    1.4  1  NACHT        NACHT domain
      0.066   13.1   0.1       0.19   11.6   0.0    1.7  2  APS_kinase   Adenylylsulphate kinase
      0.067   12.8   0.0        0.1   12.2   0.0    1.2  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.067   13.6   0.0       0.18   12.2   0.0    1.8  1  DUF4350      Domain of unknown function (DUF4350)
       0.19   11.5   0.0        0.3   10.8   0.0    1.2  1  MukB         MukB N-terminal
       0.24   10.8   0.0        2.2    7.7   0.0    2.0  2  TniB         Bacterial TniB protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.0   1.2e-34   1.1e-31       1     137 []      17     162 ..      17     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 1.2e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpe 73 
                                       l+ +++  + g +++++G+nGaGKStLlk l gll+p+ G++ +dg+ +++  ++l slr+e+g+++q+  +ql   
  gi|313125135|ref|YP_004035399.1|  17 LRGIDFRAETGDVTVLLGRNGAGKSTLLKHLNGLLEPDRGHVMIDGDRIQYddDSLLSLRQEVGFVFQDpdDQLVAP 93 
                                       57899**********************************************989999************65455444 PP

                                       SBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + v++           + +e +e als++gl + +d+ +    s LSgG+k+rvala +l+ kpk l++DEpta
  gi|313125135|ref|YP_004035399.1|  94 T-VEQDvafgpinlgtDPTEAVEWALSRVGLAGYEDRLC----SRLSGGEKKRVALAGVLAMKPKYLIFDEPTA 162
                                       4.666699****999888888******************....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.9e-07   0.00018       1      25 [.      29      53 ..      29      96 .. 0.79
   2 !   26.5   0.0   5.4e-09   5.1e-06     237     300 ..     134     194 ..     126     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      ++vl G+Ng+GKS+LL+ l +l   
  gi|313125135|ref|YP_004035399.1| 29 VTVLLGRNGAGKSTLLKHLNGLLEP 53
                                      79*****************999643 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 5.4e-09
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       lS G k+  al+  l+  +   + l++DEp +gL+   +r l++l++el+++g+ ++++TH p 
  gi|313125135|ref|YP_004035399.1| 134 LSGGEKKRVALAGVLAMKP---KYLIFDEPTAGLDGDGTRALVDLIRELTNEGISFVVSTHYPD 194
                                       688999888*******988...55*************************************985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   2.1e-09     2e-06      25     202 ..      28     196 ..      19     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.1e-09
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                        +t+++G+NG+GKs ll  +  +L  +           d i++ +++  + + ev  +f+++d++l+  + e  +  
  gi|313125135|ref|YP_004035399.1|  28 DVTVLLGRNGAGKSTLLKHLNGLLEPDRG---HVMIDGDRIQYDDDSLLSLRQEVGFVFQDPDDQLVAPTVEQDVA- 100
                                       57999999999999999999888886666...33344566777788888889999999999999943333333332. PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                                  in  +   + v+  l+++g+          LSgGek+ vala ++A++   p+   ++De  a LD
  gi|313125135|ref|YP_004035399.1| 101 --------FGPINLGTDPTEAVEWALSRVGLAGYedrlcsRLSGGEKKRVALAGVLAMK---PK-YLIFDEPTAGLD 165
                                       ........233444444444444445554444333333338**************9975...44.3589******** PP

                                       HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkekskn.aQfivislreeml 202
                                          ++++++l++e +++   f+v ++  ++ 
  gi|313125135|ref|YP_004035399.1| 166 GDGTRALVDLIRELTNEgISFVVSTHYPDFA 196
                                       *************999956777777766554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.1e-07   0.00076      20      79 ..      21      79 ..      18     112 .. 0.75
   2 ?    4.7   0.0     0.022        21     324     368 ..     152     195 ..     141     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.1e-07
                            AAA_15 20 dlsee...ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikI 79
                                      d+  e   +tvl G+N++GKS++l+ l+ +l+ +       + i+ + +++ ++   s + ++
  gi|313125135|ref|YP_004035399.1| 21 DFRAEtgdVTVLLGRNGAGKSTLLKHLNGLLEPD----RGHVMIDGDRIQYDDDSLLSLRQEV 79
                                      44444555********************999988....4555666666666665555555555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.022
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       ++ l+++EP a L  +  + l++l++el n++    +++TH p +
  gi|313125135|ref|YP_004035399.1| 152 PKYLIFDEPTAGLDGDGTRALVDLIRELTNEGI-SFVVSTHYPDF 195
                                       567899**************************9.9******8876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.5e-07   0.00024      18      50 ..      23      55 ..      15      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-07
                            AAA_29 18 eidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      + ++ ++t+l G++G+GKSTll  ++ lL p++
  gi|313125135|ref|YP_004035399.1| 23 RAETGDVTVLLGRNGAGKSTLLKHLNGLLEPDR 55
                                      4554559***************98888888876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   7.6e-07   0.00071      15      39 ..      20      47 ..       9      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.6e-07
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                      idF      +t++ G NGaGK+T+l  +
  gi|313125135|ref|YP_004035399.1| 20 IDFraeTGDVTVLLGRNGAGKSTLLKHL 47
                                      799887778***************9876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.4e-06    0.0013      24     124 ..      27     177 ..      14     188 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa..ipy............sa.laqalareellrq 84 
                                       + +++l G  G GKs+l+++l   le d+g++ + g+  q++ +  +++            ++ +a + +++  +  
  gi|313125135|ref|YP_004035399.1|  27 GDVTVLLGRNGAGKSTLLKHLNGLLEPDRGHVmIDGDRIQYDDDslLSLrqevgfvfqdpdDQlVAPTVEQDVAFGP 103
                                       36799***********************9999999999998544221112221112222222222222222222222 PP

                            AAA_16  85 lldeaesaeleawrekleeala..................................avpelagaeasrllellk 124
                                       ++  ++ +e+ +w+    + ++                                  +++ l+g++ ++l +l++
  gi|313125135|ref|YP_004035399.1| 104 INLGTDPTEAVEWALSRVGLAGyedrlcsrlsggekkrvalagvlamkpkylifdePTAGLDGDGTRALVDLIR 177
                                       22223333333333322222225556555555666655555555556666665555555555555555555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0021      99     123 ..      27      51 ..       9      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                                       TSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                       ++++vl+G  G+GKStL+++l++ l
  gi|313125135|ref|YP_004035399.1|  27 GDVTVLLGRNGAGKSTLLKHLNGLL 51 
                                       489******************9865 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.2e-06     0.003      18      50 ..      19      51 ..       9      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                       +df+ae+ d+++++G N AGKst+l+ ++ ll
  gi|313125135|ref|YP_004035399.1| 19 GIDFRAETGDVTVLLGRNGAGKSTLLKHLNGLL 51
                                      589***********************9888776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.7e-06    0.0035      17      55 ..      28      66 ..      14      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                        Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgnvvrldpDdlR 55
                                      ++ +l G  GAGKs+l++ l+  le++++ v +d+D+++
  gi|313125135|ref|YP_004035399.1| 28 DVTVLLGRNGAGKSTLLKHLNGLLEPDRGHVMIDGDRIQ 66
                                      6778889*****************************986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.011      16      49 ..      26      58 ..      19      63 .. 0.83
   2 ?   -2.8   0.0       4.7   4.5e+03      90     112 ..     153     179 ..     108     188 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                      +g  v+vl G+ G+GK+t+lk+l+ ++e + g+v
  gi|313125135|ref|YP_004035399.1| 26 TG-DVTVLLGRNGAGKSTLLKHLNGLLEPDRGHV 58
                                      44.49*******************9999875555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                            AAA_30  90 tllivDEagmv....dtkqlaallkaa 112
                                       + li DE        +t+ l +l++++
  gi|313125135|ref|YP_004035399.1| 153 KYLIFDEPTAGldgdGTRALVDLIREL 179
                                       566666643323333444444444444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00043      0.41      28      89 ..     129     177 ..     108     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00043
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       r +++lSGGek + ++la       ++        +++ +++DE  ++lD++ +++l++l++
  gi|313125135|ref|YP_004035399.1| 129 RLCSRLSGGEK-KRVALA------GVLAM------KPKYLIFDEPTAGLDGDGTRALVDLIR 177
                                       66778888888.333333......33333......4678999**********9999999987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.8e-05     0.045       4      32 ..      26      54 ..      23     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldee 32
                                      t  ++v+ G  G+GK+tll+ l   l+ +
  gi|313125135|ref|YP_004035399.1| 26 TGDVTVLLGRNGAGKSTLLKHLNGLLEPD 54
                                      67789****************99888644 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.096       2      21 ..      29      48 ..      28      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      + +l G++G GK+tLl++l 
  gi|313125135|ref|YP_004035399.1| 29 VTVLLGRNGAGKSTLLKHLN 48
                                      789**************996 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.19       4      44 ..      29      68 ..      26      88 .. 0.77
   2 ?   -1.5   0.0       2.3   2.1e+03      32      49 ..     160     179 ..     134     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg 44
                                      v  l G  g+GKst+ ++l+  L+ ++ + +++dGd +  +
  gi|313125135|ref|YP_004035399.1| 29 VTVLLGRNGAGKSTLLKHLNGLLEPDRGH-VMIDGDRIQYD 68
                                      556789*************9777666655.578****9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                                       -EEEEEHHHHTT..TTTTT- CS
                        APS_kinase  32 svylLdGdnvRh..gLnkdL 49 
                                        +  LdGd  R   +L ++L
  gi|313125135|ref|YP_004035399.1| 160 PTAGLDGDGTRAlvDLIREL 179
                                       57789999998533566666 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011       0.1       2      30 ..      29      58 ..      28      81 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                      EEEEEESTTCCHHHHHHHHH.CT--SS-EE CS
                              cobW  2 vtvltGflGsGKTtLlnhll.enraglkla 30
                                      vtvl G  G+GK+tLl+hl    + ++   
  gi|313125135|ref|YP_004035399.1| 29 VTVLLGRNGAGKSTLLKHLNgLLEPDRGHV 58
                                      89****************975444444444 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002      0.18       4      44 ..     166     209 ..     165     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                           DUF4350   4 pnGtralaelLeaq...Gvevrrvrkpfdalegedgtllvvapd 44 
                                        +Gtral++l+++    G++  + ++ +d+ ++ ++t+ +++++
  gi|313125135|ref|YP_004035399.1| 166 GDGTRALVDLIRELtneGISFVVSTHYPDFAAAVGDTFTLIDDG 209
                                       69***********7788*****9999999999999999999987 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00032       0.3      28      54 ..      29      55 ..      22      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                                      HHHHHS--SHHHHHHHHHHHHHHS--T CS
                              MukB 28 vttlsGgnGaGksttmaafvtaliPdl 54
                                      vt l G nGaGkst +  +   l Pd 
  gi|313125135|ref|YP_004035399.1| 29 VTVLLGRNGAGKSTLLKHLNGLLEPDR 55
                                      9***************99999999986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.28   2.6e+02      39      55 ..      31      47 ..      23      57 .. 0.84
   2 ?    7.7   0.0    0.0023       2.2     103     156 ..     135     185 ..      95     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.28
                              TniB 39 llvGdsnnGKtmivekF 55
                                      +l+G+   GK++++++ 
  gi|313125135|ref|YP_004035399.1| 31 VLLGRNGAGKSTLLKHL 47
                                      789**********9985 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                              TniB 103 rvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkip 156
                                       +  ++++ +l+   ++k++ Li+DE    l g     r+++ +++ L+ne  i+
  gi|313125135|ref|YP_004035399.1| 135 SGGEKKRVALAGVLAMKPKYLIFDEPTAGLDGDG--TRALVDLIRELTNE-GIS 185
                                       556677777788889***************8876..599*********98.355 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.64u 0.38s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 1212.24
//
Query:       gi|313125136|ref|YP_004035400.1|  [L=214]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-17   61.9   0.1    5.8e-17   61.2   0.1    1.3  1  HTH_10          HTH DNA binding domain
    3.7e-06   26.5   1.0      8e-05   22.2   1.0    2.3  1  Sigma70_r4_2    Sigma-70, region 4
     0.0017   17.8   1.2     0.0041   16.6   1.2    1.7  1  Sigma70_r4      Sigma-70, region 4
     0.0026   17.9   0.0      0.005   17.0   0.0    1.5  1  HTH_Tnp_1_2     Helix-turn-helix of insertion element transpo
     0.0078   16.2   0.1      0.012   15.5   0.1    1.2  1  Lipoprotein_20  YfhG lipoprotein
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.025   14.5   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.026   14.1   0.1       0.41   10.2   0.1    2.4  1  GerE            Bacterial regulatory proteins, luxR family
      0.035   14.2   0.2      0.074   13.1   0.2    1.6  1  HTH_20          Helix-turn-helix domain
      0.045   13.3   0.1      0.076   12.6   0.1    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.058   13.6   0.0       0.18   12.1   0.0    1.8  2  Coat_F          Coat F domain
      0.085   13.4   0.0       0.19   12.3   0.0    1.5  1  Mga             Mga helix-turn-helix domain
      0.086   12.6   0.5       0.46   10.3   0.5    2.1  1  LexA_DNA_bind   LexA DNA binding domain
       0.11   12.4   0.1       0.23   11.3   0.1    1.6  1  TetR_N          Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.1   4.2e-20   5.8e-17       1      52 [.     156     207 ..     156     208 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 4.2e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       L+++q+e+ +lA+e GY++ PR++t+ eLA+e GI + tl+ hLr+ e+kl+
  gi|313125136|ref|YP_004035400.1| 156 LSPRQREIFTLAHERGYYEIPRETTTTELAEEVGIQRRTLEHHLRRTEEKLA 207
                                       789***********************************************97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.0   5.8e-08     8e-05       3      54 .]     148     206 ..     147     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.8e-08
                                       HHHHHHTTS-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2   3 alrealaeLperqreifllrylegl.......sykEIAellgisegtVksrlsRArkkL 54 
                                        l+++l +L++rqreif+l ++ g+       ++ E Ae+ gi  +t +++l+R  +kL
  gi|313125136|ref|YP_004035400.1| 148 SLQALLPTLSPRQREIFTLAHERGYyeipretTTTELAEEVGIQRRTLEHHLRRTEEKL 206
                                       5899***************9888766666666888888888*************98887 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.2     3e-06    0.0041       2      48 ..     153     206 ..     152     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-06
                                       HHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   2 LasLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L +L++r+re+++l          ++ T  E++e+ gi r +   +++r+ +kL
  gi|313125136|ref|YP_004035400.1| 153 LPTLSPRQREIFTLAHergyyeiPRETTTTELAEEVGIQRRTLEHHLRRTEEKL 206
                                       889***************999988899***********9998777777766666 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.7e-06     0.005       6      47 ..     154     199 ..     149     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.7e-06
                                       HHS-HHHHHHHHHHHHHHH....--S-HHHHHHHHTS-HHHHHHHH CS
                       HTH_Tnp_1_2   6 deLtakQkkaaellvendy....ekltldeiaeevgvsrsTlykWk 47 
                                       + L+ +Q+ +  l  e+ y     ++t++e+aeevg++r+Tl + +
  gi|313125136|ref|YP_004035400.1| 154 PTLSPRQREIFTLAHERGYyeipRETTTTELAEEVGIQRRTLEHHL 199
                                       56999**************9999999***************95544 PP

>> Lipoprotein_20  YfhG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   8.7e-06     0.012      88     153 ..     141     207 ..     123     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.7e-06
                    Lipoprotein_20  88 ysaqfpaslrpllqlWreqqalqlalaeeraryqrlqeesdskl.dslreqqaaLeaeLeettrKLe 153
                                       +++q  +sl++ll +   +q    +la er  y+  +e++ ++l +++  q+++Le++L++t+ KL 
  gi|313125136|ref|YP_004035400.1| 141 FADQPVVSLQALLPTLSPRQREIFTLAHERGYYEIPRETTTTELaEEVGIQRRTLEHHLRRTEEKLA 207
                                       45666789*******************************99999568999***************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.8e-05     0.025      14      38 ..     177     201 ..     174     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                       SSEEHHHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  14 gelcvcelaeelglsqstvShHLkk 38 
                                       +e++ +elaee+g+ + t+ hHL++
  gi|313125136|ref|YP_004035400.1| 177 RETTTTELAEEVGIQRRTLEHHLRR 201
                                       689********************95 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0003      0.41       3      45 ..     156     206 ..     154     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0003
                                       S-HHHHHHHHHHCT........TS-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE   3 LskRErevLrllae........GksnkeIAeelniSekTVkvhksnimkKL 45 
                                       Ls+R+re+++l  e          +++e Aee +i  +T + h+++  +KL
  gi|313125136|ref|YP_004035400.1| 156 LSPRQREIFTLAHErgyyeiprETTTTELAEEVGIQRRTLEHHLRRTEEKL 206
                                       666666666665432111111136899********************9998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   5.4e-05     0.074      21      47 ..     175     201 ..     149     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.4e-05
                                       TCTTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  21 raegltaselaerldlskntlsyHLrv 47 
                                        +++ t +elae++++ + tl +HLr 
  gi|313125136|ref|YP_004035400.1| 175 IPRETTTTELAEEVGIQRRTLEHHLRR 201
                                       57899********************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.5e-05     0.076      18      42 ..     179     203 ..     176     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlkrLe 42 
                                       ++ +eLAe++g+ + t+  +l+r e
  gi|313125136|ref|YP_004035400.1| 179 TTTTELAEEVGIQRRTLEHHLRRTE 203
                                       799*******************955 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.18      46      61 ..     159     174 ..     149     176 .. 0.80
   2 ?   -3.1   0.1       7.1   9.8e+03      33      45 ..     192     204 ..     191     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            Coat_F  46 mqeelfnlmnqkGwYp 61 
                                        q+e+f+l++++G+Y 
  gi|313125136|ref|YP_004035400.1| 159 RQREIFTLAHERGYYE 174
                                       69*************6 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.1
                            Coat_F  33 Rqtlkqilneeie 45 
                                       R+tl ++l  ++e
  gi|313125136|ref|YP_004035400.1| 192 RRTLEHHLRRTEE 204
                                       8899999887765 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.19      29      60 ..     177     208 ..     173     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                       SEEEHHHHHHHCT--HHHHHHHHHHHHHHCHC CS
                               Mga  29 eevsieelaqelyiSestlkrkikelnklLke 60 
                                       +e++++ela+e+ i++ tl +++++ ++ L++
  gi|313125136|ref|YP_004035400.1| 177 RETTTTELAEEVGIQRRTLEHHLRRTEEKLAD 208
                                       57899**********************99986 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5   0.00034      0.46       4      53 ..     156     205 ..     154     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                                       --HHHHHHHHHHHHH.HHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind   4 LTerQrevldlikas.ieetgypPsireiaralglkSpsaveehLkaLerK 53 
                                       L++rQre++ l ++    e     +  e+a+++g++  ++ e+hL++ e K
  gi|313125136|ref|YP_004035400.1| 156 LSPRQREIFTLAHERgYYEIPRETTTTELAEEVGIQ-RRTLEHHLRRTEEK 205
                                       899*****9997643123333346999*********.9********99887 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00017      0.23      15      36 ..     177     198 ..     164     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                       TT--HHHHHHHHTSSHHHHHHH CS
                            TetR_N  15 dattvreIAkrAGvskgalYry 36 
                                       ++tt+ e+A+++G+ +++l ++
  gi|313125136|ref|YP_004035400.1| 177 RETTTTELAEEVGIQRRTLEHH 198
                                       47****************9888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1176.29
//
Query:       gi|313125137|ref|YP_004035401.1|  [L=477]
Description: hypothetical protein Hbor_03570 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-06   27.2   2.3    3.6e-06   27.2   2.3    3.8  5  Gate            Nucleoside recognition
  ------ inclusion threshold ------
      0.011   15.6   1.8      0.011   15.6   1.8    2.6  3  Nucleos_tra2_C  Na+ dependent nucleoside transporter C-termin


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4     0.097   8.7e+02       5      51 ..      84     150 ..      66     154 .. 0.61
   2 !   27.2   2.3     4e-10   3.6e-06       2     108 ..     156     253 ..     155     257 .. 0.91
   3 ?   -3.6   1.1       1.5   1.3e+04      90     106 ..     262     278 ..     259     281 .. 0.73
   4 !    8.1   6.3   0.00035       3.2       4      93 ..     345     428 ..     340     438 .. 0.75
   5 ?   -3.4   0.2       1.2   1.1e+04      46      56 ..     458     468 ..     445     476 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.097
                              Gate   5 gpiillasiliwflss..................ssllgrigkllepv.faplg.qeldwkatvsll 51 
                                       + ii+++ +l   ++                   + +l  +g +++pv f +lg   l+ + t +l+
  gi|313125137|ref|YP_004035401.1|  84 LAIIVAGGVLTTAARVgdgtvagydlsyfdtsvaFWILRLAGVVVAPVmFFKLGpSWLHTPGTGGLM 150
                                       3344444444444444777777777777775555556666666666664444665555555555555 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 4e-10
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfa.akevvvgtlgtlytsalgellq 77 
                                       + +g ii ++ ++i ++ + + l+++g + +pv++pl  + +++a+   l++++ +  v++    +++       +q
  gi|313125137|ref|YP_004035401.1| 156 YSVGVIIPIGAVFITIFVELGGLEFVGTIARPVMRPLF-KIPGRAALDSLASWVgSYSVGLYVTRNVF-------EQ 224
                                       789*********************************77.7**************88899998888887.......88 PP

                              Gate  78 gfdtpksalafllfvllytpcvatlavivre 108
                                       g +++++  +f + + ++t+++ +++v++  
  gi|313125137|ref|YP_004035401.1| 225 GGYNKRD--VFTIATCFSTVSIGFVGVVAAT 253
                                       8888888..*****************99876 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.5
                              Gate  90 lfvllytpcvatlaviv 106
                                       ++++ y+ cv ++a+i 
  gi|313125137|ref|YP_004035401.1| 262 VVFGAYFLCVIVTAAIL 278
                                       55667888998888864 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.00035
                              Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfd 80 
                                       +g+i+ ++++   +  ++ +++++g+ l+pv+a lg +    ++ + ++g++  e+ v+ l ++      +l+++f+
  gi|313125137|ref|YP_004035401.1| 345 LGTILTVGLAATLLSANTPIFDILGRPLTPVIAALGIPNAETVAPATIVGIT--EMYVPVLLVTE----TALKAKFF 415
                                       344444444444444559******************6666667777777777..88888887774....57889999 PP

                              Gate  81 tpksalafllfvl 93 
                                         + a++ l+f++
  gi|313125137|ref|YP_004035401.1| 416 IAVLAVSQLIFFS 428
                                       9999999999986 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 1.2
                              Gate  46 atvslltgfaa 56 
                                       + v++++g++ 
  gi|313125137|ref|YP_004035401.1| 458 ILVPIIAGMTH 468
                                       33444444443 PP

>> Nucleos_tra2_C  Na+ dependent nucleoside transporter C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3     0.082   7.4e+02      45     118 ..      66     149 ..      57     156 .. 0.52
   2 ?   -2.6   0.0      0.44     4e+03      54      81 ..     233     260 ..     218     305 .. 0.72
   3 ?   15.6   1.8   1.3e-06     0.011      32     169 ..     316     435 ..     272     476 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHT........-TT--HHHHHHHHHHHHHHH.TT--GGG CS
                    Nucleos_tra2_C  45 aaaegaldglklalniaamliafvalvalinall.gwlgsg........leelslelilgyvfaplafl.lGvpwed 111
                                       ++++ +++ +  a+ + a  i + + v    a +   +  g           + +  + g+v+ap++f+ lG +w +
  gi|313125137|ref|YP_004035401.1|  66 IVVSTITETFPTAVGVYALAIIVAGGVLTTAARVgDGTVAGydlsyfdtSVAFWILRLAGVVVAPVMFFkLGPSWLH 142
                                       55555666666666666555544433322222221111111122223222244455788999999998646666666 PP

                                       HHHHHHH CS
                    Nucleos_tra2_C 112 alkvgsl 118
                                       +   g l
  gi|313125137|ref|YP_004035401.1| 143 TPGTGGL 149
                                       6666655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Nucleos_tra2_C  54 lklalniaamliafvalvalinallgwl 81 
                                       +++a    ++ i+fv++va+   +l+++
  gi|313125137|ref|YP_004035401.1| 233 FTIATCFSTVSIGFVGVVAATLDILQLF 260
                                       5566666666777777777776666665 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.3e-06
                                       .....---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TT--HHHHHHHHHHHHHHHTT-- CS
                    Nucleos_tra2_C  32 keekeeekanvleaaaegaldglklalniaamliafvalvalinallgwlgsgleelslelilgyvfaplafllGvp 108
                                         ek++e +++leaa +g +dglkl   i+ ++++ v+l+a    ll++         +  ilg  ++p+   lG+p
  gi|313125137|ref|YP_004035401.1| 316 AVEKADEGESFLEAAKRGFVDGLKLTTLILGTILT-VGLAAT---LLSAN------TPIFDILGRPLTPVIAALGIP 382
                                       566777889******************99998876.455544...34333......344579*************** PP

                                       GGGHHHHHHHHHHHHHT-HHHHHHHHGGGGSSS---HHHHHHHHHHH-S--STHHHHHHHH CS
                    Nucleos_tra2_C 109 wedalkvgsllGtKlvlnefvayqeLsklkkkgelserseliatyaLcgFanfssigiqiG 169
                                        +++++ ++++G   +++ +v    ++++    +l+++   ia  a+     fss+g +  
  gi|313125137|ref|YP_004035401.1| 383 NAETVAPATIVG---ITEMYVPVLLVTET----ALKAK-FFIAVLAVSQLIFFSSVGPMTM 435
                                       ***********9...55666666555544....35444.4566666666666677764444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2789.29
//
Query:       gi|313125138|ref|YP_004035402.1|  [L=51]
Description: hypothetical protein Hbor_03580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 313.33
//
Query:       gi|313125139|ref|YP_004035403.1|  [L=177]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-14   53.3   1.4      3e-14   52.6   1.4    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      5e-13   48.4   0.4    9.9e-13   47.4   0.4    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.6e-09   37.6   0.1    2.6e-09   36.9   0.1    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    0.00064   19.6   0.1     0.0013   18.7   0.1    1.4  1  HTH_11          HTH domain
    0.00087   19.3   0.1     0.0017   18.4   0.1    1.5  1  HTH_20          Helix-turn-helix domain
     0.0044   17.0   1.0       0.01   15.8   1.0    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0053   16.6   0.2     0.0093   15.8   0.2    1.4  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.013   15.4   0.1       0.04   13.8   0.1    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.059   13.2   0.1        0.1   12.5   0.1    1.4  1  HTH_IclR        IclR helix-turn-helix domain
       0.06   13.3   0.0       0.14   12.1   0.0    1.6  1  MarR            MarR family
      0.066   12.7   0.1       0.18   11.4   0.1    1.7  1  EF-hand_5       EF hand


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   1.4   1.8e-17     3e-14       1      42 []      26      67 ..      26      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.8e-17
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDe+D +I ++L +d+Ris +eL+ervGlS+++++rR ++L+
  gi|313125139|ref|YP_004035403.1| 26 LDETDYRIYKELNRDGRISDTELGERVGLSRTAARRRREKLQ 67
                                      8***************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.4   6.1e-16   9.9e-13       1      47 [.      26      72 ..      26      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 6.1e-16
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ldetd++I+++L +++ris +eL er+glS+++ +rr ++L++eGl+
  gi|313125139|ref|YP_004035403.1| 26 LDETDYRIYKELNRDGRISDTELGERVGLSRTAARRRREKLQSEGLV 72
                                      7********************************************98 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   1.6e-12   2.6e-09       3      75 .]      92     165 ..      90     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.6e-12
                                       EEE-GGG.TTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   3 vslepgh.peqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       v+l+++  ++++++f  +++  + + e+    G yd+ll+v+ ++l ++   lr +l++++ v+r+et  v +t
  gi|313125139|ref|YP_004035403.1|  92 VTLNSDIsQDDFDDFLSKIEGEELIYEIDEYMGKYDLLLRVWHASLSDIKSYLRAQLQTHDAVERYETVPVTKT 165
                                       67774448899**********************************************************99875 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   7.7e-07    0.0013       4      46 ..      32      74 ..      30      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.7e-07
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpI 46
                                       i++ L + +g is  eL e+ ++Sr++ rr+ ++L++ g v++
  gi|313125139|ref|YP_004035403.1| 32 RIYKEL-NRDGRISDTELGERVGLSRTAARRRREKLQSEGlVDV 74
                                      588999.88899*************************9996655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1     1e-06    0.0017       7      56 ..      25      74 ..      19      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
                                      HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       ++++ +ri+++L+r++  + +el er++ls++ ++++ ++L++ gLv+v
  gi|313125139|ref|YP_004035403.1| 25 YLDETDYRIYKELNRDGRISDTELGERVGLSRTAARRRREKLQSEGLVDV 74
                                      6789999*****************************************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0   6.2e-06      0.01      19      66 ..      40      86 ..      16      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.2e-06
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHHH CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisrgrririldleaLr 66
                                      + +++ +el++++Gl+r    r   +L+ egl++  + + +l+ ++L+
  gi|313125139|ref|YP_004035403.1| 40 DGRISDTELGERVGLSRTAARRRREKLQSEGLVDVLG-VLVLQEAELA 86
                                      45899*****************************654.9999888885 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   5.7e-06    0.0093      17      52 ..      39      73 ..      28      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.7e-06
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      r+gr ++ +el +r gls+ a+ r+ ++L++ GLv 
  gi|313125139|ref|YP_004035403.1| 39 RDGR-ISDTELGERVGLSRTAARRRREKLQSEGLVD 73
                                      4443.7889*************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.5e-05      0.04       6      54 ..      26      74 ..      25      77 .. 0.96
   2 ?   -2.5   0.0       2.9   4.8e+03      33      56 ..      97     120 ..      92     127 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      L e++ ++Y+ L + g+ + +e+ e++g++r+ + +  ++L + GlV++
  gi|313125139|ref|YP_004035403.1| 26 LDETDYRIYKELNRDGRISDTELGERVGLSRTAARRRREKLQSEGLVDV 74
                                      6799*******************************************86 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                                       TSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  33 gvprskvYevLrsLedkGlVerek 56 
                                       ++++    + L++ e   l++ ++
  gi|313125139|ref|YP_004035403.1|  97 DISQDDFDDFLSKIEGEELIYEID 120
                                       555555556666666666666554 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.1e-05       0.1      19      49 ..      43      73 ..      37      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.1e-05
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyve 49
                                       + +el +r gl++++++R    L+ +G+v 
  gi|313125139|ref|YP_004035403.1| 43 ISDTELGERVGLSRTAARRRREKLQSEGLVD 73
                                      5569*************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.3e-05      0.14       3      48 ..      28      73 ..      26      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-05
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +t ++i   l + g +s +eL++++g+s++++ r   +L  +Gl++
  gi|313125139|ref|YP_004035403.1| 28 ETDYRIYKELNRDGRISDTELGERVGLSRTAARRRREKLQSEGLVD 73
                                      6778888899999*******************************96 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00011      0.18      10      23 ..      37      50 ..      36      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                      SS-SSCE-HHHHHH CS
                         EF-hand_5 10 lNgDGkIskeELkt 23
                                      lN+DG+Is  EL +
  gi|313125139|ref|YP_004035403.1| 37 LNRDGRISDTELGE 50
                                      7**********964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1128.57
//
Query:       gi|313125140|ref|YP_004035404.1|  [L=79]
Description: hypothetical protein Hbor_03600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 471.14
//
Query:       gi|313125141|ref|YP_004035405.1|  [L=228]
Description: hth DNA binding domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-20   72.5   0.1    3.2e-20   71.7   0.1    1.5  1  HTH_10      HTH DNA binding domain
  ------ inclusion threshold ------
      0.053   13.4   0.1       0.13   12.1   0.1    1.6  1  BAT         GAF and HTH_10 associated domain
      0.064   13.1   0.0       0.48   10.3   0.0    2.2  2  HTH_8       Bacterial regulatory protein, Fis family
       0.11   12.1   0.0       0.23   11.0   0.0    1.6  1  Sigma70_r4  Sigma-70, region 4
       0.11   12.5   0.0       0.28   11.2   0.0    1.7  1  HTH_1       Bacterial regulatory helix-turn-helix protein, ly


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.1     9e-24   3.2e-20       1      53 []     164     216 ..     164     216 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 9e-24
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LTd q+e+l++AyemGYF+ PR+++l+++A elGI++s+lse+Lr+a+  lie
  gi|313125141|ref|YP_004035405.1| 164 LTDPQREALRTAYEMGYFEIPRTASLDDVAGELGITASSLSERLRRAQTHLIE 216
                                       9***********************************************99985 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.7e-05      0.13       7     108 ..       6     119 ..       4     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                               BAT   7 eleirdeddvlvalaaeldcr.veleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg..... 77 
                                       e+ei+ ++++lv++aa++  + +e+      +++++   ++++++dp++++ a+e+    +++++v++ +++     
  gi|313125141|ref|YP_004035405.1|   6 EFEIDCDALPLVEVAAAVPEAmIEVAIQFN-HGNRPPFIAHITHGDPDAIERAFESGAFAAEYTLVGRAGEThryqi 81 
                                       8999********999887666377766666.5667889*******************************99866666 PP

                               BAT  78 ...tlleltv....sgpslastlaehGgtvrsaeaedg 108
                                            le+++    ++ + +++la+ ++ +++++++++
  gi|313125141|ref|YP_004035405.1|  82 lpaVGLEAKLgeqiDDLDGLRALATTDAIIERIRVTSS 119
                                       66644444440000344445577777777777777765 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.25   9.1e+02       8      21 ..      26      39 ..      24      40 .. 0.90
   2 ?   10.3   0.0   0.00013      0.48      23      41 ..     191     209 ..     185     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.25
                                      HHHHHHHHHTTT-H CS
                             HTH_8  8 elIeaALertgGnk 21
                                       +Ie A++ ++Gn+
  gi|313125141|ref|YP_004035405.1| 26 AMIEVAIQFNHGNR 39
                                      59***********8 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00013
                                       HHHHHHTS-HHHHHHHHHH CS
                             HTH_8  23 kAArlLGisRrtLyrKLkk 41 
                                       ++A +LGi+ ++L  +L++
  gi|313125141|ref|YP_004035405.1| 191 DVAGELGITASSLSERLRR 209
                                       79***************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.5e-05      0.23       3      47 ..     162     213 ..     162     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.5e-05
                                       HHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4   3 asLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrk 47 
                                       + L++ +re l+  +        +  +l +++ +lgi+ +  + +++rA  +
  gi|313125141|ref|YP_004035405.1| 162 DGLTDPQREALRTAYemgyfeiPRTASLDDVAGELGITASSLSERLRRAQTH 213
                                       579999*********99999988999**********************9665 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.9e-05      0.28      11      41 ..     184     214 ..     181     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.9e-05
                                       HHHSSHHHHHHHHTS-HHHHHHHHHHHHHHH CS
                             HTH_1  11 aeegsftrAAeeLglsqpavsrqikrLEeel 41 
                                        ++ s+   A eLg++ +++s +++r   +l
  gi|313125141|ref|YP_004035405.1| 184 PRTASLDDVAGELGITASSLSERLRRAQTHL 214
                                       588899999****************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1394.54
//
Query:       gi|313125142|ref|YP_004035406.1|  [L=377]
Description: daunorubicin resistance ABC transporter ATP-binding subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-30  104.7   0.0    9.9e-30  103.8   0.0    1.4  1  ABC_tran         ABC transporter
    1.6e-14   54.4   0.1    1.4e-08   34.9   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.8e-06   27.2   0.0    1.5e-05   25.6   0.0    1.9  1  DUF4162          Domain of unknown function (DUF4162)
    0.00044   20.7   0.0     0.0039   17.6   0.0    2.6  1  AAA              ATPase family associated with various cellul
     0.0028   17.3   0.0     0.0053   16.4   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain
     0.0059   16.3   0.2      0.014   15.1   0.2    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0087   16.0   0.1       0.49   10.4   0.1    2.4  2  A_amylase_inhib  Alpha amylase inhibitor
  ------ inclusion threshold ------
       0.01   16.2   0.2      0.048   14.0   0.0    2.0  2  AAA_16           AAA ATPase domain
      0.016   15.0   0.3      0.087   12.5   0.0    2.2  2  AAA_30           AAA domain
      0.017   14.6   0.0      0.037   13.5   0.0    1.6  1  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.018   14.7   0.0        1.4    8.6   0.0    2.1  2  AAA_15           AAA ATPase domain
       0.02   14.3   0.0        0.8    9.1   0.0    2.2  1  SMC_N            RecF/RecN/SMC N terminal domain
      0.023   15.2   0.1      0.039   14.5   0.1    1.4  1  AAA_23           AAA domain
      0.028   15.0   0.3       0.47   11.0   0.0    2.6  3  AAA_18           AAA domain
      0.038   14.3   0.0        0.2   11.9   0.0    2.0  1  AAA_22           AAA domain
      0.044   13.5   0.0      0.095   12.4   0.0    1.5  1  Thymidylate_kin  Thymidylate kinase
      0.065   13.1   0.0        0.1   12.5   0.0    1.2  1  Rad17            Rad17 P-loop domain
       0.15   11.5   0.0       0.25   10.8   0.0    1.3  1  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.0     1e-32   9.9e-30       3     136 ..      65     206 ..      63     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 1e-32
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                        v+l++++ge  +++G+nGaGK+t +k+la ll+p+ G++ ++g d+++ + + +r++ig++ qe+++++ lt+ren
  gi|313125142|ref|YP_004035406.1|  65 GVNLSVSAGEFFGFLGPNGAGKTTTIKTLAALLRPNLGSVSINGFDIEN-DSKAVRESIGYMAQETSVDEALTAREN 140
                                       599**********************************************.9************************** PP

                                       .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                    e+de+++++l+ ++l++++d+++    +++SgG+k+r+  a +l+ +p++++lDEpt
  gi|313125142|ref|YP_004035406.1| 141 vrfacdiygvpagERDERVDELLALVNLTHVADKRA----ENFSGGMKKRLDAATVLVHRPPVVFLDEPT 206
                                       ***********************************9....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     3e-06     0.003       1      52 [.      75     124 ..      75     144 .. 0.68
   2 !   34.9   0.0   1.4e-11   1.4e-08     234     299 ..     176     238 ..     151     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldly 52 
                                       + ++ GpNg+GK++ +++l  l r  +++ +  ++  ++ + +k  +++ +y
  gi|313125142|ref|YP_004035406.1|  75 FFGFLGPNGAGKTTTIKTLAALLR--PNLGSVSINGFDIENDSKAVRESIGY 124
                                       56799**************99984..55555555555555555555555555 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 1.4e-11
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       a ++S G+k+ l  +t l  ++   +++++DEp +gL+P++  r++e l++ +++g+ v+ltT+  
  gi|313125142|ref|YP_004035406.1| 176 AENFSGGMKKRLDAATVLVHRP---PVVFLDEPTTGLDPEARIRFWEYLRSINERGTTVVLTTQYL 238
                                       5678****************99...************************999999********865 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.5e-08   1.5e-05       2      80 ..     261     353 ..     261     354 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.5e-08
                                       -HHHHHTTS-SSEEEEE.....-------...........--.-EEE..E-TTS-EEEEE--.-----------.-- CS
                           DUF4162   2 tleeiKrsygknrieve.....adaeellee.........pg.veev..eeeggelelkled.eeaanellkal.ts 59 
                                       t++ +K++ g+++ie+      a     +++         ++ +e    e+++++l+++ e+  ea  +l+  l ++
  gi|313125142|ref|YP_004035406.1| 261 TPDALKSRVGGDIIELAlddpaA-----RTTeratrivreSNaFEAAtiETTDRGLIITSEHaREAVTDLFVSLdDA 332
                                       5789*************644330.....322233344554442444444666688******99***********77* PP

                                       --EEEEEEEE---HHHHHHHH CS
                           DUF4162  60 gveirsFeeeePsLndIFiek 80 
                                       +++++ +  + P+L+d+F+  
  gi|313125142|ref|YP_004035406.1| 333 DITVTGLDIRSPTLDDVFLSI 353
                                       ******************976 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     4e-06    0.0039       3      38 ..      78     171 ..      76     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4e-06
                                       EESSTTSSHHHHHHHHHHHHTHEE..EEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelgvef..leisgsellsk........................................ 37 
                                       + Gp G GKT+++k +a  l  ++  ++i+g ++ ++                                        
  gi|313125142|ref|YP_004035406.1|  78 FLGPNGAGKTTTIKTLAALLRPNLgsVSINGFDIENDskavresigymaqetsvdealtarenvrfacdiygvpage 154
                                       68******************755433888888888666777777766666666666666666666666666665555 PP

                                       ................S CS
                               AAA  38 ................y 38 
                                                       +
  gi|313125142|ref|YP_004035406.1| 155 rdervdellalvnlthV 171
                                       55555555555555553 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.3e-06    0.0053       6      38 ..      78     110 ..      74     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.3e-06
                                       EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54   6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38 
                                       ++G++GaGKTtt+  Laall+ +  +v +   D
  gi|313125142|ref|YP_004035406.1|  78 FLGPNGAGKTTTIKTLAALLRPNLGSVSINGFD 110
                                       79******************9988888777766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.4e-05     0.014      20      52 ..      71     104 ..      63     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                            AAA_29  20 dlkgatlltGpsGsGKSTllDAiqalLvpak.kv 52 
                                       +  +++ + Gp+G+GK+T +  ++alL p+  +v
  gi|313125142|ref|YP_004035406.1|  71 SAGEFFGFLGPNGAGKTTTIKTLAALLRPNLgSV 104
                                       534477799*******************986555 PP

>> A_amylase_inhib  Alpha amylase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1    0.0005      0.49      25      54 ..      48      80 ..      40      92 .. 0.70
   2 ?    3.0   0.0      0.11   1.1e+02      14      49 ..     218     256 ..     214     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0005
                                      S-EEEEEEETTS-CEEEEE...E-TTEEEEEE- CS
                   A_amylase_inhib 25 etvsVtVaYedgaeapCrt...iePgdittfaG 54
                                      ++ +V V Y+dg+ea C +   ++ g++  f G
  gi|313125142|ref|YP_004035406.1| 48 DATDVHVTYDDGTEAVCGVnlsVSAGEFFGFLG 80
                                      6789*************7522255555555544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                                       SSEEEEEE-SSS-EEEEEEETTS-CEEE...EEE-TTEE CS
                   A_amylase_inhib  14 WRYtdvtNdCaetvsVtVaYedgaeapC...rtiePgdi 49 
                                       W Y    N+   tv  t +Y ++ + +C   ++i+ g+i
  gi|313125142|ref|YP_004035406.1| 218 WEYLRSINERGTTVVLTTQYLEEVDRLCdrlAVIQDGEI 256
                                       99**************************43335566665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.8e-05     0.048      29     143 ..      78     204 ..      66     210 .. 0.55
   2 ?   -1.1   0.0       2.2   2.1e+03     101     140 ..     274     314 ..     213     336 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                            AAA_16  29 lsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                       + G+ G GK++ +++l+  l+ + g + ++g   +++s+        a  r e +  +++e++    ea  ++   +
  gi|313125142|ref|YP_004035406.1|  78 FLGPNGAGKTTTIKTLAALLRPNLGSVsINGFDIENDSK--------AV-R-ESIGYMAQETSV--DEALTARENVR 142
                                       68***************5555552444366665565222........22.2.333333333111..11111111222 PP

                            AAA_16 105 la......................avpelagaeasrllellkrll.allsrderplvlvlDd 143
                                       +a                         ++a++ a+ +   +k+ l a +   +rp v++lD+
  gi|313125142|ref|YP_004035406.1| 143 FAcdiygvpagerdervdellalvNLTHVADKRAENFSGGMKKRLdAATVLVHRPPVVFLDE 204
                                       22223323333333333333334446666666668899999988855555556689999996 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                            AAA_16 101 leealaavpelagaeasrllellkrll.allsrderplvlv 140
                                       +e al + ++ + + a+r+ ++ +++  a +++++r l+++
  gi|313125142|ref|YP_004035406.1| 274 IELALDDPAARTTERATRIVRESNAFEaATIETTDRGLIIT 314
                                       22222222222222225555555555555555555555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.7e-05     0.087      20      68 ..      75     124 ..      65     191 .. 0.76
   2 ?   -0.6   0.1      0.93   9.3e+02      47      75 ..     271     306 ..     260     325 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.7e-05
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa.ggrviglApt.gkaAkvLaeelgi 68 
                                       +    Gp G+GKtt++k+l+++++ + g +v +     ++ +k+++e++g 
  gi|313125142|ref|YP_004035406.1|  75 FFGFLGPNGAGKTTTIKTLAALLRPNlG-SVSINGFDiENDSKAVRESIGY 124
                                       55678****************9998844.4443333213334556666664 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.93
                            AAA_30  47 grviglAptgkaAkvLa.......eelgieastiak 75 
                                       g++i lA    aA++ +       e+  +ea+ti+ 
  gi|313125142|ref|YP_004035406.1| 271 GDIIELALDDPAARTTEratrivrESNAFEAATIET 306
                                       555555555555555441111111555567777764 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.8e-05     0.037      52     144 ..     165     255 ..     136     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                              KdpD  52 leglevi.prkeveykgkeleeldldailarkpevvlvDelahtnapgsrhekryqdveelLeagidVittvnvqhl 127
                                       l +l+ + ++++ + +g   ++ld  ++l ++p vv++De      p++r  + ++  +++ e+g  V+ t   q l
  gi|313125142|ref|YP_004035406.1| 165 LVNLTHVaDKRAENFSGGMKKRLDAATVLVHRPPVVFLDEPTTGLDPEAR-IRFWEYLRSINERGTTVVLT--TQYL 238
                                       33444441556667899999********************8877766665.567***********998754..3555 PP

                              KdpD 128 eslndvvekitgvrvre 144
                                       e++  +  ++  ++  e
  gi|313125142|ref|YP_004035406.1| 239 EEVDRLCDRLAVIQDGE 255
                                       55555555555555444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0014       1.4      27      50 ..      77     100 ..      66     143 .. 0.76
   2 ?    4.0   0.0     0.035        34     326     363 ..     199     235 ..     195     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                            AAA_15  27 vliGkNnsGKSsilealdlFlnnk 50 
                                        + G+N++GK++ ++ l  +l  +
  gi|313125142|ref|YP_004035406.1|  77 GFLGPNGAGKTTTIKTLAALLRPN 100
                                       588***************999966 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.035
                            AAA_15 326 illiEEPEahLHpqaqkvlikllkelandnktQviitT 363
                                       +++++EP + L p+a   ++++l+++ + +   v++tT
  gi|313125142|ref|YP_004035406.1| 199 VVFLDEPTTGLDPEARIRFWEYLRSINERGT-TVVLTT 235
                                       689***********************99996.888888 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0008       0.8     122     197 ..     164     235 ..      67     254 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0008
                                       HHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 122 evsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivisl 197
                                        + +l + a+   e++SgG k+ +  a +     v++ p+++lDe    LD + + ++ e+l++ +++   +v + 
  gi|313125142|ref|YP_004035406.1| 164 ALVNLTHVADKRAENFSGGMKKRLDAATV----LVHRPPVVFLDEPTTGLDPEARIRFWEYLRSINERGTTVVLTT 235
                                       33333333333455889998875554444....5788899999999999999999999999999887766666553 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.9e-05     0.039      21      43 ..      75      97 ..      65     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-05
                            AAA_23 21 ltlItGpNGaGKTTildAiklaL 43
                                      ++ + GpNGaGKTT +  +   L
  gi|313125142|ref|YP_004035406.1| 75 FFGFLGPNGAGKTTTIKTLAALL 97
                                      68899*********998877665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.71   7.1e+02      48     102 ..      12      71 ..       2      76 .. 0.64
   2 ?   11.0   0.0   0.00047      0.47       4      25 ..      79     109 ..      77     145 .. 0.63
   3 ?   -2.1   0.1       5.3   5.2e+03      96     113 ..     226     247 ..     212     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.71
                            AAA_18  48 eskrldedkldklldaleenss....aleegknlvidghlaeleseaakdikk.vvLtas 102
                                       + +r d  ++  + d+ +++++    ++ ++  l id   ++  +++ +++++ v L +s
  gi|313125142|ref|YP_004035406.1|  12 RADRSDAANQSGAADQSDAANQsgaaDQSDAAQLAIDATDVHVTYDDGTEAVCgVNLSVS 71 
                                       333334444444444444444445576777899999999999999999988887777665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00047
                            AAA_18   4 tGtpGvGKttlakeLskrl.gf........g 25 
                                        G+ G+GKtt  k L+ +l  +         
  gi|313125142|ref|YP_004035406.1|  79 LGPNGAGKTTTIKTLAALLrPNlgsvsingF 109
                                       69*************9998544665644431 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.3
                            AAA_18  96 k....vvLtaspeelleRlekR 113
                                            vvLt+ + e  +Rl +R
  gi|313125142|ref|YP_004035406.1| 226 ErgttVVLTTQYLEEVDRLCDR 247
                                       1455799999999999999877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002       0.2      12     114 ..      80     223 ..      78     244 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                            AAA_22  12 GesGtGKTtllrrlleqldeeakaee............................erpevvfvtlpsst..sskdllr 58 
                                       G+ G+GKTt++++l+  l  +++                                            +  + ++  r
  gi|313125142|ref|YP_004035406.1|  80 GPNGAGKTTTIKTLAALL--RPNLGSvsingfdiendskavresigymaqetsvD------------EalTARENVR 142
                                       9**************999..33333366666666655554432222222222220............1334444444 PP

                            AAA_22  59 ellralglelka.................erlsseellealeqalrarav....ielliiDEaqh.lr...seeale 110
                                         + ++g+++ +                 + ++ e +   + + l+a+ v    ++++ +DE    l+   + + +e
  gi|313125142|ref|YP_004035406.1| 143 FACDIYGVPAGErdervdellalvnlthvADKRAENFSGGMKKRLDAATVlvhrPPVVFLDEPTTgLDpeaRIRFWE 219
                                       44444444444433333333333333333355555555555555555555666666666666666665433355555 PP

                            AAA_22 111 eLrs 114
                                       +Lrs
  gi|313125142|ref|YP_004035406.1| 220 YLRS 223
                                       5544 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.5e-05     0.095       3      47 ..      80     127 ..      78     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.5e-05
                                       ESTTSSHHHHHHHHHHHHHHTTE.EE...EESSSTTSHHHHHHHHHHH CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvv...ltrepggteiGekirelll 47 
                                       G +GaGKtt +++l++ l+ +  +v    +  e+++  ++e+i  + +
  gi|313125142|ref|YP_004035406.1|  80 GPNGAGKTTTIKTLAALLRPNLGSVSingFDIENDSKAVRESIGYMAQ 127
                                       899****************99877541225678888888888877766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001       0.1      51      99 ..      79     128 ..      67     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                             Rad17  51 sGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqksdfkglteke 99 
                                        GP G gk+t++k L+  l ++l    +n+  + + +  + +  g + +e
  gi|313125142|ref|YP_004035406.1|  79 LGPNGAGKTTTIKTLAALLRPNLGSvSINGFDIENDSKAVRESIGYMAQE 128
                                       59*****************9999762689999888887777777766655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.25      13      81 ..      53     121 ..      44     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                             AAA_7  13 lVptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdi 81 
                                        V   d +     ++l ++++  + + Gp G GKt++ik+l   l ++  ++ +  f    +++ +++ 
  gi|313125142|ref|YP_004035406.1|  53 HVTYDDGTEAVCGVNLSVSAGEFFGFLGPNGAGKTTTIKTLAALLRPNLGSVSINGFDIENDSKAVRES 121
                                       5555566666666788888899999***************99988865555555557777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2232.71
//
Query:       gi|313125143|ref|YP_004035407.1|  [L=305]
Description: multidrug ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-30  104.3  17.9    8.1e-30  103.8  17.9    1.2  1  ABC2_membrane    ABC-2 type transporter
    1.7e-11   43.8  21.5    1.7e-11   43.8  21.5    1.5  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        3.1    7.4   8.7        3.4    7.3   7.3    1.8  2  CPP1-like        Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8  17.9   1.4e-33   8.1e-30       3     210 .]      28     254 ..      26     254 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 1.4e-33
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg......nsedglnr........pgllffsvlflaf 65 
                                       i++ lkr +++  r+p+ + +++l+qp+++++++  vfg++       +  d   +        p +++ s+l  a 
  gi|313125143|ref|YP_004035407.1|  28 IRVSLKRWLIKTSRNPFVT-FSSLVQPIIFFVLMAEVFGSIAggtlsqTLGD---EinyvtyltPAIVIQSALAAA- 99 
                                       788999*************.*******************9444432232333...144477799999999999999. PP

                     ABC2_membrane  66 saltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls........rf.... 130
                                        a++++++v ++e g++e+ lvsp+  + a++l+kvl+e++++++q++i+l++ y ++ l+           +    
  gi|313125143|ref|YP_004035407.1| 100 -AVSGIGLVDDIETGMFEKILVSPM-NRGAMFLGKVLSEVVRIAIQTAIILALGYAMLFLQSAasvetylqTGaiga 174
                                       .************************.*******************************98888777777776225567 PP

                     ABC2_membrane 131 flflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrs 207
                                       + ++ ++++++ ++++++ +++ ++++ e  +++a+l+++pll++s +f p++ +p+w++ +a +nP+ty+v+a+r+
  gi|313125143|ref|YP_004035407.1| 175 IGIVGIAVIFGGVFMAYSNIVALVTRDREATIMIANLLTFPLLFVSSAFLPLSVLPGWIRTFAVFNPITYGVDAIRA 251
                                       8899************************************************************************9 PP

                     ABC2_membrane 208 nlf 210
                                        ++
  gi|313125143|ref|YP_004035407.1| 252 LML 254
                                       985 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8  21.5   2.9e-15   1.7e-11     157     342 ..      80     291 ..      71     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.9e-15
                   ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl.. 231
                                        n++ +l ++i+i +++  a++   ++v + e+++ e +lvs++++ +++l+k+l+ ++  ++q+++il+l ++   
  gi|313125143|ref|YP_004035407.1|  80 INYVTYLTPAIVIQSALAAAAVSGIGLVDDIETGMFEKILVSPMNRGAMFLGKVLSEVVRIAIQTAIILALGYAMlf 156
                                       58999****************9************************************************9665556 PP

                   ABC2_membrane_3 232 .........gipfg..nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsal 297
                                                 ++ g  + + ++   ++fg ++ a +  +  ++++ e+++ ++ +++++l++++ ++ pl+ lp+++
  gi|313125143|ref|YP_004035407.1| 157 lqsaasvetYLQTGaiGAIGIVGIAVIFGGVFMAYSNIVALVTRDREATIMIANLLTFPLLFVSSAFLPLSVLPGWI 233
                                       6889999986666644667799******************************************************* PP

                   ABC2_membrane_3 298 kwifsiiPffapglgllrlitgdplwe.............illsliilalfavvylll 342
                                       ++++ ++P+++  +++  l+ g+   +             +++sli+l++  ++++ +
  gi|313125143|ref|YP_004035407.1| 234 RTFAVFNPITYGVDAIRALMLGQDTLSvlhvtvfsgfwntVIPSLIVLLGANAALGGI 291
                                       ********************66622235666666666666889999998766666555 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.42   2.5e+03     152     173 ..      62      83 ..      54     102 .. 0.65
   2 ?    7.3   7.3   0.00058       3.4      86     197 .]     108     224 ..      88     224 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.42
                         CPP1-like 152 LvvGlllGsllasllqvdvals 173
                                        v+G ++G+ l++ l  +++  
  gi|313125143|ref|YP_004035407.1|  62 EVFGSIAGGTLSQTLGDEINYV 83 
                                       5789999999999887663333 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00058
                         CPP1-like  86 esldtPssedlliraavflvlavltlvapaes...vpalllalglgasiyflnrKekklgravlltlvgLv.vGlll 158
                                       + ++t   e++l++ +  +++ +  ++++      ++a++lalg ++ ++      ++ +++ +++ +g+v +++++
  gi|313125143|ref|YP_004035407.1| 108 DDIETGMFEKILVSPMNRGAMFLGKVLSEVVRiaiQTAIILALGYAMLFLQSAASVETYLQTGAIGAIGIVgIAVIF 184
                                       55666777777777777777777777777776744556666666655555555566677777776665554399*** PP

                         CPP1-like 159 Gsllasllqvd.valsglsseellvslvtlvllwlvslfL 197
                                       G++++ + +      +   +   ++ l+t+ ll+++s+fL
  gi|313125143|ref|YP_004035407.1| 185 GGVFMAYSNIVaLVTRDREATIMIANLLTFPLLFVSSAFL 224
                                       ******99776533444445556899*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2032.22
//
Query:       gi|313125144|ref|YP_004035408.1|  [L=203]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-10   41.5   0.1    4.2e-10   40.2   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    2.2e-10   40.3   0.0    2.4e-10   40.2   0.0    1.2  1  TehB             Tellurite resistance protein TehB
      4e-10   39.8   0.0    5.8e-10   39.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.1e-08   35.5   0.1    2.6e-08   34.4   0.0    1.6  2  Methyltransf_11  Methyltransferase domain
    2.2e-06   27.2   0.0    2.9e-06   26.8   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.5e-06   26.9   0.0    4.2e-06   26.6   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.4e-05   24.5   0.1    0.00011   22.8   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
    0.00029   20.5   0.0    0.00036   20.1   0.0    1.1  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00038   20.0   0.0    0.00057   19.5   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0006   19.5   0.0    0.00073   19.3   0.0    1.1  1  TPMT             Thiopurine S-methyltransferase (TPMT)
  ------ inclusion threshold ------
      0.058   13.2   0.0      0.076   12.8   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.6e-13   4.2e-10       2      72 ..      36     106 ..      35     122 .. 0.89
   2 ?   -2.1   0.0       4.1   6.6e+03      21      42 ..     160     181 ..     150     197 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.6e-13
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEES CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssg 72 
                                       Ld+++GtGr++  la+++  ++v ++D s e l+++rera+++++  +++++q d+ + +f+++++Dl+++s+
  gi|313125144|ref|YP_004035408.1|  36 LDVAAGTGRNAVFLAEEG--YEVEAIDQSREGLRITRERARDRDVadQLDCLQVDIPSHEFPQDRYDLITVSF 106
                                       9****************5..**********************9999***********************9964 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                       SSEEEEEESSHHHHHHHHHHHH CS
                   Methyltransf_25  21 kakvtgvDiseemleaarerae 42 
                                       + +v+++D   e  +  r+ ++
  gi|313125144|ref|YP_004035408.1| 160 DLTVLAFDAKTESRDDGRTAMR 181
                                       4667777777777777666654 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.4e-13   2.4e-10      25     121 ..      26     121 ..       5     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.4e-13
                                       HCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHH.HHHHHHTT-TTEEEEE--GGG---.-S-EEEE CS
                              TehB  25 avkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafl.eeikekenlknistalydineakl.derydfi 99 
                                        v+ + pg++ld+  g grn+++l+  gy+v+a+d+  + +    e+ ++++  +++++  +di + ++ ++ryd+i
  gi|313125144|ref|YP_004035408.1|  26 YVDALPPGRALDVAAGTGRNAVFLAEEGYEVEAIDQSREGLRITrERARDRDVADQLDCLQVDIPSHEFpQDRYDLI 102
                                       578899**********************************997625678999999***********9995789**98 PP

                                       EEESSGGGS-GGGHHHHHHHHH CS
                              TehB 100 lstvvlmfleaeripsiienmq 121
                                          v  ++   +r+p++i+ + 
  gi|313125144|ref|YP_004035408.1| 103 T--V-SFYRTVDRLPDLIDALA 121
                                       4..4.34667788888887765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   3.5e-13   5.8e-10      20     126 ..      29     137 ..      10     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 3.5e-13
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                         ++gr Ld+++GtG+++  l+e+g++v+++D+s+e   i +        a++    q+d  + ++pq+++dlI+ +
  gi|313125144|ref|YP_004035408.1|  29 ALPPGRALDVAAGTGRNAVFLAEEGYEVEAIDQSREGLRITRerardrdVADQLDCLQVDIPSHEFPQDRYDLITVS 105
                                       45789******************************9999988888888888888888888889999********998 PP

                   Methyltransf_23  90 evlehvpdppellrqiatllkpgGylllseplaslke 126
                                       +   +v+ +p l++ +a+    +G+l+ + +l+s  +
  gi|313125144|ref|YP_004035408.1| 106 F-YRTVDRLPDLIDALAE----DGVLFYEHHLRSTDQ 137
                                       6.5789999998888777....999999999998743 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   1.6e-11   2.6e-08       1      82 [.      36     121 ..      36     122 .. 0.90
   2 ?   -2.7   0.0       5.9   9.7e+03      18      37 ..     158     179 ..     150     194 .. 0.57

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.6e-11
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES..-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvsse..vlhh 73 
                                       Ldv++GtGr+a  la+ g++v ++D s e l++ +e+a+++++  ++++++ d+ +  f+ + +Dl+++s+  +++ 
  gi|313125144|ref|YP_004035408.1|  36 LDVAAGTGRNAVFLAEEGYEVEAIDQSREGLRITRERARDRDVadQLDCLQVDIPSHEFPQDRYDLITVSFyrTVDR 112
                                       8******************************************************************9987555555 PP

                                       -CCHHHHHH CS
                   Methyltransf_11  74 vedpekalk 82 
                                       ++d+ +al+
  gi|313125144|ref|YP_004035408.1| 113 LPDLIDALA 121
                                       566655555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.9
                                       T..SEEEEEES-HHHHHHHHHH CS
                   Methyltransf_11  18 g..arvvgvDlskemlklakek 37 
                                       +   +v+++D  +e ++  +++
  gi|313125144|ref|YP_004035408.1| 158 CldLTVLAFDAKTESRDDGRTA 179
                                       3445566666666655544444 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.8e-09   2.9e-06      44     124 ..      28     106 ..      22     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.8e-09
                                       -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEE CS
                   Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDv 119
                                         +++ ++lDva+Gtg  a+ l+   +e ++v+ +D + + L++++++++++ +  +++ lq +    +f +d +D+
  gi|313125144|ref|YP_004035408.1|  28 DALPPGRALDVAAGTGRNAVFLA---EEGYEVEAIDQSREGLRITRERARDRDVAdQLDCLQVDIPSHEFPQDRYDL 101
                                       56678899**********99986...56789********************999989******************** PP

                                       EEEES CS
                   Ubie_methyltran 120 vtvsf 124
                                       +tvsf
  gi|313125144|ref|YP_004035408.1| 102 ITVSF 106
                                       ****9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.6e-09   4.2e-06       6      94 ..      34     120 ..      32     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.6e-09
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                       r lD+++GtG+ +  laee   + ev  iD s e ++  re+a++  +   +   q di + e  + ++++Dli+  
  gi|313125144|ref|YP_004035408.1|  34 RALDVAAGTGRNAVFLAEE---GYEVEAIDQSREGLRITRERARDRDVAdQLDCLQVDIPSHE--FPQDRYDLITVS 105
                                       579**************76...45688*******************99989********9999..999*****9886 PP

                   Methyltransf_31  82 ..evlnaladpdkil 94 
                                          +++ l+d+ ++l
  gi|313125144|ref|YP_004035408.1| 106 fyRTVDRLPDLIDAL 120
                                       443444444444443 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0     7e-08   0.00011       1      74 [.      36     106 ..      36     122 .. 0.80
   2 ?   -1.3   0.0       2.3   3.7e+03      24      57 ..     157     188 ..     150     199 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasn 74 
                                       L++ +GtG+++  l+e+  + e+ ++D s++ +  ++e+ ++r+   +++++  + d+ +++ + + +Dl+++s+
  gi|313125144|ref|YP_004035408.1|  36 LDVAAGTGRNAVFLAEE--GYEVEAIDQSREGLRITRERARDRD--VADQLDCLQVDIPSHEFPqDRYDLITVSF 106
                                       8****************..**************88888877766..57788888888877766679*****9884 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                   Methyltransf_12  24 tgvDispsaiedakeklakrennnnnnveleald 57 
                                       t++D+   a+ dak++ ++ + + + + ++ a++
  gi|313125144|ref|YP_004035408.1| 157 TCLDLTVLAF-DAKTESRDDG-RTAMRTQIVARN 188
                                       4556666666.5555544444.344455555554 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.2e-07   0.00036       4      60 ..      35      91 ..      33     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.2e-07
                   Methyltransf_15  4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60
                                       lD+ +G+G n++ +a+++ +v ai+ ++e l ++ + a+  +v+d++++ + d+ +
  gi|313125144|ref|YP_004035408.1| 35 ALDVAAGTGRNAVFLAEEGYEVEAIDQSREGLRITRERARDRDVADQLDCLQVDIPS 91
                                      69************************************************9999866 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.5e-07   0.00057      22     101 ..      22     102 ..      18     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.5e-07
                                       HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT.TSTT CS
                               MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle.evee 95 
                                       lL +++++   g++lD+++G+G  ++ la+e  e  v+++d++ + l++++e +++ +++  +++++ d+ + e+++
  gi|313125144|ref|YP_004035408.1|  22 LLEQYVDALPPGRALDVAAGTGRNAVFLAEEGYE--VEAIDQSREGLRITRERARDRDVAdqLDCLQVDIPShEFPQ 96 
                                       5556666667899****************98877..9********************9998999*****97626778 PP

                                       S-EEEE CS
                               MTS  96 kkfdli 101
                                       +++dli
  gi|313125144|ref|YP_004035408.1|  97 DRYDLI 102
                                       999998 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.5e-07   0.00073       5      78 ..       3      72 ..       1     108 [. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.5e-07
                                      HHHHHHHTT--TT--SS--HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHH CS
                              TPMT  5 fWekrweeeqipfhqeevnpllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffee 78
                                      +W++r++ ++ p +  e  pll +++da    + +r+l    G + ++v lAe+g+ev +++ s  +++   e 
  gi|313125144|ref|YP_004035408.1|  3 NWDERFRSGEYPSDP-EPAPLLEQYVDA---LPPGRALDVAAGTGRNAVFLAEEGYEVEAIDQSREGLRITRER 72
                                      7*************9.6789********...55569**99*************************999875433 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.6e-05     0.076      17      46 ..      22      52 ..      15      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                            DUF938 17 vLksylaktte.rvLEiasGtGqHAvffApa 46
                                       L++y+++    r L++a+GtG+ Avf+A++
  gi|313125144|ref|YP_004035408.1| 22 LLEQYVDALPPgRALDVAAGTGRNAVFLAEE 52
                                      57788887766689***************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1375.01
//
Query:       gi|313125145|ref|YP_004035409.1|  [L=108]
Description: thioredoxin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   47.5   0.0      2e-12   47.1   0.0    1.3  1  NifU      NifU-like domain
  ------ inclusion threshold ------
      0.054   13.3   0.3         29    4.5   0.1    3.0  3  HTH_DeoR  DeoR-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   2.2e-16     2e-12      11      66 ..      19      75 ..       6      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.2e-16
                                      GG--GG--EEEEEEEETT..EEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EE CS
                              NifU 11 PaLasdGGdielvdvdeg..vVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeV 66
                                      P+++++GG  e+ dvd++  +V+v + GaCsgC  + +t+  +i+ +L +ev+++ +V
  gi|313125145|ref|YP_004035409.1| 19 PQIQEHGGHFEIEDVDNEtgEVTVAIGGACSGCGIAPMTM-RAIRHRLPDEVDDISKV 75
                                      9**************99999********************.8************9998 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.036   3.2e+02      36      50 ..      12      26 ..       8      33 .. 0.84
   2 ?    3.9   0.0    0.0048        43      14      32 ..      41      59 ..      35      60 .. 0.88
   3 ?    4.5   0.1    0.0032        29      25      33 ..      71      79 ..      68      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.036
                          HTH_DeoR 36 neLeeqglltRthGG 50
                                      n+L++ ++ +  hGG
  gi|313125145|ref|YP_004035409.1| 12 NYLSNNVPQIQEHGG 26
                                      8999***9999***9 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0048
                          HTH_DeoR 14 klsveelvellgvSeaTiR 32
                                      ++ +  ++  +g++++T R
  gi|313125145|ref|YP_004035409.1| 41 TVAIGGACSGCGIAPMTMR 59
                                      678889999********99 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0032
                          HTH_DeoR 25 gvSeaTiRR 33
                                      ++S+ T+RR
  gi|313125145|ref|YP_004035409.1| 71 DISKVTVRR 79
                                      89******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 744.57
//
Query:       gi|313125146|ref|YP_004035410.1|  [L=139]
Description: mn-dependent transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-10   38.8   0.0    1.6e-09   37.8   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0002   21.4   0.0    0.00034   20.6   0.0    1.3  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.27   11.3   0.0    1.7  2  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.16   11.9   0.0       0.52   10.3   0.0    1.8  1  HTH_12          Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   3.5e-13   1.6e-09       8      60 .]       6      59 ..       4      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 3.5e-13
                                      HHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  8 dYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +YL ++Y ++  e+++v++  +a+ Ln s +++ e+  +L+++G+v y++y g+
  gi|313125146|ref|YP_004035410.1|  6 QYLIALYIAEHrESAPVSPGIVASMLNRSSATAIETFHRLDDEGLVTYKPYDGA 59
                                      69*************************************************997 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   7.5e-08   0.00034       1      56 [.      62     115 ..      62     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.5e-08
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHC CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldell 56 
                                       T+ Gre A +l + + +l  f+  vl++  ++ + eA+++  ++s+++++rl   l
  gi|313125146|ref|YP_004035410.1|  62 TQVGRETAAELHDTYVTLSWFFRSVLEL--DDYESEAMEMAGVVSPDIADRLASTL 115
                                       889*******************999987..778899****************8765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.9e-05      0.27      19      53 ..      19      54 ..       6      69 .. 0.78
   2 ?   -2.9   0.0       1.5   6.9e+03      27      34 ..     107     114 ..     106     116 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglis.r 53
                                        p++    Asml+ +  t   ++++L +egl++ +
  gi|313125146|ref|YP_004035410.1| 19 SAPVSPGIVASMLNRSSATAIETFHRLDDEGLVTyK 54
                                      368888889***********************9943 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                                       HHHHTTSS CS
                         HTH_Crp_2  27 lAsmlGlt 34 
                                       +A++l +t
  gi|313125146|ref|YP_004035410.1| 107 IADRLAST 114
                                       66666554 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.52      10      63 ..      18      66 ..       9      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                            HTH_12 10 sdkpigakeiaeeLkkr.gydigeravRyrLrkleergltrrvgyagreltEkGl 63
                                      +++p++ +++a+ L+     +i  +        l+++gl+  + y g+elt  G 
  gi|313125146|ref|YP_004035410.1| 18 ESAPVSPGIVASMLNRSsATAI--E----TFHRLDDEGLVTYKPYDGAELTQVGR 66
                                      5689999999999998867777..3....4678******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 896.79
//
Query:       gi|313125147|ref|YP_004035411.1|  [L=33]
Description: hypothetical protein Hbor_03670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        72  (0.00401584); expected 358.6 (0.02)
Passed bias filter:                       61  (0.00340231); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 223.48
//
Query:       gi|313125148|ref|YP_004035412.1|  [L=228]
Description: GMP synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-19   70.6   0.0      2e-19   70.1   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
      7e-12   45.6   1.0      1e-09   38.5   1.0    2.5  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.062   12.9   0.0      0.091   12.3   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   3.4e-23     2e-19      36     176 ..      51     188 ..      36     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3.4e-23
                                       HHHTHHSTSEEEEEE.ESSCTT......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEE CS
                            GATase  36 ilellknpdgilvsg.Gpgspg......vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekekehhggtm 105
                                           l+++dg+++ g G g         ++ + e+++ +++++iP+LGIC+G+Ql+ + +g++vv+  e  +   + 
  gi|313125148|ref|YP_004035412.1|  51 P--SLEDVDGVVIGGsGAGVYDepdqpwITRQKEFVEAVIDEEIPLLGICFGHQLVNEVLGGTVVNSGESRNYLVEA 125
                                       2..57899999998843333336678889999999******************************999888888888 PP

                                       EEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTS CS
                            GATase 106 rlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEstst 176
                                        l +    l++g  n+v +   H++ v++     +g+ev+++ + + ++ + +++++p++ vQ+HPE+t++
  gi|313125148|ref|YP_004035412.1| 126 SLAE--IPLFEGVRNVVPV--LHSDIVTE---PGEGMEVVGTADYN-RYFATRHHERPIWTVQYHPEFTPE 188
                                       8888..569***9888776..58999999...8999*******888.8********************986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   1.0   1.7e-13     1e-09      96     216 .]      82     184 ..      45     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.7e-13
                     Peptidase_C26  96 aLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievns 172
                                         ++a++++++P+lgiC G+ql+n +lGGt++++ e+          +++    + ++ +  l++ + +     v  
  gi|313125148|ref|YP_004035412.1|  82 EFVEAVIDEEIPLLGICFGHQLVNEVLGGTVVNSGES----------RNYL--VEASLAEIPLFEGVRN----VVPV 142
                                       57899*************************9988774..........1222..2234445555555555....99** PP

                     Peptidase_C26 173 lHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       lH+  ++e +e+++v+ +a+ +   a +++e   +++ vQ+HPE
  gi|313125148|ref|YP_004035412.1| 143 LHSDIVTEPGEGMEVVGTADYNRYFATRHHE--RPIWTVQYHPE 184
                                       *********************9987777776..57********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.5e-05     0.091      35      89 ..      51     105 ..      29     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                          GATase_3  35 eslgedadlvilpGgkdtiqdlallre.sgldeaikeaaeaggpvlgiCGGlqmLG 89 
                                        sl ed+d v+++G+   + d   +   ++ +e +++ + +++p+lgiC G q+  
  gi|313125148|ref|YP_004035412.1|  51 PSL-EDVDGVVIGGSGAGVYDEPDQPWiTRQKEFVEAVIDEEIPLLGICFGHQLVN 105
                                       345.78********98877777655543667777888899************9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1467.04
//
Query:       gi|313125149|ref|YP_004035413.1|  [L=714]
Description: catalase/peroxidase hpi [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-85  284.8   0.0    1.5e-46  158.9   0.0    2.2  2  peroxidase  Peroxidase
  ------ inclusion threshold ------
      0.041   13.8   0.0       0.11   12.5   0.0    1.6  1  STI1        STI1 domain


Domain annotation for each model (and alignments):
>> peroxidase  Peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.0   1.7e-50   1.5e-46       8     229 .]      53     374 ..      46     374 .. 0.88
   2 !  123.9   0.0   8.8e-40   7.9e-36       4     227 ..     382     686 ..     379     688 .. 0.86

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 1.7e-50
                                       CCCC........TTTHCHHHHHHHHHHHTT.......SSTTSCHHHTCCHHCSGGGTTTHHHHHHHHHHHHHCTT.. CS
                        peroxidase   8 alka........drdmgpsllrlafhdcfv.......gGcdgsvlllepektapaNaslrkgldvldaikakleaac 69 
                                       ++++        ++++gp ++r+a+h++++       gG+ g++++l p +++p+N +l+k++++l+++k+k++++ 
  gi|313125149|ref|YP_004035413.1|  53 VMTTsqewwpadYGHYGPLFIRMAWHSAGTyrtvdgrGGAAGGRQRLPPISSWPDNVNLDKARRLLWPVKQKYGRK- 128
                                       55555555555799**********************9*************************************95. PP

                                       ...S-HHHHHHHHHHHHHHCTT--..--EE---S-SSGGG.S-S................................. CS
                        peroxidase  70 pgvvScADlialaardavelaggplvpvslGRrDatessa.sevsnl.............................. 115
                                          +S+ Dli+la+++a+e +g +++ ++ GR+D+ ++++ +++ ++                              
  gi|313125149|ref|YP_004035413.1| 129 ---LSWGDLIVLAGNVALESMGFETFGFAGGREDDYVPDKaVDW-GPedewektssdrfdeegdlkeplgntvmgli 201
                                       ...*********************99**************9***.44557*************************** PP

                                       ..........-.-TS-HHHHHHHHHHHT--HHHHHHH.HGGGGC-EESHH................SS-GGGT.... CS
                        peroxidase 116 ..........PdptasvdelrdkfarkgltdeelvaL.sGaHtiGkahcssfs.rly.a...aadpaldaayaae.. 174
                                                 Pd + s++++r+ f+r+ ++dee+vaL +G+Ht+Gk h++    +l  +   a+++ ++ ++++e  
  gi|313125149|ref|YP_004035413.1| 202 yvnpegpngePDVEGSAKNIRQAFSRMAMNDEETVALiAGGHTFGKVHGADSGdNLGpEpeaAPIDLQGLGWENEyg 278
                                       ***9998888899***********************************99888888765666666667777777753 PP

                                       ..HHS..............EETS-STHHHHHHCC....................................T-EEEHH CS
                        peroxidase 175 kCasgnte.lvdld.....tptkfdnsyfknlle....................................krgllrs 209
                                       +  +g ++ ++ ++     tp ++d  y  nlle                                      ++l++
  gi|313125149|ref|YP_004035413.1| 279 S-GKGPDTiTSGIEgpwntTPIQWDMGYIDNLLEykwwpeqgpggawqwttqggelddaapgvedpsekeDVMMLTT 354
                                       1.3333335333333333688*************************************************9****** PP

                                       HHHHHHSCCCHHHHHHCCC- CS
                        peroxidase 210 Dqvllsdsetralvekyaes 229
                                       D +l++d+++r++ e+++e+
  gi|313125149|ref|YP_004035413.1| 355 DIALKRDPDFREVLERFQEN 374
                                       ****************9875 PP

  == domain 2  score: 123.9 bits;  conditional E-value: 8.8e-40
                                       HHHHCCCC.TTTHCH..HH.......HHHHHHH.......................................HTT.. CS
                        peroxidase   4 fvkaalka.drdmgp..sl.......lrlafhd.......................................cfv.. 29 
                                       f+ka++k  +rdmgp   +       + + ++d                                       +    
  gi|313125149|ref|YP_004035413.1| 382 FAKAWYKLiHRDMGPpeRFlgpevpdEVMLWQDplpdadydliddeaaaelkeeilgsdlsvsqlvktawasA-Sty 457
                                       7889999999999996522577888999999999999999999999999999999888888887776655442.158 PP

                                       ......SSTTSCHHHTCCHHCSGGGT..TTHHHHHHHHHHHHHCTT.......S-HHHHHHHHHHHHHHCT....T- CS
                        peroxidase  30 ......gGcdgsvlllepektapaNa..slrkgldvldaikakleaacpg.v.vScADlialaardavela....gg 92 
                                             gG++g++++lep+++++ N+  +l+++l++l+ i++++++++++ + vS+ADli+l++++ave+a    g 
  gi|313125149|ref|YP_004035413.1| 458 rdsdkrGGANGARIRLEPQRSWEVNEpeELETVLETLEGIQDEFNSSQSDeTrVSLADLIVLGGNAAVEKAaadaGY 534
                                       889999****************************************8866556*****************9999544 PP

                                       -...--EE---S-SSGGG.S-S.....-............-TS-HHH.HHHHHHHHT--HHHHHHH.HGGGGC-EES CS
                        peroxidase  93 p.lvpvslGRrDatessa.sev.snl.P...........dptasvde.lrdkfarkgltdeelvaL.sGaHtiGkah 152
                                          +p+++GR+Dat++++ +e+ + l P             +++ +e l+dk++ ++lt+ee+++L +G++++++++
  gi|313125149|ref|YP_004035413.1| 535 DvEIPFEPGRTDATQEQTdVESfEALkPkadgfrnyiesGVDEKPEElLVDKAELLNLTVEEMTVLvGGMRALDANY 611
                                       4555**************988865557455556666664557888998***************************** PP

                                       HH...........SS-GGGT....HHS........EETS-STHHHHHHCC.........................T- CS
                        peroxidase 153 cssfsrlyaaadpaldaayaaekCasgntelvdldtptkfdnsyfknlle.........................kr 204
                                                                 g++  v++d+p++++n++f+nll+                         ++
  gi|313125149|ref|YP_004035413.1| 612 Q-------------------------GSDLGVFTDEPETLTNDFFVNLLDmdsewepvsdsedvfelrdretgevQW 663
                                       2.........................33448999******************************************* PP

                                       EEEHHHHHHHHSCCCHHHHHHCC CS
                        peroxidase 205 gllrsDqvllsdsetralvekya 227
                                         +r D+ ++s++++r ++e+y 
  gi|313125149|ref|YP_004035413.1| 664 KGSRFDLIFGSNARLRTVAEVYG 686
                                       *********************96 PP

>> STI1  STI1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.2e-05      0.11      17      38 ..     358     379 ..     357     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                              STI1  17 llsDPefvakleeiqsNPqalq 38 
                                       l  DP+f+ +le++q+NP  +q
  gi|313125149|ref|YP_004035413.1| 358 LKRDPDFREVLERFQENPDEFQ 379
                                       568***************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 5209.57
//
Query:       gi|313125150|ref|YP_004035414.1|  [L=98]
Description: hypothetical protein Hbor_03700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 643.13
//
Query:       gi|313125151|ref|YP_004035415.1|  [L=123]
Description: hypothetical protein Hbor_03710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0021   18.1   0.0     0.0031   17.6   0.0    1.2  1  HTH_20           Helix-turn-helix domain
     0.0033   17.4   0.0     0.0047   16.9   0.0    1.2  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0097   16.2   0.0      0.013   15.8   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.022   15.1   0.0      0.032   14.6   0.0    1.2  1  Rrf2             Transcriptional regulator
      0.035   13.8   0.0      0.051   13.2   0.0    1.2  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
      0.093   12.7   0.0       0.12   12.3   0.0    1.2  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
        0.1   12.8   0.0       0.15   12.3   0.0    1.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.11   12.4   0.0       0.13   12.1   0.0    1.2  1  TFIIE_alpha      TFIIE alpha subunit
       0.11   12.4   0.0       0.15   11.9   0.0    1.2  1  MarR_2           MarR family
       0.19   11.4   0.0       0.35   10.6   0.0    1.4  1  GntR             Bacterial regulatory proteins, gntR family
       0.22   11.4   0.0       0.32   10.8   0.0    1.2  1  DUF1495          Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.9e-06    0.0031      18      61 .]      26      71 ..      22      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                                      HH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 18 aL..araegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      +L  ++++++t se+a +++ ++nt+   L  L +  Lv+  re++
  gi|313125151|ref|YP_004035415.1| 26 YLytHSDQAFTRSEIATAISEDPNTVGTALSRLKDRNLVRHKREFW 71
                                      556699*************************************987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06    0.0047      21      61 ..      34      75 ..      21      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EEES- CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrr.irild 61
                                       +t+ e+A  +   + tv  +ls+Lk+++l++ +r+   i+d
  gi|313125151|ref|YP_004035415.1| 34 AFTRSEIATAISEDPNTVGTALSRLKDRNLVRHKREfWAITD 75
                                      58******************************6556677776 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.1e-06     0.013       7      56 ..      22      69 ..      18      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.1e-06
                                      HHHHHHHHHS-..EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEE CS
                   Penicillinase_R  7 evmeilwekge..atvkevveeleeekelaysTVktllrrLvkKgllsreke 56
                                      +v  +l+++++   t +e+ ++++e+    ++TV t l+rL +++l+++++e
  gi|313125151|ref|YP_004035415.1| 22 QVVTYLYTHSDqaFTRSEIATAISED----PNTVGTALSRLKDRNLVRHKRE 69
                                      77888888876557889999999999....******************9986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     2e-05     0.032      13      59 ..      23      68 ..      19      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      +++yL +++++  ++ +eia+  +  p+ +   l++L+  +lv+ +r
  gi|313125151|ref|YP_004035415.1| 23 VVTYLYTHSDQA-FTRSEIATAISEDPNTVGTALSRLKDRNLVRHKR 68
                                      789*******98.******************************9776 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.1e-05     0.051      14      54 ..      25      65 ..      20      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                      HrcA_DNA-bdg 14 ielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLve 54
                                      + ly+++++a    eiA +++ ++ tv   l+ Lk  +Lv 
  gi|313125151|ref|YP_004035415.1| 25 TYLYTHSDQAFTRSEIATAISEDPNTVGTALSRLKDRNLVR 65
                                      569********************************999997 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.5e-05      0.12      45      89 ..      26      69 ..      24      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-05
                   Phage_rep_org_N 45 elylsenipytaemlalifnreletvrlaLkvlkdlelieisedk 89
                                      +ly   +   t  ++a+ ++++ +tv  aL+ lkd +l+ ++  +
  gi|313125151|ref|YP_004035415.1| 26 YLYTHSDQAFTRSEIATAISEDPNTVGTALSRLKDRNLVRHK-RE 69
                                      6899999999*****************************987.44 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.2e-05      0.15      12      55 ..      26      67 ..      18      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.2e-05
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                       +Yt s   +  +++++a ++   p +V   l++L++  +v ++
  gi|313125151|ref|YP_004035415.1| 26 YLYTHS--DQAFTRSEIATAISEDPNTVGTALSRLKDRNLVRHK 67
                                      455555..567789***************************998 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05      0.13      27      62 ..      34      69 ..      20      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                                      SEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                       TFIIE_alpha 27 evteedlakelkidlnelrklLnrLyearlvkykrr 62
                                       +t  ++a  ++ d+n ++ +L rL++  lv  kr+
  gi|313125151|ref|YP_004035415.1| 34 AFTRSEIATAISEDPNTVGTALSRLKDRNLVRHKRE 69
                                      588999*************************99996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.5e-05      0.15      11      54 ..      24      67 ..      21      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.5e-05
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                        +L+ + ++ +t +e+a +   ++ +v  +l rL ++ Lv+ +
  gi|313125151|ref|YP_004035415.1| 24 VTYLYTHSDQAFTRSEIATAISEDPNTVGTALSRLKDRNLVRHK 67
                                      567888888899*****************************865 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.35      28      57 ..      38      67 ..      29      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverr 57
                                      +e+a+++  + +tv  AL+rL+ ++lv  +
  gi|313125151|ref|YP_004035415.1| 38 SEIATAISEDPNTVGTALSRLKDRNLVRHK 67
                                      799999999*****************9765 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002      0.32      12      47 ..      21      56 ..      16      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                           DUF1495 12 kkvllyLysiypeksnlqeisrrvrskpsnvkGale 47
                                      ++v++yLy + +++ + +ei++++  +p+ v  al 
  gi|313125151|ref|YP_004035415.1| 21 EQVVTYLYTHSDQAFTRSEIATAISEDPNTVGTALS 56
                                      789************************999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 847.37
//
Query:       gi|313125152|ref|YP_004035416.1|  [L=492]
Description: efflux protein, mate family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-60  202.4  35.9    3.5e-31  108.0  15.5    2.7  4  MatE             MatE
    8.9e-07   29.1  12.1    8.9e-07   29.1  12.1    5.1  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0  15.5   3.9e-35   3.5e-31       1     161 []      27     191 ..      27     191 .. 0.99
   2 ?   -3.6   0.1      0.85   7.6e+03      48      56 ..     234     242 ..     222     255 .. 0.50
   3 !  106.3   5.6   1.3e-34   1.2e-30       1     160 [.     277     442 ..     277     443 .. 0.98
   4 ?   -3.7   0.0      0.93   8.4e+03      78      97 ..     461     479 ..     454     488 .. 0.53

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 3.9e-35
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       Pi+++ ll++ ++l+dt+++grl+++a+Aa+s+a+++++ll++++ g+ +a t+lv+q+ Gak    a++++ q++ 
  gi|313125152|ref|YP_004035416.1|  27 PIIVTELLQVAYNLADTIWLGRLSTDAVAAISLAFPLIFLLISVGGGFTVAGTILVAQYTGAKEEGSAGVVAGQTFA 103
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee....vlelakrylrililgipalalqlvlsgilrgagktkvplyisli 150
                                       +  ++++++ ll+++ ++ +l ++ ++++    v++ a +y+r+ +lg+p+l+ ++v+s+ +rg+g+t++p+++++i
  gi|313125152|ref|YP_004035416.1| 104 FISIIAVVVGLLGFASTDLMLGVLPSSAAtagqVIPHAGDYMRVFFLGLPFLFGFFVFSSLMRGYGNTRAPMVVMFI 180
                                       ************************999999999******************************************** PP

                              MatE 151 slllniplnyl 161
                                       s+ +n++++++
  gi|313125152|ref|YP_004035416.1| 181 SVAINVLVDPI 191
                                       *******9986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.85
                              MatE  48 lstalttlv 56 
                                       ls a++t++
  gi|313125152|ref|YP_004035416.1| 234 LSRAVATVI 242
                                       222222222 PP

  == domain 3  score: 106.3 bits;  conditional E-value: 1.3e-34
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+ale+ +  l ++++t +v  + ++ +Aa++++++++sl+f+++lgl+ a++t+vgq+lGa++++ra++a+  + +
  gi|313125152|ref|YP_004035416.1| 277 PSALEQSASALGFITLTAMVVTFAPEVVAAYGLGNRLTSLVFLPALGLGRATDTIVGQNLGAEKPERAERAVWLAAK 353
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee.....vlelakrylrililgipalalqlvlsgilrgagktkvplyisl 149
                                       +++ ++++i ++++lf+e+i+s+f ++ +      +el+++y+r+ ++   +++++++  g++rgag+tk++l++sl
  gi|313125152|ref|YP_004035416.1| 354 VGASVMVVIGVVAFLFAEPIVSVFIDTGTdsatkTIELGAEYIRVRAFEFGFIGVLQTVLGAYRGAGNTKTALAFSL 430
                                       ***************************99999********************************************* PP

                              MatE 150 isl.llniplny 160
                                       ++l   +ip+ y
  gi|313125152|ref|YP_004035416.1| 431 FALwFGRIPIVY 442
                                       ***888888876 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 0.93
                              MatE  78 lllllsliiallvllfseqi 97 
                                       ++ +l++i+a++ ++ +  +
  gi|313125152|ref|YP_004035416.1| 461 VGQILGAIAAAA-WFTRGTW 479
                                       333444444444.6666555 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.8   7.1         2   1.8e+04     119     130 ..      89     113 ..      19     126 .. 0.51
   2 !   29.1  12.1     1e-10   8.9e-07       1      77 [.     144     247 ..     144     250 .. 0.95
   3 ?   -0.9   1.4      0.17   1.5e+03      62     136 ..     285     363 ..     283     371 .. 0.52
   4 !    3.3   4.3    0.0088        79       6      77 ..     400     474 ..     395     485 .. 0.78

  Alignments for each domain:
  == domain 1  score: -5.8 bits;  conditional E-value: 2
                   Polysacc_synt_C 119 a.............alalllavlvg 130
                                                     a++ ++av+vg
  gi|313125152|ref|YP_004035416.1|  89 KeegsagvvagqtfAFISIIAVVVG 113
                                       0223333333333233444444444 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 1e-10
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgi................ 55 
                                       +++++ l+++fl+ + v+ss++ g g +++++++++i++++++++  ++i      plfg+                
  gi|313125152|ref|YP_004035416.1| 144 YMRVFFLGLPFLFGFFVFSSLMRGYGNTRAPMVVMFISVAINVLVDPIFIfgfesnPLFGMlgirgvestlfaatgf 220
                                       58999*********************************************8888777888899************** PP

                   Polysacc_synt_C  56 .....vGaaiatvlallvvavlnlyal 77 
                                            +Gaaiatvl+ +v++v+ ly +
  gi|313125152|ref|YP_004035416.1| 221 egygvTGAAIATVLSRAVATVIGLYVI 247
                                       **********************99976 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.17
                   Polysacc_synt_C  62 tvlallvvavlnlyalrrllgikl.ellrrllkpllaalvmgivvylllllllglllla....alalllavlvgalv 133
                                       ++l++++ +++ + ++   +        r +  ++l al++g ++ +++ ++lg+  ++    a+ l+++v++ + v
  gi|313125152|ref|YP_004035416.1| 285 SALGFITLTAMVVTFAPEVVAAYGlG-NRLTSLVFLPALGLGRATDTIVGQNLGAEKPEraerAVWLAAKVGASVMV 360
                                       56666666666665555544444421.33334667777777777777777777777766655533333333333333 PP

                   Polysacc_synt_C 134 Yll 136
                                        ++
  gi|313125152|ref|YP_004035416.1| 361 VIG 363
                                       333 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.0088
                   Polysacc_synt_C   6 alsiiflslstvlssiLqglgrqkialkalvigal.vklilnllli..plfgivGaaiatvlallvvavlnlyal 77 
                                       a+ + f+++ +++ +   g g +k+al ++++++    + + ++l     fg +G+ i+++++++++a+    + 
  gi|313125152|ref|YP_004035416.1| 400 AFEFGFIGVLQTVLGAYRGAGNTKTALAFSLFALWfGRIPIVYYLSfmQGFGEMGIWIGMAVGQILGAIAAAAWF 474
                                       666779999999999999******99999999988534555555554489999*************999875554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3099.89
//
Query:       gi|313125153|ref|YP_004035417.1|  [L=195]
Description: ferredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-13   50.9   0.8    2.2e-13   50.0   0.8    1.5  1  Fer2      2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.8   1.2e-17   2.2e-13       6      78 .]     109     184 ..     104     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.2e-17
                                       EEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE......CTTSSSSTHHHHHTTEEEEGGGSE CS
                              Fer2   6 kevevevadgettlldaaeenggidipysCggggCgtClvevlegev......qsdetelegeeldegklrlaCqti 76 
                                       ++ ++eva++et +l+a e+  g+d+py+C++g+C +C+ ++++g        +++++ l ++eld+g+  l+C+++
  gi|313125153|ref|YP_004035417.1| 109 QGATIEVANNET-VLEAGEDE-GMDLPYACRQGQCVSCAGQITSGGSsedyvvHDNQQMLGDAELDDGYT-LTCVAY 182
                                       6789********.******98.**********************987544455555***********999.*****9 PP

                                       ES CS
                              Fer2  77 vt 78 
                                       ++
  gi|313125153|ref|YP_004035417.1| 183 PK 184
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1216.03
//
Query:       gi|313125154|ref|YP_004035418.1|  [L=57]
Description: hypothetical protein Hbor_03750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 362.58
//
Query:       gi|313125155|ref|YP_004035419.1|  [L=298]
Description: 6-phosphogluconate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-38  131.8   0.1    3.4e-38  131.3   0.1    1.2  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    1.3e-23   83.8   0.0    1.7e-23   83.4   0.0    1.1  1  6PGD             6-phosphogluconate dehydrogenase, C-terminal
    1.9e-05   25.1   0.0    3.3e-05   24.4   0.0    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    5.9e-05   23.0   0.1      9e-05   22.4   0.1    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00016   21.1   0.0    0.00023   20.5   0.0    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00018   21.7   0.2    0.00049   20.4   0.1    1.8  2  TrkA_N           TrkA-N domain
    0.00035   20.8   0.2      0.011   16.0   0.0    2.8  3  NAD_binding_11   NAD-binding of NADP-dependent 3-hydroxyisobu
  ------ inclusion threshold ------
      0.017   15.0   0.7        2.3    8.1   0.0    2.8  3  NAD_binding_10   NAD(P)H-binding
      0.022   14.3   0.0      0.059   12.9   0.1    1.6  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.024   14.9   0.3       0.26   11.6   0.3    2.1  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.045   13.9   1.0       0.12   12.5   1.0    1.8  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.17   11.5   0.1        0.5   10.0   0.1    1.9  1  ApbA             Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.3   0.1   2.2e-41   3.4e-38       1     151 [.       2     151 ..       2     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 2.2e-41
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHC...SEEEE-SSSHHHHHHHHH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasl...dvvitmvkagkavdevie 74 
                                       ++g+iGlG MG+  ++++l+ag++v+++++++e+v +++++ga++a+sie+l+++l   + +++mv+ag+avd++++
  gi|313125155|ref|YP_004035419.1|   2 QLGVIGLGRMGQIVVNRVLDAGHDVVAFDLSEEAVATAADAGAEPASSIEDLMNRLgdeKRIWLMVPAGEAVDATLD 78 
                                       58*************************************************************************** PP

                                       SHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEE CS
                     NAD_binding_2  75 gllealkkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaiga 151
                                       +l ++l+ +d+++dg++s +e++ ++a++   +++ +ld++ SGG +gAe G  s+m+GG+e a+e+++pv++a+++
  gi|313125155|ref|YP_004035419.1|  79 ELDPHLDGQDVVVDGGNSYFEESVRRAEA---TEAAYLDCGTSGGPAGAELGF-SLMIGGPEWAYEELTPVFDAVAT 151
                                       ***********************999876...5678*****************.********************997 PP

>> 6PGD  6-phosphogluconate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.0   1.2e-26   1.7e-23       1     116 [.     165     274 ..     165     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 1.2e-26
                              6PGD   1 GhyVKmvHNGieygdmqliaEaydllkkvlglsneeiaevFeeWnkgel.esyLieitakilrkkdeedgkplvdki 76 
                                       GhyVKmvHNG+ey+ mq+ +E ++ll ++      ++++v ++Wn+g + +s+L+e +++ +r++ ++     +  +
  gi|313125155|ref|YP_004035419.1| 165 GHYVKMVHNGVEYALMQAYGEGFELLANG--RYDLDLEAVSRTWNNGAViRSWLLELCEEAFREEGND-----LGDV 234
                                       9**************************85..6778899999******555*************99874.....4567 PP

                              6PGD  77 lDkagqkGTgkwtvqealelgvpvptiaeavfaRllSslk 116
                                       +D+     Tg+wtvqeale +v+vp+i +a++ R+ S ++
  gi|313125155|ref|YP_004035419.1| 235 ADHVAGGSTGTWTVQEALEQEVSVPLIYQALAERFDSRNE 274
                                       88888899***************************99876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.2e-08   3.3e-05       2      93 ..       3      92 ..       2      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.2e-08
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH...H-SEEEE-S-H.HHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae...eadvvvlavkp.edvee 76
                                      +g+iG G+mg+ +++++l ag   h++v a + ++e ++ +a+++g++  + + e++++   + + + l v+  e+v++
  gi|313125155|ref|YP_004035419.1|  3 LGVIGLGRMGQIVVNRVLDAG---HDVV-AFDLSEEAVA-TAADAGAEPAS-SIEDLMNrlgDEKRIWLMVPAgEAVDA 75
                                      89*******************...****.8688777665.55555666666.667776656678889999987467888 PP

                                      HHHHCGHHHHTTSEEEE CS
                     F420_oxidored 77 vlselakdalkgklvis 93
                                      +l+el ++++ + +v++
  gi|313125155|ref|YP_004035419.1| 76 TLDELDPHLDGQDVVVD 92
                                      99999888888889988 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1     6e-08     9e-05       2      44 ..       3      45 ..       2      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6e-08
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                      ++viG G mG+ + + ++ ag++Vv +d seea+++a+++ ++
  gi|313125155|ref|YP_004035419.1|  3 LGVIGLGRMGQIVVNRVLDAGHDVVAFDLSEEAVATAADAGAE 45
                                      79*******************************9999887655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.6e-07   0.00023      38      90 ..       2      55 ..       1      73 [. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.6e-07
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleella 90
                                      ++G+iGlGr+Gq v +r+   g +v+a+d s+++ +++++ g+e + s+e+l++
  gi|313125155|ref|YP_004035419.1|  2 QLGVIGLGRMGQIVVNRVLDAGHDVVAFDLSEEAVATAADAGAEPAsSIEDLMN 55
                                      79*****************************99999999999966647887775 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   3.2e-07   0.00049       3      43 ..       5      45 ..       3      53 .. 0.91
   2 ?   -2.8   0.0       4.8   7.2e+03       7      19 ..     275     287 ..     275     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.2e-07
                                      EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE CS
                            TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegle 43
                                      +iGlGr+G+ +++++ + g+ dvv+ d +ee+v+++++ g+e
  gi|313125155|ref|YP_004035419.1|  5 VIGLGRMGQIVVNRVLDaGH-DVVAFDLSEEAVATAADAGAE 45
                                      9****************555.8***************99865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                                       SHHHHHHHHHHHH CS
                            TrkA_N   7 GrvGrslaeeLse 19 
                                       Gr+ r+la++L+ 
  gi|313125155|ref|YP_004035419.1| 275 GRFSRRLANRLRY 287
                                       8999*****9985 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       0.5   7.4e+02      22      47 ..      33      58 ..      15      69 .. 0.78
   2 !   16.0   0.0   7.3e-06     0.011       1      51 [.     163     216 ..     163     227 .. 0.83
   3 ?   -0.0   0.0      0.66   9.8e+02      32      60 ..     228     256 ..     222     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.5
                    NAD_binding_11 22 sEalvlaekaGldpekvlevinassg 47
                                       Ea+++a+ aG +p+  +e + + +g
  gi|313125155|ref|YP_004035419.1| 33 EEAVATAADAGAEPASSIEDLMNRLG 58
                                      599999999*9999988876666555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.3e-06
                    NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlae..kaGldpekvlevinassg.rsna 51 
                                       G+G+ vK+v+n +  + + a +E++ l++  +++ld+e+v +  n+++  rs+ 
  gi|313125155|ref|YP_004035419.1| 163 GSGHYVKMVHNGVEYALMQAYGEGFELLAngRYDLDLEAVSRTWNNGAViRSWL 216
                                       9***********************98876337********99988876425555 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.66
                    NAD_binding_11  32 Gldpekvlevinassgrsnalenklpqrv 60 
                                       G d+  v + + ++s + +++++ l+q v
  gi|313125155|ref|YP_004035419.1| 228 GNDLGDVADHVAGGSTGTWTVQEALEQEV 256
                                       7789999999**********999998865 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0015       2.3       4      41 ..       9      44 ..       7      55 .. 0.81
   2 ?   -0.5   0.0      0.68     1e+03      51      68 ..      77      94 ..      65     111 .. 0.76
   3 ?    3.8   0.0     0.031        47       2      26 ..     239     262 ..     239     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                                      SHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTC CS
                    NAD_binding_10  4 GkvGrllvkellargghevtalvRnpeklaeleaeegl 41
                                      G+ G+ +v++ l++ gh+v+a+  ++e +a  + ++g+
  gi|313125155|ref|YP_004035419.1|  9 GRMGQIVVNRVLDA-GHDVVAFDLSEEAVATAA-DAGA 44
                                      9*************.5******88888887543.4555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.68
                                      CCHHHHHHTT-SEEEES- CS
                    NAD_binding_10 51 vedlaealkgadaVvsal 68
                                       ++l  +l+g+d+Vv  +
  gi|313125155|ref|YP_004035419.1| 77 LDELDPHLDGQDVVVDGG 94
                                      48999999****999655 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.031
                                       TTSHHHHHHHHHHHHC-T-EEEEEE CS
                    NAD_binding_10   2 AtGkvGrllvkellargghevtalv 26 
                                       A G++G   v+e+l+++ ++v ++ 
  gi|313125155|ref|YP_004035419.1| 239 AGGSTGTWTVQEALEQE-VSVPLIY 262
                                       78**************5.9998876 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     4e-05     0.059       1      39 [.       1      39 [.       1      52 [. 0.93
   2 ?   -2.4   0.0       2.1   3.1e+03      99     118 ..      72      91 ..      71      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdkl 39
                                      m++ viGlG +G +    +  +gh+v+  D +ee+v++ 
  gi|313125155|ref|YP_004035419.1|  1 MQLGVIGLGRMGQIVVNRVLDAGHDVVAFDLSEEAVATA 39
                                      7889*******************************9875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHCEEEEE CS
                    UDPG_MGDP_dh_N  99 yvesaarsiaealkkgkvvv 118
                                       +v ++++++ ++l+ ++vvv
  gi|313125155|ref|YP_004035419.1|  72 AVDATLDELDPHLDGQDVVV 91 
                                       57889999**********99 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00017      0.26       2      99 ..       4     117 ..       3     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...............TTTCEEEEE--TTTHHHH. CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka...............lgvrfeaialdaenyeav. 62 
                                        +iG G++Gq v+  +++ ++    ++  d s+e ++ +a++                 ++r+  +    e ++a+ 
  gi|313125155|ref|YP_004035419.1|   4 GVIGLGRMGQIVVNRVLDAGHD---VVAFDLSEEAVATAADAGaepassiedlmnrlgDEKRIWLMVPAGEAVDATl 77 
                                       59***********999999875...8888888888766665558888889999999984444444444444444430 PP

                                       ..HHHHHTTSSEEEE-SSGGGHHHHHHHHHHHT-EEEE..S CS
                   Sacchrp_dh_NADP  63 ..LaallkegdlvvnlsppissldvlkaCietgvhyvd..t 99 
                                         L+++l ++d+vv+   ++  ++ ++ + +t ++y+d  t
  gi|313125155|ref|YP_004035419.1|  78 deLDPHLDGQDVVVDGGNSY-FEESVRRAEATEAAYLDcgT 117
                                       0067779999*****76555.55566778889999999444 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.0   8.1e-05      0.12       1      46 [.       1      56 [.       1     119 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.1e-05
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH............H CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag............e 46
                                      ++++v+G  GrmG+ vv+ v + +++ +va   ++e  + + dag            +
  gi|313125155|ref|YP_004035419.1|  1 MQLGVIGL-GRMGQIVVNRVLD-AGHDVVAFDLSEEAVATAADAGaepassiedlmnR 56
                                      7899***9.************9.78888877666666677777775555555555540 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00033       0.5       2      40 ..       4      43 ..       3     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00033
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHC CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknG 40
                                       ++G+G +G+++  +   ag+dv+  + s+  +++  ++G
  gi|313125155|ref|YP_004035419.1|  4 GVIGLGRMGQIVVNRVLDAGHDVVAFDLSEeAVATAADAG 43
                                      59*********************99988875666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1898.54
//
Query:       gi|313125156|ref|YP_004035420.1|  [L=132]
Description: signal-transduction protein containing camp-binding and cbs domains [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-13   50.1   5.6      1e-07   32.3   0.5    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.5   5.7e-12     1e-07       3      49 ..       4      49 ..       2      56 .. 0.86
   2 !   20.6   0.5   2.6e-08   0.00046       1      54 [.      66     119 ..      66     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 5.7e-12
                                      HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHH CS
                               CBS  3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlr 49
                                      ++ ++dv+t+ p+t++++++  mr+++ +++ V+d +++++Gi+t  
  gi|313125156|ref|YP_004035420.1|  4 ELLRTDVPTAAPETPIADVATVMRDTDADAVVVLD-EDRPLGIITPA 49
                                      67899*******************99999**4556.666******76 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.6e-08
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+++ + d+vt++  ++ ++++  +++++v+   V+de +++vGiv+ +D+l a
  gi|313125156|ref|YP_004035420.1|  66 VAELVSGDPVTIRRVASRSDLVAVFAREDVREAIVLDEMDQYVGIVSFKDVLTA 119
                                       67788889*****************999999664889999************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 857.50
//
Query:       gi|313125157|ref|YP_004035421.1|  [L=365]
Description: leucyl aminopeptidase (aminopeptidase t) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-58  197.7   0.0      3e-58  197.5   0.0    1.0  1  Peptidase_M29  Thermophilic metalloprotease (M29)
  ------ inclusion threshold ------
      0.072   13.5   0.8       0.39   11.2   0.1    2.6  3  3HCDH_RFF      3-hydroxybutyryl-CoA dehydrogenase reduced Ros


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.5   0.0   3.4e-62     3e-58       2     390 ..       2     348 ..       1     362 [. 0.88

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 3.4e-62
                                       HHHHHHHHHHHHHTTT---TT-EEEEEEETT-HHHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHHHS-TT-TT--- CS
                     Peptidase_M29   2 eeklekyAellvkvglnlqkgqevvinaevealelarlvaeeaykagakkvvvewsdeeltkerlknaseeqleevp 78 
                                       +++++  Ae+lv+ ++++++g++vv+++   a+ela +vae++ ++ga+ v++ + ++e+ ++ +  a+++++++ +
  gi|313125157|ref|YP_004035421.1|   2 DPRIRDHAEVLVDWSARIESGDDVVVSVAEGAHELAVAVAEKLGERGANVVTT-YASDEVLRA-YLRAHDAEFDFGA 76 
                                       678999*********************************************99.666666555.5567788885554 PP

                                       HHHHHHHHHHHHTT-EEEEEE--.-GGGSTTS-HHHHHHHHHHHHHHHHHHHHHHHTTSS-B-BEE---TTTHHHH- CS
                     Peptidase_M29  79 eweaekleelveegaarlsilae.dpkllkgvdpekiaaaqkarskalkeyreriasgklrWcvvavPteawAkkvf 154
                                         e     +l+e+++++l++ +  ++ + ++v+ e     ++a+ +a++++re+ +  ++ W+ +  Pt+++A+   
  gi|313125157|ref|YP_004035421.1|  77 -HE----LALYENADSVLFLGGGrNTFATADVPGE----TRQASDRASQPVREARM--DTDWVSTVHPTRSLAQ--- 139
                                       .44....69***********999899999999655....66777778888888888..566*************... PP

                                       --S-HHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS CS
                     Peptidase_M29 155 pdleaeealeklwdaifkavrldeedpvaaWeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWigga 231
                                          +a++a+e++ +++++av        ++Wee  +++++ +++L+e   +e+++ +  +td+++++ eg++ ++ a
  gi|313125157|ref|YP_004035421.1| 140 ---QAGMAYEEYQQFVYDAVC-------RDWEELADQMANMKEILDE--GSEVRLVKGDNTDIRMSI-EGRTAVNSA 203
                                       ...**************9986.......56*****************..9999999999********.777777776 PP

                                       ---SSS----SBSS---EEE-EEEEEEEEEEE-SS-EEETTEEEBS-EEEEETTEEEEEE-SB-HHHHHHHTTSSSG CS
                     Peptidase_M29 232 ektkkgiefvaNiPteevftaPdkrgvnGvvratkPlsysGnliegirltFedGkvveakAekGeevLkklletDeg 308
                                       +      +   N+P++evftaP     +G v ++ P+ +sG+ +++++ltF dG+v++++Ae+Ge++L ++++tD+g
  gi|313125157|ref|YP_004035421.1| 204 ASV---AYDSHNLPSGEVFTAPYD--PEGEVFFDVPMTISGSRVRNVHLTFADGEVTDFTAESGEDALAEIFDTDDG 275
                                       665...57788***********86..58************************************************* PP

                                       GGSEEEEE---TTSHHHHHT-----HHHHHT..TS-EEEEE---GGGB--..-----SHHHHT----S-EEEEE--- CS
                     Peptidase_M29 309 arrLGEvALvpndspisqsgilfyntLfDen..ascHlAlGaaypecleggeelteeelkaaglNdSlihvDfmigs 383
                                       arrLGE+ ++ n+  i++   ++ n+LfDe+   ++HlA+G+ay +cl +ge+           NdS++hvD mi +
  gi|313125157|ref|YP_004035421.1| 276 ARRLGELGIGMNR-GIDR---FTDNILFDEKmgDTIHLAVGRAYGSCLPEGES----------GNDSAVHVD-MITD 337
                                       *************.****...***********99*************999876..........9********.9986 PP

                                       ....TT-EEEE CS
                     Peptidase_M29 384 ....edldidg 390
                                           +++d+dg
  gi|313125157|ref|YP_004035421.1| 338 vseeSRMDVDG 348
                                       22224555555 PP

>> 3HCDH_RFF  3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.4e-05      0.39      20      53 ..      10      43 ..       4      53 .. 0.82
   2 ?   -2.3   0.1      0.71   6.3e+03       6      14 ..     196     204 ..     195     208 .. 0.82
   3 ?   -2.7   0.0      0.94   8.4e+03      17      34 ..     325     343 ..     322     344 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                         3HCDH_RFF 20 vvlfDlaldyraatrlAlAaaaqaspqalaqava 53
                                       vl+D+ ++ ++++ +++++a++a + a+a a +
  gi|313125157|ref|YP_004035421.1| 10 EVLVDWSARIESGDDVVVSVAEGAHELAVAVAEK 43
                                      59**********************9998876544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.71
                         3HCDH_RFF   6 GrtAtqraa 14 
                                       GrtA + aa
  gi|313125157|ref|YP_004035421.1| 196 GRTAVNSAA 204
                                       999999887 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.94
                         3HCDH_RFF  17 g.rpvvlfDlaldyraatr 34 
                                       g   +v++D + d  + +r
  gi|313125157|ref|YP_004035421.1| 325 GnDSAVHVDMITDVSEESR 343
                                       5344899999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 2025.95
//
Query:       gi|313125158|ref|YP_004035422.1|  [L=134]
Description: 30S ribosomal protein S6e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-40  137.0   0.1    3.8e-40  136.7   0.1    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.7   0.1   2.1e-44   3.8e-40       1     117 [.       4     117 ..       4     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 2.1e-44
                                       -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEE CS
                     Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLls 77 
                                       +k+++sdp+ g ++++evd++++++++g+ ig+evdg+a+G  l+g++l+itggsd++G+pm+++v +++ ++lLl+
  gi|313125158|ref|YP_004035422.1|   4 FKVVVSDPDAGDTHQFEVDGQDANRFLGRDIGDEVDGGAVG--LDGFTLEITGGSDEAGRPMRENVAGSNLKELLLE 78 
                                       79***************************************..********************************** PP

                                       TTSSSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--S CS
                     Ribosomal_S6e  78 kggvgyrprrkGerkrksvrGcivsadisqlnlvivkkge 117
                                       + gvgy+p r+Gerkr++vrG+ vs++++q+n++++  g+
  gi|313125158|ref|YP_004035422.1|  79 G-GVGYKPSRDGERKRVTVRGRQVSDETAQVNAKVIDGGD 117
                                       9.*********************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.37s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 750.75
//
Query:       gi|313125159|ref|YP_004035423.1|  [L=145]
Description: hypothetical protein Hbor_03800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 898.60
//
Query:       gi|313125160|ref|YP_004035424.1|  [L=159]
Description: hypothetical protein Hbor_03810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 882.53
//
Query:       gi|313125161|ref|YP_004035425.1|  [L=45]
Description: hypothetical protein Hbor_03820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.003   16.9   1.6       0.54    9.7   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0036   17.0   0.9       0.69    9.7   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
     0.0039   17.6   0.4       0.61   10.5   0.1    2.1  2  zf-IS66          zinc-finger binding domain of transposase IS
     0.0059   16.3   2.9       0.62    9.8   0.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
     0.0098   15.8   0.4      0.017   15.1   0.4    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.7   4.4      0.093   12.6   0.6    2.2  2  HalOD2           Halobacterial output domain 2
      0.011   15.3   1.0       0.15   11.7   0.1    2.0  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.013   14.8   0.3      0.024   14.0   0.3    1.4  1  zf-TFIIB         Transcription factor zinc-finger
      0.015   15.6   0.1      0.016   15.6   0.1    1.0  1  DUF3268          zinc-finger-containing domain
      0.015   15.3   2.4       0.29   11.2   0.3    2.1  2  YhfH             YhfH-like protein
      0.016   15.1   0.7        2.3    8.2   0.0    2.1  2  Nudix_N_2        Nudix N-terminal
      0.018   14.9   0.9       0.63    9.9   0.1    2.1  2  VATC             Vms1-associating treble clef domain
      0.019   15.0   0.4      0.033   14.2   0.4    1.4  1  DZR              Double zinc ribbon
      0.035   14.2   1.0       0.14   12.3   1.0    1.8  1  Zn-ribbon_8      Zinc ribbon domain
       0.11   12.1   1.5          3    7.5   0.0    2.1  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
       0.15   12.1   0.5       0.21   11.6   0.0    1.4  2  Pox_A3L          Poxvirus A3L Protein
       0.22   11.5   1.5        4.7    7.3   0.2    2.1  2  ADK_lid          Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.2    0.0048       5.1      18      26 .]       3      11 ..       1      11 [. 0.86
   2 !    9.7   0.1   0.00052      0.54       4      12 ..      30      38 ..      29      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0048
                       zf-ribbon_3 18 vCpyCGtkl 26
                                      +C+ CG++l
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAEL 11
                                      7*****986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00052
                       zf-ribbon_3  4 rCPnCGapl 12
                                      +C++CGa+l
  gi|313125161|ref|YP_004035425.1| 30 ECNQCGAIL 38
                                      6******65 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00065      0.69       2       9 ..       4      11 ..       3      14 .. 0.85
   2 !    6.5   0.1    0.0067       7.1      16      21 ..      31      36 ..      16      38 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00065
                     zinc_ribbon_2  2 CpnCGael 9 
                                      C+ CGael
  gi|313125161|ref|YP_004035425.1|  4 CTDCGAEL 11
                                      99999997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0067
                     zinc_ribbon_2 16 CpyCGt 21
                                      C +CG+
  gi|313125161|ref|YP_004035425.1| 31 CNQCGA 36
                                      777776 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00058      0.61       3      22 ..       3      22 ..       2      25 .. 0.70
   2 ?    5.9   0.0     0.016        17       4      15 ..      31      44 ..      26      45 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00058
                           zf-IS66  3 tCpcCGg.llkpigedrvree 22
                                      +C +CG+ l   i+ d ++ +
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAeLIEVIESD-TSAK 22
                                      7******555555555.8765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                           zf-IS66  4 CpcCGg.l.lkpig 15
                                      C +CG+ l +++ig
  gi|313125161|ref|YP_004035425.1| 31 CNQCGAiLgVTRIG 44
                                      99999888777776 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.2    0.0042       4.4      14      22 ..       1       9 [.       1      10 [. 0.82
   2 !    9.8   0.2   0.00059      0.62       1       8 [.      29      36 ..      25      37 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0042
                      Rubredoxin_2 14 fGrCpsCgs 22
                                      +G+C +Cg+
  gi|313125161|ref|YP_004035425.1|  1 MGHCTDCGA 9 
                                      699999986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00059
                      Rubredoxin_2  1 YvCsqCGf 8 
                                      ++C+qCG+
  gi|313125161|ref|YP_004035425.1| 29 WECNQCGA 36
                                      56777775 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   1.6e-05     0.017      21      44 ..       4      35 ..       2      36 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                     Zn_Tnp_IS1595 21 CPhCgsr..kayrikt......rglfqCkeCr 44
                                      C  Cg +  ++++  t      +++++C+ C+
  gi|313125161|ref|YP_004035425.1|  4 CTDCGAEliEVIESDTsakfsdARVWECNQCG 35
                                      8899988666666666888888*********8 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.015        16      33      41 ..       3      11 ..       1      25 [. 0.80
   2 ?   12.6   0.6   8.8e-05     0.093      29      41 ..      26      38 ..      22      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                            HalOD2 33 kCtrCGevq 41
                                      +Ct CG+ +
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAEL 11
                                      699999865 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.8e-05
                            HalOD2 29 ayvWkCtrCGevq 41
                                      a vW C +CG+++
  gi|313125161|ref|YP_004035425.1| 26 ARVWECNQCGAIL 38
                                      78********987 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.091        96       9      20 ..       4      16 ..       3      19 .. 0.72
   2 ?   11.7   0.1   0.00014      0.15       5      22 ..      27      44 ..      24      45 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.091
                                      -TTT--.EEEECC CS
                   Desulfoferrod_N  9 CevCGn.iVeVle 20
                                      C+ CG   +eV+e
  gi|313125161|ref|YP_004035425.1|  4 CTDCGAeLIEVIE 16
                                      999**61467766 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                                      -EEE-TTT--EEEECC-- CS
                   Desulfoferrod_N  5 evYkCevCGniVeVleaG 22
                                       v+ C+ CG i  V+  G
  gi|313125161|ref|YP_004035425.1| 27 RVWECNQCGAILGVTRIG 44
                                      5999********999877 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.3e-05     0.024       1      26 [.       3      35 ..       3      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                          zf-TFIIB  1 kCPkCqdele.......eserggveidyCpqCr 26
                                      +C  C++el         +++++  ++ C+qC+
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAELIeviesdtSAKFSDARVWECNQCG 35
                                      7*******9978877766666***********7 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   1.5e-05     0.016       4      43 ..       3      41 ..       1      44 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                           DUF3268  4 rCpyCGekvilvsaseiYkerskgkllylCpkCdayvgvh 43
                                      +C+ CG++ i v +s+   ++  ++ ++ C++C+a  gv 
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAELIEVIESDTS-AKFSDARVWECNQCGAILGVT 41
                                      69********99999998.7778889**********9996 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00027      0.29      15      29 ..       3      17 ..       1      19 [. 0.90
   2 ?    4.3   0.1     0.037        39      15      21 ..      30      36 ..      28      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                              YhfH 15 kCteCGkeieEqaec 29
                                       Ct+CG e+ E  e+
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAELIEVIES 17
                                      6********999887 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.037
                              YhfH 15 kCteCGk 21
                                      +C +CG 
  gi|313125161|ref|YP_004035425.1| 30 ECNQCGA 36
                                      7999995 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0022       2.3       2      15 ..       3      16 ..       3      21 .. 0.80
   2 ?    5.7   0.1     0.013        14       3      31 ..      31      37 ..      29      43 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0022
                                      B-TTT--B-EEE-- CS
                         Nudix_N_2  2 FCsqCGtpvelrip 15
                                      +C+ CG+++   i+
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAELIEVIE 16
                                      7******9987775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                                      -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                      C+qCG+                      i
  gi|313125161|ref|YP_004035425.1| 31 CNQCGA----------------------I 37
                                      566664......................4 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.041        43       5      15 ..       3      13 ..       1      18 [. 0.85
   2 ?    9.9   0.1   0.00059      0.63       2      11 ..      27      36 ..      26      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.041
                              VATC  5 rCsiCgesleg 15
                                      +C  Cg++l +
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAELIE 13
                                      8******9987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00059
                              VATC  2 nvlrCsiCge 11
                                      +v++C++Cg+
  gi|313125161|ref|YP_004035425.1| 27 RVWECNQCGA 36
                                      79******98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   3.1e-05     0.033      14      37 ..       3      37 ..       2      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                               DZR 14 fCseCgtklkavaa...........edrCpsCgek 37
                                       C +Cg++l +v +              C +Cg+ 
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAELIEVIEsdtsakfsdarVWECNQCGAI 37
                                      5*******999888999*****999999****986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.0   0.00014      0.14       7      35 ..       3      39 ..       3      43 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                       Zn-ribbon_8  7 rCeeCghefe......vlqsisdapltaCPeCgs..e 35
                                      +C++Cg e          +++sda   +C +Cg+   
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAELIeviesdTSAKFSDARVWECNQCGAilG 39
                                      6*****9877455554445555554555*****8655 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.043        45      13      18 ..       4       9 ..       2      10 .. 0.86
   2 ?    7.5   0.0    0.0028         3       9      21 ..      27      39 ..      23      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.043
                           zf-tcix 13 CpkCGt 18
                                      C+ CG+
  gi|313125161|ref|YP_004035425.1|  4 CTDCGA 9 
                                      *****8 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                           zf-tcix  9 GvrkCpkCGtyNG 21
                                      +v  C +CG++ G
  gi|313125161|ref|YP_004035425.1| 27 RVWECNQCGAILG 39
                                      6778******976 PP

>> Pox_A3L  Poxvirus A3L Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.21      11      28 ..       3      20 ..       2      24 .. 0.91
   2 ?   -2.4   0.1       4.6   4.9e+03      11      16 ..      30      35 ..      26      38 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                           Pox_A3L 11 rCskCaanlveylkeDre 28
                                      +C+ C a+l+e++++D  
  gi|313125161|ref|YP_004035425.1|  3 HCTDCGAELIEVIESDTS 20
                                      6***************75 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.6
                           Pox_A3L 11 rCskCa 16
                                       C +C 
  gi|313125161|ref|YP_004035425.1| 30 ECNQCG 35
                                      588885 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0044       4.7      22      32 ..       2      12 ..       1      13 [. 0.89
   2 ?    3.8   0.1     0.054        57       2      10 ..      29      37 ..      29      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0044
                                      TB-TTT--.-B CS
                           ADK_lid 22 glCDkCGepLv 32
                                      g C +CG +L+
  gi|313125161|ref|YP_004035425.1|  2 GHCTDCGAELI 12
                                      68********8 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.054
                                      EE-TTT--E CS
                           ADK_lid  2 rvCpkCGrs 10
                                      + C +CG++
  gi|313125161|ref|YP_004035425.1| 29 WECNQCGAI 37
                                      569999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 259.40
//
Query:       gi|313125162|ref|YP_004035426.1|  [L=419]
Description: dhd superfamily phosphohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.4   1.8       0.03   14.7   0.5    2.1  2  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.73   1.3e+04     125     137 ..      37      49 ..      33      63 .. 0.63
   2 ?   14.7   0.5   1.7e-06      0.03      10     134 ..     262     370 ..     253     374 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.73
                                       CHHHHHHHHHHHH CS
                             DHHA1 125 ekleealealeea 137
                                       e+++ea+e++e++
  gi|313125162|ref|YP_004035426.1|  37 ERVKEAVEDAEAV 49 
                                       4455555555543 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHCHHHHHHHHHHHHHHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEE CS
                             DHHA1  10 elekeleelkealaklkaeellekaeevk.gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvk 84 
                                       e+ ++  el++ +++++++++l++ae  + g  ++ +    ++ +    ++a+ l++   + + +++v+k      +
  gi|313125162|ref|YP_004035426.1| 262 EIVEQFIELRRVEKQQLIDAALDRAEIKQvGPWTVGV----TYGRCSQNEVAEGLRE---RgADAAVVVKPA---GS 328
                                       5555556677777777777777776544442211111....2222233556666666...447777777654...47 PP

                                       EEEEESSHSS.-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHH CS
                             DHHA1  85 vsarskkdgv.dagelakeaaaklgggGGGHdlAaGagipaekleealeal 134
                                        s+r ++ g+  a e+a +       +GGGH+ AaG + +   ++++l+ +
  gi|313125162|ref|YP_004035426.1| 329 ASIRGSD-GFeRAHEVAGQ------VNGGGHPKAAGCKPD--IYDDMLDYA 370
                                       7777777.662477*****......************997..566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.37s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 2233.66
//
Query:       gi|313125163|ref|YP_004035427.1|  [L=154]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-35  121.8   3.7    3.3e-35  121.6   3.7    1.0  1  Usp             Universal stress protein family
     0.0027   17.7   0.1     0.0036   17.3   0.1    1.1  1  DNA_photolyase  DNA photolyase
  ------ inclusion threshold ------
      0.049   12.8   0.3      0.066   12.4   0.3    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.054   13.7   0.3       0.16   12.2   0.4    1.7  2  FliG_C          FliG C-terminal domain
      0.086   13.3   0.8       0.49   10.8   0.3    1.9  2  DUF3280         Protein of unknown function (DUF2380)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6   3.7   9.2e-39   3.3e-35       1     141 []       1     137 [.       1     137 [. 0.98

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 9.2e-39
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m+++I+Va+Dgse+ ++A++ Al+la ++ga +++l+v+d+++ +++++  +++ +e+l ++++++      + +ea
  gi|313125163|ref|YP_004035427.1|   1 MFDTIVVATDGSESVRRAVDVALDLADRFGASVHALYVVDASEVDSSPERLRDEMREALTERGQRALS----EVEEA 73 
                                       99**************************************************************9985....68*** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        + +v++ v+eg pa++  ++a+e dad++ +G+rgr+g  r+l+GSv+e+v+r +p+pVl Vr
  gi|313125163|ref|YP_004035427.1|  74 TDRSVTTAVREGRPATVVGDYAREVDADMVAMGTRGRHGENRFLIGSVAERVVRTCPVPVLTVR 137
                                       *************************************************************998 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1     1e-06    0.0036      16      95 ..      22     106 ..      13     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1e-06
                                       HHHHHHCTTSEEEEEEEE-HH..HHTCG...S-CHHHHHHHHHHHHHHHH..HHHHTT--EEEEESSHHHHHHHHHH CS
                    DNA_photolyase  16 ALaaAaasgepvipvfvldpe..kahkl...rvgaarvdfllesLadLde..eLrelgirLvvrrgdpadvlpelak 85 
                                       AL  A + g++v++++v+d +  +  ++        r +++ ++ ++L e  e  ++ ++  vr+g+pa+v+ ++a+
  gi|313125163|ref|YP_004035427.1|  22 ALDLADRFGASVHALYVVDASevD--SSperLRDEMREALTERGQRALSEveEATDRSVTTAVREGRPATVVGDYAR 96 
                                       889999999************442..33554333444445555666665322557899******************* PP

                                       HCTECEEEEE CS
                    DNA_photolyase  86 elgasavvan 95 
                                       e++a+ v + 
  gi|313125163|ref|YP_004035427.1|  97 EVDADMVAMG 106
                                       ****999765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.8e-05     0.066     155     238 ..      19     111 ..      17     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHH.T-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTT......EEEEESCEEEEEEETTEEEEEEETTS CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 155 vElAaalakl.gkevtlveardrll.raldkelsaaleealekeG......vevklgtsvkeidgngeklevvledg 223
                                       v++A  la+  g+ v+ ++  d     + +++l+++++eal+++G      ve  +  sv+++ ++g+ ++vv +  
  gi|313125163|ref|YP_004035427.1|  19 VDVALDLADRfGASVHALYVVDASEvDSSPERLRDEMREALTERGqralseVEEATDRSVTTAVREGRPATVVGDYA 95 
                                       67777755444888887777766666899999999999999999944444455555666666665555666888889 PP

                                       CEEEESEEEE-S.-EE CS
                                       xxxxxxxxxxxx.xxx RF
                       Pyr_redox_2 224 eeidadlvvvav.Gvr 238
                                       +e+dad+v +++ G+ 
  gi|313125163|ref|YP_004035427.1|  96 REVDADMVAMGTrGRH 111
                                       99*****988876655 PP

>> FliG_C  FliG C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   4.5e-05      0.16      64      97 ..      48      81 ..      44      86 .. 0.88
   2 ?   -3.2   0.0       2.7   9.6e+03      36      47 ..      95     106 ..      89     116 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                                      -HHHHHHHHHHHHHC-S--HHHHHHHHHHHHHHH CS
                            FliG_C 64 Skraaemlreelealgpvrlsdveeaqkeivaii 97
                                      ++r ++++re l ++g+  ls+veea+++ v+++
  gi|313125163|ref|YP_004035427.1| 48 PERLRDEMREALTERGQRALSEVEEATDRSVTTA 81
                                      799***********************99877776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.7
                                       HTTS-HHHHHHH CS
                            FliG_C  36 lrevdkedLala 47 
                                        revd++ +a+ 
  gi|313125163|ref|YP_004035427.1|  95 AREVDADMVAMG 106
                                       566666666654 PP

>> DUF3280  Protein of unknown function (DUF2380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.18   6.4e+02      61      87 ..      13      39 ..       5      44 .. 0.78
   2 ?   10.8   0.3   0.00014      0.49      29      86 ..      49     107 ..      41     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.18
                           DUF3280 61 snlrkCngceadiArklgAdlvlvgev 87
                                      + +r+  + + d+A + gA++ ++ +v
  gi|313125163|ref|YP_004035427.1| 13 ESVRRAVDVALDLADRFGASVHALYVV 39
                                      447778888999999999999888777 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00014
                           DUF3280  29 aavteqlreaLaesgryevvdlapaaaeie.kesnlrkCngceadiArklgAdlvlvge 86 
                                       +++++++reaL+e+g+ ++ ++++a+++   ++    +      d+Ar+++Ad+v++g+
  gi|313125163|ref|YP_004035427.1|  49 ERLRDEMREALTERGQRALSEVEEATDRSVtTAVREGRPATVVGDYAREVDADMVAMGT 107
                                       6789***********9999999888886653333356677778899*********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 881.72
//
Query:       gi|313125164|ref|YP_004035428.1|  [L=152]
Description: universal stress family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-14   55.0   6.4    1.6e-14   54.6   6.4    1.1  1  Usp           Universal stress protein family
     0.0097   15.4   0.4        0.9    8.9   0.3    2.0  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   6.4   1.8e-18   1.6e-14       5     139 ..      12     151 ..      10     152 .] 0.94

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.8e-18
                                       EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.....HHHHHH CS
                               Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.....akaaae 76 
                                       +lV+vD sees +A+e+A++ a++++a+++++hv+  +   a  +++ + e+  +++++ ++ a +     + ++a 
  gi|313125164|ref|YP_004035428.1|  12 VLVPVDRSEESANAVEHAAAIAAEYDAAVHAVHVLGGDVVRAIETGAVDDEDVVADSTAIQETAGEiaaryDVELAT 88 
                                       8**********************************999999999999999998888888888888888899999999 PP

                                       CTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  77 aggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                              ++ +  +p+ + l++aee++ad +Vv +   sg  + +l   +eyvl  a+ pVl 
  gi|313125164|ref|YP_004035428.1|  89 SVAYGFSTKMKLRHPGSVVLDTAEELGADFVVVPREPVSGDPGEVLAKAAEYVLLYASQPVLS 151
                                       9999*********************************9999999*****************95 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.3    0.0001       0.9      65     128 ..      19      87 ..       3      97 .. 0.85
   2 !    4.6   0.0    0.0021        19      76     101 ..     108     129 ..     105     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHHHHHHHTBSEEEEEBCC.....GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEE CS
                      AP_endonuc_2  65 reesvdalkraielaaaLGapllvlhpGt.....agagpkgseeeawerlaeslneladyaekegvkla 128
                                       +ees +a+++a+ +aa+ +a +  +h+ +     a   +  ++e+ ++   +  + ++++a++++v+la
  gi|313125164|ref|YP_004035428.1|  19 SEESANAVEHAAAIAAEYDAAVHAVHVLGgdvvrAIETGAVDDEDVVADSTAIQETAGEIAARYDVELA 87 
                                       4678999***********999999998888899988889999999999999999************998 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0021
                                       HHHHHHHTBSEEEEEBCCGBCTTTSG CS
                      AP_endonuc_2  76 ielaaaLGapllvlhpGtagagpkgs 101
                                       +++a++LGa+++v++      + +g+
  gi|313125164|ref|YP_004035428.1| 108 LDTAEELGADFVVVP----REPVSGD 129
                                       79***********98....3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.63
# Mc/sec: 729.10
//
Query:       gi|313125165|ref|YP_004035429.1|  [L=181]
Description: acetyltransferase (gnat) family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-16   59.6   0.0    4.1e-16   59.3   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.6e-12   46.8   0.0    3.5e-12   46.4   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.5e-09   36.6   0.0    6.7e-09   36.1   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    8.6e-07   28.8   0.0    1.3e-06   28.3   0.0    1.2  1  FR47             FR47-like protein
    1.3e-05   25.9   0.0    1.6e-05   25.6   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0073   16.5   0.1       0.01   16.0   0.1    1.1  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.04   14.0   0.0        2.3    8.3   0.0    2.2  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.085   13.0   0.0       0.12   12.5   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
       0.12   12.0   0.0       0.15   11.6   0.0    1.1  1  GNAT_acetyltran  GNAT acetyltransferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   2.1e-19   4.1e-16      18     117 .]      66     160 ..      40     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.1e-19
                                       HHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
                    Acetyltransf_1  18 daseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegi 94 
                                       ++  +++ +    e++  ++a +++  +G+++l +++d     ay   ++V  ey+  G+G++L++ l+ +  e+ +
  gi|313125165|ref|YP_004035429.1|  66 ERRIRDWLDNILAEECLNVIAWDGDDAAGHATLVPDDD-----AYELAIFVLQEYQEAGIGTLLIKSLLGHGAENSV 137
                                       22222244445555556666888899************.....********************************** PP

                                       SEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  95 kkivlaveedndaairlYeklGF 117
                                       kk++l+ve +n++a++lY+k GF
  gi|313125165|ref|YP_004035429.1| 138 KKVWLTVERWNRPAVGLYKKIGF 160
                                       ******************88**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   1.8e-15   3.5e-12      25     114 ..      75     168 ..      56     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.8e-15
                   Acetyltransf_10  25 rieegealllvaeeggkivGviel.rdgshisll.fVdpeyrgqGigkaLleaveee.aekdgikl.eltvnasp.y 96 
                                        i ++e+l ++a +g+  +G+++l  d++  +l  fV +ey+  Gig+ L++ ++ + a ++  k+  ltv+  +  
  gi|313125165|ref|YP_004035429.1|  75 NILAEECLNVIAWDGDDAAGHATLvPDDDAYELAiFVLQEYQEAGIGTLLIKSLLGHgA-ENSVKKvWLTVERWNrP 150
                                       344999*****************999999777756**********************55.6667777******999* PP

                   Acetyltransf_10  97 avpfYeklGFkavgeeqe 114
                                       av++Y+k+GF++ ++e  
  gi|313125165|ref|YP_004035429.1| 151 AVGLYKKIGFETSNSESF 168
                                       ************977654 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   3.3e-12   6.7e-09       7      75 ..      85     161 ..      75     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.3e-12
                                       EEEETTEEEEEEEEEEES.TCTEEEEE-GGGTTSSHHHHHHH.HTT.SEEE.EE.EEEE..THH...HHHHHHHHTT CS
                    Acetyltransf_7   7 VaeddgkivGfialslld.aeitrlaVdpeyrgkGiGraLle.aae.kgii.le.qlel..nae...kaikfYeklG 73 
                                       +a d++   G + l+++d a++  ++V++ey+  GiG+ L++ +   +g +  + +++l  + +   +a+++Y+k G
  gi|313125165|ref|YP_004035429.1|  85 IAWDGDDAAGHATLVPDDdAYELAIFVLQEYQEAGIGTLLIKsL-LgHGAEnSVkKVWLtvE-RwnrPAVGLYKKIG 159
                                       577778888999999999888888******************42.23332221233455321.13359********* PP

                                       EE CS
                    Acetyltransf_7  74 Fe 75 
                                       Fe
  gi|313125165|ref|YP_004035429.1| 160 FE 161
                                       *8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   6.3e-10   1.3e-06      25      81 ..     107     164 ..      88     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 6.3e-10
                                       EEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEEE CS
                              FR47  25 galqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfekie 81 
                                        a+ vl+e +  G g++l+k+l  + ae   k+v l v   N p+  ly+k+Gfe  +
  gi|313125165|ref|YP_004035429.1| 107 LAIFVLQEYQEAGIGTLLIKSLLGHGAEnSVKKVWLTVERWNRPAVGLYKKIGFETSN 164
                                       6899*******************999997899**********************9875 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   7.9e-09   1.6e-05      26     138 .]      57     161 ..      29     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.9e-09
                    Acetyltransf_3  26 ry.lpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateav 101
                                       r+ + +p  +   ++wl++++ae    e +  +i   ++++ G + l + ++     el + + ++++  G++t   
  gi|313125165|ref|YP_004035429.1|  57 RAqGIPPGQERRIRDWLDNILAE----E-CLNVIAWDGDDAAGHATLVPDDDA---YELAIFVLQEYQEAGIGTLLI 125
                                       33222356677789999988775....3.444554566668****99965555...9******************** PP

                    Acetyltransf_3 102 ralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       ++ll +  e+  +++++ +++  N+  + +++k+Gfe
  gi|313125165|ref|YP_004035429.1| 126 KSLLGHGAENS-VKKVWLTVERWNRPAVGLYKKIGFE 161
                                       *******7777.************************7 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   5.1e-06      0.01      26     131 ..      37     140 ..      22     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.1e-06
                    Acetyltransf_6  26 tdpedleal...lelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgdrlyywl 99 
                                        ++e++e l   +++f    +++     +p +++ +rd l+   a++ l + +   dg  +A++++l+ +d +y + 
  gi|313125165|ref|YP_004035429.1|  37 GSDEEFESLvsmYDAFDPADRAQ---GIPPGQERRIRDWLDNILAEECLNVIA--WDGDDAAGHATLVPDDDAYELA 108
                                       35555555411155554444444...335777778888888887777755555..577789**************** PP

                    Acetyltransf_6 100 ggydpelaklspgllllweliedaaeeGlrrf 131
                                       + +  e+ + ++g+ll+  l+ + ae+ ++++
  gi|313125165|ref|YP_004035429.1| 109 IFVLQEYQEAGIGTLLIKSLLGHGAENSVKKV 140
                                       **************************999876 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0012       2.3      26      61 ..      57     100 ..      32     102 .. 0.76
   2 ?    3.7   0.0      0.03        59      79     127 ..     109     162 ..     104     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                                       -H.........HHHHHHHHHHTTS.EEEEEEETTEEEEEEEEEE CS
                    Acetyltransf_9  26 spl......e.eireyfrkllees.rvlgaedngelvgqlallp 61 
                                       +++      e +ir +++++l e+   ++a+d+++ +g+++l+p
  gi|313125165|ref|YP_004035429.1|  57 RAQgippgqErRIRDWLDNILAEEcLNVIAWDGDDAAGHATLVP 100
                                       3334444556699******99975499************99987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.03
                                       EEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  79 VavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                       + v  e++  g+ + L++ +l++ +e+ ++ ++l+       ++++Y++ G+e+
  gi|313125165|ref|YP_004035429.1| 109 IFVLQEYQEAGIGTLLIKSLLGHGAENSVKKVWLTVerwnrPAVGLYKKIGFET 162
                                       567899**********************99999999877554579999999986 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.2e-05      0.12      40     136 ..      72     162 ..      64     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                    Acetyltransf_4  40 flealdsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienlla 116
                                       +l+++ +e++    + + d+ +G a+l+ +     d + el +++  +  +++g+g  li++l    +e+++++   
  gi|313125165|ref|YP_004035429.1|  72 WLDNILAEECLNVIAWDGDDAAGHATLV-P----DDDAYELAIFVL-QEYQEAGIGTLLIKSLLGHGAENSVKKVWL 142
                                       5555534444444444477788888888.3....34799******8.78***************999********** PP

                    Acetyltransf_4 117 eiaspnensiqfhkalGFel 136
                                        +   n +++ ++k++GFe 
  gi|313125165|ref|YP_004035429.1| 143 TVERWNRPAVGLYKKIGFET 162
                                       **999*************97 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.5e-05      0.15     169     237 ..      92     163 ..      83     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.5e-05
                   GNAT_acetyltran 169 vsgasSysvyekgieieidTkedyrrkgLAtivaaalileclkrglyPsWDaa...neaSvaLaekLGYefe 237
                                        +g  + +  ++++e  i   ++y++ g  t++ ++l+ +  ++++   W +    n+++v L++k+G+e +
  gi|313125165|ref|YP_004035429.1|  92 AAGHATLVPDDDAYELAIFVLQEYQEAGIGTLLIKSLLGHGAENSVKKVWLTVerwNRPAVGLYKKIGFETS 163
                                       56666666677889999*********************************99999**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1045.47
//
Query:       gi|313125166|ref|YP_004035430.1|  [L=122]
Description: universal stress family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.9e-14   52.6   2.3    7.2e-12   46.0   2.3    2.0  1  Usp          Universal stress protein family
     0.0017   17.9   0.0      0.003   17.2   0.0    1.4  1  DAGK_cat     Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.071   11.9   0.0      0.084   11.6   0.0    1.1  1  Pneumo_ncap  Pneumovirus nucleocapsid protein
       0.12   13.0   0.2       0.16   12.6   0.2    1.1  1  PIG-L        GlcNAc-PI de-N-acetylase


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   2.3   1.6e-15   7.2e-12       4     141 .]       2     122 .]       1     122 [] 0.87

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.6e-15
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       ++l++v gs++s +A+++ ++ a+a g++l+++ v  p ++ ++ +  e ++e   e                 +gv
  gi|313125166|ref|YP_004035430.1|   2 KVLLGVGGSDDSIRAVKQTVARAAAAGDDLTVAVVENPASDRSREEITEIVREILDE-----------------EGV 61 
                                       89***************************8888887777666665555555555444.................466 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       + ev  +egdp+  ++++ae+e+ d iV+G    s   ++ +GS +e vl ++++ V +Vr
  gi|313125166|ref|YP_004035430.1|  62 EAEVRHLEGDPGSQLVDTAESENFDEIVLGGGETSPMGKINIGSIAEFVLLNSHVTVSLVR 122
                                       678999***************************************************9998 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.7e-07     0.003       2      64 ..      33      93 ..      32      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.7e-07
                                      EEEEE-TTCTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEES CS
                          DAGK_cat  2 llvivNpksGkgkgekllrkvrelleeagvelelieteepgdakelakeakeegvdlivvaGG 64
                                      + v+ Np s  ++ e++ + vre+l e+gve+e+++ e  + + +l+ +a++e++d iv  GG
  gi|313125166|ref|YP_004035430.1| 33 VAVVENPAS-DRSREEITEIVREILDEEGVEAEVRHLE-GDPGSQLVDTAESENFDEIVLGGG 93
                                      668889988.57777788*******************9.77899*****************99 PP

>> Pneumo_ncap  Pneumovirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.9e-05     0.084     284     328 ..      47      92 ..      34     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.9e-05
                       Pneumo_ncap 284 qvve.vyelvrklGgeaGllhllqspkasllslaqfpnfasvvlGn 328
                                       +++e v e+  + G ea + hl  +p + l+  a+  nf  +vlG 
  gi|313125166|ref|YP_004035430.1|  47 EITEiVREILDEEGVEAEVRHLEGDPGSQLVDTAESENFDEIVLGG 92 
                                       455524577788899*****************************85 PP

>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   3.5e-05      0.16       8      67 ..      11      69 ..      10      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                                      THHHHHHHHHHHHHHHTT-EEEEEECE--TT---STTTTHH-HHHHHHHHHHHHH.HHHCT CS
                             PIG-L  8 DDellfaggtiaklvaagvevkivcltaGdagsplatleekeelaeiRekEaraa.akhlg 67
                                      DD + ++++t+a+++aag ++ + ++ +   ++++ + +  e + ei  +E+ +a ++hl+
  gi|313125166|ref|YP_004035430.1| 11 DDSIRAVKQTVARAAAAGDDLTVAVVENPASDRSREEIT--EIVREILDEEGVEAeVRHLE 69
                                      9**************************966664444433..57889999999999888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 692.42
//
Query:       gi|313125167|ref|YP_004035431.1|  [L=277]
Description: hypothetical protein Hbor_03880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1497.82
//
Query:       gi|313125168|ref|YP_004035432.1|  [L=182]
Description: hypothetical protein Hbor_03890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.36s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1021.07
//
Query:       gi|313125169|ref|YP_004035433.1|  [L=817]
Description: oligopeptide/dipeptide ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-57  192.6   0.0    2.1e-29  102.8   0.0    2.4  2  ABC_tran         ABC transporter
    1.6e-40  137.4   0.9    4.5e-21   75.1   0.1    2.5  2  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    4.6e-11   43.1   3.9    1.1e-05   25.4   0.0    3.8  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.3e-06   27.2   0.1      0.086   12.3   0.0    3.6  3  SMC_N            RecF/RecN/SMC N terminal domain
    1.5e-05   25.3   2.9      0.023   15.0   0.2    3.7  3  AAA_22           AAA domain
      2e-05   25.0   0.1      0.043   14.2   0.0    2.9  2  AAA_16           AAA ATPase domain
     0.0001   22.0   1.3       0.21   11.3   0.1    2.3  2  AAA_29           P-loop containing region of AAA domain
     0.0006   19.8   0.2       0.77    9.8   0.1    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0048   16.4   0.3        3.5    7.1   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.013   15.1   0.7        8.1    6.0   0.0    4.0  4  AAA_25           AAA domain
      0.027   14.4   0.5        2.3    8.1   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
      0.033   13.5   3.6       0.22   10.8   0.1    2.3  2  AIG1             AIG1 family
      0.033   13.8   0.1        1.1    8.9   0.0    2.6  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.04   13.6   0.5         10    5.8   0.0    3.2  3  AAA_30           AAA domain
      0.046   14.1   0.8       0.87   10.0   0.0    3.3  3  AAA              ATPase family associated with various cellul
       0.08   12.7   0.4       0.74    9.5   0.0    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
       0.17   11.6   0.0        8.4    6.1   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
       0.29   10.8   1.5         34    4.1   0.1    3.1  3  Sigma54_activat  Sigma-54 interaction domain
       0.37   10.1   1.1         23    4.2   0.1    2.5  2  ATPase           KaiC
       0.75    9.2   2.2        4.3    6.7   0.0    3.0  4  TniB             Bacterial TniB protein
        1.1    8.4   3.0        8.5    5.5   0.1    2.2  2  NB-ARC           NB-ARC domain
        1.4    8.4   4.3         13    5.3   0.2    2.4  2  Hpr_kinase_C     HPr Serine kinase C-terminal domain
        1.7    8.7   3.8         18    5.3   0.1    2.8  3  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   1.3e-27   9.9e-25       2     136 ..      24     224 ..      23     225 .. 0.88
   2 !  102.8   0.0   2.7e-32   2.1e-29       2     136 ..     418     577 ..     417     578 .. 0.91

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 1.3e-27
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.............................EETTCEG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGei.............................lldgkdl 49 
                                       + v+l++ ege+v++vGe+G+GKS  +   +gl++ + G+i                             ++d    
  gi|313125169|ref|YP_004035433.1|  24 DGVDLEIDEGETVGLVGESGSGKSVTALSTMGLVD-DPGHIvggevtltspelatqlreeygapsfvdgdEID---- 95 
                                       789******************************98.6888888888999999999999999999965444444.... PP

                                       GG......B-HHHCCHCEEEE-SS..--S-TTSBHHHH....................................HHH CS
                                       xx......xxxxxxxxxxxxxxxx..xxxxxxxxxxxx....................................xxx RF
                          ABC_tran  50 ke......qeleslrkeigvlpqe..pqlfpeltvren....................................esd 82 
                                                 +++   e+++++q+  ++l+p ltv+e+                                    +  
  gi|313125169|ref|YP_004035433.1|  96 -LtaapeeALRSVRGGEMSMIFQDpmTSLNPALTVGEQvseslrlhqyggrkkdtwlnavrevlpkiggqeldeQVV 171
                                       .344554466677789********999******************************99999999999996665555 PP

                                       TCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  83 eeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       e++ ++ls++g++e ++++v++ p+++SgG++qrv +a al+++pkll++DEpt
  gi|313125169|ref|YP_004035433.1| 172 ERAVEVLSEVGIPE-PTSRVDEYPHEFSGGMRQRVLIAIALACRPKLLIADEPT 224
                                       55999********9.99999*********************************9 PP

  == domain 2  score: 102.8 bits;  conditional E-value: 2.7e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + v+l+++ege++++vGe+G+GKSt  +++++ll+ teG++ ++g+dl+e   ++l++ r+ +++++q+  ++l+p+
  gi|313125169|ref|YP_004035433.1| 418 DGVDLSVYEGETLGLVGESGCGKSTTGETILQLLDATEGRVVFQGEDLTElggTDLRKKRRDLQMIFQDpmSSLDPR 494
                                       789******************************************************************999***** PP

                                       SBHHHH.......................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTS CS
                                       xxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.......................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkp 127
                                       +tv++                        ++++++ ++++ +gl+  + t   + p+++SgGq+qrv +aral+ +p
  gi|313125169|ref|YP_004035433.1| 495 MTVGQIiaeplqihdlpaeepgedqnrreQRRDRVVELMRAVGLEPGQRT---RYPHEMSGGQRQRVGIARALAVDP 568
                                       *****9****************9988655555557777777777774444...559********************* PP

                                       SEEEEESTT CS
                                       xxxxxxxxx RF
                          ABC_tran 128 kllllDEpt 136
                                       +++++DEp 
  gi|313125169|ref|YP_004035433.1| 569 DFIVADEPV 577
                                       ********7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.1   5.8e-24   4.5e-21       1      65 []     276     338 ..     276     338 .. 0.98
   2 !   60.7   0.1   1.9e-19   1.5e-16       1      62 [.     629     691 ..     629     693 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 5.8e-24
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+gp++++f +p HPYT aLl+s+p +d+e+   + i+g++p+l ++++GC Fa RCp a++eC
  gi|313125169|ref|YP_004035433.1| 276 VEEGPVEEIFANPSHPYTYALLESIPTEDKERL--TPIEGNVPDLIDMPTGCNFAARCPWATDEC 338
                                       8***************************98888..****************************** PP

  == domain 2  score: 60.7 bits;  conditional E-value: 1.9e-19
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfal 62 
                                       vE++ +++lf ep+HPYT+aLl+++p++d+  +     ++g++ps+ + ++GC F++RCp++ 
  gi|313125169|ref|YP_004035433.1| 629 VETAATDDLFAEPKHPYTQALLSAIPEPDPTAEtDRIILEGDVPSPIDPPSGCHFRTRCPQVI 691
                                       8*******************************96677889********************986 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4       2.5     2e+03       3      13 ..      37      47 ..      36      49 .. 0.91
   2 !   25.4   0.0   1.5e-08   1.1e-05     220     302 ..     180     260 ..     122     261 .. 0.79
   3 ?    5.2   0.0      0.02        16       3      30 ..     431     461 ..     430     498 .. 0.74
   4 !   11.6   0.0   0.00023      0.18     224     299 ..     537     610 ..     473     614 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.5
                            AAA_21  3 vliGpNgsGKS 13
                                      +l+G  gsGKS
  gi|313125169|ref|YP_004035433.1| 37 GLVGESGSGKS 47
                                      69********9 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.5e-08
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                        v + e++++ +  ++e+S G+++   ++ al+ ++   +ll+ DEp + L+  +++ +l+l++el++  g  v++ 
  gi|313125169|ref|YP_004035433.1| 180 EVGIPEPTSRVDEYPHEFSGGMRQRVLIAIALACRP---KLLIADEPTTALDVTIQAQILDLINELQDdLGMSVLMI 253
                                       56666788889999**********977777777766...89**************************99******** PP

                            AAA_21 296 THSplll 302
                                       TH+  ++
  gi|313125169|ref|YP_004035433.1| 254 THDLGVV 260
                                       **98776 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.02
                            AAA_21   3 vliGpNgsGKSnLLdaldllarl...drdve 30 
                                       +l+G  g+GKS+  +++  l ++   +  ++
  gi|313125169|ref|YP_004035433.1| 431 GLVGESGCGKSTTGETILQLLDAtegRVVFQ 461
                                       69***************99988766633333 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_21 224 lengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                         +++ + + ++e+S G+++  +++ al+ ++   ++++ DEp + L+ ++++ +l ll++l++  g   ++  H+ 
  gi|313125169|ref|YP_004035433.1| 537 GLEPGQRTRYPHEMSGGQRQRVGIARALAVDP---DFIVADEPVSALDVSVQAQILNLLEDLQDeFGLTYLFIAHDL 610
                                       45667788899999*******99999999999...9***********************999887666666666665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.36   2.8e+02      26      38 ..      35      47 ..      20      54 .. 0.76
   2 !    8.8   0.0    0.0013         1     136     208 ..     196     267 ..      91     276 .. 0.71
   3 !   12.3   0.0   0.00011     0.086      28     198 ..     431     609 ..     420     627 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.36
                                      EEEEEESTTSSHH CS
                                      xxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKs 38
                                         +vG+ GSGKs
  gi|313125169|ref|YP_004035433.1| 35 TVGLVGESGSGKS 47
                                      3459********9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-.SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka.dkl 208
                                       ++SgG ++ v +a+ +A   ++p+ l + De   aLD +  +++ +l++e +++  + +++i+++ +++++  d++
  gi|313125169|ref|YP_004035433.1| 196 EFSGGMRQRVLIAIALA---CRPK-LLIADEPTTALDVTIQAQILDLINELQDDlgMSVLMITHDLGVVAETcDRV 267
                                       78999777666666655...4555.7899**********************9996677888888877776652433 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00011
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTT.TTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.......SSSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakk.lrseklsdlihkskekasvkkaeveitfdnedkk.......lkiekee 96 
                                        +vG+ G+GKs   + il +L  ++ +  ++ e   dl     +  + k+ +++++f+++ ++        +i +e 
  gi|313125169|ref|YP_004035433.1| 431 GLVGESGCGKSTTGETILQLLDATEGRVvFQGE---DLTELGGTDLRKKRRDLQMIFQDPMSSldprmtvGQIIAEP 504
                                       589999999999999999999987775413444...44444556777788899999988888833333222222222 PP

                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                       ++i       +e     n++e ++  v el++ +g+++        ++SgG+++ v +a  +A+    p  + + De
  gi|313125169|ref|YP_004035433.1| 505 LQIHDLPA--EEPGEDQNRREQRRDRVVELMRAVGLEPGqrtryphEMSGGQRQRVGIARALAVD---P-DFIVADE 575
                                       33322222..22223459999999************9988999999*************999975...4.4999*** PP

                                       TTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                             SMC_N 167 idaaLDeknvkkvaellkekskn..aQfivislr 198
                                         +aLD +  +++ +ll+  +++    ++ i+++
  gi|313125169|ref|YP_004035433.1| 576 PVSALDVSVQAQILNLLEDLQDEfgLTYLFIAHD 609
                                       *****************99888733445555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0082       6.4      10      51 ..      38      74 ..      31     110 .. 0.73
   2 ?   -1.2   0.0       2.9   2.3e+03      84     125 ..     208     250 ..     167     258 .. 0.66
   3 !   15.0   0.2     3e-05     0.023      10     128 ..     432     606 ..     426     612 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0082
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsst 51
                                      ++GesG+GK++++   +   d        +p+ +   +vtl+s++
  gi|313125169|ref|YP_004035433.1| 38 LVGESGSGKSVTALSTMGLVD--------DPGHIvggEVTLTSPE 74
                                      79*********9977666664........4444445666666665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                            AAA_22  84 qalraravielliiDEaqh.lr...seealeeLrsllnlsrkgvql 125
                                         + a++  +lli DE    l+   ++++l  + +l++  + g+++
  gi|313125169|ref|YP_004035433.1| 208 AIALACRP-KLLIADEPTTaLDvtiQAQILDLINELQD--DLGMSV 250
                                       33445555.99999998887877555777777777777..444444 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 3e-05
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsstsskdllrellralglelka............ 70 
                                       ++GesG+GK+t+ +++l+ ld+       + +vv      t  ++t++++ +r+l  +++++ ++            
  gi|313125169|ref|YP_004035433.1| 432 LVGESGCGKSTTGETILQLLDAT------EGRVVfqgeDLTELGGTDLRKKRRDLQMIFQDPMSSldprmtvgqiia 502
                                       79******************864......333333433333333335555555555555555555444666666666 PP

                            AAA_22  71 ........................................erlsseellealeqalrarav................ 91 
                                                                               ++                                   
  gi|313125169|ref|YP_004035433.1| 503 eplqihdlpaeepgedqnrreqrrdrvvelmravglepgqRTR-----------------Yphemsggqrqrvgiar 562
                                       6666677777778887777666555555555555554333222.................02222222222223344 PP

                            AAA_22  92 .....ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                            + +++ DE    l+   ++++l+ L +l++  ++g++ +++
  gi|313125169|ref|YP_004035433.1| 563 alavdPDFIVADEPVSaLDvsvQAQILNLLEDLQD--EFGLTYLFI 606
                                       45778888888886666777444888888888888..777777666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0055       4.3      23      45 ..      32      54 ..      21     181 .. 0.81
   2 !   14.2   0.0   5.5e-05     0.043      25      63 ..     428     466 ..     420     602 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0055
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                      ++e v l+GesG+GKs  + + +
  gi|313125169|ref|YP_004035433.1| 32 EGETVGLVGESGSGKSVTALSTM 54
                                      568899**********9987766 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.5e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       e + l+GesG+GKs+  +++l+ l +++g ++ +  d  
  gi|313125169|ref|YP_004035433.1| 428 ETLGLVGESGCGKSTTGETILQLLDATEGRVVFQGEDLT 466
                                       66779****************988888666655554444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00028      0.21      12      37 ..      23      48 ..      21      54 .. 0.86
   2 !    9.2   0.1    0.0012      0.96      15      48 ..     420     453 ..     415     460 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKST 37
                                       dg ++eid+ +++ l+G+sGsGKS 
  gi|313125169|ref|YP_004035433.1| 23 VDGVDLEIDEGETVGLVGESGSGKSV 48
                                      577899999777999**********5 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                            AAA_29  15 htieidlkgatlltGpsGsGKSTllDAiqalLvp 48 
                                        ++++ + ++  l+G+sG GKST    i  lL +
  gi|313125169|ref|YP_004035433.1| 420 VDLSVYEGETLGLVGESGCGKSTTGETILQLLDA 453
                                       5555554446679**********76666666655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0061       4.7       4      57 ..      38      91 ..      35     105 .. 0.89
   2 !    9.8   0.1   0.00099      0.77       4      27 ..     432     456 ..     429     476 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0061
                                      EE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........- CS
                             AAA_5  4 LvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvds 57
                                      LvG++G+gKs  a +   ++ ++ ++v +   +t+ +l  +++ + g  s+vd+
  gi|313125169|ref|YP_004035433.1| 38 LVGESGSGKSVTALSTMGLVDDPGHIVGGEVTLTSPELATQLREEYGAPSFVDG 91
                                      9***********************999999999999999998877777777776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00099
                                       EE--SSSSHHHHHHHGGGGB.S--E CS
                             AAA_5   4 LvGppGtgKselaerlaaal.nrev 27 
                                       LvG++G+gKs+  e ++++l  +e 
  gi|313125169|ref|YP_004035433.1| 432 LVGESGCGKSTTGETILQLLdATEG 456
                                       9******************973333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0044       3.5      30      55 ..      30      55 ..      22      79 .. 0.84
   2 !    7.1   0.0    0.0046       3.6      29      60 ..     423     454 ..     414     461 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0044
                             AAA_7 30 lknkkpvllvGptGtGKtviikdllk 55
                                      ++++  v lvG++G+GK+v++ +++ 
  gi|313125169|ref|YP_004035433.1| 30 IDEGETVGLVGESGSGKSVTALSTMG 55
                                      67888999***********9988765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0046
                             AAA_7  29 llknkkpvllvGptGtGKtviikdllkkldke 60 
                                        + ++  + lvG++G+GK+++ +++l+ ld +
  gi|313125169|ref|YP_004035433.1| 423 SVYEGETLGLVGESGCGKSTTGETILQLLDAT 454
                                       5666777889************9999998855 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0      0.01       8.1      30      53 ..      30      53 ..      10      57 .. 0.90
   2 ?   -1.1   0.0       1.6   1.2e+03     166     188 ..     233     255 ..     217     256 .. 0.86
   3 ?    2.6   0.0      0.11        88      32      48 ..     426     442 ..     405     464 .. 0.88
   4 ?    1.0   0.0      0.34   2.6e+02     154     188 ..     579     608 ..     515     609 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                            AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                      + +ge++ l+G +g+GK++ al+ 
  gi|313125169|ref|YP_004035433.1| 30 IDEGETVGLVGESGSGKSVTALST 53
                                      67999***************9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       +++++ ++++++ +g  vl++ H
  gi|313125169|ref|YP_004035433.1| 233 AQILDLINELQDDLGMSVLMITH 255
                                       68889999*************99 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.11
                            AAA_25  32 agelallaGapgtGKtt 48 
                                       +ge+  l+G +g+GK+t
  gi|313125169|ref|YP_004035433.1| 426 EGETLGLVGESGCGKST 442
                                       788889**********9 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.34
                            AAA_25 154 alggdensnsdvgalvealeriarrtgaavllvhH 188
                                       al+ + +     +++++ le++++++g + l++ H
  gi|313125169|ref|YP_004035433.1| 579 ALDVSVQ-----AQILNLLEDLQDEFGLTYLFIAH 608
                                       4444444.....899******************99 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.051        40      89     113 ..      22      47 ..       9      54 .. 0.77
   2 ?    8.1   0.0     0.003       2.3      96     121 ..     424     449 ..     387     461 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.051
                                       THHHHHHHCTT.SEEEEECSTTSSHH CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKS 113
                                       +++ +  ++++ +t+ lvG+SG GKS
  gi|313125169|ref|YP_004035433.1|  22 AVDGVDLEIDEgETVGLVGESGSGKS 47 
                                       5555666666669999*********9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.003
                                       HCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                                       + +++t  lvG+SG GKSt  +++l+
  gi|313125169|ref|YP_004035433.1| 424 VYEGETLGLVGESGCGKSTTGETILQ 449
                                       45679999**********97766665 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.8     0.066        52       3      21 ..      36      54 ..      34      57 .. 0.83
   2 ?   10.8   0.1   0.00028      0.22       3      22 ..     430     449 ..     428     462 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.066
                                      EEEESSTTSSHHHHHHHHH CS
                              AIG1  3 ivlvGktgnGkSaTgNsil 21
                                      + lvG +g+GkS T+ s +
  gi|313125169|ref|YP_004035433.1| 36 VGLVGESGSGKSVTALSTM 54
                                      669***********97766 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00028
                                       EEEESSTTSSHHHHHHHHHT CS
                              AIG1   3 ivlvGktgnGkSaTgNsilg 22 
                                       + lvG +g+GkS+Tg +il+
  gi|313125169|ref|YP_004035433.1| 430 LGLVGESGCGKSTTGETILQ 449
                                       669***************95 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.12        91      11      35 ..      30      54 ..      20     287 .. 0.71
   2 ?    8.9   0.0    0.0014       1.1       4      46 ..     416     460 ..     413     755 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                                      EBTT-EEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqsls 35
                                      i +G++++++g++g Gk+v + s +
  gi|313125169|ref|YP_004035433.1| 30 IDEGETVGLVGESGSGKSVTALSTM 54
                                      6689999999999999999875544 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                                       HHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEE CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                       ATP-synt_ab   4 vlDal.fpivqGqrtlipgafgvGktvisqslskqsnsdd.aiiy 46 
                                       ++D + +++ +G++++++g++g+Gk++  +++++  ++++  +++
  gi|313125169|ref|YP_004035433.1| 416 AVDGVdLSVYEGETLGLVGESGCGKSTTGETILQLLDATEgRVVF 460
                                       55554468899****************999999877666555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.041        32      16      69 ..      31      86 ..      14     116 .. 0.73
   2 ?   -1.4   0.0         2   1.6e+03      32     113 ..     148     243 ..     143     255 .. 0.62
   3 ?    5.8   0.0     0.013        10      21      50 ..     430     459 ..     420     464 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.041
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaag....grviglAptgkaAkvLaeelgie 69
                                      ++  ++ l+G  G+GK+ +  +   ++++ g    g+v + +p+   A +L+ee g++
  gi|313125169|ref|YP_004035433.1| 31 DEGETVGLVGESGSGKSVTALSTMGLVDDPGhivgGEVTLTSPE--LATQLREEYGAP 86
                                      34458899*********987777777777765555777776664..577888888865 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                            AAA_30  32 ttalkalreaweaaggrviglAptgkaAkvLaeelgi..eastiakllkrlk.........grarlepg.tllivDE 96 
                                        t l+a+re++ + gg+ +     ++a +vL+ e+gi  ++s+++++ ++           +  +l+ + +lli DE
  gi|313125169|ref|YP_004035433.1| 148 DTWLNAVREVLPKIGGQELDEQVVERAVEVLS-EVGIpePTSRVDEYPHEFSggmrqrvliAI-ALACRpKLLIADE 222
                                       56666667776666655555555677888888.678877888888888888788888888643.3444449999999 PP

                            AAA_30  97 agmv....dtkqlaallkaae 113
                                          +     ++q+ +l+++++
  gi|313125169|ref|YP_004035433.1| 223 PTTAldvtIQAQILDLINELQ 243
                                       776653222333444444444 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.013
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrvi 50 
                                         l+G  G GK+t+ +++ ++++a +grv+
  gi|313125169|ref|YP_004035433.1| 430 LGLVGESGCGKSTTGETILQLLDATEGRVV 459
                                       5689*****************999977876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.1   8.2e+02       3      19 ..      38      54 ..      36     126 .. 0.88
   2 ?   10.0   0.0    0.0011      0.87       3      52 ..     432     486 ..     430     613 .. 0.85
   3 ?   -2.2   0.0       6.8   5.3e+03      17      55 ..     748     798 ..     746     803 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                                      EESSTTSSHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakava 19
                                      l+G  G GK+ +a + +
  gi|313125169|ref|YP_004035433.1| 38 LVGESGSGKSVTALSTM 54
                                      89********9997765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                                       EESSTTSSHHHHHHHHHHHHTHE..........EEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakelgve..........fleisgsellskyvgesekkirelfke 52 
                                       l+G  G+GK+++ + + + l+++          + e+ g++l+     ++ ++++++f++
  gi|313125169|ref|YP_004035433.1| 432 LVGESGCGKSTTGETILQLLDATegrvvfqgedLTELGGTDLR-----KKRRDLQMIFQD 486
                                       89*****************953333333333338888888888.....678888888876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.8
                                       HHHHHH............THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHH CS
                               AAA  17 avakel............gvefleisgsellskyvgesekkirelfkeake 55 
                                       ava el            +++++e  + ++    + e+++ +r+ f+++ e
  gi|313125169|ref|YP_004035433.1| 748 AVAAELydrlfeeplqdeNRRVVESALNSIAAAEWDEAASILRDRFESVCE 798
                                       666665444444444443466777777777777777777777777777554 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3      0.43   3.4e+02       2      16 ..      36      50 ..      35      70 .. 0.87
   2 ?    9.5   0.0   0.00095      0.74       3      26 ..     431     454 ..     429     494 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.43
                               PRK  2 IgvagsSGaGkttva 16
                                      +g+ g+SG+Gk+ +a
  gi|313125169|ref|YP_004035433.1| 36 VGLVGESGSGKSVTA 50
                                      6999*******9765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00095
                               PRK   3 gvagsSGaGkttvarklekifgre 26 
                                       g+ g+SG+Gk+t+ +++ +++  +
  gi|313125169|ref|YP_004035433.1| 431 GLVGESGCGKSTTGETILQLLDAT 454
                                       899**************9999844 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.011       8.4      25      65 ..      10      51 ..       3      59 .. 0.82
   2 ?    2.5   0.0      0.13     1e+02      34      79 ..     413     459 ..     384     483 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                         IstB_IS21 25 raarsldkrkvkeLatlsf.iekkenivllGpsGvGKshlai 65
                                      r++  +d+ +vk++ + +  i++ e + l+G sG GKs  a 
  gi|313125169|ref|YP_004035433.1| 10 RTQFATDRGQVKAVDGVDLeIDEGETVGLVGESGSGKSVTAL 51
                                      5566678888899988886699****************8775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                         IstB_IS21  34 kvkeLatlsf.iekkenivllGpsGvGKshlaialgveavraglsvl 79 
                                        vk++ + +  + + e + l+G sG GKs    ++ +   +++ +v+
  gi|313125169|ref|YP_004035433.1| 413 SVKAVDGVDLsVYEGETLGLVGESGCGKSTTGETILQLLDATEGRVV 459
                                       5555555553366789999*********9877766555555555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.044        34      20      39 ..      31      50 ..      14      59 .. 0.80
   2 ?    3.9   0.0      0.05        39      24      50 ..     429     455 ..     408     462 .. 0.76
   3 ?   -1.2   0.0       1.9   1.4e+03      98     119 ..     572     594 ..     551     598 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.044
                                      TSSS-EEEECSTTSSHHHHH CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKella 39
                                      +   +v ++GesG+GK++ a
  gi|313125169|ref|YP_004035433.1| 31 DEGETVGLVGESGSGKSVTA 50
                                      55578889*********998 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.05
                                       -EEEECSTTSSHHHHHHHHHHHSTTTT CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrke 50 
                                       ++ ++GesG+GK++  ++i +  + +e
  gi|313125169|ref|YP_004035433.1| 429 TLGLVGESGCGKSTTGETILQLLDATE 455
                                       45589**********999988766655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
                                       EEET.GGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  98 fLDe.igelplelQekLlrvlqe 119
                                         De ++ l++++Q+++l++l++
  gi|313125169|ref|YP_004035433.1| 572 VADEpVSALDVSVQAQILNLLED 594
                                       555558899999****9999986 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.039        30      16      37 ..      30      51 ..      23      56 .. 0.89
   2 ?    4.2   0.1      0.03        23      17      38 ..     425     446 ..     412     476 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.039
                            ATPase 16 ipegrvvlitGepGtGKtifal 37
                                      i eg++v ++Ge+G+GK++ al
  gi|313125169|ref|YP_004035433.1| 30 IDEGETVGLVGESGSGKSVTAL 51
                                      568999************9885 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.03
                            ATPase  17 pegrvvlitGepGtGKtifalq 38 
                                       +eg++  ++Ge+G+GK++ +++
  gi|313125169|ref|YP_004035433.1| 425 YEGETLGLVGESGCGKSTTGET 446
                                       6889999***********9986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       7.1   5.5e+03      39      50 ..      37      48 ..      34      50 .. 0.84
   2 ?    6.7   0.0    0.0056       4.3     112     159 ..     207     252 ..     190     261 .. 0.84
   3 ?   -1.4   0.1       1.7   1.3e+03      38      51 ..     430     443 ..     427     451 .. 0.84
   4 ?   -0.6   0.0      0.95   7.4e+02     117     155 ..     565     601 ..     543     607 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.1
                              TniB 39 llvGdsnnGKtm 50
                                       lvG+s  GK++
  gi|313125169|ref|YP_004035433.1| 37 GLVGESGSGKSV 48
                                      58********97 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0056
                              TniB 112 lrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       +++  ++++++Li DE   +l   ++ q ++l ++  L+++l +++ +
  gi|313125169|ref|YP_004035433.1| 207 IAIALACRPKLLIADEPTTAL--DVTIQAQILDLINELQDDLGMSVLM 252
                                       4556689************99..6777889*************99976 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.7
                              TniB  38 lllvGdsnnGKtmi 51 
                                       l lvG+s +GK++ 
  gi|313125169|ref|YP_004035433.1| 430 LGLVGESGCGKSTT 443
                                       569*********86 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.95
                              TniB 117 elkvrvLiiDEihnllagsarkqreflnalksLgnelki 155
                                       ++++  ++ DE  ++l   ++ q ++ln+l  L++e+ +
  gi|313125169|ref|YP_004035433.1| 565 AVDPDFIVADEPVSAL--DVSVQAQILNLLEDLQDEFGL 601
                                       5677789999998888..66778899******9999866 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4     0.069        54      16      37 ..      31      50 ..      18      55 .. 0.78
   2 ?    5.5   0.1     0.011       8.5      22      49 ..     429     456 ..     414     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.069
                                      TTSCSEEEEEEESTTSSHHHHH CS
                            NB-ARC 16 delqslvvalvGmgGvGKttla 37
                                      de +   v+lvG  G+GK++ a
  gi|313125169|ref|YP_004035433.1| 31 DEGE--TVGLVGESGSGKSVTA 50
                                      4555..89***********966 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdeveg 49 
                                        ++lvG  G+GK+t  + il+ +d +eg
  gi|313125169|ref|YP_004035433.1| 429 TLGLVGESGCGKSTTGETILQLLDATEG 456
                                       689***********99999987777666 PP

>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.5     0.041        32       8      37 ..      22      52 ..      17      64 .. 0.80
   2 ?    5.3   0.2     0.017        13       5      37 ..     413     446 ..     410     456 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.041
                                      EEESEEEEE.TTEEEEEEESTCHHHHHHHHH CS
                      Hpr_kinase_C  8 svhGvlvdv.ygvGvLitGesgvGKselale 37
                                      +v Gv +++  g  v ++Gesg GKs +al 
  gi|313125169|ref|YP_004035433.1| 22 AVDGVDLEIdEGETVGLVGESGSGKSVTALS 52
                                      56677777733677889************96 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
                                       -EEEEESEEEEETTEEEE.EEESTCHHHHHHHHH CS
                      Hpr_kinase_C   5 eetsvhGvlvdvygvGvL.itGesgvGKselale 37 
                                       + ++v Gv ++vy+   L ++Gesg GKs ++ +
  gi|313125169|ref|YP_004035433.1| 413 SVKAVDGVDLSVYEGETLgLVGESGCGKSTTGET 446
                                       56788999999996555549*********88654 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.081        63      26      40 ..      36      50 ..      18      53 .. 0.85
   2 ?    5.3   0.1     0.024        18      26      47 ..     430     451 ..     419     460 .. 0.83
   3 ?   -2.4   0.0       5.2     4e+03     101     138 ..     752     787 ..     747     795 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.081
                             DUF87 26 lAilgsTGsGKSntv 40
                                      ++ +g++GsGKS t+
  gi|313125169|ref|YP_004035433.1| 36 VGLVGESGSGKSVTA 50
                                      7899********997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.024
                             DUF87  26 lAilgsTGsGKSntvavLleel 47 
                                       l+ +g++G GKS+t   +l+ l
  gi|313125169|ref|YP_004035433.1| 430 LGLVGESGCGKSTTGETILQLL 451
                                       6899**************9977 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.2
                             DUF87 101 elldlleeddkpaaavqrsvleealdqakakeekekls 138
                                       el d l+e  +p+ ++ r+v+e+al+++ a+e++e +s
  gi|313125169|ref|YP_004035433.1| 752 ELYDRLFE--EPLQDENRRVVESALNSIAAAEWDEAAS 787
                                       66677777..899999999***9999998877777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (817 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.89u 0.37s 00:00:01.26 Elapsed: 00:00:00.55
# Mc/sec: 4507.68
//
Query:       gi|313125170|ref|YP_004035434.1|  [L=577]
Description: peptide ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-94  317.2   4.1    2.7e-94  316.2   4.1    1.4  1  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
    2.5e-06   27.1   7.0    4.2e-06   26.4   7.0    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
       0.24   10.8   2.0       0.41   10.0   2.0    1.4  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.2   4.1   4.5e-98   2.7e-94       4     372 ..     113     475 ..     110     479 .. 0.95

  Alignments for each domain:
  == domain 1  score: 316.2 bits;  conditional E-value: 4.5e-98
                                       ESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC.......TCTEEEEEEE CS
                         SBP_bac_5   4 paLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee.......dqdikkveav 73 
                                        +LA++w   s  g+t+t++LR++v+F++G+++tA+Dvv++f+r+ +pd+ +++ +++         ++ +k+v ++
  gi|313125170|ref|YP_004035434.1| 113 EGLATDW---SLEGTTVTLTLREDVTFHNGEEFTADDVVATFNRFTNPDYEHYPGDKYISaygpftlGNWVKSVSKD 186
                                       6799995...789***************************************9988887799*************** PP

                                       ETTEEEEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEET.TTEEEEEE-TTSTTTSC CS
                         SBP_bac_5  74 ddytvrftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkp.gqkivlernpdYwgggk 149
                                        dy +++ l++ +a+fl+ la++++si   + +  ++ + d  +kpvgtGP+k+++++  +q+i+l +n dYw g+ 
  gi|313125170|ref|YP_004035434.1| 187 GDYALTIQLNQKYAPFLRNLAMFASSIL--SEKAIKELGQDLSKKPVGTGPFKFENWDTsNQQIRLSANTDYW-GEV 260
                                       ****************************..677888889*******************9888***********.*** PP

                                       SSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT.STGGGSHHHHH CS
                         SBP_bac_5 150 pkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtk.kppfddkrvRq 225
                                       pk+d+++f  + ++++ra+ l sG +d++ ++ ++  + ++++++ k+ ++++g +v+y+afN++  + f++k+vRq
  gi|313125170|ref|YP_004035434.1| 261 PKVDEVVFTSVGSNTTRAQTLDSGGADIIDGLGAQASKIVENSSNAKL-VSKAGINVGYMAFNMAkVEAFRNKKVRQ 336
                                       ************************************************.****************999********* PP

                                       HHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEE CS
                         SBP_bac_5 226 AlsyAiDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltll 302
                                       A+syAi+ e++v+++++g a++a +++p+++ g++++ +p+++  d+ekA+ lL+eaGy dg+  +l       t+ 
  gi|313125170|ref|YP_004035434.1| 337 AISYAINTEALVNNIFKGIAEQASQPIPSNVFGYNDDLSPYPQ--DLEKAESLLEEAGYGDGFSFEL------ATFK 405
                                       ****************************************955..******************9876......7888 PP

                                       EETTSHHHH.HHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHST CS
                         SBP_bac_5 303 lasgspaek.aiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflss 372
                                        + +++++   +a+l++++l+++Gi+v++++ ++ + +l+++++g++d+ +lgw++d++dpdnf++++l++
  gi|313125170|ref|YP_004035434.1| 406 NPRTYNPSPlSAAQLVKSNLAELGIEVSINQQSF-NPFLDYTNSGKHDACFLGWMTDNADPDNFFYALLHP 475
                                       8888888888************************.********************************9987 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   7.0     7e-10   4.2e-06       1      25 [.       8      32 ..       8      33 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7e-10
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalggcaa 25
                                      +++RR FLK++++aaAAa+l+gcaa
  gi|313125170|ref|YP_004035434.1|  8 DIDRRAFLKAAGGAAAAATLAGCAA 32
                                      589********************96 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.0   6.9e-05      0.41       3      30 ..       3      31 ..       1      34 [. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.9e-05
                        UCR_Fe-S_N  3 eaesdeptRRDFLyiATgavgaVG.aaaa 30
                                      e+ s++ +RR FL +A ga++a   a++a
  gi|313125170|ref|YP_004035434.1|  3 ETMSRDIDRRAFLKAAGGAAAAATlAGCA 31
                                      6778999******9999999887634555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 3186.65
//
Query:       gi|313125171|ref|YP_004035435.1|  [L=341]
Description: peptide ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-36  125.5  12.6    3.2e-36  124.8  12.6    1.3  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8  12.6   1.8e-40   3.2e-36       1     184 [.     117     340 ..     117     341 .] 0.99

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 1.8e-40
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................. 43 
                                       gi++Gi++a+++  ++d+l r+   ++ s+P+++ ++l++l+f                                  
  gi|313125171|ref|YP_004035435.1| 117 GIPFGIISAVKQDTITDHLTRVGALTGISMPIYWTGPLVILLFaqflnvlpasnriasqfdppvytglitfdtfifg 193
                                       89********************************999988888889******************************* PP

                      BPD_transp_1  44 .......vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitg 113
                                              +++s++ h+ lp+++++++++a + r++r+++l+++ +d++++ara+G + + ++ k+ l nal+p+it 
  gi|313125171|ref|YP_004035435.1| 194 iqsgdfaAFISAASHMLLPAAVIGIYGMALISRMMRSSMLEVIRQDYMRTARAKGQGAKITVMKHGLQNALIPVITV 270
                                       ***************************************************************************** PP

                      BPD_transp_1 114 lilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       ++++fg llggavl+e++++ +G+gt+l+ ai+  dy+  + g+vl++++++ l+nl +d+ + +ldpr+ 
  gi|313125171|ref|YP_004035435.1| 271 IGIQFGTLLGGAVLTETVFGIGGIGTMLVKAIEVGDYPVVQ-GTVLVFAFLFTLVNLGVDLTYSYLDPRID 340
                                       *****************************************.***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2082.95
//
Query:       gi|313125172|ref|YP_004035436.1|  [L=313]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-33  116.3   4.9    1.3e-33  116.3   4.9    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
    0.00057   19.8   0.8    0.00057   19.8   0.8    3.0  3  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3     0.046   4.1e+02     161     175 ..      36      50 ..      14      67 .. 0.54
   2 !  116.3   4.9   1.5e-37   1.3e-33       1     184 [.     122     309 ..     122     310 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.046
                      BPD_transp_1 161 lviavlllnlvadil 175
                                       l+ +vl+l+ v+ +l
  gi|313125172|ref|YP_004035436.1|  36 LAGIVLILVMVVIAL 50 
                                       222222222222222 PP

  == domain 2  score: 116.3 bits;  conditional E-value: 1.5e-37
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       g+ lGi+aa +++ ++d+++++ ++vll++Ps++la+ lv++f +   l  l+ +v +l+l++++ ++r++r aal+
  gi|313125172|ref|YP_004035436.1| 122 GVSLGIIAA-YYGDITDNIIMRSMDVLLAFPSLLLALALVAIFPNE--L-GLWRAVTALTLVYTPRFARVVRGAALK 194
                                       789******.******************************876444..3.366789********************* PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       +l++++v a  alGa++ +++ ++v+Pn l pi  +  l+fg+++ + ++l+flg    +g    ++++g ++s++ 
  gi|313125172|ref|YP_004035436.1| 195 VLEDEYVDATIALGATDPRVLARHVMPNCLAPITVQSTLNFGLAIIDLAALSFLG----FGAEPGSPSWGLMLSNGV 267
                                       *******************************************************....****************** PP

                      BPD_transp_1 155 ............nggvlalviavlllnlvadilqrlldprvr 184
                                                   +++ l+l++ vl +nl+ d + ++ldpr+r
  gi|313125172|ref|YP_004035436.1| 268 ekglltgdwwwsFFPGLFLAVTVLGFNLLGDGMRDALDPRMR 309
                                       *****************************************9 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.8   6.4e-08   0.00057       9      35 ..      28      54 ..      23      81 .. 0.70
   2 ?   -2.7   0.1      0.68   6.1e+03      16      26 ..     121     131 ..     119     133 .. 0.77
   3 ?    0.5   0.2     0.066   5.9e+02      23      32 ..     154     163 ..     152     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.4e-08
                            OppC_N  9 rFkrNklAvvglvilllllliaifaPl 35
                                       +++N+lA++g v++l++++ia++a l
  gi|313125172|ref|YP_004035436.1| 28 DLLSNRLALAGIVLILVMVVIALYARL 54
                                      5899********************732 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.68
                            OppC_N  16 Avvglvillll 26 
                                       A v+l i+++ 
  gi|313125172|ref|YP_004035436.1| 121 AGVSLGIIAAY 131
                                       77999999875 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.066
                            OppC_N  23 lllllliaif 32 
                                       ll+l+l+aif
  gi|313125172|ref|YP_004035436.1| 154 LLALALVAIF 163
                                       7899999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 2232.50
//
Query:       gi|313125173|ref|YP_004035437.1|  [L=127]
Description: hypothetical protein Hbor_03940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.038   13.4   0.1      0.054   12.9   0.1    1.3  1  Aph-1            Aph-1 protein
      0.042   14.2   1.0      0.069   13.5   1.0    1.4  1  DUF1772          Domain of unknown function (DUF1772)
       0.22   11.4   0.2       0.25   11.2   0.2    1.3  1  Pam17            Mitochondrial import protein Pam17
       0.58    9.9   8.7        2.5    7.8   3.0    2.0  2  CbtA             Probable cobalt transporter subunit (CbtA)
       0.85    9.4   3.7       0.74    9.6   2.7    1.4  1  DUF3464          Photosynthesis affected mutant 68


Domain annotation for each model (and alignments):
>> Aph-1  Aph-1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.5e-05     0.054      88     129 ..      87     127 .]      76     127 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                             Aph-1  88 eegLkkisessklkeskhqlayvsGlGfGvmsgvfslvniLa 129
                                       ++ L++ +e  +  +s++ +a + G+G Gvm +++ l ++La
  gi|313125173|ref|YP_004035437.1|  87 QRHLDTGAE-WTEMDSRRAMARIGGFGAGVMLAAMTLGSLLA 127
                                       455555555.55567999********************9996 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.0   1.9e-05     0.069      29     136 ..      21     116 ..       1     117 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                           DUF1772  29 rrlfkrg.kavfpplallsalafa.ylaaraasrgarllylaaaallllsivpyTllvmvPtNnkLaalkeedakek 103
                                       rr+  +g + ++++++ ++ala+a y + ++  +ga +++l++ ++l ++++ ++  v     ++            
  gi|313125173|ref|YP_004035437.1|  21 RRVTVVGgAFLVGVAGGGVALAVAtYHF-SSLPDGADAVFLLGILALGFGVLGWSGSVLAGRGFE------------ 84 
                                       3334445477888899999999997777.67778888888777777999**********998766............ PP

                           DUF1772 104 edeaevrelle...rWgrlnlvRavlalaaavlgll 136
                                           e+++ l+   +W+ +   Ra++ + ++ +g++
  gi|313125173|ref|YP_004035437.1|  85 ----EMQRHLDtgaEWTEMDSRRAMARIGGFGAGVM 116
                                       ....23333444679999999999999999999986 PP

>> Pam17  Mitochondrial import protein Pam17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2     7e-05      0.25      45     107 ..      32      93 ..      14     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7e-05
                             Pam17  45 lglllgaavlstleidptqqilglDplvvlglatlasgalGwllGpvlgsavfkllnrkklkq 107
                                       +g++ g   l+  +   ++   g D +++lg+  l++g+lGw  G+vl    f+ ++r+  + 
  gi|313125173|ref|YP_004035437.1|  32 VGVAGGGVALAVATYHFSSLPDGADAVFLLGILALGFGVLGW-SGSVLAGRGFEEMQRHLDTG 93 
                                       34444444455555555666679*******************.79999999999998887655 PP

>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.0   0.00069       2.5      59     120 ..      10      76 ..       5      81 .. 0.81
   2 ?    4.7   3.2    0.0062        22      16      90 ..      62     127 .]      57     127 .] 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00069
                              CbtA  59 eepelvsrgvqrtlgtvlanvltgvalglllaavfallegrlgklsara.....lalllalagflav 120
                                       ++p  +s +++r +  v +  l+gva g++  av+++  ++l+   ++      lal ++++g+   
  gi|313125173|ref|YP_004035437.1|  10 DAPTRASPTLSRRVTVVGGAFLVGVAGGGVALAVATYHFSSLPDGADAVfllgiLALGFGVLGWSGS 76 
                                       567788999*********************9999999999997766555777778888888888665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0062
                              CbtA  16 GllaflvqrlvvePlilaAeayEeaaaaaeaaeaaaeHehaeaeepelvsrgvqrtlgtvlanvltgvalgllla 90 
                                       G+la ++  l  +  +la   +Ee +++ ++          +++ +    r++ r  g +++++l+++ lg lla
  gi|313125173|ref|YP_004035437.1|  62 GILALGFGVLGWSGSVLAGRGFEEMQRHLDT---------GAEWTEMDSRRAMARIGGFGAGVMLAAMTLGSLLA 127
                                       6666666666666777777777774443222.........35677777889*********************997 PP

>> DUF3464  Photosynthesis affected mutant 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.7   0.00021      0.74      53     118 ..      13      79 ..       3      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00021
                           DUF3464  53 evVskRmirRvalfsGiPlalGlatfvvfylivskelvdlptw..vvllvslvlFglgvlGlsYGvlS 118
                                          s  + rRv+ ++G   ++G+a   v  ++++++   lp    +v+l  ++++g gvlG s +vl 
  gi|313125173|ref|YP_004035437.1|  13 TRASPTLSRRVT-VVGGAFLVGVAGGGVALAVATYHFSSLPDGadAVFLLGILALGFGVLGWSGSVLA 79 
                                       555666778888.56666999********************75227999************9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 727.25
//
Query:       gi|313125174|ref|YP_004035438.1|  [L=418]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-23   81.2   1.8      8e-23   80.2   1.8    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    8.3e-21   74.4   0.0    2.7e-20   72.8   0.0    1.8  2  OrfB_IS605       Probable transposase
     0.0038   17.5   1.6       0.01   16.2   1.6    1.7  1  C1_2             C1 domain
  ------ inclusion threshold ------
      0.085   12.8   3.8       0.23   11.5   3.8    1.7  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.12   12.5   2.9      0.096   12.8   0.7    2.0  2  Ribosomal_L37ae  Ribosomal L37ae protein family


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   1.8   2.2e-26     8e-23       1      69 []     309     378 ..     309     378 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 2.2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++ + leyka+e+Gi v  v++++TSktCs+Cg++ +  ++++ +++C++C +++++Dvn+a+Ni ++
  gi|313125174|ref|YP_004035438.1| 309 FDRFARLLEYKAEEHGILVDRVDEENTSKTCSCCGKIRDSnRVERGLYVCSSCETTMNADVNGAVNIRRK 378
                                       789************************************9999************************985 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.4   5.2e+03      58      73 ..      54      69 ..      52      85 .. 0.61
   2 !   72.8   0.0   7.5e-24   2.7e-20       3     119 ..     176     285 ..     169     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                        OrfB_IS605 58 aelqsklkksknykka 73
                                      ael s lk++k+y   
  gi|313125174|ref|YP_004035438.1| 54 AELKSELKDHKRYSDL 69
                                      6777777777766443 PP

  == domain 2  score: 72.8 bits;  conditional E-value: 7.5e-24
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       +++ e + + ++gn++agiDlGi+n ++   edg ++ly g+ lk+d+ y+++e  + +            s++ ++
  gi|313125174|ref|YP_004035438.1| 176 VCKTEIPVEDAPGNNTAGIDLGISNYLAIDYEDGPSELYPGNVLKEDKHYFTREEYQTEGENGP-------SKRARK 245
                                       56666678899******************************************99888777544.......567888 PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                         +k+srr +h+lh l++h+++++ e+gve++ vg+++di
  gi|313125174|ref|YP_004035438.1| 246 ARQKLSRRKDHFLHTLSKHIVERCVEEGVEKIAVGDLSDI 285
                                       88999********************************987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.6   2.8e-06      0.01      13      42 ..     331     365 ..     319     368 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-06
                              C1_2  13 edssesfnCsaCgrk..idgff.....YsCseCdfsl 42 
                                       ++++ s++Cs+Cg+   +  ++     Y Cs C+ ++
  gi|313125174|ref|YP_004035438.1| 331 DEENTSKTCSCCGKIrdS--NRverglYVCSSCETTM 365
                                       467788*********554..4455999******9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.8   6.4e-05      0.23      19      45 ..     337     363 ..     333     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                        +C  Cg+   + r+++ gl+ C++C +
  gi|313125174|ref|YP_004035438.1| 337 KTCSCCGKIrDSNRVER-GLYVCSSCET 363
                                       57*****9999999997.********86 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.1   7.7e+03      31      50 ..     261     280 ..     245     280 .. 0.75
   2 ?   12.8   0.7   2.7e-05     0.096      31      62 ..     334     366 ..     326     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.1
                                       HS-BEESSSSSSEEEEEETT CS
                   Ribosomal_L37ae  31 hakytCpfcgktkvkRkavg 50 
                                        +k+  ++c ++ v++ avg
  gi|313125174|ref|YP_004035438.1| 261 LSKHIVERCVEEGVEKIAVG 280
                                       56788888888888888886 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.7e-05
                                       HS-BEESSSSSS.EEEEEETTEEEETTTTEEEE CS
                   Ribosomal_L37ae  31 hakytCpfcgkt.kvkRkavgiwkCkkcgktva 62 
                                       +++ tC+ cgk  + +R+  g++ C++c+ t+ 
  gi|313125174|ref|YP_004035438.1| 334 NTSKTCSCCGKIrDSNRVERGLYVCSSCETTMN 366
                                       44569******9899**************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.57
# Mc/sec: 2226.31
//
Query:       gi|313125175|ref|YP_004035439.1|  [L=447]
Description: dihydroorotase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-21   77.3   0.0    1.1e-20   74.3   0.0    2.3  1  Amidohydro_1  Amidohydrolase family
    4.2e-15   56.2   4.9    1.3e-06   28.2   0.0    3.2  3  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.017   15.0   0.1      0.063   13.2   0.1    1.9  1  DHOase        Dihydro-orotase-like


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   1.8e-24   1.1e-20       1     344 []      62     431 ..      62     431 .. 0.72

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.8e-24
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.......HHHHHHHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.......giealleaa 70 
                                       +++PG IDaHvH++             +p+   +e+ e+g + a  +G+t vad ++t+++         +a l aa
  gi|313125175|ref|YP_004035439.1|  62 MLFPGAIDAHVHFR-------------EPGFSHKETWETGSQSAAAGGVTVVADQPNTQPPtttgsafDEKAGLAAA 125
                                       689**********9.............*******************************9999987754333334444 PP

                                       HTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTE CS
                      Amidohydro_1  71 eelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlp 147
                                       +   ++++i gg v  d++ ++  +  r  ++ g+          v+    +  ++ ++ +++ ++a++ a+++d+ 
  gi|313125175|ref|YP_004035439.1| 126 SL--IDFGISGG-VTADWDPDS--LFDRPLFALGE----------VF--LADSTGDMGIDADLFADAVERAADADVT 185
                                       44..48888877.566655555..44455555554..........22..2566799********************* PP

                                       EEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE.HHHHHHHHHHHHHHCEEHHHHHHH CS
                      Amidohydro_1 148 vaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt.pteaellkerlkeagvahcpfsns 223
                                       v++Ha + + + e a++   +++ ++   +v  ++ +++   +++++ v +  ++ea + +++          +++ 
  gi|313125175|ref|YP_004035439.1| 186 VTVHAEDADLFDESAQKRDTGGTGEAADADVWSQYRAAEAEEAAVERAVSVGsDSEADIHIAH--------TSTPEG 254
                                       *****6666666666665555666667888888877777777777777777765655553333........333333 PP

                                       H......................................SEHHHHHHHHHHHHTSCEEEEEECT...TSSCCGGHHH CS
                      Amidohydro_1 224 i......................................lrsgrealrkaldeGvkvglgtDga...asgnslnlle 259
                                       +                                      +++ re +++ + +G + +++tD+a    + + ++l++
  gi|313125175|ref|YP_004035439.1| 255 VdaakaggatcevtphhlflsradatelgtygrmnpplrSEDRREGMWERVVSGEIDIVATDHAphtRAEKDADLWD 331
                                       333444444555555556666666777777777777777*************************7773444446666 PP

                                       H..HHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.CT........... CS
                      Amidohydro_1 260 e..lrlalklqrgllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl.di........... 321
                                          +  ++++  +ll e   +g +s++++ +++  n+A+++ l+ ++G++evG dADlvv+d+  +           
  gi|313125175|ref|YP_004035439.1| 332 ApsGVPGVETMLPLLLEeARKGTISYERVRDVTAANAAEIFDLP-QKGRVEVGSDADLVVFDPeESqeihgadlhsr 407
                                       66633333333344444444999********************7.****************9972234566777778 PP

                                       ..CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 322 ..laafvglkkdgnvkkvivkGklv 344
                                          ++f+g+     + ++ v+G++v
  gi|313125175|ref|YP_004035439.1| 408 cgWTPFEGMRG-VFPEMTLVRGHVV 431
                                       87777777644.5577777777765 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1     2e-08   0.00012       1      58 [.      54     110 ..      54     126 .. 0.82
   2 !    6.8   0.8   0.00065       3.9     244     328 ..     148     228 ..     136     274 .. 0.72
   3 !   28.2   0.0   2.2e-10   1.3e-06     407     473 .]     354     432 ..     337     432 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2e-08
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkg 58 
                                       +v++a+G++++PG +D+H H  + g    +++  + + ++++g  t+v+dq +t+p++
  gi|313125175|ref|YP_004035439.1|  54 RVVNATGKMLFPGAIDAHVHFREPGFSHKETWETG-SQSAAAGGVTVVADQPNTQPPT 110
                                       69***********************7767777777.7777888888889998886554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00065
                      Amidohydro_3 244 srtalltepyf.tgwpdfedea..laelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegv 317
                                       ++ ++l e+++ ++++d+  +a  +a+ v++a+++++ v +ha +++  d       + a+k  + +  +++ a + 
  gi|313125175|ref|YP_004035439.1| 148 RPLFALGEVFLaDSTGDMGIDAdlFADAVERAADADVTVTVHAEDADLFD-------ESAQKRDTGGTGEAADADVW 217
                                       556777777779889999988889********************999888.......33333333333355555555 PP

                      Amidohydro_3 318 tesqiervaal 328
                                       ++  ++++ + 
  gi|313125175|ref|YP_004035439.1| 218 SQYRAAEAEEA 228
                                       55555555555 PP

  == domain 3  score: 28.2 bits;  conditional E-value: 2.2e-10
                      Amidohydro_3 407 elsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear............vrltvvdGr 470
                                        +s+e + + + +++A+++ l+++ G++evG dADlvv+d  +  +++ ++l++              +++t+v+G 
  gi|313125175|ref|YP_004035439.1| 354 TISYERVRDVTAANAAEIFDLPQK-GRVEVGSDADLVVFDpEESQEIHGADLHSRCgwtpfegmrgvfPEMTLVRGH 429
                                       678888889999***********8.***************8888889998888877********************* PP

                      Amidohydro_3 471 vvy 473
                                       vvy
  gi|313125175|ref|YP_004035439.1| 430 VVY 432
                                       **8 PP

>> DHOase  Dihydro-orotase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.1e-05     0.063       1     139 [.      60     251 ..      60     254 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                            DHOase   1 grllvpglidlavhlrelsgeakeliet...tvaaygvtfkaP...............................aai 43 
                                       g++l+pg id +vh re++ + ke+ et     aa gvt  a                                 ++
  gi|313125175|ref|YP_004035439.1|  60 GKMLFPGAIDAHVHFREPGFSHKETWETgsqSAAAGGVTVVADqpntqpptttgsafdekaglaaaslidfgisGGV 136
                                       689*************************9985556666666655566666788888888888876666665555344 PP

                            DHOase  44 tveddsee................afiltddt.vyvtiqllefeglkk.aeLdqalkaiaeDDevtnqsavq..... 97 
                                       t      +                 f++   + +++  + l ++++++ a+ d ++  +aeD ++ ++sa +     
  gi|313125175|ref|YP_004035439.1| 137 TA-----DwdpdslfdrplfalgeVFLADSTGdMGID-ADLFADAVERaADADVTVTVHAEDADLFDESAQKrdtgg 207
                                       44.....044445888888888755655433314554.567789999989999999999999999999986522222 PP

                            DHOase  98 dfela..rfyGvqLkGvCeaekivydvLlakaagcgfyvsiiyt 139
                                       ++e a    +  +     e+  + ++v +  ++ +  ++++++t
  gi|313125175|ref|YP_004035439.1| 208 TGEAAdaDVWSQYRAAEAEEAAVERAVSVGSDSEADIHIAHTST 251
                                       35554113455333336677777777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 2514.54
//
Query:       gi|313125176|ref|YP_004035440.1|  [L=239]
Description: lipoate-protein ligase A [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00092   19.1   0.0     0.0014   18.6   0.0    1.2  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   7.6e-08    0.0014      20     128 ..      69     173 ..      63     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.6e-08
                                       G--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHH..HHHHHHHHHHHH......HHTT-TTEE CS
                     BPL_LplA_LipB  20 elesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlely..vsllvlavlealgyrdskpgiegipvf 94 
                                         es+g  vv+r +gGr+v    +++++++ ++  e    ++   e+y   ++ v+++l++lg    + +  ++   
  gi|313125176|ref|YP_004035440.1|  69 AAESRGFPVVKRSVGGRAVAYT-GRTVAFASAVPIEND--RTGLDERYetATTAVIRALRSLGVPARRGEPANSF-- 140
                                       56899999*********55555.499999999998863..33477888888889999999995311234444444.. PP

                                       EETTTEEEE.TTEEEEEEEEEEEETTS-EEEEEEE CS
                     BPL_LplA_LipB  95 ikwpnDlyv.ngrKlaGiavtstrgktlhhivigv 128
                                          p D  v    K+ Gia++++r + l  +v++v
  gi|313125176|ref|YP_004035440.1| 141 --CPGDHSVqAHGKICGIAQRVRRDVALVSGVVVV 173
                                       ..56999995667***********65555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 1352.37
//
Query:       gi|313125177|ref|YP_004035441.1|  [L=285]
Description: hypothetical protein Hbor_03980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-05   22.9   0.0    0.00016   21.8   0.0    1.5  1  Peptidase_M23  Peptidase family M23


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   8.8e-09   0.00016      17      93 ..      41     126 ..      27     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.8e-09
                                       EESSSEEEEEEEEET.......TTEEEEEEEECTCEEEEEEEESEESS-TTEEE-TTCEEEEEBSTSSCS...SSEE CS
                     Peptidase_M23  17 lAaadGtVvfagkke.......gyGnvviidhgdgystlyahlskisvkegqkVkaGqvIGtvgstgrst...gphL 83 
                                       l++ +G+V++ ++ +         ++++i+ ++++y+ +++h++  +v++g++V+ G+ +G +  +g  +   ++h+
  gi|313125177|ref|YP_004035441.1|  41 LSPVSGEVLETRTVRappkpyaHEDEYLILVDAGEYVARILHVEP-AVEAGERVEVGDSLGPMVRSGFFApwvANHV 116
                                       68889999888885556677744588888888999********99.9********************87778899** PP

                                       EEEEEETTEE CS
                     Peptidase_M23  84 hfeirkngka 93 
                                       h  +r+++++
  gi|313125177|ref|YP_004035441.1| 117 HVGFRRHDQN 126
                                       ***9976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1781.31
//
Query:       gi|313125178|ref|YP_004035442.1|  [L=167]
Description: hypothetical protein Hbor_03990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-12   47.1   0.2    3.7e-12   46.4   0.2    1.2  1  4HBT            Thioesterase superfamily
    7.4e-08   32.6   0.0    9.3e-08   32.3   0.0    1.1  1  DUF4442         Domain of unknown function (DUF4442)
     0.0065   16.7   0.2     0.0082   16.4   0.2    1.2  1  4HBT_3          Thioesterase-like superfamily
  ------ inclusion threshold ------
      0.056   13.1   0.2       0.12   12.0   0.2    1.6  1  Docking         Erythronolide synthase docking
      0.056   14.1   0.0        1.4    9.6   0.0    2.2  2  D-ser_dehydrat  Putative serine dehydratase domain
      0.088   12.6   0.0      0.096   12.5   0.0    1.2  1  SBP_bac_8       Bacterial extracellular solute-binding protei


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.2   1.2e-15   3.7e-12       3      75 ..      61     133 ..      60     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.2e-15
                                       SB-HHHHHHHHHHHHHHHHHHTTST..TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTS CS
                              4HBT   3 vvhgGvylallDeaagaalrslggr..gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedg 75 
                                       +vhgG  ++l+D+a+g+a r+   +  + +v++v+l++++lr +  +  l+++a+v+r+g+++ v +v+v++ ++
  gi|313125178|ref|YP_004035442.1|  61 TVHGGIAATLIDTAGGIAQRTMLSDpmNGGVATVNLNVNYLRRAAGD--LRATAEVVRAGGSIGVSTVTVVSRPP 133
                                       7********************************************99..*********************99876 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   3.1e-11   9.3e-08      10      99 ..      22     115 ..      14     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.1e-11
                                       HHHSGGGGGG--EEEEEETTEEEEEE---GGGB-TTS..SB-HHHHHHHHHHHHHHHHHHHS-T..TEEEEEEEEEE CS
                           DUF4442  10 slkaPYfgtvgprieelepgraevrlkkrrrvrNhig..tvHAiAicnlaElamGllaeatlpd..thrwipkgmev 82 
                                        +   Y   +g +++e e gr++++++   ++ N     tvH++ +++l ++a G+   + l d  +  +   + +v
  gi|313125178|ref|YP_004035442.1|  22 EQEHGYLSWLGTQVNEFEDGRVVMTIPYDEKLTNTTNppTVHGGIAATLIDTAGGIAQRTMLSDpmNGGVATVNLNV 98 
                                       556678888999**********************98666*****************99999888778889999**** PP

                                       EE-S---S-EEEEEE-T CS
                           DUF4442  83 dYlakatgdltavaele 99 
                                       +Yl++a gdl+a+ae+ 
  gi|313125178|ref|YP_004035442.1|  99 NYLRRAAGDLRATAEVV 115
                                       **************986 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   2.8e-06    0.0082       6      71 ..      58     130 ..      53     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.8e-06
                                       ECTTC.-HHHHHHHHHHH...HHHT..-S....SS..EEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEEEE CS
                            4HBT_3   6 tpggagyGGyvlAlalra...aqrtv.pdp...rl..hslhvyFlrpgdagpviyhvervrdGrsfstrtvelsq 71 
                                       +p+++ +GG ++ l+  a   aqrt+ +dp   ++   +l v++lr+++   ++ ++e+vr G s+ + tv++  
  gi|313125178|ref|YP_004035442.1|  58 NPPTV-HGGIAATLIDTAggiAQRTMlSDPmngGVatVNLNVNYLRRAAG-DLRATAEVVRAGGSIGVSTVTVVS 130
                                       56666.***99998777733356885666655633668*********876.8*************9999998865 PP

>> Docking  Erythronolide synthase docking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   4.1e-05      0.12       8      20 ..      99     111 ..      98     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                           Docking   8 dYLKRvTaDLrqt 20 
                                        YL+R+  DLr t
  gi|313125178|ref|YP_004035442.1|  99 NYLRRAAGDLRAT 111
                                       5**********98 PP

>> D-ser_dehydrat  Putative serine dehydratase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00047       1.4      48      80 ..      17      48 ..       1      54 [. 0.82
   2 ?    2.6   0.0     0.071   2.1e+02      18      60 ..     115     156 ..      84     164 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00047
                                      B-..EE-SS-EEEE--TT-GGGS-TT-EEEEE- CS
                    D-ser_dehydrat 48 vsvrrlsdEhgiltleeesaddlrvGdvvrlip 80
                                      v+ + + +Ehg+l++   + ++++ G vv  ip
  gi|313125178|ref|YP_004035442.1| 17 VQ-QYIEQEHGYLSWLGTQVNEFEDGRVVMTIP 48
                                      34.6899*********9999*******999998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.071
                                       EES--HHHH-S-S..S--BT-EEE-TTSEEEEB-..EE-SS-EEE CS
                    D-ser_dehydrat  18 lvdaGskalslds..sgpgfgkvvagleegwvvsvrrlsdEhgil 60 
                                       +   Gs+ +s+ +  s+p+  +v++++e+  +  ++   dE ++ 
  gi|313125178|ref|YP_004035442.1| 115 VRAGGSIGVSTVTvvSRPP-ERVRENDEAFER--WQGTTDEEAVA 156
                                       5556777777775533333.566655443333..33556666655 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.2e-05     0.096     155     205 ..       6      58 ..       1     115 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.2e-05
                                       HHH..HHHHHHHHHHHHTT-EE-S...--SSTTTTTSBSEEEE-TTHHHHHH- CS
                         SBP_bac_8 155 kdgl.kealellkklkdngktydtg.adavsefanGevaftingswdiaaaqk 205
                                       ++g+ ++a+ +++++ ++   y ++  ++v+ef +G+v++ti +++ +++ ++
  gi|313125178|ref|YP_004035442.1|   6 PEGFpDDAASFVQQYIEQEHGYLSWlGTQVNEFEDGRVVMTIPYDEKLTNTTN 58 
                                       556668999*******999999777688999***********99999988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 992.86
//
Query:       gi|313125179|ref|YP_004035443.1|  [L=191]
Description: nicotinamidase-like amidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-50  171.9   0.7    1.6e-50  171.7   0.7    1.0  1  Isochorismatase  Isochorismatase family


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.7   8.9e-55   1.6e-50       1     175 []       9     187 ..       9     187 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 8.9e-55
                   Isochorismatase   1 talvviDmqndfv.eegvkeseeisavveninkllkaarkagipviftrdvhe...leevkgdlderkaaphfkpgt 73 
                                       ta+vv+Dmqn+f+ ++g    ++ +avv+ ++ l++ +r+ag  v++trdvh+   +++ ++ ++ +++ +h+++gt
  gi|313125179|ref|YP_004035443.1|   9 TAVVVVDMQNGFChPGGSLYAPKSEAVVDDVAALVADVRDAGAAVVYTRDVHPpeqFDDAHYYDEFDRWGEHVVEGT 85 
                                       79***********99999*********************************************************** PP

                   Isochorismatase  74 tgaelvpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaa 150
                                       +++elv+el ++e+d+vv K++++af +t+l+ +L+++gi++++++G  ++vCV++ta +a  ++y++v+v+DA++a
  gi|313125179|ref|YP_004035443.1|  86 WETELVEELDVREDDHVVVKHTYDAFHQTELEGWLDAHGIDDLLFCGTLANVCVLHTAGSAGLRDYRPVLVADAIGA 162
                                       ***************************************************************************** PP

                   Isochorismatase 151 lspelhdaalkrlkqafatvitted 175
                                       ++++++++al+++   f++v+t e+
  gi|313125179|ref|YP_004035443.1| 163 IEADHKEYALEHADWLFGEVTTREE 187
                                       **********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1188.52
//
Query:       gi|313125180|ref|YP_004035444.1|  [L=495]
Description: hypothetical protein Hbor_04010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.074   13.4   0.2       0.15   12.3   0.2    1.5  1  Peptidase_M91  Effector protein


Domain annotation for each model (and alignments):
>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   8.6e-06      0.15      58     124 ..     155     225 ..      95     235 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.6e-06
                     Peptidase_M91  58 ngtakyeekekgegtdaeinynpafsseeegkegrPs......avLyHElaHaydalngtlddgeydgkdeed 124
                                       +g ++ e  ++++g+++   y+p+ + + +  + +P+      a+L HEl Ha +  + +l +++y g++++ 
  gi|313125180|ref|YP_004035444.1| 155 SGDSQAE-ISETQGSSVAGFYSPSNDAI-TVITPSPDspridnATLIHELTHALQDQHYDLTSQTYRGDTQDR 225
                                       3333222.55566666666677777776.3333334366799788*******************999977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2941.37
//
Query:       gi|313125181|ref|YP_004035445.1|  [L=453]
Description: hypothetical protein Hbor_04020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.036   14.0   0.0    1.5  1  Peptidase_M78  IrrE N-terminal-like domain
        0.1   12.8   0.0        0.2   11.9   0.0    1.5  1  DUF4157        Domain of unknown function (DUF4157)
       0.21   11.3   0.0       0.31   10.8   0.0    1.2  1  Peptidase_M76  Peptidase M76 family


Domain annotation for each model (and alignments):
>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     6e-06     0.036      20      57 ..     147     183 ..     135     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-06
                     Peptidase_M78  20 gfrfdnsetkvivlnsnhsptrqrftlaHElgHlllhh 57 
                                       g+++++  +++++++++  p   r tlaHEl H+l ++
  gi|313125181|ref|YP_004035445.1| 147 GYYTPGD-DQIVIVSNSEQPKINRVTLAHELVHALQDQ 183
                                       5555554.999**********************98655 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.4e-05       0.2      55      77 ..     162     184 ..     144     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                           DUF4157  55 qpesaagrellaHELtHvvqqre 77 
                                       +++ + +r +laHEL+H  q ++
  gi|313125181|ref|YP_004035445.1| 162 SEQPKINRVTLAHELVHALQDQQ 184
                                       4555678999**********986 PP

>> Peptidase_M76  Peptidase M76 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.2e-05      0.31      46      96 ..     146     196 ..      90     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.2e-05
                     Peptidase_M76  46 aggfspee.gillcenrlrskehledtlahElvhayDdlrakvdwsnlrhlA 96 
                                       ag ++p   +i++++n+  + +  + tlahElvha  d ++  +  + +h A
  gi|313125181|ref|YP_004035445.1| 146 AGYYTPGDdQIVIVSNSE-QPKINRVTLAHELVHALQDQQFGFNPPQETHDA 196
                                       455555444799998875.55677889*********9999988876666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2823.83
//
Query:       gi|313125182|ref|YP_004035446.1|  [L=140]
Description: hypothetical protein Hbor_04030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.029   13.1   6.7      0.039   12.7   6.7    1.3  1  PLRV_ORF5  Potato leaf roll virus readthrough protein
      0.043   12.8   3.1      0.044   12.8   3.1    1.1  1  DEC-1_N    DEC-1 protein, N-terminal region
        1.2    6.7   9.0        1.3    6.6   9.0    1.1  1  TALPID3    Hedgehog signalling target


Domain annotation for each model (and alignments):
>> PLRV_ORF5  Potato leaf roll virus readthrough protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   6.7   6.5e-06     0.039       2      39 ..      41      81 ..      27      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-06
                         PLRV_ORF5  2 epspapqptpeptpak.hkrfieyvGip.tltisaren.dd 39
                                       p+ +p ptp+ptp+  +   i y+  p +l+i++ en +d
  gi|313125182|ref|YP_004035446.1| 41 TPTATPTPTPTPTPTAtPTETISYIDCPgVLSIDSVENvTD 81
                                      56667888888888777999*******96689999999434 PP

>> DEC-1_N  DEC-1 protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.1   7.3e-06     0.044      96     153 ..       8      66 ..       1      99 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-06
                           DEC-1_N  96 vGaalqsllplqsldgllGaaapapalaaapppapapvp.ddpapapaapqaaafaffn 153
                                       + a l s+   +++++l  + +p p+ +a+  p+p+ +p  +p+p+p a ++ + ++ +
  gi|313125182|ref|YP_004035446.1|   8 LVALLVSFAGCSGVPSLSDNGTPTPTQTATSTPTPTATPtPTPTPTPTATPTETISYID 66 
                                       556788899999999999999********999999888855789999988888777766 PP

>> TALPID3  Hedgehog signalling target
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   9.0   0.00021       1.3     945    1031 ..      35      60 ..      19     102 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00021
                           TALPID3  945 ketllptPvptPqptppqsPpssekelspvktPdsSpseseadgavsskekeaekgadtspaktlvktPvvtPva 1019
                                        ++t  ptP +tP ptp ++P+++                                                    
  gi|313125182|ref|YP_004035446.1|   35 TATSTPTPTATPTPTPTPTPTAT---------------------------------------------------- 57  
                                        22333444444444444444332.................................................... PP

                           TALPID3 1020 tPpkvatpsppl 1031
                                                 p++
  gi|313125182|ref|YP_004035446.1|   58 ---------PTE 60  
                                        .........222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 927.90
//
Query:       gi|313125183|ref|YP_004035447.1|  [L=382]
Description: nicotinic acid phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-18   66.0   0.0    4.6e-18   65.6   0.0    1.2  1  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
  ------ inclusion threshold ------
      0.024   14.7   0.0      0.092   12.8   0.0    2.0  2  QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   5.1e-22   4.6e-18       1     169 []     112     302 ..     112     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 5.1e-22
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSS..HHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaags..ive 68 
                                       +At++  + +aa + +v +++ R  +P+l ++ ++++l++G d          lg +   +++++ ++++g   ++e
  gi|313125183|ref|YP_004035447.1| 112 VATAALDVRRAAPDSTVLSFGARHVHPALTAMIERSALLAGLDgishvaaGDVLGREASGTMPHALLICFGRgnQEE 188
                                       89***************************************9999888877889999************97545*** PP

                                       HHHHHHHHHTTTSE..EEEEESSHHHHHHHHHHT......-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEE CS
                         QRPTase_C  69 avksvreavdkevk..ievevesleeleevleae......adiimLDnfsv..eelkkaveel.keknkr....vli 130
                                       a+k+++eav++ v+     +++s+ e++evl a        d ++LD+ s+   +++++v e+ +  n +    v +
  gi|313125183|ref|YP_004035447.1| 189 AWKAFDEAVEESVPrvALCDTYSD-ETDEVLRAVealgddLDSVRLDTTSSrrGDFRHIVREVqWTLNAHdhesVDV 264
                                       **********99999545566665.55555553224456699*******987799*******977777668889*** PP

                                       EEESS--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                         QRPTase_C 131 evSGgvtlenveeyaksgvdvisvgalthsvkalDislk 169
                                       +vSGg+   +++++++   d ++vg  +++++++D++l+
  gi|313125183|ref|YP_004035447.1| 265 FVSGGLGPSDLRHLRDVA-DGFGVGGYVSNANPVDFALD 302
                                       *****************9.*****************996 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05     0.092      30      89 .]      54     110 ..      50     110 .. 0.89
   2 ?   -3.8   0.0       1.5   1.4e+04      49      60 ..     349     360 ..     348     363 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                                       E-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHHH CS
                         QRPTase_N  30 vaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrlS 89 
                                       +aG++ a++++e   ++ v++  ++G  +  g  +++ieG++ ++ + E  +L +l+++S
  gi|313125183|ref|YP_004035447.1|  54 LAGVKDAAALLEGH-DVDVDAI-PEGRLFDGG-PVMRIEGSYLDFGRFETSLLGFLSHAS 110
                                       79999999999988.8888876.9**999665.99***********************98 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.5
                                       EESS-TT-EEET CS
                         QRPTase_N  49 ellvkDGervek 60 
                                       e+l++DGe v++
  gi|313125183|ref|YP_004035447.1| 349 EPLIRDGEIVRE 360
                                       67899**99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 2035.65
//
Query:       gi|313125184|ref|YP_004035448.1|  [L=200]
Description: hypothetical protein Hbor_04050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-41  141.1   0.0    2.9e-41  140.9   0.0    1.0  1  AMMECR1   AMMECR1
  ------ inclusion threshold ------
       0.15   11.7   0.2       0.21   11.2   0.2    1.2  1  DUF5549   Family of unknown function (DUF5549)


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9   0.0   3.2e-45   2.9e-41       1     166 []      18     188 ..      18     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 3.2e-45
                                       HHHHHHHHHHHTTSS-S-H.H---HHHHSEEEEEEEEE..EE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS CS
                           AMMECR1   1 lklareaieealkeekkle.eeakeelkekaglFVtlk..ekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRF 74 
                                       ++lare++e+++ ++++ +  + +++++ ++g+FV+++  +++g+LRGC G ++ +++L+++++++A++aA  D++ 
  gi|313125184|ref|YP_004035448.1|  18 VELARESVESYVLHGQREQpGSMRDAFYARTGAFVRIRstRGRGRLRGCAGAYRGKDQLGHAIVDAAIQAASGDSCG 94 
                                       689*****99999999888789999*************888888********************************* PP

                                       ----HHHHTTEEEEEEEE---EE--..GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-TT CS
                           AMMECR1  75 spvtaeElpeleveVsvLtepepiv..ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrpd 149
                                       s++++ Elp+l+++V+++ +    +  ++dle+g+hG+ i+k++++++l+P+++ve+gw+ e+fl++++rK+gl+p 
  gi|313125184|ref|YP_004035448.1|  95 SEIEPPELPNLNISVCIVCNHVLTNdpVADLELGTHGVAIDKDGKHGWLYPTIPVENGWSAEQFLTHACRKGGLSPL 171
                                       ********************9777445699**********************************************9 PP

                                       CCCSTTSEEEEE-EEEE CS
                           AMMECR1 150 ewkdseikltryevekf 166
                                       +w+d++ ++t +e+++f
  gi|313125184|ref|YP_004035448.1| 172 AWQDEDSMVTLFEGQVF 188
                                       9************9986 PP

>> DUF5549  Family of unknown function (DUF5549)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   2.3e-05      0.21      93     129 ..      34      71 ..      23     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.3e-05
                           DUF5549  93 hiqpgtvrrpprgrggwevrrrpgrgrgrqrrw.gler 129
                                       + qpg++r  + +r g  vr r  rgrgr r   g  r
  gi|313125184|ref|YP_004035448.1|  34 REQPGSMRDAFYARTGAFVRIRSTRGRGRLRGCaGAYR 71 
                                       56899***********************8886544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1108.58
//
Query:       gi|313125185|ref|YP_004035449.1|  [L=902]
Description: heavy metal-translocating p-type ATPase, cd/co/hg/pb/zn-transporting [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-51  173.1   0.6    9.8e-51  171.8   0.6    1.7  1  E1-E2_ATPase  E1-E2 ATPase
    5.2e-43  147.8   3.9    5.2e-43  147.8   3.9    1.8  2  Hydrolase     haloacid dehalogenase-like hydrolase
      8e-24   83.9   1.6    6.7e-12   45.7   0.0    4.0  5  HMA           Heavy-metal-associated domain
      0.001   18.9   0.4     0.0021   17.8   0.4    1.5  1  Hydrolase_3   haloacid dehalogenase-like hydrolase
      0.003   18.0   0.2      0.024   15.0   0.2    2.3  1  HAD           haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.013   15.3   0.0        1.6    8.4   0.0    2.6  2  CT_C_D        Carboxyltransferase domain, subdomain C and D


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.8   0.6   3.3e-54   9.8e-51       1     181 []     323     514 ..     323     514 .. 0.96

  Alignments for each domain:
  == domain 1  score: 171.8 bits;  conditional E-value: 3.3e-54
                                       SSS--EEEEE-TTS-EE..........EEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-T CS
                      E1-E2_ATPase   1 kllpptakvirdgteee..........idakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekg 67 
                                       +l+p+ta+v+r+    +          ++++++ +G  v++++gdrvp+Dg + eg++ vdes +TGEs+pv+ke g
  gi|313125185|ref|YP_004035449.1| 323 ELSPDTATVLRNSGSSKtsqaereevvVPVEDVAVGETVIVRPGDRVPLDGTVTEGTSAVDESPITGESVPVDKEPG 399
                                       5899******88844444667788888************************************************** PP

                                       TEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSST CS
                      E1-E2_ATPase  68 dmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksl 144
                                        +vf+G++v +g ++++ t+ +++++l+k++++ve+a+++kt+ ++++d+++++++p++++ a++++ + +ll++++
  gi|313125185|ref|YP_004035449.1| 400 LEVFAGSIVEEGYLEIETTTPASESTLSKVVDMVEDANREKTEAERFIDRFARYYTPIIVVGAIATATVPPLLFEEP 476
                                       **************************************************************************999 PP

                                       T.HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 145 a.eallralallvaaiPcaLplavplalalgarrlakk 181
                                       +  +++ral+llv+a+Pca+++ +p++++ g++++a++
  gi|313125185|ref|YP_004035449.1| 477 FrMWFVRALTLLVVACPCAFVISTPVSVVSGITSAARN 514
                                       989********************************996 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.6   7.8e+03       8      21 ..     371     384 ..     371     388 .. 0.85
   2 !  147.8   3.9   1.7e-46   5.2e-43       1     209 [.     530     778 ..     530     779 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                                       SBTTTBCHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                         Hydrolase   8 kdGTLttgepsved 21 
                                       +dGT+t+g++ v +
  gi|313125185|ref|YP_004035449.1| 371 LDGTVTEGTSAVDE 384
                                       69******987765 PP

  == domain 2  score: 147.8 bits;  conditional E-value: 1.7e-46
                                       SSEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakar...sgaltgfatfigrg. 67 
                                       +++v+ Dk+GTLttge  v+dv++ +       l  aaa+e  sehpi++a+v++a +r   + ++ +f+ ++g+g 
  gi|313125185|ref|YP_004035449.1| 530 VDAVAVDKTGTLTTGELGVTDVVALNgndesdVLGCAAAIESRSEHPIAQAIVEYAADRdvpERDIREFESITGKGv 606
                                       689***********************99988888888888888****************8888888*********** PP

                                       .......HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH................................ CS
                                       .......xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx................................ RF
                         Hydrolase  68 .......ayaigkpewltal..dippdlgaaigsaqsqgrtvall................................ 103
                                              +   gkp ++++l  d ++   +a+g   s+g  ++ +                                
  gi|313125185|ref|YP_004035449.1| 607 kavlddkVHYAGKPGLFESLgfDLEHTHVQADGGVRSDGGQAVEDarncdhgryldlanevvprlqaegksvvlvgt 683
                                       *******9999***********999999999999999999999999******************************* PP

                                       TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTE.EEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 104 qaralavftiadplkvkpeaaeavasLkaagi.evvlltgdnpetaeraanqlGddyfdaviasdietvakpspegk 179
                                       ++++ +v+++ad+  v+pe a av +L++ gi +vv+ltgdn++ta+ + +++G           +e+ a  +pe+k
  gi|313125185|ref|YP_004035449.1| 684 EDEIEGVVAVADT--VRPESAWAVSRLHDHGIsQVVMLTGDNERTAQVIGERVG----------VDEVRADLLPEQK 748
                                       99***********..***************************************..........5666********* PP

                                       HHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 180 vaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       v+a+reL ++   vamVGDgvnDa+alaaA
  gi|313125185|ref|YP_004035449.1| 749 VEAVRELLAEHDSVAMVGDGVNDAPALAAA 778
                                       *****************************9 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   5.5e-12   1.7e-08       2      61 ..      57     116 ..      56     117 .. 0.96
   2 !   45.7   0.0   2.2e-15   6.7e-12       1      61 [.     125     185 ..     125     186 .. 0.97
   3 ?   -3.8   0.0         6   1.8e+04      20      32 ..     524     536 ..     523     538 .. 0.88
   4 ?   -2.9   0.1       3.2   9.6e+03      34      56 ..     674     697 ..     671     699 .. 0.73
   5 ?   -4.0   0.0         6   1.8e+04      14      26 ..     750     762 ..     746     763 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 5.5e-12
                               HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                       ++v+ m+C +Ca kv+k++ +  gV++v+ +  t+t+ V +d+++t+ ++++  +e+agy
  gi|313125185|ref|YP_004035449.1|  57 LSVPEMDCPSCAEKVTKSVRGDAGVRDVDAQPTTGTLYVQYDPTATDDSAVRSRVESAGY 116
                                       689******************************************77699*********9 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 2.2e-15
                               HMA   1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                       t++v+ m+C +Ca+kve +L +++g+ + + +  +++vt+++++++++  ++++aie agy
  gi|313125185|ref|YP_004035449.1| 125 TFSVPEMDCPSCAGKVENSLDGVSGIVDFETQPTAGKVTIRYNPDEASRGDFVAAIEGAGY 185
                                       79********************************************88799*********9 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 6
                               HMA  20 LselpgVesvkvd 32 
                                       L+++++V++v vd
  gi|313125185|ref|YP_004035449.1| 524 LEAMNDVDAVAVD 536
                                       78999****9998 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 3.2
                               HMA  34 atktvtVegdaes.tklrkiieai 56 
                                       + k+v+ +g++++   + ++  ++
  gi|313125185|ref|YP_004035449.1| 674 EGKSVVLVGTEDEiEGVVAVADTV 697
                                       568999999999967666666666 PP

  == domain 5  score: -4.0 bits;  conditional E-value: 6
                               HMA  14 akvekvLselpgV 26 
                                        +v++ L+e+++V
  gi|313125185|ref|YP_004035449.1| 750 EAVRELLAEHDSV 762
                                       5789999999988 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.4   7.1e-07    0.0021     188     241 ..     748     798 ..     746     804 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.1e-07
                                       HHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS.-HHHHHHSSE CS
                       Hydrolase_3 188 KgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgna.seevkkaAdy 241
                                       K +a+++l+     +++ v+ +GDg ND + L aa +gvAmg a ++++ + Ad 
  gi|313125185|ref|YP_004035449.1| 748 KVEAVRELL----AEHDSVAMVGDGVNDAPALAAATVGVAMGAAgTDTALETADV 798
                                       555555555....78999***********************98636777777776 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2     8e-06     0.024      85     187 ..     696     775 ..     681     776 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8e-06
                               HAD  85 lldpgalellaahraaGd.rvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalre 160
                                       + +p+   ++++ ++ G+ +vv+++g +++ ++ + +++g    +++       + +           e+kv a+re
  gi|313125185|ref|YP_004035449.1| 696 TVRPESAWAVSRLHDHGIsQVVMLTGDNERTAQVIGERVG----VDE-------VRAD-------LLPEQKVEAVRE 754
                                       45687777777788****99999*****************....555.......3333.......556789999999 PP

                               HAD 161 wlaaegegidleevvayGDspsDlpll 187
                                        la++       +v  +GD+++D p+l
  gi|313125185|ref|YP_004035449.1| 755 LLAEHD------SVAMVGDGVNDAPAL 775
                                       444444......35666*******998 PP

>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00053       1.6      29      76 ..      70     117 ..      58     136 .. 0.80
   2 ?    3.7   0.0     0.015        43      44      73 ..     154     183 ..     137     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00053
                                       HHHHHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHHHHH CS
                            CT_C_D  29 alaaalrakalpgvvelvpayrsllvefdpealdaaellaalkallee 76 
                                       ++++++r +a  + v++ p+  +l v++dp+a+d ++++++++++  +
  gi|313125185|ref|YP_004035449.1|  70 KVTKSVRGDAGVRDVDAQPTTGTLYVQYDPTATDDSAVRSRVESAGYA 117
                                       56666777776777899************************9987655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.015
                                       EEEE-SSEEEEEESCCCCHHHHHH.HHHHH CS
                            CT_C_D  44 elvpayrsllvefdpealdaaellaalkal 73 
                                       e+ p++ +++++++p++ ++ +++aa++ +
  gi|313125185|ref|YP_004035449.1| 154 ETQPTAGKVTIRYNPDEASRGDFVAAIEGA 183
                                       789**********************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (902 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.91u 0.34s 00:00:01.25 Elapsed: 00:00:00.58
# Mc/sec: 4674.98
//
Query:       gi|313125186|ref|YP_004035450.1|  [L=357]
Description: matrixin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-09   37.6   0.0    1.2e-05   25.2   0.0    2.2  2  Peptidase_M10  Matrixin
    0.00014   22.4   0.0     0.0048   17.4   0.0    2.3  2  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
    0.00019   21.7   0.1    0.00075   19.7   0.0    1.9  2  Reprolysin_5   Metallo-peptidase family M12
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.022   14.6   0.0    1.3  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like
      0.015   14.9   0.0      0.032   13.8   0.0    1.4  1  Astacin        Astacin (Peptidase family M12A)
       0.03   14.0   0.0      0.075   12.7   0.0    1.7  2  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
      0.037   13.3   0.0      0.083   12.1   0.0    1.5  1  DUF4953        Met-zincin
        0.1   13.2   0.4       0.22   12.1   0.4    1.6  1  LPAM_1         Prokaryotic membrane lipoprotein lipid attachm
       0.15   11.6   2.0        0.5    9.9   0.1    2.4  3  Peptidase_M57  Dual-action HEIGH metallo-peptidase
       0.17   10.8   0.0       0.26   10.2   0.0    1.2  1  Peptidase_M66  Peptidase M66


Domain annotation for each model (and alignments):
>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   6.7e-09   1.2e-05      49     135 ..     120     196 ..      75     217 .. 0.70
   2 !   10.5   0.0   0.00023      0.41       7      59 ..     220     277 ..     214     286 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.7e-09
                                       CESEEEEEESSSSSSSSSXBSSSSESEEEBSSSSTTTTEEEEETTS-EESSTS-.SSSEEHHHHHHHHHHHHTTBES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10  49 eadikieFgrgehgdgypfdgkggvlahafapgeglggdihfdddeqWtlgeekveqgvslflVaaHEiGHalGLeH 125
                                       + di +eF     +d  ++dg++   + a      ++ + ++d  e+ +++++   ++ s +lV  HE+GH+lGL+H
  gi|313125186|ref|YP_004035450.1| 120 NPDIVVEFV----DDVPDCDGAEDAAGCAPL----ITDRRQIDTPETVSIQTR--FSNDSTVLVLEHEFGHTLGLTH 186
                                       555555555....445556666655544433....455667777777777765..46678899************** PP

                                       XSSTTSTTSS CS
                                       xxxxxxxxxx RF
                     Peptidase_M10 126 ssdkdalmyp 135
                                        +++ ++m++
  gi|313125186|ref|YP_004035450.1| 187 DDAPADVMAS 196
                                       ********85 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                                       EEEEESSSXTTSXHHHHHHHHHHHHHHHHTTS.....SSEEEEE.SSSCESEEEEEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxx.xxxxxxxxxxxxxx RF
                     Peptidase_M10   7 ltyrilnetpdleeeevrkairrAfkvwsevt.....plkFtev.kkgeadikieFgrg 59 
                                        t  +++ + + ++e+ r+++++A++ +++ +     +l+Ft v + ++adi ++F ++
  gi|313125186|ref|YP_004035450.1| 220 FTVYVDSAN-ATKSEQAREQVQHALDYYERGAegmpnNLTFTVVdDAENADIVVGFSDE 277
                                       555554444.56889999*********99998888878******88888*******876 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.7e-06    0.0048      59     124 .]     116     187 ..      83     187 .. 0.75
   2 ?    2.7   0.0     0.097   1.7e+02      47      81 ..     253     289 ..     221     313 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.7e-06
                      Reprolysin_3  59 rgqagyDlvhlftarde.....sgvgGlAyvgsvcnsskk.agvnsgssvlgkvgadtvaHEiGHnfganHt 124
                                        + a+ D+v+ f ++       ++ +G+A + +  ++ ++   v+ +++ ++++++ ++ HE GH +g+ H+
  gi|313125186|ref|YP_004035450.1| 116 PDAANPDIVVEFVDDVPdcdgaEDAAGCAPLITDRRQIDTpETVSIQTRFSNDSTVLVLEHEFGHTLGLTHD 187
                                       46789999999999555999999999999986666665554455555667799999***************7 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.097
                      Reprolysin_3  47 ldelaevtaeaergqagyDlvhlftarde....sgvgGl 81 
                                       + ++ ++t     + +++D+v+ f+++        ++G 
  gi|313125186|ref|YP_004035450.1| 253 MPNNLTFTVVD--DAENADIVVGFSDESPcspdAASCGA 289
                                       44455555555..789*********98878877777775 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.2e-07   0.00075     133     161 ..     161     189 ..     133     212 .. 0.79
   2 ?   -0.9   0.0      0.85   1.5e+03      67     101 ..     233     276 ..     217     318 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.2e-07
                      Reprolysin_5 133 nsvvvstatevqvvaHElGHnfGavHDcd 161
                                        + + s++++v v+ HE+GH++G  HD +
  gi|313125186|ref|YP_004035450.1| 161 IQTRFSNDSTVLVLEHEFGHTLGLTHDDA 189
                                       445578999******************87 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.85
                      Reprolysin_5  67 asstgdaselLnefq.........sassalrgqqnddlailflm 101
                                       ++  +++++ L+ ++           ++  ++++n+d+++ f++
  gi|313125186|ref|YP_004035450.1| 233 EQAREQVQHALDYYErgaegmpnnLTFTVVDDAENADIVVGFSD 276
                                       44445555555555444444444444555555555555555555 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.3e-05     0.022     122     147 ..     167     194 ..     147     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                      Reprolysin_2 122 etkeidvvaHEvGHaFGatHdndgs..s 147
                                       ++  ++v+ HE GH+ G tHd++     
  gi|313125186|ref|YP_004035450.1| 167 NDSTVLVLEHEFGHTLGLTHDDAPAdvM 194
                                       3677899**************9855452 PP

>> Astacin  Astacin (Peptidase family M12A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-05     0.032      54     101 ..     139     192 ..     133     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                                       --SSCEE-SS--...SSEEEEEE-CCC-...SHHHHHHHHHHHHTB--GGGSTT CS
                           Astacin  54 kaegClssvgra...ggkqevslgkgCe...klgiivHElmHalGffHeqsRtd 101
                                       +a gC+  + ++   +++++vs+++      ++ +  HE++H+lG+ H+ +  d
  gi|313125186|ref|YP_004035450.1| 139 DAAGCAPLITDRrqiDTPETVSIQTRFSndsTVLVLEHEFGHTLGLTHDDAPAD 192
                                       567888877765446678999*995443112566779***********987666 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.2e-05     0.075     134     154 ..     169     189 ..     108     232 .. 0.74
   2 ?   -3.5   0.0       3.8   6.8e+03      82     102 ..     258     278 ..     254     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                      Reprolysin_4 134 deydifAHEiGHtfGaaHdls 154
                                       ++  ++ HE GHt+G+ Hd +
  gi|313125186|ref|YP_004035450.1| 169 STVLVLEHEFGHTLGLTHDDA 189
                                       3445699***********987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.8
                      Reprolysin_4  82 tltstrdskdyDlaallrdtr 102
                                       t+t   d +++D+++ + d  
  gi|313125186|ref|YP_004035450.1| 258 TFTVVDDAENADIVVGFSDES 278
                                       788888999999998777664 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.6e-05     0.083      15      30 ..     172     187 ..     159     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.6e-05
                           DUF4953  15 fvvaHEvGhtLGLrhN 30 
                                        v  HE GhtLGL+h 
  gi|313125186|ref|YP_004035450.1| 172 LVLEHEFGHTLGLTHD 187
                                       6889***********6 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   0.00012      0.22       5      17 ..       8      20 ..       4      20 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                            LPAM_1  5 llalgalllLsGC 17
                                       +al++ll+LsGC
  gi|313125186|ref|YP_004035450.1|  8 AVALVLLLVLSGC 20
                                      689********** PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       0.4   7.1e+02      81     117 ..      33      69 ..      27      79 .. 0.81
   2 ?    9.9   0.1   0.00028       0.5     131     151 ..     168     188 ..     153     194 .. 0.76
   3 ?   -1.8   0.0       1.1     2e+03      53      92 ..     231     272 ..     218     302 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.4
                     Peptidase_M57  81 rgtntqasdmvvaditaktasgaggsaGfPsgGlPyk 117
                                        g++t++ ++++ + +a+ta++  +++ +P+g  P++
  gi|313125186|ref|YP_004035450.1|  33 VGDETPSATTSTEQAAARTATQNPSTTAAPTGASPWG 69 
                                       6788888888889999999999999999999999986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00028
                     Peptidase_M57 131 dvnehvithelGhtvGlRhsD 151
                                       d    v+ he+Ght+Gl h D
  gi|313125186|ref|YP_004035450.1| 168 DSTVLVLEHEFGHTLGLTHDD 188
                                       34445899***********98 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                     Peptidase_M57  53 stsklrtgLdlaianynal..glsltfrltrgtntqasdmvv 92 
                                        + + r+ ++ a++ y +   g+  ++++t  +  ++ d+vv
  gi|313125186|ref|YP_004035450.1| 231 KSEQAREQVQHALDYYERGaeGMPNNLTFTVVDDAENADIVV 272
                                       333455667777777765422443444445555555556554 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00014      0.26     194     257 ..     172     239 ..     164     270 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                     Peptidase_M66 194 gefiHEqGHalGLpHylageaaskg...sypyaegsllgseWGyDa.nhneflsnllaktseyknckk 257
                                        ++ HE GH lGL H  a  +  +     y   + ++ + +  +D  +   +++   a++se+++ + 
  gi|313125186|ref|YP_004035450.1| 172 LVLEHEFGHTLGLTHDDAPADVMASrsvLYTTPQPNATERAFPWDDgEFTVYVDSANATKSEQAREQV 239
                                       5678***********76644333222134555566666666666541334445555555555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.68u 0.37s 00:00:01.05 Elapsed: 00:00:00.58
# Mc/sec: 1847.71
//
Query:       gi|313125187|ref|YP_004035451.1|  [L=157]
Description: ankyrin repeat-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-26   92.2   0.1    1.6e-11   44.5   0.1    4.1  4  Ank_4     Ankyrin repeats (many copies)
      2e-20   73.2   0.0    1.8e-10   41.3   0.0    2.4  2  Ank_2     Ankyrin repeats (3 copies)
      2e-18   66.2   0.0    1.2e-08   35.0   0.0    3.1  3  Ank_5     Ankyrin repeats (many copies)
    5.6e-15   55.0   0.0      3e-06   27.4   0.0    3.7  4  Ank       Ankyrin repeat
    6.7e-14   50.7   0.0    0.00044   20.5   0.0    4.0  4  Ank_3     Ankyrin repeat
     0.0039   17.1   0.1        1.1    9.1   0.0    2.3  2  BAT       GAF and HTH_10 associated domain


Domain annotation for each model (and alignments):
>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   7.8e-07    0.0023       1      46 [.       3      46 ..       3      47 .. 0.92
   2 !   44.5   0.1   5.3e-15   1.6e-11       4      55 .]      38      88 ..      36      88 .. 0.97
   3 !   34.9   0.0   5.3e-12   1.6e-08       3      43 ..      70     109 ..      70     115 .. 0.95
   4 !    7.7   0.0    0.0018       5.4      14      38 ..     116     139 ..     110     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.8e-07
                             Ank_4  1 eltaLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrg 46
                                      e+t+L+y +++g++e  r L+ + +din   ++sG+++lh Aa  g
  gi|313125187|ref|YP_004035451.1|  3 ETTLLFYSIEEGDEEKFRDLI-NTVDINTL-DESGDNLLHAAAAYG 46
                                      5799*****************.78*****9.***********9876 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 5.3e-15
                             Ank_4  4 aLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55
                                      +Lh+aa++g+ e ++ L+++++din++  ++G t+lh+A+ +g+ ++++ Ll
  gi|313125187|ref|YP_004035451.1| 38 LLHAAAAYGQDEFAKELIDRDIDINHR-GKEGKTPLHYALEMGYEDMVRILL 88
                                      79*************************.*********************997 PP

  == domain 3  score: 34.9 bits;  conditional E-value: 5.3e-12
                             Ank_4   3 taLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAa 43 
                                       t+Lhya ++g +++vr+Ll+ gad+  + +++G+ +l+ A+
  gi|313125187|ref|YP_004035451.1|  70 TPLHYALEMGYEDMVRILLSEGADVTVT-DDYGNQPLWSAV 109
                                       79*************************9.**********98 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0018
                             Ank_4  14 lelvrlLlekgadinaqdnrsGeta 38 
                                        +++++L+++gad+  q n+ G ++
  gi|313125187|ref|YP_004035451.1| 116 DDIIQSLVAHGADPANQ-NDAGKSP 139
                                       5789*************.9999765 PP

>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   2.5e-10   7.4e-07      26      81 ..       3      63 ..       1      65 [. 0.90
   2 !   41.3   0.0   5.9e-14   1.8e-10      25      82 ..      67     132 ..      63     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.5e-10
                             Ank_2 26 gktaLhyAakngnleivklLleh.....adndgrtpLhyAarsghleivklLlekgadinl 81
                                      + t L+y++++g++e  + L++      +d++g + Lh+Aa +g+ e++k L+++++din 
  gi|313125187|ref|YP_004035451.1|  3 ETTLLFYSIEEGDEEKFRDLINTvdintLDESGDNLLHAAAAYGQDEFAKELIDRDIDINH 63
                                      5799*****************97666567799*********************999**996 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 5.9e-14
                             Ank_2  25 ngktaLhyAakngnleivklLleh......adndgrtpLhyAars..ghleivklLlekgadinlk 82 
                                       +gkt+LhyA + g++++v++Ll++      +d++g+ pL  A+ +  +  +i++ L+ +gad+  +
  gi|313125187|ref|YP_004035451.1|  67 EGKTPLHYALEMGYEDMVRILLSEgadvtvTDDYGNQPLWSAVVNeeTKDDIIQSLVAHGADPANQ 132
                                       79********************97767776669***********977578************9765 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.9e-11   5.6e-08       7      56 .]      26      75 ..      22      75 .. 0.95
   2 !   35.0   0.0   4.2e-12   1.2e-08       1      53 [.      54     105 ..      54     105 .. 0.96
   3 !    7.2   0.0    0.0022       6.6      30      56 .]     117     143 ..     115     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.9e-11
                             Ank_5  7 advnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56
                                      +d+n+ld+ g + Lh Aa yg  + +++L++r  d+n + ++G+t+l++A
  gi|313125187|ref|YP_004035451.1| 26 VDINTLDESGDNLLHAAAAYGQDEFAKELIDRDIDINHRGKEGKTPLHYA 75
                                      899**********************************************9 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 4.2e-12
                             Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltal 53 
                                       L++++ +d+n++ ++g tpLh+A + g+ d+vr+Ll +gad ++td++G+ +l
  gi|313125187|ref|YP_004035451.1|  54 LIDRD-IDINHRGKEGKTPLHYALEMGYEDMVRILLSEGADVTVTDDYGNQPL 105
                                       78998.9******************************************9987 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0022
                             Ank_5  30 dvvrlLlargadlnltdsrGltaldlA 56 
                                       d+++ L+a+gad+  +++ G+++  +A
  gi|313125187|ref|YP_004035451.1| 117 DIIQSLVAHGADPANQNDAGKSPRSIA 143
                                       78999******************9887 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.9   5.7e+03       4      29 ..       5      30 ..       2      32 .. 0.53
   2 !   10.0   0.0   0.00032      0.97       2      30 ..      35      64 ..      34      66 .. 0.84
   3 !   27.4   0.0   9.9e-10     3e-06       2      32 .]      68      99 ..      67      99 .. 0.92
   4 !   13.3   0.0     3e-05      0.09       1      31 [.     100     133 ..     100     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.9
                                      BHHHHHHHHTTHHHHHHHHTTTSTTC CS
                               Ank  4 TPLHlAatngkkriiklLLhGAnlna 29
                                      T L + + +g+++  ++L++  ++n 
  gi|313125187|ref|YP_004035451.1|  5 TLLFYSIEEGDEEKFRDLINTVDINT 30
                                      55666555555444556664356665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00032
                                      SBBHHHHHHHHTTHHHHHHHHTT.TSTTCB CS
                               Ank  2 GnTPLHlAatngkkriiklLLhG.Anlnal 30
                                      G+  LH Aa +g+ + +k+L+++  ++n +
  gi|313125187|ref|YP_004035451.1| 35 GDNLLHAAAAYGQDEFAKELIDRdIDINHR 64
                                      8889**9999***********653778765 PP

  == domain 3  score: 27.4 bits;  conditional E-value: 9.9e-10
                                      SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                               Ank  2 GnTPLHlAatngkkriiklLL.hGAnlnaldn 32
                                      G TPLH+A   g +++++ LL  GA+++ +d+
  gi|313125187|ref|YP_004035451.1| 68 GKTPLHYALEMGYEDMVRILLsEGADVTVTDD 99
                                      9******9999999*******77*****9995 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 3e-05
                                       TSBBHHHHHH....HHTTHHHHHHHH.TTTSTTCBT CS
                               Ank   1 dGnTPLHlAa....tngkkriiklLL.hGAnlnald 31 
                                       +Gn PL  A+    t +  +ii+ L+ hGA+++ ++
  gi|313125187|ref|YP_004035451.1| 100 YGNQPLWSAVvneeTKD--DIIQSLVaHGADPANQN 133
                                       68889**9998876555..8************7665 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.59   1.8e+03       4      30 ..       5      29 ..       5      30 .. 0.83
   2 !   17.3   0.0   1.6e-06    0.0049       2      31 .]      35      63 ..      34      63 .. 0.95
   3 !   20.5   0.0   1.5e-07   0.00044       1      29 [.      67      94 ..      67      96 .. 0.94
   4 !    7.3   0.0    0.0028       8.3       1      29 [.     100     129 ..     100     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.59
                             Ank_3  4 tpLhlAarsgnleivkfLlenkgadvn 30
                                      t+L++ ++ g+ e  + L++   +d+n
  gi|313125187|ref|YP_004035451.1|  5 TLLFYSIEEGDEEKFRDLIN--TVDIN 29
                                      78999999999988999999..68877 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.6e-06
                             Ank_3  2 GetpLhlAarsgnleivkfLlenkgadvna 31
                                      G ++Lh Aa +g  e +k L++ + +d+n+
  gi|313125187|ref|YP_004035451.1| 35 GDNLLHAAAAYGQDEFAKELID-RDIDINH 63
                                      789*******************.9****96 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 1.5e-07
                             Ank_3  1 nGetpLhlAarsgnleivkfLlenkgadv 29
                                      +G tpLh+A++ g  ++v+ Ll   gadv
  gi|313125187|ref|YP_004035451.1| 67 EGKTPLHYALEMGYEDMVRILLS-EGADV 94
                                      599********************.8***8 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0028
                             Ank_3   1 nGetpLhlAarsgnl..eivkfLlenkgadv 29 
                                       +G+ pL  A+ +  +  +i++ L+  +gad+
  gi|313125187|ref|YP_004035451.1| 100 YGNQPLWSAVVNEETkdDIIQSLVA-HGADP 129
                                       689999999999999645*******.9***8 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00036       1.1      38      79 ..       2      39 ..       1      62 [. 0.77
   2 !    6.1   0.0    0.0031       9.4      65      99 ..      91     128 ..      66     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00036
                               BAT 38 dgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtl 79
                                      d+++l+f++++++d e++rd+     +v d+  ++e++d  l
  gi|313125187|ref|YP_004035451.1|  2 DETTLLFYSIEEGDEEKFRDLIN---TV-DINTLDESGDNLL 39
                                      99*****************9998...55.7777887777544 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0031
                               BAT  65 vedvrvvseeddgtlleltvs...gpslastlaehGgt 99 
                                        +dv+v ++++++ l+ + v    ++++++ l++hG+ 
  gi|313125187|ref|YP_004035451.1|  91 GADVTVTDDYGNQPLWSAVVNeetKDDIIQSLVAHGAD 128
                                       469**********99999987444678999******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 934.38
//
Query:       gi|313125188|ref|YP_004035452.1|  [L=269]
Description: hypothetical protein Hbor_04090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-31  105.9   0.8    1.5e-30  105.2   0.8    1.4  1  DUF4157   Domain of unknown function (DUF4157)
    1.2e-27   96.1   3.9    1.2e-27   96.1   3.9    2.4  2  GH-E      HNH/ENDO VII superfamily nuclease with conserved GH
  ------ inclusion threshold ------
       0.06   13.1   0.3       0.06   13.1   0.3    1.8  2  SHOCT     Short C-terminal domain


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.8   2.6e-34   1.5e-30       2      78 ..       7      83 ..       6      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 2.6e-34
                           DUF4157  2 lpeavraemerafgadlsdVrvhtgsaaaraaralgAqAfTlgndivfaageyqpesaagrellaHELtHvvqqreg 78
                                      l++++++ me ++g+ l+dVr+htg++aa+a+++++A+AfT+gn+i+f++gey+p+sa+g+++laHEL+Hv qq++g
  gi|313125188|ref|YP_004035452.1|  7 LNTSIQRAMEDRMGDTLGDVRIHTGPSAAKACEDINARAFTVGNHIAFNHGEYDPSSAEGQHILAHELAHVRQQTGG 83
                                      7899**********************************************************************986 PP

>> GH-E  HNH/ENDO VII superfamily nuclease with conserved GHE residues
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5     0.023   1.4e+02      22      43 ..     130     151 ..     127     160 .. 0.83
   2 !   96.1   3.9     2e-31   1.2e-27       1      69 []     191     266 ..     191     266 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.023
                              GH-E  22 Hkpgreyrrlvkkaeeggitqk 43 
                                       H+++ ++++ +k+ e+g+ ++ 
  gi|313125188|ref|YP_004035452.1| 130 HVQRIKQWEKQKRDEKGKFSEL 151
                                       9**9*********999887754 PP

  == domain 2  score: 96.1 bits;  conditional E-value: 2e-31
                              GH-E   1 dGkvrdpntg.......gtsrerdwdmGHkpgreyrrlvkkaeeggitqkefldeynnpdnyrledpseNrShgae 69 
                                       dG+v+dpntg       g++re++wdmGHkp+reyr+l++k+++g i+++efl+ y++pdnyr+e+p++NrS+++e
  gi|313125188|ref|YP_004035452.1| 191 DGNVYDPNTGerlewdrGEPREGQWDMGHKPRREYRKLHQKYISGLISKEEFLNRYRDPDNYRPEKPKANRSRKYE 266
                                       7****************99*******************************************************98 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.89   5.3e+03       5      11 ..     150     156 ..     149     157 .. 0.78
   2 ?   13.1   0.3     1e-05      0.06       4      23 ..     226     245 ..     223     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.89
                             SHOCT   5 kLkeLya 11 
                                       +L e+y 
  gi|313125188|ref|YP_004035452.1| 150 ELEERYK 156
                                       6999996 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1e-05
                             SHOCT   4 ekLkeLyarGeIteEEFeak 23 
                                       +kL + y +G+I++EEF  +
  gi|313125188|ref|YP_004035452.1| 226 RKLHQKYISGLISKEEFLNR 245
                                       89***************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1600.19
//
Query:       gi|313125189|ref|YP_004035453.1|  [L=320]
Description: hypothetical protein Hbor_04100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.2   1.0        1.7    9.0   0.1    2.7  3  YnfE      Uncharacterized YnfE-like


Domain annotation for each model (and alignments):
>> YnfE  Uncharacterized YnfE-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1    0.0071   1.3e+02       5      50 ..      65     115 ..      61     121 .. 0.71
   2 ?    9.0   0.1   9.7e-05       1.7      40      75 ..     148     183 ..     142     184 .. 0.89
   3 ?   -3.5   0.0      0.77   1.4e+04      50      68 ..     252     270 ..     248     273 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0071
                              YnfE   5 qYvelvkknietinapDYeGkeeDlekq..keqlelYekq...Lkqesssd 50 
                                       +Y + +k+ ++t+ ap+ + +   +++   + +le++e +   L q++ss+
  gi|313125189|ref|YP_004035453.1|  65 KYYVYLKRGYDTVSAPENPVRIDAVRQAiaQMDLETFETHfgdLYQQFSSE 115
                                       688889**********99988888877522555677776422256666665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 9.7e-05
                              YnfE  40 ekqLkqesssdedfDevvdavvkcAagDlsleeLee 75 
                                       e  L +e ++++d D  ++++ ++A  Dls ee+ +
  gi|313125189|ref|YP_004035453.1| 148 ETDLGDELAAKHDLDITAESAADVAIADLSTEEIKQ 183
                                       77889999************************9865 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 0.77
                              YnfE  50 dedfDevvdavvkcAagDl 68 
                                        e f  ++d  + c   D+
  gi|313125189|ref|YP_004035453.1| 252 LEYFQSFMDHYLRCQIRDV 270
                                       5667888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2009.46
//
Query:       gi|313125190|ref|YP_004035454.1|  [L=184]
Description: hypothetical protein Hbor_04110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.072   13.2   0.1       0.33   11.1   0.1    2.0  1  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   1.8e-05      0.33      18     102 ..      80     168 ..      17     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.8e-05
                      Cupredoxin_1  18 aaektveitvkdggfePskievkagekvklk..iknkdkt.p..eefesedlgeekvlapgktttitiaplkpGeYe 89 
                                        +++  ++t+ d  ++  + +v  g ++++   + n+++t +  +e + ++l e    + +    +t+a+   G ++
  gi|313125190|ref|YP_004035454.1|  80 TEANYTNVTLHDPVCSDRVSTVSDGNSTQFVddW-NESQTtVyvVETYQNELLEVNIMQCDRDMALTFATAPDGDFR 155
                                       5556689999999****************77434.44444244466666668887999999**************** PP

                      Cupredoxin_1  90 ftcdmhmdakGkl 102
                                        t +  +d++G l
  gi|313125190|ref|YP_004035454.1| 156 TTSRCVQDVHGRL 168
                                       ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1105.35
//
Query:       gi|313125191|ref|YP_004035455.1|  [L=172]
Description: hypothetical protein Hbor_04120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0031   17.8   0.1      0.005   17.1   0.1    1.4  1  PIN_9     PIN like domain
  ------ inclusion threshold ------
      0.058   13.7   0.0      0.082   13.2   0.0    1.3  1  PIN_4     PIN domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   5.6e-07     0.005      21      91 ..      24      99 ..       4     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.6e-07
                             PIN_9 21 elerllgsvelvvpkavleELerlakagkgkertaakvalsLaer..ceiveae....eekaDdailelakeldaav 91
                                       l+r l  +++ vpk v+eEL+++ ++ ++++ +aa+v l+ + +  ++ v+ +     +++++a + la++ daa 
  gi|313125191|ref|YP_004035455.1| 24 PLSRCLTGYDVSVPKVVIEELREI-ASYDDAHGHAATVVLDQTAEllVRSVDLDvefpLDDGENAAVTLANDIDAAL 99
                                      58899999****************.899999999**99998866623344444454555667778888888888776 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.2e-06     0.082      10      59 ..      20      67 ..       4      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.2e-06
                             PIN_4 10 hdpealksfkeehdvviPitVleELdklKkgsserelarlarqanrllde 59
                                      +dp+ l +    +dv +P +V+eEL+++ +  +    +++a+ +++   e
  gi|313125191|ref|YP_004035455.1| 20 SDPNPLSRCLTGYDVSVPKVVIEELREIASYDD--AHGHAATVVLDQTAE 67
                                      467777777899***************999988..555555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1219.79
//
Query:       gi|313125192|ref|YP_004035456.1|  [L=120]
Description: hypothetical protein Hbor_04130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0043   17.8   3.8      0.011   16.5   3.8    1.7  1  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.8   6.1e-07     0.011      14      78 ..      40     116 ..      34     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.1e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............XX--HHHHHHHHHHHHHTS--SS-SSTTSTTTXXX CS
                     PSK_trans_fac  14 areLarltgeskteAvrrAleerlerlrre............raepllerllallrraaakaekedrspdekllyDe 78 
                                       a+ La++ ge  t++  +Al+e+l+   ++            + e ++e+l+al   ++a   +  +++ ++ ++De
  gi|313125192|ref|YP_004035456.1|  40 ADALAAVLGEDRTDVLVTALREYLQDAAHDdalvqeiaaayyDDEITFEQLKALVGAEEAANLRVLKQQLDDSFVDE 116
                                       899***********************986678888888777777778888888877777755555555566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 794.04
//
Query:       gi|313125193|ref|YP_004035457.1|  [L=129]
Description: hypothetical protein Hbor_04140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 893.61
//
Query:       gi|313125194|ref|YP_004035458.1|  [L=151]
Description: hypothetical protein Hbor_04150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 876.20
//
Query:       gi|313125195|ref|YP_004035459.1|  [L=31]
Description: hypothetical protein Hbor_04160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 187.15
//
Query:       gi|313125196|ref|YP_004035460.1|  [L=61]
Description: hypothetical protein Hbor_04170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 369.64
//
Query:       gi|313125197|ref|YP_004035461.1|  [L=170]
Description: ankyrin repeat-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-20   71.8   0.0    4.8e-13   49.5   0.1    2.6  2  Ank_2     Ankyrin repeats (3 copies)
    1.7e-19   69.6   0.1      5e-09   36.3   0.2    2.7  3  Ank_5     Ankyrin repeats (many copies)
      2e-18   64.6   0.0    3.1e-05   24.0   0.0    4.3  5  Ank_3     Ankyrin repeat
    4.7e-18   65.3   0.0    3.6e-08   33.8   0.1    4.1  4  Ank_4     Ankyrin repeats (many copies)
    6.7e-15   54.8   0.9     0.0017   18.7   0.1    4.1  5  Ank       Ankyrin repeat


Domain annotation for each model (and alignments):
>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.1   1.3e-16   4.8e-13       4      83 .]      19     107 ..      16     107 .. 0.85
   2 !   19.9   0.0   2.3e-07   0.00083      50      83 .]     107     142 ..     106     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.3e-16
                             Ank_2   4 AakngnlelvklLlegadpn..k.ngktaLhyAakngnleivklLleh......adndgrtpLhyAarsghleivkl 71 
                                       A+ +gn+e ++ L+  ad+   + ng t Lh Aa ++  ei++ L++       ++n g+t+L +A++  +++++++
  gi|313125197|ref|YP_004035461.1|  19 AIIQGNTEEFDELIDDADLThrSdNGSTLLHKAAGADRPEIARELIDRgidldaQNNGGHTALLHAIEVESYDTAEV 95 
                                       566788899999994455445526*************99*******977776666699*********99999***** PP

                             Ank_2  72 Llekgadinlkd 83 
                                       Lle gad+n++d
  gi|313125197|ref|YP_004035461.1|  96 LLEAGADPNIFD 107
                                       *********987 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.3e-07
                             Ank_2  50 dndgrtpLhyAarsgh..leivklLlekgadinlkd 83 
                                       dn+gr pL +A+  g+   ++vklLle+gad++++d
  gi|313125197|ref|YP_004035461.1| 107 DNKGRCPLSVAVTRGRsdRKFVKLLLEHGADPTATD 142
                                       799*********99743379*************997 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   4.5e+03      23      36 ..      19      32 ..      16      36 .. 0.82
   2 !   36.3   0.2   1.4e-12     5e-09       3      56 .]      33      84 ..      31      84 .. 0.92
   3 !   30.4   0.0   9.4e-11   3.4e-07       1      54 [.      96     150 ..      96     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                             Ank_5 23 AakygaadvvrlLl 36
                                      A+ +g+ + + +L+
  gi|313125197|ref|YP_004035461.1| 19 AIIQGNTEEFDELI 32
                                      89999999999888 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 1.4e-12
                             Ank_5  3 ehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56
                                      +  +ad+ ++  +g t Lh Aa + +++++r+L++rg dl+++++ G tal +A
  gi|313125197|ref|YP_004035461.1| 33 D--DADLTHRSDNGSTLLHKAAGADRPEIARELIDRGIDLDAQNNGGHTALLHA 84
                                      4..589999999999***********************************9766 PP

  == domain 3  score: 30.4 bits;  conditional E-value: 9.4e-11
                             Ank_5   1 LlehgpadvnrldgggntpLhvAakygaad..vvrlLlargadlnltdsrGltald 54 
                                       Lle+g ad+n  d++g  pL vA+ +g++d   v+lLl++gad+++td++G+++l+
  gi|313125197|ref|YP_004035461.1|  96 LLEAG-ADPNIFDNKGRCPLSVAVTRGRSDrkFVKLLLEHGADPTATDESGESVLE 150
                                       89***.*******************9999988999999**************9986 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   3.8e+03       9      28 ..      19      36 ..      17      39 .. 0.77
   2 !   24.0   0.0   8.7e-09   3.1e-05       1      31 []      43      72 ..      43      72 .. 0.96
   3 !   17.0   0.0   1.7e-06    0.0061       2      31 .]      77     105 ..      76     105 .. 0.96
   4 !   18.0   0.0   8.1e-07    0.0029       2      29 ..     110     138 ..     109     140 .. 0.89
   5 ?   -1.5   0.0       1.8   6.4e+03       2      22 ..     145     164 ..     144     169 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                             Ank_3  9 AarsgnleivkfLlenkgad 28
                                      A+ +gn+e  + L++   ad
  gi|313125197|ref|YP_004035461.1| 19 AIIQGNTEEFDELID--DAD 36
                                      788899977999998..666 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 8.7e-09
                             Ank_3  1 nGetpLhlAarsgnleivkfLlenkgadvna 31
                                      nG t+Lh Aa ++++ei++ L++ +g+d++a
  gi|313125197|ref|YP_004035461.1| 43 NGSTLLHKAAGADRPEIARELID-RGIDLDA 72
                                      799********************.9***985 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 1.7e-06
                             Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvna 31 
                                       G t+L +A++  +++ ++ Lle  gad+n+
  gi|313125197|ref|YP_004035461.1|  77 GHTALLHAIEVESYDTAEVLLE-AGADPNI 105
                                       89********************.9****97 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 8.1e-07
                             Ank_3   2 GetpLhlAarsgnlei..vkfLlenkgadv 29 
                                       G++pL +A+  g+ ++  vk+Lle +gad+
  gi|313125197|ref|YP_004035461.1| 110 GRCPLSVAVTRGRSDRkfVKLLLE-HGADP 138
                                       9*************9555******.9***8 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1.8
                             Ank_3   2 GetpLhlAarsgnleivkfLl 22 
                                       Ge+ L ++ ++g ++ v  Ll
  gi|313125197|ref|YP_004035461.1| 145 GESVLEWVKKHGITD-VVELL 164
                                       566666666667777.44555 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.8e-06    0.0064       6      51 ..      17      60 ..      14      61 .. 0.91
   2 !   33.8   0.1     1e-11   3.6e-08       2      55 .]      45      97 ..      44      97 .. 0.96
   3 !   13.1   0.0     3e-05      0.11      13      49 ..      89     124 ..      83     126 .. 0.88
   4 !   14.2   0.0   1.4e-05     0.052      17      39 ..     128     149 ..     125     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                             Ank_4  6 hyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveil 51
                                       +a+i+g++e  + L+  +ad+ ++ +++G t+lh+Aa   ++ei+
  gi|313125197|ref|YP_004035461.1| 17 ESAIIQGNTEEFDELI-DDADLTHR-SDNGSTLLHKAAGADRPEIA 60
                                      5799************.79******.999*********99888876 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 1e-11
                             Ank_4  2 ltaLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55
                                      +t+Lh+aa + r e++r L+++g+d++aq n+ G tal +A+  ++++ ++ Ll
  gi|313125197|ref|YP_004035461.1| 45 STLLHKAAGADRPEIARELIDRGIDLDAQ-NNGGHTALLHAIEVESYDTAEVLL 97
                                      699**************************.*************99999999997 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 3e-05
                             Ank_4  13 rlelvrlLlekgadinaqdnrsGetalhiAakrgnve 49 
                                        +++++ Lle gad+n   ++ G+ +l  A+ rg+ +
  gi|313125197|ref|YP_004035461.1|  89 SYDTAEVLLEAGADPNIF-DNKGRCPLSVAVTRGRSD 124
                                       6799**************.888*****9999999875 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 1.4e-05
                             Ank_4  17 vrlLlekgadinaqdnrsGetal 39 
                                       v+lLle+gad+ a+ ++sGe+ l
  gi|313125197|ref|YP_004035461.1| 128 VKLLLEHGADPTAT-DESGESVL 149
                                       89************.*****988 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.73   2.6e+03      18      30 ..      28      40 ..      18      42 .. 0.69
   2 !   18.7   0.1   4.6e-07    0.0017       1      32 []      43      75 ..      43      75 .. 0.92
   3 !   14.2   0.0   1.3e-05     0.046       2      32 .]      77     108 ..      76     108 .. 0.87
   4 !   17.5   0.0   1.1e-06    0.0041       2      31 ..     110     142 ..     109     143 .. 0.82
   5 ?   -3.5   0.0         5   1.8e+04      15      21 ..     158     164 ..     153     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.73
                                      HHHHHTTTSTTCB CS
                               Ank 18 iklLLhGAnlnal 30
                                        +L++ A+l+ +
  gi|313125197|ref|YP_004035461.1| 28 FDELIDDADLTHR 40
                                      4568888999876 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.6e-07
                                      TSBBHHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                               Ank  1 dGnTPLHlAatngkkriiklLL.hGAnlnaldn 32
                                      +G T LH Aa  + ++i+++L+ +G +l+a++n
  gi|313125197|ref|YP_004035461.1| 43 NGSTLLHKAAGADRPEIARELIdRGIDLDAQNN 75
                                      799*******777799******779******98 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1.3e-05
                                       SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                               Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnaldn 32 
                                       G+T+L  A+   + + ++ LL  GA++n+ dn
  gi|313125197|ref|YP_004035461.1|  77 GHTALLHAIEVESYDTAEVLLeAGADPNIFDN 108
                                       99*******666666******88*****9997 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 1.1e-06
                                       SBBHHHHHHHHTT..HHHHHHHH.TTTSTTCBT CS
                               Ank   2 GnTPLHlAatngk..kriiklLL.hGAnlnald 31 
                                       G+ PL +A+t+g      +klLL hGA+++a+d
  gi|313125197|ref|YP_004035461.1| 110 GRCPLSVAVTRGRsdRKFVKLLLeHGADPTATD 142
                                       56699999966666666**************99 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 5
                                       HHHHHHH CS
                               Ank  15 kriiklL 21 
                                       +++++lL
  gi|313125197|ref|YP_004035461.1| 158 TDVVELL 164
                                       5688876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 983.92
//
Query:       gi|313125198|ref|YP_004035462.1|  [L=417]
Description: hypothetical protein Hbor_04190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-30  103.8   1.2    1.2e-29  102.3   1.2    1.8  1  DUF4157        Domain of unknown function (DUF4157)
    1.9e-23   82.7   1.9    2.7e-23   82.1   0.1    2.2  2  GH-E           HNH/ENDO VII superfamily nuclease with conserv
  ------ inclusion threshold ------
      0.032   14.6   3.1      0.066   13.5   2.9    1.8  1  Peptidase_M91  Effector protein


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   1.2     2e-33   1.2e-29       2      78 ..     153     229 ..     152     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 2e-33
                           DUF4157   2 lpeavraemerafgadlsdVrvhtgsaaaraaralgAqAfTlgndivfaageyqpesaagrellaHELtHvvqqreg 78 
                                       l++++++ me ++g++l+dVr+htg++aa+a+++++A+AfT+gn+++f++gey p+sa+g+++laHEL+Hv qq++g
  gi|313125198|ref|YP_004035462.1| 153 LNASIQRVMEDRMGDNLGDVRIHTGPSAAKACEDINARAFTVGNHVAFNHGEYHPSSAEGQHILAHELAHVRQQTGG 229
                                       7899**********************************************************************986 PP

>> GH-E  HNH/ENDO VII superfamily nuclease with conserved GHE residues
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.71   4.3e+03       5      26 ..     286     317 ..     282     328 .. 0.65
   2 !   82.1   0.1   4.5e-27   2.7e-23       1      69 []     335     403 ..     335     403 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.71
                              GH-E   5 rdpntg..........gtsrerdwdmGHkpgr 26 
                                       r pn +          ++ ++++  +GH ++ 
  gi|313125198|ref|YP_004035462.1| 286 RRPNGEfgplkeeiakKRTKREEKPYGHDQRP 317
                                       55555555555566666667777788888764 PP

  == domain 2  score: 82.1 bits;  conditional E-value: 4.5e-27
                              GH-E   1 dGkvrdpntg...gtsrerdwdmGHkpgreyrrlvkkaeeggitqkefldeynnpdnyrledpseNrShgae 69 
                                       +G+v+++ ++   +   +++w+mGHkp+rey++lv+++++g it++efl+ey+npd+y++e++++ +S ++e
  gi|313125198|ref|YP_004035462.1| 335 NGVVFCAVDEvplD---RDEWCMGHKPRREYWYLVEYYLRGIITREEFLAEYRNPDHYQPESHRASSSGEHE 403
                                       68899999997544...89*************************************************9998 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.9   1.1e-05     0.066      71     135 ..     193     252 ..     136     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                     Peptidase_M91  71 gtdaeinynpafsseeegkegrPsavLyHElaHaydalngtlddgeydgkdeedssgvpneErqA 135
                                       + ++++ +n    +    +  + +++L+HElaH+++++ gt+   +++g+ e d +   + Er+A
  gi|313125198|ref|YP_004035462.1| 193 TVGNHVAFNHGEYHP---SSAEGQHILAHELAHVRQQTGGTVSMLPQEGELEIDPDP--RLEREA 252
                                       455556666554433...4555669****************9998888877777655..555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2359.20
//
Query:       gi|313125199|ref|YP_004035463.1|  [L=119]
Description: hypothetical protein Hbor_04200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.025   14.3   0.1    1.4  1  YpzI      YpzI-like protein
      0.029   13.7   0.0      0.035   13.4   0.0    1.0  1  HopW1-1   Type III T3SS secreted effector HopW1-1/HopPmaA


Domain annotation for each model (and alignments):
>> YpzI  YpzI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.8e-06     0.025       5      25 ..      52      72 ..      51      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-06
                              YpzI  5 RQEkkLkaskrvESDRDQsls 25
                                      RQ + L  s++vE DR Q+l 
  gi|313125199|ref|YP_004035463.1| 52 RQARDLADSGKVERDRGQPLT 72
                                      9*****************995 PP

>> HopW1-1  Type III T3SS secreted effector HopW1-1/HopPmaA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.9e-06     0.035      42     104 ..       7      72 ..       4      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-06
                           HopW1-1  42 asGelaaafGrt...stapaqdavrllsalqrelekespsfpdvaelakelaeaamteqGshllas 104
                                       asG l   f r    stap+ d+ +l+++l  e++ +++    va+ a++la+ ++ e+   ++ +
  gi|313125199|ref|YP_004035463.1|   7 ASGFLRFEFQRSrmpSTAPSFDPEELMTSLEDEFGGREAERRVVARQARDLADSGKVERDRGQPLT 72 
                                       7888888888855559****************************************9987665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 655.50
//
Query:       gi|313125200|ref|YP_004035464.1|  [L=96]
Description: hypothetical protein Hbor_04210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.9   1.8       0.13   12.9   0.3    2.0  2  DUF4404   Domain of unknown function (DUF4404)


Domain annotation for each model (and alignments):
>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   7.3e-06      0.13      17      68 ..       3      52 ..       1      70 [. 0.81
   2 ?    2.4   0.1     0.014   2.5e+02      29      59 ..      59      91 ..      52      95 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-06
                           DUF4404 17 sldeetralLeslaedieellaeedaaaeeeelaerlneaverFeeeHPkla 68
                                      s+de+tra+L++l++ + ++ ++  +++++++l e   eav+   ++ P++a
  gi|313125200|ref|YP_004035464.1|  3 SVDEATRAKLRKLHDHLAATAERPVERTASAHLGE--AEAVAGDVADDPNVA 52
                                      89********************9999999988777..566666666666666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.014
                           DUF4404 29 laedieellaeedaaaeeee..laerlneaver 59
                                       +e +++ll++ +++ ++++  ++er++e+v++
  gi|313125200|ref|YP_004035464.1| 59 RIETVSNLLSNVEKTGDDAAdkHVERARELVAE 91
                                      444455555544444444333477887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.37s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 551.99
//
Query:       gi|313125201|ref|YP_004035465.1|  [L=229]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.6e-13   48.7   0.3    1.5e-12   47.8   0.3    1.5  1  Copper-bind  Copper binding proteins, plastocyanin/azurin fam
  ------ inclusion threshold ------
       0.11   12.4   2.4       0.22   11.4   2.4    1.6  1  TAT_signal   TAT (twin-arginine translocation) pathway signal
        0.3   10.5   1.2       0.78    9.1   1.2    1.7  1  UCR_Fe-S_N   Ubiquitinol-cytochrome C reductase Fe-S subunit 


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.3   2.5e-16   1.5e-12       3      98 ..      93     188 ..      91     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.5e-16
                                       EEEEETTETSEEESSEEEEETTEEEEEEEESSSSBEEEEET.TSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSE CS
                       Copper-bind   3 vklgvesgdlqFetkeitvkkgekvtfvnlavmgHNvvldk.dgvpagvdkdkvkaedetkliggGekdsvtfdeag 78 
                                       vk+ +++g  +F+++ ++v  g +vtf n ++ +H     + d  + ++  d   a d+  l  +G +++ tf+++g
  gi|313125201|ref|YP_004035465.1|  93 VKMLSKDGGYHFSPHVVRVTVGGTVTFQN-ESGSHSTTAYHpDNGQPQLVPDGAAAWDSGILSEQGATFEHTFETEG 168
                                       6777889999******************9.77778776655566555666666666678889999************ PP

                                       EEEEEETTTTTTTSEEEEEE CS
                       Copper-bind  79 tYkffCsPHaaagMkgkvtv 98 
                                        Y+++C+PH ++gM  +v+v
  gi|313125201|ref|YP_004035465.1| 169 VYHYYCTPHESMGMISTVIV 188
                                       ******************98 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.4   3.8e-05      0.22       2      25 ..       6      28 ..       5      29 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                        TAT_signal  2 lSRRdFLKgsAAaa.AAaalggcaa 25
                                      l+RR  L+  A ++ A ++l+gc++
  gi|313125201|ref|YP_004035465.1|  6 LTRRRVLR--ATTGlAVVGLAGCTT 28
                                      79******..999966777****97 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.2   0.00013      0.78      10      28 ..       7      24 ..       2      27 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00013
                        UCR_Fe-S_N 10 tRRDFLyiATgavgaVGaa 28
                                      tRR++L  AT ++++VG a
  gi|313125201|ref|YP_004035465.1|  7 TRRRVL-RATTGLAVVGLA 24
                                      9*****.99999****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1192.86
//
Query:       gi|313125202|ref|YP_004035466.1|  [L=436]
Description: exonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-13   51.2   0.0    2.7e-13   50.2   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    6.5e-12   45.2   0.1    2.3e-11   43.4   0.0    1.9  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.3e-06   28.0   0.0    2.2e-06   27.3   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.5e-06   28.4   8.3      9e-06   25.8   6.1    2.8  2  Lactamase_B    Metallo-beta-lactamase superfamily
    1.5e-06   27.9   2.8    2.3e-05   24.0   2.8    2.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.044   13.7   0.1    2.0  1  Lactamase_B_3  Beta-lactamase superfamily domain
      0.029   14.4   0.0          4    7.5   0.0    2.4  2  RPN1_C         26S proteasome non-ATPase regulatory subunit R
      0.039   14.5   0.0      0.083   13.4   0.0    1.5  1  Rhodanese      Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.2e-16   2.7e-13      22     110 .]     260     357 ..     247     357 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.2e-16
                                       -EEEEE-HHHHHHHHHGGGGGG...........E-SHH....HHHH..HH...........HS-SSEEEEES-TTSS CS
                         Beta-Casp  22 lpiyldsplaskatevYkeyae...........veakslewmeskkeeln...........sskgpkvilassgmle 76 
                                       +  y+d+ +++++t++ ++++e           +         s++   +             k+  vi+++sgml+
  gi|313125202|ref|YP_004035466.1| 260 IDCYVDG-MGKQVTKMLRRHPEfvrdedalrraK---------SNA---RfvtgrdgqrrrIAKQNTVIVTTSGMLS 323
                                       6789999.************99966666664431.........221...122223333333345789********** PP

                                       SSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  77 gGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       gG++  ++ ++ ++p n + l+gyq+egT+gr+l
  gi|313125202|ref|YP_004035466.1| 324 GGPAMTYVPEIRSNPTNKITLTGYQVEGTPGRDL 357
                                       ********************************86 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.4   3.1e+03      31      43 ..      50      64 ..      49      72 .. 0.75
   2 !   43.4   0.0     1e-14   2.3e-11       2      59 ..     370     424 ..     369     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                             RMMBL 31 prn..vilvHGeeea 43
                                      p++  v++ HG+ ++
  gi|313125202|ref|YP_004035466.1| 50 PEPdaVVVSHGHLDH 64
                                      556669999**8665 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 1e-14
                             RMMBL   2 ipvkarieeidfSgHadknellelirklkprnvilvHGeeeatsalarllkeeegidv 59 
                                       +pv a++e++dfS+Had+++llel++  +  ++ ++HG++  ++ +a+ l  + g d+
  gi|313125202|ref|YP_004035466.1| 370 MPVSAQVEWYDFSAHADRDGLLELLSAYREAPILVNHGDR--CELFADEL-NDDGFDA 424
                                       699************************************9..77788888.6666665 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   9.6e-10   2.2e-06      34     175 ..      50     195 ..      30     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.6e-10
                     Lactamase_B_6  34 ptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgllgpedseel......... 101
                                       p+ d++++sh  l+h+Ga + l+         + p+  t p+ +L+ ++  d+ + +g++g   +            
  gi|313125202|ref|YP_004035466.1|  50 PEPDAVVVSHGHLDHVGAVPSLLSG-----DRRPPIHWTPPTRELALTLARDTLKLRGISGRGATGGSqgqrrrggt 121
                                       889***************9888854.....579**************************998777533344555555 PP

                     Lactamase_B_6 102 .....eledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnhakeshLnga 173
                                            + e+i+++ +  +t  Y  ++e  +      +t ynaGh +G +   i ++  ++ Y  d++ + ++ L +a
  gi|313125202|ref|YP_004035466.1| 122 ydcpfTEEEIRRVTQVSETHSYRETFEAAG----HEVTFYNAGHIPGSAHVLIDDGDTRLFYTADFH-TDDQRLVSA 193
                                       555557799999999999999999876664....46788**************************95.555555555 PP

                     Lactamase_B_6 174 al 175
                                       ++
  gi|313125202|ref|YP_004035466.1| 194 ST 195
                                       54 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   6.1     4e-09     9e-06      39     152 ..      46     184 ..      19     202 .. 0.83
   2 ?    0.3   0.0      0.27   6.1e+02      53      94 ..     383     424 ..     383     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4e-09
                                       TSGGGGEEEEE-SBSSHHHHTTGGGCTT.HHCCEETCCEHHHHCCHCHHHHHHHHHCCHH................. CS
                       Lactamase_B  39 glkpkdvdavilTHlHlDHiGglgglve.atdvpvgavaeeapalfmeeaddaasrkgll................. 97 
                                        ++  ++dav+++H+HlDH+G+++ l +  +  p+++ + + +  ++ ++d+   r+ +                  
  gi|313125202|ref|YP_004035466.1|  46 PVDTPEPDAVVVSHGHLDHVGAVPSLLSgDRRPPIHWTPPTRELALTLARDTLKLRGISGrgatggsqgqrrrggty 122
                                       5666789*****************988725667777777777777777777777777777***************** PP

                                       .......TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTT CS
                       Lactamase_B  98 .......lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDal 152
                                               ++ + + +++    ++++a+g++ +    g+ +g+ h+ +++g+ ++ +t D+ 
  gi|313125202|ref|YP_004035466.1| 123 dcpfteeEIRRVTQVSETHSYRETFEAAGHEVTFYNAGHIPGSAHVLIDDGDTRLFYTADFH 184
                                       ****88877777778888888889999999999999************************85 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                                       SSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHC CS
                       Lactamase_B  53 lHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrk 94 
                                       +H+D  G l+ l   + +p+ +++ + ++lf +e++d+    
  gi|313125202|ref|YP_004035466.1| 383 AHADRDGLLELLSAYREAPILVNHGDRCELFADELNDDGFDA 424
                                       69*******************************998876554 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   2.8     1e-08   2.3e-05      21     171 ..      42     214 ..      30     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1e-08
                                       --S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH..........................HC CS
                     Lactamase_B_2  21 Pve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla..........................vl 70 
                                       P + ++d+ p+ daV+++h+H DH+  +++l  +  +  p++ ++ +++                          + 
  gi|313125202|ref|YP_004035466.1|  42 PPQfPVDT-PEPDAVVVSHGHLDHVGAVPSLLSGDRR-PPIHWTPPTRElaltlardtlklrgisgrgatggsqgQR 116
                                       55556777.99**********************6543.478878888777777777777555555555555555433 PP

                                       CTTCGHHHCHTT..........TTEEEEEE-....TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECT CS
                     Lactamase_B_2  71 eanfvylaleee..........pavnvheld....wgesfelgdggleitatparhksgrrldrnagdtlGlriegg 133
                                       ++                     + +v+++       e+fe +  g e+t+  a h  g          + ++i++g
  gi|313125202|ref|YP_004035466.1| 117 RR---------GgtydcpfteeEIRRVTQVSethsYRETFEAA--GHEVTFYNAGHIPGS---------AHVLIDDG 173
                                       33.........03322222112122222222222344555555..556777777777776.........89999999 PP

                                       TEEEEEESS-S---HHHH...HHHCT-SEEEEE-S-SSTTH CS
                     Lactamase_B_2 134 gkrvyyigDtgyipeeig...erlggadllllditayedde 171
                                       + r++y++D  + ++++    +   +ad+++ + t+ + + 
  gi|313125202|ref|YP_004035466.1| 174 DTRLFYTADFHTDDQRLVsasTARPDADVIICESTYSDVEH 214
                                       99999999999888654322133344999999988555443 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     2e-05     0.044      17      52 ..      29      67 ..      21     205 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                     Lactamase_B_3 17 arilvDPf..ka.nlgyeppaeeaDlvlisqaledHahl 52
                                       r+l+D++  ++   ++  +++e+D+v++s+++ dH  +
  gi|313125202|ref|YP_004035466.1| 29 DRLLLDYGmlTGnPPQFPVDTPEPDAVVVSHGHLDHVGA 67
                                      578888884311234455556***************754 PP

>> RPN1_C  26S proteasome non-ATPase regulatory subunit RPN1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.019        43       9      43 ..     343     377 ..     338     379 .. 0.81
   2 ?    7.5   0.0    0.0018         4      17      34 ..     399     416 ..     396     418 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.019
                            RPN1_C   9 tItGfqThttPVl.LaageRAELateeYiplssvLE 43 
                                       t tG+q+  tP + L    RAE+ +e+ +p+s   E
  gi|313125202|ref|YP_004035466.1| 343 TLTGYQVEGTPGRdLLERGRAEI-DERVMPVSAQVE 377
                                       78*********976778889998.478888887776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0018
                            RPN1_C  17 ttPVlLaageRAELatee 34 
                                       ++P+l+++g+R EL  +e
  gi|313125202|ref|YP_004035466.1| 399 EAPILVNHGDRCELFADE 416
                                       78************8776 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.7e-05     0.083      24      72 ..     153     205 ..     130     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-05
                         Rhodanese  24 e...YekghIpgAvnv....skdtlsrakkseapllelpeellelgidnkktvvvy 72 
                                       e   Y++ghIpg+ +v      ++l ++     +++ l+ +  ++   ++  v++ 
  gi|313125202|ref|YP_004035466.1| 153 EvtfYNAGHIPGSAHVliddGDTRLFYTADFHTDDQRLVSASTAR---PDADVIIC 205
                                       15559***********86654444444444444444444444443...45545444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 2325.31
//
Query:       gi|313125203|ref|YP_004035467.1|  [L=396]
Description: permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-28   98.5  27.1    5.3e-28   98.1  27.1    1.1  1  AI-2E_transport  AI-2E family transporter
  ------ inclusion threshold ------
        0.4   11.2   4.7       0.45   11.0   1.8    2.7  2  TraL             TraL protein


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1  27.1     6e-32   5.3e-28       9     324 ..      21     353 ..      14     356 .. 0.79

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 6e-32
                   AI-2E_transport   9 llllalypfis.elllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltqlvk 84 
                                       + +++++ f++  +l +++++l+l+y++ pv+ +++ r  + ++ +++ ll+l++ +vllv + v   ++ +++l  
  gi|313125203|ref|YP_004035467.1|  21 VAIFVVLAFVAdAFLGTFMLGLFLYYATRPVYSRIRGRIGQPSIGAAVALLVLSLPVVLLVNYTV---LIAVQELSA 94 
                                       3444444444458888*******************555555555555555555555566665666...567777777 PP

                   AI-2E_transport  85 slpayidslqnilnelpslleele.n......liqalkqslskilsnilssilnsllsllasllglilslvlvllll 154
                                        + + ++++++ l+    ++e l+ +      l+++    ++ + +  ++ +l+s+ + ++ +l  +++l++ + + 
  gi|313125203|ref|YP_004035467.1|  95 FVGQNQQGILAALKPYLGSFESLQaPsellatLLENPSELVDMTDTATVEAVLSSIAGTASFILDAAFQLFIAFAFA 171
                                       777777777777777777777777667767855555555666666777788899999999999999999******** PP

                   AI-2E_transport 155 ffllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgv........pyall 223
                                       f+ll+d ++l   ++   +++    ++a++ ++++ l+ ++ g++l a++i+v++++++ ++++        p ++l
  gi|313125203|ref|YP_004035467.1| 172 FYLLRDDRRLSAWTRE-NLSGHGGVMDAYMTAVDRDLRTIYFGNILNAFAIAVIAAVSYNAINLfappslwiPSPTL 247
                                       *************999.77888*************************************9988444444444999** PP

                   AI-2E_transport 224 lailvglanliPyiGavivlipiaiialltgg.......ikevlivlivvllvqliegnilePklmgkrlglhplvi 293
                                       l+ l+g a+liP++G  iv++p+ +++++          + ++ +  +++++v++i + +l+P++ g+  +lh+ ++
  gi|313125203|ref|YP_004035467.1| 248 LGALTGAASLIPVVGMKIVYVPVTVLLAVEAAltapdafWVALAYGAVSLVVVDTIPDFLLRPYVSGR--NLHTGTV 322
                                       **********************766654433344325645556667778999***************9..58***** PP

                   AI-2E_transport 294 llsllaggklfGlvGlilavpltavikaile 324
                                       +++ ++g  lfG  Gl+l+++l++++  +++
  gi|313125203|ref|YP_004035467.1| 323 MFAYIIGPALFGWYGLFLGPLLLVIAVHFVR 353
                                       *************************998876 PP

>> TraL  TraL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.8     5e-05      0.45      10      57 ..      11      58 ..       5      80 .. 0.90
   2 ?   -2.6   0.0      0.87   7.8e+03      29      50 ..     153     174 ..     142     180 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                              TraL 10 perllfwelDealvillllvvgillgqfviglvlglllvlllrklkkg 57
                                       +r ++w l +a++++l +v   +lg f++gl+l +++  +++++++ 
  gi|313125203|ref|YP_004035467.1| 11 RSRAIWWVLGVAIFVVLAFVADAFLGTFMLGLFLYYATRPVYSRIRGR 58
                                      57899***************************************9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.87
                              TraL  29 vvgillgqfviglvlglllvll 50 
                                       + +++l+ ++ ++++ +++++l
  gi|313125203|ref|YP_004035467.1| 153 TASFILDAAFQLFIAFAFAFYL 174
                                       3444445444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2195.73
//
Query:       gi|313125204|ref|YP_004035468.1|  [L=264]
Description: amidohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-57  193.9   0.0    3.3e-57  193.8   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.8   0.0   1.9e-61   3.3e-57       2     260 ..       3     245 ..       2     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.8 bits;  conditional E-value: 1.9e-61
                                       EEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEE CS
                      CN_hydrolase   2 vAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiav 78 
                                       vA+vQl+   ++ ean++++++ ++ Aa++ga+L+vlPE++++gy  ++ + +aAe ++g+t+ +la+la + +i++
  gi|313125204|ref|YP_004035468.1|   3 VAAVQLTA-EESVEANVERAVSRVRDAAKRGAELVVLPEMWNVGYFAFDAYDDAAEPLDGPTATRLAELADELDIHL 78 
                                       9*******.79****************************************************************** PP

                                       EEE.EEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGG CS
                      CN_hydrolase  79 vig.liereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCy 154
                                        +g + er  ++++l  ynt +l+d+ g+ +++yrK+hLf     + ++ e++++ pg+++  ++t++g +G+  Cy
  gi|313125204|ref|YP_004035468.1|  79 HGGsIVER--DGDDL--YNTSLLFDPAGERIASYRKIHLF-----GYESEESTVLTPGEEVCAVETDLGTVGLTTCY 146
                                       ***55555..*****..***********************.....689999********86666************* PP

                                       GGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-T CS
                      CN_hydrolase 155 eigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidp 231
                                       + +fpel+r l  +g+e+l+ +s     + +   ++w+ll+r+ra+en+ f++aan +g+  + +++ +g+S+++dp
  gi|313125204|ref|YP_004035468.1| 147 DLRFPELYRQLVERGVELLLVTS----AWPAARSDHWHLLTRTRAVENQLFLVAANLTGT--NRGVELGGQSVVVDP 217
                                       *********************66....7788999**************************..*************** PP

                                       TS-EEEECCSSSTEEEEEEEEHHHHHHHH CS
                      CN_hydrolase 232 dGrilaglgeeeegvliaeidladvratr 260
                                       +G+  a +g   + +++aeid+++v+++r
  gi|313125204|ref|YP_004035468.1| 218 WGIQRANAGNGDR-TVTAEIDRETVEEVR 245
                                       *****99999997.************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:01.72
# Mc/sec: 463.72
//
Query:       gi|313125205|ref|YP_004035469.1|  [L=380]
Description: Fe3+-siderophore ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-89  297.5  35.5    2.1e-88  296.4  35.5    1.5  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
        1.9    7.9  24.8      0.067   12.7  18.3    2.0  2  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.4  35.5   2.3e-92   2.1e-88       6     312 .]      39     373 ..      33     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: 296.4 bits;  conditional E-value: 2.3e-92
                             FecCD   6 lllslllgavkispsevfeallgka..............................dsleaeivlelrlprvlaallv 52 
                                        l+ +++g++++++++ ++a+l+ +                                +e  iv+++rlprv++++lv
  gi|313125205|ref|YP_004035469.1|  39 GLVQVSFGTYSMTIEQAWRAVLDPTvifdsrwllnflvgeelmrfitgfqgelpeLANETLIVWSIRLPRVFVGILV 115
                                       5555666666666666666666555555544444444444444444333333333344445**************** PP

                             FecCD  53 GaaLavaGallQtvtrNpLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgas 129
                                       Ga La++Ga++Q+vtrN+La+P+ilG+ssga+l+++l+l+++  s  +  lpl+a +g+++a++lv+++a +++g+s
  gi|313125205|ref|YP_004035469.1| 116 GANLAISGAIFQAVTRNELASPYILGVSSGAGLAILLTLVVF--SGLAPFLPLIAAAGGAIAFFLVYIIA-WQNGTS 189
                                       ****************************************97..4555579*******************.****** PP

                             FecCD 130 plkliLaGiavsallsaltsllllll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllal 205
                                       p++l+LaG++vs+++++l + + +++ + + ++s++ w++Gsl g++w++v l+l+ ++l+++l++l ar+l++l l
  gi|313125205|ref|YP_004035469.1| 190 PVRLVLAGVIVSTVFQSLQTGIFFFAdDLAVVQSAIAWTTGSLTGVDWEQVRLALPSTTLAVILAALGARQLNVLLL 266
                                       **************************888899********************************************* PP

                             FecCD 206 gdetAkslGvnvervrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladll 282
                                       g++tA+slG++ver+r+ll  +++l++++a+a++G++gFvGLivPh++r lvg+d+++l++ + ++G +l+++ad+ 
  gi|313125205|ref|YP_004035469.1| 267 GEQTARSLGMSVERTRFLLSGVAILAASAAIAAAGIVGFVGLIVPHVVRNLVGSDYKRLMVGCLFVGPALMVIADVG 343
                                       ***************************************************************************** PP

                             FecCD 283 arlllsptelpvgivtaliGapffiylllr 312
                                       arl+++p+++pvgivt liG+p+f+yl+++
  gi|313125205|ref|YP_004035469.1| 344 ARLAMAPVQVPVGIVTGLIGGPYFLYLMRK 373
                                       ****************************97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.4      0.86   7.7e+03     178     221 ..      32      39 ..      22      52 .. 0.45
   2 ?   12.7  18.3   7.5e-06     0.067      47     225 ..     147     337 ..     109     371 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.86
                             ABC-3 178 lavvvalqavGviLvialliiPaatArrltrslesllivAillg 221
                                       +a+vv                                    l g
  gi|313125205|ref|YP_004035469.1|  32 VAMVV------------------------------------LAG 39 
                                       22222....................................222 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.5e-06
                             ABC-3  47 alayllgvn.......lllgailvgliaavalellkrktklk...edtaigivlsvfl...alglvlvslikkskvd 110
                                       +la+ll++        +l  ++++g ++a++l+++ + +        ++ g+++s+++     g++++     + ++
  gi|313125205|ref|YP_004035469.1| 147 GLAILLTLVvfsglapFLPLIAAAGGAIAFFLVYIIAWQNGTspvRLVLAGVIVSTVFqslQTGIFFFADDLAVVQS 223
                                       55555555444444432222233334444444444333332200033566887777653114577777766668889 PP

                             ABC-3 111 ldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqav 187
                                         ++  G++ +++ e++ l +  + + ++l+ l  ++l ++ + e++A++ g+sv++ ++ll  +  la ++a+ a+
  gi|313125205|ref|YP_004035469.1| 224 AIAWTTGSLTGVDWEQVRLALPSTTLAVILAALGARQLNVLLLGEQTARSLGMSVERTRFLLSGVAILAASAAIAAA 300
                                       99999************************************************************************ PP

                             ABC-3 188 GviLvialliiPaatArrltrslesllivAillglvsv 225
                                       G++  +  li+P ++  +++++ ++l++    +g   +
  gi|313125205|ref|YP_004035469.1| 301 GIVGFVG-LIVPHVVRNLVGSDYKRLMVGCLFVGPALM 337
                                       *998877.578**************9998888875554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.58
# Mc/sec: 1966.66
//
Query:       gi|313125206|ref|YP_004035470.1|  [L=282]
Description: cobalamin/Fe3+-siderophore ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-32  111.2   0.0    8.6e-32  110.5   0.0    1.3  1  ABC_tran        ABC transporter
    1.1e-13   51.7   1.0    1.7e-06   28.1   0.2    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    9.6e-11   41.5   0.2    1.1e-08   34.9   0.2    2.1  1  SMC_N           RecF/RecN/SMC N terminal domain
    4.9e-07   29.4   0.0    1.3e-06   28.1   0.0    1.7  1  AAA_29          P-loop containing region of AAA domain
    8.6e-07   28.1   0.0     0.0016   17.3   0.0    2.4  2  ABC_ATPase      Predicted ATPase of the ABC class
    5.9e-06   26.2   0.0    9.2e-05   22.3   0.0    2.0  2  AAA_15          AAA ATPase domain
    1.5e-05   25.4   0.1    2.7e-05   24.6   0.1    1.5  1  AAA_16          AAA ATPase domain
    2.6e-05   24.8   0.1    3.7e-05   24.3   0.1    1.3  1  AAA_23          AAA domain
    0.00021   21.6   1.1     0.0011   19.2   1.1    2.0  1  AAA_22          AAA domain
     0.0004   20.0   0.5    0.00098   18.7   0.4    2.0  1  AAA_25          AAA domain
    0.00062   19.9   0.5     0.0018   18.5   0.5    1.9  1  AAA_33          AAA domain
     0.0007   19.5   0.1     0.0016   18.3   0.0    1.7  2  RsgA_GTPase     RsgA GTPase
    0.00088   19.1   0.1     0.0018   18.1   0.0    1.6  1  MukB            MukB N-terminal
     0.0016   18.5   0.8      0.012   15.7   0.8    2.3  1  MMR_HSR1        50S ribosome-binding GTPase
     0.0021   18.0   0.1      0.008   16.1   0.0    1.8  2  APS_kinase      Adenylylsulphate kinase
     0.0028   18.2   0.0     0.0064   17.0   0.0    1.7  1  AAA_18          AAA domain
     0.0033   17.6   0.1     0.0097   16.1   0.0    1.7  2  HD              HD domain
     0.0047   17.2   0.1     0.0096   16.2   0.1    1.9  1  AAA_28          AAA domain
      0.005   16.6   0.2      0.012   15.4   0.2    1.8  1  AAA_30          AAA domain
     0.0062   15.8   0.0      0.016   14.5   0.0    1.6  1  Zeta_toxin      Zeta toxin
     0.0068   16.3   0.0      0.011   15.6   0.0    1.4  1  Rad17           Rad17 P-loop domain
     0.0089   16.0   0.1      0.019   14.9   0.0    1.6  1  NACHT           NACHT domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.046   13.8   0.0    1.9  2  AAA_14          AAA domain
      0.024   14.0   0.0       0.24   10.8   0.0    2.0  2  Mg_chelatase    Magnesium chelatase, subunit ChlI
      0.026   14.6   0.0      0.046   13.8   0.0    1.5  1  DUF87           Helicase HerA, central domain
      0.028   14.2   0.2       0.48   10.2   0.0    2.1  2  ATP_bind_1      Conserved hypothetical ATP binding protein
       0.03   14.8   0.1      0.073   13.5   0.0    1.9  1  AAA             ATPase family associated with various cellula
      0.031   13.9   0.5        0.1   12.2   0.1    1.9  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
      0.038   14.0   0.2       0.23   11.5   0.0    2.0  2  AAA_5           AAA domain (dynein-related subfamily)
      0.039   14.3   0.0      0.077   13.4   0.0    1.5  1  RNA_helicase    RNA helicase
      0.065   12.3   0.0       0.11   11.5   0.0    1.3  1  T2SSE           Type II/IV secretion system protein
       0.07   13.0   0.2       0.44   10.4   0.2    2.3  1  NTPase_1        NTPase
       0.07   12.7   0.0       0.13   11.9   0.0    1.3  1  AAA_27          AAA domain
      0.089   12.0   0.0       0.14   11.4   0.0    1.2  1  DUF2813         Protein of unknown function (DUF2813)
       0.09   12.5   0.5       0.21   11.3   0.1    1.7  2  Cytidylate_kin  Cytidylate kinase
       0.09   12.4   0.2       0.19   11.3   0.2    1.8  1  SRP54           SRP54-type protein, GTPase domain
       0.14   11.9   0.0       0.26   11.0   0.0    1.4  1  VirE            Virulence-associated protein E
       0.16   11.1   0.0       0.93    8.6   0.0    1.9  2  TIP49           TIP49 P-loop domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0   1.8e-34   8.6e-32       6     136 ..      49     192 ..      47     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 1.8e-34
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                       +++ +ge++a+vG+nG+GKStLlk+l+++l p+ G++lldg+ ++e   +++ +e+g l+qe+   +++tv+e    
  gi|313125206|ref|YP_004035470.1|  49 IDIPRGEITALVGPNGSGKSTLLKALSKQLAPDTGNVLLDGQTIQEYGDKEFARELGLLSQENDSPNTITVEELayh 125
                                       5799**********************************************************999999999999*** PP

                                       ..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     e++e +e+a++  g ++++d++v     +LSgGqkq   +a++l+++ ++lllDEpt
  gi|313125206|ref|YP_004035470.1| 126 gryphrgffeqvseEDEEAVERAIDLAGVDHIRDQTV----GNLSGGQKQLAWIAMVLAQDTDVLLLDEPT 192
                                       **********999777777******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2   3.5e-09   1.7e-06       1      20 [.      56      75 ..      56     124 .. 0.79
   2 !   22.4   0.0     2e-07   9.2e-05     227     287 ..     155     212 ..     123     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.5e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdald 20
                                      +++l+GpNgsGKS+LL+al+
  gi|313125206|ref|YP_004035470.1| 56 ITALVGPNGSGKSTLLKALS 75
                                      79*****************5 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2e-07
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       ++ ++ ++ +lS G+k+l a ++++l+++   ++ll+DEp + L+ + + r++e + +l++
  gi|313125206|ref|YP_004035470.1| 155 DHIRDQTVGNLSGGQKQL-AWIAMVLAQDT--DVLLLDEPTTYLDLHHQLRVMETVQQLND 212
                                       5667788999********.********998..9************9888888887765554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.2   2.2e-11   1.1e-08      25     196 ..      55     220 ..      46     240 .. 0.70

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.2e-11
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEE.EEEEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkka.eveitfdnedkklkiekeevs 98 
                                       ++ta+vGpNGSGKs ll A++         +l  ++ + l+     +e    ++a e+ ++ +++d+  +i+ ee+ 
  gi|313125206|ref|YP_004035470.1|  55 EITALVGPNGSGKSTLLKALSK--------QLAPDTGNVLLDGqtIQEYGDKEFArELGLLSQENDSPNTITVEELA 123
                                       599*****************54........55555555555554322333344441455555666666778888888 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                          r  + g  e   ++ e   +   +l    +i  +   +LSgG+k+L+ +a+++A    + + + llDe    LD
  gi|313125206|ref|YP_004035470.1| 124 YHGRYPHRGFFEQVSEEDEEAVERAIDLAGVDHIRDQtvgNLSGGQKQLAWIAMVLA----QDTDVLLLDEPTTYLD 196
                                       88877777776665555555555555555555554434449**************98....567899********** PP

                                       HHHHHHHHHHHHHHCTTSEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkeksknaQfivis 196
                                        ++  +v e +++ +++  + +  
  gi|313125206|ref|YP_004035470.1| 197 LHHQLRVMETVQQLNDRRDVTIAV 220
                                       ************998776665544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.7e-09   1.3e-06      16      50 ..      48      82 ..      43      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.7e-09
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +i+i + ++t l+Gp+GsGKSTll A++  L p++
  gi|313125206|ref|YP_004035470.1| 48 RIDIPRGEITALVGPNGSGKSTLLKALSKQLAPDT 82
                                      57777556********************9999987 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.5e-06    0.0016     242     266 ..      51      76 ..      45      82 .. 0.92
   2 !    8.3   0.0    0.0019      0.89     317     364 ..     159     206 ..     151     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.5e-06
                                       E-SS.EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAlek 266
                                       ip+G +t++vG++  GKsTLL+Al+k
  gi|313125206|ref|YP_004035470.1|  51 IPRGeITALVGPNGSGKSTLLKALSK 76 
                                       9***********************86 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0019
                                       TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHH CS
                        ABC_ATPase 317 kfstedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqe 364
                                       + +  + SG   q a+i+  l  ++++lL+DE t+   l ++ + m+ 
  gi|313125206|ref|YP_004035470.1| 159 DQTVGNLSGGQKQLAWIAMVLAQDTDVLLLDEPTTYLDLHHQLRVMET 206
                                       5677899*************************9998887776655543 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0     2e-07   9.2e-05      19      45 ..      51      76 ..      46     106 .. 0.76
   2 ?    1.7   0.0      0.36   1.7e+02     297     351 ..     165     210 ..      90     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2e-07
                            AAA_15 19 idlseeltvliGkNnsGKSsilealdl 45
                                      i+  e +t l+G+N+sGKS++l+al +
  gi|313125206|ref|YP_004035470.1| 51 IPRGE-ITALVGPNGSGKSTLLKALSK 76
                                      44455.9******************76 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.36
                            AAA_15 297 nGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkel 351
                                        + G+++l ++++ ++         +++++ll++EP ++L   +q  ++++ + l
  gi|313125206|ref|YP_004035470.1| 165 LSGGQKQLAWIAMVLA---------QDTDVLLLDEPTTYLDLHHQLRVMETVQQL 210
                                       5566666666665443.........35689*******999877777777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   5.7e-08   2.7e-05      18      88 ..      48     113 ..      44     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.7e-08
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd.ggiflrgkcdqlesaipy.sa.laqalareellrqllde 88 
                                       r+  +r+e++ l+G+ G+GKs+l+++l ++l  d g ++l g++ q      y +  +a+ l   +ll q++d 
  gi|313125206|ref|YP_004035470.1|  48 RIDIPRGEITALVGPNGSGKSTLLKALSKQLAPDtGNVLLDGQTIQE-----YgDKeFAREL---GLLSQENDS 113
                                       56667889**************************5233355555555.....2211144444...444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   7.8e-08   3.7e-05      20      43 ..      55      78 ..      44     210 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 7.8e-08
                            AAA_23 20 gltlItGpNGaGKTTildAiklaL 43
                                       +t+++GpNG+GK+T+l A+   L
  gi|313125206|ref|YP_004035470.1| 55 EITALVGPNGSGKSTLLKALSKQL 78
                                      69*****************97544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.1   2.3e-06    0.0011       6      64 ..      55     108 ..      52     228 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.3e-06
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst....sskdllrellral 64 
                                        i++++G+ G+GK+tll+ l +ql          p++  v l ++t    + k+++rel    
  gi|313125206|ref|YP_004035470.1|  55 EITALVGPNGSGKSTLLKALSKQL---------APDTGNVLLDGQTiqeyGDKEFARELGLLS 108
                                       6899*******************9.........444444444444422222333333322222 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.4   2.1e-06   0.00098      30      64 ..      51      87 ..      30     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-06
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava..tGkpwl 64
                                      +p+ge+++l+G+ g+GK+tl+  l+  +a  tG  +l
  gi|313125206|ref|YP_004035470.1| 51 IPRGEITALVGPNGSGKSTLLKALSKQLApdTGNVLL 87
                                      8********************9999999988777555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.5   3.8e-06    0.0018       3      32 ..      58      91 ..      56     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.8e-06
                            AAA_33  3 llvGlpGsGKstlaerllkklg....avllssdt 32
                                       lvG++GsGKstl++ l k+l+     vll+  t
  gi|313125206|ref|YP_004035470.1| 58 ALVGPNGSGKSTLLKALSKQLApdtgNVLLDGQT 91
                                      68*****************999888777777777 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.5e-06    0.0016      98     130 ..      53      85 ..       7      91 .. 0.89
   2 ?   -2.7   0.0       9.8   4.6e+03     122     154 ..     198     230 ..     193     233 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.5e-06
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++++++lvG+ G GKStL++al  +l   tg+v
  gi|313125206|ref|YP_004035470.1|  53 RGEITALVGPNGSGKSTLLKALSKQLAPDTGNV 85 
                                       5799********************999999887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.8
                                       T-----S--------------SEEEEEETTTEE CS
                       RsgA_GTPase 122 elelktgevseklgrGkhTTtavellelaeggl 154
                                       +++l++ e+ ++l+  +  T av l+++a+ + 
  gi|313125206|ref|YP_004035470.1| 198 HHQLRVMETVQQLNDRRDVTIAVVLHDIAQAAR 230
                                       567888888888888888888888888876655 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.8e-06    0.0018      27      79 ..      55     109 ..      46     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.8e-06
                                       HHHHHHS--SHHHHHHHHHHHHHHS--TT..T--------------------GGG CS
                              MukB  27 lvttlsGgnGaGksttmaafvtaliPdls..llhfrntteaGatsgsrdkGlyGk 79 
                                        +t+l G nG+Gkst + a+   l Pd    ll  + + e G ++ +r+ Gl  +
  gi|313125206|ref|YP_004035470.1|  55 EITALVGPNGSGKSTLLKALSKQLAPDTGnvLLDGQTIQEYGDKEFARELGLLSQ 109
                                       58*************************8533788888999999999999998765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.8   2.5e-05     0.012       3      39 ..      58      95 ..      56     253 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                                      EEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEE CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge.kaivsdkpgtTrdineg 39
                                      a+vG   +GKStL++al+++ +  +++     ++i+e+
  gi|313125206|ref|YP_004035470.1| 58 ALVGPNGSGKSTLLKALSKQlAPDTGNVLLDGQTIQEY 95
                                      89*****************9555888887555555443 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.7e-05     0.008       4      60 ..      56     116 ..      53     125 .. 0.71
   2 ?   -0.9   0.0       2.8   1.3e+03      27      72 ..     179     224 ..     163     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHT....TTTTTT--S.SHHHHHHHH CS
                        APS_kinase   4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvR....hgLnkdLgf.seedRkeni 60 
                                       +  l G  gsGKst+ +al+k+L  +  + +lLdG+++     ++  ++Lg  s+e+ + n+
  gi|313125206|ref|YP_004035470.1|  56 ITALVGPNGSGKSTLLKALSKQLAPDTGN-VLLDGQTIQeygdKEFARELGLlSQENDSPNT 116
                                       56789******************987655.68******833334677777752444444555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.8
                                       HHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHH CS
                        APS_kinase  27 vekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevakllad 72 
                                        ++ + v lLd  +   +L ++L   e   + n rr + +a  l d
  gi|313125206|ref|YP_004035470.1| 179 LAQDTDVLLLDEPTTYLDLHHQLRVMETVQQLNDRRDVTIAVVLHD 224
                                       4566777778888888888888888888888888887777766665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.4e-05    0.0064       3      25 ..      59      89 ..      58     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf........g 25
                                      l G+ G+GK+tl k+Lsk l+         g
  gi|313125206|ref|YP_004035470.1| 59 LVGPNGSGKSTLLKALSKQLAPdtgnvlldG 89
                                      89****************9733454455553 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.8   4.6e+03      40      48 ..     128     136 ..      98     156 .. 0.52
   2 !   16.1   0.0   2.1e-05    0.0097       3      74 ..     198     265 ..     197     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.8
                                       HHHTS..HH CS
                                HD  40 gpfgdafek 48 
                                       +p++ +fe+
  gi|313125206|ref|YP_004035470.1| 128 YPHRGFFEQ 136
                                       222333332 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH.HHH..CTCCHHHHHHHHHHHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk.eee..fekflaHekvgaeilrevekrl 74 
                                        H l+V++  ++l ++++       + +a  lHDi+        + + ++   ++  +  e+v++e+l +v+ ++
  gi|313125206|ref|YP_004035470.1| 198 HHQLRVMETVQQLNDRRD-------VTIAVVLHDIAQAARFADYLIAlQDGevYDWGPPREVVTEELLADVFRVE 265
                                       7*****************.......*************9776444446333567777899999999999988776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     2e-05    0.0096       3      35 ..      58     100 ..      56     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-05
                            AAA_28   3 vitGgestGKTtlleaLaar..........gypvvpEaareil 35 
                                       +++G+ ++GK+tll+aL+++          + ++++E++ + +
  gi|313125206|ref|YP_004035470.1|  58 ALVGPNGSGKSTLLKALSKQlapdtgnvllDGQTIQEYGDKEF 100
                                       799***************7766666555555557777765444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   2.5e-05     0.012      19      50 ..      55      86 ..      51     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                       +++l+Gp G+GK+t+lkal + ++ + g+v+
  gi|313125206|ref|YP_004035470.1| 55 EITALVGPNGSGKSTLLKALSKQLAPDTGNVL 86
                                      4789****************777766655554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.4e-05     0.016      19      57 ..      57      95 ..      48     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                        l+G  G+GKs+l+++l ++l+++ + v ld+ +++e+
  gi|313125206|ref|YP_004035470.1| 57 TALVGPNGSGKSTLLKALSKQLAPDTGNVLLDGQTIQEY 95
                                      5689*******************9999999*99999887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.4e-05     0.011      47      73 ..      56      82 ..      42     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-05
                             Rad17 47 iLLisGPsGCgkstvvkvLskelgikl 73
                                      i  + GP G gkst +k Lsk+l+++ 
  gi|313125206|ref|YP_004035470.1| 56 ITALVGPNGSGKSTLLKALSKQLAPDT 82
                                      77799*****************99865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   4.1e-05     0.019       3      28 ..      57      82 ..      55      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.1e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                       +l G++GsGK+tLl+ l  ++a ++
  gi|313125206|ref|YP_004035470.1| 57 TALVGPNGSGKSTLLKALSKQLAPDT 82
                                      6899***************9998665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.7e-05     0.046       3      49 ..      55     100 ..      53     125 .. 0.72
   2 ?   -0.5   0.0       2.5   1.2e+03      63      84 ..     181     202 ..     136     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.7e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49 
                                       +i +++G+  +GK+tllk l k+l  ++   + ++ ++ +++  +++
  gi|313125206|ref|YP_004035470.1|  55 EITALVGPNGSGKSTLLKALSKQLA-PDTGNVLLDGQTIQEYGDKEF 100
                                       7899****************98877.666666666666666555544 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.5
                            AAA_14  63 ekktylflDEiqevpewekalk 84 
                                       +++ +l+lDE   + ++ + l+
  gi|313125206|ref|YP_004035470.1| 181 QDTDVLLLDEPTTYLDLHHQLR 202
                                       3677899999888866666655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0005      0.24      27      62 ..      59      94 ..      54     124 .. 0.85
   2 ?    0.8   0.0      0.55   2.6e+02      90     150 ..     165     231 ..     153     239 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplseeealevakias 62
                                      lvGp GsGK+ l k+l++ l+p + +  l+ ++i+ 
  gi|313125206|ref|YP_004035470.1| 59 LVGPNGSGKSTLLKALSKQLAPDTGNVLLDGQTIQE 94
                                      89****************999999888888777765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.55
                      Mg_chelatase  90 lvGggskpkpGeislah.nGvLfLDElpef.....krkvlevLRePledgevtisrakakvefparf 150
                                       l Gg+++    ++ la+ + vL+LDE + +     + +v+e++ +  +++ vti+   +++   arf
  gi|313125206|ref|YP_004035470.1| 165 LSGGQKQLAWIAMVLAQdTDVLLLDEPTTYldlhhQLRVMETVQQLNDRRDVTIAVVLHDIAQAARF 231
                                       6677777777777777625699999976442222266788888888888888888777777777766 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.8e-05     0.046      27      82 ..      58     110 ..      55     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.8e-05
                             DUF87  27 AilgsTGsGKSntvavLleellekkgatililDpHG..EYgkalekllsekvkvitps 82 
                                       A +g  GsGKS++ + L ++l+  +++  ++lD +   EYg+     ++ ++ +++++
  gi|313125206|ref|YP_004035470.1|  58 ALVGPNGSGKSTLLKALSKQLA--PDTGNVLLDGQTiqEYGDKE---FARELGLLSQE 110
                                       788999****************..99*******88666888776...55555555554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0     0.001      0.48       2      20 ..      60      78 ..      59      87 .. 0.86
   2 ?    2.0   0.1      0.32   1.5e+02      76     142 ..     169     235 ..     140     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                        ATP_bind_1  2 vGpaGsGKttfvgalseil 20
                                      vGp GsGK+t+ +als+ l
  gi|313125206|ref|YP_004035470.1| 60 VGPNGSGKSTLLKALSKQL 78
                                      8**************9755 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.32
                        ATP_bind_1  76 resldwldeelekeeddyllfDtPGQielfthseslakiveeLes.efalvvvyLvDsqrltdptkfi 142
                                       +++l w++  l  +++d ll+D P       h     + v++L+  +  +++v+L D   ++  ++++
  gi|313125206|ref|YP_004035470.1| 169 QKQLAWIAMVL-AQDTDVLLLDEPTTYLDLHHQLRVMETVQQLNDrRDVTIAVVLHDIAQAARFADYL 235
                                       56778888888.66889999999975544444444555788888888889999999988877777665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00015     0.073       3      23 ..      59      79 ..      57     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      l+Gp G GK++l ka+ k+l 
  gi|313125206|ref|YP_004035470.1| 59 LVGPNGSGKSTLLKALSKQLA 79
                                      89****************984 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00022       0.1       2      25 ..      56      79 ..      55     107 .. 0.80
   2 ?   -2.1   0.0       5.3   2.5e+03      21      38 ..     210     227 ..     202     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                                      EEEEEESTTCCHHHHHHHHHCT-- CS
                              cobW  2 vtvltGflGsGKTtLlnhllenra 25
                                      +t l+G+ GsGK+tLl++l ++ a
  gi|313125206|ref|YP_004035470.1| 56 ITALVGPNGSGKSTLLKALSKQLA 79
                                      6899*************9986644 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.3
                                       HCT--SS-EEEEESS-SS CS
                              cobW  21 lenraglklavivNefge 38 
                                       l++r++  +av++ ++ +
  gi|313125206|ref|YP_004035470.1| 210 LNDRRDVTIAVVLHDIAQ 227
                                       477888899999988875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00048      0.23       4      23 ..      59      78 ..      57      94 .. 0.83
   2 ?   -0.2   0.0       1.9   9.1e+02      23      49 ..     187     215 ..     173     244 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00048
                                      EE--SSSSHHHHHHHGGGGB CS
                             AAA_5  4 LvGppGtgKselaerlaaal 23
                                      LvGp G+gKs+l + l++ l
  gi|313125206|ref|YP_004035470.1| 59 LVGPNGSGKSTLLKALSKQL 78
                                      9***************9988 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.9
                                       B.S--EEEEE--TT--HHHHH--B--... CS
                             AAA_5  23 l.nreveyvqltrdtteedlkgrreik.n 49 
                                       l   +++y  l+ +++  + +++++ + +
  gi|313125206|ref|YP_004035470.1| 187 LlDEPTTYLDLHHQLRVMETVQQLNDRrD 215
                                       14555556666666555555555553333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00016     0.077       3      24 ..      59      80 ..      57     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                      RNA_helicase  3 lyGpsgeGKStlakeLakallk 24
                                      l+Gp+g GKStl k L+k+l+ 
  gi|313125206|ref|YP_004035470.1| 59 LVGPNGSGKSTLLKALSKQLAP 80
                                      79****************9983 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.11     134     161 ..      59      86 ..      36      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                             T2SSE 134 vsGgTgsGKttllyallkeinksderiv 161
                                       + G+ gsGK+tll al k+++ ++ +++
  gi|313125206|ref|YP_004035470.1|  59 LVGPNGSGKSTLLKALSKQLAPDTGNVL 86 
                                       57******************99988776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00093      0.44       4      38 ..      59      95 ..      56     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00093
                                      EE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkss..gvkvgGfyteev 38
                                      + Gp G+GK+Tl+k ++++l+ +  +v ++G   +e+
  gi|313125206|ref|YP_004035470.1| 59 LVGPNGSGKSTLLKALSKQLAPDtgNVLLDGQTIQEY 95
                                      78****************9976544666777666665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027      0.13      27      48 ..      55      76 ..      46      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            AAA_27 27 dlhliyGpNEAGKstalrAisd 48
                                      +++ ++GpN +GKst+l+A+s+
  gi|313125206|ref|YP_004035470.1| 55 EITALVGPNGSGKSTLLKALSK 76
                                      567789*************986 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.14      23      50 ..      55      82 ..      46      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                           DUF2813 23 entvLiGENaWGKSSLldALslilnvek 50
                                      e t+L+G N  GKS Ll+ALs  l++++
  gi|313125206|ref|YP_004035470.1| 55 EITALVGPNGSGKSTLLKALSKQLAPDT 82
                                      6799*****************9998875 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00044      0.21       2      23 ..      58      79 ..      57      85 .. 0.89
   2 ?   -1.8   0.0       4.6   2.2e+03     135     153 ..     194     212 ..     141     231 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                                      EEE-STTSSHHHHHHHHHHHHT CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklg 23
                                      a+ GP gsGKs++ +al+++l 
  gi|313125206|ref|YP_004035470.1| 58 ALVGPNGSGKSTLLKALSKQLA 79
                                      678****************985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.6
                                       EEE--HHHHHHHHHHHHHH CS
                    Cytidylate_kin 135 fldAsveeRakRRlkqlka 153
                                       +ld   + R+   ++ql++
  gi|313125206|ref|YP_004035470.1| 194 YLDLHHQLRVMETVQQLND 212
                                       3333333333333333333 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2    0.0004      0.19       3      34 ..      56      87 ..      54     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvll 34
                                      +++lvG++G+GK t l  L+++l  +  +vll
  gi|313125206|ref|YP_004035470.1| 56 ITALVGPNGSGKSTLLKALSKQLAPDTGNVLL 87
                                      678*****************999888777776 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00054      0.26      53      79 ..      55      81 ..      40     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00054
                              VirE 53 fvlvLvGkqgsgKstfleklgeewftd 79
                                      +++ LvG+ gsgKst+l++l+++   d
  gi|313125206|ref|YP_004035470.1| 55 EITALVGPNGSGKSTLLKALSKQLAPD 81
                                      6899****************9986655 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0     0.002      0.93      50      88 ..      54      92 ..       5      99 .. 0.80
   2 ?    0.1   0.0      0.77   3.6e+02     211     243 ..     207     238 ..     190     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.002
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsev 88
                                      G    l+Gp+g+Gk+ l  a+sk+l+ d+  v l g  +
  gi|313125206|ref|YP_004035470.1| 54 GEITALVGPNGSGKSTLLKALSKQLAPDTGNVLLDGQTI 92
                                      6667799*******************9999888887655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.77
                                       S---S----XXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 211 kGevekkkevvqevtLhdlDvanarpqdllsll 243
                                         +++ +++v+  v Lhd+  a ar  d+l  l
  gi|313125206|ref|YP_004035470.1| 207 VQQLNDRRDVTIAVVLHDIAQA-ARFADYLIAL 238
                                       55788899**********9754.5666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.79u 0.41s 00:00:01.20 Elapsed: 00:00:00.61
# Mc/sec: 1400.22
//
Query:       gi|313125207|ref|YP_004035471.1|  [L=105]
Description: hypothetical protein Hbor_04280 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.2    9.1   0.0        1.2    9.1   0.0    2.0  3  LRR19-TM  Leucine-rich repeat family 19 TM domain


Domain annotation for each model (and alignments):
>> LRR19-TM  Leucine-rich repeat family 19 TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       0.2   3.6e+03      15      31 ..      10      23 ..       4      27 .. 0.47
   2 ?   -2.6   0.2      0.31   5.6e+03      12      31 ..      44      63 ..      42      68 .. 0.70
   3 ?    9.1   0.0   6.9e-05       1.2      15      43 ..      74     102 ..      71     105 .] 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.2
                          LRR19-TM 15 Waylvgvvvlalvtsll 31
                                       a +   +++al+ +ll
  gi|313125207|ref|YP_004035471.1| 10 IAVI---AATALTFALL 23
                                      3333...3444444444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.31
                          LRR19-TM 12 gksWaylvgvvvlalvtsll 31
                                      g  W    gvv   l+++l+
  gi|313125207|ref|YP_004035471.1| 44 GAGWVGAFGVVTNRLGVALV 63
                                      66788788888877777765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 6.9e-05
                          LRR19-TM  15 Waylvgvvvlalvtsllillaikckllyk 43 
                                       W+++vg+++l + ++ll+  a+ +++  +
  gi|313125207|ref|YP_004035471.1|  74 WQFTVGLAALPVAVALLVSAAATGPTRSN 102
                                       ********************999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 613.04
//
Query:       gi|313125208|ref|YP_004035472.1|  [L=388]
Description: cdc6-related protein, aaa superfamily ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-13   49.6   1.3    3.4e-12   47.1   1.3    2.2  1  AAA_16           AAA ATPase domain
    1.1e-09   38.7   0.0    2.9e-09   37.3   0.0    1.8  2  AAA_22           AAA domain
    0.00014   21.4   0.0    0.00023   20.7   0.0    1.3  1  TniB             Bacterial TniB protein
    0.00096   19.2   4.8     0.0018   18.3   0.3    3.2  3  HTH_20           Helix-turn-helix domain
     0.0014   18.4   0.2     0.0036   17.1   0.2    1.7  1  HTH_23           Homeodomain-like domain
     0.0051   16.9   0.0     0.0096   16.0   0.0    1.4  1  Sigma54_activ_2  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.014   15.2   1.1      0.025   14.4   0.1    2.0  1  HTH_IclR         IclR helix-turn-helix domain
      0.019   14.9   0.2       0.08   12.9   0.0    2.2  2  MarR             MarR family
      0.026   14.4   1.7      0.067   13.1   0.3    2.4  2  MarR_2           MarR family
      0.028   14.8   0.0      0.046   14.1   0.0    1.3  1  RNA_helicase     RNA helicase
      0.039   14.3   0.1      0.087   13.2   0.0    1.8  2  AAA_19           AAA domain
      0.047   13.8   2.7       0.11   12.7   0.0    2.7  3  AAA_33           AAA domain
      0.052   14.0   0.0       0.13   12.7   0.0    1.6  1  HTH_40           Helix-turn-helix domain
      0.055   13.4   0.0      0.079   12.9   0.0    1.2  1  ATPase_2         ATPase domain predominantly from Archaea
      0.059   12.5   0.0       0.12   11.6   0.0    1.5  1  NB-ARC           NB-ARC domain
      0.082   12.7   0.0       0.38   10.5   0.0    2.0  2  AAA_29           P-loop containing region of AAA domain
      0.093   13.2   0.0       0.17   12.3   0.0    1.5  1  AAA              ATPase family associated with various cellul
      0.094   12.0   0.0       0.19   11.0   0.0    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.11   12.4   0.0       0.23   11.4   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
       0.19   10.9   0.0       0.25   10.5   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   1.3   3.7e-15   3.4e-12       2     164 ..      35     182 ..      34     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 3.7e-15
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd.....ggiflrgkcdql.esaipysa 71 
                                         GR+  +e+Ll+ le+v ++r+ e+v+++G++G+GKs++v +l+ ++++      + i+++++  +  +++ +   
  gi|313125208|ref|YP_004035472.1|  35 PTGRGPTIERLLDRLEPVFEHRTpENVYVHGPAGSGKSAVVSALFSQFTRLlsspeDSIVTTTRGGSAdTRSFA--- 108
                                       57*******************************************99988744444333322222222233344... PP

                            AAA_16  72 laqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwad 148
                                                    ++ +++++e+e +++ l++ ++++ + +g + ++l+  ++r+l+  +     lv+ +D+   ad
  gi|313125208|ref|YP_004035472.1| 109 ------------YVDLREATSEFEFYHTILDAMTSESIPQRGLSTTDLRTRVSRHLRGGRI----LVVAMDH---AD 166
                                       ............4444444555666666555544444444444446777777777733333....6666664...44 PP

                            AAA_16 149 easlqllaaLlrlles 164
                                       e   + la+++ +les
  gi|313125208|ref|YP_004035472.1| 167 ENGTDRLASFAGELES 182
                                       5455555555555444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   3.3e-12   2.9e-09       6     102 ..      59     167 ..      54     201 .. 0.88
   2 ?   -2.3   0.0       5.4   4.9e+03      38      66 ..     205     234 ..     187     256 .. 0.61

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3.3e-12
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsstsskdllrellralglelka 70 
                                         ++v+G++G+GK+ ++  l++q+++  +  e              +++++v+l + ts  ++++ +l a+++e   
  gi|313125208|ref|YP_004035472.1|  59 ENVYVHGPAGSGKSAVVSALFSQFTRLLSSPEdsivtttrggsaDTRSFAYVDLREATSEFEFYHTILDAMTSESIP 135
                                       6689********************887777779**********8888888**********************99888 PP

                            AAA_22  71 .erlsseellealeqalraravielliiDEaqh 102
                                        ++ls+ +l++++ ++lr  +   ++  D a+ 
  gi|313125208|ref|YP_004035472.1| 136 qRGLSTTDLRTRVSRHLRGGRI-LVVAMDHADE 167
                                       999*******************.9999999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.4
                            AAA_22  38 erpevvfvtlpsstsskdl.lrellralgl 66 
                                       +  ++v+v++ +  +++dl   ++   l++
  gi|313125208|ref|YP_004035472.1| 205 RATRTVTVEPYHRAELTDLlTARVSTGLTR 234
                                       666777777777777777733344444443 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.5e-07   0.00023      17     126 ..      43     163 ..      36     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.5e-07
                              TniB  17 keilerLeeLleypkrkrmpnlllvGdsnnGKtmive....kFarlh.ppekd.......edaekvpvlvvqappkp 81 
                                       +++l+rLe ++e+     ++n++++G+   GK+++v+    +F+rl  +pe++        +a+++   +v++++  
  gi|313125208|ref|YP_004035472.1|  43 ERLLDRLEPVFEH---RTPENVYVHGPAGSGKSAVVSalfsQFTRLLsSPEDSivtttrgGSADTRSFAYVDLREAT 116
                                       4555555555554...34578***********9987522226776652233322222222445699*********** PP

                              TniB  82 dekrlyaaiLealgaplkara..rvskleqqvlrllrelkvrvLiiD 126
                                       +e ++y+ iL+a+  +  +++  ++++l+ +v r lr  ++ v+ +D
  gi|313125208|ref|YP_004035472.1| 117 SEFEFYHTILDAMTSESIPQRglSTTDLRTRVSRHLRGGRILVVAMD 163
                                       *************9997777645667888999888886655555555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.3   1.2e+03      23      46 ..     127     153 ..     121     154 .. 0.77
   2 ?    0.0   0.1         1   9.1e+02      30      50 ..     220     247 ..     217     250 .. 0.61
   3 !   18.3   0.3   2.1e-06    0.0018       7      59 ..     299     358 ..     295     360 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                                       TTB-HHHHHHHH..TS-HHH.HHHHHH CS
                            HTH_20  23 egltaselaerl..dlsknt.lsyHLr 46 
                                       +++t + + +r+   ++  t +s+HLr
  gi|313125208|ref|YP_004035472.1| 127 DAMTSESIPQRGlsTTDLRTrVSRHLR 153
                                       677777777777766788888999997 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1
                                       HHHHH......TS-HHH.HHHHHHHHHH CS
                            HTH_20  30 laerl......dlsknt.lsyHLrvLee 50 
                                       l ++l      +l++n   +++Lr L+ 
  gi|313125208|ref|YP_004035472.1| 220 LTDLLtarvstGLTRNAtTHQQLRRLAA 247
                                       5555544333345555559999999976 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 2.1e-06
                                       HS-HHHHHHHHHH.......STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20   7 LahPvRrrilraL.......araegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                       ++++ R+ +lr L       ++  g+ as +a + +ls +t+ + L + +e g+ve+v +
  gi|313125208|ref|YP_004035472.1| 299 TLSENRLTVLRRLvaldatdRSSVGRAASTIASAASLSESTITRYLYEFAESGIVERVPV 358
                                       6789*****************************************************987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2     4e-06    0.0036       2      46 ..     305     352 ..     304     356 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-06
                            HTH_23   2 asereRlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                       +++++Rl +l + ++   G   ++IA +   s++T+ r+l  ++e+G+
  gi|313125208|ref|YP_004035472.1| 305 LTVLRRLVALDATDRssvGRAASTIASAASLSESTITRYLYEFAESGI 352
                                       5789**********8899****************************95 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05    0.0096       2      47 ..      37      84 ..      36     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                                      ---HHHHHHHHHHHHHHT-SS-..EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  2 gasaaiqelkerLeqaaqsklp..vfltGekGsgkelvArlLhknsgp 47
                                      g+++ i++l +rLe + +  +p  v++ G++Gsgk+ v  +L ++ ++
  gi|313125208|ref|YP_004035472.1| 37 GRGPTIERLLDRLEPVFEHRTPenVYVHGPAGSGKSAVVSALFSQFTR 84
                                      899*************96665444***********9876666555333 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.8e-05     0.025      21      52 .]     326     357 ..     307     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR  21 lselArrtglpkStvhRlLqtLvelGyveqdg 52 
                                        s +A ++ l+ St  R+L  + e G+ve+ +
  gi|313125208|ref|YP_004035472.1| 326 ASTIASAASLSESTITRYLYEFAESGIVERVP 357
                                       688**************************975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.5   4.1e+03      32      42 ..      40      50 ..      40      50 .. 0.87
   2 ?   12.9   0.0     9e-05      0.08      21      51 ..     327     357 ..     300     360 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.5
                                      HHHHHHHHHHH CS
                              MarR 32 stvtrvldrLe 42
                                      +t+ r+ldrLe
  gi|313125208|ref|YP_004035472.1| 40 PTIERLLDRLE 50
                                      68889*****8 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9e-05
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  21 seLakklgvskstvtrvldrLekkGlieRsk 51 
                                       s +a++ ++s st+tr l +  + G +eR +
  gi|313125208|ref|YP_004035472.1| 327 STIASAASLSESTITRYLYEFAESGIVERVP 357
                                       49***************************76 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.5   3.1e+03      32      47 ..     231     247 ..     227     248 .. 0.80
   2 ?   13.1   0.3   7.4e-05     0.067      12      56 ..     312     358 ..     303     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                                       TSSH.HHHHHHHHHHHH CS
                            MarR_2  32 glsk.savsrilkrLva 47 
                                       gl++ +++++ l+rL a
  gi|313125208|ref|YP_004035472.1| 231 GLTRnATTHQQLRRLAA 247
                                       67777899999999976 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.4e-05
                                       HHHHCTTTS...EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  12 aaLgrrpgr...dltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                        aL + ++    + +++ +a +  ls s+++r l ++ + G ver+p 
  gi|313125208|ref|YP_004035472.1| 312 VALDATDRSsvgR-AASTIASAASLSESTITRYLYEFAESGIVERVPV 358
                                       4455555444434.9******************************986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.2e-05     0.046       1      36 [.      61      95 ..      61     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                      ++++Gp+g GKS ++  L +++++ l +++ ds+++
  gi|313125208|ref|YP_004035472.1| 61 VYVHGPAGSGKSAVVSALFSQFTRLLSSPE-DSIVT 95
                                      79********************98886666.55544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.7e-05     0.087       9      55 ..      57     103 ..      50     247 .. 0.85
   2 ?   -2.8   0.0         8   7.2e+03      64      78 ..     321     335 ..     305     352 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.7e-05
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAa 55 
                                       + +++ v +++G+GK+ v+ +  + + +l + + ++i+  +  g A 
  gi|313125208|ref|YP_004035472.1|  57 TPENVYVHGPAGSGKSAVVSALFSQFTRLLSSPEDSIVTTTRGGSAD 103
                                       567899************************99878887777666654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8
                            AAA_19  64 algaeatTiHrlall 78 
                                       ++g++a+Ti + a l
  gi|313125208|ref|YP_004035472.1| 321 SVGRAASTIASAASL 335
                                       344455555555443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3       1.5   1.3e+03     111     131 ..       3      23 ..       2      25 .. 0.81
   2 ?   12.7   0.0   0.00012      0.11       2      33 ..      61      93 ..      61     191 .. 0.68
   3 ?   -1.5   0.0       2.9   2.6e+03      87     122 ..     328     363 ..     297     386 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.5
                            AAA_33 111 lkeRlakRaangddrsevpee 131
                                       l+eR+ +R+++gd+r  v ee
  gi|313125208|ref|YP_004035472.1|   3 LEERILQRKRRGDRRQLVLEE 23 
                                       789*******99988766555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt..l 33
                                      v+++G++GsGKs ++  l  +  + llss++  +
  gi|313125208|ref|YP_004035472.1| 61 VYVHGPAGSGKSAVVSALFSQ-FTRLLSSPEdsI 93
                                      799***************944.455566665552 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.9
                            AAA_33  87 rflklarrlgvpvrivvvetdeetlkeRlakRaang 122
                                        + ++a+  ++ ++    e  e+ + eR+ +++ ng
  gi|313125208|ref|YP_004035472.1| 328 TIASAASLSESTITRYLYEFAESGIVERVPVKETNG 363
                                       333334444444444444455555555555555555 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015      0.13      16      41 ..     327     354 ..     321     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                            HTH_40  16 eeIAkerglkesTIegHLaelieeg..e 41 
                                         IA   +l+esTI ++L e++e+g  e
  gi|313125208|ref|YP_004035472.1| 327 STIASAASLSESTITRYLYEFAESGivE 354
                                       68*********************98443 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.8e-05     0.079       6      42 ..      44      80 ..      43     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.8e-05
                          ATPase_2  6 kelkeleeilerepneiyfiYGpegsGKtaLlkeiie 42
                                      + l++le + e  + e +++ Gp gsGK+a++  + +
  gi|313125208|ref|YP_004035472.1| 44 RLLDRLEPVFEHRTPENVYVHGPAGSGKSAVVSALFS 80
                                      5689999**********************99887655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.12      14      49 ..      54      87 ..      40     175 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                      CTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                            NB-ARC 14 ekdelqslvvalvGmgGvGKttlakqilnksdeveg 49
                                      e+  ++   v ++G +G+GK+ +++  ++++  + +
  gi|313125208|ref|YP_004035472.1| 54 EHRTPE--NVYVHGPAGSGKSAVVSALFSQFTRLLS 87
                                      455566..899******************9987765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00042      0.38      23      42 ..      59      78 ..      50      85 .. 0.81
   2 ?   -1.5   0.0       2.5   2.2e+03      37      44 ..     124     131 ..     123     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                            AAA_29 23 gatlltGpsGsGKSTllDAi 42
                                      +++ + Gp GsGKS+++ A+
  gi|313125208|ref|YP_004035472.1| 59 ENVYVHGPAGSGKSAVVSAL 78
                                      468999**********9886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                            AAA_29  37 TllDAiqa 44 
                                       T+lDA++ 
  gi|313125208|ref|YP_004035472.1| 124 TILDAMTS 131
                                       9****985 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00019      0.17       1      74 [.      61     172 ..      61     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                       EEEESSTTSSHHHHHHHHHHHH.............THE.........EEEEETTTCSSS.................S CS
                               AAA   1 vllyGppGtGKTllakavakel.............gve.........fleisgsellsk.................y 38 
                                       v+++Gp G GK+++++a+ +++               +         f  +++ e +s+                  
  gi|313125208|ref|YP_004035472.1|  61 VYVHGPAGSGKSAVVSALFSQFtrllsspedsivtT-TrggsadtrsFAYVDLREATSEfefyhtildamtsesipQ 136
                                       689*****************9633333333322330.0333333333555555555544566666666655555555 PP

                                       TTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                               AAA  39 vgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                        g s  ++r  +++  +  +  ++ +D +d+ +++r
  gi|313125208|ref|YP_004035472.1| 137 RGLSTTDLRTRVSRHLRGGRILVVAMDHADENGTDR 172
                                       666666666666553222245777777777666666 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00022      0.19      10      59 ..      29      78 ..      21      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                                      HHHT---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE 10 kfrtessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntL 59
                                       ++  ++++ +   +   ++ + +++   + ++ v+G  gsGKS ++ +L
  gi|313125208|ref|YP_004035472.1| 29 VWHSPEPTGRGPTIERLLDRLEPVFEHRTPENVYVHGPAGSGKSAVVSAL 78
                                      5666666666666667778888888888999***************9998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00026      0.23      23      58 ..     324     359 ..     299     373 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                       CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  23 atadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                         a++ia+++ +++s++ ++L +  + G+Ver++ +
  gi|313125208|ref|YP_004035472.1| 324 RAASTIASAASLSESTITRYLYEFAESGIVERVPVK 359
                                       5799****************************9876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00028      0.25       3      26 ..      60      86 ..      58     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                           DUF2075  3 vvlVtGvaGtGKtvvllnllael...e 26
                                       v V+G aG+GK+ v ++l+ +     
  gi|313125208|ref|YP_004035472.1| 60 NVYVHGPAGSGKSAVVSALFSQFtrlL 86
                                      578*****************9985551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.76u 0.37s 00:00:01.12 Elapsed: 00:00:00.59
# Mc/sec: 1980.19
//
Query:       gi|313125209|ref|YP_004035473.1|  [L=356]
Description: hypothetical protein Hbor_04300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00049   19.9   2.4    0.00092   19.0   2.4    1.4  1  RTX       N-terminal domain in RTX protein


Domain annotation for each model (and alignments):
>> RTX  N-terminal domain in RTX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   2.4   5.1e-08   0.00092      88     127 ..     277     317 ..     270     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.1e-08
                               RTX  88 savvsaaaaasgVGaPvallv.alitglisgileaskqail 127
                                        ++ +aa+aa+ VG+P+a+l+ a++ g++sg+l  + q i+
  gi|313125209|ref|YP_004035473.1| 277 MGASGAAVAAATVGSPIAILLaAGVFGALSGLLGELTQRIF 317
                                       567789999999******987358**********9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2040.52
//
Query:       gi|313125210|ref|YP_004035474.1|  [L=511]
Description: glycerol kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-78  263.6   0.0    2.1e-78  263.3   0.0    1.1  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    3.4e-61  206.4   0.4    5.5e-61  205.8   0.4    1.3  1  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
    7.4e-05   22.4   0.2     0.0037   16.8   0.0    2.2  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.3   0.0   3.6e-82   2.1e-78       1     245 []       6     263 ..       6     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 263.3 bits;  conditional E-value: 3.6e-82
                                       EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE CS
                            FGGY_N   1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisg 77 
                                       ++ ++D+Gtt+t+++v+d++g+vva a++++e+++p++gw+e+dpeeiw+ +++++  +le+ag++++q  aIgi++
  gi|313125210|ref|YP_004035474.1|   6 YVGAIDQGTTGTRFMVFDHDGRVVANAYQKHEQIYPEPGWVEHDPEEIWENTQAVMLTALEEAGLDAEQLDAIGITN 82 
                                       7899************************************************************************* PP

                                       -SS-EEEEETTT.EESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHS.CCHHCCHC. CS
                            FGGY_N  78 qreglvllDknd.kpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkene.pevfekie. 151
                                       qre++ ++Dk+  +p+ynai+w+drrt   ve l+ eg+e+ ++ektgl  +++f+++k +Wl++n  p ++++++ 
  gi|313125210|ref|YP_004035474.1|  83 QRETTLIWDKESgRPVYNAIVWQDRRTTDRVETLQDEGKEEWVREKTGLEPDAYFSATKAEWLLDNAdPIKLARMRp 159
                                       ***********99***************************************************9963778999999 PP

                                       ............EEEEHHHHHHHHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCC..EEE CS
                            FGGY_N 152 ............kflliddyLiwrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesse..iig 214
                                                   +f++id++++++Ltg++vtdvtnas++mlfni++ +wd+ell+ +++p+++LP++++ss    +g
  gi|313125210|ref|YP_004035474.1| 160 ddvreraeegelMFGTIDTWVTYKLTGAHVTDVTNASRTMLFNIHDMDWDDELLEEFDVPKAMLPEVRPSSDedLYG 236
                                       99999999*************************************************************98522688 PP

                                       EEECCCCCCTT.S-EEEEEEEEEHHHHHHHH CS
                            FGGY_N 215 elkpelaaklGlkegvpvvggggDqqaaalG 245
                                       ++ +    ++    ++pv+g++gDqqaa++G
  gi|313125210|ref|YP_004035474.1| 237 TTDSDGFLEA----EIPVAGALGDQQAALFG 263
                                       8877766665....9***************9 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.8   0.4   9.2e-65   5.5e-61       1     197 [.     272     461 ..     272     462 .. 0.97

  Alignments for each domain:
  == domain 1  score: 205.8 bits;  conditional E-value: 9.2e-65
                            FGGY_C   1 akvslGTssflll.vgtkpvisehglltpva..gedgkpeyalegsiavagslvawlldnlglreeirdageveesl 74 
                                       ak+++GT+sf+l+ +g++ v sehgllt+v+   + ++ +yalegsi+++g++++wl d   l   i+da+e+ e l
  gi|313125210|ref|YP_004035474.1| 272 AKNTYGTGSFMLMnTGDEAVMSEHGLLTTVGfqRSGEPVQYALEGSIFITGAAIEWLEDV-SL---IDDAAET-EEL 343
                                       79*****************************886669*********************98.55...9*****9.*** PP

                            FGGY_C  75 aelaaaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpld 151
                                       a     ++v ++ gv+fvpaf+gl ap+wd++argti+g++++t  +h++rA+le++a+q+r++ ea+e+dsg++l+
  gi|313125210|ref|YP_004035474.1| 344 A-----RSVDSTDGVYFVPAFTGLGAPHWDQRARGTILGMTRGTRREHVVRATLESIAFQTRDVAEAMEEDSGIDLS 415
                                       *.....99999****************************************************************** PP

                            FGGY_C 152 rlavdGGgskndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                       +l+vdGG++kn++l+ql+ +i+g++++rp  +e+talGaA++A++a
  gi|313125210|ref|YP_004035474.1| 416 TLRVDGGAVKNNFLCQLQSNIVGTDIVRPMVDETTALGAAYAAGLA 461
                                       ********************************************98 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.2e-07    0.0037       3      66 ..      10      79 ..       7     201 .. 0.91
   2 !    3.8   0.0    0.0057        34     188     267 .]     381     458 ..     378     458 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.2e-07
                                      EEE-SSEEEEEEEETTTEEEEEEEE--......TTS-HHH.........HHHHHHHHHHT--GGGECEE. CS
                       BcrAD_BadFG  3 iDgGsTttkavlmdekgevlgrgitns......anlesvrfeaaekvleealtealerageeeadieety 66
                                      iD G+T t+++++d +g v+++++ +           +++ e+ +++ + ++ +ale+ag+++++++ + 
  gi|313125210|ref|YP_004035474.1| 10 IDQGTTGTRFMVFDHDGRVVANAYQKHeqiypePGWVEHDPEEIWENTQAVMLTALEEAGLDAEQLDAIG 79
                                      9************************9944444422234677999*********************98773 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0057
                                       T--HHHHHHHHHHHHHHHHHHHHHTT---SS.....EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHH CS
                       BcrAD_BadFG 188 gekaedIlaglhraialrvialisrsggvtde....vtltGGvakneaavkelrklvkenygevkininpdsiytga 260
                                       g+ +e +++ + ++ia +   +++  ++        + + GG  kn +++      +++n+ + +  + p+ + t a
  gi|313125210|ref|YP_004035474.1| 381 GTRREHVVRATLESIAFQTRDVAEAMEEDSGIdlstLRVDGGAVKN-NFL----CQLQSNIVGTD-IVRPMVDETTA 451
                                       666677777666666655555554444444434444999*******.444....44589999965.588999999** PP

                                       HHHHHHH CS
                       BcrAD_BadFG 261 lGAalfA 267
                                       lGAa  A
  gi|313125210|ref|YP_004035474.1| 452 LGAAYAA 458
                                       ***9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2916.08
//
Query:       gi|313125211|ref|YP_004035475.1|  [L=474]
Description: NAD(fad)-dependent dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-53  181.4   1.1    2.3e-53  181.4   1.1    1.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-23   83.3   1.1    8.2e-19   67.9   0.3    4.1  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.5e-10   40.8   0.0    1.7e-05   24.3   0.0    3.0  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.8e-09   37.8   0.0    9.5e-09   35.5   0.0    2.1  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.8e-08   33.9   0.7     0.0013   18.9   0.0    3.3  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.8e-07   28.8   0.1      0.092   11.4   0.0    3.7  4  HI0933_like     HI0933-like protein
    0.00083   19.3   0.2     0.0014   18.5   0.2    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0022   17.1   9.0       0.92    8.5   0.0    4.2  5  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
      0.019   14.3   0.7       0.69    9.1   0.1    2.2  2  Amino_oxidase   Flavin containing amine oxidoreductase
      0.033   13.2   0.1        6.8    5.6   0.0    2.5  3  Lycopene_cycl   Lycopene cyclase protein
      0.037   13.4   0.7       0.68    9.2   0.0    2.5  3  FAD_oxidored    FAD dependent oxidoreductase
      0.073   13.5   0.5       0.33   11.4   0.2    2.3  2  NAD_binding_7   Putative NAD(P)-binding
      0.094   11.9   0.0        2.3    7.4   0.0    2.2  2  Thi4            Thi4 family
        0.2   11.2   0.4        1.2    8.7   0.1    2.0  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.42   10.6   3.4         15    5.5   0.0    3.0  3  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.4   1.1   1.9e-56   2.3e-53       3     279 ..       5     311 ..       3     322 .. 0.91
   2 ?   -3.7   0.0       4.7   5.6e+03     151     171 ..     418     443 ..     414     457 .. 0.50

  Alignments for each domain:
  == domain 1  score: 181.4 bits;  conditional E-value: 1.9e-56
                                       EEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..HHHHCHHHHCCCCHCCTC CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias..evvkklnqgielllgeev 75 
                                        vv+Gg +AGl+aa + ++   +  v+++e+++ + + +c  ++ + g  +    ++     +    gi+l+ ++ev
  gi|313125211|ref|YP_004035475.1|   5 FVVVGGDAAGLSAASKCRRedPERAVLVFEKGRWVSYAHCGTPYFVKGEVDSLTDLLslSPADIEDRGIDLRREHEV 81 
                                       59*****************755999*********************9999999888899444455679******99* PP

                                       EEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                       Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.......... 142
                                       v++d+++++v+++    +++++  y+ l++AtG+s+   +i+G   ++ + ++ ld+a a++  l +          
  gi|313125211|ref|YP_004035475.1|  82 VAVDTDAQTVTVRGP--DSKFTQSYGDLLVATGGSAVSAPIEGFHLDGAFTMHGLDHAAAVRAFLADpgefsvgdlg 156
                                       ************776..579************************666666678888888888777777889999999 PP

                                       ...................SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEE CS
                                       ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ...................krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvev 200
                                                          + ++vvGgGy+GvE+A a++    +v++ ++ +rll++++++++++++++l+++Gv++
  gi|313125211|ref|YP_004035475.1| 157 gatdvdrdmaarygameppETVAVVGGGYVGVEMAEAFSAHDLDVHVFQRPNRLLSPFGEAVGERVADHLREQGVTL 233
                                       99999999999999999************************************************************ PP

                                       EESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GG CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 201 klgtsvkeidgngekle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGD 276
                                       +lg++v +++g+g+ +e vv ++g+++++d  +v++G++p+t+l+ e+  +el + g+i +def+rt+v+++ya+GD
  gi|313125211|ref|YP_004035475.1| 234 HLGEEVAALRGEGQ-VEtVVCGSGTKLAVDAALVGIGIQPNTALI-EETPVELGDSGAIATDEFGRTTVENVYAAGD 308
                                       *************9.777***************************.******************************* PP

                                       GCT CS
                                       xxx RF
                       Pyr_redox_2 277 vag 279
                                       va+
  gi|313125211|ref|YP_004035475.1| 309 VAE 311
                                       **2 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.7
                                       SHHHHHHHHH.....HHHHT-EEEEE CS
                                       xxxxxxxxxx.....xxxxxxxxxxx RF
                       Pyr_redox_2 151 GyiGvElAaa.....laklgkevtlv 171
                                       + +G + Aa      ++ lg++ t+ 
  gi|313125211|ref|YP_004035475.1| 418 SIVGADRAAIridtiATALGSKMTVA 443
                                       55555544444444344444444433 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.15   1.8e+02       3      20 ..       6      23 ..       4      40 .. 0.81
   2 ?    6.4   0.0     0.011        13      50      78 ..      68      93 ..      60      98 .. 0.86
   3 !   67.9   0.3   6.9e-22   8.2e-19       2      78 ..     178     253 ..     177     256 .. 0.96
   4 ?    1.3   0.0      0.43   5.1e+02       4      35 ..     419     450 ..     415     456 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.15
                                      EEECSSHHHHHHHHHHHH CS
                         Pyr_redox  3 vvvGgGyiglElAgalae 20
                                      vvvGg+  gl +A+  ++
  gi|313125211|ref|YP_004035475.1|  6 VVVGGDAAGLSAASKCRR 23
                                      9************98766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                                      HHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox 50 lekngievllntkveeiegsedgvesvkl 78
                                      +e++gi+++ +++v+++++++++   v++
  gi|313125211|ref|YP_004035475.1| 68 IEDRGIDLRREHEVVAVDTDAQT---VTV 93
                                      799****************9997...444 PP

  == domain 3  score: 67.9 bits;  conditional E-value: 6.9e-22
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                       v+vvGgGy+g+E+A+a++++  +V+v++r ++ll+ ++e+++++++++l+++g++++l+++v++++g+++ ve+v++
  gi|313125211|ref|YP_004035475.1| 178 VAVVGGGYVGVEMAEAFSAHDLDVHVFQRPNRLLSPFGEAVGERVADHLREQGVTLHLGEEVAALRGEGQ-VETVVC 253
                                       89****************************************************************9998.898875 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.43
                                       EECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   4 vvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       +vG++  ++   +++++lg+k tv e + + l
  gi|313125211|ref|YP_004035475.1| 419 IVGADRAAIRIDTIATALGSKMTVAELERQDL 450
                                       677777777777788*********99876655 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00025       0.3     168     269 ..       6     115 ..       5     128 .. 0.72
   2 !   24.3   0.0   1.4e-08   1.7e-05     165     305 .]     176     307 ..     162     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                       Pyr_redox_3 168 vViGgknSavDaAlelvrk..gaeVtvvtrgseiekeesdpsyslkpdienrleelvke......ekikvlfnaevk 236
                                       vV+Gg   +  aA ++ r+  +  V v+ +g  ++  +    y +k  + +  + l+ +      + i++  ++ev 
  gi|313125211|ref|YP_004035475.1|   6 VVVGGDAAGLSAASKCRREdpERAVLVFEKGRWVSYAHCGTPYFVKGEVDSLTDLLSLSpadiedRGIDLRREHEVV 82 
                                       78888888888888888884445566667776666666677777777665544444333446665449999999999 PP

                       Pyr_redox_3 237 eikekeeeykvktedgkkvevkddvvlatGykp 269
                                       +++++ ++++v+ +d k ++++ d ++atG + 
  gi|313125211|ref|YP_004035475.1|  83 AVDTDAQTVTVRGPDSKFTQSYGDLLVATGGSA 115
                                       999999999999999999999999999999876 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.4e-08
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikek 241
                                       + v+V+Gg+  +v++A  + +++ +V+v+ r + + +    +       + +r+++ ++e+ ++++  +ev +++ +
  gi|313125211|ref|YP_004035475.1| 176 ETVAVVGGGYVGVEMAEAFSAHDLDVHVFQRPNRLLSP---FGE----AVGERVADHLREQGVTLHLGEEVAALRGE 245
                                       679****************************9854443...344....44555555555566**************9 PP

                       Pyr_redox_3 242 eeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                        +  +v   +g+k+ v d  ++ +G +p++ ++++  +el ++g ++ t+e   t+v++++ aG
  gi|313125211|ref|YP_004035475.1| 246 GQVETVVCGSGTKLAV-DAALVGIGIQPNTALIEETPVELGDSGAIA-TDEFGRTTVENVYAAG 307
                                       9999999******999.555888************999997666665.56666778******99 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.7     2e+03      58      78 ..     176     196 ..     171     203 .. 0.83
   2 !   35.5   0.0     8e-12   9.5e-09       5     104 ..     357     458 ..     353     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                                       TTTBEEEEEEECTTHHHHHHH CS
                     Pyr_redox_dim  58 ktgkvlGahivGpgageliqe 78 
                                       +t  v+G   vG +++e++++
  gi|313125211|ref|YP_004035475.1| 176 ETVAVVGGGYVGVEMAEAFSA 196
                                       67889*******999998865 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 8e-12
                                       EESSSEEEEEES-H.HHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHH CS
                     Pyr_redox_dim   5 vftdpevasvGlte.eeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliqe 78 
                                       + +++e +  G+   e A+ ag  ++ ++ +++a +r+ +y+  ++++v l ad+++g++lG +ivG ++a+ +i+ 
  gi|313125211|ref|YP_004035475.1| 357 KAFELECGRAGILDyERARTAG--FDPVSETITAGSRSGYYPGgSETTVTLTADRSSGRLLGGSIVGaDRAAIRIDT 431
                                       5567788888865448899999..77778888899999999999***********************677888**** PP

                                       HHHHHHTTSBHH.HHHTSBSSSSSTGG CS
                     Pyr_redox_dim  79 lavaikagltve.dladtihihPtlse 104
                                       +a+a+  ++tv+ +  ++++++P++s 
  gi|313125211|ref|YP_004035475.1| 432 IATALGSKMTVAeLERQDLAYAPPFSP 458
                                       ************668899*******94 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-06    0.0013       1      29 [.       7      37 ..       7      47 .. 0.91
   2 ?   -1.3   0.0       2.2   2.6e+03      31      66 ..     111     145 ..     110     146 .. 0.75
   3 !   11.4   0.0   0.00024      0.28       1      31 [.     180     210 ..     180     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrd 29
                                      +vG+ ++Gl+aA+ ++++   + vl++ek++
  gi|313125211|ref|YP_004035475.1|  7 VVGGDAAGLSAASKCRREdpERAVLVFEKGR 37
                                      8****************878889******85 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                                       SSGGG-EECETTCEECTS---EEETTHHHHCHHHHC CS
                     NAD_binding_8  31 lGGraasyevpgvrvdygahifhgsgyypnvrrllr 66 
                                       +GG a s+ ++g+ +d ga ++hg +   +vr++l+
  gi|313125211|ref|YP_004035475.1| 111 TGGSAVSAPIEGFHLD-GAFTMHGLDHAAAVRAFLA 145
                                       6899999999998777.6777788877777887775 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00024
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       +vG+G  G  +A + + +++dv+++++ +rl
  gi|313125211|ref|YP_004035475.1| 180 VVGGGYVGVEMAEAFSAHDLDVHVFQRPNRL 210
                                       8************************998875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   7.7e-05     0.092       4      33 ..       6      37 ..       3      40 .. 0.89
   2 !    8.0   0.0   0.00087         1     113     167 ..      62     116 ..      53     128 .. 0.82
   3 ?    4.3   0.0     0.011        13       2      36 ..     177     211 ..     176     220 .. 0.91
   4 ?   -0.8   0.0      0.41   4.9e+02     117     163 ..     224     269 ..     216     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.7e-05
                                      EEE--SHHHHHHHHHH..HHTT--EEEE-SSS CS
                       HI0933_like  4 iviGgGaAGlmaAisa..akrgkrVlllekak 33
                                      +v+Gg aAGl aA ++  ++ ++ Vl++ek++
  gi|313125211|ref|YP_004035475.1|  6 VVVGGDAAGLSAASKCrrEDPERAVLVFEKGR 37
                                      9***************7777899******986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00087
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE----SS- CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGGlSi 167
                                       ++  + ++++g++lr e+ev +v+++++  ++v+  +s+ + +   l++AtGG ++
  gi|313125211|ref|YP_004035475.1|  62 SLSPADIEDRGIDLRREHEVVAVDTDAQT-VTVRGpDSKFTQSYGDLLVATGGSAV 116
                                       55557899***************886666.8888867777778889*******876 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.011
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +v+v+GgG  G+  A++ ++++ +V ++ + ++l+
  gi|313125211|ref|YP_004035475.1| 177 TVAVVGGGYVGVEMAEAFSAHDLDVHVFQRPNRLL 211
                                       699*************************9887765 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.41
                                       HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                        +l+e+gv+l+l +ev++++  e+++ +v + s+++l+ d+ ++ +G
  gi|313125211|ref|YP_004035475.1| 224 DHLREQGVTLHLGEEVAALRG-EGQVETVVCGSGTKLAVDAALVGIG 269
                                       6799**************955.4444555556888888888877766 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.2e-06    0.0014       1      56 [.     177     232 ..     177     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56 
                                       +vav+G G +G ++a++f +++l+V+++++ ++ l    e++ ++++   +++ ++
  gi|313125211|ref|YP_004035475.1| 177 TVAVVGGGYVGVEMAEAFSAHDLDVHVFQRPNRLLSPFGEAVGERVADHLREQGVT 232
                                       69****************************99999988888888777666666555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00077      0.92       3      31 ..       6      36 ..       5      44 .. 0.82
   2 ?    2.3   0.1     0.058        70     151     237 ..      68     143 ..      58     152 .. 0.82
   3 ?   -0.8   0.1      0.52   6.2e+02       2      29 ..     178     205 ..     177     212 .. 0.89
   4 ?    0.4   0.0      0.22   2.6e+02     138     180 ..     213     254 ..     194     266 .. 0.81
   5 !    7.7   0.1    0.0014       1.7     351     402 ..     272     310 ..     256     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00077
                                      EEE--SHHHHHHHHHHHHTTT..-EEEEESS CS
                     FAD_binding_2  3 iViGsGlAGLaAAleaaeaGl..kvavveke 31
                                      +V+G+ +AGL+AA +++++     v+v ek+
  gi|313125211|ref|YP_004035475.1|  6 VVVGGDAAGLSAASKCRREDPerAVLVFEKG 36
                                      8***************996543377777776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.058
                                       HHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEES.EEEE-----GG..........GSSSBSSGTT-S CS
                     FAD_binding_2 151 arkagvdfqerteadeLivedgrvtGavvenpesgrevrirak.avvlatgGfgrallkellgaaaeaettnapavt 226
                                       ++++g+d++ ++e++++   d ++ +++v+     ++++ ++   +++atgG          +++  ++  +a +  
  gi|313125211|ref|YP_004035475.1|  68 IEDRGIDLRREHEVVAV---DTDAQTVTVR--GPDSKFT-QSYgDLLVATGGSAV------SAPIEGFHLDGAFTMH 132
                                       56889************...8899999999..5555555.445599*****9996......6678888888888999 PP

                                       -HHHHHHHCTT CS
                     FAD_binding_2 227 Gdglalalrag 237
                                       G ++a+a+ra 
  gi|313125211|ref|YP_004035475.1| 133 GLDHAAAVRAF 143
                                       99999999885 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.52
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEE CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavve 29 
                                       v V+G+G  G   A + + + l+v v  
  gi|313125211|ref|YP_004035475.1| 178 VAVVGGGYVGVEMAEAFSAHDLDVHVFQ 205
                                       89**********9999999999999875 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.22
                                       .HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEE CS
                     FAD_binding_2 138 vtghallarlvesarkagvdfqerteadeLivedgrvtGavve 180
                                         g a+ +r+++++r+ gv+++   e+++L + +g+v ++v+ 
  gi|313125211|ref|YP_004035475.1| 213 PFGEAVGERVADHLREQGVTLHLGEEVAAL-RGEGQVETVVCG 254
                                       56899999**********************.879999999987 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0014
                                       TTTSEEE.......EEEEEEEES-EEEBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 351 padrpipgpfyavkvvpaqhytmgGvetdengrvldadgqpipGLYAaGeva 402
                                       p++  i         +p  ++  g ++tde gr+      ++++ YAaG va
  gi|313125211|ref|YP_004035475.1| 272 PNTALIE-------ETPVELGDSGAIATDEFGRT------TVENVYAAGDVA 310
                                       5555555.......6677777788899*******......***********9 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.034        41     214     266 ..      66     118 ..      14     144 .. 0.80
   2 ?    9.1   0.1   0.00058      0.69     210     263 ..     220     271 ..     149     306 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.034
                                       HHHHH.TTTTEEEETSEEEEEEEEETTCEEEEETTSTEE..EESEEEE-S-HHHHH CS
                     Amino_oxidase 214 ealae.elrgldirlntrVkeikregdgvtvtledgevv..eaDaVvvTvplgvlk 266
                                           + e rg d+r +++V  +++++ +vtv+  d++ +   +D  v T   +v +
  gi|313125211|ref|YP_004035475.1|  66 A---DiEDRGIDLRREHEVVAVDTDAQTVTVRGPDSKFTqsYGDLLVATGGSAVSA 118
                                       3...2556999********************9999887787777777777766665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HH CS
                     Amino_oxidase 210 sqlpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplg 263
                                       ++++++l e   g++++l+++V  ++ eg   tv + +g+++ +Da +v + + 
  gi|313125211|ref|YP_004035475.1| 220 ERVADHLRE--QGVTLHLGEEVAALRGEGQVETVVCGSGTKLAVDAALVGIGIQ 271
                                       556666666..***********************************99987765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0057       6.8       3      40 ..       6      43 ..       4      68 .. 0.79
   2 ?    5.0   0.0    0.0089        11       2      37 ..     178     211 ..     177     222 .. 0.84
   3 ?   -2.7   0.0       1.9   2.3e+03      91     140 ..     220     269 ..     214     277 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0057
                     Lycopene_cycl  3 vviGaGpAglslAarlteakpglkvvlieaspsllfpn 40
                                      vv+G+ +Agls A +  ++ p+ +v++ e +  + ++ 
  gi|313125211|ref|YP_004035475.1|  6 VVVGGDAAGLSAASKCRREDPERAVLVFEKGRWVSYAH 43
                                      8***************9999*999*9999988776665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0089
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                       v+v+G+G  g+ +A+    ++ +l v + + ++ ll
  gi|313125211|ref|YP_004035475.1| 178 VAVVGGGYVGVEMAEAF--SAHDLDVHVFQRPNRLL 211
                                       89***************..78888887776666665 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.9
                     Lycopene_cycl  91 eellerlvengvklleak.vesveeeeageslvvleggrkirarlvvdarg 140
                                       e+++ +l e+gv+l+ +  v++ + e +   +vv+  g k+   +++++ g
  gi|313125211|ref|YP_004035475.1| 220 ERVADHLREQGVTLHLGEeVAALRGEGQ-VETVVCGSGTKLAVDAALVGIG 269
                                       5677777888888876641555555555.6788888888877777777766 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00057      0.68       3      33 ..       6      38 ..       4      39 .. 0.81
   2 ?   -2.3   0.1       1.8   2.1e+03       2      24 ..     178     200 ..     178     210 .. 0.70
   3 ?    1.9   0.0     0.096   1.1e+02      83     136 ..     213     263 ..     189     266 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00057
                      FAD_oxidored  3 vVvGGgpaGvaAAiaAaraG..akvlLveergv 33
                                      vVvGG++aG+ AA  + r++  + vl+ e+ ++
  gi|313125211|ref|YP_004035475.1|  6 VVVGGDAAGLSAASKCRREDpeRAVLVFEKGRW 38
                                      9*****************974356777777776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGak 24 
                                       v VvGGg  Gv  A a   ++  
  gi|313125211|ref|YP_004035475.1| 178 VAVVGGGYVGVEMAEAFSAHDLD 200
                                       78********9766655555555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.096
                      FAD_oxidored  83 tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirA 136
                                       +f   v ++v++++  e+gvt+ l++++ + + eg ++e v++  +  + ++ A
  gi|313125211|ref|YP_004035475.1| 213 PFGEAVGERVADHLR-EQGVTLHLGEEVAALRGEG-QVETVVCG-SGTKLAVDA 263
                                       677777788877765.66**************998.99999984.333555555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.9   2.3e+03      11      32 ..       6      27 ..       3      94 .. 0.57
   2 ?   11.4   0.2   0.00028      0.33       8      37 ..     176     205 ..     174     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.9
                     NAD_binding_7 11 lvvGgGevAarkvrklleagak 32
                                      +vvGg   +++ ++k  +++ +
  gi|313125211|ref|YP_004035475.1|  6 VVVGGDAAGLSAASKCRREDPE 27
                                      7899988888888777776633 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00028
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvva 37 
                                       ++v vvGgG v+ + ++ + + + +v+v  
  gi|313125211|ref|YP_004035475.1| 176 ETVAVVGGGYVGVEMAEAFSAHDLDVHVFQ 205
                                       5899***********************965 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0019       2.3      20      49 ..       5      35 ..       1      46 [. 0.90
   2 ?    2.0   0.0     0.084     1e+02      20      49 ..     178     206 ..     167     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0019
                                      EEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
                              Thi4 20 vvivGaGssGLtaayylakk.pdlkvailer 49
                                       v+vG+ ++GL+aa    ++ p+  v+++e+
  gi|313125211|ref|YP_004035475.1|  5 FVVVGGDAAGLSAASKCRREdPERAVLVFEK 35
                                      599**************9999*******996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.084
                                       EEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkvailer 49 
                                       v++vG+G  G+  a  ++ + dl v ++ r
  gi|313125211|ref|YP_004035475.1| 178 VAVVGGGYVGVEMAEAFSAH-DLDVHVFQR 206
                                       89****************99.999999875 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.48   5.7e+02      22      37 ..      77      92 ..      75      98 .. 0.88
   2 ?    8.7   0.1   0.00096       1.2       2      26 ..     177     201 ..     176     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.48
                                      CTSEEEEE-S-HHHHH CS
                    UDPG_MGDP_dh_N 22 ighevigvDideekvd 37
                                      + hev+ vD d+++v 
  gi|313125211|ref|YP_004035475.1| 77 REHEVVAVDTDAQTVT 92
                                      569*********9985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00096
                                       EEEEE--STTHHHHHHHHHHCTSEE CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighev 26 
                                       +++v+G GYvG+ +a +++++  +v
  gi|313125211|ref|YP_004035475.1| 177 TVAVVGGGYVGVEMAEAFSAHDLDV 201
                                       699**************99988777 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         5   5.9e+03     121     154 ..      78     112 ..      71     113 .. 0.65
   2 ?    5.5   0.0     0.013        15       1      33 [.     179     206 ..     179     215 .. 0.87
   3 ?    5.3   0.1     0.015        18      99     154 ..     214     269 ..     206     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5
                     NAD_binding_9 121 raevvdleeradgqavlladgasl.aadaVvLAlG 154
                                       ++evv+++++a++++v+  d + +  +  + +A+G
  gi|313125211|ref|YP_004035475.1|  78 EHEVVAVDTDAQTVTVRGPDSKFTqSYGDLLVATG 112
                                       56889999888888888755543325555555555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.013
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp 33 
                                       a+vG+G  G+ ++e++ a+     +l++++f +
  gi|313125211|ref|YP_004035475.1| 179 AVVGGGYVGVEMAEAFSAH-----DLDVHVFQR 206
                                       89**************999.....599999876 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.015
                     NAD_binding_9  99 YlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       + +++ e++++ l+e+    ++ +ev +l+ +++  +v+  +g++la+da  + +G
  gi|313125211|ref|YP_004035475.1| 214 FGEAVGERVADHLREQGVTLHLGEEVAALRGEGQVETVVCGSGTKLAVDAALVGIG 269
                                       556667788888865543444589*******99999**************988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.76u 0.36s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 2539.50
//
Query:       gi|313125212|ref|YP_004035476.1|  [L=215]
Description: flagellin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-29  101.0   4.1    9.1e-29  100.8   4.1    1.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   4.1   5.1e-33   9.1e-29       1     159 [.      17     196 ..      17     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 5.1e-33
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE..EEE-SSSSSEEEEEEE- CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg..dsatngtineitiyvkl 75 
                                       G+vgigtl+vfIAmVlVAA aagvli+ta flq+ a++ g+es + v +g+e++   g  +++++g+++++ ++v++
  gi|313125212|ref|YP_004035476.1|  17 GQVGIGTLVVFIAMVLVAALAAGVLIHTASFLQATAEDAGKESIDRVVNGVEVVTTAGhvTDGDDGSVDTVRLWVRP 93 
                                       89********************************************************999999999********** PP

                                       -TTS--EEGGG-EEEEEESS--EE--E....................................T-EE-TT-EEEEEE CS
                    Arch_flagellin  76 naGsspidlnkttisvtddgqetlltad.........efgivvisdtdgsltng.........devlekgekvelev 134
                                        + + +i++++ t+ ++++   ++lt +          ++  ++                   d++le+ge + l  
  gi|313125212|ref|YP_004035476.1|  94 RPAAGDINVSRLTVKWVGEQAGQSLTFSgtdpvspstASDAHTT---------FnasesigdgDKILEQGEEFVLYF 161
                                       99999***************555555552553333333333333.........2344777777************** PP

                                       E--..........TTT---TT-EEEEEEE-SSS-- CS
                    Arch_flagellin 135 nvn..........eddgitagdevsvevvpenGas 159
                                       nv+          +  ++ +gd+++ e++  +G++
  gi|313125212|ref|YP_004035476.1| 162 NVSqiesgdadpaNLAPLHPGDQATTEITVATGST 196
                                       ************99999**************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1164.25
//
Query:       gi|313125213|ref|YP_004035477.1|  [L=61]
Description: hypothetical protein Hbor_04340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 345.90
//
Query:       gi|313125214|ref|YP_004035478.1|  [L=197]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-16   60.5   0.7    2.1e-16   59.4   0.7    1.6  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    7.7e-16   57.4   0.0    1.2e-15   56.7   0.0    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    3.3e-07   30.1   0.0      5e-07   29.5   0.0    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    7.2e-07   29.2   0.1    1.8e-06   27.9   0.0    1.7  2  HTH_20           Helix-turn-helix domain
    1.1e-06   28.4   0.1    2.2e-06   27.4   0.1    1.5  1  MarR_2           MarR family
    1.3e-05   25.0   0.0      2e-05   24.4   0.0    1.3  1  MarR             MarR family
    6.1e-05   23.0   1.1    0.00011   22.2   1.1    1.3  1  YHS              YHS domain
    9.9e-05   22.1   0.0     0.0002   21.1   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
    0.00012   21.4   0.0    0.00049   19.4   0.0    2.0  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
    0.00041   20.6   1.4    0.00064   20.0   1.4    1.3  1  Arc_trans_TRASH  Archaeal TRASH domain
  ------ inclusion threshold ------
      0.012   15.8   1.5      0.018   15.3   1.5    1.3  1  LIM              LIM domain
      0.012   15.8   0.9      0.025   14.9   0.9    1.4  1  Ta0938           Ta0938
      0.018   14.9   0.0      0.073   13.0   0.0    1.8  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.021   14.8   0.0      0.044   13.7   0.0    1.5  1  HTH_1            Bacterial regulatory helix-turn-helix protei
      0.021   15.0   0.0      0.038   14.2   0.0    1.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.025   14.5   0.0      0.038   13.9   0.0    1.3  1  HTH_11           HTH domain
      0.031   14.4   0.0      0.085   13.0   0.0    1.7  1  HTH_28           Helix-turn-helix domain
      0.034   14.2   0.0      0.056   13.5   0.0    1.3  1  HTH_Mga          M protein trans-acting positive regulator (M
      0.039   14.3   0.0       0.25   11.7   0.0    2.0  2  Rrf2             Transcriptional regulator
      0.067   13.1   1.8      0.067   13.1   1.8    1.7  2  zf-FCS           MYM-type Zinc finger with FCS sequence motif
      0.068   13.9   3.5       0.12   13.1   3.5    1.4  1  ATPase-cat_bd    Putative metal-binding domain of cation tran
      0.095   12.7   0.0       0.17   11.9   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.11   13.0   0.1        0.2   12.2   0.1    1.6  1  HTH_27           Winged helix DNA-binding domain
       0.15   11.9   0.0       0.31   10.9   0.0    1.5  1  HTH_23           Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.7   2.8e-19   2.1e-16       1      42 []       4      45 ..       4      45 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 2.8e-19
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDe+D++ILe+L edaR++++++Ae+v lS+++v  Rv++L+
  gi|313125214|ref|YP_004035478.1|  4 LDETDLQILELLTEDARRPFSDIAEQVDLSPPAVSDRVDKLR 45
                                      8***************************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   1.7e-18   1.2e-15       1      48 []       4      51 ..       4      51 .. 0.99

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.7e-18
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ldetd++ILelL +++r + +++Ae+++lSp++v+ r+++L e+G+I+
  gi|313125214|ref|YP_004035478.1|  4 LDETDLQILELLTEDARRPFSDIAEQVDLSPPAVSDRVDKLRESGVIR 51
                                      7**********************************************7 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   6.7e-10     5e-07       1      46 [.       5      51 ..       5      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 6.7e-10
                                      SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      d+t l+IL lL e   + ++++ae+++ls+++vS    kLre+G+++
  gi|313125214|ref|YP_004035478.1|  5 DETDLQILELLTEdARRPFSDIAEQVDLSPPAVSDRVDKLRESGVIR 51
                                      67889********788****************************985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   2.5e-09   1.8e-06       9      56 ..       5      52 ..       4      54 .. 0.94
   2 ?   -2.5   0.0       7.6   5.7e+03      34      52 ..      55      73 ..      53      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.5e-09
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +++ + il +L++++ + +s++ae++dls+  +s+++++L+e g +++
  gi|313125214|ref|YP_004035478.1|  5 DETDLQILELLTEDARRPFSDIAEQVDLSPPAVSDRVDKLRESGVIRR 52
                                      678899**************************************9985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.6
                                      HTS-HHHHHHHHHHHHHCT CS
                            HTH_20 34 ldlskntlsyHLrvLeeag 52
                                      ldl++++l+  + vL++ +
  gi|313125214|ref|YP_004035478.1| 55 LDLDRSQLRAGVPVLVRLD 73
                                      7888999887777777665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1     3e-09   2.2e-06       8      55 ..       9      54 ..       4      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3e-09
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +++L  L    +     +++a+  +ls++avs ++++L + G ++r +
  gi|313125214|ref|YP_004035478.1|  9 LQILELLTEDAR--RPFSDIAEQVDLSPPAVSDRVDKLRESGVIRRFT 54
                                      566666666665..5*****************************9966 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.7e-08     2e-05       3      53 ..       6      56 ..       4      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.7e-08
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                      +t + iL++l e      s++a+++ +s+++v+  +d+L + G i+R    
  gi|313125214|ref|YP_004035478.1|  6 ETDLQILELLTEDARRPFSDIAEQVDLSPPAVSDRVDKLRESGVIRRFTLD 56
                                      6888999999999999*******************************8765 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.1   1.5e-07   0.00011       6      44 ..     156     192 ..     155     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-07
                               YHS   6 cgmkvdkekaeekseY.kGkeYyFcSegCkdkFedePekY 44 
                                       cg +v   ++e +s++ +G +Y+Fc+++C  +F++  e++
  gi|313125214|ref|YP_004035478.1| 156 CGNTV---TSEGESDRiGGNQYHFCCPSCAARFREQYERF 192
                                       66666...45555555379***************988877 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.7e-07    0.0002       6      50 ..       9      52 ..       9      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.7e-07
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      l+iL++l+e +++  +s++A++ +l++++v+  +  L e G +++
  gi|313125214|ref|YP_004035478.1|  9 LQILELLTEDARR-PFSDIAEQVDLSPPAVSDRVDKLRESGVIRR 52
                                      79**********9.9****************99999999998875 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.6e-07   0.00049      19      50 ..      10      43 ..       7      45 .. 0.94
   2 ?   -1.6   0.1       2.6   1.9e+03      10      18 ..      51      59 ..      51      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.6e-07
                      HTH_Tnp_ISL3 19 yilellles..rsvkavArqlgvSwtTVwrildr 50
                                      +ilell+e+  r+++++A+q+++S+  V +++d 
  gi|313125214|ref|YP_004035478.1| 10 QILELLTEDarRPFSDIAEQVDLSPPAVSDRVDK 43
                                      79****************************9985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
                      HTH_Tnp_ISL3 10 sriTlrlea 18
                                      +r+Tl+l++
  gi|313125214|ref|YP_004035478.1| 51 RRFTLDLDR 59
                                      79****986 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.4   8.5e-07   0.00064       1      36 [.     153     188 ..     153     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.5e-07
                   Arc_trans_TRASH   1 CDYCGkeivgePivyklknkvYyvCCktCkselkkk 36 
                                       C  CG+ +++e    +++   Y +CC++C   ++++
  gi|313125214|ref|YP_004035478.1| 153 CAECGNTVTSEGESDRIGGNQYHFCCPSCAARFREQ 188
                                       556******************************986 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.5   2.4e-05     0.018       1      41 [.     153     191 ..     153     197 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-05
                                       -TTT--BE-TTTEEEEETTEEEETTTSB-TTT-SB-CTT..C CS
                               LIM   1 CagCnkkiadrelvlkaldkvwHeeCFtCsdCqkeLkegs.f 41 
                                       Ca+C+++++++    ++ ++++H   F+C +C  +++e++  
  gi|313125214|ref|YP_004035478.1| 153 CAECGNTVTSEGESDRIGGNQYH---FCCPSCAARFREQYeR 191
                                       **********************9...8888888888887654 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.9   3.3e-05     0.025      16      49 ..     152     187 ..     143     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                                       S-SS---S---..SS-B-TT--BSSS--SSSS-TTS CS
                            Ta0938  16 gcalcgatwgd..yyeevdgeklffccdicakefvn 49 
                                        ca cg t       + + g++  fcc  ca+ f +
  gi|313125214|ref|YP_004035478.1| 152 TCAECGNTVTSegESDRIGGNQYHFCCPSCAARFRE 187
                                       6*****99764115678***************9976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.7e-05     0.073       6      54 ..       4      52 ..       2      56 .. 0.93
   2 ?   -1.4   0.0       3.1   2.3e+03      31      53 ..      71      93 ..      68      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.7e-05
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      L e++ ++   L +  +   ++iae+++++ + v + + +L + G+++r
  gi|313125214|ref|YP_004035478.1|  4 LDETDLQILELLTEDARRPFSDIAEQVDLSPPAVSDRVDKLRESGVIRR 52
                                      789999999999999999****************************987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.1
                                      CTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 31 elgvprskvYevLrsLedkGlVe 53
                                      +l++p + v  v  +L +   Ve
  gi|313125214|ref|YP_004035478.1| 71 RLDLPSTEVAAVTDNLRESEGVE 93
                                      67899999999999998877776 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.9e-05     0.044      20      39 ..      27      46 ..      12      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                                      HHHHTS-HHHHHHHHHHHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEe 39
                                      Ae++ ls+pavs+++ +L+e
  gi|313125214|ref|YP_004035478.1| 27 AEQVDLSPPAVSDRVDKLRE 46
                                      9*****************98 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     5e-05     0.038      26      50 ..      24      48 ..      10      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTT CS
                    Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdG 50
                                      +d+ae  + sp+ Vs  + kL++ G
  gi|313125214|ref|YP_004035478.1| 24 SDIAEQVDLSPPAVSDRVDKLRESG 48
                                      89*********************99 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.1e-05     0.038       3      44 ..       9      49 ..       7      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      lqilelL  ++   + +++Ae+ ++S  +v  ++++L+e+gv
  gi|313125214|ref|YP_004035478.1|  9 LQILELL-TEDARRPFSDIAEQVDLSPPAVSDRVDKLRESGV 49
                                      699****.666669***************************4 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.085       4      41 ..      10      49 ..       9      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            HTH_28  4 eiikllaa..GhsvreaArelgisrrtvyrWikryeegGi 41
                                      +i++ll +   ++ +++A+++ +s+  v++ + +++e G+
  gi|313125214|ref|YP_004035478.1| 10 QILELLTEdaRRPFSDIAEQVDLSPPAVSDRVDKLRESGV 49
                                      677777751245999**********************995 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.6e-05     0.056       5      46 ..       6      46 ..       4      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.6e-05
                           HTH_Mga  5 krklkLlelLteneksltldelakeLglseltlqsdiseLne 46
                                      +++l++lelLte + + + +++a++ +ls  ++ +++++L+e
  gi|313125214|ref|YP_004035478.1|  6 ETDLQILELLTE-DARRPFSDIAEQVDLSPPAVSDRVDKLRE 46
                                      689*********.9999*************999999999875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00034      0.25      21      56 ..      16      51 ..       8      54 .. 0.81
   2 ?   -0.1   0.0       1.6   1.2e+03       6      42 ..      61      97 ..      58      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00034
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                       e+     ++iae++++sp+ ++  + kLr++g+++
  gi|313125214|ref|YP_004035478.1| 16 TEDARRPFSDIAEQVDLSPPAVSDRVDKLRESGVIR 51
                                      344445789*************************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHH CS
                              Rrf2  6 kteyalhallyLakeeeeepvsseeiaerqnispsyl 42
                                      +++ ++ +l+ L + ++e  + ++++ e+ +++++++
  gi|313125214|ref|YP_004035478.1| 61 QLRAGVPVLVRLDLPSTEVAAVTDNLRESEGVEHVFV 97
                                      6778888899999888888888888888888888876 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       6.9   5.2e+03      22      32 ..      86      96 ..      82      96 .. 0.81
   2 ?   13.1   1.8   8.9e-05     0.067       5      41 .]     152     185 ..     150     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.9
                            zf-FCS 22 vlendgvvgqF 32
                                       +e +gv+++F
  gi|313125214|ref|YP_004035478.1| 86 LRESEGVEHVF 96
                                      56889**9999 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.9e-05
                            zf-FCS   5 rCwfCkkyikgkpeftyvlendgvvgqFCStsCldsY 41 
                                       +C  C++  +   e      ++g +++FC+ sC++++
  gi|313125214|ref|YP_004035478.1| 152 TCAECGNTVTSEGE---SDRIGGNQYHFCCPSCAARF 185
                                       67777777766666...57889************998 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.5   0.00016      0.12       1      33 [.     152     183 ..     152     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                     ATPase-cat_bd   1 aCyHCglpveesaklkaeiegeerefCCkGCqa 33 
                                       +C  Cg+ v+++   + +i g++ +fCC+ C+a
  gi|313125214|ref|YP_004035478.1| 152 TCAECGNTVTSE-GESDRIGGNQYHFCCPSCAA 183
                                       5999*****875.67899*************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.17      26      66 ..      25      63 ..      12      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHHH CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglisrgrririldleaLr 66
                                      ++A+ + l++  vs    +L++ g+i+r      ld+ +Lr
  gi|313125214|ref|YP_004035478.1| 25 DIAEQVDLSPPAVSDRVDKLRESGVIRRF--TLDLDRSQLR 63
                                      9*************************952..2336777776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00027       0.2       5      56 ..       8      58 ..       4      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdead 56
                                      + ++L+l+  +++r   +d+++ ++++  ++s  ++kL e G++ r + + d
  gi|313125214|ref|YP_004035478.1|  8 DLQILELLT-EDARRPFSDIAEQVDLSPPAVSDRVDKLRESGVIRRFTLDLD 58
                                      7899*****.9999999***************************88765555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00042      0.31       8      46 ..       9      49 ..       9      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                            HTH_23  8 lrillllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      l+il ll e  + + ++IA++ + s+  v+  + + re+G+
  gi|313125214|ref|YP_004035478.1|  9 LQILELLTEdaRRPFSDIAEQVDLSPPAVSDRVDKLRESGV 49
                                      6889999988999***********************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1076.89
//
Query:       gi|313125215|ref|YP_004035479.1|  [L=434]
Description: pkd domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-05   22.2   2.4      0.045   12.5   0.1    2.2  2  REJ         REJ domain
     0.0026   16.6   8.3      0.048   12.4   1.0    2.1  2  Presenilin  Presenilin
  ------ inclusion threshold ------
        4.7    6.0  22.2        2.2    7.1   7.6    2.1  2  Apt1        Golgi-body localisation protein domain


Domain annotation for each model (and alignments):
>> REJ  REJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   7.6e-06     0.045      89     126 ..     109     143 ..      86     161 .. 0.90
   2 !    9.5   0.3   6.3e-05      0.38     386     426 ..     172     214 ..     158     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-06
                               REJ  89 GGssrvigyrgnltLdGseSyDpdeddhsqsqlsYeWl 126
                                        G+ r+++    +++d+++S+Dpd +d    +l+YeW+
  gi|313125215|ref|YP_004035479.1| 109 AGANRTVPEWLRVHFDATSSSDPDGND---ANLTYEWT 143
                                       58999999999************9998...67*****7 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 6.3e-05
                               REJ 386 kvtvmvsVyDnkgarvsvsltitVkppavnns..tieellenr 426
                                       ++t++ +V+D+ g +++ + titV+pp+ ++s   ++e  + +
  gi|313125215|ref|YP_004035479.1| 172 DLTFQLTVTDEAGETATDTVTITVRPPDRDDSddEQTESDNST 214
                                       679999*************************943222222222 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   1.1   0.00014      0.86     241     306 ..      38     100 ..       7     124 .. 0.40
   2 !   12.4   1.0   8.1e-06     0.048     199     307 ..     152     259 ..     145     305 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00014
                        Presenilin 241 aekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessesseeee 306
                                       a++++++  es+ +++s++++++++++s e   ++++es +++s a+ s+++++s++s+++++ e+
  gi|313125215|ref|YP_004035479.1|  38 ANDASAAVGESTPTAQSSNSNNQQTETSGE---SDSSESGDVTSGADDSDTTSSSSNSTDAQSVER 100
                                       222222222222222222222222211111...111111111111111111111111111111111 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 8.1e-06
                        Presenilin 199 LvelaqerneeifpaLiYsatvvvlaaeekkaevaeseeeeeaekkkeeasesskeeeseeesseksaqsseseees 275
                                       +v+    + + + p ++Y ++ + + + +++a ++++++ + + +  ++++++++++es++++ e+ ++++e +++s
  gi|313125215|ref|YP_004035479.1| 152 IVDADTAKPNILTPEIVYRTDLTFQLTVTDEAGETATDTVTITVRPPDRDDSDDEQTESDNSTDESDNSTDE-SDDS 227
                                       566666666777899999999999887777544444444444444444444433333333333222222222.2222 PP

                        Presenilin 276 eeesseaessaeesseekeseessesseeeee 307
                                       ++e+ +++++++  s+++++++s++s +++++
  gi|313125215|ref|YP_004035479.1| 228 DSEQPSDPNDDAGDSDDDSDDSSDDSGDSDDS 259
                                       22222222222222222222222222111111 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   6.6    0.0014       8.3     332     387 ..      46     100 ..      23     159 .. 0.42
   2 ?    7.1   7.6   0.00036       2.2     299     374 ..     200     261 ..     174     387 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0014
                              Apt1 332 ssssssassssssssrssslelrlkptsstssssssessssssskkrsseessles 387
                                        +s+ +a+ss+s++++++++ ++++++s + +s + +s+++sss ++s++ +s+e+
  gi|313125215|ref|YP_004035479.1|  46 GESTPTAQSSNSNNQQTETSGESDSSESGDVTSGADDSDTTSSS-SNSTDAQSVER 100
                                       11122222222222222222222222222222222222222222.12222222221 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00036
                              Apt1 299 rdsdaqeasmvkessseeddesdeesessssss.ssssssassssssssrssslelrlkpt.....sstsssssses 369
                                       rd+++ e+                 +es++s   s++s+++s++s+s++ s+ +++          s +ss+ s +s
  gi|313125215|ref|YP_004035479.1| 200 RDDSDDEQ-----------------TESDNSTDeSDNSTDESDDSDSEQPSDPNDDA---GdsdddSDDSSDDSGDS 256
                                       22222222.................11111111111111111111111111111111...01111111111111111 PP

                              Apt1 370 sssss 374
                                       ++s s
  gi|313125215|ref|YP_004035479.1| 257 DDSDS 261
                                       11111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1210  (0.0674884); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.08u 0.39s 00:00:01.47 Elapsed: 00:00:00.58
# Mc/sec: 2249.11
//
Query:       gi|313125216|ref|YP_004035480.1|  [L=65]
Description: copper chaperone [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-18   67.3   1.0    1.3e-18   67.2   1.0    1.0  1  HMA       Heavy-metal-associated domain
      0.003   15.9   0.1     0.0033   15.8   0.1    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   1.0   1.5e-22   1.3e-18       1      62 []       4      62 ..       4      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.5e-22
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      t+ v+gm C++C+++ve++Ls+++gVes+  d ++ +vtV+gd++    +k++ a+e+agy+
  gi|313125216|ref|YP_004035480.1|  4 TLTVEGMSCGHCEQTVEDALSNVDGVESAAADHESASVTVRGDVSV---NKLVTAVEDAGYD 62
                                      689*******************************************...************7 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.6e-07    0.0033     501     546 ..      14      60 ..      10      65 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.6e-07
                           DUF2070 501 lvlelvekAiadlepvevgyaterve.vkvfgedrfeelvstvnsvv 546
                                       +++++ve+A+++++ ve ++a ++   v+v g+ + ++lv++v++++
  gi|313125216|ref|YP_004035480.1|  14 HCEQTVEDALSNVDGVESAAADHESAsVTVRGDVSVNKLVTAVEDAG 60 
                                       6899************88877777777****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 395.70
//
Query:       gi|313125217|ref|YP_004035481.1|  [L=226]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-18   67.7   0.0    1.5e-18   67.2   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
      3e-18   66.1   0.0    3.4e-18   65.9   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    2.3e-17   63.5   0.0    3.1e-17   63.0   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      2e-15   57.2   0.0      3e-15   56.7   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    3.5e-14   53.3   0.0      5e-14   52.8   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    6.4e-14   51.9   0.0    7.7e-14   51.6   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.1e-10   40.7   0.0    2.6e-10   40.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      2e-06   27.3   0.0    2.7e-06   26.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    6.8e-05   22.6   0.0    0.00021   21.0   0.0    1.7  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00055   19.4   0.0    0.00094   18.7   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
    0.00061   19.4   0.0      0.002   17.7   0.0    1.7  1  MTS              Methyltransferase small domain
     0.0012   18.6   0.0     0.0016   18.2   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
     0.0026   17.9   0.0       0.01   15.9   0.0    1.6  2  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.079   12.0   0.0        0.1   11.6   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.096   12.3   0.0       0.12   11.9   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
       0.13   11.3   0.0       0.16   11.0   0.0    1.1  1  Fibrillarin      Fibrillarin
        0.2   11.7   0.0        0.3   11.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.0   1.5e-21   1.5e-18       1      97 []      52     147 ..      52     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.5e-21
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       vLd+GcG+G +  al +++g +++v+g+D+s++m+ +ar+r++++g+ nv++v+gda + pfe   fD+ +++  l+
  gi|313125217|ref|YP_004035481.1|  52 VLDVGCGPGVNFPALREAVGpDGTVVGLDYSAGMCHRARKRVRKAGWeNVHVVRGDAARPPFET-PFDAAYAT--LS 125
                                       9******************66*****************************************98.*******7..45 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       ++  +++ ++++ +++ L+pgG
  gi|313125217|ref|YP_004035481.1| 126 MTAMPEATAVIDAVYDSLRPGG 147
                                       55566889*************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   3.2e-21   3.4e-18       2     114 ..      47     161 ..      46     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 3.2e-21
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       d g +vlD+GCG G    +l e +gp+++vvG+D+s+ +  +Ar++ +k g +nv++ +gd+   +  +e  +fD  
  gi|313125217|ref|YP_004035481.1|  47 DPGDTVLDVGCGPGVNFPALREAVGPDGTVVGLDYSAGMCHRARKRVRKAGWENVHVVRGDAARPP--FE-TPFDAA 120
                                       56889***********************************************************99..99.9****9 PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr.....l 114
                                        +   + a+++  +++  + + l+pgg++++ d r      
  gi|313125217|ref|YP_004035481.1| 121 YATLSMTAMPEATAVIDAVYDSLRPGGRFVVVDTRpiqdaP 161
                                       999999**************************999444441 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0   2.9e-20   3.1e-17      66     171 ..      41     151 ..      35     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2.9e-20
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-S CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaP 142
                                       +  l l++g+ vL+vG+G G +   l + vg++g+vv++++++ ++++a+++++k + env+vv gD     + ++P
  gi|313125217|ref|YP_004035481.1|  41 VTSLALDPGDTVLDVGCGPGVNFPALREAVGPDGTVVGLDYSAGMCHRARKRVRKAGWENVHVVRGDAARP-PFETP 116
                                       56689**************************************************************9874.6679* PP

                                       EEEEEESSBBSS--HH......HHHTEEEEEEEEE CS
                              PCMT 143 YdaihvgaaapeiPea......lidQLkeGGrlvv 171
                                       +da + + +   +Pea        d L +GGr+vv
  gi|313125217|ref|YP_004035481.1| 117 FDAAYATLSMTAMPEAtavidaVYDSLRPGGRFVV 151
                                       *****999999999752222226789******997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   2.8e-18     3e-15       1      96 []      53     151 ..      53     151 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 2.8e-18
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       LdvGcG G ++ al +++   ++vvg+D+s+ m  +a+++++++g  +v +v++da + pfe   fD+ +++ +++ 
  gi|313125217|ref|YP_004035481.1|  53 LDVGCGPGVNFPALREAVgpdGTVVGLDYSAGMCHRARKRVRKAGWeNVHVVRGDAARPPFET-PFDAAYATLSMTA 128
                                       8**************7777******************************************99.************* PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                       +++  ++++ ++  L+pgG++v+
  gi|313125217|ref|YP_004035481.1| 129 MPEATAVIDAVYDSLRPGGRFVV 151
                                       ********************996 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   4.7e-17     5e-14       1      99 []      53     149 ..      53     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 4.7e-17
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L++GcG G +  al+e+  pd +++g+D+s+ ++++a+++ +k + +n+++v+ +a     +     fD+ +a   +
  gi|313125217|ref|YP_004035481.1|  53 LDVGCGPGVNFPALREAVgPDGTVVGLDYSAGMCHRARKRVRKAGWENVHVVRGDAARPPFE---TPFDAAYATLSM 126
                                       8********************************************98888888888886644...69********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                        ++++  +v+d +++ L+pgGr+
  gi|313125217|ref|YP_004035481.1| 127 TAMPEATAVIDAVYDSLRPGGRF 149
                                       *********************96 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   7.3e-17   7.7e-14      42     157 ..      43     157 ..       8     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 7.3e-17
                                       H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EE CS
                   Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfD 118
                                         a  +g +vlDv +G g    +l ++vg  g+vv+lD+++ m + ++k++++ g  n++ + ++a + pfe   fD
  gi|313125217|ref|YP_004035481.1|  43 SLALDPGDTVLDVGCGPGVNFPALREAVGPDGTVVGLDYSAGMCHRARKRVRKAGWENVHVVRGDAARPPFET-PFD 118
                                       55667899**********9999************************************************985.799 PP

                                       EEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE--- CS
                   Ubie_methyltran 119 vvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskv 157
                                           +  +  +++ + ++  +y  l+pGGr+vv+++  +
  gi|313125217|ref|YP_004035481.1| 119 AAYATLSMTAMPEATAVIDAVYDSLRPGGRFVVVDTRPI 157
                                       9999999**************************998655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   2.5e-13   2.6e-10      17     128 ..      45     164 ..      27     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.5e-13
                   Methyltransf_23  17 lpklraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqg 81 
                                       +  l++g  vLd+GcG G + + lre  g   +v+g D s  + ++a+         + +  + d +    +++ + 
  gi|313125217|ref|YP_004035481.1|  45 A--LDPGDTVLDVGCGPGVNFPALREAvGPdgTVVGLDYSAGMCHRARkrvrkagweNVHVVRGDAA----RPPFET 115
                                       3..67889****************777477899*************988887666543333333333....444566 PP

                   Methyltransf_23  82 kfdlIvlrevlehvpdppellrqiatllkpgGylllse..plaslkedr 128
                                        fd ++++ ++  +p  +++++ +++ l+pgG++++ +  p +++++dr
  gi|313125217|ref|YP_004035481.1| 116 PFDAAYATLSMTAMPEATAVIDAVYDSLRPGGRFVVVDtrPIQDAPWDR 164
                                       ***********************************99966333444544 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.5e-09   2.7e-06      56     119 ..      42     107 ..      35     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.5e-09
                                       TTTT--TT-EEEEES-TTSH...HHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES CS
                              CMAS  56 eklelkpGmtlLdiGcGWGs...lvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevkll 119
                                         l l+pG+t+Ld+GcG G     +r+av   d  vvgl  S+   ++a+krv +++ e+ + v+  
  gi|313125217|ref|YP_004035481.1|  42 TSLALDPGDTVLDVGCGPGVnfpALREAVGP-DGTVVGLDYSAGMCHRARKRVRKAGWENVHVVRGD 107
                                       6799***************733356778887.9************************9988777654 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     2e-07   0.00021       2      72 ..      42     112 ..      41     121 .. 0.94
   2 ?   -1.6   0.0       1.6   1.7e+03     118     135 ..     133     150 ..     126     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2e-07
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCH CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkid 72 
                                       + La+ +++t+lD+ ++PG     + e + + gtvv +d ++   +r  + +++ g +n+ v+++Da +++
  gi|313125217|ref|YP_004035481.1|  42 TSLALDPGDTVLDVGCGPGVNFPALREAVGPDGTVVGLDYSAGMCHRARKRVRKAGWENVHVVRGDAARPP 112
                                       6799999***********************************************************98875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                                       HHHHHHHCCCEEEEEEEE CS
                   Methyltr_RsmB-F 118 kellsaaidllkkgGvlv 135
                                        ++++a+ d+l++gG  v
  gi|313125217|ref|YP_004035481.1| 133 TAVIDAVYDSLRPGGRFV 150
                                       578999********9876 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.9e-07   0.00094       4      61 ..      51     109 ..      49     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.9e-07
                                       EEEEET-TTSHHHHHHHHH.STTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CC CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkk.nPdknflGiEirvkvvakvlkkiealelkNlrilrgdal 61 
                                       +vl++GcG G    al ++  Pd +++G++ +  + +++ k++++ + +N++++rgda 
  gi|313125217|ref|YP_004035481.1|  51 TVLDVGCGPGVNFPALREAvGPDGTVVGLDYSAGMCHRARKRVRKAGWENVHVVRGDAA 109
                                       689*******99999987637************************************95 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.9e-06     0.002      28     144 ..      45     158 ..      34     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                                       HCCTCSEEEEET-TTSH.HHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEE CS
                               MTS  28 pkelsgkvlDlGcGaGv.lgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdliv 102
                                         +  ++vlD+GcG Gv   a   +  p+ +v+ +d +a   + a++ +++ + e v+vv  d+     e  fd+  
  gi|313125217|ref|YP_004035481.1|  45 ALDPGDTVLDVGCGPGVnFPALREAVGPDGTVVGLDYSAGMCHRARKRVRKAGWEnVHVVRGDAARPPFETPFDAAY 121
                                       5556789*********944555566789999***********************************99999999875 PP

                                       E---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSC CS
                               MTS 103 sNPPfhagkatelavaeeliaeAkeaLkegGeLliVanrklg 144
                                                 t    a+++i +  + L++gG++++V  r ++
  gi|313125217|ref|YP_004035481.1| 122 ATLS-----MTAMPEATAVIDAVYDSLRPGGRFVVVDTRPIQ 158
                                       5433.....333444777888888888888888888777665 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0016      34     113 ..      42     120 ..      38     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                             GCD14  34 mkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeev 110
                                       ++L l pG  v++ G G g    a+  +v+P G +  +++ +   ++ar+  r+ +  ++v+v   D+ +  f++  
  gi|313125217|ref|YP_004035481.1|  42 TSLALDPGDTVLDVGCGPGVNFPALREAVGPDGTVVGLDYSAGMCHRARKRVRKAGW-ENVHVVRGDAARPPFETPF 117
                                       57999*************************************************997.5799999999999997766 PP

                             GCD14 111 sgk 113
                                       +  
  gi|313125217|ref|YP_004035481.1| 118 DAA 120
                                       443 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-05      0.01      19      73 ..      46     111 ..      41     126 .. 0.82
   2 ?   -1.0   0.0       1.6   1.6e+03     118     133 ..     136     151 ..     118     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                                       S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS..........HHH..TTEEEECS-CCCS CS
                              FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..........apl..pgvttiqgditdp 73 
                                       ++pg+tv+D+g++PG     l + +g++g vv++D   +          +    ++v++++gd  +p
  gi|313125217|ref|YP_004035481.1|  46 LDPGDTVLDVGCGPGVNFPALREAVGPDGTVVGLDYSAGmchrarkrvrK-AgwENVHVVRGDAARP 111
                                       5799********************************88768877654431.1457888889988665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                                       HCCHCCCCECCCEEEE CS
                              FtsJ 118 lelalkllkpggtfvl 133
                                       +    + l+pgg fv+
  gi|313125217|ref|YP_004035481.1| 136 IDAVYDSLRPGGRFVV 151
                                       5555678888888885 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.8e-05       0.1      24      86 ..      42     109 ..      37     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.8e-05
                                       HHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CC CS
                            RrnaAD  24 dklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqDfl 86 
                                         l l + +tvl++g G+G+    L + +     vv l     ++ + +k+++    e++ vv  D+ 
  gi|313125217|ref|YP_004035481.1|  42 TSLALDPGDTVLDVGCGPGVNFPALREAVgpdGTVVGLDYSAGMCHRARKRVRkaGWENVHVVRGDAA 109
                                       5677899**********************98778888999999*********977779*****99985 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.12      11      46 ..      46      83 ..      38     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                              MetW 11 ikpgsrvldlGcGdGellellkeekqvdgr..Glelde 46
                                      ++pg +vld+GcG G  +  l+e  + dg   Gl+ ++
  gi|313125217|ref|YP_004035481.1| 46 LDPGDTVLDVGCGPGVNFPALREAVGPDGTvvGLDYSA 83
                                      57999****************99988777522444444 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.16      60     131 ..      38     111 ..      32     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                       HTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH.HHHTT.STTEEEEES-TTSG CS
                       Fibrillarin  60 lkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreli.evakk.RknivPileDArkP 131
                                        +g+++l + +g+ vL +G + G     + + vg++g+v ++++s  + +    +v k   +n+  + +DA +P
  gi|313125217|ref|YP_004035481.1|  38 ARGVTSLALDPGDTVLDVGCGPGVNFPALREAVGPDGTVVGLDYSAGMCHRARkRVRKAgWENVHVVRGDAARP 111
                                       5799****************************************987765544144433257888888888777 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028       0.3      26      83 ..      49     102 ..      40     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                   Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrls 83 
                                         tv+DvG+G g    +l   ++     vvg+d ++ ++++a+kr +k g  + ++++
  gi|313125217|ref|YP_004035481.1|  49 GDTVLDVGCGPGVNFPALRE-AVGPDGTVVGLDYSAGMCHRARKRVRKAG--W-ENVH 102
                                       579*********87777777.77799**********************99..8.5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1245.83
//
Query:       gi|313125218|ref|YP_004035482.1|  [L=138]
Description: hypothetical protein Hbor_04390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.036   14.2   0.0      0.047   13.8   0.0    1.3  1  EcoEI_R_C  EcoEI R protein C-terminal


Domain annotation for each model (and alignments):
>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-06     0.047      70     159 ..      24     113 ..       5     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-06
                         EcoEI_R_C  70 tdlidlirkiagldeeletrserverafkrwikekkft..eeqrewLelildhiaangvielddldeape.fkqkgg 143
                                       + l   i +++ +  +l+t++++v +a++++++ ++++  +  +ew ++++dh    g+++ + ++e+ + f++ g 
  gi|313125218|ref|YP_004035482.1|  24 HELQLGIEHVYRGYGTLLTFHHQVGHAMDHLANAEAYLreAGHKEWANILRDHHLPAGAVDDQWTYELVQaFRE-GL 99 
                                       5555567788888888*****************9999977778******************9999999984444.55 PP

                         EcoEI_R_C 144 lgkayklFGgkqelde 159
                                       l+++ + F   +  d+
  gi|313125218|ref|YP_004035482.1| 100 LQDV-ADFEH-DVRDD 113
                                       5555.88854.33344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 809.98
//
Query:       gi|313125219|ref|YP_004035483.1|  [L=98]
Description: hypothetical protein Hbor_04400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.16   11.7   0.0    1.5  1  DUF4325   STAS-like domain of unknown function (DUF4325)


Domain annotation for each model (and alignments):
>> DUF4325  STAS-like domain of unknown function (DUF4325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.9e-06      0.16      18      48 ..      10      40 ..       3      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.9e-06
                           DUF4325 18 ekvelDFdgvesigssFldeaFgglirefge 48
                                         ++D+ + e +g+ F +eaF +l    ++
  gi|313125219|ref|YP_004035483.1| 10 AYTTFDMLDAEAVGHDFTEEAFAVLNVTAPR 40
                                      56789******************99766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 570.10
//
Query:       gi|313125220|ref|YP_004035484.1|  [L=220]
Description: hypothetical protein Hbor_04410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-43  147.7   0.0      4e-43  147.6   0.0    1.0  1  AIM24     Mitochondrial biogenesis AIM24


Domain annotation for each model (and alignments):
>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.6   0.0   2.2e-47     4e-43       2     201 .]       4     209 ..       3     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 2.2e-47
                                       EEESS.SS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE.....--------------EEEEEEE.S.SS-EEEEE- CS
                             AIM24   2 evlge.pssllsvtLspgeelyaerGalvamsgkvemet.....gllkalkrlltgeslfllkft.akissgtvlla 71 
                                       e+ +  +++ l+++ ++ge++ +e+G++v  s++v++et     g++++lkr+++ e   +++++ a++++ ++lla
  gi|313125220|ref|YP_004035484.1|   4 EIADGhSYATLEIDFDEGERVGIEPGSMVTRSENVRVETtsgddGIGGMLKRAVSDEIDVMTTYFiAESDGAHALLA 80 
                                       5555559**************************************************98888888677777****** PP

                                       -SSSEEEEEEEGGTT.EEEEEGGGEEEEETT-EEEEEEEE--SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE. CS
                             AIM24  72 pklpgtivtlelgggdwlivqkdafLAatgnveldikfqkglkglfggeglflqkltGrGlvalsgyGaiyeielka 148
                                       p+++g+i+ +el+g++ + vq++ +LA++++ve ++++++  +++f++ +l ++kl G+G++++s++Ga+ + +++a
  gi|313125220|ref|YP_004035484.1|  81 PDYLGDIARVELDGTEGVKVQSGGLLAWSEGVERGTARNE-ASNFFSSGELTVLKLDGKGSAFISAFGAVRKETVTA 156
                                       ************9999**********************95.588998878*************************** PP

                                       EEEEEEEGGGEEEEETTEEEEEEEETT---STTTTS-EEEEEEEEEEEEEESS CS
                             AIM24 149 geelvvdpghlvafsgslkfdiervgglkrrligGeglflkltGpgtvllqsr 201
                                       +++l+vd +hl+a++++l+ + ++ ++l+++l+gGeg+++kl+G+g  ++q+r
  gi|313125220|ref|YP_004035484.1| 157 EDPLIVDEDHLLAWTDGLSASRQKDSNLTSSLLGGEGFVTKLSGEGSAWVQTR 209
                                       ***************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1423.15
//
Query:       gi|313125221|ref|YP_004035485.1|  [L=590]
Description: sulfite reductase subunit beta (hemoprotein) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-41  141.2   0.0    1.9e-31  108.7   0.1    2.5  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
      7e-37  125.1   0.0    3.4e-18   65.3   0.0    3.1  2  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.1   2.1e-35   1.9e-31       2     154 ..     138     293 ..     137     298 .. 0.94
   2 !   29.9   0.0   3.7e-11   3.3e-07       5     152 ..     401     545 ..     398     550 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 2.1e-35
                                       SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdeke 78 
                                       g++ rn++++p ag ++++++D+ +++++++++++++ + ++lPrK+K++v+g  + +++  +nD+++ + +k+   
  gi|313125221|ref|YP_004035485.1| 138 GDSWRNIVGNPVAGKDAQEVIDAWPVIRELNETFKGNEDHSNLPRKWKVSVTGSADGSGQGDINDLAFEPAYKEVDV 214
                                       7889*******************************************************************998554 PP

                                       E...EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH. CS
                                       x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                           NIR_SIR  79 i...gfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv. 151
                                       +   gfn+ vGGgl r++++ +  ++ ++v +e+v +v+ ++  ++rd+gdr+nr+++R+k lv+++G ek r+++ 
  gi|313125221|ref|YP_004035485.1| 215 EekvGFNVRVGGGLARNEERFARDID-VWVAPENVSDVAGGLSALFRDNGDRENRYNARIKFLVDEWGPEKVRNVLq 290
                                       4666**********************.7************************************************5 PP

                                       HHC CS
                                       xxx RF
                           NIR_SIR 152 eee 154
                                       ee+
  gi|313125221|ref|YP_004035485.1| 291 EEY 293
                                       555 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 3.7e-11
                                       CCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                           NIR_SIR   5 lrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei.. 79 
                                       +r  ++c+g+++c   +++t++   +  ++l+++ + ++   +f i +sgc   c++ ++ Di+l g+k  +  +  
  gi|313125221|ref|YP_004035485.1| 401 MRGSVACTGTEFCSLSIVETKNRQVRYARWLKENVELPDDIDQFHIHLSGCTASCAQPQIADISLRGMKTRKNGEpv 477
                                       678899***************99999999*********999***************************976665567 PP

                                       .EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  80 .gfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                         + + +GGglg++++ ++       +p +ev  ++ ++++ ++    ++ +  e ++++v+r   e++ e ve
  gi|313125221|ref|YP_004035485.1| 478 eALDVGLGGGLGEEPQFARWVT--QRIPVDEVPGAISNLLDQFK----ANREDGESFREFVARHDDEELDEFVE 545
                                       79**********9998877777..68******************....99999999999999998888887775 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   3.3e-19   2.9e-15       3      68 ..      53     128 ..      51     129 .. 0.91
   2 !   65.3   0.0   3.8e-22   3.4e-18       1      62 [.     325     384 ..     325     387 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 3.3e-19
                      NIR_SIR_ferr   3 qkdgkgyymvrlrvpnGritaeqlraladia..........ekygsgeirlTtrQnlqlhgvpeedleeileeLae 68 
                                           ++y+m+r+ +pnG + + qlr + +ia            +g+ ++++TtrQ++qlh+++ ed+++i+e++++
  gi|313125221|ref|YP_004035485.1|  53 RNGQESYFMMRIGTPNGVLEPGQLRVVGEIAaeyatgpgtnPIFGDAYADFTTRQSIQLHWINIEDVPAIFEKMEK 128
                                       45557888***********************999988888779*****************************9976 PP

  == domain 2  score: 65.3 bits;  conditional E-value: 3.8e-22
                      NIR_SIR_ferr   1 hkqkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleei 62 
                                       h+qkdg   y+v+l+v  Gr+ ae   +lad+a++ygsge+rl+ rQn+++++vpeedl++ 
  gi|313125221|ref|YP_004035485.1| 325 HEQKDGN--YFVGLNVLVGRMGAEDVLELADLADEYGSGEVRLSQRQNVIVTDVPEEDLDDF 384
                                       899**88..8*************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 3510.76
//
Query:       gi|313125222|ref|YP_004035486.1|  [L=103]
Description: hypothetical protein Hbor_04430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.6   0.8      0.033   14.3   0.4    1.7  2  NifU      NifU-like domain


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.19   3.5e+03      40      53 ..      37      50 ..      36      51 .. 0.82
   2 ?   14.3   0.4   1.8e-06     0.033      23      47 ..      51      75 ..      45      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.19
                                      G-....THHHHHHH CS
                              NifU 40 gCpsstvtlkegie 53
                                      gC   ++ ++  +e
  gi|313125222|ref|YP_004035486.1| 37 GCDLTDMVVEGFVE 50
                                      89999999988887 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-06
                                      EEEETTEEEEEEESGGGG-....TH CS
                              NifU 23 vdvdegvVkvrlqGaCsgCpsstvt 47
                                      v+vd+++V vr  G+C  C ++++t
  gi|313125222|ref|YP_004035486.1| 51 VGVDGRTVEVRAYGQCIACGAAETT 75
                                      6899****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 707.44
//
Query:       gi|313125223|ref|YP_004035487.1|  [L=56]
Description: hypothetical protein Hbor_04440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 335.25
//
Query:       gi|313125224|ref|YP_004035488.1|  [L=228]
Description: hypothetical protein Hbor_04450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1349.98
//
Query:       gi|313125225|ref|YP_004035489.1|  [L=422]
Description: acetylornithine deacetylase/succinyldiaminopimelate desuccinylase-like deacylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-28   97.6   0.7      1e-27   97.2   0.7    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    8.8e-06   25.6   0.0    2.4e-05   24.2   0.0    1.8  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.7   1.2e-31     1e-27       1     205 [.      92     415 ..      92     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 1.2e-31
                                       EEEEES-BSS.TTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHH.....TTT-SSEEEEEEEST CS
                                       xxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVp.eeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkde.....gikpkgtivllfqpd 70 
                                       +l++H DvVp + e+  w++ pf +   dG + +rGa+dmk g++a + a+r l+++        ++g +v+  ++ 
  gi|313125225|ref|YP_004035489.1|  92 VLNGHCDVVPvDREN--WSSdPFDPVWSDGEVTARGAADMKSGLAACVFAVRDLQERvgdgeLDGLDGRVVVESVVG 166
                                       589*******77777..*********999***************************976655233488888877777 PP

                                       TSSTTTHH.HHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE............................... CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                     Peptidase_M20  71 EEggrgGa.kallegleerekvdavfelhieepgileagklaigvv............................... 115
                                       EE g+ Ga +a l+   + +++d    +++ ep+ l         +                               
  gi|313125225|ref|YP_004035489.1| 167 EEEGGIGAaAAALD---NPYPFDRDA-AIVAEPTELRCV------Tategtvmkrlrlrgraahaatrwngedvlph 233
                                       77533555344444...567777766.77899*****22......2446678************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|313125225|ref|YP_004035489.1| 234 ferirkaffelesersesvshplydafpipwpvcigtvragswassvagtltaecrfgvapgetvdeveeayearla 310
                                       ***************************************************************************** PP

                                       ..............EEEEEEE.EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEES.SSBHTHHHH..TTTEEEE CS
                                       ..............xxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx..xxxxxxx RF
                     Peptidase_M20 116 ..............kvevell.eggapvtln.dsplvkalaeaaeelfgekvelivsg.pggtdarff..agiptvm 173
                                                     +  +e++  + +p++++ d+++v+ l+ a+  + g++++++  g ++g d+r++  agiptv 
  gi|313125225|ref|YP_004035489.1| 311 evvaesdwlseqppT--FERFsIQFEPAEIDaDEDVVRSLQTAMGVT-GHDTTDP-VGaTYGADSRHYvaAGIPTV- 382
                                       *********998551..444446688*****************9876.9665555.4459*********99***99. PP

                                       EEESSG.GCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 174 ifgpgs.glaHspnEyvdledlekgikvlarll 205
                                       ++gpgs ++aH p+E ++ +d+e++ +++++++
  gi|313125225|ref|YP_004035489.1| 383 LYGPGSiEQAHFPDETINWDDVETARETYTEAA 415
                                       7****88*********************99986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.6e-09   2.4e-05       5     107 ..     206     315 ..     202     317 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.6e-09
                                       EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC............TCCTCCCCCEECCE-CCCCEESS CS
                         M20_dimer   5 GlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia.......eerslprttlnvtgiegGsaknvipd 74 
                                       G +  +++ +g+a+H++ + +g++ + +  r+  ++ ++e++          + ++ +  + ++++++Gs++ ++++
  gi|313125225|ref|YP_004035489.1| 206 GTVMKRLRLRGRAAHAATRWNGEDVLPHFERIRKAFFELESERSesvshplYDAFPIPWPVCIGTVRAGSWASSVAG 282
                                       666667889***************************999888889*****999999999999*************** PP

                                       EEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCST CS
                         M20_dimer  75 eaeakidiRllpgedpeevleeieeilekeape 107
                                       + +a+  + + pge+++ev+e+ e+ l+++ +e
  gi|313125225|ref|YP_004035489.1| 283 TLTAECRFGVAPGETVDEVEEAYEARLAEVVAE 315
                                       ***************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2543.69
//
Query:       gi|313125226|ref|YP_004035490.1|  [L=599]
Description: oligopeptidase f [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-70  237.3   4.3    4.2e-70  237.3   4.3    2.0  2  Peptidase_M3    Peptidase family M3
    2.3e-25   88.7   0.3    2.3e-25   88.7   0.3    3.2  2  Peptidase_M3_N  Oligopeptidase F
  ------ inclusion threshold ------
      0.026   15.2   0.3        4.8    7.9   0.0    2.9  2  Phage_ABA_S     Phage ABA sandwich domain
      0.061   13.8   0.8       0.39   11.2   0.1    2.6  3  MitMem_reg      Maintenance of mitochondrial structure and fu


Domain annotation for each model (and alignments):
>> Peptidase_M3  Peptidase family M3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.031   1.4e+02      32     124 ..      53     150 ..      32     177 .. 0.57
   2 !  237.3   4.3   9.3e-74   4.2e-70       2     456 ..     204     582 ..     203     584 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHHHHH....HHHTT-SSHHHHHHTTSTT-SHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHC.. CS
                      Peptidase_M3  32 sklleellklrael....Akllgyesyaelaledkmaknpetvldfleelvkkl...rpllekelkllkelkkke.. 99 
                                        ++l ell+l++e     +k+ +y s ++++  +  ++  ++++   e+l++++   ++ +e el++l+e   ++  
  gi|313125226|ref|YP_004035490.1|  53 PETLLELLELQEEImrevSKVANYASLRSAEDTR--DQEYQALQAKAESLSSEAqstVSFVEPELQELSE---ADve 124
                                       4555555555554454447777777776666555..5555555555555555540004555566666666...3333 PP

                                       ..CT-S.SS--CCCHHHHHHHHHCCCCS CS
                      Peptidase_M3 100 ..lgle.gelqpwDvaYYsekqreekyd 124
                                           ++ +el  + + Y++   r + ++
  gi|313125226|ref|YP_004035490.1| 125 sfI-ETePELVDYEH-YFDDVLRMKPHT 150
                                       442.22468888888.777665554444 PP

  == domain 2  score: 237.3 bits;  conditional E-value: 9.3e-74
                                       HHC-S-HHHHHHHHHHHCTTTCCSS..THHHHHHHHHHHHHHHHHHHTT-SSHHHHHHTTSTT-SHHHHHHHHHHHH CS
                      Peptidase_M3   2 lkespdrelRkeayeashskaaeqrntlensklleellklraelAkllgyesyaelaledkmaknpetvldfleelv 78 
                                       l++ p+r+ R+e+y++++++  + rnt+   + l++ +k+  + A++++ye+++e+al+    + p +v+d+l e+v
  gi|313125226|ref|YP_004035490.1| 204 LQKHPNRQFRREVYQQFYDEWGDVRNTV--GTALKNSVKKDVKYANARNYETAREAALDG--TNVPVEVYDNLVETV 276
                                       6789************************..99*********999****************..*************** PP

                                       HHHHHHHHHHHHHHHHHHHHCCT-SSS--CCCHHHHHHHHHCCCCS.--CCCCGGG-BHHHHHHCHHHHHHHHHTEE CS
                      Peptidase_M3  79 kklrpllekelkllkelkkkelglegelqpwDvaYYsekqreekyd.ldqeelkeyfpletvleGllelfeeLfGik 154
                                       + +  +l++  +l++      lg+e el++wD+           y  l   +  +++++e++ e         + i+
  gi|313125226|ref|YP_004035490.1| 277 RDNLDYLHRHAELKRG----ALGVE-ELEMWDL-----------YMsLTG-DEGPEITYEEAKE---------YIIE 327
                                       ************9999....9****.*******...........553555.4799999999999.........5555 PP

                                       EEEETTS..--SSTT-EEEEEEET.TT-EEEEEEEEEEC--TTS-SS-EEEEEE--BTTS-B--EEEEEEEEE---B CS
                      Peptidase_M3 155 fveekdakgevwhedVrkleVvdeilsegligeiylDlyerkgKrggAasfglvksredgtrqlpviylllNftkps 231
                                        v   +  ge++ +          +l +gl +++++D+ye++gKr+gA+s+g ++         + +++++N+++  
  gi|313125226|ref|YP_004035490.1| 328 AV--APL-GEEYQS----------QLAQGL-EDRWVDVYENRGKRSGAFSSGTYD---------TQPFIMMNYQE-- 379
                                       55..333.99****..........89****.************************.........79*********.. PP

                                       TTS--B--HHHHHHHHHHHHHHHHHHC--BSSGGGSTT-S-CCCCCHHHHHHHHGGGSHHHHHCC-B-TTT--B--H CS
                      Peptidase_M3 232 skkPsLLtldevetLfHEfGHsmHsllsrteysnvsgtnvpidfvElpSqlmEnlltepevlkslskhyetgeaipe 308
                                              ++++++tL+HE+GHs+Hs l+++e++  ++ +++i+++E++S+++E llt++++ +    ++e +  +++
  gi|313125226|ref|YP_004035490.1| 380 -------DISSMFTLAHELGHSLHSELAKEEQPW-HYADYTIFVAEVASTVNETLLTQYLLENVE--DDEFRMHVLD 446
                                       .......************************999.****************************99..99******** PP

                                       HHHHHHHCCCCTTHHHHHHHHHHHHHHHHHCTT-TCCGHH.....HHHHHHHHHHCTTSCTTBTTSSGGGC-CCCHT CS
                      Peptidase_M3 309 elleklikaknvnaalellrqlvfaafdqelHeeaeeeqilk.kdlletyaelrkkflglpvapdeasqasFghlfa 384
                                       e le+++        ++l+rq++fa+f++++H+  ee+ +l+ + l++ y +l+++f+    ++d+ +    + +  
  gi|313125226|ref|YP_004035490.1| 447 EYLERFR--------STLYRQTMFADFEHQMHTISEEGGALTpDRLDQLYGDLKREFYAPANVDDR-IAREWMRI-P 513
                                       *******........***************************99**************96555555.44444556.3 PP

                                       SS-TTTTCHHHHHHHH..HHHHHHCCHHCCTT-CCHHHHHHHHTTTTTTSS-HHHHHHCCCSS---SHHHHHHC CS
                      Peptidase_M3 385 hgYaanYYsylyaevl..aldifekffeedplnretGeryrkeiLsrGgskdplellkkflgrepsadallkal 456
                                       h+Y+ nYY+y+y++++  a++i e++ +e++  +      +++ L+ Gg k+p+e+l+++++++ s+++++ al
  gi|313125226|ref|YP_004035490.1| 514 HFYY-NYYVYQYSTGIsaAVAIVERILNEGEDAA----ADYRDALALGGAKYPIEVLETAGVDMASPEPIESAL 582
                                       ****.***********9999********995556....999*****************************9987 PP

>> Peptidase_M3_N  Oligopeptidase F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.3      0.13   5.8e+02       1      51 [.      58     106 ..      58     109 .. 0.75
   2 !   88.7   0.3   5.1e-29   2.3e-25       1      70 []     114     183 ..     114     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.13
                    Peptidase_M3_N   1 EllaldeekleellkeepelaeyrfyleeilrqkphtLseeeEklLaelse 51 
                                       Ell+l ee ++e+ k     a   ++ e++++q    L ++ E l +e++ 
  gi|313125226|ref|YP_004035490.1|  58 ELLELQEEIMREVSKV-ANYASL-RSAEDTRDQEYQALQAKAESLSSEAQS 106
                                       7888888888888775.555554.678999999999999999999888765 PP

  == domain 2  score: 88.7 bits;  conditional E-value: 5.1e-29
                    Peptidase_M3_N   1 EllaldeekleellkeepelaeyrfyleeilrqkphtLseeeEklLaelsevggaawnifsdltnadlkF 70 
                                       El +l+e+++e+++++epel +y++y++++lr+kpht s+e+E++Lael+ev++a+++if +l+nad++F
  gi|313125226|ref|YP_004035490.1| 114 ELQELSEADVESFIETEPELVDYEHYFDDVLRMKPHTRSAEVEEVLAELGEVASAPSDIFGMLSNADMTF 183
                                       899******************************************************************9 PP

>> Phage_ABA_S  Phage ABA sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.017        74      23      68 ..     365     409 ..     345     424 .. 0.84
   2 ?    7.9   0.0    0.0011       4.8      31      53 ..     520     542 ..     499     560 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.017
                       Phage_ABA_S  23 ldegeflvevfeysedisaAweVveklknegieikvkslekkyqvl 68 
                                        ++++ ++   +y edis+ + ++ +l  + ++ +++++e+ +++ 
  gi|313125226|ref|YP_004035490.1| 365 GTYDTQPFIMMNYQEDISSMFTLAHELG-HSLHSELAKEEQPWHYA 409
                                       45688888899****************9.99999999999999875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0011
                       Phage_ABA_S  31 evfeysedisaAweVveklkneg 53 
                                        v +ys+ isaA  +ve + neg
  gi|313125226|ref|YP_004035490.1| 520 YVYQYSTGISAAVAIVERILNEG 542
                                       47799**************8654 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   8.6e-05      0.39      30      74 ..      29      80 ..       5     119 .. 0.74
   2 ?   -2.5   0.0       1.5   6.9e+03      28      28 ..     164     164 ..     130     222 .. 0.55
   3 ?   -1.0   0.0      0.51   2.3e+03      79      97 ..     403     431 ..     376     435 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.6e-05
                        MitMem_reg 30 yyslkilqerldlikdYlkkveege......lpvnheilrnlqkllnllP.h 74
                                      +++ + +qerl++i +Y  +v e        l+ ++ei+r+++k+ n     
  gi|313125226|ref|YP_004035490.1| 29 ETAFEDVQERLSEIAAYEGRVTESPetllelLELQEEIMREVSKVANYASlR 80
                                      356666****************553566667788899********9766533 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                        MitMem_reg  28 r 28 
                                       +
  gi|313125226|ref|YP_004035490.1| 164 E 164
                                       1 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.51
                        MitMem_reg  79 e..........lekefnvetnDvllvvyL 97 
                                       e          +  e+++ +n++ll+ yL
  gi|313125226|ref|YP_004035490.1| 403 EqpwhyadytiFVAEVASTVNETLLTQYL 431
                                       23444444444667788999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 3564.16
//
Query:       gi|313125227|ref|YP_004035491.1|  [L=52]
Description: hypothetical protein Hbor_04490 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 349.06
//
Query:       gi|313125228|ref|YP_004035492.1|  [L=51]
Description: hypothetical protein Hbor_04500 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0027   17.1   1.0        0.4   10.2   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
     0.0032   17.4   0.2     0.0052   16.8   0.2    1.3  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.024   14.5   1.3       0.33   10.8   1.3    2.1  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
      0.029   13.9   1.1      0.044   13.3   1.1    1.3  1  RecR            RecR protein
      0.036   14.0   0.7       0.18   11.8   0.7    2.0  1  Nudix_N_2       Nudix N-terminal
       0.04   14.0   3.0      0.086   13.0   3.0    1.6  1  Zn-ribbon_8     Zinc ribbon domain
       0.12   12.5   4.7        3.7    7.7   0.1    2.1  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        1.6    8.8   5.8         16    5.6   5.8    2.0  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00018       0.4       4      12 ..       3      11 ..       1      15 [. 0.66
   2 !    5.9   0.1     0.004         9      18      22 ..      29      33 ..      28      40 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                       zf-ribbon_3  4 rCPnCGapl 12
                                      +C nCG+ +
  gi|313125228|ref|YP_004035492.1|  3 KCDNCGSFV 11
                                      578888744 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.004
                       zf-ribbon_3 18 vCpyC 22
                                      vCp+C
  gi|313125228|ref|YP_004035492.1| 29 VCPSC 33
                                      56666 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   2.3e-06    0.0052      15      40 ..       4      39 ..       2      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                               DZR 15 CseCgtklkavaa..........edrCpsCgekvdp 40
                                      C++Cg+ +  +            +++CpsC+ kv  
  gi|313125228|ref|YP_004035492.1|  4 CDNCGSFVTTEYVrvfapegmnnPRVCPSCEDKVRD 39
                                      *******9854449999**************99875 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.3   0.00015      0.33       3      28 ..       3      34 ..       2      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                      B-TTT--BBEEEEC......TTEEEEE-TTTT CS
                      zf-FPG_IleRS  3 pCpRCwryiervgq......agrstyfCprCq 28
                                      +C+ C+  ++++ +      + +++ +Cp C 
  gi|313125228|ref|YP_004035492.1|  3 KCDNCGSFVTTEYVrvfapeGMNNPRVCPSCE 34
                                      8******988887778999999*********6 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.1     2e-05     0.044      18      40 .]       3      39 ..       1      39 [. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                      E-TTT--EESSS..............S-CCCCSTTSE CS
                              RecR 18 hCsrCgnlteed..............lCaICsdprRD 40
                                       C +Cg + +++              +C+ C d+ RD
  gi|313125228|ref|YP_004035492.1|  3 KCDNCGSFVTTEyvrvfapegmnnprVCPSCEDKVRD 39
                                      6*******888889**********999*********9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   7.9e-05      0.18       3      29 ..       4      34 ..       4      35 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.9e-05
                                      -TTT--B-E.....EE--TT-SS-EEEETTTT CS
                         Nudix_N_2  3 CsqCGtpve.....lripdgDnreRlvCpaCg 29
                                      C +CG+ v+        p+g n +R vCp+C+
  gi|313125228|ref|YP_004035492.1|  4 CDNCGSFVTteyvrVFAPEGMNNPR-VCPSCE 34
                                      999**9987455323459999***9.9****6 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.0   3.8e-05     0.086       7      37 ..       3      38 ..       1      39 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                       Zn-ribbon_8  7 rCeeCghefe......vlqsisdap...lta.CPeCgsevr 37
                                      +C++Cg  f       v    + ++   ++  CP+C  +vr
  gi|313125228|ref|YP_004035492.1|  3 KCDNCG-SFVtteyvrV----FAPEgmnNPRvCPSCEDKVR 38
                                      7*****.5554866433....33334455556****88886 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0017       3.7       3      11 ..       3      11 ..       3      16 .. 0.87
   2 ?    6.1   1.4    0.0053        12      19      26 .]      26      33 ..      24      34 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0017
                            zf-ACC  3 KCpsCgeml 11
                                      KC+ Cg+ +
  gi|313125228|ref|YP_004035492.1|  3 KCDNCGSFV 11
                                      9*****987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0053
                            zf-ACC 19 nlyVCPkC 26
                                      n  VCP+C
  gi|313125228|ref|YP_004035492.1| 26 NPRVCPSC 33
                                      55799999 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   5.8     0.007        16       2      25 ..       1      33 [.       1      35 [. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.007
                    PhnA_Zn_Ribbon  2 lpkCplCaSeytY.........edgallvCpeC 25
                                      +pkC +C+S +t            +   vCp C
  gi|313125228|ref|YP_004035492.1|  1 MPKCDNCGSFVTTeyvrvfapeGMNNPRVCPSC 33
                                      7********665333777777666666677777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 337.71
//
Query:       gi|313125229|ref|YP_004035493.1|  [L=441]
Description: aminopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-34  118.5   0.3    4.3e-34  117.9   0.3    1.2  1  Peptidase_M28  Peptidase family M28
    1.2e-12   47.7   0.3    2.3e-12   46.8   0.3    1.5  1  PA             PA domain
    0.00039   20.2   0.3     0.0011   18.8   0.3    1.7  1  Peptidase_M20  Peptidase family M20/M25/M40
     0.0018   17.4   0.2     0.0029   16.7   0.2    1.3  1  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.9   0.3   9.6e-38   4.3e-34       1     197 [.     216     399 ..     216     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 9.6e-38
                                       EEEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHH CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllG 77 
                                       Nv+++l +++ de +ll AHyD + +  ++   GA Dn++g+a++++ ar+la+   ++  gvr++ +++EE gl G
  gi|313125229|ref|YP_004035493.1| 216 NVVGRLGPDT-DEEILLLAHYDAHDI--AE---GALDNGCGIAVVVTAARILAQ--FDLSVGVRIAGVGCEETGLTG 284
                                       9*****9999.**************9..99...********************8..59******************* PP

                                       HHHHHHHHCCCTTEEEEEEECS-SSSS--EEE.HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHH CS
                     Peptidase_M28  78 SkafakakpelkkiaavlnlDmvgsggkellf.esgdkssselekelkalakpvgraaaedpfdersgrgrsDhspf 153
                                       S+++a ++ + ++i+av+n+D +g+ ++ + + +++++++s  e+ ++++ +p++ + +++pf        sD++pf
  gi|313125229|ref|YP_004035493.1| 285 SEHLA-EQLAHDRIKAVVNVDGAGRFRDLIAMtHTSEATASVAERVADETRHPIQIETEPHPF--------SDQWPF 352
                                       *****.989*******************99987888888888888888999998775444444........9***** PP

                                       HTTT--EEEE..CTSSS-TTT.TSTTSSGGGB-HHHHHHHHHHHHHH CS
                     Peptidase_M28 154 lkagvpvldl..aetgfpevy.HtprDtldnidkdtlariaelvlel 197
                                       ++agvp+l+l   + + ++ + Ht +Dt d++d ++++++a l + l
  gi|313125229|ref|YP_004035493.1| 353 ARAGVPALQLhsDSGERGRGWgHTHADTRDKVDDRNIREHAMLTALL 399
                                       **********6555666999*******************99988765 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.3   5.1e-16   2.3e-12       1      89 []      99     191 ..      99     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 5.1e-16
                                PA   1 vtgplVyscfagygisadfegvdvkGkivLvqr......tf...aeKarnAqaaGAagviiv..ndge.lgaatgas 65 
                                       vtg+lV   ++g+g++++ ++ dv+Gkiv+ +        f    eK+  A +aGA+++++v  +  + + ++t  +
  gi|313125229|ref|YP_004035493.1|  99 VTGELV---YVGHGTPDEVDEHDVAGKIVVASTttppggRFvhrMEKFGYAIDAGAEAFVFVnhV--PgQLPPT-GA 169
                                       89****...*********99***********6444444412666******************543..3223333.23 PP

                                PA  66 gnegepdgitiPavgvsredgeal 89 
                                         +ge  +   Pavgvs+e+g+ l
  gi|313125229|ref|YP_004035493.1| 170 LKFGE--EAVAPAVGVSKESGAWL 191
                                       33344..489***********876 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   2.3e-07    0.0011      33     100 ..     242     304 ..     239     433 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-07
                                       TTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  33 rGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhie 100
                                        Ga d+ +g++ ++ a+r l++    +   ++++ ++ EE+g  G+++l+e+l   ++++av+ +   
  gi|313125229|ref|YP_004035493.1| 242 EGALDNGCGIAVVVTAARILAQFD--LSVGVRIAGVGCEETGLTGSEHLAEQLA-HDRIKAVVNV--D 304
                                       5999***************99997..588***********988********887.5678886632..2 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   6.5e-07    0.0029     126     185 ..     238     297 ..     226     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.5e-07
                                       ECEEETTHHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHHHHHHHHHH--SEE CS
                     Peptidase_M42 126 gkivskalDdragvavllellkelkeeeleatvylvatvqEEvGlrGaktsaekikpdia 185
                                       + i+  alD+  g+av++++++ l++ +l++ v +++   EE Gl G++ +ae++  d +
  gi|313125229|ref|YP_004035493.1| 238 HDIAEGALDNGCGIAVVVTAARILAQFDLSVGVRIAGVGCEETGLTGSEHLAEQLAHDRI 297
                                       4577789*********************************************99877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 3204.53
//
Query:       gi|313125230|ref|YP_004035494.1|  [L=81]
Description: hypothetical protein Hbor_04520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 469.71
//
Query:       gi|313125231|ref|YP_004035495.1|  [L=220]
Description: haloacid dehalogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-16   61.5   0.0    1.3e-16   61.2   0.0    1.1  1  HAD_2            Haloacid dehalogenase-like hydrolase
    2.7e-11   44.1   0.5    1.1e-10   42.2   0.5    1.8  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.3e-09   38.0   0.0    2.9e-09   36.8   0.0    1.6  1  Hydrolase_like   HAD-hyrolase-like
  ------ inclusion threshold ------
      0.018   15.5   0.8      0.049   14.0   0.8    1.9  1  HAD              haloacid dehalogenase-like hydrolase
      0.024   14.0   0.0       0.26   10.7   0.0    2.0  2  Put_Phosphatase  Putative Phosphatase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   3.7e-20   1.3e-16       1     176 [.      11     190 ..      11     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 3.7e-20
                             HAD_2   1 iiFDlDgTlldtee..liiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkk 75 
                                       +iFD Dg+l   +   ++ +a++ ++ e+g+ e++ e ++++i+ s   + r  ++ +    ++e ++ + +++   
  gi|313125231|ref|YP_004035495.1|  11 VIFDNDGVLTRPTAttVHREAVRAAFSEFGV-EPTTEGVDSVIHGSFARVQRICEIHDV---DYEAFWPRREANAAA 83 
                                       7********9765501455799999999988.99***********99776666666433...555555555555555 PP

                             HAD_2  76 ........kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk....KPdpev 140
                                                e ++yd+v ++L +L   + ++g+v+++++e+ve  l+++++ + F+v ++ + + +     KP+p  
  gi|313125231|ref|YP_004035495.1|  84 aqaaaierGEKTLYDDV-SVLSDL---DRTMGVVSNNQHETVETILDAFELRDQFEVAYGRSPTVEGyrnrKPSPHY 156
                                       11111221233445554.455666...889*****************************988764333444****** PP

                             HAD_2 141 iekaleklklkkeeviyvGDsptDieaakkagikvi 176
                                       +e+a+++l  ++e+v+yvGDs+ D+ aa +ag +++
  gi|313125231|ref|YP_004035495.1| 157 LERAIDEL--DAESVLYVGDSNVDVLAATRAGADSA 190
                                       ******86..6799******************9987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.5     3e-14   1.1e-10       1     210 []       8     186 ..       8     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 3e-14
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.HHHHHHHHHETTTEHHHHTHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar.sgaltgfatfigrgayaigkpew 76 
                                       +++v+fD dG+Lt  +p  ++v ++a                   + aa+ +   +++t+         +  g+   
  gi|313125231|ref|YP_004035495.1|   8 YDAVIFDNDGVLT--RPTATTVHREA-------------------VRAAFSEFgVEPTTEGVD-----SVIHGSFAR 58 
                                       589**********..67788999999...................555555556444466666.....788888888 PP

                                       HHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  77 ltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraan 153
                                       +++     + ++ +++a    r++    a+a a+   + +  +++++  ++  L +    +++++++++et+e +++
  gi|313125231|ref|YP_004035495.1|  59 VQRI---CEIHDVDYEAFWPRREANAAAAQAAAIERGEKT--LYDDV-SVLSDLDRT---MGVVSNNQHETVETILD 126
                                       8888...555666666666777777776689999999999..****9.788888844...888************** PP

                                       HTT.GGGESEEEEHHCES....STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxx.xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 154 qlG.ddyfdaviasdiet....vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        +  +d f++ ++++ ++      kpsp  +++ai+eL ++   v+ VGD+  D+ a+ +Ag
  gi|313125231|ref|YP_004035495.1| 127 AFElRDQFEVAYGRSPTVegyrNRKPSPHYLERAIDELDAES--VLYVGDSNVDVLAATRAG 186
                                       ****9999999999888889******************8777..**************9998 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   8.2e-13   2.9e-09       3      74 ..     150     215 ..     149     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 8.2e-13
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                       +KP+p  +++a  +l  d e vl++GD+ + D+++A +aG++s+++++   ++ +l+   ++pty +++l++
  gi|313125231|ref|YP_004035495.1| 150 RKPSPHYLERAIDEL--DAESVLYVGDS-NVDVLAATRAGADSAFIRRPHRDDYQLA---ANPTYEVESLDD 215
                                       7************97..6699*******.*******************998887755...89***9999987 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8   1.4e-05     0.049       1     187 [.      11     182 ..      11     183 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                               HAD   1 alfDfDgTLldgdsle....lllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaael 73 
                                       ++fD+Dg L++    +    + + ++ + g +++ + +   ++ +++r   ++   ++  + ++++ + +e+ aa +
  gi|313125231|ref|YP_004035495.1|  11 VIFDNDGVLTRPTATTvhreAVRAAFSEFGVEPTTEGVDSVIHGSFARVQRIC---EIHDVDYEAFWPRREANAAAA 84 
                                       68999999988833333464333334444444444444444555554443333...334444444444444444444 PP

                               HAD  74 erfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd....rltgelgleg 146
                                       +++  e  ++ l+  + + +l+   +   +  vvS++  + ve +l+++     l  ++ev       + g      
  gi|313125231|ref|YP_004035495.1|  85 QAAAIERGEKTLY--DDVSVLS---DLDRTMGVVSNNQHETVETILDAFE----LRDQFEVAYgrspTVEGY----- 147
                                       4444222222244..3445555...7778999******************....999888654334433333..... PP

                               HAD 147 kpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                           ++ k++      +++  ++d e+v ++GDs  D+ ++
  gi|313125231|ref|YP_004035495.1| 148 ----RNRKPSPHYL--ERAIDELDAESVLYVGDSNVDVLAA 182
                                       ....3333322222..334444666779999******9776 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.064   2.3e+02      92     118 ..     110     136 ..      98     146 .. 0.81
   2 ?   10.7   0.0   7.2e-05      0.26     162     202 ..     159     198 ..     154     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.064
                   Put_Phosphatase  92 liiiSDaNsffieeileaagledlFse 118
                                       + ++S+  +  +e+il+a +l+d F+ 
  gi|313125231|ref|YP_004035495.1| 110 MGVVSNNQHETVETILDAFELRDQFEV 136
                                       568888888999999999999999976 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.2e-05
                   Put_Phosphatase 162 qaregveyerliYvGDganDlCpvlklrekDvampRkgfpl 202
                                       +a ++   e ++YvGD++ D+ + ++ + +D a++R+ +  
  gi|313125231|ref|YP_004035495.1| 159 RAIDELDAESVLYVGDSNVDVLAATR-AGADSAFIRRPHRD 198
                                       466778899************99887.56899999986654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1273.12
//
Query:       gi|313125232|ref|YP_004035496.1|  [L=272]
Description: pseudouridylate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-16   59.1   0.0      2e-12   47.5   0.0    2.3  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   7.6e-05       1.4       4     105 ..       7     101 ..       5     104 .. 0.66
   2 !   47.5   0.0   1.1e-16     2e-12       1     108 []     127     227 ..     127     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 7.6e-05
                   PseudoU_synth_1   4 elvGthdfgsfckqkqekkntvrtileaaieevsge.ekellvvtvkgsgFldhqVRamvgvl.favgqgklspedv 78 
                                       +++G+ ++g f  q+q++  tv   +  a++ +    e+        ++g++d++V a+ +++ f+  + ++     
  gi|313125232|ref|YP_004035496.1|   7 AYDGRPFYG-F--QRQPSVPTVEDSIFDALRSLGVLdEDARKPTGYAAAGRTDAGVSALAQTVaFD--CPEW---CT 75 
                                       689999999.9..5666666666666666664443303344488899***************9333..3222...24 PP

                   PseudoU_synth_1  79 kellnakkrkkiavetapavglvlfhv 105
                                       ++++na++++++ +  a +vg+  fh+
  gi|313125232|ref|YP_004035496.1|  76 PRAMNAELPESVRAWAAADVGE-RFHA 101
                                       6777777777777777777776.6655 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 1.1e-16
                   PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklsped 77 
                                       Aa +l G+hdf ++   +++++ tvr ++   +e     ++e+lv++v + gF ++ VR++  ++  v  g+++  d
  gi|313125232|ref|YP_004035496.1| 127 AADALTGEHDFHNL---TPDDTGTVRDVTVS-VE----ADGEFLVLSVAAGGFPYNLVRRLASIVHSVATGDRPLAD 195
                                       8999********88...88889999999865.44....467899********************************* PP

                   PseudoU_synth_1  78 vkellnakk.rkkiavetapavglvlfhvrYd 108
                                       ++++l  ++ +    v+tapa++lvl++v Y+
  gi|313125232|ref|YP_004035496.1| 196 IETVLGPETvPGPEGVPTAPAEPLVLERVVYP 227
                                       *********987789****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1546.42
//
Query:       gi|313125233|ref|YP_004035497.1|  [L=431]
Description: histidyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-49  169.2   0.2    1.6e-49  168.9   0.2    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    1.6e-13   50.6   0.1    3.1e-13   49.7   0.1    1.4  1  HGTP_anticodon  Anticodon binding domain
    1.2e-06   28.6   0.0      2e-06   27.9   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.9   0.2   2.7e-53   1.6e-49       1     305 [.       7     313 ..       7     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 2.7e-53
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqva 76 
                                       g+rd++p+e+ +++++  ++ d+++++G++++ +P lE+++ + +++ge+   +++ + D+ gr ++l +++Tp va
  gi|313125233|ref|YP_004035497.1|   7 GFRDFYPDEMSARRQVFDAVEDAAARYGFREIATPRLERTQMYVDKSGEEIVeELYAFEDKGGREVSLTPELTPTVA 83 
                                       89************************************************6549*********************** PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTS..SSEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagv..kelrld 150
                                       R++    +  ++p +++++ + +r ++ ++gr re++Q+ + ++G++++ead+E+l  +++al  ++g+  +++++ 
  gi|313125233|ref|YP_004035497.1|  84 RMVVAKQQaLSKPIKWVSSRPFWRFEQVQQGRFREFYQTNVDIFGSSEPEADAEILAFAADALT-SLGLtaDDFEFR 159
                                       **9998887******************************************************6.99965599**** PP

                                       EEETCHHHHHHHHTT--HHHHHHHHHHHHCT-HHH..HHHHHHCCTTHHHCCHCC...HCCHCCCHHHHCHCCHCTH CS
                     tRNA-synt_His 151 lghvglvralleaaglsesleeallaalarkdlae..lkelaaeaglkealrellkalelygdaevleealealaaa 225
                                       ++h +++  ll++++ + ++++a++a+ +r ++++  +  l+++agl+ ++++ ++ l ++gd ++++e      + 
  gi|313125233|ref|YP_004035497.1| 160 VSHRDILGGLLDSFDADVDTRNAIRAVDKRAKVEDeeYLGLLSDAGLSYDQAREFDNLIVAGDLDAIAEF-----GG 231
                                       ***************9999999999888888776511445667889999999999999888887777774.....66 PP

                                       HHHHHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT..-SS-SEEEEEECTTTGGG.T---E CS
                     tRNA-synt_His 226 palqaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayaeg..vgqaiarGGrYdelgaaf.grarp 299
                                       +++++a+++l+++ a+ e+++  +  + + l+  rg++YytG+vF+++ +   v++a  +GGrYd+l+++f g++ p
  gi|313125233|ref|YP_004035497.1| 232 DDVKDAVENLRAVLAATEDFG-VRQYCDISLTTARGLDYYTGVVFECFDSTgdVSRAAFGGGRYDNLIEDFgGQPTP 307
                                       789999************998.566777778999**************97544889********************* PP

                                       EEEEEE CS
                     tRNA-synt_His 300 AtGfsl 305
                                       A+G +l
  gi|313125233|ref|YP_004035497.1| 308 AVGVAL 313
                                       ****98 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.1   5.1e-17   3.1e-13       3      88 ..     338     419 ..     336     420 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 5.1e-17
                                       EEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEE CS
                    HGTP_anticodon   3 vviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreq 79 
                                       +v+++++       +a+++a++Lr+ g  ve+d  ++s+g ++ +ad ++   +v+vGe++le+++vtv+d+dt++q
  gi|313125233|ref|YP_004035497.1| 338 YVLTVGD----TRAVASRVARDLRDRGNVVEMDVADRSFGAQMGYADSINAETVVIVGEQDLENDEVTVKDMDTGDQ 410
                                       5777777....4579************99************************************************ PP

                                       EEEETTHHH CS
                    HGTP_anticodon  80 ervsldelv 88 
                                        + ++++++
  gi|313125233|ref|YP_004035497.1| 411 TTAPVSDFP 419
                                       ****99986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   3.4e-10     2e-06       1      98 [.      62     153 ..      62     306 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.4e-10
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEE.EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevl.rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasl 76 
                                       Y +ed+ +re  L P+ ++t+++++  +    sk  P+k +   + +R E+  ++G  R reF q +  +f++ +  
  gi|313125233|ref|YP_004035497.1|  62 YAFEDKGGREVSLTPELTPTVARMVVAKQQaLSK--PIKWVSSRPFWRFEQV-QQG--RFREFYQTNVDIFGSSE-- 131
                                       89**********************9876222456..****************.9**..***************99.. PP

                                       HHHHHHHHHHHHHHHHHTT.SC CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  77 ddslrdlikaisriferlglef 98 
                                       ++ +++++  +++ + +lgl  
  gi|313125233|ref|YP_004035497.1| 132 PEADAEILAFAADALTSLGLTA 153
                                       9999999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 2305.54
//
Query:       gi|313125234|ref|YP_004035498.1|  [L=398]
Description: hypothetical protein Hbor_04560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-24   86.4  14.9    8.5e-14   51.7   3.2    2.9  3  PQQ_2     PQQ-like domain
    3.6e-21   75.0  30.9    1.6e-06   28.4   1.1    7.1  7  PQQ_3     PQQ-like domain
    1.2e-15   56.5  14.0    1.8e-06   27.6   0.9    5.3  5  PQQ       PQQ enzyme repeat


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   3.2   1.4e-17   8.5e-14      35     151 ..      59     190 ..      37     191 .. 0.91
   2 !   48.2   3.9   1.6e-16   9.8e-13       4     139 ..     171     295 ..     168     297 .. 0.85
   3 !    7.3   0.2   0.00054       3.2      35     225 ..     277     337 ..     263     365 .. 0.53

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.4e-17
                             PQQ_2  35 sggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrse.epa 110
                                       ++g+  ++++  rl+al+   G+  W+t  eg   g p v e+rv+  ++d++++alda++G+  W+ +++++ e  
  gi|313125234|ref|YP_004035498.1|  59 PEGYGTTGGDQHRLAALN-HHGQAEWTTVSEGGGFGVPAVHENRVYIGTGDDTVRALDAATGRIEWT-YDAGGvEEY 133
                                       5666666789999****9.9***********************************************.777777999 PP

                             PQQ_2 111 elrssaspavagdtvvvges...............sgklvaldpkdGkvlWerel.a 151
                                         +  ++p va+++v+vg s                 ++vald +dG++lW +e+ a
  gi|313125234|ref|YP_004035498.1| 134 GGGAWGQPLVADGRVYVGIShsnkpdpdpsdesqyTHRVVALDSTDGSELWATEVtA 190
                                       9999******************************99*****************9944 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 1.6e-16
                             PQQ_2   4 vvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgap.lvaegrv 79 
                                       +v+ald ++G+elW ++++    +g+  a+ + + ++++++   l +++++tG v+W+++l+g++   p +v+e  v
  gi|313125234|ref|YP_004035498.1| 171 RVVALDSTDGSELWATEVTAMVEHGP--AL-ASDIVVSGSEDSVLRGFNPETGDVRWTVSLPGKTWWQPvFVNESLV 244
                                       799*************9977899999..88.99******************************99999857777777 PP

                             PQQ_2  80 vvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldp 139
                                       ++    +++++++a+ G+++ + +   +e+a+         + dtv++g++sg++val +
  gi|313125234|ref|YP_004035498.1| 245 FAT--TETVAKVNAAEGTVQQT-KNPLDEMAS------FDHDEDTVYLGGTSGRVVALTA 295
                                       666..5************9988.333323333......33349**************975 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00054
                             PQQ_2  35 sggtlfvatgggrlvaldaatG......kvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqr 105
                                       +++t++ ++++gr+val a+        +v+We+++e  v ++    +  v+vv++                     
  gi|313125234|ref|YP_004035498.1| 277 DEDTVYLGGTSGRVVALTATPEaetsewSVKWEYDAEISVGAI-AAGDAGVFVVDQS-------------------- 332
                                       4444444444444444443322111111233444444443333.3333334444444.................... PP

                             PQQ_2 106 seepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtselsrvgdisgrpvvaegtVyassgq 182
                                                                                                                    
  gi|313125234|ref|YP_004035498.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                             PQQ_2 183 grllaldlatgrrlwskeissinglpildgdllyvvsagelia 225
                                                                             g+l++
  gi|313125234|ref|YP_004035498.1| 333 --------------------------------------GYLHR 337
                                       ......................................44443 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       0.5     3e+03      21      37 ..      60      76 ..      39      76 .. 0.58
   2 !   28.4   1.1   2.6e-10   1.6e-06       5      40 .]      83     118 ..      79     118 .. 0.86
   3 !   18.6   0.6   3.3e-07     0.002       1      38 [.     119     177 ..     119     179 .. 0.82
   4 !   16.2   0.0   1.9e-06     0.011       1      40 []     180     219 ..     180     219 .. 0.98
   5 !   15.1   0.5   4.1e-06     0.025       1      36 [.     220     254 ..     220     261 .. 0.77
   6 !    9.5   0.1   0.00024       1.4      20      38 ..     277     295 ..     270     296 .. 0.91
   7 !    5.3   0.6     0.005        30       3      34 ..     306     336 ..     304     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.5
                             PQQ_3 21 gglvyvgtgdGtlyAlD 37
                                      +g+  +g+++++l Al+
  gi|313125234|ref|YP_004035498.1| 60 EGYGTTGGDQHRLAALN 76
                                      45555667789998885 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.6e-10
                             PQQ_3   5 WsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       W++   g + + pav +++vy+gtgd t++AlDa+t
  gi|313125234|ref|YP_004035498.1|  83 WTTVSEGGGFGVPAVHENRVYIGTGDDTVRALDAAT 118
                                       888666677799**********************98 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 3.3e-07
                             PQQ_3   1 GevlWsv......qlpgpvnsspavdgglvyvgtg...............dGtlyAlDa 38 
                                       G++ W++      + +g ++++p+v++g+vyvg +                ++++AlD 
  gi|313125234|ref|YP_004035498.1| 119 GRIEWTYdaggveEYGGGAWGQPLVADGRVYVGIShsnkpdpdpsdesqyTHRVVALDS 177
                                       7889***7777777788999999**********88888888888888888888888885 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 1.9e-06
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       G +lW++++ + v  +pa++ ++v+ g++d  l+ +++et
  gi|313125234|ref|YP_004035498.1| 180 GSELWATEVTAMVEHGPALASDIVVSGSEDSVLRGFNPET 219
                                       899***********************************98 PP

  == domain 5  score: 15.1 bits;  conditional E-value: 4.1e-06
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                       G+v+W+v+lpg+++ +p++++  ++++t+  t+  +
  gi|313125234|ref|YP_004035498.1| 220 GDVRWTVSLPGKTWWQPVFVNESLVFATT-ETVAKV 254
                                       99***************999866555555.455554 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.00024
                             PQQ_3  20 dgglvyvgtgdGtlyAlDa 38 
                                       d+++vy g++ G+++Al a
  gi|313125234|ref|YP_004035498.1| 277 DEDTVYLGGTSGRVVALTA 295
                                       689*************976 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.005
                             PQQ_3   3 vlWsvqlpgpvnsspavdgglvyvgtgdGtly 34 
                                       v+W+++    v ++ a+++  v+v++  G l+
  gi|313125234|ref|YP_004035498.1| 306 VKWEYDAEISV-GAIAAGDAGVFVVDQSGYLH 336
                                       78999976555.667999999******99987 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.9   2.9e-10   1.8e-06       1      30 [.     100     129 ..     100     130 .. 0.94
   2 !   12.7   0.0   1.6e-05     0.094      11      28 ..     171     188 ..     167     190 .. 0.87
   3 !   17.7   0.1   4.1e-07    0.0024       2      37 ..     202     237 ..     201     238 .. 0.92
   4 !    4.2   0.1    0.0077        46       1      17 [.     279     295 ..     279     296 .. 0.90
   5 ?   -1.7   0.1      0.57   3.4e+03      22      28 ..     306     312 ..     305     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.9e-10
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSS CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktgg 30 
                                       ++vy+g+ d +++AlDa+TG++ W++++gg
  gi|313125234|ref|YP_004035498.1| 100 NRVYIGTGDDTVRALDAATGRIEWTYDAGG 129
                                       78****9999*****************998 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.6e-05
                                       EEEEEETTTCCEEEEEES CS
                               PQQ  11 ylyAlDadTGkvlWrfkt 28 
                                       +++AlD ++G +lW +++
  gi|313125234|ref|YP_004035498.1| 171 RVVALDSTDGSELWATEV 188
                                       89************9886 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 4.1e-07
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                        v+ gs d +l+ ++ +TG+v+W++ ++g+ +++p+
  gi|313125234|ref|YP_004035498.1| 202 IVVSGSEDSVLRGFNPETGDVRWTVSLPGKTWWQPV 237
                                       577789999*************************97 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.0077
                                       TEEEEEETTSEEEEEET CS
                               PQQ   1 gvvylgsadGylyAlDa 17 
                                       ++vylg   G+++Al a
  gi|313125234|ref|YP_004035498.1| 279 DTVYLGGTSGRVVALTA 295
                                       69************976 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 0.57
                                       EEEEEES CS
                               PQQ  22 vlWrfkt 28 
                                       v+W++++
  gi|313125234|ref|YP_004035498.1| 306 VKWEYDA 312
                                       89***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 2158.93
//
Query:       gi|313125235|ref|YP_004035499.1|  [L=305]
Description: cysteine transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-29  100.8  23.6    3.7e-17   62.8   9.0    2.1  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.051   13.6   0.3      0.051   13.6   0.3    3.0  4  TMEM234   Putative transmembrane family 234
       0.24   10.7  11.2        1.9    7.7   2.4    2.9  2  TPT       Triose-phosphate Transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   9.0   6.1e-21   3.7e-17       2     136 ..      19     156 ..      18     157 .. 0.91
   2 !   44.3   6.6   3.1e-15   1.9e-11       4     136 ..     175     304 ..     172     305 .] 0.88

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 6.1e-21
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkd....wllllllgllg 74 
                                        gi +a++aa++w++y+++ k+ + +++   +t+v  ++a +  l+i+l +      ++        + ++ll ++ 
  gi|313125235|ref|YP_004035499.1|  19 PGIAYAVVAAFVWGTYIFALKRYFDDYPGTVFTVVVNVAAVLWYLPITLSTPTAE-IPDAGTfgigDAGIILLTVVM 94 
                                       5999*******************************************99999998.33333344445667888889* PP

                              EamA  75 tvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       t+ afl+f++al  +++s +++i+ ++Pvf+l + +l+l+e+l  +ql+g++++ l+v++ +
  gi|313125235|ref|YP_004035499.1|  95 TATAFLVFLSALDAGEVSYVAPINKIVPVFVLPIEILFLHEQLRPIQLVGVGVATLAVYVAN 156
                                       **********************************************************9976 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 3.1e-15
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                       + lal++al++ai+ v  + +l++++   +  v +l++g++++++ l+ + +     + d+   + l+  g++l+  
  gi|313125235|ref|YP_004035499.1| 175 AQLALVSALCYAIGDVGKRLVLQEMNIPPTIWVPTLLGGVVVVLLPLVVRDWV--SVRGDLPK-FALAGAGVALGEH 248
                                       579***********************************999855544444333..23566555.666668******* PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       l   a+   +as+as++++++ v++++l+ +ll+e+   + l++++l+++Gv+li 
  gi|313125235|ref|YP_004035499.1| 249 LTSLAFAVAPASIASPVVNTQAVVAVLLGGVLLRERAFGTRLVAAALAVIGVALIA 304
                                       ******************************************************96 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.54   3.2e+03       2      16 ..      25      39 ..      24      47 .. 0.73
   2 ?   -3.4   0.0       1.6   9.5e+03      50      61 ..      51      62 ..      48      69 .. 0.61
   3 ?    1.4   1.4     0.054   3.2e+02      49     112 ..      90     152 ..      87     155 .. 0.76
   4 ?   13.6   0.3   8.5e-06     0.051      66     115 ..     255     303 ..     235     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.54
                           TMEM234  2 llvgilWGitnPllk 16
                                      ++++++WG     lk
  gi|313125235|ref|YP_004035499.1| 25 VVAAFVWGTYIFALK 39
                                      68999***7655555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.6
                           TMEM234 50 plllNqsgSvlf 61
                                      ++++N+ + +++
  gi|313125235|ref|YP_004035499.1| 51 TVVVNVAAVLWY 62
                                      556666665555 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.054
                           TMEM234  49 iplllNqsgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgi 112
                                       +++++  ++ ++f  +l   ++s + pi N +  vf + +e l   ++l+  +++g+++ ++++
  gi|313125235|ref|YP_004035499.1|  90 LTVVMTATAFLVFLSALDAGEVSYVAPI-NKIVPVFVLPIEILFLHEQLRPIQLVGVGVATLAV 152
                                       566777888999************9998.67777787877877767777777777877766665 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 8.5e-06
                           TMEM234  66 gkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       + a+ s+a+p++N+ a+v+ +l + ll+e+  +++ v   +l v+g+al+
  gi|313125235|ref|YP_004035499.1| 255 AVAPASIASPVVNTQAVVAVLLGGVLLRERAFGTRLV-AAALAVIGVALI 303
                                       56789**************************998765.567888899987 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.4   0.00032       1.9      81     282 ..     101     148 ..      34     155 .. 0.52
   2 ?    6.6   1.7   0.00069       4.1      19     136 ..     190     304 ..     177     305 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00032
                               TPT  81 lavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalasvtElsFnligfisAlisnltf 157
                                       +   +l +  VS+   +  + P+F   + +l+l e+l                                        
  gi|313125235|ref|YP_004035499.1| 101 VFLSALDAGEVSYVAPINKIVPVFVLPIEILFLHEQL---------------------------------------- 137
                                       3333455555666666666666665555555555554........................................ PP

                               TPT 158 slrnifsKkllkklkdldalnlfaiitilslllllPvallvegvlktpsllkstkvslkevllllllsgvlfhlynq 234
                                                                                                                    
  gi|313125235|ref|YP_004035499.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                               TPT 235 vaymvLervspvthsvantvKrvvvIvlsvlvfknpvsllnaiGtava 282
                                                                            ++++++G+ va
  gi|313125235|ref|YP_004035499.1| 138 -------------------------------------RPIQLVGVGVA 148
                                       .....................................44444444444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00069
                               TPT  19 ilnKkilnvfpyPltvsavqllvgsvlilvlwalglkkrpkisseflkailplalvktlghvlavvslskvaVSfth 95 
                                       +  + +l+ +++P t+ +  ll g+v+  vl+ l +++   +  ++ k  l  +   +lg+ l+ ++++  + S + 
  gi|313125235|ref|YP_004035499.1| 190 VGKRLVLQEMNIPPTIWVPTLLGGVVV--VLLPLVVRDWVSVRGDLPKFAL-AGAGVALGEHLTSLAFAVAPASIAS 263
                                       555779999999999999999999998..4455555665556555555544.45566788888999*********** PP

                               TPT  96 tvKasePiFtvilsrlllgeklsllvylsLlpivgGvalas 136
                                        v  ++ + +v+l  +ll+e+   + +++    v Gval +
  gi|313125235|ref|YP_004035499.1| 264 PVVNTQAVVAVLLGGVLLRERAFGTRLVAAALAVIGVALIA 304
                                       ********************999888888888899999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1584.69
//
Query:       gi|313125236|ref|YP_004035500.1|  [L=196]
Description: subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0014   18.7   0.0      0.002   18.2   0.0    1.2  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
  ------ inclusion threshold ------
       0.01   15.5   0.2      0.015   15.0   0.2    1.4  1  Asn_synthase     Asparagine synthase
      0.062   12.8   0.0        0.1   12.0   0.0    1.4  1  QueC             Queuosine biosynthesis protein QueC
       0.15   11.5   0.0       0.28   10.7   0.0    1.5  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.5e-07     0.002       2     138 ..       3     134 ..       2     148 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.5e-07
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssly 78 
                                       l++++sgGkds+ l  L+l  f++v++v +  g + + +     + ++r+g ++ v+e +e va++ +++    + y
  gi|313125236|ref|YP_004035500.1|   3 LALLYSGGKDST-LAALLLDSFYDVTLVTAHFGITDDWV-H-ARDAADRLGYEFDVVELDEAVAREAAEQM-VNDGY 75 
                                       6899******98.56777889999887776666554332.2.23455666666666666666655554444.34445 PP

                                       HCHHHHHHTH..HHHHHHHHCTTECEEE----CCCTT...TTTTSSSEEECTTT-SCEEE-CCCT CS
                       PAPS_reduct  79 eeaaeriaKv..eplkkaLekldedalltGaRrdesk...sraklpiveidedfekslrvfPlln 138
                                        +  + i +v  ++l+  + +ld  a+  G Rrd+     sra+ + +e + d      + Pl+ 
  gi|313125236|ref|YP_004035500.1|  76 PR--NGIQQVheHALE-RIAELDVAAIADGTRRDDRVptiSRAQAQSLEDRHDV---DYLAPLSG 134
                                       55..445555104455.5*****************8654566666666655553...34556655 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   3.3e-06     0.015      20      85 ..       3      64 ..       1      97 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-06
                      Asn_synthase 20 vGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeell 85
                                      +++l SGG DS+l a l++ +   +++ ++++f     d+  +a+ +a++lg e   ++l+e+ + 
  gi|313125236|ref|YP_004035500.1|  3 LALLYSGGKDSTLAALLLDSFY--DVTLVTAHF--GITDDWVHARDAADRLGYEFDVVELDEAVAR 64
                                      67788****************9..799999999..99***************99777777665544 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.3e-05       0.1       5      51 ..       6      53 ..       3      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                                      E--SSHHHHHHHHHHHHH-SEEEEEEEESS-T..TSHHHHHHHHHHHHT CS
                              QueC  5 llSGGlDSttvlalakkegkevealtfdYgqr..hkkeleaakkiakel 51
                                      l SGG DSt + al +++++ v+++t ++g    + +  +aa+++  e+
  gi|313125236|ref|YP_004035500.1|  6 LYSGGKDSTLA-ALLLDSFYDVTLVTAHFGITddWVHARDAADRLGYEF 53
                                      78******865.667899*********9997622233334444444444 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.2e-05      0.28       1      17 [.       1      17 [.       1      38 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.2e-05
                   Diphthami_syn_2  1 mkvavlysGGkDsilaL 17
                                      m  a lysGGkDs+la 
  gi|313125236|ref|YP_004035500.1|  1 MELALLYSGGKDSTLAA 17
                                      67799**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1059.79
//
Query:       gi|313125237|ref|YP_004035501.1|  [L=119]
Description: DNA-binding tfar19-related protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-26   91.7  13.9    3.8e-26   91.5  13.9    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain
     0.0014   18.4   2.9     0.0017   18.2   2.9    1.2  1  RMI1_N      RecQ mediated genome instability protein
  ------ inclusion threshold ------
      0.085   11.7   3.1      0.093   11.6   3.1    1.1  1  DUF759      Borrelia burgdorferi protein of unknown function 
       0.19   12.0   0.0       0.23   11.8   0.0    1.2  1  FpoO        F420H2 dehydrogenase subunit FpoO
       0.28   11.3   5.7       0.25   11.4   4.0    1.9  2  FLYWCH_u    FLYWCH-type zinc finger-containing protein 1
          2    9.1   8.8        1.4    9.6   5.9    2.2  2  DUF4404     Domain of unknown function (DUF4404)


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5  13.9   1.3e-29   3.8e-26       1     106 [.      13     116 ..      13     119 .] 0.90

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 1.3e-29
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       +r+++++elq++a++++g++++++q+++++  ++e++k a+L+q L++ Ar+RL+ ++++kp+ ae+v+++L+ laq
  gi|313125237|ref|YP_004035501.1|  13 LRQEKMEELQERAEGQGGQQNEAAQEAARE--RAEAQKDALLKQYLTDGARQRLNAVEMSKPDFAEKVKQQLVALAQ 87 
                                       69***********99988665555555544..5******************************************** PP

                                       --SS-----HHHHHHHHHHHS---XXXXX CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvaekkketki 106
                                       sG+++ +++e+q+k+LL++++ ++k+ +i
  gi|313125237|ref|YP_004035501.1|  88 SGRIQDRIDEDQMKDLLRELQPDSKSFNI 116
                                       **********************9998888 PP

>> RMI1_N  RecQ mediated genome instability protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.9   5.7e-07    0.0017     101     165 ..       9      71 ..       3      89 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.7e-07
                            RMI1_N 101 rgeetrgrevirt...e.saaaasakadeenseekeeaqatsseskkrrmlkLeLtDg.gqkvkAiElkp 165
                                       r e+ r++++++    +  + +++++a++e+    +    + +e++k ++lk  LtDg  q++ A+E+++
  gi|313125237|ref|YP_004035501.1|   9 RLEKLRQEKMEELqerAeGQGGQQNEAAQEA----A--R-ERAEAQKDALLKQYLTDGaRQRLNAVEMSK 71 
                                       3344444444444211212222222222222....1..1.224567899******************975 PP

>> DUF759  Borrelia burgdorferi protein of unknown function (DUF759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.1   3.1e-05     0.093      50     131 ..       4      88 ..       1     102 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                            DUF759  50 nlsdkkkelsrqskfeslrervekyrltqtkklikqgmgfekarkeafrrslmsdrdkrrleykelak...eskaks 123
                                       n  d + e  rq k+e l+er e     q             a+k+a+ +  ++d  ++rl+  e++k     k k 
  gi|313125237|ref|YP_004035501.1|   4 NPDDERLEKLRQEKMEELQERAEGQGGQQNEAAQEAARERAEAQKDALLKQYLTDGARQRLNAVEMSKpdfAEKVKQ 80 
                                       5568889999**************9999999988888888999************************9333357788 PP

                            DUF759 124 kmlaasqg 131
                                       +++a +q 
  gi|313125237|ref|YP_004035501.1|  81 QLVALAQS 88 
                                       88887775 PP

>> FpoO  F420H2 dehydrogenase subunit FpoO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.8e-05      0.23      41      95 ..      33      87 ..      22     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.8e-05
                              FpoO 41 lkaakktydelskeeasgtaGkcdlcgkktrlydvevqvPsfskgsekktaklck 95
                                       +aa++++ e ++ ++ +   +    g+ +rl  ve++ P+f ++++++ + l +
  gi|313125237|ref|YP_004035501.1| 33 NEAAQEAARERAEAQKDALLKQYLTDGARQRLNAVEMSKPDFAEKVKQQLVALAQ 87
                                      579999999999999998888888889******************9999888865 PP

>> FLYWCH_u  FLYWCH-type zinc finger-containing protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.0   8.4e-05      0.25       2      36 ..       5      37 ..       4      43 .. 0.86
   2 ?   -2.1   0.0       1.4   4.1e+03       1      12 [.     108     119 .]     108     119 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.4e-05
                          FLYWCH_u  2 PDvEgLeaRRqQEkAmetLqarPgGpggqadkllq 36
                                      PD E Le  R QEk me Lq r +G+ggq++   q
  gi|313125237|ref|YP_004035501.1|  5 PDDERLEKLR-QEK-MEELQERAEGQGGQQNEAAQ 37
                                      8999999766.788.7*************998766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                          FLYWCH_u   1 pPDvEgLeaRRq 12 
                                       +PD  + + RR+
  gi|313125237|ref|YP_004035501.1| 108 QPDSKSFNIRRR 119
                                       699999999996 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.9   0.00048       1.4       3      80 ..       8      87 ..       5      90 .. 0.72
   2 ?    1.0   0.1      0.23   6.8e+02       2      29 ..      79     107 ..      78     113 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00048
                           DUF4404  3 elLekLhee.LeqnesldeetralLeslaedieellaeedaaaeeee.laerlneaverFeeeHPklagvlreildsLa 79
                                      e+LekL++e +e+ ++  e + ++ +++a++  +  ae ++ a  ++ l++++++ ++  e + P++a+ +++ l +La
  gi|313125237|ref|YP_004035501.1|  8 ERLEKLRQEkMEELQERAEGQGGQQNEAAQEAARERAEAQKDALLKQyLTDGARQRLNAVEMSKPDFAEKVKQQLVALA 86
                                      678888765355555555555555555555555555555555554457**************************99999 PP

                           DUF4404 80 n 80
                                      +
  gi|313125237|ref|YP_004035501.1| 87 Q 87
                                      8 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.23
                           DUF4404   2 kelLekLheeLeqnesldeetra.lLesl 29 
                                       k++L +L +  + ++++de++ + lL++l
  gi|313125237|ref|YP_004035501.1|  79 KQQLVALAQSGRIQDRIDEDQMKdLLREL 107
                                       56777777777777777777644034444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2090  (0.116571); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 691.65
//
Query:       gi|313125238|ref|YP_004035502.1|  [L=151]
Description: 30S ribosomal protein S19e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-47  159.1   0.0    5.4e-47  158.9   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
    2.7e-05   23.7   0.5     0.0014   18.3   0.2    2.3  2  GntR            Bacterial regulatory proteins, gntR family
     0.0008   19.3   0.1     0.0019   18.1   0.1    1.7  1  HTH_12          Ribonuclease R winged-helix domain
     0.0045   17.1   0.2      0.024   14.8   0.1    1.9  2  Mrr_N           Mrr N-terminal domain
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.049   13.6   0.0    1.3  1  HTH_45          Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.0   1.5e-50   5.4e-47       1     136 [.       3     140 ..       3     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 1.5e-50
                                       TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS CS
                    Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGg 77 
                                       t++dVpa++li+ +a++L+++  +e Pew++++Ktg+++el+p++++++yvR+As+lRkv+++gpvGv+rl+++YGg
  gi|313125238|ref|YP_004035502.1|   3 TLYDVPADALIEDVADRLEDR--IEEPEWMAFAKTGQTRELPPQQDNFWYVRTASLLRKVAMNGPVGVDRLSTEYGG 77 
                                       789***************997..****************************************************** PP

                                       ------.....-THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                    Ribosomal_S19e  78 kkrrgv.....rpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                       +kr g+     + +h+ ++s+++ir++lqqLe+ gl+++++++gr++t++G+++ld+ a++v++
  gi|313125238|ref|YP_004035502.1|  78 RKR-GTnryvvSGKHSDTGSKNIIRTALQQLEEEGLIRTAQGEGRVITDEGRSFLDNAAADVFE 140
                                       *99.3324455889***********************9999*******************9976 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.013        48       2      19 ..      13      30 ..      12      41 .. 0.87
   2 !   18.3   0.2   3.8e-07    0.0014      37      62 ..      96     121 ..      94     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.013
                                      HHHHHHHHHHHHHTTSS- CS
                              GntR  2 yeqvyerLredIlsgelr 19
                                       e+v++rL+++I + e++
  gi|313125238|ref|YP_004035502.1| 13 IEDVADRLEDRIEEPEWM 30
                                      689*********998876 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.8e-07
                                       -HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR  37 srttvReALrrLeaeglverrqgrGt 62 
                                       s++ +R AL++Le+egl+   qg+G 
  gi|313125238|ref|YP_004035502.1|  96 SKNIIRTALQQLEEEGLIRTAQGEGR 121
                                       7899*******************996 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   5.3e-07    0.0019      34      65 ..      99     130 ..      90     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.3e-07
                            HTH_12  34 avRyrLrkleergltrrvgyagreltEkGlee 65 
                                        +R  L+ lee+gl+r     gr +t+ G + 
  gi|313125238|ref|YP_004035502.1|  99 IIRTALQQLEEEGLIRTAQGEGRVITDEGRSF 130
                                       599*************************9765 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.22   7.9e+02      22      47 ..      11      38 ..       6      56 .. 0.71
   2 !   14.8   0.1   6.7e-06     0.024      44      85 ..      88     131 ..      68     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.22
                             Mrr_N 22 eirervaerf..glseeeraellpsgkq 47
                                       ++e va+r+   + e e+    ++g++
  gi|313125238|ref|YP_004035502.1| 11 ALIEDVADRLedRIEEPEWMAFAKTGQT 38
                                      5677788888777888888888888866 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.7e-06
                             Mrr_N  44 sgkq..trfknrvgWartyLkkagllespkrgvwkiTekGrevl 85 
                                       sgk   t  kn ++ a+++L ++gl+ + +     iT++Gr++l
  gi|313125238|ref|YP_004035502.1|  88 SGKHsdTGSKNIIRTALQQLEEEGLIRTAQGEGRVITDEGRSFL 131
                                       555555677999******************999********998 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05     0.049      38      68 ..     102     133 ..      96     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                            HTH_45  38 kYLdmLvekglikk.skekYvlTekGlellek 68 
                                         L++L e+gli++ ++e  v+T++G+ +l++
  gi|313125238|ref|YP_004035502.1| 102 TALQQLEEEGLIRTaQGEGRVITDEGRSFLDN 133
                                       5699********6648999**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 871.71
//
Query:       gi|313125239|ref|YP_004035503.1|  [L=362]
Description: hypothetical protein Hbor_04610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-41  143.2  35.4    1.5e-41  142.9  35.4    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.9  35.4   8.3e-46   1.5e-41       4     301 .]      33     348 ..      26     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 8.3e-46
                   LPG_synthase_TM   4 glalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrW....rlllrslgarislrrllrayli 76 
                                       ++++++ll++++    ++ +l+++++++     ++ ++l++l++l++ ++W    +++l  lg+ +++++++ +++ 
  gi|313125239|ref|YP_004035503.1|  33 AFVVFVLLFYFA----GVDELIDTFQKAE----AAPVGLVILVTLVWLAAWsfslKTVLDILGVSVTFPKAFFIFAG 101
                                       344445555555....*************....99999999999988889966667777777*************** PP

                   LPG_synthase_TM  77 glfvnnvtPgalg.Gevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa..vlllla 150
                                       ++f nnvtP++ + Ge+v ayl+++ ++ +++++la++     l+ +  + + l+++++   ++  g++  +ll+l+
  gi|313125239|ref|YP_004035503.1| 102 AMFSNNVTPFGQAgGEPVTAYLISQASDAEYETSLAAIASVDTLNFVPSITIALVGAGYYATEVTLGTNrnLLLALV 178
                                       **************************************************************9999999999***** PP

                   LPG_synthase_TM 151 lallllavlalllllllrrrlarlarvlkrlarllarfarklasakr....................klvlasprrl 207
                                       ++++l++v+  +++ +++rr +   rv++++++l++++ar    a r                    ++++++pr l
  gi|313125239|ref|YP_004035503.1| 179 AVVALAVVVPSVGYVAWQRRYRLEDRVVSAFVPLIQTVAR---YAPRvpvptedgierringffraiERIATNPRGL 252
                                       **********************************999994...4444669*************************** PP

                   LPG_synthase_TM 208 llafllslliwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllall...Gvsaae 281
                                       +la++ s++ w +++l l+l +ra+g++v+l  ++l++++ +++g + plPgG+G++E +l++ll ++    v+++ 
  gi|313125239|ref|YP_004035503.1| 253 ALALGGSAIGWFCQMLGLWLSFRAIGIEVPLSIAMLVVPIGAIAG-VTPLPGGAGGIESVLVVLLLAVplpSVTKSV 328
                                       *******************************98877777666655.6789***********999999999******* PP

                   LPG_synthase_TM 282 alaaallyrlitlylllllG 301
                                       a+aa++++r++ ++l++llG
  gi|313125239|ref|YP_004035503.1| 329 AVAAIVIFRGAVYWLPTLLG 348
                                       ******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1977.68
//
Query:       gi|313125240|ref|YP_004035504.1|  [L=308]
Description: thiamine-phosphate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-19   69.9   2.8    6.6e-19   68.4   2.8    1.8  1  AIRS      AIR synthase related protein, N-terminal domain
    8.2e-09   35.8   0.0    1.5e-08   34.9   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   2.8   7.3e-23   6.6e-19       1      93 [.      35     139 ..      35     140 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 7.3e-23
                                       SSSEE....EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHH CS
                              AIRS   1 dDaav....vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp.....wleevvr 60 
                                       dDaav    vvttd     +l e ++f        +G+++va+ lsD+aamGA+ +a++ ++  p     +l+++vr
  gi|313125240|ref|YP_004035504.1|  35 DDAAVvdglVVTTD-----MLHESTDFpagttrytAGWRSVAASLSDVAAMGADATAAVAAYGAPsleesELRDFVR 106
                                       89**55555*****.....**************************************9******************* PP

                                       HHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEE CS
                              AIRS  61 glaeaaeelgvplvgGdtsfsneptisvtavGl 93 
                                       g +e ++++g++ vgGd+  ++e+t+++ta+G+
  gi|313125240|ref|YP_004035504.1| 107 GAREVCAAVGAEYVGGDLDTHEEFTVATTALGE 139
                                       ********************************7 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   1.7e-12   1.5e-08       2     149 ..     151     290 ..     150     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.7e-12
                                       TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHH CS
                            AIRS_C   2 pGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalae 78 
                                       pG+v+ +tg lG  +a+ + + + +   ++d       d+++   ++ +  al   +  ++a+ D ++ GL+ +l++
  gi|313125240|ref|YP_004035504.1| 151 PGNVVCVTGALGRSAAA-LRAFEAG---DCD----RANDLFRFTPRVAAGVAL---RPYATAMMDSSD-GLARSLHQ 215
                                       89999999998888888.3333233...333....234555554444444444...468*********.8******* PP

                                       HHHTTTEEEEEECGTHHHHHHHH.......HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEE CS
                            AIRS_C  79 mapasgvgaeidldkvpifdele.......splemllsensGrllvavppeea.davlaileeeglpeaavIGevta 147
                                       +a+as++g+ +++d++p+ d +        ++  m+  + +   lv+  p++a d+++++l+   +p  +v+G+vt+
  gi|313125240|ref|YP_004035504.1| 216 IAEASDCGFAFEWDALPVHDAVTeyardtdDERAMAAYFGEDFELVFTLPADAvDTARDALS---IP-ITVVGQVTD 288
                                       **************9999999988888888666666666666667777777776******99...76.********9 PP

                                       SS CS
                            AIRS_C 148 ke 149
                                       ++
  gi|313125240|ref|YP_004035504.1| 289 EQ 290
                                       87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1698.40
//
Query:       gi|313125241|ref|YP_004035505.1|  [L=379]
Description: membrane-associated zn-dependent protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-15   55.3   6.5    5.6e-07   29.1   2.0    2.4  2  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   2.0   3.1e-11   5.6e-07       2     109 ..     128     216 ..     127     258 .. 0.79
   2 !   28.6   0.2   4.5e-11     8e-07     190     229 ..     256     295 ..     226     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.1e-11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp....LGGyVkmageepeeelsee 74 
                                       f ++++ +++ HElGH+ + + +gv v                 +++Y i+++     LG++++m+g+ p+++    
  gi|313125241|ref|YP_004035505.1| 128 FTAAVLGVLTTHELGHYALSRYHGVDV-----------------SLPYLIPFIVpfgtLGAIIQMRGQIPDRK---- 183
                                       788999999******************.................45666666655666***********9999.... PP

                                       ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.........- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........x RF
                     Peptidase_M50  75 eakaflkkspwqrllivlAGplanfilailvfvv.........p 109
                                                  + + i +AGpla++  +i+v +v         p
  gi|313125241|ref|YP_004035505.1| 184 -----------ALFDIGVAGPLAGLAATIVVTAVglslppmtvP 216
                                       ...........99******************9997777655551 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 4.5e-11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 190 sflqllalisvnLgilNLlPipvLDGghllfalleairrk 229
                                       +++ +  ++++ +++lNLlP+ +LDGgh+++a+l + +++
  gi|313125241|ref|YP_004035505.1| 256 HPVIIGGWVGMFFTVLNLLPVGQLDGGHIIRAMLGEAQER 295
                                       6777889**************************9987754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2232.84
//
Query:       gi|313125242|ref|YP_004035506.1|  [L=86]
Description: hypothetical protein Hbor_04640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.15   12.0   0.0       0.31   11.0   0.0    1.5  1  IstB_IS21_ATP  IstB-like ATP binding N-terminal


Domain annotation for each model (and alignments):
>> IstB_IS21_ATP  IstB-like ATP binding N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.7e-05      0.31       4      17 ..       9      22 ..       8      23 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.7e-05
                     IstB_IS21_ATP  4 qqpdyaeLSFEERL 17
                                      + p+++eLS E+RL
  gi|313125242|ref|YP_004035506.1|  9 TEPTANELSKEDRL 22
                                      569**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 515.76
//
Query:       gi|313125243|ref|YP_004035507.1|  [L=261]
Description: molybdopterin synthase subunit moae;molybdopterin guanine dinucleotide biosynthesis accessory protein mobb [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-26   93.1   0.4    2.2e-26   92.3   0.4    1.4  1  MoaE      MoaE protein


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.4   1.3e-30   2.2e-26       8     112 ..     134     240 ..     124     241 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 1.3e-30
                                       HHHHHHHH--TT--EEEEEEEE------..TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEET CS
                              MoaE   8 vaeiealvaspkaGAvvlFvGtvRdsfd..gkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelev 82 
                                       v++++++ + ++aGA+++F+G vR ++   ++++t+L++e y+++ae++++ i +e+++r ++e+v+++Hr+G +e 
  gi|313125243|ref|YP_004035507.1| 134 VEQVKQSPRADRAGAIATFTGRVRAKEGddDARTTQLTFEKYDGVAEEKMRTIESEIAARDGVEEVTMFHRTGVIED 210
                                       445666666889************77657789********************************************* PP

                                       TSEEEEEEEEESSHHHHHHHHHHHHHHHHH CS
                              MoaE  83 geasvvvavssahRkeafeaceylidelKk 112
                                       ge +v+v+v + hR+e+f+a+e+ id+lK+
  gi|313125243|ref|YP_004035507.1| 211 GEDIVFVVVLAGHRRESFRAVEDGIDRLKD 240
                                       *****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1535.95
//
Query:       gi|313125244|ref|YP_004035508.1|  [L=239]
Description: uridylate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-23   83.2   6.9    1.2e-22   80.8   6.9    1.8  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   6.9   6.4e-27   1.2e-22       1     240 [.       1     202 [.       1     203 [. 0.89

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 6.4e-27
                                       TEEEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHH CS
                         AA_kinase   1 krvVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagev 76 
                                       +rvVv +GGs+l+ d ++ ++++ a+ i+ l+++g +l  V+Ggg++++ +++++++l ++e ++            
  gi|313125244|ref|YP_004035508.1|   1 MRVVVSIGGSVLApDLDARRVEDHADVIEHLAREGVELGAVVGGGGVARDYITAARDLGANEVQL------------ 65 
                                       79***********88888************************************99999999996............ PP

                                       HHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTT CS
                         AA_kinase  77 atrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeeg 153
                                          d++++  +r++a+ll a+l   +++++                   +d e   + + +g + v++g      +g
  gi|313125244|ref|YP_004035508.1|  66 ---DQIGIDVTRINARLLIAAL-GPKVDPKVA-----------------HDYEGAGDAIRRGDISVMGGVM----PG 117
                                       ...******************9.344444433.................36899999************88....88 PP

                                       EEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH...CSSS.TTTHHHHCHHHHH CS
                         AA_kinase 154 elgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee...saselatgGmkvkhpaal 227
                                       +    ++D +aa+lAe+++Ad li++t+ dGV+dadp++++da++++e+s++++ +     s +a g   ++++ a+
  gi|313125244|ref|YP_004035508.1| 118 Q----TTDAVAAALAEYVDADLLIYATSADGVFDADPNVDDDATRYEELSASKLVDviaPMSRDA-GASAPVDLLAA 189
                                       8....9**************************************************875444444.44445788888 PP

                                       HHHHCTT-EEEEE CS
                         AA_kinase 228 aaarrggipvvIt 240
                                       ++++r++++++++
  gi|313125244|ref|YP_004035508.1| 190 KLIERSRMRTIVL 202
                                       8888888998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1319.78
//
Query:       gi|313125245|ref|YP_004035509.1|  [L=549]
Description: lysyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.8e-101  339.0   0.0   3.8e-101  338.6   0.0    1.1  1  tRNA-synt_1f  tRNA synthetases class I (K)
    6.8e-08   31.7   0.0    2.7e-06   26.4   0.0    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
    0.00056   19.4   0.0     0.0052   16.2   0.0    2.2  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.6   0.0  6.4e-105  3.8e-101       2     344 ..      22     376 ..      21     389 .. 0.95

  Alignments for each domain:
  == domain 1  score: 338.6 bits;  conditional E-value: 6.4e-105
                      tRNA-synt_1f   2 aWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvp 78 
                                        Wad++a+++ ++   +    + +v++ G+spSG  H+Gn++e++++++va+ lr+rg+evr++++sDd D+lRk+p
  gi|313125245|ref|YP_004035509.1|  22 FWADSVADDIEARD-PD----EPIVIKGGVSPSGVAHLGNFNEIMRGYFVAEVLRERGHEVRQVFTSDDKDPLRKLP 93 
                                       6*********9444.44....79****************************************************** PP

                      tRNA-synt_1f  79 e.............nlpekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglyde 142
                                       +             +++  +l ++lgkp+t+iPdp+g+ +sya hf+  l++  d+lg+ ve++s+telY +g +d 
  gi|313125245|ref|YP_004035509.1|  94 RkladaegnivglgDVDAGALGRNLGKPYTEIPDPFGEADSYAAHFADLLKADADRLGVPVEMVSNTELYDDGTFDP 170
                                       *9999***99999999999********************************************************** PP

                      tRNA-synt_1f 143 aikealenrekikeilekyrgeereetyspylpvcekcgrvdttevvevdaeeeeieYkc..........eecGeee 209
                                        ++++l++ ++ +++l ky +++  e+y+p++pvce+cg++ t +v+++d +++++eY+c          e cG+e+
  gi|313125245|ref|YP_004035509.1| 171 VVERVLSDIDNARDVLGKY-QRKVDEEYVPFNPVCEECGKI-TETVTDIDLDAKTVEYACtdmtvgdetiEGCGHEG 245
                                       *******************.788999**************7.667******************************** PP

                      tRNA-synt_1f 210 evdiregngKLqWkvdwamrWaalgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmssS 285
                                       +++ r+  gKL+W+ +w+ +W++lgVdfEp+GkDha+  gS   +++ia ++l +e+P++++Ye+++l+g+ ++ssS
  gi|313125245|ref|YP_004035509.1| 246 TATFRQ--GKLPWRFEWPGQWQVLGVDFEPFGKDHAE--GSWPSGKDIAeNVLTIEPPVPMTYEWFTLNGE-ALSSS 317
                                       ****99..7****************************..*****************************999.***** PP

                      tRNA-synt_1f 286 kGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf..aeqe 344
                                        Gn++t+ ++le++epevlr++++  +P+ka +ldl+  + +lvd++d++er+yf   ++e
  gi|313125245|ref|YP_004035509.1| 318 AGNIVTVPEILELLEPEVLRYFFAL-NPRKARDLDLS-RLDQLVDDFDRFERAYFgdVDDE 376
                                       *************************.***********.*****************542222 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.0    0.0062        37      11      46 ..      49      84 ..      46      87 .. 0.90
   2 !   26.4   0.0   4.6e-10   2.7e-06     317     368 ..     303     354 ..     283     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0062
                                      SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE- CS
                      tRNA-synt_1g 11 ngklHlGhllevisaDifaRykrlrgeevlfvcgtD 46
                                      +g+ HlG+  e++ +  +a   r rg+ev  v  +D
  gi|313125245|ref|YP_004035509.1| 49 SGVAHLGNFNEIMRGYFVAEVLRERGHEVRQVFTSD 84
                                      6899*************************9887777 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 4.6e-10
                                       EE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-H CS
                      tRNA-synt_1g 317 aheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfsw 368
                                       + e++t++g+ lS+S g++v++ e+le l++++lRY++a +  + +Dld+s 
  gi|313125245|ref|YP_004035509.1| 303 TYEWFTLNGEALSSSAGNIVTVPEILELLEPEVLRYFFALNPRKARDLDLSR 354
                                       679*********************************************9985 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.7e-07    0.0052     245     283 ..     305     343 ..     301     357 .. 0.86
   2 ?   -0.0   0.0     0.076   4.5e+02      60     113 ..     434     486 ..     394     499 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.7e-07
                                       --EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                      tRNA-synt_1e 245 ghlkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                                       ++ +++ge +s s +n++t+ ++l+  +p++lR++++ +
  gi|313125245|ref|YP_004035509.1| 305 EWFTLNGEALSSSAGNIVTVPEILELLEPEVLRYFFALN 343
                                       67899******************************9865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.076
                                       HHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHH CS
                      tRNA-synt_1e  60 kiikrareeeksvkelaekfieefkkdleaLnvlkptleprvsekvdeiielve 113
                                         +++a e+ ++ +++ae++ ++++  l+ +++ ++++   v   +d++ ++v+
  gi|313125245|ref|YP_004035509.1| 434 WAVEEALERVEKARAWAERMDNAYNYRLQ-VEMPETDFDDDVVAALDDLADFVD 486
                                       35667777777788888888888887664.566667788889999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 3062.44
//
Query:       gi|313125246|ref|YP_004035510.1|  [L=178]
Description: hypothetical protein Hbor_04680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   12.5   0.0       0.12   11.9   0.0    1.4  1  DUF3833   Protein of unknown function (DUF3833)


Domain annotation for each model (and alignments):
>> DUF3833  Protein of unknown function (DUF3833)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.8e-06      0.12      57     109 ..      31      82 ..       9     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.8e-06
                           DUF3833  57 wegdeltLdEdfvyddgekqkRiWtltkeedgkyegtAdDvvgeakgeaaGna 109
                                        ++++++L+Edf ++d ++    ++++ ++  ++ + A D+v++ +ge  G+ 
  gi|313125246|ref|YP_004035510.1|  31 SKQKKFRLKEDFSFTDPDTGAERFRVKADSVLDI-SAAYDIVDSQTGERVGSV 82 
                                       467899************9999999998887655.5699********999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.56
# Mc/sec: 961.93
//
Query:       gi|313125247|ref|YP_004035511.1|  [L=91]
Description: hypothetical protein Hbor_04690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.073   12.4   0.1      0.073   12.4   0.1    1.0  1  DUF1616     Protein of unknown function (DUF1616)
      0.077   12.9   0.0        0.1   12.5   0.0    1.2  1  DUF1467     Protein of unknown function (DUF1467)
        0.1   12.6   0.1       0.14   12.2   0.1    1.2  1  MitoNEET_N  Iron-containing outer mitochondrial membrane prot


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.2e-05     0.073     126     180 ..      29      83 ..      11      91 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                           DUF1616 126 keeleeksesrldkalnvlLvvsivlavaalgyavvaPkegekfTelyllgedgd 180
                                        +e ++ks+s  +k+l   +++++v+a++ l y  +++++  +f e+    e+ +
  gi|313125247|ref|YP_004035511.1|  29 DDESSSKSSSTGRKLLRTTVLLALVAAAGYLLYRRATAADDSEFAEIVFEDETAE 83 
                                       5566666777889*********************************999888874 PP

>> DUF1467  Protein of unknown function (DUF1467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05       0.1      34      74 ..      23      63 ..       9      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                           DUF1467 34 evkvpGtdasAParprllrkvlitTivaavvfalvlliils 74
                                      +v++p  d+s+ +  + +rk+l+tT++ a+v a+ +l+++ 
  gi|313125247|ref|YP_004035511.1| 23 QVEIPIDDESSSKSSSTGRKLLRTTVLLALVAAAGYLLYRR 63
                                      34567789999999********************9999975 PP

>> MitoNEET_N  Iron-containing outer mitochondrial membrane protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.3e-05      0.14      36      61 ..      43      68 ..      38      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                        MitoNEET_N 36 wLalvpfaavtaalgYlaykaflpkk 61
                                       L+ ++++a +aa gYl+y++  +++
  gi|313125247|ref|YP_004035511.1| 43 LLRTTVLLALVAAAGYLLYRRATAAD 68
                                      68999***************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 545.19
//
Query:       gi|313125248|ref|YP_004035512.1|  [L=158]
Description: ankyrin repeat-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-20   71.5   0.1    5.8e-09   36.3   0.0    3.8  4  Ank_4     Ankyrin repeats (many copies)
    3.3e-16   59.1   0.1      6e-07   29.6   0.0    3.1  3  Ank_5     Ankyrin repeats (many copies)
    2.3e-15   57.0   0.0    2.8e-10   40.6   0.0    2.2  2  Ank_2     Ankyrin repeats (3 copies)
    1.1e-13   50.9   0.0    2.5e-05   24.5   0.0    3.5  4  Ank       Ankyrin repeat
    2.7e-13   48.8   0.0     0.0011   19.3   0.0    3.8  4  Ank_3     Ankyrin repeat


Domain annotation for each model (and alignments):
>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00033       1.2      29      50 ..      31      51 ..      13      56 .. 0.89
   2 !   29.2   0.0   2.8e-10     1e-06       5      47 ..      40      81 ..      36      85 .. 0.93
   3 !   36.3   0.0   1.6e-12   5.8e-09       3      47 ..      71     114 ..      71     117 .. 0.95
   4 !    9.6   0.0   0.00038       1.4      16      42 ..     119     144 ..     116     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                             Ank_4 29 aqdnrsGetalhiAakrgnvei 50
                                      a+ ++sG++ lh Aa+rg+++i
  gi|313125248|ref|YP_004035512.1| 31 AV-DESGNNMLHVAASRGKIDI 51
                                      67.99*************9986 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 2.8e-10
                             Ank_4  5 LhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgn 47
                                      Lh aa+ g++++   L+e+g+ +n+q  ++G t+lh+A+ +g+
  gi|313125248|ref|YP_004035512.1| 40 LHVAASRGKIDIGSDLIERGIFLNRQ-GKEGKTPLHYALEMGD 81
                                      9*************************.**************97 PP

  == domain 3  score: 36.3 bits;  conditional E-value: 1.6e-12
                             Ank_4   3 taLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgn 47 
                                       t+Lhya ++g+ e++ lL++ gad+  + +++G+ +l+ A++++ 
  gi|313125248|ref|YP_004035512.1|  71 TPLHYALEMGDNEMATLLISAGADVTVT-DDYGNQPLWSAVMNEE 114
                                       79*************************9.*************985 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00038
                             Ank_4  16 lvrlLlekgadinaqdnrsGetalhiA 42 
                                       ++rlL+++gad+  q n+ G ++l+ A
  gi|313125248|ref|YP_004035512.1| 119 VIRLLVQHGADPVNQ-NEAGKSPLDVA 144
                                       79*********9999.*******9877 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.7e-10     6e-07      11      56 .]      31      76 ..      26      76 .. 0.95
   2 !   25.8   0.0   2.6e-09   9.4e-06       1      53 [.      55     106 ..      55     106 .. 0.95
   3 !   12.6   0.0   3.6e-05      0.13      31      56 .]     118     144 ..     116     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.7e-10
                             Ank_5 11 rldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56
                                      + d+ gn+ LhvAa++g  d+   L++rg  ln + ++G+t+l++A
  gi|313125248|ref|YP_004035512.1| 31 AVDESGNNMLHVAASRGKIDIGSDLIERGIFLNRQGKEGKTPLHYA 76
                                      67999****************************************9 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2.6e-09
                             Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltal 53 
                                       L+e+g + +nr+ ++g tpLh+A + g  +++ lL+  gad ++td++G+ +l
  gi|313125248|ref|YP_004035512.1|  55 LIERG-IFLNRQGKEGKTPLHYALEMGDNEMATLLISAGADVTVTDDYGNQPL 106
                                       67888.889****************************************9987 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 3.6e-05
                             Ank_5  31 vvrlLl.argadlnltdsrGltaldlA 56 
                                        v++Ll  +gad+  +++ G+++ld+A
  gi|313125248|ref|YP_004035512.1| 118 NVIRLLvQHGADPVNQNEAGKSPLDVA 144
                                       5677777******************98 PP

>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   7.9e-14   2.8e-10      24      83 .]      34      99 ..       4      99 .. 0.83
   2 !   14.6   0.0     1e-05     0.037      25      64 ..     101     148 ..      99     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 7.9e-14
                             Ank_2 24 kngktaLhyAakngnleivklLleh...ad...ndgrtpLhyAarsghleivklLlekgadinlkd 83
                                      + g++ Lh+Aa++g+++i + L+e    ++   ++g+tpLhyA + g  e++ lL+  gad++++d
  gi|313125248|ref|YP_004035512.1| 34 ESGNNMLHVAASRGKIDIGSDLIERgifLNrqgKEGKTPLHYALEMGDNEMATLLISAGADVTVTD 99
                                      3799*************99****966774445699***********999*******88*****997 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1e-05
                             Ank_2  25 ngktaLhyAakngnl..eivklLleh......adndgrtpLhyAarsg 64 
                                        g+ +L+ A++n  +  ++++lL++h      +++ g++pL +A r  
  gi|313125248|ref|YP_004035512.1| 101 YGNQPLWSAVMNEEVddNVIRLLVQHgadpvnQNEAGKSPLDVARRRE 148
                                       578899999999844337899999999666444466999999996544 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0012       4.2       2      24 ..      36      59 ..      35      66 .. 0.84
   2 !   24.5   0.0   6.9e-09   2.5e-05       2      32 .]      69     100 ..      68     100 .. 0.90
   3 !   14.5   0.0     1e-05     0.037       1      28 [.     101     132 ..     101     135 .. 0.84
   4 ?   -3.4   0.0       4.8   1.7e+04       2       9 ..     137     144 ..     137     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                                      SBBHHHHHHHHTTHHHHHHHH.TT CS
                               Ank  2 GnTPLHlAatngkkriiklLL.hG 24
                                      Gn  LH+Aa++gk +i ++L+ +G
  gi|313125248|ref|YP_004035512.1| 36 GNNMLHVAASRGKIDIGSDLIeRG 59
                                      7888*********99999999666 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 6.9e-09
                                       SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                               Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnaldn 32 
                                       G TPLH+A   g+ +++ lL+  GA+++ +d+
  gi|313125248|ref|YP_004035512.1|  69 GKTPLHYALEMGDNEMATLLIsAGADVTVTDD 100
                                       9******99889999******77*****9995 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 1e-05
                                       TSBBHHHHHHHHTT..HHHHHHHH.TTTST.T CS
                               Ank   1 dGnTPLHlAatngk..kriiklLL.hGAnl.n 28 
                                       +Gn PL  A++n     ++i+lL+ hGA++ n
  gi|313125248|ref|YP_004035512.1| 101 YGNQPLWSAVMNEEvdDNVIRLLVqHGADPvN 132
                                       6889*****977778888******99***846 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 4.8
                                       SBBHHHHH CS
                               Ank   2 GnTPLHlA 9  
                                       G +PL +A
  gi|313125248|ref|YP_004035512.1| 137 GKSPLDVA 144
                                       78999775 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   4.4e-05      0.16       2      27 ..      36      60 ..      35      63 .. 0.92
   2 !   19.3   0.0   3.1e-07    0.0011       1      29 [.      68      95 ..      68      97 .. 0.94
   3 !   12.5   0.0     5e-05      0.18       1      29 [.     101     130 ..     101     131 .. 0.93
   4 ?   -1.6   0.0       1.9   6.7e+03       2      13 ..     137     148 ..     136     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                             Ank_3  2 GetpLhlAarsgnleivkfLlenkga 27
                                      G+++Lh+Aa+ g+++i   L+e +g+
  gi|313125248|ref|YP_004035512.1| 36 GNNMLHVAASRGKIDIGSDLIE-RGI 60
                                      99**************999999.776 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 3.1e-07
                             Ank_3  1 nGetpLhlAarsgnleivkfLlenkgadv 29
                                      +G tpLh+A++ g+ e++ +L+   gadv
  gi|313125248|ref|YP_004035512.1| 68 EGKTPLHYALEMGDNEMATLLIS-AGADV 95
                                      599********************.8***8 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 5e-05
                             Ank_3   1 nGetpLhlAarsgnle..ivkfLlenkgadv 29 
                                       +G+ pL  A+++  ++  ++++L++ +gad+
  gi|313125248|ref|YP_004035512.1| 101 YGNQPLWSAVMNEEVDdnVIRLLVQ-HGADP 130
                                       6999***********778*******.9**97 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.9
                             Ank_3   2 GetpLhlAarsg 13 
                                       G +pL +A r  
  gi|313125248|ref|YP_004035512.1| 137 GKSPLDVARRRE 148
                                       789998886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 823.83
//
Query:       gi|313125249|ref|YP_004035513.1|  [L=125]
Description: hypothetical protein Hbor_04710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-07   31.4   0.1    2.7e-07   31.0   0.1    1.2  1  Colicin_immun  Bacterial self-protective colicin-like immunit
  ------ inclusion threshold ------
       0.38   10.8   3.0          5    7.1   0.2    2.1  2  P4Ha_N         Prolyl 4-Hydroxylase alpha-subunit, N-terminal


Domain annotation for each model (and alignments):
>> Colicin_immun  Bacterial self-protective colicin-like immunity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1     3e-11   2.7e-07       4      88 .]      36     116 ..      32     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3e-11
                     Colicin_immun   4 klieliksFvnneisaeeFeeaylelfkteqdngsllklneklsevldslFlavdlYnpdselreeyeld..eeeLr 78 
                                       k+i+ ++ + ++e+sa+e +  yle fk e +      ++e+ +++l ++F + d Y++ +  re+      e+eL 
  gi|313125249|ref|YP_004035513.1|  36 KYINPLQRYTEGEMSASELSTGYLEEFKNESQ-----GFSEETYQILQNMFRKSDAYCEPEI-REDVRGSigEQELL 106
                                       899999**************************.....********************97654.776554455***** PP

                     Colicin_immun  79 kevrkllekL 88 
                                       + + ++++kL
  gi|313125249|ref|YP_004035513.1| 107 EAATQTIKKL 116
                                       ********98 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2   0.00055         5      13      57 ..      35      79 ..      31      83 .. 0.89
   2 ?    4.1   0.3     0.005        45      12      34 ..     102     124 ..     101     125 .] 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00055
                            P4Ha_N 13 relveeLesyieeeekkleklkrfleeleeehesakedkeeylsn 57
                                      +++++ L++y+e e +  e    +lee+++e++  +e++ + l+n
  gi|313125249|ref|YP_004035513.1| 35 KKYINPLQRYTEGEMSASELSTGYLEEFKNESQGFSEETYQILQN 79
                                      67899***************************8888888888877 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.005
                            P4Ha_N  12 ErelveeLesyieeeekkleklk 34 
                                       E+el+e+ ++ i+++e++le++ 
  gi|313125249|ref|YP_004035513.1| 102 EQELLEAATQTIKKLEERLERID 124
                                       899*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 718.58
//
Query:       gi|313125250|ref|YP_004035514.1|  [L=612]
Description: membrane-associated zn-dependent protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-22   78.3   0.0    3.4e-21   75.7   0.0    2.2  1  Peptidase_M50  Peptidase family M50
    1.9e-17   63.4   1.0    4.2e-07   30.2   0.0    3.4  3  PDZ_2          PDZ domain
    5.7e-09   35.7   1.9    1.3e-07   31.4   0.1    3.3  4  PDZ_6          PDZ domain
    6.6e-09   35.6   0.7    0.00011   22.1   0.1    2.9  3  Tricorn_PDZ    Tricorn protease PDZ domain
      3e-05   24.3   0.3    0.00047   20.4   0.0    2.9  3  PDZ            PDZ domain
  ------ inclusion threshold ------
        0.4   11.3   1.3       0.83   10.3   0.1    2.0  2  MBG            MBG domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   1.1e-24   3.4e-21       3     242 ..     123     589 ..     121     601 .. 0.76

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.1e-24
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaf 79 
                                       ++ l++ +vvHE GH+++ + +++++e++++ +               ++llpLG++V+ ++e              
  gi|313125250|ref|YP_004035514.1| 123 VFGLLVGLVVHEGGHGILCRVEDIEIESMGLVL---------------FTLLPLGAFVEPDEES------------Q 172
                                       78899999********************99999...............9************999............3 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX................................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................ RF
                     Peptidase_M50  80 lkkspwqrllivlAGplanfilailvfvv................................................ 108
                                       ++++   + ++++AG  +nf ++i++f++                                                
  gi|313125250|ref|YP_004035514.1| 173 RNADRGGKSRMFAAGVTNNFAVTIVAFALlfgpviasisvapgmaisgaydgspaatadisqgdritavagmpvnne 249
                                       4678899*******************************************************************999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M50 109 ............................................................................. 108
                                                                                                                    
  gi|313125250|ref|YP_004035514.1| 250 ttldaalystsdqrvevelnggesaadrekrtvsverslivagtvagnpaglsvgdddsaasqnddpirvtqvngta 326
                                       99999999999999999888888888877777777777777777777777777777777777777776666666666 PP

                                       ........................................................................-EEEC CS
                                       ........................................................................xxxxx RF
                     Peptidase_M50 109 ........................................................................pkksk 113
                                                                                                                    
  gi|313125250|ref|YP_004035514.1| 327 vhtqrgfseavgdgrfatittsrgtvtipvgayltrvsadgplgstgaptdggaivtaigdervtssaslsrV---- 399
                                       6666666666666666666666666666666666666666666655555555555555555555555555550.... PP

                                       ECTTTSCEE-SEEEC-............................................................. CS
                                       xxxxxxxxxxxxxxxx............................................................. RF
                     Peptidase_M50 114 eseeekrgviGvspkp............................................................. 129
                                                      +                                                             
  gi|313125250|ref|YP_004035514.1| 400 ---------------Mgdtqpgetvpvelyhdgafktydvtlgenprdnggflgvnlfpgtsgllltdfgvqsypag 461
                                       ...............05555555555555555555555555555556666666666666999999999999999999 PP

                                       ...................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 130 ...................vkkegllealkegvektlkvvvltvkalgklitgklslktlggpisiaqlaseaaeag 187
                                                           ++ ++l+a+  ++   l + vl +  + ++    +++  ++gp ++           
  gi|313125250|ref|YP_004035514.1| 462 tyvsllggdggpdalglsgAVADSPLSAVYVALILPLASLVLGIPNFPGFTDSVANFYAVSGPFGFLGSG----VFL 534
                                       9999999999977777777777777777777777777777777777777777777788888887665444....245 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlv 242
                                       l ++ +++a+i+++Lg++N +P  +LDGg++l+  +ea+  +    +  +v+  +
  gi|313125250|ref|YP_004035514.1| 535 LANVCFWMAWINLQLGLFNCIPGYPLDGGRILRTSVEAVVSRLPVSEPYTVVRTI 589
                                       66************************************99776665554444443 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1     1e-09   3.1e-06      15      68 ..     215     267 ..     206     286 .. 0.79
   2 ?    2.7   0.1     0.053   1.6e+02      37      56 ..     318     337 ..     278     344 .. 0.83
   3 !   30.2   0.0   1.4e-10   4.2e-07      15      82 .]     357     426 ..     343     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1e-09
                                       -EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEE CS
                             PDZ_2  15 gvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVklt 68 
                                       g+ +   ++g+Paa a++ +gD+i++v g +v+++++l+ +l++++  + V+++
  gi|313125250|ref|YP_004035514.1| 215 GMAISGAYDGSPAATADISQGDRITAVAGMPVNNETTLDAALYSTSD-QRVEVE 267
                                       555666789**********************************8764.445554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.053
                                       EEEEETTB--SSHHHHHHHH CS
                             PDZ_2  37 vilkvdgkkvksledlisll 56 
                                       ++++v+g++v++++ + +++
  gi|313125250|ref|YP_004035514.1| 318 RVTQVNGTAVHTQRGFSEAV 337
                                       589*********99887766 PP

  == domain 3  score: 30.2 bits;  conditional E-value: 1.4e-10
                                       -EEEEEE-TTSGGGGT...--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEEE- CS
                             PDZ_2  15 gvlvvsVkeggPaakag..lkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvevkl 82 
                                       g++ + V  +gP    g     g +++++++ +v+s+++l + +  ++pG+tV +++++dg  kt++v+l
  gi|313125250|ref|YP_004035514.1| 357 GAYLTRVSADGPLGSTGapTDGGAIVTAIGDERVTSSASLSRVMGDTQPGETVPVELYHDGAFKTYDVTL 426
                                       566667888888777773344499********************************************97 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   4.2e-11   1.3e-07       4      53 ..     220     267 ..     217     269 .. 0.90
   2 ?   -1.5   0.1      0.79   2.3e+03       5      20 ..     289     305 ..     287     305 .. 0.86
   3 ?    1.0   0.0      0.13   3.9e+02      21      34 ..     318     329 ..     318     338 .. 0.83
   4 ?   -1.5   0.0      0.77   2.3e+03      20      48 ..     380     407 ..     379     413 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.2e-11
                             PDZ_6   4 aVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesvvlv 53 
                                         + gsPA++A + +GD+i++v G pv   + + + a+l +  +++v+++
  gi|313125250|ref|YP_004035514.1| 220 GAYDGSPAATADISQGDRITAVAGMPV--NNETTLDAALYSTSDQRVEVE 267
                                       5678***********************..999999999999999999987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.79
                             PDZ_6   5 VdpgsPAdr.AGlrvGD 20 
                                       +++g++A + AGl vGD
  gi|313125250|ref|YP_004035514.1| 289 IVAGTVAGNpAGLSVGD 305
                                       6789999999******9 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.13
                             PDZ_6  21 iilsvNGqpvegls 34 
                                       ++++vNG+ v  ++
  gi|313125250|ref|YP_004035514.1| 318 RVTQVNGTAV--HT 329
                                       699******9..44 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.77
                             PDZ_6  20 DiilsvNGqpveglsladvaallr.gsage 48 
                                        i+++++++ v  +s a +++ +  + +ge
  gi|313125250|ref|YP_004035514.1| 380 AIVTAIGDERV--TSSASLSRVMGdTQPGE 407
                                       58999******..99999998876555555 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   3.6e-08   0.00011      39      82 ..     231     278 ..     220     284 .. 0.84
   2 ?   -1.6   0.0      0.91   2.7e+03      46      63 ..     319     336 ..     317     341 .. 0.86
   3 !   10.6   0.0   0.00014      0.43      28      78 ..     364     415 ..     352     425 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.6e-08
                                       --.TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE-STT....- CS
                       Tricorn_PDZ  39 nvreGdlilavdgepvskekgiaelLvgkagkeveLtvkrkdg....k 82 
                                       ++++Gd i+av g pv++e+ ++ +L +++++ ve++++ +++    +
  gi|313125250|ref|YP_004035514.1| 231 DISQGDRITAVAGMPVNNETTLDAALYSTSDQRVEVELNGGESaadrE 278
                                       6789**********************************9987754334 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.91
                                       EEEETTEE-BTTB-HHHH CS
                       Tricorn_PDZ  46 ilavdgepvskekgiael 63 
                                       +++v+g  v++++g++e+
  gi|313125250|ref|YP_004035514.1| 319 VTQVNGTAVHTQRGFSEA 336
                                       799*******99998775 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00014
                                       S-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTT.TSEEEEEEE- CS
                       Tricorn_PDZ  28 earSPLaepGvnvreGdlilavdgepvskekgiaelLvgka.gkeveLtvkr 78 
                                        a +PL  +G     G++++a+ +e+v++++++++++ +++ g++v +++ +
  gi|313125250|ref|YP_004035514.1| 364 SADGPLGSTGAPTDGGAIVTAIGDERVTSSASLSRVMGDTQpGETVPVELYH 415
                                       6889******************************999876525667666655 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.6e-07   0.00047      21      71 ..     212     259 ..     202     269 .. 0.78
   2 ?   -0.7   0.1      0.62   1.9e+03      40      48 ..     297     305 ..     259     332 .. 0.62
   3 ?   -0.8   0.0      0.69   2.1e+03      27      79 ..     357     411 ..     342     413 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.6e-07
                                       TSSSSSSEEEEEECTT.SHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHH CS
                               PDZ  21 dqrgdkgifvsevlpg.gaaeadglkvGDkIlsvNgvdvenvsheeavqaik 71 
                                        +   +g  +s    g +aa ad ++ GD+I++v g +v+n + ++a++  +
  gi|313125250|ref|YP_004035514.1| 212 VA---PGMAISGAYDGsPAATAD-ISQGDRITAVAGMPVNNETTLDAALYST 259
                                       43...699999999**7777777.*****************99999987555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.62
                                       HHHTSSTTE CS
                               PDZ  40 eadglkvGD 48 
                                       + +gl+vGD
  gi|313125250|ref|YP_004035514.1| 297 NPAGLSVGD 305
                                       333444444 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.69
                                       SEEEEEECTT.SHHHHHT.SSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEE CS
                               PDZ  27 gifvsevlpg.gaaeadg.lkvGDkIlsvNgvdvenvsheeavqaikgskgkvtL 79 
                                       g++ ++v+++ +   ++     G ++++++++ v++ + +  v   ++++++v++
  gi|313125250|ref|YP_004035514.1| 357 GAYLTRVSADgPLGSTGApTDGGAIVTAIGDERVTSSASLSRVMGDTQPGETVPV 411
                                       6777888888777777777778889999999888888777777666666666665 PP

>> MBG  MBG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00028      0.83       3      46 ..     221     262 ..     219     275 .. 0.84
   2 ?   -1.3   0.1       1.1   3.4e+03      36      67 ..     337     367 ..     300     368 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                               MBG   3 tYdGqaatlddsnsnnkittittngkdatktytltagDfewkta 46 
                                        YdG++a+++d ++++ it   ++g  +++ +tl+a+ ++++++
  gi|313125250|ref|YP_004035514.1| 221 AYDGSPAATADISQGDRIT--AVAGMPVNNETTLDAALYSTSDQ 262
                                       7***********9999888..89999999999999998888544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                               MBG  36 ltagDfew.ktadgnttaptnvGtYtvkLtaag 67 
                                       + +g f + +t+ g+    + vG Y  + +a+g
  gi|313125250|ref|YP_004035514.1| 337 VGDGRFATiTTSRGT--VTIPVGAYLTRVSADG 367
                                       333333321333444..6777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 3517.90
//
Query:       gi|313125251|ref|YP_004035515.1|  [L=174]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-24   83.7   0.1    1.1e-23   83.0   0.1    1.3  1  PadR      Transcriptional regulator PadR-like family
     0.0029   18.2   0.0     0.0046   17.6   0.0    1.2  1  RTP       Replication terminator protein
  ------ inclusion threshold ------
      0.058   13.4   0.3      0.089   12.8   0.3    1.3  1  DUF1007   Protein of unknown function (DUF1007)
       0.24    9.7   0.1       0.31    9.4   0.1    1.1  1  DUF505    Protein of unknown function (DUF505)


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.1   2.4e-27   1.1e-23       1      75 []      15      87 ..      15      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 2.4e-27
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                      +L+ll+e+p+yGyei ke+++ s+g++e+s+Gs+Yp+L ++e++g+ ++ ++e  ++  rky++lTd Gr+elae
  gi|313125251|ref|YP_004035515.1| 15 VLELLDEKPRYGYEILKEINDISGGHWEPSYGSVYPILYKFEDKGWATRIERE--TESDRKYFELTDSGREELAE 87
                                      8**********************************************999887..599**************986 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     1e-06    0.0046      12      93 ..      13      89 ..       8      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1e-06
                                      HHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHHH CS
                               RTP 12 lylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkekak 90
                                        +++l+++k+ yg+++l e+ +      ++P+   +y  l  + ++g  +r+++   +++++   +++ltd+G+e++ 
  gi|313125251|ref|YP_004035515.1| 13 YLVLELLDEKPRYGYEILKEIND-ISGGHWEPSYGSVYPILYKFEDKGWATRIERET-ESDRK---YFELTDSGREELA 86
                                      457899**************965.66667***********************98776.45555...7899999999987 PP

                                      HHH CS
                               RTP 91 lyk 93
                                        +
  gi|313125251|ref|YP_004035515.1| 87 EKR 89
                                      655 PP

>> DUF1007  Protein of unknown function (DUF1007)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3     2e-05     0.089      25      63 ..     111     149 ..     106     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                           DUF1007  25 telvfdddgrltglrhtWtfDelySafllqgldknkdgv 63 
                                       + + +dd  +++    +W+fDe++S+++++ l ++++ +
  gi|313125251|ref|YP_004035515.1| 111 VAFATDDRFEVETPDDVWRFDETFSSWIIEQLIRHHERD 149
                                       4566677777888999*************9987766655 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   6.9e-05      0.31     336     406 ..      19      90 ..      15      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 6.9e-05
                            DUF505 336 leempkkkeeiakkfeeakdlekWyednfdlreaLysLesfeLiesev..eekgkevyvlTeyGekvledqek 406
                                       l+e p+   ei k+ +++    +W  ++ ++   Ly+ e ++  ++ +  +e  +++++lT+ G++ l+++++
  gi|313125251|ref|YP_004035515.1|  19 LDEKPRYGYEILKEINDISGG-HWEPSYGSVYPILYKFEDKGWATRIEreTESDRKYFELTDSGREELAEKRR 90 
                                       556666666777777777776.6*9***************99865544337889***********99887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 989.44
//
Query:       gi|313125252|ref|YP_004035516.1|  [L=510]
Description: hypothetical protein Hbor_04740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-68  229.4   0.3    4.8e-68  228.6   0.3    1.5  1  Chlor_dismutase  Chlorite dismutase
      1e-07   31.9   0.4      1e-07   31.9   0.4    4.0  4  ABM              Antibiotic biosynthesis monooxygenase
  ------ inclusion threshold ------
       0.26   11.1   0.0       0.43   10.4   0.0    1.3  1  ATP-synt_D       ATP synthase subunit D


Domain annotation for each model (and alignments):
>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.6   0.3     8e-72   4.8e-68       9     194 .]      47     245 ..      33     245 .. 0.95

  Alignments for each domain:
  == domain 1  score: 228.6 bits;  conditional E-value: 8e-72
                                       HHHHHHTTSCEEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHSTGGGGEEEEEEEEEEEEEESS....... CS
                   Chlor_dismutase   9 ealleeaeegvlralysvlGlradaDlmlwllretleelqeaerelrrtalgkvlepaysyvsvtelseY....... 78 
                                       ++++e+ae+g ++a++s+lG++  aDl+++++r+tl++l++aer+++rtal++++e+a+syvsvte+s Y       
  gi|313125252|ref|YP_004035516.1|  47 HEAVEDAEDG-TSAVFSILGHK--ADLLVIHFRPTLDALSRAERQFERTALAAYTEQATSYVSVTEVSGYvsqdyfe 120
                                       4556668999.***********..***************************************************** PP

                                       ....SSS-GGGHHHCHHHHS----SSSEEEEEEEEE-EE....GGGS-HHHHHHHHHHHHHHHHGC.TTEEEEEEE- CS
                   Chlor_dismutase  79 ....keedeenkshvearlapelpkkkyvcvYPmsksre....WYllpeeeRrelmaeHgeigrkY.gkVrqiitgs 146
                                           ++ de+ ++++e +l p+ p+++yv +YPmsk+r     WY+l++eeR+e+m+ Hg++gr+Y gk++q+i +s
  gi|313125252|ref|YP_004035516.1| 121 egedADVDEGLRRYIEGKLEPDVPDDQYVAFYPMSKRRGekynWYDLSFEERAEMMSVHGDTGREYaGKIKQVIASS 197
                                       **999999******************************99************************************* PP

                                       TTTSSSSEEEEEEESSTHHHHHHHHHHCTSHHHHHHEEE-S-EEEEEE CS
                   Chlor_dismutase 147 fGldDyEwgvaleaddleefkdlvyelRfdeasakvaeegpfyvGrrl 194
                                       +G+dD+Ewgv+l+++d++e+k++vy++Rfd++s+k++e+g+fy+Grr+
  gi|313125252|ref|YP_004035516.1| 198 VGFDDFEWGVTLFSEDPTEIKNIVYDMRFDDVSSKYGEFGQFYIGRRF 245
                                       *********************************************985 PP

>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.23   1.4e+03      62      74 ..      21      33 ..      20      36 .. 0.86
   2 ?    1.1   0.1     0.075   4.5e+02      12      49 ..      91     126 ..      83     127 .. 0.81
   3 ?   -0.1   0.1      0.17     1e+03      41      64 ..     375     397 ..     347     401 .. 0.73
   4 !   31.9   0.4   1.8e-11     1e-07       7      78 .]     425     495 ..     420     495 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.23
                                      HHHHHHTSHHHHH CS
                               ABM 62 aleahlksphfka 74
                                      +++a++++p++++
  gi|313125252|ref|YP_004035516.1| 21 DWDAWRDAPEHER 33
                                      699******9986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.075
                                       TTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTT CS
                               ABM  12 pgqaeafldafaeavesllaeepGclgyellrstedpd 49 
                                       + + +a+ ++ +++v+ ++ e+ G+ + +++++ ed d
  gi|313125252|ref|YP_004035516.1|  91 RTALAAYTEQATSYVS-VT-EVSGYVSQDYFEEGEDAD 126
                                       55668999999***99.96.******999999877765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.17
                                       EEEEETSTTEEEEEEEESSHHHHH CS
                               ABM  41 llrstedpdevvvieeWeseaale 64 
                                       ++ + +++++  v++ W+++ a e
  gi|313125252|ref|YP_004035516.1| 375 VY-EAKERGRSAVVSIWDTQSAAE 397
                                       33.478888889999999998876 PP

  == domain 4  score: 31.9 bits;  conditional E-value: 1.8e-11
                                       EEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHHHHH CS
                               ABM   7 eirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaahea 78 
                                        ++vk++++e+f+++f  +   +la+ +G+ + +l+ + ed+d +++ ++W  +++  ++ +s++f++++++
  gi|313125252|ref|YP_004035516.1| 425 FYTVKSEHREDFVEKFDTVGD-VLADTDGHQETDLMVNIEDEDDMFIASQWNAQEDAMEFFRSDAFRDTVQW 495
                                       578***************766.99*******************************************99876 PP

>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.2e-05      0.43      15      62 ..      60     107 ..      49     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTS CS
                        ATP-synt_D  15 ghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaag 62 
                                       + s+L  K+d L++ fr +l+ l ++++++e+   +ay   a  +++ 
  gi|313125252|ref|YP_004035516.1|  60 VFSILGHKADLLVIHFRPTLDALSRAERQFERTALAAYTEQATSYVSV 107
                                       56899*********************************9988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2950.19
//
Query:       gi|313125253|ref|YP_004035517.1|  [L=162]
Description: hypothetical protein Hbor_04750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-09   34.7   2.9    1.5e-08   34.1   2.9    1.3  1  SHOCT     Short C-terminal domain
    0.00027   21.0   2.5    0.00027   21.0   2.5    1.7  2  DUF1707   Domain of unknown function (DUF1707)
  ------ inclusion threshold ------
      0.012   15.6   0.7      0.017   15.1   0.7    1.3  1  GvpG      Gas vesicle protein G
      0.053   13.3   0.0      0.069   12.9   0.0    1.1  1  Connexin  Connexin
      0.059   12.7   0.1      0.078   12.3   0.1    1.2  1  DUF4820   Domain of unknown function (DUF4820)
      0.066   13.3   0.1      0.095   12.8   0.1    1.3  1  DUF3288   Protein of unknown function (DUF3288)


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   2.9     5e-12   1.5e-08       1      28 []     110     137 ..     110     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5e-12
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakLL 28 
                                       +a+++L+e+ya+GeI +EEFe++ + LL
  gi|313125253|ref|YP_004035517.1| 110 TAIARLRERYAAGEIGDEEFERRLDALL 137
                                       589*********************9998 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.5   8.9e-08   0.00027       9      39 ..     109     139 ..     106     143 .. 0.91
   2 ?   -3.2   0.2       3.2   9.4e+03       5      13 ..     148     156 ..     147     157 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.9e-08
                           DUF1707   9 eravelLrealaeGrLtldEfdeRleaalaA 39 
                                       e a+++Lre +a+G +  +Ef++Rl+a l+ 
  gi|313125253|ref|YP_004035517.1| 109 ETAIARLRERYAAGEIGDEEFERRLDALLQT 139
                                       789************************9875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                           DUF1707   5 dadRerave 13 
                                       d  R r+++
  gi|313125253|ref|YP_004035517.1| 148 DRARTRVLD 156
                                       555666665 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.7   5.8e-06     0.017      26      64 ..     101     139 ..      92     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-06
                              GvpG  26 qlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdr 64 
                                         +++++ ++ +a+L  +  aGeI +eeF+rr + lL+ 
  gi|313125253|ref|YP_004035517.1| 101 ASYEPTEDETAIARLRERYAAGEIGDEEFERRLDALLQT 139
                                       567788888999**********************99974 PP

>> Connexin  Connexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.3e-05     0.069      82     140 ..      50     107 ..      46     127 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                          Connexin  82 lvstPsllylvyvlhkiakeekeke.keeeekeeeekeeekkkkkekkkkkkkeeekekk 140
                                       l  tP+++ l y++h++   + ++e k+++++++ ++e ++++++++   +++++ + ++
  gi|313125253|ref|YP_004035517.1|  50 LTVTPTVMLLSYAVHRLTGPSGDEEsKTTDSHRAAHRETSRRRTATQ--GQESASYEPTE 107
                                       6789************9988884440334444444444433332222..22222222222 PP

>> DUF4820  Domain of unknown function (DUF4820)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.6e-05     0.078     171     227 ..      73     129 ..      37     131 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                           DUF4820 171 rksekesaesseskkrnkeerdaeseeessede..eeeetvkellekyanenseddsdf 227
                                       ++s+++  +++++++ +++++ ++ +e+ s  e  e+e ++  l e+ya  +  +d++f
  gi|313125253|ref|YP_004035517.1|  73 EESKTTDSHRAAHRETSRRRTATQGQESAS-YEptEDETAIARLRERYAAGEI-GDEEF 129
                                       344444444444555555333333344433.34447777788889****6653.57777 PP

>> DUF3288  Protein of unknown function (DUF3288)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.2e-05     0.095      24      73 ..     107     157 ..      82     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                           DUF3288  24 denlaelArLliRYe.gFpGardiqkdldkvlkkWqlteeeL.fektreiha 73 
                                       +++ + +ArL+ RY+ g  G ++ ++ ld +l++ +lt ++   ++tr + +
  gi|313125253|ref|YP_004035517.1| 107 EDE-TAIARLRERYAaGEIGDEEFERRLDALLQTEDLTGDKSdRARTRVLDH 157
                                       433.569*******73667*******************88752577887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 950.51
//
Query:       gi|313125254|ref|YP_004035518.1|  [L=261]
Description: kinase, sugar kinase superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-10   39.2   1.7    5.9e-10   39.2   1.7    1.7  2  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   1.7   3.3e-14   5.9e-10       1      66 []      71     136 ..      71     136 .. 0.82
   2 ?   -2.8   0.0      0.45   8.1e+03      39      58 ..     229     248 ..     215     251 .. 0.66

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.3e-14
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       d++++ +iPvg+G+G S+A+++a+++A+++ ++l+l  e+ +  a +ae +   + ++ gDv++   Gg
  gi|313125254|ref|YP_004035518.1|  71 DVSLEADIPVGCGFGASGAATLATALAAADVFDLELsrEDvLTAAHRAEVA---AGTGLGDVFVQEQGG 136
                                       688999***************************999533366666666654...559999999987776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHHHSHH CS
                    GHMP_kinases_N  39 aklaleaerlaqggngsggD 58 
                                       a +a ++e   ++g+ +  D
  gi|313125254|ref|YP_004035518.1| 229 ATMAMVGETVLATGVEGVLD 248
                                       56777777666667777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1536.04
//
Query:       gi|313125255|ref|YP_004035519.1|  [L=133]
Description: hypothetical protein Hbor_04770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-08   31.7   3.8    8.3e-08   31.7   3.8    1.9  2  SHOCT     Short C-terminal domain
    1.7e-05   24.8   6.8    2.8e-05   24.1   6.8    1.4  1  DUF1707   Domain of unknown function (DUF1707)
     0.0021   18.0   1.2     0.0032   17.5   1.2    1.3  1  GvpG      Gas vesicle protein G
     0.0084   16.7   2.2       0.15   12.6   0.0    2.7  2  DUF883    Bacterial protein of unknown function (DUF883)
  ------ inclusion threshold ------
      0.044   13.7   1.1      0.044   13.7   1.1    2.0  2  VbhA      Antitoxin VbhA


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   3.8   2.3e-11   8.3e-08       1      28 []      88     115 ..      88     115 .. 0.98
   2 ?   -1.5   0.2      0.66   2.4e+03      17      24 ..     124     131 ..     124     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.3e-11
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakLL 28 
                                       daL +L+e+ya+G I+e+EFe++ ++LL
  gi|313125255|ref|YP_004035519.1|  88 DALGRLRERYAEGKIDEAEFERRVEQLL 115
                                       89*************************8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.66
                             SHOCT  17 eEEFeakK 24 
                                       e+EF + K
  gi|313125255|ref|YP_004035519.1| 124 EAEFVREK 131
                                       79**9988 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   6.8   7.9e-09   2.8e-05       2      40 ..      80     118 ..      79     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 7.9e-09
                           DUF1707   2 RasdadReravelLrealaeGrLtldEfdeRleaalaAr 40 
                                       Ra+ ++ ++a+ +Lre +aeG ++ +Ef++R+e+ l+ +
  gi|313125255|ref|YP_004035519.1|  80 RANADQHDDALGRLRERYAEGKIDEAEFERRVEQLLRTQ 118
                                       8888999***************************99765 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.2   8.8e-07    0.0032      35      66 ..      88     119 ..      68     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.8e-07
                              GvpG  35 keLaaLqqeLdaGeIdeeeFdrrEeelLdrLe 66 
                                         L +L  +  +G+Ide+eF+rr e+lL   +
  gi|313125255|ref|YP_004035519.1|  88 DALGRLRERYAEGKIDEAEFERRVEQLLRTQD 119
                                       4688999********************97655 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   4.3e-05      0.15      66      90 ..      12      36 ..       9      39 .. 0.92
   2 ?    1.5   1.9      0.13   4.7e+02      19      39 ..      80     100 ..      63     133 .] 0.53

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                            DUF883 66 ddyVrenPwqavGiAagvGlllGlL 90
                                      d+++r +Pw+  +++agv  l++l+
  gi|313125255|ref|YP_004035519.1| 12 DEFIRTRPWTFSAVVAGVVSLIALI 36
                                      899******************9986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                            DUF883  19 keaadeageeaeelRerleer 39 
                                       ++ ad+ ++ + +lRer  e 
  gi|313125255|ref|YP_004035519.1|  80 RANADQHDDALGRLRERYAEG 100
                                       455566666666666664433 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         2     7e+03      18      28 ..      61      71 ..      60      72 .. 0.70
   2 ?   13.7   1.1   1.2e-05     0.044      19      45 ..      86     112 ..      80     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                              VbhA 18 epsaetvadle 28
                                      + ++ t+a++e
  gi|313125255|ref|YP_004035519.1| 61 RLTDFTRAMTE 71
                                      56788888876 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.2e-05
                              VbhA  19 psaetvadleayvrGeIdadElvrrvr 45 
                                       +++++ ++ e+y+ G+Id +E  rrv 
  gi|313125255|ref|YP_004035519.1|  86 HDDALGRLRERYAEGKIDEAEFERRVE 112
                                       889999999***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 800.39
//
Query:       gi|313125256|ref|YP_004035520.1|  [L=56]
Description: hypothetical protein Hbor_04780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.2   0.1      0.011   16.1   0.1    1.1  1  DUF4281   Domain of unknown function (DUF4281)


Domain annotation for each model (and alignments):
>> DUF4281  Domain of unknown function (DUF4281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.1   6.3e-07     0.011      88     127 .]      14      50 ..       6      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.3e-07
                           DUF4281  88 DLfvgrwiyldglrrgvpalltahsllltllfGPlGlllh 127
                                        L ++ wi +d+++r++    ++++ lltll+G +Gll +
  gi|313125256|ref|YP_004035520.1|  14 HLTLAAWIRRDAKKRDI---DASPWDLLTLLTGVFGLLGY 50 
                                       6899*************...89999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 365.42
//
Query:       gi|313125257|ref|YP_004035521.1|  [L=358]
Description: oxidoreductase, aryl-alcohol dehydrogenase like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-49  167.8   0.0    3.4e-49  167.6   0.0    1.0  1  Aldo_ket_red   Aldo/keto reductase family
  ------ inclusion threshold ------
       0.16   12.2   0.1        0.9    9.8   0.0    2.1  2  ETC_C1_NDUFA4  ETC complex I subunit conserved region


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.6   0.0   3.8e-53   3.4e-49       1     292 [.      15     315 ..      15     317 .. 0.93

  Alignments for each domain:
  == domain 1  score: 167.6 bits;  conditional E-value: 3.8e-53
                                       .EEEE-SSS-ST...TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE..... CS
                      Aldo_ket_red   1 elglGtwqlgsk..eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv..... 70 
                                       e+g+G+w +g++  +  +k++++e++++a+e+Gi++fDt++vYg g+se+++Gea+++    r+ev +atKv     
  gi|313125257|ref|YP_004035521.1|  15 EVGFGAWVVGTDwwGDRTKDDSIEMIHHAIEEGITYFDTGDVYGHGESEKVIGEAIAD---YRDEVTLATKVgydfy 88 
                                       68************9*******************************************...***********99998 PP

                                       ...--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEE.S--H CS
                      Aldo_ket_red  71 ...dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvS.nfsv 143
                                          + + +e +  ++ e++r + e+sl+rLg+d+v +l+lH+ +++ +  e+vl+al+el++eG++ aiG + + s+
  gi|313125257|ref|YP_004035521.1|  89 nnpQAGHGELPKEMTGEWVRSATEKSLERLGVDHVEVLQLHNANVDEV-DEDVLEALDELREEGLVDAIGWAlGPSI 164
                                       88888888888888889*******************************.***********************65558 PP

                                       HHHHHHHHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-E..EEEBSTTGGGTTGTTTSS---SSSCCC------ CS
                      Aldo_ket_red 144 eqlekakkkkkvkivavqveynllreleeegllelckkkgvp..liaysplggGlltgkyqseedkedkeprkdlkr 218
                                       + l +     + ++ ++q  +n+++++  ++ l++++  g p  li+  p ++Gll +++++e+  +d + ++ ++ 
  gi|313125257|ref|YP_004035521.1| 165 GWLAEGDMAIEEEFDSLQLVWNMFEQEVGNHFLDTVERTGSPtsLIPRVPHSSGLLNEQVTPETG-HDLDDHRGFRP 240
                                       8888776677888*************************75442289***********88886666.56777778899 PP

                                       -TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG-.---HHHHHHHHHH CS
                      Aldo_ket_red 219 dertsknldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalel.klseeevaeldel 292
                                       d +++   +++e+l+ l ++   ++ q+a++y+ls++av +v p   + e +++ ++a ++ klseee++++  l
  gi|313125257|ref|YP_004035521.1| 241 DAWYETGWEKLETLRFLERDGERTMGQAAIAYLLSHDAVASVTPTFHTKEDITEWAAASDVpKLSEEEMTRVSDL 315
                                       9*********************************************************************99776 PP

>> ETC_C1_NDUFA4  ETC complex I subunit conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.21   1.9e+03      36      48 ..     162     174 ..     158     183 .. 0.80
   2 ?    9.8   0.0    0.0001       0.9      32      92 ..     264     322 ..     245     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.21
                                       TTT-SSSS--SEE CS
                     ETC_C1_NDUFA4  36 plmGWtssaDtls 48 
                                       p +GW +++D++ 
  gi|313125257|ref|YP_004035521.1| 162 PSIGWLAEGDMAI 174
                                       889*******975 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0001
                                       S---TTT-SSSS--SEEECEEEESSHHHHHHHHHHCT-EEEEE-SST-XXXXXXXXXXXXX CS
                     ETC_C1_NDUFA4  32 rwenplmGWtssaDtlsqvslkFdskedAiayaekqgweyeveepkkrkvkpksYadnfsv 92 
                                       ++ +  + +  s+D++++v+ +F++ked  ++a ++ +    ee+   ++    Y dnf +
  gi|313125257|ref|YP_004035521.1| 264 TMGQAAIAYLLSHDAVASVTPTFHTKEDITEWAAASDVPKLSEEE--MTRVSDLYEDNFGI 322
                                       44456677888***********************99988544444..66677899999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2120.58
//
Query:       gi|313125258|ref|YP_004035522.1|  [L=310]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-07   29.1   4.8     0.0025   17.5   0.7    3.3  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
      0.002   17.9   9.2      0.042   13.6   0.5    3.5  4  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1     6e-05      0.54      17      34 ..     146     163 ..     132     165 .. 0.88
   2 ?    1.5   0.0     0.031   2.8e+02       3      16 ..     170     183 ..     167     186 .. 0.59
   3 !   17.5   0.7   2.8e-07    0.0025       1      35 [.     200     234 ..     200     235 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6e-05
                                       ETTEEE-TTEEEETTEEE CS
                           Hexapep  17 ggnVkIGdnvkIgagvvi 34 
                                       g+n+ IGdn++++ gv +
  gi|313125258|ref|YP_004035522.1| 146 GHNISIGDNTVVHDGVHL 163
                                       699999999999999865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.031
                                       EEETTEEE-TTEEE CS
                           Hexapep   3 vIGsnvlIgpfavi 16 
                                       +IG+ v +  ++++
  gi|313125258|ref|YP_004035522.1| 170 TIGDRVSLSDGVHL 183
                                       56666666666655 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 2.8e-07
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +t++++n+ I   a++++++ IG n+++ga +v+ 
  gi|313125258|ref|YP_004035522.1| 200 HTIVEDNARITYDAMVRAGIRIGANSVVGARSVVQ 234
                                       68999***************************995 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.24   2.2e+03       5       9 ..     132     136 ..     132     138 .. 0.66
   2 !    5.5   0.1    0.0017        15      18      30 ..     149     161 ..     140     165 .. 0.70
   3 !    7.8   0.2    0.0003       2.7       2      33 ..     149     184 ..     148     185 .. 0.79
   4 !   13.6   0.5   4.7e-06     0.042       2      29 ..     201     230 ..     200     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.24
                                       -TT-E CS
                         Hexapep_2   5 GdnCl 9  
                                       GdnC 
  gi|313125258|ref|YP_004035522.1| 132 GDNCR 136
                                       66664 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0017
                                       EEE-TT-EE-TT- CS
                         Hexapep_2  18 vslGdncvvgaGv 30 
                                       +s+Gdn vv  Gv
  gi|313125258|ref|YP_004035522.1| 149 ISIGDNTVVHDGV 161
                                       5666666666555 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0003
                                       EEE-TT-EE-TT-EE...S.EEE-TT-EE-TT-EE- CS
                         Hexapep_2   2 viIGdnCliGanagi...G.vslGdncvvgaGvvit 33 
                                       ++IGdn++++        G  ++Gd++ ++ Gv ++
  gi|313125258|ref|YP_004035522.1| 149 ISIGDNTVVHDGVHLddrGkLTIGDRVSLSDGVHLY 184
                                       899999999999887666788888888888888665 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 4.7e-06
                                       EEE-TT-EE-TT-EE..SEEE-TT-EE-TT CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaG 29 
                                       +i++dn  i  +a +  G+ +G n+vvga 
  gi|313125258|ref|YP_004035522.1| 201 TIVEDNARITYDAMVraGIRIGANSVVGAR 230
                                       688999999999998889999999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1855.78
//
Query:       gi|313125259|ref|YP_004035523.1|  [L=108]
Description: hypothetical protein Hbor_04810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0026   17.7   1.1     0.0034   17.4   1.1    1.2  1  DZR             Double zinc ribbon
     0.0029   17.2   5.5      0.012   15.3   5.5    1.9  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.025   14.0   6.8      0.079   12.4   0.9    2.3  2  zf-ribbon_3     zinc-ribbon domain
      0.028   14.1   1.9      0.054   13.2   1.9    1.6  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.037   13.9   0.8      0.055   13.4   0.8    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.1   9.5e-07    0.0034      10      36 ..      79     105 ..      71     108 .] 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.5e-07
                               DZR  10 pdarfCseCgtklkavaaedrCpsCge 36 
                                       +  r+C++Cg++ ++  + drC++C  
  gi|313125259|ref|YP_004035523.1|  79 STGRYCPHCGSENEPDHTFDRCWNCAN 105
                                       456899999999998888999999975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   5.5   3.3e-06     0.012       1      19 [.      83     103 ..      83     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-06
                     zinc_ribbon_2   1 fCpnCGaelqdnakF..CpyC 19 
                                       +Cp+CG e++++ +F  C +C
  gi|313125259|ref|YP_004035523.1|  83 YCPHCGSENEPDHTFdrCWNC 103
                                       8**************888666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   2.2e-05     0.079       3      17 ..      82      96 ..      81      97 .. 0.83
   2 ?    5.2   0.5     0.004        14       3      11 ..      98     107 ..      96     108 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                       zf-ribbon_3  3 vrCPnCGa.plssddn 17
                                      ++CP+CG+ + ++d +
  gi|313125259|ref|YP_004035523.1| 82 RYCPHCGSeN-EPDHT 96
                                      69*****999.98865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.004
                       zf-ribbon_3   3 vrCPnCGa.p 11 
                                        rC+nC + +
  gi|313125259|ref|YP_004035523.1|  98 DRCWNCANrL 107
                                       59****8755 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.9   1.5e-05     0.054       4      17 ..      82      95 ..      79     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                     zf-NADH-PPase  4 rFCgrCGaptepae 17
                                      r+C++CG+++ep +
  gi|313125259|ref|YP_004035523.1| 82 RYCPHCGSENEPDH 95
                                      9*********9987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   1.5e-05     0.055      21      50 ..      74     104 ..      69     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                    OrfB_Zn_ribbon  21 evnpayTSktCseCgsknke.alsgrtfkCp 50 
                                       e +   T   C++Cgs+n++    +r ++C 
  gi|313125259|ref|YP_004035523.1|  74 ERDDQSTGRYCPHCGSENEPdHTFDRCWNCA 104
                                       5677789*************55556666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 577.23
//
Query:       gi|313125260|ref|YP_004035524.1|  [L=62]
Description: hypothetical protein Hbor_04820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.021   14.1   0.2      0.024   13.9   0.2    1.0  1  O_anti_polymase  Putative O-antigen polymerase
      0.024   14.8   1.9      0.027   14.7   1.9    1.1  1  DMT_6            Putative member of DMT superfamily (DUF486)


Domain annotation for each model (and alignments):
>> O_anti_polymase  Putative O-antigen polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.7e-06     0.024     154     195 ..      13      54 ..      11      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-06
                   O_anti_polymase 154 ttvlaillsilitlYytkkikikeivllilllvllllgigyl 195
                                       +++l+++++++ + Y ++ + +++++ + +l+++++l+i  l
  gi|313125260|ref|YP_004035524.1|  13 MQTLVVFVVFFAYDYLQNAVDWSYLFAATALFFVMMLVIDGL 54 
                                       689**********************************99766 PP

>> DMT_6  Putative member of DMT superfamily (DUF486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.9     3e-06     0.027      68     104 ..      13      50 ..       4      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-06
                             DMT_6  68 vitlvvfvlfsvl.llkeklklnhlvaflllvlavyfv 104
                                       + tlvvfv+f ++ +l++++ +++l+a++ l+  +++v
  gi|313125260|ref|YP_004035524.1|  13 MQTLVVFVVFFAYdYLQNAVDWSYLFAATALFFVMMLV 50 
                                       458999988654449*************9999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 341.08
//
Query:       gi|313125261|ref|YP_004035525.1|  [L=250]
Description: hypothetical protein Hbor_04830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-61  207.0   0.0    3.8e-61  206.8   0.0    1.0  1  Nmad3     Nucleotide modification associated domain 3


Domain annotation for each model (and alignments):
>> Nmad3  Nucleotide modification associated domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.8   0.0   2.1e-65   3.8e-61       1     248 [.       3     236 ..       3     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 206.8 bits;  conditional E-value: 2.1e-65
                             Nmad3   1 kiilsrkGfDssaggvpsPilpdGsfvslPIPek....adesritYadlkldgeelgdlvadltegklkaestvHlD 73 
                                       ++++++++++++ +gv++P++pdG+f+++PIPe+    +d++++tYad++ +     +++ad+++       +vHlD
  gi|313125261|ref|YP_004035525.1|   3 RALAINVAANTNLPGVRGPVYPDGTFAYVPIPERkptrPDATVPTYADIDPP----VEIPADARD------APVHLD 69 
                                       7899*****************************889855**********999....*******99......78**** PP

                             Nmad3  74 PdlaeetlewrptyGq.hgaaqghlrnqgveeGDlflFfglfrrvekenerlrfv.......kgaewghylfGylqv 142
                                       P++a+++ ++r+tyG+ hg+++g+l++  +++GD+++F+++++ +e +++  +++        +++wg yl+G ++v
  gi|313125261|ref|YP_004035525.1|  70 PEFAGYPFCDRYTYGDeHGVKAGPLSD--LDAGDWLFFYATLDLHEATGNGDTVDaddgtnyLAPDWGTYLIGGFEV 144
                                       ***************************..****************8885444444445666678999********** PP

                             Nmad3 143 devl.kveedevpeaewarhphnahkkran.dntlyvasekegsglfdrlealpLskpeagkesnwklpsffkkelv 217
                                       d ++  +e++++p+ e+ar+++nah+kr++ d++++va+ +++s+lfd  +++pLs+ eag+++n         ++v
  gi|313125261|ref|YP_004035525.1| 145 DIAVtGSEYESLPAPERARFATNAHVKRESfDAAVLVAG-TDRSRLFD--RVVPLSTREAGADAN---------RIV 209
                                       ****99999999999**********************99.9*******..9**************.........99* PP

                             Nmad3 218 telsyhsgkgrWwrreedaalksaargqefv 248
                                       t+ls++sgkg+Wwrr     l+++a+++ ++
  gi|313125261|ref|YP_004035525.1| 210 TDLSNDSGKGPWWRR----VLRFDAKATDEL 236
                                       ***************....999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1383.11
//
Query:       gi|313125262|ref|YP_004035526.1|  [L=156]
Description: hypothetical protein Hbor_04840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.11   12.4   6.8       0.19   11.6   6.8    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   6.8   1.1e-05      0.19       2      25 ..       8      29 ..       7      30 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      lSRR +L   A +a  aal+gc++
  gi|313125262|ref|YP_004035526.1|  8 LSRRRLLA--ASTAGVAALAGCGG 29
                                      8*******..99999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 904.01
//
Query:       gi|313125263|ref|YP_004035527.1|  [L=277]
Description: nh(3)-dependent NAD(+) synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-82  275.4   0.0    3.4e-82  275.2   0.0    1.0  1  NAD_synthase   NAD synthase
    4.3e-07   29.0   0.1    0.00019   20.4   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
    0.00064   19.3   0.0     0.0033   17.0   0.0    1.9  2  QueC           Queuosine biosynthesis protein QueC
     0.0011   18.8   0.0     0.0013   18.5   0.0    1.3  1  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
       0.19   11.5   0.0       0.29   10.9   0.0    1.4  1  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.2   0.0   9.4e-86   3.4e-82       3     242 .]      28     269 ..      26     269 .. 0.98

  Alignments for each domain:
  == domain 1  score: 275.2 bits;  conditional E-value: 9.4e-86
                                       HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE- CS
                      NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkti 79 
                                       +++ +f+++ v+ aga+g+vlGlSGG+DS+ +a+la +algken ++l++Ps+v+s+e++ da  +a++l+ie+ ++
  gi|313125263|ref|YP_004035527.1|  28 NHILQFIRDVVDGAGAEGAVLGLSGGIDSTATAYLAAEALGKENLHGLVMPSVVNSDENMSDAERVAQELEIEYDVV 104
                                       67899************************************************************************ PP

                                       --HHHHHHHHHHHHHHH.-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS- CS
                      NAD_synthase  80 dikpivrafeqelkeak.edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaell 155
                                       +i+pi ++f +++ ea+ + +a+gN+  R+R +++y +an++n++vlgTgn+sE+++GyfTkyGD a+d +pi++l+
  gi|313125263|ref|YP_004035527.1| 105 EIQPIAETFFDTFPEAAnDRMAAGNVYVRVRGVLNYFVANHENKIVLGTGNRSEALTGYFTKYGDQAVDCNPIGNLY 181
                                       *************9998789********************************************************* PP

                                       HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHH CS
                      NAD_synthase 156 KtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekiekl 231
                                       K++v++La++++vP+ ++ k PsA++++gqtDe+e+g++Yd+lD iL   v+   s+  ++++ ++  e++ ++++l
  gi|313125263|ref|YP_004035527.1| 182 KQQVRQLAAHVGVPQDLVMKTPSAGMWTGQTDEDEMGMHYDTLDAILAlHVDGPLSKSATMDHIDVTGEQIDRVVEL 258
                                       ************************************************779999999******************** PP

                                       HHHTGGGGSSS CS
                      NAD_synthase 232 vkksehKrklp 242
                                       +++s+hKr++p
  gi|313125263|ref|YP_004035527.1| 259 YEQSAHKRQMP 269
                                       *********98 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.3e-08   0.00019       4      71 ..      47     107 ..      45     130 .. 0.84
   2 !    7.0   0.0   0.00061       2.2     167     187 ..     176     198 ..     111     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.3e-08
                     tRNA_Me_trans   4 vvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfe 71 
                                       v +lSgG+DS+ +a+l +e+    ++ g+++  + +         ++e+++daerva++l+i+++vv+++
  gi|313125263|ref|YP_004035527.1|  47 VLGLSGGIDSTATAYLAAEALgkENLHGLVMPSVVN---------SDENMSDAERVAQELEIEYDVVEIQ 107
                                       579**************9986446788888887766.........456679***************9976 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00061
                     tRNA_Me_trans 167 PlgeltKeevrkiAkeagla..v 187
                                       P+g+l K++vr++A++ g++  +
  gi|313125263|ref|YP_004035527.1| 176 PIGNLYKQQVRQLAAHVGVPqdL 198
                                       ***************99987444 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.1e-07    0.0033       2      65 ..      46     110 ..      45     153 .. 0.87
   2 ?   -0.1   0.0      0.15   5.5e+02     156     178 ..     175     197 ..     161     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.1e-07
                                       EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGG CS
                              QueC   2 avvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildldllk 65 
                                       av+ lSGG+DSt+ ++la ++   ++++ l +    + +++++ a+++a+el++ e  +++++ ++
  gi|313125263|ref|YP_004035527.1|  46 AVLGLSGGIDSTATAYLAAEALgkENLHGLVMPSVVNSDENMSDAERVAQELEI-EYDVVEIQPIA 110
                                       8999**********99999886557799999999999*****************.99999998665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.15
                                       -TTTT--HHHHHHHHHHTTHHHH CS
                              QueC 156 aPlidlsKaeivklgkelgvple 178
                                        P+ +l K+++ +l++++gvp +
  gi|313125263|ref|YP_004035527.1| 175 NPIGNLYKQQVRQLAAHVGVPQD 197
                                       5999999*******999998865 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.7e-07    0.0013      24      93 ..      50     122 ..      45     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.7e-07
                      Asn_synthase  24 LSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgte..htelvlteeelldalpdviy 93 
                                       LSGG+DS++ a+laa+ +  ++l+   +     +++ ++ a++va++l++e   +e++  +e ++d++p+++ 
  gi|313125263|ref|YP_004035527.1|  50 LSGGIDSTATAYLAAEALGkENLHGLVMPSVVNSDENMSDAERVAQELEIEydVVEIQPIAETFFDTFPEAAN 122
                                       9***************98777888888777558889999***********94445666667888888888876 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     8e-05      0.29       3      63 ..      47     103 ..      45     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8e-05
                                       EEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEE CS
                        ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklniklei 63 
                                       ++++SgG+DS+a  +l+a+   k+++  lv+  v      +s+e++   ++++++l+i++ +
  gi|313125263|ref|YP_004035527.1|  47 VLGLSGGIDSTATAYLAAEALGKENLhGLVMPSV-----VNSDENMSDAERVAQELEIEYDV 103
                                       799*************999877666533433333.....23444444444455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1645.34
//
Query:       gi|313125264|ref|YP_004035528.1|  [L=241]
Description: enoyl-CoA hydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-42  145.5   0.0    2.1e-42  145.2   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
      5e-26   92.0   0.0    5.8e-26   91.8   0.0    1.0  1  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.041   14.4   1.5      0.083   13.4   1.5    1.6  1  MccV      Microcin V bacteriocin


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.2   0.0   3.5e-46   2.1e-42       6     221 ..      10     216 ..       5     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 3.5e-46
                                       EEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHH CS
                             ECH_1   6 vaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwt 82 
                                       v v++++rPe  Nal ++ l+El++a  +++ + +  ++ L G ++ F+aGadl  + e   a+ + + ++ ++  +
  gi|313125264|ref|YP_004035528.1|  10 VRVVTIDRPERRNALRPTDLDELAAAVTDADSN-ETPVIYLRGAGGHFCAGADLDSVSEL--ADPEAFAQKGQQVAN 83 
                                       889****************************99.99*********************996..99999********** PP

                                       HHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EE CS
                             ECH_1  83 klytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkki 159
                                        + +   +v+a + Gaa gGG+e+alacD+++a  +a f+ + + +Gl+ + ggt +l+r+vG+ +A+ i+l g+ +
  gi|313125264|ref|YP_004035528.1|  84 TIADASAVVVAGIDGAARGGGVEMALACDVRVATPDATFAEPGVEFGLFGAWGGTVRLPRIVGEGEAMDIALSGRVV 160
                                       ***************************************************************************** PP

                                       EHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             ECH_1 160 saqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaea 221
                                        a+ea ++Glv++vv      e  + +a ++a++ ++alr +k  l+ +++d+  e  eaea
  gi|313125264|ref|YP_004035528.1| 161 DAAEARRIGLVSRVV------EDPRTVADEIASNRSDALRVVKRRLRDDADDKARERAEAEA 216
                                       ************987......6678999**********************977777666664 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   9.7e-30   5.8e-26       1     211 [.      10     212 ..      10     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 9.7e-30
                                       .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHH CS
                             ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeY 77 
                                       v+v+t++rp+  NaL  + +++l++a+++ ++++e+ +++l+gag   fCAG D+ ++ e a+ +     +f ++  
  gi|313125264|ref|YP_004035528.1|  10 VRVVTIDRPERRNALRPTDLDELAAAVTD-ADSNETPVIYLRGAG-GHFCAGADLDSVSELADPE-----AFAQKGQ 79 
                                       689*************************9.5788899******99.79***********998883.....4999*** PP

                                       HHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH CS
                             ECH_2  78 klnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalT 153
                                       ++ ++ia+ +  vva +dG + GgGv +++ + +rv+t +++fA P ++ Glf   Gg+  L+r+ g   ++ +al+
  gi|313125264|ref|YP_004035528.1|  80 QVANTIADASAVVVAGIDGAARGGGVEMALACDVRVATPDATFAEPGVEFGLFGAWGGTVRLPRIVGeGEAMDIALS 156
                                       ****************************************************************977467999**** PP

                                       ---B-HHHHHHTTS--EE--GGGHHHHHHHHHTT........--------......-- CS
                             ECH_2 154 GarlkgadalaaglathyvpseklealeeaLaelessdeeaveevleelaeeaeeeee 211
                                       G+ +++a+a  +gl + +v++ +  ++++++a+ +s++ + v++ l++ a+++++e+ 
  gi|313125264|ref|YP_004035528.1| 157 GRVVDAAEARRIGLVSRVVEDPR--TVADEIASNRSDALRVVKRRLRDDADDKARERA 212
                                       *******************8875..788999997666666666666655544444333 PP

>> MccV  Microcin V bacteriocin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.5   1.4e-05     0.083      17      64 ..      75     122 ..      49     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                              MccV  17 ddsgrdiakgigaaagtfvaGaiGaivggivaga.vydvastktpdaal 64 
                                        ++g+++a++i+ a++ +vaG  Ga+ gg v  a + dv   +tpda +
  gi|313125264|ref|YP_004035528.1|  75 AQKGQQVANTIADASAVVVAGIDGAARGGGVEMAlACDV-RVATPDATF 122
                                       56899********************99886654404444.445666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1536.71
//
Query:       gi|313125265|ref|YP_004035529.1|  [L=226]
Description: hypothetical protein Hbor_04880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.8   0.3       0.12   12.7   0.3    1.5  1  DIMCO_N   Dinitrogenase iron-molybdenum cofactor, N-terminal


Domain annotation for each model (and alignments):
>> DIMCO_N  Dinitrogenase iron-molybdenum cofactor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   6.7e-06      0.12      12      60 ..      10      61 ..       2      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.7e-06
                           DIMCO_N 12 Aar.aLpgvdvaqLlevLqerlg.eplteekLakltvtdLktala.sadgee 60
                                      Aar aL+++++ +L evL +rl+   +t  +L+ l ++ Lk ++  +adg  
  gi|313125265|ref|YP_004035529.1| 10 AAReALDDIEPDRLREVLFDRLDeTSMTPGALTILSARALKPGVDaDADGLA 61
                                      66637*****************94579**************98855555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1411.00
//
Query:       gi|313125266|ref|YP_004035530.1|  [L=197]
Description: membrane-bound metal-dependent hydrolase (duf457) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.47    9.7  13.6        5.6    6.2  13.7    2.2  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  13.7   0.00031       5.6      12     114 ..       5      89 ..       1     166 [. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00031
                              YdjM  12 alglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllflallalvlllllr 88 
                                       ++++++ +  +a++   +la+a+lg+l+PD+D            l++      gHR   H  +   +la+ +l++++
  gi|313125266|ref|YP_004035530.1|   5 VVAVVFPESAAATTPVPVLAAAALGGLFPDFD------------LYA------GHRKTLHFPVYFSGLAVPALVAAA 63 
                                       333333333344434899**************............444......6********999999999999999 PP

                              YdjM  89 lfgrsalrlglllllg.vlsHlllDll 114
                                       l   + l+l ++l+l+ +++H + D++
  gi|313125266|ref|YP_004035530.1|  64 LSPST-LTLSVALFLAaAALHSVMDAF 89 
                                       99988.88888855554999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1197.52
//
Query:       gi|313125267|ref|YP_004035531.1|  [L=228]
Description: hypothetical protein Hbor_04910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   16.0   3.8      0.012   16.0   3.8    2.9  3  DUF4233   Protein of unknown function (DUF4233)
      0.015   15.1   5.3      0.074   12.8   5.3    1.9  1  DUF2238   Predicted membrane protein (DUF2238)


Domain annotation for each model (and alignments):
>> DUF4233  Protein of unknown function (DUF4233)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   3.8   1.3e-06     0.012      17      90 ..      38     107 ..      26     116 .. 0.80
   2 ?   -0.8   1.1      0.21   1.9e+03      75      90 ..     141     157 ..     109     171 .. 0.55
   3 ?    1.4   0.2     0.046   4.1e+02      18      45 ..     177     204 ..     162     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                           DUF4233  17 LallvaiglrdtepatvlsvggvlavallllagllrrpwglalglvlQvlliaagfvvpamfvvgvvFaavWvy 90 
                                        a + ++g+ +   ++ +++ +++a+a+  l +ll+r wg+ l   l +++  ++++++a+++vg  +  vW+y
  gi|313125267|ref|YP_004035531.1|  38 IAGILGFGIAKL--NASITINAAAALAVTYLPALLSRDWGIRLSPSLTLWVT-TAVLLHAVGMVGP-YSEVWWY 107
                                       444556777444..666677778888888999******************99.999********95.8889998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.21
                           DUF4233  75 p.amfvvgvvFaavWvy 90 
                                       p  mfv  + F +++ +
  gi|313125267|ref|YP_004035531.1| 141 PrFMFVYILTFTLAFGV 157
                                       34444444444333333 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.046
                           DUF4233  18 allvaiglrdtepatvlsvggvlavall 45 
                                       a+lv++gl+dt  ++++  +g+++val+
  gi|313125267|ref|YP_004035531.1| 177 AVLVQYGLHDTIVDLMFDTVGAAIVALF 204
                                       6788999999967777777776666665 PP

>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.3   8.3e-06     0.074      59     139 ..     107     193 ..      61     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.3e-06
                           DUF2238  59 YDrlvHfaqGlllalvvrelllrkkkl.......rkwllllavlvvlaisalYEliEwlvalllggeaaeaflGtqG 128
                                       YD + H +  +l+a v +  ++   k+        +++++ +++++la++ l+E++E+++ l ++  + ea l ++G
  gi|313125267|ref|YP_004035531.1| 107 YDHVTHTLSAMLVAAVGYATARAVDKYsdsvflpPRFMFVYILTFTLAFGVLWEVLEFFARLSAEFFGIEAVLVQYG 183
                                       99999999999988887777666666566678866699999*******************99999899999999999 PP

                           DUF2238 129 diWDaqkDmll 139
                                        + D+  D+++
  gi|313125267|ref|YP_004035531.1| 184 -LHDTIVDLMF 193
                                       .9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.83
# Mc/sec: 827.33
//
Query:       gi|313125268|ref|YP_004035532.1|  [L=219]
Description: k+ transporter, NAD-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-27   94.2   0.3    8.8e-27   93.7   0.3    1.2  1  TrkA_N           TrkA-N domain
    4.1e-11   42.5   1.0    6.1e-11   42.0   0.3    1.7  1  TrkA_C           TrkA-C domain
    2.8e-10   40.1   0.2    4.9e-10   39.3   0.2    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    6.2e-07   29.2   0.1    9.6e-07   28.6   0.1    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
    7.3e-07   29.6   0.2    1.1e-06   29.0   0.2    1.3  1  NAD_binding_7    Putative NAD(P)-binding
    4.1e-06   26.5   0.1    6.4e-06   25.8   0.1    1.3  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    7.1e-05   22.8   0.2    0.00011   22.1   0.2    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      8e-05   22.6   0.1    0.00013   22.0   0.1    1.3  1  NAD_binding_10   NAD(P)H-binding
    0.00011   22.4   0.3    0.00017   21.9   0.3    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00023   20.6   0.2    0.00037   19.9   0.2    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00029   21.0   0.0    0.00071   19.8   0.0    1.6  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0004   19.7   0.1    0.00047   19.5   0.1    1.2  1  FAD_binding_3    FAD binding domain
    0.00061   20.3   1.0     0.0015   19.0   1.0    1.8  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0025   17.3   0.1     0.0034   16.9   0.1    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0028   17.7   0.1     0.0046   17.0   0.1    1.4  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
     0.0041   16.4   0.9     0.0061   15.9   0.9    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0043   16.3   0.2     0.0043   16.3   0.2    1.4  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0046   17.5   0.1     0.0077   16.8   0.1    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.017   15.1   0.0    1.2  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.012   15.2   0.1      0.023   14.3   0.1    1.4  1  DAO              FAD dependent oxidoreductase
      0.016   14.8   0.1      0.022   14.3   0.1    1.3  1  NmrA             NmrA-like family
      0.018   15.5   0.0      0.027   14.9   0.0    1.4  1  XdhC_C           XdhC Rossmann domain
      0.066   13.3   0.1      0.097   12.7   0.1    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.081   12.5   0.1       0.11   12.0   0.1    1.2  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
       0.11   12.4   0.3        3.5    7.6   0.3    2.3  1  ADH_zinc_N       Zinc-binding dehydrogenase
       0.12   13.2   0.1       0.18   12.6   0.1    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
       0.21   10.3   0.0       0.28    9.8   0.0    1.1  1  HI0933_like      HI0933-like protein
       0.73    9.8   4.9        5.8    6.9   1.0    2.9  3  DUF2118          Uncharacterized protein conserved in archaea


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.3   1.4e-29   8.8e-27       1     116 []       3     118 ..       3     118 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.4e-29
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddean 76 
                                       ++i+G+GrvG + a  L+e g+ +v+v+d+de++ve++++eg+evv gd+++e vL++agie+ada+  +tgd  +n
  gi|313125268|ref|YP_004035532.1|   3 VVIVGYGRVGARTALVLREeGH-EVTVVDNDEQKVERIEKEGFEVVEGDGSNETVLRRAGIEDADAIGGLTGDPNVN 78 
                                       79*****************555.7***************************************************** PP

                                       HHHHHHHHHHTSSSEEEEEESSGGGHHHHHH..HTTSEEEEH CS
                            TrkA_N  77 ilavllakelnpkkkiiaraqdpehaellkk..lgadvvisp 116
                                        +a+++ ke ++ ++ + r++++ ++e++++    +d+vi+p
  gi|313125268|ref|YP_004035532.1|  79 FAACMIGKE-FG-CRAVMRVSEDYRKEIYERyaDDVDEVIYP 118
                                       ********8.55.689*************9976779999997 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.3   9.5e-14   6.1e-11       2      69 ..     148     215 ..     147     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 9.5e-14
                                       EEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                        +v++p+++p+vG+++++++l     ++ a+ R+ + ++ip + t+ e+GD+l +++++++l+++r+ l
  gi|313125268|ref|YP_004035532.1| 148 SRVVIPEDAPVVGQKVSDIDLDS-VGRIYAHGRKrEPMTIPLPGTKVEAGDQLALLTEKDGLDAVRRTL 215
                                       699********************.999999966668*****************************9865 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.2   7.7e-13   4.9e-10       1      50 [.       1      50 [.       1      64 [. 0.92

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 7.7e-13
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TT CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepg 50
                                      mk++++G G vG+ ta+vl e ghev++vD+de+kv+ ++++ ++++e +
  gi|313125268|ref|YP_004035532.1|  1 MKVVIVGYGRVGARTALVLREEGHEVTVVDNDEQKVERIEKEGFEVVEGD 50
                                      89*******************************************99965 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   1.5e-09   9.6e-07       1      56 [.       3      60 ..       3      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.5e-09
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppe 56
                                      ++i+G G +G   a  L + g++vt++++++ ++e+++k+G+++ + +  +e+++ ++
  gi|313125268|ref|YP_004035532.1|  3 VVIVGYGRVGARTALVLREEGHEVTVVDNDEqKVERIEKEGFEVVEGDgSNETVLRRA 60
                                      68******************************************99997555555554 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.2   1.7e-09   1.1e-06       9      80 ..       2      83 ..       1     104 [. 0.74

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.7e-09
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeel...ekd...........legadlviaatddre 73
                                      kv++vG G+v+ar +  l e+g +vtvv+++   e ++  ++++e +   e+d           +e+ad +   t d++
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDND---E-QKVERIEKEGFevvEGDgsnetvlrragIEDADAIGGLTGDPN 76
                                      79*****************************...3.2223333333322233344445555555999**9999999999 PP

                     NAD_binding_7 74 lneriae 80
                                      +n + + 
  gi|313125268|ref|YP_004035532.1| 77 VNFAACM 83
                                      9977665 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   9.9e-09   6.4e-06       6      53 ..       2      48 ..       1      64 [. 0.90

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9.9e-09
                                      -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEE CS
                              IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevlt 53
                                      k++++GyG  G   al lr+ g +v+v  ++++ +v++ ++egfev++
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDEQ-KVERIEKEGFEVVE 48
                                      89************************9877666.9***********97 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   1.8e-07   0.00011       1      41 [.       2      42 ..       2      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.8e-07
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalek 41
                                      kv ++G G +Ga  a v+ ++g+eV++vd +e+++e+ +++
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDEQKVERIEKE 42
                                      699********************************998776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1     2e-07   0.00013       4      64 ..       9      68 ..       7     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2e-07
                                      SHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEE CS
                    NAD_binding_10  4 GkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaV 64
                                      G+vG + +  l ++ ghevt++  +++k++++e +eg evvegd +++  l++a +++ada+
  gi|313125268|ref|YP_004035532.1|  9 GRVGARTALVLREE-GHEVTVVDNDEQKVERIE-KEGFEVVEGDGSNETVLRRAgIEDADAI 68
                                      99*****9999999.6******999*****998.7***************999867999997 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.3   2.6e-07   0.00017       1      71 [.       3      66 ..       3      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.6e-07
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSS CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegd 71
                                      v+i+G+G+vG  +a +l ++++   e+tv+d +++k+e++     ++ fe ++ d +n++  L ++ ++++d
  gi|313125268|ref|YP_004035532.1|  3 VVIVGYGRVGARTALVLREEGH---EVTVVDNDEQKVERI----EKEGFEVVEGDGSNETV-LRRAgIEDAD 66
                                      89************99999987...6**********9999....46788888888888887.5444477666 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   5.7e-07   0.00037      38      84 ..       2      48 ..       1      60 [. 0.91

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.7e-07
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECS CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvs 84
                                      +v i+G+Gr+G ++a +l++ g +v+++d  ++k e+ e++g+e+v+
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDEQKVERIEKEGFEVVE 48
                                      799******************************99999999998876 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-06   0.00071       2      47 ..       3      48 ..       2      65 .. 0.90
   2 ?   -2.1   0.0         6   3.8e+03     129     139 ..     128     138 ..      95     160 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-S CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaae 47
                                      + ++G G  G+  al l ++g++v+v++ +++kve++ +eg++++e
  gi|313125268|ref|YP_004035532.1|  3 VVIVGYGRVGARTALVLREEGHEVTVVDNDEQKVERIEKEGFEVVE 48
                                      6789************************************987765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6
                                       EEEEEE-HHHH CS
                     NAD_binding_2 129 simvGGseeaf 139
                                       + ++GG+ +a+
  gi|313125268|ref|YP_004035532.1| 128 TALLGGNFNAI 138
                                       33344443333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   7.3e-07   0.00047       3      39 ..       2      38 ..       1     109 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.3e-07
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                      +V+IVG G +G+ +al+L+e G +v++v+  +++v+ 
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDEQKVER 38
                                      7*****************************9998865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.0   2.4e-06    0.0015       1      35 [.       2      36 ..       2      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.4e-06
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      kvv+vG G +g   A +l+e g++Vtvv++ ++  
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDEQKV 36
                                      79***************************988755 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   5.3e-06    0.0034       5      68 ..       7      68 ..       3      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.3e-06
                                      TTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEE CS
                         Epimerase  5 GatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdav 68
                                      G  G +G+ ++  l e+g+ev+++d+++++ ++ ++e  e+ve+d  +++ l+r+  e ++da+
  gi|313125268|ref|YP_004035532.1|  7 GY-GRVGARTALVLREEGHEVTVVDNDEQKVERIEKEGFEVVEGDGSNETVLRRAGIE-DADAI 68
                                      44.99**********************888888888888***********99998764.66665 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   7.3e-06    0.0046      25      71 ..       2      48 ..       1      64 [. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.3e-06
                                      EEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE-- CS
                     AdoHcyase_NAD 25 vavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvt 71
                                      ++v++GyG vG  +a  l++ G  v+v + d     +   eGfevv+
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDEQKVERIEKEGFEVVE 48
                                      589*****************************9999999*****986 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.9   9.6e-06    0.0061      30      93 ..       2      66 ..       1      73 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.6e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHH.HHH-S CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaea.vkead 93
                                      kv+++G G +G   + + ++ g +Vtv+D ++++ e++e+ g ++ve   s+e  l++a +++ad
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDEQKVERIEKEGFEVVEGDGSNETVLRRAgIEDAD 66
                                      8***************************************9999998888887777654355555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   6.7e-06    0.0043       2      33 ..       2      33 ..       1     209 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.7e-06
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      +vv++G G  G ++al l++ g++vt+v+ ++
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDE 33
                                      89**************************6333 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.2e-05    0.0077       1      46 [.       2      43 ..       2      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeel 46
                                      k+ i+G+G++g+  a+ l ++g   he++v+ +++++k+e +++e 
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEG---HEVTVV-DNDEQKVERIEKEG 43
                                      68899*****************...****88.********999874 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.7e-05     0.017       1      41 [.       2      42 ..       2      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeinee 41
                                      k+ ++G G  G   A vl e+ghev++  ++e+ +e+i++e
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDEQKVERIEKE 42
                                      799***********************************976 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.7e-05     0.023       1      29 [.       2      32 ..       2      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      +vvi+G G +G+ tA+ L ++g  Vt+++ +
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGheVTVVDND 32
                                      59****************88899******88 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.4e-05     0.022       3      67 ..       4      67 ..       3      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                                      ESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SE CS
                              NmrA  3 viGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdv 67
                                      vi + Gr G+  + +l ++gh+v ++  d ++++++ ++++G e+v+gd  ++ +l++a ++++d+
  gi|313125268|ref|YP_004035532.1|  4 VIVGYGRVGARTALVLREEGHEVTVV--DNDEQKVERIEKEGFEVVEGDGSNETVLRRAgIEDADA 67
                                      77788*****************9876..888999**********************9885777776 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.3e-05     0.027       1      50 [.       3      71 ..       3     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-05
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.......................-EEEE- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.......................tavvvl 50
                                      +vi+G g v++  a ++++ g +vtvvd++e+  ++er+++  e                       +a+  l
  gi|313125268|ref|YP_004035532.1|  3 VVIVGYGRVGARTALVLREEGHEVTVVDNDEQ--KVERIEK--EgfevvegdgsnetvlrragiedaDAIGGL 71
                                      69*****************************6..4455542..122334445544444444444444444444 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00015     0.097      14      55 ..       2      42 ..       1      67 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHH CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaee 55
                                      kv+++G G+++ ++a  L ++g + v+v+  + ++++++ +e
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHE-VTVVDNDEQKVERIEKE 42
                                      89*****************99998.***********999876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00018      0.11       6      59 ..      11      60 ..       9      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                      HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHH CS
                      adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqveal 59
                                      +G+ +A  l eeG ev ++d +e++   ve++++e g ev+e D ++e+ ++++
  gi|313125268|ref|YP_004035532.1| 11 VGARTALVLREEGHEVTVVDNDEQK---VERIEKE-GFEVVEGDGSNETVLRRA 60
                                      5899*******************99...9999987.889999999999887766 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3    0.0054       3.5       9      41 ..      18      50 ..      11     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0054
                                      HHHHTT-EEEEEESSHHHHHHHHHTTESEEEET CS
                        ADH_zinc_N  9 lAkalGaeviavdsseeklelakklGadeviny 41
                                      +++  G ev++vd +e+k+e  +k G ++v   
  gi|313125268|ref|YP_004035532.1| 18 VLREEGHEVTVVDNDEQKVERIEKEGFEVVEGD 50
                                      556668899999999999999999988777555 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00029      0.18       1      47 [.       1      43 [.       1      80 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00029
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTT CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfg 47
                                      ++v+i+G+G++g + +  l+e+  ++ev+ ++d+d+++ e++ e+ g
  gi|313125268|ref|YP_004035532.1|  1 MKVVIVGYGRVGARTALVLREE--GHEVT-VVDNDEQKVERI-EKEG 43
                                      69*************9677666..66666.89****999998.4444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00043      0.28       2      39 ..       2      39 ..       1      44 [. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00043
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKi 39
                                      +v+++G G  G  +A+ ++++g++V+++++ ++  ++i
  gi|313125268|ref|YP_004035532.1|  2 KVVIVGYGRVGARTALVLREEGHEVTVVDNDEQKVERI 39
                                      79****************************99877776 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.0     0.009       5.8      69     107 ..       9      50 ..       1      62 [. 0.78
   2 ?    0.8   0.1      0.67   4.3e+02      38      55 ..      98     115 ..      77     120 .. 0.76
   3 ?    2.1   0.0      0.26   1.7e+02      97     117 ..     187     207 ..     169     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.009
                           DUF2118  69 p..derklill.kkGdklklipvegvkvtlivdvGdrveegd 107
                                          + r++++l ++G ++  ++ +  kv  i ++G +v egd
  gi|313125268|ref|YP_004035532.1|   9 GrvGARTALVLrEEGHEVTVVDNDEQKVERIEKEGFEVVEGD 50 
                                       34456666666258***************************9 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.67
                           DUF2118  38 klkgkvvYeelldeivdv 55 
                                       + + k++Ye+ +d++++v
  gi|313125268|ref|YP_004035532.1|  98 EDYRKEIYERYADDVDEV 115
                                       345689999988888776 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.26
                           DUF2118  97 vdvGdrveegdtlaavttrkg 117
                                          G++ve gd+la +t + g
  gi|313125268|ref|YP_004035532.1| 187 PLPGTKVEAGDQLALLTEKDG 207
                                       4579**********9886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1210.48
//
Query:       gi|313125269|ref|YP_004035533.1|  [L=286]
Description: dihydrodipicolinate synthase/n-acetylneuraminate lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-62  208.9   0.0      7e-62  208.8   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.8   0.0   3.9e-66     7e-62       4     287 ..       3     284 ..       1     286 [] 0.96

  Alignments for each domain:
  == domain 1  score: 208.8 bits;  conditional E-value: 3.9e-66
                                       EEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---S CS
                             DHDPS   4 giitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsn 80 
                                       gi ++lvtpf  dg +d+ alr l+ +   +gvd lv +G+  E++++  e ++ ++e+++  a+ ++pv+ag+Gs+
  gi|313125269|ref|YP_004035533.1|   3 GIGPPLVTPFTADGLIDETALRDLVSWVESRGVDFLVPCGSNSEAELMTAEGRARVIEVVA--AEASVPVLAGTGSP 77 
                                       67789*****************************************************996..5668********** PP

                                       SHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTE CS
                             DHDPS  81 stseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaeleni 157
                                         +e  ++++ a++aGad++l+vtP+Y++     l+ +++  + + + p+ lY+vp+ t ++ls+ +v++La+ +ni
  gi|313125269|ref|YP_004035533.1|  78 GYEETRQATAAAADAGADAALVVTPFYYPHDDTALEAYYRDLADEAEIPIYLYSVPAFTDVKLSVSVVEALATHPNI 154
                                       *******************************************9999****************************** PP

                                       EEEEE-SS-CTHHH.HHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHH CS
                             DHDPS 158 vgvKeavgdleevi.kikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaeln 233
                                       +g+K+ +gd+e+ + +++ +++ d+ ++ G   +l +al +GadG + + +n+a+e   ++++a +eGd+  a+e n
  gi|313125269|ref|YP_004035533.1| 155 AGMKDSSGDIETFVrERRLTADADFDLLVGSGSMLSHALDIGADGGVLALANVAPEATTAIYDAHREGDVTAARERN 231
                                       **********8766156667889****************************************************** PP

                                       HHHHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHH CS
                             DHDPS 234 ekllplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleallk 287
                                       e l +l+ ++  +  + ++k+a++  G +v++ +r+P  p++++ +eele+l+ 
  gi|313125269|ref|YP_004035533.1| 232 EALVELNRAVTTTHGIPGLKAAMRARGAPVGH-VRRPHQPVSDDTREELERLVA 284
                                       ********************************.****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1759.15
//
Query:       gi|313125270|ref|YP_004035534.1|  [L=235]
Description: ModE family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-10   40.3   1.8    5.5e-10   39.0   1.8    1.7  1  HTH_1          Bacterial regulatory helix-turn-helix protein,
    2.4e-10   40.5   1.3    2.4e-10   40.5   1.3    2.7  2  TOBE           TOBE domain
    0.00049   20.2   1.0    0.00049   20.2   1.0    2.5  2  TOBE_2         TOBE domain
  ------ inclusion threshold ------
      0.043   13.4   0.3       0.12   12.0   0.3    1.8  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.49   10.3   3.1        2.7    7.9   3.1    2.4  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   1.8   1.5e-13   5.5e-10       4      60 .]      21      81 ..      19      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.5e-13
                                      HHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEE.....SSSEEEE-HHHH CS
                             HTH_1  4 lrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeR.....tgrglrLTeaGe 60
                                       rl+ ++ae+gs+++AAe Lg s +   +++++LE++lg pL+eR     +g+g +LT+a++
  gi|313125270|ref|YP_004035534.1| 21 ARLLATIAETGSVSGAAESLGRSRARCLARLRELEDALG-PLVERrrggsDGGGSELTAAAR 81
                                      599***********************************9.9***8555544455*****986 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.6      0.14     5e+02      25      63 ..     119     151 ..     101     152 .. 0.69
   2 !   40.5   1.3   6.8e-14   2.4e-10       1      62 [.     164     225 ..     164     227 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                              TOBE  25 vdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvh 63 
                                       v++++g+ + A+ t +s++     +++ V++++ a +v 
  gi|313125270|ref|YP_004035534.1| 119 VETDAGT-IRAVAT-ESVRT----VEKAVTVSVRADAVT 151
                                       4455566.788887.77777....788888888888875 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 6.8e-14
                              TOBE   1 ssarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakv 62 
                                       +sarN+l gtV+ v  +++ ++V v +g  ++L A vt +s+++L L+pG  V+a+ ka+++
  gi|313125270|ref|YP_004035534.1| 164 TSARNRLSGTVEGVKRGDAVATVSVNVGLSTPLRAFVTVESVRRLSLEPGTSVVASWKATAT 225
                                       7**********************************************************986 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       0.3   1.1e+03      18      27 ..     104     113 ..      88     142 .. 0.65
   2 !   20.2   1.0   1.4e-07   0.00049       1      73 [.     143     225 ..     143     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.3
                            TOBE_2  18 glsGtVedve 27 
                                        lsG V++ve
  gi|313125270|ref|YP_004035534.1| 104 VLSGIVTHVE 113
                                       6677777765 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.4e-07
                            TOBE_2   1 laiRPEklrla.........aagganglsGtVedveylGsstryv.velaggqlvvvrqpnadr.dsalapGdtVel 66 
                                       +++R ++++l+         a +++n+lsGtVe v  +G+ + +v v ++  + +++ + +++  +  l+pG+ V  
  gi|313125270|ref|YP_004035534.1| 143 VSVRADAVTLHdpsdtpaesATSARNRLSGTVEGVK-RGDAVATVsVNVGLSTPLRAFVTVESVrRLSLEPGTSVVA 218
                                       79**********99888764333358*******996.899998888*******999999999987899********* PP

                            TOBE_2  67 swdpdda 73 
                                       sw++ ++
  gi|313125270|ref|YP_004035534.1| 219 SWKATAT 225
                                       **99775 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   3.3e-05      0.12      24      43 ..      37      56 ..      16      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.3e-05
                            HTH_24 24 AerlglSpstvnrrlkrLee 43
                                      Ae lg S++ +++rl++Le+
  gi|313125270|ref|YP_004035534.1| 37 AESLGRSRARCLARLRELED 56
                                      99*****************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.1   0.00075       2.7       2      42 .]      17      55 ..      16      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00075
                     HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      D+ D ++L+ + e ++ s a  Ae +G S++++l+R+r Le
  gi|313125270|ref|YP_004035534.1| 17 DRSDARLLATIAETGSVSGA--AESLGRSRARCLARLRELE 55
                                      66777777777777766665..9****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1551.86
//
Query:       gi|313125271|ref|YP_004035535.1|  [L=275]
Description: polar amino acid ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-32  112.6   0.0    2.7e-32  112.2   0.0    1.2  1  ABC_tran     ABC transporter
    2.5e-10   40.7   0.0    0.00053   19.9   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    7.5e-05   23.2   0.9    0.00014   22.2   0.9    1.6  1  AAA_16       AAA ATPase domain
    0.00017   22.2   0.1       0.01   16.3   0.0    2.2  2  AAA_18       AAA domain
    0.00024   20.6   0.0       0.11   11.9   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00045   19.9   0.6    0.00084   19.0   0.6    1.5  1  AAA_25       AAA domain
     0.0007   19.3   0.0     0.0017   18.0   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
     0.0017   18.7   0.0     0.0026   18.0   0.0    1.5  1  AAA_22       AAA domain
     0.0023   17.7   1.6      0.025   14.3   1.6    2.1  1  AAA_30       AAA domain
     0.0023   18.1   0.1     0.0037   17.4   0.1    1.6  1  AAA_33       AAA domain
     0.0072   16.7   0.0      0.014   15.7   0.0    1.5  1  AAA_19       AAA domain
     0.0075   16.5   0.1      0.017   15.4   0.0    1.7  1  AAA_28       AAA domain
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.029   14.0   0.0    1.5  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.018   15.0   0.0      0.043   13.7   0.0    1.6  2  NACHT        NACHT domain
      0.019   14.8   0.0       0.15   12.0   0.0    2.1  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.023   14.9   0.1       0.73   10.1   0.1    2.5  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.034   14.0   0.0      0.067   13.1   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.035   13.2   0.0      0.057   12.5   0.0    1.4  1  T2SSE        Type II/IV secretion system protein
      0.049   14.1   0.0        0.5   10.8   0.0    2.1  2  AAA          ATPase family associated with various cellular a
      0.071   13.0   0.0        0.1   12.5   0.0    1.2  1  Rad17        Rad17 P-loop domain
       0.09   13.3   0.0       0.14   12.7   0.0    1.2  1  AAA_23       AAA domain
      0.094   12.6   0.0       0.15   11.9   0.0    1.2  1  ATPase_2     ATPase domain predominantly from Archaea
       0.12   11.6   0.0       0.28   10.3   0.0    1.6  2  NB-ARC       NB-ARC domain
       0.14   12.1   0.1       0.25   11.3   0.0    1.6  1  NTPase_1     NTPase
       0.16   11.7   0.0       0.26   11.0   0.0    1.3  1  AAA_24       AAA domain
       0.18   10.5   0.0        7.8    5.2   0.0    2.4  3  ABC_ATPase   Predicted ATPase of the ABC class
       0.22   11.0   0.0       0.66    9.4   0.0    1.7  2  Pox_A32      Poxvirus A32 protein
       0.22   11.5   0.0       0.46   10.5   0.0    1.5  1  AAA_14       AAA domain
       0.26    9.9   0.0        1.1    7.8   0.0    1.8  2  AAA_13       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.0   4.3e-35   2.7e-32       2     137 .]      39     198 ..      38     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 4.3e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpelt 75 
                                       ++vsl +++ge++a+vG++G+GK+tLl+lla l++p+eG ++ +g+++ e   +e+ ++r+++g++ q+ +lf+ + 
  gi|313125271|ref|YP_004035535.1|  39 SDVSLAVEPGEVLAVVGPSGSGKTTLLRLLACLESPAEGVVTANGRNVGEmseEERLHVRRRLGMVLQHRCLFSAT- 114
                                       68*********************************************9999989999*****************99. PP

                                       HHHH..........................HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHH CS
                                       xxxx..........................xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren..........................esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalaral 123
                                       v++n                          e       + +al+++g+++++d+++    +sLSgG+ qrva+aral
  gi|313125271|ref|YP_004035535.1| 115 VASNaayglrvratwneriraairgflgtaE---TplaAVDALETVGMVDKQDRHA----ASLSGGEAQRVAIARAL 184
                                       99999******99887777666666665444...1555999*********999999....***************** PP

                                       HHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxx RF
                          ABC_tran 124 lkkpkllllDEpta 137
                                       + +p++ll+DEpt+
  gi|313125271|ref|YP_004035535.1| 185 APEPDVLLFDEPTS 198
                                       ************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.6e-07   0.00053       3      42 ..      52      88 ..      50      99 .. 0.80
   2 !   19.0   0.0   1.6e-06   0.00099     236     298 ..     169     228 ..     118     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.6e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggi 42
                                      +++Gp gsGK++LL++l +l    + +eg  + +++++g+
  gi|313125271|ref|YP_004035535.1| 52 AVVGPSGSGKTTLLRLLACL---ESPAEGVVTANGRNVGE 88
                                      79******************...77777777777777665 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.6e-06
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +lS G  +  a++ al+  +   ++ll+DEp ++L+P+ ++ + + + +++++g  v l+TH+
  gi|313125271|ref|YP_004035535.1| 169 SLSGGEAQRVAIARALAPEP---DVLLFDEPTSNLDPRNTAIVEKAICDARDRGMGVCLATHD 228
                                       55555555444444555444...***************9999999999999999999999997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.9   2.3e-07   0.00014      24     107 ..      47     156 ..      36     243 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.3e-07
                            AAA_16  24 p.elvllsGesGvGKsslvrellralekd.ggiflrgkcdql.esa.......ipysalaqalareellrqlldeae 90 
                                       p e++ ++G+sG+GK++l+r l+   + + g+++++g+++   + +       +++ +++q     +   + +++  
  gi|313125271|ref|YP_004035535.1|  47 PgEVLAVVGPSGSGKTTLLRLLACLESPAeGVVTANGRNVGEmS-EeerlhvrRRLGMVLQHRCLFSATVASNAAYG 122
                                       44899**************9999533333245558888777631.22343332111222222222233333333344 PP

                            AAA_16  91 saeleawrekleeala.................a 107
                                        + ++ w e++++a++                  
  gi|313125271|ref|YP_004035535.1| 123 LRVRATWNERIRAAIRgflgtaetplaavdaleT 156
                                       4455555555555555555555554444444440 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.7e-05      0.01       3      37 ..      53      95 ..      51     107 .. 0.80
   2 ?    3.8   0.0      0.13        82      78     114 ..     207     239 ..     149     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf.........gvnlrdvakengl 37
                                      + G++G+GKttl + L+ ++ +         g+n++++  e++l
  gi|313125271|ref|YP_004035535.1| 53 VVGPSGSGKTTLLRLLACLE-SpaegvvtanGRNVGEMSEEERL 95
                                      89**************6653.34566688889998888888776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                            AAA_18  78 vidghlaeleseaakdikkvvLtaspeelleRlekRg 114
                                       +++  +++ ++  +     v+L +++ + ++R+++R 
  gi|313125271|ref|YP_004035535.1| 207 IVEKAICDARDRGMG----VCLATHDMQQAQRVSDRT 239
                                       455555554444443....****************95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0057       3.5      26      41 ..      50      65 ..      38      72 .. 0.83
   2 !   11.9   0.0   0.00018      0.11     134     203 ..     167     233 ..      80     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0057
                                      EEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnll 41
                                      + a+vGp GSGK+ ll
  gi|313125271|ref|YP_004035535.1| 50 VLAVVGPSGSGKTTLL 65
                                      679**********987 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00018
                                       TTCS-HHHHHHHHHHHHHHHHCCS--S.EEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpap.lyllDeidaaLDeknvkkvaellkekskn.aQfivislreemle 203
                                         +LSgGe + va+a  +A     p+p + l+De  ++LD +n+++v + +  ++++ + +   +++ ++ +
  gi|313125271|ref|YP_004035535.1| 167 AASLSGGEAQRVAIARALA-----PEPdVLLFDEPTSNLDPRNTAIVEKAICDARDRgMGVCLATHDMQQAQ 233
                                       4489*****9999997766.....44436799*******************988866355555555555544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.6   1.4e-06   0.00084      32     125 ..      47     144 ..      41     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                            AAA_25  32 agelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.........rd 99 
                                        ge+ +++G++g+GKttl+  la+  +   p  g v++ +g+ +    E+ + ++rrRl  v++++         ++
  gi|313125271|ref|YP_004035535.1|  47 PGEVLAVVGPSGSGKTTLLRLLACLES---PAEG-VVTANGRNVGEMSEEERLHVRRRLGMVLQHRclfsatvasNA 119
                                       699***************999988666...4446.556555555555555555***********9988888886533 PP

                            AAA_25 100 darllvldlagv.eslpLfakdrggtl 125
                                         +l+v    ++ e+++ +  ++ gt+
  gi|313125271|ref|YP_004035535.1| 120 AYGLRVRA--TWnERIRAAIRGFLGTA 144
                                       44444443..34356666655555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.8e-06    0.0017      12      39 ..      38      65 ..      34      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.8e-06
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                      f++ ++ +++ ++  ++GpsGsGK+Tll
  gi|313125271|ref|YP_004035535.1| 38 FSDVSLAVEPGEVLAVVGPSGSGKTTLL 65
                                      788889999999***************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.3e-06    0.0026       6      26 ..      49      69 ..      45     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-06
                            AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                       +l+v+G+sG+GKTtllr l+
  gi|313125271|ref|YP_004035535.1| 49 EVLAVVGPSGSGKTTLLRLLA 69
                                      6899**************987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.6     4e-05     0.025      15      45 ..      45      75 ..      41     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaa 45
                                       ++  v +++Gp G+GKtt+l+ l+ +   a
  gi|313125271|ref|YP_004035535.1| 45 VEPGEVLAVVGPSGSGKTTLLRLLACLESPA 75
                                      5566799***************998766655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     6e-06    0.0037       1      33 [.      50      97 ..      50     206 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6e-06
                            AAA_33  1 lvllvGlpGsGKstlaerl.lkklgavllssdt..............l 33
                                      ++ +vG++GsGK+tl++ l + + +a+ + + +              +
  gi|313125271|ref|YP_004035535.1| 50 VLAVVGPSGSGKTTLLRLLaCLESPAEGVVTANgrnvgemseeerlhV 97
                                      6789*************9832333355444444455555555555553 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-05     0.014       9     123 ..      47     209 ..      42     235 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.............atTi 72 
                                       + +vl+v+++ G+GKT++l+   a+l++  +       +v+ +gr + e++e+ + l ++               T+
  gi|313125271|ref|YP_004035535.1|  47 PGEVLAVVGPSGSGKTTLLRLL-ACLESPAE------GVVTANGRNVGEMSEEER-LHVRrrlgmvlqhrclfSATV 115
                                       56899***********998754.45544443......36999********99663.233336776777777775555 PP

                            AAA_19  73 Hrlal....................................ldfddlltealelle.....eaeeekklqeee.lli 107
                                        + a                                     +++ d+++  ++ l      + +  + l  e  +l+
  gi|313125271|ref|YP_004035535.1| 116 ASNAAyglrvratwneriraairgflgtaetplaavdaletVGMVDKQDRHAASLSggeaqRVAIARALAPEPdVLL 192
                                       54444566667777777777777777766677666666666333333333344555665653344444544444777 PP

                            AAA_19 108 vDE.fqdvdelqyrLlk 123
                                        DE ++++d+   ++++
  gi|313125271|ref|YP_004035535.1| 193 FDEpTSNLDPRNTAIVE 209
                                       77755677766666664 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.7e-05     0.017       3      39 ..      52      94 ..      50     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-05
                            AAA_28  3 vitGgestGKTtlleaLa.....argypvv.pEaareileekl 39
                                      +++G++++GKTtll+ La     a+g+++   + + e+ ee+ 
  gi|313125271|ref|YP_004035535.1| 52 AVVGPSGSGKTTLLRLLAclespAEGVVTAnGRNVGEMSEEER 94
                                      789***************7765555777776666666666665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.6e-05     0.029       2      21 ..      50      69 ..      49     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      v+ ++G+ GsGKTtLl+ l 
  gi|313125271|ref|YP_004035535.1| 50 VLAVVGPSGSGKTTLLRLLA 69
                                      6789************8765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     7e-05     0.043       2      21 ..      50      69 ..      49      73 .. 0.89
   2 ?   -3.0   0.0       9.5   5.9e+03     100     120 ..      92     112 ..      80     142 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7e-05
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      ++++ G++GsGKTtLl+ la
  gi|313125271|ref|YP_004035535.1| 50 VLAVVGPSGSGKTTLLRLLA 69
                                      789*************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.5
                                       .........HHHHHCTTTTT- CS
                             NACHT 100 kekqpvrtlLselirkkllpe 120
                                       +e+ +vr+ L+  ++   l +
  gi|313125271|ref|YP_004035535.1|  92 EERLHVRRRLGMVLQHRCLFS 112
                                       455556666666655533333 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.15       1      21 [.      50      69 ..      50      81 .. 0.82
   2 ?    0.2   0.0       1.1   6.6e+02      13      40 ..     205     232 ..     203     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                              MobB  1 vlgivgksgsGKTtLleklip 21
                                      vl++vg sgsGKTtLl  l++
  gi|313125271|ref|YP_004035535.1| 50 VLAVVGPSGSGKTTLLR-LLA 69
                                      799************95.444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                              MobB  13 TtLleklipelkarglrvgtiKhahhgf 40 
                                       T+++ek i   ++rg+ v++  h+ ++ 
  gi|313125271|ref|YP_004035535.1| 205 TAIVEKAICDARDRGMGVCLATHDMQQA 232
                                       899****************999998765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0012      0.73      25      82 ..     162     206 ..     149     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                           SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesia 82 
                                       + +r++++lSGGe+q    +a+a al           p ++++++DE  s+lD++++a
  gi|313125271|ref|YP_004035535.1| 162 KQDRHAASLSGGEAQR---VAIARAL----------APEPDVLLFDEPTSNLDPRNTA 206
                                       5678888999999943...3333222..........3568999999999999999986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.067      99     121 ..      48      70 ..      31      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                       TSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                       +++ ++vG+SG GK+tL+  l+ 
  gi|313125271|ref|YP_004035535.1|  48 GEVLAVVGPSGSGKTTLLRLLAC 70 
                                       38999*************99976 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.3e-05     0.057     124     180 ..      43      98 ..      18     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.3e-05
                             T2SSE 124 kavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqln 180
                                        av+   ++ v G+ gsGKttll  ll+ +++  e +vt+      +++++++++++
  gi|313125271|ref|YP_004035535.1|  43 LAVEPGEVLAVVGPSGSGKTTLLR-LLACLESPAEGVVTANGRNVGEMSEEERLHVR 98 
                                       56666778889**********996.67777777788888765555555555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00081       0.5       3      20 ..      53      70 ..      51     111 .. 0.78
   2 ?    1.1   0.0      0.79   4.9e+02      51      66 ..     179     195 ..     135     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00081
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      ++Gp G GKT+l + +a 
  gi|313125271|ref|YP_004035535.1| 53 VVGPSGSGKTTLLRLLAC 70
                                      79************9985 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.79
                                       HHHHHTS.TSEEEEEET CS
                               AAA  51 keakeka.kpsilfiDE 66 
                                       + a++ a +p +l++DE
  gi|313125271|ref|YP_004035535.1| 179 AIARALApEPDVLLFDE 195
                                       3455555779******9 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017       0.1      38      67 ..      41      70 ..      33      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                             Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                       +L  ++ ++L + GPsG gk+t ++ L+ 
  gi|313125271|ref|YP_004035535.1| 41 VSLAVEPGEVLAVVGPSGSGKTTLLRLLAC 70
                                      5677788899****************9985 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00022      0.14      22      39 ..      51      68 ..      35      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00022
                            AAA_23 22 tlItGpNGaGKTTildAi 39
                                       +++Gp G+GKTT+l+ +
  gi|313125271|ref|YP_004035535.1| 51 LAVVGPSGSGKTTLLRLL 68
                                      5789**********9866 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.15      17      39 ..      45      67 ..      41      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                          ATPase_2 17 repneiyfiYGpegsGKtaLlke 39
                                       ep e++ + Gp gsGKt+Ll+ 
  gi|313125271|ref|YP_004035535.1| 45 VEPGEVLAVVGPSGSGKTTLLRL 67
                                      58999****************95 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00046      0.28      18      38 ..      47      66 ..      35      69 .. 0.85
   2 ?   -2.3   0.0       3.3   2.1e+03     124     149 ..     212     237 ..     161     242 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00046
                                      SCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlak 38
                                      ++  v+a+vG  G+GKttl++
  gi|313125271|ref|YP_004035535.1| 47 PG-EVLAVVGPSGSGKTTLLR 66
                                      55.699*************85 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.3
                                       HHHHCHTTSEEEEEESBCCCCCCS-S CS
                            NB-ARC 124 vlparenrlrvllTTRdeevanavsa 149
                                          ar++++ v l T d++ a++vs+
  gi|313125271|ref|YP_004035535.1| 212 ICDARDRGMGVCLATHDMQQAQRVSD 237
                                       34568888888888888888888776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0004      0.25       3      43 ..      52      88 ..      50     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                                      EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE----- CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggr 43
                                      ++ Gp+G+GKtTl++ +++ l   + + +G++t + r+ g+
  gi|313125271|ref|YP_004035535.1| 52 AVVGPSGSGKTTLLRLLAC-L---ESPAEGVVTANGRNVGE 88
                                      688**********976655.4...46889999988887665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00042      0.26       5      22 ..      51      68 ..      48      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++++Gpsg+GKTtl++ l
  gi|313125271|ref|YP_004035535.1| 51 LAVVGPSGSGKTTLLRLL 68
                                      789***********9877 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.013       7.8     241     264 ..      44      68 ..      41      85 .. 0.86
   2 ?    2.6   0.0     0.077        47     324     351 ..     171     198 ..     160     213 .. 0.89
   3 ?   -2.0   0.0       1.9   1.2e+03      93     125 ..     217     249 ..     198     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                                       EE-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAl 264
                                       ++  G v ++vG+   GK+TLL+ l
  gi|313125271|ref|YP_004035535.1|  44 AVEPGeVLAVVGPSGSGKTTLLRLL 68 
                                       56667799*************9865 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.077
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDts 351
                                       SG   q ++i++al  + ++lL+DE ts
  gi|313125271|ref|YP_004035535.1| 171 SGGEAQRVAIARALAPEPDVLLFDEPTS 198
                                       8999999******************998 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.9
                                       T-SSS--S-EE-----SEE--BSSEEE--EEEE CS
                        ABC_ATPase  93 sagsgksgalaidkksqevlersavelsdekie 125
                                        +g g   a + +++ q v +r+av l +e ie
  gi|313125271|ref|YP_004035535.1| 217 DRGMGVCLATHDMQQAQRVSDRTAVLLGGEIIE 249
                                       5555555566677899999*****999888776 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0011      0.66      16      32 ..      51      67 ..      35      73 .. 0.72
   2 ?   -1.3   0.0         2   1.2e+03     193     226 ..     203     238 ..     197     244 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                           Pox_A32 16 lalvGgsGsGktvyLls 32
                                      la+vG sGsGkt+ L+ 
  gi|313125271|ref|YP_004035535.1| 51 LAVVGPSGSGKTTLLRL 67
                                      79**********98764 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                           Pox_A32 193 rkvliiedsvfsegear...iCldsaDesviekeldk 226
                                       r+  i+e ++ ++ + r   +Cl + D +  ++  d 
  gi|313125271|ref|YP_004035535.1| 203 RNTAIVEKAI-CDARDRgmgVCLATHDMQQAQRVSDR 238
                                       6677899998.7776665559**99999998887775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00074      0.46       3      32 ..      49      77 ..      47     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00074
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkes 32
                                      ++l+++G+  +GKTtll+ l+  +  ++e 
  gi|313125271|ref|YP_004035535.1| 49 EVLAVVGPSGSGKTTLLRLLACLES-PAEG 77
                                      6899*************99885544.5555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0017       1.1      23      43 ..      55      75 ..      47      98 .. 0.75
   2 ?   -0.5   0.0      0.57   3.5e+02     463     510 ..     133     180 ..     130     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                            AAA_13 23 GwNGaGKTtLSrllrslelge 43
                                      G  G+GKTtL rll++le+ +
  gi|313125271|ref|YP_004035535.1| 55 GPSGSGKTTLLRLLACLESPA 75
                                      788**************8754 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.57
                            AAA_13 463 inkeLkaf.GlgeleLkfeeekkgYrivrkggsqaaetLSeGEktaIaf 510
                                       i   ++ f G  e  L+++++ ++  +v k ++ +a++LS GE   +a+
  gi|313125271|ref|YP_004035535.1| 133 IRAAIRGFlGTAETPLAAVDALETVGMVDK-QDRHAASLSGGEAQRVAI 180
                                       556677788888888888888888887776.5589999**999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1736.72
//
Query:       gi|313125272|ref|YP_004035536.1|  [L=249]
Description: tungstate ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-13   48.4   7.0    1.6e-12   47.6   7.0    1.3  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   7.0   8.7e-17   1.6e-12       2     180 ..      38     225 ..      37     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 8.7e-17
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...vilsilghlilp..viillllsaapyvrlirr 73 
                                       +++++ +a ++ ++++ +l+ +i +++++Ps+v++++++l++     l+++  l++p  +i++ ++ a+p+v+ +  
  gi|313125272|ref|YP_004035536.1|  38 LPIAVTVA-FSDFRGKSVLTSIISTGMGFPSVVIGLVVLLALsnsGPLGDFELLFTPqaMILAQTILATPVVLSVSL 113
                                       79999999.99****************************9999995555555555554389999************* PP

                      BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydy 150
                                       +a++s+ +dl+eaa+  G ++   +   vl+ a   i+t ++   g+++ +   ++++g++  +  +  +++  + +
  gi|313125272|ref|YP_004035536.1| 114 SAVESVGDDLREAAYGAGGTTTD-VGLAVLREARYGIVTAILAGYGRAISEVGSVLIVGGN--IVFPADQTSYTRTL 187
                                       ***********************.888********************************54..33333333333333 PP

                      BPD_transp_1 151 seis...........nggvlalviavlllnlvadilqrlld 180
                                          +           + + lal++++l+l+l +++l  +l 
  gi|313125272|ref|YP_004035536.1| 188 ---TtaitvearkgnVETGLALGAILLALVLGVNALGSHLR 225
                                       ...23447999999999999999999999999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1501.05
//
Query:       gi|313125273|ref|YP_004035537.1|  [L=156]
Description: hypothetical protein Hbor_04970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0091   16.8   1.2      0.012   16.4   1.2    1.3  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.2   6.5e-07     0.012       1      72 [.       8      76 ..       8     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.5e-07
                             PIN_3  1 rvvlDtnvlldallfdspaarkildal.etgaitlvvsprlldElervlarelaypqfklraadkaallakva 72
                                      rvv D++vl + ll+ + +ar  ld l ++   tlv+s +lld+ e v+  el++p  +l a+++a  +  + 
  gi|313125273|ref|YP_004035537.1|  8 RVVADADVLAADLLVGG-DARDALDHLrAHSWTTLVASDALLDDAESVI-AELTDP--ELAADWRARVEVWCE 76
                                      8*********6666666.466666666377788999************9.555666..456666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 992.90
//
Query:       gi|313125274|ref|YP_004035538.1|  [L=211]
Description: ditpase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-48  164.5   0.0      3e-48  164.2   0.0    1.1  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.2   0.0   1.7e-52     3e-48       2     187 .]       3     205 ..       2     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 1.7e-52
                                       EEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTT CS
                        Ham1p_like   2 vfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLngl 76 
                                        ++T+N+gK+re+ ++la    +v++l    + +++E+q +++  +a++ ar+a++ ag pvl+dD gL++d ++g+
  gi|313125274|ref|YP_004035538.1|   3 HYVTTNAGKVREALQYLA----DVEQL----DYDYTEVQaSDLGPIAAHGAREAYRhAGEPVLVDDAGLFIDGFEGF 71 
                                       689**********99*95....34444....34677***999999**********967999**************** PP

                                       BGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEET..............................T CS
                        Ham1p_like  77 PGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladp..............................e 123
                                       PG+ys+ ++++ +   e + +l e   ee   r+A+f cvla++d+                              e
  gi|313125274|ref|YP_004035538.1|  72 PGPYSSFVEDTLGV--ETVYRLAESELEE--PRRASFDCVLAYCDGegfeatpdpvdrddrtvaaargaeqddeetE 144
                                       ******99664433..3555555544334..5****************************************99988 PP

                                       TTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
                        Ham1p_like 124 eeeellfeGeveGeiveeprgeggfGyDpiFvpeegektfaelskeeknaiShRgkAlekllef 187
                                         +++lf+G+v+G+iv+ prgeggfGyDpiF++ e ++tfae+s+eeknaiShRg+Al+k+ e+
  gi|313125274|ref|YP_004035538.1| 145 ALPVKLFRGTVRGRIVP-PRGEGGFGYDPIFEH-E-GTTFAEMSSEEKNAISHRGRALAKFGEW 205
                                       8899************7.*************99.5.78**********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1232.89
//
Query:       gi|313125275|ref|YP_004035539.1|  [L=97]
Description: hypothetical protein Hbor_04990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.14   13.2   0.0       0.71   10.9   0.0    1.9  2  Pheromone  Fungal mating-type pheromone


Domain annotation for each model (and alignments):
>> Pheromone  Fungal mating-type pheromone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     4e-05      0.71      38      63 ..       5      31 ..       2      35 .. 0.82
   2 ?    0.2   0.0     0.088   1.6e+03      19      28 ..      76      85 ..      53      93 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4e-05
                         Pheromone 38 sssasasddevlavpvDaErrggg.ta 63
                                      +++++ +  e+l+vp ++Er+  g ++
  gi|313125275|ref|YP_004035539.1|  5 VMADKPQKGEILGVPYNFERPSLGrML 31
                                      677889999************988644 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.088
                         Pheromone 19 ssesalfass 28
                                      ss+s+ ++ +
  gi|313125275|ref|YP_004035539.1| 76 SSSSTDLEDE 85
                                      3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 640.95
//
Query:       gi|313125276|ref|YP_004035540.1|  [L=540]
Description: o-sialoglycoprotein endopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-74  249.2   0.0      7e-74  248.9   0.0    1.1  1  Peptidase_M22  Glycoprotease family
    3.9e-06   27.0   1.2    0.00095   19.2   0.2    2.4  2  APH            Phosphotransferase enzyme family
     0.0006   19.2   0.1     0.0048   16.3   0.1    2.0  1  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0042   16.7   0.0     0.0089   15.6   0.0    1.5  1  RIO1           RIO1 family


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.9   0.0   1.6e-77     7e-74       5     270 ..      24     295 ..      20     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: 248.9 bits;  conditional E-value: 1.6e-77
                                       EEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHH....TSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHH CS
                     Peptidase_M22   5 nvvasqkelhakyGGvvPelasraHserllplieealaea....glsledldaIavtkgPGlftgLrvGvsfAkgla 77 
                                       +v+++++ + ++ GG++P++a+++   +++ ++  +l+ a    + +  ++d++a+++gPGl+++Lr++ ++A+ la
  gi|313125276|ref|YP_004035540.1|  24 EVFIESDPYEPDSGGIHPREAAEHMGDAIPAVVSTVLDHAvetaEGDSPEIDGVAFSRGPGLGPCLRIVGTAARSLA 100
                                       5666667788999****************999888777764333666669*************************** PP

                                       HHCT--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSC CS
                     Peptidase_M22  78 lalnkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypg 154
                                        +l++PlvgVnh+ ah++ +r++++ + Pv+l  sG + +++ +++gry++lget+d  +g+a+dk++r +g+ +pg
  gi|313125276|ref|YP_004035540.1| 101 QTLDVPLVGVNHMVAHLEIGRYQSGFDSPVCLNASGANAHLLGYHNGRYRVLGETMDTGVGNAIDKFTRHVGWTHPG 177
                                       *********************997669*****************99******************************* PP

                                       CHHHHHHHCTCS.......EETTEEE.CHHHHHHHHHHSTT..HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEE CS
                     Peptidase_M22 155 gpkieklakegkkiefprplkgldfsfsGlktavlkeleke..vedlaasfqeavvdhlvekteralklpkakelvi 229
                                       gpk+e++ak+g+++++p+++kg+dfsfsG+ +a+ ++  +   ved+++ +qe+++++l+e++eral+l++ +elv+
  gi|313125276|ref|YP_004035540.1| 178 GPKVERAAKDGEYHDLPYVVKGMDFSFSGIMSAAKQASDDGvpVEDVCCGLQETIFAMLTEVAERALSLTGTDELVL 254
                                       ***********99*****************8888887744368********************************** PP

                                       ESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHH CS
                     Peptidase_M22 230 lGGvaankrLrealeeeaeelglkliiPplkyctdnaamia 270
                                       +GGv++n+rLre+l+e+++++g+++++P++++++dna mia
  gi|313125276|ref|YP_004035540.1| 255 GGGVGQNARLREMLSEMCDQRGADFYAPEPRFLRDNAGMIA 295
                                       ****************************************8 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2   0.00027       1.2      33     108 ..     378     444 ..     347     445 .. 0.76
   2 !   19.2   0.2   2.1e-07   0.00095     154     229 ..     435     510 ..     422     532 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00027
                                       -HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH CS
                               APH  33 aaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhqv 108
                                        +e++r+e++l  + ++ gvp+P++ +    d  +g  + ++e+v+  +l+     a + e ++ +g  la +h++
  gi|313125276|ref|YP_004035540.1| 378 RKERTRAEARLTSQARREGVPTPVIRD---VDPTEG--VIVFESVGKSDLAG----ALTTERCRTVGKHLATVHDA 444
                                       467888*********************...455555..77888888888888....67777778888877777776 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.1e-07
                                       HHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH.....HH.CSCHCCCHCHHHH CS
                               APH 154 aalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll.....rs.wtseldpeflaal 224
                                        +++a+++   +++++HgD+ ++N+ vd    + t++iDf++  +   + D a+ l         t ++ + +l+a+
  gi|313125276|ref|YP_004035540.1| 435 GKHLATVH---DAGFVHGDPTTRNVRVD--AEK-TYLIDFGLGYYTGHVEDHAMDLhvfgqSVeGTAAEPEPLLQAF 505
                                       56677777...8****************..455.469***9988888888887777444432223333334444444 PP

                                       HHHHC CS
                               APH 225 lraye 229
                                        ++y+
  gi|313125276|ref|YP_004035540.1| 506 EEGYA 510
                                       44444 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.1e-06    0.0048      97     167 ..     403     469 ..     327     491 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
                               Kdo  97 erlegaqdLedllakwae.laeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                       +++++++ + ++   +++ la++l+ +  + vg+  a  h+ag  H+d   +n+ +++e+      +liD+ 
  gi|313125276|ref|YP_004035540.1| 403 RDVDPTEGVIVFESVGKSdLAGALTTERCRTVGKHLATVHDAGFVHGDPTTRNVRVDAEK-----TYLIDFG 469
                                       55555555555555444458999999*******************************997.....9****95 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     2e-06    0.0089      45     150 ..     372     469 ..     349     483 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-06
                                       S-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEE..ETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHH CS
                              RIO1  45 tnprklvklwaekEfrnLkrleeagvpvPkpiel..krhvlvmefigedgvaapklkdveeeeeaeelyeevleemr 119
                                           kl k  ++ E r  ++++++gvp P   ++   + v+v e +g +   a  l   +     +     ++ +  
  gi|313125276|ref|YP_004035540.1| 372 ELDDKLRKERTRAEARLTSQARREGVPTPVIRDVdpTEGVIVFESVG-KSDLAGALTTER----CR-----TVGKHL 438
                                       445567788889999999999999999997655522799********.333333333333....23.....233334 PP

                                       HHHHTSTEEESS-STTSEEEETTEEEE--GT CS
                              RIO1 120 klykeaglvHaDLSeyNvlvdedkvviIDvs 150
                                       + +++ag vH+D    Nv vd +k ++ID++
  gi|313125276|ref|YP_004035540.1| 439 ATVHDAGFVHGDPTTRNVRVDAEKTYLIDFG 469
                                       45789************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3240.01
//
Query:       gi|313125277|ref|YP_004035541.1|  [L=105]
Description: 30S ribosomal protein S24e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-25   89.2   0.1    1.6e-25   88.9   0.1    1.1  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.1   8.8e-30   1.6e-25       2      77 ..      21      95 ..      20      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 8.8e-30
                                      EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS--- CS
                    Ribosomal_S24e  2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekk 77
                                      +++ H++ atps+ ++r++la++++ d+d+vv+++++t+fG++kt G+ak+Y+s+e a+++E++++l Rn+++ ++
  gi|313125277|ref|YP_004035541.1| 21 FEIVHDE-ATPSRLSVRDSLAAKLNKDSDEVVIHELDTKFGMRKTAGYAKVYESPEFARDVEQDYMLDRNKIEAEE 95
                                      89*****.****************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 640.54
//
Query:       gi|313125278|ref|YP_004035542.1|  [L=175]
Description: hypothetical protein Hbor_05020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-42  144.1   0.2      2e-42  143.8   0.2    1.1  1  DUF359    Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.049   13.7   1.9       0.36   11.0   0.1    2.5  3  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
      0.098   12.8   0.4       0.13   12.4   0.4    1.5  1  DUF1525   Protein of unknown function (DUF1525)
       0.12   12.4   0.0       0.27   11.2   0.0    1.6  1  DUF4911   Domain of unknown function (DUF4911)
       0.79   10.0   5.7       0.28   11.5   1.0    2.0  2  acVLRF1   Actinobacteria/chloroflexi VLRF1 release factor


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.8   0.2   5.5e-46     2e-42       1     125 [.      41     162 ..      41     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 5.5e-46
                            DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdG 77 
                                       vt++l++ag++Pd+a++DgktkRe+v+ee ++     ++ +++ +v+NpaG+ite l ++i++al+ +++v+++V G
  gi|313125278|ref|YP_004035542.1|  41 VTHHLRRAGRTPDVAVIDGKTKREAVDEEIRRAL---SDPETRRDVNNPAGEITEALADTIRDALDADDPVTVVVAG 114
                                       8***********************9988555555...6799999********************************* PP

                            DUF359  78 EEDLavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekf 125
                                       EEDLa+lpa+++ap+g++vvYGqpdeG+vl++vt+++k+e+++ll+++
  gi|313125278|ref|YP_004035542.1| 115 EEDLATLPAVVAAPTGASVVYGQPDEGMVLIDVTDDSKAEMRSLLRRM 162
                                       **********************************************99 PP

>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.92   3.3e+03      21      45 ..      45      73 ..      34      76 .. 0.56
   2 ?   11.0   0.1    0.0001      0.36      24      56 ..      76     112 ..      73     119 .. 0.81
   3 ?    1.3   0.1      0.11   3.8e+02       8      26 ..     143     165 ..     140     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.92
                                      EETT--EEE.EEGG.......GB-HHHHTT CS
                            eIF-5a 21 mdddgetkeDlklpeg.....elgkqikek 45
                                      + + g t + + + +g      ++++i+++
  gi|313125278|ref|YP_004035542.1| 45 LRRAGRTPD-VAVIDGktkreAVDEEIRRA 73
                                      555555644.66665544454666666665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0001
                                       T--EEE.EEGG......GB-HHHHTT--TT-E..EEE CS
                            eIF-5a  24 dgetkeDlklpeg....elgkqikekfeegkdvlVtV 56 
                                       d et+ D++ p g     l++ i++++++++ v V+V
  gi|313125278|ref|YP_004035542.1|  76 DPETRRDVNNPAGeiteALADTIRDALDADDPVTVVV 112
                                       679********44457799*************66666 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.11
                                       EEEEE-SS....EEEEEE.TT-- CS
                            eIF-5a   8 qLidIqdDg...flsLmd.ddge 26 
                                        Lid++dD    + sL+   dg+
  gi|313125278|ref|YP_004035542.1| 143 VLIDVTDDSkaeMRSLLRrMDGD 165
                                       59****99877777777766665 PP

>> DUF1525  Protein of unknown function (DUF1525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   3.7e-05      0.13      73     100 ..     110     139 ..      35     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                           DUF1525  73 vadawqlgikkiPAVvvd..rraVvYGead 100
                                       v+ a +  ++ +PAVv      +VvYG++d
  gi|313125278|ref|YP_004035542.1| 110 VVVAGEEDLATLPAVVAAptGASVVYGQPD 139
                                       667788899*******987799******99 PP

>> DUF4911  Domain of unknown function (DUF4911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.6e-05      0.27      29      54 ..     138     163 ..     132     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.6e-05
                           DUF4911  29 kkkGlvrirttpdtkeellelLesLk 54 
                                       +++G+v i +t d k+e++ lL  ++
  gi|313125278|ref|YP_004035542.1| 138 PDEGMVLIDVTDDSKAEMRSLLRRMD 163
                                       689*******************9985 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.4      0.15   5.5e+02      67      94 ..      24      50 ..      19      82 .. 0.39
   2 ?   11.5   1.0   7.7e-05      0.28      49     124 ..      81     162 ..      78     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.15
                           acVLRF1 67 arllaeesaevvlgGdrslvaevledar 94
                                      +rlla++   ++ +Gd  + +  ++  r
  gi|313125278|ref|YP_004035542.1| 24 DRLLADAGTPIIAVGDVVTHHLRRAG-R 50
                                      56664444446666665333333332.2 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.7e-05
                           acVLRF1  49 Rrrenqadalleavaeaaarllaeesae.vvlgGdrslva..evledar.laplatlare..elldvpdprravLed 119
                                       R ++n a +  ea a+++++ l+++++  vv++G++ l+   +v + ++  + + +++ e   l+dv d+++a ++ 
  gi|313125278|ref|YP_004035542.1|  81 RDVNNPAGEITEALADTIRDALDADDPVtVVVAGEEDLATlpAVVAAPTgASVVYGQPDEgmVLIDVTDDSKAEMRS 157
                                       778999999*************9999989*****9987652266666553455777777764444999999999999 PP

                           acVLRF1 120 avrra 124
                                        +rr+
  gi|313125278|ref|YP_004035542.1| 158 LLRRM 162
                                       88886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1153.06
//
Query:       gi|313125279|ref|YP_004035543.1|  [L=65]
Description: DNA-directed RNA polymerase subunit e'' [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-14   53.4   0.1    2.5e-14   53.1   0.1    1.1  1  Spt4           Spt4/RpoE2 zinc finger
     0.0022   17.3   2.0     0.0029   16.9   2.0    1.3  1  zf-RanBP       Zn-finger in Ran binding protein and others
     0.0022   18.0   1.0     0.0028   17.6   1.0    1.2  1  DZR            Double zinc ribbon
     0.0023   17.6   2.1     0.0032   17.1   2.1    1.2  1  zinc_ribbon_2  zinc-ribbon domain
  ------ inclusion threshold ------
      0.039   14.0   0.3      0.045   13.8   0.3    1.2  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.042   13.8   3.4       0.26   11.2   0.3    2.2  2  Nudix_N_2      Nudix N-terminal


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.1   8.3e-18   2.5e-14       2      77 .]       6      65 .]       5      65 .] 0.97

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 8.3e-18
                              Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                       AC++C++++  d+   + C+nC           + ++++e++ G+v+i++pe+S +A    ++ ++pg YAlkv+
  gi|313125279|ref|YP_004035543.1|  6 LACRECHYINMPDS---QACENC-----------GASSLTEDWAGYVVITHPEESDIATE--MNVTEPGGYALKVR 65
                                      59************...******...........9*************************..************96 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.0   9.8e-07    0.0029       7      28 ..       8      29 ..       7      31 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.8e-07
                                      -SSS--EEESSSSB-TTT--BT CS
                          zf-RanBP  7 CskClvqNfawstkCvaCqapk 28
                                      C  C + N + s++C++C+a+ 
  gi|313125279|ref|YP_004035543.1|  8 CRECHYINMPDSQACENCGASS 29
                                      99*****************975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.0   9.5e-07    0.0028      31      49 .]       8      26 ..       2      35 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.5e-07
                               DZR 31 CpsCgekvdpearfCpeCG 49
                                      C +C++ + p+++ C +CG
  gi|313125279|ref|YP_004035543.1|  8 CRECHYINMPDSQACENCG 26
                                      5556666555666666655 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.1   1.1e-06    0.0032       2      21 ..       8      27 ..       7      29 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                      C +C++ + ++++ C++CG+
  gi|313125279|ref|YP_004035543.1|  8 CRECHYINMPDSQACENCGA 27
                                      *******************8 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   1.5e-05     0.045      68      98 ..       3      31 ..       1      43 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                      --EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 68 pvkvrCreCgkefeleekalrCpkCgsadve 98
                                      + ++ CreC++    +++   C++Cg+++++
  gi|313125279|ref|YP_004035543.1|  3 KPRLACRECHYINMPDSQ--ACENCGASSLT 31
                                      67899*****87777644..8*****98765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   8.8e-05      0.26      20      31 ..       3      14 ..       2      15 .. 0.91
   2 ?    3.5   0.2     0.023        70       3       8 ..      22      27 ..      20      32 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.8e-05
                                      S-EEEETTTTEE CS
                         Nudix_N_2 20 reRlvCpaCgti 31
                                      ++Rl C  C++i
  gi|313125279|ref|YP_004035543.1|  3 KPRLACRECHYI 14
                                      79*********9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.023
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      C++CG+
  gi|313125279|ref|YP_004035543.1| 22 CENCGA 27
                                      777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 405.84
//
Query:       gi|313125280|ref|YP_004035544.1|  [L=192]
Description: DNA-directed RNA polymerase subunit e' [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-15   57.2   0.1    2.5e-15   56.6   0.1    1.3  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    1.4e-14   54.2   0.4    3.5e-14   52.9   0.4    1.7  1  S1             S1 RNA binding domain
      0.007   16.4   0.0       0.64   10.1   0.0    2.4  1  S1_2           S1 domain
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.022   15.0   0.0    1.3  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.1   5.6e-19   2.5e-15       1      70 []       8      77 ..       8      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 5.6e-19
                                      EEEEEE-GGGTTS.THHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  1 edtvrlePsylgs.tledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      +dtv+++P++l++ t+ + +++ l++k+eg++++++G +v+v ++ +++eg+vl+g ++vy++++f+a+ F
  gi|313125280|ref|YP_004035544.1|  8 KDTVEVPPEHLADvTP-QRVKRLLQDKLEGRMDEDVGSVVSVVNVHDIGEGTVLPGRAGVYYEAEFDAVTF 77
                                      69**********9555.5677***********************************************998 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.4   7.8e-18   3.5e-14       6      67 ..      83     153 ..      78     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 7.8e-18
                                       CEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEETTT CS
                                S1   6 evveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvdkdr 67 
                                       ev++GeV++v+++GafV +g +v+g++++s++s++              +++++l vGd v+v+v     d+
  gi|313125280|ref|YP_004035544.1|  83 EVIDGEVVEVVEFGAFVGIG-PVDGLLHVSQISDEylaydgenqqLASTESNRTLAVGDSVRVRVVTKSIDE 153
                                       8*******************.************************99999**************98765555 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00014      0.64       5      37 ..      85     116 ..      83     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                              S1_2   5 ntlkvlretdfgyfLqkdesgevlLpkkevpee 37 
                                          +v++  +fg+f+  +  ++ lL+ +++ +e
  gi|313125280|ref|YP_004035544.1|  85 IDGEVVEVVEFGAFVGIGP-VDGLLHVSQISDE 116
                                       5678999999999997777.7777777777643 PP

>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   4.8e-06     0.022       1      93 [.      79     177 ..      79     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-06
                                       -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE- CS
                     RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrveeeifv 77 
                                       P ++ev+ g + +  + g +v +g +d ++   +   e+ ++d e+q        e++  l vg+++r+rv+ ++  
  gi|313125280|ref|YP_004035544.1|  79 PDMQEVIDGEVVEVVEFGAFVGIGPVDGLLHVSQISDEYLAYDGENQQLAS---TESNRTLAVGDSVRVRVVTKSID 152
                                       6689************************999999999********998653...56888999**************9 PP

                                       ------HHHHHCHHH.........C CS
                     RNA_pol_Rbc25  78 dvkpkspkeaeleee.........e 93 
                                       +++p+++k   ++++         e
  gi|313125280|ref|YP_004035544.1| 153 ERNPRDSKIGLTAKQpglgkhgwlE 177
                                       9999998876666556665554331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1232.78
//
Query:       gi|313125281|ref|YP_004035545.1|  [L=142]
Description: SSU processome protein utp24 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-39  133.2   0.7    5.9e-39  133.0   0.7    1.0  1  PIN_9     PIN like domain
    1.2e-07   31.5   0.1    2.2e-07   30.6   0.1    1.4  1  DUF188    Uncharacterized BCR, YaiI/YqxD family COG1671
    0.00034   20.9   0.0     0.0008   19.7   0.0    1.5  2  PIN_4     PIN domain
      0.007   16.7   0.0     0.0096   16.3   0.0    1.2  1  Fcf1      Fcf1
  ------ inclusion threshold ------
       0.14   12.7   0.0       0.22   12.0   0.0    1.3  1  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.0   0.7   1.6e-42   5.9e-39       1     115 [.      19     133 ..      19     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 1.6e-42
                             PIN_9   1 vilDtnaLmipvqfgvdifeelerll.gsvelvvpkavleELerlakagkgkertaakvalsL.aerceiveaeeek 75 
                                       v+lDtnaLm+pv+++v++f+el+rll  +v+lvvp+av+ ELe+l +ag+g+e  aa+v+++L a+rc++v++e+ +
  gi|313125281|ref|YP_004035545.1|  19 VVLDTNALMMPVELDVRVFDELDRLLaANVDLVVPSAVVGELEKL-SAGAGNEGVAASVGADLaADRCRVVDTEATY 94 
                                       8*************************999****************.99***************9999********** PP

                             PIN_9  76 aDdailelakeldaavlvTnDreLkkrllekgipvilLRq 115
                                       aDda++ela++   +++vTnD++L++rlle+g++vi +R+
  gi|313125281|ref|YP_004035545.1|  95 ADDAVVELAERG-FDYVVTNDKPLRDRLLERGVRVIGIRG 133
                                       *********976.79999*********************8 PP

>> DUF188  Uncharacterized BCR, YaiI/YqxD family COG1671
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1     6e-11   2.2e-07      30      79 ..      84     134 ..      72     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 6e-11
                            DUF188  30 etvvVdsgadaaDdaIveraeag.DlvvTqDipLAarvlekgaaalsprGe 79 
                                       +  vVd++a  aDda+ve ae+g D vvT+D pL +r+le+g++++  rG+
  gi|313125281|ref|YP_004035545.1|  84 RCRVVDTEATYADDAVVELAERGfDYVVTNDKPLRDRLLERGVRVIGIRGH 134
                                       5689*****************988***********************9997 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.2e-07    0.0008       1      44 [.      19      86 ..      19     117 .. 0.76
   2 ?   -1.1   0.0       0.6   2.1e+03     109     126 ..     110     127 ..      90     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.2e-07
                             PIN_4  1 fVlDTnvlLhdpealksf........keehdvviPitVleELdklKkgsse................r 44
                                      +VlDTn l+  +e+  ++          + d+v+P  V+ EL+kl  g  +                r
  gi|313125281|ref|YP_004035545.1| 19 VVLDTNALMMPVELDVRVfdeldrllAANVDLVVPSAVVGELEKLSAGAGNegvaasvgadlaadrcR 86
                                      69*******9998766667888****99*****************99988766666555555444444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.6
                             PIN_4 109 LvskDinlrikAkalgie 126
                                        v++D+ lr +    g++
  gi|313125281|ref|YP_004035545.1| 110 VVTNDKPLRDRLLERGVR 127
                                       689999999776666665 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.7e-06    0.0096       2      80 ..      43     122 ..      42     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.7e-06
                                       HCTS-EEEEEEHHHHHHHHHCT....-HHHHHHHT.TSEEE----..SS---HHHHHHHHH-BTB-TT-EEEE-S-H CS
                              Fcf1   2 tLqakvkpliTqCviaeleklg..kklkealkiak.tferlkCnh..kkptsaddClvsvvkkkknkkryivAtqDk 73 
                                       +L a+v +++ + v+ elekl+  + ++++ + +   +   +C    +++t+add +v++ ++      y+v t+Dk
  gi|313125281|ref|YP_004035545.1|  43 LLAANVDLVVPSAVVGELEKLSagAGNEGVAASVGaDLAADRCRVvdTEATYADDAVVELAER---GFDYVV-TNDK 115
                                       799******************955335566666663699999988878999**********95...477765.99** PP

                                       HHHHHHH CS
                              Fcf1  74 dlrrrlr 80 
                                        lr rl 
  gi|313125281|ref|YP_004035545.1| 116 PLRDRLL 122
                                       9999974 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.1e-05      0.22       1      47 [.      19      62 ..      19      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-05
                            PIN_12  1 ifiDTnifldeffrlseeealkklleliesgkiklivpdivldEflk 47
                                      +++DTn ++    +l+   ++++l +l+ + ++ l+vp+ v+ E++k
  gi|313125281|ref|YP_004035545.1| 19 VVLDTNALMM-PVELDVR-VFDELDRLLAA-NVDLVVPSAVVGELEK 62
                                      79*******5.9999999.*****666666.6************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 953.57
//
Query:       gi|313125282|ref|YP_004035546.1|  [L=410]
Description: translation initiation factor 2 subunit gamma (aeif-2g) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-30  105.2   0.1    4.2e-30  103.8   0.1    1.8  1  eIF2_C        Initiation factor eIF2 gamma, C terminal
    2.7e-29  102.1   3.5    2.1e-28   99.2   3.5    2.0  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    6.9e-09   36.0   1.6    1.7e-08   34.7   1.6    1.8  1  GTP_EFTU_D2   Elongation factor Tu domain 2
    5.6e-05   23.2   0.0    0.00012   22.1   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
    5.7e-05   23.1   2.3     0.0027   17.6   0.2    2.7  3  RsgA_GTPase   RsgA GTPase
     0.0013   18.4   0.9       0.25   11.1   0.0    2.3  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0075   15.9   0.8       0.23   11.0   0.2    2.3  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.029   14.4   0.1    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.032   13.8   2.5        6.6    6.2   2.5    2.4  1  FeoB_N        Ferrous iron transport protein B
       0.15   11.5   0.0        9.6    5.6   0.0    2.2  2  SRPRB         Signal recognition particle receptor beta subun


Domain annotation for each model (and alignments):
>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.1   2.3e-33   4.2e-30       2      85 ..     326     408 ..     325     409 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 2.3e-33
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSE CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrW 78 
                                       e+++++ell+r+vg +ee +ve+++++E+Lml++G+a+t+g vts+++ ea+v+Lk+Pvca  g+kia++Rrv++rW
  gi|313125282|ref|YP_004035546.1| 326 EFTMDVELLNRVVGEDEE-TVEEISTGEPLMLTVGTATTVGAVTSARTGEAEVSLKRPVCAADGAKIAINRRVGARW 401
                                       799***********8886.9********************************************************* PP

                                       EEEEEEE CS
                            eIF2_C  79 rLiGwGe 85 
                                       rLiG+G+
  gi|313125282|ref|YP_004035546.1| 402 RLIGIGT 408
                                       ******8 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   3.5   1.2e-31   2.1e-28       4     193 ..      11     201 ..       8     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 1.2e-31
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................ CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................ 64 
                                       +nig++ghvDhGKtTL+ +L                 + +D+++eE +rgi+i    +                   
  gi|313125282|ref|YP_004035546.1|  11 VNIGLVGHVDHGKTTLVQALSG---------------SWTDQHSEEMKRGISIRLGYADATfrkipgadppecytve 72 
                                       7******************981...............2489999999999999999998888899999999999999 PP

                                       .......TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESC CS
                          GTP_EFTU  65 .......ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKm 132
                                              ++   ++++++D+PGH+  + ++  g++++Dgavlvv+a+e  +++qtee+l  +   g+  i+++ NK+
  gi|313125282|ref|YP_004035546.1|  73 etdddgnETDVLRTVSFVDAPGHETLMATMLSGAAIMDGAVLVVSATENvPQAQTEEHLMALDIIGIDnIVIAQNKI 149
                                       999877445667899*********************************9669****************9******** PP

                                       GST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 133 Drl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       D + +++  e  e+++ ++      ++  +++   + p+v++Sa +  +++ l++a+ + +p
  gi|313125282|ref|YP_004035546.1| 150 DLVdRDRAVENYEQIQ-EF------VQGTVAE---DAPIVPISAQQEVNIDLLIDAIEREIP 201
                                       ***7677777788887.77......4444444...57********************99887 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   1.6   9.6e-12   1.7e-08       1      69 [.     233     310 ..     233     315 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 9.6e-12
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE......EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS...GS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke......ivtrissletfhededeavaganaGvivaikgled...ai 67 
                                       G+v++g+v++G+l +G+e+++++  ++++ +      i+t+i+sl++  +  de+++g+ +Gv++++++  +   a 
  gi|313125282|ref|YP_004035546.1| 233 GGVIGGSVVEGKLTEGEELELRPgREVDEGGqtewrpITTDIRSLQAGGQMTDEVRPGGLCGVGTGLDPSLTkgdA- 308
                                       89*********************88886666************************************987774433. PP

                                       ST CS
                       GTP_EFTU_D2  68 iv 69 
                                       ++
  gi|313125282|ref|YP_004035546.1| 309 LA 310
                                       55 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     7e-08   0.00012       1      94 [.      12     126 ..      12     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7e-08
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE..ETTEE........................... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk..lkgke........................... 47 
                                       ++++vG+   GK+tL++al+g+ + + s++    + i+ g  +  ++  +                           
  gi|313125282|ref|YP_004035546.1|  12 NIGLVGHVDHGKTTLVQALSGSwTDQHSEEMKRGISIRLGYADatFR--Kipgadppecytveetdddgnetdvlrt 86 
                                       589******************98667777776666666665553333..1234555666666667777777888888 PP

                                       EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHH CS
                          MMR_HSR1  48 ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpld 94 
                                       + +vD pG  e       l  ++l+    +d ++lvv+a+ e++ + +
  gi|313125282|ref|YP_004035546.1|  87 VSFVDAPG-HE------TLMATMLSGAAiMDGAVLVVSAT-ENVPQAQ 126
                                       ********.54......7888888877767*******988.4343322 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.02        36     104     137 ..      15      45 ..       7      48 .. 0.82
   2 !   17.6   0.2   1.5e-06    0.0027      13      98 ..     106     197 ..      83     201 .. 0.81
   3 ?   -1.9   0.0       1.5   2.7e+03     115     132 ..     333     350 ..     332     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.02
                                       EECSTTSSHHHHHHHHCTT-----S--------- CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrG 137
                                       lvG+   GK+tL+ al ++    t + se+++rG
  gi|313125282|ref|YP_004035546.1|  15 LVGHVDHGKTTLVQALSGS---WTDQHSEEMKRG 45 
                                       7899999**********98...666677777666 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.5e-06
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllv 82 
                                       +a +d +++vvs++ +++ + + +  L+++   gi ++vi+ nKiDl+++++      +++e+ + + a + +++ +
  gi|313125282|ref|YP_004035546.1| 106 AAIMDGAVLVVSAT-ENVPQAQTEEHLMALDIIGIdNIVIAQNKIDLVDRDRavenyeQIQEFVQGTVAEDAPIVPI 181
                                       7889**********.89999999************88999*********9997776666666666666778888899 PP

                                       -TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  83 saktkegleelkellk 98 
                                       sa+++ +++ l ++++
  gi|313125282|ref|YP_004035546.1| 182 SAQQEVNIDLLIDAIE 197
                                       9988888887776665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
                                       HHHHHCTT-----S---- CS
                       RsgA_GTPase 115 Linallpelelktgevse 132
                                       L+n++++e+e  ++e+s+
  gi|313125282|ref|YP_004035546.1| 333 LLNRVVGEDEETVEEIST 350
                                       89*************997 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00014      0.25       4      24 ..      13      33 ..      10      43 .. 0.87
   2 !    5.6   0.4    0.0068        12      40     142 ..      89     197 ..      80     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      i l+G+v+ GKttL qal+g 
  gi|313125282|ref|YP_004035546.1| 13 IGLVGHVDHGKTTLVQALSGS 33
                                      669***************984 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0068
                         PduV-EutP  40 viDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGi....i..tkidlaedeeniea 110
                                       ++D+PG    +++l+ ++ + +a  d  +lv++ate+    +++  ++++ ++iGi    i   kidl++ + ++e+
  gi|313125282|ref|YP_004035546.1|  89 FVDAPG----HETLMATMLSGAAIMDGAVLVVSATENV-PQAQTEEHLMALDIIGIdnivIaqNKIDLVDRDRAVEN 160
                                       567777....4667777777888888888888888754.567777899999****7654333359999988877776 PP

                         PduV-EutP 111 vee...lLksaGaek..ifevsavekegieellkyle 142
                                        e+   +++   ae   i  +sa ++++i+ l++ +e
  gi|313125282|ref|YP_004035546.1| 161 YEQiqeFVQGTVAEDapIVPISAQQEVNIDLLIDAIE 197
                                       5541104544444433389999999999999998876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.039        70       3      22 ..      13      35 ..      11      46 .. 0.76
   2 !   11.0   0.2   0.00013      0.23     103     167 ..     100     166 ..      86     174 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.039
                                      EEEEESTTCCHHHHHHHHH...C CS
                              cobW  3 tvltGflGsGKTtLlnhll...e 22
                                      ++l+G +  GKTtL+++l    +
  gi|313125282|ref|YP_004035546.1| 13 IGLVGHVDHGKTTLVQALSgswT 35
                                      578999999******99875552 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                                       SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEE..E-HHHHCHC..HHHHHHHHH CS
                              cobW 103 eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvl..nKtDlldeeallekleerlr 167
                                       ++ l+ ++ +d+ v vv+a++   + +++e+++   +   d +v+  nK+Dl+d ++ +e+ e++ +
  gi|313125282|ref|YP_004035546.1| 100 ATMLSGAAIMDGAVLVVSATENVPQAQTEEHLMALDIIGIDNIVIaqNKIDLVDRDRAVENYEQIQE 166
                                       5667778899*********87755556666666666666666665579********88888877655 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.6e-05     0.029      59     100 ..     143     196 ..     112     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                      MMR_HSR1_Xtn  59 lyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                       +++ NKiDl++ +   e +++              +v+iSa++e+n+d L ++i
  gi|313125282|ref|YP_004035546.1| 143 VIAQNKIDLVDRDRAVENYEQiqefvqgtvaedAPIVPISAQQEVNIDLLIDAI 196
                                       6788*****77655444444334557778887668999************9988 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.5    0.0037       6.6      60      60 ..      71      71 ..      11     196 .. 0.41

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0037
                                      S CS
                            FeoB_N 60 l 60
                                      +
  gi|313125282|ref|YP_004035546.1| 71 V 71
                                      2 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.022        39       7      26 ..      14      33 ..       8      62 .. 0.80
   2 ?    5.6   0.0    0.0054       9.6      50     123 ..      86     150 ..      68     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.022
                                      EEE-STTSSHHHHHHHHHHS CS
                             SRPRB  7 llvGlsdsGKTslftrLttd 26
                                       lvG  d GKT+l + L+  
  gi|313125282|ref|YP_004035546.1| 14 GLVGHVDHGKTTLVQALSGS 33
                                      589***********999865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0054
                                       T-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TT CS
                             SRPRB  50 kltliDfPGheklrqklleklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqe 123
                                       ++ ++D PGhe l   +l      + + g v vv +t +  +  ++ E l+ + +i +      +i+iA nK +
  gi|313125282|ref|YP_004035546.1|  86 TVSFVDAPGHETLMATMLSG---AAIMDGAVLVVSATENVPQ-AQTEEHLMALDIIGI-----DNIVIAQNKID 150
                                       5789*********9999988...5567778888865554443.456666665544444.....23455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2607.48
//
Query:       gi|313125283|ref|YP_004035547.1|  [L=270]
Description: hypothetical protein Hbor_05070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.043   13.2   0.0      0.066   12.5   0.0    1.2  1  Cthe_2159  Carbohydrate-binding domain-containing protein Cth


Domain annotation for each model (and alignments):
>> Cthe_2159  Carbohydrate-binding domain-containing protein Cthe_2159
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.7e-06     0.066     191     255 ..     160     227 ..     151     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-06
                         Cthe_2159 191 tinggtltittgggseessakddeSakGika...dgsitingGtitidsaddaihakgsitingGtlt 255
                                       ++  gt+++ +g+ ++ ++ +++ S +G++     ++iti+gG+i++  +  a  a++s+ ++gG + 
  gi|313125283|ref|YP_004035547.1| 160 QVGTGTFDVASGTSARLTEYEASYSFEGFSVnvgTEDITIEGGEISVAGHLAAWIADNSVLVAGGAYP 227
                                       67789*******9999999**********97555899****************99999******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1783.09
//
Query:       gi|313125284|ref|YP_004035548.1|  [L=51]
Description: hypothetical protein Hbor_05080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       147  (0.00819901); expected 358.6 (0.02)
Passed bias filter:                      119  (0.00663729); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 358.03
//
Query:       gi|313125285|ref|YP_004035549.1|  [L=283]
Description: hypothetical protein Hbor_05090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1600.07
//
Query:       gi|313125286|ref|YP_004035550.1|  [L=70]
Description: hypothetical protein Hbor_05100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 441.94
//
Query:       gi|313125287|ref|YP_004035551.1|  [L=274]
Description: metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-20   71.8   0.4    6.7e-20   71.5   0.4    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
      0.001   19.1   2.8     0.0014   18.7   2.8    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.4   7.5e-24   6.7e-20       3     200 ..      50     250 ..      48     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 7.5e-24
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEE....HHHHHHCCTTC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyap....kgvlavleanf 74 
                                       +LiD +pd+rqq   ++       e+p  da l+th H+DH+ gl    + +  ++lp++a     +++++ +++  
  gi|313125287|ref|YP_004035551.1|  50 LLIDFSPDFRQQ-FLTH-------EVPLPDAGLITHVHFDHIDGLGNAYRvF--DDLPVHAAdetdPKTGQSVAETV 116
                                       79**********.5555.......8999*****************9999955..45999977355566666777776 PP

                                       GHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE..CTTEEEEEESS-S-.--H CS
                     Lactamase_B_2  75 vylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie..gggkrvyyigDtgy.ipe 148
                                          ++  + +++v+  ++ e+f+    gl++t++p++h            ++Gl ie  ++g ++  +gDt y ipe
  gi|313125287|ref|YP_004035551.1| 117 ASKFDYLD-RISVRAQTPFETFRTC--GLDVTLVPVEHPPLL--------CYGLTIEdsETGAKLSLSGDTSYgIPE 182
                                       66666666.7777777777777774..899********9999........*******9999***********83569 PP

                                       HHHHHHCT-SEEEEE-S-SSTTHHHH..................HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 149 eigerlggadllllditayeddemir..................hmgHltpeeaveaaadlgakrlvliH 200
                                       + +  l ++dlll ++ +  +    +                  +  H+t e+a+++a+dl+a+++ l+H
  gi|313125287|ref|YP_004035551.1| 183 DSRSVLSDPDLLLAEAIVPASLC--QhhplggkhfddegvprtfGTKHMTREGALALADDLNAEQTRLVH 250
                                       9************8866554444..4469999*************************************9 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.8   1.6e-07    0.0014      49     162 ..      74     187 ..      36     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.6e-07
                                       E-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEH CS
                       Lactamase_B  49 ilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyv 125
                                       ++TH H+DHi glg   + +d  +++ a+e+   ++  +      k+++l + s+++  ++e  ++ +++  +  + 
  gi|313125287|ref|YP_004035551.1|  74 LITHVHFDHIDGLGNAYRVFDDLPVHAADETDPKTGQSVAETVASKFDYLDRISVRAQTPFETFRTCGLDVTLVPVE 150
                                       89*************************************99988888889999999999****************** PP

                                       ECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 126 tggpghghghgvveygggkvlftGDallagetgridl 162
                                       ++  +  ++ +  +  g+k+ ++GD+++  ++ + + 
  gi|313125287|ref|YP_004035551.1| 151 HPPLLCYGLTIEDSETGAKLSLSGDTSYGIPEDSRSV 187
                                       ****************************888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1759.64
//
Query:       gi|313125288|ref|YP_004035552.1|  [L=196]
Description: hypothetical protein Hbor_05120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1382.72
//
Query:       gi|313125289|ref|YP_004035553.1|  [L=456]
Description: ATPase AAA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-40  137.4   0.0    9.1e-40  136.1   0.0    1.7  1  AAA              ATPase family associated with various cellul
      4e-09   36.1   0.3      1e-08   34.9   0.3    1.7  1  AAA_lid_3        AAA+ lid domain
    1.2e-06   29.1   0.1    4.1e-05   24.1   0.0    2.7  2  AAA_18           AAA domain
    1.6e-06   28.1   0.0    8.8e-06   25.8   0.0    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
    2.7e-06   27.7   0.2    0.00013   22.3   0.0    2.9  2  AAA_28           AAA domain
    4.3e-06   27.0   0.0    1.3e-05   25.4   0.0    1.9  1  AAA_33           AAA domain
    2.4e-05   24.1   0.1    8.9e-05   22.3   0.1    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.8e-05   22.8   3.2     0.0063   16.8   0.9    3.1  2  AAA_22           AAA domain
    0.00021   21.5   0.0    0.00056   20.1   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    0.00036   20.9   2.1       0.02   15.3   0.1    3.1  3  AAA_16           AAA ATPase domain
    0.00099   19.5   0.3     0.0039   17.6   0.0    2.2  2  AAA_17           AAA domain
     0.0013   18.3   0.0     0.0032   17.0   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
     0.0018   17.9   2.1     0.0096   15.5   0.0    2.9  3  AAA_25           AAA domain
      0.002   17.3   0.0     0.0036   16.4   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
     0.0021   18.2   0.0     0.0057   16.8   0.0    1.8  1  SKI              Shikimate kinase
     0.0023   17.2   0.0     0.0045   16.3   0.0    1.6  1  TIP49            TIP49 P-loop domain
     0.0041   17.3   0.0     0.0098   16.0   0.0    1.6  1  Cytidylate_kin2  Cytidylate kinase-like family
     0.0071   16.4   0.0      0.017   15.2   0.0    1.7  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0084   15.9   0.1      0.029   14.1   0.0    2.0  2  IstB_IS21        IstB-like ATP binding protein
     0.0096   15.3   0.1        1.1    8.7   0.0    2.6  2  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.021   14.8   0.0    1.4  1  Rad17            Rad17 P-loop domain
      0.013   15.3   0.0      0.026   14.3   0.0    1.5  1  Cytidylate_kin   Cytidylate kinase
      0.014   15.4   0.0       0.03   14.3   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.014   15.9   0.1      0.078   13.5   0.0    2.5  2  ABC_tran         ABC transporter
      0.015   15.7   0.0      0.033   14.6   0.0    1.6  1  RNA_helicase     RNA helicase
      0.019   15.1   0.0      0.035   14.2   0.0    1.4  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.02   14.7   0.0      0.042   13.6   0.0    1.5  1  AAA_11           AAA domain
      0.023   14.5   0.0       0.92    9.2   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.025   14.6   0.0      0.077   13.0   0.0    1.9  1  AAA_14           AAA domain
      0.029   14.2   0.0      0.064   13.1   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
       0.05   13.0   0.0      0.092   12.1   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.072   13.0   0.0        6.9    6.6   0.0    2.5  2  NACHT            NACHT domain
       0.08   12.6   1.8       0.41   10.2   0.0    2.4  2  SRP54            SRP54-type protein, GTPase domain
      0.095   12.4   0.1       0.23   11.1   0.0    1.8  1  AAA_30           AAA domain
       0.15   11.4   2.4        1.9    7.8   0.2    2.7  2  ATPase           KaiC
        1.1    9.5   3.8       0.83   10.0   0.5    2.4  1  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.1   0.0   1.8e-42   9.1e-40       1     132 []     222     351 ..     222     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 1.8e-42
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +l++GppGtGKT++ +a+a+elg +f+e+++s ++s+y+ge++k+++++f+ ak+ + p+ilfiDE+d++ak+r+++
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHELGLPFVEVKLSMITSQYLGETAKNVEKTFEVAKRLS-PCILFIDEFDSVAKTRRSD 297
                                       69******************************************************9.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETTS CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieiel 132
                                       e+   +r+vn+Ll+ +d+ +  +++vi+igatn+pd+ld+a   +Rfd+++++++
  gi|313125289|ref|YP_004035553.1| 298 EHAALKRAVNTLLKSIDDISLIRDEVILIGATNHPDQLDSAAW-RRFDEIVNFPR 351
                                       *******************************************.7******9985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.3     2e-11     1e-08       1      43 [.     372     414 ..     372     422 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2e-11
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                       d+d +++A rTeG +G Dl  + reA+l+Al + ++++t+ d+
  gi|313125289|ref|YP_004035553.1| 372 DFDPEAVADRTEGLTGSDLRMVLREAVLEALTEERTALTQTDI 414
                                       8999***********************************9987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.51   2.6e+02      53     105 ..     128     181 ..      85     207 .. 0.72
   2 !   24.1   0.0   8.2e-08   4.1e-05       1      44 [.     222     286 ..     222     342 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.51
                            AAA_18  53 dedkldklldaleenssaleegknlvidghlaeleseaakdikk...vvLtaspee 105
                                       d d +d+ +++ +e   ++ +++ + id++l ++++e+     +   v ++a++e+
  gi|313125289|ref|YP_004035553.1| 128 DHDDVDVSHTEARERT-RSIQADRVWIDSLLDQYFDEEEDAE-MldlVQVRAPEEI 181
                                       3344444444444433.5788899999999999998866543.3478888888875 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 8.2e-08
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe 44 
                                       Il  G+pG+GKtt++++L+ +lg+                     +++  +vak   +++ + +e
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHELGLpfvevklsmitsqylgetaknVEKTFEVAKRLSPCILFIDE 286
                                       8999**************99998888877777777555555555555555555555555555444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.8e-08   8.8e-06       2     138 .]     222     343 ..     221     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.8e-08
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEvera 77 
                                       +l vGppGtgK+++++ la+ l+ ++++v l+  +t+ + +g++       + v++ +  a r +++il++DE++ +
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHELGLPFVEVKLSM-ITS-QYLGETA------KNVEKTFEVAKRlSPCILFIDEFDSV 290
                                       789****************************87.333.3344444......23333333333359**********99 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                        +   +  +  l +    l ++   ++  +d+    + +i+++n +d    +l++a ++Rf
  gi|313125289|ref|YP_004035553.1| 291 AKTRRSDEHAALKRAVNTLLKSIDDISLIRDE----VILIGATNHPD----QLDSAAWRRF 343
                                       98888888888888888888888888887776....99999999999....8888988888 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.41     2e+02      94     125 ..      19      50 ..       6      77 .. 0.79
   2 !   22.3   0.0   2.5e-07   0.00013       1      49 [.     221     270 ..     221     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.41
                            AAA_28  94 geaeaeleaaarekrydlvfllpp.apeidddg 125
                                        e ++el++     ry++vf ++p + e +dd+
  gi|313125289|ref|YP_004035553.1|  19 TE-NRELDENDLPPRYRRVFWTDPpDDEDEDDE 50 
                                       34.7899999999**********8455555555 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 2.5e-07
                            AAA_28   1 kivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv 49 
                                       ki ++G+++tGKTt+++aLa + g p v+    +i+++ l ++ ++ +++
  gi|313125289|ref|YP_004035553.1| 221 KILFVGPPGTGKTTVSRALAHElGLPFVEVKLSMITSQYLGETAKNVEKT 270
                                       799*****************877999998777777777666555555554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.6e-08   1.3e-05       2      92 ..     222     347 ..     222     383 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.6e-08
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt......................lrrrlfgtdqqskt........ 46 
                                       +l+vG+pG+GK+t+++ l+ +lg  +v +                          l            +        
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHELGlpFVEVKLSMitsqylgetaknvektfevakrL------------Spcilfide 286
                                       69*********************885555555523333444444444444433330............033333333 PP

                            AAA_33  47 ..........dytrvldrlyqilnelarkalsagrnvil.dat....nlsrrerarflkla 92 
                                                 d   +l+r+ ++l + +++    +  vil  at     l+ ++++rf++++
  gi|313125289|ref|YP_004035553.1| 287 fdsvaktrrsDEHAALKRAVNTLLKSIDDISLIRDEVILiGATnhpdQLDSAAWRRFDEIV 347
                                       3333333332444466677777777777776666666664555333334566666666665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   1.8e-07   8.9e-05      32     101 ..     218     295 ..     183     348 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-07
                            RuvB_N  32 aldhvllyGpPGlGkttlakiiakelg.....vklk.itsgPvlekagdlaalltnlee..kdvlfideihrlsrav 100
                                       ++  +l++GpPG Gktt+++ +a+elg     vkl  its    e a+++   +   ++    +lfide   ++++ 
  gi|313125289|ref|YP_004035553.1| 218 EIGKILFVGPPGTGKTTVSRALAHELGlpfveVKLSmITSQYLGETAKNVEKTFEVAKRlsPCILFIDEFDSVAKTR 294
                                       45689********************9833311333323444444555555444333332113589999988777665 PP

                            RuvB_N 101 e 101
                                        
  gi|313125289|ref|YP_004035553.1| 295 R 295
                                       5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.9   1.3e-05    0.0063       8     128 ..     222     326 ..     217     335 .. 0.55
   2 ?   -0.9   0.1       3.7   1.8e+03      56      84 ..     394     420 ..     354     439 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelkaerlsseell.ea 81 
                                       ++ +G++GtGKTt+ r l+++l         + ++v+v+l+  t   + + ++++ + +++    +rls   l+ + 
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHEL---------GLPFVEVKLSMITsqYLGETAKNVEKTFEVA---KRLSPCILFiDE 286
                                       7889*****************9.........7777766666555222222233333333321...334555555555 PP

                            AAA_22  82 leqalraravielliiDEaqhlrseealeeL.rsllnlsrkgvqliLv 128
                                       +   +++r+       DE   l  ++a+++L +s+ ++s     +iL+
  gi|313125289|ref|YP_004035553.1| 287 FDSVAKTRRS------DEHAAL--KRAVNTLlKSIDDISLIRDEVILI 326
                                       5555555555......444444..333333335555544444455555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.7
                            AAA_22  56 llrellralglelkaerlsseellealeq 84 
                                       l++++l+al++e+ a  l++ ++l+a+e+
  gi|313125289|ref|YP_004035553.1| 394 LREAVLEALTEERTA--LTQTDILDAVED 420
                                       345555555555555..444444444443 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.1e-06   0.00056       1     105 [.     217     315 ..     217     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.1e-06
                                       -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS...EEEE CS
                             AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG...ivll 74 
                                       r+i++il++gp g+Gkt +++ala  l +    +++ +  s ++      +++ +   + +   +++++    i+++
  gi|313125289|ref|YP_004035553.1| 217 REIGKILFVGPPGTGKTTVSRALAHELGL----PFVEVKLSMITS-----QYLGETAKNVEKTFEVAKRLspcILFI 284
                                       5799***********************98....777777766666.....33333333333333333222334**** PP

                                       ETGGG-------------HHHHHHHHHHHH- CS
                             AAA_2  75 DEidKihpkessgadvSregVqrdLLqileg 105
                                       DE d ++++++s +    +  ++ LL+ +++
  gi|313125289|ref|YP_004035553.1| 285 DEFDSVAKTRRSDEHAALKRAVNTLLKSIDD 315
                                       ********97777777777778888888877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1     4e-05      0.02      25      49 ..     220     244 ..     195     258 .. 0.82
   2 ?    3.4   0.0      0.18        89     129     161 ..     273     305 ..     263     326 .. 0.67
   3 ?   -1.0   0.1       4.2   2.1e+03     116     135 ..     378     406 ..     304     427 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4e-05
                            AAA_16  25 elvllsGesGvGKsslvrellrale 49 
                                       + +l++G++G+GK+++ r+l+++l 
  gi|313125289|ref|YP_004035553.1| 220 GKILFVGPPGTGKTTVSRALAHELG 244
                                       5689****************99875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.18
                            AAA_16 129 llsrderplvlvlDdlqwadeaslql.laaLlrl 161
                                        ++r  +p +l++D+++ +  + ++   aaL r+
  gi|313125289|ref|YP_004035553.1| 273 VAKR-LSPCILFIDEFDSVAKTRRSDeHAALKRA 305
                                       4555.568*********54443333334444444 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4.2
                            AAA_16 116 a.........srllellkrll.allsrder 135
                                                 s+l+ +l++++ + l++ er
  gi|313125289|ref|YP_004035553.1| 378 VadrtegltgSDLRMVLREAVlEALTE-ER 406
                                       122222334455555555555333333.33 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       6.5   3.2e+03      75     114 ..     156     197 ..     108     213 .. 0.59
   2 !   17.6   0.0   7.8e-06    0.0039       1      25 [.     225     249 ..     225     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 6.5
                                       EEEE-SEEEETTEEEESSHHHHHHHH....SEEEEEE--HHH CS
                            AAA_17  75 lvdghprikeqagfldglpkevleelkp..daiilleadpee 114
                                       l+d ++  +e+a++ld +++   ee++   + ++l ++++ e
  gi|313125289|ref|YP_004035553.1| 156 LLDQYFDEEEDAEMLDLVQVRAPEEIEMtlEDLVLTQDQEGE 197
                                       566666666666666666655555554411334444444444 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7.8e-06
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG GK+t+++ l++++g+++++
  gi|313125289|ref|YP_004035553.1| 225 VGPPGTGKTTVSRALAHELGLPFVE 249
                                       7*********************997 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.3e-06    0.0032      23     110 ..     209     288 ..     204     300 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.3e-06
                             AAA_7  23 syllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpgg 99 
                                       +yl +  l++  ++l+vGp GtGKt++ + l ++l    ++ +++++  +    ++ + +e+ +e       +++  
  gi|313125289|ref|YP_004035553.1| 209 EYLADIGLREIGKILFVGPPGTGKTTVSRALAHELG-LPFVEVKLSMITSQYLGETAKNVEKTFE-------VAKRL 277
                                       5777778888889******************99999.3444444433333333444444444443.......34445 PP

                             AAA_7 100 kklvvFvDDln 110
                                         +++F+D+++
  gi|313125289|ref|YP_004035553.1| 278 SPCILFIDEFD 288
                                       55666666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.4       2.6   1.3e+03     103     103 ..      83      83 ..      21     173 .. 0.59
   2 !   15.5   0.0   1.9e-05    0.0096      12      56 ..     198     242 ..     190     254 .. 0.85
   3 ?   -0.1   0.0       1.2   5.9e+02     130     172 ..     267     309 ..     244     319 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.6
                            AAA_25 103 l 103
                                       l
  gi|313125289|ref|YP_004035553.1|  83 L 83 
                                       2 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.9e-05
                            AAA_25  12 vadlaapppprrwlvk.gllpagelallaGapgtGKttlaldlala 56 
                                       +++l +++++r++l + gl ++ + +l++G+pgtGKtt+   la++
  gi|313125289|ref|YP_004035553.1| 198 IHKLMKAIEHREYLADiGL-REIGKILFVGPPGTGKTTVSRALAHE 242
                                       67788999********666.79****************99888875 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.2
                            AAA_25 130 vdaleaaieevegvrlvviDplsralggdensnsdv.galveal 172
                                       v++  +++++   +  + iD ++++      +++++ +++v+ l
  gi|313125289|ref|YP_004035553.1| 267 VEKTFEVAKR-LSPCILFIDEFDSVAKTRRSDEHAAlKRAVNTL 309
                                       5556666666.348889999999999997777777667777765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.3e-06    0.0036      93     153 ..     173     243 ..     163     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.3e-06
                             T2SSE  93 lviRkksakeltlddlgaeealk..........ekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                       + +R +++ e+tl+dl+ +++++          e+ + +    +re g il+ G+ g+GKtt+  al +e+
  gi|313125289|ref|YP_004035553.1| 173 VQVRAPEEIEMTLEDLVLTQDQEgeihklmkaiEHREYLADIGLREIGKILFVGPPGTGKTTVSRALAHEL 243
                                       67999******************7777676665444444455678889***************99998886 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.1e-05    0.0057       1      23 [.     228     250 ..     228     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+tv ++lA++lgl+f+++
  gi|313125289|ref|YP_004035553.1| 228 PGTGKTTVSRALAHELGLPFVEV 250
                                       69******************986 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     9e-06    0.0045      52      93 ..     221     260 ..     180     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                        +L++Gp+gtGkt ++ a+++elg  +pfv ++ s + s+ +
  gi|313125289|ref|YP_004035553.1| 221 KILFVGPPGTGKTTVSRALAHELG--LPFVEVKLSMITSQYL 260
                                       489*********************..9***999998877654 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-05    0.0098       8      60 ..     228     281 ..     224     327 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-05
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde.rsrlssfl 60 
                                        G+g++t+ +aLA++Lglpf++ ++   +++ lg + + ve+  e ++rls  +
  gi|313125289|ref|YP_004035553.1| 228 PGTGKTTVSRALAHELGLPFVEVKLSMITSQYLGETAKNVEKTFEvAKRLSPCI 281
                                       59********************************99999977666455544443 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.4e-05     0.017       1      45 [.     221     275 ..     221     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-05
                                       EEEEEESTTSSHHHHHHHHHT.........S.TEEESSSTTSSSSEEEEEEEETT CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltg.........e.kaivsdkpgtTrdinegrvklkg 45 
                                       ++++vG p +GK+t+ +al           +   i+s++ g T + +e+++++ +
  gi|313125289|ref|YP_004035553.1| 221 KILFVGPPGTGKTTVSRALAHelglpfvevKlSMITSQYLGETAKNVEKTFEVAK 275
                                       589****************97666777654446799*********9999988443 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.7   3.3e+03     101     137 ..     140     176 ..     131     182 .. 0.80
   2 !   14.1   0.0   5.7e-05     0.029      46      71 ..     218     243 ..     176     308 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.7
                         IstB_IS21 101 ralkrllkvdllilDdlgllpldqaeaellfeviekr 137
                                       r+ +r +++d + +D l  + +d++e ++++++++ r
  gi|313125289|ref|YP_004035553.1| 140 RERTRSIQADRVWIDSLLDQYFDEEEDAEMLDLVQVR 176
                                       4556667778888899999999999999999998766 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.7e-05
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgvea 71 
                                       +   i+++Gp+G+GK+ ++ al++e 
  gi|313125289|ref|YP_004035553.1| 218 EIGKILFVGPPGTGKTTVSRALAHEL 243
                                       445799*****************986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.06        30      35      54 ..     219     238 ..     194     244 .. 0.83
   2 !    8.7   0.0    0.0022       1.1     104     144 ..     263     303 ..     252     350 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.06
                              TniB  35 mpnlllvGdsnnGKtmivek 54 
                                       + ++l+vG++ +GKt++ + 
  gi|313125289|ref|YP_004035553.1| 219 IGKILFVGPPGTGKTTVSRA 238
                                       56799***********9875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0022
                              TniB 104 vskleqqvlrllrelkvrvLiiDEihnllagsarkqrefln 144
                                       ++k  +++ ++ ++l++ +L iDE++++ + ++++ +++l 
  gi|313125289|ref|YP_004035553.1| 263 TAKNVEKTFEVAKRLSPCILFIDEFDSVAKTRRSDEHAALK 303
                                       56677788999******************998887655442 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.2e-05     0.021      46      81 ..     221     255 ..     183     316 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.2e-05
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvs 81 
                                       + +L  GP+G gk+tv + L+ elg  + e   ++ 
  gi|313125289|ref|YP_004035553.1| 221 K-ILFVGPPGTGKTTVSRALAHELGLPFVEVKLSMI 255
                                       3.5678*******************98888665554 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.2e-05     0.026       5      28 ..     226     249 ..     222     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.2e-05
                                       -STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                       GP g+GK +v+rala++lgl +++
  gi|313125289|ref|YP_004035553.1| 226 GPPGTGKTTVSRALAHELGLPFVE 249
                                       9******************99986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     6e-05      0.03       8      47 ..     199     249 ..     191     260 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-05
                                       HHHHHHHHHCH..TEE.......EEEEESTTSSHHHHHHHHHHHTT--..- CS
                              TsaE   8 ealgkklakal..gdv.......ilLeGdLGaGKTtlvrglakalgve..e 47 
                                       ++l k++ +    +d+       il+ G+ G+GKTt +r+la++lg+   e
  gi|313125289|ref|YP_004035553.1| 199 HKLMKAIEHREylADIglreigkILFVGPPGTGKTTVSRALAHELGLPfvE 249
                                       555555544323322244555679*********************986444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       7.1   3.6e+03      76      89 ..     139     157 ..      82     208 .. 0.53
   2 ?   13.5   0.0   0.00016     0.078      10      67 ..     218     273 ..     211     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.1
                                       HHHH.....HHHTCHHHHH CS
                                       xxxx.....xxxxxxxxxx RF
                          ABC_tran  76 vren.....esdeeiekal 89 
                                       +re+     +++++i+ +l
  gi|313125289|ref|YP_004035553.1| 139 ARERtrsiqADRVWIDSLL 157
                                       3333444432222233333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00016
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       e  k+ +vG+ G+GK+t+ ++la++l     e++l +  +++  l ++ k+++  ++ 
  gi|313125289|ref|YP_004035553.1| 218 EIGKILFVGPPGTGKTTVSRALAHELGLPFVEVKLSMITSQY--LGETAKNVEKTFEV 273
                                       5567899****************9998877777777777777..55555555555544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.5e-05     0.033       1      27 [.     222     251 ..     222     310 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.5e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...k 27 
                                       i+++Gp+g+GK+t+++ La++l   +   k
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHELGLPFvevK 251
                                       6899*****************985554442 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.1e-05     0.035      24      86 ..     222     295 ..     202     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.1e-05
                                       EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..............HHHHHHTTTSEEEEEE-TT--HHHH CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp..............ldlleqakggtLylkdiadlskaeq 86 
                                       ++ +G++G+gk++v+r+L+++ g    +fv+ +l+ ++               ++ +++++ +L++ ++++  k   
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHELGL---PFVEVKLSMITsqylgetaknvektFEVAKRLSPCILFIDEFDSVAKTRR 295
                                       7889**************987654...44444444333223344444554446666667999****99999888765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.4e-05     0.042      16      42 ..     218     244 ..     190     283 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-05
                            AAA_11  16 eseitliqGPPGtgKTktivellsqll 42 
                                       e +  l+ GPPGtgKT++  +l ++l 
  gi|313125289|ref|YP_004035553.1| 218 EIGKILFVGPPGTGKTTVSRALAHELG 244
                                       33478999************9999985 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.14        70      95     142 ..     111     159 ..      95     204 .. 0.80
   2 ?    9.2   0.0    0.0018      0.92       5      71 ..     226     287 ..     222     293 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                   Viral_helicase1  95 GDplQipfhsrnasfllahlpsslshrvgrrttyllpsdvaeilsak.v 142
                                       +D+ Q +++++ a +   h  + +sh + r +t  +++d++ i s    
  gi|313125289|ref|YP_004035553.1| 111 ADRDQLETNPTIAAAVEDHDDVDVSHTEARERTRSIQADRVWIDSLLdQ 159
                                       7999*************************************99998743 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0018
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+t+ r l+++  l +++++    ++t +   +++++v+  ++f+ a+  s    il++DE+
  gi|313125289|ref|YP_004035553.1| 226 GPPGTGKTTVSRALAHELgLPFVEVK--LSMITSQYLGETAKNVE--KTFEVAKRLS--PCILFIDEF 287
                                       88*************99554443333..35555554333344444..4444444433..349999997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00015     0.077       6      77 ..     223     296 ..     218     332 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                            AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev.....p 77 
                                       + +G+  +GKTt+ + l++el      +++++l   + + l +++k+ e  +e +k+    +lf+DE   v     +
  gi|313125289|ref|YP_004035553.1| 223 LFVGPPGTGKTTVSRALAHELG---LPFVEVKLSMITSQYLGETAKNVEKTFEVAKRLSPCILFIDEFDSVaktrrS 296
                                       568999************9999...8899999888888776666555666666545556799******999544441 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00013     0.064       2      58 ..     222     275 ..     221     337 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkk 58 
                                       +l+ g PG++kt++ +ala+ l+l f  +++   ++ s  lG +  +  ek+fe+ k
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHELGLPFVEVKLS--MITSQYLGETAKNV-EKTFEVAK 275
                                       788999********************988874..78888888765544.34454443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019     0.092      24      44 ..     221     241 ..     204     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlps 44 
                                       ++l+vGppG+GKt + ++l+ 
  gi|313125289|ref|YP_004035553.1| 221 KILFVGPPGTGKTTVSRALAH 241
                                       69*************999975 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.014       6.9       3      24 ..     222     243 ..     221     250 .. 0.89
   2 ?    3.7   0.0      0.11        54      57     111 ..     254     312 ..     249     339 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.014
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       ++  G++G GKTt  + la+++
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHEL 243
                                       6789************999987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                                       HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHH CS
                             NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLse 111
                                       +++sq++ + a+  e+  +++++     l +D +D +++  +     + k++v+tlL++
  gi|313125289|ref|YP_004035553.1| 254 MITSQYLGETAKNVEKTFEVAKRLSPCILFIDEFDSVAKTRRSdehaALKRAVNTLLKS 312
                                       57788877766666667777888888888899999999877774444555555555544 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6      0.77   3.8e+02      45     124 ..     113     188 ..     102     208 .. 0.72
   2 ?   10.2   0.0   0.00083      0.41       4      25 ..     222     243 ..     220     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.77
                                       HHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEE CS
                             SRP54  45 veQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvl 121
                                        +QL+t+ + +     + + ++d      ea e+ ++ ++d v +D+   +  d+e  +e+ ++ +v +p+e+ ++l
  gi|313125289|ref|YP_004035553.1| 113 RDQLETNPTIAA----AVEDHDDVDVSHTEARERTRSIQADRVWIDSLLDQYFDEEEDAEMLDLVQVRAPEEIEMTL 185
                                       567776666555....12333344445667888899999********999999999999**9999999999999888 PP

                                       ETT CS
                             SRP54 122 dat 124
                                       + +
  gi|313125289|ref|YP_004035553.1| 186 EDL 188
                                       644 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00083
                                       EEEEESTTSSHHHHHHHHHHHH CS
                             SRP54   4 illvGlqGaGKTttlaKLaall 25 
                                       il+vG+ G+GKTt    La+ l
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHEL 243
                                       89**************999976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00047      0.23      22      40 ..     223     241 ..     217     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00047
                            AAA_30  22 vltGpAGtGKttalkalre 40 
                                       + +Gp+GtGKtt+ +al++
  gi|313125289|ref|YP_004035553.1| 223 LFVGPPGTGKTTVSRALAH 241
                                       579**********999864 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.13        64      98     131 ..     125     159 ..     110     207 .. 0.77
   2 ?    7.8   0.2    0.0038       1.9      14      38 ..     214     238 ..     197     334 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
                            ATPase  98 e.kdkedleelieelaeaikeikakrvviDsitgl 131
                                       + +d++d++   +e +e  ++i+a rv iDs+   
  gi|313125289|ref|YP_004035553.1| 125 AvEDHDDVDVSHTEARERTRSIQADRVWIDSLLDQ 159
                                       247888999999999999*************8554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0038
                            ATPase  14 gGipegrvvlitGepGtGKtifalq 38 
                                        G+ e   +l +G pGtGKt+++  
  gi|313125289|ref|YP_004035553.1| 214 IGLREIGKILFVGPPGTGKTTVSRA 238
                                       588899999************9875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5    0.0017      0.83      13      35 ..     222     244 ..     217     326 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0017
                            AAA_19  13 llvtaGpGtGKTrvlkhivallv 35 
                                       +l +++pGtGKT+v ++  ++l 
  gi|313125289|ref|YP_004035553.1| 222 ILFVGPPGTGKTTVSRALAHELG 244
                                       6789*********9887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.79u 0.39s 00:00:01.18 Elapsed: 00:00:00.57
# Mc/sec: 2403.37
//
Query:       gi|313125290|ref|YP_004035554.1|  [L=377]
Description: 3-ketoacyl-CoA thiolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-79  264.8   0.4    2.1e-78  263.3   0.8    1.5  2  Thiolase_N     Thiolase, N-terminal domain
    7.1e-42  141.9   0.8    9.8e-42  141.5   0.1    1.7  2  Thiolase_C     Thiolase, C-terminal domain
    0.00011   21.9   0.8    0.00019   21.1   0.1    1.7  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.065   13.1   4.9       0.51   10.2   0.1    2.8  3  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
       0.13   12.3   0.0       0.62   10.2   0.0    2.0  2  HTH_7          Helix-turn-helix domain of resolvase
       0.81    9.9   4.0       0.97    9.6   1.0    2.3  2  YfhD           YfhD-like protein
       0.97    9.3   3.7        4.2    7.3   0.1    3.2  3  DUF433         Protein of unknown function (DUF433)


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.3   0.8   8.2e-82   2.1e-78       2     259 ..       5     247 ..       4     248 .. 0.93
   2 ?   -2.7   0.0       1.1   2.9e+03       4      37 ..     279     312 ..     279     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 263.3 bits;  conditional E-value: 8.2e-82
                                       EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSCHHHHHHHHTTS-TTSE CS
                        Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqniarqaalkagipeevp 77 
                                       vi++a rtp+gk gg+++d+++e+L+ +++ ++l+++ +d+e+vd++++G   q  ++++n+ar +al +++ e +p
  gi|313125290|ref|YP_004035554.1|   5 VIAAAHRTPFGKAGGVFEDVRSEDLSVALIDHILDETDLDAEDVDDLMWGVAQQRgEQDNNVARVIALLSELGEGTP 81 
                                       899**************************************************99555666**************** PP

                                       EEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSE CS
                        Thiolase_N  78 avtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneeh 154
                                       a+t+n+ c+S+++av+ a +++aag+ d+vvagGvE+ms++p++ +  + ++l  + ++  ++             +
  gi|313125290|ref|YP_004035554.1|  82 ATTINRWCASSMQAVISASDAVAAGNRDCVVAGGVENMSRVPMDGD--SYEHLHPELSEEYNIFQ----------LQ 146
                                       *******************************************997..44555555555555553..........56 PP

                                       HHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-B CS
                        Thiolase_N 155 mGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkp 231
                                       mG+tae++a++y++sReeqde+A++s+q+aa+a+++g+F+deivP++++      ++++de+ir+++t+++L+ l p
  gi|313125290|ref|YP_004035554.1| 147 MGMTAEKVAEEYDVSREEQDEYALQSQQRAAEAAESGRFDDEIVPIETEA----GVITEDEGIRPDTTMDALSGLPP 219
                                       **********************************************9988....57********************* PP

                                       SSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 232 aFkkeGtvtAgnasqisDGaaavllmse 259
                                       aF  +GtvtAgn+sqi+DGaaavl++s+
  gi|313125290|ref|YP_004035554.1| 220 AFTGDGTVTAGNSSQITDGAAAVLVTSR 247
                                       *************************997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                       EEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHH CS
                        Thiolase_N   4 vsaartpigkfggslkdlsaeeLlaealkallek 37 
                                       v a+rt + + g  + d   +eL ++++++++  
  gi|313125290|ref|YP_004035554.1| 279 VPATRTLLERNGRDVDDYDLVELNEAFASQCVYA 312
                                       5689999999999999999999999999999875 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.7     7e+03      28      43 ..      34      49 ..      31      51 .. 0.84
   2 !  141.5   0.1   3.8e-45   9.8e-42       3     120 ..     257     374 ..     255     377 .] 0.97

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.7
                                      HHHHHHHHT--GGGES CS
                        Thiolase_C 28 ikkvlkkagltvedid 43
                                      i ++l+++ l+ ed+d
  gi|313125290|ref|YP_004035554.1| 34 IDHILDETDLDAEDVD 49
                                      678999999*999998 PP

  == domain 2  score: 141.5 bits;  conditional E-value: 3.8e-45
                                       -SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH- CS
                        Thiolase_C   3 plakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialG 79 
                                       +la +   a++gvdp+ +g+gP++a++ +l+++g +v+d dl+E+nEAFa+q+++++ +l++d + +NvnGGaialG
  gi|313125290|ref|YP_004035554.1| 257 ILADVGMNAVAGVDPTVMGIGPVPATRTLLERNGRDVDDYDLVELNEAFASQCVYAMDELGIDHDIFNVNGGAIALG 333
                                       688889999******************************************************************** PP

                                       B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEE CS
                        Thiolase_C  80 HPlGasGaRivvtllselkkeggklgvaalCigggqgvalv 120
                                       HPlGasGaR+ vtl++e+ k++++ g+a+lC g gqg+a+ 
  gi|313125290|ref|YP_004035554.1| 334 HPLGASGARLPVTLIHEMIKRDAERGLATLCVGFGQGAAIE 374
                                       **************************************985 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   7.5e-08   0.00019     151     205 ..      63     119 ..      31     132 .. 0.83
   2 ?   -3.3   0.0       2.1   5.4e+03      39      75 ..     161     190 ..     151     198 .. 0.53

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.5e-08
                                       TTHHHHHHHHH..HT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE-- CS
                     ketoacyl-synt 151 anviagrisya..lglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvell 205
                                        n +a  i++   lg   p+ t+   C+Ss  av  a +++ +g+ d+++aGGve +
  gi|313125290|ref|YP_004035554.1|  63 DNNVARVIALLseLGEGTPATTINRWCASSMQAVISASDAVAAGNRDCVVAGGVENM 119
                                       5666666666666888889999********99999999****************966 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                                       TSSCGTTSBTSSTTEEE-BSS.EEE..STTEGGTTST CS
                     ketoacyl-synt  39 drwdadklydpparaagkiktklggfldvddfdpeff 75 
                                       +r ++d++  ++++ a+++ +         +fd+e+ 
  gi|313125290|ref|YP_004035554.1| 161 SREEQDEYALQSQQRAAEAAE-------SGRFDDEIV 190
                                       455555555333333333333.......355666555 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0002      0.51       3      40 ..      85     122 ..      84     130 .. 0.91
   2 ?    4.0   0.1     0.017        44      53      65 ..     236     248 ..     228     261 .. 0.77
   3 ?   -2.4   0.1       1.8   4.5e+03      47      57 ..     362     372 ..     354     372 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGC CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlski 40 
                                       +n  C++ ++a+  A++++++g+  +v+  g e++s++
  gi|313125290|ref|YP_004035554.1|  85 INRWCASSMQAVISASDAVAAGNRDCVVAGGVENMSRV 122
                                       6778********************************95 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                                       -EEEEEEEEEEES CS
                       ACP_syn_III  53 GDGAgAvvlease 65 
                                        DGA+Av+++  e
  gi|313125290|ref|YP_004035554.1| 236 TDGAAAVLVTSRE 248
                                       6********9873 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.8
                                       HHHTTB-EEEE CS
                       ACP_syn_III  47 stavlfGDGAg 57 
                                       + +v fG GA+
  gi|313125290|ref|YP_004035554.1| 362 TLCVGFGQGAA 372
                                       67999999996 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   2.9e+03       9      20 ..      64      75 ..      61      86 .. 0.63
   2 ?   10.2   0.0   0.00024      0.62      19      36 ..     146     163 ..     143     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                      HHHGGGGSSTTT CS
                             HTH_7  9 ndinrvvkLlee 20
                                      n  +rv++Ll+e
  gi|313125290|ref|YP_004035554.1| 64 NNVARVIALLSE 75
                                      457888888764 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00024
                                       TTT--STTTSSSS---SS CS
                             HTH_7  19 eeGisiskIAkevnisRs 36 
                                       + G+++ k+A+e+++sR+
  gi|313125290|ref|YP_004035554.1| 146 QMGMTAEKVAEEYDVSRE 163
                                       67***************5 PP

>> YfhD  YfhD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.0   0.00038      0.97      30      53 ..     159     180 ..     138     183 .. 0.82
   2 ?   -0.2   0.1      0.44   1.1e+03      34      44 ..     246     256 ..     245     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00038
                              YfhD  30 DvEfSkelADheDleAnaRakaAd 53 
                                       D  +S+e  D++ l++++Ra++A 
  gi|313125290|ref|YP_004035554.1| 159 D--VSREEQDEYALQSQQRAAEAA 180
                                       3..5****************9996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.44
                              YfhD  34 SkelADheDle 44 
                                       S+e+A++ Dl+
  gi|313125290|ref|YP_004035554.1| 246 SREFAAEHDLD 256
                                       89*****9986 PP

>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4      0.24   6.1e+02      34      51 ..      34      50 ..      31      52 .. 0.88
   2 ?    7.3   0.1    0.0016       4.2      28      47 ..     145     163 ..     142     167 .. 0.91
   3 ?   -0.6   0.0      0.47   1.2e+03      16      31 ..     340     355 ..     338     358 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.24
                                      HHHHHHHH.TS-HHHHHH CS
                            DUF433 34 ieeiledyPdLtlediqa 51
                                      i+ il++  dL++ed+ +
  gi|313125290|ref|YP_004035554.1| 34 IDHILDET-DLDAEDVDD 50
                                      689*****.******976 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                                       HHTT--HHHHHHHH.TS-HH CS
                            DUF433  28 laaGesieeiledyPdLtle 47 
                                       l++G++ e ++e+y d+++e
  gi|313125290|ref|YP_004035554.1| 145 LQMGMTAEKVAEEY-DVSRE 163
                                       899***********.99998 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.47
                                       TT--BTHHHHHHHHTT CS
                            DUF433  16 gtRipVetilellaaG 31 
                                       g R+pV  i e+++ +
  gi|313125290|ref|YP_004035554.1| 340 GARLPVTLIHEMIKRD 355
                                       88*******9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2052.63
//
Query:       gi|313125291|ref|YP_004035555.1|  [L=620]
Description: sodium/proton antiporter, cpa1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-34  117.9  42.0    5.9e-34  117.5  42.0    1.0  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
    2.5e-33  114.8   1.0    6.2e-33  113.5   1.0    1.7  1  TrkA_N           TrkA-N domain
    5.7e-12   45.3   0.9      2e-10   40.4   0.1    2.6  2  TrkA_C           TrkA-C domain
    2.7e-09   37.4   0.2    9.4e-09   35.7   0.1    2.0  1  NAD_binding_7    Putative NAD(P)-binding
    4.3e-06   26.7   1.9      1e-05   25.5   1.9    1.7  1  NAD_binding_10   NAD(P)H-binding
      4e-05   24.1   2.9    0.00017   22.1   0.4    3.0  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0001   21.9   0.4    0.00016   21.2   0.4    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00047   20.7   0.2     0.0024   18.4   0.1    2.3  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00074   19.2   0.0     0.0021   17.7   0.0    1.8  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0011   18.7   0.0     0.0016   18.1   0.0    1.4  1  DAO              FAD dependent oxidoreductase
     0.0015   17.8   0.0     0.0022   17.3   0.0    1.2  1  FAD_binding_3    FAD binding domain
     0.0021   18.1   0.1     0.0044   17.1   0.1    1.6  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
     0.0043   16.3   1.2     0.0055   16.0   0.2    1.6  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0045   17.2   2.3      0.013   15.8   0.4    2.7  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0046   17.1   0.1      0.011   15.9   0.1    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0047   16.9   0.0      0.012   15.6   0.0    1.7  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.027   14.3   0.0    1.4  1  DFP              DNA / pantothenate metabolism flavoprotein
       0.02   14.5   0.0      0.037   13.6   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.02   14.0   0.0      0.029   13.4   0.0    1.2  1  Lycopene_cycl    Lycopene cyclase protein
      0.022   14.7   0.2      0.022   14.7   0.2    2.2  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.043   13.4   0.1      0.083   12.5   0.1    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
       0.06   13.9   0.0       0.15   12.6   0.0    1.7  1  XdhC_C           XdhC Rossmann domain
       0.11   11.9   0.1       0.32   10.3   0.1    1.8  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.12   11.1   0.0       0.16   10.6   0.0    1.2  1  HI0933_like      HI0933-like protein
       0.16   12.3   0.0       0.16   12.3   0.0    2.5  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
       0.27   10.9   0.3        1.1    8.9   0.0    1.9  2  DUF4564          Domain of unknown function (DUF4564)


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5  42.0   8.6e-37   5.9e-34       8     375 ..      12     390 ..       7     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 8.6e-37
                                       HHHHHH......HHHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTH CS
                    Na_H_Exchanger   8 allvgl......larrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrknl 76 
                                       a+++g+      l+ r+ +p++++li  G++lGp +l++++p+   + l+ +  l + +++F+ +++l +++lr+  
  gi|313125291|ref|YP_004035555.1|  12 AAIIGIgvvsqiLSDRFQVPSVLFLITSGIILGPEVLNVVHPDsfGSGLSAIVGLSVAIIVFEGAFHLRIEKLREAP 88 
                                       333333345553699999*************************99999999999*********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHH CS
                    Na_H_Exchanger  77 ksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDa 153
                                        +++ l ++g  i++++++ ++++  +lg p++ ++l+ga+l at p v+++il e    + r+   l+ e+++nD+
  gi|313125291|ref|YP_004035555.1|  89 AATIRLITVGAGIALIGTAAAIHY--LLGSPWSVSFLIGALLVATGPTVIAPIL-EVVPARDRVEAALETEGIVNDV 162
                                       *****************9999998..799*************************.********************** PP

                                       HCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS....CTHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 154 vavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft....dddrelevllvlllalla 226
                                       +a +l +v+ +++   + g+t+ ++l   f+  +++g+++g ++   +++++r++     + ++   llvl+ al+a
  gi|313125291|ref|YP_004035555.1| 163 TAAILAVVIFEAI---IEGATEPGALMTLFAERLGVGVVVGTLVAAAMFYALRYVdlspGNAPQNARLLVLAGALVA 236
                                       *****99999999...7888888888888888888888888888888888888888888****************** PP

                                       HHHHHTS.XXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH...HHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHH CS
                    Na_H_Exchanger 227 allaell.gvsgilgaflaGlvlseyefsnklseklesfre...glfnplfFvlvGlsldlkvlnnhlsvlilvlli 299
                                       +++a+ +    gi ++  aG++l++ ++    +e++++f      +++ ++F+ + + l ++ l  +l +  l +++
  gi|313125291|ref|YP_004035555.1| 237 YGAADFIaTEAGIAAVATAGILLGNADVPY--EEDISAFKGditLIVLSFVFIALAALLEFETLL-RLGLGGLGVVV 310
                                       *******77788888999******777777..577888887755777777777777788877774.99999999999 PP

                                       HHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHH......XHHHHTTSSTTTCSTSXHHHH CS
                    Na_H_Exchanger 300 lvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpal......gllarelyallivvvlftvlv 370
                                       +va+ + r+l vfl +   ++++ e+++++f g  rg + + +a l+  +      g  a +l+ ++++v+l+tv++
  gi|313125291|ref|YP_004035555.1| 311 VVAL-VLRPLLVFLSAQGDRFTTGEKWFMSFVGP-RGIIPASVATLFAIQlraeglGQAADTLVGTVFLVILVTVVF 385
                                       9999.6****************************.**99998888877776677667777788*************9 PP

                                       HHHHH CS
                    Na_H_Exchanger 371 qGlsl 375
                                        G+  
  gi|313125291|ref|YP_004035555.1| 386 EGGLA 390
                                       98765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   1.0     9e-36   6.2e-33       1     114 [.     404     517 ..     404     519 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 9e-36
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       +++iG G+vGr+lae+L+++g++vv+i++d+e +e++r+eg +v +gd+td++vL++ag+++a++v+aatgdd++n+
  gi|313125291|ref|YP_004035555.1| 404 VLVIGGGKVGRTLAERLEDRGENVVLIEQDPEIIETARNEGHTVHQGDGTDTDVLRSAGADNAKIVVAATGDDDVNL 480
                                       68*****************7778****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvi 114
                                       l+++la++ ++  +iiara++p++++++++lg+ ++ 
  gi|313125291|ref|YP_004035555.1| 481 LVAQLANSKFDPETIIARANNPDNVDAFEELGVRTIS 517
                                       ******999999********************98875 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.13        92      13      36 ..     412     435 ..     402     451 .. 0.78
   2 !   40.4   0.1   2.9e-13     2e-10       2      69 ..     549     616 ..     548     617 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.13
                                       TTSBHHHHTHHHHS-EEEEEE-T.- CS
                            TrkA_C  13 vGktlkelnlrargvlvvairRg.g 36 
                                       vG+tl+e +l++rg +vv i  + +
  gi|313125291|ref|YP_004035555.1| 412 VGRTLAE-RLEDRGENVVLIEQDpE 435
                                       8******.*****999999976533 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 2.9e-13
                                       EEEEEE--GGGTTSBHHHHT..HHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkeln..lrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                        e++v+++  +vGkt+++++  l++ g+l+  i R+ge  +ps d++ + GD+++++g  ++++e+  ++
  gi|313125291|ref|YP_004035555.1| 549 QEIEVTSEE-IVGKTVRDIGpeLPN-GCLITLISRDGESSVPSADFTVQHGDHITIIGGHDAVREAMQFI 616
                                       689999666.********9988999.*************************************9988765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1   1.4e-11   9.4e-09       4      97 ..     398     504 ..     396     508 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.4e-11
                     NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele....elvklaeeelekd...........legadlv 65 
                                       d+   +vlv+GgG+v+ + +++l + g +v+++ ++  e++e    e  ++++     d            ++a++v
  gi|313125291|ref|YP_004035555.1| 398 DVIPMRVLVIGGGKVGRTLAERLEDRGENVVLIEQDP-EIIEtarnEGHTVHQG----DgtdtdvlrsagADNAKIV 469
                                       566679***************************9993.3333222221222222....122223555555999**** PP

                     NAD_binding_7  66 iaatddrelneriaeaaka...rrilvnvadkpel 97 
                                       +aat d+++n  +a++a +    +  + +a++p++
  gi|313125291|ref|YP_004035555.1| 470 VAATGDDDVNLLVAQLANSkfdPETIIARANNPDN 504
                                       ***************99764455667777777765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   1.9   1.5e-08     1e-05       3      95 ..     409     518 ..     408     545 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.5e-08
                                       TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S.EEEES---TCC..... CS
                    NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgad.aVvsalggggk..... 73 
                                        GkvGr l+++l +rg  +v+++  +pe ++   ++eg +v +gd td++ l++a ++   +Vv+a+g ++      
  gi|313125291|ref|YP_004035555.1| 409 GGKVGRTLAERLEDRG-ENVVLIEQDPEIIETA-RNEGHTVHQGDGTDTDVLRSAGADNAkIVVAATGDDDVnllva 483
                                       6**************6.8************965.69*******************9977725666665555466544 PP

                                       ...HHHH............HHHHHHHHHHCT--EEEE CS
                    NAD_binding_10  74 ...deeg............aknivdaakeagvkRfvl 95 
                                          +  +                vda +e gv+ +  
  gi|313125291|ref|YP_004035555.1| 484 qlaN--SkfdpetiiaranNPDNVDAFEELGVRTISS 518
                                       4331..1444444554433333488888888877644 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       5.5   3.8e+03       3      18 ..      13      28 ..      12      30 .. 0.88
   2 !   22.1   0.4   2.5e-07   0.00017       2      93 ..     404     497 ..     403     501 .. 0.79
   3 ?    3.5   0.0      0.15     1e+02      13      52 ..     480     517 ..     467     529 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.5
                                      EEETTSHHHHHHHHHH CS
                     F420_oxidored  3 giiGaGnmgealasgl 18
                                      +iiG G + + l  ++
  gi|313125291|ref|YP_004035555.1| 13 AIIGIGVVSQILSDRF 28
                                      89******99998877 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.5e-07
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......-EEECECHHHHHHH-SEEEE-S-H CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......vkvtavdneeaaeeadvvvlavkp 71 
                                       + +iG+G++g++la++l  +g   +++v++ +++pe +e +++e            t v  +  a++a++vv a   
  gi|313125291|ref|YP_004035555.1| 404 VLVIGGGKVGRTLAERLEDRG---ENVVLI-EQDPEIIETARNEGHtvhqgdgT-DTDVLRSAGADNAKIVVAATGD 475
                                       669******************...****89.*****998888886677666532.2222344456689999999999 PP

                                       HHHHHHHHHCGHHHHTTSEEEE CS
                     F420_oxidored  72 edveevlselakdalkgklvis 93 
                                        dv  ++++la++++  +++i 
  gi|313125291|ref|YP_004035555.1| 476 DDVNLLVAQLANSKFDPETIIA 497
                                       9999999999888888888875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.15
                                       HHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEEC CS
                     F420_oxidored  13 alasgllaagaqpheivvansrnpekaeelaeelgvkvta 52 
                                        l+ +l+++ ++p+ i+ a  +np+ ++++ eelgv++++
  gi|313125291|ref|YP_004035555.1| 480 LLVAQLANSKFDPETII-ARANNPDNVDAF-EELGVRTIS 517
                                       57889999999******.99*****99888.667777766 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.4   2.4e-07   0.00016       1      71 [.     404     472 ..     404     486 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.4e-07
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihl 71 
                                       +lV+G+ G +G+ l+++l+++g +v+ + ++++  +tar+e  +++++d td + l+ + ++ ++ +v+ +
  gi|313125291|ref|YP_004035555.1| 404 VLVIGG-GKVGRTLAERLEDRGENVVLIEQDPEIIETARNEGHTVHQGDGTDTDVLRSAGAD-NAKIVVAA 472
                                       699999.***************************************************9998.45555544 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.4e-06    0.0024       1      35 [.     403     437 ..     403     449 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.4e-06
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       +v+v+GgG +g  lA+ l + g +V ++e  +++ 
  gi|313125291|ref|YP_004035555.1| 403 RVLVIGGGKVGRTLAERLEDRGENVVLIEQDPEII 437
                                       79******************************998 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.1e-06    0.0021       1      56 [.     404     461 ..     404     495 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.1e-06
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECE CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppe 56 
                                       ++++G G +G++la +L   g++v+li +++  +e+ +++G ++++ + +++ ++ ++
  gi|313125291|ref|YP_004035555.1| 404 VLVIGGGKVGRTLAERLEDRGENVVLIEQDPeIIETARNEGHTVHQGDgTDTDVLRSA 461
                                       68*****************************99999********99996666655554 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.4e-06    0.0016       1      48 [.     403     451 ..     403     574 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl 48 
                                       +v++iGGG +G + A  L  rg  V+l+e+++++  ++  + +  +h+g 
  gi|313125291|ref|YP_004035555.1| 403 RVLVIGGGKVGRTLAERLEDRGenVVLIEQDPEII-ETARNEGHTVHQGD 451
                                       59****************99999********9999.88888888888886 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.2e-06    0.0022       3      48 ..     403     450 ..     401     514 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS..--EEEHH CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr..adglnqr 48 
                                        Vl++G+G +G +la  L  +G +vvl+e+  + +++ r  +++++q 
  gi|313125291|ref|YP_004035555.1| 403 RVLVIGGGKVGRTLAERLEDRGENVVLIEQDPEIIETARneGHTVHQG 450
                                       7********************************999996336777764 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   6.4e-06    0.0044      25      92 ..     403     479 ..     392     537 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.4e-06
                                       EEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HH....HC.....TTT-SEEEE-SSSSSSB CS
                     AdoHcyase_NAD  25 vavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtle....ev.....vkkadivvtttGnkdii 92 
                                        ++v+G G vG+  a+ l+  G  v++ e dP     a  eG+ v++ +    +v     +++a+ivv++tG +d+ 
  gi|313125291|ref|YP_004035555.1| 403 RVLVIGGGKVGRTLAERLEDRGENVVLIEQDPEIIETARNEGHTVHQGDgtdtDVlrsagADNAKIVVAATGDDDVN 479
                                       578999***************************999*********87542222442222346789*******99984 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       5.5   3.8e+03     164     164 ..     113     113 ..      82     162 .. 0.55
   2 !   16.0   0.2     8e-06    0.0055     142     193 ..     401     448 ..     388     485 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.5
                                       H CS
                                       x RF
                       Pyr_redox_2 164 l 164
                                       l
  gi|313125291|ref|YP_004035555.1| 113 L 113
                                       1 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8e-06
                                       TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 142 pkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleeal 193
                                       p r++v+GgG +G  lA  l + g++v+l+e+ +++     + ++++ + ++
  gi|313125291|ref|YP_004035555.1| 401 PMRVLVIGGGKVGRTLAERLEDRGENVVLIEQDPEII----ETARNEGHTVH 448
                                       5799******************************999....44555555555 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       5.6   3.8e+03      48      91 ..     134     177 ..     126     180 .. 0.77
   2 !   15.8   0.4   1.8e-05     0.013       1      80 [.     404     476 ..     404     489 .. 0.74
   3 ?    1.2   0.1      0.59   4.1e+02      16      54 ..     456     495 ..     448     515 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.6
                                       CEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGHHHHHHHHHH CS
                   Sacchrp_dh_NADP  48 rfeaialdaenyeavLaallkegdlvvnlsppissldvlkaCie 91 
                                       +++a  l +   ++ ++a+l+  ++v +++  i++  + +a ie
  gi|313125291|ref|YP_004035555.1| 134 TVIAPILEVVPARDRVEAALETEGIVNDVTAAILAVVIFEAIIE 177
                                       55555566666677789999999999999999999999999998 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.8e-05
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE- CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnl 76 
                                       vl+iG+G+vG+ +ae l+++++   ++++++++ e      ++a+++ ++ ++ d  + +  L ++    +++vv +
  gi|313125291|ref|YP_004035555.1| 404 VLVIGGGKVGRTLAERLEDRGE---NVVLIEQDPEII----ETARNEGHTVHQGDGTDTDV-LRSAgADNAKIVVAA 472
                                       89******************98...5*****999984....44477778888888887776.555525555888777 PP

                                       SSGG CS
                   Sacchrp_dh_NADP  77 sppi 80 
                                       +++ 
  gi|313125291|ref|YP_004035555.1| 473 TGDD 476
                                       7765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.59
                                       HHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE- CS
                   Sacchrp_dh_NADP  16 llarhfdvda.eitvadrskeklealaakalgvrfeaial 54 
                                       +++r+   d+ +i+va   ++ ++ l+a++++++f+++++
  gi|313125291|ref|YP_004035555.1| 456 DVLRSAGADNaKIVVAATGDDDVNLLVAQLANSKFDPETI 495
                                       556666666669*****************97777776554 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.6e-05     0.011       3      89 ..     405     499 ..     403     526 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                                       EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHC....SEEEE-SSSHHHHHHH CS
                     NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...akaaesieelvasl....dvvitmvkagkavdev 72 
                                        +iG G+ G+ +a++l+++g +v++++ ++e +e++ +eg    ++  +  ++++s+     ++++  + +++v+ +
  gi|313125291|ref|YP_004035555.1| 405 LVIGGGKVGRTLAERLEDRGENVVLIEQDPEIIETARNEGhtvHQGDGTDTDVLRSAgadnAKIVVAATGDDDVNLL 481
                                       58*************************************97765555667788888788777777888888999999 PP

                                       HHSHC.CC--TT-EEEE- CS
                     NAD_binding_2  73 iegll.ealkkgdilidg 89 
                                       + +l+ +++++++i+   
  gi|313125291|ref|YP_004035555.1| 482 VAQLAnSKFDPETIIARA 499
                                       999662566777776555 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05     0.012       2      43 ..     404     445 ..     403     500 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSS CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehe 43 
                                       + v+G+G+ G +lA  l+++g++v+l+ +++e ie+ ++e +
  gi|313125291|ref|YP_004035555.1| 404 VLVIGGGKVGRTLAERLEDRGENVVLIEQDPEIIETARNEGH 445
                                       789****************************99998776655 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.9e-05     0.027      28      98 ..     409     479 ..     395     519 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                                       --HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT-SEEEE---S--EEES CS
                               DFP  28 SGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealkeadivimaAAvaDyrpk 98 
                                        Gk G +lAe++ +rG +V l+    ++ + ++ e + v++ +   + v + + + ++ i++AA  D  ++
  gi|313125291|ref|YP_004035555.1| 409 GGKVGRTLAERLEDRGENVVLIEQDPEIIETARNEGHTVHQGDGTDTDVLRSAGADNAKIVVAATGDDDVN 479
                                       59********************999887777788999999999999****999999999999999996664 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.3e-05     0.037       1      42 [.     402     443 ..     402     465 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.3e-05
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTT CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsg 42 
                                       m++ viG G vG + a  l  +g +v+++  d e +++ +++
  gi|313125291|ref|YP_004035555.1| 402 MRVLVIGGGKVGRTLAERLEDRGENVVLIEQDPEIIETARNE 443
                                       89********************************99987765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.3e-05     0.029       2      41 ..     404     441 ..     403     467 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnn 41 
                                       v+viG+G  g  lA+rl  +  g +vvlie  p+++ +++
  gi|313125291|ref|YP_004035555.1| 404 VLVIGGGKVGRTLAERL--EDRGENVVLIEQDPEIIETAR 441
                                       89***************..999************998876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4       1.4     1e+03      58      88 ..     147     177 ..     134     181 .. 0.81
   2 ?   14.7   0.2   3.1e-05     0.022       2      42 ..     404     444 ..     403     473 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                                       HHHCCCHHCEEEES-HHHHHC-SEEEE-S-S CS
                           3HCDH_N  58 eeveaalarisfttdleeavdadlviEavvE 88 
                                       + veaal++  + +d+ +a+ a +++Ea++E
  gi|313125291|ref|YP_004035555.1| 147 DRVEAALETEGIVNDVTAAILAVVIFEAIIE 177
                                       5677778888888899999999999999998 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.1e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42 
                                       v viG G +G+ +a+ +  +g +Vvl++ ++e++e+a+++ 
  gi|313125291|ref|YP_004035555.1| 404 VLVIGGGKVGRTLAERLEDRGENVVLIEQDPEIIETARNEG 444
                                       78**********************************99875 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00012     0.083       6      53 ..     403     449 ..     400     475 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                       -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEE CS
                              IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevlt 53 
                                       ++ viG G  G++ a+ l d g +vv+   ++ + +++A++eg++v++
  gi|313125291|ref|YP_004035555.1| 403 RVLVIGGGKVGRTLAERLEDRGENVVLIE-QDPEIIETARNEGHTVHQ 449
                                       689*********************99865.55559*********9986 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00021      0.15       1      92 [.     404     489 ..     404     507 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE-EEEE--S-HHHHHHHHHHHSSS--SEEEESS- CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeadetavvvlthdhklDaealeaalrkkaayigllGS 77 
                                       ++++G+g+v++ la+ ++  g +v+++++++e+ +++r ++        ++++  +D+++l+ a +++a+ + +   
  gi|313125291|ref|YP_004035555.1| 404 VLVIGGGKVGRTLAERLEDRGENVVLIEQDPEIIETARNEGH------TVHQGDGTDTDVLRSAGADNAKIVVAATG 474
                                       689****************************98766666533......34444444444555554444444433333 PP

                                       HHHHHHHCTTS.--. CS
                            XdhC_C  78 rkkaarrlerlraag 92 
                                           + ++++l++++
  gi|313125291|ref|YP_004035555.1| 475 DDDVNLLVAQLANSK 489
                                       334444444444444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00047      0.32      36      79 ..     401     444 ..     386     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00047
                                       TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHT CS
                      2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelg 79 
                                        ++v +iG G++G+++a+rl+  g +v+ +++ ++  e+++++g
  gi|313125291|ref|YP_004035555.1| 401 PMRVLVIGGGKVGRTLAERLEDRGENVVLIEQDPEIIETARNEG 444
                                       5799************************9999888666555554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.16       2      35 ..     403     436 ..     402     445 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       +v+viGgG  G   A+++++rg++V+l+e+ +++
  gi|313125291|ref|YP_004035555.1| 403 RVLVIGGGKVGRTLAERLEDRGENVVLIEQDPEI 436
                                       699**************************99876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00023      0.16       1      31 [.     406     436 ..     406     453 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       ++G+G  G ++A +L ++g +v+l+e+ + +
  gi|313125291|ref|YP_004035555.1| 406 VIGGGKVGRTLAERLEDRGENVVLIEQDPEI 436
                                       8**************************9987 PP

>> DUF4564  Domain of unknown function (DUF4564)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0016       1.1      19      58 ..      91     130 ..      81     133 .. 0.89
   2 ?   -1.1   0.1       1.9   1.3e+03      37      67 ..     264     297 ..     252     299 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                           DUF4564  19 girswsllvgiasvGlaaayyssDsllwklvyvigcllva 58 
                                        ir   ++ gia +G aaa++    + w + ++ig llva
  gi|313125291|ref|YP_004035555.1|  91 TIRLITVGAGIALIGTAAAIHYLLGSPWSVSFLIGALLVA 130
                                       678888999******************************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                           DUF4564  37 ayyssDsllwk...lvyvigcllvalqnleewee 67 
                                       + y++D ++ k    + v++++++al++l e e 
  gi|313125291|ref|YP_004035555.1| 264 VPYEEDISAFKgdiTLIVLSFVFIALAALLEFET 297
                                       56666666444333467899******99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.84u 0.35s 00:00:01.19 Elapsed: 00:00:00.56
# Mc/sec: 3354.62
//
Query:       gi|313125292|ref|YP_004035556.1|  [L=677]
Description: amp-forming long-chain acyl-CoA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-91  306.6   0.0    2.6e-91  306.4   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.4   0.0   1.4e-95   2.6e-91      17     422 ..      59     537 ..      24     538 .. 0.83

  Alignments for each domain:
  == domain 1  score: 306.4 bits;  conditional E-value: 1.4e-95
                                       CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHH CS
                       AMP-binding  17 sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayileds 93 
                                       sg+   lTY+e++e v++lAag+r+lGv+ g+rV+i++++++ew  ++++il aG++v ++++++++++++y+l+d 
  gi|313125292|ref|YP_004035556.1|  59 SGDFSELTYGEMREIVRNLAAGFRELGVEAGSRVGIFSHTRMEWAQSDFGILAAGGAVTTVYTSSSERQVRYLLSDP 135
                                       678899*********************************************************************** PP

                                       TESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS..................-TS CS
                       AMP-binding  94 eakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae..................kpe 151
                                       +a+ ++  v++++ l+++l+++++l + + ++++d  ++++ + + ++  ++++ +                  +  
  gi|313125292|ref|YP_004035556.1| 136 GATGVV--VENAElLQRVLAVEDEL-DLSFIVLID--DPADGSGMGGAVRDRDDIYtlgdvheigatafdeeayQ-S 206
                                       ******..9****9******99986.555555566..55666677777766665536788999********9954.4 PP

                                       CCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHC.SCCTT.......T-EEEESS-TTSCHHHH CS
                       AMP-binding 152 eeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk..letr.fklke.......ddvvlsilplahifgli 218
                                         +e +p++la +iYTSGTTG+PKGV l+h+n+ +nv +++  + +r +k  e       + v ls+lplah+++  
  gi|313125292|ref|YP_004035556.1| 207 WINERDPSSLASLIYTSGTTGQPKGVKLTHNNFRSNVNQCYkrFGPRpDK--EdvptltnGMVTLSFLPLAHVLERL 281
                                       77899****************************99999987664444322..145677779999************* PP

                                       HHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHH.......HHCCCHHCHHHHC........ CS
                       AMP-binding 219 lelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleal.......lesgalkaakkak........ 280
                                       ++ +l+++sGa+v +++  ++     l e+++  ++tv ++vPrv+e+l       +     k     +        
  gi|313125292|ref|YP_004035556.1| 282 AGHFLMFASGACVAYAESPDT-----LREDFQLVRPTVGTSVPRVYEKLydairseA----SK-----Sptkkrife 344
                                       ***************996666.....5599*******************66644331....11.....012234566 PP

                                       ....................................CGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGG CS
                       AMP-binding 281 ....................................dlss.lrlvllggeplspellrffralfgeevlegYGlTEt 320
                                                                            l++ ++++++gg++ls+el   ++  +  ++legYGlTEt
  gi|313125292|ref|YP_004035556.1| 345 wavdvgreyhesdspgvilsakhaladklvfdqvreALGGrIEFFISGGGSLSAELCALYHGMGL-PILEGYGLTET 420
                                       667777778888888888888888888888888888888889999************88888765.6********** PP

                                       SSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE..TTSEEEEEEEETTS-SEBTT-HHHHHHHEEE.... CS
                       AMP-binding 321 tgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvp..dgeeGellvrgpgvmkgYlkkpeataeafds.... 391
                                       ++v++ ++++e+ +k+g++G+p+ +vevk+     g   +   g +Gellv+gp+v++gY+++pe+ta af++    
  gi|313125292|ref|YP_004035556.1| 421 SPVIA-VNPPEE-PKIGTIGTPVVDVEVKLDKTVVGDVTGdaGGDVGELLVKGPNVTEGYWNRPEETAAAFTDdvps 495
                                       ****9.563444.69**************85444333333446888*************************988999 PP

                                       ..........T.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 392 ..........e.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                                 + g+w+rTGD+++l++dGy+ +  R+k++++l
  gi|313125292|ref|YP_004035556.1| 496 dangesesegDsGGWFRTGDVVELRPDGYIAFRERAKQILVL 537
                                       *******9873467************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (677 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 3726.90
//
Query:       gi|313125293|ref|YP_004035557.1|  [L=304]
Description: zn-dependent hydrolase, glyoxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-25   89.5   4.4    4.2e-25   88.9   4.4    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0022   17.6   0.7      0.005   16.4   0.7    1.7  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   4.4   4.7e-29   4.2e-25       6     197 .]      29     225 ..      24     225 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 4.7e-29
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       +++y+i + ++   +DtG++t  + ++++l  l++  +dv++++ TH HlDH+Gg+g+l++a ++++++ +e++ ++
  gi|313125293|ref|YP_004035557.1|  29 GSVYII-DAERPAFVDTGIGTNHEHLLDALDELDIAREDVEYLLPTHIHLDHAGGAGYLADACPNATVMTHEIGVSH 104
                                       677888.55555668************************************************************** PP

                                       HCHHHHHHHHHCCHH........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTT CS
                       Lactamase_B  83 fmeeaddaasrkgll........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDa 151
                                       + + ++  a+ k +          + +++ + ++++ ++ ++++g+r+l v++ pgh +++  + +  +++lftGDa
  gi|313125293|ref|YP_004035557.1| 105 LIDPEKLIAGTKAAVgdqwefyvEPKPVPEDRIEPLTDGNEIDLGDRTLSVFHAPGHAPHQTMFLDSKDDLLFTGDA 181
                                       *****9999999998************************************************************** PP

                                       TSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 152 llagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                         +   +r+    r   ++ + d e +ld+++ +++  +e++++gH
  gi|313125293|ref|YP_004035557.1| 182 AGIYVPERGQV--RQTSPPSQFDLEACLDDVRTIEEIAPERICFGH 225
                                       **999999999..99******************************* PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.7   5.6e-07     0.005      24     116 ..      63     164 ..      38     198 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.6e-07
                                       SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE..............HHHHHHCCTTCGHHHCHTT.... CS
                     Lactamase_B_2  24 lrdelppidaVllthaHyDHlaglltlrelrpkklplyap..............kgvlavleanfvylaleee.... 82 
                                       +r   ++++ +l th H DH  g+  l+  +p+ ++++ +              +g+               +    
  gi|313125293|ref|YP_004035557.1|  63 AR---EDVEYLLPTHIHLDHAGGAGYLADACPN-ATVMTHeigvshlidpekliAGTK--------------Aavgd 121
                                       33...3699********************9995.677766333323333333333333..............22333 PP

                                       ...........TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C CS
                     Lactamase_B_2  83 ...........pavnvheldwgesfelgdggleitatparhksgr 116
                                                  p+ ++++l+ g++++lgd   ++ ++ a++ ++ 
  gi|313125293|ref|YP_004035557.1| 122 qwefyvepkpvPEDRIEPLTDGNEIDLGDR--TLSVFHAPGHAPH 164
                                       3333334444699**************975..5777877777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1664.31
//
Query:       gi|313125294|ref|YP_004035558.1|  [L=329]
Description: hypothetical protein Hbor_05180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-06   26.2   1.2      0.056   13.4   0.1    2.8  2  META      META domain


Domain annotation for each model (and alignments):
>> META  META domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   2.7e-05      0.48      40      70 ..     150     180 ..     128     186 .. 0.88
   2 !   13.4   0.1   3.1e-06     0.056      40      75 ..     279     315 ..     267     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.7e-05
                                       SSSEEEEEEEEC.TTEEEESSEEE-----SCH CS
                              META  40 gCNrfsGsytle.ggrltlgalasTrmaCspa 70 
                                        CN+ + +++++ +g++ +   asTrmaC+  
  gi|313125294|ref|YP_004035558.1| 150 DCNTTTTTAAIQsDGTVDV-MTASTRMACPGV 180
                                       5**********97888887.789******765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.1e-06
                                       SSSEEEEEEEEC.TTEEEESSEEE-----.SCHHHHCH CS
                              META  40 gCNrfsGsytle.ggrltlgalasTrmaC.spalmelE 75 
                                        CN+ s s++++ gg+l++ a  sT maC +p+++  E
  gi|313125294|ref|YP_004035558.1| 279 DCNSSSTSVSVTdGGELKI-ASISTLMACvPPEEAGNE 315
                                       7**********97889**9.7789*****766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2072.83
//
Query:       gi|313125295|ref|YP_004035559.1|  [L=205]
Description: bacterial regulatory protein, arsr family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-12   46.2   0.1    1.3e-11   44.4   0.0    1.8  2  HTH_20          Helix-turn-helix domain
      9e-10   38.3   0.0    2.2e-09   37.0   0.0    1.6  2  HTH_5           Bacterial regulatory protein, arsR family
    7.7e-07   28.6   0.0    1.4e-06   27.8   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.4e-06   26.8   0.4    1.8e-05   24.5   0.0    2.1  2  MarR_2          MarR family
     0.0015   18.4   0.0     0.0025   17.7   0.0    1.4  1  MarR            MarR family
     0.0027   17.6   0.2     0.0059   16.6   0.0    1.7  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0053   17.2   0.0       0.01   16.3   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
       0.02   15.2   0.0       0.04   14.3   0.0    1.5  1  Rrf2            Transcriptional regulator
      0.026   14.4   0.3       0.07   13.0   0.1    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.035   14.3   0.0      0.053   13.7   0.0    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.086   12.4   0.0       0.14   11.7   0.0    1.3  1  Sigma70_r4      Sigma-70, region 4
       0.14   12.5   0.0       0.22   11.8   0.0    1.3  1  DUF2513         Hypothetical protein (DUF2513)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   8.5e-15   1.3e-11       2      58 ..      30      85 ..      29      86 .. 0.95
   2 ?   -1.3   0.0       1.6   2.4e+03      34      49 ..     111     127 ..     105     134 .. 0.68

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 8.5e-15
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +i +++++++ r+il+a   +e++t s+la  +d+s +++syHL+ L eag ve v+
  gi|313125295|ref|YP_004035559.1| 30 EIVSVVTSETAREILAAV-YEEPQTTSDLASSVDTSVQNVSYHLDRLKEAGVVEAVG 85
                                      678899************.**********************************9875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                                       HTS-HHHHHHHH.HHHH CS
                            HTH_20  34 ldlskntlsyHL.rvLe 49 
                                        d +++++s+ L r L+
  gi|313125295|ref|YP_004035559.1| 111 TDQARSSVSDTLrRSLA 127
                                       56678999999955555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.5e-12   2.2e-09       2      46 ..      38      82 ..      37      83 .. 0.96
   2 ?   -2.0   0.0       2.4   3.5e+03      23      37 ..     109     123 ..     107     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.5e-12
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +t ++IL ++ e++++ ++la  ++ s  +vS+HL +L+eaG+Ve
  gi|313125295|ref|YP_004035559.1| 38 ETAREILAAVYEEPQTTSDLASSVDTSVQNVSYHLDRLKEAGVVE 82
                                      7899****************************************7 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                                       HHHTS-HHHHHHHHH CS
                             HTH_5  23 eelglsqstvShHLk 37 
                                       +e++  +s vS  L+
  gi|313125295|ref|YP_004035559.1| 109 AETDQARSSVSDTLR 123
                                       788999999998776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   9.1e-10   1.4e-06       3      48 .]      38      82 ..      36      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 9.1e-10
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      et r+IL +++++p  + ++LA  ++ S+++v+++l+rL+e+G+++
  gi|313125295|ref|YP_004035559.1| 38 ETAREILAAVYEEPQ-TTSDLASSVDTSVQNVSYHLDRLKEAGVVE 82
                                      7899********776.569*************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.2e-08   1.8e-05       6      53 ..      39      83 ..      36      93 .. 0.92
   2 ?   -0.1   0.1      0.61   9.1e+02      29      44 ..     109     124 ..     105     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.2e-08
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      + + +Laa++ +p    t ++la   + s ++vs++l+rL +aG ve 
  gi|313125295|ref|YP_004035559.1| 39 TAREILAAVYEEP---QTTSDLASSVDTSVQNVSYHLDRLKEAGVVEA 83
                                      56789********...5*****************************96 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.61
                                       HHHTSSHHHHHHHHHH CS
                            MarR_2  29 rrlglsksavsrilkr 44 
                                       ++++  +s+vs +l+r
  gi|313125295|ref|YP_004035559.1| 109 AETDQARSSVSDTLRR 124
                                       7888899*****9998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06    0.0025      13      48 ..      48      82 ..      37      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                                      HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      y ++p++ s+La+ + +s  +v+  ldrL ++G +e
  gi|313125295|ref|YP_004035559.1| 48 Y-EEPQTTSDLASSVDTSVQNVSYHLDRLKEAGVVE 82
                                      4.468999*************************886 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.9e-06    0.0059      21      54 ..      51      85 ..      32      89 .. 0.87
   2 ?   -3.4   0.1       6.9     1e+04      35      44 ..     115     124 ..     114     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.9e-06
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rg 54
                                      p t  +lAs + ++ + vs  l +Lk++g+++  g
  gi|313125295|ref|YP_004035559.1| 51 PQTTSDLASSVDTSVQNVSYHLDRLKEAGVVEaVG 85
                                      67899*************************99555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.9
                                       HHHHHHHHHH CS
                         HTH_Crp_2  35 retvsrilse 44 
                                       r++vs +l++
  gi|313125295|ref|YP_004035559.1| 115 RSSVSDTLRR 124
                                       8999999985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.8e-06      0.01       7      50 ..      42      83 ..      37      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.8e-06
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                       +L  ++  +++++ +dl+  ++++ +++sy l++L e+G+ve 
  gi|313125295|ref|YP_004035559.1| 42 EILAAVY--EEPQTTSDLASSVDTSVQNVSYHLDRLKEAGVVEA 83
                                      6788888..99*******************************75 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.7e-05      0.04      17      58 ..      44      84 ..      37      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      La+ +ee p +++++a+++++s + ++  l +L++ag+v++v
  gi|313125295|ref|YP_004035559.1| 44 LAAVYEE-PQTTSDLASSVDTSVQNVSYHLDRLKEAGVVEAV 84
                                      5555554.5899***************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.7e-05      0.07      18      55 ..      47      84 ..      40     100 .. 0.92
   2 ?   -3.7   0.0       7.7   1.1e+04      35      45 ..     114     124 ..     109     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      + ++p t++++a+ ++ + ++v   L +L+++G+Ve +
  gi|313125295|ref|YP_004035559.1| 47 VYEEPQTTSDLASSVDTSVQNVSYHLDRLKEAGVVEAV 84
                                      6799*******************************986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.7
                                       SCHCHHHHHHH CS
                              TrmB  35 prskvYevLrs 45 
                                        rs+v ++Lr+
  gi|313125295|ref|YP_004035559.1| 114 ARSSVSDTLRR 124
                                       58999999985 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.053      20      59 ..      53      92 ..      49     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                    B-block_TFIIIC 20 tqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatk 59
                                      t+sdLa++++ ++ ++ y+l+ L++ g ++ + +  sa++
  gi|313125295|ref|YP_004035559.1| 53 TTSDLASSVDTSVQNVSYHLDRLKEAGVVEAVGTWYSAQG 92
                                      89***************************98877655555 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.6e-05      0.14       7      40 ..      38      71 ..      37      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.6e-05
                                      HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHH CS
                        Sigma70_r4  7 ererevlelrfgeglTleEIgerlgiSrerVrqi 40
                                      e  re+l  +++e++T ++++   + S   V+ +
  gi|313125295|ref|YP_004035559.1| 38 ETAREILAAVYEEPQTTSDLASSVDTSVQNVSYH 71
                                      678************************9999865 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.22       6      65 ..      39      91 ..      36     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                           DUF2513  6 lvRdiLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakss 65
                                        R+iL ++ e +++++ l        ++d +s ++++yhl  l eag +ea+ ++++ +
  gi|313125295|ref|YP_004035559.1| 39 TAREILAAVYEEPQTTSDLAS------SVD-TSVQNVSYHLDRLKEAGVVEAVGTWYSAQ 91
                                      568888887777777766655......455.56667*****************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1256.78
//
Query:       gi|313125296|ref|YP_004035560.1|  [L=460]
Description: seryl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-29  100.5   5.9    1.1e-28   99.6   5.9    1.5  1  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
    8.5e-28   97.5   0.0    3.3e-27   95.6   0.0    1.8  2  tRNA-synt_2b   tRNA synthetase class II core domain (G, H, P,
  ------ inclusion threshold ------
      0.056   12.0   3.5      0.086   11.4   3.5    1.2  1  FapA           Flagellar Assembly Protein A
       0.31   10.7   4.3       0.59    9.8   4.3    1.5  1  Syntaxin       Syntaxin
       0.32    9.8   2.6       0.52    9.1   2.6    1.3  1  Fmp27_WPPW     RNA pol II promoter Fmp27 protein domain
       0.54    9.3   1.0       0.82    8.7   1.0    1.2  1  YdfA_immunity  SigmaW regulon antibacterial
       0.94    8.9   6.7        1.4    8.3   6.7    1.2  1  Golgin_A5      Golgin subfamily A member 5


Domain annotation for each model (and alignments):
>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   5.9   4.2e-32   1.1e-28       1     108 []       1     110 [.       1     110 [. 0.99

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 4.2e-32
                                       ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT..S-TCCCCCC CS
                      Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk..edaeeliae 75 
                                       M+  +++renpe+v+e+l+++g+d+ d+d++le+de++r+l+++ ++l++erNe s +Ig++k+++  e+a+e i++
  gi|313125296|ref|YP_004035560.1|   1 MISRQFLRENPETVREALRSKGVDDVDLDHILEVDEEWRSLKKRGDDLRHERNETSSKIGELKAEGkdEEAQEAIER 77 
                                       9999************************************************************************* PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHCTS---- CS
                      Seryl_tRNA_N  76 vkelkeelkaleaelkeleaeleklllaiPNip 108
                                       ++elk el+++e++ +eleaele+ ll++P ip
  gi|313125296|ref|YP_004035560.1|  78 SQELKSELAEVEDRADELEAELEERLLELPQIP 110
                                       ******************************997 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.45   1.2e+03      76     146 ..      23     100 ..       4     106 .. 0.64
   2 !   95.6   0.0   1.3e-30   3.3e-27       4     178 ..     230     419 ..     222     420 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHHHHTT.SCEEEEEE.......GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  76 lddslrdlikaisriferlglefraiiel.......msaksadykdkkefeavsesltkgieigtiqklgtrlserl 145
                                       +dd++ d i ++++ +++l      +++         ++ +a++kd++  ea+  s++ + e++ ++ + ++l  +l
  gi|313125296|ref|YP_004035560.1|  23 VDDVDLDHILEVDEEWRSLKKRGDDLRHErnetsskIGELKAEGKDEEAQEAIERSQELKSELAEVEDRADELEAEL 99 
                                       56666666666666666664333222222111222355555888888888888888888888888888877766665 PP

                                       T CS
                                       x RF
                      tRNA-synt_2b 146 g 146
                                       +
  gi|313125296|ref|YP_004035560.1| 100 E 100
                                       5 PP

  == domain 2  score: 95.6 bits;  conditional E-value: 1.3e-30
                                       EETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   4 edrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeasl 76 
                                       ++r+d+++ L Pt+e ++++++rde+l + +LP+k  ++++ +R+E+     ++rG++Rv++F++ + + f+ ++++
  gi|313125296|ref|YP_004035560.1| 230 KERDDDDLWLCPTAEVPVTNMYRDEILLDDDLPVKHQAYTPNFRREAGehgtETRGIVRVHQFNKVEMVNFVRPENS 306
                                       47899********************999999****************778999************************ PP

                                       HHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETT.........TSEEEEEEEEEEEETHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  77 ddslrdlikaisriferlglefraiielmsaksadykdkkefeavses.........ltkgieigtiqklgtrlser 144
                                       ++++++l+ +++++++rl l++r ++ ++++  +  ++k+++e++ +           ++ +e++++++ ++ +++r
  gi|313125296|ref|YP_004035560.1| 307 YEQFEELLDEAEEVLRRLELPYRILEMCTGDLGFTQAKKYDIEVWAPGddmedgpeeGGRWLEVSSVSNFEDFQARR 383
                                       *********************9988888****************************99******************* PP

                                       TTEEEECTTS.SEEEEEEEEEE.EEHHHHHHHHHHH CS
                                       xxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxx RF
                      tRNA-synt_2b 145 lgatvldenn.reksvimicaa.igveRllsaileq 178
                                        g+++  e   + +  ++++ + +++ R++ ai+e 
  gi|313125296|ref|YP_004035560.1| 384 AGLRYRPERHeSAEYLHTLNGSgLAIPRVVVAIMEY 419
                                       *****988874667789999888**********996 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.5   3.4e-05     0.086     333     411 ..      32     102 ..      25     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                              FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                       +e++e+ + l+++  +l+ e ++  +ki +l++        + k e+ ++++e  ++lk+el+e+e++ +el++ele
  gi|313125296|ref|YP_004035560.1|  32 LEVDEEWRSLKKRGDDLRHERNETSSKIGELKA--------EGKDEEAQEAIERSQELKSELAEVEDRADELEAELE 100
                                       578899999999999999999999999999999........345689*****************************9 PP

                              FapA 410 sk 411
                                       ++
  gi|313125296|ref|YP_004035560.1| 101 ER 102
                                       87 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.3   0.00023      0.59     134     188 ..      55     109 ..      30     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00023
                          Syntaxin 134 seeeieelietgesevflqkllqeqrgarealseieeRhkev.lelekslkeLhql 188
                                       +  +i el  +g+ e+  q++++ ++  ++ l+e+e+R +e+  ele++l eL q+
  gi|313125296|ref|YP_004035560.1|  55 TSSKIGELKAEGKDEE-AQEAIERSQELKSELAEVEDRADELeAELEERLLELPQI 109
                                       5667778888888555.677777777779*************559********998 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.6    0.0002      0.52     175     235 ..      40     101 ..      34     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0002
                        Fmp27_WPPW 175 lleeRleeleeqiekleekleelelkseke.deelkeeieelekeikelkeklefletlled 235
                                        l++R ++l+++++++++k++el+ + + e  +e  e+++el++e++e++++ + le+ le+
  gi|313125296|ref|YP_004035560.1|  40 SLKKRGDDLRHERNETSSKIGELKAEGKDEeAQEAIERSQELKSELAEVEDRADELEAELEE 101
                                       689**********************9999777777778888888888888888777766654 PP

>> YdfA_immunity  SigmaW regulon antibacterial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.0   0.00032      0.82     187     275 ..       8      98 ..       3     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00032
                     YdfA_immunity 187 lenPdsisktvlekgldagtafeilsidiadvdvgenigaklqadqaeadkkiaqakaeerr...amavakeqemka 260
                                        enP+++ +++ +kg+d     +il +d  +    +  g  l+ ++ e+  ki + kae +      a+ + qe k+
  gi|313125296|ref|YP_004035560.1|   8 RENPETVREALRSKGVDDVDLDHILEVDE-EWRSLKKRGDDLRHERNETSSKIGELKAEGKDeeaQEAIERSQELKS 83 
                                       59**************************6.56666778********************9775111457888999999 PP

                     YdfA_immunity 261 kvqemrakvveaeae 275
                                       +  e + +  e eae
  gi|313125296|ref|YP_004035560.1|  84 ELAEVEDRADELEAE 98 
                                       988765555554444 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.7   0.00056       1.4      34     151 ..      21     134 ..      10     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00056
                         Golgin_A5  34 sgeeglessta..lsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerka 108
                                       +g++++++ ++  +  e  +lk++ d lr+e ++++++i +l++e +d      +ea+++ e+ qel+++l+e + +
  gi|313125296|ref|YP_004035560.1|  21 KGVDDVDLDHIleVDEEWRSLKKRGDDLRHERNETSSKIGELKAEGKD------EEAQEAIERSQELKSELAEVEDR 91 
                                       4555555544412556677889999999999999*****999999444......55666777778888888888888 PP

                         Golgin_A5 109 keeveaelerlkeelryleeelvrskatlqsrikdrekeiekl 151
                                         e+eaele+   el  +  + v + ++  +++++r +  ++l
  gi|313125296|ref|YP_004035560.1|  92 ADELEAELEERLLELPQIPHDDVPVGEDESENVERRREGFDDL 134
                                       8899999999888888888777777777666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 2702.38
//
Query:       gi|313125297|ref|YP_004035561.1|  [L=89]
Description: hypothetical protein Hbor_05210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00086   19.5   0.1     0.0015   18.8   0.1    1.4  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   8.3e-08    0.0015      31      74 ..      45      86 ..      33      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.3e-08
                            HalOD1 31 iDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVe 74
                                      iDp+  ++L++s  ++ea  d +v+F ++g  V ++ +g + V+
  gi|313125297|ref|YP_004035561.1| 45 IDPEEAERLLRS--AREAGVDLEVRFCVDGRPVKIDTKGVVSVK 86
                                      9***********..788899*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 549.86
//
Query:       gi|313125298|ref|YP_004035562.1|  [L=135]
Description: ntf2 domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-12   46.5   3.3    6.3e-12   46.0   3.3    1.2  1  SnoaL_2   SnoaL-like domain
    4.2e-09   36.8   0.6    6.6e-09   36.1   0.6    1.3  1  DUF4440   Domain of unknown function (DUF4440)
    6.1e-06   26.5   0.1    9.1e-06   25.9   0.1    1.4  1  SnoaL_3   SnoaL-like domain
    8.9e-06   26.3   0.0    1.1e-05   25.9   0.0    1.1  1  NTF2      Nuclear transport factor 2 (NTF2) domain
    1.4e-05   25.2   0.5    1.7e-05   25.0   0.5    1.2  1  SnoaL_4   SnoaL-like domain
    0.00013   21.7   0.2     0.0002   21.2   0.2    1.4  1  SnoaL     SnoaL-like polyketide cyclase
  ------ inclusion threshold ------
      0.077   13.8   0.0      0.098   13.4   0.0    1.3  1  DUF4829   Domain of unknown function (DUF4829)


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   3.3   2.4e-15   6.3e-12       1      97 [.      14     107 ..      14     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 2.4e-15
                                       HHHHHHHHHTTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEE..EEETTEEEEEEEEEE CS
                           SnoaL_2   1 vraflaalnagdldalaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdv..vadgdrvavewtvtg 75 
                                       v+a+++a++agd+d+la+l++p +v+  p ++l+Gre +  f+r  +    d r+++++    ++gd  +v++++ g
  gi|313125298|ref|YP_004035562.1|  14 VEAYYDAIDAGDYDRLASLLSPAFVHDRPDQTLSGRETFVSFMRDDRP-ETDTRHDVTATyrQTEGDGWVVRGRLLG 89 
                                       89*******************************************985.8888888888888999**********86 PP

                                       EEETTSSEEEEEEEEEEEEETT CS
                           SnoaL_2  76 tipatgrgvtvrgvdvfrvrdG 97 
                                            +  v++++vdvf+v  G
  gi|313125298|ref|YP_004035562.1|  90 ----ADGDVRFTFVDVFTVGAG 107
                                       ....55669*********9666 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.6   2.6e-12   6.6e-09       2      98 ..      11     102 ..      11     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.6e-12
                                       HHHHHHHHHHHHCT-HHHHHHCEEEEEEEE-TTS-EEEHHHHHHHHHCCHCEEEEEEEEEEEEEEE.TTEEEEEEEE CS
                           DUF4440   2 aaleealeeafvagdaealaallapdavlvgpsgtvldkeellealeagfaagrslelteeevrvl.gdlAvvtgry 77 
                                       ++l+ea+++a+ agd+++la+ll+p +v   p+ t+ ++e+++  +++ + ++ + +  ++++r + gd+ vv+gr 
  gi|313125298|ref|YP_004035562.1|  11 RQLVEAYYDAIDAGDYDRLASLLSPAFVHDRPDQTLSGRETFVSFMRDDRPETDTRHDVTATYRQTeGDGWVVRGRL 87 
                                       5899********************************************9888777755557777777*********8 PP

                                       EEEECCTTEEEEEEEEEEEEE CS
                           DUF4440  78 tfegrgdgepvegrgrftsvw 98 
                                         +   dg   ++r++f+ v+
  gi|313125298|ref|YP_004035562.1|  88 LGA---DG---DVRFTFVDVF 102
                                       876...66...4677777666 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   3.5e-09   9.1e-06       2      72 ..      11      80 ..      11     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.5e-09
                           SnoaL_3  2 ealldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakg.egisfeltdvrvtesg 72
                                      ++l++a+y+a+ +gd+d+l +l+++ +v+    +d+ l+gre ++ +++++  ++ ++ + ++t ++ + +g
  gi|313125298|ref|YP_004035562.1| 11 RQLVEAYYDAIDAGDYDRLASLLSPAFVHDR--PDQTLSGRETFVSFMRDDRPETdTRHDVTATYRQTEGDG 80
                                      6899*********************987755..677999***********9999866666666666666555 PP

>> NTF2  Nuclear transport factor 2 (NTF2) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.4e-09   1.1e-05       2     107 ..      10     108 ..       9     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.4e-09
                                       HHHHHHHHHHHHHHHGGGGGGGGEEEEEEEEEETTEEEEESHHHHHHHHHHSSCSCE.EEEEEEEEEEETSEGGGCE CS
                              NTF2   2 akafvqqYYaaldagdregllalyaadaslltpegsspvkgreaIteffrslpftri.elkittvdaqpdeaslstg 77 
                                       ++++v+ YY+a+dagd + l+ l    a + +++++ +++gre  + f+r    ++  ++++t    q   +    g
  gi|313125298|ref|YP_004035562.1|  10 GRQLVEAYYDAIDAGDYDRLASLL-SPAFVHDRPDQ-TLSGRETFVSFMRDDRPETDtRHDVTATYRQ---T---EG 78 
                                       6789*******************9.***********.************9887776447777777777...2...35 PP

                                       EEEEEEEEEEETTSCCEEEEEEEEEEEEET CS
                              NTF2  78 vlvmvtGelkvddfkkrrkfsqtfilapqs 107
                                         ++v G+l ++d+  r  f+ +f + + +
  gi|313125298|ref|YP_004035562.1|  79 DGWVVRGRLLGADGDVRFTFVDVFTVGAGQ 108
                                       67999*********999*******998876 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.5   6.6e-09   1.7e-05      10      92 ..      11      89 ..       5     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.6e-09
                                      HHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH-EEEEE---EEEEETTEEEEEE CS
                           SnoaL_4 10 rdlvarygyylDtkdweeladlFtedavvdytgvgegvlegrdairaalrealdgfaltqHllsnplieldgdtAtgra 88
                                      r+lv +y  ++D++d++ la+l  +  v+d +    ++l+gr+ ++ ++r+  +++ +t+H ++++    +gd   +r+
  gi|313125298|ref|YP_004035562.1| 11 RQLVEAYYDAIDAGDYDRLASLLSPAFVHDRPD---QTLSGRETFVSFMRDD-RPETDTRHDVTATYRQTEGDGWVVRG 85
                                      79******************************6...7**************9.5888********99999999999998 PP

                                      EEEE CS
                           SnoaL_4 89 ylla 92
                                      +ll+
  gi|313125298|ref|YP_004035562.1| 86 RLLG 89
                                      8876 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   7.7e-08    0.0002       2      75 ..      12      85 ..      11     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.7e-08
                                      HHHHHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEE..EETTEEEEEE CS
                             SnoaL  2 lvlrfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlv..aegdkvaarl 75
                                      +++++y ++++ gd d+l+ l+++ +v+  p+ + + G+e f  f+++++ +  D +++v+ ++  +egd  ++r 
  gi|313125298|ref|YP_004035562.1| 12 QLVEAYYDAIDAGDYDRLASLLSPAFVHDRPD-QTLSGRETFVSFMRDDRPET-DTRHDVTATYrqTEGDGWVVRG 85
                                      68999*********************999554.999**************998.9999777665225667666665 PP

>> DUF4829  Domain of unknown function (DUF4829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.8e-05     0.098       2      26 ..      12      36 ..      11      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                           DUF4829  2 evieeYFkalnkkdaeaakallske 26
                                      + +e Y+ a++++d++++ +lls+ 
  gi|313125298|ref|YP_004035562.1| 12 QLVEAYYDAIDAGDYDRLASLLSPA 36
                                      89********************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 818.99
//
Query:       gi|313125299|ref|YP_004035563.1|  [L=171]
Description: hypothetical protein Hbor_05230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-45  153.0   0.0    3.8e-45  152.7   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    4.5e-08   32.8   0.0    6.6e-08   32.2   0.0    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.7   0.0   4.2e-49   3.8e-45       1     127 []      46     167 ..      46     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 152.7 bits;  conditional E-value: 4.2e-49
                                       EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHH CS
                     Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaal 77 
                                       +vl+p+a+++lsp+D+++    +++++dcsW+++ e+ f+      +r+LPyLvAaNpvn+g+p++L++vEAlaaal
  gi|313125299|ref|YP_004035563.1|  46 VVLNPHAERALSPEDSDT---GTLVALDCSWESAGEAMFSLP--GDHRALPYLVAANPVNFGRPMQLTTVEALAAAL 117
                                       89*************665...89***********99997765..69******************************* PP

                                       HHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                     Ribo_biogen_C  78 yilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                       +i+g +++ae++lskf+wg++Fleln+e+l++Ya+c+ds+ +vevq+eyl
  gi|313125299|ref|YP_004035563.1| 118 CIFGRDDHAERILSKFTWGHTFLELNEEPLRRYANCEDSTAIVEVQQEYL 167
                                       ************************************************97 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   7.4e-12   6.6e-08       3      33 ..       9      39 ..       7      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.4e-12
                                      EEEES---------TTHHHHHTTSEEEESS- CS
                               RLI  3 lAivdadqCdPKKCtgkkcarfcpvrlvrtg 33
                                      l++ +++ +dP KCt++k+a+f++++l+++ 
  gi|313125299|ref|YP_004035563.1|  9 LHVRYEGDDDPAKCTARKLAKFDLAELHHSD 39
                                      89***********************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1149.69
//
Query:       gi|313125300|ref|YP_004035564.1|  [L=324]
Description: GTPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-43  146.1   0.0    1.4e-42  145.4   0.0    1.4  1  NOG1_N       NOG1 N-terminal helical domain
    6.8e-22   77.0   0.0    1.3e-21   76.1   0.0    1.5  1  NOG1         Nucleolar GTP-binding protein 1 (NOG1)
    1.7e-21   76.4   0.0    3.3e-21   75.5   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
    3.6e-11   42.8   0.0    6.9e-11   41.9   0.0    1.5  1  FeoB_N       Ferrous iron transport protein B
      3e-06   27.4   0.3      0.022   14.8   0.0    3.1  3  Dynamin_N    Dynamin family
    0.00016   21.1   0.0    0.00025   20.4   0.0    1.3  1  AIG1         AIG1 family
    0.00018   21.1   0.0     0.0043   16.6   0.0    2.6  2  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0028   17.6   0.0      0.038   13.9   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
     0.0052   16.1   0.0       0.21   10.9   0.0    2.2  2  6PF2K        6-phosphofructo-2-kinase
     0.0057   17.1   0.1      0.022   15.1   0.0    2.0  2  AAA_16       AAA ATPase domain
     0.0059   16.1   0.0      0.018   14.5   0.0    1.8  1  SRPRB        Signal recognition particle receptor beta subuni
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.021   14.6   0.1    1.2  1  DUF2451      Protein of unknown function C-terminus (DUF2451)
      0.055   14.0   0.0        9.2    6.8   0.0    2.3  2  DUF4174      Domain of unknown function (DUF4174)
        0.1   12.8   0.0        3.5    7.9   0.0    2.8  3  Roc          Ras of Complex, Roc, domain of DAPkinase
        0.1   13.1   0.0       0.35   11.4   0.0    1.9  2  AAA_18       AAA domain
       0.11   12.4   0.0       0.41   10.5   0.0    1.8  2  SIS          SIS domain
       0.14   11.8   0.1       0.91    9.1   0.0    2.3  2  Ras          Ras family


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.0   1.3e-45   1.4e-42       1     159 [.       3     152 ..       3     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 1.3e-45
                            NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrel 77 
                                       Fe++pt+p seel+dka++ra r +++++ +  e      +++++++tas +lsd+Le++v+++P++ +++pFy+el
  gi|313125300|ref|YP_004035564.1|   3 FESLPTTPRSEELLDKAFSRAARSGRAKSGH--E------AQESMLQTASSILSDNLENVVTEWPDFGTVDPFYYEL 71 
                                       9************************999665..3......5799********************************* PP

                            NOG1_N  78 ldvlvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLr 154
                                       +d++vd+del++sL++v+wa++ i++i++ey++k++k+d+ ++a++ r++af r+a+++ +++++l  + ++r  L+
  gi|313125300|ref|YP_004035564.1|  72 ADAIVDVDELRQSLSEVTWASRQIAEIRSEYLSKMRKTDK-DTARKHRKQAFARMADIMDEIEDDLLQIGEARDSLK 147
                                       ************************************8876.88********************************** PP

                            NOG1_N 155 kLpai 159
                                        Lp+i
  gi|313125300|ref|YP_004035564.1| 148 GLPDI 152
                                       ***98 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   1.2e-24   1.3e-21       1      58 []     223     282 ..     223     282 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.2e-24
                              NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfan..kpvivvlnKiD 58 
                                       +IEkqA++AL+hlada lF++D+s++cgy+l+ Ql+L++ ++++fa+  +pv++v+nK+D
  gi|313125300|ref|YP_004035564.1| 223 DIEKQAVSALEHLADAALFVVDASGDCGYPLDAQLELRDAVEARFAErnVPVLTVCNKSD 282
                                       6********************************************986678********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   3.1e-24   3.3e-21       2     114 .]     159     280 ..     158     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 3.1e-24
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH..HHHHHHHHHHC. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek..glgkaflalee. 75 
                                       ++++G+pNvGKS+++n  t++  +++++p+tT+ ++ g+++ ++ +++++DtpGl+++ +e++   +++a+ ale  
  gi|313125300|ref|YP_004035564.1| 159 IVVAGYPNVGKSSFVNHVTRASNEIARYPFTTKGVQIGHFERDRIRYQIIDTPGLLDRPEEDRndIEKQAVSALEHl 235
                                       899**************************************888**********99744444443555555556668 PP

                                       TSEEEEEEETT.......TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  76 adlillvvdas.......eeklkpldeeleelleeakkplilvlnk 114
                                       ad++l+vvdas       +++l+ l+  +e+   e++ p++ v+nk
  gi|313125300|ref|YP_004035564.1| 236 ADAALFVVDASgdcgyplDAQLE-LRDAVEARFAERNVPVLTVCNK 280
                                       9********99766555422222.2233333334478888989887 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   6.5e-14   6.9e-11       3      89 ..     159     246 ..     157     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6.5e-14
                                       EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH..CT CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll..ee 77 
                                       ++++G pnvGk++++n++t a+++++ +p +t   + g+++ ++ +++i+D PG  +  +  + + + ++ +   e+
  gi|313125300|ref|YP_004035564.1| 159 IVVAGYPNVGKSSFVNHVTRASNEIARYPFTTKGVQIGHFERDRIRYQIIDTPGLLDRPEEDR-NDIEKQAVSalEH 234
                                       899**************************************999**********988633332.2333333321267 PP

                                       SSSEEEEEEEGG CS
                            FeoB_N  78 epdvvvnvvdat 89 
                                        +d+ + vvda+
  gi|313125300|ref|YP_004035564.1| 235 LADAALFVVDAS 246
                                       789999999996 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.41   4.4e+02      31      79 ..      91     139 ..      71     149 .. 0.57
   2 !    8.1   0.0    0.0024       2.5       1      22 [.     159     180 ..     159     203 .. 0.79
   3 !   14.8   0.0   2.1e-05     0.022     102     141 ..     204     248 ..     195     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.41
                                       ---S-EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHHHHH CS
                         Dynamin_N  31 tTrrplelqlgeeeeaseravkeelkekekkledfsevreeieketeki 79 
                                        +r + e++ +  ++++++  +   k +++ +  + ++ +eie+   +i
  gi|313125300|ref|YP_004035564.1|  91 ASRQIAEIRSEYLSKMRKTDKDTARKHRKQAFARMADIMDEIEDDLLQI 139
                                       3344444444444444443444444444888888888888888876665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0024
                                       EEEEEBTTTTHHHHHHHHHTS- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlged 22 
                                       i+v G  + GKSS++n+++++ 
  gi|313125300|ref|YP_004035564.1| 159 IVVAGYPNVGKSSFVNHVTRAS 180
                                       8999*************98766 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.1e-05
                                       SEEEEE---B-SSSGTTS....HHHHHHH.STTEEEEEEEETTS- CS
                         Dynamin_N 102 gltlvDlPGldsvnkrdq....elvkeyi.kkadiilavtsanhd 141
                                       ++ ++D+PGl +++++d     + + +++ + ad+ l+v++a+ d
  gi|313125300|ref|YP_004035564.1| 204 RYQIIDTPGLLDRPEEDRndieKQAVSALeHLADAALFVVDASGD 248
                                       578**************988887777778799*********9976 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.4e-07   0.00025       3     124 ..     159     276 ..     157     310 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.4e-07
                                       EEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTC.CHHCHHHHHHHHHH CS
                              AIG1   3 ivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsv.sadkiskeivrcll 78 
                                       iv+ G   +GkS+ +N + + +    +      tk +q  + ++d  + ++iDTPgl+d  + + ++i+k+ v  l 
  gi|313125300|ref|YP_004035564.1| 159 IVVAGYPNVGKSSFVNHVTRASNEIAR--YPFTTKGVQIGHFERDRIRYQIIDTPGLLDRPEeDRNDIEKQAVSAL- 232
                                       9999**************877654444..5677888999999*****************87625677888776544. PP

                                       HCTT-ESEEEEEEETT.B-SHHHHHHHHHHHHHHCGGGGGGEEEEEE CS
                              AIG1  79 lseegihalllvlslg.rfteedekalktlkelFGekilkylivvft 124
                                         e+  +a l+v++++ +       a  +l+++ ++++ +  + v+t
  gi|313125300|ref|YP_004035564.1| 233 --EHLADAALFVVDASgDCG-YPLDAQLELRDAVEARFAERNVPVLT 276
                                       ..444567777777764444.33344445566666666666665555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.2   2.2e+02       6      32 ..     159     185 ..     156     194 .. 0.87
   2 !   16.6   0.0   4.1e-06    0.0043      62     146 ..     197     298 ..     180     312 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.2
                                       EEEEESTTSSHHHHHHHHHHHTTSSCH CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaisk 32 
                                       i+++g  + GK++++ +++ ++++i++
  gi|313125300|ref|YP_004035564.1| 159 IVVAGYPNVGKSSFVNHVTRASNEIAR 185
                                       78999999**********999999875 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.1e-06
                                       EEETTCSSEEEEEEEESSSGGGHHH........HHHH.HHT-SEEEEEEETTTB......STHHHHHHHHH.HHHTT CS
                          GTP_EFTU  62 sleketkkylinliDtPGHvdFske........virg.lrvlDgavlvvdaveG......vepqteevlrl.alkeg 122
                                       ++  e ++ ++++iDtPG  d  +e           +    +D a++vvda+ +       +   +  ++    +++
  gi|313125300|ref|YP_004035564.1| 197 HF--ERDRIRYQIIDTPGLLDRPEEdrndiekqAVSAlEHLADAALFVVDASGDcgypldAQLELRDAVEArFAERN 271
                                       33..489999********766543311111111334435689**********7777875555555555544156788 PP

                                       TEEEEEEESCGST...HHHHHHHHHHH CS
                          GTP_EFTU 123 vpiivfiNKmDrl...kaelkeiveev 146
                                       vp+ +++NK Dr    +a++ ++ve+ 
  gi|313125300|ref|YP_004035564.1| 272 VPVLTVCNKSDRStdvEADYYMSVENE 298
                                       99**********988878877777765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.6e-05     0.038      64     161 ..     121     213 ..     100     216 .. 0.72
   2 ?    0.4   0.0       0.5   5.2e+02      43      78 ..     268     302 ..     257     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S----------- CS
                       RsgA_GTPase  64 eleelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkh 139
                                       ++ ++++ + +++ ++l + +  +++l+ l +   d   +v++G   vGKS+++n+++          s++  r   
  gi|313125300|ref|YP_004035564.1| 121 AFARMADIMDEIEDDLLQIGEA-RDSLKGLPDIRPDePAIVVAGYPNVGKSSFVNHVTRA--------SNEIARYPF 188
                                       5566666677777777777444.6666666666555478999*************98877........777778899 PP

                                       ---SEEEEEETT...TEEEESS-SS CS
                       RsgA_GTPase 140 TTtavellelae...gglliDtPGf 161
                                       TT+ v++ ++++      +iDtPG+
  gi|313125300|ref|YP_004035564.1| 189 TTKGVQIGHFERdriRYQIIDTPGL 213
                                       9999999999993334569****97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.5
                                       HHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSE CS
                       RsgA_GTPase  43 eekgiepvivlnKiDlleeeeeleelkeelealgye 78 
                                        e++++++ v nK D  ++ e ++ +++  ++ g+e
  gi|313125300|ref|YP_004035564.1| 268 AERNVPVLTVCNKSDRSTDVE-ADYYMSVENEEGVE 302
                                       67899999999****999999.66666666666654 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.058        61      54      99 ..      93     139 ..      82     141 .. 0.79
   2 !   10.9   0.0    0.0002      0.21      15     123 ..     158     271 ..     149     288 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.058
                                       HHHHSS---G.GGGSTT-HHHHHHHHHHHHHHHHHHHHHHHTS--SE CS
                             6PF2K  54 reaskalsda.effrpdneealklreklalaalkdllaylneeegqv 99 
                                       r++++  s++ + +r+++++  ++++k a a + d++++++++  q+
  gi|313125300|ref|YP_004035564.1|  93 RQIAEIRSEYlSKMRKTDKDTARKHRKQAFARMADIMDEIEDDLLQI 139
                                       677777666525578889999999999*************9986666 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0002
                                       EEEEESSTTSSHHHHHHHHHHHHH...HTT--EEEEEHHHHHHHHHSS..---GGGGSTT-HHHHHHHHH..HHHHH CS
                             6PF2K  15 vivlvGLpargKtyiskkltrylk...wlgvrtkvFnvgkyrreaska..lsdaeffrpdneealklrek..lalaa 84 
                                       +iv+ G p  gK+   +++tr  +      ++tk  ++g++ r+  +          +  +e+ +++ ++   al+ 
  gi|313125300|ref|YP_004035564.1| 158 AIVVAGYPNVGKSSFVNHVTRASNeiaRYPFTTKGVQIGHFERDRIRYqiIDTPGLLDRPEEDRNDIEKQavSALEH 234
                                       6999******************9965544578898899988888766643233334444445555544441157788 PP

                                       HHHHHHHHHTS--SEEEEES---SHHHHHHHHHHHHHTT CS
                             6PF2K  85 lkdllaylneeegqvaifDAtNttrerRklilefveenn 123
                                       l d + ++ + +g+ +    +  + e R+ + +++ e+n
  gi|313125300|ref|YP_004035564.1| 235 LADAALFVVDASGDCGY--PLDAQLELRDAVEARFAERN 271
                                       88888888888888774..23334555555555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.4   1.5e+03      71      88 ..      70      87 ..      15     144 .. 0.51
   2 !   15.1   0.0   2.1e-05     0.022      21      88 ..     153     210 ..     137     290 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                            AAA_16 71 alaqalareellrqllde 88
                                       la+a+   + lrq l+e
  gi|313125300|ref|YP_004035564.1| 70 ELADAIVDVDELRQSLSE 87
                                      344444444444444444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.1e-05
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqllde 88 
                                       +++++++++ G++ vGKss v+++ ra ++  + + +++k +q             ++r+++  q+ d 
  gi|313125300|ref|YP_004035564.1| 153 RPDEPAIVVAGYPNVGKSSFVNHVTRASNEI-ARYpFTTKGVQI----------GHFERDRIRYQIIDT 210
                                       455599*******************765555.333477777776..........333333333333333 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.7e-05     0.018       3     126 ..     156     285 ..     154     301 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                       --EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT....-GCCSHHHHHHHHHHG CS
                             SRPRB   3 kpavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPG....heklrqklleklkaks 74 
                                       +pa++++G  + GK s+ +++t  s + +      + +     +++  + ++iD PG     e+ r+++ ++ +   
  gi|313125300|ref|YP_004035564.1| 156 EPAIVVAGYPNVGKSSFVNHVTRASNEIARYPFtTKGVQIGHFERDRIRYQIIDTPGlldrPEEDRNDIEKQAVSAL 232
                                       689*******************998777777663333444444778899********44333566777766654433 PP

                                       G..EEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT CS
                             SRPRB  75 s..lkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelfl 126
                                       +  + + +fvvD++ d     +    l +  ++   ++ +v++l  CnK++ ++
  gi|313125300|ref|YP_004035564.1| 233 EhlADAALFVVDASGDCGYPLDAQLELRDA-VEARFAERNVPVLTVCNKSDRST 285
                                       33578899****999987766644444444.44455688899*********887 PP

>> DUF2451  Protein of unknown function C-terminus (DUF2451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     2e-05     0.021      30     125 ..      38     136 ..      30     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                           DUF2451  30 sllpekkrglleeFyeqtvsavadl..repiykavasrllnleslleaianvkWdvkevatehssYvdqllkevesf 104
                                       s+l ++ +++l++ +e++v+  +d+   +p+y  +a  ++++++l +++++v W  +++a   s+Y +++ k  ++ 
  gi|313125300|ref|YP_004035564.1|  38 SML-QTASSILSDNLENVVTEWPDFgtVDPFYYELADAIVDVDELRQSLSEVTWASRQIAEIRSEYLSKMRKTDKDT 113
                                       444.66689999999999999997633689***************************************99887775 PP

                           DUF2451 105 skklqe..lkerlklpeevkkal 125
                                       ++k ++  +++ +++ +e+++ l
  gi|313125300|ref|YP_004035564.1| 114 ARKHRKqaFARMADIMDEIEDDL 136
                                       44433212555556666666666 PP

>> DUF4174  Domain of unknown function (DUF4174)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.037        39      73     111 ..      93     132 ..      72     137 .. 0.83
   2 ?    6.8   0.0    0.0088       9.2      24      57 ..     253     286 ..     238     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.037
                           DUF4174  73 rkelklsekd.fsmvLigkdggvkeryekpisleelfdlI 111
                                       r+  ++++++  +m  ++kd   k+r+++  ++++++d I
  gi|313125300|ref|YP_004035564.1|  93 RQIAEIRSEYlSKMRKTDKDTARKHRKQAFARMADIMDEI 132
                                       55556677776789999********************998 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0088
                           DUF4174  24 ykqqreeleeqecelaeRklvvltivgsgaketg 57 
                                       +  q+e  ++ e+++aeR++ vlt+ +++ ++t+
  gi|313125300|ref|YP_004035564.1| 253 LDAQLELRDAVEARFAERNVPVLTVCNKSDRSTD 286
                                       56677777899***************99998876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.86   9.1e+02      69      99 ..      61      91 ..      59     107 .. 0.73
   2 ?    7.9   0.0    0.0033       3.5       2      35 ..     159     194 ..     158     221 .. 0.65
   3 ?    0.4   0.0      0.68   7.2e+02     106     119 ..     269     282 ..     223     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.86
                                      TTTT-HHHHCTSCEEEEEEEGHHHHCHHHHH CS
                               Roc 69 frslhplylreaalailvydsrssenlkeWl 99
                                      f ++ p+y++ a++++ v + r+s +  +W 
  gi|313125300|ref|YP_004035564.1| 61 FGTVDPFYYELADAIVDVDELRQSLSEVTWA 91
                                      7789999999999998777766655545665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0033
                                       EEEESSTTSSHHHHHHCHCT-CCC..-EEETTTTEE CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfs..ekekstigvd 35 
                                       +v+ G  +vGK+s+++++++ + +  +   +t gv+
  gi|313125300|ref|YP_004035564.1| 159 IVVAGYPNVGKSSFVNHVTRASNEiaRYPFTTKGVQ 194
                                       7899************99864443102233344443 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.68
                                       CSSS-EEEEEE-TT CS
                               Roc 106 agkspvilvgnkiD 119
                                        ++ pv+ v+nk D
  gi|313125300|ref|YP_004035564.1| 269 ERNVPVLTVCNKSD 282
                                       34669999****99 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.5   4.8e+03      53      53 ..      99      99 ..      41     135 .. 0.54
   2 ?   11.4   0.0   0.00033      0.35       1      44 [.     159     211 ..     159     258 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.5
                            AAA_18 53 d 53
                                      +
  gi|313125300|ref|YP_004035564.1| 99 R 99
                                      2 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00033
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf........gvnlrdvakenglllevdpe 44 
                                       I+++G+p vGK+++ +++ +   ++        gv++++  +++  +   d +
  gi|313125300|ref|YP_004035564.1| 159 IVVAGYPNVGKSSFVNHVTRASnEIarypfttkGVQIGHFERDRIRYQIIDTP 211
                                       89****************77743447777777766666655554444444444 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.7   2.8e+03      38      61 ..     140     162 ..     125     171 .. 0.73
   2 ?   10.5   0.0   0.00039      0.41      68     116 ..     258     310 ..     254     314 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.7
                                       EEHHHHHHTGGGG-STTCEEEEEE CS
                               SIS  38 edaselkhgvlalideddlvilis 61 
                                        +a +   g l+ i++d + i+++
  gi|313125300|ref|YP_004035564.1| 140 GEARDSLKG-LPDIRPDEPAIVVA 162
                                       455555666.88999999999987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00039
                                       HHHHHHH.HHHHTTSEEEEEESSTTSHHHHHSSEEEEEEEECHC...SSSHCH CS
                               SIS  68 dlvaaae.lakergakiiaITdskgsplareadlalyinaepet...lvastk 116
                                       +l +a+e   +er++++++++++++ +   ead+ + +  e+ +   l as++
  gi|313125300|ref|YP_004035564.1| 258 ELRDAVEaRFAERNVPVLTVCNKSDRSTDVEADYYMSVENEEGVeevLTASVD 310
                                       7788999999**********************988888777766666666655 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.5   3.7e+03      63     103 ..      63     101 ..      60     129 .. 0.57
   2 ?    9.1   0.0   0.00086      0.91       2      57 ..     159     212 ..     158     313 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.5
                                       HHHHHHHTTESEEEEEEETTB.HHHHHTHHHHHHHHHHHSTT CS
                               Ras  63 slrelyyrdaegillvydits.resfenvkkwveeikrvaee 103
                                       ++ + yy+ a++i+   d+++ r+s+++v+   ++i ++ +e
  gi|313125300|ref|YP_004035564.1|  63 TVDPFYYELADAIV---DVDElRQSLSEVTWASRQIAEIRSE 101
                                       55566666666655...3333256666666556666555554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00086
                                       EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETT CS
                               Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAG 57 
                                       +v+ G  +vGK+s++++ ++ + +    +     + ++  +++  +++ +i DT G
  gi|313125300|ref|YP_004035564.1| 159 IVVAGYPNVGKSSFVNHVTRASNEIARYPFT--TKGVQIGHFERDRIRYQIIDTPG 212
                                       7999***********9988877665544433..35566666778999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      815  (0.0454571); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2034.71
//
Query:       gi|313125301|ref|YP_004035565.1|  [L=248]
Description: hypothetical protein Hbor_05250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-43  148.9  10.3    3.1e-43  148.6  10.3    1.1  1  SIMPL     Protein of unknown function (DUF541)
  ------ inclusion threshold ------
       0.02   14.8   0.5       0.18   11.7   0.2    2.4  2  Flg_hook  Flagellar hook-length control protein FliK


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6  10.3   3.4e-47   3.1e-43       1     200 []      47     245 ..      47     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 3.4e-47
                             SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysyengknki 77 
                                       ItV+G++ev++++D+a+l++ v++++ +a+ea+a+va++++++++al+++g++++ ++ts+++++ +y+ +++++++
  gi|313125301|ref|YP_004035565.1|  47 ITVSGNGEVKAESDLAVLSVAVTATASSADEARAQVADRSETMRQALREAGVADDAVTTSHFRVRAQYNHNGKERNV 123
                                       9***********************************************99*************************** PP

                             SIMPL  78 tgyeasqsltvkfrdldklgevldaavka.aneingvsfslsde..delrdeareeAvkdArakAealAkalgvklg 151
                                       tgyea +++++++   d++gevld av + ane++ vsf+ls+e  ++lr++a+++A++ Ar+ A++lA+a+++++ 
  gi|313125301|ref|YP_004035565.1| 124 TGYEAVHTYSIEV-SPDRAGEVLDVAVGNgANEVQHVSFTLSEEarADLRNDALNAAMDSARTDADTLASAANLSIT 199
                                       *************.5577************************776788899************************** PP

                             SIMPL 152 kvvsisesgsnpyappapamaaaaaaaasaatpfepgeievtasVtvvf 200
                                       +v+s+s sg+ + +  +++++ ++  aa ++t+fepg ++v+a+Vtv++
  gi|313125301|ref|YP_004035565.1| 200 GVQSVSTSGGYH-PVEPRMEYDTP--AANSGTSFEPGPVTVSATVTVTY 245
                                       *****9943333.22222233333..699******************98 PP

>> Flg_hook  Flagellar hook-length control protein FliK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2     2e-05      0.18      40      77 ..      68     106 ..      46     112 .. 0.77
   2 ?    0.4   0.0     0.067     6e+02      15      56 ..     132     174 ..     124     191 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                                       EEEEE.-SCHHHHHHHHTHHHHHHHHHCCTTCCEEEEEE CS
                          Flg_hook  40 vqlta.enpetrelLeqnlprLreaLaaaGlklddlsvs 77 
                                       v+ ta +  e+r+++ + ++++r+aL++aG+  d ++ s
  gi|313125301|ref|YP_004035565.1|  68 VTATAsSADEARAQVADRSETMRQALREAGVADDAVTTS 106
                                       4444414568*********************99887765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.067
                                       EEEEECCCCCEEE.EEEEEEETTEE.EEEEEE-SCHHHHHHHHT CS
                          Flg_hook  15 atlrLdppeLGkv.evkltlrggql.svqltaenpetrelLeqn 56 
                                        +++  p++ G+v +v +   ++++ +v++t  ++e+r+ L+++
  gi|313125301|ref|YP_004035565.1| 132 YSIEVSPDRAGEVlDVAVGNGANEVqHVSFTL-SEEARADLRND 174
                                       56677777777753566655566440444444.55566666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1621.81
//
Query:       gi|313125302|ref|YP_004035566.1|  [L=428]
Description: hypothetical protein Hbor_05260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-33  113.3  17.4    9.1e-33  113.3  17.4    2.4  3  DUF389    Domain of unknown function (DUF389)


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.13   2.3e+03      75     100 ..     112     137 ..      92     138 .. 0.66
   2 !  113.3  17.4   5.1e-37   9.1e-33       1     142 []     139     284 ..     139     284 .. 0.95
   3 ?   -0.3   0.0     0.056     1e+03      34      50 ..     317     333 ..     304     363 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.13
                            DUF389  75 dllvAlasGaagalallsgnssslvG 100
                                        +l+A++s ++++  +l ++ +++vG
  gi|313125302|ref|YP_004035566.1| 112 FVLLAVVSAVVATAGVLLDSPAVVVG 137
                                       46677777777777766666666666 PP

  == domain 2  score: 113.3 bits;  conditional E-value: 5.1e-37
                            DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplk...vlg.eeelptsemlsrtepnl 73 
                                       M+i+Pl+gp++a+++g+v+ dr+l+ rg+k +++g +la+  + lf+++l+++   +l+ ee +   e+++r  p++
  gi|313125302|ref|YP_004035566.1| 139 MVIAPLVGPAMATSIGTVVDDRELAIRGVKLQVLGGILAISSASLFAAALRFSgivPLTaEEVFAIGEVRERLAPDV 215
                                       ***********************************************7766666776666899999*********** PP

                            DUF389  74 vdllvAlasGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgIvl 142
                                       ++l++Al +Gaaga++++sg s++lvGv+IaaaL+PP++++G+++a+g++  ++g l+l+lvN++ I++
  gi|313125302|ref|YP_004035566.1| 216 LSLVIALGAGAAGAMSISSGVSTALVGVMIAAALVPPIAVVGISIAWGQPLTMIGPLVLVLVNVLSINF 284
                                       *******************************************************************86 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.056
                            DUF389  34 iglllallvgflfglll 50 
                                       +g +l +l ++l+g+ +
  gi|313125302|ref|YP_004035566.1| 317 LGAILLILSSVLVGVTY 333
                                       33334444444444322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2761.38
//
Query:       gi|313125303|ref|YP_004035567.1|  [L=237]
Description: 5-formyltetrahydrofolate cyclo-ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-31  109.5   0.0    2.1e-31  109.2   0.0    1.1  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.0   1.2e-35   2.1e-31       1     187 []       3     200 ..       3     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 1.2e-35
                                       HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-.SEE........EE----TTS---HHHHHHHHHTTEE CS
                    5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqea.krv........alyvsvkgeidtkelikklleegke 68 
                                       Kq+lR++   +++++++e++a+ + + + r+++++++++a +r+        a ++++++++++ +l++++l +gk 
  gi|313125303|ref|YP_004035567.1|   3 KQDLRER---IWDRMEAEGIARFPFPPHDRVPNFVGAEDAaERLaetdayteASVLKCNPDSPQLPLRRRALHDGKT 76 
                                       899***9...*****************************999*********************************** PP

                                       EEEEEECSSCTEECEEEEEECCCCCCCCCHCTSSCE--TTECCBCGGG...G-SEEEE--SEEETTS-EE-SSTTHH CS
                    5-FTHF_cyc-lig  69 vllPrvrlesgslkvvrlttlkeedslesgkyglkePeeeeerelale...kldlvlvPgvAfdkeGaRlGkGkGyy 142
                                       v+l  +rl+++++ +     + + ++  + +    + ++e++r+   +    +dlv+ ++vA+ ++G R+GkG+Gy 
  gi|313125303|ref|YP_004035567.1|  77 VYLAAPRLRDKKPFLALDPAEIPPEEYDRAPTV--SHAAEYARPVGPKdvpHVDLVVSGSVAVTETGTRVGKGEGYS 151
                                       **9888888844333333333333333322222..22333333333333448************************* PP

                                       HHHHHHHTS.T-SS--EEEEE--GGGEES...-----ST----SEEE-S CS
                    5-FTHF_cyc-lig 143 Drflarlkg.gagdkpltvglaldeqlve...rlPleehDvpvdevvte 187
                                       D ++a l++  a d+++tv+++++e +v     +   +hDvp+d+v+t+
  gi|313125303|ref|YP_004035567.1| 152 DLEFAVLSElEAVDSETTVATTVHEVQVVgddAVTPADHDVPMDIVCTP 200
                                       *************************9998888899999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1413.80
//
Query:       gi|313125304|ref|YP_004035568.1|  [L=206]
Description: small GTP-binding protein domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-20   72.9   0.0    3.1e-20   72.4   0.0    1.2  1  MMR_HSR1       50S ribosome-binding GTPase
    1.1e-13   51.0   0.1    1.5e-12   47.3   0.1    2.0  1  FeoB_N         Ferrous iron transport protein B
    1.2e-06   28.2   0.0    0.00027   20.5   0.0    2.3  2  GTP_EFTU       Elongation factor Tu GTP binding domain
    4.3e-06   26.7   0.0      0.002   18.0   0.0    2.3  2  RsgA_GTPase    RsgA GTPase
    4.4e-06   26.2   0.0    1.7e-05   24.3   0.0    1.8  2  AIG1           AIG1 family
     0.0028   18.2   0.0     0.0036   17.8   0.0    1.5  1  ABC_tran       ABC transporter
     0.0091   16.5   0.0      0.014   16.0   0.0    1.3  1  AAA_18         AAA domain
  ------ inclusion threshold ------
      0.012   15.7   0.1      0.029   14.4   0.1    1.6  2  Dynamin_N      Dynamin family
      0.013   14.7   0.2      0.023   13.9   0.2    1.3  1  TIP49          TIP49 P-loop domain
      0.014   15.6   0.1      0.041   14.1   0.0    1.8  2  Roc            Ras of Complex, Roc, domain of DAPkinase
      0.032   14.0   0.4       0.73    9.6   0.0    2.2  2  ATP_bind_1     Conserved hypothetical ATP binding protein
      0.038   14.3   0.1       0.24   11.7   0.1    2.3  2  AAA_22         AAA domain
      0.039   14.3   0.1       0.14   12.5   0.1    1.9  1  AAA_16         AAA ATPase domain
      0.048   13.1   0.0      0.097   12.1   0.0    1.6  1  SRPRB          Signal recognition particle receptor beta subu
      0.054   13.1   0.1       0.12   12.0   0.0    1.6  2  Ras            Ras family
      0.078   13.4   0.0       0.14   12.5   0.0    1.4  1  RNA_helicase   RNA helicase
       0.11   12.0   0.0        4.1    6.8   0.0    2.1  2  Arf            ADP-ribosylation factor family
       0.12   12.1   0.0       0.55    9.9   0.0    1.9  2  AAA_24         AAA domain
       0.12   12.0   0.0       0.19   11.4   0.0    1.2  1  Guanylate_kin  Guanylate kinase
       0.14   11.9   0.0       0.43   10.3   0.0    1.7  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
       0.18   11.8   0.0       0.32   11.0   0.0    1.5  1  MIP-T3         Microtubule-binding protein MIP-T3 CH-like dom
       0.19   11.1   0.0       0.36   10.2   0.0    1.4  1  TniB           Bacterial TniB protein


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0   3.7e-23   3.1e-20       1     114 []      10     141 ..      10     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 3.7e-23
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC.....SSHHHHHHHHHHHHH CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGl.....iegaseekglgkafl 71 
                                       ev++vGr+NvGKStL++ ltg  k  +++kpg+Tr++n++ ++  g+++ ++D+pG+     + +++++++++ ++ 
  gi|313125304|ref|YP_004035568.1|  10 EVVLVGRSNVGKSTLMRELTGHsKFTTGKKPGVTRQPNHFDWS--GEKFMFTDLPGFgfmsgV-EEHRREEIKTDIV 83 
                                       699******************8799***************999..99*********5433222.3444444444444 PP

                                       HHHC.....TSEEEEEEETT............TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  72 alee.....adlillvvdas............eeklkpldeeleelleeakkplilvlnk 114
                                       +  e       + +lvvd +            +e   p d e+  +l+e + p+++++nk
  gi|313125304|ref|YP_004035568.1|  84 RYLEsnaddILAGVLVVDGKsvvdiidrhsgpDE--IPHDVEMFHFLRELGVPVVVAVNK 141
                                       4333231123345667774477777776555322..4678999999999*******9998 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1   1.8e-15   1.5e-12       2     127 ..      10     154 ..       9     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.8e-15
                                       EEEEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETTEEEEEEE----SSS...SSSSHHHHHHHHHH CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkgkeveivDlPGiYsl...sayseeekvardfl 74 
                                       +v+lvG  nvGk+tl+ +ltg +  + g  pGvt +    +++++g+++ ++DlPG   +   +   + e++ +d++
  gi|313125304|ref|YP_004035568.1|  10 EVVLVGRSNVGKSTLMRELTGHSkFTTGKKPGVTRQ--PNHFDWSGEKFMFTDLPGFGFMsgvE-EHRREEIKTDIV 83 
                                       699******************762689*****9965..5667777***********86663332.233344554443 PP

                                       H...CTSSSE...........EEEEEEGG....GHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-H CS
                            FeoB_N  75 l...eeepdv...........vvnvvdat....nlernLyLtlqllelgvpvvlalnmideaekkgieidl 127
                                           ++  d+           vv+++d +    ++  ++ ++  l elgvpvv+a+n++d++++k  ++d+
  gi|313125304|ref|YP_004035568.1|  84 RyleSNADDIlagvlvvdgksVVDIIDRHsgpdEIPHDVEMFHFLRELGVPVVVAVNKMDKVDDKDERLDE 154
                                       2221333332111111111115666665422225788999************************9999885 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.01       8.6       5      29 ..      10      34 ..       6      64 .. 0.80
   2 !   20.5   0.0   3.3e-07   0.00027      98     144 ..     106     157 ..      90     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.01
                                      EEEEEESTTSSHHHHHHHHHHHTTS CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktga 29
                                       ++++g  + GK+TL+ +L+ +++ 
  gi|313125304|ref|YP_004035568.1| 10 EVVLVGRSNVGKSTLMRELTGHSKF 34
                                      6889999***********9966654 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.3e-07
                                       EEEEETTTBST..HHHHHHHHHHHHTTTEEEEEEESCGST...HHHHHHHHH CS
                          GTP_EFTU  98 vlvvdaveGve..pqteevlrlalkegvpiivfiNKmDrl...kaelkeive 144
                                       v ++d ++G+   p   e+++ ++++gvp++v++NKmD++   +++l+e+ +
  gi|313125304|ref|YP_004035568.1| 106 VDIIDRHSGPDeiPHDVEMFHFLRELGVPVVVAVNKMDKVddkDERLDELCD 157
                                       445777777542256678999*******************777677776655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.5e-06     0.002     100     129 ..       9      38 ..       3      64 .. 0.89
   2 !    6.5   0.0    0.0087       7.1      41      71 ..     127     155 ..     120     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.5e-06
                                       SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktge 129
                                       + +vlvG S vGKStL+ +l+++ +  tg+
  gi|313125304|ref|YP_004035568.1|   9 QEVVLVGRSNVGKSTLMRELTGHSKFTTGK 38 
                                       5689******************99998876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0087
                                       HHHHTT-EEEEEEE-GGG--HHHHHHHHHHH CS
                       RsgA_GTPase  41 laeekgiepvivlnKiDlleeeeeleelkee 71 
                                       ++ e g+++v+++nK+D +++++  e+l e 
  gi|313125304|ref|YP_004035568.1| 127 FLRELGVPVVVAVNKMDKVDDKD--ERLDEL 155
                                       5678899*************999..444444 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   2.1e-08   1.7e-05       2      92 ..      10     101 ..       9     111 .. 0.83
   2 ?    0.3   0.0      0.46   3.8e+02      58     102 ..     107     151 ..      96     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.1e-08
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SC.CCTTC...CHHCHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPgl.fdlsv...sadkiskeiv 74 
                                       ++vlvG++ +GkS+    + g++ F++  ++ +vt+++++    w+g+k    D Pg  f + v   + ++i+ +iv
  gi|313125304|ref|YP_004035568.1|  10 EVVLVGRSNVGKSTLMRELTGHSKFTTG-KKPGVTRQPNHF--DWSGEKFMFTDLPGFgFMSGVeehRREEIKTDIV 83 
                                       69************************99.899***988765..799***********764444322358999***** PP

                                       HHHHHCTT-ESEEEEEEE CS
                              AIG1  75 rclllseegihalllvls 92 
                                       r l+ +++ i a +lv++
  gi|313125304|ref|YP_004035568.1|  84 RYLESNADDILAGVLVVD 101
                                       *99999988888888876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.46
                                       SCCCTTCCHHCHHHHHHHHHHHCTT-ESEEEEEEETTB-SHHHHH CS
                              AIG1  58 glfdlsvsadkiskeivrclllseegihalllvlslgrfteedek 102
                                       +++d ++  d+i +++     l e g+ +++ v ++++++++de 
  gi|313125304|ref|YP_004035568.1| 107 DIIDRHSGPDEIPHDVEMFHFLRELGVPVVVAVNKMDKVDDKDER 151
                                       356666678899999998889999999******999999999986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.4e-06    0.0036      12      41 ..       9      38 ..       6     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.4e-06
                                      SEEEEEESTTSSHHHHHHHHTTSS--SEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGe 41
                                      + v++vG++  GKStL++ l+g++k t G+
  gi|313125304|ref|YP_004035568.1|  9 QEVVLVGRSNVGKSTLMRELTGHSKFTTGK 38
                                      5699*********************99997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-05     0.014       1      89 [.      11     119 ..      11     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..................gvnlrdvakenglllevdpealdeskrldedkldk 59 
                                       ++l G + vGK+tl +eL  + +f                  g++ +++   +    +  +e  ++ +++++d + +
  gi|313125304|ref|YP_004035568.1|  11 VVLVGRSNVGKSTLMRELTGHSKFttgkkpgvtrqpnhfdwsGEKFMFTDLPGFGFMSGVEE--HRREEIKTDIVRY 85 
                                       6899**************77767788888888855555555555555554444444444444..7888888888888 PP

                            AAA_18  60 lldaleenss....aleegknlvidghlaelese 89 
                                       l ++ + + +      ++  + +id h +  e +
  gi|313125304|ref|YP_004035568.1|  86 LESNADDILAgvlvVDGKSVVDIIDRHSGPDEIP 119
                                       8888888887887666666666888877766644 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.5e-05     0.029       1      38 [.      11      49 ..      11      81 .. 0.89
   2 ?   -1.2   0.0       2.2   1.8e+03      98     112 ..      51      65 ..      47      97 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-05
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS.---S-EEE CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnp.tTrrplel 38
                                      +++vG  + GKS+++  L+g+  + +g+ p +Tr p++ 
  gi|313125304|ref|YP_004035568.1| 11 VVLVGRSNVGKSTLMRELTGHSKFTTGKKPgVTRQPNHF 49
                                      799*******************99999996489999875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                                       TTS-SEEEEE---B- CS
                         Dynamin_N  98 llvkgltlvDlPGld 112
                                       +  ++  + DlPG+ 
  gi|313125304|ref|YP_004035568.1|  51 WSGEKFMFTDLPGFG 65 
                                       566777888999974 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.8e-05     0.023     254     292 ..      70     108 ..      64     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 254 iteklreeinkkvakyveegkaeivpGvlfiDevhmlDi 292
                                       ++e+ reei + + +y+e+   +i++Gvl +D   ++Di
  gi|313125304|ref|YP_004035568.1|  70 VEEHRREEIKTDIVRYLESNADDILAGVLVVDGKSVVDI 108
                                       78999****************************999998 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     5e-05     0.041       2      25 ..      11      35 ..      10      52 .. 0.80
   2 ?   -2.0   0.0         5   4.1e+03     110     120 .]     134     144 ..     125     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                                      EEEESSTTSSHHHHHHCHCT.-CCC CS
                               Roc  2 vvlvGdsgvGKtsllkrfve.dkfs 25
                                      vvlvG s+vGK++l+++++  +kf+
  gi|313125304|ref|YP_004035568.1| 11 VVLVGRSNVGKSTLMRELTGhSKFT 35
                                      89**************998624454 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5
                                       -EEEEEE-TTT CS
                               Roc 110 pvilvgnkiDl 120
                                       pv++ +nk+D+
  gi|313125304|ref|YP_004035568.1| 134 PVVVAVNKMDK 144
                                       899999**995 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.11        93       2      20 ..      14      32 ..      13      41 .. 0.85
   2 ?    9.6   0.0    0.0009      0.73     149     174 ..     125     150 ..      66     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                        ATP_bind_1  2 vGpaGsGKttfvgalseil 20
                                      vG   +GK+t++++l+ + 
  gi|313125304|ref|YP_004035568.1| 14 VGRSNVGKSTLMRELTGHS 32
                                      78899*********99876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0009
                        ATP_bind_1 149 lsamlrlelPhvvvlnkfDllkekle 174
                                          + +l++P vv++nk+D +++k+e
  gi|313125304|ref|YP_004035568.1| 125 FHFLRELGVPVVVAVNKMDKVDDKDE 150
                                       4556789*************996643 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0003      0.24       8      29 ..      11      32 ..       5     132 .. 0.68
   2 ?   -0.7   0.0       1.9   1.5e+03     114     114 ..     157     157 ..     102     202 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                            AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                      +v++G s +GK+tl+r+l+   
  gi|313125304|ref|YP_004035568.1| 11 VVLVGRSNVGKSTLMRELTGHS 32
                                      699**************98764 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                            AAA_22 114 s 114
                                       +
  gi|313125304|ref|YP_004035568.1| 157 D 157
                                       2 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00017      0.14      25     160 ..       9     157 ..       2     165 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesa...............ipysalaqalareellrqll 86 
                                       + v+l+G s vGKs+l+rel  + +     f++gk    +++               +p   + +   +e+  ++++
  gi|313125304|ref|YP_004035568.1|   9 QEVVLVGRSNVGKSTLMRELTGHSK-----FTTGKKPGVTRQpnhfdwsgekfmftdLPGFGFMSGV-EEHRREEIK 79 
                                       5589****************96333.....4444444443332222222222344334445555555.335555555 PP

                            AAA_16  87 deaesaeleawrekleeala.avpelagaea......srllellkrll...allsrderplvlvlDdlqwadeaslq 153
                                       ++    + + +++ l ++l  ++++            ++  +++ + +    +l++ + p+v+ +  ++++d+ +  
  gi|313125304|ref|YP_004035568.1|  80 TDIVRYLESNADDILAGVLVvDGKS-----VvdiidrHSGPDEIPHDVemfHFLRELGVPVVVAVNKMDKVDDKDER 151
                                       5533322222222222222242222.....13333355555555544433356677777888888888888886655 PP

                            AAA_16 154 llaaLlr 160
                                       l ++L++
  gi|313125304|ref|YP_004035568.1| 152 L-DELCD 157
                                       5.55555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012     0.097       4      59 ..       9      64 ..       6     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                      -EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG.....GGTT-SEEEETT- CS
                             SRPRB  4 pavllvGlsdsGKTslftrLttdsvkktvtSqessaalkv..ksekgskltliDfPGh 59
                                      + v+lvG s+ GK +l+  Lt  s+ +t    ++ ++ +    +  g+k+ + D+PG 
  gi|313125304|ref|YP_004035568.1|  9 QEVVLVGRSNVGKSTLMRELTGHSKFTTGK--KPGVTRQPnhFDWSGEKFMFTDLPGF 64
                                      679*****************9986655543..33333333112557889999999995 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.12       2      32 ..      11      42 ..      10      58 .. 0.82
   2 ?   -2.9   0.0       5.3   4.3e+03     104     118 ..     132     146 ..     109     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                      EEEEESTTSSHHHHHHHHH.HSSCSSSCTTTS CS
                               Ras  2 lvlvGdsavGKtslllrfv.kdkFkeeyesTi 32
                                      +vlvG s+vGK++l+ + + ++kF++ +++ +
  gi|313125304|ref|YP_004035568.1| 11 VVLVGRSNVGKSTLMRELTgHSKFTTGKKPGV 42
                                      89*************99984567887777765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.3
                                       TSEEEEEEETTTGGG CS
                               Ras 104 nvpivLvGnKvDlee 118
                                        vp+v+  nK+D  +
  gi|313125304|ref|YP_004035568.1| 132 GVPVVVAVNKMDKVD 146
                                       578888889998655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017      0.14       1      26 [.      11      32 ..      11      58 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      ++l+G+s++GKStl++eL+ +    +
  gi|313125304|ref|YP_004035568.1| 11 VVLVGRSNVGKSTLMRELTGH----S 32
                                      689**************5543....3 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0051       4.1      16      65 ..      10      61 ..       3      67 .. 0.77
   2 ?    3.3   0.0     0.059        48     115     134 ..     132     151 ..      91     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0051
                                      EEEEEESTTSSHHHHHHHHHHSSCEE..CSSSSSEEEEEEEETTEEEEEEEE CS
                               Arf 16 rilllGLDnaGKtTilkklkleelvt..tvPTigfnveeleiknlkftvwDv 65
                                       ++l+G  n GK+T++ +l+ ++  t   +P +  + ++    + kf + D+
  gi|313125304|ref|YP_004035568.1| 10 EVVLVGRSNVGKSTLMRELTGHSKFTtgKKPGVTRQPNHFDWSGEKFMFTDL 61
                                      5899***************987766534677777777777777777776666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.059
                                       TSEEEEEEE-TTSTTSS-HH CS
                               Arf 115 evallvlaNKqDlpealsee 134
                                        v+++v  NK+D  ++ +e+
  gi|313125304|ref|YP_004035568.1| 132 GVPVVVAVNKMDKVDDKDER 151
                                       799*********99987763 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00067      0.55       3      22 ..       9      28 ..       7      44 .. 0.83
   2 ?   -0.5   0.0         1   8.5e+02     125     142 ..     134     151 ..     122     179 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00067
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      + ++++G s +GK+tl++el
  gi|313125304|ref|YP_004035568.1|  9 QEVVLVGRSNVGKSTLMREL 28
                                      679***************99 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1
                            AAA_24 125 vifiahektrkdedpege 142
                                        +++a  k++k++d++++
  gi|313125304|ref|YP_004035568.1| 134 PVVVAVNKMDKVDDKDER 151
                                       466677777777777655 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.19       4      53 ..      10      58 ..       7      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                      EEEEESTTTSSHHHHHHHHHHHSTTTEE.E--EEESS---TTS-TTTSEEE CS
                     Guanylate_kin  4 pvvlvgpsgaGksslkkaLlselpekfg.vsvshtTrdprkgevdGkdYyF 53
                                       vvlvg s +Gks+l  +L  +  +kf+    + +Tr+p + +  G+++ F
  gi|313125304|ref|YP_004035568.1| 10 EVVLVGRSNVGKSTLMRELTGH--SKFTtGKKPGVTRQPNHFDWSGEKFMF 58
                                      69****************9765..455436789***************999 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00053      0.43       2      24 ..       9      31 ..       8      57 .. 0.83
   2 ?   -1.3   0.0       2.1   1.7e+03      88     104 ..     131     147 ..      95     158 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                         PduV-EutP  2 kkilliGkvgsGKttLtqalkge 24
                                      ++++l+G++++GK tL+++l+g+
  gi|313125304|ref|YP_004035568.1|  9 QEVVLVGRSNVGKSTLMRELTGH 31
                                      5799****************985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.1
                         PduV-EutP  88 fnkeviGiitkidlaed 104
                                       +  +v+  + k+d+++d
  gi|313125304|ref|YP_004035568.1| 131 LGVPVVVAVNKMDKVDD 147
                                       33345555555555544 PP

>> MIP-T3  Microtubule-binding protein MIP-T3 CH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00039      0.32      17      67 ..     154     203 ..     139     206 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                                       ---TTTTTS--HHHHHHHHHHHHHHT-SSTTTS-HHHH-GGG--SHHHHHH CS
                            MIP-T3  17 kltekLLskPPFkylvDivtevikatGflkglytddeldsenvkdkdakia 67 
                                       +l ++L   PP+k   D++  +  + G+++ ly++ ++ +++ + +d  ++
  gi|313125304|ref|YP_004035568.1| 154 ELCDRLGLMPPWKQWSDVIAPICAKRGSIDPLYESLQTYFHE-QKRDDLLK 203
                                       68999999*************************998877766.55555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00045      0.36      32      56 ..       5      29 ..       2      45 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                              TniB 32 rkrmpnlllvGdsnnGKtmivekFa 56
                                      r   + ++lvG+sn+GK++++++ +
  gi|313125304|ref|YP_004035568.1|  5 RPNCQEVVLVGRSNVGKSTLMRELT 29
                                      5667899*************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1307.88
//
Query:       gi|313125305|ref|YP_004035569.1|  [L=224]
Description: hypothetical protein Hbor_05290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-45  153.1   0.0    3.7e-26   92.2   0.0    2.0  2  DUF3179   Protein of unknown function (DUF3179)


Domain annotation for each model (and alignments):
>> DUF3179  Protein of unknown function (DUF3179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   2.1e-30   3.7e-26      19      93 ..      49     122 ..      35     128 .. 0.92
   2 !   59.1   0.0   2.4e-20   4.3e-16      94     151 ..     153     210 ..     136     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 2.1e-30
                           DUF3179  19 sksldddepVigvelngearaYPlrilvwheiVNdtlggepvavTYCpLcgtalaferridggelefgvsGkLvn 93 
                                        + l+ + +V+gve +g araYPl++l+whe+VNd l+g pv vTYCpLc+++++ +r +d++  +f+vsG L++
  gi|313125305|ref|YP_004035569.1|  49 GDGLTAQSQVVGVERDGAARAYPLSVLWWHEVVNDDLNG-PVLVTYCPLCQSGMVAKRVVDEQAATFRVSGHLWQ 122
                                       457999*******************************96.9********************************87 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 2.4e-20
                           DUF3179  94 snlvmyDreteslwqQllgeaiaGklegteLeelpvvtttwekwkeahpdtkVlseet 151
                                        nlv+ D +tes+w+Qll++a++G+  gt+L++lp+++ttw++w+ +hp+t Vl  + 
  gi|313125305|ref|YP_004035569.1| 153 GNLVLVDDATESYWSQLLARAVCGSASGTRLDILPSTVTTWDAWRDDHPKTDVLLPPP 210
                                       499***************************************************6554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1372.35
//
Query:       gi|313125306|ref|YP_004035570.1|  [L=423]
Description: translation initiation factor 2b subunit, eif-2b alpha/beta/delta family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-33  114.5   1.1    6.6e-33  114.1   1.1    1.1  1  IF-2B     Initiation factor 2 subunit family
      1e-07   32.0   2.0      1e-07   32.0   2.0    2.1  2  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   1.1   7.3e-37   6.6e-33       2     280 ..     141     403 ..     140     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 7.3e-37
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       ++Gs++i+ +ale+l++++ +a+       +  + k +++L+ arP++  ++n ++ +l      +s+ + +++ + 
  gi|313125306|ref|YP_004035570.1| 141 THGSAWISARALEALRDAAIEAD------DWAAVAKIGRELRDARPSMAAVCNRVNHVLS-----TSERTPESVATV 206
                                       689************99877666......26788999***********************.....555666666666 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLv 155
                                       +i++++   +++e+a +  ++  ++   +   + T ++s+tv + lr++   +     +++EsrP+ +G  +a++++
  gi|313125306|ref|YP_004035570.1| 207 AIRELDAAFESDEKAARTLVRRLRD--AEVSGVATLSRSGTVSAALRKLDPTS----LLAAESRPEREGVTVAETVA 277
                                       6666666666655555554444333..23456****************99965....9***********76666665 PP

                                       HT.TXEEEEEEGGGHHHHHHC...TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSS CS
                             IF-2B 156 qa.gipvtlitdsavayvmse...evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservql 228
                                       ++ +  vt++t +a+ + +s+    vd+v+vGAd++  +G+++nk+GTs lA +A+++ +pv+vva s k+ +    
  gi|313125306|ref|YP_004035570.1| 278 EEtDAAVTVTTEAALPAALSRcetAVDAVVVGADAVHPDGSVVNKTGTSVLASAAQSAGVPVYVVAASDKVRPAGTA 354
                                       4326789**************9999************************************************9888 PP

                                       GGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEE CS
                             IF-2B 229 dedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvl 280
                                       ++d   e+ ++     + + +    +++v+ p+f  + ++l++++ Te+G+l
  gi|313125306|ref|YP_004035570.1| 355 SRDAADEMCAESPHEAVYDGDA---DVDVFAPTFERVSADLVDGLATEKGLL 403
                                       8887777665555545555444...89***********************98 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   2.0   1.2e-11     1e-07       6     117 ..       5     115 ..       2     129 .. 0.74
   2 ?   -3.9   0.1       1.5   1.4e+04      42      52 ..     402     412 ..     391     414 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.2e-11
                                       EEEEEEETTSEEEEEEES..SSSTTT.EESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   6 vgvvllnekgevLlvrrs..kkpfpg.WelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhylapydgpy 78 
                                       v ++++n   +vLl+ rs    + +g W+ + G +e +  ++e+ A REl+EEtGl +++lel+       +++  +
  gi|313125306|ref|YP_004035570.1|   5 VTCFVRNCG-AVLLTLRSeeTGTYSGrWAGISGYIEGDPdDAEADAWRELREETGLGEDDLELVRAG---ETVEVED 77 
                                       677888888.7*******886666668*********887899999***********88999998833...3333333 PP

                                       EEEEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHH CS
                             NUDIX  79 gdeheilyvfl.eevegelepndenevsevrwvpleellk 117
                                       ++  ++++ fl e+++ ++++   +e++e+ w +++++  
  gi|313125306|ref|YP_004035570.1|  78 EEGSFVVHPFLfESDTRTVTT--NEELAEIAWTDPTAIRN 115
                                       335677777774455555444..59**********99933 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHH CS
                             NUDIX  42 tpeeAArREle 52 
                                        + +AA+R+++
  gi|313125306|ref|YP_004035570.1| 402 LLDAAAVRRVA 412
                                       45689999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2765.26
//
Query:       gi|313125307|ref|YP_004035571.1|  [L=168]
Description: phosphoesterase, mj0936 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-26   91.8   0.8    6.2e-26   91.5   0.8    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    0.00093   19.7   0.8      0.019   15.5   0.1    2.0  2  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.8     7e-30   6.2e-26       3     163 ..       5     157 ..       4     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 7e-30
                     Metallophos_2   3 laiiSDlH...snldaleavlealkevgvdaiihaGDleeeepevleellela....pvlaVrGNnDeevveedvlr 72 
                                       la++SD+H   ++ ++++ v+e+++++  d+++haGD+   ++++ +++ ela     ++aV GN+D          
  gi|313125307|ref|YP_004035571.1|   5 LAVVSDTHipsRAERIPDWVAERIRAA--DHVVHAGDF--DSLDAYDRVVELAggaaNLTAVAGNID---------- 67 
                                       79********88888899999999999..*********..9999999999999999***********.......... PP

                     Metallophos_2  73 eaaelgtdlpeeaelelagekvlliHgdpl..gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvg 147
                                          + + dlpe  +++++ +++ ++Hg+ +  g++d++a+++ e ++ +++ ++GHtH+   +  +gv+++nPGs++
  gi|313125307|ref|YP_004035571.1|  68 ---PRSFDLPEVTTFDVEAVRFVVTHGSGPraGYRDRVAATVHEVADSDAISISGHTHEVMDDVVDGVRLLNPGSAT 141
                                       ...77779********************99**************999999*************************** PP

                     Metallophos_2 148 eprdgdpetyaildtd 163
                                       +++ +d+ t+ +++++
  gi|313125307|ref|YP_004035571.1| 142 GAAPADETTMYTITVE 157
                                       ****999988888775 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.1e-06     0.019       3      76 ..       5      70 ..       3      92 .. 0.71
   2 ?    3.4   0.2      0.01        92     164     203 ..      86     123 ..      80     124 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-06
                                      EEEEESBTBTTCCTHHHHHHHHH.HHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS..C CS
                       Metallophos  3 ilvigDlHlalgggqlddllkll.ddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe..g 76
                                      ++v++D+H    + + +++ +++ +++++   +d v++aGD+     ++  ++el a   +   ++ +++GN +   
  gi|313125307|ref|YP_004035571.1|  5 LAVVSDTH---IPSRAERIPDWVaERIRA---ADHVVHAGDFDSLDAYDR-VVEL-AGGAA---NLTAVAGNIDprS 70
                                      68******...889999999999555555...5********555555555.8888.44444...5799999999441 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                                       EEEESSESSCSSSCSCCHHHHHHHHHHTTESEE.EEESSSS CS
                       Metallophos 164 ivlgHsplyrgsgylfgdealedllkkygvdlv.isGHtHv 203
                                       +v++H   +      + d++++++ +  + d++ isGHtH+
  gi|313125307|ref|YP_004035571.1|  86 FVVTHGSGP---RAGYRDRVAATVHEVADSDAIsISGHTHE 123
                                       566666666...33445555556677777788779*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1048.32
//
Query:       gi|313125308|ref|YP_004035572.1|  [L=250]
Description: coenzyme f420-0 gamma-glutamyl ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-57  194.7   0.0    1.9e-57  194.4   0.0    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.4   0.0   1.1e-61   1.9e-57       4     244 .]       9     219 ..       8     219 .. 0.98

  Alignments for each domain:
  == domain 1  score: 194.4 bits;  conditional E-value: 1.1e-61
                                       -----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH......TS-H... CS
                       F420_ligase   4 tplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklk.....vidpilS 75 
                                       +p+i++gddla+++ ++ +     l+++D+v+v+++vv+kaeg++++l+d+ ++++A+eia++l+     ++dp   
  gi|313125308|ref|YP_004035572.1|   9 VPEIRPGDDLAAVIRDRAD-----LREDDVVCVASTVVSKAEGRLFDLADFPAGPRAREIASNLEavtgdEKDP--- 77 
                                       69****************9.....****************************************878999****... PP

                                       ...............HHHHHHHHTEEEEEE-..S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHH CS
                       F420_ligase  76 rnrfsliLkalakatrkvevvlsepsdevgn..qlidekytdevlvklGllgsnagidesnveegllkllPedpdks 150
                                                      r+ ++vl+e+ + +++  +l++e+       ++G++g+nagid+snv+++ l+llP+ p +s
  gi|313125308|ref|YP_004035572.1|  78 ---------------RFAQAVLEESVELLMEspFLLTET-------RFGHVGVNAGIDRSNVPDNDLLLLPKRPAES 132
                                       ...............****************99******.......******************************* PP

                                       HHHHHHHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHH CS
                       F420_ligase 151 aeeikkklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgslad 227
                                       ae+i++++ +      +V++  +D++gr++++++ +va+g++g++a rd+rg++d+dg+elg+t+++v+del+++a+
  gi|313125308|ref|YP_004035572.1| 133 AERIRAEIPA-----DRVIV--TDTCGRPFRHGQRGVALGWAGMSASRDWRGETDRDGRELGVTVESVVDELAAAAN 202
                                       ********75.....58***..******************************************************* PP

                                       HHC-SSSS---EEEEES CS
                       F420_ligase 228 LvsGsadegtPvvlvrg 244
                                       LvsG++d+gtPvv+vr+
  gi|313125308|ref|YP_004035572.1| 203 LVSGEGDDGTPVVVVRD 219
                                       ***************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1665.23
//
Query:       gi|313125309|ref|YP_004035573.1|  [L=357]
Description: methylenetetrahydromethanopterin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-60  205.5   3.9    1.4e-60  205.4   3.0    1.4  2  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
       0.18   11.6   0.0       0.29   10.9   0.0    1.2  1  Phage_Nu1       Phage DNA packaging protein Nu1


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   3.0   1.5e-64   1.4e-60      20     307 ..      15     320 ..       4     327 .. 0.92
   2 ?   -0.7   0.0     0.081   7.3e+02     183     212 ..     321     354 ..     319     357 .] 0.63

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 1.5e-64
                    Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhl 96 
                                       +++  +ve  ++aE++G+d+++v+ h+++    +d+f+ l+ la +Te +rlg +v ++y +hP++lA   at+ +l
  gi|313125309|ref|YP_004035573.1|  15 HPIPAVVERGVRAEKAGYDTAFVSCHYNN----RDPFAALSRLADETEELRLGPGVANPYEMHPVTLAAKTATVAEL 87 
                                       588999**********************9....******************************************** PP

                    Bac_luciferase  97 sgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsv.kgalllprpgqgpiPvyva 172
                                       s+GR+++g+g g p +  r+ G++ ++ ++   E+ +v +r+w ge+v+++G f  + + + ++  p  g+iPvyv+
  gi|313125309|ref|YP_004035573.1|  88 SEGRAVFGIGPGDPSTL-RNLGLEDERGLRSVLEAFKVAQRVWDGERVSHDGTF-EAqNAGVNFDVP--GEIPVYVG 160
                                       *************9999.************************************.773555555555..349***** PP

                    Bac_luciferase 173 aaspaglelaarhadglllageppeeaaelierlragaae......................agrdpadirvgislt 227
                                       + +p + ++a++hadgll++g++p+++a++ +r+++g ae                         d ad+++++ ++
  gi|313125309|ref|YP_004035573.1| 161 GEGPHMCRMAGKHADGLLFNGSHPDDVAWARARVEEGIAErpdggdagndgdsgddgdsgddGNTDTADFELLAYAS 237
                                       ****************************************9************999998887777777********* PP

                    Bac_luciferase 228 vivadteeeAraea...raliagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqva 301
                                       v+++ ++e+Ar+ a    a+ia++ + +   ++  ++  a+ i+++ +a+++ +a+d+v++++++a+ ++Gtp++va
  gi|313125309|ref|YP_004035573.1| 238 VSIDSDREAAREAArppVAFIASGAAPPVLDRHGIDASLADDIGKKISAGAFSEAFDLVTPAMIDAFSMAGTPDTVA 314
                                       **************8888888887788888888888888889*********************************** PP

                    Bac_luciferase 302 erlaay 307
                                       +r+aa+
  gi|313125309|ref|YP_004035573.1| 315 DRMAAV 320
                                       ****94 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.081
                    Bac_luciferase 183 arhadglllag....eppeeaaelierlragaae 212
                                        +hadg+++ +    +p e++  +++  r + + 
  gi|313125309|ref|YP_004035573.1| 321 FEHADGVVVGSplgpNPDEAITLAADATRRARSH 354
                                       589******9999955555555555555543333 PP

>> Phage_Nu1  Phage DNA packaging protein Nu1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.2e-05      0.29      29      71 ..      20      62 ..      13      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.2e-05
                         Phage_Nu1 29 vvkgGGkGnevvfdtaavirWyaerdaeieneklrkeveelra 71
                                      vv++G + + + +dta v   y +rd      +l  e eelr 
  gi|313125309|ref|YP_004035573.1| 20 VVERGVRAEKAGYDTAFVSCHYNNRDPFAALSRLADETEELRL 62
                                      899***********************9999999******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2221.40
//
Query:       gi|313125310|ref|YP_004035574.1|  [L=80]
Description: hypothetical protein Hbor_05340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 528.73
//
Query:       gi|313125311|ref|YP_004035575.1|  [L=98]
Description: hypothetical protein Hbor_05350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0041   16.5   2.0        0.5    9.8   0.0    2.3  2  zf-ribbon_3    zinc-ribbon domain
  ------ inclusion threshold ------
      0.078   13.2   2.6       0.11   12.7   2.6    1.1  1  dbPDZ_assoc    Unstructured region between two PDZ domains on
      0.082   13.0   3.1       0.45   10.7   3.1    2.1  1  Zn-ribbon_8    Zinc ribbon domain
        0.1   12.6   1.8       0.28   11.2   1.8    1.7  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        0.1   12.5   1.9       0.23   11.4   1.9    1.6  1  Nudix_N_2      Nudix N-terminal
        0.3   11.0   3.3        4.6    7.2   0.2    2.3  2  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.68    9.9   4.7        1.7    8.6   4.7    1.7  1  Prok-RING_1    Prokaryotic RING finger family 1
        3.7    7.8   6.6        1.5    9.0   3.0    1.9  2  DUF2387        Probable metal-binding protein (DUF2387)


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00022       0.5       3      13 ..      69      79 ..      68      82 .. 0.78
   2 !    5.8   0.5    0.0043       9.5      13      23 ..      86      96 ..      86      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                       zf-ribbon_3  3 vrCPnCGa.pls 13
                                      v+CP CG+ + +
  gi|313125311|ref|YP_004035575.1| 69 VECPTCGEmV-E 79
                                      79*****944.5 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0043
                       zf-ribbon_3 13 ssddnvCpyCG 23
                                      ++d++vC+ C 
  gi|313125311|ref|YP_004035575.1| 86 DTDAQVCADCK 96
                                      689*******6 PP

>> dbPDZ_assoc  Unstructured region between two PDZ domains on Dlg5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.6   4.9e-05      0.11      11      55 ..      14      58 ..      10      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                       dbPDZ_assoc 11 hsRsssrlesvsnqstpqgsGattPdnhsiidtlseqDeGtmtPp 55
                                       s + s  +++++  t  ++   +Pd+    dtl + D Gt+ P+
  gi|313125311|ref|YP_004035575.1| 14 DSSAESETDTAQSAETNDEADENAPDSSVQTDTLEDGDSGTVSPA 58
                                      577789999999999****************************97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.1    0.0002      0.45       7      32 ..      70      95 ..      52      97 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeC 32
                                      +C  Cg+  e+l   +++ + + C +C
  gi|313125311|ref|YP_004035575.1| 70 ECPTCGEMVERLW-LDEDTDAQvCADC 95
                                      4666666666665.3433333336666 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.8   0.00013      0.28      13      44 ..      62      96 ..      58      97 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                     Zn_Tnp_IS1595 13 lrW.pngfvCPhCgsr..kayriktrglfqCkeCr 44
                                       rW p+g+ CP Cg +  +++  ++     C++C+
  gi|313125311|ref|YP_004035575.1| 62 YRWdPDGVECPTCGEMveRLWLDEDTDAQVCADCK 96
                                      588456688*****998777666666666677776 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.9    0.0001      0.23       3      29 ..      71      96 ..      71      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                      -TTT--B-EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCg 29
                                      C+ CG+ ve+   d+D+    vC++C 
  gi|313125311|ref|YP_004035575.1| 71 CPTCGEMVERLWLDEDTDA-QVCADCK 96
                                      *************999988.8999996 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0021       4.6      18      32 ..      60      75 ..      53      78 .. 0.88
   2 ?    4.6   0.4     0.014        31      11      20 ..      89      98 .]      88      98 .] 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0021
                           DUF35_N 18 GtvqfPPr.avCphCg 32
                                      Gt+++ P    Cp Cg
  gi|313125311|ref|YP_004035575.1| 60 GTYRWDPDgVECPTCG 75
                                      999************9 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
                           DUF35_N 11 gqrCpdCGtv 20
                                      +q C+dC ++
  gi|313125311|ref|YP_004035575.1| 89 AQVCADCKAW 98
                                      69*****988 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.7   0.00077       1.7       4      28 ..      68      97 ..      65      98 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00077
                       Prok-RING_1  4 gkkCpvCgke.....lkeedDiVvCpeCgt 28
                                      g +Cp Cg+      l+e+ D+ vC +C++
  gi|313125311|ref|YP_004035575.1| 68 GVECPTCGEMverlwLDEDTDAQVCADCKA 97
                                      789*****983333345679********96 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.56   1.3e+03      54      66 ..      20      32 ..       9      47 .. 0.49
   2 ?    9.0   3.0   0.00067       1.5       8      37 ..      68      96 ..      67      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.56
                           DUF2387 54 ktrvnkdeekeas 66
                                      +t  ++++e++++
  gi|313125311|ref|YP_004035575.1| 20 ETDTAQSAETNDE 32
                                      3333333332222 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00067
                           DUF2387  8 GavCPrCsemDkirmweedeveyrECvsCg 37
                                      G+ CP C em + r+w +++++   C +C+
  gi|313125311|ref|YP_004035575.1| 68 GVECPTCGEMVE-RLWLDEDTDAQVCADCK 96
                                      899*******76.899999999999**995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 664.26
//
Query:       gi|313125312|ref|YP_004035576.1|  [L=586]
Description: DNA mismatch repair protein mutl [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-30  104.5   0.0    7.6e-30  103.6   0.0    1.4  1  MutL_C          MutL C terminal dimerisation domain
    1.2e-26   92.7   0.0      2e-26   92.0   0.0    1.4  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    1.2e-10   41.4   0.1    1.9e-10   40.7   0.1    1.4  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    6.5e-06   26.6   0.3    1.7e-05   25.3   0.1    1.9  2  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
  ------ inclusion threshold ------
        3.4    8.0  11.3        4.5    7.6   0.1    4.8  4  Se-cys_synth_N  Selenocysteine synthase N terminal


Domain annotation for each model (and alignments):
>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.0   2.1e-33   7.6e-30       4     147 .]     394     538 ..     393     538 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 2.1e-33
                                       EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHSS...B-EEEEEEEEEEE--HHHHHHHHHCHHHHH CS
                            MutL_C   4 kalgqvhgtyilaenedglvlvDqhaAherilyeklkeqlkeee...lksQpLliPlvlelspeeaalleehkeeLa 77 
                                       +++gq+ + y+l+e++d+l ++D haAher++ye+l++++ ++e   ++s p     +++lsp +aa+  e ++eLa
  gi|313125312|ref|YP_004035576.1| 394 RVIGQFRDLYLLCEADDDLLVIDHHAAHERVNYERLRAAVGAGEvnaVESIPIDPAATVSLSPAQAAATAEWRDELA 470
                                       68*************************************99988778899999999********************* PP

                                       HCT-EEEE-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS-H-HCCHHHHHHHHCTTSSSSSS--- CS
                            MutL_C  78 klGfeleefgpnslivravPallrqqnleelirelleelaekgkesleekleellatmachssvkagrrl 147
                                       +lG el +fg+++++vr vPa+++ + ++e +r+ l+ l+  ++    +  ++ll+ +ach s kag+ l
  gi|313125312|ref|YP_004035576.1| 471 HLGYELDSFGGDTVRVRGVPAPMGRAAAPESVRDALDALRGGET--PGDATDRLLKDLACHPSLKAGDAL 538
                                       ****************************************9995..56799****************986 PP

>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.0   5.7e-30     2e-26      14     118 ..     255     361 ..     236     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 5.7e-30
                                       EEEEEEETT......EEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EEEEEEEESS CS
                    DNA_mis_repair  14 leiekeeeq......lkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgrypvvvLnleidp 84 
                                        ei+    +      +++eG++++p+++rs+rd+++++vNgR+  s+ l++a+ ++Y ++lp gr pv+v++++++p
  gi|313125312|ref|YP_004035576.1| 255 REIT----DngetvtVSVEGLLAHPSVTRSRRDHIYTAVNGRAFPSEPLRRAVVAGYGDVLPDGRAPVAVVSVSLPP 327
                                       3344....03344669************************************************************* PP

                                       GGEE-TSSTT----EETTHHCHHHHHHHHHHHHH CS
                    DNA_mis_repair  85 eevDvNvhPtKreVrfqdeeevieaieealkeal 118
                                         +D NvhP+KreVr++ +++v ++++ea+++al
  gi|313125312|ref|YP_004035576.1| 328 PWCDHNVHPAKREVRLRAQRAVERTVREAVHDAL 361
                                       *******************************998 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.1   5.4e-14   1.9e-10       3      63 ..      29      87 ..      26     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 5.4e-14
                       HATPase_c_3  3 lekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskea 63
                                      +e+A++elv+N+ldA+a++v+++v  +   t+ ++++D+G Gmse +   a + +t+sk  
  gi|313125312|ref|YP_004035576.1| 29 PEDAVVELVENALDAEATRVEVTVVGDG--TDLLRVRDNGRGMSETDAALAVERHTTSKLG 87
                                      499***********************84..799*************999888888877764 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   4.8e-09   1.7e-05       5      64 ..      28      90 ..      24     166 .. 0.76
   2 ?   -3.1   0.0       3.2   1.1e+04      41      52 ..     256     267 ..     244     283 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.8e-09
                                      HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH......H CS
                         HATPase_c  5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq......d 64
                                      r + ++ +lv+Na+++  +a+++ev++   +++  ++v+DnG+G+++ d  +  e++++      +
  gi|313125312|ref|YP_004035576.1| 28 RPEDAVVELVENALDA--EATRVEVTVV-GDGTDLLRVRDNGRGMSETDAALAVERHTTsklgdvA 90
                                      6667899********6..8999999999.446999**************99777766664543331 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.2
                                       EEEESSSSSTTH CS
                         HATPase_c  41 sveDnGiGipke 52 
                                       +++DnG  ++++
  gi|313125312|ref|YP_004035576.1| 256 EITDNGETVTVS 267
                                       677777766654 PP

>> Se-cys_synth_N  Selenocysteine synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.15   5.5e+02      24      38 ..      29      43 ..      26      43 .. 0.89
   2 ?   -0.1   0.5      0.32   1.1e+03      15      31 ..     344     360 ..     267     364 .. 0.55
   3 ?    7.6   0.1    0.0013       4.5      21      40 .]     491     510 ..     469     510 .. 0.89
   4 ?    3.0   0.1     0.034   1.2e+02       6      24 ..     518     551 ..     518     552 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.15
                    Se-cys_synth_N 24 pRalvrdavrafLdr 38
                                      p ++v+++v  +Ld+
  gi|313125312|ref|YP_004035576.1| 29 PEDAVVELVENALDA 43
                                      7789*********95 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                    Se-cys_synth_N  15 earallaalpRalvrda 31 
                                       +a+ ++++  R++v da
  gi|313125312|ref|YP_004035576.1| 344 RAQRAVERTVREAVHDA 360
                                       44444444444444444 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0013
                    Se-cys_synth_N  21 aalpRalvrdavrafLdrcR 40 
                                       a ++Ra+  + vr++Ld++R
  gi|313125312|ref|YP_004035576.1| 491 APMGRAAAPESVRDALDALR 510
                                       669****************9 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.034
                    Se-cys_synth_N   6 sVDaLLtal...............earallaalp 24 
                                       ++D+LL++l               ea  l+++l+
  gi|313125312|ref|YP_004035576.1| 518 ATDRLLKDLachpslkagdalnteEATRLVERLG 551
                                       58*******7777777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 3252.19
//
Query:       gi|313125313|ref|YP_004035577.1|  [L=941]
Description: DNA mismatch repair protein muts [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-79  266.0   0.0    3.3e-79  265.3   0.0    1.3  1  MutS_V    MutS domain V
    5.9e-38  131.0   1.9    1.2e-37  130.1   1.9    1.5  1  MutS_III  MutS domain III
    3.2e-36  124.0   0.0    5.9e-36  123.1   0.0    1.5  1  MutS_I    MutS domain I
    2.5e-31  107.9   0.4    5.4e-31  106.8   0.4    1.6  1  MutS_IV   MutS family domain IV
    4.7e-08   33.4   0.0    1.5e-07   31.7   0.0    1.9  1  MutS_II   MutS domain II
  ------ inclusion threshold ------
       0.06   13.9   0.0       0.31   11.5   0.0    2.1  2  AAA_23    AAA domain
      0.074   12.8   0.0       0.18   11.6   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
       0.11   12.5   0.0       0.35   10.9   0.0    1.8  1  AAA_14    AAA domain
        1.2    9.1  13.9        1.7    8.6   0.1    4.1  5  TerB      Tellurite resistance protein TerB


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.3   0.0   1.6e-82   3.3e-79       2     185 ..     632     820 ..     631     823 .. 0.96

  Alignments for each domain:
  == domain 1  score: 265.3 bits;  conditional E-value: 1.6e-82
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TT CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatek 78 
                                       +itGpnm+Gksty+rqvali++laq Gsfvpa++a+++i+d+iftRvgasDd+a g+stFm Em+E++ il+nate+
  gi|313125313|ref|YP_004035577.1| 632 VITGPNMSGKSTYMRQVALIAILAQAGSFVPARAARLPILDRIFTRVGASDDIAGGQSTFMREMAELTDILHNATED 708
                                       8**************************************************************************** PP

                                       SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEE.....EETTEEEEE CS
                            MutS_V  79 slvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavk.....eeeedivfl 150
                                       slv+lDE+GRGtst+dGlaia a +e++++++ a+tlfatHyh+lt+l+e+l+e  nlh++v+     + e d++fl
  gi|313125313|ref|YP_004035577.1| 709 SLVLLDEVGRGTSTTDGLAIARATTEFVHDEVGATTLFATHYHDLTALSERLPEAFNLHFTVEktereSGEPDVTFL 785
                                       **************************************************************95544333468**** PP

                                       EEEEES--SS--HHHHHHHTT--HHHHHHHHHHHH CS
                            MutS_V 151 ykvkegaaeksyGikvaklaglPesvverArevlk 185
                                       ++v++g +++syG++vaklag+P++vverAre ++
  gi|313125313|ref|YP_004035577.1| 786 HRVADGPSSSSYGVEVAKLAGVPSTVVERAREYIR 820
                                       *******************************9876 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   1.9   5.8e-41   1.2e-37       2     191 .]     294     583 ..     293     583 .. 0.94

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 5.8e-41
                                       HHHHTTSSS-.TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          MutS_III   2 TlrnLeilen.lrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVee.leneelreelrellrr 76 
                                       ++r+Le++e+ + + +   +L+gvld+T  a G+R L  wl +P++d +eI++R+daV e ++++  re++r+ l +
  gi|313125313|ref|YP_004035577.1| 294 AIRSLELFESrSPS-G-GRTLVGVLDETACALGRRRLTAWLRRPSVDEREIRRRHDAVGElIDRPLARETVRDHLSE 368
                                       89*****9973332.2.34*****************************************9999999********** PP

                                       ---HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH.....HHHH...HHHHHHB-SS--SSGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxx...xxxxxxxxxxxxxxxxx RF
                          MutS_III  77 lpDleRllsrislgkakardlkallealkaleelvallekeklaesee.....esla...elleeaideeplaleke 145
                                       ++DleRl+sr+s ++a+ardl+al ++l+a++e + +l++ ++++ +      ++la   +l+ eai  +p+++  e
  gi|313125313|ref|YP_004035577.1| 369 VYDLERLVSRVSRERANARDLRALKTTLDAVPEVKSALSEMETDPLQRlcdslDELAdvrDLIGEAIRPDPPQEITE 445
                                       *********************************9999988887766669988833445559**************** PP

                                       S--B-T....................................................................... CS
                                       xxxxxx....................................................................... RF
                          MutS_III 146 gedlra....................................................................... 151
                                       g+++r+                                                                       
  gi|313125313|ref|YP_004035577.1| 446 GGVIREgfddeldeirateregrewvsnleeqeqertgidslevgynqvhgyyievtnpnldsvpddytrrqtlkns 522
                                       ***************************************************************************** PP

                                       .....................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                       .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 .....................iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                                            ++ale+e+f +++++v+e++erl++la++la+LDvl+ +A
  gi|313125313|ref|YP_004035577.1| 523 erfytpelkrredeilsasekADALEYEVFTNVRADVAEEVERLQSLADSLATLDVLATFA 583
                                       ********************999999***********999*******************99 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.0     3e-39   5.9e-36       1     113 []      37     148 ..      37     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 3e-39
                                       HHHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC.EEEEEEEHHHHHHHHHHHHHTT CS
                            MutS_I   1 tplmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkkssekeipmagvPehalekylrkLvekg 77 
                                       tp+++qyl+l ++++da+++f+vGdfYe+f e A+ +ar++e+tltkr++s++  +pmag+P  ++ +yl+ L+++g
  gi|313125313|ref|YP_004035577.1|  37 TPMLSQYLDLCESHPDAIVMFQVGDFYEAFCEAAEEVARVCEVTLTKREDSTGT-YPMAGIPIDNAASYLEALLDAG 112
                                       8*********************************************99987777.********************** PP

                                       -EEEEEEE-S-HHHHS.S--EEEEEEEBTTC-TTSC CS
                            MutS_I  78 ykVavveqtetpaekkgvvkrevvrviTpGtltdee 113
                                       y+Vav++q+e+++e++g+v+r v++viTpGt++d+e
  gi|313125313|ref|YP_004035577.1| 113 YRVAVADQVEDASEASGLVDRAVTQVITPGTVVDDE 148
                                       ********************************9985 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.4   2.7e-34   5.4e-31       1      91 [.     452     542 ..     452     543 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 2.7e-34
                                       TTSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECC CS
                           MutS_IV   1 gfdeeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknserytta 77 
                                       gfd+eLde+r++ +e +++  +lee+e+e++gi+sl v+yn+v+Gyy+evt+ + ++vp++++r+qtlknser++t+
  gi|313125313|ref|YP_004035577.1| 452 GFDDELDEIRATEREGREWVSNLEEQEQERTGIDSLEVGYNQVHGYYIEVTNPNLDSVPDDYTRRQTLKNSERFYTP 528
                                       8**************************************************************************** PP

                                       CHHHHHHHHHHHHH CS
                           MutS_IV  78 elkkleaelleaee 91 
                                       elk+ e+e+l+a e
  gi|313125313|ref|YP_004035577.1| 529 ELKRREDEILSASE 542
                                       **********9987 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   7.8e-11   1.5e-07       2     130 ..     157     269 ..     156     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 7.8e-11
                                       EEEEEEEETTTSEEEEEEEETTTTEEEEEEEEE-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTTT-EEEEE CS
                           MutS_II   2 ylaAisekregrrvGlafiDlstgefvvsefedfeeleaeLsrlsPkElllpedlsestaeeessklrelrsrvgvr 78 
                                       yl A++   +g+  +la +D+stge++v++ +   e+  eL rl+P+Ell   d+ +         +      v++ 
  gi|313125313|ref|YP_004035577.1| 157 YLGAVAG--SGDETALATVDVSTGECQVTSGS-AYEIGEELDRLAPAELLSAADAPDF--------ELGFETLVSNP 222
                                       7788888..9999******************9.79*******************9655........34444555666 PP

                                       SCCCCSHCCHHHHCHHHB--STTTTTTTGGG-HHHHHHHHHHHHHCCCCCSC CS
                           MutS_II  79 etvefesekaserleedfsvedldgfglekekklalaAlgalisYleetqke 130
                                       + + f+++ ase+l  ++     + +    e++ +++A+g l++Y+e tq +
  gi|313125313|ref|YP_004035577.1| 223 DPEAFDVDGASETLS-AYVSAPESVV----ENESEMRAVGGLLDYAEYTQGD 269
                                       6788********996.5666664444....7899***************976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.2   2.4e+03     159     184 ..     454     480 ..     362     573 .. 0.68
   2 ?   11.5   0.0   0.00016      0.31      16      37 ..     624     646 ..     617     654 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                            AAA_23 159 ekeleeledekkl.lekleqekekeke 184
                                        +el+e+ +++++  e++ +++e+e+e
  gi|313125313|ref|YP_004035577.1| 454 DDELDEIRATEREgREWVSNLEEQEQE 480
                                       444444443222202222233222222 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00016
                            AAA_23  16 dFsk.gltlItGpNGaGKTTild 37 
                                       dFs+  + +ItGpN +GK+T ++
  gi|313125313|ref|YP_004035577.1| 624 DFSDgHVAVITGPNMSGKSTYMR 646
                                       78553799************876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.1e-05      0.18      18      39 ..     624     645 ..     616     660 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-05
                            AAA_29  18 eidlkg.atlltGpsGsGKSTll 39 
                                       +++ +g + ++tGp+ sGKST +
  gi|313125313|ref|YP_004035577.1| 624 DFS-DGhVAVITGPNMSGKSTYM 645
                                       566.45599************87 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00017      0.35       3      73 ..     629     716 ..     627     729 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell......vkkesilyinldderd...........kkladpe......klleli 56 
                                       ++ vitG+  +GK+t+++q++   +            +     + +            +     +      ++++++
  gi|313125313|ref|YP_004035577.1| 629 HVAVITGPNMSGKSTYMRQVALIAIlaqagsF-----VPARAARLPIldriftrvgasD-----DiaggqsTFMREM 695
                                       689****************9854446333332.....3333333222222223333221.....1222223333333 PP

                            AAA_14  57 leklke.....ekktylflDEi 73 
                                        e+ ++      ++++++lDE+
  gi|313125313|ref|YP_004035577.1| 696 AEL-TDilhnaTEDSLVLLDEV 716
                                       333.112334556777778877 PP

>> TerB  Tellurite resistance protein TerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3    0.0013       2.5      64     122 ..      70     127 ..      62     135 .. 0.85
   2 ?   -1.4   0.2         1     2e+03      71     132 ..     359     421 ..     341     422 .. 0.73
   3 ?   -2.0   0.3       1.6   3.2e+03      18      43 ..     570     591 ..     539     599 .. 0.58
   4 ?    8.6   0.1   0.00086       1.7      49      89 ..     812     852 ..     795     861 .. 0.87
   5 ?   -2.2   0.0       1.8   3.5e+03      25      51 ..     884     911 ..     865     924 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                              TerB  64 peeakallelfeeaeeeavdleqftralkrklspeqrraliealweiAlADGeldeaEd 122
                                       +ee++ + e+    +e++++++ ++    ++ +   ++al++a +++A AD+  d++E 
  gi|313125313|ref|YP_004035577.1|  70 AEEVARVCEVTLTKREDSTGTYPMAGIPIDN-AASYLEALLDAGYRVAVADQVEDASEA 127
                                       5778888888888899999999999877775.7999****************9999997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                              TerB  71 lelfeeaeeeavdleqftralkrkls.peqrraliealweiAlADGeldeaEdavlrrvaelL 132
                                       +e+  ++ +e+ dle+ ++++ r+ +   ++ral ++l ++      l+e+E + l+r ++ L
  gi|313125313|ref|YP_004035577.1| 359 RETVRDHLSEVYDLERLVSRVSRERAnARDLRALKTTLDAVPEVKSALSEMETDPLQRLCDSL 421
                                       566666677788888888888777555666666666666666666778888888888888766 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.6
                              TerB  18 ktdaakeafalalaallaevakaDgq 43 
                                       ++    +  +l ++a +a va+a   
  gi|313125313|ref|YP_004035577.1| 570 AD----SLATLDVLATFAAVAAANDY 591
                                       11....23355566666666655444 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.00086
                              TerB  49 rqafrellksrfglspeeakallelfeeaeeeavdleqftr 89 
                                       +++ re++++++g ++ +a+ ++e++e+ae++++ + q+t 
  gi|313125313|ref|YP_004035577.1| 812 VERAREYIREADGADNGQADRAVETAEAAESDSPTATQATT 852
                                       6789****************************999999886 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 1.8
                              TerB  25 afalalaallaevakaDgqvses.Erqa 51 
                                       + +la+ +  +e  + Dg+v+++ E + 
  gi|313125313|ref|YP_004035577.1| 884 DGTLAAYVDGIEATETDGRVTSDaEDDV 911
                                       4567777777777777777765413333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.81u 0.36s 00:00:01.17 Elapsed: 00:00:00.55
# Mc/sec: 5181.15
//
Query:       gi|313125314|ref|YP_004035578.1|  [L=324]
Description: moxr-like ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-59  198.1   0.1    6.3e-59  197.5   0.1    1.2  1  AAA_3            ATPase family associated with various cellul
    4.7e-20   71.2   1.0    1.7e-19   69.4   1.0    2.0  1  AAA_lid_2        AAA lid domain
    5.2e-13   49.2   0.0    8.8e-13   48.4   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    1.4e-06   28.8   0.0    2.5e-06   27.9   0.0    1.5  1  AAA              ATPase family associated with various cellul
    1.7e-05   24.6   0.0     0.0019   17.9   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
    4.1e-05   23.1   0.3    0.00094   18.6   0.1    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00017   20.8   0.0    0.00037   19.7   0.0    1.6  1  MCM              MCM P-loop domain
     0.0016   18.2   0.0      0.011   15.4   0.0    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.086   12.9   0.0       0.39   10.8   0.0    2.1  1  AAA_2            AAA domain (Cdc48 subfamily)


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.5   0.1   3.2e-62   6.3e-59       1     130 [.      59     188 ..      59     189 .. 1.00

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 3.2e-62
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       h+lle+vPG++kt+l++a+a +l+ +fkr+qftpdllPsd++G++vf+++++efef++Gpvfan++l deinrappk
  gi|313125314|ref|YP_004035578.1|  59 HLLLEDVPGVGKTMLARAVAISLGGSFKRVQFTPDLLPSDVTGVNVFNQQTREFEFQPGPVFANVVLGDEINRAPPK 135
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                       tq+alle+mee+qvtv+ge+h++p+pf+v+atqn +e + ty+lp a++drf+
  gi|313125314|ref|YP_004035578.1| 136 TQAALLEVMEEQQVTVDGESHRVPDPFTVIATQNDVEPNRTYELPIAEIDRFM 188
                                       ****************************************************8 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   1.0   8.4e-23   1.7e-19       5      63 ..     253     310 ..     249     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 8.4e-23
                         AAA_lid_2   5 ahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaeg 63 
                                       +++ ++lgvs+r + +al+ra++A+A ++grdyV+p+Dv++ a+ V+aHR+r +  + g
  gi|313125314|ref|YP_004035578.1| 253 TREHAQLGVSPR-GGIALVRASQARAVFDGRDYVIPDDVQTEAQSVWAHRIRTDGDDTG 310
                                       56789*******.***************************************7766655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   4.4e-16   8.8e-13       1     138 []      59     187 ..      59     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 4.4e-16
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       ++lL   pG+gK++la+ +a  l+ ++  vq+t d+ ++d++g   ++   ++ +++++p+      + +++ DE++
  gi|313125314|ref|YP_004035578.1|  59 HLLLEDVPGVGKTMLARAVAISLGGSFKRVQFTPDLLPSDVTGVNVFNqqTREFEFQPGPVF-----ANVVLGDEIN 130
                                       5677778************************************9999966777788999999.....99******** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra+++++++Ll ++ee+++ + +g      ++      f+viat n+++ ++  el  a ++Rf
  gi|313125314|ref|YP_004035578.1| 131 RAPPKTQAALLEVMEEQQVTV-DGESHRVPDP------FTVIATQNDVEpNRTYELPIAEIDRF 187
                                       ********************4.4444444555......*********99877777777766666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.3e-09   2.5e-06       2     130 ..      61     193 ..      60     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.3e-09
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SS..STTHHHHHHHHH.HHHHHHTSTSEEEEEETGGGHHHH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisg.sell.sk..yvgesekkirel.fkeakekakpsilfiDEidalaks 73 
                                       ll   pG+GKT+la+ava +lg +f +++  ++ll s+   v   ++++re+ f+     a   +++ DEi +  ++
  gi|313125314|ref|YP_004035578.1|  61 LLEDVPGVGKTMLARAVAISLGGSFKRVQFtPDLLpSDvtGVNVFNQQTREFeFQPGPVFA--NVVLGDEINRAPPK 135
                                       66668*****************999999862677744455555555555555344444444..9**********999 PP

                                       HTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS...GGGSTHHHHS.TTSSEEEET CS
                               AAA  74 rsgseseeeervvnqLlteldgvkkk........eskvivigatnr...pdkldpallr.gRfdrkiei 130
                                                   +++Ll+++++++           ++++vi++ n+    ++++ ++   +Rf +k+++
  gi|313125314|ref|YP_004035578.1| 136 T-----------QAALLEVMEEQQVTvdgeshrvPDPFTVIATQNDvepNRTYELPIAEiDRFMKKLRL 193
                                       9...........************999*******777******99976434444555556777777665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.014        29      10      42 ..      45      77 ..      41      91 .. 0.85
   2 !   17.9   0.0   9.4e-07    0.0019     100     144 ..     127     170 ..     120     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellarai 42
                                      +++e+i  ++  + ++l++   G+GK++lara+
  gi|313125314|ref|YP_004035578.1| 45 DAIENILIAVLARGHLLLEDVPGVGKTMLARAV 77
                                      56777778888889999*************997 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 9.4e-07
                                       ETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS- CS
                   Sigma54_activat 100 DeigelplelQekLlrvlqegevervGsskeikvdvriiaatned 144
                                       Dei++ p+++Q+ Ll+v++e++v+  G+s+ ++  + +ia+ n d
  gi|313125314|ref|YP_004035578.1| 127 DEINRAPPKTQAALLEVMEEQQVTVDGESHRVPDPFTVIATQN-D 170
                                       9***************************999998888886544.4 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   4.7e-07   0.00094       5      43 ..      40      78 ..      37      90 .. 0.92
   2 ?    2.2   0.0      0.05        99     109     158 ..     123     170 ..     112     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.7e-07
                      Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlp 43
                                      ++G+++a + + ia+  + +lll   pG GKtmla++++
  gi|313125314|ref|YP_004035578.1| 40 IVGHRDAIENILIAVLARGHLLLEDVPGVGKTMLARAVA 78
                                      899********************************9876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.05
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       v++ DE+     k+  +L e +e+++vt+   +++v  p  f+++a+ N 
  gi|313125314|ref|YP_004035578.1| 123 VVLGDEINRAPPKTQAALLEVMEEQQVTVDGESHRV--PDPFTVIATQND 170
                                       5666999999*******************9877766..666888888775 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.8e-07   0.00037      57     153 ..      57     152 ..      22     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
                                       S-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSS...SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESG CS
                               MCM  57 dinvllvgdpgtaKsqlLkyveklapravytsgkgssa...agLtaavvrdeetgefvleaGalvladkGvcciDef 130
                                       + ++ll   pg++K+ l ++v+ ++  + +   + +     ++ t   v +++t+ef ++ G +      v++ De+
  gi|313125314|ref|YP_004035578.1|  57 RGHLLLEDVPGVGKTMLARAVA-ISLGGSFKRVQFTPDllpSDVTGVNVFNQQTREFEFQPGPVFAN---VVLGDEI 129
                                       5577888889****99888887.888888888887754233788999999************98754...9****** PP

                                       GGSTCHHHHHHHHHHHHSEEEEE CS
                               MCM 131 dkmkeedrsalhEamEqqtisia 153
                                       ++   +++ al+E+mE+q++++ 
  gi|313125314|ref|YP_004035578.1| 130 NRAPPKTQAALLEVMEEQQVTVD 152
                                       ********************986 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.7e-06     0.011      33     113 ..      57     149 ..      41     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.7e-06
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklkits.gPvlekagdlaallt.nleek...........dvlfideihrl 96 
                                         h+ll   PG+Gkt la+ +a  lg ++k    +P l  ++d++++ + n +++           +v++ dei r 
  gi|313125314|ref|YP_004035578.1|  57 RGHLLLEDVPGVGKTMLARAVAISLGGSFKRVQfTPDL-LPSDVTGVNVfNQQTRefefqpgpvfaNVVLGDEINRA 132
                                       56************************999865415555.34555554321222211111111222245556777777 PP

                            RuvB_N  97 sraveevlysamedfrl 113
                                        ++++  l   me+ ++
  gi|313125314|ref|YP_004035578.1| 133 PPKTQAALLEVMEEQQV 149
                                       77777777777776665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.39       6     113 ..      60     154 ..      56     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHH.TTS.....EEEEET CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgae.egG.....ivllDE 76 
                                       +ll +  gvGkt+la+a+a  l      ++ r+  +  l      + v+   + ++   ++e + G     +vl DE
  gi|313125314|ref|YP_004035578.1|  60 LLLEDVPGVGKTMLARAVAISLGG----SFKRVQFTPDLL----PSDVTGVNVFNQQTREFEfQPGpvfanVVLGDE 128
                                       567777899999999999999984....888888888888....666666666665555555344588888****** PP

                                       GGG-------------HHHHHHHHHHHH--EE----- CS
                             AAA_2  77 idKihpkessgadvSregVqrdLLqileggtltdkqg 113
                                       i ++ p             q +LL ++e+ ++t   +
  gi|313125314|ref|YP_004035578.1| 129 INRAPP-----------KTQAALLEVMEEQQVTVDGE 154
                                       ******...........99***********9996655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1861.17
//
Query:       gi|313125315|ref|YP_004035579.1|  [L=339]
Description: hypothetical protein Hbor_05390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-18   66.6   0.4    7.1e-18   64.7   0.2    2.2  2  DUF58     Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       0.5     9e+03      39      52 ..      67      80 ..      65      89 .. 0.78
   2 !   64.7   0.2     4e-22   7.1e-18       2      85 ..     178     253 ..     177     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.5
                             DUF58 39 rartvllvldlspe 52
                                      +++tv+l +d++++
  gi|313125315|ref|YP_004035579.1| 67 TTGTVTLSFDTERS 80
                                      67889999998876 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 4e-22
                             DUF58   2 ldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqll 78 
                                       ++f+glReYv+gD+lr+++Wk+tA++++l+v+ef ae++++ + +    +         ++ +++++aaa+++ +++
  gi|313125315|ref|YP_004035579.1| 178 EEFDGLREYVRGDSLRDVHWKSTAKRDDLIVKEFVAETDASSVHIAAGAAR--------TASDRMAEAAATICLTFV 246
                                       69*********************************9999665555444444........6789************** PP

                             DUF58  79 degdrvg 85 
                                        +g +v 
  gi|313125315|ref|YP_004035579.1| 247 TSGIPVT 253
                                       ***9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2314.91
//
Query:       gi|313125316|ref|YP_004035580.1|  [L=745]
Description: transglutaminase-like enzyme, cysteine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-30  105.1   0.9    7.6e-30  103.7   0.1    2.1  2  Transglut_core   Transglutaminase-like superfamily
    3.1e-10   40.1  10.4    1.7e-09   37.8  10.4    2.4  1  DUF4129          Domain of unknown function (DUF4129)
      1e-05   25.4   0.0    4.4e-05   23.4   0.0    2.1  1  Transglut_core3  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.1   1.3e-33   7.6e-30       1     112 []     400     514 ..     400     514 .. 0.97
   2 ?   -1.6   0.1      0.61   3.7e+03      14      60 ..     660     703 ..     649     710 .. 0.54

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 1.3e-33
                    Transglut_core   1 ralaeeltagakdplekakaiyewvrknveysaprrtpgsrdaeavle.tgkGncedfaslfvallRalGipaRvvt 76 
                                       ra a+++ta a++p++ka+ai++ ++ + +ys + ++p+++ a+++l+   +G+c+ +a+++v++lR+ G+paR+vt
  gi|313125316|ref|YP_004035580.1| 400 RARAAAVTADADNPYDKAVAIEQTLEAEKRYSLSVPQPSGDIADSFLFeMDAGYCTYYATTMVVMLRSQGVPARFVT 476
                                       578999******************************************8899************************* PP

                    Transglut_core  77 gylsgeeekeq..svasedaHawvevylegygWvplDp 112
                                       gy++g++  e+   v++ d+Hawvevy+e+ gWv++Dp
  gi|313125316|ref|YP_004035580.1| 477 GYTPGQQVSENeyVVRGLDSHAWVEVYFEDVGWVRFDP 514
                                       ******999999*************************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.61
                    Transglut_core  14 plekakaiyewvrknveysaprrtpgsrdaeavletgkGncedfasl 60 
                                          + +++++ ++ +++ +  r++ ++r+  + l ++ G   d+a +
  gi|313125316|ref|YP_004035580.1| 660 TIRAYRRLEYVLERRYRPR--RTGETPRTYLQSL-SRVGLDADVARV 703
                                       3356666666665444444..4444444444443.588888888876 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8  10.4   2.8e-13   1.7e-09       1      66 [.     663     726 ..     663     729 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.8e-13
                           DUF4129   1 ayrallraLaergldrrpgeTprEyarrv.riapspaaalaalaelfeearYGgrpasaeeyrrlve 66 
                                       ayr+l+  L++r+++rr+geTpr y++ + r+   + a +a++ e++e+arY g  + +e+++ + +
  gi|313125316|ref|YP_004035580.1| 663 AYRRLEYVLERRYRPRRTGETPRTYLQSLsRV--GLDADVARVGEAYERARY-GDGVARETADDAIA 726
                                       7****************************766..7999**************.78888888888766 PP

>> Transglut_core3  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   7.4e-09   4.4e-05      56      97 ..     451     502 ..     387     508 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.4e-09
                   Transglut_core3  56 s.kCLpralalalllrrrgipatlviGvrkedd.........pfaaHAWvev 97 
                                       +  C   a++++++lr +g+pa++v+G    ++          +  HAWvev
  gi|313125316|ref|YP_004035580.1| 451 AgYCTYYATTMVVMLRSQGVPARFVTGYTPGQQvseneyvvrGLDSHAWVEV 502
                                       347*************************999989888788777*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.58
# Mc/sec: 3843.24
//
Query:       gi|313125317|ref|YP_004035581.1|  [L=97]
Description: translation initiation factor 1 (eif-1/sui1) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-22   79.9   0.0    1.8e-22   79.7   0.0    1.1  1  SUI1      Translation initiation factor SUI1
     0.0031   17.8   0.0     0.0047   17.2   0.0    1.5  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
  ------ inclusion threshold ------
       0.01   15.6   0.5      0.012   15.3   0.5    1.1  1  DTW       DTW domain


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.0     3e-26   1.8e-22       2      76 ..      24      94 ..      23      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 3e-26
                              SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                       ++i+ir+++r+ +K vT+++g++++++d+++l+++lk+kfac+g+v +dg   i++QG++  +v+++L +k g+
  gi|313125317|ref|YP_004035581.1| 24 SQEITIRIDERRYGKEVTVIEGFDPKDVDMDSLSSDLKSKFACGGTV-EDG--SIELQGNHTGRVEDFLRNK-GF 94
                                      689*******************************************9.999..8*****************9.87 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.9e-07    0.0047      36      80 .]      52      94 ..      12      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.9e-07
                              Img2 36 DiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                      D+  l +dL++ ++  +  + + g+ie++G+++ +v++fL++kgF
  gi|313125317|ref|YP_004035581.1| 52 DMDSLSSDLKSKFA--CGGTVEDGSIELQGNHTGRVEDFLRNKGF 94
                                      77788888888888..7788899*********************9 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.5   2.1e-06     0.012       2      29 ..       3      29 ..       2      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-06
                               DTW  2 elCerCllpaevclcsslppleklpikv 29
                                      e+C +C lp+e+c+c+ + + e+++i +
  gi|313125317|ref|YP_004035581.1|  3 EVCSTCGLPEELCVCEDVAK-ESQEITI 29
                                      68*****************9.6665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 618.80
//
Query:       gi|313125318|ref|YP_004035582.1|  [L=119]
Description: rhodanese-related sulfurtransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.3e-13   48.8   0.0      1e-12   48.5   0.0    1.1  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   5.8e-17     1e-12       2     105 ..       7      99 ..       6     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 5.8e-17
                         Rhodanese   2 akelkellekgkva.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdggg 77 
                                       ++e++ ll+++++  ++D+R+p  +++ hIpg+ nv             p++elp+++++l     +++v++c +g+
  gi|313125318|ref|YP_004035582.1|   7 PSEVESLLDSEDPPrVVDIRSPGSFARFHIPGSENV-------------PFAELPDRVASL--EGADRIVTVCPHGK 68 
                                       789999997777667*********************.............************..************** PP

                         Rhodanese  78 raaaaaallkk....lGyknvsvldGGfkawk 105
                                        + +aa+l+k+    +   +v  ++GG++aw 
  gi|313125318|ref|YP_004035582.1|  69 ASIQAARLIKSyegtAD-ARVESMRGGLEAWE 99 
                                       *******9995444344.77***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 772.79
//
Query:       gi|313125319|ref|YP_004035583.1|  [L=187]
Description: ADP-ribose pyrophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-15   57.1   0.9    2.9e-15   56.5   0.9    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.9   1.6e-19   2.9e-15       5     116 ..      54     163 ..      51     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.6e-19
                                       EEEEEEEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   5 avgvvllnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpyg 79 
                                       ++ vv+  e+g+v+ v++++ + +    elP+G ve gE++ +AA REl+EEtG++a    +l+         +++ 
  gi|313125319|ref|YP_004035583.1|  54 TAVVVIAVEDGQVIFVEQYRPTIRQtqLELPAGIVEGGESYTQAAERELREETGFDATSSSVLE---------ECWC 121
                                       455668888889*****994444444467****************************9999999.........5555 PP

                                       E....EEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHH.H CS
                             NUDIX  80 d....eheilyvfleevegelepndenevsevrwvpleel.l 116
                                       +    +h   +vf+e ++   +  d+ne+ +v  vp+ee+ +
  gi|313125319|ref|YP_004035583.1| 122 StgvlRHRRGFVFAEGLTPVERDLDDNEFLSVHTVPVEEAvK 163
                                       5567899999****66666666667***************42 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1175.96
//
Query:       gi|313125320|ref|YP_004035584.1|  [L=154]
Description: hypothetical protein Hbor_05440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.5   0.0      0.089   12.8   0.0    1.4  1  DUF98     p-hydroxybenzoic acid synthase


Domain annotation for each model (and alignments):
>> DUF98  p-hydroxybenzoic acid synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     5e-06     0.089      12      74 ..      58     121 ..      50     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-06
                                       HHHHSS-EEEEEEEEEEEE.--HHHHHHHTS-TT-EEEEEEEEEEETTEEEEEEEEEEEGGGS- CS
                             DUF98  12 elltqekveveliemeaee.seeeeapkeveelkkpllrRqVwlrangqklayAeSwwneeele 74 
                                       ++l +e+ +v++ ++e  +  ++++   ev++l++p + R+Vw  a  + +a A+ + ne  ++
  gi|313125320|ref|YP_004035584.1|  58 NVLFAERLAVHVGAHEEFDaWTDDHPAYEVTQLGSPNVERVVWHAAPFADVAVAATFQNERDAA 121
                                       57888889999877665551555777789****************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 999.31
//
Query:       gi|313125321|ref|YP_004035585.1|  [L=141]
Description: hypothetical protein Hbor_05450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-05   23.2   0.1    7.9e-05   22.4   0.1    1.3  1  zf-C2H2_9  C2H2 type zinc-finger (1 copy)


Domain annotation for each model (and alignments):
>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   4.4e-09   7.9e-05       4      54 ..       5      56 ..       3      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.4e-09
                                      -TTT--B-SSHHHHHHHHHHHTSSS--HHHHHHHHHT-S.S---HHHHHHHH CS
                         zf-C2H2_9  4 CPvCevkfnswkdlseHilsaasksdaeHvmWLNRnisk.krlskdELekkl 54
                                      CPvC v  ++ ++l++H+  +a    aeH +WL   + +    s dEL+ ++
  gi|313125321|ref|YP_004035585.1|  5 CPVCDVPQQDGEHLANHLAFTAMTHGAEHESWLDEHVPEwSSSSPDELAARV 56
                                      *********************************9998762445668887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 922.29
//
Query:       gi|313125322|ref|YP_004035586.1|  [L=123]
Description: hypothetical protein Hbor_05460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-12   45.9   3.6    5.5e-11   42.6   3.6    2.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   3.6   3.1e-15   5.5e-11       7      75 .]      33     116 ..      27     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 3.1e-15
                            HalOD1   7 taVveavaav...egvdptelepLydaiDpdALdaLfas.radgearad...........gsvsFtyegyeVtVrsd 68 
                                       +++++a a++   +  d + l+p  + +DpdAL++Lf++ r++g+  +d            +v+Fty gy Vt+ +d
  gi|313125322|ref|YP_004035586.1|  33 VTIARAAAEAwtgNPDDAMTLPPVGSIVDPDALESLFEPaRSRGRPATDggypstdgaaqSRVRFTYVGYNVTISED 109
                                       556666665521122466778******************5555554444889999999999**************** PP

                            HalOD1  69 geieVep 75 
                                       g ++Ve+
  gi|313125322|ref|YP_004035586.1| 110 GVVVVED 116
                                       ****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 854.21
//
Query:       gi|313125323|ref|YP_004035587.1|  [L=1069]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-30  105.8   5.3      5e-16   58.9   0.8    3.9  3  PAS_4      PAS fold
    1.1e-27   96.8  13.6    1.1e-27   96.8  13.6    4.9  6  BAT        GAF and HTH_10 associated domain
    8.9e-25   86.9   0.1    5.7e-16   58.5   0.1    2.8  2  PAS        PAS fold
    1.3e-22   80.6  14.0    2.7e-10   40.7   0.5    5.3  5  GAF_2      GAF domain
    3.7e-20   72.1   0.0    9.7e-11   41.9   0.0    3.6  3  PAS_9      PAS domain
    9.6e-18   63.7   0.0    3.1e-17   62.1   0.0    2.0  1  HTH_10     HTH DNA binding domain
      3e-14   53.8   2.6    4.6e-08   33.8   0.1    4.3  4  GAF        GAF domain
      3e-13   49.4   1.0    3.4e-07   30.1   0.1    3.2  3  PAS_8      PAS domain
    6.5e-11   42.7   0.7    7.4e-08   32.8   0.0    4.1  4  GAF_3      GAF domain
    6.4e-10   39.2   3.0     0.0002   21.5   0.3    4.0  3  PAS_7      PAS fold
    2.9e-08   33.9   0.1    0.00013   22.2   0.0    2.6  2  PAS_3      PAS fold
    5.5e-07   30.1   0.4     0.0027   18.3   0.0    3.6  4  PAS_10     PAS domain
  ------ inclusion threshold ------
       0.55    9.8   3.7       0.46   10.1   0.0    2.1  2  PTRF_SDPR  PTRF/SDPR family


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   2.9e-15     4e-12       3     109 ..     292     390 ..     290     391 .. 0.94
   2 !   58.9   0.8   3.6e-19     5e-16       1     109 [.     403     513 ..     403     514 .. 0.97
   3 ?   -1.6   0.0       2.3   3.1e+03      48      75 ..     759     787 ..     743     794 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.9e-15
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                       ++ ++l+ ld d rv+y+N++a++l+  ++ e++G  +++l+  ++  ++++ ++++++++e ++f+ +  +   +r
  gi|313125323|ref|YP_004035587.1| 292 RMDQGLIGLDNDWRVTYMNPEAERLLDTAASEVVGTNYWDLFDSDAVKPFRERYEKAVKTGEKVSFESYFPP--HDR 366
                                       67789999************************************************************7766..*** PP

                             PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerr 109
                                       +ye++++P  +      g+ v++ DiT+r 
  gi|313125323|ref|YP_004035587.1| 367 WYEVEAYPSQA------GLSVYFADITDRT 390
                                       ********976......***********96 PP

  == domain 2  score: 58.9 bits;  conditional E-value: 3.6e-19
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +++  d++++ld+d++++ +N+a+ae+f +++e+l+G++  el  e+ aa+ + + +++++++ep +++    l +g
  gi|313125323|ref|YP_004035587.1| 403 VEAADDGVYALDSDQHIVQVNQAFAEMFSREQESLIGMHTTELIDEDTAAESALIQAEAARTGEPKRMEFKAELpDG 479
                                       57889****************************************************************999999** PP

                             PAS_4  77 eerhyelrllPlrdesGe.vigvlvisrDiTerr 109
                                        e+++e++++ + de+ +  +g+++++rD+Terr
  gi|313125323|ref|YP_004035587.1| 480 TEVWIETHFSAIVDEETDqFVGTVGVARDVTERR 513
                                       *********************************8 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.3
                             PAS_4  48 daarleralrrvlegeepiefleelll.p 75 
                                       +  ++ + l rv+++++++   ++l++  
  gi|313125323|ref|YP_004035587.1| 759 QTSPFPELLSRVASTGRRAVVNDVLDDpA 787
                                       6778889999******9999988888743 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3       2.9   4.1e+03      43      98 ..      69      99 ..      34     114 .. 0.54
   2 ?   -4.2   5.5       9.7   1.3e+04      16     103 ..     382     470 ..     377     534 .. 0.57
   3 ?   -0.8   0.1      0.91   1.3e+03      28      47 ..     603     622 ..     594     655 .. 0.81
   4 ?   -2.1   0.2       2.3   3.2e+03      37      37 ..     734     734 ..     677     788 .. 0.53
   5 ?   -3.2   0.0       4.9   6.8e+03      92     111 ..     813     832 ..     806     835 .. 0.84
   6 !   96.8  13.6   8.1e-31   1.1e-27       2     156 .]     856    1007 ..     855    1007 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.9
                               BAT 43 vfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpslastlaehGg 98
                                      v + + g+  +                        +  e+++ +++++  la +G+
  gi|313125323|ref|YP_004035587.1| 69 VPVLLIGDRED------------------------SIAEIAL-STDVVDYLAVRGV 99
                                      33333333444........................4444444.3444444444443 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 9.7
                               BAT  16 vlvalaaeldcr...veleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpsl 89 
                                        +++++++++++   +++e++v+  d++v ++ + ++    +v +a++++ + e+ ++++ + ++   e t +++ l
  gi|313125323|ref|YP_004035587.1| 382 YFADITDRTEREmelLRYERMVEAADDGVYALDSDQH--IVQVNQAFAEMFSREQESLIGMHTTELIDEDTAAESAL 456
                                       5677777777776667788888888888755433333..33555555555555555555555554444444444444 PP

                               BAT  90 astlaehGgtvrsa 103
                                       +++ a++ g ++++
  gi|313125323|ref|YP_004035587.1| 457 IQAEAARTGEPKRM 470
                                       44444444444444 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.91
                               BAT  28 veleglvprsdgevlvfftv 47 
                                       ++ e++v+ ++g++++f+ v
  gi|313125323|ref|YP_004035587.1| 603 FTEERMVRVEEGTTVQFVPV 622
                                       45589999999999999876 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.3
                               BAT  37 s 37 
                                       s
  gi|313125323|ref|YP_004035587.1| 734 S 734
                                       1 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 4.9
                               BAT  92 tlaehGgtvrsaeaedgrar 111
                                        l+ hG ++ +++ edg++ 
  gi|313125323|ref|YP_004035587.1| 813 LLVVHGTRPDTFAGEDGDVL 832
                                       57889999999999999875 PP

  == domain 6  score: 96.8 bits;  conditional E-value: 8.1e-31
                               BAT    2 avveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseedd 76  
                                        + +e+eleird++++lv+l+++++ + ++ g+vp+ +g ++ f++++  +  +vrda+   ++    ++ +e+dd
  gi|313125323|ref|YP_004035587.1|  856 RQTEVELEIRDDQHFLVRLSTATGETATVTGVVPTAEGDYRTFVRTAAPK-NAVRDALP--PGTLARELTDEDDD 927 
                                        679*******************************************9855.9******9..9999999******* PP

                               BAT   77 gtlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtr 151 
                                        + l+e++ +++++++t+ +  g++r+++ae+g +++ + +P+++ vRsvv+a++++y++++L arr+ ++p+++ 
  gi|313125323|ref|YP_004035587.1|  928 EHLYEVQPADTTPFETVYAGRGRLREMVAENGVCTVSLTIPSDVSVRSVVDAFAATYSRTTLAARRTLTEPTDSV 1002
                                        *************************************************************************** PP

                               BAT  152 refra 156 
                                        ++fra
  gi|313125323|ref|YP_004035587.1| 1003 GSFRA 1007
                                        99986 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   8.1e-09   1.1e-05       3      73 ..     286     356 ..     284     374 .. 0.85
   2 !   58.5   0.1   4.1e-19   5.7e-16       2     109 ..     398     502 ..     397     509 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.1e-09
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH..HHHHHHHHHHHHTT-EC CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda..elaelleqlleqgeesr 73 
                                       l+++++ ++ + +++D d r++y+N++ae+ll  +++ev+g ++ dl+  +  a   ++e++e++ ++ge+ +
  gi|313125323|ref|YP_004035587.1| 286 LEEMFSRMDQGLIGLDNDWRVTYMNPEAERLLDTAASEVVGTNYWDLFDSD--AvkPFRERYEKAVKTGEKVS 356
                                       577888999***************************************766..33477777777777777654 PP

  == domain 2  score: 58.5 bits;  conditional E-value: 4.1e-19
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++++++e+++d++ ++D d  i+ vN+a++e++  ++e ++g +  +li e++ ae a +  +++++ge++r+ e +
  gi|313125323|ref|YP_004035587.1| 398 RYERMVEAADDGVYALDSDQHIVQVNQAFAEMFSREQESLIGMHTTELIDEDTAAESALIQAEAARTGEPKRM-EFK 473
                                       79***********************************************999888888888888888888877.666 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEE CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgv 109
                                        +l+dg+++++e++ s ++d++    +f+g+
  gi|313125323|ref|YP_004035587.1| 474 AELPDGTEVWIETHFSAIVDEETD--QFVGT 502
                                       6667****************9876..55444 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.5     2e-13   2.7e-10       5     138 .]     147     278 ..     144     278 .. 0.83
   2 ?   -2.8   0.0       5.1   7.1e+03     122     130 ..     313     321 ..     280     372 .. 0.48
   3 ?   -0.9   0.0       1.4   1.9e+03      22      68 ..     408     467 ..     394     471 .. 0.48
   4 !    6.2   0.2    0.0088        12      93     135 ..     617     655 ..     532     657 .. 0.60
   5 !   38.5   0.6   9.3e-13   1.3e-09       2     138 .]     701     844 ..     700     844 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2e-13
                                       HHHHHHHHHHHHH.SS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG-S- CS
                             GAF_2   5 eelldlvldelve.lg.aalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleedpd 79 
                                       ee++ ++++ ++e l+  +++ +    ++g+l ++a+ + +    + +   l++g+ g+al +++pv+ ndl ++  
  gi|313125323|ref|YP_004035587.1| 147 EEVFAETVEIVTEtLDaGRAALLQSRPEHGDLSIVAAKGWPQVYVGGVAVGLDSGP-GRALTNREPVVENDLSSE-- 220
                                       899********995685667788888899998888666666666666656778885.**************6663.. PP

                                       HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  80 kkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                          +  +h + +s+l+v + ++ ++ Gvl++ +++ +afde+d ++ e +a++ia +ie
  gi|313125323|ref|YP_004035587.1| 221 -TTELTAHLDAGSELSVVVGGGTEPWGVLTVHSSESGAFDETDARFTENVAALIAAVIE 278
                                       .3444589999******998899********9999999*******************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.1
                                       HHHHHHHHH CS
                             GAF_2 122 dlelLeela 130
                                         +lL++ a
  gi|313125323|ref|YP_004035587.1| 313 AERLLDTAA 321
                                       222222222 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.4
                                       EEEEEEE-TTS-EEEE.............EEEES-TTSTT-S-B--.......-TTH.HHHHHHHTS- CS
                             GAF_2  22 lgyillvdddgglrla.............awgeaeeefgaaldrpl.......gegl.vgealrtgrp 68 
                                        g+++l+  d+++  +                  e   g ++   l       +++l  +ea+rtg+p
  gi|313125323|ref|YP_004035587.1| 408 DGVYALDS-DQHI--VqvnqafaemfsreQ----ESLIGMHTTE-LidedtaaESALiQAEAARTGEP 467
                                       56655544.3332..112344444422221....2222222211.12222343566548899999998 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0088
                                       EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHH CS
                             GAF_2  93 flavPlisegrvvGvlnlyankppafdeedlelLeelaeqiai 135
                                         +vP+   g  +Gvl++ +    +  e+d e+L +la++++ 
  gi|313125323|ref|YP_004035587.1| 617 VQFVPV---G-QYGVLAVERLSGATIRETDAEMLGLLAATMGE 655
                                       368899...8.99999998888888999999999999999986 PP

  == domain 5  score: 38.5 bits;  conditional E-value: 9.3e-13
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-....EEEE.......EEEES-TTSTT-S-B---TTHHHHHHHHT CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgg....lrla.......awgeaeeefgaaldrplgeglvgealrtg 66 
                                       ++ ee   +++++lve    +++++ +  ++ +    +  +         ++a +   aa+ +p+   l+ +++ tg
  gi|313125323|ref|YP_004035587.1| 701 TTTEEATARACERLVEAEpYQFAWLCEAPEEANsddrV--VpmtttgvEDSYAARLTEAAQTSPF-PELLSRVASTG 774
                                       67899999********845********66443323332..2343445433333333333332233.44899****** PP

                                       S-EEES-GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  67 rpvilndleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       r+ ++nd+ +dp++ +++  a + g+rs+++vP   ++  + v++  +++p++f  ed ++L el+e+++ +i+
  gi|313125323|ref|YP_004035587.1| 775 RRAVVNDVLDDPAWEPHRrdALAQGFRSIAVVPA--GNDRLLVVH--GTRPDTFAGEDGDVLVELGETLGAVID 844
                                       **********************************..444555555..69**********************996 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.2e-08   4.4e-05       5      85 ..     298     375 ..     294     391 .. 0.74
   2 !   41.9   0.0     7e-14   9.7e-11       2     104 .]     408     511 ..     407     511 .. 0.88
   3 ?    2.1   0.0      0.17   2.3e+02      17      81 ..     810     875 ..     804     887 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.2e-08
                             PAS_9   5 lidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                       +  ++d r++y+N+ a+rll + + ev+g++++dlf  +  +  +er ++a+++g+    ++e  +   ++   w++
  gi|313125323|ref|YP_004035587.1| 298 IGLDNDWRVTYMNPEAERLLDTAASEVVGTNYWDLFdsDAVKPFRERYEKAVKTGE--KVSFESYFPPHDR---WYE 369
                                       44667889****************************55555555555555555555..8999988888888...888 PP

                             PAS_9  80 ltaspv 85 
                                       + a+p 
  gi|313125323|ref|YP_004035587.1| 370 VEAYPS 375
                                       888876 PP

  == domain 2  score: 41.9 bits;  conditional E-value: 7e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       dg+   ++d +i+ +N+a+++++    e ++g + t+l+  +t++e++   ++a ++g+  +++ e     ++g+++
  gi|313125323|ref|YP_004035587.1| 408 DGVYALDSDQHIVQVNQAFAEMFSREQESLIGMHTTELIdeDTAAESALIQAEAARTGE--PKRMEFKAELPDGTEV 482
                                       67776668888************999999**********66666666666666666666..**************** PP

                             PAS_9  77 wvlltaspvkdd.dgelvgiivilrDite 104
                                       w++ ++s++ d+  + +vg +++ rD+te
  gi|313125323|ref|YP_004035587.1| 483 WIETHFSAIVDEeTDQFVGTVGVARDVTE 511
                                       *********9999***************8 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.17
                             PAS_9  17 NeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.....kerevevvlirkngetfwvllt 81 
                                       N+ +l + G+ p+ + g + + l+    e  e+l a+++++ +      er+ ev+l  ++++ f+v+l+
  gi|313125323|ref|YP_004035587.1| 810 NDRLLVVHGTRPDTFAGEDGDVLV----ELGETLGAVIDRLGRtqpilDERQTEVELEIRDDQHFLVRLS 875
                                       777777788888888888888888....777788888888877899999*****************9976 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   2.2e-20   3.1e-17       2      53 .]    1014    1065 ..    1013    1065 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.2e-20
                            HTH_10    2 TdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53  
                                        T++q+e++ +A++ G +d+PR+++++ L++++++s +t+++hLr+ae+klie
  gi|313125323|ref|YP_004035587.1| 1014 TERQREAISAALHGGLYDWPRKTSVSTLSEAFDVSSPTFQYHLRAAERKLIE 1065
                                        9*************************************************96 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   3.3e-11   4.6e-08       2     132 ..     146     276 ..     145     277 .. 0.77
   2 ?   -0.6   0.0       1.4   1.9e+03       4      75 ..     280     369 ..     279     381 .. 0.47
   3 ?    1.3   0.1      0.36     5e+02       4     109 ..     537     632 ..     517     671 .. 0.47
   4 !   15.0   0.1   2.1e-05     0.029      30     129 ..     744     839 ..     685     843 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.3e-11
                                       HHHHHHHHHHHHHHHHTESEEEEEE..EEETTEEECEEEEECCEEEET.TSHHHH......HHHHHSSSEEEST.GG CS
                               GAF   2 leelldtvveelrellgadrvalyl..pdydGlhydipqasrwlfmkn.grgicg......qvlatgqplvipd.st 68 
                                       +ee+++++ve + e+l+a r+al++  p ++G    i +a  w+   + g   +g      ++l++++p+v +d s+
  gi|313125323|ref|YP_004035587.1| 146 REEVFAETVEIVTETLDAGRAALLQsrP-EHGDLS-IVAAKGWPQVYVgGVA-VGldsgpgRALTNREPVVENDlSS 219
                                       699********************87755.777555.9999999555553222.44566677************9533 PP

                                       TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE.SSS.CSHHHHHHHHHHHHHHHHHH CS
                               GAF  69 pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn.psp.pftreelellqvladqvava 132
                                       ++    +        +    s l+v +  + e wG+l++h+ +    f++ + ++ + +a+++a  
  gi|313125323|ref|YP_004035587.1| 220 ETTELTA--------HLDAGSELSVVVGGGTEPWGVLTVHSsE-SgAFDETDARFTENVAALIAAV 276
                                       3333222........3666666888888899**********53.458**************99975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHTE.......SEEEEEE.EEETTEEE....CEEEEECC.EEEETTSHHHH.........HHHHH CS
                               GAF   4 elldtvveelrellga.......drvalyl.pdydGlhy....dipqasrw.lfmkngrgicg.........qvlat 58 
                                       e+l+t++ee+++ ++        d+ + y+ p+++ l      ++     w lf+++     +         ++++t
  gi|313125323|ref|YP_004035587.1| 280 ETLRTTLEEMFSRMDQgligldnDWRVTYMnPEAERLLDtaasEVVGTNYWdLFDSD-----AvkpfreryeKAVKT 351
                                       678888888887777533333333333333322222111122222222222433333.....033333445588889 PP

                                       SSSEEESTGG.TSTTHHT CS
                               GAF  59 gqplvipdst.pdprfaq 75 
                                       g+ ++++ +  p++r+ +
  gi|313125323|ref|YP_004035587.1| 352 GEKVSFESYFpPHDRWYE 369
                                       999999953247777665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHTESEEEEEEEEETTEEE....CEEEEECC...EEEETTSHHHHHHHHHSSSEEESTGGTSTTH CS
                               GAF   4 elldtvveelrellgadrvalylpdydGlhy....dipqasrw...lfmkngrgicgqvlatgqplvipdstpdprf 73 
                                        ++ +++e +++l++  r+a++   yd   +    + pq+++     ++++g       ++ + p+  +   +dp++
  gi|313125323|ref|YP_004035587.1| 537 AVVTRTIEGCHSLFDPCRAAFFD--YDAT-TrtleRHPQSDEVdrgRYQSDG-------VNRDAPVESE---NDPCW 600
                                       33444444444455544555543..3331.0223312222222211222222.......2245555555...66665 PP

                                       HTT.HHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE CS
                               GAF  74 aqy.nrrdllenmgirsslvvPlvndgelwGllvlhn 109
                                        +  ++r++  + g+ ++  vP+ +    +G+l++ +
  gi|313125323|ref|YP_004035587.1| 601 VAFtEERMVRVEEGT-TVQFVPVGQ----YGVLAVER 632
                                       554433333333333.344444443....44444444 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 2.1e-05
                                       TTEEE....CEEEEECCEEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEE CS
                               GAF  30 dGlhy....dipqasrwlfmkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelw 102
                                        G++     ++++a++ ++ ++  +   +v++tg+  v++d+ +dp + +  +r+ + + g+rs +vvP  nd+   
  gi|313125323|ref|YP_004035587.1| 744 TGVEDsyaaRLTEAAQTSPFPELLS---RVASTGRRAVVNDVLDDPAWEP--HRRDALAQGFRSIAVVPAGNDR--- 812
                                       3322233445666666666666555...999*******************..*******************976... PP

                                       EEEEEEESSS.CSHHHHHHHHHHHHHHH CS
                               GAF 103 Gllvlhnpsp.pftreelellqvladqv 129
                                        llv+h ++p  f  e+ ++l +l++ +
  gi|313125323|ref|YP_004035587.1| 813 -LLVVHGTRPdTFAGEDGDVLVELGETL 839
                                       .799999888878777777776666655 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.7e-06    0.0079       3      56 ..     286     337 ..     282     349 .. 0.77
   2 !   30.1   0.1   2.4e-10   3.4e-07       2      43 ..     398     436 ..     397     460 .. 0.79
   3 ?   -1.9   0.0       2.6   3.6e+03      31      53 ..     643     661 ..     643     677 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.7e-06
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGysadlkgellg.qllpvlrpll 56 
                                       l+ +f  +++g++ +d+++r++++N+ a++ll  +     e++g ++++ +++  
  gi|313125323|ref|YP_004035587.1| 286 LEEMFSRMDQGLIGLDNDWRVTYMNPEAERLLD-T--AASEVVGtNYWDLFDSDA 337
                                       566788899*******999*************7.3..444555567777776655 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 2.4e-10
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGysadlkge 43 
                                       r++ ++e+++dg+  +d +++iv+vNqa++e++  +    ++
  gi|313125323|ref|YP_004035587.1| 398 RYERMVEAADDGVYALDSDQHIVQVNQAFAEMFSRE---QES 436
                                       9****************8888************522...333 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.6
                             PAS_8  31 lellGysadlkgellgqllpvlr 53 
                                       +e+lG    l+++++g+ll  ++
  gi|313125323|ref|YP_004035587.1| 643 AEMLG----LLAATMGELLGSVE 661
                                       699**....99999998776655 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   5.4e-11   7.4e-08       3     129 .]     147     279 ..     146     279 .. 0.79
   2 ?    1.0   0.1      0.37   5.1e+02      15     106 ..     401     511 ..     395     532 .. 0.61
   3 ?    4.0   0.0     0.045        62      85     124 ..     619     654 ..     534     657 .. 0.73
   4 ?   -1.7   0.0       2.5   3.4e+03      97     129 .]     813     845 ..     766     845 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 5.4e-11
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse..sldedsalarralssgevvsepsfaeedg 77 
                                       +e+++++++ + ++l+a ++all+ +++  +l ++a+++  ++ +   ++   ++   ral+ +e+v+e++   e++
  gi|313125323|ref|YP_004035587.1| 147 EEVFAETVEIVTETLDAGRAALLQSRPEHGDLSIVAAKGWPQVYVGgvAV-GLDSGPGRALTNREPVVENDLSSETT 222
                                       78999*******************88887777777665223333333333.33333468888899999966644433 PP

                             GAF_3  78 .....lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                            l+ ++ l v +  g ++ Gvl ++s++ +afd++d+++ e++A++ia  ier
  gi|313125323|ref|YP_004035587.1| 223 eltahLDAGSELSVVVGGGTEPWGVLTVHSSESGAFDETDARFTENVAALIAAVIER 279
                                       33444888******9***99***********************************98 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.37
                             GAF_3  15 kllgaevgalllldedgnklqvaagw.dgkpalse.........sldedsalarralssgevvse..psfaeedglp 79 
                                       +++ a    ++ ld d+  +qv+ ++ ++  + +e          +ded+a+ +++++ + + ++  ++++ +  lp
  gi|313125323|ref|YP_004035587.1| 401 RMVEAADDGVYALDSDQHIVQVNQAFaEMFSREQEsligmhtteLIDEDTAAESALIQAEAARTGepKRMEFKAELP 477
                                       55555555678889999999999888555444444666666663334777777777776666666655555556677 PP

                             GAF_3  80 draa.....lavPLvagr..qviGvlalastkpr 106
                                       d+       ++  +v+++  q +G++++a++ ++
  gi|313125323|ref|YP_004035587.1| 478 DGTEvwietHFSAIVDEEtdQFVGTVGVARDVTE 511
                                       7555455556667777767777777777777654 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.045
                             GAF_3  85 avPLvagrqviGvlalastkprafdaedlelleslArqia 124
                                       +vP+      +Gvla+++ ++  ++++d+e+l  lA+ ++
  gi|313125323|ref|YP_004035587.1| 619 FVPVG----QYGVLAVERLSGATIRETDAEMLGLLAATMG 654
                                       55554....4********99999************99876 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2.5
                             GAF_3  97 vlalastkprafdaedlelleslArqiataier 129
                                       +l+++ t+p  f  ed + l +l+  ++  i+r
  gi|313125323|ref|YP_004035587.1| 813 LLVVHGTRPDTFAGEDGDVLVELGETLGAVIDR 845
                                       478899999999999999999999999988886 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05      0.02       2     114 ..     291     393 ..     290     394 .. 0.77
   2 !   21.5   0.3   1.5e-07    0.0002       2     114 ..     404     516 ..     403     517 .. 0.71
   3 ?   -1.1   0.1       1.5     2e+03      14      91 ..     670     694 ..     651     718 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsf 78 
                                       + m+qG++ +D+d r++ +N +  +lld  ++ v vg+++ +l++  a +  f+     + +e+    +++g++ sf
  gi|313125323|ref|YP_004035587.1| 291 SRMDQGLIGLDNDWRVTYMNPEAERLLDTAASEV-VGTNYWDLFDSDAVKP-FR-----ERYEKA---VKTGEKVSF 357
                                       68********************************.****999998775443.23.....233333...355666666 PP

                             PAS_7  79 erer.pdgrvievrgnplpdgGfVttytDiTerrrae 114
                                       e    p  r+ ev++ p +  G+ + + DiT+r + e
  gi|313125323|ref|YP_004035587.1| 358 ESYFpPHDRWYEVEAYPSQA-GLSVYFADITDRTERE 393
                                       66541678999999998765.6667899999998876 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.5e-07
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg..agdveaeverrlaaaragkph 76 
                                       e  ++G+  +D+d+ +v +N+ + e+++  +e + +g++ +el++  ++ ++    a++++    +r+ + +a+ p+
  gi|313125323|ref|YP_004035587.1| 404 EAADDGVYALDSDQHIVQVNQAFAEMFSREQESL-IGMHTTELIDEDTAAESALiqAEAARTGEPKRM-EFKAELPD 478
                                       66789***************************99.*********987444433311333333344444.45555555 PP

                             PAS_7  77 sfererpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                        +e+  +++    v +++ +  G+V +  D+Terr  e
  gi|313125323|ref|YP_004035587.1| 479 GTEVWIETHFSAIVDEETDQFVGTVGVARDVTERRHRE 516
                                       5555555555555555555779***********99887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.5
                             PAS_7  14 dlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpdgrviev 90 
                                       d++L   N+r  +l  +                                                       +v ev
  gi|313125323|ref|YP_004035587.1| 670 DQQLEQQNERLTQLNRIN-----------------------------------------------------RTVREV 693
                                       334444444444443333.....................................................333333 PP

                             PAS_7  91 r 91 
                                       +
  gi|313125323|ref|YP_004035587.1| 694 T 694
                                       3 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0012       1.6       2      55 ..     307     358 ..     306     372 .. 0.94
   2 !   22.2   0.0   9.4e-08   0.00013       2      88 ..     420     505 ..     419     506 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyege 55 
                                       +y++++ e++l+  ++e+ g+  ++ dl   +  + +re +++a+k+ge++++e
  gi|313125323|ref|YP_004035587.1| 307 TYMNPEAERLLDTAASEVVGT--NYWDLFDSDAVKPFRERYEKAVKTGEKVSFE 358
                                       79*******************..**************************98887 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 9.4e-08
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvi.rd 77 
                                       + v++++ e++  ++e+l+g   +  +l+  +  ++     +ea+++gep   e++   +dG+ +w+e++ ++i   
  gi|313125323|ref|YP_004035587.1| 420 VQVNQAFAEMFSREQESLIGM--HTTELIDEDTAAESALIQAEAARTGEPKRMEFKAELPDGTEVWIETHFSAIvDE 494
                                       789******************..99999999998888888899*******************************666 PP

                             PAS_3  78 engkpvrvigv 88 
                                       e  + v  +gv
  gi|313125323|ref|YP_004035587.1| 495 ETDQFVGTVGV 505
                                       66666666666 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     2e-06    0.0027       1     104 [.     286     385 ..     286     387 .. 0.84
   2 !    7.5   0.0    0.0045       6.2       8     106 .]     406     510 ..     400     510 .. 0.80
   3 ?   -2.0   0.1       3.9   5.4e+03      30      75 ..     644     689 ..     639     705 .. 0.64
   4 ?   -1.0   0.0       1.9   2.6e+03      68      99 ..     854     888 ..     837     891 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-06
                            PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknvee.viealrtgekdevevvvp 75 
                                       l+ +++ ++ +l+ lD++ ++++ +p+a++l++  +++ vG +  d+  ++avk ++e   +a++tgek+  e + p
  gi|313125323|ref|YP_004035587.1| 286 LEEMFSRMDQGLIGLDNDWRVTYMNPEAERLLDTAASEvVGTNYWDLFDSDAVKPFRErYEKAVKTGEKVSFESYFP 362
                                       57899***************************99876527*******99988777755267899************* PP

                            PAS_10  76 kngkwvlvrylpyrdedgeiaGvvetfvD 104
                                         ++w+ v+  p +      aG+ ++f D
  gi|313125323|ref|YP_004035587.1| 363 PHDRWYEVEAYPSQ------AGLSVYFAD 385
                                       *******9998866......555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0045
                            PAS_10   8 tpieltflDdnlqirrFtpaakklfklipad.vGrpladihpk.kavknveeviealrtgekdevevvvp...kngk 79 
                                       ++ ++  lD++ +i   ++a +++f++ ++  +G + +++  +  a +++    ea rtge +++e++ +     + 
  gi|313125323|ref|YP_004035587.1| 406 ADDGVYALDSDQHIVQVNQAFAEMFSREQESlIGMHTTELIDEdTAAESALIQAEAARTGEPKRMEFKAElpdGTEV 482
                                       55567779***********99999998765438**999998774667777777899*************87566699 PP

                            PAS_10  80 wvlvrylpyrded.geiaGvvetfvDit 106
                                       w+    +++ de+ +++ G+v +  D+t
  gi|313125323|ref|YP_004035587.1| 483 WIETHFSAIVDEEtDQFVGTVGVARDVT 510
                                       **99999998865278999999988875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.9
                            PAS_10  30 klfklipadvGrpladihpkkavknveeviealrtgekdevevvvp 75 
                                       +++ l +a +G+ l ++ +k+a+ +  + +e+  ++ ++  ++ ++
  gi|313125323|ref|YP_004035587.1| 644 EMLGLLAATMGELLGSVETKQALRSRDQQLEQQNERLTQLNRINRT 689
                                       6667778888888888887766666666665555555555554444 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.9
                            PAS_10  68 devevvvp...kngkwvlvrylpyrdedgeiaGvv 99 
                                       de +++v+   ++++++lvr +    e+  + Gvv
  gi|313125323|ref|YP_004035587.1| 854 DERQTEVEleiRDDQHFLVRLSTATGETATVTGVV 888
                                       33333343447899*******99999999999998 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.4      0.82   1.1e+03      26      65 ..     678     716 ..     652     718 .. 0.71
   2 ?   10.1   0.0   0.00034      0.46       8      58 ..     833     883 ..     829     887 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.82
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         PTRF_SDPR  26 krlEerqaelenavksiqgdllkLakshssTsntvnklle 65 
                                       +rl ++ + ++++v+ +   +++ + +  +T+ + ++l+e
  gi|313125323|ref|YP_004035587.1| 678 ERL-TQLNRINRTVREVTRSVVHATTTEEATARACERLVE 716
                                       222.223456889999999999999999999999999987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         PTRF_SDPR   8 lalLdkvvgivdsvqesqkrlEerqaelenavksiqgdllkLakshssTsn 58 
                                       + l + + +++d + ++q  l+erq+e+e  ++  q  l++L+ +  +T++
  gi|313125323|ref|YP_004035587.1| 833 VELGETLGAVIDRLGRTQPILDERQTEVELEIRDDQHFLVRLSTATGETAT 883
                                       556678889***********************************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1069 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.84u 0.35s 00:00:01.19 Elapsed: 00:00:00.56
# Mc/sec: 5795.65
//
Query:       gi|313125324|ref|YP_004035588.1|  [L=181]
Description: (SSU ribosomal protein s18p)-alanine acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-16   58.1   0.0    1.2e-15   57.7   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    9.4e-13   48.4   0.0    1.4e-12   47.9   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.7e-11   44.1   0.0    2.1e-11   43.8   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.8e-06   27.2   0.0    4.8e-06   26.4   0.0    1.4  1  FR47             FR47-like protein
    4.3e-06   26.8   0.0    8.6e-06   25.9   0.0    1.5  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.021   14.5   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   4.1e-19   1.2e-15       3     117 .]      44     153 ..      42     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 4.1e-19
                                       HHHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHH CS
                    Acetyltransf_1   3 dlvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGs 79 
                                       ++  +++ +f++p++ + +e f +      +g+lva  +g+++G+i +   p++ ++ ++i ++aV pe+rg GlG+
  gi|313125324|ref|YP_004035588.1|  44 EVLGIEKTCFTEPWPYTAFESFLDE-----PGFLVAVNEGNVVGYIVADVMPNHGRDLGHIKDIAVTPEARGIGLGR 115
                                       6677889999999999999995544.....78999******************9*********************** PP

                                       HHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  80 aLlealeeraree.gikkivlaveedndaairlYeklGF 117
                                       +Ll+  +   ++  g+  + l+v++ n++a  lY+k+GF
  gi|313125324|ref|YP_004035588.1| 116 RLLQRGLV-SLSFsGAALVKLEVRVGNEPALSLYRKMGF 153
                                       *****997.5555477778***************99**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   4.6e-16   1.4e-12       5      76 .]      71     155 ..      67     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 4.6e-16
                                       EEEEEETTEEEEEEEEEEES......TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEEEE..EEEE.THHHHHH CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld......aeitrlaVdpeyrgkGiGraLlea..ae...kgiile..qlel.naekaik 67 
                                       ++Va ++g++vG+i++ +        ++i+ +aV pe+rg G+Gr+Ll+   +    +g  l+  ++++ n e+a++
  gi|313125324|ref|YP_004035588.1|  71 FLVAVNEGNVVGYIVADVMPnhgrdlGHIKDIAVTPEARGIGLGRRLLQRglVSlsfSGAALVklEVRVgN-EPALS 146
                                       899**********999998899988777777*****************95331245566333323455533.49*** PP

                                       HHHHTTEEE CS
                    Acetyltransf_7  68 fYeklGFee 76 
                                       +Y+k+GFe+
  gi|313125324|ref|YP_004035588.1| 147 LYRKMGFEP 155
                                       *******95 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   7.1e-15   2.1e-11      33     110 ..      71     159 ..      38     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 7.1e-15
                   Acetyltransf_10  33 llvaeeggkivGvi...elrdgs....hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpf 100
                                       +lva ++g++vG+i    + +++    hi  ++V pe+rg G+g++Ll++ +  ++  g +l +l+v+  +  a ++
  gi|313125324|ref|YP_004035588.1|  71 FLVAVNEGNVVGYIvadVMPNHGrdlgHIKDIAVTPEARGIGLGRRLLQRGLVSLSFSGAALvKLEVRVGNePALSL 147
                                       67888889******8853355557888********************************************9***** PP

                   Acetyltransf_10 101 YeklGFkav..g 110
                                       Y+k+GF++    
  gi|313125324|ref|YP_004035588.1| 148 YRKMGFEPArrV 159
                                       *******98544 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.6e-09   4.8e-06      19      80 ..      94     156 ..      81     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.6e-09
                                       -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfeki 80 
                                       +d g +  + v pe+r+ Glg+rl +     ++  g   v l v+ +N+p+ +ly k+Gfe +
  gi|313125324|ref|YP_004035588.1|  94 RDLGHIKDIAVTPEARGIGLGRRLLQRGLVSLSFSGAAlVKLEVRVGNEPALSLYRKMGFEPA 156
                                       567999*******************999999999887615688*****************965 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.9e-09   8.6e-06       1     127 [.      33     155 ..      33     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.9e-09
                                       .EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEE CS
                    Acetyltransf_9   1 eirelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvt 77 
                                       +ir+++ +dl evl + k++F +  +++     +f+  l+e  +l+a ++g +vg +    +   +p+   + + + 
  gi|313125324|ref|YP_004035588.1|  33 TIRRAERADLLEVLGIEKTCFTEPWPYT-----AFESFLDEPGFLVAVNEGNVVGYI----VADVMPNHGRDLGHIK 100
                                       59************************95.....799******************965....455668888999**** PP

                                       EEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--...SSH..HHHHTTT-EE CS
                    Acetyltransf_9  78 gVavapehrgrgvlskLlaraleemreegqplsllfP...ssi..piYrrfGyei 127
                                       ++av pe rg g+ ++Ll+r l  +   g+ l+ l      ++  ++Yr++G+e+
  gi|313125324|ref|YP_004035588.1| 101 DIAVTPEARGIGLGRRLLQRGLVSLSFSGAALVKLEVrvgNEPalSLYRKMGFEP 155
                                       ********************************999876665544499******97 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.9e-06     0.021      88     143 ..     105     159 ..      79     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-06
                                       SHHHCTTTCHHHHHHH.HHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                    Acetyltransf_8  88 eaeargkglttallra.lvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                        +earg gl+++ll++ lv++ f+  +++ v +E +v Ne a++l++k+Gfe++++v
  gi|313125324|ref|YP_004035588.1| 105 TPEARGIGLGRRLLQRgLVSLSFS--GAALVKLEVRVGNEPALSLYRKMGFEPARRV 159
                                       478889999999998725555555..599***********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1086.97
//
Query:       gi|313125325|ref|YP_004035589.1|  [L=659]
Description: aconitase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   3.3e-105  352.8   0.3     2e-103  346.9   0.3    2.3  1  Aconitase    Aconitase family (aconitate hydratase)
    1.8e-21   76.8   0.0    3.6e-21   75.9   0.0    1.5  1  Aconitase_C  Aconitase C-terminal domain
  ------ inclusion threshold ------
      0.049   12.4   0.0      0.068   11.9   0.0    1.2  1  DUF521       Protein of unknown function (DUF521)
      0.066   13.1   0.2        0.3   11.0   0.0    2.1  3  Barwin       Barwin family


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.9   0.3  4.5e-107    2e-103       1     461 []       7     407 ..       7     407 .. 0.91

  Alignments for each domain:
  == domain 1  score: 346.9 bits;  conditional E-value: 4.5e-107
                         Aconitase   1 ekiwdahlvee.....egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeeal 72 
                                       eki+d+hlve      e+i    d+vl+qd+tg ++  +++a + +          +++   ++  +dh+      +
  gi|313125325|ref|YP_004035589.1|   7 EKILDDHLVEGelepgEEIGIEIDQVLTQDTTGTMVWLQFEALELDE---------VQTELAAQ-YCDHQT-----Y 68 
                                       79*****9944455443355558*******************99998.........55556666.667766.....3 PP

                         Aconitase  73 eknledefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgie 149
                                       + +++     n+   +fL+saa ++g ++  pg+GI+H v  E+ +a pgkt++g+DSHT++ gglG laiG Gg +
  gi|313125325|ref|YP_004035589.1|  69 QFDFK-----NTDDHRFLRSAAGTYGAHFSRPGNGICHNVHKEN-FAAPGKTLLGSDSHTPTPGGLGQLAIGAGGLD 139
                                       34444.....355669****************************.******************************** PP

                         Aconitase 150 aeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaE 226
                                       +  ++ g  +++++p+vv+++l+G+l+e++takD++l++ ++l +kg+vgkv E++G+gve+L++ +r Ti+NM++E
  gi|313125325|ref|YP_004035589.1| 140 ISVAMGGGAYYVEMPEVVNIRLEGELPEWATAKDVILELLRRLSVKGGVGKVFEYTGPGVETLTVPERTTITNMGTE 216
                                       ***************************************************************************** PP

                         Aconitase 227 vGAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavpl 303
                                       +GAt+++fp+de+t +YL+ +gre++             +el+ dedaey++++ +dls+lep +a p  P+++vp+
  gi|313125325|ref|YP_004035589.1| 217 LGATSSIFPTDEETKDYLARQGREDEY------------VELSPDEDAEYADEIVVDLSDLEPLIACPSMPDKVVPV 281
                                       *******************88885555............46889********************************* PP

                         Aconitase 304 selvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsv 380
                                       +e +                              +v+++++gSCTN+ +ed+  aa++l+     +++v+++ +++v
  gi|313125325|ref|YP_004035589.1| 282 REVA----------------------------GESVEQVIVGSCTNGGYEDILPAAKMLE-----DREVNKKTEMIV 325
                                       3333............................235899**********************.....99999999**** PP

                         Aconitase 381 aPGSevvkayleaeGlleiLekaGfevvgagCstCignsdrleegeaivsssNRNFegRqgpntra.yLaSPelvva 456
                                       aPGS++ ++ l ++G    +++aG+++ +a C+ Cig     +++++++ ++NRNFegR g +  + yL+SPe+++a
  gi|313125325|ref|YP_004035589.1| 326 APGSKQASEILARQGWAAEMMAAGVNFSEATCGACIGIGHVPASDSVSLRTFNRNFEGRSGIEDDNvYLCSPEVAAA 402
                                       *************************************888878999***************555555********** PP

                         Aconitase 457 aAlaG 461
                                       aAl+G
  gi|313125325|ref|YP_004035589.1| 403 AALKG 407
                                       ***98 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0     8e-25   3.6e-21      77     130 ..     527     580 ..     497     581 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 8e-25
                                       EEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
                       Aconitase_C  77 vviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefke 130
                                       v++ag+n+G+GSSRehAA+ ++ lGi+av+a+SF+rI++ nl++ g+Lpl ++e
  gi|313125325|ref|YP_004035589.1| 527 VLVAGENYGQGSSREHAAMCPQYLGIEAVLAQSFARIHKANLFNFGILPLAIDE 580
                                       66778*********************************************9986 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.5e-05     0.068     287     358 ..     285     358 ..     188     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                            DUF521 287 keekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvtt.srevkeeaerlglveklekaGvkvlsdtCm 358
                                         e+v+ v++G c    +e++   a++l+++++++k+e++v   s++  e + r g+++++ +aGv++ + tC 
  gi|313125325|ref|YP_004035589.1| 285 AGESVEQVIVGsCTNGGYEDILPAAKMLEDREVNKKTEMIVAPgSKQASEILARQGWAAEMMAAGVNFSEATCG 358
                                       4555665555547778899999******************997245688999*********************5 PP

>> Barwin  Barwin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.2   5.5e+03      72      88 ..     286     302 ..     282     313 .. 0.80
   2 ?   11.0   0.0   6.6e-05       0.3      36      92 ..     332     391 ..     324     409 .. 0.80
   3 ?   -3.9   0.0       2.7   1.2e+04      77     104 ..     510     537 ..     500     544 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                            Barwin  72 naqvtvrivdqcsngGl 88 
                                       + +v   iv  c+ngG 
  gi|313125325|ref|YP_004035589.1| 286 GESVEQVIVGSCTNGGY 302
                                       56677789999***996 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.6e-05
                            Barwin  36 plakrskygwtafcgpag.argqascGkclrvtntatnaqvtvrivdqcsng..Gldldv 92 
                                         + + + gw+a    ag ++ +a+cG c+ +    ++ +v +r  +   +g  G++ d+
  gi|313125325|ref|YP_004035589.1| 332 ASEILARQGWAAEMMAAGvNFSEATCGACIGIGHVPASDSVSLRTFNRNFEGrsGIEDDN 391
                                       55667899***9877665389*************99999999999887666555777664 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 2.7
                            Barwin  77 vrivdqcsngGldldvalfnkldtdGvG 104
                                        r+ d  ++  +d+d  ++ + +  G G
  gi|313125325|ref|YP_004035589.1| 510 SRVDDTFAQRSMDADGGVLVAGENYGQG 537
                                       4666677888888888777666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4400.71
//
Query:       gi|313125326|ref|YP_004035590.1|  [L=132]
Description: hypothetical protein Hbor_05500 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 880.77
//
Query:       gi|313125327|ref|YP_004035591.1|  [L=160]
Description: deoxycytidine deaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-12   44.9   0.0    1.2e-11   44.4   0.0    1.3  1  dUTPase   dUTPase
  ------ inclusion threshold ------
      0.044   12.6   0.0        0.1   11.3   0.0    1.8  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   1.4e-15   1.2e-11      24     106 ..      63     142 ..      58     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.4e-15
                                       EEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEE CS
                           dUTPase  24 ltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLi 100
                                       ++++pg+++l++    i++p+g+ +++ pRS+l ++  +  + v+d+ y+G+ +  l ++ +  ++++ g+RiAqL+
  gi|313125327|ref|YP_004035591.1|  63 YVLPPGGYILQYA-ETIHIPEGHVGFLYPRSSLMRNSCMLNTAVWDAGYEGKGEGLLQVHHD--IELEPGARIAQLV 136
                                       5677888877775.579**********************************88888888876..************* PP

                                       EEEBEC CS
                           dUTPase 101 farilt 106
                                       +ar ++
  gi|313125327|ref|YP_004035591.1| 137 LARGNH 142
                                       **9888 PP

>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.2e-05       0.1      21     113 ..      11      99 ..       1     147 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.2e-05
                               DCD  21 aeepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelklheldLtegavlekgcvYivplleslaLpad 97 
                                         ep++++q+qP+ +DL L +   +v    l  +g+++ ++    +  + d  +g+++     Yi++  e++++p+ 
  gi|313125327|ref|YP_004035591.1|  11 HVEPIADSQVQPNGVDLTLDSLYEQVSPGRLGVDGKEIGDR----EPVSADSDDGSYVLPPGGYILQYAETIHIPEG 83 
                                       45799***************999999988888887777665....55566777787777777799999999999999 PP

                               DCD  98 lsaaanpksstGRlDv 113
                                         +   p+ss  R  +
  gi|313125327|ref|YP_004035591.1|  84 HVGFLYPRSSLMRNSC 99 
                                       9999999999877555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 904.62
//
Query:       gi|313125328|ref|YP_004035592.1|  [L=338]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-15   57.2   0.0    7.9e-15   55.0   0.0    2.0  2  PAS_9        PAS domain
    2.7e-13   50.4   0.0    5.3e-13   49.5   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.1e-09   36.7   0.1    1.3e-08   35.1   0.0    1.9  2  PAS_4        PAS fold
    5.1e-09   36.1   0.0      1e-08   35.2   0.0    1.6  1  PAS          PAS fold
    6.4e-07   29.3   0.5    2.6e-06   27.3   0.0    2.4  3  PAS_8        PAS domain
     0.0002   21.6   0.0    0.00065   19.9   0.0    2.0  1  PAS_3        PAS fold
    0.00027   20.9   0.0    0.00055   19.9   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.013   15.1   0.1       0.02   14.5   0.1    1.3  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
      0.035   14.0   0.0      0.065   13.2   0.0    1.4  1  HATPase_c_5  GHKL domain


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0     4e-18   7.9e-15       1     104 []      17     116 ..      17     116 .. 0.94
   2 ?   -0.7   0.0      0.86   1.7e+03      36      60 ..     168     197 ..     155     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 4e-18
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       p++++i+++++ i+++Nea l+++Gy++ee+lg +   l+ +d+++ e++ + l +g+  ++e+e++ ++k ge+++
  gi|313125328|ref|YP_004035592.1|  17 PNPTVITDESFSIVDVNEACLEFTGYTREEILGSPPLFLV-NDSQTYEEMVDTLAAGE--PWEGEIEAVTKYGERVF 90 
                                       68899*99********************************.*****************..***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                            +p++ +dgelvg+++i++D++e
  gi|313125328|ref|YP_004035592.1|  91 GYGATFPLI-TDGELVGYAGIFIDLSE 116
                                       886667776.589************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.86
                             PAS_9  36 itdlfvtdpeanerlraaleqgrk......k 60 
                                       i+ l+ + +e++++l+++le+ ++       
  gi|313125328|ref|YP_004035592.1| 168 IERLL-DRAETARDLHQLLERSSTalvprdL 197
                                       55566.8888888999999888876654441 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   2.7e-16   5.3e-13       6     108 ..     232     331 ..     228     334 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2.7e-16
                                       HHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                       L + +  +v+Nav++++  ++ i+++++++ d++v++veDnG+Gi +e+ + lf+   +    ++   g Gl+l  v
  gi|313125328|ref|YP_004035592.1| 232 LSRGVAAVVENAVEYNQdASPMIWIHVETTPDEVVLTVEDNGPGIEPEQAEFLFGQCED----SQLRHGQGLSLFFV 304
                                       66668889*******66577799999997679*******************99996665....445679******** PP

                                       HHHHHHTTTEEEEEEETTTEEEEEEEE CS
                         HATPase_c  82 kklvelmgGeiwvesepgrGttftftl 108
                                       ++l + +gG+++++ ++  G+ f +++
  gi|313125328|ref|YP_004035592.1| 305 DRLLDFYGGSVTYRPRSPTGSIFELRF 331
                                       *************999999***99876 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   6.5e-12   1.3e-08       1     110 []      13     119 ..      13     119 .. 0.89
   2 ?   -1.7   0.1       1.7   3.4e+03      56      73 ..     168     185 ..     157     217 .. 0.58

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.5e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++ +p ++++ d+ + ++++N+a  e  g+++ee+lG+++  l++  d + +e+ ++ +++g ep+e ++e ++  +
  gi|313125328|ref|YP_004035592.1|  13 FHETPNPTVITDESFSIVDVNEACLEFTGYTREEILGSPPLFLVN--DSQTYEEMVDTLAAG-EPWEGEIEAVTKYG 86 
                                       577899***********************************5555..899***********9.6**********666 PP

                             PAS_4  78 erhyelrl.lPlrdesGevigvlvisrDiTerrr 110
                                       er++   + +Pl  ++Ge +g+ +i++D++errr
  gi|313125328|ref|YP_004035592.1|  87 ERVFGYGAtFPL-ITDGELVGYAGIFIDLSERRR 119
                                       666666665998.68*****************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                             PAS_4  56 lrrvlegeepiefleell 73 
                                       ++r+l+  e++++l+ ll
  gi|313125328|ref|YP_004035592.1| 168 IERLLDRAETARDLHQLL 185
                                       344444444444443333 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0     5e-12     1e-08       3      99 ..       9     101 ..       7     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5e-12
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       +r+i++ +p+p++++De+  i+ vN+a  e++G++ree+lg++ l l++ +++  ++e++   l++ge+++++   +
  gi|313125328|ref|YP_004035592.1|   9 YRSIFHETPNPTVITDESFSIVDVNEACLEFTGYTREEILGSPPLFLVN-DSQ--TYEEMVDTLAAGEPWEGEIEAV 82 
                                       89*******************************************6665.444..***************9954444 PP

                                       ECTTSSEEEEEEEEEEEEET CS
                               PAS  80 klrdgrpihlevraspvrda 99 
                                       ++  g+ +     + p++  
  gi|313125328|ref|YP_004035592.1|  83 TK-YGERVFGYGATFPLITD 101
                                       44.66666555555555555 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.3e-09   2.6e-06       2      57 ..       8      64 ..       7      76 .. 0.85
   2 ?   -2.9   0.0       3.9   7.9e+03      41      60 ..     161     179 ..     154     186 .. 0.51
   3 ?   -3.2   0.1       4.9   9.7e+03      12      18 ..     222     228 ..     218     238 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.3e-09
                             PAS_8  2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57
                                       +r++f+  p++ +++d     ivdvN+a le++Gy+ ++++g++   l+++++ ++e
  gi|313125328|ref|YP_004035592.1|  8 IYRSIFHETPNPTVITDeSFS-IVDVNEACLEFTGYTrEEILGSPPLFLVNDSQTYEE 64
                                      69***************7777.*********************999888888877776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.9
                             PAS_8  41 kgellgqllpvlrplledae 60 
                                        ++ l ++++ l +  e+a+
  gi|313125328|ref|YP_004035592.1| 161 VEKAL-ERIERLLDRAETAR 179
                                       44444.55555555555444 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.9
                             PAS_8  12 dgiavvd 18 
                                       d+++++ 
  gi|313125328|ref|YP_004035592.1| 222 DPVWILA 228
                                       5999842 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.3e-07   0.00065       2      87 ..      30     109 ..      29     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.3e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + v+e++ e +Gy++ee+lg+      l    D ++++e++ + l+ gep+ege+  ++k Ge +     ++++   
  gi|313125328|ref|YP_004035592.1|  30 VDVNEACLEFTGYTREEILGS----PPLFLVND-SQTYEEMVDTLAAGEPWEGEIEAVTKYGERVFGYGATFPL-IT 100
                                       789******************....55666667.778888888999****************977666555555.56 PP

                             PAS_3  79 ngkpvrvig 87 
                                       +g+ v + g
  gi|313125328|ref|YP_004035592.1| 101 DGELVGYAG 109
                                       666655555 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.8e-07   0.00055      40     110 ..     240     309 ..     225     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.8e-07
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpe.tlpdpteeepkeslkegGrGlalikglvD 110
                                       + Nave++++  p   + +++e ++++++++v+D+Gpg +pe +    ++ e+++ +  +G+ l+++ +l D
  gi|313125328|ref|YP_004035592.1| 240 VENAVEYNQDASP--MIWIHVETTPDEVVLTVEDNGPGIEPEqAEFLFGQCEDSQLRHGQGLSLFFVDRLLD 309
                                       56*******9988..8888888****************6666144555555667777777888888888877 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     1e-05      0.02     126     163 ..     113     150 ..      98     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                         HisKA_4TM 126 dasrakrisdalafvndlirhdlrndlvvirgyaeaie 163
                                       d s  +r  ++++ +n ++rh++rnd +vi g   +i+
  gi|313125328|ref|YP_004035592.1| 113 DLSERRRSEQTVSVLNRVLRHNIRNDANVIGGVLSTIK 150
                                       6666778899********************99877775 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.3e-05     0.065      10      88 ..     236     318 ..     228     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                       HATPase_c_5  10 lgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ekkkle....sskskkeehGiGlksireivk 79 
                                       +  + +NA+e  ++ +   ++I ++v+++ + +++++e +  g   e+ ++     + ++ ++ +G+ l  ++++++
  gi|313125328|ref|YP_004035592.1| 236 VAAVVENAVEYNQDAS---PMIWIHVETTPDEVVLTVEDNGPGiepEQAEFLfgqcEDSQLRHGQGLSLFFVDRLLD 309
                                       5667899999988876...9******************9955543355333345333344445555556789***** PP

                       HATPase_c_5  80 kykgnlsie 88 
                                        y+g+++++
  gi|313125328|ref|YP_004035592.1| 310 FYGGSVTYR 318
                                       ****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.38s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 1854.43
//
Query:       gi|313125329|ref|YP_004035593.1|  [L=409]
Description: proteasome-activating nucleotidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-43  146.3   0.1    1.5e-42  145.1   0.1    1.6  1  AAA              ATPase family associated with various cellul
    4.7e-12   45.5   0.9    1.3e-11   44.1   0.9    1.8  1  AAA_lid_3        AAA+ lid domain
    6.3e-08   32.9   0.0    1.7e-07   31.5   0.0    1.8  1  AAA_2            AAA domain (Cdc48 subfamily)
    2.1e-07   30.9   0.1      1e-06   28.6   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      2e-06   27.8   0.2    8.9e-06   25.8   0.2    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
    4.8e-06   27.1   3.9    0.00048   20.6   0.0    3.2  3  AAA_16           AAA ATPase domain
    2.4e-05   24.6   1.7     0.0012   19.1   0.0    2.9  3  AAA_22           AAA domain
    0.00018   21.4   0.3    0.00058   19.8   0.1    2.0  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    0.00042   19.5   0.0    0.00083   18.6   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
    0.00049   19.4   0.0     0.0012   18.2   0.0    1.6  1  TIP49            TIP49 P-loop domain
    0.00068   19.8   0.1     0.0024   18.0   0.0    2.1  2  AAA_33           AAA domain
     0.0019   18.2   0.0     0.0046   17.0   0.0    1.6  1  AAA_14           AAA domain
     0.0027   18.0   0.3      0.012   15.9   0.0    2.3  2  AAA_28           AAA domain
     0.0031   16.9   0.0     0.0065   15.9   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0036   17.1   0.0      0.021   14.5   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
     0.0055   17.2   0.5      0.032   14.8   0.0    2.5  2  AAA_18           AAA domain
     0.0061   16.4   0.3      0.075   12.8   0.0    2.2  2  AAA_11           AAA domain
     0.0078   16.1   0.2      0.043   13.7   0.0    2.2  2  NACHT            NACHT domain
     0.0095   14.4   0.9      0.014   13.8   0.9    1.2  1  MAD              Mitotic checkpoint protein
     0.0096   15.6   0.1      0.043   13.5   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.01   16.3   0.9      0.056   13.9   0.0    2.6  2  AAA_17           AAA domain
      0.016   14.7   0.0      0.046   13.2   0.0    1.7  1  AAA_7            P-loop containing dynein motor region
      0.016   15.5   0.4      0.016   15.5   0.4    2.6  2  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.019   14.8   0.5       0.26   11.2   0.1    2.6  2  NTPase_1         NTPase
       0.02   14.2   1.1      0.032   13.6   1.1    1.3  1  CASP_C           CASP C terminal
      0.022   14.6   0.0      0.045   13.6   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
      0.023   13.9   0.0      0.051   12.7   0.0    1.7  1  NB-ARC           NB-ARC domain
      0.028   14.8   0.0      0.072   13.5   0.0    1.8  1  RNA_helicase     RNA helicase
      0.029   14.0   0.2       0.11   12.2   0.1    2.1  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
       0.03   14.3   0.0      0.057   13.4   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.036   13.9   0.0        0.1   12.5   0.0    1.8  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.038   13.7   0.5       0.14   11.8   0.1    2.2  2  AAA_24           AAA domain
       0.04   13.6   1.6       0.07   12.9   1.6    1.3  1  DUF4201          Domain of unknown function (DUF4201)
      0.043   13.9   0.0      0.087   12.9   0.0    1.4  1  Torsin           Torsin
      0.044   14.2   5.1      0.064   13.7   1.7    2.6  2  ZapB             Cell division protein ZapB
      0.053   13.6   5.7       0.06   13.5   3.7    2.2  1  DMPK_coil        DMPK coiled coil domain like
      0.063   12.4   0.2      0.098   11.7   0.2    1.3  1  DUF3086          Protein of unknown function (DUF3086)
        0.1   10.8   0.9       0.15   10.2   0.9    1.2  1  COG6             Conserved oligomeric complex COG6
       0.11   13.0   1.4       0.24   11.9   0.0    2.3  2  ABC_tran         ABC transporter
       0.15   11.1   0.0       0.34   10.0   0.0    1.5  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.17   12.0   0.6       0.47   10.6   0.6    1.7  1  Swi5             Swi5
       0.22   11.7   0.2       0.22   11.7   0.2    1.7  1  Myc-LZ           Myc leucine zipper domain
       0.31   10.3   2.2        1.1    8.6   0.0    2.6  3  ATPase           KaiC
       0.72    9.5   4.3       0.16   11.7   0.3    2.0  1  AAA_30           AAA domain
        0.8    9.6   2.4        1.5    8.7   2.4    1.4  1  DUF2721          Protein of unknown function (DUF2721)
        1.5    8.7   3.4         12    5.8   3.4    2.4  1  DivIC            Septum formation initiator
        2.3    7.7  11.3       0.67    9.5   0.1    3.5  3  AAA_25           AAA domain
        3.9    7.7   4.9        9.2    6.5   0.5    2.4  2  NYD-SP28_assoc   Sperm tail C-terminal domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.1   0.1     4e-45   1.5e-42       1     131 [.     188     320 ..     188     321 .. 0.95

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 4e-45
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vll+GppGtGKT+lakava+e++++f+++ gsel+ k++ge+++ +r+lf+ a   + p ++fiDEida+a++r   
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETDATFIKMAGSELVRKFIGEGARLVRDLFELAADRE-PAVIFIDEIDAVASKRtds 263
                                       79**************************************************99987.****************986 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++s + e +r++ qLl+e+dg++++ +++ +++atnr d+ld+a+lr gRfdr ie++
  gi|313125329|ref|YP_004035593.1| 264 KTSGDAEVQRTMMQLLSEMDGFDDR-GEIRIMAATNRFDMLDEAILRpGRFDRLIEVP 320
                                       666888999***************7.66***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.9   3.5e-14   1.3e-11       1      44 [.     343     386 ..     343     387 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 3.5e-14
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       dvd++eLAe+ +G SGAD+a+l  eA++ A+r++++e+   df+
  gi|313125329|ref|YP_004035593.1| 343 DVDFEELAEELDGQSGADIASLTTEAGMFAIRDDRTEVRRVDFD 386
                                       9**************************************99997 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   4.6e-10   1.7e-07       5     105 ..     187     281 ..     183     294 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4.6e-10
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG-- CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKih 81 
                                        +ll gp g+Gkt+laka+a+  ++    ++i +  sel    +     +rl+       +  e  ++++DEid ++
  gi|313125329|ref|YP_004035593.1| 187 GVLLHGPPGTGKTMLAKAVANETDA----TFIKMAGSELVR--KFIGEGARLVRDLFELAADREPAVIFIDEIDAVA 257
                                       57999******************96....899999999988..22222234444444455566778*********** PP

                                       -----------HHHHHHHHHHHH- CS
                             AAA_2  82 pkessgadvSregVqrdLLqileg 105
                                       +k++ ++     +Vqr ++q+l +
  gi|313125329|ref|YP_004035593.1| 258 SKRTDSKTSGDAEVQRTMMQLLSE 281
                                       *87777777888*********965 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.9   2.6e+03      88     130 ..      99     142 ..      62     145 .. 0.68
   2 !   28.6   0.0   2.8e-09     1e-06      30      97 ..     182     257 ..     164     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.9
                            RuvB_N  88 lfideihrlsraveevlysamed.frldivigkGpsarsikldl 130
                                       ++ d    l+++ve     a++d f+++ v+++ + ar+  +++
  gi|313125329|ref|YP_004035593.1|  99 VLTDTSPHLESQVEAGDRVAINDsFAIQTVLDDETDARAQAMEV 142
                                       34566666777777777777776577888888888888777765 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 2.8e-09
                            RuvB_N  30 eealdhvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl......eekdvlfideihrls 97 
                                        e+   vll+GpPG Gkt lak +a+e ++++   +g  l ++  g+ a l+ +l      +e  v+fidei  ++
  gi|313125329|ref|YP_004035593.1| 182 VEPPSGVLLHGPPGTGKTMLAKAVANETDATFIKMAGSELVRKfiGEGARLVRDLfelaadREPAVIFIDEIDAVA 257
                                       5667789**********************998777777666543445444444432213223457*******8765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   2.4e-08   8.9e-06       1     124 [.     187     301 ..     187     310 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.4e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL GppGtgK++la+ +a  + +++  +++++      l+ +    +g +  +d     a re++++++DE++ +
  gi|313125329|ref|YP_004035593.1| 187 GVLLHGPPGTGKTMLAKAVANETDATFIKMAGSE------LVRKFIG-EGARLVRDLFELAADREPAVIFIDEIDAV 256
                                       59*********************99988888776......5555543.3333345554455999***********99 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS-- CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkaknddller..frviatanpld 124
                                        s+ ++s  s   e ++ ++++  +++   d    r  +r++a++n+ d
  gi|313125329|ref|YP_004035593.1| 257 ASKRTDSKTSGDAEVQRTMMQLLSEMDGFDD----RgeIRIMAATNRFD 301
                                       8666555444444444444444444433222....22366666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1         3   1.1e+03      59      88 ..      31      62 ..      12     120 .. 0.58
   2 !   20.6   0.0   1.3e-06   0.00048      24      48 ..     184     209 ..     157     226 .. 0.75
   3 ?    5.8   0.2     0.045        17     121     149 ..     231     258 ..     215     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3
                            AAA_16 59 kcdql.esaipysa.laqalareellrqllde 88
                                      ++++l e +++++  l++a +r++ l+ + d+
  gi|313125329|ref|YP_004035593.1| 31 HFERLrEVNRELDDrLTEATDRRDDLQSEVDQ 62
                                      22222111122222233333333333332222 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.3e-06
                            AAA_16  24 p.elvllsGesGvGKsslvrellral 48 
                                       p + vll+G++G+GK+ l+++++++ 
  gi|313125329|ref|YP_004035593.1| 184 PpSGVLLHGPPGTGKTMLAKAVANET 209
                                       2599*****************99743 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.045
                            AAA_16 121 ellkrllallsrderplvlvlDdlqwade 149
                                       +l+++l++l++  ++p v+++D+++ + +
  gi|313125329|ref|YP_004035593.1| 231 RLVRDLFELAAD-REPAVIFIDEIDAVAS 258
                                       567777888888.777*********5544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       9.2   3.5e+03      67      81 ..      45      59 ..      22      89 .. 0.53
   2 !   19.1   0.0   3.2e-06    0.0012       8      30 ..     188     210 ..     183     228 .. 0.82
   3 ?    3.5   0.1      0.21        79      82     106 ..     236     273 ..     213     294 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 9.2
                            AAA_22 67 elkaerlsseellea 81
                                      +l ++++++++l + 
  gi|313125329|ref|YP_004035593.1| 45 RLTEATDRRDDLQSE 59
                                      333322222222222 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.2e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                       ++++G++GtGKT+l++ ++++ d
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETD 210
                                       689*****************984 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.21
                            AAA_22  82 leqalraravielliiDEaqhlr.....s.........e 106
                                       l + + +r   +++ iDE++ +      s          
  gi|313125329|ref|YP_004035593.1| 236 LFELAADREP-AVIFIDEIDAVAskrtdSktsgdaevqR 273
                                       3333344444.8********9875543314445544444 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   1.6e-06   0.00058       1      47 [.      77     121 ..      77     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.6e-06
                                       EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEET CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdk 47 
                                       +atV Ev dd  ++++k+++ ++ v+  +++  ++++ +gD+Va++ 
  gi|313125329|ref|YP_004035593.1|  77 IATVEEVTDD--GVVIKQHGNNQEVLTDTSPHLESQVEAGDRVAIND 121
                                       89******98..********99999999999999***********95 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.2e-06   0.00083      15     116 ..     138     253 ..     124     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                            DUF815  15 alepveevdevklddLvgidkqkealve.......nteqfle..glpannvLLwGarGtGKSslvkallneyaeegL 82 
                                       +   v+    v+ dd+ gid+q +++ e       n e f++   +p + vLL G  GtGK  l ka+ ne+ ++ +
  gi|313125329|ref|YP_004035593.1| 138 QAMEVDASPDVTYDDIGGIDDQVREVREavedplsNPEMFAKvgVEPPSGVLLHGPPGTGKTMLAKAVANETDATFI 214
                                       4566777888999999999999877754122222266778763247899**************************98 PP

                            DUF815  83 rli..evekedlkelpklvellr...erperfilfvDDL 116
                                       ++   e+ ++ + e  +lv+ l    + +e  ++f+D +
  gi|313125329|ref|YP_004035593.1| 215 KMAgsELVRKFIGEGARLVRDLFelaADREPAVIFIDEI 253
                                       886558889999988888876541215567788998875 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.1e-06    0.0012      52      90 ..     187     223 ..     183     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                       +vLl Gp+gtGkt la a+++e   d  f++++gse+ +
  gi|313125329|ref|YP_004035593.1| 187 GVLLHGPPGTGKTMLAKAVANET--DATFIKMAGSELVR 223
                                       79*******************96..589********976 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       9.7   3.6e+03      61      94 ..      33      66 ..      15     104 .. 0.56
   2 !   18.0   0.0   6.4e-06    0.0024       2      28 ..     188     214 ..     188     277 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.7
                            AAA_33 61 elarkalsagrnvildatnlsrrerarflklarr 94
                                      e++r++ ++  + ++ at ++ + ++++++l rr
  gi|313125329|ref|YP_004035593.1| 33 ERLREVNRELDDRLTEATDRRDDLQSEVDQLKRR 66
                                      4444444444444444444444444555554443 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 6.4e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavll 28 
                                       vll+G+pG+GK+ la+ ++++++a+++
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETDATFI 214
                                       799****************99987765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.2e-05    0.0046       5      77 ..     188     257 ..     186     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       +++ G+  +GKT+l+k +++e       ++ ++  +   k + + ++l + ++e++ +++  ++f+DEi  v 
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETD---ATFIKMAGSELVRKFIGEGARLVRDLFELAADREPAVIFIDEIDAVA 257
                                       6899**************98877...778888777765555555557899999986666999*******9885 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       8.1     3e+03      43      58 ..      47      59 ..      16      89 .. 0.52
   2 !   15.9   0.0   3.2e-05     0.012       2      40 ..     188     231 ..     187     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 8.1
                            AAA_28 43 edalpwv.edllafaer 58
                                      ++    + +++ +++++
  gi|313125329|ref|YP_004035593.1| 47 TE----AtDRRDDLQSE 59
                                      21....11233333333 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.2e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekla 40 
                                       + + G+++tGKT l++a a++     +++   E +r+++ e+++
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANEtdatFIKMAgSELVRKFIGEGAR 231
                                       6799***************6554446666677888887766654 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.8e-05    0.0065      25      42 ..     188     205 ..     177     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll GppG+GKtmlak++
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAV 205
                                       89*************987 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   5.7e-05     0.021      48      70 ..     186     208 ..     173     222 .. 0.88
   2 ?   -1.0   0.0       3.3   1.2e+03      54      98 ..     355     400 ..     345     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                        +++l Gp+G+GK+ la a++ e
  gi|313125329|ref|YP_004035593.1| 186 SGVLLHGPPGTGKTMLAKAVANE 208
                                       6799***************9976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.3
                         IstB_IS21  54 GpsGvGKshlaialgveavrag.lsvlfvrvedLveelkrarrdgk 98 
                                       G+sG+  + l++  g+ a+r++ ++v+ v  +d +e+++ a++  +
  gi|313125329|ref|YP_004035593.1| 355 GQSGADIASLTTEAGMFAIRDDrTEVRRVDFDDAIEKMRDAEDSRS 400
                                       888999999999999****965268999999999999999987766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       6.6   2.5e+03      55      68 ..      51      64 ..      22     121 .. 0.54
   2 !   14.8   0.0   8.7e-05     0.032       1      25 [.     188     220 ..     188     293 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 6.6
                            AAA_18 55 dkldklldaleens 68
                                      d++d l++++++  
  gi|313125329|ref|YP_004035593.1| 51 DRRDDLQSEVDQLK 64
                                      33333333333322 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.7e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......g 25 
                                       +ll G+pG+GKt lak++++++ +         
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETdATfikmagsE 220
                                       7899**************998733255555540 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3      0.71   2.7e+02     151     202 ..      30      79 ..      10     113 .. 0.64
   2 !   12.8   0.0    0.0002     0.075      19      39 ..     187     207 ..     158     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.71
                            AAA_11 151 klkkskekskskleqerrklkkerkelskeleeaeesleeevldeaeivltT 202
                                       ++ +  ++ +++l  ++++ ++ r++l++e+++ +++  +e l+++++ ++T
  gi|313125329|ref|YP_004035593.1|  30 QHFERLREVNRELDDRLTEATDRRDDLQSEVDQLKRR--NETLKTSSLYIAT 79 
                                       3334444555555555555555555555555555555..3455555555555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0002
                            AAA_11  19 itliqGPPGtgKTktivells 39 
                                        +l++GPPGtgKT    ++ +
  gi|313125329|ref|YP_004035593.1| 187 GVLLHGPPGTGKTMLAKAVAN 207
                                       689**********76666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00012     0.043       3      23 ..     188     208 ..     186     215 .. 0.90
   2 ?   -0.9   0.0       3.6   1.3e+03      76     114 ..     239     280 ..     219     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l+G++G GKT+L++ +a +
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANE 208
                                       79**************99876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.6
                                       HCCSCCCEEEEEE-STT-SS-TCH............HHHHHC CS
                             NACHT  76 llelperlLlilDglDelvtdlgq...kekqpvrtlLselir 114
                                       l++ +e +++ +D +D ++++      ++ ++v++ + +l++
  gi|313125329|ref|YP_004035593.1| 239 LAADREPAVIFIDEIDAVASKRTDsktSGDAEVQRTMMQLLS 280
                                       455556667778999988887666666677777777777665 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.9   3.8e-05     0.014     125     200 ..      23     101 ..      14     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                               MAD 125 lelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqs...qeddslivknskselar 198
                                         ls+ ++  e+l+e + +l+ +l+e+++++ +l+++ ++l+ +++++k+ +  i+     +dd +++k+  ++++ 
  gi|313125329|ref|YP_004035593.1|  23 ERLSALRQHFERLREVNRELDDRLTEATDRRDDLQSEVDQLKRRNETLKTSSLYIATveeVTDDGVVIKQHGNNQEV 99 
                                       46899999******************************************988887766588999999987555544 PP

                               MAD 199 ip 200
                                       + 
  gi|313125329|ref|YP_004035593.1| 100 LT 101
                                       43 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00012     0.043      20      54 ..     183     214 ..     164     228 .. 0.76
   2 ?   -1.4   0.0       4.3   1.6e+03      97     107 ..     248     258 ..     236     317 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                                       TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfv 54 
                                       + ++ vl++G  GtGK++la+a+ ++++   + f+
  gi|313125329|ref|YP_004035593.1| 183 EPPSGVLLHGPPGTGKTMLAKAVANETD---ATFI 214
                                       45588*****************987654...4455 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.3
                                       EEEETGGGS-H CS
                   Sigma54_activat  97 lfLDeigelpl 107
                                       +f+Dei  +  
  gi|313125329|ref|YP_004035593.1| 248 IFIDEIDAVAS 258
                                       56666554433 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3       3.2   1.2e+03      65      80 ..      90     105 ..      22     164 .. 0.60
   2 ?   13.9   0.0   0.00015     0.056       2      48 ..     192     239 ..     191     287 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.2
                                       HHHHHHSSEEEEEE-S CS
                            AAA_17  65 iaeeakkkgvlvdghp 80 
                                       i+++ ++++vl d+ p
  gi|313125329|ref|YP_004035593.1|  90 IKQHGNNQEVLTDTSP 105
                                       2233333334444444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00015
                                       E-TTSSHHHHHHHHHHHHTEEEEEH..HHHHHHHHHTTTSHSSHHHHCT CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsa..Gdllreeakrgglakardemrk 48 
                                       G+PG GK+ +++ ++ + + t++ +  ++l+r+ +  +g+   rd ++ 
  gi|313125329|ref|YP_004035593.1| 192 GPPGTGKTMLAKAVANETDATFIKMagSELVRKFI-GEGARLVRDLFEL 239
                                       9********************99877455555555.5555455666653 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.046      31      61 ..     183     212 ..     173     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                             AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkek 61 
                                       +    vll Gp GtGKt+++k + ++ d  +
  gi|313125329|ref|YP_004035593.1| 183 EPPSGVLLHGPPGTGKTMLAKAVANETD-AT 212
                                       555679****************999998.43 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.4   4.4e-05     0.016      15      72 ..      25      82 ..      22      86 .. 0.91
   2 ?   -0.7   0.1       4.9   1.8e+03      62      82 ..     148     168 ..     125     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-05
                           BLOC1_2 15 leatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiek 72
                                      l+a +++++ L ++N++   + ++ +d+ ++l++++++l++++e+l+     i  +e+
  gi|313125329|ref|YP_004035593.1| 25 LSALRQHFERLREVNRELDDRLTEATDRRDDLQSEVDQLKRRNETLKTSSLYIATVEE 82
                                      78999*****************************************999888888776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.9
                           BLOC1_2  62 pylqqidqiekqvteLeeavs 82 
                                          + i  i++qv+e  eav+
  gi|313125329|ref|YP_004035593.1| 148 VTYDDIGGIDDQVREVREAVE 168
                                       556789999999999999886 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.2   4.4e+02      95     125 ..     145     174 ..     115     182 .. 0.80
   2 ?   11.2   0.1    0.0007      0.26       2      59 ..     188     246 ..     187     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                                       HH-EEEE---STTGGG-HHHHHHHHHHHTTT CS
                          NTPase_1  95 eadviviDEiGkmElkskkfkeaveevLkse 125
                                       ++dv   D iG +  ++++++eave+ L++ 
  gi|313125329|ref|YP_004035593.1| 145 SPDVT-YDDIGGIDDQVREVREAVEDPLSNP 174
                                       45554.599****************999854 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0007
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T--EEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasgeegi 59 
                                       v++ GppG+GKt l k v+++ +   +k++G  ++++   +g r   ++ +la ++e  
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETDATFIKMAGSeLVRKFIGEGARLVRDLFELAADREPA 246
                                       6789******************9999999996345666688888888888887777655 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.1   8.5e-05     0.032      94     154 ..      33      93 ..      17     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.5e-05
                            CASP_C  94 DRFrkrnaeLEeelrkqeetvsslraeiaslqkDNlkLYEkvRYlqsYnrgskastkssse 154
                                       +R r+ n+eL++ l + ++  ++l++e+++l++ N  L     Y+++ ++ +   +  +++
  gi|313125329|ref|YP_004035593.1|  33 ERLREVNRELDDRLTEATDRRDDLQSEVDQLKRRNETLKTSSLYIATVEEVTDDGVVIKQH 93 
                                       79************************************99999999988877666333333 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00012     0.045       2      30 ..     188     216 ..     187     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++kt+l+ka+a+  d++f ++
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETDATFIKM 216
                                       89********************9999664 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014     0.051      23      47 ..     188     212 ..     182     351 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                       EEEEESTTSSHHHHHHHHCCSHCCC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksdev 47 
                                       v l+G +G GKt lak + n+ d +
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETDAT 212
                                       679*****************96654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00019     0.072       1      43 [.     188     221 ..     188     267 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00019
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddf 43 
                                       ++l+Gp+g+GK++lak +a++          d ++++ + ++ 
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANET---------DATFIKMAGSEL 221
                                       689**************65544.........444444444444 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00028      0.11       2      58 ..      77     132 ..      76     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                     Prot_ATP_OB_N   2 yGtflavnsqdgtadVlvg.grrmrVavsPlvdaeeLrpGqeVlLnEalvvVealgye 58 
                                       ++t+ +v+ +dg +   +g ++++    sP+++ ++ ++G++V +n+++++  +l+ e
  gi|313125329|ref|YP_004035593.1|  77 IATVEEVT-DDGVVIKQHGnNQEVLTDTSPHLE-SQVEAGDRVAINDSFAIQTVLDDE 132
                                       57888888.45555555541455666799***9.9***************98888766 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00015     0.057      20      59 ..     186     225 ..     159     258 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00015
                                       EEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEE CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeY 59 
                                       + +lL+G+ G+GKT+l++++a++ + + +k     lv+++
  gi|313125329|ref|YP_004035593.1| 186 SGVLLHGPPGTGKTMLAKAVANETDATFIKMAGSELVRKF 225
                                       349******************9998776666666666666 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00027       0.1       4      39 ..     188     223 ..     186     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00027
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafve 39 
                                       +lL+G + +GK+ la+a+ + +d+++++++  ++v 
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETDATFIKMAGSELVR 223
                                       89**************************98776665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00038      0.14       5      31 ..     188     216 ..     185     272 .. 0.69
   2 ?   -2.2   0.0       7.4   2.8e+03      25      56 ..     360     392 ..     349     400 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidt 31 
                                       +l+ Gp+g+GKT+lak    + ++ fi +
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVanETDATFIKM 216
                                       789*************9976666666654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.4
                            AAA_24  25 kplfidtekGlksldadkfpdie.swedfldev 56 
                                       +++ + te+G+ ++ +d+ +  +  ++d ++++
  gi|313125329|ref|YP_004035593.1| 360 DIASLTTEAGMFAIRDDRTEVRRvDFDDAIEKM 392
                                       566788999999999999764447444444443 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.6   0.00019      0.07      91     155 ..      23      84 ..      18      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                           DUF4201  91 selselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekve 155
                                       + ls+l++  +++ e  ++l+++l+++  +rd l+ + ++lk++++ l+  +L   Y+ t+e+v 
  gi|313125329|ref|YP_004035593.1|  23 ERLSALRQHFERLREVNRELDDRLTEATDRRDDLQSEVDQLKRRNETLKTSSL---YIATVEEVT 84 
                                       56788888888888999999999999999999999999999999999888888...788888876 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00023     0.087      56      92 ..     188     227 ..     177     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00023
                                       EEEEE-TTSSHHHHHHHHHHH...HSTTGGGSTTEEEEEH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaen...lyrdGlrsdyvkkfva 92 
                                       + +hG +GtGk  +a+ +a++   ++ +   s+ v+kf++
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANEtdaTFIKMAGSELVRKFIG 227
                                       569***************9752227999999999*99996 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2       0.1        38      18      43 ..      23      48 ..      21      50 .. 0.86
   2 ?   13.7   1.7   0.00017     0.064       8      39 ..      41      72 ..      37     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.1
                              ZapB 18 dtitlLqmeieeLkeeneelkeenre 43
                                      +++++L++  e+L+e n+el ++  e
  gi|313125329|ref|YP_004035593.1| 23 ERLSALRQHFERLREVNRELDDRLTE 48
                                      67789***************998766 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00017
                              ZapB  8 qLEskiqkaidtitlLqmeieeLkeeneelke 39
                                      +L  +  +a d+ + Lq e+++Lk++ne+lk 
  gi|313125329|ref|YP_004035593.1| 41 ELDDRLTEATDRRDDLQSEVDQLKRRNETLKT 72
                                      79999*************************97 PP

>> DMPK_coil  DMPK coiled coil domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.7   0.00016      0.06      16      59 ..      28      71 ..      23      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00016
                         DMPK_coil 16 lqeeLekvkaanlafeskLkeaEkknreLeeeleqLkkemEelr 59
                                      l++  e+ ++ n + + +L ea  +  +L++e++qLk++ E l+
  gi|313125329|ref|YP_004035593.1| 28 LRQHFERLREVNRELDDRLTEATDRRDDLQSEVDQLKRRNETLK 71
                                      6677889999******************************9987 PP

>> DUF3086  Protein of unknown function (DUF3086)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00026     0.098       3     128 ..      44     178 ..      42     180 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                           DUF3086   3 ealkeleerkqalqieveqLerrkerieke...lrtsfaGvsqdlairvqgf.kdyLvgslqdLaaaaeqlelvake 75 
                                       ++l+e  +r+++lq ev+qL+rr+e +++    + t    + + + i+ +g  ++ L+++   L +++e  + va +
  gi|313125329|ref|YP_004035593.1|  44 DRLTEATDRRDDLQSEVDQLKRRNETLKTSslyIATVEEVTDDGVVIKQHGNnQEVLTDTSPHLESQVEAGDRVAIN 120
                                       689999********************998532233333444455777777642677777777776666665555444 PP

                           DUF3086  76 kavkpePa..dekeeeekeeeeeaepqfaeqe...fkeeakkirklldqyrekPdyyg 128
                                          + + +  de+ +++++ e +a+p+++ +     +++ +++r++++   ++P+ ++
  gi|313125329|ref|YP_004035593.1| 121 DSFAIQTVldDETDARAQAMEVDASPDVTYDDiggIDDQVREVREAVEDPLSNPEMFA 178
                                       4332222211334444444445555555544311156666777777777777777665 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.9   0.00041      0.15      43      93 ..      22      72 ..      19      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                              COG6 43 aeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklel 93
                                      ae+L+++++++e l e++ e+ ++l++a+++ +dl +e+++Lk++++ l++
  gi|313125329|ref|YP_004035593.1| 22 AERLSALRQHFERLREVNRELDDRLTEATDRRDDLQSEVDQLKRRNETLKT 72
                                      589******************************************999886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.5       6.9   2.6e+03      82     102 ..      50      70 ..      11     168 .. 0.64
   2 ?   11.9   0.0   0.00064      0.24       7      37 ..     181     211 ..     178     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 6.9
                                       HTCHHHHHHHSTTGGTTCBGE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  82 deeiekalsklglkelkdtvv 102
                                       +++ +++ s++++ + +++++
  gi|313125329|ref|YP_004035593.1|  50 TDRRDDLQSEVDQLKRRNETL 70 
                                       333444444444333333333 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00064
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkp 37 
                                        +++ + v + G+ G+GK+ L+k++a++++ 
  gi|313125329|ref|YP_004035593.1| 181 GVEPPSGVLLHGPPGTGKTMLAKAVANETDA 211
                                       677778899*****************99876 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0009      0.34     117     138 ..     188     209 ..     182     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0009
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                       v+++Gp+ tGkt+la+a a+ +
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANET 209
                                       789***************9865 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6    0.0013      0.47       4      48 ..      24      68 ..      22      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0013
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHH CS
                              Swi5  4 eikeleeqleelekelaelkeelkekkdpeetvkrhIklLheYNE 48
                                      ++++l+++ e+l++   el+++l e +d  + +++ +++L+++NE
  gi|313125329|ref|YP_004035593.1| 24 RLSALRQHFERLREVNRELDDRLTEATDRRDDLQSEVDQLKRRNE 68
                                      7899****************************************9 PP

>> Myc-LZ  Myc leucine zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00058      0.22       6      21 ..      56      71 ..      54      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00058
                            Myc-LZ  6 LlSekEqLRkrrEqLK 21
                                      L Se +qL++r E LK
  gi|313125329|ref|YP_004035593.1| 56 LQSEVDQLKRRNETLK 71
                                      78*************9 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       8.3   3.1e+03      98     130 ..      50      82 ..      31      91 .. 0.66
   2 ?    8.6   0.0    0.0028       1.1      15      37 ..     181     203 ..     155     211 .. 0.87
   3 ?    0.1   0.0       1.2   4.4e+02     107     151 ..     232     282 ..     214     286 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.3
                            ATPase  98 ekdkedleelieelaeaikeikakrvviDsitg 130
                                        ++++dl++ +++l++  +++k + + i +++ 
  gi|313125329|ref|YP_004035593.1|  50 TDRRDDLQSEVDQLKRRNETLKTSSLYIATVEE 82 
                                       356667777777777777776666666666555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0028
                            ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                       G+   + vl+ G pGtGKt++a+
  gi|313125329|ref|YP_004035593.1| 181 GVEPPSGVLLHGPPGTGKTMLAK 203
                                       66666789*************97 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                            ATPase 107 lieelaeaikeikakrvviDsitgl.ayeek.....eavaReilrqlvrvl 151
                                       l+++l e  ++ +   + iD i+++ +++++     +a++ ++++ql++++
  gi|313125329|ref|YP_004035593.1| 232 LVRDLFELAADREPAVIFIDEIDAVaSKRTDsktsgDAEVQRTMMQLLSEM 282
                                       667777778888888899999998844333311111234555555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00043      0.16      21      43 ..     188     210 ..     176     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00043
                            AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                       ++l+Gp+GtGKt++ ka+++  +
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAVANETD 210
                                       6899**********999976554 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.4    0.0041       1.5      17      69 ..      27      76 ..      23      80 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0041
                           DUF2721 17 vltnRlariadrirqLedeleelaeeeeedeelakeiknlrrRarlirraill 69
                                      +l   + r+ +  r+L d+l e++++   +++l+ e+++l+rR + ++ + l 
  gi|313125329|ref|YP_004035593.1| 27 ALRQHFERLREVNRELDDRLTEATDR---RDDLQSEVDQLKRRNETLKTSSLY 76
                                      55566667777777777777744444...678***********9999887665 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   3.4     0.031        12      22      55 ..      35      68 ..      20      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.031
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                             DivIC 22 lkqeiaalqaelaklkaeneeLeaevkdLksded 55
                                      l++   +l + l + ++++++L++ev++Lk   +
  gi|313125329|ref|YP_004035593.1| 35 LREVNRELDDRLTEATDRRDDLQSEVDQLKRRNE 68
                                      4555567788888888999999999999975544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4      0.26        98      87     139 ..      22      69 ..       9     117 .. 0.78
   2 ?    9.5   0.1    0.0018      0.67      36      53 ..     188     205 ..     181     209 .. 0.86
   3 ?    1.8   0.1       0.4   1.5e+02     130     165 ..     233     269 ..     213     288 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.26
                            AAA_25  87 rrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaiee 139
                                       ++Rl+a+++++   +rl+ +++  + + +L++++++   l+++vd+l ++ e 
  gi|313125329|ref|YP_004035593.1|  22 AERLSALRQHF---ERLREVNR--ELDDRLTEATDRRDDLQSEVDQLKRRNET 69 
                                       68999999999...55555543..22457888888888889999999887655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0018
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll G+pgtGKt+la  +
  gi|313125329|ref|YP_004035593.1| 188 VLLHGPPGTGKTMLAKAV 205
                                       69************9665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.4
                            AAA_25 130 vdaleaaieevegvrlvviDplsralgg..densnsdv 165
                                       v++l + + +  +++++ iD ++++ +   d++ + d+
  gi|313125329|ref|YP_004035593.1| 233 VRDLFELAAD-REPAVIFIDEIDAVASKrtDSKTSGDA 269
                                       6677888888.56***********98886655544443 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3      0.37   1.4e+02      37      58 ..      27      48 ..      23      50 .. 0.83
   2 ?    6.5   0.5     0.025       9.2      34      54 ..      52      72 ..      51      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.37
                    NYD-SP28_assoc 37 klieetesLekqNeeLrnlLkq 58
                                      +l ++ e L++ N eL ++L++
  gi|313125329|ref|YP_004035593.1| 27 ALRQHFERLREVNRELDDRLTE 48
                                      5667789**********99986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.025
                    NYD-SP28_assoc 34 eRaklieetesLekqNeeLrn 54
                                      +R  l +e+++L++ Ne L++
  gi|313125329|ref|YP_004035593.1| 52 RRDDLQSEVDQLKRRNETLKT 72
                                      69999**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1237  (0.0689944); expected 358.6 (0.02)
Passed bias filter:                      888  (0.0495287); expected 358.6 (0.02)
Passed Vit filter:                       195  (0.0108762); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              48  [number of targets reported over threshold]
# CPU time: 0.89u 0.38s 00:00:01.27 Elapsed: 00:00:00.56
# Mc/sec: 2196.25
//
Query:       gi|313125330|ref|YP_004035594.1|  [L=156]
Description: arginine decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-34  117.9   0.2    4.1e-34  117.7   0.2    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC
  ------ inclusion threshold ------
      0.065   13.8   0.0       0.11   13.0   0.0    1.4  1  DUF5629   Family of unknown function (DUF5629)


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.2   4.6e-38   4.1e-34       4     161 ..       3     149 ..       1     150 [. 0.90

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 4.6e-38
                          PvlArgDC   4 kvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrli 80 
                                       ++ +++Gvg++++e+as+d+AL++A+I+n+NLv+vSS++P+++++ +v++++++ p+G++++vv ara+++  g ++
  gi|313125330|ref|YP_004035594.1|   3 TIYVVRGVGTAPTEMASYDAALAAANIHNYNLVAVSSVIPADTTVEEVDTAPDLGPAGNRLTVVEARATTSDAG-TV 78 
                                       6889******************************************************************9999.7* PP

                          PvlArgDC  81 aaavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrgllee.kiietkeievaaveakvekygtvl 156
                                       +a++g+++      +G+++E+sg       + ee+++ ++ +l++ r+l+++ +  +++++++++++a+ e y+t++
  gi|313125330|ref|YP_004035594.1|  79 SAGLGWTVGP---GPGLFYEASG------ADAEEVRHAIEAGLSSGRNLRDWqF--DNERVTTTTADADGEGYTTAI 144
                                       *******964...6*********......5688888888999999999966644..4457777788899******** PP

                          PvlArgDC 157 aaavf 161
                                       ++a++
  gi|313125330|ref|YP_004035594.1| 145 TVAAY 149
                                       99976 PP

>> DUF5629  Family of unknown function (DUF5629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05      0.11      51      82 ..     110     141 ..      94     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                                       EEEEETTEEEEEEEEHHHHHS-EE-TTSSEEE CS
                           DUF5629  51 iealdGrerrkWkfsynavmearydaeddsWl 82 
                                            Gr+ r W+f  ++v   + da+ + ++
  gi|313125330|ref|YP_004035594.1| 110 AGLSSGRNLRDWQFDNERVTTTTADADGEGYT 141
                                       33468*********************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 994.78
//
Query:       gi|313125331|ref|YP_004035595.1|  [L=126]
Description: hypothetical protein Hbor_05550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 711.28
//
Query:       gi|313125332|ref|YP_004035596.1|  [L=87]
Description: hypothetical protein Hbor_05560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.4   0.6      0.019   15.0   0.6    1.1  1  DUF3561   Protein of unknown function (DUF3561)


Domain annotation for each model (and alignments):
>> DUF3561  Protein of unknown function (DUF3561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.6   1.1e-06     0.019      60     101 ..      22      64 ..      17      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-06
                           DUF3561  60 fflallPvsvlvGvalsvllrgkllysilatll.avvllfwll 101
                                       ++lallP+ +l+G+ + v+ + ++ + + + +l +v++l   l
  gi|313125332|ref|YP_004035596.1|  22 WLLALLPLPMLLGILVAVITDIRVAFGVSLGGLpSVAMLVYGL 64 
                                       68**************************998873455554445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 507.85
//
Query:       gi|313125333|ref|YP_004035597.1|  [L=94]
Description: hypothetical protein Hbor_05570, partial [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.36s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 515.52
//
Query:       gi|313125334|ref|YP_004035598.1|  [L=452]
Description: divergent aaa domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.6   0.0      3e-07   30.8   0.0    1.5  1  AlbA_2    Putative DNA-binding domain


Domain annotation for each model (and alignments):
>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.7e-11     3e-07      18     122 .]      56     189 ..      39     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.7e-11
                            AlbA_2  18 rers......iakticAfaNs...eg.GtlliGVeDdgkvvGv......ecsdqeedqlrlelksiikrfkpkvlpd 78 
                                       + +       ++k+icA+aN+   +   +l+iG  D+g ++G         ++  e ++++ ++ +++ ++p ++++
  gi|313125334|ref|YP_004035598.1|  56 SDQGkernfrLLKHICALANTrgeQRyRYLFIGFGDSGGFIGAsdwdanGGEHVVEVDEARVQDLLSDSLDPVPEVE 132
                                       2222234577**********944323479**************99888756667777888888889*********** PP

                            AlbA_2  79 iervelkgkkvlvvkvekskkkp.............lyeneegvvyiRrggsskrlr 122
                                        + +  ++++  v+ v +s+++p             +   ++gv y+R+g++s+++r
  gi|313125334|ref|YP_004035598.1| 133 RTVLTQDDNTAAVLSVRRSDSPPvlfdtsittsggaTTLVKSGVGYVRKGSQSRPMR 189
                                       ***********************9888776666666555666***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 2451.67
//
Query:       gi|313125335|ref|YP_004035599.1|  [L=605]
Description: translation initiation factor eaif-5b [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-33  114.0   0.0    5.8e-32  110.8   0.0    2.4  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.7e-25   88.1   0.3    8.1e-25   86.6   0.1    2.0  2  GTP_EFTU_D4  Elongation factor Tu domain 4
    3.9e-22   78.4   0.7    9.2e-22   77.2   0.7    1.6  1  IF-2         Translation-initiation factor 2
    5.4e-14   52.3   7.9      2e-09   37.7   0.2    2.9  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    6.2e-08   32.7   0.0    1.8e-07   31.2   0.0    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
      0.003   17.6   0.1        0.5   10.4   0.0    2.6  2  Dynamin_N    Dynamin family
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.044   13.6   0.0    1.9  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.074   13.3   0.0       0.21   11.8   0.0    1.8  2  Roc          Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   2.6e-35   5.8e-32       4     189 ..      20     225 ..      17     230 .. 0.79
   2 ?   -2.6   0.0       1.5   3.3e+03     138     141 ..     452     455 ..     377     536 .. 0.57

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 2.6e-35
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE..TTCSSEEEEEEEES CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle..ketkkylinliDtP 78 
                                         ++++ghvDhGKtTL+d++  ++    ++g+ ++ +      +       T++  a sl   ++ +   + +iDtP
  gi|313125335|ref|YP_004035599.1|  20 PIVAVLGHVDHGKTTLLDKIRGSAVSEGEAGAITQ-HIGATAVPL-----DTVSQMAGSLVnpDDFDLPGLLFIDTP 90 
                                       5789*****************77777776555553.222222222.....23333333333223666789******* PP

                                       SSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHH CS
                          GTP_EFTU  79 GHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeive 144
                                       GH +Fs   +rg + +D+a++vvd+++G +pqt e l ++++ g+p++v+ NK+D +           +++++++ +
  gi|313125335|ref|YP_004035599.1|  91 GHHSFSTLRSRGGALADIAIVVVDVNDGFQPQTIEALDILKRTGTPFVVAANKIDTTpgwnpndgspiQETYENQSD 167
                                       ****************************************************************9999999999999 PP

                                       HHHHHHHHH...............HHHHHHHHHTTT........TTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 145 evkqklsrk...............eeklekygekge........kevpvvfgSalkgegvktllealv 189
                                       +++q+l+++               +                   k+v vv+ Sa++geg+ +ll +l+
  gi|313125335|ref|YP_004035599.1| 168 NARQRLDQNlyeiignlsdegfsaD----------LywrvqnfqKNVGVVPLSAMTGEGIPDLLAVLM 225
                                       9999998887777666555555433..........04444555568******************9887 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                       HHHH CS
                          GTP_EFTU 138 elke 141
                                       e++e
  gi|313125335|ref|YP_004035599.1| 452 EYEE 455
                                       2222 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.1   6.9e+03      13      29 ..     270     285 ..     264     299 .. 0.71
   2 !   86.6   0.1   3.6e-28   8.1e-25       1      85 [.     474     561 ..     474     562 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.1
                                       EETCCCEEEEEEEEEEE CS
                       GTP_EFTU_D4  13 frrsdpaivGvevlgGv 29 
                                        r+sd ++vG  v g +
  gi|313125335|ref|YP_004035599.1| 270 VRESDTIVVG-GVNGPI 285
                                       5889999999.555444 PP

  == domain 2  score: 86.6 bits;  conditional E-value: 3.6e-28
                                       S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE....EEEEEEEEEETTEEESEEETT-EEEEEEESS- CS
                       GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGr...evGeilqiqdkgkkleeakaGqevaisiegki 74 
                                       rP +++il++ vfr+s pa+vGvevl+G++k + +++k +G+   +vG+++ iq++g+ ++ea+aG++v+++i+g++
  gi|313125335|ref|YP_004035599.1| 474 RPCRFRILEDHVFRQSSPAVVGVEVLSGTLKNNANVVKWEGNettRVGQLSGIQEQGEDVSEARAGNRVSVAIDGPT 550
                                       799***********************************999733369****************************** PP

                                       TTTS--TT-EE CS
                       GTP_EFTU_D4  75 vGrqikegdil 85 
                                       vGrqi+egd+l
  gi|313125335|ref|YP_004035599.1| 551 VGRQIEEGDEL 561
                                       *********98 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.7   4.1e-25   9.2e-22       2     105 .]     351     454 ..     350     454 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 4.1e-25
                                       CCHHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH....STEEEEEESS CS
                              IF-2   2 eelfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa....snaiiigFnv 74 
                                       e++++ei+ +++e +v++kaD+ GsleA+++aL++      +v++++++vG++  +Dv  as+    +n++i+gFnv
  gi|313125335|ref|YP_004035599.1| 351 ESELAEIEVDTEEEGVVVKADTLGSLEAMANALREA-----EVPILRAEVGDVAPRDVAVASTaremENKVILGFNV 422
                                       5677889988899**********************8.....5*******************99776677******** PP

                                       SCTHHHHHCCCCC.TSEEEEESSHHHHHHHHH CS
                              IF-2  75 kvskkakklaeke.gvkirlynvIYkliddvk 105
                                       +v ++a+++ ek  +v++++ +vIY+li++++
  gi|313125335|ref|YP_004035599.1| 423 DVLANAEDELEKTgDVRLFKDDVIYQLIEEYE 454
                                       **********99868**************985 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.2   9.1e-13     2e-09       1      73 [.     258     335 ..     258     336 .. 0.95
   2 ?   -2.6   0.0       3.3   7.5e+03      33      48 ..     371     386 ..     355     399 .. 0.62
   3 !   18.0   1.1   1.2e-06    0.0027       3      71 ..     493     559 ..     492     561 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 9.1e-13
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEE.........ETTSEEEEEEEESSCCSGS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededea.........vaganaGvivaikgledai 67 
                                       G ++++++y+G +++ d+++++g n+    +ivt++++l+ ++++ ++          ++ a+aG+++a+++l+da 
  gi|313125335|ref|YP_004035599.1| 258 GATVDVVLYDGSVRESDTIVVGGvNG----PIVTEVRALLQPRPNAEIRtekrfdkveEVRAAAGIKIAAPDLDDA- 329
                                       789******************99887....9***********998888899************************8. PP

                                       STTCEE CS
                       GTP_EFTU_D2  68 ivGdtl 73 
                                       ++G+++
  gi|313125335|ref|YP_004035599.1| 330 MAGAPI 335
                                       ***986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.3
                                       EEEEEEEEETEEESEE CS
                       GTP_EFTU_D2  33 trissletfhededea 48 
                                        + +sle++ + ++ea
  gi|313125335|ref|YP_004035599.1| 371 DTLGSLEAMANALREA 386
                                       4567777777777777 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.2e-06
                                       EEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTC CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGd 71 
                                       v+++ v sGtlk + +v+    n+t     v++ s+++   ed+ ea+ag ++ v + ++ +   i+ Gd
  gi|313125335|ref|YP_004035599.1| 493 VVGVEVLSGTLKNNANVVKWEgNET---TRVGQLSGIQEQGEDVSEARAGNRVSVAIDGPTVGRQIEEGD 559
                                       899****************888887...455999999999999999999999999998888887777777 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   8.2e-11   1.8e-07       2     114 .]      22     143 ..      21     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 8.2e-11
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE................EEEEECGGCSSHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke................ielvDtpGliegase 62 
                                       va++G+   GK+tL+ ++ g+++  ++    T++i    v l+  +                + ++DtpG  +    
  gi|313125335|ref|YP_004035599.1|  22 VAVLGHVDHGKTTLLDKIRGSAVSEGEAGAITQHIGATAVPLDTVSqmagslvnpddfdlpgLLFIDTPG-HH---- 93 
                                       89*****************98777777777888887777764432234455555566666669*******.44.... PP

                                       HHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  63 ekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       + +  ++       ad++++vvd++ ++++p+  e  ++l++++ p+++++nk
  gi|313125335|ref|YP_004035599.1|  94 SFSTLRSRGG--AlADIAIVVVDVN-DGFQPQTIEALDILKRTGTPFVVAANK 143
                                       2222222222..237********87.88**********************998 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00022       0.5       1      33 [.      22      54 ..      22      61 .. 0.90
   2 ?    4.3   0.0     0.017        37      93     117 ..      74      98 ..      65     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33
                                      +av+G++ +GK+++l+++ g+++   +++ +T+
  gi|313125335|ref|YP_004035599.1| 22 VAVLGHVDHGKTTLLDKIRGSAVSEGEAGAITQ 54
                                      79********************98888888886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.017
                                       EEEEETTS-SEEEEE---B-SSSGT CS
                         Dynamin_N  93 lkilsllvkgltlvDlPGldsvnkr 117
                                       +++ +++ +gl ++D+PG +s  + 
  gi|313125335|ref|YP_004035599.1|  74 VNPDDFDLPGLLFIDTPGHHSFSTL 98 
                                       567789999*********9996554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   3.6e+03       1      17 [.      24      40 ..      24      52 .. 0.81
   2 ?   13.6   0.0     2e-05     0.044      84     233 ..      71     222 ..      45     229 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                        ATP_bind_1  1 vvGpaGsGKttfvgals 17
                                      v+G++  GKtt+  ++ 
  gi|313125335|ref|YP_004035599.1| 24 VLGHVDHGKTTLLDKIR 40
                                      7899999****998765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                        ATP_bind_1  84 eelekeed....dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrle 156
                                        +l + +d     +l +DtPG   + t+++ +     +L+     +++++vD++       f  +++ al ++ r++
  gi|313125335|ref|YP_004035599.1|  71 GSLVNPDDfdlpGLLFIDTPGHHSFSTLRSRGG----ALA----DIAIVVVDVNDG-----FQPQTIEALDILKRTG 134
                                       44434444423348999*************999....444....566666666544.....33444556999***** PP

                        ATP_bind_1 157 lPhvvvlnkfDllkek...lekeleffedvealslllekee........ekykklaeaiaelleefalvlrflplss 222
                                       +P+vv+ nk+D        +   ++   + ++ ++ + +++           +   +++   +++f+ +  ++pls+
  gi|313125335|ref|YP_004035599.1| 135 TPFVVAANKIDTTPGWnpnDGSPIQETYENQSDNARQRLDQnlyeiignLSDEGFSADLYWRVQNFQKNVGVVPLSA 211
                                       ***********965433332223333333333333333333556666432223344556666777777777777777 PP

                        ATP_bind_1 223 ekeesiedlls 233
                                        ++e+i dll+
  gi|313125335|ref|YP_004035599.1| 212 MTGEGIPDLLA 222
                                       77777777765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.4e-05      0.21       2     119 ..      22     145 ..      21     146 .. 0.72
   2 ?   -3.2   0.0       4.3   9.5e+03      22      44 ..     484     506 ..     479     517 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.4e-05
                                       EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEE.EECGGSG.GCTTBTTTTCEEEEEEEE-SGGCTTTT CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdflt.kevtkik.gvendkkvkkvklniWDtaGqerfrsl 72 
                                       v ++G    GKt+ll+++  + +se e    ++ ig++ +   +v+++  ++ n ++ +   l + Dt G+  f++l
  gi|313125335|ref|YP_004035599.1|  22 VAVLGHVDHGKTTLLDKIRGSAVSEGEagaiTQHIGATAVPlDTVSQMAgSLVNPDDFDLPGLLFIDTPGHHSFSTL 98 
                                       5789****************999987622224667777665344445542445777777788999************ PP

                                       -HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                               Roc  73 hplylreaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiD 119
                                       ++     a++ai+v+d ++  +  + ++ l+   +  +p+++ +nkiD
  gi|313125335|ref|YP_004035599.1|  99 RSRGGALADIAIVVVDVNDGFQ-PQTIEALDILKRtGTPFVVAANKID 145
                                       ***************9765433.2334455444331468889999998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.3
                                       -CCC-EEETTTTEEEEEEECGGS CS
                               Roc  22 dkfsekekstigvdfltkevtki 44 
                                       + f++++ + +gv++l+ ++++ 
  gi|313125335|ref|YP_004035599.1| 484 HVFRQSSPAVVGVEVLSGTLKNN 506
                                       45778888899999988776543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 3356.68
//
Query:       gi|313125336|ref|YP_004035600.1|  [L=81]
Description: hypothetical protein Hbor_05600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-10   39.7   0.0    4.3e-10   39.5   0.0    1.1  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   2.4e-14   4.3e-10       4      73 ..       4      80 ..       1      81 [] 0.94

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.4e-14
                                      CCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.............-EEEEEGG.CEECCCTEEEET CS
                               PRC  4 frasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi........gekevliPfdlavkigkdriivd 73
                                      + a +l Gk V+ +dG++lG ++++ ++ k+g+++ l+vs  +   +        ++ ++ +P+  +v ++kd+i+v+
  gi|313125336|ref|YP_004035600.1|  4 VLAENLSGKAVMGSDGTELGMLYNITMNLKTGKLHDLLVSPHEEIHPdqfsfqqdEQGRFCVPVS-RVQAVKDYIVVQ 80
                                      67899************************************998766******************.**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 474.84
//
Query:       gi|313125337|ref|YP_004035601.1|  [L=152]
Description: nucleic acid-binding protein with pin domain and zn ribbon [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-10   41.8   0.0    2.1e-10   41.0   0.0    1.4  1  PIN_6           PIN domain of ribonuclease
    0.00021   20.8   0.1    0.00029   20.3   0.1    1.3  1  PIN_5           PINc domain ribonuclease
      0.002   18.1   1.0     0.0033   17.4   1.0    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0025   17.9   2.2     0.0061   16.6   2.2    1.6  1  Zn-ribbon_8     Zinc ribbon domain
     0.0066   16.4   0.1      0.017   15.0   0.1    1.8  2  DUF4411         Domain of unknown function (DUF4411)
  ------ inclusion threshold ------
      0.012   15.5   0.7      0.019   14.9   0.7    1.2  1  zinc-ribbons_6  zinc-ribbons
      0.014   15.7   0.1      0.025   14.9   0.1    1.4  1  C1_2            C1 domain
      0.028   14.3   1.1      0.041   13.8   1.1    1.2  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.036   14.5   0.1      0.058   13.8   0.1    1.3  1  DUF2710         Protein of unknown function (DUF2710)
      0.048   14.4   0.2      0.065   14.0   0.2    1.2  1  zinc_ribbon_15  zinc-ribbon family
      0.049   13.7   0.9      0.074   13.1   0.9    1.2  1  DZR             Double zinc ribbon
      0.063   13.4   0.1      0.078   13.1   0.1    1.2  1  Mut7-C          Mut7-C RNAse domain
       0.07   13.6   1.9        5.4    7.7   0.5    2.4  2  zf-C2H2         Zinc finger, C2H2 type
       0.13   12.4   0.4       0.24   11.6   0.4    1.4  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.14   13.1   1.3         12    7.1   0.3    2.4  2  zf-C2H2_4       C2H2-type zinc finger
       0.17   11.8   1.3       0.27   11.1   1.3    1.4  1  Prok-RING_4     Prokaryotic RING finger family 4
       0.21   11.4   1.1        1.4    8.8   0.7    2.2  2  Rad50_zn_hook   Rad50 zinc hook motif
       0.29   11.0   2.7       0.46   10.4   2.7    1.3  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
       0.34   10.9   3.2       0.96    9.4   3.2    1.7  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.51   10.3   8.0       0.23   11.4   0.8    2.4  2  zf-C2HC_2       zinc-finger of a C2HC-type


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   2.3e-13   2.1e-10       2      89 .]       3      85 ..       2      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.3e-13
                             PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktDi 80
                                      VlD++a+i++      ++ ++   +p V +E+  +++ +  ++   ++++  P +  v+k++++a +tGD ++LS+tDi
  gi|313125337|ref|YP_004035601.1|  3 VLDSSAFIHE-----YHTDDQTASIPLVSDELEGEASFRFDAMEGAGMHIHIPASGTVEKIRRAAGETGDRETLSDTDI 76
                                      9*******99.....567889999*********9998876666668********************************* PP

                             PIN_6 81 evlALtyeL 89
                                      ++lA ++eL
  gi|313125337|ref|YP_004035601.1| 77 RLLAAAFEL 85
                                      *****9997 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   3.2e-07   0.00029     156     190 ..      72     106 ..      25     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.2e-07
                             PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlr 190
                                       s  D+ +l  A ELda++v++D  ++++ae++ ++
  gi|313125337|ref|YP_004035601.1|  72 SDTDIRLLAAAFELDATLVTDDYAMQNVAERVNVH 106
                                       455666666678*******************9886 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.0   3.7e-06    0.0033      63      95 ..     106     145 ..      48     149 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                                       E.........EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  63 e.........ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       +          e+ + +++C+ Cg+ef+++++  rCp Cg +
  gi|313125337|ref|YP_004035601.1| 106 HvnviaqdgiEEQRDWRFQCQGCGREFDEHKD--RCPICGME 145
                                       3445555553457789************8866..9****975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.2   6.8e-06    0.0061       6      38 ..     123     148 ..     121     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.8e-06
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsevrr 38 
                                       ++C+ Cg+ef++           CP Cg e+ r
  gi|313125337|ref|YP_004035601.1| 123 FQCQGCGREFDEHK-------DRCPICGMELAR 148
                                       99*********663.......45*****97766 PP

>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         2   1.8e+03       2      13 ..       3      14 ..       3      23 .. 0.80
   2 !   15.0   0.1   1.9e-05     0.017      91     146 ..      61     115 ..       8     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                           DUF4411  2 llDtnvfieakr 13
                                      +lD+++fi+++ 
  gi|313125337|ref|YP_004035601.1|  3 VLDSSAFIHEYH 14
                                      69*****98764 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.9e-05
                           DUF4411  91 ekyskaakkeflsvaDpfliAaAlaknatvVTkEvkkpnkkknkvkI.Pdvcealgi 146
                                       ++ ++  + e ls  D +l+AaA + +at+VT + + +n  + +v +  +v ++ gi
  gi|313125337|ref|YP_004035601.1|  61 AAGET-GDRETLSDTDIRLLAAAFELDATLVTDDYAMQNVAE-RVNVhVNVIAQDGI 115
                                       33333.367888***********************9666666.66665555555555 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.7   2.2e-05     0.019      12      40 ..     118     147 ..     109     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                                       E-SSEEE-TTT--EEEEE.EE-SSS-S--- CS
                    zinc-ribbons_6  12 krgeqyhCeaCqedlkke.alCpeCeqele 40 
                                       +r+ +++C+ C ++++++   Cp C+ el 
  gi|313125337|ref|YP_004035601.1| 118 QRDWRFQCQGCGREFDEHkDRCPICGMELA 147
                                       666899*********976268*****9986 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   2.8e-05     0.025      11      40 ..     115     144 ..      99     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                              C1_2  11 kgedssesfnCsaCgrkidgffYsCseCdf 40 
                                       ++e+++ +f+C++Cgr+ d+ + +C++C  
  gi|313125337|ref|YP_004035601.1| 115 IEEQRDWRFQCQGCGREFDEHKDRCPICGM 144
                                       6789999**********888889***9*75 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.1   4.5e-05     0.041      26      46 ..     125     145 ..     121     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-05
                                       -HHHHHHHHHTT-B-TTT--B CS
                        zf-C3HC4_3  26 CeeCaekllkrkkkCpiCrrp 46 
                                       C+ C +++ ++k++CpiC  +
  gi|313125337|ref|YP_004035601.1| 125 CQGCGREFDEHKDRCPICGME 145
                                       ********99********876 PP

>> DUF2710  Protein of unknown function (DUF2710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.5e-05     0.058      47      97 ..      64     118 ..      53     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
                           DUF2710  47 dlgdvravansdgrllelt..lhpgvvs.dyayselaerlnlvitalr.eeveae 97 
                                       + gd  +++++d rll  +  l  ++v+ dya  ++aer+n+ +  +  + +e +
  gi|313125337|ref|YP_004035601.1|  64 ETGDRETLSDTDIRLLAAAfeLDATLVTdDYAMQNVAERVNVHVNVIAqDGIEEQ 118
                                       5689999999*****975522677766537************9987751445544 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   7.3e-05     0.065      64      86 .]     116     143 ..      86     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.3e-05
                    zinc_ribbon_15  64 e.....kkeCknCgkeveeefkyCpkCg 86 
                                       e       +C+ Cg+e +e+ + Cp Cg
  gi|313125337|ref|YP_004035601.1| 116 EeqrdwRFQCQGCGREFDEHKDRCPICG 143
                                       144455789******************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.9   8.3e-05     0.074       1      22 [.     125     146 ..     115     151 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-05
                               DZR   1 CpqCgeelppdarfCseCgtkl 22 
                                       C+ Cg+e ++++  C+ Cg +l
  gi|313125337|ref|YP_004035601.1| 125 CQGCGREFDEHKDRCPICGMEL 146
                                       5555555555555555555554 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.7e-05     0.078      29     102 ..      73     148 ..      52     152 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.7e-05
                            Mut7-C  29 vedeellalaakekrillTrdreLlkraklkkg.vll.tsrdveeqlreviarlglklslkpelsrCvaCngelee 102
                                        +d +lla a + + +l+T d ++ + a+ ++  v +  ++ +eeq    ++  g+  +++++ +rC  C  el++
  gi|313125337|ref|YP_004035601.1|  73 DTDIRLLAAAFELDATLVTDDYAMQNVAERVNVhVNViAQDGIEEQRDWRFQCQGCGREFDEHKDRCPICGMELAR 148
                                       3788999***************9998888887664343888899999888999999999************99986 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.5     0.006       5.4       1      10 [.     123     132 ..     123     136 .. 0.91
   2 ?    5.0   0.0     0.042        38       2      12 ..     138     148 ..     137     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.006
                                       EEETTTTEEE CS
                           zf-C2H2   1 ykCpdCgksF 10 
                                       ++C +Cg+ F
  gi|313125337|ref|YP_004035601.1| 123 FQCQGCGREF 132
                                       89******99 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.042
                                       EETTTTEEESS CS
                           zf-C2H2   2 kCpdCgksFkr 12 
                                       +Cp+Cg+   r
  gi|313125337|ref|YP_004035601.1| 138 RCPICGMELAR 148
                                       7*****97766 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00027      0.24       1      32 [.     115     145 ..     115     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                      NOB1_Zn_bind   1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnk 32 
                                       i++ + w  +C++C + + d +k  Cp CG +
  gi|313125337|ref|YP_004035601.1| 115 IEEQRDWRFQCQGCGREF-DEHKDRCPICGME 145
                                       78899**********976.567888*****75 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3     0.013        12       1      13 [.     123     135 ..     123     137 .. 0.84
   2 ?    4.7   0.0     0.077        69       2      13 ..     138     149 ..     138     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                         zf-C2H2_4   1 fkCpiCgksFssk 13 
                                       f+C  Cg+ F  +
  gi|313125337|ref|YP_004035601.1| 123 FQCQGCGREFDEH 135
                                       89********765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.077
                         zf-C2H2_4   2 kCpiCgksFssk 13 
                                       +CpiCg    +k
  gi|313125337|ref|YP_004035601.1| 138 RCPICGMELARK 149
                                       6****9887665 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3    0.0003      0.27      21      45 ..     125     151 ..     123     152 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                       Prok-RING_4  21 CkeCfdskdls..sCPlCqrrisksdp 45 
                                       C+ C  + d    +CP+C  ++++++p
  gi|313125337|ref|YP_004035601.1| 125 CQGCGREFDEHkdRCPICGMELARKNP 151
                                       99998887655579*******998876 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.032        29      25      33 ..     128     136 ..     125     138 .. 0.88
   2 ?    8.8   0.7    0.0015       1.4      16      29 ..     133     146 ..     130     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.032
                                       T--EE-HHH CS
                     Rad50_zn_hook  25 CgReldeeh 33 
                                       CgRe+de++
  gi|313125337|ref|YP_004035601.1| 128 CGREFDEHK 136
                                       *******98 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                                       TT-SEE-TTT--EE CS
                     Rad50_zn_hook  16 keakgcCPlCgRel 29 
                                        e+k++CP Cg el
  gi|313125337|ref|YP_004035601.1| 133 DEHKDRCPICGMEL 146
                                       68999******888 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.7   0.00051      0.46      23      40 .]     125     142 ..     121     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00051
                        zf-C3HC4_2  23 CqkCilrsLeekneCPlC 40 
                                       Cq C ++  e+k++CP+C
  gi|313125337|ref|YP_004035601.1| 125 CQGCGREFDEHKDRCPIC 142
                                       *******766666***** PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.2    0.0011      0.96       6      27 ..     124     143 ..     119     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                       Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCg 27 
                                       +C+ Cg+e++e +D   Cp Cg
  gi|313125337|ref|YP_004035601.1| 124 QCQGCGREFDEHKD--RCPICG 143
                                       8***********99..7****9 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   0.00026      0.23       3      12 ..     123     132 ..     122     135 .. 0.88
   2 ?    2.4   1.3      0.17   1.5e+02       5       9 ..     139     143 ..     138     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                         zf-C2HC_2   3 vpCpkCgRsF 12 
                                        +C++CgR F
  gi|313125337|ref|YP_004035601.1| 123 FQCQGCGREF 132
                                       69******** PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.17
                         zf-C2HC_2   5 CpkCg 9  
                                       Cp+Cg
  gi|313125337|ref|YP_004035601.1| 139 CPICG 143
                                       ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 883.00
//
Query:       gi|313125338|ref|YP_004035602.1|  [L=249]
Description: metal-dependent membrane protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-14   53.4  11.1    8.7e-14   51.7  11.1    2.1  1  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7  11.1   4.9e-18   8.7e-14       5      92 .]     140     233 ..      18     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 4.9e-18
                                       HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG......HHHHHHHHHHHHHHHHHHHH CS
                              CPBP   5 llvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn......gpsvllaalaGlvlgylylk 75 
                                       l  + ++lll++ +EEl+fRg+++ l+++ ++  +ai+ ss+ F+ +H+         +s+++++++G vlg++y+k
  gi|313125338|ref|YP_004035602.1| 140 LYYIPVTLLLVAPTEELVFRGVVQGLFRREYGVPFAIAGSSLTFASIHATSftgegaVVSLIVVLILGGVLGIVYEK 216
                                       4455569999******************998889***************999999855559**************** PP

                                       TT-HHHHHHHHHHHHHH CS
                              CPBP  76 tgsllaaillHallnll 92 
                                       + sl++++++H+l+n++
  gi|313125338|ref|YP_004035602.1| 217 SESLVVPVVAHGLYNTV 233
                                       ***************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1398.65
//
Query:       gi|313125339|ref|YP_004035603.1|  [L=430]
Description: glucose-6-phosphate isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-27   94.9   0.0    3.4e-25   88.6   0.0    2.1  2  PGI       Phosphoglucose isomerase


Domain annotation for each model (and alignments):
>> PGI  Phosphoglucose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   1.9e-29   3.4e-25      97     309 ..      70     276 ..      62     285 .. 0.88
   2 !    4.1   0.0   0.00077        14     415     464 ..     359     408 ..     351     422 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 1.9e-29
                                       -EEEEE--GGGTHHHHHHHHHTGGG-TT-EEEEE--SSHHHHHHHHTT--GGGEEEEEE-SSS--HHHHHHHHHHHH CS
                               PGI  97 tdvvniGiGGsdlGPvlvtealkkeserlkvafvsnvdgthiaevlkkldpettlfivasktfttaetllnaesake 173
                                       + vv +GiGGs+lG   + + l    +  +  ++ nvd+ h+ + l +l   +t++ v+s+  ttaetl n   +++
  gi|313125339|ref|YP_004035603.1|  70 EAVVTVGIGGSALGAATLSAGLSGP-DDPEAYYLDNVDPEHVTRLLDSLSLSETVVNVVSRSGTTAETLSNFLVVRD 145
                                       679***************9999865.556699********************************************* PP

                                       HHHHHH--GGGGGGTEEEESS-HHHHHHHT-.-GGGEEE--TTS-GGG-TTSGGGHHHHHHH-HHHHHHHHHHHHHH CS
                               PGI 174 wllkalkedsavakhfvalstnaekveefGi.deknmfefwdwvGGryslwsaiGlsvalsiGfenfeelleGaaai 249
                                       ++ +a ++ +  ++ fv+    + + +++    +   +   d v Gr+s  s++Gl+va   G++ +e+ll Ga+a 
  gi|313125339|ref|YP_004035603.1| 146 AMESAGVDWT--ERTFVTTGE-EGNLRNLAAkHDLPSLPVPDGVPGRFSALSTVGLAVAAIQGHD-LEALLAGAQAE 218
                                       ****999644..778877555.455555554156789***********************99987.8********99 PP

                                       HHHHHHS-GGG-HHHHHHHHHHHHHHTS---EEEEEES-GGGTTHHHHHHHHHHHHH--- CS
                               PGI 250 dkhfleaplekniPvllalvgvwyvnflgaeteailpydqylerlaaylqqldmesnGks 309
                                          +  + +e   P  +  +  +  + +ga t+a++py++ le +a ++ ql  es Gk 
  gi|313125339|ref|YP_004035603.1| 219 ADRLSGSLFES--PAYAYGAASYALANRGALTNAMMPYSEDLEYFAEWFAQLWAESLGKD 276
                                       99999999997..555555678999*********************************95 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.00077
                                       EEEEEEE--HHHHHHHHHHHHHHHHHHHHHHTB-TT--GGGHHHHHHHHH CS
                               PGI 415 nsillekltpaelGalialyehkilvqGviwginsfdqwGvelGkelakk 464
                                         + ++++  + lG l+   e   +  G + g+ +f q  ve Gk+ a+ 
  gi|313125339|ref|YP_004035603.1| 359 IRVEIDDVDERGLGELLYGMEAACVLYGELAGVSTFTQPAVEWGKRAARG 408
                                       556677888899*********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2421.34
//
Query:       gi|313125340|ref|YP_004035604.1|  [L=177]
Description: hypothetical protein Hbor_05640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.4   1.1       0.23   11.7   1.1    1.4  1  DUF872    Eukaryotic protein of unknown function (DUF872)
       0.27   11.4   3.2        7.9    6.7   0.0    2.4  2  DUF3976   Domain of unknown function (DUF3976)
       0.72    8.8   9.0          2    7.4   9.0    1.8  1  DUF898    Bacterial protein of unknown function (DUF898)
        2.1    8.8   5.5        4.4    7.8   5.5    1.7  1  DUF805    Protein of unknown function (DUF805)
        7.2    6.4  10.7        9.4    6.0   4.4    2.5  2  DUF2157   Predicted membrane protein (DUF2157)
        7.7    7.3  13.0        2.8    8.8   5.3    2.2  2  DUF4282   Domain of unknown function (DUF4282)


Domain annotation for each model (and alignments):
>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.1   7.6e-05      0.23      47      97 ..      34      86 ..      10      96 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.6e-05
                            DUF872 47 laallLlllGlvLl.llgvvilvep.seGvssavflvlGlllfiPGvYhvvyi 97
                                      + a++ l++ ++L+ l+g + +++  +   s a ++v+Gll+++P v  + ++
  gi|313125340|ref|YP_004035604.1| 34 AVAFISLFIVIALIvLVGQTAAIQGgQLTLSRAFYIVVGLLVILPAVAPTLVV 86
                                      34444444444443145666555552445666777**********99877665 PP

>> DUF3976  Domain of unknown function (DUF3976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.5      0.04   1.2e+02      24      41 .]      30      47 ..      22      50 .. 0.67
   2 ?    6.7   0.0    0.0026       7.9       9      30 ..      56      77 ..      54      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.04
                           DUF3976 24 iGCLvVmliaviVmiVLv 41
                                         L+V +i++ ++i L+
  gi|313125340|ref|YP_004035604.1| 30 CSALAVAFISLFIVIALI 47
                                      456999999965555444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0026
                           DUF3976  9 vtkdnTLT.KRGFYKliGCLvVm 30
                                      + +++ LT  R FY ++G Lv++
  gi|313125340|ref|YP_004035604.1| 56 I-QGGQLTlSRAFYIVVGLLVIL 77
                                      4.89999966********99874 PP

>> DUF898  Bacterial protein of unknown function (DUF898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   9.0   0.00068         2     166     250 ..       9      86 ..       5     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00068
                            DUF898 166 fGasrfkfeakvgdfykiwlaavllfllglvlliallaalltevlakeaaatadaskseaellklavllilalvlll 242
                                       fGa +  f+++ ++++k +++  +l+++++ l+i++++++l +  a+ +  + + s++  +++     ++ +lv+l+
  gi|313125340|ref|YP_004035604.1|   9 FGAFPYAFRQSRSRLFKSYVVCSALAVAFISLFIVIALIVLVGQTAAIQGGQLTLSRA--FYI-----VVGLLVILP 78 
                                       899999*******************************999887777666555554443..322.....222222223 PP

                            DUF898 243 lallaaay 250
                                       ++++++++
  gi|313125340|ref|YP_004035604.1|  79 AVAPTLVV 86 
                                       33333332 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.5    0.0015       4.4      16      68 ..      38      94 ..      14     172 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                            DUF805 16 fvlfllllvivlallaavlaa.........aavasalsvvlallllvps..lavtvRRlHDtgr 68
                                      + lf++++ ivl+       +          ++  a+ +v++ll+++p+   +++v R H +g 
  gi|313125340|ref|YP_004035604.1| 38 ISLFIVIALIVLV-------GqtaaiqggqLTLSRAFYIVVGLLVILPAvaPTLVVARRHRRGI 94
                                      1222222222222.......24455677888899999999999999999663455555565554 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.4    0.0032       9.4      97     139 ..      34      76 ..       8      83 .. 0.82
   2 ?    5.6   1.1    0.0041        12      69     138 ..      74     148 ..      62     159 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0032
                           DUF2157  97 allllaalllgaaialvgqifqlsgdaysllllwalllllmay 139
                                       a+++++ +++ a+i+lvgq+  ++g   +l  +  +++ l+++
  gi|313125340|ref|YP_004035604.1|  34 AVAFISLFIVIALIVLVGQTAAIQGGQLTLSRAFYIVVGLLVI 76 
                                       7789999*****************9999998666555555544 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0041
                           DUF2157  69 lllvllllslllgavlwrdr.......rvpprlgeallllaalllgaaialvgqifqlsgdaysllllwalllllma 138
                                       l+++++++  l++a+  r+r       r + +l+ a +l+   l+++a+a + ++f l g++ +  +  +l++ +++
  gi|313125340|ref|YP_004035604.1|  74 LVILPAVAPTLVVAR--RHRrgiesspRYEVALAIAGYLFLLSLYLGAVASMPETFVLDGETVARPAPTGLFAPVIS 148
                                       223333333333333..333678777666666677777777788999999999999999998877776666665555 PP

>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.3   0.00093       2.8       4      63 ..      24      87 ..      23      96 .. 0.72
   2 ?    3.2   0.8     0.049   1.5e+02      20      60 ..     104     157 ..     100     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00093
                           DUF4282  4 FnrfitpkllkvlYilgivlialvllslivgafaal....seslsagggllllllaviafllmi 63
                                      F++++  + l v++i ++++ial++l++  +a++      s+++ +++gll +l av   l+ +
  gi|313125340|ref|YP_004035604.1| 24 FKSYVVCSALAVAFISLFIVIALIVLVGQTAAIQGGqltlSRAFYIVVGLLVILPAVAPTLVVA 87
                                      999**********************966665555554434666666666666666666665554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.049
                           DUF4282  20 givlialvllslivgafaal.............seslsagggllllllaviafl 60 
                                       ++++  l+llsl +ga+a++              +++++++ +++ll+a+ +++
  gi|313125340|ref|YP_004035604.1| 104 LAIAGYLFLLSLYLGAVASMpetfvldgetvarPAPTGLFAPVISLLYAIPQAF 157
                                       456667788888899999998888988887777777777777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.38s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 994.54
//
Query:       gi|313125341|ref|YP_004035605.1|  [L=227]
Description: hypothetical protein Hbor_05650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-24   84.8   6.2    1.4e-23   83.7   6.2    1.6  1  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   6.2   7.6e-28   1.4e-23       1     119 [.      74     191 ..      74     192 .. 0.99

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 7.6e-28
                       SNARE_assoc   1 lPsevllvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrll 77 
                                       +P+++l +++G+lfg++ gt +++lg+++G+++++ l+r++g + ++++++  + +++++++  ++g++ l+ + ll
  gi|313125341|ref|YP_004035605.1|  74 IPGQTLGIVGGYLFGTVAGTAYSMLGVVIGSTVVFCLARRYG-RPFVERVIAADVLDRFDSFAAEHGVIGLFAVFLL 149
                                       79****************************************.********************************** PP

                       SNARE_assoc  78 pivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                       p++P+d+++++aG+t +++++F++  ++G +p+  ++a++G+
  gi|313125341|ref|YP_004035605.1| 150 PTFPDDAICALAGITTLRYRTFIALVAVGRLPTFALVALVGD 191
                                       ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1300.34
//
Query:       gi|313125342|ref|YP_004035606.1|  [L=201]
Description: phosphatidylserine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-08   34.9   0.1    1.9e-08   34.9   0.1    2.6  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
      0.019   14.7   1.2      0.019   14.7   1.2    1.8  2  PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-t
      0.069   13.1   0.1       0.16   11.9   0.1    1.6  1  Flavi_NS4A       Flavivirus non-structural protein NS4A
        0.9    8.9   6.1       0.11   11.9   1.4    1.7  2  ThrE             Putative threonine/serine exporter


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   4.2e-12   1.9e-08       2      66 .]       7      70 ..       6      70 .. 0.89
   2 ?   -0.8   2.3      0.61   2.7e+03       9       9 ..     155     155 ..      72     196 .. 0.63

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 4.2e-12
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      ++++++l+ l+ + + ++l+ +   + ++i+ +l  +++D lDG+ AR+ ++ s++G+++Ds++D
  gi|313125342|ref|YP_004035606.1|  7 VADWLSLAALFWAWVGAVLF-VQGEVNWGIVAVLGGFVFDKLDGYYAREHGTPSSFGRQIDSFID 70
                                      6899*******999999866.4444799999999******************9*********998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.61
                                       H CS
                   CDP-OH_P_transf   9 l 9  
                                       +
  gi|313125342|ref|YP_004035606.1| 155 A 155
                                       1 PP

>> PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.16   7.2e+02     175     232 ..      17      78 ..       4      88 .. 0.47
   2 ?   14.7   1.2   4.3e-06     0.019     118     189 ..      90     163 ..      84     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.16
                   PhoLip_ATPase_C 175 twtliliililgsillyflfl............llyssllpsssefygvleelfsspsfwlvlllvvvva 232
                                       +w ++  +l++                      +++ +l  ++ +  g+ +++ +++  ++ ++  +v a
  gi|313125342|ref|YP_004035606.1|  17 FWAWVGAVLFVQ--------GevnwgivavlggFVFDKLDGYYAREHGTPSSFGRQIDSFIDIFTYLVSA 78 
                                       343333332222........02222222223333444444447777777777777766555555555444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.3e-06
                   PhoLip_ATPase_C 118 wileglyqsliifflsylvlddssfs..dgktndlqlfgtlvftalvlvvnlkvaletktwtliliililgsil 189
                                       wi+ +++  ++++f  + +++ ++    +  +++++   t+v t+lv++vn  ++  + +w+ ++  l+++ ++
  gi|313125342|ref|YP_004035606.1|  90 WIASAVVGFVVLMFGGLRLIRHNDEGfvGDGDTSYYHGTTVVHTHLVVLVNYFLLQFVPFWNGWVAGLTIVAVC 163
                                       99999999999999988885555544668888999999999*************99999**9655555555443 PP

>> Flavi_NS4A  Flavivirus non-structural protein NS4A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.5e-05      0.16      79     112 ..      69     102 ..      61     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                        Flavi_NS4A  79 ialltviassallflasvkpthiaavillefvlm 112
                                       i + t + s+al++  +++p++ia +++ + vlm
  gi|313125342|ref|YP_004035606.1|  69 IDIFTYLVSAALVYHVAMRPHWIASAVVGFVVLM 102
                                       567788899******************9999999 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.4   2.4e-05      0.11     107     202 ..       8     109 ..       2     119 .. 0.81
   2 ?   -1.4   0.2      0.27   1.2e+03     141     168 ..     163     190 ..     129     197 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                              ThrE 107 prwlvvlaaglaaaafallfggdwidflvaflagllggllrlll.akrglnsfvleavaaflasllallavsl..gl 180
                                         wl ++a   a ++ +l+++g+++  +va+l+g++ + l  +  +++g++s +   + +f+  +++l+ ++l  ++
  gi|313125342|ref|YP_004035606.1|   8 ADWLSLAALFWAWVGAVLFVQGEVNWGIVAVLGGFVFDKLDGYYaREHGTPSSFGRQIDSFIDIFTYLVSAALvyHV 84 
                                       67999888888888888888********************98886889999**********9999997777753355 PP

                              ThrE 181 gln...pdaiiigsillLvPGlplt 202
                                       ++    ++ +++g ++l+  Gl l+
  gi|313125342|ref|YP_004035606.1|  85 AMRphwIASAVVGFVVLMFGGLRLI 109
                                       5554345888999999888888776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.27
                              ThrE 141 llggllrlllakrglnsfvleavaafla 168
                                       + ++   ++ +k    +f++ + +a+++
  gi|313125342|ref|YP_004035606.1| 163 CPLMTSEYKAPKTDNAHFLVAVGGAVTV 190
                                       3333333333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1141.75
//
Query:       gi|313125343|ref|YP_004035607.1|  [L=202]
Description: acetyltransferase (gnat) family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-14   53.2   0.0    4.7e-14   52.6   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.5e-08   34.7   0.0    4.6e-08   33.1   0.0    1.8  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.7e-08   34.3   0.0      5e-08   32.8   0.0    1.7  2  FR47             FR47-like protein
    2.6e-08   34.2   0.0    4.6e-08   33.4   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.1e-05   24.6   0.0    3.6e-05   23.8   0.0    1.3  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00013   22.7   0.0     0.0002   22.1   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0023   17.9   0.1     0.0043   17.0   0.1    1.4  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
     0.0078   16.3   0.0      0.017   15.3   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   2.1e-17   4.7e-14      23     117 .]      60     167 ..      43     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.1e-17
                                       H...HHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET.........TSTTEEEEEEEEESGGGTTSSHHHHHHHHHH CS
                    Acetyltransf_1  23 e...feesfsleae.gllvaeedgeliGfisllkipd.........ekggvayieslaVspeyrgkGlGsaLleale 86 
                                       +   +  +++l +e + ++a++d++++G++ ++ ++          ++ + +y+++++V p+yr++G+++aL+  + 
  gi|313125343|ref|YP_004035607.1|  60 VgneYGAFAELLPEeRVICALDDETIVGYLFVSLDTRhrihpleetLRFDGGYVRRVFVQPDYRNRGIATALVSRAR 136
                                       2334334444455527777***********555555455666677999999************************** PP

                                       HHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  87 erareegikkivlaveedndaairlYeklGF 117
                                       e+a ++ +++  + v  dn++++ l+e  GF
  gi|313125343|ref|YP_004035607.1| 137 EWAADRDATAAHALVARDNKPSRWLFEANGF 167
                                       ******9988866699**********99998 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0     2e-11   4.6e-08      30     111 ..      73     172 ..      52     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2e-11
                   Acetyltransf_10  30 ealllvaeeggkivGvi..elrdgs..............hisllfVdpeyrgqGigkaLleaveeeaekdgikl..e 88 
                                       e  ++ a ++++ivG++  +l++++              ++ ++fV+p+yr +Gi++aL+ +++e a +++     +
  gi|313125343|ref|YP_004035607.1|  73 EERVICALDDETIVGYLfvSLDTRHrihpleetlrfdggYVRRVFVQPDYRNRGIATALVSRAREWAADRDATAahA 149
                                       556677777888888875555333357778888888888**************************965555555577 PP

                   Acetyltransf_10  89 ltvnaspyavpfYeklGFkavge 111
                                       l ++ ++  + ++e  GF+av e
  gi|313125343|ref|YP_004035607.1| 150 LVARDNKPSRWLFEANGFEAVHE 172
                                       7777777*************965 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   3.1e+03      64      75 ..       9      20 ..       2      24 .. 0.73
   2 !   32.8   0.0   2.2e-11     5e-08      15      84 ..     104     174 ..      95     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                                      T-HHHHHHHHHH CS
                              FR47 64 sNtpsirlyekl 75
                                        + ++r+ye l
  gi|313125343|ref|YP_004035607.1|  9 RTDHARRVYETL 20
                                      456899999977 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 2.2e-11
                                       EEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEEEEEE CS
                              FR47  15 wilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfekieete 84 
                                       + lr dgg++  + v+p+ r+rG ++ lv+   +  a r+ t + ++v+ +N+ps+ l+e+ Gfe+  e +
  gi|313125343|ref|YP_004035607.1| 104 ETLRFDGGYVRRVFVQPDYRNRGIATALVSRAREWAADRDATaAHALVARDNKPSRWLFEANGFEAVHEHV 174
                                       78999**************************9999999887725799******************995543 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0     2e-11   4.6e-08       3      75 ..      74     168 ..      72     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2e-11
                                       EEEEEEEETTEEEEEEEEEEES...............TCTEEEEE-GGGTTSSHHHHHHH.HTT....SEEEEE.EE CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld...............aeitrlaVdpeyrgkGiGraLle.aae....kgiile.ql 58 
                                       ++v+ a dd+ ivG++ +sl+                ++  r++V p+yr++Gi++aL+  a+e    +  +   ++
  gi|313125343|ref|YP_004035607.1|  74 ERVICALDDETIVGYLFVSLDTrhrihpleetlrfdgGYVRRVFVQPDYRNRGIATALVSrAREwaadRDAT-AaHA 149
                                       6788899*******9999999899999998888877666666*****************7453233332211.2223 PP

                                       EE..THHHHHHHHHHTTEE CS
                    Acetyltransf_7  59 el..naekaikfYeklGFe 75 
                                        +  ++++++ ++e +GFe
  gi|313125343|ref|YP_004035607.1| 150 LVarDNKPSRWLFEANGFE 168
                                       33433335666*******8 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.6e-08   3.6e-05      34     108 ..      66     145 ..      52     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.6e-08
                                       HHHHHHTTSEEEEEEETTEEEEEEEE...EEEEEEETTEEEEE..EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT CS
                    Acetyltransf_9  34 yfrklleesrvlgaedngelvgqlal...lplelnvpGktlka..agvtgVavapehrgrgvlskLlaraleemree 105
                                       +f +ll e+rv+ a d++++vg l +   ++++++  ++tl+   ++v  V v p++r+rg++++L+ ra e ++++
  gi|313125343|ref|YP_004035607.1|  66 AFAELLPEERVICALDDETIVGYLFVsldTRHRIHPLEETLRFdgGYVRRVFVQPDYRNRGIATALVSRAREWAADR 142
                                       57889999**************875432356666665555544439**********************998877777 PP

                                       T-- CS
                    Acetyltransf_9 106 gqp 108
                                       +++
  gi|313125343|ref|YP_004035607.1| 143 DAT 145
                                       665 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.7e-08    0.0002      85     138 .]     116     168 ..      46     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.7e-08
                    Acetyltransf_3  85 ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                         ++p+++++G+at  v+ + e+a ++  ++   a ++ +N+ S+ ++e  Gfe
  gi|313125343|ref|YP_004035607.1| 116 VFVQPDYRNRGIATALVSRAREWAADRD-ATAAHALVARDNKPSRWLFEANGFE 168
                                       456799******************6666.999*********************7 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.9e-06    0.0043       7      31 ..     113     137 ..     112     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-06
                   Acetyltransf_13   7 isriWvssshRrkgiAtkLldaare 31 
                                       ++r++v +++R++giAt+L+  are
  gi|313125343|ref|YP_004035607.1| 113 VRRVFVQPDYRNRGIATALVSRARE 137
                                       89******************99986 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.5e-06     0.017      29      57 ..     115     143 ..     108     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.5e-06
                   Acetyltransf_CG  29 hTeVpeelrGkGiAkkLvkaalddareeg 57 
                                        ++V++ +r +GiA +Lv +a ++a +++
  gi|313125343|ref|YP_004035607.1| 115 RVFVQPDYRNRGIATALVSRAREWAADRD 143
                                       689******************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.58
# Mc/sec: 1050.01
//
Query:       gi|313125344|ref|YP_004035608.1|  [L=158]
Description: hypothetical protein Hbor_05680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 875.51
//
Query:       gi|313125345|ref|YP_004035609.1|  [L=304]
Description: glycosyl transferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-12   46.4   0.0    5.1e-12   45.6   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
    2.3e-10   40.6   0.1    3.7e-10   39.9   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.2e-06   28.6   0.0    1.9e-06   28.0   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   8.5e-16   5.1e-12       3     139 ..      54     183 ..      51     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 8.5e-16
                   Glyco_transf_21   3 vrrllvsgdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaal 79 
                                       vr l+++gdp+g++ K n+++ ++ aa++d +v+ D+d + +pd L++l a  e+   g V+ +p+ ++++ l +  
  gi|313125345|ref|YP_004035609.1|  54 VR-LVIAGDPEGCSGKANAIAVGMGAARHDRIVWTDDDFVHPPDWLDSLHADYER--HGPVSEVPFFVGRDPLSTLT 127
                                       66.9**************************************************7..9*****************99 PP

                   Glyco_transf_21  80 eaafl.ntlagvlqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraa 139
                                       e ++  +   g++q      + a+G ++++ r+++ +   ++al +++ +D  l+++l   
  gi|313125345|ref|YP_004035609.1| 128 EPLYAiGGTLGTYQD-----NKAWGGAVMFERDDIGETAFLAALCQTVSDDGLLSEHLDLT 183
                                       999976778888888.....789*****************************999988655 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.1   6.1e-14   3.7e-10      18     120 ..      20     121 ..      14     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 6.1e-14
                                       HHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHHHH--SSEEEEEESSEEE- CS
                   Glycos_transf_2  18 esllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv.GkagalnaglraatgdyilflDaDdepd 93 
                                       + +++q   pd+e+++v D++ D  ++ +++l  e+ r+ +   +e+  Gka+a+  g+ aa++d i++ D+D +++
  gi|313125345|ref|YP_004035609.1|  20 DDVASQ-LGPDDELLIVCDNDADPVAARADDLP-EGVRLVIAGDPEGCsGKANAIAVGMGAARHDRIVWTDDDFVHP 94 
                                       678999.9************************5.3555555566777789*************************** PP

                                       TTHHHHHHHHHHH.TTCEEEEEEEEEE CS
                   Glycos_transf_2  94 pdwleklvealekdgadvvlgqrprif 120
                                       pdwl  l + +e++g+   ++ ++ ++
  gi|313125345|ref|YP_004035609.1|  95 PDWLDSLHADYERHGPVSEVPFFVGRD 121
                                       ***************966666555554 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   3.1e-10   1.9e-06      24     121 ..      22     112 ..       4     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.1e-10
                   Glyco_tranf_2_3  24 llaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdDtvv 100
                                       +++q  p++e+ +v+d++ + ++++a+     lp  +vr+v+  +  g  gk++a++ ++ a+++d ++  DdD v 
  gi|313125345|ref|YP_004035609.1|  22 VASQLGPDDELLIVCDNDADPVAARADD----LPE-GVRLVIAGDPEGCSGKANAIAVGMGAARHDRIVWTDDDFVH 93 
                                       44544588***************99997....676.67777776655888*************************** PP

                   Glyco_tranf_2_3 101 ePdtlkrllqffltpkvgavg 121
                                        Pd l++l + +  +++g v 
  gi|313125345|ref|YP_004035609.1|  94 PPDWLDSLHADY--ERHGPVS 112
                                       ****99965544..6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1781.97
//
Query:       gi|313125346|ref|YP_004035610.1|  [L=128]
Description: hypothetical protein Hbor_05700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.0   2.3       0.24   11.0   2.3    1.5  1  Docking   Erythronolide synthase docking


Domain annotation for each model (and alignments):
>> Docking  Erythronolide synthase docking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.3   1.4e-05      0.24       2      17 ..      38      53 ..      38      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.4e-05
                           Docking  2 nEeKLRdYLKRvTaDL 17
                                      + ++ R YL+Rv  DL
  gi|313125346|ref|YP_004035610.1| 38 DTDRFRKYLRRVLDDL 53
                                      6799*********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 803.67
//
Query:       gi|313125347|ref|YP_004035611.1|  [L=296]
Description: protein translocase subunit secf [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-27   96.6  13.3    1.2e-27   96.6  13.3    1.7  2  SecD_SecF  Protein export membrane protein
      3e-06   26.5   0.0    9.2e-06   25.0   0.0    1.9  1  Sec_GG     SecD/SecF GG Motif
  ------ inclusion threshold ------
       0.12   10.4  14.3       0.17    9.9  14.3    1.1  1  Patched    Patched family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.15   8.9e+02      57      82 ..      20      45 ..      12      49 .. 0.57
   2 !   96.6  13.3     2e-31   1.2e-27      12     187 ..     119     290 ..     108     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.15
                                      HHHHHHHHHHHHHHHHHHHHHTT--- CS
                         SecD_SecF 57 alaaiialvhDviitvgvlsllgiev 82
                                      a   ++ l+  +++++g ++++g +v
  gi|313125347|ref|YP_004035611.1| 20 AAVPLAVLAVALLVVAGWYVATGAPV 45
                                      44444455555666666666666555 PP

  == domain 2  score: 96.6 bits;  conditional E-value: 2e-31
                                       -EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT----HHHH CS
                         SecD_SecF  12 daekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgievdlatv 87 
                                        +e++s+++v+++++++ ++ a+  +++a++++ i v+  F+  v++ a++  +++D++i v+++ +lgie++l tv
  gi|313125347|ref|YP_004035611.1| 119 GFEVRSISSVSANFGSDTQWLALGGVAAAFLGMSILVFAMFRSFVPSIAVVIsAFSDIVIPVALMNILGIELSLGTV 195
                                       5799*****************************************98776555************************ PP

                                       HHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHH CS
                         SecD_SecF  88 aalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalal 164
                                       aalL++iGYSv++++++ + +  +       ++ e + +++ + +t+t++ ++ ++++ ++  ++g + l+ + ++l
  gi|313125347|ref|YP_004035611.1| 196 AALLMLIGYSVDSDILLNNHILRR-----SGDFYESTYRAMRTGVTMTLTSIAAMIVMTITATIFGIQLLAAIGTVL 267
                                       *******************99987.....567777777777777777777777788899999*************** PP

                                       HHHTSTTTTTHHHHHHHHHHHHH CS
                         SecD_SecF 165 lvGlivgtyssifiasplllllk 187
                                       ++Gl+++ +++  ++  ll ++k
  gi|313125347|ref|YP_004035611.1| 268 VFGLAADLMNTYMLNLSLLRWYK 290
                                       *******************9997 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.5e-09   9.2e-06       6      26 ..      43      63 ..      39      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.5e-09
                                      C--EE-TTTS-EEEEEEEE-T CS
                            Sec_GG  6 kGlNLGlDFtGGthielqfdq 26
                                       ++N+G++FtGGt+i++ +d 
  gi|313125347|ref|YP_004035611.1| 43 APVNQGIEFTGGTEIQVVVDD 63
                                      699**************9986 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  14.3   2.9e-05      0.17     663     779 ..     144     267 ..     138     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 2.9e-05
                           Patched 663 ivlallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvd....lsaHi...a 732
                                       ++ a+l m++  + +  +++ ++++++s  s  +  + ++ + g++L   ++++++m iG+svd    l  Hi   +
  gi|313125347|ref|YP_004035611.1| 144 VAAAFLGMSILVFAMFRSFVPSIAVVISAFSDIVIPVALMNILGIELSLGTVAALLMLIGYSVDsdilLNNHIlrrS 220
                                       67889999999998888888888888888886666678**************************6666688993333 PP

                           Patched 733 yafvrsekddakeRvvealealgwPvvqgalSTilgvlvLlfvdsym 779
                                         f++s +   +  v+++l  ++  +v   + Ti g+ +L+ + + +
  gi|313125347|ref|YP_004035611.1| 221 GDFYESTYRAMRTGVTMTLTSIAAMIVMTITATIFGIQLLAAIGTVL 267
                                       46999999899999***************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1749.92
//
Query:       gi|313125348|ref|YP_004035612.1|  [L=523]
Description: preprotein translocase subunit secd [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-12   44.7   9.9    2.1e-11   43.6   9.9    1.5  1  SecD_SecF       Protein export membrane protein
    0.00054   19.8   3.1      0.001   18.9   3.1    1.4  1  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
  ------ inclusion threshold ------
      0.019   13.9  16.5      0.043   12.8  16.5    1.5  1  MMPL            MMPL family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   9.9   3.5e-15   2.1e-11      20     173 ..     355     505 ..     348     516 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.5e-15
                                       EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-H.HHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTT CS
                         SecD_SecF  20 tvgpsvskelaekavlallialvliliyvalrFew.rvalaaiialvhDviitvgvlsllgievdlatvaalLtiiG 95 
                                        +++  +  ++ ++++  +ia++++  +v++r+ + +va   i+++++ v+i++g+ +++g ++dl+++a+ + +iG
  gi|313125348|ref|YP_004035612.1| 355 YISSGQGASFKIDSLITGIIAVLAVSGVVFVRYSDvKVAAPMIVTALSEVVILLGFAAAIGYPLDLSVIAGFIAVIG 431
                                       5777788889999999999**************7538999************************************* PP

                                       SSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTT CS
                         SecD_SecF  96 YSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgt 172
                                         v+d +++ d v  + + ++r+ ++  + ++         ++ +tt++++  l +l  + l++fa+  ++G++vg+
  gi|313125348|ref|YP_004035612.1| 432 TGVDDLIIIADEVMAEGEVSSRRVFQSRFRKAF----WVIGAAAATTIIAMSPLAVLSLGDLQGFAIFTILGVLVGV 504
                                       *************99977777766666666665....5444678889999999***********************9 PP

                                       T CS
                         SecD_SecF 173 y 173
                                       +
  gi|313125348|ref|YP_004035612.1| 505 L 505
                                       7 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   3.1   1.7e-07     0.001       5     123 ..     389     505 ..     385     517 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-07
                                       HHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHH.HHHHCHHCCHHCHHHHHHHHTTTCHHHHHHHHHHH CS
                    Sterol-sensing   5 kfgLglagviivllsvasslgllaylgltltliilevlPfl.vlavgvdnifvlvkavqrtsrsldeseriaealge 80 
                                        + +++ +++++l+ v+  lg+ a++g++l l ++  + f+ v+  gvd+  ++  +v +  +  +     +  +++
  gi|313125348|ref|YP_004035612.1| 389 DVKVAAPMIVTALSEVVILLGFAAAIGYPLDLSVI--AGFIaVIGTGVDDLIIIADEVMAEGEV-SSRRVFQSRFRK 462
                                       567888899*********************99888..77774789*****99999998665444.434445566888 PP

                                       HCCCCHHCCCHHHHHHH.HHHHCCHHHHHHHHHHHHHHHHHHHH CS
                    Sterol-sensing  81 vgpsilltsltellall.lgaltdvpavqeFclfaavavlvdFl 123
                                       + + i + ++t ++a+  l+ + ++  +q F++f++++vlv  l
  gi|313125348|ref|YP_004035612.1| 463 AFWVIGAAAATTIIAMSpLA-VLSLGDLQGFAIFTILGVLVGVL 505
                                       88888888888888888777.77899*************98655 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  16.5   7.2e-06     0.043     140     292 ..     363     508 ..     320     511 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-06
                              MMPL 140 asdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGt 216
                                       +++ d+ ++++++++ +  + ++ y  +  a+ +++t++ ++++ lg+++    + g  l  +v+   ++ +i++G+
  gi|313125348|ref|YP_004035612.1| 363 SFKIDSLITGIIAVLAVSGVVFVRYSDVKVAAPMIVTALSEVVILLGFAA----AIGYPLDLSVI-AGFIAVIGTGV 434
                                       4455777778888888889999999999999999**********999944....34444544443.3688899**** PP

                              MMPL 217 DYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivl 292
                                       D  +++      e +  ++r   ++  ++++  v+ aa++t +iam  L+v++l+ l+++++   lGvlv vli++
  gi|313125348|ref|YP_004035612.1| 435 DDLIIIADEVMAEGEVSSRR--VFQSRFRKAFWVIGAAAATTIIAMSPLAVLSLGDLQGFAIFTILGVLVGVLITR 508
                                       *8888776655555555555..89999**********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3266.74
//
Query:       gi|313125349|ref|YP_004035613.1|  [L=69]
Description: hypothetical protein Hbor_05730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 441.30
//
Query:       gi|313125350|ref|YP_004035614.1|  [L=122]
Description: molecular chaperone [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.8e-19   67.7   0.0      1e-18   67.3   0.0    1.2  1  HSP20       Hsp20/alpha crystallin family
    4.7e-09   35.7   0.0    6.8e-09   35.2   0.0    1.2  1  ArsA_HSP20  HSP20-like domain found in ArsA


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   1.2e-22     1e-18       3     101 ..      31     120 ..      29     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.2e-22
                                       -SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETT CS
                             HSP20   3 keeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdG 79 
                                        ee+ ef +++++pg+++ee++v+ +d ++ v +ehe    de   ++    + + r+f+ P+nvd++ ++a++++G
  gi|313125350|ref|YP_004035614.1|  31 YEEDGEFVLSVEMPGFDPEEITVTWDDAVLNVAAEHE----DEARGRR----KTYHRRFRFPKNVDDEGIAATYNNG 99 
                                       68999********************************....4444555....699********************** PP

                                       EEEEEEEBSS--..-------- CS
                             HSP20  80 vLtvtvpkkepekkkkerkiqi 101
                                       +L+vt+p  +   +   ++i+i
  gi|313125350|ref|YP_004035614.1| 100 ILQVTLPVATGTTA-AGKQIEI 120
                                       ********999976.9999998 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   7.5e-13   6.8e-09       1      63 []      34     105 ..      34     105 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 7.5e-13
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig..........nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                       d+e+vl++++P++d+eei ++ ++  L + ++           ++R++  P+ ++++ +  A++++g L +++
  gi|313125350|ref|YP_004035614.1|  34 DGEFVLSVEMPGFDPEEITVTWDDAVLNVAAEhedeargrrkTYHRRFRFPKNVDDEGI-AATYNNGILQVTL 105
                                       79*******************************************************99.***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 782.76
//
Query:       gi|313125351|ref|YP_004035615.1|  [L=224]
Description: rnase hii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.9e-41  140.5   0.0    6.8e-41  140.3   0.0    1.0  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.3   0.0   3.8e-45   6.8e-41       1     198 []       9     209 ..       9     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 3.8e-45
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH....SEEEEEEE-HHHHH.HHTT CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik....kkiekrklvaeeikyasen 73 
                                       iG+DEaG+GpvlGp+v+aav  + ++ +     g++DSK L++ +ree+ + ++     ++  +++    i+     
  gi|313125351|ref|YP_004035615.1|   9 IGSDEAGKGPVLGPMVAAAVRAPADALP----DGIDDSKRLTSAQREEIDQTLRgrddVTVGVATIDPVRID---DP 78 
                                       7**********************99995....8*********************884444445555554444...56 PP

                                       TS-HHHHHHHHHHHHHHHHHHT..CEECCECCCE--SSHHHHHHHHHHHHC.....CEEEEETTGGGT-HHHHHHHH CS
                         RNase_HII  74 einlneikaaltlavikllekl..gvkvdeilvdgvttpeslkkkleqiik.....ikvtvekkadekyllvaaASi 143
                                       + + n++ +a++ a+  +++++   v  d+ +vd      ++ + +++ ++     + v+ e++ade+y+ v aAS+
  gi|313125351|ref|YP_004035615.1|  79 TTDMNSLTVAAHVAAVAAVAQDadEVVTDAGDVDE----SRFGRRVRTGVGdegtdVTVVSEHRADETYPHVGAASV 151
                                       66777777777777766666553377778888884....4555555555555554689999**************** PP

                                       HHHHHHHHHHHHHHHHCS.H.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHHH CS
                         RNase_HII 144 iAkverdeelellkrkpg.tldkgsGyasdektrallkkgats..klpdivrlsfktv 198
                                       +Akv+rd  +e + + ++   + gsGy+sd+ tr++l+ ++ +  +lpd++r s++t+
  gi|313125351|ref|YP_004035615.1| 152 VAKVRRDTLMETIGERYEdYGPVGSGYPSDPTTREFLRTYVSEtgELPDCARASWATC 209
                                       ******************************************999***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1447.82
//
Query:       gi|313125352|ref|YP_004035616.1|  [L=54]
Description: hypothetical protein Hbor_05760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 344.54
//
Query:       gi|313125353|ref|YP_004035617.1|  [L=427]
Description: hypothetical protein Hbor_05770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-08   33.1   0.1    1.1e-07   32.1   0.1    1.5  1  THUMP          THUMP domain
    8.4e-05   22.9   0.3    8.4e-05   22.9   0.3    2.6  3  DnaJ_CXXCXGXG  DnaJ central domain
  ------ inclusion threshold ------
      0.015   15.2   0.9      0.015   15.2   0.9    2.5  2  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1   1.8e-11   1.1e-07      56     143 ..      63     164 ..      42     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.8e-11
                                       EEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS.................SSHHHHHHHHHHHHHHCC CS
                             THUMP  56 vcevceadledileaakeivkkkfeeeketFaVrvkrrgkhf.................eftsreinrevGkaivek 115
                                       vce+ +a+++d  e   e v++  ++   t++V+++++   +                 e  + e+nrevGk++ ++
  gi|313125353|ref|YP_004035617.1|  63 VCEGECARFDDWAERCAESVEDVEFD---TYQVGTRAPPLVEenevllregaglpddagELFKSEFNREVGKRFGRL 136
                                       4999*********************9...**********9999********************************** PP

                                       TT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP 116 tglkVdlenPdivvrveiikdkayisid 143
                                       t+  V++ +Pd+ ++++i+ d++++ ++
  gi|313125353|ref|YP_004035617.1| 137 TETDVEFGRPDVQFLLDIDADTVEVEVN 164
                                       ***********************99776 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.7     1e+04      17      22 ..      17      22 ..      11      30 .. 0.64
   2 ?    2.0   0.2     0.047   2.8e+02      41      54 ..      58      71 ..      45      81 .. 0.60
   3 !   22.9   0.3   1.4e-08   8.4e-05       1      29 [.     186     213 ..     174     240 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                     DnaJ_CXXCXGXG 17 CktCkG 22
                                      C+ C G
  gi|313125353|ref|YP_004035617.1| 17 CDPCLG 22
                                      444444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.047
                     DnaJ_CXXCXGXG 41 qstCpeCeGtGkvi 54
                                      +++C  CeG+   +
  gi|313125353|ref|YP_004035617.1| 58 REDCWVCEGECARF 71
                                      34555566655555 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 1.4e-08
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsG.vvree 29 
                                       C+kC+Gsg     k+ C++C+G+G + +++
  gi|313125353|ref|YP_004035617.1| 186 CNKCHGSGY--LGKQPCDKCDGTGyMYQDS 213
                                       777777775..2345577777777333333 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.5      0.21   1.2e+03      11      18 ..      59      66 ..      50      71 .. 0.81
   2 ?   15.2   0.9   2.5e-06     0.015       6      42 ..     179     209 ..     175     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.21
                                      EE-TTTTT CS
                         Anti-TRAP 11 tkCdaCng 18
                                      + C+ C+g
  gi|313125353|ref|YP_004035617.1| 59 EDCWVCEG 66
                                      67999988 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.5e-06
                                       HHHCEEE-TTTTTTSEETTE......E-TTTTTSSEE CS
                         Anti-TRAP   6 lpeLEtkCdaCngsGkiepeeprasleCPkCsGkgli 42 
                                       +p+ E +C++C+gsG    +      +C kC G g +
  gi|313125353|ref|YP_004035617.1| 179 IPQTEWPCNKCHGSGYLGKQ------PCDKCDGTGYM 209
                                       68899************999......*******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.36s 00:00:01.04 Elapsed: 00:00:00.58
# Mc/sec: 2202.14
//
Query:       gi|313125354|ref|YP_004035618.1|  [L=103]
Description: hypothetical protein Hbor_05780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.0   0.1      0.078   12.5   0.0    1.7  2  DUF374    Domain of unknown function (DUF374)


Domain annotation for each model (and alignments):
>> DUF374  Domain of unknown function (DUF374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.3e-06     0.078       7      65 ..      20      78 ..      15      82 .. 0.92
   2 ?    0.8   0.0      0.02   3.6e+02      12      34 ..      75      98 ..      68     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-06
                            DUF374  7 klaaliSrsrDGeliarvlerlGiktirGSsskggaealremlralkegesvaitpDgP 65
                                       l +l+ r +DG+l  +v +rl+      S ++  +++lr +l+ ++ + ++a+ + gP
  gi|313125354|ref|YP_004035618.1| 20 SLTVLVTRDADGDLQEGVRARLDAVECVASVDRVDVSGLRPALNDMRVDLDAALRVSGP 78
                                      5789******************************************9999999988888 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.02
                            DUF374 12 iSrsrDGeliarvler.lGiktir 34
                                      +S   D+e +a++le  +G+k +r
  gi|313125354|ref|YP_004035618.1| 75 VSGPPDAESVADALEAgFGVKEVR 98
                                      677789999999998646888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 598.68
//
Query:       gi|313125355|ref|YP_004035619.1|  [L=347]
Description: pep phosphonomutase-like enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.5e-41  140.4   0.0    8.1e-41  140.0   0.0    1.1  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
    9.1e-30  103.6   1.5    2.4e-14   52.7   0.0    2.1  2  ICL         Isocitrate lyase family


Domain annotation for each model (and alignments):
>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   0.0     9e-45   8.1e-41       1     220 [.      27     264 ..      27     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 9e-45
                        PEP_mutase   1 lra.LhakgeplvlpnawDalsakiveeagfkalatsSlavaasl.GvpDgeelpleellaavraiaevvslPlivD 75 
                                       +r+ L ++ + +++p ++ al a+++e a  +a  +s++++   + G+pD e ++++e+++++++i+e+++lP+i+D
  gi|313125355|ref|YP_004035619.1|  27 FRRmLDEQ-NFVFAPGIYHALDARLAELADLDAAYMSGYSTVLGQfGFPDLEMVTMTEMVENAKRIVEATNLPVIAD 102
                                       78856666.9****************************98887767******************************* PP

                        PEP_mutase  76 ledGygespeevaetvrrliaaGvvgvniEDk....kknd.aerqlldieefaekiaaaraaaeeagfvinARtdal 147
                                       +++Gyg  + +v+++vr+ ++aGv++++iED+    +++  a++q+++ +++ ++ +aa++a+++++ +i+ARtda+
  gi|313125355|ref|YP_004035619.1| 103 CDTGYGG-VHNVRRAVREYEKAGVAAIHIEDQttpkRCGHiAGKQIISRDKARARFEAAVDAKQSEDTFIIARTDAY 178
                                       ******9.9***********************77643335699*********************************9 PP

                        PEP_mutase 148 llsagagleeaieRaraYaeAGAdgvfvpgl....qkdaeiaelvaavd.....vplnvvplkgt.........lsv 206
                                         s +++ ee +eR+r Ya+AG d+v   +     ++     + ++ ++     + l    + ++         l++
  gi|313125355|ref|YP_004035619.1| 179 G-SSNGDWEEHLERGRIYADAGVDMVWPEMPdpsrED---AVNYAETIHethpdLKLAFNYS-SSfawskeedpLTF 250
                                       9.68888*******************99777432222...3333333322323433333331.11234555678999 PP

                        PEP_mutase 207 aelaelGvarislg 220
                                       +el +lG + i + 
  gi|313125355|ref|YP_004035619.1| 251 EELGDLGYEYIFIT 264
                                       99999999999876 PP

>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.7     2e-17   1.8e-13     150     234 ..      97     178 ..      77     182 .. 0.83
   2 !   52.7   0.0   2.7e-18   2.4e-14     366     465 ..     186     282 ..     178     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 2e-17
                                       --EEEE-TT-SSSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHHT.T--- CS
                               ICL 150 rpiiadadtGhGGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadil.gsdl 225
                                        p+iad+dtG+GG+  v + ++ + + G a ihiedq+ + k+cGh+aGk +++ ++   r+ a+   +d     d+
  gi|313125355|ref|YP_004035619.1|  97 LPVIADCDTGYGGVHNVRRAVREYEKAGVAAIHIEDQT-TPKRCGHIAGKQIISRDKARARFEAA---VDAKqSEDT 169
                                       49***********************************8.579***********999988887654...444405689 PP

                                       EEEEE--GG CS
                               ICL 226 lvvartdse 234
                                       +++artd+ 
  gi|313125355|ref|YP_004035619.1| 170 FIIARTDAY 178
                                       9******85 PP

  == domain 2  score: 52.7 bits;  conditional E-value: 2.7e-18
                                       HHHHHHHHHHTTS.-SEEE---SS--HHHHHHHHHHHHTT-TT-EEEEE--SSS-GGGTS-HHHHHSHHHHHHHTTE CS
                               ICL 366 qcsvvravafapy.adliwmesklpdyaqakefaeGvkakvpeqklaynlspsfnwkkamsadeqetyikrlaklGy 441
                                       +  + r++ +a   +d++w e   p  ++a ++ae +++++p+ kla+n s sf w+k    ++  t  + l++lGy
  gi|313125355|ref|YP_004035619.1| 186 EEHLERGRIYADAgVDMVWPEMPDPSREDAVNYAETIHETHPDLKLAFNYSSSFAWSKE---EDPLT-FEELGDLGY 258
                                       556789999997537*****************************************863...44455.589****** PP

                                       EEEEETTHHHHHHHHHHHHHHHHH CS
                               ICL 442 vwqfitlaGlhtnalisdkfakdy 465
                                        + fitl Glh+ a  + +  ++ 
  gi|313125355|ref|YP_004035619.1| 259 EYIFITLFGLHSGAHSVYEDFRAL 282
                                       ************998765554555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2151.81
//
Query:       gi|313125356|ref|YP_004035620.1|  [L=115]
Description: hypothetical protein Hbor_05800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.047   14.0   0.1      0.073   13.4   0.1    1.3  1  Csm1_N          Csm1 N-terminal domain
       0.12   13.4   0.0       0.17   12.9   0.0    1.3  1  DUF5320         Family of unknown function (DUF5320)


Domain annotation for each model (and alignments):
>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.1e-06     0.073      37      66 ..      84     113 ..      77     115 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.1e-06
                            Csm1_N  37 etkdqeiesLkeqlaeleekvkeleerrkk 66 
                                       +t d+ei +L++ +a+l+++++++e+r ++
  gi|313125356|ref|YP_004035620.1|  84 QTSDNEIRNLRRDIAALRTQLDRIETRMEE 113
                                       7899*********************99876 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05      0.17      62      98 ..      71     113 ..      37     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                           DUF5320  62 a......aaetaeaskeeekelLeeqaeaLeeeleaikkrlke 98 
                                                 ++e+++++e++ L++ ++aL+ +l+ i+ r++e
  gi|313125356|ref|YP_004035620.1|  71 EaplvpfIIDPTEQTSDNEIRNLRRDIAALRTQLDRIETRMEE 113
                                       23344556788999**************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 671.75
//
Query:       gi|313125357|ref|YP_004035621.1|  [L=317]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-30  106.2   0.0    3.3e-30  105.4   0.0    1.4  1  ABC_tran         ABC transporter
    3.1e-14   53.5   3.1    3.8e-09   36.8   0.1    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    7.3e-07   29.8   0.0    3.2e-06   27.8   0.0    2.1  2  DUF4162          Domain of unknown function (DUF4162)
     0.0014   18.5   0.1       0.75    9.7   0.0    3.1  3  NTPase_1         NTPase
      0.003   18.1   0.0     0.0046   17.5   0.0    1.3  1  AAA_23           AAA domain
     0.0037   17.0   0.0          2    8.0   0.0    2.1  2  AAA_15           AAA ATPase domain
      0.005   16.6   0.0      0.034   13.9   0.0    2.1  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.052   13.3   0.1        1.8    8.2   0.0    2.2  2  AAA_24           AAA domain
      0.052   13.0   0.0        2.7    7.4   0.1    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
      0.053   13.3   0.0       0.11   12.3   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.084   11.7   0.0       0.13   11.0   0.0    1.2  1  DLIC             Dynein light intermediate chain (DLIC)
       0.14   12.0   0.2         57    3.6   0.0    3.7  4  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   2.2e-33   3.3e-30       1     137 []      20     164 ..      20     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 2.2e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ v+l++ eg+  +++G+nGaGK+t++++l gl+++  Ge ++ g d+++ + +++r +ig  pqe ++++   +r
  gi|313125357|ref|YP_004035621.1|  20 LDGVDLDVPEGSFFGLLGPNGAGKTTFINILVGLVRKSGGEARVFGYDVED-DYREARDRIGLAPQEFNVDRFFPIR 95 
                                       789************************************************.999************7766666666 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e              e++e+++++l+++g+ +++dt+       LSgG+k+r +laral+++p+ll+lDEpta
  gi|313125357|ref|YP_004035621.1|  96 EVlehkagyhgipadEARERADEVLKRVGIYDKRDTRF----DWLSGGMKRRFVLARALITDPDLLILDEPTA 164
                                       66666********9999999*****************9....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.7   1.9e-06    0.0028       1      23 [.      32      54 ..      32      94 .. 0.77
   2 !   36.8   0.1   2.5e-12   3.8e-09     186     297 ..      96     193 ..      62     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + +l GpNg+GK++++ +l +l 
  gi|313125357|ref|YP_004035621.1| 32 FFGLLGPNGAGKTTFINILVGLV 54
                                      6789***************8883 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 2.5e-12
                            AAA_21 186 qrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgslll 262
                                       + l+++    +i+++  +e+ ++            +  +   d +++ ++ lS G+kr  ++l+  l +++  +ll+
  gi|313125357|ref|YP_004035621.1|  96 EVLEHKAGYHGIPADEARERADE-----------VLKRVGIYDKRDTRFDWLSGGMKRR-FVLARALITDP--DLLI 158
                                       44444444444444444444444...........44455567889999***********.77777777776..9*** PP

                            AAA_21 263 iDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +DEp +g + +l ++l+e + el++ g+ ++ltTH
  gi|313125357|ref|YP_004035621.1| 159 LDEPTAGVDVQLRHELWETITELNDSGTTILLTTH 193
                                       *********************************** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.5   5.3e+03       2      12 ..       6      16 ..       6      20 .. 0.85
   2 !   27.8   0.0   2.1e-09   3.2e-06       3      81 .]     219     304 ..     218     304 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.5
                                      -HHHHHTTS-S CS
                           DUF4162  2 tleeiKrsygk 12
                                      t++++++syg+
  gi|313125357|ref|YP_004035621.1|  6 TIRDLRKSYGG 16
                                      689******97 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 2.1e-09
                                       HHHHHTTS-SSEEEEE.....-------..--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE-- CS
                           DUF4162   3 leeiKrsygknrieve.....adaeelleepg.veeveeeggelelkled.eeaanellkal.tsgveirsFeeeeP 71 
                                       ++e++++ g++ i+v+     + + ++   ++ ve ve +g++l+++ ++ + +a+e+ ++l ++g ei+ +e  + 
  gi|313125357|ref|YP_004035621.1| 219 PDELMDR-GTDDIVVTlrdqpTAVPDFTVDDErVEAVELDGTRLVVTAREgGLVAPEVVRRLdAAGHEIVDLEISRT 294
                                       5667777.4444555544433223333333556****************99***********77************* PP

                                       -HHHHHHHHH CS
                           DUF4162  72 sLndIFiekv 81 
                                       sL+++F+e +
  gi|313125357|ref|YP_004035621.1| 295 SLEEVFVEMT 304
                                       *******975 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0005      0.75       4      46 ..      35      80 ..      33      89 .. 0.75
   2 ?    2.8   0.0     0.065        97      94     156 ..     152     217 ..     132     228 .. 0.78
   3 ?    2.0   0.0      0.11   1.7e+02      31      64 ..     268     300 ..     261     317 .] 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0005
                                      EE--TTSSHHHHHHHHHHHH...G..GGEEEEEEE.EE-------E CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssg..vkvgGfyte.evreggrrig 46
                                      + Gp G GKtT+++ ++ l+++sg   +v G  +e ++re   rig
  gi|313125357|ref|YP_004035621.1| 35 LLGPNGAGKTTFINILVGLVRKSGgeARVFGYDVEdDYREARDRIG 80
                                      569*****************99972255666655424566666666 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.065
                                       HHH-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE-- CS
                          NTPase_1  94 seadviviDE..iGkmElkskkfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvfevt 156
                                       +++d++++DE   G      +++ e+++e+ +s++ +l + h  +  ++l +e+     ++v+ev 
  gi|313125357|ref|YP_004035621.1| 152 TDPDLLILDEptAGVDVQLRHELWETITELNDSGTTILLTTHYIEeAERLCDEVAILDSGRVLEVA 217
                                       677888888853344334456788899999999999999999988788999999888888888875 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.11
                                       EEEEEEEE-------EEEEEET.T--EEEEEETT CS
                          NTPase_1  31 gGfyteevreggrrigFkivdlasgeegiLarve 64 
                                       gG++++ev ++    g +ivdl + +++ L +v 
  gi|313125357|ref|YP_004035621.1| 268 GGLVAPEVVRRLDAAGHEIVDL-EISRTSLEEVF 300
                                       799*******************.77788887776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.1e-06    0.0046      12      39 ..      22      50 ..       7     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.1e-06
                            AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAi 39
                                      ++++d  +  ++ + GpNGaGKTT+++ +
  gi|313125357|ref|YP_004035621.1| 22 GVDLDVpEGSFFGLLGPNGAGKTTFINIL 50
                                      4555556667999************9865 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0014         2      28      49 ..      35      56 ..      20      91 .. 0.83
   2 !    6.9   0.0    0.0029       4.3     321     364 ..     151     193 ..     108     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0014
                            AAA_15 28 liGkNnsGKSsilealdlFlnn 49
                                      l G+N++GK++++++l  +  +
  gi|313125357|ref|YP_004035621.1| 35 LLGPNGAGKTTFINILVGLVRK 56
                                      78*************9776664 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0029
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                        +++++l+++EP a    q+  +l++++ el +++   +++tTH
  gi|313125357|ref|YP_004035621.1| 151 ITDPDLLILDEPTAGVDVQLRHELWETITELNDSGT-TILLTTH 193
                                       34679**************************99996.9****** PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.3e-05     0.034      22     110 ..      34     176 ..      28     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                            AAA_30  22 vltGpAGtGKttalkalreaweaag.................grviglAptgkaAkvLa.......eelgi...... 68 
                                        l Gp G+GKtt ++ l+ +++++g                 ++ iglAp++   ++         +++g       
  gi|313125357|ref|YP_004035621.1|  34 GLLGPNGAGKTTFINILVGLVRKSGgearvfgydveddyreaRDRIGLAPQEFNVDRFFpirevleHKAGYhgipad 110
                                       578*********************76888888777777777777777777776666543333333322221222222 PP

                            AAA_30  69 .eastiakllkrlk......................grarlepgtllivDE.agmvdtkqlaallk 110
                                        + ++ +++lkr +                      +ra +++ +lli DE ++ vd +  ++l +
  gi|313125357|ref|YP_004035621.1| 111 eARERADEVLKRVGiydkrdtrfdwlsggmkrrfvlARALITDPDLLILDEpTAGVDVQLRHELWE 176
                                       111222223322225556666666666666677766555666667777777333455555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0012       1.8       7      22 ..      35      50 ..      32      86 .. 0.82
   2 ?    2.6   0.0     0.063        95     106     134 ..     169     197 ..     164     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                            AAA_24  7 iyGpsgiGKTtlakel 22
                                      + Gp+g+GKTt+++ l
  gi|313125357|ref|YP_004035621.1| 35 LLGPNGAGKTTFINIL 50
                                      89**********9876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.063
                            AAA_24 106 elaeefrrllkklqelrknvifiahektr 134
                                       +l++e++++++ l++ + ++ ++ h  ++
  gi|313125357|ref|YP_004035621.1| 169 QLRHELWETITELNDSGTTILLTTHYIEE 197
                                       6899*********************8776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0018       2.7      24      42 ..      30      48 ..       6      58 .. 0.83
   2 ?    3.5   0.0     0.028        41     136     197 ..     135     193 ..      85     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                                      SSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlld 42
                                       sf  ++GpNG+GK+ +++
  gi|313125357|ref|YP_004035621.1| 30 GSFFGLLGPNGAGKTTFIN 48
                                      468889*********9986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.028
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivisl 197
                                        LSgG k      +++A   +    l +lDe  a  D + ++++ e + e +++ + ++ +++
  gi|313125357|ref|YP_004035621.1| 135 WLSGGMKR----RFVLARALITDPDLLILDEPTAGVDVQLRHELWETITELNDSgTTILLTTH 193
                                       68888776....566666667777899**********************99987333444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.1e-05      0.11      13      39 ..      21      47 ..      18      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                            AAA_29 13 dghtieidlkg.atlltGpsGsGKSTll 39
                                      dg ++++  +g ++ l Gp+G+GK+T++
  gi|313125357|ref|YP_004035621.1| 21 DGVDLDVP-EGsFFGLLGPNGAGKTTFI 47
                                      56667776.4448889**********99 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     9e-05      0.13      24      76 ..      29      80 ..      24      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                              DLIC 24 sgksvlvlGedgsGkttliaklqGveeekkGrGleylyldvkdedrddltrln 76
                                       g    +lG +g+Gktt+i  l G+  +  G    + y dv+d++r+   r++
  gi|313125357|ref|YP_004035621.1| 29 EGSFFGLLGPNGAGKTTFINILVGLVRKSGGEARVFGY-DVEDDYREARDRIG 80
                                      55556689*****************9988888887777.*******9999986 PP

>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.038        57       4      20 ..     107     123 ..     105     125 .. 0.92
   2 ?   -2.0   0.0       2.1   3.2e+03      15      32 ..     176     193 ..     169     212 .. 0.64
   3 ?    1.3   0.0       0.2   3.1e+02      24      38 ..     227     241 ..     218     241 .. 0.81
   4 ?    2.0   0.1      0.13   1.9e+02      17      67 ..     251     298 ..     248     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.038
                                       EEHHHHHHTHHHHHHHH CS
                   PhdYeFM_antitox   4 vsiseakanlselldev 20 
                                       +++ ea+ ++ e+l++v
  gi|313125357|ref|YP_004035621.1| 107 IPADEARERADEVLKRV 123
                                       899************99 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.1
                                       HHHHHHHHHT-EEEEEET CS
                   PhdYeFM_antitox  15 elldeveegeepviItrr 32 
                                       e + e ++ ++++++t +
  gi|313125357|ref|YP_004035621.1| 176 ETITELNDSGTTILLTTH 193
                                       556666666666666655 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.2
                                       T-EEEEEETTEEEEE CS
                   PhdYeFM_antitox  24 eepviItrrGkpvaV 38 
                                        +++++t r+ p+aV
  gi|313125357|ref|YP_004035621.1| 227 TDDIVVTLRDQPTAV 241
                                       345**********98 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.13
                                       HHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH.HHHHHCSHHHHHHHHH CS
                   PhdYeFM_antitox  17 ldeveegeepviItrrGkpvaVlvsleeyerlqeltekllslplnaerlae 67 
                                       +++ve +++++++t r +    lv++e  +rl ++ + + +l+ ++ +l+e
  gi|313125357|ref|YP_004035621.1| 251 VEAVELDGTRLVVTAREGG---LVAPEVVRRLDAAGHEIVDLEISRTSLEE 298
                                       7899999*******99987...99999999999988888888888887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1777.09
//
Query:       gi|313125358|ref|YP_004035622.1|  [L=255]
Description: polysaccharide/polyol phosphate ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-32  110.1  19.4    1.3e-31  109.7  19.4    1.2  1  ABC2_membrane    ABC-2 type transporter
    0.00029   20.1  21.8    0.00038   19.7  21.8    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7  19.4   1.4e-35   1.3e-31       3     209 ..       8     217 ..       6     218 .. 0.94

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 1.4e-35
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg.nsedglnr.....pgllffsvlflafsaltsvap 73 
                                       ++allkre+l+++r+p  +++ ++i+ +l++ vfg++ g    n+  g+ +     pgl++  ++ +a + ++s ++
  gi|313125358|ref|YP_004035622.1|   8 FLALLKREVLRFVRRPRNTFVPPFITNVLYFSVFGVILGE-RiNEIAGVPYilfilPGLIVLGAVSNA-FENASFSI 82 
                                       899************************************4.134444443379999************.99999999 PP

                     ABC2_membrane  74 vferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgll 150
                                       +  r ++ +e+ l+spl s  ++v a+vl+++++++++++++ +i +f++ + + r f++++++l+++l++ slg++
  gi|313125358|ref|YP_004035622.1|  83 FHGRWNRYIEEVLTSPL-SYRSMVGAYVLSSATRGIFVGALVAVIGVFFTTVGVVRPFYLIAFMLVITLLFASLGVV 158
                                       9999*************.******************************998888778******************** PP

                     ABC2_membrane 151 isalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                        + +a++f+d +++ +++l pl++++G+f++++ +p  lq ++ lnP+ y+v+++r+++
  gi|313125358|ref|YP_004035622.1| 159 GGLWAEDFDDLTMMNQFILRPLVFFGGVFYSLNELPATLQQVSLLNPMIYMVNGVRYGF 217
                                       ************************************9*******************987 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  21.8   4.2e-08   0.00038     159     339 ..      58     239 ..      26     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.2e-08
                   ABC2_membrane_3 159 vasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afglgip 234
                                       +  +l gli++ +++  + ++++si + + +r +e  l+s++s  +++ + +l++++ ++++ +l+ ++ +f + + 
  gi|313125358|ref|YP_004035622.1|  58 ILFILPGLIVLGAVSNAFENASFSIFHGRWNRYIEEVLTSPLSYRSMVGAYVLSSATRGIFVGALVAVIgVFFTTVG 134
                                       33445559999999999999999****************************************99999987773555 PP

                   ABC2_membrane_3 235 fgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffggl.fpledlpsalkwifsiiPffapg 310
                                       +   ++l+ ++l+  l++++lg + +    + ++    +  +il +++ffgg+ ++l+ lp +l++++ ++P+ +  
  gi|313125358|ref|YP_004035622.1| 135 VVRPFYLIAFMLVITLLFASLGVVGGLWAEDFDDLTM-MNQFILRPLVFFGGVfYSLNELPATLQQVSLLNPMIYMV 210
                                       5599************************888777554.555555455555555166********************* PP

                   ABC2_membrane_3 311 lgllrlitgdplweillsliilalfavvy 339
                                       +g      g++ ++  +sl++l++++v++
  gi|313125358|ref|YP_004035622.1| 211 NGVRYGFLGVSEVDPNMSLAVLVALTVAV 239
                                       *9955557774455667777777666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1459.12
//
Query:       gi|313125359|ref|YP_004035623.1|  [L=106]
Description: hypothetical protein Hbor_05830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 679.60
//
Query:       gi|313125360|ref|YP_004035624.1|  [L=561]
Description: gamma-glutamyltransferase 2 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-144  482.9   0.0   1.3e-144  482.7   0.0    1.0  1  G_glu_transpept  Gamma-glutamyltranspeptidase


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.7   0.0  7.5e-149  1.3e-144       2     512 .]      39     556 ..      38     556 .. 0.96

  Alignments for each domain:
  == domain 1  score: 482.7 bits;  conditional E-value: 7.5e-149
                                       HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTT.........TSCB CS
                   G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmf.........dkeg 69 
                                       ++Lr+GGnA+DAavA+a++l+vvep+s+G+GG++f+l+++a++    a+ a++ APa+at +++          +++
  gi|313125360|ref|YP_004035624.1|  39 QMLREGGNAFDAAVATAAALNVVEPTSTGLGGDVFALYRTADGDVG-AMRACGGAPAEATIENVresvaeendVDSE 114
                                       69**************************************999866.9********************998876788 PP

                                       CCHHHHSSGGG-BB--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEE CS
                   G_glu_transpept  70 dsklsktgalavgVPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlp 146
                                       d++++ tga+ v+VPG+ +g+e++++ +G+l++ad l+pai++a +G+pvse +a+a+   ee +++d ++++ Fl 
  gi|313125360|ref|YP_004035624.1| 115 DAEMPDTGAHTVTVPGTARGWEATVDAFGRLTLADALQPAIRYATDGYPVSEVIADAWTHGEEVFETD-NAREAFLF 190
                                       9999***********************************************************99999.788***** PP

                                       TTSE--TTSEE--HHHHHHHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEE CS
                   G_glu_transpept 147 egevlkagellkqpalAktLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytv 223
                                       ++e++++g++++ p+l +t+e++ae+Ga+  Y+G++Ae++++e+q +gG +t +DLa+++ve+ +p+s++y +g +v
  gi|313125360|ref|YP_004035624.1| 191 DDEAPDVGQTVTFPKLGATMEQIAEKGADVVYEGDIAEQIADEVQSQGGFMTVDDLADFEVEFPDPISTTY-NGVEV 266
                                       ***********************************************************************.99*** PP

                                       EE-TTCSHHHHHHHHHHHHCTTTGGGCTTTCHHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHH CS
                   G_glu_transpept 224 yepppssggivllqiLnilegfdlkslssnsaetlhllvEamklayadRsrylgDpdfvknptelveellskeyake 300
                                       +e pp+ +g+++l++Lni e++  ++++ +sa+++h + Eamkla++d +ry++Dp + +     +  l ske+a++
  gi|313125360|ref|YP_004035624.1| 267 FELPPNNQGLIALEALNIAEEIGAHESELGSADRIHYFGEAMKLAFHDGHRYITDPAYEE-----IPPLASKEWAEK 338
                                       ***********************999*********************************8.....679********* PP

                                       HHTT.BTTB..SG................GGCSCGGCSCG.TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTT CS
                   G_glu_transpept 301 raklIkdkaatps................seyykaaeaaeesggTthlsvvDregnaVSltstinllFGsgvvvpgt 361
                                       ra+ I ++a+++                 +   ++ ++++e+++T+ l+v+D+egn+VS++++   +FGsg+v  +t
  gi|313125360|ref|YP_004035624.1| 339 RATAIGEEANDDVsfgvpdasneapgrqrPPNPQEPPEPPEDSDTVLLTVADDEGNVVSYINSRFAGFGSGLVAGDT 415
                                       *********99889*********998765323334445556************************************ PP

                                       TEBE--GGGGSBSTS..TTSCSTTSTTB--TT----B----EEEEETTEEEEEEEEESGGGHHHHHHHHHHHHHTT- CS
                   G_glu_transpept 362 GilLnnemddfstgvenafgldpspanaiePgkRplssmaPtivlkdgkpvlvlGaaGGsriisavlqvlvnvldlg 438
                                       Gi+L+n++++fs        ldps++n++ePgkRp+++++P+++  d++ ++++G++GG ++++++lqv+ n++d+g
  gi|313125360|ref|YP_004035624.1| 416 GIALQNRGSSFS--------LDPSHPNRLEPGKRPFHTLIPGLLKFDEDDWAAFGVMGGYMQPQGHLQVVSNIVDYG 484
                                       ************........************************99******************************* PP

                                       S-HHHHHHS--EEESSSSTEEEESTTS.HHHHHHHHHTTSEEEESSSTCCCEEEEEEEETTTEEEEEE-TTTTT CS
                   G_glu_transpept 439 ldlqeavdaprihhqllpdkvevEegfseevveeLearGhkvkevedsssvvaavavakekgvleaasDprkdg 512
                                       ++lq+a+d pr+  +     + +Ee+ +++v ++L++rGh+v+  ++s  ++a++a+  ++g+l+aa++prkdg
  gi|313125360|ref|YP_004035624.1| 485 MPLQAALDFPRWRYR-EDGSLAIEERTGDSVGTKLTRRGHDVRLLSPSLFGGAQIARS-DHGTLSAATEPRKDG 556
                                       **************6.3459*****************************999999997.9************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3483.91
//
Query:       gi|313125361|ref|YP_004035625.1|  [L=68]
Description: hypothetical protein Hbor_05850 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.018   15.1   1.2      0.019   15.1   1.2    1.0  1  FUSC_2           Fusaric acid resistance protein-like
       0.37   10.7   0.2       0.37   10.7   0.2    1.7  2  Deltameth_res    Deltamethrin resistance
       0.67    9.9   0.0       0.67    9.9   0.0    2.2  2  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> FUSC_2  Fusaric acid resistance protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.2   3.1e-06     0.019      35      82 ..       9      60 ..       3      68 .] 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-06
                            FUSC_2 35 ravqRilGtvlGavlall.llyllpgn...lalallvfllvfliafflkrny 82
                                      r++  +lGt++G +l  l l+++l +n   ++la+ ++ll+  + ++++++ 
  gi|313125361|ref|YP_004035625.1|  9 RVLTSLLGTMFGTLLIGLgLVHVLGSNeppWQLAFGIVLLSGAALLVKSASV 60
                                      677778999999977666255666665689********99999988887665 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.35   2.1e+03      35      36 ..      21      22 ..       9      34 .. 0.57
   2 ?   10.7   0.2   6.2e-05      0.37      24      45 ..      40      61 ..      39      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                     Deltameth_res 35 Ti 36
                                      T+
  gi|313125361|ref|YP_004035625.1| 21 TL 22
                                      33 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.2e-05
                     Deltameth_res 24 vLaaGiviligTialakesgli 45
                                      +La+Giv l+g++ l+k+  + 
  gi|313125361|ref|YP_004035625.1| 40 QLAFGIVLLSGAALLVKSASVT 61
                                      8****************98765 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   3.8      0.54   3.2e+03      21      29 ..      17      25 ..       2      31 .. 0.56
   2 ?    9.9   0.0   0.00011      0.67      14      36 ..      34      56 ..      33      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.54
                                      XXXXXXXXX CS
                   Gram_pos_anchor 21 taaGllall 29
                                      t +G l++ 
  gi|313125361|ref|YP_004035625.1| 17 TMFGTLLIG 25
                                      223333333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00011
                                      XXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 14 engnifltaaGllallggllLlv 36
                                      +n+ ++ +a+G+ +l g++lL++
  gi|313125361|ref|YP_004035625.1| 34 SNEPPWQLAFGIVLLSGAALLVK 56
                                      56667889***999999999955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 473.80
//
Query:       gi|313125362|ref|YP_004035626.1|  [L=167]
Description: hypothetical protein Hbor_05860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00079   19.9   0.0     0.0012   19.3   0.0    1.2  1  Arrestin_C  Arrestin (or S-antigen), C-terminal domain


Domain annotation for each model (and alignments):
>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.7e-08    0.0012       4      31 ..      40      67 ..      38      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.7e-08
                                      -EEEEEEES-SEEETT--EEEEEEEEE- CS
                        Arrestin_C  4 kvsleaslpkkgyvpGetipvtvkidnd 31
                                      ++sl++ ++k+ y+pGe +++tv+i+n 
  gi|313125362|ref|YP_004035626.1| 40 SLSLSVRTDKETYAPGEPVELTVEIENR 67
                                      689***********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1132.33
//
Query:       gi|313125363|ref|YP_004035627.1|  [L=430]
Description: oligopeptide/dipeptide ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-32  111.2   0.0    8.8e-32  110.5   0.0    1.4  1  ABC_tran      ABC transporter
    1.1e-16   61.1   0.1    2.1e-16   60.1   0.1    1.5  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    3.7e-07   30.5   0.0    2.4e-06   27.9   0.0    2.0  1  AAA_22        AAA domain
      8e-05   23.1   0.0    0.00023   21.6   0.0    1.8  1  AAA_16        AAA ATPase domain
    0.00022   21.6   0.0      0.002   18.6   0.0    2.4  1  AAA           ATPase family associated with various cellular 
    0.00024   21.0   0.0      0.061   13.1   0.0    2.4  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      0.001   18.5   0.0     0.0021   17.6   0.0    1.4  1  SMC_N         RecF/RecN/SMC N terminal domain
      0.005   16.8   0.0     0.0092   15.9   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
     0.0073   16.0   0.0      0.014   15.1   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0078   15.9   0.0      0.012   15.3   0.0    1.3  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
     0.0089   16.0   0.0      0.019   15.0   0.0    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0099   16.0   0.0      0.027   14.6   0.0    1.8  1  AAA_33        AAA domain
  ------ inclusion threshold ------
       0.02   14.2   0.0      0.037   13.3   0.0    1.3  1  Zeta_toxin    Zeta toxin
      0.035   13.3   0.0      0.047   12.9   0.0    1.2  1  G-alpha       G-protein alpha subunit
      0.039   13.1   0.0      0.077   12.2   0.0    1.4  1  NB-ARC        NB-ARC domain
      0.043   13.7   0.1       0.11   12.4   0.0    1.7  2  NACHT         NACHT domain
      0.048   13.2   0.0        1.5    8.4   0.0    2.3  2  AAA_25        AAA domain
      0.054   12.9   0.0       0.13   11.7   0.0    1.6  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.14   12.5   0.0       0.29   11.5   0.0    1.5  1  RNA_helicase  RNA helicase
       0.15   11.8   0.0       0.33   10.6   0.0    1.6  1  PRK           Phosphoribulokinase / Uridine kinase family


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0   9.8e-35   8.8e-32       2     137 .]      49     199 ..      48     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 9.8e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       ++v++++ +ge++++vGe+G+GKStL++++++ll+pt G +++++++l e   +el+ +r+ +++++q+  ++l+p+
  gi|313125363|ref|YP_004035627.1|  49 DDVTFNIAKGETLGLVGESGCGKSTLARTVLRLLEPTDGAVWFKDDNLAEmsgEELRTMREDMQMIFQDpqSSLDPR 125
                                       89******************************************999999999****************88889999 PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++v+               +++e++  +l+k+gl+  +    ++ p+++SgGq+qrv laral+ +p+++++DEpt+
  gi|313125363|ref|YP_004035627.1| 126 MKVGPIveepmkahglykgQREERARMLLEKVGLDPQHY---NRYPHQFSGGQRQRVNLARALAVNPDFIVCDEPTS 199
                                       9988778999******87777777888888888777555...5569*****************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.1   2.4e-19   2.1e-16       1      60 [.     250     310 ..     250     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2.4e-19
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpf 60 
                                       vE +++++lf++p+HPYT aLl+s+p +d++   +   ++g++ps+ + ++GC+F++RCp 
  gi|313125363|ref|YP_004035627.1| 250 VELAETEELFENPQHPYTNALLQSIPVPDPRHGgQRGVLEGDVPSPIDPPSGCRFRTRCPR 310
                                       8*****************************99999999*********************95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   2.6e-09   2.4e-06      10     128 ..      63     227 ..      57     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.6e-09
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka............... 70 
                                       ++GesG+GK+tl+r++l+ l+    a + +++ ++++   ++ + ++ +++++++ +++l+                
  gi|313125363|ref|YP_004035627.1|  63 LVGESGCGKSTLARTVLRLLEPTDGAVWfKDDNLAEMSGEELRTMREDMQMIFQDPQSSLDPrmkvgpiveepmkah 139
                                       79******************755555558888888999999999999999999999999999*************** PP

                            AAA_22  71 ...........................erlsseellealeqalrarav.ielliiDEaqh.lr...seealeeLrsl 115
                                                                  ++++ +   ++  + +ra av + +++ DE    l+   ++++l++ r+l
  gi|313125363|ref|YP_004035627.1| 140 glykgqreerarmllekvgldpqhynrYPHQFSGGQRQRVNLARALAVnPDFIVCDEPTSaLDasiQAQVLNTMRDL 216
                                       ***9998888888888877766666555555555555555555555559********9999989555********** PP

                            AAA_22 116 lnlsrkgvqliLv 128
                                       ++  ++g++ +++
  gi|313125363|ref|YP_004035627.1| 217 QD--EFGLTYLFI 227
                                       **..999988776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.6e-07   0.00023       8      55 ..      44      89 ..      42     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.6e-07
                            AAA_16  8 eleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                      e++++ ++  ++++g  e + l+GesG+GKs+l+r++lr le ++g +
  gi|313125363|ref|YP_004035627.1| 44 EVKAVDDVTFNIAKG--ETLGLVGESGCGKSTLARTVLRLLEPTDGAV 89
                                      555665555556666..56889****************9998885332 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.2e-06     0.002       3      38 ..      63     154 ..      61     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                                       EESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS................................ CS
                               AAA   3 lyGppGtGKTllakavakel..........gvefleisgsellsk................................ 37 
                                       l+G  G+GK++la+ v + l          + ++ e+sg el+ +                                
  gi|313125363|ref|YP_004035627.1|  63 LVGESGCGKSTLARTVLRLLeptdgavwfkDDNLAEMSGEELRTMredmqmifqdpqssldprmkvgpiveepmkah 139
                                       89*****************955554444444779*********5556666666666666666666666666666666 PP

                                       ..............S CS
                               AAA  38 ..............y 38 
                                                     +
  gi|313125363|ref|YP_004035627.1| 140 glykgqreerarmlL 154
                                       664444444444440 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.015        13       3      23 ..      62      82 ..      61     123 .. 0.81
   2 !   13.1   0.0   6.8e-05     0.061     230     302 ..     164     234 ..     145     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      +l+G  g+GKS+L ++   l 
  gi|313125363|ref|YP_004035627.1| 62 GLVGESGCGKSTLARTVLRLL 82
                                      69***********99997775 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.8e-05
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       +++ ++++S G+++   l+ al+  +   ++++ DEp + L+ ++++ +l  +++l++  g   ++ +H+ +++
  gi|313125363|ref|YP_004035627.1| 164 YNRYPHQFSGGQRQRVNLARALAVNP---DFIVCDEPTSALDASIQAQVLNTMRDLQDeFGLTYLFISHDLSVI 234
                                       6778999******999*******999...9***********************9999999**********9887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.3e-06    0.0021      27     210 ..      61     242 ..      42     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                                       EEEEESTTSSHHHHHHHHHHHCTT.T.TTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGers.akklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                         +vG+ G+GKs l   +l +L  ++ a  ++ ++l ++   s e+ ++++ +++++f++++++    ++++++   
  gi|313125363|ref|YP_004035627.1|  61 LGLVGESGCGKSTLARTVLRLLEPTDgAVWFKDDNLAEM---SGEELRTMREDMQMIFQDPQSS---LDPRMKVGPI 131
                                       469***************999986641445666666665...5679999999*********999...7888999999 PP

                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                       v++  + +   +g++ ++   + lle++g++++       ++SgG+++ v la  +A++      + + De  +aLD
  gi|313125363|ref|YP_004035627.1| 132 VEEPMKAHGLYKGQREER--ARMLLEKVGLDPQhynryphQFSGGQRQRVNLARALAVNP----DFIVCDEPTSALD 202
                                       999999888888886555..56799*****9999999999**************999863....599********** PP

                                       HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkekskn..aQfivislreemlekadklvg 210
                                       ++  ++v + ++  +++    ++ is++  ++++ +  v 
  gi|313125363|ref|YP_004035627.1| 203 ASIQAQVLNTMRDLQDEfgLTYLFISHDLSVIRHISDRVA 242
                                       ************9998844567888888877777655554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-05    0.0092      83     119 ..      41      78 ..      26      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                                       -TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  83 saktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                       + ++ +++++++ ++++ +t  lvG+SG GKStL  ++
  gi|313125363|ref|YP_004035627.1|  41 NDDEVKAVDDVTFNIAKgETLGLVGESGCGKSTLARTV 78 
                                       5566788999999998889***************8876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.014      13      49 ..      49      85 ..      44      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      d+ t++i   ++  l+G+sG GKSTl   +  lL p+
  gi|313125363|ref|YP_004035627.1| 49 DDVTFNIAKGETLGLVGESGCGKSTLARTVLRLLEPT 85
                                      66788888555777************88888888776 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.4e-05     0.012       6      38 ..      50      82 ..      45     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                                      HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslskqs 38
                                      D+ f i++G++++++g++g+Gk+++++++++  
  gi|313125363|ref|YP_004035627.1| 50 DVTFNIAKGETLGLVGESGCGKSTLARTVLRLL 82
                                      7889**********************9998765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.1e-05     0.019       4      26 ..      63      89 ..      60     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                                      EE--SSSSHHHHHHHGGGGB....S-- CS
                             AAA_5  4 LvGppGtgKselaerlaaal....nre 26
                                      LvG++G+gKs+la+ ++++l    ++ 
  gi|313125363|ref|YP_004035627.1| 63 LVGESGCGKSTLARTVLRLLeptdGAV 89
                                      9******************97655444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     3e-05     0.027       4      33 ..      63     107 ..      61     218 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                            AAA_33   4 lvGlpGsGKstlaerllkklg....avllssdt...........l 33 
                                       lvG +G+GKstla+ +l+ l     av    d+           +
  gi|313125363|ref|YP_004035627.1|  63 LVGESGCGKSTLARTVLRLLEptdgAVWFKDDNlaemsgeelrtM 107
                                       69*************988777777666666666555555533332 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.1e-05     0.037      21      57 ..      63      99 ..      56     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.1e-05
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                      l+G +G+GKs+la+ + + le+++++v ++ D+l e+
  gi|313125363|ref|YP_004035627.1| 63 LVGESGCGKSTLARTVLRLLEPTDGAVWFKDDNLAEM 99
                                      78*****************************998765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.2e-05     0.047      25     111 ..      60     166 ..      41     256 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                       EEEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT.............. CS
                           G-alpha  25 kllllGqseSGKsTilkqlkllykkg.....fseeelatwraviqlnivrsiktilealesleselsesf....... 89 
                                       +l l+G+s++GKsT+ + + +l +++     f++++la++      ++ +++++i++  +s+ ++    +       
  gi|313125363|ref|YP_004035627.1|  60 TLGLVGESGCGKSTLARTVLRLLEPTdgavwFKDDNLAEMSGEELRTMREDMQMIFQDPQSSLDPR---Mkvgpive 133
                                       5779***************999999999***99999999888888888888888888777743222...23455666 PP

                                       ...........HHHC-SS-SCCCS-HCHHHH.. CS
                           G-alpha  90 ...........elqelkerldplkkveasliak 111
                                                  + +e+ + l +   ++++++++
  gi|313125363|ref|YP_004035627.1| 134 epmkahglykgQREERARMLLEKVGLDPQHYNR 166
                                       667777777776666666666666677776665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.6e-05     0.077      22      43 ..      60      81 ..      42      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                                      EEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnk 43
                                       ++lvG  G+GK+tla+ +l+ 
  gi|313125363|ref|YP_004035627.1| 60 TLGLVGESGCGKSTLARTVLRL 81
                                      689**************99875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013      0.11       3      24 ..      61      82 ..      59      88 .. 0.86
   2 ?   -3.3   0.0       8.5   7.7e+03      52      71 ..     367     386 ..     358     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                      EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                      + l Ge+G+GK+tL++ + +++
  gi|313125363|ref|YP_004035627.1| 61 LGLVGESGCGKSTLARTVLRLL 82
                                      6689************998876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.5
                                       .-HCHHHCCCCTS--SSS-C CS
                             NACHT  52 rsladllfsqlpepaapvse 71 
                                       +s++d+l +++++ +++ +e
  gi|313125363|ref|YP_004035627.1| 367 TSIDDVLNDDWDAAEERLTE 386
                                       58889999999998888877 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0017       1.5      30      50 ..      55      75 ..      48     117 .. 0.87
   2 ?    2.4   0.0      0.11     1e+02     153     188 ..     199     229 ..     169     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +++ge+  l+G +g+GK+tla
  gi|313125363|ref|YP_004035627.1| 55 IAKGETLGLVGESGCGKSTLA 75
                                      57899999************8 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                            AAA_25 153 ralggdensnsdvgalvealeriarrtgaavllvhH 188
                                       +al+++ +     +++++ ++++++++g + l++ H
  gi|313125363|ref|YP_004035627.1| 199 SALDASIQ-----AQVLNTMRDLQDEFGLTYLFISH 229
                                       44444433.....99*******************99 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.13      19      65 ..      55     101 ..      42     131 .. 0.73
   2 ?   -3.5   0.0       6.2   5.6e+03     174     196 ..     160     182 ..     155     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                      Mg_chelatase  19 aaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65 
                                       +a g  l lvG +G+GK+ la+ +  ll p + +  ++  ++a ++g
  gi|313125363|ref|YP_004035627.1|  55 IAKGETLGLVGESGCGKSTLARTVLRLLEPTDGAVWFKDDNLAEMSG 101
                                       56677889********************9988776666666666665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.2
                      Mg_chelatase 174 sekeierYlsklsgplldRidlq 196
                                        +++ +rY ++ sg    R++l 
  gi|313125363|ref|YP_004035627.1| 160 DPQHYNRYPHQFSGGQRQRVNLA 182
                                       57889999999999999999885 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00032      0.29       3      23 ..      63      83 ..      61     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                      RNA_helicase  3 lyGpsgeGKStlakeLakall 23
                                      l+G+sg+GKStla+++ + l+
  gi|313125363|ref|YP_004035627.1| 63 LVGESGCGKSTLARTVLRLLE 83
                                      78************9655444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00037      0.33       3      24 ..      62      83 ..      60     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                               PRK  3 gvagsSGaGkttvarklekifg 24
                                      g+ g+SG+Gk+t+ar++  +++
  gi|313125363|ref|YP_004035627.1| 62 GLVGESGCGKSTLARTVLRLLE 83
                                      899************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2934.93
//
Query:       gi|313125364|ref|YP_004035628.1|  [L=371]
Description: oligopeptide/dipeptide ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-26   93.0   0.0    4.1e-26   92.1   0.0    1.5  1  ABC_tran   ABC transporter
    7.1e-19   68.1   0.1    1.3e-18   67.3   0.1    1.5  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    0.00035   20.5   0.1     0.0016   18.4   0.0    1.9  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
  ------ inclusion threshold ------
      0.011   16.0   0.1       0.45   10.8   0.1    2.4  1  AAA_22     AAA domain
      0.093   13.1   0.0       0.21   12.0   0.0    1.6  2  AAA_16     AAA ATPase domain
        0.2   11.2   0.3       0.74    9.3   0.1    2.0  2  AAA_25     AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.0   1.4e-29   4.1e-26       2     136 ..      26     199 ..      25     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 1.4e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....................B-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....................xxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....................qel 54 
                                       + +s++++ege+v++vGe+GaGKS   + +++l+++      G+++++gk+l +                     ++
  gi|313125364|ref|YP_004035628.1|  26 DGISFEVNEGELVGLVGESGAGKSVATSSIMRLVEDpgevVGGTVTYKGKKLIDieegsdgelrqssemlsneeMRK 102
                                       789******************************99655555666666666555556666666666666666775556 PP

                                       HHCCHCEEEE-SS..--S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHH CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  55 eslrkeigvlpqe..pqlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkq 115
                                       ++  +ei++++q+  + l+p  tv+ +              +++e + ++l+++g++e ++++ +s p+++SgG++q
  gi|313125364|ref|YP_004035628.1| 103 QIRGREIAIIFQDpmEALNPVFTVGGQlrefieinrdvsseQAKEIAIDMLREVGIPE-PEKRYDSYPHQFSGGMRQ 178
                                       7788999******98899999999999*******99987655555599**********.888889************ PP

                                       HHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 116 rvalarallkkpkllllDEpt 136
                                       rv +a+al+++p+l+++DEpt
  gi|313125364|ref|YP_004035628.1| 179 RVIIAMALACEPDLIIADEPT 199
                                       ********************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.1   4.3e-22   1.3e-18       1      65 []     251     315 ..     251     315 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 4.3e-22
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E++++++lf++ +HPYT aLl+s+pr+d+  d+l  ikg  p++ + ++GC+F++RCp a+  C
  gi|313125364|ref|YP_004035628.1| 251 IEQADVDDLFHKTRHPYTDALLDSIPRPDQSVDELNPIKGVMPEAINPPSGCRFHTRCPEARTVC 315
                                       79***********************************************************9999 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.21   6.1e+02       2      14 ..      38      50 ..      37      82 .. 0.83
   2 !   18.4   0.0   5.2e-07    0.0016     173     302 ..     101     235 ..      70     236 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.21
                            AAA_21  2 nvliGpNgsGKSn 14
                                       +l+G  g+GKS 
  gi|313125364|ref|YP_004035628.1| 38 VGLVGESGAGKSV 50
                                      689********96 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 5.2e-07
                            AAA_21 173 adyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer.......gvvflengdgqelparelSdGtk 242
                                       ++ + + ++  ++q+ +  l++v+     l+e++e + +v+  +  +        v + e++++++  ++++S G++
  gi|313125364|ref|YP_004035628.1| 101 RKQIRGREIAIIFQDPMEALNPVFTVGGQLREFIEINRDVSSEQAKEiaidmlrEVGIPEPEKRYDSYPHQFSGGMR 177
                                       5555555555555555555555555555555554444444444333367777778999999999999********** PP

                            AAA_21 243 rllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       +   ++ a++ a+++ +l++ DEp + L+  +   +l+l+kel++  ++ ++ +TH+  ++
  gi|313125364|ref|YP_004035628.1| 178 QR--VIIAMALACEP-DLIIADEPTTALDVTVEGQILDLVKELQEkYNTSFVWVTHDLGVV 235
                                       *8..55555555555.************************9999999*********98776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00015      0.45      10     113 ..      40     134 ..      33     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseell.ealeqa 85 
                                       ++GesG+GK++    +++  +        + evv  t++ ++  k+ l ++ +  + el     sse l  e ++++
  gi|313125364|ref|YP_004035628.1|  40 LVGESGAGKSVATSSIMRLVED-------PGEVVGGTVTYKG--KK-LIDIEEGSDGELRQ---SSEMLSnEEMRKQ 103
                                       89**********9999998752.......6677755555555..22.45777777776666...7777778888888 PP

                            AAA_22  86 lraravielliiDEaqhlr...s.eealeeLr 113
                                       +r r   +++  D ++ l+   +   +l+e+ 
  gi|313125364|ref|YP_004035628.1| 104 IRGREI-AIIFQDPMEALNpvfTvGGQLREFI 134
                                       888888.8887788888864432455555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.9e-05      0.21      23      52 ..      34      67 ..      21     163 .. 0.73
   2 ?   -2.7   0.0       2.2   6.5e+03      42      82 ..     215     260 ..     213     306 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd....g 52
                                      ++elv l+GesG GKs    +++r +e+     g
  gi|313125364|ref|YP_004035628.1| 34 EGELVGLVGESGAGKSVATSSIMRLVEDPgevvG 67
                                      348999*****************76665554432 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                            AAA_16  42 rellralekd......ggiflrgkcdqlesaipysa.laqalareell 82 
                                       +el++ ++++      +  ++++ cd+   ++ y+  ++++++ ++l+
  gi|313125364|ref|YP_004035628.1| 215 KELQEKYNTSfvwvthDLGVVAEICDRV--NVMYLGeIIEQADVDDLF 260
                                       5555555555444443344455555555..555544444444443333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00025      0.74      31      58 ..      33      60 ..      25     167 .. 0.75
   2 ?   -0.5   0.0      0.26   7.9e+02     143     188 ..     190     230 ..     134     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00025
                            AAA_25 31 pagelallaGapgtGKttlaldlalava 58
                                       +gel+ l+G +g+GK++++++++  v 
  gi|313125364|ref|YP_004035628.1| 33 NEGELVGLVGESGAGKSVATSSIMRLVE 60
                                      689******************9987776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.26
                            AAA_25 143 vrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                       ++l++ D  + al+   +     g++++ +++++++++  ++ v H
  gi|313125364|ref|YP_004035628.1| 190 PDLIIADEPTTALDVTVE-----GQILDLVKELQEKYNTSFVWVTH 230
                                       555555555555554444.....78888888888888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2088.96
//
Query:       gi|313125365|ref|YP_004035629.1|  [L=339]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-31  108.8   6.8    2.5e-31  108.8   6.8    1.9  3  BPD_transp_1     Binding-protein-dependent transport system i
      0.003   17.5   0.2      0.003   17.5   0.2    3.6  4  OppC_N           N-terminal TM domain of oligopeptide transpo
  ------ inclusion threshold ------
        3.1    7.7  10.4       0.14   12.1   2.1    2.3  2  ABC2_membrane_4  ABC-2 family transporter protein
        3.5    7.5   7.8        5.4    6.9   0.9    2.5  2  YqhR             Conserved membrane protein YqhR
        8.3    5.8  10.7       0.12   11.9   2.3    2.1  2  DUF3169          Protein of unknown function (DUF3169)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5      0.69   2.5e+03     149     172 ..      34      56 ..      19      65 .. 0.52
   2 ?   -2.6   1.8       1.1   3.8e+03     126     127 ..      59      60 ..      35     154 .. 0.55
   3 !  108.8   6.8     7e-35   2.5e-31       1     184 [.     155     338 ..     155     339 .] 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.69
                      BPD_transp_1 149 dyseisnggvlalviavlllnlva 172
                                       d ++   g+ ++++  +++l++++
  gi|313125365|ref|YP_004035629.1|  34 DPTALV-GLGVIALMTTVALIAFI 56 
                                       444444.44444444444444444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                      BPD_transp_1 126 vl 127
                                       vl
  gi|313125365|ref|YP_004035629.1|  59 VL 60 
                                       22 PP

  == domain 3  score: 108.8 bits;  conditional E-value: 7e-35
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g+l+G++a+ ++++++d++l++ +++l+++P+++l+i +       +++g   ++ +i +++ +++ ++rlir+++l
  gi|313125365|ref|YP_004035629.1| 155 GMLVGAVAG-YYGGWIDDALMRASETLYAIPFLILVIAFM------TAFGKNLTYaMIGVGIATIPTFARLIRSRVL 224
                                       7899*****.************************999999......****99999799999**************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       +++++d++eaa a G++++ i+ ++v+Pn++ p++ ++ l++g ++   + l+flg     g +  ++++g+++s+ 
  gi|313125365|ref|YP_004035629.1| 225 SVREEDYIEAAQAAGVRDRDIILRHVIPNSFAPVLVQATLQVGVNILIIAGLSFLG----YGAQPPTPSWGQMLSNS 297
                                       ********************************************************....***************88 PP

                      BPD_transp_1 154 s..........nggvlalviavlllnlvadilqrlldprvr 184
                                                  +++ +a++i v+ +nl+ d l ++ldpr+ 
  gi|313125365|ref|YP_004035629.1| 298 ReymlpnpwfsIWPGIAILITVVGFNLIGDGLRDALDPRIN 338
                                       8**************************************96 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   8.4e-07     0.003       4      33 ..      25      54 ..      24     101 .. 0.84
   2 ?   -0.5   0.7      0.35   1.3e+03      21      35 ..     185     199 ..     184     213 .. 0.77
   3 ?   -2.3   0.0       1.2   4.4e+03      23      39 ..     270     286 ..     267     302 .. 0.66
   4 ?   -2.0   0.1       1.1   3.8e+03      19      34 ..     312     327 ..     312     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.4e-07
                            OppC_N  4 qdawrrFkrNklAvvglvilllllliaifa 33
                                      + ++ + +r+++A+vgl +++l++ +a++a
  gi|313125365|ref|YP_004035629.1| 25 RYTLSQVRRDPTALVGLGVIALMTTVALIA 54
                                      5677899*******************9986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                            OppC_N  21 villlllliaifaPl 35 
                                       +++l+++++ +f+  
  gi|313125365|ref|YP_004035629.1| 185 FLILVIAFMTAFGKN 199
                                       568888888888754 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
                            OppC_N  23 lllllliaifaPliaPy 39 
                                       +l+++ +++++    P+
  gi|313125365|ref|YP_004035629.1| 270 ILIIAGLSFLGYGAQPP 286
                                       67788888887444344 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.1
                            OppC_N  19 glvilllllliaifaP 34 
                                       g +il++++ + ++++
  gi|313125365|ref|YP_004035629.1| 312 GIAILITVVGFNLIGD 327
                                       6789999998877775 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   1.4       0.2   7.3e+02     106     131 ..      43      69 ..      36      88 .. 0.52
   2 ?   12.1   2.1   3.8e-05      0.14      95     177 ..     129     215 ..     124     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.2
                   ABC2_membrane_4 106 svllmlvtflitvlfallsgfvg.fsv 131
                                       +++lm + +li+++ ++l+gf + f++
  gi|313125365|ref|YP_004035629.1|  43 VIALMTTVALIAFIDGVLFGFLAeFKT 69 
                                       445555555566666666666421333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.8e-05
                   ABC2_membrane_4  95 llaKlivllllsvllmlvtflitvlfallsgfvgfsvklvl.ellkkclelgllvffavlpiialvllkksy...vl 167
                                       +la l++   +++ + +v++ i+++f++l+g v+   ++ +  +l++  e+   + f++l+i +++++ k+    ++
  gi|313125365|ref|YP_004035629.1| 129 ILARLFYGTRIAITVAIVSTGIAMIFGMLVGAVAGYYGGWIdDALMRASETLYAIPFLILVIAFMTAFGKNLtyaMI 205
                                       5677778888899999***************9987766666379999999999999****99999998887522466 PP

                   ABC2_membrane_4 168 pliltlvyti 177
                                       +++++ + t+
  gi|313125365|ref|YP_004035629.1| 206 GVGIATIPTF 215
                                       6667777665 PP

>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.9    0.0015       5.4      15      44 ..      44      73 ..      41      89 .. 0.79
   2 ?    3.8   1.0     0.013        48      67     100 ..     136     168 ..     131     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0015
                              YqhR 15 lsllakvviiGfvGGvlWsllaylaylfnf 44
                                      ++l+++v++i f+ Gvl+++la +  + n+
  gi|313125365|ref|YP_004035629.1| 44 IALMTTVALIAFIDGVLFGFLAEFKTFANM 73
                                      67999*****************98766553 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.013
                              YqhR  67 Gtvisivligvvsigvallyyvllkkikslwagi 100
                                       Gt i+i  +++vs g+a+++ +l+  +++++ g 
  gi|313125365|ref|YP_004035629.1| 136 GTRIAIT-VAIVSTGIAMIFGMLVGAVAGYYGGW 168
                                       7777765.79*************99999999875 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   1.4      0.87   3.1e+03       7      35 ..      43      71 ..      40      87 .. 0.63
   2 ?   11.9   2.3   3.3e-05      0.12       4      62 ..     145     203 ..     143     238 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.87
                           DUF3169  7 fillmliggliGgiiGfllgafeaekgle 35
                                      +i+lm+  +li +i G l+g++ ++k++ 
  gi|313125365|ref|YP_004035629.1| 43 VIALMTTVALIAFIDGVLFGFLAEFKTFA 71
                                      56677777777777777777776665444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.3e-05
                           DUF3169   4 llkfillmliggliGgiiGfllgafeaekgleelsaalkelllligskilpllli..iavl 62 
                                       ++++ + m++g+l+G+++G+++g+++++  l  +s+ l ++ +li   +++ ++   ++ +
  gi|313125365|ref|YP_004035629.1| 145 IVSTGIAMIFGMLVGAVAGYYGGWIDDA--LMRASETLYAIPFLILVIAFMTAFGknLTYA 203
                                       6778899******************999..4557777777766655533333332553333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2195.40
//
Query:       gi|313125366|ref|YP_004035630.1|  [L=332]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-48  162.9  11.7    6.8e-48  162.9  11.7    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        6.4    6.7  12.3        9.1    6.2   3.4    2.8  2  Trep_Strep    Hypothetical bacterial integral membrane protei


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.0   0.3    0.0084        75      21      44 ..       6      38 ..       2     114 .. 0.67
   2 !  162.9  11.7   7.6e-52   6.8e-48       1     184 [.     115     327 ..     115     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0084
                      BPD_transp_1 21 rpliivllslPsfv....laillvlvf.........v 44
                                      ++++ +l+s+P++v    + ++    +          
  gi|313125366|ref|YP_004035630.1|  6 YTISRLLQSIPVIVgvitITFF----LtdaipgdpvQ 38
                                      689999********54333333....12333444440 PP

  == domain 2  score: 162.9 bits;  conditional E-value: 7.6e-52
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..............................vils 47 
                                       +++lGi++a +rnk++d+++r++  ++ s+Psf+++++l+ +f                              vil+
  gi|313125366|ref|YP_004035630.1| 115 AVPLGIISAKRRNKPTDHVSRIVALLGVSTPSFWIGLMLIIIFsfwldifpatnivlpwaapaavdgaanqidVILT 191
                                       58*************************************************************************** PP

                      BPD_transp_1  48 ilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllgg 124
                                       +++hlilp i+l++l++a+++r+ r+++l++l +++v++ara+G+s+ +i+rk++++na  p+it+++l+++++lgg
  gi|313125366|ref|YP_004035630.1| 192 SIHHLILPTITLGTLQMAAFTRIERSSMLEVLGEEYVKLARAYGVSESKIVRKHAFRNAQLPLITLVGLQLTSALGG 268
                                       ***************************************************************************** PP

                      BPD_transp_1 125 avlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       avl+e+++s +G+g+l+++ai+++d+++ + g++l++++++++ ++++d+ ++++dprv+
  gi|313125366|ref|YP_004035630.1| 269 AVLTETVFSINGMGRLIITAIQNQDFQLVM-GTTLVFGLVFVIGVILTDLSYAYVDPRVS 327
                                       ******************************.***************************96 PP

>> Trep_Strep  Hypothetical bacterial integral membrane protein (Trep_Strep)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.9     0.002        18      30      92 ..     101     162 ..      73     168 .. 0.69
   2 ?    6.2   3.4     0.001       9.1      29      95 ..     253     319 ..     245     328 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.002
                        Trep_Strep  30 vlmlllpaivallagivymllvakvpkfgailimglllgllllltGhgwlvlllaiiggliae 92 
                                       + +ll+++++al+++++  +++ak +++ +   ++ +++ll + t  +w+ l+l+ii+++  +
  gi|313125366|ref|YP_004035630.1| 101 LYLLLSSFTFALITAVPLGIISAKRRNKPT-DHVSRIVALLGVSTPSFWIGLMLIIIFSFWLD 162
                                       445568888888888888888888666544.44555667777888888888888888877555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.001
                        Trep_Strep  29 pvlmlllpaivallagivymllvakvpkfgailimglllgllllltGhgwlvlllaiiggliaelia 95 
                                       p+++l+   +++ l+g v +  v  ++ +g ++i+++    + l++G ++++ l+++ig ++ +l +
  gi|313125366|ref|YP_004035630.1| 253 PLITLVGLQLTSALGGAVLTETVFSINGMGRLIITAIQNQDFQLVMGTTLVFGLVFVIGVILTDLSY 319
                                       889999999999***************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2070.43
//
Query:       gi|313125367|ref|YP_004035631.1|  [L=550]
Description: peptide ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.6e-68  230.7   7.6    3.5e-68  230.3   7.6    1.1  1  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
  ------ inclusion threshold ------
       0.11   12.3   3.0       0.18   11.7   3.0    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.3   7.6   3.9e-72   3.5e-68       2     371 ..      97     452 ..      96     457 .. 0.92

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 3.9e-72
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       +vpaLA+  +evs+ gk y +kL+ ++++s+G+++tAeDv++s+   +  +t   +  ++     i+++++vd+ tv
  gi|313125367|ref|YP_004035631.1|  97 IVPALAKGEPEVSKEGKRYVVKLNSDATYSNGDKVTAEDVKYSYTAPVTEETENASELNM-----IDTITVVDEETV 168
                                       79******99***********************************999999998887777.....9*********** PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSEE CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldri 155
                                       +f lk ++a+f+t+l+ +  +       +ed++  ++ + ++g+GP+++++++ gq++++++n++Ywg  kpk+ +i
  gi|313125367|ref|YP_004035631.1| 169 QFDLKYAYAPFMTTLTWYVVPKS---VREEDKNAFKSGDSLIGSGPFVFDSWQEGQYARIKANENYWGEPKPKVPEI 242
                                       *********99999887666444...5899999**********************************99******** PP

                                       EEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS- CS
                         SBP_bac_5 156 efkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAiD 232
                                       ef  ++++++r++ l++ e d+++e+pp++ ++++  ++  + +e pg g++y afN+k  p +d++vR+A+ yA+D
  gi|313125367|ref|YP_004035631.1| 243 EFVPVTEATTRVTTLKNSENDVIEEIPPKQYPTVRSISDASI-QEVPGIGYFYAAFNCKEGPTADPKVREAIDYAFD 318
                                       ******************************************.********************************** PP

                                       HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH....SHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEET CS
                         SBP_bac_5 233 reeivkavlegyatpansllppsspgadeeykpayka....ydpekAkklLkeaGykdgdggglrekklkltlllas 305
                                        ++ v  + e ++++++s+ p s++  ++ + +++k      d++k k l++eaG  d+           +++++++
  gi|313125367|ref|YP_004035631.1| 319 MDQAVSSYVEPTGIRQYSPYPKSISEDWGFPLDEWKSiphsKDIDKTKSLFDEAGVSDDYS---------FQVIVPP 386
                                       *****************************99999877*********************973.........7776666 PP

                                       TSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHH...HHCTTESEEEEEEECTTSTTHHHHHHHHS CS
                         SBP_bac_5 306 gspaekaiaeliqqqlkkiGikvevktvdwaatyler...vkdgdfdmillgwgadypdpdnflnpfls 371
                                       +   +++i   i +  k++G +++v+ +dw  ++l++    ++ d++++ lgw+++ pdpd+f + +++
  gi|313125367|ref|YP_004035631.1| 387 D-DKREQIGISISNGIKEAGWDASVQRLDW-GAFLDKyvsGSEDDYNIYTLGWSGS-PDPDAFSYFLFG 452
                                       5.56789999********************.6666654558899**********98.666666665554 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.0     2e-05      0.18       1      25 [.      11      34 ..      11      36 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalggcaa 25
                                      kl+RR  L+g ++a+ A+++ gca+
  gi|313125367|ref|YP_004035631.1| 11 KLNRRRVLQGLGGAGIAGLA-GCAG 34
                                      68*******99999977755.5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3680.25
//
Query:       gi|313125368|ref|YP_004035632.1|  [L=198]
Description: hypothetical protein Hbor_05920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-62  210.1   0.0    2.8e-62  209.9   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.9   0.0   1.6e-66   2.8e-62       1     197 [.       1     194 [.       1     195 [. 0.99

  Alignments for each domain:
  == domain 1  score: 209.9 bits;  conditional E-value: 1.6e-66
                                       -EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S-- CS
                   Methyltrn_RNA_2   1 mrefvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvs 77 
                                       mr+fv+++++apT+++++lddl+G agrldvl+rcv+ a+f+sh iRe v v+lvL     ++ t+++e+ e+++ +
  gi|313125368|ref|YP_004035632.1|   1 MRQFVIIGHDAPTTPEFSLDDLAGGAGRLDVLCRCVNSAFFLSHAIRESVRVHLVLG----DEFTVRFEGAELRRLN 73 
                                       9********************************************************....9*************** PP

                                       SSHHHHHHHHHHHHCHCC.TGCCSEEEEETTEEEE---HHHHHHHHHCTSEEEEESTTSEEGGGS---SSEEEEEE- CS
                   Methyltrn_RNA_2  78 pderniailikkalkave.eikkqekkvrpgltVrkegfealleelsekksiillkekGedisnakielnPvFilgd 153
                                       pder+ a li+ al+ +e +i++  ++++pg+ +r+ gf+a l++++    +i l+e+G+ + +++ + +PvF+l+d
  gi|313125368|ref|YP_004035632.1|  74 PDERSTAALIRGALDVREeAIGHMPAEASPGVSIRRMGFDATLDAVATDGTVIELHENGDPVADVEPPEDPVFVLSD 150
                                       ***************999899******************************************************** PP

                                       TT-SHHHHHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHHHH CS
                   Methyltrn_RNA_2 154 HidlpeeeekllerlkakrvslgPlsLhadhcvtlihneldkke 197
                                       H d++++e+  l++++++rv+lgP +Lhadh +t++hn ld+  
  gi|313125368|ref|YP_004035632.1| 151 HHDFTDDEAAALADAADERVRLGPEVLHADHSITVAHNYLDTDG 194
                                       *****************************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 1074.79
//
Query:       gi|313125369|ref|YP_004035633.1|  [L=240]
Description: hypothetical protein Hbor_05940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   14.9   0.0        1.1    8.6   0.0    2.1  2  FliD_C    Flagellar hook-associated protein 2 C-terminus
      0.037   13.4   0.0      0.054   12.9   0.0    1.2  1  DUF5040   Domain of unknown function (DUF5040)


Domain annotation for each model (and alignments):
>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0029        26      54      90 ..      98     133 ..      86     156 .. 0.73
   2 ?    8.6   0.0   0.00012       1.1      47      74 ..     208     235 ..     206     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0029
                                       CCHCHHHHHHHHCCCCCCCCCS..-----XXXXXXXX CS
                            FliD_C  54 ealkeFVdaYNalvteinektkekedeikdeekaksG 90 
                                       ++ ++FV++YN+ v++ ++ ++ +  +   e  ++sG
  gi|313125369|ref|YP_004035633.1|  98 QDYESFVESYNDYVESRSGVLD-DVSTDFPEPHETSG 133
                                       45678********999888777.33333335555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00012
                                       C-SCCCCCCHCHHHHHHHHCCCCCCCCC CS
                            FliD_C  47 tDtdkikealkeFVdaYNalvteinekt 74 
                                        D+ +++  ++ FV++YN+ v+e+++ +
  gi|313125369|ref|YP_004035633.1| 208 PDVRQLVGGFEGFVESYNDYVAELESDL 235
                                       69999******************99876 PP

>> DUF5040  Domain of unknown function (DUF5040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     6e-06     0.054      77     153 ..     115     190 ..      94     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-06
                           DUF5040  77 eanlkekytdyktpfdrsnyaaaydyvikrylsecyelkddpkskyyntkygkpavivlctdwhdartvynesirkl 153
                                        + l +  td+  p ++s   a  d ++ r    c e+  +   +y +t+yg  a+ v  t w   r +  +s  ++
  gi|313125369|ref|YP_004035633.1| 115 SGVLDDVSTDFPEPHETSGVVAERDRIVDRIREVCDEIAVQ-LHRYDGTDYGTFATTVSGTRWELKRELDRTSYLRV 190
                                       45678889***********************9999998776.579******************99988777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.58
# Mc/sec: 1243.36
//
Query:       gi|313125370|ref|YP_004035634.1|  [L=339]
Description: membrane-bound metal-dependent hydrolase (duf457) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-10   39.1  24.5    2.8e-08   33.3  24.5    3.0  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3  24.5   1.6e-12   2.8e-08       4     162 ..       3     245 ..       1     335 [. 0.82

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.6e-12
                              YdjM   4 ltHallGaalglalaallgaakeavllavavlg..AllPDiDhpsstlgrklgllskklak........lvgHRgft 70 
                                         H  l++al+  l  l+g+++ ++l+a++v++  AllPD+D+   + ++ l+ + +++ +        ++ HR +t
  gi|313125370|ref|YP_004035634.1|   3 VGHEFLAFALAGTLTRLTGRDARTALFAGGVAAlcALLPDLDVAYGFATYLLAVADGTTLSwdafwgvtNGVHRVVT 79 
                                       589999*************9999999999998888*******88888888888888876669*************** PP

                              YdjM  71 HSllflallalvlllllrlfgrsa..................................................... 94 
                                       H l++ a+++l ++++++ + ++                                                      
  gi|313125370|ref|YP_004035634.1|  80 HPLPVGAAATLCFAAAVAIVPARGrgketrmqnrtphgllihttlavvasvvaaaviwamarvssesaavvaatylg 156
                                       ***99666666666666555555456699************************************************ PP

                              YdjM  95 .......................lrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltll.. 146
                                                               +l+++  +g+l+H+++D+l  ++ pl++P  ++  + +++f   d+ + ll  
  gi|313125370|ref|YP_004035634.1| 157 tvcvvgaavsrrfgkesrlgigtPTLAFAAGVGFLTHPFGDVLMAAPPPLFAPAAPSPLTDRVVFS-ADETVNLLni 232
                                       ******************999777777777777*********************976666666666.5554444323 PP

                              YdjM 147 ...srrglvalelvllvly 162
                                          +      +++v+++l+
  gi|313125370|ref|YP_004035634.1| 233 lfvE------VATVWAGLF 245
                                       3320......333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1845.61
//
Query:       gi|313125371|ref|YP_004035635.1|  [L=420]
Description: hypothetical protein Hbor_05960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-10   40.8   3.1    5.7e-07   29.2   0.9    3.2  2  Arylsulfotran_2  Arylsulfotransferase (ASST)
    4.8e-06   25.7   3.1    6.3e-05   22.0   2.0    2.9  2  Arylsulfotrans   Arylsulfotransferase (ASST)
    0.00013   21.8   0.5       0.86    9.8   0.3    4.1  3  NHL              NHL repeat
  ------ inclusion threshold ------
        1.5    8.8   5.5       0.31   11.1   1.0    2.1  2  DUF3185          Protein of unknown function (DUF3185)


Domain annotation for each model (and alignments):
>> Arylsulfotran_2  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0018       8.3     148     182 ..     150     182 ..     142     188 .. 0.90
   2 !   29.2   0.9   1.3e-10   5.7e-07     139     296 ..     194     337 ..     183     339 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0018
                   Arylsulfotran_2 148 svekfedgdyLiSlrelsslflirpkegkvlWqlq 182
                                       +ve  + g++L+S  e+  +f ++  +g+v+Wq +
  gi|313125371|ref|YP_004035635.1| 150 DVELLDSGEFLVSDMEYERIFTVK--NGEVTWQWN 182
                                       89999******************9..9*****965 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 1.3e-10
                   Arylsulfotran_2 139 kpedyfHlNsvekfedgdyLiSlrelsslflirpkegkvlWqlqGpkggdfeldnstfsrQHdariveetedkivis 215
                                       +  d  H+N+v+  ++  yL+S+r+ + l++i+  eg v+   +  ++gd + d    + QH+++      ++ ++ 
  gi|313125371|ref|YP_004035635.1| 194 TTTDWLHINDVDALSEDRYLVSVRNANQLVVIERGEG-VVEVINKDENGDGTGDPEVLLQQHNPQWL----NNGSVL 265
                                       56799******999999****************5554.33333334456666666679999999999....444444 PP

                   Arylsulfotran_2 216 lfnNentdtnerepttglildvdlq..nkevtllrklkdaedeissvsqGsyqllpnghvlveegsigrveeydang 290
                                       + +           ++ +i++++ +  + e +   +++ +++ +   +   ++ l+ng+ l+++  + rv e+++ g
  gi|313125371|ref|YP_004035635.1| 266 VADS----------HNDRIVELHRNntTDEWEVAWAVY-EAEGVPFSWPRDADRLANGNTLITDSLNQRVVEVNESG 331
                                       4444..........344455444432122222333333.55556666666677777777777777777777777777 PP

                   Arylsulfotran_2 291 kivlea 296
                                         v+++
  gi|313125371|ref|YP_004035635.1| 332 MTVWSY 337
                                       777766 PP

>> Arylsulfotrans  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   2.0   1.4e-08   6.3e-05     132     211 ..     173     235 ..     145     286 .. 0.79
   2 ?    0.4   0.0     0.052   2.3e+02      62     141 ..     315     338 ..     291     359 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.4e-08
                    Arylsulfotrans 132 ktGkvvkewdlakiLdpyrdallkaakapfgdiagvgagrdWlHiNsveydekddsiivSsRhqsavvkidyrtkkv 208
                                       k+G+v+++w                +   + d++ + ++ dWlHiN v+    +d  +vS+R+ + +v i++ ++ v
  gi|313125371|ref|YP_004035635.1| 173 KNGEVTWQW----------------NASSMYDAPADPTTTDWLHINDVDALS-EDRYLVSVRNANQLVVIERGEGVV 232
                                       333333333................33445566677899**********888.99****************888877 PP

                    Arylsulfotrans 209 kWi 211
                                       + i
  gi|313125371|ref|YP_004035635.1| 233 EVI 235
                                       655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.052
                    Arylsulfotrans  62 lilsgqklaefdllGrvikeyrlpggyidlhHdivelpngnllvlvaeenykrkdgkkvktveDtiievdktGkvvk 138
                                       li+                                                        ++++  ++ev+++G  v+
  gi|313125371|ref|YP_004035635.1| 315 LIT--------------------------------------------------------DSLNQRVVEVNESGMTVW 335
                                       333........................................................445555666666666666 PP

                    Arylsulfotrans 139 ewd 141
                                       +++
  gi|313125371|ref|YP_004035635.1| 336 SYK 338
                                       554 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.016        73       5      20 ..     149     166 ..     146     168 .. 0.83
   2 !    9.8   0.3   0.00019      0.86      11      26 ..     260     275 ..     259     277 .. 0.90
   3 ?    3.3   0.0     0.021        94       1      26 [.     300     325 ..     300     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.016
                                       EEEEEETTTEEEEEE..C CS
                               NHL   5 hGvavdsnGdiyVaD..s 20 
                                       h+v ++++G+++V+D  +
  gi|313125371|ref|YP_004035635.1| 149 HDVELLDSGEFLVSDmeY 166
                                       889999*********644 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00019
                                       TTTEEEEEECCCTEEE CS
                               NHL  11 snGdiyVaDsenhrvq 26 
                                       +nG ++VaDs+n r++
  gi|313125371|ref|YP_004035635.1| 260 NNGSVLVADSHNDRIV 275
                                       79**********9986 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.021
                                       BSSEEEEEEETTTEEEEEECCCTEEE CS
                               NHL   1 fnyPhGvavdsnGdiyVaDsenhrvq 26 
                                       f++P++   + nG+ +++Ds n+rv+
  gi|313125371|ref|YP_004035635.1| 300 FSWPRDADRLANGNTLITDSLNQRVV 325
                                       78999999999*************96 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.0     7e-05      0.31       4      48 ..      13      56 ..      10      58 .. 0.87
   2 ?   -1.3   0.2      0.52   2.3e+03       3      16 ..     404     417 ..     403     418 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7e-05
                           DUF3185  4 GiiLlvaGivLlvfGynasdSlgsqvseaftGsttdktlllligG 48
                                      G +L+v G+vLlv  +  s +l+ +v  a+  + t++tl+   gG
  gi|313125371|ref|YP_004035635.1| 13 GTMLIVFGVVLLVSSLVVSAALAPSVGAAG-NDGTPQTLVGSQGG 56
                                      899***********************9999.77888888776666 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.52
                           DUF3185   3 iGiiLlvaGivLlv 16 
                                       +++ + +aG vL+v
  gi|313125371|ref|YP_004035635.1| 404 VSLTMTIAGTVLIV 417
                                       67788899999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 2281.77
//
Query:       gi|313125372|ref|YP_004035636.1|  [L=191]
Description: nudix family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-14   52.4   0.4    7.2e-14   51.9   0.4    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.4     4e-18   7.2e-14       4     121 ..      53     169 ..      50     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 4e-18
                                       EEEEEEEEETTSEEEEEEES....SSSTTTEESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   4 ravgvvllnekgevLlvrrs....kkpfpgWelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhylapyd 75 
                                        av v+ + +++ v+lv++     ++  +g  lP+G +e ++ ++++AArREl EEtG+ea  le++g++    p +
  gi|313125372|ref|YP_004035636.1|  53 EAVVVLPFTPDDDVVLVEEWrqavGRVNRG--LPAGSLESDDdDIAAAARRELTEETGYEAGSLEYVGSV---EPAN 124
                                       5899999999989*****885466666666..*****************************999***943...4444 PP

                                       EEEEEEEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTH CS
                             NUDIX  76 gpygdeheilyvfl.eevegelepndenevsevrwvpleellkekla 121
                                       g   + h++ +v + +e++ge+e++  ne   v   p++++l ++l+
  gi|313125372|ref|YP_004035636.1| 125 GLLNSVHHH-FVARdCEPTGEQELD-FNESIRVAVEPYDDVLTAALD 169
                                       444433333.33337******9999.999888889999999555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1097.50
//
Query:       gi|313125373|ref|YP_004035637.1|  [L=260]
Description: caax amino terminal protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-17   62.7   2.9    3.1e-17   62.7   2.9    2.5  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   4.0      0.19   3.4e+03      48      77 ..      26      83 ..      10     121 .. 0.62
   2 !   62.7   2.9   1.7e-21   3.1e-17       4      91 ..     142     237 ..     138     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.19
                                      HHHCSGGGHHHH............................HHHHHHHHHHHHHHHHTT CS
                              CPBP 48 FglaHlpngpsv............................llaalaGlvlgylylktg 77
                                       ++a  + g+++                             +  + G+++ yl++++ 
  gi|313125373|ref|YP_004035637.1| 26 LAIAGPALGIAFvflvsvplvltgieitpilnisislvflTWGGIGGMAFLYLRYRNE 83
                                      4444444433322333333334444444444444455444666777777777777776 PP

  == domain 2  score: 62.7 bits;  conditional E-value: 1.7e-21
                                       THHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG........HHHHHHHHHHHHHHHHH CS
                              CPBP   4 lllvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn........gpsvllaalaGlvlgyl 72 
                                       lll++ + +l+ +++EEllfRg+++++l+e +s+++ il++s++F+++H+            s+  ++l ++v+g++
  gi|313125373|ref|YP_004035637.1| 142 LLLLIPASFLFIGVGEELLFRGVVQSRLRESFSPAVGILLASVIFAAIHFFAiggtpmarLTSISILLLPSVVFGIV 218
                                       5667778999*********************999*********************9999765699************ PP

                                       HHHTT-HHHHHHHHHHHHH CS
                              CPBP  73 ylktgsllaaillHallnl 91 
                                       y++t +ll++i++H+++++
  gi|313125373|ref|YP_004035637.1| 219 YEYTDNLLVPIFIHGAYDA 237
                                       ****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1444.94
//
Query:       gi|313125374|ref|YP_004035638.1|  [L=193]
Description: hypothetical protein Hbor_05990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1094.23
//
Query:       gi|313125375|ref|YP_004035639.1|  [L=515]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-41  141.4  65.6      1e-40  139.4  23.0    4.7  5  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
    6.6e-07   29.5  43.1      0.025   14.9   1.4    5.9  5  DUF948          Bacterial protein of unknown function (DUF948
    0.00023   21.5   2.5     0.0035   17.7   0.1    3.8  3  HAMP            HAMP domain
     0.0049   15.6  39.8       0.12   11.0  20.1    2.2  2  AAA_13          AAA domain
     0.0053   17.3   3.7     0.0053   17.3   3.7    5.1  5  Syntaxin-6_N    Syntaxin 6, N-terminal
  ------ inclusion threshold ------
      0.031   14.3  47.2       0.32   11.0   1.7    5.3  5  Laminin_II      Laminin Domain II
      0.042   13.9  39.2       0.22   11.6   2.0    5.2  5  DUF1664         Protein of unknown function (DUF1664)
      0.048   14.0  37.4      0.056   13.7   4.8    6.1  6  BLOC1_2         Biogenesis of lysosome-related organelles com
      0.063   12.2  44.4      0.022   13.7  13.6    4.2  4  Spc7            Spc7 kinetochore protein
       0.14   12.9  37.4      0.065   14.0   5.2    5.0  5  DUF2203         Uncharacterized conserved protein (DUF2203)
       0.32   11.2   3.3       0.26   11.5   0.4    2.2  2  BLYB            Borrelia hemolysin accessory protein
       0.92    7.6  36.2      0.039   12.1   9.6    3.1  2  EzrA            Septation ring formation regulator, EzrA
       0.99    9.5   8.4          2    8.5   0.0    4.2  3  Mis12           Mis12 protein
          1    7.5  42.3          1    7.5  40.2    1.7  2  FPP             Filament-like plant protein, long coiled-coil
        1.5    7.7  43.3        0.1   11.5   2.0    4.9  5  IFT57           Intra-flagellar transport protein 57
        1.6    6.1  42.6      0.015   12.8  19.0    2.3  2  DUF3584         Protein of unknown function (DUF3584)
        1.7    7.7  35.7       0.35    9.9   4.1    4.3  5  APG17           Autophagy protein Apg17
        2.1    8.4  35.2       0.75    9.9   0.3    5.7  5  COG2            COG (conserved oligomeric Golgi) complex comp
        2.7    7.8  24.7       0.29   10.9   1.6    4.6  6  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
        3.3    7.6  33.7       0.87    9.5   2.8    5.3  5  Sec34           Sec34-like family
        3.6    8.1  36.8      0.086   13.3   2.5    6.2  6  ZapB            Cell division protein ZapB
          4    7.6  15.7        3.9    7.6   1.3    4.8  5  bZIP_1          bZIP transcription factor
        4.3    7.7  15.1       0.33   11.4   3.5    3.0  3  SLX9            Ribosome biogenesis protein SLX9
          5    7.3  45.8        1.4    9.1  12.5    3.9  3  ATG16           Autophagy protein 16 (ATG16)
        7.1    6.5  18.6        6.5    6.6   0.3    5.8  7  DASH_Duo1       DASH complex subunit Duo1
          8    5.6  34.3      0.058   12.6   4.3    4.6  5  TMPIT           TMPIT-like protein
        8.5    6.5  36.6        2.9    8.0   4.5    5.0  5  Mod_r           Modifier of rudimentary (Mod(r)) protein
        9.8    5.1  38.6          1    8.3  10.0    3.1  3  AIP3            Actin interacting protein 3


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.8      0.14        93     117     163 ..      82     128 ..      69     137 .. 0.78
   2 !    6.9   9.7    0.0079       5.1      75     169 ..      93     194 ..      84     197 .. 0.82
   3 ?    6.4  16.1     0.011       7.2      76     153 ..     168     245 ..     137     257 .. 0.56
   4 !  139.4  23.0   1.6e-43     1e-40       4     171 ..     250     424 ..     247     425 .. 0.93
   5 !    8.7   7.9    0.0023       1.4     109     165 ..     411     467 ..     409     473 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 117 eegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnq 163
                                       + g + +    e++k +v+ ++e +++++ ++ + e+q++s +e  +
  gi|313125375|ref|YP_004035639.1|  82 AIGGTATLAIVEDMKVLVSDAEEKSEELNALTETLEQQAESYSEKME 128
                                       55666666677899999999999999999999999999999876554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0079
                                       HHHHHHHHHHHHHHHHHHHHH..............HHHHH.....HH..HHHHHHHHHHCCHHHHHHHHHHHHHHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrq.....rv..eegselveetgealkeiveavaevadlv 144
                                       ++ + L + + ++++e++al + ++++ ++  e +e +       rv  ++ s+ + + g+a++++v+ +++v+ ++
  gi|313125375|ref|YP_004035639.1|  93 EDMKVLVSDAEEKSEELNALTETLEQQAESYSEKMEAASDgdltvRVdpDSESDAMTRIGQAFNSMVADIESVTLQI 169
                                       678999999999**********9*999999999988653222222552256678899999***************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 145 qeiaaaseeqsasieevnqaveeva 169
                                       q  a+ ++e s+ ++  ++av++ +
  gi|313125375|ref|YP_004035639.1| 170 QSFAQRVDEESTEVTTSANAVKQTS 194
                                       ***************9999999876 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  76 EVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaase 152
                                        +++ A+r  + + e+++   ++++ + d+++s+ee    +e+     +++  +l++++++++e+a++ +e+aa s+
  gi|313125375|ref|YP_004035639.1| 168 QIQSFAQRVDEESTEVTTSANAVKQTSTDVASSVEEISAATETQHRNLDNASGELSNLSATIEEIASSADEVAAESQ 244
                                       34445555555555555555555555555555555555555555555555555555555555555555555555544 PP

                                       H CS
                         MCPsignal 153 e 153
                                        
  gi|313125375|ref|YP_004035639.1| 245 R 245
                                       3 PP

  == domain 4  score: 139.4 bits;  conditional E-value: 1.6e-43
                                       HHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHH CS
                         MCPsignal   4 aeeaseeAeeg.......gkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVV 73 
                                       a+e+++ A++g       +   +++v+++ee+++s+++i +++e id+iad+TN+LALNA+iEAA AG++G+GFaVV
  gi|313125375|ref|YP_004035639.1| 250 AKESRKAANKGtekmeqlESRASETVAEVEELQSSVEQIGEVVELIDDIADKTNILALNASIEAASAGDAGEGFAVV 326
                                       6666666666644444447777899**************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  74 AdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaa 150
                                       A+EV++LAe++a+a++e+e+li  ++  ++++++ + et+++++ + ++v e+ e+l ++v +++e ++++q i+ a
  gi|313125375|ref|YP_004035639.1| 327 ASEVKSLAEETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSISDA 403
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 151 seeqsasieevnqaveevakv 171
                                       ++eqs+s + v + v+ev+++
  gi|313125375|ref|YP_004035639.1| 404 TDEQSKSTQGVVSMVDEVTDL 424
                                       *************99999876 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0023
                                       .HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 109 leetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqav 165
                                        + +++ v+e ++l ++t+++ +++++a++e ++  qeia+as+e+s+ +++ +  v
  gi|313125375|ref|YP_004035639.1| 411 TQGVVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQAIV 467
                                       67889999*****************************************99987655 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0082       5.2      52      85 ..      91     124 ..      83     133 .. 0.73
   2 !    9.2   2.9    0.0022       1.4      28      75 ..     162     209 ..     147     219 .. 0.76
   3 !   11.0   4.7   0.00062       0.4      29      88 ..     223     282 ..     213     309 .. 0.55
   4 !   14.9   1.4   3.8e-05     0.025      23      88 ..     336     401 ..     322     402 .. 0.78
   5 ?    7.0   7.1     0.011       7.1      23      88 ..     399     464 ..     396     465 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0082
                            DUF948  52 llakvnelledvneklekvdplteavadlgesvs 85 
                                       +++ +++l++d +ek+e++++lte +++ +es s
  gi|313125375|ref|YP_004035639.1|  91 IVEDMKVLVSDAEEKSEELNALTETLEQQAESYS 124
                                       5666777788888888888888887777666654 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplte 75 
                                       +++++ +i++  ++vd+ ++ev++  + v+++  dv + +e++ + te
  gi|313125375|ref|YP_004035639.1| 162 IESVTLQIQSFAQRVDEESTEVTTSANAVKQTSTDVASSVEEISAATE 209
                                       456666677777999999999999999999999999999999988876 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00062
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       ++++atiee+ + +d++  e+++++++++e  +  n+ +ek+++l + + ++ + v+el+
  gi|313125375|ref|YP_004035639.1| 223 SNLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASETVAEVEELQ 282
                                       455555555555555555555555555555444444444444443333333333333332 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 3.8e-05
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       + +k  +e+++ i+++e  ++++++++ ++ +++++  + v e +ek+  ++  +++  es+++++
  gi|313125375|ref|YP_004035639.1| 336 ETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSIS 401
                                       447778888888888889999999999999999999999999999999999999999998888875 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.011
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       ++++  de +++ +++ + vd++++ ++++ ++++++ +  +e++++ +++ +a ++l+e+ ++l+
  gi|313125375|ref|YP_004035639.1| 399 SISDATDEQSKSTQGVVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQ 464
                                       6778899999***************************************************99986 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   5.5e-06    0.0035      16      51 ..     126     162 ..     114     164 .. 0.88
   2 ?    0.6   0.1       1.2   7.5e+02       6      21 ..     225     240 ..     196     255 .. 0.75
   3 ?   -1.1   0.0       4.1   2.6e+03      16      28 ..     445     459 ..     440     488 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.5e-06
                                       HHHHHTTTBTSSTCCT.TSSSHHHHHHHHHHHHHHHH CS
                              HAMP  16 aarriaaGdldtrlpv.sgrDEiGeLarafNaMldrL 51 
                                        +++ ++Gdl++r+++ s  D + ++++afN M+  +
  gi|313125375|ref|YP_004035639.1| 126 KMEAASDGDLTVRVDPdSESDAMTRIGQAFNSMVADI 162
                                       5777788******9999****************9776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.2
                                       THHHHHHHHHHHHHHT CS
                              HAMP   6 ilrPLrrLaraarria 21 
                                       +++ ++++a++a+++a
  gi|313125375|ref|YP_004035639.1| 225 LSATIEEIASSADEVA 240
                                       3444566666666666 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.1
                                       HHHHHTT..TBTSST CS
                              HAMP  16 aarriaa..Gdldtr 28 
                                       a+++ia+  ++l+++
  gi|313125375|ref|YP_004035639.1| 445 ATQEIASasNELSEQ 459
                                       555555322333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0  20.1   0.00019      0.12     281     466 ..     102     298 ..      86     314 .. 0.71
   2 !    9.6  12.6    0.0005      0.32     317     455 ..     328     465 ..     299     477 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                            AAA_13 281 feekqerLekliekveskkselleklkavsde........asensafeed...keelkaeaealeeqLkglqralea 346
                                        eek e+L+ l e++e++ ++++ek++a+sd         +se  a+ +     + + a +e ++ q+++  +++++
  gi|313125375|ref|YP_004035639.1| 102 AEEKSEELNALTETLEQQAESYSEKMEAASDGdltvrvdpDSESDAMTRIgqaFNSMVADIESVTLQIQSFAQRVDE 178
                                       56677888888888888888888888888875344332223332222222222344444556666666666666666 PP

                            AAA_13 347 KrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykkl 421
                                         +e+ +s   + vk+ ++ + ++v+ei +  +   +  +n   e +++   +e     + e+ +e ++  ++ k+ 
  gi|313125375|ref|YP_004035639.1| 179 ESTEVTTS--ANAVKQTSTDVASSVEEISAATETQHRNLDNASGELSNLSATIEEIAssADEVAAESQRTVEQAKES 253
                                       66666663..4556666677788888888888888888888888888888888874322466667777666888888 PP

                            AAA_13 422 ekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinke 466
                                        ka++k ++++++ e+++ +  +e++eL+ +++++ + +e i ++
  gi|313125375|ref|YP_004035639.1| 254 RKAANKGTEKMEQLESRASETVAEVEELQSSVEQIGEVVELIDDI 298
                                       9999999999***************************99999875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0005
                            AAA_13 317 safeedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkakiesikklvaeineliakhNekvanleeek 392
                                       s+ ++  ee  +++e++e+ ++g++   e+  +++ + + e++++ + + ++ +++ ++   i++ Ne ++++ +++
  gi|313125375|ref|YP_004035639.1| 328 SEVKSLAEETAKATEEVESLIDGVETSTENVTDDIYEtQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSISDAT 404
                                       55667788889999999999**************998456699999999888899999999**************99 PP

                            AAA_13 393 eeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                        e  k+ +   v ++ +e++ + ++ +  +++++ + +e++++++e++ + +e +e  +ql+ 
  gi|313125375|ref|YP_004035639.1| 405 DEQSKSTQG--VVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQA 465
                                       999999888..5556688888888888888888888888888888888888887777777665 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2       0.6   3.8e+02      29      58 ..     100     128 ..      88     143 .. 0.69
   2 ?    3.8   6.9      0.13        86       3      74 ..     155     239 ..     153     252 .. 0.67
   3 ?    3.3   5.1      0.19   1.2e+02       8      66 ..     230     287 ..     224     310 .. 0.59
   4 !   17.3   3.7   8.3e-06    0.0053       3      88 ..     323     411 ..     322     425 .. 0.77
   5 ?    6.1   3.7     0.026        16      10      80 ..     414     483 ..     399     494 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.6
                      Syntaxin-6_N  29 edtssstseeldetrteLrkalrsiewdle 58 
                                       +d+++ +seel+ +++ L+++ +s ++++e
  gi|313125375|ref|YP_004035639.1| 100 SDAEE-KSEELNALTETLEQQAESYSEKME 128
                                       34333.377777777777777777666554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrw.erlledtsss.............tseeldetrteLrkalrsiewdledLeetvr 65 
                                       F+++ +++++   +++s  +r  e+  e+t+ s             + ee++ +++  +++l++++ +l++L  t++
  gi|313125375|ref|YP_004035639.1| 155 FNSMVADIESVTLQIQSFAQRVdEESTEVTT-SanavkqtstdvasSVEEISAATETQHRNLDNASGELSNLSATIE 230
                                       6777777777777888888888323333333.224666777777777888888888899999999999999999997 PP

                      Syntaxin-6_N  66 iveknpskf 74 
                                        + ++ +++
  gi|313125375|ref|YP_004035639.1| 231 EIASSADEV 239
                                       666655543 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.19
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrw.erlledtssstseeldetrteLrkalrsiewdledLeetvri 66 
                                       ee+ +s++++++  +r  e+ +e+   +  ++  e +++L++  ++   ++e+L+ +v+ 
  gi|313125375|ref|YP_004035639.1| 230 EEIASSADEVAAESQRTvEQAKESR--KAANKGTEKMEQLESRASETVAEVEELQSSVEQ 287
                                       6788888888887777733322222..334555555566666666666666666666632 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 8.3e-06
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrwerlledtss...stseeldetrteLrkalrsiewdledLeetvriveknpsk.fk 75 
                                       F +v++eV++ ++++++  ++ e+l +  ++   + ++++ et++e++++ +++ + +e L ++v+ +e++++   +
  gi|313125375|ref|YP_004035639.1| 323 FAVVASEVKSLAEETAKATEEVESLIDGVETsteNVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESiQS 399
                                       8899******************999888777434489****************************999888877355 PP

                      Syntaxin-6_N  76 idekelsrrrafv 88 
                                       i++ + +++ +  
  gi|313125375|ref|YP_004035639.1| 400 ISD-ATDEQSKST 411
                                       554.444443333 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.026
                      Syntaxin-6_N  10 Vqkslnkaeslyrrwerlledtsss......tseeldetrteLrkalrsiewdledLeetvriveknpskfkideke 80 
                                       V + +++++ l ++         ++        ee   +++e+ +a ++++++ ++L+  v+  e +++ ++++e e
  gi|313125375|ref|YP_004035639.1| 414 VVSMVDEVTDLSDQT-------ATEaqnvsaAAEEQTAATQEIASASNELSEQAQQLQAIVSGFEVSQTPMELNEGE 483
                                       333333334444333.......3323444456899999999999999999999999999998777766666666655 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.013       8.3      16      84 ..      89     129 ..      83     140 .. 0.53
   2 ?    4.7  11.2     0.044        28       8     107 ..     169     258 ..     145     259 .. 0.54
   3 ?    9.5  10.8    0.0015      0.94       6     100 ..     202     296 ..     197     319 .. 0.59
   4 ?   11.0   1.7   0.00049      0.32       1      69 [.     330     398 ..     330     402 .. 0.88
   5 ?    2.3   8.1      0.25   1.6e+02       1      72 [.     393     464 ..     393     474 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                       l++++++                            +  + dA++++ +L+ l + L+++ ++  ++ ea
  gi|313125375|ref|YP_004035639.1|  89 LAIVEDM----------------------------KVLVSDAEEKSEELNALTETLEQQAESYSEKMEA 129
                                       4444444............................4445555555555555555555554444444333 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                       +++ a+ v e  +++ +  + +k+    +++svee+ +  +   + ++ A+ + ++L  +++++ +         ++
  gi|313125375|ref|YP_004035639.1| 169 IQSFAQRVDEESTEVTTSANAVKQTSTDVASSVEEISAATETQHRNLDNASGELSNLSATIEEIASS-------ADE 238
                                       3444555555555555555555555555555555555555555555555555555555555555444.......222 PP

                                       ...HHHHHHHHHHHHHHHHHHHH CS
                        Laminin_II  85 ssslsdniseikelIaqARkaAn 107
                                          + ++ ++  e+ +  RkaAn
  gi|313125375|ref|YP_004035639.1| 239 ---VAAESQRTVEQAKESRKAAN 258
                                       ...55555555555555666666 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       +e++  ++   + l + s +l+n+++ ++ei++s++e+ ++ +   ++ ++ r++  k +++++qL+++ +e     
  gi|313125375|ref|YP_004035639.1| 202 EEISAATETQHRNLDNASGELSNLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASETVAEV 278
                                       33333333333444444557888888888888888887777777777777777777777777777777765544444 PP

                                       HH...HHHHHHHHHHHHH CS
                        Laminin_II  83 eassslsdniseikelIa 100
                                       e+ +s  ++i e+ elI 
  gi|313125375|ref|YP_004035639.1| 279 EELQSSVEQIGEVVELID 296
                                       443333344555555554 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00049
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                       +k+la+e  + ++ev++ + ++++ +en+ +++ e ++++++  + v +a + + d+   + + ++ ++
  gi|313125375|ref|YP_004035639.1| 330 VKSLAEETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQ 398
                                       5899***************************************99999999999888777776666655 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.25
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLl 72 
                                       s+e ++++++ + e  + ++++   ++++ +   + +++++++ + +++ + a+++  +++ +L ++a+qL 
  gi|313125375|ref|YP_004035639.1| 393 SNESIQSISDATDEQSKSTQGVVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQ 464
                                       578888899999999999999999999988888888999999999999888888888888888888888874 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2       1.2   7.5e+02      93     119 ..      96     122 ..      86     133 .. 0.45
   2 ?   10.9   3.8   0.00055      0.35      42     120 ..     154     232 ..     142     243 .. 0.52
   3 ?    9.1   4.3     0.002       1.3      37     121 ..     213     296 ..     212     304 .. 0.79
   4 ?   11.6   2.0   0.00034      0.22      44     121 ..     324     401 ..     320     404 .. 0.86
   5 ?    4.8   4.6     0.042        27      37     103 ..     398     467 ..     395     480 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                           DUF1664  93 redlseigedvesvkeavegleskler 119
                                       +  +s+ +e++e+++++ e+le++ e+
  gi|313125375|ref|YP_004035639.1|  96 KVLVSDAEEKSEELNALTETLEQQAES 122
                                       333333344444444444444433332 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00055
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                       a +s+  ++e+v  ++++  ++  ++  +v ++ +++k++s+++++ v+e++  +++ ++++++ +   ++l +++e
  gi|313125375|ref|YP_004035639.1| 154 AFNSMVADIESVTLQIQSFAQRVDEESTEVTTSANAVKQTSTDVASSVEEISAATETQHRNLDNASGELSNLSATIE 230
                                       44444444444444444444444444445555555555555555555555555555555555555555555555555 PP

                           DUF1664 119 ri 120
                                       +i
  gi|313125375|ref|YP_004035639.1| 231 EI 232
                                       44 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.002
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       r+l +a  ++s +l    e++a+  ++ +++ +r  ++ +e+ +++++ +e+++++++  se+  +ve++++ ve++
  gi|313125375|ref|YP_004035639.1| 213 RNLDNASGELS-NLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASETVAEVEELQSSVEQI 288
                                       77777777776.47778888888888888888888888888888888888888888888888888888888888888 PP

                           DUF1664 114 esklerie 121
                                       ++ +e i+
  gi|313125375|ref|YP_004035639.1| 289 GEVVELID 296
                                       88777665 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00034
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       + v+++++++ e+ a++ ++ +s id v+++ +++++ + e+++e+++ r+ + e  e++  v   +e+ ++++++i
  gi|313125375|ref|YP_004035639.1| 324 AVVASEVKSLAEETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSI 400
                                       67899999999********************************9999999988888888888888888888888877 PP

                           DUF1664 121 e 121
                                       +
  gi|313125375|ref|YP_004035639.1| 401 S 401
                                       6 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.042
                           DUF1664  37 rslsdavesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv 103
                                       +s+sda ++ sk+ + v    +++++  ++ + + ++v +  +eq+++++ei++  +e++e+ ++++  v
  gi|313125375|ref|YP_004035639.1| 398 QSISDATDEQSKSTQGVVsmvDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQAIV 467
                                       4667777777776666652334555556666667777777777777777777777777777777666655 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.6     0.031        20      36      64 ..      92     120 ..      86     131 .. 0.80
   2 ?    1.3   0.1      0.67   4.3e+02      44      75 ..     153     184 ..     142     193 .. 0.45
   3 ?    5.5   1.2     0.032        21      39      86 ..     194     241 ..     181     249 .. 0.79
   4 ?   13.7   4.8   8.8e-05     0.056       5      79 ..     233     307 ..     230     311 .. 0.87
   5 ?    3.5   1.2      0.14        88      17      86 ..     340     392 ..     323     409 .. 0.39
   6 ?    4.2   4.1     0.086        55      15      70 ..     411     466 ..     394     472 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.031
                           BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpyl 64 
                                       ++++k  ++++e+k+e+ln++ e+l+++ 
  gi|313125375|ref|YP_004035639.1|  92 VEDMKVLVSDAEEKSEELNALTETLEQQA 120
                                       67899999999999999999999888775 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.67
                           BLOC1_2  44 aslekkleklnekyeelqpylqqidqiekqvt 75 
                                       + +++ + ++++   ++q++ q++d+  ++vt
  gi|313125375|ref|YP_004035639.1| 153 QAFNSMVADIESVTLQIQSFAQRVDEESTEVT 184
                                       33444444444444444444444444444444 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.032
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                        +dva+s+e+ + +++ ++ +l++   ++ ++ ++++e+ + ++e+ +
  gi|313125375|ref|YP_004035639.1| 194 STDVASSVEEISAATETQHRNLDNASGELSNLSATIEEIASSADEVAA 241
                                       467788888888888888889999999999999999999999988765 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 8.8e-05
                           BLOC1_2   5 ekvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       +++++ + ae + tve+ k   k  ++ +ek ++l+++a+++ +++e+l++  e++ + ++ id+i ++++ L  
  gi|313125375|ref|YP_004035639.1| 233 ASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASETVAEVEELQSSVEQIGEVVELIDDIADKTNILAL 307
                                       567777889999999999999999999999999999999999999999999999999999999999999888765 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.14
                           BLOC1_2  17 atvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                       at e  +l+  + +++++  +++ +  ++++++ +                  + + +++L ++v +++e
  gi|313125375|ref|YP_004035639.1| 340 ATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDT-----------------VGEAIEKLGDVVGRIEE 392
                                       222222222222222222223333333333333333.................34444444444444443 PP

  == domain 6  score: 4.2 bits;  conditional E-value: 0.086
                           BLOC1_2  15 leatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqi 70 
                                       ++++v+ ++ ++ l  +++++ ++++ +a++ ++  +++ + ++el+++ qq+++i
  gi|313125375|ref|YP_004035639.1| 411 TQGVVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQAI 466
                                       34444455555667778888888888888888888899999999999999999887 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.7      0.03        19     202     240 ..      93     131 ..      87     140 .. 0.78
   2 ?   13.7  13.6   3.4e-05     0.022     151     280 ..     155     290 ..     144     313 .. 0.69
   3 ?    7.6   4.5    0.0024       1.6     176     257 ..     330     411 ..     321     431 .. 0.48
   4 ?    2.0   6.8      0.12        77     165     236 ..     414     484 ..     401     507 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.03
                              Spc7 202 eelreelaelkaeieekkkelaelqeqleeleekieelk 240
                                       e ++  +++++++ ee+++ +++l++q e+ +ek+e+++
  gi|313125375|ref|YP_004035639.1|  93 EDMKVLVSDAEEKSEELNALTETLEQQAESYSEKMEAAS 131
                                       667777888888888888888888888888888887765 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.4e-05
                              Spc7 151 leedkelLekqeeeldellpeleeekaeleeeleklqe.......aaeeles...idkeeLeelreelaelkaeiee 217
                                       +++  + +e+   +++++ ++++ee +e++  ++  ++        +ee+++    ++ +L ++  el++l+a+iee
  gi|313125375|ref|YP_004035639.1| 155 FNSMVADIESVTLQIQSFAQRVDEESTEVTTSANAVKQtstdvasSVEEISAateTQHRNLDNASGELSNLSATIEE 231
                                       444444455555555555555555555555555555553333222666665566577999999999***99999995 PP

                              Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkalee 280
                                            +e+    +e++ ++e++ke+++ +++ +++ e+ le + + +  ev++l+++v+++ e
  gi|313125375|ref|YP_004035639.1| 232 IASSADEV---AAESQRTVEQAKESRKAANKGTEKMEQ-LESRASETVAEVEELQSSVEQIGE 290
                                       55444444...455667788888999999999887776.5667888999********999865 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0024
                              Spc7 176 kaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiae 252
                                        ++l ee +k  e++e+l +  +++ e++ +++ e ++ei++ ++ + e  e+l ++  +iee +e+++++ +++ e
  gi|313125375|ref|YP_004035639.1| 330 VKSLAEETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSISDATDE 406
                                       33333333333333333333335555555555555555555555555555555555555555555555555555554 PP

                              Spc7 253 aervl 257
                                       + + +
  gi|313125375|ref|YP_004035639.1| 407 QSKST 411
                                       44433 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.12
                              Spc7 165 ldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleeki 236
                                       + ++++e++   ++   e+++  +aaee ++   +e++++ +el+e+ +++++     +  q+ +e  e + 
  gi|313125375|ref|YP_004035639.1| 414 VVSMVDEVTDLSDQTATEAQNVSAAAEE-QTAATQEIASASNELSEQAQQLQAIVSGFEVSQTPMELNEGES 484
                                       4455555666666666666666665554.5555666666666666666666666655555555555444444 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.3     0.024        16      11      80 ..      91     173 ..      86     177 .. 0.76
   2 ?    5.7   0.5     0.036        23       9      72 ..     156     218 ..     146     235 .. 0.55
   3 ?   14.0   5.2    0.0001     0.065       5      79 ..     215     288 ..     211     307 .. 0.80
   4 ?    4.3   0.5     0.098        62      14      69 ..     329     383 ..     318     390 .. 0.68
   5 ?    6.5   4.8     0.021        14       5      78 ..     390     465 ..     387     474 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.024
                           DUF2203  11 lLpllkelleelralrkeleeleeeleeakaeaekse.............aaeleaeleeleaeieelveeieelGv 74 
                                       ++  +k l++++ ++ +el+ l e le++ ++++++                ++  +++++ + ++++v+ ie++  
  gi|313125375|ref|YP_004035639.1|  91 IVEDMKVLVSDAEEKSEELNALTETLEQQAESYSEKMeaasdgdltvrvdPDSESDAMTRIGQAFNSMVADIESVTL 167
                                       56677778888888888888888888887777665557788888998887677777888888999999999999888 PP

                           DUF2203  75 evkdle 80 
                                       ++++++
  gi|313125375|ref|YP_004035639.1| 168 QIQSFA 173
                                       888775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.036
                           DUF2203   9 nalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieel 72 
                                       n+++  +++++ ++++ ++++ e ++e++++ ++ +++  +  ++++ee++a  e   +++++ 
  gi|313125375|ref|YP_004035639.1| 156 NSMVADIESVTLQIQSFAQRVDEESTEVTTSANAVKQT-STDVASSVEEISAATETQHRNLDNA 218
                                       56677777777777777777777666666666655443.3333333333333333333333333 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 0.0001
                           DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdl 79 
                                       l++A   L  l+ ++ee+++ ++e++  +++  e+ +e+ +++a++  +++e+le++++e+v+e+eel   v ++
  gi|313125375|ref|YP_004035639.1| 215 LDNASGELSNLSATIEEIASSADEVAAESQRTVEQAKES-RKAANKGTEKMEQLESRASETVAEVEELQSSVEQI 288
                                       678999999**********99999998777666666664.44589999999999999999999999998877766 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.098
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveei 69 
                                       ++k+l ee +++++e+e+l + +e+++++ + ++  e ++e+++ ++ + e++e++
  gi|313125375|ref|YP_004035639.1| 329 EVKSLAEETAKATEEVESLIDGVETSTENVT-DDIYETQNEIQRSRDTVGEAIEKL 383
                                       5667777777777777777776666666643.447777777777777777777666 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.021
                           DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkd 78 
                                       +ee n+ ++ +++ ++e  + ++ + ++++e+++ ++++++++   +++++e +++++ei ++ +e++e   +++ 
  gi|313125375|ref|YP_004035639.1| 390 IEESNESIQSISDATDEQSKSTQGVVSMVDEVTDLSDQTATEAqnVSAAAEEQTAATQEIASASNELSEQAQQLQA 465
                                       68999999***********999999999999999999987766775555566666666666666666665554444 PP

>> BLYB  Borrelia hemolysin accessory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00041      0.26       9      95 ..     222     309 ..     214     314 .. 0.77
   2 ?   -1.3   0.1       3.8   2.4e+03      60      99 ..     330     368 ..     326     383 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                              BLYB   9 LtvLssLieifaksdteiDelfqkgfkkvidlykyykkiYtkslkklesaeskki..vkeledilekiaklidains 83 
                                       L  Ls+ ie  a s +e+    q+++++  +  k   +  t+++++les+ s+ +  v+el++  e+i +++++i+ 
  gi|313125375|ref|YP_004035639.1| 222 LSNLSATIEEIASSADEVAAESQRTVEQAKESRKA-ANKGTEKMEQLESRASETVaeVEELQSSVEQIGEVVELIDD 297
                                       66677777766888888888888888888887754.555799******9988776336899999999********98 PP

                              BLYB  84 DknkkiiedLkf 95 
                                        ++k+ i  L +
  gi|313125375|ref|YP_004035639.1| 298 IADKTNILALNA 309
                                       899887776665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.8
                              BLYB  60 skkivkeledilekiaklidainsDknkkiiedLkfernk 99 
                                        k + +e ++  e +  lid +++  + ++ +d+   +n+
  gi|313125375|ref|YP_004035639.1| 330 VKSLAEETAKATEEVESLIDGVETSTE-NVTDDIYETQNE 368
                                       556667777777777888888877643.455666666665 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1  17.7      0.32     2e+02     274     432 ..     121     280 ..      94     285 .. 0.78
   2 ?   12.1   9.6   6.1e-05     0.039      98     222 ..     336     462 ..     328     466 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTT.HHHH CS
                              EzrA 274 edveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeelek.lrel 349
                                       e+ +e+++  ++   ++  d + E +A  ++ + ++++   +e ++ q++   + +d+ + + + s + +++   ++
  gi|313125375|ref|YP_004035639.1| 121 ESYSEKMEAASDGDLTVRVDPDSESDAMTRIGQAFNSMVADIESVTLQIQSFAQRVDEESTEVTTSANAVKQtSTDV 197
                                       44555555555555556666678888999999999999999999999999999999999999999888886515689 PP

                                       HHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 350 ekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkei 426
                                        + ++e+++  e+ + +l++ +   S+l+  +ee+ ++ +e+  + +++ e+ k+ rk  ++  e++++++++ +e+
  gi|313125375|ref|YP_004035639.1| 198 ASSVEEISAATETQHRNLDNASGELSNLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASET 274
                                       99999999999999999999999999999999999999999999999999999999999999999999999999998 PP

                                       HHHSSS CS
                              EzrA 427 krkiek 432
                                         ++e+
  gi|313125375|ref|YP_004035639.1| 275 VAEVEE 280
                                       888876 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.1e-05
                                       HTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH- CS
                              EzrA  98 kakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqlenie 174
                                       ++ k+ +e+e+ +d ve++++++ +++ e ++  +++r+ + ++ ek  ++  ++++ ++s +++ ++ ++q +  +
  gi|313125375|ref|YP_004035639.1| 336 ETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSISDATDEQSKSTQ 412
                                       6778999********************************************************************** PP

                                       -----------..----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTT CS
                              EzrA 175 kefsefeelte..ngdyveakeilkkleeeideleevieeiPelleelkk 222
                                          s  +e+t+  ++  +ea+++  ++ee++++ +e+     el e++++
  gi|313125375|ref|YP_004035639.1| 413 GVVSMVDEVTDlsDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQ 462
                                       *********9722455789***************9999888888777775 PP

>> Mis12  Mis12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       2.3   1.5e+03     113     127 ..     106     120 ..      80     132 .. 0.50
   2 ?    8.5   0.0    0.0031         2      19      67 ..     188     267 ..     181     281 .. 0.80
   3 ?   -0.7   3.9       2.2   1.4e+03      52      74 ..     339     361 ..     268     468 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHH CS
                             Mis12 113 deeieelrrkleael 127
                                        ee+++l + le++ 
  gi|313125375|ref|YP_004035639.1| 106 SEELNALTETLEQQA 120
                                       233333333332222 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHHHHHH.......................................TTSTHHHH-HHHHHHHHHHH CS
                             Mis12  19 navndllyravdavekvL...............................dkkleedeeeekaaeesteeieeGtakl 64 
                                       nav+++  ++ ++ve++                                d+ ++e++++ ++a+es++  ++Gt+k+
  gi|313125375|ref|YP_004035639.1| 188 NAVKQTSTDVASSVEEISaatetqhrnldnasgelsnlsatieeiassaDEVAAESQRTVEQAKESRKAANKGTEKM 264
                                       7888888888888888657777777777888888888888887777777666777777999999************* PP

                                       HHH CS
                             Mis12  65 etl 67 
                                       e+l
  gi|313125375|ref|YP_004035639.1| 265 EQL 267
                                       *97 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.2
                                       H-HHHHHHHHHHHHHHHHHHHHH CS
                             Mis12  52 esteeieeGtakletlleasvDk 74 
                                       ++tee+e+ +  +et  e+ +D 
  gi|313125375|ref|YP_004035639.1| 339 KATEEVESLIDGVETSTENVTDD 361
                                       44444444444444444444442 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  40.2    0.0016         1     478     844 ..      89     458 ..      82     463 .. 0.67
   2 ?    4.6  12.9     0.011       7.3     513     665 ..     338     489 ..     321     512 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                               FPP 478 ekiledirvalkevneesaeasdslasseeeeedassdektlkedslevekeeevseeeksseeeskqkiqqelska 554
                                        +i+ed++v +++++e+s+e ++ + + e+++e+ s++ ++ ++  l+v    ++ +++++   +  +++  ++++ 
  gi|313125375|ref|YP_004035639.1|  89 LAIVEDMKVLVSDAEEKSEELNALTETLEQQAESYSEKMEAASDGDLTVRVDPDSESDAMTRIGQAFNSMVADIESV 165
                                       57*************99877755544444444444444444444478888888888889999999************ PP

                               FPP 555 iskiielveslskealklqdkss....ksselsevleqFsavvndllsgkadledfvleLssvldeiselkfslldv 627
                                        ++i+ + + +++e+++++++ +     s+++ +++e+ sa  +    +  + +  +++Ls +++ei +   ++  +
  gi|313125375|ref|YP_004035639.1| 166 TLQIQSFAQRVDEESTEVTTSANavkqTSTDVASSVEEISAATETQHRNLDNASGELSNLSATIEEIASSADEVAAE 242
                                       *****************977777555566677777777777777666666666666666666666666665555555 PP

                               FPP 628 ssmeeeikksddidkvalsenkvaqk.ges.snecaeisklssekeipselplvsgsneskkeenkllkeeleelks 702
                                       s+ + e  k  +  k+a +  + +++ + + s+++ae+++l+s+ e++ e  +v+  ++  +++n l+ +  +e  s
  gi|313125375|ref|YP_004035639.1| 243 SQRTVEQAK--ESRKAANKGTEKMEQlESRaSETVAEVEELQSSVEQIGE--VVELIDDIADKTNILALNASIEAAS 315
                                       544433332..233333333333233355568899999999998887544..4444344444444444444444444 PP

                               FPP 703 ...ekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcm..kesyesletrateleael 774
                                            e  +v  ++ ++  e++    +e E l++ +++  e++ +   + etq + +    +  +   ++ ++   +
  gi|313125375|ref|YP_004035639.1| 316 agdAGEGFAVVASEVKSLAEETAKATEEVESLIDGVETSTENVTDD--IYETQNEIQrsRDTVGEAIEKLGDVVGRI 390
                                       0114566777777777788888888899999999998888877664..55555444300333333344566677889 PP

                               FPP 775 nelkqkieaLeveLeeekksheeleakckelqeqlervekkevskssaeeedkklkqekeiaAAaeKLae 844
                                       +e ++ i++++   +e++ks +   + + e+    ++++ +e  +++ + +++++ + +eia+A++ L e
  gi|313125375|ref|YP_004035639.1| 391 EESNESIQSISDATDEQSKSTQGVVSMVDEVTDLSDQTA-TEA-QNVSAAAEEQTAATQEIASASNELSE 458
                                       999999999999999999999999998888876665554.444.4566677778888999*****99987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                               FPP 513 ssdektlkedslevekeeevseeeksseeeskqkiqqelskaiskiielveslskealklqdkssksselsevleqF 589
                                       ++ ++++++    ve+++e +++++ +++++ q+++  + +ai k+ ++v  +++++  +q+ s  ++e s++ +  
  gi|313125375|ref|YP_004035639.1| 338 AKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSISDATDEQSKSTQGV 414
                                       22222333334556666666777777777777778888888888888888888888888877777666666666666 PP

                               FPP 590 savvndllsgkadledfvleLssv.......ldeiselkfslldvssmeeeikksddidkvalsenkvaqkgessne 659
                                       +++v+++ + + +    ++++s +        +ei +   +l ++ ++ ++i + +++ ++ ++ n+         e
  gi|313125375|ref|YP_004035639.1| 415 VSMVDEVTDLSDQTATEAQNVSAAaeeqtaaTQEIASASNELSEQAQQLQAIVSGFEVSQTPMELNEG--------E 483
                                       66666665554444444444444400000004444444444444444444444444444422222222........2 PP

                               FPP 660 caeisk 665
                                       + e+++
  gi|313125375|ref|YP_004035639.1| 484 SDETDE 489
                                       222222 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8    0.0015      0.93     290     335 ..      92     137 ..      86     140 .. 0.89
   2 ?   11.5   2.0   0.00016       0.1     238     326 ..     146     234 ..     142     240 .. 0.94
   3 ?    5.8   5.2    0.0088       5.7     253     341 ..     224     311 ..     222     314 .. 0.89
   4 ?    6.5   3.5    0.0053       3.4     237     321 ..     327     411 ..     323     426 .. 0.76
   5 ?    1.0   3.2      0.27   1.7e+02     269     322 ..     425     478 ..     418     493 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                             IFT57 290 kekykqlsegvseltrelaeiseelekvkqemeergssmtDgsplv 335
                                        e++k l +  +e+++el+ ++e le+  +   e+ + ++Dg+  v
  gi|313125375|ref|YP_004035639.1|  92 VEDMKVLVSDAEEKSEELNALTETLEQQAESYSEKMEAASDGDLTV 137
                                       57788899999******************************97655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00016
                             IFT57 238 eslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseel 314
                                       ++++++ ++++ +  di+ +  +i+s  ++++++  e ++  ++++++ ++v  +++++s+  + + r+l++ s el
  gi|313125375|ref|YP_004035639.1| 146 DAMTRIGQAFNSMVADIESVTLQIQSFAQRVDEESTEVTTSANAVKQTSTDVASSVEEISAATETQHRNLDNASGEL 222
                                       57889999********************************************************************* PP

                             IFT57 315 ekvkqemeergs 326
                                       ++++  +ee  s
  gi|313125375|ref|YP_004035639.1| 223 SNLSATIEEIAS 234
                                       *****9998655 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0088
                             IFT57 253 disktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmt 329
                                       ++s t+e+i s    +  + + ++++ +e ++  ++ +ek++ql+++ se   e +e++  +e++  e+ e  + ++
  gi|313125375|ref|YP_004035639.1| 224 NLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASETVAEVEELQSSVEQIG-EVVELIDDIA 299
                                       67889999999999*************************************************985.6667889999 PP

                             IFT57 330 Dgsplvkikkal 341
                                       D +++  +  ++
  gi|313125375|ref|YP_004035639.1| 300 DKTNILALNASI 311
                                       999988877666 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0053
                             IFT57 237 eeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeisee 313
                                       +++++++ ++ +k  e+++  ++ +e+  ++++  + e+ +e +  ++++ e+ ek+ ++ ++++e ++  ++is+ 
  gi|313125375|ref|YP_004035639.1| 327 ASEVKSLAEETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSISDA 403
                                       56777777778888888888888888888888888888888888888888888888888888888888888888887 PP

                             IFT57 314 lekvkqem 321
                                        ++ ++  
  gi|313125375|ref|YP_004035639.1| 404 TDEQSKST 411
                                       77766554 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.27
                             IFT57 269 nsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqeme 322
                                         q  ++ q+ ++a ee +++++++  +s+++se+ ++l+ i   +e  ++ me
  gi|313125375|ref|YP_004035639.1| 425 SDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQAIVSGFEVSQTPME 478
                                       567777788888888888999999999999999999999988776655554444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  19.0   2.4e-05     0.015     714     912 ..      87     287 ..      84     301 .. 0.82
   2 ?   -1.9  15.6      0.66   4.2e+02     285     415 ..     333     461 ..     321     509 .. 0.36

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                           DUF3584 714 erlekkakwqevvgeldeqlaelkkaieaartqakarlkeleeaykreLksk.dvDpetvkelkrkieeLekkieri 789
                                       ++l+  + ++++v++ +e+ +el++  e  ++qa+   +++e a + +L  + d+D e + ++ r  +++++ +++i
  gi|313125375|ref|YP_004035639.1|  87 ATLAIVEDMKVLVSDAEEKSEELNALTETLEQQAESYSEKMEAASDGDLTVRvDPDSESD-AMTRIGQAFNSMVADI 162
                                       577778999****************************************97747777777.66777789******** PP

                           DUF3584 790 ekrreevreYraflqetwlkvdslaeerpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqldql 866
                                       e+   +++++ + + e+  +   ++   +a k++  ++ s++ee+    +++ +++ +   +l++ + ++e+ ++ +
  gi|313125375|ref|YP_004035639.1| 163 ESVTLQIQSFAQRVDEESTE---VTTSANAVKQTSTDVASSVEEISAATETQHRNLDNASGELSNLSATIEEIASSA 236
                                       **********9999999866...788888888889999999999999999999999999999999998888888888 PP

                           DUF3584 867 denlr....klrdllskl.aelkldadaeqaegelaerlaaleelkrkrer 912
                                       de        +++  +   a++k  ++ eq+e  ++e++a +eel+++ e+
  gi|313125375|ref|YP_004035639.1| 237 DEVAAesqrTVEQAKESRkAANKGTEKMEQLESRASETVAEVEELQSSVEQ 287
                                       765540001555555545588888889999999999999999999887665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.66
                           DUF3584 285 vqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirsele 361
                                        +e+ a+  +++++l d ++++ ++++ ++ ++++++++ ++ + ++ e+  +    +ie+ ++    +    +e +
  gi|313125375|ref|YP_004035639.1| 333 LAEETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVV-GRIEESNESIQSISDATDEQS 408
                                       3333344444444444444444444444444444444444444433333333221.122222222222222222222 PP

                           DUF3584 362 eleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlka 415
                                       +  + +  + ++++d+  ++ ++ q+++   ee+ +  +e + a+ e  ++  +
  gi|313125375|ref|YP_004035639.1| 409 KSTQGVVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQ-AQ 461
                                       222222222233333333333333333333333333333322222221111.11 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   4.9      0.14        89     230     321 ..      95     191 ..      89     195 .. 0.69
   2 ?    9.9   4.1   0.00055      0.35     247     324 ..     194     268 ..     186     271 .. 0.90
   3 ?    5.7   5.0      0.01       6.5     225     294 ..     221     290 ..     205     312 .. 0.52
   4 ?    6.2   0.2    0.0072       4.6      17      96 ..     306     385 ..     298     387 .. 0.87
   5 ?    8.1   4.5    0.0019       1.2     239     323 ..     382     466 ..     373     481 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHH CS
                             APG17 230 leVlekDaaeledVvkelqerleem........ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifka 298
                                       ++Vl  Da+e ++ ++ l+e+le+         e+a++   + + + ++ ++a++++ + ++++ + ++++     +
  gi|313125375|ref|YP_004035639.1|  95 MKVLVSDAEEKSEELNALTETLEQQaesysekmEAASDGDLTVRVDPDSESDAMTRIGQAFNSMVADIESVTL---Q 168
                                       68999***99999999999999988744433333333333333445566777777777777777777777777...8 PP

                                       HHHHHHH...HHHHHHHHHHHHH CS
                             APG17 299 eeeflerweeekekieekleele 321
                                       ++ f +r +ee +++ +  + ++
  gi|313125375|ref|YP_004035639.1| 169 IQSFAQRVDEESTEVTTSANAVK 191
                                       88888888888777777766665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00055
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHH CS
                             APG17 247 lqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekleeleeL 323
                                        +++++++e+++++ +++++++++++ +l+++ +++ee+ +  +e+ a   ++++ +e+ +e ++  ++++e++e+L
  gi|313125375|ref|YP_004035639.1| 194 STDVASSVEEISAATETQHRNLDNASGELSNLSATIEEIASSADEVAA---ESQRTVEQAKESRKAANKGTEKMEQL 267
                                       45677888****************************************...999999999****************9 PP

                                       H CS
                             APG17 324 r 324
                                       +
  gi|313125375|ref|YP_004035639.1| 268 E 268
                                       7 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHH CS
                             APG17 225 ereelleVlekDaaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeyla 294
                                       e  +l + +e+ a+  ++V +e q ++e+ +++ k+ ++ +e++e+l s  +++++e+ee+++ ++++ +
  gi|313125375|ref|YP_004035639.1| 221 ELSNLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASETVAEVEELQSSVEQIGE 290
                                       3444444445555556666666666666665555555555555555555555555555544443333333 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0072
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHHH CS
                             APG17  17 cqrAnelltsarqeleeavkllakteflrdglkqQlkllekirkslerklekgkeefkdlikeldaanerLektlek 93 
                                         +A+  ++sa ++ e  ++++++++ l +  ++  + +e++ +++e+ +e++ +++ ++++e++++ +   + +ek
  gi|313125375|ref|YP_004035639.1| 306 ALNASIEAASAGDAGEGFAVVASEVKSLAEETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEK 382
                                       566667777777777888999999999******************************************99999999 PP

                                       HHT CS
                             APG17  94 Lrk 96 
                                       L +
  gi|313125375|ref|YP_004035639.1| 383 LGD 385
                                       976 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHH CS
                             APG17 239 eledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekiee 315
                                        l dVv  ++e+ e++++++++ +e+ ++++ ++s + ++ +  ++  ++ +++ a  +++++ +++ ++  +++ e
  gi|313125375|ref|YP_004035639.1| 382 KLGDVVGRIEESNESIQSISDATDEQSKSTQGVVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSE 458
                                       46678888888888888888888888888887777777777777766777777777555555555555555555555 PP

                                       HHHHHHHH CS
                             APG17 316 kleeleeL 323
                                       + ++l++ 
  gi|313125375|ref|YP_004035639.1| 459 QAQQLQAI 466
                                       55555544 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   6.2      0.33   2.1e+02      57     103 ..     148     194 ..      94     222 .. 0.65
   2 ?    2.5   6.9      0.22   1.4e+02      69     132 ..     213     281 ..     194     282 .. 0.65
   3 ?    3.0   0.8      0.15        97      69     100 ..     262     293 ..     258     313 .. 0.77
   4 ?    9.9   0.3    0.0012      0.75      69     131 ..     328     392 ..     322     394 .. 0.83
   5 ?    6.2   1.5     0.016        10      69     115 ..     405     451 ..     396     472 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.33
                              COG2  57 FvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskl 103
                                          ++++  ++ +++e v+ +++++ ++v++   ++    ++v++  
  gi|313125375|ref|YP_004035639.1| 148 MTRIGQAFNSMVADIESVTLQIQSFAQRVDEESTEVTTSANAVKQTS 194
                                       55677777778888888888888888887777777777777776653 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.22
                              COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekr.....ellklllkldevvekleal 132
                                       ++l++ + +l+++   +e++ ++ +e  +e +  +e+ake +++      ++ +l  + +e+v ++e+l
  gi|313125375|ref|YP_004035639.1| 213 RNLDNASGELSNLSATIEEIASSADEVAAESQRTVEQAKESRKAAnkgteKMEQLESRASETVAEVEEL 281
                                       556666666666666666666666666666666666666666655555666777777888899998876 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.15
                              COG2  69 eeleevesplaaarkkvesvreklsereeeve 100
                                       e++e++es  ++++ +ve++++++++  e ve
  gi|313125375|ref|YP_004035639.1| 262 EKMEQLESRASETVAEVEELQSSVEQIGEVVE 293
                                       78999999999999999999999988766554 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0012
                              COG2  69 eeleevesplaaarkkvesvreklsereeevesklee.akeleekr.ellklllkldevveklea 131
                                       +e++ +  + a+a+++ves+++ ++   e+v++ + e ++e+++ r  + +++ kl +vv ++e+
  gi|313125375|ref|YP_004035639.1| 328 SEVKSLAEETAKATEEVESLIDGVETSTENVTDDIYEtQNEIQRSRdTVGEAIEKLGDVVGRIEE 392
                                       678889999999*****************999988662567888887888899999999988886 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.016
                              COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekrel 115
                                       +e ++ ++ + +++++v+++ ++ +   ++v++  ee+++++++ ++
  gi|313125375|ref|YP_004035639.1| 405 DEQSKSTQGVVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIAS 451
                                       55566677888888999999999999999999999988888777633 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.26   1.6e+02      92     123 ..      96     129 ..      90     145 .. 0.67
   2 ?   10.9   1.6   0.00045      0.29     101     173 ..     163     235 ..     148     238 .. 0.85
   3 ?   -1.6   0.0       3.2   2.1e+03     121     167 ..     271     285 ..     246     313 .. 0.54
   4 ?    3.0   0.2      0.13        81     105     168 ..     321     384 ..     297     393 .. 0.62
   5 ?    4.0   0.5     0.063        40      97     160 ..     352     415 ..     321     418 .. 0.73
   6 ?    3.3   4.1       0.1        65     102     155 ..     416     469 ..     394     474 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.26
                      Bacillus_HBL  92 veav..dkkdkaellellekLqeeiqqnqkevkq 123
                                       + +v   +++++el +l e L++++ ++++++++
  gi|313125375|ref|YP_004035639.1|  96 KVLVsdAEEKSEELNALTETLEQQAESYSEKMEA 129
                                       4444433556666777777788888887777765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00045
                      Bacillus_HBL 101 aellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgk 173
                                       ++++ +++   + + + + ev+++++++k+  +++a+ +++ ++++++    l + sg++s+l ++ie++ ++
  gi|313125375|ref|YP_004035639.1| 163 ESVTLQIQSFAQRVDEESTEVTTSANAVKQTSTDVASSVEEISAATETQHRNLDNASGELSNLSATIEEIASS 235
                                       6677778888889999999999999999999999999999999999999999999999999999999999876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.2
                      Bacillus_HBL 121 vkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqnei 167
                                       + ++++e+++l+                                  +
  gi|313125375|ref|YP_004035639.1| 271 ASETVAEVEELQ--------------------------------SSV 285
                                       222222222222................................222 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.13
                      Bacillus_HBL 105 ellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneie 168
                                       e+     +e+ +  +e+ +  +e+++l + ++  ++n + d+ e ++ ++ +  ++ +  +++ 
  gi|313125375|ref|YP_004035639.1| 321 EGFAVVASEVKSLAEETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLG 384
                                       5555555666666666666666666666666666666666666666666666655555555555 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.063
                      Bacillus_HBL  97 kkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvi 160
                                       ++  +++++++ + q+eiq    +v + i++L +   ++++ +++ ++  d  ++  ++++gv+
  gi|313125375|ref|YP_004035639.1| 352 ETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSISDATDEQSKSTQGVV 415
                                       4556777888888888888888888888888888888888888887777777777777777776 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.1
                      Bacillus_HBL 102 ellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilag 155
                                       ++++ +++L+++  +  ++v + ++e ++  +++a+ s+++++++++l++i++g
  gi|313125375|ref|YP_004035639.1| 416 SMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQAIVSG 469
                                       467788999999999999999999999999999999999999999999999876 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.26   1.6e+02      23      62 ..      89     128 ..      85     133 .. 0.63
   2 ?    5.0   1.9     0.032        20       9      66 ..     177     234 ..     170     236 .. 0.91
   3 ?    6.7   2.6    0.0094         6       6      69 ..     230     293 ..     226     311 .. 0.88
   4 ?    3.7   0.3     0.081        52       5      66 ..     337     399 ..     333     402 .. 0.81
   5 ?    9.5   2.8    0.0014      0.87       5      73 ..     404     472 ..     400     487 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.26
                             Sec34  23 leqLeeleekfksvsektsslheaceqlleeqkrleelae 62 
                                       l  +e+++  +++ +ek+++l++ +e+l ++ ++++e  e
  gi|313125375|ref|YP_004035639.1|  89 LAIVEDMKVLVSDAEEKSEELNALTETLEQQAESYSEKME 128
                                       5556666666666677777777777777666666666554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.032
                             Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                        ee +e+ +++++++++ +++ ++++++s+ t++ h++ ++   e ++l+ + eei +
  gi|313125375|ref|YP_004035639.1| 177 DEESTEVTTSANAVKQTSTDVASSVEEISAATETQHRNLDNASGELSNLSATIEEIAS 234
                                       678899999********************************99999999999999976 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0094
                             Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       e+  ++ de+ ++ +++ eq +e ++  ++ +ek+++l++++ + ++e ++l++ +e+i e ++
  gi|313125375|ref|YP_004035639.1| 230 EEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASETVAEVEELQSSVEQIGEVVE 293
                                       56677899999************************************************98766 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.081
                             Sec34   5 LeskeeecdelleqtdealeqL.eeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                         + +ee+++l++ +++  e++ +++ e  ++++ +  ++ ea e+l +   r+ee +e+i++
  gi|313125375|ref|YP_004035639.1| 337 TAKATEEVESLIDGVETSTENVtDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQS 399
                                       556788999999999877766625799999999999999999999999999999999999986 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0014
                             Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFee 73 
                                        ++++++++ +++ +de+ ++ ++  ++ ++vs+  ++  +a++++ +  ++l+e a+++++ ++ Fe 
  gi|313125375|ref|YP_004035639.1| 404 TDEQSKSTQGVVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQAIVSGFEV 472
                                       567889999****************************************************99999975 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.6      0.25   1.6e+02      38      61 ..     103     126 ..      91     133 .. 0.48
   2 ?    0.2   0.2       1.7   1.1e+03      25      56 ..     174     209 ..     153     224 .. 0.47
   3 ?    1.1   1.3      0.86   5.5e+02      30      59 ..     229     258 ..     216     264 .. 0.54
   4 ?   13.3   2.5   0.00013     0.086       4      67 ..     262     349 ..     259     353 .. 0.86
   5 ?    2.1   1.4      0.42   2.7e+02      10      70 ..     352     391 ..     328     414 .. 0.52
   6 ?    9.2   3.3    0.0026       1.7      14      66 ..     415     467 ..     411     471 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.25
                              ZapB  38 keenreleeeneqlkeereawqer 61 
                                       +e+ +el++  e l+++ e+  e+
  gi|313125375|ref|YP_004035639.1| 103 EEKSEELNALTETLEQQAESYSEK 126
                                       333333333333333333333333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.7
                              ZapB  25 meieeLkeeneelkeenrele....eeneqlkeere 56 
                                       ++++e   e+ + ++  ++ +    +++e+  +  e
  gi|313125375|ref|YP_004035639.1| 174 QRVDEESTEVTTSANAVKQTStdvaSSVEEISAATE 209
                                       333333333322222222222333344444444444 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.86
                              ZapB  30 Lkeeneelkeenreleeeneqlkeereawq 59 
                                        +e  ++  e ++e ++ +eq ke r+a +
  gi|313125375|ref|YP_004035639.1| 229 IEEIASSADEVAAESQRTVEQAKESRKAAN 258
                                       233333344444455577777777777655 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00013
                              ZapB   4 elLeqLEskiqkaidtitlLqmeieeLkeeneelkeenrele........................eeneqlkeere 56 
                                       e +eqLEs+ ++++ ++++Lq  +e+  e +e   + +++ +                        +e++ l ee +
  gi|313125375|ref|YP_004035639.1| 262 EKMEQLESRASETVAEVEELQSSVEQIGEVVELIDDIADKTNilalnasieaasagdagegfavvaSEVKSLAEETA 338
                                       789***********************999887666655555566788999999999999999999999999999999 PP

                              ZapB  57 awqerlkkLLg 67 
                                       + +e +++L++
  gi|313125375|ref|YP_004035639.1| 339 KATEEVESLID 349
                                       99999999986 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.42
                              ZapB  10 EskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgkle 70 
                                       E++ ++  d i + q                      e+++ +++  +  e+l  ++g++e
  gi|313125375|ref|YP_004035639.1| 352 ETSTENVTDDIYETQ---------------------NEIQRSRDTVGEAIEKLGDVVGRIE 391
                                       333333333333333.....................5555555555555555555555554 PP

  == domain 6  score: 9.2 bits;  conditional E-value: 0.0026
                              ZapB  14 qkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLL 66 
                                        +++d++t L+ + +   + +++ +ee+ + ++e+    +e +++ + l++++
  gi|313125375|ref|YP_004035639.1| 415 VSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQAIV 467
                                       589*******************************************9999887 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.1      0.26   1.6e+02      32      57 ..     103     128 ..      99     132 .. 0.74
   2 ?    7.6   1.3    0.0061       3.9      17      57 ..     250     293 ..     243     297 .. 0.82
   3 ?    1.8   0.1      0.42   2.7e+02      27      55 ..     329     357 ..     325     360 .. 0.62
   4 ?    1.7   0.0      0.44   2.8e+02      19      56 ..     371     408 ..     369     413 .. 0.81
   5 ?   -2.5   0.0       8.7   5.6e+03      48      60 ..     452     464 ..     442     468 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  32 errvkaLekeNksLkseleelkkeve 57 
                                       e+++++L++  ++L +++e++++++e
  gi|313125375|ref|YP_004035639.1| 103 EEKSEELNALTETLEQQAESYSEKME 128
                                       67777787878888777777777665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0061
                                       HHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  17 ArrsRq...RKqaeieeLerrvkaLekeNksLkseleelkkeve 57 
                                       A++sR+   +  +++e+Le+r+++  +e ++L+s +e++ + ve
  gi|313125375|ref|YP_004035639.1| 250 AKESRKaanKGTEKMEQLESRASETVAEVEELQSSVEQIGEVVE 293
                                       56666544366789***********************9977665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  27 eieeLerrvkaLekeNksLkseleelkke 55 
                                       e++ L+++ ++ ++e +sL++ +e+ +++
  gi|313125375|ref|YP_004035639.1| 329 EVKSLAEETAKATEEVESLIDGVETSTEN 357
                                       55666666666666666666666666655 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  19 rsRqRKqaeieeLerrvkaLekeNksLkseleelkkev 56 
                                       rsR    + ie+L + v  +e+ N+s +s  +   +++
  gi|313125375|ref|YP_004035639.1| 371 RSRDTVGEAIEKLGDVVGRIEESNESIQSISDATDEQS 408
                                       6666667899***************9999877776665 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 8.7
                                       HHHHHHHHHHHHH CS
                            bZIP_1  48 eleelkkevekLk 60 
                                         +el+++ ++L+
  gi|313125375|ref|YP_004035639.1| 452 ASNELSEQAQQLQ 464
                                       3444555555444 PP

>> SLX9  Ribosome biogenesis protein SLX9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.8   5.7e+03     111     130 ..      99     118 ..      92     137 .. 0.59
   2 ?   11.4   3.5   0.00051      0.33      15     106 ..     170     271 ..     166     317 .. 0.73
   3 ?    2.9   1.7      0.21   1.3e+02      18     112 ..     387     457 ..     327     503 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.8
                              SLX9 111 LahpsfksnpfaaLrehisn 130
                                       +++ + ks  ++aL e +++
  gi|313125375|ref|YP_004035639.1|  99 VSDAEEKSEELNALTETLEQ 118
                                       45555555555555554443 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00051
                              SLX9  15 eaflsKieksisksaskkkkkrkrrpskklvtdlesLadaLpdle..............eeegekkekkekeqaqqg 77 
                                       ++f +++++  ++++ +++ +  +++s+++++++e++  a +                 ++ +e  ++ ++ +a+++
  gi|313125375|ref|YP_004035639.1| 170 QSFAQRVDE--ESTEVTTSANAVKQTSTDVASSVEEISAATETQHrnldnasgelsnlsATIEEIASSADEVAAESQ 244
                                       589999999..777778888888888888888888888888844488888888888765222222333333344444 PP

                              SLX9  78 kvkkaekslkskpgalkrkkklekkEmer 106
                                       ++ +  + ++s++ a+k+ +k+e+ E+  
  gi|313125375|ref|YP_004035639.1| 245 RTVE--QAKESRKAANKGTEKMEQLESRA 271
                                       4444..56789999999999998888654 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.21
                              SLX9  18 lsKiek.sisksaskkkkkrkrrpskklvtdlesLadaLpdleeeegekkekkekeqaqqgkvkkae.........k 84 
                                       + +ie+ + s ++ + +      ++ k    + s+                               +          
  gi|313125375|ref|YP_004035639.1| 387 VGRIEEsNESIQSISDATD----EQSKSTQGVVSMV------------------------------DevtdlsdqtA 429
                                       3344442111111111111....2222222222223..............................23333333211 PP

                              SLX9  85 slkskpgalkrkkklekkEmerfkkvLa 112
                                       ++ ++ +a+   +  + +E++  ++ L+
  gi|313125375|ref|YP_004035639.1| 430 TEAQNVSAAAEEQTAATQEIASASNELS 457
                                       3333333333333333444443333333 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.1      0.83   5.3e+02     118     141 ..     102     125 ..      89     138 .. 0.51
   2 ?    6.1  17.1     0.018        12      14     155 ..     145     287 ..     139     290 .. 0.79
   3 ?    9.1  12.5    0.0022       1.4      24     176 ..     330     486 ..     289     493 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.83
                             ATG16 118 lkedeerlaeleaeraaletklkd 141
                                       ++e++e+l++l+++ ++  + +++
  gi|313125375|ref|YP_004035639.1| 102 AEEKSEELNALTETLEQQAESYSE 125
                                       444444444444443333333332 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.018
                             ATG16  14 ekafaeliqaynrLldrtsaleaenaklekaaasaks..sksskksakekeasasqsnskqsakiqsleqklaqlre 88 
                                        +a   + qa+n +   +++   + ++  ++  ++++  ++s +++++++++ as s ++ sa +++++ +l     
  gi|313125375|ref|YP_004035639.1| 145 SDAMTRIGQAFNSMVADIESVTLQIQSFAQRVDEESTevTTSANAVKQTSTDVAS-SVEEISAATETQHRNLDNASG 220
                                       5666677778888777777777777777555555555543333322222222222.46799999999********** PP

                             ATG16  89 elaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqd 155
                                       el++l  + +e a++  e+ +e q+  e++ke +++ ++ +++ ++le + ++  +e++e++  v++
  gi|313125375|ref|YP_004035639.1| 221 ELSNLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASETVAEVEELQSSVEQ 287
                                       *************************************************************999887 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0022
                             ATG16  24 ynrLldrtsaleaenaklekaaasaks..sksskksakekeasasq...........snskqsakiqsleqklaqlr 87 
                                        + L++ t++  +e ++l    +++++  +     ++  +++++ q           +  +   +i+++++ +++  
  gi|313125375|ref|YP_004035639.1| 330 VKSLAEETAKATEEVESLIDGVETSTEnvT-----DDIYETQNEIQrsrdtvgeaieKLGDVVGRIEESNESIQS-- 399
                                       455677777777777777555555554431.....3333333333332233554444334444444444444444.. PP

                             ATG16  88 eelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLq 164
                                          +++  ++++++q ++++ +e+ +l +++ ++++++ ++ +e +a ++++++  +el e+++ +q++    +  q
  gi|313125375|ref|YP_004035639.1| 400 --ISDATDEQSKSTQGVVSMVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQAIVSGFEVSQ 474
                                       ..56777889999999************************************************9999877777766 PP

                             ATG16 165 lqlnqaEeklrk 176
                                         ++ +E ++++
  gi|313125375|ref|YP_004035639.1| 475 TPMELNEGESDE 486
                                       666666666655 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3      0.01       6.5       5      41 ..     144     180 ..     142     195 .. 0.89
   2 ?    1.9   0.2      0.31     2e+02       8      39 ..     200     231 ..     197     251 .. 0.82
   3 ?    0.7   0.2      0.69   4.4e+02       7      40 ..     220     253 ..     209     269 .. 0.71
   4 ?   -0.6   0.1       1.8   1.2e+03       5      27 ..     277     299 ..     273     315 .. 0.56
   5 ?    0.8   0.1      0.64   4.1e+02      10      37 ..     349     376 ..     336     380 .. 0.69
   6 ?    5.6   0.1      0.02        13       6      54 ..     380     428 ..     376     435 .. 0.86
   7 ?   -1.8   0.0       4.1   2.6e+03       2      39 ..     456     493 ..     455     499 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.01
                         DASH_Duo1   5 EleqLrkinevienviesLkkaksniervketvestn 41 
                                       E + +++i ++++++++++++++ +i++++++v++ +
  gi|313125375|ref|YP_004035639.1| 144 ESDAMTRIGQAFNSMVADIESVTLQIQSFAQRVDEES 180
                                       7888999************************998765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.31
                         DASH_Duo1   8 qLrkinevienviesLkkaksniervketves 39 
                                       ++++i ++ e+ + +L++a++++++++ t+e+
  gi|313125375|ref|YP_004035639.1| 200 SVEEISAATETQHRNLDNASGELSNLSATIEE 231
                                       57788888888888999999988888888876 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.69
                         DASH_Duo1   7 eqLrkinevienviesLkkaksniervketvest 40 
                                        +L ++ ++ie + +s +++  + +r  e+ +++
  gi|313125375|ref|YP_004035639.1| 220 GELSNLSATIEEIASSADEVAAESQRTVEQAKES 253
                                       4677777788888887777776666666665554 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.8
                         DASH_Duo1   5 EleqLrkinevienviesLkkak 27 
                                       E+e+L++  e i  v+e ++++ 
  gi|313125375|ref|YP_004035639.1| 277 EVEELQSSVEQIGEVVELIDDIA 299
                                       45555555555555555554444 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.64
                         DASH_Duo1  10 rkinevienviesLkkaksniervketv 37 
                                       + + +  env++++ +++++i+r   tv
  gi|313125375|ref|YP_004035639.1| 349 DGVETSTENVTDDIYETQNEIQRSRDTV 376
                                       4455666788888888888888776666 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.02
                         DASH_Duo1   6 leqLrkinevienviesLkkaksniervketvestntLLdkWirIlsqt 54 
                                       +e+L ++   ie ++es++++++ +++ +++++ + +++d+ +++  qt
  gi|313125375|ref|YP_004035639.1| 380 IEKLGDVVGRIEESNESIQSISDATDEQSKSTQGVVSMVDEVTDLSDQT 428
                                       5788889999999999999999999999999999999999988888888 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 4.1
                         DASH_Duo1   2 LekEleqLrkinevienviesLkkaksniervketves 39 
                                       L ++ +qL+ i + +e ++  ++  +++ ++  e +++
  gi|313125375|ref|YP_004035639.1| 456 LSEQAQQLQAIVSGFEVSQTPMELNEGESDETDEPTQT 493
                                       78889999999999888877777666666666665555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   2.7      0.95   6.1e+02       4      76 ..     106     181 ..     100     205 .. 0.52
   2 ?    6.8   0.7    0.0053       3.4       6      61 ..     175     230 ..     170     237 .. 0.78
   3 ?   12.6   4.3   9.1e-05     0.058       4      89 ..     215     299 ..     212     311 .. 0.87
   4 ?    7.4   0.9    0.0036       2.3      13      89 ..     329     404 ..     321     418 .. 0.67
   5 ?    2.3   2.7      0.13        82       7      61 ..     417     471 ..     411     509 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.95
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..........eeeeeevee 70 
                                        eel+  +++le++a++y +k+e  s    +++ + ++++  ++++ ++++++ ++++          +       +
  gi|313125375|ref|YP_004035639.1| 106 SEELNALTETLEQQAESYSEKMEAASDGDLTVRVDPDSESDAMTRIGQAFNSMVADIEsvtlqiqsfaQ-------R 175
                                       566666677777777777777777777666666666666666666666666666554323222222221.......2 PP

                             TMPIT  71 lkeelk 76 
                                       ++ee  
  gi|313125375|ref|YP_004035639.1| 176 VDEEST 181
                                       222222 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0053
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk 61 
                                       ++ +e  e+ ++a+ +kq++ +++++ +++s ++++q+++l + + +l++l+++++
  gi|313125375|ref|YP_004035639.1| 175 RVDEESTEVTTSANAVKQTSTDVASSVEEISAATETQHRNLDNASGELSNLSATIE 230
                                       67778888888888888888888888888888888888888888888888877654 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 9.1e-05
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       +++ + e+ +l++t +e+ ++ +e+++  +++++++k+ +k +++ ++++++l++++ +e+  eveel+++++++ +
  gi|313125375|ref|YP_004035639.1| 215 LDNASGELSNLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRA-SETVAEVEELQSSVEQIGE 290
                                       5677889999********************************************996.699999*********9999 PP

                             TMPIT  81 vlkevesll 89 
                                       v++ ++++ 
  gi|313125375|ref|YP_004035639.1| 291 VVELIDDIA 299
                                       988666654 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0036
                             TMPIT  13 eleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesll 89 
                                       e+++ a+e  + +ee+++l++ + +++++ + ++ e ++++++ + +v+ e  e++ ++  +++e +++++++++  
  gi|313125375|ref|YP_004035639.1| 329 EVKSLAEETAKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVG-EAIEKLGDVVGRIEESNESIQSISDAT 404
                                       5555566667788888888888888888888888888888888887764.666666666666666666666555543 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.13
                             TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk 61 
                                       + +e+ +l+++  +  q++   ++ q++ ++ei++ +++l+e  ++l+ + +  +
  gi|313125375|ref|YP_004035639.1| 417 MVDEVTDLSDQTATEAQNVSAAAEEQTAATQEIASASNELSEQAQQLQAIVSGFE 471
                                       5567777777777777777777777777777777777777777777777766643 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.0      0.21   1.4e+02      59      90 ..      98     129 ..      86     143 .. 0.57
   2 ?    2.9   1.2      0.17   1.1e+02      29     100 ..     156     225 ..     139     241 .. 0.55
   3 ?    8.0   4.5    0.0046       2.9      13     102 ..     224     313 ..     220     317 .. 0.80
   4 ?    7.4   0.5    0.0067       4.3      19      95 ..     331     408 ..     321     412 .. 0.80
   5 ?    6.0   6.2     0.019        12       7      83 ..     399     476 ..     393     503 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.21
                             Mod_r  59 lrselqekleelkelekefeekeqeldellqk 90 
                                       l s+ +ek eel++l +++e+  + ++e+++ 
  gi|313125375|ref|YP_004035639.1|  98 LVSDAEEKSEELNALTETLEQQAESYSEKMEA 129
                                       34444555555555555555555555555444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                             Mod_r  29 kqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspdallarL 100
                                       +++ ++ e++  +++s+a++  ++ +e++   + ++++   +++  +e  + ++ +++ l++ s +  l++L
  gi|313125375|ref|YP_004035639.1| 156 NSMVADIESVTLQIQSFAQRVDEESTEVTTSANAVKQTSTDVASSVEEISAATETQHRNLDNASGE--LSNL 225
                                       455556666666666666666666666666666666666665555555555555555555444433..2222 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0046
                             Mod_r  13 edeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellq 89 
                                       +    +e+++++++ev +  ++  e  +e ++ a+k  ++ ++le   se+ ++ eel++  ++  e  +  d++ +
  gi|313125375|ref|YP_004035639.1| 224 NLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASETVAEVEELQSSVEQIGEVVELIDDIAD 300
                                       55567888898898888888888888899999999999999999999999999999999999999888888888888 PP

                             Mod_r  90 kfspdallarLqt 102
                                       k++  al a  ++
  gi|313125375|ref|YP_004035639.1| 301 KTNILALNASIEA 313
                                       8887777766655 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0067
                             Mod_r  19 ealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspd 94 
                                       ++l++++ + ++++++  + +++++e++ ++  + ++e++  r+ + e++e+l  +  + ee ++  +++++ ++++
  gi|313125375|ref|YP_004035639.1| 331 KSLAEETaKATEEVESLIDGVETSTENVTDDIYETQNEIQRSRDTVGEAIEKLGDVVGRIEESNESIQSISDATDEQ 407
                                       4555544355677777777777788888888889999*************************999999999888777 PP

                             Mod_r  95 a 95 
                                       +
  gi|313125375|ref|YP_004035639.1| 408 S 408
                                       5 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.019
                             Mod_r   7 eLqelledeeklealvktl.pevkqlkeekeellaenesla.eknlslepeleelrselqekleelkelekefeeke 81 
                                        + +  ++++k  + v ++ +ev +l ++     a+n+s a e++ +  +e+   ++el+e+ ++l+++ + fe  +
  gi|313125375|ref|YP_004035639.1| 399 SISDATDEQSKSTQGVVSMvDEVTDLSDQTATE-AQNVSAAaEEQTAATQEIASASNELSEQAQQLQAIVSGFEVSQ 474
                                       444444444333333335558888887766555.6666665266666699999999999999999999999888776 PP

                             Mod_r  82 qe 83 
                                       + 
  gi|313125375|ref|YP_004035639.1| 475 TP 476
                                       65 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  18.5    0.0097       6.2      80     217 ..     150     288 ..      86     292 .. 0.53
   2 ?    8.3  10.0    0.0016         1      87     223 ..     217     360 ..     212     392 .. 0.63
   3 ?    3.0  12.3     0.068        44      58     203 ..     295     463 ..     290     484 .. 0.41

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0097
                                       XXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXX. CS
                              AIP3  80 hideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefk. 155
                                       +i + ++s+ +++++++ +i+s +++ +e       +++e +++   ++  k+  ++v s  +++++  ++++ +  
  gi|313125375|ref|YP_004035639.1| 150 RIGQAFNSMVADIESVTLQIQSFAQRVDE-------ESTEVTTS---ANAVKQTSTDVASSVEEISAATETQHRNLd 216
                                       34444444444444444444443333333.......22222221...122333333333333333333333333330 PP

                                       ......XXXXXXXXXXXXXXXXXX.XXXX.XXXXXXHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 156 ......seikeslselrekakkvk.easlastkkssnrayiekgkkk...LseesdklvtkvddLqDlvedl 217
                                             s+++++++e+ + a++v  e++ +  + +++r+  +kg +k   L++++++ v++v++Lq  ve++
  gi|313125375|ref|YP_004035639.1| 217 nasgelSNLSATIEEIASSADEVAaESQRTVEQAKESRKAANKGTEKmeqLESRASETVAEVEELQSSVEQI 288
                                       00000044445555555555555543333334446677777777654222788999*************987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                                       XXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXX.XXXXXXXXXXXXX..XXXX CS
                              AIP3  87 slskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrd.Lavlrqlysefks..eike 160
                                       + s el +l+++ie+ ++s++ev++++++++++++++  a+++ ++++++++s   + +a + +l+s+ ++  e+ e
  gi|313125375|ref|YP_004035639.1| 217 NASGELSNLSATIEEIASSADEVAAESQRTVEQAKESRKAANKGTEKMEQLESRASEtVAEVEELQSSVEQigEVVE 293
                                       55566677777777777777777777777777666666666666666666665444325556655554433227777 PP

                                       XXXXXXXXXXXXX.XXXX.XXXX...XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 161 slselrekakkvk.easlastkk...ssnrayiekgkkkLseesdklvtkvddLqDlvedlrkDVvq 223
                                        + ++ +k++ +  +as++ ++    +++ a++ +  k+L ee+ k  ++v+ L D ve   + V++
  gi|313125375|ref|YP_004035639.1| 294 LIDDIADKTNILAlNASIEAASAgdaGEGFAVVASEVKSLAEETAKATEEVESLIDGVETSTENVTD 360
                                       788888888877663333333322236777889999999******************9987777764 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.068
                                       XXXXXXXX.XXXXX.........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...X.XXXX CS
                              AIP3  58 lsdvkdrs.vLsLn.........................iepldevkkhideslaslskelkelkssiesqk.aslq 107
                                       ++d+ d++ +L Ln                                     e++a+ ++e+++l + +e+++ + ++
  gi|313125375|ref|YP_004035639.1| 295 IDDIADKTnILALNasieaasagdagegfavvasevkslA-----------EETAKATEEVESLIDGVETSTeNVTD 360
                                       5677777557888877777777666555444322222221...........22222233333333333222101122 PP

                                       XXXXXXXXXXXXXXXXXXX...................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3 108 evserqeeaakekasesla..........kkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvke 174
                                       ++ e+q+e ++++ +   a           +e++++++++++   + +   q   ++ +e+++   +  ++a++v  
  gi|313125375|ref|YP_004035639.1| 361 DIYETQNEIQRSRDTVGEAieklgdvvgrIEESNESIQSISDATDEQSKSTQGVVSMVDEVTDLSDQTATEAQNVS- 436
                                       2222222222222222222111222222233333333333333333333333333333333333333333333333. PP

                                       XXX.XXXXXXHHHHHHHHHHHHHHHHHHH CS
                              AIP3 175 aslastkkssnrayiekgkkkLseesdkl 203
                                          a  +++++ + i ++ ++Lse++++l
  gi|313125375|ref|YP_004035639.1| 437 --AAAEEQTAATQEIASASNELSEQAQQL 463
                                       ..333444455555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3180  (0.177366); expected 358.6 (0.02)
Passed bias filter:                      841  (0.0469072); expected 358.6 (0.02)
Passed Vit filter:                       183  (0.0102069); expected 17.9 (0.001)
Passed Fwd filter:                       129  (0.00719505); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 2.29u 0.43s 00:00:02.72 Elapsed: 00:00:00.73
# Mc/sec: 2142.76
//
Query:       gi|313125376|ref|YP_004035640.1|  [L=89]
Description: hypothetical protein Hbor_06010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0018   18.2   0.3      0.002   18.1   0.3    1.0  1  7TMR-DISM_7TM  7TM diverse intracellular signalling
  ------ inclusion threshold ------
      0.019   14.4   1.6      0.021   14.2   1.6    1.1  1  NnrS           NnrS protein
      0.047   13.3   1.2      0.057   13.0   1.2    1.1  1  YhhN           YhhN family
       0.91    9.1   3.5       0.63    9.6   2.4    1.4  1  TMEM100        Transmembrane protein 100
        1.8    8.7   8.1        1.8    8.7   2.5    2.2  2  DUF2892        Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.3   5.5e-07     0.002     133     199 ..      12      77 ..       3      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.5e-07
                     7TMR-DISM_7TM 133 villllligikawrkgnkparyfliawlllligvlidilsllgllpsnffteyllqigvllevllls 199
                                       +++++l+ ++ ++ + +   ++f+++++ll++g++ + l+++ l p+  + e+++ ig++  v+l +
  gi|313125376|ref|YP_004035640.1|  12 GLVVSLIGLVPVLTQYRDETKLFTAGYVLLVVGMVATNLETFALEPVLNVVEHAIGIGAAGVVFL-A 77 
                                       344444444444456677899**********************999998999*****99975555.4 PP

>> NnrS  NnrS protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.6   5.8e-06     0.021     247     291 ..      34      77 ..      12      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-06
                              NnrS 247 LhlgylwlplgllllglaalgaglvlesaalHaltvGalglmila 291
                                         +gy++l++g++++ l  ++ ++vl + + Ha+++Ga g+++la
  gi|313125376|ref|YP_004035640.1|  34 FTAGYVLLVVGMVATNLETFALEPVL-NVVEHAIGIGAAGVVFLA 77 
                                       579***************99988888.999************998 PP

>> YhhN  YhhN family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   1.6e-05     0.057      85     144 ..      10      71 ..       2      82 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                              YhhN  85 llllllaaavllalllprlgklkipvlvYalvistmvatAlesl.....lslsslaallaalGal 144
                                       + +l++  ++l+ +l +  ++ k+  + Y+l+++ mvat le++     l   +  + ++ +Ga+
  gi|313125376|ref|YP_004035640.1|  10 VTGLVVSLIGLVPVLTQYRDETKLFTAGYVLLVVGMVATNLETFalepvL---NVVEHAIGIGAA 71 
                                       455566666666667777788*********************99774433...444444444443 PP

>> TMEM100  Transmembrane protein 100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.4   0.00018      0.63      59     105 ..      35      81 ..      23      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                           TMEM100  59 PfgvvvLvaGvvvtav.aytfnshgsvisvlglvLLsaGlvllassav 105
                                         g v Lv+G+v+t   +++     +v  + ++ + +aG+v+la++ v
  gi|313125376|ref|YP_004035640.1|  35 TAGYVLLVVGMVATNLeTFALEPVLNV-VEHAIGIGAAGVVFLAAAYV 81 
                                       5689**********9768999999999.556788899****9998765 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3     0.025        88      26      46 ..       5      25 ..       1      26 [. 0.74
   2 ?    8.7   2.5    0.0005       1.8      15      50 ..      35      82 ..      31      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.025
                           DUF2892 26 lglsggwgwllglvGavlllt 46
                                      l+   ++g+++ l+G+v++lt
  gi|313125376|ref|YP_004035640.1|  5 LSPLEVTGLVVSLIGLVPVLT 25
                                      444455699999*****9987 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0005
                           DUF2892 15 vvGlvllllallglsggw............gwllglvGavllltgltg 50
                                      ++G vll+++++++   +            ++  g++G+v+l+++ ++
  gi|313125376|ref|YP_004035640.1| 35 TAGYVLLVVGMVATNLETfalepvlnvvehAIGIGAAGVVFLAAAYVR 82
                                      6899999999999988889999999*****9999**********9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 548.29
//
Query:       gi|313125377|ref|YP_004035641.1|  [L=500]
Description: archaeosine tRNA-ribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-79  267.9   0.0    1.8e-79  267.5   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase
  ------ inclusion threshold ------
      0.085   13.2   0.0        5.6    7.3   0.0    2.5  2  TGT_C1    C1 domain of tRNA-guanine transglycosylase dimerisa


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.5   0.0     2e-83   1.8e-79       3     349 ..      14     340 ..      10     341 .. 0.95

  Alignments for each domain:
  == domain 1  score: 267.5 bits;  conditional E-value: 2e-83
                                       EEEEEEEETT.E.EEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S- CS
                               TGT   3 aRlGklelph.g.tietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkp 77 
                                       +R+G+l++p+ g t+etPa++pv  ++++ +++p  l++e+gaqi+++n+y+++++   +  a + glh++l++d++
  gi|313125377|ref|YP_004035641.1|  14 GRIGELTVPRaGvTVETPALLPV-INPNIVTVSPARLESEFGAQILITNSYIIHKNDDLHEEALDVGLHEMLDFDGA 89 
                                       8*******997668*********.999***************************888888878888*********** PP

                                       EEEE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHH CS
                               TGT  78 iltdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrw 154
                                       i+tdsg+fq+               ++ G+ +++t +e++++q ++g Di +++d ++p++  ++++e+++  T++ 
  gi|313125377|ref|YP_004035641.1|  90 IMTDSGSFQLA--------------EY-GD-ITVTTREILQFQYDIGTDIGTPVDIPTPPDVPREQAERELAVTEEA 150
                                       *********44..............36.**.********************************************** PP

                                       HHHHHHHH..SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EE CS
                               TGT 155 ldrcleah..qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkpry 225
                                       l+++ +    ++ + ++vqG++y+dlree+ + + ++d+d+++ig+ +++++  +++++++vv+ +++ l +d p++
  gi|313125377|ref|YP_004035641.1| 151 LQDAEDVDtgEMlVNAPVQGSTYPDLREEAGRAAYETDLDVFPIGAvVPLMNsyRYDDMVDVVAGAKRGLGRDAPIH 227
                                       ****987789777*********************************8788887899********************* PP

                                       ETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHH CS
                               TGT 226 lmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhll 302
                                       l+G+g+P++++ ava+G+D+fd+++++++ar+gr+lt +g+ +l++  y     p    CsC++C+++++ +l+   
  gi|313125377|ref|YP_004035641.1| 228 LFGAGHPMMFALAVAMGCDLFDSAAYALYARDGRYLTVRGTEHLEDLDYL----P----CSCPICTSHSPDELRAAD 296
                                       *********************************************88877....9....*****************9 PP

                                       HTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 303 ktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                       +t++    +Ll++HNlh+ +e++ r+++aI++g++ e+vee+ar+++
  gi|313125377|ref|YP_004035641.1| 297 ETEQ---ERLLAEHNLHVSFEELHRVKQAIRSGNLLELVEERARSHP 340
                                       9999...************************************9987 PP

>> TGT_C1  C1 domain of tRNA-guanine transglycosylase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00062       5.6       2      31 ..     362     390 ..     361     394 .. 0.83
   2 ?    2.9   0.0     0.015   1.3e+02      42      58 ..     417     433 ..     410     439 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00062
                            TGT_C1   2 vtkksaffkvseealkwpiverakeraekv 31 
                                       v+k  +ff +see+   p v+r ++r  ++
  gi|313125377|ref|YP_004035641.1| 362 VSK-GSFFYLSEESAFRPEVRRHHDRLARL 390
                                       555.46999***************998776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.015
                            TGT_C1  42 pifGeipkylslsypfa 58 
                                       p fG  p+ ls +yp++
  gi|313125377|ref|YP_004035641.1| 417 PPFGPFPRALSETYPLT 433
                                       77*************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3126.45
//
Query:       gi|313125378|ref|YP_004035642.1|  [L=91]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-09   36.5   0.0    4.3e-09   36.1   0.0    1.1  1  HTH_5            Bacterial regulatory protein, arsR family
    1.2e-07   31.7   0.2    1.7e-07   31.2   0.2    1.2  1  HTH_20           Helix-turn-helix domain
    0.00021   21.2   0.0    0.00032   20.6   0.0    1.4  1  HTH_45           Winged helix-turn-helix
     0.0019   18.2   0.0     0.0027   17.8   0.0    1.3  1  DprA_WH          DprA winged helix domain
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.033   13.8   0.0    1.6  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.016   15.1   0.0      0.025   14.5   0.0    1.2  1  MarR_2           MarR family
      0.026   14.4   0.0      0.036   14.0   0.0    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.037   14.4   0.0      0.041   14.2   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
      0.045   13.6   0.0      0.058   13.2   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
      0.049   13.6   0.0      0.083   12.9   0.0    1.3  1  HTH_29           Winged helix-turn helix
      0.073   13.0   0.1      0.099   12.6   0.1    1.2  1  HTH_11           HTH domain
      0.099   12.5   0.0       0.13   12.2   0.0    1.1  1  TFIIE_alpha      TFIIE alpha subunit
       0.18   11.9   0.0        0.2   11.7   0.0    1.3  1  DUF2089          Protein of unknown function (DUF2089)


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   3.1e-12   4.3e-09       3      46 ..      17      60 ..      16      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.1e-12
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +R +IL++L ++++ + +lae+l+l   tv+hHL +L+e  +V+
  gi|313125378|ref|YP_004035642.1| 17 NRARILRALDSRPRNANQLAEDLDLDYKTVRHHLDVLMENSVVQ 60
                                      699***********************************987776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.2   1.2e-10   1.7e-07      11      51 ..      17      56 ..      16      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.2e-10
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHC CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeea 51
                                       R+rilraL + +++ a++lae ldl+ +t+++HL+vL e 
  gi|313125378|ref|YP_004035642.1| 17 NRARILRAL-DSRPRNANQLAEDLDLDYKTVRHHLDVLMEN 56
                                      69*******.****************************775 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.3e-07   0.00032      10      56 ..      20      66 ..      18      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.3e-07
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekY 56
                                       IL+a+++   +  ++  + +L+yk+++  Ld L+e+ +++ s++ Y
  gi|313125378|ref|YP_004035642.1| 20 RILRALDSRPRNANQLAEDLDLDYKTVRHHLDVLMENSVVQSSGDDY 66
                                      69**************************************8877766 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     2e-06    0.0027      13      46 ..      17      50 ..      13      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-06
                           DprA_WH 13 lerrvLaaLgpePvhvDqLvrrtglpaaevsaaL 46
                                       ++r+L aL + P+   qL++++ l+  +v ++L
  gi|313125378|ref|YP_004035642.1| 17 NRARILRALDSRPRNANQLAEDLDLDYKTVRHHL 50
                                      699***************************9988 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05     0.033       7      47 ..      20      59 ..      16      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +IL++L   pr   ++LAe l+l   tv+ +l+ L+e+ ++
  gi|313125378|ref|YP_004035642.1| 20 RILRALDSRPRN-ANQLAEDLDLDYKTVRHHLDVLMENSVV 59
                                      788888887775.568********************98776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.8e-05     0.025       7      52 ..      18      60 ..      15      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                       ar+L aL  rp+   ++++la+ l+l+  +v  +l+ L +   v+
  gi|313125378|ref|YP_004035642.1| 18 RARILRALDSRPR---NANQLAEDLDLDYKTVRHHLDVLMENSVVQ 60
                                      68**********6...********************9999877766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.6e-05     0.036      19      59 ..      26      66 ..      17      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                       + p +a+++ae+l++++ +v   L  L++  +V+ +   +
  gi|313125378|ref|YP_004035642.1| 26 DSRPRNANQLAEDLDLDYKTVRHHLDVLMENSVVQSSGDDY 66
                                      67899***************************999886664 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     3e-05     0.041      25      65 ..      33      73 ..      20      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                                      HT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
                   Penicillinase_R 25 eeleeekelaysTVktllrrLvkKgllsrekegrafiYspl 65
                                      ++l+e+ +l y+TV+  l  L++  ++++  +    +Y p+
  gi|313125378|ref|YP_004035642.1| 33 NQLAEDLDLDYKTVRHHLDVLMENSVVQSSGDDYGAVYLPT 73
                                      689999*********************************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.2e-05     0.058       6      49 ..      19      60 ..      16      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      ++iL+al ++p+     +lA+ ++l   tv+++L  L+e   v+
  gi|313125378|ref|YP_004035642.1| 19 ARILRALDSRPRN--ANQLAEDLDLDYKTVRHHLDVLMENSVVQ 60
                                      69**********7..9**********************998887 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     6e-05     0.083       1      33 [.      18      50 ..      18      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwl 33
                                      Ra++l++l+    +  q+A+ l+l+++tv+++l
  gi|313125378|ref|YP_004035642.1| 18 RARILRALDSRPRNANQLAEDLDLDYKTVRHHL 50
                                      8999999999755*****************987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.2e-05     0.099       4      41 ..      20      55 ..      17      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.2e-05
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLee 41
                                       il+ L ++r+  ++++LAe L++  +tvr +++ L e
  gi|313125378|ref|YP_004035642.1| 20 RILRAL-DSRP-RNANQLAEDLDLDYKTVRHHLDVLME 55
                                      577777.7775.8*******************998854 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.1e-05      0.13       3      58 ..       5      60 ..       3      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.1e-05
                                      HHHHHHHCS-.HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha  3 lkevvrkfyg.eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                      l +v+++  g  + + +l +L ++   + ++la++l +d + +r+ L  L e  +v+
  gi|313125378|ref|YP_004035642.1|  5 LWYVLTGTRGgANRARILRALDSRPR-NANQLAEDLDLDYKTVRHHLDVLMENSVVQ 60
                                      56788888876788999999996655.5689********************999886 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015       0.2      51      79 ..      31      59 ..      15      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                           DUF2089 51 nlkevekelgisYpTvrnrldeileaLgy 79
                                      n +++++ l++ Y Tvr++ld ++e+  +
  gi|313125378|ref|YP_004035642.1| 31 NANQLAEDLDLDYKTVRHHLDVLMENSVV 59
                                      668999***************99987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 539.45
//
Query:       gi|313125379|ref|YP_004035643.1|  [L=101]
Description: hypothetical protein Hbor_06040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 652.22
//
Query:       gi|313125380|ref|YP_004035644.1|  [L=677]
Description: hypothetical protein Hbor_06050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-12   46.3   5.5       0.31   11.2   0.0    5.7  6  PAS_7           PAS fold
    8.1e-07   28.8   6.8    2.2e-06   27.4   6.8    1.8  1  PGF-CTERM       PGF-CTERM motif
    0.00028   21.0   1.6         12    6.1   0.0    5.6  5  PrcB_C          PrcB C-terminal
  ------ inclusion threshold ------
      0.039   14.1   0.0        1.8    8.6   0.0    3.1  4  Nanovirus_C8    Nanovirus component 8 (C8) protein
      0.056   14.0   4.7        4.3    7.9   0.1    4.8  5  DUF4369         Domain of unknown function (DUF4369)


Domain annotation for each model (and alignments):
>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   8.7e-05      0.31      68     104 ..      28      64 ..      16      66 .. 0.86
   2 !    8.3   0.0    0.0007       2.5      47     105 ..     122     181 ..     109     188 .. 0.69
   3 !   10.1   0.0   0.00019      0.67      58     104 ..     252     298 ..     225     301 .. 0.81
   4 ?    4.1   0.0     0.013        48      75     104 ..     385     414 ..     359     416 .. 0.82
   5 !    9.7   0.0   0.00025      0.89      77     105 ..     499     527 ..     460     532 .. 0.82
   6 ?   -2.1   0.1       1.2   4.3e+03      46      86 ..     607     645 ..     596     662 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.7e-05
                             PAS_7  68 aaaragkphsfererpdgrvievrgnplpdgGfVtty 104
                                       a+ ++g++ sf  + + g ++ v++ +lpdgGfVt++
  gi|313125380|ref|YP_004035644.1|  28 AQQSSGASVSFAAQSSGGSTVVVENVTLPDGGFVTIH 64 
                                       566778999999***********************98 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0007
                             PAS_7  47 ynaergefg.agdveaeverrlaaaragkphsfererpdgrvievrgnplpdgGfVttyt 105
                                       + a++ge + + +++  +    a+++  +  s+  + +dg+ + v + +l dgGfVt+++
  gi|313125380|ref|YP_004035644.1| 122 FVADNGETDgPYTADGSAVISQANVTVSATVSMSDQPTDGTSVVVDRVELSDGGFVTVHD 181
                                       55555555532222222222233455566778889999*******************985 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00019
                             PAS_7  58 dveaeverrlaaaragkphsfererpdgrvievrgnplpdgGfVtty 104
                                       + +a v++    +++ ++ +f  + + g+ + v +  lp+gGfVt++
  gi|313125380|ref|YP_004035644.1| 252 NGSAVVDTAAVTLSETANVTFSAQSSGGQSVVVDSAYLPEGGFVTVH 298
                                       455666666677888999999************************98 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.013
                             PAS_7  75 phsfererpdgrvievrgnplpdgGfVtty 104
                                       +  +  + +dg+ + v + +l +gGfV+++
  gi|313125380|ref|YP_004035644.1| 385 SVDMSMQASDGHSVVVDRVELSEGGFVVVH 414
                                       455667889******************987 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.00025
                             PAS_7  77 sfererpdgrvievrgnplpdgGfVttyt 105
                                       +   +++dg+++ + + +l dgGfVt+++
  gi|313125380|ref|YP_004035644.1| 499 TAADQTTDGQTVTIDSVTLHDGGFVTVHD 527
                                       4567889******************9974 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 1.2
                             PAS_7  46 rynaergefgagdveaeverrlaaaragkphsfererpdgr 86 
                                       +  +e ge++  ++e+ +e++++   a++++ +e  ++ ++
  gi|313125380|ref|YP_004035644.1| 607 EASVEDGEMT--ETEMNAETMTETEMADEETEMETGTEMNE 645
                                       5556667776..44444445554444455555555444444 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   6.8   6.1e-10   2.2e-06       1      23 []     654     676 ..     654     676 .. 0.98

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 6.1e-10
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       tPGFG+v+A+++L aaal+a Rr
  gi|313125380|ref|YP_004035644.1| 654 TPGFGVVVAIIALVAAALIAVRR 676
                                       9*******************998 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.94   3.4e+03      10      23 ..      41      54 ..      29      63 .. 0.65
   2 !    6.1   0.0    0.0035        12       9      25 ..     156     172 ..     151     186 .. 0.81
   3 ?    2.7   0.0     0.038   1.4e+02      10      24 ..     275     291 ..     270     303 .. 0.80
   4 ?    3.0   0.0     0.031   1.1e+02      10      32 ..     391     415 ..     388     430 .. 0.79
   5 ?    2.2   0.1     0.054   1.9e+02       5      24 ..     498     518 ..     496     563 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.94
                            PrcB_C 10 qptgGYsievdkvy 23
                                      q++gG  + v++v+
  gi|313125380|ref|YP_004035644.1| 41 QSSGGSTVVVENVT 54
                                      66677777777666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0035
                            PrcB_C   9 eqptgGYsievdkvyet 25 
                                        qpt+G s+ vd+v+++
  gi|313125380|ref|YP_004035644.1| 156 DQPTDGTSVVVDRVELS 172
                                       69************944 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.038
                            PrcB_C  10 qptgGYsievdkvy..e 24 
                                       q++gG s+ vd+ y  e
  gi|313125380|ref|YP_004035644.1| 275 QSSGGQSVVVDSAYlpE 291
                                       99***********9543 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.031
                            PrcB_C  10 qptgGYsievdkvy..etenaiyvk 32 
                                       q ++G s+ vd+v+  e++ +++ +
  gi|313125380|ref|YP_004035644.1| 391 QASDGHSVVVDRVElsEGGFVVVHD 415
                                       7899**********66555566655 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.054
                            PrcB_C   5 vgyGeqptgGYsievdkvy.e 24 
                                       v++  q t+G  +++d+v+  
  gi|313125380|ref|YP_004035644.1| 498 VTAADQTTDGQTVTIDSVTlH 518
                                       6666799**********9952 PP

>> Nanovirus_C8  Nanovirus component 8 (C8) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.32   1.2e+03      59     128 ..     142     213 ..     134     221 .. 0.68
   2 ?    0.2   0.0       0.2     7e+02      79     123 ..     282     326 ..     267     341 .. 0.76
   3 ?    8.6   0.0   0.00052       1.8      62     120 ..     379     439 ..     370     454 .. 0.84
   4 ?   -3.2   0.0       2.2   7.8e+03      68     119 ..     497     550 ..     489     559 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                      Nanovirus_C8  59 sgsnrnvrgflqlsirdddgvvrpvlivpi..ggylyhddyyyyegkkkveldiesdylkpdidfskdlevs 128
                                       s +n  v   + +s +  dg    v  v +  gg++  +d    eg+    +   s yl+ ++    +++++
  gi|313125380|ref|YP_004035644.1| 142 SQANVTVSATVSMSDQPTDGTSVVVDRVELsdGGFVTVHDASVTEGEVFESIRGTSAYLEAGVHENVRITLD 213
                                       334444555555555667998888877766558999999999999998888888899998887766666655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.2
                      Nanovirus_C8  79 vvrpvlivpiggylyhddyyyyegkkkveldiesdylkpdidfsk 123
                                       vv    ++p gg++  +d    +g     +   s yl+p+     
  gi|313125380|ref|YP_004035644.1| 282 VVVDSAYLPEGGFVTVHDATLNDGAVFESIRGTSAYLAPGLHKNV 326
                                       45556899******9999999999999999999******975433 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00052
                      Nanovirus_C8  62 nrnvrgflqlsirdddgvvrpvlivpi..ggylyhddyyyyegkkkveldiesdylkpdid 120
                                       n  +   + +s++  dg    v  v +  gg++  +d   + g+ +  +   sdyl+p++ 
  gi|313125380|ref|YP_004035644.1| 379 NVTLSASVDMSMQASDGHSVVVDRVELseGGFVVVHDSSLFAGEVEGSILGTSDYLEPGVH 439
                                       555677899********9888888765559****************99999*******975 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 2.2
                      Nanovirus_C8  68 flqlsirdddgvvrpvlivpi..ggylyhddyyyyegkkkveldiesdylkpdi 119
                                        +  + +  dg+   +  v +  gg++  +d    eg     +   s yl+p+ 
  gi|313125380|ref|YP_004035644.1| 497 VVTAADQTTDGQTVTIDSVTLhdGGFVTVHDATVSEGAVFESVRGTSAYLSPGT 550
                                       555566677787777777765557888888888888887777788888888875 PP

>> DUF4369  Domain of unknown function (DUF4369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.71   2.5e+03      44      70 ..     112     129 ..      43     157 .. 0.62
   2 ?    1.2   0.1      0.15   5.3e+02      22      46 ..     158     184 ..     135     255 .. 0.76
   3 ?    2.4   0.0     0.061   2.2e+02      16      47 ..     271     303 ..     231     333 .. 0.76
   4 ?   -2.4   0.0       1.9     7e+03      21      40 ..     393     412 ..     374     420 .. 0.75
   5 ?    7.9   0.1    0.0012       4.3      20      59 ..     504     543 ..     488     583 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.71
                           DUF4369  44 vdeprlaylliddkgg....alpfflengti 70 
                                        d             +    ++ f+++ng++
  gi|313125380|ref|YP_004035644.1| 112 MD-------------TdgdrVYDFVADNGET 129
                                       22.............1222345555555543 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                           DUF4369  22 d..ngvvklDsavvknGkFtfkgkvde 46 
                                          ++ v++D +++++G F+  ++++ 
  gi|313125380|ref|YP_004035644.1| 158 PtdGTSVVVDRVELSDGGFVTVHDASV 184
                                       145788899999999999987665544 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.061
                           DUF4369  16 vy.lsyddngvvklDsavvknGkFtfkgkvdep 47 
                                        +  ++++++ v++Dsa + +G F+  ++++  
  gi|313125380|ref|YP_004035644.1| 271 TFsAQSSGGQSVVVDSAYLPEGGFVTVHDATLN 303
                                       333444448999999999999999877766655 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.9
                           DUF4369  21 ddngvvklDsavvknGkFtf 40 
                                       +d+  v++D +++++G F+ 
  gi|313125380|ref|YP_004035644.1| 393 SDGHSVVVDRVELSEGGFVV 412
                                       34678899999999998875 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0012
                           DUF4369  20 yddngvvklDsavvknGkFtfkgkvdeprlaylliddkgg 59 
                                       ++d+++v++Ds+++ +G F+  ++++  ++a++   ++++
  gi|313125380|ref|YP_004035644.1| 504 TTDGQTVTIDSVTLHDGGFVTVHDATVSEGAVFESVRGTS 543
                                       33489**************998877776666555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (677 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.38s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 3690.13
//
Query:       gi|313125381|ref|YP_004035645.1|  [L=167]
Description: hypothetical protein Hbor_06060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-08   33.2   0.0    5.1e-08   33.0   0.0    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
     0.0069   16.6   0.0      0.011   16.0   0.0    1.3  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.032   14.2   0.0      0.037   14.0   0.0    1.2  1  APH             Phosphotransferase enzyme family
      0.077   12.6   0.1       0.11   12.1   0.1    1.2  1  DSHCT           DSHCT (NUC185) domain


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   1.1e-11   5.1e-08       3     140 ..      10     147 ..       8     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.1e-11
                                       HHHHHHHHC-SE.EEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCC.T--.ECEEEEEEEEEEE-SE.GG CS
                      Pyridox_ox_2   3 eeilalLdegev.grlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalr.gap.vcvvvtevdglvlars.fn 75 
                                       +e++ +L+e+ v  rla+ + +   ++ ++ +++    ++ g+++s+l++a++ +a+ v +  ++ d++ ++ s + 
  gi|313125381|ref|YP_004035645.1|  10 DEAETFLRESTVpVRLACRT-PSDDLWMLSLWYE----WVGGEDSSELCCATSaDADvVRFLRAN-DDVAFEIStN- 79 
                                       899999*9655449******.888**********....999999********9544445555555.8888888833. PP

                                       EEEEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB....---CCCCCT.EEEEEEEEEEEEEE CS
                      Pyridox_ox_2  76 slnyrSVvvrGraeevtdeeekaealellvekivpgrwenlr....pptrkelka.tsvlrlkieevsgr 140
                                       +  yr V  rG+a+    ++e++++l++l+e+++ g+ ++l     +++r+e++  ++  rl+ ++ sgr
  gi|313125381|ref|YP_004035645.1|  80 DPPYRGVRGRGTASIE--PDEEKTLLRSLLERYLGGTENELGsfllDDDREEVRIrITPTRLHSWDYSGR 147
                                       445***********99..***************9999554445788999999988899999999999998 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.4e-06     0.011       3      88 .]      10      99 ..       9      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHHHS.SEEEEEEEETTSEEEEEEEEEEEETTT..TEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEE CS
                    Putative_PNPOx  3 eelreflaes.kavvlATvdedGrPnvspvllkagdgr..dgivfatnadsrklrnleenprvallfldde.lgrgvri 77
                                      +e+++fl+es   v+lA+ +++   ++  +++ +  g+    +  at+ad++ +r l++n  va+ +  ++  +rgvr 
  gi|313125381|ref|YP_004035645.1| 10 DEAETFLREStVPVRLACRTPSDDLWMLSLWYEWVGGEdsSELCCATSADADVVRFLRANDDVAFEISTNDpPYRGVRG 88
                                      5677777766345899999999999999999999888888899************************99999******* PP

                                      EEEEEEESCHH CS
                    Putative_PNPOx 78 eGtaelvsdge 88
                                      +Gta +  d+e
  gi|313125381|ref|YP_004035645.1| 89 RGTASIEPDEE 99
                                      ******99986 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.2e-06     0.037      48     126 ..      17      97 ..       9     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.2e-06
                                       HHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS....HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHC CS
                               APH  48 akagvpvPevlagdtddeeigllfalieyvpgrsllr....klsaaqlpellealgeflaalhqvdpaalpladfla 120
                                       +++  +vP+ la++t  +++++l++ +e+v+g++ ++    +  +a+  ++l+a  ++ ++++  dp+ +++++++ 
  gi|313125381|ref|YP_004035645.1|  17 RES--TVPVRLACRTPSDDLWMLSLWYEWVGGEDSSElccaTSADADVVRFLRANDDVAFEISTNDPPYRGVRGRGT 91 
                                       444..7899****************************8887667777777777777777777777777777776665 PP

                                       HTCCHH CS
                               APH 121 qdlell 126
                                         +e++
  gi|313125381|ref|YP_004035645.1|  92 ASIEPD 97 
                                       444433 PP

>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.5e-05      0.11      89     134 ..      31      76 ..       7      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
                             DSHCT  89 l.dlglvevvyaWakgasfaellektdldeGdiVRllrrleellrql 134
                                         dl +  + y+W+ g++ +el+ +t++d+ d+VR lr  +++  ++
  gi|313125381|ref|YP_004035645.1|  31 SdDLWMLSLWYEWVGGEDSSELCCATSADA-DVVRFLRANDDVAFEI 76 
                                       44788999*******************988.*******999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1115.32
//
Query:       gi|313125382|ref|YP_004035646.1|  [L=585]
Description: tRNA-archaeosine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-58  196.7   0.8    2.8e-58  196.2   0.8    1.2  1  DUF5591   Domain of unknown function (DUF5591)
    1.5e-24   85.9   0.0    3.5e-24   84.7   0.0    1.7  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    1.4e-15   57.3   0.1    4.5e-15   55.7   0.0    1.8  2  TGT       Queuine tRNA-ribosyltransferase
      4e-12   45.9   0.5    9.3e-12   44.7   0.5    1.6  1  PUA       PUA domain


Domain annotation for each model (and alignments):
>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.2   0.8   6.2e-62   2.8e-58       1     154 []     283     432 ..     283     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 196.2 bits;  conditional E-value: 6.2e-62
                                       X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT------- CS
                           DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqY 77 
                                       ++rf+erv++rY++++ +++lvL+Pcsa+kPyses+sh++f++a++ r   +h  ++tsP+GvvP ele++YPa++Y
  gi|313125382|ref|YP_004035646.1| 283 IQRFAERVTSRYKNRF-DNPLVLVPCSATKPYSESQSHSQFHDAVQFR---AHLASMTSPIGVVPSELELTYPAQHY 355
                                       89*************9.******************************9...9************************* PP

                                       ---------HHHHHHHHHHHHHHHHHHT-SEEEE---TH.HHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHHH CS
                           DUF5591  78 diavtgewseeeiefvaellakylektkyekviahleee.yreiveevaeelgleiiytvvedkptskeslknLkea 153
                                       d++vtg+wse+e++fva++l++yle+++y++v+ah++e+ yr+i+e+v++e+++ ++ytv ed+pt+++s++nL ++
  gi|313125382|ref|YP_004035646.1| 356 DTVVTGRWSEDEKQFVASVLTQYLERNDYPRVVAHVPEHgYRDICERVEQEVDVPFEYTV-EDHPTTTDSIANLMST 431
                                       **************************************99********************.*************998 PP

                                       H CS
                           DUF5591 154 L 154
                                       L
  gi|313125382|ref|YP_004035646.1| 432 L 432
                                       7 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   7.7e-28   3.5e-24       1      70 [.     446     515 ..     446     516 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 7.7e-28
                            TGT_C2   1 nrlraiadYqFGagagdaLfpedvtitrsatgrirqvlv...dgerlatlraqdgrltLsleGarrlheslpp 70 
                                       n+++aiadYqFG+gagdaLf + v+++   t r+++++v   dg++la++++q+g+l+++l+Gar + +s++p
  gi|313125382|ref|YP_004035646.1| 446 NTVKAIADYQFGDGAGDALFAD-VDVQ--MTSRYPKLQVrngDGDQLAAMVPQYGVLSFTLAGARVWSDSDAP 515
                                       79******************75.****..***********999**************************9876 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.36   1.6e+03       2      20 ..      13      30 ..      11      32 .. 0.86
   2 !   55.7   0.0     1e-18   4.5e-15     188     344 ..      99     237 ..      85     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.36
                                      TEEEEEEEETTEEEEESEE CS
                               TGT  2 gaRlGklelphgtietPaf 20
                                      +aRlG+l+l++ +++tPa+
  gi|313125382|ref|YP_004035646.1| 13 AARLGELRLAD-PVTTPAL 30
                                      39*******98.7****87 PP

  == domain 2  score: 55.7 bits;  conditional E-value: 1e-18
                                       H--SEEEE-SSS..SSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEE CS
                               TGT 188 rdfdgyaigGls..vgeekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngralt 262
                                        + d y ++  +  vg   + + + + a+++ lp+d   yl Gv tP +++ +v +GvD++d  ++   +r+g++lt
  gi|313125382|ref|YP_004035646.1|  99 AGSDAYILSNAQgfVG-HASAFRDAIVAAKDALPADTALYLSGVATPRNVATLVYAGVDLVDAKLARVKGRQGMYLT 174
                                       5556666666553233.4788999999************************************************** PP

                                       TTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHH CS
                               TGT 263 segelnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfee 339
                                       se+e+ l++     d  p    C+C +C+   r++  h            ++ HN+  ++ +++++R+ I++g++ +
  gi|313125382|ref|YP_004035646.1| 175 SENEYFLED----LDELP----CTCAACQ-TPREEFTHED----------CAAHNVNALRAELATVRQRIRDGRLRD 232
                                       *99999984....35557....******9.6777777654..........788************************ PP

                                       HHHHH CS
                               TGT 340 fveef 344
                                       ++e  
  gi|313125382|ref|YP_004035646.1| 233 YIEGQ 237
                                       99865 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.5   2.1e-15   9.3e-12      17      73 ..     528     582 ..     517     582 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.1e-15
                                       -EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA  17 asLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                        s+lapGvv++++d++ gd+V +  +  ++ avG+a++ ++e+++ ++g++ve+++v
  gi|313125382|ref|YP_004035646.1| 528 GSVLAPGVVDADDDIRVGDEVIVEGP--KAFAVGRAEMFGAEMTESTRGVAVEVRHV 582
                                       49*******************99888..***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3565.80
//
Query:       gi|313125383|ref|YP_004035647.1|  [L=134]
Description: hypothetical protein Hbor_06080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 869.57
//
Query:       gi|313125384|ref|YP_004035648.1|  [L=90]
Description: moad family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-20   71.0   0.2      1e-19   70.9   0.2    1.0  1  ThiS      ThiS family
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.011   16.1   0.0    1.2  1  Urm1      Urm1 (Ubiquitin related modifier)


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.2   1.2e-23     1e-19       1      77 []       1      87 [.       1      87 [. 0.98

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.2e-23
                                      EEETTCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG........TTTTEEEEETTEEEGC.CTTTSB--TTCEEE CS
                              ThiS  1 vllfaelrelag.eeelelaegstvaelleaLgerypela........lerrvavavNgeivpr.lwldtelkdgDeva 69
                                      +++fa+ re++g ++ + + e +tv+++l++L+++y++la         +++v+v++Ng++v++ ++ +tel d D+++
  gi|313125384|ref|YP_004035648.1|  1 MRFFANFREAVGtKTIERDYEVTTVGDALRELEAEYSGLAgelledghVRPQVNVLLNGRDVQHeQGIETELGDEDTLS 79
                                      58**********************************************99**************99************* PP

                                      EEESTTC- CS
                              ThiS 70 ilppVaGG 77
                                      i+ppVaGG
  gi|313125384|ref|YP_004035648.1| 80 IFPPVAGG 87
                                      *******9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.0   1.2e-06     0.011      53      96 .]      44      87 ..       5      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-06
                                      BSTTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                              Urm1 53 lekdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                      le+++vrP + vL+n  D++ ++  ++el d+D+++    + GG
  gi|313125384|ref|YP_004035648.1| 44 LEDGHVRPQVNVLLNGRDVQHEQGIETELGDEDTLSIFPPVAGG 87
                                      7899******************************9877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 605.79
//
Query:       gi|313125385|ref|YP_004035649.1|  [L=92]
Description: hypothetical protein Hbor_06100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.7   0.0       0.34   11.2   0.0    1.2  1  DUF5376   Family of unknown function (DUF5376)


Domain annotation for each model (and alignments):
>> DUF5376  Family of unknown function (DUF5376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.9e-05      0.34      40      81 ..      18      59 ..       2      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.9e-05
                           DUF5376 40 ldlelakkvldklkdkeieeedigseawdaeieedkvkigfl 81
                                      ++++la + l++l  + + e+ ++ ++w a +  +kv ig +
  gi|313125385|ref|YP_004035649.1| 18 ISMRLAGQYLENLGGERVAEDRVEGDGWTASLSAQKVPIGPT 59
                                      457889999****************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 605.71
//
Query:       gi|313125386|ref|YP_004035650.1|  [L=119]
Description: hypothetical protein Hbor_06110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 762.42
//
Query:       gi|313125387|ref|YP_004035651.1|  [L=98]
Description: hypothetical protein Hbor_06120, partial [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-13   49.2   0.0    8.7e-13   49.0   0.0    1.0  1  ABC_tran     ABC transporter
    0.00065   19.4   0.1    0.00096   18.8   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0063   17.0   0.0     0.0076   16.8   0.0    1.1  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.015   14.3   0.1      0.015   14.3   0.1    1.1  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.018   14.6   0.0      0.022   14.3   0.0    1.1  1  AAA_7        P-loop containing dynein motor region
       0.02   14.8   0.0       0.02   14.8   0.0    1.1  1  RsgA_GTPase  RsgA GTPase
      0.051   13.4   0.0      0.051   13.4   0.0    1.1  1  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      0.058   13.0   0.0      0.078   12.6   0.0    1.1  1  SRP54        SRP54-type protein, GTPase domain
      0.071   13.5   0.0      0.071   13.5   0.0    1.1  1  AAA_16       AAA ATPase domain
       0.13   11.8   0.0       0.15   11.6   0.0    1.2  1  AAA_27       AAA domain
       0.16   11.7   0.1        0.2   11.4   0.1    1.1  1  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.24   10.3   0.0       0.25   10.2   0.0    1.1  1  AAA_10       AAA-like domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   5.8e-16   8.7e-13       2      77 ..      20      94 ..      19      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 5.8e-16
                                      EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77
                                       ++sl+++ege+++++G+nGaGKSt + +l+  ++pt+G+ ++ g d ++ + +  +++ g+lp    + + lt r
  gi|313125387|ref|YP_004035651.1| 20 TDLSLSVREGEVYGFLGPNGAGKSTTIDMLMDYTRPTSGNATVLGIDAQT-NASAIHARTGILPDRFGVYSSLTRR 94
                                      689*********************************************99.8888999999998887777776655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   6.4e-07   0.00096      19      43 ..      26      50 ..      18      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.4e-07
                            AAA_29 19 idlkg.atlltGpsGsGKSTllDAiq 43
                                      +++ g ++ + Gp+G+GKST +D ++
  gi|313125387|ref|YP_004035651.1| 26 VRE-GeVYGFLGPNGAGKSTTIDMLM 50
                                      443.348889*************765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.1e-06    0.0076      21      39 ..      31      49 ..      19      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.1e-06
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                      ++ + GpNGaGK+T +d +
  gi|313125387|ref|YP_004035651.1| 31 VYGFLGPNGAGKSTTIDML 49
                                      67899***********976 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     1e-05     0.015      28      70 ..      28      70 ..       9      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      + +v G+ G  GaGkst+++ l+   r      +vl +D   +
  gi|313125387|ref|YP_004035651.1| 28 EGEVYGFLGPNGAGKSTTIDMLMDYTRPTSGNATVLGIDAQTN 70
                                      56789******************99999999999**9997654 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.5e-05     0.022      29      78 ..      25      74 ..      18      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                             AAA_7 29 llknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanql 78
                                       ++++    + Gp G GK+++i  l++   +++ + +++ + aqt+a+ +
  gi|313125387|ref|YP_004035651.1| 25 SVREGEVYGFLGPNGAGKSTTIDMLMDYTRPTSGNATVLGIDAQTNASAI 74
                                      56666777799**********************************99876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.4e-05      0.02      91     122 ..      20      52 ..       4      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       ++l+  +++ ++  ++G+ G+GKSt i++l+  
  gi|313125387|ref|YP_004035651.1|  20 TDLSLSVREgEVYGFLGPNGAGKSTTIDMLMDY 52 
                                       55665666659999***************9875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.4e-05     0.051       3      19 ..      33      49 ..      31      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                            AAA_21  3 vliGpNgsGKSnLLdal 19
                                      ++ GpNg+GKS+ +d l
  gi|313125387|ref|YP_004035651.1| 33 GFLGPNGAGKSTTIDML 49
                                      789**********9987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.2e-05     0.078       4      39 ..      32      67 ..      30      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      + ++G++GaGK tt+  L ++ +    ++ +   D 
  gi|313125387|ref|YP_004035651.1| 32 YGFLGPNGAGKSTTIDMLMDYTRPTSGNATVLGIDA 67
                                      5689****************9999877777776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.8e-05     0.071      19      63 ..      26      70 ..       9      94 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.8e-05
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd...ggiflrgkcdql 63
                                      vr+g  e+  + G+ G GKs+ +++l++ +++    ++ +l  +++ +
  gi|313125387|ref|YP_004035651.1| 26 VREG--EVYGFLGPNGAGKSTTIDMLMD-YTRPtsgNATVLGIDAQTN 70
                                      5555..566689***************5.5555243344444444444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.15      21      48 ..      24      51 ..      15      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                            AAA_27 21 fsaeeadlhliyGpNEAGKstalrAisd 48
                                      +s  e ++   +GpN AGKst+++ + d
  gi|313125387|ref|YP_004035651.1| 24 LSVREGEVYGFLGPNGAGKSTTIDMLMD 51
                                      444466666679**********988776 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00013       0.2       2      34 ..      35      67 ..      34      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDP 34
                                      +Gp G+GK+t +  l+++++ +  +  v+ +D 
  gi|313125387|ref|YP_004035651.1| 35 LGPNGAGKSTTIDMLMDYTRPTSGNATVLGIDA 67
                                      7*****************999988888888875 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00017      0.25      26      60 ..      34      70 ..      21      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                            AAA_10 26 iiGdlGnGKSvlakllvlyisllg..gkaliiDpkke 60
                                      ++G+ G+GKS ++ +l+ y +       +l iD + +
  gi|313125387|ref|YP_004035651.1| 34 FLGPNGAGKSTTIDMLMDYTRPTSgnATVLGIDAQTN 70
                                      89*****************987762245566787766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 653.21
//
Query:       gi|313125388|ref|YP_004035652.1|  [L=154]
Description: o-6-methylguanine DNA methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-23   80.8   0.1    8.3e-23   80.3   0.1    1.2  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.1   4.6e-27   8.3e-23       5      80 ..      52     128 ..      49     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 4.6e-27
                                       HHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTT....TTCHHHHHHHHH CS
                     DNA_binding_1   5 rVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggy....agglerkralLe 77 
                                       +V++ +rqIpyG++ tYgeiA +l+  +a+ aVgqa+++np++ilvPcHR+vg++  lgg+    ++g + k++lL+
  gi|313125388|ref|YP_004035652.1|  52 AVMRCMRQIPYGETRTYGEIATELQ--TAPVAVGQACGRNPVPILVPCHRIVGTES-LGGFsaggEHGETLKHRLLA 125
                                       799**********************..***************************98.99997544449999*****9 PP

                                       HTT CS
                     DNA_binding_1  78 aEg 80 
                                        E+
  gi|313125388|ref|YP_004035652.1| 126 LER 128
                                       996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 967.79
//
Query:       gi|313125389|ref|YP_004035653.1|  [L=57]
Description: hypothetical protein Hbor_06140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 355.40
//
Query:       gi|313125390|ref|YP_004035654.1|  [L=350]
Description: o-methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-20   71.2   0.0    9.4e-20   70.8   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    2.7e-07   30.5   0.0    7.1e-07   29.1   0.0    1.7  1  Dimerisation2    Dimerisation domain
    8.6e-07   28.9   0.0    3.2e-06   27.1   0.0    1.8  2  Methyltransf_23  Methyltransferase domain
    5.8e-06   27.0   0.0    1.5e-05   25.6   0.0    1.8  1  Methyltransf_12  Methyltransferase domain
    1.3e-05   25.8   0.0      3e-05   24.6   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    0.00019   21.4   0.0    0.00048   20.1   0.0    1.6  1  Dimerisation     Dimerisation domain
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.031   13.8   0.0    1.4  1  MTS              Methyltransferase small domain
      0.033   14.8   0.0      0.066   13.9   0.0    1.5  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   4.2e-23   9.4e-20      24     209 ..     139     328 ..     123     329 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 4.2e-23
                                       -HHHHHTSSHHHHHHHHHHHHTTHHHHHHHHHHSS-.GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHH CS
                    Methyltransf_2  24 slfeaikrdeeerakfnkglqessslvakkvleafd.leglkslvDvGGGtGalakaivsayPtikvivfDlpeVve 99 
                                       s++e   +d+   +  ++g++ + sl +++v+ ++    g ++l+DvGGG G  a +  + +P+++++vfD p  + 
  gi|313125390|ref|YP_004035654.1| 139 SIYEWFDEDPARWETAQEGFRATASLLVDDVVDSMTvPAGQSRLLDVGGGHGLYAMELCRRHPKLSATVFDYPGAID 215
                                       5899999999999***********************77899************************************ PP

                                       HHHHHS-----TTEEEEES-TTTS-----.SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS-- CS
                    Methyltransf_2 100 aAkehlsageeervefvgGdffkdslPea.DaillkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsg 175
                                       a ++ +  +++ r+    Gd++ d l e+ D+ ll +v+h +s ++ + l +rv++al +gG+++v +   g +++ 
  gi|313125390|ref|YP_004035654.1| 216 AMEDDIPDELAGRLGTRTGDYWTDDLGEGyDMALLFNVVHAHSPAENTALFERVRDALAPGGRIVVLDQWEGSGRTP 292
                                       ******99*******************655**************************************998877666 PP

                                       -HHHHHHHHHHHHC..SS-----HHHHHHHHHHCT- CS
                    Methyltransf_2 176 eletelvdlimlvq..teGkeRteaeyeellseaGf 209
                                         ++ l  + +  +   + ++ +  e ++ l++aGf
  gi|313125390|ref|YP_004035654.1| 293 VSRAGLRFVALTYHttLGANVYEHDEVSSWLQAAGF 328
                                       555555433333333144456667789999999998 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.2e-10   7.1e-07      17      89 ..      37     105 ..      25     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.2e-10
                     Dimerisation2  17 tAceLgvFdlLke.eeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelastyLvsssp 89 
                                        A e+g+F+++++ ++pl+ae++a++l+a ++G+  +++ +v+ g Le       ++ Y+ t +++++L  +s+
  gi|313125390|ref|YP_004035654.1|  37 LALEIGLFETIADvDRPLTAEDLADRLDAHPDGIAVFCNFLVSEGYLEAV-----GDRYRLTGMTEKWLLAESE 105
                                       589*********************************************55.....467************9997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.68   1.5e+03     111     135 ..      67     101 ..      41     134 .. 0.64
   2 !   27.1   0.0   1.4e-09   3.2e-06      23     163 ..     179     331 ..     156     333 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.68
                   Methyltransf_23 111 pgGylllseplasl..........kedrllldwly 135
                                       p+G ++++ +l+s             + + ++wl+
  gi|313125390|ref|YP_004035654.1|  67 PDGIAVFCNFLVSEgyleavgdryRLTGMTEKWLL 101
                                       88999999888877666666666523333333433 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.4e-09
                   Methyltransf_23  23 ggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaaepqg................ 81 
                                       ++r+Ld+G G+G + +e++r++++ s t++D    a++           ++d +  +e +g                
  gi|313125390|ref|YP_004035654.1| 179 QSRLLDVGGGHGlYAMELCRRHPKlSATVFDYP-GAID----------AMEDDI-PDELAGrlgtrtgdywtddlge 243
                                       579*********8899999999989*******4.3333..........333111.1222224455555555666666 PP

                   Methyltransf_23  82 kfdlIvlrevlehvpd..ppellrqiatllkpgGylllseplasl...kedrllldwlylvpagrhi.sffsarslk 152
                                        +d + l++v +   +   ++l+ ++++ l+pgG+++++++ + +   +  r+ l   +l  + +++ +++  +++ 
  gi|313125390|ref|YP_004035654.1| 244 GYDMALLFNVVHAHSPaeNTALFERVRDALAPGGRIVVLDQWEGSgrtPVSRAGLRFVALTYHTTLGaNVYEHDEVS 320
                                       **********9877643377********************6332234456666666544444447779********* PP

                   Methyltransf_23 153 elleeaGlevv 163
                                        +l++aG++ +
  gi|313125390|ref|YP_004035654.1| 321 SWLQAAGFTGI 331
                                       ********976 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   6.8e-09   1.5e-05       1      99 []     183     279 ..     183     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.8e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++G+G G ++++l++++p ++ t+ D+ p ai d  +   ++ ++ + ++  ++ d   +d g+ +D+ +++nv+h
  gi|313125390|ref|YP_004035654.1| 183 LDVGGGHGLYAMELCRRHPKLSATVFDY-PGAI-D--AMEDDIPDELAGRLGTRTGDYWTDDLGEGYDMALLFNVVH 255
                                       8**************************9.6667.2..3344445555667777777777778888************ PP

                   Methyltransf_12  78 hl..kdirevldnirklLkpgGrl 99 
                                       +   ++  ++++++r++L+pgGr+
  gi|313125390|ref|YP_004035654.1| 256 AHspAENTALFERVRDALAPGGRI 279
                                       **888888**************96 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.3e-08     3e-05       2      97 .]     183     277 ..     182     277 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       Ld+G G+G ++++l +r +k + t +D+ +++++a++  + +e + ++  ++gd  + ++  + +D+ ++++++h  
  gi|313125390|ref|YP_004035654.1| 183 LDVGGGHGLYAMELCRRHPKLSATVFDY-PGAIDAMEDDIPDELAgRLGTRTGDYWTDDLG-EGYDMALLFNVVHAH 257
                                       9****************989*******8.899********887558999999999665554.59******8889999 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       s+++  +++++++++L pgG
  gi|313125390|ref|YP_004035654.1| 258 SPAENTALFERVRDALAPGG 277
                                       99999**************9 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.2e-07   0.00048       6      39 ..      38      69 ..      34      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.2e-07
                      Dimerisation  6 AiELglldiiakaggkplspsEiaskLptknpea 39
                                      A+E gl+++ia   ++pl+++++a +L   +p+ 
  gi|313125390|ref|YP_004035654.1| 38 ALEIGLFETIADV-DRPLTAEDLADRLD-AHPDG 69
                                      9************.7*************.99985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05     0.031      31     137 ..     178     281 ..     155     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE--- CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPP 106
                                        + ++lD+G G G+ +++l +++p+++ t++d    A+++ +  + ++ +  + +++ d   +   + +d+ +    
  gi|313125390|ref|YP_004035654.1| 178 GQSRLLDVGGGHGLYAMELCRRHPKLSATVFDY-PGAIDAMEDDIPDELAGrLGTRTGDYWTDDLGEGYDMALL--- 250
                                       45679**************************97.5799999999888777668888888777666688998887... PP

                                       STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                               MTS 107 fhagkatelavaeeliaeAkeaLkegGeLli 137
                                       f   +a + a  ++l++  ++aL++gG++++
  gi|313125390|ref|YP_004035654.1| 251 FNVVHAHSPAENTALFERVRDALAPGGRIVV 281
                                       4455555557777888888999999998876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.9e-05     0.066       1      96 []     183     281 ..     183     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       LdvG G G++a +l +r    + + +D  + ++++ ++ +++e   ++  + +d  +  + +  +D+ ++++v+h  
  gi|313125390|ref|YP_004035654.1| 183 LDVGGGHGLYAMELCRRHpkLSATVFD-YPGAIDAMEDDIPDELAgRLGTRTGDYWTDDLGE-GYDMALLFNVVHAH 257
                                       8**************888888999999.7999999999999998899999999999877877.89*******99988 PP

                                       ..CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 ..edpekalkeiaRvLkpgGllvi 96 
                                         ++  ++++ ++  L pgG++v+
  gi|313125390|ref|YP_004035654.1| 258 spAENTALFERVRDALAPGGRIVV 281
                                       89999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2286.42
//
Query:       gi|313125391|ref|YP_004035655.1|  [L=218]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-17   61.8   0.0    5.9e-17   61.2   0.0    1.3  1  HTH_10          HTH DNA binding domain
  ------ inclusion threshold ------
      0.023   14.9   0.0      0.041   14.1   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.058   13.0   0.0       0.15   11.6   0.0    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.063   13.2   0.0       0.12   12.2   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   1.3e-20   5.9e-17       1      52 [.     162     213 ..     162     214 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.3e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       +T++q evl +A+++GY+++PR++tl+++ +  GI+++t+ ehLrk+e+ ++
  gi|313125391|ref|YP_004035655.1| 162 FTPRQEEVLETAVDLGYYNEPRQATLEDIGEVVGIAPATVGEHLRKVEECVF 213
                                       7**********************************************98665 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.1e-06     0.041       1      48 [.     161     210 ..     161     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.1e-06
                                       X--HHHHHHHHHHHHHHH..HHSSB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                    Fe_dep_repress   1 dLvestEdYLetIYtlse..ekkvvktkdlaerLnvspssVsemlkkLek 48 
                                       +++++ E++Let  +l    e   ++  d+ e+ +++p++V e l+k e+
  gi|313125391|ref|YP_004035655.1| 161 MFTPRQEEVLETAVDLGYynEPRQATLEDIGEVVGIAPATVGEHLRKVEE 210
                                       7999*********999766689999*********************9876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.4e-05      0.15      15      43 ..     181     210 ..     179     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                            HTH_24  15 npr.isqreLAerlglSpstvnrrlkrLee 43 
                                       +pr  +  ++ e +g+ p+tv ++l++ ee
  gi|313125391|ref|YP_004035655.1| 181 EPRqATLEDIGEVVGIAPATVGEHLRKVEE 210
                                       56668999******************9887 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.8e-05      0.12      16      42 ..     185     211 ..     180     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                                       EEHHHHHHHHTS-HHHHHHHHHHHHHT CS
                             HTH_5  16 lcvcelaeelglsqstvShHLkkLrea 42 
                                       ++  ++ e +g+ ++tv +HL+k +e+
  gi|313125391|ref|YP_004035655.1| 185 ATLEDIGEVVGIAPATVGEHLRKVEEC 211
                                       67789999**************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1327.42
//
Query:       gi|313125392|ref|YP_004035656.1|  [L=441]
Description: transposase, is605 orfb family, central region [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-26   92.1   0.0    6.6e-26   90.9   0.0    1.6  1  OrfB_IS605      Probable transposase
    3.8e-20   71.6   2.2    7.6e-20   70.6   1.3    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0003   21.1   1.1    0.00078   19.7   1.1    1.7  1  C1_2            C1 domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.0   1.1e-29   6.6e-26       2     118 ..     192     299 ..     180     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 1.1e-29
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                       ++++ e e p+++g+++agiDlGi+n+a+v+ +++++ ly g+rlk+d +y+ keia+++              + +
  gi|313125392|ref|YP_004035656.1| 192 LVCKDEIEAPTAPGTETAGIDLGICNFAAVAYSTEEADLYPGNRLKQDGYYFPKEIAKCDDS---------GGDRAT 259
                                       5566666799*************************************************988.........35679* PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkd 118
                                       rlh+k+s+rr+h++h+la+h+++++ e+gv+ +nvg+++ 
  gi|313125392|ref|YP_004035656.1| 260 RLHHKWSERRTHFFHSLAKHIVEKCIERGVGRINVGKLAG 299
                                       ************************************9985 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.56   3.4e+03       1      19 [.     273     291 ..     273     296 .. 0.82
   2 !   70.6   1.3   1.3e-23   7.6e-20       1      67 [.     324     391 ..     324     393 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.56
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikv 19 
                                       f++l + + +k+ e+G+  
  gi|313125392|ref|YP_004035656.1| 273 FHSLAKHIVEKCIERGVGR 291
                                       788999999******9865 PP

  == domain 2  score: 70.6 bits;  conditional E-value: 1.3e-23
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f++++++l ykak +Gi v+ev+++ TSktC +Cg+k++  ++++ +++C++C + +++Dvn+a Ni 
  gi|313125392|ref|YP_004035656.1| 324 FDRFTKILTYKAKVEGIDVVEVSERDTSKTCCVCGRKDDSqRVERGLYVCDECDAAFNADVNGAENIR 391
                                       889************************************999*************************7 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.1   1.3e-07   0.00078      13      42 ..     346     382 ..     327     385 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-07
                              C1_2  13 edssesfnCsaCgrkidgff.....YsCseCd..fsl 42 
                                       ++++ s++C +Cgrk d+ +     Y C+eCd  f+ 
  gi|313125392|ref|YP_004035656.1| 346 SERDTSKTCCVCGRKDDSQRverglYVCDECDaaFNA 382
                                       578899*********4444456899******944554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 2380.30
//
Query:       gi|313125393|ref|YP_004035657.1|  [L=254]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-20   73.8   7.5    3.4e-20   73.6   7.5    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.8e-11   44.2   0.0    5.1e-09   36.1   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    3.7e-09   36.2   0.1    1.7e-08   34.0   0.1    1.9  1  Hydrolase_4    Serine aminopeptidase, S33
    2.9e-06   27.6   0.0    5.9e-06   26.6   0.0    1.3  1  Thioesterase   Thioesterase domain
     0.0012   18.5   0.0      0.002   17.8   0.0    1.3  1  Abhydrolase_8  Alpha/beta hydrolase
     0.0056   16.4   0.1      0.036   13.7   0.0    2.0  2  Esterase       Putative esterase
     0.0057   16.5   0.0      0.011   15.6   0.0    1.6  2  Ser_hydrolase  Serine hydrolase
  ------ inclusion threshold ------
      0.095   12.8   0.0       0.16   12.1   0.0    1.3  1  Abhydrolase_4  TAP-like protein
       0.15   11.0   0.0       0.37    9.8   0.0    1.5  2  DUF1057        Alpha/beta hydrolase of unknown function (DUF1


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   7.5   1.7e-23   3.4e-20       1     220 []      23     246 ..      23     246 .. 0.68

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 1.7e-23
                                       EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-.GGCS--HHH.CHHHHHHHCCTT..TTSEEEEEETCH CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrs.dpppldled.ladlaalldelaagggpvvlvGHSlG 75 
                                       ++llHG+++++ +W    L++ l+++++  +pD++G G+s d++ +dl++ +adl+al++++   +gp  ++GHS+G
  gi|313125393|ref|YP_004035657.1|  23 LILLHGGSGTRQHWD--ALRPHLTDDFTLSIPDRRGRGESgDGDKYDLSReVADLRALVEAV---DGPTTVFGHSFG 94 
                                       79************9..999999***98899******844488889999999**********...6999******** PP

                                       HHHHHHHHHCC...EE.EEES-..----TTT.....S----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHCCCCHC CS
                     Abhydrolase_6  76 Galalaaapla.lvvg.vlldppptalpagl.....laaalelllallallrllawlsreplprlfladedadaawr 145
                                       G++alaaa+   l  + vl++p   al  g+     la ++e  l ++++  + +++ +   + ++ +     ++  
  gi|313125393|ref|YP_004035657.1|  95 GLVALAAASEIsL-DRlVLYEP---ALLVGDhrgddLASRMESRLNAGQRQDAMRLFLE--EAGGIPD-----VEQL 160
                                       ******7777754.555*****...6666665655666666666666665555333332..2224444.....3333 PP

                                       HCCCGHHHHCC.........HHCHTTCCHHTT-TTGCEEE.CTT-C.HHHHCHHCCCH.STTEEETCE...SSS-HH CS
                     Abhydrolase_6 146 arlarlaalla.........glgllpaaawadlpvpllvl.ggeDp.lvprllerlla.qagarlpvvlpgaGHlph 210
                                       +++ + a l            ++++ ++a +d+ vp+l+l g+  p ++++ + +l   + + r+ v++ g GH+  
  gi|313125393|ref|YP_004035657.1| 161 PWWPEEAGLSLaetvvrenyEVEAYELPAEPDIDVPTLLLtGEYGPaHLRDAVFELDErLSDSRV-VEFDGVGHVAT 236
                                       33333322222122222222444666778888888888775444444444443333335478888.99********* PP

                                       HHSHHHHHHH CS
                     Abhydrolase_6 211 leepdevaea 220
                                       ++ep+ va+a
  gi|313125393|ref|YP_004035657.1| 237 QSEPELVADA 246
                                       ********96 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   2.6e-12   5.1e-09       1      93 [.      21     104 ..      21     122 .. 0.86
   2 !    6.5   0.0    0.0029       5.8     209     252 ..     192     235 ..     114     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.6e-12
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEE CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltl 77 
                                       p+l++lhG+ g+   w +  l p+L + +f++ ++D rG g+S  +       y +    +dl+++++a + ++ t+
  gi|313125393|ref|YP_004035657.1|  21 PSLILLHGGSGTRQHWDA--LRPHLTD-DFTLSIPDRRGRGESGDGDK-----YDLSREVADLRALVEAVD-GPTTV 88 
                                       79****************..******9.***************88876.....666556777778888875.6667* PP

                                       EEETHHHHHHHHHHHH CS
                     Abhydrolase_1  78 vGhSmGGmialayaae 93 
                                        GhS+GG++ala+a+e
  gi|313125393|ref|YP_004035657.1|  89 FGHSFGGLVALAAASE 104
                                       **************97 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0029
                                       HHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSH CS
                     Abhydrolase_1 209 nvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHla 252
                                       ++ +ptl++ g++ p+   +a  +l++ l+++r+v +++ gH a
  gi|313125393|ref|YP_004035657.1| 192 DIDVPTLLLTGEYGPAHLRDAVFELDERLSDSRVVEFDGVGHVA 235
                                       4566**************************************87 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   8.8e-12   1.7e-08       7     115 ..      23     121 ..      20     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 8.8e-12
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                       ++l+HG   + +  + l  +L++ +f   + D rG G+s    g+  ++++ v+Dl+a+ve+v       p +++Gh
  gi|313125393|ref|YP_004035657.1|  23 LILLHGGSGTRQHWDALRPHLTD-DFTLSIPDRRGRGES--GDGDKYDLSREVADLRALVEAVD-----GPTTVFGH 91 
                                       68899999999999999999975.8**************..5666779************9998.....8999**** PP

                       Hydrolase_4  84 SmGGliallyllrypdkvaglilsaPalkika 115
                                       S GGl+al+++ + +   ++l+l  Pal +  
  gi|313125393|ref|YP_004035657.1|  92 SFGGLVALAAASEISL--DRLVLYEPALLVGD 121
                                       **********999887..9*****99998775 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.9e-09   5.9e-06       3      86 ..      23     104 ..      21     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.9e-09
                                       EEEE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTST.SHHHCTTCHHHHHHHHHHHHH.HH-SSSSEEEEEETHHH CS
                      Thioesterase   3 LflfppagGsasvfrslasklsdpvvevlavqlpgre.rdepplesieelaaeyaealr.qiqpegPyalfGhSlGg 77 
                                       L+l++++ G  ++   l+ +l d+    +++  p+r  r+e+   +  +l  e+a+     +  +gP+++fGhS+Gg
  gi|313125393|ref|YP_004035657.1|  23 LILLHGGSGTRQHWDALRPHLTDD----FTLSIPDRRgRGESGDGDKYDLSREVADLRAlVEAVDGPTTVFGHSFGG 95 
                                       99*********************9....66666666668999999******999997540455677*********** PP

                                       HHHHHHHHH CS
                      Thioesterase  78 llAfevArq 86 
                                       l+A ++A++
  gi|313125393|ref|YP_004035657.1|  96 LVALAAASE 104
                                       *****9986 PP

>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     1e-06     0.002      93     134 ..      67     107 ..      58     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-06
                     Abhydrolase_8  93 eLnallrdlrats.vpgqhlallgHSYGSlvaslAlddaaseV 134
                                       +L++ + dlra   + +++++++gHS+G lva  A+ +     
  gi|313125393|ref|YP_004035657.1|  67 DLSREVADLRALVeAVDGPTTVFGHSFGGLVALAAASE--ISL 107
                                       78899999999988899**************9888887..444 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.3   5.9e+02      18      42 ..      14      38 ..      11      46 .. 0.85
   2 !   13.7   0.0   1.8e-05     0.036     116     135 ..      84     104 ..      67     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.3
                                      .GGTTTEEEEEEE--TTHHCCHHHH CS
                          Esterase 18 yspgrkypvvylldGltgwdqnfra 42
                                      y+++++ p ++ll+G +g+ q++ a
  gi|313125393|ref|YP_004035657.1| 14 YERHGEGPSLILLHGGSGTRQHWDA 38
                                      7788999999999998999998865 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.8e-05
                                       C.EEEEEETHHHHHHHHHHHC CS
                          Esterase 116 g.ravaGqSmGGlgALilalk 135
                                       g ++v+G+S+GGl+AL +a++
  gi|313125393|ref|YP_004035657.1|  84 GpTTVFGHSFGGLVALAAASE 104
                                       349***************986 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.6e-06     0.011      13      88 ..      34     120 ..      23     166 .. 0.70
   2 ?   -3.4   0.0       3.9   7.8e+03     141     157 ..     222     238 ..     217     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.6e-06
                                       TTCH...HHHHHHHCCT.....EEEEEC--TS--HHHHHHHHHHHHHC-STTEEEEEETCHHHHHHHHHH.HTTSSS CS
                     Ser_hydrolase  13 eHWq...srwekklpaa.....rrveqadwlkPdledWvaaleaaveaaeekvvlvAHSlgclavlhaae.lqlakk 80 
                                       +HW     ++ ++++ +      r e  d +k dl++ va l+a vea+ +++++  HS+g l++l+aa+   l + 
  gi|313125393|ref|YP_004035657.1|  34 QHWDalrPHLTDDFTLSipdrrGRGESGDGDKYDLSREVADLRALVEAVDGPTTVFGHSFGGLVALAAASeISLDRL 110
                                       67752223555555432221023556666689999999***************************999984333333 PP

                                       E..EEEEEET CS
                     Ser_hydrolase  81 v..agalLVa 88 
                                       v  + alLV 
  gi|313125393|ref|YP_004035657.1| 111 VlyEPALLVG 120
                                       3234566665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.9
                                       T-EEEEETT-TTSSGGG CS
                     Ser_hydrolase 141 gaelvdlgeaGHinads 157
                                       ++++v+    GH+  +s
  gi|313125393|ref|YP_004035657.1| 222 DSRVVEFDGVGHVATQS 238
                                       78899999999998776 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05      0.16      32      90 ..     191     250 ..     174     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                     Abhydrolase_4  32 kg.aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaY 90 
                                       ++ ++p+Lll++e+ pa       +l ++l ++++v  +g GH a +++ + v +av+++
  gi|313125393|ref|YP_004035657.1| 191 PDiDVPTLLLTGEYGPAHLRDAVFELDERLSDSRVVEFDGVGHVATQSEPELVADAVRRF 250
                                       33369****************************************998888898998887 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00019      0.37     102     152 ..      82     133 ..      64     147 .. 0.89
   2 ?   -2.2   0.0      0.85   1.7e+03     273     293 ..     228     248 ..     220     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                           DUF1057 102 lkgklillghsRGcenaLqlavtleahGlvlinptGlr.vhkgirplsrlet 152
                                       ++g   ++ghs G+  aL  a+++ +  lvl  p+ l+  h+g    sr+e+
  gi|313125393|ref|YP_004035657.1|  82 VDGPTTVFGHSFGGLVALAAASEISLDRLVLYEPALLVgDHRGDDLASRMES 133
                                       55777899**************************988747*********985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.85
                           DUF1057 273 vakdghfqnkkraelvaevvk 293
                                       +   gh   ++ +elva++v+
  gi|313125393|ref|YP_004035657.1| 228 FDGVGHVATQSEPELVADAVR 248
                                       55568999999******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1420.48
//
Query:       gi|313125394|ref|YP_004035658.1|  [L=414]
Description: respiratory-chain NADH dehydrogenase 51 kd subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-20   72.5   0.0    5.1e-20   71.9   0.0    1.3  1  Complex1_51K   Respiratory-chain NADH dehydrogenase 51 Kd sub
      5e-05   23.2   0.2     0.0001   22.2   0.2    1.5  1  RnfC_N         RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.035   13.9   0.1    1.6  1  Biotin_lipoyl  Biotin-requiring enzyme


Domain annotation for each model (and alignments):
>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   8.5e-24   5.1e-20       2     151 ..      21     176 ..      20     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 8.5e-24
                      Complex1_51K   2 keagivGrGGagfPthvKlkakakkkkkylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgvigvrd 78 
                                       ++agi G+GGagfPt+ K++   +   ++l+vN +E+EP+++ D+ l + +  ++   + ++ e +    ++ + + 
  gi|313125394|ref|YP_004035658.1|  21 RNAGISGAGGAGFPTYAKWERLDE--VPFLLVNHQESEPIYYIDKWLGKSHTADFASLFDALLEETFEVIVICAKET 95 
                                       78*********************8..89**********************************999876667777788 PP

                      Complex1_51K  79 ekpeaiealekalaeakaagl.........ldievvklagkYpaGeekaLiesltgrevprgkppadvgvvvnNveT 146
                                       +  +++ +le+al+++                i  +  +++Y  G+e++L++ + +  ++  ++p+d g +v+N+eT
  gi|313125394|ref|YP_004035658.1|  96 DRAQWMGELEAALDGTVYTAAqlpidpadeSGIVFAYTDDRYEYGMESVLLRLVADVVLQ-NELPMDHGWIVQNTET 171
                                       899*********88654332245889999899********************99987655.56************** PP

                      Complex1_51K 147 laavy 151
                                       +++v 
  gi|313125394|ref|YP_004035658.1| 172 MFNVL 176
                                       ***95 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2   1.8e-08    0.0001      40      86 ..     314     361 ..     296     370 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.8e-08
                            RnfC_N  40 apakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlva 86 
                                       a+ +p+v+ g +V++G++ia   +  +s   has+ GtV a+++  + 
  gi|313125394|ref|YP_004035658.1| 314 AKSRPIVEAGAEVTEGEMIAVPAQdGISNSQHASIDGTVAAVTETHIE 361
                                       6789****************8765577***************998765 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.9e-06     0.035       3      56 ..     304     355 ..     302     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-06
                                       EEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEE CS
                     Biotin_lipoyl   3 iksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkei 56 
                                       i+ P++G +v+    + +v++G +V++g+ +a+   +  ++   a  +G+v+ +
  gi|313125394|ref|YP_004035658.1| 304 ITNPDFGDVVA--KSRPIVEAGAEVTEGEMIAVPAQDGISNSQHASIDGTVAAV 355
                                       788********..69***********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2417.72
//
Query:       gi|313125395|ref|YP_004035659.1|  [L=56]
Description: hypothetical protein Hbor_06200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 311.42
//
Query:       gi|313125396|ref|YP_004035660.1|  [L=368]
Description: sulfate permease-like transporter, mfs superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-40  136.6  37.8    5.9e-23   81.4  10.7    3.3  3  MFS_MOT1         Molybdate transporter of MFS superfamily
    6.1e-09   35.1  22.8    1.2e-08   34.1   7.9    2.5  2  Sulfate_transp   Sulfate permease family
  ------ inclusion threshold ------
       0.16   11.3   0.0       0.23   10.8   0.0    1.1  1  Glyco_transf_24  Glucosyltransferase 24


Domain annotation for each model (and alignments):
>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9  10.1   6.4e-22   3.8e-18       2     111 .]      19     132 ..      18     132 .. 0.97
   2 ?    0.7   1.5      0.11   6.8e+02       7      54 ..     143     189 ..     138     196 .. 0.80
   3 !   81.4  10.7   9.9e-27   5.9e-23       2     111 .]     206     319 ..     205     319 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 6.4e-22
                          MFS_MOT1   2 elsgalgdlglTllnlvialaalaslsltalllsvGlmnlltglfggvPmc.....hgAgglaaqyrfgartgaagi 73 
                                       +++ga+gd   T+l++v+a+aal++lsl++lll ++++++++g+ +g+P++     + A+ ++a      ++++ag+
  gi|313125396|ref|YP_004035660.1|  19 AFTGAIGDSV-TVLPVVVAIAALTELSLSHLLLGFAVFQVVWGVRYGLPVSvepmkALAALVIAGSLTTDELVVAGL 94 
                                       679*******.******************************************************777********* PP

                          MFS_MOT1  74 llGlvllllgltgllerllrliPksvlgglllgaGleL 111
                                       l G++l++ g t++l+r+ +++ ++v++g++l+++l L
  gi|313125396|ref|YP_004035660.1|  95 LAGVILFTAGSTRTLRRVSHYVGEPVVRGVQLAVALLL 132
                                       ***********************************987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.11
                          MFS_MOT1   7 lgdlglTllnlvialaalaslsltalllsvGlmnlltglfggvPmchg 54 
                                        + ++ Tl   v a++++a+   +++l+++++   ++ +  g+P +h+
  gi|313125396|ref|YP_004035660.1| 143 SPAFA-TLAVGVAAIVSVAGYRRASALVVLAVGFGVVIPQTGLPTPHV 189
                                       55666.777788888889998899999999999999999999999986 PP

  == domain 3  score: 81.4 bits;  conditional E-value: 9.9e-27
                          MFS_MOT1   2 elsgalgdlglTllnlvialaala......slsltalllsvGlmnlltglfggvPmchgAgglaaqyrfgartgaag 72 
                                       +l+g+ ++l++T+ n+++a+++l       ++s+++l++s+G+mnll++++g+vPmchg+gg+a++y+fgart+ ++
  gi|313125396|ref|YP_004035660.1| 206 ALEGTAAQLAMTVGNAAVATSLLLsdyydaDVSPDELATSMGVMNLLAVPLGAVPMCHGSGGVAGKYAFGARTAWSN 282
                                       678999****************88899999999******************************************** PP

                          MFS_MOT1  73 illGlvllllgltgllerllrliPksvlgglllgaGleL 111
                                       i+lG ++ l +++   + +++++P s+lg++l+ +++eL
  gi|313125396|ref|YP_004035660.1| 283 IVLGTLYALAAVFA--VGIVAAFPLSMLGVVLALVAVEL 319
                                       *****999999986..8999****************998 PP

>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   9.2    0.0014       8.3      42     142 ..      53     148 ..       7     162 .. 0.76
   2 !   34.1   7.9   2.1e-12   1.2e-08     204     357 ..     155     319 ..     143     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0014
                    Sulfate_transp  42 lvyalfGtsrqlavGpvavlslivgeiiakvaeeepekgieiattltllaGviqvllGllR.LgflveflseavlsG 117
                                       +v+ +++++r     +v  +  +++ +ia           + ++++ llaGvi++ +G  R L +++ ++ e+v++G
  gi|313125396|ref|YP_004035660.1|  53 AVFQVVWGVRYGLPVSVEPMKALAALVIAGS------LTTDELVVAGLLAGVILFTAGSTRtLRRVSHYVGEPVVRG 123
                                       4555555555555555555555555555554......4556678999************9989************** PP

                    Sulfate_transp 118 fiaGaaivillsqikvllglervsk 142
                                          ++a+ +l + i  +lg   +++
  gi|313125396|ref|YP_004035660.1| 124 VQLAVALLLLETGIRLSLGSPAFAT 148
                                       ***************9999876555 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 2.1e-12
                    Sulfate_transp 204 tlvsaifelkreagvki.......vgei.psglpelslp.....kvdwsllsall..pdalaialvglleaiavsks 265
                                        +vs++  ++r    ++       v  i ++glp++++p       + s+ls+ +   +a+ +a++    a+a+s+ 
  gi|313125396|ref|YP_004035660.1| 155 AIVSVAG-YRRASALVVlavgfgvV--IpQTGLPTPHVPnvtfvLPSLSALSSSAleGTAAQLAMTVGNAAVATSLL 228
                                       3333333.22222222222332212..41578*******6654422334444333114566778888888******* PP

                    Sulfate_transp 266 ldkkkgykvdsnkELvAlGfsNilsslfgglpatgafsrsavnikaGaktqlsglvsalvvllvllvltplleyiPk 342
                                       l   ++  v+++     +G++N+l+  +g++p   +    a +++ Ga+t+ s++v++ + +l+ +++ ++++ +P 
  gi|313125396|ref|YP_004035660.1| 229 LSDYYDADVSPDELATSMGVMNLLAVPLGAVPMCHGSGGVAGKYAFGARTAWSNIVLGTLYALAAVFAVGIVAAFPL 305
                                       ***********987789************************************************************ PP

                    Sulfate_transp 343 avLaaiiivagkglL 357
                                       ++L++++ +++++ L
  gi|313125396|ref|YP_004035660.1| 306 SMLGVVLALVAVE-L 319
                                       *******999988.4 PP

>> Glyco_transf_24  Glucosyltransferase 24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.8e-05      0.23     113     167 ..     244     299 ..     230     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.8e-05
                   Glyco_transf_24 113 kelveldlegapygytPlcdsrkem.egfrfwkqgywkehlkgkkyhisalyvvdl 167
                                       + +  ++l   p+g +P+c+ +  +  ++ f  +  w++ + g  y ++a++ v +
  gi|313125396|ref|YP_004035660.1| 244 TSMGVMNLLAVPLGAVPMCHGSGGVaGKYAFGARTAWSNIVLGTLYALAAVFAVGI 299
                                       4556799999**********76665167************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2105.25
//
Query:       gi|313125397|ref|YP_004035661.1|  [L=252]
Description: branched-chain amino acid permease (azaleucine resistance) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-40  137.0   7.0    5.4e-40  137.0   7.0    1.8  2  AzlC             AzlC protein
  ------ inclusion threshold ------
      0.058   13.3   0.3      0.058   13.3   0.3    1.8  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra


Domain annotation for each model (and alignments):
>> AzlC  AzlC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0   7.0     6e-44   5.4e-40       1     134 [.      17     162 ..      17     164 .. 0.93
   2 ?   -1.1   0.3      0.26   2.3e+03     123     130 ..     223     230 ..     181     241 .. 0.66

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 6e-44
                              AzlC   1 PillgylpvgiafGvlavqaglsvweavlmSllvfAGsaqfaavgllaagasllaivlttllvNlRhllyglslapk 77 
                                       Pil+g++p+g++ Gv+av+agls+++av +S++vfAG++q+a+++ll ++a l+++++t++++NlR+++y++s+ap+
  gi|313125397|ref|YP_004035661.1|  17 PILVGIIPFGLVAGVAAVNAGLSPLQAVGLSVVVFAGASQLAIIDLLGQNAELVVVFVTAVVINLRMMMYSASIAPH 93 
                                       9***********************************************999************************** PP

                              AzlC  78 lkklsrlkrlllaflltDetfalasar............klsrayflglglllylawvlgtllGallgs 134
                                       +++++ +++++ ++lltD+++al++ar            + +r+y+l++++ l+++w+++t+lG+llg+
  gi|313125397|ref|YP_004035661.1|  94 FRRVRSRWKAVSSYLLTDQAYALSIARynegapaerpnsNERRNYYLAVAASLWIVWQVCTVLGILLGT 162
                                       ***9999999999***********856677777766655444*************************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.26
                              AzlC 123 vlgtllGa 130
                                        lg+l+G+
  gi|313125397|ref|YP_004035661.1| 223 LLGALAGV 230
                                       22222222 PP

>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   6.5e-06     0.058     130     181 ..      44      95 ..      40      96 .. 0.88
   2 ?   -2.3   0.8      0.39   3.5e+03     155     169 ..     147     161 ..     139     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.5e-06
                   Peptidase_M48_N 130 lalviglpllaallwiiewggeyfylylwlfllvfslllmtiyPtlIaPLFn 181
                                       ++l +++   a  l ii+ +g++  l+++++++v+  l m++y+  IaP F 
  gi|313125397|ref|YP_004035661.1|  44 VGLSVVVFAGASQLAIIDLLGQNAELVVVFVTAVVINLRMMMYSASIAPHFR 95 
                                       555666667778899**********************************996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.39
                   Peptidase_M48_N 155 lylwlfllvfslllm 169
                                       +++w +++v+ +ll 
  gi|313125397|ref|YP_004035661.1| 147 WIVWQVCTVLGILLG 161
                                       445555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1424.09
//
Query:       gi|313125398|ref|YP_004035662.1|  [L=124]
Description: hypothetical protein Hbor_06230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-21   74.9  12.2      4e-20   71.8  12.2    1.9  1  AzlD      Branched-chain amino acid transport protein (AzlD)


Domain annotation for each model (and alignments):
>> AzlD  Branched-chain amino acid transport protein (AzlD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8  12.2   2.3e-24     4e-20       1      99 []      10     121 ..      10     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 2.3e-24
                              AzlD   1 illaillmalvtyltRylplllfrr.lklppwlqrllryvPiavLaaliapell............aetgklsaslg 64 
                                       i+ +++++++ t+++R++++ lf+r  ++pp+l+++lryvP+av+aal++p+l+             + + ls+++g
  gi|313125398|ref|YP_004035662.1|  10 IWGVVIAVGITTFAIRASFIYLFGRiDTVPPRLKHALRYVPPAVFAALVVPALVvsegsahfapisVSLSDLSVAVG 86 
                                       799**********************99***************************9999999999776666677777* PP

                              AzlD  65 larllaalvavlvalltrnlllsilvGmavyallr 99 
                                       + rlla++va++va+l   ++++i++Gm+++++lr
  gi|313125398|ref|YP_004035662.1|  87 NERLLAGIVAAIVAWLAEDVFATIAAGMVTLWVLR 121
                                       *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 757.13
//
Query:       gi|313125399|ref|YP_004035663.1|  [L=645]
Description: aldehyde:ferredoxin oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.7e-118  394.5   2.2   5.9e-118  394.2   2.2    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    1.3e-74  250.4   0.1    1.8e-74  249.9   0.1    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.2   2.2  6.6e-122  5.9e-118       4     382 .]     228     626 ..     225     626 .. 0.94

  Alignments for each domain:
  == domain 1  score: 394.2 bits;  conditional E-value: 6.6e-122
                                       HHHHHHHHHSH.HHH....HHHHH-GGGHHHHHHHTT---BTTTTB.S-.-T..........TGGGGSHHHHHHHTE CS
                            AFOR_C   4 kkiqkeiksspqvta....elrkyGTaelvnianetgalptknfqe.gt.fe..........kaekisgealeekyl 64 
                                       +++++ i++s+ vt+    +l+ yGT++l+n+++e++ lpt+n ++ +t  e          +aek+sge+++e++l
  gi|313125399|ref|YP_004035663.1| 228 QQAMELIRESD-VTGpnegGLSLYGTNVLMNLTEEMDGLPTRNARYtSThSEaegspddpniEAEKVSGENVRENIL 303
                                       56777788888.44447779**************************666533678888888888************* PP

                                       EEE.E-TT-SS--EEEEE.......ET....EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHH CS
                            AFOR_C  65 vknegCfsCpiaCgrevkveegkk.vk....vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntia 136
                                       v++  C+sCp+aC++ev+v+ ++k  +    +e +eye+++alG+n ++dd ++i+ + ++c++lG+Dti+ Gn+ia
  gi|313125399|ref|YP_004035663.1| 304 VDEPTCHSCPVACKKEVEVTYERKgEElnvrGESYEYESAFALGPNSMNDDRDSIAVMIDMCNDLGMDTIESGNMIA 380
                                       ***88**************999985559***99******************************************** PP

                                       HHHHHHHTTSS-HHHHTS----TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-G CS
                            AFOR_C 137 famelyekGllkkedtdglelefgdaeallellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydp 212
                                       +ame++e+G l+++d    ++e+gd e ++++le+iA++e+ +g+ll++G++r+ae+ ga++   +vkG+ +paydp
  gi|313125399|ref|YP_004035663.1| 381 MAMEMTEQGKLDDVDE---DIEWGDVEHMMDVLEDIAHQESeLGELLGNGAERVAEEKGAHDNKLSVKGQTIPAYDP 454
                                       *************998...99******************************************************** PP

                                       GG-HHHHHHHHH-TTSS-SGGG-THHHH.....S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH..... CS
                            AFOR_C 213 rgakgmalaYatsnrGacHlrayliale.....ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldle 284
                                       r++kgm+++YatsnrGacHlr+y+ ++e     ekvdp e+egk+el++ fqd++a+ ds+ +Ckf++       +e
  gi|313125399|ref|YP_004035663.1| 455 RAMKGMGIGYATSNRGACHLRGYTPSAEimgipEKVDPREWEGKGELCALFQDMHAISDSFDICKFNAF---AEGIE 528
                                       ********************************************************************4...45699 PP

                                       .HHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHT--HHHS---HHHH..HS--.-SSTTTT---..-HHHHHH CS
                            AFOR_C 285 lyakllsavtGidvteeellkaGeRiynleRlfnlreGltrkddtlperll..eepl.kegpakgkvledeleemld 358
                                       +y+ +++ +tG dvte+el+++G+Riy+leR++n+ +G++ +ddtlp r+l  +e++  +g ++g+++  el+em++
  gi|313125399|ref|YP_004035663.1| 529 EYVLQYNGMTGRDVTEDELMETGDRIYTLERYYNNLAGFDGSDDTLPGRFLegDEAIpGQGASDGQLC--ELDEMKE 603
                                       9**************************************************87666645888889999..9****** PP

                                       HHHHHHT--TTS---HHHHHHCT- CS
                            AFOR_C 359 eyYelrGWdetGvPtketlkrLgL 382
                                       eyY++r W  +Gv+  e+l++Lg+
  gi|313125399|ref|YP_004035663.1| 604 EYYARRQWV-DGVVPDERLEELGI 626
                                       *********.*************7 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.9   0.1     2e-78   1.8e-74       2     196 ..      10     209 ..       9     211 .. 0.96

  Alignments for each domain:
  == domain 1  score: 249.9 bits;  conditional E-value: 2e-78
                                       EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE- CS
                            AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaks 78 
                                       +++rvdLs+g++++e +++e a+ky+Ggrgl++k+++d+  p+vdp++p+n l+f+ Gpltgt+ap+sgr++v++ks
  gi|313125399|ref|YP_004035663.1|  10 HVARVDLSSGEVQYEGIDDEDARKYIGGRGLGVKYVFDQG-PDVDPMGPDNLLAFVNGPLTGTQAPMSGRIAVCTKS 85 
                                       689***********************************65.99********************************** PP

                                       TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS..... CS
                            AFOR_N  79 PltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd..... 150
                                       Pltgt+++s+ Gg+ ga+lk++G+d++ +eGk+e+pvy ++ed++ e++da++lwg++++et e+l++e +      
  gi|313125399|ref|YP_004035663.1|  86 PLTGTVTDSHHGGWSGARLKWSGFDGLLFEGKSEDPVYAYVEDGELELRDASHLWGKGVHETMETLESEIEGafgkn 162
                                       ********************************************************************655567779 PP

                                       .EEEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE CS
                            AFOR_N 151 .kvaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvr 196
                                        +v+++GpaGen+vr+A+i+ +d+ra grgG+G+vmgsK+lka+vv+
  gi|313125399|ref|YP_004035663.1| 163 lSVMAVGPAGENEVRYACIINEDDRASGRGGTGCVMGSKGLKAVVVK 209
                                       9999***************66699**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 3728.10
//
Query:       gi|313125400|ref|YP_004035664.1|  [L=358]
Description: hypothetical protein Hbor_06250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2395.77
//
Query:       gi|313125401|ref|YP_004035665.1|  [L=34]
Description: hypothetical protein Hbor_06260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   18.0   0.2     0.0022   17.8   0.2    1.1  1  SH3_4     Bacterial SH3 domain
  ------ inclusion threshold ------
      0.046   14.0   0.3      0.051   13.9   0.3    1.1  1  SH3_3     Bacterial SH3 domain


Domain annotation for each model (and alignments):
>> SH3_4  Bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   2.4e-07    0.0022      34      52 ..       9      27 ..       3      28 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-07
                             SH3_4 34 gnWcrvrDadGatGWiyqs 52
                                      ++W+++r +d a+GWi+ s
  gi|313125401|ref|YP_004035665.1|  9 DGWVEIRESDNADGWIATS 27
                                      89**************865 PP

>> SH3_3  Bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   5.6e-06     0.051      32      52 ..       9      27 ..       3      29 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-06
                             SH3_3 32 gggeWykvrtddgteGwvssg 52
                                      +g  W+ +r++d+  Gw++++
  gi|313125401|ref|YP_004035665.1|  9 DG--WVEIRESDNADGWIATS 27
                                      34..**************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 234.50
//
Query:       gi|313125402|ref|YP_004035666.1|  [L=262]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-21   75.5   0.0      8e-21   74.5   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    3.5e-20   72.5   0.1    9.6e-20   71.1   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    6.8e-18   64.9   0.0    9.6e-18   64.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.5e-12   48.1   0.0    2.8e-12   47.3   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    2.2e-12   47.2   0.0    3.3e-12   46.5   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    5.1e-12   45.6   0.0    8.7e-12   44.9   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.7e-08   32.0   0.0    1.8e-07   31.1   0.0    1.4  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.2e-07   30.4   0.0    3.4e-07   29.8   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.024   14.1   0.0       0.92    9.0   0.0    2.1  2  CheR             CheR methyltransferase, SAM binding domain
      0.027   14.1   0.0      0.043   13.4   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.054   13.1   0.0       0.07   12.7   0.0    1.2  1  NodS             Nodulation protein S (NodS)
      0.061   12.4   0.0      0.092   11.8   0.0    1.2  1  Fibrillarin      Fibrillarin
      0.093   12.6   0.1       0.19   11.5   0.1    1.5  1  Methyltransf_8   Hypothetical methyltransferase
       0.16   11.5   0.0       0.25   10.9   0.0    1.4  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   6.2e-24     8e-21       1      96 []      44     141 ..      44     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 6.2e-24
                                       EEET-TTSHHHHHHH.HTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaeala.krg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       L +GcG G   ++la   g  + v g+D s++ml+la+++  + +    + +++a +lp++d+sfD+ v+ +v++++
  gi|313125402|ref|YP_004035666.1|  44 LSIGCGPGFEPAELAgAVGesGYVHGIDRSEAMLTLANQRCDDLPQ-AALSKGNALDLPVADESFDAAVAVQVFEYL 119
                                       789************6444889********************9995.789*************************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                       +++++a++e+aRvL+pgG+ v+
  gi|313125402|ref|YP_004035666.1| 120 DRVDAAVNELARVLRPGGRAVV 141
                                       ******************9885 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   7.5e-23   9.6e-20       1      97 []      43     137 ..      43     137 .. 0.95
   2 ?   -2.2   0.0       5.5   7.1e+03      17      42 ..     217     243 ..     209     253 .. 0.64

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 7.5e-23
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vL +GcG+G   ++la ++g ++ v+g+D se+ml  a++r+++  +++ + +g+a dlp +d+sfD+ v+++++++
  gi|313125402|ref|YP_004035666.1|  43 VLSIGCGPGFEPAELAGAVGeSGYVHGIDRSEAMLTLANQRCDDL-PQAALSKGNALDLPVADESFDAAVAVQVFEY 118
                                       89*****************769********************654.6************************988*** PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       l+  ++++a++e+arvL+pgG
  gi|313125402|ref|YP_004035666.1| 119 LD--RVDAAVNELARVLRPGG 137
                                       99..5679************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.5
                                       CTS.TSSEEEEEESSHHHHHHHHHHHH CS
                   Methyltransf_25  17 krl.gkakvtgvDiseemleaarerae 42 
                                       k +  +++ +g D +++ ++  re+ e
  gi|313125402|ref|YP_004035666.1| 217 KDYaANHDSIGSDEASAWVADLREHEE 243
                                       444235777888888888888887764 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   7.5e-21   9.6e-18       2     123 ..      38     160 ..      37     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 7.5e-21
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       ++g rvl +GCG G+   ela  +g+ + v+GiD+se +++lA++++++l    + +++g++ +l+  ++de+fD  
  gi|313125402|ref|YP_004035666.1|  38 QRGDRVLSIGCGPGFEPAELAGAVGESGYVHGIDRSEAMLTLANQRCDDL--PQAALSKGNALDLP--VADESFDAA 110
                                       56889****************************************97755..567***********..9******** PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr.....llaelpakve 123
                                       ++ +v+ +l   d++ +e+ rvl+pgg+ +++d++     + + +pa +e
  gi|313125402|ref|YP_004035666.1| 111 VAVQVFEYLDRVDAAVNELARVLRPGGRAVVCDADfdslvWRSPNPARME 160
                                       **********************************9777663334444443 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   2.2e-15   2.8e-12       1      98 [.      44     138 ..      44     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.2e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L iGcG G   ++l+ +  ++ y+ g+D s+++++ a ++  +  +   ++ +  +l ++d+    sfD+ va +v+
  gi|313125402|ref|YP_004035666.1|  44 LSIGCGPGFEPAELAGAVGESGYVhGIDRSEAMLTLANQRCDDLPQAALSKGNALDLPVADE----SFDAAVAVQVF 116
                                       789***************7777777*********9999999999987766666666666655....*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGr 98 
                                       ++l+ +++++++++++L+pgGr
  gi|313125402|ref|YP_004035666.1| 117 EYLDRVDAAVNELARVLRPGGR 138
                                       *********************7 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   2.6e-15   3.3e-12       8     162 ..      23     190 ..      12     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.6e-15
                   Methyltransf_23   8 elsdklerllpk..lraggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiaekakkaqkdqfdeqeaaep 79 
                                       +++d +e + ++  l++g rvL+iGcG G + +e++ + g    v g+D s+++  +a      ++ + d  +aa +
  gi|313125402|ref|YP_004035666.1|  23 AAADRRELVRETldLQRGDRVLSIGCGPGfEPAELAGAVGEsgYVHGIDRSEAMLTLA------NQRCDDLPQAALS 93 
                                       444444433333438999***********88888888888855577*******99997......3333333333333 PP

                   Methyltransf_23  80 qg..........kfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl.....kedrllldwlylvpagr 141
                                       +g          +fd +v+ +v+e ++ + ++++ +a+ l+pgG++++++ + ++     ++  +++    l+  ++
  gi|313125402|ref|YP_004035666.1|  94 KGnaldlpvadeSFDAAVAVQVFEYLDRVDAAVNELARVLRPGGRAVVCDADFDSlvwrsPNPARMER--VLDAFDD 168
                                       334555566666**************************************865553443223333333..3344448 PP

                   Methyltransf_23 142 hisffs.arslkelleeaGlev 162
                                       h+ +    + l+ ll++aGl++
  gi|313125402|ref|YP_004035666.1| 169 HCPWPHlGSRLAPLLRDAGLTI 190
                                       9977651467999999999998 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   6.8e-15   8.7e-12      38     152 ..      30     142 ..      19     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 6.8e-15
                                       HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS- CS
                   Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed 114
                                        v ++   +rg +vl + +G g   ++l+ +vge+g v+++D +e mL  ++++  +  +    + ++na +Lp  d
  gi|313125402|ref|YP_004035666.1|  30 LVRETLDLQRGDRVLSIGCGPGFEPAELAGAVGESGYVHGIDRSEAMLTLANQRCDDLPQ--AALSKGNALDLPVAD 104
                                       5666777799********************************************998765..56779********** PP

                                       T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 115 dsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                       +sfD       +  +   + a++e+ rvl+pGGr vv 
  gi|313125402|ref|YP_004035666.1| 105 ESFDAAVAVQVFEYLDRVDAAVNELARVLRPGGRAVVC 142
                                       ****86555455555556889************98876 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.4e-10   1.8e-07      64     121 ..      30      87 ..       8     108 .. 0.86
   2 ?   -3.7   0.0       6.5   8.3e+03     158     171 ..     128     141 ..     120     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.4e-10
                                       HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHC CS
                              PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkl 121
                                       l+ e l+l++g+rvL +G+G G++ a la  vge+g v +i+r++ + + a+++   l
  gi|313125402|ref|YP_004035666.1|  30 LVRETLDLQRGDRVLSIGCGPGFEPAELAGAVGESGYVHGIDRSEAMLTLANQRCDDL 87 
                                       5668899*****************************************9999987655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.5
                                       HHHHTEEEEEEEEE CS
                              PCMT 158 alidQLkeGGrlvv 171
                                       +l + L +GGr vv
  gi|313125402|ref|YP_004035666.1| 128 ELARVLRPGGRAVV 141
                                       67778899999876 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.7e-10   3.4e-07      45     163 ..      22     140 ..      12     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.7e-10
                                       HHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHH...HHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEE CS
                              CMAS  45 eAqlaKldlileklelkpGmtlLdiGcGWGslvrr...averydvkvvglTlSkeqaklakkrvdeldlerkvevkl 118
                                       +A  ++++l+ e l+l+ G+++L iGcG G    +   av +    v g+  S+    la++r+d+l  +   + + 
  gi|313125402|ref|YP_004035666.1|  22 QAAADRRELVRETLDLQRGDRVLSIGCGPGFEPAElagAVGE-SGYVHGIDRSEAMLTLANQRCDDLPQAALSKGNA 97 
                                       5777899999********************765541115555.568******************************* PP

                                       S-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEE CS
                              CMAS 119 ldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGlll 163
                                       ld    de +d+ v+v++fe +  ++ d+ +++l ++l+++G+ +
  gi|313125402|ref|YP_004035666.1|  98 LDLPVADESFDAAVAVQVFEYL--DRVDAAVNELARVLRPGGRAV 140
                                       ********************97..6889999*********99865 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00072      0.92      32      81 ..      40      81 ..      15      86 .. 0.78
   2 ?    3.1   0.0     0.046        59     126     173 ..      96     141 ..      88     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00072
                                      SEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHH CS
                              CheR 32 rvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAk 81
                                        r++s+gc+ G Ep  lA ++ e      +    ++++D ++++l+ A+
  gi|313125402|ref|YP_004035666.1| 40 GDRVLSIGCGPGFEPAELAGAVGE-----SG---YVHGIDRSEAMLTLAN 81
                                      4589***************99998.....33...6778888888887776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.046
                                       -TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                              CheR 126 nllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                                       n+l+   + +++D  ++  v+ Y+d+ +  + ++++a+ l+pgg+ ++
  gi|313125402|ref|YP_004035666.1|  96 NALDLPVADESFDAAVAVQVFEYLDRVD--AAVNELARVLRPGGRAVV 141
                                       66666677899*************9875..679***********9877 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.3e-05     0.043      12     112 ..      38     146 ..      26     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                              MetW  12 kpgsrvldlGcGdGellellkeekqvdgr..GleldeegvaecvakGlsviqgdldkdlen...fedksfdyvvlsq 83 
                                       + g rvl +GcG G     l+   + +g+  G++ +e+ ++ + ++   + q  l k+ +     +d+sfd +v  q
  gi|313125402|ref|YP_004035666.1|  38 QRGDRVLSIGCGPGFEPAELAGAVGESGYvhGIDRSEAMLTLANQRCDDLPQAALSKGNALdlpVADESFDAAVAVQ 114
                                       6789**********988888887777764449******************9999998754322479*********** PP

                              MetW  84 tlqatrnpkevldellri...grraivsfPnf 112
                                        +  + + +  ++el r+   g ra+v+  +f
  gi|313125402|ref|YP_004035666.1| 115 VFEYLDRVDAAVNELARVlrpGGRAVVCDADF 146
                                       98888777777666554422277888876666 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.5e-05      0.07      44     146 ..      40     143 ..      13     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                              NodS  44 iadalevGcaaGalterlapyckr...ltvvdvveeaiararervkesshiswivsdvqqfs.tdekfdlivvaevl 116
                                          +l +Gc  G    +la        +  +d  e  ++ a++r ++ ++ +  + +   +  +de fd  v  +v+
  gi|313125402|ref|YP_004035666.1|  40 GDRVLSIGCGPGFEPAELAGAVGEsgyVHGIDRSEAMLTLANQRCDDLPQAALSKGNALDLPvADESFDAAVAVQVF 116
                                       446889999999888888865433111445777777889999999999999999888877752689*********** PP

                              NodS 117 yyiedvaelraavrnlvsllapdgqlvfGs 146
                                        y++   ++ aav++l ++l+p+g+ v   
  gi|313125402|ref|YP_004035666.1| 117 EYLD---RVDAAVNELARVLRPGGRAVVCD 143
                                       **96...6789*************988655 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.2e-05     0.092      51     108 ..      19      77 ..       3      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                                       TTSHHHHHHHTT-.S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH CS
                       Fibrillarin  51 frsKlaaailkgl.kelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl 108
                                       +r + aa   + + ++l +++g++vL +G + G  ++ ++  vge+g v++++ s+ +l
  gi|313125402|ref|YP_004035666.1|  19 YRTQAAADRRELVrETLDLQRGDRVLSIGCGPGFEPAELAGAVGESGYVHGIDRSEAML 77 
                                       4555555444444245789**********************************998764 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00015      0.19     113     157 ..      97     142 ..      27     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                       TTS-S--TT-EEEEEEES---S.S-HHHHHHHHHHHEEEEEEEEEE CS
                    Methyltransf_8 113 lakvPledesvdvavfclslmg.tnladflkeanrvlkvGGllkva 157
                                          +P++des d av    +   + +   ++e  rvl++GG   v 
  gi|313125402|ref|YP_004035666.1|  97 ALDLPVADESFDAAVAVQVFEYlDRVDAAVNELARVLRPGGRAVVC 142
                                       3469********99988776541567889************98876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.25      21     101 ..      29     110 ..      12     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                                       HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTT CS
                               MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvle.evee 95 
                                       +l  etl+ ++ ++vl +GcG G+  a+la +  e   v+ +d + + l++a++ + +    + + + ++l+  v++
  gi|313125402|ref|YP_004035666.1|  29 ELVRETLDLQRGDRVLSIGCGPGFEPAELAGAVGESGyVHGIDRSEAMLTLANQRCDDLPQ-AALSKGNALDlPVAD 104
                                       5667899999999*****************99999888***********999998776554.334444433315556 PP

                                       S-EEEE CS
                               MTS  96 kkfdli 101
                                       ++fd+ 
  gi|313125402|ref|YP_004035666.1| 105 ESFDAA 110
                                       666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1631.63
//
Query:       gi|313125403|ref|YP_004035667.1|  [L=227]
Description: phosphoribosylformylglycinamidine synthase subunit i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-44  151.8   0.0    2.4e-44  151.4   0.0    1.1  1  GATase_5   CobB/CobQ-like glutamine amidotransferase domain
    1.3e-06   28.4   0.0    1.6e-06   28.0   0.0    1.2  1  GATase     Glutamine amidotransferase class-I
      7e-06   25.8   0.0    1.1e-05   25.2   0.0    1.3  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
    0.00095   19.0   0.0     0.0012   18.7   0.0    1.2  1  DJ-1_PfpI  DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.4   0.0   5.4e-48   2.4e-44       3     230 ..       2     207 ..       1     216 [. 0.93

  Alignments for each domain:
  == domain 1  score: 151.4 bits;  conditional E-value: 5.4e-48
                          GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklr 79 
                                        v ++ + G+n+++++ +a+e+ G +a++v  +d l      +d+ +++lpGGfsygD l +g+++a+s      + 
  gi|313125403|ref|YP_004035667.1|   2 TVSVIQFGGSNCDRDAVRALEHLGIDAERVWHEDELP-----EDVTGIMLPGGFSYGDYLRAGSMAAQSP-----IL 68 
                                       589**************************98877765.....5689*******************99765.....56 PP

                          GATase_5  80 ealekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsv.vvsekspsvfl.kgmeg 154
                                       +++++  ++ +t +LG+CnG q+ ++  l  g          ++t N+s rf+++ v++ v ++++p+ +  +++++
  gi|313125403|ref|YP_004035667.1|  69 DDVREAAAD-GTPVLGVCNGAQVGCESSLTEG----------AFTTNESARFQCEHVYLrVENAETPWTAAyEEGDV 134
                                       888887788.*****************99999..........9****************889999****99899*** PP

                          GATase_5 155 lslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervv 230
                                       +++p+ahGeGrf++ se+ +++l+++  + +rY+d++g++tee  +NPNgS  ++agi  +d  v +lmpHper++
  gi|313125403|ref|YP_004035667.1| 135 IEIPIAHGEGRFEI-SEDRYEQLVEEDRILFRYCDADGNVTEE--ANPNGSRGNVAGIRGDDENVGVLMPHPERAT 207
                                       **************.999**********************996..7****************************87 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   3.5e-10   1.6e-06      14      88 ..      18      95 ..       7     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.5e-10
                                      HHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT......TTTHHHH...HHHHCTSTS-EEEETHHHHH CS
                            GATase 14 vhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg......vegkiea...ikearenkiPiLGICLGmQl 83
                                      v+al +lg++ e v+++ +  e       ++gi+++gG+ +        +  +  +   ++ea+  ++P+LG+C G Q+
  gi|313125403|ref|YP_004035667.1| 18 VRALEHLGIDAERVWHEDELPED------VTGIMLPGGFSYGDylragsMAAQSPIlddVREAAADGTPVLGVCNGAQV 90
                                      7999***********99776666......8*********999999655522222231114555559************9 PP

                                      HHHHT CS
                            GATase 84 laief 88
                                       ++++
  gi|313125403|ref|YP_004035667.1| 91 GCESS 95
                                      77765 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.4e-09   1.1e-05      27      91 ..      28      94 ..       8     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.4e-09
                          GATase_3 27 vrfvplkdeslgedadlvilpGgkdt...iqdlallresgldeaikeaaeaggpvlgiCGGlqmLGee 91
                                       + v  ++++l+ed+  ++lpGg+++   +++  ++++s + ++++eaa++g+pvlg+C G q+ +e+
  gi|313125403|ref|YP_004035667.1| 28 AERVW-HEDELPEDVTGIMLPGGFSYgdyLRAGSMAAQSPILDDVREAAADGTPVLGVCNGAQVGCES 94
                                      44555.7899*************97611155667789999**********************987766 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.6e-07    0.0012      40     120 ..      18     103 ..       1     130 [. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-07
                                       EEETTSEEEE-SEEGG.GCTCCG-SEEEE--BHHHHHHHHTSH.....HHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                         DJ-1_PfpI  40 vkgsrGlkvtvdasld.dvkaaeyDalvlpGGragperlrene.....kvvelvkefaekgklvaaICagpqlLaaa 110
                                       v+  ++l + +++++  d  +++   ++lpGG +  ++lr+ +      +++ v+e+a +g++v  +C g+q+  + 
  gi|313125403|ref|YP_004035667.1|  18 VRALEHLGIDAERVWHeDELPEDVTGIMLPGGFSYGDYLRAGSmaaqsPILDDVREAAADGTPVLGVCNGAQVGCES 94 
                                       55555566666666652334568899**********99997652222267888*******************99988 PP

                                       TTTTTSEE-- CS
                         DJ-1_PfpI 111 gvlkgrrvTs 120
                                       ++ +g   T+
  gi|313125403|ref|YP_004035667.1|  95 SLTEGAF-TT 103
                                       8876654.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1523.44
//
Query:       gi|313125404|ref|YP_004035668.1|  [L=90]
Description: phosphoribosylformylglycinamidine synthase, purs protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-25   89.5   0.1    1.3e-25   89.3   0.1    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase
     0.0095   16.4   0.3     0.0098   16.4   0.3    1.1  1  SIMPL     Protein of unknown function (DUF541)


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.1   1.5e-29   1.3e-25       2      77 .]      13      87 ..      12      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 1.5e-29
                                      EEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEEE CS
                              PurS  2 akveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeiel 77
                                      a+v+V+lK+gvlDp++++ k+al++lg+e  e++r + ++e+e++ae+ ++ae++++em+e+lLaNp i+dy +e+
  gi|313125404|ref|YP_004035668.1| 13 ATVTVRLKQGVLDPEAETTKRALERLGFE-LESLRSADRFEVEMDAESVAAAEDRADEMAERLLANPTIHDYDVEV 87
                                      89**************************9.*******************************************986 PP

>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   1.1e-06    0.0098      77     152 ..       8      82 ..       1      90 [] 0.57

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-06
                             SIMPL  77 itgyeasqsltvkfrdldklgevldaavkaaneingvsf.slsdedelrdeareeAvkdArakAealAk..algvkl 150
                                       +t+y+a+ ++++k   ld  +e  ++a+++     g ++ sl+ +d  + e+ +e v++A+++A+++A+   ++ ++
  gi|313125404|ref|YP_004035668.1|   8 MTTYTATVTVRLKQGVLDPEAETTKRALER----LGFELeSLRSADRFEVEMDAESVAAAEDRADEMAErlLANPTI 80 
                                       444555555554432333333333333331....1455555555588899*******************43334455 PP

                             SIMPL 151 gk 152
                                        +
  gi|313125404|ref|YP_004035668.1|  81 HD 82 
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 550.62
//
Query:       gi|313125405|ref|YP_004035669.1|  [L=363]
Description: formyltetrahydrofolate deformylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-40  136.4   0.0    1.3e-39  135.8   0.0    1.3  1  Formyl_trans_N  Formyl transferase
      2e-07   30.9   0.3    4.3e-07   29.8   0.3    1.5  1  ACT_6           ACT domain
      5e-06   26.2   0.1    1.8e-05   24.4   0.1    2.0  1  ACT             ACT domain
    0.00015   22.2   0.1     0.0013   19.2   0.1    2.3  2  ACT_4           ACT domain


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.0   2.9e-43   1.3e-39       2     181 .]      89     263 ..      88     263 .. 0.97

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 2.9e-43
                                       EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCT CS
                    Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkel 78 
                                       +i+vl+++++++l+al +a  +g+l+ad+ +v++n+d+++    ae+ + p+  +  +k +p    e+el + l+e+
  gi|313125405|ref|YP_004035669.1|  89 QIAVLATKESHCLEALFEAWANGDLDADISVVIGNRDHLR--PLAERYDVPFYNVGDEKGSPD---EDELLDLLDEY 160
                                       69************************************99..88999******9999999998...99********* PP

                                       T-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE CS
                    Formyl_trans_N  79 kadlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkve 155
                                        adl+vla ym++l++++v +++ +i+niHpSLLP+f+Gaaa+++a e+G++ +Gvt h+v+ +lD+G+i+ q + +
  gi|313125405|ref|YP_004035669.1| 161 DADLVVLARYMRILSPNVVFRYEDRIINIHPSLLPAFPGAAAYRQAKEEGVRIAGVTAHYVTTDLDQGPIITQRAFD 237
                                       ***************************************************************************** PP

                                       --TT--HHHHHHHHHHHHHHHHHHHH CS
                    Formyl_trans_N 156 iiaedtkeeleqrvadaehkalveal 181
                                       +  + ++ee++   + +e  al+ea+
  gi|313125405|ref|YP_004035669.1| 238 VPDDASLEEIKSLGQPLEADALLEAV 263
                                       ************99999999999886 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.3   9.7e-11   4.3e-07       5      75 ..       7      79 ..       7      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 9.7e-11
                             ACT_6  5 itvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgped..alarlekaLlflakelgltvef 75
                                      itv+G d++Gl+a +t +l e g+n+ D+ qav  g +  +l  + +e   +++ l+ aL+ l  +lg++v++
  gi|313125405|ref|YP_004035669.1|  7 ITVIGGDKTGLIANVTTLLFERGINVEDLDQAVRDGIFRMTLHADTSEMvcTEETLRDALHDLGDDLGVDVQV 79
                                      9**********************************************8878*******************987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1     4e-09   1.8e-05       3      54 ..       7      54 ..       5      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4e-09
                                      EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHH CS
                               ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeed 54
                                      + v   D+ Gl+a v+++l +rgiN++ + q+  +     i+ +++++d+++
  gi|313125405|ref|YP_004035669.1|  7 ITVIGGDKTGLIANVTTLLFERGINVEDLDQAVRDG----IFRMTLHADTSE 54
                                      778888****************************65....888887777655 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1     3e-07    0.0013       7      53 ..       5      49 ..       4      55 .. 0.92
   2 ?   -0.1   0.0      0.32   1.4e+03      48      63 ..     113     128 ..      91     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3e-07
                             ACT_4  7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikit 53
                                      ++++v++ d++gl+a++t+++ e ++n++++      +dg+++++++
  gi|313125405|ref|YP_004035669.1|  5 TEITVIGGDKTGLIANVTTLLFERGINVEDLDQAV--RDGIFRMTLH 49
                                      689********************************..589**99986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                             ACT_4  48 aeikitveVkdvehLs 63 
                                        + +i+v + +++hL+
  gi|313125405|ref|YP_004035669.1| 113 LDADISVVIGNRDHLR 128
                                       4556677777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2167.75
//
Query:       gi|313125406|ref|YP_004035670.1|  [L=343]
Description: phosphoribosylaminoimidazolesuccinocarboxamide synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-25   89.1   0.0    3.6e-24   85.8   0.0    1.9  1  SAICAR_synt  SAICAR synthetase
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.051   13.7   0.1    1.5  1  DUF4110      Domain of unknown function (DUF4110)


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0     4e-28   3.6e-24      20     249 ..      22     277 ..      12     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 4e-28
                                       EEEEESEEEECCC.TEEEEETTHHHHHHHHHHHHHHHHH.H.--BSEEEE........................... CS
                       SAICAR_synt  20 llvakDrisAfdv.vlkeeipgKGkvltqlsafwfekle.k.ipnhliksld.........pe.............. 70 
                                        +v++++ s+fd+  +++++p+KG+ l+++ af fe+le + ip+h++  ++          e              
  gi|313125406|ref|YP_004035670.1|  22 RFVFTNQYSVFDWgEMPDHVPKKGASLCTMGAFNFELLEvNdIPTHYVGVIEdgettdlkeCEspptemvieltqvp 98 
                                       689*********6489***********************736******77667777666550055567777788888 PP

                                       ..............-SSSEEEEE-EEEESEEEEEEEE-.-HHH.......HH....HH..T--TT-EEEEEEEEEEE CS
                       SAICAR_synt  71 .............qlegrsmlvkklkmlpvEvvvRgyl.tGslwkeykksgkvcgirlpeglkegeklpepiftpst 133
                                                     ++  +  + +  ++p+E+v+R+++  Gs +++  + +  +g+   +   e+  lpep++++st
  gi|313125406|ref|YP_004035670.1|  99 dlpyvggsgadayDYDAYHEAADENYLIPLEIVFRNTVpVGSSLRTRGEPAD-YGLDADAWPDEAVSLPEPVVEFST 174
                                       888999999998878888888999999999******8758999888877788.9***99999*************** PP

                                       --CCCT.S-EE-HHHHH.HTT-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STT CS
                       SAICAR_synt 134 KaeegehDeniseeevvealgteeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpD 210
                                       K ee+  D  +++ee+ +++g ++e++++eelal v+++++e a++ g +  D K+E   +  dg++ +aD v t D
  gi|313125406|ref|YP_004035670.1| 175 KYEEQ--DRYLDREEAESIAG-RAELDRLEELALSVNHILNERAERAGFTHEDGKIECLYH--DGTIKVADVVGTFD 246
                                       ***94..9*********9988.99*********************************9998..8************* PP

                                       TEEEEETTT.....GGGB-STHHHHTT-STHHHHHHHHH CS
                       SAICAR_synt 211 ssRfwdaetyeegkeqeslDKqfvRdwleeveekwkekl 249
                                         Rf    +        ++ K++vR++ ++++ +w e +
  gi|313125406|ref|YP_004035670.1| 247 ENRFSYDGQ--------EVSKEVVRQYYKRTDPEWVEAV 277
                                       ****88666........899********99999998876 PP

>> DUF4110  Domain of unknown function (DUF4110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.6e-06     0.051      13      41 ..     259     287 ..     255     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-06
                           DUF4110  13 gEslrdFfaRTseeWqelaieslkekgae 41 
                                        E +r++++RT+ eW+e++ e ++++++e
  gi|313125406|ref|YP_004035670.1| 259 KEVVRQYYKRTDPEWVEAVSEAKDRSREE 287
                                       699**************999988765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2065.90
//
Query:       gi|313125407|ref|YP_004035671.1|  [L=270]
Description: NAD-dependent protein deacetylase, sir2 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-39  135.9   0.0    1.7e-39  135.5   0.0    1.1  1  SIR2          Sir2 family
     0.0025   17.5   0.0      0.048   13.4   0.0    2.3  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.0   1.9e-43   1.7e-39       1     177 []      23     203 ..      23     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 1.9e-43
                                       -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEE CS
                              SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllveevfyniarellaeeaepnaaHkalkklekkgkllr 77 
                                       GAG+S +sG+p+fR++eG++++  +      + +++++   ++   ++ ++++   + pn aH+al+ le+ g +  
  gi|313125407|ref|YP_004035671.1|  23 GAGVSNASGVPTFRGEEGIWNNEFDPADFRMDRFERDPAGFWTDRLELHERMFGDVTGPNDAHRALARLEDLGVVDV 99 
                                       9*******************98777666788999999999998566666666666899******************* PP

                                       EEES-SSSHHHHTT-SSEEETTEEEEEEEETTTSBEEECCGGHCHHHCCTT..B-T..TTCCBEEEEE--CTSB-S. CS
                              SIR2  78 liTQNiDgLekkaGskkvvelHGslakakcvkcekkldkeelqeeieaekvp.ece..kcgkllkpdvvfFGealp. 150
                                       ++TQN DgL+ +aG+++++elHG+ a+  cv+c++++ +e++ ++++a + p +c+   c++ lkpdvv+FGe lp 
  gi|313125407|ref|YP_004035671.1| 100 VVTQNTDGLHAEAGTNRLIELHGNNARSVCVECGESVPTETALDDVRAGNSPpSCPvvGCTGHLKPDVVLFGERLPg 176
                                       **********************************************9876553665336999**************9 PP

                                       HHHHHHHHHHHH-SEEEEES--STSTT CS
                              SIR2 151 dklkkliekveeadlllviGtSlkVap 177
                                        +++++ + + e d+++v+G+Sl+V p
  gi|313125407|ref|YP_004035671.1| 177 GAYDSARRMAWESDVFIVVGSSLTVVP 203
                                       99999999*****************87 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.02   1.8e+02       2      26 ..       6      30 ..       5      36 .. 0.86
   2 !   13.4   0.0   5.3e-06     0.048      48     137 .]     159     246 ..     123     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.02
                                      HHHHHHHHH-SSEEEEE-CHHCHTT CS
                      TPP_enzyme_M  2 ekaaellkaakrpvilvGggvarsg 26
                                      +++a+ ++aa  + +l G gv+++ 
  gi|313125407|ref|YP_004035671.1|  6 AALADEISAADGVTVLTGAGVSNAS 30
                                      67899****************9664 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.3e-06
                                       GTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEEES-SSSTCCCTTTTT.TTTTT-EEEEEESSCCCCTTCC--S CS
                      TPP_enzyme_M  48 gkgvipedhplylgmlglhgskaanealeeaDlvlalGarfddirttgsep.efapeakiihididpaeigknyqvd 123
                                       + g ++ d  l+  +l   + ++a++++ e+D+ +++G+ ++ +  +++ p e a+++++  +d+   e  k + ++
  gi|313125407|ref|YP_004035671.1| 159 CTGHLKPDVVLFGERLPGGAYDSARRMAWESDVFIVVGSSLTVVP-ASTLPeEAAERGQLAIFDTG--ETEKDHLAH 232
                                       5566666667777777778889999999*************9954.44555366666688888755..555555689 PP

                                       EEEECTHHHHHHHH CS
                      TPP_enzyme_M 124 laivgdvketleaL 137
                                       + + gd++etl aL
  gi|313125407|ref|YP_004035671.1| 233 YLVRGDATETLPAL 246
                                       ***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1637.03
//
Query:       gi|313125408|ref|YP_004035672.1|  [L=164]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-17   64.1   0.1    1.5e-17   63.9   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    8.2e-15   54.9   0.0      1e-14   54.6   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.2e-07   31.2   0.0    2.9e-07   30.8   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    9.9e-07   29.0   0.0    1.4e-06   28.6   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00012   22.0   0.0    0.00018   21.4   0.0    1.2  1  FR47             FR47-like protein
  ------ inclusion threshold ------
       0.07   13.3   0.0       0.15   12.2   0.0    1.7  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.13   12.0   0.1        4.3    7.2   0.0    2.3  2  DUF4597          Domain of unknown function (DUF4597)


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.1     6e-21   1.5e-17      16     115 ..      40     140 ..      16     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 6e-21
                                       HHHHHHHH..HHHHHHSTTC.EEEE..EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHH CS
                    Acetyltransf_1  16 nedaseee..feesfsleae.gllv..aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealee 87 
                                       + ++ +++  f+ +   +++ ++++  a e+g+++G+i ++++ d ++ +  + s++V + ++g G+G++Ll+++e+
  gi|313125408|ref|YP_004035672.1|  40 FLSEYYDAesFQAR---IDCdETILdvAVEGGTVVGYILASPNAD-DETTFDLSSIYVTRMRWGEGIGQQLLDHVER 112
                                       33334444323333...55555555679*****************.99***************************** PP

                                       HHHHTTESEEEEEEETTEHHHHHHHHHT CS
                    Acetyltransf_1  88 rareegikkivlaveedndaairlYekl 115
                                       r+re+g+++i l v + nd+a+r+Ye  
  gi|313125408|ref|YP_004035672.1| 113 RVREHGGERIQLGVMAENDRAVRFYEAA 140
                                       *************************865 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   3.9e-18     1e-14       7     113 ..      34     149 ..      26     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 3.9e-18
                   Acetyltransf_10   7 eegietf.kefispealrerieegealllvaeeggkivGviel.rdgs.....hisllfVdpeyrgqGigkaLleav 76 
                                        +++e f +e+ ++e++++ri+  e++l va egg++vG+i    + +      +s ++V +   g Gig++Ll++v
  gi|313125408|ref|YP_004035672.1|  34 TDAMESFlSEYYDAESFQARIDCDETILDVAVEGGTVVGYILAsPNADdettfDLSSIYVTRMRWGEGIGQQLLDHV 110
                                       567899***********************************554444467789************************ PP

                   Acetyltransf_10  77 eeeaekdgikl.eltvnasp.yavpfYeklGFkavgeeq 113
                                       e++++++g++  +l v a +  av+fYe   +++ ge  
  gi|313125408|ref|YP_004035672.1| 111 ERRVREHGGERiQLGVMAENdRAVRFYEAADYRQDGEFH 149
                                       *********************************998765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.2e-10   2.9e-07       7      75 ..      63     143 ..      40     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.2e-10
                                       EEEETTEEEEEEEEEEES....TCTEE....EEE-GGGTTSSHHHHHHHH......TTSE...EEEEEEEE..THHH CS
                    Acetyltransf_7   7 VaeddgkivGfialslld....aeitr....laVdpeyrgkGiGraLlea......aekg...iileqlel..naek 64 
                                       Va ++g +vG+i +s+++    +   +    ++V     g GiG++Ll++      + +g   i+l    +  ++++
  gi|313125408|ref|YP_004035672.1|  63 VAVEGGTVVGYILASPNAddetT---FdlssIYVTRMRWGEGIGQQLLDHverrvrE-HGgerIQLG---VmaENDR 132
                                       788899**********9985541...35567******************95554421.332223222...2433349 PP

                                       HHHHHHHTTEE CS
                    Acetyltransf_7  65 aikfYeklGFe 75 
                                       a++fYe   ++
  gi|313125408|ref|YP_004035672.1| 133 AVRFYEAADYR 143
                                       ******98776 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   5.3e-10   1.4e-06       1     141 [.       5     149 ..       5     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.3e-10
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvntait..............feyevssveefekflealdsekeyvflvaesdrivGy 63 
                                       iraa + D ++i+++ +      a++              f +e + +e f+ +++    ++ ++  + e +++vGy
  gi|313125408|ref|YP_004035672.1|   5 IRAAAPTDVASIRDVAKR-----AWKaahepivgtdamesFLSEYYDAESFQARIDC---DETILDVAVEGGTVVGY 73 
                                       899999999999999864.....2222222444466655655555666677766666...4555556666******* PP

                    Acetyltransf_4  64 aylg.qfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgi 139
                                         ++ + ++  ++   + s+y+  r    eg+g++l+d++e + +e + e++   ++++n+ ++ f++a  ++  g+
  gi|313125408|ref|YP_004035672.1|  74 ILASpNADD--ETTFDLSSIYVT-RMRWGEGIGQQLLDHVERRVREHGGERIQLGVMAENDRAVRFYEAADYRQDGE 147
                                       *99955555..9999999****7.899******************************************99999998 PP

                    Acetyltransf_4 140 fk 141
                                       f+
  gi|313125408|ref|YP_004035672.1| 148 FH 149
                                       87 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     7e-08   0.00018      24      80 ..      88     145 ..      80     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7e-08
                                       EEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  24 lgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfeki 80 
                                       l++++v     ++G g++l   + ++++e  g+ + l v a+N+++ r+ye+  ++++
  gi|313125408|ref|YP_004035672.1|  88 LSSIYVTRMRWGEGIGQQLLDHVERRVREhGGERIQLGVMAENDRAVRFYEAADYRQD 145
                                       78899999999******************88999*****************9999876 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.9e-05      0.15      19      57 ..      80     118 ..      45     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                   Acetyltransf_CG  19 vrkegvldfthTeVpeelrGkGiAkkLvkaalddareeg 57 
                                       +++e ++d+  ++V     G+Gi+++L +++   +re+g
  gi|313125408|ref|YP_004035672.1|  80 ADDETTFDLSSIYVTRMRWGEGIGQQLLDHVERRVREHG 118
                                       456779******************************998 PP

>> DUF4597  Domain of unknown function (DUF4597)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.044   1.1e+02      24      47 ..       2      25 ..       1      32 [. 0.85
   2 ?    7.2   0.0    0.0017       4.3      40      61 ..     129     150 ..     122     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.044
                           DUF4597 24 diiitPPtPtgmtlpRDsrravwl 47
                                      d+ i    Pt ++  RD  +  w 
  gi|313125408|ref|YP_004035672.1|  2 DVAIRAAAPTDVASIRDVAKRAWK 25
                                      56677889**********999995 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0017
                           DUF4597  40 DsrravwlDetgsysDDGeida 61 
                                       +  rav+  e++ y  DGe   
  gi|313125408|ref|YP_004035672.1| 129 ENDRAVRFYEAADYRQDGEFHD 150
                                       5679***************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1064.60
//
Query:       gi|313125409|ref|YP_004035673.1|  [L=570]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-48  165.7  24.4      2e-48  165.4  24.4    1.1  1  HisKA_7TM    N-terminal 7TM region of histidine kinase
    2.9e-16   59.7   1.0    2.9e-16   59.7   1.0    1.8  2  PAS_4        PAS fold
    5.7e-16   59.0   0.1    1.3e-15   57.8   0.1    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    6.6e-14   51.7   1.7    8.1e-14   51.4   0.3    1.9  2  HisKA        His Kinase A (phospho-acceptor) domain
    1.7e-09   37.6   0.1    4.4e-09   36.3   0.1    1.7  1  PAS          PAS fold
      5e-09   36.4   0.2    2.2e-08   34.3   0.1    2.1  2  PAS_9        PAS domain
    1.1e-07   31.7   0.3      4e-07   29.9   0.3    2.0  1  PAS_8        PAS domain
     0.0002   21.5   0.8     0.0018   18.5   0.3    2.7  2  PAS_7        PAS fold
     0.0024   17.8   0.1     0.0062   16.5   0.1    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.027   14.2   0.0      0.063   13.0   0.0    1.6  1  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain
       0.13   12.2   0.0       0.21   11.5   0.0    1.3  1  M20_dimer    Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4  24.4   1.2e-51     2e-48       1     220 []      11     238 ..      11     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 1.2e-51
                         HisKA_7TM   1 lllisallslvlaiyawrrrskpgaraflllllavalwslgyalellattleakllwaklqylgivfipvlwllfal 77 
                                       lll++a +s+ l++++wrr s++g+ af+l +lav lw++g+++e++at+ + +  wa++q++++ ++++ w+lf++
  gi|313125409|ref|YP_004035673.1|  11 LLLVAAAISVTLCVMTWRR-SVTGSVAFSLNMLAVTLWLVGHTAEVMATSEALIRYWANVQWVAAIVVAPTWFLFVM 86 
                                       699*************987.689************************9998************************** PP

                         HisKA_7TM  78 eytgkrrwltrrrlallllvpvltlilvltnplhhlfy............vsagsfvvlef.........ehGplfw 133
                                       +y gk++wl ++rla+l+++pv++l+l++tn+  hl++                      f         e+ +   
  gi|313125409|ref|YP_004035673.1|  87 AYLGKDQWLDPKRLAVLAVEPVVMLLLLATNNQFHLLWnephidtvtlgwL---------FgetvtlaaaEPAVGTL 154
                                       ******************************777788885555444333332.........03333444346666666 PP

                         HisKA_7TM 134 vhlaysyllliagvvlliralirssglyrrqalllligllvPwlanllyllglsplpgidltplafaltglllaiai 210
                                       +h+a+sy+ll++g++ l+r ++ s ++yr+q++++l+g+ vPw+a+++ l +     +idltp+af++tg++l +++
  gi|313125409|ref|YP_004035673.1| 155 AHVAFSYTLLFVGSLYLVRLALASASVYRWQSAAVLLGVSVPWVASAAALSD---ATSIDLTPVAFSVTGVALSFGL 228
                                       6*************************************************74...3489****************** PP

                         HisKA_7TM 211 fryrlldivP 220
                                       +ryrlld+vP
  gi|313125409|ref|YP_004035673.1| 229 IRYRLLDLVP 238
                                       *********9 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   1.0   1.8e-19   2.9e-16       1     110 []     245     348 ..     245     348 .. 0.96
   2 ?   -2.8   0.1       4.7   7.6e+03      55      81 ..     436     463 ..     434     466 .. 0.73

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.8e-19
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +++l+d ++v+d++gr++++N aa +   ++  +++G + ae+++e   ++l + +r v++ +e i  ++    +g 
  gi|313125409|ref|YP_004035673.1| 245 VENLNDSVIVFDRHGRIVDVNDAALAFTDLDEPDVIGASAAEVFTE--YTDLIERYRGVADMREEIAIEH----EGV 315
                                       689******************************************7..9999999999999999999999....899 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       erhye+ l+P+  ++G  +g+l ++rDiTerrr
  gi|313125409|ref|YP_004035673.1| 316 ERHYEVDLTPITGRDGSRVGTLTVCRDITERRR 348
                                       9******************************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                             PAS_4  55 alrrvlegeepiefleelll.pgeerhy 81 
                                       a+r v++g+++++ + e +   +++r +
  gi|313125409|ref|YP_004035673.1| 436 AWRNVATGDAALTVEAEAVVeADRDRLV 463
                                       7999999999998887766655666655 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.1   8.1e-19   1.3e-15       2     106 ..     458     567 ..     457     569 .. 0.79

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 8.1e-19
                                       HHHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEE.........TEEEEEEEESSSSSTTHHHTGTCS.TTCHHCS CS
                         HATPase_c   2 dekrLrqiisnlvdNavkf..atkageieveikase.........ddlvisveDnGiGipkedlkklfe.kfsqdds 66 
                                       d +rL q++ nl  Nav++  +++++e  ve +             ++ + v DnG+Gip+ +++ +fe  +++   
  gi|313125409|ref|YP_004035673.1| 458 DRDRLVQLLENLFRNAVEHgsSGETSEPAVEADG-GgslrvwvgtTENGFFVADNGPGIPVTERDTVFEaGHTT--- 530
                                       889****************652244444444442.0223333334689999******************66666... PP

                                       TCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEE CS
                         HATPase_c  67 tkrggggtGlGlsivkklvelmgGeiwvesepgrGttftf 106
                                          g+ gtGlGlsiv ++++ +g +++v+++  +G +f +
  gi|313125409|ref|YP_004035673.1| 531 ---GSDGTGLGLSIVSQIANVHGWDVSVDESRAGGARFEL 567
                                       ...789**********************999999**9987 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.3     5e-17   8.1e-14       2      66 ..     360     419 ..     359     420 .. 0.94
   2 ?   -2.4   0.1       3.2   5.2e+03      47      58 ..     458     469 ..     448     473 .. 0.63

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 5e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l+rf++ v+H+Lr+PL +  gn+e+ ++         + l+++e+  +r+d++++d+L+l+r ++
  gi|313125409|ref|YP_004035673.1| 360 LERFASVVSHDLRNPLQVATGNVELARE-----TGSDDRLDRVEDALDRMDQIIDDMLELTRVDG 419
                                       79***********************999.....788899**********************9886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHH CS
                             HisKA  47 earrldhlvedl 58 
                                         +rl +l+e+l
  gi|313125409|ref|YP_004035673.1| 458 DRDRLVQLLENL 469
                                       334777777776 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.1   2.7e-12   4.4e-09       4     113 .]     242     343 ..     240     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.7e-12
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       +a++e+l d ++v D+ gri+ vN+aa  ++ l++ +v+g s  +++ e +d      l ++++   + r  ei ++
  gi|313125409|ref|YP_004035673.1| 242 DAVVENLNDSVIVFDRHGRIVDVNDAALAFTDLDEPDVIGASAAEVFTEYTD------LIERYRGVADMRE-EIAIE 311
                                       799********************************************97654......3333333322222.33334 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                          g ++h ev  +p++ ++g + g l v+rdi
  gi|313125409|ref|YP_004035673.1| 312 H-EGVERHYEVDLTPITGRDGSRVGTLTVCRDI 343
                                       4.77889***************99***999998 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   1.3e-11   2.2e-08       2     104 .]     250     345 ..     249     345 .. 0.86
   2 ?   -1.1   0.0       1.3   2.2e+03      43      77 ..     390     423 ..     357     435 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.3e-11
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       d++++ + +gri+++N+aal ++  ++ +v+g s  ++f        +  +++e+ r  +  +e + i  +g + ++
  gi|313125409|ref|YP_004035673.1| 250 DSVIVFDRHGRIVDVNDAALAFTDLDEPDVIGASAAEVF-------TEYTDLIERYRGVADMREEIAIEHEGVERHY 319
                                       5667756********************************.......55555666666556778888888889999** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       ++ ++p+   dg  vg + ++rDite
  gi|313125409|ref|YP_004035673.1| 320 EVDLTPITGRDGSRVGTLTVCRDITE 345
                                       *******88899999999*******8 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                             PAS_9  43 dpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       ++++ +r+++al++++ +  ++ ++l+r +g  + 
  gi|313125409|ref|YP_004035673.1| 390 SDDRLDRVEDALDRMD-QIIDDMLELTRVDGDSIE 423
                                       5666667777777777.888888888888887665 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.3   2.5e-10     4e-07       5      63 ..     243     302 ..     240     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.5e-10
                             PAS_8   5 alfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplledaeqll 63 
                                       a++e+++d+++v+d+ +rivdvN+aal ++ ++ +d++g+   +++++ ++l+e+++ ++
  gi|313125409|ref|YP_004035673.1| 243 AVVENLNDSVIVFDRHGRIVDVNDAALAFTDLDePDVIGASAAEVFTEYTDLIERYRGVA 302
                                       699***********6568***********************************9999877 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   1.1e-06    0.0018       1     114 [.     245     350 ..     245     351 .. 0.79
   2 ?   -0.7   0.0      0.98   1.6e+03      53      93 ..     387     427 ..     376     433 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphs 77 
                                       +en+++ ++vfD+ +r+v +N+  l   dl e  v +g++ +e++   ++  e  +g v a +++ +a  ++g + +
  gi|313125409|ref|YP_004035673.1| 245 VENLNDSVIVFDRHGRIVDVNDAALAFTDLDEPDV-IGASAAEVFTEYTDLIERYRG-V-ADMREEIAIEHEGVERH 318
                                       699*****************************999.999988887766555444423.3.33344444555566666 PP

                             PAS_7  78 fererpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                       +e+         ++g+     G++t++ DiTerrr e
  gi|313125409|ref|YP_004035673.1| 319 YEV-----DLTPITGRDGSRVGTLTVCRDITERRRRE 350
                                       666.....46789*********************998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.98
                             PAS_7  53 efgagdveaeverrlaaaragkphsfererpdgrvievrgn 93 
                                       e g++d+ + ve  l+++ +   + +e +r dg  ie  + 
  gi|313125409|ref|YP_004035673.1| 387 ETGSDDRLDRVEDALDRMDQIIDDMLELTRVDGDSIETSAV 427
                                       55678888999999999999999999999999999997765 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   3.8e-06    0.0062      22     110 ..     452     547 ..     433     561 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.8e-06
                       HATPase_c_2  22 aglseelldeirlaveEactNavehayleapegpv.......evrlesdeealtvevaDsGpgfdpetlpdpteeep 91 
                                         + e+++d++   +e ++ Naveh+  +++++p        ++r+++++++  + vaD+Gpg ++++++   e + 
  gi|313125409|ref|YP_004035673.1| 452 EAVVEADRDRLVQLLENLFRNAVEHGSSGETSEPAveadgggSLRVWVGTTENGFFVADNGPGIPVTERDTVFEAGH 528
                                       567778888999999999*************66654555555555888888888899*********99999988888 PP

                       HATPase_c_2  92 keslkegGrGlalikglvD 110
                                       ++  +  G+Gl ++ ++++
  gi|313125409|ref|YP_004035673.1| 529 TTGSDGTGLGLSIVSQIAN 547
                                       99999999**999998876 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.9e-05     0.063      17      59 ..     365     407 ..     349     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                            SPOB_a  17 rsqRHDflNhLQvIsGylqLgkydkaeeyieevvkelkeeski 59 
                                       ++  HD  N LQv +G+++L + +  ++ +++v ++l ++ +i
  gi|313125409|ref|YP_004035673.1| 365 SVVSHDLRNPLQVATGNVELARETGSDDRLDRVEDALDRMDQI 407
                                       5678******************999999999998888888776 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.21      25     106 ..     396     475 ..     378     478 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                       TTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHH CS
                         M20_dimer  25 agaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRllpgedpeevleeieeil 101
                                       ++++A+  + ++++++ ++++  +   s+ ++++n+ +++   ++nv  + a ++++   + + d++++ + +e+++
  gi|313125409|ref|YP_004035673.1| 396 RVEDALDRMDQIIDDMLELTRVDG--DSIETSAVNIDSVSNAAWRNVATGDAALTVEAEAVVEADRDRLVQLLENLF 470
                                       567899999999999999988755..*************************************************99 PP

                                       TSCCS CS
                         M20_dimer 102 ekeap 106
                                       +++ +
  gi|313125409|ref|YP_004035673.1| 471 RNAVE 475
                                       98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3571.88
//
Query:       gi|313125410|ref|YP_004035674.1|  [L=462]
Description: fo synthase subunit 2 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-12   46.4   0.1    9.5e-12   45.6   0.1    1.4  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.1   5.3e-16   9.5e-12       2     165 ..      87     294 ..      86     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 5.3e-16
                                       EEESEESS--TTTSCCTT.......HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.......vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerla 71 
                                       +vt +Cn +C fC+++ t        +   +g ++++ e  + v+ +  + g+ ev++++g   l+p fv   +++ 
  gi|313125410|ref|YP_004035674.1|  87 NVTTACNTGCLFCNFKNTahqfeseYEGDHTGFTKTPAESRAVVEDA-LDTGIYEVTSVSG---LHPAFVLNEDHRE 159
                                       6899********************999999*****************.8***777777777...5566666666666 PP

                                       HTC................................CCTEEEEEEECSSCHG.........HHHHHHHHHTT.-SEEE CS
                                       xxx................................xxxxxxxxxxxxxxxx.........xxxxxxxxxxx.xxxxx RF
                       Radical_SAM  72 kla................................vpgiritvetngtlpd.........eeklerllelg.vdrvs 106
                                        l+                                v g++++  t++             ee+ ++l+++g      
  gi|313125410|ref|YP_004035674.1| 160 ILEsyenpyaevdykppeaydkdpgtyveqmramsVGGVHLHSMTPEEAYHarrgtdwsyEEVYRELKDAGlDSAPG 236
                                       66666778888899999999999999999999999**************99********************777889 PP

                                       EEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 107 lgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeeleelle 165
                                         +e++ +e v++ ++ ++ +  e++e++e + +ag++ v+ +i+ ++ en ++++ +l+
  gi|313125410|ref|YP_004035674.1| 237 TAAEILVPE-VREVICpGKISTAEWVEGMEGAIAAGLD-VTATIMYGHVENAAHRVMHLK 294
                                       999******.****************************.9************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3117.93
//
Query:       gi|313125411|ref|YP_004035675.1|  [L=182]
Description: hypothetical protein Hbor_06360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-06   26.7  13.4    3.5e-05   23.2  13.4    2.2  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
       0.85   10.0   7.5      0.052   13.9   2.0    1.7  2  DUF4149   Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2  13.4   3.9e-09   3.5e-05       1     147 [.       1     144 [.       1     174 [. 0.69

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.9e-09
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllfla 77 
                                       M+  tHa+ +++ ++   al ++++ a+++++a+lg+++PD+D            l++     + HR   H  + + 
  gi|313125411|ref|YP_004035675.1|   1 MMVTTHAAAALLFFATPVALFAPEFTAAAIIGALLGGIVPDVD------------LFV-----GTHRKSLHFPVYAS 60 
                                       999****************************************............222.....24999999888877 PP

                              YdjM  78 llalvlllllrlfgrsalrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltll........ 146
                                       l+++++ +++     +a  ++ ++llg+ +H + D++   G   l P+  + +r   l   +  +l+          
  gi|313125411|ref|YP_004035675.1|  61 LAGVGAGIVALVAPSTASVAAAAFLLGAGLHAASDWF--GGSDELRPWERTSRRAVYLHP-RRRWLRPRhiirydga 134
                                       77777766666666663445555************98..688899999764444444444.3332322256666665 PP

                              YdjM 147 .........s 147
                                                 
  gi|313125411|ref|YP_004035675.1| 135 pedffltvvL 144
                                       4333333330 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.0   5.8e-06     0.052      11      68 ..       9      80 ..       2      97 .. 0.85
   2 ?   -1.7   0.3      0.41   3.7e+03      68      82 ..     156     170 ..     138     176 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-06
                           DUF4149 11 lwvtfvvapvlfrsLprhqfgelqskl....................Fplyfglglalsvlllltevavgseklasee 68
                                       ++ f+++pv+ ++ p++++ ++ + l                    Fp+y+ l ++ +++++l  +        s +
  gi|313125411|ref|YP_004035675.1|  9 AALLFFATPVALFA-PEFTAAAIIGALlggivpdvdlfvgthrkslhFPVYASLAGVGAGIVALVAPSTA-----SVA 80
                                      56779999999999.**************************************************99543.....333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.41
                           DUF4149  68 ellqlllllvvlllt 82 
                                       +l+ + +l+v ++ t
  gi|313125411|ref|YP_004035675.1| 156 RLVVAAGLVVGAVYT 170
                                       333444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1149.45
//
Query:       gi|313125412|ref|YP_004035676.1|  [L=203]
Description: hypothetical protein Hbor_06370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-07   30.8  13.4    3.1e-06   26.6  13.2    2.4  1  YdjM      LexA-binding, inner membrane-associated putative hy
     0.0053   16.5   1.8     0.0094   15.7   1.8    1.5  1  DUF4184   Domain of unknown function (DUF4184)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6  13.2   3.5e-10   3.1e-06       1     114 [.       1      96 [.       1     176 [. 0.86

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.5e-10
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllfla 77 
                                       M+  tH++ G+al++ +a l ++ +   ++a+av+g+++PD+D++                  ++HR   H + + a
  gi|313125412|ref|YP_004035676.1|   1 MMAPTHVAAGIALAVPIAFLVPELAP-LVVAAAVAGSVFPDFDMV-----------A------GEHRRTLHAVEAYA 59 
                                       99*****************9998775.****************22...........2......25**********99 PP

                              YdjM  78 llalvlllllrlfgrsalrlglllllgvlsHlllDll 114
                                       +l++++++++       ++++ ++++++++H+llDl 
  gi|313125412|ref|YP_004035676.1|  60 VLTALVTFAAIVAPSPPVIAAAVFFAAAAVHPLLDLA 96 
                                       999999999988888867777779999********75 PP

>> DUF4184  Domain of unknown function (DUF4184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.8     1e-06    0.0094      10      83 ..      13      97 ..       4     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-06
                           DUF4184 10 avlpl..kllkrkrlslsaLviGslaPDveyf..........lrlkakstltHtllglllvdlplalllalvfhlvikk 76
                                      +++p+     +  +l+++a v+Gs+ PD+ +           +++ a  t   t+++++   +p++ +++++  + ++ 
  gi|313125412|ref|YP_004035676.1| 13 LAVPIafLVPELAPLVVAAAVAGSVFPDFDMVagehrrtlhaVEAYAVLTALVTFAAIVAPSPPVIAAAVFFAAAAVH- 90
                                      4555522234557899****************8888888777777777777777777777777777777777666666. PP

                           DUF4184 77 pllallP 83
                                      pll+l+ 
  gi|313125412|ref|YP_004035676.1| 91 PLLDLAG 97
                                      7777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1194.98
//
Query:       gi|313125413|ref|YP_004035677.1|  [L=194]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-15   57.9   0.0    1.9e-15   57.3   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.9e-15   57.3   0.0    3.7e-15   56.4   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      2e-15   56.9   0.0    2.2e-15   56.7   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    3.4e-13   50.2   0.0    4.9e-13   49.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
      3e-09   36.7   0.0    5.2e-09   35.9   0.0    1.3  2  MTS              Methyltransferase small domain
    6.5e-09   35.5   0.0    8.8e-09   35.0   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    4.6e-07   29.5   0.0    9.9e-07   28.4   0.0    1.5  1  Methyltransf_4   Putative methyltransferase
    2.1e-06   27.2   0.0    2.8e-06   26.8   0.0    1.1  1  GidB             rRNA small subunit methyltransferase G
    2.3e-06   27.5   0.0    2.7e-06   27.3   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    4.2e-06   26.7   0.0    4.2e-06   26.6   0.0    1.2  1  Met_10           Met-10+ like-protein
    9.4e-06   25.6   0.0    1.2e-05   25.3   0.0    1.1  1  Methyltransf_18  Methyltransferase domain
    4.2e-05   23.4   0.0    7.2e-05   22.6   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00034   20.6   0.0    0.00042   20.3   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0015   19.5   0.0     0.0025   18.8   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
     0.0021   17.7   0.0     0.0029   17.3   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0033   16.6   0.0     0.0037   16.4   0.0    1.1  1  Fibrillarin      Fibrillarin
     0.0055   15.8   0.0     0.0067   15.5   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0059   16.0   0.0     0.0078   15.6   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0066   15.8   0.0     0.0086   15.4   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.063   13.4   0.0    1.9  1  FtsJ             FtsJ-like methyltransferase
      0.069   12.9   0.0       0.12   12.1   0.0    1.3  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   2.2e-18   1.9e-15       2      96 .]      37     135 ..      36     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.2e-18
                                       EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTS.S-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklp.fednsfDlvvssevlhhv 74 
                                       dvG+G+G+++ +la+ +  + v+++D+++e+l    e+a e++  +++++++da++lp +  + +D v++ +++h v
  gi|313125413|ref|YP_004035677.1|  37 DVGSGNGYFTLPLAELVdgEPVYAIDINDELLGELAEAAAERQCqNIDCIHGDARNLPeLLPEPVDTVLVANTFHGV 113
                                       9*************88888*************55555555555559***********769999************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                       e++ ++ ++++ +L+p+G +v+
  gi|313125413|ref|YP_004035677.1| 114 EKQVEFARQARELLRPDGQFVV 135
                                       *******************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   4.3e-18   3.7e-15       1      97 []      35     131 ..      35     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 4.3e-18
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS.SSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp.fedgsfDlvvssgal 74 
                                       v d+G G+G +tl la+ + g + v+++Di++e+l + +e a+e+++ n+++++gda++lp +  + +D v++++++
  gi|313125413|ref|YP_004035677.1|  35 VADVGSGNGYFTLPLAELVdG-EPVYAIDINDELLGELAEAAAERQCqNIDCIHGDARNLPeLLPEPVDTVLVANTF 110
                                       78*****************66.9************9999999999999************954888*******9999 PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       h ++  ++ ++ ++++++L+p+G
  gi|313125413|ref|YP_004035677.1| 111 HGVE--KQVEFARQARELLRPDG 131
                                       9887..5679************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   2.6e-18   2.2e-15       1     113 [.      29     139 ..      29     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 2.6e-18
                   Methyltransf_31   1 ldkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDl 77 
                                       +d+g +v D+G+G+G++t+ la el ++  v+ iDi+ e +    e a++ + +n+   +gd+ +l++ll  e++D 
  gi|313125413|ref|YP_004035677.1|  29 IDSGQSVADVGSGNGYFTLPLA-ELVDGEPVYAIDINDELLGELAEAAAERQCQNIDCIHGDARNLPELLP-EPVDT 103
                                       578999****************.8889899***********999999********************9766.89*** PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedpr 113
                                       +l  ++++ +  + ++ +++ ++l+p+g +++ + +
  gi|313125413|ref|YP_004035677.1| 104 VLVANTFHGVEKQVEFARQARELLRPDGQFVVVNWH 139
                                       *******************************98877 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   5.8e-16   4.9e-13       2      99 .]      37     133 ..      36     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 5.8e-16
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       ++G+G+G ++ +l+e   +  ++++Di+ + +   +e  a+r+ +n ++++ +a++l +l ++  +D+v+++n++h 
  gi|313125413|ref|YP_004035677.1|  37 DVGSGNGYFTLPLAELVDGEPVYAIDINDELLGELAEAAAERQCQNIDCIHGDARNLPELLPE-PVDTVLVANTFHG 112
                                       8***************99999***********9999999999999*************99997.************* PP

                   Methyltransf_12  79 lkdirevldnirklLkpgGrl 99 
                                       +++  e+ +++r+lL+p+G++
  gi|313125413|ref|YP_004035677.1| 113 VEKQVEFARQARELLRPDGQF 133
                                       *******************96 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   6.1e-12   5.2e-09      26     145 ..      26     143 ..      20     151 .. 0.84
   2 ?   -3.8   0.0       9.5   8.1e+03     145     158 ..     166     179 ..     162     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 6.1e-12
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS-EE CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve..ekkfd 99 
                                       t+  +  ++v+D+G+G+G+ ++ la+  +   v ++d++ + l    e +++ +++ +++++ d+ +  e  ++ +d
  gi|313125413|ref|YP_004035677.1|  26 TVGIDSGQSVADVGSGNGYFTLPLAELVDGEPVYAIDINDELLGELAEAAAERQCQnIDCIHGDARNLPEllPEPVD 102
                                       444556789*********************99***********777777777777779999999977544448**** PP

                                       EEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCH CS
                               MTS 100 livsNPPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgy 145
                                       +++    fh  ++       e+ ++A+e L+++G++++V  + ++ 
  gi|313125413|ref|YP_004035677.1| 103 TVLVANTFHGVEK-----QVEFARQARELLRPDGQFVVVNWHDMPK 143
                                       ****99***9888.....789*****************98777765 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.5
                                       HHHHHHHHHS--EE CS
                               MTS 145 yeslleelfgnvev 158
                                        +++l+++fg+ve+
  gi|313125413|ref|YP_004035677.1| 166 TRDVLRKVFGSVEQ 179
                                       56789999999885 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0     1e-11   8.8e-09      35     154 ..      17     138 ..      13     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1e-11
                                       HHH..HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT CS
                   Ubie_methyltran  35 Wkk..fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaee 109
                                       W +   v k+v+  +g++v Dv +G g +++ l++ v+ +  v  +Din+++L +  + + e+  +ni+ ++++a +
  gi|313125413|ref|YP_004035677.1|  17 WPEpkAVLKTVGIDSGQSVADVGSGNGYFTLPLAELVDGE-PVYAIDINDELLGELAEAAAERQCQNIDCIHGDARN 92 
                                       65544688999999**********************9876.6999**********999999999************* PP

                                       -TTS-.T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran 110 Lpfed.dsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                       Lp+   +  D+v v+  +  v  + +  ++a+  l+p G++vv++ 
  gi|313125413|ref|YP_004035677.1|  93 LPELLpEPVDTVLVANTFHGVEKQVEFARQARELLRPDGQFVVVNW 138
                                       **98779***********************************9976 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.2e-09   9.9e-07       4      70 ..      34      99 ..      31     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.2e-09
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-T CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelled 70
                                       v+++G+G+G f++ lA+      + +i+i+ +++ ++ +++++++++N+ +++gda + l+ell++
  gi|313125413|ref|YP_004035677.1| 34 SVADVGSGNGYFTLPLAELVDGEPVYAIDINDELLGELAEAAAERQCQNIDCIHGDA-RNLPELLPE 99
                                      689******************************************************.888888765 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.2e-09   2.8e-06      46     147 ..      30     136 ..      22     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.2e-09
                                       -CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC..TTTTT-EEEE. CS
                              GidB  46 kekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee..kqeeekydvv. 119
                                       ++ + +v+DvGsG+G   +pLa +     ++ ++ +      L+e+ +e + +n+  ++ +a +      e++d+v 
  gi|313125413|ref|YP_004035677.1|  30 DSGQ-SVADVGSGNGYFTLPLAELVDGEPVYAIDINDELLGELAEAAAERQCQNIDCIHGDARNlpELLPEPVDTVl 105
                                       4455.6*******************999************************************8767788999984 PP

                                       ...EEC-SSSHHHHHHHHCCCEEEEEEEEEE CS
                              GidB 120 ...tsRAlaslnelteillkllkegglilal 147
                                          t+ ++ +  e++  +++ll++ g+++++
  gi|313125413|ref|YP_004035677.1| 106 vanTFHGVEKQVEFARQARELLRPDGQFVVV 136
                                       34456788888999999999********986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   3.2e-09   2.7e-06      20     120 ..      29     138 ..      12     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.2e-09
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlren..gfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg........kfdlI 86 
                                        ++g++v d+G G G+++  l+e   g  v+++D+++e+ ++++    a+ ++ + +++  +++          d++
  gi|313125413|ref|YP_004035677.1|  29 IDSGQSVADVGSGNGYFTLPLAELvdGEPVYAIDINDELLGELA-EAAAERQCQNIDCIHGDARnlpellpePVDTV 104
                                       56788999*********99998873466**********999984.444444444455555555577778888***** PP

                   Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllsep 120
                                          ++++ v+   e  rq+++ll+p+G +++  +
  gi|313125413|ref|YP_004035677.1| 105 LVANTFHGVEKQVEFARQARELLRPDGQFVVVNW 138
                                       ****************************999875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0     5e-09   4.2e-06      93     171 ..      22     103 ..      11     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5e-09
                                       HHHTT..--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.. CS
                            Met_10  93 rlakl..veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.. 165
                                        + k+  ++ g+ V dv  G G+f++p+a + +++ v+aid+n e    l e+ +  + +  +  i +D+r++ +  
  gi|313125413|ref|YP_004035677.1|  22 AVLKTvgIDSGQSVADVGSGNGYFTLPLAELVDGEPVYAIDINDELLGELAEAAAERQCQ-NIDCIHGDARNLPEll 97 
                                       5555535689****************************************9998877765.5789*****9987555 PP

                                       TT-EEE CS
                            Met_10 166 eqladr 171
                                       ++ +d 
  gi|313125413|ref|YP_004035677.1|  98 PEPVDT 103
                                       444454 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.4e-08   1.2e-05      12      89 ..      29     107 ..      21     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.4e-08
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk..eeevdtv 86 
                                       +++g++vaD+G+  gy ++ l++    + v+a+Din++ l +  e +++ +++ +i+++ +d  +  +  +e vdtv
  gi|313125413|ref|YP_004035677.1|  29 IDSGQSVADVGSGNGYFTLPLAELVDGEPVYAIDINDELLGELAEAAAERQCQ-NIDCIHGDARNLPEllPEPVDTV 104
                                       67899********************************************9995.7******9866554426669999 PP

                   Methyltransf_18  87 via 89 
                                       ++a
  gi|313125413|ref|YP_004035677.1| 105 LVA 107
                                       887 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   8.4e-08   7.2e-05      65     135 ..      23      92 ..      20     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.4e-08
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGG CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrk 135
                                       +l+ + ++ g++v +vGsG Gy t  la+lv  +  v +i+   el  e  +   + + +n+  ++gD r+
  gi|313125413|ref|YP_004035677.1|  23 VLKTVGIDSGQSVADVGSGNGYFTLPLAELVDGEP-VYAIDINDELLGELAEAAAERQCQNIDCIHGDARN 92 
                                       5667889*************************999.99********999999999999**********875 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.9e-07   0.00042      26      83 ..      32      84 ..      21     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.9e-07
                   Methyltransf_32 26 altvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrls 83
                                       ++v+DvG+G+gY +  la       +  v++id+++el  +  + a++ +    +++ 
  gi|313125413|ref|YP_004035677.1| 32 GQSVADVGSGNGYFTLPLAE---LvDGEPVYAIDINDELLGELAEAAAERQ--C-QNID 84
                                      5789***************9...44799***********999888888877..4.5555 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.9e-06    0.0025       3     103 ..      38     135 ..      36     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.9e-06
                   Methyltransf_24   3 iGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiD.llfiDg 77 
                                       +G+ +G+ tl l++++ + +   ++a+d + +   e a+ a+e    ++++ i++d++++ + l  +++D +l+   
  gi|313125413|ref|YP_004035677.1|  38 VGSGNGYFTLPLAELV-DGE--PVYAIDINDElLGELAEAAAE-RQCQNIDCIHGDARNLPELLP-EPVDtVLVANT 109
                                       7999******999765.455..49*****99654444444444.67788*********9955555.****4555577 PP

                   Methyltransf_24  78 ghaaeavledleallprlapggvvlf 103
                                        h  e+  e+ + ++++l+p+g +++
  gi|313125413|ref|YP_004035677.1| 110 FHGVEKQVEFARQARELLRPDGQFVV 135
                                       7888999**************94443 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.4e-06    0.0029       9      85 ..      32     106 ..      25     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-06
                                       T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEE CS
                   Methyltr_RsmB-F   9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLl 85 
                                       ++ + D+ ++ G  T  +ael  +   v+A+d+n+e l ++ae      ++n+ ++++Dar+ ++ l +  +D +L+
  gi|313125413|ref|YP_004035677.1|  32 GQSVADVGSGNGYFTLPLAEL-VDGEPVYAIDINDELLGELAEAAAERQCQNIDCIHGDARNLPELLPE-PVDTVLV 106
                                       567889999999999999**9.67789**************************************9995.9999997 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.4e-06    0.0037      63     173 ..      24     135 ..      21     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.4e-06
                                       -S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTS..TTEEEEES-TTS.GGGGTT CS
                       Fibrillarin  63 lkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkR..knivPileDArk.PekYra 136
                                       lk++ i +g++v  +G++ G     ++++v+    vya++  +  l el e a +R  +ni  i +DAr+ Pe   +
  gi|313125413|ref|YP_004035677.1|  24 LKTVGIDSGQSVADVGSGNGYFTLPLAELVD-GEPVYAIDINDELLGELAEAAAERqcQNIDCIHGDARNlPELLPE 99 
                                       78899*************************9.678******************999445*********964776666 PP

                                       TS--EEEEEEESSSTTHHHHHHHHHHHHEEEEEEEEE CS
                       Fibrillarin 137 lvekvDvifaDvaqpdqarilaknaklflkeggylli 173
                                        v++v v  +     +q++ +a+ a+  l+ +g++++
  gi|313125413|ref|YP_004035677.1| 100 PVDTVLVANTFHGVEKQVE-FARQARELLRPDGQFVV 135
                                       6665544322222233444.56667777777777766 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.8e-06    0.0067      22      87 ..      23      92 ..      20     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.8e-06
                                      HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCG CS
                            RrnaAD 22 IldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflk 87
                                      +l+++ +   + v ++g+G G +T +La+ +  + v ++ +  +L+ +l ++    + +++  +h D+ +
  gi|313125413|ref|YP_004035677.1| 23 VLKTVGIDSGQSVADVGSGNGYFTLPLAELVdgEPVYAIDINDELLGELAEAAAerQCQNIDCIHGDARN 92
                                      67777888999********************9999******999999999977778999*******9876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.2e-06    0.0078     160     258 ..      30     135 ..      22     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.2e-06
                              PrmA 160 kegeevlDvGtGSGiLaiaaa.kLgakkvvavDiDevAvkvakeNaelNkveakleva.lseellk..eekad.viv 231
                                        +g++v DvG G G  ++  a +++ + v+a+Di++  +   +e a+  ++++   ++  +++l++   e++d v+v
  gi|313125413|ref|YP_004035677.1|  30 DSGQSVADVGSGNGYFTLPLAeLVDGEPVYAIDINDELLGELAEAAAERQCQNIDCIHgDARNLPEllPEPVDtVLV 106
                                       6789***********9997551567899******8888877777777777877555653334444444467873679 PP

                              PrmA 232 aNILaev..lielaedikklvkeggllil 258
                                       aN    v   +e+a ++ +l++++g++++
  gi|313125413|ref|YP_004035677.1| 107 ANTFHGVekQVEFARQARELLRPDGQFVV 135
                                       ***9766326899************9985 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05    0.0086      52     167 ..      21     138 ..       6     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--E.EEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---. CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvk.vvglTlSkeqaklakkrvdeldlerkvevklldyedlde. 126
                                       + +l+ ++++ G+ + d+G G G+ +   +e  d + v ++ + +e      ++ +e++ ++   ++  d ++l+e 
  gi|313125413|ref|YP_004035677.1|  21 KAVLKTVGIDSGQSVADVGSGNGYFTLPLAELVDGEpVYAIDINDELLGELAEAAAERQCQNIDCIH-GDARNLPEl 96 
                                       6789999************************998765889999999998888888888877665554.566776666 PP

                                       ...--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEE CS
                              CMAS 127 ...kvdrvvsvgafehvgkenydtffkklkkllkedGllllhti 167
                                          +vd v   + f   g+e+  +f +++ +ll++dG +++   
  gi|313125413|ref|YP_004035677.1|  97 lpePVDTVLVANTFH--GVEKQVEFARQARELLRPDGQFVVVNW 138
                                       555999999888886..667789**************9987554 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.4e-05     0.063      15      73 ..      26      93 ..      21     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.4e-05
                                      HHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHH..TTEEEECS-CCCS CS
                              FtsJ 15 kfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........apl..pgvttiqgditdp 73
                                       ++ ++ g+ v D+g++ G ++  l++ +     v+a+D++           a +  +++ +i+gd ++ 
  gi|313125413|ref|YP_004035677.1| 26 TVG-IDSGQSVADVGSGNGYFTLPLAELVDG-EPVYAIDINDEllgelaeaaAERqcQNIDCIHGDARNL 93
                                      555.78999*******************965.77******88889999988733346999999**99775 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.12      16     137 ..      22     133 ..      19     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                            DUF938  16 evLksylakttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtaevapv 92 
                                       +vLk +  ++++ v +++sG G     +A+++      + d ++el + +a  a+e   +n+   ++ d+ + +   
  gi|313125413|ref|YP_004035677.1|  22 AVLKTVGIDSGQSVADVGSGNGYFTLPLAELVDGEPVYAIDINDELLGELAEAAAERQCQNIDC-IHGDARNLP--- 94 
                                       6788876666667************************************************975.666665542... PP

                            DUF938  93 ereappapasidailsinllHispwsaveglfagagellkkkavl 137
                                            + p+++d++l +n++H   ++    + + a ell++ + +
  gi|313125413|ref|YP_004035677.1|  95 ----ELLPEPVDTVLVANTFHGVEKQ--VEFARQARELLRPDGQF 133
                                       ....247899***********65554..45667777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1156.04
//
Query:       gi|313125414|ref|YP_004035678.1|  [L=385]
Description: fo synthase subunit 1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-16   59.6   0.0    7.9e-16   58.9   0.0    1.4  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   4.4e-20   7.9e-16       3     164 ..      46     213 ..      44     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 4.4e-20
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.............TTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.............xxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly.............pdfve 65 
                                        t +C++ C++C+ +      g +  +s+e++ e ++ + a+ g ++ ++ +g+ep+++             +d+  
  gi|313125414|ref|YP_004035678.1|  46 LTTACRYTCTYCTYYD---VPGEATLMSPEDVRETLRVG-ADAGcTEALFTFGDEPDDRytaiheqlsewgyDDILA 118
                                       6899***********9...7*******************.8***9**************************999999 PP

                                       HHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  66 llerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreag 141
                                       +l+ +++ a  +  +   +n++ ++e   erl++ +   + + le++ d  v+ + + r++t+ ++l++++++ ++g
  gi|313125414|ref|YP_004035678.1| 119 YLRDCCEMA-MEEGLLAHSNPGDLTESAFERLAPVN-ASMGVMLETTAD--VRAHSGgRRKTPGQRLNTIRAAGKVG 191
                                       999999997.999999999999999*********99.************..8899989******************* PP

                                       SETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 142 ikrvvdrivglpGendeeleell 164
                                       ++  +++++++ Ge+++++ e l
  gi|313125414|ref|YP_004035678.1| 192 VP-FTTGLLIGIGETWRDRAESL 213
                                       **.***************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1983.19
//
Query:       gi|313125415|ref|YP_004035679.1|  [L=207]
Description: phospholactate guanylyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-39  133.6   0.0    6.2e-39  133.4   0.0    1.0  1  CofC          Guanylyl transferase CofC like
    8.1e-05   23.0   2.3    9.4e-05   22.8   2.3    1.3  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.4   0.0   6.9e-43   6.2e-39       1     207 [.       1     199 [.       1     206 [. 0.88

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 6.9e-43
                              CofC   1 mkviiPvsainsaktrlseilseeerkellkamlldvidalkrld..vlvvsedeevleyaldelgvevvkekekdl 75 
                                       m+v+iP+ + + +k+rl+ +l e+er+ +++am  dv+ a+        +++ d +    + d  ++ v+ ++ + l
  gi|313125415|ref|YP_004035679.1|   1 MQVVIPYTTRD-PKSRLAGVLDEDERRAFARAMRTDVVRAVRAAGgaPTILTTDAD----DIDDVDAPVIGDD-RAL 71 
                                       89*****9988.****************************9883222233333332....2345567899999.*** PP

                              CofC  76 ntavekafeeieekeviiipsdiPlikkedvkdllelekradvviaPargGGtnllllrksalevkyedfsflkhle 152
                                         av+ +  +   ++v ++++d+ l++ + +++l+e e+  +vviaP+rgGGtn l++r+  ++v y+++s+ +h  
  gi|313125415|ref|YP_004035679.1|  72 TPAVNAV-LDDATSDVSVVMADLALVTPDALRRLFESEG--EVVIAPGRGGGTNALVVRHPDFRVDYHGASYRDHQA 145
                                       ******9.5577889************************..************************************ PP

                              CofC 153 earkrglkvkiydsfylsvdinteedlgeillhGegtkakeylrklgfsvepees 207
                                        a + gl+v++ ds+ l+ d++++ dl e+llhG g+ a+ +l   gf++e  ++
  gi|313125415|ref|YP_004035679.1| 146 IADDAGLSVTVIDSMRLATDVDEPADLAEVLLHGAGN-ARTWLEDAGFELEVTDG 199
                                       **********************************995.899*******9987654 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   2.3     1e-08   9.4e-05      25     133 ..      31     126 ..      14     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1e-08
                                       CHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--H CS
                      NTP_transf_3  25 pllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltp 101
                                        +   v++a+raag ++ ++ ++++++     + +++v+ d+   +    ++ a l+ a  ++ v v+++D++l+tp
  gi|313125415|ref|YP_004035679.1|  31 AMRTDVVRAVRAAGGAPTILTTDADDID----DVDAPVIGDD---RALTPAVNAVLDDA--TSDVSVVMADLALVTP 98 
                                       6778899******988999999999886....689******7...889999*****987..89************** PP

                                       HHHHHHHHCHHHHTSSEEEEESSSEEEECCEE CS
                      NTP_transf_3 102 elverllaaaaasgadvvvptyegerghpllf 133
                                       ++++rl+++   +g+ v++p + g+  + l+ 
  gi|313125415|ref|YP_004035679.1|  99 DALRRLFES---EGEVVIAPGRGGGT-NALVV 126
                                       ********7...45555666555554.54443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1132.27
//
Query:       gi|313125416|ref|YP_004035680.1|  [L=261]
Description: hypothetical protein Hbor_06410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0019   18.5   2.0     0.0019   18.5   2.0    1.8  2  DUF1771    Domain of unknown function (DUF1771)
     0.0035   17.0   0.3     0.0076   15.9   0.3    1.5  1  DUF1411    Protein of unknown function (DUF1411)
     0.0064   16.5   1.3      0.012   15.6   1.3    1.5  1  PTS_IIA    PTS system, Lactose/Cellobiose specific IIA subuni
  ------ inclusion threshold ------
      0.012   15.9   0.4      0.039   14.2   0.4    1.8  1  DUF4878    Domain of unknown function (DUF4878)
      0.028   14.6   1.4        3.3    8.0   0.2    2.3  2  TrbC       TrbC/VIRB2 family
      0.039   14.6  10.2       0.15   12.7  10.2    1.8  1  DUF4398    Domain of unknown function (DUF4398)
      0.042   13.4   4.6      0.072   12.7   4.6    1.4  1  PspA_IM30  PspA/IM30 family
      0.082   13.6   1.3       0.16   12.6   1.3    1.5  1  TPR_16     Tetratricopeptide repeat
       0.42   10.7   2.9         10    6.2   0.1    2.4  2  TPPK_C     Thiamine pyrophosphokinase C terminal


Domain annotation for each model (and alignments):
>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1         1     2e+03      11      34 ..     164     187 ..     160     190 .. 0.65
   2 !   18.5   2.0   9.8e-07    0.0019      15      51 ..     187     223 ..     183     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                           DUF1771  11 harkrnelfekAaeAyrrGdgaaA 34 
                                       + +  + +++++++A +  +  +A
  gi|313125416|ref|YP_004035680.1| 164 ESQSARDALDESKAAVEGVNSDEA 187
                                       455666777777777776665555 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 9.8e-07
                           DUF1771  15 rnelfekAaeAyrrGdgaaAkelseqGkehgekmeea 51 
                                        +  f+ A  A+++G+ + A el++++++  +++e+ 
  gi|313125416|ref|YP_004035680.1| 187 AQASFDNAVSAFENGNFELATELANEAQTKAQQAEQS 223
                                       6788******************************986 PP

>> DUF1411  Protein of unknown function (DUF1411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   3.8e-06    0.0076      15      82 ..       8      69 ..       3      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.8e-06
                           DUF1411 15 kvaklmlasvvvlsalsgnvladeaevskkpvekkkegglfskewneadivkedkkklkalsdltkte 82
                                      + +kl la +vvl+al+  v a+ +     p ++++e+ +++       ++ ++  k  +l + t + 
  gi|313125416|ref|YP_004035680.1|  8 RFSKLALACLVVLTALAAPVAAVSVGEEDVPSDAQVESKVTTS------VTLNELYKNPQLESWTLAG 69
                                      779*******************999999999999999998887......3333333333333333333 PP

>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.3   6.2e-06     0.012      12      56 ..     186     231 ..     182     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.2e-06
                           PTS_IIA  12 eArslameAlkaakegdfeeaeellkeAeeelkeAhk.aqteliqk 56 
                                       eA+ ++ +A++a ++g+fe a el +eA+++ ++A + +qt+ +  
  gi|313125416|ref|YP_004035680.1| 186 EAQASFDNAVSAFENGNFELATELANEAQTKAQQAEQsSQTQQMLI 231
                                       7899999****************************87246665544 PP

>> DUF4878  Domain of unknown function (DUF4878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4     2e-05     0.039       4      50 ..     182     228 ..     179     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                           DUF4878   4 gekqtpeeavknFleavkeGdvedaikyltestreedalaeklkgkf 50 
                                        +++++++  +n ++a+++G++e a ++++e++ +  +  ++ ++++
  gi|313125416|ref|YP_004035680.1| 182 VNSDEAQASFDNAVSAFENGNFELATELANEAQTKAQQAEQSSQTQQ 228
                                       567799999***********************999998888877776 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0017       3.3       1      36 [.       1      37 [.       1      53 [. 0.79
   2 ?    5.7   0.1    0.0086        17      43      75 ..     224     255 ..     205     261 .] 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0017
                              TrbC  1 MkalkskarrlllalalalvllllaspalAqaagg..d 36
                                      M+ ++s++r+ +lala+++vl++la p+ A + g    
  gi|313125416|ref|YP_004035680.1|  1 MT-KTSWSRFSKLALACLVVLTALAAPVAAVSVGEedV 37
                                      55.789************************98877651 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0086
                              TrbC  43 qnivdfltgplakviatiaiivaGimlafgrls 75 
                                        + +++l   +a ++  ia++v G+ ++  ++s
  gi|313125416|ref|YP_004035680.1| 224 SQTQQMLIY-AAGGLLAIAVVVGGVFYWRSQQS 255
                                       456788888.99**************9987765 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  10.2   7.4e-05      0.15      11      69 ..     166     227 ..     162     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.4e-05
                           DUF4398  11 eaAraagaeeyApae...leeAreaLaqAeaamaekdyeeAdhlaylAerdaelAearAkaa 69 
                                       ++Ar+a +e  A++e     eA+ +++ A +a ++++ e A +la +A+ +a+ Ae+ +++ 
  gi|313125416|ref|YP_004035680.1| 166 QSARDALDESKAAVEgvnSDEAQASFDNAVSAFENGNFELATELANEAQTKAQQAEQSSQTQ 227
                                       67888888888888888899************************************999886 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.6   3.6e-05     0.072      64     108 ..     184     228 ..     159     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                         PspA_IM30  64 keqakklekkAkaALtkgeeeLArealaeikslekqaealetqla 108
                                       +++a++  ++A +A+++g+ eLA e++ e+++ ++qae+ ++ ++
  gi|313125416|ref|YP_004035680.1| 184 SDEAQASFDNAVSAFENGNFELATELANEAQTKAQQAEQSSQTQQ 228
                                       4556667799****************************9887655 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.3   8.3e-05      0.16      25      67 ..     178     220 ..     163     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-05
                            TPR_16  25 krdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +  ++ +d a+A++  +++a+++g++++A +l ++a++ a +a
  gi|313125416|ref|YP_004035680.1| 178 AVEGVNSDEAQASFDNAVSAFENGNFELATELANEAQTKAQQA 220
                                       44556799****************************9888776 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.6     0.024        47      10      31 ..       8      30 ..       6      36 .. 0.49
   2 ?    6.2   0.1    0.0053        10      10      31 ..     223     244 ..     221     246 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.024
                            TPPK_C 10 risggallllvl.AaLvAvaval 31
                                      r+s  al+ lv+ +aL+A ++a+
  gi|313125416|ref|YP_004035680.1|  8 RFSKLALACLVVlTALAAPVAAV 30
                                      55555555554404444444443 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0053
                            TPPK_C  10 risggallllvlAaLvAvaval 31 
                                       ++++ ++l  ++++L+A+av++
  gi|313125416|ref|YP_004035680.1| 223 SSQTQQMLIYAAGGLLAIAVVV 244
                                       678889999***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1722  (0.0960455); expected 358.6 (0.02)
Passed bias filter:                      870  (0.0485247); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1605.89
//
Query:       gi|313125417|ref|YP_004035681.1|  [L=393]
Description: cell division GTPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-27   95.0   0.0    1.4e-26   93.9   0.0    1.6  1  Tubulin      Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
      0.013   14.7   0.3      0.029   13.6   0.2    1.5  1  Tubulin_2    Tubulin like
      0.091   12.3   0.0       0.22   11.0   0.0    1.6  1  Mu-like_Pro  Mu-like prophage I protein


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.0   2.3e-30   1.4e-26       3     194 ..       4     174 ..       2     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 2.3e-30
                                       EEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE-- CS
                           Tubulin   3 ivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllg 79 
                                        +ig+Gq+G++i+++++e + + hg               g v+    +va++  + +l  ++      + +++l+g
  gi|313125417|ref|YP_004035681.1|   4 AMIGFGQAGGKIVDKFVE-YDQRHGS--------------GIVR---AAVAVNSAKADLMGLEHI---PQDQRVLIG 59 
                                       68****************.7777775..............5344...358999966665544443...344****** PP

                                       CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE...SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  80 kegagnngaggypevgkeaaeeileeirkevekcds..lqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       ++  +++g+g+++e+g+e+aee  +e++ ++++     +++f+++++lgGGTGSG +pv+++ lk+ y   +v++  
  gi|313125417|ref|YP_004035681.1|  60 QSRVKGHGVGADNELGAEIAEEDIDEVQGAIDSIPVheVDAFLVVSGLGGGTGSGGAPVLAKHLKRIY-TEPVYGLG 135
                                       ********************************86544499***************************9.778***** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHC CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlk 194
                                       vlP ++ e+ ++  na+ + +++++e+d ++v+dNda+ k
  gi|313125417|ref|YP_004035681.1| 136 VLPGGD-EGGIYTLNAARSFQTFVREVDNLMVFDNDAWRK 174
                                       ***998.******************************976 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   4.9e-06     0.029     154     220 ..      97     153 ..      72     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-06
                         Tubulin_2 154 eglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvfplnkeggervkaNayaa 220
                                       e+  + Vv++L GGTGSG +  +a  l+ i+ e       +gl +lP       ++g  + +Na+++
  gi|313125417|ref|YP_004035681.1|  97 EVDAFLVVSGLGGGTGSGGAPVLAKHLKRIYTEPV-----YGLGVLPGG-----DEGGIYTLNAARS 153
                                       445678*************9999999999998754.....577777775.....3456666666665 PP

>> Mu-like_Pro  Mu-like prophage I protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.7e-05      0.22     106     147 ..     335     377 ..     330     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.7e-05
                       Mu-like_Pro 106 tgevle.llsaALTntPaldgmeelaalaaateqeeekekeee 147
                                       +g+v   +l  ++Tn P+++ ++++a  a+++ +e ++e+e++
  gi|313125417|ref|YP_004035681.1| 335 SGKVASvILLSGVTNVPRIKELQQVAIEAQENIDEIQQESEQN 377
                                       677765167789***************9999999999997653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2415.66
//
Query:       gi|313125418|ref|YP_004035682.1|  [L=300]
Description: nucleoside-diphosphate sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-28   97.9   0.0    8.9e-28   97.4   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    1.9e-19   70.1   0.0    1.2e-18   67.5   0.0    2.1  1  Epimerase        NAD dependent epimerase/dehydratase family
      1e-13   50.9   0.0    4.5e-12   45.6   0.0    2.2  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.5e-13   50.5   0.0    6.6e-12   45.1   0.0    2.2  1  RmlD_sub_bind    RmlD substrate binding domain
    2.4e-11   43.6   0.0    3.1e-11   43.3   0.0    1.1  1  NmrA             NmrA-like family
    7.6e-07   28.8   0.0    1.3e-05   24.8   0.0    2.2  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      8e-06   25.2   0.0     0.0063   15.7   0.0    2.2  2  NAD_binding_4    Male sterility protein
      6e-05   22.3   0.2    0.00035   19.8   0.2    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00037   20.7   0.0     0.0027   17.9   0.0    2.0  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0019   18.2   0.0      0.003   17.6   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0063   16.9   0.0      0.014   15.8   0.0    1.6  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
      0.015   15.8   0.0      0.041   14.4   0.0    1.7  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.021   14.8   0.0       0.44   10.4   0.0    2.1  2  KR               KR domain
      0.022   15.2   0.0      0.044   14.2   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      0.037   13.5   0.0      0.074   12.5   0.0    1.4  1  adh_short        short chain dehydrogenase
      0.043   13.9   0.0      0.069   13.3   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.0   7.9e-31   8.9e-28       1     147 [.       7     151 ..       7     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 7.9e-31
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-......... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal......... 68 
                                       G++G vG  l++el +r ghevtal R+p++ + l+  +g++ + g+vt  +++++a++g daV+  +         
  gi|313125418|ref|YP_004035682.1|   7 GGSGFVGTNLCRELKER-GHEVTALSRSPSSDE-LP--KGVNKTMGNVTVYDSIKDAFEGMDAVYNLValsplfkps 79 
                                       9****************.5************76.87..7*************************8777779999885 PP

                                       --TCC.....HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEE CS
                    NAD_binding_10  69 ggggk.....deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTi 140
                                       g g++      ++g++n+v+aa++++v Rfv +sa+g++            +   ay++ak +ae+++ +s ldwTi
  gi|313125418|ref|YP_004035682.1|  80 G-GNEmhdkvHRHGTENVVRAAEKHEVDRFVQMSALGADP-----------DGPTAYIRAKGEAEQIVTESVLDWTI 144
                                       3.333454445555************************93...........34568********************* PP

                                       EEE-CEE CS
                    NAD_binding_10 141 vrpggLt 147
                                        rp+ + 
  gi|313125418|ref|YP_004035682.1| 145 FRPSVIF 151
                                       ***9875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0     1e-21   1.2e-18       1     241 []       3     209 ..       3     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1e-21
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       +lV+G++Gf+G++l+++l+e+g+ev++l+r +s+++  +   ++ + +++t  ++++++f+  ++dav++l a +  
  gi|313125418|ref|YP_004035682.1|   3 VLVVGGSGFVGTNLCRELKERGHEVTALSRSPSSDELPK--GVNKTMGNVTVYDSIKDAFE--GMDAVYNLVALSPL 75 
                                       79*****************************77777554..558889**************..9*******998888 PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                          s  ++   + + +gt n++ aa k++v+r++++s     G+d++ p             ++Y +aK  +e++v+
  gi|313125418|ref|YP_004035682.1|  76 FKPSGGNEMHDKVHRHGTENVVRAAEKHEVDRFVQMSA---LGADPDGP-------------TAYIRAKGEAEQIVT 136
                                       887777777777999**********************9...77666632.............48************* PP

                                       HHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                       +      l+ +i+r++ ++G + ++ ++ + + p ++           l g g+ + + lyv+Dv+ ++  ++e  d
  gi|313125418|ref|YP_004035682.1| 137 ES----VLDWTIFRPSVIFGDGgEFVSFTKLLAPPYV---------SALPGGGKTRFQPLYVDDVVGMMADAIED-D 199
                                       75....5777************444444333333333.........357899**********************9.3 PP

                                       T-STTEEEEES CS
                         Epimerase 231 agdkgeiyniG 241
                                       a   ge y iG
  gi|313125418|ref|YP_004035682.1| 200 A-HIGERYEIG 209
                                       3.568999998 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0     4e-15   4.5e-12       1     118 [.       4     115 ..       4     119 .. 0.87
   2 ?    3.1   0.0     0.035        39     145     224 ..     123     191 ..     116     199 .. 0.62

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 4e-15
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +v+Gg+GF+G +l++eL ++++  ev +  l  sp+  e  + vn +    g vt  d++++a eg+d+v  l +l+
  gi|313125418|ref|YP_004035682.1|   4 LVVGGSGFVGTNLCRELKERGH--EVTA--LSRSPSSDELPKGVNKT---MGNVTVYDSIKDAFEGMDAVYNLVALS 73 
                                       69***************99996..6655..66777775555555555...9************************** PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsae 118
                                       ++++    ++  +kv  +GT+nv+ a+ k++v ++v +S+++
  gi|313125418|ref|YP_004035682.1|  74 PLFKpSGGNEMHDKVHRHGTENVVRAAEKHEVDRFVQMSALG 115
                                       ****677788889***********************999865 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.035
                         3Beta_HSD 145 aypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglalfkigdeevlsdrvYvgNv 221
                                       ay + K  aE++v ++                Rp++i+G+g ++++ +  +l+   +     g  ++ +++ Yv+ v
  gi|313125418|ref|YP_004035682.1| 123 AYIRAKGEAEQIVTESVL---------DWTIFRPSVIFGDGGEFVS-FT-KLLAPPYVSALPGGGKTRFQPLYVDDV 188
                                       566667777777766543.........234689******9987653.33.333333344444555555666777666 PP

                         3Beta_HSD 222 awa 224
                                       + +
  gi|313125418|ref|YP_004035682.1| 189 VGM 191
                                       655 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   5.9e-15   6.6e-12       1     241 [.       1     236 [.       1     241 [. 0.87

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 5.9e-15
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.............T--TTSHHHHHHHHHHH--SEEEE------H CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.............eldltdaeavaellkeakpdvvvnaAAytav 64 
                                       mk+lv+G++G +G++L ++l+e+g+ev+al+r+               ++t  ++++++++    d+v+n+ A    
  gi|313125418|ref|YP_004035682.1|   1 MKVLVVGGSGFVGTNLCRELKERGHEVTALSRSpssdelpkgvnktMGNVTVYDSIKDAFEG--MDAVYNLVALSPL 75 
                                       89******************************999999999888877788888888888887..899********** PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH- CS
                     RmlD_sub_bind  65 DkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaag 140
                                       +k    +e   +v  +++e++ +aa+++++  ++++S      G         d+ +P ++Y r+K + Eq v +++
  gi|313125418|ref|YP_004035682.1|  76 FKPSGGNEMHDKVHRHGTENVVRAAEKHEVdRFVQMSAL----G--------ADPDGP-TAYIRAKGEAEQIVTESV 139
                                       *****************************9569999973....4........477788.589*************** PP

                                       SSEEEEEE-SEESSSSS-HHHHHHHHH.HH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS CS
                     RmlD_sub_bind 141 kkalivRtswvygekgknfvktmlrla.kereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlaneg 216
                                        +++i+R s+++g+ g +fv+    la      l        +P +++d+  ++++++e  a+   + + y +++ +
  gi|313125418|ref|YP_004035682.1| 140 LDWTIFRPSVIFGD-GGEFVSFTKLLApPYVSALPGGGKTRFQPLYVDDVVGMMADAIEDDAH---IGERYEIGGPD 212
                                       *************9.667887766666456677777788888999999999999999999887...88999999999 PP

                                       -EEHHHHHHHHHHHHCHTTSEEEEE CS
                     RmlD_sub_bind 217 etswlefArailkeagadseevkpi 241
                                       +++ +e+A+ i k+ g + + + pi
  gi|313125418|ref|YP_004035682.1| 213 KLTLAEIAKMIHKSNGRS-TTIVPI 236
                                       999999999998887764.466666 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   2.7e-14   3.1e-11       1     228 [.       3     230 ..       3     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2.7e-14
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.. CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.. 75 
                                       +lv+G++G  G  + r l ++gh+v al R ++s+++     +Gv+   g++  ++s++ a++g d+v+  +++   
  gi|313125418|ref|YP_004035682.1|   3 VLVVGGSGFVGTNLCRELKERGHEVTALSRSPSSDELP----KGVNKTMGNVTVYDSIKDAFEGMDAVYNLVALSpl 75 
                                       79******************************999986....5888889999999*****************99899 PP

                                       ..........S-HHHHH.HHHHHHHHHHS-SEEEE.EE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEE CS
                              NmrA  76 ..........skeiedg.kklvdAakeaGvkhfiy.SslgddndrsnaeepavphfdsKaeieeyvralgipytfvy 140
                                                 +k  + g  ++v+Aa +  v +f+  S lg+d d             +K e e+ v ++ +  t+++
  gi|313125418|ref|YP_004035682.1|  76 fkpsggnemhDKVHRHGtENVVRAAEKHEVDRFVQmSALGADPDGP------TAYIRAKGEAEQIVTESVLDWTIFR 146
                                       9****8888633334452589*************626666666444......345589******************* PP

                                       E-EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHH CS
                              NmrA 141 agffmenflsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgnei 217
                                       + +  +    ++    ++ +app    +l+g g++   +l  ++D+  +++ +++d + +  ++     + l++ ei
  gi|313125418|ref|YP_004035682.1| 147 PSVIFGDGGEFVSF--TKLLAPPY-VSALPGGGKTRFQPL-YVDDVVGMMADAIEDDAHIGERYEIGGPDKLTLAEI 219
                                       98877777665544..78899997.889999999999999.*******************8888888889******* PP

                                       HHHHHHHHTS- CS
                              NmrA 218 velfekkigkt 228
                                       ++++ k  g++
  gi|313125418|ref|YP_004035682.1| 220 AKMIHKSNGRS 230
                                       *******9986 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.2e-08   1.3e-05       1     128 [.       4     112 ..       4     114 .. 0.85
   2 ?    1.5   0.0      0.14   1.6e+02     224     273 ..     183     226 ..     170     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.2e-08
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+ G++Gf+G +l++ L e+g+ev+ + r  ss +      l k  +           g++t  +s++++++ +  d
  gi|313125418|ref|YP_004035682.1|   4 LVVGGSGFVGTNLCRELKERGHEVTALSRSPSSDE------LPKGVN--------KTMGNVTVYDSIKDAFEGM--D 64 
                                       89************************999888844......433222........2356666677888899987..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEE CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaS 128
                                       +vynL A s   +     e   +v   Gt +++ a+ +++++   rf+q+S
  gi|313125418|ref|YP_004035682.1|  65 AVYNLVALSPLFKPSGGNEMHDKVHRHGTENVVRAAEKHEVD---RFVQMS 112
                                       **********99999999*******************99886...999988 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                                       EEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH CS
                     GDP_Man_Dehyd 224 ghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewe 273
                                       ++v+D+v +m  +++ d         ge +++++  +l+++e+ k i ++
  gi|313125418|ref|YP_004035682.1| 183 LYVDDVVGMMADAIEDDA------HIGERYEIGGPDKLTLAEIAKMIHKS 226
                                       79**********999987......58999999999999999998877654 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0021       2.4       2      50 ..       6      52 ..       5      67 .. 0.80
   2 !   15.7   0.0   5.6e-06    0.0063     153     209 ..     101     153 ..      82     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                                      E-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-H CS
                     NAD_binding_4  2 TGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkel 50
                                       G++GF+G+ L ++L ++    ++++l R+ s+++  + +++++ +  +
  gi|313125418|ref|YP_004035682.1|  6 VGGSGFVGTNLCRELKERGH--EVTALSRSPSSDELPKGVNKTMGNVTV 52
                                      6*************998887..8******99988877777666665555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 5.6e-06
                                       H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-- CS
                     NAD_binding_4 153 eegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitge 209
                                       e++e +  ++  ++  + + p++Y + K +aE++v e      l ++i+Rps+i g+
  gi|313125418|ref|YP_004035682.1| 101 EKHEVDRFVQMSALGADPDGPTAYIRAKGEAEQIVTESV----LDWTIFRPSVIFGD 153
                                       3344555566666777778899**************999....889********984 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   3.1e-07   0.00035       1     128 [.       3     113 ..       3     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.1e-07
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlv G++G +G +l+r++ + + +++  l+r+  + +e+ k +              +++g+v+  +++++a+e  +
  gi|313125418|ref|YP_004035682.1|   3 VLVVGGSGFVGTNLCRELKE-RGHEVTALSRSPSS-DELPKGV-------------NKTMGNVTVYDSIKDAFE--G 62 
                                       8999***********99755.56778888887543.3333332.............2348**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHH..HHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNv..lgtenvieaaieagvkkvvliSt 128
                                       +d+v++  Al   Pl      + ++  v  +gtenv++aa +++v+++v +S+
  gi|313125418|ref|YP_004035682.1|  63 MDAVYNLVALS--PLFKPSGGNEMHDKVhrHGTENVVRAAEKHEVDRFVQMSA 113
                                       *********97..555554444444444227*******************995 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.4e-06    0.0027       6      63 ..       8      70 ..       4      75 .. 0.82
   2 ?    0.1   0.0      0.74   8.3e+02      11      44 ..      81     114 ..      80     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.4e-06
                                      --SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT......EEE-SSHHHHHHHCSEEEE-S CS
                     NAD_binding_2  6 GlGvMGsnmalnllkagykvavynrtkekveelvaeg......akaaesieelvasldvvitmv 63
                                      G G  G+n++++l+++g++v++  r++++ +el +        +++++si+++++++d+v  +v
  gi|313125418|ref|YP_004035682.1|  8 GSGFVGTNLCRELKERGHEVTALSRSPSS-DELPKGVnktmgnVTVYDSIKDAFEGMDAVYNLV 70
                                      7899*********************9754.3333332344788****************98877 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEE CS
                     NAD_binding_2  11 Gsnmalnllkagykvavynrtkekveelvaegak 44 
                                       G++m  ++ ++g + +v   +k +v+++v+  a 
  gi|313125418|ref|YP_004035682.1|  81 GNEMHDKVHRHGTENVVRAAEKHEVDRFVQMSAL 114
                                       8899999999999999999999999999998754 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.7e-06     0.003       1      36 [.       6      41 ..       6      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                    Glyco_transf_4  1 vGGverhvleLaraLarrGheVtvvtpgddgpleee 36
                                      vGG + +  +L+r+L +rGheVt ++++++ ++  +
  gi|313125418|ref|YP_004035682.1|  6 VGGSGFVGTNLCRELKERGHEVTALSRSPSSDELPK 41
                                      69999999*****************99988776655 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-05     0.014       1      70 [.       2      66 ..       2      72 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEE CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdiv 70
                                      kv +vG++G vG++l r L+e    e+++l+ s +   +  + ++k   +  +++v d  +++++++d v
  gi|313125418|ref|YP_004035682.1|  2 KVLVVGGSGFVGTNLCRELKER-GHEVTALSRSPS-SDELPKGVNK---TMGNVTVYDSIKDAFEGMDAV 66
                                      799*****************93.345666555555.4444444433...566777877777888888876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.7e-05     0.041       2      34 ..       4      36 ..       2      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                      +vv G+G++g  l  +l+e g++Vt + rs+  
  gi|313125418|ref|YP_004035682.1|  4 LVVGGSGFVGTNLCRELKERGHEVTALSRSPSS 36
                                      355567**********************99764 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00039      0.44       3      39 ..       3      38 ..       2      58 .. 0.82
   2 ?    2.0   0.0      0.15   1.7e+02     114     138 ..      91     115 ..      82     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                                      EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--H CS
                                KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaade 39
                                      +l++GG G +G+ l+r l e+g  ++  lsRs+++de
  gi|313125418|ref|YP_004035682.1|  3 VLVVGGSGFVGTNLCRELKERGH-EVTALSRSPSSDE 38
                                      69********************7.5888999965443 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                                       HHHHHHHHHTTTS--SEEEEEEEHH CS
                                KR 114 kGawnLhelledesldffvlfSSia 138
                                       +G++n+ ++ e++++d fv +S ++
  gi|313125418|ref|YP_004035682.1|  91 HGTENVVRAAEKHEVDRFVQMSALG 115
                                       69******************99765 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.9e-05     0.044       1      34 [.       7      40 ..       7      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                   Glyco_trans_4_4  1 gGigryvaelaraLaarGheVtvltpapapgape 34
                                      gG+g +  +l+r+L +rGheVt l ++p  ++ +
  gi|313125418|ref|YP_004035682.1|  7 GGSGFVGTNLCRELKERGHEVTALSRSPSSDELP 40
                                      899999*******************988877654 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.6e-05     0.074       3      36 ..       3      36 ..       1      71 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-05
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseek 36
                                      vlv+G+s+ +G ++++el ++G +v++++rs++ 
  gi|313125418|ref|YP_004035682.1|  3 VLVVGGSGFVGTNLCRELKERGHEVTALSRSPSS 36
                                      9***************************999764 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.1e-05     0.069       1      70 [.       1      65 [.       1     109 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.1e-05
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SE CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadv 70
                                      +kv+vvG sG +G+++++ ++e +++e++a   +++s     ++ + ++++  +v+v+d++++++e  d 
  gi|313125418|ref|YP_004035682.1|  1 MKVLVVGGSGFVGTNLCRELKE-RGHEVTALSRSPSS----DELPKGVNKTMGNVTVYDSIKDAFEGMDA 65
                                      89*******************9.99999998888774....55555556666679999999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 1680.99
//
Query:       gi|313125419|ref|YP_004035683.1|  [L=199]
Description: thymidylate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-38  130.0   0.0    9.6e-38  129.7   0.0    1.1  1  Thymidylate_kin  Thymidylate kinase
    1.7e-06   28.0   0.0    2.3e-06   27.6   0.0    1.2  1  dNK              Deoxynucleoside kinase
    2.7e-06   27.6   0.0    5.2e-06   26.7   0.0    1.5  1  AAA_33           AAA domain
    0.00057   20.2   0.2    0.00074   19.8   0.2    1.2  1  AAA_28           AAA domain
    0.00085   19.9   0.0     0.0023   18.5   0.0    1.8  1  AAA_18           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7   0.0   2.7e-41   9.6e-38       1     184 [.       5     184 ..       5     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 2.7e-41
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpal 77 
                                       +EGlDG+GKtt  e+l + ++++     +trep+++ +G+ + ++++  e+ ++++e++lf+ad+++hl++++ pal
  gi|313125419|ref|YP_004035683.1|   5 LEGLDGSGKTTAWEALHDVYPDAV----FTREPTESWYGDAVYRSMS-DEDADSLAELFLFTADHADHLSRVVRPAL 76 
                                       6********************988....9****************99.99*************************** PP

                                       HTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTS......E-SEEEEEESSHHHHHTSCCTTSSTTTSHHHH CS
                   Thymidylate_kin  78 kqgktvivdRylfSslaYqgakegvdldlvlslnedvll......kPdltflldvdpevalkRlakrdeldeeeeeq 148
                                       +++k+vi+dRy +S  aYq+a+ + d+dl + l +  +        Pd+t++ldvdpe+a++R++++++     +e+
  gi|313125419|ref|YP_004035683.1|  77 ADDKLVISDRYSDSRFAYQAATLE-DADLRRPLDYIRGIhaafsrPPDATIFLDVDPETAAARAGATNK-----FER 147
                                       ********************9764.666655555443334444569***********************.....*** PP

                                       HHHHHHHHHHHHHHHH.TTSTEEEEETTS-HHHHHHH CS
                   Thymidylate_kin 149 ldflrkvrerylelak.ederiliidasksieevhee 184
                                        ++lr+v+++y +l++ e+er++ ida+++ e+v+e+
  gi|313125419|ref|YP_004035683.1| 148 ASYLREVKANYERLIDaEPERFVRIDATQPPEDVVEM 184
                                       **********************************987 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   6.4e-10   2.3e-06       1     169 [.       3     164 ..       3     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.4e-10
                                       EEEEESTTSSHHHHHHHHHCCST.CEEEE-HHHHCCSSSSHHHHHHHHSHHHHH..HHHHHHHHHHHHHHHHCHHSS CS
                               dNK   1 ivveGnIgaGKstlvklLskklg.vkvfeEpvdkwtnvqknlLekfYkdpsrws..falqtyvllsrlkqqlealat 74 
                                       i++eG  g+GK+t  + L++ ++  ++ +Ep + w    + + ++  +d+  ++  f +      +  ++   ala 
  gi|313125419|ref|YP_004035683.1|   3 ITLEGLDGSGKTTAWEALHDVYPdAVFTREPTESW-YGDAVYRSMSDEDADSLAelFLFTADHADHLSRVVRPALAD 78 
                                       789*******************9899999******.33445666666666666633444445555555555556677 PP

                                       S-EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH.-SEEEEEE--HHHHHHHHHHCTTCCCTT CS
                               dNK  75 kqvvvleRsiysdryiFakalaekgtlseeelkiykelldnlleelak.pdlliYLkasletclerikkRgreeekk 150
                                       ++ v+ +R  ysd       +++  tl++ +l    +    +   +++ pd  i+L++++et   r    ++ e   
  gi|313125419|ref|YP_004035683.1|  79 DKLVISDR--YSDS----RFAYQAATLEDADLRRPLDYIRGIHAAFSRpPDATIFLDVDPETAAARAGATNKFE--- 146
                                       78888887..6776....55567788888888887777777777778879**************9988877777... PP

                                       S-HHHHHHHHHHHHHHHTS CS
                               dNK 151 ieldYlekLhekyeewlkk 169
                                          +Yl++++ +ye  ++ 
  gi|313125419|ref|YP_004035683.1| 147 -RASYLREVKANYERLIDA 164
                                       .789*********998765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.4e-09   5.2e-06       1     120 [.       2     144 ..       2     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.4e-09
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.avllssdt.......lrrrlfgtdqqsktdytrvldrlyqilnelarkalsa 69 
                                       l+ l Gl GsGK+t  e l+   + av+ +++t       ++r +  +d +s+ ++  ++ +  ++l++++r al+ 
  gi|313125419|ref|YP_004035683.1|   2 LITLEGLDGSGKTTAWEALHDVYPdAVFTREPTeswygdaVYRSMSDEDADSLAELFLFTADHADHLSRVVRPALAD 78 
                                       68899*****************99*********99999999999999****************************** PP

                            AAA_33  70 grnvil...........datnlsrrerarflklarrlgvp.....vrivvvetdeetlkeRlakRaa 120
                                        + vi             at+ +++ r+ ++ +   +  +     ++ +++++d+et+++R  + ++
  gi|313125419|ref|YP_004035683.1|  79 DKLVISdrysdsrfayqAATLEDADLRRPLDYIRGIHA-AfsrppDATIFLDVDPETAAARAGATNK 144
                                       ******66654444433333333444433333322111.1233348999999999999999877665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   2.1e-07   0.00074       2     144 ..       3     164 ..       2     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.1e-07
                            AAA_28   2 ivitGgestGKTtlleaLaar..gypvvpEaareileeklakge.dalpwv.edllafaervleeqleeeaaa.aan 73 
                                       i + G  ++GKTt  eaL++   + +  +E+    + +   +   d+ +++ ++l  f +   ++  +  + a a++
  gi|313125419|ref|YP_004035683.1|   3 ITLEGLDGSGKTTAWEALHDVypDAVFTREPTESWYGDAVYRSMsDEDADSlAELFLFTADHADHLSRVVRPAlADD 79 
                                       6677889************88443334478777777777633320222222355666666666666666666689** PP

                            AAA_28  74 kvlfcDrglldtlaYaraygge..aeaelea....aarekr.ydlvfllppapei.......dddgeRredleerea 136
                                       k++++Dr +   +aY  a  ++    ++l+     +a+++r  d+ ++l+++pe+       ++  eR   l+e +a
  gi|313125419|ref|YP_004035683.1|  80 KLVISDRYSDSRFAYQAATLEDadLRRPLDYirgiHAAFSRpPDATIFLDVDPETaaaragaTNKFERASYLREVKA 156
                                       ***************98887764455556656688777777578899999999664432232333445555666666 PP

                            AAA_28 137 iderlrea 144
                                        +erl++a
  gi|313125419|ref|YP_004035683.1| 157 NYERLIDA 164
                                       66666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.3e-07    0.0023       1     111 [.       3     140 ..       3     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.3e-07
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss........ 69 
                                       I l G  G+GKtt  ++L      ++++ d ++ +++ +++  +    ++ + ++  d+l +++   ++        
  gi|313125419|ref|YP_004035683.1|   3 ITLEGLDGSGKTTAWEAL------HDVYPDAVFTREPTESWYGD--AVYRSMSDEDADSLAELFLFTADhadhlsrv 71 
                                       899***************......788*****************..9999999999999999999988888899999 PP

                            AAA_18  70 ...aleegknlvidghlaeleseaakdikk.........................vvLtaspeelleRle 111
                                          al++ k  vi+++ ++ +++++                              ++L+++pe+ + R  
  gi|313125419|ref|YP_004035683.1|  72 vrpALADDKL-VISDRYSDSRFAYQAATLEdadlrrpldyirgihaafsrppdatIFLDVDPETAAARAG 140
                                       9985444444.66666666655555433335777777888888888888888888999999999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1171.00
//
Query:       gi|313125420|ref|YP_004035684.1|  [L=106]
Description: hypothetical protein Hbor_06450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   11.7   6.1       0.21   11.5   6.1    1.1  1  YqhR      Conserved membrane protein YqhR
        7.2    4.8   8.1        7.8    4.7   8.1    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   6.1   2.3e-05      0.21      69     131 ..       4      71 ..       1      92 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.3e-05
                              YqhR  69 visivligvvsigvallyyvllk....kikslwagilyGvvlwllvfyvlnPlfPdvkava.eleknt 131
                                       v+ +vl gvv ++ +l+  v+ +    ++k+ w  ++y + l  +v++v   +f ++ ++  +l  +t
  gi|313125420|ref|YP_004035684.1|   4 VLNLVLFGVVLVVHTLIAAVMTRffriRLKTQWGYVIYSLLLIPVVLFVTTLVFSGILQIGpDLGDTT 71 
                                       667888888877766665554433324899*************************9988842555444 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   8.1   0.00087       7.8      40     110 ..       6      84 ..       1      94 [. 0.66

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.00087
                           DUF2070  40 gillfglpalvaflltlpvlrilggrltykrslflalltelivviisllaillsall......qalvllalvls..l 108
                                        ++lfg+ ++v +l+   + r++++rl++++ +++  l +++vv++++  ++  +l        + + + ++++  l
  gi|313125420|ref|YP_004035684.1|   6 NLVLFGVVLVVHTLIAAVMTRFFRIRLKTQWGYVIYSLLLIPVVLFVTTLVFSGILQigpdlgDTTTAFGVMIGmpL 82 
                                       67899*********************999999877777777777766666665544467444423333333333223 PP

                           DUF2070 109 al 110
                                       al
  gi|313125420|ref|YP_004035684.1|  83 AL 84 
                                       33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 641.45
//
Query:       gi|313125421|ref|YP_004035685.1|  [L=357]
Description: pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase component subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-71  239.8   0.0    3.9e-71  239.4   0.0    1.1  1  E1_dh            Dehydrogenase E1 component
    5.8e-05   22.2   0.0    9.1e-05   21.6   0.0    1.3  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    0.00074   18.8   0.0     0.0014   17.9   0.0    1.3  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
      0.002   17.9   1.4      0.027   14.2   0.3    2.6  2  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.4   0.0   8.8e-75   3.9e-71       4     295 ..      36     317 ..      33     321 .. 0.94

  Alignments for each domain:
  == domain 1  score: 239.4 bits;  conditional E-value: 8.8e-75
                                       HHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TTTS CS
                             E1_dh   4 vllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvkgk 80 
                                       ++ +r +d+++  ++r + ++ y +  gqea +vg+a+a+ ++D+++++YR     +arg+++  ila  +g++++ 
  gi|313125421|ref|YP_004035685.1|  36 MIRTRRFDERALALQRRGWMSGYPPFLGQEASQVGAAHAMREDDMLFPTYRSNALQIARGVPMSDILAFRRGRAEY- 111
                                       6778999******************************************************************944. PP

                                       SGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEE CS
                             E1_dh  81 ggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifv 157
                                             l+++     ++++  ++++q pl+ G+ +aa + +++++ ++ +GDgA+++Gd++e+ln+a ++++pv+f+
  gi|313125421|ref|YP_004035685.1| 112 ------LSDHDI--PVFPQAVPIATQIPLATGAGMAANYSDDDHAILVCFGDGATSEGDFHEGLNFAGVFDAPVVFF 180
                                       ......443333..49999********************************************************** PP

                                       EEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTS CS
                             E1_dh 158 veNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHsesD 234
                                       +eNN ++is ++++++as+++a +a ++g  g++VdgnDplav+e v +A   ar g  p+l+e +tYR g H++ D
  gi|313125421|ref|YP_004035685.1| 181 CENNAWAISLPRDRQTASDSIAVKAEAYGFEGVQVDGNDPLAVRETVSEALSDARDG-NPILVESLTYRQGAHTTAD 256
                                       *******************************************************96.6****************** PP

                                       HSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS- CS
                             E1_dh 235 dpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskk 295
                                       dps+yr  +     +  +dp++r++e+L ++g++++  ++ +++ v+ e +eav+++e+ +
  gi|313125421|ref|YP_004035685.1| 257 DPSAYRDGDPDLPEWRVRDPVERYEEYLREEGIIDDAFVESVREDVEDELKEAVERVEELP 317
                                       ******776555666666***************************************9976 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     2e-08   9.1e-05     135     240 ..     142     243 ..     120     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2e-08
                                       H-BTTB-S----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGG.GT--S-HHHHHHHTT-EE CS
                   Transketolase_N 135 ynkpgfdivdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGete.isftedvakrfeaygWhv 210
                                       y+       dh + v  gDg   eG  +e  ++ag+     ++ + ++n  +i    + ++ ++++a + eayg++ 
  gi|313125421|ref|YP_004035685.1| 142 YS-----DDDHAILVCFGDGATSEGDFHEGLNFAGVFDA-PVVFFCENNAWAISLPRDrQTASDSIAVKAEAYGFEG 212
                                       33.....3478999*********************9864.3555556776666654441566788999********9 PP

                                       EEETTTT-HHHHHHHHHHHHH-..TTS-EEEE CS
                   Transketolase_N 211 ievedgedveaikaaieeakae..kdkPslik 240
                                       ++  dg+d  a+++ ++ea ++     P l++
  gi|313125421|ref|YP_004035685.1| 213 VQ-VDGNDPLAVRETVSEALSDarDGNPILVE 243
                                       99.56777777777777775431034676665 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     3e-07    0.0014     114     176 ..     127     189 ..     109     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-07
                    DXP_synthase_N 114 stsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsis 176
                                       +t i  a+G  +a++++++++ ++   GDga + G  +e+ln +g  ++ ++    +N ++is
  gi|313125421|ref|YP_004035685.1| 127 ATQIPLATGAGMAANYSDDDHAILVCFGDGATSEGDFHEGLNFAGVFDAPVVFFCENNAWAIS 189
                                       689999*****************9********************************9999987 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   6.1e-06     0.027      31     152 ..     127     243 ..     120     244 .. 0.73
   2 ?   -1.9   0.0      0.58   2.6e+03     125     144 ..     293     311 ..     275     315 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-06
                                       TTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT.GGG.HHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTT CS
                      TPP_enzyme_C  31 GyglpaAiGakla....kpdrevvaivGDGgflmi.lqe.latavrrnlpitvvvlnNegygmtggqqepfggkrks 101
                                         ++p A+Ga +a    + d+ + +  GDG++    ++e l  a   ++p+++++ nN++         p+  ++  
  gi|313125421|ref|YP_004035685.1| 127 ATQIPLATGAGMAanysDDDHAILVCFGDGATSEGdFHEgLNFAGVFDAPVVFFCENNAWAIS-----LPRDRQT-- 196
                                       5689********645433468899999****99888666155555667788888888887622.....2333222.. PP

                                       TSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH...CSSSEEEEE CS
                      TPP_enzyme_C 102 gpagkdlkpvdfaklaealGakgarvekadveeleealkeal...ekkgpalie 152
                                       +       + ++a  aea+G +g++v+ +d+  ++e++ eal   + + p l+e
  gi|313125421|ref|YP_004035685.1| 197 AS------D-SIAVKAEAYGFEGVQVDGNDPLAVRETVSEALsdaRDGNPILVE 243
                                       21......2.57888**************************9886666677765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.58
                                       EEESSH.HHHHHHHHHHHHC CS
                      TPP_enzyme_C 125 arvekadveeleealkeale 144
                                       a ve+   e++e+ lkea+e
  gi|313125421|ref|YP_004035685.1| 293 AFVESV-REDVEDELKEAVE 311
                                       444443.4778888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2373.70
//
Query:       gi|313125422|ref|YP_004035686.1|  [L=135]
Description: hypothetical protein Hbor_06470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 833.36
//
Query:       gi|313125423|ref|YP_004035687.1|  [L=77]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-11   42.1   0.2    7.2e-11   41.9   0.2    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.2     4e-15   7.2e-11       1      73 [.       6      75 ..       6      77 .] 0.96

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 4e-15
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      v+v++  g+    e++ + ++el+ V+e++ v+G yd +++v ++ +    +  + k++ l+gv++t+t+i +
  gi|313125423|ref|YP_004035687.1|  6 VMVKTGAGE---SERLLAPIRELETVTEAHIVAGAYDVIAEVDAEEVYNVLQTASSKIQGLEGVTDTKTYISM 75
                                      788999899...***********************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 502.35
//
Query:       gi|313125424|ref|YP_004035688.1|  [L=227]
Description: k+ transporter, NAD-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-25   87.6   1.0    8.6e-25   87.3   0.5    1.5  2  TrkA_N           TrkA-N domain
    1.3e-07   31.4   0.9      2e-07   30.7   0.1    1.8  2  TrkA_C           TrkA-C domain
      4e-06   27.2   0.3      8e-06   26.2   0.1    1.6  2  NAD_binding_7    Putative NAD(P)-binding
    0.00037   20.1   0.0    0.00068   19.3   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00039   20.9   0.1      0.001   19.6   0.1    1.8  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00051   19.4   0.2    0.00082   18.7   0.2    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.001   18.4   0.2     0.0014   17.9   0.2    1.4  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0017   17.9   0.2     0.0086   15.7   0.0    2.2  3  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0025   17.7   0.1     0.0061   16.5   0.1    1.7  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0053   16.4   0.3     0.0077   15.9   0.3    1.3  1  DAO              FAD dependent oxidoreductase
      0.009   16.2   0.0       0.66   10.1   0.0    2.5  3  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.023   14.9   0.0    1.5  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
      0.012   15.3   0.1       0.02   14.6   0.1    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.016   14.7   0.0      0.032   13.7   0.0    1.5  1  CutC             CutC family
      0.027   14.7   0.2      0.043   14.1   0.2    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.031   13.5   0.1      0.033   13.4   0.1    1.2  1  FAD_binding_3    FAD binding domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.5   7.7e-28   8.6e-25       1     116 []       3     118 ..       3     118 .. 0.94
   2 ?   -3.3   0.0       9.2     1e+04      40      56 ..     143     159 ..     136     166 .. 0.57

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 7.7e-28
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       ++iiG GrvG + a+ L++++++v++++ d +r+e++re g+ev+ gd+++ee+Le+ag+++ada+ a+tgd  +n 
  gi|313125424|ref|YP_004035688.1|   3 FVIIGGGRVGLRTARVLRDEEHEVTIVELDTDRIERAREAGFEVIDGDGSREETLERAGVADADAIGALTGDLNVNF 79 
                                       79*****************5557****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHH..HTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkk..lgadvvisp 116
                                       +a+ + k+  ++++++ r++++ + e++kk    +d+v++p
  gi|313125424|ref|YP_004035688.1|  80 AACSIGKH--HGLRTVLRVDEDYRDEVYKKyaEEVDEVVYP 118
                                       ******95..5589*************99976779***997 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.2
                                       TTSEEEES-TTSHHHHH CS
                            TrkA_N  40 eglevvvgdatdeevLe 56 
                                       ++l+vv   +tde+ ++
  gi|313125424|ref|YP_004035688.1| 143 QNLQVVLMTVTDESPMR 159
                                       34556666666665555 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.3   4.8e+03      26      38 ..      12      26 ..      10      39 .. 0.53
   2 !   30.7   0.1   1.8e-10     2e-07       2      68 ..     148     214 ..     147     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.3
                                      S-EEEEEE-T..-EE CS
                            TrkA_C 26 gvlvvairRg..gel 38
                                      g + +++ R+   e+
  gi|313125424|ref|YP_004035688.1| 12 GLRTARVLRDeeHEV 26
                                      556666666644222 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.8e-10
                                       EEEEEE--GGGTTSBHHHHTHHHHS-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       v +tv+ +sp+ G ++ e+ l+   ++++a  + g+++ ip+ d+ Le GD+l v+++ + l  +r l
  gi|313125424|ref|YP_004035688.1| 148 VLMTVTDESPMRGYSIEEVALPG-QARILAFgKAGEQMGIPMRDDSLETGDRLAVLADFDVLGNVRQL 214
                                       6789*******************.*******7777*********************998887777665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   7.1e-09     8e-06       9      86 ..       2      89 ..       1     105 [. 0.72
   2 ?   -2.9   0.0       8.3   9.3e+03      77      94 ..     137     155 ..     135     159 .. 0.57

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.1e-09
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele.......elvk...laeeele.kdlegadlviaatddrelne 76
                                      + +++GgG+v++r +r l +++ +vt+v  ++ + +e       e ++    +ee+le + +++ad + a t d ++n 
  gi|313125424|ref|YP_004035688.1|  2 RFVIIGGGRVGLRTARVLRDEEHEVTIVELDT-DRIErareagfEVIDgdgSREETLErAGVADADAIGALTGDLNVNF 79
                                      679****************************4.4445233443333333323445554256999*************99 PP

                     NAD_binding_7 77 riaeaakarr 86
                                      + +   k  +
  gi|313125424|ref|YP_004035688.1| 80 AACSIGKHHG 89
                                      9888877555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.3
                     NAD_binding_7  77 riaeaakarri.lvnvadk 94 
                                       +ia+ a++ ++ l+ v+d+
  gi|313125424|ref|YP_004035688.1| 137 AIADIAQNLQVvLMTVTDE 155
                                       5677776655525555554 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.1e-07   0.00068       1      46 [.       1      46 [.       1      60 [. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.1e-07
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipi 46
                                      m+ ++iG G vGl ta vl    hev++v  d+ +++  ++  +++
  gi|313125424|ref|YP_004035688.1|  1 MRFVIIGGGRVGLRTARVLRDEEHEVTIVELDTDRIERAREAGFEV 46
                                      7889*********************************988876665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   8.9e-07     0.001       1      30 [.       2      31 ..       2      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.9e-07
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvver 30
                                      + v++GgG +gl  A +l++  ++Vt+ve 
  gi|313125424|ref|YP_004035688.1|  2 RFVIIGGGRVGLRTARVLRDEEHEVTIVEL 31
                                      579*************************95 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   7.3e-07   0.00082      30      93 ..       2      66 ..       1      72 [. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.3e-07
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHH.HHH-S CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaea.vkead 93
                                      + ++iGgG +Gl  +++ +  + +Vt+++++++r+e+ ++ g ++++   s ee+l++a v++ad
  gi|313125424|ref|YP_004035688.1|  2 RFVIIGGGRVGLRTARVLRDEEHEVTIVELDTDRIERAREAGFEVIDGDGSREETLERAgVADAD 66
                                      579***************************************99999988888888765366666 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.3e-06    0.0014       2      33 ..       2      33 ..       1     154 [. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE.TTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.leg 33
                                      + v+iGgG  Gl++a+ l+  +++vt+ve + +
  gi|313125424|ref|YP_004035688.1|  2 RFVIIGGGRVGLRTARVLRDEEHEVTIVElD-T 33
                                      5688888888888888888888888888742.3 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.7e-06    0.0086       7      54 ..       3      49 ..       1      75 [. 0.85
   2 ?   -0.9   0.0      0.96   1.1e+03      50      77 ..     134     161 ..     114     184 .. 0.76
   3 ?   -2.3   0.0       2.5   2.8e+03       9      28 ..     174     193 ..     166     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.7e-06
                                      EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEH CS
                              IlvN  7 iaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltv 54
                                       ++iG G  G   a+ lrd   +v++   +++  +++A+e+gfev++ 
  gi|313125424|ref|YP_004035688.1|  3 FVIIGGGRVGLRTARVLRDEEHEVTIVELDTD-RIERAREAGFEVIDG 49
                                      589*********************99877666.8***********864 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.96
                                       EEEEHHHHHHT-SEEEE-S-HHHHHHHH CS
                              IlvN  50 evltvaeavkkadvvmiliPDelqkevy 77 
                                       ++  +a+++++ +vv++ + De   + y
  gi|313125424|ref|YP_004035688.1| 134 SIRAIADIAQNLQVVLMTVTDESPMRGY 161
                                       5677889999999999999998766555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.5
                                       EES-SHHHHHHHHHHHHTT- CS
                              IlvN   9 viGyGsqGhaqalnlrdsgl 28 
                                       ++ +G  G+  +  +rd  l
  gi|313125424|ref|YP_004035688.1| 174 ILAFGKAGEQMGIPMRDDSL 193
                                       88999999999999999876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   5.5e-06    0.0061       4      44 ..       5      45 ..       2      79 .. 0.85
   2 ?   -2.1   0.0       2.8   3.1e+03      16      29 ..     138     151 ..      89     162 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.5e-06
                                      EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                      +iG G +G   a v+  +++eV++v+ +++++e+a+e+  +
  gi|313125424|ref|YP_004035688.1|  5 IIGGGRVGLRTARVLRDEEHEVTIVELDTDRIERAREAGFE 45
                                      9**********************************997655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                                       HHHHHTT-EEEEE- CS
                           3HCDH_N  16 avfasagleVvlvd 29 
                                        + ++++l+Vvl+ 
  gi|313125424|ref|YP_004035688.1| 138 IADIAQNLQVVLMT 151
                                       22233344444444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   6.9e-06    0.0077       2      28 ..       3      31 ..       2      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.9e-06
                                      EEEECTSHHHHHHHHHHHHTT...EEEEES CS
                               DAO  2 vviiGGGiiGlstAyeLarrg...Vtllek 28
                                       viiGGG +Gl tA+ L       Vt++e 
  gi|313125424|ref|YP_004035688.1|  3 FVIIGGGRVGLRTARVLR-DEeheVTIVEL 31
                                      79***************4.32358****95 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00059      0.66       3      46 ..       4      47 ..       2      70 .. 0.85
   2 ?    3.6   0.0     0.059        67      45      71 ..     134     160 ..      91     176 .. 0.74
   3 ?   -3.0   0.0       6.6   7.4e+03       9      27 ..     183     201 ..     182     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00059
                                      EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE- CS
                     NAD_binding_2  3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaa 46
                                       +iG G  G   a+ l +++++v++++++++++e++ ++g++++
  gi|313125424|ref|YP_004035688.1|  4 VIIGGGRVGLRTARVLRDEEHEVTIVELDTDRIERAREAGFEVI 47
                                      589***********************************996654 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.059
                                       E-SSHHHHHHHCSEEEE-SSSHHHHHH CS
                     NAD_binding_2  45 aaesieelvasldvvitmvkagkavde 71 
                                        +  i++++++l+vv++ v+++++++ 
  gi|313125424|ref|YP_004035688.1| 134 SIRAIADIAQNLQVVLMTVTDESPMRG 160
                                       456789999***********9998775 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.6
                                       HHHHHHHHHHHHTT-EEEE CS
                     NAD_binding_2   9 vMGsnmalnllkagykvav 27 
                                       +MG +m    l+ g ++av
  gi|313125424|ref|YP_004035688.1| 183 QMGIPMRDDSLETGDRLAV 201
                                       5999**9999999999887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.1e-05     0.023       1      27 [.       5      31 ..       5      36 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                      I+G+G  Gl +A+ L+++ ++v+++e 
  gi|313125424|ref|YP_004035688.1|  5 IIGGGRVGLRTARVLRDEEHEVTIVEL 31
                                      9***********************996 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.8e-05      0.02       2      56 ..       4      61 ..       3      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT..CEEEEEECE CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg..geeilrppe 56
                                      +i+G G +G   a  L    ++vt++  +  r+e+ +++G+++ + +  +ee+l+   
  gi|313125424|ref|YP_004035688.1|  4 VIIGGGRVGLRTARVLRDEEHEVTIVELDTdRIERAREAGFEVIDGDgsREETLERAG 61
                                      7***************99********99999***********9998866666655555 PP

>> CutC  CutC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.9e-05     0.032      91     153 ..     121     183 ..     100     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                              CutC  91 lGaltadgeiDlkaleklieaaegLgvtfHrAfDvvadpeealeqlielgvervLtsGqkssa 153
                                       lGa+ a++++    ++ +   a+ L+v++    D+++ + +++e++   g +r+L  G++ ++
  gi|313125424|ref|YP_004035688.1| 121 LGAIGAKNALLGGSIRAIADIAQNLQVVLMTVTDESPMRGYSIEEVALPGQARILAFGKAGEQ 183
                                       7999999999999*********************************************98665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   3.8e-05     0.043       2      63 ..       4      57 ..       3     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHH CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavL 63
                                      +iiG+G+vG  +a++l ++++   e+t+++ + ++ e++     +  fe i  d + +e  L
  gi|313125424|ref|YP_004035688.1|  4 VIIGGGRVGLRTARVLRDEEH---EVTIVELDTDRIERAR----EAGFEVIDGDGSREET-L 57
                                      8***************99876...6**********88885....4455555555555444.4 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.9e-05     0.033       5      61 ..       4      65 ..       1     144 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                                      EEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEH.....HHHHHHHHTT-HHH CS
                     FAD_binding_3  5 lIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnq.....rtmellrqlGledr 61
                                      +I+G+G +Gl +a++L+    +v++ve  +++++  r  g++         e+l+ +G++d 
  gi|313125424|ref|YP_004035688.1|  4 VIIGGGRVGLRTARVLRDEEHEVTIVELDTDRIERAREAGFEVidgdgSREETLERAGVADA 65
                                      7******************99******99999999987776642222123355555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1415.60
//
Query:       gi|313125425|ref|YP_004035689.1|  [L=76]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-09   36.3   0.2      5e-09   36.0   0.2    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0013   18.7   0.4     0.0014   18.6   0.4    1.1  1  GYD             GYD domain
  ------ inclusion threshold ------
      0.063   13.4   0.6      0.078   13.1   0.6    1.3  1  IF-2            Translation-initiation factor 2
       0.12   12.8   0.0       0.16   12.4   0.0    1.2  1  HAMP            HAMP domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.2   1.1e-12     5e-09       1      73 [.       6      75 ..       6      76 .] 0.88

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.1e-12
                                      EEEEE-GGGTTHHHHHHHHHHT.STTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealae.lpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      v+v+ + g+   +++++e + +  + V+++  v+Gd d+++k+ v++ ++  ++    ++++ g++rt+t+i++
  gi|313125425|ref|YP_004035689.1|  6 VMVKASTGD---VDRLKESMLNlDDGVKSVSIVAGDVDFIVKADVESPAEVKTIAAS-IHEMSGIERTQTYIAM 75
                                      567777777...88888888873468****************************999.**************99 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.4   3.1e-07    0.0014      16      82 ..       9      75 ..       3      76 .] 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.1e-07
                               GYD 16 kdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslala.asGtvrtetlraf 82
                                      k s+ ++++ ke +  +l+  ++s+ ++ G+ D++v  +++  +++ +++ +++ +sG  rt+t+ a+
  gi|313125425|ref|YP_004035689.1|  9 KASTGDVDRLKESM-LNLDDGVKSVSIVAGDVDFIVKADVESPAEVKTIAASIHeMSGIERTQTYIAM 75
                                      77888899999999.999999***************************99998625788888*99988 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   1.7e-05     0.078      17      63 ..       6      51 ..       2      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                                      EEEEESSHHHHHHHHHHHHCTT.SSTE.EEECEEEESSB-HHHHHHHH CS
                              IF-2 17 viikaDvqGsleAlkeaLekleseevk.vkvihsgvGaitesDvelas 63
                                      v++ka++ G ++ lke++ +l ++ vk v+++  +v+ i + Dve  +
  gi|313125425|ref|YP_004035689.1|  6 VMVKAST-GDVDRLKESMLNL-DDGVKsVSIVAGDVDFIVKADVESPA 51
                                      7899975.9************.5666659***************8754 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.5e-05      0.16       9      48 ..      14      64 ..       6      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                                      HHHHHHHHHHHHTTT...........BTSSTCCTTSSSHHHHHHHHHHHHH CS
                              HAMP  9 PLrrLaraarriaaG...........dldtrlpvsgrDEiGeLarafNaMl 48
                                       + rL++++ ++++G           d+ +  +v+++ E+ ++a+++ +M+
  gi|313125425|ref|YP_004035689.1| 14 DVDRLKESMLNLDDGvksvsivagdvDFIVKADVESPAEVKTIAASIHEMS 64
                                      578************9999999998877777999999**********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 481.62
//
Query:       gi|313125426|ref|YP_004035690.1|  [L=166]
Description: hypothetical protein Hbor_06510 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1178.46
//
Query:       gi|313125427|ref|YP_004035691.1|  [L=840]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-38  129.9  54.6    1.1e-36  126.2  24.6    4.4  4  MCPsignal     Methyl-accepting chemotaxis protein (MCP) signa
    9.2e-11   42.0  16.3      1e-09   38.6   0.9    5.5  5  HAMP          HAMP domain
    4.8e-09   36.4   0.0    4.8e-09   36.4   0.0    3.8  4  dCache_1      Cache domain
    5.3e-07   29.9  20.9       0.18   12.1   0.1    5.4  5  BLOC1_2       Biogenesis of lysosome-related organelles compl
    1.1e-06   28.8  37.7     0.0043   17.3   1.3    7.1  7  DUF948        Bacterial protein of unknown function (DUF948)
     0.0072   15.3  15.9      0.063   12.2   4.1    2.9  2  DUF677        Protein of unknown function (DUF677)
  ------ inclusion threshold ------
      0.013   15.7   2.7      0.013   15.7   2.7    5.5  5  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
      0.045   14.3  25.0      0.064   13.8   0.5    5.6  4  Syntaxin-6_N  Syntaxin 6, N-terminal
        0.1   12.6  27.3       0.59   10.2   3.1    5.2  5  DUF1664       Protein of unknown function (DUF1664)
       0.51   10.3   4.6         13    5.7   0.2    4.1  4  Cauli_AT      Aphid transmission protein
       0.52   10.2   3.2        0.4   10.5   0.4    2.1  2  LapA_dom      Lipopolysaccharide assembly protein A domain
       0.98    7.5  14.0       0.13   10.4   3.5    2.9  3  EzrA          Septation ring formation regulator, EzrA
        1.1    7.2   9.0        0.4    8.6   5.4    1.9  2  Prominin      Prominin
          3    5.6  18.0        2.6    5.9   8.4    2.6  2  V_ATPase_I    V-type ATPase 116kDa subunit family
        4.3    7.0   4.8         67    3.2   0.0    4.1  4  RPW8          Arabidopsis broad-spectrum mildew resistance pr
        5.3    6.1   8.2          1    8.5   1.7    2.6  3  Taxilin       Myosin-like coiled-coil protein
        7.1    5.2  11.9        3.1    6.4   0.7    3.5  4  Tweety        Tweety
        7.8    5.0  23.6        4.7    5.7  12.0    2.5  2  AAA_13        AAA domain


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.2   2.2e+03     111     156 ..     350     378 ..     315     389 .. 0.47
   2 !    9.0   8.1    0.0011       1.1      76     159 ..     423     499 ..     388     507 .. 0.68
   3 !  126.2  24.6   1.1e-39   1.1e-36       4     170 ..     505     678 ..     502     680 .. 0.94
   4 !    7.3   3.5    0.0038       3.8      60     100 ..     691     729 ..     687     783 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 111 etrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsa 156
                                       e r                  ++  +++e +++   + +a++e  +
  gi|313125427|ref|YP_004035691.1| 350 EMRD-----------------TLQRRIEESEETAATLERAADEYGE 378
                                       2222.................2222223333333333333333333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  76 EVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaase 152
                                       EV + Aer+a a++ +         +++++ ++ +++ + ++e ++ +++  ++l+ +++++a+++++v+eiaa ++
  gi|313125427|ref|YP_004035691.1| 423 EVGAFAERAAAASERVG-------VGTDEVSNASQQVSRSTQEITSGAADQLDTLQAVSDQTADLSATVEEIAAQAD 492
                                       55555555555554444.......34444444444444444444555667788899999999999999999999999 PP

                                       HHHHHHH CS
                         MCPsignal 153 eqsasie 159
                                       e+s+ ++
  gi|313125427|ref|YP_004035691.1| 493 ELSTLSK 499
                                       9998665 PP

  == domain 3  score: 126.2 bits;  conditional E-value: 1.1e-39
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHH CS
                         MCPsignal   4 aeeaseeAeeggkevanvvkqmeeieks.......skeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVV 73 
                                       ++e +e A   g+e+a++ +q e+++ +       +++i+ +++ id+ia+QTN+LALNA+iEA RAGe+G+GFaVV
  gi|313125427|ref|YP_004035691.1| 505 GDEGREAAMAVGQEMAEIADQAETVTARvsrldeeVSDIASVVDLIDDIAEQTNILALNASIEASRAGEAGEGFAVV 581
                                       56677888888999999998888888888888888****************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  74 AdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaa 150
                                       A+EV++LAe++a a+ +i + i+ + + + ++ve ++e ++ ve+g+e+++   +a++e v+ v++v++ v+ i  a
  gi|313125427|ref|YP_004035691.1| 582 ANEVKQLAEETAAATDDIGDSIESVRRATTEAVEEMDEMQSSVESGAETIDGGVDAIREAVDIVEDVDHGVHSIDEA 658
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 151 seeqsasieevnqaveevak 170
                                       ++ q+++ ++ ++ ++  a+
  gi|313125427|ref|YP_004035691.1| 659 TDSQATATQQAAERIDDAAS 678
                                       **********9999887766 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0038
                                       HHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..... CS
                         MCPsignal  60 AARAGeqGrGFaVVAdEVrkLAersaqaakeiealiieiqk 100
                                       AA A +q      VAdEV +LAe+++  a+ +e+    +  
  gi|313125427|ref|YP_004035691.1| 691 AAAAQQQTASLETVADEVDELAEQTQVLAERVETFT--VSD 729
                                       6778888888899*****************999876..444 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.9     1e-12     1e-09       2      53 .]     306     357 ..     305     357 .. 0.93
   2 ?    6.1   3.1     0.014        14      15      50 ..     378     416 ..     377     416 .. 0.86
   3 ?    0.8   0.0      0.64   6.4e+02      12      40 ..     451     497 ..     450     506 .. 0.62
   4 ?   -2.9   0.1       9.5   9.5e+03      13      39 ..     546     576 ..     540     576 .. 0.70
   5 ?   -0.4   0.1       1.6   1.6e+03       9      42 ..     700     713 ..     689     729 .. 0.62

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1e-12
                                       HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                              HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                       l r+++ +LrrL++ a+r+a+Gd d++l  ++ DE+G+L  +f +M+d L++
  gi|313125427|ref|YP_004035691.1| 306 LGRSTVVSLRRLRKRAERLADGDMDVDLSSRRVDEFGTLYNSFAEMRDTLQR 357
                                       689*******************888888888*******************96 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                                       HHHHHHTTTBTSST..CCTTSSSH.HHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtr..lpvsgrDE.iGeLarafNaMldr 50 
                                       +++++ aaGdl++r  ++  g+ E ++e++r fN+M+d+
  gi|313125427|ref|YP_004035691.1| 378 ETMDQAAAGDLTARmdPDAAGDAEaMAEIGRRFNRMMDE 416
                                       68999*********855558999988**********985 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.64
                                       HHHHHHHHHTTT................BTSSTCCT.T.SSSHHHHH CS
                              HAMP  12 rLaraarriaaG................dldtrlpv.s.grDEiGeL 40 
                                       +++r++++i +G                dl++++++     DE+ +L
  gi|313125427|ref|YP_004035691.1| 451 QVSRSTQEITSGaadqldtlqavsdqtaDLSATVEEiAaQADELSTL 497
                                       56777777777777766666666655666666655443355555555 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 9.5
                                       HHHHHHHHTTT....BTSSTCCTTSSSHHHH CS
                              HAMP  13 LaraarriaaG....dldtrlpvsgrDEiGe 39 
                                       +++ ++ ia+      l+++++ s+  E Ge
  gi|313125427|ref|YP_004035691.1| 546 VVDLIDDIAEQtnilALNASIEASRAGEAGE 576
                                       5566666676445666888999999999875 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHH CS
                              HAMP   9 PLrrLaraarriaaGdldtrlpvsgrDEiGeLar 42 
                                       +L+ +a                    DE++eLa+
  gi|313125427|ref|YP_004035691.1| 700 SLETVA--------------------DEVDELAE 713
                                       444444....................55555543 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   4.8e-12   4.8e-09       7     248 ..      49     270 ..      44     271 .. 0.77
   2 ?   -1.4   1.5       1.7   1.7e+03       4      43 ..     449     488 ..     446     513 .. 0.71
   3 ?   -1.4   0.1       1.7   1.7e+03      10      47 ..     584     625 ..     579     675 .. 0.56
   4 ?    0.7   0.7      0.38   3.8e+02       5      37 ..     691     723 ..     685     751 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.8e-12
                          dCache_1   7 aeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksn.pdisgvylvd. 81 
                                        +++l ++ae+ a+n+++++d+ e+ a++l+++  l    ++      ++++s+++ l   +    +d++++ +vd 
  gi|313125427|ref|YP_004035691.1|  49 KHDELRTIAELEAENLNEWVDTNEQRARMLSEHRGL----QS------DDPDSVDQSLLREHGQLpSDVYAIHYVDl 115
                                       57899*************************998655....44......46677776666544333156678877777 PP

                          dCache_1  82 adGqviassdpssppnlegtddpadrdwykealaggg.gkpvisdpyvdqtggkpvitiavpiyddsgkfiGvlaad 157
                                       + G+v+ s+  +++ +     d++d  w +  l++   +++ +s++y+  +gg   +++a+p+  ++ +   ++ + 
  gi|313125427|ref|YP_004035691.1| 116 ETGDVVRSTAGEMETKS---LDDVDITWQSGELDFSQsTDVAVSEVYR--NGGLQLVAFASPVPGTD-R---AVLLI 183
                                       8*****99999998776...58889999999999998999999**996..4599*********9864.4...45555 PP

                          dCache_1 158 ldldnlqdllsniklgetgyvfivdsdGniiahpdkdllgknlrdelkaq......ealekalakiesgvssvklng 228
                                        d+++  + +++    e++++ +v +dG+++++   + +       l+a       + l++a+a +  ++  v++  
  gi|313125427|ref|YP_004035691.1| 184 TDATQHAKAFREPV--ERSHTQVVREDGTVLFDRYGKNV-------LTAYrdgddtPGLDAAVAATDDKSGVVERAA 251
                                       67777777666543..669*************9653332.......222222333456999999999999******* PP

                          dCache_1 229 eeylvayapiptglgWylvv 248
                                       +e+ vayap+++ ++Wy++v
  gi|313125427|ref|YP_004035691.1| 252 DEQVVAYAPVKG-TDWYVLV 270
                                       ***9*******6.*****97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                          dCache_1   4 eeqaeeqllglaeqlanniedvldslenlaetlasnpslq 43 
                                        +q+ ++++++  ++a+++++  +  +++a + a+ ++++
  gi|313125427|ref|YP_004035691.1| 449 SQQVSRSTQEITSGAADQLDTLQAVSDQTADLSATVEEIA 488
                                       5788899999999999998888766555555555555544 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.7
                          dCache_1  10 qllglaeqlanniedvldsle....nlaetlasnpslqdlle 47 
                                       ++++lae++a++ +d  ds+e    +++e + ++ ++q+++e
  gi|313125427|ref|YP_004035691.1| 584 EVKQLAEETAAATDDIGDSIEsvrrATTEAVEEMDEMQSSVE 625
                                       555566666655555544433222244444444444444333 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.38
                          dCache_1   5 eqaeeqllglaeqlanniedvldslenlaetla 37 
                                       ++a +q+++++e++a+++++  ++ + lae++ 
  gi|313125427|ref|YP_004035691.1| 691 AAAAQQQTASLETVADEVDELAEQTQVLAERVE 723
                                       568888889999999999998888888887764 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.73   7.2e+02      22      55 ..     345     378 ..     333     385 .. 0.69
   2 !    9.3   0.3    0.0014       1.4      30      91 ..     432     494 ..     410     499 .. 0.77
   3 !    9.1   0.3    0.0016       1.6      32      80 ..     515     563 ..     510     566 .. 0.89
   4 !   12.1   0.1   0.00018      0.18       6      81 ..     584     659 ..     580     668 .. 0.88
   5 !    7.9   3.4    0.0037       3.7      30      88 ..     667     722 ..     660     726 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.73
                           BLOC1_2  22 yklLeklNeaasekykklkdvaaslekkleklne 55 
                                       y+   ++  + ++++++ ++ aa le+ ++++ e
  gi|313125427|ref|YP_004035691.1| 345 YNSFAEMRDTLQRRIEESEETAATLERAADEYGE 378
                                       5666666777777777777777777777666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                        aase++   +d+++++++++++  ++     + +l+ ++++ +q+++L ++v+e+ +   eL
  gi|313125427|ref|YP_004035691.1| 432 AAASERVGVGTDEVSNASQQVSRSTQEITsGAADQLDTLQAVSDQTADLSATVEEIAAQADEL 494
                                       6777788777888888888877655544438999*********************99988887 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0016
                           BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       + ++ ++++d+a+ +++ +++l+e+   +++ ++ id+i +q++ L  +
  gi|313125427|ref|YP_004035691.1| 515 VGQEMAEIADQAETVTARVSRLDEEVSDIASVVDLIDDIAEQTNILALN 563
                                       56788999**********************************9988755 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00018
                           BLOC1_2   6 kvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                       +v+++ e++ +at +  + +e + +a++e +++++++ +s+e+ +e ++   +++++ ++ +++++  v ++ ea 
  gi|313125427|ref|YP_004035691.1| 584 EVKQLAEETAAATDDIGDSIESVRRATTEAVEEMDEMQSSVESGAETIDGGVDAIREAVDIVEDVDHGVHSIDEAT 659
                                       5666666777777777799**************************************************9999876 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0037
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                       ++a+e++++ +++aa++++++e++ +   + q++  +++ + ++v+eL e  ++L e +
  gi|313125427|ref|YP_004035691.1| 667 QQAAERIDDAASIAAQTHSESEQVAA---AAQQQTASLETVADEVDELAEQTQVLAERV 722
                                       67889999999999999999999887...888888888888899999988888887765 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.1   2.1e+03      25      47 ..     356     378 ..     339     386 .. 0.52
   2 !   12.2   0.0   0.00017      0.17      33      86 ..     401     454 ..     396     457 .. 0.94
   3 !   16.2   1.5   9.2e-06    0.0091      23      87 ..     423     487 ..     409     489 .. 0.76
   4 !    6.8   0.4    0.0081         8      29      83 ..     506     556 ..     492     562 .. 0.66
   5 !   17.3   1.3   4.3e-06    0.0043      18      87 ..     579     648 ..     577     650 .. 0.93
   6 ?    3.6   6.3     0.081        80      33      87 ..     664     718 ..     651     727 .. 0.54
   7 ?    0.2   0.4       0.9     9e+02      29      72 ..     772     811 ..     761     817 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.1
                            DUF948  25 kktldeaaatieelekqvdpilk 47 
                                       ++ ++e ++t ++le+ +d++ +
  gi|313125427|ref|YP_004035691.1| 356 QRRIEESEETAATLERAADEYGE 378
                                       34444444444444444433333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00017
                            DUF948  33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       ++++e++++ + +++e e+++a+v + +e     +e+v   t++v +++++vs 
  gi|313125427|ref|YP_004035691.1| 401 EAMAEIGRRFNRMMDEWEETVAEVGAFAERAAAASERVGVGTDEVSNASQQVSR 454
                                       67899***********************************************97 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 9.2e-06
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +++  +++aaa+ e ++  +d++++ ++++ + ++e++++  ++l++++++ ++ adl+++v+e+
  gi|313125427|ref|YP_004035691.1| 423 EVGAFAERAAAASERVGVGTDEVSNASQQVSRSTQEITSGAADQLDTLQAVSDQTADLSATVEEI 487
                                       33344445555555555888899999999999999999999*********************987 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0081
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                       de +++   +++++ +i +++e+++a v +    + e++ ++ ++++ + d++e+
  gi|313125427|ref|YP_004035691.1| 506 DEGREAAMAVGQEMAEIADQAETVTARVSR----LDEEVSDIASVVDLIDDIAEQ 556
                                       666677777888888888888888888888....445555555555555555544 PP

  == domain 5  score: 17.3 bits;  conditional E-value: 4.3e-06
                            DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +vv +++k++++e+aa+ +++++ ++++ + ++++++++ e+++ v++  e++d  ++a++++ + v+++
  gi|313125427|ref|YP_004035691.1| 579 AVVANEVKQLAEETAAATDDIGDSIESVRRATTEAVEEMDEMQSSVESGAETIDGGVDAIREAVDIVEDV 648
                                       678999******************************************************9987777665 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.081
                            DUF948  33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       ++ ++  +++d     ++++ ++++++++  ++++++++++ ++v +l+e+ + l
  gi|313125427|ref|YP_004035691.1| 664 TATQQAAERIDDAASIAAQTHSESEQVAAAAQQQTASLETVADEVDELAEQTQVL 718
                                       3444444444444444555555555555666666666666666666666554433 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 0.9
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdp 72 
                                       dea++  + + +++++++ e++   +     ++d ++k+e+vd+
  gi|313125427|ref|YP_004035691.1| 772 DEAESETNAIDEETGGTTPETDPRDE----ATDDSESKTEAVDE 811
                                       66666666666777776666655444....44457777777775 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   2.9   0.00069      0.69     218     325 ..     433     547 ..     410     553 .. 0.72
   2 !   12.2   4.1   6.3e-05     0.063     205     303 ..     581     676 ..     577     704 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00069
                            DUF677 218 vPleavgkwvasawkkyeealkrqkeivssmekg...ievakkdvenisilverleseiksilktvefAvekeen.. 289
                                       +  e vg   +++ + ++++ +  +ei s        +++   ++ ++s  ve++  +   ++   + A e++++  
  gi|313125427|ref|YP_004035691.1| 433 AASERVGVGTDEVSNASQQVSRSTQEITSGAADQldtLQAVSDQTADLSATVEEIAAQADELSTLSKRAAERGDEgr 509
                                       55555554455555555555555666655444331114555678899999******999999999999999877522 PP

                            DUF677 290 e..aavklaleeikkkvekltekieevgeeaakcskli 325
                                       e  +av + + ei ++ e +t  +  ++ee+ + ++++
  gi|313125427|ref|YP_004035691.1| 510 EaaMAVGQEMAEIADQAETVTARVSRLDEEVSDIASVV 547
                                       322678888**********************9988876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.3e-05
                            DUF677 205 aapavvavagalavPleavgkwvasawkkyeealkrqkeivssmekgievakkdvenisilverleseiksilktve 281
                                        a  v  +a  +a+    +g  ++s+++  +ea+    e+ ss+e+g e+    v+ i+  v+ +e++ ++ +++++
  gi|313125427|ref|YP_004035691.1| 581 VANEVKQLAEETAAATDDIGDSIESVRRATTEAVEEMDEMQSSVESGAETIDGGVDAIREAVDIVEDVDHG-VHSID 656
                                       455566699999999999***********************************************998887.5789* PP

                            DUF677 282 fAvekeeneaavklaleeikkk 303
                                       +A+++++  +a+++a e i++ 
  gi|313125427|ref|YP_004035691.1| 657 EATDSQA--TATQQAAERIDDA 676
                                       ****988..9999999998765 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1         1     1e+03      69      69 ..     385     385 ..     333     453 .. 0.57
   2 ?   15.7   2.7   1.3e-05     0.013      23     103 ..     462     546 ..     449     548 .. 0.90
   3 ?    1.1   0.3      0.47   4.7e+02      66     102 ..     586     622 ..     579     628 .. 0.67
   4 ?    2.0   3.4      0.25   2.5e+02      31      90 ..     662     722 ..     635     728 .. 0.48
   5 ?   -1.0   0.7       2.1   2.1e+03      43      92 ..     769     818 ..     751     828 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1
                                       T CS
                      Seryl_tRNA_N  69 a 69 
                                       a
  gi|313125427|ref|YP_004035691.1| 385 A 385
                                       1 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-05
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkelea 95 
                                       +++ ++d+l ++ ++   l +++ee+ a+  els   ++a +++    e a ++ +e++e+ ++ ++++a+++ l++
  gi|313125427|ref|YP_004035691.1| 462 GAADQLDTLQAVSDQTADLSATVEEIAAQADELSTLSKRAAERGdegrEAAMAVGQEMAEIADQAETVTARVSRLDE 538
                                       678899***************************99999999999988999999999********************* PP

                                       HHHHHHCT CS
                      Seryl_tRNA_N  96 elekllla 103
                                       e+ +++++
  gi|313125427|ref|YP_004035691.1| 539 EVSDIASV 546
                                       ***99875 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.47
                                       TS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  66 kedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       k+ aee  a ++++++ ++ +  + +e+ +e++++ +
  gi|313125427|ref|YP_004035691.1| 586 KQLAEETAAATDDIGDSIESVRRATTEAVEEMDEMQS 622
                                       3456667777777777777777777777777776654 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  31 lleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleael 90 
                                          + ++  e + ++ ++ a+  + s++++ a +++ +  e + +ev+el e+++ l +++
  gi|313125427|ref|YP_004035691.1| 662 QATATQQAAERIDDAASIAAQTHSESEQVAAAAQQQtASLETVADEVDELAEQTQVLAERV 722
                                       3333344444444444444555555555555555554455555555555555555554444 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelke 92 
                                       +e++e+ +e N++ +e g    + + ++e  +++++  e +++++ + + 
  gi|313125427|ref|YP_004035691.1| 769 SETDEAESETNAIDEETGGTTPETDPRDEATDDSESKTEAVDEADRADES 818
                                       57889999999999999988888844444444444444444444444444 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.1     0.029        29       3      95 ..     348     459 ..     313     462 .. 0.79
   2 ?    1.1   5.4      0.59   5.9e+02      23      62 ..     455     496 ..     442     566 .. 0.65
   3 ?   13.8   0.5   6.4e-05     0.064       3      96 ..     578     674 ..     577     677 .. 0.82
   4 ?    4.2   4.1     0.062        62      15      82 ..     664     733 ..     654     738 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.029
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrwerlledtsss...................tseeldetrteLrkalrsiewdledL 60 
                                       F e+++  q  +++ e++ ++ er  ++  ++                     e + e  + +++ +++ e+++ + 
  gi|313125427|ref|YP_004035691.1| 348 FAEMRDTLQRRIEESEETAATLERAADEYGETmdqaaagdltarmdpdaagDAEAMAEIGRRFNRMMDEWEETVAEV 424
                                       66667777777777777777776666665553456777778888777777777777777777788888888888888 PP

                      Syntaxin-6_N  61 eetvriveknpskfkidekelsrrrafveevreev 95 
                                           + + +  +++++  +e+s+  + v++  +e+
  gi|313125427|ref|YP_004035691.1| 425 GAFAERAAAASERVGVGTDEVSNASQQVSRSTQEI 459
                                       7777778888899**********999999999998 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.59
                      Syntaxin-6_N  23 rwerlledtss..stseeldetrteLrkalrsiewdledLee 62 
                                       + +++ + + +  +t + +++++ +L +++++i  + ++L  
  gi|313125427|ref|YP_004035691.1| 455 STQEITSGAADqlDTLQAVSDQTADLSATVEEIAAQADELST 496
                                       223333333332335666777777777777777777777654 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 6.4e-05
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrw.erlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfki 76 
                                       F +v++eV++ ++++++  +    ++ ++ ++  +  ee+de ++ +++  ++i+  ++ ++e+v+ive   + ++ 
  gi|313125427|ref|YP_004035691.1| 578 FAVVANEVKQLAEETAAATDDIgDSIESVRRAttEAVEEMDEMQSSVESGAETIDGGVDAIREAVDIVEDVDHGVHS 654
                                       7889999999999999999988634444444333579*********************************9888888 PP

                      Syntaxin-6_N  77 dekelsrrrafveevreevk 96 
                                        +++ +++    +++ e+++
  gi|313125427|ref|YP_004035691.1| 655 IDEATDSQATATQQAAERID 674
                                       88888888888888888876 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.062
                      Syntaxin-6_N  15 nkaeslyrrw...erlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekels 82 
                                         +++  +r     ++  +t+ s+se++  + ++  ++l+++  ++++L e  +++ +  + f ++++ ls
  gi|313125427|ref|YP_004035691.1| 664 TATQQAAERIddaASIAAQTH-SESEQVAAAAQQQTASLETVADEVDELAEQTQVLAERVETFTVSDDVLS 733
                                       444444444421123333333.4699999***************************999999999998776 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.77   7.7e+02      53      84 ..     344     375 ..     334     425 .. 0.65
   2 ?    2.4   0.2      0.15   1.5e+02      69     120 ..     436     487 ..     387     489 .. 0.72
   3 ?   10.2   3.1   0.00059      0.59      41     114 ..     471     544 ..     442     553 .. 0.53
   4 ?    9.9   1.1    0.0007       0.7      44     119 ..     579     654 ..     575     661 .. 0.62
   5 ?    4.8   2.1     0.027        26      43      92 ..     676     725 ..     665     747 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.77
                           DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiske 84 
                                       +++s a+ ++ L++ri++ +++    ++++ e
  gi|313125427|ref|YP_004035691.1| 344 LYNSFAEMRDTLQRRIEESEETAATLERAADE 375
                                       55666666666666666655544444433333 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                           DUF1664  69 drvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       +rv+   de++++s+++++  +e+ ++ ++  + +++v++   +l +++e+i
  gi|313125427|ref|YP_004035691.1| 436 ERVGVGTDEVSNASQQVSRSTQEITSGAADQLDTLQAVSDQTADLSATVEEI 487
                                       5666667777777777777777777777777777777777777777777766 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00059
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       +av++ + +l    e++aa+ ++Ls   +r  ++ de  e++ ++ +e++e+ ++ +++   v+ ++e v++++
  gi|313125427|ref|YP_004035691.1| 471 QAVSDQTADLSATVEEIAAQADELSTLSKRAAERGDEGREAAMAVGQEMAEIADQAETVTARVSRLDEEVSDIA 544
                                       23333344444444444445555555445555555555555555555555555555555555555555554444 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0007
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       + v+++++q+ e+ aa+ +++ + i++v +   e  e   e+++ v++  e ++   + +++  ++ve++++ +++
  gi|313125427|ref|YP_004035691.1| 579 AVVANEVKQLAEETAAATDDIGDSIESVRRATTEAVEEMDEMQSSVESGAETIDGGVDAIREAVDIVEDVDHGVHS 654
                                       6788899999999999999999999999877666666666666555544333333333333333344444444444 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.027
                           DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtev 92 
                                        +s++ q  + se++aa+ ++ ++ +++v +++de +e ++ ++e v++ 
  gi|313125427|ref|YP_004035691.1| 676 AASIAAQTHSESEQVAAAAQQQTASLETVADEVDELAEQTQVLAERVETF 725
                                       46788888888999999999999999999999999999999888888653 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.5   3.4e+03      36      79 ..      49      93 ..      45      99 .. 0.76
   2 ?    2.3   0.1      0.15   1.5e+02      89     133 ..     446     490 ..     433     504 .. 0.80
   3 ?   -0.1   0.0       0.8     8e+02      96     150 ..     502     556 ..     491     563 .. 0.77
   4 ?    5.7   0.2     0.013        13      97     137 ..     685     725 ..     661     734 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.5
                          Cauli_AT 36 kkssiksiia.hcnnlneivarslLklskllsylGLekDeseals 79
                                      k+ ++++i++ +  nlne v  +  +   l  + GL+ D+ +++ 
  gi|313125427|ref|YP_004035691.1| 49 KHDELRTIAElEAENLNEWVDTNEQRARMLSEHRGLQSDDPDSVD 93
                                      455677777635789999999999998888889999999888654 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                          Cauli_AT  89 fkklkkifkeggedkekktklletLkeaqnrikkleeetkklaek 133
                                        +  +++ ++++e ++ ++++l+tL+ ++++  +l+ +++++a +
  gi|313125427|ref|YP_004035691.1| 446 SNASQQVSRSTQEITSGAADQLDTLQAVSDQTADLSATVEEIAAQ 490
                                       55566677788888889999999******9999999999999876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.8
                          Cauli_AT  96 fkeggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlder 150
                                        ++g+e +e+++   + + e+ ++ + +  ++ +l+e++   + + + + d+ e+
  gi|313125427|ref|YP_004035691.1| 502 AERGDEGREAAMAVGQEMAEIADQAETVTARVSRLDEEVSDIASVVDLIDDIAEQ 556
                                       4556677777788888899999999999999999999998888888888888776 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.013
                          Cauli_AT  97 keggedkekktklletLkeaqnrikkleeetkklaekivte 137
                                        e+++   ++ +++ +L+ + + +++l e+t+ lae+++t 
  gi|313125427|ref|YP_004035691.1| 685 SESEQVAAAAQQQTASLETVADEVDELAEQTQVLAERVETF 725
                                       56666777888999************************985 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.8   2.8e+03      16      31 ..      18      33 ..      10      36 .. 0.63
   2 ?   10.5   0.4    0.0004       0.4      21      54 ..     289     323 ..     277     326 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.8
                          LapA_dom 16 elpLsllllvafgiGa 31
                                      ++ L+l +l+a  +G+
  gi|313125427|ref|YP_004035691.1| 18 KYVLVLAVLLASMVGV 33
                                      5666677777666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0004
                          LapA_dom  21 llllvafgiGallgwllsl.wsylrlrrelrrlkk 54 
                                       ++l++++++G++l++l+   ++++ lrr  +r+++
  gi|313125427|ref|YP_004035691.1| 289 TVLIGTAVAGFILMGLTLGrSTVVSLRRLRKRAER 323
                                       689999**********9995444444444444433 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.1      0.11   1.1e+02     381     477 ..     403     501 ..     350     526 .. 0.65
   2 ?    1.7   1.3     0.058        58     312     399 ..     474     558 ..     455     592 .. 0.55
   3 ?   10.4   3.5   0.00013      0.13      99     222 ..     592     717 ..     578     723 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.11
                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-..SS-S-TTTHHHHSTTTSTTTHH CS
                              EzrA 381 leeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkieks..nLPgiPesyleelkeasdeiee 455
                                       + e+ ++ +++ ++ ee+  ++++  +  + A e++     e++++ +++++s  ++ +  ++ l+ l+++sd+  +
  gi|313125427|ref|YP_004035691.1| 403 MAEIGRRFNRMMDEWEETVAEVGAFAERAAAASERVGVGTDEVSNASQQVSRStqEITSGAADQLDTLQAVSDQTAD 479
                                       45555555555555555555555555555555555555555555555555543114555555555555555555555 PP

                                       HHHHHT-TT--HHHHHHHHHTT CS
                              EzrA 456 lakeLekkpinikevnkrldea 477
                                       l+  +e+   + +e+++  + a
  gi|313125427|ref|YP_004035691.1| 480 LSATVEEIAAQADELSTLSKRA 501
                                       5555555555555554444444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.058
                                       SHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHH CS
                              EzrA 312 keklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekl 388
                                       +++   l + ++e+ ++ d+l+   +Ls++  e+ +e  +    + +++ e+ ++ e+ ++  S+l ee+ ++ + +
  gi|313125427|ref|YP_004035691.1| 474 SDQTADLSATVEEIAAQADELS---TLSKRAAERGDEGREAAMAVGQEMAEIADQAETVTARVSRLDEEVSDIASVV 547
                                       3333444444444444444444...4555555555555555566666666666666666666666666666655555 PP

                                       HHHHHHHHHHH CS
                              EzrA 389 eeieekqeeil 399
                                       + i++  e+++
  gi|313125427|ref|YP_004035691.1| 548 DLIDDIAEQTN 558
                                       55555555554 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00013
                                       TTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH-- CS
                              EzrA  99 akkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniek 175
                                       + ++ +++ + +++v+  + +  ee++e+++s e   e i+   +  re  + +++  +   ++ e+ ++q  + ++
  gi|313125427|ref|YP_004035691.1| 592 TAAATDDIGDSIESVRRATTEAVEEMDEMQSSVESGAETIDGGVDAIREAVDIVEDVDHGVHSIDEATDSQATATQQ 668
                                       5667889999**************************************************************99999 PP

                                       ----------..----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTT CS
                              EzrA 176 efsefeelte..ngdyveakeilkkleeeideleevieeiPelleelkk 222
                                         + ++++ +  ++ ++e +++  ++++++++le+v +e+ el e+++ 
  gi|313125427|ref|YP_004035691.1| 669 AAERIDDAASiaAQTHSESEQVAAAAQQQTASLETVADEVDELAEQTQV 717
                                       99999988643399*****************************999875 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.27   2.6e+02     645     690 ..     446     494 ..     408     534 .. 0.55
   2 ?    8.6   5.4    0.0004       0.4     192     390 ..     515     715 ..     491     733 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.27
                          Prominin 645 knlkqslkneaqdlraiqqelvlple...ssvkklkksvkkldeensdl 690
                                       +n++q++ ++ q++ +  +++ ++l+    ++++l  +v+++ +++ +l
  gi|313125427|ref|YP_004035691.1| 446 SNASQQVSRSTQEITSGAADQLDTLQavsDQTADLSATVEEIAAQADEL 494
                                       3333333333333333333333322211123333333333333333333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0004
                          Prominin 192 vpqhidhvlvqnyeelekhvs...ddLddag..khlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklek 263
                                       v q++ ++++q  e++ ++vs   ++++d+     l++d+a++ +   l+a  e  r +e+ +      ++v++l +
  gi|313125427|ref|YP_004035691.1| 515 VGQEMAEIADQ-AETVTARVSrldEEVSDIAsvVDLIDDIAEQTNILALNASIEASRAGEAGEGFAVVANEVKQLAE 590
                                       66777777777.4444444331114555555344577788888777767777788899999999999999******* PP

                          Prominin 264 eLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcl.....dqlpnvdevlealeevletnl 335
                                       e    ++++ d++++v+r  ++a+++  ++e  s+++s +e+  +d + +      d +++vd+ +++++e+++++ 
  gi|313125427|ref|YP_004035691.1| 591 ETAAATDDIGDSIESVRRATTEAVEE--MDEMQSSVESGAET--IDGGVDAireavDIVEDVDHGVHSIDEATDSQ- 662
                                       **************************..33445555555555..66666655655788888888888888886555. PP

                          Prominin 336 ssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdav 390
                                       + + +++ +r+++    ++ qt++  +++  a +++++ ++++a ++ +e ++++
  gi|313125427|ref|YP_004035691.1| 663 ATATQQAAERIDDA-ASIAAQTHSESEQVAAAAQQQTASLETVADEV-DELAEQT 715
                                       45678899999996.56889999**********************99.6555544 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.1    0.0039       3.9      18     165 ..     403     547 ..     395     563 .. 0.73
   2 ?    5.9   8.4    0.0026       2.6       3     148 ..     588     757 ..     586     785 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0039
                        V_ATPase_I  18 vnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenlek 94 
                                       ++++ r+f + +   +e   ++  + e  + +++ v   ++++++ +++ +++++e+++   +  + l+ +++++ +
  gi|313125427|ref|YP_004035691.1| 403 MAEIGRRFNRMMDEWEETVAEVGAFAERAAAASERVGVGTDEVSNASQQVSRSTQEITSGAADQLDTLQAVSDQTAD 479
                                       667889999999999**999**99*999999999999999999999999999********99999************ PP

                        V_ATPase_I  95 lkkelnelvelkavlekakefleee.eeeeeeeeseeeeeekeeeeeeeseeeeeeelleeeeelsfvaGvi 165
                                       l+++++e+  +   l++ ++  +e+ +e +e++ +  +    e++e ++++e+ ++++++ +ee+s +a v+
  gi|313125427|ref|YP_004035691.1| 480 LSATVEEIAAQADELSTLSKRAAERgDEGREAAMAVGQ----EMAEIADQAETVTARVSRLDEEVSDIASVV 547
                                       ***99999999888888887776663333333222222....222222222222333333334455555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0026
                        V_ATPase_I   3 LGelglvqfrDlnedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeea.................... 59 
                                       L+e +     D+ ++++++ r+ ++ v  +dem+ +++   e+i+   +a++++ ++                    
  gi|313125427|ref|YP_004035691.1| 588 LAEETAAATDDIGDSIESVRRATTEAVEEMDEMQSSVESGAETIDGGVDAIREAVDIvedvdhgvhsideatdsqat 664
                                       66666677778888888888888888888888888888888888775555555544477788888888888777655 PP

                        V_ATPase_I  60 ...........eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleeeeeeeee 125
                                                  ++s +a+++       +e e++ +  ++++++le++ +e+ el e+++vl +  e ++ +++  ++
  gi|313125427|ref|YP_004035691.1| 665 atqqaaeriddAASIAAQTH-------SESEQVAAAAQQQTASLETVADEVDELAEQTQVLAERVETFTVSDDVLSA 734
                                       55443333443334444444.......44555555555555555555555555555555555544444433222222 PP

                        V_ATPase_I 126 eeseeeeeekeeeeeeeseeeee 148
                                       + ++ +e+++ +++++e++ e++
  gi|313125427|ref|YP_004035691.1| 735 DGDHGSETDAVDTSAAETTPETD 757
                                       22222222211111111111111 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.68   6.8e+02      32      62 ..     475     506 ..     457     513 .. 0.81
   2 ?    0.8   0.0      0.35   3.5e+02      23      58 ..     522     557 ..     510     566 .. 0.79
   3 ?    3.2   0.0     0.067        67      26      81 ..     592     647 ..     574     650 .. 0.73
   4 ?   -0.0   0.1      0.64   6.4e+02      13      67 ..     666     724 ..     663     727 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.68
                              RPW8  32 silkrLestleritPvvkeieklnkel.drpr 62 
                                        +  +L +t+e+i+   +e+ +l+k+  +r +
  gi|313125427|ref|YP_004035691.1| 475 DQTADLSATVEEIAAQADELSTLSKRAaERGD 506
                                       56789999*******99999999998866655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.35
                              RPW8  23 akkksldfksilkrLestleritPvvkeieklnkel 58 
                                        ++++ ++   + rL++ +++i+ vv+ i+ + ++ 
  gi|313125427|ref|YP_004035691.1| 522 IADQAETVTARVSRLDEEVSDIASVVDLIDDIAEQT 557
                                       4555566667899*****************998875 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.067
                              RPW8  26 ksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkklLekaekLVek 81 
                                       +++ ++ i +++es   + t  v+e+++++  +++  e i+   + +++a ++Ve 
  gi|313125427|ref|YP_004035691.1| 592 TAAATDDIGDSIESVRRATTEAVEEMDEMQSSVESGAETIDGGVDAIREAVDIVED 647
                                       34444455555555555567789999****99999999999999999999999985 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.64
                              RPW8  13 lgellkaileakkksldfksilkrLestle....ritPvvkeieklnkeldrpreeiee 67 
                                        ++ ++ i +a+  +++++s +++ ++  +    ++++v +e+++l ++ +   e +e 
  gi|313125427|ref|YP_004035691.1| 666 TQQAAERIDDAASIAAQTHSESEQVAAAAQqqtaSLETVADEVDELAEQTQVLAERVET 724
                                       56777888888888888888888887655411115777777788887777766666665 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   1.5e+03      24      60 ..     342     378 ..     331     386 .. 0.59
   2 ?    0.0   0.2      0.39   3.8e+02       7      26 ..     481     500 ..     411     553 .. 0.51
   3 ?    8.5   1.7     0.001         1     102     229 ..     586     726 ..     580     728 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                           Taxilin  24 vkkyaelleerkrlqkqlkklkkkleqlqkekeqlqa 60 
                                        + y+ + e r +lq+ + ++++++++l +  ++  +
  gi|313125427|ref|YP_004035691.1| 342 GTLYNSFAEMRDTLQRRIEESEETAATLERAADEYGE 378
                                       5556666666666666666666666666666655544 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.39
                           Taxilin   7 keslsklespeekleaLvkk 26 
                                       + ++++++ + ++l +L k+
  gi|313125427|ref|YP_004035691.1| 481 SATVEEIAAQADELSTLSKR 500
                                       22222222222222222222 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.001
                           Taxilin 102 kelaekfqakLkdiqaqieekserneklreenaelteKlkslieqye....lreehf..............ekllkt 160
                                       k+lae   a   di ++ie+ +    + +ee  e+++  +s +e  +         +              +++ ++
  gi|313125427|ref|YP_004035691.1| 586 KQLAEETAAATDDIGDSIESVRRATTEAVEEMDEMQSSVESGAETIDggvdA----IreavdivedvdhgvHSIDEA 658
                                       7788888999999999999999999999999999999999999999955550....444444566666666777777 PP

                           Taxilin 161 kelelqlaeaKlqqadallkeeqekkkrekeyllkeakeltkkvkalketekelkeqlnlYaeKfeefq 229
                                        + +    ++  +++d  ++ + + + + +++ ++ a++ t++++++ ++  el eq ++ ae+ e f+
  gi|313125427|ref|YP_004035691.1| 659 TDSQATATQQAAERIDDAASIAAQTHSESEQV-AAAAQQQTASLETVADEVDELAEQTQVLAERVETFT 726
                                       77777666666666666666677766655555.899**************************9999986 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.43   4.3e+02      66      87 ..      20      41 ..      15      54 .. 0.82
   2 ?    6.4   0.7    0.0031       3.1      88     183 ..     446     552 ..     432     566 .. 0.47
   3 ?   -1.2   0.0      0.62   6.2e+02     124     166 ..     582     625 ..     578     649 .. 0.62
   4 ?    2.5   2.3     0.045        45      98     167 ..     645     714 ..     626     737 .. 0.44

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.43
                            Tweety 66 vviatlvccaaigvGfYGNset 87
                                      v + ++++++ +gvG+Y  +++
  gi|313125427|ref|YP_004035691.1| 20 VLVLAVLLASMVGVGLYTEEQV 41
                                      56777888999******87765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0031
                            Tweety  88 ndGvlqltyslrkan.......htlagikklvseteesleeklee..eLtkleeifakrtd.lletlrlvqeqveev 154
                                       ++  +q+  s +++         tl+++++++ ++++++ee  ++  eL +l++  a+r d   e+  +v +++ e+
  gi|313125427|ref|YP_004035691.1| 446 SNASQQVSRSTQEITsgaadqlDTLQAVSDQTADLSATVEEIAAQadELSTLSKRAAERGDeGREAAMAVGQEMAEI 522
                                       33333333333322111111113555555555555555554333211455555555555553233333344444444 PP

                            Tweety 155 vqqlselp.flkkkdvsltelaeqvelvel 183
                                       ++q++ ++  +++ d +++++a+ v+l++ 
  gi|313125427|ref|YP_004035691.1| 523 ADQAETVTaRVSRLDEEVSDIASVVDLIDD 552
                                       444444443555556666666666666655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.62
                            Tweety 124 eeeLtkleeifa.krtdlletlrlvqeqveevvqqlselpflkk 166
                                       ++e+++l e  a +  d+  +++ v++ ++e+v++++e++   +
  gi|313125427|ref|YP_004035691.1| 582 ANEVKQLAEETAaATDDIGDSIESVRRATTEAVEEMDEMQSSVE 625
                                       55666665544404455778889999999999999999884322 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.045
                            Tweety  98 lrkanhtlagikklvseteesleekleeeLtkleeifakrtd.lletlrlvqeqveevvqqlselpflkkk 167
                                       +++++h + +i++ + +++++ +++ +e++    +i a+ ++   ++  ++q+q+ ++ + ++e+  l ++
  gi|313125427|ref|YP_004035691.1| 645 VEDVDHGVHSIDEATDSQATA-TQQAAERIDDAASIAAQTHSeSEQVAAAAQQQTASLETVADEVDELAEQ 714
                                       455555555555554433332.3333334444444444433312222222333333333333333222111 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.3     0.012        12     310     455 ..     352     496 ..     313     537 .. 0.49
   2 ?    5.7  12.0    0.0047       4.7     281     461 ..     540     723 ..     525     728 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                            AAA_13 310 sde.asensafeedkeelkaeaealeeqLkg.lqraleaKrkepfksvelesvkakiesikklvaeineliakhNek 384
                                        d+ +++ +++ee  ++l+++a++  e++++ +   l+a+  +p +  + e +++   +++  ++e +e++a+  ++
  gi|313125427|ref|YP_004035691.1| 352 RDTlQRRIEESEETAATLERAADEYGETMDQaAAGDLTARM-DPDAAGDAEAMAEIGRRFNRMMDEWEETVAEVGAF 427
                                       22112223333444444444444444444432333444444.33333333333333334444444444444433333 PP

                            AAA_13 385 vanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                        ++ +++ e  ++ +  ++v+++ +++++ ++++ + +++  ++ +++++++a+l +  eei++   +l++
  gi|313125427|ref|YP_004035691.1| 428 AERAAAASE--RVGVGTDEVSNASQQVSRSTQEITSGAADQLDTLQAVSDQTADLSATVEEIAAQADELST 496
                                       333333222..222333444555555555554444444444444445555555555555555444444443 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0047
                            AAA_13 281 feekqerLekliekveskkselleklkavsde..........asensafeedkeelkaeaealeeqLkglqraleaK 347
                                       + + +++  +li++++++++ +l  l+a +++          a   ++ ++  ee  a+++ + +++++++ra ++ 
  gi|313125427|ref|YP_004035691.1| 540 VSD-IASVVDLIDDIAEQTN-IL-ALNASIEAsrageagegfAVVANEVKQLAEETAAATDDIGDSIESVRRATTEA 613
                                       444.6666667777777663.43.33344443233332222222222333334444445555555566677777666 PP

                            AAA_13 348 rkepfk.svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklek 423
                                       ++e+ + + ++es ++ i+ + +++ e+ +++++    v++++e++ + +++ ++     + + +d   +  +++  
  gi|313125427|ref|YP_004035691.1| 614 VEEMDEmQSSVESGAETIDGGVDAIREAVDIVEDVDHGVHSIDEATDSQATATQQ-----AAERIDDAASIAAQTHS 685
                                       6666664455666666666677777777777777777777777666666666555.....66677777788889999 PP

                            AAA_13 424 aieklekelkeeeaelkkleeeikeLekqlrdekpaae 461
                                       + e++ +++++++a l+++++e+ eL +q++   + +e
  gi|313125427|ref|YP_004035691.1| 686 ESEQVAAAAQQQTASLETVADEVDELAEQTQVLAERVE 723
                                       99999999******************999986666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (840 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2224  (0.124045); expected 358.6 (0.02)
Passed bias filter:                      798  (0.0445089); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        67  (0.00373696); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 1.64u 0.41s 00:00:02.04 Elapsed: 00:00:00.61
# Mc/sec: 4169.53
//
Query:       gi|313125428|ref|YP_004035692.1|  [L=61]
Description: hypothetical protein Hbor_06530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.8    9.5   5.6       0.92    9.3   5.6    1.0  1  IncD      Inclusion membrane protein D


Domain annotation for each model (and alignments):
>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.6   5.1e-05      0.92      51      91 ..      16      57 ..      10      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 5.1e-05
                              IncD 51 lvvagl.lfsgvlcspvsvlaaslffgvgafllggalvggvl 91
                                      l v g+ l+s  l   +s +   l  gvg+++  g lvgg l
  gi|313125428|ref|YP_004035692.1| 16 LGVMGVsLLSAALLGAISAVPLHLAAGVGSLIAAGVLVGGTL 57
                                      55555438999*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 382.74
//
Query:       gi|313125429|ref|YP_004035693.1|  [L=289]
Description: hypothetical protein Hbor_06540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0026   18.0   0.2     0.0067   16.7   0.1    1.7  2  CARDB     CARDB
  ------ inclusion threshold ------
        0.2   11.6   4.9        0.7    9.9   4.9    1.9  1  DUF3558   Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         1     9e+03      40      45 ..     110     115 ..      86     127 .. 0.46
   2 !   16.7   0.1   7.5e-07    0.0067       5      81 ..     188     269 ..     184     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1
                                       EEEEET CS
                             CARDB  40 valyld 45 
                                       v++  d
  gi|313125429|ref|YP_004035693.1| 110 VSVATD 115
                                       222222 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.5e-07
                                       EE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEE.SEE-CTEEEEEEEEEE-S..-S- CS
                             CARDB   5 tvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtv.psLaagesttvsftwtte..ate 75 
                                       +v + ++p++++ g+e+t+t+tv+N G+a+ g++ + l  +g ++    t+ +  +++ag+++t + ++t++     
  gi|313125429|ref|YP_004035693.1| 188 EVREFSAPDTVTSGTESTLTLTVENVGSAD-GTFVAGLNRSGPQTaymPTTAIsIEVDAGATATWTHSYTPPvvSRD 263
                                       56778999*******************987.6677778777777767744444368999999999999999955555 PP

                                       CEEEEE CS
                             CARDB  76 gevtlt 81 
                                       g++ ++
  gi|313125429|ref|YP_004035693.1| 264 GDISFQ 269
                                       655555 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.9   7.8e-05       0.7       1      35 [.      26      62 ..      26      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.8e-05
                           DUF3558  1 lllaGCssttdGt.....apaasssassssttsssaapav 35
                                      +llaGC+s    +     +++++s++ ++ tt++++ap v
  gi|313125429|ref|YP_004035693.1| 26 ALLAGCTSG---SpfggdTQQSPSGTEPAETTTPTSAPHV 62
                                      69*****44...3344669999999999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1839.60
//
Query:       gi|313125430|ref|YP_004035694.1|  [L=543]
Description: peptide ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-68  230.9   2.2      3e-68  230.5   2.2    1.1  1  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
  ------ inclusion threshold ------
      0.081   12.8   2.0       0.13   12.1   2.0    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.5   2.2   3.3e-72     3e-68       2     374 ..      96     454 ..      95     457 .. 0.92

  Alignments for each domain:
  == domain 1  score: 230.5 bits;  conditional E-value: 3.3e-72
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       ++p+LA   +evs+ g+ y + L++g++F++G+p+tAeDv++s+   ++ +t  g+ +++     i+++  vdd+tv
  gi|313125430|ref|YP_004035694.1|  96 LTPQLANGDPEVSKSGQRYVVSLKDGITFHNGDPITAEDVKYSYLAPAREETENGSEFTM-----IDTISIVDDKTV 167
                                       78******************************************************9998.....9*********** PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSEE CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldri 155
                                       +f lk p+ +f   la  p +      + e+dk++++  +pvg+GP+ ++e+++g+ ++++r++dYwg +  +++ +
  gi|313125430|ref|YP_004035694.1| 168 QFDLKYPFGPFKHSLAWSPVPKS----VREADKKAFNTSNPVGSGPFEFDEWQQGSFVRMQRHDDYWGENGSNIETL 240
                                       *********99999887777666....889999**********************************88999***** PP

                                       EEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS- CS
                         SBP_bac_5 156 efkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAiD 232
                                       +f  ++++++r++ l++Ge + v+ +pp+   +++  +   v  e++g+g++ylafN++  p  dk+vR+A+ yAi 
  gi|313125430|ref|YP_004035694.1| 241 VFTPVKEPTTRITTLRNGENHAVQTVPPKLYSTVEGIEEASV-TEQTGLGYFYLAFNCNEGPTTDKKVREAIDYAIS 316
                                       ******************************************.********************************** PP

                                       HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH....SHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEET CS
                         SBP_bac_5 233 reeivkavlegyatpansllppsspgadeeykpayka....ydpekAkklLkeaGykdgdggglrekklkltlllas 305
                                        +e v+++ e  +t+++s+lp+++  +++ + ++++      d e A++lL+eaG  ++ +         +t+ +++
  gi|313125430|ref|YP_004035694.1| 317 LDEAVNRYVEPAGTRMTSPLPQTLIDSWGFPGEKWDQipheKDQEMARQLLDEAGVSKDYD---------WTI-IVP 383
                                       *********************98777777777666557779****************9975.........555.555 PP

                                       TSHHHHHHHHHHHHHHHHTTE.EEEEEEECHH..HHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTC CS
                         SBP_bac_5 306 gspaekaiaeliqqqlkkiGi.kvevktvdwa..atylervkdgdfdmillgwgadypdpdnflnpflsssg 374
                                        +  +++i   + ++lk +G+ +++v+ +dw      +++ k+ d++m+ lgw  d  dpd +l++++++s+
  gi|313125430|ref|YP_004035694.1| 384 PDKKREQIGISVSNALKSLGFsNASVQRLDWGafLDKYATGKESDYNMYALGWL-DEVDPDGYLYYLFHESE 454
                                       6677899*************548********65633335699************.66999999999999875 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.0   1.5e-05      0.13       2      24 ..       8      30 ..       7      32 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                       SRR  L++ +A++ A+++g  a
  gi|313125430|ref|YP_004035694.1|  8 PSRRRVLQAIGATGVAGLAGCTA 30
                                      7************9777655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 3105.61
//
Query:       gi|313125431|ref|YP_004035695.1|  [L=117]
Description: hypothetical protein Hbor_06570 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   19.6   0.9     0.0024   18.5   0.7    1.8  1  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.7   1.4e-07    0.0024       1      62 [.      32      86 ..      32      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-07
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvd 62
                                      + ++ ++C g g C+++a++       gla+ +       +  +++de e+  +Aa++CP++
  gi|313125431|ref|YP_004035695.1| 32 IIFEANKCFGAGKCAEVADNWEMDIASGLARPK-------SYYFDEDELEENVRAAEVCPAK 86
                                      567899***********9755555558999666.......5799999999999*******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 742.54
//
Query:       gi|313125432|ref|YP_004035696.1|  [L=170]
Description: peptidyl-prolyl cis-trans isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-52  176.1   0.0    6.6e-52  176.0   0.0    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0   0.0   3.7e-56   6.6e-52       3     156 ..       7     166 ..       5     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 3.7e-56
                     Pro_isomerase   3 dietsskGrivieLfadkaPktvenFlklvkeg................fYdgttFhRvikgfmvqgGdptgktsag 63 
                                       +++t  +G+i++eLf+++aP tvenF++l++ g                 Y+gt+FhR+i++fm+qgGdp+g+++  
  gi|313125432|ref|YP_004035696.1|   7 TLHTT-RGDITVELFEERAPRTVENFIDLAT-GekewedpetgetrtdsLYEGTIFHRIIDDFMIQGGDPEGTGR-- 79 
                                       78895.************************5.55777777777888888********************999965.. PP

                     Pro_isomerase  64 eqekkggesiraipdEitsklkh.krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiek 139
                                            gg   ++++dE++++l+h ++G l+ma++g  p+++gsqFfItl+++phld++++vFG+VveGmdvve+i +
  gi|313125432|ref|YP_004035696.1|  80 -----GG-PGYTFDDEFHDELRHdSAGKLSMANRG--PDTNGSQFFITLGAQPHLDDRHAVFGEVVEGMDVVEEIGS 148
                                       .....33.2469******999**899*******98..8*************************************** PP

                     Pro_isomerase 140 vetde.erpkknvkivsa 156
                                       ++td+ ++p k+v i+s+
  gi|313125432|ref|YP_004035696.1| 149 LPTDRnDKPMKDVEIESI 166
                                       ***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1087.20
//
Query:       gi|313125433|ref|YP_004035697.1|  [L=324]
Description: deacylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-39  136.2   0.0    1.3e-39  136.0   0.0    1.0  1  AstE_AspA      Succinylglutamate desuccinylase / Aspartoacyla
  ------ inclusion threshold ------
      0.047   13.5   0.0        2.3    7.9   0.0    2.2  2  Peptidase_M14  Zinc carboxypeptidase


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.0   0.0   1.5e-43   1.3e-39       2     289 ..      30     314 ..      29     316 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 1.5e-43
                                       S-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSS....TT-S-CTTTTTCCCCCS CS
                         AstE_AspA   2 gpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyip....idredLNRaFpgrslgr 74 
                                       gp+v+++A+ HG E++G+e++r++ ++l++ d++g+ + vp+a p+ + + s + p       +++NR++pg+++g 
  gi|313125433|ref|YP_004035697.1|  30 GPTVYVQAAQHGREINGTEVIRRIHERLDSDDLSGTLVTVPVADPLTFDRVSYTTPesldAVHSNMNRVWPGDEEG- 105
                                       9***************************************************88888877888*************. PP

                                       STCHHHHHHHHHHHHHHHCHCTCCCGCEEEEEEEESSTBCCSSEEEE---SSHHHHHHHHHHTTTSEEEEEESS--S CS
                         AstE_AspA  75 sldealrateaerladalfaaalpeadivlDLHtgtrglkhllfaeadiaeaqlqslallkalglpavllldekesa 151
                                               +  er+a al++ a  ead+++DLHtg   +  +  +++d +++     +l++a+g++++l  +    +
  gi|313125433|ref|YP_004035697.1| 106 --------SLHERMAAALWEYA-GEADYIVDLHTGSPEM-LTHTVYLDGDDDC---RRLAEAFGTELLLAEAAG--D 167
                                       ........***********888.7***************.7777778887774...4999*********33333..3 PP

                                       ............SHHHHHHHHCTSEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT.-.SCC.CEEEEEEE CS
                         AstE_AspA 152 ............gfletaaeelgalaftlElGgagrlgaedisrtakgvlnvlahigvvagq.e.avepaklyrvlr 214
                                                   g+l+ aa ++g++++t+El+    l + +i+  ++gv+nvl+++++++g+ e ++e++ ++ +l 
  gi|313125433|ref|YP_004035697.1| 168 dadtewsernfgGKLRVAATRAGIPSITPELAHNKQLVEPAIETGVRGVFNVLREVEMLSGDpEiPAEQTTARNHLG 244
                                       369***********************************************************666666666666666 PP

                                       EEEGGSCCCSSCSEEECC..CCSTTTTETCTEEEETTEEEEECTSTEEEEESSSSEEEESCCTSCCTTTTEEEEEEE CS
                         AstE_AspA 215 eldeprdiraeeaGlvef..kvklgddveagellakalvldslggekvelrapqdgvivfineaalvekgaalvkva 289
                                        ++  ++      Gl+++  +++lg +ve g+ l +++  ++++  + e +a++ gvi +  ++a v  g+ lv va
  gi|313125433|ref|YP_004035697.1| 245 RVSAAES------GLFHPgpDAELGRQVEEGDHLGRVYHPTTYEVLQ-EATADRAGVIYSVCREATVTAGQTLVGVA 314
                                       6666665......****5449****************9999996666.***********************999876 PP

>> Peptidase_M14  Zinc carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00026       2.3      44      70 ..      28      54 ..      13      63 .. 0.84
   2 ?    3.4   0.0    0.0063        57     180     275 ..     106     205 ..      72     218 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00026
                                      ST-CEEEEEE-SSTT-HHHHHHHHHHH CS
                     Peptidase_M14 44 egkpvvlidggiHarEwigsalllyll 70
                                       + p+v +++ +H+rE+ g+++  ++ 
  gi|313125433|ref|YP_004035697.1| 28 GTGPTVYVQAAQHGREINGTEVIRRIH 54
                                      56799****************987665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0063
                                       EEEESSSEEEESHSSSS--..............-SS-TTHHHHHHHHHHHHHHHCHTTTTEEE-EEEEEHHHHT--- CS
                     Peptidase_M14 180 dlhsysqvilypygstrde..............ispppddeelkslarkyaealqkmvrgteylsegitngaliyea 242
                                       +lh  ++++l++y+  +d               +   + d+++++la+++  +l    +     ++g+ +++ + e+
  gi|313125433|ref|YP_004035697.1| 106 SLHERMAAALWEYAGEADYivdlhtgspemlthTVYLDGDDDCRRLAEAFGTELLL-AE-----AAGDDADTEWSER 176
                                       56666666666666333333333322223333223333444477777777777755.33.....6676777779999 PP

                                       S.S-HHHHHHHHTT-SEEEEEEESSSSSSTTS-- CS
                     Peptidase_M14 243 s.ggmddwayertgvkfeytlelrdegkqgflpp 275
                                       + gg  + a +r+g+  ++t el  ++    ++ 
  gi|313125433|ref|YP_004035697.1| 177 NfGGKLRVAATRAGI-PSITPELAHNK----QLV 205
                                       999999*********.9*****99988....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2056.89
//
Query:       gi|313125434|ref|YP_004035698.1|  [L=423]
Description: amidohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-19   70.0   4.4    3.4e-19   69.4   4.4    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
    5.7e-14   52.0   0.4    1.3e-13   50.8   0.4    1.5  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   4.4   3.8e-23   3.4e-19       2     206 ..     105     417 ..     104     418 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 3.8e-23
                                       EEEES-BSS.TTCGGGSSS.....TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTS CS
                                       xxxxxxxxx.xxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVp.eeetdgwtt.....pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEE 72 
                                       ++ ++D++   e +d+ ++      f++t++ + ++++G+d++++  ++++ a+    +eg+  +gt++l fqp+EE
  gi|313125434|ref|YP_004035698.1| 105 VRVDMDALArSEASDD-DHrpareGFASTHP-NEMHACGHDGHTAVGIGIARAFD---AEGF--DGTLKLFFQPAEE 174
                                       5789999998666644.22222356777788.67*****************9985...5886..89*********** PP

                                       STTTHHHHHHHHHHTTTCESEEEEEEEE..SSSBTCHSTETEEEE................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx................................ RF
                     Peptidase_M20  73 ggrgGakallegleerekvdavfelhie..epgileagklaigvv................................ 115
                                       gg +G k + e     ++vda+++lh++  e+++ +        v                                
  gi|313125434|ref|YP_004035698.1| 175 GG-RGGKPMSETTH-VDDVDALLALHLGldEETGTV--------Vggydrplsnakldvtfegepahaggapnegrn 241
                                       98.999*****444.569********6600333333........3367788889*********************** PP

                                       ...........................................................................EE CS
                                       ...........................................................................xx RF
                     Peptidase_M20 116 ...........................................................................kv 117
                                                                                                                  +v
  gi|313125434|ref|YP_004035698.1| 242 alqamttaiqnlyaiprhadgktrinvgqvhadnaqnviceeaqmrvevrgedadlndymmqkaervvehaagmhDV 318
                                       *************************************************************************9758 PP

                                       EEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEES.SSBHTHHHH.TTT.E.....EEEEEESSG.GCTTS CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxx.x.....xxxxxxxxx.xxxxx RF
                     Peptidase_M20 118 evelleggapvtln.dsplvkalaeaaeelfgekvelivsg.pggtdarff.agi.p.....tvmifgpgs.glaHs 184
                                        +e    g  +t++ d+ +v+++ +aae + g+++ +  s+  g++da+f+  ++       +++++g ++ ++ H+
  gi|313125434|ref|YP_004035698.1| 319 AYETSLYGMTTTFEnDGFVVETVMDAAETVEGVTQICGRSPfGGSEDASFLiRRVqEnggvaSYIGIGASNpAGHHT 395
                                       8887788888888867888**********98977666677788********96664134433666677444477777 PP

                                       TTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 185 pnEyvdledlekgikvlarlle 206
                                          ++d+++l  ++ v++++++
  gi|313125434|ref|YP_004035698.1| 396 AYFDIDEAALDIAVGVVEEAVR 417
                                       8888889999999999998876 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.4   1.5e-17   1.3e-13       8     105 ..     220     313 ..     217     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.5e-17
                                       EEEEEEE-B-EEGG.-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEE CS
                         M20_dimer   8 ggkitvkgkagHsg.apgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiR 83 
                                          +t++g+ +H+g ap+ g+NA+ ++  +++ l + +++       ++t +nv+++++ +a nvi++ea++ +++R
  gi|313125434|ref|YP_004035698.1| 220 KLDVTFEGEPAHAGgAPNEGRNALQAMTTAIQNLYAIPRH-----ADGKTRINVGQVHADNAQNVICEEAQMRVEVR 291
                                       57899********************************877.....56****************************** PP

                                       HHHHHHHHHHHHHHHHHHTSCC CS
                         M20_dimer  84 llpgedpeevleeieeilekea 105
                                        ++ +  +  +++ e ++e++a
  gi|313125434|ref|YP_004035698.1| 292 GEDADLNDYMMQKAERVVEHAA 313
                                       9999999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2805.15
//
Query:       gi|313125435|ref|YP_004035699.1|  [L=357]
Description: anthranilate phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-31  108.6   0.0      8e-31  107.5   0.0    1.4  2  Glycos_transf_3  Glycosyl transferase family, a/b domain
    1.3e-07   31.3   0.7    5.4e-07   29.4   0.1    2.3  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
  ------ inclusion threshold ------
      0.013   15.0   0.1      0.022   14.3   0.1    1.3  1  DUF455           Protein of unknown function (DUF455)
       0.16   12.2   0.1       0.45   10.8   0.0    1.7  2  DndE             DNA sulphur modification protein DndE


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.84   3.8e+03     195     214 ..      34      53 ..      21      61 .. 0.75
   2 !  107.5   0.0   1.8e-34     8e-31      20     252 ..     108     347 ..      94     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.84
                                       SHHHHHHHHTTHHTSCHHHH CS
                   Glycos_transf_3 195 epkenaeilkavlegkksaa 214
                                       + +++ e+++++l+g+ +++
  gi|313125435|ref|YP_004035699.1|  34 TREQATEAMQRILAGEPDHT 53 
                                       44778889999999988765 PP

  == domain 2  score: 107.5 bits;  conditional E-value: 1.8e-34
                                       HHHHHHHHHHHTT-BEEEEE-.STCTTCS-H.HHHHCTST--ST--HHHHHHHHHHHSEEEEEHHSSSSHHHHHHHH CS
                   Glycos_transf_3  20 iStaaaivvAaaGvkvakhgn.rsvssksGs.aDvLealgvnleltpeeveklleevgvgflfapeyhkamkhvapv 94 
                                       +  aa+iv+A+aG++v+ h++ r  + k  +   vL++lg++ el+pee +  ++e+g+gf  +p +++ ++   + 
  gi|313125435|ref|YP_004035699.1| 108 LGAAAGIVAAGAGTPVVAHSGdRVPTQKQDAyKHVLDELGIRTELSPEESADQVDETGFGFYYQPAFNPVIHDLWER 184
                                       5678999********99887626667777762579****************************************** PP

                                       HHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEE...EEEESTTSSCCS.TSHHHHHHHHHHHHHHHH CS
                   Glycos_transf_3  95 rrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlk...elgveralvvhg.dGldevsllakttvaelk 167
                                       r ++g+rT  n +  + npa+++ +l + y+  +a+k+  +++   +l   r+++++g +G+d++++ + t v e +
  gi|313125435|ref|YP_004035699.1| 185 RDQMGVRTFVNTIETIANPAKADVHLGSFYHLAFAKKVVDTFEqseQLSPRRVVMFQGmEGYDDIRP-GYTKVGEST 260
                                       ********************************9999998887622268999**************98.89******* PP

                                       TTEEEEEEEEEGSSTSSSEEESHHHHSSH...HHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHH CS
                   Glycos_transf_3 168 dgeiteytlepedfglkraelealeggep...kenaeilkavlegkksaakrdlvllnagaalvlagkadslkegva 241
                                       dge t +++e ++ g+  +  e+le++ +   + +aei ++v++g++++  +d++ lna+  +++ ++a++l+eg++
  gi|313125435|ref|YP_004035699.1| 261 DGEFTDFEIETAEYGMDFE-TEDLEVDPDdvaDDSAEITESVITGDRDDHFADAIELNAAFRIYAREDAETLEEGLE 336
                                       ***************9875.688999654334789**************99************************** PP

                                       HHHHHHHTSHH CS
                   Glycos_transf_3 242 kaeevidsGkA 252
                                        a+e+i+sG+A
  gi|313125435|ref|YP_004035699.1| 337 MARESIESGAA 347
                                       *********99 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.2e-10   5.4e-07      11      62 ..      31      82 ..      24      82 .. 0.95
   2 ?   -2.6   0.0       1.1   5.1e+03       8      20 ..     147     159 ..     140     163 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.2e-10
                                      .---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
                   Glycos_trans_3N 11 eeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmres 62
                                      e+ t+e++ +a++ il ge     ++Af  A r k  +aeE+aa +++m e+
  gi|313125435|ref|YP_004035699.1| 31 EDMTREQATEAMQRILAGEPDHTTLGAFWLANRWKHNNAEELAAYTDVMCEH 82
                                      799**********************************************886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                                       HTT.---HHHHHH CS
                   Glycos_trans_3N   8 rdgeeLtaeeirf 20 
                                         + eL++ee ++
  gi|313125435|ref|YP_004035699.1| 147 GIRTELSPEESAD 159
                                       4557999999776 PP

>> DUF455  Protein of unknown function (DUF455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.9e-06     0.022     171     224 ..      31      84 ..      20      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-06
                            DUF455 171 raagdeesaeiLevIledEitHVaaGvrWfrylcekegldpvetFrelvreyfr 224
                                       + +  e+++e++++Il+ E +H + G  W+    ++++ ++ +++++ + e+++
  gi|313125435|ref|YP_004035699.1|  31 EDMTREQATEAMQRILAGEPDHTTLGAFWLANRWKHNNAEELAAYTDVMCEHVE 84 
                                       34445999*************************************999888765 PP

>> DndE  DNA sulphur modification protein DndE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         2   9.2e+03      50      81 ..      36      69 ..      29      81 .. 0.60
   2 ?   10.8   0.0    0.0001      0.45      43      93 ..     286     335 ..     279     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2
                              DndE 50 dsglelnkktllGe..yqdifeallkqrcqkdgl 81
                                      ++  e  +++l+Ge  ++++    l+ r ++++ 
  gi|313125435|ref|YP_004035699.1| 36 EQATEAMQRILAGEpdHTTLGAFWLANRWKHNNA 69
                                      5666666777777532555555555555555544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0001
                              DndE  43 dakeikddsglelnkktllGeyqdifeallkqrcqkdgletldeeelekal 93 
                                       d+ ++ +d++ e+++++++G+ +d f ++++ ++    +   d e+le+ l
  gi|313125435|ref|YP_004035699.1| 286 DP-DDVADDSAEITESVITGDRDDHFADAIELNAAFRIYAREDAETLEEGL 335
                                       44.788999**********************87777777777888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2241.39
//
Query:       gi|313125436|ref|YP_004035700.1|  [L=347]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-44  148.4   0.0    1.3e-20   73.3   0.0    2.4  2  AsnC_trans_reg2  AsnC-like ligand binding domain
    2.2e-08   33.8   2.3    0.00013   21.7   0.0    3.0  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0064   16.0   0.0        3.5    7.3   0.0    2.9  3  HTH_24           Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.1   3.3e-24     2e-20       6      81 ..      75     149 ..      73     150 .. 0.95
   2 !   73.3   0.0   2.3e-24   1.3e-20       3      82 .]     248     333 ..     246     333 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 3.3e-24
                   AsnC_trans_reg2   6 analvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLpstref 81 
                                       +++l+a+++pe+r+eevaev++ +++v H+Y+R++++n++f+v a+s+++ +e+laei+++tgl+ + +Lp + ++
  gi|313125436|ref|YP_004035700.1|  75 SSTLAAVSAPEDRFEEVAEVINGYRQVNHNYRRDHEWNMWFVVTAASRKKRDEILAEIEEQTGLT-VLNLPMLTDY 149
                                       479**************************************************************.9999987766 PP

  == domain 2  score: 73.3 bits;  conditional E-value: 2.3e-24
                   AsnC_trans_reg2   3 GfkanalvawkvpeerveevaevvaelpevtHcYeR......ewpynlyfmvharseeeveevlaeiaaatgledye 73 
                                       Gf an++v+w+vp+++++  +e v +lp vt+cY R      +w+y l++m+h+r+ ++v+e ++e+aa+    d+e
  gi|313125436|ref|YP_004035700.1| 248 GFDANCMVVWDVPDDELDVRGEDVGRLPYVTLCYHRprrpeqDWQYSLFTMIHGREADAVDEKIDELAAEHLPFDHE 324
                                       9***********************************8888777******************************9*** PP

                   AsnC_trans_reg2  74 vLpstrefK 82 
                                        L+st+++K
  gi|313125436|ref|YP_004035700.1| 325 RLYSTETLK 333
                                       ******998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.2e-08   0.00013       1      42 []      12      56 ..      12      56 .. 0.97
   2 ?   -3.7   0.0       1.9   1.1e+04      29      35 ..     168     174 ..     167     175 .. 0.83
   3 !   11.1   0.3   4.7e-05      0.28       2      41 ..     187     229 ..     186     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.2e-08
                     HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42
                                      LDe+D  ++++ q       +++  L+e +G+Se+++l+Rvr L+
  gi|313125436|ref|YP_004035700.1| 12 LDEVDATLIDEYQSGfpvVERPFDVLGEVLGVSEDEALARVRSLR 56
                                      8*****************************************996 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.9
                     HTH_AsnC-type  29 lSestvl 35 
                                       lSe++v 
  gi|313125436|ref|YP_004035700.1| 168 LSETAVN 174
                                       89**996 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4.7e-05
                     HTH_AsnC-type   2 DeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrL 41 
                                         +D + L ++q     + ++y+++A++v  + + vl+ ++rL
  gi|313125436|ref|YP_004035700.1| 187 SSLDAAVLVEIQDGfplSATPYRDVADAVDADVDDVLAAIQRL 229
                                       578999999999999999************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0     0.002        12      23      46 ..      37      60 ..      33      62 .. 0.91
   2 ?   -1.9   0.1      0.41   2.5e+03       7      20 ..     127     140 ..     127     143 .. 0.80
   3 !    7.3   0.0   0.00058       3.5      19      48 .]     207     236 ..     204     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.002
                            HTH_24 23 LAerlglSpstvnrrlkrLeeeGl 46
                                      L e lg+S    ++r++ L e+G+
  gi|313125436|ref|YP_004035700.1| 37 LGEVLGVSEDEALARVRSLREKGI 60
                                      77999******************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.41
                            HTH_24   7 kILelLqknprisq 20 
                                       +IL +++++ +++ 
  gi|313125436|ref|YP_004035700.1| 127 EILAEIEEQTGLTV 140
                                       59999999988885 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00058
                            HTH_24  19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       ++r++A++++  +  v++ ++rL ++G Ik
  gi|313125436|ref|YP_004035700.1| 207 PYRDVADAVDADVDDVLAAIQRLLDDGCIK 236
                                       7899***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2103.06
//
Query:       gi|313125437|ref|YP_004035701.1|  [L=105]
Description: hypothetical protein Hbor_06630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 626.65
//
Query:       gi|313125438|ref|YP_004035702.1|  [L=119]
Description: hypothetical protein Hbor_06640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 770.72
//
Query:       gi|313125439|ref|YP_004035703.1|  [L=96]
Description: hypothetical protein Hbor_06650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   11.1   1.0       0.25   10.7   1.0    1.2  1  DUF4407   Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0   1.4e-05      0.25      19      64 ..      45      89 ..      37      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.4e-05
                           DUF4407 19 vvlltallAalsgayAlytvlksplllallvGllwgllIfnlDRfi 64
                                      +vl+ ++ A ++g++++y v  + +   +++G ++gl +  + R +
  gi|313125439|ref|YP_004035703.1| 45 LVLVLGFTALVFGTSFAYDVSPVTI-QTVIFGSVVGLTVHVVSRIL 89
                                      699*********************9.************99988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 626.94
//
Query:       gi|313125440|ref|YP_004035704.1|  [L=259]
Description: metal-dependent phosphoesterase, php family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-21   73.6   0.1      2e-20   72.3   0.1    1.8  1  PHP_C     PHP-associated
    7.1e-07   29.7   0.0    7.1e-07   29.7   0.0    1.2  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.1   2.3e-24     2e-20       2      56 .]     142     201 ..     141     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 2.3e-24
                             PHP_C   2 eaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepia.....tpdelleairegrt 56 
                                       ++NrrArrfA+  g+pg++GSDAH++++VGrayTe++ p       t+d +l+air g+t
  gi|313125440|ref|YP_004035704.1| 142 WKNRRARRFARSGGYPGVAGSDAHKVGYVGRAYTEIDIPDVqrvglTADVILDAIRDGAT 201
                                       78**********************************7777778899************87 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0     8e-11   7.1e-07       3      73 ..      10      76 ..       8     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 8e-11
                                      EE--CCC..--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE........ CS
                                      xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  3 HvHteys..lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse 73
                                      HvH++ s  +  +++  e ++++a+e gl+a+ iTDh+++++ v++++ a      g+  i G+e++ ad++ 
  gi|313125440|ref|YP_004035704.1| 10 HVHSDASydAH-DPV--ELILEQAAEIGLDAVVITDHDVIHESVRAAELA---PMYGLVGIPGVEVSTADGHL 76
                                      *******8555.677..******************************999...44589999999988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1757.32
//
Query:       gi|313125441|ref|YP_004035705.1|  [L=587]
Description: ferredoxin subunit of nitrite reductase and ring-hydroxylating dioxygenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-13   48.3   0.0    1.4e-12   47.4   0.0    1.4  1  Rieske    Rieske [2Fe-2S] domain
    3.4e-10   39.8   0.0    6.3e-10   38.9   0.0    1.5  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   1.5e-16   1.4e-12      10      87 ..      20      95 ..      14      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.5e-16
                                      GC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTHHHEEE CS
                            Rieske 10 dvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPaprplat 87
                                      +++++  ++++v g++l+++ + +ge+++++++C+H+g plseg++ e+gvl+C +H ++++   G+  + P  ++++t
  gi|313125441|ref|YP_004035705.1| 20 ELEREGRVQTSVDGRALALFHH-EGEIRVVDNRCPHMGFPLSEGSV-EDGVLTCHWHHARFElSCGDTFD-PWADDVQT 95
                                      66656678899**********6.***********************.899************66665544.55555555 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   7.1e-14   6.3e-10       3     103 ..      13     107 ..      11     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 7.1e-14
                                       EEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT- CS
                          Rieske_2   3 vpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktG 79 
                                        + ++l++l +e +v   vdg++ alf+  ++e+  +dn++p     +ls+G v+d     v+++  +  +f+L+ G
  gi|313125441|ref|YP_004035705.1|  13 RETVPLAELEREGRVQTSVDGRALALFHH-EGEIRVVDNRCPH-MGFPLSEGSVEDG----VLTCHWHHARFELSCG 83 
                                       5678999*********************9.9************.69********998....9*************** PP

                                       BBSS-TTSB-BEE-EEESTSEEEE CS
                          Rieske_2  80 ecledeevslkvypvrvedgkvev 103
                                       + ++  +  ++++pv ++dg+v+v
  gi|313125441|ref|YP_004035705.1|  84 DTFDPWADDVQTFPVEIRDGSVYV 107
                                       **********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 4011.90
//
Query:       gi|313125442|ref|YP_004035706.1|  [L=346]
Description: NAD/fad-dependent oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-20   73.0   2.2    1.5e-11   44.3   0.7    2.0  2  Amino_oxidase    Flavin containing amine oxidoreductase
      1e-14   54.5   0.3      2e-14   53.5   0.3    1.6  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    3.1e-05   23.4   5.4    0.00018   20.8   1.1    2.8  3  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00016   22.1   0.8     0.0013   19.3   0.5    2.3  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00021   21.0   0.1      0.068   12.8   0.1    2.2  2  ApbA             Ketopantoate reductase PanE/ApbA
    0.00029   20.3   0.2     0.0005   19.5   0.2    1.3  1  FAD_oxidored     FAD dependent oxidoreductase
    0.00053   19.7   7.7    0.00066   19.4   6.1    2.1  1  DAO              FAD dependent oxidoreductase
     0.0006   19.2   1.5    0.00099   18.4   1.5    1.3  1  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
     0.0026   17.6   0.1      0.004   17.0   0.1    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0062   15.8   1.5      0.018   14.3   0.4    1.9  2  FAD_binding_3    FAD binding domain
     0.0077   15.4   5.2      0.015   14.4   4.6    1.8  2  FAD_binding_2    FAD binding domain
     0.0088   14.8   2.9      0.012   14.3   2.3    1.5  2  HI0933_like      HI0933-like protein
  ------ inclusion threshold ------
      0.014   14.7   0.9      0.025   13.8   0.9    1.4  1  Thi4             Thi4 family
      0.015   14.4   2.6      0.033   13.3   2.3    1.7  2  GIDA             Glucose inhibited division protein A
      0.025   14.4   0.2      0.054   13.4   0.2    1.6  1  Rossmann-like    Rossmann-like domain
      0.027   14.5   0.1       0.39   10.7   0.0    2.2  2  NAD_binding_9    FAD-NAD(P)-binding
      0.091   12.0   0.1       0.13   11.5   0.1    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
       0.14   12.4   0.1        0.3   11.4   0.1    1.6  1  TrkA_N           TrkA-N domain
        0.2   10.7   0.0       0.27   10.3   0.0    1.1  1  Prenylcys_lyase  Prenylcysteine lyase


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     1e-09   9.8e-07       2      66 ..      13      77 ..      12      89 .. 0.93
   2 !   44.3   0.7   1.6e-14   1.5e-11     199     451 ..     100     341 ..      86     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1e-09
                                      HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHHTTCCCC CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellkelgleds 66
                                      aG  aA+ L +a  +Vt++E +  v GR++t+r+ + +++ Ga+ +  +++ +  l+++lg + +
  gi|313125442|ref|YP_004035706.1| 13 AGVGAAYALRNADAEVTIVEKSRGVCGRAATRRKHDCYYDHGANYIKESDQRTESLIRDLGTDGV 77
                                      8999********************************************************98755 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 1.6e-14
                                       TSCCCEETTHTHHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEE...EESEEEE-S-HHHHH....SS CS
                     Amino_oxidase 199 ggslllprgGlsqlpealaeelrgldirlntrVkeikregdgvtvtledgevv...eaDaVvvTvplgvlk....ai 268
                                       +++ ++ ++G+ ql+++l + + + ++r +trV +i  ++++ t  l d e     ++D+ ++T p +  +    a+
  gi|313125442|ref|YP_004035706.1| 100 DSHKWTWTEGITQLAKRLLA-RTDAEVRRETRVESIVCDDSEATWSLIDTEGEthgPFDRLLLTPPAPQTAeilrAT 175
                                       45667779************.*****************999988888877777778***************777777 PP

                                       EEES.CCSHHHHHHHHHSEEEEEEEEEEEESSGGSGCSTS.E.CECECCCEEETTTEEEEECCECCCSTTTEEEEEE CS
                     Amino_oxidase 269 lfsP.plpdekaeairnlgfgsvnkvilefdrkfwednal.g.qgvlvseltttlgeafissdfpsrappgkglvll 342
                                       +++  +l  ++++a+  + + ++   +l+++  f e+ ++ g   v+ ++   +  ++ +    +++ p+g +l l+
  gi|313125442|ref|YP_004035706.1| 176 EWDGeRLG-DATAAVSDVSYRTIRTFVLHYP--FREEYSWyGlVNVDKAHEVGWVSREECK---DGHVPDGESL-LI 245
                                       77776665.*********************9..8778777654445555555555554444...7899999999.99 PP

                                       EEECHHHHHHHTTS-HHHHHHHHHHHHHHHHTGTSSTCSEEEEEECCT.ETTTSSSEEE.BTTHHHHHHHHHHCHHC CS
                     Amino_oxidase 343 vyvggdaaneleslsdeelvqavlrdLrklfgeevpepkatlvtrWht.dplargsysyvsvgpghedydplakpeg 418
                                       + ++ ++  e      ++ ++++ +d + l+  e  ++ ++   +W + + ++   y   +   ++ d d+++++  
  gi|313125442|ref|YP_004035706.1| 246 AQMSPEWSAE----RYDDPLAEAGDDAAALVA-ELLDDDRYADPDWVDdQGWR---Y---ALPNDGVDTDAVRAT-E 310
                                       *999888877....455555555555666666.66668888999998855677...6...455566788888888.8 PP

                                       STTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 419 dprlffAGehtsreypgtvegAilSGlraAari 451
                                       d +lffAG+++     g+v+ A+  G +aA+ri
  gi|313125442|ref|YP_004035706.1| 311 DAGLFFAGDWVV--GEGRVHHALWNGHEAAERI 341
                                       88*********9..999***************9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.3   2.2e-17     2e-14       1      67 [.       7      71 ..       7      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2.2e-17
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllre 67
                                      IvGaG++G  aAy+L++a+++v+++ek+++++Graa+++ +++ +d+ga++++ s+  +++  l+r+
  gi|313125442|ref|YP_004035706.1|  7 IVGAGAAGVGAAYALRNADAEVTIVEKSRGVCGRAATRRKHDCYYDHGANYIKESD--QRTESLIRD 71
                                      9****************************************************975..888888776 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   1.1     2e-07   0.00018       2      36 ..       4      38 ..       3     103 .. 0.72
   2 ?    0.2   0.0      0.38   3.6e+02     183     225 ..     108     152 ..      97     162 .. 0.82
   3 ?    2.8   0.1     0.058        55     254     292 ..     297     332 ..     282     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtcl 36
                                      +v ++G+G+AG+ aa  l++a a+vt+ve+ + + 
  gi|313125442|ref|YP_004035706.1|  4 RVGIVGAGAAGVGAAYALRNADAEVTIVEKSRGVC 38
                                      57799*********************998333333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE..EEETTSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                       Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgngekle..vvledgee 225
                                       + +++ +++ l + + ev+ +t+v+ i  ++++++  +++++ge+
  gi|313125442|ref|YP_004035706.1| 108 EGITQLAKRLLARTDAEVRRETRVESIVCDDSEATwsLIDTEGET 152
                                       77899999999999***********99999996666788888876 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.058
                                       ETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 254 erggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvq 292
                                       +++g+ +d   +t++ g++ +GD +    g  ++++A  
  gi|313125442|ref|YP_004035706.1| 297 PNDGVDTDAVRATEDAGLFFAGDWV---VGEGRVHHALW 332
                                       67889999999************99...77777777765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   1.3e-06    0.0013       1      35 [.       4      38 ..       4      48 .. 0.89
   2 ?   -0.0   0.0       1.4   1.4e+03      43      72 ..     111     140 ..     106     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      +v +vG+G  g+ +A al++  ++Vt+ve s  ++
  gi|313125442|ref|YP_004035706.1|  4 RVGIVGAGAAGVGAAYALRNADAEVTIVEKSRGVC 38
                                      688**************************998776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  43 skilqeklekngievllntkveeiegsedg 72 
                                        ++ ++ l +   ev+ +t+ve+i+ ++++
  gi|313125442|ref|YP_004035706.1| 111 TQLAKRLLARTDAEVRRETRVESIVCDDSE 140
                                       555566667778899999999999977765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   7.2e-05     0.068       1      33 [.       5      38 ..       5      71 .. 0.81
   2 !    5.9   0.0    0.0096         9      43      87 ..     125     174 ..     108     177 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rl 33
                                      + i+GaGa G   a+ L +a a+vt++ +sr  +
  gi|313125442|ref|YP_004035706.1|  5 VGIVGAGAAGVGAAYALRNADAEVTIVEKSRgVC 38
                                      57***************99********9988554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0096
                                       EEETT..CEEEEEECEEECCH...SCCCCS-ESEEEE-SSGGGHHHHHHH CS
                              ApbA  43 ltseg..geeilrppealsae...ekselepidlvivtvKayqteealee 87 
                                       +++e+  ++ ++ ++ea+++    e +  +p+d +++t +a qt+e l++
  gi|313125442|ref|YP_004035706.1| 125 VRRETrvESIVCDDSEATWSLidtEGETHGPFDRLLLTPPAPQTAEILRA 174
                                       33333323333333333333377778899****************99875 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   5.3e-07    0.0005       3     117 ..       6     138 ..       5     154 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.3e-07
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdig....nkaee..qvvtgiaref.lerlrqrgg 72 
                                        +vG+g+aGv AA+a  +a+a+v +ve+++ + G ++             n+++e  q ++ ++r++ ++ + + ++
  gi|313125442|ref|YP_004035706.1|   6 GIVGAGAAGVGAAYALRNADAEVTIVEKSRGVCGRAATRRKHDCYYdhgaNYIKEsdQRTESLIRDLgTDGVVDIEK 82 
                                       59*************************87776666655443322222234444447756666555552223333222 PP

                      FAD_oxidored  73 a.............rlkkrskwntfepevakavleemlaeagvtvllntrlvevekeg 117
                                                     + ++ +k      e  +++++ +la+ + +v  +tr+++++ ++
  gi|313125442|ref|YP_004035706.1|  83 PvwvfdesgeitegDDGDSHK--WTWTEGITQLAKRLLARTDAEVRRETRVESIVCDD 138
                                       234454444332211112222..46677788888888888888888888888877776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   6.1     7e-07   0.00066       2      44 ..       5      50 ..       4     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7e-07
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEE CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgll 44
                                      v i+G+G +G+++Ay+L  +   Vt++ek++ ++  +a+ r     
  gi|313125442|ref|YP_004035706.1|  5 VGIVGAGAAGVGAAYALRNADaeVTIVEKSRGVCGrAATRRKHDCY 50
                                      78***************555589*******8877437777765555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.5   1.1e-06   0.00099       2      31 ..       7      35 ..       6      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgn 31
                                      I+GaG+aG++aa++l++a+  +++i+Ek +
  gi|313125442|ref|YP_004035706.1|  7 IVGAGAAGVGAAYALRNADA-EVTIVEKSR 35
                                      9*******************.69****975 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   4.3e-06     0.004       2      56 ..       5      59 ..       4      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.3e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56
                                      v+++GaG  G g a+++ +a+ eV++v+ s+    +a+ + ++ +   + ++ +k
  gi|313125442|ref|YP_004035706.1|  5 VGIVGAGAAGVGAAYALRNADAEVTIVEKSRGVCGRAATRRKHDCYYDHGANYIK 59
                                      9*****************************9999999888877666555555555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.4   1.9e-05     0.018       3      34 ..       4      35 ..       2      48 .. 0.91
   2 ?    0.2   0.0      0.37   3.5e+02     112     146 ..     114     149 ..      60     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                       V IVGaG aG+ +a  L++a  +v++vek +
  gi|313125442|ref|YP_004035706.1|  4 RVGIVGAGAAGVGAAYALRNADAEVTIVEKSR 35
                                      699***************************87 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.37
                                       HHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECC CS
                     FAD_binding_3 112 vehaeerg.lqvrfktevesleqdeegvtaevrdke 146
                                       ++++ +r  ++vr++t+ves+  d+++ t  + d e
  gi|313125442|ref|YP_004035706.1| 114 AKRLLARTdAEVRRETRVESIVCDDSEATWSLIDTE 149
                                       44444555599**********999999887777765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   4.6   1.6e-05     0.015       4      35 ..       7      38 ..       4      44 .. 0.89
   2 ?   -2.6   0.0       2.3   2.1e+03     144     174 ..     110     141 ..      95     151 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                      EE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      ++G+G+AG  AA+++++a ++v++vek   + 
  gi|313125442|ref|YP_004035706.1|  7 IVGAGAAGVGAAYALRNADAEVTIVEKSRGVC 38
                                      9**************************87655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                                       HHHHHHHHHTCT.EEEEESEEEEEEEECTTEE CS
                     FAD_binding_2 144 larlvesarkag.vdfqerteadeLivedgrv 174
                                       +  l+++++++   +++ +t++++++ +d ++
  gi|313125442|ref|YP_004035706.1| 110 ITQLAKRLLARTdAEVRRETRVESIVCDDSEA 141
                                       44455555555558888888888888877655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.3   1.3e-05     0.012       3      34 ..       5      36 ..       3      42 .. 0.91
   2 ?   -3.5   0.0       3.4   3.2e+03     116     144 ..     115     142 ..     107     161 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      v ++G+GaAG+ aA ++++++++V+++ek + 
  gi|313125442|ref|YP_004035706.1|  5 VGIVGAGAAGVGAAYALRNADAEVTIVEKSRG 36
                                      679*************************9875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.4
                                       HHHHHHHT-EEE-S--EEEEECETTE.EE CS
                       HI0933_like 116 lkelkeagvklrletevksvekeedgkfr 144
                                       ++ l +++ ++r et+v+s+  ++++  +
  gi|313125442|ref|YP_004035706.1| 115 KRLLARTDAEVRRETRVESIVCDDSE-AT 142
                                       45567788899999999999776665.33 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   2.6e-05     0.025      20      55 ..       5      39 ..       1      43 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                      v ivGaG++G+ aay l ++ d +v+i+e+s  + G
  gi|313125442|ref|YP_004035706.1|  5 VGIVGAGAAGVGAAYALRNA-DAEVTIVEKSRGVCG 39
                                      679**************998.********9876655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.3   3.5e-05     0.033       2      35 ..       5      38 ..       4      47 .. 0.86
   2 ?   -2.2   0.0       1.7   1.6e+03     350     369 ..     306     325 ..     294     342 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldti 35
                                      v ++G+G AG+ AA+a+ ++ a+v+++ ++ + +
  gi|313125442|ref|YP_004035706.1|  5 VGIVGAGAAGVGAAYALRNADAEVTIVEKSRGVC 38
                                      779**********************997666555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                                       SBBSSSBTEEE-CGGGTB-S CS
                              GIDA 350 LetkkvkgLflAGqinGteG 369
                                       ++  +  gLf+AG+    eG
  gi|313125442|ref|YP_004035706.1| 306 VRATEDAGLFFAGDWVVGEG 325
                                       55667899*****9765555 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   5.7e-05     0.054      11      45 ..       3      37 ..       1      69 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-05
                     Rossmann-like 11 lsvGiisaGrvGtalgaaleraghvvvgisaisaa 45
                                      l vGi++aG  G+  ++al  a+  v+ +     +
  gi|313125442|ref|YP_004035706.1|  3 LRVGIVGAGAAGVGAAYALRNADAEVTIVEKSRGV 37
                                      89*********************999877654433 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00042      0.39       2      47 ..       7      47 ..       6      69 .. 0.83
   2 ?    1.4   0.0       0.3   2.8e+02     106     152 ..     112     162 ..     106     163 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdqs 47
                                      ivGaG++G+ ++ +L +      + e+t++++s    gr++ ++++
  gi|313125442|ref|YP_004035706.1|  7 IVGAGAAGVGAAYALRNA-----DAEVTIVEKSRGVCGRAATRRKH 47
                                      9***********999766.....79*******66655787766654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.3
                     NAD_binding_9 106 ellarlpegvtvevhra.evvdleeradgq..avlladgasl.aadaVvLA 152
                                       +l++rl ++++ ev r+ +v+++ ++++++   ++ ++g+++  +d++ L+
  gi|313125442|ref|YP_004035706.1| 112 QLAKRLLARTDAEVRREtRVESIVCDDSEAtwSLIDTEGETHgPFDRLLLT 162
                                       455555555566665444888888887775225566777766588888776 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00014      0.13      30      61 ..       4      35 ..       2      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                      +v ++G+G aG+ A+ + ++ +a+Vt+++++ 
  gi|313125442|ref|YP_004035706.1|  4 RVGIVGAGAAGVGAAYALRNADAEVTIVEKSR 35
                                      689************************99875 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00031       0.3       3      41 ..       7      45 ..       5      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                                      EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT CS
                            TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg 41
                                      i+G+G  G   a  L++ +  +v++++k++ ++ +++ + 
  gi|313125442|ref|YP_004035706.1|  7 IVGAGAAGVGAAYALRNaDA-EVTIVEKSRGVCGRAATRR 45
                                      9****************555.6********9998886544 PP

>> Prenylcys_lyase  Prenylcysteine lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00029      0.27     118     186 ..     101     166 ..      98     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                   Prenylcys_lyase 118 sglwavegGnkqvcsgllkkskanv.inatVtsielksgessslYevtykkesgtesklyDiVviAtPlq 186
                                       s+ w+  +G  q++++ll +++a+v  +++V+si  +++e   ++++  ++  g+++  +D  +++ P  
  gi|313125442|ref|YP_004035706.1| 101 SHKWTWTEGITQLAKRLLARTDAEVrRETRVESIVCDDSE--ATWSLIDTE--GETHGPFDRLLLTPPAP 166
                                       6789999******************999*******96666..478877775..89999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2077.04
//
Query:       gi|313125443|ref|YP_004035707.1|  [L=234]
Description: haloacid dehalogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-15   58.0   0.0    2.1e-15   57.2   0.0    1.4  1  HAD_2           Haloacid dehalogenase-like hydrolase
    4.9e-11   42.5   0.0      1e-10   41.5   0.0    1.6  1  Hydrolase_like  HAD-hyrolase-like
    6.9e-08   33.0   0.1    1.1e-06   29.1   0.1    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
    3.2e-06   27.7   1.3    4.2e-06   27.3   1.3    1.2  1  HAD             haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   4.7e-19   2.1e-15       1     177 [.       6     188 ..       6     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 4.7e-19
                             HAD_2   1 iiFDlDgTlldteelii..qafnelleeyglselseeelrkli.glslrellrklgeseeeee.......kieellr 67 
                                       +iFD Dg+l+  ++l +  +a + ++e  g+ ++  e++++++ g +  ++ + +++ +  +        +     +
  gi|313125443|ref|YP_004035707.1|   6 VIFDNDGVLVRLSPLAVlrEASRAAFEAVGVTDPAAEHVEQMMlGVTPADVREVSEV-YSLDPdafwaarDG-AAAD 80 
                                       799999999987766443389999999999999999999987636666555544444.44444466664322.2223 PP

                             HAD_2  68 kyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedv....ekkKPdpev 140
                                          +e+ +  ++ yd+v      L++ +   giv+++++e+++  l+++++ ++F + ++ e +     +kKP+p  
  gi|313125443|ref|YP_004035707.1|  81 AQISEMRDGRLSCYDDVA----ALEHIRAPRGIVSTNQQETIDAVLDHHDFSHLFATAYGREPTieslRRKKPEPHY 153
                                       344444446777777764....455558899****************************998762222677****** PP

                             HAD_2 141 iekaleklklkkeeviyvGDsptDieaakkagikvia 177
                                       +e+a+  l  ++e +++vGDs tD+ aa++agi+++ 
  gi|313125443|ref|YP_004035707.1| 154 LERAMADL--DAETALFVGDSETDVLAAHRAGIDSAF 188
                                       *****875..7899*******************9875 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   2.3e-14     1e-10       3      74 ..     147     212 ..     145     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.3e-14
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                        KPep  +++a+++l  d e  l++GD+ +tD+++A++aG++s+++++   ++++l    ++pty +++l++
  gi|313125443|ref|YP_004035707.1| 147 KKPEPHYLERAMADL--DAETALFVGDS-ETDVLAAHRAGIDSAFIRRPHRSDTELD---ASPTYEIETLYD 212
                                       6************97..6699*******.*********************9998876...799**9999987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   2.4e-10   1.1e-06       1     210 []       3     183 ..       3     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.4e-10
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH..HHHHHHHHHETTTEHHHHTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar..sgaltgfatfigrgayaigkpe 75 
                                       +++v+fD dG+L++ +p    v+++a                     aa++a+  + + ++  +     + + g   
  gi|313125443|ref|YP_004035707.1|   3 YDAVIFDNDGVLVRLSPLA--VLREA-------------------SRAAFEAVgvTDPAAEHVE-----QMMLGVTP 53 
                                       589**********888544..44444...................3355555554555555555.....56666555 PP

                                       HHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  76 wltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraa 152
                                          ++   +++ + + +a  ++r+ a  +a++ ++     +   ++++a a+++++    + ++++ +++et ++++
  gi|313125443|ref|YP_004035707.1|  54 ADVRE--VSEVYSLDPDAFWAARDGAAADAQISEMRDGRLS--CYDDVA-ALEHIR---APRGIVSTNQQETIDAVL 122
                                       55555..3666666666666666666666666666666666..777774.444445...45778************* PP

                                       HHTT.GGGESEEEEHHCES....STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxx.xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 153 nqlG.ddyfdaviasdiet....vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       ++ +  + f+  ++++ +      +kp+p  +++a+  L ++    ++VGD+ +D+ a+ +Ag
  gi|313125443|ref|YP_004035707.1| 123 DHHDfSHLFATAYGREPTIeslrRKKPEPHYLERAMADLDAET--ALFVGDSETDVLAAHRAG 183
                                       **998666655555554446799****************8777..***************998 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   1.3   9.3e-10   4.2e-06       1     187 [.       6     179 ..       6     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.3e-10
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaellea....llagls.eelaae 72 
                                       ++fD+Dg L++ ++l +l+++ ++ ++    +  +++  ++++      d +++ e+++     ++a+ + ++ +a+
  gi|313125443|ref|YP_004035707.1|   6 VIFDNDGVLVRLSPLAVLREASRAAFEAVGVTDPAAEHVEQMMLGVTPADVREVSEVYSLdpdaFWAARDgAAADAQ 82 
                                       79**************9999888887777777777779999999999999999999998777879999997777777 PP

                               HAD  73 lerfvaevirpklldp.galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkp 148
                                       + +++ + ++ + +d   ale ++   a   +  +vS + ++ + ++l+++++ ++ at       + +e   ++++
  gi|313125443|ref|YP_004035707.1|  83 ISEMR-DGRLSC-YDDvAALEHIR---A---PRGIVSTNQQETIDAVLDHHDFSHLFAT------AYGRE-PTIESL 144
                                       77777.888888.54559*****9...3...4469************************......66666.555666 PP

                               HAD 149 vrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                        r++  ++ l++    + +++d e+  ++GDs++D+ ++
  gi|313125443|ref|YP_004035707.1| 145 RRKKPEPHYLER----AMADLDAETALFVGDSETDVLAA 179
                                       666555566666....888999999**********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1486.98
//
Query:       gi|313125444|ref|YP_004035708.1|  [L=55]
Description: hypothetical protein Hbor_06700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 362.46
//
Query:       gi|313125445|ref|YP_004035709.1|  [L=234]
Description: RecA-superfamily ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-42  143.7   0.0    6.3e-42  143.5   0.0    1.0  1  ATPase          KaiC
    1.8e-06   27.6   0.0    3.1e-06   26.9   0.0    1.3  1  AAA_25          AAA domain
    8.1e-06   25.3   0.0    1.2e-05   24.8   0.0    1.4  1  DnaB_C          DnaB-like helicase C terminal domain
    1.6e-05   24.8   0.0    3.7e-05   23.6   0.0    1.6  1  MEDS            MEDS: MEthanogen/methylotroph, DcmR Sensory d
    1.7e-05   23.7   0.0    4.7e-05   22.2   0.0    1.5  1  GvpD            GvpD gas vesicle protein
    8.6e-05   22.1   0.0    0.00056   19.4   0.0    2.0  2  RecA            recA bacterial DNA recombination protein
      0.001   19.1   0.0     0.0018   18.3   0.0    1.5  1  AAA_14          AAA domain
     0.0016   18.6   0.1     0.0036   17.5   0.1    1.8  1  AAA_33          AAA domain
     0.0017   18.7   0.0     0.0027   18.1   0.0    1.4  1  AAA_19          AAA domain
     0.0024   17.6   0.0     0.0051   16.6   0.0    1.6  1  IstB_IS21       IstB-like ATP binding protein
     0.0032   16.6   0.2       0.25   10.4   0.1    2.1  2  T2SSE           Type II/IV secretion system protein
     0.0081   15.8   0.0      0.018   14.6   0.0    1.6  1  cobW            CobW/HypB/UreG, nucleotide-binding domain
     0.0083   16.4   0.1      0.022   15.1   0.1    1.8  1  AAA_22          AAA domain
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.035   13.8   0.1    1.8  1  AAA_30          AAA domain
      0.014   15.4   0.0      0.019   14.9   0.0    1.2  1  ATPase_2        ATPase domain predominantly from Archaea
      0.017   14.8   0.0      0.058   13.1   0.0    1.9  2  AAA_24          AAA domain
      0.018   15.6   0.1      0.028   15.0   0.1    1.5  1  AAA_18          AAA domain
      0.023   14.7   0.0      0.039   14.0   0.0    1.4  1  AAA_5           AAA domain (dynein-related subfamily)
      0.024   15.1   0.0      0.046   14.1   0.0    1.5  1  AAA             ATPase family associated with various cellula
      0.027   14.2   0.0      0.029   14.1   0.0    1.1  1  Glyco_hydro_18  Glycosyl hydrolases family 18
      0.034   13.3   0.0      0.067   12.3   0.0    1.4  1  DAP3            Mitochondrial ribosomal death-associated prot
      0.034   14.5   0.1      0.064   13.6   0.1    1.7  1  AAA_16          AAA ATPase domain
      0.044   14.0   0.0       0.11   12.8   0.0    1.6  2  AAA_28          AAA domain
      0.075   12.3   0.0       0.17   11.1   0.0    1.5  2  Zeta_toxin      Zeta toxin
      0.098   11.8   0.0        2.1    7.4   0.0    2.0  2  PAXNEB          PAXNEB protein
       0.14   12.2   0.0       0.27   11.2   0.0    1.4  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.5   0.0   9.2e-45   6.3e-42       1     228 [.       3     228 ..       3     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.5 bits;  conditional E-value: 9.2e-45
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       +++g+ g+D++++gG+  gr + ++G pG+GKt+f  q++ +g+++ ge+++++t+ e+ e+l ++++s +  +e l
  gi|313125445|ref|YP_004035709.1|   3 IPSGVSGFDHLIQGGFLPGRLYVLSGPPGSGKTTFTTQYVAEGLRN-GENCMYITMHESREELVNDMSSYDFGFETL 78 
                                       699****************************************999.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaee.....kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvr 149
                                        e++++ +i++++++ ++  +      +++ +++l++++   +++ k+ r+viDs   l +   +    +++ ++++
  gi|313125445|ref|YP_004035709.1|  79 TESDQFRFINLASQKGKHVLNqfsggGGSSGVQSLTDKIVAFVNSRKVDRLVIDSTMLL-QLLFTGD-DQEMTRFLT 153
                                       ***********99998876667999999***************************9999.5555444.58999**** PP

                            ATPase 150 vlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikv 226
                                        lk+ + T++l+se+    +  + y  e+f++ gvi  ++ ++++ ++R +++vkmRgt+++ ++  ++ t+eg +v
  gi|313125445|ref|YP_004035709.1| 154 ALKQGDATTLLISEM----TDPSSYSDEHFLAHGVIFFHNYLEATGMTRGIQVVKMRGTDIDCDIRSLNFTDEGLVV 226
                                       **************6....45577888999999*****************************************999 PP

                            ATPase 227 le 228
                                        +
  gi|313125445|ref|YP_004035709.1| 227 DP 228
                                       76 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   4.5e-09   3.1e-06      24     174 ..      12     157 ..       9     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.5e-09
                            AAA_25  24 wlvk.gllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg...e 95 
                                       +l++ g+lp g l +l G+pg+GKtt++++ +++ +  G+           +++y+   +s++el + ++      e
  gi|313125445|ref|YP_004035709.1|  12 HLIQgGFLP-GRLYVLSGPPGSGKTTFTTQYVAEGLrNGE-----------NCMYITMHESREELVNDMSSYDfgfE 76 
                                       678846776.*********************999993333...........89***************998663346 PP

                            AAA_25  96 alrddarllvldlagv.eslpLfak.drggtl.ltadvdaleaaieevegvrlvviDplsralggdensnsdvgalv 169
                                       +l++ ++ ++++la++ ++  L +  + gg+  +++ +d++ a +++  +v+ +viD+   +      ++ ++++++
  gi|313125445|ref|YP_004035709.1|  77 TLTESDQFRFINLASQkGKHVLNQFsGGGGSSgVQSLTDKIVAFVNS-RKVDRLVIDSTMLLQLLFTGDDQEMTRFL 152
                                       6689999999999988766666544144455589*************.67*******98777777777777888888 PP

                            AAA_25 170 ealer 174
                                       +al++
  gi|313125445|ref|YP_004035709.1| 153 TALKQ 157
                                       88877 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.7e-08   1.2e-05       2      70 ..       3      71 ..       3     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-08
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllss 70
                                      +++g + +D+l++ G+ +g l+++ + p+ Gkt+++++ +++    +  +++++ +  s+e+lv+ + s 
  gi|313125445|ref|YP_004035709.1|  3 IPSGVSGFDHLIQgGFLPGRLYVLSGPPGSGKTTFTTQYVAEGLR-NGENCMYITMHESREELVNDMSSY 71
                                      678899999887527***********************9988775.456899************998775 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.4e-08   3.7e-05      17      69 ..      38      90 ..      35     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.4e-08
                              MEDS 17 lvpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildae 69
                                      + +++++gl++ge ++y++  ++++el + ++++    + + es+q+++++ +
  gi|313125445|ref|YP_004035709.1| 38 TTQYVAEGLRNGENCMYITMHESREELVNDMSSYDFGFETLTESDQFRFINLA 90
                                      579********************************************999865 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.9e-08   4.7e-05      10     201 ..      21     215 ..      17     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.9e-08
                              GvpD  10 GktllikGaPGtGktlftlrgl.dvlrresdvlyvstr.vddetvseay.....fsgeaeldktalldl.lkdplel 78 
                                       G+  ++ G PG+Gkt+ft +++ + lr+ ++ +y++   + +e v+++      f+  +e d+  +++l ++ + ++
  gi|313125445|ref|YP_004035709.1|  21 GRLYVLSGPPGSGKTTFTTQYVaEGLRNGENCMYITMHeSREELVNDMSsydfgFETLTESDQFRFINLaSQKGKHV 97 
                                       778899*************9973679999******975267788998866688888888888888888834566666 PP

                              GvpD  79 dldvdvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvle 155
                                         +         ++sl + + +  +  +   + +ds  ++++ l +  d     + ++  l +l +++   l l++e
  gi|313125445|ref|YP_004035709.1|  98 LNQFSGGGGSSGVQSLTDKIVAFVNSRKVDRLVIDS-TMLLQLLFTGDD-----QEMTRFLTALKQGDATTL-LISE 167
                                       666667777889999999888777777777788899.566666654433.....345666777777766555.6777 PP

                              GvpD 156 taansrl...eyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlq 201
                                          +s+     +++ Gv+ ++   +  g++ r +++ k+rG  i+  ++
  gi|313125445|ref|YP_004035709.1| 168 MTDPSSYsdeHFLAHGVIFFHNYLEATGMT-RGIQVVKMRGTDIDCDIR 215
                                       77766543326899******8877778887.7899******99987665 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   8.2e-07   0.00056      34      90 ..       3      58 ..       1      69 [. 0.89
   2 ?    0.3   0.0      0.58     4e+02     122     141 ..     116     135 ..     104     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.2e-07
                                      E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS CS
                              RecA 34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidae 90
                                      i+sG  ++d  +  GG+  Gr+  + Gp  sGktt++ + +ae  ++g  + +i   
  gi|313125445|ref|YP_004035709.1|  3 IPSGVSGFDHLIQ-GGFLPGRLYVLSGPPGSGKTTFTTQYVAEGLRNGENCMYITMH 58
                                      6788888888665.99999**********************************9764 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.58
                                       HHHHHHTTT--SEEEEE-TT CS
                              RecA 122 iadalvrsgaidlivvdsva 141
                                        + a+v+s  +d +v+ds  
  gi|313125445|ref|YP_004035709.1| 116 KIVAFVNSRKVDRLVIDSTM 135
                                       44568999*********975 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.7e-06    0.0018       3      49 ..      22      68 ..      20      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-06
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                      +++v++G+  +GKTt+  q++ e l + e+++yi++ + r++  +d 
  gi|313125445|ref|YP_004035709.1| 22 RLYVLSGPPGSGKTTFTTQYVAEGLRNGENCMYITMHESREELVNDM 68
                                      6799*********************99*********99888655543 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.2e-06    0.0036       2      39 ..      24      66 ..      23     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.2e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklg......avllssdtlrrrlfg 39
                                       +l G+pGsGK+t+ ++++++ g      +  ++  + r+ l++
  gi|313125445|ref|YP_004035709.1| 24 YVLSGPPGSGKTTFTTQYVAE-GlrngenCMYITMHESREELVN 66
                                      5789*************9844.3345566555666665555554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.8e-06    0.0027       9      78 ..      20     108 ..      14     182 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.8e-06
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal........ 77 
                                       + ++ ++ ++pG+GKT+ +++ va+ +++g    e+++ +++   + +el + +++++   +T+ +           
  gi|313125445|ref|YP_004035709.1|  20 PGRLYVLSGPPGSGKTTFTTQYVAEGLRNG----ENCMYITMH-ESREELVNDMSSYDFGFETLTESDQfrfinlas 91 
                                       567899*******************99999....778888874.456666666666666666655554444555555 PP

                            AAA_19  78 ................l 78 
                                                        
  gi|313125445|ref|YP_004035709.1|  92 qkgkhvlnqfsggggsS 108
                                       55555555555555551 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.4e-06    0.0051      50      91 ..      24      65 ..      10      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.4e-06
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelk 91
                                       vl Gp+G GK+ +++    e+ r+g + +++++++  eel 
  gi|313125445|ref|YP_004035709.1| 24 YVLSGPPGSGKTTFTTQYVAEGLRNGENCMYITMHESREELV 65
                                      5899******************************98766664 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00036      0.25     132     152 ..      24      44 ..      10      62 .. 0.78
   2 ?    4.7   0.0      0.02        14      96     160 ..      61     128 ..      48     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                             T2SSE 132 ilvsGgTgsGKttllyallke 152
                                        ++sG+ gsGKtt++   ++e
  gi|313125445|ref|YP_004035709.1|  24 YVLSGPPGSGKTTFTTQYVAE 44 
                                       589***********9776665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                             T2SSE  96 Rkksakeltlddlgaeealkekiaevlrkavrerglil..vs.GgTgsGKttllyallkeinksderi 160
                                       R++ +++++  d+g+e  ++ ++ ++++ a ++ + +l  +s Gg +sG   l+  +++++n+++   
  gi|313125445|ref|YP_004035709.1|  61 REELVNDMSSYDFGFETLTESDQFRFINLASQKGKHVLnqFSgGGGSSGVQSLTDKIVAFVNSRKVDR 128
                                       66778899999*******************666666665556255678999999********995433 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.6e-05     0.018       3      91 ..      24     134 ..      22     155 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                                       EEEEESTTCCHHHHHHHHH...........CT--SS-EEEEESS-SSCHCCCCCCHCCCT..............EEE CS
                              cobW   3 tvltGflGsGKTtLlnhll...........enraglklavivNefgevsiDaellretgve.............ive 55 
                                       +vl+G++GsGKTt+ ++++             + +++   +vN++++ +   e l+e+++              + +
  gi|313125445|ref|YP_004035709.1|  24 YVLSGPPGSGKTTFTTQYVaeglrngencmYITMHESREELVNDMSSYDFGFETLTESDQFrfinlasqkgkhvLNQ 100
                                       79*************99998865433322211223333345666666555555553332223333344444443444 PP

                                       ETTTTECCHCTT-HHHHHHHHHHHHTT-SEEEEEEC CS
                              cobW  56 lenGciCctlredllkelealeereerldviliEtt 91 
                                       ++ G+      + l+ ++ a+++ + ++d+++i +t
  gi|313125445|ref|YP_004035709.1| 101 FSGGGGSSG-VQSLTDKIVAFVNSR-KVDRLVIDST 134
                                       554444444.556666666666666.6777777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.1e-05     0.022       6      46 ..      22      56 ..      20     170 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvt 46
                                      ++ v+ G++G+GKTt   +++ +  +       +  ++++t
  gi|313125445|ref|YP_004035709.1| 22 RLYVLSGPPGSGKTTFTTQYVAEGLRN------GENCMYIT 56
                                      6789***********999988875432......33333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.1e-05     0.035      19     118 ..      22     161 ..      17     169 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaag..................................grviglAptgkaAkv 61 
                                       r+ vl Gp+G+GKtt  +++++   ++g                                  +r i lA+++   +v
  gi|313125445|ref|YP_004035709.1|  22 RLYVLSGPPGSGKTTFTTQYVAEGLRNGencmyitmhesreelvndmssydfgfetltesdqFRFINLASQKG-KHV 97 
                                       6899***********9998855444455245444444444444444444444444444444444444443322.233 PP

                            AAA_30  62 Lae.elgieastiakllkrlkgrarlepgtllivDEagmv......dtkqlaallkaaekagak 118
                                       L++ + g  +s +++l+++  + ++ ++ + l++D + ++      d ++++++l+a+++ +a+
  gi|313125445|ref|YP_004035709.1|  98 LNQfSGGGGSSGVQSLTDKIVAFVNSRKVDRLVIDSTMLLqllftgDDQEMTRFLTALKQGDAT 161
                                       3321222344444444444444444445566666655444566666666666666666665555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.8e-05     0.019      20      71 ..      21      76 ..      17     139 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie.....e 71
                                       + y++ Gp gsGKt++  + + + +  +++ +y++ ++e++++ ++++       e
  gi|313125445|ref|YP_004035709.1| 21 GRLYVLSGPPGSGKTTFTTQYVAEGLRNGENCMYIT-MHESREELVNDMSSydfgfE 76
                                      568999*******************99888777765.55566666666533445552 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.5e-05     0.058       5      29 ..      24      55 ..      21     139 .. 0.69
   2 ?   -1.4   0.0       2.4   1.6e+03     109     131 ..     146     168 ..     141     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.5e-05
                            AAA_24  5 iliyGpsgiGKTtlakel.......gpkplfi 29
                                      +++ Gp+g+GKTt+ +++       g++  +i
  gi|313125445|ref|YP_004035709.1| 24 YVLSGPPGSGKTTFTTQYvaeglrnGENCMYI 55
                                      5799*************988877777777777 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                            AAA_24 109 eefrrllkklqelrknvifiahe 131
                                       +e++r+l++l++ + +  +i+++
  gi|313125445|ref|YP_004035709.1| 146 QEMTRFLTALKQGDATTLLISEM 168
                                       79999999999988888777765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   4.1e-05     0.028       3      34 ..      26      66 ..      25     154 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.1e-05
                            AAA_18  3 ltGtpGvGKttla.keLskrlgf........gvnlrdvake 34
                                      l+G+pG+GKtt++ +++++ l +          ++r+ + +
  gi|313125445|ref|YP_004035709.1| 26 LSGPPGSGKTTFTtQYVAEGLRNgencmyitMHESREELVN 66
                                      89*********862455555444344455543333333333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.6e-05     0.039       3      42 ..      25      65 ..      24      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                                      EEE--SSSSHHHHHHH.GGGGB..S--EEEEE--TT--HHHHH CS
                             AAA_5  3 lLvGppGtgKselaer.laaal..nreveyvqltrdtteedlk 42
                                      +L GppG+gK++++ + +a+ l  + +  y+ +++  ++e+l+
  gi|313125445|ref|YP_004035709.1| 25 VLSGPPGSGKTTFTTQyVAEGLrnGENCMYITMHE--SREELV 65
                                      699*******9987651566778888999999998..555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.7e-05     0.046       2      40 ..      25      66 ..      24     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.7e-05
                                      EEESSTTSSHHHHHHHHHHH.H..THEEEEEETTTCSSSSTT CS
                               AAA  2 llyGppGtGKTllakavake.l..gvefleisgsellskyvg 40
                                      +l+GppG GKT++  + + e l  g +++ i ++e ++++v 
  gi|313125445|ref|YP_004035709.1| 25 VLSGPPGSGKTTFTTQYVAEgLrnGENCMYITMHESREELVN 66
                                      699********9887655553444577777777777766554 PP

>> Glyco_hydro_18  Glycosyl hydrolases family 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.2e-05     0.029      47     149 ..      71     165 ..       7     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-05
                                       H.......HHHHHHHHHHHHTSTT-EEEEEEEETTTTTHHHHHHTSHHHHHHHHHHHHHHHHHCT-SEEEEEES-TT CS
                                       x.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Glyco_hydro_18  47 l.......gnfeqlkklkkkknpgvkvllsiGGwtdssgfslaastdasrkkfadsvvsllrkygfDGiDidweypg 116
                                       +       ++  q++ +  ++++g+ vl  + G+++ss            +++ d++v++++  ++D + id  +  
  gi|313125445|ref|YP_004035709.1|  71 YdfgfetlTESDQFRFINLASQKGKHVLNQFSGGGGSS----------GVQSLTDKIVAFVNSRKVDRLVIDSTMLL 137
                                       13344444666678888877777999999999999844..........45556689*****************9432 PP

                                       TS...TCHHHHHHHHHHHHHHHHHHHHHHTSTTCEE CS
                                       xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Glyco_hydro_18 117 gn...pedkenytallkelrealdkakategkkllL 149
                                        +   + d + +t++l++l++     +    ++ll+
  gi|313125445|ref|YP_004035709.1| 138 -QllfTGDDQEMTRFLTALKQ----GD---ATTLLI 165
                                       .146777899**********9....32...234444 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.7e-05     0.067      26      70 ..      24      71 ..      20      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.7e-05
                                      EEEE-SSSSSTTTTHHHHHHHGGGS..--EEEEES-G.GGGTSS-S-- CS
                              DAP3 26 lvltGekgsGKSvlLlqalayAlek..gwvvlhvpea.edlvngttey 70
                                      +vl+G +gsGK++  +q +a +l +  + + ++ +e  e+lvn  ++y
  gi|313125445|ref|YP_004035709.1| 24 YVLSGPPGSGKTTFTTQYVAEGLRNgeNCMYITMHESrEELVNDMSSY 71
                                      89*********************9977677777766525677776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.3e-05     0.064      25      46 ..      22      43 ..      10     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-05
                            AAA_16 25 elvllsGesGvGKsslvrellr 46
                                      +l +lsG++G+GK++  ++   
  gi|313125445|ref|YP_004035709.1| 22 RLYVLSGPPGSGKTTFTTQYVA 43
                                      8899***********9976654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00016      0.11       2      48 ..      24      80 ..      23     101 .. 0.64
   2 ?   -1.7   0.0       4.3     3e+03     134     155 ..     184     205 ..     126     210 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                            AAA_28  2 ivitGgestGKTtlleaLaar........gypvvpEaareileekl..akgedalpw 48
                                      +v++G++++GKTt + +  a+         y +++E+  e++++ +  ++g+++l +
  gi|313125445|ref|YP_004035709.1| 24 YVLSGPPGSGKTTFTTQYVAEglrngencMYITMHESREELVNDMSsyDFGFETLTE 80
                                      69***********98554433233334334446688888888776655555555554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
                            AAA_28 134 reaiderlrealrelgipviiv 155
                                          +++ l+++  ++gi+v+ +
  gi|313125445|ref|YP_004035709.1| 184 VIFFHNYLEATGMTRGIQVVKM 205
                                       3445666666666666666666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.17      18      55 ..      23      61 ..      21      72 .. 0.78
   2 ?   -3.0   0.0       5.1   3.5e+03      80     104 ..     110     135 ..     107     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                        Zeta_toxin 18 lillgGqpGAGKselael.lkdelerqgnvvrldpDdlR 55
                                      l++l+G pG+GK++  +  +++ l++++n+  +   + R
  gi|313125445|ref|YP_004035709.1| 23 LYVLSGPPGSGKTTFTTQyVAEGLRNGENCMYITMHESR 61
                                      799*********997665055556688888888766666 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.1
                        Zeta_toxin  80 aselvekllqeaiengyn.iivegtl 104
                                       ++ l++k+++ + +++++ +++++t+
  gi|313125445|ref|YP_004035709.1| 110 VQSLTDKIVAFVNSRKVDrLVIDSTM 135
                                       56788888888888888757788887 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0031       2.1      21      84 ..       5      67 ..       2      71 .. 0.85
   2 ?    2.4   0.0     0.098        68     190     243 ..     112     157 ..      78     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0031
                            PAXNEB 21 tGtpsLDklLgGGLplGsillie...EdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlre 84
                                      +G++ +D+l+ GG+  G + ++     +g+t+f       ++AeG+ ++ + +++++++++ee++++
  gi|313125445|ref|YP_004035709.1|  5 SGVSGFDHLIQGGFLPGRLYVLSgppGSGKTTFT----TQYVAEGLRNGENCMYITMHESREELVND 67
                                      899***************9999844456666665....58******************999999876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.098
                            PAXNEB 190 qiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLra 243
                                       +++ ++ +  f ++ k  v R+vi s +  +l        +++++++FL++L++
  gi|313125445|ref|YP_004035709.1| 112 SLTDKIVA--FVNSRK--VDRLVIDSTMLLQLLF----TGDDQEMTRFLTALKQ 157
                                       33334433..444455..99****9966666634....78999*********97 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00039      0.27      19      41 ..      21      43 ..      10      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                                      TEEEEEEESTTSSHHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglak 41
                                      g++ +L+G+ G+GKTt++ + ++
  gi|313125445|ref|YP_004035709.1| 21 GRLYVLSGPPGSGKTTFTTQYVA 43
                                      56789************976554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1361.49
//
Query:       gi|313125446|ref|YP_004035710.1|  [L=137]
Description: hypothetical protein Hbor_06720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 859.27
//
Query:       gi|313125447|ref|YP_004035711.1|  [L=135]
Description: methionine-r-sulfoxide reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-52  175.0   0.0    6.2e-52  174.8   0.0    1.0  1  SelR            SelR domain
  ------ inclusion threshold ------
      0.013   15.2   2.7        1.5    8.7   0.2    2.6  2  zinc_ribbon_2   zinc-ribbon domain
      0.052   13.8   0.2       0.14   12.4   0.2    1.7  2  Yippee-Mis18    Yippee zinc-binding/DNA-binding /Mis18, centr
        0.1   12.6   2.1       0.51   10.4   2.1    2.1  1  DZR             Double zinc ribbon
       0.12   12.4   0.0       0.12   12.4   0.0    2.9  4  DUF1610         Domain of unknown function (DUF1610)
       0.15   11.7   2.8        9.4    5.9   0.1    2.6  3  GATA            GATA zinc finger
       0.18   11.3   6.4       0.93    9.1   0.2    2.9  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.27   11.4   1.8        2.1    8.6   0.1    2.4  2  Ribosomal_L37e  Ribosomal protein L37e


Domain annotation for each model (and alignments):
>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.8   0.0   2.8e-55   6.2e-52       1     121 []      15     133 ..      15     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 174.8 bits;  conditional E-value: 2.8e-55
                                       HHHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEEC CS
                              SelR   1 elkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdts 77 
                                       e++++L++e+y++lre+gte+ f+g++ +  e+G+y c++cg++Lf++etkfdsgcGwpsF++a+++ a+++++dt+
  gi|313125447|ref|YP_004035711.1|  15 EWRERLSEEEYHILRERGTEPRFSGDHVDRDEDGAYLCTGCGAELFDAETKFDSGCGWPSFFAAHDD-AIETETDTR 90 
                                       7***************************************************************999.********* PP

                                       TTSEEEEEEETTCECEEEEEECTSSSSS.SEEEEE-CCCEEEEE CS
                              SelR  78 lgmertevvcakcdahlGhvFedgpkpttgkrycinsvslkfkp 121
                                       +gm+r+ev c++c++hlGhvF+dgp+pt gkrycinsv+l+f p
  gi|313125447|ref|YP_004035711.1|  91 HGMRRIEVLCENCGGHLGHVFDDGPEPT-GKRYCINSVALEFDP 133
                                       **************************95.*************86 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2   0.00065       1.5      10      23 .]      46      59 ..      46      59 .. 0.90
   2 ?    5.9   0.2    0.0047        11      14      22 ..      98     106 ..      97     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00065
                     zinc_ribbon_2 10 qdnakFCpyCGtpl 23
                                      +d+a  C+ CG++l
  gi|313125447|ref|YP_004035711.1| 46 EDGAYLCTGCGAEL 59
                                      59999******997 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0047
                     zinc_ribbon_2  14 kFCpyCGtp 22 
                                       + C++CG +
  gi|313125447|ref|YP_004035711.1|  98 VLCENCGGH 106
                                       679999855 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.79   1.8e+03      57      65 ..      51      59 ..      30      60 .. 0.78
   2 ?   12.4   0.2   6.3e-05      0.14      35      84 ..      81     128 ..      48     132 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.79
                                      EETTT--EE CS
                      Yippee-Mis18 57 sCkgCnsvl 65
                                       C+gC+++l
  gi|313125447|ref|YP_004035711.1| 51 LCTGCGAEL 59
                                      688888765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.3e-05
                                       CCEEEECEEEETTSTTEEEEEEEETTT--EEEEEEEECSCC..CCCCCTCEE CS
                      Yippee-Mis18  35 rnvvvgkelvtdeegkctystlsCkgCnsvlGwkYksteee..lkykrglfi 84 
                                       +++ +++ + +         ++ C++C+ +lG ++ + +e    +y+++   
  gi|313125447|ref|YP_004035711.1|  81 DAIETETDTRHG----MRRIEVLCENCGGHLGHVFDDGPEPtgKRYCINSVA 128
                                       444444444444....677899*************99988744555555554 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.1   0.00023      0.51      10      35 ..      47     104 ..      26     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                               DZR  10 pdarfCseCgtklkavaa................................edrCpsCg 35 
                                       ++a  C  Cg++l  +++                                e  C +Cg
  gi|313125447|ref|YP_004035711.1|  47 DGAYLCTGCGAELFDAETkfdsgcgwpsffaahddaietetdtrhgmrriEVLCENCG 104
                                       6788999999999876668999999999999999999999999999999999999998 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.3   9.7e+03      11      16 ..      29      34 ..      29      34 .. 0.82
   2 ?   12.4   0.0   5.2e-05      0.12       1      17 [.      52      66 ..      52      67 .. 0.94
   3 ?   -1.0   0.1      0.81   1.8e+03       2       7 ..      68      73 ..      67      73 .. 0.75
   4 ?   -1.9   2.2       1.5   3.4e+03      19      23 ..     100     104 ..      99     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.3
                           DUF1610 11 rEravv 16
                                      rEr+++
  gi|313125447|ref|YP_004035711.1| 29 RERGTE 34
                                      899995 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.2e-05
                           DUF1610  1 CtSCGaelaprEravvF 17
                                      Ct CGael ++E  ++F
  gi|313125447|ref|YP_004035711.1| 52 CTGCGAELFDAE--TKF 66
                                      ************..998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.81
                           DUF1610  2 tSCGae 7 
                                      + CG++
  gi|313125447|ref|YP_004035711.1| 68 SGCGWP 73
                                      679996 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.5
                           DUF1610  19 CPNCG 23 
                                       C NCG
  gi|313125447|ref|YP_004035711.1| 100 CENCG 104
                                       789*9 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       3.5   7.9e+03      11      14 ..      15      18 ..      11      20 .. 0.71
   2 ?    5.7   0.0     0.005        11      14      27 ..      44      56 ..      40      58 .. 0.89
   3 ?    5.9   0.1    0.0042       9.4      13      27 ..      90     104 ..      82     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.5
                              GATA 11 lWRr 14
                                      +WR+
  gi|313125447|ref|YP_004035711.1| 15 EWRE 18
                                      7996 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.005
                              GATA 14 rgpdgnksLCnaCG 27
                                      r++dg++ LC+ CG
  gi|313125447|ref|YP_004035711.1| 44 RDEDGAY-LCTGCG 56
                                      7899***.*****9 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0042
                              GATA  13 RrgpdgnksLCnaCG 27 
                                       R+g++    LC++CG
  gi|313125447|ref|YP_004035711.1|  90 RHGMRRIEVLCENCG 104
                                       777444445999999 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00041      0.93      15      29 ..      45      59 ..      35      75 .. 0.81
   2 ?    4.5   1.0     0.011        24      18      26 ..      96     104 ..      83     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00041
                                      TSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon 15 pergelvCtdCGlVl 29
                                       e g ++Ct CG+ l
  gi|313125447|ref|YP_004035711.1| 45 DEDGAYLCTGCGAEL 59
                                      4779********876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                                       TCEEESSSS CS
                      TF_Zn_Ribbon  18 gelvCtdCG 26 
                                        e++C++CG
  gi|313125447|ref|YP_004035711.1|  96 IEVLCENCG 104
                                       5899****7 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00095       2.1      18      41 ..      51      74 ..      44      75 .. 0.93
   2 ?    1.6   0.3      0.14   3.1e+02      14      25 ..      95     106 ..      87     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00095
                    Ribosomal_L37e 18 lCrrCgkrsyhvqkktCascGyps 41
                                      lC  Cg + +  ++k  + cG+ps
  gi|313125447|ref|YP_004035711.1| 51 LCTGCGAELFDAETKFDSGCGWPS 74
                                      8*********************96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                    Ribosomal_L37e  14 ktHilCrrCgkr 25 
                                       ++ +lC+ Cg +
  gi|313125447|ref|YP_004035711.1|  95 RIEVLCENCGGH 106
                                       46689****965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 886.60
//
Query:       gi|313125448|ref|YP_004035712.1|  [L=69]
Description: hypothetical protein Hbor_06740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:00.47
# Mc/sec: 438.79
//
Query:       gi|313125449|ref|YP_004035713.1|  [L=810]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-41  142.3  28.5    1.3e-41  142.3  28.5    3.8  3  MCPsignal      Methyl-accepting chemotaxis protein (MCP) sign
    9.7e-13   48.3   5.7    2.3e-09   37.5   0.8    4.0  3  HAMP           HAMP domain
    1.1e-05   25.4   0.2    1.1e-05   25.4   0.2    3.7  3  dCache_1       Cache domain
     0.0074   16.2  10.8     0.0074   16.2  10.8    2.0  1  DUF5089        Domain of unknown function (DUF5089)
  ------ inclusion threshold ------
      0.014   14.7   0.8      0.047   13.0   0.8    1.9  1  Vps54_N        Vacuolar-sorting protein 54, of GARP complex
      0.019   14.7   0.1      0.073   12.8   0.1    2.0  1  Phage_Mu_Gp45  Bacteriophage Mu Gp45 protein
      0.019   14.6   1.2         16    5.2   0.1    3.7  3  RPW8           Arabidopsis broad-spectrum mildew resistance p
      0.067   12.1   9.2       0.27   10.2   2.2    3.3  3  IFT57          Intra-flagellar transport protein 57
       0.14   11.6  18.2      0.046   13.2   3.2    3.3  3  Mce4_CUP1      Cholesterol uptake porter CUP1 of Mce4, putati
       0.23   10.5   3.1       0.13   11.3   0.5    1.9  2  Atg14          Vacuolar sorting 38 and autophagy-related subu
       0.34   11.2  21.4        7.2    7.0   1.3    5.7  5  BLOC1_2        Biogenesis of lysosome-related organelles comp
       0.36   10.8  35.7      0.032   14.2   5.3    5.3  5  Laminin_II     Laminin Domain II
       0.39   11.0  42.5      0.097   12.9   6.2    7.2  8  DUF948         Bacterial protein of unknown function (DUF948)
        0.4   10.8   3.6        1.3    9.1   0.4    2.7  2  TPPK_C         Thiamine pyrophosphokinase C terminal
       0.63    9.1  18.4        1.4    7.9   6.6    2.5  2  AIP3           Actin interacting protein 3
        2.2    6.1  11.4          5    4.9   5.1    2.2  2  Prominin       Prominin
        2.4    7.3   8.9        5.6    6.1   1.5    3.2  3  TMPIT          TMPIT-like protein
        3.4    7.8  13.7        4.1    7.5   4.4    3.5  3  Nup54          Nucleoporin complex subunit 54
        4.8    7.9  23.0        1.4    9.7   1.2    4.7  4  DUF2203        Uncharacterized conserved protein (DUF2203)
        5.5    7.0  26.4       0.84    9.7   4.8    5.4  5  DUF1664        Protein of unknown function (DUF1664)
        9.3    6.2  11.2         17    5.4   0.3    4.4  5  BORCS8         BLOC-1-related complex sub-unit 8


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   6.9    0.0075       6.4      87     169 ..     439     521 ..     423     529 .. 0.77
   2 !  142.3  28.5   1.5e-44   1.3e-41       5     171 ..     539     705 ..     531     706 .. 0.92
   3 ?    1.9   2.0       0.2   1.7e+02     110     169 ..     707     738 ..     698     759 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0075
                                       HHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  87 aakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnq 163
                                          e++a++ + q  ++ ++++  +t  +v+   +  ++  e++ +i + + + +d +++ a   +e sa++++++ 
  gi|313125449|ref|YP_004035713.1| 439 MVDELAAVVGDAQSFSEGVADASAQTSANVAAVKDASADVSESMTNILDDAVRQDDHLTDAADRMNEFSATVQQMSA 515
                                       45667777777777778888888888888888888888889999999999888888888888888888888888888 PP

                                       HHHHHH CS
                         MCPsignal 164 aveeva 169
                                       + + va
  gi|313125449|ref|YP_004035713.1| 516 SAADVA 521
                                       877765 PP

  == domain 2  score: 142.3 bits;  conditional E-value: 1.5e-44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHH CS
                         MCPsignal   5 eeaseeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLA 81 
                                       e+a  e +  ++  a++v+++ee+e+  ++i+ +++ id+ia+QTN+LALNA+iEAARAGe+G+GFaVVA+EV++LA
  gi|313125449|ref|YP_004035713.1| 539 EDAVAELQVIDEATAETVSTVEELESVIEDIESVVSFIDGIAEQTNILALNASIEAARAGEAGEGFAVVAEEVKSLA 615
                                       33333333346677899************************************************************ PP

                                       HHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  82 ersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasi 158
                                       ++++ a+++ie+ i ++ ++++++++ +  tr+rv  gse+v e+ +a+++iv+ v++ ++ vqei aa+e q++++
  gi|313125449|ref|YP_004035713.1| 616 AETQAATEDIESSIDRVREQTETTADDIRRTRERVVDGSETVTEAMDAIETIVDDVEQTSEAVQEIRAATERQAETA 692
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHH CS
                         MCPsignal 159 eevnqaveevakv 171
                                       +ev   v+ v+++
  gi|313125449|ref|YP_004035713.1| 693 TEVVGVVADVSEI 705
                                       *****99999876 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 110 eetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                       + t + +                            ++ aa++++q+as+  v+++v+ +a
  gi|313125449|ref|YP_004035713.1| 707 DRTSSAA----------------------------EDAAATAQQQTASLVAVSDSVDSLA 738
                                       2233333............................3444444444444444444444332 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.8   2.7e-12   2.3e-09       1      52 [.     333     384 ..     333     385 .. 0.97
   2 !   10.7   0.0   0.00062      0.53      16      52 ..     407     444 ..     405     445 .. 0.89
   3 ?   -2.1   0.0       6.2   5.3e+03      16      39 ..     733     746 ..     720     762 .. 0.58

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.7e-12
                                       HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                       ++ rr++r L  L++ a+ +a+G+l+++l+ s+ DE+G+L  a++aM+ +Lr
  gi|313125449|ref|YP_004035713.1| 333 VIGRRTTRTLTHLTDRAEMMADGHLEEPLESSREDEFGRLYDAVDAMRASLR 384
                                       589***********************************************98 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00062
                                       HHHHHTTTBTSSTCCT.TSSSHHHHHHHHHHHHHHHHH CS
                              HAMP  16 aarriaaGdldtrlpv.sgrDEiGeLarafNaMldrLr 52 
                                       ++++ a+Gdl+ r ++ + +  ++++a+a+N+M+d+L 
  gi|313125449|ref|YP_004035713.1| 407 VMEQCADGDLTCRMDPdDENKAMADVAHAYNRMVDELA 444
                                       6788899******888899999*************995 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.2
                                       HHHHHTTTBTSSTCCTTSSSHHHH CS
                              HAMP  16 aarriaaGdldtrlpvsgrDEiGe 39 
                                       +++++a+          + DE+ +
  gi|313125449|ref|YP_004035713.1| 733 SVDSLAD----------RADELQQ 746
                                       4444442..........3344433 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.2   1.3e-08   1.1e-05       4     247 ..      79     297 ..      76     299 .. 0.73
   2 ?   -2.4   0.3       3.7   3.2e+03       8      43 ..     548     586 ..     543     599 .. 0.50
   3 ?   -0.8   4.3       1.3   1.1e+03      10      44 ..     613     645 ..     605     773 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.3e-08
                          dCache_1   4 eeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgv.yl 79 
                                        +q+e q++++ae+ a+ ++++l+s  ++++ l++ +++q           + r++   l+ + ++  +d+ ++ y+
  gi|313125449|ref|YP_004035713.1|  79 DSQVETQVTSTAELQADGMDEWLASKSAQTRALSQAKEFQL---------GQERKIDLYLFSQANDLSSDVVAIhYV 146
                                       579******************************99777664.........344555555566677777888888777 PP

                          dCache_1  80 vdadGqviassdpssppnlegtddpadrdw..ykealaggg...gkpvisdp.yvdqtggkpvitiavpiyddsgkf 150
                                         a+G+v++s+ +++++     +     +w   ++a++++      +++s++ y +++ +   +++++++ ++  + 
  gi|313125449|ref|YP_004035713.1| 147 RVASGDVVSSTAREMKGEN---AAEMGLPWaeNRTAIDSKTndaSVVHVSKTpYESPVADGKALAFISAVPSN-TEH 219
                                       789*****98888876443...455555566556788888788855555555367777677889999999875.466 PP

                          dCache_1 151 iGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpdkdllgknlrdelkaqealekalakiesgvssvkln 227
                                         v++++l+  ++ ++++++ +   g++ i d +G +++++ +d  + n++          +a  ++  +     + 
  gi|313125449|ref|YP_004035713.1| 220 AVVVTVNLT-HRVGQFYQTMAE---GETTIYDVEGDPVVSTGPDAEATNVS----------HAALGTSAQF----SR 278
                                       666666666.679999999975...668************99977444333..........3322222222....46 PP

                          dCache_1 228 geeylva.yapiptglgWylv 247
                                       g++  va yap++ + +W + 
  gi|313125449|ref|YP_004035713.1| 279 GDDA-VAaYAPLD-DMNWVVG 297
                                       9999.888****9.6***986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.7
                          dCache_1   8 eeqllglaeqlanniedvldsle...nlaetlasnpslq 43 
                                       ++++++   ++ +++e+v++ +e   ++   +a+  ++ 
  gi|313125449|ref|YP_004035713.1| 548 IDEATAETVSTVEELESVIEDIEsvvSFIDGIAEQTNIL 586
                                       555555555566666666655552222222334444443 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.3
                          dCache_1  10 qllglaeqlanniedvldslenlaetlasnpslqd 44 
                                       +l +  + ++++ie+ +d+++ ++et a +  +++
  gi|313125449|ref|YP_004035713.1| 613 SLAAETQAATEDIESSIDRVREQTETTADD--IRR 645
                                       555667778889999999999999999887..333 PP

>> DUF5089  Domain of unknown function (DUF5089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  10.8   8.7e-06    0.0074      18     186 ..     538     715 ..     522     721 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.7e-06
                           DUF5089  18 akkarkkLesaartqkkTtkelrkQgekLekakqsaikvhknaekgeelakk..ik..regkvfvfkspvvdkikkw 90 
                                       a +a ++L+ + + + +T  ++++ + ++e+++     +   ae+ + la +  i+  r+g++ +  + v +++k++
  gi|313125449|ref|YP_004035713.1| 538 AEDAVAELQVIDEATAETVSTVEELESVIEDIESVVSFIDGIAEQTNILALNasIEaaRAGEAGEGFAVVAEEVKSL 614
                                       6778888898999999999999999999999999999999999999988754224422789999999999******* PP

                           DUF5089  91 fkkdkkaeeeveeiknkeeeakeeeedkk.eeeefipedkel....vpgeektdkeLekilnglkslkkeaevQnke 162
                                       +++ + a e++e++ ++  e+ e ++d   +  e++ ++ e+    +++ e+  +  e++ ++++++++ +e Q + 
  gi|313125449|ref|YP_004035713.1| 615 AAETQAATEDIESSIDRVREQTETTADDIrRTRERVVDGSETvteaMDAIETIVDDVEQTSEAVQEIRAATERQAET 691
                                       *********************888888876888999999998666678899999*********************** PP

                           DUF5089 163 ikkqkskikdItkvneksekevkk 186
                                       +++    + d+++++ +++  +++
  gi|313125449|ref|YP_004035713.1| 692 ATEVVGVVADVSEISDRTSSAAED 715
                                       ******************999886 PP

>> Vps54_N  Vacuolar-sorting protein 54, of GARP complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.8   5.6e-05     0.047      19      99 ..     610     694 ..     601     704 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
                           Vps54_N  19 eLkklpdde.lsyesiekevkklksqhdvvskkl...sqlilekreefvkelseveeiekelkesvvickngrraLd 91 
                                       e k+l ++  ++ e+ie++++++++q +  ++ +    +++++ +e +++ ++++e i ++++++   ++++r a +
  gi|313125449|ref|YP_004035713.1| 610 EVKSLAAETqAATEDIESSIDRVREQTETTADDIrrtRERVVDGSETVTEAMDAIETIVDDVEQTSEAVQEIRAATE 686
                                       677777766699999************9999765222689*********************************9988 PP

                           Vps54_N  92 lakkeltr 99 
                                          + +t+
  gi|313125449|ref|YP_004035713.1| 687 RQAETATE 694
                                       87777666 PP

>> Phage_Mu_Gp45  Bacteriophage Mu Gp45 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   8.6e-05     0.073      44      93 ..     203     256 ..     175     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                                       XX.XXXXXXXXXXXXXXXXXXXXXX--S--....-SSSTT-EEEE-TTS-EEEEE CS
                     Phage_Mu_Gp45  44 aG.aeaivlavgGdrshgvviavedrryRl....kglkeGevalYddegqkvvlk 93 
                                       +G a a++ av  +++h+vv+ v+   +R+    + ++eGe+++Yd eg+ vv +
  gi|313125449|ref|YP_004035713.1| 203 DGkALAFISAVPSNTEHAVVVTVN-LTHRVgqfyQTMAEGETTIYDVEGDPVVST 256
                                       443667778888999999998876.555552223679*************99866 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2     1e+03      36      70 ..     375     409 ..     363     415 .. 0.64
   2 ?    5.1   0.0     0.019        16      25      58 ..     550     583 ..     536     595 .. 0.80
   3 ?    5.2   0.1     0.018        16      36      86 ..     656     706 ..     641     714 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                              RPW8  36 rLestleritPvvkeieklnkeldrpreeieeLkk 70 
                                         +++  +++++++e e ln++l++  e+    ++
  gi|313125449|ref|YP_004035713.1| 375 AVDAMRASLRTSLHEAEALNNHLESTAEDYRAVME 409
                                       44555566777777777777777777766665555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.019
                              RPW8  25 kksldfksilkrLestleritPvvkeieklnkel 58 
                                       + ++++ s++++Les +e+i+ vv  i+ + ++ 
  gi|313125449|ref|YP_004035713.1| 550 EATAETVSTVEELESVIEDIESVVSFIDGIAEQT 583
                                       3456677889**************9999988765 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.018
                              RPW8  36 rLestleritPvvkeieklnkeldrpreeieeLkklLekaekLVekcsklk 86 
                                          + + +i+++v+++e+ ++++++ r+ +e+  ++ ++    V   s+++
  gi|313125449|ref|YP_004035713.1| 656 TVTEAMDAIETIVDDVEQTSEAVQEIRAATERQAETATEVVGVVADVSEIS 706
                                       567899*****************9999999998888888888887777776 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.21   1.8e+02     267     331 ..     392     460 ..     356     472 .. 0.63
   2 ?    2.9   0.1      0.05        42     250     320 ..     460     530 ..     444     551 .. 0.75
   3 ?   10.2   2.2   0.00031      0.27     247     330 ..     611     694 ..     592     750 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                             IFT57 267 ylnsqleellqeyreaqeelsevkekyk....qlsegvseltrelaeiseelekvkqemeergssmtDg 331
                                        ln+ le++ ++yr++ e+ ++    ++    + ++ + +  + ++++ +el +v  + ++ ++ ++D+
  gi|313125449|ref|YP_004035713.1| 392 ALNNHLESTAEDYRAVMEQCADGDLTCRmdpdDENKAMADVAHAYNRMVDELAAVVGDAQSFSEGVADA 460
                                       466666666666666666666544333311114455555555666666666666655555555555555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.05
                             IFT57 250 lhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqe 320
                                        + + s  +  ++     + +++ + l++   + ++l+++ +++++ s++v++++   a++ e+ +++ ++
  gi|313125449|ref|YP_004035713.1| 460 ASAQTSANVAAVKDASADVSESMTNILDDAVRQDDHLTDAADRMNEFSATVQQMSASAADVAERADAAAER 530
                                       55555566666666666677777888888888889999999999999999999999999999988877655 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00031
                             IFT57 247 lkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemee 323
                                       +k l  + + + e ies   ++ +q e++ ++ r ++e++ + +e + ++ + ++   ++ +++se ++++    e 
  gi|313125449|ref|YP_004035713.1| 611 VKSLAAETQAATEDIESSIDRVREQTETTADDIRRTRERVVDGSETVTEAMDAIETIVDDVEQTSEAVQEIRAATER 687
                                       33444444444444444444444444444444444444444444444444444444444444444444444333333 PP

                             IFT57 324 rgssmtD 330
                                       + +++t+
  gi|313125449|ref|YP_004035713.1| 688 QAETATE 694
                                       3333332 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.2   5.4e-05     0.046      57     174 ..     425     543 ..     415     557 .. 0.92
   2 ?    5.6   2.1     0.011       9.4      34     113 ..     601     681 ..     582     696 .. 0.79
   3 ?    0.1   0.2      0.54   4.6e+02      56      92 ..     725     761 ..     714     766 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-05
                         Mce4_CUP1  57 direladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadllerngdnLirlaadlrptle 133
                                       + +++ad+a++Y+   ++l  ++ +a   s+ +++ +a+ +a ++a+  +s ++++ +++  d+ +r  ++l  +++
  gi|313125449|ref|YP_004035713.1| 425 ENKAMADVAHAYNRMVDELAAVVGDAQSFSEGVADASAQTSANVAAVKDASADVSESMTNILDDAVRQDDHLTDAAD 501
                                       57899************************************************************************ PP

                         Mce4_CUP1 134 lLakYspeltCllrnladvepkvaka.lggtngyslrldatl 174
                                        ++++s +   + + +adv++++++a   g++g+++  da  
  gi|313125449|ref|YP_004035713.1| 502 RMNEFSATVQQMSASAADVAERADAAaERGERGRAAAEDAVA 543
                                       ************************999999999988766554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                         Mce4_CUP1  34 GesltdlnevLdelNprlpqlredire.ladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsnt 109
                                       Ge  + + e ++ l +++  ++edi++ + ++ +  +  a+d+ ++ + +v  s+T++e  +++++++ ++ ++s+ 
  gi|313125449|ref|YP_004035713.1| 601 GEGFAVVAEEVKSLAAETQAATEDIESsIDRVREQTETTADDIRRTRERVVDGSETVTEAMDAIETIVDDVEQTSEA 677
                                       55555666667778888888889987525678888999999999999999999999999999999999999999998 PP

                         Mce4_CUP1 110 gadl 113
                                       ++++
  gi|313125449|ref|YP_004035713.1| 678 VQEI 681
                                       8876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.54
                         Mce4_CUP1  56 edireladladvYadaapdlldaLdnavttsrTiveq 92 
                                       + + ++ d  d  ad a++l +aLd + +t + +v+ 
  gi|313125449|ref|YP_004035713.1| 725 ASLVAVSDSVDSLADRADELQQALDRFDVTGSVVVAD 761
                                       4444555666788999999999999999998888765 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       3.1   2.6e+03      23      55 ..     502     534 ..     462     572 .. 0.50
   2 ?   11.3   0.5   0.00015      0.13      29     143 ..     609     737 ..     596     762 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.1
                             Atg14  23 rlyelrerlaklksekeslkkkiekalegkeea 55 
                                       r++e    ++++ +  + + ++ ++a e+ e++
  gi|313125449|ref|YP_004035713.1| 502 RMNEFSATVQQMSASAADVAERADAAAERGERG 534
                                       333333333333333333333333333333333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00015
                             Atg14  29 erlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkkla 105
                                       e++++l +e ++  + ie  + + +      ++ +++++++++++ ++ d +e + e +d +++  + +e++++ ++
  gi|313125449|ref|YP_004035713.1| 609 EEVKSLAAETQAATEDIESSIDRVR------EQTETTADDIRRTRERVVDGSETVTEAMDAIETIVDDVEQTSEAVQ 679
                                       4566666666666666666666666......7777777778888888888888877777777777777777777777 PP

                             Atg14 106 klsdklk....................kRrsdleslqneleerrkkqiaklqdaikri 143
                                       + ++++                     +R+s+++      ++ +++++  ++d++   
  gi|313125449|ref|YP_004035713.1| 680 EIRAATErqaetatevvgvvadvseisDRTSSAAEDAAATAQQQTASLVAVSDSVDSL 737
                                       7777776666666688888888888888888877777777777777777776666644 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.9   7.7e+02      38      64 ..     375     401 ..     368     413 .. 0.51
   2 ?    3.0   0.3      0.15   1.3e+02      40      84 ..     476     520 ..     457     527 .. 0.62
   3 ?    6.3   0.5     0.013        11      47      88 ..     539     580 ..     522     585 .. 0.77
   4 ?    7.0   1.3    0.0084       7.2      38      91 ..     635     688 ..     605     693 .. 0.78
   5 ?    3.9   0.6     0.078        66      37      83 ..     703     750 ..     686     754 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.9
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpyl 64 
                                       +++ + asl+++l++ ++++++l++  
  gi|313125449|ref|YP_004035713.1| 375 AVDAMRASLRTSLHEAEALNNHLESTA 401
                                       445555555555555555555544432 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.15
                           BLOC1_2  40 kdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseL 84 
                                       +dv +s+++ l++  +++++l    ++++++ ++v+++ + ++ +
  gi|313125449|ref|YP_004035713.1| 476 ADVSESMTNILDDAVRQDDHLTDAADRMNEFSATVQQMSASAADV 520
                                       334444444455566777777778888888888888877777655 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.013
                           BLOC1_2  47 ekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                       e+ + +l+  +e+ ++ ++ ++++e  ++++e++vs +D + 
  gi|313125449|ref|YP_004035713.1| 539 EDAVAELQVIDEATAETVSTVEELESVIEDIESVVSFIDGIA 580
                                       555666777777888888888888888888888888888765 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0084
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                       + ++ a++++++ e++   +e++ + ++ i+ i ++v++  eav+e+ + + ++
  gi|313125449|ref|YP_004035713.1| 635 QTETTADDIRRTRERVVDGSETVTEAMDAIETIVDDVEQTSEAVQEIRAATERQ 688
                                       456778899999999999999999999999999999999999999988777765 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.078
                           BLOC1_2  37 kklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavse 83 
                                        +++d+++s+++++ ++ +++  +l    +++d + ++ +eL++a ++
  gi|313125449|ref|YP_004035713.1| 703 SEISDRTSSAAEDAAATAQQQTaSLVAVSDSVDSLADRADELQQALDR 750
                                       444555555554444444433335566666666666666666665555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.5      0.78   6.7e+02      33      56 ..     390     413 ..     371     474 .. 0.52
   2 ?    2.3   3.3      0.18   1.5e+02      11      56 ..     467     512 ..     424     532 .. 0.49
   3 ?    2.5   0.6      0.16   1.4e+02       7      53 ..     547     593 ..     541     600 .. 0.73
   4 ?   14.2   5.3   3.8e-05     0.032       4      78 ..     607     681 ..     605     688 .. 0.89
   5 ?    7.4   3.8    0.0049       4.2       5      76 ..     681     749 ..     677     755 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.78
                                       XXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  33 lseinrsveetnekvkdankaird 56 
                                       ++ +n+++e t e+ ++ +++ +d
  gi|313125449|ref|YP_004035713.1| 390 AEALNNHLESTAEDYRAVMEQCAD 413
                                       444444444444444444443333 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankaird 56 
                                        +++v++  a++s+ + n+ +++ + ++++    + +++++ ++++
  gi|313125449|ref|YP_004035713.1| 467 NVAAVKDASADVSESMTNILDDAVRQDDHLTDAADRMNEFSATVQQ 512
                                       2233333333333333333333333333333333333333333333 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.16
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdanka 53 
                                        ++e ++e+ + +++l+  +e +++ +s i++ +e+tn ++ +a+  
  gi|313125449|ref|YP_004035713.1| 547 VIDEATAETVSTVEELESVIEDIESVVSFIDGIAEQTNILALNASIE 593
                                       57788888888888888888888888888888888888777665544 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 3.8e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       +a+e+++ a+e+++ +++++  +++++e+ ++ ++++++t e v d ++++ +A +++ ++   ++q  + ++e+
  gi|313125449|ref|YP_004035713.1| 607 VAEEVKSLAAETQAATEDIESSIDRVREQTETTADDIRRTRERVVDGSETVTEAMDAIETIVDDVEQTSEAVQEI 681
                                       68999************************************************9999998888887766666555 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0049
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklk 76 
                                       +++a e  +e+   + ++ ++++++++  s+++++     + +++ +  ++ +++sv  L   a++L + l 
  gi|313125449|ref|YP_004035713.1| 681 IRAATERQAETATEVVGVVADVSEISDRTSSAAED---AAATAQQQTASLVAVSDSVDSLADRADELQQALD 749
                                       78888899999999999999999999999999999...5555778999999999999999999999977665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       7.4   6.3e+03      11      39 ..      55      83 ..      52      98 .. 0.44
   2 ?    0.3   0.1      0.97   8.3e+02      32      64 ..     373     405 ..     322     413 .. 0.62
   3 ?   10.9   0.9   0.00049      0.42      32      86 ..     426     480 ..     422     484 .. 0.94
   4 ?    3.4   0.3      0.11        93      39      83 ..     479     523 ..     477     529 .. 0.74
   5 ?   -0.2   8.7       1.4   1.2e+03      40      77 ..     602     639 ..     495     642 .. 0.76
   6 ?   12.9   6.2   0.00011     0.097      20      86 ..     607     680 ..     603     686 .. 0.60
   7 ?    9.8   3.3    0.0011      0.91      31      82 ..     653     704 ..     642     711 .. 0.83
   8 ?    2.1   2.8      0.26   2.3e+02      26      84 ..     690     748 ..     683     753 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.4
                            DUF948 11 vvLviflivvllklkktldeaaatieele 39
                                      ++Lv++l++  + + +  + +++   ++e
  gi|313125449|ref|YP_004035713.1| 55 AMLVAMLVMGSVGAVSYTQVTESLDSQVE 83
                                      44555554443333322222222223333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.97
                            DUF948  32 aatieelekqvdpilkevedllakvnelledvn 64 
                                        ++++ ++  ++  l+e+e+l ++ + ++ed +
  gi|313125449|ref|YP_004035713.1| 373 YDAVDAMRASLRTSLHEAEALNNHLESTAEDYR 405
                                       344555556666666666666666666665544 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00049
                            DUF948  32 aatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       +++++++ +  + +++e+++++  ++   e+v + +++  + ++av+d+++ vse
  gi|313125449|ref|YP_004035713.1| 426 NKAMADVAHAYNRMVDELAAVVGDAQSFSEGVADASAQTSANVAAVKDASADVSE 480
                                       7889999999*****************************************9986 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.11
                            DUF948  39 ekqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                        + +++il+++ +  ++  + ++ +ne +++v+++ +++ad++e 
  gi|313125449|ref|YP_004035713.1| 479 SESMTNILDDAVRQDDHLTDAADRMNEFSATVQQMSASAADVAER 523
                                       566777777777777788888888888888888888888887765 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.4
                            DUF948  40 kqvdpilkevedllakvnelledvneklekvdplteav 77 
                                       +    + +ev+ l a++++ +ed+++ +++v + te  
  gi|313125449|ref|YP_004035713.1| 602 EGFAVVAEEVKSLAAETQAATEDIESSIDRVREQTETT 639
                                       55566778888888888888888888888888887765 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 0.00011
                            DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvne.......lledvneklekvdplteavadlgesvse 86 
                                       v  ++k+++ e++a+ e++e+ +d + +++e++ + +++         e v+e +++++++++ v++++e+v+e
  gi|313125449|ref|YP_004035713.1| 607 VAEEVKSLAAETQAATEDIESSIDRVREQTETTADDIRRtrervvdGSETVTEAMDAIETIVDDVEQTSEAVQE 680
                                       55666777777777777777777777777777777766611111114555555666666666666666666665 PP

  == domain 7  score: 9.8 bits;  conditional E-value: 0.0011
                            DUF948  31 aaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                        ++t++e ++ ++ i+++ve++ + v+e+ +  +++ e+  +++  vad++e
  gi|313125449|ref|YP_004035713.1| 653 GSETVTEAMDAIETIVDDVEQTSEAVQEIRAATERQAETATEVVGVVADVSE 704
                                       4678899999999999999999999999999999999999999999999987 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.26
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       +t++e+   ++++ +  d ++  +ed+ a++++ ++ +   +++vd+l + + +l +++
  gi|313125449|ref|YP_004035713.1| 690 ETATEVVGVVADVSEISDRTSSAAEDAAATAQQQTASLVAVSDSVDSLADRADELQQAL 748
                                       56677777777777788888888888888888888888888888888888887777665 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.38   3.2e+02      21      37 ..      54      67 ..      43      76 .. 0.61
   2 ?    9.1   0.4    0.0015       1.3      14      37 ..     313     338 ..     306     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.38
                            TPPK_C 21 lAaLvAvavallvsp.ag 37
                                      +    A++va+lv + +g
  gi|313125449|ref|YP_004035713.1| 54 A----AMLVAMLVMGsVG 67
                                      3....5555555555444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0015
                            TPPK_C  14 g.allllvlAaLvAvavallvsp.ag 37 
                                       g +ll+ vlAa+ A++va++v +  +
  gi|313125449|ref|YP_004035713.1| 313 GqSLLWTVLAAVGALGVAAVVIGrRT 338
                                       4489*****************98644 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.9    0.0046       3.9      81     218 ..     429     570 ..     373     575 .. 0.74
   2 ?    7.9   6.6    0.0017       1.4      67     215 ..     586     749 ..     576     758 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0046
                                       XXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XX..XXXXXXXXXXXXXXXXXX CS
                              AIP3  81 ideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkev..qslrrdLavlrqlysefk 155
                                       + +  +   +++ el + + + ++ ++ v++ +++++++ a  + a+++ +++++++   ++r+d   l    ++ +
  gi|313125449|ref|YP_004035713.1| 429 MADVAHAYNRMVDELAAVVGDAQSFSEGVADASAQTSANVAAVKDASADVSESMTNIldDAVRQDD-HLTD-AADRM 503
                                       455556667777777777777787788888888877777777555555555555555222344443.3333.35678 PP

                                       XXXXXXXXXXXXXXXXXX.XXXX.XXXXXXHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 156 seikeslselrekakkvk.easlastkkssnrayiekgkkkL...seesdklvtkvddLqDlvedlr 218
                                       +e++++++++++ a++v  +a+ a   ++ +ra  e++ ++L   +e + + v+ v++L+ ++ed+ 
  gi|313125449|ref|YP_004035713.1| 504 NEFSATVQQMSASAADVAeRADAAAERGERGRAAAEDAVAELqviDEATAETVSTVEELESVIEDIE 570
                                       8899999999999999985566777777999*****999987333589999*************985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0017
                                       XXXX..................XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3  67 LsLn..................iepldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekasesl 125
                                       L Ln                   e+++++  + +  ++++++++ ++++++e+++  +++++er  + +++ ++ + 
  gi|313125449|ref|YP_004035713.1| 586 LALNasieaarageagegfavvAEEVKSLAAETQAATEDIESSIDRVREQTETTADDIRRTRERVVDGSETVTEAMD 662
                                       55554444444444444444334455555556666666666666666666666666666666666666655555444 PP

                                       X.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXX.XXXXXXHHHHHHHHHHHHHHHHH CS
                              AIP3 126 akkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvk.easlastkkssnrayiekgkkkLseesd 201
                                       a    ++ +++v++  + ++ +r   +  + e+ +++  + + ++++  ++s a  +  ++ +  +++   +s+ +d
  gi|313125449|ref|YP_004035713.1| 663 A---IETIVDDVEQTSEAVQEIRAATER-QAETATEVVGVVADVSEISdRTSSAAEDAAATAQQQTASLVAVSDSVD 735
                                       4...555555555555555555544333.333333344444444444421122222222223333344445555566 PP

                                       HHHHHHHHHHHHHH CS
                              AIP3 202 klvtkvddLqDlve 215
                                       +l  + d+Lq  ++
  gi|313125449|ref|YP_004035713.1| 736 SLADRADELQQALD 749
                                       66666666665544 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.1    0.0079       6.8     210     374 ..     356     530 ..     336     589 .. 0.63
   2 ?    4.9   5.1    0.0059         5     243     384 ..     596     735 ..     558     756 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0079
                          Prominin 210 hvsddLddagkhlgldladt...lesnvlpaLaelerllenlkea....keqLeqvnklekeLrksgsqLrdglrgv 279
                                       h+++ L++  +  +++l d+   +++++  +L+e e+l ++l+++    ++ +eq+ +     r+  ++ ++++ +v
  gi|313125449|ref|YP_004035713.1| 356 HLEEPLESSREDEFGRLYDAvdaMRASLRTSLHEAEALNNHLESTaedyRAVMEQCADGDLTCRMDPDDENKAMADV 432
                                       55666666666666666554111456677788888888887776611114568888888888899999999999999 PP

                          Prominin 280 krdlnqalsnlCqs.eeCskilssleiekldtskcldqlpnvd.evlealeevletnlss..ivkeglarlneipek 352
                                        +  n+++ +l     + +++++ +   + +ts+++ ++++ + +v e+++++l++ + +    +++ +r+ne + +
  gi|313125449|ref|YP_004035713.1| 433 AHAYNRMVDELAAVvGDAQSFSEGVADASAQTSANVAAVKDASaDVSESMTNILDDAVRQddHLTDAADRMNEFSAT 509
                                       99999999996664499999999999999999999988866542678899999999886522677899999999999 PP

                          Prominin 353 vknqtaevvpdlkkalakgreq 374
                                       v++ ++   +d+ +  + + e 
  gi|313125449|ref|YP_004035713.1| 510 VQQ-MSASAADVAERADAAAER 530
                                       974.555555555444433332 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0059
                          Prominin 243 rllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcl.dql 317
                                       r +e+ +      e+v++l  e +  ++++++++  v+++ ++++ +   ++e+  + +++++   +d  +++ d +
  gi|313125449|ref|YP_004035713.1| 596 RAGEAGEGFAVVAEEVKSLAAETQAATEDIESSIDRVREQTETTADDiRRTRERVVDGSETVTE-AMDAIETIvDDV 671
                                       5555555556666788999999999999999999999999999999954444555555555533.578777777888 PP

                          Prominin 318 pnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkipr 384
                                       ++++e +++++ ++e + + + +e +  + +++e + + t++  +d   + +++++ +  ++ ++ +
  gi|313125449|ref|YP_004035713.1| 672 EQTSEAVQEIRAATERQAETA-TEVVGVVADVSE-ISDRTSSAAEDAAATAQQQTASLVAVSDSV-D 735
                                       888888888888866665544.467777777764.777888888888888888888877777776.3 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.74   6.4e+02       6      62 ..     389     451 ..     384     488 .. 0.68
   2 ?    3.7   0.1     0.035        30       6      86 ..     498     577 ..     493     591 .. 0.83
   3 ?    6.1   1.5    0.0066       5.6      20      91 ..     610     687 ..     599     706 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.74
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......e 62 
                                       e e   ++le+ta+ y++ +e+++    +c+ + + ++k + ++ ++ +++  ++       +
  gi|313125449|ref|YP_004035713.1| 389 EAEALNNHLESTAEDYRAVMEQCADGDLTCRMDPDDENKAMADVAHAYNRMVDELAavvgdaQ 451
                                       555566789999999999999999999999999999999999999999988777544443331 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.035
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82 
                                       + +++++e+++t +++ ++ +++++  ++ +++ ++ +  +++  ++l+ ++++ ++e+ ++veel++ ++++++v+
  gi|313125449|ref|YP_004035713.1| 498 DAADRMNEFSATVQQMSASAADVAERADAAAERGERGRAAAEDAVAELQVIDEA-TAETVSTVEELESVIEDIESVV 573
                                       566778889999999999999999999999999999999999999999999988.5799999999999999999988 PP

                             TMPIT  83 keve 86 
                                       + ++
  gi|313125449|ref|YP_004035713.1| 574 SFID 577
                                       7554 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0066
                             TMPIT  20 eykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeelkerkkvlkevesllp 90 
                                       e+k+  +e+++  +++ ++i++ +++ +   +++++++++v       +e  +++e++ ++++++++ ++e+ +   
  gi|313125449|ref|YP_004035713.1| 610 EVKSLAAETQAATEDIESSIDRVREQTETTADDIRRTRERVVdgsetvTEAMDAIETIVDDVEQTSEAVQEIRAATE 686
                                       33444444444445555555555555555555555554443333333356666666666666666666666665543 PP

                             TMPIT  91 k 91 
                                       +
  gi|313125449|ref|YP_004035713.1| 687 R 687
                                       3 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         5   4.2e+03      33      63 ..     378     408 ..     372     413 .. 0.68
   2 ?    4.7   0.4     0.036        31      42     124 ..     472     553 ..     452     574 .. 0.73
   3 ?    7.5   4.4    0.0048       4.1      46     139 ..     655     747 ..     600     755 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  33 dLakRvkaQqkevaqhrerlkeisdrleele 63 
                                       +++  +++  +e+++++++l+++++++++++
  gi|313125449|ref|YP_004035713.1| 378 AMRASLRTSLHEAEALNNHLESTAEDYRAVM 408
                                       5555555666777888888888888887776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHH CS
                             Nup54  42 qkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarlet 118
                                       ++++a   e +++i d++      h ++++ r+++   + +++s     ++ + + ++ rg   +a  e + a+l+ 
  gi|313125449|ref|YP_004035713.1| 472 KDASADVSESMTNILDDAVRQD-DHLTDAADRMNEFSATVQQMSASAADVAERADAAAERGERGRAAAEDAVAELQV 547
                                       4444455555555555555555.899999999999999999999999999999999988888777788888888877 PP

                                       HHHHHS CS
                             Nup54 119 leaqln 124
                                       ++++  
  gi|313125449|ref|YP_004035713.1| 548 IDEATA 553
                                       766655 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0048
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHH.HHHHHHHHHHH CS
                             Nup54  46 aqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEe.elrarletlea 121
                                       +   e++++i++ ++++e  +  e+ ++++ a  r++e  + ++ +++ ++ ++ r ++ +++    ++++  +l a
  gi|313125449|ref|YP_004035713.1| 655 ETVTEAMDAIETIVDDVE--QTSEAVQEIRAATERQAETATEVVGVVADVSEISDRTSSAAEDAAaTAQQQTASLVA 729
                                       455667777777777777..56688999999********************66555554344443044444444444 PP

                                       HHS-HHH.HHHHHHHHHH CS
                             Nup54 122 qlndpaqlkgrvnelwar 139
                                         ++  +l  r +el ++
  gi|313125449|ref|YP_004035713.1| 730 VSDSVDSLADRADELQQA 747
                                       444447777777777654 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.27   2.3e+02      15      85 ..     383     459 ..     371     471 .. 0.60
   2 ?    9.7   1.2    0.0016       1.4       7      87 ..     498     576 ..     493     587 .. 0.78
   3 ?    3.7   3.5      0.12     1e+02      14      78 ..     610     680 ..     599     685 .. 0.69
   4 ?    4.0   2.3     0.093        79       5      50 ..     671     729 ..     670     758 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.27
                           DUF2203  15 lkelleelralrkeleeleeeleeakaeaekse......aaeleaeleeleaeieelveeieelGvevkdleaglvD 85 
                                       l+  l+e+ al+++le+++e+ ++  ++ +  +         ++++++ +++ ++++v+e+ ++  + +++++g+ D
  gi|313125449|ref|YP_004035713.1| 383 LRTSLHEAEALNNHLESTAEDYRAVMEQCADGDltcrmdPDDENKAMADVAHAYNRMVDELAAVVGDAQSFSEGVAD 459
                                       55555555555566665555555555554444455554444555556666666667777776666666666666666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleagl 83 
                                       +A + + + + +++++ a +++++e++++ +e  ++ +  +a+ + ael+ +++   e+v+++eel  ++ d+e  +
  gi|313125449|ref|YP_004035713.1| 498 DAADRMNEFSATVQQMSASAADVAERADAAAERGERGR-AAAEDAVAELQVIDEATAETVSTVEELESVIEDIE-SV 572
                                       56666777778888888888888887777777776654.44889999**************************6.67 PP

                           DUF2203  84 vDFp 87 
                                       v F 
  gi|313125449|ref|YP_004035713.1| 573 VSFI 576
                                       7775 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.12
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekse.......aaeleaeleeleaeieelveeieelGvevkd 78 
                                       ++k+l +e +a+++++e+  ++++e++++++  +            ++++e+++ ie +v+ +e++   v++
  gi|313125449|ref|YP_004035713.1| 610 EVKSLAAETQAATEDIESSIDRVREQTETTAD-DirrtrerVVDGSETVTEAMDAIETIVDDVEQTSEAVQE 680
                                       57777778888888888777777777666543.235566666677777777788888888777777665555 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.093
                           DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekse.............aae 50 
                                       +e+  + +++++  +e+ +++++e+  ++++++e+++++++ +               +
  gi|313125449|ref|YP_004035713.1| 671 VEQTSEAVQEIRAATERQAETATEVVGVVADVSEISDRTSSAAedaaataqqqtasLVA 729
                                       67888999999999999999999999999999999998765544444442222222222 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.5     3e+03      39      71 ..     372     404 ..     341     416 .. 0.63
   2 ?    6.2   0.9     0.011       9.7      42     117 ..     442     517 ..     427     524 .. 0.67
   3 ?    1.7   4.8      0.29   2.4e+02      41      85 ..     473     517 ..     469     588 .. 0.54
   4 ?    9.7   4.8   0.00099      0.84      44     120 ..     605     681 ..     601     687 .. 0.85
   5 ?    1.0   0.2      0.48   4.1e+02      74     105 ..     680     711 ..     675     722 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.5
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrv 71 
                                       l dav+ +  +l +  ++ +a  +hL+s  +  
  gi|313125449|ref|YP_004035713.1| 372 LYDAVDAMRASLRTSLHEAEALNNHLESTAEDY 404
                                       344555555555555555555555554444444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                        ++ v  + +++se +a++  + s++++ v +   +++e  ++i ++  +  ++l++  + +++ +++v+++ ++ 
  gi|313125449|ref|YP_004035713.1| 442 ELAAVVGDAQSFSEGVADASAQTSANVAAVKDASADVSESMTNILDDAVRQDDHLTDAADRMNEFSATVQQMSASA 517
                                       4445555556777777777777777777777777777777777777777777777777777777777777776654 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.29
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskei 85 
                                       da ++vs++++++ ++  ++ +hL++  dr+++    ++++s++ 
  gi|313125449|ref|YP_004035713.1| 473 DASADVSESMTNILDDAVRQDDHLTDAADRMNEFSATVQQMSASA 517
                                       666666666666666666666666655555443322222222221 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00099
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       + v+++++++ ++ +a+ ++++s idrv ++ + +++ ++ ++e v + +e ++e  + +e++ + ve+  + +++i
  gi|313125449|ref|YP_004035713.1| 605 AVVAEEVKSLAAETQAATEDIESSIDRVREQTETTADDIRRTRERVVDGSETVTEAMDAIETIVDDVEQTSEAVQEI 681
                                       67899999999999***********************9999999998888888888888888888877777777766 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.48
                           DUF1664  74 kldeqkeiskeikeevtevredlseigedves 105
                                       ++ + +e ++e++ ev  v  d+sei++  +s
  gi|313125449|ref|YP_004035713.1| 680 EIRAATERQAETATEVVGVVADVSEISDRTSS 711
                                       56678889999999999999999999987665 PP

>> BORCS8  BLOC-1-related complex sub-unit 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.7   5.7e+03      77      94 ..      19      36 ..      16      42 .. 0.84
   2 ?   -0.8   0.1       1.6   1.4e+03      67     105 ..     463     502 ..     432     516 .. 0.62
   3 ?   -0.9   0.1       1.8   1.5e+03      50      77 ..     554     581 ..     537     593 .. 0.61
   4 ?    4.8   0.2      0.03        25      49      78 ..     609     638 ..     605     641 .. 0.89
   5 ?    5.4   0.3      0.02        17      37      81 ..     643     687 ..     640     717 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.7
                            BORCS8 77 esessfeniqelLknsif 94
                                       ++++f+ni + L  s+ 
  gi|313125449|ref|YP_004035713.1| 19 AIQDTFRNIRSYLSRSVV 36
                                      67899******9999985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                            BORCS8  67 yaisavksikesessf.eniqelLknsiflkqqlkaeesr 105
                                          + v ++k+++  + e++ ++L  ++   ++l+ ++ r
  gi|313125449|ref|YP_004035713.1| 463 QTSANVAAVKDASADVsESMTNILDDAVRQDDHLTDAADR 502
                                       3344466667777777677788888888777777665555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.8
                            BORCS8  50 evkeleeelqgacydveyaisavksike 77 
                                       e  +  eel+  ++d+e  +s +  i e
  gi|313125449|ref|YP_004035713.1| 554 ETVSTVEELESVIEDIESVVSFIDGIAE 581
                                       3344445555566666666655555555 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.03
                            BORCS8  49 kevkeleeelqgacydveyaisavksikes 78 
                                       +evk+l+ e+q a++d+e +i  v++ +e+
  gi|313125449|ref|YP_004035713.1| 609 EEVKSLAAETQAATEDIESSIDRVREQTET 638
                                       699*********************987765 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.02
                            BORCS8  37 vrkalPelvekkkevkeleeelqgacydveyaisavksikesess 81 
                                       +r++   +v+  + v+e    ++  + dve   +av++i+ +++ 
  gi|313125449|ref|YP_004035713.1| 643 IRRTRERVVDGSETVTEAMDAIETIVDDVEQTSEAVQEIRAATER 687
                                       8999999999*****************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (810 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2028  (0.113113); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        65  (0.00362541); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 1.41u 0.38s 00:00:01.79 Elapsed: 00:00:00.59
# Mc/sec: 4144.46
//
Query:       gi|313125450|ref|YP_004035714.1|  [L=161]
Description: flavin-nucleotide-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-15   56.6   0.0      4e-14   52.6   0.0    2.1  2  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
    3.7e-10   39.9   0.1    4.8e-10   39.6   0.1    1.1  1  Pyridox_ox_2     Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.025   14.7   0.1    1.6  1  F420H2_quin_red  F420H(2)-dependent quinone reductase
      0.017   14.7   0.0      0.024   14.2   0.0    1.1  1  Pyrid_ox_like    Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   8.9e-18     4e-14       5      88 .]       9      91 ..       5      91 .. 0.85
   2 ?    1.9   0.0     0.056   2.5e+02      28      61 ..     124     152 ..     122     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 8.9e-18
                                      HHHHHH.HSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT...GSEEEEEEE CS
                    Putative_PNPOx  5 lrefla.eskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde...lgrgvrieG 79
                                      ++ +l  e+ ++++AT+ ++GrP++ pv++ + dg     +   +   klrnl+enprval++  de   + + v++ G
  gi|313125450|ref|YP_004035714.1|  9 IERLLTsEPLMAHVATC-RNGRPHAAPVWYRYEDGV--VELV--TSGTKLRNLRENPRVALSIQKDEngdAKWMVSLLG 82
                                      5555552455679****.******************..4444..34669****************************** PP

                                      EEEEESCHH CS
                    Putative_PNPOx 80 taelvsdge 88
                                      ta++++d+e
  gi|313125450|ref|YP_004035714.1| 83 TATVIDDEE 91
                                      ******997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.056
                                       EEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-E CS
                    Putative_PNPOx  28 vspvllkagdgrdgivfatnadsrklrnleenpr 61 
                                       +s++++ +  +   +++++ ++s++lr   +npr
  gi|313125450|ref|YP_004035714.1| 124 ASYRTYLNQGES--PDVYGGRESDTLR---HNPR 152
                                       577777755555..*********9998...7777 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.1   1.1e-13   4.8e-10       4     140 ..       8     127 ..       6     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.1e-13
                                       HHHHHHHC-S.EEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGG.EE CS
                      Pyridox_ox_2   4 eilalLdege.vgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfn.sl 77 
                                       ei++lL +++ ++++a+ ++g+p++ Pv y ++++ + + ++ g++l + lr++p v+ ++++ d+       n + 
  gi|313125450|ref|YP_004035714.1|   8 EIERLLTSEPlMAHVATCRNGRPHAAPVWYRYEDGVVELVTS-GTKL-RNLRENPrVALSIQK-DE-------NgDA 74 
                                       8899999655279*******************9775555544.4555.555546669999999.66.......3366 PP

                                       EEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTT..GGCSB---CCCCCTEEEEEEEEEEEEEE CS
                      Pyridox_ox_2  78 nyrSVvvrGraeevtdeeekaealellvekivpgr..wenlrpptrkelkatsvlrlkieevsgr 140
                                       ++  V + G+a++++dee  +ea +++ +k+  ++  w            ++ ++r+++ ++s r
  gi|313125450|ref|YP_004035714.1|  75 KW-MVSLLGTATVIDDEEATREATRKINRKYGAEEdaWS-----------ENVLVRIDVGTASYR 127
                                       7*.****************************54443555...........567788887777765 PP

>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   5.6e-06     0.025      24      86 ..      16      71 ..       4     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.6e-06
                                      --EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEETTEEE CS
                   F420H2_quin_red 24 pvllLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevqvgakkl 86
                                      + l+ ++   + g+p   p+ ++ +++ + +v s          ++Nl+ nPrv + +++++ 
  gi|313125450|ref|YP_004035714.1| 16 EPLMAHVATCRNGRPHAAPVWYRYEDGVVELVTSGT-------KLRNLRENPRVALSIQKDEN 71
                                      55777888899*********************9976.......589************99875 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.3e-06     0.024      51     124 ..      50     126 ..      44     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-06
                     Pyrid_ox_like  51 sdkvkeirkdsqvnlafsdesk..kky.vsvsGtaevvedrakieelWspvvkawfpegkddpnltlikvtpeeaey 124
                                         k +++r++++v l +++ ++   k+ vs+ Gta+v +d++  +e   ++ +++ +e    ++ +l+++++ +a y
  gi|313125450|ref|YP_004035714.1|  50 GTKLRNLRENPRVALSIQKDENgdAKWmVSLLGTATVIDDEEATREATRKINRKYGAEEDAWSENVLVRIDVGTASY 126
                                       57889***********99765422566479*****************999999998777777778888888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1049.29
//
Query:       gi|313125451|ref|YP_004035715.1|  [L=271]
Description: hypothetical protein Hbor_06770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1406.90
//
Query:       gi|313125452|ref|YP_004035716.1|  [L=271]
Description: hypothetical protein Hbor_06780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1732.35
//
Query:       gi|313125453|ref|YP_004035717.1|  [L=241]
Description: 2-keto-4-pentenoate hydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-44  152.2   0.0    1.9e-44  152.0   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   0.0   1.1e-48   1.9e-44       2     217 ..      51     240 ..      50     241 .] 0.92

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 1.1e-48
                                       EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--H CS
                     FAA_hydrolase   2 ivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsv 78 
                                       ++c+g+n+a+ +++++    e p+   p+    f+k++ s+ +p++p+++Pa++e+l y +ELa+vi  +++++ ++
  gi|313125453|ref|YP_004035717.1|  51 CYCVGRNFAATLEQME---YETPE--VPD---WFIKPPVSVHPPDEPVEYPAWTEELTYAGELAAVIDERCTDL-AI 118
                                       69************97...34444..355...******************************************.89 PP

                                       HHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGG CS
                     FAA_hydrolase  79 eeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkd 155
                                       +e++da++Gyt+lnD+ a d        +g ++ k+fd+++p+Gpwi t  +l dpe +++++ v ge++q+snt+ 
  gi|313125453|ref|YP_004035717.1| 119 DEVDDAVRGYTILNDLDALDQ-------AGRTARKAFDGSAPLGPWIET--DL-DPEGIDMTTHVGGEQRQESNTEL 185
                                       ****************99883.......366789*************44..66.568******************** PP

                                       TTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE CS
                     FAA_hydrolase 156 mifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrV 217
                                       m+fsp e+i+ ls+ +t++pGd+++ G+p+++        ++++g+ v++  eg+G+l+n+V
  gi|313125453|ref|YP_004035717.1| 186 MLFSPREIISFLSERYTFQPGDVVSFGSPANP-------GLVEPGEDVTIWYEGIGKLQNTV 240
                                       *****************************775.......59********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1300.00
//
Query:       gi|313125454|ref|YP_004035718.1|  [L=137]
Description: hypothetical protein Hbor_06810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-12   47.5   0.1    4.7e-12   47.2   0.1    1.1  1  DUF393    Protein of unknown function, DUF393


Domain annotation for each model (and alignments):
>> DUF393  Protein of unknown function, DUF393
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.1   2.6e-16   4.7e-12       1     111 [.       6     112 ..       6     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 2.6e-16
                            DUF393   1 vlyDgeCplCnravqflerrdrkgrirfadlqsasgkallkelgidaeqldslllvieagrvysgsdAaleiaralp 77 
                                       ++yD++C +C+++++fle+r   + + f +l    + +l ++l  d+e +++l+    +++vys+ + ++e++ ++ 
  gi|313125454|ref|YP_004035718.1|   6 LVYDDDCGFCTWWADFLEARSDLRIVGFSAL----DPSLRDRLPPDYESCSHLVT---DDAVYSCGASIEEAMLRTD 75 
                                       68******************66555555555....55544555666666666655...899*********9966555 PP

                            DUF393  78 g...lwrllalllvlprlkklrdalYrliarnRyrlf 111
                                           +  ++  l+++  ++ +r+++Yr +a nR  + 
  gi|313125454|ref|YP_004035718.1|  76 LgsgARPIVRSLRSVGLYRDVREWGYRHVAHNRSLWG 112
                                       434466778888999999***************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.37s 00:00:00.94 Elapsed: 00:00:00.58
# Mc/sec: 715.78
//
Query:       gi|313125455|ref|YP_004035719.1|  [L=56]
Description: hypothetical protein Hbor_06820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.56    9.7   2.3       0.62    9.6   2.3    1.0  1  DUF4225          Protein of unknown function (DUF4225)
        2.1    8.4   7.8        2.5    8.2   7.8    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        2.7    7.6   5.6        3.5    7.3   5.6    1.1  1  Tetraspanin      Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF4225  Protein of unknown function (DUF4225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.3    0.0001      0.62      46      84 ..       8      46 ..       5      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0001
                           DUF4225 46 vVagglqivaGvalvskasetvvgavaGalLilhGannv 84
                                      +Vagg+ +v+G+  v+    + +   +G++L++ G++++
  gi|313125455|ref|YP_004035719.1|  8 LVAGGVTLVTGLWTVTFLDSGSLLWAFGVVLVVAGVGGL 46
                                      69*************8999999999**********9876 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   7.8   0.00041       2.5      35      87 ..       6      48 ..       1      53 [. 0.52

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00041
                   Phage_holin_3_6 35 sgagllgaagvlallalllllvalalalaalwlaalivaavllvlagvlalvg 87
                                      +++++ g+++v +l ++++l  + +l+           ++v+lv+agv +l+g
  gi|313125455|ref|YP_004035719.1|  6 KLLVAGGVTLVTGLWTVTFLDSGSLLWA----------FGVVLVVAGVGGLAG 48
                                      4444444444444444444444443333..........677777777777766 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.6   0.00059       3.5      12      75 ..       7      53 ..       3      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00059
                                      XXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 12 fwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalken 75
                                      ++++g v l+ G+w+               +  d+ +l   l+++Gv+l++ g+ G+ g + +n
  gi|313125455|ref|YP_004035719.1|  7 LLVAGGVTLVTGLWT--------------VTFLDSGSL---LWAFGVVLVVAGVGGLAGGIWRN 53
                                      678999999999999..............235667777...99999999999999999977766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 325.22
//
Query:       gi|313125456|ref|YP_004035720.1|  [L=83]
Description: hypothetical protein Hbor_06830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.8    8.9   5.4       0.26   11.6   2.0    1.4  2  DUF3040   Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.0   1.4e-05      0.26      38      81 ..      16      60 ..       5      62 .. 0.83
   2 ?   -3.5   0.1      0.72   1.3e+04      13      20 ..      73      80 ..      72      82 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                           DUF3040 38 rrslrrlavlavllfva.GllllvlGvaaaavvlgvvGfvvmlag 81
                                       +++  l v++v+l+ a G+ +lv G+    v++ v+G+++ +++
  gi|313125456|ref|YP_004035720.1| 16 PGRTAALSVAPVVLASAqGINALVHGTHSPLVAVFVIGMLATAIA 60
                                      445566789999999999********99999********998766 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.72
                           DUF3040 13 eiEraLaa 20
                                       +Er+L +
  gi|313125456|ref|YP_004035720.1| 73 SLERDLFE 80
                                      57888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 489.36
//
Query:       gi|313125457|ref|YP_004035721.1|  [L=124]
Description: spw hypothetical protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-14   52.3  18.4    5.3e-08   32.3   6.0    2.3  2  SPW              SPW repeat
  ------ inclusion threshold ------
       0.56    9.5   9.6       0.68    9.2   9.6    1.1  1  ThrE             Putative threonine/serine exporter
        1.1    9.5   4.1       0.46   10.7   0.3    1.9  2  DPM3             Dolichol-phosphate mannosyltransferase subun


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   4.4   9.6e-10   5.8e-06       5      43 ..      13      49 ..       9      54 .. 0.88
   2 !   32.3   6.0   8.8e-12   5.3e-08       2      45 ..      66     107 ..      65     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9.6e-10
                               SPW  5 lllGlwlivSPWvlGfsattgaawnnvivGavvavLala 43
                                       l G+wl++S +v+G  +    +wn++i+Ga++a+La +
  gi|313125457|ref|YP_004035721.1| 13 ALFGAWLFASAFVFGMGGA--QFWNSLIIGAAIALLAGY 49
                                      689************7776..7**************976 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 8.8e-12
                               SPW   2 WanlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafa 45 
                                       +++ llG+w+i++P+v G  a t ++ ++vi G+vvavL+ + a
  gi|313125457|ref|YP_004035721.1|  66 GLAGLLGVWMIAAPFVYG--AATTVMASSVISGLVVAVLSGYEA 107
                                       7889**************..55569**************87765 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   9.6   0.00011      0.68     106     199 ..       8     105 ..       2     114 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00011
                              ThrE 106 yprwlvvlaaglaaaafallfgg..dwidflvaflagllggllrlllakrglnsfvleavaaflasllallavslgl 180
                                       ++ + ++++a l+a af++ +gg   w+ +++ ++++ll+g+  + +++ g+ +  +  +a++l  +++++ + +g 
  gi|313125457|ref|YP_004035721.1|   8 FNSISALFGAWLFASAFVFGMGGaqFWNSLIIGAAIALLAGYGAYRTRETGMGNTWTSGLAGLLGVWMIAAPFVYGA 84 
                                       45555666666666666666655333555555555666666666666666666666666666655555555444555 PP

                              ThrE 181 gln..pdaiiigsillLvPGl 199
                                       + +  ++ +i g ++ +++G+
  gi|313125457|ref|YP_004035721.1|  85 ATTvmASSVISGLVVAVLSGY 105
                                       444434888888888888887 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   7.7e-05      0.46       1      54 [.       1      54 [.       1      61 [. 0.90
   2 ?    0.3   0.3      0.13   7.9e+02       7      26 ..      63      82 ..      58     109 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.7e-05
                              DPM3  1 MtraqktlalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGaysl 54
                                      M    +++  +++l+++wl++ + ++ +   + ++++++ + + +l+ +Gay  
  gi|313125457|ref|YP_004035721.1|  1 MVDTSQWFNSISALFGAWLFASAFVFGMGGAQFWNSLIIGAAIALLAGYGAYRT 54
                                      566789****************99998888**********************65 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                              DPM3  7 tlalallllalwlalllrlv 26
                                      + + ++ ll++w+++   + 
  gi|313125457|ref|YP_004035721.1| 63 WTSGLAGLLGVWMIAAPFVY 82
                                      66666666777766653333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 707.32
//
Query:       gi|313125458|ref|YP_004035722.1|  [L=279]
Description: ion channel [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-17   64.2  13.8    1.3e-17   63.8  13.8    1.1  1  Ion_trans       Ion transport protein
    4.8e-16   58.5   5.0    4.8e-16   58.5   5.0    2.1  3  Ion_trans_2     Ion channel
    5.7e-05   22.4   3.8    8.5e-05   21.8   3.8    1.3  1  zf-ribbon_3     zinc-ribbon domain
     0.0045   17.0   0.2     0.0069   16.4   0.2    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.024   14.3   2.5      0.046   13.4   2.5    1.5  1  zinc_ribbon_2   zinc-ribbon domain
      0.077   13.1   0.6       0.37   10.9   0.6    2.3  1  DUF962          Protein of unknown function (DUF962)
       0.42   10.6   2.1          6    6.9   0.1    2.2  2  zinc_ribbon_4   zinc-ribbon domain
       0.56    9.8   2.4        3.8    7.1   2.4    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.74    9.8   4.3        1.7    8.7   4.3    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
          1    9.4   3.2        3.4    7.7   0.2    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.7    8.6   4.1         11    6.0   4.9    2.0  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        1.7    7.2  10.4        3.4    6.2  10.4    1.5  1  PKD_channel     Polycystin cation channel
          2    8.1   4.8        8.6    6.1   0.3    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        2.1    8.5   5.4        1.5    9.0   0.3    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8  13.8     1e-20   1.3e-17       8     220 ..      35     227 ..      29     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1e-20
                                       HHHHHHHHHHHHHCCCSSSSHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCHSHHHHHHHHHHHHHHHH CS
                         Ion_trans   8 illlillncvflaletyfpedelektileilelvftaiftlemllkilalgllikkrYlrdpwnilDflvvlpslls 84 
                                        l l l+ + ++  +ty+ ++ ++  +l  +e+++  +f++e +l++++ ++  ++  +++p  ++D+l++lp++ +
  gi|313125458|ref|YP_004035722.1|  35 LLALNLVFVGVFVAQTYPVSSATD-AWLWRAEVAIASVFVVEYVLRLYGSRN--RLQEFTNPYTVVDLLSILPTISV 108
                                       344444555555557777777777.99999**********************..9*********************9 PP

                                       H...HHHHHHHHHHHHHHHHGGGGGGHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCC CS
                         Ion_trans  85 l...vlseesllllsvlrlfrvlrllklisrleglrtlvtalirsvkdllnvlllllvvlfifaligvqlfkgklre 158
                                       +   v+   ++l + +lr++rv+r+l++ + ++  + +  ++      ++++ll +lvv+f+ a +++         
  gi|313125458|ref|YP_004035722.1| 109 FllpVP--AVVLTVGFLRVARVVRVLRFYRFTRDEEFFFGTVSVETLRVMKLLLTVLVVFFVSAGLFYSAE------ 177
                                       965533..678999999999999999999999998886665444444444444444444444444443333...... PP

                                       CCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHH CS
                         Ion_trans 159 knecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiil 220
                                                   + n+ ++nf++a++ ++ ++tt+g+gdi+++t  ++ +v+++ +++ iil
  gi|313125458|ref|YP_004035722.1| 178 -----------FQTNPDVNNFGDAFYYMVITLTTVGFGDIIPVTSAGR-WVTVASVLAAIIL 227
                                       ...........33444777*****************************.4444444444443 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.4   3.1e+03      48      71 ..      25      48 ..      23      54 .. 0.73
   2 ?   -3.5   0.0       8.2   1.1e+04      35      41 ..     116     122 ..     106     125 .. 0.73
   3 !   58.5   5.0   3.8e-19   4.8e-16       2      75 ..     162     237 ..     160     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.4
                                      -----HHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2 48 tdagrlftivyillGlalfalfla 71
                                      t++g+++ + ++ l l+++++f+a
  gi|313125458|ref|YP_004035722.1| 25 TAVGKAIDVTLLALNLVFVGVFVA 48
                                      566777777777788888888776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.2
                                       HHTTS-- CS
                       Ion_trans_2  35 tltTiGY 41 
                                       +++T+G+
  gi|313125458|ref|YP_004035722.1| 116 VVLTVGF 122
                                       5667776 PP

  == domain 3  score: 58.5 bits;  conditional E-value: 3.8e-19
                                       HHHHTCHHHHHHHHT......T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   2 vlllvlifgaviysl..eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgk 75 
                                       vl+++++++ ++ys   +++   ++f da+Y++++tltT+G+Gdi+p+t agr++t++ +l  ++l+ +   ++++
  gi|313125458|ref|YP_004035722.1| 162 VLVVFFVSAGLFYSAefQTNPDVNNFGDAFYYMVITLTTVGFGDIIPVTSAGRWVTVASVLAAIILVPWQAGKIVR 237
                                       56667777777777788777889*******************************************9998887765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.8   6.6e-08   8.5e-05       3      24 ..     247     269 ..     245     271 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.6e-08
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGt 24 
                                       v+CPnCG  + ++d+++C++CG+
  gi|313125458|ref|YP_004035722.1| 247 VTCPNCGLsHHDPDASHCKSCGH 269
                                       89*****9889***********7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   5.4e-06    0.0069      28      49 .]     246     268 ..     221     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.4e-06
                               DZR  28 edrCpsCgek.vdpearfCpeCG 49 
                                       + +Cp+Cg +  dp+a+ C++CG
  gi|313125458|ref|YP_004035722.1| 246 NVTCPNCGLShHDPDASHCKSCG 268
                                       689*****9999**********9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.5   3.6e-05     0.046       2      21 ..     249     269 ..     248     271 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                     zinc_ribbon_2   2 CpnCGael.qdnakFCpyCGt 21 
                                       CpnCG  + +++a  C  CG+
  gi|313125458|ref|YP_004035722.1| 249 CPNCGLSHhDPDASHCKSCGH 269
                                       ********778*********9 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6   0.00029      0.37       3      77 ..      11     100 ..       9     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                            DUF962   3 sleefyafYlaeHsnpinrllHfigvplilltvlllllrak.............lklllalfvvgyifafvGHf..v 64 
                                       +++e+ +fYl +H+ ++ +++ +    l l++v ++++ +                 ++ +fvv y++   G    +
  gi|313125458|ref|YP_004035722.1|  11 DFREQVRFYLLDHRTAVGKAIDVTLLALNLVFVGVFVAQTYpvssatdawlwraEVAIASVFVVEYVLRLYGSRnrL 87 
                                       799*******************9999998888887777766789999998877422333456666666666632114 PP

                            DUF962  65 fEkrkPAlfknpl 77 
                                        E  +P ++ ++l
  gi|313125458|ref|YP_004035722.1|  88 QEFTNPYTVVDLL 100
                                       4444444444444 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0047         6      23      32 ..     244     253 ..     238     255 .. 0.79
   2 ?    3.0   0.3     0.078        99      28      35 ..     264     271 ..     263     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0047
                     zinc_ribbon_4  23 gvkvrCskCg 32 
                                       +v+v+C++Cg
  gi|313125458|ref|YP_004035722.1| 244 KVNVTCPNCG 253
                                       6788888887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.078
                     zinc_ribbon_4  28 CskCghvF 35 
                                       C+ Cgh++
  gi|313125458|ref|YP_004035722.1| 264 CKSCGHII 271
                                       9****986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3    0.0042       5.4      17      27 ..     244     254 ..     239     263 .. 0.72
   2 ?    7.1   2.4    0.0029       3.8       2      29 ..     248     271 ..     247     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0042
                                       TTCEEESSSSB CS
                      TF_Zn_Ribbon  17 rgelvCtdCGl 27 
                                         +++C++CGl
  gi|313125458|ref|YP_004035722.1| 244 KVNVTCPNCGL 254
                                       56778888887 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0029
                                       EETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVl 29 
                                       +CPnCg ++   Dp+     C++CG ++
  gi|313125458|ref|YP_004035722.1| 248 TCPNCGLSH--HDPD--ASHCKSCGHII 271
                                       7*****886..7888..77899999987 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.3    0.0013       1.7      15      45 ..     239     269 ..     236     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                     Zn_Tnp_IS1595  15 Wpng....fvCPhCgsrkayriktrglfqCkeCrk 45 
                                       W n+    ++CP+Cg +++    ++   +Ck+C++
  gi|313125458|ref|YP_004035722.1| 239 WTNRekvnVTCPNCGLSHH----DPDASHCKSCGH 269
                                       8888888799*****5533....366668999987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0027       3.4      36      57 ..     234     257 ..     231     262 .. 0.78
   2 ?    1.8   0.3      0.18   2.3e+02      30      40 ..     263     273 ..     260     279 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0027
                    OrfB_Zn_ribbon  36 sknke..alsgrtfkCpnCgfead 57 
                                       ++++e  ++++ +++CpnCg++++
  gi|313125458|ref|YP_004035722.1| 234 KIVREwtNREKVNVTCPNCGLSHH 257
                                       56666667889999******9976 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                    OrfB_Zn_ribbon  30 tCseCgsknke 40 
                                        C  Cg++ ++
  gi|313125458|ref|YP_004035722.1| 263 HCKSCGHIIYQ 273
                                       69999999887 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.9    0.0088        11      14      32 ..     249     268 ..     247     269 .. 0.93
   2 ?    5.3   0.3     0.014        18      11      22 ..     261     272 ..     260     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0088
                           DUF35_N  14 CpdCGtvqfPPr.avCphCg 32 
                                       Cp+CG  ++ P   +C  Cg
  gi|313125458|ref|YP_004035722.1| 249 CPNCGLSHHDPDaSHCKSCG 268
                                       ************99999997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
                           DUF35_N  11 gqrCpdCGtvqf 22 
                                       +++C++CG+ ++
  gi|313125458|ref|YP_004035722.1| 261 ASHCKSCGHIIY 272
                                       579*****9875 PP

>> PKD_channel  Polycystin cation channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  10.4    0.0027       3.4     298     407 ..     117     228 ..      18     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHGGGGG------------------------HHHHHHHHHHHHHHHHHHSSSS-STTSSHHHHHHH CS
                       PKD_channel 298 riilavlvflttlkllkvlrfnktlslltktlaralkdvlgfalvivilflayaqlgvllfGtqasnfsnlvksilt 374
                                         + ++l +  ++++l++ rf ++ + +  t++     v+ + l ++++f++ a l +    +  ++ +n+  ++  
  gi|313125458|ref|YP_004035722.1| 117 VLTVGFLRVARVVRVLRFYRFTRDEEFFFGTVSVETLRVMKLLLTVLVVFFVSAGLFYSAEFQTNPDVNNFGDAFYY 193
                                       3345566666778889999999999**************************************************99 PP

                                       HHHHHTT---HHHH...HHH-TTHHHHHHHHHHHHH CS
                       PKD_channel 375 lfrlilgdfqytel...esgnrvLGpllllalvflv 407
                                       +  ++l  +++ ++    s++r+  +  +la ++lv
  gi|313125458|ref|YP_004035722.1| 194 M-VITLTTVGFGDIipvTSAGRWVTVASVLAAIILV 228
                                       9.6778889999653338999999999888887776 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.036        46      24      31 ..     249     256 ..     247     256 .. 0.89
   2 ?    6.1   0.3    0.0067       8.6      23      32 .]     263     272 ..     261     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.036
                     zf-NADH-PPase  24 CpaCgleh 31 
                                       Cp+Cgl h
  gi|313125458|ref|YP_004035722.1| 249 CPNCGLSH 256
                                       9****987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0067
                     zf-NADH-PPase  23 vCpaCglehY 32 
                                       +C +Cg++ Y
  gi|313125458|ref|YP_004035722.1| 263 HCKSCGHIIY 272
                                       9******998 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.8      0.27   3.5e+02      23      26 .]     249     252 ..     246     253 .. 0.58
   2 ?    9.0   0.3    0.0012       1.5       4      13 ..     264     273 ..     262     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.27
                            zf-ACC  23 CPkC 26 
                                       CP+C
  gi|313125458|ref|YP_004035722.1| 249 CPNC 252
                                       5555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0012
                            zf-ACC   4 CpsCgemlyk 13 
                                       C sCg+++y+
  gi|313125458|ref|YP_004035722.1| 264 CKSCGHIIYQ 273
                                       *********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1503.69
//
Query:       gi|313125459|ref|YP_004035723.1|  [L=156]
Description: hypothetical protein Hbor_06860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.001   19.3   1.5     0.0016   18.7   1.5    1.3  1  End3             Actin cytoskeleton-regulatory complex protei
     0.0077   16.6   0.5      0.014   15.8   0.5    1.5  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
  ------ inclusion threshold ------
       0.03   14.2   0.4      0.063   13.2   0.4    1.6  1  Pox_A_type_inc   Viral A-type inclusion protein repeat
      0.045   14.2   1.6      0.048   14.1   0.3    1.8  2  DUF4094          Domain of unknown function (DUF4094)
      0.052   13.9   3.3      0.055   13.8   1.8    1.7  2  Csm1_N           Csm1 N-terminal domain
       0.13   12.2   0.2       0.23   11.4   0.1    1.4  1  Bys1             Blastomyces yeast-phase-specific protein
       0.28   11.4   1.8       0.43   10.8   1.8    1.4  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> End3  Actin cytoskeleton-regulatory complex protein END3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.5   6.1e-07    0.0016      67     123 ..       6      62 ..       1      80 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.1e-07
                              End3  67 akfgdsylsrlGvgsksekgtdfsatkgtdweevrLkreLaeLeeklekveeeaekr 123
                                        k   +yl+ l +  +++++  f a +  d+e +rLk+++++Le++l+ ++++ +++
  gi|313125459|ref|YP_004035723.1|   6 YKNTSKYLHELIQEARATRAEGFLAPQSSDQEVQRLKKKIEKLEDRLAVAKQQRRDS 62 
                                       456689*****999999*******************************999976643 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   5.4e-06     0.014      48      89 ..      32      87 ..       2      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.4e-06
                       Uso1_p115_C 48 keleaenkklekeleklraelkeekekekek..............qkEldDLLlll 89
                                      ++ ++e+++l+k++ekl+ +l+ +k++ +++               ++ldDL++ +
  gi|313125459|ref|YP_004035723.1| 32 QSSDQEVQRLKKKIEKLEDRLAVAKQQRRDSvtirtikrfrlirrDTDLDDLFVGI 87
                                      456899**********************9889********************9855 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   2.5e-05     0.063       1      18 [.      36      53 ..      36      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                    Pox_A_type_inc  1 rEmsrlRsRIsDLErqLs 18
                                      +E++rl+ +I+ LE +L+
  gi|313125459|ref|YP_004035723.1| 36 QEVQRLKKKIEKLEDRLA 53
                                      7*************9998 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   1.9e-05     0.048      63      88 .]      33      58 ..       3      58 .. 0.85
   2 ?   -2.7   0.0       3.2   8.2e+03      15      28 ..     127     141 ..     125     153 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                           DUF4094 63 kthkaiqtLdktissLemeLaaarae 88
                                         +++q+L+k+i +Le  La+a+++
  gi|313125459|ref|YP_004035723.1| 33 SSDQEVQRLKKKIEKLEDRLAVAKQQ 58
                                      46789*******************86 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                           DUF4094  15 agllftnRlwtvp.s 28 
                                       +g++ft+ ++++  s
  gi|313125459|ref|YP_004035723.1| 127 VGTVFTTLMRNQGrS 141
                                       677888877644332 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.8   2.1e-05     0.055      38      67 ..      33      62 ..      29      63 .. 0.91
   2 ?   -3.0   0.0       3.8   9.8e+03      26      37 ..     101     112 ..      94     118 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                            Csm1_N 38 tkdqeiesLkeqlaeleekvkeleerrkkq 67
                                      + dqe+++Lk+++++le +++ ++++r+++
  gi|313125459|ref|YP_004035723.1| 33 SSDQEVQRLKKKIEKLEDRLAVAKQQRRDS 62
                                      579*********************999875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.8
                            Csm1_N  26 vhENsvLsqkle 37 
                                       v E  v++  le
  gi|313125459|ref|YP_004035723.1| 101 VREAAVKESILE 112
                                       444444444443 PP

>> Bys1  Blastomyces yeast-phase-specific protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   8.8e-05      0.23      26      80 ..      98     152 ..      71     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.8e-05
                              Bys1  26 dveagevstrkildgrsydyynekyrggsgdgvsltlshtegrdssnsettfryk 80 
                                       +    e++ ++ +   s d +++k+ + +   v  tl   +gr s+ s t+ r +
  gi|313125459|ref|YP_004035723.1|  98 QCAVREAAVKESILEDSEDRFHKKFTPHTVGTVFTTLMRNQGRSSTSSSTSVRMR 152
                                       444556677777777899********************************99975 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.8   0.00017      0.43      33     142 ..      33     151 ..      14     152 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                       ESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHH CS
                   CTP_transf_like  33 psdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklkpdklylvigadvledfsewkeleeilgn 109
                                        sd+++++ kk++ ++e+Rl+  ++ ++++   +++ ++  r ++++ + d+l++ i +d l+++    +++e   +
  gi|313125459|ref|YP_004035723.1|  33 SSDQEVQRLKKKIEKLEDRLAVAKQQRRDSV--TIRTIKRFRLIRRDTDLDDLFVGIRDDRLTKTVIQCAVREAAVK 107
                                       699**********************954444..55555555567788888888887777777776444466666666 PP

                                       HHHEEEEEE...........HTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like 110 vklvvvsrp...........ekqanvllkaekrtngiSstkire 142
                                         +   s++            + ++ l+ ++ r++  Sst +r 
  gi|313125459|ref|YP_004035723.1| 108 ESILEDSEDrfhkkftphtvGTVFTTLMRNQGRSSTSSSTSVRM 151
                                       66665555577777666544444455688999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1693  (0.094428); expected 358.6 (0.02)
Passed bias filter:                      879  (0.0490267); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 884.23
//
Query:       gi|313125460|ref|YP_004035724.1|  [L=135]
Description: doxx protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-08   32.5   8.9    9.9e-08   32.5   8.9    1.8  2  DoxX      DoxX


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   8.9   5.5e-12   9.9e-08       2      84 ..      12      92 ..      11      93 .. 0.97
   2 ?   -0.1   0.0      0.08   1.4e+03      34      49 ..     112     127 ..     102     134 .. 0.52

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 5.5e-12
                              DoxX  2 llllRlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllvat 80
                                       l++R+llg+++ + G++ +   + e   ++  ++g+p + l++ +  ++ ++ggl++llG+++ +a+++++++ +++t
  gi|313125460|ref|YP_004035724.1| 12 FLIGRVLLGGVLAYLGVSNML--DAENKIEYARSTGIPFAGLAVPVSFVLLILGGLGILLGVYPMIASVGVIAFFAGVT 88
                                      69*******************..******************************************************** PP

                              DoxX 81 ltvh 84
                                       ++h
  gi|313125460|ref|YP_004035724.1| 89 PAMH 92
                                      9999 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.08
                              DoxX  34 aalglpppellaylaa 49 
                                       +++ l+  +l +++++
  gi|313125460|ref|YP_004035724.1| 112 VNFALLGSALIVLVIG 127
                                       4444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 715.68
//
Query:       gi|313125461|ref|YP_004035725.1|  [L=115]
Description: carboxymuconolactone decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-07   31.4   1.7    1.9e-07   31.1   1.7    1.2  1  CMD          Carboxymuconolactone decarboxylase family
     0.0091   15.9   0.8       0.17   11.8   0.1    2.3  2  Phage-MuB_C  Mu B transposition protein, C terminal
     0.0097   15.4   0.0      0.012   15.1   0.0    1.1  1  DUF908       Domain of Unknown Function (DUF908)


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   1.7   3.1e-11   1.9e-07       1      85 []      32     115 .]      32     115 .] 0.95

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.1e-11
                                       HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHH CS
                               CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaar 77 
                                       p++++ ++a++ ++   +++L+++++ Li+la  aa g  + v+  ++ A+ +Gv+e+e+ae++ + a  +g  ++ 
  gi|313125461|ref|YP_004035725.1|  32 PDFADHVAAIARNAGT-DDALSAQTKTLITLALDAADGNTNGVKDLAAVARSQGVSEQELAETVKVIANQGGLGKLA 107
                                       899999999999**99.999***********************999**************************99999 PP

                                       HHHHHHHH CS
                               CMD  78 aAlaaaee 85 
                                        A++a++e
  gi|313125461|ref|YP_004035725.1| 108 VAAHALTE 115
                                       99999875 PP

>> Phage-MuB_C  Mu B transposition protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.017     1e+02      27      60 ..      30      66 ..      24      74 .. 0.72
   2 !   11.8   0.1   2.8e-05      0.17      15      43 ..      74     102 ..      66     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.017
                                      SSSHHHHHHHTTSSS-S...-HHHHHHHHGGGT-TT- CS
                       Phage-MuB_C 27 tdeelmkllqeiaekpG...aLRaltktLrlAamfAk 60
                                       d++  + + +ia+ +G   aL a tktL   a+ A+
  gi|313125461|ref|YP_004035725.1| 30 HDPDFADHVAAIARNAGtddALSAQTKTLITLALDAA 66
                                      6888899999999998866678888888755444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.8e-05
                                       GGTTHHHHSSSSSSSHHHHHHHTTSSS-S CS
                       Phage-MuB_C  15 eDvkaiaaAwgltdeelmkllqeiaekpG 43 
                                       +D+ a+a++ g+ ++el + +  ia+++G
  gi|313125461|ref|YP_004035725.1|  74 KDLAAVARSQGVSEQELAETVKVIANQGG 102
                                       7************************9865 PP

>> DUF908  Domain of Unknown Function (DUF908)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     2e-06     0.012     282     338 ..      20      78 ..      13      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-06
                            DUF908 282 esefqtkllkqdpdlvyqLaeLihpe..esevprelqtaaleaLealarkkaklsdvls 338
                                       e+ef+tkl  +dpd++ ++a + +    +++++ +++t+++ aL+a    ++ ++d+++
  gi|313125461|ref|YP_004035725.1|  20 EPEFLTKLRAHDPDFADHVAAIARNAgtDDALSAQTKTLITLALDAADGNTNGVKDLAA 78 
                                       899**********************9978*****************9999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 628.31
//
Query:       gi|313125462|ref|YP_004035726.1|  [L=128]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-22   78.8   0.0    2.7e-22   78.4   0.0    1.1  1  HxlR           HxlR-like helix-turn-helix
     0.0025   17.7   0.0     0.0037   17.1   0.0    1.2  1  MarR_2         MarR family
     0.0069   16.5   0.0     0.0095   16.1   0.0    1.2  1  HTH_34         Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.018   14.9   0.0    1.3  1  MarR           MarR family
      0.033   14.3   0.0      0.041   13.9   0.0    1.2  1  Replic_Relax   Replication-relaxation
      0.043   13.9   0.0      0.067   13.3   0.0    1.2  1  Trp_repressor  Trp repressor protein
      0.047   13.6   0.0      0.065   13.1   0.0    1.2  1  HTH_5          Bacterial regulatory protein, arsR family
      0.072   13.1   0.0       0.11   12.5   0.0    1.3  1  PadR           Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0   1.2e-25   2.7e-22       3      89 ..      34     119 ..      32     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.2e-25
                                       HSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHH CS
                              HxlR   3 ggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqel 79 
                                       g kW+l il++l++g +Rf+elkra  + s  +L++ L  Le+d +++r+v +  P+   YsltekG +l+pv++++
  gi|313125462|ref|YP_004035726.1|  34 GTKWRLRILYNLFDGDHRFNELKRAS-GASSYTLSRVLESLEEDAIVDRRVEEGPPVETHYSLTEKGAALKPVFDAI 109
                                       89**********************98.8899********************************************** PP

                                       HHHHHHHHHC CS
                              HxlR  80 kkwgeeylee 89 
                                        +w +e++ e
  gi|313125462|ref|YP_004035726.1| 110 DEWNAEWVGE 119
                                       ******9865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.6e-06    0.0037       8      54 ..      39      82 ..      35      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +r+L++L +++    + +el r+ g s  ++sr+l+ L++   v rr
  gi|313125462|ref|YP_004035726.1| 39 LRILYNLFDGDH---RFNELKRASGASSYTLSRVLESLEEDAIVDRR 82
                                      699*******95...*****************************998 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.2e-06    0.0095       2      66 ..      38     100 ..      37     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.2e-06
                            HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGr 66 
                                       Rl +l  L + d   f+elk a +a++  Ls  l+ Le+   + ++ e +g    t++++T++G 
  gi|313125462|ref|YP_004035726.1|  38 RLRILYNLFDGD-HRFNELKRASGASSYTLSRVLESLEEDAIVDRRVE-EGPPVETHYSLTEKGA 100
                                       666666666554.58***********************9987766554.555578*********5 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   8.1e-06     0.018      10      50 ..      40      82 ..      37      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.1e-06
                                      HHHHHS..TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 10 rilyeq..gplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      rily+   g+++  eL +++g s+ t++rvl  Le++  ++R+
  gi|313125462|ref|YP_004035726.1| 40 RILYNLfdGDHRFNELKRASGASSYTLSRVLESLEEDAIVDRR 82
                                      5555543388**************************9999886 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.8e-05     0.041      16      69 ..      56     103 ..      42     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                      Replic_Relax  16 arllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarll 69 
                                        r+  as   t++r+L  L+e  +++r  ++  g      +++Y Lt+kGa+l 
  gi|313125462|ref|YP_004035726.1|  56 KRASGASSY-TLSRVLESLEEDAIVDRRVEE--GPP---VETHYSLTEKGAALK 103
                                       444444444.5****************4444..233...489********9876 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05     0.067      38      75 ..      38      75 ..      30      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                     Trp_repressor 38 RlqvvkeLLkeelsqreIaeelgvSiAtItRvsrsLkt 75
                                      Rl+++ +L ++++ ++e++   g+S  t +Rv  sL+ 
  gi|313125462|ref|YP_004035726.1| 38 RLRILYNLFDGDHRFNELKRASGASSYTLSRVLESLEE 75
                                      9*******************************999984 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.9e-05     0.065       4      45 ..      38      79 ..      35      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      Rl+IL+ L +g + + el ++ g s  t+S+ L  L+e  +V
  gi|313125462|ref|YP_004035726.1| 38 RLRILYNLFDGDHRFNELKRASGASSYTLSRVLESLEEDAIV 79
                                      9**********************************9997766 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.8e-05      0.11      33      71 ..      65     101 ..      49     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-05
                                       HHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR  33 slYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71 
                                       +l ++L++Le++ +v+++ ee    p   +Y lT++G +
  gi|313125462|ref|YP_004035726.1|  65 TLSRVLESLEEDAIVDRRVEE--GPPVETHYSLTEKGAA 101
                                       45568*************886..5788899*******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 728.68
//
Query:       gi|313125463|ref|YP_004035727.1|  [L=313]
Description: glutathione s-transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-17   62.6   0.0    3.7e-16   59.2   0.0    2.3  2  GST_N_2   Glutathione S-transferase, N-terminal domain
      1e-12   47.9   0.1    2.5e-12   46.6   0.1    1.6  1  GST_C_2   Glutathione S-transferase, C-terminal domain
    4.6e-08   33.2   0.0      7e-08   32.6   0.0    1.4  1  GST_C     Glutathione S-transferase, C-terminal domain
    1.6e-06   28.2   0.0    2.7e-06   27.5   0.0    1.4  1  GST_C_3   Glutathione S-transferase, C-terminal domain
     0.0065   16.9   0.1        3.9    8.0   0.0    2.9  3  GST_N_3   Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.027   14.2   0.0    1.5  1  GST_C_6   Glutathione S-transferase, C-terminal domain


Domain annotation for each model (and alignments):
>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   1.2e-19   3.7e-16       1      69 [.      51     147 ..      51     148 .. 0.78
   2 ?    0.7   0.0      0.22   6.5e+02      25      48 ..     278     299 ..     253     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.2e-19
                                       S-HHHHHHHHHHHHCT--EEEEE................EH...-TTSHHHHH......................HH CS
                           GST_N_2   1 aCPwahRvlialalkglediisv................vvlepkgfekseef......................pr 39 
                                       aCPwah + ++++l+gled+is                                                     p+
  gi|313125463|ref|YP_004035727.1|  51 ACPWAHGAALVRKLLGLEDVISLdivdpyrgaggwqftpD------------KpgctpdsihdsdflhevytaadPE 115
                                       7*********************998666544444333330............34555555666666888888888** PP

                                       HCTTTSSSEEE-C.TTE.EEESHHHHHHHHHH CS
                           GST_N_2  40 lnprgtVPvLwdk.dgq.vineSseIlrylet 69 
                                       +++ +t PvLwd  +g+ v+neS eI+++l+t
  gi|313125463|ref|YP_004035727.1| 116 YSGGVTTPVLWDReNGTiVNNESIEIMQMLAT 147
                                       ************868889999*********98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.22
                                       H...-TTSHHHHHHHHCTTTSSSE CS
                           GST_N_2  25 vlepkgfekseefprlnprgtVPv 48 
                                       ++  k++++s    ++np+g VPv
  gi|313125463|ref|YP_004035727.1| 278 DHIKKHYYRS--HTDINPTGFVPV 299
                                       5555555554..899********8 PP

>> GST_C_2  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   8.4e-16   2.5e-12       3      66 ..     193     261 ..     191     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 8.4e-16
                                       HHCHHHHHCCHCHHHCTTT---SS.CTTCS--HHHHHHHHHHHHHHHHHHS-...---..TT-HHHHHH CS
                           GST_C_2   3 averaleqldaaldaleahLadspflfGdqptlaDialapflvrlraagpgf...dir..eaypnlraW 66 
                                        +era+e+++ al  +e  L+d++fl Gd +t+aD +l+p lvr++ +++ +   +ir   +ypnl+ +
  gi|313125463|ref|YP_004035727.1| 193 TYERAVETMFDALNHWEGVLGDQRFLVGDSLTIADLRLFPALVRFDPVYYTHfkcNIRrlVDYPNLWGY 261
                                       689*********************************************9987899888888*****988 PP

>> GST_C  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.3e-11     7e-08      17      92 ..     182     268 ..     141     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.3e-11
                                       H.....HHHHHHHHHHHHHHHHHHHHHHHHHHTSSSSSTTSSCHHHHHHHHHHH.....HHHHHTTTTT.TTTSHHH CS
                             GST_C  17 e.....ekkeelvdealekvaevlsaleeelkkqdylvGdkltlADialvpiln.....wlqrlglafg.qekfpnl 82 
                                       +     + ++ +++ a e ++ +l+  e++l +q +lvGd lt+AD+ l+p+l      ++ +++ ++    ++pnl
  gi|313125463|ref|YP_004035727.1| 182 AytagfAESQDTYERAVETMFDALNHWEGVLGDQRFLVGDSLTIADLRLFPALVrfdpvYYTHFKCNIRrLVDYPNL 258
                                       14444477899999**************************************9977766666666666688999999 PP

                                       HHHHHHHHTS CS
                             GST_C  83 kawlerimar 92 
                                         ++  i+++
  gi|313125463|ref|YP_004035727.1| 259 WGYTRDIYQH 268
                                       9998888765 PP

>> GST_C_3  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0     9e-10   2.7e-06       3      81 ..     174     260 ..     172     274 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 9e-10
                                       HHHHHHCCCC.SHCHHHHHHHHHHHHHHHCHHHHHHHHHHCHGTSSSSTTS--HHHHHHHHHHHHHHHH........ CS
                           GST_C_3   3 lhhpiaklly.dqkeeaekkkefleerlpkflkyfekvlkkkgggylvgdklTyADlalfqvldgleea........ 70 
                                       lh+pi + +y    +e++ + e   e++ + l+++e vl    + +lvgd+lT+ADl lf +l  +  +        
  gi|313125463|ref|YP_004035727.1| 174 LHEPILQGAYtAGFAESQDTYERAVETMFDALNHWEGVLG--DQRFLVGDSLTIADLRLFPALVRFDPVyythfkcn 248
                                       6889999999655555577777788888889999999999..899***************99988777655555332 PP

                                       TCC..CC-HHHHH CS
                           GST_C_3  71 eal..kkfpklka 81 
                                             ++p+l  
  gi|313125463|ref|YP_004035727.1| 249 I-RrlVDYPNLWG 260
                                       0.13345566555 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0057        17       1      24 [.      46      69 ..      46      83 .. 0.88
   2 !    8.0   0.0    0.0013       3.9      39      73 ..     114     151 ..      96     180 .. 0.87
   3 ?   -3.7   0.0       5.6   1.7e+04      56      65 ..     218     227 ..     212     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0057
                                      EES-TTSHHHHHHHHHHHHHT--E CS
                           GST_N_3  1 LygfpaSpyarrvrlaLnekglpv 24
                                      Ly ++a+p+a  ++l+ +++gl+ 
  gi|313125463|ref|YP_004035727.1| 46 LYIARACPWAHGAALVRKLLGLED 69
                                      899******************975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
                                       HHH-TT--SSEE..ETTS-EEE.SHHHHHHHHHHHH-G CS
                           GST_N_3  39 laknplgkvPvL..eddgealt.dSlaIidyLeelypg 73 
                                       +++++  + PvL  + +g+++  +S +I++ L +++++
  gi|313125463|ref|YP_004035727.1| 114 PEYSGGVTTPVLwdRENGTIVNnESIEIMQMLATAFAD 151
                                       5778889*****76677996655*********999875 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.6
                                       EEESHHHHHH CS
                           GST_N_3  56 altdSlaIid 65 
                                        + dSl I+d
  gi|313125463|ref|YP_004035727.1| 218 LVGDSLTIAD 227
                                       6789*99987 PP

>> GST_C_6  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.2e-06     0.027       4      63 ..     204     264 ..     201     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.2e-06
                           GST_C_6   4 dleaLselLgdkkyFfGdkPtslDAlvFGhla...qilytplespelrellkeypNLvaycer 63 
                                       +l+    +Lgd+ ++ Gd+ t +D  +F  l+   +++yt ++ + +r+l+  ypNL  y++ 
  gi|313125463|ref|YP_004035727.1| 204 ALNHWEGVLGDQRFLVGDSLTIADLRLFPALVrfdPVYYTHFKCN-IRRLVD-YPNLWGYTRD 264
                                       67777889********************99972335677777777.777776.****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1770.37
//
Query:       gi|313125464|ref|YP_004035728.1|  [L=134]
Description: glyoxalase/bleomycin resistance protein/dioxygenase superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-08   33.7   0.7    4.7e-08   33.3   0.7    1.2  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
     0.0021   18.3   0.0      0.003   17.8   0.0    1.2  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.7   5.2e-12   4.7e-08       2     128 .]       6     126 ..       5     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 5.2e-12
                                       EEEEE..EEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEE CS
                        Glyoxalase   2 idhva..llvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhh 76 
                                       idhv   ++ +++e +++FY+++LGf l   ++++ +++   +  +++++  +  +  e  ++++  +        h
  gi|313125464|ref|YP_004035728.1|   6 IDHVHlrIPEDEIEHAIEFYQGHLGFPLEGFDEYEAGETPIFHFRLTEDTIIHIRPTDEFVHPERENF-------DH 75 
                                       66666559999**********************75555666666677777766677777777777776.......57 PP

                                       EEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEE.EEEETTSEEEEE CS
                        Glyoxalase  77 vafialdvedvgkaldrlkeagvkvvaepgrhyfgalysf.yfrDpdGillei 128
                                       +a i   +ed+ +  ++l++agv + +e + ++ ++   + y+rDp+G+lle+
  gi|313125464|ref|YP_004035728.1|  76 LAIIL--DEDIKDVKQELEDAGVIIEREGTPYGATGEAPAiYVRDPFGYLLEL 126
                                       77665..6999***********9999887777766655447**********96 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.3e-07     0.003       8     104 ..      16     109 ..       8     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-07
                                       S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEEES.-HHHHH CS
                      Glyoxalase_4   8 eDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflaehgeglhhlaywvd.dldaav 83 
                                       +++e a+++++++lG+  +   ++e  e  +  ++l +       i+ ++++ef++  +e + hla+  d d++ + 
  gi|313125464|ref|YP_004035728.1|  16 DEIEHAIEFYQGHLGFPLEGFDEYEAGETPIFHFRLTED--T--IIHIRPTDEFVHPERENFDHLAIILDeDIKDVK 88 
                                       57999**********966655555555555444555554..3..456666667***************976****** PP

                                       HHHCTTTEEEEEEEE-GGGTT CS
                      Glyoxalase_4  84 arleeqGfevvqkgvragaag 104
                                       ++le++G+ +  +g+  ga g
  gi|313125464|ref|YP_004035728.1|  89 QELEDAGVIIEREGTPYGATG 109
                                       ********9989888888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 836.97
//
Query:       gi|313125465|ref|YP_004035729.1|  [L=100]
Description: hypothetical protein Hbor_06920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   14.4   0.3      0.062   13.5   0.2    1.6  2  Cohesin   Cohesin domain
      0.074   13.3   0.1       0.08   13.2   0.1    1.2  1  FixG_C    IG-like fold at C-terminal of FixG, putative oxidor
       0.11   12.7   0.3       0.31   11.2   0.3    1.8  1  fn3_6     Fibronectin type-III domain


Domain annotation for each model (and alignments):
>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2     1e-05     0.062      15      46 ..       7      40 ..       2      65 .. 0.84
   2 ?   -2.0   0.0      0.66     4e+03       3      22 ..      69      88 ..      67      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                                      EEEEEEEEESECTT..EEEEEEEEEE.TTTEEEE CS
                           Cohesin 15 tvtvpvtvsnvskk..vaaaqftikYDpavlevv 46
                                       +tv++t++nv+++  v++ ++ + YD ++   v
  gi|313125465|ref|YP_004035729.1|  7 PITVQLTITNVASDaeVYSESVSVDYDEELANRV 40
                                      59*************************9987655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.66
                                      EEESEEEE-TTSEEEEEEEE CS
                           Cohesin  3 vkidkvsakvGdtvtvpvtv 22
                                      + +++++++++  v + +tv
  gi|313125465|ref|YP_004035729.1| 69 WDVPGNQGQPDGAVGLDITV 88
                                      67778888887777777776 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.3e-05      0.08      40     105 ..       1      63 [.       1      93 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                       EE-SSS-EEEEEEEES.-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEEEGG CS
                            FixG_C  40 lNktekprrytlsveg.lpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvtddd 105
                                       +N+t++p +++l++++   ++e+    +++++v+ +e++  +v+ +++   ++++++ i+++++dd+
  gi|313125465|ref|YP_004035729.1|   1 MNQTTSPITVQLTITNvASDAEV-Y--SESVSVDYDEELANRVT-TIEGVIEEPGEHLISVELKDDN 63 
                                       8**************94459999.4..48*******99999887.4445555677778888887543 PP

>> fn3_6  Fibronectin type-III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   5.3e-05      0.31      14      41 ..       3      40 ..       1     100 [] 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.3e-05
                             fn3_6 14 elkgtvtvtRtvtnVgsseatYkakve..........a 41
                                      ++++ +tv+ t+tnV+s +++Y+ +v+           
  gi|313125465|ref|YP_004035729.1|  3 QTTSPITVQLTITNVASDAEVYSESVSvdydeelanrV 40
                                      5678899***************9888744444443330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 643.14
//
Query:       gi|313125466|ref|YP_004035730.1|  [L=206]
Description: hypothetical protein Hbor_06930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0013   19.0   3.3     0.0018   18.5   3.3    1.3  1  Reprolysin_5  Metallo-peptidase family M12
     0.0038   17.7   0.3     0.0068   16.9   0.3    1.5  1  Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
  ------ inclusion threshold ------
      0.093   12.6   1.8      0.088   12.7   0.5    1.6  2  Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like


Domain annotation for each model (and alignments):
>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.3     3e-07    0.0018      29     173 ..      24     177 ..       6     190 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3e-07
                      Reprolysin_5  29 ivnlvnrasnvyeres...nislglanvtildeedpstaseasstgdaselLnefqsassalrgqqnddlailflmt 102
                                       ++n  + +sn+ e ++   + + +l+  t +d++ + ++     +++++ + ++++  +++  +++++d   ++ ++
  gi|313125466|ref|YP_004035730.1|  24 LNNRADAISNAWETDIedsSGDYSLRTHTHWDKPVSISS-----DDAGTARQEAAEYVHNNYSFSSKYDSILVIHDE 95 
                                       444444555555555544334455555555555555442.....222222222222244445566677777777777 PP

                      Reprolysin_5 103 nfsgg.vGlAwlgqlcnsgsagsvstrveksnsvvvstatevqvva..HElGHnfGavH.Dcdsss........... 164
                                       + + +  G+A    ++++++  +  +++   + v++ t+ ++++ a  HE+GH++ a+H D+++             
  gi|313125466|ref|YP_004035730.1|  96 KWNDNvTGMAPIPPTDGDSDEIAAGNNP---QPVAIATTGTLIAAAdtHEMGHMYSARHsDHEN-Wgvaeftvmgnp 168
                                       7777655666665555555533322222...23445555555554344***********66665.458888888888 PP

                      Reprolysin_5 165 esqsCslsn 173
                                       +s++C+++ 
  gi|313125466|ref|YP_004035730.1| 169 SSTTCNGND 177
                                       888887754 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   1.1e-06    0.0068      39     124 .]      61     152 ..      26     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                      Reprolysin_3  39 tkkdatealdelaevtaeaergqagyDlvhlftarde.sgvgGlAyvgsvcnsskk.agvnsgssvlgkvga....d 109
                                       ++ da +a +e+ae++++++  +++yD   ++++++  + v G+A +      s++ a+ n  + v  +++      
  gi|313125466|ref|YP_004035730.1|  61 SSDDAGTARQEAAEYVHNNYSFSSKYDSILVIHDEKWnDNVTGMAPIPPTDGDSDEiAAGNNPQPVAIATTGtliaA 137
                                       3445588899999999**99**************88799********544444444244444444444433346657 PP

                      Reprolysin_3 110 tvaHEiGHnfganHt 124
                                       + +HE+GH  +a+H+
  gi|313125466|ref|YP_004035730.1| 138 ADTHEMGHMYSARHS 152
                                       778***********6 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.47   2.8e+03     156     168 ..      65      76 ..      17     107 .. 0.63
   2 ?   12.7   0.5   1.5e-05     0.088     130     192 ..     140     199 ..     113     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.47
                      Reprolysin_2 156 aatsvedaggkfi 168
                                       a+t + ++  +++
  gi|313125466|ref|YP_004035730.1|  65 AGT-ARQEAAEYV 76 
                                       222.333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.5e-05
                      Reprolysin_2 130 aHEvGHaFGatHdndgs..sasegveenaatsvedaggkfiMapasksnndlFSpcsislisdvl 192
                                        HE+GH + a H ++ +   a+  v  n  +++++++ +     +    +  FS+c i  i+d +
  gi|313125466|ref|YP_004035730.1| 140 THEMGHMYSARHSDHENwgVAEFTVMGNPSSTTCNGNDH-----TFRTRKNRFSDCDITPIRDYM 199
                                       5***********999777633323322222223444433.....333444459999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1235.31
//
Query:       gi|313125467|ref|YP_004035731.1|  [L=194]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-27   95.1   0.0    6.3e-27   94.5   0.0    1.3  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.015   15.0   0.3        1.7    8.4   0.0    2.2  2  DDE_3          DDE superfamily endonuclease
      0.027   14.6   0.0      0.062   13.5   0.0    1.6  2  rve            Integrase core domain
      0.033   14.3   0.0      0.049   13.7   0.0    1.2  1  DUF1115        Protein of unknown function (DUF1115)
       0.19   11.8   0.0       0.43   10.6   0.0    1.5  2  PilJ           Type IV pili methyl-accepting chemotaxis trans


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   1.8e-30   6.3e-27       2     134 ..      67     193 ..      66     194 .] 0.95

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 1.8e-30
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkel 77 
                                       k+++vDET+vki+G+w++ly+a+D e++ ild+ ++ r +t++a+afl+++ +k++l++ ++++D+++  ++al++l
  gi|313125467|ref|YP_004035731.1|  67 KRVAVDETAVKINGEWSWLYAAIDIETKlILDVELFGRHGTDPAAAFLHRLSEKHDLSDTVFLVDGYG-HQTALSRL 142
                                       789*****************************************************************.9******* PP

                     DDE_Tnp_IS240  78 kregelfdevshvqvkylnnriEsdhrtlKkrl..rptrgfkslksaaktlagfeavkn 134
                                       + +g  +d+       +++n iE+++  lK+r+  ++++++ s  s++ ++ +f+ ++ 
  gi|313125467|ref|YP_004035731.1| 143 GLSGL-LDY-------VERNLIEKWFHILKMRVerFHNSWVGSHGSVHGWIIQFAQYYD 193
                                       **865.556.......789**************8889****************999985 PP

>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00047       1.7      29      87 ..      74     132 ..      44     140 .. 0.85
   2 ?    4.5   0.5    0.0078        28     120     135 ..     154     169 ..     152     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00047
                             DDE_3  29 leeygrrgrvnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDn 87 
                                        + +++++  +l++a+d +++l++ v   ++  ++  a+fl rl e+++ +  +v+++D+
  gi|313125467|ref|YP_004035731.1|  74 TAVKINGEWSWLYAAIDIETKLILdVELFGRHGTDPAAAFLHRLSEKHDLS-DTVFLVDG 132
                                       5677889999**************99999999999999***********98.77777776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0078
                             DDE_3 120 NpiEivwsklkrellk 135
                                       N iE+++++lk ++ +
  gi|313125467|ref|YP_004035731.1| 154 NLIEKWFHILKMRVER 169
                                       9**********99887 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.7e-05     0.062       6      65 ..      67     124 ..      62     145 .. 0.84
   2 ?   -2.9   0.0       2.1   7.5e+03     107     112 ..     166     171 ..     150     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                               rve   6 elwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggv 65 
                                       +++ vD t v+i   g++++l++++d  ++lil + l  ++ ++ ++a+l+r  ++   +
  gi|313125467|ref|YP_004035731.1|  67 KRVAVDETAVKIN--GEWSWLYAAIDIETKLILDVELFGRHGTDPAAAFLHRLSEKHDLS 124
                                       67889***99955..447*********************************998887665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                               rve 107 kvErfh 112
                                       +vErfh
  gi|313125467|ref|YP_004035731.1| 166 RVERFH 171
                                       355555 PP

>> DUF1115  Protein of unknown function (DUF1115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.4e-05     0.049      14      59 ..      11      54 ..       5      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                           DUF1115 14 rfkvdknAkqlsltGvvllgpkfnlvvveGgekaikkYkklmlrri 59
                                      r  v+ +A ql+ tG+ l + k  ++ + G e++ +++++++ +r+
  gi|313125467|ref|YP_004035731.1| 11 RTPVRVFAVQLHATGCSLRETK-EILRILGVERSHQAFWQWV-HRL 54
                                      77799***************99.9*****************9.776 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012      0.43      48      95 ..      41      89 ..      39      97 .. 0.89
   2 ?   -3.8   0.0       3.7   1.3e+04      41      58 ..     157     174 ..     153     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                              PilJ 48 retiaqfdrtlaalrlgdpapgllvpae.avraqleaveqlWqelkkpa 95
                                      +++ ++f +++++l++++ +p+ ++p+  av +   +++ +W+ l  ++
  gi|313125467|ref|YP_004035731.1| 41 ERSHQAFWQWVHRLADSGHTPPEAKPKRvAVDETAVKINGEWSWLYAAI 89
                                      67778999**********************************9776665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.7
                              PilJ  41 aearaqlretiaqfdrtl 58 
                                       ++ +  l+ ++++f +++
  gi|313125467|ref|YP_004035731.1| 157 EKWFHILKMRVERFHNSW 174
                                       566777888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1157.97
//
Query:       gi|313125468|ref|YP_004035732.1|  [L=55]
Description: hypothetical protein Hbor_06950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 341.17
//
Query:       gi|313125469|ref|YP_004035733.1|  [L=277]
Description: hypothetical protein Hbor_06960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.48   10.6   3.5       0.87    9.8   3.5    1.4  1  YbgT_YccB  Membrane bound YbgT-like protein


Domain annotation for each model (and alignments):
>> YbgT_YccB  Membrane bound YbgT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.5   4.9e-05      0.87       5      22 ..      46      63 ..      45      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.9e-05
                         YbgT_YccB  5 aWiLGvlLAvlfgilnal 22
                                       W++G l A+lf++l a 
  gi|313125469|ref|YP_004035733.1| 46 LWFVGPLIAILFAVLGAA 63
                                      6*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1807.07
//
Query:       gi|313125470|ref|YP_004035734.1|  [L=79]
Description: hypothetical protein Hbor_06970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 469.32
//
Query:       gi|313125471|ref|YP_004035735.1|  [L=86]
Description: hypothetical protein Hbor_06980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 563.28
//
Query:       gi|313125472|ref|YP_004035736.1|  [L=137]
Description: hypothetical protein Hbor_06990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0084   16.6   0.1      0.024   15.1   0.1    1.9  1  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.017   14.7   3.4      0.017   14.7   3.4    1.4  1  MscS_porin       Mechanosensitive ion channel porin domain
      0.038   14.1   0.9      0.079   13.1   0.3    1.8  2  DUF2250          Uncharacterized protein conserved in archaea
       0.07   13.8   6.5        1.8    9.2   1.1    2.2  2  YabA             Initiation control protein YabA
       0.09   12.7   0.0       0.32   11.0   0.0    2.0  2  MarR             MarR family
        2.6    8.5   7.9       0.98    9.9   0.5    2.6  2  Snapin_Pallidin  Snapin/Pallidin


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   7.9e-06     0.024       3      54 ..      10      58 ..       8      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.9e-06
                            HTH_27  3 rqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                      + + +vL++i   ++ +    + +++ +e  h+ y+ +kL+  GL+ +  ++
  gi|313125472|ref|YP_004035736.1| 10 EKDQVVLNQID--QGNDDVQKITEATTLENYHVTYAFEKLEDLGLL-KVSKP 58
                                      667899*****..999999***************************.44444 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.4   5.8e-06     0.017      51     110 ..      80     135 ..      69     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.8e-06
                        MscS_porin  51 kelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlve 110
                                       +++++ +q+le+l    e++  +++++ls +eL ++  q +++  +l++ l+++ +q+ve
  gi|313125472|ref|YP_004035736.1|  80 ALTEKGRQHLEQL----ETDGFDEYENLSHRELVKKTHQLEADIRQLENSLNTFRQQVVE 135
                                       5677778888888....9999999999999999999999999999999999998888776 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   2.6e-05     0.079      11      63 ..      13      65 ..       3      92 .. 0.71
   2 ?   -0.8   0.1      0.58   1.7e+03      40      54 ..      86     100 ..      75     121 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                           DUF2250 11 lkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve.gktikrt 63
                                        vl+ +++ n d  + i++ + ++  +v+ +++kLe+lGLl+  + + t+ r 
  gi|313125472|ref|YP_004035736.1| 13 QVVLNQIDQGNDDV-QKITEATTLENYHVTYAFEKLEDLGLLKVSKpEGTVERI 65
                                      45677777766665.5689999********************976645555544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.58
                           DUF2250  40 rellkkLeelGLler 54 
                                       r+ l++Le+ G  e+
  gi|313125472|ref|YP_004035736.1|  86 RQHLEQLETDGFDEY 100
                                       555666666554333 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.1   0.00062       1.8       7      81 ..       2      97 ..       1      99 [. 0.77
   2 ?    7.7   0.4    0.0018       5.5       3      33 ..     105     135 ..     103     137 .] 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00062
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHH.................XXXXXXXXXXXX CS
                              YabA  7 fdkleeleeqleelleeleelkeelaelle....enaeLeleneklrerl.................eeeekkekekkk 64
                                      +++le+l e+ + +l+++++ ++++++++e    en +++   ekl ++                  +++  ++ ++ +
  gi|313125472|ref|YP_004035736.1|  2 TEALENLREKDQVVLNQIDQGNDDVQKITEattlENYHVTYAFEKLEDLGllkvskpegtveriingQKRVFQHPKQAA 80
                                      5677888888888888888777777766652223566666666666655489999********9998888888999999 PP

                                      XXXXXXXXXXXXXXXXX CS
                              YabA 65 elsegkenLarlYeeGF 81
                                       +++g+++L++l ++GF
  gi|313125472|ref|YP_004035736.1| 81 LTEKGRQHLEQLETDGF 97
                                      99**************9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   3 kkelfdkleeleeqleelleeleelkeelae 33 
                                       ++el++k ++le ++++l ++l++ +++++e
  gi|313125472|ref|YP_004035736.1| 105 HRELVKKTHQLEADIRQLENSLNTFRQQVVE 135
                                       689***********************99976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.32      15      52 ..      21      58 ..      14      60 .. 0.90
   2 ?   -3.0   0.0       2.5   7.3e+03      38      46 ..      89      97 ..      88      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      qg+  v+++ ++  +++ +vt +  +Le+ Gl++ sk 
  gi|313125472|ref|YP_004035736.1| 21 QGNDDVQKITEATTLENYHVTYAFEKLEDLGLLKVSKP 58
                                      6777899**************************98875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                                      HHHHHHTTS CS
                              MarR 38 ldrLekkGl 46
                                      l +Le +G+
  gi|313125472|ref|YP_004035736.1| 89 LEQLETDGF 97
                                      678999998 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5   0.00033      0.98      19      53 ..       2      37 ..       1      50 [. 0.85
   2 ?    2.3   0.6     0.074   2.2e+02      23      48 ..     106     131 ..     102     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                   Snapin_Pallidin 19 deklkelrqsQeeLleqldrlnekLkeleeaqe.ae 53
                                      +e l++lr++ + +l+q+d+ n++++++ ea+  ++
  gi|313125472|ref|YP_004035736.1|  2 TEALENLREKDQVVLNQIDQGNDDVQKITEATTlEN 37
                                      6789*************************9998444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.074
                   Snapin_Pallidin  23 kelrqsQeeLleqldrlnekLkelee 48 
                                       +el ++  +L +++++l ++L+ +++
  gi|313125472|ref|YP_004035736.1| 106 RELVKKTHQLEADIRQLENSLNTFRQ 131
                                       56777777788888888887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1258  (0.0701657); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.58
# Mc/sec: 707.25
//
Query:       gi|313125473|ref|YP_004035737.1|  [L=149]
Description: hypothetical protein Hbor_07000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 968.04
//
Query:       gi|313125474|ref|YP_004035738.1|  [L=569]
Description: hypothetical protein Hbor_07010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-07   29.9  43.7    4.7e-06   25.7  15.4    2.3  2  Spc7             Spc7 kinetochore protein
    1.8e-06   28.0  33.3     0.0061   16.6   4.7    4.3  4  DUF1664          Protein of unknown function (DUF1664)
    3.2e-05   22.8  12.3    3.2e-05   22.8  12.3    2.3  2  AAA_13           AAA domain
    0.00011   21.4  11.3    0.00011   21.4  11.3    2.6  2  Atg14            Vacuolar sorting 38 and autophagy-related su
    0.00017   21.7   4.4    0.00017   21.7   4.4    3.9  3  Laminin_II       Laminin Domain II
    0.00021   21.5   7.4    0.00021   21.5   7.4    4.6  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
    0.00094   19.2   0.6    0.00094   19.2   0.6    3.7  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
     0.0015   18.5  10.6     0.0015   18.5  10.6    4.9  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
     0.0022   18.2   0.0     0.0061   16.8   0.0    1.7  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0032   17.1   0.5     0.0032   17.1   0.5    1.7  1  DpnI             Dam-replacing family
      0.005   17.1  12.6      0.005   17.1  12.6    3.4  3  ATG16            Autophagy protein 16 (ATG16)
  ------ inclusion threshold ------
      0.013   15.8   5.8      0.013   15.8   5.8    4.7  4  DUF4164          Domain of unknown function (DUF4164)
      0.016   14.9   3.1      0.016   14.9   3.1    4.2  4  DUF4201          Domain of unknown function (DUF4201)
      0.024   14.5   0.0      0.024   14.5   0.0    6.3  4  Rad50_zn_hook    Rad50 zinc hook motif
      0.036   14.3   1.9        2.4    8.5   0.0    2.9  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
      0.066   11.8  32.6      0.049   12.2  12.4    3.1  2  FapA             Flagellar Assembly Protein A
      0.068   13.1   0.5       0.17   11.8   0.5    1.7  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.073   12.7  10.5       0.11   12.1  10.5    1.3  1  DUF885           Bacterial protein of unknown function (DUF88
      0.075   12.7  38.8      0.045   13.5  17.6    2.4  2  SHE3             SWI5-dependent HO expression protein 3
       0.14   12.6  16.6        4.5    7.8   7.3    4.3  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.18   11.4   0.1       0.18   11.4   0.1    4.3  4  AAA_27           AAA domain
       0.54    9.7   2.2         19    4.6   0.1    3.1  3  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
       0.55   10.1  24.8      0.042   13.7   2.3    4.0  3  CK2S             Casein Kinase 2 substrate
       0.69    9.5  48.7        2.7    7.6  23.9    2.7  2  Lebercilin       Ciliary protein causing Leber congenital ama
       0.87    9.2  45.5        4.9    6.7   6.2    4.0  3  DUF4795          Domain of unknown function (DUF4795)
        1.1    9.3  46.8         11    6.1   5.3    4.3  4  Mod_r            Modifier of rudimentary (Mod(r)) protein
        1.2    8.7   3.1          5    6.8   0.1    2.4  2  Sgf11            Sgf11 (transcriptional regulation protein)
        1.5    9.3  48.2      0.044   14.2  16.9    3.3  3  Fez1             Fez1
        1.5    9.1  14.9        9.1    6.6   0.6    4.0  3  DUF948           Bacterial protein of unknown function (DUF94
        1.5    9.5  29.9      0.081   13.7   2.6    4.4  2  DUF2203          Uncharacterized conserved protein (DUF2203)
        2.1    8.2  31.2       0.43   10.5   3.0    4.0  4  Sec34            Sec34-like family
        2.2    8.8  65.3       0.15   12.6  23.1    4.3  4  APG6_N           Apg6 coiled-coil region
        2.3    7.7  35.2    1.8e+04  -11.3  35.2    2.8  0  Exonuc_VII_L     Exonuclease VII, large subunit
        2.6    6.1  40.3        1.7    6.7  13.9    2.1  2  FPP              Filament-like plant protein, long coiled-coi
        2.7    8.3  44.0       0.15   12.4   4.0    5.4  3  DUF5082          Domain of unknown function (DUF5082)
        2.8    8.4  55.9    1.8e+04  -17.1  55.9    3.4  0  AAA_23           AAA domain
        3.8    6.9  44.4          2    7.8  20.7    2.5  2  Golgin_A5        Golgin subfamily A member 5
        4.8    7.0  12.8        3.7    7.3   2.8    3.2  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
        5.3    7.2  12.5          1    9.5   1.2    2.9  2  GIT1_C           G protein-coupled receptor kinase-interactin
        5.7    7.0   8.8         20    5.3   3.0    3.3  2  CpXC             CpXC protein
        6.2    5.8  50.4        2.7    7.0  19.7    2.2  2  DUF4686          Domain of unknown function (DUF4686)
        6.5    6.4   7.3         19    4.9   0.1    3.5  3  DUF4988          Domain of unknown function
        7.7    6.7  35.7          8    6.6   6.7    4.3  4  Fib_alpha        Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8  20.3   0.00078      0.33     133     253 ..     134     262 ..     133     267 .. 0.75
   2 !   25.7  15.4   1.1e-08   4.7e-06     133     264 ..     294     425 ..     291     467 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00078
                              Spc7 133 RmqllegLke.gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles....idkeeLeel 204
                                       R++l+ ++ + +le++++ le+ +e+L++   e ++ + +l+eek++l +++ +l++++e+ +     i++ eL++l
  gi|313125474|ref|YP_004035738.1| 134 RTKLIRSVTNrELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDRlesqIESGELAKL 210
                                       6677777654279***************************************99999776665555478999***** PP

                              Spc7 205 reela...elkaeieekkkelaelqeqleeleekieelkeqkseleeeiaea 253
                                        ++l+   el++ ++e+ ke + l+++l +l  k  + ++  se+++ iaea
  gi|313125474|ref|YP_004035738.1| 211 SQQLRrdeELENRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDIIAEA 262
                                       ****722144555555566666666666666666666666666666666665 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.1e-08
                              Spc7 133 RmqllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqe....aaeelesidkeeLeelr 205
                                       R   legLk++l++++e+ ++  ++L+++ eel++  +e++++  el+ee  +l+e     ++ l+++d+ ++++++
  gi|313125474|ref|YP_004035738.1| 294 RNHSLEGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEEldgfTKRRLDNYDH-NIQQIQ 369
                                       6778999999999999999999999999999999999999999999999999999944444444444443.233333 PP

                              Spc7 206 eelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgws 264
                                       +    +++e+e+ +  l+el++++++leek+ee++ + + + e+ ++a +++ee  + s
  gi|313125474|ref|YP_004035738.1| 370 D---HVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTEQS 425
                                       3...3456677777899999999999999999999999999999999998888866544 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   4.3    0.0032       1.3      60     119 ..     142     204 ..     133     212 .. 0.73
   2 ?    5.6   0.7     0.037        15      48      94 ..     218     264 ..     206     268 .. 0.87
   3 !   12.9   2.0    0.0002     0.083      55     107 ..     296     348 ..     293     353 .. 0.90
   4 !   16.6   4.7   1.5e-05    0.0061      48     115 ..     356     423 ..     347     428 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0032
                           DUF1664  60 tkrhLssridrvdkkldeqkei...skeikeevtevredlseigedvesvkeavegleskler 119
                                       t r+L++ri r+++  ++ +e+   +k++k+ ++e ++dl++  +d+es ke    les++e+
  gi|313125474|ref|YP_004035738.1| 142 TNRELEQRISRLEDAEEQLSELvveTKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQIES 204
                                       678999999998876666655511156667777777777887788888888888888888875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.037
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevre 94 
                                       ++le+  ++l + k+ L +r+ ++ +k  +q++  +e+++ ++e+ +
  gi|313125474|ref|YP_004035738.1| 218 EELENRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDIIAEAVN 264
                                       57899999************************999999998887655 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.0002
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                       +sl+  k++Ls++i++ d+ lde ke ++e++++ +ev++++ e++e+  +++
  gi|313125474|ref|YP_004035738.1| 296 HSLEGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELE 348
                                       578899***********************************999998866655 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 1.5e-05
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       ++l++  +++++ ++h +++++++ ++lde k   ++++e+v+e++++ ++ +e  ++ +e+ve+l +
  gi|313125474|ref|YP_004035738.1| 356 RRLDNYDHNIQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTE 423
                                       579999**********************************************************9976 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1  13.2       1.3   5.3e+02     352     467 ..     138     259 ..     123     267 .. 0.42
   2 !   22.8  12.3   7.6e-08   3.2e-05     255     428 ..     286     447 ..     277     459 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                            AAA_13 352 fksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeyk.....kkykklek 423
                                        +sv+  +++++i++++++ +++ el+ +   +  +l eek+++  ++   +    ++++d+++      +++kl++
  gi|313125474|ref|YP_004035738.1| 138 IRSVTNRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLES--QKEKYDRLEsqiesGELAKLSQ 212
                                       44444444444444444444444444444444444444444444444444222..1222222221111122222222 PP

                            AAA_13 424 ai...eklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeL 467
                                       ++   e+le++l+e  +e++ l+++ + L ++ r++++  +e+n+++
  gi|313125474|ref|YP_004035738.1| 213 QLrrdEELENRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDII 259
                                       22111344444444444444444444444444444444444444444 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 7.6e-08
                            AAA_13 255 sdtCpFCgqplp.aerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaea 330
                                       ++ Cp+Cg++ + + +k++L + +++ +++  ++L++ ie+++ +++e+++++ ++ +e+   ++ ee     k+++
  gi|313125474|ref|YP_004035738.1| 286 RGYCPYCGRNHSlEGLKQRLSQKIEE-SDDLLDELKEEIEELQDQRDEVSNQIGELKEEK---PELEELDGFTKRRL 358
                                       578****9865414466677777665.666677777777777777777777776555532...33444444444455 PP

                            AAA_13 331 ealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveel 407
                                       ++ + +++++q+ +++         eles+++ ++++k++ ++++e +++ N+k++ + e+ ++a + +e    +++
  gi|313125474|ref|YP_004035738.1| 359 DNYDHNIQQIQDHVQE---------ELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTEQSF 426
                                       5555555555555444.........667777788888899999********************************** PP

                            AAA_13 408 eseldeykkkykklekaiekl 428
                                       e+ ++e+ ++++++ ++++++
  gi|313125474|ref|YP_004035738.1| 427 EAGIQEFSEAWEEAYNQMNSN 447
                                       *********999988888764 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3  18.4       1.1   4.6e+02      38     151 ..     143     252 ..     128     262 .. 0.58
   2 !   21.4  11.3   2.6e-07   0.00011       1     139 [.     268     424 ..     268     453 .. 0.52

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                             Atg14  38 keslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkR 114
                                       + +l+++i++++  +e+ ++l  + k +k +l+e ks+  ++ + l+  k+k ++l ++ie  + +lakls++l +R
  gi|313125474|ref|YP_004035738.1| 143 NRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQIE--SGELAKLSQQL-RR 216
                                       5566666666666666666666666666666666666666666666666666666666554..34666666666.44 PP

                             Atg14 115 rsdleslqnelee..rrkkqiaklqdaikrieqklssls 151
                                        ++   l+n+l e  ++k+ ++k +++++r+++k+++ +
  gi|313125474|ref|YP_004035738.1| 217 DEE---LENRLDElfKEKEGLRKRLRKLHRKKRKQENYE 252
                                       444...444444422234444555555555555555444 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.6e-07
                             Atg14   1 CplCerss.........rpfiCesClrngperlyelrerlaklksekeslkkkiekalegke............... 53 
                                       Cp C+r+          ++ +C+ C rn  ++l+ l++rl +  +e++ l  ++++++e+ +               
  gi|313125474|ref|YP_004035738.1| 268 CPTCDRRIttekaknriQRGYCPYCGRN--HSLEGLKQRLSQKIEESDDLLDELKEEIEELQdqrdevsnqigelke 342
                                       999999888889999999**********..89999999999999998888888888888888544444444443333 PP

                             Atg14  54 .......eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk........... 112
                                                                       +++rl +  + ++q ++ ++e  + +++  d+lk           
  gi|313125474|ref|YP_004035738.1| 343 ekpeleeL---------------------DGFTKRRLDNYDHNIQQIQDHVQEELESISSSLDELKsdrqsleekve 398
                                       22222221.....................222223322222222222222222222222222222211111112222 PP

                             Atg14 113 ..kRrsdleslqneleerrkkqiaklqda 139
                                          R+s+   +++e ++   + +++l+++
  gi|313125474|ref|YP_004035738.1| 399 eiNRKSK---AYSEAHNHASEMVEELTEQ 424
                                       2233333...4444444444444444443 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   9.2       2.5     1e+03      21      77 ..     145     204 ..     135     262 .. 0.68
   2 ?    5.2   1.5     0.049        20      67      97 ..     311     342 ..     298     343 .. 0.76
   3 !   21.7   4.4     4e-07   0.00017       7      67 ..     364     424 ..     360     428 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.5
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TT...TTTGGGHHH CS
                        Laminin_II  21 plsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekla...pqLldklke 77 
                                       +l+q+++++++  +++ + v et++  + +++   d  r+v++Le +    ++L++++++
  gi|313125474|ref|YP_004035738.1| 145 ELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKekyDRLESQIES 204
                                       567777777777777777777777777777777777777777777554111344444432 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.049
                                       TTTTTGGGHH.HHHHHHHH...HHHHHHHHHH CS
                        Laminin_II  67 lapqLldklk.elkqleeassslsdniseike 97 
                                       + ++Lld lk e+++l++++  +s++i e+ke
  gi|313125474|ref|YP_004035738.1| 311 ESDDLLDELKeEIEELQDQRDEVSNQIGELKE 342
                                       45778888753588888888889999999997 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 4e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--T CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekl 67 
                                       +++++  +v+e l+ +s  l+++k++ ++++++vee+n k k++++a + A++ v +L+++
  gi|313125474|ref|YP_004035738.1| 364 NIQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTEQ 424
                                       5789999***************************************************997 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   6.6      0.12        50      38      95 ..     143     204 ..     136     214 .. 0.86
   2 ?    1.2   5.4         1   4.2e+02      28      79 ..     207     258 ..     203     264 .. 0.78
   3 !   21.5   7.4   5.1e-07   0.00021      27     104 ..     305     379 ..     297     383 .. 0.86
   4 ?    5.4   6.0      0.05        21      41     100 ..     365     421 ..     357     449 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  38 rrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkelea 95 
                                        rel++++  l     +ls+ + + k+ k    e++++l  +v++l  + ++++  ++++e+
  gi|313125474|ref|YP_004035738.1| 143 NRELEQRISRLEDAEEQLSELVVETKDTKrrlsEEKSDLDRQVSDLESQKEKYDRLESQIES 204
                                       69999*********************999999999999999999999999999998888875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHH CS
                      Seryl_tRNA_N  28 vdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkel 79 
                                       +++l +  ++ +el+++l+el +e+  l k   k+ +kk + e    ev+++
  gi|313125474|ref|YP_004035738.1| 207 LAKLSQQLRRDEELENRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDI 258
                                       5666666777788999999999999999999999999998888888888776 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 5.1e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  27 dvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekllla 103
                                       + +++ e d+   el+ e+eelq +r e+s++Ig++k++k + eel       k +l++++ + +++++ +++ l +
  gi|313125474|ref|YP_004035738.1| 305 LSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELD---GFTKRRLDNYDHNIQQIQDHVQEELES 378
                                       6789999******************************9886666555...778899999999999999999998888 PP

                                       S CS
                      Seryl_tRNA_N 104 i 104
                                       i
  gi|313125474|ref|YP_004035738.1| 379 I 379
                                       7 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  41 lqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                       +q+  + +q+e  ++s +  ++k    d+++l ++v+e++ + ka++++ + +++ +e+l
  gi|313125474|ref|YP_004035738.1| 365 IQQIQDHVQEELESISSSLDELKS---DRQSLEEKVEEINRKSKAYSEAHNHASEMVEEL 421
                                       555555566666666666666664...455555555555555555555555555544443 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.8      0.47     2e+02      45      87 ..     151     202 ..     130     264 .. 0.64
   2 !   19.2   0.6   2.2e-06   0.00094      31     100 ..     322     389 ..     310     402 .. 0.88
   3 ?   -0.8   0.0       3.4   1.4e+03      48      83 ..     415     448 ..     390     453 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.47
                      Baculo_PEP_C  45 tqLnalsedlksllaeldt...rldtlltnLtdalnalq......dtlrneL 87 
                                       ++L++ +e+l++l+ e ++   rl++  + L++++  l+      d l++++
  gi|313125474|ref|YP_004035738.1| 151 SRLEDAEEQLSELVVETKDtkrRLSEEKSDLDRQVSDLEsqkekyDRLESQI 202
                                       4555556666666555444444666666666666666654433333333333 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.2e-06
                      Baculo_PEP_C  31 qilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlss 100
                                       +i  +l+ + d++ +q+++l+e+  + l+eld   +  l+n ++ ++++qd +++eL+++ s l +L s+
  gi|313125474|ref|YP_004035738.1| 322 EI-EELQDQRDEVSNQIGELKEEKPE-LEELDGFTKRRLDNYDHNIQQIQDHVQEELESISSSLDELKSD 389
                                       45.78999999999999999998777.8899999999******************************996 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.4
                      Baculo_PEP_C  48 nalsedlksllaeldtrldtlltnLtdalnalqdtl 83 
                                       +++ e+l++  +++++ +++++++ ++a n+++ +l
  gi|313125474|ref|YP_004035738.1| 415 SEMVEELTE--QSFEAGIQEFSEAWEEAYNQMNSNL 448
                                       333333443..4566688888888888888887665 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6  10.4       3.2   1.3e+03      27      69 ..     142     184 ..     139     206 .. 0.52
   2 !   18.5  10.6   3.5e-06    0.0015       4      69 ..     306     371 ..     303     374 .. 0.94
   3 ?    1.3   9.0      0.84   3.5e+02      17      68 ..     372     423 ..     370     427 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.2
                        TMF_DNA_bd  27 kelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                       ++++l++ i++L   +++l + + e+k+ +++l++e + l + 
  gi|313125474|ref|YP_004035738.1| 142 TNRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQ 184
                                       5566666666666666666655555553333333333333222 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.5e-06
                        TMF_DNA_bd   4 ekklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                         k++e D+ +++L+eE e+L+++ ++ +n+i +L+++  ele+    +k++l++++ +++++++ 
  gi|313125474|ref|YP_004035738.1| 306 SQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNIQQIQDH 371
                                       578********************************************************9999985 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.84
                        TMF_DNA_bd  17 LmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleelee 68 
                                       ++eE+e  s++ ++l+    +L +k++e + + k +++  +  ++ +eel+e
  gi|313125474|ref|YP_004035738.1| 372 VQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTE 423
                                       6899999999999999999999999999999999999999999999999876 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-05    0.0061      22      85 ..     466     527 ..     446     531 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-05
                           SbcCD_C  22 kekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDee.siatll 85 
                                       ++ + +++ g+lSG e   l+ + +a  l+   +++ g     ++++LDE Fs+l ee +++++l
  gi|313125474|ref|YP_004035738.1| 466 NNLREYDRGGNLSGSEF-HLLNISFACTLSRFATEN-G-VIEWDTIVLDEPFSNLQEEeNRDAAL 527
                                       445568999********.9****************7.5.99*************98761555555 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.5   7.7e-06    0.0032      16      79 ..     252     312 ..     239     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.7e-06
                                       -TTHHHHHHHHHHHHH---TTT--SS-EE--------EEE-TTT--EEEEEEEESS--SEEEEE CS
                              DpnI  16 ksqkaRvltEkWvaknlyCpkCgskklsefennkpvaDfyCesckeefeLkskksklskkivdg 79 
                                       +s++  +++E+   +++ Cp+C+++ +++ ++ +++   yC  c  ++ L   k++ls+ki ++
  gi|313125474|ref|YP_004035738.1| 252 ESEVNDIIAEA--VNDFVCPTCDRR-ITTEKAKNRIQRGYCPYCGRNHSLEGLKQRLSQKIEES 312
                                       44455556664..57899******9.888899999**************************976 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  17.7      0.19        79      96     178 ..     142     225 ..     130     238 .. 0.86
   2 !   17.1  12.6   1.2e-05     0.005       3     144 ..     211     377 ..     209     382 .. 0.92
   3 ?    2.1   6.4      0.47     2e+02     114     153 ..     372     407 ..     354     432 .. 0.46

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.19
                             ATG16  96 srgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdl.qDElsaLqlqlnqaE 171
                                       ++ el+qr+ +l+++ ++l e   e + + ++l++e+++l ++++d+e + +  ++l  ++   El+ L  ql   E
  gi|313125474|ref|YP_004035738.1| 142 TNRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQIeSGELAKLSQQLRRDE 218
                                       6899*************************************************99996555167*********9888 PP

                             ATG16 172 eklrkle 178
                                       e  ++l 
  gi|313125474|ref|YP_004035738.1| 219 ELENRLD 225
                                       7666654 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.2e-05
                             ATG16   3 laqLreRdarqekafaeliqaynrLldrtsaleaenaklekaaasaks...........sksskksakekeasasq. 67 
                                       ++qLr+ ++  e+   el++    L +r ++l+++++k e+  ++++            ++  ++ ++ek++++ q 
  gi|313125474|ref|YP_004035738.1| 211 SQQLRRDEE-LENRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDiiaeavndfvcPTCDRRITTEKAKNRIQr 286
                                       667775555.6****************************999999998999****9999888899999999999999 PP

                             ATG16  68 ..............snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaelea 130
                                                      +++ s+ki++++++l +l+ee +el+ +r e ++++ el+ee  +lee     ++rl++  +
  gi|313125474|ref|YP_004035738.1| 287 gycpycgrnhslegLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDH 363
                                       ************99899999********************************************************* PP

                             ATG16 131 eraaletklkdree 144
                                       +++++++ +++  e
  gi|313125474|ref|YP_004035738.1| 364 NIQQIQDHVQEELE 377
                                       ******99987766 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.47
                             ATG16 114 leeklkedeerlaeleaeraaletklkdreeelrekeklv 153
                                        +e+l++ +++l+el+++r++le+k++    e++ k k+ 
  gi|313125474|ref|YP_004035738.1| 372 VQEELESISSSLDELKSDRQSLEEKVE----EINRKSKAY 407
                                       233334444444444444444444433....333333322 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   8.2       2.9   1.2e+03      17      75 ..     126     184 ..     123     191 .. 0.84
   2 ?    0.8  10.6       1.5   6.2e+02      17      79 ..     195     262 ..     187     265 .. 0.78
   3 ?   15.8   5.8   3.1e-05     0.013      16      86 ..     297     368 ..     295     371 .. 0.94
   4 ?    2.4   1.6      0.45   1.9e+02      35      72 ..     377     414 ..     370     424 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.9
                           DUF4164  17 ldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrr 75 
                                       ld+L +    +l +  +++ele++i++l++ +++L e   ++++  +rl+e ++++ r+
  gi|313125474|ref|YP_004035738.1| 126 LDELSRGQRTKLIRSVTNRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQ 184
                                       67777777788888889999************999999999999999999988888775 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.5
                           DUF4164  17 ldsLEkavd....rrleaerkr.deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaa 79 
                                        d+LE+ ++    ++l+++  r +ele+++ +l ++++ L ++L +   + ++ e+  +Ev++ +  a
  gi|313125474|ref|YP_004035738.1| 195 YDRLESQIEsgelAKLSQQLRRdEELENRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDIIAEA 262
                                       5677777763222355444333599************************************9877665 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 3.1e-05
                           DUF4164  16 aldsLEkavdrrleaerkr.deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietirav 86 
                                       +l+ L +++ +++e+  +  del++eie+l++ r    +++ + + +  +lee+   ++rrL+  + +i+++
  gi|313125474|ref|YP_004035738.1| 297 SLEGLKQRLSQKIEESDDLlDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNIQQI 368
                                       789999*******9999988*************************************************998 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.45
                           DUF4164  35 deleaeiealgedrsRLaeeLdqaearaarleevnrEv 72 
                                       +++ + + +l++dr+ L+e+  + + + ++ +e+ + +
  gi|313125474|ref|YP_004035738.1| 377 ESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHA 414
                                       55556666677777777776666666655555554444 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   9.3       1.1   4.6e+02      55     119 ..     143     207 ..     132     216 .. 0.67
   2 ?   -1.9  10.1       5.8   2.4e+03      82     135 ..     191     245 ..     185     257 .. 0.61
   3 ?   14.9   3.1   3.9e-05     0.016      90     138 ..     299     347 ..     292     350 .. 0.89
   4 ?    6.6   4.6     0.014         6      73     135 ..     363     425 ..     355     431 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                           DUF4201  55 nkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkl 119
                                       n ++e r   L+   ++    v +++++k +l++ +s l ++ ++l++++e+ ++l+ ++++ +l
  gi|313125474|ref|YP_004035738.1| 143 NRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQIESGEL 207
                                       45566666666666666666666667777777777777777777777777777777666666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.8
                           DUF4201  82 lkeklhmleselse.lkkelkekeerlaklrkelykvklerdklrkqneklkqqg 135
                                        kek + les+ +     +l+++ +r ++l+ +l ++ +e++ lrk+ +kl++++
  gi|313125474|ref|YP_004035738.1| 191 QKEKYDRLESQIESgELAKLSQQLRRDEELENRLDELFKEKEGLRKRLRKLHRKK 245
                                       5666665555554313456666666666666666666666666666666666654 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3.9e-05
                           DUF4201  90 eselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggll 138
                                       e   ++l ++++e ++ l++l++e+++++ +rd + +q  +lk+++ +l
  gi|313125474|ref|YP_004035738.1| 299 EGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPEL 347
                                       5567899************************************987665 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.014
                           DUF4201  73 tktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqg 135
                                       ++  ++  h++e l  ++s l elk++ +++ee+ +++ ++     + ++++ +  e+l +q+
  gi|313125474|ref|YP_004035738.1| 363 HNIQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTEQS 425
                                       455566679999999999999999999999999999999999999999999999999998886 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.7e-05     0.024      12      40 ..     259     287 ..     249     288 .. 0.75
   2 ?    5.2   0.3     0.047        19      21      42 ..     288     310 ..     285     312 .. 0.87
   3 ?    2.5   1.0       0.3   1.3e+02      33      50 ..     311     328 ..     310     330 .. 0.84
   4 ?   -1.1   0.1       4.1   1.7e+03      32      48 ..     362     379 ..     358     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-05
                                       HHHHTT-SE.E-TTT--EE-HHH.HHHHHHH CS
                     Rad50_zn_hook  12 ieelkeakg.cCPlCgReldeeh.rseLike 40 
                                       i e  +  +  CP C+R +++e+ ++++++ 
  gi|313125474|ref|YP_004035738.1| 259 IAEAVN--DfVCPTCDRRITTEKaKNRIQRG 287
                                       444443..359***************99875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.047
                                       E-TTT--EE-HHH.HHHHHHHHH CS
                     Rad50_zn_hook  21 cCPlCgReldeeh.rseLikelq 42 
                                        CP CgR+ + e  +++L+++++
  gi|313125474|ref|YP_004035738.1| 288 YCPYCGRNHSLEGlKQRLSQKIE 310
                                       6*******999999999999987 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHH. CS
                     Rad50_zn_hook  33 hrseLikelqsklerlpe 50 
                                       +  +L++el++++e+l++
  gi|313125474|ref|YP_004035738.1| 311 ESDDLLDELKEEIEELQD 328
                                       56799*********9987 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 4.1
                                       HH.HHHHHHHHHHHHHHH CS
                     Rad50_zn_hook  32 eh.rseLikelqsklerl 48 
                                       +h  ++++++ q++le++
  gi|313125474|ref|YP_004035738.1| 362 DHnIQQIQDHVQEELESI 379
                                       57799999******9997 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.13        53      31      43 ..     265     277 ..     260     284 .. 0.64
   2 ?    8.5   0.0    0.0058       2.4       5      22 ..     289     306 ..     285     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                           zf-Di19  31 evvCPvCaekvtk 43 
                                         vCP C  ++t 
  gi|313125474|ref|YP_004035738.1| 265 DFVCPTCDRRITT 277
                                       4566666665554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0058
                           zf-Di19   5 CPyCgkeltvkeLveHve 22 
                                       CPyCg++++ + L + ++
  gi|313125474|ref|YP_004035738.1| 289 CPYCGRNHSLEGLKQRLS 306
                                       ********9999876655 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  12.9     0.036        15     333     441 ..     172     287 ..     106     299 .. 0.71
   2 ?   12.2  12.4   0.00012     0.049     294     426 ..     278     413 ..     270     434 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.036
                              FapA 333 pelkeklkeleeeleeleeeleklkkk.....ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkel 404
                                         l e+ ++l++++ +le++ ek+++        +l kl+++ + ++e ++ l++l ++ke l+++l++l++++   
  gi|313125474|ref|YP_004035738.1| 172 RRLSEEKSDLDRQVSDLESQKEKYDRLesqieSGELAKLSQQLRRDEELENRLDELFKEKEGLRKRLRKLHRKKR-K 247
                                       344455566777777775555555555555663345555556777899999999999999999999999998877.5 PP

                              FapA 405 keeleskkeea.kikvnkeiypgvkikig..kkkliikre 441
                                       +e+ es  +++   +vn+ ++p ++ +i   k+k++i+r 
  gi|313125474|ref|YP_004035738.1| 248 QENYESEVNDIiAEAVNDFVCPTCDRRITteKAKNRIQRG 287
                                       5555555456657788999999998777744666666665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                              FapA 294 ngrkgkivggn.ikalkevkakklGselgtkteievgldepelkeklkeleeeleeleeeleklkkk......ikkl 363
                                       ++ k  i  g+   ++++++++ l  +l +k+e +  l   elke+++el+++  e+ +++ +lk++      ++ +
  gi|313125474|ref|YP_004035738.1| 278 EKAKNRIQRGYcPYCGRNHSLEGLKQRLSQKIEESDDLL-DELKEEIEELQDQRDEVSNQIGELKEEkpeleeLDGF 353
                                       555566666664455555555544446666776666555.699999999999999999999999999***8888888 PP

                              FapA 364 pklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeeakikvnkeiypg 426
                                        k +  +++++++++ ++ ++e++e+++++l el+ ++++l+e++e+   + k k+ +e+++ 
  gi|313125474|ref|YP_004035738.1| 354 TK-RRLDNYDHNIQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEI--NRKSKAYSEAHNH 413
                                       88.778999*************************************99..4466666666655 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5    0.0004      0.17      64     116 ..     243     294 ..     187     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                                       EEEESSSSSCCHHHHHHHHHHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  64 rlilngkfeakkleklldkyieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                       r   +++  ++++++++ + ++++V C++C++  t+ + ++r++   C  Cg+
  gi|313125474|ref|YP_004035738.1| 243 RKKRKQENYESEVNDIIAEAVNDFV-CPTCDRRITTEKAKNRIQRGYCPYCGR 294
                                       44555666778999**********8.*********9999************96 PP

>> DUF885  Bacterial protein of unknown function (DUF885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  10.5   0.00026      0.11      61     326 ..     142     409 ..      86     444 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHS..HHHHTT-CCCCHHHHHHHHHCGTTSSCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHTT.-S-H CS
                            DUF885  61 leleletaeag..ypleqlralagpvqqlpsllseepfateedleaylarlaavpaaldqaranlregaaaglvppr 135
                                        ++ele+++++     eql   +  v +  ++  ++  +++ dl++ ++ l++ ++ +d + +++++g  a+l +  
  gi|313125474|ref|YP_004035738.1| 142 TNRELEQRISRleDAEEQL---SELVVETKDTK-RRLSEEKSDLDRQVSDLESQKEKYDRLESQIESGELAKLSQQL 214
                                       3334444444422222333...33333333332.2345577888888888888888888888888888888888888 PP

                                       HHHHHHHHHHHHHHGTSSHHCCCHH.CCCCCC......HHHHHHHHHH.HHHHHHHHHHHHHHHHHCCHHHS-BSS. CS
                            DUF885 136 rqvekvieqlrgllagaaaeasalvaplaele...aekealraeleaalaeavkpayaeladfleeellpaarkda. 208
                                       r  e+  + l++l+++    ++ l++ l++l     ++e+++ e+++++aeav   +    d   +  + +    + 
  gi|313125474|ref|YP_004035738.1| 215 RRDEELENRLDELFKE----KEGLRKRLRKLHrkkRKQENYESEVNDIIAEAVNDFVCPTCDRRITTEKAK----Nr 283
                                       8888888888888874....223344444443322334555555555555555444433333332222222....13 PP

                                       .........HHHHHHHHHHHHHSSSS-.HHHHHHHHHHHHHHHHHHHHHHHHHHHH.-.HHHHHHHHHCH-GGGEEE CS
                            DUF885 209 ......pd.GeelYarllrsftttdlt.peeihelglaelariraemeaiakevgf.kgdlaevlaalrtdprfyle 276
                                             p  G+    + l++ + +++   +++ +  ++e+++++ + +++ +++g+ k + +  l++l+   +++l 
  gi|313125474|ref|YP_004035738.1| 284 iqrgycPYcGRNHSLEGLKQRLSQKIEeSDDLLDELKEEIEELQDQRDEVSNQIGElK-EEKPELEELDGFTKRRLD 359
                                       445678779****99*****99976654999***********************8856.567789999966667789 PP

                                       SHHHHHHHHHHHHHHHHHHHCCHHHCCT---TTS-GCCCEEEEEE-SS.- CS
                            DUF885 277 etdagreellaaaraaiaeldaklpehfgllpkaplevrrvpefiapsas 326
                                       + d + ++++++++++++ +   l+e +++ +  + +v+++    ++++ 
  gi|313125474|ref|YP_004035738.1| 360 NYDHNIQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSE 409
                                       999999**********************8888899999988887777654 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  13.2     0.051        21      75     197 ..     143     264 ..     129     268 .. 0.88
   2 ?   13.5  17.6   0.00011     0.045      54     187 ..     295     427 ..     293     457 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.051
                                       HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHH CS
                              SHE3  75 lselkesveelklekkqlkkrlenssaseteleeelerlkvqYdalvdsqkeYkehYqqeie..eLkesleklklen 149
                                       + el++++  l+  ++ql++ + ++++++ +l+ee + l+ q   l +sqke  ++ +++ie  eL +  ++l++++
  gi|313125474|ref|YP_004035738.1| 143 NRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDL-ESQKEKYDRLESQIEsgELAKLSQQLRRDE 218
                                       6799999999*******************************98776.888887788889888446999999999999 PP

                                       HSSSXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 150 ekqleelqerissndkdidtkldsynnkkknlesieeeknkkllkkle 197
                                       e  le+  +++ ++++ + ++l ++  kk++ e+ e e n  + + ++
  gi|313125474|ref|YP_004035738.1| 219 E--LENRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDIIAEAVN 264
                                       9..9******************************99999999988776 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  54 NdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqYdalvdsqkeYkeh 130
                                       N  L  l +R  +++ + ++ l elke++eel+ +++++++++ ++++++ elee     k   d      ++ ++h
  gi|313125474|ref|YP_004035738.1| 295 NHSLEGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNIQQIQDH 371
                                       788999999**************************************999999887777777777777888999*** PP

                                       HHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 131 YqqeieeLkesleklklenekqleelqerissndkdidtkldsynnkkknlesieee 187
                                        q+e+e+++ sl++lk +++  lee  e+i++++k+  +  ++ ++ +++l + + e
  gi|313125474|ref|YP_004035738.1| 372 VQEELESISSSLDELKSDRQ-SLEEKVEEINRKSKAYSEAHNHASEMVEELTEQSFE 427
                                       ******************99.99***********99999888888888887665443 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.0       0.4   1.7e+02      21      46 ..     179     204 ..     163     258 .. 0.72
   2 ?    7.8   7.3     0.011       4.5       4      59 ..     314     373 ..     303     405 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.4
                           NPV_P10  21 dalqqqvddvqenlpdvtelnekLda 46 
                                       + l+ qv d++++ ++ + l++++++
  gi|313125474|ref|YP_004035738.1| 179 SDLDRQVSDLESQKEKYDRLESQIES 204
                                       45677777777777776666665542 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
                           NPV_P10   4 niLlvIradikavddkVdalqqqvddvqenlpdvtel....nekLdaqsaqLaeletkve 59 
                                         L   +++i++++d+ d +++q+ +++e+ p+++el    + +Ld+   ++++++++v+
  gi|313125474|ref|YP_004035738.1| 314 DLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELdgftKRRLDNYDHNIQQIQDHVQ 373
                                       567778899999999999999999999999999887633333456666666666665443 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00043      0.18       1      54 [.       1      54 [.       1      61 [. 0.92
   2 ?    1.4   2.1      0.49   2.1e+02     126     199 ..     142     216 ..     126     223 .. 0.80
   3 ?    0.8   1.1      0.73     3e+02     161     194 ..     216     249 ..     204     263 .. 0.66
   4 ?    6.7   3.4     0.012       4.9     119     200 ..     347     428 ..     305     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                            AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGip 54
                                      M++++L++e + + + r +++++ ++d hl+ G   +GK+ +++Ai   l G +
  gi|313125474|ref|YP_004035738.1|  1 MKIDSLNIEEFASGEHRGMEIESVSSDSHLLRGGSRTGKTLTFNAILYNLLGAK 54
                                      9********************************************987777765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.49
                            AAA_27 126 dherLreGGealleaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskk.rainealeeleeakkelre 199
                                       ++++L++  ++l +ae++l++l++e +   ++l+e   +L+++ ++l +++++ +  + + +  el++++++lr+
  gi|313125474|ref|YP_004035738.1| 142 TNRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDrLESQIESGELAKLSQQLRR 216
                                       66778888889999999**************************99999888888733444455566666666665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.73
                            AAA_27 161 vleaLeaeadelfkprkskkrainealeeleeak 194
                                         e+Le++ delfk+++  ++++++ +++ ++++
  gi|313125474|ref|YP_004035738.1| 216 RDEELENRLDELFKEKEGLRKRLRKLHRKKRKQE 249
                                       4578999999999998877766655555444333 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.012
                            AAA_27 119 FealFgLdherLreGGealleaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakk 195
                                        e+l g +++rL +  +++ + ++ + + L + s++l +l++ +++Le++ +e+ +++k+ ++a n+a e +ee+++
  gi|313125474|ref|YP_004035738.1| 347 LEELDGFTKRRLDNYDHNIQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTE 423
                                       566668889999999999************************************99999999889999988888887 PP

                            AAA_27 196 elrea 200
                                       +  ea
  gi|313125474|ref|YP_004035738.1| 424 QSFEA 428
                                       76665 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.86   3.6e+02      59     103 ..     144     188 ..     139     228 .. 0.80
   2 ?    4.6   0.1     0.045        19      24      61 ..     296     333 ..     294     350 .. 0.87
   3 ?    2.3   0.0      0.23        97      35      84 ..     374     423 ..     369     459 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.86
                         Mce4_CUP1  59 reladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaa 103
                                       rel++     +da ++l + + ++  t+r + e++++Ld+ ++++
  gi|313125474|ref|YP_004035738.1| 144 RELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDL 188
                                       556666667789999999999999999999999999999876655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.045
                         Mce4_CUP1  24 eALeGrGerlGesltdlnevLdelNprlpqlredirel 61 
                                       ++LeG+ +rl +++++ +++Ldel +++++l++   e+
  gi|313125474|ref|YP_004035738.1| 296 HSLEGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEV 333
                                       589***************************99876655 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.23
                         Mce4_CUP1  35 esltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavt 84 
                                       e l+ + + Ldel +   +l+e ++e+++ +++Y++a ++  +++++++ 
  gi|313125474|ref|YP_004035738.1| 374 EELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTE 423
                                       567788899999***********************998877777776654 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.9       0.6   2.5e+02       7      62 ..     186     240 ..     180     263 .. 0.63
   2 ?   13.7   2.3    0.0001     0.042      52      93 ..     297     337 ..     290     349 .. 0.88
   3 ?    6.8   3.2     0.014       5.7      61     105 ..     365     409 ..     348     449 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.6
                              CK2S   7 rkveeqrekWkellseseslleslsnlaeqlqalqnvkl..ygtplrdfpdlqerLre 62 
                                       + +e+q+ek+++l+s+ es  + l+ l +ql+  ++ ++  ++  +++ ++l++rLr+
  gi|313125474|ref|YP_004035738.1| 186 SDLESQKEKYDRLESQIES--GELAKLSQQLRRDEELENrlDEL-FKEKEGLRKRLRK 240
                                       5677888888888888877..34444444444433333200332.6666666666664 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.0001
                              CK2S  52 dfpdlqerLrekqlealeevlakLrekleelqkvrdsleklv 93 
                                       ++++l++rL +k+ e+ + +l++L+e++eelq+ rd+++++ 
  gi|313125474|ref|YP_004035738.1| 297 SLEGLKQRLSQKIEES-DDLLDELKEEIEELQDQRDEVSNQI 337
                                       67899*******9765.99********************986 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.014
                              CK2S  61 rekqlealeevlakLrekleelqkvrdsleklvrdalqlyeekad 105
                                       +++++  ++e+l+++++ l+el++ r+sle++v++ ++  +  ++
  gi|313125474|ref|YP_004035738.1| 365 IQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSE 409
                                       5789999**************************888774443333 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  23.9    0.0066       2.7      38     152 ..     139     250 ..     124     259 .. 0.83
   2 ?    7.1  16.8    0.0095       3.9       8     113 ..     318     420 ..     297     450 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0066
                        Lebercilin  38 krlqkrq.ekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsed 113
                                       + +  r  e+++s++ed+e++L++l+ + ++  r l e+  ++  ++++le++ kek ++l+  + +  +l kLs  
  gi|313125474|ref|YP_004035738.1| 139 RSVTNRElEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQ-KEKYDRLE-SQIESGELAKLS-- 211
                                       55555543789*******************************99999999875.55555554.456678999999.. PP

                        Lebercilin 114 knLaereeLqkkLeeleakleekeekikeLerkleleek 152
                                       ++L+  eeL+++L+el ++ e  ++++++L+rk + +e+
  gi|313125474|ref|YP_004035738.1| 212 QQLRRDEELENRLDELFKEKEGLRKRLRKLHRKKRKQEN 250
                                       89******************************9887765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0095
                        Lebercilin   8 arllkikeLqnelaelqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqeker 84 
                                       + +++i+eLq++ +e+ +++ el++E   L++l    +++L++y+ +    +q+ +  +eE++ +   l +++   +
  gi|313125474|ref|YP_004035738.1| 318 ELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNI---QQIQDHVQEELESISSSLDELKSDRQ 391
                                       55789************************************8887665...55555556666666666666666666 PP

                        Lebercilin  85 elekklkekeaellrlkdklkklkkLsed 113
                                       +le+k+ e + + +  ++++++ ++++e+
  gi|313125474|ref|YP_004035738.1| 392 SLEEKVEEINRKSKAYSEAHNHASEMVEE 420
                                       66666666666666666666666666543 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.2     0.012       4.9       7      69 ..     141     203 ..     130     205 .. 0.90
   2 ?    3.1  20.9      0.14        60      18     154 ..     209     377 ..     204     385 .. 0.62
   3 ?    5.7  18.4     0.024        10       5     125 ..     312     451 ..     309     462 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                           DUF4795   7 ellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeela 69 
                                       ++  +l++ i+ l++  e+l+e v e+++++++++++   l  q+++le++k++ + +e +++
  gi|313125474|ref|YP_004035738.1| 141 VTNRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQIE 203
                                       55667899**********************************************999998875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                           DUF4795  18 klqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelae...kadkeaLatkvsrdq.fDeak 90 
                                       kl+++l     + +ele+rl ++ k+ e+l+k +++l+ +k ++e+ e e++     a  + ++ +++r    ++ak
  gi|313125474|ref|YP_004035738.1| 209 KLSQQL----RRDEELENRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDiiaEAVNDFVCPTCDRRItTEKAK 281
                                       556666....67899**************************9999999998532225666789*****999977777 PP

                           DUF4795  91 keLekml..........eellekleeqeealkkaldtLqeelkekld...............rlelepLkeqle... 139
                                       ++++++           e l ++l+++ e+ + +ld+L+ee++e  d               + el       e   
  gi|313125474|ref|YP_004035738.1| 282 NRIQRGYcpycgrnhslEGLKQRLSQKIEESDDLLDELKEEIEELQDqrdevsnqigelkeeKPEL-------Eeld 351
                                       777777755544444444444444455555555555555444444444334433311111133333.......2333 PP

                           DUF4795 140 ...........erlkelqkelqeame 154
                                                   +++++q+ +qe +e
  gi|313125474|ref|YP_004035738.1| 352 gftkrrldnydHNIQQIQDHVQEELE 377
                                       33335555666666666666666555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.024
                           DUF4795   5 saellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvk........adkeeveeel.aeka 72 
                                       s  ll++l+e+ie+lq++ ++++++  el++++ ++e+ +   k  +++ + +         ++ e ++  l ++k+
  gi|313125474|ref|YP_004035738.1| 312 SDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNIqqiqdhvqEELESISSSLdELKS 388
                                       67899999999999999999999999999998888877666666556555554433323223555555555645799 PP

                           DUF4795  73 dkeaLatkvsrdq.....fDeakkeLekmleellekle.........eqeealkkaldtLqeelkek 125
                                       d++ L+ kv++ +       ea +  ++m+eel    +         e +ea+++a+++++++l+  
  gi|313125474|ref|YP_004035738.1| 389 DRQSLEEKVEEINrkskaYSEAHNHASEMVEEL----TeqsfeagiqEFSEAWEEAYNQMNSNLQLG 451
                                       999999999888876666444444444445555....334445555599999999999999888765 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   9.5     0.029        12      29      86 ..     144     204 ..     126     217 .. 0.78
   2 ?    4.6  12.1     0.077        32      25     125 ..     220     333 ..     205     344 .. 0.56
   3 ?    6.1   5.3     0.026        11      29      80 ..     299     350 ..     295     364 .. 0.60
   4 ?    4.1  18.1      0.11        46       5      98 ..     320     414 ..     320     456 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.029
                             Mod_r  29 kqlkeekeellaeneslaeknlslep...eleelrselqekleelkelekefeekeqelde 86 
                                       ++l+++ + l++++e+l e   + ++   +l e++s+l  + + l++ +++++++e++ ++
  gi|313125474|ref|YP_004035738.1| 144 RELEQRISRLEDAEEQLSELVVETKDtkrRLSEEKSDLDRQVSDLESQKEKYDRLESQIES 204
                                       57888888888888888887777766677***************************99853 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.077
                             Mod_r  25 l.pevkqlkeekeellaeneslaeknlslepeleelrselqeklee.....lkelekefeekeqeldell....... 88 
                                       l +++++l++eke l++  ++l +k+ ++e+   e+ + ++e+ +      +++  ++ ++k++             
  gi|313125474|ref|YP_004035738.1| 220 LeNRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDIIAEAVNDfvcptCDRRITTEKAKNRI----Qrgycpyc 292
                                       32334666667777766666666655555554444444445555544433222222222223333....24445889 PP

                             Mod_r  89 .qkfspdallarLqtavaeaeeeSealaeefle...geiel 125
                                        ++ s++ l++rL ++++e++++ ++l ee+ e   +  e+
  gi|313125474|ref|YP_004035738.1| 293 gRNHSLEGLKQRLSQKIEESDDLLDELKEEIEElqdQRDEV 333
                                       99999999999999999999999999999887654333444 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.026
                             Mod_r  29 kqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeek 80 
                                       + lk+++++ ++e  +l+++  ++ +el+++r+e+++++ elke + e+ee+
  gi|313125474|ref|YP_004035738.1| 299 EGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEEL 350
                                       4455566666666666666555556666666666666666666666666555 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.11
                             Mod_r   5 keeLqelledeeklealvktlpevkqlkeekeellaeneslaeknlsl.epeleelrselqekleelkelekefeek 80 
                                       kee++el ++ + +++ + +l+e k   ee++   +   +  ++n+++ +++++e+ ++++++l+elk+ ++++eek
  gi|313125474|ref|YP_004035738.1| 320 KEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNIQQiQDHVQEELESISSSLDELKSDRQSLEEK 396
                                       58999999999999999999977788888888888999999999999999999999999999999999999999999 PP

                             Mod_r  81 eqeldellqkfspdalla 98 
                                        +e +++++ +s++++ a
  gi|313125474|ref|YP_004035738.1| 397 VEEINRKSKAYSEAHNHA 414
                                       999999999998887654 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.012         5       4      15 ..     265     276 ..     262     278 .. 0.86
   2 ?    1.7   0.4      0.46   1.9e+02       7      12 ..     289     294 ..     287     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                                       EEE-TTTSSEEE CS
                             Sgf11   4 yvtCpnCgRqia 15 
                                       +++Cp C+R i 
  gi|313125474|ref|YP_004035738.1| 265 DFVCPTCDRRIT 276
                                       79*******996 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.46
                                       -TTTSS CS
                             Sgf11   7 CpnCgR 12 
                                       Cp+CgR
  gi|313125474|ref|YP_004035738.1| 289 CPYCGR 294
                                       ****** PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   8.3       1.9   7.8e+02      40      96 ..     146     202 ..     123     204 .. 0.63
   2 ?   14.2  16.9   0.00011     0.044       8     128 ..     203     348 ..     199     355 .. 0.78
   3 ?    4.4  17.4      0.11        47      18     144 ..     325     448 ..     319     464 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.9
                              Fez1  40 lrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeel 96 
                                       l +  ++le+ ee+++el  ++++ ++ l + +++l+r+ s+ e  +ek ++le+++
  gi|313125474|ref|YP_004035738.1| 146 LEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQI 202
                                       333334556666666666666666666666667777777777777777777777665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00011
                              Fez1   8 ksGEislLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektle...............le 69 
                                        sGE++ L qQL+    e+ ++l+e+++ k  lr    kl++k ++ +++e+++++  +e                e
  gi|313125474|ref|YP_004035738.1| 203 ESGELAKLSQQLRR-DEELENRLDELFKEKEGLRKRLRKLHRKKRKQENYESEVNDIIAEavndfvcptcdrritTE 278
                                       59**********95.78**************************************9999999999988888888877 PP

                              Fez1  70 vcenelqrk...........kseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqeae 128
                                       + +n++qr            +  ++ l++k+e+ ++ l el+ee++el+ +++e +++  e k+++ e e
  gi|313125474|ref|YP_004035738.1| 279 KAKNRIQRGycpycgrnhslEGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELE 348
                                       7777777777777777776655666666677777777777777777766666666666666666665544 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.11
                              Fez1  18 QLkdsqaevtqklseivalkaqlrel....rakleekeeeikeleesleektlelevcenelqrkkseaellrekve 90 
                                        L+d + ev+++++e+ + k +l el    + +l++ +++i+++++++   ++ele + + l++ ks+ + l+ekve
  gi|313125474|ref|YP_004035738.1| 325 ELQDQRDEVSNQIGELKEEKPELEELdgftKRRLDNYDHNIQQIQDHV---QEELESISSSLDELKSDRQSLEEKVE 398
                                       477888888888888888888888862222345555566666666555...55777777777777888888888888 PP

                              Fez1  91 kleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeL 144
                                       +++++ k   e+ +++s+  ee +++s ea  q+ +    e+ ++  ++++++L
  gi|313125474|ref|YP_004035738.1| 399 EINRKSKAYSEAHNHASEMVEELTEQSFEAGIQEFS----EAWEEAYNQMNSNL 448
                                       888888888777777666666666666555555444....33333344444444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.7      0.15        64      30      78 ..     148     196 ..     135     204 .. 0.70
   2 ?    6.6   0.2     0.023       9.4      34      76 ..     297     339 ..     294     352 .. 0.64
   3 ?    6.6   0.6     0.022       9.1      27      81 ..     357     411 ..     346     429 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                            DUF948  30 eaaatieelekqvdpilkevedllakvnelledvneklekvdplteava 78 
                                       +  +++e+ e+q+ +++ e++d+ +   e  +d+ +++ ++++  e+  
  gi|313125474|ref|YP_004035738.1| 148 QRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYD 196
                                       3334556666999999999999999999988888888888776655555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.023
                            DUF948  34 tieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                       ++e+l++++ + ++e++dll++ +e  e+++++ ++v + + +
  gi|313125474|ref|YP_004035738.1| 297 SLEGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGE 339
                                       5666666777777777777777777666666666666555444 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.022
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81 
                                        ld+  + i++++++v++ l+ +   l++ +   + ++ek+e++++  +a  ++ 
  gi|313125474|ref|YP_004035738.1| 357 RLDNYDHNIQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAH 411
                                       5666666666666666666666666666666655666666666655444444333 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.6   0.00019     0.081       5      68 ..     309     374 ..     308     388 .. 0.73
   2 ?    8.1   2.1      0.01       4.2       9      60 ..     373     435 ..     370     470 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00019
                           DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelvee 68 
                                       +ee  +lL +lke +eel+++r+e+ +   el+e+k e e+ +   +++  ++++  ++i+++v+e
  gi|313125474|ref|YP_004035738.1| 309 IEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDgfTKRRLDNYDHNIQQIQDHVQE 374
                                       68999*********************************9988888444444444444444433332 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.01
                           DUF2203   9 nalLpllkelleelralrkeleeleeeleeakaeaekse...........aaeleaeleelea 60 
                                       ++ L  +++ l+el++ r+ lee++ee++++++++++ +           +++ ea ++e ++
  gi|313125474|ref|YP_004035738.1| 373 QEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHnhasemveeltEQSFEAGIQEFSE 435
                                       566778888888888888888888888888887766554454545544442222333333322 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   4.8      0.26   1.1e+02      11      66 ..     145     204 ..     140     217 .. 0.70
   2 ?    1.1   2.1      0.77   3.2e+02       4      59 ..     187     243 ..     185     262 .. 0.51
   3 ?   10.5   3.0     0.001      0.43      13      73 ..     303     363 ..     296     371 .. 0.89
   4 ?    8.0   5.2    0.0058       2.4      12      66 ..     369     423 ..     357     434 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.26
                             Sec34  11 ecdelleqtdealeqLeel....eekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                       e+++ ++++++a+eqL+el    ++  ++ se+ s+l+++  +l ++++++++l  +ie+
  gi|313125474|ref|YP_004035738.1| 145 ELEQRISRLEDAEEQLSELvvetKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQIES 204
                                       555555566666666665511114555667888889999999999999999999888875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.77
                             Sec34   4 qLeskeeecdelleqtdea.leqLeeleekfksvsektsslheaceqlleeqkrlee 59 
                                        Les++e++d+l +q+++  l +L++   + ++ +++  +l ++ e l +  ++l++
  gi|313125474|ref|YP_004035738.1| 187 DLESQKEKYDRLESQIESGeLAKLSQQLRRDEELENRLDELFKEKEGLRKRLRKLHR 243
                                       678888888888888876313333333333333444444443344433333333333 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.001
                             Sec34  13 delleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFee 73 
                                       ++l ++++e  ++L+el+e+ ++ +++  +++++  +l ee+ +leel    + +L+ +++
  gi|313125474|ref|YP_004035738.1| 303 QRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDH 363
                                       57899999************************************99999888888888875 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0058
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                        d++ e+++++ ++L+el+++ +s +ek ++++++++   e +++ +e++ee++e
  gi|313125474|ref|YP_004035738.1| 369 QDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTE 423
                                       3456667777777777777777777777777777777777777777777777665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  14.6     0.062        26      48     115 ..     142     210 ..     123     216 .. 0.80
   2 ?    5.9  13.2     0.042        17      14      80 ..     181     248 ..     181     264 .. 0.72
   3 ?   12.6  23.1   0.00037      0.15      12     119 ..     218     372 ..     217     374 .. 0.90
   4 ?    5.4  11.3      0.06        25      22      98 ..     355     425 ..     352     447 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.062
                            APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne.lqlellel 115
                                         +ele+++++le++ee+l e   e+++++++l +e ++l ++ ++le ++e++ r  ++  + el++l
  gi|313125474|ref|YP_004035738.1| 142 TNRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQiESGELAKL 210
                                       45789999*****************************************99999777776455555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.042
                            APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeek.qdeeleeleeeleklekeeeelleeLkelekereel 80 
                                       ld+q++++e+++++Y + ++++++ +  + + q   +eele++l++l ke+e l + L++l +++++ 
  gi|313125474|ref|YP_004035738.1| 181 LDRQVSDLESQKEKYDRLESQIESGELAKLSqQLRRDEELENRLDELFKEKEGLRKRLRKLHRKKRKQ 248
                                       68999*****************9884443225566667788888888888888888777777766543 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00037
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeek............................................ 44 
                                       eel+++l+++ ke++ +++ l+kl+++k+++e+                                            
  gi|313125474|ref|YP_004035738.1| 218 EELENRLDELFKEKEGLRKRLRKLHRKKRKQENyesevndiiaeavndfvcptcdrrittekaknriqrgycpycgr 294
                                       6899***********************99998899999999999999999999999999999999999999999997 PP

                            APG6_N  45 ...qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleee 118
                                           +   ++l +++e+ ++  +el ee++el+++r+e+ +++ +l+ee+ +lee      r+  +++++ ++ ++ 
  gi|313125474|ref|YP_004035738.1| 295 nhsLEGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNIQQIQDH 371
                                       77655555667777888999999999******************************999999999999999999987 PP

                            APG6_N 119 l 119
                                        
  gi|313125474|ref|YP_004035738.1| 372 V 372
                                       5 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.06
                            APG6_N  22 ekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98 
                                       ++  d+Y    ++++++ ++     eele++  +l++l++++++l+e+ +e+ ++ ++  ++ + ++e  e+l e+ 
  gi|313125474|ref|YP_004035738.1| 355 KRRLDNYDHNIQQIQDH-VQ-----EELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTEQS 425
                                       67778888888888888.33.....4799999999999999999999999999999999999999999999998764 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  13.9    0.0042       1.7     668     802 ..     117     255 ..      56     285 .. 0.74
   2 ?    5.4  18.4      0.01       4.3     719     829 ..     303     417 ..     293     426 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0042
                               FPP 668 sekeipselplvsgsneskkee.nkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslk 743
                                        +++i  ++pl++ s +++++  + +++ ele+  s+ e+ e +l++   + + +k +l+e    l+   s+Les k
  gi|313125474|ref|YP_004035738.1| 117 VHSHI-GKMPLDELSRGQRTKLiRSVTNRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQK 192
                                       34443.56777777777776541567889999999999999999999999999999999999999999999999999 PP

                               FPP 744 eskslaetqlkcmkesyeslet.rateleaelnelkqkieaLeveLee...ekksheeleakc 802
                                       e    +e+q+++ ++ + s +  r +ele+ l el ++ e L + L +   +k+  e+ e+++
  gi|313125474|ref|YP_004035738.1| 193 EKYDRLESQIESGELAKLSQQLrRDEELENRLDELFKEKEGLRKRLRKlhrKKRKQENYESEV 255
                                       999999999999888877666514578999999999999999987655111444444444444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.01
                               FPP 719 eslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLev....eLeee 791
                                       + l  +++es  ll+elk+e+e+l++ +  + +q+ + ke + +le      +  l +  ++i++++     eLe+ 
  gi|313125474|ref|YP_004035738.1| 303 QRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNIQQIQDhvqeELESI 379
                                       56778899***************************************999999999999999998765111155666 PP

                               FPP 792 kksheeleakckelqeqlervekkevskssaeeedkkl 829
                                       ++s  el++  + l+e++e +++k+   s+a+++ +++
  gi|313125474|ref|YP_004035738.1| 380 SSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEM 417
                                       77889999999*********998887766666655554 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.1     0.026        11      20      74 ..     144     201 ..     139     205 .. 0.59
   2 ?   12.4   4.0   0.00035      0.15      75     117 ..     301     343 ..     291     349 .. 0.82
   3 ?    4.7   5.4     0.081        34       9      58 ..     380     429 ..     374     453 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.026
                           DUF5082  20 aaleekIerLkeaktklsdekeslkqkkkklekplnsse...sWkGkeennydgirsn 74 
                                       + le+ I+rL+ a ++ls+   ++k++k+ l++   + +   s   +++++yd  +s+
  gi|313125474|ref|YP_004035738.1| 144 RELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDrqvSDLESQKEKYDRLESQ 201
                                       4567777777777777777777777777766655444443344444555555555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00035
                           DUF5082  75 lessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsq 117
                                       l++  ++ +++ d+l d+++eEIe+L+ q+ e ++ ++ l+++
  gi|313125474|ref|YP_004035738.1| 301 LKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEE 343
                                       6777778889999999999999999999999999999988865 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.081
                           DUF5082   9 qaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse 58 
                                        +  +el+s++++leek+e+  + +++ s++ +++++  ++l+++ ++  
  gi|313125474|ref|YP_004035738.1| 380 SSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTEQSFEAG 429
                                       56778999999999999999999999999999999998888888877765 PP

>> AAA_23  AAA domain
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  15.7     0.047        19      55     144 ..     145     241 ..     114     264 .. 0.64
   2 ?    7.8  20.7    0.0049         2      30     155 ..     301     425 ..     294     453 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.047
                         Golgin_A5  55 erdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeevea.elerlkeelrylee.. 128
                                       e ++  + l+++++q+++l  e +d++++ ++e + l  q+++le+q e+  + + ++e+ el++l+++lr+ ee  
  gi|313125474|ref|YP_004035738.1| 145 ELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQIESgELAKLSQQLRRDEEle 221
                                       33333467888888899999999999999999999999999999988877766666666447887777777644311 PP

                         Golgin_A5 129 ....elvrskatlqsrikdr 144
                                           el ++k+ l++r+++ 
  gi|313125474|ref|YP_004035738.1| 222 nrldELFKEKEGLRKRLRKL 241
                                       11114444444444444332 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0049
                         Golgin_A5  30 Lkegsgeeglesstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeer 106
                                       Lk+   ++++e s  l +el e  +e + +r+e+ ++ +++++ + el++l+  ++   +++  ++q+++++++ee 
  gi|313125474|ref|YP_004035738.1| 301 LKQR-LSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNIQQIQDHVQEEL 376
                                       4432.344445555555666666666666667777777777777888888888888899999999999999999999 PP

                         Golgin_A5 107 kakeeveaelerlkeelryleeelvrskatlqsrikdrekeieklrnql 155
                                       ++  +  +el++ ++ l+   ee  r+ + + + +++  +++e+l++q 
  gi|313125474|ref|YP_004035738.1| 377 ESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTEQS 425
                                       9999999999999999999999999888888888888888899888885 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3      0.59   2.4e+02     100     148 ..     144     189 ..     130     210 .. 0.48
   2 ?    3.9   0.1       0.1        43     110     149 ..     303     342 ..     258     349 .. 0.80
   3 ?    7.3   2.8     0.009       3.7      93     167 ..     363     439 ..     345     445 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.59
                                       ..........HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 100 keindsvesleetrqrveegselveetgealkeiveavaevadlvqeia 148
                                       +e ++ ++ le+++++    selv et+++ ++++e+ ++++ +v+++ 
  gi|313125474|ref|YP_004035738.1| 144 RELEQRISRLEDAEEQL---SELVVETKDTKRRLSEEKSDLDRQVSDLE 189
                                       23333333333333333...33334444444444444444444444444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 110 eetrqrveegselveetgealkeiveavaevadlvqeiaa 149
                                       +   q++ee+ +l +e +e+++e+ ++ +ev++++ e++ 
  gi|313125474|ref|YP_004035738.1| 303 QRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKE 342
                                       3456788888888888888888888888888888888765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.009
                                       HHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHH CS
                         MCPsignal  93 aliieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs..asieevnqavee 167
                                       + i++iq ++++ +es++++  + ++  +  ee  e++++ ++a +e  +  +e+    +eqs  a+i+e ++a ee
  gi|313125474|ref|YP_004035738.1| 363 HNIQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTEQSfeAGIQEFSEAWEE 439
                                       55777777777777777777777777777777777777777777777777777777766666644678887777665 PP

>> GIT1_C  G protein-coupled receptor kinase-interacting protein 1 C term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.2    0.0024         1      29     104 ..     190     262 ..     162     264 .. 0.86
   2 ?    2.6   3.2      0.35   1.4e+02      56      99 ..     374     420 ..     321     428 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0024
                            GIT1_C  29 ekkesfvpcaerIqsaVqdlvalfpenlseetlrtaLkqLtssaerLqeeCeelqeaeseskedikketqqviqcA 104
                                       ++ke++ ++ ++I+s   +l++l  +  ++e+l++ L++L ++ e L+++ ++l++ ++ ++e+ ++e++++i  A
  gi|313125474|ref|YP_004035738.1| 190 SQKEKYDRLESQIES--GELAKLSQQLRRDEELENRLDELFKEKEGLRKRLRKLHR-KKRKQENYESEVNDIIAEA 262
                                       555666666666665..3899999999*****************************.7889999********9887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.35
                            GIT1_C  56 lseetlrtaLkqLtssaerLqeeCeelqe...aeseskedikketqq 99 
                                        + e+++++L++L+s  + L+e+ ee ++   a se+++++ +++++
  gi|313125474|ref|YP_004035738.1| 374 EELESISSSLDELKSDRQSLEEKVEEINRkskAYSEAHNHASEMVEE 420
                                       44567777888888888888888888888433333333344444444 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3       7.2     3e+03      64     102 ..     162     195 ..     134     209 .. 0.52
   2 ?    5.3   3.0     0.047        20      28      50 ..     256     278 ..     247     396 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.2
                              CpXC  64 illvpeserseeeeieeaeek...egytl.RlvidmaelaEki 102
                                        l+v ++++++             e+  l R v+d ++ +Ek 
  gi|313125474|ref|YP_004035738.1| 162 ELVVETKDTKR---------RlseEKSDLdRQVSDLESQKEKY 195
                                       22222222211.........01112222236666666666665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.047
                              CpXC  28 eklldgslfeatCpkCgatakle 50 
                                       ++++++ +++++Cp C+++++ e
  gi|313125474|ref|YP_004035738.1| 256 NDIIAEAVNDFVCPTCDRRITTE 278
                                       67888888888888888887765 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  19.7    0.0066       2.7     149     261 ..     139     251 ..     126     283 .. 0.80
   2 ?    4.5  22.7     0.037        15     153     264 ..     302     414 ..     294     425 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0066
                           DUF4686 149 rilekkqLeekikeaseneaklkqqlqeeqqkrklLdqnveeLqqqvrslrdkeaqlertnsqqql.riqqqeaqlk 224
                                       r+ ++ +Le++i  +++ e++l + + e + +++ L +++ +L +qv  l+++ ++ +r  sq ++  + +  +ql+
  gi|313125474|ref|YP_004035738.1| 139 RSVTNRELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKEKYDRLESQIESgELAKLSQQLR 215
                                       4567889*******************************************999999999888876425666666666 PP

                           DUF4686 225 klenekrksdehlksnqeLsekLsslqqekealqeel 261
                                       + e+ ++  de  k ++ L+++L +l++ k ++ e++
  gi|313125474|ref|YP_004035738.1| 216 RDEELENRLDELFKEKEGLRKRLRKLHRKKRKQ-ENY 251
                                       644444457888899999999999998866554.444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.037
                           DUF4686 153 kkqLeekikeaseneaklkqqlqeeqqkrklLdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlkk.len 228
                                       k++L +ki+e  + +++lk++++e q +r    +++ eL++    l++ +   +r   +  + iqq +  +++ le+
  gi|313125474|ref|YP_004035738.1| 302 KQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEEKPELEELDGFTKRRLDNYDHNIQQIQDHVQEeLES 378
                                       899***************************************************************99988873777 PP

                           DUF4686 229 ekrksdehlksnqeLsekLsslqqekealqeelqqv 264
                                         +  de +  +q L+ek+ ++ + ++a  e ++++
  gi|313125474|ref|YP_004035738.1| 379 ISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHA 414
                                       77779999999*************999998887765 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.081        34       3      30 ..     314     341 ..     312     361 .. 0.90
   2 ?    4.9   0.1     0.045        19       3      44 ..     381     423 ..     379     450 .. 0.82
   3 ?   -2.2   0.0       6.6   2.7e+03     138     171 ..     534     566 ..     525     567 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.081
                           DUF4988   3 ddvndlkdrvaaleeqvkelndniealk 30 
                                       d +++lk++++ l+ q +e+ ++i  lk
  gi|313125474|ref|YP_004035738.1| 314 DLLDELKEEIEELQDQRDEVSNQIGELK 341
                                       5689******************999887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.045
                           DUF4988   3 ddvndlkdrvaaleeqvkelndniealkkll.eegkvitevee 44 
                                       + +++lk+  ++lee+v+e+n + +a ++   + ++++ e++e
  gi|313125474|ref|YP_004035738.1| 381 SSLDELKSDRQSLEEKVEEINRKSKAYSEAHnHASEMVEELTE 423
                                       6799******************999988776445555555555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.6
                           DUF4988 138 kGepvkAvgdkssedsffksvevdeeenlvvtlk 171
                                       + + +  +++ s  ds f++ve+ e e l+ +l 
  gi|313125474|ref|YP_004035738.1| 534 DKQMIVTTSNTS-IDSRFDQVEILEREPLQTKLG 566
                                       455555555555.899999999988777777765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   6.7      0.13        53      38     104 ..     144     210 ..     133     230 .. 0.83
   2 ?    0.7   9.1       1.3   5.3e+02      75     124 ..     294     343 ..     204     349 .. 0.70
   3 ?    6.6   6.7     0.019         8      45     118 ..     303     379 ..     293     389 .. 0.60
   4 ?    6.4   7.2     0.023       9.6      26      85 ..     365     424 ..     355     457 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.13
                                       CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHH CS
                         Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.sni 104
                                       ++le++++++++ +++ +elv+e+kd+ r+  ++k+d d+ +++++++ e ++ rl+ +i + e  ++
  gi|313125474|ref|YP_004035738.1| 144 RELEQRISRLEDAEEQLSELVVETKDTKRRLSEEKSDLDRQVSDLESQKE-KYDRLESQIESGElAKL 210
                                       5899***********************99999999999*********999.99999999988765444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  75 ndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqd 124
                                        ++ ++ ++++l ++i++ ++ +d+  ++i++Lq+  ++ +++i +L+++
  gi|313125474|ref|YP_004035738.1| 294 RNHSLEGLKQRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEE 343
                                       46777888999999999999999999999999999999999999999976 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.019
                                       CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  45 eeisnstkeaeelvkeikdslrekqkskkdndnvikkssk...eleeeilrlketidaqesnirvLqnvlesneqki 118
                                       +++s++ +e+++l  e+k+ ++e q + ++ +n i ++++   elee     k+++d+  +ni+++q+ +++  ++i
  gi|313125474|ref|YP_004035738.1| 303 QRLSQKIEESDDLLDELKEEIEELQDQRDEVSNQIGELKEekpELEELDGFTKRRLDNYDHNIQQIQDHVQEELESI 379
                                       44556666666666666666666666666666665555542225776666667777777777777777777665555 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.023
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksske 85 
                                       +++ + +v+++le++ ++l+e+++  ++ ee v+ei+ + ++  + +++ ++++++++++
  gi|313125474|ref|YP_004035738.1| 365 IQQIQDHVQEELESISSSLDELKSDRQSLEEKVEEINRKSKAYSEAHNHASEMVEELTEQ 424
                                       667777888888888888888888888888888888887777777777666666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2743  (0.152992); expected 358.6 (0.02)
Passed bias filter:                      944  (0.0526521); expected 358.6 (0.02)
Passed Vit filter:                       269  (0.0150036); expected 17.9 (0.001)
Passed Fwd filter:                       171  (0.00953762); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              43  [number of targets reported over threshold]
# CPU time: 2.13u 0.46s 00:00:02.59 Elapsed: 00:00:00.70
# Mc/sec: 2454.84
//
Query:       gi|313125475|ref|YP_004035739.1|  [L=171]
Description: hypothetical protein Hbor_07020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1099.59
//
Query:       gi|313125476|ref|YP_004035740.1|  [L=1399]
Description: hypothetical protein Hbor_07030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-06   24.4   1.6    1.2e-05   23.7   1.6    1.2  1  EzrA          Septation ring formation regulator, EzrA
  ------ inclusion threshold ------
      0.012   16.0   0.8       0.17   12.3   0.0    2.8  2  AAA_16        AAA ATPase domain
      0.013   15.5   0.0      0.083   12.8   0.0    2.4  3  NACHT         NACHT domain
       0.02   14.1   0.0      0.061   12.5   0.0    1.8  1  NB-ARC        NB-ARC domain
      0.026   12.5   0.7       0.04   11.9   0.7    1.1  1  Prominin      Prominin
      0.043   13.6   0.0        0.1   12.3   0.0    1.6  1  IstB_IS21     IstB-like ATP binding protein
      0.057   13.1   1.9       0.11   12.2   1.9    1.4  1  TEX13         Testis-expressed sequence 13 protein family
      0.097   12.9   0.0        0.3   11.4   0.0    1.8  1  AAA_22        AAA domain
       0.17   11.7   0.2       0.52   10.1   0.0    1.8  2  Bac_DnaA      Bacterial dnaA  protein
       0.62   10.7   4.9         11    6.7   2.4    2.6  2  Ead_Ea22      Ead/Ea22-like protein
       0.94   10.0   5.4        3.1    8.3   4.9    2.3  1  Spectrin      Spectrin repeat
          1    9.8   5.6       0.76   10.2   2.7    2.2  2  CC2-LZ        Leucine zipper of domain CC2 of NEMO, NF-kappa-


Domain annotation for each model (and alignments):
>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   1.6   8.2e-09   1.2e-05      65     195 ..     218     346 ..     203     354 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8.2e-09
                                       HHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHH CS
                              EzrA  65 wkkkwdeiktkklpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeiekl 141
                                       +k + d ++++     +++ +e+ +++d+ +f++++ +++++   l+++e+   +i   ++el++  e+ +++i +l
  gi|313125476|ref|YP_004035740.1| 218 VKDRLDALSEEASSLFTQRSIEVLKQADEESFHELHDAIEQIPVLLQDIEQVDTDI--PIQELVDTLEQAEQAISSL 292
                                       677778888888888899999*****************************988877..6****************** PP

                                       HHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH----------------HHHHHH CS
                              EzrA 142 kekYrelrkkllanrfsygealeelekqleniekefsefeeltengdyveakei 195
                                       + + r+l+++ +++++s g+++++  +++ ++++e  +f+   +++d + a++ 
  gi|313125476|ref|YP_004035740.1| 293 EPELRTLKEQAEEEQDSVGTTEKHTLNRFRQVQSEVYSFQRYVQSKDLQVAQDP 346
                                       **********************************************99988875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.9      0.64   9.5e+02     117     124 ..     250     257 ..     144     330 .. 0.46
   2 ?   12.3   0.0   0.00011      0.17      25      80 ..     346     398 ..     326     448 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.64
                            AAA_16 117 srllellk 124
                                       + l++++ 
  gi|313125476|ref|YP_004035740.1| 250 HELHDAIE 257
                                       22222222 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00011
                            AAA_16  25 elvllsGesGvGKsslv.rellralekdggif.lrgkcdqlesaipysalaqalaree 80 
                                       +++ l Ge+G+GK+ l+ + +++++e+ +  + l g++  +     + +++q+++r +
  gi|313125476|ref|YP_004035740.1| 346 PALKLLGEAGMGKTHLLcNVAKDRIEEGYPTVlLLGENFYN-----RNIWTQIIERFG 398
                                       677799***********666666888887444588888888.....234777776544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.3   6.4e+03      23      58 ..     152     184 ..     147     188 .. 0.70
   2 ?   12.8   0.0   5.5e-05     0.083       5      24 ..     350     369 ..     347     380 .. 0.82
   3 ?   -3.4   0.0       5.4   8.1e+03      82     132 ..     420     465 ..     417     495 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.3
                                       HHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHH CS
                             NACHT  23 awaegklpqgafklvFflslrelsrsgnarsladll 58 
                                       ++ ++k ++   +l F+++  +l+ s+    l +++
  gi|313125476|ref|YP_004035740.1| 152 LLSKEKHKG---RLYFWFNTNQLTGSKLRSELEETI 184
                                       555555444...899999999999888776666666 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.5e-05
                                       EEC-TTTCHHHHHHHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlqklalaw 24 
                                       l GeaG+GKT+Ll+ +a + 
  gi|313125476|ref|YP_004035740.1| 350 LLGEAGMGKTHLLCNVAKDR 369
                                       78*************99865 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 5.4
                                       CEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCH CS
                             NACHT  82 rlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpral 132
                                       r L+ +D+l+e ++       +++  +L++l +    p   + +++r++  
  gi|313125476|ref|YP_004035740.1| 420 RSLIMIDALNESSDPRMW--SRQLPGVLRKLEN---YPHIGICVSCRTGYE 465
                                       568899999998864333..4444444444433...366666666666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-05     0.061      22      79 ..     347     400 ..     332     437 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLsls 79 
                                        + l G +G+GKt l+ ++ ++   +e+ ++ v    +++++  ++i+ +i+++++l+
  gi|313125476|ref|YP_004035740.1| 347 ALKLLGEAGMGKTHLLCNVAKD--RIEEGYPTVL--LLGENFYNRNIWTQIIERFGLT 400
                                       3889****************99..9******985..689**************99876 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   2.7e-05      0.04     186     310 ..     212     342 ..     201     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                          Prominin 186 rtflkdvpqhidhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerllenl..keakeqLeqvnk 260
                                         f+ dv + +d++ ++  + + ++ ++ L++a+++ +++l+d++e+     L+++e++ +++  +e  + Leq ++
  gi|313125476|ref|YP_004035740.1| 212 PAFVGDVKDRLDALSEEASSLFTQRSIEVLKQADEESFHELHDAIEQI-PVLLQDIEQVDTDIpiQELVDTLEQAEQ 287
                                       579******************************************987.7789******9986336999******** PP

                          Prominin 261 lekeLrksgsqLrdglrgvkrdlnqalsnlCq.....seeCskilssleiekldt 310
                                         ++L  + ++L++  ++ ++++ ++ +++ +     ++e +++++ ++ + l++
  gi|313125476|ref|YP_004035740.1| 288 AISSLEPELRTLKEQAEEEQDSVGTTEKHTLNrfrqvQSEVYSFQRYVQSKDLQV 342
                                       ************9999999999988777744435554567777777776666655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.9e-05       0.1      45      77 ..     343     375 ..     317     385 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavragls 77 
                                       ++  ++ llG +G+GK+hl + ++++ +++g+ 
  gi|313125476|ref|YP_004035740.1| 343 AQDPALKLLGEAGMGKTHLLCNVAKDRIEEGYP 375
                                       55667889*********************9985 PP

>> TEX13  Testis-expressed sequence 13 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.9   7.4e-05      0.11      86     139 ..     275     328 ..     264     338 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
                             TEX13  86 vqkLqdqveehksaaqaLaselkrlreqqemerkeaasqlqlaqaalaevqker 139
                                       +q L d +e+ + a ++L  el++l+eq e e++ + +  + + ++ ++vq+e 
  gi|313125476|ref|YP_004035740.1| 275 IQELVDTLEQAEQAISSLEPELRTLKEQAEEEQDSVGTTEKHTLNRFRQVQSEV 328
                                       899***********************************************9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002       0.3       7      98 ..     347     426 ..     342     440 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                        l + Ge+G+GKT+ll ++++   e      e+ ++v+    +    +++++++ + +gl + +     ee+l al 
  gi|313125476|ref|YP_004035740.1| 347 ALKLLGEAGMGKTHLLCNVAKDRIE------EGYPTVLLLGENFY-NRNIWTQIIERFGLTCGT-----EEFLGALD 411
                                       57899***************99843......36666666666666.99***********98888.....89999999 PP

                            AAA_22  84 qalraravielliiD 98 
                                          ++r+v++l++iD
  gi|313125476|ref|YP_004035740.1| 412 SLGESRGVRSLIMID 426
                                       999999988888888 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.3   4.9e+03      74     111 ..     232     271 ..     229     284 .. 0.64
   2 ?   10.1   0.0   0.00035      0.52      37      76 ..     348     385 ..     315     395 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHTT-HHHHHHHHT...T-SEEEEE-GGGGTT CS
                          Bac_DnaA  74 eFlnelvkalrdkkaeefkeklr...kvDvLliDDiqflag 111
                                        F+++ ++ l++ + e+f+e      ++ vL + Di+ + +
  gi|313125476|ref|YP_004035740.1| 232 LFTQRSIEVLKQADEESFHELHDaieQIPVL-LQDIEQVDT 271
                                       6999999999998888887755411044444.456666655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00035
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHH CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFl 76 
                                       l + ge G+GktHLl  +++  +e+      v l +e+F 
  gi|313125476|ref|YP_004035740.1| 348 LKLLGEAGMGKTHLLCNVAKDRIEE--GYPTVLLLGENFY 385
                                       3478***********9998765443..2233445555555 PP

>> Ead_Ea22  Ead/Ea22-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.11   1.6e+02      37     109 ..     116     183 ..     105     202 .. 0.76
   2 ?    6.7   2.4    0.0071        11      66     105 ..     272     317 ..     233     346 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                          Ead_Ea22  37 ctgegnddefklgrtvakeh..daefiaaanpatvlaLLDelekkqqrikeleeeaenedialtvgklrveleaa 109
                                          e+++d ++  ++ a+e   d+ef+     +  l+LL++ ++    + +l  +  +   +lt +klr+ele++
  gi|313125476|ref|YP_004035740.1| 116 TALEKYNDRKEKWERWADERdmDVEFVFW-GQSRLLELLSKEKH----KGRLYFW--FNTNQLTGSKLRSELEET 183
                                       45578889988999999999999999999.58888888876554....3444434..667899999999999986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0071
                          Ead_Ea22  66 patvlaLLDelekkqqrikeleee.....aenedialtvgklrv.e 105
                                       +  +++L+D le+++q i++le e      ++e+ ++ vg +++  
  gi|313125476|ref|YP_004035740.1| 272 DIPIQELVDTLEQAEQAISSLEPElrtlkEQAEEEQDSVGTTEKhT 317
                                       55689*****************875555555555555555555542 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.9    0.0021       3.1      12      99 ..     251     338 ..     240     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHH CS
                          Spectrin  12 eleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelner 88 
                                       el++ ie++  ll++ +   +   +q+l++++++ e+ +++ ++++++l+e+ae+ +d+ + +++++ +r  ++++ 
  gi|313125476|ref|YP_004035740.1| 251 ELHDAIEQIPVLLQDIEQVDTDIPIQELVDTLEQAEQAISSLEPELRTLKEQAEEEQDSVGTTEKHTLNRFRQVQSE 327
                                       7777788888888777776666679******************************************9999999887 PP

                                       HHHHHHHHHHH CS
                          Spectrin  89 WeeLkelaaer 99 
                                         + ++ ++++
  gi|313125476|ref|YP_004035740.1| 328 VYSFQRYVQSK 338
                                       77766666665 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.4   2.1e+03      33      59 ..     234     264 ..     215     272 .. 0.62
   2 ?   10.2   2.7   0.00051      0.76      13      65 ..     272     330 ..     262     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.4
                            CC2-LZ  33 kqeeidelkeeikkkee....eletisvlka 59 
                                        q+ i+ lk+ +++  +     +e+i+vl +
  gi|313125476|ref|YP_004035740.1| 234 TQRSIEVLKQADEESFHelhdAIEQIPVLLQ 264
                                       6788888888888776633335558888865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00051
                            CC2-LZ  13 keeieeLkaqlqaaeealaakqeeidelkeeikkkee.....eletisvlk.aQaevYr 65 
                                          i+eL   l++ae+a+++ + e+  lke+++++++     e +t++ ++ +Q+evY+
  gi|313125476|ref|YP_004035740.1| 272 DIPIQELVDTLEQAEQAISSLEPELRTLKEQAEEEQDsvgttEKHTLNRFRqVQSEVYS 330
                                       45699*****************************9996664333388877526****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 1.07u 0.33s 00:00:01.40 Elapsed: 00:00:00.53
# Mc/sec: 7985.28
//
Query:       gi|313125477|ref|YP_004035741.1|  [L=310]
Description: site-specific recombinase xerd [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-25   89.9   0.2    2.8e-25   89.1   0.2    1.3  1  Phage_integrase  Phage integrase family
    2.8e-12   46.9   1.6    5.5e-12   46.0   1.0    1.8  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    3.7e-09   36.8   1.7    4.6e-09   36.5   0.4    1.9  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    0.00028   20.8   0.3      0.023   14.6   0.1    2.3  2  Phage_integr_3   Archaeal phage integrase
    0.00033   20.9   0.3     0.0012   19.1   0.2    1.9  2  Phage_int_SAM_5  Phage integrase SAM-like domain
  ------ inclusion threshold ------
       0.02   14.8   0.1       0.11   12.5   0.0    2.2  2  Sdh5             Flavinator of succinate dehydrogenase
       0.06   14.0   0.1       0.24   12.1   0.1    2.0  1  Phage_int_SAM_2  Phage integrase, N-terminal


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.2   1.1e-28   2.8e-25       6     170 ..     128     293 ..     125     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.1e-28
                                       HHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHH CS
                   Phage_integrase   6 deverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellke 82 
                                       +++e++++a+++    rdk+++ +l +tG R+ E+l+++ +dl le+g i++  ++ Kg+k +++p+ +e ++++++
  gi|313125477|ref|YP_004035741.1| 128 ENAEKIVHAIDD---PRDKTVAVVLAKTGCRVTEALTITREDLLLEDGFIRL--TNRKGGKTTVIPVDDETVRMIQR 199
                                       67899*******...9************************************..999*******************9 PP

                                       HHHHHCHCCTTTSBSSBET.TSSB--HHHHHHHHHHHHHHCT-S........SC--TTHHHHHHHHHHHHHCTSHHH CS
                   Phage_integrase  83 llskaleeaeksellfask.rgkplsrqtvrkafkraveeagie........kpltpHtlRhsfataLleagvdlrv 150
                                       l       ++ se+lfas   g++l+r+ +r+ +++a+ ++g+         k++tpHt+R  f t + ++g++ + 
  gi|313125477|ref|YP_004035741.1| 200 LQFID---QNTSEYLFASSrTGNQLTRERIRRKVREAAVKTGVMeegetrfhKKFTPHTFRTVFTTLMRNQGMPDHI 273
                                       98888...89*******986899*****************999889999**************************** PP

                                       HHHHHT-SSCCHHHHHHCCC CS
                   Phage_integrase 151 vqkllGHssisttqiYthva 170
                                       +q++ G s+ +t+ iYt+ +
  gi|313125477|ref|YP_004035741.1| 274 LQYIRGDSESETIDIYTRID 293
                                       *****************976 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   1.0   2.1e-15   5.5e-12       3      82 ..      18      97 ..      17     100 .. 0.92
   2 ?   -3.0   0.0       4.3   1.1e+04      17      28 ..     296     307 ..     294     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 2.1e-15
                   Phage_int_SAM_4  3 erfrealrlaglserTiksYlsaikrflrfl.kkkapeeltkedieaYlnyLanerklsastqknalnalsffykkvle 80
                                      ++f+   +  g s rTi+ Y ++++rf + +  +  pe+++ +++e+Yl  L+ er l+ +t +++l +ls+fy ++ +
  gi|313125477|ref|YP_004035741.1| 18 NEFLTSKTTTGRSHRTINEYSRTLQRFFHEHfPELDPEDVEVHHVEQYLRILV-ERDLAQNTKRRYLESLSSFYAWAMK 95
                                      5788889999******************99952469*****************.***********************99 PP

                   Phage_int_SAM_4 81 re 82
                                      r+
  gi|313125477|ref|YP_004035741.1| 96 RP 97
                                      86 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.3
                   Phage_int_SAM_4  17 rTiksYlsaikr 28 
                                       + ++ Yl+aik+
  gi|313125477|ref|YP_004035741.1| 296 QAQQEYLQAIKP 307
                                       568899999987 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.4   1.8e-12   4.6e-09      10      83 ..      25      96 ..      17      97 .. 0.90
   2 ?   -2.7   0.0         3   7.8e+03      16      27 ..     220     231 ..     207     236 .. 0.53

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.8e-12
                                      HTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHHHHT CS
                   Phage_int_SAM_1 10 kerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqflvre 83
                                      + +g+s+ T+++Y r L+rf++ +    + + e ++ ++v ++l+ l+e++l++++ +r+l +l sF+++++++
  gi|313125477|ref|YP_004035741.1| 25 TTTGRSHRTINEYSRTLQRFFHEHFP--ELDPEDVEVHHVEQYLRILVERDLAQNTKRRYLESLSSFYAWAMKR 96
                                      46789**************9876666..6******************************************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3
                                       HHHHHHHHHHHH CS
                   Phage_int_SAM_1  16 pnTlraYrrdLr 27 
                                       + T++  rr++r
  gi|313125477|ref|YP_004035741.1| 220 QLTRERIRRKVR 231
                                       334444444444 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.017        44      20      58 ..     139     173 ..     126     186 .. 0.77
   2 !   14.6   0.1   9.1e-06     0.023      83     140 ..     224     287 ..     210     306 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                                       -HHHHHHHHHHHHH---HHHHHHHHHS..GGG-EEETTE CS
                    Phage_integr_3  20 seevelvykllvfsGiRLkevlklLreyDpekliveddi 58 
                                       +++ ++v+ +l+ +G R  e+l++ re     l+ ed++
  gi|313125477|ref|YP_004035741.1| 139 DPRDKTVAVVLAKTGCRVTEALTITRE----DLLLEDGF 173
                                       45678999***************9998....44555555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.1e-06
                                       ....--B--HHHHHHHHHT-T.......--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CCTTS CS
                    Phage_integr_3  83 kelerlelseeavkefeakkk.......vkakyiRkwvatklaelgvpeevidFiqGrkpssvle 140
                                       ++++r ++ e avk+   +++       ++ +++R  ++t + ++g+p  + ++i G  +s+   
  gi|313125477|ref|YP_004035741.1| 224 ERIRR-KVREAAVKTGVMEEGetrfhkkFTPHTFRTVFTTLMRNQGMPDHILQYIRGDSESETID 287
                                       55666.8888888844444334455556*****************************99876554 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   4.7e-07    0.0012       6      86 ..      17      96 ..      14     103 .. 0.85
   2 ?   -2.2   0.0       2.1   5.3e+03      77      93 ..     228     244 ..     215     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.7e-07
                                      HHHHTHHHHTTS-HHHHHHHHHHHHHTTTS-....S---TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5  6 fkeyiekkkkkgskgtlrnykstlkhlkkFlkk..kditfeeidkefleeFedYLkkkkglsentiskyfkklkavlnk 82
                                      ++e+++ k+ +g   + r+++++ + l++F ++  +++  e++ +  +e++   L  ++ l++nt ++y++ l  ++  
  gi|313125477|ref|YP_004035741.1| 17 INEFLTSKTTTG--RSHRTINEYSRTLQRFFHEhfPELDPEDVEVHHVEQYLRIL-VERDLAQNTKRRYLESLSSFYAW 92
                                      667777777777..77788888888888888333588******************.9********************** PP

                                      HHHT CS
                   Phage_int_SAM_5 83 Aike 86
                                      A+k+
  gi|313125477|ref|YP_004035741.1| 93 AMKR 96
                                      *996 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                                       HHHHHHHHHTTS--S-H CS
                   Phage_int_SAM_5  77 kavlnkAikegilkknp 93 
                                       ++v  +A+k g++++  
  gi|313125477|ref|YP_004035741.1| 228 RKVREAAVKTGVMEEGE 244
                                       67778899999998765 PP

>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-05      0.11       7      37 ..      29      58 ..      26      74 .. 0.88
   2 ?   -1.8   0.0       1.2   3.1e+03      50      64 ..      89     102 ..      87     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                                      HH.--SSHHHHHTTTTHHHHHTTT--HHHHH CS
                              Sdh5  7 rsrrRGmlElDllLgrFaekhlatlseeeld 37
                                      rs +R + E    L+rF+++h+++l+ e+++
  gi|313125477|ref|YP_004035741.1| 29 RS-HRTINEYSRTLQRFFHEHFPELDPEDVE 58
                                      78.***********************99876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                       HHHHHHT-.---S-H CS
                              Sdh5  50 Lldwltgrkeepeda 64 
                                        ++w+++r +  ed 
  gi|313125477|ref|YP_004035741.1|  89 FYAWAMKR-PRYEDI 102
                                       699****9.777665 PP

>> Phage_int_SAM_2  Phage integrase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.5e-05      0.24      15      85 ..      27      93 ..      18      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.5e-05
                   Phage_int_SAM_2 15 agGsykTvndrerilqrla.reLlalniqvrdvkslKarHieayieerlaeeiskrtlqNemaalRsvlrka 85
                                      +g s++T n+  r lqr+  +++ +l     d +++ ++H+e+y++   + ++++ t +  + +l s+ ++a
  gi|313125477|ref|YP_004035741.1| 27 TGRSHRTINEYSRTLQRFFhEHFPEL-----DPEDVEVHHVEQYLRILVERDLAQNTKRRYLESLSSFYAWA 93
                                      567**************851567777.....5678999******************9999999998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1834.56
//
Query:       gi|313125478|ref|YP_004035742.1|  [L=163]
Description: hypothetical protein Hbor_07050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.019   14.8   2.6      0.025   14.4   2.6    1.2  1  RB_A            Retinoblastoma-associated protein A domain
      0.026   14.5   0.4        0.1   12.6   0.1    1.8  2  Anticodon_1     Anticodon-binding domain of tRNA
      0.042   13.4   3.9      0.048   13.2   3.9    1.1  1  Exonuc_VII_L    Exonuclease VII, large subunit
      0.047   13.1   0.3      0.057   12.8   0.3    1.1  1  Peptidase_C11   Clostripain family
      0.054   14.4   3.7      0.082   13.8   3.7    1.2  1  CDC37_N         Cdc37 N terminal kinase binding
      0.058   12.7   0.0       0.07   12.5   0.0    1.1  1  aGPT-Pplase3    Alpha-glutamyl/putrescinyl thymine pyrophosph
      0.071   13.5   2.9       0.09   13.2   2.9    1.2  1  eIF3_N          eIF3 subunit 6 N terminal domain
      0.082   12.5   2.4      0.089   12.4   2.4    1.1  1  HXXSHH          Protein of unknown function (DUF1552)
       0.11   11.2   1.7       0.13   10.9   1.7    1.1  1  HlyD_2          HlyD family secretion protein
       0.16   13.0   0.0       0.82   10.7   0.0    2.0  2  KCNQ2_u3        Unstructured region on Potassium channel subu
       0.19   11.5   2.2       0.31   10.8   1.5    1.6  2  Imm49           Immunity protein 49
       0.23   11.3   2.2       0.36   10.7   0.7    2.1  2  IF2_N           Translation initiation factor IF-2, N-termina
       0.39   11.4   3.0        1.8    9.2   3.0    2.0  1  ParE_toxin      ParE toxin of type II toxin-antitoxin system,
       0.63   10.0   6.4       0.11   12.4   2.2    2.0  2  Pox_A_type_inc  Viral A-type inclusion protein repeat
       0.79   10.1   9.8          1    9.8   6.6    2.2  2  Csm1_N          Csm1 N-terminal domain
          3    7.9   5.2        2.5    8.2   2.1    2.5  3  PspB            Phage shock protein B


Domain annotation for each model (and alignments):
>> RB_A  Retinoblastoma-associated protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.6   2.2e-05     0.025      35     100 ..      63     127 ..      34     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                              RB_A  35 ctedpteeiekrvkelsekflkkyaesseeeessslaeelakkrlklaekLYykvLesilksEkkr 100
                                        +++  e++++rv+el++++ ++ +++++++ ++++ eel +k l++  + + ++Le++lk+ + r
  gi|313125478|ref|YP_004035742.1|  63 GDKRKVEQLQQRVEELEQQLESQSSNRVTSQ-TQTIDEELVEKILSENYTPFDQLLEELLKQPEFR 127
                                       46678899************99999999888.99**************************997744 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   9.2e-05       0.1     107     150 ..      20      68 ..       3      70 .. 0.65
   2 ?    0.8   0.1      0.39   4.4e+02       5      33 ..      68      96 ..      64     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.2e-05
                       Anticodon_1 107 wpe..kaeelekele...eeevellkeivkairklrselkikpsselkv 150
                                       +p    +e +++e+e    +++++l+++++ +r lr++ ++k   + kv
  gi|313125478|ref|YP_004035742.1|  20 YPPetHKETWKAEAEergTSMIQYLQDLIQEARYLREQGQLKLGDKRKV 68 
                                       44323333333333235688********************998887666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.39
                       Anticodon_1  5 lselnklvkevteayeeyrfnkaasalye 33
                                      + +l++ v+e ++ +e+ + n++ s+ ++
  gi|313125478|ref|YP_004035742.1| 68 VEQLQQRVEELEQQLESQSSNRVTSQTQT 96
                                      56899999999999999999999988776 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.9   4.2e-05     0.048     142     221 ..      26     105 ..      18     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                      Exonuc_VII_L 142 kaeleeqleelerrlekaikrlleekkqrleklasrlk.speellerkrqrldeleerleralkkqlkkkrerleel 217
                                       k++++++ ee   ++ + ++ l++e++   e+   +lk   ++++e+ +qr++ele++le++ ++++++++++++e 
  gi|313125478|ref|YP_004035742.1|  26 KETWKAEAEERGTSMIQYLQDLIQEARYLREQG--QLKlGDKRKVEQLQQRVEELEQQLESQSSNRVTSQTQTIDEE 100
                                       667788888888888888888888776544444..4554678999999999********999999998888888765 PP

                      Exonuc_VII_L 218 k.erl 221
                                         e++
  gi|313125478|ref|YP_004035742.1| 101 LvEKI 105
                                       42333 PP

>> Peptidase_C11  Clostripain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   5.1e-05     0.057     185     269 ..      26     111 ..      23     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.1e-05
                     Peptidase_C11 185 setkessaeevgrkivdsyresyssvrve..elsLsvydlskveevlksvdalaedlvkkakkeisidlksfykvlv 259
                                       +et +++aee g  +++  ++  ++ r+   + +L + d  kve++ + v++l ++l ++ ++ +  +++ + + lv
  gi|313125478|ref|YP_004035742.1|  26 KETWKAEAEERGTSMIQYLQDLIQEARYLreQGQLKLGDKRKVEQLQQRVEELEQQLESQSSNRVTSQTQTIDEELV 102
                                       5678899******************998776889***********************99999988888888888888 PP

                     Peptidase_C11 260 eseltegsys 269
                                       e+ l   +y+
  gi|313125478|ref|YP_004035742.1| 103 EKILS-ENYT 111
                                       77766.4455 PP

>> CDC37_N  Cdc37 N terminal kinase binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.7   7.3e-05     0.082      28     103 ..      39     113 ..      34     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.3e-05
                           CDC37_N  28 sfirwKqrdihekreqrkaeikklklereindkllkridkllealkekeveeeevvfkalnesleekkekedkpka 103
                                       s+i+  q  i e r  r++   kl  +r++ ++l++r+++l ++l++++++  ++ ++++ e+l ek  +e++ + 
  gi|313125478|ref|YP_004035742.1|  39 SMIQYLQDLIQEARYLREQGQLKLGDKRKV-EQLQQRVEELEQQLESQSSNRVTSQTQTIDEELVEKILSENYTPF 113
                                       999**********************99887.57***************9999778888888887665555554443 PP

>> aGPT-Pplase3  Alpha-glutamyl/putrescinyl thymine pyrophosphorylase clade 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.2e-05      0.07     102     200 ..      39     142 ..      14     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                      aGPT-Pplase3 102 afekWLekna.......qeiggkfgnhrkyeslkpakkrgtgkviesYvewiaeagshealf.aqlvrqagndpeai 170
                                       ++ ++L++         ++ + k+g++rk e l+++ + ++++++es  +     +s ++++ ++lv+++ ++  + 
  gi|313125478|ref|YP_004035742.1|  39 SMIQYLQDLIqearylrEQGQLKLGDKRKVEQLQQRVE-ELEQQLESQSSNRV--TSQTQTIdEELVEKILSENYTP 112
                                       34444444333345777666889***********9999.89999998766433..355565516789999999**** PP

                      aGPT-Pplase3 171 Fdelykslekvkrfgrlgkfdyltllgklg 200
                                       Fd+l+++l k  +f r ++ d  t l klg
  gi|313125478|ref|YP_004035742.1| 113 FDQLLEELLKQPEFRRRVRLDLETGLYKLG 142
                                       *********************988887775 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.9     8e-05      0.09      42     127 ..      36     121 ..      18     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-05
                            eIF3_N  42 kkTnmvdyaadlykelegeeevpeelekkreevleeleeleeeaekvlelledeevvsnlrsdkkqnle.fLkeehg 117
                                       ++T+m++y++dl +e    +e   +l+   +  +e+l++  ee e+ le  +++ v+s+ ++  ++++e +L+e++ 
  gi|313125478|ref|YP_004035742.1|  36 RGTSMIQYLQDLIQEARYLREQG-QLKLGDKRKVEQLQQRVEELEQQLESQSSNRVTSQTQTIDEELVEkILSENYT 111
                                       68**************9876644.55555555689999999*******************99555555559999997 PP

                            eIF3_N 118 itpemidaly 127
                                          + +++l 
  gi|313125478|ref|YP_004035742.1| 112 PFDQLLEELL 121
                                       6555555555 PP

>> HXXSHH  Protein of unknown function (DUF1552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.4   7.9e-05     0.089     157     217 ..      30      95 ..      14     134 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                            HXXSHH 157 aarrlarrksvlDlvle...dakslkr..kLgaadrqKLdeylesvreiekrlekaekwaptakae 217
                                       +a++ +r++s++ ++++   +a+ l++  +L   d++K+++  + v+e+e++le++++ + t++ +
  gi|313125478|ref|YP_004035742.1|  30 KAEAEERGTSMIQYLQDliqEARYLREqgQLKLGDKRKVEQLQQRVEELEQQLESQSSNRVTSQTQ 95 
                                       445556777776666651115555776447999********************5555433333332 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.7   0.00012      0.13     103     166 ..      64     123 ..      48     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                            HlyD_2 103 lkekletlnerikeienneaieniekdiekldreInvlekdikesiknedikkieelKeelnal 166
                                       +k+k+e+l++r++e+e++      ++  +++ ++ ++  +++ e+i +e++   ++l eel ++
  gi|313125478|ref|YP_004035742.1|  64 DKRKVEQLQQRVEELEQQL----ESQSSNRVTSQTQTIDEELVEKILSENYTPFDQLLEELLKQ 123
                                       7899************998....3456799999************************9999875 PP

>> KCNQ2_u3  Unstructured region on Potassium channel subunit alpha KvLQT2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00073      0.82      66      91 ..       3      28 ..       1      33 [. 0.87
   2 ?   -0.1   0.0       1.7   1.9e+03      19      40 ..      72      94 ..      60     125 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00073
                          KCNQ2_u3 66 awngssPvgdsgslvRiPPPPahers 91
                                       w++ss ++d++slv++ PP +h  +
  gi|313125478|ref|YP_004035742.1|  3 GWKSSSGISDDTSLVKLYPPETHKET 28
                                      589******************99875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                          KCNQ2_u3 19 eekitkivrs.sssmgqknfsap 40
                                      ++ +++++++  s+++++ +s++
  gi|313125478|ref|YP_004035742.1| 72 QQRVEELEQQlESQSSNRVTSQT 94
                                      34444444443333333433333 PP

>> Imm49  Immunity protein 49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0         1   1.2e+03     164     181 ..      23      40 ..      22      49 .. 0.77
   2 ?   10.8   1.5   0.00028      0.31     104     165 ..      64     123 ..      30     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1
                             Imm49 164 eahrayyaadeeerredp 181
                                       e h++ ++a++eer  + 
  gi|313125478|ref|YP_004035742.1|  23 ETHKETWKAEAEERGTSM 40 
                                       6799*****999887654 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00028
                             Imm49 104 dpdaaeellaaleaalpreaaiaaaegkrldqlatpelrllraLlegDeeaFeeaLeeaLea 165
                                       d++++e+l +++e+ +++   + ++      q+ t + +l + +l+ +   F++ Lee+L++
  gi|313125478|ref|YP_004035742.1|  64 DKRKVEQLQQRVEELEQQLESQSSNRV--TSQTQTIDEELVEKILSENYTPFDQLLEELLKQ 123
                                       467777788888877777777777777..9******************************85 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.7     3e+03      33      43 ..       4      14 ..       3      15 .. 0.87
   2 ?   10.7   0.7   0.00032      0.36      13      50 ..      71     108 ..      69     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.7
                             IF2_N 33 kshsssLDeet 43
                                      ++ ss+++++t
  gi|313125478|ref|YP_004035742.1|  4 WKSSSGISDDT 14
                                      6789*****98 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00032
                             IF2_N  13 LgvkskevikkLfkelGievkshsssLDeetaeliaee 50 
                                       L+ +++e+ ++L+++    v s ++++Dee +e+i+ e
  gi|313125478|ref|YP_004035742.1|  71 LQQRVEELEQQLESQSSNRVTSQTQTIDEELVEKILSE 108
                                       66677888888855445559***************875 PP

>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.0    0.0016       1.8       8      48 ..      44      87 ..      42     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                                      HHHHHHHHHHHHCC-H...HHHHHHHHHHHHHHHHHHHTTTSEE CS
                        ParE_toxin  8 lkdlkkiadyiardgp...aakrfldaleealellaenpalgrp 48
                                      l+dl   a+y++++g+     kr +++l++++e+l+++ ++ ++
  gi|313125478|ref|YP_004035742.1| 44 LQDLIQEARYLREQGQlklGDKRKVEQLQQRVEELEQQLESQSS 87
                                      799*********55544766******************998877 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.2   9.9e-05      0.11       3      18 ..      68      83 ..      66      84 .. 0.92
   2 ?   -2.5   0.1       4.9   5.5e+03       7      14 ..     127     135 ..     126     136 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                    Pox_A_type_inc  3 msrlRsRIsDLErqLs 18
                                      +++l+ R+++LE+qL+
  gi|313125478|ref|YP_004035742.1| 68 VEQLQQRVEELEQQLE 83
                                      79*************7 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.9
                    Pox_A_type_inc   7 RsRIs.DLE 14 
                                       R+R++ DLE
  gi|313125478|ref|YP_004035742.1| 127 RRRVRlDLE 135
                                       778764665 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.6   0.00089         1      23      65 ..      45      90 ..      30      96 .. 0.84
   2 ?    1.2   0.1      0.42   4.7e+02      20      31 ..     100     111 ..      95     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00089
                            Csm1_N 23 sklvhENsvLsqkletk...dqeiesLkeqlaeleekvkeleerrk 65
                                      + l++E + L+++ + k   ++++e+L+++++ele++++++ ++r 
  gi|313125478|ref|YP_004035742.1| 45 QDLIQEARYLREQGQLKlgdKRKVEQLQQRVEELEQQLESQSSNRV 90
                                      56899999999988776555789**************999887765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.42
                            Csm1_N  20 llvsklvhENsv 31 
                                        lv+k++ EN +
  gi|313125478|ref|YP_004035742.1| 100 ELVEKILSENYT 111
                                       59********75 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.85   9.5e+02      41      55 ..      42      56 ..      27      59 .. 0.82
   2 ?    8.2   2.1    0.0022       2.5      47      70 ..      65      88 ..      40      90 .. 0.76
   3 ?   -3.4   0.0       9.4   1.1e+04      60      71 ..     117     126 ..     114     128 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.85
                              PspB 41 krLeellekAeklee 55
                                      + L++l+++A+ l+e
  gi|313125478|ref|YP_004035742.1| 42 QYLQDLIQEARYLRE 56
                                      77999***9999876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0022
                              PspB 47 lekAekleeRietLEriLdaespn 70
                                       +k e+l++R+e LE+ L+++s n
  gi|313125478|ref|YP_004035742.1| 65 KRKVEQLQQRVEELEQQLESQSSN 88
                                      467899999999999999998865 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 9.4
                              PspB  60 LEriLdaespnw 71 
                                       LE++L   +p++
  gi|313125478|ref|YP_004035742.1| 117 LEELLK--QPEF 126
                                       555553..4555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2886  (0.160968); expected 358.6 (0.02)
Passed bias filter:                     1349  (0.0752412); expected 358.6 (0.02)
Passed Vit filter:                       185  (0.0103185); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 1001.68
//
Query:       gi|313125479|ref|YP_004035743.1|  [L=456]
Description: signal transduction histidine kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-20   71.9   0.2    8.8e-19   68.2   0.0    2.6  2  GAF_2        GAF domain
    1.7e-17   64.0   0.0    1.3e-16   61.1   0.0    2.0  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.7e-13   49.0   0.2    4.7e-13   49.0   0.2    2.7  3  HisKA        His Kinase A (phospho-acceptor) domain
      3e-09   37.6   0.0    1.1e-07   32.6   0.0    2.8  3  GAF          GAF domain
    2.8e-05   24.5   0.0    5.1e-05   23.6   0.0    1.5  1  GAF_3        GAF domain
     0.0012   18.5   1.5      0.029   13.9   0.3    2.8  3  HisKA_4TM    Archaeal 4TM region of histidine kinase
  ------ inclusion threshold ------
      0.049   13.5   0.0       0.16   11.8   0.0    1.8  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.063   13.2   0.0       0.35   10.8   0.0    2.0  2  HATPase_c_2  Histidine kinase-like ATPase domain
       0.18   11.9   0.1       0.47   10.6   0.1    1.7  1  sCache_like  Single Cache-like


Domain annotation for each model (and alignments):
>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   4.4e-22   8.8e-19       4     137 ..      84     226 ..      81     227 .. 0.87
   2 ?    0.8   0.0      0.29   5.7e+02       9      38 ..     319     348 ..     317     414 .. 0.62

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 4.4e-22
                                       HHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--.....-TTHHHHHHHHTS-EEES- CS
                             GAF_2   4 leelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrpl.....geglvgealrtgrpvilnd 73 
                                        + l ++v+d+++e g  ++++i+ +d+ ++ +r +aw++ +ee +++l   +     g+g  g+a+++g+   + +
  gi|313125479|ref|YP_004035743.1|  84 RSALEQAVCDRVIESGpYDAAWIGRYDPTDSrVRPVAWTGFDEEYFESLVVTVdddptGKGAGGRAIKSGEIQCIPN 160
                                       567889********999**********5555488889998888887777663334446999789************* PP

                                       GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       + edp ++++    ++ +  s ++vP+++++ v+G +++ya++++ fde++ e+L+el+++i+ ai
  gi|313125479|ref|YP_004035743.1| 161 VFEDPTMQPWWdqFEALDAESLAVVPIRDDETVYGLISIYADRQNVFDEREKEVLSELGDTIGHAI 226
                                       ***********88888888888*******999*********************************9 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.29
                                       HHHHHHHHHS.S..EEEEEEE-TTS-EEEE.E CS
                             GAF_2   9 dlvldelvel.gaalgyillvdddgglrla.a 38 
                                       ++v + ++e+ g+  + + l+dd +   +a  
  gi|313125479|ref|YP_004035743.1| 319 ETVAEDAWETaGSPSATLRLLDDLRT--VAcD 348
                                       67777777776777777777775444..3332 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.54   1.1e+03       7      63 ..      72     168 ..      68     179 .. 0.49
   2 !   61.1   0.0   6.3e-20   1.3e-16       2     107 ..     348     444 ..     347     448 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHHHSTTTEEEEEEEE..........................EE...TEEEEEEEE..SSSSSTTH CS
                         HATPase_c   7 rqiisnlvdNavkfatkageieveika..........................se...ddlvisveD..nGiGipke 52 
                                       r + ++lv+N+ + a ++  ++  i++                          +e   + lv++v D  +G+G    
  gi|313125479|ref|YP_004035743.1|  72 RIATQELVSNSERSALEQAVCDRVIESgpydaawigrydptdsrvrpvawtgfDEeyfESLVVTVDDdpTGKGAGGR 148
                                       55566667776666222222222122122222222222222211111333333225667888999997777776665 PP

                                       HHT........GTCS.TTCH CS
                         HATPase_c  53 dlk........klfe.kfsq 63 
                                        +k        ++fe + +q
  gi|313125479|ref|YP_004035743.1| 149 AIKsgeiqcipNVFEdPTMQ 168
                                       55555555666666666665 PP

  == domain 2  score: 61.1 bits;  conditional E-value: 6.3e-20
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlG 77 
                                       d +rLr+++ nl  N+ ++   ++++++ ++    d  + veD+G+Gip +d++++fe  +s+      +  gtG+G
  gi|313125479|ref|YP_004035743.1| 348 DRSRLRELFENLFRNSREH--AGSDVTIIVR--PIDSGFAVEDDGPGIPAADRQEVFEaGYST------NEDGTGFG 414
                                       789***************9..6788888888..55899********************88888......889***** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftft 107
                                       l ivk+++e +g ++++ ++p++G +f ft
  gi|313125479|ref|YP_004035743.1| 415 LNIVKSIAEAHGWTVSLAESPDGGVRFEFT 444
                                       ***************************996 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       2.9   5.7e+03      47      63 ..      60      75 ..      56      78 .. 0.52
   2 !   49.0   0.2   2.3e-16   4.7e-13       2      65 ..     249     307 ..     248     309 .. 0.95
   3 ?    0.1   0.0      0.42   8.4e+02      39      66 ..     340     367 ..     321     368 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.9
                                      HHHHHHHHHHHHHHHCC CS
                             HisKA 47 earrldhlvedlLdlsr 63
                                      + ++l+++ +d L++++
  gi|313125479|ref|YP_004035743.1| 60 SLEQLNRI-NDTLRIAT 75
                                      44455554.44445554 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 2.3e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l++f+  v+H+Lr+PL++  g++e+ ++        ++y++++ +   r+++l+edlL+l++ +
  gi|313125479|ref|YP_004035743.1| 249 LEEFTGAVSHDLRNPLNVAEGFLELAQE-----HGDEQYFDRVADALARMNELIEDLLTLAQQG 307
                                       789*************************.....899************************9876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA  39 eyletiesearrldhlvedlLdlsriea 66 
                                       + l+t+     rl++l e+l + sr+ a
  gi|313125479|ref|YP_004035743.1| 340 DDLRTVACDRSRLRELFENLFRNSREHA 367
                                       4555555555688888888877777655 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.2   2.4e+03      92     107 ..      30      48 ..      29      75 .. 0.78
   2 !   32.6   0.0   5.3e-11   1.1e-07      45     133 .]     139     226 ..      83     226 .. 0.82
   3 ?    1.3   0.0      0.25     5e+02       2      43 ..     352     403 ..     351     438 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.2
                                       EEEEEE...TTEEEEEEEE CS
                               GAF  92 vvPlvn...dgelwGllvl 107
                                       vvP++n    g l+Gllv 
  gi|313125479|ref|YP_004035743.1|  30 VVPMLNvatAGALIGLLVG 48 
                                       799999899999****985 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 5.3e-11
                                       EETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHH CS
                               GAF  45 mkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreele 120
                                       +++g+g  g+++++g++ +ip++ +dp  ++  + d++e+    s++vvP+++d+ ++Gl++++  ++  f++ e e
  gi|313125479|ref|YP_004035743.1| 139 DPTGKGAGGRAIKSGEIQCIPNVFEDPTMQP--WWDQFEALDAESLAVVPIRDDETVYGLISIYADRQnVFDEREKE 213
                                       444666556*************99****999..8889****************************88889******* PP

                                       HHHHHHHHHHHHH CS
                               GAF 121 llqvladqvaval 133
                                       +l +l+d ++ a+
  gi|313125479|ref|YP_004035743.1| 214 VLSELGDTIGHAI 226
                                       ********99886 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHHTESEEEEEEEEETTEEE.....CEEEEECC.....E CS
                               GAF   2 leelldtvveelrellgadrvalylpdydGlhy.....dipqasrw.....l 43 
                                       l el++++ +  re+ g d  ++ +p  +G  +     +ip+a+r       
  gi|313125479|ref|YP_004035743.1| 352 LRELFENLFRNSREHAGSDVTIIVRPIDSGFAVeddgpGIPAADRQevfeaG 403
                                       67999***************99999555553223455568888887544441 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.6e-08   5.1e-05      27     127 ..     109     226 ..      87     228 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.6e-08
                             GAF_3  27 ldedgnklqvaagw.dgkpalse.sldedsalar.....ralssgevvsepsfaeedg..........lpdraalav 86 
                                       +d+  ++++++a + + ++ ++  +++ d+  +      ra++sge++  p + e ++          l+ +++ +v
  gi|313125479|ref|YP_004035743.1| 109 YDPTDSRVRPVAWTgFDEEYFESlVVTVDDDPTGkgaggRAIKSGEIQCIPNVFEDPTmqpwwdqfeaLDAESLAVV 185
                                       56666666666655556666644422233333333455577777777666555444442222222222777999*** PP

                             GAF_3  87 PLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       P+++ ++v+G++ ++ ++   fd++++e l++l++ i+ ai
  gi|313125479|ref|YP_004035743.1| 186 PIRDDETVYGLISIYADRQNVFDEREKEVLSELGDTIGHAI 226
                                       ****99**********99666*****************999 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.3   1.5e-05     0.029      73     129 ..       4      60 ..       1      82 [. 0.72
   2 ?    1.5   0.0     0.097   1.9e+02     141     160 ..     253     272 ..     233     276 .. 0.78
   3 ?   -0.4   0.0      0.38   7.5e+02     126     145 ..     279     298 ..     274     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                         HisKA_4TM  73 Gavvvgavigltvlv.rllegrtiaePvfvvlvaaevGavaGllaGylaararadasr 129
                                       G+v+++ ++g  v+v  ++ g  + +Pv ++l  a  Ga+ Gll G + ar  +  + 
  gi|313125479|ref|YP_004035743.1|   4 GVVALT-ILGGWVFVaTVIRGFPLIDPVVPMLNVATAGALIGLLVGVYDARGLEQQRS 60 
                                       555555.445555551577899999**************************8766543 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.097
                         HisKA_4TM 141 ndlirhdlrndlvvirgyae 160
                                        + + hdlrn l+v +g+ e
  gi|313125479|ref|YP_004035743.1| 253 TGAVSHDLRNPLNVAEGFLE 272
                                       56689*********999866 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.38
                         HisKA_4TM 126 dasrakrisdalafvndlir 145
                                       d +  +r++dala +n+li 
  gi|313125479|ref|YP_004035743.1| 279 DEQYFDRVADALARMNELIE 298
                                       5566689***********96 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.4   4.8e+03       4      16 ..      72      84 ..      70      90 .. 0.76
   2 ?   11.8   0.0   7.8e-05      0.16      10      62 ..     359     408 ..     352     417 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                       HATPase_c_3  4 ekAlaelvdNsld 16
                                      ++A  elv Ns  
  gi|313125479|ref|YP_004035743.1| 72 RIATQELVSNSER 84
                                      68999*****965 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.8e-05
                       HATPase_c_3  10 lvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                                       l +Ns +     v+i v   +   + + +eDdG G++ ++ +++++ + s++e
  gi|313125479|ref|YP_004035743.1| 359 LFRNSREHAGSDVTIIVRPID---SGFAVEDDGPGIPAADRQEVFEAGYSTNE 408
                                       557777777778999999986...69*******************99999887 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.69   1.4e+03      30      49 ..      69      88 ..      58     146 .. 0.75
   2 ?   10.8   0.0   0.00018      0.35      38     111 ..     354     424 ..     349     438 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.69
                       HATPase_c_2 30 deirlaveEactNavehayl 49
                                      d +r+a +E+++N  + a +
  gi|313125479|ref|YP_004035743.1| 69 DTLRIATQELVSNSERSALE 88
                                      57889999999997665554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00018
                       HATPase_c_2  38 EactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDe 111
                                       E++ N ++  +++a   +v++   +++    + v+D+Gpg +++++++  e +++++++  G+Gl ++k++++ 
  gi|313125479|ref|YP_004035743.1| 354 ELFENLFRNSREHAG-SDVTII--VRPIDSGFAVEDDGPGIPAADRQEVFEAGYSTNEDGTGFGLNIVKSIAEA 424
                                       666677776666665.444444..2344445789******9999999999999****************99875 PP

>> sCache_like  Single Cache-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00024      0.47      17      71 ..     196     247 ..     194     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                       HHHHHS-GGG-SSHHHHHHHHHHHHHHT-EEEEEETTS-EEEETTS...S---HH CS
                       sCache_like  17 llasllenenlkaaenkkvleeasekldaritivdadgkvlydtgqeieeaesea 71 
                                       l++++++ +n+ ++++k+vl e+++ ++  it ++++++   +  +    a++++
  gi|313125479|ref|YP_004035743.1| 196 LISIYADRQNVFDEREKEVLSELGDTIGHAITSIETHEQLAERERE---LARQNQ 247
                                       6899**********************************98777666...444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 2457.98
//
Query:       gi|313125480|ref|YP_004035744.1|  [L=202]
Description: translation initiation factor 2 subunit beta (aeif-2b) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-30  105.0   0.0      3e-30  104.5   0.0    1.2  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
    5.4e-06   26.3   0.8    9.1e-06   25.6   0.8    1.3  1  TRAM             TRAM domain
  ------ inclusion threshold ------
      0.082   12.5   0.1       0.11   12.1   0.1    1.3  1  DUF2271          Predicted periplasmic protein (DUF2271)
       0.11   12.8   1.2        1.6    9.1   1.2    2.2  1  Lar_restr_allev  Restriction alleviation protein Lar
        0.2   11.8   2.5        2.1    8.5   2.5    2.2  2  Zn-ribbon_8      Zinc ribbon domain
       0.78    9.5   2.9         24    4.7   3.5    2.2  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0     1e-33     3e-30       6     116 ..      19     127 ..      15     128 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 1e-33
                                       SSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHH CS
                      eIF-5_eIF-2B   6 dkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldk 82 
                                        +++r+++p+++ +++g+  t ++N+ +ia+aL r+++h+++ +++elgt+g++ +++r+ +ng+f+ +++e+++d+
  gi|313125480|ref|YP_004035744.1|  19 YEESRLSVPDPEGETDGA-FTRLTNLGQIADALGREASHLHRNIQRELGTNGQF-DGDRARYNGSFSVANFEAAIDE 93 
                                       5678**************.***********************************.8899****************** PP

                                       HHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  83 yieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                       y+ eyV+C+eC+ p+t+l++e+ + +l+C+aCga
  gi|313125480|ref|YP_004035744.1|  94 YVAEYVTCTECGLPDTRLVTEDGVDMLRCEACGA 127
                                       *********************************7 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.8   3.1e-09   9.1e-06       3      61 ..     147     201 ..     146     202 .] 0.95

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.1e-09
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61 
                                       ++G+t+e +++g + ++g+g++    ++++fv g+ +  Gd+V + I+++    ++++ 
  gi|313125480|ref|YP_004035744.1| 147 EEGKTYELEITGTG-RKGDGVAEKG-KYTIFVTGARE--GDTVRAIIERTSGTLAFARK 201
                                       58************.**********.***********..***********999999986 PP

>> DUF2271  Predicted periplasmic protein (DUF2271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.7e-05      0.11      59     108 ..     133     184 ..      86     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                           DUF2271  59 klkeeidgvsgaTrapGk.yklkvdekddklkkl.kaGkYklvvEaaredgg 108
                                       k+++++ + +g+ +++Gk y+l+++++ +k++ + ++GkY+++v  are ++
  gi|313125480|ref|YP_004035744.1| 133 KQAAKTQTQTGPAIEEGKtYELEITGTGRKGDGVaEKGKYTIFVTGAREGDT 184
                                       455689999********74799*****9999988468***********9765 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.2   0.00055       1.6       5      36 ..     100     127 ..      62     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00055
                   Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCadCga 36 
                                        C  Cg +++   ++++v     +  C+ Cga
  gi|313125480|ref|YP_004035744.1| 100 TCTECGLPDTRLVTEDGVD----MLRCEACGA 127
                                       4667888888777778877....888888888 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.5   0.00071       2.1       6      38 ..      98     133 ..      86     134 .. 0.78
   2 ?    7.7   0.2    0.0013         4       7      22 ..     121     135 ..     119     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00071
                       Zn-ribbon_8   6 Yr.CeeCghefevlqsisdaplta.CPeCgs..evrr 38 
                                       Y  C+eCg   ++l++  d  +   C +Cg+  +v++
  gi|313125480|ref|YP_004035744.1|  98 YVtCTECGLPDTRLVT-EDGVDMLrCEACGAfrPVQK 133
                                       4469****99999984.56666666****99877776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0013
                       Zn-ribbon_8   7 rCeeCghefevlqsis 22 
                                       rCe+Cg  f ++q+ +
  gi|313125480|ref|YP_004035744.1| 121 RCEACG-AFRPVQKQA 135
                                       8*****.9**999855 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.012        35      16      24 ..      97     105 ..      95     112 .. 0.86
   2 ?    4.7   3.5    0.0081        24       3      24 ..     101     126 ..     100     134 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                                       S----SSS- CS
                    DNA_RNApol_7kD  16 dpiRCkeCG 24 
                                       + + C+eCG
  gi|313125480|ref|YP_004035744.1|  97 EYVTCTECG 105
                                       6789****9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0081
                                       -SSS--B.----SS...S----SSS- CS
                    DNA_RNApol_7kD   3 CgeCgae.vslkkg...dpiRCkeCG 24 
                                       C eCg + ++l  +   d +RC  CG
  gi|313125480|ref|YP_004035744.1| 101 CTECGLPdTRLVTEdgvDMLRCEACG 126
                                       88888541446555122678*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1089.61
//
Query:       gi|313125481|ref|YP_004035745.1|  [L=357]
Description: hypothetical protein Hbor_07080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.21   11.5   2.2       0.35   10.7   2.2    1.4  1  Sigma70_ner  Sigma-70, non-essential region
        9.9    4.1   6.3         14    3.6   6.3    1.1  1  DNA_pol_phi  DNA polymerase phi


Domain annotation for each model (and alignments):
>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.2   3.9e-05      0.35      34      77 ..     124     169 ..      57     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.9e-05
                       Sigma70_ner  34 eeeeeeeeeedeeeeeee.......edddeeeseseaadeeelkeealekf 77 
                                        e++e  eee+e     +       + d+++++++e++ ee+++ ea +++
  gi|313125481|ref|YP_004035745.1| 124 PEDDETTEEEQE-----TdwlgepvDGDGDDADDDEEETEEIDRREAVKTV 169
                                       222222222222.....1245557777778899*************99876 PP

>> DNA_pol_phi  DNA polymerase phi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   6.3    0.0015        14     642     685 ..     125     162 ..     113     192 .. 0.49

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0015
                       DNA_pol_phi 642 dedeeddeeeeeeddeededse...edddeeesdedeededdedvde 685
                                       ++de+++ee+e          +   e  d + +d d+++e+ e++d 
  gi|313125481|ref|YP_004035745.1| 125 EDDETTEEEQET---------DwlgEPVDGDGDDADDDEEETEEIDR 162
                                       111111111111.........12232222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2007.00
//
Query:       gi|313125482|ref|YP_004035746.1|  [L=175]
Description: hypothetical protein Hbor_07090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-05   24.8   2.4    2.1e-05   24.1   2.4    1.4  1  SHOCT     Short C-terminal domain
  ------ inclusion threshold ------
      0.027   14.5   0.5      0.046   13.7   0.5    1.3  1  GvpG      Gas vesicle protein G


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   2.4   2.3e-09   2.1e-05       1      27 [.     123     149 ..     123     149 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.3e-09
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakL 27 
                                       daL+ Lk+ y + eIte+EFe+k ++L
  gi|313125482|ref|YP_004035746.1| 123 DALASLKRQYVEDEITEAEFERKLDRL 149
                                       89**********************998 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   5.1e-06     0.046      35      63 ..     123     151 ..     112     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-06
                              GvpG  35 keLaaLqqeLdaGeIdeeeFdrrEeelLd 63 
                                         La+L+++  + eI+e+eF+r+ ++l  
  gi|313125482|ref|YP_004035746.1| 123 DALASLKRQYVEDEITEAEFERKLDRLVA 151
                                       579********************999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1033.97
//
Query:       gi|313125483|ref|YP_004035747.1|  [L=360]
Description: deacetylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-31  109.1   0.0    2.8e-31  108.8   0.0    1.1  1  DUF2334          Uncharacterized protein conserved in bacteri
      4e-05   23.5   0.0    0.00036   20.4   0.0    2.1  2  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
       0.13   11.8   0.4        0.2   11.2   0.4    1.3  1  LIME1            Lck-interacting transmembrane adapter 1


Domain annotation for each model (and alignments):
>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.0   4.8e-35   2.8e-31       2     208 ..     100     322 ..      99     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 4.8e-35
                           DUF2334   2 alirleDvspgedleklkeiadyldkegipfsvavIPrykdpktgskvnlsenpefvevLkylqak...GgeialHG 75 
                                       a++r +D++p+ d+++++++ +++ +e++p++ avIP    +      ++s+++e++++L++l+++     e+alHG
  gi|313125483|ref|YP_004035747.1| 100 AVFRNDDIKPNPDPTTMQAVDRVFADENVPVTNAVIPFPGGE------PISSSKETCSYLRELRRDnptTFEFALHG 170
                                       789*************************************99......9***************87455789***** PP

                           DUF2334  76 YtHqygtvksevsgegfeflseseakeriekGieilkklg.ikpkgFeaPhyaaseetykalkky.fsiiyer...y 147
                                       YtH+ +t  + + +++f     ++++e+i+ G ++l+ +  ++p++F++P  +++++t++a++ + +++i+ +    
  gi|313125483|ref|YP_004035747.1| 171 YTHEKRT--EFYGASEFGSVPSETQQEWITVGTRELTVCTgVRPTTFVPPMNTYDKNTTRAVAASnLTVISGGswfT 245
                                       ******8..8899999999*******************9758*********************888*****999954 PP

                           DUF2334 148 keykgq.....kegltyipenlgyvee.....dee....i.enaealkvrdglasffyHpyl..tysgrselkelle 207
                                       ++y+g+     +++++++ +++gyv++     + +    + ++ ++   ++g++++++H  +  t++ rs+l++ll+
  gi|313125483|ref|YP_004035747.1| 246 EPYYGErgvfrASNVVHVGNTTGYVANwttmeT-KsrsdLrADFDKAYAEGGTYAMMLHYPHfdTAERRSDLRALLR 321
                                       555533456789**************9987641.2556666666665566************************998 PP

                           DUF2334 208 e 208
                                       +
  gi|313125483|ref|YP_004035747.1| 322 Y 322
                                       6 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     6e-08   0.00036      18     120 ..     113     234 ..      92     238 .. 0.78
   2 ?    0.5   0.0     0.092   5.5e+02      59      86 ..     261     291 ..     252     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6e-08
                                       CSCHHHHHHHHHHCT--EEEEE-HHH......HCH-......HHHHHHHHHTTEEEEE--SS--EG.........GG CS
                   Polysacc_deac_1  18 rdntteilpvLkkykvkatffviggl......vedy......pdevremaasGveignHtinhsnl.........kr 73 
                                       +++++++  v+++++v+ t  vi+                    e+r+     +e++ H+++h++           +
  gi|313125483|ref|YP_004035747.1| 113 PTTMQAVDRVFADENVPVTNAVIPFPggepisS--SketcsyLRELRRDNPTTFEFALHGYTHEKRtefygasefGS 187
                                       567778888888888888888887553444440..1444444666666666679**********8778888888799 PP

                                       SHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHHHHHTT CS
                   Polysacc_deac_1  74 lseeevrreierakdalrkalgreprlfryPygsasatvlevarelg 120
                                       + +e++++ i   ++ l   +g +p++f +P   +++++ +++++ +
  gi|313125483|ref|YP_004035747.1| 188 VPSETQQEWITVGTRELTVCTGVRPTTFVPPMNTYDKNTTRAVAASN 234
                                       999999999999***************************88877655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.092
                                       EEEEE--...SS--EGGGSHHHHHHHHHHHH CS
                   Polysacc_deac_1  59 veignHt...inhsnlkrlseeevrreiera 86 
                                       v++gn t    n++ ++++s++++r+++++a
  gi|313125483|ref|YP_004035747.1| 261 VHVGNTTgyvANWTTMETKSRSDLRADFDKA 291
                                       7778888777899999**********99886 PP

>> LIME1  Lck-interacting transmembrane adapter 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   3.4e-05       0.2      93     144 ..      58     108 ..      45     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                             LIME1  93 rasPaaaspsigpeatYsnvgLaaiPraslaasplvvaEYaciqklkgteqg 144
                                        ++Paa+ + ++  at    + +++Pr s aa+   + EY  +  +++ + +
  gi|313125483|ref|YP_004035747.1|  58 TSPPAATPDATADAATQTPAAPTTTPRPSSAANT-TWKEYQLVAVFRNDDIK 108
                                       346789999999*****************99999.*****999877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2036.44
//
Query:       gi|313125484|ref|YP_004035748.1|  [L=360]
Description: deoxyhypusine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-94  315.1   0.0    4.9e-94  314.8   0.0    1.1  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.8   0.0   2.7e-98   4.9e-94       1     287 [.      41     351 ..      41     352 .. 0.96

  Alignments for each domain:
  == domain 1  score: 314.8 bits;  conditional E-value: 2.7e-98
                                DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       el  +y+k+g+ a++l++a+d++++m  ++++t ++gl+++++++G+r+i++dl++e+++d++vtT++++++D+i+a
  gi|313125484|ref|YP_004035748.1|  41 ELAGEYGKAGIGAANLQRAVDVYAEMIGRDDVTNLFGLAGAMVPAGMRQIVVDLIREGHIDALVTTGANLTHDAIEA 117
                                       57889************************************************************************ PP

                                DS  78 lgkktylg...................dfelddeeLrekginRignllvpnenyckfedwvre.ildkleeeqkvws 134
                                       +g k+++g                   + + +de+Lr+++++Ri+n+++p+e +  fe+++re ++ ++e+   + s
  gi|313125484|ref|YP_004035748.1| 118 IGGKHHHGraephdphptnedaeptgeTLRDHDEHLRDEQVDRIYNVYLPQEYFALFESHLREnVFPEIER---TVS 191
                                       *******9*****************9888999*****************************9978999987...58* PP

                                DS 135 pselikelG.........keindeeSilywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelnd 202
                                       ++e+++elG         + i+++ +i+++Ay++d+p++cpa++D++lG+q+++++   ++++++ld++ D+++l+d
  gi|313125484|ref|YP_004035748.1| 192 IREFTAELGranlernraEGIEEDAGIAAAAYEHDVPIYCPAIQDSVLGIQAWIYS---QTSEFTLDALTDMTHLSD 265
                                       *********988888888888899********************************...7899************** PP

                                DS 203 ialkakktgaiilGGGvpKhhilnanlm.rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaT 278
                                       +a++a+k+ga+++GGGvpK+++l+++l+  + +dy v++t++ +++G+lsgatldEa+Swgk++++ak+v+v++DaT
  gi|313125484|ref|YP_004035748.1| 266 LAFEAEKAGAMVVGGGVPKNYVLQTMLTiPDAYDYGVQLTMDPDHTGGLSGATLDEARSWGKLEKSAKNVTVVGDAT 342
                                       **************************665789********************************************* PP

                                DS 279 ivlPLlvaa 287
                                       i+lP+++aa
  gi|313125484|ref|YP_004035748.1| 343 ITLPFVAAA 351
                                       *****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2070.70
//
Query:       gi|313125485|ref|YP_004035749.1|  [L=256]
Description: hypothetical protein Hbor_07120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-54  185.0   0.0      2e-54  184.8   0.0    1.0  1  NIF3          NIF3 (NGG1p interacting factor 3)
    0.00097   18.6   0.4      0.011   15.2   0.1    2.5  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
     0.0082   16.7   0.8       0.63   10.6   0.2    2.3  2  Usp           Universal stress protein family
  ------ inclusion threshold ------
       0.01   16.1   0.4        0.3   11.4   0.2    2.5  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
      0.075   13.8   0.3       0.17   12.7   0.3    1.6  1  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.8   0.0   5.6e-58     2e-54       3     241 ..      10     243 ..       7     247 .. 0.93

  Alignments for each domain:
  == domain 1  score: 184.8 bits;  conditional E-value: 5.6e-58
                              NIF3   3 vevleelaplelae.swDnvGlqvgdpekevkkvllaldlteevleeAiekgadliithHPlifkplkrlteddykk 78 
                                       +++ e+la  ++a+ +   +Glqvg+ + +v++v++a+d+ e+++e A+e+gadl++thH+li+++l+r+t++  ++
  gi|313125485|ref|YP_004035749.1|  10 ARYDEKLATDAYADvDASANGLQVGSESGTVEHVAFAVDAAEATIEAAVEAGADLLVTHHGLIWGGLDRVTGQ--EY 84 
                                       45557778888888888999*****************************************************..99 PP

                              NIF3  79 rllkkliknnislysaHtnlDaapg.Gvndwlakalglekieplepskeekkeeeeglgrigeleepvsleelakkl 154
                                        +++ l++n+i ly  H++lD ++  G+++ +a++l+le  ep+++          ++g  g+ ++p s+e+l + l
  gi|313125485|ref|YP_004035749.1|  85 DRIAPLVENDIGLYVSHLPLDGHQSlGNAAGVADQLELEAREPFGEMG------PVHIGQRGQASQPYSVEKLREAL 155
                                       *********************************************987......799***************87777 PP

                              NIF3 155 kkkl.glekvrvagdldkkvkkvaicaGsGaslieeakakgaDlliTGelkhhealdakekgiavidvgHyatErvf 230
                                        +   g +  +v    + +++++ai++GsG ++++ea a gaD+l+TGe k + +++a+e+g++v+++gHyatE+++
  gi|313125485|ref|YP_004035749.1| 156 DEFDnGGTPTQVLDFGPDEISEIAIVTGSGVDWLSEAEAVGADALVTGEGKQQVYHEAREAGLNVFLAGHYATETFG 232
                                       7766344558888899************************************************************* PP

                              NIF3 231 lealaelLkek 241
                                       ++ la+l +e+
  gi|313125485|ref|YP_004035749.1| 233 VRNLAALAQEW 243
                                       ****9987765 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     3e-06     0.011      54     114 ..      36     156 ..      16     167 .. 0.68
   2 ?    0.5   0.0     0.096   3.5e+02      75     102 ..     188     214 ..     183     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-06
                                       STCTHCHTTCS..HHHHHHHHHHHHHHHHHHTBSEEEEEBCC................................... CS
                      AP_endonuc_2  54 gypdederear..reesvdalkraielaaaLGapllvlhpGt................................... 93 
                                       ++        +   +++vda++ +ie+a + Ga+llv+h G                                    
  gi|313125485|ref|YP_004035749.1|  36 ESGT------VehVAFAVDAAEATIEAAVEAGADLLVTHHGLiwggldrvtgqeydriaplvendiglyvshlpldg 106
                                       3322......1345666**********************77688887777777777777777777777777777777 PP

                                       .............................GBCTTTSGHHHHHHHHHHHHH CS
                      AP_endonuc_2  94 .............................agagpkgseeeawerlaesln 114
                                                                     g+++  s +  +e+l+e+l+
  gi|313125485|ref|YP_004035749.1| 107 hqslgnaagvadqlelearepfgemgpvhIGQRGQASQPYSVEKLREALD 156
                                       76666666666666666666666666655555555555555555555555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.096
                                       HHHHHHHHTBSEEEEEBCCGBCTTTSGH CS
                      AP_endonuc_2  75 aielaaaLGapllvlhpGtagagpkgse 102
                                       ++  a+a+Ga+ lv++ G   + + + +
  gi|313125485|ref|YP_004035749.1| 188 WLSEAEAVGADALVTGEGK-QQVYHEAR 214
                                       6667889999999998773.23333333 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2   0.00018      0.63      59     109 ..      21      67 ..       3      88 .. 0.71
   2 ?    4.8   0.0     0.011        38      70     113 ..     157     206 ..      97     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEE CS
                               Usp  59 leleeaeleadaakaaaeaggvkvevvveegdpaeeilevaeeedadliVv 109
                                       +++  a +    +  +   +  +ve+v    d+ae+ +e+a e +adl+V+
  gi|313125485|ref|YP_004035749.1|  21 YADVDASA----NGLQVGSESGTVEHVAFAVDAAEATIEAAVEAGADLLVT 67 
                                       33333333....3445778888999************************97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                                       H.......HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCC CS
                               Usp  70 a.......akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrg 113
                                       +       ++ +  + +++ e+ ++ g++ + +  +ae+ +ad +V+G  +
  gi|313125485|ref|YP_004035749.1| 157 EfdnggtpTQVLDFGPDEISEIAIVTGSGVDWL-SEAEAVGADALVTGEGK 206
                                       144555667777888899999999999999976.568999*******9776 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   8.4e-05       0.3      66      96 ..      37      67 ..      15      74 .. 0.87
   2 ?    1.9   0.0     0.075   2.7e+02       5      45 ..     146     184 ..     144     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.4e-05
                                      S-EEEEEEEEES-HHHHHHHHCTTTEEEEEE CS
                      Glyoxalase_4 66 geglhhlaywvddldaavarleeqGfevvqk 96
                                       + + h+a++vd  +a+++++ e+G+ ++  
  gi|313125485|ref|YP_004035749.1| 37 SGTVEHVAFAVDAAEATIEAAVEAGADLLVT 67
                                      56799********************998754 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.075
                                       EE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEE CS
                      Glyoxalase_4   5 ivVeDleaavarfsallGvgpwqryrdepqevdlafallgs 45 
                                       + Ve l +a+++f++  G +p+q   + p e++     +gs
  gi|313125485|ref|YP_004035749.1| 146 YSVEKLREALDEFDN--GGTPTQVLDFGPDEISEIAIVTGS 184
                                       668999999999999..999999999888877665555555 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   4.7e-05      0.17      60      88 ..      41      69 ..       8      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                      Glyoxalase_6 60 vHldlavedldaevarlvalGArvlrepr 88
                                       H+ +av+ ++a+++++v++GA  l +++
  gi|313125485|ref|YP_004035749.1| 41 EHVAFAVDAAEATIEAAVEAGADLLVTHH 69
                                      4*********************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1461.65
//
Query:       gi|313125486|ref|YP_004035750.1|  [L=282]
Description: agmatinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-54  185.7   0.2    1.5e-54  185.4   0.2    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.4   0.2   8.2e-59   1.5e-54       3     277 ..      14     263 ..      12     266 .. 0.91

  Alignments for each domain:
  == domain 1  score: 185.4 bits;  conditional E-value: 8.2e-59
                                       EEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHH CS
                          Arginase   3 vallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavae 78 
                                        +++G+P+d+++++rpG+rfGP+ ir+  + ++    y+ +++  ++++ ++d gd++    d +e +e+++ ++++
  gi|313125486|ref|YP_004035750.1|  14 YVVVGAPLDISTTFRPGTRFGPERIRRFARTFDD---YDRRTDLhFSDCCVHDEGDIHPWD-DAQEYVEWVAGTLRD 86 
                                       79**************************999997...6766666799**********8764.66669********** PP

                                       HHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEE CS
                          Arginase  79 ilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqi 155
                                       +  ++++p++lGG+H+++++ + a+          + +DAH+Dlr ++ +g+++sh+t+ rr++  + l +++ +++
  gi|313125486|ref|YP_004035750.1|  87 VRFDDAVPLLLGGEHTVTYAGVDAVEPD-----VFVCLDAHLDLRSEY-DGNEWSHATITRRVL--DTLGAEEAIIL 155
                                       ********************99999843.....5689***********.9**************..788999***** PP

                                       EE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HH CS
                          Arginase 156 GirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlr 232
                                       G r+ ++ee++ a+   ++v+  + + + +         +r++   + vylS+DiD+ Dpa+aPGtGtpep G+ +r
  gi|313125486|ref|YP_004035750.1| 156 GARTGSPEEWDRAEAEDVTVVAPEAVADFDF-------GDRLD--GRSVYLSVDIDGADPAFAPGTGTPEPFGMAPR 223
                                       *************999**********99876.......78884..479***************************** PP

                                       HHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 233 ellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                       e+++++r++a   n  g+DvvEvn+  d    q a+l+ +l+re+
  gi|313125486|ref|YP_004035750.1| 224 EMRDVVRTVAP--NADGFDVVEVNDRDDG---QAASLGGKLLREF 263
                                       *********77..89**********9443...789******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1769.23
//
Query:       gi|313125487|ref|YP_004035751.1|  [L=124]
Description: translation initiation factor 5a (eif-5a) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0063   16.5   0.0      0.014   15.4   0.0    1.6  2  EFP_N      Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
      0.039   14.1   0.2       0.07   13.2   0.2    1.5  1  eIF-5a     Eukaryotic elongation factor 5A hypusine, DNA-bind
       0.15   12.0   0.3         11    6.0   0.0    2.8  3  Gemini_C4  Geminivirus C4 protein


Domain annotation for each model (and alignments):
>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.4e-06     0.014       3      41 ..       9      48 ..       7      56 .. 0.83
   2 ?   -2.8   0.0       1.1   6.6e+03       6      16 ..      73      83 ..      71      90 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-06
                                      GG--TT-EEEETTEEEEEEEEEEEEETT.S--EEEEEEEE CS
                             EFP_N  3 selkkGlvieidgklyvVlefehvkpGk.Gqafvrvklkn 41
                                       el  G  +++d  ++++  +   kpGk G+a  r++ k 
  gi|313125487|ref|YP_004035751.1|  9 RELQEGSYVMMDESPCKINAYSTAKPGKhGSAKARIEGKG 48
                                      68999**********************6367777777765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                                      -TT-EEEETTE CS
                             EFP_N  6 kkGlvieidgk 16
                                      k G+v+ + g 
  gi|313125487|ref|YP_004035751.1| 73 KQGQVVSVTGS 83
                                      56666666554 PP

>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.2e-05      0.07       1      39 [.      69     107 ..      69     124 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                       --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG...GB- CS
                            eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklp.egelg 39 
                                       +++rk+ q++++++    ++md +++et+   ++p +++l 
  gi|313125487|ref|YP_004035751.1|  69 IIERKQGQVVSVTGS-DAQIMDlSTYETFT-MRIPeDEDLS 107
                                       599*********987.79************.****644553 PP

>> Gemini_C4  Geminivirus C4 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.031   1.8e+02      14      36 ..      20      40 ..      14      46 .. 0.78
   2 ?    6.0   0.0    0.0019        11       8      35 ..      48      79 ..      42      82 .. 0.79
   3 ?    0.8   0.0     0.075   4.5e+02      14      26 ..      81      93 ..      75      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.031
                         Gemini_C4 14 enssakikdsstWyPqPGqhisi 36
                                      ++s +ki+ +st   +PG+h s 
  gi|313125487|ref|YP_004035751.1| 20 DESPCKINAYSTA--KPGKHGSA 40
                                      567899*****95..78999876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0019
                         Gemini_C4  8 slfnskenssakikdsstWyP....qPGqhis 35
                                       +f+sk++s ++  d+  W P    + Gq +s
  gi|313125487|ref|YP_004035751.1| 48 GVFDSKKRSLSQPVDAKVWVPiierKQGQVVS 79
                                      58*****************9944444566665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.075
                         Gemini_C4 14 enssakikdsstW 26
                                      + s a+i d st+
  gi|313125487|ref|YP_004035751.1| 81 TGSDAQIMDLSTY 93
                                      5689*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 737.83
//
Query:       gi|313125488|ref|YP_004035752.1|  [L=196]
Description: hypothetical protein Hbor_07150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.096   12.9   0.7       0.18   12.0   0.2    1.7  2  PEP-utilisers_N  PEP-utilising enzyme, N-terminal


Domain annotation for each model (and alignments):
>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.26   4.6e+03      31      48 ..      17      34 ..      11      51 .. 0.65
   2 ?   12.0   0.2   9.9e-06      0.18      27      68 ..     108     158 ..      81     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.26
                                      HHHHHHHHHHHHHHHHHH CS
                   PEP-utilisers_N 31 aelerleeAlekvreele 48
                                      +  +r ++A+ +v  +l+
  gi|313125488|ref|YP_004035752.1| 17 DTTARTDAAVSTVVYRLR 34
                                      556777777777776664 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.9e-06
                                       GGHHHHHHHHHHHHHHHHHHHHHHHHHH.........T-HHHHHHHHHHHH CS
                   PEP-utilisers_N  27 edveaelerleeAlekvreelealaeka.........lgeeeaaifeahlm 68 
                                          e+e++rl++A++  r++l++++++             e+aa ++ahl 
  gi|313125488|ref|YP_004035752.1| 108 PADEDEQQRLDDAIQSIRNRLQTAEDDGnpghhgrmvCPGESAAELRAHLD 158
                                       33589******************9877766554444422233666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1210.19
//
Query:       gi|313125489|ref|YP_004035753.1|  [L=117]
Description: hypothetical protein Hbor_07160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-06   27.3  10.9    4.1e-06   26.9  10.9    1.2  1  DUF5518   Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9  10.9   2.3e-10   4.1e-06      26      96 ..       1      85 [.       1      93 [. 0.63

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.3e-10
                           DUF5518 26 gsllgllvgGlvaGylaggdskdgavaGalaGligaipv...lvlllvlll...........glvaaigglagfvallv 90
                                      ++l+g+l g++ aGyl+g d  dga++G+l++l  +i++   lv l+v++            +l++++g++++ v+l+v
  gi|313125489|ref|YP_004035753.1|  1 MTLVGGLAGSAFAGYLVGPDPADGAWHGLLSALTWGIVLipgLVALAVVGGgtlpfpfeylaPLFDTPGEATTGVLLAV 79
                                      57899****************************9888876534444444446666555544444444444444444444 PP

                           DUF5518 91 alllvv 96
                                      +l  v+
  gi|313125489|ref|YP_004035753.1| 80 TLPNVA 85
                                      333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 727.16
//
Query:       gi|313125490|ref|YP_004035754.1|  [L=559]
Description: protein kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-28   97.9   0.0    2.3e-27   95.5   0.0    2.1  2  ABC1      ABC1 family
    0.00059   19.8   0.2      0.029   14.3   0.2    2.5  2  APH       Phosphotransferase enzyme family
    0.00084   18.8   0.0     0.0019   17.6   0.0    1.5  1  Pkinase   Protein kinase domain
  ------ inclusion threshold ------
       0.12   11.6   0.2       0.18   11.0   0.2    1.2  1  LtrA      Bacterial low temperature requirement A protein (Lt


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   5.2e-31   2.3e-27       3     118 ..     111     225 ..     108     226 .. 0.96
   2 ?   -0.6   0.0      0.31   1.4e+03      74      97 ..     396     419 ..     364     448 .. 0.71

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 5.2e-31
                              ABC1   3 lgkkleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkflkelr.ldlee 78 
                                       lg +++e+F++fd+ Pi  AS++qV++A+  +g++VavKv+rpg+++ +++Dl+++++ +  + +f+ + r  +le+
  gi|313125490|ref|YP_004035754.1| 111 LG-PVDEVFESFDNDPISGASLGQVYTAQY-DGDDVAVKVRRPGIESLVEADLRVIRWSLPFIMRFIGQGRaFSLEN 185
                                       44.99***********************96.8**********************************9999989**** PP

                              ABC1  79 lvdefskslleEldferEAknaekfrenfaklkevkvPkv 118
                                       l+def+k++++E+d++rE +  e++++nf+   ++++Pk 
  gi|313125490|ref|YP_004035754.1| 186 LADEFAKTIRQEMDYSRERRILEQIQSNFNGNGTIRIPKP 225
                                       **************************************96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.31
                              ABC1  74 ldleelvdefskslleEldferEA 97 
                                       l++ ++v+ +  +l +E df   A
  gi|313125490|ref|YP_004035754.1| 396 LRVATVVEGVCVTLDQEFDFISVA 419
                                       347777777888888888876544 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.026   1.2e+02      37      86 ..     200     253 ..     169     272 .. 0.70
   2 !   14.3   0.2   6.5e-06     0.029     167     201 ..     277     309 ..     257     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHTT-......B--B-CTTBS-EEETTEEEEEEE----EE-SS....HH CS
                               APH  37 irrevallrlLakagv......pvPevlagdtddeeigllfalieyvpgrsllr....kl 86 
                                        +re ++l +++ + +      ++P+++      e +g +++ +ey+pg+ + +     +
  gi|313125490|ref|YP_004035754.1| 200 YSRERRILEQIQSN-FngngtiRIPKPVE-----ERSGPRVLTMEYLPGTKINDletiDM 253
                                       45666666444433.22344478999999.....99999***********9999664433 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.5e-06
                                       EEE-SS-SGGGEEEC..TTEEEEE---TT-EEEEC CS
                               APH 167 vllHgDlhpgNllvdpddgrvtGviDfedaglgpp 201
                                       ++ H D+hpgNl vd ++gr+  + Df+++g  +p
  gi|313125490|ref|YP_004035754.1| 277 GVFHADPHPGNLAVD-EEGRI-IFYDFGMSGRVDP 309
                                       678************.77887.688***9987776 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.2e-07    0.0019      43     149 ..     198     308 ..     177     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHHHHHHS....CTTB--EEEEEEE.SSEEEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHHHHHHHH CS
                           Pkinase  43 kkvlrEikilkklk....hpnivrlyevfee.kdelylvleyveggeladlle.rkgslseeeakkiakqilegley 113
                                        ++ rE +il++++     +  +r+ + +ee +  ++l +ey++g++++dl + +   ++ +e+   +++i   l+ 
  gi|313125490|ref|YP_004035754.1| 198 MDYSRERRILEQIQsnfnGNGTIRIPKPVEErSGPRVLTMEYLPGTKINDLETiDMEGIDRTELATRLQRIY--LQM 272
                                       4566777777766643335567888777766467799**************995444599999999999987..899 PP

                                       HHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESS CS
                           Pkinase 114 lHskgiiHrDlKpeNiLidekgelKitDFGlakele 149
                                       + + g++H D  p N+ +de+g +   DFG++ +++
  gi|313125490|ref|YP_004035754.1| 273 IIDDGVFHADPHPGNLAVDEEGRIIFYDFGMSGRVD 308
                                       *******************************98876 PP

>> LtrA  Bacterial low temperature requirement A protein (LtrA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2     4e-05      0.18      64     121 ..     487     544 ..     480     554 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4e-05
                              LtrA  64 vrllllvqmaavlvlalsipeafeerglvfalayvvmrlvlvlqylraaradpklsar 121
                                        r ++   ++av vl+++i +af+++++v a+  +++ l +++q +r++r+++ l++ 
  gi|313125490|ref|YP_004035754.1| 487 ARRIVYGLLLAVGVLSTAILYAFDQTSVVPAAVAAALTLPIIIQLYRSFRKKRGLKTT 544
                                       45667778999**************************************999887633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3467.06
//
Query:       gi|313125491|ref|YP_004035755.1|  [L=123]
Description: molecular chaperone [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-12   48.0   0.0    1.2e-12   47.8   0.0    1.0  1  HSP20       Hsp20/alpha crystallin family
    2.9e-06   26.7   0.1    6.2e-06   25.7   0.1    1.6  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0091   16.1   0.6      0.026   14.6   0.3    1.7  2  GvpH        GvpH
  ------ inclusion threshold ------
       0.14   11.4   0.0       0.19   11.0   0.0    1.1  1  CNF1        Rho-activating domain of cytotoxic necrotizing fa


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   2.7e-16   1.2e-12       2     101 ..      19     115 ..      18     116 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.7e-16
                                       --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEET CS
                             HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkd 78 
                                         e+++++ + ld+pg+ ++ ++v ve++r+++++ ++++   e  +++e +s   + ++ LP ++     +++++ 
  gi|313125491|ref|YP_004035755.1|  19 LLESDDAYLLVLDLPGVTPDTVEVRVEKGRLVIEARRDKQLPPEFRYVREDRSLFLDAEIPLPPDATGAGADSEIDR 95 
                                       6789**********************************9999999999999999999******************** PP

                                       TEEEEEEEBSS--..-------- CS
                             HSP20  79 GvLtvtvpkkepekkkkerkiqi 101
                                       GvLt+ +pk+ ++    er+i++
  gi|313125491|ref|YP_004035755.1|  96 GVLTIRLPKRDAA---PERTIPV 115
                                       *********9998...7899998 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   1.4e-09   6.2e-06       1      63 []      23     102 ..      23     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.4e-09
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig............nfrRq......itLPsvlarkevtsAkfedgvL 59 
                                       dd y l+ldLP+v+++ ++++ +   L+I++             ++ R+      i+LP    +  + + ++  gvL
  gi|313125491|ref|YP_004035755.1|  23 DDAYLLVLDLPGVTPDTVEVRVEKGRLVIEARrdkqlppefryvREDRSlfldaeIPLPPDATGAGA-DSEIDRGVL 98 
                                       799*****************************99999998866644444777777999998888866.888889999 PP

                        ArsA_HSP20  60 eIrF 63 
                                       +Ir+
  gi|313125491|ref|YP_004035755.1|  99 TIRL 102
                                       9886 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   5.7e-06     0.026      99     130 ..      22      51 ..      13      59 .. 0.81
   2 ?   -0.6   0.0      0.27   1.2e+03     107     132 ..      76     102 ..      62     113 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-06
                              GvpH  99 dsdelvvvadlpGvtdedvdvaletdeqaltl 130
                                       + d  ++v dlpGvt ++v+v +e  ++ l +
  gi|313125491|ref|YP_004035755.1|  22 SDDAYLLVLDLPGVTPDTVEVRVE--KGRLVI 51 
                                       56778999***************9..555555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                              GvpH 107 adlpGvtded.vdvaletdeqaltlrv 132
                                       a++p   d +   +  e d + lt+r+
  gi|313125491|ref|YP_004035755.1|  76 AEIPLPPDATgAGADSEIDRGVLTIRL 102
                                       555555555545555666777777765 PP

>> CNF1  Rho-activating domain of cytotoxic necrotizing factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.2e-05      0.19      15      53 ..      42      78 ..      38      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.2e-05
                              CNF1 15 isvLrgrgaiGgkrdvkLPskltidfvriDkdllmdaae 53
                                      + v +gr +i  +rd +LP++    +vr D+ l +da  
  gi|313125491|ref|YP_004035755.1| 42 VRVEKGRLVIEARRDKQLPPEFR--YVREDRSLFLDAEI 78
                                      67889***************975..6******9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 767.76
//
Query:       gi|313125492|ref|YP_004035756.1|  [L=425]
Description: molybdopterin molybdochelatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-39  135.9   3.5    1.6e-39  135.2   3.5    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    2.6e-26   92.0   0.1    4.1e-26   91.4   0.1    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain
    3.2e-18   65.6   0.4    1.9e-17   63.2   0.1    2.6  2  MoeA_C         MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.2   3.5   2.7e-43   1.6e-39       3     157 .]      18     180 ..      16     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 2.7e-43
                                       HHHHHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--.............. CS
                            MoeA_N   3 veealaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep.......sa 70 
                                       +++a++++laa+ + +++  +pl  +  gr lae v+A+ +vP++d++amDG+Avrae++ gas ++p       s+
  gi|313125492|ref|YP_004035756.1|  18 LADARETLLAAAtPHQRTDtLPL-GRVDGRSLAEAVTAANPVPNYDRAAMDGWAVRAEDTFGASDRSPsilrvavSE 93 
                                       68999999999966677777***.8889***********************************************88 PP

                                       ....-S---TT-.EEEE-TTSB--TT--EEEEGGGE.E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB- CS
                            MoeA_N  71 ageeperllpgg.avrimTGaplPegadaVvpvEdteeeeaketvev.kavkpgenvrraGedikaGevllragtrl 145
                                       a++++++ +++g avr++TG+ lP+gadaVv+vE+++   + ++ ev +av++genv  aGed+++G+ l+  g+ l
  gi|313125492|ref|YP_004035756.1|  94 AESDADAAVEPGsAVRVHTGSELPPGADAVVMVEHAD--VVGSELEVfDAVTEGENVGDAGEDVAEGQELFDIGHEL 168
                                       8888888888888**********************94..33444444799*************************** PP

                                       -CCCHHHHHHCT CS
                            MoeA_N 146 tpaeigllasvG 157
                                       +p+++gll svG
  gi|313125492|ref|YP_004035756.1| 169 RPSDLGLLKSVG 180
                                       **********98 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.1   6.8e-30   4.1e-26       1     144 []     193     327 ..     193     327 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 6.8e-30
                                       EEEEE-HHHH.....TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT- CS
                     MoCF_biosynth   1 avitvGdell.....sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdD 72 
                                       +vi +G el+     +g+++ tng ++++l+++ g  +  + vv Dd++++++a+ + l + dv++ttGG +++++D
  gi|313125492|ref|YP_004035756.1| 193 GVIPTGEELVqsdpePGEVVETNGLTVSRLVHRWGGVATYRNVVTDDPAALRAAVQRDLTK-DVVVTTGGSSVGERD 268
                                       6999***************************************************888677.*************** PP

                                       -HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHHH CS
                     MoCF_biosynth  73 vtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpaleh 144
                                       + pe++ +l+e       +++++v+lkpg+pv ++ +   +++   ++++LPG+p+a+ + +  +l+p l+h
  gi|313125492|ref|YP_004035756.1| 269 LIPEVVDELGE-------VLVHGVALKPGHPVALGVV---EDT---PVVMLPGYPVACIVNAVQFLRPLLKH 327
                                       ***********.......8************999999...665...7**********************998 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.65   3.9e+03       7       7 ..      76      76 ..      47     108 .. 0.56
   2 !   63.2   0.1   3.1e-21   1.9e-17       2      70 ..     341     419 ..     340     421 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.65
                                      - CS
                            MoeA_C  7 d 7 
                                       
  gi|313125492|ref|YP_004035756.1| 76 T 76
                                      1 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 3.1e-21
                                       EEESS-EE--SSS-EEEEEEEE..S-S.........-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EE CS
                            MoeA_C   2 arlaedlksdpgrreflRvilt..eed.........geyvaeptgkqgSglLsslaeAnglivipegtegleaGeeV 67 
                                       arl ++++s+pg r+f Rv+l+  + d          e +aept+++gSg+Lss a A+g++ +pe+teg+++Ge+V
  gi|313125492|ref|YP_004035756.1| 341 ARLERKIPSEPGVRTFARVRLReeN-DegdnggndpVERIAEPTRTSGSGVLSSVALADGWVAVPEETEGYAKGETV 416
                                       89********************753.1468888887677************************************** PP

                                       EEE CS
                            MoeA_C  68 evi 70 
                                        v+
  gi|313125492|ref|YP_004035756.1| 417 TVE 419
                                       996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2664.03
//
Query:       gi|313125493|ref|YP_004035757.1|  [L=647]
Description: molybdopterin molybdochelatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-39  133.6   6.0    1.1e-38  132.4   6.0    1.6  1  MoeA_N         MoeA N-terminal region (domain I and II)
    9.9e-25   86.9   0.0    1.8e-24   86.1   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
    5.9e-24   84.2   0.0    5.2e-23   81.2   0.0    2.3  1  PBP_like       PBP superfamily domain
    6.1e-14   52.0   0.8    1.6e-13   50.6   0.1    2.1  2  MoeA_C         MoeA C-terminal region (domain IV)
     0.0014   18.5   0.1     0.0029   17.4   0.1    1.6  1  SBP_bac_11     Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.098   12.7   0.1       0.28   11.3   0.0    1.7  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   6.0   3.8e-42   1.1e-38       8     157 .]      20     177 ..      13     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 3.8e-42
                                       HHHHHH-HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...................- CS
                            MoeA_N   8 aiilaaleleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........saageep 75 
                                       ++i+ +  ++e+e vpl +e+ grvlae + A++dvP+fd++ mDGYAvra+++ ga+e +p        ++ag ep
  gi|313125493|ref|YP_004035757.1|  20 EAIAGLDLTPETErVPL-RESRGRVLAERIDAEMDVPGFDRASMDGYAVRARDTFGADEASPaeleligeVHAGVEP 95 
                                       33333323367777***.9999************************************************9999999 PP

                                       S---TT-.EEEE-TTSB--TT--EEEEGGGE.E....EETTES--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHH CS
                            MoeA_N  76 erllpgg.avrimTGaplPegadaVvpvEdteeeeaketvevkavkpgenvrraGedikaGevllragtrltpaeig 151
                                       + ++ +g a++i TGa++P+gadaVv vE+te e+  + v ++av+pg+ v  aG d++aG+ +l  gt ltp+eig
  gi|313125493|ref|YP_004035757.1|  96 DVVVGEGeAAEISTGAVMPDGADAVVIVERTE-ERDGTLVVRDAVAPGDSVMLAGADVAAGARALGPGTYLTPREIG 171
                                       99999999***********************5.33333333389********************************* PP

                                       HHHHCT CS
                            MoeA_N 152 llasvG 157
                                       ll ++G
  gi|313125493|ref|YP_004035757.1| 172 LLSALG 177
                                       ***998 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.0     6e-28   1.8e-24       1     143 [.     190     346 ..     190     347 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 6e-28
                                       EEEEE-HHHH.........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SS CS
                     MoCF_biosynth   1 avitvGdell.........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGp 68 
                                       ++i++Gdel+         +g+i+D n++++a  ++e+g ev+ y + +Dd+ee+++ l +a+ee d+++++G t++
  gi|313125493|ref|YP_004035757.1| 190 GIISTGDELVrpgdplnsdAGQIYDVNSYTIATGVEEAGGEVRMYPHAGDDYEEMERILVQAAEECDLVLSSGSTSA 266
                                       69*********************************************************9998999*********** PP

                                       STT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE..........TTE..EEEE-SSHHHHHHH CS
                     MoCF_biosynth  69 tpdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav..........gkt..iigLPGspkavkea 133
                                       ++ Dv ++++++ +e        ++++v+ kpgkp++v+++   ++a           +++   +gLPG+p+++ ++
  gi|313125493|ref|YP_004035757.1| 267 SAVDVIYRVIEERGE-------LLLHGVAVKPGKPMLVGTLGGERGAKsenkgdtaatDSPsaYVGLPGYPVSALTI 336
                                       ***************.......8**************9999666555599999**9994445599************ PP

                                       HHHHHHGGHH CS
                     MoCF_biosynth 134 leeillpale 143
                                       +++++ pa++
  gi|313125493|ref|YP_004035757.1| 337 FQTFVAPAIR 346
                                       ******9997 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.0   1.7e-26   5.2e-23      15     192 ..     462     632 ..     459     633 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 1.7e-26
                                       EEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC-S CS
                          PBP_like  15 vanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdlad 91 
                                       +  vGs +Gl++lr+g  d+a +  + ++t       ++        v + +++re gl+v +gnp ++++++dl+ 
  gi|313125493|ref|YP_004035757.1| 462 YLPVGSREGLRRLRDGVPDVAVVAGPTERT-------VE-------SVDIGGWTREWGLIVPAGNPDDVSGLSDLVA 524
                                       678999999999999999999999999855.......22.......36689************************** PP

                                       -B-EEEEE-TTSHHHHHHHHHHC-CEECT........E-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCC CS
                          PBP_like  92 aplrlvnRetGSGtrdlfdellkkegisk........ssikgyaqearshlavaaaVaagradvgvgieavaeelkg 160
                                       ++lr+vnR+t +G r  +d +l +  +++        ++i g + + +   + a+aV +g+ad+g+g++a+a+el +
  gi|313125493|ref|YP_004035757.1| 525 RDLRFVNRDTNAGLRASLDAALDELAAERdtskreltARIDGFELTTKATESPARAVLRGKADAGLGLRATANEL-D 600
                                       **********************99988889999*****************************************8.* PP

                                       CECTTCE-EEEEEEEECTCCCSHHHHHHHHHH CS
                          PBP_like 161 ldfvplaeerydlvvrkealddpevqaflefl 192
                                        +f+ + +e+  +  + ++ ++p v+a+ ++l
  gi|313125493|ref|YP_004035757.1| 601 MGFIRVGDESVRVHANPDRTEKPSVEAITALL 632
                                       **************************998876 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       3.3   9.9e+03      48      60 ..     117     129 ..     116     145 .. 0.65
   2 !   50.6   0.1   5.4e-17   1.6e-13       7      72 .]     366     431 ..     361     431 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.3
                                       --EEEEE-TT--E CS
                            MoeA_C  48 Anglivipegteg 60 
                                       A++ +++++ +e+
  gi|313125493|ref|YP_004035757.1| 117 ADAVVIVERTEER 129
                                       8888888888874 PP

  == domain 2  score: 50.6 bits;  conditional E-value: 5.4e-17
                                       -EE--SSS-EEEEEEEE.S-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   7 dlksdpgrreflRvilt.eedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       + + ++gr ++++v l  +e+ge  ++p+  +gSg+++sl+eA+g +++ ++te+l+ Ge+Vev l+
  gi|313125493|ref|YP_004035757.1| 366 RERYAEGRLRLMPVGLLeNESGETLVYPV-DKGSGATTSLVEADGVVEVHPDTEYLADGESVEVRLF 431
                                       5566899*******9999***********.**********************************986 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   9.8e-07    0.0029      79     170 ..     502     597 ..     464     633 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.8e-07
                                       EEEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.H.HHHG..GG--HHHHHHHHHTEEEEESSH...HH CS
                        SBP_bac_11  79 splviavpkgnpkkikgwadLlkpglklavadPttspsGlaal.alle..aagaqellkalekkvvklgess...rq 149
                                           ++vp+gnp++++g+ dL + +l+++  d  t+++ +a l a+l+  aa+++ + ++l  ++ +++ ++   ++
  gi|313125493|ref|YP_004035757.1| 502 REWGLIVPAGNPDDVSGLSDLVARDLRFVNRD--TNAGLRASLdAALDelAAERDTSKRELTARIDGFELTTkatES 576
                                       567899*******************9998777..6666665554555566668888888888888877544444366 PP

                                       HHHHHHTTT-SEEEEEHHHHH CS
                        SBP_bac_11 150 lltaveageadagivyeseak 170
                                        + av +g+adag++ +  a+
  gi|313125493|ref|YP_004035757.1| 577 PARAVLRGKADAGLGLRATAN 597
                                       7777**********9999886 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.3e-05      0.28      16      52 ..      97     133 ..      93     140 .. 0.92
   2 ?   -3.4   0.0       3.1   9.3e+03      70      86 ..     249     265 ..     241     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.3e-05
                                       EEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHH CS
                      Shikimate_DH  16 lliGaGemaelvakhLlakgvkkvvvaNRtlerakel 52 
                                       +++G Ge ae  + + +  g+++vv++ Rt er  +l
  gi|313125493|ref|YP_004035757.1|  97 VVVGEGEAAEISTGAVMPDGADAVVIVERTEERDGTL 133
                                       69******************************97776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.1
                                       HHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  70 kellaeadvvisatase 86 
                                        ++ +e+d+v+s+ +++
  gi|313125493|ref|YP_004035757.1| 249 VQAAEECDLVLSSGSTS 265
                                       56789999999987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3893.74
//
Query:       gi|313125494|ref|YP_004035758.1|  [L=253]
Description: response regulator with chey-like receiver, aaa-type ATPase, and DNA-binding domains [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-16   59.8   0.8    7.3e-16   58.2   0.0    2.2  3  HalOD1        Halobacterial output domain 1
    9.3e-10   38.7   0.0    1.9e-09   37.7   0.0    1.5  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.37   3.3e+03      29      42 ..      90     103 ..      89     118 .. 0.66
   2 ?   -2.4   0.0      0.68   6.1e+03      22      22 ..     129     129 ..     108     156 .. 0.56
   3 !   58.2   0.0   8.1e-20   7.3e-16       2      75 .]     173     246 ..     172     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.37
                            HalOD1  29 daiDpdALdaLfas 42 
                                       d++  dAL+a +++
  gi|313125494|ref|YP_004035758.1|  90 DTVALDALEARVSE 103
                                       56666777665554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.68
                            HalOD1  22 t 22 
                                       t
  gi|313125494|ref|YP_004035758.1| 129 T 129
                                       2 PP

  == domain 3  score: 58.2 bits;  conditional E-value: 8.1e-20
                            HalOD1   2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75 
                                       ++++ t+++++  a++g d  e epL+++ D dALd+L+++ra+++ r d++v+F ye+ e  V sdg i V+p
  gi|313125494|ref|YP_004035758.1| 173 DDELATTIAQVMEAYTGIDALEAEPLFSSLDMDALDSLLEPRASETPRYDIQVRFPYEEWELSVSSDGFISVRP 246
                                       57899*******************************************************************97 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   2.1e-13   1.9e-09       1     109 [.       7     115 ..       7     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.1e-13
                                       EEEESSSHHHHHHHHHHHH...HTTEEEEEEESSHHHHHHHHHHHHESEEEEE.SSCSSSEHHHHHHHHHHCTTTSE CS
                      Response_reg   1 vlivdDdplvrellrqlle...eegyeevaeaedgkealellkeekvdlillD.inmpgmdGlellkeireedpelp 73 
                                       vl vdDdp+++el +  ++   ++++ e  +a+d+ + l+ l++++vd+++ D +++p+ + +  +   r+++p++p
  gi|313125494|ref|YP_004035758.1|   7 VLHVDDDPDLLELSAFSFDqaaSDEL-EMVTASDAVAGLDTLESQSVDCLVSDsLRLPDDTPF--IVAARQREPSIP 80 
                                       789****************6555566.6779**********************7799999765..5555788899** PP

                                       EEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHH CS
                      Response_reg  74 viiltahseeedavealkagaddflsKpfdpeeLlk 109
                                       ++++ta++ +++a +al+a +++++ K  d+ ++ +
  gi|313125494|ref|YP_004035758.1|  81 IVFYTAKGWDTVALDALEARVSEYIRKG-DEGDIAA 115
                                       ***************************8.7666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1581.49
//
Query:       gi|313125495|ref|YP_004035759.1|  [L=227]
Description: phosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-16   58.4   0.0    1.6e-15   57.7   0.0    1.4  1  HAD_2           Haloacid dehalogenase-like hydrolase
    4.5e-07   30.4   2.2    7.4e-07   29.7   2.2    1.3  1  HAD             haloacid dehalogenase-like hydrolase
    8.9e-07   29.4   0.0    5.7e-05   23.5   0.0    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.048   13.7   0.0       0.13   12.3   0.0    1.7  1  Hydrolase_like  HAD-hyrolase-like
       0.16   11.7   0.0        3.7    7.3   0.0    2.0  2  NIF             NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   4.4e-19   1.6e-15       2     177 ..      10     188 ..       9     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 4.4e-19
                             HAD_2   2 iFDlDgTlldte.eliiqafnelleeygls..elseeelrkliglslrellrklgeseeeeekieellrkyneekkk 75 
                                       +FDlDgTl+d    +  ++f ++ ++ g +  + + e + + +g   +  lr   ++ +  + ++ + + +++ + +
  gi|313125495|ref|YP_004035759.1|  10 LFDLDGTLVDADwSYTREVFDRVGDRLGREftDREAEIIWHGLGGARDPQLRAWDIDPD--DFWPAF-HAVEDPQAR 83 
                                       8*********7527788999999999965322445555566677777777887777655..466666.888888888 PP

                             HAD_2  76 .kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklk 151
                                        + + + d++ +lL +L   +  +g+vT  ++  ++  +++l++ + Fd++v+ ++  + KPdpe+++ +++ l+l+
  gi|313125495|ref|YP_004035759.1|  84 aEATYLHDDATDLLADL-VDDRPVGVVTHCQQFLADPVIDHLDVRDWFDTVVCCTEELGWKPDPEPVHHTMKALGLD 159
                                       899**************.8899*****************************************************99 PP

                             HAD_2 152 ke...eviyvGDsptDieaakkagikvia 177
                                       ++   + +  GD ++Di aa +ag++ i 
  gi|313125495|ref|YP_004035759.1| 160 PNsdsQGVLAGDGSSDIGAAWNAGLDGIH 188
                                       863326899***************99775 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   2.2   2.1e-10   7.4e-07       2     187 ..      10     179 ..       9     179 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.1e-10
                               HAD   2 lfDfDgTLldgdsle..lllrfllrrgaprlwralreklllalfrellrldraglaellea....llagls.eelaa 71 
                                       lfD+DgTL+d d  +  + ++    r + rl+r+   +  +++ +++l   r+   ++++     ++ ++   e+ +
  gi|313125495|ref|YP_004035759.1|  10 LFDLDGTLVDADWSYtrEVFD----RVGDRLGREFTDREAEII-WHGLGGARDPQLRAWDIdpddFWPAFHaVEDPQ 81 
                                       7**********7555564444....444445555555555555.333333344444455442333333333333333 PP

                               HAD  72 elerfvaevirpklldpgalella.ahraaGdrvvvvSgglrplvepllaelg....adevlatelevddrltgelg 143
                                         +++        +l+ +a +lla        +v vv+ + ++l+ p+ ++l+    +d+v++           +++
  gi|313125495|ref|YP_004035759.1|  82 ARAEAT-------YLHDDATDLLAdL--VDDRPVGVVTHCQQFLADPVIDHLDvrdwFDTVVCC------TEELGWK 143
                                       333333.......6889*******33..4556*********************77777777666......5556688 PP

                               HAD 144 legkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                       +++ pv+   k+  l+       + +  +  v  GD+ sD+ ++
  gi|313125495|ref|YP_004035759.1| 144 PDPEPVHHTMKALGLDP------NSD--SQGVLAGDGSSDIGAA 179
                                       99999999566555555......222..224888******9875 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.6e-08   5.7e-05       5     210 .]      10     183 ..       6     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.6e-08
                                       EEESBTTTBCHH.HHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH..HHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   5 vfDkdGTLttge.psvedvivsaalalaaaletgsehpigkalvaaakarsgal..tgfatfigrgayaigkpewlt 78 
                                       +fD+dGTL++   +  ++v++++                g +l +++ +r+ ++  +g +      a     + w  
  gi|313125495|ref|YP_004035759.1|  10 LFDLDGTLVDADwSYTREVFDRV----------------GDRLGREFTDREAEIiwHGLGG-----ARDPQLRAWDI 65 
                                       69999999988888888888888................8888888888855554466666.....55555555555 PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                       +                ++   a++   +    + a+  ++ ++a +++a L +    v+++t  ++  a+ ++++l
  gi|313125495|ref|YP_004035759.1|  66 DP---------------DDFWPAFH--AVEDPQARAEATYLHDDATDLLADLVDDRP-VGVVTHCQQFLADPVIDHL 124
                                       55...............55555555..5555555556666999********997755.******************* PP

                                       T.GGGESEEEEHHCESSTTTSHHHHHHHHHHHT...STGGGEEEEESSHHHHHHHHHTT CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 156 G.ddyfdaviasdietvakpspegkvaaireLq...gkpeevamVGDgvnDaaalaaAg 210
                                       + +d fd v++ ++e   kp+pe ++++++ L+    + ++ +  GDg  D+ a+ +Ag
  gi|313125495|ref|YP_004035759.1| 125 DvRDWFDTVVCCTEELGWKPDPEPVHHTMKALGldpNSDSQGVLAGDGSSDIGAAWNAG 183
                                       ******99999999999****************7665688999**********998887 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.6e-05      0.13       4      49 ..     143     190 ..     142     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                                       TTSSHHHHHHHHHH---...GGGEEEEES-TTTHHHHHHHCT-EEEEES CS
                    Hydrolase_like   4 KPepemydfalevlgsd...peevlmiGDrlatDiagAnnaGwksvLVl 49 
                                       KP pe +   +++lg+d    ++ ++ GD   +Di +A naG++++ V 
  gi|313125495|ref|YP_004035759.1| 143 KPDPEPVHHTMKALGLDpnsDSQGVLAGDG-SSDIGAAWNAGLDGIHVE 190
                                       888888888999997774444568999***.***************996 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.036   1.3e+02       5      19 ..      11      25 ..      10      48 .. 0.70
   2 ?    7.3   0.0     0.001       3.7      41      80 ..      95     133 ..      87     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.036
                               NIF  5 LDLDetLvhskleks 19
                                      +DLD+tLv + ++ +
  gi|313125495|ref|YP_004035759.1| 11 FDLDGTLVDADWSYT 25
                                      7*******9988544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.001
                               NIF  41 efLkelsklyevvifTasseeyaeavidildpekkllshr 80 
                                       ++L  l+    v++ T +++  a++vid+ld   + ++ +
  gi|313125495|ref|YP_004035759.1|  95 DLLADLVDDRPVGVVTHCQQFLADPVIDHLDVRDW-FDTV 133
                                       567778888889*******************9876.6555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1400.71
//
Query:       gi|313125496|ref|YP_004035760.1|  [L=149]
Description: hypothetical protein Hbor_07230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 928.37
//
Query:       gi|313125497|ref|YP_004035761.1|  [L=124]
Description: hypothetical protein Hbor_07240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 857.41
//
Query:       gi|313125498|ref|YP_004035762.1|  [L=91]
Description: pterin-4-alpha-carbinolamine dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-26   91.4   0.0    3.5e-26   91.2   0.0    1.0  1  Pterin_4a        Pterin 4 alpha carbinolamine dehydratase
  ------ inclusion threshold ------
       0.18   11.3   0.0       0.23   10.9   0.0    1.1  1  Peptidase_S9     Prolyl oligopeptidase family
       0.31   11.3   0.0       0.31   11.3   0.0    1.8  2  Par3_HAL_N_term  N-terminal of Par3 and HAL proteins


Domain annotation for each model (and alignments):
>> Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.0   5.9e-30   3.5e-26       3      89 ..       5      88 ..       3      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 5.9e-30
                         Pterin_4a  3 lseeeiqkllaelpgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilvsynkvtvrltThdaggltenD 81
                                      l+++ei+++l + ++W++ +++e++++++f+d+  +i+fv++v+++aeee Hhp+i v y++v+vrlt+h+ gg+te+D
  gi|313125498|ref|YP_004035762.1|  5 LDDDEIESQL-P-DEWER-DGDEITKTYEFDDYLRGIEFVTKVGEVAEEEFHHPEIIVGYKTVEVRLTSHEEGGITEKD 80
                                      8999******.3.69**9.8889******************************************************** PP

                         Pterin_4a 82 fklAakid 89
                                      ++lA  +d
  gi|313125498|ref|YP_004035762.1| 81 IRLADLFD 88
                                      ****9887 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.9e-05      0.23      30      64 ..      16      50 ..      11      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.9e-05
                                      CHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GG CS
                      Peptidase_S9 30 eafhdagkrklgqnefdDfiaaaealakegyvdse 64
                                      ++++++g++ ++++efdD++ ++e+++k g v +e
  gi|313125498|ref|YP_004035762.1| 16 DEWERDGDEITKTYEFDDYLRGIEFVTKVGEVAEE 50
                                      69************************999876665 PP

>> Par3_HAL_N_term  N-terminal of Par3 and HAL proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5      0.47   2.8e+03      58      71 ..       4      17 ..       2      33 .. 0.59
   2 ?   11.3   0.0   5.2e-05      0.31      44      72 ..      62      90 ..      41      91 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.47
                   Par3_HAL_N_term 58 iLDpDDlladvvdD 71
                                      +LD+D++ +++ d+
  gi|313125498|ref|YP_004035762.1|  4 LLDDDEIESQLPDE 17
                                      67777776666553 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.2e-05
                   Par3_HAL_N_term 44 slvkvhsleskdggiLDpDDlladvvdDr 72
                                      ++v+v+  ++++ggi ++D +lad+ dD 
  gi|313125498|ref|YP_004035762.1| 62 KTVEVRLTSHEEGGITEKDIRLADLFDDE 90
                                      6799999999*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 640.92
//
Query:       gi|313125499|ref|YP_004035763.1|  [L=451]
Description: glutamyl-tRNA reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-33  115.9   0.1    2.7e-33  115.0   0.1    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.7e-33  115.4   0.2    3.6e-33  114.4   0.2    1.5  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    1.8e-19   70.0   1.3    3.9e-19   68.9   1.3    1.6  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
      1e-07   31.6   0.4      1e-07   31.6   0.4    2.3  3  Glu_dehyd_C      Glucose dehydrogenase C-terminus
    9.2e-06   26.2   0.3    2.9e-05   24.6   0.3    1.9  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00038   20.7   2.2    0.00092   19.5   0.1    2.6  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00046   20.6   0.1     0.0017   18.8   0.1    1.9  1  NAD_binding_7    Putative NAD(P)-binding
    0.00084   19.5   0.0     0.0022   18.2   0.0    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0032   16.9   1.3     0.0081   15.5   0.7    1.9  2  ThiF             ThiF family
     0.0038   16.6   0.0     0.0071   15.7   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.028   13.7   0.3       0.05   12.8   0.3    1.4  1  UPF0052          Uncharacterised protein family UPF0052
      0.051   13.8   0.7       0.31   11.3   0.7    2.4  1  TrkA_N           TrkA-N domain
      0.086   12.1   0.3        1.1    8.5   0.3    2.4  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      0.093   12.6   1.7       0.65    9.9   0.1    2.5  3  KR               KR domain
        0.1   12.7   0.3       0.32   11.0   0.3    1.7  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
       0.14   11.8   0.2       0.31   10.7   0.2    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.19   12.0   0.0       0.32   11.3   0.0    1.3  1  zf-C4H2          Zinc finger-containing protein
        1.1    9.1   4.8       0.85    9.5   0.2    2.7  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0   0.1   2.7e-36   2.7e-33       2     138 .]     167     296 ..     166     296 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 2.7e-36
                                       HHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SE CS
                      Shikimate_DH   2 lakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadv 78 
                                       lak+++ +l+++++l+iGaGem++l+a+ L+a+g+ ++vvaNRtl +a+++aee+ ++ ++al+l+ +++++++adv
  gi|313125499|ref|YP_004035763.1| 167 LAKSET-TLDGATALVIGAGEMGTLAAESLAAAGIGELVVANRTLPHAEHVAEEV-DVPARALPLSAVEAAIEAADV 241
                                       677777.59**********************************************.778****************** PP

                                       EEE-SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHHH CS
                      Shikimate_DH  79 visataseepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLkev 138
                                       visat+s+e++l++ +ve + +     + l+D+a+PRdv+p+v +l d+ ++++D L++v
  gi|313125499|ref|YP_004035763.1| 242 VISATGSPEYVLSSPHVETSGE-----TTLIDLAQPRDVDPAVDSLPDIVVHDMDGLEAV 296
                                       ******************8874.....59****************************986 PP

>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.2   3.6e-36   3.6e-33       2     146 .]      11     151 ..      10     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 3.6e-36
                           GlutR_N   2 ginhktapvelreklafseeelkellkel.ee.kvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelke 76 
                                        ++h +a+v+     + s+++++ ++++l ++ +v+ea+ L TCNR E y++++++++ +++l+++      +  + 
  gi|313125499|ref|YP_004035763.1|  11 RVSHDHATVDEVA--SASDDDVRTTVESLlTNeEVSEAFALHTCNRAEAYVVTDAQATGRRALTDFA----PDVRDG 81 
                                       6789998888776..667788888999987554999**************99998888888777777....555567 PP

                           GlutR_N  77 klyvlegeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                       ++  +++e+++rHl+rVa+GL+SlvlGEdqIlgQ+k+++e+a+ ag +g++L+  + kai+v+ r+rtet
  gi|313125499|ref|YP_004035763.1|  82 AVVEMDHEQSLRHLMRVAAGLESLVLGEDQILGQIKRSFEEARGAGGIGPMLDDAVTKAIHVGERARTET 151
                                       88999****************************************************************8 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   1.3   3.9e-22   3.9e-19       2      96 ..     311     410 ..     310     411 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 3.9e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S......--------TTHHHHHHHHHHHHHH CS
                       GlutR_dimer   2 AeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla....ldgedreelekltrslvnkllhept 74 
                                       +e++I++e+e++++ +k+++++ +I+ ++e aee++++ele al+kl+    l++++re++ +l+++lv +ll +pt
  gi|313125499|ref|YP_004035763.1| 311 VESMIDDEFERLLKSFKRKRADRAISGMYEAAEEVKQRELETALAKLDaqgeLTDDQRETVAALADALVGQLLSAPT 387
                                       89*************************************************************************** PP

                                       HHHHSS-TTTT.HHHHHHHHH.. CS
                       GlutR_dimer  75 arLkeaedeee.ellealrrlFn 96 
                                       ++L+ea+ e++ ++++++ +lF+
  gi|313125499|ref|YP_004035763.1| 388 KSLREAAVEDDwDTIQTAMTLFD 410
                                       ******5555569********97 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.74   7.4e+02     164     200 ..      12      48 ..       2      58 .. 0.83
   2 !   31.6   0.4   1.1e-10     1e-07      23     176 ..     168     313 ..     153     350 .. 0.79
   3 ?   -2.8   0.1       3.6   3.6e+03     175     211 ..     372     407 ..     364     408 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.74
                       Glu_dehyd_C 164 rrhfeaavdtLaalpeslldelvtkvvdldeleeAfe 200
                                       ++h +a+vd++a+++++ +++ v + ++ +e++eAf+
  gi|313125499|ref|YP_004035763.1|  12 VSHDHATVDEVASASDDDVRTTVESLLTNEEVSEAFA 48 
                                       5667788999999999999999999999999999997 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.1e-10
                       Glu_dehyd_C  23 srsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipease 99 
                                       ++s+ + + ++alv+GaG +G La+  l+a   g+ ++ v++ r  p+ +  + ee++   v  r  p++ + +a e
  gi|313125499|ref|YP_004035763.1| 168 AKSETTLDGATALVIGAGEMGTLAAESLAA--AGIGEL-VVANRTLPHAEH-VAEEVD---VPARALPLSAVEAAIE 237
                                       678889999*******************97..789866.677677777665.778877...678999********** PP

                       Glu_dehyd_C 100 emdlvvEaTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaa 176
                                         d+v+ aTGs++ ++ +  ++++ G ++L+ + ++++v+  +++l + +v + + l   +   r+  ++a++++++
  gi|313125499|ref|YP_004035763.1| 238 AADVVISATGSPEYVLSS-PHVETSGETTLIDLAQPRDVDPAVDSLPDIVVHDMDGLEAVTDETRELRREAAERVES 313
                                       **************9987.799**************99999999987665555444444444444444556665555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.6
                       Glu_dehyd_C 175 aalpeslldelvtkvvdldeleeAfedddetiKtvve 211
                                       aal + l+ +l++  +  +  e+A edd +ti t++ 
  gi|313125499|ref|YP_004035763.1| 372 AALADALVGQLLSAPT-KSLREAAVEDDWDTIQTAMT 407
                                       4444444444444322.23346677888889988875 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.3   2.9e-08   2.9e-05       4      70 ..     181     247 ..     179     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.9e-08
                                       EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..-EEECECHHHH.HHH-SEEEE-S- CS
                     F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..vkvtavdneea.aeeadvvvlavk 70 
                                       +iGaG+mg   a+ l+aag    e+vva +r+   ae+ aee+   +++ + ++ ea +e advv+ a  
  gi|313125499|ref|YP_004035763.1| 181 VIGAGEMGTLAAESLAAAG--IGELVVA-NRTLPHAEHVAEEVDvpARALPLSAVEAaIEAADVVISATG 247
                                       79*****************..8999988.**************966555555665550568899987764 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       2.1   2.1e+03      30      91 ..      23      89 ..      12     100 .. 0.65
   2 !   19.5   0.1   9.3e-07   0.00092       2      79 ..     180     248 ..     179     259 .. 0.88
   3 ?   -2.6   0.0       6.1   6.1e+03     109     123 ..     294     308 ..     262     325 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.1
                                      EESSHHHHHHHHCHH.....TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGHHHHHHHHHH CS
                   Sacchrp_dh_NADP 30 adrskeklealaaka.....lgvrfeaialdaenyeavLaallkegdlvvnlsppissldvlkaCie 91
                                      a+ s++ ++ +++++      ++ f  +++++++   v++a  +++ ++ + +p++ + +v+++ +e
  gi|313125499|ref|YP_004035763.1| 23 ASASDDDVRTTVESLltneeVSEAFALHTCNRAEAYVVTDAQATGRRALTDFAPDVRDGAVVEMDHE 89
                                      5555555555555555555555666666666666666667777777777777777777777776555 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 9.3e-07
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsp 78 
                                       l+iGaG +G  +ae la+ +    e++va r++ ++e++a    +v++ a+al  + +ea    +++ +d+v+++++
  gi|313125499|ref|YP_004035763.1| 180 LVIGAGEMGTLAAESLAAAGIG--ELVVANRTLPHAEHVA---EEVDVPARALPLSAVEA----AIEAADVVISATG 247
                                       89****************9855..***************9...57889999998888887....88899****9987 PP

                                       G CS
                   Sacchrp_dh_NADP  79 p 79 
                                       +
  gi|313125499|ref|YP_004035763.1| 248 S 248
                                       6 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.1
                                       HCCSHHHHHTHHHHH CS
                   Sacchrp_dh_NADP 109 yalreavlklkekak 123
                                        a+++++++l+++a+
  gi|313125499|ref|YP_004035763.1| 294 EAVTDETRELRREAA 308
                                       334455555555544 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.7e-06    0.0017       5      73 ..     174     250 ..     172     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapev...keeleelvklaeeel.....ekdlegadlviaatddre 73 
                                       l+g + lv+G+Ge+++  +++l++ag    vva+++   +e + e v++  + l     e+ +e ad+vi at  +e
  gi|313125499|ref|YP_004035763.1| 174 LDGATALVIGAGEMGTLAAESLAAAGIGELVVANRTlphAEHVAEEVDVPARALplsavEAAIEAADVVISATGSPE 250
                                       7899**********************999999999745433333556654444333333999***********9876 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.2e-06    0.0022       4      66 ..     181     249 ..     178     271 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-06
                                       EE--SHHHHHHHHHHHHTT-.EEEEE-SSHHHHHHHHHTT.....EEE-SSHHHHHHHCSEEEE-SSSH CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagy.kvavynrtkekveelvaeg.....akaaesieelvasldvvitmvkag 66 
                                       +iG G+MG+  a+ l++ag+ +++v nrt  ++e++++e      a +++ +e++++++dvvi    + 
  gi|313125499|ref|YP_004035763.1| 181 VIGAGEMGTLAAESLAAAGIgELVVANRTLPHAEHVAEEVdvparALPLSAVEAAIEAADVVISATGSP 249
                                       7*****************97589**************9988888899999999999999**99876555 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.7   8.1e-06    0.0081      15      48 ..     173     206 ..     160     208 .. 0.87
   2 ?   -1.9   0.0       1.8   1.8e+03      83     119 ..     215     248 ..     211     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.1e-06
                                       HHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  15 kLrdskvllvGaGglGsellknLalsGvgkltlv 48 
                                        L  ++ l++GaG  G  +++ La++G+g+l ++
  gi|313125499|ref|YP_004035763.1| 173 TLDGATALVIGAGEMGTLAAESLAAAGIGELVVA 206
                                       5777899***********************9985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                                       HT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  83 einpdveveavteritdetvleellesvDlVvdalDn 119
                                       +++ +v+v a   ++++   +e  +e +D+V+ a+ +
  gi|313125499|ref|YP_004035763.1| 215 HVAEEVDVPARALPLSA---VEAAIEAADVVISATGS 248
                                       55666777777777766...35789******999866 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.2e-06    0.0071      27      96 ..     167     243 ..     142     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.2e-06
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH......CHHHHTCEECSHHHHHHH-SEEE CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee......eeeelgvelvsleellaesDivs 96 
                                        a + ++l g t  +iG+G++G+ +a+ l+a g+ ++++ +r+  + e      ++ +  + l  +e++++ +D+v+
  gi|313125499|ref|YP_004035763.1| 167 LAKSETTLDGATALVIGAGEMGTLAAESLAAAGIgELVVANRTLPHAEhvaeevDVPARALPLSAVEAAIEAADVVI 243
                                       45667899***********************9998888888877655544422222222233446677777777776 PP

>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3     5e-05      0.05      50     186 ..      28     249 ..      16     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                                       HHHHHHHHHH--S-CHHHHHCH-B-SS...........SSSST.....................T-BHHHHHHHH.. CS
                           UPF0052  50 gDirnvlvalidderlleeLfqyRfkg...........dgdla.....................ghslgnllLaa.. 92 
                                        D+r+ + +l+++e++ e+++ +  ++                                     ++sl+ l+  a  
  gi|313125499|ref|YP_004035763.1|  28 DDVRTTVESLLTNEEVSEAFALHTCNRaeayvvtdaqaT---GrraltdfapdvrdgavvemdhEQSLRHLMRVAag 101
                                       588888888888888888887776655666665544441...04445566666666666677776777777766633 PP

                                       HHHH...HS-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-EEESTTTGG...................... CS
                           UPF0052  93 lael...tgsleeaiealskilkvrgrvlPatddpvelsaeledGeeitgeskis...................... 144
                                       l++l   + ++   i+   +  +  g + P+ dd v+  +++  Ge  + e++i+                      
  gi|313125499|ref|YP_004035763.1| 102 LESLvlgEDQILGQIKRSFEEARGAGGIGPMLDDAVTKAIHV--GERARTETEINegalslgsaavrlaksettldg 176
                                       333333223555555555555555667889999999999999..888899999977889999999999999999999 PP

                                       ..............................GG-S....-EEEEEEESTT----HHHHHHHHH-SEEEE-SS-I CS
                           UPF0052 145 ..............................eark.lkapikrvflepegaeaapevleaikeAdlivlgpGsl 186
                                                                     ++   +++++ +    p++a + + v +ai++Ad+++ + Gs+
  gi|313125499|ref|YP_004035763.1| 177 atalvigagemgtlaaeslaaagigelvvaNRTLpHAEHVAEEVDVPARALPLSAVEAAIEAADVVISATGSP 249
                                       999999999999999999999999999986333334556777777788888*********************8 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   0.00031      0.31       2      74 ..     180     250 ..     179     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                       EEES-SHHHHHHHHHHHHTT..EEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLsegg..kdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgdde 74 
                                       ++iG+G++G+  ae L ++g  +  vv  +   ++e+++ee  ++   + a  +    ea ie ad+vi atg+ e
  gi|313125499|ref|YP_004035763.1| 180 LVIGAGEMGTLAAESLAAAGigE-LVVANRTLPHAEHVAEEVdVP---ARAL-PLSAVEAAIEAADVVISATGSPE 250
                                       79****************77444.666666667788888777533...3333.223347889*********99987 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3    0.0011       1.1      72      95 ..     231     254 ..     156     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                                       CHHHHHCCSSEEEE-SS-TT-B-G CS
                     THF_DHG_CYH_C  72 dlaeitreadivvvavGkpelika 95 
                                        +++ ++ ad+v++a+G+pe + +
  gi|313125499|ref|YP_004035763.1| 231 AVEAAIEAADVVISATGSPEYVLS 254
                                       5788999*************9854 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.7   6.6e+03      80     121 ..      32      73 ..      13      80 .. 0.57
   2 ?    9.9   0.1   0.00065      0.65       2      46 ..     178     221 ..     177     255 .. 0.68
   3 ?    1.1   0.0      0.32   3.2e+02      66      99 ..     317     352 ..     294     358 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.7
                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhe 121
                                        +++  +    v++  +l +++ ++   v+ +  +G + L  
  gi|313125499|ref|YP_004035763.1|  32 TTVESLLTNEEVSEAFALHTCNRAEAYVVTDAQATGRRALTD 73 
                                       455555555555555666666666666666666666666665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00065
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskalia 46 
                                       t l++G +G +G+  a+ la+ g  +lv+  R+ +  e+ +++++
  gi|313125499|ref|YP_004035763.1| 178 TALVIG-AGEMGTLAAESLAAAGIGELVVANRTLPHAEHVAEEVD 221
                                       667887.8*************************755555554333 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHS..S---EEEE---------TTT CS
                                KR  66 davealleeikaee..ppikGvihaAgvlrdkllee 99 
                                       d+ e+ll+++k++   ++i+G + aA  ++++ le+
  gi|313125499|ref|YP_004035763.1| 317 DEFERLLKSFKRKRadRAISGMYEAAEEVKQRELET 352
                                       78899999999888889*********9999988875 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00032      0.32      18      93 ..     171     253 ..     164     271 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                                       -S--TTSEEEEE--SHHHHHHHHHHHHCT-..EEEEE-S-HHHH.....HHHHCTT-EE--HHHCTTT-SEEEE-SS CS
                     AdoHcyase_NAD  18 dvllaGkvavvaGyGdvGkGcaaslkglGa..rvivtevdPica.....lqaameGfevvtleevvkkadivvtttG 87 
                                       ++ l G +a+v+G G++G  +a+sl ++G    v+     P +      +      + +  +e +++ ad+v+++tG
  gi|313125499|ref|YP_004035763.1| 171 ETTLDGATALVIGAGEMGTLAAESLAAAGIgeLVVANRTLPHAEhvaeeVDVPARALPLSAVEAAIEAADVVISATG 247
                                       567899*******************9887511444444445432100113333446677899*************** PP

                                       SSSSB- CS
                     AdoHcyase_NAD  88 nkdiit 93 
                                       + + + 
  gi|313125499|ref|YP_004035763.1| 248 SPEYVL 253
                                       977554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00031      0.31       2      38 ..     180     218 ..     179     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                       EEES-SHHHHHHHHHHHHHTHC.EEEE-SCH.HHHHHHH CS
                              ApbA   2 ailGaGaiGsllaakLakagad.vtlilrsr.rlealkk 38 
                                       +++GaG +G+l a +La+ag    ++ +r+  ++e++ +
  gi|313125499|ref|YP_004035763.1| 180 LVIGAGEMGTLAAESLAAAGIGeLVVANRTLpHAEHVAE 218
                                       69****************876547777888789998876 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.32      58     145 ..     287     375 ..     278     426 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                           zf-C4H2  58 haDinalEsvikeaeeekekslekakkly.eeykklkeevnelrselglekledleeeeeellkeeifekqklkaaa 133
                                        +D++ lE v+ e++e ++++ e++++++ +e+++l+++  + r +  ++ + + +ee ++   e+ ++k   + + 
  gi|313125499|ref|YP_004035763.1| 287 VHDMDGLEAVTDETRELRREAAERVESMIdDEFERLLKSFKRKRADRAISGMYEAAEEVKQRELETALAKLDAQGEL 363
                                       5799********************99988579******************999988888777777777777666555 PP

                           zf-C4H2 134 velkkesstapa 145
                                       ++ ++e++ a a
  gi|313125499|ref|YP_004035763.1| 364 TDDQRETVAALA 375
                                       555555555444 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00086      0.85       4      24 ..     181     201 ..     178     242 .. 0.82
   2 ?    0.3   0.8      0.57   5.7e+02      32      64 ..     340     372 ..     296     397 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00086
                                       EE--SCCHHHHHHHHHHTT-E CS
                           3HCDH_N   4 viGaGtmGagiaavfasagle 24 
                                       viGaG mG+  a+ +a+ag+ 
  gi|313125499|ref|YP_004035763.1| 181 VIGAGEMGTLAAESLAAAGIG 201
                                       9*****************985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCH CS
                           3HCDH_N  32 eealekalekieksleklvekgklkeeeveaal 64 
                                       e+a e  ++++e+ l+kl ++g+l+++++e+++
  gi|313125499|ref|YP_004035763.1| 340 EAAEEVKQRELETALAKLDAQGELTDDQRETVA 372
                                       444444555666677777777777766665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 2943.33
//
Query:       gi|313125500|ref|YP_004035764.1|  [L=220]
Description: siroheme synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-21   74.8   0.0    1.3e-20   73.7   0.0    1.6  1  NAD_binding_7   Putative NAD(P)-binding
    2.6e-10   39.6   0.1      2e-09   36.7   0.0    2.3  2  Sirohm_synth_M  Sirohaem biosynthesis protein central
     0.0078   15.9   1.6     0.0078   15.9   1.6    2.9  4  CysG_dimeriser  Sirohaem synthase dimerisation region
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.19   11.1   0.0    1.3  1  PcrB            PcrB family


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   2.9e-24   1.3e-20       1      96 [.       4     105 ..       4     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 2.9e-24
                     NAD_binding_7   1 lfldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele......elvkla..eeelekdlegad..lvia 67 
                                       l++d+++++vlv+GgG+v+ark+r+++++ a+v+vv+p++    e      e v+++  ++++++++++++  lv+a
  gi|313125500|ref|YP_004035764.1|   4 LYHDFTDESVLVFGGGPVGARKARRFAAE-ANVIVVSPRF---EEddygdaECVRAEptPDDVSDWVSRVEpaLVVA 76 
                                       79*************************99.*********4...333477776666643378899999999899**** PP

                     NAD_binding_7  68 atddrelneriaeaakarrilvnvadkpe 96 
                                       at+d  +n++  +aa++ ++lvn+ad+++
  gi|313125500|ref|YP_004035764.1|  77 ATPDGGVNDAAERAAQETGALVNRADESA 105
                                       **************************764 PP

>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   4.4e-13     2e-09       1      27 [.     125     151 ..     125     152 .. 0.94
   2 ?   -0.1   0.0      0.15   6.6e+02      17      27 ..     162     172 ..     162     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 4.4e-13
                    Sirohm_synth_M   1 rGpLQIaiSTnGksPrLAaliRreier 27 
                                       +G+  +aiST+G+sP+LA+ +R++ie+
  gi|313125500|ref|YP_004035764.1| 125 DGDVRVAISTGGASPALAKYLRERIES 151
                                       68888*********************7 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.15
                    Sirohm_synth_M  17 LAaliRreier 27 
                                       L+ ++R+e+ +
  gi|313125500|ref|YP_004035764.1| 162 LTGQLRQELRE 172
                                       6889****976 PP

>> CysG_dimeriser  Sirohaem synthase dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.51   2.3e+03      44      56 ..      81      93 ..      74      94 .. 0.73
   2 ?   -1.1   0.4      0.37   1.6e+03      36      52 ..      99     115 ..      95     117 .. 0.77
   3 ?   -2.1   0.0      0.75   3.4e+03       7      19 ..     140     152 ..     140     154 .. 0.79
   4 !   15.9   1.6   1.7e-06    0.0078       3      56 ..     157     210 ..     155     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.51
                                      TT-HHHHHHHHHH CS
                    CysG_dimeriser 44 aGdeeeAealleq 56
                                       G  ++Ae++ ++
  gi|313125500|ref|YP_004035764.1| 81 GGVNDAAERAAQE 93
                                      5778999999886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.37
                                       HHHHHHHHTT-HHHHHH CS
                    CysG_dimeriser  36 gpvaelvlaGdeeeAea 52 
                                        ++ e+++aGd ++A +
  gi|313125500|ref|YP_004035764.1|  99 NRADESAAAGDGDRAAR 115
                                       56778899999999876 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.75
                                       HHHHHHHHHHHHH CS
                    CysG_dimeriser   7 elagrlRdrVkar 19 
                                       +la  lR+r+++ 
  gi|313125500|ref|YP_004035764.1| 140 ALAKYLRERIESE 152
                                       5889999999875 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHT-HHHHHHHHTT-HHHHHHHHHH CS
                    CysG_dimeriser   3 GrLAelagrlRdrVkarlpdvaaRRrFWerffdgpvaelvlaGdeeeAealleq 56 
                                       G++Ael g+lR++ +++  ++++RR+  ++++++p    +l+  e++A+++ ++
  gi|313125500|ref|YP_004035764.1| 157 GAMAELTGQLRQELRETDYTPDERRAAVRAVVQSPKVWKALRTGESKARQEADR 210
                                       99********************************99999999999999998875 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.3e-05      0.19     179     215 ..      10      46 ..       4      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                                       SSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHH CS
                              PcrB 179 ekarlivGGGirsaEkAkevveaADvivvGnvveekd 215
                                       +++ l++GGG   a kA++ +  A+vivv    ee+d
  gi|313125500|ref|YP_004035764.1|  10 DESVLVFGGGPVGARKARRFAAEANVIVVSPRFEEDD 46 
                                       67899************************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1525.19
//
Query:       gi|313125501|ref|YP_004035765.1|  [L=363]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-49  164.6   0.6    8.3e-24   83.6   0.1    2.8  2  AsnC_trans_reg2  AsnC-like ligand binding domain
  ------ inclusion threshold ------
      0.024   14.6   0.5      0.035   14.0   0.5    1.4  1  GvpL_GvpF        Gas vesicle synthesis protein GvpL/GvpF
       0.03   14.3   0.0       0.11   12.6   0.0    1.9  2  HTH_29           Winged helix-turn helix


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.1   1.4e-27   8.3e-24       2      82 .]      77     156 ..      76     156 .. 0.97
   2 !   78.6   0.0   4.9e-26   2.9e-22       2      82 .]     250     348 ..     249     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 1.4e-27
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeRew.pynlyfmvharseeeveevlaeiaaatgledyevLps 77 
                                       +G + ++lva+++pe+r++evae+v++++ev+H+YeRe+ ++n++f+v++++e++veevl ei+++tg+  +++Lp+
  gi|313125501|ref|YP_004035765.1|  77 IGGT-ATLVAMHAPEDRYDEVAEQVNAHREVAHNYEREHpHLNMWFVVSVADESRVEEVLGEIEEETGQP-TYNLPK 151
                                       8999.9********************************9899***************************9.99**** PP

                   AsnC_trans_reg2  78 trefK 82 
                                       + ef+
  gi|313125501|ref|YP_004035765.1| 152 QDEFR 156
                                       *9995 PP

  == domain 2  score: 78.6 bits;  conditional E-value: 4.9e-26
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeRe.....wpynlyfmvharseeeveevlaeiaaatgl.... 69 
                                       lG+++n++++w+vp++ v+ev+ +va+l+ vtHcY+R+     wpyn+++m+h+rse+e +e+++++++ +      
  gi|313125501|ref|YP_004035765.1| 250 LGYTENGMTVWNVPDDVVQEVGPAVASLDFVTHCYRRPrhegvWPYNFFAMTHGRSEAESQERIEQVRDVMAEywdv 326
                                       9************************************445577**************99999999998877664444 PP

                   AsnC_trans_reg2  70 ......e...dyevLpstrefK 82 
                                             +   d+++L+str +K
  gi|313125501|ref|YP_004035765.1| 327 gdqttdDeqgDWDTLFSTRILK 348
                                       4443331456777777777776 PP

>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   5.9e-06     0.035      31     118 ..      76     159 ..      40     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-06
                         GvpL_GvpF  31 ragg.laavvsdvpeeeydaerleqverwllaHqrVvealmaegtvlPlrFgtvlkdeeavrelLeeeadelreaLe 106
                                       + gg  ++v  ++pe++yd+ +++     + aH +V     +e++ l + F + + de++v+e+L e ++e  +   
  gi|313125501|ref|YP_004035765.1|  76 EIGGtATLVAMHAPEDRYDEVAEQ-----VNAHREVAHNYEREHPHLNMWFVVSVADESRVEEVLGEIEEETGQPTY 147
                                       455523455568999999999999.....***************************************999998888 PP

                         GvpL_GvpF 107 rlagkvEygvkv 118
                                       +l  + E++v++
  gi|313125501|ref|YP_004035765.1| 148 NLPKQDEFRVEA 159
                                       888888888876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.4   8.2e+03      39      59 ..      75      95 ..      67     105 .. 0.48
   2 ?   12.6   0.0   1.8e-05      0.11      16      40 ..     212     236 ..     206     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                            HTH_29 39 gGlaalldrrrsgrprnrlse 59
                                      ++++++    + ++p +r +e
  gi|313125501|ref|YP_004035765.1| 75 EEIGGTATLVAMHAPEDRYDE 95
                                      555554333333333333333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.8e-05
                            HTH_29  16 sqiAkllglsrrtvyrwlkrfeegG 40 
                                       +++A+ l  +  +v r++krf+++G
  gi|313125501|ref|YP_004035765.1| 212 ADVAAELETDTEWVVRTIKRFNQEG 236
                                       678999******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2447.17
//
Query:       gi|313125502|ref|YP_004035766.1|  [L=122]
Description: hypothetical protein Hbor_07290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.7   4.1       0.02   14.4   4.1    1.1  1  BaxI_1    Bax inhibitor 1 like


Domain annotation for each model (and alignments):
>> BaxI_1  Bax inhibitor 1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   4.1   1.1e-06      0.02      60     161 ..       6     111 ..       3     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-06
                            BaxI_1  60 alvglvlalvasfkkkvspalvllYAvleGlflGgislvfea....pgivvqAvlgTlgvfavmlvlYktgairvtp 132
                                       +l+g  + l+ ++  +++ ++ l + vl Gl+ G +s  fe+     g++  +    +gv +++l l +  ++ +++
  gi|313125502|ref|YP_004035766.1|   6 ILFGSLVQLALTIAAELAGMTLLPFGVLGGLVAGSVSRSFEKeyrdAGLAGWSAWFVFGVGIAVLSLLSGSKLFTDQ 82 
                                       5677788999999**************************************************************** PP

                            BaxI_1 133 kftkivvaaligilllylvnlvlslfgvg 161
                                        f  + +++  +i+   +  l+ +++gv 
  gi|313125502|ref|YP_004035766.1|  83 SFVGVWFGVGYAIVGAGISGLLSAIVGVA 111
                                       *****999999999988888888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 858.01
//
Query:       gi|313125503|ref|YP_004035767.1|  [L=132]
Description: hypothetical protein Hbor_07300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 861.85
//
Query:       gi|313125504|ref|YP_004035768.1|  [L=310]
Description: undecaprenyl pyrophosphate synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-66  221.5   0.0    1.2e-65  221.1   0.0    1.1  1  Prenyltransf  Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
        0.1   11.7   0.0       0.16   11.1   0.0    1.2  1  Cas_Cas1      CRISPR associated protein Cas1


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.1   0.0   1.4e-69   1.2e-65       1     222 [.      31     253 ..      31     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: 221.1 bits;  conditional E-value: 1.4e-69
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHH.H CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkee.l 76 
                                       i DGNrR+A++rg  e+ +Ghk+Ga++ +++l++c e+gv+ +t+Y+fSteNf R++ee++ l++l++e+l +   +
  gi|313125504|ref|YP_004035768.1|  31 IQDGNRRYARRRG-DEAPDGHKEGAKTAEQVLHWCEEFGVEELTLYTFSTENFDRPQEELEPLFDLIEEKLYEFAdA 106
                                       78***********.77777************************************************9777765535 PP

                                       HHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHS CS
                      Prenyltransf  77 kellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeid 152
                                       +++++ gvr+ +iG++++lp++v+ea+e ae++t+   ++++lnia++Yg+r+e++ avr++++++++ + + ++++
  gi|313125504|ref|YP_004035768.1| 107 ERVHEAGVRICTIGETDRLPPRVREAIEYAESRTR-GYDGFCLNIALAYGGRAELLGAVRDVARDVTSGTLSpDDVT 182
                                       688888*****************************.6666**********************999987776646678 PP

                                       HHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-E..EEEESSSGGG--HHHHHHHHHHHHHCHHH CS
                      Prenyltransf 153 eetlekhlytakalpdpDlliRtsGeeRlSnFllwqlayse..lyfldvlWPdfskedllealleyqkrerr 222
                                        e+++++l   + + d+Dl+iRt+G eR SnFl w++  +e  +yf+  +WP+fsk d+l+ l++y++re+ 
  gi|313125504|ref|YP_004035768.1| 183 VEEIDSRLCQ-HPTRDVDLIIRTGGAERTSNFLPWHANGNEaaVYFCAPYWPEFSKVDFLRGLRTYESREKS 253
                                       899******7.556**********************9888899**************************986 PP

>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.7e-05      0.16      15     137 ..     179     302 ..     172     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.7e-05
                                       TEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHH.TT-EEEEE-TTS-EEEEEEE.SSSSTHHHHHHHHH CS
                          Cas_Cas1  15 erlvvekegeekkeiplediesivifgevslstkalrllae.kgipvvflsengkylgrlep.eesgnvelrraQyr 89 
                                       + ++ve+ ++++ + p +d++ i+ +g ++ ++++l + a+ ++ +v f+ ++   ++++   +  ++ e r + ++
  gi|313125504|ref|YP_004035768.1| 179 DDVTVEEIDSRLCQHPTRDVDLIIRTGGAERTSNFLPWHANgNEAAVYFCAPYWPEFSKVDFlRGLRTYESREKSWQ 255
                                       56778887888999**********************998873667777777776666667668999*********** PP

                                       HHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHH CS
                          Cas_Cas1  90 aaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieelee 137
                                       + ++e+ +++l++++ +  l   r+v  rl+++ +++  ee ++ele+
  gi|313125504|ref|YP_004035768.1| 256 RTRTER-AVALVRSVAETELAEARAVTARLREKLPSAGAEEVAAELER 302
                                       *98776.************************99977666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1929.27
//
Query:       gi|313125505|ref|YP_004035769.1|  [L=202]
Description: undecaprenyl diphosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-24   85.9   0.0      2e-23   83.1   0.0    1.9  2  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.017     3e+02      24      45 ..      37      58 ..      29      64 .. 0.89
   2 !   83.1   0.0   1.1e-27     2e-23     119     224 .]      99     201 ..      71     201 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.017
                                      HHHHHHHHHHHHHHTT-SEEEE CS
                      Prenyltransf 24 Gaealkeilelclelgvkvvtv 45
                                       +e+l+++l+++ e+g + vtv
  gi|313125505|ref|YP_004035769.1| 37 AYETLERFLRWAFEFGAERVTV 58
                                      46899***************98 PP

  == domain 2  score: 83.1 bits;  conditional E-value: 1.1e-27
                                       EEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EE CS
                      Prenyltransf 119 lniavnYgsrdeiveavrelvkekseekkk.eeideetlekhlytakalpdpDlliRtsGeeRlSnFllwqlaysel 194
                                       +++ +  g+++e ++ vr++++++ + + + e+i +e++e++l     + +pDlli+t+  eRlS+F++wq++ysel
  gi|313125505|ref|YP_004035769.1|  99 VQVSIGLGGKREFADVVRDIAEDVDAGDLSpEDIGAEHVEERLVF---QDEPDLLIKTG-AERLSDFMIWQSVYSEL 171
                                       7888999*************9999666555467778999999998...368******97.579************** PP

                                       EEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 195 yfldvlWPdfskedllealleyqkrerrfg 224
                                       yf+dv W df+k+d+l+a+l++q+r+rrfg
  gi|313125505|ref|YP_004035769.1| 172 YFTDVNWRDFRKRDYLRAVLDFQNRQRRFG 201
                                       ****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 1164.80
//
Query:       gi|313125506|ref|YP_004035770.1|  [L=435]
Description: hypothetical protein Hbor_07330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-46  157.1  20.1    4.9e-46  157.1  20.1    3.1  3  DUF92     Integral membrane protein DUF92


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   1.4      0.48   8.6e+03     171     175 ..      25      35 ..       8      48 .. 0.32
   2 ?  -10.4  12.4         1   1.8e+04     139     157 ..     117     134 ..      61     167 .. 0.52
   3 !  157.1  20.1   2.7e-50   4.9e-46       2     198 ..     204     409 ..     203     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.48
                             DUF92 171 l......lill 175
                                       +      ++++
  gi|313125506|ref|YP_004035770.1|  25 KaatfapFVAI 35 
                                       11111111111 PP

  == domain 2  score: -10.4 bits;  conditional E-value: 1
                             DUF92 139 GtnGgVsllGllasllGal 157
                                       Gt+G V + G l ++lG +
  gi|313125506|ref|YP_004035770.1| 117 GTSGFV-VGGFLGGVLGQV 134
                                       222222.233333333333 PP

  == domain 3  score: 157.1 bits;  conditional E-value: 2.7e-50
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdav 76 
                                       lt++++l+++  k+ ++sG+l++vl+ +l+++  +g+ +f++l+ Ff +g l tk+++++K   +++e+++gaR+  
  gi|313125506|ref|YP_004035770.1| 204 LTVAFGLVSYVLKAASVSGMLSGVLLSLLVTVF-GGFGWFAVLMSFFAIGALSTKFRYDEKLdrGVAEDNDGARGTR 279
                                       68999***********************99999.7778***********************9999************ PP

                             DUF92  77 qVlanslvalllally.......lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsl 146
                                       +V++n++val+ ++ +       + + l+ +++++s+Aa+++DTl+SE+G ++ + +prlittl++v pGt+GgV++
  gi|313125506|ref|YP_004035770.1| 280 NVFGNAAVALASVIGFaasahtaVDGMLFQYAFAGSMAAALSDTLSSEIGGLY-D-NPRLITTLERVDPGTDGGVTW 354
                                       ***********9999988887653378899********************777.4.7******************** PP

                             DUF92 147 lGllasllGalliallavlllllel....lillltlaGllGsllDSlLGatlqasv 198
                                        G la+l+G++++a++a++ll   +      ++++l Gl+G+++DS+LGat++   
  gi|313125506|ref|YP_004035770.1| 355 QGELAGLVGSAIVAAIAAFLLSG-VtgllGGAVVLLGGLAGMTVDSFLGATVEGAR 409
                                       **************884444322.2356666678888***************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2893.39
//
Query:       gi|313125507|ref|YP_004035771.1|  [L=138]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-13   49.4   0.0    4.7e-13   49.2   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    5.1e-11   42.8   0.0    6.1e-11   42.6   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.4e-11   42.3   0.0    1.5e-10   41.4   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.6e-08   32.9   0.0    1.2e-07   31.5   0.0    1.7  2  FR47             FR47-like protein
    7.7e-05   22.8   0.0    0.00028   21.0   0.0    1.8  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.028   15.1   0.0      0.037   14.7   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.029   14.2   0.0      0.041   13.7   0.0    1.2  1  Acetyltransf_18  Acetyltransferase (GNAT) domain
      0.042   13.5   0.1      0.057   13.1   0.1    1.3  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.075   13.0   0.0       0.72    9.9   0.0    2.2  2  Acetyltransf_13  ESCO1/2 acetyl-transferase
       0.12   12.5   0.0       0.25   11.5   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.17   11.6   0.0       0.22   11.3   0.0    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   2.9e-16   4.7e-13      32     115 ..      38     125 ..      27     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.9e-16
                   Acetyltransf_10  32 lllvaeeggkivGvi.el.rdgs.hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnasp.yavpfYekl 104
                                       +++     +++vG++ ++ +d++ h++ l+V+peyr++G ++ Llea+ +e   +++++++tv a + +a+++Ye++
  gi|313125507|ref|YP_004035771.1|  38 VFVSTAHRNRPVGYLlAVaSDDGcHVAELVVHPEYRRTGRARDLLEALFDER-PAESAVTVTVAAGNdAARSLYESV 113
                                       456666778*****9766655557***************************7.666777********9********* PP

                   Acetyltransf_10 105 GFkav.geeqee 115
                                       GF++   ++ ++
  gi|313125507|ref|YP_004035771.1| 114 GFEESdCRPGYF 125
                                       ***985555555 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   3.7e-14   6.1e-11      36     117 .]      39     115 ..       4     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 3.7e-14
                                       EE.EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHH CS
                    Acetyltransf_1  36 lv.aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairl 111
                                       +v   + ++++G++ +   +d     +++ +l+V+peyr+ G ++ Lleal ++   e   ++ ++v + ndaa+ l
  gi|313125507|ref|YP_004035771.1|  39 FVsTAHRNRPVGYLLAVASDD----GCHVAELVVHPEYRRTGRARDLLEALFDERPAE--SAVTVTVAAGNDAARSL 109
                                       223555599*****9999999....9**************************966666..4578889999******* PP

                                       HHHTTE CS
                    Acetyltransf_1 112 YeklGF 117
                                       Ye +GF
  gi|313125507|ref|YP_004035771.1| 110 YESVGF 115
                                       *99**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   9.1e-14   1.5e-10       5      76 .]      38     117 ..      20     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 9.1e-14
                                       EEE.EEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH......TTSEEEEE.EEEE...THHHHHHH CS
                    Acetyltransf_7   5 vfV.aeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea......aekgiile.qlel...naekaikf 68 
                                       vfV   + +++vG++ ++ +d  ++  +l+V+peyr+ G +r Llea      a +      ++++   n+ +a+++
  gi|313125507|ref|YP_004035771.1|  38 VFVsTAHRNRPVGYLLAVASDdgCHVAELVVHPEYRRTGRARDLLEAlfderpA-ES---AvTVTVaagND-AARSL 109
                                       4442234489999999888888777777******************74543221.11...12233333333.7888* PP

                                       HHHTTEEE CS
                    Acetyltransf_7  69 YeklGFee 76 
                                       Ye+ GFee
  gi|313125507|ref|YP_004035771.1| 110 YESVGFEE 117
                                       ******96 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0         1   1.7e+03      25      43 ..      36      54 ..      33      59 .. 0.75
   2 !   31.5   0.0   7.6e-11   1.2e-07      21      80 ..      60     118 ..      44     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1
                                      EEEEE-GGG-SSSHHHHHH CS
                              FR47 25 galqvlpehrrrGlgsrlv 43
                                      g + v   hr+r  g +l+
  gi|313125507|ref|YP_004035771.1| 36 GTVFVSTAHRNRPVGYLLA 54
                                      6777888888888777776 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 7.6e-11
                                       TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       g  +  l v+pe rr G ++ l +al  e + ++  v++ v+a+N+++++lye++Gfe+ 
  gi|313125507|ref|YP_004035771.1|  60 GCHVAELVVHPEYRRTGRARDLLEALFDE-RPAESAVTVTVAAGNDAARSLYESVGFEES 118
                                       46677899******************998.77999**********************986 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   1.9e+03      75      90 ..      34      49 ..      28      58 .. 0.69
   2 !   21.0   0.0   1.7e-07   0.00028      76     127 ..      63     117 ..      59     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                                      EEEEEEE-CCGTTS-H CS
                    Acetyltransf_9 75 gvtgVavapehrgrgv 90
                                       v+ V v   hr+r v
  gi|313125507|ref|YP_004035771.1| 34 VVGTVFVSTAHRNRPV 49
                                      5666777777777654 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.7e-07
                                       EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--...SSHHHHHTTT-EE CS
                    Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegqplsllfP...ssipiYrrfGyei 127
                                       v+   v+pe+r+ g +++Ll+++++e  +e +  ++  +   +++++Y++ G+e 
  gi|313125507|ref|YP_004035771.1|  63 VAELVVHPEYRRTGRARDLLEALFDERPAESAVTVTVAAgndAARSLYESVGFEE 117
                                       77889**********************999877777777899999********95 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.2e-05     0.037      66     138 .]      49     116 ..       3     116 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                    Acetyltransf_3  66 iGsvglrdleeedeeaelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       +G+      ++    +++  ++++p++++ G a++ ++al +     +  + + +++++ N a + ++e++Gfe
  gi|313125507|ref|YP_004035771.1|  49 VGYLLAVASDDG---CHVAeLVVHPEYRRTGRARDLLEALFDER---PAESAVTVTVAAGNDAARSLYESVGFE 116
                                       444433333333...44433888999999999988777766544...444579********************7 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-05     0.041      29     102 ..      40     118 ..      28     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                   Acetyltransf_18  29 vvveedgeivGyglarktrkglkiGPlvAene....eiAeaLlkalvanaeg.kkvridvpeenkalielleklgfk 100
                                       v  +  ++ vGy la+   +g  +  lv + e      A++Ll+al+ +    + v++ v + n+a+ +l e++gf+
  gi|313125507|ref|YP_004035771.1|  40 VSTAHRNRPVGYLLAVASDDGCHVAELVVHPEyrrtGRARDLLEALFDERPAeSAVTVTVAAGNDAARSLYESVGFE 116
                                       55667788999*9*9999999999999987542211579********98876478*********************9 PP

                   Acetyltransf_18 101 ev 102
                                       e 
  gi|313125507|ref|YP_004035771.1| 117 ES 118
                                       86 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.5e-05     0.057      77     139 ..      56     117 ..      28     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
                                       TT-EEEEE..EESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EE CS
                    Acetyltransf_8  77 pgdrGiHl..ligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfek 139
                                         d G+H+  l+  +e+r+ g+++ ll+al +   ++p+ + v v   + N +a++l+e++Gfe+
  gi|313125507|ref|YP_004035771.1|  56 ASDDGCHVaeLVVHPEYRRTGRARDLLEALFD---ERPAESAVTVTVAAGNDAARSLYESVGFEE 117
                                       56777787556888999999999888877655...4667799999999***************97 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.28   4.6e+02       9      23 ..      37      51 ..      34      66 .. 0.79
   2 ?    9.9   0.0   0.00044      0.72       7      31 ..      63      87 ..      59     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.28
                   Acetyltransf_13  9 riWvssshRrkgiAt 23
                                       ++vs +hR++ +  
  gi|313125507|ref|YP_004035771.1| 37 TVFVSTAHRNRPVGY 51
                                      689******998865 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00044
                   Acetyltransf_13  7 isriWvssshRrkgiAtkLldaare 31
                                      +  + v++++Rr+g A+ Ll+a+ +
  gi|313125507|ref|YP_004035771.1| 63 VAELVVHPEYRRTGRARDLLEALFD 87
                                      77788****************9866 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.25      24      52 ..      60      88 ..      39      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                   Acetyltransf_CG 24 vldfthTeVpeelrGkGiAkkLvkaaldd 52
                                        ++   +V++e+r+ G A+ L +a +d+
  gi|313125507|ref|YP_004035771.1| 60 GCHVAELVVHPEYRRTGRARDLLEALFDE 88
                                      56677889******************997 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.22      47     112 ..      46     107 ..      14     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                              PanZ  47 dRlLgAvkveledkeaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvkeldlavlq 112
                                       +R  g      +d+  ++ +l+V  + Rr G ++ Lle   ++ P+ ++ +++ ++++++     +
  gi|313125507|ref|YP_004035771.1|  46 NRPVGYLLAVASDDGCHVAELVVHPEYRRTGRARDLLEALFDERPAESAVTVTVAAGNDAA----R 107
                                       566666666667888899***************************9888888877766544....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 853.89
//
Query:       gi|313125508|ref|YP_004035772.1|  [L=558]
Description: DNA primase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-13   49.5   0.1    1.4e-12   47.9   0.1    1.9  1  Toprim_4   Toprim domain
    5.9e-06   26.6   0.0    1.7e-05   25.2   0.0    1.8  1  Toprim_2   Toprim-like
  ------ inclusion threshold ------
      0.013   15.7   0.7       0.12   12.6   0.1    2.9  2  Toprim     Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.1   2.3e-16   1.4e-12       2      70 ..     168     245 ..     167     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2.3e-16
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGe 68 
                                       +ii+VEg+aDvl l ++g+kn++av g+++ p + +r+++ +t +++++    +e +++e+++++d D+     +G+
  gi|313125508|ref|YP_004035772.1| 168 AIIVVEGRADVLTLLRYGVKNAIAVEGTNI-PDAVARLTQDRTvTAFLDgdrgGELILRELVQVGDVDYvafapDGQ 243
                                       79****************************.******999999999999*******************966666666 PP

                          Toprim_4  69 at 70 
                                        +
  gi|313125508|ref|YP_004035772.1| 244 SV 245
                                       55 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.8e-09   1.7e-05       1      66 [.     170     229 ..     170     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.8e-09
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlae 66 
                                       +v+Eg  D+l l+++g k   n++a+ Gt++++a ++l +++   +v   lD D+ G+   ++l++
  gi|313125508|ref|YP_004035772.1| 170 IVVEGRADVLTLLRYGVK---NAIAVEGTNIPDAVARLTQDR---TVTAFLDGDRGGELILRELVQ 229
                                       69***************9...********9999999998888...69999********99998876 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     2e-05      0.12       2      87 ..     169     231 ..     168     253 .. 0.84
   2 ?   -2.5   0.0      0.98   5.9e+03      70      78 ..     356     364 ..     355     366 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                       EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHH CS
                            Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGea 78 
                                       +++vEg +d+ t+ ++   g ++++a+ G+ +  +                      ++ +   +   +D+Dr Ge 
  gi|313125508|ref|YP_004035772.1| 169 IIVVEGRADVLTLLRY---GVKNAIAVEGTNIPDAV--------------------ARLTQDRTVTAFLDGDRGGEL 222
                                       89**************...9*********9887776....................3444566777779******** PP

                                       HHHHHHHHH CS
                            Toprim  79 iawellevl 87 
                                       i  el++v 
  gi|313125508|ref|YP_004035772.1| 223 ILRELVQVG 231
                                       *99999875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.98
                                       CSSSHHHHH CS
                            Toprim  70 tDpDreGea 78 
                                       tD+ +eGe+
  gi|313125508|ref|YP_004035772.1| 356 TDASVEGEH 364
                                       9*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 3349.36
//
Query:       gi|313125509|ref|YP_004035773.1|  [L=73]
Description: hypothetical protein Hbor_07360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-11   41.9  18.9    8.6e-11   41.6  18.9    1.1  1  DUF3311        Protein of unknown function (DUF3311)


Domain annotation for each model (and alignments):
>> DUF3311  Protein of unknown function (DUF3311)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6  18.9   4.8e-15   8.6e-11       1      54 [.      10      63 ..      10      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.8e-15
                           DUF3311  1 vlllvpvlvalllvpfynrvdpvllGlPffywwqllwvllasvvtwlayrlakr 54
                                      ++ +++vlv  ++++f++r++ ++ GlP ++ww+ +w++las  ++l++  a+ 
  gi|313125509|ref|YP_004035773.1| 10 WVGVFAVLVTFAIPWFLWRDAATWAGLPVWLWWHIGWMVLASGAFYLFTLGAWD 63
                                      899*********************************************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 493.48
//
Query:       gi|313125510|ref|YP_004035774.1|  [L=500]
Description: Na+/proline symporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-50  171.2  27.2    4.1e-50  170.8  27.2    1.1  1  SSF         Sodium:solute symporter family
  ------ inclusion threshold ------
      0.043   13.4   0.0      0.082   12.5   0.0    1.4  1  Herpes_UL4  Herpesvirus UL4 family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8  27.2   4.6e-54   4.1e-50       1     403 [.      38     430 ..      38     433 .. 0.89

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 4.6e-54
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr......nagalTl 71 
                                       y+la+rsl+ +vl  +++a+ +sa  f G++ +++  G +++l  +g++ +vl+++l  a  +r      n g +Tl
  gi|313125510|ref|YP_004035774.1|  38 YYLASRSLGTVVLLFTTFATLLSAFTFFGGPNLAYGAGPEWIL-VMGLMDGVLFAVLWYAVGYRqwligqNRGYVTL 113
                                       9*************************************99865.466665555544444444555578*9******* PP

                               SSF  72 pdylskRfkgkrilvylsalslllvitlklsvdlvggaklielalG.lnyetavlllaaltalYtviGGllAvvytd 147
                                        ++l  Rf+++ ++ +++ +sl+ ++   +  ++ +g +++ l+ G + y ++  l+ + ++lY+v+ Gl+ v +td
  gi|313125510|ref|YP_004035774.1| 114 GEMLGDRFGSRALRAMVATISLFWLFPYVMLQQMGAGEAIVGLTGGtVPYWAGAALITVFMILYVVLAGLRGVAWTD 190
                                       ************999999999999999999999999999999998857899999*********************** PP

                               SSF 148 tiqavlmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvR 224
                                       tiq++ ml    + +  v++++Ggl+++   ++e +p   ++l  ++   l +p  ++s  + + +Gv++ p i +R
  gi|313125510|ref|YP_004035774.1| 191 TIQGLFMLSIVWVAVAWVVSSAGGLSAISASMAETKP---EFLALGG--GLYSPEWMISTAVTIAFGVIMFPQINQR 262
                                       *************************************...7777555..3799************************ PP

                               SSF 225 flaakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavm 301
                                       f+ akd + + +++    ++l+l+l+        ++ l g   +  g +v +   ++p L ++  p ++a+l++a +
  gi|313125510|ref|YP_004035774.1| 263 FFMAKDDRVLKRSFAL-WPILVLLLFV-------PAFLLGSWAAGLGVQVPEGSNVIPALLNEYTPVWFAALVVAGA 331
                                       ********99999754.3333333333.......444555555556888889999********************** PP

                               SSF 302 lAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafagla 378
                                       +Aa+ms+ +s+lls+ss +t+DlY  ++    a++ ++ +++ri v v + l++++ + ++   ++ +  +af+g+a
  gi|313125510|ref|YP_004035774.1| 332 MAAMMSSSDSMLLSGSSYLTRDLYRPFVNPT-ASDEREGWIARIGVAVFATLSFVASLFQPGT-LINVGDTAFGGFA 406
                                       *****************************99.7777889******************999999.************* PP

                               SSF 379 savlavillalfwkrvneqGAlagl 403
                                          l+v++ al+w + ++ G lag+
  gi|313125510|ref|YP_004035774.1| 407 QMALPVMV-ALYWPKTTKLGMLAGI 430
                                       99999876.9**********99986 PP

>> Herpes_UL4  Herpesvirus UL4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.1e-06     0.082      47     102 ..       1      56 [.       1      95 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-06
                        Herpes_UL4  47 lpsgkvviqhtpvgtlivvDcetefcaYllearesgselerslpeellaipFtact 102
                                       ++++ +++q + vg+ +vv     f aY+l++r++++ +  s    ++++ Ft+  
  gi|313125510|ref|YP_004035774.1|   1 MAESDLLVQMGVVGVYLVVSLLVGFVAYRLTSRDAEDYYLASRSLGTVVLLFTTFA 56 
                                       568999****************************9999998888888888887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2839.50
//
Query:       gi|313125511|ref|YP_004035775.1|  [L=272]
Description: hypothetical protein Hbor_07380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-79  265.6   0.0    3.9e-79  265.4   0.0    1.1  1  YqcI_YcgG  YqcI/YcgG family


Domain annotation for each model (and alignments):
>> YqcI_YcgG  YqcI/YcgG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.4   0.0   2.2e-83   3.9e-79       7     210 ..      45     249 ..      35     250 .. 0.97

  Alignments for each domain:
  == domain 1  score: 265.4 bits;  conditional E-value: 2.2e-83
                         YqcI_YcgG   7 dkeFPCvfaksalkkgelryafvesledeeaakelaaaLeeylelareskgkrtslvvffeppeeelseeeyeellW 83 
                                        ++FPC+f+++++++ge  y++v+s++d++a+ ++++aL eyl+++r +   rts+v+ff+ppe+e se +y+e lW
  gi|313125511|ref|YP_004035775.1|  45 GTPFPCFFGAQSVRDGEPVYTAVPSMTDKDALLDFRDALLEYLDVYR-DLPGRTSFVTFFKPPEREFSEGDYHEILW 120
                                       689********************************************.8889************************* PP

                         YqcI_YcgG  84 klLqsLhelDeepwpediptdpddpewefsfaGepfFvvgltPayksrksRrlpv.lvlvfqprevFeklraetekg 159
                                       +lLq+Lh +D+epwpediptdpddp+wef+f+Gep+F+++++P+y++rksR++pv l+++fqpr++F++++++te+g
  gi|313125511|ref|YP_004035775.1| 121 HLLQFLHVHDPEPWPEDIPTDPDDPHWEFCFGGEPMFPTCRAPFYDERKSRYCPVgLEITFQPRTLFDGITHDTEAG 197
                                       ***************************************************************************** PP

                         YqcI_YcgG 160 ekarekirkrleaydqgsvnpdLgdygeesnreakqYslrddeee.sskcPf 210
                                       +kare+i++r+e+yd +++++dLgd+g es+re++qY++r+d ++ +++cP+
  gi|313125511|ref|YP_004035775.1| 198 QKARETIQSRMEEYDGVCPHADLGDWGVESDREWPQYLFREDPDDsPDECPI 249
                                       *********************************************9*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1654.44
//
Query:       gi|313125512|ref|YP_004035776.1|  [L=195]
Description: nicotinamidase-like amidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-33  115.5   0.0    3.4e-33  115.3   0.0    1.1  1  Isochorismatase  Isochorismatase family


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   1.9e-37   3.4e-33       2     175 .]      18     190 ..      17     190 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 1.9e-37
                   Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgael 78 
                                       alv++D+q +f  + ++ + + +++ +n+++ll+a+r+++ p  ++r+              +    ++ + +g + 
  gi|313125512|ref|YP_004035776.1|  18 ALVLVDLQTGFD-ADGWGDRNNPDAESNAARLLDAWRERDFPRAHVRHDST-----------EPTSPLRGDGPGFAW 82 
                                       9**********9.9*************************************...........899999999****** PP

                   Isochorismatase  79 vpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaals... 152
                                        pe ap+  +++++K+  s+f gt+l+ +L+e+  +t+v++G++td C+ +t+r a +lG+ ++vvsDA+a+++   
  gi|313125512|ref|YP_004035776.1|  83 KPETAPVDEEPTFTKQVNSGFIGTELESWLRENDCETVVIVGLTTDHCISTTTRMAENLGFAPIVVSDATATFDreg 159
                                       ***************************************************************************** PP

                   Isochorismatase 153 ........pelhdaalkrlkqafatvitted 175
                                               +e h++al++l   fa+v tt+d
  gi|313125512|ref|YP_004035776.1| 160 pdgerysaEEMHRTALAHLYREFADVATTDD 190
                                       *******6666*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1309.27
//
Query:       gi|313125513|ref|YP_004035777.1|  [L=124]
Description: hypothetical protein Hbor_07400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.035   14.2  10.6       0.04   14.0  10.6    1.0  1  HisKA_7TM  N-terminal 7TM region of histidine kinase


Domain annotation for each model (and alignments):
>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0  10.6   2.2e-06      0.04       4     104 ..      10     110 ..       7     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-06
                         HisKA_7TM   4 isallslvlaiya.wrrrskpgaraflllllavalwslgyalell.attleakllwaklqylgivfipvlwllfale 78 
                                       +++ll+l+la+ a w +   ++  a++ ll+ +al  ++ +++++ +   +++l w+++  +g+  +  ++ l++++
  gi|313125513|ref|YP_004035777.1|  10 AVVLLTLALAYAAfWPHT--TTIIALIELLVFGALCYFATGFRISiSVG-SWTLPWYSIYGIGTLALGGALPLLVMQ 83 
                                       6799*********88653..3355555599999999********96666.*************************** PP

                         HisKA_7TM  79 ytgkrrwltrrrlallll.vpvltlil 104
                                        +g  r+ +  +++ll+l +p++++ +
  gi|313125513|ref|YP_004035777.1|  84 MAGGGRLGPFYIVLLLILeIPMVVVGV 110
                                       ***777766678888888999888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.34s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 731.19
//
Query:       gi|313125514|ref|YP_004035778.1|  [L=104]
Description: hypothetical protein Hbor_07410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 666.50
//
Query:       gi|313125515|ref|YP_004035779.1|  [L=308]
Description: hypothetical protein Hbor_07420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.11   12.5   0.1        0.4   10.7   0.0    1.9  2  SRP_TPR_like  Putative TPR-like repeat
       0.12   12.0   0.1       0.17   11.5   0.1    1.2  1  LMWSLP_N      Low molecular weight S layer protein N terminal


Domain annotation for each model (and alignments):
>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.5e-05       0.4      52     114 ..      40     105 ..      30     107 .. 0.77
   2 ?   -1.5   0.0      0.28   2.5e+03       5      23 ..     216     234 ..     212     261 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.5e-05
                      SRP_TPR_like  52 aYvlYklkkykkalkilkkveaeekvkvlksqvlYrlgsyekAYklL.skekked..elvvNllAv 114
                                       a v+Y  +  +k  k ++++ + +  +v+   v+ +   +e+AY+l+ ++ +k+d  e+ vN+ A+
  gi|313125515|ref|YP_004035779.1|  40 ANVEYSQNLSTKLEKDFQNLLGADTERVVIEDVYDYDAAFEQAYDLInTELDKSDdtEVWVNVSAM 105
                                       5566666666677777777778888899*****************997455555511677899998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.28
                      SRP_TPR_like   5 yekilrlegkelkkfkvva 23 
                                       +e+i+  e  e+ +f  v+
  gi|313125515|ref|YP_004035779.1| 216 FEEIILFELGEYGQFESVS 234
                                       6677777777777775554 PP

>> LMWSLP_N  Low molecular weight S layer protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   1.9e-05      0.17      51      78 ..      73     101 ..      47     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHHHHHHHHHT--TT-.EEE CS
                          LMWSLP_N  51 adrdaaaeklynlvntqldklgdgd.yvd 78 
                                        d daa e+ y+l+nt+ldk  d + +v+
  gi|313125515|ref|YP_004035779.1|  73 YDYDAAFEQAYDLINTELDKSDDTEvWVN 101
                                       699*****************999863344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2078.93
//
Query:       gi|313125516|ref|YP_004035780.1|  [L=260]
Description: hypothetical protein Hbor_07430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-51  173.3  11.5      5e-51  172.8  11.5    1.2  1  DUF1405   Protein of unknown function (DUF1405)
  ------ inclusion threshold ------
       0.24   11.9   5.7        2.7    8.5   0.2    3.0  3  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF1405  Protein of unknown function (DUF1405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8  11.5   5.5e-55     5e-51       1     156 [.      58     241 ..      58     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 5.5e-55
                           DUF1405   1 gtvyGyiyYgk............qlaetplllwpfvpDSPtAtlffalallllllgrelellealAfvtlikyGlWt 65 
                                       gtv+G++yYg+            q+a++p+++wpfvpDSP+Atlf+a a++l++l+r++e+++alAf++++k+GlWt
  gi|313125516|ref|YP_004035780.1|  58 GTVFGFWYYGFhplplsdplivwQFASEPVVMWPFVPDSPMATLFIAGAFALWRLDRTNEYVNALAFFGCWKLGLWT 134
                                       8**************************************************************************** PP

                           DUF1405  66 vvvlllvllkgg.......leelmLilsHlamavealllarilrfsvkalavalawlllndvvDYvlgvlpelhetl 135
                                       ++vl+++            ++ l+L++sHlam+vea++l+ri +f+v+a+ava++w+++ndvvDY++++++++h+t 
  gi|313125516|ref|YP_004035780.1| 135 PFVLTAFSD--AfldqtalPMYLFLFFSHLAMVVEAFVLHRISDFPVRAVAVAIVWYGFNDVVDYFIPIVGDPHHTS 209
                                       ******982..1334444444555****************************************************9 PP

                           DUF1405 136 ...........eeeleliaafavvltvlslll 156
                                                  ++ l+++aa+a+vlt++++++
  gi|313125516|ref|YP_004035780.1| 210 ipladgvivggSSVLQIAAAGAIVLTLVATFF 241
                                       **********5555***************997 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.25   2.2e+03      40      62 ..      44      66 ..       5      69 .. 0.70
   2 ?    8.5   0.2    0.0003       2.7      16      54 ..      98     134 ..      97     150 .. 0.73
   3 ?    4.8   0.3    0.0044        39      20      62 ..     164     243 ..     156     249 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.25
                            DUF202 40 gkilglilivlgiltllvglvry 62
                                      g  l ++ +++ ++  ++g++ y
  gi|313125516|ref|YP_004035780.1| 44 GLNLVWTVVAINLVGTVFGFWYY 66
                                      45555555555555555555544 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0003
                            DUF202  16 tslalialglallrffltgepsalgkilglilivlgilt 54 
                                       +++++ia ++al+r+ +t+e  +  +++ ++++ lg++t
  gi|313125516|ref|YP_004035780.1|  98 MATLFIAGAFALWRLDRTNEYVN--ALAFFGCWKLGLWT 134
                                       7899***********88777777..44444455555554 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0044
                            DUF202  20 lialglallrffl...........................tgepsa..........lgkilglilivlgiltllvgl 59 
                                       +++ +++l r+                             ++++++          ++++l ++++++ +ltl+  +
  gi|313125516|ref|YP_004035780.1| 164 MVVEAFVLHRISDfpvravavaivwygfndvvdyfipivgDPHHTSipladgvivgGSSVLQIAAAGAIVLTLVATF 240
                                       44555555555445566666666666666677777777775555552322222222123333444444444444444 PP

                            DUF202  60 vry 62 
                                       ++ 
  gi|313125516|ref|YP_004035780.1| 241 FSL 243
                                       443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1676.71
//
Query:       gi|313125517|ref|YP_004035781.1|  [L=164]
Description: ankyrin repeat-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-30  105.5   1.6    6.6e-14   52.3   0.0    2.3  3  Ank_2     Ankyrin repeats (3 copies)
    3.1e-20   72.0   1.8    2.4e-08   34.1   0.0    2.9  3  Ank_5     Ankyrin repeats (many copies)
    1.8e-17   63.5   0.1    2.5e-07   31.1   0.0    3.3  3  Ank_4     Ankyrin repeats (many copies)
    1.5e-16   60.0   0.3    1.6e-05   25.1   0.0    4.2  5  Ank       Ankyrin repeat
    1.9e-15   55.4   0.2      3e-06   27.1   0.0    4.1  4  Ank_3     Ankyrin repeat
  ------ inclusion threshold ------
      0.025   14.5   0.0        5.3    7.0   0.0    2.2  2  PEGA      PEGA domain


Domain annotation for each model (and alignments):
>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   2.2e-17   6.6e-14       4      83 .]      17     105 ..      14     105 .. 0.86
   2 !   45.2   0.0   3.4e-15     1e-11      25      82 ..      74     137 ..      74     138 .. 0.90
   3 !   18.5   0.1   7.6e-07    0.0023      52      82 ..     107     137 ..     101     163 .. 0.65

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 2.2e-17
                             Ank_2   4 AakngnlelvklLlegadpn..k.ngktaLhyAakngnleivklLleh......adndgrtpLhyAarsghleivkl 71 
                                       A+ ++n e + +L++ ad+n  + +g + Lh+Aa  g  e++  L+e        dn+grtpLh A+  gh eiv++
  gi|313125517|ref|YP_004035781.1|  17 AIIQNNKEQFYQLISDADLNhrSgDGGNLLHIAAWTGEPEFAAELIERgieldaKDNQGRTPLHEAVDRGHHEIVEM 93 
                                       555666789999998888886548**********************9677766555********************* PP

                             Ank_2  72 Llekgadinlkd 83 
                                       L+e+ga +++ d
  gi|313125517|ref|YP_004035781.1|  94 LVENGARLDIED 105
                                       ******998876 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 3.4e-15
                             Ank_2  25 ngktaLhyAakngnleivklLleh...ad...ndgrtpLhyAarsghleivklLlekgadinlk 82 
                                       +g+t+Lh A+ +g++eiv++L+e+   +d    +g  pLh A+ +g++e+ +lL+ +gad++  
  gi|313125517|ref|YP_004035781.1|  74 QGRTPLHEAVDRGHHEIVEMLVENgarLDiedMYGAQPLHKAVANGNYELTNLLVTHGADPTHE 137
                                       599********************88774465788*********************99***9875 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 7.6e-07
                             Ank_2  52 dgrtpLhyAarsghleivklLlekgadinlk 82 
                                       +g  pLh A+ +g++e+ +lL+ +gad++  
  gi|313125517|ref|YP_004035781.1| 107 YGAQPLHKAVANGNYELTNLLVTHGADPTHE 137
                                       4566666666666666666666666666543 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0     8e-12   2.4e-08       6      56 .]      32      82 ..      29      82 .. 0.93
   2 !   26.4   0.0   2.1e-09   6.1e-06       1      49 [.      61     108 ..      61     110 .. 0.94
   3 !   22.1   0.2   4.7e-08   0.00014       1      43 [.      94     135 ..      94     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 8e-12
                             Ank_5  6 padvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56
                                      +ad+n++ g+g + Lh+Aa+ g ++ + +L++rg  l+++d++G+t+l+ A
  gi|313125517|ref|YP_004035781.1| 32 DADLNHRSGDGGNLLHIAAWTGEPEFAAELIERGIELDAKDNQGRTPLHEA 82
                                      489999999999************************************866 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 2.1e-09
                             Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrG 49 
                                       L+e+g + ++++d+ g tpLh A+ +g+ ++v++L+++ga l++ d +G
  gi|313125517|ref|YP_004035781.1|  61 LIERG-IELDAKDNQGRTPLHEAVDRGHHEIVEMLVENGARLDIEDMYG 108
                                       89999.*********************************9999888777 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 4.7e-08
                             Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadln 43 
                                       L+e+g a+++ +d +g  pLh A+ +g+ ++ +lL+ +gad++
  gi|313125517|ref|YP_004035781.1|  94 LVENG-ARLDIEDMYGAQPLHKAVANGNYELTNLLVTHGADPT 135
                                       899**.***********************************87 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     1e-05     0.031      21      49 ..      30      56 ..      10      59 .. 0.80
   2 !   31.1   0.0   8.4e-11   2.5e-07      16      55 .]      57      95 ..      53      95 .. 0.92
   3 !   26.5   0.0   2.3e-09   6.8e-06       8      55 .]      82     128 ..      81     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                             Ank_4 21 lekgadinaqdnrsGetalhiAakrgnve 49
                                      + ++ad+n++ +++G ++lhiAa++g +e
  gi|313125517|ref|YP_004035781.1| 30 I-SDADLNHR-SGDGGNLLHIAAWTGEPE 56
                                      4.689*****.*************99665 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 8.4e-11
                             Ank_4 16 lvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55
                                       ++ L+e+g++++a  +++G+t+lh A+ rg+ ei+++L+
  gi|313125517|ref|YP_004035781.1| 57 FAAELIERGIELDAK-DNQGRTPLHEAVDRGHHEIVEMLV 95
                                      57889*********9.**********************96 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 2.3e-09
                             Ank_4   8 aaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                       a+  g++e+v+ L+e+ga ++   + +G  +lh+A+ +gn+e + lL+
  gi|313125517|ref|YP_004035781.1|  82 AVDRGHHEIVEMLVENGARLDIE-DMYGAQPLHKAVANGNYELTNLLV 128
                                       6779************9987774.77999*************998885 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.36   1.1e+03      15      30 ..      24      38 ..      16      39 .. 0.65
   2 !   12.6   0.0   4.9e-05      0.15       5      32 .]      45      73 ..      41      73 .. 0.92
   3 !   25.1   0.0   5.3e-09   1.6e-05       2      31 ..      75     105 ..      74     105 .. 0.93
   4 !   16.4   0.1     3e-06    0.0089       5      30 ..     111     137 ..     107     139 .. 0.90
   5 ?   -3.1   0.0       4.4   1.3e+04       4      10 ..     143     149 ..     142     160 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.36
                                      HHHHHHHHTTTSTTCB CS
                               Ank 15 kriiklLLhGAnlnal 30
                                      ++  + L++ A+ln +
  gi|313125517|ref|YP_004035781.1| 24 EQFYQ-LISDADLNHR 38
                                      44445.88779**986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.9e-05
                                      HHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                               Ank  5 PLHlAatngkkriiklLL.hGAnlnaldn 32
                                       LH+Aa+ g ++ + +L+ +G +l+a+dn
  gi|313125517|ref|YP_004035781.1| 45 LLHIAAWTGEPEFAAELIeRGIELDAKDN 73
                                      6*****99**********99********8 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 5.3e-09
                                       SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                               Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                       G+TPLH A+ +g+++i+++L+ +GA l++ d
  gi|313125517|ref|YP_004035781.1|  75 GRTPLHEAVDRGHHEIVEMLVeNGARLDIED 105
                                       9********************99**998866 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 3e-06
                                       HHHHHHHHTTHHHHHHHH.TTTSTTCB CS
                               Ank   5 PLHlAatngkkriiklLL.hGAnlnal 30 
                                       PLH A+ ng+ + + lL+ hGA+++  
  gi|313125517|ref|YP_004035781.1| 111 PLHKAVANGNYELTNLLVtHGADPTHE 137
                                       9****99*****************876 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 4.4
                                       BHHHHHH CS
                               Ank   4 TPLHlAa 10 
                                       +PL lA 
  gi|313125517|ref|YP_004035781.1| 143 SPLSLAR 149
                                       6787763 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0077        23       2      30 ..      42      69 ..      41      70 .. 0.89
   2 !   27.1   0.0     1e-09     3e-06       2      30 ..      75     102 ..      74     103 .. 0.92
   3 !   17.5   0.0   1.4e-06    0.0041       1      30 [.     107     135 ..     107     136 .. 0.90
   4 ?   -1.6   0.0       2.3     7e+03       4      24 ..     143     162 ..     141     163 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0077
                             Ank_3  2 GetpLhlAarsgnleivkfLlenkgadvn 30
                                      G ++Lh+Aa  g +e +  L+e +g++++
  gi|313125517|ref|YP_004035781.1| 42 GGNLLHIAAWTGEPEFAAELIE-RGIELD 69
                                      7789******************.999987 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1e-09
                             Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvn 30 
                                       G+tpLh+A+  g++eiv++L+e +ga ++
  gi|313125517|ref|YP_004035781.1|  75 GRTPLHEAVDRGHHEIVEMLVE-NGARLD 102
                                       9*********************.899776 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.4e-06
                             Ank_3   1 nGetpLhlAarsgnleivkfLlenkgadvn 30 
                                       +G  pLh A+ +gn+e+  +L+  +gad+ 
  gi|313125517|ref|YP_004035781.1| 107 YGAQPLHKAVANGNYELTNLLVT-HGADPT 135
                                       5778************9999999.9***85 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.3
                             Ank_3   4 tpLhlAarsgnleivkfLlen 24 
                                       +pL lA  ++  +   +Llen
  gi|313125517|ref|YP_004035781.1| 143 SPLSLARDADAED-FVALLEN 162
                                       6777776666666.6667764 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0062        19      21      38 ..      73      90 ..      65      92 .. 0.88
   2 ?    7.0   0.0    0.0018       5.3      11      39 ..      97     124 ..      95     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0062
                              PEGA 21 ylGkTPvtlsleaGnysl 38
                                      + G+TP+  +++ G +++
  gi|313125517|ref|YP_004035781.1| 73 NQGRTPLHEAVDRGHHEI 90
                                      67**************98 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0018
                              PEGA  11 eGatVyidGkylGkTPvtlsleaGnyslr 39 
                                       +Ga+  i +  +G  P+  ++++Gny+l+
  gi|313125517|ref|YP_004035781.1|  97 NGARLDI-EDMYGAQPLHKAVANGNYELT 124
                                       6888888.6799***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 991.17
//
Query:       gi|313125518|ref|YP_004035782.1|  [L=418]
Description: hypothetical protein Hbor_07450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-31  107.4   2.3    7.7e-31  106.2   2.3    1.7  1  DUF4157        Domain of unknown function (DUF4157)
    3.3e-24   85.1  10.3    1.6e-23   82.9   6.2    2.6  2  GH-E           HNH/ENDO VII superfamily nuclease with conserv
  ------ inclusion threshold ------
       0.03   14.7   1.3       0.03   14.7   1.3    1.9  2  Peptidase_M91  Effector protein


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   2.3   1.3e-34   7.7e-31       2      78 ..     147     223 ..     146     224 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.3e-34
                           DUF4157   2 lpeavraemerafgadlsdVrvhtgsaaaraaralgAqAfTlgndivfaageyqpesaagrellaHELtHvvqqreg 78 
                                       l++++++ me+++g++l+dVr+htgs+aa+a+++++A+AfT+gn+++f++gey+p+s +g++llaHEL+Hv qq++g
  gi|313125518|ref|YP_004035782.1| 147 LDSSIQQAMEERMGESLDDVRIHTGSRAANACEDINARAFTVGNHVAFNHGEYDPSSTEGQHLLAHELAHVRQQTGG 223
                                       89************************************************************************986 PP

>> GH-E  HNH/ENDO VII superfamily nuclease with conserved GHE residues
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.01        62       2      26 ..     283     306 ..     282     326 .. 0.75
   2 !   82.9   6.2   2.6e-27   1.6e-23       1      69 []     324     399 ..     324     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.01
                              GH-E   2 GkvrdpntggtsrerdwdmGHkpgr 26 
                                       G+++ ++t+ +++++++ ++H+p++
  gi|313125518|ref|YP_004035782.1| 283 GRFAEKDTE-QYKQKKYSIDHRPPY 306
                                       778889999.9***********987 PP

  == domain 2  score: 82.9 bits;  conditional E-value: 2.6e-27
                              GH-E   1 dGkvrdpntg.......gtsrerdwdmGHkpgreyrrlvkkaeeggitqkefldeynnpdnyrledpseNrShgae 69 
                                       d+kvrdpnt+       +++r ++w+mGHk++reyr+l +++++g i+++ef +ey+npd+y++e p+eN+++++e
  gi|313125518|ref|YP_004035782.1| 324 DDKVRDPNTEevltwdkDRGRGEQWHMGHKKQREYRYLLEYYQQGIISEEEFVKEYQNPDHYQAEAPRENMGRRHE 399
                                       679**************999******************************************************98 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.3   4.9e-06      0.03      30     135 ..     144     246 ..     117     250 .. 0.67
   2 ?   -1.9   0.1      0.62   3.7e+03     147     166 ..     377     396 ..     317     402 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.9e-06
                     Peptidase_M91  30 GqqlLeelksskse....gerkltikelvdedngtakyeekekgegtdaeinynpafsseeegkegrPsavLyHEla 102
                                       Gqql ++++++++e      +++ i+ +    n  ++   + + ++ ++++ +n         + ++ ++ L+HEla
  gi|313125518|ref|YP_004035782.1| 144 GQQLDSSIQQAMEErmgeSLDDVRIHTGSRAANACEDI--NARAFTVGNHVAFNHGEYDP---SSTEGQHLLAHELA 215
                                       77777777777776554344456666644444444443..45677777778887774333...56666789****** PP

                     Peptidase_M91 103 HaydalngtlddgeydgkdeedssgvpneErqA 135
                                       H+++++ g +   +++gk e d +   + Er+A
  gi|313125518|ref|YP_004035782.1| 216 HVRQQTGGAVSMLPQEGKLEIDPDE--RLEREA 246
                                       ********99988888887777766..555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.62
                     Peptidase_M91 147 pevrdpdsahpeeltENglR 166
                                        e ++pd+++ e+++EN  R
  gi|313125518|ref|YP_004035782.1| 377 KEYQNPDHYQAEAPRENMGR 396
                                       44556667777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2643.52
//
Query:       gi|313125519|ref|YP_004035783.1|  [L=302]
Description: pyridoxal phosphate synthase yaad subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   3.6e-103  343.8   8.2   4.5e-103  343.4   8.2    1.1  1  SOR_SNZ      SOR/SNZ family
    1.5e-10   40.8   5.7      2e-05   24.0   0.6    2.2  2  ThiG         Thiazole biosynthesis protein ThiG
     0.0021   17.2   1.5       0.84    8.7   0.1    2.5  2  Dus          Dihydrouridine synthase (Dus)
     0.0074   15.5   0.0       0.22   10.7   0.0    2.3  2  IGPS         Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.016   14.8   0.6      0.049   13.2   0.3    1.8  1  OMPdecase    Orotidine 5'-phosphate decarboxylase / HUMPS fam
       0.14   11.5   0.1        5.6    6.4   0.0    2.5  2  MttA_Hcf106  mttA/Hcf106 family


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.4   8.2  1.5e-106  4.5e-103       3     207 .]      16     220 ..      14     220 .. 0.99

  Alignments for each domain:
  == domain 1  score: 343.4 bits;  conditional E-value: 1.5e-106
                                       HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEET CS
                           SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvri 79 
                                        vk+g+a+m+kgGvimdvv aeqa+iaeeaGavavmale vpadirk+ggv+rm+dp+++kei++avsipvm k+ri
  gi|313125519|ref|YP_004035783.1|  16 LVKRGFAQMQKGGVIMDVVDAEQARIAEEAGAVAVMALEAVPADIRKRGGVSRMADPETVKEIIDAVSIPVMGKARI 92 
                                       69*************************************************************************** PP

                                       T-HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHH CS
                           SOR_SNZ  80 GhfveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveav 156
                                       Gh +eaqile++gvd+iDesevlt+ad+++hidk++f++pfvcGarnlgealrri+eGaamirtkGeagtGdv +av
  gi|313125519|ref|YP_004035783.1|  93 GHHTEAQILESIGVDMIDESEVLTMADDRYHIDKRDFTAPFVCGARNLGEALRRINEGAAMIRTKGEAGTGDVNQAV 169
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                           SOR_SNZ 157 rhvrkikeeirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                       +h r+ik +irkl+ ++++e  ++a+e++ap elv+e+ae+grlpvvnfaa
  gi|313125519|ref|YP_004035783.1| 170 HHQRNIKGSIRKLQGMTHQEREKWAREHEAPAELVHETAEMGRLPVVNFAA 220
                                       *************************************************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.5   1.6e-07   0.00048     113     212 ..      10     120 ..       1     137 [. 0.74
   2 !   24.0   0.6   6.7e-09     2e-05     175     225 ..     212     264 ..     197     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHTT-EEEEE..E-S-HH...HHHHHHHTT-SEBEEBSS...STTS---...-S-HHHHHHHHHH-SS-B CS
                              ThiG 113 lkaaeiLvkeGFevlpY..vsdDlv...larrleevGcaavmPlaa...piGsglG...llnkealkiiieeakvPv 178
                                       l+    Lvk GF+ +    v  D+v    ar  ee+G+ avm l a    i    G   ++++e++k ii+ +++Pv
  gi|313125519|ref|YP_004035783.1|  10 LRRGTELVKRGFAQMQKggVIMDVVdaeQARIAEEAGAVAVMALEAvpaDIRKRGGvsrMADPETVKEIIDAVSIPV 86 
                                       4455679999999986433555665111566679********9965222565555511157899************* PP

                                       EEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                              ThiG 179 ivDAGigspsdaaqamelGadavllntavaeakd 212
                                       +  A ig+ ++a     +G+d +     +++a+d
  gi|313125519|ref|YP_004035783.1|  87 MGKARIGHHTEAQILESIGVDMIDESEVLTMADD 120
                                       ************999999*998877777777766 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 6.7e-09
                                       SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 175 kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                       ++Pv+  A  Gi +p daa  m   +d++++ + +  a+dp am +a+  av+
  gi|313125519|ref|YP_004035783.1| 212 RLPVVNFAagGIATPADAALMMHHECDGIFVGSGIFGAEDPEAMGKAIVEAVN 264
                                       78888544349****************************************97 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00028      0.84      96     138 ..      61      99 ..      36     109 .. 0.72
   2 !    7.5   0.1   0.00065         2     182     218 ..     213     248 ..     169     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00028
                                       TEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC CS
                               Dus  96 rggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeee 138
                                       r+ +G + +++p++v++i+    +av+iPv  k rig + e +
  gi|313125519|ref|YP_004035783.1|  61 RKRGGVSRMADPETVKEII----DAVSIPVMGKARIGHHTEAQ 99 
                                       5666667777777665555....67889999999998884444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00065
                                       -SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCC CS
                               Dus 182 vsipviaNGdIkdaedaqaileetGadgvmigrgalg 218
                                       ++++ +a G+I ++ da  ++++  +dg+ +g g  g
  gi|313125519|ref|YP_004035783.1| 213 LPVVNFAAGGIATPADAALMMHH-ECDGIFVGSGIFG 248
                                       56777899**********99999.9*******99764 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.021        63      61      87 ..      26      52 ..      18     109 .. 0.86
   2 !   10.7   0.0   7.2e-05      0.22     210     250 ..     215     255 ..     198     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.021
                                      TEESBSS--HHHHHHHHTTT.-SEEEE CS
                              IGPS 61 kgliredfdpaeiAkkyeeagAsaiSV 87
                                      kg + +d++ ae+A+  eeagA a+  
  gi|313125519|ref|YP_004035783.1| 26 KGGVIMDVVDAEQARIAEEAGAVAVMA 52
                                      7889999999************99855 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.2e-05
                                       SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHH CS
                              IGPS 210 vllvaeSGiktredveklkeegvnafLvGeslmrqedveka 250
                                       v+  a  Gi+t++d+  + +++ +++ vG+ +  +ed e++
  gi|313125519|ref|YP_004035783.1| 215 VVNFAAGGIATPADAALMMHHECDGIFVGSGIFGAEDPEAM 255
                                       6777899**************************99998875 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.6e-05     0.049     122     224 ..     154     258 ..     142     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                       TSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHTH.HHHHH.TTCSCEEEHHHTT..EEEEECTTCCGGGH CS
                         OMPdecase 122 msskgnlmlqekgytqacveaarehkaedfvmGfvaqetln.ateed.addfihltpgigl..eqggdgkgqqyntp 194
                                       + +kg++ +++  + qa+ ++++ +    ++ G+  qe+++ a e +   +++h t  +g    +   ++g+     
  gi|313125519|ref|YP_004035783.1| 154 IRTKGEAGTGD--VNQAVHHQRNIKGSIRKLQGMTHQEREKwAREHEaPAELVHETAEMGRlpVVNFAAGGIATPAD 228
                                       45566666666..6666666666555559999*********944444577999999999988878888889988888 PP

                                       HHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 195 ekligiagadiiivGRgIlkagdpveeaer 224
                                        +l+   ++d i vG gI++a+dp++  ++
  gi|313125519|ref|YP_004035783.1| 229 AALMMHHECDGIFVGSGIFGAEDPEAMGKA 258
                                       99999999****************997765 PP

>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.038   1.1e+02      26      35 ..     137     146 ..     136     149 .. 0.91
   2 ?    6.4   0.0    0.0019       5.6      19      34 ..     269     284 ..     269     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.038
                                       HHHHHHHHHH CS
                       MttA_Hcf106  26 araLGktLre 35 
                                       ar+LG++Lr 
  gi|313125519|ref|YP_004035783.1| 137 ARNLGEALRR 146
                                       8*******95 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0019
                                       TTTHHHHHHHHHHHHH CS
                       MttA_Hcf106  19 pkkLPEvaraLGktLr 34 
                                       p++L+E+a + Gk+++
  gi|313125519|ref|YP_004035783.1| 269 PDQLAEIASGIGKGMK 284
                                       899***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1886.05
//
Query:       gi|313125520|ref|YP_004035784.1|  [L=161]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-17   62.0   0.4      1e-16   61.7   0.4    1.1  1  Usp             Universal stress protein family
  ------ inclusion threshold ------
      0.021   15.5   0.1      0.031   14.9   0.1    1.3  1  Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.4   1.1e-20     1e-16       3     139 ..       2     145 ..       1     146 [. 0.97

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.1e-20
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.......HH CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.......ak 72 
                                       k  lV+v   +  +++++ A e a  +++el+ll++i+++++++   a +e + + + ++++++e +a       a 
  gi|313125520|ref|YP_004035784.1|   2 KQALVVVTPGKRGRRLIREAGEYATGTDTELVLLTIIPEDEFEEKRRAVSEIGSSDAIYTLEQAEGTAereameiAD 78 
                                       66789999999****************************************************************** PP

                                       HHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  73 aaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                       + + +  v+ + v ++g +a++il+vae e++d + +G r+rs   ++l+G+v+++vl   + pV++
  gi|313125520|ref|YP_004035784.1|  79 DVLSELNVSYRAVSTVGRKADTILDVAETEGVDHVFLGGRRRSPAGKALFGDVAQKVLLTFEGPVTL 145
                                       ***********************************************************99999986 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   3.4e-06     0.031      39      82 ..      68     111 ..      40     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-06
                    Mg_chelatase_C  39 eldeeaeelleeaierlglsaRaydrilkvArTiADLegseeie 82 
                                       + ++ea+e+ ++++++l++s Ra++ + + A Ti D++++e ++
  gi|313125520|ref|YP_004035784.1|  68 TAEREAMEIADDVLSELNVSYRAVSTVGRKADTILDVAETEGVD 111
                                       5688999********************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1068.18
//
Query:       gi|313125521|ref|YP_004035785.1|  [L=291]
Description: homoserine kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-12   45.1   4.1      9e-12   45.1   4.1    2.3  3  GHMP_kinases_N  GHMP kinases N terminal domain
    1.9e-07   31.3   0.0    5.1e-07   30.0   0.0    1.7  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.52   4.7e+03      53      60 ..      13      20 ..       8      24 .. 0.73
   2 !   45.1   4.1     1e-15     9e-12       1      66 []      72     139 ..      72     139 .. 0.90
   3 ?   -3.9   0.5       1.9   1.7e+04      15      23 ..     189     197 ..     189     201 .. 0.48

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.52
                                      HHHSHHHH CS
                    GHMP_kinases_N 53 ngsggDva 60
                                       gsg+Dv+
  gi|313125521|ref|YP_004035785.1| 13 LGSGFDVF 20
                                      48999996 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 1e-15
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       +i i++ + +++GLGSSAA a+++++Al+al++     +e +  a+e+e  +  g+ + ++va++++Gg
  gi|313125521|ref|YP_004035785.1|  72 HIQIDKGVRPSSGLGSSAASAAGAALALNALYDRGYsrSElVPAAAEGEAVVS-GEAHVDNVAPALLGG 139
                                       799*****************************877434336999*****8887.**************8 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.9
                                       CHHHHHHHH CS
                    GHMP_kinases_N  15 GSSAAlava 23 
                                       GS A+lav+
  gi|313125521|ref|YP_004035785.1| 189 GSAATLAVG 197
                                       444444444 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   5.7e-11   5.1e-07       5      80 ..     198     267 ..     194     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.7e-11
                    GHMP_kinases_C   5 lergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralr 80 
                                       ++r d el+g+++ +    ++   + +l    e++  a++++Ga g+ +sGa  Gp+v a +  +d+  qva a+ 
  gi|313125521|ref|YP_004035785.1| 198 MCRSDPELVGRGMDERLV-TP--ARSELITGYENVRTAALDAGATGVTVSGA--GPSVLAAC-YPDDRRQVAAAMV 267
                                       6899**********6666.68..*****************************..********.9999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1918.51
//
Query:       gi|313125522|ref|YP_004035786.1|  [L=450]
Description: protoporphyrinogen oxidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-38  132.7   0.1    4.1e-38  131.8   0.1    1.4  1  Amino_oxidase   Flavin containing amine oxidoreductase
    1.6e-14   53.9   0.2    4.6e-14   52.4   0.2    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.5e-09   36.1   0.5    3.6e-06   26.8   0.2    2.2  2  DAO             FAD dependent oxidoreductase
      2e-07   30.5   2.1    1.6e-05   24.3   0.1    2.5  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-05   24.4   0.9    1.3e-05   24.4   0.9    1.5  2  FAD_binding_2   FAD binding domain
    0.00021   20.8   0.4    0.00042   19.8   0.1    1.6  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0006   19.0   0.1     0.0011   18.1   0.1    1.5  1  GIDA            Glucose inhibited division protein A
     0.0012   17.6   0.4     0.0066   15.2   0.5    1.8  2  HI0933_like     HI0933-like protein
     0.0017   18.9   2.4     0.0047   17.4   0.4    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0019   18.2   0.7       0.24   11.4   0.1    2.3  2  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.015   14.1   0.4       0.11   11.4   0.1    2.0  2  Trp_halogenase  Tryptophan halogenase
      0.027   12.9   0.0      0.038   12.4   0.0    1.2  1  FMO-like        Flavin-binding monooxygenase-like
      0.047   12.9   0.4       0.17   11.1   0.3    1.8  2  FAD_binding_3   FAD binding domain
      0.066   12.5   0.1      0.066   12.5   0.1    1.5  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.075   12.3   0.1       0.26   10.5   0.0    1.8  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
        0.1   11.7   0.0       0.16   11.0   0.0    1.2  1  Lycopene_cycl   Lycopene cyclase protein
       0.11   12.6   0.6       0.38   10.8   0.2    2.0  2  PepSY_2         Peptidase propeptide and YPEB domain
       0.14   11.4   3.3       0.14   11.4   0.5    2.3  3  Thi4            Thi4 family
       0.15   11.9   0.1       0.24   11.3   0.1    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.8   0.1   4.4e-41   4.1e-38       1     451 [.       9     433 ..       9     434 .. 0.90

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 4.4e-41
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHHTTCCCCEEEESCCGCEE CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellkelgledslslpdpgapkr 77 
                                       +aGLaaA++L ++G+dV+v+Ea+d vGG ++ ++ dG  ie   + ++ ++  + el++elgl ++l+++   + ++
  gi|313125522|ref|YP_004035786.1|   9 IAGLAAAYRLRQHGYDVQVFEATDDVGGLAAVYETDGDDIEKFYHHLSKSEETIVELAQELGLGNRLEWKIGKNSYY 85 
                                       8*******************************************************************999884444 PP

                                       EEETTEECCTTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH......HHHCCCCHHHHHHHHHCHHHHHH CS
                     Amino_oxidase  78 vlskggrefpgdlspvpaewealleqgalsaellsleeklrlgleall......qktldeldldskslaesleelgr 148
                                       v        +g+ +p++ +w++ +         +sl +k rlg+  +          +d  ++ s++ + s++++  
  gi|313125522|ref|YP_004035786.1|  86 V--------DGTAHPLDTAWQIAAY------PHMSLYDKFRLGMLTQGidvrggIPDFDAYNELSEYEHVSIRDFVV 148
                                       4........999*************......9********************9988999999999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEE......TTHTHHHHHHHHHT CS
                     Amino_oxidase 149 repgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllp......rgGlsqlpealaee 219
                                        + +   v +++++p       ++ g f+   ++   ++a++l + ++  +++ll++      +gG++ l +al + 
  gi|313125522|ref|YP_004035786.1| 149 EHTTR-GVYENFVDP-------LLDGKFGH--RKDDISAAWFLGRIRFRGERDLLRGeilgyfDGGFRPLLDALVDA 215
                                       99999.9********.......99999998..9999999************************************** PP

                                       TTTEEEETSEEEEEEEE...ETTCEEEEETTSTEE.EESEEEE-S-HHHHHSSEEESCCSHHHHHHHHHSEEEEEEE CS
                     Amino_oxidase 220 lrgldirlntrVkeikr...egdgvtvtledgevv.eaDaVvvTvplgvlkailfsPplpdekaeairnlgfgsvnk 292
                                        ++ +i +++rV e+++   + d  tv++ dg+++ ++D+Vvv++ ++vl        l    +     ++f +++ 
  gi|313125522|ref|YP_004035786.1| 216 VGRENITTGARVAELATdgeSVDSLTVETADGTTThDVDSVVVAAMPNVLE------DL----TGYECDIEFQGAVC 282
                                       *****************6555555999999*********************......66....55555679999999 PP

                                       EEEEESSGG....SGCSTSECECECCCEEETTTEEEEECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHH CS
                     Amino_oxidase 293 vilefdrkf....wednalgqgvlvseltttlgeafissdfpsrappgkglvllvyvggdaaneleslsdeelvqav 365
                                         +++ +      w++ a+    + + ++   +++fi     +r+  ++ l + +yv  ++ +++ +++d+e+ +  
  gi|313125522|ref|YP_004035786.1| 283 GLVTMSESLldtyWLNVAH----DAPFGSLIEHTNFIPK---ERYGGDHLLYIASYVQSREEELW-QMDDDEVEELW 351
                                       9999999998888888886....9999999999999994...46666677777888876666665.*********** PP

                                       HHHHHHHHTGTSSTCSEEEEEECCTETTTSSSEEE.BTTH.HHHHHHHHHCH.....HCSTTEEE.SGGGCTTTTTS CS
                     Amino_oxidase 366 lrdLrklfgeevpepkatlvtrWhtdplargsysyvsvgp.ghedydplakp.....egdprlffAGehtsreypgt 436
                                       l++++++++    +  + +v  ++  +++       ++gp  ++ y +l  p     e   ++++AG + +++yp +
  gi|313125522|ref|YP_004035786.1| 352 LDEIESMYP----DFDRSTVEEFRIARNP-------RAGPiYERGYLDLVVPydlgdEVSEGVYYAGMASASQYPER 417
                                       *********....9999999999999999.......6666666667777777666888888**************** PP

                                       .HHHHHHHHHHHHHHH CS
                     Amino_oxidase 437 .vegAilSGlraAari 451
                                        ++g i +G + A+ri
  gi|313125522|ref|YP_004035786.1| 418 sLNGGIVAGYECADRI 433
                                       ***************9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.2   4.9e-17   4.6e-14       1      60 [.       4      61 ..       4      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 4.9e-17
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHH CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypn 60
                                      +vG+G++Gl+aAy+L+++g+dv+++e+ d++GG aa ye +g  ++   h + +s+  + 
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRLRQHGYDVQVFEATDDVGGLAAVYETDGDDIEKFYHHLSKSE--ET 61
                                      8***************************************9988887777776653..55 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.2   3.8e-09   3.6e-06       2      35 ..       2      36 ..       1      77 [. 0.91
   2 !    7.7   0.0    0.0024       2.3     162     322 ..     220     385 ..     149     431 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.8e-09
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                      + ++GGGi+Gl++Ay L ++g  V ++e+ d++g g
  gi|313125522|ref|YP_004035786.1|  2 IGVVGGGIAGLAAAYRLRQHGydVQVFEATDDVG-G 36
                                      679**************9999*********9998.3 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0024
                                       EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGHHHHHTTCTT...TSEE...EEEEEEEEEEEEC CS
                               DAO 162 eilegtevtgleeedgkvwgverttp.gen.daadavVnaaGawsdllgllkel...dlpi...spvrgqvlvlkpl 230
                                       +i +g++v +l  +++ v  + ++t+ g++ + +d vV+aa + +  l   ++l   ++ i    +v g v + + l
  gi|313125522|ref|YP_004035786.1| 220 NITTGARVAELATDGESVDSLTVETAdGTTtHDVDSVVVAAMPNV--L---EDLtgyECDIefqGAVCGLVTMSESL 291
                                       466777777775544445555556666988777799*****8885..6...44443445532012233333333333 PP

                                       CTHSTGSGCSEEEEEEEETTTTEEEEEE....TTSEEEEEESSEEETTCSS.TSCSHHHHHH.HHHHHHHHSGGG.. CS
                               DAO 231 seklvspaailpvpetdddgrgvyvtpr....kdgrvlvGgtadeesgddd.pevdeedide.llealrklfPql.. 299
                                        ++    +     p       ++ ++p      d+ +++ +    +s++++  + d+++++e  l++++ ++P++  
  gi|313125522|ref|YP_004035786.1| 292 LDTYW-LNVAHDAP-FGSLIEHTNFIPKerygGDHLLYIASYV--QSREEElWQMDDDEVEElWLDEIESMYPDFdr 364
                                       33332.22333333.6666677788885666566678888876..333334578888888885689********633 PP

                                       CGEEEEEEEEEEETTSSEEEEEE CS
                               DAO 300 gdvlrkwaGlrplpdglpliget 322
                                       + v++ +   r  p  +p+  ++
  gi|313125522|ref|YP_004035786.1| 365 STVEEFRI-ARN-PRAGPIYERG 385
                                       33554333.333.5666666663 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   1.7e-08   1.6e-05       5      35 ..       4      34 ..       2      88 .. 0.81
   2 !    5.4   0.1    0.0095         9     199     235 ..     220     260 ..     204     274 .. 0.90
   3 ?   -2.8   0.0       3.1   2.9e+03       7      22 ..     421     436 ..     421     438 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.7e-08
                                      EE--SHHHHHHHHHHHHHTS-EEEEETTHCH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  5 viGgGpAGlaaaltlaqagakvtlvelegtc 35
                                      v+GgG+AGlaaa +l+q+g++v ++e+++ +
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRLRQHGYDVQVFEATDDV 34
                                      9************************855544 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0095
                                       EEEESCEEEEEEETTE...EEEEEETTSCE.EEESEEEE-S CS
                                       xxxxxxxxxxxxxxxx...xxxxxxxxxxx.xxxxxxxxxx RF
                       Pyr_redox_2 199 evklgtsvkeidgnge...klevvledgee.idadlvvvav 235
                                       ++ +g++v e+  +ge   +l+v++ dg++  d+d vvva+
  gi|313125522|ref|YP_004035786.1| 220 NITTGARVAELATDGEsvdSLTVETADGTTtHDVDSVVVAA 260
                                       57899*********99777777******9999*******96 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.1
                                       --SHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   7 GgGpAGlaaaltlaqa 22 
                                       Gg +AG+++a ++aq+
  gi|313125522|ref|YP_004035786.1| 421 GGIVAGYECADRIAQK 436
                                       5558******999996 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.9   1.4e-08   1.3e-05       4      37 ..       4      38 ..       2      43 .. 0.91
   2 ?   -3.4   0.0         4   3.8e+03      69      88 ..     241     260 ..     211     279 .. 0.51

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.4e-08
                                      EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.G CS
                     FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefgg.a 37
                                      V+G+G+AGLaAA++++++G +v v e ++ +gg a
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRLRQHGYDVQVFEATDDVGGlA 38
                                      9***************************9999843 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4
                                       HHHHTTT-S-HHHHHHHHHT CS
                     FAD_binding_2  69 tlkaldeladqplveafvea 88 
                                       t++++d+   +++  ++v+a
  gi|313125522|ref|YP_004035786.1| 241 TVETADGTTTHDVDSVVVAA 260
                                       23333333333333333333 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   4.4e-07   0.00042       4      39 ..       4      39 ..       2      91 .. 0.85
   2 ?   -2.4   0.0       2.4   2.3e+03     103     133 ..     220     250 ..     206     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.4e-07
                      FAD_oxidored  4 VvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                                      VvGGg+aG+aAA+   ++G  v + e ++ +GGl++
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRLRQHGYDVQVFEATDDVGGLAA 39
                                      9********************************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                      FAD_oxidored 103 tvllntrlvevekegkriesvtveskegrkt 133
                                       ++ +++r+ e  ++g+ ++s+tve+ +g++t
  gi|313125522|ref|YP_004035786.1| 220 NITTGARVAELATDGESVDSLTVETADGTTT 250
                                       67789999999999999*****998777554 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.2e-06    0.0011       3      38 ..       3      37 ..       1      66 [. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                                      EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-- CS
                              GIDA  3 iViGgGhAGceAAlaaarlGakvlLithkldtiael 38
                                       V+GgG AG++AA+ + + G++v  + + +d+++ l
  gi|313125522|ref|YP_004035786.1|  3 GVVGGGIAGLAAAYRLRQHGYDVQVF-EATDDVGGL 37
                                      69**********************99.777777765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.5     7e-06    0.0066       5      36 ..       4      35 ..       1      37 [. 0.94
   2 ?   -0.2   0.0      0.34   3.2e+02     111     178 ..     208     272 ..     205     307 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7e-06
                                      EE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  5 viGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      v+GgG AGl aA +++++g +V ++e+++ +g
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRLRQHGYDVQVFEATDDVG 35
                                      9*************************999887 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE----SS-GGGT--SHHHH CS
                       HI0933_like 111 ivdallkelkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGGlSiPklGstgkgyk 178
                                       ++dal+ ++ +++++   + +  + + e+  +++v+t +++++   d++v+A    ++P++  +  gy+
  gi|313125522|ref|YP_004035786.1| 208 LLDALVDAVGRENITTGARVAELATDGESVDSLTVETaDGTTTHDVDSVVVA----AMPNVLEDLTGYE 272
                                       6777777777777766555555555555555688888778889999*****9....7777666655555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4     5e-06    0.0047       2      35 ..       2      35 ..       1      44 [. 0.91
   2 ?   -0.2   0.0       1.6   1.5e+03      56      79 ..     220     243 ..     194     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      + vvGgG  gl +A  l+++g +V+v+e+ d + 
  gi|313125522|ref|YP_004035786.1|  2 IGVVGGGIAGLAAAYRLRQHGYDVQVFEATDDVG 35
                                      579*************************999876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                                       EEECSEEEEEEEEETTSEEEEEEE CS
                         Pyr_redox  56 evllntkveeiegsedgvesvklk 79 
                                       ++ ++++v+e+ ++++ v s++++
  gi|313125522|ref|YP_004035786.1| 220 NITTGARVAELATDGESVDSLTVE 243
                                       478999******999989988886 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00025      0.24       2      45 ..       4      44 ..       3      51 .. 0.80
   2 ?    5.0   0.0     0.023        22     120     152 ..     223     259 ..     193     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdp.sep.gagrvwrtd 45
                                      +vG+G++Gla++ rL ++       ++++f+  +   g   v++td
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRLRQH-----GYDVQVFEAtDDVgGLAAVYETD 44
                                      8**************999.....599*****955554555566665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.023
                     NAD_binding_9 120 hraevvdleeradgq...avlladgasl.aadaVvLA 152
                                         a+v +l+++++++   +v +adg+++ ++d+Vv+A
  gi|313125522|ref|YP_004035786.1| 223 TGARVAELATDGESVdslTVETADGTTThDVDSVVVA 259
                                       35577777777755333389999**7654******99 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00011      0.11       2      88 ..       2      85 ..       1     102 [. 0.75
   2 ?    0.6   0.0      0.21     2e+02     360     381 ..     129     150 ..     126     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-..SSS---SS-EE--THHHHTHHHHT--HHHHCHHCT-EEE-EEEEE CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlves..eeigtvgvGeatipsirkllrlLgideeeflreteatfKlgikFe 78
                                      i +vGGG+aG  aA  l++++   ++v++ e+  +  g   v e     i+k+++ L  +ee  + e    + lg +  
  gi|313125522|ref|YP_004035786.1|  2 IGVVGGGIAGLAAAYRLRQHG---YDVQVFEAtdDVGGLAAVYETDGDDIEKFYHHLSKSEE-TIVELAQELGLGNRL- 75
                                      89************9999999...77888776213345667888888888888888888877.455666677777777. PP

                                      SSSSCESEEE CS
                    Trp_halogenase 79 dWgkkgeryi 88
                                      +W+  +++y+
  gi|313125522|ref|YP_004035786.1| 76 EWKIGKNSYY 85
                                      7776666666 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                    Trp_halogenase 360 iaefnrevarelervrdfiilh 381
                                        + +n+  ++e   +rdf++ h
  gi|313125522|ref|YP_004035786.1| 129 FDAYNELSEYEHVSIRDFVVEH 150
                                       589*****************99 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     4e-05     0.038       4      55 ..       2      53 ..       1      62 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                          FMO-like  4 vaviGaGvsGlasikccleegleptcfersddiGGlwrfkenveeGrasiyk 55
                                      + v+G+G++Gla+     + g +   fe +dd+GGl    e   +   + y 
  gi|313125522|ref|YP_004035786.1|  2 IGVVGGGIAGLAAAYRLRQHGYDVQVFEATDDVGGLAAVYETDGDDIEKFYH 53
                                      689*********************************9998888777777775 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00018      0.17       5      33 ..       3      31 ..       1      35 [. 0.89
   2 ?   -1.4   0.0       1.1   1.1e+03     182     239 ..     291     351 ..     277     374 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                      EEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  5 lIVGaGpaGlmlallLseaGvrvvlvekr 33
                                       +VG+G aGl +a  L+++G +v + e  
  gi|313125522|ref|YP_004035786.1|  3 GVVGGGIAGLAAAYRLRQHGYDVQVFEAT 31
                                      59********************9998865 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                       EEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEE...EEEECCETEEEEEEEEECCE-GGGS CS
                     FAD_binding_3 182 vyeagvldvlfdadlsdiveplvlilsaesrgv...mviPlentlerfyvqvearaekeer 239
                                       + +  +l+v  da++ ++ e+  +i+++  +g     + ++ + +e+ ++q++ ++ +e +
  gi|313125522|ref|YP_004035786.1| 291 LLDTYWLNVAHDAPFGSLIEHTNFIPKERYGGDhllYIASYVQSREEELWQMDDDEVEELW 351
                                       4556777777777777777776666665555444445555555555566665555544444 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.9e-05     0.066      33      63 ..       4      34 ..       1      69 [. 0.80
   2 ?   -3.9   0.1       7.4     7e+03     134     162 ..     236     262 ..     221     264 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.9e-05
                                      EESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C 33 viGgGvaGlqAiatakglgakVtvlDvrpar 63
                                      v+GgG+aGl+A+   ++ g +V+v++   ++
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRLRQHGYDVQVFEATDDV 34
                                      9************************987665 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.4
                                       SBTT--TBBTTSEEEEETTEEEEEBSTGG CS
                       AlaDh_PNT_C 134 nvetsrltthgepvveekgvvhygvanlp 162
                                       +v+   lt ++   +++++v  + va +p
  gi|313125522|ref|YP_004035786.1| 236 SVDS--LTVETADGTTTHDVDSVVVAAMP 262
                                       4552..23333333333444444444444 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00027      0.26       2      31 ..       4      33 ..       3      56 .. 0.85
   2 ?   -1.2   0.0         1   9.6e+02     235     264 ..     230     259 ..     206     289 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg.n 31
                                      ++G+G aGlaaa+ l+++g  d+ + E    
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRLRQHGY-DVQVFEATdD 33
                                      79*****************9.7999998744 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                       Pyr_redox_3 235 vkeikekeeeykvktedgkkvevkddvvla 264
                                       +    e+  + +v+t+dg++++  d vv+a
  gi|313125522|ref|YP_004035786.1| 230 LATDGESVDSLTVETADGTTTHDVDSVVVA 259
                                       333334445557778887777776666654 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.16       4      53 ..       4      50 ..       2      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                     Lycopene_cycl  4 viGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga 53
                                      v+G+G Agl+ A rl   + g  v + ea +++  ++   v++  + d+++
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRL--RQHGYDVQVFEATDDV--GGLAaVYETDGDDIEK 50
                                      9**************..9999999999999999..5555577777777665 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0004      0.38      38      73 ..      17      52 ..      12      56 .. 0.77
   2 ?   -1.1   0.0       2.1     2e+03      30      62 ..      57      89 ..      52      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                           PepSY_2 38 kleaqGykvkkievddggcyEvegldkdGkkveikl 73
                                       l+++Gy+v+ +e++d+    + +   dG  +e  +
  gi|313125522|ref|YP_004035786.1| 17 RLRQHGYDVQVFEATDDVGGLAAVYETDGDDIEKFY 52
                                      699**************5555557777888777555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                           PepSY_2 30 lpreklvakleaqGy.kvkkievddggcyEvegl 62
                                       ++e++v+ +++ G  +  + ++ ++  y v+g+
  gi|313125522|ref|YP_004035786.1| 57 KSEETIVELAQELGLgNRLEWKIGKN-SYYVDGT 89
                                      57999999999999999999999666.7888876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00015      0.14      22      55 ..       4      36 ..       1      40 [. 0.90
   2 ?   -3.2   0.1       4.2     4e+03     140     171 ..     240     274 ..     220     282 .. 0.54
   3 ?   -1.0   0.0      0.92   8.7e+02     209     224 ..     397     412 ..     388     418 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                      EE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 22 ivGaGssGLtaayylakkpdlkvailersvspGG 55
                                      +vG+G +GL+aay l ++ +  v ++e+   +GG
  gi|313125522|ref|YP_004035786.1|  4 VVGGGIAGLAAAYRLRQH-GYDVQVFEATDDVGG 36
                                      8***************99.********9988887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                                       HHHHTC.TTTSS.-B-EEEEEE..EEEE--GSSST CS
                              Thi4 140 tlvela.hdtqscvDPlvirak..vvvdatGhdge 171
                                        +ve+a   t   vD  v+ a   v+ d tG++++
  gi|313125522|ref|YP_004035786.1| 240 LTVETAdGTTTHDVDSVVVAAMpnVLEDLTGYECD 274
                                       33333321122235555554433255566666665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.92
                                       CEEETTEEE-THHHHH CS
                              Thi4 209 revvpnlyvaGmevae 224
                                        ev +++y aGm++a 
  gi|313125522|ref|YP_004035786.1| 397 DEVSEGVYYAGMASAS 412
                                       68999********986 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00025      0.24       2      34 ..       2      34 ..       1      77 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      ++v+G G+ G   a+ + ++g++V++++ +++ 
  gi|313125522|ref|YP_004035786.1|  2 IGVVGGGIAGLAAAYRLRQHGYDVQVFEATDDV 34
                                      89*************************997764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2883.17
//
Query:       gi|313125523|ref|YP_004035787.1|  [L=209]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-09   38.2   4.5    1.4e-09   38.2   4.5    2.7  3  TetR_C_6   BetI-type transcriptional repressor, C-terminal
    1.9e-08   34.0   0.1    3.4e-08   33.2   0.1    1.5  1  TetR_N     Bacterial regulatory proteins, tetR family
    1.8e-07   31.4   0.3    5.5e-06   26.6   0.1    2.5  2  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
    3.2e-07   30.4   1.1    9.8e-07   28.8   0.0    2.4  4  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
    8.6e-06   25.9   4.3    3.3e-05   24.0   0.8    2.5  2  TetR_C_31  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.038   14.1   0.0    1.8  2  TetR_C_17  Tetracyclin repressor-like, C-terminal domain
      0.069   13.2   0.0       0.17   11.9   0.0    1.7  1  TetR_C_29  Tetracyclin repressor-like, C-terminal domain
      0.073   13.4   0.4        1.3    9.4   0.0    2.8  3  TetR_C_25  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.85   1.9e+03      47      83 ..      15      45 ..       9      46 .. 0.61
   2 ?   -1.6   0.1       1.4   3.1e+03      48      64 ..      50      68 ..      30      77 .. 0.61
   3 !   38.2   4.5   6.3e-13   1.4e-09       1     110 [.      79     198 ..      79     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.85
                                      HHHHHHHHHHHHHHHHHTTSCTTSTHHHHHHHHHHHH CS
                          TetR_C_6 47 yarlrsnlrallaelaegglradadaeaaAerlaAli 83
                                      +a++r++++  +a l        +d +++Ae  ++l+
  gi|313125523|ref|YP_004035787.1| 15 EATYRALCANGFASLTM------QDIADEAEKSTSLL 45
                                      44555555555555555......88888888777765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHHHH..T CS
                          TetR_C_6 48 arlrsnlrallaelae..g 64
                                      ++ r++l+a l+ l+e  +
  gi|313125523|ref|YP_004035787.1| 50 DTKRDLLVAFLRYLLErfE 68
                                      4445555666665555333 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 6.3e-13
                                       HHHHHHHHHHCCSTHSHHHHH..........HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSC CS
                          TetR_C_6   1 prerlraileallpldqerra..........elavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglr 67 
                                       p+erlr ++  +lp+d+++++          +  + l++  +a+++++++e++r+n + +rs l+ +++++ e g +
  gi|313125523|ref|YP_004035787.1|  79 PEERLRLLVSRMLPADETTDEnrvdesdydrFGLAILEVRMQAPYEEDYREQLRTNMEVIRSGLANVIEDGIETGAF 155
                                       89************999998666676766668889****************************************** PP

                                       TTSTHHHHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHH CS
                          TetR_C_6  68 adadaeaaAerlaAlidGLwlraalapeeldaeraralvrrhl 110
                                       +d+d+++ A+ ++  +dG   + ++ ++  ++ ++ a++++++
  gi|313125523|ref|YP_004035787.1| 156 RDVDPDRTARLIVDALDGARSERVTLDDNDAPTEVAAALDEFV 198
                                       *******************887777778888888888888887 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.1   1.5e-11   3.4e-08       2      46 ..      14      58 ..      13      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.5e-11
                                      HHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                            TetR_N  2 ldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                      ++a+ + +  +G++++t+++IA++A  s ++l++++++K++Ll a
  gi|313125523|ref|YP_004035787.1| 14 MEATYRALCANGFASLTMQDIADEAEKSTSLLHYHYDTKRDLLVA 58
                                      6899999999********************************987 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0       0.1   2.3e+02       2      16 ..      77      91 ..      76     100 .. 0.86
   2 !   26.6   0.1   2.4e-09   5.5e-06      35      85 ..     122     172 ..     106     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.1
                                      SSHHHHHHHHHHHHH CS
                         TetR_C_24  2 gspaerLralvrahv 16
                                      ++p+erLr lv +++
  gi|313125523|ref|YP_004035787.1| 77 EDPEERLRLLVSRML 91
                                      79********98876 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 2.4e-09
                                       GS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHH CS
                         TetR_C_24  35 aLspehreeiralrreyerllrdlieeGvaagefedldpklaalailgmln 85 
                                         ++++re++r+  + +++ l+++ie+G+++g f+d+dp+ +a++i+ +l 
  gi|313125523|ref|YP_004035787.1| 122 PYEEDYREQLRTNMEVIRSGLANVIEDGIETGAFRDVDPDRTARLIVDALD 172
                                       56899*****************************************99985 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.9   4.3e+03      24      37 ..       7      20 ..       6      38 .. 0.73
   2 ?   -2.5   0.0       2.3   5.2e+03       7      23 ..      61      77 ..      59      81 .. 0.76
   3 ?   -2.4   0.0       2.1   4.8e+03       1      13 [.      79      91 ..      79      97 .. 0.82
   4 !   28.8   0.0   4.4e-10   9.8e-07      35      82 ..     125     172 ..     118     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.9
                                      HHHHHHHHHHHHH- CS
                         TetR_C_27 24 pelFatyvvlieee 37
                                      p +++t+++++ ++
  gi|313125523|ref|YP_004035787.1|  7 PDVHETVMEATYRA 20
                                      56777777766544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                      HHHHHHHHHHHHHHHH- CS
                         TetR_C_27  7 ewlaalfeakrrkardd 23
                                      ++l+++fe k ++ +d+
  gi|313125523|ref|YP_004035787.1| 61 RYLLERFEEKFEDTEDE 77
                                      68889999998888764 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.1
                                      HHHHHHHHHHHHH CS
                         TetR_C_27  1 AeerLrewlaalf 13
                                      +eerLr ++++++
  gi|313125523|ref|YP_004035787.1| 79 PEERLRLLVSRML 91
                                      799***9999876 PP

  == domain 4  score: 28.8 bits;  conditional E-value: 4.4e-10
                                       HH-HHHHHHHHHHHHHHHHHHHHHHHHCT-STT--HHHHHHHHHHHSG CS
                         TetR_C_27  35 eeelevvekhieeleeqlaeIireGvaaGeFkaadpeaaaravfdata 82 
                                       e+++e  +  +e ++  la++i++G+++G+F+  dp+++ar+++da+ 
  gi|313125523|ref|YP_004035787.1| 125 EDYREQLRTNMEVIRSGLANVIEDGIETGAFRDVDPDRTARLIVDALD 172
                                       5667778888999999*****************************985 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.066   1.5e+02      41      76 ..      53      88 ..      43      93 .. 0.72
   2 !   24.0   0.8   1.5e-08   3.3e-05      25     104 ..     112     197 ..     103     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.066
                                      HHHHHHHHHHHHHHHHHHHHHHCSS-HHHHHHHHHH CS
                         TetR_C_31 41 raalarlrralrealaallaalGlpdpeeaarllva 76
                                      r++l +  r l+e+ ++ +++   +dpee+ rllv 
  gi|313125523|ref|YP_004035787.1| 53 RDLLVAFLRYLLERFEEKFEDTEDEDPEERLRLLVS 88
                                      556666666667777777777777777777777774 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHH......HHCSS-HHHHHHHHHHHHHHHHHHHHHSG.TS-HH CS
                         TetR_C_31  25 lAryelfleaarrPeLraalarlrralrealaalla......alGlpdpeeaarllvaaldGllldrLagp.aadpr 94 
                                       lA +e +++a   ++ r+ l+  ++ +r  la + +      a+   dp+++arl+v aldG+  +r++++ +++p 
  gi|313125523|ref|YP_004035787.1| 112 LAILEVRMQAPYEEDYREQLRTNMEVIRSGLANVIEdgietgAFRDVDPDRTARLIVDALDGARSERVTLDdNDAP- 187
                                       7999********************999999999999888554444479**********************954444. PP

                                       HHHHHHHHHH CS
                         TetR_C_31  95 aevrellral 104
                                       +ev+++l+++
  gi|313125523|ref|YP_004035787.1| 188 TEVAAALDEF 197
                                       6777777665 PP

>> TetR_C_17  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.1   2.6e+03      41      57 ..      45      61 ..      30      74 .. 0.52
   2 ?   14.1   0.0   1.7e-05     0.038      20      96 ..     110     185 ..      98     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHHHHHHH CS
                         TetR_C_17 41 leeRyerlvealkellq 57
                                      l+  y+   + l+++l 
  gi|313125523|ref|YP_004035787.1| 45 LHYHYDTKRDLLVAFLR 61
                                      44444444444444443 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.7e-05
                                       SHHHHHHHHHGGGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHHHHHHHHHS-HHH CS
                         TetR_C_17  20 lllakyEyfltsyreeerrayleeRyerlvealkellqeGvergEfkPqlplesiakylisfldGliletlalgeek 96 
                                       + la +E  +++  ee+ r+ l +  e +   l +++++G+e+g f+ + p +  a++++  ldG   e+++l+ + 
  gi|313125523|ref|YP_004035787.1| 110 FGLAILEVRMQAPYEEDYREQLRTNMEVIRSGLANVIEDGIETGAFRDVDP-DRTARLIVDALDGARSERVTLDDND 185
                                       56777788888877888888899999999999***************8877.5679**********99999998765 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.8e-05      0.17      41      87 ..     129     174 ..     109     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.8e-05
                                       --SS-.THHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHHHHHH CS
                         TetR_C_29  41 esirelnspliekleeilerGqaagvFrpgvdaldlyllisslcffr 87 
                                       e++r+ ++ + + l++++e G ++g+Fr+ vd+     li+      
  gi|313125523|ref|YP_004035787.1| 129 EQLRTNMEVIRSGLANVIEDGIETGAFRD-VDPDRTARLIVDALDGA 174
                                       5566655666678***************9.***99999988765555 PP

>> TetR_C_25  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.51   1.1e+03      53      85 ..      16      48 ..       9      67 .. 0.62
   2 ?   -0.0   0.0      0.49   1.1e+03      62      90 ..     109     136 ..      95     144 .. 0.80
   3 ?    9.4   0.0   0.00058       1.3      30      89 ..     140     198 ..     130     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.51
                         TetR_C_25 53 arArylalsslGalllelqlheeedptdlravl 85
                                      a+ r l ++++++l+++  ++e e++t l ++ 
  gi|313125523|ref|YP_004035787.1| 16 ATYRALCANGFASLTMQDIADEAEKSTSLLHYH 48
                                      555566666666666666555555555555554 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.49
                         TetR_C_25  62 slGalllelqlheeedptdlravlreyle 90 
                                        +G  +le+++++   ++d+r+ lr  +e
  gi|313125523|ref|YP_004035787.1| 109 RFGLAILEVRMQA-PYEEDYREQLRTNME 136
                                       5788999999999.677888888887665 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00058
                         TetR_C_25  30 edaeayleegvaaGtirpsrdpkarArylalsslGalllelqlheeedptdlravlreyl 89 
                                       ++  +++e+g+++G  r+  dp  +Ar+++ +  Ga    ++l++++ pt+++a+l e++
  gi|313125523|ref|YP_004035787.1| 140 SGLANVIEDGIETGAFRD-VDPDRTARLIVDALDGARSERVTLDDNDAPTEVAAALDEFV 198
                                       5667899**********8.69*********************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1096.43
//
Query:       gi|313125524|ref|YP_004035788.1|  [L=492]
Description: efflux protein, mate family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-60  202.1  38.1    4.1e-37  127.3  10.8    2.9  3  MatE             MatE
    3.2e-05   24.0  11.9    3.2e-05   24.0  11.9    4.9  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3  10.8   4.6e-41   4.1e-37       1     160 [.      23     184 ..      23     185 .. 0.99
   2 ?   -2.9   1.8      0.52   4.6e+03      36      62 ..     207     234 ..     203     235 .. 0.73
   3 !   88.7   9.9   3.4e-29   3.1e-25      20     160 ..     297     440 ..     280     441 .. 0.94

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 4.6e-41
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       Pi+l+++++++++l+dt++vgr+g++a++a+s++++i++l+++++ g+ +a t+lv+q+ Ga+n +r+++++ q++ 
  gi|313125524|ref|YP_004035788.1|  23 PIILSQMMQVCYNLADTFWVGRVGENAVSALSFSWPIVFLMISIGGGFTVAGTVLVAQNKGAGNDDRVNHVAGQTIA 99 
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee..vlelakrylrililgipalalqlvlsgilrgagktkvplyislisl 152
                                       +++lls+i+++l+++f++ +l l+++++   v +l+  y r ++lg+ +++ ++++++ lrg g+t++p+y++++++
  gi|313125524|ref|YP_004035788.1| 100 FVILLSAIFSALGYIFAPSLLNLIGTTPGteVHALSVSYTRTIFLGVYFMFGFFIFQALLRGWGDTRTPMYLMAFGV 176
                                       ***************************9888********************************************** PP

                              MatE 153 llniplny 160
                                       +ln+++++
  gi|313125524|ref|YP_004035788.1| 177 VLNVIIDP 184
                                       ****9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.52
                              MatE  36 silsllfvfllgl.stalttlvgqalGa 62 
                                       +++sl+++ ++g+ ++a++t+ ++ +Ga
  gi|313125524|ref|YP_004035788.1| 207 TLFSLTGFTGMGVqGAAVATVFSRGVGA 234
                                       5778888888887457778888887776 PP

  == domain 3  score: 88.7 bits;  conditional E-value: 3.4e-29
                              MatE  20 vgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfse 95 
                                       v+++  s a+Aa +i++++ sl+f++++gl  +++t+vgq+lGa +++r k++++ g+ l  +  ++++++ + f+e
  gi|313125524|ref|YP_004035788.1| 297 VAGIdTSAAVAAFGIGNRLNSLVFLPAIGLQQGVETVVGQNLGADKPERSKQTVFLGVGLISAALAVVSVVSYQFAE 373
                                       44554789********************************************************************* PP

                              MatE  96 qilslftqdee.vlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llniplny 160
                                       +i+ +f   e  v++++ ++lri +lg ++l+++ v sg +rg g t++++++sl++l +l+ip +y
  gi|313125524|ref|YP_004035788.1| 374 PIVAVFIPGEPnVIAIGVNFLRINALGFVFLGIFRVVSGGFRGSGSTRTAMAFSLLALwVLRIPPAY 440
                                       ****99976655****************************************************998 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.6      0.18   1.7e+03       5      30 ..     102     116 ..      93     126 .. 0.43
   2 !   24.0  11.9   3.5e-09   3.2e-05       5      85 ..     142     250 ..     138     300 .. 0.84
   3 ?   -2.6   0.1      0.57   5.1e+03      96     101 ..     359     364 ..     344     382 .. 0.46
   4 !   14.0   4.6   4.5e-06     0.041       2      78 ..     394     474 ..     393     482 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.18
                   Polysacc_synt_C   5 lalsiiflslstvlssiLqglgrqki 30 
                                       + ls+if++l            +  +
  gi|313125524|ref|YP_004035788.1| 102 ILLSAIFSALG-----------YIFA 116
                                       22333333333...........2222 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 3.5e-09
                   Polysacc_synt_C   5 lalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgi.................... 55 
                                       + l++ f++ + +++++L g g ++++++ +++g+++++i+  +li      p fg+                    
  gi|313125524|ref|YP_004035788.1| 142 IFLGVYFMFGFFIFQALLRGWGDTRTPMYLMAFGVVLNVIIDPFLIlgfqnnPIFGMlgfdglqatlfsltgftgmg 218
                                       568999****************************************88888888888******************** PP

                   Polysacc_synt_C  56 .vGaaiatvlallvvavlnlyalrr.llgikl 85 
                                         Gaa+atv++  v+a++ +y+l   ++gi+l
  gi|313125524|ref|YP_004035788.1| 219 vQGAAVATVFSRGVGALVGFYLLFSgRVGIHL 250
                                       ******************98877554777776 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.57
                   Polysacc_synt_C  96 laalvm 101
                                       +a +v+
  gi|313125524|ref|YP_004035788.1| 359 AALAVV 364
                                       111111 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 4.5e-06
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalviga.lvklilnllliplf..givGaaiatvlallvvavln.l 74 
                                       L+i al+++fl++++v+s+ + g g +++a+ ++++++ ++ +   + l+ +   g+ G+ +a++++ +++a++  l
  gi|313125524|ref|YP_004035788.1| 394 LRINALGFVFLGIFRVVSGGFRGSGSTRTAMAFSLLALwVLRIPPAYALVEWTglGLDGIWYAMAFSNVAAAIVAgL 470
                                       899**************************998777766279*********776336799999999999999999866 PP

                   Polysacc_synt_C  75 yalr 78 
                                       ++lr
  gi|313125524|ref|YP_004035788.1| 471 WFLR 474
                                       6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2729.88
//
Query:       gi|313125525|ref|YP_004035789.1|  [L=70]
Description: hypothetical protein Hbor_07520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 449.61
//
Query:       gi|313125526|ref|YP_004035790.1|  [L=199]
Description: hypothetical protein Hbor_07530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   12.0   2.1        1.3    9.3   0.0    2.2  2  DUF3546   Domain of unknown function (DUF3546)


Domain annotation for each model (and alignments):
>> DUF3546  Domain of unknown function (DUF3546)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0     7e-05       1.3      45      93 ..      37      85 ..      34     103 .. 0.87
   2 ?    2.2   0.6     0.012   2.1e+02      13      29 ..     102     118 ..      95     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7e-05
                           DUF3546 45 frekYhPeelakrkeelrellkkrlevFlellesgvfdevsleadnske 93
                                      f ek +P+++++r+  +++++  +++++   lesg  +    e+++ ++
  gi|313125526|ref|YP_004035790.1| 37 FGEKADPDHREEREPHMEAFFDCTFDTYVAALESGFSEAKAREITHIQA 85
                                      67999******************************99888777776665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.012
                           DUF3546  13 keeaqkkYdeYkeefqk 29 
                                         e++++Y++Y+e fq+
  gi|313125526|ref|YP_004035790.1| 102 ADELEAHYERYEEFFQR 118
                                       57899999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1321.13
//
Query:       gi|313125527|ref|YP_004035791.1|  [L=298]
Description: hypothetical protein Hbor_07540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-07   29.4   0.0    1.9e-06   27.8   0.0    1.9  1  HTH_20           Helix-turn-helix domain
     0.0052   16.7   0.4        4.1    7.5   0.0    2.9  2  ADK_lid          Adenylate kinase, active site lid
  ------ inclusion threshold ------
       0.21   11.4   0.0       0.37   10.6   0.0    1.3  1  SoxZ             Sulphur oxidation protein SoxZ
       0.33   10.6   6.8         31    4.3   0.0    3.8  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.37   10.9  13.4        3.3    7.9   0.8    4.0  4  Zn-ribbon_8      Zinc ribbon domain
        1.9    8.5  10.5       0.13   12.3   2.3    2.6  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        3.7    8.0   6.2         24    5.4   1.5    3.0  2  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   7.5e-10   1.9e-06       2      50 ..      23      73 ..      22      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 7.5e-10
                                      HHHHHHS-HHHHHHHHHH..STCTTB-HHHHHHHHTS-HHH.HHHHHHHHHH CS
                            HTH_20  2 qiaeALahPvRrrilraL..araegltaselaerldlsknt.lsyHLrvLee 50
                                      +++ ++++++R++il aL  + ++++ +s+l +r++++++   +yHL +L  
  gi|313125527|ref|YP_004035791.1| 23 EAFAVVGNETRLAILEALwrSADRPVAFSDLRRRVGMRDSAqFNYHLGKL-T 73
                                      78999*************9999**************999999*******9.4 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0033       8.6      16      32 ..     109     125 ..      99     126 .. 0.73
   2 !    7.5   0.0    0.0016       4.1       4      30 ..     137     188 ..     135     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0033
                                       B--SSTTB-TTT--.-B CS
                           ADK_lid  16 npPkveglCDkCGepLv 32 
                                        p  v+g C +CG++L+
  gi|313125527|ref|YP_004035791.1| 109 EPFEVPGECADCGGTLT 125
                                       56689*********995 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0016
                                       -TTT--EE.ETTTB--S.........................STTB-TTT--. CS
                           ADK_lid   4 CpkCGrsY.hvvfnpPk.........................veglCDkCGep 30 
                                       C+ CGr   h +  pP                          ++g+C +CG+ 
  gi|313125527|ref|YP_004035791.1| 137 CRECGRLHaH-APFPPGgltdrsdeevahafdqrvrhlhclaADGVCPECGGR 188
                                       8888888743.44566677777777777777777777777779********85 PP

>> SoxZ  Sulphur oxidation protein SoxZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.37      43      87 ..      85     132 ..      74     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                                       EEEETTEEEEEE---SS--SS-EEE.EEEE...--S-EEEEEEEEETT CS
                              SoxZ  43 evtlngkevleaelgiaiSknPylr.fkfkg..akkgdtlkvtwtDnk 87 
                                       e+++ g++v++a l+ +  +nP+++ f++ g  a+ g+tl+++++D++
  gi|313125527|ref|YP_004035791.1|  85 EFRHAGEKVVRAVLSGSFNENPTVEpFEVPGecADCGGTLTASYVDEH 132
                                       7899*******************9779999988999*********986 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.013        34       5      21 ..     117     133 ..     115     133 .. 0.93
   2 ?   -2.3   0.3       1.3   3.5e+03       5      10 ..     137     142 ..     135     143 .. 0.86
   3 ?    4.3   0.0     0.012        31       4      15 ..     181     192 ..     178     196 .. 0.81
   4 ?    3.8   0.3     0.017        44       4      13 ..     209     218 ..     206     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.013
                            zf_UBZ   5 CerCgkeipeselqEHe 21 
                                       C++Cg ++  s ++EH+
  gi|313125527|ref|YP_004035791.1| 117 CADCGGTLTASYVDEHL 133
                                       ****************5 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                            zf_UBZ   5 CerCgk 10 
                                       C +Cg+
  gi|313125527|ref|YP_004035791.1| 137 CRECGR 142
                                       99**96 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.012
                            zf_UBZ   4 lCerCgkeipes 15 
                                       +C++Cg ++ ++
  gi|313125527|ref|YP_004035791.1| 181 VCPECGGRMATT 192
                                       8*****888765 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.017
                            zf_UBZ   4 lCerCgkeip 13 
                                        Ce+C+++i 
  gi|313125527|ref|YP_004035791.1| 209 RCEQCDHRIR 218
                                       7******995 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.6   4.1e+03      24      32 ..      10      18 ..       4      23 .. 0.65
   2 ?    7.9   0.8    0.0013       3.3       7      35 ..     116     144 ..     111     147 .. 0.81
   3 ?    7.1   0.2    0.0023       5.8      24      36 ..     177     189 ..     163     192 .. 0.67
   4 ?    2.9   0.1     0.047   1.2e+02       7      15 ..     209     217 ..     207     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.6
                       Zn-ribbon_8 24 apltaCPeC 32
                                      + lt+C +C
  gi|313125527|ref|YP_004035791.1| 10 RLLTDCVDC 18
                                      335569999 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0013
                       Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgs.e 35 
                                       +C +Cg + ++     d+ l + C eCg  +
  gi|313125527|ref|YP_004035791.1| 116 ECADCGGTLTAS--YVDEHLSVgCRECGRlH 144
                                       6*****888844..347889999****9755 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0023
                       Zn-ribbon_8  24 apltaCPeCgsev 36 
                                       a++ +CPeCg+++
  gi|313125527|ref|YP_004035791.1| 177 AADGVCPECGGRM 189
                                       45667*****954 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.047
                       Zn-ribbon_8   7 rCeeCghef 15 
                                       rCe+C+h+ 
  gi|313125527|ref|YP_004035791.1| 209 RCEQCDHRI 217
                                       8****9985 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.2      0.31   7.8e+02      21      44 ..     117     141 ..     112     143 .. 0.62
   2 ?   12.3   2.3     5e-05      0.13       3      45 ..     160     215 ..     158     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.31
                     Zn_Tnp_IS1595  21 CPhCgsr.kayriktrglfqCkeCr 44 
                                       C  Cg++ +a  +       C+eC+
  gi|313125527|ref|YP_004035791.1| 117 CADCGGTlTASYVDEHLSVGCRECG 141
                                       7788888744444443666677776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5e-05
                     Zn_Tnp_IS1595   3 EeearalLealrWpng....fvCPhCgsrkayrikt.........rglfqCkeCrk 45 
                                       Ee a+a+ +++r  +      vCP Cg+r a+++++           +++C+ C +
  gi|313125527|ref|YP_004035791.1| 160 EEVAHAFDQRVRHLHClaadGVCPECGGRMATTLSQdagpldvaaCSVHRCEQCDH 215
                                       5555555555555554555589*******999999999*****9999*******87 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.05   1.3e+02      28      61 ..     134     169 ..     112     170 .. 0.55
   2 ?    5.4   1.5    0.0093        24       6      34 ..     182     213 ..     181     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.05
                   Lar_restr_allev  28 cvyCadCga..stpwfkiaedeaeaekeaieaWNrR 61 
                                        v C +Cg   ++  f+  +   ++++e+++a+ +R
  gi|313125527|ref|YP_004035791.1| 134 SVGCRECGRlhAHAPFPPGGLTDRSDEEVAHAFDQR 169
                                       567777777665556666666666666666666665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0093
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigq...cvyCadC 34 
                                       CP Cggr     sq+          +  C++C
  gi|313125527|ref|YP_004035791.1| 182 CPECGGRMATTLSQDAGPLDVAacsVHRCEQC 213
                                       **********9999998754334444444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1771.50
//
Query:       gi|313125528|ref|YP_004035792.1|  [L=39]
Description: hypothetical protein Hbor_07550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 250.90
//
Query:       gi|313125529|ref|YP_004035793.1|  [L=415]
Description: NAD(P)H-nitrite reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-45  153.7   0.1    7.8e-45  153.3   0.1    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      4e-09   36.9   0.2    6.8e-05   23.3   0.0    3.1  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    7.6e-09   35.4   0.0    2.3e-07   30.7   0.0    2.8  3  Rubredoxin_C   Rubredoxin NAD+ reductase C-terminal domain
    4.9e-07   29.3   0.0    1.5e-06   27.7   0.0    1.7  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0041   15.9   0.0        1.9    7.1   0.0    3.2  3  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.025   14.8   4.1       0.34   11.2   0.0    3.5  4  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.25   10.4   5.3          3    6.8   0.0    3.6  4  FAD_binding_2  FAD binding domain
       0.82    9.2   4.2        1.6    8.3   0.0    3.0  4  DAO            FAD dependent oxidoreductase
        1.4    8.9   3.5        5.9    6.9   0.0    3.2  4  NAD_binding_9  FAD-NAD(P)-binding
        2.1    8.9   4.3        1.4    9.5   0.6    2.6  3  RHS_repeat     RHS Repeat


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.1   4.3e-48   7.8e-45       2     279 ..       4     282 ..       3     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 4.3e-48
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.......HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias.......evvkklnqgiel 69 
                                       ++v+iG G+AG +aa+tl++    a++t+v +eg+ l++++l+++ + g   +a i         e       +iel
  gi|313125529|ref|YP_004035793.1|   4 SYVIIGDGIAGSSAAETLREeePDADITVVTDEGEALYNRILIKEFAKGKLPEAPISIhepewydE------RDIEL 74 
                                       68******************766********************99999998888877777755532......35999 PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.kri 145
                                        l++ v+++dp+ ++++       ++e++  dkl++  G++p  l+++    +++++  t+++a+++++++ + ++ 
  gi|313125529|ref|YP_004035793.1|  75 KLNTLVTDVDPDGHTIET-----HEGETLSWDKLLVSVGGTPTQLPVDNSDAEGIHHFWTFQDARKIRSHMEEaDSS 146
                                       99988********99999.....6789*********************9988888888***************8899 PP

                                       EEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.EEE.EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xx RF
                       Pyr_redox_2 146 vvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgnge.kle.vv 219
                                       vvvG+G+ G++lAa  a  g+e  ++ +++     al +e ++++++al++++ve ++++ v  ++ +++ +++  v
  gi|313125529|ref|YP_004035793.1| 147 VVVGAGLLGIDLAAITAAQGVEGKYLMRGNCWWrYALSEEGGEIIHNALRERNVEPVFESGVDHFEVDDDgRVTtAV 223
                                       **********************77777766666599***************************888888886667** PP

                                       ETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC..T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Pyr_redox_2 220 ledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva..g 279
                                       + +g+e+dad v +a+G+  +te+l +   +e+  ++gi vde++rtn+++++a+GD++  +
  gi|313125529|ref|YP_004035793.1| 224 DPNGDEYDADFVGIAIGLDFNTEIL-QGTDIEC--DNGIIVDEYMRTNHEDVFAAGDITqfH 282
                                       *************************.999****..***********************9552 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00093       1.7       2      35 ..       5      40 ..       4      55 .. 0.82
   2 ?   -0.2   0.0      0.85   1.5e+03      52      72 ..      69      89 ..      66      95 .. 0.81
   3 !   23.3   0.0   3.8e-08   6.8e-05       3      74 ..     147     220 ..     145     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00093
                                      EEEECSSHHHHHHHHHHHHTT..SEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvversdkll 35
                                       v++G G  g  +A++l+e    +++tvv  + + l
  gi|313125529|ref|YP_004035793.1|  5 YVIIGDGIAGSSAAETLREEEpdADITVVTDEGEAL 40
                                      59***************99887799****9999988 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.85
                                      HTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox 52 kngievllntkveeiegsedg 72
                                      ++ ie+ lnt v+ ++ ++ +
  gi|313125529|ref|YP_004035793.1| 69 ERDIELKLNTLVTDVDPDGHT 89
                                      5689***********988765 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 3.8e-08
                                       EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EE CS
                         Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedg.ve 74 
                                       vvvG+G++g++lA++ a+ g + + + r++     +l ee ++i+++ l+++++e ++++ v  +e ++dg v+
  gi|313125529|ref|YP_004035793.1| 147 VVVGAGLLGIDLAAITAAQGVEGKYLMRGNCWWrYALSEEGGEIIHNALRERNVEPVFESGVDHFEVDDDGrVT 220
                                       9*********************9888888877779***********************************9665 PP

>> Rubredoxin_C  Rubredoxin NAD+ reductase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.23   4.2e+02      21      44 ..      25      48 ..      19      50 .. 0.82
   2 ?   -2.1   0.0       2.1   3.7e+03      11      22 ..     271     282 ..     270     292 .. 0.78
   3 !   30.7   0.0   1.3e-10   2.3e-07       8      69 ..     328     386 ..     323     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.23
                                      ---SEEEEEE-SS-..EEEEEEET CS
                      Rubredoxin_C 21 eekaeelveedkekgkYkklfikn 44
                                      e +a++ v  d+ +  Y +++ik+
  gi|313125529|ref|YP_004035793.1| 25 EPDADITVVTDEGEALYNRILIKE 48
                                      333888999999999******986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.1
                                       EEEEES--TT-- CS
                      Rubredoxin_C  11 dlfSvGdieeee 22 
                                       d+f +Gdi +  
  gi|313125529|ref|YP_004035793.1| 271 DVFAAGDITQFH 282
                                       799999999866 PP

  == domain 3  score: 30.7 bits;  conditional E-value: 1.3e-10
                                       TTEEEEEES--TT---SEEEEEE-SS-..EEEEEEETTEEEEEEEES-HHHHHHHHHHHHTT CS
                      Rubredoxin_C   8 sgidlfSvGdieeeekaeelveedkekgkYkklfikngklvGAiliGDtkesaklkkliekk 69 
                                       +++   S+G     ++  e +++d+e    ++l +k+gk+vG +liGD +  +k+kkl++++
  gi|313125529|ref|YP_004035793.1| 328 FDFPFLSFGHPTLGDDEAEAKYSDTE---WRRLAFKDGKIVGGVLIGDLAPQSKYKKLMREE 386
                                       66677899999999966666666655...59****************************986 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.74   1.3e+03       1     193 [.       6      33 ..       2      43 .. 0.52
   2 !   27.7   0.0   8.3e-10   1.5e-06      92     305 .]      68     276 ..      49     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.74
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyrypkemtfispsftsekleipdlnaiseetspafslkeek 77 
                                       +IiG G aG +aa +l++                                                           
  gi|313125529|ref|YP_004035793.1|   6 VIIGDGIAGSSAAETLRE----------------------------------------------------------- 23 
                                       455555555555554444........................................................... PP

                       Pyr_redox_3  78 lsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhys 154
                                                                                                                    
  gi|313125529|ref|YP_004035793.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                       Pyr_redox_3 155 kvkefhkyagqkvvViGgknSavDaAlelvrk..gaeVtvv 193
                                                                      +  +a++tvv
  gi|313125529|ref|YP_004035793.1|  24 -------------------------------EepDADITVV 33 
                                       ...............................3334444444 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 8.3e-10
                       Pyr_redox_3  92 ksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeeklvk.hyskvkefhkya... 163
                                       ++ +++ kl++ V++v+++  g ++et ++ t++ +k++++ G    P +l +  ++   + h+ ++++++k++   
  gi|313125529|ref|YP_004035793.1|  68 DERDIELKLNTLVTDVDPD--GHTIETHEGeTLSWDKLLVSVGG--TPTQLPVDNSDAEGIhHFWTFQDARKIRshm 140
                                       677899999*******997..68999998769999********8..9******999976661555667776654222 PP

                       Pyr_redox_3 164 ..gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkei 238
                                          +  vV+G++  ++D A  ++++g e + ++rg+ + +      y l+    + ++++++e++++ +f++ v+  
  gi|313125529|ref|YP_004035793.1| 141 eeADSSVVVGAGLLGIDLAAITAAQGVEGKYLMRGNCWWR------YALSEEGGEIIHNALRERNVEPVFESGVDHF 211
                                       226789*****************************98765......7899999999999999988**********98 PP

                       Pyr_redox_3 239 kekeeeykvk..tedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       + ++     +   ++g++ ++ d+v +a+G + ++++l+   +e  ++g+  + +e + tn +++f aG
  gi|313125529|ref|YP_004035793.1| 212 EVDDDGRVTTavDPNGDEYDA-DFVGIAIGLDFNTEILQGTDIEC-DNGI--IVDEYMRTNHEDVFAAG 276
                                       876655433323566666554.666678**********9655555.3443..34789*********999 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.039        70       3      39 ..       5      44 ..       3      47 .. 0.67
   2 !    7.1   0.0    0.0011       1.9     119     165 ..      67     110 ..      63     123 .. 0.91
   3 ?    2.6   0.0     0.025        46     109     163 ..     185     240 ..     156     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.039
                                      EEEE--SHHHHHHHHHH..HHTT--EEE.E-SSSSS-HHH CS
                       HI0933_like  3 viviGgGaAGlmaAisa..akrgkrVll.lekakklgrKi 39
                                       ++iG G AG  aA+++  ++ ++++++  +++++l ++i
  gi|313125529|ref|YP_004035793.1|  5 YVIIGDGIAGSSAAETLreEEPDADITVvTDEGEALYNRI 44
                                      69**************944444555544146666555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0011
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                        +e++++l+l+t v++v  + dg ++++t+++e+l+ dkl++++GG+
  gi|313125529|ref|YP_004035793.1|  67 YDERDIELKLNTLVTDV--DPDG-HTIETHEGETLSWDKLLVSVGGT 110
                                       57899************..6777.899999****************7 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE--- CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtG 163
                                       e+  +++ ++l+e++v+   e+ v ++e ++dg+++ ++  +++e+ ad + +A+G
  gi|313125529|ref|YP_004035793.1| 185 EEGGEIIHNALRERNVEPVFESGVDHFEVDDDGRVTTAVdPNGDEYDADFVGIAIG 240
                                       44456778889999999999999999999999988888855888888888888877 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.34       1      24 [.       7      32 ..       7      37 .. 0.90
   2 ?   -1.2   0.0       1.4   2.4e+03      48      65 ..     123     140 ..     119     143 .. 0.82
   3 ?    2.0   1.0      0.14   2.6e+02       1      20 [.     148     167 ..     148     172 .. 0.85
   4 ?   -2.0   0.0       2.5   4.5e+03      32      56 ..     293     322 ..     281     330 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                      EE--SHHHHHHHHHHHCC..TEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvll 24
                                      I+G G++G++aA +L+++  ++d+++
  gi|313125529|ref|YP_004035793.1|  7 IIGDGIAGSSAAETLREEepDADITV 32
                                      89**************9878888887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                                       S---EEETTHHHHCHHHH CS
                     NAD_binding_8  48 gahifhgsgyypnvrrll 65 
                                       g h f+++++ +++r  +
  gi|313125529|ref|YP_004035793.1| 123 GIHHFWTFQDARKIRSHM 140
                                       889*****9999888765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.14
                                       EE--SHHHHHHHHHHHCCTE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagf 20 
                                       +vGaGl G  +A+  a +g+
  gi|313125529|ref|YP_004035793.1| 148 VVGAGLLGIDLAAITAAQGV 167
                                       8*******999988887765 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.5
                                       SGGG-EECETT....CEECTS---E.EETT CS
                     NAD_binding_8  32 GGraasyevpg....vrvdygahif.hgsg 56 
                                       G + + +e +     + vdyg   f + s+
  gi|313125529|ref|YP_004035793.1| 293 GAWGSAKEQGTiaakNMVDYGTEEFrWVSS 322
                                       555554544334445889999887755544 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0017         3       3      32 ..       6      37 ..       4      41 .. 0.81
   2 ?   -1.3   1.7       0.5   8.9e+02       3      20 ..     147     165 ..     145     172 .. 0.79
   3 ?    3.2   0.0     0.022        39     372     402 ..     255     279 ..     187     287 .. 0.76
   4 ?   -3.0   0.0       1.6   2.9e+03     162     194 ..     352     393 ..     349     403 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0017
                                      EEE--SHHHHHHHHHHHHTTT..-EEEEESSS CS
                     FAD_binding_2  3 iViGsGlAGLaAAleaaeaGl..kvavvekeq 32
                                      ++iG G+AG +AA +++e+    +++vv+ e+
  gi|313125529|ref|YP_004035793.1|  6 VIIGDGIAGSSAAETLREEEPdaDITVVTDEG 37
                                      9***************9954325888888776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.5
                                       EEE--SHHHH.HHHHHHHH CS
                     FAD_binding_2   3 iViGsGlAGL.aAAleaae 20 
                                       +V+G+Gl G   AA++aa+
  gi|313125529|ref|YP_004035793.1| 147 VVVGAGLLGIdLAAITAAQ 165
                                       9********9457777776 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.022
                                       ES-EEEBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 372 tmgGvetdengrvldadgqpipGLYAaGeva 402
                                       +  G+ +de +r+      ++++ +AaG  +
  gi|313125529|ref|YP_004035793.1| 255 CDNGIIVDEYMRT------NHEDVFAAGDIT 279
                                       55699999****9......9*******9887 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.6
                                       EEEEEEEECTTEEEEEEEEET........TTTCEEEEEES.E CS
                     FAD_binding_2 162 teadeLivedgrvtGavvenp........esgrevrirak.a 194
                                       te ++L  +dg+++G v+  +        + +re+r++a+ +
  gi|313125529|ref|YP_004035793.1| 352 TEWRRLAFKDGKIVGGVLIGDlapqskykKLMREERVVADqK 393
                                       667889999999999998877788777776677777777654 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00088       1.6       2      27 ..       5      34 ..       4      39 .. 0.81
   2 ?   -1.5   0.0      0.81   1.5e+03     161     202 ..      72     109 ..      68     138 .. 0.75
   3 ?   -3.1   1.1       2.4   4.4e+03       3      15 ..     147     159 ..     145     168 .. 0.76
   4 ?    0.7   0.0      0.18   3.2e+02     154     205 ..     193     244 ..     177     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00088
                                      EEEECTSHHHHHHHHHHHHT.T...EEEEE CS
                               DAO  2 vviiGGGiiGlstAyeLarr.g...Vtlle 27
                                       viiG Gi+G+s+A  L ++ +   +t++ 
  gi|313125529|ref|YP_004035793.1|  5 YVIIGDGIAGSSAAETLREEePdadITVVT 34
                                      69***************6553479988875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.81
                                       -EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GG CS
                               DAO 161 veilegtevtgleeedgkvwgverttp.gendaadavVnaaGa 202
                                       +e+ ++t vt+++  d  ++++  +t+ ge+ + d++ ++ G 
  gi|313125529|ref|YP_004035793.1|  72 IELKLNTLVTDVDP-D--GHTI--ETHeGETLSWDKLLVSVGG 109
                                       67889999999944.3..7899..6666887445888888885 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.4
                                       EEECTSHHHHHHH CS
                               DAO   3 viiGGGiiGlstA 15 
                                       v++G+G  G+  A
  gi|313125529|ref|YP_004035793.1| 147 VVVGAGLLGIDLA 159
                                       8******998666 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.18
                                       HHHHHTT-EEEESECEEEEEEEE.TCEEEEEEECT.EEE.EEEEEEEE--GGGHH CS
                               DAO 154 raaealGveilegtevtgleeed.gkvwgverttp.gen.daadavVnaaGawsd 205
                                       +a++++ ve ++++ v ++e +d g+v++   + p g + da d v +a G+  +
  gi|313125529|ref|YP_004035793.1| 193 NALRERNVEPVFESGVDHFEVDDdGRVTTA--VDPnGDEyDA-DFVGIAIGLDFN 244
                                       567788888888899999988666999999..5555877343.668888887765 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0033       5.9       1      32 [.       6      34 ..       6      49 .. 0.83
   2 ?    0.2   0.0      0.37   6.6e+02     123     154 ..      79     108 ..      68     110 .. 0.78
   3 ?   -3.1   0.4       3.9     7e+03       1      13 [.     147     159 ..     147     165 .. 0.82
   4 ?   -0.1   0.0      0.45   8.2e+02     128     154 ..     212     240 ..     190     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0033
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfd 32
                                      +i+G G++G +++e L ++   + + +it++ 
  gi|313125529|ref|YP_004035793.1|  6 VIIGDGIAGSSAAETLREE---EPDADITVVT 34
                                      7***************999...5888888874 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.37
                     NAD_binding_9 123 evvdleeradgqavlladgaslaadaVvLAlG 154
                                        v+d++  +dg ++ +++g++l  d++ + +G
  gi|313125529|ref|YP_004035793.1|  79 LVTDVD--PDGHTIETHEGETLSWDKLLVSVG 108
                                       566665..566779999********9999988 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.9
                     NAD_binding_9   1 aivGaGprGlavl 13 
                                       ++vGaG  G+ ++
  gi|313125529|ref|YP_004035793.1| 147 VVVGAGLLGIDLA 159
                                       69****9998776 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.45
                     NAD_binding_9 128 eeradgq..avlladgaslaadaVvLAlG 154
                                       e ++dg+  + +  +g++++ad V +A+G
  gi|313125529|ref|YP_004035793.1| 212 EVDDDGRvtTAVDPNGDEYDADFVGIAIG 240
                                       5555664235667899**********998 PP

>> RHS_repeat  RHS Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.7     3e+03      11      17 ..      83      89 ..      77     103 .. 0.55
   2 ?   -3.2   0.0       7.7   1.4e+04       7      16 ..     158     167 ..     157     168 .. 0.60
   3 ?    9.5   0.6   0.00078       1.4       2      16 ..     214     228 ..     213     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.7
                        RHS_repeat 11 tdpsGrv 17
                                      +dp+G +
  gi|313125529|ref|YP_004035793.1| 83 VDPDGHT 89
                                      4777766 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.7
                        RHS_repeat   7 LtevtdpsGr 16 
                                       L ++t+++G+
  gi|313125529|ref|YP_004035793.1| 158 LAAITAAQGV 167
                                       5566777664 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00078
                        RHS_repeat   2 DaaGrLtevtdpsGr 16 
                                       D++Gr+t+ +dp+G+
  gi|313125529|ref|YP_004035793.1| 214 DDDGRVTTAVDPNGD 228
                                       888999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2333.71
//
Query:       gi|313125530|ref|YP_004035794.1|  [L=367]
Description: serine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-27   96.9   2.5      2e-27   96.9   2.5    1.7  2  Trypsin_2      Trypsin-like peptidase domain
      1e-12   48.2   0.1    2.4e-12   47.0   0.1    1.7  1  PDZ_2          PDZ domain
      2e-12   47.4   0.4      6e-12   45.8   0.4    1.7  1  Trypsin        Trypsin
    0.00029   20.6   0.2     0.0074   16.1   0.0    2.4  2  PDZ_6          PDZ domain
     0.0049   16.9   0.2     0.0089   16.0   0.2    1.3  1  Pico_P2A       Picornavirus core protein 2A
  ------ inclusion threshold ------
      0.032   14.6   0.1       0.41   11.0   0.0    2.4  2  PDZ            PDZ domain
      0.038   12.7   0.9      0.059   12.0   0.9    1.2  1  Peptidase_S46  Peptidase S46
      0.055   12.6   3.7        2.7    7.1   0.3    2.8  3  Peptidase_S32  Equine arteritis virus serine endopeptidase S3


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.3   5.3e+03      92     125 ..      27      59 ..      13      66 .. 0.70
   2 !   96.9   2.5     9e-31     2e-27       1     150 []      83     220 ..      83     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.3
                         Trypsin_2  92 yplggeksgsvssGivsgvvesesaasgegesfl 125
                                        p+g++ + s+++ + s+v +++s+++ + +s +
  gi|313125530|ref|YP_004035794.1|  27 APQGKTTG-SATETSTSAVAPRRSSDDSKYDSAI 59 
                                       36777776.8888888888886666666666655 PP

  == domain 2  score: 96.9 bits;  conditional E-value: 9e-31
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgp 77 
                                       Gs+f+++++  ++Tn Hvv++a+++ +           + g++ +a++v++d+  DlA+l+v ++ + +++pl+++ 
  gi|313125530|ref|YP_004035794.1|  83 GSAFVINDTS-VVTNEHVVSGAERVDI---------QYTTGEWTSAEIVGTDMFADLAILDV-DHVPESVRPLQFSL 148
                                       8*********.****************.........9***************777*******.***********999 PP

                         Trypsin_2  78 sealkggepvyvvGyplggeksgsvssGivsgvve..sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                       +++  g+ +v ++G p g ++  s+s+Gi+sgv++   +   + + ++ +qtdaa++pG+SGGpl++++G vvG+
  gi|313125530|ref|YP_004035794.1| 149 RPPQIGT-EVSAIGSPFGLKG--SMSKGIISGVNRtaFNPITGVSIPNAVQTDAAVNPGNSGGPLVNTEGSVVGV 220
                                       8888888.************9..9***********555555555556666************************8 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.1   1.1e-15   2.4e-12      11      82 .]     264     360 ..     254     360 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.1e-15
                                       --............-EEEEEE-TTSGGGGT.--T...............T-EEEEETTB--SSHHHHHHHHH.TS-T CS
                             PDZ_2  11 ed..........tggvlvvsVkeggPaakaglka...............gDvilkvdgkkvksledlislll.kkkp 61 
                                        +           +gv+vv+V ++gPa++  l+a                D+il+vdg++v ++ +l   l+ +++p
  gi|313125530|ref|YP_004035794.1| 264 GPlvaeandltePNGVIVVTVIDDGPAEGI-LRAsdetverrgvsipvgSDIILEVDGVPVRDRNELLAHLSlETSP 339
                                       55555555555579************9988.7778****************************************** PP

                                       T-EEEEEEEETTEEEEEEEE- CS
                             PDZ_2  62 GdtVkltvlRdgkkktvevkl 82 
                                       G+t+ lt++R+g ++ ve++l
  gi|313125530|ref|YP_004035794.1| 340 GETIPLTIYRNGITQPVELTL 360
                                       ******************997 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.4   2.7e-15     6e-12      27     203 ..      83     228 ..      71     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.7e-15
                                       EEEEEEETTEEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSS CS
                           Trypsin  27 CgGslisenwvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdt 103
                                        ++++i++  v+T+ H+vs+a++v++       + + g+    + ++++     +  +   D+a+l ++      ++
  gi|313125530|ref|YP_004035794.1|  83 GSAFVINDTSVVTNEHVVSGAERVDI-------QYTTGE---WTSAEIVG---TDMFA---DLAILDVDHV---PES 140
                                       469****************9666655.......445552...33333322...44455...********98...*** PP

                                       BHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTT CS
                           Trypsin 104 vrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGD 180
                                       vrp++     +  ++g    vs++g+++  +   ++ ++ ++ v+r   +  + g   +n ++++a     + ++G+
  gi|313125530|ref|YP_004035794.1| 141 VRPLQFSLRPP--QIG--TEVSAIGSPFGLK--GSMSKGIISGVNRTAFNP-ITGVSIPNAVQTDA-----AVNPGN 205
                                       *******9333..777..5566666665555..789999999999966666.667778999*****.....****** PP

                                       TTSEEEETTTEEEEEEEEESSSS CS
                           Trypsin 181 SGGPlvcsdgelvGivswgkgca 203
                                       SGGPlv+ +g +vG++s+g  ++
  gi|313125530|ref|YP_004035794.1| 206 SGGPLVNTEGSVVGVISAGGAEN 228
                                       ******************95554 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.09     2e+02       2      18 ..     281     296 ..     280     300 .. 0.81
   2 !   16.1   0.0   3.3e-06    0.0074      20      56 .]     313     349 ..     312     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.09
                             PDZ_6   2 VtaVdpgsPAdrAG.lrv 18 
                                       V +V+ ++PA+  G lr+
  gi|313125530|ref|YP_004035794.1| 281 VVTVIDDGPAE--GiLRA 296
                                       899*******9..76666 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.3e-06
                             PDZ_6  20 DiilsvNGqpveglsladvaallr..gsagesvvlvvrr 56 
                                       Diil+v+G+pv  ++ +++ a l   +s+ge + l++ r
  gi|313125530|ref|YP_004035794.1| 313 DIILEVDGVPV--RDRNELLAHLSleTSPGETIPLTIYR 349
                                       9**********..****9988876678999999998876 PP

>> Pico_P2A  Picornavirus core protein 2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2     4e-06    0.0089      85     117 ..     199     232 ..     185     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4e-06
                          Pico_P2A  85 GfaePGdCGGilrCehG.viGivtaGGeglvafa 117
                                          +PG+ GG l+ + G v+G+++aGG + ++fa
  gi|313125530|ref|YP_004035794.1| 199 AAVNPGNSGGPLVNTEGsVVGVISAGGAENIGFA 232
                                       5679******9998887589*************8 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       0.3   6.8e+02      17      49 ..     268     299 ..     261     309 .. 0.79
   2 ?   11.0   0.0   0.00018      0.41      48      81 ..     313     347 ..     302     348 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.3
                                       EEETTSSSSSSEEEEEECTTSHHHHHTSSTTEE CS
                               PDZ  17 kggsdqrgdkgifvsevlpggaaeadglkvGDk 49 
                                       ++ +d  + +g++v  v  +g+ae   l++ D+
  gi|313125530|ref|YP_004035794.1| 268 AEANDLTEPNGVIVVTVIDDGPAEGI-LRASDE 299
                                       55555557789999999999999988.888775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00018
                                       EEEEEETTEETTTSHHHHHHHHHHTTTS.EEEEEE CS
                               PDZ  48 DkIlsvNgvdvenvsheeavqaikgskg.kvtLti 81 
                                       D+Il+v+gv+v++ +++ a + ++ s g +++Lti
  gi|313125530|ref|YP_004035794.1| 313 DIILEVDGVPVRDRNELLAHLSLETSPGeTIPLTI 347
                                       9**********************999998999998 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.9   2.6e-05     0.059     624     660 ..     194     230 ..     184     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                                       EEEES----TT-TT-EEE-TTS-EEEEEEEE-GGGTT CS
                     Peptidase_S46 624 nflstnDitGGNSGSPvlngkgelvGlaFDgniesls 660
                                       ++ +++    GNSG P++n++g++vG++  g  e+++
  gi|313125530|ref|YP_004035794.1| 194 AVQTDAAVNPGNSGGPLVNTEGSVVGVISAGGAENIG 230
                                       5556677778*****************9999888886 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.39   8.7e+02     218     247 ..      16      45 ..      12      58 .. 0.67
   2 ?    5.3   0.0    0.0043       9.6     113     143 ..      80     110 ..      69     154 .. 0.70
   3 ?    7.1   0.3    0.0012       2.7     205     226 ..     201     222 ..     177     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.39
                                       TE.EEEEEEEEETTTEEEEE-TT--EETSS CS
                     Peptidase_S32 218 dgelvGvhtGsnkkGsglvttpsGkllgva 247
                                        + + G +tGs  +G ++    +  + +va
  gi|313125530|ref|YP_004035794.1|  16 GAGVFGTYTGSAPQGKTTGSATETSTSAVA 45 
                                       455899999999998776666555555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0043
                                       EEEEEEEECTTEEEEEEEHHHH-.TSEEEEEE CS
                     Peptidase_S32 113 lGsGgvftidgevvvvtashvlg.dnkarvsi 143
                                        G G+ f i++ + vvt  hv++ +++  +++
  gi|313125530|ref|YP_004035794.1|  80 RGQGSAFVIND-TSVVTNEHVVSgAERVDIQY 110
                                       699****9975.6789******9344444443 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0012
                                       --GGGTT-EEEETTE.EEEEEE CS
                     Peptidase_S32 205 tkcGDsGspvvdedgelvGvht 226
                                        ++G+sG p+v+ +g++vGv  
  gi|313125530|ref|YP_004035794.1| 201 VNPGNSGGPLVNTEGSVVGVIS 222
                                       479****************964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 2132.80
//
Query:       gi|313125531|ref|YP_004035795.1|  [L=82]
Description: hypothetical protein Hbor_07580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 514.65
//
Query:       gi|313125532|ref|YP_004035796.1|  [L=138]
Description: hypothetical protein Hbor_07590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 969.47
//
Query:       gi|313125533|ref|YP_004035797.1|  [L=310]
Description: GTP cyclohydrolase mpta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-75  252.7   1.2    4.5e-75  252.5   1.2    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2


Domain annotation for each model (and alignments):
>> GCHY-1  Type I GTP cyclohydrolase folE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.5   1.2   2.5e-79   4.5e-75       1     259 []       5     293 ..       5     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 252.5 bits;  conditional E-value: 2.5e-79
                                       .XXXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHH.HS-SSEEG.. CS
                            GCHY-1   1 lpDvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevle.eaeeelee.. 74 
                                       lpDvq++++++++ l++VGv+gv+++vk+++++k++  l+ae+++fvdLp+ +kGi+mSR+++v++   e+++ e  
  gi|313125533|ref|YP_004035797.1|   5 LPDVQASRPDVTVGLSQVGVTGVDKLVKIARDGKRPLILMAEFEVFVDLPSGRKGIDMSRNMQVIDeILEDAVAEpt 81 
                                       79****************************************************************54455555467 PP

                                       GGHHH....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE..TTEEEEEEEEEEEEEEE- CS
                            GCHY-1  75 kslee....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaelerkeevkltvgvevpvttlC 147
                                       +++e+    ++e+ll+k++y+++aev++++e+++++++p+s+ +++ +++++++a +++ + ++ ++g+ev+++t+C
  gi|313125533|ref|YP_004035797.1|  82 YRVEDmcgdTAERLLAKHDYTSKAEVRMTAELVLREDTPASELQTQSTANIIASAVATE-DGTREEIGAEVVGMTVC 157
                                       6666666679***********************************************77.36*************** PP

                                       HHHHHHS.........................SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S-- CS
                            GCHY-1 148 PCskeisrell.....................eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyell 203
                                       PCs+ +s + +                     +++ H+QR+++t++ve +e + +v++ d+++++++s+s+++y+l 
  gi|313125533|ref|YP_004035797.1| 158 PCSQGMSASRArdvlrdldvedetieefleqvPQPGHSQRGHATLTVE-TEGSPDVDLIDIVDIARDSMSARIYNLA 233
                                       *******8888*************************************.67999*********************** PP

                                       -HHHHHHHHHHHHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                            GCHY-1 204 KReDEkavtekayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                       KR+DE+++t +a++n+kFvED+vR++a ++     ++ef         +++++n ESiH+Hna A
  gi|313125533|ref|YP_004035797.1| 234 KRPDEDHMTYHAHANAKFVEDCVRSMADQV-----LTEFdhladdavvHMKQSNDESIHQHNAHA 293
                                       *****************************9.....4455555888999***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2090.45
//
Query:       gi|313125534|ref|YP_004035798.1|  [L=236]
Description: sigma-70 family RNA polymerase sigma factor [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-10   40.3   0.1    1.7e-08   33.9   0.1    2.6  2  HTH_24          Winged helix-turn-helix DNA-binding
    4.2e-07   29.8   0.0      1e-06   28.5   0.0    1.7  1  MarR_2          MarR family
    6.2e-07   28.8   0.1    1.2e-06   27.9   0.1    1.5  1  Sigma70_r4      Sigma-70, region 4
    2.3e-06   27.4   0.0    1.6e-05   24.7   0.0    2.2  2  MarR            MarR family
    5.6e-06   26.1   0.5    6.1e-05   22.8   0.1    2.6  3  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    6.7e-05   23.1   0.0      0.001   19.4   0.0    2.4  2  HTH_WhiA        WhiA C-terminal HTH domain
    0.00012   21.9   0.1    0.00081   19.3   0.0    2.3  3  HTH_11          HTH domain
     0.0002   21.1   0.5      0.011   15.5   0.2    2.9  1  HTH_10          HTH DNA binding domain
    0.00051   19.9   0.1     0.0056   16.5   0.0    2.5  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0035   17.6   0.0       0.39   11.0   0.0    2.5  2  HTH_Tnp_Tc3_2   Transposase
     0.0049   16.6   0.0      0.012   15.4   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.005   16.9   0.0       0.04   14.0   0.0    2.3  2  HTH_20          Helix-turn-helix domain
     0.0068   16.4   0.0      0.019   15.0   0.0    1.7  1  HTH_3           Helix-turn-helix
     0.0099   15.7   0.0      0.039   13.8   0.0    2.0  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   14.6   0.0       0.14   11.6   0.0    2.4  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.024   14.6   0.7      0.062   13.3   0.0    2.0  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.033   14.3   0.1      0.089   12.9   0.1    1.7  1  MbeD_MobD       MbeD/MobD like
      0.045   13.5   0.0      0.086   12.6   0.0    1.4  1  HTH_Tnp_4       Helix-turn-helix of DDE superfamily endonucle
      0.046   13.5   0.1       0.13   12.0   0.1    1.8  1  LexA_DNA_bind   LexA DNA binding domain
      0.061   12.9   0.0       0.12   12.0   0.0    1.4  1  HTH_CodY        CodY helix-turn-helix domain
      0.061   13.1   0.2        3.2    7.6   0.0    2.9  3  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.076   12.6   0.0       0.77    9.4   0.0    2.5  3  HTH_50          Helix-turn-helix domain
      0.094   12.4   0.0       0.52   10.0   0.0    2.2  1  Sigma70_r4_2    Sigma-70, region 4
      0.097   12.9   0.1       0.23   11.7   0.0    1.6  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13
      0.099   12.6   0.0       0.25   11.3   0.0    1.7  1  HTH_37          Helix-turn-helix domain
        0.1   12.5   0.0       0.25   11.2   0.0    1.6  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
       0.11   12.2   0.0       0.46   10.3   0.0    2.0  1  HTH_psq         helix-turn-helix, Psq domain
       0.12   12.8   5.0       0.17   12.3   3.0    2.0  2  DUF1690         Protein of Unknown function (DUF1690)
       0.12   12.3   0.2         23    5.0   0.1    2.8  2  HTH_1           Bacterial regulatory helix-turn-helix protein
       0.12   12.2   0.0       0.39   10.6   0.0    1.9  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.13   12.0   0.0       0.26   11.1   0.0    1.5  1  HTH_38          Helix-turn-helix domain
       0.16   12.3   1.7       0.81   10.0   0.1    2.6  2  ABC_tran_CTD    ABC transporter C-terminal domain
       0.94    9.9   5.1       0.25   11.8   0.8    2.3  2  LPP             Lipoprotein leucine-zipper


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.084        46       4      28 ..       2      26 ..       2      26 .. 0.91
   2 !   33.9   0.1   3.1e-11   1.7e-08       1      39 [.      91     129 ..      91     130 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.084
                            HTH_24  4 tdrkILelLqknprisqreLAerlg 28
                                      +++kIL + +  p+ +  eL+  ++
  gi|313125534|ref|YP_004035798.1|  2 IHKKILDVAESRPDATVEELSSVVN 26
                                      689*****************98775 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 3.1e-11
                            HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlk 39 
                                       l e++r++L+++q+ p+ +q+eLA+r g+++st+n rl+
  gi|313125534|ref|YP_004035798.1|  91 LTEKQREVLRAIQDSPDATQSELADRFGVTQSTINNRLN 129
                                       5789*********************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.8e-09     1e-06       3      45 ..      91     131 ..      89     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.8e-09
                                       --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrL 45 
                                       lt  q+ vL a+ ++p+   t++ela+r+g+++s+++++l+  
  gi|313125534|ref|YP_004035798.1|  91 LTEKQREVLRAIQDSPD--ATQSELADRFGVTQSTINNRLNSI 131
                                       67789***********9..9*******************9975 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   2.2e-09   1.2e-06       4      41 ..      90     128 ..      89     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.2e-09
                                       HS-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.geglTleEIgerlgiSrerVrqie 41 
                                       +L+e++revl+      + T++E+++r+g++++++  ++
  gi|313125534|ref|YP_004035798.1|  90 ELTEKQREVLRAIQdSPDATQSELADRFGVTQSTINNRL 128
                                       7*************99*******************9876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.9   1.6e+03       8      28 ..       6      26 ..       4      36 .. 0.79
   2 !   24.7   0.0   2.9e-08   1.6e-05       1      43 [.      91     133 ..      91     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.9
                                      HHHHHHHSTTEEHHHHHHHHT CS
                              MarR  8 iLrilyeqgplsvseLakklg 28
                                      iL   +++++++v eL + ++
  gi|313125534|ref|YP_004035798.1|  6 ILDVAESRPDATVEELSSVVN 26
                                      77778889999**99998765 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.9e-08
                                       --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                              MarR   1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLek 43 
                                       lt+ q ++Lr + +++++++seLa+++gv++st+ + l   e 
  gi|313125534|ref|YP_004035798.1|  91 LTEKQREVLRAIQDSPDATQSELADRFGVTQSTINNRLNSIEG 133
                                       7999*******************************99987775 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.2   6.5e+02       6      33 ..       4      31 ..       2      36 .. 0.75
   2 !   22.8   0.1   1.1e-07   6.1e-05       6      39 ..      96     129 ..      91     132 .. 0.91
   3 ?   -2.6   0.0       9.3     5e+03      19      31 ..     163     176 ..     157     179 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.2
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSest 33
                                      +kIL+  +  + ++++eL+  v+ +  t
  gi|313125534|ref|YP_004035798.1|  4 KKILDVAESRPDATVEELSSVVNGASVT 31
                                      5788888888999*****9999755555 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.1e-07
                     HTH_AsnC-type   6 rkILeaLqedaRisyaeLAervGlSestvlrRvr 39 
                                       r  L+a+q  + ++ +eLA+r G+++st+ +R++
  gi|313125534|ref|YP_004035798.1|  96 REVLRAIQDSPDATQSELADRFGVTQSTINNRLN 129
                                       788*****************************86 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9.3
                     HTH_AsnC-type  19 syaeLAe.rvGlSe 31 
                                       s++ L+e  + lSe
  gi|313125534|ref|YP_004035798.1| 163 SVKNLSEqLTDLSE 176
                                       66666663334444 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.3   6.9e+02      45      65 ..       6      26 ..       3      31 .. 0.76
   2 !   19.4   0.0   1.9e-06     0.001      36      81 ..      89     132 ..      67     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.3
                                      HHHHHHH-TTS-HHHHHHTT. CS
                          HTH_WhiA 45 vaelRlenpdaSLkeLgelle 65
                                      + ++  + pda+ +eL+++++
  gi|313125534|ref|YP_004035798.1|  6 ILDVAESRPDATVEELSSVVN 26
                                      55666778********99874 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.9e-06
                                       GGS-HHHHHHHHHHHH-TTS-HHHHHHTT..T--HHHHHHHHHHHH CS
                          HTH_WhiA  36 eklpeklkevaelRlenpdaSLkeLgelleppisKSgvnhrlrklk 81 
                                        +l+ek +ev ++  + pda+ +eL++ +   ++ S++n+rl+ ++
  gi|313125534|ref|YP_004035798.1|  89 VELTEKQREVLRAIQDSPDATQSELADRF--GVTQSTINNRLNSIE 132
                                       489**************************..9***********997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.3   2.9e+03       4      22 ..       5      22 ..       3      26 .. 0.79
   2 !   19.3   0.0   1.5e-06   0.00081       2      40 ..      95     132 ..      94     134 .. 0.85
   3 ?   -1.6   0.0       4.9   2.6e+03      14      25 ..     160     171 ..     157     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.3
                            HTH_11  4 qilelLleargpisgeeLA 22
                                      +il    e+r++ + eeL+
  gi|313125534|ref|YP_004035798.1|  5 KILDVA-ESRPDATVEELS 22
                                      677777.899999999997 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.5e-06
                            HTH_11   2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLe 40 
                                       ++ +l+ + +  ++ + +eLA++++v+ +t+ +++ ++e
  gi|313125534|ref|YP_004035798.1|  95 QREVLRAI-QDSPDATQSELADRFGVTQSTINNRLNSIE 132
                                       56677777.77777********************99987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.9
                            HTH_11  14 gpisgeeLAeeL 25 
                                       g +s + L+e+L
  gi|313125534|ref|YP_004035798.1| 160 GSVSVKNLSEQL 171
                                       459999999998 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.1e-05     0.011       1      48 [.      91     132 ..      91     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkae 48 
                                       LT+kq+evl++ ++    d P ++t +eLA+++G+++st+ ++L+++e
  gi|313125534|ref|YP_004035798.1|  91 LTEKQREVLRA-IQ----DSP-DATQSELADRFGVTQSTINNRLNSIE 132
                                       77788887774.33....344.88999*****************9987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     1e-05    0.0056       2      37 ..      93     129 ..      92     133 .. 0.90
   2 ?   -0.0   0.1       1.5   8.2e+02      27      41 ..     162     176 ..     161     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5   2 ptRlkILklLaege.lcvcelaeelglsqstvShHLk 37 
                                       ++++++L++ ++++ ++ +ela+ +g++qst+   L+
  gi|313125534|ref|YP_004035798.1|  93 EKQREVLRAIQDSPdATQSELADRFGVTQSTINNRLN 129
                                       7899********999*****************87666 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.5
                                       S-HHHHHHHHHHHHH CS
                             HTH_5  27 lsqstvShHLkkLre 41 
                                       +s  ++S++L  L e
  gi|313125534|ref|YP_004035798.1| 162 VSVKNLSEQLTDLSE 176
                                       79999*****99976 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.11        60       2      30 ..       4      28 ..       3      41 .. 0.76
   2 !   11.0   0.0   0.00072      0.39       1      43 [.      95     132 ..      95     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                     HTH_Tnp_Tc3_2  2 rrIvrlvrkdPritlreLanelkeeGksv 30
                                       +I+ +++ +P +t +eL+++++  G   
  gi|313125534|ref|YP_004035798.1|  4 KKILDVAESRPDATVEELSSVVN--G--A 28
                                      58999***************993..3..3 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00072
                     HTH_Tnp_Tc3_2   1 krrIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkag 43 
                                       +r+++r ++ +P +t  eLa ++      v ++Ti +rL ++ 
  gi|313125534|ref|YP_004035798.1|  95 QREVLRAIQDSPDATQSELADRF-----GVTQSTINNRLNSIE 132
                                       599********************.....8999*******9865 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.2e-05     0.012       9      40 ..      96     130 ..      89     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                            HTH_23   9 r.illllae..GlsvreIAreLgvsrrTvyrwlkr 40 
                                       r +l++ ++   ++++e A+++gv+++T+ + l+ 
  gi|313125534|ref|YP_004035798.1|  96 ReVLRAIQDspDATQSELADRFGVTQSTINNRLNS 130
                                       447888888889*****************987665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   7.3e-05      0.04      12      46 ..      95     129 ..      91     133 .. 0.92
   2 ?   -0.5   0.0       2.5   1.3e+03      36      52 ..     162     179 ..     150     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  12 RrrilraLaraegltaselaerldlskntlsyHLr 46 
                                       +r++lra+ +   +t sela+r++++++t++++L+
  gi|313125534|ref|YP_004035798.1|  95 QREVLRAIQDSPDATQSELADRFGVTQSTINNRLN 129
                                       899*****99999*******************997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.5
                                       S-HHHHHHHHHHHHH.CT CS
                            HTH_20  36 lskntlsyHLrvLee.ag 52 
                                       +s ++ls +L  L+e + 
  gi|313125534|ref|YP_004035798.1| 162 VSVKNLSEQLTDLSEqVA 179
                                       556666666666666444 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.5e-05     0.019      11      31 ..     109     129 ..     108     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3  11 sqeeLAeklGvsrstisriEn 31 
                                       +q eLA++ Gv++sti++  n
  gi|313125534|ref|YP_004035798.1| 109 TQSELADRFGVTQSTINNRLN 129
                                       8***************98776 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   7.1e-05     0.039       7      40 ..      97     129 ..      93     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.1e-05
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHH CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLq 40 
                                       ++L+a+   p + t selA+r+g++ St  + L+
  gi|313125534|ref|YP_004035798.1|  97 EVLRAIQDSPDA-TQSELADRFGVTQSTINNRLN 129
                                       69*********8.***************877666 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.4   7.4e+02      40      51 ..      29      40 ..      26      41 .. 0.86
   2 ?   11.6   0.0   0.00026      0.14      19      50 ..      97     130 ..      95     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.4
                      HTH_Tnp_ISL3 40 SwtTVwrildry 51
                                      S t V+r+ld+y
  gi|313125534|ref|YP_004035798.1| 29 SVTLVERVLDEY 40
                                      8899*****998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00026
                      HTH_Tnp_ISL3  19 yilellles..rsvkavArqlgvSwtTVwrildr 50 
                                        +l++ ++s  ++ ++ A+++gv+ +T++++l++
  gi|313125534|ref|YP_004035798.1|  97 EVLRAIQDSpdATQSELADRFGVTQSTINNRLNS 130
                                       567777777778*******************986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.062      21      44 ..     107     130 ..      89     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                       EHHHHHHHHHTTSSHHHHHHHHHH CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilse 44 
                                       + tq elA++ G+t++t++  l+ 
  gi|313125534|ref|YP_004035798.1| 107 DATQSELADRFGVTQSTINNRLNS 130
                                       68*****************98875 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00016     0.089      46      65 ..     166     185 ..     135     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                         MbeD_MobD  46 aLseqvtgLsqQVesLseqv 65 
                                        Lseq t+Ls QV  L +q+
  gi|313125534|ref|YP_004035798.1| 166 NLSEQLTDLSEQVAALEQQL 185
                                       68999999999999998887 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00016     0.086      21      44 ..     109     132 ..     107     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                         HTH_Tnp_4  21 tyqdLayrFgvsestvsrifhkwv 44 
                                       t++ La rFgv +st+++  + ++
  gi|313125534|ref|YP_004035798.1| 109 TQSELADRFGVTQSTINNRLNSIE 132
                                       7899**************999887 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00025      0.13       3      49 ..      90     130 ..      89     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                                       ---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHH CS
                     LexA_DNA_bind   3 kLTerQrevldlikasieetgypPsireiaralglkSpsaveehLka 49 
                                       +LTe+Qrevl+ i++s + t+      e+a+++g++  s+++++L+ 
  gi|313125534|ref|YP_004035798.1|  90 ELTEKQREVLRAIQDSPDATQ-----SELADRFGVT-QSTINNRLNS 130
                                       69**************99987.....6999999998.8888888876 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00022      0.12       6      29 ..     109     132 ..     107     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                          HTH_CodY   6 taskiaDriGitrsvivnaLrkLe 29 
                                       t s++aDr G+t+s i n L  +e
  gi|313125534|ref|YP_004035798.1| 109 TQSELADRFGVTQSTINNRLNSIE 132
                                       6799**************998877 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.8     1e+03       2      25 ..       3      26 ..       3      32 .. 0.81
   2 ?    7.6   0.0    0.0059       3.2       4      39 ..      97     132 ..      94     139 .. 0.82
   3 ?    1.7   0.0      0.41   2.2e+02      11      24 ..     158     171 ..     157     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                          HTH_DeoR  2 ieqilellkqqgklsveelvellg 25
                                      +++il+  +++   +veel+   +
  gi|313125534|ref|YP_004035798.1|  3 HKKILDVAESRPDATVEELSSVVN 26
                                      78999999999999****987765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0059
                          HTH_DeoR   4 qilellkqqgklsveelvellgvSeaTiRRDLneLe 39 
                                       + l  ++++   +  el++++gv++ Ti + Ln +e
  gi|313125534|ref|YP_004035798.1|  97 EVLRAIQDSPDATQSELADRFGVTQSTINNRLNSIE 132
                                       566777777788889*************88888776 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.41
                          HTH_DeoR  11 qqgklsveelvell 24 
                                       ++g++sv+ l+e+l
  gi|313125534|ref|YP_004035798.1| 158 SSGSVSVKNLSEQL 171
                                       589********998 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       8.9   4.8e+03       4      23 ..      21      40 ..      19      41 .. 0.74
   2 ?    9.4   0.0    0.0014      0.77      29      44 ..     113     128 ..     111     130 .. 0.92
   3 ?   -0.8   0.0       2.2   1.2e+03       3      15 ..     173     185 ..     172     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.9
                            HTH_50  4 LkeyveefErelikkayekY 23
                                      L+ +v+    +l+++++ +Y
  gi|313125534|ref|YP_004035798.1| 21 LSSVVNGASVTLVERVLDEY 40
                                      56677777778888888888 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                            HTH_50  29 lAkrLGvShtaiankl 44 
                                       lA r Gv++++i n+l
  gi|313125534|ref|YP_004035798.1| 113 LADRFGVTQSTINNRL 128
                                       899************8 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.2
                            HTH_50   3 sLkeyveefErel 15 
                                       +L+e v++ E++l
  gi|313125534|ref|YP_004035798.1| 173 DLSEQVAALEQQL 185
                                       79********997 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00096      0.52      10      47 ..      90     128 ..      89     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00096
                                       TS-HHHHHHHHHHHTS.---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2  10 eLperqreifllryle.glsykEIAellgisegtVksrl 47 
                                       eL+e+qre++  ++   + ++ E A ++g++ +t+++rl
  gi|313125534|ref|YP_004035798.1|  90 ELTEKQREVLRAIQDSpDATQSELADRFGVTQSTINNRL 128
                                       699999999888654445689****************98 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00042      0.23      18      57 ..      91     131 ..      89     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00042
                           UPF0122  18 LTekqanylelyyad.DlSlsEiAeefnvsrqavydnikrt 57 
                                       LTekq+++l+   +  D   sE+A++f v+++++ + ++ +
  gi|313125534|ref|YP_004035798.1|  91 LTEKQREVLRAIQDSpDATQSELADRFGVTQSTINNRLNSI 131
                                       9********9877644******************9998876 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00046      0.25      23      53 ..      99     129 ..      85     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00046
                                       HHHHHHHCT--HHHHHHHHT--HHHHHHHHT CS
                            HTH_37  23 iaeliekrelsqseaaqllgiaqPkvsrllr 53 
                                       +++++++ + +qse+a ++g++q+ +++ l+
  gi|313125534|ref|YP_004035798.1|  99 LRAIQDSPDATQSELADRFGVTQSTINNRLN 129
                                       5677788899***************998765 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00046      0.25      10      30 ..     109     129 ..     102     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00046
                    YdaS_antitoxin  10 gqkaLAealgvsqqaVsqWlk 30 
                                       +q++LA++ gv+q+++++ l+
  gi|313125534|ref|YP_004035798.1| 109 TQSELADRFGVTQSTINNRLN 129
                                       69***************9776 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00085      0.46      18      39 ..     109     130 ..      99     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00085
                           HTH_psq  18 SirkAArkYgiPrsTLwrrkrg 39 
                                       +++++A+++g+  sT+ +r++ 
  gi|313125534|ref|YP_004035798.1| 109 TQSELADRFGVTQSTINNRLNS 130
                                       799**************99876 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.8      0.18        96      26      86 ..      72     129 ..      50     132 .. 0.66
   2 ?   12.3   3.0   0.00031      0.17      13     105 ..      98     191 ..      84     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                           DUF1690  26 sraqalekliqerVaeeLkkLraeeeetlkkfeeklekellkdeadakdelsskalnekie 86 
                                       s + +++ +  ++Va++  +L +++ e+l+++++  ++ +++    +  +++++++n+ ++
  gi|313125534|ref|YP_004035798.1|  72 SMS-KTDTHHVRKVAQDPVELTEKQREVLRAIQDSPDATQSELA--DRFGVTQSTINNRLN 129
                                       333.4455555689999999999999999999887666555444..445555556666555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00031
                           DUF1690  13 lvsqLessketdasraqalekl..iqerVaeeLkkLraeeeetlkkfee.klekellkdeadakdelsskalnekie 86 
                                       ++  +++s+  da++++ ++++   q+ ++++L+ ++  + + +++f e  l+++  + ++d++ ++s k+l+e+++
  gi|313125534|ref|YP_004035798.1|  98 VLRAIQDSP--DATQSELADRFgvTQSTINNRLNSIEGFDWKHRQAFTEvMLDDSDTSADDDSSGSVSVKNLSEQLT 172
                                       344444443..34555555654328999********87777777777651566666666689999************ PP

                           DUF1690  87 eLrkkleefkkkeeeklpe 105
                                       +L++++++++++ +e  ++
  gi|313125534|ref|YP_004035798.1| 173 DLSEQVAALEQQLNEPAQD 191
                                       ********99888755543 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.071        39      20      38 ..     114     132 ..      95     133 .. 0.90
   2 ?    5.0   0.1     0.042        23      30      44 ..     174     188 ..     164     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.071
                                       HHHHTS-HHHHHHHHHHHH CS
                             HTH_1  20 AeeLglsqpavsrqikrLE 38 
                                       A++ g++q+++  ++++ E
  gi|313125534|ref|YP_004035798.1| 114 ADRFGVTQSTINNRLNSIE 132
                                       899***********99887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHTS- CS
                             HTH_1  30 vsrqikrLEeelgvp 44 
                                       +s q+++LE++l++p
  gi|313125534|ref|YP_004035798.1| 174 LSEQVAALEQQLNEP 188
                                       799*********986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00072      0.39       5      48 ..      90     133 ..      86     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00072
                                       HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHH CS
                              TrmB   5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLed 48 
                                        L+e   +v  a+  +  at +e+a + gv +s++++ L+s e 
  gi|313125534|ref|YP_004035798.1|  90 ELTEKQREVLRAIQDSPDATQSELADRFGVTQSTINNRLNSIEG 133
                                       68888999999999999***********************9876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00047      0.26       5      39 ..      91     126 ..      90     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00047
                            HTH_38   5 LsleeReeIerll.aeGlslreIArrLgrspsTIsR 39 
                                       L+  +Re++ +   + + +++e A r g+  sTI++
  gi|313125534|ref|YP_004035798.1|  91 LTEKQREVLRAIQdSPDATQSELADRFGVTQSTINN 126
                                       788888888888525779****************97 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.3   7.3e+02      43      56 ..      84      97 ..      51     117 .. 0.60
   2 ?   10.0   0.1    0.0015      0.81      11      39 ..     165     191 ..     162     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.3
                      ABC_tran_CTD 43 laelsaeleeleae 56
                                      +a+   el+e + e
  gi|313125534|ref|YP_004035798.1| 84 VAQDPVELTEKQRE 97
                                      33333333333333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0015
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpelysd 39 
                                       ++l +++  L e+ a+le++l++p+  +d
  gi|313125534|ref|YP_004035798.1| 165 KNLSEQLTDLSEQVAALEQQLNEPA--QD 191
                                       5677888888888899999988887..55 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       9.5   5.2e+03      10      30 ..      89     109 ..      80     114 .. 0.63
   2 ?   11.8   0.8   0.00046      0.25       2      30 ..     164     192 ..     163     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 9.5
                               LPP  10 sqLkskvdqlssdvnsakaaa 30 
                                        +L +k+ ++   ++++ +a 
  gi|313125534|ref|YP_004035798.1|  89 VELTEKQREVLRAIQDSPDAT 109
                                       567777777766666666655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00046
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaa 30 
                                       +++Ls+q+ +L+++v++l++++n+ +++ 
  gi|313125534|ref|YP_004035798.1| 164 VKNLSEQLTDLSEQVAALEQQLNEPAQDT 192
                                       789*****************999877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1278  (0.0712812); expected 358.6 (0.02)
Passed bias filter:                      810  (0.0451782); expected 358.6 (0.02)
Passed Vit filter:                       142  (0.00792013); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1546.58
//
Query:       gi|313125535|ref|YP_004035799.1|  [L=273]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-20   71.7   0.1    7.4e-20   70.6   0.1    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00024   20.4   0.0     0.0004   19.6   0.0    1.3  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
     0.0011   19.0   0.0     0.0022   18.0   0.0    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
     0.0028   17.6   0.0     0.0068   16.3   0.0    1.6  1  PadR            Transcriptional regulator PadR-like family
     0.0038   17.1   0.0      0.013   15.4   0.0    1.9  2  PLDc_2          PLD-like domain
     0.0089   16.0   0.5      0.018   15.0   0.2    1.6  2  Holin_BhlA      BhlA holin family
  ------ inclusion threshold ------
      0.018   14.8   0.2      0.043   13.6   0.2    1.7  1  HTH_IclR        IclR helix-turn-helix domain
      0.037   13.1   0.1      0.052   12.7   0.1    1.2  1  PDCD7           Programmed cell death protein 7
      0.076   13.1   0.1        0.2   11.8   0.1    1.7  1  HTH_20          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.1   3.7e-23   7.4e-20       1      67 [.       4      71 ..       4      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 3.7e-23
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravdp 67
                                      L++lGLseyEa++Y  Ll+ g  ta+e++++++vp  ++Y+vL+sLe+  lV+ +  +rpk+Y+av+p
  gi|313125535|ref|YP_004035799.1|  4 LRDLGLSEYEARAYRSLLRTGATTAKELSRASDVPMGRIYDVLNSLEQHSLVRSQAaSRPKKYVAVEP 71
                                      789****************************************************9566*******99 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     2e-07    0.0004      38     134 ..     159     264 ..     155     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2e-07
                                       HHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S.EE...........EEETTTEEEEE-SSS-EEE CS
                    Regulator_TrmB  38 lreeliaaaergvtVllliypdedleeldleevatevrvrrsgapll...........vivDrkrgvvaprevlrdk 103
                                       + eel+aa +rgv+V++l++pd   + +++ ++  + r+ + +++++           +i D + ++ +p+ +l+  
  gi|313125535|ref|YP_004035799.1| 159 ITEELEAALDRGVNVSVLMSPDLVASLPKTVGKRYVTRLENHPQFEVrtteqlsgtfnLIDDVEVCIEVPN-PLDPG 234
                                       789*****************************************999777777777755555554444444.67777 PP

                                       E--HHHHHHHHHHHHHH........HHH-EE CS
                    Regulator_TrmB 104 eeeyaiifkekelihvlshyFlttlWktsev 134
                                       e +  i  k+ e+++ +  +F  + W+++e 
  gi|313125535|ref|YP_004035799.1| 235 EAFAMIDLKDAEFATDIREMFDPR-WDEAEP 264
                                       777778888888888888888888.887775 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.1e-06    0.0022      19      57 ..      17      55 ..      13      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 19 vetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      ++ Llr+g+ t++el+++++++   + ++L +L qh lV
  gi|313125535|ref|YP_004035799.1| 17 YRSLLRTGATTAKELSRASDVPMGRIYDVLNSLEQHSLV 55
                                      578***********************************9 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.4e-06    0.0068      17      62 ..      29      66 ..      22      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.4e-06
                                      HHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEE CS
                              PadR 17 keleelsegllelseGslYpaLkrLekeglveseweesgegpprky 62
                                      kel++      ++ +G++Y++L++Le++ lv s+ +     +p+ky
  gi|313125535|ref|YP_004035799.1| 29 KELSRA----SDVPMGRIYDVLNSLEQHSLVRSQAAS----RPKKY 66
                                      444444....5899******************99775....57766 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.4e-06     0.013       1      73 [.     128     206 ..     128     221 .. 0.71
   2 ?   -1.9   0.0       1.5   2.9e+03     116     133 .]     242     259 ..     237     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.4e-06
                            PLDc_2   1 liqliksAkksidiatyyf.......vsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagv 70 
                                       l+++++ A +s+ i+ +++        + + i ++l +a +rgv+v +l++++   a++++   +++  +l  + + 
  gi|313125535|ref|YP_004035799.1| 128 LLERLSAADSSLVIVAGTLspqfdigRVGELITEELEAALDRGVNVSVLMSPDL-VASLPKTVGKRYVTRLENHPQF 203
                                       578999*************44444443444469******************954.4555555555555555455555 PP

                            PLDc_2  71 evr 73 
                                       evr
  gi|313125535|ref|YP_004035799.1| 204 EVR 206
                                       555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                            PLDc_2 116 iedkelakeleeeFerlw 133
                                       ++d+e+a+ ++e F+  w
  gi|313125535|ref|YP_004035799.1| 242 LKDAEFATDIREMFDPRW 259
                                       67899*********9888 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   9.3e-06     0.018      32      62 ..      81     111 ..      77     114 .. 0.86
   2 ?   -4.0   0.0       7.6   1.5e+04      50      62 ..     210     222 ..     208     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.3e-06
                        Holin_BhlA  32 kreekqeerekkyqeiikkltekfeiveeik 62 
                                       ++   +ee+ ++yq+++++lt+++e+ e ++
  gi|313125535|ref|YP_004035799.1|  81 TKHRELEEKAEQYQAVVDDLTDELETAEPVQ 111
                                       5566789*******************99886 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 7.6
                        Holin_BhlA  50 kltekfeiveeik 62 
                                       +l+  f+++++++
  gi|313125535|ref|YP_004035799.1| 210 QLSGTFNLIDDVE 222
                                       6788899998875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   2.2e-05     0.043      16      50 ..      23      57 ..      19      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +++ t +el+r++++p    +  L++L+++ +v+ 
  gi|313125535|ref|YP_004035799.1| 23 TGATTAKELSRASDVPMGRIYDVLNSLEQHSLVRS 57
                                      455689***************************96 PP

>> PDCD7  Programmed cell death protein 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.6e-05     0.052     146     210 ..      41     105 ..      32     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                             PDCD7 146 rmldilrsleklrklrkeaaerkgillekeadeafesklekLrkvlkkrteeyskEEkaLkvmLe 210
                                       r++d+l+sle+   +r +aa+r ++++  e d a++  le+  ++l+++ e+y++    L + Le
  gi|313125535|ref|YP_004035799.1|  41 RIYDVLNSLEQHSLVRSQAASRPKKYVAVEPDTALDRLLETKHRELEEKAEQYQAVVDDLTDELE 105
                                       89***************************************************987666666666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.9e-05       0.2      19      57 ..      20      58 ..      10      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.9e-05
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      L r ++ ta+el ++ d+++  +++ L+ Le++ Lv+++
  gi|313125535|ref|YP_004035799.1| 20 LLRTGATTAKELSRASDVPMGRIYDVLNSLEQHSLVRSQ 58
                                      458899******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1763.96
//
Query:       gi|313125536|ref|YP_004035800.1|  [L=546]
Description: hypothetical protein Hbor_07630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-24   86.7   0.0    2.7e-24   86.0   0.0    1.4  1  Thioredox_DsbH  Protein of unknown function, DUF255
    1.7e-12   47.4   0.0      4e-12   46.1   0.0    1.7  2  Thioredoxin_7   Thioredoxin-like
    4.1e-07   29.9   0.0    7.6e-07   29.1   0.0    1.3  1  Thioredoxin     Thioredoxin
    0.00018   21.9   0.0    0.00033   21.1   0.0    1.4  1  Thioredoxin_2   Thioredoxin-like domain
    0.00048   19.5   2.8      0.063   12.5   0.3    3.0  3  GlcNAc_2-epim   N-acylglucosamine 2-epimerase (GlcNAc 2-epime
  ------ inclusion threshold ------
       0.43   10.0   2.9        3.7    7.0   0.3    2.8  3  Glyco_hydro_76  Glycosyl hydrolase family 76


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   8.9e-28   2.7e-24      17     150 ..       5     124 ..       1     134 [. 0.93

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 8.9e-28
                    Thioredox_DsbH  17 knpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDreerPdldkiymea 93 
                                       ++ v+W++wg ea+e+a++++kp+lls+  ++c  Ch m+ e++ ++++aa +n+ fv+v+vD + +P + + y   
  gi|313125536|ref|YP_004035800.1|   5 ETRVEWHKWGPEAFEEARADEKPVLLSLTATWCDGCHEMDVETYGEPRIAANVNDDFVPVRVDVDRHPRVRERYN-- 79 
                                       789*******************************************************************99994.. PP

                    Thioredox_DsbH  94 vqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeeree 150
                                              gg+P +vf+tp ++ + g+ Y+ +       g+++vl++++e+w+e+ ++
  gi|313125536|ref|YP_004035800.1|  80 ------MGGFPSTVFCTPSGELITGAMYLGP------DGMRQVLDRVRETWSEKGDS 124
                                       ......6**********************98......5899**********998665 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   1.3e-15     4e-12       1      83 []       9      91 ..       9      91 .. 0.88
   2 ?   -3.9   0.0       5.6   1.7e+04      40      58 ..     216     234 ..     216     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.3e-15
                                      ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEE CS
                     Thioredoxin_7  1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvva 79
                                      ew+++ +ea+++a++++kpvl+ ++a+wc  C+ ++ ++  +++++a ++++fv +rvdv++  +   ++ + g+P  +
  gi|313125536|ref|YP_004035800.1|  9 EWHKWGPEAFEEARADEKPVLLSLTATWCDGCHEMDVETYGEPRIAANVNDDFVPVRVDVDRHPRVRERYNMGGFPSTV 87
                                      79**********************************************************9888733233346699998 PP

                                      EE-T CS
                     Thioredoxin_7 80 fldp 83
                                      f +p
  gi|313125536|ref|YP_004035800.1| 88 FCTP 91
                                      8766 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.6
                                       HH-HHHHH.HHHT-EEEEE CS
                     Thioredoxin_7  40 lsdeevkaalaekfvllrv 58 
                                       +sd+   ++l+++ +l+r+
  gi|313125536|ref|YP_004035800.1| 216 WSDPHHEKLLDSNAALVRA 234
                                       7788888889999999987 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.5e-10   7.6e-07       7      82 ..      15      92 ..      10     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.5e-10
                                      HHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHH...HHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETT CS
                       Thioredoxin  7 kenFeeevakekklvlveFyApwCghCkalaPele...klaeelkdkvklakvdvdenedlakkyevegiPtlklfkng 82
                                       e+Fee+ a+ +k+vl+  +A+wC  C ++  e     ++a +++d+++ ++vdvd ++ + ++y+  g+P  +++  +
  gi|313125536|ref|YP_004035800.1| 15 PEAFEEARAD-EKPVLLSLTATWCDGCHEMDVETYgepRIAANVNDDFVPVRVDVDRHPRVRERYNMGGFPSTVFCTPS 92
                                      5789999888.*******************9876423379999999*************************99887655 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.1e-07   0.00033       2     100 ..      22     100 ..      21     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-07
                     Thioredoxin_2   2 kgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygv 78 
                                       ++++kpvl+  t+++C  C+ +  e+   +++        ++++f+p+ v++++ + +              ++y++
  gi|313125536|ref|YP_004035800.1|  22 RADEKPVLLSLTATWCDGCHEMDVETYGEPRIAAN-----VNDDFVPVRVDVDRHPRVR-------------ERYNM 80 
                                       6789****************************999.....****999999999988886.............88*** PP

                     Thioredoxin_2  79 rgtPtivfldgkeivarlpGyv 100
                                        g+P++vf  ++   + ++G++
  gi|313125536|ref|YP_004035800.1|  81 GGFPSTVFCTPS--GELITGAM 100
                                       *****9987777..33677766 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.03        91      47     118 ..     190     264 ..     178     279 .. 0.67
   2 !   12.5   0.3   2.1e-05     0.063      74     175 ..     291     396 ..     271     405 .. 0.69
   3 ?    3.4   0.0     0.013        38     277     307 ..     424     454 ..     412     461 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.03
                                       HHHHHTTTTTB-TTTSSB-SEEETTEEEE--EEHHHHHHHHH..HHHH.HHTTT-TTHHHHHHHHHHHHHHHTEE CS
                     GlcNAc_2-epim  47 hGlkflekvlrdaehggyfsalrdggvldaskdaYdhaFvll..alas.alaageeeakdlldetlavlekhlwe 118
                                       + l+ +++ l d+ +gg+f+ +  ++  d+ ++    + ++l  a+a+  l++g+++  + ++et ++l  +lw+
  gi|313125536|ref|YP_004035800.1| 190 ETLRTIAETLFDDVEGGFFRYADGRDWSDPHHEKLLDSNAALvrAFANgYLYTGDDDLLNPAMETRDFLADRLWN 264
                                       444555555557777888877766666666555444333333247777677888888888888888888888887 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
                                       EE--EE..HHHHHHHHHHHHH...HHTTT-TTHHHHHHHHHHHHHHHTEETTTTEE--EE-TTSS-BEEHHHHHHHH CS
                     GlcNAc_2-epim  74 ldaskd..aYdhaFvllalas...alaageeeakdlldetlavlekhlweekaglvkeesdkefsklrgsnpnMhll 145
                                       + +++d  aY  a +l a a     +++ +  a+d +  tl++l+++l ++   +++  + +   ++   + + +++
  gi|313125536|ref|YP_004035800.1| 291 AGPRRDltAYAGANALAADALltlTAYTDDGTARDYAVRTLDFLDTRLIDDG-DVTHFDAGETTGETHLLEDHARTV 366
                                       44444411566666666555541122344445689999*********99984.444555555556666799****** PP

                                       HHHHHHHHTT-BTHHHHHHHHHHHHHTTTT CS
                     GlcNAc_2-epim 146 eAmLalaeatgdkeyleraeeiaelvisef 175
                                        A+  + ++ gd+ yl+ra+ +a+++i+e+
  gi|313125536|ref|YP_004035800.1| 367 SAFVRARQVLGDDWYLDRAQAVADVAIDEL 396
                                       ***************************876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHH--CHHHHHHHHHHHHH CS
                     GlcNAc_2-epim 277 qtEalkaaaalaeltgearylewyarvaeyl 307
                                        +E ++a+  la+ tge+ y++ +++++ ++
  gi|313125536|ref|YP_004035800.1| 424 NVEMANALCDLAAATGEEPYEDAAQEAIGAF 454
                                       4677777777777788888877777776654 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.72   2.2e+03     151     188 ..     223     260 ..     187     268 .. 0.67
   2 ?    7.0   0.3    0.0012       3.7     155     209 ..     303     356 ..     296     405 .. 0.87
   3 ?    1.9   0.1     0.042   1.3e+02     155     181 ..     423     449 ..     372     452 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.72
                                       EEHHHHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHH CS
                    Glyco_hydro_76 151 knsisngplfqlaarLarytgnetYlewAekvwdWved 188
                                       k   sn++l  + a  + ytg++ +l+ A ++ d+++d
  gi|313125536|ref|YP_004035800.1| 223 KLLDSNAALVRAFANGYLYTGDDDLLNPAMETRDFLAD 260
                                       55557888888888888888888888888877777665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHHHSCSBTTTS-B-SEEETTTCC CS
                    Glyco_hydro_76 155 sngplfqlaarLarytgnetYlewAekvwdWvedvgliddedwlvyDgasvednc 209
                                       +n+ ++ + + L  yt++ t  ++A ++ d++ + +lidd d++ +D  ++++++
  gi|313125536|ref|YP_004035800.1| 303 ANALAADALLTLTAYTDDGTARDYAVRTLDFLDT-RLIDDGDVTHFDAGETTGET 356
                                       7999999999**********************99.9***********98766655 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHHHHH--CHHHHHHHH CS
                    Glyco_hydro_76 155 sngplfqlaarLarytgnetYlewAek 181
                                       +n +++++ + La +tg+e Y + A++
  gi|313125536|ref|YP_004035800.1| 423 ANVEMANALCDLAAATGEEPYEDAAQE 449
                                       678888999999999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 3239.33
//
Query:       gi|313125537|ref|YP_004035801.1|  [L=160]
Description: protein affecting phage t7 exclusion by the f plasmid [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-33  114.0   7.9    4.4e-33  113.7   7.9    1.1  1  FxsA      FxsA cytoplasmic membrane protein


Domain annotation for each model (and alignments):
>> FxsA  FxsA cytoplasmic membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   7.9   2.5e-37   4.4e-33       2     108 ..       9     115 ..       8     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 2.5e-37
                              FxsA   2 lllllpvlEilllvlvasaiGvlatllllvltallGallvrrqgrralrrlqeklaqgelpaeelldglllllggvL 78 
                                       +ll +p+l+ lllv +as+iG+ +t+ll+vlt+l+G+llvr++gr++l++lq+k+a+g++p++elldg ll+++g++
  gi|313125537|ref|YP_004035801.1|   9 ALLSIPLLDTLLLVPLASTIGFAPTVLLVVLTGLVGMLLVRAEGRHTLSKLQQKVATGGIPTDELLDGGLLIAAGAF 85 
                                       57799************************************************************************ PP

                              FxsA  79 LllPGfvtdvlGlllllPptRkllrrllkr 108
                                       Ll+PG+vtd+lG+ll +P+tR  +r+++kr
  gi|313125537|ref|YP_004035801.1|  86 LLTPGVVTDLLGFLLAIPVTRYPIRKVVKR 115
                                       **************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1032.67
//
Query:       gi|313125538|ref|YP_004035802.1|  [L=222]
Description: hypothetical protein Hbor_07660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1220.04
//
Query:       gi|313125539|ref|YP_004035803.1|  [L=142]
Description: hypothetical protein Hbor_07670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.054   13.3   0.0    1.4  1  SplA      Transcriptional regulator protein (SplA)


Domain annotation for each model (and alignments):
>> SplA  Transcriptional regulator protein (SplA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-06     0.054       7      23 ..      50      66 ..      44      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-06
                              SplA  7 agdeVyViyrNPHtanV 23
                                        d V+ iy+NP t+ V
  gi|313125539|ref|YP_004035803.1| 50 RQDDVFMIYKNPTTQVV 66
                                      4699********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 785.47
//
Query:       gi|313125540|ref|YP_004035804.1|  [L=250]
Description: hypothetical protein Hbor_07680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   13.3   0.8          1    9.9   0.0    2.5  2  YflT      Heat induced stress protein YflT


Domain annotation for each model (and alignments):
>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   5.8e-05         1      69      97 ..      21      52 ..      13      52 .. 0.85
   2 ?    1.0   0.5     0.033     6e+02      28      84 ..     116     176 ..      98     178 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 5.8e-05
                              YflT 69 delre...kleslGltedeaeeyeeeldeGki 97
                                      d +++   +l+++Gl+++ ++e+e+ +d++k+
  gi|313125540|ref|YP_004035804.1| 21 DTVASplvALKEMGLSDELLAELEQTVDDDKY 52
                                      5555555589********************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.033
                              YflT  28 yvvakdkdrlerla.entdaetettse...eglwdsiknlfrskgdelrekleslGltede 84 
                                       +v+++++ ++++l  ++ + e++++ e    ++ d+ ++   ++++   + +++ G+++de
  gi|313125540|ref|YP_004035804.1| 116 HVYTEENPEIDKLImDKEKGEVVKAVEektGSSNDDHAREAIKQAENKIADIQNSGIPQDE 176
                                       6777777777776643333344444442333333333333333333333366666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1437.89
//
Query:       gi|313125541|ref|YP_004035805.1|  [L=580]
Description: hypothetical protein Hbor_07690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-31  106.8   0.9    1.2e-30  105.6   0.9    1.7  1  DUF4157        Domain of unknown function (DUF4157)
  ------ inclusion threshold ------
       0.03   14.7   0.3      0.058   13.7   0.3    1.5  1  Peptidase_M91  Effector protein


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.9   1.3e-34   1.2e-30       2      78 ..      98     174 ..      97     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 1.3e-34
                           DUF4157   2 lpeavraemerafgadlsdVrvhtgsaaaraaralgAqAfTlgndivfaageyqpesaagrellaHELtHvvqqreg 78 
                                       l++++++ me ++g++l+dVr+htg++aa+a+++++A+AfT+gn+i+f++gey+p+sa+g+++laHEL+Hv qq++g
  gi|313125541|ref|YP_004035805.1|  98 LDTSIQRAMEDRMGDNLGDVRIHTGPSAAKACEDINARAFTVGNHIAFNHGEYDPSSAEGQHILAHELAHVRQQTGG 174
                                       899***********************************************************************986 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   6.5e-06     0.058      67     135 ..     134     197 ..      73     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-06
                     Peptidase_M91  67 ekgegtdaeinynpafsseeegkegrPsavLyHElaHaydalngtlddgeydgkdeedssgvpneErqA 135
                                        + ++ +++i +n         +  + +++L+HElaH+++++ g +   +++g+ e d +   + Er+A
  gi|313125541|ref|YP_004035805.1| 134 ARAFTVGNHIAFNHGEYDP---SSAEGQHILAHELAHVRQQTGGAVSMLPQEGELEIDPDP--RLEREA 197
                                       4555666666666663333...5556669***************99888887776666654..555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 3405.16
//
Query:       gi|313125542|ref|YP_004035806.1|  [L=127]
Description: hypothetical protein Hbor_07700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.87    9.9   6.2         13    6.1   3.4    2.1  2  DUF3267   Putative zincin peptidase


Domain annotation for each model (and alignments):
>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0018        32       1      17 [.      23      39 ..      23      47 .. 0.85
   2 ?    6.1   3.4   0.00073        13      50     100 ..      81     126 ..      59     127 .] 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0018
                           DUF3267  1 llvlvilHEllHglffk 17
                                      +++ v+ HEl H+ + +
  gi|313125542|ref|YP_004035806.1| 23 MFPAVLAHELTHAAVAW 39
                                      588999******99875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00073
                           DUF3267  50 fiiillaPfvllgilllllalllpsstlllllllalnaagsagDllialll 100
                                       ++ +ll Pfv+    +++ +l +p  + +++   al + +sa Dl ++++l
  gi|313125542|ref|YP_004035806.1|  81 MVGALLTPFVV----PWAFGLEVPLMA-YVFGAWALYTWPSADDLAVLSAL 126
                                       33334444433....555555555332.999999***********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 736.92
//
Query:       gi|313125543|ref|YP_004035807.1|  [L=119]
Description: hypothetical protein Hbor_07710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.6   1.6        0.2   11.7   0.3    2.1  2  Melittin  Melittin
       0.27   11.5   5.1       0.14   12.4   0.4    2.1  2  TrbC      TrbC/VIRB2 family


Domain annotation for each model (and alignments):
>> Melittin  Melittin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   2.2e-05       0.2       1      18 [.      56      76 ..      56      79 .. 0.92
   2 ?   -1.0   0.1      0.24   2.2e+03       2      16 ..      93     107 ..      92     111 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                                      -HHHHHHHHHTH...HHHHHH CS
                          Melittin  1 GiGAvLKvLttG...LPALis 18
                                      GiG +L +Lt G   LPA+is
  gi|313125543|ref|YP_004035807.1| 56 GIGTILYILTEGradLPAVIS 76
                                      9*********998889****9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                                       HHHHHHHHHTHHHHH CS
                          Melittin   2 iGAvLKvLttGLPAL 16 
                                       iGA + +L     AL
  gi|313125543|ref|YP_004035807.1|  93 IGAFMSILFGAALAL 107
                                       899888886555555 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   1.5e-05      0.14      35      88 ..      25      83 ..       1      86 [. 0.77
   2 ?    1.3   0.5     0.043   3.9e+02      80      93 ..      91     104 ..      86     110 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                              TrbC 35 g......dpvetvlqnivdfltgplakviatiaiivaGimlafgrlswrtlvmvviGivi 88
                                             d + ++++ ++d l gp+a+++  i+i  + + l  gr+++++++ ++iG+++
  gi|313125543|ref|YP_004035807.1| 25 DdpwkegDAWAGFVKPFMDLL-GPVAPAMLGIGIGTILYILTEGRADLPAVISILIGGFL 83
                                      256666788999999998865.88*********************************998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.043
                              TrbC  80 vmvviGiviifgAs 93 
                                       + + ++++i+fgA+
  gi|313125543|ref|YP_004035807.1|  91 AKIGAFMSILFGAA 104
                                       55667777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 702.15
//
Query:       gi|313125544|ref|YP_004035808.1|  [L=103]
Description: hypothetical protein Hbor_07720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 604.23
//
Query:       gi|313125545|ref|YP_004035809.1|  [L=276]
Description: hypothetical protein Hbor_07730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.031   13.8   0.4      0.054   13.1   0.4    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
       0.07   12.6   0.1       0.16   11.5   0.1    1.6  1  SieB            Super-infection exclusion protein B
       0.11   12.8   2.6       0.18   12.1   2.6    1.3  1  TctB            Tripartite tricarboxylate transporter TctB fa
       0.15   12.2   0.2       0.74   10.0   0.2    2.1  2  Mrr_N           Mrr N-terminal domain
       0.42    8.9   1.8       0.31    9.3   0.3    1.5  2  SpecificRecomb  Site-specific recombinase


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   1.5e-05     0.054       4      47 ..     203     247 ..     200     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                            HTH_24   4 tdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +d++I+e++q++       ++++++g S+  + +r + L ++Gl+
  gi|313125545|ref|YP_004035809.1| 203 IDYRIIEAVQQEDQaQRVDQISKKVGKSIELTEKRCELLLNKGLL 247
                                       8**********6665***************************985 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.3e-05      0.16       4      79 ..      32     106 ..      29     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.3e-05
                              SieB   4 LiiasglllllPdslleklnlgkfleeyglwig.lvflisiayllaqvvskllaeikekikkkreqkkvekklknLt 79 
                                       ++++  +l ++++s ++++++++++++y+ +ig l  ++s+ ++l++  +k  + + + ++    + ++++ +++Lt
  gi|313125545|ref|YP_004035809.1|  32 ISAFLTALAVVSNSNIKSVSVSNAVNSYATIIGgLLWIFSVTLVLVSQTHKKPKGADSGWS--DYNAREISSFSRLT 106
                                       67888999************************64788999*****9999888777777777..66666666666666 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.6   5.1e-05      0.18      30     101 ..      58     151 ..      29     170 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.1e-05
                              TctB  30 ffPlllgvllallgllllv................aadgekeekearedwrkllklvlallaalllyalllepl... 87 
                                        + +++g+ll+++++ l++                     ++++ ++++  + + l++ +l  lll++ l   +   
  gi|313125545|ref|YP_004035809.1|  58 SYATIIGGLLWIFSVTLVLvsqthkkpkgadsgwsD---YNAREISSFSRLTDASLFFSTLTTLLLFIGLASGVitg 131
                                       46789*********8877789999776655553321...22222222333333333344444444444444443455 PP

                              TctB  88 ......Gfilatalflllll 101
                                              +++++++++l+l 
  gi|313125545|ref|YP_004035809.1| 132 yygggkSYLISSIILILVLT 151
                                       55544445555553332222 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00021      0.74       8      45 ..     207     245 ..     203     255 .. 0.91
   2 ?    2.0   0.0     0.065   2.3e+02      63      84 ..     243     264 ..     241     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                             Mrr_N   8 lLealad.gsehrlkeirervaerfglseeeraellpsg 45 
                                       ++ea+++ ++++r+++i ++v ++++l+e+ ++ ll++g
  gi|313125545|ref|YP_004035809.1| 207 IIEAVQQeDQAQRVDQISKKVGKSIELTEKRCELLLNKG 245
                                       78899888***************************9988 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.065
                             Mrr_N  63 kagllespkrgvwkiTekGrev 84 
                                       + gll+++   ++++++ Gr++
  gi|313125545|ref|YP_004035809.1| 243 NKGLLDRDMYKQYEVSDLGRRF 264
                                       679*****************87 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.3   8.7e-05      0.31     418     488 ..      59     133 ..      42     139 .. 0.82
   2 ?   -3.1   0.1      0.49   1.8e+03     217     239 ..     212     234 ..     205     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 8.7e-05
                    SpecificRecomb 418 laAvlGNvlvvipvalli.allilallgapliseekaeallesldplgslallyAaitGvlLFl...ssLiaGya 488
                                        a ++G +l ++ v+l++ +   ++  ga    ++  ++ ++s++ l+ ++l++ ++t +lLF+   s++i+Gy+
  gi|313125545|ref|YP_004035809.1|  59 YATIIGGLLWIFSVTLVLvSQTHKKPKGADSGWSDYNAREISSFSRLTDASLFFSTLTTLLLFIglaSGVITGYY 133
                                       578899999999888765145555667777777888889999*********************65559******8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.49
                    SpecificRecomb 217 qcreavdrvrkhleenGvsvslv 239
                                       q +++++rv +  ++ G s++l+
  gi|313125545|ref|YP_004035809.1| 212 QQEDQAQRVDQISKKVGKSIELT 234
                                       55678888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1555.85
//
Query:       gi|313125546|ref|YP_004035810.1|  [L=265]
Description: hypothetical protein Hbor_07740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0056   15.9   0.0      0.011   15.0   0.0    1.6  1  Ion_trans  Ion transport protein
  ------ inclusion threshold ------
      0.034   12.8   1.1      0.045   12.4   1.1    1.1  1  Ndc1_Nup   Nucleoporin protein Ndc1-Nup


Domain annotation for each model (and alignments):
>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-06     0.011      89     160 ..      47     159 ..       5     258 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-06
                                       H.....HHHHHHHHHHHHGGGGGGHHHCHSHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCC CS
                         Ion_trans  89 e.....esllllsvlrlfrvlrllklisrleg.lrtlvtalirsvkdllnvlllllvvlfifaligvqlfkgklrek 159
                                       +      sl+ll++++ f +l l ++ s+l+g l ++    i+   +  ++l+l+++++++ ++  + lf++++ +k
  gi|313125546|ref|YP_004035810.1|  47 SaltslISLVLLYLFSGFYLLNLRRIASSLSGfLGIISINGIELSATSALFLYLSHIFVIFVGSSLLGLFDRNILNK 123
                                       03333445677999999999999999999999544433346677777777888888888888888888****99999 PP

                                       ...................................C CS
                         Ion_trans 160 ...................................n 160
                                                                          +
  gi|313125546|ref|YP_004035810.1| 124 deildprepweyafdeipvdgeeldiylqdgvqlrG 159
                                       777776666666666666665555555555544440 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.1     5e-06     0.045      53     178 ..      22     141 ..       3     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-06
                          Ndc1_Nup  53 lpilvlrkaqlhvgprttssrlstllaslfsl..qtletllvyllSallfaevyiwslpedarlgwvtskssrerpr 127
                                       l+ l +  ++  +++r+++sr    ++ ++s   +++ ++l yl+S++ + ++   + + +  lg     s ++   
  gi|313125546|ref|YP_004035810.1|  22 LVGLQIFFKY--AQRRPSPSR---TKWVAWSAltSLISLVLLYLFSGFYLLNLRRIASSLSGFLG---IISINGIEL 90 
                                       4444444443..467778888...566666666699************99999986555433344...444556677 PP

                          Ndc1_Nup 128 lNerplflllsglvlalvysllhllfdrdrlsfkssfpivqpskyllkrlp 178
                                          + lfl+ls++++ +v s l  lfdr+ l++++  +  +p +y++ ++p
  gi|313125546|ref|YP_004035810.1|  91 SATSALFLYLSHIFVIFVGSSLLGLFDRNILNKDEILDPREPWEYAFDEIP 141
                                       7789***************************99988888889988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1458.76
//
Query:       gi|313125547|ref|YP_004035811.1|  [L=180]
Description: transcriptional regulator padr-like family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-05   24.4   0.0    4.2e-05   23.4   0.0    1.5  1  PadR          Transcriptional regulator PadR-like family
    0.00013   21.7   0.0    0.00027   20.7   0.0    1.7  1  HxlR          HxlR-like helix-turn-helix
    0.00077   20.3   0.3     0.0012   19.7   0.3    1.4  1  DUF4065       Protein of unknown function (DUF4065)
     0.0014   18.7   0.0      0.002   18.2   0.0    1.3  1  Replic_Relax  Replication-relaxation
     0.0034   15.8   0.1     0.0043   15.5   0.1    1.1  1  DUF505        Protein of unknown function (DUF505)
     0.0091   16.6   0.1      0.014   16.0   0.1    1.4  1  RTP           Replication terminator protein
  ------ inclusion threshold ------
      0.021   15.0   0.1      0.035   14.3   0.1    1.4  1  HTH_34        Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.6e-08   4.2e-05      38      74 ..      89     125 ..      68     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                                       HHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  38 LkrLekeglveseweesgegpprkyYrlTdaGrrela 74 
                                        k+Le++g++e++ e++++g ++ +Y lTd+Grr ++
  gi|313125547|ref|YP_004035811.1|  89 IKTLENKGIIERRTETTVSGNEKYIYSLTDEGRRVVK 125
                                       589******************************9875 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.1e-07   0.00027      35      75 ..      84     126 ..      48     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHHHTTSEEEEEESSSS..-EEEEEE-TCGGGGHHH CS
                              HxlR  35 mLaqrLreLeqdglierevypevP..pkveYsltekGrslepv 75 
                                        La +++ Le++g+ier++  +v   +k  Yslt++Gr + + 
  gi|313125547|ref|YP_004035811.1|  84 SLAGSIKTLENKGIIERRTETTVSgnEKYIYSLTDEGRRVVKS 126
                                       68999************998887533799*********98765 PP

>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   4.8e-07    0.0012      13     109 ..      60     163 ..      54     179 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.8e-07
                           DUF4065  13 lkrtgkpitg.lkyiawkyGPVvpevydeikelgskpieekeeeisdeklekkekkeveeleddkeae......lse 82 
                                       l +++k i++  ++   kyGP++p++  +ik+l++k i+e+++e++ +  ek  +     l d++  +      +++
  gi|313125547|ref|YP_004035811.1|  60 LTQKEKDISElHEFKSDKYGPFSPSLAGSIKTLENKGIIERRTETTVSGNEKYIY----SLTDEG--RrvvkslIND 130
                                       5667778888457999********************9999988888433333222....222222..1235787888 PP

                           DUF4065  83 eekev......idkvikkykdlsaseLselthk 109
                                       e ++v       + + k+y+d   ++L +++++
  gi|313125547|ref|YP_004035811.1| 131 ENRDVdhvlkaAESIKKRYQDTPLDRLLRYVYQ 163
                                       888888888885555555665555555555554 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   7.7e-07     0.002      16      72 ..      68     132 ..      55     159 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.7e-07
                      Replic_Relax  16 arllfashra......tarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarll.....aaq 72 
                                        +l++ + ++      ++   +++L+ +g+++r ++      +g e+y+Y Lt  G+r++     +++
  gi|313125547|ref|YP_004035811.1|  68 SELHEFKSDKygpfspSLAGSIKTLENKGIIERRTET---TVSGNEKYIYSLTDEGRRVVkslinDEN 132
                                       55555444445667777778899**********5554...5556789*************44433222 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.7e-06    0.0043     346     411 ..      60     135 ..      49     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                            DUF505 346 iakkfeeakdlekWyednf.....dlreaLysLesfeLiesev....eekgkevyvlTeyGekvledqekk.lrev 411
                                       +++k++++ +l+++++d++     +l  ++++Le +++ie++     + + k +y+lT++G++v++ + ++  r+v
  gi|313125547|ref|YP_004035811.1|  60 LTQKEKDISELHEFKSDKYgpfspSLAGSIKTLENKGIIERRTettvSGNEKYIYSLTDEGRRVVKSLINDeNRDV 135
                                       556666666666666666543344688899**********9985543445599***********998765545665 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   5.5e-06     0.014      34     103 ..      71     138 ..      51     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.5e-06
                                       HHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHHHHHHHHHHHHHHHH CS
                               RTP  34 keFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkekaklykkqvkidldrc 103
                                       +eFk+  y P    +  +++ l ++gi++rr e    +  +e +iYsltdeG+  +k + +    d+d+ 
  gi|313125547|ref|YP_004035811.1|  71 HEFKSDKYGPFSPSLAGSIKTLENKGIIERRTETT--VSGNEKYIYSLTDEGRRVVKSLINDENRDVDHV 138
                                       6899999************************9998..67778899*******988887766666666655 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.4e-05     0.035      31      71 ..      85     126 ..      52     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                            HTH_34  31 LsvhlkkLekagYievdke.fkgkkprtllriTpeGreafkk 71 
                                       L+  +k+Le++g ie++ e  +++ ++ ++++T+eGr   k+
  gi|313125547|ref|YP_004035811.1|  85 LAGSIKTLENKGIIERRTEtTVSGNEKYIYSLTDEGRRVVKS 126
                                       67789**********9875267899************97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1097.66
//
Query:       gi|313125548|ref|YP_004035812.1|  [L=331]
Description: phosphoribosyl transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-11   44.6   0.0    7.4e-11   41.8   0.0    2.0  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
       0.34   11.2   1.8       0.58   10.5   0.3    2.2  2  HAD_SAK_2     HAD domain in Swiss Army Knife RNA repair prote


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   8.3e-15   7.4e-11      13     154 ..       7     145 ..       2     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 8.3e-15
                                       EEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSE CS
                      Pribosyltran  13 davarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkk 89 
                                          ++ a+++ +e + ++d+v+gi+r G+  a+ l   L+vp+++++  +     +++            +  + ++
  gi|313125548|ref|YP_004035812.1|   7 SQLNSSARQLARELPTRIDLVAGIPRSGLLAANLLCLNLDVPMTDIEGLCEGRLLQTGRRYDG-----VDSFEDVET 78 
                                       556677899999999*******************************99888877777775443.....33556779* PP

                                       EEEE-SEESSSHHHHHHHHHHHCC-BS.EEEEEEEEE-HHHHHHHHHH-TTS......EEEEEEE-S CS
                      Pribosyltran  90 VliVDDildtGgTllaalelLkekgpe.evriavlvdkpateeevdknakrvfsls.pdnfvavvgf 154
                                       Vl+VDD +dtG+ ++++ + L+e++    ++  + +  +++ ++vd+++++v ++  ++++  ++++
  gi|313125548|ref|YP_004035812.1|  79 VLVVDDSVDTGRQMQETKRQLAEHDFPfDIEYGAMYISSQGHKHVDHWVDVVSKPRvFEWNMMHHPM 145
                                       *******************666666555********************************9988875 PP

>> HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.47   4.2e+03     104     114 ..      75      90 ..      69     107 .. 0.58
   2 ?   10.5   0.3   6.5e-05      0.58       4      27 ..     151     172 ..     149     264 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.47
                         HAD_SAK_2 104 eveawvalDD.....k 114
                                       +ve  +++DD     +
  gi|313125548|ref|YP_004035812.1|  75 DVETVLVVDDsvdtgR 90 
                                       5677788888533221 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.5e-05
                         HAD_SAK_2   4 LDiDGVLnpekskkrregeedeal 27 
                                        DiDGVL++++++++++++ +  +
  gi|313125548|ref|YP_004035812.1| 151 VDIDGVLCRDPTREENDDGRR--Y 172
                                       6************99875533..2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1908.62
//
Query:       gi|313125549|ref|YP_004035813.1|  [L=42]
Description: hypothetical protein Hbor_07770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 265.54
//
Query:       gi|313125550|ref|YP_004035814.1|  [L=311]
Description: hypothetical protein Hbor_07780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   13.6   0.1       0.09   12.7   0.1    1.3  1  ApoO      Apolipoprotein O


Domain annotation for each model (and alignments):
>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     5e-06      0.09      50     107 ..     116     174 ..     102     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-06
                              ApoO  50 qsvtdtiasLkepp.edllPrlgyilvagLaGsilarrrsilkRvlyPlalgglaaslf 107
                                        ++ d++a+L +      +P+l+ + va+LaG + + +++ l+ +++ ++ g+l++ ++
  gi|313125550|ref|YP_004035814.1| 116 DFTHDAFAYLGPMAvWAAVPSLVTVSVAMLAGGFGTVEGNTLLPLVFVIIAGALVFGYL 174
                                       5667777777777677789*********************************9999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2073.76
//
Query:       gi|313125551|ref|YP_004035815.1|  [L=366]
Description: Fe3+-siderophore ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-89  300.1  33.0    1.8e-89  299.8  33.0    1.1  1  FecCD     FecCD transport family
    0.00013   21.5  15.6    0.00013   21.5  15.6    2.2  2  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.8  33.0     2e-93   1.8e-89       2     312 .]      31     359 ..      30     359 .. 0.96

  Alignments for each domain:
  == domain 1  score: 299.8 bits;  conditional E-value: 2e-93
                             FecCD   2 lllllllslllgavkispsevfeallgka....................dsleaeivlelrlprvlaallvGaaLav 58 
                                       ll+++ll +++ga+++++se ++ +++++                     s ++ iv+++rlpr+l+++lvGa Lav
  gi|313125551|ref|YP_004035815.1|  31 LLVATLLQVSFGAYPLTLSEAWHTVFDGQvlfseavwraflfgddipawLSRQQLIVWNIRLPRILVGILVGANLAV 107
                                       7899**********************98899999888888888888888677777********************** PP

                             FecCD  59 aGallQtvtrNpLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliL 135
                                       +Ga++Q vt+N+La+P+ilG+s ga+l+++lal+++  +  l  lp++a lg++ a+llv+++a ++ g++p++l+L
  gi|313125551|ref|YP_004035815.1| 108 SGAIFQVVTQNELASPYILGVSDGAGLVVLLALTTF--TGLLPFLPILAALGGAGAFLLVYIIA-WKDGTNPVRLVL 181
                                       **********************************97..444446999999**************.************ PP

                             FecCD 136 aGiavsallsaltsllllll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAk 211
                                       aG++v++++++l  +l +++ n   ++s+++wl+Gsl g +w+++ ++l++++l++ll+ll++r+ld+l lg+etAk
  gi|313125551|ref|YP_004035815.1| 182 AGVIVGTVFGSLQRALFFFIdNLGVAMSAQMWLSGSLLGTDWEQIRIALPFTVLAVLLALLVTRQLDVLLLGEETAK 258
                                       ********************899999*************************************************** PP

                             FecCD 212 slGvnvervrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarllls 288
                                       slG++vervr++++++++l ta+a+a++G igFvGLivPh++r +vg++ ++ll+ + ++G +ll+ ad+ arl+ls
  gi|313125551|ref|YP_004035815.1| 259 SLGMPVERVRFFVAAIAILSTAAAIAVAGLIGFVGLIVPHMVRNIVGSNSKRLLIGCLFVGPALLVGADVGARLALS 335
                                       ***************************************************************************** PP

                             FecCD 289 ptelpvgivtaliGapffiylllr 312
                                       p++lpvgi+  l+G+p+f+yl+++
  gi|313125551|ref|YP_004035815.1| 336 PVQLPVGIISGLVGGPYFLYLMRK 359
                                       **********************97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.21   1.9e+03     186     197 ..      27      38 ..      19      77 .. 0.73
   2 !   21.5  15.6   1.5e-08   0.00013      84     221 ..     180     319 ..      92     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.21
                             ABC-3 186 avGviLvialli 197
                                         Gv+Lv++ll 
  gi|313125551|ref|YP_004035815.1|  27 SLGVLLVATLLQ 38 
                                       567777777774 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.5e-08
                             ABC-3  84 taigivlsvfl.alglvlvslikk..skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeel 157
                                       ++ g+++ +++ +l  +l+  i++  ++++ + +L G++l+ + e++ + +  +++ +ll+ll+ ++l ++ + ee+
  gi|313125551|ref|YP_004035815.1| 180 VLAGVIVGTVFgSLQRALFFFIDNlgVAMSAQMWLSGSLLGTDWEQIRIALPFTVLAVLLALLVTRQLDVLLLGEET 256
                                       56677777766345555555555555*************************************************** PP

                             ABC-3 158 AkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillg 221
                                       Ak+ g++v+++++  +a+  l+ ++a+ ++G+i  + l i+P ++   ++++ ++lli    +g
  gi|313125551|ref|YP_004035815.1| 257 AKSLGMPVERVRFFVAAIAILSTAAAIAVAGLIGFVGL-IVPHMVRNIVGSNSKRLLIGCLFVG 319
                                       *******************************9988775.6788888888888887777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2458.09
//
Query:       gi|313125552|ref|YP_004035816.1|  [L=397]
Description: ferrichrome ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-11   44.2   0.0    3.7e-11   43.0   0.0    1.5  2  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
          2    8.4   8.5        3.7    7.5   8.5    1.4  1  DUF3558       Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.32   2.8e+03     184     202 ..     133     151 ..     119     174 .. 0.70
   2 !   43.0   0.0   4.2e-15   3.7e-11      94     235 ..     183     342 ..     155     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.32
                                       E-HHHHHHH--SEEEEEEH CS
                      Peripla_BP_2 184 isaEqilasdpdvifvsgr 202
                                        + E+++a+d+dv ++++r
  gi|313125552|ref|YP_004035816.1| 133 FDKENFYAADVDVHLIDPR 151
                                       5778888888888888777 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 4.2e-15
                                       S.........HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEEETTE.......EEE CS
                      Peripla_BP_2  94 g.........eslkeqiralgellgledeaeklvaeidsklaaaksaidse...kpkpvlvfggade.....ggyvv 153
                                                 ++l+  ++  g++++++++++++++ +d+ + +++s+++ +      ++++ g +++        + 
  gi|313125552|ref|YP_004035816.1| 183 SssinehepyYDLYGAFEKAGQIFQRQARFRAWQSLYDEFISNIESKLPPKserPTVAAIWRGVNPDsgtfrI--SP 257
                                       344457777799999************************************9844444556666666544322..23 PP

                                       E-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.....HHHT-S--HHHHT-SHHHHTSHH CS
                      Peripla_BP_2 154 agsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.....aeadnktgleflkenpllaelpA 225
                                       ++ + + +   + lg++++++   +   ++i+ E +l  dpd+i   g      ++++ +t++e +++n   +el+A
  gi|313125552|ref|YP_004035816.1| 258 IHAKQNNTRTYRVLGLKDAFEG--QIPDGPIGYEKLLDIDPDYIGAVGGltsltHDEFVSTVVEPFENNSNGQELTA 332
                                       44555555666779*****999..8*******************999999*************************** PP

                                       HHTT-EEEE- CS
                      Peripla_BP_2 226 vkngrVyald 235
                                       vk+g+ ++++
  gi|313125552|ref|YP_004035816.1| 333 VKEGNLVRTG 342
                                       ******9987 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.5   0.00041       3.7       2      43 ..      18      61 ..      17      64 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00041
                           DUF3558  2 llaGCssttdGtapaasssassssttsssaapav..pldtsgvl 43
                                       +aGCss+t+ t+pa ++s+ + +t++s ++ +   ++d + v+
  gi|313125552|ref|YP_004035816.1| 18 GVAGCSSSTTETSPADDESTQTGNTAQSETESKAttEDDSYTVT 61
                                      79****99999966666666666665554444444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2380.84
//
Query:       gi|313125553|ref|YP_004035817.1|  [L=286]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00031   20.6   0.2    0.00056   19.8   0.2    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain
    0.00032   20.5   0.1    0.00064   19.6   0.1    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00033   20.5   0.5     0.0008   19.3   0.5    1.7  1  MarR_2         MarR family
    0.00036   20.3   0.1    0.00096   19.0   0.1    1.6  1  HxlR           HxlR-like helix-turn-helix
    0.00096   19.0   0.2     0.0018   18.2   0.2    1.4  1  MarR           MarR family
     0.0035   17.2   0.2      0.013   15.4   0.1    1.9  2  HTH_5          Bacterial regulatory protein, arsR family
     0.0067   16.2   0.3      0.016   15.0   0.3    1.7  1  HTH_IclR       IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.046   13.7   0.0      0.071   13.1   0.0    1.3  1  HTH_45         Winged helix-turn-helix
      0.059   13.5   0.2       0.16   12.1   0.2    1.7  1  DprA_WH        DprA winged helix domain
      0.064   13.3   0.9      0.064   13.3   0.9    1.8  2  HTH_20         Helix-turn-helix domain
      0.085   12.7   0.0       0.12   12.2   0.0    1.2  1  DUF4370        Domain of unknown function (DUF4370)
       0.16   12.2   0.0       0.28   11.4   0.0    1.4  1  DUF1724        Domain of unknown function (DUF1724)
       0.18   11.6   0.0       0.34   10.7   0.0    1.4  1  Arg_repressor  Arginine repressor, DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   4.1e-07   0.00056      32      55 ..      55      78 ..      27      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.1e-07
                                      TSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 32 GltretvsrilseLkreglisrgr 55
                                       +tr+t+sril++L+++g+++r++
  gi|313125553|ref|YP_004035817.1| 55 SVTRVTLSRILRDLEERGWVRRNH 78
                                      69*******************763 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   4.6e-07   0.00064      16      58 ..      38      80 ..      34      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.6e-07
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       Ll+ g+ t de+   + v r +  ++Lr Le++G+V+r++++
  gi|313125553|ref|YP_004035817.1| 38 ELLSDGSRTRDELKVGTSVTRVTLSRILRDLEERGWVRRNHET 80
                                      69**************************************987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   5.8e-07    0.0008       8      54 ..      34      77 ..      22      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.8e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       rvL  L ++ +   t  el   + +++ ++sril++L+++G+v+r 
  gi|313125553|ref|YP_004035817.1| 34 VRVLELLSDGSR---TRDELKVGTSVTRVTLSRILRDLEERGWVRRN 77
                                      567777766664...999**************************985 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   6.9e-07   0.00096       8      79 ..      34      99 ..      30     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.9e-07
                                      HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHH CS
                              HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqel 79
                                      + +l  l +g++   elk    ++++ +L++ Lr Le+ g + r+         eY+lt++G+ +++ +++l
  gi|313125553|ref|YP_004035817.1| 34 VRVLELLSDGSRTRDELKVGT-SVTRVTLSRILRDLEERGWVRRNHET-----SEYCLTAYGKLVYEDFSQL 99
                                      567777888988889998887.9********************98654.....48********998877665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   1.3e-06    0.0018      28      53 ..      55      80 ..      36      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                                      TS-HHHHHHHHHHHHHTTSEEEEEET CS
                              MarR 28 gvskstvtrvldrLekkGlieRsksp 53
                                      +v++ t++r+l+ Le++G+++R + +
  gi|313125553|ref|YP_004035817.1| 55 SVTRVTLSRILRDLEERGWVRRNHET 80
                                      68899*****************9876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   9.1e-06     0.013       2      45 ..      31      74 ..      30      76 .. 0.94
   2 ?   -1.2   0.0       1.4   1.9e+03      11      20 ..     128     137 ..     127     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.1e-06
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      + R+++L lL++g+++  el   + +++ t+S+ L+ L+e G V
  gi|313125553|ref|YP_004035817.1| 31 EHRVRVLELLSDGSRTRDELKVGTSVTRVTLSRILRDLEERGWV 74
                                      67**************************************9976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                                       HTTSSEEHHH CS
                             HTH_5  11 Laegelcvce 20 
                                       Laege+ v+e
  gi|313125553|ref|YP_004035817.1| 128 LAEGERVVSE 137
                                       99******98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   1.2e-05     0.016       7      51 ..      35      77 ..      32      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      ++L++l+ + +     el   t +++ t +R+L+ L+e+G+v+++
  gi|313125553|ref|YP_004035817.1| 35 RVLELLSDGSRT--RDELKVGTSVTRVTLSRILRDLEERGWVRRN 77
                                      678888888884..78888999999******************98 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.2e-05     0.071      11      72 ..      36      99 ..      29     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli..kkskekYvlTekGlelleklkel 72
                                      +Le +s+g+ +  ++      +  +l++ L  L e+g +  ++++++Y+lT+ G+ ++e++ +l
  gi|313125553|ref|YP_004035817.1| 36 VLELLSDGSRTRDELKVGTSVTRVTLSRILRDLEERGWVrrNHETSEYCLTAYGKLVYEDFSQL 99
                                      7888888888888888888889999**************86668999********999998776 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00011      0.16      11      57 ..      30      76 ..      19      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                           DprA_WH 11 ddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                      ++ + rvL++L+  +++ D+L   t ++  ++s++L  LE  G v+r
  gi|313125553|ref|YP_004035817.1| 30 SEHRVRVLELLSDGSRTRDELKVGTSVTRVTLSRILRDLEERGWVRR 76
                                      78899***********************************9999998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9   4.7e-05     0.064       9      57 ..      29      77 ..      18      80 .. 0.88
   2 ?   -3.6   0.3       9.1   1.3e+04       5      14 ..     146     155 ..     146     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                                      -.HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  9 h.PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                        + R r+l +L +++ +t  el+   ++++ tls+ Lr Lee g v++ 
  gi|313125553|ref|YP_004035817.1| 29 RsEHRVRVLELL-SDGSRTRDELKVGTSVTRVTLSRILRDLEERGWVRRN 77
                                      4489********.*******************************988875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.1
                                       HHHS-HHHHH CS
                            HTH_20   5 eALahPvRrr 14 
                                       +A+a+ vRr+
  gi|313125553|ref|YP_004035817.1| 146 RAVANAVRRA 155
                                       5899999995 PP

>> DUF4370  Domain of unknown function (DUF4370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.9e-05      0.12      92     148 ..     116     172 ..      90     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-05
                           DUF4370  92 laaswdelPdavvedakkalskntddkaGqealknvfraaeaveefgGilvslkmel 148
                                       l ++w ++   v+ + ++++s n+d  a   a++n  r a +v  + G ++sl m  
  gi|313125553|ref|YP_004035817.1| 116 LPTEWFDFNIGVLAEGERVVSENADPMAAPRAVANAVRRASSVRALVGSFTSLPMHA 172
                                       6689999999*******************************************9975 PP

>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.28      12      61 ..     227     275 ..     218     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                           DUF1724  12 plsltvtDkflslslfdkdg.kydhkdlisfdesAlkWGeeLFeyYlkrSe 61 
                                       p  + + D+ ++ls+ d+ g ++d   + +  ++++ W++eLFe  +  ++
  gi|313125553|ref|YP_004035817.1| 227 PCNVDLIDDEVYLSVGDEHGrTFDV--IRCGHPAVVTWARELFERKRTHAT 275
                                       5556666777888888888855654..7899************98666655 PP

>> Arg_repressor  Arginine repressor, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.34      31      69 ..      51      90 ..      47      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                      TTT----HHHHHHHHHHHT-E.EEETTSTSEEEE-B-SS- CS
                     Arg_repressor 31 eeGidvtQatvSRdLkelglv.kvraengeyvYvlpaets 69
                                      + G  vt  t+SR L++l+ +  vr + ++  Y+l+a+++
  gi|313125553|ref|YP_004035817.1| 51 KVGTSVTRVTLSRILRDLEERgWVRRNHETSEYCLTAYGK 90
                                      4688999999998666666542345567888999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1829.14
//
Query:       gi|313125554|ref|YP_004035818.1|  [L=345]
Description: ca2+/na+ antiporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-42  142.6  34.4    6.3e-25   87.9  15.7    2.1  2  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8  10.7   7.7e-21   1.4e-16       6     150 ..      15     168 ..       7     169 .. 0.80
   2 !   87.9  15.7   3.5e-29   6.3e-25       5     150 ..     195     334 ..     192     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 7.7e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHT.TTHHHHHHHHHHHHHHHHHT CS
                          Na_Ca_ex   6 filslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaalt.gevdlaignvlGsnifnlll 81 
                                        +++ +l   + ++lv++a++++ + g+++ v G ++ A g+s+pEl+s++ia ++ g  ++++g+v+Gs++fn+l+
  gi|313125554|ref|YP_004035818.1|  15 AVVGAALAFRGGELLVEAADSLGAYYGLPPVVQGAVVAAVGSSFPELASTVIASVRyGAFEIGVGAVVGSAVFNILI 91 
                                       55666667777899**************************************9999678****************** PP

                                       HHHHHHHHHH...BTTSSCE.CCHHHHHHHHHHHHHHHHHHHTCHHHHH.......HTEEHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  82 viGlialigs...lkvdses.lkldlgllllvallllllvlllllplfv.......pgrltvleglvllllYalylv 147
                                       + +++ l g+   ++++ +  ++ ++ +ll +a+++l ++l++  + ++       +g++t   ++  lllY+ly++
  gi|313125554|ref|YP_004035818.1|  92 IPAISTLAGGgslASNRDLVfKEAQF-YLLSIAVVFLTFTLAV--VYDGtavgdplTGEITPGIAMFPLLLYGLYIF 165
                                       ********997664444444133444.3344444443433332..2344799************************* PP

                                       HHH CS
                          Na_Ca_ex 148 lsl 150
                                       +++
  gi|313125554|ref|YP_004035818.1| 166 IQY 168
                                       997 PP

  == domain 2  score: 87.9 bits;  conditional E-value: 3.5e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHT CS
                          Na_Ca_ex   5 lfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlll 81 
                                        +++sl++i+v+a++lv++a  +++ +g s  + Glt++A+g+slp++++s++aa++g++d++++nvlGsnif ll+
  gi|313125554|ref|YP_004035818.1| 195 RLVVSLAVIVVSAELLVRAAVGFGDAFGTSTFLWGLTVVAAGTSLPDTFVSVVAARRGNADVSLANVLGSNIFALLV 271
                                       5899************************************************************************* PP

                                       HHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  82 viGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       v+++ +l ++    +   +++lg+ + ++ +l+++ ++++ +l++++rlt+ e+ +l+++Y+++l++++
  gi|313125554|ref|YP_004035818.1| 272 VLPVGVLAAG----R--ATISLGAVVPMMGFLVVASVAFFAVLRTEMRLTRREAYLLVGTYLAFLAWLT 334
                                       ********66....3..25666444444444445555556677789*******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2327.45
//
Query:       gi|313125555|ref|YP_004035819.1|  [L=402]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-24   86.7   0.1    1.8e-23   83.0   0.0    2.5  3  Acetyltransf_9   Acetyltransferase (GNAT) domain
    6.4e-21   75.3   1.8    6.4e-21   75.3   1.8    2.4  3  Acetyltransf_17  Acetyltransferase (GNAT) domain
    4.7e-20   71.9   0.4      9e-20   71.0   0.4    1.5  1  SCP2_2           Sterol carrier protein domain
  ------ inclusion threshold ------
      0.016   15.4   0.0       0.29   11.4   0.0    2.4  2  Acetyltransf_1   Acetyltransferase (GNAT) family
      0.044   13.3   0.0      0.081   12.5   0.0    1.4  1  FBP_C            FBP C-terminal treble-clef zinc-finger


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   5.1e-27   1.8e-23       3     127 ..       4     134 ..       3     135 .. 0.91
   2 ?    0.4   0.0      0.18   6.4e+02      19      52 ..     181     214 ..     162     230 .. 0.67
   3 ?   -2.9   0.0       1.9   6.7e+03      14      28 ..     233     247 ..     231     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 5.1e-27
                                       EEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEE........TTEEEEEEEEEEEEEEETTEEE CS
                    Acetyltransf_9   3 relteedldevlellkyaFqdeespleeireyfrklleesrvlgaed........ngelvgqlallplelnvpGktl 71 
                                       r+l  ++ d++ ++++yaF  +e p    +e+ r+l +    +g +d         ++l  +++ ++++++++G   
  gi|313125555|ref|YP_004035819.1|   4 RQLPADHRDAFRAMVDYAFRPTEGPD--WQEQDRPLPDLFTRFGYYDappdeepdPDDLRTVCGSYDFTVRIRGDWH 78 
                                       78888999*****************4..456678888888888999999977776677******************* PP

                                       EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHTTT-EE CS
                    Acetyltransf_9  72 kaagvtgVavapehrgrgvlskLlaraleemreegqplsllfPssipiYrrfGyei 127
                                        a+gv++Va+ pe r++g +s++l+++le++reeg  +s+l+P+++++Yrr+G+ +
  gi|313125555|ref|YP_004035819.1|  79 AAGGVSAVASPPEGRRQGAVSAMLDALLEHYREEGTAFSVLWPFEYEFYRRLGWAT 134
                                       ******************************************************86 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.18
                                       HHTT----H...HHHHHHHHHHTTSEEEEEEETTE CS
                    Acetyltransf_9  19 yaFqdeespl.eeireyfrklleesrvlgaednge 52 
                                       +a ++++++  + +++ fr    +  v+g++d++e
  gi|313125555|ref|YP_004035819.1| 181 EALAVRRTDGwW-RERTFRGWETDPYVYGWFDDEE 214
                                       567777777733.23455555666699*****776 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.9
                                       HHHHHHHTT----H. CS
                    Acetyltransf_9  14 lellkyaFqdeespl 28 
                                       ++++++aF d+e ++
  gi|313125555|ref|YP_004035819.1| 233 MRVWERAFTDHEARA 247
                                       578999999998775 PP

>> Acetyltransf_17  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         2     7e+03      59      76 ..       6      23 ..       2      52 .. 0.70
   2 !   75.3   1.8   1.8e-24   6.4e-21       2     116 .]     184     296 ..     183     296 .. 0.90
   3 ?   -3.0   0.0       3.5   1.2e+04      86     103 ..     378     395 ..     368     398 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2
                                      EEESSHHHHHHHHHHHHC CS
                   Acetyltransf_17 59 lvaltpeayraLlrflas 76
                                      l a++++a ra+  + ++
  gi|313125555|ref|YP_004035819.1|  6 LPADHRDAFRAMVDYAFR 23
                                      567777888887777554 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 1.8e-24
                                       EBE--HHHHHHHHHTTTTSTGCSEEEEEE.TTSEETEEEEEEEETTE.TTC.EEEEEEEEESSHHHHHHHHHHHHCG CS
                   Acetyltransf_17   2 aleRseawWrrrllkrrearegalayvvyrdddgpeGyllYrvkeesgaeg.tleVrelvaltpeayraLlrflash 77 
                                       a++R++ wWr+r+++  e   + ++y +++d++  +Gyl+Y+++  +g++g +++V e +++++ea++ Llrf+ +h
  gi|313125555|ref|YP_004035819.1| 184 AVRRTDGWWRERTFRGWE--TDPYVYGWFDDEETLRGYLIYTIS--EGDDGrDMRVWERAFTDHEARAHLLRFCRDH 256
                                       789********8887654..667******999988********3..3456679************************ PP

                                       TGTESEEEEEEESTT-SCGGGCSSGG..EECEEEEEEEEE CS
                   Acetyltransf_17  78 dslveeveawkappddplpllledpri.keaarpgamlRi 116
                                       ds+ve+v++ +++  +     l+dpr+ + ++++g m+Ri
  gi|313125555|ref|YP_004035819.1| 257 DSQVETVTFTTLSEWSRPIEGLPDPRAaTLEIKTGPMARI 296
                                       ********9999988888999*****99999********8 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.5
                                       EEEESTT-SCGGGCSSGG CS
                   Acetyltransf_17  86 awkappddplpllledpr 103
                                       + +a + ++l  l++d+r
  gi|313125555|ref|YP_004035819.1| 378 VSDATVRETLADLFPDER 395
                                       456778888999999998 PP

>> SCP2_2  Sterol carrier protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.4   2.5e-23     9e-20       1     103 [.     299     398 ..     299     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 2.5e-23
                                       HHHHHHHS--SS-SSEEEEEEEE-TTSGGGSEEEEEEEETTSEEEECSCE-SCE..EEEEHHHHHHHHTTSS-HHHH CS
                            SCP2_2   1 veaalearpyekeekgeltleveDpllpwnngrfrltiedgkgeevgkeeeada.dltldiqtLaqlllGyrsaseL 76 
                                       veaal a++y+   +++++l v+D+ + wn+ +f+l+++++++ +v + e     d +ld+++L+ql +G+r a+eL
  gi|313125555|ref|YP_004035819.1| 299 VEAALTALSYD--VQESVVLAVSDERCAWNDDTFELRVDAAGA-RVNRVE--TTpDAELDVGALSQLAVGAREAAEL 370
                                       79********5..688***********************9999.555554..23369******************** PP

                                       HHTTSSBSSH.HHHHHHHHHS-SS--B- CS
                            SCP2_2  77 arlgriegae.ealatldalfpkekpyl 103
                                        r+g ++ ++  + +tl++lfp+e++yl
  gi|313125555|ref|YP_004035819.1| 371 ERTGDLTVSDaTVRETLADLFPDERTYL 398
                                       *******6662667************97 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.2e-05      0.29      61     116 ..      81     131 ..      28     132 .. 0.82
   2 ?    1.6   0.1     0.087   3.1e+02      23      55 ..     193     227 ..     171     253 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.2e-05
                                       EEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTT CS
                    Acetyltransf_1  61 ayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklG 116
                                       + +  +a  pe r++G+ sa+l+al+e+ reeg    vl+ +e      ++Y++lG
  gi|313125555|ref|YP_004035819.1|  81 GGVSAVASPPEGRRQGAVSAMLDALLEHYREEGTAFSVLWPFE-----YEFYRRLG 131
                                       555566777899********************88554664433.....67887788 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.087
                                       H...HHHHHHSTTC.EEEEEEET.TEEEEEEEEEEEET CS
                    Acetyltransf_1  23 e...feesfsleae.gllvaeed.geliGfisllkipd 55 
                                       +   f+ +   e++ + + + +d ++l G++ +++   
  gi|313125555|ref|YP_004035819.1| 193 RertFRGW---ETDpYVYGWFDDeETLRGYLIYTISEG 227
                                       33456666...444233334444366999998888766 PP

>> FBP_C  FBP C-terminal treble-clef zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.2e-05     0.081      28      92 ..     200     266 ..     193     271 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                             FBP_C  28 wddldf.lgWrDpkaperaylvvelddelvGvaLraae.aakagarrrsmCslCetvhassevsLft 92 
                                       w++  + +gW D +   r+yl++++ ++  G  +r  e a + +++r+++ ++C++  ++ e + ft
  gi|313125555|ref|YP_004035819.1| 200 WETDPYvYGWFDDEETLRGYLIYTISEGDDGRDMRVWErAFTDHEARAHLLRFCRDHDSQVETVTFT 266
                                       55544427***************************9873567899999********99887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2822.30
//
Query:       gi|313125556|ref|YP_004035820.1|  [L=103]
Description: hypothetical protein Hbor_07840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 683.78
//
Query:       gi|313125557|ref|YP_004035821.1|  [L=83]
Description: hypothetical protein Hbor_07850 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 547.78
//
Query:       gi|313125558|ref|YP_004035822.1|  [L=177]
Description: hypothetical protein Hbor_07860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.094   13.0   0.3       0.14   12.5   0.1    1.3  2  PSII_Pbs27  Photosystem II Pbs27
       0.19   11.9   1.6       0.33   11.1   1.4    1.4  2  Mod_r       Modifier of rudimentary (Mod(r)) protein


Domain annotation for each model (and alignments):
>> PSII_Pbs27  Photosystem II Pbs27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.7   1.5e+04      52      66 ..      60      74 ..      59      79 .. 0.59
   2 ?   12.5   0.1   1.5e-05      0.14      51      99 ..     128     176 ..     111     177 .] 0.78

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.7
                        PSII_Pbs27 52 vktlresleldkkdd 66
                                      v+ lre++e+  +d+
  gi|313125558|ref|YP_004035822.1| 60 VEVLREAIETTSEDM 74
                                      556666666666554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.5e-05
                        PSII_Pbs27  51 vvktlresleldkkddakrera.akaakesireyvskYrsakkvsgeesY 99 
                                       vv+ ++ ++ ++  dd+ ++++  k +  +++e+v +Yr+++  s++  Y
  gi|313125558|ref|YP_004035822.1| 128 VVELMEHAVSHAE-DDSAVSEFeTKMLDFDVSEFVEQYRQQRDLSEDDVY 176
                                       4555666666666.666665551678899*****************9999 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.1   9.9e+03      90     107 ..      53      70 ..      51      73 .. 0.66
   2 ?   11.1   1.4   3.6e-05      0.33      98     138 ..     130     170 ..     125     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                             Mod_r  90 kfspdallarLqtavaea 107
                                       +f p++l + L++a++ +
  gi|313125558|ref|YP_004035822.1|  53 RFLPEFLVEVLREAIETT 70 
                                       566777777777777655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.6e-05
                             Mod_r  98 arLqtavaeaeeeSealaeefle..geieldeFvkefkekRkl 138
                                       +++++av+ ae++S    +ef     + +++eFv++++++R l
  gi|313125558|ref|YP_004035822.1| 130 ELMEHAVSHAEDDSAV--SEFETkmLDFDVSEFVEQYRQQRDL 170
                                       5789999999999987..77775224578899*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1096.52
//
Query:       gi|313125559|ref|YP_004035823.1|  [L=93]
Description: hypothetical protein Hbor_07870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 570.95
//
Query:       gi|313125560|ref|YP_004035824.1|  [L=1079]
Description: carbamoyl-phosphate synthase large subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-96  321.0   0.2      2e-58  197.4   0.0    2.7  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    7.7e-25   87.6   0.1    1.7e-24   86.5   0.1    1.6  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    1.4e-14   54.0   0.0    7.7e-09   35.3   0.0    2.5  2  ATP-grasp        ATP-grasp domain
    7.8e-14   51.7   0.0    2.5e-09   37.0   0.0    2.7  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      3e-13   49.6   0.0    2.4e-05   24.1   0.0    3.0  3  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      7e-11   42.4   0.1    1.2e-05   25.4   0.0    2.4  2  ATP-grasp_3      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.4   0.0   6.7e-62     2e-58       1     210 [.     138     361 ..     138     362 .. 0.88
   2 !  120.8   0.0   1.8e-38   5.3e-35       1     210 [.     701     903 ..     701     904 .. 0.95

  Alignments for each domain:
  == domain 1  score: 197.4 bits;  conditional E-value: 6.7e-62
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHH............HHHHHH.-SSEEEEETTCCTTTTEEEESSHHHHH CS
                       CPSase_L_D2   1 Dkesakealkkinvpvvpssaapvetleeal............aiakei.gyPviikaafglGGkGmrvarneeela 64 
                                       D++ +++ +++i++pv +s++   e+ e ++            a+++e+ g Pvi +++++lGG+G++v+++ +el+
  gi|313125560|ref|YP_004035824.1| 138 DRDLFRQRMENIGQPVPRSTTISLEDDESVTsiteddlsdrveAAVEEVgGLPVIARTTYTLGGSGSGVVHEMDELV 214
                                       999****************998777666544111111111111334555479************************* PP

                                       HHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHH CS
                       CPSase_L_D2  65 elvkkalaeakaafgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerq 139
                                       + v+k+l+ ++    n++vl+ +s++g+ e+E+ev+rDa++ +i++c++en++++  +t+++++v Psq++ de +q
  gi|313125560|ref|YP_004035824.1| 215 ARVRKGLRLSR----NSEVLITESISGWVELEYEVMRDADDSCIIICNMENIDPMgiHTGESMVVTPSQVIPDEGHQ 287
                                       **********7....9************************************************************* PP

                                       HHHHHHHHHHHHHT-EEEEEEEEEEET...TTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 140 alreaavkvvrevgvvgagtveflldp...kskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       ++r aa++v+re+g++g+++++f+ +      +ey v+EvN+R+s++sala+kaTG++++ ++ak+alg++L+e
  gi|313125560|ref|YP_004035824.1| 288 EMRDAALEVIRELGIQGGCNIQFAWHDdgtPGGEYRVVEVNPRVSRSSALASKATGYPIARVTAKVALGKRLHE 361
                                       *************************98332368***************************************87 PP

  == domain 2  score: 120.8 bits;  conditional E-value: 1.8e-38
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+++++ +++++++   ++ +a  +++eeal++a++igyPv++++++ lGG+ m v++++eel+  +++a++ ++  
  gi|313125560|ref|YP_004035824.1| 701 DRDRFNVLMDELGILQPEGGTA--TSEEEALELARDIGYPVLVRPSYVLGGRAMDVVHSDEELKTYIEEAVRVSP-- 773
                                       99*****************999..9*************************************************7.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEE.EEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvit.vcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevg 153
                                         +k +lv+++l+   e++v+ ++D +   i  v+e   s  ++ +++  + P + L++e+  ++re +  ++ +++
  gi|313125560|ref|YP_004035824.1| 774 --DKPILVDEFLADAVELDVDAVADGRRALIGgVMEHVESAGVHSGDSACMIPPRSLDEETMGRVREVTEDIATALD 848
                                       ..9***********************99888525555566666********************************** PP

                                       -EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 154 vvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                        vg  +v+ +++  +++ yv+E N+R s+  +  +kaT ++++k aak+ +ge+Le+
  gi|313125560|ref|YP_004035824.1| 849 TVGLLNVQLAVK--DGDVYVLEANPRSSRTVPFVSKATDVPIAKLAAKVMAGETLET 903
                                       ***********9..6****************************************85 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.1   5.9e-28   1.7e-24       2     121 ..     448     555 ..     447     555 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 5.9e-28
                       CPSase_L_D3   2 elkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiae 78 
                                       +l++pt++R +ai+ea++rg++ve++ elt+++ w++e+++++++  ++ ++         ++ a  +G ++++ia+
  gi|313125560|ref|YP_004035824.1| 448 YLEKPTPDRPYAIFEAFERGYTVEDVVELTDMKTWYVERFKRVTDSVAAAQDG-------DFTAAATAGHTNAEIAT 517
                                       799*****************************************999985544.......699************** PP

                       CPSase_L_D3  79 lleeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYst 121
                                        ++ ++   v ++  ++    +yk+vDtcA+eF+a+tpY+Ys+
  gi|313125560|ref|YP_004035824.1| 518 TTG-SD---VSAVEADVP-GRTYKQVDTCAGEFAAQTPYYYSS 555
                                       965.44...666665555.469*******************96 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.5e-06    0.0075      18     160 ..     177     331 ..     167     339 .. 0.84
   2 !   35.3   0.0   2.6e-12   7.7e-09       3     160 ..     711     873 ..     709     876 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEEETTC-E CS
                         ATP-grasp  18 eeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvrsaeGet 90 
                                       + +e+a+ee+g   v+ + +    G G+ vv++ ++l   ++      ++ +v++ e ++  +El   v+r+a+ + 
  gi|313125560|ref|YP_004035824.1| 177 DRVEAAVEEVGGLPVIARTTYTLGGSGSGVVHEMDELVARVRKGlrlsRNSEVLITESISGWVELEYEVMRDADDSC 253
                                       478999****8888888899999********99887655554444666999************************** PP

                                       EE--EEEEEEETTEEE...EEEECEE-.SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCT....EEEEEEESS CS
                         ATP-grasp  91 afypvvetvqedgilr...lsvapaev.sekaqkkaeeiakkiveeLggvGvfavElFvledge....llvnElapR 159
                                        ++  +e++   gi     ++v p++v +++ +++ ++ a ++++eLg+ G   + +   +dg+      v E+ pR
  gi|313125560|ref|YP_004035824.1| 254 IIICNMENIDPMGIHTgesMVVTPSQViPDEGHQEMRDAALEVIRELGIQGGCNIQFAWHDDGTpggeYRVVEVNPR 330
                                       **********999985333788888752677899999***************9999999988877777888899998 PP

                                       - CS
                         ATP-grasp 160 p 160
                                       +
  gi|313125560|ref|YP_004035824.1| 331 V 331
                                       7 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 2.6e-12
                                       TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----S CS
                         ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfe 75 
                                       +lg+  p+  +++s+ee+ e+a+++g+pv+v+ +     G+   vv+s+e+l++ +e++     +++++v ef    
  gi|313125560|ref|YP_004035824.1| 711 ELGILQPEGGTATSEEEALELARDIGYPVLVR-PSYVLGGRAMDVVHSDEELKTYIEEAvrvsPDKPILVDEFLADA 786
                                       5677777777899999****************.99999***************999999999899**********9* PP

                                       EEEEEEEEEETTC-EEE--EEEEEE....ETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETT CS
                         ATP-grasp  76 kElsvlvvrsaeGetafypvvetvq....edgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvled 148
                                       +El v +v + +    +  v+e+v+    ++g+    + p +++e+   +++e++++i+ +L+ vG++ v l v+ d
  gi|313125560|ref|YP_004035824.1| 787 VELDVDAVADGRR-ALIGGVMEHVEsagvHSGDSACMIPPRSLDEETMGRVREVTEDIATALDTVGLLNVQLAVK-D 861
                                       **99988865443.344455555551111445666788899999****************************999.* PP

                                       CTEEEEEEESS- CS
                         ATP-grasp 149 gellvnElapRp 160
                                       g+++v E  pR 
  gi|313125560|ref|YP_004035824.1| 862 GDVYVLEANPRS 873
                                       **********96 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   4.9e-05      0.15      24     173 ..     176     328 ..     155     331 .. 0.72
   2 !   37.0   0.0   8.3e-13   2.5e-09      16     174 ..     716     871 ..     706     883 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.9e-05
                                       H-HHHHHHHHHC-SSEEEEESSS..STTTTEEEESSGGGHHHHHHHHHT..T-SCEEEEE--.ESEEEEEEEEETSS CS
                   Dala_Dala_lig_C  24 kkellekveeelgypvfVKpare..GSSvGvskveseeelkeaieeafk..ydekvlvEeai.egreievavlgnek 95 
                                       ++ + ++vee  g+pv+ +   +  GS  G   v+ ++el + +++ ++  ++++vl+ e i    e+e  v+ + +
  gi|313125560|ref|YP_004035824.1| 176 SDRVEAAVEEVGGLPVIARTTYTlgGS--GSGVVHEMDELVARVRKGLRlsRNSEVLITESIsGWVELEYEVMRDAD 250
                                       4456788899999*****997642144..66669***********9875226789*****995668*******9555 PP

                                       CEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS--.--HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTT....EE CS
                   Dala_Dala_lig_C  96 levsevgeivvkkgfydyeakysddkaqlevpak.lekeveekiqelalkaykaldlrGlaRvDfflteeg....ei 167
                                         +     i+ + + +d    ++  +++++ p + +++e +++++++al++ + l+++G + + f  +++g    e 
  gi|313125560|ref|YP_004035824.1| 251 DSCI----IICNMENIDPMGIHT-GESMVVTPSQvIPDEGHQEMRDAALEVIRELGIQGGCNIQFAWHDDGtpggEY 322
                                       4444....344444455555555.455666666526889999***********************998876111145 PP

                                       EEEEEE CS
                   Dala_Dala_lig_C 168 vlnEvN 173
                                        + EvN
  gi|313125560|ref|YP_004035824.1| 323 RVVEVN 328
                                       666666 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 8.3e-13
                                       ETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--.ESEEEEEE CS
                   Dala_Dala_lig_C  16 ekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai.egreieva 89 
                                       ++e+ + +++e   ++   +gypv+V+p+       +  v+s eelk +ieea++   d+ +lv+e++ ++ e++v 
  gi|313125560|ref|YP_004035824.1| 716 QPEGGTATSEEEALELARDIGYPVLVRPSYVLGGRAMDVVHSDEELKTYIEEAVRVspDKPILVDEFLaDAVELDVD 792
                                       555666667778889999***********98778899****************97655999*******9*******6 PP

                                       EEETSS.CEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTT CS
                   Dala_Dala_lig_C  90 vlgnek.levsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteeg 165
                                        + +++   +  v e+v + g+       s+d+a +  p +l++e+  +++e+  ++ +ald  Gl  v + ++ +g
  gi|313125560|ref|YP_004035824.1| 793 AVADGRrALIGGVMEHVESAGVH------SGDSACMIPPRSLDEETMGRVREVTEDIATALDTVGLLNVQLAVK-DG 862
                                       666555388999*****999986......67899999**********************************998.9* PP

                                       EEEEEEEES CS
                   Dala_Dala_lig_C 166 eivlnEvNt 174
                                       ++++ E N+
  gi|313125560|ref|YP_004035824.1| 863 DVYVLEANP 871
                                       *******97 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.5e-08   0.00011      46     122 ..     286     368 ..     279     376 .. 0.82
   2 !   24.1   0.0   7.9e-09   2.4e-05       5     119 ..     777     907 ..     774     919 .. 0.66
   3 ?   -3.4   0.0       2.6   7.7e+03      21      56 ..    1013    1045 ..    1011    1054 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.5e-08
                      ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededg.p....kLLEiNpRasGGlg.ysalaGvnlpylalklllgleteev 116
                                       ++e+ ++a ++++e+g++g  n+Q+ +++dg p    ++ E+NpR+s      s ++G  ++++ +k +lg+  +e+
  gi|313125560|ref|YP_004035824.1| 286 HQEMRDAALEVIRELGIQGGCNIQFAWHDDGtPggeyRVVEVNPRVSRSSAlASKATGYPIARVTAKVALGKRLHEI 362
                                       789999*********************99865555558********96555156777**************987777 PP

                      ATPgrasp_Ter 117 eepeeg 122
                                       e+  +g
  gi|313125560|ref|YP_004035824.1| 363 ENEITG 368
                                       776655 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 7.9e-09
                      ATPgrasp_Ter   5 llvmeyLegp.EySvDvlae.k..................gevlaavpRrKekgglq........elekdeeliela 53 
                                       +lv e+L+ + E  vD +a+ +                  g                          e+  ++ e++
  gi|313125560|ref|YP_004035824.1| 777 ILVDEFLADAvELDVDAVADgRraliggvmehvesagvhsGDS-------------AcmipprslDEETMGRVREVT 840
                                       5666666543366666666644444433333333333333222.............022333311234556789999 PP

                      ATPgrasp_Ter  54 erlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveep 119
                                       e++a+++   gl nvQ+  +++  ++LE NpR s ++  +s ++ v +++la+k + g+  e+  ++
  gi|313125560|ref|YP_004035824.1| 841 EDIATALDTVGLLNVQLAVKDGDVYVLEANPRSSRTVPfVSKATDVPIAKLAAKVMAGETLETLGAT 907
                                       *************************************83567779*************844444433 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.6
                      ATPgrasp_Ter   21 laekgevlaavpRrKekgglqelekdeelielaerl 56  
                                          ++gev  +v R+++     el  +ee++  +++ 
  gi|313125560|ref|YP_004035824.1| 1013 AIRAGEVDLVVSRNRD---FLELCVEEEITYFSTHA 1045
                                        5568999999999999...45555555555555444 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1     9e-06     0.027      35     158 ..     192     331 ..     139     334 .. 0.73
   2 !   25.4   0.0     4e-09   1.2e-05      15     157 ..     713     872 ..     700     876 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9e-06
                                       EEEESS-------B--SS--TTE...............EEEE---S.EEEEEEEEE.SSSEEEEEEEEEEEET.... CS
                       ATP-grasp_3  35 vvKprdGaggesvrvveekeeaeaaieeve........lvqefieG.kplSvsllsdgekvlvlavnrqliekaeke 102
                                       ++   +  gg++  vv+e +e+ a + +          l+ e i+G  +l  +++ d+ +  ++ +n + i+  + +
  gi|313125560|ref|YP_004035824.1| 192 IARTTYTLGGSGSGVVHEMDELVARVRKGLrlsrnsevLITESISGwVELEYEVMRDADDSCIIICNMENIDPMGIH 268
                                       55555555666666666655555444433345555566888888885578888899999999999999999875554 PP

                                       ...TEEEEEEES...----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS......SEEEEEEESS- CS
                       ATP-grasp_3 103 ...fvyaGnvtp...ietelkeevvelaeevvekleglaGyvGvDlvlkd.....eepyviEvNPRl 158
                                                vtp   i+ e ++e++++a ev+++l g+ G   + +  +d     +e  v+EvNPR+
  gi|313125560|ref|YP_004035824.1| 269 tgeS---MVVTPsqvIPDEGHQEMRDAALEVIREL-GIQGGCNIQFAWHDdgtpgGEYRVVEVNPRV 331
                                       3332...234441114556699*************.***********999888877889*******8 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 4e-09
                                       .S---.......-EESS--....SSSEEEEESS-------B--SS--TTE...............EEEE--.-SEEE CS
                       ATP-grasp_3  15 gvkvP...tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefi.eGkpl 75 
                                       g+  P   t +++ee+ e      +++ v p++  gg ++ vv+ +ee+++ iee          lv ef+ +  +l
  gi|313125560|ref|YP_004035824.1| 713 GILQPeggTATSEEEALELardiGYPVLVRPSYVLGGRAMDVVHSDEELKTYIEEAVrvspdkpiLVDEFLaDAVEL 789
                                       5666666533344433333344599****************************99989************94578** PP

                                       EEEEEE.SSSEEEEEEEEEEEET....TEEEE...EEES----HHHHHHHHHHHHHTTST...T--EEEEEEEEESS CS
                       ATP-grasp_3  76 SvsllsdgekvlvlavnrqliekaekefvyaG...nvtpietelkeevvelaeevvekle...glaGyvGvDlvlkd 146
                                        v++++dg ++l+  v + +        v +G   +++p + +l+ee++  ++ev+e++    +++G++ v l +kd
  gi|313125560|ref|YP_004035824.1| 790 DVDAVADGRRALIGGVMEHVESA----GVHSGdsaCMIPPR-SLDEETMGRVREVTEDIAtalDTVGLLNVQLAVKD 861
                                       ********999988887766654....55555111555554.4466655555555555555559************* PP

                                       .SEEEEEEESS CS
                       ATP-grasp_3 147 eepyviEvNPR 157
                                       ++ yv+E NPR
  gi|313125560|ref|YP_004035824.1| 862 GDVYVLEANPR 872
                                       *********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1079 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.47
# Mc/sec: 6950.86
//
Query:       gi|313125561|ref|YP_004035825.1|  [L=151]
Description: hypothetical protein Hbor_07890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.33   10.8   3.2       0.29   11.0   1.7    1.6  2  Flavi_NS2B  Flavivirus non-structural protein NS2B


Domain annotation for each model (and alignments):
>> Flavi_NS2B  Flavivirus non-structural protein NS2B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.7   1.6e-05      0.29       7      59 ..      26      77 ..      21     102 .. 0.82
   2 ?   -1.6   0.0      0.13   2.3e+03      13      41 ..     105     133 ..      95     139 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.6e-05
                        Flavi_NS2B  7 avGlvsvl.lslllkedvnllGPlivGGllialvvvaGrvddlelkklaevswe 59
                                      ++G+v  l +++l++e   ++  +++GG+l a+v+vaG    +  + l+ vsw+
  gi|313125561|ref|YP_004035825.1| 26 TAGVVNNLyAAVLVRELDRVIDLVLIGGILSAVVIVAGFLTAV--NWLGWVSWD 77
                                      578887552677889999********************98765..568999997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.13
                        Flavi_NS2B  13 vllslllkedvnllGPlivGGllialvvv 41 
                                       v++s  + e   +    +vGG +    +v
  gi|313125561|ref|YP_004035825.1| 105 VVISFGIMETTAFYASRVVGGEVRDTATV 133
                                       44455555666666666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 859.55
//
Query:       gi|313125562|ref|YP_004035826.1|  [L=262]
Description: nmra-like family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-47  160.2   0.1    6.1e-47  159.9   0.1    1.1  1  NAD_binding_10   NAD(P)H-binding
      7e-15   55.2   0.0    1.3e-14   54.4   0.0    1.4  1  NmrA             NmrA-like family
    5.8e-11   41.9   0.1    7.7e-11   41.5   0.1    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.5e-10   41.0   0.0    2.4e-10   40.3   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    7.5e-05   23.2   0.0    0.00011   22.6   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0031   16.7   0.1       0.02   14.1   0.1    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0047   16.8   0.1       0.19   11.6   0.1    2.1  2  KR               KR domain
  ------ inclusion threshold ------
      0.011   16.0   0.2      0.016   15.4   0.2    1.3  1  TrkA_N           TrkA-N domain
      0.025   14.7   0.1      0.043   13.9   0.1    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.041   13.0   0.0         15    4.7   0.0    2.9  3  NAD_binding_4    Male sterility protein
       0.11   13.2   0.4        1.6    9.5   0.0    2.2  2  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.9   0.1   3.7e-50   6.1e-47       1     183 [.      21     214 ..      21     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 159.9 bits;  conditional E-value: 3.7e-50
                                       TTTSHHHHHHHHHHHHC-.T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC... CS
                    NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk... 73 
                                       GAtG++Gr++++ l  ++ ++ v+al+R+p++ + l+++ + evv gdv++++d a+a++++daV++alg++ +   
  gi|313125562|ref|YP_004035826.1|  21 GATGGTGRRVLDVLHTSDsEVVVRALTRSPDSESPLRDRGADEVVIGDVMNPDDAARAVADVDAVICALGSSLGldt 97 
                                       9*************9999999****************99999***************************88777666 PP

                                       ......HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCH..HHHHHHHHHHHHHHHSSSEEEEEE CS
                    NAD_binding_10  74 ......deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellk..aylaakraaeellrasgldwTivr 142
                                             d eg+kn++daa +agv++fvlvs++gvgd++pg      + l++   +l ak++ae++lr+sgl++Ti+r
  gi|313125562|ref|YP_004035826.1|  98 ltsdsaDGEGTKNLIDAACKAGVEQFVLVSSLGVGDSAPGMPLG-LRLLFRglGVLPAKARAEAHLRDSGLTYTILR 173
                                       6555456666***************************9997433.344554225689******************** PP

                                       E-CEE-ST.--SEEEEETTSS----EEEHHHHHHHHHHHCTX CS
                    NAD_binding_10 143 pggLtdep.ttkyrvvekgepfkggsisradVAdvlvavldd 183
                                       pggLt+ + t++++v+e+g+   +gsi+radVA ++va+l  
  gi|313125562|ref|YP_004035826.1| 174 PGGLTNADaTGDIVVGEGGD-TVSGSIPRADVAGLCVASLFT 214
                                       ******99455565555555.56789************9976 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   7.8e-18   1.3e-14       1     143 [.      17     176 ..      17     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 7.8e-18
                                       EEESSTTSHHHHHHHHHHHH..HT-EEEEEES-S-SHHHHHHHHSTT.EEEES-TT-HHHHHHHHTT-SEEEE---G CS
                              NmrA   1 IlviGaTGrqGksvvrallk..aghkvralvRdtkselakslkeaGv.elvkgdlddkeslvealkgvdvvfsvtgf 74 
                                       +lv GaTG  G+ v ++l    ++  vral+R ++se    l ++G+ e+v gd+ + +  ++a+ +vd+v++++g+
  gi|313125562|ref|YP_004035826.1|  17 VLVAGATGGTGRRVLDVLHTsdSEVVVRALTRSPDSES--PLRDRGAdEVVIGDVMNPDDAARAVADVDAVICALGS 91 
                                       79***************9986678889*******9995..79****94466*************************9 PP

                                       G.........S-HHHHHHHHHHHHHHHS-SEEEE.EE---GG.GT.SSS-......--TTTHHHHHHHHHHHHCTS- CS
                              NmrA  75 y.........skeiedgkklvdAakeaGvkhfiy.Sslgddndrsnaeep......avphfdsKaeieeyvralgip 135
                                                 s+  e  k+l+dAa +aGv++f+  Sslg  + +            ++ +  +Ka+ e ++r +g+ 
  gi|313125562|ref|YP_004035826.1|  92 SlgldtltsdSADGEGTKNLIDAACKAGVEQFVLvSSLGVGDSAPGMPLGlrllfrGLGVLPAKARAEAHLRDSGLT 168
                                       99**99987777777789**************8637777766555444331111114455679************** PP

                                       EEEEEE-E CS
                              NmrA 136 ytfvyagf 143
                                       yt++++g 
  gi|313125562|ref|YP_004035826.1| 169 YTILRPGG 176
                                       ***99985 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.1   4.7e-14   7.7e-11       1     119 [.      18     131 ..      18     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.7e-14
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +v G++G  Gr++   L   ++  ev v  l  sp   + l+  + ++v+ gDv++ d+  +a+ +vd+vi   + +
  gi|313125562|ref|YP_004035826.1|  18 LVAGATGGTGRRVLDVLHTSDS--EVVVRALTRSPDSESPLRDRGADEVVIGDVMNPDDAARAVADVDAVICALGSS 92 
                                       699***********99999986..888888899999999*******************************9874444 PP

                         3Beta_HSD  78 dvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaev 119
                                           +lt    +++  +GT+n+++a+ kagv+ +v +Ss++v
  gi|313125562|ref|YP_004035826.1|  93 LGLDTLT---SDSADGEGTKNLIDAACKAGVEQFVLVSSLGV 131
                                       4444444...558889***********************987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   1.4e-13   2.4e-10       1     116 [.      17     129 ..      17     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.4e-13
                                       EEEETTTSHHHHHHHHHHHHCTSE..EEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgye..vigldrlssasntarledl.elveldltdrsalerlfkeeqpdavihlAav 74 
                                       +lV+GatG  G+ +++ l + + e  v +l+r ++++   r++ + e+v +d++++++ +r+++  ++davi + + 
  gi|313125562|ref|YP_004035826.1|  17 VLVAGATGGTGRRVLDVLHTSDSEvvVRALTRSPDSESPLRDRGAdEVVIGDVMNPDDAARAVA--DVDAVICALGS 91 
                                       79********************773355667776666666666669******************..89******887 PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEG CS
                         Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsSs 116
                                       +   ++ ++ ++    + +gt nl++aa kagv++++ +sS 
  gi|313125562|ref|YP_004035826.1|  92 SLGLDTLTSDSA----DGEGTKNLIDAACKAGVEQFVLVSSL 129
                                       777777777655....799*********************94 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     7e-08   0.00011       1      78 [.      16      93 ..      16     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7e-08
                                      EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSG.GGTTTECEBEEEGGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavk.aleegkdlkvedvdeeelkevdivflalpag 77
                                      +v + GatG +G+++l +L++ + ev + +l+ s     ++l+++   ++  g  ++ +d  + ++++vd v++al+++
  gi|313125562|ref|YP_004035826.1| 16 RVLVAGATGGTGRRVLDVLHTsDSEVVVRALTRSPD-SESPLRDRGAdEVVIGDVMNPDD-AARAVADVDAVICALGSS 92
                                      6899*****************778888888777777.77888888663555555555555.77778**********987 PP

                                      H CS
                    Semialdhyde_dh 78 v 78
                                       
  gi|313125562|ref|YP_004035826.1| 93 L 93
                                      5 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.2e-05      0.02       1     128 [.      17     128 ..      17     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEE..EES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT. CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiil..lerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekalee 75 
                                       vlv+Ga+G  G+++++ + +++  ++++  l r+  +   +++    + ++        +vigdv + +  ++a+  
  gi|313125562|ref|YP_004035826.1|  17 VLVAGATGGTGRRVLDVLHTSDS-EVVVraLTRSPDSESPLRD----RGAD-------EVVIGDVMNPDDAARAVA- 80 
                                       79999999999998876655544.4433003333333333332....2233.......357999999999999999. PP

                                       .T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  76 lkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                        +vd+v+ a        +   +l   +    gt+n+i+aa +agv+++vl+S+
  gi|313125562|ref|YP_004035826.1|  81 -DVDAVICALGS----SLGLDTLTSDSADGEGTKNLIDAACKAGVEQFVLVSS 128
                                       .99999876543....344455555566678********************96 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00012      0.19       1      76 [.      15      83 ..      15      89 .. 0.79
   2 ?    3.1   0.0      0.05        81     114     138 ..     106     130 ..     101     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                      SEEEEETTTSHHHHHHHHHHHHHHS-EEE.EE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                                KR  1 gtylitGGlGgLGlelarwlaekgarhlv.llsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                                      g +l++G++Gg G+ + + l  +  + +v  l+Rs    +ds+   + l+++ga+ evv  Dv ++d+ ++++++++
  gi|313125562|ref|YP_004035826.1| 15 GRVLVAGATGGTGRRVLDVLHTSDSEVVVrALTRS----PDSE---SPLRDRGAD-EVVIGDVMNPDDAARAVADVD 83
                                      678*****************987755554267777....4444...569999998.56668**********999987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.05
                                       HHHHHHHHHTTTS--SEEEEEEEHH CS
                                KR 114 kGawnLhelledesldffvlfSSia 138
                                       +G++nL  +  +  ++ fvl+SS++
  gi|313125562|ref|YP_004035826.1| 106 EGTKNLIDAACKAGVEQFVLVSSLG 130
                                       6999**999999***********75 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2     1e-05     0.016       2      73 ..      18      92 ..      17     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                      EEES.-SHHHHHHHHHHHH.TT.EEEEEEESSHHHHHHHHHTTSE.EEES-TTSHHHHHHTTGGGESEEEE-SSSH CS
                            TrkA_N  2 iiiG.lGrvGrslaeeLse.gg.kdvvvidkdeerveelreegle.vvvgdatdeevLeeagiekadaviaatgdd 73
                                      +++G  G +Gr++++ L++ ++   v +  ++++    lr++g++ vv+gd+ +++  ++a ++++davi+a+g+ 
  gi|313125562|ref|YP_004035826.1| 18 LVAGaTGGTGRRVLDVLHTsDSeVVVRALTRSPDSESPLRDRGADeVVIGDVMNPDDAARA-VADVDAVICALGSS 92
                                      56664699***********55542245699*************555**********99998.899*******9875 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.7e-05     0.043       2      45 ..      16      60 ..      15      89 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC.STTTTTBHH CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrke.selegkdag 45
                                      +v+v+Ga+G  G++v+++++++++  +v a+ r++ se   +d g
  gi|313125562|ref|YP_004035826.1| 16 RVLVAGATGGTGRRVLDVLHTSDSEVVVRALTRSPdSESPLRDRG 60
                                      79*******************998889999999885333333333 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0092        15       2      38 ..      20      56 ..      19      80 .. 0.83
   2 ?    2.4   0.0     0.046        75     111     139 ..     104     132 ..      63     140 .. 0.68
   3 ?    2.8   0.0     0.035        56     184     227 ..     159     197 ..     153     222 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0092
                                      E-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHH CS
                     NAD_binding_4  2 TGaTGFLGkvLlekLLrttpevkiyllvRaksgesae 38
                                       GaTG  G+++l  L ++++ev + +l R+ ++es++
  gi|313125562|ref|YP_004035826.1| 20 AGATGGTGRRVLDVLHTSDSEVVVRALTRSPDSESPL 56
                                      7****************************88887754 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHTSSS--.-EEEEEE.GGG CS
                     NAD_binding_4 111 NveGtrevlelakklkklkvllhvST.ayv 139
                                         eGt+++++ a k     +++ vS+ ++ 
  gi|313125562|ref|YP_004035826.1| 104 DGEGTKNLIDAACKAGVE-QFVLVSSlGVG 132
                                       458*********998877.9*****95554 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.035
                                       HHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHH CS
                     NAD_binding_4 184 EklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllg 227
                                       E  +    r sgl  +i+Rp+ +t    tG i   + g +++ g
  gi|313125562|ref|YP_004035826.1| 159 EAHL----RDSGLTYTILRPGGLTNADATGDIVVGE-GGDTVSG 197
                                       4444....445799**********966666554444.4444433 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00097       1.6       1      33 [.      17      49 ..      17      59 .. 0.88
   2 ?    1.8   0.0      0.22   3.7e+02      82     106 ..      75      97 ..      51     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00097
                                      EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEES CS
                   DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaag 33
                                      v++ G+TG  G+  Ldv++  + +  v al+ +
  gi|313125562|ref|YP_004035826.1| 17 VLVAGATGGTGRRVLDVLHTSDSEVVVRALTRS 49
                                      6789******************99999999865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.22
                                       HHHHHCHTT-SEEEE--SSGGGHHH CS
                   DXP_reductoisom  82 lkelaeeeeadvvvaaivGaaGLkp 106
                                       +++++   ++d+v+ a+ ++ GL  
  gi|313125562|ref|YP_004035826.1|  75 AARAV--ADVDAVICALGSSLGLDT 97 
                                       33333..379************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1493.38
//
Query:       gi|313125563|ref|YP_004035827.1|  [L=274]
Description: sugar kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-32  113.2   1.4    1.9e-32  112.7   1.4    1.3  1  NAD_kinase      ATP-NAD kinase
  ------ inclusion threshold ------
      0.028   14.0   0.1      0.049   13.3   0.1    1.3  1  DAGK_cat        Diacylglycerol kinase catalytic domain
       0.12   12.6   0.1       0.22   11.7   0.1    1.4  1  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   1.4   3.1e-36   1.9e-32      77     289 ..      53     259 ..       2     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 3.1e-36
                                       TSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE CS
                        NAD_kinase  77 agvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskg 153
                                       + +dl++ +GGDGT+l+ ar       P+lgvn+G +gfl  + p++a e+  + +e   r  + e l   +++  +
  gi|313125563|ref|YP_004035827.1|  53 ETADLVVSIGGDGTFLFTARGAG--GTPILGVNLGEVGFLNAVGPDDAVEAVMAEVE---RFRDGESLA--VREVPR 122
                                       689********************..8*****************88888877777777...566666666..333333 PP

                                       ......EEEEEEESSEEEEEESSSSS-EE..EEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EE CS
                        NAD_kinase 154 eediadiviensvlnevviirgpgstlie..lelyvdtelleadqldglivstPtGstayslsaGgplisPgvlail 228
                                         + ad   e+ ++nevv+   ++ +     le+ vd++l +   +dg++v+tPtGstay ls  gpl++P+v+ ++
  gi|313125563|ref|YP_004035827.1| 123 IAAEADGWTEHPAMNEVVVQGPRRGHGGGvsLEVRVDGSLYSGGHADGVLVATPTGSTAYNLSERGPLVHPSVEGLV 199
                                       2245777889999*****9998888888788********************************************99 PP

                                       EEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEE CS
                        NAD_kinase 229 ivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfkl 289
                                       i  + P      p+Vvs++ +++i+v + +ea+++ dG+++ +++p  ev++ ++d +++l
  gi|313125563|ref|YP_004035827.1| 200 INEMAPDGG-MPPLVVSPDAEVTITVTDAEEAVVVSDGRQRQYVTPPTEVTIATADDPVRL 259
                                       999999765.68******************************************9998876 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.1e-06     0.049      11      69 ..      10      68 ..       3      85 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.1e-06
                                      TTTTHHHHHHHCHHHHHHCTCEEEEEE--STTH..HHHHHHHHHHCC-SEEEEEESHHHHH CS
                          DAGK_cat 11 Gkgkgekllrkvrelleeagvelelieteepgd..akelakeakeegvdlivvaGGDGtvs 69
                                      G+ +++ l++ +re l +a ve+++   + +    + + ++++++  +dl+v +GGDGt+ 
  gi|313125563|ref|YP_004035827.1| 10 GNSRAAYLADDLRERLLNADVEVRVDAETAETLgvEGHPVETVET--ADLVVSIGGDGTFL 68
                                      566677777888888888888666666554443113344555555..6***********85 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.7e-05      0.22       1      43 [.       2      44 ..       2      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                                      SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHH CS
                    HGTP_anticodon  1 qvvviplnekaeeleeyakklaeeLraagirveldd.snesigk 43
                                      qv++++   +++ +  +a++l+e+L++a+++v +d   +e++g 
  gi|313125563|ref|YP_004035827.1|  2 QVAIVAQRGNSR-AAYLADDLRERLLNADVEVRVDAeTAETLGV 44
                                      788888887544.7889*******************99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1473.68
//
Query:       gi|313125564|ref|YP_004035828.1|  [L=420]
Description: RecA-superfamily ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-52  175.7   0.0    1.1e-51  175.4   0.0    1.1  1  ATPase         KaiC
    7.6e-07   28.9   0.0    1.3e-06   28.2   0.0    1.3  1  AAA_25         AAA domain
    2.8e-06   26.2   0.1    6.3e-06   25.1   0.1    1.5  1  GvpD           GvpD gas vesicle protein
    0.00013   21.4   0.0      0.006   15.9   0.0    2.2  2  DnaB_C         DnaB-like helicase C terminal domain
    0.00035   20.1   0.0    0.00055   19.5   0.0    1.2  1  RecA           recA bacterial DNA recombination protein
     0.0012   18.6   0.0     0.0029   17.3   0.0    1.6  1  AAA_24         AAA domain
     0.0021   17.9   0.0     0.0041   17.0   0.0    1.4  1  MEDS           MEDS: MEthanogen/methylotroph, DcmR Sensory do
     0.0032   17.5   0.0     0.0081   16.2   0.0    1.6  1  AAA_14         AAA domain
     0.0042   16.4   0.0     0.0058   15.9   0.0    1.2  1  Rad51          Rad51
  ------ inclusion threshold ------
      0.036   14.2   0.0       0.08   13.1   0.0    1.7  1  AAA_33         AAA domain
      0.057   13.7   0.0       0.15   12.4   0.0    1.7  1  AAA_22         AAA domain
      0.067   12.9   0.0        0.1   12.3   0.0    1.3  1  IstB_IS21      IstB-like ATP binding protein
      0.071   12.0   0.0       0.11   11.4   0.0    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.13   11.7   0.1       0.22   11.0   0.1    1.2  1  PhoH           PhoH-like protein
       0.18   10.6   0.0       0.27   10.0   0.0    1.1  1  PPV_E1_C       Papillomavirus helicase


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.4   0.0   9.2e-55   1.1e-51       3     229 ..     195     416 ..     193     418 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 9.2e-55
                            ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdleklee 79 
                                        gIeglDe++ gG+p+++ +   G++GtGKt+f+lqFl + +e+ ge+ v++t+ee+   +   a++ Gw ++k+ +
  gi|313125564|ref|YP_004035828.1| 195 IGIEGLDEMILGGVPKRSLMVTIGTAGTGKTTFGLQFLNHALEN-GEKAVYITLEESRDRIFDTAEEKGWPFRKYAD 270
                                       7*************************************999888.******************************** PP

                            ATPase  80 egklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkklg 155
                                       e++laiid+   +         ++l ++ ++l + +++++a+r+v+Ds++ l + ++++++ R++++ ++r lk+ g
  gi|313125564|ref|YP_004035828.1| 271 EDRLAIIDLDPVEM-------ANSLASIQNDLPRLVADFGAERLVLDSVSLLeMMYDHPSKRRSQVFDFARALKDAG 340
                                       *********99965.......599*****************************9*********************** PP

                            ATPase 156 vTailvsekssseeaaggygveefivdgvivLdlkeiee..elvRtleivkmRgtkhskkehpfeIteegikvlee 229
                                       vT++l+se+++++   +++g+ e+++d v+vL++ + ++  e++  +ei k+R ++hs+++ p++ t++gi+v+ +
  gi|313125564|ref|YP_004035828.1| 341 VTTLLTSEAKENNPYSSRHGLVEYLADAVFVLQYVRPSDfrETRLAIEIQKIRDANHSRETKPYDLTSDGISVYRQ 416
                                       ************************************9999899999***************************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.1e-09   1.3e-06      12     151 ..     190     312 ..     180     347 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.1e-09
                            AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelr 87 
                                       +++l+  ++ ++  + g +p+ +l + +G  gtGKtt+ l+   + +  G+           k +y+ +E+s+d++ 
  gi|313125564|ref|YP_004035828.1| 190 IDRLDIGIEGLDEMILGGVPKRSLMVTIGTAGTGKTTFGLQFLNHALeNGE-----------KAVYITLEESRDRIF 255
                                       5556666667777777777****************************4444...........89************* PP

                            AAA_25  88 rRlravg...ealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDpl 151
                                         +++ g   ++++d +rl+++dl+ v + + L++       ++ d+ +l   + +  g++ +v+D++
  gi|313125564|ref|YP_004035828.1| 256 DTAEEKGwpfRKYADEDRLAIIDLDPVeMANSLAS-------IQNDLPRL---VAD-FGAERLVLDSV 312
                                       ****988888999**********988855555544.......55554333...333.34445566655 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   5.3e-09   6.3e-06      13     206 ..     214     407 ..     204     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.3e-09
                              GvpD  13 llikGaPGtGktlftlrgld.vlrresdvlyvstrvddetvseay......fsgeaeldktalldllkdpleldldv 82 
                                       ++  G  GtGkt+f l++l+ +l++ ++ +y++     + +++        f   a+ d+ a++dl  dp+e+    
  gi|313125564|ref|YP_004035828.1| 214 MVTIGTAGTGKTTFGLQFLNhALENGEKAVYITLEESRDRIFDTAeekgwpFRKYADEDRLAIIDL--DPVEMANSL 288
                                       5667***************74688999999**9988888888877778889999999999999998..898876543 PP

                              GvpD  83 dvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvletaan 159
                                          i +   + l   v      a++l+  lds    +  l   yd+P + +    d++   +++gv  +l +e+++n
  gi|313125564|ref|YP_004035828.1| 289 -ASI-Q---NDLPRLVA--DFGAERLV--LDS----VSLLEMMYDHPSKRRSQVFDFARALKDAGVTTLLTSEAKEN 352
                                       .344.3...34445555..34567765..799....7788999******999999999999**************99 PP

                              GvpD 160 sr.......leyivdGvvtl.nvkeddrgrlrrdlrleklrGvrignrlqPftla 206
                                       ++       +ey++d v  l  v+  d   +r  + ++k+r  +     +P+ l+
  gi|313125564|ref|YP_004035828.1| 353 NPyssrhglVEYLADAVFVLqYVRPSDFRETRLAIEIQKIRDANHSRETKPYDLT 407
                                       7644445557**********6799999999***********99988888888875 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     5e-06     0.006       3      63 ..     194     254 ..     193     258 .. 0.82
   2 ?    3.1   0.0     0.043        51     111     163 ..     285     338 ..     269     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
                                       XSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHH CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   3 stgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeql 63 
                                       + g + LD+++ +G+ k  l++  + +++Gkt++ l++ ++a ++ + + +++ le s++++
  gi|313125564|ref|YP_004035828.1| 194 DIGIEGLDEMIlGGVPKRSLMVTIGTAGTGKTTFGLQFLNHALENGE-KAVYITLEESRDRI 254
                                       568899998752789999*********************99887555.66677888888776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.043
                                       SXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBTS.CSSSCCCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 111 altvseirskarrlkkekglgliviDyLqlmegs.eekenreqevseisrsLka 163
                                       a ++++i++ + rl ++ g + +v+D + l+e    + ++r+++v + +r+Lk 
  gi|313125564|ref|YP_004035828.1| 285 ANSLASIQNDLPRLVADFGAERLVLDSVSLLEMMyDHPSKRRSQVFDFARALKD 338
                                       5578889999999999999999**********87555779999*********96 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.6e-07   0.00055      24      97 ..     183     255 ..     175     266 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.6e-07
                                       S--.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHH CS
                              RecA  24 dekeklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpky 97 
                                       de+ + +++ +  G  +ld  + +GG+pk  ++   G+  +Gktt+ l+ + +a ++g  a++i  e + d  +
  gi|313125564|ref|YP_004035828.1| 183 DEEFESDIDRLDIGIEGLDEMI-LGGVPKRSLMVTIGTAGTGKTTFGLQFLNHALENGEKAVYITLEESRDRIF 255
                                       6677889999999*9***9866.79******************************************9988765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.5e-06    0.0029       5      91 ..     214     329 ..     211     340 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.5e-06
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel............... 59 
                                       ++ +G +g+GKTt+ +++       g+k+++i +e++ +++ ++  +  ++w  f+++++e+               
  gi|313125564|ref|YP_004035828.1| 214 MVTIGTAGTGKTTFGLQFlnhalenGEKAVYITLEESRDRIFDTAEE--KGW-PFRKYADEDrlaiidldpvemans 287
                                       5779********************************88777666543..244.377777777777777777777777 PP

                            AAA_24  60 ............aaeladyktlviDtideleelclaevirqnek 91 
                                                   a+  a  + lv+D+++ le + ++  +r++++
  gi|313125564|ref|YP_004035828.1| 288 lasiqndlprlvADFGA--ERLVLDSVSLLEMMYDHPSKRRSQV 329
                                       77777777654333333..7788888888877777777666665 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.5e-06    0.0041      19      73 ..     230     284 ..     227     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.5e-06
                              MEDS  19 pfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetyl 73 
                                       +f+  +l++gek +y++ ++++d++ +  +++g +  ++ ++++l i+d + + +
  gi|313125564|ref|YP_004035828.1| 230 QFLNHALENGEKAVYITLEESRDRIFDTAEEKGWPFRKYADEDRLAIIDLDPVEM 284
                                       79***********************************************987655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.8e-06    0.0081       4      50 ..     213     259 ..     210     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.8e-06
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe 50 
                                       ++v  G   +GKTt+  q++++ l + e+ +yi+l++ rd+ +++ e
  gi|313125564|ref|YP_004035828.1| 213 LMVTIGTAGTGKTTFGLQFLNHALENGEKAVYITLEESRDRIFDTAE 259
                                       566778899***************99************997665443 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.9e-06    0.0058      14     141 ..     188     312 ..     176     337 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-06
                                       HSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHH CS
                             Rad51  14 sellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlve 90 
                                       s++ +l  G + lDe++ GG++  s+   +G  ++Gkt +  ++     l+  l+ g +kavyi  e +   +r+++
  gi|313125564|ref|YP_004035828.1| 188 SDIDRLDIGIEGLDEMILGGVPKRSLMVTIGTAGTGKTTFGLQF-----LNHALENG-EKAVYITLEES--RDRIFD 256
                                       66778999*******************************99886.....33334433.46889988875..568888 PP

                                       HH.....HHT.T--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETT CS
                             Rad51  91 ia.....ery.kldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsv 141
                                        a       + k  +e+ l  +  + +  +++ +++ + ++ l+a+     l++Dsv
  gi|313125564|ref|YP_004035828.1| 257 TAeekgwP-FrKYADEDRLAIIDLDPVEMANSLASIQNDLPRLVADFGAERLVLDSV 312
                                       88443320.344444555555555555556666666666666666666666666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.7e-05      0.08       1      46 [.     213     263 ..     213     349 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg......avllssdtlrrrlfgtdqqskt 46 
                                       l++++G +G+GK+t+  + l++ +      av ++  + r+r+f t +++ +
  gi|313125564|ref|YP_004035828.1| 213 LMVTIGTAGTGKTTFGLQFLNH-AlengekAVYITLEESRDRIFDTAEEKGW 263
                                       6899***********9886422.22355999999999999999998777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.15       5      50 ..     211     250 ..     209     331 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpss 50 
                                       ++++v +G +GtGKTt   ++l+ + e       + + v++tl +s
  gi|313125564|ref|YP_004035828.1| 211 RSLMVTIGTAGTGKTTFGLQFLNHALEN------GEKAVYITLEES 250
                                       678899**********999998888654......555555555544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.8e-05       0.1      46     115 ..     210     280 ..     197     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-05
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveel.krarrdgklaralkrllkvdllilD 115
                                       k+  +v +G +G+GK+ +   +  +a ++g + +++++e+   ++  +a+++g   r+ +   + +++ lD
  gi|313125564|ref|YP_004035828.1| 210 KRSLMVTIGTAGTGKTTFGLQFLNHALENGEKAVYITLEESRDRIfDTAEEKGWPFRKYADEDRLAIIDLD 280
                                       55668899*****************************9986655425666666666666666666666665 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.2e-05      0.11      18      47 ..     214     243 ..     208     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.2e-05
                     TrwB_AAD_bind  18 ilivGttGsGKtqalekllrairargdrai 47 
                                       ++ +Gt+G+GKt+   ++l+++ + g++a+
  gi|313125564|ref|YP_004035828.1| 214 MVTIGTAGTGKTTFGLQFLNHALENGEKAV 243
                                       6779***********************998 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00018      0.22      18      48 ..     210     240 ..     200     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                       H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS CS
                              PhoH  18 kndivfaiGpaGtGKtylavalavealkkkk 48 
                                       k ++++ iG aGtGKt + ++   +al++++
  gi|313125564|ref|YP_004035828.1| 210 KRSLMVTIGTAGTGKTTFGLQFLNHALENGE 240
                                       78899************99998888887765 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00022      0.27     255     283 ..     204     232 ..     199     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                          PPV_E1_C 255 fLkgvPkknclvllGppntGkslfamsli 283
                                        L gvPk++ +v +G++ tGk++f+  ++
  gi|313125564|ref|YP_004035828.1| 204 ILGGVPKRSLMVTIGTAGTGKTTFGLQFL 232
                                       5889********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2489.41
//
Query:       gi|313125565|ref|YP_004035829.1|  [L=76]
Description: hypothetical protein Hbor_07930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-05   25.4   0.9      0.017   15.2   0.1    2.2  2  Zn-ribbon_8     Zinc ribbon domain
      6e-05   22.9   1.1      0.025   14.5   0.1    2.4  2  Nudix_N_2       Nudix N-terminal
     0.0002   20.8   3.9       0.11   12.0   0.1    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00033   19.9   2.0       0.38   10.2   0.1    2.3  2  zf-ribbon_3     zinc-ribbon domain
    0.00057   20.1   0.4      0.081   13.2   0.0    2.1  2  Ribosomal_L32p  Ribosomal L32p protein family
    0.00087   18.9   0.9       0.12   12.1   0.2    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
     0.0013   18.9   1.0        1.2    9.5   0.1    2.4  2  zinc_ribbon_9   zinc-ribbon
     0.0023   17.9   1.7          1    9.4   0.0    2.4  2  Rubredoxin      Rubredoxin
     0.0087   16.1   2.7        0.2   11.7   0.1    2.2  2  UPF0547         Uncharacterised protein family UPF0547
     0.0089   16.0   3.9       0.63   10.1   0.6    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.5   1.2        3.2    7.6   0.0    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.017   15.1   0.4        3.7    7.5   0.0    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.03   14.3   0.4        7.8    6.5   0.1    2.3  2  Prok-RING_1     Prokaryotic RING finger family 1
      0.035   13.8   4.6       0.15   11.8   0.0    2.5  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
      0.035   14.1   0.7        0.1   12.7   0.7    1.7  1  DZR             Double zinc ribbon
       0.04   13.9   0.1      0.052   13.6   0.1    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.044   13.5   0.1          1    9.0   0.0    2.0  2  TackOD1         Thaumarchaeal output domain 1
      0.049   13.1   0.2       0.16   11.4   0.2    1.6  1  NMD3            NMD3 family
      0.067   13.2   1.4        3.4    7.7   0.1    2.6  2  ADK_lid         Adenylate kinase, active site lid
      0.071   13.0   4.9        0.3   11.0   0.4    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.076   12.7   3.4        3.4    7.4   0.1    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.12   13.1   1.9        1.5    9.6   0.2    2.1  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
       0.19   12.2   2.8         18    6.0   1.0    2.6  2  zf-H2C2_2       Zinc-finger double domain
       0.22   11.5   8.0       0.34   10.9   1.0    2.4  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.24   11.5   4.9       0.59   10.3   0.3    2.3  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.26   11.3   3.1        7.9    6.5   0.1    2.3  2  DUF1610         Domain of unknown function (DUF1610)
       0.33   11.0   1.7        7.9    6.6   0.1    2.1  2  CpXC            CpXC protein
        0.5   10.3   5.3          4    7.4   1.4    2.3  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        0.7    9.7   2.7        4.8    7.0   0.2    2.3  2  zinc_ribbon_5   zinc-ribbon domain
        1.3    9.1   6.5        2.6    8.1   0.6    2.4  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        7.8    7.2   7.2         32    5.2   0.3    3.0  3  zf-C2H2         Zinc finger, C2H2 type
        9.2    6.4   6.8         18    5.5   1.7    2.4  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     3e-05     0.017      13      33 ..       9      29 ..       6      32 .. 0.89
   2 !    8.9   0.1     0.003       1.7      28      37 ..      51      59 ..      44      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                       Zn-ribbon_8 13 hefevlqsisdapltaCPeCg 33
                                      + fe+l+s ++ ++ +CP+Cg
  gi|313125565|ref|YP_004035829.1|  9 TPFERLRSHMEHEDLVCPDCG 29
                                      68*****888*999******9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.003
                       Zn-ribbon_8 28 aCPeCgsevr 37
                                      +CP+Cgs vr
  gi|313125565|ref|YP_004035829.1| 51 VCPSCGS-VR 59
                                      4999998.44 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1     0.008       4.5      21      30 ..      21      30 ..      12      30 .. 0.83
   2 !   14.5   0.1   4.4e-05     0.025      21      31 ..      48      58 ..      34      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.008
                                      -EEEETTTTE CS
                         Nudix_N_2 21 eRlvCpaCgt 30
                                      e lvCp+Cg+
  gi|313125565|ref|YP_004035829.1| 21 EDLVCPDCGY 30
                                      558*****97 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.4e-05
                                      -EEEETTTTEE CS
                         Nudix_N_2 21 eRlvCpaCgti 31
                                       R+vCp+Cg +
  gi|313125565|ref|YP_004035829.1| 48 YRHVCPSCGSV 58
                                      5********98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1    0.0002      0.11      16      27 ..      19      30 ..       7      34 .. 0.86
   2 !    9.6   0.6    0.0011      0.63      20      28 ..      50      58 ..      48      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                      STTCEEESSSSB CS
                      TF_Zn_Ribbon 16 ergelvCtdCGl 27
                                      e+ +lvC+dCG+
  gi|313125565|ref|YP_004035829.1| 19 EHEDLVCPDCGY 30
                                      6789*******7 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                                      EEESSSSBE CS
                      TF_Zn_Ribbon 20 lvCtdCGlV 28
                                      +vC++CG+V
  gi|313125565|ref|YP_004035829.1| 50 HVCPSCGSV 58
                                      589999998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00068      0.38      15      24 ..      21      30 ..      17      31 .. 0.85
   2 !    9.4   0.2    0.0012       0.7       5      11 ..      52      58 ..      50      61 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00068
                       zf-ribbon_3 15 ddnvCpyCGt 24
                                      +d vCp CG+
  gi|313125565|ref|YP_004035829.1| 21 EDLVCPDCGY 30
                                      6889*****8 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                       zf-ribbon_3  5 CPnCGap 11
                                      CP+CG++
  gi|313125565|ref|YP_004035829.1| 52 CPSCGSV 58
                                      6666654 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.04        22      41      49 ..      24      32 ..      15      34 .. 0.83
   2 !   13.2   0.0   0.00014     0.081      32      53 ..      42      63 ..      38      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.04
                                      -BTTTTBSS CS
                    Ribosomal_L32p 41 vcpscGyYk 49
                                      vcp+cGy +
  gi|313125565|ref|YP_004035829.1| 24 VCPDCGYED 32
                                      9*****975 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00014
                                      TCCEECTTC-BTTTTBSSSBXS CS
                    Ribosomal_L32p 32 cgelklpHrvcpscGyYkgrev 53
                                       g  +l ++vcpscG  + r++
  gi|313125565|ref|YP_004035829.1| 42 NGDQILYRHVCPSCGSVRKRTF 63
                                      577889*********9999876 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.2   0.00021      0.12      18      30 ..      19      31 ..      18      32 .. 0.85
   2 ?    5.4   0.0     0.027        15      23      30 ..      51      58 ..      42      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                     A2L_zn_ribbon 18 eqgylvCieCgas 30
                                      e+ +lvC++Cg++
  gi|313125565|ref|YP_004035829.1| 19 EHEDLVCPDCGYE 31
                                      5679*******95 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.027
                     A2L_zn_ribbon 23 vCieCgas 30
                                      vC+ Cg++
  gi|313125565|ref|YP_004035829.1| 51 VCPSCGSV 58
                                      9*****97 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0021       1.2      13      28 ..      15      29 ..      12      31 .. 0.71
   2 !    7.9   0.1    0.0067       3.7      13      29 ..      38      57 ..      36      58 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0021
                     zinc_ribbon_9 13 svspdedsdvlCPhCg 28
                                      + ++++++ v CP+Cg
  gi|313125565|ref|YP_004035829.1| 15 RSHMEHEDLV-CPDCG 29
                                      4555666667.****8 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0067
                     zinc_ribbon_9 13 svspdedsd....vlCPhCgg 29
                                      +++++ d++    v CP+Cg+
  gi|313125565|ref|YP_004035829.1| 38 TAETNGDQIlyrhV-CPSCGS 57
                                      56666666666545.****97 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.3    0.0048       2.7      33      43 ..      21      31 ..       4      34 .. 0.73
   2 !    9.4   0.0    0.0018         1      23      47 .]      38      63 ..      30      63 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0048
                                      TT-BBTTTB-B CS
                        Rubredoxin 33 ddWvCPdCgve 43
                                      +d vCPdCg e
  gi|313125565|ref|YP_004035829.1| 21 EDLVCPDCGYE 31
                                      6889****975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                                      -TT--GGGS-TT-BBTTT.B-BGGGE CS
                        Rubredoxin 23 apgTkFedlPddWvCPdC.gvekeqF 47
                                      ++ T+ +++    vCP+C +v+k  F
  gi|313125565|ref|YP_004035829.1| 38 TAETNGDQILYRHVCPSCgSVRKRTF 63
                                      5667777777889*****44667766 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00036       0.2      16      24 ..      24      32 ..      23      33 .. 0.87
   2 ?    4.6   0.4      0.06        34       2       7 ..      51      56 ..      50      58 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                           UPF0547 16 fCphCGyvF 24
                                      +Cp+CGy++
  gi|313125565|ref|YP_004035829.1| 24 VCPDCGYED 32
                                      6******97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.06
                           UPF0547  2 vCPeCe 7 
                                      vCP C 
  gi|313125565|ref|YP_004035829.1| 51 VCPSCG 56
                                      566664 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0055       3.1      19      27 ..      23      31 ..      11      49 .. 0.83
   2 !   10.1   0.6    0.0011      0.63      18      28 ..      49      60 ..      37      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0055
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                       vCP Cg++
  gi|313125565|ref|YP_004035829.1| 23 LVCPDCGYE 31
                                      79*****87 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.k 28
                                      ++vCP Cgs  k
  gi|313125565|ref|YP_004035829.1| 49 RHVCPSCGSVrK 60
                                      489*****9854 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0056       3.2       2       8 ..      25      31 ..      22      32 .. 0.76
   2 ?    6.4   0.3     0.014       7.8       2       6 ..      52      56 ..      51      58 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0056
                     zinc_ribbon_2  2 CpnCGae 8 
                                      Cp CG+e
  gi|313125565|ref|YP_004035829.1| 25 CPDCGYE 31
                                      7888765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                     zinc_ribbon_2  2 CpnCG 6 
                                      Cp+CG
  gi|313125565|ref|YP_004035829.1| 52 CPSCG 56
                                      88887 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0067       3.7      42      57 ..      18      33 ..       8      43 .. 0.82
   2 ?    6.2   0.1     0.017       9.6      30      40 ..      51      61 ..      48      72 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0067
                    OrfB_Zn_ribbon 42 lsgrtfkCpnCgfead 57
                                       +++ ++Cp+Cg+e d
  gi|313125565|ref|YP_004035829.1| 18 MEHEDLVCPDCGYEDD 33
                                      5678899999999876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                    OrfB_Zn_ribbon 30 tCseCgsknke 40
                                       C+ Cgs+ k+
  gi|313125565|ref|YP_004035829.1| 51 VCPSCGSVRKR 61
                                      58888888887 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.018        10      19      27 ..      22      29 ..      14      31 .. 0.75
   2 ?    6.5   0.1     0.014       7.8      22      32 ..      51      61 ..      41      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                       Prok-RING_1 19 DiVvCpeCg 27
                                      D+ vCp+Cg
  gi|313125565|ref|YP_004035829.1| 22 DL-VCPDCG 29
                                      54.7****9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                       Prok-RING_1 22 vCpeCgtpyHr 32
                                      vCp Cg++  r
  gi|313125565|ref|YP_004035829.1| 51 VCPSCGSVRKR 61
                                      8*****98665 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.9      0.21   1.2e+02       2      11 ..      20      29 ..      19      37 .. 0.85
   2 ?   11.8   0.0   0.00027      0.15       4      18 ..      49      67 ..      47      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                           zf-RRN7  2 ekgppCgvCg 11
                                      +   +C+ Cg
  gi|313125565|ref|YP_004035829.1| 20 HEDLVCPDCG 29
                                      56689****9 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00027
                           zf-RRN7  4 gppCgvCgc...rsftl.d 18
                                      + +C+ Cg+   r+ftl d
  gi|313125565|ref|YP_004035829.1| 49 RHVCPSCGSvrkRTFTLdD 67
                                      559********99****55 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   0.00018       0.1       9      38 ..      19      59 ..      12      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                               DZR  9 ppdarfCseCgtk....lkavaa...........edrCpsCgekv 38
                                      ++++ +C++Cg +                      ++CpsCg+  
  gi|313125565|ref|YP_004035829.1| 19 EHEDLVCPDCGYEddggE----WtaetngdqilyRHVCPSCGSVR 59
                                      667789999999944440....1445668999999******9875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.3e-05     0.052      61      96 ..      13      59 ..       5      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-05
                                      EEEEEEE--EEEETTTS-EEECHHH.HH..........S-TTTSSS- CS
                              HypA 61 eLeieevpvkvrCreCgkefeleek.al..........rCpkCgsad 96
                                      +L+ + ++  + C +Cg+e +  e  a+           Cp+Cgs +
  gi|313125565|ref|YP_004035829.1| 13 RLRSHMEHEDLVCPDCGYEDDGGEWtAEtngdqilyrhVCPSCGSVR 59
                                      67778888899******987755432225778889999******976 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.14        77     117     130 ..      16      29 ..       2      33 .. 0.77
   2 ?    9.0   0.0    0.0018         1      80      97 ..      42      59 ..      38      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.14
                           TackOD1 117 eflkegkleCpkCk 130
                                       + +++++l+Cp C 
  gi|313125565|ref|YP_004035829.1|  16 SHMEHEDLVCPDCG 29 
                                       56777888999885 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                           TackOD1 80 ksghlnvrevCpkCkSid 97
                                      ++ ++ +r+vCp+C+S++
  gi|313125565|ref|YP_004035829.1| 42 NGDQILYRHVCPSCGSVR 59
                                      567899*********986 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00028      0.16      13      59 ..      22      72 ..      16      76 .] 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                              NMD3 13 nglCedCllke.....vditegiekievevCkeCgrylpkgkWvkaelesee 59
                                      + +C+dC  ++     +  t+g + +  +vC++Cg+++++ +++  ++es+e
  gi|313125565|ref|YP_004035829.1| 22 DLVCPDCGYEDdggewTAETNGDQILYRHVCPSCGSVRKR-TFTLDDDESSE 72
                                      55899998888664333333344447799********988.88666666665 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.07        39       3       8 ..      24      29 ..      20      31 .. 0.79
   2 ?    7.7   0.1     0.006       3.4       1      10 [.      49      58 ..      49      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.07
                                      E-TTT- CS
                           ADK_lid  3 vCpkCG 8 
                                      vCp+CG
  gi|313125565|ref|YP_004035829.1| 24 VCPDCG 29
                                      788887 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.006
                                      EEE-TTT--E CS
                           ADK_lid  1 RrvCpkCGrs 10
                                      R vCp+CG +
  gi|313125565|ref|YP_004035829.1| 49 RHVCPSCGSV 58
                                      88******76 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.5      0.09        51       6      12 ..      24      30 ..      24      31 .. 0.81
   2 ?   11.0   0.4   0.00054       0.3       3      19 ..      48      64 ..      48      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.09
                    Zn_ribbon_SprT  6 rCtgCgr 12
                                      +C++Cg 
  gi|313125565|ref|YP_004035829.1| 24 VCPDCGY 30
                                      6*****4 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00054
                    Zn_ribbon_SprT  3 yvYrCtgCgreythhls 19
                                      y ++C++Cg+  +++++
  gi|313125565|ref|YP_004035829.1| 48 YRHVCPSCGSVRKRTFT 64
                                      899******77777766 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0061       3.4      22      30 ..      23      31 ..      22      31 .. 0.88
   2 ?    5.7   0.7      0.02        11      23      29 ..      51      57 ..      50      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0061
                     zf-NADH-PPase 22 rvCpaCgle 30
                                      +vCp+Cg+e
  gi|313125565|ref|YP_004035829.1| 23 LVCPDCGYE 31
                                      59*****86 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                     zf-NADH-PPase 23 vCpaCgl 29
                                      vCp+Cg 
  gi|313125565|ref|YP_004035829.1| 51 VCPSCGS 57
                                      7999985 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1       0.3   1.7e+02       4      10 ..      24      30 ..      22      34 .. 0.85
   2 ?    9.6   0.2    0.0027       1.5       2      13 ..      49      60 ..      48      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.3
                           zf-ISL3  4 rCPnCgs 10
                                      +CP Cg 
  gi|313125565|ref|YP_004035829.1| 24 VCPDCGY 30
                                      6****95 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0027
                           zf-ISL3  2 phrCPnCgsktv 13
                                      +h+CP Cgs+ +
  gi|313125565|ref|YP_004035829.1| 49 RHVCPSCGSVRK 60
                                      599******965 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.0     0.031        18       7      22 ..      15      30 ..       6      31 .. 0.71
   2 ?    5.5   0.0     0.046        26      15      22 ..      50      57 ..      40      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.031
                         zf-H2C2_2  7 rkHtgekpyeCplCdk 22
                                      r+H+    + Cp C++
  gi|313125565|ref|YP_004035829.1| 15 RSHMEHEDLVCPDCGY 30
                                      4555555579****98 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.046
                         zf-H2C2_2 15 yeCplCdk 22
                                      + Cp+C+ 
  gi|313125565|ref|YP_004035829.1| 50 HVCPSCGS 57
                                      89****85 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.0   0.00061      0.34      17      28 ..      20      31 ..      17      31 .. 0.86
   2 ?    4.0   0.9     0.085        48      21      27 ..      51      57 ..      50      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                    PhnA_Zn_Ribbon 17 gallvCpeCahE 28
                                      ++ lvCp+C++E
  gi|313125565|ref|YP_004035829.1| 20 HEDLVCPDCGYE 31
                                      5669******98 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.085
                    PhnA_Zn_Ribbon 21 vCpeCah 27
                                      vCp C++
  gi|313125565|ref|YP_004035829.1| 51 VCPSCGS 57
                                      7888875 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3    0.0011      0.59      11      24 ..      17      30 ..       2      46 .. 0.83
   2 ?    3.9   0.6      0.11        60      16      24 ..      49      57 ..      36      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                          zf-Mss51 11 apkhvdfeCpdCGi 24
                                      + +h d+ CpdCG+
  gi|313125565|ref|YP_004035829.1| 17 HMEHEDLVCPDCGY 30
                                      578999*******7 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                          zf-Mss51 16 dfeCpdCGi 24
                                      ++ Cp CG 
  gi|313125565|ref|YP_004035829.1| 49 RHVCPSCGS 57
                                      678****96 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.5     0.041        23      19      23 ..      25      29 ..      24      30 .. 0.91
   2 ?    6.5   0.1     0.014       7.9      17      23 ..      50      56 ..      49      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.041
                           DUF1610 19 CPNCG 23
                                      CP CG
  gi|313125565|ref|YP_004035829.1| 25 CPDCG 29
                                      ****9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                           DUF1610 17 FpCPNCG 23
                                      + CP CG
  gi|313125565|ref|YP_004035829.1| 50 HVCPSCG 56
                                      89****9 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.075        42      37      46 ..      22      31 ..      12      37 .. 0.81
   2 ?    6.6   0.1     0.014       7.9      35      51 ..      47      63 ..      39      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.075
                              CpXC 37 eatCpkCgat 46
                                      + +Cp+Cg++
  gi|313125565|ref|YP_004035829.1| 22 DLVCPDCGYE 31
                                      5679999875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                              CpXC 35 lfeatCpkCgataklea 51
                                      l +++Cp+Cg  +k ++
  gi|313125565|ref|YP_004035829.1| 47 LYRHVCPSCGSVRKRTF 63
                                      67899*****9887766 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.063        35      14      18 ..      25      29 ..      20      32 .. 0.70
   2 ?    7.4   1.4    0.0072         4      25      33 ..      49      57 ..      49      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.063
                           DUF35_N 14 CpdCG 18
                                      CpdCG
  gi|313125565|ref|YP_004035829.1| 25 CPDCG 29
                                      55555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0072
                           DUF35_N 25 ravCphCgs 33
                                      r+vCp Cgs
  gi|313125565|ref|YP_004035829.1| 49 RHVCPSCGS 57
                                      788888886 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.19   1.1e+02       5       9 ..      25      29 ..      23      31 .. 0.87
   2 ?    7.0   0.2    0.0086       4.8       5      18 ..      52      69 ..      49      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.19
                     zinc_ribbon_5  5 CpdCd 9 
                                      CpdC+
  gi|313125565|ref|YP_004035829.1| 25 CPDCG 29
                                      ****8 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0086
                     zinc_ribbon_5  5 CpdCdt....kFklvdsk 18
                                      Cp C++    +F l+d++
  gi|313125565|ref|YP_004035829.1| 52 CPSCGSvrkrTFTLDDDE 69
                                      *****9666679999998 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.7     0.093        52       2       6 ..      25      29 ..      24      31 .. 0.90
   2 ?    8.1   0.6    0.0047       2.6       2       7 ..      52      57 ..      51      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.093
                    DNA_ligase_ZBD  2 CPvCG 6 
                                      CP CG
  gi|313125565|ref|YP_004035829.1| 25 CPDCG 29
                                      ****9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0047
                    DNA_ligase_ZBD  2 CPvCGs 7 
                                      CP+CGs
  gi|313125565|ref|YP_004035829.1| 52 CPSCGS 57
                                      *****9 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       2.6   1.5e+03      16      20 ..      14      18 ..      10      20 .. 0.83
   2 ?    5.2   0.3     0.057        32       2       8 ..      24      30 ..      23      31 .. 0.85
   3 ?    4.7   0.2     0.083        47       1      10 [.      50      63 ..      50      66 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.6
                                      HHHHH CS
                           zf-C2H2 16 LkrHi 20
                                      L++H+
  gi|313125565|ref|YP_004035829.1| 14 LRSHM 18
                                      89999 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.057
                                      EETTTTE CS
                           zf-C2H2  2 kCpdCgk 8 
                                      +CpdCg+
  gi|313125565|ref|YP_004035829.1| 24 VCPDCGY 30
                                      7****96 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.083
                                      EEETTTT....EEE CS
                           zf-C2H2  1 ykCpdCg....ksF 10
                                      ++Cp Cg    ++F
  gi|313125565|ref|YP_004035829.1| 50 HVCPSCGsvrkRTF 63
                                      79*****5555554 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.17        95      22      26 .]      24      28 ..      18      29 .. 0.75
   2 ?    4.5   2.2     0.067        37      21      26 .]      50      55 ..      48      55 .. 0.91
   3 ?    5.5   1.7     0.033        18       4       7 ..      52      55 ..      50      58 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.17
                            zf-ACC 22 VCPkC 26
                                      VCP C
  gi|313125565|ref|YP_004035829.1| 24 VCPDC 28
                                      56655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.067
                            zf-ACC 21 yVCPkC 26
                                      +VCP+C
  gi|313125565|ref|YP_004035829.1| 50 HVCPSC 55
                                      8****9 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.033
                            zf-ACC  4 CpsC 7 
                                      CpsC
  gi|313125565|ref|YP_004035829.1| 52 CPSC 55
                                      5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.50u 0.35s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 425.32
//
Query:       gi|313125566|ref|YP_004035830.1|  [L=131]
Description: hypothetical protein Hbor_07940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0031   17.3   0.1     0.0062   16.3   0.1    1.5  1  HTH_23        Homeodomain-like domain
     0.0036   16.8   0.0     0.0054   16.3   0.0    1.2  1  GerE          Bacterial regulatory proteins, luxR family
     0.0055   16.3   0.2     0.0094   15.6   0.2    1.4  1  Sigma70_r4_2  Sigma-70, region 4
     0.0077   15.8   0.0      0.011   15.3   0.0    1.2  1  CENP-B_N      CENP-B N-terminal DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.021   14.9   0.0    1.5  1  HTH_7         Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.7e-06    0.0062      12      41 ..      38      68 ..      25      77 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-06
                            HTH_23 12 lllae.GlsvreIAreLgvsrrTvyrwlkry 41
                                       +  e G+s+r+IAre+ + ++Tv  ++++ 
  gi|313125566|ref|YP_004035830.1| 38 VAWSElGYSRRAIAREMEIGESTVKGYHEKA 68
                                      334456******************9887764 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.5e-06    0.0054       6      42 ..      33      69 ..      29      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-06
                                      HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH CS
                              GerE  6 RErevLrllaeGksnkeIAeelniSekTVkvhksnim 42
                                      +E++  ++   G+s   IA+e++i e TVk + + +m
  gi|313125566|ref|YP_004035830.1| 33 KEATAVAWSELGYSRRAIAREMEIGESTVKGYHEKAM 69
                                      78888899999*******************9999888 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   2.6e-06    0.0094      24      51 ..      42      69 ..      30      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
                                      TS---HHHHHHHHT--HHHHHHHHHHHH CS
                      Sigma70_r4_2 24 leglsykEIAellgisegtVksrlsRAr 51
                                      + g+s + IA++++i e+tVk +  +A+
  gi|313125566|ref|YP_004035830.1| 42 ELGYSRRAIAREMEIGESTVKGYHEKAM 69
                                      78*******************9998887 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.2e-06     0.011      19      41 ..      41      63 ..      33      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-06
                                      HHCTT-HHHHHHHHT--CCHHHH CS
                          CENP-B_N 19 leegeSkaelarrfnvpestlsd 41
                                      +e g S++++ar+  ++est+ +
  gi|313125566|ref|YP_004035830.1| 41 SELGYSRRAIAREMEIGESTVKG 63
                                      67789***************986 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.9e-06     0.021      14      44 ..      37      67 ..      30      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.9e-06
                                      GGSSTTTT--STTTSSSS---SSSS--SS-- CS
                             HTH_7 14 vvkLleeGisiskIAkevnisRsTvYRylad 44
                                      +v+  e G+s+++IA+e  i+ sTv+ y+++
  gi|313125566|ref|YP_004035830.1| 37 AVAWSELGYSRRAIAREMEIGESTVKGYHEK 67
                                      5556677******************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 803.83
//
Query:       gi|313125567|ref|YP_004035831.1|  [L=290]
Description: hypothetical protein Hbor_07950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1833.42
//
Query:       gi|313125568|ref|YP_004035832.1|  [L=232]
Description: nitroreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-31  108.7   0.0      5e-31  108.0   0.0    1.4  1  Nitroreductase  Nitroreductase family
    1.1e-07   31.6   0.0    0.00033   20.3   0.0    2.8  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   0.0   5.6e-35     5e-31       2     170 .]       8     183 ..       7     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 5.6e-35
                                       HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGG. CS
                    Nitroreductase   2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrke. 77 
                                        +RrS+ ++ de +p e++e+i e  r+aPs+ nlqpw+f+v++d+e+r++l+e a ++  + ea+ + +    k+ 
  gi|313125568|ref|YP_004035832.1|   8 TSRRSVHQYADEDLPTEVIESIFERVRHAPSSYNLQPWEFLVLTDDEKRQQLREVAYDQEHVTEAPVAVVVLGNKDp 84 
                                       69****************************************************************99999999889 PP

                                       ............HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-G CS
                    Nitroreductase  78 ............elklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpigg 142
                                                   +    + ++ ++ +   v+  + + + + ++++++ +++ ++ +aa+ l+ aA+++G++scp+gg
  gi|313125568|ref|YP_004035832.1|  85 sahadavlddwlA----KGYLPNEDARDAVL-GNIEGMADLPEAERRVWTVRSTTIAATELMNAAWEEGVASCPMGG 156
                                       9999999965552....33333322222222.355677777************************************ PP

                                       GGGGHHHHHHHHT-S...SEEEEEEEEE- CS
                    Nitroreductase 143 fdeaaeevrkllglp.deeeivvliavGy 170
                                       fd +   v + ++++ d++e+v+l+++Gy
  gi|313125568|ref|YP_004035832.1| 157 FDPEG--VLDTFDIDgDQYEPVMLVTLGY 183
                                       *****..*********99**********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.6e-08   0.00033     148     188 ..      13      54 ..       8      71 .. 0.78
   2 !    7.7   0.0   0.00026       2.4      96     155 ..     145     211 ..     138     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.6e-08
                                       HBSS-GGGS-HH.HHHHHHHHHTS--GGG----EEE.E-SSE CS
                    TM1586_NiRdase 148 lcevkeeelpew.fkeileaarlAPsAlNqqpwrfelkddde 188
                                       + ++ +e+lp++ +++i e +r APs+ N qpw+f + +dde
  gi|313125568|ref|YP_004035832.1|  13 VHQYADEDLPTEvIESIFERVRHAPSSYNLQPWEFLVLTDDE 54 
                                       667777788755278999*****************9877764 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00026
                                       HHTT-EEEEES--SST.............T-S-EEEEE-BS----......-----HHHHBSS-GGG CS
                    TM1586_NiRdase  96 talGlgtcWvggtykk.kkakvelkk.geklvivIalGyaktklv.....eakrkpleelcevkeee 155
                                        ++G+++c +gg  ++ +  ++++   + + v++++lGy++++        + r+p++e+++++e +
  gi|313125568|ref|YP_004035832.1| 145 WEEGVASCPMGGFDPEgVLDTFDIDGdQYEPVMLVTLGYPDDEAAdveneRKYRRPVDEIVHYDEFD 211
                                       5788999999987777655566777635678999*********966667688899******999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1489.65
//
Query:       gi|313125569|ref|YP_004035833.1|  [L=140]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-31  109.7   0.2    1.8e-31  109.5   0.2    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.2     1e-35   1.8e-31       1     141 []       1     140 []       1     140 [] 0.95

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 1e-35
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.HHHHHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.akaaae 76 
                                       m ++ l++vDgs++s +Al++A+ +  +    ++ll+vi p + g++  a+++  ee++e +++++     +++ + 
  gi|313125569|ref|YP_004035833.1|   1 MAHHLLLPVDGSPQSVEALRFAASEWGNA--NVTLLNVINPIEAGYRLSAFPAGSEEWYEAAREQASTVFeDAKDEL 75 
                                       7899********************87774..59******************************99987778888888 PP

                                       CTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  77 aggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                         + + ++ +e+g pa +ileva+e ++d iV+Gs+gr g+sr+llGSv+e+++r++p+pV+vV+
  gi|313125569|ref|YP_004035833.1|  76 SPEMDIDTRIEVGRPAATILEVAREGEVDHIVIGSHGREGISRILLGSVAEAIVRRSPVPVTVVH 140
                                       89999**********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 870.22
//
Query:       gi|313125570|ref|YP_004035834.1|  [L=618]
Description: ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-13   49.2   0.0    1.3e-12   48.3   0.0    1.4  1  DUF87            Helicase HerA, central domain
      1e-05   24.4   0.1      0.041   12.5   0.0    2.3  2  DUF853           Bacterial protein of unknown function (DUF85
     0.0016   18.5   0.0        1.1    9.3   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
     0.0029   16.6   0.0     0.0065   15.4   0.0    1.5  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.008   15.6   0.0      0.036   13.4   0.0    2.0  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.013   15.8   0.0       0.13   12.5   0.0    2.4  3  AAA_22           AAA domain
      0.018   15.2   0.1      0.061   13.5   0.0    1.9  2  AAA_33           AAA domain
      0.037   13.8   0.0        1.3    8.8   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
      0.049   12.7   0.0      0.093   11.8   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
      0.059   13.7   0.2       0.27   11.6   0.2    2.2  1  AAA_16           AAA ATPase domain
        0.1   12.7   0.0       0.28   11.4   0.0    1.7  1  HAS-barrel       HAS barrel domain
       0.14   11.9   0.0       0.37   10.5   0.0    1.7  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   8.9e-16   1.3e-12      15     224 ..     235     478 ..     231     481 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 8.9e-16
                             DUF87  15 yldlnklvtrHlAilgsTGsGKSntvavLleelle...........kkgatililDpHGEYgkal............ 68 
                                       y d + lv rH+++ g TGsGK++  + Ll++ll            + +  ++ +Dp+ EY+++             
  gi|313125570|ref|YP_004035834.1| 235 YTDGDPLVFRHTLVAGGTGSGKTHASKNLLRQLLDsdrtyemddgrDARMAVVQFDPQDEYAQMHddnpemtesvar 311
                                       668899***********************************999888888***************998666666666 PP

                             DUF87  69 .......ekllsekvkvitpspsa.........................kdkelkinpwsldpeelldlleeddkpa 113
                                              +               +                         ++ e++i+++  + +  l      ++++
  gi|313125570|ref|YP_004035834.1| 312 ryeregvA---------------HgghddtialvpkedgvpyggdnhraEQLEFTIPFSMARDRPWLVAGSSLNENQ 373
                                       66666653...............044444444444445589******99999****999888777665555599*** PP

                             DUF87 114 aavqrsvleealdqaka.keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdl 189
                                        ++++++l+++++q+ + ++++e l++ + ++ l+eel+    e+ +  + +  +++++++ + +   +    s+++
  gi|313125570|ref|YP_004035834.1| 374 FPALKELLRRFFRQYGDeGTYDEFLTFLD-DPALKEELH----ESGRVHEATFDAVKRRVRGVPNGVFDQ---SARP 442
                                       *************9997666666666666.677888888....777777777777777777777666555...9999 PP

                             DUF87 190 iallleklekegkitiidlsgvd.elaqqlvvsvil 224
                                       i++l  +l ++g +t+i+   ++ ++a++++v +++
  gi|313125570|ref|YP_004035834.1| 443 ITELDHELVRPGGLTVIPTYHLStSRAKEMFVLAVS 478
                                       99999999*********6655441555556776665 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00021      0.31      20      45 ..     242     267 ..     232     277 .. 0.88
   2 !   12.5   0.0   2.7e-05     0.041     247     315 ..     488     560 ..     401     566 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00021
                            DUF853  20 anrhGliaGatGtGktvtLqvlaesl 45 
                                       + rh l+aG tG Gkt + + l  +l
  gi|313125570|ref|YP_004035834.1| 242 VFRHTLVAGGTGSGKTHASKNLLRQL 267
                                       67***************999988776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.7e-05
                            DUF853 247 eLPevGdldkPklvfffdeahLLfndapka....llekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGn 315
                                       + P+   + +  lv+ +deah ++ da ++    ++ k     +  r    G++++tq+P+ + + v+ q+ +
  gi|313125570|ref|YP_004035834.1| 488 NTPDSQRIKQTPLVLGMDEAHNFLADADNVqarkVVSKFTEAAKQGRKERLGLFLITQDPQGVAEPVFKQVNT 560
                                       4555556666779*************9877222255666778899999********************99866 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0043       6.4      25      52 ..     244     271 ..     228     308 .. 0.89
   2 !    9.3   0.0   0.00072       1.1      98     159 ..     464     528 ..     381     539 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0043
                                       SEEEEEESTTSTHHHHHHHHHHHH-S.. CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkg 52 
                                       ++ l++  TG+GKT  + +l ++ll + 
  gi|313125570|ref|YP_004035834.1| 244 RHTLVAGGTGSGKTHASKNLLRQLLDSD 271
                                       57899999***********999999874 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00072
                                       ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHHHT--- CS
                            ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreilekfke 159
                                        + s  k+++v  ++s+  d +  +  + +  +++ +v+ +DEaH++ a++   + r+++ kf e
  gi|313125570|ref|YP_004035834.1| 464 LSTSRAKEMFVLAVSSMLIDDKLSNTPDSQRIKQTPLVLGMDEAHNFLADAdnvQARKVVSKFTE 528
                                       5567788999999999999998889999999999999***********98455677777777765 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.3e-06    0.0065      16      40 ..     244     268 ..     240     296 .. 0.90
   2 ?   -3.4   0.0       2.2   3.3e+03     294     314 ..     551     571 ..     548     575 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.3e-06
                     TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrair 40 
                                       +h+l++G+tGsGKt a ++llr++ 
  gi|313125570|ref|YP_004035834.1| 244 RHTLVAGGTGSGKTHASKNLLRQLL 268
                                       8*********************986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.2
                     TrwB_AAD_bind 294 aqsilslvntklilrvsdaet 314
                                       a+ +++ vntkl+l+  d+++
  gi|313125570|ref|YP_004035834.1| 551 AEPVFKQVNTKLVLNLGDEDA 571
                                       6778899********999876 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.4e-05     0.036      40      63 ..     244     267 ..     220     272 .. 0.83
   2 ?   -1.8   0.0       1.1   1.6e+03     193     241 ..     499     547 ..     486     548 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                                       .SEEEE--TTSSHHHHHHHHHHHH CS
                      FtsK_SpoIIIE  40 shllvaGatgsGKStalntLilSl 63 
                                        h+lvaG+tgsGK+ a ++L+  l
  gi|313125570|ref|YP_004035834.1| 244 RHTLVAGGTGSGKTHASKNLLRQL 267
                                       6***************99998665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                       EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES-- CS
                      FtsK_SpoIIIE 193 slvvivderieLrlaapkdssvlvedaivRlarkgraaglHlllatqrl 241
                                       +lv + de      +a + + + v + +++ a++gr+++l l l+tq +
  gi|313125570|ref|YP_004035834.1| 499 PLVLGMDEAHNFLADADNVQARKVVSKFTEAAKQGRKERLGLFLITQDP 547
                                       5555555555555555555566677777777888998888888888876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     9e-05      0.13       7      31 ..     245     269 ..     244     323 .. 0.76
   2 ?   -2.7   0.0       4.5   6.7e+03      52      70 ..     376     394 ..     343     427 .. 0.73
   3 ?   -0.3   0.0      0.83   1.2e+03      92     103 ..     499     511 ..     480     545 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqlde 31 
                                       +++v G +G+GKT+  ++ll+ql  
  gi|313125570|ref|YP_004035834.1| 245 HTLVAGGTGSGKTHASKNLLRQLLD 269
                                       7899******************953 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.5
                            AAA_22  52 sskdllrellralglelka 70 
                                        +k+llr+++r++g+e+ +
  gi|313125570|ref|YP_004035834.1| 376 ALKELLRRFFRQYGDEGTY 394
                                       5677777777777766655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.83
                            AAA_22  92 ielliiDEaqh.l 103
                                       + +l  DEa++ l
  gi|313125570|ref|YP_004035834.1| 499 PLVLGMDEAHNfL 511
                                       6789999999944 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.1e-05     0.061       3      70 ..     247     317 ..     246     321 .. 0.81
   2 ?   -3.4   0.0       6.8     1e+04      70      94 ..     507     532 ..     493     541 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrr.rlfgtdqqsktdytrvldrlyqilnelarkalsag 70 
                                       l+ G  GsGK++ +++ll++l     + + d+ r+ r+++ + +++ +y++  d+  ++++ +ar++ ++g
  gi|313125570|ref|YP_004035834.1| 247 LVAGGTGSGKTHASKNLLRQLLdsDRTYEMDDGRDaRMAVVQFDPQDEYAQMHDDNPEMTESVARRYEREG 317
                                       578999************99888777788888887777777888888889988888888888888777766 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.8
                            AAA_33  70 grnvildatnlsrrer.arflklarr 94 
                                       + n+++da n+++r+  ++f ++a++
  gi|313125570|ref|YP_004035834.1| 507 AHNFLADADNVQARKVvSKFTEAAKQ 532
                                       56778888888886664677776664 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00086       1.3      15      42 ..     244     270 ..     237     489 .. 0.72
   2 ?    2.9   0.0     0.057        85     125     159 ..     502     536 ..     472     544 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00086
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyet 42 
                                       ++ lva+ TGsGKT a +  +l++++++
  gi|313125570|ref|YP_004035834.1| 244 RHTLVAGGTGSGKTHA-SKNLLRQLLDS 270
                                       5789***********9.55555555554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.057
                                       EEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 125 lVlDEadrlldqgfsdfinrilnqlpqitcdgklq 159
                                       l +DEa+++l +    + +++++++ ++ ++g+++
  gi|313125570|ref|YP_004035834.1| 502 LGMDEAHNFLADADNVQARKVVSKFTEAAKQGRKE 536
                                       448*********999********998888887754 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.2e-05     0.093     132     167 ..     246     280 ..     242     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.2e-05
                             T2SSE 132 ilvsGgTgsGKttllyallkeinksderivtvEDpv 167
                                        lv+GgTgsGKt     ll ++ +s +r   + D +
  gi|313125570|ref|YP_004035834.1| 246 TLVAGGTGSGKTHASKNLLRQLLDS-DRTYEMDDGR 280
                                       59***********999999988887.6666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00018      0.27      20      88 ..     236     301 ..     229     538 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                            AAA_16  20 rsgrp...elvllsGesGvGKsslvrellralekd............ggiflrgkcdqlesaipysalaqalareel 81 
                                        +g+p   + +l+ G  G+GK+   + llr+l ++            +                +   + +++  + 
  gi|313125570|ref|YP_004035834.1| 236 TDGDPlvfRHTLVAGGTGSGKTHASKNLLRQLLDSdrtyemddgrdaR----------------M--AVVQFDPQDE 294
                                       5788888899**********************9994333333333222................2..3333333333 PP

                            AAA_16  82 lrqllde 88 
                                       ++q++d+
  gi|313125570|ref|YP_004035834.1| 295 YAQMHDD 301
                                       4444443 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.28      11      49 ..      88     125 ..      67     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                        HAS-barrel  11 sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrg 49 
                                       + ++++ +++ dv++G+y+ +++pd+e +++++t ++  
  gi|313125570|ref|YP_004035834.1|  88 RAFVTTGNRD-DVRLGKYLLVPYPDDELLFCRITALEYA 125
                                       4555555555.************************9994 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025      0.37       1      25 [.     246     268 ..     246     293 .. 0.81
   2 ?   -3.5   0.0       4.7     7e+03      71      96 ..     543     568 ..     515     570 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                   Viral_helicase1   1 ivvhGvpGcGKStlirkllrtslil 25 
                                       ++v+G  G+GK+++ ++llr+   l
  gi|313125570|ref|YP_004035834.1| 246 TLVAGGTGSGKTHASKNLLRQ--LL 268
                                       589*****************9..33 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.7
                   Viral_helicase1  71 ylllhaGyilllaalskaklvilfGD 96 
                                       +++ ++G+ + + ++ + klv+ +GD
  gi|313125570|ref|YP_004035834.1| 543 ITQDPQGVAEPVFKQVNTKLVLNLGD 568
                                       67788888899999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4071.03
//
Query:       gi|313125571|ref|YP_004035835.1|  [L=113]
Description: hypothetical protein Hbor_07990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.027   14.3   0.0    1.4  1  DUF5633   Family of unknown function (DUF5633)
      0.086   13.0   0.3       0.17   12.1   0.3    1.5  1  DUF2188   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF5633  Family of unknown function (DUF5633)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     3e-06     0.027       2      16 ..      72      86 ..      71      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-06
                           DUF5633  2 GYatkeeAekAAkkA 16
                                      G++t+e A++AAk+ 
  gi|313125571|ref|YP_004035835.1| 72 GFDTREQAVEAAKEH 86
                                      9************96 PP

>> DUF2188  Uncharacterized protein conserved in bacteria (DUF2188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   1.8e-05      0.17      25      46 ..      73      93 ..      71     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                           DUF2188 25 fdTqeeAieaArelAkeqggse 46
                                      fdT+e+A+eaA+e+ + q  + 
  gi|313125571|ref|YP_004035835.1| 73 FDTREQAVEAAKEHVRTQ-FAR 93
                                      9************99876.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 659.17
//
Query:       gi|313125572|ref|YP_004035836.1|  [L=418]
Description: nura domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-17   64.1   0.0    1.9e-17   63.8   0.0    1.1  1  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0     1e-21   1.9e-17       3     242 .]      77     385 ..      75     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1e-21
                                       EEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE......................... CS
                              NurA   3 vaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel......................... 54 
                                        ++ D++ + +++  +++++ +a a+++    +l  +   + v +++ +d +                         
  gi|313125572|ref|YP_004035836.1|  77 AHGLDSGTINPTTFKNGIVLDVAQAAMAAVPSDLDLHRHRSIVATTHANDSTlkldepwrklddgycrwriihaprv 153
                                       5799*******************************************99999****************999996666 PP

                                       ....HHHHHHHHHHHHHH........HHHHHCGGCCSCEEEEECSHHCCCH........HHHHHHHHHHHHHHHHHH CS
                              NurA  55 ....errirllmetlElk........lgallleekgedllllDGsligslv........efdelheeleyeeylysl 111
                                           e  +         +        ++al +     dll+lDG+l+++ +        e  +l  e +  e+++ +
  gi|313125572|ref|YP_004035836.1| 154 sryaEGVVH--------AlalylsesTHALEYADRVDDLLILDGPLYPKELlnwrdrdsELRNLSREAKPKEVVKNY 222
                                       644444444........3444446559999999**************************999*************** PP

                                       HHHTT-....TTCEEEEESS-SCTCCHCCC......S--HHHHCCHHCCHCH........---STTS-HHHHTT... CS
                              NurA 112 srllea....glnlvgvaKsfrskellnllletlligesisDiallgallrk........pgytspllkilrek... 173
                                       +rl+e+     ++l+g +K+  sk l+n + ++  + ++  D+a++ +ll++                         
  gi|313125572|ref|YP_004035836.1| 223 MRLVERfverDVPLCGFVKNPASKHLVNAVRDRGMEAPWADDTAFFTRLLERravgngetE------------Rrdt 287
                                       **************************************************66555533330............3334 PP

                                       ........................-HCCHHHHHH-.EEEEEEES..STTTTEEEEEHHHHHHCCHHHHHHHHHH... CS
                              NurA 174 ........................pllrealidke.iyfaYvrl..egggsilrleipaevstakdedvlslla... 220
                                                                +  e + d++ + +a+  +   ++++++r+e p+    a+de+v  +l+   
  gi|313125572|ref|YP_004035836.1| 288 seltftnwfvsrggsdrtfaadgdAYGLERNLDDDlYEVAFFVVydPRTDVLYRVEAPVA--FARDETVRRQLTtqm 362
                                       5666777777888888899999995555555555434444444445**********9988..5************** PP

                                       ...TTB-SSSBCCHHHHHHHHCC CS
                              NurA 221 .sqrlsisGYprpLalAhelaki 242
                                        ++ + ++G p++ a+A+ela+i
  gi|313125572|ref|YP_004035836.1| 363 lRDIAAERGPPEAVAKADELARI 385
                                       *********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2676.85
//
Query:       gi|313125573|ref|YP_004035837.1|  [L=219]
Description: haloacid dehalogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-20   74.3   0.0    1.6e-20   74.0   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    4.6e-13   49.9   1.7    6.7e-13   49.4   1.7    1.3  1  Hydrolase       haloacid dehalogenase-like hydrolase
    1.4e-09   37.9   0.3    3.4e-09   36.7   0.3    1.7  1  Hydrolase_like  HAD-hyrolase-like
    1.1e-06   29.2   1.8    1.5e-06   28.7   1.8    1.1  1  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.011   14.7   0.3       0.11   11.4   0.0    2.4  3  5_nucleotid     5' nucleotidase family


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   4.4e-24   1.6e-20       3     174 ..       8     183 ..       6     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 4.4e-24
                             HAD_2   3 FDlDgTlldteeliiqafnelleeyglselseeel.....rkliglslrellrklgeseeeeekieellrkyneekk 74 
                                       FDlD Tl+  +   +++++ ++ + g + ls++ +     ++l   +   ++r l +  e + + + +   y+e+  
  gi|313125573|ref|YP_004035837.1|   8 FDLDYTLAVPTRDRATILRDAATDAGAPPLSRDAYldahqQHLTQETRTPIFRTLLDGRESDTDPAAVATAYREHIA 84 
                                       99*****98888888888888888877766655441111145555566678899998888888************** PP

                             HAD_2  75 kkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklk 151
                                       +  + ++d++ ++L eL + +y++g+ T++ r a+++kl+ lg+++ Fdv +++ +    KP+ + +e++l+ l+++
  gi|313125573|ref|YP_004035837.1|  85 D-ALVLIDNAAQFLAEL-RGQYTVGLLTNGPRVAQRDKLDTLGWNDAFDVALVTGELPAGKPNSAAFEALLDALGTD 159
                                       *.***************.99********************************************************* PP

                             HAD_2 152 keeviyvGDsp.tDieaakkagik 174
                                       ++e+ yvGD    Di +a +ag+ 
  gi|313125573|ref|YP_004035837.1| 160 AAETAYVGDDVdADIGGAANAGLV 183
                                       ***********9**********75 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   1.7   1.9e-16   6.7e-13      67     210 .]      35     181 ..       3     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.9e-16
                                       E.....HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTE.EE CS
                                       x.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                         Hydrolase  67 g.....ayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagi.ev 137
                                             ay+   ++ lt+++ +p ++   +  +s+   +a+          iad l + + aa+++a+L+  g   v
  gi|313125573|ref|YP_004035837.1|  35 PplsrdAYLDAHQQHLTQETRTPIFRTLLDGRESDTDPAAVA---TAYREHIADALVLIDNAAQFLAELR--GQyTV 106
                                       255555667777777777777788888888888888888888...344455678888*************..6669* PP

                                       EEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 138 vlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                       +llt++ +  ++  ++ lG +d+fd+ + + +   +kp+  +++a+++ L+ + +e+a VGD v  D+ ++a+Ag
  gi|313125573|ref|YP_004035837.1| 107 GLLTNGPRVAQRDKLDTLGwNDAFDVALVTGELPAGKPNSAAFEALLDALGTDAAETAYVGDDVDaDIGGAANAG 181
                                       ********9999*************************************************************98 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.3   9.4e-13   3.4e-09       2      48 ..     141     187 ..     140     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 9.4e-13
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEE CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLV 48 
                                       +gKP+  ++++ l +lg d +e+ ++GD++++Di gA naG+  + V
  gi|313125573|ref|YP_004035837.1| 141 AGKPNSAAFEALLDALGTDAAETAYVGDDVDADIGGAANAGLVPIQV 187
                                       69***************************************987765 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   1.8   4.3e-10   1.5e-06       2     180 ..       7     169 ..       6     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.3e-10
                               HAD   2 lfDfDgTL.ldg.dslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaeler 75 
                                        fD+D TL +++ d ++ l+++ +  gap+l r +   ++++++ +  r         ++ ll g + + + a ++ 
  gi|313125573|ref|YP_004035837.1|   7 GFDLDYTLaVPTrDRATILRDAATDAGAPPLSRDAYLDAHQQHLTQETR------TPIFRTLLDGREsDTDPAAVAT 77 
                                       6*******888899999****9999999999888888888888333333......3566777788887********* PP

                               HAD  76 fvaevirpk.lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltge..lglegkpv 149
                                       +++e+i+ + +l   a ++la  ++  ++v ++++g+r   + +l+ lg     +  ++v   +tge  +g +++  
  gi|313125573|ref|YP_004035837.1|  78 AYREHIADAlVLIDNAAQFLA-ELRGQYTVGLLTNGPRVAQRDKLDTLG----WNDAFDVA-LVTGElpAGKPNS-- 146
                                       **999999953448*******.55899**********************....66655555.7777722223333.. PP

                               HAD 150 rgegkvaalrewlaaegegidleevvayGDs 180
                                             aa ++       g d +e+ ++GD 
  gi|313125573|ref|YP_004035837.1| 147 ------AAFEA--LLDALGTDAAETAYVGDD 169
                                       ......44444..333477788889999995 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.1e-05      0.11      11      25 ..       2      16 ..       1      26 [. 0.87
   2 ?   -1.5   0.0      0.25     9e+02     234     251 ..     123     140 ..     114     146 .. 0.80
   3 ?    0.1   0.0      0.08   2.9e+02     291     315 ..     150     174 ..     145     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                                      T--EEEE-TBTTTBE CS
                       5_nucleotid 11 kIkvvGFDmDYTLaq 25
                                       I++vGFD DYTLa+
  gi|313125573|ref|YP_004035837.1|  2 TIRAVGFDLDYTLAV 16
                                      599**********97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.25
                                       T--GGGGESEEEES--TT CS
                       5_nucleotid 234 kkswrdlFDvvivkarKP 251
                                       +  w+d FDv  v  + P
  gi|313125573|ref|YP_004035837.1| 123 TLGWNDAFDVALVTGELP 140
                                       567*******99987665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.08
                                       HHHHHHTT--GGGEEEEESS--S-H CS
                       5_nucleotid 291 kelekllgvkgkevLYvGDhiygDi 315
                                       + l + lg++ +e  YvGD + +Di
  gi|313125573|ref|YP_004035837.1| 150 EALLDALGTDAAETAYVGDDVDADI 174
                                       56778889999999*******9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1433.75
//
Query:       gi|313125574|ref|YP_004035838.1|  [L=123]
Description: hypothetical protein Hbor_08020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.029   13.9   0.0    1.2  1  MR_MLE_C  Enolase C-terminal domain-like


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-06     0.029     124     157 ..      62      95 ..      52     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-06
                                       EEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSC CS
                          MR_MLE_C 124 ivqpdvsrvgGitearkvaalaeafgvpvapHsg 157
                                       +vqpd +rv  +te+ +va++ae+ g++v p ++
  gi|313125574|ref|YP_004035838.1|  62 FVQPDRARVEFVTEMATVADVAEQEGLRVRPKAV 95 
                                       79***************************99984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 803.73
//
Query:       gi|313125575|ref|YP_004035839.1|  [L=148]
Description: hypothetical protein Hbor_08030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-51  173.5   0.1    2.2e-51  173.3   0.1    1.0  1  DUF2240   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.3   0.1   1.2e-55   2.2e-51       2     143 ..       5     143 ..       4     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 173.3 bits;  conditional E-value: 1.2e-55
                           DUF2240   2 lkiavaapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpde 78 
                                       l +ava+pfk++++d+l+e +fv+alsldr+w+spdqak+l+d a+ +gL++++dg++v++fd+a+v++P++++pd+
  gi|313125575|ref|YP_004035839.1|   5 LDVAVAVPFKQRGTDQLGEGEFVVALSLDRDWFSPDQAKRLIDVAAGRGLVSRDDGNVVAEFDPAGVTVPEDYEPDQ 81 
                                       789************************************************************************** PP

                           DUF2240  79 ellkekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddliee 143
                                       ++l+e+s+ferilda++a  g +k+++va +n++q++l+  v+veaaa ++ak++gv+v d++++
  gi|313125575|ref|YP_004035839.1|  82 SILREQSAFERILDALVA-DGHDKQSAVADVNDVQRRLG--VSVEAAAALYAKQHGVEVGDAAQK 143
                                       ******************.999*****************..********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 984.09
//
Query:       gi|313125576|ref|YP_004035840.1|  [L=125]
Description: 30S ribosomal protein S8e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-33  114.6   2.4    4.2e-33  114.4   2.4    1.0  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   2.4   2.4e-37   4.2e-33       4     137 .]       2     122 ..       1     122 [. 0.97

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 2.4e-37
                                       BXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEE CS
                     Ribosomal_S8e   4 srdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlg 80 
                                       + ++++krk tGg+ ++ +kk++++lgr++++t +g+ r++vv  rg+++k ral ++ a+v++   + + +++I +
  gi|313125576|ref|YP_004035840.1|   2 KDQGRSKRKRTGGRLRPSHKKKRYQLGREPTETTVGEPRFRVVDSRGNQKKLRALSTNVAQVAD--GGDVSEAEIEN 76 
                                       5799**********************************************************99..5778899**** PP

                                       EECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  81 VkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       V++npsn +y+r++++tKgaiie+++++           A+vtsrPgqdG+vnavl+
  gi|313125576|ref|YP_004035840.1|  77 VVDNPSNVNYIRRNIITKGAIIETSAGR-----------ARVTSRPGQDGQVNAVLV 122
                                       ****************************...........****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 768.05
//
Query:       gi|313125577|ref|YP_004035841.1|  [L=333]
Description: phosphate uptake regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-23   80.7   9.1    4.8e-18   65.4   1.3    2.4  2  PhoU            PhoU domain
    4.8e-11   42.3   0.0    1.1e-10   41.2   0.0    1.7  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.47   10.5   5.5       0.43   10.6   0.4    3.1  3  HisKA           His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   1.3     8e-22   4.8e-18       2      88 ..     137     226 ..     136     227 .. 0.81
   2 !   19.6   1.3   1.6e-07   0.00094       2      88 ..     243     324 ..     242     325 .. 0.78

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 8e-22
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HGG-SHHHHHH.HHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak....rqplaedlrel.lsllriar 73 
                                        rm  i+++ml+da+ a++e d+++ar+vi+rdd++drl + ++r  ++a  +     ++l+   re+ +++ ++ar
  gi|313125577|ref|YP_004035841.1| 137 TRMRLISLSMLEDAIAAIAELDDDMARDVIQRDDDVDRLWMVVSRI-FRATLRtpkaAEELGL-PREVcFDYQSAAR 211
                                       79*************************************7766555.6666431222444444.5555599****** PP

                                       HHHHHHHHHHHHHHH CS
                              PhoU  74 dlERigDhavniaer 88 
                                        lERigDha++ia  
  gi|313125577|ref|YP_004035841.1| 212 QLERIGDHATKIAHL 226
                                       *************75 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHHHHHHHHHHHCT-H....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdt....elarevierddeidrlekeiersllealak.rqplaedlrellsllriar 73 
                                       +++   +++ +dd ++al+++d      la++ +e+ ++id+  ++i++  l+ l   r +l         l  i+ 
  gi|313125577|ref|YP_004035841.1| 243 EELYMEARKVVDDGMDALFTDDPdeasRLANDARENVQQIDERARKIDEL-LRDLDPaRAQL---------LGLIVD 309
                                       5677788999************7455577777778899999999999877.88884322222.........3469** PP

                                       HHHHHHHHHHHHHHH CS
                              PhoU  74 dlERigDhavniaer 88 
                                       +  R +D+  niae 
  gi|313125577|ref|YP_004035841.1| 310 SVSRSADYGGNIAET 324
                                       *************95 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   1.8e-14   1.1e-10       1      43 [.       9      51 ..       9      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.8e-14
                                      EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHH CS
                    MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilrplks 43
                                      +++G+++ v+iPk+++ e+ +++G+eve++++gd++ l+p  +
  gi|313125577|ref|YP_004035841.1|  9 VTGGSTYTVSIPKDWATENSVSAGSEVEFYPEGDSLFLTPRTE 51
                                      699***********************************99865 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4      0.12   7.3e+02      37      63 ..      95     129 ..      82     148 .. 0.70
   2 ?   -1.1   0.0      0.33     2e+03      36      57 ..     208     229 ..     199     237 .. 0.77
   3 ?   10.6   0.4   7.2e-05      0.43      31      64 ..     269     301 ..     239     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                                       CHHHHHHHHHHHH........HHHHHHHHHHHHCC CS
                             HisKA  37 lkeyletiesear........rldhlvedlLdlsr 63 
                                       +++ ++ + ++          r + ++ dlLd s 
  gi|313125577|ref|YP_004035841.1|  95 QRRTIREATQSLVglevleetRDRVVIRDLLDSSE 129
                                       44444444444446666666677778888887665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.33
                                       SCHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  36 elkeyletiesearrldhlved 57 
                                       + +++le+i ++a  + hl  +
  gi|313125577|ref|YP_004035841.1| 208 SAARQLERIGDHATKIAHLTLN 229
                                       5678899999999999888755 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 7.2e-05
                                       .T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
                             HisKA  31 gklteelkeyletiesearrldhlvedlLdlsri 64 
                                        +l  + +e++++i + ar +d+l+ dl d +r 
  gi|313125577|ref|YP_004035841.1| 269 SRLANDARENVQQIDERARKIDELLRDL-DPARA 301
                                       5688999********************8.99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 1806.34
//
Query:       gi|313125578|ref|YP_004035842.1|  [L=372]
Description: phosphate ABC transporter substrate-binding protein, phot family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-21   77.6   4.0    2.7e-21   76.5   1.9    2.3  2  PBP_like_2  PBP superfamily domain
    8.3e-11   41.4   0.0    1.3e-10   40.8   0.0    1.2  1  PBP_like    PBP superfamily domain
  ------ inclusion threshold ------
       0.28   11.1   6.0       0.49   10.3   6.0    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.5     0.063   3.7e+02     202     251 ..      50      74 ..      11     106 .. 0.51
   2 !   76.5   1.9   4.6e-25   2.7e-21      41     275 ..     110     334 ..      50     340 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.063
                        PBP_like_2 202 vtngagkfvlptaataasalkvakiasnplawslqpveeniadgayPlsr 251
                                        t                         +++++s+ p+ ++  ++ yP+++
  gi|313125578|ref|YP_004035842.1|  50 ST-------------------------SSDSGSVTPLTADGSSTVYPVTN 74 
                                       22.........................22222333333222233333332 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 4.6e-25
                        PBP_like_2  41 n..................yastGSgagikalrngdvdfagsdrplteseia.agwaangaggliqvpvaigaialv 98 
                                                          +  + Sg g+++l++g+vd++ s++p+ ++ +  a  +     +++ + va++a  +v
  gi|313125578|ref|YP_004035842.1| 110 AglygfegnddgtppfrtsIGLSHSGVGLEKLKKGQVDIGDSSAPVGAE-FPdASDDE--LEPFTDHVVAVDAQPVV 183
                                       044444455555455444478889**********************666.76444444..56*************** PP

                        PBP_like_2  99 vnkd...npln.lsreaLakIfsgkItnWnd..vlglpadgpIkvvhrsdgsgttflfstalaeqgpwtasgigasg 169
                                       v+k+    +++ l+ e+L++I++g+It+W++  +  +p d+ I+ v r +gsgt ++f  +++  ++++ sg+   +
  gi|313125578|ref|YP_004035842.1| 184 VSKEiydAGVTkLTLEQLQDIYRGEITKWSEidGYDGP-DKEIQAVGRAEGSGTDTAFRLNVLGDPDASMSGVDIRK 259
                                       ****99977778********************998988.************************99999987776433 PP

                        PBP_like_2 170 ..segvasav.snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqpveenia 243
                                         + +v++ v + n+a +y+ +a+  ++               v+p       ++          ++ + +  en +
  gi|313125578|ref|YP_004035842.1| 260 gqNQQVKTLVsKSNNAVAYLALAFVDEEA--------------VPPV----SLEI----------EGTTYTYGENLG 308
                                       5688888888677**********999663..............4444....2222..........335666777888 PP

                        PBP_like_2 244 dgayPlsrftyiivyqpyayhgnnaalakaFl 275
                                       +++yPlsr++++++ + +      +++  aFl
  gi|313125578|ref|YP_004035842.1| 309 AKEYPLSRDLHAYTWDGT------SKKEAAFL 334
                                       899999999999988876......55555555 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   2.1e-14   1.3e-10       9     157 ..     123     287 ..     118     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.1e-14
                                       TTCEEEEEES-HHHHHHHHHTTS-SEEEESS-.......--CCCHHCCCCCEEEEEEEEEEE........E-CC-HC CS
                          PBP_like   9 pgvrvavanvGsggGlkalrageadiagshll.......dketeeynapalrkaldgievvl........vnlarre 70 
                                       p +r +++ + sg Gl++l++g++di+ s+ +       ++++e   +     a+d+++vv+        v+ ++ e
  gi|313125578|ref|YP_004035842.1| 123 PPFRTSIGLSHSGVGLEKLKKGQVDIGDSSAPvgaefpdASDDELEPFTDHVVAVDAQPVVVskeiydagVTKLTLE 199
                                       67788899999********************9777777522222233333345678888777777777777777778 PP

                                       HCCCCHCCHHHS--BGGGC.....-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCC CS
                          PBP_like  71 qglvvakgnpkkitnwkdl.....adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaa 142
                                       q   +++g   +it+w+++     +d++++ v+R++GSGt   f   + +     +s++g++    ++++v++ V++
  gi|313125578|ref|YP_004035842.1| 200 QLQDIYRG---EITKWSEIdgydgPDKEIQAVGRAEGSGTDTAFRLNVLG--DPDASMSGVDIRKGQNQQVKTLVSK 271
                                       88888888...8**********999********************99966..4779********************* PP

                                       ETTCCEC.CCGG-HCC CS
                          PBP_like 143 gradvgv.gieavaee 157
                                        + +v++ +++ v+ee
  gi|313125578|ref|YP_004035842.1| 272 SNNAVAYlALAFVDEE 287
                                       **99998787777765 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   6.0   8.2e-05      0.49       2      25 ..       1      23 [.       1      25 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.2e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      +SRR F  +++A++ A+++g c++
  gi|313125578|ref|YP_004035842.1|  1 MSRRKFVVAAGATGLAGLAG-CSG 23
                                      8************9777555.543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1943.24
//
Query:       gi|313125579|ref|YP_004035843.1|  [L=362]
Description: phosphate ABC transporter substrate-binding protein, phot family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-20   71.9   2.8    4.9e-19   69.1   2.8    2.2  1  PBP_like_2  PBP superfamily domain
    2.1e-11   43.3   0.1    3.4e-11   42.6   0.1    1.2  1  PBP_like    PBP superfamily domain
  ------ inclusion threshold ------
       0.27   11.2   0.2       0.27   11.2   0.2    1.6  2  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   2.8   8.1e-23   4.9e-19       5     276 ..      48     326 ..      29     331 .. 0.72

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 8.1e-23
                        PBP_like_2   5 eatsvgeifgaGsttpapalrkladafekaapgakvn.......................................y 42 
                                       e+t+   +++ Gs+t++p+ +k+   + +++p+a+ +                                       +
  gi|313125579|ref|YP_004035843.1|  48 ESTEL--LKAGGSSTVYPIANKAG-SYWNSNPPAEDEeywgptqygidtdenladywagrygfesdsgssvpftvsV 121
                                       44555..77777777777777775.4333334444222333334455555555555566666666666666665558 PP

                        PBP_like_2  43 astGSgagikalrngdvdfagsdrplteseia.agwaangaggliqvpvaigaialvvnkd...npln.lsreaLak 114
                                         + Sg+g++++rn++ d++ +++p++++  + + + + +  +++++ v+++a  +vv+k+    +++ l+++ +++
  gi|313125579|ref|YP_004035843.1| 122 GLSHSGTGLEKVRNEQLDIGNASAPVSAE--LpD-ASQEELDKFVNHVVGVDAQPIVVSKEiydAGVTkLTADKIRA 195
                                       9999**********************999..424.4444479*******************99977778******** PP

                        PBP_like_2 115 IfsgkItnWnd..vlglpadgpIkvvhrsdgsgttflfstalaeqgpwtasgigasg..segvasav.snngaigyv 186
                                       I++g+ItnW++    g+p d  I+ + rs gsgt ++f  +l+    ++  g+ + +  + +v+++v + n+ai+y 
  gi|313125579|ref|YP_004035843.1| 196 IYRGEITNWSEidSYGGP-DREIQTIGRSVGSGTDTAFRANLLGDSEAEMPGVDVRKgqNQQVKTTVsKSNNAIAYM 271
                                       ***********9866766.***********************9885555555554447899999999677******* PP

                        PBP_like_2 187 svaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqpveeniadgayPlsrftyiivyqpyay 263
                                        +a+  ++ + +++                   ++            ++ +  en  d  yPl r+++ ++y+++  
  gi|313125579|ref|YP_004035843.1| 272 ALAFVDDS-VPAISL------------------EVGG----------KTYTRGENLSDPGYPLARDLHCYTYEDT-- 317
                                       ***99877.444443..................1111..........2222335566788888888888888877.. PP

                        PBP_like_2 264 hgnnaalakaFld 276
                                           ++   aFl 
  gi|313125579|ref|YP_004035843.1| 318 ----SKREAAFLR 326
                                       ....555555555 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1   5.6e-15   3.4e-11      11     155 ..     117     277 ..     111     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 5.6e-15
                                       CEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS..... CS
                          PBP_like  11 vrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkk..... 82 
                                       ++v+v+ + sg+Gl+++r+++ di++++ + +  e  +a+  +++ld+  +v   +  ++q +vv k+   +     
  gi|313125579|ref|YP_004035843.1| 117 FTVSVGLSHSGTGLEKVRNEQLDIGNASAPVS-AELPDAS--QEELDK--FVNHVVGVDAQPIVVSKEIYDAgvtkl 188
                                       5789999**********************965.2233333..333444..455555556666666666555345555 PP

                                       ............--BGGGC.....-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCC CS
                          PBP_like  83 ............itnwkdl.....adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaa 142
                                                   itnw+++     +d++++ ++R  GSGt   f   l +   s+++++g++    ++++v+++V++
  gi|313125579|ref|YP_004035843.1| 189 tadkiraiyrgeITNWSEIdsyggPDREIQTIGRSVGSGTDTAFRANLLG--DSEAEMPGVDVRKGQNQQVKTTVSK 263
                                       555666677777*******9999999**********************65..599********************** PP

                                       ETTCCEC.CCGG-H CS
                          PBP_like 143 gradvgv.gieava 155
                                        + ++++ +++ v+
  gi|313125579|ref|YP_004035843.1| 264 SNNAIAYmALAFVD 277
                                       **999986666665 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   4.5e-05      0.27       2      25 ..       6      27 ..       5      28 .. 0.88
   2 ?   -3.9   0.3       2.5   1.5e+04       8      12 ..      53      57 ..      52      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.5e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      + RR++L   ++a+  a l+gc +
  gi|313125579|ref|YP_004035843.1|  6 VHRRSLLV--GGAGLVASLAGCIS 27
                                      68******..99999999999976 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.5
                        TAT_signal  8 LKgsA 12
                                      LK+++
  gi|313125579|ref|YP_004035843.1| 53 LKAGG 57
                                      99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2005.71
//
Query:       gi|313125580|ref|YP_004035844.1|  [L=351]
Description: phosphate ABC transporter membrane protein 1, phot family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-18   65.9  13.3    3.6e-18   65.9  13.3    2.9  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        0.4   10.7   2.3        1.4    9.0   2.3    2.1  1  YpmT          Uncharacterized YmpT-like


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   9.8      0.35   3.1e+03     116     175 ..      26      89 ..      19      97 .. 0.74
   2 ?   -4.2   9.8       1.4   1.2e+04     114     169 ..      72     138 ..      64     152 .. 0.44
   3 !   65.9  13.3   4.1e-22   3.6e-18       2     183 ..     143     343 ..     138     346 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.35
                      BPD_transp_1 116 lafggllggavlleflgswpGlgtllleailgydyseis....nggvlalviavlllnlvadil 175
                                       la+ ++l +++++  +  +p +  l+  a+ +y y+e +    ++ + + ++++l l++v+ ++
  gi|313125580|ref|YP_004035844.1|  26 LALLAVLLAFLVAAQFVVYPFVVFLVSVAYGWYAYQESTakilMFFTTVSTVIILGLITVYLFI 89 
                                       5666666666666666668889999999999999999999988777777777777777776666 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 1.4
                      BPD_transp_1 114 lilafggllggavlleflgswpGlgtllleailgydyseis...........nggvlalviavllln 169
                                         ++ +++lg  ++ +f+ s p++ t+ l+++l  + +++            ++g++ ++i+ +++ 
  gi|313125580|ref|YP_004035844.1|  72 TTVSTVIILGLITVYLFIKSIPAFRTMGLDILLKTNQPLWErasntyslapmIWGTVLTTIIAMVIA 138
                                       3334444444444555555555555555555444444444444544445554233333333333322 PP

  == domain 3  score: 65.9 bits;  conditional E-value: 4.1e-22
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....vilsilghlilp.viillllsaapyvrlir 72 
                                       i +++++     k+ ++++ p i++l ++Ps+v ++l  +v+     + l+   ++ l+ + i++ ++a+p+v+ + 
  gi|313125580|ref|YP_004035844.1| 143 IAGALFISEIAPKWAREIIKPAIEMLAGIPSIVYGFLGWVVVteyfySELQLSNFSSLMvAGIMVGVMALPTVVSVA 219
                                       4445555577789************************888888999977777777777777889999********** PP

                      BPD_transp_1  73 raalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..........lgt 139
                                       ++a+ s+p + +  ++alGas+wq+++ v++P a++ i + +il +g+++g+++++  +++ +            gt
  gi|313125580|ref|YP_004035844.1| 220 EDAIASVPGSTKDGSLALGASDWQTIKSVTFPTAFSGISAAVILGVGRAVGETMAATVILGHQQafpdplydvwEGT 296
                                       ************************************************************76668999999999777 PP

                      BPD_transp_1 140 llleailgydyseis....nggvlalviavlllnlvadilqrlldprv 183
                                        +l+++++++y  ++     ++++a+vi++l +++ + i  ++++ r 
  gi|313125580|ref|YP_004035844.1| 297 ETLTSLIASQYGIATgtqlSALFAAGVILFLTVLT-LSIGSQIIEDRR 343
                                       77777777777766677854444444444444444.444444554444 PP

>> YpmT  Uncharacterized YmpT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.3   0.00016       1.4       4      28 ..      40      64 ..      37      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00016
                              YpmT  4 iyvyFsllsllfslyFGglayqhlv 28
                                       +v + ++ +l+s+ +G++ayq+  
  gi|313125580|ref|YP_004035844.1| 40 QFVVYPFVVFLVSVAYGWYAYQEST 64
                                      689999***************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 1968.62
//
Query:       gi|313125581|ref|YP_004035845.1|  [L=546]
Description: phosphate ABC transporter membrane protein 2, phot family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-24   85.3   9.8    4.3e-24   85.3   9.8    4.8  4  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
        1.7    8.3   6.5       0.41   10.3   0.7    3.2  2  DUF3149          Protein of unknown function (DUF3149)
          4    7.3   7.0        1.5    8.7   2.1    3.1  2  Phage_holin_2_3  Bacteriophage holin family HP1


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.5   5.6         3   1.8e+04     117     169 ..      30      74 ..      16      83 .. 0.44
   2 ?  -12.5  15.9         3   1.8e+04      48      48 ..     180     180 ..      90     250 .. 0.54
   3 ?   -2.0   0.3      0.42   2.5e+03      32      70 ..     278     316 ..     272     319 .. 0.58
   4 !   85.3   9.8   7.2e-28   4.3e-24       2     183 ..     318     544 ..     317     546 .] 0.90

  Alignments for each domain:
  == domain 1  score: -5.5 bits;  conditional E-value: 3
                      BPD_transp_1 117 afggllggavlleflgswpGlgtllleailgydyseisnggvlalviavllln 169
                                       a+g+++ g + +  ++      t++++ ++++dy     g+ +++v +vl+ +
  gi|313125581|ref|YP_004035845.1|  30 ALGIAVAGIATIFGVF----DLTTTVSGLSAFDYF----GIGFVGVGVVLVGI 74 
                                       2333333333333333....334444445555555....44444444444444 PP

  == domain 2  score: -12.5 bits;  conditional E-value: 3
                      BPD_transp_1  48 i 48 
                                       +
  gi|313125581|ref|YP_004035845.1| 180 Y 180
                                       0 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.42
                      BPD_transp_1  32 sfvlaillvlvfvilsilghlilpviillllsaapyvrl 70 
                                        +++  ++v+  v l    ++i+p+i+ +++  ++ v++
  gi|313125581|ref|YP_004035845.1| 278 LVWFYWPFVMEGVALMTEINGIFPAIVGTVWVVFGAVVF 316
                                       555555555444445555566666666666666665554 PP

  == domain 4  score: 85.3 bits;  conditional E-value: 7.2e-28
                      BPD_transp_1   2 illGilaa.....lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirr 73 
                                       i+lG+ aa     ++ +++++kl+ + ++ l+s+Ps+v +++ ++++v   + +++ l+++++l ++++p+v+++ r
  gi|313125581|ref|YP_004035845.1| 318 IPLGVGAAvflteYAERGWFTKLVEISTDGLWSTPSIVYGLFGLAFLVPRLGNTTSLLSGMLVLGFMMLPLVVITSR 394
                                       677777777777**************************999999888888899999999****************** PP

                      BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydy 150
                                       +al+s+p+d++ a+ alG+++w++++ vvlP+a+p +itg+il +g++ g+++ +++++    +++++ +       
  gi|313125581|ref|YP_004035845.1| 395 EALKSVPDDYRDASAALGVGKWETIKSVVLPAAMPGVITGAILGIGRIAGETAPILLVM----VSDPFPSRATDVFA 467
                                       ***********************************************************....77777777777777 PP

                      BPD_transp_1 151 seis............................................nggvlalviavlllnlvadilqrlldprv 183
                                       +e +                                            +g++l+l+++vl + +v      ++ +++
  gi|313125581|ref|YP_004035845.1| 468 PEFAfvsdfpfvhaqvidpnallqptsalpyqlyaiitagvgqresfaWGTALVLLLVVLSFYVVGIGSRMYFRRKL 544
                                       76667777777779999999999999999999999999999999999999999999999999999888887777776 PP

>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.7      0.71   4.2e+03       9      23 ..      29      44 ..      27      45 .. 0.67
   2 ?   10.3   0.7   6.9e-05      0.41       7      23 ..     224     240 ..     223     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.71
                           DUF3149  9 vGLl.SliVIvftigm 23
                                      v L   +++I+ ++g+
  gi|313125581|ref|YP_004035845.1| 29 VALGiAVAGIATIFGV 44
                                      5566677788888875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.9e-05
                           DUF3149   7 sdvGLlSliVIvftigm 23 
                                       + vG lSl+VI++++++
  gi|313125581|ref|YP_004035845.1| 224 NAVGMLSLLVILVAFVV 240
                                       78*************97 PP

>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.1   0.00024       1.5       4      32 ..      16      44 ..      13      55 .. 0.81
   2 ?   -3.6   0.2       1.6   9.7e+03      10      23 ..     348     361 ..     348     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00024
                   Phage_holin_2_3  4 sslaAYisSava.vvlGllsLseWAiviGI 32
                                      ssl+AY+sSav+ v lG+   +  A+++G+
  gi|313125581|ref|YP_004035845.1| 16 SSLLAYVSSAVTaVALGI-AVAGIATIFGV 44
                                      89********86256999.99999999997 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.6
                   Phage_holin_2_3  10 isSavavvlGllsL 23 
                                       ++S+  +v Gl+ L
  gi|313125581|ref|YP_004035845.1| 348 LWSTPSIVYGLFGL 361
                                       58999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 3022.35
//
Query:       gi|313125582|ref|YP_004035846.1|  [L=302]
Description: phosphate ABC transporter ATP-binding protein, phot family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-31  107.1   0.0    1.6e-30  106.4   0.0    1.3  1  ABC_tran      ABC transporter
    1.1e-12   48.3   0.0      3e-06   27.3   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.1e-08   32.1   0.2    5.5e-06   26.0   0.2    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.1e-07   30.5   0.0    2.7e-05   24.0   0.0    2.3  2  AAA_15        AAA ATPase domain
    5.3e-05   23.5   0.0    0.00022   21.5   0.0    2.0  1  AAA_22        AAA domain
    0.00032   20.4   0.0    0.00074   19.2   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
    0.00033   21.1   0.2    0.00093   19.6   0.2    1.8  1  AAA_16        AAA ATPase domain
    0.00074   19.5   0.0     0.0014   18.6   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
     0.0026   18.3   0.1     0.0043   17.6   0.1    1.6  1  AAA_23        AAA domain
     0.0029   17.2   0.1      0.014   15.0   0.0    2.0  2  AAA_25        AAA domain
     0.0089   16.0   0.0      0.015   15.3   0.0    1.3  1  Rad17         Rad17 P-loop domain
  ------ inclusion threshold ------
      0.041   13.0   0.0      0.065   12.4   0.0    1.3  1  G-alpha       G-protein alpha subunit
      0.042   14.4   0.1       0.17   12.4   0.0    2.1  2  AAA_18        AAA domain
      0.044   14.0   0.0       0.11   12.7   0.0    1.7  1  AAA_33        AAA domain
      0.056   13.2   0.1       0.97    9.1   0.0    2.1  2  AAA_30        AAA domain
      0.058   12.6   0.0      0.074   12.2   0.0    1.3  1  NB-ARC        NB-ARC domain
      0.065   13.0   0.0       0.11   12.2   0.0    1.4  1  PRK           Phosphoribulokinase / Uridine kinase family
      0.098   12.6   0.0       0.17   11.8   0.0    1.3  1  DeoRC         DeoR C terminal sensor domain
       0.11   12.9   0.1       0.53   10.7   0.0    2.0  2  RNA_helicase  RNA helicase
       0.16   10.7   0.0        2.8    6.7   0.0    2.1  2  Adeno_IVa2    Adenovirus IVa2 protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.0   1.8e-33   1.6e-30       1     136 [.      58     225 ..      58     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 1.8e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepql 70 
                                       l+++s+++ e +++a++G++G+GKSt+l++l ++ +        G+++++++++ +  ++l +lrk++g ++q p+ 
  gi|313125582|ref|YP_004035846.1|  58 LHDISMDIPEKSVTALIGPSGCGKSTFLRCLNRMNDRiksarVDGSVKFENQEIYQdgTDLVELRKRVGQVFQSPNP 134
                                       789*******************************9998888889**********99999****************** PP

                                       -TTSBHHHH..........................HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHH CS
                                       xxxxxxxxx..........................xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren..........................esdee...iekalsklglkelkdtvvksspssLSgGqkqrva 118
                                       fp++ +r+n                              e   +e+ l++  l +   ++++++++ LSgGq+qr++
  gi|313125582|ref|YP_004035846.1| 135 FPKS-IRKNisygprkhgdintgllarltgrddsdR---EdelVERSLKQAALWDEVSDRLGDNATGLSGGQQQRLC 207
                                       ****.*************************985544...3456********************************** PP

                                       HHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxx RF
                          ABC_tran 119 larallkkpkllllDEpt 136
                                       +aral+++p+++l+DEp 
  gi|313125582|ref|YP_004035846.1| 208 IARALATDPEVILMDEPA 225
                                       *****************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.6e-07   0.00041       1      26 [.      70      98 ..      70     117 .. 0.73
   2 !   27.3   0.0   3.3e-09     3e-06     126     298 ..     100     255 ..      92     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.6e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl...d 26
                                      +++liGp g+GKS++L++l  + +    +
  gi|313125582|ref|YP_004035846.1| 70 VTALIGPSGCGKSTFLRCLNRMNDRiksA 98
                                      69*****************9996654430 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3.3e-09
                            AAA_21 126 slkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdl 202
                                       ++ +   ++++++q g +l+++++r  +  ++       +  + +i ++  +++++ + +   +  +++ ++  + +
  gi|313125582|ref|YP_004035846.1| 100 VDGSVKFENQEIYQDGTDLVELRKRVGQVFQSP------NPFPKSIRKNISYGPRKHGDINTGLLARLTGRDDSDRE 170
                                       555566667777777777777777777777777......77777777777777777777777777777777777777 PP

                            AAA_21 203 gegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll 279
                                       +e +e + + + +++e        +d+   +a+ lS G+++ l+++ al+ ++    ++l DEp + L+P +++++ 
  gi|313125582|ref|YP_004035846.1| 171 DELVERSLKQAALWDE-------VSDRLGDNATGLSGGQQQRLCIARALATDP---EVILMDEPASALDPVATSKIE 237
                                       7777777777777666.......9999***************99999999988...9******************** PP

                            AAA_21 280 ellkelsrngaQviltTHS 298
                                       +l+ +l++ +  v+++TH+
  gi|313125582|ref|YP_004035846.1| 238 DLIVDLAE-DYTVVVVTHN 255
                                       ***88888.8********8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.2   6.1e-09   5.5e-06      23     212 ..      67     269 ..      57     274 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.1e-09
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEE........EEEEEEETTEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkae........veitfdnedkklk 91 
                                       +ks+ta++Gp G+GKs +l  +     +r +  ++s++++  ++  ++++  + ++        v  +f+ ++    
  gi|313125582|ref|YP_004035846.1|  67 EKSVTALIGPSGCGKSTFLRCL-----NRMNDRIKSARVDGSVKF-ENQEIYQDGTdlvelrkrVGQVFQSPNPFP- 136
                                       6889***************999.....566668888888888876.444444444311000000444444444432. PP

                                       SSSSCEEEEEEEETTSEEEEEE...........TTEEE-HHHHHHHHHCTT-STT..........CS-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxx RF
                             SMC_N  92 iekeevsisrrvkrkgeseyki...........ngkevtkkevsellesagiske..........lLSgGektLval 147
                                             si+++++ + + +  i           ++++ + + v++ l++a +  e           LSgG+++ + +
  gi|313125582|ref|YP_004035846.1| 137 -----KSIRKNISYGPRKHGDIntgllarltgrDDSDREDELVERSLKQAALWDEvsdrlgdnatGLSGGQQQRLCI 208
                                       .....2333333322222222211112333333344444444555555555555588888888889******98888 PP

                                       HHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 148 aLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                       a  +A+   +p+ + l+De ++aLD   ++k+ +l+    ++  ++v++++ ++ ++ +    v+
  gi|313125582|ref|YP_004035846.1| 209 ARALAT---DPE-VILMDEPASALDPVATSKIEDLIVDLAEDYTVVVVTHNMQQAARISDQTAVF 269
                                       888775...454.679***********************************99998887776665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     3e-08   2.7e-05      14      83 ..      58     129 ..      56     182 .. 0.80
   2 ?    4.2   0.0     0.033        29     322     365 ..     214     255 ..     202     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3e-08
                            AAA_15  14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn...kkvikiekedleifeniseskdikIdvef 83 
                                       l d+++d+ e+ +t liG+ ++GKS++l+ l+ + ++ +  +   +  +k+e++++ +   +  + + ++   f
  gi|313125582|ref|YP_004035846.1|  58 LHDISMDIPEKsVTALIGPSGCGKSTFLRCLNRMNDRIK--SarvDGSVKFENQEIYQDGTDLVELRKRVGQVF 129
                                       678899998888************************774..345988888888888777666666655555555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.033
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++ ++l++EP   L p a + + +l+ +la+d    v++ TH+
  gi|313125582|ref|YP_004035846.1| 214 TDPEVILMDEPASALDPVATSKIEDLIVDLAEDYT--VVVVTHN 255
                                       67899*****************************6..******8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.5e-07   0.00022       5      66 ..      68     121 ..      65     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralgl 66 
                                       +++++++G+sG+GK+t lr l + +d        r + ++v+ +++ + ++++++    ++l
  gi|313125582|ref|YP_004035846.1|  68 KSVTALIGPSGCGKSTFLRCLNRMND--------RIKSARVDGSVKFENQEIYQDGTDLVEL 121
                                       7899********************98........7777788888777777777776665555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.2e-07   0.00074      11      39 ..      57      85 ..      47      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.2e-07
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTll 39
                                       +++ +++i +k++t l+GpsG GKST+l
  gi|313125582|ref|YP_004035846.1| 57 ALHDISMDIPEKSVTALIGPSGCGKSTFL 85
                                      3445556666666**************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2     1e-06   0.00093      14      52 ..      56     102 ..      55     272 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-06
                            AAA_16  14 salervrsgrp..elvllsGesGvGKsslvrellralekd.......g 52 
                                       +al++++++ p  +++ l+G+sG+GKs+ +r+l r ++++       g
  gi|313125582|ref|YP_004035846.1|  56 HALHDISMDIPekSVTALIGPSGCGKSTFLRCLNR-MNDRiksarvdG 102
                                       5677777777777999*****************95.555543223331 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.6e-06    0.0014      87     124 ..      55      94 ..      24     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT.T-- CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallp.ele 124
                                        ++l++++  + + ++++l+G+SG GKSt++  l+  +++
  gi|313125582|ref|YP_004035846.1|  55 DHALHDISMDIPEkSVTALIGPSGCGKSTFLRCLNRmNDR 94 
                                       5567777777777699***************999873444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   4.8e-06    0.0043      18      40 ..      67      89 ..      56     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.8e-06
                            AAA_23 18 skgltlItGpNGaGKTTildAik 40
                                      +k +t+++Gp G+GK+T+l+++ 
  gi|313125582|ref|YP_004035846.1| 67 EKSVTALIGPSGCGKSTFLRCLN 89
                                      7889*****************96 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.5e-05     0.014      30      50 ..      65      85 ..      55      89 .. 0.88
   2 ?   -0.8   0.1       1.1   9.7e+02     121     148 ..     227     252 ..     168     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +p++++++l+G++g+GK+t++
  gi|313125582|ref|YP_004035846.1| 65 IPEKSVTALIGPSGCGKSTFL 85
                                      69*****************97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                            AAA_25 121 rggtlltadvdaleaaieevegvrlvvi 148
                                       + ++++t+++++l+ ++ e  ++ +vv+
  gi|313125582|ref|YP_004035846.1| 227 ALDPVATSKIEDLIVDLAE--DYTVVVV 252
                                       2334467777777766666..3444443 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-05     0.015      43      68 ..      66      91 ..      54     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                             Rad17 43 rkkriLLisGPsGCgkstvvkvLske 68
                                       +k +  + GPsGCgkst ++ L + 
  gi|313125582|ref|YP_004035846.1| 66 PEKSVTALIGPSGCGKSTFLRCLNRM 91
                                      456688899************99875 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.3e-05     0.065      27     163 ..      72     270 ..      62     287 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.3e-05
                                       EEEESTTSSHHHHHHHHHHHCS--..........--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT........... CS
                           G-alpha  27 lllGqseSGKsTilkqlkllykkg..........fseeelatwraviqlnivrsiktilealesleselsesf.... 89 
                                        l+G s++GKsT+l+ l ++ +            f             + i+++  +++e  ++ ++ ++++     
  gi|313125582|ref|YP_004035846.1|  72 ALIGPSGCGKSTFLRCLNRMNDRIksarvdgsvkF-----------ENQEIYQDGTDLVELRKRVGQVFQSPNpfpk 137
                                       589***************99977733343333333...........4455555555555555553333322223344 PP

                                       .................................................HHHC-SS-SCCCS-HCHHHH........ CS
                           G-alpha  90 .................................................elqelkerldplkkveasliaklssate 117
                                                                                                           ++       
  gi|313125582|ref|YP_004035846.1| 138 sirknisygprkhgdintgllarltgrddsdredelverslkqaalwdeV------------------SD------- 189
                                       44666677777766666666666666655554222222222111111110..................11....... PP

                                       ...................................HHCCHHC..-HCHHHHHHHHCCSHHHHHHHCCG.CCTT--TT CS
                           G-alpha 118 ee.................................qeiefnp..raevgedikaLwndpgiqelyerr.nkikledn 158
                                        +                                   + + p  + ++ + i++L +d+++  +  +  +  +++d+
  gi|313125582|ref|YP_004035846.1| 190 -RlgdnatglsggqqqrlciaralatdpevilmdePASALDPvaTSKIEDLIVDLAEDYTVVVVTHNMqQAARISDQ 265
                                       .0222223334444555666555555544444443222222255556777888888888888776644356668888 PP

                                       HHHHH CS
                           G-alpha 159 aeyFl 163
                                       +++Fl
  gi|313125582|ref|YP_004035846.1| 266 TAVFL 270
                                       88887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019      0.17       3      25 ..      73      98 ..      72     129 .. 0.75
   2 ?   -2.8   0.1       9.6   8.6e+03     106     120 ..     157     171 ..     156     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                            AAA_18  3 ltGtpGvGKttlakeLskrl.gf..g 25
                                      l G++G+GK+t+ + L++++  +   
  gi|313125582|ref|YP_004035846.1| 73 LIGPSGCGKSTFLRCLNRMNdRIksA 98
                                      89**************9997333541 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.6
                            AAA_18 106 lleRlekRgyeeaki 120
                                       ll Rl  R+ ++++ 
  gi|313125582|ref|YP_004035846.1| 157 LLARLTGRDDSDRED 171
                                       678888888777664 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012      0.11       1      22 [.      70      91 ..      70     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                            AAA_33  1 lvllvGlpGsGKstlaerllkk 22
                                      ++ l+G++G+GKst+++ l + 
  gi|313125582|ref|YP_004035846.1| 70 VTALIGPSGCGKSTFLRCLNRM 91
                                      5679***********9987655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0011      0.97      18      42 ..      68      92 ..      63     103 .. 0.84
   2 ?    1.6   0.3      0.22     2e+02      86     129 ..     213     259 ..     168     270 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                            AAA_30 18 drvavltGpAGtGKttalkalreaw 42
                                      + v++l Gp G GK+t l+ l+++ 
  gi|313125582|ref|YP_004035846.1| 68 KSVTALIGPSGCGKSTFLRCLNRMN 92
                                      46999**************998775 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
                            AAA_30  86 lepgtllivDEagmv....dtkqlaallkaaekagakvilvGDerQla 129
                                        ++ ++++ DE + +    +t+++++l+  +++ + +v++v  + Q a
  gi|313125582|ref|YP_004035846.1| 213 ATDPEVILMDEPASAldpvATSKIEDLIVDLAE-DYTVVVVTHNMQQA 259
                                       334478888886655566677778877777777.56666665555544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.2e-05     0.074      15     110 ..      63     222 ..      55     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                                       TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE................................. CS
                            NB-ARC  15 kdelqslvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv................................. 57 
                                       +d +++ v al G  G+GK+t ++  ++  d +++ r d+ +                                   
  gi|313125582|ref|YP_004035846.1|  63 MDIPEKSVTALIGPSGCGKSTFLRCLNRMNDRIKSaRVDGSVKFenqeiyqdgtdlvelrkrvgqvfqspnpfpksi 139
                                       566778899******************99999999899988888888888888888888888888888888888888 PP

                                       .................................EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCC CS
                            NB-ARC  58 .................................vvsktdkseeiletilkeLslseddleekeeveslkrklvrlLl 101
                                                                         v ++ k+  +++++  +L+++   l+  +++      + r+L 
  gi|313125582|ref|YP_004035846.1| 140 rknisygprkhgdintgllarltgrddsdredeLVERSLKQAALWDEVSDRLGDNATGLSGGQQQR---LCIARALA 213
                                       888888888888888888888888888888888888888888888888888888876666666544...67777888 PP

                                       CTTEEEEEE CS
                            NB-ARC 102 tkrfllvlD 110
                                       t   ++++D
  gi|313125582|ref|YP_004035846.1| 214 TDPEVILMD 222
                                       877777777 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.11       3      47 ..      72     114 ..      70     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                               PRK   3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekd 47 
                                       ++ g+SG+Gk+t+ r l+ +     +k+a ++g + ++ +++++d
  gi|313125582|ref|YP_004035846.1|  72 ALIGPSGCGKSTFLRCLNRMND--RIKSARVDGSVKFENQEIYQD 114
                                       788***********99987655..677778877777776666655 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.17      32      72 ..     237     275 ..     228     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                             DeoRC  32 lelaraLaekknltvvTnslnvaeeLsekedikvillGGev 72 
                                       + l+  Lae+ +++vvT++++ a+++s++    v+l+GG +
  gi|313125582|ref|YP_004035846.1| 237 EDLIVDLAEDYTVVVVTHNMQQAARISDQ--TAVFLTGGYL 275
                                       5678889999*****************97..99******76 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00059      0.53       3      26 ..      73      95 ..      71     117 .. 0.74
   2 ?   -1.0   0.0       2.5   2.3e+03      49      94 ..     215     261 ..     211     271 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                      l Gpsg+GKSt+ +   +++ +++
  gi|313125582|ref|YP_004035846.1| 73 LIGPSGCGKSTFLRC-LNRMNDRI 95
                                      78**********998.55555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.5
                      RNA_helicase  49 gqevvvidDfgqvkdee.npsdlaelirlvsstpyplnmasleekgt 94 
                                       ++ev+++d+ ++  d   + +++  ++ l++ +++ + + ++++ ++
  gi|313125582|ref|YP_004035846.1| 215 DPEVILMDEPASALDPVaTSKIEDLIVDLAEDYTVVVVTHNMQQAAR 261
                                       67788888877777777566688888888888888887777766555 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0031       2.8      90     107 ..      71      88 ..      34      96 .. 0.83
   2 ?    2.0   0.0     0.082        73     224     251 ..     234     262 ..     205     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                        Adeno_IVa2  90 GviyGPtGsGksqllrnl 107
                                         + GP G+Gks +lr l
  gi|313125582|ref|YP_004035846.1|  71 TALIGPSGCGKSTFLRCL 88 
                                       4567************88 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.082
                        Adeno_IVa2 224 sklsakfkk.ctgfsvlvvlhnlnPrsdi 251
                                       sk+ +     +  ++v+vv hn++  + i
  gi|313125582|ref|YP_004035846.1| 234 SKIEDLIVDlAEDYTVVVVTHNMQQAARI 262
                                       5665554431457**********977666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 1719.17
//
Query:       gi|313125583|ref|YP_004035847.1|  [L=225]
Description: phosphate uptake regulator, phou [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-40  135.0  11.5    6.7e-21   74.6   2.1    2.3  2  PhoU      PhoU domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   2.1   3.7e-25   6.7e-21       4      88 ..      20     104 ..      17     105 .. 0.97
   2 !   65.7   2.1   2.1e-22   3.8e-18       2      88 ..     119     212 ..     118     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 3.7e-25
                                       HHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   4 maeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigD 80 
                                       m+e+v e l++ l+ale+kd+ la+evie d ei+r++ ++e +++ ++a +qp+a+dlr++ ++ +i++dlERigD
  gi|313125583|ref|YP_004035847.1|  20 MSEVVAERLRMGLDALEQKDDQLAEEVIEGDGEINRMYLDLEQDCIDLIALQQPVASDLRFIAASFKIITDLERIGD 96 
                                       99*************************************************************************** PP

                                       HHHHHHHH CS
                              PhoU  81 havniaer 88 
                                        a+n+a++
  gi|313125583|ref|YP_004035847.1|  97 LATNLANY 104
                                       *****986 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 2.1e-22
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH.......HHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae.......dlrellsllri 71 
                                       +++++ ++emld++++a++e++ el+r+v  +dd+id+++++ ++ +++ l + +p +e        l +++ ll  
  gi|313125583|ref|YP_004035847.1| 119 QQIGDGTLEMLDKSMDAYAEENPELCRAVATQDDDIDAMCEAASEMVVRDLIETDPFGEedrdaeaYLSDISRLLLT 195
                                       6788999********************************************7766666667756665666777**** PP

                                       HHHHHHHHHHHHHHHHH CS
                              PhoU  72 ardlERigDhavniaer 88 
                                       +rdlER+gDhavnia r
  gi|313125583|ref|YP_004035847.1| 196 VRDLERVGDHAVNIAAR 212
                                       ***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1287.52
//
Query:       gi|313125584|ref|YP_004035848.1|  [L=61]
Description: hypothetical protein Hbor_08120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.26   11.7   6.2       0.29   11.5   6.2    1.1  1  DUF2628   Protein of unknown function (DUF2628)
        2.1    8.8   7.7       0.34   11.4   3.1    1.9  2  DUF2583   Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> DUF2628  Protein of unknown function (DUF2628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   6.2   3.2e-05      0.29      21      62 ..      13      55 ..       3      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                           DUF2628 21 rlsfnvwA.fffgfiwLlyrklwlkalvllviavavsvvlavl 62
                                       +s+++ A f + f++++   lw++++   +  v v +vl  +
  gi|313125584|ref|YP_004035848.1| 13 WWSWQWTAtFAVMFGYFFGAMLWVAGFKISAALVGVIAVLLGM 55
                                      69****984667899****************999999998655 PP

>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.1   3.8e-05      0.34      45      64 ..      23      42 ..       7      44 .. 0.85
   2 ?    0.6   0.1     0.087   7.8e+02       6      20 ..      43      57 ..      40      60 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                           DUF2583 45 aallgifiGallWlaGarvg 64
                                      a ++g f Ga+lW+aG +++
  gi|313125584|ref|YP_004035848.1| 23 AVMFGYFFGAMLWVAGFKIS 42
                                      5689************9998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.087
                           DUF2583  6 alllGnvlmglGlll 20
                                      a+l+G + + lG+ +
  gi|313125584|ref|YP_004035848.1| 43 AALVGVIAVLLGMSV 57
                                      566777666677655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 361.93
//
Query:       gi|313125585|ref|YP_004035849.1|  [L=741]
Description: ATPase AAA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.7e-101  335.9   0.0    7.9e-50  168.7   0.0    2.4  2  AAA              ATPase family associated with various cellul
    1.3e-30  105.4   0.0    7.9e-30  102.9   0.0    2.4  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    4.2e-30  103.3   5.2    4.4e-15   55.2   1.3    2.5  2  AAA_lid_3        AAA+ lid domain
    9.1e-17   60.6   0.1    6.6e-16   57.8   0.1    2.4  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.6e-15   57.2   0.0    5.3e-07   29.5   0.0    3.0  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.4e-14   54.3   1.4    3.4e-06   27.1   0.0    3.9  2  AAA_5            AAA domain (dynein-related subfamily)
    2.5e-14   54.0   1.7    3.9e-06   27.3   0.1    4.1  3  AAA_16           AAA ATPase domain
    4.7e-13   49.6   0.0    8.6e-06   26.0   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.7e-11   43.9   0.0    5.8e-05   22.5   0.0    3.2  3  TIP49            TIP49 P-loop domain
    5.4e-11   42.9   1.3     0.0013   19.0   0.1    4.4  4  AAA_22           AAA domain
    1.4e-10   41.5   0.0    0.00011   22.3   0.0    2.8  2  AAA_33           AAA domain
    1.8e-08   34.5   0.0     0.0048   16.9   0.0    2.4  2  AAA_14           AAA domain
    6.8e-08   33.1   0.0      0.011   16.3   0.0    3.0  2  AAA_18           AAA domain
    8.1e-08   32.2   0.0      0.017   14.9   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    2.1e-07   30.7   0.5        2.1    7.8   0.0    4.4  4  AAA_25           AAA domain
    4.5e-07   29.7   0.1      0.045   13.5   0.0    3.6  3  Sigma54_activat  Sigma-54 interaction domain
    9.1e-07   28.5   0.1      0.046   13.1   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.3e-06   28.7   0.0      0.059   13.8   0.0    2.5  2  RNA_helicase     RNA helicase
      2e-06   27.5   0.0       0.04   13.4   0.0    2.4  2  AAA_7            P-loop containing dynein motor region
    5.3e-06   25.9   0.3        0.5    9.7   0.0    3.7  3  ATPase           KaiC
    6.6e-06   26.5   0.0      0.038   14.2   0.0    2.6  2  AAA_28           AAA domain
    1.1e-05   26.0   0.0       0.22   12.0   0.0    2.7  2  ABC_tran         ABC transporter
    1.2e-05   24.6   0.0       0.17   11.1   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    1.7e-05   24.7   0.0       0.21   11.5   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    1.9e-05   24.2   0.1       0.43   10.0   0.0    3.2  3  PhoH             PhoH-like protein
    2.6e-05   24.3   0.1       0.73    9.7   0.0    4.0  3  ATPase_2         ATPase domain predominantly from Archaea
    2.8e-05   24.1   0.0       0.18   11.8   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    3.1e-05   23.8   0.0       0.15   11.8   0.0    2.5  2  AAA_24           AAA domain
    3.3e-05   23.8   0.2       0.29   10.9   0.0    2.6  2  AAA_11           AAA domain
    4.7e-05   22.8   0.2      0.083   12.2   0.0    2.6  2  Zeta_toxin       Zeta toxin
    5.6e-05   22.5   0.0       0.12   11.5   0.0    2.4  2  NB-ARC           NB-ARC domain
    6.8e-05   22.3   0.0       0.34   10.1   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    8.9e-05   22.3   0.1       0.51   10.0   0.0    2.8  2  AAA_30           AAA domain
    0.00017   20.8   0.1       0.21   10.7   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0003   21.2   0.0       0.83   10.1   0.0    3.4  2  AAA_17           AAA domain
    0.00035   20.5   1.9      0.034   14.2   0.0    3.0  2  Vps4_C           Vps4 C terminal oligomerisation domain
    0.00063   19.9   0.0        1.3    9.2   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00063   20.1   0.6        1.3    9.3   0.0    3.0  2  AAA_19           AAA domain
    0.00075   19.5   0.5       0.57   10.1   0.0    3.1  2  NACHT            NACHT domain
     0.0017   18.3   0.4        3.6    7.5   0.0    3.3  2  NTPase_1         NTPase
     0.0031   17.3   0.1        2.3    7.9   0.0    2.4  2  Cytidylate_kin   Cytidylate kinase
      0.005   16.3   1.0        1.2    8.4   0.0    2.7  2  IPT              Isopentenyl transferase
     0.0056   16.5   0.0        3.7    7.3   0.0    2.7  2  Bac_DnaA         Bacterial dnaA  protein
     0.0059   16.5   0.0          1    9.3   0.0    2.6  2  Rad17            Rad17 P-loop domain
     0.0084   16.1   0.0          5    7.1   0.0    2.6  2  ResIII           Type III restriction enzyme, res subunit
     0.0093   14.9   0.0        2.1    7.1   0.0    2.2  2  AFG1_ATPase      AFG1-like ATPase
  ------ inclusion threshold ------
       0.01   16.0   0.0        5.5    7.1   0.0    2.5  2  SKI              Shikimate kinase
      0.011   15.9   0.1        7.9    6.6   0.0    2.7  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.012   14.9   0.1        4.1    6.5   0.0    3.1  3  KAP_NTPase       KAP family P-loop domain
      0.012   15.0   0.0         10    5.4   0.0    3.4  3  TniB             Bacterial TniB protein
      0.023   14.3   0.0        2.9    7.5   0.0    2.5  2  Zot              Zonular occludens toxin (Zot)
      0.026   14.4   0.0        3.7    7.4   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.029   14.5   0.0        4.5    7.4   0.0    2.4  2  Torsin           Torsin
      0.038   14.3   0.1        4.8    7.4   0.0    2.4  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.038   13.7   0.0        3.4    7.4   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.05   13.3   0.2         55    3.4   0.0    3.6  3  Guanylate_kin    Guanylate kinase
      0.071   12.9   0.0         15    5.5   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
        0.1   12.0   0.0         47    3.3   0.0    3.1  3  KTI12            Chromatin associated protein KTI12


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.7   0.0   2.6e-52   7.9e-50       1     131 [.     226     355 ..     226     356 .. 0.98
   2 !  165.0   0.0   3.6e-51   1.1e-48       1     131 [.     499     629 ..     499     630 .. 0.96

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 2.6e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKTllakava+e++++f++i g+e++sky gese+++re+f++ake++ psi+fiDE+d++a++r++ 
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSIAGPEIISKYYGESEQQLREIFEDAKEES-PSIIFIDELDSIAPKREDV 301
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLlt++dg++++ ++vivi+atnr+d++dpal+r gRfdr+iei+
  gi|313125585|ref|YP_004035849.1| 302 TGEVERRVVAQLLTMMDGLETR-GQVIVIAATNRVDSVDPALRRpGRFDREIEIG 355
                                       *********************7.56***************************996 PP

  == domain 2  score: 165.0 bits;  conditional E-value: 3.6e-51
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       vllyGppGtGKTl+akava+e++++f+++ g++llsk+vgesek ir++f++a++ + p+i+f+DE+d+la+sr ++
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNANFISVRGPQLLSKWVGESEKAIRQTFRKARQVS-PTIIFFDELDSLAPSRgND 574
                                       79******************************************************9.****************888 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                         ++++ervvnqLlteldg++++ ++v+vigatnrpd++dpal+r gRfdr + i+
  gi|313125585|ref|YP_004035849.1| 575 MGNNVSERVVNQLLTELDGLEEN-GDVMVIGATNRPDMIDPALIRsGRFDRLVLIG 629
                                       89********************6.77************************988775 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.0   2.5e-32   7.9e-30       1      84 [.       5      88 ..       5      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 2.5e-32
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +L Va+a+++d+grgi+r+dp+++ +l+l+pgd++eieg ++T+a+vw+a+++d++++++r+dg+tR+na+v+iG++Vt
  gi|313125585|ref|YP_004035849.1|  5 QLEVAKAYPNDSGRGIARLDPDTLLHLKLSPGDIIEIEGGETTAAKVWRADRQDWNTDTVRIDGFTRQNADVGIGERVT 83
                                      699*****99*****************************999************************************* PP

                                      EEEE- CS
                           CDC48_N 80 Vrkae 84
                                      +rkae
  gi|313125585|ref|YP_004035849.1| 84 IRKAE 88
                                      ***97 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1     1e-15   3.2e-13       1      41 [.     378     418 ..     378     422 .. 0.92
   2 !   55.2   1.3   1.4e-17   4.4e-15       1      45 []     652     698 ..     652     698 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1e-15
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitme 41 
                                       dv+l++LA +T+G++GAD+++l +eAa+ Alrr ++ei+ +
  gi|313125585|ref|YP_004035849.1| 378 DVSLDHLADETHGFVGADIESLTKEAAMKALRRYLPEIDLD 418
                                       9*********************************9998754 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 1.4e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfee 45 
                                       dv+l e+Ae TeGy+G Dl+++ reAa++Alr++ +  ei+m++f++
  gi|313125585|ref|YP_004035849.1| 652 DVSLREIAEITEGYVGSDLESIAREAAIEALREDDDakEIEMRHFRK 698
                                       9********************************999756******86 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       3.9   1.2e+03      19      29 ..      33      43 ..       2      70 .. 0.78
   2 !   57.8   0.1   2.1e-18   6.6e-16       2      63 ..     107     177 ..     106     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.9
                                      E-TTEEEEECC CS
                           CDC48_2 19 vtkGdlvvfef 29
                                      +++Gd++ +e 
  gi|313125585|ref|YP_004035849.1| 33 LSPGDIIEIEG 43
                                      78899988775 PP

  == domain 2  score: 57.8 bits;  conditional E-value: 2.1e-18
                                       .SCCCCH.HHHCCCTTEEE-TTEEEEECCT.........CCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2   2 idgdema.ylkrqFlgrpvtkGdlvvfefk.........gqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                       + +d +a ++krq+l+rpv++ d+v+++ +         gq+i+l +v+t+P g++ +te+Te+el+++p +
  gi|313125585|ref|YP_004035849.1| 107 FGSD-AAgMVKRQILKRPVVERDIVPVMSStnhpfmrspGQAIPLIAVETDPEGVCLVTEDTEVELREEPIS 177
                                       6778.666*****************998877778889********************************976 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   1.7e-09   5.3e-07      32     103 ..     222     301 ..     199     343 .. 0.86
   2 !   24.2   0.0   7.6e-08   2.4e-05      31      70 ..     494     533 ..     471     577 .. 0.79
   3 ?   -1.8   0.0       7.3   2.2e+03      23      43 ..     612     632 ..     600     642 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.7e-09
                            RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsrav 100
                                       +   vll+GpPG Gkt lak +a+e  +++ + +gP +      e +++l  ++ + +e+   ++fide+  ++++ 
  gi|313125585|ref|YP_004035849.1| 222 PPQGVLLHGPPGTGKTLLAKAVANETSASFFSIAGPEIiskyygESEQQLREIFEDAKEEspSIIFIDELDSIAPKR 298
                                       56679*******************************875544444568899999988776337********999988 PP

                            RuvB_N 101 eev 103
                                       e+v
  gi|313125585|ref|YP_004035849.1| 299 EDV 301
                                       876 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 7.6e-08
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                                       e+   vllyGpPG Gkt +ak +a+e ++++ +  gP l 
  gi|313125585|ref|YP_004035849.1| 494 EPPKGVLLYGPPGTGKTLIAKAVANETNANFISVRGPQLL 533
                                       556779*******************************874 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 7.3
                            RuvB_N  23 ieaakkreealdhvllyGpPG 43 
                                       i+ a  r+   d ++l+G PG
  gi|313125585|ref|YP_004035849.1| 612 IDPALIRSGRFDRLVLIGQPG 632
                                       667778888899999999998 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   2.1e-07   6.6e-05       1     136 [.     225     344 ..     225     345 .. 0.73
   2 !   27.1   0.0   1.1e-08   3.4e-06       1     136 [.     498     618 ..     498     619 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.1e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ la+ +a  + ++++ +++++      ++ ++    g+ + +  ++ + a+  +++i+++DE++
  gi|313125585|ref|YP_004035849.1| 225 GVLLHGPPGTGKTLLAKAVANETSASFFSIAGPE------IISKYY---GESEQQLREIFEDAKeeSPSIIFIDELD 292
                                       59******************************98......555554...4555555677777777899********* PP

                                       G--...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  76 rae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        +     +v++++ +    + l +++g e  +        ++ via++n++d    +++palr+
  gi|313125585|ref|YP_004035849.1| 293 SIApkrEDVTGEVERRVVAQLLTMMDGLETRG--------QVIVIAATNRVD----SVDPALRR 344
                                       98722234555554444444444444444443........399999999999....88999886 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.1e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +vlL GppGtgK+ +a+ +a  +n+++  v +++      l+ ++   ++ ++   + + +a + ++ i+++DE++ 
  gi|313125585|ref|YP_004035849.1| 498 GVLLYGPPGTGKTLIAKAVANETNANFISVRGPQ------LLSKWV--GESEKAIRQTFRKARQvSPTIIFFDELDS 566
                                       59*****************************998......888888..45555555666655559************ PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                       + ++  n + +  +er +    ++el + ++++   +++vi+++n++d     ++pal++
  gi|313125585|ref|YP_004035849.1| 567 LAPSRGNDMGNNVSERVVN-QLLTELDGLEENG---DVMVIGATNRPD----MIDPALIR 618
                                       ****************998.5555666555543...4***********....88888875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   1.3e-08   3.9e-06      24     141 ..     223     329 ..     197     342 .. 0.75
   2 !   19.2   0.0     4e-06    0.0012      23      63 ..     495     532 ..     485     549 .. 0.78
   3 ?    3.9   0.0      0.21        64     122     149 ..     543     569 ..     538     603 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.3e-08
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqlldeaesaeleawr 98 
                                       p+ vll+G++G+GK+ l+++++++ +++  +f ++g    +     y+    q+l r e++++ ++e   +    + 
  gi|313125585|ref|YP_004035849.1| 223 PQGVLLHGPPGTGKTLLAKAVANETSAS--FFsIAGPEIIS----KYYGeSEQQL-R-EIFEDAKEE---SPSIIFI 288
                                       589*******************988877..33355555555....5544466777.6.777777777...4445555 PP

                            AAA_16  99 ekleealaavpelagaeasrllellkrllallsrderplvlvl 141
                                       ++l++ +    +++g+ ++r+ ++l  +++ l+++++  v+v+
  gi|313125585|ref|YP_004035849.1| 289 DELDSIAPKREDVTGEVERRVVAQLLTMMDGLETRGQ--VIVI 329
                                       656666667777777777***********99999887..4444 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                        p  vll+G++G+GK+ ++++++++ +++   f++ +  ql
  gi|313125585|ref|YP_004035849.1| 495 PPKGVLLYGPPGTGKTLIAKAVANETNAN---FISVRGPQL 532
                                       4589*******************977776...666666555 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.21
                            AAA_16 122 llkrllallsrderplvlvlDdlqwade 149
                                       ++++ ++++++  +p+++++D+l+ + +
  gi|313125585|ref|YP_004035849.1| 543 AIRQTFRKARQ-VSPTIIFFDELDSLAP 569
                                       56777889999.889*********5544 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.8e-08   8.6e-06       6     105 ..     226     319 ..     222     333 .. 0.88
   2 !   20.6   0.0   1.3e-06   0.00039       6     103 ..     499     591 ..     495     597 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.8e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    ++  +   e++     + + +++++ ++    a+e+   i+++DE+d i
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSA----SFFSIAGPEIIS----KYYGESEQQLREIFEDAKEESpsIIFIDELDSI 294
                                       6889*****************996....99999999**99....99999999999999999999889********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e  + +v r  V+  LL +++g
  gi|313125585|ref|YP_004035849.1| 295 APKrEDVTGEVERR-VVAQLLTMMDG 319
                                       **866777777665.77778899997 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.3e-06
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++aka+a+  ++    ++i +   +ll     + + ++++  ++   +a +    i+++DE+d  
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNA----NFISVRGPQLLS----KWVGESEKAIRQTFRKARQVSptIIFFDELDSL 567
                                       6789******************96....999999999999....44444444444555555555467********** PP

                                       ---..---------HHHHHHHHHHH CS
                             AAA_2  81 hpk..essgadvSregVqrdLLqil 103
                                       +p+  + +g++vS+  V++ LL  l
  gi|313125585|ref|YP_004035849.1| 568 APSrgNDMGNNVSER-VVNQLLTEL 591
                                       **9988888889876.555555544 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.7   1.7e+03     165     196 ..      27      58 ..      25      67 .. 0.79
   2 !   17.3   0.0   6.9e-06    0.0021      51      97 ..     224     268 ..     214     292 .. 0.88
   3 !   22.5   0.0   1.9e-07   5.8e-05      51     109 ..     497     554 ..     490     557 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.7
                                       HHHHHT--TT-EEEEETTT--EEE-SSS-SS- CS
                             TIP49 165 ellkekvkegDviviekesGkvkklGrseara 196
                                       +ll+ k++ gD+i ie    +  k+ r++ + 
  gi|313125585|ref|YP_004035849.1|  27 TLLHLKLSPGDIIEIEGGETTAAKVWRADRQD 58 
                                       57788999********9988888888887654 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6.9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl Gp+gtGkt la a+++e +    f +++g e+ s     +e
  gi|313125585|ref|YP_004035849.1| 224 QGVLLHGPPGTGKTLLAKAVANETS--ASFFSIAGPEIISKYYGESE 268
                                       68*********************87..789********998766665 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 1.9e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksigv 109
                                       ++vLl Gp+gtGkt +a a+++e +    f+++ g ++ s  v  +e ++ q++rk+ +v
  gi|313125585|ref|YP_004035849.1| 497 KGVLLYGPPGTGKTLIAKAVANETN--ANFISVRGPQLLSKWVGESEkAIRQTFRKARQV 554
                                       89********************987..78**************99985799*****9665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   4.2e-06    0.0013       8      59 ..     226     277 ..     221     281 .. 0.79
   2 ?    4.1   0.0      0.17        53      73     127 ..     266     328 ..     258     337 .. 0.66
   3 !   15.1   0.0     7e-05     0.022       8      45 ..     499     527 ..     494     537 .. 0.82
   4 ?    1.6   0.0      0.97     3e+02      81     114 ..     543     581 ..     538     611 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.2e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllre 59 
                                       ++++G++GtGKT+l++ ++++   +++   ++pe++ +++  s+  +++++++
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETS-ASFFSIAGPEIIsKYYGESEQQLREIFED 277
                                       689*****************984.34444478888888888888888888876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.17
                            AAA_22  73 lsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliL 127
                                        s+++l+e +e+a ++     ++ iDE + +   +         +++ +L ++++  ++  q+i+
  gi|313125585|ref|YP_004035849.1| 266 ESEQQLREIFEDAKEESPS--IIFIDELDSIApkRedvtgeveRRVVAQLLTMMDGLETRGQVIV 328
                                       5667777777777776666..*********98762445555667777777777666444444444 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 7e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45 
                                       ++++G++GtGKT+ ++ ++++          ++ +++v
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANET---------NANFISV 527
                                       689*****************98.........5555555 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.97
                            AAA_22  81 aleqalrarav..ielliiDEaqhlr.s..eealeeLrs 114
                                       a++q +r+++   + ++  DE + l  s  +++ +++++
  gi|313125585|ref|YP_004035849.1| 543 AIRQTFRKARQvsPTIIFFDELDSLApSrgNDMGNNVSE 581
                                       566666666667889**********87345555544433 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.7e-07   0.00011       2      80 ..     226     334 ..     226     359 .. 0.75
   2 !   16.2   0.0     3e-05    0.0092       2      50 ..     499     549 ..     499     608 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.7e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll+G+pG+GK+ la+ +++++   ++ ++ ++++++++g+ +q+++                              
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSasFFSIAGPEIISKYYGESEQQLReifedakeespsiifideldsiapkredVT 302
                                       799****************999999999************8888777677777777777777777777776555322 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnl 80 
                                        +v+ r+ ++l  + +   ++g+ +++ atn+
  gi|313125585|ref|YP_004035849.1| 303 GEVERRVVAQLLTMMDGLETRGQVIVIAATNR 334
                                       33555566666666666666666666666664 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdytr 50 
                                       vll G+pG+GK+  a+ +++++   ++ ++ ++l+++ +g+ ++ +++  r
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNanFISVRGPQLLSKWVGESEKAIRQTFR 549
                                       7899***************99998899999999999999876666554333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.5e-05    0.0048       5      76 ..     226     294 ..     223     350 .. 0.76
   2 !   15.1   0.0   5.6e-05     0.017       5     102 ..     499     607 ..     496     628 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k +++e      s++ i+  +   k + ++e+ l++i+e +kee  +++f+DE   +
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETS---ASFFSIAGPEIISKYYGESEQQLREIFEDAKEESPSIIFIDELDSI 294
                                       7899***************8888...89999988887777777777667777777677799*******9888 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 5.6e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT ++k +++e      +++ +   +   k   ++ek ++  ++k+++   t++f+DE   +     
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETN---ANFISVRGPQLLSKWVGESEKAIRQTFRKARQVSPTIIFFDELDSLapsrg 572
                                       7899**************98877...777777776666666666554554444444445789*******99989999 PP

                            AAA_14  77 .....pewekalkslvd..eg..knldvivtGSns 102
                                            +  e+++++l+   +g  +n+dv+v G  +
  gi|313125585|ref|YP_004035849.1| 573 ndmgnNVSERVVNQLLTelDGleENGDVMVIGATN 607
                                       88887444555555555332234678888888765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00023      0.07       1      25 [.     226     268 ..     226     338 .. 0.64
   2 !   16.3   0.0   3.6e-05     0.011       1      78 [.     499     602 ..     499     656 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00023
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                                       +ll G+pG+GKt lak++++++ ++                  
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETsASffsiagpeiiskyygesE 268
                                       7899**************9998433565555544444444441 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe...........alde 48 
                                       +ll G+pG+GKt +ak++++++ ++                    +r+++++ + + +   +             d 
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETnANfisvrgpqllskwvgesEKAIRQTFRKARQVSPTIIFfdeldslapsrGNDM 575
                                       799***************99984337888888888888888844444444444444444333333444444444466 PP

                            AAA_18  49 skrldedkldklldaleenssaleegknlv 78 
                                        + + e ++++ll++l++     e+g++ v
  gi|313125585|ref|YP_004035849.1| 576 GNNVSERVVNQLLTELDGLE---ENGDVMV 602
                                       66667777777777776654...3444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.5e-05     0.017      45      71 ..     221     247 ..     211     256 .. 0.85
   2 !   14.7   0.0   6.3e-05      0.02      48      78 ..     497     527 ..     489     572 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.5e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgvea 71 
                                       e  ++++l Gp+G+GK+ la a++ e+
  gi|313125585|ref|YP_004035849.1| 221 EPPQGVLLHGPPGTGKTLLAKAVANET 247
                                       566899****************99876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.3e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsv 78 
                                       ++++l Gp+G+GK+ +a a++ e+ ++ +sv
  gi|313125585|ref|YP_004035849.1| 497 KGVLLYGPPGTGKTLIAKAVANETNANFISV 527
                                       6899****************99887766665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.011       3.4      36      54 ..     226     244 ..     222     257 .. 0.87
   2 !    7.6   0.0    0.0085       2.6     128     184 ..     269     327 ..     261     334 .. 0.79
   3 !    7.8   0.0    0.0069       2.1      36      52 ..     499     515 ..     475     522 .. 0.87
   4 ?    2.6   0.0      0.28        87     128     184 ..     542     603 ..     525     606 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll G+pgtGKt la  +a
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVA 244
                                       689***********97666 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0085
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar..rtgaavl 184
                                       ++++++ ++++e e +  + iD l+++ +  e+   +v +++v++l  + +  +t+  v+
  gi|313125585|ref|YP_004035849.1| 269 QQLREIFEDAKE-ESPSIIFIDELDSIAPKREDVTGEVeRRVVAQLLTMMDglETRGQVI 327
                                       67899999****.99***************999889987888888776655344444444 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0069
                            AAA_25  36 allaGapgtGKttlald 52 
                                       +ll+G+pgtGKt +a  
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKA 515
                                       69**********99865 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.28
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsd......vgalvealeriarrtgaavl 184
                                        ++++  +++++v  +  + +D l+++ +   n+         v++l++ l+ ++++ ++ v+
  gi|313125585|ref|YP_004035849.1| 542 KAIRQTFRKARQVS-PTIIFFDELDSLAPSRGNDMGNnvservVNQLLTELDGLEENGDVMVI 603
                                       57888889999975.9********999998444443333334348888888888777777776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0011      0.33      22      46 ..     223     247 ..     205     259 .. 0.84
   2 ?   -1.9   0.0       7.4   2.3e+03      95     142 ..     284     333 ..     263     336 .. 0.54
   3 !   13.5   0.0   0.00014     0.045      22     143 ..     496     608 ..     483     628 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                                       SS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheas 46 
                                       +  vl++G  GtGK+lla+a+ +++
  gi|313125585|ref|YP_004035849.1| 223 PQGVLLHGPPGTGKTLLAKAVANET 247
                                       4679****************98765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.4
                                       SEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSS...EEE--EEEEEEES CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqegevervGssk...eikvdvriiaatn 142
                                       +++f+De+ ++ ++  e +   ++++ v ++ +     e++ +v +iaatn
  gi|313125585|ref|YP_004035849.1| 284 SIIFIDELDSIAPKR-EDVTGEVERRVVAQLLTMMdglETRGQVIVIAATN 333
                                       578888888877653.33344444444444332211114455566666665 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 0.00014
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEE CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlf 98 
                                       +  vl+ G  GtGK+l+a+a+ ++++   ++f++v      ++ll s+  G ++ a      +   + ++ +  ++f
  gi|313125585|ref|YP_004035849.1| 496 PKGVLLYGPPGTGKTLIAKAVANETN---ANFISVRG----PQLL-SKWVGESEKAIR----QTFRKARQVSPTIIF 560
                                       4679****************987654...77888754....3333.444555554443....333345666777777 PP

                                       EETGGGS-HHHHHHHHHHHHHSEEESBTSS...SEEE--EEEEEEESS CS
                   Sigma54_activat  99 LDeigelplelQekLlrvlqegevervGss...keikvdvriiaatne 143
                                       +De+ +l ++  + + + + e+ v+++ ++    e + dv++i atn+
  gi|313125585|ref|YP_004035849.1| 561 FDELDSLAPSRGNDMGNNVSERVVNQLLTEldgLEENGDVMVIGATNR 608
                                       777777777777777777777777776544221356667777777775 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   0.00024     0.074      25      43 ..     226     244 ..     222     249 .. 0.90
   2 !   13.1   0.0   0.00015     0.046      25      43 ..     499     517 ..     496     553 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt+lak+++
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVA 244
                                       79*************9875 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00015
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt++ak+++
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVA 517
                                       79*************9875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00019     0.059       1      32 [.     226     257 ..     226     333 .. 0.74
   2 !   12.6   0.0   0.00043      0.13       1      26 [.     499     524 ..     499     587 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00019
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkd 32 
                                       ++l+Gp+g+GK++lak +a++ + ++ ++  +
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSIAGP 257
                                       689**************988888766222222 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00043
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++lyGp+g+GK+++ak +a++   ++
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNANF 524
                                       689**************999887665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00051      0.16      31      61 ..     221     251 ..     211     296 .. 0.83
   2 !   13.4   0.0   0.00013      0.04      33      62 ..     496     524 ..     487     536 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00051
                             AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkek 61 
                                       +  + vll Gp GtGKt+++k + ++ + + 
  gi|313125585|ref|YP_004035849.1| 221 EPPQGVLLHGPPGTGKTLLAKAVANETSASF 251
                                       556789****************999888554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00013
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkeky 62 
                                        k vll+Gp GtGKt+i+k + ++ +  ++
  gi|313125585|ref|YP_004035849.1| 496 PKGVLLYGPPGTGKTLIAKAVANETN-ANF 524
                                       5789****************999988.444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0016       0.5      13      37 ..     217     241 ..     212     250 .. 0.84
   2 ?    2.1   0.0      0.34   1.1e+02     109     155 ..     269     321 ..     256     337 .. 0.68
   3 !    9.5   0.0    0.0019      0.58      14      37 ..     491     514 ..     484     527 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                            ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                       k Gi   + vl+ G pGtGKt++a+
  gi|313125585|ref|YP_004035849.1| 217 KLGIEPPQGVLLHGPPGTGKTLLAK 241
                                       568888899**************97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.34
                            ATPase 109 eelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkklg 155
                                       ++l+e+ ++ k+   + + iD ++++    ++ + +v R+ + ql++++ +l+
  gi|313125585|ref|YP_004035849.1| 269 QQLREIFEDAKEespSIIFIDELDSIapkREDVTGEVERRVVAQLLTMMDGLE 321
                                       5555555555553336677777666632145556677899******9998765 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0019
                            ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                        Gi   + vl++G pGtGKt++a+
  gi|313125585|ref|YP_004035849.1| 491 MGIEPPKGVLLYGPPGTGKTLIAK 514
                                       577888899************997 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   0.00012     0.038       2      49 ..     226     274 ..     225     307 .. 0.73
   2 !    9.6   0.0    0.0034         1       2      24 ..     499     522 ..     498     557 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00012
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv 49 
                                       + + G+++tGKT l++a a++   + +  a+ ei+++ + + e++l++ 
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANEtSASFFSIAGPEIISKYYGESEQQLREI 274
                                       6799***************765455555555555555555555555544 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0034
                            AAA_28   2 ivitGgestGKTtlleaLaar.gy 24 
                                       + + G+++tGKT +++a a++ + 
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANEtNA 522
                                       6799***************65443 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0015      0.48       6      37 ..     218     249 ..     216     332 .. 0.80
   2 !   12.0   0.0   0.00071      0.22       7      92 ..     492     591 ..     490     607 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0015
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp 37 
                                       l +++ + v + G+ G+GK+ L+k++a++++ 
  gi|313125585|ref|YP_004035849.1| 218 LGIEPPQGVLLHGPPGTGKTLLAKAVANETSA 249
                                       678888999******************99876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00071
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx... RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren... 79 
                                        +++ + v + G+ G+GK+ ++k++a++++  +  i ++g +l ++   +++k i+  + +  q+ p++   ++   
  gi|313125585|ref|YP_004035849.1| 492 GIEPPKGVLLYGPPGTGKTLIAKAVANETN--ANFISVRGPQLLSKWVGESEKAIRQTFRKaRQVSPTIIFFDElds 566
                                       577778899*******************97..578888999999988888888888888876777777766655677 PP

                                       ............HHHTCHHHHHHHS CS
                                       ............xxxxxxxxxxxxx RF
                          ABC_tran  80 ............esdeeiekalskl 92 
                                                    s++ ++++l++l
  gi|313125585|ref|YP_004035849.1| 567 lapsrgndmgnnVSERVVNQLLTEL 591
                                       6666666666554444456655555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00054      0.17      52     116 ..     222     291 ..     214     337 .. 0.64
   2 !   11.0   0.0   0.00057      0.18      51      82 ..     494     525 ..     443     570 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00054
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..ev.ek...edlkelpklvellrerperfilfvDDL 116
                                       p + vLL G  GtGK  l ka+ ne++++   +   e+ +k   e+ ++l +++e  +e +   i+f+D L
  gi|313125585|ref|YP_004035849.1| 222 PPQGVLLHGPPGTGKTLLAKAVANETSASFFSIAgpEIiSKyygESEQQLREIFEDAKE-ESPSIIFIDEL 291
                                       56789*********************999965543344133111444555555555443.45578999987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00057
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegL 82 
                                       +p + vLL+G  GtGK  + ka+ ne++++ +
  gi|313125585|ref|YP_004035849.1| 494 EPPKGVLLYGPPGTGKTLIAKAVANETNANFI 525
                                       57789*********************998764 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00098       0.3       2      30 ..     226     254 ..     225     337 .. 0.91
   2 !   11.5   0.0   0.00068      0.21       2      31 ..     499     528 ..     498     608 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00098
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++ktll+ka+a+  +++f  i
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSI 254
                                       89******************999998665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00068
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       vll g PG++ktl++ka+a+  +++f  ++
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNANFISVR 528
                                       7999********************998775 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0014      0.43      22      42 ..     226     246 ..     212     254 .. 0.86
   2 !    9.7   0.0    0.0017      0.51      22      42 ..     499     519 ..     481     527 .. 0.84
   3 ?   -0.6   0.0       2.5   7.7e+02     159     205 .]     669     716 ..     661     716 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt+la a+a e
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANE 246
                                       6789***********999865 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt++a a+a e
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANE 519
                                       7789***********999865 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.5
                                       ---------THHHHHHTTT-TTEEEEE--GG.G----HHHHHHHHHH- CS
                              PhoH 159 dlpkgkksGlaealevlknvegieivelkkk.dvvRhplvkkivkaye 205
                                       dl++  +++  eal+  ++ ++ie+ +++k+ + vR +++ ++++ ye
  gi|313125585|ref|YP_004035849.1| 669 DLESIAREAAIEALREDDDAKEIEMRHFRKAmEAVRPTITDELMDYYE 716
                                       666667778888888888999999999976438999999999998886 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0024      0.73      15      83 ..     218     290 ..     212     331 .. 0.57
   2 ?    6.4   0.0     0.025       7.7      19      44 ..     495     520 ..     489     528 .. 0.79
   3 ?    1.6   0.0       0.7   2.2e+02     115     161 ..     549     603 ..     529     607 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0024
                          ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal......... 82 
                                       l  ep + +++ Gp g GKt L k ++++ +      ++ ia  e+ ++++ e+   e++ +++ + +         
  gi|313125585|ref|YP_004035849.1| 218 LGIEPPQGVLLHGPPGTGKTLLAKAVANETS----ASFFSIAGPEIISKYYGES---EQQLREIFEDAkeespsiif 287
                                       556777778999********99999999883....4678888888888888888...33333333333133322222 PP

                          ATPase_2  83 ..g 83 
                                          
  gi|313125585|ref|YP_004035849.1| 288 idE 290
                                       230 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.025
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienl 44 
                                       p + +++YGp g GKt + k ++++ 
  gi|313125585|ref|YP_004035849.1| 495 PPKGVLLYGPPGTGKTLIAKAVANET 520
                                       5666899*********8888888765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.7
                          ATPase_2 115 kkgkk...iiiiiDelqkli.....dlglngaellvkeLlnliesltkekhlcvv 161
                                       +k+++    ii++Del  l      d+g n +e +v++Ll+ ++ l ++ +++v+
  gi|313125585|ref|YP_004035849.1| 549 RKARQvspTIIFFDELDSLApsrgnDMGNNVSERVVNQLLTELDGLEENGDVMVI 603
                                       33333666899*****998644444788888999999999888887777776665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0    0.0006      0.18      19      51 ..     223     257 ..     200     274 .. 0.75
   2 !    9.8   0.0    0.0025      0.78      20      51 ..     497     530 ..     472     534 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0006
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        + +lL+G+ G+GKT l++++a++   +  ++  P
  gi|313125585|ref|YP_004035849.1| 223 PQGVLLHGPPGTGKTLLAKAVANETSASffSIAGP 257
                                       4559******************9987766666666 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0025
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       + +lL+G+ G+GKT +++++a++ + +  +v+ P
  gi|313125585|ref|YP_004035849.1| 497 KGVLLYGPPGTGKTLIAKAVANETNANfiSVRGP 530
                                       359******************9998876666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0027      0.84       5      23 ..     226     246 ..     223     302 .. 0.66
   2 !   11.8   0.0   0.00049      0.15       5      22 ..     499     516 ..     496     553 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0027
                            AAA_24   5 iliyGpsgiGKTtlakel..g 23 
                                       +l+ Gp+g+GKT lak    +
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVanE 246
                                       799************998332 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00049
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+yGp+g+GKT +ak  
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAV 516
                                       89*************987 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00095      0.29      20      40 ..     226     246 ..     213     283 .. 0.79
   2 !   10.4   0.1    0.0013      0.41      18      43 ..     497     528 ..     483     723 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00095
                            AAA_11  20 tliqGPPGtgKTktivellsq 40 
                                       +l++GPPGtgKT    ++ ++
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANE 246
                                       79**********766665555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0013
                            AAA_11  18 eitliqGPPGtgKTktivellsqll......s 43 
                                       + +l+ GPPGtgKT    ++ ++ +       
  gi|313125585|ref|YP_004035849.1| 497 KGVLLYGPPGTGKTLIAKAVANETNanfisvR 528
                                       45799*********888888877753333330 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0059       1.8      14      40 ..     221     247 ..     213     256 .. 0.87
   2 !   12.2   0.0   0.00027     0.083      14      50 ..     494     528 ..     482     533 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0059
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdel 40 
                                       e P  +ll G pG GK+ la+++++e+
  gi|313125585|ref|YP_004035849.1| 221 EPPQGVLLHGPPGTGKTLLAKAVANET 247
                                       56899******************9997 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00027
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       e Pk +ll G pG GK+ +a+++++e+  + n++ + 
  gi|313125585|ref|YP_004035849.1| 494 EPPKGVLLYGPPGTGKTLIAKAVANET--NANFISVR 528
                                       789***********************9..88888775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00039      0.12      10      44 ..     216     247 ..     210     281 .. 0.80
   2 !    8.3   0.0    0.0039       1.2      23      44 ..     499     520 ..     489     551 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                                       HHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  10 ekLlekdelqslvvalvGmgGvGKttlakqilnks 44 
                                       +kL   + +q   v l+G +G GKt lak + n+ 
  gi|313125585|ref|YP_004035849.1| 216 KKLG-IEPPQ--GVLLHGPPGTGKTLLAKAVANET 247
                                       5555.44455..689****************9993 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0039
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l+G +G GKt +ak + n+ 
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANET 520
                                       779***************9983 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0011      0.34       4      33 ..     226     249 ..     223     307 .. 0.70
   2 !   10.0   0.0    0.0012      0.37       4      36 ..     499     524 ..     496     566 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeert 33 
                                       vl +G +GtGKt+++ ++++e       + 
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANET------SA 249
                                       6889*************99998......23 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavy 36 
                                       vl  G +GtGKt+++ ++++e        +a++
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANET-------NANF 524
                                       6789*************99998.......3334 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0016      0.51      21      42 ..     226     247 ..     213     257 .. 0.81
   2 !    9.0   0.0    0.0034       1.1      21      44 ..     499     522 ..     488     530 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                            AAA_30  21 avltGpAGtGKttalkalreaw 42 
                                       ++l+Gp+GtGKt + ka+++  
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANET 247
                                       789*************998755 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0034
                            AAA_30  21 avltGpAGtGKttalkalreawea 44 
                                       ++l Gp+GtGKt + ka+++  +a
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNA 522
                                       5789*************9876655 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0051       1.6     117     137 ..     226     246 ..     219     250 .. 0.89
   2 !   10.7   0.0   0.00067      0.21     117     137 ..     499     519 ..     492     525 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0051
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v+++Gp+ tGkt la+a a+ 
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANE 246
                                       899**************9985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00067
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++yGp+ tGkt +a+a a+ 
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANE 519
                                       89***************9985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.025       7.8       2      31 ..     230     260 ..     229     302 .. 0.75
   2 !   10.1   0.0    0.0027      0.83       1      49 [.     502     551 ..     502     572 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.025
                                       E-TTSSHHHHHHHHHHHHTEEEEEH.HHHHH CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsa.Gdllr 31 
                                       G+PG GK+ +++ ++ +   +++s  G  ++
  gi|313125585|ref|YP_004035849.1| 230 GPPGTGKTLLAKAVANETSASFFSIaGPEII 260
                                       9**************9999998875355555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0027
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrkl 49 
                                       +G+PG GK+ +++ ++ + +  ++s  G  l +    ++ +  r+ +rk+
  gi|313125585|ref|YP_004035849.1| 502 YGPPGTGKTLIAKAVANETNANFISVrGPQLLSKWVGESEKAIRQTFRKA 551
                                       7*****************99988886665555554444444556666655 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1       0.1        31      17      45 ..     420     448 ..     414     458 .. 0.85
   2 !   14.2   0.0   0.00011     0.034      27      56 ..     689     718 ..     678     722 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.1
                            Vps4_C  17 mdipsdkllePpvtlkDflkalkkarptV 45 
                                       +dip++ +    v+++Df+ al ++ p+ 
  gi|313125585|ref|YP_004035849.1| 420 EDIPPSLIDRMIVKRSDFEGALTEVEPSA 448
                                       68998889999***************996 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00011
                            Vps4_C  27 PpvtlkDflkalkkarptVskeDLekheeF 56 
                                        ++++++f ka++ +rpt+++e ++ +e+ 
  gi|313125585|ref|YP_004035849.1| 689 KEIEMRHFRKAMEAVRPTITDELMDYYEQM 718
                                       589******************999888875 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0      0.01       3.2      24      47 ..     226     249 ..     220     299 .. 0.66
   2 !    9.2   0.0    0.0041       1.3      24      49 ..     499     524 ..     494     587 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.01
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       v+l G++G+gk+l A++ +++ + 
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSA 249
                                       9****************9998765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0041
                                       EEEEEETT--HHHHHHCC--TTS-EE CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwl 49 
                                       v+l G++G+gk+l+A++ +++   + 
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNANF 524
                                       9****************998766543 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2     0.016         5      12      33 ..     225     246 ..     220     281 .. 0.84
   2 !    9.3   0.0    0.0044       1.3      11      34 ..     497     520 ..     492     571 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.016
                            AAA_19  12 vllvtaGpGtGKTrvlkhival 33 
                                        +l+ ++pGtGKT + k++ ++
  gi|313125585|ref|YP_004035849.1| 225 GVLLHGPPGTGKTLLAKAVANE 246
                                       5899*********988877665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0044
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivall 34 
                                       k +l+ ++pGtGKT + k++ ++ 
  gi|313125585|ref|YP_004035849.1| 497 KGVLLYGPPGTGKTLIAKAVANET 520
                                       56899*********9988877665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0018      0.57       3      23 ..     226     246 ..     224     251 .. 0.89
   2 ?    6.1   0.0     0.032       9.7       3      23 ..     499     519 ..     497     525 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0018
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l+G++G GKT L++ +a +
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANE 246
                                       79**************99976 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.032
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT  ++ +a +
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANE 519
                                       799************999876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.012       3.6       2      32 ..     226     256 ..     225     270 .. 0.89
   2 ?    7.2   0.0     0.014       4.2       2      32 ..     499     529 ..     498     545 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.012
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+++ + s ++++G
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSIAG 256
                                       6789***************999888777777 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + k v+++ + + ++v+G
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNANFISVRG 529
                                       6788***************999888888887 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.014       4.4       3      28 ..     228     253 ..     226     256 .. 0.90
   2 !    7.9   0.0    0.0076       2.3       4      28 ..     502     526 ..     499     528 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g+GK  +a+a+a++ ++++++
  gi|313125585|ref|YP_004035849.1| 228 LHGPPGTGKTLLAKAVANETSASFFS 253
                                       68******************999986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0076
                                       E-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                                        GP g+GK  +a+a+a++ ++++++
  gi|313125585|ref|YP_004035849.1| 502 YGPPGTGKTLIAKAVANETNANFIS 526
                                       6********************9986 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.032       9.9       5      30 ..     227     252 ..     224     255 .. 0.90
   2 !    8.4   0.0     0.004       1.2       5      37 ..     500     532 ..     497     555 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                               IPT   5 lifGatttGKtaeaiklaketgapvi 30 
                                       l++G+ +tGKt  a ++a+et+a+  
  gi|313125585|ref|YP_004035849.1| 227 LLHGPPGTGKTLLAKAVANETSASFF 252
                                       899*******************9865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.004
                               IPT   5 lifGatttGKtaeaiklaketgapvivlDRvqc 37 
                                       l++G+ +tGKt  a ++a+et a  i++   q 
  gi|313125585|ref|YP_004035849.1| 500 LLYGPPGTGKTLIAKAVANETNANFISVRGPQL 532
                                       89*********************9999765555 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.028       8.8      37      61 ..     226     250 ..     219     255 .. 0.89
   2 ?    7.3   0.0     0.012       3.7      37      66 ..     499     528 ..     493     613 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.028
                                       EEEE-SSSSSHHHHHHHHHHHHHHH CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlen 61 
                                       ++++g+ G Gkt L ka++ne+ ++
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSAS 250
                                       79******************98765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.012
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelr 66 
                                       +++yg+ G Gkt + ka++ne+ +n+ + r
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNANFISVR 528
                                       79*******************999887665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.14        43      46      73 ..     224     251 ..     215     276 .. 0.83
   2 !    9.3   0.0    0.0033         1      46     119 ..     497     572 ..     470     594 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgikl 73 
                                       + +L+ GP+G gk+   k ++ e + ++
  gi|313125585|ref|YP_004035849.1| 224 QGVLLHGPPGTGKTLLAKAVANETSASF 251
                                       55799**********9999999887765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0033
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkele.Lkdaky 119
                                       + +L+ GP+G gk+ + k ++ e   +++    p +l +     ++ ++  + k  +  + i  f el  L  ++ 
  gi|313125585|ref|YP_004035849.1| 497 KGVLLYGPPGTGKTLIAKAVANETNANFISVRGPQLLSKWVGeSEKAIRQTFRKARQVSPTIIFFDELDsLAPSRG 572
                                       457899************************9999988664433788899999999999999999999952455555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.028       8.7      21      50 ..     220     249 ..     195     300 .. 0.81
   2 ?    7.1   0.0     0.016         5      21      71 ..     490     537 ..     441     578 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.028
                                       ..TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  21 skrdkrglikmaTGtGKTlvaaklierllk 50 
                                       ++  + +l++ + GtGKTl+a +++ + + 
  gi|313125585|ref|YP_004035849.1| 220 IEPPQGVLLHGPPGTGKTLLAKAVANETSA 249
                                       46778899************9888777665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.016
                                       .....TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH CS
                            ResIII  21 s...krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl 71 
                                           +  k +l+  + GtGKTl+a +++ +   +      ++ v + +ll+++ 
  gi|313125585|ref|YP_004035849.1| 490 RmgiEPPKGVLLYGPPGTGKTLIAKAVANETNAN------FISVRGPQLLSKWV 537
                                       15556778899999*********98888877764......22345555555555 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0     0.007       2.1      53      79 ..     215     240 ..     194     247 .. 0.81
   2 ?    5.3   0.0     0.024       7.4      51      78 ..     487     512 ..     462     520 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.007
                       AFG1_ATPase  53 grkrksvepvrglYlwGgvGrGKtylm 79 
                                       ++k    ep++g+ l+G+ G GKt l 
  gi|313125585|ref|YP_004035849.1| 215 FKK-LGIEPPQGVLLHGPPGTGKTLLA 240
                                       444.3678****************985 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.024
                       AFG1_ATPase  51 lfgrkrksvepvrglYlwGgvGrGKtyl 78 
                                       +f r     ep++g+ l+G+ G GKt +
  gi|313125585|ref|YP_004035849.1| 487 KFER--MGIEPPKGVLLYGPPGTGKTLI 512
                                       4443..3579****************76 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.028       8.6       1      45 [.     232     281 ..     232     282 .. 0.76
   2 ?    7.1   0.0     0.018       5.5       1      22 [.     505     526 ..     505     551 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.028
                                       TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHHT...S-HHHHHHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrtg...ksiaeifeeegee 45 
                                       +G+GK+ ++k++A++ + +f+ +   e+i+k  g   ++ +eife+  ee
  gi|313125585|ref|YP_004035849.1| 232 PGTGKTLLAKAVANETSASFFSIagPEIISKYYGeseQQLREIFEDAKEE 281
                                       69******************987445688887764335577777777665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.018
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ ++k++A++ + +fi 
  gi|313125585|ref|YP_004035849.1| 505 PGTGKTLIAKAVANETNANFIS 526
                                       69******************95 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.026       7.9       8      53 ..     232     281 ..     228     328 .. 0.76
   2 ?    6.4   0.0     0.029       8.9       8      61 ..     505     559 ..     501     603 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.026
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde...r 53 
                                        G+g++ +++a+A++    f++ + +e ++k  g se+++ e +++   +
  gi|313125585|ref|YP_004035849.1| 232 PGTGKTLLAKAVANETSASFFSIAGPEIISKYYGESEQQLrEIFEDakeE 281
                                       69*********************999999999999999995555554222 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.029
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersrlssfls 61 
                                        G+g++ i++a+A++ + +f++ + ++ ++k  g se+ + +++ +++ +s ++ 
  gi|313125585|ref|YP_004035849.1| 505 PGTGKTLIAKAVANETNANFISVRGPQLLSKWVGESEKAIrQTFRKARQVSPTII 559
                                       59********************************999999777777555555554 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.1   1.6e+03      19      44 ..     222     247 ..     213     255 .. 0.83
   2 ?    6.5   0.0     0.013       4.1     170     198 ..     277     307 ..     255     315 .. 0.75
   3 ?    3.8   0.0      0.09        28      24      68 ..     500     574 ..     489     594 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.1
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledel 44 
                                       +p  v L g+ G+GK+ l + + +e 
  gi|313125585|ref|YP_004035849.1| 222 PPQGVLLHGPPGTGKTLLAKAVANET 247
                                       56668999999*****9999887775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                        KAP_NTPase 170 a..lqkrlVvviDdLDrceteevlqlleavk 198
                                       +  ++++ +++iD+LD++ +++   + e+ +
  gi|313125585|ref|YP_004035849.1| 277 DakEESPSIIFIDELDSIAPKREDVTGEVER 307
                                       23458999************99888777655 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.09
                        KAP_NTPase  24 gLygkWGsGKssllnkledelkefa..............................kpvrflfaefnawsfkggdd 68 
                                        Lyg+ G+GK+ + + + +e + +                                p+ ++f e+++++++ g+d
  gi|313125585|ref|YP_004035849.1| 500 LLYGPPGTGKTLIAKAVANETNANFisvrgpqllskwvgesekairqtfrkarqvSPTIIFFDELDSLAPSRGND 574
                                       566666666666666665555555445555555555555555555555555544444444444444444444444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.072        22      34      59 ..     222     247 ..     203     259 .. 0.84
   2 ?    5.4   0.0     0.034        10      35      60 ..     496     521 ..     482     529 .. 0.84
   3 ?   -0.1   0.0       1.7   5.3e+02     105     133 ..     541     569 ..     534     587 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.072
                              TniB  34 rmpnlllvGdsnnGKtmivekFarlh 59 
                                        ++ +ll+G++ +GKt +++  a++ 
  gi|313125585|ref|YP_004035849.1| 222 PPQGVLLHGPPGTGKTLLAKAVANET 247
                                       56899*************99877665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.034
                              TniB  35 mpnlllvGdsnnGKtmivekFarlhp 60 
                                       ++ +ll+G++ +GKt i++  a++ +
  gi|313125585|ref|YP_004035849.1| 496 PKGVLLYGPPGTGKTLIAKAVANETN 521
                                       4689**************98887665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.7
                              TniB 105 skleqqvlrllrelkvrvLiiDEihnlla 133
                                       +k+ +q+ r  r++++ ++ +DE+++l  
  gi|313125585|ref|YP_004035849.1| 541 EKAIRQTFRKARQVSPTIIFFDELDSLAP 569
                                       556678889999************99875 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0093       2.9       4      65 ..     227     293 ..     226     311 .. 0.81
   2 ?    3.9   0.0      0.11        35       4      62 ..     500     563 ..     499     576 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0093
                               Zot   4 lvtGapGsgKts..gavkkdllp..alkegRkiitnidGlrlerieqvlgekvs.tarliridnpeg 65 
                                       l +G+pG+gKt+  +av ++     ++ +g +ii +  G   ++++ +++++++ ++ +i+id+ ++
  gi|313125585|ref|YP_004035849.1| 227 LLHGPPGTGKTLlaKAVANETSAsfFSIAGPEIISKYYGESEQQLREIFEDAKEeSPSIIFIDELDS 293
                                       789********722567776665545558*********************99999999***995443 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                               Zot   4 lvtGapGsgKts..gavkkdllp..alkegRkiitnidGlrlerieqvlgekvs.tarliridn 62 
                                       l +G+pG+gKt+  +av ++ +    ++ g ++  +  G   ++i+q ++++ + ++ +i+ d+
  gi|313125585|ref|YP_004035849.1| 500 LLYGPPGTGKTLiaKAVANETNAnfISVRGPQLLSKWVGESEKAIRQTFRKARQvSPTIIFFDE 563
                                       679********72256877776642333688888888888888888888888888888888774 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.012       3.7       4      34 ..     226     256 ..     224     329 .. 0.87
   2 ?    4.4   0.0     0.094        29       4      33 ..     499     528 ..     497     557 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.012
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                                       +lL+G + +GK+ la+a+ + + ++++ ++ 
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSIAG 256
                                       89************************99875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.094
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       +lL G + +GK+ +a+a+ + +++ ++ + 
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNANFISVR 528
                                       89******************9999998876 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.015       4.5      56      77 ..     226     247 ..     214     254 .. 0.88
   2 ?    4.3   0.0      0.13        39      57      77 ..     500     520 ..     489     528 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.015
                                       EEEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaenl 77 
                                       + +hG +GtGk  +a+ +a+++
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANET 247
                                       569***************9986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                                       EEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  57 sfhGwtGtGknfvaeiiaenl 77 
                                        ++G +GtGk  +a+ +a+++
  gi|313125585|ref|YP_004035849.1| 500 LLYGPPGTGKTLIAKAVANET 520
                                       5789*************9986 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.016       4.8       2      30 ..     226     254 ..     225     280 .. 0.90
   2 ?    4.4   0.0      0.13        40       2      30 ..     499     527 ..     498     529 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.016
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++hG+P +GKt  a ++a +  a++++i
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSI 254
                                       689******************99999998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.13
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++ G+P +GKt +a ++a + +a ++++
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNANFISV 527
                                       5789******************9999987 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0       0.1        32       2      22 ..     227     247 ..     226     291 .. 0.71
   2 ?    7.4   0.0     0.011       3.4       5      71 ..     503     564 ..     499     570 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts 22 
                                       + hG pG GK+ l + ++++ 
  gi|313125585|ref|YP_004035849.1| 227 LLHGPPGTGKTLLAKAVANET 247
                                       68*************999994 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ + + ++++   ++ ++r    ll++++ ++++    t++++ +         i+++DE 
  gi|313125585|ref|YP_004035849.1| 503 GPPGTGKTLIAKAVANETnANFISVRG-PQLLSKWVGESEKAIRQTFRKARQVS-----PTIIFFDEL 564
                                       78*******999999999977777777.99******888888888787655532.....359999996 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.28        85       5      30 ..     226     251 ..     223     258 .. 0.86
   2 ?    2.4   0.0      0.37   1.1e+02      76      95 ..     261     280 ..     254     298 .. 0.84
   3 ?    3.4   0.0      0.18        55       4      30 ..     498     524 ..     496     530 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.28
                                       EEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   5 vvlvgpsgaGksslkkaLlselpekf 30 
                                       v l gp g+Gk  l ka+ +e + +f
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSASF 251
                                       7899**************99999888 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.37
                                       TEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  76 gnlygtsveaieevlekgki 95 
                                       +++yg+s ++ +e++e +k+
  gi|313125585|ref|YP_004035849.1| 261 SKYYGESEQQLREIFEDAKE 280
                                       78**************9997 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.18
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        v l gp g+Gk  + ka+ +e + +f
  gi|313125585|ref|YP_004035849.1| 498 GVLLYGPPGTGKTLIAKAVANETNANF 524
                                       6899***************99998887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.081        25      21      39 ..     223     240 ..     213     245 .. 0.75
   2 ?    5.5   0.0     0.047        15      18      38 ..     492     512 ..     477     518 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.081
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       ++g +ll Gp G+GK+ l 
  gi|313125585|ref|YP_004035849.1| 223 PQG-VLLHGPPGTGKTLLA 240
                                       356.9**********8765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.047
                            AAA_29  18 eidlkgatlltGpsGsGKSTl 38 
                                        i++   +ll Gp G+GK+ +
  gi|313125585|ref|YP_004035849.1| 492 GIEPPKGVLLYGPPGTGKTLI 512
                                       4444444***********866 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.15        47       4      28 ..     226     258 ..     225     322 .. 0.64
   2 ?    3.2   0.0      0.16        50       4      28 ..     499     523 ..     498     551 .. 0.86
   3 ?    1.1   0.0      0.71   2.2e+02     175     233 ..     638     696 ..     623     706 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.15
                                       EEEE--TTSSHHHHHHHHHHHHHH........T CS
                             KTI12   4 vvltGlPssGKstrakeLakalee........e 28 
                                       v+l G P +GK+ +ak +a++ ++        e
  gi|313125585|ref|YP_004035849.1| 226 VLLHGPPGTGKTLLAKAVANETSAsffsiagpE 258
                                       7999*************9998887566555551 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.16
                                       EEEE--TTSSHHHHHHHHHHHHHHT CS
                             KTI12   4 vvltGlPssGKstrakeLakaleee 28 
                                       v+l G P +GK+ +ak +a++ +++
  gi|313125585|ref|YP_004035849.1| 499 VLLYGPPGTGKTLIAKAVANETNAN 523
                                       899*************999877664 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.71
                                       S--SSSTT-------HHHHHHHHHHHHHHHHHHH....HTT--HHH............. CS
                             KTI12 175 lkpnqatlskplaeanflqeLdketseivkeileaqksavaidkltlpgsseslelpak 233
                                       +     t+s pla+  +l+e+ ++t+  v + le +++  ai+ l+ ++  +++e+   
  gi|313125585|ref|YP_004035849.1| 638 QILRIHTQSSPLAPDVSLREIAEITEGYVGSDLESIAREAAIEALREDDDAKEIEMRHF 696
                                       5556789***************************************9999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (741 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        58  (0.00323498); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              58  [number of targets reported over threshold]
# CPU time: 0.87u 0.30s 00:00:01.17 Elapsed: 00:00:00.49
# Mc/sec: 4518.20
//
Query:       gi|313125586|ref|YP_004035850.1|  [L=536]
Description: hypothetical protein Hbor_08140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-123  413.0  17.1   8.9e-123  410.1  17.1    1.9  1  DUF111    Protein of unknown function DUF111


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.1  17.1    5e-127  8.9e-123       1     373 []       4     525 ..       4     525 .. 0.96

  Alignments for each domain:
  == domain 1  score: 410.1 bits;  conditional E-value: 5e-127
                            DUF111   1 lyldcssGisGDmllgALldlgadkeeleealeklgleeveleiekvkksgisatkvdve................. 60 
                                       l +d ++G+sGDm+l++Ll +gad+++l    ++l++   ++++++v k+gisa +v+v+                 
  gi|313125586|ref|YP_004035850.1|   4 LAFDGRMGASGDMILASLLAAGADRDALAPVENALDV---HYDVSTVVKNGISARRVRVRlddtagggegandghda 77 
                                       679***********************99888888986...9************************************ PP

                            DUF111  61 ............................................................................. 60 
                                                                                                                    
  gi|313125586|ref|YP_004035850.1|  78 dgghehahehgdhshghehhhhahdhshgeghthdhshgaghthdhshgaghthdhshgaghthdhshgaghthdhs 154
                                       ***************************************************************************** PP

                            DUF111  61 ...............................................eeehehehrslaeieeiieaaslsekvkek 90 
                                                                                       +e + +hr +ae+ ei+e++ l++ v+++
  gi|313125586|ref|YP_004035850.1| 155 hgaghthdhshgaghthdhshgaghthdhshgdhtehphdddhahetPAEGHGPHRAYAEVVEIVESMGLPNGVERD 231
                                       ****999999999999999999988888877777776666665555544555556********************** PP

                            DUF111  91 alaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgvekvvasplalGsGtvrcahGilPvPaPA 167
                                       a+aif++l eAea+vhg++l+e+hfhEvGa Dai+divga+l+l++L+ve+vv+spl++G+G+ ++ahG++PvP+PA
  gi|313125586|ref|YP_004035850.1| 232 AKAIFRILGEAEAAVHGTELDETHFHEVGADDAIADIVGACLLLADLDVERVVTSPLSTGGGEQSMAHGTYPVPTPA 308
                                       ***************************************************************************** PP

                            DUF111 168 vlellkelklkl..gevegElvTPTGaAilaalaeefgslpamkvekiGyGaGkrdleeipnvlRvlleeeeeelek 242
                                       v+e++++++++l  g+ve+El+TPTGaAila++ae ++slp+++++++GyGaG  d++++pnvlR+l+++ + +l +
  gi|313125586|ref|YP_004035850.1| 309 VVEIAQRADWSLkgGPVEAELLTPTGAAILAHVAEGVESLPTLEIDASGYGAGGYDFPDHPNVLRTLVGDGAGRLIR 385
                                       **********99999************************************************************** PP

                            DUF111 243 eevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeedaeeleellfretttlGvRes 319
                                       +e++vletn+DD+ pe+lg ++++L + GA+Dv++ p++mKK+Rp++l++v++k+edae++++ l+ et+tlG+Re+
  gi|313125586|ref|YP_004035850.1| 386 DEITVLETNLDDAAPELLGGLQSTLKDVGARDVTILPATMKKSRPGHLVKVIVKPEDAERVANRLAVETGTLGIREH 462
                                       ***************************************************************************** PP

                            DUF111 320 e.verlvlereietvetelg....evrvKva...ee.vvkvkpEyedvkkiAeetglplkevl 373
                                          +r++++r++et e+e++    ev+vKva   e+ v+++++E+++++++A+etglp++ev+
  gi|313125586|ref|YP_004035850.1| 463 GaGHRWTASRRFETAELEIEderhEVAVKVAsdaEGaVYDYSAEFDEAQAVADETGLPIREVM 525
                                       989****************99999*******986336************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.38s 00:00:01.08 Elapsed: 00:00:00.58
# Mc/sec: 2787.54
//
Query:       gi|313125587|ref|YP_004035851.1|  [L=257]
Description: hypothetical protein Hbor_08150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   13.9   1.6      0.088   12.5   1.1    2.0  2  DUF460    Protein of unknown function (DUF460)
       0.13   11.9   0.1       0.29   10.8   0.1    1.5  1  Big_3_3   Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.34   3.1e+03      78      97 ..      43      62 ..      37      75 .. 0.76
   2 ?   12.5   1.1   9.8e-06     0.088      31      51 ..      83     103 ..      53     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.34
                            DUF460 78 vivAtDvspppetvkklars 97
                                      v+  tD  ++p+ v+ + +s
  gi|313125587|ref|YP_004035851.1| 43 VVSGTDEVEIPSGVETVVAS 62
                                      44468999999999887665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.8e-06
                            DUF460  31 klivGiDPGittgiavldldg 51 
                                       ++++G+DPG+  giavl+ d 
  gi|313125587|ref|YP_004035851.1|  83 RTVIGVDPGTRPGIAVLSGDT 103
                                       689*************98655 PP

>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   3.2e-05      0.29      39      77 ..     122     160 ..     101     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
                           Big_3_3  39 ilvdntpPtvsisegkkisdgavvkglenlritladald 77 
                                        + d     v+i +g++ +++++v++le++ ++l+d++ 
  gi|313125587|ref|YP_004035851.1| 122 EVEDSPDAIVRIGDGARLQGSTIVNELEDVTVELVDETG 160
                                       344555667999************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.58
# Mc/sec: 1339.96
//
Query:       gi|313125588|ref|YP_004035852.1|  [L=231]
Description: DNA repair and recombination protein radb [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-29  101.3   0.0    6.3e-29  101.0   0.0    1.0  1  Rad51           Rad51
    1.2e-13   51.1   0.4    1.7e-13   50.6   0.4    1.1  1  AAA_25          AAA domain
      2e-12   47.1   0.4    3.3e-12   46.5   0.4    1.4  1  RecA            recA bacterial DNA recombination protein
    7.6e-12   45.1   0.0    2.5e-11   43.4   0.0    1.7  1  ATPase          KaiC
    3.7e-10   39.8   0.0    4.3e-10   39.5   0.0    1.1  1  Zot             Zonular occludens toxin (Zot)
    7.1e-07   29.1   0.0    1.5e-06   28.1   0.0    1.7  1  AAA_24          AAA domain
    7.6e-05   22.2   0.0    0.00014   21.3   0.0    1.6  1  DnaB_C          DnaB-like helicase C terminal domain
    0.00017   22.0   0.2    0.00023   21.6   0.2    1.2  1  AAA_16          AAA ATPase domain
      0.005   16.4   0.7      0.028   14.0   0.7    1.9  1  CobU            Cobinamide kinase / cobinamide phosphate guan
  ------ inclusion threshold ------
      0.019   14.7   0.2      0.062   13.0   0.0    1.8  2  IstB_IS21       IstB-like ATP binding protein
      0.043   14.1   1.6       0.15   12.3   1.6    1.9  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
      0.052   14.0   0.1       0.12   12.9   0.1    1.6  1  AAA             ATPase family associated with various cellula
      0.077   12.9   0.0       0.11   12.4   0.0    1.3  1  ATPase_2        ATPase domain predominantly from Archaea
       0.18   10.9   0.1       0.33   10.1   0.1    1.3  1  PAXNEB          PAXNEB protein


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   4.9e-32   6.3e-29      19     254 ..       5     228 ..       2     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 4.9e-32
                                       E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHT CS
                             Rad51  19 lttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaery 95 
                                       +ttG+++lD+lLgGG+e g++t ++G   +Gkt ++ + +v v        + g +vyidteg +  +r  ++ae+ 
  gi|313125588|ref|YP_004035852.1|   5 VTTGCRSLDDLLGGGFERGTVTQVYGPPAAGKTNVALSAAVRVA------AAGGTVVYIDTEG-LSVDRFQQLAEHV 74 
                                       8*********************************9988888764......34578*******7.99********998 PP

                                       ...T--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHH CS
                             Rad51  96 ...kldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtL 169
                                          +   e+v ++  +  a+  e+qee ++ +++ +a ++  l+++Ds+t  yR + +   +  +  +++++ +++L
  gi|313125588|ref|YP_004035852.1|  75 agpEQSIEDVTSRLIVSEAHDFEEQEEAVRDTTE-FA-EQADLVVLDSATGFYRLERTMDKDGGESLRRVARQVTHL 149
                                       6434556899999***************998765.44.5679**************8888888889999******** PP

                                       HHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-E.EEE CS
                             Rad51 170 rkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpele.avf 245
                                         la ++++avvitnqv +++d        d+ +  gG+ l h +   l + + +g +R + + +    p  e a+f
  gi|313125588|ref|YP_004035852.1| 150 LSLARKHDLAVVITNQVFSDPDS-------DQIRALGGHTLEHWTGAVLRIDRFRGGNRRATLEKHRAKPAGEtATF 219
                                       **********************9.......9999***************************999999999877368* PP

                                       EEETTEEE- CS
                             Rad51 246 aigeeGied 254
                                        i++ Gi +
  gi|313125588|ref|YP_004035852.1| 220 EITDGGISS 228
                                       ******986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.4   1.4e-16   1.7e-13      21     188 ..      11     165 ..       3     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.4e-16
                            AAA_25  21 prrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                       ++++l++g   +g+++ ++G+p++GKt +al+ a+ va             g+V+y+++E+       R++++ e++
  gi|313125588|ref|YP_004035852.1|  11 SLDDLLGGGFERGTVTQVYGPPAAGKTNVALSAAVRVAA----------AGGTVVYIDTEGLS---VDRFQQLAEHV 74 
                                       6788999888****************************6..........458**********9...89********9 PP

                            AAA_25  98 rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsd.......vga 167
                                       + +++  + d   v+s+ ++++ ++ +    + +a++++ e +e+++lvv+D+ + +++ + + ++d       v++
  gi|313125588|ref|YP_004035852.1|  75 AGPEQS-IED---VTSRLIVSEAHDFEE---QEEAVRDTTEFAEQADLVVLDSATGFYRLERTMDKDggeslrrVAR 144
                                       444333.222...222333444444433...334566666666779*****************99999999998899 PP

                            AAA_25 168 lvealeriarrtgaavllvhH 188
                                        v++l ++ar+++ av+++ +
  gi|313125588|ref|YP_004035852.1| 145 QVTHLLSLARKHDLAVVITNQ 165
                                       9***************99865 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.4   2.5e-15   3.3e-12      32     189 ..       3     166 ..       1     195 [. 0.78

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.5e-15
                                       -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS-.---H..HHHHHT.T.. CS
                              RecA  32 etissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaeh.aldp..kyakkl.G.. 102
                                       e++++G  +ld  lG GG+ +G ++++yGp ++Gkt +al+a +++  +gg++++id+e  ++d   + a+++ G  
  gi|313125588|ref|YP_004035852.1|   3 ESVTTGCRSLDDLLG-GGFERGTVTQVYGPPAAGKTNVALSAAVRVAAAGGTVVYIDTEGlSVDRfqQLAEHVaGpe 78 
                                       6899***********.******************************************9536664223444332222 PP

                                       ..-.-.GGG-EEE--.SSHHHHHHHHHHHHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHH CS
                              RecA 103 ..v.d.idellvsqp.dtGeqaleiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltg 174
                                         + d +  l+vs+  d  eq   + d+   +   dl+v+ds + +     +e  m d+  g   r +++ +  l +
  gi|313125588|ref|YP_004035852.1|  79 qsIeDvTSRLIVSEAhDFEEQEEAVRDTTEFAEQADLVVLDSATGFY---RLERTM-DKDGGESLRRVARQVTHLLS 151
                                       1122224579999863777888888899999999********87764...455555.44556666667777777777 PP

                                       HHTTT--EEEEEEE- CS
                              RecA 175 aisksntvvifinqi 189
                                         +k + +v+  nq+
  gi|313125588|ref|YP_004035852.1| 152 LARKHDLAVVITNQV 166
                                       778888888888886 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0     2e-14   2.5e-11       1     225 [.       5     227 ..       5     230 .. 0.70

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2e-14
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa....edlrenakslGwd 73 
                                       v tg   lD++l gG+ +g+v+ ++G p +GKt +al  +++ a+  g  +v++ +e  +    ++l e+++     
  gi|313125588|ref|YP_004035852.1|   5 VTTGCRSLDDLLGGGFERGTVTQVYGPPAAGKTNVALSAAVRVAAA-GGTVVYIDTEGLSvdrfQQLAEHVAGPEQS 80 
                                       689****************************************999.**********98877778888888888888 PP

                            ATPase  74 lekleeegklaiidasesaeesaee...kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrql 147
                                       +e++ ++  l++ +a   +e+ +e+   +++++ ++ +  l +a   ++ +r++ D+ +g     +   + +++ +l
  gi|313125588|ref|YP_004035852.1|  81 IEDVTSR--LIVSEAHDFEEQ-EEAvrdTTEFAEQADLVVLDSATGFYRLERTM-DKDGGE----SLRRVARQVTHL 149
                                       8888888..554444443333.21112233333333334444444444444432.332222....222333455566 PP

                            ATPase 148 vrvlkklgvTailvsekss.....seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeI 219
                                       ++  +k ++  ++++++ s     + +a gg+ +e+     v+++d +   ++++      k R ++   ++ +feI
  gi|313125588|ref|YP_004035852.1| 150 LSLARKHDLAVVITNQVFSdpdsdQIRALGGHTLEH-WTGAVLRID-RFRGGNRRA--TLEKHRAKPAG-ETATFEI 221
                                       6666999*********9889998888999*******.555555555.444444444..55799998875.6789*** PP

                            ATPase 220 teegik 225
                                       t++gi+
  gi|313125588|ref|YP_004035852.1| 222 TDGGIS 227
                                       **9996 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   3.4e-13   4.3e-10       5     147 ..      28     188 ..      24     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 3.4e-13
                               Zot   5 vtGapGsgKtsgavkkdllpalkegRkiitnidGlrlerieqvlgekvs........tarliridnpegaetlkefa 73 
                                       v+G+p +gKt +a++  ++ a   g +++ + +Gl ++r++q+ +++          t rli  + ++++e+ ++++
  gi|313125588|ref|YP_004035852.1|  28 VYGPPAAGKTNVALSAAVRVAAAGGTVVYIDTEGLSVDRFQQLAEHVAGpeqsiedvTSRLIVSEAHDFEEQEEAVR 104
                                       79****************************************66555434344445555577766999999999999 PP

                               Zot  74 kwatid.kgallviDEcqeifpvrakegrkd.........pevinaftehRhlgwDivlltqdiskihk.evralae 139
                                       +    + +  l+v+D +  ++  +++   kd          +v + +  +R++   +v++ q +s  ++ ++ral +
  gi|313125588|ref|YP_004035852.1| 105 DTTEFAeQADLVVLDSATGFYRLERTM-DKDggeslrrvaRQVTHLLSLARKHDLAVVITNQVFSDPDSdQIRALGG 180
                                       9999886777****************6.5567******97777799*******************987527888888 PP

                               Zot 140 kavklkrk 147
                                       +  ++   
  gi|313125588|ref|YP_004035852.1| 181 HTLEHWTG 188
                                       87777655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.1e-09   1.5e-06       4      82 ..      25     129 ..      22     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.1e-09
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie........swedfldevvel...... 59 
                                         ++yGp+ +GKT +a+++       g ++++idte+    l +d+f+++         s+ed+ +           
  gi|313125588|ref|YP_004035852.1|  25 VTQVYGPPAAGKTNVALSAavrvaaaGGTVVYIDTEG----LSVDRFQQLAehvagpeqSIEDVTS----Rlivsea 93 
                                       678**********************************....7788888877788877774444333....2333366 PP

                            AAA_24  60 .............aaeladyktlviDtideleelcl 82 
                                                     +  ++ + +v+D+++ +++l +
  gi|313125588|ref|YP_004035852.1|  94 hdfeeqeeavrdtTEFAEQADLVVLDSATGFYRLER 129
                                       77777777777778889999***********99654 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.1e-07   0.00014       2     108 ..       5     119 ..       4     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                                       BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXH....HHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                            DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsa....eqlvqRllsseae 73 
                                       ++tg ++LD+l++ G+++g+++ + + p+ Gkt +al+ a ++a+    +v+++  e  +    +ql++ +   e++
  gi|313125588|ref|YP_004035852.1|   5 VTTGCRSLDDLLGgGFERGTVTQVYGPPAAGKTNVALSAAVRVAAAGG-TVVYIDTEGLSvdrfQQLAEHVAGPEQS 80 
                                       7899*****988537*************************99997544.5666666643311225677777777777 PP

                                       XXHHHHHHTTSXHHHHHHHHHHH....HHHHHSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx RF
                            DnaB_C  74 idskklrtgklkeedweklteai....eelseaklfidd 108
                                       i+  + r    + +d+e+ +ea+    e  ++a+l++ d
  gi|313125588|ref|YP_004035852.1|  81 IEDVTSRLIVSEAHDFEEQEEAVrdttEFAEQADLVVLD 119
                                       765444433323333333333321111444555555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.2   1.8e-07   0.00023      22     139 ..      22     162 ..       9     178 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.8e-07
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqllde...aesael 94 
                                        +  ++ ++G+++ GK+ ++ +++ ++ ++gg +++ +++ l s  ++++    ++  e+ ++++ ++   +   e+
  gi|313125588|ref|YP_004035852.1|  22 RG-TVTQVYGPPAAGKTNVALSAAVRVAAAGGTVVYIDTEGL-SVDRFQQlAEHVAGPEQSIEDVTSRlivS---EA 93 
                                       33.6778*************9999999999999999999999.22233332222233344444444443332...22 PP

                            AAA_16  95 eawrekleeala...........................avpelagaeasrllellkrllallsrderplvl 139
                                        ++ e  ee  a                             +++ g++ +r+++++++ll+l+++++  +v+
  gi|313125588|ref|YP_004035852.1|  94 HDFEE-QEE--AvrdttefaeqadlvvldsatgfyrlerTMDKDGGESLRRVARQVTHLLSLARKHDLAVVI 162
                                       22222.122..13356668888889999999999999988888888888**************995554444 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.7   2.2e-05     0.028       3     127 ..      28     167 ..      26     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-05
                              CobU   3 vtGgarSGKSefAekla...eeskekvvYiATaeal.De..emaeRiarHre......rR...paeWetveepldla 64 
                                       v G+  +GK ++A + a   ++++++vvYi T     D+  ++ae +a  ++      +R   ++  +  e++++++
  gi|313125588|ref|YP_004035852.1|  28 VYGPPAAGKTNVALSAAvrvAAAGGTVVYIDTEGLSvDRfqQLAEHVAGPEQsiedvtSRlivSEAHDFEEQEEAVR 104
                                       78999999999999988777778899999999887755433555555543331111114456555555556666777 PP

                              CobU  65 ealkeeekkevvLvDcltlw..ltnllleeeaekveekleeeveellealkelkatvvlVsnEvg 127
                                       ++ + +e+++ v++D+ t +  l+++++++  e + ++++++v++ll+ +++++  v +++n v 
  gi|313125588|ref|YP_004035852.1| 105 DTTEFAEQADLVVLDSATGFyrLERTMDKDGGE-SLRRVARQVTHLLSLARKHDLAV-VITNQVF 167
                                       7776677799********984467888886654.8899*********9999987665.5678775 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.9e-05     0.062      46      86 ..      22      62 ..       4      90 .. 0.81
   2 ?   -0.7   0.0      0.77   9.9e+02      97     117 ..     101     121 ..      79     168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                         IstB_IS21 46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedL 86
                                      +     + Gp+ +GK+ +a + +v+ ++ag  v+++ +e L
  gi|313125588|ref|YP_004035852.1| 22 RGTVTQVYGPPAAGKTNVALSAAVRVAAAGGTVVYIDTEGL 62
                                      45556789****************************99877 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.77
                         IstB_IS21  97 gklaralkrllkvdllilDdl 117
                                       + +  + +   ++dl++lD  
  gi|313125588|ref|YP_004035852.1| 101 EAVRDTTEFAEQADLVVLDSA 121
                                       333333334445577777753 PP

>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.6   0.00012      0.15       5     112 ..      26     128 ..      21     169 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                    CobA_CobO_BtuR   5 ihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKgekesgElaal.kkl...eielerlgkegfvkmeeeekeed 77 
                                        +vy     GKt  Al  a+R ++ag  v+++       +++  + l +++   e ++e + ++  v +    +++d
  gi|313125588|ref|YP_004035852.1|  26 TQVYGPPAAGKTNVALSAAVRVAAAGGTVVYIDTEGL--SVDRFQQLaEHVagpEQSIEDVTSRLIV-S----EAHD 95 
                                       577777889*******************998874333..2333333313335544666666633333.3....3455 PP

                    CobA_CobO_BtuR  78 aaaakealekakealaseeydlvvlDEinyalklg 112
                                        ++ +ea++ ++e ++  ++dlvvlD  +  ++l+
  gi|313125588|ref|YP_004035852.1|  96 FEEQEEAVRDTTEFAE--QADLVVLDSATGFYRLE 128
                                       6666666666666663..47999999999888874 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     9e-05      0.12       3     110 ..      28     164 ..      26     178 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-05
                                       EESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS.............................STTHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel...gvefleisgsellsk.............................yvgesekkir 47 
                                       +yGpp  GKT +a + a  +   g +++ i+   l  +                              ++e+e+ +r
  gi|313125588|ref|YP_004035852.1|  28 VYGPPAAGKTNVALSAAVRVaaaGGTVVYIDTEGLSVDrfqqlaehvagpeqsiedvtsrlivseahDFEEQEEAVR 104
                                       7*************999996334555555555555533245555666666666666666676666666777778888 PP

                                       HHHHHHHHTSTSEEEEEETGGGHHHHH...TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEES CS
                               AAA  48 elfkeakekakpsilfiDEidalaksr...sgseseeeervvnqLlteldgvkkkeskvivigatn 110
                                       ++ + a++      +++D +  + + +   +++  e+ +rv+ q  + l+  +k+ +  + +++tn
  gi|313125588|ref|YP_004035852.1| 105 DTTEFAEQA---DLVVLDSATGFYRLErtmDKDGGESLRRVARQVTHLLSLARKH-D--LAVVITN 164
                                       887776544...5777777766666555555556666666666666666666662.2..4444444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.7e-05      0.11      20      76 ..      23      83 ..      19     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.7e-05
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie.....eeeekk 76
                                       ++  +YGp   GKt +   ++ +    +  v+y+ + ++ s +++++  e     e++ ++
  gi|313125588|ref|YP_004035852.1| 23 GTVTQVYGPPAAGKTNVALSAAVRVAAAGGTVVYI-DTEGLSVDRFQQLAEhvagpEQSIED 83
                                      67888********************9999888876.56677777777765544444333333 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00026      0.33      19      40 ..       5      26 ..       3      31 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                            PAXNEB 19 tStGtpsLDklLgGGLplGsil 40
                                      + tG++sLD+lLgGG+  G++ 
  gi|313125588|ref|YP_004035852.1|  5 VTTGCRSLDDLLGGGFERGTVT 26
                                      67**************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.73u 0.37s 00:00:01.10 Elapsed: 00:00:00.60
# Mc/sec: 1166.65
//
Query:       gi|313125589|ref|YP_004035853.1|  [L=380]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-37  127.2  13.1    2.4e-14   53.5   0.4    4.4  4  CBS              CBS domain
  ------ inclusion threshold ------
       0.04   14.7   0.9       0.13   13.0   0.1    2.2  2  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma
      0.061   13.8   0.1        1.2    9.6   0.0    2.7  2  Ribosomal_L9_C   Ribosomal protein L9, C-terminal domain
       0.11   12.8   0.0       0.74   10.1   0.0    2.3  3  Big_6            Bacterial Ig domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   7.7e-08   0.00034       2      54 ..       4      55 ..       3      58 .. 0.90
   2 !   19.6   0.0   2.1e-07   0.00095       2      56 ..      64     116 ..      63     117 .. 0.85
   3 !   53.5   0.4   5.3e-18   2.4e-14       1      55 [.     124     178 ..     124     180 .. 0.96
   4 !   39.4   1.0   1.3e-13   5.9e-10       1      55 [.     202     258 ..     202     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.7e-08
                                      HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                      +di t+d+v v+ d  l+++  ++++++ +++ +V +dg++ G++ ++ l+r 
  gi|313125589|ref|YP_004035853.1|  4 ADIATPDFVEVDADKRLGKVRSIFERENSRGV-IVTNDGEYAGVIGEKQLVRS 55
                                      7999********************999999**.6657*********9999986 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.1e-07
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllrall 56 
                                       +++m + +  ++  ++++ea+++++e +  r+ P   e +kl Gi+t  D+l+a+l
  gi|313125589|ref|YP_004035853.1|  64 SAVMKSAP-KIDRHEDVREAARMLVEGDT-RIaPAY-EGEKLYGIITGNDILEAVL 116
                                       56776666.9*************988776.888***.5667************987 PP

  == domain 3  score: 53.5 bits;  conditional E-value: 5.3e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+di t+dvvt+ + + +++a++++re+g+srlPV+dedgkl G++t +D++++ 
  gi|313125589|ref|YP_004035853.1| 124 VEDILTKDVVTIGEKSHVGQAINRLRENGISRLPVTDEDGKLTGVLTTHDIIEFS 178
                                       89***********************9999***********************985 PP

  == domain 4  score: 39.4 bits;  conditional E-value: 1.3e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE...ETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV...dedgklvGivtlrDllral 55 
                                       V d+m+++v+t++p + +  ++ +m ++++ ++ VV   d+d +++Gi+t++D+lral
  gi|313125589|ref|YP_004035853.1| 202 VYDLMSSPVITATPGEKIDTVVSRMFDNDIEGV-VVtptDSDTEVLGILTKTDVLRAL 258
                                       669*********************65888****.766*99999*************98 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.94   4.2e+03      50      76 ..      49      75 ..       6      87 .. 0.58
   2 ?   13.0   0.1     3e-05      0.13      13      82 ..     283     361 ..     276     363 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.94
                                      TTEEEEEEEEESSHHHHHHHHHHHHHH CS
                   Ribosomal_S30AE 50 kgkviraeeesedlyaaidlavdkler 76
                                       ++ +r+  e+++  +a+ + + k++r
  gi|313125589|ref|YP_004035853.1| 49 EKQLVRSRMEDDTKASAVMKSAPKIDR 75
                                      344555555556666666666666665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3e-05
                                       HHHHHHHHHHCCGGGG..-EEEEEEE.EE........EEEEEEEEECTTEEEEEEEEESSHHHHHHHHHHHHHHHHH CS
                   Ribosomal_S30AE  13 alkeyvekklekleky.fieadVtls.kk........kkvevtirlakgkviraeeesedlyaaidlavdklerqlr 79 
                                       ++ + ++k ++k +++ + +a+V+++ +k         + +v++r++ +  + ++ e    + a++ a+dkler + 
  gi|313125589|ref|YP_004035853.1| 283 SVVDSITKVVDKYQQMqVHHAHVRFHeHKeklrgtplIQSQVRLRTS-HGQVAGSGEGYGAEHAFHVALDKLERNVL 358
                                       44444555555555444499999999944557777666678888666.5555656778****************998 PP

                                       HCH CS
                   Ribosomal_S30AE  80 kyk 82 
                                         k
  gi|313125589|ref|YP_004035853.1| 359 ELK 361
                                       776 PP

>> Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00027       1.2      20      52 ..      94     125 ..      77     140 .. 0.71
   2 ?    0.8   0.0      0.15   6.8e+02      22      39 ..     159     176 ..     137     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                                       --B-TT-BBSS---HHHHHHHHHHHT-----GG CS
                    Ribosomal_L9_C  20 akagedgklFGsVtakdIaealkkklgieidkk 52 
                                       a a e++kl+G +t +dI ea+ ++l+  i  +
  gi|313125589|ref|YP_004035853.1|  94 APAYEGEKLYGIITGNDILEAVLDNLD-AISVE 125
                                       4567899**************998852.34444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.15
                                       B-TT-BBSS---HHHHHH CS
                    Ribosomal_L9_C  22 agedgklFGsVtakdIae 39 
                                       + edgkl G  t++dI+e
  gi|313125589|ref|YP_004035853.1| 159 TDEDGKLTGVLTTHDIIE 176
                                       478*************87 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   7.8e+03      40      56 ..      35      51 ..      29      58 .. 0.72
   2 ?   -1.6   0.0      0.76   3.4e+03      27      50 ..     156     179 ..     152     189 .. 0.62
   3 ?   10.1   0.0   0.00017      0.74       9      69 ..     306     367 ..     301     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                             Big_6 40 gtadadGeFsvtlepaq 56
                                      +++++dGe++  + ++q
  gi|313125589|ref|YP_004035853.1| 35 VIVTNDGEYAGVIGEKQ 51
                                      46788999887776655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.76
                             Big_6  27 VtvkdadgtvlgtgtadadGeFsv 50 
                                       + v+d+dg+++g  t  +  eFsv
  gi|313125589|ref|YP_004035853.1| 156 LPVTDEDGKLTGVLTTHDIIEFSV 179
                                       557777777776666555555555 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00017
                             Big_6   9 avsedgttltGkaeagatVtvkdadgtvlgtgta.dadGeFsvtlepaqangetlsvvatDa 69 
                                        + e  ++l G+    ++V+++++ g+v g+g   +a+ +F+v+l++ ++n  +l+ v +D+
  gi|313125589|ref|YP_004035853.1| 306 RFHEHKEKLRGTPLIQSQVRLRTSHGQVAGSGEGyGAEHAFHVALDKLERNVLELKGVNADE 367
                                       5677889999**********************8769999********999999999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2093.31
//
Query:       gi|313125590|ref|YP_004035854.1|  [L=435]
Description: subtilase protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-24   87.2   2.6    3.4e-22   79.1   2.6    2.7  1  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
       0.86   10.2   3.6         52    4.5   0.1    4.0  3  PQQ_3         PQQ-like domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   2.6   3.8e-26   3.4e-22       1     298 []      57     412 ..      57     413 .. 0.75

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 3.8e-26
                                       -TT-EEEEEC.S-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B. CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlD.tGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaana 76 
                                       g++v+v+v+D tG+d++hp l+ +++               ++   se+t +n ++++      HGt     aaa  
  gi|313125590|ref|YP_004035854.1|  57 GENVTVGVIDaTGFDTEHPTLNGHVTA--------------THAFGSEPTVRNRGQNG------HGT-----AAAA- 107
                                       789*******99**********66444..............34445666666666666......995.....4444. PP

                                       .SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEE..E-EESCETTCHHCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  77 peegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvin..mslgestslpktgrsiealainrav 151
                                           ++n vap+a++  +  +d + g         +a+++ +e++vdvi   +s+  +t  + ++ +++  ++ ra+
  gi|313125590|ref|YP_004035854.1| 108 ----TVNRVAPNASLV-LATFDSPRG-------FRDAVNWMVESNVDVIVapVSFL-GTAGDGSSLISR--VATRAT 169
                                       ....689********9.555555443.......3469**********765115555.666666666666..888888 PP

                                       .CCT-EEEEE--SS-.............................................................. CS
                                       xxxxxxxxxxxxxxx.............................................................. RF
                      Peptidase_S8 152 nkkgvlvviSaGNng.............................................................. 166
                                         +gv++v+SaGN                                                                
  gi|313125590|ref|YP_004035854.1| 170 -LEGVVFVASAGNLArghwsgqydtvrngtlqfgadrrlylsgddrritvwlswperfrshdytaelyrtgggrttl 245
                                       .68***********977888888888888888888888888888888888888888888888888888888888777 PP

                                       ..............................................T-HH....EEE-TTCEECTTTSTTCEEEEEE CS
                                       ..............................................xxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 167 ..............................................ktgs....slqagspvgtpstsknvitvgay 193
                                                                                     +  +    + + + +  +p+t+ +v+tvga 
  gi|313125590|ref|YP_004035854.1| 246 iarsqpyhgdntpnkrfvvrtrpggiyhvvvrgpqnathvplelssP--ThdfrQPTPSGSLTAPATAPGVLTVGAL 320
                                       77777777777777777777777777777777665554444444432..0434444455555557777788888888 PP

                                       S.TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT-- CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 194 t.tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpklt 269
                                       + + g + pfSsrGp+sdg+l++d+vap   +++t + +            + G+S ++P a g+aAl+ls  p+ +
  gi|313125590|ref|YP_004035854.1| 321 DpNTGRLEPFSSRGPTSDGRLGVDVVAPDRGVSPTFEGR------------FIGSSVSAPYAGGVAALVLSVDPDQS 385
                                       888899**********************99855554444............58************************ PP

                                       HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 270 petvraallntAqdlgkadniesfaqGaG 298
                                       p++v+ +l++tA+d+gk+    + a G+G
  gi|313125590|ref|YP_004035854.1| 386 PREVEVLLEQTATDIGKP--NADPATGYG 412
                                       ***************888..555566665 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.02   1.8e+02      16      33 ..     159     182 ..     149     186 .. 0.71
   2 ?    0.6   0.0     0.099   8.9e+02      20      34 ..     203     217 ..     187     219 .. 0.87
   3 ?    4.5   0.1    0.0058        52       6      30 ..     297     321 ..     296     329 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.02
                             PQQ_3  16 sp.......avdgglvyvgtgdGtl 33 
                                       s+       a+ +g+v+v++  G+l
  gi|313125590|ref|YP_004035854.1| 159 SLisrvatrATLEGVVFVASA-GNL 182
                                       3444446667779*******8.876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.099
                             PQQ_3  20 dgglvyvgtgdGtly 34 
                                       +++++y +++d +++
  gi|313125590|ref|YP_004035854.1| 203 ADRRLYLSGDDRRIT 217
                                       6999******99987 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0058
                             PQQ_3   6 svqlpgpvnsspavdgglvyvgtgd 30 
                                       ++++p+   ++pa++ g++ vg+ d
  gi|313125590|ref|YP_004035854.1| 297 RQPTPSGSLTAPATAPGVLTVGALD 321
                                       67999988899***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2710.28
//
Query:       gi|313125591|ref|YP_004035855.1|  [L=199]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-15   55.3   0.1      9e-15   54.5   0.1    1.4  1  HTH_20          Helix-turn-helix domain
    5.6e-06   26.1   0.0    1.1e-05   25.1   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
    9.7e-06   25.4   0.2      5e-05   23.1   0.0    2.2  3  MarR_2          MarR family
     0.0012   18.4   0.0      0.002   17.7   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0017   18.8   0.1     0.0052   17.2   0.0    1.8  2  HTH_27          Winged helix DNA-binding domain
     0.0068   16.2   0.0      0.027   14.3   0.0    2.1  2  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.038   14.0   0.0       0.13   12.3   0.0    1.8  2  Dimerisation2   Dimerisation domain
      0.078   13.3   0.0       0.13   12.6   0.0    1.3  1  DUF2513         Hypothetical protein (DUF2513)
      0.081   12.8   0.0       0.17   11.8   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
        0.1   12.2   0.0       0.18   11.4   0.0    1.5  1  Sigma70_r4      Sigma-70, region 4
       0.11   12.7   0.0       0.17   12.0   0.0    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.13   11.9   0.0       0.39   10.4   0.0    1.7  1  Sigma70_r4_2    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.1     6e-18     9e-15       1      60 [.      30      88 ..      30      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 6e-18
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      d +++AL++ +Rr+++r L  +e+ tas++a+rld+s ++++yHL +L +a+Lve+v+++
  gi|313125591|ref|YP_004035855.1| 30 DAVIDALSSDTRRAVFRSL-FDEPGTASDVADRLDTSVQNVHYHLSTLTDAELVESVDTR 88
                                      5789***************.************************************9876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   7.6e-09   1.1e-05       2      47 .]      39      84 ..      38      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.6e-09
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                       tR+ + ++L +++ ++++ a+ l+ s  +v +HL+ L +a LVe+
  gi|313125591|ref|YP_004035855.1| 39 DTRRAVFRSLFDEPGTASDVADRLDTSVQNVHYHLSTLTDAELVES 84
                                      69999***************************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.3e-08     5e-05       6      54 ..      40      85 ..      35      91 .. 0.90
   2 ?   -2.8   0.0         4     6e+03      22      31 ..     120     129 ..     114     132 .. 0.57
   3 ?   -1.9   0.0       2.1   3.2e+03       9      16 ..     180     187 ..     176     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.3e-08
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + + v   L ++pg   t++++a+rl+ s ++v+++l  L +a Lve +
  gi|313125591|ref|YP_004035855.1| 40 TRRAVFRSLFDEPG---TASDVADRLDTSVQNVHYHLSTLTDAELVESV 85
                                      67788889999**9...*****************************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4
                                       EEHHHHHHHH CS
                            MarR_2  22 ltvgelarrl 31 
                                        + +++++ l
  gi|313125591|ref|YP_004035855.1| 120 QSLTDIVAGL 129
                                       3445555555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.1
                                       HHHHHHHC CS
                            MarR_2   9 rvLaaLgr 16 
                                        vL++Lg+
  gi|313125591|ref|YP_004035855.1| 180 GVLFFLGC 187
                                       59****98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.3e-06     0.002      19      48 .]      54      83 ..      38      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + +++A+rl+ S+++v+++l  L++++l++
  gi|313125591|ref|YP_004035855.1| 54 TASDVADRLDTSVQNVHYHLSTLTDAELVE 83
                                      5689***********************996 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.5   6.7e+03      26      42 ..      20      36 ..       8      38 .. 0.65
   2 !   17.2   0.0   3.5e-06    0.0052      16      51 ..      50      85 ..      41      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.5
                            HTH_27 26 grlnvedshisyslkkL 42
                                      ++l+v+d+ +  ++++L
  gi|313125591|ref|YP_004035855.1| 20 RVLDVDDAEADAVIDAL 36
                                      45666666666666555 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.5e-06
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                      +++ +++d+++rl+++ ++++y l+ Lt ++Lve+ 
  gi|313125591|ref|YP_004035855.1| 50 DEPGTASDVADRLDTSVQNVHYHLSTLTDAELVESV 85
                                      78999****************************654 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.8e-05     0.027       8      50 ..      32      84 ..      29      86 .. 0.85
   2 ?   -2.3   0.0       2.7   4.1e+03      20      29 ..     121     130 ..     116     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                                      HHCT-CTTBSS..........-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqe..........ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++dal++ +++           t s++A+r++ +  +vh +L+tL+   +ve 
  gi|313125591|ref|YP_004035855.1| 32 VIDALSSDTRRavfrslfdepGTASDVADRLDTSVQNVHYHLSTLTDAELVES 84
                                      6777777777777777777778*************************999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.7
                                       BHHHHHHHHT CS
                          HTH_IclR  20 tlselArrtg 29 
                                       +l+++ + +g
  gi|313125591|ref|YP_004035855.1| 121 SLTDIVAGLG 130
                                       7999999998 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.6e-05      0.13      22      66 ..      43      86 ..      31      99 .. 0.84
   2 ?   -2.1   0.0       2.6   3.8e+03      44      62 ..     114     132 ..     110     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.6e-05
                     Dimerisation2 22 gvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerek 66
                                      +vF  L + ep +a++va++l++sv+ ++  l +++  +L e+  
  gi|313125591|ref|YP_004035855.1| 43 AVFRSLFD-EPGTASDVADRLDTSVQNVHYHLSTLTDAELVESVD 86
                                      79999*99.9*************************9999998653 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                     Dimerisation2  44 asvkGterLldacvaLgLL 62 
                                       +s++  + L d +++Lg L
  gi|313125591|ref|YP_004035855.1| 114 ISPHVRQSLTDIVAGLGVL 132
                                       5667778899999999988 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.6e-05      0.13      37      65 ..      64      92 ..      43     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.6e-05
                           DUF2513 37 yskeeiiyhlkllaeagLieaekkkakss 65
                                      +s +++ yhl+ l +a+L+e+++++++++
  gi|313125591|ref|YP_004035855.1| 64 TSVQNVHYHLSTLTDAELVESVDTRYSEK 92
                                      445689*******************9988 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.17      20      58 ..      50      88 ..      43     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       +p ta+++a +l+ + ++v   L+ L d+ lVe ++ r
  gi|313125591|ref|YP_004035855.1| 50 DEPGTASDVADRLDTSVQNVHYHLSTLTDAELVESVDTR 88
                                      5799******************************99877 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.18       7      38 ..      39      70 ..      32      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4  7 ererevlelrfgeglTleEIgerlgiSrerVr 38
                                      +  r v++  f+e+ T +++++rl+ S   V+
  gi|313125591|ref|YP_004035855.1| 39 DTRRAVFRSLFDEPGTASDVADRLDTSVQNVH 70
                                      45688999999****************99886 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.17      20      53 ..      54      87 ..      53      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                    B-block_TFIIIC 20 tqsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                      t sd+a  ++ ++ +++y+l +L++  L++ + +
  gi|313125591|ref|YP_004035855.1| 54 TASDVADRLDTSVQNVHYHLSTLTDAELVESVDT 87
                                      6789999999*******************98876 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00026      0.39       5      48 ..      30      74 ..      27      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                                      HHHHTTS-HHHHHHHHHHHTS-.--HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2  5 realaeLperqreifllryleg.lsykEIAellgisegtVksrls 48
                                      ++ +++L+ + r+++  + +++  +  ++A +l++s+++V ++ls
  gi|313125591|ref|YP_004035855.1| 30 DAVIDALSSDTRRAVFRSLFDEpGTASDVADRLDTSVQNVHYHLS 74
                                      5678888888888888876666346789***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1212.62
//
Query:       gi|313125592|ref|YP_004035856.1|  [L=337]
Description: hypothetical protein Hbor_08200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0042   17.5   1.0      0.055   13.9   0.1    3.0  4  MG2       MG2 domain


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.25   4.5e+03      50      71 ..      37      58 ..      29      67 .. 0.76
   2 !   13.9   0.1   3.1e-06     0.055      52      88 ..      79     115 ..      37     121 .. 0.71
   3 ?   -0.1   0.0     0.074   1.3e+03      63      84 ..     233     253 ..     181     265 .. 0.69
   4 ?   -1.7   0.0      0.23   4.2e+03      34      53 ..     277     296 ..     260     309 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.25
                                      EEEEEE-CTTEEEEEEE--TT- CS
                               MG2 50 elplatdetggaesefalpeaa 71
                                      +l+l +++ +++++e +lpe++
  gi|313125592|ref|YP_004035856.1| 37 TLTLHQSTGQTVSGETTLPEGT 58
                                      5566677777788888888765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.1e-06
                                       EEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT- CS
                               MG2  52 platdetggaesefalpeaaklGeysvelsadsaees 88 
                                       + + +e g++e  f+ +e++k+G+++v++s d+++ +
  gi|313125592|ref|YP_004035856.1|  79 ETTVTEHGTFEAHFDMSEGPKTGTFEVTVSHDGDSLT 115
                                       237789999********************55554443 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.074
                                       EEEE--TT--SEEEEEEEEECS CS
                               MG2  63 sefalpeaaklGeysvelsads 84 
                                        e++l +   +G+y++e+ + +
  gi|313125592|ref|YP_004035856.1| 233 EEWELEDLIHRGDYQMEI-YPG 253
                                       578888888899999998.433 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.23
                                       EEEEEEEE-TTSSEEEEEEE CS
                               MG2  34 lplkltirdpdgkevkelpl 53 
                                       +p++ +++ +  +++ ++  
  gi|313125592|ref|YP_004035856.1| 277 TPTETKVTETTTQQTTNTAA 296
                                       66666666666665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1950.67
//
Query:       gi|313125593|ref|YP_004035857.1|  [L=85]
Description: hypothetical protein Hbor_08210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 558.68
//
Query:       gi|313125594|ref|YP_004035858.1|  [L=570]
Description: hypothetical protein Hbor_08220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0002   20.7   0.0    0.00052   19.4   0.0    1.6  2  Glyco_trans_1_3  Glycosyl transferase family 1
     0.0016   18.4   0.0      0.004   17.2   0.0    1.7  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.083   13.1   0.0       0.55   10.4   0.0    2.3  2  UPF0180          Uncharacterised protein family (UPF0180)
      0.097   13.5   0.0       0.27   12.1   0.0    1.8  1  DUF3349          Protein of unknown function (DUF3349)
        3.1    7.2   6.4       0.61    9.5   1.7    2.4  2  UCR_Fe-S_N       Ubiquitinol-cytochrome C reductase Fe-S subu


Domain annotation for each model (and alignments):
>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.5e-07   0.00052      10     122 ..      12     122 ..       5     140 .. 0.85
   2 ?   -2.9   0.1      0.89   3.2e+03     251     270 ..     231     250 ..     227     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-07
                   Glyco_trans_1_3  10 eGaGhasRsrvvlehL.arghevkvvvsgraldvLekef.dvneivglsivyeenrvrklktllknlqv.aaklakn 83 
                                       eGaGha+R ++++++L   g e++++  g + ++++ +  d +e +++  + +     +  t++  l++ +++++++
  gi|313125594|ref|YP_004035858.1|  12 EGAGHATRMLAIARALeSAGCEIQIAGGGAGARFVDLNGyDAFEPTTVDYIGDY----QDGTVTDLLAGsIPDTTRR 84 
                                       9***************666****************9886699998888877543....3467777786559****** PP

                   Glyco_trans_1_3  84 vkalvelvedfrpdlvvtDFealtallakrhkLPvisvd 122
                                       ++++ve +++  pd vvtD + +++++a r ++P   v 
  gi|313125594|ref|YP_004035858.1|  85 ISEIVEWLRKTDPDAVVTD-DMFAVMAAVRVGIPQYVVK 122
                                       *******************.7888889999988866555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.89
                   Glyco_trans_1_3 251 LataraviagagftLmteal 270
                                       L++a av++++  t+m  a+
  gi|313125594|ref|YP_004035858.1| 231 LRAADAVVCSGYSTVMDAAV 250
                                       899******99999998876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06     0.004       3     126 ..      15     136 ..      13     152 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                    Glyco_transf_4   3 GverhvleLaraLarrGheVtvvtpgddgpleeev............elvvrvprvplpllkrllrslaflrrlrrl 67 
                                       G ++ +l +araL  +G+e+++   g + ++ +              +  ++ + v  +l +  + + + ++ + ++
  gi|313125594|ref|YP_004035858.1|  15 GHATRMLAIARALESAGCEIQIAGGGAGARFVDLNgydafepttvdyIGDYQDGTVTDLLAGSIPDTTRRISEIVEW 91 
                                       78899******************6666666655556666666666652223333333366667777888889999** PP

                    Glyco_transf_4  68 lkrekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllral 126
                                       l++ +pD v + + +a++aa    r   gip  +  H++          + ++ + ++l
  gi|313125594|ref|YP_004035858.1|  92 LRKTDPDAVVTDDMFAVMAA---VR--VGIPQYVVKHDMP---------SIYEDRTERL 136
                                       *********99997776555...45..5999999999998.........3444444444 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.92   3.3e+03      12      25 ..      23      36 ..      20      48 .. 0.81
   2 ?   10.4   0.0   0.00015      0.55       7      48 ..     197     247 ..     196     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.92
                           UPF0180 12 vkeaLrekGYeVvd 25
                                      +++aL++ G+e+  
  gi|313125594|ref|YP_004035858.1| 23 IARALESAGCEIQI 36
                                      899*******9975 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                           UPF0180   7 egLsnvkeaLrekGYeVvdlet...........eedaqsvdaiVvtGqdtnvm 48 
                                       ++L+ v e L+++G +Vv++++           +   + +da+V++G +t + 
  gi|313125594|ref|YP_004035858.1| 197 SNLESVGERLTDRGLSVVNVGSegweavpsllpY--LRAADAVVCSGYSTVMD 247
                                       58********************999999988544..999********887664 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.4e-05      0.27       3      31 ..      85     113 ..      83     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHHHH-TT-B-HHHHHHHHHHHC CS
                           DUF3349   3 lasileWLragYPegvPeqdyvpLlalLr 31 
                                       +++i+eWLr+  P+ v  +d+++++a  r
  gi|313125594|ref|YP_004035858.1|  85 ISEIVEWLRKTDPDAVVTDDMFAVMAAVR 113
                                       579**********************9876 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       1.7   6.2e+03      19      33 ..     244     259 ..     242     259 .. 0.54
   2 ?    9.5   1.7   0.00017      0.61       4      32 ..     323     351 ..     320     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                        UCR_Fe-S_N  19 TgavgaV.GaaaaawP 33 
                                       T++ +aV G+ ++++P
  gi|313125594|ref|YP_004035858.1| 244 TVMDAAVaGTHCVVYP 259
                                       6665555266666666 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00017
                        UCR_Fe-S_N   4 aesdeptRRDFLyiATgavgaVGaaaaaw 32 
                                       ++ ++ptRR  L +A++ vg+ + ++aa+
  gi|313125594|ref|YP_004035858.1| 323 DQTGKPTRRGMLRAAAATVGTTVIGTAAV 351
                                       67899*********999999877776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3710.92
//
Query:       gi|313125595|ref|YP_004035859.1|  [L=444]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-30  105.2   0.1      5e-30  104.2   0.1    1.6  1  OrfB_IS605      Probable transposase
      1e-19   70.2   0.5      2e-19   69.2   0.5    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
        1.3    8.6   4.5        3.1    7.4   4.5    1.6  1  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.1   8.4e-34     5e-30       2     119 ..     180     295 ..     179     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 8.4e-34
                        OrfB_IS605   2 ipveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       +pv+v+++ l++p  ++ a++D+G+nnL+++ t++g++ ly+gr l+ +++++++eia+lqs+l++    ++ s ++
  gi|313125595|ref|YP_004035859.1| 180 QPVTVDDSrLAQPLASEEAALDIGANNLVACTTTTGQQLLYEGRDLFDRFRETTREIARLQSLLEEG---RYSSHRI 253
                                       6888888889*********************************************************...7****** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       +rl+++r++rr+h++++la++li++l+++gv+t++vg+++d+
  gi|313125595|ref|YP_004035859.1| 254 RRLYDRRTKRRDHAQDALARDLIERLYDEGVSTVYVGALTDV 295
                                       **************************************9986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.5   3.4e-23     2e-19       1      69 []     314     381 ..     314     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 3.4e-23
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       fr + +++++ akeyG++ve+ ++a+TS++C++Cgs+ +++++++t++Cp Cgfe ++D++A+   l+r
  gi|313125595|ref|YP_004035859.1| 314 FRAFVNRVACTAKEYGMSVEVRSEAWTSQECPNCGSTEETTRHRDTLTCP-CGFEGHADLVASETFLRR 381
                                       899***********************************************.************988876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.5   0.00052       3.1       2      23 ..     343     363 ..     342     365 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00052
                                       EETTTTCEECHEETSTTCEEES CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCt 23 
                                        CPnCgst+ ++   r +l+C+
  gi|313125595|ref|YP_004035859.1| 343 ECPNCGSTE-ETTRHRDTLTCP 363
                                       5******98.444445566776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2762.79
//
Query:       gi|313125596|ref|YP_004035860.1|  [L=45]
Description: hypothetical protein Hbor_08240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 268.32
//
Query:       gi|313125597|ref|YP_004035861.1|  [L=303]
Description: glycosyl transferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-10   40.8   0.1    4.7e-10   39.2   0.0    1.8  2  Glyco_transf_21  Glycosyl transferase family 21
    7.8e-06   25.8   2.3    2.9e-05   24.0   1.8    2.1  2  Glycos_transf_2  Glycosyl transferase family 2
     0.0011   18.9   0.0     0.0016   18.3   0.0    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   7.8e-14   4.7e-10       3     172 ..      53     207 ..      50     208 .. 0.85
   2 ?   -1.8   0.1      0.31   1.8e+03      66     103 ..     250     287 ..     242     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 7.8e-14
                   Glyco_transf_21   3 vrrllvsgdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaal 79 
                                       v+ ++v+g p g++ K n++  ++e+a++d +v+ D+d + + d L++l a  e+   g V+ +p+ ++++ l   l
  gi|313125597|ref|YP_004035861.1|  53 VE-VVVAGVPDGCSGKANAIDVGMERARHDRIVWTDDDFHHPDDWLATLNADYET--HGPVSEVPFFVGQDPLSILL 126
                                       55.999************************************************7..9***************9999 PP

                   Glyco_transf_21  80 eaafl.ntlagvlqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsv 155
                                       e  +  +    v++      + ++G ++++ r++L+     ++l++++ +D  lg+++    l+ +         ++
  gi|313125597|ref|YP_004035861.1| 127 EPGYAfGGTFSVWAG-----DVIWGGAVIFERSDLDVDAFRKELRQTISDDGLLGEYIDVTTLRRARRV------EM 192
                                       888754555666666.....99**************999999**************9986655543322......33 PP

                   Glyco_transf_21 156 prrsslrallaRqlrWa 172
                                       +   s+r+ l+R +r++
  gi|313125597|ref|YP_004035861.1| 193 G--GSVRETLERHVRFM 207
                                       3..26778888888886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.31
                   Glyco_transf_21  66 lpvgsdakglaaaleaafl.ntlagvlqaklsglgfavG 103
                                       ++++ +++ ++a l+   + ++++ +++a  ++  f++G
  gi|313125597|ref|YP_004035861.1| 250 IYLAFGQRRWTALLAYPSVlAMVPLMAYA-YARRTFVWG 287
                                       55566666677777666665677777777.788888887 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   1.8   4.8e-09   2.9e-05      65     110 ..      65     110 ..      14     125 .. 0.73
   2 ?   -3.0   0.0      0.91   5.4e+03      52      73 ..     177     198 ..     159     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.8e-09
                                       -HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTC CS
                   Glycos_transf_2  65 vGkagalnaglraatgdyilflDaDdepdpdwleklvealekdgad 110
                                        Gka+a+  g+++a++d i++ D+D  +++dwl  l + +e +g+ 
  gi|313125597|ref|YP_004035861.1|  65 SGKANAIDVGMERARHDRIVWTDDDFHHPDDWLATLNADYETHGPV 110
                                       39********************************999999998884 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.91
                                       C-TTEEEEEESSS-HHHHHHHH CS
                   Glycos_transf_2  52 edprvrvirreenvGkagalna 73 
                                       e+ +v+ +rr ++v  +g++++
  gi|313125597|ref|YP_004035861.1| 177 EYIDVTTLRRARRVEMGGSVRE 198
                                       6778888899888888777665 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.8e-07    0.0016      27     126 ..      25     123 ..       4     187 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.8e-07
                   Glyco_tranf_2_3  27 qeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnl.gstgksralnealravksdlvllvDdDtvveP 102
                                       q  p++e+ vv+d +++ +++  +     lp+ +v vvv    + g  gk++a+  +++++++d ++  DdD    +
  gi|313125597|ref|YP_004035861.1|  25 QLGPDDELLVVCDDESDRVAD-RD----GLPA-GVEVVVAGV-PdGCSGKANAIDVGMERARHDRIVWTDDDFHHPD 94 
                                       334778999999776666655.24....4676.566665533.33667************************99999 PP

                   Glyco_tranf_2_3 103 dtlkrllqffltp.....kvgavgtpvfl 126
                                       d l+ l++ ++t+      + +vg++ ++
  gi|313125597|ref|YP_004035861.1|  95 DWLATLNADYETHgpvseVPFFVGQDPLS 123
                                       99998888774443333345555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1620.28
//
Query:       gi|313125598|ref|YP_004035862.1|  [L=89]
Description: hypothetical protein Hbor_08270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0017   18.0   4.8     0.0021   17.8   4.8    1.1  1  CAF-1_p150  Chromatin assembly factor 1 complex p150 subunit,


Domain annotation for each model (and alignments):
>> CAF-1_p150  Chromatin assembly factor 1 complex p150 subunit, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   4.8   1.1e-07    0.0021      38      90 ..      20      72 ..       9      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-07
                        CAF-1_p150 38 kkrlkeekkeekerakeearrkkeeekekkekerrekkekdekekaeklrlke 90
                                      ++ l+ee+k +++r++    r++eee e   +er e   +d   +ae+   k 
  gi|313125598|ref|YP_004035862.1| 20 ADGLREEAKPVERRIRSALGREREEESEPTGRERLESELRDVPRRAERGGKKA 72
                                      6789*************************************999999865544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 543.33
//
Query:       gi|313125599|ref|YP_004035863.1|  [L=177]
Description: ATP:cob(i)alamin adenosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-55  187.5   0.0      2e-55  187.4   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase
     0.0078   16.4   1.3       0.42   10.9   0.0    2.4  2  Osmo_CC          Osmosensory transporter coiled coil
  ------ inclusion threshold ------
       0.04   14.3   0.3         17    5.8   0.1    2.6  3  CLZ              C-terminal leucine zipper domain of cyclic n
       0.12   13.0   2.1       0.18   12.4   2.1    1.6  1  ABATE            Putative stress-induced transcription regula


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.4   0.0   4.5e-59     2e-55       1     163 [.       3     163 ..       3     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 4.5e-59
                                       XXXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BT CS
                   Cob_adeno_trans   1 iyTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekk 77 
                                       iyT +GD+G+T+l +++rvsK++pr+eayGtvDe+n+++g +r   ++  ++++e+Le+iqn+L+ ++a++a+p+ +
  gi|313125599|ref|YP_004035863.1|   3 IYTGRGDEGMTDLRDMSRVSKTSPRIEAYGTVDEVNALVGSVR---PTGYDDIDEKLERIQNHLHIVQADFANPDPE 76 
                                       9******************************************...66689***********************999 PP

                                       CCG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHH CS
                   Cob_adeno_trans  78 kekkkiteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRL 153
                                        ++  i e++vee+e+ id++e+el+pl+sfilpgg+ + a+lh+aR+v RraER++v+la ++ v+e++++ylNRL
  gi|313125599|ref|YP_004035863.1|  77 DDDPVIAEAHVEEVESYIDDVEEELEPLQSFILPGGGDSGAKLHHARAVSRRAERRAVALATDQsVNEQAIQYLNRL 153
                                       99999*******************************************************998889*********** PP

                                       HHHHHHHHHH CS
                   Cob_adeno_trans 154 SDlLfvlarv 163
                                       SD Lfv ar 
  gi|313125599|ref|YP_004035863.1| 154 SDALFVFARL 163
                                       ********97 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.012        55      14      27 ..      49      62 ..      47      68 .. 0.70
   2 !   10.9   0.0   9.4e-05      0.42      13      33 ..      86     106 ..      81     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                                      XTHHHHHHHHHHHH CS
                           Osmo_CC 14 YdnIEqkvedidee 27
                                      Yd+I +k+e i + 
  gi|313125599|ref|YP_004035863.1| 49 YDDIDEKLERIQNH 62
                                      77777777777655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.4e-05
                                       XXTHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  13 hYdnIEqkvedideeIaaLee 33 
                                       h +++E  ++d++ee++ L+ 
  gi|313125599|ref|YP_004035863.1|  86 HVEEVESYIDDVEEELEPLQS 106
                                       5589**************995 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0043        19      26      48 ..      49      71 ..      32      72 .. 0.84
   2 ?    5.8   0.1    0.0038        17      18      44 ..      79     105 ..      76     107 .. 0.85
   3 ?   -2.3   0.0       1.3   5.9e+03      26      37 ..     143     154 ..     130     166 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0043
                               CLZ 26 qkeleekverLessLeaLqtrla 48
                                       ++++ek+er++++L + q  +a
  gi|313125599|ref|YP_004035863.1| 49 YDDIDEKLERIQNHLHIVQADFA 71
                                      5799************9998876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0038
                               CLZ  18 eaakagaeqkeleekverLessLeaLq 44 
                                       ++  a+a+ +e+e+ ++ +e++Le Lq
  gi|313125599|ref|YP_004035863.1|  79 DPVIAEAHVEEVESYIDDVEEELEPLQ 105
                                       556688999***************999 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.3
                               CLZ  26 qkeleekverLe 37 
                                       ++++ + ++rL 
  gi|313125599|ref|YP_004035863.1| 143 NEQAIQYLNRLS 154
                                       233333333333 PP

>> ABATE  Putative stress-induced transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.1   4.1e-05      0.18      49     105 ..     109     173 ..      13     177 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                                       ...........HHHHHH.HHHHHHHHTHHHH.........HHHHHHHHHS----EEEE-TTS-E.. CS
                             ABATE  49 a........elararaL.RealrallaaaaagdpppaaalaalnallaaappaprLvrhddgpvdr 105
                                                 l  ara+ R a r+ + a a+++++ ++a++ ln+l +a  + +rLv++ dg +++
  gi|313125599|ref|YP_004035863.1| 109 LpgggdsgaKLHHARAVsRRAERRAV-ALATDQSVNEQAIQYLNRLSDALFVFARLVNQRDGVPEE 173
                                       03344444444555555333334444.3445569************************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1081.53
//
Query:       gi|313125600|ref|YP_004035864.1|  [L=88]
Description: glutaredoxin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-15   56.2   0.0    4.2e-15   55.9   0.0    1.0  1  GST_N_3        Glutathione S-transferase, N-terminal domain
    1.4e-14   54.1   0.0    1.7e-14   53.7   0.0    1.1  1  Glutaredoxin   Glutaredoxin
      6e-14   52.1   0.0    6.9e-14   51.9   0.0    1.1  1  GST_N_2        Glutathione S-transferase, N-terminal domain
    2.2e-07   31.1   0.0    2.7e-07   30.8   0.0    1.1  1  GST_N          Glutathione S-transferase, N-terminal domain
      0.004   17.2   0.1     0.0051   16.8   0.1    1.2  1  Thioredoxin_3  Thioredoxin domain
     0.0091   16.4   0.1      0.013   15.9   0.1    1.3  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.012   16.1   0.0    1.2  1  Thioredoxin_2  Thioredoxin-like domain
       0.18   12.1   0.0       0.22   11.8   0.0    1.2  1  Tom37          Outer mitochondrial membrane transport complex


Domain annotation for each model (and alignments):
>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   1.9e-18   4.2e-15       2      69 ..      15      85 ..      14      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 1.9e-18
                                      ES-TTSHHHHHHHHHHHHHT--EEEE---TTTT.HHHHHHH-TT--SSEEETTS-..EEESHHHHHHHHHH CS
                           GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevtpgeh.deellaknplgkvPvLeddge..altdSlaIidyLee 69
                                      y   ++py+ +v+ aL+e g+++e+++v+  ++ ++e++++++++ vPvL+dd++   + +S+ I++y+e+
  gi|313125600|ref|YP_004035864.1| 15 YALDGCPYCEKVHDALEEHGVEYETEWVEALHSeRNEVKRVSGQRSVPVLVDDERgiTMGESDNIVQYIER 85
                                      77899***********************8555459*****************95555************97 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   7.7e-18   1.7e-14       1      56 [.      12      67 ..      12      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 7.7e-18
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEET CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfid 56
                                      ++++   +CpyC k+ ++L+e+gv++e+  v++ +++r e+k++sg+r+vP+++ d
  gi|313125600|ref|YP_004035864.1| 12 ITVYALDGCPYCEKVHDALEEHGVEYETEWVEALHSERNEVKRVSGQRSVPVLVDD 67
                                      79**************************************************9844 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   3.1e-17   6.9e-14       2      69 ..      20      85 ..      19      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 3.1e-17
                                      -HHHHHHHHHHHHCT--EEEEEEH...-TTSHHHHHHHHCTTTSSSEEE-CTTE.EEESHHHHHHHHHH CS
                           GST_N_2  2 CPwahRvlialalkglediisvvvlepkgfekseefprlnprgtVPvLwdkdgq.vineSseIlrylet 69
                                      CP++ +v+ al+++g+e+++++v  e  + e+  e++r++++ +VPvL+d++      eS  I++y+e+
  gi|313125600|ref|YP_004035864.1| 20 CPYCEKVHDALEEHGVEYETEWV--EALHSER-NEVKRVSGQRSVPVLVDDERGiTMGESDNIVQYIER 85
                                      ***********************..4455555.6****************85553666*********97 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.2e-10   2.7e-07       1      76 []      10      85 ..      10      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.2e-10
                                      EEEEEESSSTSHTHHHHHHHHHHTT-EEEEEEECSTTTCGGCHHHHHHCTTS-SSEEEET..TEEEESHHHHHHHHHH CS
                             GST_N  1 avltlysirgsprahrirlllaakgveyevvpldfeageekspellklnplgkvPaLedn..gkkltESraIleYiar 76
                                      +++t+y   g+p+ ++++ +l++ gveye+  ++   +e+   e +++     vP+L+d+  g +  ES  I++Yi+r
  gi|313125600|ref|YP_004035864.1| 10 MSITVYALDGCPYCEKVHDALEEHGVEYETEWVEALHSER--NEVKRVSGQRSVPVLVDDerGITMGESDNIVQYIER 85
                                      789***************************9999744433..899999999*********9999999*********86 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.3e-06    0.0051       1      63 [.      10      74 ..      10      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                                      EEEEE.ESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEEECTTCEEEES CS
                     Thioredoxin_3  1 meikv.lgpgCakCpklekavkeaaaekgikaevekvtdfeei.ekygVmsvPalvidgkvvvsG 63
                                      m i v    gC++C+k+  a++e   e +++     +++ +e+    g +svP lv d++  ++G
  gi|313125600|ref|YP_004035864.1| 10 MSITVyALDGCPYCEKVHDALEEHGVEYETEWVEALHSERNEVkRVSGQRSVPVLVDDERGITMG 74
                                      6788866789*****99888888777776555333334445554677889999999888877777 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   5.6e-06     0.013       2      31 ..      12      41 ..      11      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.6e-06
                                      EEEEE-TT-HHHHHHHHHHHHHCCCTTEEE CS
                            DUF836  2 ltLyskpgChlCeqakekLkelkleeglel 31
                                      +t y  +gC+ Ce+++++L+e ++e + e+
  gi|313125600|ref|YP_004035864.1| 12 ITVYALDGCPYCEKVHDALEEHGVEYETEW 41
                                      899999**************9888877554 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.0   5.2e-06     0.012       9      60 ..      12      62 ..       9      86 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.2e-06
                     Thioredoxin_2  9 lvvftdpdCpyCkklkkelkelddvtvrvllfp.lkpsfepkavaiwcakekk 60
                                      ++v++ ++CpyC+k ++ l+e  +v+  +  +  l+++   ++ +++++++++
  gi|313125600|ref|YP_004035864.1| 12 ITVYALDGCPYCEKVHDALEEH-GVEYETEWVEaLHSE-RNEVKRVSGQRSVP 62
                                      6788899************999.666665566666665.55555555555554 PP

>> Tom37  Outer mitochondrial membrane transport complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.22      25      55 ..      54      85 ..      36      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                             Tom37 25 slsptgeLPaLkdge.gtwisgfdnIveylrk 55
                                       +s ++++P+L d+e g ++ + dnIv+y+++
  gi|313125600|ref|YP_004035864.1| 54 RVSGQRSVPVLVDDErGITMGESDNIVQYIER 85
                                      4588889******99655569*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 593.98
//
Query:       gi|313125601|ref|YP_004035865.1|  [L=1592]
Description: hypothetical protein Hbor_08300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-14   54.8  33.1      0.075   13.3   0.5   13.7 13  DUF4625         Domain of unknown function (DUF4625)
    8.3e-05   22.3   9.3        1.6    8.5   0.0    7.4  7  Big_3_4         Domain of unknown function
    0.00047   19.8  76.5     0.0092   15.7   4.5   11.0 11  Big_3_3         Bacterial Ig-like domain (group 3)
     0.0086   16.1   5.1       0.19   11.7   0.1    4.0  4  DUF2213         Uncharacterized protein conserved in bacteria
  ------ inclusion threshold ------
      0.011   15.7   2.1        7.1    6.7   0.0    4.3  4  Y_Y_Y           Y_Y_Y domain
      0.011   15.9   6.1      0.011   15.9   6.1   16.8 11  Big_3_5         Bacterial Ig-like domain (group 3)
      0.012   15.5   1.7      0.029   14.3   1.7    1.6  1  PGF-CTERM       PGF-CTERM motif
      0.014   15.8  25.7         11    6.5   0.0    9.5 10  MG2             MG2 domain
      0.031   15.0 190.6      0.064   14.0   9.2   15.6 14  Big_7           Bacterial Ig domain
      0.057   13.7   8.3       0.56   10.5   0.1    5.0  6  DUF3416         Domain of unknown function (DUF3416)
          1   10.0   5.4        1.5    9.5   0.1    3.4  2  Porphyrn_cat_1  Porphyranase catalytic subdomain 1
        2.6    9.0  21.5       0.42   11.5   0.2    7.4  8  DUF756          Domain of unknown function (DUF756)
        3.9    8.0   6.9         21    5.6   0.0    5.2  5  MG1             Macroglobulin domain MG1


Domain annotation for each model (and alignments):
>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.04        55       6      54 ..     100     150 ..      96     183 .. 0.82
   2 !   13.3   0.5   5.4e-05     0.075      11     127 ..     211     311 ..     191     315 .. 0.71
   3 ?   -1.6   0.0       2.2     3e+03      43      87 ..     338     384 ..     323     393 .. 0.74
   4 !    9.6   0.3   0.00076         1       6      67 ..     407     469 ..     402     513 .. 0.77
   5 !    6.8   0.4    0.0055       7.6     100     125 ..     590     615 ..     498     621 .. 0.66
   6 ?    2.0   0.1      0.16   2.3e+02       3      54 ..     615     665 ..     613     670 .. 0.83
   7 ?   -2.3   0.0       3.6     5e+03      99     125 ..     693     720 ..     678     723 .. 0.78
   8 ?    3.3   0.0     0.065        90       9      57 ..     831     881 ..     817     887 .. 0.82
   9 ?    4.5   0.1     0.028        38     105     124 ..     911     930 ..     900     937 .. 0.84
  10 ?    4.7   0.0     0.024        33      11      57 ..     939     984 ..     932    1032 .. 0.77
  11 !   10.2   0.0   0.00049      0.68      10      56 ..    1043    1089 ..    1025    1095 .. 0.90
  12 ?    2.9   0.0     0.089   1.2e+02      91     126 ..    1109    1144 ..    1097    1150 .. 0.87
  13 ?   -3.2   0.0       6.8   9.3e+03      31      57 ..    1160    1186 ..    1152    1198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.04
                           DUF4625   6 ddee.edtekPvidllevsaepeeeevlkiGetlhfeaklsdne.alasyk 54 
                                       +d++  dt++P+++ +++  + + + +++ ++t+ ++a++ d    ++s++
  gi|313125601|ref|YP_004035865.1| 100 NDSAyVDTTEPSVTNVQLLDDSDGDGIVASDDTVRVRADVVDATaSVQSVE 150
                                       455558**********9988999****************999651466655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.4e-05
                           DUF4625  11 dtekPvidllevsaepeeeevlkiGetlhfeaklsdn.ealasykvdihnnfDhhshsseakegekewsfeksydls 86 
                                       dt++P+ + +++s+   ++ ++  Get+++e+++ d   a++s++ d+ ++f   + +s ++  +++ +++ ++++s
  gi|313125601|ref|YP_004035865.1| 211 DTNAPTYSSTTLSE-AGDDGTVDAGETVTVEVDVADAtTAIESVTADL-SDFGAGTSESLTN-ETESSVYNATITVS 284
                                       77777777775544.777788889999999999988525799999999.7775555444443.37777788888777 PP

                           DUF4625  87 gskkeyelheeieiPadaeaGdYhlvirvtDasGneteesr 127
                                       ++                ++GdY +++rv Da+Gn +++ +
  gi|313125601|ref|YP_004035865.1| 285 EG--------------GTTDGDYPVTVRVRDAAGNVNQTTV 311
                                       77..............4678999999999999999998876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.2
                           DUF4625  43 klsdnealasykvdihnnfDhhshsseakeg...ekewsfeksydlsg 87 
                                        +  +e l++++v++ +  D  + ++ a  +     ++++e +y+++ 
  gi|313125601|ref|YP_004035865.1| 338 SFDSDETLGNITVSV-SGADSTTVTEAAFSTadgSAPYTYEATYNAPT 384
                                       566788899999999.66777777665443355599999999997765 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00076
                           DUF4625   6 ddee..edtekPvidllevsaepeeeevlkiGetlhfeaklsdne.alasykvdihnnfDhhshs 67 
                                       + e+   dt+ P i+ l+++   + +  ++ G+++++ea++sd+   ++s++ d+ + fD  s  
  gi|313125601|ref|YP_004035865.1| 407 ESETvvVDTTGPDISPLSLTD-GDADGNVTDGDEITVEATVSDDTsGVQSVTADL-SAFDLGSSV 469
                                       33333569****999996655.78899999************98537********.999965544 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0055
                           DUF4625 100 iPadaeaGdYhlvirvtDasGnetee 125
                                         + a +G+Y l++ +tD  Gn +  
  gi|313125601|ref|YP_004035865.1| 590 GTNAAGDGNYSLTVEATDDLGNANSA 615
                                       33456778888888888888887765 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.16
                           DUF4625   3 cssddeeedtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasyk 54 
                                       + +++ ++d++ P+++  +++   + + v++  et+++e++++d   +  ++
  gi|313125601|ref|YP_004035865.1| 615 ATTNELTQDVNPPTLSAGSLTG-TDGDGVVADEETVTVELTVTDATTVDTVT 665
                                       567777799*******997766.788889999999*********99998776 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 3.6
                           DUF4625  99 eiPad.aeaGdYhlvirvtDasGnetee 125
                                       +++a+ +++G+  + + + D +G ++++
  gi|313125601|ref|YP_004035865.1| 693 VVDASgVADGEHSVSVEAADSQGKTNQT 720
                                       55554478999999*********99887 PP

  == domain 8  score: 3.3 bits;  conditional E-value: 0.065
                           DUF4625   9 e.edtekPvidllevsaepeeeevlkiGetlhfeaklsdne.alasykvdi 57 
                                          dt kP+++ + v+ + + +++++ Ge++++ a+ +d    ++s++ d+
  gi|313125601|ref|YP_004035865.1| 831 LtLDTAKPTLSSVGVTDDADGDSIVADGESVTVSATATDSTaGVQSVTADL 881
                                       3369*********9*999*******************99751577777776 PP

  == domain 9  score: 4.5 bits;  conditional E-value: 0.028
                           DUF4625 105 eaGdYhlvirvtDasGnete 124
                                       ++GdY +++ vtD +Gn + 
  gi|313125601|ref|YP_004035865.1| 911 PDGDYSVAVDVTDGAGNVRS 930
                                       47***************765 PP

  == domain 10  score: 4.7 bits;  conditional E-value: 0.024
                           DUF4625  11 dtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdi 57 
                                       dt+ P+++  +++ + + + vl+ Ge++++ea+ +d + +a ++ d+
  gi|313125601|ref|YP_004035865.1| 939 DTTGPTVSSPTLT-DETGDGVLTDGENVTVEATATDANGVATVTTDL 984
                                       8888988888444.479999**********************99998 PP

  == domain 11  score: 10.2 bits;  conditional E-value: 0.00049
                           DUF4625   10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvd 56  
                                         dt+ P+++ l+++ + + + v++ G+++ + a++sd + ++s++vd
  gi|313125601|ref|YP_004035865.1| 1043 LDTTGPSVTGLTFTDATDGDGVVAPGDQIDISATVSDAAGIGSVTVD 1089
                                        499******9999999*****************************98 PP

  == domain 12  score: 2.9 bits;  conditional E-value: 0.089
                           DUF4625   91 eyelheeieiPadaeaGdYhlvirvtDasGnetees 126 
                                        +y+++ +++ +a+a++Gd  + ++ tD  Gn++  +
  gi|313125601|ref|YP_004035865.1| 1109 TYTATLTVDFDATAADGDRSVPVTTTDTVGNKRSAQ 1144
                                        7889999999*********************98765 PP

  == domain 13  score: -3.2 bits;  conditional E-value: 6.8
                           DUF4625   31 vlkiGetlhfeaklsdnealasykvdi 57  
                                        ++  G++ ++++++ + e l++++v +
  gi|313125601|ref|YP_004035865.1| 1160 SVSAGSDSSVDIAFDASETLNDVNVTL 1186
                                        567899999999999999999999876 PP

>> Big_3_4  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.1   1.5e+03      15      48 ..     162     199 ..     156     202 .. 0.66
   2 ?    3.9   0.0     0.032        44      16      52 ..     269     311 ..     260     350 .. 0.76
   3 !    8.5   0.0    0.0012       1.6      11      51 ..     466     509 ..     462     521 .. 0.83
   4 ?   -0.3   0.1      0.64   8.8e+02      33      50 ..     596     613 ..     587     624 .. 0.88
   5 ?   -1.6   0.0       1.6   2.2e+03      32      54 ..     700     724 ..     681     730 .. 0.79
   6 ?    1.7   0.0      0.15   2.1e+02      20      62 ..     790     836 ..     777     844 .. 0.76
   7 ?    4.6   0.2     0.019        27      14      48 ..     889     927 ..     877     933 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                           Big_3_4  15 efdrseGdiWn....vpvPldedGeyvvellaedeaGn 48 
                                        +  ++Gd +     v   +  dGe  v ++a d+  n
  gi|313125601|ref|YP_004035865.1| 162 SLSLTNGDTYAatftVGGSVPADGETNVTIVAADNQSN 199
                                       55556666554111133356689***********9877 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.032
                           Big_3_4  16 fdrseGdiWnvpvPl....dedGeyvvellaedeaGn..qayi 52 
                                        + +e  ++n ++ +     +dG+y v +   d aGn  q+ +
  gi|313125601|ref|YP_004035865.1| 269 TNETESSVYNATITVseggTTDGDYPVTVRVRDAAGNvnQTTV 311
                                       5667777777777662222479**************8224444 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0012
                           Big_3_4  11 gievefdrseGdiWnvpvPld...edGeyvvellaedeaGnqay 51 
                                       g+ v +  s+G  Wn++  +    ++G+ +  + a d+ Gn a 
  gi|313125601|ref|YP_004035865.1| 466 GSSVSLTSSDGSTWNLTTAVGqspTEGDQLASVTATDDEGNTAS 509
                                       678999**********9987522368***************985 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.64
                           Big_3_4  33 dGeyvvellaedeaGnqa 50 
                                       dG+y + + a d+ Gn  
  gi|313125601|ref|YP_004035865.1| 596 DGNYSLTVEATDDLGNAN 613
                                       9**************975 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 1.6
                           Big_3_4  32 edGeyvvellaedeaG..nqayiak 54 
                                        dGe+ v + a d  G  nq+ + +
  gi|313125601|ref|YP_004035865.1| 700 ADGEHSVSVEAADSQGktNQTTVGT 724
                                       699**********998557776665 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.15
                           Big_3_4  20 eGdiWnvpvPlde.....dGeyvvellaedeaGnqayiakllyvvdie 62 
                                       +G  W+v+v +d      dG +   +   deaG  + +++   ++d++
  gi|313125601|ref|YP_004035865.1| 790 DG-TWDVTVSVDAanadpDGSHGGSVTVSDEAGQTSVVTTETLTLDTA 836
                                       33.6999998864334448999999***********999877777765 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.019
                           Big_3_4  14 vefdrseGdiWn.vpvP...ldedGeyvvellaedeaGn 48 
                                       v++  + Gd+ + v+v     d dG+y v++   d aGn
  gi|313125601|ref|YP_004035865.1| 889 VTLTDTGGDWSKtVTVNganADPDGDYSVAVDVTDGAGN 927
                                       77888899997647774333689***************9 PP

>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.99   1.4e+03      31      84 ..      95     149 ..      65     167 .. 0.65
   2 !    5.9   6.5    0.0067       9.3      13     143 ..     183     312 ..     169     319 .. 0.74
   3 !    6.7   0.2    0.0037       5.2       3      84 ..     374     456 ..     372     475 .. 0.74
   4 !   12.4   3.0   6.7e-05     0.092      13     139 ..     490     614 ..     477     616 .. 0.74
   5 !   15.7   4.5   6.6e-06    0.0092      10     107 ..     592     692 ..     580     696 .. 0.74
   6 !   11.6   0.3   0.00012      0.16       4      83 ..     691     769 ..     688     775 .. 0.82
   7 !    6.0   0.9    0.0061       8.5      10      85 ..     803     878 ..     793     882 .. 0.78
   8 !    6.6   0.7    0.0039       5.4       9      73 ..     907     970 ..     899     986 .. 0.78
   9 !    6.8   2.4    0.0035       4.9      13     139 ..    1016    1142 ..    1004    1154 .. 0.80
  10 !    5.6   0.5    0.0084        12       5      79 ..    1116    1193 ..    1112    1213 .. 0.70
  11 ?   -0.4   0.2      0.56   7.7e+02     120     140 ..    1335    1355 ..    1331    1360 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.99
                           Big_3_3  31 vtksllstilvdntpPtvsisegkkisdgavvkglenlritladaldks.kltsi 84 
                                        + sl+    vd+t P+v+ ++    sdg  +   ++ +   ad +d++ +++s+
  gi|313125601|ref|YP_004035865.1|  95 KESSLNDSAYVDTTEPSVTNVQLLDDSDGDGIVASDDTVRVRADVVDATaSVQSV 149
                                       3445556778999999998766666676666666666665666766665566665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0067
                           Big_3_3  13 peGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlrit..ladaldkskltsia.. 85 
                                       ++G+ n++++a+d+  n+  + +   + +d+ +Pt s ++ ++  d+ +v   e + ++  +ada+++  ++s++  
  gi|313125601|ref|YP_004035865.1| 183 ADGETNVTIVAADNQSNTNRTDSP-SLRLDTNAPTYSSTTLSEAGDDGTVDAGETVTVEvdVADATTA--IESVTad 256
                                       579999999998888776655555.89*********99888888899999877766655005665555..8888733 PP

                           Big_3_3  86 lsGGpasDkVelswveegkdvysleYPrlFPsleegesYtltvkaeDeagNaktkask 143
                                       ls   a  + +l ++e+   vy+    +    +++g+ Y +tv+++D+agN+++++++
  gi|313125601|ref|YP_004035865.1| 257 LSDFGAGTSESL-TNETESSVYNATITVSEGGTTDGD-YPVTVRVRDAAGNVNQTTVE 312
                                       555444444445.455556799999988888888886.9************9999875 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0037
                           Big_3_3   3 ytvtfdlkelpeGkynlvl.aakdtfnnqvtksllstilvdntpPtvsi.segkkisdgavvkglenlritladald 77 
                                       yt++  +++  +G+y+ +l  a+d  +     s ++t++vd+t P +s  s     +dg v    +++ ++ + + d
  gi|313125601|ref|YP_004035865.1| 374 YTYEATYNAPTDGTYTFTLdEAADGTGKDGASSESETVVVDTTGPDISPlSLTDGDADGNVTD-GDEITVEATVSDD 449
                                       677778889999*****9988999999999999999*********998633344444444433.3445444444445 PP

                           Big_3_3  78 kskltsi 84 
                                       +s ++s+
  gi|313125601|ref|YP_004035865.1| 450 TSGVQSV 456
                                       5555555 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 6.7e-05
                           Big_3_3  13 peGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdg.avvkglenlritladaldkskltsialsG 88 
                                        eG + ++++a+d  +n++ +++  t++vd++ P++s  + ++ s+g +vv++ + ++++ +  +d+   t i+ + 
  gi|313125601|ref|YP_004035865.1| 490 TEGDQLASVTATDDEGNTASTETG-TLSVDTSGPSLSSLTLRNGSGGmSVVRDGDTVVVSATV-TDT---TGITAVT 561
                                       5899999999*******9999999.***********985555555441555555555554433.333...4455555 PP

                           Big_3_3  89 GpasD.kVel.swveegkdvysleYPrlFPsleegesYtltvkaeDeagNakt 139
                                         asD  V   + ++ g d+y+  + +   +     +Y+ltv+a+D  gNa+ 
  gi|313125601|ref|YP_004035865.1| 562 TDASDfGVGTeTLSNVGGDTYETSFTVNGTNAAGDGNYSLTVEATDDLGNANS 614
                                       566763454414578899*********999999999**************976 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 6.6e-06
                           Big_3_3  10 kelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsi.segkkisdgavv.kglenlritladaldks..klt 82 
                                       ++  +G+y+l++ a+d  +n    +++ ++++d+ pPt+s  s  ++  dg+v  ++ + ++ t++da++    + +
  gi|313125601|ref|YP_004035865.1| 592 NAAGDGNYSLTVEATDDLGNANSATTN-ELTQDVNPPTLSAgSLTGTDGDGVVAdEETVTVELTVTDATTVDtvTAD 667
                                       56779*************998877776.*************655555556655524567778889998776634677 PP

                           Big_3_3  83 sialsGGpasDkVelswveegkdvy 107
                                          l GG+a    +++ ++  ++++
  gi|313125601|ref|YP_004035865.1| 668 ATELGGGSAVSLSQVGSSDVYNGTF 692
                                       899****997777776666655555 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00012
                           Big_3_3   4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlritladaldksk 80 
                                       t++ d++ +++G++++++ a+d  ++++++++  t+++d+ +P+ s  + +    ++ v g e+l ++++ + + s+
  gi|313125601|ref|YP_004035865.1| 691 TFVVDASGVADGEHSVSVEAADS-QGKTNQTTVGTLTLDTVTPSTSGLSLSDSDADSYVAGGEDLTVSVTPDGTGSE 766
                                       567789999******99866665.6677777777*********9987677778888999**********99988887 PP

                           Big_3_3  81 lts 83 
                                       +  
  gi|313125601|ref|YP_004035865.1| 767 VRT 769
                                       765 PP

  == domain 7  score: 6.0 bits;  conditional E-value: 0.0061
                           Big_3_3  10 kelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsi.segkkisdgavvkglenlritladaldkskltsia 85 
                                       ++ p+G++  +++ +d+ + +  +++  t+++d++ Pt+s         ++++v + e++ ++ + +  ++ ++s++
  gi|313125601|ref|YP_004035865.1| 803 NADPDGSHGGSVTVSDEAGQTSVVTTE-TLTLDTAKPTLSSvGVTDDADGDSIVADGESVTVSATATDSTAGVQSVT 878
                                       67799****999999998777777666.***********87355566667788888899888887777776777765 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.0039
                           Big_3_3   9 lkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlritla 73 
                                       +++ p+G y++ +  +d  +n    ++   +++d+t Ptvs ++ +  +++ v+ + en+ ++ +
  gi|313125601|ref|YP_004035865.1| 907 ANADPDGDYSVAVDVTDGAGNVRSGTTG-SLTLDTTGPTVSSPTLTDETGDGVLTDGENVTVEAT 970
                                       57789*****999999998887766666.89**********977777777777777788776544 PP

  == domain 9  score: 6.8 bits;  conditional E-value: 0.0035
                           Big_3_3   13 peGkynlvlaakdtfnnqvtksllstilvdntpPtvsi.segkkisdgavvkglenlritladaldkskltsial 86  
                                        ++G+ ++ ++a+d  + +v   ++  +++d+t P+v+  ++   + ++ vv   ++++i+ +  +d++ + s+++
  gi|313125601|ref|YP_004035865.1| 1016 ADGSVSAPIQASDDRG-TVGSGTTGSLTLDTTGPSVTGlTFTDATDGDGVVAPGDQIDISAT-VSDAAGIGSVTV 1088
                                        5677777776666544.4555555589*********97566666777778888899999865.678889****** PP

                           Big_3_3   87 sGGpasDkVelswve.egkdvysleYPrlFPsleegesYtltvkaeDeagNakt 139 
                                         G +      +s  +  ++++y+    + F ++ +    ++ v+++D+ gN+  
  gi|313125601|ref|YP_004035865.1| 1089 DGSAFGSGSAVSIADgDSDGTYTATLTVDFDATAADGDRSVPVTTTDTVGNKRS 1142
                                        **99988888887653799********************************865 PP

  == domain 10  score: 5.6 bits;  conditional E-value: 0.0084
                           Big_3_3    5 vtfdlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsi...segkkisdgavv...kglenlritla 73  
                                        v fd+   ++G  ++ ++ +dt++n+   ++  t+++d tpPtvs    s g+  s + ++   ++l+++++tl+
  gi|313125601|ref|YP_004035865.1| 1116 VDFDAT-AADGDRSVPVTTTDTVGNKRSAQTG-TLTLD-TPPTVSNfsvSAGSDSSVDIAFdasETLNDVNVTLT 1187
                                        566654.57899999999*******9999988.77777.899998722234444444444433368999999999 PP

                           Big_3_3   74 daldks 79  
                                         +++++
  gi|313125601|ref|YP_004035865.1| 1188 GSANAT 1193
                                        888764 PP

  == domain 11  score: -0.4 bits;  conditional E-value: 0.56
                           Big_3_3  120 egesYtltvkaeDeagNaktk 140 
                                        ++e+Y++ ++++D a Na+  
  gi|313125601|ref|YP_004035865.1| 1335 QNETYSVQATVHDDAPNATID 1355
                                        79***************9865 PP

>> DUF2213  Uncharacterized protein conserved in bacteria (DUF2213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       4.9   6.7e+03     117     132 ..      69      84 ..      61      95 .. 0.70
   2 ?    3.7   0.0      0.04        55      81     120 ..     530     568 ..     519     587 .. 0.83
   3 !   11.7   0.1   0.00013      0.19      78     136 ..     631     690 ..     607     704 .. 0.79
   4 ?   -1.8   0.1       1.9   2.7e+03      85     122 ..     954     990 ..     949    1006 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.9
                           DUF2213 117 relSagYeadldmtpg 132
                                       +++S gY+++  ++ +
  gi|313125601|ref|YP_004035865.1|  69 TNISGGYHYETTTNVS 84 
                                       689****999876433 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.04
                           DUF2213  81 avGtvgrdvrfegeylvadllitdaeaiaaiesgklrelS 120
                                         G+ g  v ++g+++v++ ++td + i a++++  ++  
  gi|313125601|ref|YP_004035865.1| 530 RNGSGGMSVVRDGDTVVVSATVTDTTGITAVTTDA-SDFG 568
                                       5677778899*********************9998.6655 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00013
                           DUF2213  78 kelavGtvgrdvrfegeylvadllitdaeaiaaiesgklrelSagYeadldm.tpg.eydG 136
                                       +    Gt g++v +++e+++++l++tda+++++++++  +el  g +++l +  ++ +y+G
  gi|313125601|ref|YP_004035865.1| 631 AGSLTGTDGDGVVADEETVTVELTVTDATTVDTVTADA-TELGGGSAVSLSQvGSSdVYNG 690
                                       3445677799****************************.9999998888877543336666 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.9
                           DUF2213  85 vgrdvrfegeylvadllitdaeaiaaiesgklrelSag 122
                                       +g++v ++ge ++++ + tda+ +a+++++  + + ag
  gi|313125601|ref|YP_004035865.1| 954 TGDGVLTDGENVTVEATATDANGVATVTTDL-SAIGAG 990
                                       5677888999999999999999999998887.555555 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.12   1.6e+02      37      61 ..     289     314 ..     268     318 .. 0.84
   2 ?    2.6   0.0     0.099   1.4e+02      29      44 ..     367     391 ..     352     408 .. 0.78
   3 ?    6.7   0.0    0.0052       7.1      39      58 ..     597     616 ..     592     622 .. 0.86
   4 ?   -2.8   0.0       4.6   6.3e+03      37      52 ..     911     926 ..     911     928 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.12
                                       -SEEEEEEEEEEETTS-B-SS-.EEE CS
                             Y_Y_Y  37 ppGdYtlkVkakdndgqwnydi.tsl 61 
                                         GdY ++V+++d  g+ n+ +  +l
  gi|313125601|ref|YP_004035865.1| 289 TDGDYPVTVRVRDAAGNVNQTTvETL 314
                                       57***********9999887765555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.099
                                       ..........EEEEES--SEEEEEE CS
                             Y_Y_Y  29 q.........easytnlppGdYtlk 44 
                                       +         ea+y+    G+Yt++
  gi|313125601|ref|YP_004035865.1| 367 TadgsapytyEATYNAPTDGTYTFT 391
                                       44444556679*************7 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0052
                                       EEEEEEEEEEETTS-B-SS- CS
                             Y_Y_Y  39 GdYtlkVkakdndgqwnydi 58 
                                       G+Y l+V+a+d++g+ n+ +
  gi|313125601|ref|YP_004035865.1| 597 GNYSLTVEATDDLGNANSAT 616
                                       9**************99985 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 4.6
                                       -SEEEEEEEEEEETTS CS
                             Y_Y_Y  37 ppGdYtlkVkakdndg 52 
                                       p GdY + V ++d  g
  gi|313125601|ref|YP_004035865.1| 911 PDGDYSVAVDVTDGAG 926
                                       78*******9999766 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   4.7       1.7   2.3e+03       9      53 ..     139     191 ..     131     208 .. 0.65
   2 ?   -2.5  14.2       4.2   5.8e+03       3      83 ..     230     316 ..     228     323 .. 0.70
   3 ?   -0.5  11.9         1   1.4e+03      17      85 ..     342     412 ..     326     418 .. 0.63
   4 ?    2.9  16.5     0.092   1.3e+02       6      89 ..     541     628 ..     536     629 .. 0.73
   5 ?   -1.5   4.5       2.1   2.9e+03      11      60 ..     755     813 ..     745     818 .. 0.53
   6 ?   -0.6  18.3       1.1   1.6e+03       4      65 ..     928     994 ..     909    1000 .. 0.79
   7 ?    0.9  13.7      0.38   5.3e+02       7      49 ..     962    1014 ..     959    1037 .. 0.57
   8 ?   -2.3   4.5       3.8   5.3e+03      11      58 ..    1002    1050 ..     996    1067 .. 0.62
   9 ?    3.0   4.8     0.085   1.2e+02      12      57 ..    1182    1226 ..    1168    1240 .. 0.76
  10 ?   -1.7   0.7       2.5   3.5e+03      57      75 ..    1335    1353 ..    1287    1367 .. 0.63
  11 ?   15.9   6.1   7.8e-06     0.011       4      64 ..    1463    1526 ..    1460    1528 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.7
                                       EEEEEEE--CCCCTT...S--EEEEEE.TTEE-SS-EE--T....TSEEEEEE CS
                           Big_3_5   9 tvtltatVtaasggt...ptGtVtftd.ggttlgtavllsa....nGtAtltv 53 
                                        v  ta+V+++++ +     GtV++   +g+t++++ ++ +    +G  ++t+
  gi|313125601|ref|YP_004035865.1| 139 VVDATASVQSVEADAsdfGAGTVSLSLtNGDTYAATFTVGGsvpaDGETNVTI 191
                                       57788999988663312356999998636677777666664333345555554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                                       -EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTS....EEEEEEE-..SS-EEEEEEEEEE-T.TS CS
                           Big_3_5   3 svtagqtvtltatVtaasggtptGtVtftdggttlgtavllsanG....tAtltvsa..laaGthsitAtYsGd.an 72 
                                       +v ag+tvt+ + V++a+++  + t  + d g+   +  +++ +     +At+tvs   ++ G + +t++  +  +n
  gi|313125601|ref|YP_004035865.1| 230 TVDAGETVTVEVDVADATTAIESVTADLSDFGAGTSESLTNE-TEssvyNATITVSEggTTDGDYPVTVRVRDAaGN 305
                                       7899*************8877778888999555554433333.222344889998776789*******998765356 PP

                                       ---S--EEEEE CS
                           Big_3_5  73 yaastssavtv 83 
                                       +++ t ++ t+
  gi|313125601|ref|YP_004035865.1| 306 VNQTTVETLTL 316
                                       66666665554 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1
                                       -CCCCTTS--EEEEEE...TTEE-SS-EE--TTSEEEEEEE-....SS-EEEEEEEEEE-TTS---S--EEEEEEE CS
                           Big_3_5  17 taasggtptGtVtftd...ggttlgtavllsanGtAtltvsa....laaGthsitAtYsGdanyaastssavtvtV 85 
                                        ++      G++t+ +   ++tt+ +a+ ++a+G+A +t++a     + Gt++ t   + d++ ++ +ss++   V
  gi|313125601|ref|YP_004035865.1| 342 DET-----LGNITVSVsgaDSTTVTEAAFSTADGSAPYTYEAtynaPTDGTYTFTLDEAADGTGKDGASSESETVV 412
                                       444.....5788888755566888888888889*888887663333679******998877664444444332222 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.092
                                       TTSEEEEEEE--CCCCTTS--EEEEEETTEE-..SS-EE--TTS....EEEEEEE-SS...-EEEEEEEEEE-T.TS CS
                           Big_3_5   6 agqtvtltatVtaasggtptGtVtftdggttl..gtavllsanG....tAtltvsala...aGthsitAtYsGd.an 72 
                                        g+tv ++atVt++     tG   +t+++  +  gt +l++  G      ++tv++++    G++s+t++ ++d +n
  gi|313125601|ref|YP_004035865.1| 541 DGDTVVVSATVTDT-----TGITAVTTDASDFgvGTETLSNV-GgdtyETSFTVNGTNaagDGNYSLTVEATDDlGN 611
                                       589***********.....66666666554442255555553.3244466677666544448************899 PP

                                       ---S--EEEEEEEES-- CS
                           Big_3_5  73 yaastssavtvtVtkaa 89 
                                        +++t+++ t+ V++++
  gi|313125601|ref|YP_004035865.1| 612 ANSATTNELTQDVNPPT 628
                                       9999**********986 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 2.1
                                       EEEEE--CCCCTTS-..........-EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EE CS
                           Big_3_5  11 tltatVtaasggtpt..........GtVtftdggttlgtavllsanGtAtltvsalaaGt 60 
                                       t+++t  ++++++ t          GtVt+ dg+      v++s    A+++  +   G+
  gi|313125601|ref|YP_004035865.1| 755 TVSVTPDGTGSEVRTveadlsafgaGTVTLADGDSDGTWDVTVS-VDAANADPDGSHGGS 813
                                       33333333333333333445555558888888776666666666.455665555555555 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 1.1
                                       EETTSEEEEEEE--CCCC.....TTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEE CS
                           Big_3_5   4 vtagqtvtltatVtaasg.....gtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitA 65 
                                       v +g+t +lt   t+ +      ++ tG   +tdg+++  +a++++anG+At+t+ + a G+ ++t 
  gi|313125601|ref|YP_004035865.1| 928 VRSGTTGSLTLDTTGPTVssptlTDETGDGVLTDGENVTVEATATDANGVATVTTDLSAIGAGTVTL 994
                                       5667777777777755331222356779999***999999999999*********888877777774 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.38
                                        TSEEEEEEE--CCCC.TTS-........-EEEEEE..TTEE-SS-EE--TTSEE CS
                           Big_3_5    7 gqtvtltatVtaasg.gtpt........GtVtftd..ggttlgtavllsanGtA 49  
                                        g++vt+ at t+a+g +t+t        GtVt+td  ++ t  ++v++++  +A
  gi|313125601|ref|YP_004035865.1|  962 GENVTVEATATDANGvATVTtdlsaigaGTVTLTDgdDDGTWNATVAVDE-SNA 1014
                                        67777777777776653444467777778888887432233345555652.222 PP

  == domain 8  score: -2.3 bits;  conditional E-value: 3.8
                                        EEEEE--CCCC.TTS--EEEEEE....TTEE-SS-EE--TTSEEEEEEE-SS- CS
                           Big_3_5   11 tltatVtaasg.gtptGtVtftd....ggttlgtavllsanGtAtltvsalaa 58  
                                        t +atV+  ++ +++ G+V+  +    +  t+g+     ++G+ tl++++ ++
  gi|313125601|ref|YP_004035865.1| 1002 TWNATVAVDESnASADGSVSAPIqasdDRGTVGSG----TTGSLTLDTTGPSV 1050
                                        66777774443267888887766211144444444....46888888887654 PP

  == domain 9  score: 3.0 bits;  conditional E-value: 0.085
                                        EEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS CS
                           Big_3_5   12 ltatVtaasggtptGtVtftdggttlgtavllsanGtAtltvsala 57  
                                        +++t+t++ ++++     f + gt++ t  ++ +nG++t+t++ la
  gi|313125601|ref|YP_004035865.1| 1182 VNVTLTGS-ANATLDETDFSVSGTSYETSHAVGSNGSVTVTLARLA 1226
                                        34455555.233447779***********************99886 PP

  == domain 10  score: -1.7 bits;  conditional E-value: 2.5
                                        S-EEEEEEEEEE-TTS--- CS
                           Big_3_5   57 aaGthsitAtYsGdanyaa 75  
                                        +  t+s++At ++da  a+
  gi|313125601|ref|YP_004035865.1| 1335 QNETYSVQATVHDDAPNAT 1353
                                        3455666666555543332 PP

  == domain 11  score: 15.9 bits;  conditional E-value: 7.8e-06
                                        EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS.-EE--TTS...EEEEEEE-SS-EEEEEE CS
                           Big_3_5    4 vtagqtvtltatVtaasggtptGtVtftdggttlgt.avllsanG...tAtltvsalaaGthsit 64  
                                        +  g+tvt++a Vt  ++ ++tG V++ ++++t  t  v+l  +G   t  +tv++ ++Gt+++ 
  gi|313125601|ref|YP_004035865.1| 1463 IRPGETVTVSAGVTNDGTRAATGYVSLAVDNATTDTrRVTLG-AGdseTERFTVQFDEVGTYNLS 1526
                                        5689************99**********99988866366666.555558999**********986 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.7   2.1e-05     0.029       2      23 .]    1570    1591 ..    1569    1591 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                         PGF-CTERM    2 PGFGavlAlaGLLaaalLaRRr 23  
                                        PGFG + A+  L  ++ La+Rr
  gi|313125601|ref|YP_004035865.1| 1570 PGFGPLAAILSLFVVVTLAWRR 1591
                                        ****************777776 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.095   1.3e+02      13      93 ..     233     310 ..     226     313 .. 0.67
   2 ?    1.9   0.2      0.23   3.1e+02      22      53 ..     281     312 ..     270     366 .. 0.75
   3 ?    1.5   0.1      0.29     4e+02      35      84 ..     347     396 ..     327     411 .. 0.75
   4 ?    2.3   0.1      0.17   2.3e+02      36      90 ..     557     613 ..     537     620 .. 0.68
   5 ?    0.6   0.1      0.59   8.1e+02      36      69 ..     675     708 ..     636     722 .. 0.52
   6 ?    6.5   0.0    0.0081        11      37      86 ..     755     803 ..     739     817 .. 0.67
   7 ?   -2.3   0.0       4.6   6.3e+03      68      90 ..     907     929 ..     887     933 .. 0.64
   8 ?    5.2   0.1     0.021        28      34      89 ..     963    1015 ..     941    1032 .. 0.63
   9 ?   -0.8   0.0       1.5   2.1e+03      50      82 ..    1085    1116 ..    1059    1143 .. 0.51
  10 ?    5.1   0.1     0.023        32      12      80 ..    1464    1527 ..    1458    1539 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.095
                                       TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--S.EEEEEEEEECSTTT- CS
                               MG2  13 PgetVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefalpeaakl.Geysvelsadsaees 88 
                                       +getV +++ + d+t  ++   +++++++d + ++ ++l+ + +e+++++ +++++e+  + G+y v+++ ++a+++
  gi|313125601|ref|YP_004035865.1| 233 AGETVTVEVDVADATT-AI--ESVTADLSDFGAGTSESLT-NETESSVYNATITVSEGGTTdGDYPVTVRVRDAAGN 305
                                       6777777766644433.22..3578888888888888888.555555788888887765544888888877777777 PP

                                       EEEEE CS
                               MG2  89 lssgs 93 
                                       +++++
  gi|313125601|ref|YP_004035865.1| 306 VNQTT 310
                                       66665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.23
                                       EEESTTCSB---EEEEEEEE-TTSSEEEEEEE CS
                               MG2  22 llrdetlqglaklplkltirdpdgkevkelpl 53 
                                       ++  e +++  ++p+++++rd+ g++ +++  
  gi|313125601|ref|YP_004035865.1| 281 ITVSEGGTTDGDYPVTVRVRDAAGNVNQTTVE 312
                                       44455666666799******999986555443 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.29
                                       EEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--S.EEEEEEEEECS CS
                               MG2  35 plkltirdpdgkevkelplatdetggaesefalpeaakl.Geysvelsads 84 
                                       +++++++ +d+ +v e  + ++++g+a ++++   +a++ G+y+ +l++  
  gi|313125601|ref|YP_004035865.1| 347 NITVSVSGADSTTVTEAAF-STADGSAPYTYEATYNAPTdGTYTFTLDEAA 396
                                       5788888888888888885.55567888888888777766******93222 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.17
                                       EEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--..TT--SEEEEEEEEECSTTT-EE CS
                               MG2  36 lkltirdpdgkevkelplatdetggaesefalp..eaaklGeysvelsadsaeesls 90 
                                       ++++ +d+++  v +++l +    ++e++f+++  +aa  G+ys++++a ++ ++++
  gi|313125601|ref|YP_004035865.1| 557 ITAVTTDASDFGVGTETLSNVGGDTYETSFTVNgtNAAGDGNYSLTVEATDDLGNAN 613
                                       555566666666777777777777899999997224577789*99996655555444 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.59
                                       EEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--T CS
                               MG2  36 lkltirdpdgkevkelplatdetggaesefalpe 69 
                                         +++++ ++ +v++ +++ d++g+a++e  ++ 
  gi|313125601|ref|YP_004035865.1| 675 SAVSLSQVGSSDVYNGTFVVDASGVADGEHSVSV 708
                                       3344444455555555555555555444444433 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.0081
                                       EEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEE...EECSTT CS
                               MG2  37 kltirdpdgkevkelplatdetggaesefalpeaaklGeysvel...sadsae 86 
                                       +++++ pdg   +  ++++d + +  ++++l ++ + G++ v++       a+
  gi|313125601|ref|YP_004035865.1| 755 TVSVT-PDGTGSEVRTVEADLSAFGAGTVTLADGDSDGTWDVTVsvdA---AN 803
                                       55554.44444444455666666788******************5542...32 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 4.6
                                       -TT--SEEEEEEEEECSTTT-EE CS
                               MG2  68 peaaklGeysvelsadsaeesls 90 
                                        +a + G+ysv ++  + +++++
  gi|313125601|ref|YP_004035865.1| 907 ANADPDGDYSVAVDVTDGAGNVR 929
                                       45667899999996555555555 PP

  == domain 8  score: 5.2 bits;  conditional E-value: 0.021
                                        EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT-E CS
                               MG2   34 lplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsaeesl 89  
                                         +++++ + +d + v + +  td + +  ++++l ++   G++++++ a ++++++
  gi|313125601|ref|YP_004035865.1|  963 ENVTVEATATDANGVATVT--TDLSAIGAGTVTLTDGDDDGTWNATV-AVDESNAS 1015
                                        4455555555555555444..66667788999999999999999988.22222222 PP

  == domain 9  score: -0.8 bits;  conditional E-value: 1.5
                                        EEEEEE-CTTEEEEEEE--TT--SEEEEEEEEE CS
                               MG2   50 elplatdetggaesefalpeaaklGeysvelsa 82  
                                        + +++ +++g+  s + + ++ + G+y+++l  
  gi|313125601|ref|YP_004035865.1| 1085 SVTVDGSAFGS-GSAVSIADGDSDGTYTATLTV 1116
                                        33333333333.344555555555555555522 PP

  == domain 10  score: 5.1 bits;  conditional E-value: 0.023
                                        -TT-EEEEEEEEESTTCSB---..........EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEE CS
                               MG2   12 rPgetVslkallrdetlqglak..........lplkltirdpdgkevkelplatdetggaesefalpeaaklGey 76  
                                        rPgetV ++a + ++  +++++          + ++ +   +++ e+++++++ de g+++ +            
  gi|313125601|ref|YP_004035865.1| 1464 RPGETVTVSAGVTNDGTRAATGyvslavdnatTDTRRVTLGAGDSETERFTVQFDEVGTYNLS------------ 1526
                                        9***********998888888844444444443333333444444455555555555554444............ PP

                                        EEEE CS
                               MG2   77 svel 80  
                                           +
  gi|313125601|ref|YP_004035865.1| 1527 ---V 1527
                                        ...4 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.9       1.3   1.8e+03      36      67 ..      51      90 ..      22      91 .. 0.72
   2 ?   -1.5  11.6       3.2   4.5e+03      14      69 ..     128     190 ..     120     223 .. 0.76
   3 ?    5.9  11.4     0.016        21       9      70 .]     226     297 ..     219     297 .. 0.80
   4 ?    9.3   3.8    0.0014       1.9      17      69 ..     346     391 ..     313     403 .. 0.70
   5 ?   12.4   6.4   0.00015      0.21      12      59 ..     432     493 ..     423     518 .. 0.67
   6 ?   12.9   9.9   0.00011      0.15      12      70 .]     537     603 ..     531     603 .. 0.78
   7 ?    8.2   8.9     0.003       4.1      13      70 .]     642     708 ..     634     708 .. 0.70
   8 ?    1.8   3.6       0.3   4.1e+02      10      66 ..     744     810 ..     737     817 .. 0.77
   9 ?   14.0   9.2   4.6e-05     0.064       9      70 .]     849     919 ..     842     919 .. 0.78
  10 ?   11.7   7.8   0.00025      0.34      13      60 ..     958    1011 ..     943    1046 .. 0.78
  11 ?   13.4   7.0   7.4e-05       0.1       4      67 ..    1054    1128 ..    1048    1150 .. 0.76
  12 ?    1.4   3.6      0.42   5.7e+02      13      58 ..    1178    1222 ..    1154    1248 .. 0.68
  13 ?   -2.9   0.2       8.7   1.2e+04      18      28 ..    1338    1348 ..    1325    1366 .. 0.58
  14 ?    5.0   3.4     0.031        42      13      70 .]    1462    1527 ..    1450    1527 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                                      EEETTEE.........EEEE-SSSEEEEEE--...SEEEE CS
                             Big_7 36 fyvdgtl.g.......lgtdtsapysltwtttaltagtht 67
                                      +y +g + +       + t+ s++y ++ tt+   +g +t
  gi|313125601|ref|YP_004035865.1| 51 LYRNGDSdQvlgadtfTETNISGGYHYETTTNVSRDGYYT 90
                                      56677765577777767777789*****999888888887 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                                       EBTSEEEEEEEEE-S.S-EEEEEEEET.....TEE.EEEE-SSSEEEEEE--.....SEEEEEE CS
                             Big_7  14 vsggtvtisasAsdd.ggvskVefyvd.....gtlglgtdtsapysltwttta..ltagthtlt 69 
                                        s +tv ++a++ d+  +v++Ve  +      +++ l+ ++ ++y +t+t      ++g+ ++t
  gi|313125601|ref|YP_004035865.1| 128 ASDDTVRVRADVVDAtASVQSVEADASdfgagTVS-LSLTNGDTYAATFTVGGsvPADGETNVT 190
                                       34789*****************9876633331334.7777789999999984443445555555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.016
                                       -TT--EB.TSEEEEEEEEE-S.S-EEEEEEEET....TEE...EEEE-SSSEEEEEE--.....SEEEEEEE CS
                             Big_7   9 angatvs.ggtvtisasAsdd.ggvskVefyvd....gtl.g.lgtdtsapysltwttta..ltagthtltV 70 
                                        +  tv+ g+tvt+++++ d+ +++++V+  +     gt+   ++++ s+ y++t+t +    t+g + +tV
  gi|313125601|ref|YP_004035865.1| 226 GDDGTVDaGETVTVEVDVADAtTAIESVTADLSdfgaGTSeSlTNETESSVYNATITVSEggTTDGDYPVTV 297
                                       567799*9********************99666454455534677777899*******88889999999998 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0014
                                       SEEEEEEEEE-SS-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEE CS
                             Big_7  17 gtvtisasAsddggvskVefyvdgtlglgtdtsapysltwtttaltagthtlt 69 
                                       g++t+s+s  d+++v++  f+       ++d sapy+++ t +a t+gt+t t
  gi|313125601|ref|YP_004035865.1| 346 GNITVSVSGADSTTVTEAAFS-------TADGSAPYTYEATYNAPTDGTYTFT 391
                                       456666666666666666665.......4445556666666655577887766 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 0.00015
                                       --EB.TSEEEEEEEEE-S.S-EEEEEEEET....TEE..EEEE-SSSEEEEEE-.......- CS
                             Big_7  12 atvs.ggtvtisasAsdd.ggvskVefyvd....gtl.glgtdtsapysltwtt.......t 59 
                                        +v+ g+ +t++a++sdd +gv++V+  +     g++  l+++  ++++lt          +
  gi|313125601|ref|YP_004035865.1| 432 GNVTdGDEITVEATVSDDtSGVQSVTADLSafdlGSSvSLTSSDGSTWNLTTAVgqsptegD 493
                                       45777********************9966644567773355555555555544455554440 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 0.00011
                                       --EB.TSEEEEEEEEE-SS-EEEEEEEET.....TEE.EEEE-SSSEEEEEE-..-....SEEEEEEE CS
                             Big_7  12 atvs.ggtvtisasAsddggvskVefyvd.....gtlglgtdtsapysltwtt..ta.ltagthtltV 70 
                                       ++v  g+tv +sa+++d +g++ V+  +      +++ l++   ++y++++t   t+ + +g+++ltV
  gi|313125601|ref|YP_004035865.1| 537 SVVRdGDTVVVSATVTDTTGITAVTTDASdfgvgTET-LSNVGGDTYETSFTVngTNaAGDGNYSLTV 603
                                       5788899*****************8765533221444.7888888888888885433699*******9 PP

  == domain 7  score: 8.2 bits;  conditional E-value: 0.003
                                       -EB.TSEEEEEEEEE-SS-EEEEEEEET...TEE......EEEE-SSSEEEEEE--.....SEEEEEEE CS
                             Big_7  13 tvs.ggtvtisasAsddggvskVefyvd...gtlg.....lgtdtsapysltwttta..ltagthtltV 70 
                                       +v  ++tvt++ +++d+++v++V+  +    g ++     +g++  + y+ t+  +a  +++g+h+++V
  gi|313125601|ref|YP_004035865.1| 642 VVAdEETVTVELTVTDATTVDTVTADATelgGGSAvslsqVGSS--DVYNGTFVVDAsgVADGEHSVSV 708
                                       455689*****************986543324443578555555..5555555555555********98 PP

  == domain 8  score: 1.8 bits;  conditional E-value: 0.3
                                       TT--EB.TSEEEEEEEEE-S.S-EEEEEEEET....TEE..EEEE-SSSEEEEEE--......SEEE CS
                             Big_7  10 ngatvs.ggtvtisasAsdd.ggvskVefyvd....gtlg.lgtdtsapysltwttta...ltagth 66 
                                       + ++v  g+++t+s++     ++v +Ve  +     gt++  + d+++++ +t++ +a    ++g+h
  gi|313125601|ref|YP_004035865.1| 744 ADSYVAgGEDLTVSVTPDGTgSEVRTVEADLSafgaGTVTlADGDSDGTWDVTVSVDAanaDPDGSH 810
                                       6789999999999999999999*****986555544665349999999**99999976334455555 PP

  == domain 9  score: 14.0 bits;  conditional E-value: 4.6e-05
                                       -TT--EB..TSEEEEEEEEE-S.S-EEEEEEEET....TEE.EEEE-SSSEEEEEE--......SEEEEEEE CS
                             Big_7   9 angatvs..ggtvtisasAsdd.ggvskVefyvd....gtlglgtdtsapysltwttta...ltagthtltV 70 
                                       a+g+++   g++vt+sa+A+d+  gv++V+  +     g++ + tdt + +s t+t +     ++g +++ V
  gi|313125601|ref|YP_004035865.1| 849 ADGDSIVadGESVTVSATATDStAGVQSVTADLSafgaGVV-TLTDTGGDWSKTVTVNGanaDPDGDYSVAV 919
                                       66665555788******************986555555778.99************9443347888888876 PP

  == domain 10  score: 11.7 bits;  conditional E-value: 0.00025
                                        -EB.TSEEEEEEEEE-SS-EEEEEEEET....TEE..EEEE-SSSEEEEEE--. CS
                             Big_7   13 tvs.ggtvtisasAsddggvskVefyvd....gtlg.lgtdtsapysltwttta 60  
                                        +++ g++vt++a+A+d++gv++V+  +     gt++ ++ d ++++++t+  + 
  gi|313125601|ref|YP_004035865.1|  958 VLTdGENVTVEATATDANGVATVTTDLSaigaGTVTlTDGDDDGTWNATVAVDE 1011
                                        567799*****************8855544445542488888899999998865 PP

  == domain 11  score: 13.4 bits;  conditional E-value: 7.4e-05
                                        EEEE--TT-.-EB.TSEEEEEEEEE-SS-EEEEEEEETTEE.........EEEE-SSSEEEEEE-..-....SEE CS
                             Big_7    4 titsPanga.tvs.ggtvtisasAsddggvskVefyvdgtl.g.......lgtdtsapysltwtt..ta.ltagt 65  
                                        t+t  ++g+ +v  g++++isa++sd+ g+ +V++  dg+  g        + d++++y++t+t   +a +++g 
  gi|313125601|ref|YP_004035865.1| 1054 TFTDATDGDgVVApGDQIDISATVSDAAGIGSVTV--DGSAfGsgsavsiADGDSDGTYTATLTVdfDAtAADGD 1126
                                        5666677775667899*****************97..44443344457788888889999988884422355555 PP

                                        EE CS
                             Big_7   66 ht 67  
                                         +
  gi|313125601|ref|YP_004035865.1| 1127 RS 1128
                                        55 PP

  == domain 12  score: 1.4 bits;  conditional E-value: 0.42
                                        -EBTSEEEEEEEEE-SS-EEEEEEEETTEE......EEEE-SSSEEEEEE- CS
                             Big_7   13 tvsggtvtisasAsddggvskVefyvdgtl.g....lgtdtsapysltwtt 58  
                                        t++  +vt+++sA+     ++ +f+v gt+ +    +     ++ s+t+t 
  gi|313125601|ref|YP_004035865.1| 1178 TLNDVNVTLTGSANAT--LDETDFSVSGTSyEtshaV----GSNGSVTVTL 1222
                                        4444456666666655..9999999999996633333....3445555554 PP

  == domain 13  score: -2.9 bits;  conditional E-value: 8.7
                                        EEEEEEEEE-S CS
                             Big_7   18 tvtisasAsdd 28  
                                        t +++a++ dd
  gi|313125601|ref|YP_004035865.1| 1338 TYSVQATVHDD 1348
                                        44444444444 PP

  == domain 14  score: 5.0 bits;  conditional E-value: 0.031
                                        -EB.TSEEEEEEEEE-S...S-EEEEEEEETTEE.......EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7   13 tvs.ggtvtisasAsdd...ggvskVefyvdgtl.g.....lgtdtsapysltwtttaltagthtltV 70  
                                         +  g+tvt+sa +++d    +   V + vd+ +       lg+  s + ++t++ +  + gt++l+V
  gi|313125601|ref|YP_004035865.1| 1462 RIRpGETVTVSAGVTNDgtrAATGYVSLAVDNATtDtrrvtLGAGDSETERFTVQFD--EVGTYNLSV 1527
                                        678899***********76545588999***99965899998888888888888888..789999998 PP

>> DUF3416  Domain of unknown function (DUF3416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.7   2.3e+03      24      88 ..     130     195 ..     127     205 .. 0.64
   2 ?   -3.4   0.0       7.2   9.9e+03      65      85 ..     373     393 ..     349     397 .. 0.74
   3 ?   -1.5   0.0       1.9   2.7e+03      21      45 ..     434     460 ..     419     497 .. 0.76
   4 ?    3.2   0.0     0.071        98      24      89 ..     542     608 ..     537     614 .. 0.80
   5 ?   -1.0   0.0       1.4   1.9e+03      63      86 ..     683     710 ..     647     723 .. 0.70
   6 ?   10.5   0.1    0.0004      0.56      23      84 ..    1465    1527 ..    1458    1529 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.7
                           DUF3416  24 GetvpVeAdvfrdGhdalaAtlvlrragekewqevpMtpggndrweasftpdel....GryeftveAWv 88 
                                       ++tv+V+Adv+    +  ++++   + g + + ++ +t+g  d ++a+ft+       G+ ++t+ A  
  gi|313125601|ref|YP_004035865.1| 130 DDTVRVRADVVDATASVQSVEADASDFG-AGTVSLSLTNG--DTYAATFTVGGSvpadGETNVTIVAAD 195
                                       6788888888776666666666666555.55556666666..999999987644344466666666655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.2
                           DUF3416  65 ndrweasftpdelGryeftve 85 
                                       +  +ea+ ++ + G+y+ft +
  gi|313125601|ref|YP_004035865.1| 373 PYTYEATYNAPTDGTYTFTLD 393
                                       6789999999********975 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.9
                           DUF3416  21 avvGetvpVeAdvfrd..GhdalaAtl 45 
                                       ++ G++++VeA+v  d  G +++ A+l
  gi|313125601|ref|YP_004035865.1| 434 VTDGDEITVEATVSDDtsGVQSVTADL 460
                                       56699********98844555666655 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.071
                           DUF3416  24 GetvpVeAdvfrdGhdalaAtlvlrragekewqevpMtpggndrweasftpdel.....GryeftveAWvD 89 
                                       G+tv+V+A+v     d+ + t+v ++a++      +++++g d +e+sft++ +     G+y+ tveA  D
  gi|313125601|ref|YP_004035865.1| 542 GDTVVVSATVT----DTTGITAVTTDASDFGVGTETLSNVGGDTYETSFTVNGTnaagdGNYSLTVEATDD 608
                                       66777777774....56666666666666777788899999**********99999999*********877 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 1.4
                           DUF3416  63 ggndrweasftpdel....GryeftveA 86 
                                       g  d+++++f +d+     G++++ veA
  gi|313125601|ref|YP_004035865.1| 683 GSSDVYNGTFVVDASgvadGEHSVSVEA 710
                                       4567788888887775555667777776 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.0004
                           DUF3416   23 vGetvpVeAdvfrdGhdalaAtlvlr.ragekewqevpMtpggndrweasftpdelGryeftv 84  
                                         Getv+V+A v  dG  a    + l  ++ ++++++v++ +g+ +  + ++++de+G+y+  v
  gi|313125601|ref|YP_004035865.1| 1465 PGETVTVSAGVTNDGTRAATGYVSLAvDNATTDTRRVTLGAGDSETERFTVQFDEVGTYNLSV 1527
                                        69****************999988886444589999999988788888888999****99877 PP

>> Porphyrn_cat_1  Porphyranase catalytic subdomain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0011       1.5      26      93 ..     188     253 ..     183     256 .. 0.82
   2 ?    1.1   0.1      0.43   5.9e+02      34      91 ..     608     663 ..     596     669 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                    Porphyrn_cat_1  26 tvtLnllglsgnsvqsvtikrlkitkngapvlseetlksapksltLaaeetviLeytyeseiaiketv 93 
                                       +vt+ +++++ +++++ +  +l+  +++ap++s++tl++a +  t++a+etv +e++++ ++++ e+v
  gi|313125601|ref|YP_004035865.1| 188 NVTIVAADNQ-SNTNRTDSPSLR-LDTNAPTYSSTTLSEAGDDGTVDAGETVTVEVDVADATTAIESV 253
                                       5555544444.448888999999.999*******************************9998877766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.43
                    Porphyrn_cat_1  34 lsgnsvqsvtikrlkitkngapvlseetlksapksltLaaeetviLeytyeseiaike 91 
                                         gn ++s+t+ +l+ ++ + p+ls  +l+ +     +a eetv +e+t++ ++++++
  gi|313125601|ref|YP_004035865.1| 608 DLGN-ANSATTNELT-QDVNPPTLSAGSLTGTDGDGVVADEETVTVELTVTDATTVDT 663
                                       4455.8899999999.99999*****************************88887765 PP

>> DUF756  Domain of unknown function (DUF756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.029        40       8      48 ..     155     197 ..     139     249 .. 0.74
   2 ?   -2.2   0.0       5.8     8e+03      21      37 ..     290     306 ..     266     356 .. 0.61
   3 ?   -0.8   0.1       2.3   3.1e+03      27      68 ..     585     606 ..     543     617 .. 0.63
   4 ?    0.5   0.0      0.85   1.2e+03      12      55 ..     752     796 ..     741     835 .. 0.74
   5 ?   -2.6   0.0         8   1.1e+04      12      35 ..     990    1014 ..     973    1049 .. 0.54
   6 ?   -2.3   0.1       6.3   8.6e+03      26      48 ..    1112    1137 ..    1105    1190 .. 0.45
   7 ?   -0.5   0.1       1.8   2.4e+03      19      67 ..    1292    1345 ..    1285    1349 .. 0.83
   8 ?   11.5   0.2   0.00031      0.42      18      65 ..    1475    1527 ..    1452    1531 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.029
                            DUF756   8 dlaagnlrltlrNtgkaaarftVydnaka..pwtytveagdql 48 
                                       d+ ag++ l+l+N  + aa+ftV     a   +++t+ a d+ 
  gi|313125601|ref|YP_004035865.1| 155 DFGAGTVSLSLTNGDTYAATFTVGGSVPAdgETNVTIVAADNQ 197
                                       344599*****************76544466555555444433 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.8
                            DUF756  21 tgkaaarftVydnakap 37 
                                       +g+ ++++ V+d a+  
  gi|313125601|ref|YP_004035865.1| 290 DGDYPVTVRVRDAAGNV 306
                                       34444555555543333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.3
                            DUF756  27 rftVydnakapwtytveagdqledhwklassg.gwYdltVtgp 68 
                                        ftV   + a                     g g Y ltV + 
  gi|313125601|ref|YP_004035865.1| 585 SFTVNGTNAA---------------------GdGNYSLTVEAT 606
                                       3444333322.....................334566666543 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.85
                            DUF756  12 gnlrltlrNtgkaaarftVydnaka..pwtytveagdqledhwkla 55 
                                        +l+++ +++g+++ + tV++   a  + t+t++ g  ++ +w++ 
  gi|313125601|ref|YP_004035865.1| 752 EDLTVSVTPDGTGSEVRTVEADLSAfgAGTVTLADG-DSDGTWDVT 796
                                       567788888888888888888777788777777444.444555544 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 8
                            DUF756   12 gnlrltlrN.tgkaaarftVydnak 35  
                                        g+++lt  + +g+  a+++V + + 
  gi|313125601|ref|YP_004035865.1|  990 GTVTLTDGDdDGTWNATVAVDESNA 1014
                                        4444444443466666666655433 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 6.3
                            DUF756   26 arftVydnaka...pwtytveagdql 48  
                                        a++tV   a+a    +++ v+  d++
  gi|313125601|ref|YP_004035865.1| 1112 ATLTVDFDATAadgDRSVPVTTTDTV 1137
                                        55555444444444222222222222 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 1.8
                            DUF756   19 rNtgkaaarftVydnaka.....pwtytveagdqledhwklassggwYdltVtg 67  
                                          tg+ +  + V++ +       p + t e ++ + d++++as+++ Y ++ t 
  gi|313125601|ref|YP_004035865.1| 1292 ERTGRNGSSVRVESAQPSslvdlPLNTTSESKNVSLDTLSIASQNETYSVQATV 1345
                                        56899999999999877799999999999999999999***9999999987765 PP

  == domain 8  score: 11.5 bits;  conditional E-value: 0.00031
                            DUF756   18 lrNtgkaaa....rftVydnaka.pwtytveagdqledhwklassg.gwYdltV 65  
                                         +N+g++aa     ++V dna++ ++++t+ agd+ +++++++ ++ g Y l+V
  gi|313125601|ref|YP_004035865.1| 1475 VTNDGTRAAtgyvSLAV-DNATTdTRRVTLGAGDSETERFTVQFDEvGTYNLSV 1527
                                        67888765533336667.444448****************************99 PP

>> MG1  Macroglobulin domain MG1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.9   3.9e+03      28      58 ..     184     214 ..     139     223 .. 0.79
   2 ?   -0.1   0.2      0.92   1.3e+03      14      38 ..     231     255 ..     230     284 .. 0.67
   3 ?    5.6   0.0     0.015        21      19      62 ..     280     324 ..     277     328 .. 0.86
   4 ?    0.3   0.0       0.7   9.6e+02      19      56 ..     691     729 ..     688     737 .. 0.87
   5 ?   -2.1   0.0         4   5.5e+03      34      66 ..     813     845 ..     795     867 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.9
                                       SS-EEEEEEEEETTTTTSEEEEEEEEESTTT CS
                               MG1  28 tkeveVtitvkdfpqkkkelasesvtLnsdn 58 
                                       ++e++Vti+  d + +++  +s s++L+ + 
  gi|313125601|ref|YP_004035865.1| 184 DGETNVTIVAADNQSNTNRTDSPSLRLDTNA 214
                                       5678888888888888888888888887765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.92
                                       TTSEEEEEEEEES-SS-EEEEEEEE CS
                               MG1  14 vgseetivveahgltkeveVtitvk 38 
                                       v++ et++ve++ ++++++++ +  
  gi|313125601|ref|YP_004035865.1| 231 VDAGETVTVEVDVADATTAIESVTA 255
                                       7889999999998766665554333 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.015
                                       EEEEEEES-.SS-EEEEEEEEETTTTTSEEEEEEEEESTTTTTEE CS
                               MG1  19 tivveahgl.tkeveVtitvkdfpqkkkelasesvtLnsdnnfqa 62 
                                       ti+v   g  +++ +Vt+ v d + + ++ + e++tLn d n ++
  gi|313125601|ref|YP_004035865.1| 280 TITVSEGGTtDGDYPVTVRVRDAAGNVNQTTVETLTLNTDPNITS 324
                                       6777777744899**************************988765 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.7
                                       EEEEEEES-.SS-EEEEEEEEETTTTTSEEEEEEEEEST CS
                               MG1  19 tivveahgl.tkeveVtitvkdfpqkkkelasesvtLns 56 
                                       t vv+a g+ ++e +V++   d + k+++ +  ++tL+ 
  gi|313125601|ref|YP_004035865.1| 691 TFVVDASGVaDGEHSVSVEAADSQGKTNQTTVGTLTLDT 729
                                       67999999559999*************999999999975 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 4
                                       EEEEEETTTTTSEEEEEEEEESTTTTTEEEEEE CS
                               MG1  34 titvkdfpqkkkelasesvtLnsdnnfqalvki 66 
                                       ++tv d + +++++++e++tL+ ++  +++v +
  gi|313125601|ref|YP_004035865.1| 813 SVTVSDEAGQTSVVTTETLTLDTAKPTLSSVGV 845
                                       688999999999999999999999887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.13u 0.35s 00:00:01.48 Elapsed: 00:00:02.05
# Mc/sec: 2358.98
//
Query:       gi|313125602|ref|YP_004035866.1|  [L=153]
Description: acyl-CoA hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-18   64.6   0.1    1.2e-17   64.0   0.1    1.3  1  4HBT      Thioesterase superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.1   6.8e-22   1.2e-17       4      77 ..      26      98 ..      23     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 6.8e-22
                                      B-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT  4 vhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77
                                       hgG++++++De++++ +++ +g+ ++v+++  s++f+rp+  gd  ++e  v  +g+ts++v+ +v++ed+ +
  gi|313125602|ref|YP_004035866.1| 26 AHGGNVMKWMDEVGAMSAMRFAGE-TCVTARMESVNFHRPIPRGDAALIESYVYGAGTTSVKVRLRVFREDPLT 98
                                      7**********************9.*********************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 943.19
//
Query:       gi|313125603|ref|YP_004035867.1|  [L=310]
Description: phosphoglycerate dehydrogenase-like oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-50  170.2   0.0    3.4e-50  169.9   0.0    1.1  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    8.4e-08   31.9   0.0      1e-07   31.7   0.0    1.1  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    1.3e-06   28.7   0.0    2.1e-06   28.0   0.0    1.3  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    6.6e-05   23.4   0.0    0.00012   22.6   0.0    1.5  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.045   13.8   0.0    1.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
       0.04   13.8   0.1      0.074   12.9   0.1    1.5  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.11   12.7   0.1       0.42   10.9   0.0    2.1  2  TrkA_N         TrkA-N domain


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9   0.0   1.3e-53   3.4e-50       2     178 .]     103     278 ..     102     278 .. 0.96

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 1.3e-53
                                       HHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                      2-Hacid_dh_C   2 alllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                       ++ll+++r l++++    ++ew+ ++     +l g+ v+++GlG +G+ +a+r+ a+gm v ++ r++++ +   e+
  gi|313125603|ref|YP_004035867.1| 103 GYLLQFARGLHRYRLHEPDHEWNPPAWDDTFTLDGESVCVVGLGTLGRGIARRADALGMSVSGVRRTPTPVD-HVET 178
                                       789*******************999999999**************************************998.5555 PP

                                       TCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--S CS
                      2-Hacid_dh_C  79 gvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfe 155
                                       ++  ++l +++++  +v++++plt+ t+++++ae+l++m+++a+l+N+aRG++vd+ aL++aL+s  iagaalDvfe
  gi|313125603|ref|YP_004035867.1| 179 RYGPQELLDAVSDVRFVVVAVPLTDRTEEMVGAEALSAMRDDAYLVNVARGPVVDQSALVDALRSASIAGAALDVFE 255
                                       77889************************************************************************ PP

                                       SSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 156 eeplpedspllelpnviltPHia 178
                                       eeplp++spl+e+++v++tPH a
  gi|313125603|ref|YP_004035867.1| 256 EEPLPPESPLWEMEHVVITPHAA 278
                                       *********************87 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0     4e-11     1e-07      53     133 ..      54     309 ..      18     310 .] 0.94

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4e-11
                                       HHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                        2-Hacid_dh  53 aevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt........................... 102
                                         +l+a  +L +i+ + +G+D + ld+++ + i+++n  g + ++v E +                           
  gi|313125603|ref|YP_004035867.1|  54 PSFLDA--GLDWIHVVRAGYDEFPLDTLRDHEITLSNSTGIHGDAVSEAVvgyllqfarglhryrlhepdhewnppa 128
                                       666666..89******************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|313125603|ref|YP_004035867.1| 129 wddtftldgesvcvvglgtlgrgiarradalgmsvsgvrrtptpvdhvetrygpqelldavsdvrfvvvavpltdrt 205
                                       ***************************************************************************** PP

                                       .........................................................................T-BH CS
                                       .........................................................................xxxx RF
                        2-Hacid_dh 103 .........................................................................aaTe 106
                                                                                                                aaTe
  gi|313125603|ref|YP_004035867.1| 206 eemvgaealsamrddaylvnvargpvvdqsalvdalrsasiagaaldvfeeeplppesplwemehvvitphaaAATE 282
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 107 eaqeniaeeaaenlvaflkgespanav 133
                                       +  ++ia+ + en ++ ++ges+an+v
  gi|313125603|ref|YP_004035867.1| 283 DYPNRIAALVRENSRRLAAGESLANRV 309
                                       *************************98 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   8.1e-10   2.1e-06       2     104 ..     140     241 ..     139     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 8.1e-10
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       + ++GlG++G+ +a++  + g++v+++ rt+  v+++ ++   + +++ ++v+++++v++ v+ ++ ++e++    l
  gi|313125603|ref|YP_004035867.1| 140 VCVVGLGTLGRGIARRADALGMSVSGVRRTPTPVDHVETR--YGPQELLDAVSDVRFVVVAVPLTDRTEEMVGAeAL 214
                                       789********************************98755..45678889********************9988899 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHH CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakel 104
                                       +a++ +++l++++   + d+  l ++l
  gi|313125603|ref|YP_004035867.1| 215 SAMRDDAYLVNVARGPVVDQSALVDAL 241
                                       99**99999988766666666665555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.7e-08   0.00012       2      75 ..     140     205 ..     139     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.7e-08
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedve 75 
                                       ++++G G +g+++a+++ a g    ++  + +r+p  +++ + ++g   +  +  +a+++  +vv+av+ +d +
  gi|313125603|ref|YP_004035867.1| 140 VCVVGLGTLGRGIARRADALG---MSVS-GVRRTPTPVDHVETRYG--PQ--ELLDAVSDVRFVVVAVPLTDRT 205
                                       789******************...****.88**************9..33..589**************98754 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-05     0.045      21     110 ..     135     227 ..     130     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-....SSSSSSB- CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtt....tGnkdiit 93 
                                       l G  ++v+G G +G+G a+   +lG  v      P   +  +   +  ++l ++v+++ +vv +      +++++ 
  gi|313125603|ref|YP_004035867.1| 135 LDGESVCVVGLGTLGRGIARRADALGMSVSGVRRTPT-PVDHVETRYGPQELLDAVSDVRFVVVAvpltDRTEEMVG 210
                                       7899******************999999987777774.45666778889999999999998887612213467899* PP

                                       HHHHCCS-TTEEEEE-S CS
                     AdoHcyase_NAD  94 lehlkkmkddaivcniG 110
                                       +e l++m+dda + n+ 
  gi|313125603|ref|YP_004035867.1| 211 AEALSAMRDDAYLVNVA 227
                                       *************9986 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.9e-05     0.074       2      37 ..     140     175 ..     139     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealek 37 
                                       v v+G Gt+G+gia  + + g++V  v +++  +++
  gi|313125603|ref|YP_004035867.1| 140 VCVVGLGTLGRGIARRADALGMSVSGVRRTPTPVDH 175
                                       89***************999****988887766665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.3     6e+03      43      54 ..      90     101 ..      72     103 .. 0.65
   2 ?   10.9   0.0   0.00016      0.42       1      40 [.     140     179 ..     140     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.3
                                       EEEES-TTSHHH CS
                            TrkA_N  43 evvvgdatdeev 54 
                                       + ++gda +e+v
  gi|313125603|ref|YP_004035867.1|  90 TGIHGDAVSEAV 101
                                       379999999987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00016
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHT CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelree 40 
                                       + ++GlG++Gr +a++  + g  +v+++ + +  v++++ +
  gi|313125603|ref|YP_004035867.1| 140 VCVVGLGTLGRGIARRADAlGM-SVSGVRRTPTPVDHVETR 179
                                       579****************555.7********999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1962.60
//
Query:       gi|313125604|ref|YP_004035868.1|  [L=97]
Description: translation initiation factor 1 (eif-1/sui1) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.8e-16   58.2   0.0    1.1e-15   57.9   0.0    1.1  1  SUI1       Translation initiation factor SUI1
    0.00036   20.8   0.0    0.00045   20.5   0.0    1.2  1  Img2       Mitochondrial large subunit ribosomal protein (Img
  ------ inclusion threshold ------
      0.027   14.5   0.0      0.048   13.7   0.0    1.4  1  ThiS-like  ThiS-like ubiquitin


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   1.8e-19   1.1e-15       3      76 ..      25      93 ..      23      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.8e-19
                              SUI1  3 pkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                      ++++ r+eqr+ +K+v +++g+   + dl++l ++lk+ ++++g+v kd+   i++QGd+  +v+elL e+ g+
  gi|313125604|ref|YP_004035868.1| 25 EELTTRTEQRRYGKHVVIIEGF-QTDTDLDDLGSDLKSALGTGGTV-KDD--HIEIQGDHESRVRELLRER-GY 93
                                      567789****************.888*******************9.777..8*****************9.86 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   7.5e-08   0.00045      24      80 .]      37      93 ..      21      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.5e-08
                              Img2 24 tkkltvirkie..GDiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                       k++++i   +   D+ +l +dL++al+  +  + +  +iei+Gd++++v++ L+++g+
  gi|313125604|ref|YP_004035868.1| 37 GKHVVIIEGFQtdTDLDDLGSDLKSALG--TGGTVKDDHIEIQGDHESRVRELLRERGY 93
                                      45666666544115778***********..67777899******************996 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     8e-06     0.048      20      43 ..      29      52 ..      21      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8e-06
                         ThiS-like 20 alkekikpdaDvvIlNGFpikeDt 43
                                         e+ + +++vvI++GF++ +D+
  gi|313125604|ref|YP_004035868.1| 29 TRTEQRRYGKHVVIIEGFQTDTDL 52
                                      56678888999*********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 636.94
//
Query:       gi|313125605|ref|YP_004035869.1|  [L=54]
Description: hypothetical protein Hbor_08340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-05   23.3   1.2      0.013   15.9   0.0    2.1  2  zf-H2C2_2        Zinc-finger double domain
    0.00015   21.7   0.9     0.0002   21.3   0.9    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0062   16.5   2.3        1.7    8.7   0.2    2.2  2  Rubredoxin       Rubredoxin
  ------ inclusion threshold ------
      0.016   14.9   0.5        3.2    7.5   0.1    2.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.02   15.2   0.6      0.023   15.1   0.6    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.022   15.2   1.0        2.6    8.6   0.1    2.3  2  zf-C2H2          Zinc finger, C2H2 type
      0.023   14.8   0.3        3.3    7.9   0.1    2.1  2  Zn-ribbon_8      Zinc ribbon domain
      0.043   13.7   1.4          1    9.3   0.1    2.1  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.055   13.2   4.5       0.25   11.1   0.5    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.062   13.3   0.4      0.097   12.7   0.4    1.4  1  Ogr_Delta        Ogr/Delta-like zinc finger
      0.074   13.1   1.5        0.6   10.2   1.5    1.9  1  Ribosomal_L37ae  Ribosomal L37ae protein family
       0.11   12.5   2.0        2.1    8.3   0.3    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.22   11.6   8.5        1.7    8.8   1.2    2.2  2  UPF0547          Uncharacterised protein family UPF0547
       0.43   10.7   4.7          4    7.6   4.5    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.55    9.9   3.8         11    5.8   0.5    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
        1.8    8.4   5.1         16    5.3   5.1    2.1  2  zinc_ribbon_5    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.3    0.0094        11      14      22 ..       6      14 ..       4      18 .. 0.83
   2 !   15.9   0.0   1.2e-05     0.013       8      24 ..      25      42 ..      23      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0094
                         zf-H2C2_2 14 pyeCplCdk 22
                                      +y Cp+Cd 
  gi|313125605|ref|YP_004035869.1|  6 EYDCPECDS 14
                                      699****96 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-05
                         zf-H2C2_2  8 kHtgekp.yeCplCdkaF 24
                                       H g+k  ++C+ C++ F
  gi|313125605|ref|YP_004035869.1| 25 IHLGKKTkWQCSDCGYGF 42
                                      59999755********99 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.9   1.7e-07    0.0002      21      45 ..       9      40 ..       5      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-07
                     Zn_Tnp_IS1595 21 CPhCgsrkayrikt.......rglfqCkeCrk 45
                                      CP C s+k+++++          ++qC++C++
  gi|313125605|ref|YP_004035869.1|  9 CPECDSTKFWKTAYmeihlgkKTKWQCSDCGY 40
                                      *************9****************97 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0025       2.8      34      44 ..       6      16 ..       2      18 .. 0.86
   2 !    8.7   0.2    0.0015       1.7       1      12 [.      32      43 ..      32      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                                      T-BBTTTB-BG CS
                        Rubredoxin 34 dWvCPdCgvek 44
                                      ++ CP+C+ +k
  gi|313125605|ref|YP_004035869.1|  6 EYDCPECDSTK 16
                                      799****9987 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                                      EEEETTT-BEEE CS
                        Rubredoxin  1 kyeCkvCgyvYd 12
                                      k++C+ Cgy + 
  gi|313125605|ref|YP_004035869.1| 32 KWQCSDCGYGFI 43
                                      799*****9875 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0081       9.1      42      52 ..       4      14 ..       2      16 .. 0.84
   2 ?    7.5   0.1    0.0029       3.2      41      51 ..      29      39 ..      19      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0081
                    zinc_ribbon_10 42 evkyrCpkCga 52
                                      e++y Cp+C +
  gi|313125605|ref|YP_004035869.1|  4 EMEYDCPECDS 14
                                      689******86 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0029
                    zinc_ribbon_10 41 eevkyrCpkCg 51
                                      +++k++C+ Cg
  gi|313125605|ref|YP_004035869.1| 29 KKTKWQCSDCG 39
                                      789*******9 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.6   2.1e-05     0.023       4      47 ..       7      49 ..       4      54 .] 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigq.cvyCadCgastpwfkiaede 47
                                      ++CP C + + +++++     + +   +C dCg+    ++i +d 
  gi|313125605|ref|YP_004035869.1|  7 YDCPECDSTKFWKTAYMEIHLGKKtKWQCSDCGY--GFIQINDDI 49
                                      78**************99987666999*******..333444433 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.022        25       1       8 [.       7      15 ..       7      28 .. 0.75
   2 ?    8.6   0.1    0.0024       2.6       2      11 ..      34      43 ..      33      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.022
                                      EEETTTT.E CS
                           zf-C2H2  1 ykCpdCg.k 8 
                                      y Cp+C+  
  gi|313125605|ref|YP_004035869.1|  7 YDCPECDsT 15
                                      89****964 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0024
                                      EETTTTEEES CS
                           zf-C2H2  2 kCpdCgksFk 11
                                      +C+dCg+ F 
  gi|313125605|ref|YP_004035869.1| 34 QCSDCGYGFI 43
                                      8******996 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0029       3.3      27      34 ..       6      14 ..       1      20 [. 0.65
   2 ?    5.6   0.0     0.015        17       7      16 ..      34      43 ..      28      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 27 ta.CPeCgs 34
                                      +  CPeC s
  gi|313125605|ref|YP_004035869.1|  6 EYdCPECDS 14
                                      333777766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                       Zn-ribbon_8  7 rCeeCghefe 16
                                      +C +Cg  f 
  gi|313125605|ref|YP_004035869.1| 34 QCSDCGYGFI 43
                                      7999998885 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.047        53      22      29 ..       7      14 ..       2      16 .. 0.68
   2 ?    9.3   0.1   0.00093         1      13      30 ..      25      41 ..      22      42 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.047
                                      EEESSSS- CS
                    RNA_POL_M_15KD 22 feCrqCgY 29
                                      ++C  C++
  gi|313125605|ref|YP_004035869.1|  7 YDCPECDS 14
                                      67777765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00093
                                      EEECSCCCEEEESSSS-E CS
                    RNA_POL_M_15KD 13 pkedkegknfeCrqCgYe 30
                                      +  +k++k   C+ CgY 
  gi|313125605|ref|YP_004035869.1| 25 IHLGKKTK-WQCSDCGYG 41
                                      55556655.57******5 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.042        47      17      22 ..       9      14 ..       7      16 .. 0.75
   2 ?   11.1   0.5   0.00022      0.25       1      12 [.      33      44 ..      33      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.042
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+C s
  gi|313125605|ref|YP_004035869.1|  9 CPECDS 14
                                      888865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00022
                      Rubredoxin_2  1 YvCsqCGfesak 12
                                      ++Cs+CG+ +++
  gi|313125605|ref|YP_004035869.1| 33 WQCSDCGYGFIQ 44
                                      89******8876 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   8.7e-05     0.097       2      38 ..       9      43 ..       8      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-05
                         Ogr_Delta  2 CPhCgapaaartsrnlskd.vreryyqCsnfeCgatfv 38
                                      CP+C +    +++ ++  + +++   qCs+  Cg+ f+
  gi|313125605|ref|YP_004035869.1|  9 CPECDST-KFWKTAYMEIHlGKKTKWQCSD--CGYGFI 43
                                      ****997.677777777661566*******..***997 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5   0.00053       0.6      31      59 ..       4      40 ..       1      44 [. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00053
                                      HS-BEESSSSSSEEEEEE.TTE.......EEETTTTE CS
                   Ribosomal_L37ae 31 hakytCpfcgktkvkRka.vgi.......wkCkkcgk 59
                                      + +y Cp+c++tk  ++a ++i       w+C+ cg+
  gi|313125605|ref|YP_004035869.1|  4 EMEYDCPECDSTKFWKTAyMEIhlgkktkWQCSDCGY 40
                                      5689********9988873455445555577777776 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.039        44       5      12 ..       7      14 ..       6      17 .. 0.82
   2 ?    8.3   0.3    0.0019       2.1       4      14 ..      32      40 ..      29      43 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.039
                    Zn_ribbon_SprT  5 YrCtgCgr 12
                                      Y C+ C++
  gi|313125605|ref|YP_004035869.1|  7 YDCPECDS 14
                                      99****95 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0019
                    Zn_ribbon_SprT  4 vYrCtgCgrey 14
                                      +++C +Cg  y
  gi|313125605|ref|YP_004035869.1| 32 KWQCSDCG--Y 40
                                      7*******..4 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.1    0.0044       4.9       3       8 ..       9      14 ..       8      15 .. 0.84
   2 ?    8.8   1.2    0.0015       1.7      17      25 ..      35      43 ..      33      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0044
                           UPF0547  3 CPeCea 8 
                                      CPeC++
  gi|313125605|ref|YP_004035869.1|  9 CPECDS 14
                                      ****97 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                           UPF0547 17 CphCGyvFq 25
                                      C++CGy F+
  gi|313125605|ref|YP_004035869.1| 35 CSDCGYGFI 43
                                      ******996 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.5     0.026        29      15      23 ..       5      13 ..       2      27 .. 0.78
   2 ?    7.6   4.5    0.0035         4       2      24 ..       9      40 ..       8      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.026
                          zf-Mss51 15 vdfeCpdCG 23
                                      ++++Cp+C 
  gi|313125605|ref|YP_004035869.1|  5 MEYDCPECD 13
                                      789*****5 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0035
                          zf-Mss51  2 CPvpkhkqt.........apkhvdfeCpdCGi 24
                                      CP +++++            k+ + +C dCG+
  gi|313125605|ref|YP_004035869.1|  9 CPECDSTKFwktaymeihLGKKTKWQCSDCGY 40
                                      999976666889999999999**********8 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5    0.0095        11       3      10 ..       7      14 ..       6      16 .. 0.86
   2 ?    5.3   0.2     0.013        14       2       9 ..      32      39 ..      31      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0095
                            zf_UBZ  3 ylCerCgk 10
                                      y C++C++
  gi|313125605|ref|YP_004035869.1|  7 YDCPECDS 14
                                      89****96 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.013
                            zf_UBZ  2 tylCerCg 9 
                                       ++C++Cg
  gi|313125605|ref|YP_004035869.1| 32 KWQCSDCG 39
                                      689****9 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.1     0.015        16       4      32 ..       8      39 ..       5      43 .. 0.66
   2 ?    3.6   0.3     0.051        58       4      12 ..      34      42 ..      31      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                     zinc_ribbon_5  4 rCpdCdtk.F.klvdsklKksgkkVr..CakCa 32
                                       Cp+Cd++ F k +  ++  +gkk +  C  C+
  gi|313125605|ref|YP_004035869.1|  8 DCPECDSTkFwKTAYMEI-HLGKKTKwqCSDCG 39
                                      6****9754547777775.45665544488886 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.051
                     zinc_ribbon_5  4 rCpdCdtkF 12
                                      +C dC+  F
  gi|313125605|ref|YP_004035869.1| 34 QCSDCGYGF 42
                                      899998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 330.50
//
Query:       gi|313125606|ref|YP_004035870.1|  [L=471]
Description: glycine dehydrogenase subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-09   35.9   0.0    5.7e-09   35.4   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    1.9e-07   30.3   0.0      1e-05   24.6   0.0    2.1  2  GDC-P            Glycine cleavage system P-protein
  ------ inclusion threshold ------
      0.018   14.3   0.0      0.035   13.4   0.0    1.4  2  Beta_elim_lyase  Beta-eliminating lyase
       0.03   13.5   0.0      0.041   13.1   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   1.3e-12   5.7e-09      73     207 ..     141     274 ..     135     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.3e-12
                                       HHHHHHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESB CS
                       Aminotran_5  73 ainlvalslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithv 148
                                       a  lva+++ +s  +++ e+v+ ++ h  n+ + +++    g++v+ +p  e+g++d+d+l+++l+e+t+++++t  
  gi|313125606|ref|YP_004035870.1| 141 AGILVAKAYHESqGNDRSEVVIPASAHGTNF-ASAAM---AGYDVVELPSGEDGRVDMDALDAALSEDTAALMLTNP 213
                                       5668999999987778889999999999999.33333...59********************************977 PP

                                       ETTTTE.B--HHHHHHHHHHTT-EEEEE-TT.TTTTS---HHHHTESEEEEETTT.TTSSTT CS
                       Aminotran_5 149 snvtGt.iqpveeigklakkkgalvlvDaaq.avghipidvkklgvDflafsghK.llgPtG 207
                                       ++v G    ++ ei+++++++g l+  D+a  +++  +    ++g D++    hK +  P G
  gi|313125606|ref|YP_004035870.1| 214 NTV-GLfERDIVEIAEMVHDVGGLLYYDGANlNALLGRGRPGDMGFDIMHYNVHKtFATPHG 274
                                       666.66599********************985677888889999999999999997777777 PP

>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.3e-09     1e-05     103     285 ..     103     294 ..      87     299 .. 0.80
   2 !    3.7   0.0     0.005        22     330     393 ..     328     391 ..     322     429 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.3e-09
                                       GG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHH.HHHHHHHH-SSS....--EEEEETTS-HHHHHHHHHH CS
                             GDC-P 103 EisqGrLeallnfqtlvadltGldianasllDegtAaaE.Avllaaraskkk....akkvvvdkkvhpqtlevlktr 174
                                       E sqG+Le l + q  +  + G+d     l   + Aa+E A +l+a+a ++     +++vv+ ++ h  + +     
  gi|313125606|ref|YP_004035870.1| 103 ESSQGTLELLYDLQDYLGRIGGMDA--VTLQPPAGAAGEfAGILVAKAYHESqgndRSEVVIPASAHGTNFA----S 173
                                       89*********************96..468999999999433444333322211134567777777766654....5 PP

                                       HGGGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB--.--HHHHHHHHHTT-EEEE.EE-TTGGGTB CS
                             GDC-P 175 akglgieivevdlteekvtd.......kekevagvlvqypnteGrie.dlkelvekakkkkslvvv.aadllaLtll 242
                                       a   g ++ve ++ e++  d        ++++a++++  pnt G  e d+ e++e +++   l+    a+l aL   
  gi|313125606|ref|YP_004035870.1| 174 AAMAGYDVVELPSGEDGRVDmdaldaaLSEDTAALMLTNPNTVGLFErDIVEIAEMVHDVGGLLYYdGANLNALLGR 250
                                       777888999998888888777888898899**************98747**********987776527889999999 PP

                                       --HHHHT-SEEEEE.-TTTT---GGG----EEEEE-GGGGGG-- CS
                             GDC-P 243 kpPgelgaDivvGs.aqrfGvPlgyGGPhagffAvkeklkRkiP 285
                                         Pg++g Di+  +  + f  P g GGP ag + v e+l+  +P
  gi|313125606|ref|YP_004035870.1| 251 GRPGDMGFDIMHYNvHKTFATPHGGGGPGAGPVGVVEELAPFLP 294
                                       99********97661578*************9999998876665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.005
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--SSBSSEEEEE--TTTHHHHHH CS
                             GDC-P 330 nlaalyavyhGkeglkeiarrihkkteilakelkkkleeelkkkkffdtllieveekaaekvlk 393
                                       + a  y+  +G  gl + + +   ++++la++l  ++  +  +++f  t   + +   a+++l+
  gi|313125606|ref|YP_004035870.1| 328 VKAYAYIARLGDAGLADASAKAVLNANYLAEQLDYEVPYSPFHHEFAATAGDKDAADVAKRMLD 391
                                       567789999************************9988777777777777666555544445554 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.9e-06     0.035      33     169 ..     111     242 ..      83     256 .. 0.70
   2 ?   -3.6   0.0       1.1   5.2e+03     220     240 ..     347     366 ..     327     401 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-06
                                       HHHHHHHHHHHHTT-SEEEEES.-HHHHHHHHH.......HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE CS
                   Beta_elim_lyase  33 tvnrLedavaelfgkeaalfvp.qGtaAnsill.......killqrgeevivtepahihfdetgaiaelagvklrdl 101
                                         ++L+d++ ++ g++a+   p  G a++   +       +   +  +ev++   ah+    + a a++ag  +++l
  gi|313125606|ref|YP_004035870.1| 111 LLYDLQDYLGRIGGMDAVTLQPpAGAAGEFAGIlvakayhESQGNDRSEVVIPASAHGT---NFASAAMAGYDVVEL 184
                                       45566666666777776665442566666544422331111111222344444445554...44667789999**** PP

                                       -EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 102 knkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       ++ e+G +d+++l aa+ e  +    +++++lt+ n +  G  +    + e+a+++++ g  l +DgA
  gi|313125606|ref|YP_004035870.1| 185 PSGEDGRVDMDALDAALSE--D----TAALMLTNPNTV--G--LFERDIVEIAEMVHDVGGLLYYDGA 242
                                       *******************..4....789999999998..4..6678999999999999999999999 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHT---SSTHHHH CS
                   Beta_elim_lyase 220 aerveqrkylggglrqagvla 240
                                       a++v  ++yl+++l+ ++v++
  gi|313125606|ref|YP_004035870.1| 347 AKAVLNANYLAEQLD-YEVPY 366
                                       556666777777776.55554 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.1e-06     0.041      43     158 ..     105     214 ..      73     242 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.1e-06
                                       TTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH...HHHHHHHHHHH..HTTT-EEEEEESS-THHHHHHHHTT CS
                     Aminotran_1_2  43 idglpeleealakflgrseklklkreaavvvgsGag...aliealifllk..lnpgdeilvpdptyasyknilrlsg 114
                                       ++g  el ++l ++lgr  ++  ++  +++   Ga    a+i ++++  +   n  +e+++p+  ++     + ++g
  gi|313125606|ref|YP_004035870.1| 105 SQGTLELLYDLQDYLGRIGGM--DAV-TLQPPAGAAgefAGILVAKAYHEsqGNDRSEVVIPASAHGTNFASAAMAG 178
                                       566666777777777722221..111.2222222221113333333333244577789******************* PP

                                       SEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS- CS
                     Aminotran_1_2 115 gevvryplyseedfhldlealeealkeapegnkktkvilvesph 158
                                         vv+ p  s ed ++d++al++al+e       t  + +++p+
  gi|313125606|ref|YP_004035870.1| 179 YDVVELP--SGEDGRVDMDALDAALSE------DTAALMLTNPN 214
                                       *******..78****************......77888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3222.33
//
Query:       gi|313125607|ref|YP_004035871.1|  [L=440]
Description: glycine dehydrogenase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-105  353.2   0.0   2.2e-105  353.0   0.0    1.0  1  GDC-P            Glycine cleavage system P-protein
    3.8e-06   26.1   0.1    6.1e-06   25.4   0.1    1.2  1  Aminotran_5      Aminotransferase class-V
      8e-05   21.3   0.0    0.00012   20.8   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.024   14.1   0.0      0.054   12.9   0.0    1.6  1  RtcR             Regulator of RNA terminal phosphate cyclase


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.0   0.0  4.9e-109  2.2e-105       3     416 ..       7     423 ..       5     436 .. 0.92

  Alignments for each domain:
  == domain 1  score: 353.0 bits;  conditional E-value: 4.9e-109
                                       H-SS-HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S---------HHHHHHHHHHHHTTB---EE--BTTB----- CS
                             GDC-P   3 higpsekdqkemLetlGlkslddliekavPkeiklkkelkleapksEeellaelekiasknkvvksfiGaGyydtil 79 
                                       + +++++++  mL+++G+++ ++l+  ++P+++++  e+ +e + sE++++ el +  +kn+ +++f+G G   +++
  gi|313125607|ref|YP_004035871.1|   7 YAPHTDEETAAMLDAVGVEDEESLF--DIPEDVRFDGEFGIE-ARSERDIRSELATTFKKNQDLTEFLGRGHHSHYI 80 
                                       77999********************..9*********99997.589******************************* PP

                                       -HHHHHHTTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--E CS
                             GDC-P  80 PaviqrnilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakk 156
                                       P+ ++  i  ++e++t+Yt Yq+Ei+qG L+al+++q+++++ltGl++an s++D +tA+aEA+ la r+ +   ++
  gi|313125607|ref|YP_004035871.1|  81 PSLVDD-ITRRSEFLTSYTQYQPEITQGFLQALFEYQSILVELTGLPVANCSMYDAATALAEAARLAGRVRRVSGTQ 156
                                       ****99.********************************************************************** PP

                                       EEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-.........S-EEEEEEEES-TTSB---.-HHHHHHHHHT CS
                             GDC-P 157 vvvdkkvhpqtlevlktrakglgieivevdlteekvtd......kekevagvlvqypnteGried.lkelvekakkk 226
                                       ++v + +h+ +++vl  +  g+++ +++ ++ + +v+         +++a v    p + G+ie+ l+++ + a + 
  gi|313125607|ref|YP_004035871.1| 157 ILVPEILHEGKRSVLDNYVAGTDLTVETYPMDDGNVDLdavaelADEDTAMVYAENPTVRGTIEEhLSDIGDVADDA 233
                                       *****************************9877776657899988999***************9879********** PP

                                       T-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GGGGGG--S-EEEEEEBTTS-EEEEE CS
                             GDC-P 227 kslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkeklkRkiPGRlvGvskDaegkralrl 303
                                        +l+++ +d +aL+ll+ P+ +gaDivvG+a  +G+P +yG    g fA++e++ R++PGRlvG s+Da gkra++l
  gi|313125607|ref|YP_004035871.1| 234 GALFCLGTDTVALALLEEPASVGADIVVGEADALGMPTAYGM-GLGLFATRESFLRQVPGRLVGASEDAGGKRAYTL 309
                                       ****************************************85.589******************************* PP

                                       E-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT...T-EE--SSBSSE CS
                             GDC-P 304 alqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkk..leeelkkkkffdt 378
                                       +lqtREqHir+++AtsniCt+qa +A+ aa++a y+G++gl+++a++  + ++ la++l +   ++  ++++++f  
  gi|313125607|ref|YP_004035871.1| 310 TLQTREQHIRKERATSNICTNQAWVALRAAMHAAYLGPDGLTDLAKQCVTDAASLASDLTELrgIKAPVHDRHHFRE 386
                                       ***********************************************************987656666766666655 PP

                                       EEEE--TTTHHHHHHHHHHTTEE-EEESTTEEEEE--T CS
                             GDC-P 379 llieveekaaekvlkkaekeglnlrkvelktvgialdE 416
                                        +++++ + a+++ +  e+eg+ +  v ++++ + +++
  gi|313125607|ref|YP_004035871.1| 387 FVAHTD-QPAQAIASDLEAEGFAVHVVGEHELQVCITD 423
                                       444333.4455677777777777777777777776665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   1.4e-09   6.1e-06      85     350 ..     151     425 ..     134     430 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.4e-09
                                       -TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHH CS
                       Aminotran_5  85 lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpvee 160
                                          g++i+v e+ h +++    +    t ++v+ +p+ ++g++dld++++l +e+t++v ++ + +v Gt  + + +
  gi|313125607|ref|YP_004035871.1| 151 RVSGTQILVPEILHEGKRSVLDNYVAGTDLTVETYPM-DDGNVDLDAVAELADEDTAMV-YAENPTVRGTiEEHLSD 225
                                       557999************99999999**********9.89********99999999877.6789******66789** PP

                                       HHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSST....T-EEEEEEHHHHHTS..SS.STTSEEE CS
                       Aminotran_5 161 igklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPt....GiGvlyvrkellekleplllggemvee 233
                                       ig++a ++gal+++   + ++    + + +g+D+++  +  l  Pt    G+G+   r++ l +++  l+g +  + 
  gi|313125607|ref|YP_004035871.1| 226 IGDVADDAGALFCLGTDTVALALLEEPASVGADIVVGEADALGMPTaygmGLGLFATRESFLRQVPGRLVGASE-DA 301
                                       *************98888888888889999******999999888777779**************776666552.22 PP

                                       EETTEEE....EHCTTGGGS.SS--HH...HHHHHHHHH..HHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES CS
                       Aminotran_5 234 vsleett....faeapskfeaGTpnva...giiglgaal..eyleeigleaiekhekelaeyllerlkslpgvrlyg 301
                                            +t    ++e+  + e  T n+    ++++l+aa+   yl   gl+  +k+  + a+ l + l +l g++   
  gi|313125607|ref|YP_004035871.1| 302 GGKRAYTltlqTREQHIRKERATSNICtnqAWVALRAAMhaAYLGPDGLTDLAKQCVTDAASLASDLTELRGIKA-- 376
                                       2222222233345566666666999954448******96226889999999****999***************99.. PP

                                       .-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEE.E-TTTHHHHHHTT CS
                       Aminotran_5 302 pdkaerrasivsfnfkgvhaedvatlLdeegIavrs.Ghhcaqplmkrla 350
                                         +++r++    +++++  a+ +a+ L+ eg av+  G+h +q+  + l+
  gi|313125607|ref|YP_004035871.1| 377 -PVHDRHHFREFVAHTDQPAQAIASDLEAEGFAVHVvGEHELQVCITDLN 425
                                       .35566666666666788889**************99***9998877766 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.6e-08   0.00012      90     193 ..     153     261 ..     125     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.6e-08
                                       TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHH CS
                   Cys_Met_Meta_PP  90 aGdeivvsddlYggtqrllkkvlkklgievkfvdt....sdleelekaikentklvylEtptnpllkvvDiekiakl 162
                                       +G++i+v + l++g +++l++++  + ++v+ + +     dl+++++  +e t +vy E pt        + +i ++
  gi|313125607|ref|YP_004035871.1| 153 SGTQILVPEILHEGKRSVLDNYVAGTDLTVETYPMddgnVDLDAVAELADEDTAMVYAENPTVRGTIEEHLSDIGDV 229
                                       69*********************99888888877722334678999****************9999999999999** PP

                                       HHHTT-EEEEE.GTTTHTTTS-GGGGT-SEEE CS
                   Cys_Met_Meta_PP 163 akkagvlvvvD.ntfaspllqrplklgaDivv 193
                                       a +ag+l ++   t+a  ll +p + gaDivv
  gi|313125607|ref|YP_004035871.1| 230 ADDAGALFCLGtDTVALALLEEPASVGADIVV 261
                                       *****8888852688999*************8 PP

>> RtcR  Regulator of RNA terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.2e-05     0.054      23     122 ..     318     421 ..     306     428 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                              RtcR  23 werWrPtvslvqqedllvdrleL....lyekresklaeevaediaevspe.tevrlkevelkdpWdfeevyaalldf 94 
                                        ++ r t ++++++ ++  r  +    l  +  ++la++ ++d a+++ + te+r  +  ++d   f e  a+  + 
  gi|313125607|ref|YP_004035871.1| 318 IRKERATSNICTNQAWVALRAAMhaayLGPDGLTDLAKQCVTDAASLASDlTELRGIKAPVHDRHHFREFVAHTDQP 394
                                       5556666666666666655543311114455678999999999998766549************************* PP

                              RtcR  95 akaykfdtekedYlvhittGthvaqicl 122
                                       a+a + d e+e + vh+  G h  q+c+
  gi|313125607|ref|YP_004035871.1| 395 AQAIASDLEAEGFAVHV-VGEHELQVCI 421
                                       ****************9.59*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 2390.83
//
Query:       gi|313125608|ref|YP_004035872.1|  [L=126]
Description: glycine cleavage system h protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-45  153.3   0.0    2.8e-45  153.2   0.0    1.0  1  GCV_H          Glycine cleavage H-protein
     0.0013   18.5   0.2     0.0037   17.1   0.2    1.7  1  Biotin_lipoyl  Biotin-requiring enzyme
     0.0018   18.2   0.0      0.011   15.6   0.0    1.9  2  RnfC_N         RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.069   13.1   0.0        0.1   12.6   0.0    1.2  1  DUF2118        Uncharacterized protein conserved in archaea (
       0.07   12.7   0.1        5.2    6.7   0.0    2.1  2  AOC_like       Allene oxide cyclase barrel like domain


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.2   0.0   7.7e-49   2.8e-45       2     118 ..       9     124 ..       8     126 .] 0.98

  Alignments for each domain:
  == domain 1  score: 153.2 bits;  conditional E-value: 7.7e-49
                                       EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGG CS
                             GCV_H   2 yytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekl 78 
                                        y ++he+ ++++d vat+Gitdfaq+elgdvvfvelp++g+++ +ge++++vEs Ka+s++yapvsG+vv+vNe+l
  gi|313125608|ref|YP_004035872.1|   9 NYLESHEYATTDGD-VATIGITDFAQDELGDVVFVELPDEGDELTQGEEFGVVESIKAVSDLYAPVSGTVVDVNEDL 84 
                                       599**********9.************************************************************** PP

                                       TT-TTHHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHHH CS
                             GCV_H  79 eeepeliNkdpyeegWliklklsnleeleeLlsaeeyekl 118
                                        + pel+N+dpy++gW++k+++s++   +eLls eey++ 
  gi|313125608|ref|YP_004035872.1|  85 FDRPELVNEDPYGDGWMLKVEVSDEGAFDELLSPEEYRDQ 124
                                       *************************************976 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2     1e-06    0.0037      22      56 ..      46      80 ..      37      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                                      STTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEE CS
                     Biotin_lipoyl 22 kvGdkVkagqvlaeveamKmemeieapkaGvvkei 56
                                       +Gd+ ++g+   +ve+ K++ ++ ap++G+v+++
  gi|313125608|ref|YP_004035872.1| 46 DEGDELTQGEEFGVVESIKAVSDLYAPVSGTVVDV 80
                                      58******************************998 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.13   4.6e+02      62      97 ..       8      43 ..       3      47 .. 0.74
   2 !   15.6   0.0   3.1e-06     0.011      48      86 ..      47      86 ..      42      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                            RnfC_N 62 egfvsapvhasvsGtVkaiekrlvahgsgveavvie 97
                                      ++++ ++ +a + G V +i     a+ +  + v +e
  gi|313125608|ref|YP_004035872.1|  8 SNYLESHEYATTDGDVATIGITDFAQDELGDVVFVE 43
                                      556677779999*****9998888877766666665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.1e-06
                            RnfC_N 48 vgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlva 86
                                      +gd+ ++G+  +  e+    +  +a+vsGtV+++++ l  
  gi|313125608|ref|YP_004035872.1| 47 EGDELTQGEEFGVVESiKAVSDLYAPVSGTVVDVNEDLFD 86
                                      79**********9998555789************987665 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.8e-05       0.1      95     138 ..      43      85 ..      32      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                           DUF2118  95 livdvGdrveegdtlaavttrkgevrylrapvegvVvfikeepa 138
                                          d+Gd++ +g+ ++ v + k  v  l apv g+Vv ++e+  
  gi|313125608|ref|YP_004035872.1|  43 ELPDEGDELTQGEEFGVVESIKA-VSDLYAPVSGTVVDVNEDLF 85 
                                       5669****************995.9*************999876 PP

>> AOC_like  Allene oxide cyclase barrel like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.009        32      61      80 ..      14      33 ..       6      44 .. 0.82
   2 ?    6.7   0.0    0.0015       5.2       4      54 ..      60     110 ..      58     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.009
                                      EEEEETTEEEEEEEEEEHHH CS
                          AOC_like 61 eeitleDGtirvaGlvdlta 80
                                       e+ ++DG + + G+ d+++
  gi|313125608|ref|YP_004035872.1| 14 HEYATTDGDVATIGITDFAQ 33
                                      589999***********987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0015
                                       EEEEE---TTS.--TT-EEEEEEEEE-TTS-EEEEEEEEEEEEEEETTTTE CS
                          AOC_like   4 vkaetddetlanptvgdvatvedelldadgkkiGttsGkgrilyqrpedgh 54 
                                       v++ + + +l +p  g+v+ v+++l+d+ +       G g++l+ + +d +
  gi|313125608|ref|YP_004035872.1|  60 VESIKAVSDLYAPVSGTVVDVNEDLFDRPELVNEDPYGDGWMLKVEVSDEG 110
                                       566678889999****************999999999*****999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 723.75
//
Query:       gi|313125609|ref|YP_004035873.1|  [L=368]
Description: glycine cleavage system protein T [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-83  278.0   0.1    7.9e-83  277.7   0.1    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    1.1e-23   82.9   0.1    2.2e-23   82.0   0.1    1.5  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain
  ------ inclusion threshold ------
      0.071   13.3   0.1        3.9    7.6   0.0    2.2  2  SoxG      Sarcosine oxidase, gamma subunit family
      0.096   13.0   0.0        3.5    8.0   0.0    2.2  2  TrmE_N    GTP-binding protein TrmE N-terminus


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.7   0.1   1.8e-86   7.9e-83       3     256 ..      10     263 ..       8     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 277.7 bits;  conditional E-value: 1.8e-86
                             GCV_T   3 drhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkat 79 
                                       + h a+ akf+ef+gw+mPv++  +si+ eh avre++g+fDvShmg+ievsGpda++l+qrl+tnd++ l+pg+++
  gi|313125609|ref|YP_004035873.1|  10 EAHAARDAKFTEFGGWDMPVEF--DSIRTEHTAVRESVGIFDVSHMGEIEVSGPDATRLMQRLTTNDVTLLDPGDSQ 84 
                                       689*******************..***************************************************** PP

                             GCV_T  80 ytlllnedGgvidDlivarlde...defllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarev 153
                                       y+++++ +G ++dD++v+rl +   d++l++ na++ e++++ +++++++++ld+++ ++tee+a++a+qGP a++ 
  gi|313125609|ref|YP_004035873.1|  85 YAMITDAEGTILDDTVVYRLPDeetDRYLFIPNAGHDEEMHDRWTSHRDEWELDARIANTTEEWAMFAVQGPDAKDA 161
                                       ********************965558***************777777999**************************9 PP

                             GCV_T 154 lskllgadlselkffsfaevelaggkkvlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtl 230
                                       + +  + d+ +l+ f+++  ++  g++ +v+RtgytGedGfei++p eeae +w+a    +++++ +p+GlgArdtl
  gi|313125609|ref|YP_004035873.1| 162 VVAAADGDVGSLSKFEATYEDVV-GVRSWVARTGYTGEDGFEILCPVEEAETVWNAF---VEDHESQPCGLGARDTL 234
                                       999999****************9.*********************************...68999************ PP

                             GCV_T 231 RlEaglrlyghdldee...ttPleaglgw 256
                                       R+E+g+ l g+d+d+e    +P+eag+g+
  gi|313125609|ref|YP_004035873.1| 235 RMEMGFLLSGEDFDPEsepRNPYEAGVGF 263
                                       ****************99999*****987 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.1   4.8e-27   2.2e-23       2      78 ..     288     364 ..     287     366 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 4.8e-27
                           GCV_T_C   2 rlvgleld.dgapllrggepilr.dgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkk 76 
                                       ++vgl+l  +g  ++r+g+ i++ d+ vvGhvTSg++sptlg +ial+yv+ e+a++gt++ v vrg++ +a+vv++
  gi|313125609|ref|YP_004035873.1| 288 KFVGLKLLdRG--VPRHGYDIVDaDNHVVGHVTSGTMSPTLGEPIALGYVPVEHADPGTTLSVVVRGQEKRAKVVST 362
                                       78*****7355..88*******549999************************************************* PP

                           GCV_T_C  77 pf 78 
                                       pf
  gi|313125609|ref|YP_004035873.1| 363 PF 364
                                       *9 PP

>> SoxG  Sarcosine oxidase, gamma subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00088       3.9      60      97 ..      41      77 ..      30     103 .. 0.77
   2 ?    3.4   0.0     0.017        77     119     142 ..     195     218 ..     143     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00088
                              SoxG 60 laelasvvdlShgrvlisisGakaeavlakltaiDlsa 97
                                      + e+  + d+Sh    i++sG+ a +++++lt+ D+ +
  gi|313125609|ref|YP_004035873.1| 41 VRESVGIFDVSHMG-EIEVSGPDATRLMQRLTTNDVTL 77
                                      55556678999975.8*******************976 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.017
                              SoxG 119 rtgsdafevlvfrsFaeslwkaLl 142
                                        tg+d fe+l+    ae +w+a+ 
  gi|313125609|ref|YP_004035873.1| 195 YTGEDGFEILCPVEEAETVWNAFV 218
                                       699*****************9876 PP

>> TrmE_N  GTP-binding protein TrmE N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00078       3.5      14      65 ..      53     106 ..      45     110 .. 0.78
   2 ?    2.6   0.0     0.037   1.7e+02      55      79 ..     181     205 ..     141     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00078
                                       EEEEEEESTTHHHHHHTTEEE...T--CTEEEEEEEECT..TCEEEEEEEEEEBT CS
                            TrmE_N  14 iaiiRvsGpkaleiakklfkk...elkprkallgklvdeeekevlDevlvlvfka 65 
                                       ++ i vsGp+a++++++l+++    l+p   ++  ++d+ e+++lD+++v   + 
  gi|313125609|ref|YP_004035873.1|  53 MGEIEVSGPDATRLMQRLTTNdvtLLDPGDSQYAMITDA-EGTILDDTVVYRLPD 106
                                       56799*************988554344778888888876.777899999987765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.037
                                       EEEEEEEEEBTTCSTTSSEEEEEEE CS
                            TrmE_N  55 lDevlvlvfkaprsyTgedvvElhl 79 
                                        D v v  + a   yTged +E+ +
  gi|313125609|ref|YP_004035873.1| 181 EDVVGVRSWVARTGYTGEDGFEILC 205
                                       46666777788999********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 1945.86
//
Query:       gi|313125610|ref|YP_004035874.1|  [L=71]
Description: hypothetical protein Hbor_08390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.074   12.7   2.7      0.083   12.5   2.7    1.1  1  Wzy_C     O-Antigen ligase
       0.11   12.4   2.7       0.14   12.1   2.7    1.2  1  MerE      MerE protein


Domain annotation for each model (and alignments):
>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.7   9.3e-06     0.083      21      73 ..      18      70 ..       9      71 .] 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.3e-06
                             Wzy_C 21 gllvalivlliifykrripfllllgilvgvilliilfvlstnletlknitkaf 73
                                      ++l+ l v+l+i + + i  l+l+g+ v ++++++l v+s ++  ++n + af
  gi|313125610|ref|YP_004035874.1| 18 AVLGSLTVALFISPTWVIDTLGLAGFGVYIVVILALPVFSFKYDLVGNAKEAF 70
                                      579999******************************************99887 PP

>> MerE  MerE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.7   1.6e-05      0.14      34      65 ..      15      46 ..       8      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                              MerE 34 ilaivlaGttaGaflgeywviaalaltGlfvl 65
                                      +l +vl   t   f++  wvi +l+l+G+ v 
  gi|313125610|ref|YP_004035874.1| 15 LLGAVLGSLTVALFISPTWVIDTLGLAGFGVY 46
                                      7899***********************97554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 435.27
//
Query:       gi|313125611|ref|YP_004035875.1|  [L=66]
Description: hypothetical protein Hbor_08400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.35s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 379.01
//
Query:       gi|313125612|ref|YP_004035876.1|  [L=383]
Description: signal transduction histidine kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-18   67.2   0.0    2.8e-18   66.5   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.1e-16   59.9   1.7    6.5e-16   58.3   1.7    1.8  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
    2.9e-07   30.5   0.0    6.3e-07   29.4   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
    1.2e-06   28.3   0.0    2.3e-06   27.4   0.0    1.4  1  HATPase_c_5  GHKL domain
     0.0005   20.0   0.5     0.0011   19.0   0.5    1.6  1  HisKA        His Kinase A (phospho-acceptor) domain
      0.006   16.4   0.0      0.011   15.5   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.067   12.9   0.2       0.17   11.6   0.2    1.7  1  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   1.1e-21   2.8e-18       6     110 ..     253     351 ..     249     353 .. 0.87

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.1e-21
                                       HHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                       L +++ nl++Navk++    +++++++ ++ d+ v++++DnG+Gip+e+++ lfe  ++       ++ +GlGl++v
  gi|313125612|ref|YP_004035876.1| 253 LPRVFCNLLQNAVKHNDsAVPRVSITLATDADTAVVTITDNGRGIPEEKRETLFEGDTR-------TSNHGLGLYLV 322
                                       568999*********33355577777776679**********************97677.......79********* PP

                                       HHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  82 kklvelmgGeiwvesepgrGttftftlpl 110
                                       + l+e++gG i+++++  +G+ ft++lp 
  gi|313125612|ref|YP_004035876.1| 323 RTLTERYGGAIELRETGPEGSVFTVELPR 351
                                       *************99999*******9996 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   1.7   2.5e-19   6.5e-16      28     161 ..      27     168 ..       2     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 2.5e-19
                         HisKA_4TM  28 svrGPvlalaldGllalglvyagyrlastdlpaeqewtvlvwslgGavvvgavigltvlvrllegrtiaePvfvvlv 104
                                         r  vl+l+++G++alg+ y+gy+l+++d+ a+q   v++w+lgG +++ ++  l v++ l       e +     
  gi|313125612|ref|YP_004035876.1|  27 YTRDYVLTLLFNGIPALGISYTGYWLRRSDIEADQYRRVVAWCLGGMAAFLSLN-L-VIIALWPADHFIENLGWARG 101
                                       467789****************************************99987753.3.33444444444555555556 PP

                         HisKA_4TM 105 aaevGavaGllaGylaararadasrakr.......i...sdalafvndlirhdlrndlvvirgyaea 161
                                       +a   a  Gl+ G  +ara + a+ a+r       +    + l ++n+l+rh++ n  +vi+gy+e 
  gi|313125612|ref|YP_004035876.1| 102 SAVYAACGGLIMGVIEARAIKRARVAEReiartkrVeakRQWLGYMNSLLRHEVLNTANVIEGYSEL 168
                                       66677888899999888888777665542111111211145699********************986 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   2.4e-10   6.3e-07      40     112 ..     261     329 ..     258     348 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.4e-10
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDev 112
                                       + Nav+h+    p  +v+++l  d+++ +v+++D+G+g + e+++   e +  +   ++G+Gl+l+++l++ +
  gi|313125612|ref|YP_004035876.1| 261 LQNAVKHNDSAVP--RVSITLATDADTAVVTITDNGRGIPEEKRETLFEGD--TRTSNHGLGLYLVRTLTERY 329
                                       67********999..8889999****************9999877776655..99**************9876 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   8.9e-10   2.3e-06       7      89 ..     254     337 ..     249     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 8.9e-10
                       HATPase_c_5   7 cvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkklesskskkeehGiGlksireivk 79 
                                        ++++nlL NA+   +      + +++t+ ++ ++ +++i+ + +g    + ++l++  +++++hG+Gl  +r +++
  gi|313125612|ref|YP_004035876.1| 254 PRVFCNLLQNAVKHNDSAV---PRVSITLATDADTAVVTITDNGRGipeeKRETLFEGDTRTSNHGLGLYLVRTLTE 327
                                       579*********9888766...67777777777776666665544434324477889999***************** PP

                       HATPase_c_5  80 kykgnlsiea 89 
                                       +y+g+++++ 
  gi|313125612|ref|YP_004035876.1| 328 RYGGAIELRE 337
                                       ****998654 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   4.3e-07    0.0011       6      65 ..     148     208 ..     143     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.3e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHH..HHHCCHH CS
                             HisKA   6 lagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedl..Ldlsrie 65 
                                        + + HE  +  ++i g++e+L +e ++++  ++ le+i++++r l+++++d+  L  +++e
  gi|313125612|ref|YP_004035876.1| 148 NSLLRHEVLNTANVIEGYSELLLEE-DTNDLSADRLEVIRQQSRNLSEVINDVqvLIEATEE 208
                                       566889999999*********9664.67899999******************9666666655 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.4e-06     0.011       7      52 ..     257     304 ..     253     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-06
                       HATPase_c_3   7 laelvdNsld...AdaenvkievnknrgktgeivieDdGkGmseeelkn 52 
                                        + l++N++    +   +v+i++ ++  +t+ ++i+D+G G++ee+ + 
  gi|313125612|ref|YP_004035876.1| 257 FCNLLQNAVKhndSAVPRVSITLATDA-DTAVVTITDNGRGIPEEKRET 304
                                       578899998644466777*******86.89**************98665 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   6.5e-05      0.17       8      42 ..     139     174 ..     133     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.5e-05
                            SPOB_a   8 elkeliklL.rsqRHDflNhLQvIsGylqLgkydka 42 
                                         ++++ ++ + +RH+ lN   vI Gy +L   ++ 
  gi|313125612|ref|YP_004035876.1| 139 AKRQWLGYMnSLLRHEVLNTANVIEGYSELLLEEDT 174
                                       5567777775668***************99666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2289.13
//
Query:       gi|313125613|ref|YP_004035877.1|  [L=263]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-07   31.0   0.0    3.8e-07   30.2   0.0    1.4  1  DUF1724    Domain of unknown function (DUF1724)
    2.6e-05   24.0   0.1    7.5e-05   22.5   0.1    1.8  1  MarR_2     MarR family
    9.5e-05   22.2   0.0     0.0003   20.6   0.0    1.9  2  HTH_5      Bacterial regulatory protein, arsR family
     0.0014   18.7   0.0     0.0054   16.8   0.0    2.1  1  HemN_C     HemN C-terminal domain
     0.0089   16.0   0.1      0.023   14.7   0.1    1.7  1  HTH_Crp_2  Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.049   13.4   1.0       0.16   11.8   0.0    2.4  3  HTH_IclR   IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.3e-10   3.8e-07       2      61 ..     198     255 ..     197     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.3e-10
                           DUF1724   2 klyvydeeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSe 61 
                                       ++++ de+i pl++t+tD+++ l l d+dg   +  l  +d+++l+W+++ +e Y++ + 
  gi|313125613|ref|YP_004035877.1| 198 EIRLHDEPI-PLAVTITDDVVHLLLRDEDGLL-RAALDTDDDAVLSWARDMHEQYWQAAS 255
                                       7999*****.********************55.557999*****************9886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   2.5e-08   7.5e-05       2      53 ..      12      60 ..      11      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.5e-08
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +l+     vL aL+ +    lt  el+++++ s++++ ril+++ ++G++e 
  gi|313125613|ref|YP_004035877.1| 12 ALSANRVEVLDALRKAS---LTRHELEAETDASQPTLGRILRDFTDRGWIEH 60
                                      67888899*******99...9*****************************95 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   9.9e-08    0.0003       3      37 ..      16      50 ..      14      59 .. 0.90
   2 ?   -2.5   0.0       1.7   4.9e+03      30      42 ..     182     194 ..     181     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.9e-08
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLk 37
                                      +R+++L +L++ +l+ +el +e++ sq+t+ + L+
  gi|313125613|ref|YP_004035877.1| 16 NRVEVLDALRKASLTRHELEAETDASQPTLGRILR 50
                                      7*****************************98776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHT CS
                             HTH_5  30 stvShHLkkLrea 42 
                                       st+++ L  L +a
  gi|313125613|ref|YP_004035877.1| 182 STLRQRLEDLLDA 194
                                       8999999999998 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.8e-06    0.0054      26      66 .]      34      73 ..      27      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                            HemN_C 26 feqrfgldleellaaaleklqeqGLLeldggrlrltprGrl 66
                                      +e+++  + +++l+ +l++++++G++e+dg+r+ +t  Grl
  gi|313125613|ref|YP_004035877.1| 34 LEAETDAS-QPTLGRILRDFTDRGWIEHDGNRYAATATGRL 73
                                      67778887.9999**************************96 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   7.7e-06     0.023      19      55 ..      26      63 ..       8      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.7e-06
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglis.rgr 55
                                      + +lt+ el +   +++ t+ ril+++ ++g+i+  g+
  gi|313125613|ref|YP_004035877.1| 26 KASLTRHELEAETDASQPTLGRILRDFTDRGWIEhDGN 63
                                      5689999999999*********************6453 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.2e-05      0.16       7      52 .]      19      62 ..      16      62 .. 0.89
   2 ?   -2.2   0.1       1.2   3.6e+03      10      25 ..      80      95 ..      75      96 .. 0.78
   3 ?   -3.0   0.0       2.3   6.9e+03       4      13 ..     129     135 ..     127     138 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      ++Ldal++a    t  el ++t+ + +t  R+L+ ++ +G++e dg
  gi|313125613|ref|YP_004035877.1| 19 EVLDALRKASL--TRHELEAETDASQPTLGRILRDFTDRGWIEHDG 62
                                      67888877765..699***************************996 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                      CT-CTTBSS-BHHHHH CS
                          HTH_IclR 10 dalaeapqeltlselA 25
                                      d+l++   el+l+++ 
  gi|313125613|ref|YP_004035877.1| 80 DLLETMETELKLRDVV 95
                                      6788888889998876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.3
                                       HHHHHHCT-C CS
                          HTH_IclR   4 RalaiLdala 13 
                                       R   +L++l+
  gi|313125613|ref|YP_004035877.1| 129 R---VLELLR 135
                                       4...555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1676.34
//
Query:       gi|313125614|ref|YP_004035884.1|  [L=331]
Description: dmt(drug/metabolite transporter) superfamily permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-37  127.8  31.6    9.8e-21   74.4   9.8    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.083   12.9   2.8        3.8    7.6   0.2    2.5  2  TMEM234   Putative transmembrane family 234
        9.4    6.6   6.6        1.2    9.5   0.4    2.4  3  DUF2919   Protein of unknown function (DUF2919)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   9.8   1.6e-24   9.8e-21       4     136 ..       7     142 ..       5     143 .. 0.90
   2 !   59.7  13.8   5.5e-20   3.3e-16       3     135 ..     156     290 ..     154     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.6e-24
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkd..wllllllgllgtvla 78 
                                       ++++l+a+ f++ +fv++k++l++++pl ++++rf i+++lll + l++  + ++l+++   ++ +l  g++++ ++
  gi|313125614|ref|YP_004035884.1|   7 LVFFLAASAFFGGTFVAAKAGLEFFPPLLFVAYRFDIGAALLLSVVLYRFPRERWLPRTRadIAGILAAGVFAIGAT 83 
                                       57899*******************************99999977766666666344444344*************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlll.gekltlkqllgivlillGvllil 136
                                       + l+f +++++++++ s+i sl P++t il+++ll  e+l+ +   g++l+l+Gv+l++
  gi|313125614|ref|YP_004035884.1|  84 NALIFVGQQYVTSGVSSIIYSLNPIMTPILAAFLLsDERLSRSGAGGMLLGLVGVALVV 142
                                       ***********************************99********************96 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 5.5e-20
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtvl 77 
                                       g  l+l+aa++ a++ vl++++ +++++   t++ + +a++l+ + ++  +++     +++ ++++l ++g+++++l
  gi|313125614|ref|YP_004035884.1| 156 GKALVLAAAVSGALGSVLIRRADSTLDSTVRTAWALPVAAVLCHVSSFAAGEQAsaVTWTPAALAALGYVGVFSGAL 232
                                       66799**************************************88888888888778999999************** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       af+++f +l +++a +  l+++ +P+++++ ++lllge+++ ++++g+++i lG +l+
  gi|313125614|ref|YP_004035884.1| 233 AFIAYFGLLDDVGAIRGNLVFYAVPIVATLGGWLLLGETISALTVVGFGVICLGFVLL 290
                                       ******************************************************9997 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2   0.00063       3.8      73     116 .]      98     142 ..      78     142 .. 0.85
   2 ?    5.3   0.3    0.0033        20      61     115 ..     237     290 ..     228     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00063
                           TMEM234  73 avpiaNslafvfTvlte.lllgekvlkkktvlgmllvvvgialcv 116
                                       ++ i  sl+ ++T + +  ll ++ l+++   gmll +vg+al+v
  gi|313125614|ref|YP_004035884.1|  98 VSSIIYSLNPIMTPILAaFLLSDERLSRSGAGGMLLGLVGVALVV 142
                                       5678899**999977665999**********************86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0033
                           TMEM234  61 fflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       +f ll  +    +  +  ++ +v+T l ++ll  +++++ tv+g +++++g +l+
  gi|313125614|ref|YP_004035884.1| 237 YFGLLDDVGAIRGNLVFYAVPIVAT-LGGWLLLGETISALTVVGFGVICLGFVLL 290
                                       5556666666666666777777766.67888888899999***********9986 PP

>> DUF2919  Protein of unknown function (DUF2919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4    0.0002       1.2      49     138 ..      30     121 ..       4     126 .. 0.74
   2 ?   -0.5   0.3      0.23   1.4e+03      58     124 ..     159     220 ..     158     228 .. 0.58
   3 ?   -2.5   0.0      0.97   5.8e+03       6      27 ..     241     262 ..     240     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0002
                           DUF2919  49 fYPdkssfylgLalgvpalllllligrrkkssewleklwragrplllllllvdlllqlyrlalsheafsw....lta 121
                                       f+P    ++++   +++a lll ++ +r ++++wl++       +l + +++  + +++ ++ +++  s     ++ 
  gi|313125614|ref|YP_004035884.1|  30 FFP--PLLFVAYRFDIGAALLLSVVLYRFPRERWLPRTRADIAGILAAGVFAIGATNALIFVGQQYVTSGvssiIYS 104
                                       444..479999999********999999999*******************999999999888888887772222444 PP

                           DUF2919 122 ltlllllwvllyllksk 138
                                       l+ +++ +++++ll ++
  gi|313125614|ref|YP_004035884.1| 105 LNPIMTPILAAFLLSDE 121
                                       44455555556666555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.23
                           DUF2919  58 lgLalgvpalllllligrrkkssewleklwragrplllllllvdlllqlyrlalsheafswltaltl 124
                                       l La++v + l  +li+r ++    l+  +r+   l ++++l  + +  + +  +  a++w+ a+ +
  gi|313125614|ref|YP_004035884.1| 159 LVLAAAVSGALGSVLIRRADS---TLDSTVRTAWALPVAAVL--CHVSSFAAGEQASAVTWTPAALA 220
                                       568888888888888877744...455555444333333333..33344556677777777666555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.97
                           DUF2919   6 yDehgrlkpPlllwlvllflaR 27 
                                       +D+ g ++  l+++ v ++ + 
  gi|313125614|ref|YP_004035884.1| 241 LDDVGAIRGNLVFYAVPIVATL 262
                                       5899999999999998666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1984.73
//
Query:       gi|313125615|ref|YP_004035885.1|  [L=455]
Description: GTP-binding protein HflX [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-19   70.1   0.0    5.7e-19   68.6   0.0    1.8  1  GTP-bdg_N       GTP-binding GTPase N-terminal
    1.3e-14   54.2   0.4    7.7e-14   51.7   0.1    2.2  2  MMR_HSR1        50S ribosome-binding GTPase
    1.7e-08   34.3   0.7    5.1e-08   32.7   0.7    1.8  1  GTP_EFTU        Elongation factor Tu GTP binding domain
    3.5e-08   33.9   3.7    1.1e-07   32.3   1.7    2.6  2  GTP-bdg_M       GTP-binding GTPase Middle Region
    3.2e-07   30.4   0.4     0.0046   16.9   0.5    2.6  2  RsgA_GTPase     RsgA GTPase
     0.0017   18.4   0.0     0.0054   16.7   0.0    1.8  2  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
     0.0038   16.8   0.5       0.72    9.4   0.3    2.5  2  FeoB_N          Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.027   14.7   2.6      0.092   13.1   0.3    2.9  3  DUF11           Domain of unknown function DUF11
      0.069   13.5   2.5      0.086   13.2   0.5    2.2  2  AAA_16          AAA ATPase domain
        0.1   12.0   0.3        2.6    7.5   0.0    2.3  2  Arf             ADP-ribosylation factor family
       0.11   12.0   0.0       0.18   11.4   0.0    1.3  1  SapC            SapC
       0.13   12.1   0.8       0.57   10.1   0.0    2.4  2  Pox_A_type_inc  Viral A-type inclusion protein repeat


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   3.8e-22   5.7e-19       4      89 .]      46     132 ..      44     132 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 3.8e-22
                         GTP-bdg_N   4 leEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekel..evkVi 78 
                                        eE+++La++ag++v++ev+q r + dp t +G+Gkv+ +++ +e+++a+++++d  L+psq  nL++ l  e++++
  gi|313125615|ref|YP_004035885.1|  46 TEEIRALASAAGYRVIDEVTQVR-REDPGTHFGSGKVDSLSDRIEATDASVLVIDGGLTPSQTTNLRDCLpdETEIF 121
                                       68*******************97.78******************************************98768**** PP

                         GTP-bdg_N  79 DRtqLILdIFA 89 
                                       DR  L+L IFA
  gi|313125615|ref|YP_004035885.1| 122 DRYRLVLSIFA 132
                                       **********8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.53     8e+02      48      86 ..      58     101 ..       5     128 .. 0.60
   2 !   51.7   0.1   5.2e-17   7.7e-14       2     113 ..     211     344 ..     210     345 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.53
                                       EEEEECGGCSS....HHHHHHHHHHHHHHHHC.TSEEEEEEETT CS
                          MMR_HSR1  48 ielvDtpGlie....gaseekglgkaflalee.adlillvvdas 86 
                                       ++++D +  +     g + + g  +++ + +e +d+ +lv+d  
  gi|313125615|ref|YP_004035885.1|  58 YRVIDEVTQVRredpGTHFGSGKVDSLSDRIEaTDASVLVIDGG 101
                                       55555555332223344455566677777666459999999933 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 5.2e-17
                                       EEEEESTTSSHHHHHHHHHT...............STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg...............ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegasee 63 
                                       v ++G++N+GKStL+ +l +               ++a v+d+ ++T++++++r +l+g+++  +Dt+G+++  +  
  gi|313125615|ref|YP_004035885.1| 211 VTVAGYTNAGKSTLLHRLADdlsldsterhpdeanSVAAVEDRLFKTLQTTTRRATLEGRPVLATDTVGFVD--DLP 285
                                       789****************5555555555555543699*******************************776..455 PP

                                       HHHHHHHHHHHC....TSEEEEEEETTTTCSHHHHHHHHHHHHH......TTSEEEEEEE CS
                          MMR_HSR1  64 kglgkaflalee....adlillvvdaseeklkpldeeleellee......akkplilvln 113
                                       ++l ++f   ++    ad+++lv das ++++ l+e++   l+       ++++++ +ln
  gi|313125615|ref|YP_004035885.1| 286 HWLVESFSTTISeaaaADIVVLVADAS-DDVETLREKIRVSLSVfdaqgvETQNVVTALN 344
                                       56777777644334448********99.54666655554443223334445555555665 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.7   3.4e-11   5.1e-08       6     193 ..     211     391 ..     208     400 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.4e-11
                                       EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvd 82 
                                       ++++g +++GK+TL+ rL  +++ +s   e++  +++   ++ E +   T ++++       + + +   Dt G vd
  gi|313125615|ref|YP_004035885.1| 211 VTVAGYTNAGKSTLLHRLADDLSLDST--ERHP-DEANSVAAVEDRLFKTLQTTTRRAT--LEGRPVLATDTVGFVD 282
                                       679999**************9999888..5552.3356778888888999999999999..9999999999999998 PP

                                       ....GH....HHHHHHHHT-SEEEEEEETTTBST...HHHHHHHHHHHHTTTE...EEEEEESCGST.HHHHHHHHH CS
                          GTP_EFTU  83 ....Fs....kevirglrvlDgavlvvdaveGve...pqteevlrlalkegvp...iivfiNKmDrl.kaelkeive 144
                                           +     +++i  ++++D++vlv da+++ve   ++ +  l +  ++gv+   +++++NK D l +ae++  v 
  gi|313125615|ref|YP_004035885.1| 283 dlphWLvesfSTTISEAAAADIVVLVADASDDVEtlrEKIRVSLSVFDAQGVEtqnVVTALNKTDLLtDAECESRVA 359
                                       6666441111345666999***********99761115677788999999998899***********9999999998 PP

                                       HHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 145 evkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       +++ +l                   vv++S ++  +++tl+e++ + lp
  gi|313125615|ref|YP_004035885.1| 360 AAE-SL------------AP----RVVPVSVVEETNLETLVEVVCDRLP 391
                                       888.55............12....4777777777777777777777666 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   1.7   7.3e-11   1.1e-07       2      79 .]     135     203 ..     134     203 .. 0.79
   2 ?   -3.3   0.0       9.8   1.5e+04      23      39 ..     432     448 ..     426     453 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 7.3e-11
                                       --SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH..... CS
                         GTP-bdg_M   2 ArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrkk 78 
                                       A t+ a+lQVelAqlky lpr+   ++e + q+  i +    e+   ++ + +r+ria+l+++L+++ +  ++ r++
  gi|313125615|ref|YP_004035885.1| 135 AGTRRAQLQVELAQLKYALPRI---ETESDPQAMNIAL----EKG--TRVKGVRDRIAELESKLADLPNPAAQYRSR 202
                                       99********************...5555555333332....443..5667899**********9999999999998 PP

                                       T CS
                         GTP-bdg_M  79 R 79 
                                       R
  gi|313125615|ref|YP_004035885.1| 203 R 203
                                       8 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.8
                                       HCXXXXXXXXX..X..X CS
                         GTP-bdg_M  23 LeglgkelsrqgGgigt 39 
                                       L+g+ + l+r++G++  
  gi|313125615|ref|YP_004035885.1| 432 LQGRPEILERMRGKVES 448
                                       56777788888887443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00025      0.37     101     161 ..     210     280 ..     181     283 .. 0.85
   2 !   16.9   0.5   3.1e-06    0.0046      12      99 ..     298     388 ..     289     393 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                                       EEEEECSTTSSHHHHHHHHCTT...........-----S--------------SEEEEEETTTEEEESS-SS CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpe...........lelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                       +++++G + +GKStL+ +l+ +           +  ++++v ++l +   TTt++  le     l  Dt Gf
  gi|313125615|ref|YP_004035885.1| 210 LVTVAGYTNAGKSTLLHRLADDlsldsterhpdEANSVAAVEDRLFKTLQTTTRRATLEGR-PVLATDTVGF 280
                                       67899****************9899999999988899999999999999999988877766.5666666665 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.1e-06
                                       TEES--EEEEEEEST.TTT--HHHHHHHHHHHHHTT-...EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--T CS
                       RsgA_GTPase  12 kvaNvdqllivvslk.epelslnlldrfLvlaeekgi...epvivlnKiDlleeeeeleelkeelealgyevllvsa 84 
                                       ++a  d +++v  ++ + e+  + +   L ++ ++g+   ++v +lnK+Dll+++e +e+  ++ e+l  +v+ vs+
  gi|313125615|ref|YP_004035885.1| 298 EAAAADIVVLVADASdDVETLREKIRVSLSVFDAQGVetqNVVTALNKTDLLTDAE-CESRVAAAESLAPRVVPVSV 373
                                       466677777777554044555678888899999999855557889***********.******************** PP

                                       TTHTTHHHHHHHCTT CS
                       RsgA_GTPase  85 ktkegleelkellkd 99 
                                        ++++le+l e++ d
  gi|313125615|ref|YP_004035885.1| 374 VEETNLETLVEVVCD 388
                                       *********998766 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.5   1.1e+04      80     100 ..     302     322 ..     294     327 .. 0.70
   2 !   16.7   0.0   3.6e-06    0.0054      58     104 ..     339     390 ..     333     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.5
                      MMR_HSR1_Xtn  80 pnsvviSaekelnldeLkeki 100
                                        ++vv+ a+   ++++L eki
  gi|313125615|ref|YP_004035885.1| 302 ADIVVLVADASDDVETLREKI 322
                                       467777788888888888887 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.6e-06
                      MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare.....pnsvviSaekelnldeLkekiweeL 104
                                       ++++lNK+Dl++++e+++         p++v++S+ +e+nl++L+e + ++L
  gi|313125615|ref|YP_004035885.1| 339 VVTALNKTDLLTDAECESRVAAaeslaPRVVPVSVVEETNLETLVEVVCDRL 390
                                       6889******999998875553356779*****************9988776 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.011        17       3      22 ..     211     230 ..     210     233 .. 0.89
   2 !    9.4   0.3   0.00048      0.72      75     154 ..     298     384 ..     256     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                                       EEEEESTTSSHHHHHHHHHT CS
                            FeoB_N   3 valvGnpnvGkttlfnaltg 22 
                                       v+++G  n+Gk+tl+ +l++
  gi|313125615|ref|YP_004035885.1| 211 VTVAGYTNAGKSTLLHRLAD 230
                                       6799***********99975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00048
                                       HCTSSSEEEEEEEGG....GHHHHHHHHHHHHHTT....SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBT CS
                            FeoB_N  75 leeepdvvvnvvdat....nlernLyLtlqllelg....vpvvlalnmideaekkgieidlkkLsekLgvpvvktsa 143
                                           +d+vv v+da+    +l+ ++ + l +++ +    ++vv aln++d +++++ e  +++ +e+L   vv++s 
  gi|313125615|ref|YP_004035885.1| 298 EAAAADIVVLVADASddveTLREKIRVSLSVFDAQgvetQNVVTALNKTDLLTDAECESRVAA-AESLAPRVVPVSV 373
                                       556789999999986333368888999999988764444789**************9988776.7789********* PP

                                       TTTBTHHHHHH CS
                            FeoB_N 144 kkkegieellk 154
                                        +++++e+l++
  gi|313125615|ref|YP_004035885.1| 374 VEETNLETLVE 384
                                       ******99987 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.9e+03      29      45 ..     104     120 ..      99     166 .. 0.68
   2 ?   -1.3   0.1       1.9   2.8e+03      71      71 ..     317     317 ..     241     383 .. 0.55
   3 ?   13.1   0.3   6.2e-05     0.092      34      74 ..     385     432 ..     373     441 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                             DUF11  29 sangvvvtDtlPaglay 45 
                                       +++++ ++D lP  +++
  gi|313125615|ref|YP_004035885.1| 104 PSQTTNLRDCLPDETEI 120
                                       45678899999987764 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                             DUF11  71 t 71 
                                       t
  gi|313125615|ref|YP_004035885.1| 317 T 317
                                       0 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 6.2e-05
                             DUF11  34 vvtDtlPaglayvsvsas......qgtasaltsv......gsLeagesa.tlsf 74 
                                       vv+D lP+++++vs s++             + +      +s+e+g+++ tl++
  gi|313125615|ref|YP_004035885.1| 385 VVCDRLPTATETVSMSTGdeamsvV------SWAydharvESVEYGAETvTLTL 432
                                       89****************4333222......32256666688999875314444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.3     2e+03      74     106 ..     119     147 ..      46     198 .. 0.59
   2 ?   13.2   0.5   5.8e-05     0.086      18     145 ..     202     313 ..     185     346 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                            AAA_16  74 qalareellrqlldeaesaeleawrekleeala 106
                                       ++++r +l+  + ++    +++  r++l+ +la
  gi|313125615|ref|YP_004035885.1| 119 EIFDRYRLVLSIFAA----QAGTRRAQLQVELA 147
                                       344444444444444....44444444444444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.8e-05
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesael 94 
                                       r r+++  lv + G+   GKs+l+ +l++ l+ d     +++  +       +  + a  +++l++ l + ++ a l
  gi|313125615|ref|YP_004035885.1| 202 RRREQGFDLVTVAGYTNAGKSTLLHRLADDLSLD----STERHPDE------ANSVAAV-EDRLFKTLQTTTRRATL 267
                                       444444599********************99999....55555555......3467777.66999999999888777 PP

                            AAA_16  95 eawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                       e  +   +++++      +++++ l e ++  ++ ++  ++ +vlv D  +
  gi|313125615|ref|YP_004035885.1| 268 EGRPVLATDTVG----FVDDLPHWLVESFSTTISEAAA-ADIVVLVADASD 313
                                       777777777666....4444445555555555544444.334666666544 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0017       2.6      19      37 ..     213     231 ..     199     254 .. 0.83
   2 ?    1.9   0.4     0.088   1.3e+02      82     134 ..     302     355 ..     298     390 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0017
                                       EEESTTSSHHHHHHHHHHS CS
                               Arf  19 llGLDnaGKtTilkklkle 37 
                                       + G  naGK+T+l++l ++
  gi|313125615|ref|YP_004035885.1| 213 VAGYTNAGKSTLLHRLADD 231
                                       56999***********987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.088
                                       ESEEEEEEETT-.CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HH CS
                               Arf  82 tdavifvvDsad.reRleeakeeLkalleeeelkevallvlaNKqDlpealsee 134
                                        d v+ v D++d  e l+e  +   ++++ + +++  ++   NK Dl ++++ e
  gi|313125615|ref|YP_004035885.1| 302 ADIVVLVADASDdVETLREKIRVSLSVFDAQGVETQNVVTALNKTDLLTDAECE 355
                                       68899999987625677777666678899999999999999*****97766543 PP

>> SapC  SapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.18     131     192 ..     320     383 ..     307     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                              SapC 131 ekvlefleeleegkertqafiaaLeeldLlepvelkvtlddgekln..lsglytideekLnaLs 192
                                       ek+  +l+ ++++  +tq+++ aL++ dLl+++e++ + +  e+l   +  + +++e  L++L 
  gi|313125615|ref|YP_004035885.1| 320 EKIRVSLSVFDAQGVETQNVVTALNKTDLLTDAECESRVAAAESLAprVVPVSVVEETNLETLV 383
                                       677888999*************************999888866654448889999999998885 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00038      0.57       7      19 ..     179     191 ..     177     191 .. 0.95
   2 ?   -1.4   0.1       1.6   2.5e+03       3      11 ..     315     323 ..     314     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00038
                    Pox_A_type_inc   7 RsRIsDLErqLse 19 
                                       R+RI +LE++L++
  gi|313125615|ref|YP_004035885.1| 179 RDRIAELESKLAD 191
                                       9**********97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                    Pox_A_type_inc   3 msrlRsRIs 11 
                                       ++ lR++I+
  gi|313125615|ref|YP_004035885.1| 315 VETLREKIR 323
                                       5779****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2793.46
//
Query:       gi|313125616|ref|YP_004035886.1|  [L=133]
Description: hypothetical protein Hbor_08450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0053   16.9  19.8     0.0076   16.4  19.8    1.2  1  DUF5518          Family of unknown function (DUF5518)
  ------ inclusion threshold ------
       0.29   10.9   8.0        2.9    7.6   2.4    2.7  2  EpuA             DNA-directed RNA polymerase subunit beta
       0.64    9.8   9.9        2.2    8.0   9.9    1.8  1  7TM-7TMR_HD      7TM receptor with intracellular HD hydrolase
       0.82    9.8   4.7       0.19   11.9   0.9    1.8  2  DUF872           Eukaryotic protein of unknown function (DUF8
        5.1    7.5  11.6        2.8    8.3   6.8    2.5  2  DUF1269          Protein of unknown function (DUF1269)


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  19.8   2.1e-06    0.0076       8     112 ..      10     110 ..       4     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-06
                           DUF5518   8 avvaivlslllglllpsvgsllgl.lvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlllglvaaiggla 83 
                                        vv++ l++++g ++ +++ + ++ l++G ++Gy + + ++d+  + +l+G++g+i +lvl+ +l   +++ i++++
  gi|313125616|ref|YP_004035886.1|  10 TVVSALLGTVVG-FAFGWVAMQPMgLIAGGIVGYSVSR-TSDAIFDSLLSGFLGGILALVLVNALN--YTTQITQAG 82 
                                       555666666666.444455556666***********66.689****************99988888..477777777 PP

                           DUF5518  84 gfvallvalllvvllllvvllvilgaiGG 112
                                        ++a++  ++++++  l+ ++ +  a+G+
  gi|313125616|ref|YP_004035886.1|  83 DAAAAGQQAIFLTIYGLL-FVPGAYAVGA 110
                                       777777777766333333.2233334665 PP

>> EpuA  DNA-directed RNA polymerase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.4   0.00082       2.9       3      22 ..       5      24 ..       4      25 .. 0.91
   2 ?    5.6   0.3    0.0036        13      12      22 ..      34      44 ..      30      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00082
                              EpuA  3 iVivLavlalaiGlmiGYgv 22
                                      +V+  +v+++++G+++G+++
  gi|313125616|ref|YP_004035886.1|  5 VVLSVTVVSALLGTVVGFAF 24
                                      79999*************86 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0036
                              EpuA 12 laiGlmiGYgv 22
                                      l++G ++GY+v
  gi|313125616|ref|YP_004035886.1| 34 LIAGGIVGYSV 44
                                      899*******8 PP

>> 7TM-7TMR_HD  7TM receptor with intracellular HD hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.9   0.00062       2.2      67     148 ..       8      97 ..       1     118 [. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00062
                       7TM-7TMR_HD  67 plaavalLlsllldsrlalvvsvllsllisilf........gnnlellllalvsglvgallvrklrsRsdllragll 135
                                        +++v+ Ll+  ++  ++ v++  + l+++ ++        +  + +ll ++++g+++ +lv+ l+  +++ +ag  
  gi|313125616|ref|YP_004035886.1|   8 SVTVVSALLGTVVGFAFGWVAMQPMGLIAGGIVgysvsrtsDAIFDSLLSGFLGGILALVLVNALNYTTQITQAGDA 84 
                                       45566666666666666666666666666665566777777888999999*************************99 PP

                       7TM-7TMR_HD 136 valvnvlvilals 148
                                       +a+++ +++l+++
  gi|313125616|ref|YP_004035886.1|  85 AAAGQQAIFLTIY 97 
                                       9999999988876 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.3      0.38   1.3e+03      46      71 ..       5      32 ..       1      60 [. 0.65
   2 ?   11.9   0.9   5.4e-05      0.19      59      96 ..      72     110 ..      42     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.38
                            DUF872 46 vlaallLl..llGlvLlllgvvilveps 71
                                      v++++ ++  llG+v+ +   +++++p+
  gi|313125616|ref|YP_004035886.1|  5 VVLSVTVVsaLLGTVVGFAFGWVAMQPM 32
                                      3333333211566666555556666665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.4e-05
                            DUF872  59 Llllgvvilvep.seGvssavflvlGlllfiPGvYhvvy 96 
                                       L  ++ + +++   +  ++a+fl +  llf+PG+Y v  
  gi|313125616|ref|YP_004035886.1|  72 LNYTTQITQAGDaAAAGQQAIFLTIYGLLFVPGAYAVGA 110
                                       22223333333334455788999888899******9865 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.8   0.00079       2.8       1      41 [.      14      53 ..      14      98 .. 0.88
   2 ?   -0.3   2.5      0.37   1.3e+03       9      26 ..      95     110 ..      55     131 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00079
                           DUF1269  1 AlsGalwGllvGllflnPllGaavGAaaGAlvgalsdvgid 41
                                      Al G+++G+ +G ++++P +G+++G+ +G  v++ sd+ +d
  gi|313125616|ref|YP_004035886.1| 14 ALLGTVVGFAFGWVAMQP-MGLIAGGIVGYSVSRTSDAIFD 53
                                      788***************.9*********999988876555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.37
                           DUF1269   9 llvGllflnPllGaavGA 26 
                                       ++ Gllf +P    avGA
  gi|313125616|ref|YP_004035886.1|  95 TIYGLLF-VP-GAYAVGA 110
                                       3445544.55.2355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.34s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 852.48
//
Query:       gi|313125617|ref|YP_004035887.1|  [L=421]
Description: translation elongation factor 1a (ef-1a/ef-tu) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-57  192.8   0.0    5.2e-57  192.5   0.0    1.1  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    7.7e-37  126.0   0.0    2.9e-36  124.2   0.0    2.0  2  GTP_EFTU_D3   Elongation factor Tu C-terminal domain
    1.9e-16   60.2   1.8    9.2e-16   58.0   0.6    2.4  2  GTP_EFTU_D2   Elongation factor Tu domain 2
    2.8e-08   33.9   0.2    4.3e-07   30.0   0.2    2.6  1  MMR_HSR1      50S ribosome-binding GTPase
    0.00072   19.5   2.0      0.041   13.8   0.2    2.5  2  RsgA_GTPase   RsgA GTPase
    0.00095   18.8   1.6     0.0037   16.9   0.7    2.1  2  Ras           Ras family
     0.0028   17.5   0.3      0.008   16.1   0.3    1.8  1  GTP_EFTU_D4   Elongation factor Tu domain 4
     0.0037   16.6   0.6      0.011   15.0   0.0    1.9  2  Septin        Septin
     0.0052   16.8   0.1        1.8    8.6   0.0    2.5  2  Dynamin_N     Dynamin family
  ------ inclusion threshold ------
      0.012   14.9   0.1        1.2    8.4   0.0    2.2  2  Gtr1_RagA     Gtr1/RagA G protein conserved region
      0.023   14.2   0.6       0.41   10.2   0.4    2.6  2  FeoB_N        Ferrous iron transport protein B
      0.026   14.0   0.1        0.5    9.8   0.1    2.3  1  SRPRB         Signal recognition particle receptor beta subun
      0.047   13.9   0.0        5.3    7.3   0.0    2.5  2  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.064   13.6   0.0       0.16   12.3   0.0    1.6  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.5   0.0     4e-60   5.2e-57       1     183 [.       4     193 ..       4     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 192.5 bits;  conditional E-value: 4e-60
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHST.............HCHSHHHHHHTSCSSCEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka..eeerv.............lDtlkeErergiTiksaais 62 
                                       k++ n++iighvDhGK+TL++rLl++tg i ++  ++  e  ++             +D+l+eErerg+Ti++a+  
  gi|313125617|ref|YP_004035887.1|   4 KPHQNLAIIGHVDHGKSTLVGRLLFETGSIPEHIIEQhrE--EAeekgksgfefayvMDNLAEERERGVTIDIAHQR 78 
                                       5799*************************99987777441..2235678999************************* PP

                                       EETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST... CS
                          GTP_EFTU  63 leketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl... 135
                                       ++  t+ky ++++DtPGH+dF+k++i+g++++D avlvv+a++Gv pqt+e++ la+++g++ +i+++NKmD +   
  gi|313125617|ref|YP_004035887.1|  79 FD--TDKYYFTIVDTPGHRDFVKNMITGASQADHAVLVVAADDGVAPQTREHVFLARTLGIEeLIIAVNKMDIVdys 153
                                       **..**********************************************************************996 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHH CS
                          GTP_EFTU 136 kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvkt 183
                                       ++++k+++ ev+ +l      l+++++++  + +++++Sa++g++v +
  gi|313125617|ref|YP_004035887.1| 154 EDTYKQVKAEVQ-EL------LKQVQFNTA-DASFIPISAFEGDNVAE 193
                                       666777777777.66......577777774.889**********9984 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.2   4.1e+03      36      74 ..     261     290 ..     256     294 .. 0.61
   2 !  124.2   0.0   2.3e-39   2.9e-36       4     111 ..     313     418 ..     310     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.2
                                       -EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEE CS
                       GTP_EFTU_D3  36 advtgkvveLlskldkktekvsekkpefvkpGdnvivev 74 
                                       +dv+g+v+++    + ++e+v       + pGdnv ++v
  gi|313125617|ref|YP_004035887.1| 261 SDVSGEVKTI----EMHHEEV-----PKAEPGDNVGFNV 290
                                       5666666666....2233333.....5578888887776 PP

  == domain 2  score: 124.2 bits;  conditional E-value: 2.3e-39
                                       EECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEE CS
                       GTP_EFTU_D3   4 phtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpi 80 
                                        +++f+Aq++++++  ++ itagY+pv++++ta+v+++++++ +k+d+++++v+e++p+f+k Gd+++v+++++kp+
  gi|313125617|ref|YP_004035887.1| 313 VAETFQAQIVVMQH--PSVITAGYTPVIHAHTAQVACTFESIDKKIDPSSGEVAEEEPDFIKAGDAAVVTLRPQKPL 387
                                       6899**********..************************************************************* PP

                                       EE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  81 alekgseypqlGrFaiReggrTvaaGvvtei 111
                                       +le  se+p+lG FaiR++g+T+aaG+v e+
  gi|313125617|ref|YP_004035887.1| 388 VLEPSSEIPELGSFAIRDMGQTIAAGKVLEV 418
                                       ****************************998 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.62   7.9e+02      14      52 ..       4      40 ..       4      49 .. 0.84
   2 !   58.0   0.6   7.1e-19   9.2e-16       1      73 [.     238     304 ..     238     305 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.62
                                      ETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTS CS
                       GTP_EFTU_D2 14 kkGdevrilg.ndtskkeivtrissletfhededeavaga 52
                                      k+ +++ i+g +d +k+   t +++l+ + +   e + ++
  gi|313125617|ref|YP_004035887.1|  4 KPHQNLAIIGhVDHGKS---TLVGRLLFETGSIPEHIIEQ 40
                                      67789999999999999...******99999888876554 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 7.1e-19
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       Gtv  grv++G+l++Gd+v +  ++++ +   ++++ +e++he++  a++g+n+G++v+++g +d i++Gd+ 
  gi|313125617|ref|YP_004035887.1| 238 GTVPVGRVETGILNTGDNVSF--QPSDVS---GEVKTIEMHHEEVPKAEPGDNVGFNVRGIGKDD-IRRGDVC 304
                                       99*******************..777678...*********************************.*****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.2   3.4e-10   4.3e-07       2     113 ..       9     145 ..       8     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.4e-10
                                       EEEEESTTSSHHHHHHHHH.....................T..........STEEESSSTTSSSSEEEEEEEETTEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt.....................g..........ekaivsdkpgtTrdinegrvklkgke 47 
                                        ai+G+   GKStL+ +l+                     g          ++   +++ g+T+di + r+++++  
  gi|313125617|ref|YP_004035887.1|   9 LAIIGHVDHGKSTLVGRLLfetgsipehiieqhreeaeekGksgfefayvmDNLAEERERGVTIDIAHQRFDTDKYY 85 
                                       69****************988877777777777666655515566555543466678888************9999* PP

                                       EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSE.EEEEEE CS
                          MMR_HSR1  48 ielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkp.lilvln 113
                                       +++vDtpG  +    +  +++ +    +ad+++lvv a  ++++p+ +e   l +  +++ li+++n
  gi|313125617|ref|YP_004035887.1|  86 FTIVDTPG--H----RDFVKNMITGASQADHAVLVVAAD-DGVAPQTREHVFLARTLGIEeLIIAVN 145
                                       ********..3....223555555566789988888766.557776655444433322221444554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.024        30     101     160 ..       8      93 ..       3     100 .. 0.61
   2 !   13.8   0.2   3.2e-05     0.041      13      81 ..     105     173 ..      97     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.024
                                       EEEEECSTTSSHHHHHHHHCTT.........................-----S--------------SEEEEEETT. CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpe.........................lelktgevseklgrGkhTTtavellelae. 151
                                         +++G+   GKStL+ +ll e                             + ++ e+ +rG     a + ++ ++ 
  gi|313125617|ref|YP_004035887.1|   8 NLAIIGHVDHGKSTLVGRLLFEtgsipehiieqhreeaeekgksgfeFAYVMDNLAEERERGVTIDIAHQRFDTDKy 84 
                                       5678999999******9998875666666655555555555555554444455555555555555555555555542 PP

                                       TEEEESS-S CS
                       RsgA_GTPase 152 gglliDtPG 160
                                         +++DtPG
  gi|313125617|ref|YP_004035887.1|  85 YFTIVDTPG 93 
                                       334566666 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.2e-05
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee.eleelkeelealgyevll 81 
                                       ++  d++++vv+++ + + +++ + + +la + gi e++i++nK+D+++ +e +++++k+e+++l  +v +
  gi|313125617|ref|YP_004035887.1| 105 ASQADHAVLVVAAD-DGVAPQTREHV-FLARTLGIeELIIAVNKMDIVDYSEdTYKQVKAEVQELLKQVQF 173
                                       6789**********.77777776665.5567777768999********98887889999998888655554 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.5   6.4e+02       2      19 ..       9      26 ..       8      38 .. 0.85
   2 !   16.9   0.7   2.9e-06    0.0037      11     152 ..      49     194 ..      45     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.5
                                      EEEEESTTSSHHHHHHHH CS
                               Ras  2 lvlvGdsavGKtslllrf 19
                                      l ++G    GK++l+ r 
  gi|313125617|ref|YP_004035887.1|  9 LAIIGHVDHGKSTLVGRL 26
                                      679***********9774 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.9e-06
                                       SHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHH CS
                               Ras  11 GKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresf 87 
                                       GK+ + + +v d+  ee e  + +d      ++d  ++ ++i DT G  +f +   +  ++a+ ++lv + ++  + 
  gi|313125617|ref|YP_004035887.1|  49 GKSGFEFAYVMDNLAEERERGVTIDIAH--QRFDTDKYYFTIVDTPGHRDFVKNMITGASQADHAVLVVAADDGVAP 123
                                       9******************999777655..566777899************99999999999999999888887776 PP

                                       HTHHHHHHHHHHHSTTTSEEEEEEETTTGGG.....G-SS-HHHHHHHH....HHHTSEEEEEBTTTTCTHHHH CS
                               Ras  88 envkkwveeikrvaeenvpivLvGnKvDlee.....kravsteegeela....kelglkfletSAktnenveea 152
                                       ++ ++ +  + r+     ++++  nK+D+ +      ++v++e  e l     +  ++ f+ +SA +  nv e 
  gi|313125617|ref|YP_004035887.1| 124 QTREHVF--LARTLG-IEELIIAVNKMDIVDysedtYKQVKAEVQELLKqvqfNTADASFIPISAFEGDNVAES 194
                                       6655444..344444.23588889*****999999855555443332222222556689*********999886 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   6.3e-06     0.008      21      83 ..     242     302 ..     231     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.3e-06
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT.S--TT- CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr.qikegd 83 
                                       vG +v +G++++g ++  +     Ge++ i+ +++++ +a+ G++v+  ++g  +G+ +i  gd
  gi|313125617|ref|YP_004035887.1| 242 VG-RVETGILNTGDNVSFQPSDVSGEVKTIEMHHEEVPKAEPGDNVGFNVRG--IGKdDIRRGD 302
                                       88.9************99999999************************9998..3442466665 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     9e-06     0.011       6      78 ..       8     100 ..       5     106 .. 0.87
   2 ?   -2.2   0.1       1.5     2e+03     145     179 ..     141     177 ..     133     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9e-06
                                       EEEEEEBTTSSCCCCCCT.TSSSS----.....................--------------S-EEEEEEEEETTC CS
                            Septin   6 tlmvvGesglGkttlint.lfetdliee.....................ekleeasekkkktveikkkkvvieedgv 60 
                                       +l ++G+   Gk+tl+   lfet  i+e                       +++ +e+ ++ v+i+ +++  + d  
  gi|313125617|ref|YP_004035887.1|   8 NLAIIGHVDHGKSTLVGRlLFETGSIPEhiieqhreeaeekgksgfefaYVMDNLAEERERGVTIDIAHQRFDTD-- 82 
                                       7899************76268998888889999999999999999999866778888999999999999999988.. PP

                                       EEEEEEEE---BSSSSSH CS
                            Septin  61 klnltviDtpgfGdavdn 78 
                                       k  +t++Dtpg+ d+v n
  gi|313125617|ref|YP_004035887.1|  83 KYYFTIVDTPGHRDFVKN 100
                                       8899***********998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                       EEEESSGGGS-HHH..HHHHHHHHHHHHHHTT----- CS
                            Septin 145 iPviaKaDtltkeE..lkefKkkireeleeeeikiyk 179
                                       i  + K D++  +E   k++K +++e l++ +++  +
  gi|313125617|ref|YP_004035887.1| 141 IIAVNKMDIVDYSEdtYKQVKAEVQELLKQVQFNTAD 177
                                       4456667766544322677888888888777776654 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0093        12       1      19 [.       9      27 ..       9      35 .. 0.88
   2 !    8.6   0.0    0.0014       1.8      53     135 ..      43     115 ..      28     147 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0093
                                      EEEEEBTTTTHHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                      +a++G++ +GKS+++  Ll
  gi|313125617|ref|YP_004035887.1|  9 LAIIGHVDHGKSTLVGRLL 27
                                      589***********98887 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0014
                                       SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTT CS
                         Dynamin_N  53 eelkekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikka 129
                                       ee +ek k   +f  v +++ +e+e+         ++ i ++ ++ ++   t+vD+PG  +  k   ++++ + +  
  gi|313125617|ref|YP_004035887.1|  43 EEAEEKGKSGFEFAYVMDNLAEERERGV-------TIDIAHQRFDTDKYYFTIVDTPGHRDFVK---NMITGASQAD 109
                                       4444444444455555555555555544.......4578999999*************887433...3555555444 PP

                                       EEEEEE CS
                         Dynamin_N 130 diilav 135
                                       +++l+v
  gi|313125617|ref|YP_004035887.1| 110 HAVLVV 115
                                       444444 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00096       1.2      29      67 ..      66     103 ..      47     117 .. 0.80
   2 ?    4.3   0.0     0.017        21     116     154 ..     142     180 ..     130     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00096
                         Gtr1_RagA  29 lrlgatidveksevrflgnltlnlwDcgGqeafveeyls 67 
                                       ++ g+tid+ ++++  +++ ++ ++D +G ++fv+++++
  gi|313125617|ref|YP_004035887.1|  66 RERGVTIDIAHQRF-DTDKYYFTIVDTPGHRDFVKNMIT 103
                                       45589*******99.58999****************765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.017
                         Gtr1_RagA 116 vlihKmDliqedereeifeerkeeireeiekleke..eiqf 154
                                       + ++KmD +  d  e+++++ k+e++e +++++++  + +f
  gi|313125617|ref|YP_004035887.1| 142 IAVNKMDIV--DYSEDTYKQVKAEVQELLKQVQFNtaDASF 180
                                       6789*****..89999*************999877444444 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.33   4.2e+02       2      20 ..       8      26 ..       7      36 .. 0.86
   2 ?   10.2   0.4   0.00032      0.41      32      62 ..      69      99 ..      67     194 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.33
                                      EEEEEESTTSSHHHHHHHH CS
                            FeoB_N  2 tvalvGnpnvGkttlfnal 20
                                      ++a++G  + Gk+tl+ +l
  gi|313125617|ref|YP_004035887.1|  8 NLAIIGHVDHGKSTLVGRL 26
                                      5799***********9877 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00032
                                      TSSSEEEEEEEEETTEEEEEEE----SSSSS CS
                            FeoB_N 32 GvtvekkegklklkgkeveivDlPGiYslsa 62
                                      Gvt++ ++ +++++++ ++ivD PG  ++ +
  gi|313125617|ref|YP_004035887.1| 69 GVTIDIAHQRFDTDKYYFTIVDTPGHRDFVK 99
                                      9************************866633 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00039       0.5      44     104 ..      79     136 ..       4     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00039
                                       ...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHH CS
                             SRPRB  44 ksekgskltliDfPGheklrqklleklkaksslkglvfvvDStidpkevkevAEllyeill 104
                                        ++++  +t++D PGh  + +++++    ++    lv   D  + p+  ++v  +l   l 
  gi|313125617|ref|YP_004035887.1|  79 FDTDKYYFTIVDTPGHRDFVKNMITGA-SQADHAVLVVAADDGVAPQTREHV--FLARTLG 136
                                       36678899***************9993.333344555556777776655544..4555554 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.04        52       2      22 ..       9      29 ..       8      39 .. 0.86
   2 ?    7.3   0.0    0.0041       5.3       9     119 ..      47     148 ..      45     149 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.04
                                      EEEESSTTSSHHHHHHCHCT- CS
                               Roc  2 vvlvGdsgvGKtsllkrfved 22
                                      + ++G    GK++l+ r++ +
  gi|313125617|ref|YP_004035887.1|  9 LAIIGHVDHGKSTLVGRLLFE 29
                                      679*************99755 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0041
                                       TSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEE CS
                               Roc   9 gvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalail 85 
                                       + GK+ +   +v d+  e+++  + +d++++++           ++k+ + i Dt G+ +f + +    ++a+ a+l
  gi|313125617|ref|YP_004035887.1|  47 EKGKSGFEFAYVMDNLAEERERGVTIDIAHQRFD----------TDKYYFTIVDTPGHRDFVKNMITGASQADHAVL 113
                                       5799999999************999999988762..........23578***********99866666666665555 PP

                                       EEEGH..HHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  86 vydsr..ssenlkeWlkelkkvagkspvilvgnkiD 119
                                       v+ ++     + +e +  l +  g + +i+ +nk+D
  gi|313125617|ref|YP_004035887.1| 114 VVAADdgVAPQTREHV-FLARTLGIEELIIAVNKMD 148
                                       5543301233333333.3444455566666777776 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012      0.16      64     127 ..      60     121 ..      16     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                       E-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                      NTP_transf_3  64 ededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                        +  +++  + ++  a ++  d+d ++++ +D+P   +++v+ ++  a +++++v+v++++++ 
  gi|313125617|ref|YP_004035887.1|  60 DNLAEERERGVTIDIAHQRF-DTDKYYFTIVDTPG-HRDFVKNMITGASQADHAVLVVAADDGV 121
                                       33444677777888888888.9*************.89**********9999988777777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2662.26
//
Query:       gi|313125618|ref|YP_004035888.1|  [L=515]
Description: subtilisin-like serine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-51  173.4  12.5    9.6e-51  172.8  12.5    1.2  1  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
      0.055   13.3   0.5      0.055   13.3   0.5    2.7  3  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8  12.5   1.1e-54   9.6e-51       2     298 .]     145     391 ..     144     391 .. 0.91

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 1.1e-54
                                       TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   2 kgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanape 78 
                                       ++v+vav+D Gv+++hpdls+            +++g++f+++ds+++ +  +++       HGthvAGiaa+++++
  gi|313125618|ref|YP_004035888.1| 145 SDVTVAVVDQGVKYDHPDLSAR---------FGSNTGYDFVDDDSDPMPDVLSDEF------HGTHVAGIAAGTTDN 206
                                       689*****************54.........45678889*********99999887......************555 PP

                                       SSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  79 egekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnkkg 155
                                       ++  +g   + ++ls ++l++sg  ++  +++++ai++aa +++dv+n+slg++  +++ ++     a+ +a+  +g
  gi|313125618|ref|YP_004035888.1| 207 NE-GVGGISNSTLLSGRALSESGRGST--SDIADAIQWAADQGADVVNLSLGGGGYTQTMKN-----AVSYAT-TNG 274
                                       55.5555569*************9986..8**********************7777766665.....899999.88* PP

                                       -EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 156 vlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrqs 232
                                       + v+++aGN++        + +v++p+ + ++i+v+a ++++ +a++S++G++       d++apG+n++s w++ +
  gi|313125618|ref|YP_004035888.1| 275 TAVIAAAGNDS--------SGSVSYPAAYSEAIAVSALDPDETLASYSNYGSKL------DLAAPGTNVLSCWTTST 337
                                       ***********........788******************************88......7**************** PP

                                       HHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 233 nnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                              +y+ +sGTSmA+P+++g+aAl ls++  l+p+++r+ l ntA     +    s++qGaG
  gi|313125618|ref|YP_004035888.1| 338 -------QYKEISGTSMATPVVSGVAALALSEYS-LSPADLRQHLKNTAV----NVGLPSNKQGAG 391
                                       .......399***********************9.**************3....34899999*998 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   6.2e-06     0.055       4      19 ..       9      24 ..       6      31 .. 0.82
   2 ?   -4.9   3.0         2   1.8e+04      10      17 ..     274     281 ..     274     282 .. 0.58
   3 ?   -2.7   0.9      0.72   6.4e+03      12      16 ..     354     358 ..     344     361 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-06
                        TAT_signal  4 RRdFLKgsAAaaAAaa 19
                                      RR+FLK +AA+  +++
  gi|313125618|ref|YP_004035888.1|  9 RRSFLKSTAALSLLGM 24
                                      **********998876 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 2
                        TAT_signal  10 gsAAaaAA 17 
                                       g+A+ aAA
  gi|313125618|ref|YP_004035888.1| 274 GTAVIAAA 281
                                       56666666 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.72
                        TAT_signal  12 AAaaA 16 
                                       ++aa 
  gi|313125618|ref|YP_004035888.1| 354 GVAAL 358
                                       33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.50
# Mc/sec: 3126.05
//
Query:       gi|313125619|ref|YP_004035889.1|  [L=177]
Description: hypothetical protein Hbor_08480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-19   69.8   0.1    4.3e-19   69.4   0.1    1.1  1  NYN           NYN domain
    0.00012   21.8   0.1    0.00015   21.4   0.1    1.2  1  Peripla_BP_4  Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.1   4.8e-23   4.3e-19       1     141 [.      31     158 ..      31     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 4.8e-23
                               NYN   1 rvavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgikvkhkplkkrggsgkk 77 
                                       rva+f+Dg n+    ++ +vd++ ++e++++ g+ + +r y++  + +  ++ +a ++ g++v+          + +
  gi|313125619|ref|YP_004035889.1|  31 RVALFVDGPNVLR--DEFDVDLDDVREAAAEIGRPTATRLYLD--EHATPGLIQAAEARGFEVVI---------TSG 94 
                                       89**********9..6678************************..44456777999*****9966.........458 PP

                               NYN  78 avDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaad 141
                                       +vDv+lavd++++a++ + d i + s+D DF p++e ++++g r+  ++  e   s++L++aa+
  gi|313125619|ref|YP_004035889.1|  95 DVDVRLAVDITQFAVEGRADVIAVASRDTDFKPAIETANAYGLRTFAIAPGEFGRSDALRNAAT 158
                                       9******************************************99999987779********96 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   1.7e-08   0.00015      16     104 ..      74     160 ..      66     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-08
                                       HHHHHHHHHHHTTCEEEEEECSTT-HHHHHHHHHHHHHTT-SEEEE--SSHHHHHHHHHHHHHTT-EEEEESTTGCT CS
                      Peripla_BP_4  16 aregleeaakelgaevtvvgdaendaaeQvaqiedaiakgvdgiivapvdstalapalkkakaaGIpVvafdsddap 92 
                                       a+ gl +aa++ g+ev+++  ++ d++  v++ + a++  +d+i+va+ d t  +pa+++a+a G   +a+   +  
  gi|313125619|ref|YP_004035889.1|  74 ATPGLIQAAEARGFEVVIT-SGDVDVRLAVDITQFAVEGRADVIAVASRD-TDFKPAIETANAYGLRTFAIAPGEFG 148
                                       677999************6.***************************999.7*************987776555555 PP

                                       TT-CEEEEEC-H CS
                      Peripla_BP_4  93 sgerlayvgfdn 104
                                        ++ l + ++d+
  gi|313125619|ref|YP_004035889.1| 149 RSDALRNAATDS 160
                                       555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1037.13
//
Query:       gi|313125620|ref|YP_004035890.1|  [L=282]
Description: metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.3e-17   62.7   0.0    1.4e-15   57.4   0.0    2.0  2  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   7.7e-20   1.4e-15       2     159 ..      10     196 ..       9     207 .. 0.86
   2 !    3.4   0.0    0.0022        40     198     234 ..     220     254 ..     206     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 7.7e-20
                                       EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG..................GGHHHHHHHHTT.TTTEEEEE- CS
                        TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvvvgtss..................kdskavlelakkypnkvyavlG 60 
                                       D+H Hld  +      +++  +++ g+++++vv+  s                  ++++ v+e ++  p++ ++vlG
  gi|313125620|ref|YP_004035890.1|  10 DNHLHLDP-R-YGRGIDAVDDFRRLGGTHLLVVNKPSwhldveaseggdfravfeETITTVEEASEALPGRAWPVLG 84 
                                       9*******.4.47888999************999999999***********9997799999999999********** PP

                                       --GGGGGC..........C.CCHH..HHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTT CS
                        TatD_DNase  61 iHPnevde..........asedll..eelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelk 124
                                       +HP  v +          +  d l  + l+ + ++v+  ++ a+ + G+++y++ ++ +ea ++v+++ ++l +el+
  gi|313125620|ref|YP_004035890.1|  85 VHPGLVSRlvderdfspaEARD-LmqAGLDVAaEYVRAGDALAL-KSGRPHYDVPDAVWEASNDVMRHAFSLGAELD 159
                                       ***9998876667776652333.256899999999*********.******************************** PP

                                       EEEEEEEES-HHHHHHHHHHCGGCCS...EEEETT--S CS
                        TatD_DNase 125 lplviHlrkaeedlleilkeaaeaka...kvvlHsfsg 159
                                       +++++H++++ +dl +++  a++a++   kvv H   g
  gi|313125620|ref|YP_004035890.1| 160 CAVQLHTEAS-DDLTAVAAWAEDAGMprkKVVKHYAGG 196
                                       *******875.555555555555566666999998766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0022
                                       GGEEE---TTSSEECCCTT.SE--GGGHHHHHHHHHHH CS
                        TatD_DNase 198 drlLiETDaPyltpkpyrg.krnepanvayvveklael 234
                                       + +L+ETD  + ++   r+ ++  p++v++ v+ + + 
  gi|313125620|ref|YP_004035890.1| 220 EPFLMETD--FVDD-ADRPgAVLGPKTVPRRVRWMLDE 254
                                       569*****..8888.55555**********99988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1881.29
//
Query:       gi|313125621|ref|YP_004035891.1|  [L=196]
Description: hypothetical protein Hbor_08500 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-71  240.7   6.9    1.3e-71  240.5   6.9    1.0  1  DUF2150   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.5   6.9   7.4e-76   1.3e-71       1     188 []       7     194 ..       7     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 240.5 bits;  conditional E-value: 7.4e-76
                           DUF2150   1 eFYteeRwqNWlnrvkeedldle.edseeleaavllnlqdDvilavlkiikaveeeelskeeAleeleevreivlee 76 
                                       ++Yt++RwqNWl+rv+ee+ld+e eds    a++llnlqdD+++av+ki++a+ee++ls+e+Al+ele vr+ivl+e
  gi|313125621|ref|YP_004035891.1|   7 TYYTKDRWQNWLTRVEEEELDPEnEDS----ARLLLNLQDDAAIAVAKIVSAYEEDTLSEEDALDELEGVRDIVLSE 79 
                                       69*********************8888....********************************************** PP

                           DUF2150  77 vee...ddeekeeliesvqtsllvvfaaaeeyieggvakekdieelvkaaaeaeaeedleaaleivaqiGakvidge 150
                                        ++   d eek +li++vqtsl++vf+aaeeyi  g a+ +++ee+v+aaaeae+ee+++aal++++q+G+++i+g+
  gi|313125621|ref|YP_004035891.1|  80 PTFegdDVEEKVMLIDGVQTSLVCVFYAAEEYIVAGPAEAAPLEEYVTAAAEAEQEENMDAALGYLVQAGTRIIEGD 156
                                       **9444468999***************************************************************** PP

                           DUF2150 151 klpekvledleyglvaewldgidslaaamsssesveee 188
                                       +l+++++e+leyglv+ewl+g+dsl++ams++e+vee+
  gi|313125621|ref|YP_004035891.1| 157 ELDMSIAEELEYGLVSEWLNGLDSLQSAMSDPEVVEED 194
                                       ************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1214.41
//
Query:       gi|313125622|ref|YP_004035892.1|  [L=594]
Description: hypothetical protein Hbor_08510 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3606.14
//
Query:       gi|313125623|ref|YP_004035893.1|  [L=595]
Description: rej domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-13   48.1   2.0    9.2e-05   21.4   0.0    3.3  3  REJ             REJ domain
    3.4e-06   27.9   2.1    0.00094   20.1   0.2    3.7  4  Pilin_N         Archaeal Type IV pilin, N-terminal
    0.00014   21.6  14.4      0.036   13.9   0.9    5.6  5  PKD             PKD domain
  ------ inclusion threshold ------
          2    8.6  13.9       0.74   10.0   0.2    3.5  3  Arch_flagellin  Archaebacterial flagellin
          3    8.0   5.6         47    4.1   0.4    3.6  4  BiPBP_C         Penicillin-Binding Protein C-terminus Family


Domain annotation for each model (and alignments):
>> REJ  REJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.6e-08   9.2e-05      89     198 ..     186     278 ..     181     288 .. 0.84
   2 !   16.5   0.0   7.8e-07    0.0028      99     132 ..     401     435 ..     385     454 .. 0.74
   3 !    7.7   0.3   0.00037       1.3      55     146 ..     458     538 ..     451     581 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.6e-08
                               REJ  89 GGssrvigyr.gnltLdGseSyDpdeddhsqsqlsYeWlcrrsqpmngrnndnpllnidpealsgtllssstssltf 164
                                       GG+  v+g+  +++tLdGs+  Dpd d+     l+YeW +++ +   g   d + l +d++  +       + ++++
  gi|313125623|ref|YP_004035893.1| 186 GGT--VVGRAgETVTLDGSDTTDPDGDS-----LTYEWRIVDGD---GLPPDAVRLVDDSTGTP-------NATFEV 245
                                       554..67777799***********9995.....9******8777...99999999999999999.......999999 PP

                               REJ 165 paselvanltynftltvskrsrksasteqtilvv 198
                                         +     +  ++ l+vs+++  sa    t+ v+
  gi|313125623|ref|YP_004035893.1| 246 RENVTDRSHSVTVELVVSDGND-SARDRATVEVE 278
                                       99999999999999***99997.77666666665 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.8e-07
                               REJ  99 gnltLdGseSyDpdeddhsqsqlsYeWlcrrsq......p 132
                                        ++ LdGs SyDpd dd     l+Y+W++++++      +
  gi|313125623|ref|YP_004035893.1| 401 AEVRLDGSGSYDPDGDD-----LTYRWEIVDTDgigdilE 435
                                       6778***********96.....9******88885554444 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00037
                               REJ  55 vflltvslsgepsleatdiikvrvep...spLvavIkGGssrvigyrgnltLdGseSyDpdeddhsqsqlsYeWlcr 128
                                       + +++++++++++ + td+++v+v++   +p+v  I G     i+y ++ +L ++   Dpd+dd     l+YeW+ +
  gi|313125623|ref|YP_004035893.1| 458 TVTVRLTVTDDDGATDTDTVNVTVRArnrAPVVSAIYG-----IRYGDEHYLYAE-TTDPDDDD-----LTYEWTYV 523
                                       56778888888888888888888875222577777777.....777788888875.46888775.....88888762 PP

                               REJ 129 rsqpmngrnndnpllnid 146
                                           ++g ++d+  l++d
  gi|313125623|ref|YP_004035893.1| 524 ---GFEGASGDTWSLTDD 538
                                       ...344666666555555 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   2.6e-07   0.00094       7      79 ..      18      92 ..      14      94 .. 0.77
   2 ?    4.4   0.0      0.02        73      32      77 ..     233     278 ..     228     282 .. 0.84
   3 ?   -1.9   0.0       1.8   6.5e+03       5       8 ..     444     447 ..     437     488 .. 0.56
   4 ?   -0.5   0.0       0.7   2.5e+03      45      69 ..     510     535 ..     479     543 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.6e-07
                           Pilin_N  7 iGviLmvaitvIlaAviaafvlgl...asneekapqasievkidssastgknavslehkgGdsidtkdlkivlnse 79
                                      iGv+L++ ++++ a+ ++ f l     ++++  ++ as  ++++  ++ ++++++l h gG s++ + l iv+ ++
  gi|313125623|ref|YP_004035893.1| 18 IGVVLLLGVVIVSASTFGFFYLTDgfsNDVSGGSNGASG-ESVNIAGEVSHDQLELAHTGGRSLSMDRLDIVVRNA 92
                                      9*******************9976534444444555555.4455555556666******************99765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.02
                           Pilin_N  32 sneekapqasievkidssastgknavslehkgGdsidtkdlkivln 77 
                                       ++++ +p+a++ev+ + ++ +++++v+l  ++G++ + + +++ ++
  gi|313125623|ref|YP_004035893.1| 233 DDSTGTPNATFEVRENVTDRSHSVTVELVVSDGNDSARDRATVEVE 278
                                       678899*******988888888899**********99999888765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.8
                           Pilin_N   5 pViG 8  
                                       pViG
  gi|313125623|ref|YP_004035893.1| 444 PVIG 447
                                       4444 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.7
                           Pilin_N  45 kidssastgkna...vslehkgGdsidt 69 
                                       + d+++ t   +   v +e  +Gd+ ++
  gi|313125623|ref|YP_004035893.1| 510 DPDDDDLTY--EwtyVGFEGASGDTWSL 535
                                       333333333..244799*******9876 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.9     1e-05     0.036       9      62 ..     192     260 ..     182     269 .. 0.79
   2 !    7.8   0.0   0.00078       2.8       6      34 ..     395     426 ..     389     435 .. 0.80
   3 ?    1.3   0.2     0.086   3.1e+02      57      69 ..     460     472 ..     446     492 .. 0.68
   4 ?    1.8   0.4     0.061   2.2e+02      19      31 ..     509     521 ..     502     536 .. 0.84
   5 ?    0.9   0.0      0.12   4.2e+02      57      71 .]     558     572 ..     552     572 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                                       BSSEEEEEEEES....-SS-SEEEEE--SS.........--EEEEETTEEEEEE-S...SEEEEEEEEE CS
                               PKD   9 vpgatvaftaav...pdganvtysWdfgdg.........svvqvlseptvthtYls...pGeYeVtvta 62 
                                        +g+tv++ ++    pdg+++ty+W   dg          v  ++  p++t  +++    +++ Vtv +
  gi|313125623|ref|YP_004035893.1| 192 RAGETVTLDGSDttdPDGDSLTYEWRIVDGdglppdavrLVDDSTGTPNATFEVREnvtDRSHSVTVEL 260
                                       5799*********9***************9999999998777777778888777766666777777654 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00078
                                       S--BSSEEEEEEEES....-SS-SEEEEE--S CS
                               PKD   6 tvlvpgatvaftaav...pdganvtysWdfgd 34 
                                       t +   a+v++ ++    pdg+++ty+W+  d
  gi|313125623|ref|YP_004035893.1| 395 TLVGGIAEVRLDGSGsydPDGDDLTYRWEIVD 426
                                       556666788888888889**********9877 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.086
                                       EEEEEEE-SS-EE CS
                               PKD  57 eVtvtasnavgsa 69 
                                       +V++t+++++g++
  gi|313125623|ref|YP_004035893.1| 460 TVRLTVTDDDGAT 472
                                       4566666655544 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.061
                                       ES.-SS-SEEEEE CS
                               PKD  19 avpdganvtysWd 31 
                                       + pd++++ty+W+
  gi|313125623|ref|YP_004035893.1| 509 TDPDDDDLTYEWT 521
                                       349*********8 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.12
                                       EEEEEEE-SS-EEEE CS
                               PKD  57 eVtvtasnavgsata 71 
                                        V++t+++a+g +t+
  gi|313125623|ref|YP_004035893.1| 558 IVDLTVTDARGESTT 572
                                       599********9986 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   4.8     0.047   1.7e+02      49     153 ..      57     278 ..      20     286 .. 0.67
   2 ?   10.0   0.2    0.0002      0.74     120     159 ..     443     488 ..     403     492 .. 0.77
   3 ?   -1.9   0.1      0.96   3.4e+03     104     150 ..     522     575 ..     506     576 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.047
                                       T--EEEEEEE........EEE-SSSSSEEEEEEE--TTS--EEGGG-EEEEEESS--EE--E............... CS
                    Arch_flagellin  49 sgleitgdvg........dsatngtineitiyvklnaGsspidlnkttisvtddgqetlltad.............. 103
                                       ++++i g v         +++++ +++ + i+v+++ G ++ d++   i+  d +  +++ a               
  gi|313125623|ref|YP_004035893.1|  57 ESVNIAGEVShdqlelahTGGRSLSMDRLDIVVRNASGTTEYDFEPALIIAGDGD--ETFEAGerwrldwnqpvgek 131
                                       5566666666666666667777778888999999999999999999999876666..55555567778888888888 PP

                                       ............................................................................. CS
                    Arch_flagellin 104 ............................................................................. 103
                                                                                                                    
  gi|313125623|ref|YP_004035893.1| 132 lrvtvvdadrnrilfsetlvipttptpepdnpargetptatpeddgdppsavahggtvvgragetvtldgsdttdpd 208
                                       88888888888888887777777777777777777777777777777777777777777777777766666666666 PP

                                       ..........................................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE CS
                    Arch_flagellin 104 .....................efgivvisdtdgsltng....devlekgekvelevnvneddgitagdevsvevv 153
                                                            ++   ++ + ++    +     +v +++  v++e+ v+ d +  a+d+++vev 
  gi|313125623|ref|YP_004035893.1| 209 gdsltyewrivdgdglppdavRLVDDSTGTPNA----TfevrENVTDRSHSVTVELVVS-DGNDSARDRATVEVE 278
                                       666666666666666654422222222223333....2445588888888888888885.666778888888876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0002
                                       .......T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS-- CS
                    Arch_flagellin 120 g......devlekgekvelevnvneddgitagdevsvevvpenGas 159
                                              d vl+++ +v++ ++v++ddg t++d+v+v+v++ n a+
  gi|313125623|ref|YP_004035893.1| 443 RpvigltDVVLDRDRTVTVRLTVTDDDGATDTDTVNVTVRARNRAP 488
                                       1344666999*******************************99887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.96
                                       ........................T-EE-TT-EEEEEEE--TTT---TT-EEEE CS
                    Arch_flagellin 104 efgivvisdtdgsltng.......devlekgekvelevnvneddgitagdevsv 150
                                        +g    s+ ++slt++        +  ++   +++ v+++++d  +++++v+v
  gi|313125623|ref|YP_004035893.1| 522 YVGFEGASGDTWSLTDDsgrvariEQRTDEFAAGRVIVDLTVTDARGESTTVRV 575
                                       445555555566666665555555666677777777777766666666666665 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.51   1.8e+03      58      81 ..     116     140 ..      69     141 .. 0.75
   2 ?    4.1   0.4     0.013        47      73      88 ..     461     478 ..     458     479 .. 0.85
   3 ?   -2.5   0.0       1.5   5.5e+03      77      87 ..     535     545 ..     533     548 .. 0.86
   4 ?    3.9   0.1     0.015        54      74      89 .]     560     575 ..     546     575 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.51
                           BiPBP_C  58 tkrgrelawqp.epGrhrLtvvDaa 81 
                                       ++ + +l w      + r+tvvDa+
  gi|313125623|ref|YP_004035893.1| 116 AGERWRLDWNQpVGEKLRVTVVDAD 140
                                       4555556666633336899999985 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.013
                           BiPBP_C  73 hrLtvvDaaGrvdd..vr 88 
                                       +rLtv+D++G++d+  v+
  gi|313125623|ref|YP_004035893.1| 461 VRLTVTDDDGATDTdtVN 478
                                       69**********986665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.5
                           BiPBP_C  77 vvDaaGrvddv 87 
                                       ++D++Grv+++
  gi|313125623|ref|YP_004035893.1| 535 LTDDSGRVARI 545
                                       89******986 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.015
                           BiPBP_C  74 rLtvvDaaGrvddvri 89 
                                        Ltv+Da+G++++vr+
  gi|313125623|ref|YP_004035893.1| 560 DLTVTDARGESTTVRV 575
                                       69***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 3700.48
//
Query:       gi|313125624|ref|YP_004035894.1|  [L=445]
Description: hydroxymethylglutaryl-CoA synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-25   88.3   0.0    9.3e-25   87.5   0.0    1.4  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
    3.6e-22   79.3   0.0    7.2e-22   78.3   0.0    1.4  1  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
  ------ inclusion threshold ------
      0.011   15.9   0.3      0.029   14.6   0.3    1.6  1  DUF1257         Protein of unknown function (DUF1257)
       0.22   11.4   2.1       0.56   10.2   0.0    2.9  3  TPR_10          Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   2.1e-28   9.3e-25       5     171 ..       4     175 ..       2     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 2.1e-28
                    HMG_CoA_synt_N   5 vgilaleiylpaqyvdqaelek.fdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlev 80 
                                       vgi a+ei+     +d  +      g +  kyt glg    +f ++ edi ++     ++l++r+ l+ d igr++v
  gi|313125624|ref|YP_004035894.1|   4 VGIDAIEIWTGKLRLDLPNTFApEMGEDPEKYTKGLGLESSSFPDVYEDIVTMGANAAKQLMDRKGLTPDDIGRIDV 80 
                                       788888888888888876544304467889*********************************************** PP

                    HMG_CoA_synt_N  81 gtetiidksksvksvlmqlfeesgntdiegi...dtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsg 154
                                        te+  d+sk v + +   +e+  + d       +   ac  gt+++ +a nwi++    gr alv+a d a+y++ 
  gi|313125624|ref|YP_004035894.1|  81 ATESAFDNSKPVSTYIAGCLEQVYDGDFHHAnkgERKFACLAGTQSIDDAYNWIKAGRNRGRAALVIATDTALYERD 157
                                       ***************99999998888887661114678*************************************98 PP

                    HMG_CoA_synt_N 155 na.rptggagavalligp 171
                                       ++   t gagava+li  
  gi|313125624|ref|YP_004035894.1| 158 DPgEATQGAGAVAMLITE 175
                                       873689*********975 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   1.6e-25   7.2e-22      17     238 ..     195     407 ..     188     432 .. 0.79

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.6e-25
                                       SEE---TT-S--EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH------GGG-SEEEE--SSHHHHHHHHHHHHHH CS
                    HMG_CoA_synt_C  17 DFykPdlaseYPvvDGklslscYlkaldrcYksyskkvkkitkdadkeftlddfdyvifhsPfcklvqkslarllyn 93 
                                       DF kP+    +P vDGk s++ Yl  ++++ + y + +         ++  ddf+y+ fh+Pf  +v+k+ a+l y 
  gi|313125624|ref|YP_004035894.1| 195 DFLKPN--QQFPSVDGKRSVQVYLARMREALEDYESVS--------GDTHPDDFEYIPFHTPFPGMVRKA-AVLGYR 260
                                       9****8..57************************9874........455689*****************8.99***9 PP

                                       HHHH.S-HHHHHHH-GGGGGG...TT--GGGGGT-....HHHHHHHHHHHHHHHHHHTGGGGHHHHHH---GGGHHH CS
                    HMG_CoA_synt_C  94 Dflanassdkeeevkekleek...ddlkldesltd....kdlekallkiakelfkkkvkpsllvptevGnmYtasly 163
                                        ++++++   e+e+++++ ++    d++  e +t+       + + ++  +e + + ++p+l ++++vGn Yt s++
  gi|313125624|ref|YP_004035894.1| 261 HMTRDTE--IEDELTSEIGRQpreADFESREEYTEairdYMDDLKGMDQYREWYAETIEPTLSISRNVGNWYTGSVH 335
                                       9999876..445555555444333455555555542200555667788899************************** PP

                                       HHHHHHHHHS..-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHHHHHTTTTHHHHHHTSEEE-HHHHHHHH CS
                    HMG_CoA_synt_C 164 aalasllskv..sadelagkriglfsYGsGlaaslfslrvkqdvsedsildiakvldlkkkLdsRkevtPeefeeal 238
                                        a +s l ++    +elag+++++ sYGsG  a +++ ++ +  +e    ++ +v +++++L+ R  ++ +e+e   
  gi|313125624|ref|YP_004035894.1| 336 IARLSALRHAleRGEELAGQQMLVGSYGSGAQAEVHAETIVDGWTE----HVEAV-EVEDQLARRYDISFDEYELVH 407
                                       9999999886224689***********************9999988....45555.999**********99997443 PP

>> DUF1257  Protein of unknown function (DUF1257)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   6.5e-06     0.029      10      67 ..     369     422 ..     365     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.5e-06
                           DUF1257  10 kegee.evrgyrgqtrsaevvirqkngydigFrwngegeYelvaDlqfwkqslsveefl 67 
                                       ++++e  v+g+ ++ + +ev  + +++ydi F+     eYelv+D +  +++++ve f 
  gi|313125624|ref|YP_004035894.1| 369 EVHAEtIVDGWTEHVEAVEVEDQLARRYDISFD-----EYELVHDVHNHEKEVDVEAFT 422
                                       44444479*****99999*999999*******4.....8*****************996 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00012      0.56      25      42 .]     219     236 ..     216     236 .. 0.93
   2 ?   -3.4   0.0       2.2   9.9e+03      15      25 ..     288     298 ..     287     300 .. 0.77
   3 ?   -2.6   0.1       1.3   5.8e+03      25      37 ..     342     354 ..     339     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                            TPR_10  25 leealairrrllGpdHPd 42 
                                       ++eal+ ++ + G+ HPd
  gi|313125624|ref|YP_004035894.1| 219 MREALEDYESVSGDTHPD 236
                                       79***************9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.2
                            TPR_10  15 rgrydeAeall 25 
                                       r +y+eA +++
  gi|313125624|ref|YP_004035894.1| 288 REEYTEAIRDY 298
                                       67899998876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.3
                            TPR_10  25 leealairrrllG 37 
                                       l++al++ ++l G
  gi|313125624|ref|YP_004035894.1| 342 LRHALERGEELAG 354
                                       6899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2799.01
//
Query:       gi|313125625|ref|YP_004035895.1|  [L=235]
Description: XRE family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-10   39.8   0.1    1.6e-09   37.9   0.1    2.1  1  HTH_31          Helix-turn-helix domain
    1.7e-08   34.4   0.0    4.3e-08   33.1   0.0    1.7  1  HTH_3           Helix-turn-helix
    1.6e-06   28.0   0.0    3.3e-06   27.0   0.0    1.6  1  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.7   0.1        0.4   10.6   0.0    2.7  2  HTH_11          HTH domain
      0.016   15.1   0.0       0.05   13.5   0.0    1.9  2  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.034   14.6   0.0       0.23   11.9   0.0    2.3  2  HTH_26          Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   5.5e-13   1.6e-09       2      54 ..      23      75 ..      22      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 5.5e-13
                            HTH_31  2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                       Ga+Lr +R+   +sq+++Ae+l vs s +s++E+Grr  p  +v++++++al
  gi|313125625|ref|YP_004035895.1| 23 AGATLRKWRTDFDISQTALAEQLDVSSSVISDYESGRRESPGIGVVRRMVEAL 75
                                      69************************************************996 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.4e-11   4.3e-08       1      48 [.      27      75 ..      27      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.4e-11
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                      l+++R   ++sq+ LAe l+vs s is++E+G + +P + ++ ++ +aL
  gi|313125625|ref|YP_004035895.1| 27 LRKWRTDFDISQTALAEQLDVSSSVISDYESGrRESPGIGVVRRMVEAL 75
                                      899*****************************9888*******999987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.1e-09   3.3e-06       1      52 [.      24      75 ..      24      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.1e-09
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                                      G  L++ R  + ++q +lae+l++s s is +E+g+++ p+++++++ +eal
  gi|313125625|ref|YP_004035895.1| 24 GATLRKWRTDFDISQTALAEQLDVSSSVISDYESGRRESPGIGVVRRMVEAL 75
                                      56799************************************99998877765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014       0.4      14      33 ..      34      53 ..      27      55 .. 0.85
   2 ?    2.1   0.0     0.065   1.9e+02      26      42 ..     134     150 ..     131     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                            HTH_11 14 gpisgeeLAeeLnvSrrtvr 33
                                       +is   LAe+L+vS +++ 
  gi|313125625|ref|YP_004035895.1| 34 FDISQTALAEQLDVSSSVIS 53
                                      459************99985 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.065
                            HTH_11  26 nvSrrtvrrdIkaLeel 42 
                                       +vS  tv + I+a++ l
  gi|313125625|ref|YP_004035895.1| 134 HVSGHTVINSIQAITRL 150
                                       6999********99876 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.7e-05      0.05      10      34 ..      37      61 ..      34      84 .. 0.86
   2 ?   -2.9   0.0       2.1   6.4e+03      24      47 ..     102     125 ..      97     127 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkq 34
                                      +q+aLAe+l+vs++ +s+  +g+++
  gi|313125625|ref|YP_004035895.1| 37 SQTALAEQLDVSSSVISDYESGRRE 61
                                      8*****************9988887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                    YdaS_antitoxin  24 aVsqWlkgkkqvpaervpeIekat 47 
                                        V+++ + ++++p er  +   at
  gi|313125625|ref|YP_004035895.1| 102 IVQDLREYSTSIPLERLYDAMDAT 125
                                       566776666679999877665555 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.7e-05      0.23       2      41 ..      27      66 ..      26      75 .. 0.86
   2 ?   -0.8   0.0      0.72   2.1e+03      17      33 ..     145     161 ..     122     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.7e-05
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsld 41
                                      Lr++  d +i+++ La+++++s++ +s + +g+ e++ ++
  gi|313125625|ref|YP_004035895.1| 27 LRKWRTDFDISQTALAEQLDVSSSVISDYESGRRESPGIG 66
                                      89999999***********************997776655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.72
                            HTH_26  17 argtgisaatlsrlvkg 33 
                                       +  t +s+  ++rl+ +
  gi|313125625|ref|YP_004035895.1| 145 QAITRLSSEEFYRLYGQ 161
                                       45667777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1530.34
//
Query:       gi|313125626|ref|YP_004035896.1|  [L=221]
Description: hypothetical protein Hbor_08550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-07   29.5   2.1    5.4e-07   29.1   2.1    1.4  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
        0.1   12.5   0.0        0.2   11.6   0.0    1.3  1  GATase_7  Glutamine amidotransferase domain
       0.17   11.5   0.0       0.27   10.9   0.0    1.2  1  UL45      UL45 protein, carbohydrate-binding C-type lectin-li


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   2.1   9.1e-11   5.4e-07       4     142 ..       5     137 ..       1     210 [. 0.71

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.1e-11
                              YdjM   4 ltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllflalla 80 
                                       + H+++G +lg+al+     +   + ++v+++  +lPD+D     +++ +  +       + HR++ H++l  a+l 
  gi|313125626|ref|YP_004035896.1|   5 IVHLAIGGLLGAALLGDEFDR---RSVLVIFAFTALPDVD----VFAEPIF-A-------GAHRSLGHTFLLPAVLF 66 
                                       479999999999999888776...55555555567*****....5555552.2.......34**********88888 PP

                              YdjM  81 lvlllllrlfgrsa..........lrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidpl 142
                                       ++l++ +r+  +s+          + ++++ ++ +   +l Dll   Gv  l+P+ ++ ++++  +   +++
  gi|313125626|ref|YP_004035896.1|  67 AFLIWDTRRGVASVlrgrfgvrgvKLAWVGTFCLLGAGILPDLL-VGGVNALYPLHDRFYTVDGRLLYSTDR 137
                                       88888888888888899999966533344455556679999*76.68********98666666666655553 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.3e-05       0.2      78     107 ..      66      95 ..      64     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
                          GATase_7  78 fAfaiwdeeekrlllaRDrlGikPLyyged 107
                                       fAf+iwd++++   + R r+G++ + +++ 
  gi|313125626|ref|YP_004035896.1|  66 FAFLIWDTRRGVASVLRGRFGVRGVKLAWV 95 
                                       9*********************99888877 PP

>> UL45  UL45 protein, carbohydrate-binding C-type lectin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.5e-05      0.27       9      68 ..     150     206 ..     145     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.5e-05
                              UL45   9 plepvkaelrfevrailedepsvlsstsssrtkrkspaaalllilggialGvlltvfviv 68 
                                       +  ++++  +fe r +l+  p+  ++++++ +++    + +++ l g+ +G++l  +v+v
  gi|313125626|ref|YP_004035896.1| 150 EPKQTRTTKNFEFRTVLDAAPTQRTAETPDEKRV---ERIFPVALTGFRFGIVLLSAVVV 206
                                       4567888899**************9999999999...88899************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1370.45
//
Query:       gi|313125627|ref|YP_004035897.1|  [L=173]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-14   54.6   0.0    1.6e-14   54.2   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.2e-11   43.5   0.0    4.9e-11   42.9   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.5e-11   42.1   0.0    9.7e-11   41.7   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.1e-07   31.2   0.0    4.4e-07   30.6   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    4.6e-06   26.7   0.0      9e-06   25.7   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    1.4e-05   24.8   0.0      3e-05   23.7   0.0    1.5  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
    0.00017   21.7   0.0    0.00045   20.3   0.0    1.8  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00097   19.3   0.0     0.0012   18.9   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0096   15.9   0.0      0.018   15.0   0.0    1.4  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
  ------ inclusion threshold ------
      0.023   14.6   0.0      0.043   13.8   0.0    1.4  1  FR47             FR47-like protein
      0.055   13.3   0.0        1.8    8.4   0.0    2.1  2  Acetyltransf_18  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   9.6e-18   1.6e-14      24     117 .]      62     162 ..      43     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 9.6e-18
                                       HHHH...HHSTTC.EEEEEEETTEEEEEE.....EEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHH CS
                    Acetyltransf_1  24 fees...fsleae.gllvaeedgeliGfi.....sllkipdekggvayieslaVspeyrgkGlGsaLlealeerare 91 
                                       + ++      ++e +  va   + l+G++     sl+ i+d     a++++++V++eyrg G++  L++a++e are
  gi|313125627|ref|YP_004035897.1|  62 WLDWvdrCVSTDEsSVTVAATADGLVGYAfvlpeSLSFIWD----AAVLNEIFVASEYRGTGVADDLMDAAIECARE 134
                                       445544433344425555888889*****999999999999....8******************************* PP

                                       T..TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  92 e..gikkivlaveedndaairlYeklGF 117
                                       +   ++++vl+v+  nd+a+++Ye+ GF
  gi|313125627|ref|YP_004035897.1| 135 QdlPLDRMVLDVDRENDRAQAFYERYGF 162
                                       *7666**********************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0     3e-14   4.9e-11       3      75 ..      75     163 ..      69     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3e-14
                                       EEEEEEEETTEEEEEEEEEEES.......TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEEE.....EEEEEE.. CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld.......aeitrlaVdpeyrgkGiGraLleaae.....kgii.....leqlel.. 60 
                                       ++v Va   ++ vG++ + +++       a +++++V+ eyrg G++  L++aa+     +        + +l +  
  gi|313125627|ref|YP_004035897.1|  75 SSVTVAATADGLVGYAFVLPESlsfiwdaAVLNEIFVASEYRGTGVADDLMDAAIecareQ--DlpldrM-VLDVdr 148
                                       5677888889999*99999999988877555555******************732233322..0333331.222232 PP

                                       THH.HHHHHHHHTTEE CS
                    Acetyltransf_7  61 nae.kaikfYeklGFe 75 
                                       + + +a++fYe++GFe
  gi|313125627|ref|YP_004035897.1| 149 E-NdRAQAFYERYGFE 163
                                       2.149**********8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0     6e-14   9.7e-11      27     112 ..      71     168 ..      48     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 6e-14
                   Acetyltransf_10  27 eegealllvaeeggkivGviel.rdgs.......hisllfVdpeyrgqGigkaLleaveeeaekdgikl...eltvn 92 
                                       ++ e  + va   + +vG++ +  ++         +  +fV++eyrg+G++  L++a++e a+++++ l    l v+
  gi|313125627|ref|YP_004035897.1|  71 STDESSVTVAATADGLVGYAFVlPESLsfiwdaaVLNEIFVASEYRGTGVADDLMDAAIECAREQDLPLdrmVLDVD 147
                                       4556666677777899999966344436777778999*************************999988886778888 PP

                   Acetyltransf_10  93 asp.yavpfYeklGFkavgee 112
                                         +  a++fYe++GF+  ge+
  gi|313125627|ref|YP_004035897.1| 148 RENdRAQAFYERYGFEHWGEM 168
                                       8889************98876 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   2.7e-10   4.4e-07       3     138 .]      14     163 ..      12     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.7e-10
                    Acetyltransf_3   3 lLrplteeDlealfelrsdpevm..rylpepltleea..........eewlerawaeeseeeg.ygwaivlkdtgvi 66 
                                       ++rp++++D+ +l el +  e+   +  + p++  e+          ++wl+  w ++  +++    ++   ++g +
  gi|313125627|ref|YP_004035897.1|  14 TIRPYEADDATDLWELKQGFELGigE-NTGPADKGETyegkltdhyrTRWLD--WVDRCVSTDeSSVTVAATADGLV 87 
                                       79***********9999988866223.2235555555433333222244444..55444444423466655777678 PP

                    Acetyltransf_3  67 Gsvglrdleeedee...aelgymlapsfwgkGyateavralleyaf.eelglerlvavidkeNeaSirvleklGfe 138
                                       G++ + + + +  +   +  ++ +a++++g G+a + + a++e a  ++l l+r+v  +d eN + ++ +e+ Gfe
  gi|313125627|ref|YP_004035897.1|  88 GYAFVLPESLSFIWdaaVLNEIFVASEYRGTGVADDLMDAAIECAReQDLPLDRMVLDVDRENDRAQAFYERYGFE 163
                                       888666544444447746667999999******************6477799***********************7 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   5.5e-09     9e-06      25      58 ..     104     137 ..      85     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.5e-09
                   Acetyltransf_CG  25 ldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                        +++ ++V  e+rG G+A  L++aa+++are++l
  gi|313125627|ref|YP_004035897.1| 104 AVLNEIFVASEYRGTGVADDLMDAAIECAREQDL 137
                                       57899**************************987 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.8e-08     3e-05      87     143 ..     112     168 ..     107     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.8e-08
                                       SSHHHCTTTCHHHHHHHHHHHHHC.CTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                    Acetyltransf_8  87 geaeargkglttallralvhylfa.dprtrrvvvEPdvrNerairllekaGfekekev 143
                                       +  e+rg g+++ l+ a ++ + + d   +r+v++ d +N ra +++e+ Gfe+++e+
  gi|313125627|ref|YP_004035897.1| 112 A-SEYRGTGVADDLMDAAIECAREqDLPLDRMVLDVDRENDRAQAFYERYGFEHWGEM 168
                                       4.689******************6366***************************9986 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.7e-07   0.00045      43     127 ..      76     164 ..      48     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.7e-07
                                       EEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..... CS
                    Acetyltransf_9  43 rvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP..... 114
                                        v +a   + lvg + +lp +l++   +++aa +  + va e+rg gv+ +L+++a+e +re++ pl   +      
  gi|313125627|ref|YP_004035897.1|  76 SVTVAATADGLVGYAFVLPESLSF---IWDAAVLNEIFVASEYRGTGVADDLMDAAIECAREQDLPLDRMVLdvdre 149
                                       556666666666666666666665...68999999****************************99996665555777 PP

                                       ..SSHHHHHTTT-EE CS
                    Acetyltransf_9 115 ..ssipiYrrfGyei 127
                                         ++ ++Y+r+G+e+
  gi|313125627|ref|YP_004035897.1| 150 ndRAQAFYERYGFEH 164
                                       777779999999986 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.6e-07    0.0012      46     139 ..      72     167 ..      47     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.6e-07
                    Acetyltransf_4  46 sekeyvflvaesdrivGyaylgqfkkr.akdwkaelsvylaerdnnkeglgrelidaleqvlkeqn..ienllaeia 119
                                       ++++ v  +a +d +vGya +         d +++ ++++a    + +g++ +l+da +++++eq   + +++  + 
  gi|313125627|ref|YP_004035897.1|  72 TDESSVTVAATADGLVGYAFVLPESLSfIWDAAVLNEIFVA-SEYRGTGVADDLMDAAIECAREQDlpLDRMVLDVD 147
                                       455566566669999***999743333477999999****9.78******************888733689****** PP

                    Acetyltransf_4 120 spnensiqfhkalGFelvgi 139
                                        +n+ +++f+++ GFe  g+
  gi|313125627|ref|YP_004035897.1| 148 RENDRAQAFYERYGFEHWGE 167
                                       9**************98775 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.018       8      31 ..     107     130 ..     104     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                   Acetyltransf_13   8 sriWvssshRrkgiAtkLldaare 31 
                                       + i+v+s++R +g+A  L+daa+e
  gi|313125627|ref|YP_004035897.1| 107 NEIFVASEYRGTGVADDLMDAAIE 130
                                       78*******************986 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-05     0.043      23      79 ..     105     164 ..     100     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                       SEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-...S-EEEEEETT-HHHHHHHHHHT-EE CS
                              FR47  23 elgalqvlpehrrrGlgsrlvkalakeiaerg...ktvllvvvasNtpsirlyeklGfek 79 
                                        l  + v  e r+ G +  l  a ++  +e++   + ++l v  +N++++++ye+ Gfe 
  gi|313125627|ref|YP_004035897.1| 105 VLNEIFVASEYRGTGVADDLMDAAIECAREQDlplDRMVLDVDRENDRAQAFYERYGFEH 164
                                       577789999*************999998887655567889999***************96 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.062     1e+02      19      46 ..      68      95 ..      56     100 .. 0.81
   2 ?    8.4   0.0    0.0011       1.8      62     102 ..     120     165 ..     116     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.062
                   Acetyltransf_18 19 rrlkqaeqklvvveedgeivGyglarkt 46
                                      r+++  e+++ v ++++ +vGy+++ + 
  gi|313125627|ref|YP_004035897.1| 68 RCVSTDESSVTVAATADGLVGYAFVLPE 95
                                      667777888888889999*****99876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                   Acetyltransf_18  62 iAeaLlkalvanaegk.....kvridvpeenkalielleklgfkev 102
                                       +A +L++a+++ a+++      +++dv  en++++++ e++gf+  
  gi|313125627|ref|YP_004035897.1| 120 VADDLMDAAIECAREQdlpldRMVLDVDRENDRAQAFYERYGFEHW 165
                                       5777777777777765111114689******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1018.58
//
Query:       gi|313125628|ref|YP_004035898.1|  [L=186]
Description: hypothetical protein Hbor_08570 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.15   12.0   7.4       0.09   12.7   3.4    2.2  2  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.028   5.1e+02      94     118 ..      12      36 ..       7      46 .. 0.74
   2 ?   12.7   3.4     5e-06      0.09      67     113 ..      93     139 ..      87     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.028
                         RseC_MucC  94 llaalgallglvlgflivrllskrl 118
                                       l+ +  ++ ++++g+l+v+l ++ +
  gi|313125628|ref|YP_004035898.1|  12 LVGVGSGFGAAIVGYLLVYLSASGT 36 
                                       5667778888899999998877664 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5e-06
                         RseC_MucC  67 allvYllPllllilgallgsallgssellaalgallglvlgflivrl 113
                                       + l+Y++P+++l+++ ++  al+g+++ +  +++ ++++lg+l+v l
  gi|313125628|ref|YP_004035898.1|  93 STLLYAVPVVCLLVAGAVSAALAGAESPADGALSGAAIALGYLVVAL 139
                                       6799*********9999999999999999999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1156.56
//
Query:       gi|313125629|ref|YP_004035899.1|  [L=207]
Description: acetyltransferase, ribosomal protein n-acetylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-16   59.2   0.0    9.3e-16   58.8   0.0    1.2  1  Acetyltransf_3  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   5.2e-20   9.3e-16       1     134 [.      13     153 ..      13     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 5.2e-20
                    Acetyltransf_3   1 RLlLrpl.tee.Dlealfelrsdpevmry...lpe..pltleeaeewlera...waeeseeegygwaivlkdtgv.i 66 
                                       RL L ++ +++ D+ +l++++s  + +++   +p   ++t+ e+ ++l ++   w++   +e+  +ai+ +++g+ +
  gi|313125629|ref|YP_004035899.1|  13 RLRLERAgRDTvDVRELYRVASGDDAEEMfahVPFspHETPKETFDFLVSCeerWES---GEAAEYAIRRPEDGEfV 86 
                                       788888844448999999999988888863342223356666666666655444654...47788***88777755* PP

                    Acetyltransf_3  67 GsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvlek 134
                                       G+ g++ + ++d+ ae g++l+++fwg+Gy  e +rall++af++l+   + + ++++Ne+S+r   k
  gi|313125629|ref|YP_004035899.1|  87 GMTGVTCYWDRDT-AEPGIWLRKPFWGRGYSGERARALLTLAFDRLDFGLVGVSVAADNEKSRRAVGK 153
                                       ******9888776.**************************************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 1413.62
//
Query:       gi|313125630|ref|YP_004035900.1|  [L=208]
Description: acetyltransferase, ribosomal protein n-acetylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-16   59.9   0.7    7.6e-16   59.0   0.1    1.7  2  Acetyltransf_3  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.1   4.3e-20   7.6e-16       1     134 [.      10     156 ..      10     157 .. 0.79
   2 ?   -1.4   0.0      0.19   3.5e+03      21      93 ..     178     193 ..     167     205 .. 0.60

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 4.3e-20
                    Acetyltransf_3   1 RLlLrplteeDleal.f.el.rs....dpevmrylpe..pltleeaeewlerawaeeseeegygwaivlkdtg.... 64 
                                       RL Lr++t e +++l   e+ r+      ev++y+++   +t+ e++e+l+r+ ++ +++e+  +ai+ +d++    
  gi|313125630|ref|YP_004035900.1|  10 RLRLRRATREVIPPLeQyEYtREgaegIDEVTEYVSWnpVKTPKESDEFLARCEEKWDDGEAAIYAIFPRDGEdgag 86 
                                       7778888877777774223322222223467789777779999999999998855555567788***9766634466 PP

                    Acetyltransf_3  65 .viGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvlek 134
                                        + G+ gl+ +++++++a +g++l++ fwg+Gy  e +ra+ e+afee +++   a++ +eNe+S r ++k
  gi|313125630|ref|YP_004035900.1|  87 eFAGTTGLH-FQWDRDTAVFGIWLRKRFWGRGYSGERARAFFEVAFEEFDVSLCAAEYLPENEQSGRAIQK 156
                                       46*******.7777777**************************************************9998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.19
                    Acetyltransf_3  21 dpevmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwg 93 
                                       dpe                                                         a + y + +s w+
  gi|313125630|ref|YP_004035900.1| 178 DPE---------------------------------------------------------ATVRYSITQSEWR 193
                                       333.........................................................5566666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1164.05
//
Query:       gi|313125631|ref|YP_004035901.1|  [L=150]
Description: flavin-nucleotide-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-21   74.8   0.2    7.5e-21   74.6   0.2    1.0  1  Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.2   4.2e-25   7.5e-21       2     141 .]      10     142 ..       9     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 4.2e-25
                                       HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEE..TTEEEEEEETTSHCCHCCCT--ECEEEEEEEEEEE-SEGGE CS
                      Pyridox_ox_2   2 reeilalLdegevgrlafvddgepvilPvnyvvd..gdslyfhgakgsrlaaalrgapvcvvvtevdglvlarsfns 76 
                                       +eei ++L++g+++++a++++++ +++Pv+y++d  ++++y++ a  s+  +        v ++ vd+lv  ++  +
  gi|313125631|ref|YP_004035901.1|  10 HEEIVEFLETGGTAVIALAKGDDSYAIPVSYGFDdeEEHFYLRLAFDSESEKREY-----VDAAGVDSLVIHEQ--T 79 
                                       89********************************66667*******887777666.....99999999999999..4 PP

                                       EE.EEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEEEEEEEEEE CS
                      Pyridox_ox_2  77 ln.yrSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelkatsvlrlkieevsgrr 141
                                        + ++SVv+rG+++evt+++ +++++e++    +p  + ++ ++  +el   +++rl++ee++gr+
  gi|313125631|ref|YP_004035901.1|  80 DEgWKSVVARGHLAEVTEAALDSTIVEAMRTMDIP--FVTIFEHPSTELDF-EMYRLAPEELTGRK 142
                                       456***************************999**..*****999999999.************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.36s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 851.32
//
Query:       gi|313125632|ref|YP_004035902.1|  [L=225]
Description: transposase, is605 orfb family, central region [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-23   80.4   1.8    1.1e-21   76.5   0.6    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.5e-09   37.4   0.1    4.5e-09   36.6   0.1    1.5  1  HMA             Heavy-metal-associated domain
  ------ inclusion threshold ------
      0.055   12.7   0.1       0.34   10.0   0.1    1.9  1  RuvC_1          RuvC nuclease domain
       0.21   11.6   4.8       0.88    9.6   2.0    2.3  2  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
       0.29   11.2   2.8          2    8.6   0.3    2.2  2  DUF2752         Protein of unknown function (DUF2752)
       0.33   11.0   5.9        0.3   11.1   3.5    2.1  2  HypA            Hydrogenase/urease nickel incorporation, meta
        9.4    6.4  12.6       0.92    9.7   0.2    2.9  3  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.042   1.1e+02      25      42 ..       8      25 ..       1      38 [. 0.75
   2 !   76.5   0.6   4.2e-25   1.1e-21       1      69 []     109     176 ..     109     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.042
                    OrfB_Zn_ribbon 25 ayTSktCseCgsknkeal 42
                                        T  +C+ C +++++al
  gi|313125632|ref|YP_004035902.1|  8 DITGMSCPGCERTVETAL 25
                                      458999*****9999844 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 4.2e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l +++eyka+++Gi v +v+++ TSktC++C +++ +  ++ +f+Cp+Cg+  ++D n+a+Ni kr
  gi|313125632|ref|YP_004035902.1| 109 FARLLNYIEYKAHDAGIDVRLVEEYDTSKTCNRCACEGVR-ETQGRFECPECGLDDNADKNGALNIGKR 176
                                       899*************************************.*************************987 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   1.8e-12   4.5e-09       2      62 .]       7      66 ..       6      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.8e-12
                               HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaes.tklrkiieaiekagyk 62
                                      +++ gm C gC+++ve +L++++gV+ ++ + +++tv+ +++++  +   ++  ai++agyk
  gi|313125632|ref|YP_004035902.1|  7 IDITGMSCPGCERTVETALKSVDGVRRADANRESGTVETVVEDDVgD--DDLGDAIHSAGYK 66
                                      5789*****************************88887777777755..88*********97 PP

>> RuvC_1  RuvC nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00013      0.34      94     210 ..      67     178 ..      61     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RuvC_1  94 vvhkiaklaikynaivvlEdLnlgFkrgrqkvekqvyqkfEkaLidk.lnylvdkkkkeeeaggllkayqltakves 169
                                       + ++i++ a + na++v+ dL     r+ ++  + v  k  k+  ++ lny+  k +++     l++ y  +++ + 
  gi|313125632|ref|YP_004035902.1|  67 IARQIVEDAEERNAVIVVGDLGGI--RKDNHKGRYVNDKTHKMPFARlLNYIEYKAHDAGIDVRLVEEYDTSKTCNR 141
                                       557788888888899999988654..444455677888888886655268888888888888888888888887765 PP

                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RuvC_1 170 feklg..kqaGilfyvpaayTkklslpedadaNgayniarkgl 210
                                        +  g    +G           ++ l  +ad+Nga ni+++ l
  gi|313125632|ref|YP_004035902.1| 142 CACEGvrETQGR------FECPECGLDDNADKNGALNIGKRAL 178
                                       543222144443......2346779999***********9976 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.074   1.9e+02      29      37 ..      10      18 ..       5      27 .. 0.79
   2 ?    9.6   2.0   0.00034      0.88      11      37 ..     137     160 ..     126     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.074
                                      ...E-TTTT CS
                         Anti-TRAP 29 asleCPkCs 37
                                      +++ CP C+
  gi|313125632|ref|YP_004035902.1| 10 TGMSCPGCE 18
                                      578888885 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00034
                                       EE-TTTTTTSEETTE......E-TTTT CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCs 37 
                                       ++C+ C   G  e++   + +eCP+C+
  gi|313125632|ref|YP_004035902.1| 137 KTCNRCACEGVRETQ---GRFECPECG 160
                                       578888888888777...99******6 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3   0.00077         2       6      14 ..       9      17 ..       8      20 .. 0.91
   2 ?    2.7   0.1     0.053   1.4e+02       9      16 ..     154     161 ..     150     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00077
                           DUF2752  6 ltGipCPGC 14
                                      +tG++CPGC
  gi|313125632|ref|YP_004035902.1|  9 ITGMSCPGC 17
                                      8******** PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.053
                           DUF2752   9 ipCPGCGl 16 
                                       ++CP CGl
  gi|313125632|ref|YP_004035902.1| 154 FECPECGL 161
                                       89*****7 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.5   1.3e+03      88      95 ..      13      20 ..       4      32 .. 0.61
   2 ?   11.1   3.5   0.00012       0.3      64      96 ..     130     163 ..      65     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.5
                                      S-TTTSSS CS
                              HypA 88 rCpkCgsa 95
                                      +Cp C+++
  gi|313125632|ref|YP_004035902.1| 13 SCPGCERT 20
                                      45555543 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00012
                                       EEEE--EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                              HypA  64 ieevpvkvrCreCgkefeleek.alrCpkCgsad 96 
                                       +ee + + +C++C  e+  e++ +++Cp+Cg  d
  gi|313125632|ref|YP_004035902.1| 130 VEEYDTSKTCNRCACEGVRETQgRFECPECGLDD 163
                                       78889999********998877799*****9765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00036      0.92       3      14 ..      14      25 ..      13      27 .. 0.84
   2 ?   -4.0   3.0       6.5   1.7e+04       1       7 [.     137     143 ..     137     145 .. 0.70
   3 ?    5.7   0.2    0.0062        16      16      21 ..     155     160 ..     154     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                           UPF0547  3 CPeCeakvPvaa 14
                                      CP+Ce++v +a 
  gi|313125632|ref|YP_004035902.1| 14 CPGCERTVETAL 25
                                      ********8886 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.5
                           UPF0547   1 KvCPeCe 7  
                                       K+C +C+
  gi|313125632|ref|YP_004035902.1| 137 KTCNRCA 143
                                       7777775 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0062
                           UPF0547  16 fCphCG 21 
                                       +Cp+CG
  gi|313125632|ref|YP_004035902.1| 155 ECPECG 160
                                       588887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1242.99
//
Query:       gi|313125633|ref|YP_004035903.1|  [L=771]
Description: copper/silver-translocating p-type ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-49  166.5   0.1    4.3e-49  166.5   0.1    2.4  3  E1-E2_ATPase  E1-E2 ATPase
    4.3e-44  151.3   3.8    7.9e-44  150.4   3.8    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
      1e-06   29.1   0.6    4.4e-06   27.1   0.1    2.3  2  HMA           Heavy-metal-associated domain
    3.6e-06   26.9   0.5    9.5e-05   22.3   0.4    2.2  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.069   13.6   0.2       0.53   10.7   0.1    2.5  2  HAD           haloacid dehalogenase-like hydrolase
      0.083   12.8   0.0      0.083   12.8   0.0    3.1  4  DUF2721       Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.41   1.2e+03     112     140 ..      70     100 ..      61     122 .. 0.43
   2 !  166.5   0.1   1.4e-52   4.3e-49       2     180 ..     210     399 ..     209     400 .. 0.96
   3 ?   -3.8   0.1       2.5   7.6e+03     121     142 ..     700     721 ..     692     733 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHHHHHHH..HHHS-STT CS
                      E1-E2_ATPase 112 qkkldklgkvlvpvvlliall..vflialll 140
                                       q+++++ ++ +++++ +++++  ++l+++++
  gi|313125633|ref|YP_004035903.1|  70 QQEVKRATRRVTLAGAAALVTagLMLFMIFV 100
                                       3333344443333322222220022222222 PP

  == domain 2  score: 166.5 bits;  conditional E-value: 1.4e-52
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       l+p+ta+++rdgt+ee++++el+++D v +++g+r+p+Dg+++ g+++vdes++TGEs+p +k  gd+v +G+++  
  gi|313125633|ref|YP_004035903.1| 210 LQPDTARRVRDGTVEEVEISELETDDHVRVNPGERIPVDGIVIAGETTVDESVVTGESVPGDKIPGDEVVGGSINET 286
                                       89*************************************************************************** PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.......... CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.......... 145
                                       g++ ++Vt+tg d +l+++ar++e+a+  k+ +++ +d++ k++vp vl++a++ fl+++l+   ++          
  gi|313125633|ref|YP_004035903.1| 287 GTLLVEVTTTGDDAFLNQVARQIEKARTMKPGVVQLADRVLKYFVPSVLAVAAASFLFWVLVPVLWTggplgsepnv 363
                                       *************************************************************7777777777888889 PP

                                       .HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 146 .eallralallvaaiPcaLplavplalalgarrlak 180
                                        +  + ala+lv   PcaL++a+plal+ g + +a+
  gi|313125633|ref|YP_004035903.1| 364 kRGAFAALAVLVLGYPCALGMATPLALIRGGGLAAN 399
                                       9****************************9988876 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHS-STTTS CS
                      E1-E2_ATPase 121 vlvpvvlliallvflialllgk 142
                                       v++++++++++ ++l++ + g+
  gi|313125633|ref|YP_004035903.1| 700 VFAMIAMILSVSAVLVNSFAGQ 721
                                       4566666666666666665554 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.4   3.8   2.7e-47   7.9e-44       1     210 []     416     632 ..     416     632 .. 0.93

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 2.7e-47
                                       SSEEEEESBTTTBCHHHHHHHHHHHH.....CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH...HHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.....alalaaaletgsehpigkalvaaakarsgal...tgfatfigrg.. 67 
                                       ++t+v+Dk+GT ttgep ve v++ +      + +aa  e+ sehp++ a+ ++a++rs++    + f  ++g+g  
  gi|313125633|ref|YP_004035903.1| 416 VDTIVLDKTGTMTTGEPAVEAVVALRgdehsVIRRAASAEVFSEHPLADAIREYANERSIEFsdpETFDSVTGKGvr 492
                                       68************************9998666666666666****************88886678888899999** PP

                                       ......HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTE CS
                                       ......xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ......ayaigkpewltal.dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagi 135
                                             + ++gkp wlt++       + +i+ +q++g+tv+ +  +  + ++++i dp  vk +a  +v++ +aagi
  gi|313125633|ref|YP_004035903.1| 493 atvegeQTLVGKPGWLTEEgVDLMVARGDIDRLQERGETVVCVadDESVIGLVAIGDP--VKNDADSTVERMRAAGI 567
                                       *******************9888899999*************9888899*********..***************** PP

                                       EEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 136 evvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                         v+ tgdn++ta+++a  +G           i+   a ++p++k+a ir+Lq  +e+vamVGDg+nDa+al +A+
  gi|313125633|ref|YP_004035903.1| 568 TPVMSTGDNERTANAVAATVG-----------IDRvMADVLPDDKRAEIRRLQDGGERVAMVGDGINDAPALTQAD 632
                                       *********************...........6666*****************99*******************98 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   1.5e-09   4.4e-06       7      62 .]       1      56 [.       1      56 [. 0.98
   2 ?   -1.2   0.0      0.99     3e+03      35      59 ..     288     312 ..     284     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.5e-09
                               HMA  7 mhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      m C  C+ +++k+ ++ +gVe+v+v+la  +  + +d ++++  +++ +++++gy+
  gi|313125633|ref|YP_004035903.1|  1 MSCSFCVESIRKAYERTEGVEEVNVSLAHEEIRIQYDSAALSEVELKDTLRDLGYT 56
                                      99**************************************999***********95 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.99
                               HMA  35 tktvtVegdaestklrkiieaieka 59 
                                       t  v+V+++ +++ l+++ ++ieka
  gi|313125633|ref|YP_004035903.1| 288 TLLVEVTTTGDDAFLNQVARQIEKA 312
                                       5567888888886669999999986 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.041   1.2e+02      19      58 ..     554     593 ..     545     596 .. 0.87
   2 !   22.3   0.4   3.2e-08   9.5e-05     203     253 ..     612     662 ..     604     663 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  19 ktkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                        + +++++++++gi+ v +TG + r++  v+  +g+d  +
  gi|313125633|ref|YP_004035903.1| 554 DADSTVERMRAAGITPVMSTGDNERTANAVAATVGIDRVM 593
                                       5667899***************************999665 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3.2e-08
                                       GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHH CS
                       Hydrolase_3 203 leeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVak 253
                                        e+v+ +GDg ND + L++a++g+A+g +++ +++ Ad +      +GV +
  gi|313125633|ref|YP_004035903.1| 612 GERVAMVGDGINDAPALTQADIGIAVGAGTDIAIESADIILMGDRLGGVMD 662
                                       5899**********************************9987777777765 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.7   1.1e+04      71      95 ..     300     324 ..     296     329 .. 0.76
   2 ?   10.7   0.1   0.00018      0.53      93     187 ..     558     628 ..     538     629 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.7
                               HAD  71 aelerfvaevirpklldpgalella 95 
                                       a l++  +++ + ++++pg+++l +
  gi|313125633|ref|YP_004035903.1| 300 AFLNQVARQIEKARTMKPGVVQLAD 324
                                       5677777888888899999998765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                               HAD  93 llaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaegegi 169
                                        +++ raaG++ v+ +g +++ + +++a +g+d+v+a       +l           ++    a++r+        +
  gi|313125633|ref|YP_004035903.1| 558 TVERMRAAGITPVMSTGDNERTANAVAATVGIDRVMAD------VLPDD--------KR----AEIRR------LQD 610
                                       455566*************************8888888......44333........45....66666......555 PP

                               HAD 170 dleevvayGDspsDlpll 187
                                         e+v  +GD+++D p+l
  gi|313125633|ref|YP_004035903.1| 611 GGERVAMVGDGINDAPAL 628
                                       777799999999999987 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.8e-05     0.083      28     110 ..      49     124 ..      44     126 .. 0.67
   2 ?   -2.2   0.1       1.2   3.5e+03      59     100 ..     139     179 ..     133     191 .. 0.52
   3 ?   -2.3   0.0       1.3   3.9e+03     106     116 ..     334     344 ..     303     377 .. 0.66
   4 ?   -1.5   1.4      0.74   2.2e+03      96     118 ..     693     715 ..     675     723 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                           DUF2721  28 rirqLedeleelaeeeeedeelakeiknlrrRarlirrailllvlsallvvlvvlllflsallsldlsllaailfvl 104
                                        +r+L   +++ ++++ + ee ++e+k+  r      r  l+++++++++ l+ +++f++  ++ +  ++  ++ +l
  gi|313125633|ref|YP_004035903.1|  49 TLRDLGYTIRDPDKQT-QFEEQQQEVKRATR------RVTLAGAAALVTAGLMLFMIFVRGTFESEARWMDLVTLGL 118
                                       5555555555333332.23444555555555......5556677788888888899999999999999999999999 PP

                           DUF2721 105 alllll 110
                                       al  ++
  gi|313125633|ref|YP_004035903.1| 119 ALGTMF 124
                                       998875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                           DUF2721  59 Rarlirrailllvlsallvvlvvlllflsall.sldlsllaai 100
                                       R r+ ++ +ll + +++ +v   l lf+  +     ++++a+ 
  gi|313125633|ref|YP_004035903.1| 139 RRRIFNQHVLLEAGAFAGLVGGFLGLFV--FPsFPTVHFFAVS 179
                                       4455566666666666666666666666..1111222333333 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.3
                           DUF2721 106 lllllvslllf 116
                                       +l+++++++lf
  gi|313125633|ref|YP_004035903.1| 334 VLAVAAASFLF 344
                                       22222222222 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.74
                           DUF2721  96 llaailfvlalllllvslllflr 118
                                       ++  +  v+a++++++s+  +l+
  gi|313125633|ref|YP_004035903.1| 693 TTGLVHPVFAMIAMILSVSAVLV 715
                                       44444445666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (771 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.82u 0.38s 00:00:01.20 Elapsed: 00:00:00.58
# Mc/sec: 3986.36
//
Query:       gi|313125634|ref|YP_004035904.1|  [L=184]
Description: bacterial regulatory protein, arsr family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-12   45.7   0.2    9.3e-12   44.8   0.2    1.5  1  HTH_20           Helix-turn-helix domain
    1.5e-09   37.6   0.2    7.3e-09   35.4   0.2    2.0  1  HTH_5            Bacterial regulatory protein, arsR family
    3.3e-05   23.8   1.7    4.2e-05   23.4   0.4    1.8  2  HTH_12           Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
       0.01   15.9   0.7      0.022   14.9   0.6    1.6  1  FUR              Ferric uptake regulator family
      0.011   15.5   1.3       0.03   14.2   0.2    2.0  2  TFIIE_alpha      TFIIE alpha subunit
      0.016   15.1   0.2      0.027   14.4   0.2    1.4  1  PadR             Transcriptional regulator PadR-like family
      0.021   14.7   0.3      0.032   14.1   0.2    1.4  1  BCDHK_Adom3      Mitochondrial branched-chain alpha-ketoacid 
      0.037   14.4   0.5       0.15   12.5   0.0    2.1  2  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.2   4.1e-15   9.3e-12       4      58 ..      21      79 ..      18      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 4.1e-15
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH....T.S-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerl....d.lskntlsyHLrvLeeagLvevvr 58
                                      a+AL++ vR +il++L  ++++t +e++e+l    +    +t+++H+++L +agLve  r
  gi|313125634|ref|YP_004035904.1| 21 AKALDNDVRVKILDML-ADQEMTIGEIHEELarrgEkKVETTVRHHVNILKDAGLVEIAR 79
                                      89**************.**************87652477777**************9765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.2   3.2e-12   7.3e-09       2      46 ..      27      76 ..      26      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3.2e-12
                                      HHHHHHHHHHTTSSEEHHHHHHHH.....TS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeel.....glsqstvShHLkkLreaGLVe 46
                                        R+kIL +La++e++++e+ eel     ++ + tv+hH ++L++aGLVe
  gi|313125634|ref|YP_004035904.1| 27 DVRVKILDMLADQEMTIGEIHEELarrgeKKVETTVRHHVNILKDAGLVE 76
                                      57**********************999989*******************6 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.4   1.9e-08   4.2e-05       1      49 [.      30      76 ..      30      85 .. 0.90
   2 ?   -1.5   0.0       1.2   2.6e+03      25      40 ..     131     144 ..     108     172 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.9e-08
                            HTH_12  1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                                      v+IL++la+++  ig  ei eeL  rg++  e +vR +  +l + gl++
  gi|313125634|ref|YP_004035904.1| 30 VKILDMLADQEMTIG--EIHEELARRGEKKVETTVRHHVNILKDAGLVE 76
                                      689****98887665..9**********999***************997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                            HTH_12  25 krgydigeravRyrLr 40 
                                       + ++ i  ++v + ++
  gi|313125634|ref|YP_004035904.1| 131 DHDEVI--ETVAREMQ 144
                                       344444..44444444 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.6   9.7e-06     0.022      10      67 ..      29      84 ..      26     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.7e-06
                                      HHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSE CS
                               FUR 10 RekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedge 67
                                      R kil++l+++e  +++ e+++el +++++   +TV   +++l++aglv+   +ed++
  gi|313125634|ref|YP_004035904.1| 29 RVKILDMLADQE--MTIGEIHEELARRGEKKVETTVRHHVNILKDAGLVEIARLEDAS 84
                                      889999998877..8**********************************988777432 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.3e-05      0.03      15      73 ..      29      91 ..      20     102 .. 0.76
   2 ?   -0.0   0.1      0.35     8e+02      30      54 ..     107     131 ..     104     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHHHCTTSEBHHHHHHHH.....TS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEE CS
                       TFIIE_alpha 15 avlvldvLlekgevteedlakel.....kidlnelrklLnrLyearlvkykrrrdeekswykyy 73
                                       v++ld+L+ + e+t  ++ +el     k   + +r+ +n L++a+lv++ r  d + ++ kyy
  gi|313125634|ref|YP_004035904.1| 29 RVKILDMLA-DQEMTIGEIHEELarrgeKKVETTVRHHVNILKDAGLVEIARLEDASGGTLKYY 91
                                      578899988.556666666666522222233578*********************999999988 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.35
                                       HHHHHHHHTS-HHHHHHHHHHHHHC CS
                       TFIIE_alpha  30 eedlakelkidlnelrklLnrLyea 54 
                                       +++l++  +  ++e+  l+ +L+ +
  gi|313125634|ref|YP_004035904.1| 107 DDELNEVQETAREEITALVEQLFRD 131
                                       7888888888888888888888754 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.2e-05     0.027       1      64 [.      32      92 ..      32      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEE CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYr 64
                                      iL +l++q++   ei +el+++  g ++  e+++    + L++ glve  + e+++g++ kyY+
  gi|313125634|ref|YP_004035904.1| 32 ILDMLADQEMTIGEIHEELARR--G-EKKVETTVRHHVNILKDAGLVEIARLEDASGGTLKYYK 92
                                      8999******************..9.8999*********************************7 PP

>> BCDHK_Adom3  Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.4e-05     0.032      68     109 ..     110     152 ..      56     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                       BCDHK_Adom3  68 llelpkpeleenekftelLekikkrHddvvttlaqGvlelk....e 109
                                       l e+++      e++t l+e++ ++Hd+v++t+a+ ++ ++    +
  gi|313125634|ref|YP_004035904.1| 110 LNEVQE---TAREEITALVEQLFRDHDEVIETVAREMQPCEycetQ 152
                                       333333...22579***********************999854321 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.5e-05      0.15      14      53 ..      37      77 ..      28     100 .. 0.86
   2 ?   -0.5   0.1      0.68   1.5e+03      70      98 ..     115     142 ..     109     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-05
                                      HHS-EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EE CS
                   Penicillinase_R 14 ekgeatvkevveeleee.kelaysTVktllrrLvkKgllsr 53
                                      + +e+t++e++eel+++  +  ++TV+  ++ L + gl++ 
  gi|313125634|ref|YP_004035904.1| 37 ADQEMTIGEIHEELARRgEKKVETTVRHHVNILKDAGLVEI 77
                                      45789***********967779*************999975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.68
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Penicillinase_R  70 eavasavkqlldklfegsvkelvaafvee 98 
                                       e  +++   l+++lf +++ e++  +++e
  gi|313125634|ref|YP_004035904.1| 115 ETAREEITALVEQLF-RDHDEVIETVARE 142
                                       555666677777777.4777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.38s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 995.01
//
Query:       gi|313125635|ref|YP_004035905.1|  [L=719]
Description: type i restriction-modification system methyltransferase subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-17   62.1   0.0    1.1e-16   61.0   0.0    1.5  1  N6_Mtase         N-6 DNA Methylase
    3.2e-08   34.0   0.0    6.7e-08   33.0   0.0    1.5  1  Eco57I           Eco57I restriction-modification methylase
    5.2e-05   23.0   0.0    0.00058   19.6   0.0    2.4  2  UPF0020          Putative RNA methylase family UPF0020
    7.3e-05   22.4   0.0    0.00016   21.3   0.0    1.5  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.026   14.3   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
      0.014   15.5   0.0      0.034   14.2   0.0    1.7  1  TaqI_C           TaqI-like C-terminal specificity domain
      0.036   14.8   0.0       0.12   13.1   0.0    2.0  2  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   4.2e-20   1.1e-16       9     214 ..     143     349 ..     136     383 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 4.2e-20
                          N6_Mtase   9 vYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqek 85 
                                       ++E++     +e+ ++ G+f TP e+  +++    ++s  +v+Dp +G+g+l   a k   + + +++  +++G ++
  gi|313125635|ref|YP_004035905.1| 143 LFEQITP---QESRRKLGQFRTPPEIADIMATWCVQESTDTVLDPGVGAGALSAPAYKRKLKLSSDASLATMHGIDL 216
                                       5554433...4567788***************998888888*************998876668999999******** PP

                          N6_Mtase  86 nettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkew...kektlekderfrea....v 155
                                       ne +  ++ + l l +      + ++gd le   ++ d ++d+v++Npp++ + +   +e +   + + ++     v
  gi|313125635|ref|YP_004035905.1| 217 NELALVMGATTLRLLDHGGP-HNLQTGDFLELSPEDIDAEVDAVISNPPYSRH-HelsEEYKTRVNTQIEQElgcdV 291
                                       ************99999999.689******9888888**************99.33553333334444444456644 PP

                          N6_Mtase 156 apksnadla.fllhiieslkpkGraavvlangvLfrggkegkIrkalvekdlveavialp 214
                                          s   +a f  h+ + l+p+Gra+ + ++  L +++ +++++++l+++ +++a++ + 
  gi|313125635|ref|YP_004035905.1| 292 SALSPM-YAyFYFHAEKFLSPGGRASYITPSEFL-ETNYGESLKQYLTNEFNLNALVLFD 349
                                       444444.444999***************999877.789999**************99875 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.6e-11   6.7e-08       3      98 ..     256     366 ..     254     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.6e-11
                            Eco57I   3 fdviiGNPPYqeseakkelkaleek.............akdiyqkFvekalkle..dkylaliiparflasgkglke 64 
                                       +d++i NPPY ++++  e  +++ +              +++y +F  +a k     ++ + i+p+ fl + +++++
  gi|313125635|ref|YP_004035905.1| 256 VDAVISNPPYSRHHELSEEYKTRVNtqieqelgcdvsaLSPMYAYFYFHAEKFLspGGRASYITPSEFL-ETNYGES 331
                                       69**********99887777665558999*******9999***********9887768899********.99***** PP

                            Eco57I  65 frekllkdkklkklvefedsk.evFkdveikggil 98 
                                       +++ l ++ +l+ lv f   +  vF+++ ++  ++
  gi|313125635|ref|YP_004035905.1| 332 LKQYLTNEFNLNALVLFDRDEdSVFSEAMTTSLVS 366
                                       ****************9765516888876655444 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.3e-07   0.00058      22     134 ..     171     268 ..     151     287 .. 0.74
   2 ?   -1.6   0.0      0.69   1.8e+03     140     169 ..     293     322 ..     290     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.3e-07
                                       HHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHH.HH--EEEEES-HHHHHHHHHHHH CS
                           UPF0020  22 rlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeear.aelklygsDldrrvvqgareNae 97 
                                       + + ++ +++ lDP  G G++   a                   k++++ +     + + g+Dl++ ++  + + ++
  gi|313125635|ref|YP_004035905.1| 171 TWCVQESTDTVLDPGVGAGALSAPA------------------YKRKLKLSSDaSLATMHGIDLNELALVMGATTLR 229
                                       5555555555555544444433221..................3444555555345559****************** PP

                                       HTT-GGGEEEEE--GGG--..STTS---EEEE------- CS
                           UPF0020  98 kagvgdliefsqadaakLr..lkegevdvivtnpPYGer 134
                                           g+  ++++ d+ +L     ++evd++++npPY + 
  gi|313125635|ref|YP_004035905.1| 230 LLDHGGPHNLQTGDFLELSpeDIDAEVDAVISNPPYSRH 268
                                       *******************865566***********875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.69
                                       HHHHHHHHHHHHHHHH-TT..-EEEEEESS CS
                           UPF0020 140 alekLYseflrelkrvlrgggrlvlltsen 169
                                       al  +Y  f   +++ l+ ggr+ ++t+++
  gi|313125635|ref|YP_004035905.1| 293 ALSPMYAYFYFHAEKFLSPGGRASYITPSE 322
                                       67789999*****************99875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   6.1e-08   0.00016      29     120 ..     175     278 ..     166     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.1e-08
                                       CCTCSEEEEET-TTSHHHHHHHHHTTC.....E...EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST.. CS
                               MTS  29 kelsgkvlDlGcGaGvlgaalakespe....ae...vtlvdvdarAlesakenleankle..vevvasdvleeve.. 94 
                                       +e +++vlD G GaG+l+a + k++ +    a+   ++ +d +  Al +  ++l+  ++    ++ + d le  +  
  gi|313125635|ref|YP_004035905.1| 175 QESTDTVLDPGVGAGALSAPAYKRKLKlssdASlatMHGIDLNELALVMGATTLRLLDHGgpHNLQTGDFLELSPed 251
                                       446778*************9877653311113321267789999999999999887666666999999999866534 PP

                                       .TS-EEEEEE---STTTCHCHHHHHHH CS
                               MTS  95 .ekkfdlivsNPPfhagkatelavaee 120
                                        ++++d+++sNPP+ ++++ +++  ++
  gi|313125635|ref|YP_004035905.1| 252 iDAEVDAVISNPPYSRHHELSEEYKTR 278
                                       4689**********9999877766555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05     0.026       3     113 ..     177     321 ..     175     356 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelae...elgpkae...vvGiDiseeaielArenaqklgld.nveFeqgdieelekl.le 71 
                                       ++ +vlD+G G+G+l+  +++   +l ++a    ++GiD +e a+    + ++ l      +++ gd+ el+   + 
  gi|313125635|ref|YP_004035905.1| 177 STDTVLDPGVGAGALSAPAYKrklKLSSDASlatMHGIDLNELALVMGATTLRLLDHGgPHNLQTGDFLELSPEdID 253
                                       7789*****************9986666665666********998777775554444446788999**997644344 PP

                   Methyltransf_31  72 dekfDlilsn.......................evl.naladpdkile....eiervlkpggilliedpr 113
                                        + +D ++sn                       e l ++++++   +      +e+ l+pgg+    +p+
  gi|313125635|ref|YP_004035905.1| 254 -AEVDAVISNppysrhhelseeyktrvntqieqE-LgCDVSALSPMYAyfyfHAEKFLSPGGRASYITPS 321
                                       .999999999777666666666666555555542.13444444444445555777777777776666665 PP

>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.3e-05     0.034      20     120 .]     556     669 ..     544     669 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                            TaqI_C  20 Yldlikkklkneka.......kelfe....ekpKilvrdisk.kldaaydekayyvlntlylliakdelev.slkyl 83 
                                       Yl++  +k  ++++       + ++     +   ilv  +s+   +++++e +   ln+l+ ++ + +l++ + k l
  gi|313125635|ref|YP_004035905.1| 556 YLKYGMSKNVEAHDsylarnrDPWYVvdrrDPAPILVTYMSRgGCRFILNETESRNLNNLHSIYLNVDLDTdEMKSL 632
                                       7777777766666634444433444477777777888888876899****************9999999861579** PP

                            TaqI_C  84 lgiLNSklikfyykkiystlrggysrlkrkeleklPi 120
                                       l++LNS   +  ++   +t ++g+ ++ ++el++ P+
  gi|313125635|ref|YP_004035905.1| 633 LAYLNSGFADDVVRRSGRTYSTGMDKIEPNELQSVPV 669
                                       ***********************************98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         7   1.8e+04      40      59 ..      69      88 ..      65     107 .. 0.64
   2 ?   13.1   0.0   4.8e-05      0.12       1      71 [.     181     262 ..     181     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7
                                      HHHHTTTTEEEEESBCCGBS CS
                   Methyltransf_25 40 raeeeglnvefvqgdaedlp 59
                                      +++++ +n +f + da+d  
  gi|313125635|ref|YP_004035905.1| 69 HYQKNTPNTSFNELDASDAR 88
                                      55556666666666665543 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.8e-05
                                       EEEET-TTSHHHHHHHCT.......STSSEEEEEESSHHHHHHHHHHHHH..TTTTEEEEESBCCGBS..SSTTTEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakr.......lgkakvtgvDiseemleaareraee..eglnvefvqgdaedlp..fedgsfD 66 
                                       vLd G G G l++ + kr        + a+++g+D++e +l   ++ ++   +g   ++++gd+ +l+    d+++D
  gi|313125635|ref|YP_004035905.1| 181 VLDPGVGAGALSAPAYKRklklssdASLATMHGIDLNELALVMGATTLRLldHGGPHNLQTGDFLELSpeDIDAEVD 257
                                       8***********9999995544333137999*********998888776633555***********98334688*** PP

                                       EEEEE CS
                   Methyltransf_25  67 lvvss 71 
                                       +v+s+
  gi|313125635|ref|YP_004035905.1| 258 AVISN 262
                                       ***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 4032.98
//
Query:       gi|313125636|ref|YP_004035906.1|  [L=54]
Description: hypothetical protein Hbor_08650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-05   26.1   0.0    1.3e-05   25.9   0.0    1.1  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
      0.044   13.8   0.1      0.045   13.8   0.1    1.0  1  IBD           Transcription-initiator DNA-binding domain IBD


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.5e-09   1.3e-05       1      32 [.      11      42 ..      11      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.5e-09
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLle 32
                                      K+I + +++Y++L++  + geSF+d+I+r+l+
  gi|313125636|ref|YP_004035906.1| 11 KSIKVYESTYDRLQSHGNMGESFDDLINRILD 42
                                      89***************************997 PP

>> IBD  Transcription-initiator DNA-binding domain IBD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     5e-06     0.045       3      49 ..       5      52 ..       3      54 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-06
                                      ..HHHHHCS-HHHHHHHHS-S-SSGGGSHHHHHHHHHHHHTT-HH... CS
                               IBD  3 d.keeymslrksisssstknsrnkkksrFkeklenilkyterhpeddw 49
                                      d +e+y s++ + s++ + +s+++  ++F++ ++ il++ e++p d +
  gi|313125636|ref|YP_004035906.1|  5 DeREKYKSIKVYESTYDRLQSHGNMGESFDDLINRILDIYENGPTDTE 52
                                      54789***************************************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 329.08
//
Query:       gi|313125637|ref|YP_004035907.1|  [L=316]
Description: xami restriction endonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-15   55.2   0.1    1.2e-14   54.7   0.1    1.1  1  RE_XamI   XamI restriction endonuclease


Domain annotation for each model (and alignments):
>> RE_XamI  XamI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   6.4e-19   1.2e-14       2     228 ..      51     264 ..      50     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 6.4e-19
                           RE_XamI   2 dltnitpdvlrqspeiLptlRmlacPPiarDrLiglaevskslvksleeekrlkkrmeaakldeelrkvaeiilrla 78 
                                       ++ +i+++ +r+ p i+ +lR+l  P i++ +  ++a+v +   ++ e e  l +  +     + ++ +a+     +
  gi|313125637|ref|YP_004035907.1|  51 NFRDIEKEDIREDPRIVRILRYLVKPKISQMKFGQFAGVNS--TNNYE-EYTLAEASTP--NHQIAQDLADFTAANL 122
                                       78899*********************************644..45666.5555544444..34556778899999** PP

                           RE_XamI  79 DrdiFtWleeerepteaeieraavivadrLlgavadpiirnaqerRqlaaiksyLesrGyrevpag.kavrfdemkP 154
                                       D+++ +Wl+  +  +e+eie +   + d++    a    rn ++ +q++++++ L+  Gy+    + k+ + + +  
  gi|313125637|ref|YP_004035907.1| 123 DPEKVPWLSDPTIDEEEEIEYSRRWICDKIAEQEATTHYRNWRKDKQEQTVAEMLDDAGYTDSGYSgKISSTNDIPV 199
                                       *************************************************************9876505455566655 PP

                           RE_XamI 155 gtfsFrlnvpveedGekvnikvDvvvrlldarkGdlllliEaksagdftnsnkRrkeeAakkaqlrityGnave 228
                                       gt  +  +++v   G  v  k+D +vr+++      +++iEak+ g   +s kR ke   k ++ + ++  a +
  gi|313125637|ref|YP_004035907.1| 200 GT--YAEESKV--AGADV-QKADFIVRPTEDT----VIFIEAKAIGVRVDSHKRVKEIRNKASDWKDEFEGAET 264
                                       55..6789999..66663.49*******9988....********************999999888888755444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1766.57
//
Query:       gi|313125638|ref|YP_004035908.1|  [L=487]
Description: replication factor c large subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-11   42.7   0.2    3.8e-10   40.3   0.0    2.3  2  AAA              ATPase family associated with various cellul
      6e-06   26.1   0.9    1.2e-05   25.1   0.9    1.5  1  AAA_30           AAA domain
    1.6e-05   24.7   0.0    2.9e-05   23.9   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00017   21.9   0.0    0.00092   19.5   0.0    2.1  1  AAA_22           AAA domain
    0.00033   21.2   0.1      0.052   14.1   0.0    2.7  2  AAA_18           AAA domain
    0.00053   20.4   0.1     0.0014   19.0   0.1    1.9  1  AAA_16           AAA ATPase domain
    0.00059   20.1   0.0     0.0018   18.6   0.0    1.9  1  AAA_28           AAA domain
     0.0032   17.8   2.4     0.0042   17.4   0.2    2.4  2  AAA_assoc_2      AAA C-terminal domain
     0.0033   17.6   0.1      0.017   15.3   0.0    2.1  2  AAA_33           AAA domain
     0.0067   16.2   0.0      0.013   15.2   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0091   16.0   0.0      0.025   14.6   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.026   13.8   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.013   15.5   0.0      0.031   14.3   0.0    1.7  1  AAA_14           AAA domain
      0.015   14.9   0.6       0.46   10.0   0.1    2.7  2  AAA_25           AAA domain
      0.015   15.2   0.0      0.026   14.5   0.0    1.4  1  Rad17            Rad17 P-loop domain
       0.02   15.3   0.0       0.05   14.0   0.0    1.8  1  RNA_helicase     RNA helicase
      0.021   14.6   0.0      0.037   13.8   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.024   14.6   0.0       0.29   11.0   0.0    2.2  2  NACHT            NACHT domain
      0.038   14.3   0.1      0.085   13.1   0.1    1.6  1  Hydin_ADK        Hydin Adenylate kinase-like domain
       0.15   11.9   0.0       0.28   11.1   0.0    1.3  1  RsgA_GTPase      RsgA GTPase
       0.18   11.6   0.0       0.35   10.7   0.0    1.4  1  AAA_3            ATPase family associated with various cellul


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   4.5e-13   3.8e-10       1      74 [.      40     122 ..      40     165 .. 0.77
   2 ?   -1.4   0.0       3.5     3e+03      38      57 ..     405     424 ..     386     428 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 4.5e-13
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SS....STTHHHHHHHHHHHHHHHTS....TSEEEEEETGG CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsell.sk....yvgesekkirelfkeakeka....kpsilfiDEid 68 
                                       v+l+G pG+GKT++a+a+a+++g e +e+++s+ +  +    + g +++++    ++a   +    +   +++DE+d
  gi|313125638|ref|YP_004035908.1|  40 VVLHGAPGVGKTSAAHALANDMGWETVELNASDQRtADvierFAGRAAMNTTLAGASAGDANgereGRQLVIMDEAD 116
                                       689*******************************9555555555555555555555554444888666********* PP

                                       GHHHHH CS
                               AAA  69 alaksr 74 
                                       +++++ 
  gi|313125638|ref|YP_004035908.1| 117 NIHGNY 122
                                       **9987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                                       STTHHHHHHHHHHHHHHHTS CS
                               AAA  38 yvgesekkirelfkeakeka 57 
                                         ge+ +k++ ++++a+e++
  gi|313125638|ref|YP_004035908.1| 405 GSGETTNKVQSIVEDAREMR 424
                                       67999999999999999875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.9   1.4e-08   1.2e-05      17     124 ..      36     146 ..      29     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.4e-08
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepg.tll 92 
                                       ++  +vl+G++G GKt a  al++ +    ++v + A+ ++ A+v+++ +g +a+++     + ++++  ++g +l+
  gi|313125638|ref|YP_004035908.1|  36 HREAVVLHGAPGVGKTSAAHALANDMGW--ETVELNASDQRTADVIERFAGRAAMNTTLAGASAGDANGEREGrQLV 110
                                       56789************99888766554..5799**************99999998887776666434444445*** PP

                            AAA_30  93 ivDEagmv....dtkqlaallkaaekagakvilvGD 124
                                       i DEa  +    d   + a+++ ++k++  ++l+  
  gi|313125638|ref|YP_004035908.1| 111 IMDEADNIhgnyDRGGAGAITRLVKKSNQPIVLIAN 146
                                       *****8776666888899999999998888888765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.4e-08   2.9e-05       2      61 ..       9      65 ..       8      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.4e-08
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl 61
                                      rP++l+e  g +k ++ l+   e  k+ +++ + v+l+G+PG+Gkt+ a+ +a+++g + 
  gi|313125638|ref|YP_004035908.1|  9 RPSTLAEVRGNNKARDALA---EWGKTWDDHREAVVLHGAPGVGKTSAAHALANDMGWET 65
                                      9**************9986...678888999999**********************9653 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.1e-06   0.00092       4     117 ..      36     135 ..      33     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelle 80 
                                       ++  +v++G +G+GKT  +  l++           + e+v+ +++ + + +d+ ++++           +++ +  +
  gi|313125638|ref|YP_004035908.1|  36 HREAVVLHGAPGVGKTSAAHALANDM---------GWETVELNASDQRT-ADVIERFAGRAA---M---NTTLAGAS 96 
                                       77899*******************97.........88988888888883.333333333333...3...48888889 PP

                            AAA_22  81 aleqalraravielliiDEaqhlr.s.....eealeeLrslln 117
                                       a   + ++ ++ +l+i DEa+++  +     + a++ L   ++
  gi|313125638|ref|YP_004035908.1|  97 AGDANGEREGR-QLVIMDEADNIHgNydrggAGAITRL---VK 135
                                       99999999999.**********9551443445555555...33 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   6.1e-05     0.052       1      24 [.      40      63 ..      40     146 .. 0.79
   2 ?    4.5   0.0     0.056        48      25      95 ..     173     256 ..     151     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf 24
                                      ++l G+pGvGKt+ a++L++ +g 
  gi|313125638|ref|YP_004035908.1| 40 VVLHGAPGVGKTSAAHALANDMGW 63
                                      6899**************987644 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.056
                            AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenss...............aleegknl..vidghla 84 
                                       + +lrd+++++g++++ d+   d+  + + + l ++++ l+++++               + + g  l  +id++l 
  gi|313125638|ref|YP_004035908.1| 173 VPVLRDILRKEGIEFDSDAL--DRIAETNSGDLRSAVKDLQAAADgadrltvedvvtgsrDKAIG--LfeYIDSVLK 245
                                       56799***************..********99999999999998877777777776664333333..2336666666 PP

                            AAA_18  85 eleseaakdik 95 
                                       e    +a++  
  gi|313125638|ref|YP_004035908.1| 246 EDTAQDAIQSA 256
                                       66555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.6e-06    0.0014      18      91 ..      32      97 ..      18     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.6e-06
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaes 91
                                      ++ ++r e+v+l+G++GvGK+s + +l++ +  +   +++ ++ +     + + +++ +a +  ++  l+ a++
  gi|313125638|ref|YP_004035908.1| 32 TWDDHR-EAVVLHGAPGVGKTSAAHALANDMGWE---TVELNASDQ----RTADVIERFAGRAAMNTTLAGASA 97
                                      555666.89***************9999755433...455555554....113366666665655555555444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.1e-06    0.0018       2      28 ..      40      67 ..      39     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvvp 28
                                      +v+ G+++ GKT+ + aLa++ g+++v+
  gi|313125638|ref|YP_004035908.1| 40 VVLHGAPGVGKTSAAHALANDmGWETVE 67
                                      9******************987**9995 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       9.7   8.3e+03      13      23 ..      90     100 ..      77     125 .. 0.78
   2 !   17.4   0.2   4.9e-06    0.0042       3      56 ..     183     254 ..     181     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.7
                                       XXXXXXXXXXX CS
                       AAA_assoc_2  13 ealaeladGDa 23 
                                       ++la ++ GDa
  gi|313125638|ref|YP_004035908.1|  90 TTLAGASAGDA 100
                                       56777777776 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.9e-06
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...................XXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak..................egkieitledleealq 56 
                                       + +++++dal+ +ae+ +GD R+a + L++aa+ a++                     + +++++++++a+q
  gi|313125638|ref|YP_004035908.1| 183 EGIEFDSDALDRIAETNSGDLRSAVKDLQAAADGADRLtvedvvtgsrdkaiglfeYIDSVLKEDTAQDAIQ 254
                                       5799****************************9998656666666655555555443344455555555554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-05     0.017       2      32 ..      40      70 ..      40     161 .. 0.80
   2 ?   -0.8   0.1       1.8   1.5e+03      29      82 ..     292     342 ..     280     367 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt 32
                                      v+l+G+pG+GK+  a+ l++  g+++++ ++
  gi|313125638|ref|YP_004035908.1| 40 VVLHGAPGVGKTSAAHALANDMGWETVELNA 70
                                      799********************99988776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                            AAA_33  29 ssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsr 82 
                                       + d+++ r+ +t++ s   +  ++d++ + + + ar + + g++    a+++s 
  gi|313125638|ref|YP_004035908.1| 292 NADVWLGRVMATQDYSY--WRYATDNVAAGV-AAARNRTRGGWTQYGGAPYRST 342
                                       56788888887755444..444667777777.7777777777776666666663 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.5e-05     0.013      40      70 ..      30      60 ..      14      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                         IstB_IS21 40 tlsfiekkenivllGpsGvGKshlaialgve 70
                                      +  + +++e++vl G +GvGK+  a al+ +
  gi|313125638|ref|YP_004035908.1| 30 GKTWDDHREAVVLHGAPGVGKTSAAHALAND 60
                                      578999******************9999865 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.9e-05     0.025       2      41 ..      40      79 ..      39     121 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-05
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHH CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedl 41
                                      v+L G+pG+gK++ a  la  +++e+++ + +++ t++ +
  gi|313125638|ref|YP_004035908.1| 40 VVLHGAPGVGKTSAAHALANDMGWETVELNASDQRTADVI 79
                                      89***********************999988887666544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05     0.026      14      56 ..      35      75 ..      24      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                        Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                                      ++  +++l G+pG GK+++a++l++++  + + v+l++ d R+
  gi|313125638|ref|YP_004035908.1| 35 DHREAVVLHGAPGVGKTSAAHALANDM--GWETVELNASDQRT 75
                                      566899*********************..89999999988776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.6e-05     0.031       2      88 ..      37     135 ..      36     165 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-05
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk.ladpe..kllelileklke..........ekk 65 
                                       r+++v+ Ga  vGKT  ++ l+++      +++++n  d+r+++ ++ ++    ++  l+   +          e++
  gi|313125638|ref|YP_004035908.1|  37 REAVVLHGAPGVGKTSAAHALANDMG---WETVELNASDQRTADvIERFAgrAAMNTTLA---GasagdangerEGR 107
                                       6799******************9988...9999999999999552333323322233333...1233567789999* PP

                            AAA_14  66 tylflDEiqev.....pewekalkslvd 88 
                                       +++++DE+ ++     ++   a+ +lv+
  gi|313125638|ref|YP_004035908.1| 108 QLVIMDEADNIhgnydRGGAGAITRLVK 135
                                       ********99944444444445555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00054      0.46      28      56 ..      32      60 ..       7      69 .. 0.78
   2 ?    2.1   0.0      0.14   1.2e+02     139     171 ..     103     136 ..      71     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                            AAA_25 28 gllpagelallaGapgtGKttlaldlala 56
                                       +    e ++l Gapg+GKt +a  la +
  gi|313125638|ref|YP_004035908.1| 32 TWDDHREAVVLHGAPGVGKTSAAHALAND 60
                                      455667899**************999865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                            AAA_25 139 evegvrlvviDplsralgg.densnsdvgalvea 171
                                       e+eg +lv+ D  + ++g+ d   + ++++lv++
  gi|313125638|ref|YP_004035908.1| 103 EREGRQLVIMDEADNIHGNyDRGGAGAITRLVKK 136
                                       448899*************999999999999987 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     3e-05     0.026       8      75 ..       3      67 ..       1      93 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
                             Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75
                                       W eky+P +++e+    k  +++ ew k+    ++    +++ G +G gk+ + + L+  +g +  e
  gi|313125638|ref|YP_004035908.1|  3 DWTEKYRPSTLAEVRGNNKARDALAEWGKTWDDHRE---AVVLHGAPGVGKTSAAHALANDMGWETVE 67
                                      6*****************99*******998754444...7889*****************99988776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.9e-05      0.05       1      25 [.      40      64 ..      40     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      ++l+G++g+GK+++a+ La+++  +
  gi|313125638|ref|YP_004035908.1| 40 VVLHGAPGVGKTSAAHALANDMGWE 64
                                      689*****************99843 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.3e-05     0.037       2      75 ..      41     119 ..      40     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts....liltvnrptaelltegk..pklpnlsvrtvdsflmalvkstkgkililDEyl 72 
                                       v hG+pG GK+++   l+++     + l+++ ++++++ e++    + n +  ++ +   +  +  + +++i+DE+ 
  gi|313125638|ref|YP_004035908.1|  41 VLHGAPGVGKTSAAHALANDMgwetVELNASDQRTADVIERFagRAAMNTTLAGASAGDANGER-EGRQLVIMDEAD 116
                                       89*****************999999888888888999999986544444444444433333333.468899999986 PP

                   Viral_helicase1  73 llh 75 
                                         h
  gi|313125638|ref|YP_004035908.1| 117 NIH 119
                                       655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.29       3      25 ..      40      62 ..      38      73 .. 0.84
   2 ?    1.0   0.0      0.42   3.6e+02      78     127 ..     103     145 ..      99     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                                      EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                      v+l+G++G+GKT  ++ la ++ 
  gi|313125638|ref|YP_004035908.1| 40 VVLHGAPGVGKTSAAHALANDMG 62
                                      89****************98765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.42
                                       CSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEE CS
                             NACHT  78 elperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltv 127
                                       e++ r L i+D +D ++   +          +++l++k   ++ +++l++
  gi|313125638|ref|YP_004035908.1| 103 EREGRQLVIMDEADNIHGNYDR----GGAGAITRLVKK---SNQPIVLIA 145
                                       578899**********996666....777777777777...555555554 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.9e-05     0.085       1      22 [.      39      60 ..      39      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                         Hydin_ADK  1 aiivhGaPlsGKtatavtLakk 22
                                      a+++hGaP  GKt++a +La  
  gi|313125638|ref|YP_004035908.1| 39 AVVLHGAPGVGKTSAAHALAND 60
                                      89*****************976 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032      0.28      81     136 ..      17      74 ..       2      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                                       E--TTTHTTHHHHHHHCTT..SEEEEECSTTSSHHHHHHHHCTT-----S-------- CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd..ktsvlvGqSGvGKStLinallpelelktgevseklgr 136
                                         ++k +++l+e  + ++d  + +vl G  GvGK++   al++++  +t e+ ++++r
  gi|313125638|ref|YP_004035908.1|  17 RGNNKARDALAEWGKTWDDhrEAVVLHGAPGVGKTSAAHALANDMGWETVELNASDQR 74 
                                       555566666666666666655789********************99999999888776 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00041      0.35       2      30 ..      40      68 ..      39      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                             AAA_3  2 vllegvPGlaktllvkalakaldlefkri 30
                                      v+l+g+PG++kt +++ala+ ++ e   +
  gi|313125638|ref|YP_004035908.1| 40 VVLHGAPGVGKTSAAHALANDMGWETVEL 68
                                      789*****************998776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3021.01
//
Query:       gi|313125639|ref|YP_004035909.1|  [L=243]
Description: amino acid ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-35  120.7   0.0    8.1e-35  120.3   0.0    1.1  1  ABC_tran     ABC transporter
      3e-10   40.4   0.0    0.00015   21.7   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    5.4e-09   35.8   0.0    2.3e-05   23.9   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    3.9e-05   24.1   0.1      6e-05   23.5   0.1    1.4  1  AAA_16       AAA ATPase domain
    0.00012   21.7   0.0    0.00025   20.7   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00044   20.0   0.0     0.0007   19.4   0.0    1.5  1  AAA_30       AAA domain
    0.00073   19.8   0.1     0.0023   18.2   0.1    1.9  1  AAA_22       AAA domain
     0.0018   17.1   0.0        1.8    7.3   0.1    2.9  2  ABC_ATPase   Predicted ATPase of the ABC class
     0.0022   17.9   0.0     0.0037   17.2   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.025   14.7   0.0    1.4  1  CSD2         Cold shock domain
      0.015   15.2   0.0      0.063   13.2   0.0    1.8  2  ATPase_2     ATPase domain predominantly from Archaea
      0.018   15.6   0.0      0.028   14.9   0.0    1.3  1  AAA_23       AAA domain
      0.023   14.9   0.0      0.033   14.3   0.0    1.4  1  AAA_33       AAA domain
       0.04   14.3   0.4          1    9.8   0.1    2.7  2  AAA          ATPase family associated with various cellular a
      0.044   13.0   0.0        0.2   10.8   0.0    1.8  2  NB-ARC       NB-ARC domain
      0.055   13.1   0.1       0.13   11.8   0.0    1.7  2  AAA_27       AAA domain
      0.059   13.1   0.0        0.1   12.3   0.0    1.3  1  AAA_15       AAA ATPase domain
      0.066   12.8   0.0        0.2   11.2   0.0    1.7  2  AAA_25       AAA domain
      0.071   13.1   0.1          4    7.4   0.0    2.4  2  AAA_5        AAA domain (dynein-related subfamily)
       0.08   12.8   0.0       0.19   11.6   0.0    1.6  2  Rad17        Rad17 P-loop domain
      0.082   12.0   0.0       0.14   11.2   0.0    1.3  1  T2SSE        Type II/IV secretion system protein
       0.11   13.0   0.0        0.2   12.2   0.0    1.6  1  AAA_18       AAA domain
       0.13   11.9   0.0       0.27   10.8   0.0    1.5  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.13   12.2   0.0       0.22   11.4   0.0    1.3  1  NACHT        NACHT domain
       0.15   11.5   0.0         10    5.5   0.0    2.2  2  TniB         Bacterial TniB protein
       0.16   11.7   0.0       0.32   10.7   0.0    1.5  1  IstB_IS21    IstB-like ATP binding protein
       0.16   12.2   0.3        2.4    8.5   0.3    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.17   10.7   0.0       0.53    9.0   0.0    1.7  2  Adeno_IVa2   Adenovirus IVa2 protein
       0.21   11.3   0.0       0.36   10.5   0.0    1.3  1  AAA_24       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0   1.3e-37   8.1e-35       1     137 []      20     168 ..      20     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 1.3e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpelt 75 
                                       lknvsl+++e e+ ++vG++G+GKStLl++  +l++ + Gei+ldg +l++   + ++lr++ig+++q  +lfp++t
  gi|313125639|ref|YP_004035909.1|  20 LKNVSLDIEETEVCVVVGPSGSGKSTLLRCANRLEEIQGGEIRLDGIPLSDpnADVNFLRQRIGMVFQSFNLFPHKT 96 
                                       79*************************************************9999********************** PP

                                       HHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + en              e++++ e++l+++gl    ++     p++LSgGq+qrva+aral+ +pk++l+DE t+
  gi|313125639|ref|YP_004035909.1|  97 ALENvtlaprkvrgldanEARARGEELLERVGLGAQMNSY----PNQLSGGQQQRVAIARALAMDPKVMLFDEVTS 168
                                       ***************99999999*********99955555....5****************************985 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.6e-06    0.0035       3      24 ..      34      55 ..      32      87 .. 0.78
   2 !   21.7   0.0   2.4e-07   0.00015     233     297 ..     136     197 ..      67     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.6e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                      v++Gp gsGKS+LL++   l  
  gi|313125639|ref|YP_004035909.1| 34 VVVGPSGSGKSTLLRCANRLEE 55
                                      89**************998843 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.4e-07
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                        +++lS G+++  a++ al+ ++   ++ l+DE+ + L+P+l+ ++le++  l+++g   +++TH
  gi|313125639|ref|YP_004035909.1| 136 YPNQLSGGQQQRVAIARALAMDP---KVMLFDEVTSALDPELVGEVLEVMGTLADEGMTMMVVTH 197
                                       46788*****9999999999999...9***********************777777888888888 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00066      0.41      24      41 ..      30      47 ..       8      51 .. 0.81
   2 !   23.9   0.0   3.8e-08   2.3e-05     132     208 ..     135     209 ..      76     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00066
                                      SSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnll 41
                                      +++ ++vGp GSGKs ll
  gi|313125639|ref|YP_004035909.1| 30 TEVCVVVGPSGSGKSTLL 47
                                      46889**********987 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.8e-08
                                       -STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.x RF
                             SMC_N 132 iskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemleka.d 206
                                        ++++LSgG+++ va+a  +A+    p+ ++l+De+ +aLD + v +v e++ +  ++ + ++v++++ ++ +++ d
  gi|313125639|ref|YP_004035909.1| 135 SYPNQLSGGQQQRVAIARALAMD---PK-VMLFDEVTSALDPELVGEVLEVMGTLADEgMTMMVVTHEMGFAREVgD 207
                                       34569************999875...44.679*********************98877799******9998877645 PP

                                       CE CS
                                       xx RF
                             SMC_N 207 kl 208
                                       ++
  gi|313125639|ref|YP_004035909.1| 208 RI 209
                                       54 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   9.7e-08     6e-05      23      52 ..      29      74 ..      17     187 .. 0.58

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 9.7e-08
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd.................g 52
                                      ++e+++++G+sG+GKs+l+r++ r le+                  +
  gi|313125639|ref|YP_004035909.1| 29 ETEVCVVVGPSGSGKSTLLRCANR-LEEIqggeirldgiplsdpnaD 74
                                      5599****************9996.3332233333333333333330 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.1e-07   0.00025      13      39 ..      21      47 ..      16      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.1e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      ++ +++i++ ++++++GpsGsGKSTll
  gi|313125639|ref|YP_004035909.1| 21 KNVSLDIEETEVCVVVGPSGSGKSTLL 47
                                      56778888888***************8 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-06    0.0007      17      80 ..      29      96 ..      24     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvi..glAptgkaAkv..Laeelgieastiakllkrl 80
                                      +  v+v++Gp G+GK+t+l+ ++++ e +gg++   g+  +   A+v  L++ +g+  ++ + + +++
  gi|313125639|ref|YP_004035909.1| 29 ETEVCVVVGPSGSGKSTLLRCANRLEEIQGGEIRldGIPLSDPNADVnfLRQRIGMVFQSFNLFPHKT 96
                                      45699**********************99866653344444444444446666666555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.7e-06    0.0023       5      32 ..      30      57 ..      26     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldee 32
                                        ++vv+G+sG+GK+tllr   +  +++
  gi|313125639|ref|YP_004035909.1| 30 TEVCVVVGPSGSGKSTLLRCANRLEEIQ 57
                                      5689**************9888876544 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0094       5.8     245     263 ..      31      49 ..      21      52 .. 0.85
   2 !    7.3   0.1    0.0029       1.8     322     353 ..     139     170 ..     131     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0094
                                       SEEEEEE-TTSSHHHHHHH CS
                        ABC_ATPase 245 GvtlIvGggfhGKsTLLeA 263
                                        v ++vG+   GKsTLL+ 
  gi|313125639|ref|YP_004035909.1|  31 EVCVVVGPSGSGKSTLLRC 49 
                                       499**************85 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0029
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAt 353
                                       + SG   q ++i++al ++ k++L+DE tsA 
  gi|313125639|ref|YP_004035909.1| 139 QLSGGQQQRVAIARALAMDPKVMLFDEVTSAL 170
                                       5699999**********************995 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.9e-06    0.0037      92     131 ..      22      62 ..      11      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.9e-06
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       +++  +++ +++v+vG+SG GKStL+   +  +e++ ge++
  gi|313125639|ref|YP_004035909.1|  22 NVSLDIEEtEVCVVVGPSGSGKSTLLRCANRLEEIQGGEIR 62 
                                       55556666699***************987776677776665 PP

>> CSD2  Cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     4e-05     0.025      42      72 ..     174     204 ..     151     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-05
                              CSD2  42 peGevievLGkkgdpgveilsilakhglpee 72 
                                       ++Gev+ev+G   d g+ ++++ ++ g+ +e
  gi|313125639|ref|YP_004035909.1| 174 LVGEVLEVMGTLADEGMTMMVVTHEMGFARE 204
                                       79*************************9765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.063      16      39 ..      26      49 ..      20      61 .. 0.81
   2 ?   -1.0   0.0       2.1   1.3e+03     121     162 ..     160     195 ..     149     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlke 39
                                      + e+ e+ ++ Gp gsGK++Ll+ 
  gi|313125639|ref|YP_004035909.1| 26 DIEETEVCVVVGPSGSGKSTLLRC 49
                                      557789***************984 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                          ATPase_2 121 iiiiDelqklidlglngaellvkeLlnliesltkekhlcvvi 162
                                       ++++De+  +     +   +lv e l+++  l  e  +++v+
  gi|313125639|ref|YP_004035909.1| 160 VMLFDEVTSAL----D--PELVGEVLEVMGTLADEGMTMMVV 195
                                       78999999999....4..778888888888877666666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.6e-05     0.028      11      38 ..      21      49 ..      12      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-05
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildA 38
                                      +++++d  +  + +++Gp G+GK+T+l++
  gi|313125639|ref|YP_004035909.1| 21 KNVSLDIeETEVCVVVGPSGSGKSTLLRC 49
                                      56666665567889*************98 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.4e-05     0.033       1      17 [.      32      48 ..      32      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.4e-05
                            AAA_33  1 lvllvGlpGsGKstlae 17
                                      + ++vG++GsGKstl++
  gi|313125639|ref|YP_004035909.1| 32 VCVVVGPSGSGKSTLLR 48
                                      6799***********87 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         6   3.7e+03      62      74 ..       5      17 ..       2      29 .. 0.76
   2 ?    9.8   0.1    0.0017         1       2      72 ..      34     171 ..      33     203 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6
                                      EEEETGGGHHHHH CS
                               AAA 62 lfiDEidalaksr 74
                                      l +DE+d+ +++ 
  gi|313125639|ref|YP_004035909.1|  5 LEFDEVDKYFGET 17
                                      5689999988776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0017
                                       EEESSTTSSHHHHHHHHHHH...................HTHEEEEEETTTCSSS...................... CS
                               AAA   2 llyGppGtGKTllakavake...................lgvefleisgsellsk...................... 37 
                                       +++Gp G GK++l +   +                    ++v+fl+     ++++                      
  gi|313125639|ref|YP_004035909.1|  34 VVVGPSGSGKSTLLRCANRLeeiqggeirldgiplsdpnADVNFLRQRIGMVFQSfnlfphktalenvtlaprkvrg 110
                                       57899999999998864333233222222222222111112334444444444336666666666666666666666 PP

                                       .........................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHH CS
                               AAA  38 .........................yvgesekkirelfkeakeka.kpsilfiDEidalak 72 
                                                                y  + +   ++ ++ a++ a +p+++++DE+ +   
  gi|313125639|ref|YP_004035909.1| 111 ldanearargeellervglgaqmnsYPNQLSGGQQQRVAIARALAmDPKVMLFDEVTSALD 171
                                       6666666667777777777777777888888888888888888888899999999987655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00033       0.2      16      48 ..      28      57 ..      17      62 .. 0.80
   2 ?   -0.3   0.0      0.81     5e+02      92     149 ..     146     207 ..     122     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                                      TTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCC CS
                            NB-ARC 16 delqslvvalvGmgGvGKttlakqilnksdeve 48
                                      +e +  v  +vG  G+GK+tl++ +++  +e++
  gi|313125639|ref|YP_004035909.1| 28 EETE--VCVVVGPSGSGKSTLLRCANRL-EEIQ 57
                                      4555..8899************998876.6665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.81
                                       HHHHHHHHCCCTTEEEEEEEE-SHHHH.....HHH....HCHTTSEEEEEESBCCCCCCS-S CS
                            NB-ARC  92 lkrklvrlLltkrfllvlDDVweeedwdkigvvlp....arenrlrvllTTRdeevanavsa 149
                                           + r+L     ++++D V    d + +g vl       ++++ +++ T ++  a +v++
  gi|313125639|ref|YP_004035909.1| 146 QRVAIARALAMDPKVMLFDEVTSALDPELVGEVLEvmgtLADEGMTMMVVTHEMGFAREVGD 207
                                       56678888988888999999988877444444443111135677778887777777777665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.13      19      48 ..      23      52 ..      12      54 .. 0.80
   2 ?   -2.7   0.1       5.8   3.6e+03     124     142 ..     110     128 ..     106     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisd 48
                                      ++++ ee+++ +++Gp  +GKst+lr  ++
  gi|313125639|ref|YP_004035909.1| 23 VSLDIEETEVCVVVGPSGSGKSTLLRCANR 52
                                      44445599*****************98766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.8
                            AAA_27 124 gLdherLreGGealleaeg 142
                                       gLd+++ r+ Ge+lle  g
  gi|313125639|ref|YP_004035909.1| 110 GLDANEARARGEELLERVG 128
                                       8999999999999998766 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017       0.1      14      41 ..      20      48 ..      19     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsile 41
                                      lk+v++d++e  + v++G+ +sGKS++l+
  gi|313125639|ref|YP_004035909.1| 20 LKNVSLDIEETeVCVVVGPSGSGKSTLLR 48
                                      7999****999899*************97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033       0.2      30      50 ..      27      47 ..       9      50 .. 0.88
   2 ?   -1.5   0.0       2.5   1.6e+03     134     155 ..     151     170 ..     100     198 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + + e+++++G++g+GK+tl+
  gi|313125639|ref|YP_004035909.1| 27 IEETEVCVVVGPSGSGKSTLL 47
                                      67899**************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                            AAA_25 134 eaaieevegvrlvviDplsral 155
                                       ++a+    ++++  +D +++al
  gi|313125639|ref|YP_004035909.1| 151 ARALAM--DPKVMLFDEVTSAL 170
                                       333333..44555555544444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0065         4       3      17 ..      34      48 ..      32      57 .. 0.85
   2 ?    3.5   0.0       0.1        64      64     104 ..     152     200 ..     114     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0065
                                      EEE--SSSSHHHHHH CS
                             AAA_5  3 lLvGppGtgKselae 17
                                      ++vGp+G+gKs+l +
  gi|313125639|ref|YP_004035909.1| 34 VVVGPSGSGKSTLLR 48
                                      579*********987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                                       -....G-SEEEEESGGG--.HHHHHHHHHH...HHSSEEE..-SSSEEE CS
                             AAA_5  64 r....egeilvlDEverae.sevlnsLlsl...leerrllleeggelvk 104
                                       r     ++++++DEv+ a  +e ++++l +   l ++ + ++  +++++
  gi|313125639|ref|YP_004035909.1| 152 RalamDPKVMLFDEVTSALdPELVGEVLEVmgtLADEGMTMMVVTHEMG 200
                                       23346899********999899888877651113444555555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00031      0.19      34      70 ..      19      55 ..      12     103 .. 0.81
   2 ?   -1.8   0.0         4   2.5e+03     104     145 ..     131     170 ..     102     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                             Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                       lk  +L+ ++ ++ ++ GPsG gkst ++   +   
  gi|313125639|ref|YP_004035909.1| 19 VLKNVSLDIEETEVCVVVGPSGSGKSTLLRCANRLEE 55
                                      5788889999999***************997665544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4
                             Rad17 104 sqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkf 145
                                       +q++s+++  L + + +++      l  d k++l +++ +  
  gi|313125639|ref|YP_004035909.1| 131 AQMNSYPNQ-LSGGQQQRVA-IARALAMDPKVMLFDEVTSAL 170
                                       678888876.7777776666.667777788888888876655 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.14     120     149 ..      21      50 ..       5      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                             T2SSE 120 evlrkavrerglilvsGgTgsGKttllyal 149
                                       + ++  ++e  + +v G+ gsGK+tll  +
  gi|313125639|ref|YP_004035909.1|  21 KNVSLDIEETEVCVVVGPSGSGKSTLLRCA 50 
                                       5556667888999*************9543 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00032       0.2       2      25 ..      34      65 ..      33     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00032
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf........g 25
                                      ++ G++G+GK+tl +  ++++++        g
  gi|313125639|ref|YP_004035909.1| 34 VVVGPSGSGKSTLLRCANRLEEIqggeirldG 65
                                      589***********999888766654444441 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00044      0.27       2      18 ..      32      48 ..      31      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00044
                                      EEEEEESTTCCHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLln 18
                                      v v++G+ GsGK+tLl+
  gi|313125639|ref|YP_004035909.1| 32 VCVVVGPSGSGKSTLLR 48
                                      789*************8 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00036      0.22       2      18 ..      32      48 ..      31      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                                      CEEEEC-TTTCHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlq 18
                                      ++++ G++GsGK+tLl+
  gi|313125639|ref|YP_004035909.1| 32 VCVVVGPSGSGKSTLLR 48
                                      799************97 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.017        10      34      54 ..      29      49 ..       9      62 .. 0.84
   2 ?    3.9   0.0     0.048        30     105     133 ..     143     171 ..     117     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
                              TniB 34 rmpnlllvGdsnnGKtmivek 54
                                      +++ +++vG+s  GK+++++ 
  gi|313125639|ref|YP_004035909.1| 29 ETEVCVVVGPSGSGKSTLLRC 49
                                      567899***********9875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.048
                              TniB 105 skleqqvlrllrelkvrvLiiDEihnlla 133
                                        ++++ +++   +++++v+++DE+ ++l 
  gi|313125639|ref|YP_004035909.1| 143 GQQQRVAIARALAMDPKVMLFDEVTSALD 171
                                       445555566666899*********99984 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00052      0.32      44      63 ..      27      46 ..       8      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                         IstB_IS21 44 iekkenivllGpsGvGKshl 63
                                      ie+ e +v++GpsG GKs l
  gi|313125639|ref|YP_004035909.1| 27 IEETEVCVVVGPSGSGKSTL 46
                                      78999************976 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3    0.0039       2.4      63      88 ..     157     182 ..     106     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0039
                           SbcCD_C  63 alrlvfLDEAFsklDeesiatllell 88 
                                       +++++++DE  s lD+e + ++le++
  gi|313125639|ref|YP_004035909.1| 157 DPKVMLFDEVTSALDPELVGEVLEVM 182
                                       47889999999999999999999876 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00085      0.53      89     106 ..      32      49 ..       6      54 .. 0.80
   2 ?   -1.7   0.0       1.5   9.5e+02     235     255 ..     189     209 ..     186     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00085
                        Adeno_IVa2  89 iGviyGPtGsGksqllrn 106
                                       + v+ GP GsGks llr 
  gi|313125639|ref|YP_004035909.1|  32 VCVVVGPSGSGKSTLLRC 49 
                                       6799************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                        Adeno_IVa2 235 gfsvlvvlhnlnPrsdiagni 255
                                       g +++vv h++   +++++ i
  gi|313125639|ref|YP_004035909.1| 189 GMTMMVVTHEMGFAREVGDRI 209
                                       789********9999998776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00059      0.36       5      22 ..      33      50 ..      30      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00059
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++++Gpsg+GK+tl++ +
  gi|313125639|ref|YP_004035909.1| 33 CVVVGPSGSGKSTLLRCA 50
                                      799***********9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.62u 0.38s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 1344.38
//
Query:       gi|313125640|ref|YP_004035910.1|  [L=277]
Description: amino acid ABC transporter membrane protein, paat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.2e-20   71.3   3.8    8.2e-20   71.3   3.8    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.017   3.1e+02     155     178 ..      30      53 ..      10      82 .. 0.72
   2 !   71.3   3.8   4.6e-24   8.2e-20       2     182 ..      85     269 ..      84     271 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.017
                      BPD_transp_1 155 nggvlalviavlllnlvadilqrl 178
                                        g++l +++a+ +l lva+i+++ 
  gi|313125640|ref|YP_004035910.1|  30 LGASLSALFALGILGLVAYIIATQ 53 
                                       566666666666666666666654 PP

  == domain 2  score: 71.3 bits;  conditional E-value: 4.6e-24
                      BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf....vilsilghlilp.viillllsaapyvrl 70 
                                       + +Gi+++   +++ + ++ + + +i++++++P +  ++++++ +         ++++ +p +ii+l+l  a+yv  
  gi|313125640|ref|YP_004035910.1|  85 VSAGIFVGlarVSKTSLTSGIAQSYIQFFRGTPLLFQIFVIYFGIpalwPGTFPIQDWEFPtAIIALTLNHAAYVGE 161
                                       668999999999999999******************99998866699885555688899999*************** PP

                      BPD_transp_1  71 irraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailg 147
                                        +r++++s+p++++eaar lG+s++q +r v+lP+a + +++ +++  ++l+++++l+  ++       l   +++ 
  gi|313125640|ref|YP_004035910.1| 162 AVRGGINSVPEGQMEAARSLGMSYIQSMREVILPQAWRNALAAIGNDQVILVKDTSLMTVIA-------LPELIQQF 231
                                       **************************************************************.......44555555 PP

                      BPD_transp_1 148 ydyseis...nggvlalviavlllnlvadilqrlldpr 182
                                       +d++++    ++++++++ia+l +++ +  l+++l+ r
  gi|313125640|ref|YP_004035910.1| 232 RDVNSAVfdpWTPLVIVAIAYLSITIPLGKLVDHLENR 269
                                       5666555666889*************999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1557.67
//
Query:       gi|313125641|ref|YP_004035911.1|  [L=300]
Description: amino acid ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-66  224.5   1.5    1.3e-66  224.3   1.5    1.1  1  SBP_bac_3        Bacterial extracellular solute-binding prote
    5.7e-08   33.0   0.6    7.7e-07   29.3   0.3    2.6  2  Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine
    1.1e-05   25.5   0.2    1.7e-05   24.9   0.2    1.3  1  NMT1             NMT1/THI5 like
    0.00013   21.7   0.5    0.00013   21.7   0.5    2.3  3  TAT_signal       TAT (twin-arginine translocation) pathway si
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.015   14.7   0.1    1.3  1  NMT1_3           NMT1-like family
      0.029   14.0   0.0        1.5    8.4   0.0    2.1  2  OpuAC            Substrate binding domain of ABC-type glycine


Domain annotation for each model (and alignments):
>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.3   1.5   4.4e-70   1.3e-66       1     224 [.      64     299 ..      64     300 .] 0.95

  Alignments for each domain:
  == domain 1  score: 224.3 bits;  conditional E-value: 4.4e-70
                                       EEEEE-S-BTTTBEE-TTS-EESHHHHHHHHHHH.HCT-EEEEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHTTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3   1 lrvgvdadypPfsykdengeltGfdvdlakaiak.rlgvkvefvpvswdelipalksgkvDiaiaaititpeReekv 76 
                                       +++g+d  y+Pf+y++++gel+Gfdv++a+a+ + +lgv++ef+++s+d++ip+l+sg++ i+++a+ti+++R+ekv
  gi|313125641|ref|YP_004035911.1|  64 VVIGSDIPYRPFEYETTSGELKGFDVEIAQAVFEeELGVEYEFKKTSFDSIIPSLNSGRFRIIMSAMTINEKRKEKV 140
                                       689****************************988467**************************************** PP

                                       EEESESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC...TSEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  77 dFsqpyfsagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkk...gaeivefdtleealqaLkn 150
                                       dFs+pyf+a q+++++k+     ssi+s +dLkg ++gvq+g+t +++++e + +   + +++ +d++++a+qaL n
  gi|313125641|ref|YP_004035911.1| 141 DFSEPYFTAYQTVIIKKD-----SSISSKEDLKGATIGVQKGTTGASAAEELKTEfdgDLTLKKYDQIPSAFQALIN 212
                                       ****************65.....3688888**************9999888666688899999************** PP

                                       TSSSEEEEEHHHHHHHHHHCCGCCEEEE.............ECGGCECEEEEEEETTTHHHHHHHHHHHHHHHHTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 151 grvdavvadspvlaylvkknpdkkvvlv.............eeplsseeyaiavrkgdseLrkainkalaelkadgt 214
                                       g++da+v+d++v  ++++k++d  + +              + +l+ e+y+i++rk+d+e+rk++n+ala++k++gt
  gi|313125641|ref|YP_004035911.1| 213 GQIDAIVNDNTVNSEFADKRDDVVFLEGegaaaaegenappYLTLTVENYGIGFRKADDEFRKKVNEALAAVKENGT 289
                                       **************************99************************************************* PP

                                       HHHHHHHHHC CS
                                       xxxxxxxxxx RF
                         SBP_bac_3 215 lakisekWfg 224
                                       +++i+  +f+
  gi|313125641|ref|YP_004035911.1| 290 YDEIYSTYFS 299
                                       ********96 PP

>> Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine-binding site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.3   2.6e-10   7.7e-07      53     114 ..      96     158 ..      62     159 .. 0.81
   2 ?   -0.8   0.0      0.56   1.7e+03      72      91 ..     208     227 ..     199     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.6e-10
                                       TT-----BET.TTTEB-HHHHHHHTTS-SEE-SS-B--HHHHTTSEEESESEEE-EEEEEESX CS
                   Lig_chan-Glu_bd  53 edgkyGskke.kkkewnGmigellekkadlavapltitaeReevvdFtkpfmelgisilikkp 114
                                        ++++G + e kk++ + +i +l +++  ++++++ti+++R+e vdF++p+ +   +++ikk 
  gi|313125641|ref|YP_004035911.1|  96 FEEELGVEYEfKKTSFDSIIPSLNSGRFRIIMSAMTINEKRKEKVDFSEPYFTAYQTVIIKKD 158
                                       44555544331456899**************************************99999986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.56
                                       HHHHTTS-SEE-SS-B--HH CS
                   Lig_chan-Glu_bd  72 gellekkadlavapltitae 91 
                                       + l+++++d +v + t+++e
  gi|313125641|ref|YP_004035911.1| 208 QALINGQIDAIVNDNTVNSE 227
                                       5799999****999999986 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   5.5e-09   1.7e-05      74     145 ..     150     219 ..     128     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.5e-09
                                       -EEEEEECCC--SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEE CS
                              NMT1  74 lsglivlkdsgikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaai 145
                                        +++i +kds i+s +DLkG +ig++++  +    ++l  +  gd    +  +    s+++al++g++Da++
  gi|313125641|ref|YP_004035911.1| 150 YQTVIIKKDSSISSKEDLKGATIGVQKGTTGASAAEELKTEFDGDLTL-KKYDQ-IPSAFQALINGQIDAIV 219
                                       5789***********************99999999***9999994433.23333.566888*********98 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.5   4.2e-08   0.00013       2      25 ..       1      24 [.       1      25 [. 0.95
   2 ?   -3.5   1.9       3.9   1.2e+04       9      17 ..     176     184 ..     176     184 .. 0.47
   3 ?   -5.1   3.0         6   1.8e+04      16      19 ..     243     246 ..     242     246 .. 0.28

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.2e-08
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR+ LK++A++ A+++ +gc++
  gi|313125641|ref|YP_004035911.1|  1 MDRRTYLKTGAGVVAGGLIAGCTG 24
                                      79********************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.9
                        TAT_signal   9 KgsAAaaAA 17 
                                       Kg+ +a AA
  gi|313125641|ref|YP_004035911.1| 176 KGTTGASAA 184
                                       555555554 PP

  == domain 3  score: -5.1 bits;  conditional E-value: 6
                        TAT_signal  16 AAaa 19 
                                       AAaa
  gi|313125641|ref|YP_004035911.1| 243 AAAA 246
                                       3332 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   5.1e-06     0.015      92     165 ..     150     219 ..     125     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
                            NMT1_3  92 vfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesadalkdgqldgaa 165
                                       + +++++kds i+s +dlkg +++v  ++ +t +sa + l++    + dl+l ++ +   + +al +gq+d+++
  gi|313125641|ref|YP_004035911.1| 150 YQTVIIKKDSSISSKEDLKGATIGV--QKGTTGASAAEELKTEF--DGDLTLKKYDQIPSAFQALINGQIDAIV 219
                                       4456689*************87655..55666666666666444..3566666787899999*********987 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.012        36      18     113 ..      90     172 ..      87     195 .. 0.71
   2 ?    8.4   0.0    0.0005       1.5      34      63 ..     198     247 ..     181     298 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.012
                                       HHHHHHHHHT.TEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEEEEEEESEEECEEEEEE CS
                             OpuAC  18 eilkqllekk.GykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkglevlgplgagnteglavp 93 
                                       ei+++++e+  G++ e  + +  ++++ +l sG + ++++      + +++++ +ek +    ++ ++ ++++++++
  gi|313125641|ref|YP_004035911.1|  90 EIAQAVFEEElGVEYEFKKTSF-DSIIPSLNSGRFRIIMS------AMTINEKRKEKVDF---SEPYFTAYQTVIIK 156
                                       6888888888888666666666.66899999999999993......33455655544444...47899999999999 PP

                                       HHHHHHHTTTBHHHHCTHHG CS
                             OpuAC  94 kyvaekygiksisDLkkpae 113
                                       k+      i+s +DLk    
  gi|313125641|ref|YP_004035911.1| 157 KDS----SISSKEDLKGATI 172
                                       996....9999999987776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0005
                                       EEEESHHHHHHHHHTTSSSEEEEEEHHHH....................H CS
                             OpuAC  34 tnlgstavlfaalasGdiDvypeewtgta....................y 63 
                                        + ++ +++f+al +G+iD+++++ t ++                    +
  gi|313125641|ref|YP_004035911.1| 198 KKYDQIPSAFQALINGQIDAIVNDNTVNSefadkrddvvflegegaaaaE 247
                                       556677889*************7777665444444444444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1805.49
//
Query:       gi|313125642|ref|YP_004035912.1|  [L=37]
Description: hypothetical protein Hbor_08710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.35s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 212.97
//
Query:       gi|313125643|ref|YP_004035913.1|  [L=274]
Description: hypothetical protein Hbor_08720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-10   39.8  30.4    5.3e-10   38.9  13.8    2.9  3  COX15-CtaA  Cytochrome oxidase assembly protein


Domain annotation for each model (and alignments):
>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   1.6   8.5e-06      0.15       2      39 ..       7      45 ..       6      55 .. 0.89
   2 !   38.9  13.8     3e-14   5.3e-10      77     196 ..      56     165 ..      48     184 .. 0.79
   3 ?    0.6   1.4     0.013   2.3e+02     148     204 ..     179     235 ..     171     257 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.5e-06
                        COX15-CtaA  2 rwlllvlllvllvvvlGgltRltdsGlsitd.WppctGa 39
                                      r++ l++ l+ ++ vlG +t + ++Gl +   Wp c G 
  gi|313125643|ref|YP_004035913.1|  7 RLVALTVPLTGFLMVLGVYTAAAGAGLTCAGrWPFCDGF 45
                                      7889999999*******************988*****98 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 3e-14
                        COX15-CtaA  77 wiEwiHRllgrllGllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLll 153
                                       +iEw+HRl+++l+G+lil  ++  ++   ++r++++ l+++++l+  Q +lG+ +V+           ++l+aH+++
  gi|313125643|ref|YP_004035913.1|  56 FIEWFHRLVAMLVGFLILGTTIQTWR-TGADRRVRRALAVATVLLPSQIILGALTVTTY-------EWLILSAHFIT 124
                                       89***********************8.578999999999******************99.......78********* PP

                        COX15-CtaA 154 aflllalllwlalrllakeaesaeeeaaakklrllallllall 196
                                       a ++++++++ a+  ++   ++++e +++ ++ ++ +++l++l
  gi|313125643|ref|YP_004035913.1| 125 ASTIFTGVVLAAAWSFET--PAVAEIRRMMGVLAAGVVALVVL 165
                                       ************998888..43444444444444444444444 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.013
                        COX15-CtaA 148 aaHLllaflllalllwlalrllakeaesaeeeaaakklrllallllallllqialGa 204
                                       a+ ++l++++++ l++ ++ l a +a   ++++ a++  +l+l++l++l  q++ G+
  gi|313125643|ref|YP_004035913.1| 179 AIYYTLGLVVYGSLVAATVWLGATDADGLDRVRLATGGAALILVSLLVLGRQVYGGT 235
                                       556778899999998888888877533445555555555555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1561.31
//
Query:       gi|313125644|ref|YP_004035914.1|  [L=375]
Description: xaa-pro aminopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-10   41.5   0.1    1.6e-10   41.0   0.1    1.2  1  Peptidase_M24  Metallopeptidase family M24
    5.8e-06   27.0   0.0    1.4e-05   25.8   0.0    1.7  1  Creatinase_N   Creatinase/Prolidase N-terminal domain
  ------ inclusion threshold ------
      0.088   12.6   0.0       0.14   11.9   0.0    1.3  1  NUDIX_5        NUDIX, or N-terminal NPxY motif-rich,  region 


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.1   2.7e-14   1.6e-10       2     209 .]     141     338 ..     140     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.7e-14
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGG..STTTBCSSSB--TTEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaa..vlhytpndrvlkegdl 76 
                                        +r+ +r ++ a+e+v+++++p  te+e+aa+++   l+    rg+  p++ a g + a  + h+tp+ ++l  gd 
  gi|313125644|ref|YP_004035914.1| 141 RYRELGRETADAVERVARELEPEDTEHEVAAALKIS-LS---TRGINAPVVLAGGSERAqkYRHFTPTFTEL--GDY 211
                                       799*******************************33.44...556666666666655554678999965555..9** PP

                                       EEEEEEEEETTEEEEEEEEEECSSGSHH.....HHHHHHHHHHHHHHHHHC-.STTSBHHHHHHHHHHHHHHTTB.C CS
                     Peptidase_M24  77 vlidagaeydgyasDitrTvlvGkftpe.....qrelyeavleaqeaaikav.kpGvtlseidaaarevlesagl.a 146
                                        ++ ++ae  g ++ +trTv+++   pe     + +++++   a+ aa++av +   t+s + + + +  e+ g+ +
  gi|313125644|ref|YP_004035914.1| 212 AILSVTAERGGLYASTTRTVAFD--PPEwlserHSQAMQVETSAL-AATQAVsRLNGTASSVFDNIMAAYEHLGIpE 285
                                       **********************7..33333333555565555555.4444441556678888888888888778865 PP

                                       CGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                     Peptidase_M24 147 kffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                       +   h+ G   G   ++   + s  ++++r++e  m ++  p +       g++ edtvlvte
  gi|313125644|ref|YP_004035914.1| 286 EWREHHQGGAAGYAGREW--FAS--PDTERPVETPMAYAYNPTVQ------GAKSEDTVLVTE 338
                                       666677777777777754..333..6789*************877......9**********7 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.3e-09   1.4e-05       1      89 [.      15     109 ..      15     147 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.3e-09
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS.......-SSSEEEEEE..ESSCE.EEEEECTTHHHHHHHH.TTSE CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfa....tetgsrglalvv..tadga.lllvdalryteaaeesatvee 70 
                                       R+erl + ++++glda++  +p ++++ltG            g+a+     +d+  + ++d  ++++ a e++++e 
  gi|313125644|ref|YP_004035914.1|  15 RRERLDEYLDREGLDAVWFARPNSFSWLTGGSnvisR-DADVGVAA-AgyDRDDGwVVITDNIEAQRLADEELPDEF 89 
                                       9******************************999953.44444444.234888899****************44443 PP

                                       EEEEST.HSSHHHHHHHHHH CS
                      Creatinase_N  71 vveydd.pvealadllkell 89 
                                        ve +   +++lad+++++ 
  gi|313125644|ref|YP_004035914.1|  90 TVEETAwYESSLADAVADRT 109
                                       34433345567777777763 PP

>> NUDIX_5  NUDIX, or N-terminal NPxY motif-rich,  region of KRIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.3e-05      0.14     103     155 ..     197     251 ..     183     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                           NUDIX_5 103 skspgsPsFycLqd..ilrvcsessdkfatvtarllsaldkwlkeqhavphaiea 155
                                       +++  +P+F  L d  il v +e +  +a++t+++     +wl+e+h+++  +e+
  gi|313125644|ref|YP_004035914.1| 197 KYRHFTPTFTELGDyaILSVTAERGGLYASTTRTVAFDPPEWLSERHSQAMQVET 251
                                       556668999999866699*******************************998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 2174.48
//
Query:       gi|313125645|ref|YP_004035915.1|  [L=748]
Description: allosteric nADP-dependent malic enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-97  327.3   0.0    1.7e-97  326.6   0.0    1.3  1  PTA_PTB   Phosphate acetyl/butaryl transferase
    2.3e-30  105.8   0.0    4.4e-28   98.3   0.0    2.4  1  malic     Malic enzyme, N-terminal domain
    1.1e-22   80.6   0.2    2.9e-22   79.2   0.2    1.7  1  Malic_M   Malic enzyme, NAD binding domain
  ------ inclusion threshold ------
      0.089   12.2   0.1        2.8    7.3   0.1    2.2  2  DUF3798   Protein of unknown function (DUF3798)


Domain annotation for each model (and alignments):
>> PTA_PTB  Phosphate acetyl/butaryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.6   0.0  3.7e-101   1.7e-97       3     318 ..     427     741 ..     425     742 .. 0.97

  Alignments for each domain:
  == domain 1  score: 326.6 bits;  conditional E-value: 3.7e-101
                                       HHHHHHHHCTS--EEEES-TTSHHHHHHHHHHHHTTSSEEEEES-HHHHHHHHHHCTB--TT-EEE-TTT-CCHHHH CS
                           PTA_PTB   3 lerivekakkekkrivlpegedervlkAakelleegiadviLigdeaeikakaleldldlsgieivdpetsekleey 79 
                                       ++ +++kak+++kr++l+eg+de++++Aa +l+e+gia ++L+g++ +i++ a+ l+ld +  e+ dp++ +  ++y
  gi|313125645|ref|YP_004035915.1| 427 MRVVLNKAKSDPKRVALAEGTDEKMIRAAYQLQEQGIAYPVLVGNREKINQTAERLGLDFE-PEVADPRNGD-WDHY 501
                                       67899***************************************99999998888888876.6999*99988.99** PP

                                       HHHHHHHCCCC.S-HCCHHHHTT.SHHHHHHHHHHTTSSSEEEE-TTS-HHHHHHHHHHCT-B-TT----EEEEEEE CS
                           PTA_PTB  80 adelyelrkrkgvtieearevvr.datyfaamlvklgeaDglvsGavnttadtlrpalqiiktkpgvklvSsvfiml 155
                                       ad+lyelr+rkg+t++ea+e +r d++yfa  +v++++aD++++G+++ +  +lrp lq+i+t+p +  +++v ++ 
  gi|313125645|ref|YP_004035915.1| 502 ADRLYELRRRKGMTKNEAHELIRrDTNYFASVMVEENDADAMLTGLTHHYPSALRPPLQVIGTAPDADYAAGVYMLT 578
                                       ***************************************************************************** PP

                                       ETTEEEEEESSSS-SS--HHHHHHHHHHHHHHHHHCCSS--EEEEE-SSSTTSS-SHHHHHHHHHHHHHH.HH-TTS CS
                           PTA_PTB 156 ledrlllfaDcavnvnPtaeelaeialesaktakalgeeeprvAlLSyStkgsakgesvekvrealkivk.ekapdl 231
                                        ++r+++ aD+ vn  P+++ laei+  +a+ a++++ +epr+A+LSyS++gs k e + k r+a+k+++   ++d+
  gi|313125645|ref|YP_004035915.1| 579 FKNRVIFCADATVNLAPDSDVLAEITKHTAELARRFN-IEPRAAMLSYSNFGSVKNEGTRKPRDAVKLLHdDPEVDF 654
                                       *************************************.*****************************98615699** PP

                                       EEEEEE-HHHHH-HHHHHHH-TTSTTTT--SEEE-SSHHHHHHHHHHHHHCCTEEEEEEEEESBSS-EEE--TT--H CS
                           PTA_PTB 232 vvdGelqlDaAlseevaekkapesevaGkAnvlvfPdLeagnigykivqrlakaeaiGPilqGlakPvndlSrgasv 308
                                        vdGe+q+D A++e++ e  +  s++   AnvlvfP+Leagnigyk++qrl++aeaiGP+l+G++kPv++l rg++v
  gi|313125645|ref|YP_004035915.1| 655 DVDGEMQADTAVVEDILEGTYEFSDLDDPANVLVFPNLEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEV 731
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                           PTA_PTB 309 edivnvaait 318
                                       +divn+a ++
  gi|313125645|ref|YP_004035915.1| 732 KDIVNLAGVA 741
                                       *****98665 PP

>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.0   9.9e-32   4.4e-28       2     182 .]      17     149 ..      16     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 9.9e-32
                                       TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSB CS
                             malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeri 78 
                                       +k+e++++k ++++  ++l+++Y+P+v+++c++++++ ++a+ +y+++++                 v vv++g+++
  gi|313125645|ref|YP_004035915.1|  17 GKIEISTTKSTNTQ--RDLSLAYSPGVAAPCRDIADDADRAY-EYTAKGNL----------------VGVVSNGSAV 74 
                                       57888899998888..**************************.********................9********* PP

                                       TTTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHH CS
                             malic  79 LGlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveav 154
                                       LGlGd+G  a++++m+GK +L++++a+id   v++v+ld +                           + + ++e+v
  gi|313125645|ref|YP_004035915.1|  75 LGLGDIGaQASKPVMEGKGVLFKRFADID---VFDVELDLE---------------------------DPESIIETV 121
                                       *******9999******************...*********...........................89******* PP

                                       HHHHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 155 kelfppkaliqfEDfkaknafeileryr 182
                                       ++++p++++i++ED+ka+++fei++r+r
  gi|313125645|ref|YP_004035915.1| 122 SAMEPTFGGINLEDIKAPECFEIESRLR 149
                                       *************************997 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.2   6.5e-26   2.9e-22       3     229 ..     163     356 ..     161     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 6.5e-26
                                       HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S--- CS
                           Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekle 79 
                                       gTa+++ a+ll+a+ i +k l++ +iv+ GaG+++i  a      +v+ G+     k++i + D++G++t dre+++
  gi|313125645|ref|YP_004035915.1| 163 GTAIISGAALLNAADIVDKDLEDLNIVFSGAGASAIATARF----YVSLGAR----KENIVMCDSDGVITPDREDIN 231
                                       9*********************************9977665....4555644....5689***************** PP

                                       TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHH CS
                           Malic_M  80 eekkpfakkkeelkeakdkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEataed 156
                                       e+k +fa++           tL+e+++   ++v +Gls ++g+ ++e+v +ma   + Pii+++ NP+   E   e+
  gi|313125645|ref|YP_004035915.1| 232 EFKAEFANDVPAD-------TLAEAMEG--ADVFVGLS-IGGLVDQEMVASMA---DDPIIFAMANPDP--EIGYEE 293
                                       ******9876543.......79**9997..69*****8.79********9997...58*********97..778899 PP

                                       HHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHH CS
                           Malic_M 157 vlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseee 229
                                       + +  d+++++a+G          +  +++Q NN++ fP +  g++ +ra++i++em  aaa+ala+l++++ 
  gi|313125645|ref|YP_004035915.1| 294 AKAARDDTVIMATG----------RSDYPNQVNNVLGFPFIFRGALDVRATEINEEMKRAAAKALADLARKDV 356
                                       99999********8..........56789**************************************998876 PP

>> DUF3798  Protein of unknown function (DUF3798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1   0.00062       2.8      50     103 ..     269     318 ..     264     351 .. 0.86
   2 ?    2.3   0.0     0.021        92     140     169 ..     463     492 ..     449     506 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00062
                                       HHHGGGG-TTEEEEEEE-SS---HHHHHHHHHH-TTSEEEESS--S-HHHHHHH CS
                           DUF3798  50 qivslAdDpkvkaivvaqavpgtleAirkvkekrpdilliagepeedpavlssa 103
                                        ++s+AdDp    i++a a+p     ++++k+ r+d +++a+  ++ p++++++
  gi|313125645|ref|YP_004035915.1| 269 MVASMADDP----IIFAMANPDPEIGYEEAKAARDDTVIMATGRSDYPNQVNNV 318
                                       578999999....99*********************************999886 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.021
                                       GGSHHHHHHHHHHHHHHHHCT--EEEEEE- CS
                           DUF3798 140 lsyellakrreimektckelGlefvevtap 169
                                       ++y++l   re +++t++ lGl+f  + a 
  gi|313125645|ref|YP_004035915.1| 463 IAYPVLVGNREKINQTAERLGLDFEPEVAD 492
                                       78999999****************877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 4379.08
//
Query:       gi|313125646|ref|YP_004035916.1|  [L=232]
Description: sec-independent protein translocase (tatc) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-10   38.9  13.3    8.2e-10   38.9   8.7    2.1  2  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   0.1    0.0064   1.1e+02     174     199 ..      22      48 ..      20      56 .. 0.85
   2 !   38.9   8.7   4.6e-14   8.2e-10     100     207 .]     109     217 ..      63     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0064
                                       HHHTTHHHHHHHHHHHHHHH-S..SHH CS
                              TatC 174 tlrkkrryaivvilvvaavltP.pdvi 199
                                       t+r++ r  + v+l v+av+t  ++ i
  gi|313125646|ref|YP_004035916.1|  22 TVRRNLRPLLAVFLLVSAVVTAaASGI 48 
                                       78999999*************866665 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 4.6e-14
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHT..TTTSSTTEEHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHH CS
                              TatC 100 liaslllfllGaafayfvvlplvlkfll..seevepllslseylsfvlllllafgiaFelPlvlvllarlglvsaet 174
                                       ++++ + f +G+a++  ++lp+v + +   +++  + l++  y ++ l++++a g a  +P++l+ ++r+g+v + t
  gi|313125646|ref|YP_004035916.1| 109 AVVAAFAFTVGVAVGV-ILLPAVAEAVSrvTATSAAGLDVYWYTEVWLFFPVALGGAAATPFLLIAAVRAGVVGRFT 184
                                       4566777888888887.47888888777222222446**************************************** PP

                                       HHTTHHHHHHHHHHHHHHH-S.SHHHHHHHHHH CS
                              TatC 175 lrkkrryaivvilvvaavltPpdvisqlllavP 207
                                        +++r ya ++++v+aa  +P+d  + +lla+P
  gi|313125646|ref|YP_004035916.1| 185 STRQRGYAALAFVVFAACYSPADSATFVLLAAP 217
                                       *******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1496.45
//
Query:       gi|313125647|ref|YP_004035917.1|  [L=78]
Description: hypothetical protein Hbor_08760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-05   25.1   7.9    1.4e-05   24.8   7.9    1.1  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   7.9   7.9e-10   1.4e-05       2      50 ..      19      67 ..      17      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.9e-10
                              TauE  2 llagllaGfvagllGiGggliavPlLllllppavavatsllavvatsls 50
                                      +++++++Gfv gl G+G+++i + lL+++++p++ava+ +l ++a ++s
  gi|313125647|ref|YP_004035917.1| 19 AAIVAFGGFVTGLNGFGFAVIGTALLAFVMDPQTAVALMILPILAANTS 67
                                      56778899********************77**************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 513.21
//
Query:       gi|313125648|ref|YP_004035918.1|  [L=460]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-22   78.9   0.0    7.6e-22   77.8   0.0    1.6  1  OrfB_IS605       Probable transposase
    5.2e-22   77.6   0.8    1.3e-21   76.3   0.8    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0012   19.1   0.6      0.003   17.8   0.6    1.6  1  C1_2             C1 domain
  ------ inclusion threshold ------
      0.091   12.9   2.2       0.19   11.8   2.2    1.6  1  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        0.1   12.7   0.3       0.23   11.6   0.3    1.5  1  Ribosomal_L37ae  Ribosomal L37ae protein family
       0.19   11.2   1.9       0.46   10.0   1.9    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.24   11.2   1.6       0.53   10.1   1.6    1.6  1  A2L_zn_ribbon    A2L zinc ribbon domain
       0.24   11.4   1.1        0.6   10.1   1.1    1.7  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        4.8    7.2   5.0       0.93    9.5   0.1    2.2  3  DUF4298          Domain of unknown function (DUF4298)


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   3.8e-25   7.6e-22       8     117 ..     222     321 ..     205     324 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 3.8e-25
                        OrfB_IS605   8 velpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkr 84 
                                       ++ p+p+g ++ag+DlGi+n+a+v+ +  ++ ly g  lk+d++y++k++a+++            sr+ +rl+rkr
  gi|313125648|ref|YP_004035918.1| 222 TIDPEPPGDEVAGVDLGICNFAAVSFGG-ESVLYPGGALKEDEYYFTKKKAKCDDS---------SSREATRLDRKR 288
                                       447999********************98.99999999***************9987.........57999******* PP

                        OrfB_IS605  85 srrrkhllhklathliktlkevgvetLnvgnmk 117
                                       + rr+h+lh+l++++++++ e+gv+tL+vg++ 
  gi|313125648|ref|YP_004035918.1| 289 AGRRTHFLHALSKSIVNECVERGVGTLVVGDLG 321
                                       ******************************985 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.8   6.6e-25   1.3e-21       1      69 []     348     417 ..     348     417 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 6.6e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++++ l yka+ +Gi ve+v+++ TSk+Cs Cg+++++ ++++ +++C++C+++a++Dvn+a Ni ++
  gi|313125648|ref|YP_004035918.1| 348 FDRFTTLLDYKAEAEGIDVELVSERDTSKSCSACGHTDDNqRVERGLYVCEKCNTVANADVNGAENIRQK 417
                                       889*************************************99*************************875 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6   1.5e-06     0.003      13      41 ..     370     403 ..     364     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
                              C1_2  13 edssesfnCsaCgrkidgff.....YsCseCdfs 41 
                                       ++++ s++CsaCg++ d+ +     Y C++C+ +
  gi|313125648|ref|YP_004035918.1| 370 SERDTSKSCSACGHTDDNQRverglYVCEKCNTV 403
                                       467899*********6665577899******976 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.2   9.7e-05      0.19       4      26 .]     378     400 ..     376     400 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.7e-05
                            zf-ACC   4 CpsCgemlykkeLernlyVCPkC 26 
                                       C +Cg++  ++ +er lyVC kC
  gi|313125648|ref|YP_004035918.1| 378 CSACGHTDDNQRVERGLYVCEKC 400
                                       99********************* PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00011      0.23      30      60 ..     372     403 ..     365     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                       HHS-BEESSSSSS.EEEEEETTEEEETTTTEE CS
                   Ribosomal_L37ae  30 qhakytCpfcgkt.kvkRkavgiwkCkkcgkt 60 
                                       + ++  C+ cg+t + +R+  g++ C+kc+ +
  gi|313125648|ref|YP_004035918.1| 372 RDTSKSCSACGHTdDNQRVERGLYVCEKCNTV 403
                                       445568******9899*************875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.9   0.00023      0.46       3      28 ..     378     403 ..     377     412 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                                       ETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCGlV 28 
                                       C  Cg+t++    erg +vC++C +V
  gi|313125648|ref|YP_004035918.1| 378 CSACGHTDDNQRVERGLYVCEKCNTV 403
                                       999*****9999***********666 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.6   0.00027      0.53       4      30 ..     376     403 ..     373     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                     A2L_zn_ribbon   4 kvCsvCggngiln.seqgylvCieCgas 30 
                                       k Cs Cg+  + +  e+g +vC +C+++
  gi|313125648|ref|YP_004035918.1| 376 KSCSACGHTDDNQrVERGLYVCEKCNTV 403
                                       5699****9999989***********97 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.1    0.0003       0.6      20      44 ..     377     401 ..     372     403 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                     Zn_Tnp_IS1595  20 vCPhCgsr.kayriktrglfqCkeCr 44 
                                        C +Cg++    r+++ gl+ C++C+
  gi|313125648|ref|YP_004035918.1| 377 SCSACGHTdDNQRVER-GLYVCEKCN 401
                                       4*******99999997.********7 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00047      0.93      15      61 ..      51      97 ..      47     100 .. 0.90
   2 ?   -3.7   0.0       6.2   1.2e+04      32      45 ..     201     214 ..     200     217 .. 0.80
   3 ?   -1.7   0.2       1.5     3e+03      36      54 ..     262     280 ..     260     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00047
                                      HHHHHHHHHHHHHTHHHHHHHHHHHTSHHHHHHHTS--SS.....-- CS
                           DUF4298 15 lqqLeealeqwkklqkklakLdeYYqseqwredleasnkgelpqelk 61
                                      +qq  + l+q+  + +kl ++ +YY+ +qw e  +  ++gel+ elk
  gi|313125648|ref|YP_004035918.1| 51 QQQVRDDLDQLGWAASKLWNVGRYYAQKQWDETGKIPDDGELKAELK 97
                                      68999999*************************99999999988765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.2
                                       HHHHHHHHTSHHHH CS
                           DUF4298  32 lakLdeYYqseqwr 45 
                                       ++++++ Y+ ++wr
  gi|313125648|ref|YP_004035918.1| 201 IQQVRAVYKHDEWR 214
                                       68888999999998 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.5
                                       HHHHTSHHHHHHHTS--SS CS
                           DUF4298  36 deYYqseqwredleasnkg 54 
                                       deYY +++  ++ ++s ++
  gi|313125648|ref|YP_004035918.1| 262 DEYYFTKKKAKCDDSSSRE 280
                                       79****9998888776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2673.58
//
Query:       gi|313125649|ref|YP_004035919.1|  [L=216]
Description: hypothetical protein Hbor_08780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00019   21.2   0.0    0.00028   20.7   0.0    1.2  1  RVT_3     Reverse transcriptase-like
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.027   14.7   0.0    1.2  1  RNase_H   RNase H


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.2e-08   0.00028       2      79 ..      36     113 ..      35     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.2e-08
                             RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLqlalklgirr..lvvegDsktvvqll 76 
                                       +dg++ + +g+gg+gvvi + +G +++ +a + ++  ++ ++E++AL  GL + +++   +  + v +D+++++ ++
  gi|313125649|ref|YP_004035919.1|  36 TDGSY-RPTGDGGLGVVIETRDGTRVARVAVP-DTAPNNNVSEYRALHLGLDVLAARAPPNarVGVLIDHDSLAANV 110
                                       57866.7799********************99.99999*************98777665443488888888888888 PP

                             RVT_3  77 ngr 79 
                                       n +
  gi|313125649|ref|YP_004035919.1| 111 NTE 113
                                       765 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     3e-06     0.027       4      60 ..      32      89 ..      29     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-06
                                      EEEEEEEEEECTTTCEEEEEEE.CTT..EEEEEEEC.CCCHHHHHHHHHHHHHHHTT.S CS
                           RNase_H  4 vvvYtDGsclgnpgeggagavl.ykegarnisaple.eaqtnnraELsAvieaLkalks 60
                                        v tDGs++  +g gg g+v+  ++g+r  + +++  a  nn  E +A++  L  l +
  gi|313125649|ref|YP_004035919.1| 32 FYVATDGSYR-PTGDGGLGVVIeTRDGTRVARVAVPdTAPNNNVSEYRALHLGLDVLAA 89
                                      5688****77.799******9967777888888888788999********999985533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1425.79
//
Query:       gi|313125650|ref|YP_004035920.1|  [L=167]
Description: cbs-domain-containing membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-30  104.6   9.4    1.4e-15   57.4   0.7    2.1  2  CBS       CBS domain
  ------ inclusion threshold ------
       0.23   11.6   4.0       0.56   10.3   0.2    2.5  2  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.7   1.6e-19   1.4e-15       1      53 [.       5      57 ..       5      60 .. 0.95
   2 !   51.7   2.3     1e-17     9e-14       2      56 ..     105     160 ..     104     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.6e-19
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                      ++d+mt+dv tv+pd++++++l ++++++++++PVVded+++vGivt++Dl+ 
  gi|313125650|ref|YP_004035920.1|  5 ARDLMTEDVETVSPDDDVSDVLGRLARADFNGFPVVDEDDHVVGIVTQHDLVG 57
                                      589**********************9999*********************985 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 1e-17
                                       HHHSBSSCEEEETTSBHHHHHHHHH.HHT.SSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmr.ekg.vsrlPVVdedgklvGivtlrDllrall 56 
                                       + +mt+dvvtv pd++l  +l+l++ +++ ++rlPV+ edg+lvG+v + D++ra+ 
  gi|313125650|ref|YP_004035920.1| 105 KKVMTPDVVTVEPDADLDAILDLLAdDERdINRLPVI-EDGRLVGVVARQDVIRAIR 160
                                       789*********************954447*******.9***************985 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   6.2e-05      0.56       5      60 ..      30      86 ..      27     100 .. 0.71
   2 ?    2.0   0.3     0.025   2.2e+02       7      29 ..     133     156 ..     129     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.2e-05
                                      CS---TT-EEEETTSSEEEEE..EEEEEETTTTEEEEEEEEETTT.....-EEEEEGG CS
                               PRC  5 rasdliGkeVytedGeklGkV..kDvvidekegrvralvvsvggflgigekevliPfd 60
                                      + +d+ G +V++ed+  +G V   D+ +   e + r l ++ g  ++++  ++++++ 
  gi|313125650|ref|YP_004035920.1| 30 ARADFNGFPVVDEDDHVVGIVtqHDL-VGLFETKDRTLWIPIGLPPFMETVTYAVDIS 86
                                      5789*****************77777.5555666666666666666666666666555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.025
                                       ---TT-EEEETTSSEEEEE..EEEE CS
                               PRC   7 sdliGkeVytedGeklGkV..kDvv 29 
                                       +d+  ++V+ + G+ +G+V  +Dv+
  gi|313125650|ref|YP_004035920.1| 133 RDINRLPVIED-GRLVGVVarQDVI 156
                                       57888888876.8******888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 977.27
//
Query:       gi|313125651|ref|YP_004035921.1|  [L=321]
Description: dmt(drug/metabolite transporter) superfamily permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-34  119.1  30.8    2.4e-21   76.4  14.2    2.1  2  EamA           EamA-like transporter family
  ------ inclusion threshold ------
        1.2    9.0  23.9        5.6    6.8   5.6    3.5  3  7TMR-DISM_7TM  7TM diverse intracellular signalling


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   8.6   8.4e-17   7.5e-13       6     135 ..       9     149 ..       6     150 .. 0.92
   2 !   76.4  14.2   2.6e-25   2.4e-21       4     135 ..     165     298 ..     162     300 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 8.4e-17
                              EamA   6 lallaalfwaiyfvlskillrkv........spltltfvrfliagillliiallkegklaklslkd.wllllllgll 73 
                                       l+l  a +w+++f+++k++l +          p+ ++++r+ +ag+l+l +a++    + +++ +d w+ +++ ++l
  gi|313125651|ref|YP_004035921.1|   9 LFLFLAAVWGAAFMAIKAGLGTPsdpggffeTPVLFAAIRYDVAGVLMLGYAVYATDHP-VPRGRDeWATVVVGSVL 84 
                                       44556667***********999999999999**************************99.88888889999****** PP

                              EamA  74 gtvlafllffyalkk..tsasnaslitslePvftlilsvlll.gekltlkqllgivlillGvlli 135
                                        ++ ++ l+f++ ++  ++++ a++i+sl+Pv+t+ ++ ++l  e+lt + l+g++l+l+Gv+++
  gi|313125651|ref|YP_004035921.1|  85 IMAGYHALLFIGETDpaVTSAAAAVIVSLSPVLTAGFARAFLpVERLTTFGLAGLLLGLVGVAIL 149
                                       *************9755777899*******************99******************997 PP

  == domain 2  score: 76.4 bits;  conditional E-value: 2.6e-25
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtvla 78 
                                        ll+++aa+++a++ vl++++ ++++  t+ ++++l +++l+ i+++  +++     ++ + +l++ +l++++++++
  gi|313125651|ref|YP_004035921.1| 165 KLLIFAAAICFALGSVLTRRIDADFPIETMEAWTMLGGAVLMHIVSVGIGESVsdVTWTGETLLAVGYLSVVASAIG 241
                                       589***************************************99999999999888999999*************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       fl++f +l++++a ++ l+++++Pvf+++ ++l+ ge +t+++++g+++i++G ll+
  gi|313125651|ref|YP_004035921.1| 242 FLVYFVLLERLGALEINLVSYVAPVFAALTGWLFRGEIPTVYTVVGFIVIFVGFLLL 298
                                       *****************************************************9996 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4   0.00089         8       7      26 ..      78      97 ..      74     103 .. 0.85
   2 ?    6.8   5.6   0.00062       5.6      66     197 ..     104     248 ..      96     252 .. 0.56
   3 ?    2.8   9.2     0.011        95     106     168 ..     238     297 ..     225     303 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00089
                     7TMR-DISM_7TM  7 lllGvllalalynlflffsl 26
                                      +++G +l++a y+ +lf+  
  gi|313125651|ref|YP_004035921.1| 78 VVVGSVLIMAGYHALLFIGE 97
                                      789**************965 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00062
                     7TMR-DISM_7TM  66 nkllyltlllllilfll.Farsflelkkkprllklllllavllsllllllpllpyteslslaq..llallvilllll 139
                                       + +  + ++l+  ++++ Far fl  +   rl  + l+ ++l  +l+ +++l   + ++ l    +  ll++  +++
  gi|313125651|ref|YP_004035921.1| 104 SAAAAVIVSLSP-VLTAgFARAFLPVE---RLTTFGLAGLLL--GLVGVAILSDPDPNNLLTGgtVAKLLIFAAAIC 174
                                       555566666776.55555********4...455554444444..333333444333333333333555555556666 PP

                     7TMR-DISM_7TM 140 igikawrkgnkparyfl...iawlllligvlidils...........llg..llpsnffteyllqigvllevll 197
                                       +++ +++ ++ +a + +    aw++l  +vl++i+s            +g  ll +++++  ++ ig+l+  +l
  gi|313125651|ref|YP_004035921.1| 175 FALGSVLTRRIDADFPIetmEAWTMLGGAVLMHIVSvgigesvsdvtWTGetLLAVGYLSVVASAIGFLVYFVL 248
                                       66666666666666655555788888888888887766666655553222445555555556666666655555 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.011
                     7TMR-DISM_7TM 106 llsllllllpllpyteslslaqllallvillllligikaw.rkgnkparyfliawlllligvli 168
                                        ++++l+ + ll    +l++  l+++++ ++++   +  w ++g+ p  y +++++++++g+l+
  gi|313125651|ref|YP_004035921.1| 238 SAIGFLVYFVLLERLGALEI-NLVSYVAPVFAA---LTGWlFRGEIPTVYTVVGFIVIFVGFLL 297
                                       11122222222222222222.233333444444...444449*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1914.10
//
Query:       gi|313125652|ref|YP_004035922.1|  [L=94]
Description: hypothetical protein Hbor_08810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.098   12.8   0.4       0.17   12.0   0.4    1.5  1  RRP7      Ribosomal RNA-processing protein 7 (RRP7) C-termina
       0.12   12.4   0.0       0.18   11.7   0.0    1.5  1  DUF1344   Protein of unknown function (DUF1344)
       0.12   12.5   0.0       0.13   12.5   0.0    1.1  1  OstA      OstA-like protein


Domain annotation for each model (and alignments):
>> RRP7  Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   2.8e-05      0.17      13      49 ..      49      85 ..      32      94 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                              RRP7 13 evdeymeefdkeeeeekkeekkkeeevDeDGfvtVtr 49
                                      +vde+ +e+    +e +++    ++  DeDG+++V +
  gi|313125652|ref|YP_004035922.1| 49 RVDEADAEYRLITSEDNESVLIGRSGADEDGWTMVGE 85
                                      55666666666666666666666999*********88 PP

>> DUF1344  Protein of unknown function (DUF1344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     3e-05      0.18       7      25 ..      10      28 ..       5      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                           DUF1344  7 tIkkidkkalsitLdDGkt 25
                                       I++++++   +tLdDG t
  gi|313125652|ref|YP_004035922.1| 10 RIHNVSPDPVQLTLDDGST 28
                                      699**************87 PP

>> OstA  OstA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.2e-05      0.13      34     105 ..      17      87 ..       7      94 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                              OstA  34 dkvtvtqdkkskkierleakgtatfrqkvdlvgeqi.rGkAerieydskkeiivLtgnatltqnsnsveGsei 105
                                       d v++t d++s ++     + t++f+q+ + +ge + +++Ae    +s++++ vL+g    +++++++ G++ 
  gi|313125652|ref|YP_004035922.1|  17 DPVQLTLDDGSTAVY--RMHSTEFFQQEFQAEGERVdEADAEYRLITSEDNESVLIGRSGADEDGWTMVGEVT 87 
                                       678888888855555..555555*********999847*******************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 650.08
//
Query:       gi|313125653|ref|YP_004035923.1|  [L=204]
Description: cytidylate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-21   76.0   0.0    5.1e-21   75.6   0.0    1.2  1  AAA_18           AAA domain
    2.6e-18   66.8   0.1      3e-17   63.3   0.1    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    7.7e-11   42.6   0.0    1.8e-10   41.4   0.0    1.6  1  AAA_17           AAA domain
    2.2e-08   34.1   0.4    0.00039   20.2   0.2    2.2  2  Cytidylate_kin   Cytidylate kinase
    3.2e-05   24.4   0.0    5.2e-05   23.7   0.0    1.4  1  AAA              ATPase family associated with various cellul
      4e-05   23.9   0.2    8.7e-05   22.8   0.2    1.6  1  AAA_28           AAA domain
    5.4e-05   23.4   0.1    0.00012   22.3   0.1    1.5  1  AAA_33           AAA domain
    0.00038   20.6   0.0     0.0011   19.2   0.0    1.7  2  ADK              Adenylate kinase
     0.0029   17.7   0.3      0.026   14.7   0.3    2.0  1  SKI              Shikimate kinase
     0.0037   17.7   0.2      0.008   16.6   0.2    1.7  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.024   14.5   0.2      0.044   13.7   0.2    1.4  1  RHH_4            Ribbon-helix-helix domain
      0.038   13.9   0.0      0.062   13.2   0.0    1.4  1  Rad17            Rad17 P-loop domain
        0.1   12.9   0.2       0.21   11.9   0.2    1.6  1  AAA_22           AAA domain
       0.13   12.1   0.0       0.22   11.4   0.0    1.3  1  NTPase_1         NTPase
       0.18   10.9   0.0        0.3   10.2   0.0    1.4  1  NB-ARC           NB-ARC domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   4.2e-24   5.1e-21       1     124 [.      18     144 ..      18     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 4.2e-24
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I ++G+pG+G ttl+k Ls++l++     g++ r++a e+g++l++  ++ des+++d+  + +l +  e++ +   
  gi|313125653|ref|YP_004035923.1|  18 ITVSGPPGCGATTLCKGLSRSLECgyvsgGDIFRELAEERGMSLSQLIAKADESDEIDRALDRRLRTVAEQWGA--- 91 
                                       89********************9999**********************************************75... PP

                            AAA_18  73 egknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik..ene 124
                                       ++k+ v++++la ++  ++ d+  ++L+a++e++ eR ++R++ ea+++  e +
  gi|313125653|ref|YP_004035923.1|  92 SNKPFVLESRLAGWLAGNRADLR-IWLDAPEEVRVERTRDREELEAEMRvrEVS 144
                                       9**********************.********************9998765444 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.1   2.5e-20     3e-17       2     178 ..      18     170 ..      17     171 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 2.5e-20
                   Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeev.eevdersrlssflskllaarvagdtldek 76 
                                       IT+s+  G+g++t+++ L+  L+  +++  +i++e+a+e g+s +++ +++de                     + +
  gi|313125653|ref|YP_004035923.1|  18 ITVSGPPGCGATTLCKGLSRSLECGYVSGgDIFRELAEERGMSLSQLiAKADE---------------------SDE 73 
                                       9***************************99*****************999999.....................677 PP

                   Cytidylate_kin2  77 lddelfeaqervirela.aeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkr 152
                                       +d +l ++ ++v ++ + +++++V+  R a  +  + +  lr++l+ap+e+rv+r ++re+l+      +++ ++  
  gi|313125653|ref|YP_004035923.1|  74 IDRALDRRLRTVAEQWGaSNKPFVLESRLAGWLAGN-RADLRIWLDAPEEVRVERTRDREELE-----AEMRVREVS 144
                                       888899999999999997788**********65555.55*********************884.....456666778 PP

                   Cytidylate_kin2 153 rakyykkytgqdwgdaenYdlvlnts 178
                                       +a +y+ y+g d++d + Ydl +nt+
  gi|313125653|ref|YP_004035923.1| 145 EAGRYESYYGIDVSDQSFYDLQMNTA 170
                                       99**********************97 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   1.5e-13   1.8e-10       2     123 ..      22     132 ..      21     145 .. 0.67

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.5e-13
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC...TSHHHHHHHHHHHHHHHHHHHH..HSSE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr...klpleekkelqkeaaekiaeea..kkkg 73 
                                       G+PG+G +t+c+ l + ++  ++s Gd++re a+++g+  + +++    +++ e++++l++++  ++ae+   ++k 
  gi|313125653|ref|YP_004035923.1|  22 GPPGCGATTLCKGLSRSLECGYVSGGDIFRELAEERGM--SLSQLIakaDESDEIDRALDRRLR-TVAEQWgaSNKP 95 
                                       9************************************9..334433111334444445554443.455543334555 PP

                                       EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  74 vlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                       ++++            +g+ +   + +  d+ i l+a++e+ +er   ++
  gi|313125653|ref|YP_004035923.1|  96 FVLESRL---------AGWLAG--NRA--DLRIWLDAPEEVRVERTRDRE 132
                                       6665554.........445542..333..778889998888887766554 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   3.3e-07   0.00039       1      50 [.      18      70 ..      18      88 .. 0.79
   2 !   13.4   0.1   3.9e-05     0.047      92     153 ..      68     133 ..      55     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.3e-07
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHH...HHHHTT--TT-H CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalal...aalrrkvdllde 50
                                      i++ GP g G  ++++ l++ l++ y++ g ++R la    ++l + ++ +de
  gi|313125653|ref|YP_004035923.1| 18 ITVSGPPGCGATTLCKGLSRSLECGYVSGGDIFRELAEergMSLSQLIAKADE 70
                                      899*******************************9985222345555555555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.9e-05
                                       HTTSHHHHHHHHHHHHTT-B.....SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHH CS
                    Cytidylate_kin  92 vaaipavRailvkklrelvk.....karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlka 153
                                            ++ ++l ++lr++++     ++ +v+e R  g      a+l+i+ldA  e+R++R  +  ++
  gi|313125653|ref|YP_004035923.1|  68 ADESDEIDRALDRRLRTVAEqwgasNKPFVLESRLAGWLAGNRADLRIWLDAPEEVRVERTRDR-EE 133
                                       55566677777778887776554456789*****************************985443.32 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   4.4e-08   5.2e-05       2      74 ..      19      81 ..      18     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.4e-08
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr 74
                                       ++GppG+G T+l+k + ++l  e+  +sg +++ ++ +e+ +++++l+++a e+        DEid+   +r
  gi|313125653|ref|YP_004035923.1| 19 TVSGPPGCGATTLCKGLSRSL--ECGYVSGGDIFRELAEERGMSLSQLIAKADES--------DEIDRALDRR 81
                                      589*****************6..567799*********************99876........7888877777 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   7.3e-08   8.7e-05       2      80 ..      18     100 ..      17     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.3e-08
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaa..aan 73 
                                       i ++G++++G Ttl++ L++    gy+   +++re+ ee++ +  + ++++++  ++ ++ l+ +l++ a++  a+n
  gi|313125653|ref|YP_004035923.1|  18 ITVSGPPGCGATTLCKGLSRSlecGYVSGGDIFRELAEERGMSLSQLIAKADESDEIDRA-LDRRLRTVAEQwgASN 93 
                                       789****************7776799999************9999988877777777765.9999999999998888 PP

                            AAA_28  74 kvlfcDr 80 
                                       k ++++ 
  gi|313125653|ref|YP_004035923.1|  94 KPFVLES 100
                                       8887765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1     1e-07   0.00012       4     122 ..      20     135 ..      17     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1e-07
                            AAA_33   4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldr...lyqilnelarkalsagrnvilda 77 
                                       + G+pG+G +tl ++l + l +  +s  +++r l+++   s+++++  +d+   + + l +++r   ++ +++    
  gi|313125653|ref|YP_004035923.1|  20 VSGPPGCGATTLCKGLSRSLECGYVSGGDIFRELAEERGMSLSQLIAKADEsdeIDRALDRRLRT-VAEQWGA-SNK 94 
                                       78**********************************99999998777444412255555555542.2333332.478 PP

                            AAA_33  78 tnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaang 122
                                       +++ +++ a +l+  r    +++ ++++++ee+  eR++ R++ +
  gi|313125653|ref|YP_004035923.1|  95 PFVLESRLAGWLAGNR----ADLRIWLDAPEEVRVERTRDREELE 135
                                       8999999999998887....7788*****************9963 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.8e-07    0.0011       1      37 [.      20      56 ..      20      88 .. 0.83
   2 ?   -1.5   0.0         2   2.4e+03     102     126 ..     110     133 ..      97     152 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.8e-07
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevks 37
                                      + G+Pg+G  t ++ l +++++  +s Gd++R+  ++
  gi|313125653|ref|YP_004035923.1| 20 VSGPPGCGATTLCKGLSRSLECGYVSGGDIFRELAEE 56
                                      57******************************97653 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                                       EESEEEEEE--HHHHHHHHHTGSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 102 kldlvleldvpeevlveRltgDnee 126
                                       + dl + ld+peev veR  + +ee
  gi|313125653|ref|YP_004035923.1| 110 RADLRIWLDAPEEVRVERTRD-REE 133
                                       567778888888888888544.333 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   2.1e-05     0.026       1     132 [.      24     153 ..      24     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                                       TTSSHHHHHHHHHHHHTSEEE...EHHHHHHHHHTS-HHHHHHHHHHHH..HHHHHHHHHHHHCCCSSEEEEE-TTG CS
                               SKI   1 mGaGKstvGkllAkklglefi...DlDeliekrtgksiaeifeeegeeg..FrelEsevlkelleeeglViatGGGa 72 
                                       +G+G +t+ k l+++l++ ++   D+ +++ ++ g+s ++++++ +e+   +r+l+++ l+ ++e+ g   a     
  gi|313125653|ref|YP_004035923.1|  24 PGCGATTLCKGLSRSLECGYVsggDIFRELAEERGMSLSQLIAKADESDeiDRALDRR-LRTVAEQWG---ASNKPF 96 
                                       69******************943344456788889*******9876654224444443.333333321...222235 PP

                                       GGSHHHHHHHH..HHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHC CS
                               SKI  73 vlseenrellk..ekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplye 132
                                       vl+++    l+  +  + i+Ld++ e+ +er+++++e   l+++++ +e+ e    r ++y 
  gi|313125653|ref|YP_004035923.1|  97 VLESRLAGWLAgnRADLRIWLDAPEEVRVERTRDREE---LEAEMRVREVSEA--GRYESYY 153
                                       666666655555577789**************99999...7777774443333..4455554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   6.7e-06     0.008      24     100 ..      11      92 ..       4     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.7e-06
                            AAA_16  24 p....elvllsGesGvGKsslvrellralekdggiflrgkcdql...esaipysa.laqalareellrqlldeaesa 92 
                                       +      + +sG++G+G ++l + l r+le   g++  g+  +    e+++++s+ +a+a + +e+ r+l++++++ 
  gi|313125653|ref|YP_004035923.1|  11 SvdsnLFITVSGPPGCGATTLCKGLSRSLE--CGYVSGGDIFRElaeERGMSLSQlIAKADESDEIDRALDRRLRT- 84 
                                       333347899*****************9999..67887777777668888999999677777666666666666444. PP

                            AAA_16  93 eleawrek 100
                                        +e+w + 
  gi|313125653|ref|YP_004035923.1|  85 VAEQWGAS 92 
                                       88888764 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   3.7e-05     0.044      23      47 ..      48      72 ..      48      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHHHTT--HHHHHHHH.HHH CS
                             RHH_4 23 daLeeiArregltvnaLiaeidadr 47
                                      d+++e+A+++g+++++Lia+ d++ 
  gi|313125653|ref|YP_004035923.1| 48 DIFRELAEERGMSLSQLIAKADESD 72
                                      5789****************98665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.2e-05     0.062      48      71 ..      18      41 ..       5      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                             Rad17 48 LLisGPsGCgkstvvkvLskelgi 71
                                      + +sGP+GCg +t  k Ls+ l  
  gi|313125653|ref|YP_004035923.1| 18 ITVSGPPGCGATTLCKGLSRSLEC 41
                                      5689***************98765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00018      0.21       4      29 ..      14      39 ..      10      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      +  +++v G++G+G Ttl++ l ++l
  gi|313125653|ref|YP_004035923.1| 14 SNLFITVSGPPGCGATTLCKGLSRSL 39
                                      5679****************999887 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.22       2      39 ..      18      54 ..      16      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                                      + ++GppG G tTl+k +++ l + g+  gG + +e  
  gi|313125653|ref|YP_004035923.1| 18 ITVSGPPGCGATTLCKGLSRSL-ECGYVSGGDIFRELA 54
                                      6799******************.788888887777665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00025       0.3      19      84 ..      15      90 ..       8     113 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                                      CSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE..............EEESXXHHHHHHHXXHHHHHCCCTTS CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqilnksdevegrFdsvawv..............vvsktdkseeiletilkeLslseddl 83
                                      + l+++++G +G+G ttl k   ++   +e  + s   +               ++k d+s ei +++ ++L +  +++
  gi|313125653|ref|YP_004035923.1| 15 N-LFITVSGPPGCGATTLCKGLSRS---LECGYVSGGDIfrelaeergmslsqLIAKADESDEIDRALDRRLRTVAEQW 89
                                      4.89***************998877...333333333333333666666666666666666666666666666666666 PP

                                      S CS
                            NB-ARC 84 e 84
                                       
  gi|313125653|ref|YP_004035923.1| 90 G 90
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1251.09
//
Query:       gi|313125654|ref|YP_004035924.1|  [L=328]
Description: l-asparaginase/glutrnagln amidotransferase subunit d [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-51  174.8   0.0    2.2e-51  174.1   0.0    1.3  1  Asparaginase    Asparaginase, N-terminal
    6.6e-19   68.2   2.5    1.9e-18   66.7   0.3    2.2  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.1   0.0   2.4e-55   2.2e-51       2     189 ..       4     189 ..       3     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 2.4e-55
                                       EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHC.CT-S CS
                      Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.eeyd 77 
                                       v+v+++GGTiase  e+g  +apa +++el++++p+++++a+l++ ++ + +  +m++  ++  ae++++a+ +++d
  gi|313125654|ref|YP_004035924.1|   4 VHVVGCGGTIASEPAEDG--AAPAKAGDELVRSVPDISEYADLRVTDVGSRPGFDMDFGVVAAAAEEVRTAVaDGAD 78 
                                       89***************9..88899***********************************************666** PP

                                       EEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTEEEETT CS
                      Asparaginase  78 gfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngkllran 154
                                       g+Vv+hGTDTla tA+aL+++++  ++pv++tGsqr ++e++sD+p+Nll+A+++a + +  +gv ++f+++l++a+
  gi|313125654|ref|YP_004035924.1|  79 GVVVTHGTDTLADTAYALDIACNV-PVPVIVTGSQRRFDEPGSDAPSNLLTAVRAAVDGQFAPGVHIAFDDELHAAR 154
                                       **********************77.*********************************9999*************** PP

                                       TEEE-BSSSSS-EEETTT--SEEEETTEEEESEEE CS
                      Asparaginase 155 rvtKvhtssldaFespnlgplaevegskvkvnkel 189
                                       ++ K+ht++ld+F+sp  gp+a+++++++++++++
  gi|313125654|ref|YP_004035924.1| 155 DAVKTHTNALDTFQSPGKGPVATFTRETTRLHRDP 189
                                       ************************99999988876 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.046   4.1e+02      14      32 ..      67      85 ..      59     110 .. 0.77
   2 !   66.7   0.3   2.1e-22   1.9e-18       5     114 .]     218     327 ..     214     327 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.046
                                      HHHHHHHHTT--EEEEEEB CS
                    Asparaginase_C 14 kvlkallkkgakGvvlegt 32
                                      + ++ +++ ga+Gvv+  +
  gi|313125654|ref|YP_004035924.1| 67 EEVRTAVADGADGVVVTHG 85
                                      446678889******9765 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 2.1e-22
                                       EE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.......HHHH CS
                    Asparaginase_C   5 lklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseye..agkeler 79 
                                       +++  g+d++ l+ +l   a+G+v+egtG Gn++ +l +a+++a  + ++vv++s+c+ g +++ ++   +g  l++
  gi|313125654|ref|YP_004035924.1| 218 VHSGTGVDGASLERFL-PDADGIVVEGTGLGNATGSLGDAVADA-LESVPVVVSSRCHAGPTEAVYGTagGGVTLRD 292
                                       5667799999999998.7**************************.678****************97768999***** PP

                                       HTEEE-TT--HHHHHHHHHHHCTT---HHHHHHHH CS
                    Asparaginase_C  80 lgvisaddmtpeaarikLmlllgkgldpaevrklf 114
                                        gv +a+ +++++ar+kL l l+ gl+ ++v++ f
  gi|313125654|ref|YP_004035924.1| 293 HGVAYAGTLSTAKARVKLVLGLTAGLSREAVEATF 327
                                       *******************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1881.01
//
Query:       gi|313125655|ref|YP_004035925.1|  [L=63]
Description: hypothetical protein Hbor_08840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.083   12.7   0.3      0.094   12.5   0.3    1.0  1  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain


Domain annotation for each model (and alignments):
>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   5.2e-06     0.094     101     146 ..       8      53 ..       6      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-06
                                       ETTEEGTTSBHHHHHHHHHHHTHHHHHHHHHTTCCCCTTSSSEEEE CS
                   mRNA_cap_enzyme 101 ingvtvaeeplskRleilkkelikprneekktglletdkepfsvrl 146
                                       + +v+++++  ++Rl +l++ +++ + e++k++++ ++ +p ++r 
  gi|313125655|ref|YP_004035925.1|   8 CANVQYQKRRKYRRLPTLETAVQERQIEKRKSNCYPERDKPNRIRD 53 
                                       778999*******************************999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 398.06
//
Query:       gi|313125656|ref|YP_004035926.1|  [L=324]
Description: oxidoreductase, aryl-alcohol dehydrogenase like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-79  265.4   0.0    6.3e-79  265.2   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.2   0.0   3.5e-83   6.3e-79       1     291 [.      17     320 ..      17     323 .. 0.96

  Alignments for each domain:
  == domain 1  score: 265.2 bits;  conditional E-value: 3.5e-83
                                       .EEEE-SSS-ST......TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE.. CS
                      Aldo_ket_red   1 elglGtwqlgsk.....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv.. 70 
                                       e+ +Gtw++g +      e+ +e+a +ll+++ +aG +f+DtA++Yg g++ee++G +l++   +re+++ia+K+  
  gi|313125656|ref|YP_004035926.1|  17 EIAFGTWRFGREndegdIEVGPEQAHRLLDAYADAGGTFIDTADMYGGGRAEEYIGDWLAD--RDRENFVIASKIyw 91 
                                       699*******9999998899*****************************************..************99 PP

                                       --SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEE..S--HHH CS
                      Aldo_ket_red  71 dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvS..nfsveq 145
                                       + r +++ +gl+++++r++++e+l rLgtdyvD+l+ Hr+d ++p   e +++l+e+v+ Gk+ ++G+S  + ++++
  gi|313125656|ref|YP_004035926.1|  92 PTREDPNGVGLNRKHLRRNIDEILDRLGTDYVDVLYTHRWDDDTP-AREFMRTLDEFVRDGKVNYLGTStlEPNAWK 167
                                       99999****************************************.***********************77556888 PP

                                       HHHH....HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC------ CS
                      Aldo_ket_red 146 leka....kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkr 218
                                       + ka     k ++ +++++q +yn+++++ e ++l++c++++v+++++spl+gG+ltgky ++++++ ++++ + ++
  gi|313125656|ref|YP_004035926.1| 168 IAKAneiaDKRGYEPFTVSQPRYNVVNREIEGNYLDMCADYDVGVVPWSPLAGGFLTGKYSRNKEPPADSRAASDQQ 244
                                       8888899999*******************************************************999888887767 PP

                                       -...TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 219 d...ertsknldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                       +     t++n+da+e+++++a++ g s+ q+al+++l++++v+ +i+ga++++qle+nl+a e+ l+++++++l+ 
  gi|313125656|ref|YP_004035926.1| 245 FvdsYLTPENFDALEAVESVAADVGASPGQVALAWLLHHDQVTAPIVGARTVDQLEENLAAAEVSLTPDQFERLAD 320
                                       6999********************************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2038.17
//
Query:       gi|313125657|ref|YP_004035927.1|  [L=194]
Description: hypothetical protein Hbor_08860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-51  174.1   0.1    2.3e-51  173.8   0.1    1.1  1  DUF1684   Protein of unknown function (DUF1684)


Domain annotation for each model (and alignments):
>> DUF1684  Protein of unknown function (DUF1684)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.8   0.1   1.3e-55   2.3e-51       2     140 .]      45     187 ..      44     187 .. 0.98

  Alignments for each domain:
  == domain 1  score: 173.8 bits;  conditional E-value: 1.3e-55
                                       C--S-EE----GGGEEEEEEEE-CCEEEEEEEBSSSSCEEEEEEEEEEEEETTEE.EEEEEECTT.-CSSEEEEEEE CS
                           DUF1684   2 eFegleyfepdpawrveaelepadepeevevetstgeeveyervgevefelegkg.eLtvyreee.ekealfvpfrD 76 
                                       eF+gl+yf+p+p+ rv+a+++ +d+pe+v++et++g+ev+y r+ +++fel+g++ eL+ y++e+ +++a+fvpfrD
  gi|313125657|ref|YP_004035927.1|  45 EFSGLDYFDPNPDARVSATVTVHDDPEPVTMETTAGNEVRYLRLVTFSFELRGESvELHGYQQEReDDNAIFVPFRD 121
                                       7**************************************************9999*******99988999******* PP

                                       CCCCTTC-TT-EEEEE--TTTTT..EEEEEEGGGEB--HHHHTTTS--BB--GGGEESS---SSEE CS
                           DUF1684  77 atsgketYgggRyleleakkada..gtvvlDfNrAynppcAysdafsCPlppeeNrLdvaveAGek 140
                                       +t+g+++Y++gRylel+++++ a  ++vvlDfN+Ay+p+cAysd+fsCPlppeeN+L+vav AGe+
  gi|313125657|ref|YP_004035927.1| 122 KTTGQQSYRNGRYLELHPEGELAdgESVVLDFNLAYTPFCAYSDTFSCPLPPEENWLEVAVAAGER 187
                                       *******************99889999**************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 1176.83
//
Query:       gi|313125658|ref|YP_004035928.1|  [L=61]
Description: hypothetical protein Hbor_08870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.2    9.6   3.4        2.5    8.6   3.4    1.5  1  DUF2583   Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.4   0.00014       2.5      16      66 ..      11      59 ..       3      60 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00014
                           DUF2583 16 lGlllmvaslaysvlnqlpelelpellaeaallgifiGallWlaGarvgGr 66
                                      +Gl+lmv++    v + l + ++p +   +   ++ + a  Wl+G++  Gr
  gi|313125658|ref|YP_004035928.1| 11 VGLVLMVVGTLAFVPSALGTASVPVYALAV--AALVLTAGTWLVGTSGDGR 59
                                      788888888777788888888888776554..4555556679999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.32s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 386.81
//
Query:       gi|313125659|ref|YP_004035929.1|  [L=167]
Description: flagellin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-24   85.6   5.2    3.9e-24   85.4   2.3    2.0  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   2.3   2.1e-28   3.9e-24       1      75 [.      11      84 ..      11      94 .. 0.92
   2 ?    1.2   0.1     0.039     7e+02      49      79 ..     117     151 ..      86     153 .. 0.53

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.1e-28
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgknavslehkgGdsidtkdlkiv 75
                                      +AVSpViGviLmvaitvIlaAvi++fvl+l  s+++++pqas+ ++ d++as   ++v+++h+ Gd+i+t+ l++ 
  gi|313125659|ref|YP_004035929.1| 11 SAVSPVIGVILMVAITVILAAVIGTFVLNLgGSVSQTTPQASFGFDFDDDASG--DNVTITHETGDTIETDRLALK 84
                                      69****************************99***********9999999875..67*************998865 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.039
                           Pilin_N  49 sastgkna....vslehkgGdsidtkdlkivlnse 79 
                                       ++ +++++     +l   gG +++ +d ++v ns+
  gi|313125659|ref|YP_004035929.1| 117 GSFQSGETvgagDTLYAGGGMDLNGEDFRVVWNSQ 151
                                       22222222334467888889999999988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1040.18
//
Query:       gi|313125660|ref|YP_004035930.1|  [L=142]
Description: flagellin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-24   86.3   3.1    5.3e-24   85.0   1.9    1.9  2  Pilin_N   Archaeal Type IV pilin, N-terminal
     0.0083   16.0   5.2       0.51   10.2   0.2    2.1  2  PKD       PKD domain


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   1.9   5.9e-28   5.3e-24       1      72 [.      11      80 ..      11      90 .. 0.93
   2 ?    0.3   0.0      0.15   1.3e+03      57      80 ..     104     127 ..      91     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 5.9e-28
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgknavslehkgGdsidtkdl 72
                                      +AVSpViGviLmvaitvIlaAvi++fvl+l  s+++++pqas+ +++++s+++   +v+++h+ Gd+i+ + l
  gi|313125660|ref|YP_004035930.1| 11 SAVSPVIGVILMVAITVILAAVIGTFVLNLgGSVSQTTPQASFGFEYETSGDN---NVTITHETGDTIEGARL 80
                                      69****************************99***********9999999986...5***********98765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
                           Pilin_N  57 vslehkgGdsidtkdlkivlnseg 80 
                                        s+e k+G + + +++++v nse+
  gi|313125660|ref|YP_004035930.1| 104 SSVELKNGADWSGETIRVVWNSEN 127
                                       468899999999999999999876 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2   5.7e-05      0.51       7      61 ..      16      68 ..      11      73 .. 0.83
   2 !    7.7   1.1   0.00035       3.2       5      45 ..      97     138 ..      93     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.7e-05
                                      --BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEE CS
                               PKD  7 vlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvt 61
                                      v+ +   va t  +  +++ t+  ++g  sv q++ + ++   Y++ G+ +Vt t
  gi|313125660|ref|YP_004035930.1| 16 VIGVILMVAITVIL-AAVIGTFVLNLGG-SVSQTTPQASFGFEYETSGDNNVTIT 68
                                      55555556666666.788999*******.********************999987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00035
                                       -S--BSSEEEEEEEES..-SS-SEEEEE--SS--EEEEETTE CS
                               PKD   5 ptvlvpgatvaftaav.pdganvtysWdfgdgsvvqvlsept 45 
                                       ++ +++g +v++ ++  ++g+ ++  W+ ++  + ++lse+t
  gi|313125660|ref|YP_004035930.1|  97 GGTVSAGSSVELKNGAdWSGETIRVVWNSENNENSATLSEST 138
                                       6789************************99987777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 879.36
//
Query:       gi|313125661|ref|YP_004035931.1|  [L=932]
Description: hypothetical protein Hbor_08900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-07   31.4   7.1    2.4e-07   30.5   7.1    1.5  1  PGF-CTERM  PGF-CTERM motif
  ------ inclusion threshold ------
      0.068   13.6   6.4        1.3    9.6   0.0    4.8  5  MG2        MG2 domain


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   7.1   2.6e-11   2.4e-07       1      23 []     909     931 ..     909     931 .. 0.98

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.6e-11
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       tPGFG+v+A+++LLaaalLa Rr
  gi|313125661|ref|YP_004035931.1| 909 TPGFGVVVAVTALLAAALLAVRR 931
                                       9********************98 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.12   1.1e+03      33      80 ..      84     135 ..      67     151 .. 0.54
   2 ?    2.5   0.0     0.023     2e+02      38      82 ..     296     340 ..     275     350 .. 0.69
   3 ?    9.6   0.0   0.00014       1.3      32      93 ..     377     441 ..     360     444 .. 0.79
   4 ?   -2.8   0.0         1   9.2e+03      35      52 ..     577     594 ..     555     607 .. 0.53
   5 ?   -1.9   0.0      0.52   4.6e+03      55      86 ..     810     838 ..     775     847 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.12
                                       -EEEEEEEE-TTSSEEEEEEE.EE-CTTEEEEEEE--TT--S...EEEEEEE CS
                               MG2  33 klplkltirdpdgkevkelpl.atdetggaesefalpeaakl...Geysvel 80 
                                        ++ +lti+++ +++  + ++ +++++ +a+++    e++ l   G++++++
  gi|313125661|ref|YP_004035931.1|  84 LDSQSLTIKNATSGNEISATVsTSNNDISADFSQSAGENTTLyvnGTFTITA 135
                                       3555666666655544444441444443355555555554322235555555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.023
                                       EEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEE CS
                               MG2  38 ltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsa 82 
                                       + +++ ++++++ ++  ++ t++  + f + +++ +G+y++++ +
  gi|313125661|ref|YP_004035931.1| 296 VIVQSGEDEDFDAFQDGSTGTNSKVYVFSTDSDTNTGQYNITIGD 340
                                       55555555555555555556666788999************9933 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00014
                                       --EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT-...-SEEEEEEEEECSTTT-EEEEE CS
                               MG2  32 aklplkltirdpdgkevkelplatdetggaesefalpeaa...klGeysvelsadsaeeslssgs 93 
                                        ++p+++++ d+dg +v+e   + + +  +e++f+ +e+      G+y++ + +++ + +++s s
  gi|313125661|ref|YP_004035931.1| 377 GDRPITVELLDSDGDTVEERGARLSGQAKYEFTFNASEDKlnlDAGNYTILATDNQSSVDAESSS 441
                                       349**********************9999******9997622257*****996666555555555 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1
                                       EEEEEEE-TTSSEEEEEE CS
                               MG2  35 plkltirdpdgkevkelp 52 
                                         +l+++  +   +++++
  gi|313125661|ref|YP_004035931.1| 577 AGTLELTERNTTSIQTWT 594
                                       334444444444444444 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 0.52
                                       E-CTTEEEEEEE--TT--SEEEEEEEEECSTT CS
                               MG2  55 tdetggaesefalpeaaklGeysvelsadsae 86 
                                        +e+ +++ +++ +e+a   +y++++   +++
  gi|313125661|ref|YP_004035931.1| 810 VTENRTFSATVDFSEQAVGDTYEISI---DDS 838
                                       45666777788888888777888888...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (932 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 5606.59
//
Query:       gi|313125662|ref|YP_004035932.1|  [L=232]
Description: hypothetical protein Hbor_08910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-11   42.4   3.6    1.1e-10   41.6   3.6    1.5  1  DUF4129          Domain of unknown function (DUF4129)
  ------ inclusion threshold ------
      0.018   14.8   0.9      0.018   14.8   0.9    2.3  2  Trp_oprn_chp     Tryptophan-associated transmembrane protein 
      0.028   14.5   0.0       0.08   13.0   0.0    1.8  1  DUF3185          Protein of unknown function (DUF3185)
       0.59    9.6   1.6        1.1    8.7   1.6    1.4  1  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   3.6   2.5e-14   1.1e-10      13      69 .]     157     213 ..     145     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.5e-14
                           DUF4129  13 gldrrpgeTprEyarrvriapspaaalaalaelfeearYGgrpasaeeyrrlvealr 69 
                                          r + eTp+E+a+r+ +a+ p+ a+++l++lf  +rYGg+p++a+  +r+  al+
  gi|313125662|ref|YP_004035932.1| 157 EAHREAQETPTEFAQRASRAGLPRNAVERLTALFCSVRYGGEPPTADREKRAQNALE 213
                                       5678899**********77899*****************************999885 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.29   1.3e+03      73      83 ..      13      23 ..       4      52 .. 0.51
   2 ?   14.8   0.9   4.1e-06     0.018      64     114 ..      83     130 ..      80     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.29
                      Trp_oprn_chp 73 llalagagaav 83
                                      +lal+ +g+a+
  gi|313125662|ref|YP_004035932.1| 13 VLALSTVGVAA 23
                                      12222222222 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.1e-06
                      Trp_oprn_chp  64 glgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaave 114
                                        +gr vvgv+l lag+++++  ++l +d+++aar++++++++ ++ + + e
  gi|313125662|ref|YP_004035932.1|  83 TVGRLVVGVVLFLAGIALVL--WRLTSDDSQAARESEKETDV-STDEVTSE 130
                                       589***********998887..56677888888888855333.33333322 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.8e-05      0.08       2      31 ..      88     117 ..      87     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                           DUF3185   2 iiGiiLlvaGivLlvfGynasdSlgsqvse 31 
                                       ++G++L+ aGi+L+ + +++ dS + + se
  gi|313125662|ref|YP_004035932.1|  88 VVGVVLFLAGIALVLWRLTSDDSQAARESE 117
                                       69****************999997766555 PP

>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.6   0.00025       1.1      18      33 ..      87     102 ..      83     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHHHHHH CS
                   ATP1G1_PLM_MAT8  18 LifAglLfivGiliil 33 
                                       L+++++Lf++Gi+++l
  gi|313125662|ref|YP_004035932.1|  87 LVVGVVLFLAGIALVL 102
                                       99***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1429.64
//
Query:       gi|313125663|ref|YP_004035933.1|  [L=656]
Description: hypothetical protein Hbor_08920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-17   62.7   0.0      6e-17   61.7   0.0    1.6  1  DUF58        Protein of unknown function DUF58
    2.1e-07   31.1   1.7    2.1e-07   31.1   1.7    2.1  2  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.014   15.6   0.4      0.047   14.0   0.4    1.9  1  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0     1e-20     6e-17       1      85 [.     426     513 ..     426     514 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1e-20
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg...dekletavsaaasla 74 
                                       g++f+++ReY++gDpl+r+dW+  A+tgel + +f ++r ++v++v+d++pe++l  t+   +  + ++++aa  + 
  gi|313125663|ref|YP_004035933.1| 426 GIEFHSVREYRSGDPLSRVDWNRKAKTGELTTIDFRESRLAKVMIVVDTRPEAYLTPTEecdRPIIRRSLTAARKIT 502
                                       78*****************************************************9888887778888888888888 PP

                             DUF58  75 rqlldegdrvg 85 
                                       +++ +e  +vg
  gi|313125663|ref|YP_004035933.1| 503 THFSSERIPVG 513
                                       88888888877 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2      0.54   3.2e+03      28      68 ..     215     254 ..     207     262 .. 0.67
   2 !   31.1   1.7   3.5e-11   2.1e-07       1      78 [.     290     359 ..     290     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.54
                             DUF11  28 asangvvvtDtlPaglayvsvsasqgtasaltsv.gsLeage 68 
                                       +   +v+ +  +P+ ++  s +++  ++++++ +   L ag+
  gi|313125663|ref|YP_004035933.1| 215 DRGRTVTTRQYWPSHTSETSRTTK--SGRTRWVTtAALVAGG 254
                                       555678888889999998888888..4455555445666665 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 3.5e-11
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftv 76 
                                       +t+t + +++ p +++++t+t +Nt+ +++++++v D +Pagl+   +  +         + + L +g++at+++tv
  gi|313125663|ref|YP_004035933.1| 290 ITRTISDPNPEPQQEIDVTVTIQNTSESTLTDLRVIDGVPAGLTVTDGVPR---------FtTALRPGNEATFTYTV 357
                                       79999**************************************95555554.........2368************* PP

                             DUF11  77 rv 78 
                                       r 
  gi|313125663|ref|YP_004035933.1| 358 RG 359
                                       96 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   7.8e-06     0.047       5      69 ..     303     367 ..     300     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.8e-06
                       NPCBM_assoc   5 etvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGd 69 
                                       ++  +t+t+ n+ ++++t++++   +P+G tv+   p+  ++l+pG ++++t +V+   g  a+d
  gi|313125663|ref|YP_004035933.1| 303 QEIDVTVTIQNTSESTLTDLRVIDGVPAGLTVTDGVPRFTTALRPGNEATFTYTVRGVGGSHAFD 367
                                       67789**************************9999999999**************8776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 3562.93
//
Query:       gi|313125664|ref|YP_004035934.1|  [L=141]
Description: hypothetical protein Hbor_08930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        4.5    7.8  16.9        6.3    7.3   2.6    2.5  2  MerC         MerC mercury resistance protein
        6.4    7.1  21.7       0.13   12.6   7.4    2.5  2  DUF4395      Domain of unknown function (DUF4395)


Domain annotation for each model (and alignments):
>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.6    0.0019        17      64     112 ..       3      51 ..       1      68 [. 0.76
   2 ?    7.3   2.6    0.0007       6.3      19      59 ..      94     135 ..      84     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0019
                              MerC  64 tsvlvlgalGllillvalflgteaeetl..lfgslwqvltvlGaalLaiah 112
                                       ++vl+lg+lGl++l+v+lf  +   +t+   +g l+  ++v+G++ +a++ 
  gi|313125664|ref|YP_004035934.1|   3 PYVLALGILGLVLLAVGLFRAS--PKTFavGTGLLFVGVVVAGILGMASVY 51 
                                       689****************992..333344666777777777777777654 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0007
                              MerC  19 Pvllallpllglsf.lasellhqvllilvvaigllalvvgyr 59 
                                        ++l++ +++g ++ la+   + vl+++++++g++al+vg r
  gi|313125664|ref|YP_004035934.1|  94 MAILVVGASVGFGVfLAATGGQPVLALVALLVGVVALLVGLR 135
                                       567777888888886779999999999999999999999986 PP

>> DUF4395  Domain of unknown function (DUF4395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   7.4   1.4e-05      0.13      70     123 ..      23      75 ..      17      76 .. 0.78
   2 ?    1.6   4.5     0.036   3.2e+02      79     111 ..      99     131 ..      83     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                           DUF4395  70 aapkrFAqliGlvfllvalvlfllgapvlglvltalllvaafleaafgfClGCl 123
                                       a pk FA + Gl+f++v +++ l g++ + l l+a+l+v+a+     gf +G +
  gi|313125664|ref|YP_004035934.1|  23 ASPKTFAVGTGLLFVGVVVAGIL-GMASVYLLLAAFLVVIAWTVGQNGFSIGAE 75 
                                       78************988776665.566666777777777777769999999865 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.036
                           DUF4395  79 iGlvfllvalvlfllgapvlglvltalllvaaf 111
                                       +G+ + +  +++ + g pvl+lv++++ +va +
  gi|313125664|ref|YP_004035934.1|  99 VGASVGFGVFLAATGGQPVLALVALLVGVVALL 131
                                       566666666666666666666665555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 842.18
//
Query:       gi|313125665|ref|YP_004035935.1|  [L=41]
Description: hypothetical protein Hbor_08950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       122  (0.00680462); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 283.46
//
Query:       gi|313125666|ref|YP_004035936.1|  [L=355]
Description: hypothetical protein Hbor_08960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.55    8.9   3.1       0.68    8.6   3.1    1.1  1  MCLC      Mid-1-related chloride channel (MCLC)


Domain annotation for each model (and alignments):
>> MCLC  Mid-1-related chloride channel (MCLC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.1   3.8e-05      0.68     434     535 ..     196     299 ..     140     312 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 3.8e-05
                              MCLC 434 nkspevlrafdlpda..earehpevvpsekssvlntslketaellgestkkesstessqsakavsgqdaagtaegsp 508
                                         s + lr  + pd   e     +v   + +  l+++++e +e + ++t++es +  +++a+a+ gq++ g+  gs 
  gi|313125666|ref|YP_004035936.1| 196 VSSLDELREANEPDEddEPAGDKDVSFGDGPDPLSANPTELSEEPANATRAESESPPAETADAAGGQQSGGQQSGSQ 272
                                       5566677777777751134455667777888899*********************************9999999999 PP

                              MCLC 509 iaekaqlkldsegspeegstespasav 535
                                        +   q+++ s++   e+ t++p++  
  gi|313125666|ref|YP_004035936.1| 273 QSVSQQVETASQTVEAEAQTQTPTNEA 299
                                       999999999999999999999988643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1259  (0.0702214); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.94
# Mc/sec: 1142.39
//
Query:       gi|313125667|ref|YP_004035937.1|  [L=173]
Description: hypothetical protein Hbor_08970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 1045.09
//
Query:       gi|313125668|ref|YP_004035938.1|  [L=220]
Description: hypothetical protein Hbor_08980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.5e-11   42.4   8.5    8.5e-11   42.4   8.5    2.0  3  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
        4.3    6.9   8.3         13    5.4   7.9    2.1  2  Wzy_C        O-Antigen ligase


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.64   5.7e+03       3       3 ..      29      29 ..      11      59 .. 0.51
   2 !   42.4   8.5   9.5e-15   8.5e-11       2     118 ..      62     169 ..      61     171 .. 0.89
   3 ?   -2.6   0.1      0.85   7.7e+03      24      35 ..     189     200 ..     176     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.64
                       SNARE_assoc  3 s 3 
                                       
  gi|313125668|ref|YP_004035938.1| 29 E 29
                                      1 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 9.5e-15
                       SNARE_assoc   2 PsevllvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrllp 78 
                                       P+++l++++G+ fg+  g++ +++ ++l ++  yl++r++g + +r ++  e  v++          + ++l+rl+p
  gi|313125668|ref|YP_004035938.1|  62 PTTLLALVVGFGFGFA-GLPFALTLIVLTSVPPYLFARRYG-RTGRLAAAGESFVERTGD------LRSVVLSRLVP 130
                                       899999*******997.************************.777777777777776444......468******** PP

                       SNARE_assoc  79 ivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylG 118
                                         P+d+v++ aG+++v+f+ F+++t+iG  pwa+  +++G
  gi|313125668|ref|YP_004035938.1| 131 A-PSDVVSVGAGIAGVRFRWFVVGTAIGETPWAVAGVLAG 169
                                       5.8******************************9988888 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.85
                       SNARE_assoc  24 slgallGaslay 35 
                                       +++a l+a+l +
  gi|313125668|ref|YP_004035938.1| 189 VVAAALAAVLLF 200
                                       345555555555 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.9    0.0014        13      14     110 ..      32     147 ..       8     175 .. 0.71
   2 ?   -1.7   0.0      0.21   1.9e+03      48      64 ..     189     205 ..     183     216 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0014
                             Wzy_C  14 tsRsgiigl....lvalivlliifykrri..............pfllllgilvgvilliilfvlstnletlknitka 72 
                                        sR++++++    lva  v+l+i+   +                f++l+++l +++l  ++ +l  + ++ + +  a
  gi|313125668|ref|YP_004035938.1|  32 LSRAAWVAAdpvrLVAATVALAIVRPLLAwpttllalvvgfgfGFAGLPFALTLIVLTSVPPYLFARRYGRTGRLAA 108
                                       69999999997765555555544444444466666666666666666666666666666666677777777777777 PP

                             Wzy_C  73 fgkldkkkgkdksgssRlyiwkralplikdspilGtG.....v 110
                                        g     ++ +++g+ R  + +r++p+  d    G G     +
  gi|313125668|ref|YP_004035938.1| 109 AGE----SFVERTGDLRSVVLSRLVPAPSDVVSVGAGiagvrF 147
                                       775....999************999998888888888555443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.21
                             Wzy_C  48 vgvilliilfvlstnle 64 
                                       v++++l++++++  + +
  gi|313125668|ref|YP_004035938.1| 189 VVAAALAAVLLFAPTAY 205
                                       33333333333333334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1347.53
//
Query:       gi|313125669|ref|YP_004035939.1|  [L=504]
Description: phosphoglycerate mutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-80  268.6   0.1    4.3e-80  268.2   0.1    1.2  1  iPGM_N         BPG-independent PGAM N-terminus (iPGM_N)
    1.8e-72  243.7   0.1    2.1e-72  243.5   0.1    1.0  1  Metalloenzyme  Metalloenzyme superfamily
    5.3e-07   29.5   0.1    5.3e-06   26.3   0.1    2.3  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
    1.3e-06   28.1   0.1      2e-05   24.2   0.0    2.7  3  Sulfatase      Sulfatase
  ------ inclusion threshold ------
      0.019   15.1   0.2      0.039   14.0   0.2    1.4  1  PglZ           PglZ domain
        1.2    9.8   4.4         25    5.6   0.5    3.6  4  PGM_PMM_II     Phosphoglucomutase/phosphomannomutase, alpha/b


Domain annotation for each model (and alignments):
>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.2   0.1   1.4e-83   4.3e-80       1     215 []      79     290 ..      79     290 .. 0.95

  Alignments for each domain:
  == domain 1  score: 268.2 bits;  conditional E-value: 1.4e-83
                                       HHHHHHCTGGGG-HHHHHHHHHHHHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT CS
                            iPGM_N   1 inkaiedgslfenealkeaiekakkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapk 77 
                                       i++ai+dgs++en+al++a+++++++g+++H++GL+SdGgVHS+++hl+al+e+a+++gv ++v+haf+DGRDt+p+
  gi|313125669|ref|YP_004035939.1|  79 IEDAIADGSFYENDALNSAFDHVESTGGRVHFMGLVSDGGVHSEQQHLHALIEMAADRGV-EAVTHAFMDGRDTDPH 154
                                       789*********************************************************.899************* PP

                                       -HHHHHHHHHHHHHHCT--EEEEEEEHHHHT--SS-HHHHHHHHHHHCCSSSEEECTTHHHHHHHHHHTT--GGG-- CS
                            iPGM_N  78 saleyleeleeklkelgvgkiasvsGRyyaMDRdkrwervekaydalvkgegeskaesaveaieesyakgetDefve 154
                                        +++yl+ele+ ++  g+g++a+vsGRyyaMDRd++wer+++ayda+v++e+e +a++av+a++esy++getDefve
  gi|313125669|ref|YP_004035939.1| 155 GGEDYLTELESVAAAEGTGDVATVSGRYYAMDRDQNWERTRRAYDAIVNREAEFEAATAVDAVTESYDRGETDEFVE 231
                                       **************************************************9999999******************** PP

                                       -EEE...TCCGGS--TT-EEEE----CCCCHHHHHHHHSTT.HHCC..--TT-EEEESS-S-T CS
                            iPGM_N 155 ptviaeegkkegtikdgDaviffNFRaDRareltraltdke.fkefe.kakklklvtmteYde 215
                                       pt++    +  ++++dgDa iffNFR+DRar+l+r+l+d e   +f+ ++ +l+lvtmteYde
  gi|313125669|ref|YP_004035939.1| 232 PTLV----EGGAALEDGDAGIFFNFRPDRARQLCRMLADVEpEWAFDtSPPELRLVTMTEYDE 290
                                       ****....56799*************************643244444578999********96 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.5   0.1   6.9e-76   2.1e-72       2     247 ..       2     492 ..       1     493 [. 0.98

  Alignments for each domain:
  == domain 1  score: 243.5 bits;  conditional E-value: 6.9e-76
                                       EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH........SEEEEEESSSTT----HHHHHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                     Metalloenzyme   2 kvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerw.likahgtavglpeddmgnsevgHlel.......... 67 
                                       +++lv+lDG+G +  d+ +a++ A+tP++d+++++   ++ +++ +g +vglp+++mgnsevgHl++          
  gi|313125669|ref|YP_004035939.1|   2 QTALVILDGWGLGDHDRRDAVKAAETPNFDRFADT--GAYgTLEVSGRNVGLPDGQMGNSEVGHLNIgagrvvkqay 76 
                                       678********************************..8899************************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|313125669|ref|YP_004035939.1|  77 triedaiadgsfyendalnsafdhvestggrvhfmglvsdggvhseqqhlhaliemaadrgveavthafmdgrdtdp 153
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|313125669|ref|YP_004035939.1| 154 hggedyltelesvaaaegtgdvatvsgryyamdrdqnwertrraydaivnreaefeaatavdavtesydrgetdefv 230
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|313125669|ref|YP_004035939.1| 231 eptlveggaaledgdagiffnfrpdrarqlcrmladvepewafdtsppelrlvtmteydetfpfpvafppqepqdtl 307
                                       ***************************************************************************** PP

                                       ...........HHHHTT-----EEEEEEEE-S---SSHHHHHT--EEEE--SHHSTT--HHHHHHHHHHHH.CC.-S CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ...........lrisetvkfahvtffwnggrsgyfnpleereeipsdtvitfdlqpemkavevaekaldailsgkfd 133
                                                  lr++e +k+ahvt+f nggr+ +f++ e r  i+s+ v t+d +pem+a++v++ a++ i s++ d
  gi|313125669|ref|YP_004035939.1| 308 getlsavgktqLRLAESEKYAHVTYFLNGGREVEFDG-EIRRIIESPDVPTYDQKPEMSAEDVTDTAIELIDSDDPD 383
                                       ***********99************************.*************************************** PP

                                       EEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 134 lvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPil 210
                                        +v+n++n+DmvGHtgd+ a+iaa+ea+De+++++++a++  +g +++tADHgna+dm +  ++p+T+Ht++pVP++
  gi|313125669|ref|YP_004035939.1| 384 AMVLNYANPDMVGHTGDFDAAIAAVEAVDEQLGRLVEAVQTAGGHVLITADHGNADDMGT-AETPHTAHTTNPVPLV 459
                                       ************************************************************.99************** PP

                                       EESTT----S--SSHHHHTT-TTEEEEGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 211 ivgkglapdkvkegakfrekggLanvaatllnllgle 247
                                        + ++ +     +  ++r+ g+L+++a+t+l+l+ +e
  gi|313125669|ref|YP_004035939.1| 460 SLTPDGDD----GARTVRSFGSLCDIAPTMLELMEIE 492
                                       99998665....5557888**************9987 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.14   4.2e+02       3      35 ..       5      41 ..       3      45 .. 0.67
   2 !   26.3   0.1   1.8e-09   5.3e-06     163     235 ..     371     438 ..     286     453 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                                      EEEETT-B......TTHHHHHGSTSHHHHHHHHHSEEES CS
                      Phosphodiest  3 vislDGlr......adlldrlaellpnlaaLakegvsap 35
                                      +++lDG         d +++   ++pn++++a++g +++
  gi|313125669|ref|YP_004035939.1|  5 LVILDGWGlgdhdrRDAVKA--AETPNFDRFADTGAYGT 41
                                      56677776433222344444..5************9987 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.8e-09
                                       SHHHHHCT...SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---E CS
                      Phosphodiest 163 kvvlekel...ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGma 235
                                       + ++e  l   ++pd +++++ ++D vgH  G d  +  +a++ vD+ +g+L+ea++         +++++DHG a
  gi|313125669|ref|YP_004035939.1| 371 DTAIE--LidsDDPDAMVLNYANPDMVGH-TG-DFDAAIAAVEAVDEQLGRLVEAVQTA----GGHVLITADHGNA 438
                                       33333..13469*****************.55.6567899*****************99....789********66 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0       2.9   8.6e+03      24      36 ..      25      37 ..       6      44 .. 0.60
   2 ?   -0.8   0.0      0.26   7.7e+02      76     124 ..     120     163 ..     103     223 .. 0.70
   3 !   24.2   0.0   6.7e-09     2e-05     209     308 ..     399     490 ..     310     491 .. 0.70

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 2.9
                                      CSSHHHHHHHHTS CS
                         Sulfatase 24 attpnldrlaeeg 36
                                      a+tpn+dr a+ g
  gi|313125669|ref|YP_004035939.1| 25 AETPNFDRFADTG 37
                                      3466666666554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.26
                                       HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEET CS
                         Sulfatase  76 gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgf 124
                                        + +q+ ++L+e+  ++G++      +h +++ r++  +++g d++ + 
  gi|313125669|ref|YP_004035939.1| 120 HSEQQHLHALIEMAADRGVEA----VTHAFMDGRDTD-PHGGEDYLTEL 163
                                       678899999999999999998....778888888884.44444444443 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 6.7e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTS CS
                         Sulfatase 209 qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgek 285
                                          +a  ++ve vD+++gr+++a+    +     v++t+Dhg + + +++   +     + +    vPl+   p++ 
  gi|313125669|ref|YP_004035939.1| 399 GDFDAAIAAVEAVDEQLGRLVEAV----QTAGGHVLITADHGNADDMGTAETPH-----TAHTTNPVPLVSLTPDGD 466
                                       55678899****************....777778*********66442222222.....22334459********** PP

                                       HC.EEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 286 ap.rvseelvshiDlfptildlag 308
                                          r++  + s+ D++pt+l+l+ 
  gi|313125669|ref|YP_004035939.1| 467 DGaRTVRSFGSLCDIAPTMLELME 490
                                       999*******************96 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.3e-05     0.039     123     169 ..     393     437 ..     359     439 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                              PglZ 123 DalgdkasteqksfeaveeslkelkelvkslleengykvlltaDHGf 169
                                       D++g+ +    +  +ave   ++l +lv+ +  + g +vl+taDHG+
  gi|313125669|ref|YP_004035939.1| 393 DMVGH-TGDFDAAIAAVEAVDEQLGRLVEAVQTA-GGHVLITADHGN 437
                                       66666.2233333444444444788888888888.99*********7 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.9   1.2e+04      65      82 ..     121     137 ..      91     142 .. 0.70
   2 ?   -0.4   0.0      0.61   1.8e+03      52      83 ..     286     319 ..     281     322 .. 0.75
   3 ?    5.6   0.5    0.0083        25      55      95 ..     352     394 ..     345     402 .. 0.89
   4 ?    2.7   0.1     0.064   1.9e+02      62      99 ..     407     444 ..     394     448 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.9
                                       --TT-TTTTHHHHGGGGG CS
                        PGM_PMM_II  65 peekealkllielvkkeg 82 
                                        e+ ++l++lie++ + g
  gi|313125669|ref|YP_004035939.1| 121 SEQ-QHLHALIEMAADRG 137
                                       444.77777777777655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.61
                                       ----TT-TT..SS----TT-TTTTHHHHGGGGG- CS
                        PGM_PMM_II  52 aepdpdfpt..kapnpeekealkllielvkkega 83 
                                        e d++fp    +p  e++++l +   +v k++ 
  gi|313125669|ref|YP_004035939.1| 286 TEYDETFPFpvAFPPQEPQDTLGETLSAVGKTQL 319
                                       5789999999777777777788888887777665 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0083
                                       -TT-TT..SS----TT-TTTTHHHHGGGGG-SEEEEE-TTS-B CS
                        PGM_PMM_II  55 dpdfpt..kapnpeekealkllielvkkegadlglafDgDaDR 95 
                                       +pd pt  + p++ ++++ + +iel+++++ d+++ ++ + D 
  gi|313125669|ref|YP_004035939.1| 352 SPDVPTydQKPEMSAEDVTDTAIELIDSDDPDAMVLNYANPDM 394
                                       6888998899*****99******************99988775 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.064
                                       S----TT-TTTTHHHHGGGGG-SEEEEE-.TTS-BEEEE CS
                        PGM_PMM_II  62 apnpeekealkllielvkkegadlglafD.gDaDRlgvv 99 
                                       a++  + e+l +l+e+v+  g ++ +  D g+aD +g +
  gi|313125669|ref|YP_004035939.1| 407 AVEAVD-EQLGRLVEAVQTAGGHVLITADhGNADDMGTA 444
                                       444444.78888888888888866666664677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3183.80
//
Query:       gi|313125670|ref|YP_004035940.1|  [L=240]
Description: hypothetical protein Hbor_09000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-35  121.0   9.5      6e-35  120.6   9.5    1.1  1  DUF1405   Protein of unknown function (DUF1405)


Domain annotation for each model (and alignments):
>> DUF1405  Protein of unknown function (DUF1405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   9.5   3.4e-39     6e-35       2     157 .]      44     217 ..      43     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 3.4e-39
                           DUF1405   2 tvyGyiyYgk...qlaetplllwpfvpDSPtAtlffalallllll...........grelellealAfvtlikyGlW 64 
                                       +++G+ +Y++    l++ + ll+p+++DSPtA ++ +l+l++ll+           ++ l+++++lAfv+l+kyG+W
  gi|313125670|ref|YP_004035940.1|  44 FLVGVSFYVHsdpSLRDVSSLLYPLFGDSPTALALGTLSLATLLPhlgnrvrdaptNYPLTVIHTLAFVWLVKYGVW 120
                                       689*****9655578888**********************************9999999****************** PP

                           DUF1405  65 tvvvlllvllkgg..........leelmLilsHlamavealllarilrfsvkalavalawlllndvvDYvlgvlpel 131
                                       tvv+l+l     +          ++ + ++l+Hl+++veall++ + ++++ ala+ala++++ndv+DY++g++p+l
  gi|313125670|ref|YP_004035940.1| 121 TVVALNLRP---DlyfgftpdllWDYWGIMLTHLFFLVEALLIPYYGKTTRSALALALALAFVNDVYDYGFGFYPPL 194
                                       *****9987...2224577789999999************************************************* PP

                           DUF1405 132 hetleeeleliaafavvltvlsllla 157
                                       ++++     l++a++++l+vls++la
  gi|313125670|ref|YP_004035940.1| 195 KYEA---GVLLTAITIALSVLSVALA 217
                                       *777...999***********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1510.82
//
Query:       gi|313125671|ref|YP_004035941.1|  [L=222]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-19   67.8   0.9    4.7e-16   58.4   0.1    2.8  3  HTH_5            Bacterial regulatory protein, arsR family
    2.8e-16   59.3   6.5      4e-13   49.2   0.1    3.1  3  HTH_20           Helix-turn-helix domain
      8e-16   57.7   5.3    5.7e-09   35.7   0.1    3.2  3  MarR_2           MarR family
    4.7e-13   48.8   0.0      4e-06   26.6   0.0    2.5  2  TrmB             Sugar-specific transcriptional regulator Trm
    7.1e-13   48.3   0.4    1.3e-07   31.4   0.1    2.8  2  MarR             MarR family
    1.5e-09   37.7   0.4    8.7e-05   22.4   0.1    2.5  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    1.7e-09   37.1   2.6    3.1e-06   26.6   0.2    3.6  3  HTH_24           Winged helix-turn-helix DNA-binding
    1.7e-09   37.7   0.0     0.0002   21.5   0.0    2.3  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    4.6e-08   33.4   0.2     0.0009   19.7   0.1    2.5  2  HTH_27           Winged helix DNA-binding domain
      5e-07   30.0   0.0     0.0045   17.3   0.0    2.3  2  Rrf2             Transcriptional regulator
      9e-07   28.6   0.1      0.018   14.8   0.0    2.7  2  LexA_DNA_bind    LexA DNA binding domain
    1.5e-06   28.0   0.0     0.0035   17.1   0.0    2.5  2  DUF4423          Domain of unknown function (DUF4423)
    4.1e-06   26.8   3.2    0.00018   21.6   0.0    2.9  2  DprA_WH          DprA winged helix domain
      1e-05   25.3   0.5    6.8e-05   22.7   0.0    2.4  2  HTH_11           HTH domain
    1.5e-05   24.8   0.3     0.0026   17.7   0.1    3.6  3  PadR             Transcriptional regulator PadR-like family
      2e-05   24.1   0.1       0.14   11.8   0.1    2.6  2  GntR             Bacterial regulatory proteins, gntR family
    6.2e-05   22.7   0.0      0.012   15.4   0.0    3.2  3  HTH_10           HTH DNA binding domain
    7.4e-05   22.8   0.0      0.062   13.4   0.0    2.4  2  DUF2250          Uncharacterized protein conserved in archaea
    0.00011   22.1   0.9       0.85    9.6   0.3    3.0  2  HTH_1            Bacterial regulatory helix-turn-helix protei
    0.00014   21.3   0.0    0.00027   20.4   0.0    1.4  1  HTH_CodY         CodY helix-turn-helix domain
    0.00014   21.9   3.4      0.019   15.1   0.2    2.8  2  HTH_28           Helix-turn-helix domain
    0.00021   21.0   0.0       0.07   12.8   0.0    2.4  2  RP-C             Replication protein C N-terminal domain
    0.00047   20.1   0.4        1.3    9.1   0.1    2.5  2  HTH_29           Winged helix-turn helix
    0.00049   19.9   2.5       0.16   11.8   0.0    3.7  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    0.00055   19.8   0.0      0.053   13.5   0.0    2.4  2  HTH_36           Helix-turn-helix domain
    0.00057   19.4   0.0       0.37   10.4   0.0    2.4  2  HTH_47           winged helix-turn-helix
     0.0015   18.3   0.3        2.8    7.9   0.1    2.8  2  HTH_23           Homeodomain-like domain
      0.002   18.1   0.0        1.5    9.0   0.0    3.1  3  HemN_C           HemN C-terminal domain
     0.0033   16.8   0.0        1.5    8.3   0.0    2.7  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
     0.0041   17.2   0.2        2.8    8.2   0.0    2.7  2  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
     0.0045   16.6   0.0     0.0093   15.6   0.0    1.4  1  DDRGK            DDRGK domain
     0.0065   16.1   0.0       0.17   11.5   0.0    2.2  2  ArsR             ArsR transcriptional regulator
     0.0067   16.1   0.1        1.2    8.8   0.0    2.7  2  Sigma70_r4_2     Sigma-70, region 4
  ------ inclusion threshold ------
       0.01   15.9   0.0       0.05   13.6   0.0    1.9  2  DUF2089          Protein of unknown function (DUF2089)
      0.012   15.8   0.1       0.55   10.5   0.1    2.4  2  PaaX             PaaX-like protein
      0.014   15.2   0.1        1.8    8.5   0.0    2.3  2  TFIIE_alpha      TFIIE alpha subunit
      0.018   14.8   0.2       0.17   11.6   0.0    2.4  2  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.018   15.2   0.0       0.71   10.1   0.0    2.3  2  B-block_TFIIIC   B-block binding subunit of TFIIIC
       0.02   15.6   0.0        3.1    8.5   0.0    2.3  2  RPA_C            Replication protein A C terminal
       0.02   14.8   0.1       0.18   11.8   0.0    2.4  2  Cdc6_C           CDC6, C terminal winged helix domain
      0.025   14.9   0.0       0.33   11.3   0.0    2.1  2  DUF2513          Hypothetical protein (DUF2513)
      0.029   14.1   0.5       0.73    9.7   0.1    3.0  2  MerR             MerR family regulatory protein
      0.037   13.9   0.0       0.21   11.5   0.0    2.0  2  HxlR             HxlR-like helix-turn-helix
      0.039   14.0   0.1        9.8    6.3   0.0    3.0  3  Sulfolobus_pRN   Sulfolobus plasmid regulatory protein
      0.039   13.8   0.1        1.5    8.7   0.0    3.0  3  IF2_N            Translation initiation factor IF-2, N-termin
      0.049   13.5   6.0       0.31   10.9   0.1    3.4  3  HTH_IclR         IclR helix-turn-helix domain
       0.05   13.9   0.0        6.1    7.2   0.0    2.5  2  Penicillinase_R  Penicillinase repressor
      0.059   12.9   0.0         14    5.3   0.0    2.5  2  GerE             Bacterial regulatory proteins, luxR family
      0.064   13.3   0.0         15    5.8   0.0    2.5  2  FeoC             FeoC like transcriptional regulator
        0.1   12.6   4.1       0.64   10.1   0.1    2.8  2  BLACT_WH         Beta-lactamase associated winged helix domai
       0.11   12.8   0.1       0.53   10.5   0.1    2.0  2  DUF3572          Protein of unknown function (DUF3572)
       0.11   11.4   0.0       0.22   10.5   0.0    1.4  2  TnsD             Tn7-like transposition protein D
       0.18   12.2   0.0       0.38   11.2   0.0    1.6  1  FaeA             FaeA-like protein
       0.18   12.3   0.1        5.9    7.4   0.0    2.5  2  HTH_40           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   1.4e-18   4.7e-16       1      47 []      12      58 ..      12      58 .. 0.97
   2 ?   -1.9   0.0       9.8   3.3e+03      35      40 ..     127     132 ..     116     134 .. 0.67
   3 ?    7.2   0.0     0.014       4.6       9      46 ..     171     208 ..     168     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.4e-18
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +++R++IL+lL+ ++++v+e++e+lg+s+ +v  HL+kL++aGL+e+
  gi|313125671|ref|YP_004035941.1| 12 NENRRRILRLLSHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIES 58
                                      589******************************************86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 9.8
                                       HHHHHH CS
                             HTH_5  35 HLkkLr 40 
                                       HL+ L+
  gi|313125671|ref|YP_004035941.1| 127 HLADLE 132
                                       666666 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.014
                                       HHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   9 klLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                        + a+ge++v   a+el+ s+ +v +   +L e GL++
  gi|313125671|ref|YP_004035941.1| 171 AAIARGEQTVDGVARELNASPEAVEEAVHRLAERGLIS 208
                                       57899****************99988777777777775 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   1.2e-15     4e-13       3      58 ..       6      60 ..       4      63 .. 0.96
   2 ?    1.5   0.2      0.92   3.1e+02      20      35 ..     111     126 ..     103     154 .. 0.78
   3 !   11.0   0.2   0.00099      0.33      17      61 .]     171     214 ..     147     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.2e-15
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      ++++L+++ Rrrilr+L + ++  ++e+ e l++s++ + +HLr+Le+agL+e+++
  gi|313125671|ref|YP_004035941.1|  6 LLDLLGNENRRRILRLL-SHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIESRT 60
                                      6899*************.***********************************998 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.92
                                       STCTTB-HHHHHHHHT CS
                            HTH_20  20 araegltaselaerld 35 
                                       +r++++ ++ela++l+
  gi|313125671|ref|YP_004035941.1| 111 PREDAQDLNELARELG 126
                                       78999999*****995 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00099
                                       HHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  17 raLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       +a+  ++++t+  +a++l  s+  +   ++ L+e gL+ +++eg+
  gi|313125671|ref|YP_004035941.1| 171 AAI-ARGEQTVDGVARELNASPEAVEEAVHRLAERGLISREDEGW 214
                                       455.788999999******************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1   1.7e-11   5.7e-09       7      62 .]      15      65 ..       8      65 .. 0.95
   2 ?   -0.6   0.0       3.8   1.3e+03      24      32 ..     118     126 ..     108     129 .. 0.76
   3 !   22.5   0.2   2.4e-07     8e-05      10      55 ..     169     211 ..     166     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.7e-11
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                       +r+L  L + p   + v+e+ ++lg+s+ av  +l++L++aGL+e r++  D R+
  gi|313125671|ref|YP_004035941.1| 15 RRRILRLLSHKP---CYVTEISEYLGVSPKAVIDHLRKLEDAGLIESRTD--DQRR 65
                                      5899*******9...9*********************************9..9886 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.8
                                       HHHHHHHHT CS
                            MarR_2  24 vgelarrlg 32 
                                        +elar+lg
  gi|313125671|ref|YP_004035941.1| 118 LNELARELG 126
                                       679999998 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 2.4e-07
                                       HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                        Laa++r++    tv  +ar+l+ s+ av  ++ rL ++GL+ r++
  gi|313125671|ref|YP_004035941.1| 169 TLAAIARGE---QTVDGVARELNASPEAVEEAVHRLAERGLISRED 211
                                       799*****9...5*****************************9985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.2e-08     4e-06      16      64 ..      20      69 ..      18      73 .. 0.89
   2 !   19.6   0.0   1.8e-06   0.00061      11      57 ..     163     212 ..     159     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.2e-08
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYra 64
                                       Ll+++p  ++ei+e lgv+   v + Lr+Led+Gl+e +    +++Y  
  gi|313125671|ref|YP_004035941.1| 20 RLLSHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIESRTDDqRRKYFH 69
                                      69************************************999664667765 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.8e-06
                                       CCHCHHHH...HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  11 akvYlaLl...klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                       ++ Y+  l   ++g+ t+d +a+el+ +   v e++ +L ++Gl+ re++
  gi|313125671|ref|YP_004035941.1| 163 SRFYAETLaaiARGEQTVDGVARELNASPEAVEEAVHRLAERGLISREDE 212
                                       5556544446689*********************************9976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1     4e-10   1.3e-07       8      56 ..      18      63 ..      12      66 .. 0.85
   2 !   14.0   0.0    0.0001     0.035      15      50 ..     175     210 ..     173     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4e-10
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTST CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDr 56
                                      iLr+l ++ p++v+e+ + lgvs+ +v   l++Le++Glie++ +  D+
  gi|313125671|ref|YP_004035941.1| 18 ILRLL-SHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIESRTD--DQ 63
                                      56655.5789********************************998..44 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.0001
                                       STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  15 qgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       +g+++v   a+ l+ s+ +v ++++rL ++Gli+R+
  gi|313125671|ref|YP_004035941.1| 175 RGEQTVDGVARELNASPEAVEEAVHRLAERGLISRE 210
                                       578888899**************************7 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   2.6e-07   8.7e-05      20      53 ..      25      59 ..       3      77 .. 0.70
   2 !   13.4   0.0   0.00017     0.055      27      54 ..     183     210 ..     144     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.6e-07
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis.r 53
                                       p   +e++++lG+++  v   l++L+++gli+ r
  gi|313125671|ref|YP_004035941.1| 25 KPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIEsR 59
                                      377779***************************64 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00017
                                       HHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2  27 lAsmlGltretvsrilseLkreglisrg 54 
                                        A+ l++++e v  + ++L ++glisr+
  gi|313125671|ref|YP_004035941.1| 183 VARELNASPEAVEEAVHRLAERGLISRE 210
                                       6999**********************74 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.2   9.3e-09   3.1e-06       2      48 .]      12      57 ..      11      57 .. 0.92
   2 ?   -1.5   0.0       5.6   1.9e+03      21      28 ..     119     126 ..     118     127 .. 0.86
   3 !    7.8   0.0    0.0071       2.4      19      47 ..     179     207 ..     170     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9.3e-09
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +e++r+IL+lL  +p +  +e++e lg+Sp +v  +l++Le++GlI+
  gi|313125671|ref|YP_004035941.1| 12 NENRRRILRLLSHKP-CYVTEISEYLGVSPKAVIDHLRKLEDAGLIE 57
                                      789999999999966.5589**************************7 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.6
                            HTH_24  21 reLAerlg 28 
                                       +eLA++lg
  gi|313125671|ref|YP_004035941.1| 119 NELARELG 126
                                       69****99 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0071
                            HTH_24  19 sqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +   +A++l+ Sp +v + + rL e GlI
  gi|313125671|ref|YP_004035941.1| 179 TVDGVARELNASPEAVEEAVHRLAERGLI 207
                                       55668***********************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     6e-07    0.0002      12      53 ..      17      57 ..      16      62 .. 0.91
   2 !   13.8   0.0   0.00016     0.052      26      53 ..     181     208 ..     174     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6e-07
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                       I++l  ++k+  +++++e L+vsp  V   l+kLe++G++e
  gi|313125671|ref|YP_004035941.1| 17 RILRLL-SHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIE 57
                                      577888.99999****************************97 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00016
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  26 kdlaerLnvspssVsemlkkLekdGyve 53 
                                         +a++Ln sp  V e + +L++ G++ 
  gi|313125671|ref|YP_004035941.1| 181 DGVARELNASPEAVEEAVHRLAERGLIS 208
                                       569**********************986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   2.7e-06    0.0009      21      62 ..      29      68 ..       7      71 .. 0.83
   2 !   11.3   0.0    0.0011      0.37       8      52 ..     169     210 ..     166     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.7e-06
                            HTH_27 21 ladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrv 62
                                       ++++++l v+  +++  l+kL+ +GL+e+ +d+  +r+k +
  gi|313125671|ref|YP_004035941.1| 29 VTEISEYLGVSPKAVIDHLRKLEDAGLIESRTDD--QRRKYF 68
                                      589*************************999986..555544 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0011
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52 
                                       +L  i+  r++++   +++ ln +  ++ +++ +L e+GL+ r +
  gi|313125671|ref|YP_004035941.1| 169 TLAAIA--RGEQTVDGVARELNASPEAVEEAVHRLAERGLISR-E 210
                                       677777..88999999*************************33.3 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.4e-05    0.0045      24      58 ..      25      59 ..      17      60 .. 0.90
   2 !   10.4   0.0     0.002      0.66      22      56 ..     175     208 ..     163     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-05
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksv 58
                                      +p+ ++ei+e  ++sp+ +   l+kL+ agl++s+
  gi|313125671|ref|YP_004035941.1| 25 KPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIESR 59
                                      56899****************************97 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.002
                                       TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  22 eeepvsseeiaerqnispsylekilakLrkaglvk 56 
                                       ++e  +++ +a++ n sp+ +e  +++L++ gl+ 
  gi|313125671|ref|YP_004035941.1| 175 RGE-QTVDGVARELNASPEAVEEAVHRLAERGLIS 208
                                       333.5999*************************96 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.4e-05     0.018      28      61 ..      29      61 ..      16      65 .. 0.85
   2 !   11.0   0.0   0.00082      0.27      30      60 ..     182     211 ..     178     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.4e-05
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyierdpg 61
                                      + ei++ lg++ p+av  hL++Le  G+ie    
  gi|313125671|ref|YP_004035941.1| 29 VTEISEYLGVS-PKAVIDHLRKLEDAGLIESRTD 61
                                      789******96.*****************96544 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00082
                                       HHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                     LexA_DNA_bind  30 eiaralglkSpsaveehLkaLerKGyierdp 60 
                                        +ar+l+ +Sp+avee  ++L+ +G+i r++
  gi|313125671|ref|YP_004035941.1| 182 GVARELN-ASPEAVEEAVHRLAERGLISRED 211
                                       5778888.57*****************9987 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0045       1.5      29      74 ..      21      62 ..      12      81 .. 0.81
   2 !   17.1   0.0   1.1e-05    0.0035      28      79 ..     169     217 ..     165     222 .] 0.90

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0045
                           DUF4423 29 llplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedg 74
                                      ll+ k+    + e+++ l+  +s + v + l+ L+++gl++   d+
  gi|313125671|ref|YP_004035941.1| 21 LLSHKPC--YVTEISEYLG--VSPKAVIDHLRKLEDAGLIESRTDD 62
                                      5555555..689*******..********************99883 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.1e-05
                           DUF4423  28 ellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqt 79 
                                       +l+++  ++++++ +a+ l+  +s e ve+a+ +L + gl+ ++ +  ++++
  gi|313125671|ref|YP_004035941.1| 169 TLAAIARGEQTVDGVARELN--ASPEAVEEAVHRLAERGLISREDE-GWVVA 217
                                       5899999*************..**********************98.77665 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.4e-07   0.00018      12      58 ..      13      59 ..       3      61 .. 0.94
   2 ?    5.0   0.2      0.08        27      17      46 ..     169     198 ..     158     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.4e-07
                           DprA_WH 12 dlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverl 58
                                      + +rr+L +L++ P+ v ++++ +g+++ +v  +L  LE aGl+e++
  gi|313125671|ref|YP_004035941.1| 13 ENRRRILRLLSHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIESR 59
                                      689*****************************************975 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.08
                           DprA_WH  17 vLaaLgpePvhvDqLvrrtglpaaevsaaL 46 
                                        Laa++    +vD ++r++ +++++v  a 
  gi|313125671|ref|YP_004035941.1| 169 TLAAIARGEQTVDGVARELNASPEAVEEAV 198
                                       589999999***************997765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.1e-07   6.8e-05       2      49 ..      15      59 ..      14      61 .. 0.88
   2 ?   -0.5   0.0       3.6   1.2e+03      22      43 ..     184     205 ..     174     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.1e-07
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIese 49
                                      ++ il+lL +++ p    e++e+L+vS ++v  ++++Le++g  Ies+
  gi|313125671|ref|YP_004035941.1| 15 RRRILRLL-SHK-PCYVTEISEYLGVSPKAVIDHLRKLEDAG-LIESR 59
                                      68899999.555.5999*************************.77775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.6
                            HTH_11  22 AeeLnvSrrtvrrdIkaLeelg 43 
                                       A+eLn S  +v   + +L e g
  gi|313125671|ref|YP_004035941.1| 184 ARELNASPEAVEEAVHRLAERG 205
                                       8899999999999999987766 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     8e-06    0.0026       1      66 [.      18      71 ..      18      78 .. 0.81
   2 ?    0.1   0.0       2.4   7.9e+02      19      43 ..     131     155 ..     125     157 .. 0.73
   3 ?    1.2   0.0       1.1   3.5e+02      37      52 ..     197     212 ..     184     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8e-06
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEES CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlT 66
                                      iL ll+++p y +ei + l         +s+  + + L++Le+ gl+es+ +++    +rky+++ 
  gi|313125671|ref|YP_004035941.1| 18 ILRLLSHKPCYVTEISEYLG--------VSPKAVIDHLRKLEDAGLIESRTDDQ----RRKYFHIS 71
                                      78888888888888776554........455568899*************9986....9****996 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.4
                                       HHCCSTT-CCTTHHHHHHHHHHHHH CS
                              PadR  19 leelsegllelseGslYpaLkrLek 43 
                                       le+ ++ + +  +G++ ++L+rL +
  gi|313125671|ref|YP_004035941.1| 131 LENELSLAQRWVHGRITDVLDRLNE 155
                                       4555555567789999999999976 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.1
                                       HHHHHHHTTSEEEEEE CS
                              PadR  37 aLkrLekeglvesewe 52 
                                       a +rL + gl+++e e
  gi|313125671|ref|YP_004035941.1| 197 AVHRLAERGLISREDE 212
                                       689********99865 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0024      0.79      27      57 ..      29      59 ..      20      62 .. 0.93
   2 !   11.8   0.1   0.00042      0.14      30      58 ..     183     211 ..     178     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0024
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverr 57
                                      + e+++ +gVs   v   Lr+Le +gl+e+r
  gi|313125671|ref|YP_004035941.1| 29 VTEISEYLGVSPKAVIDHLRKLEDAGLIESR 59
                                      57999***********************998 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00042
                                       HHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR  30 LaaefgVsrttvReALrrLeaeglverrq 58 
                                       +a e++ s   v eA  rL+++gl+ r++
  gi|313125671|ref|YP_004035941.1| 183 VARELNASPEAVEEAVHRLAERGLISRED 211
                                       6899*********************9986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.6e-05     0.012      25      48 ..      28      51 ..      24      53 .. 0.89
   2 ?    1.5   0.0      0.76   2.5e+02      18      34 ..     108     126 ..     108     138 .. 0.86
   3 ?    1.4   0.0      0.82   2.7e+02      25      46 ..     179     200 ..     177     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-05
                            HTH_10 25 tlkeLAkelGIskstlsehLrkae 48
                                       + e+++ lG+s+ ++ +hLrk e
  gi|313125671|ref|YP_004035941.1| 28 YVTEISEYLGVSPKAVIDHLRKLE 51
                                      5789*****************976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.76
                            HTH_10  18 FdyPRr..vtlkeLAkelG 34 
                                       Fd PR+   +l+eLA elG
  gi|313125671|ref|YP_004035941.1| 108 FDIPREdaQDLNELARELG 126
                                       888886336899***9998 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.82
                            HTH_10  25 tlkeLAkelGIskstlsehLrk 46 
                                       t++ +A el+ s+ +++e + +
  gi|313125671|ref|YP_004035941.1| 179 TVDGVARELNASPEAVEEAVHR 200
                                       566799***********99876 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00019     0.062      13      56 ..      18      60 ..       8      75 .. 0.83
   2 ?    6.9   0.0      0.02       6.8      28      57 ..     183     212 ..     180     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00019
                           DUF2250 13 vlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      +l+ l   ++ Y   i+++l ++ + v + l+kLe++GL+e  +
  gi|313125671|ref|YP_004035941.1| 18 ILRLL-SHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIESRT 60
                                      55444.357889999*************************9876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.02
                           DUF2250  28 iakeleipleevrellkkLeelGLlerveg 57 
                                       +a+el+++ e v+e++++L e GL+ r ++
  gi|313125671|ref|YP_004035941.1| 183 VARELNASPEAVEEAVHRLAERGLISREDE 212
                                       578999999****************99765 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0029      0.98      21      39 ..      34      52 ..      29      54 .. 0.91
   2 !    9.6   0.3    0.0026      0.85       5      39 ..     168     203 ..     167     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0029
                                      HHHTS-HHHHHHHHHHHHH CS
                             HTH_1 21 eeLglsqpavsrqikrLEe 39
                                      e Lg+s++av +++++LE+
  gi|313125671|ref|YP_004035941.1| 34 EYLGVSPKAVIDHLRKLED 52
                                      679***************8 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1   5 rlfvavaeeg.sftrAAeeLglsqpavsrqikrLEe 39 
                                       +++ a+a+ + ++ + A+eL+ s+ av  ++ rL e
  gi|313125671|ref|YP_004035941.1| 168 ETLAAIARGEqTVDGVARELNASPEAVEEAVHRLAE 203
                                       68999999888*********************9965 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   8.2e-07   0.00027       9      38 ..      31      60 ..      28      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.2e-07
                          HTH_CodY  9 kiaDriGitrsvivnaLrkLesaGiiesrs 38
                                      +i++ +G+    +++ LrkLe aG+iesr 
  gi|313125671|ref|YP_004035941.1| 31 EISEYLGVSPKAVIDHLRKLEDAGLIESRT 60
                                      6888899999999****************7 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1      0.02       6.7      11      50 ..      23      65 ..      14      67 .. 0.73
   2 !   15.1   0.2   5.8e-05     0.019       4      41 ..     168     206 ..     167     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.02
                            HTH_28 11 aGh..svreaArelgisrrtvyrWikryeegG.iagLvprrrr 50
                                      +++   v+e+++ lg+s+  v + ++++e  G i++  +  rr
  gi|313125671|ref|YP_004035941.1| 23 SHKpcYVTEISEYLGVSPKAVIDHLRKLEDAGlIESRTDDQRR 65
                                      44446689*********************99955655554444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 5.8e-05
                            HTH_28   4 eiikllaaGh.svreaArelgisrrtvyrWikryeegGi 41 
                                       e + ++a+G+ +v+ +Arel+ s++ v   ++r+ e G+
  gi|313125671|ref|YP_004035941.1| 168 ETLAAIARGEqTVDGVARELNASPEAVEEAVHRLAERGL 206
                                       6788999*****************************996 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00021      0.07      76     114 ..      31      69 ..      29      85 .. 0.84
   2 ?    5.6   0.0     0.033        11      78     106 ..     184     212 ..     180     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00021
                              RP-C  76 qLsralglsestlrrhlaaLveaGliirrDspngkRyar 114
                                       ++s++lg+s++++  hl++L +aGli  r     + y +
  gi|313125671|ref|YP_004035941.1|  31 EISEYLGVSPKAVIDHLRKLEDAGLIESRTDDQRRKYFH 69 
                                       6899**********************9997777777765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.033
                              RP-C  78 sralglsestlrrhlaaLveaGliirrDs 106
                                       +r+l+ s++++++ + +L+e Gli r D 
  gi|313125671|ref|YP_004035941.1| 184 ARELNASPEAVEEAVHRLAERGLISREDE 212
                                       589999********************995 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0038       1.3       4      47 ..      18      58 ..      15      75 .. 0.73
   2 !    9.0   0.1    0.0042       1.4       3      41 ..     168     206 ..     167     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0038
                            HTH_29  4 allllaeG.vstvsqiAkllglsrrtvyrwlkrfeegGlaalldr 47
                                      +l+ll++  ++ v +i + lg+s++ v ++l+  e  G   l+++
  gi|313125671|ref|YP_004035941.1| 18 ILRLLSHKpCY-VTEISEYLGVSPKAVIDHLRKLEDAG---LIES 58
                                      55555554144.99*********************999...3332 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0042
                            HTH_29   3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41 
                                       + l+++a+G+ tv  +A+ l+ s+  v  +++r  e Gl
  gi|313125671|ref|YP_004035941.1| 168 ETLAAIARGEQTVDGVARELNASPEAVEEAVHRLAERGL 206
                                       56899******************************9995 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0    0.0005      0.16       6      42 .]      16      51 ..      16      51 .. 0.85
   2 ?   -1.8   0.0       8.8   2.9e+03      22      28 ..     120     126 ..     118     126 .. 0.84
   3 ?    5.6   0.1     0.041        14      23      41 ..     183     201 ..     174     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0005
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      r+IL++L +     ++e++e +G+S+ +v+  +r+Le
  gi|313125671|ref|YP_004035941.1| 16 RRILRLLSHK-PCYVTEISEYLGVSPKAVIDHLRKLE 51
                                      6778777755.46799*******************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 8.8
                     HTH_AsnC-type  22 eLAervG 28 
                                       eLA+++G
  gi|313125671|ref|YP_004035941.1| 120 ELARELG 126
                                       99**998 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.041
                     HTH_AsnC-type  23 LAervGlSestvlrRvrrL 41 
                                       +A++++ S+++v + v+rL
  gi|313125671|ref|YP_004035941.1| 183 VARELNASPEAVEEAVHRL 201
                                       79****************9 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00016     0.053      29      55 .]      30      56 ..      19      56 .. 0.93
   2 ?    4.1   0.0      0.14        46      28      55 .]     180     207 ..     168     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00016
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                        +++ lg+s + v+ ++++Le++G+i
  gi|313125671|ref|YP_004035941.1| 30 TEISEYLGVSPKAVIDHLRKLEDAGLI 56
                                      57999********************98 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
                            HTH_36  28 qetlakrlglsknTvsraikeLeqlGyi 55 
                                       ++  a+ l+ s + v  a+  L++ G+i
  gi|313125671|ref|YP_004035941.1| 180 VDGVARELNASPEAVEEAVHRLAERGLI 207
                                       56679999******************98 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.015         5      50      77 ..      30      57 ..      25      58 .. 0.93
   2 !   10.4   0.0    0.0011      0.37      41      77 ..     172     208 ..     148     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                                      HHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 50 ldiAeriglpfdrvaaiaraLaeaglla 77
                                       +i+e +g++ ++v++ +r+L++agl++
  gi|313125671|ref|YP_004035941.1| 30 TEISEYLGVSPKAVIDHLRKLEDAGLIE 57
                                      5899**********************97 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                                       HH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47  41 nlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77 
                                       ++a G++++ ++A +++++ ++v++++++Lae gl++
  gi|313125671|ref|YP_004035941.1| 172 AIARGEQTVDGVARELNASPEAVEEAVHRLAERGLIS 208
                                       6789999****************************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0097       3.2      20      46 ..      29      55 ..      13      59 .. 0.84
   2 !    7.9   0.1    0.0084       2.8      12      47 ..     171     207 ..     167     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0097
                            HTH_23 20 vreIAreLgvsrrTvyrwlkryreeGl 46
                                      v+eI++ Lgvs+  v   l++ +  Gl
  gi|313125671|ref|YP_004035941.1| 29 VTEISEYLGVSPKAVIDHLRKLEDAGL 55
                                      68************9988888755664 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0084
                            HTH_23  12 lllae.GlsvreIAreLgvsrrTvyrwlkryreeGle 47 
                                        + a+  ++v  +AreL+ s+  v   ++r +e Gl 
  gi|313125671|ref|YP_004035941.1| 171 AAIARgEQTVDGVARELNASPEAVEEAVHRLAERGLI 207
                                       555556689999*******************999985 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.089        29      26      53 ..      32      58 ..      18      62 .. 0.81
   2 ?   -0.2   0.0       3.1     1e+03      23      40 ..     150     168 ..     150     178 .. 0.64
   3 !    9.0   0.0    0.0044       1.5      36      60 ..     193     216 ..     180     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.089
                            HemN_C 26 feqrfgldleellaaaleklqeqGLLel 53
                                      + ++ g++  ++ ++ l+kl+++GL+e 
  gi|313125671|ref|YP_004035941.1| 32 ISEYLGVSPKAV-IDHLRKLEDAGLIES 58
                                      678888887666.677**********85 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.1
                            HemN_C  23 laafeqrfgldleell.aa 40 
                                       l+++++r+g d   ++ a 
  gi|313125671|ref|YP_004035941.1| 150 LDRLNERIGADADSRFyAE 168
                                       6789999999944444333 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0044
                            HemN_C  36 ellaaaleklqeqGLLeldggrlrl 60 
                                       + ++ a+ +l e+GL++ +++++++
  gi|313125671|ref|YP_004035941.1| 193 A-VEEAVHRLAERGLISREDEGWVV 216
                                       3.4677*****************87 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.027         9      30      46 ..      29      45 ..      15      50 .. 0.85
   2 !    8.3   0.0    0.0045       1.5      22      51 ..     171     201 ..     163     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
                      HTH_Tnp_ISL3 30 vkavArqlgvSwtTVwr 46
                                      v+++++ lgvS++ V++
  gi|313125671|ref|YP_004035941.1| 29 VTEISEYLGVSPKAVID 45
                                      89***********9986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0045
                      HTH_Tnp_ISL3  22 ellles.rsvkavArqlgvSwtTVwrildry 51 
                                       ++  ++ ++v  vAr+l+ S+  V+ +++r+
  gi|313125671|ref|YP_004035941.1| 171 AAIARGeQTVDGVARELNASPEAVEEAVHRL 201
                                       44445559*****************999997 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0084       2.8      18      39 ..      31      57 ..      29      57 .. 0.90
   2 ?    6.3   0.1     0.033        11      19      40 ..     183     209 ..     171     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0084
                           AbiEi_4 18 elea.aGispsa....lrrLvrkGwLv 39
                                      e+ + +G+sp+a    lr+L ++G+++
  gi|313125671|ref|YP_004035941.1| 31 EISEyLGVSPKAvidhLRKLEDAGLIE 57
                                      778889******************997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.033
                           AbiEi_4  19 lea.aGispsa....lrrLvrkGwLvr 40 
                                       +++ ++ sp a    ++rL ++G++ r
  gi|313125671|ref|YP_004035941.1| 183 VAReLNASPEAveeaVHRLAERGLISR 209
                                       666689999999999*********988 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.8e-05    0.0093     110     158 ..      23      72 ..      13      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-05
                                       H-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T.T--EEE--- CS
                             DDRGK 110 ekKvvlleelavkfklktqevierikeLeeqgsltGvlDd.rGkyiyitd 158
                                       ++K + ++e++  ++++ + vi+ +++Le+ g ++   Dd r ky +i+ 
  gi|313125671|ref|YP_004035941.1|  23 SHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIESRTDDqRRKYFHISR 72 
                                       68999******************************999884689****97 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0    0.0005      0.17      10      60 ..       6      59 ..       2      78 .. 0.86
   2 ?    2.4   0.0      0.33   1.1e+02     113     145 ..     169     201 ..     143     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0005
                              ArsR 10 llqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsq 60
                                      ll ++++e+ +++++ ls++ +  +e++e+lg +   v + l+ L+ ++liEs+
  gi|313125671|ref|YP_004035941.1|  6 LLDLLGNENRRRILRLLSHKPCYVTEISEYLGVSpkaVIDHLRKLEDAGLIESR 59
                                      789999**************************88444566667777799***97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.33
                              ArsR 113 iekeveegntsisdlsrklglsplfiralakrs 145
                                         + + +g++ +  ++r+l+ sp  +   ++r 
  gi|313125671|ref|YP_004035941.1| 169 TLAAIARGEQTVDGVARELNASPEAVEEAVHRL 201
                                       4467999****************9998877775 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0037       1.2      31      43 ..      31      43 ..      13      49 .. 0.86
   2 ?    4.4   0.0     0.092        30      28      49 ..     179     200 ..     166     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0037
                                      HHHHHHT--HHHH CS
                      Sigma70_r4_2 31 EIAellgisegtV 43
                                      EI+e+lg+s+++V
  gi|313125671|ref|YP_004035941.1| 31 EISEYLGVSPKAV 43
                                      9***********9 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.092
                                       -HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsR 49 
                                       + + +A++l+ s+ +V+ +++R
  gi|313125671|ref|YP_004035941.1| 179 TVDGVARELNASPEAVEEAVHR 200
                                       66779************99998 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       3.3   1.1e+03      49      75 ..      26      52 ..       7      75 .. 0.66
   2 ?   13.6   0.0   0.00015      0.05      34     113 ..     110     187 ..      98     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.3
                           DUF2089 49 rGnlkevekelgisYpTvrnrldeile 75
                                         + e+ + lg+s  +v  +l ++  
  gi|313125671|ref|YP_004035941.1| 26 PCYVTEISEYLGVSPKAVIDHLRKLED 52
                                      456778888888888888887777654 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00015
                           DUF2089  34 LskeqlefvelfikarGnlkevekelgisYpTvrnrldeileaLgyeeeeeeeeeeeerkeileklekgeisveeAl 110
                                       + +e+ + ++ + +  G+l ++e+el ++   v+ r+ ++l +L+ +  ++   +++  +e l+++++ge +v+  +
  gi|313125671|ref|YP_004035941.1| 110 IPREDAQDLNELARELGHLADLENELSLAQRWVHGRITDVLDRLNERIGAD--ADSRFYAETLAAIARGEQTVDGVA 184
                                       567778888889999******************************999966..334678999999999999988766 PP

                           DUF2089 111 erL 113
                                       ++L
  gi|313125671|ref|YP_004035941.1| 185 REL 187
                                       665 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.4   1.3e+02      29      67 ..      32      71 ..      29      74 .. 0.80
   2 ?   10.5   0.1    0.0017      0.55      32      59 ..     186     213 ..     183     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.4
                              PaaX 29 llaelGiseslvRaalsRlakaGwlvrekegr.rsfYrLs 67
                                      + + lG+s ++v   l  l+ aG++ +  + + r +++ s
  gi|313125671|ref|YP_004035941.1| 32 ISEYLGVSPKAVIDHLRKLEDAGLIESRTDDQrRKYFHIS 71
                                      677899999999999**********987766637777666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0017
                              PaaX  32 elGiseslvRaalsRlakaGwlvrekeg 59 
                                       el  s ++v  a++Rla++G++ re+eg
  gi|313125671|ref|YP_004035941.1| 186 ELNASPEAVEEAVHRLAERGLISREDEG 213
                                       56667789999**************998 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0053       1.8      13      61 ..      13      60 ..       3      73 .. 0.76
   2 ?    4.7   0.0     0.082        27      18      58 ..     169     208 ..     145     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEE CS
                       TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykr 61
                                      e+   +l  L  k +    ++++ l++ ++ +   L +L +a+l++ + 
  gi|313125671|ref|YP_004035941.1| 13 ENRRRILRLLSHKPCY-VTEISEYLGVSPKAVIDHLRKLEDAGLIESRT 60
                                      4556667766655554.457*************************9764 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.082
                                       HHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha  18 vldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58 
                                        l +++ +ge t + +a+el+  ++ + +++ rL e +l++
  gi|313125671|ref|YP_004035941.1| 169 TLAAIA-RGEQTVDGVARELNASPEAVEEAVHRLAERGLIS 208
                                       566666.899999**************************98 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00052      0.17       9      45 ..      21      57 ..      16      60 .. 0.89
   2 ?    0.0   0.0       2.2   7.4e+02      15      46 ..     178     209 ..     174     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00052
                          HTH_DeoR  9 lkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      l ++  + v+e++e+lgvS++ +   L++Le +gl++
  gi|313125671|ref|YP_004035941.1| 21 LLSHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIE 57
                                      678999*****************99999999999985 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.2
                          HTH_DeoR  15 lsveelvellgvSeaTiRRDLneLeeqglltR 46 
                                        +v+ ++ +l+ S++ +      L+e gl+ R
  gi|313125671|ref|YP_004035941.1| 178 QTVDGVARELNASPEAVEEAVHRLAERGLISR 209
                                       57777888888888888777788888888887 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0021      0.71      23      52 ..      31      60 ..      28      77 .. 0.84
   2 ?    2.7   0.0      0.43   1.4e+02      23      51 ..     182     210 ..     169     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0021
                    B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvkqs 52
                                      +++ +++ +p+ +  +l++Le+ gLI+ ++
  gi|313125671|ref|YP_004035941.1| 31 EISEYLGVSPKAVIDHLRKLEDAGLIESRT 60
                                      5678999*******************9987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.43
                    B-block_TFIIIC  23 dLakeskqdprslfyrlksLekkgLIvkq 51 
                                       ++a+e++ +p+ +   +  L + gLI + 
  gi|313125671|ref|YP_004035941.1| 182 GVARELNASPEAVEEAVHRLAERGLISRE 210
                                       5779999*******************985 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.15        50      70     104 .]      29      63 ..      25      63 .. 0.93
   2 ?    8.5   0.0    0.0094       3.1      70      97 ..     180     207 ..     178     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.15
                                       HHHHHHHSTSXHHHHHHHHHHHHHTTSEEESSSTT CS
                             RPA_C  70 vdeiaqklrlsvndvkqavdeLsneGiiYsTiDde 104
                                       v ei++ l++s + v   +++L+++G+i s  Dd+
  gi|313125671|ref|YP_004035941.1|  29 VTEISEYLGVSPKAVIDHLRKLEDAGLIESRTDDQ 63 
                                       67999***********************9999986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0094
                                       HHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C  70 vdeiaqklrlsvndvkqavdeLsneGii 97 
                                       vd +a++l+ s + v++av  L++ G+i
  gi|313125671|ref|YP_004035941.1| 180 VDGVARELNASPEAVEEAVHRLAERGLI 207
                                       6889**********************98 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00053      0.18      37      67 ..      38      69 ..      27      83 .. 0.72
   2 ?   -0.4   0.0       3.6   1.2e+03      44      59 ..     196     211 ..     186     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00053
                                      --HHHHHHHHHHHHHTTSEEEEEEE-CC.C.- CS
                            Cdc6_C 37 ltqrevsdllseLemlgileleksskGrre.g 67
                                      ++ + v d+l++Le+ g++e+++  + r++  
  gi|313125671|ref|YP_004035941.1| 38 VSPKAVIDHLRKLEDAGLIESRTDDQRRKYfH 69
                                      67889*****************9865555553 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.6
                                       HHHHHHHHTTSEEEEE CS
                            Cdc6_C  44 dllseLemlgilelek 59 
                                       + + +L+ +g++++e 
  gi|313125671|ref|YP_004035941.1| 196 EAVHRLAERGLISRED 211
                                       5577899999999886 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00099      0.33      33      65 ..      34      66 ..       5      78 .. 0.77
   2 ?    1.3   0.0       1.2   4.1e+02      38      59 ..     190     211 ..     167     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00099
                           DUF2513 33 aidgyskeeiiyhlkllaeagLieaekkkakss 65
                                      +  g+s + +i hl++l++agLie+  + ++ +
  gi|313125671|ref|YP_004035941.1| 34 EYLGVSPKAVIDHLRKLEDAGLIESRTDDQRRK 66
                                      566888999***************999888777 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.2
                           DUF2513  38 skeeiiyhlkllaeagLieaek 59 
                                       s e + ++++ lae gLi+ e+
  gi|313125671|ref|YP_004035941.1| 190 SPEAVEEAVHRLAERGLISRED 211
                                       56779999**********9876 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0022      0.73       4      38 .]      31      67 ..      29      67 .. 0.75
   2 ?    0.0   0.0       2.3   7.5e+02      15      26 ..     197     208 ..     195     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0022
                                      HHHHHHTTTHHH....HHHHHHTTSSTSEEETTTSSEEE CS
                              MerR  4 evAeltGvsprt....LRyYEreGLipppeRtegGyRlY 38
                                      e++e +Gvsp++    LR +E+ GLi    Rt+  +R Y
  gi|313125671|ref|YP_004035941.1| 31 EISEYLGVSPKAvidhLRKLEDAGLIE--SRTDDQRRKY 67
                                      78888999988866668*********5..4555567776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.3
                                       HHHHHHHTTSST CS
                              MerR  15 tLRyYEreGLip 26 
                                       +++++ ++GLi 
  gi|313125671|ref|YP_004035941.1| 197 AVHRLAERGLIS 208
                                       578899*****4 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00063      0.21       3      53 ..      11      60 ..       9      69 .. 0.87
   2 ?   -0.4   0.0       3.1     1e+03      12      52 ..     171     210 ..     162     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00063
                                      HSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE CS
                              HxlR  3 ggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierev 53
                                      g+  +  il+ l +++   +e+++ l ++s k  + +Lr+Le  glie ++
  gi|313125671|ref|YP_004035941.1| 11 GNENRRRILRLLSHKPCYVTEISEYL-GVSPKAVIDHLRKLEDAGLIESRT 60
                                      55556789999***************.9*******************9765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.1
                                       HHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEE CS
                              HxlR  12 vellkgkkRfselkralpkisqkmLaqrLreLeqdgliere 52 
                                        ++ +g++    ++r+l + s +   +  ++L + gli+re
  gi|313125671|ref|YP_004035941.1| 171 AAIARGEQTVDGVAREL-NASPEAVEEAVHRLAERGLISRE 210
                                       55666677777777777.66777778888999999999997 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0      0.03       9.8       6      50 ..      14      58 ..      10      71 .. 0.88
   2 ?    0.9   0.0       1.4   4.6e+02      20      33 ..     149     162 ..     141     170 .. 0.82
   3 ?    2.9   0.0      0.35   1.2e+02      39      51 ..     198     210 ..     167     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.03
                    Sulfolobus_pRN  6 lsekillilsrrcatleeleektGiekeellvyltrlykrGlisr 50
                                      +  +il  ls++   + e+ e  G+  + ++ +l +l + Gli  
  gi|313125671|ref|YP_004035941.1| 14 NRRRILRLLSHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIES 58
                                      5678999*****999***************************964 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.4
                    Sulfolobus_pRN  20 tleeleektGieke 33 
                                        l++l+e+ G++ +
  gi|313125671|ref|YP_004035941.1| 149 VLDRLNERIGADAD 162
                                       699*******9865 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.35
                    Sulfolobus_pRN  39 ltrlykrGlisrk 51 
                                       + rl +rGlisr+
  gi|313125671|ref|YP_004035941.1| 198 VHRLAERGLISRE 210
                                       6799*******96 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0046       1.5       6      26 ..      29      49 ..      25      54 .. 0.90
   2 ?    0.9   0.0       1.3   4.2e+02       7      14 ..     119     126 ..     117     161 .. 0.75
   3 ?   -1.2   0.0       5.5   1.8e+03       6      20 ..     180     194 ..     179     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0046
                             IF2_N  6 VyeLAkeLgvkskevikkLfk 26
                                      V e+ + Lgv++k vi++L k
  gi|313125671|ref|YP_004035941.1| 29 VTEISEYLGVSPKAVIDHLRK 49
                                      889****************76 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.3
                             IF2_N   7 yeLAkeLg 14 
                                       +eLA+eLg
  gi|313125671|ref|YP_004035941.1| 119 NELARELG 126
                                       68999998 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.5
                             IF2_N   6 VyeLAkeLgvkskev 20 
                                       V  +A+eL+ +++ v
  gi|313125671|ref|YP_004035941.1| 180 VDGVARELNASPEAV 194
                                       556799999776554 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00094      0.31       7      50 ..      17      58 ..       4      60 .. 0.82
   2 ?   -0.1   0.1       2.5   8.2e+02      21      29 ..     118     126 ..     112     139 .. 0.74
   3 ?    3.8   0.1      0.16        51       9      51 ..     170     210 ..     167     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00094
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +iL++l++ p    ++e+++ +g+++ +v  +L+ L+  G++e 
  gi|313125671|ref|YP_004035941.1| 17 RILRLLSHKPC--YVTEISEYLGVSPKAVIDHLRKLEDAGLIES 58
                                      46666666665..5***************************985 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.5
                                       HHHHHHHHT CS
                          HTH_IclR  21 lselArrtg 29 
                                       l elAr++g
  gi|313125671|ref|YP_004035941.1| 118 LNELARELG 126
                                       778888776 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.16
                                       HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR   9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       L a+a++ q  t+  +Ar++  ++ +v   ++ L e+G++ ++
  gi|313125671|ref|YP_004035941.1| 170 LAAIARGEQ--TVDGVARELNASPEAVEEAVHRLAERGLISRE 210
                                       667777777..599999999999999*************9876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.18        61      16      63 ..      25      68 ..      16      77 .. 0.77
   2 ?    7.2   0.0     0.018       6.1      15      57 ..     175     213 ..     170     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.18
                                      S-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
                   Penicillinase_R 16 geatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYs 63
                                      +++ v+e+ e l     ++++ V   lr+L++ gl++++++ ++  Y 
  gi|313125671|ref|YP_004035941.1| 25 KPCYVTEISEYLG----VSPKAVIDHLRKLEDAGLIESRTDDQRRKYF 68
                                      5555666655555....56999***************99997776664 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.018
                                       HS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEET CS
                   Penicillinase_R  15 kgeatvkevveeleeekelaysTVktllrrLvkKgllsrekeg 57 
                                       +ge+tv+ v  el++     ++ V   + rL ++gl+sre eg
  gi|313125671|ref|YP_004035941.1| 175 RGEQTVDGVARELNAS----PEAVEEAVHRLAERGLISREDEG 213
                                       6777777777777777....999*****************988 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.041        14      20      40 ..      29      49 ..      27      51 .. 0.88
   2 ?    4.8   0.0     0.059        20       9      37 ..     168     197 ..     167     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.041
                                      HHHHHHHHTS-HHHHHHHHHH CS
                              GerE 20 nkeIAeelniSekTVkvhksn 40
                                      ++eI+e l++S+k V  h++ 
  gi|313125671|ref|YP_004035941.1| 29 VTEISEYLGVSPKAVIDHLRK 49
                                      579************988875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.059
                                       HHHHHHCTTS.-HHHHHHHHTS-HHHHHHH CS
                              GerE   9 evLrllaeGk.snkeIAeelniSekTVkvh 37 
                                       e L+ +a G+ ++  +A+eln S++ V+  
  gi|313125671|ref|YP_004035941.1| 168 ETLAAIARGEqTVDGVARELNASPEAVEEA 197
                                       568888999526788**********99855 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.091        30      12      49 ..      24      61 ..      20      66 .. 0.86
   2 ?    5.8   0.0     0.044        15      13      50 ..     176     213 ..     170     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.091
                              FeoC 12 rgrvslkeLsrhfkaspealeamLeqwvrkGrvekvaa 49
                                      ++   + e+s ++ +sp+a+ + L  ++  G +e ++ 
  gi|313125671|ref|YP_004035941.1| 24 HKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIESRTD 61
                                      6667789*****************99999999998876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.044
                              FeoC  13 grvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50 
                                       g+  ++  +r+++aspea+e  +  +  +G + +++++
  gi|313125671|ref|YP_004035941.1| 176 GEQTVDGVARELNASPEAVEEAVHRLAERGLISREDEG 213
                                       556677789*********************99998875 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0019      0.64      25      43 ..      43      61 ..      41      65 .. 0.82
   2 ?    3.1   0.1       0.3        98      16      42 ..     197     211 ..     192     214 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0019
                          BLACT_WH 25 vlahLeKLeeeGkVkregd 43
                                      v+ hL+KLe+ G++++  d
  gi|313125671|ref|YP_004035941.1| 43 VIDHLRKLEDAGLIESRTD 61
                                      889***********98665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.3
                          BLACT_WH  16 slhpaAergvlahLeKLeeeGkVkreg 42 
                                        +h+            L e+G+++re+
  gi|313125671|ref|YP_004035941.1| 197 AVHR------------LAERGLISRED 211
                                       4455............55555555555 PP

>> DUF3572  Protein of unknown function (DUF3572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       6.5   2.2e+03      60      82 ..      29      51 ..      18      53 .. 0.72
   2 ?   10.5   0.1    0.0016      0.53      41      83 ..     161     203 ..     152     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 6.5
                           DUF3572 60 llafaeaaglkpeevaaAraaLa 82
                                      +++++e  g++p++v+   ++L+
  gi|313125671|ref|YP_004035941.1| 29 VTEISEYLGVSPKAVIDHLRKLE 51
                                      67788888888888887777775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0016
                           DUF3572  41 aepeflaavLdFllsdealllafaeaaglkpeevaaAraaLag 83 
                                       a+ +f a  L+ + + e+++  +a++ + +pe+v +A ++La+
  gi|313125671|ref|YP_004035941.1| 161 ADSRFYAETLAAIARGEQTVDGVARELNASPEAVEEAVHRLAE 203
                                       577899999999****************************985 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00066      0.22     184     238 ..      11      65 ..       7      95 .. 0.83
   2 ?   -3.1   0.0       8.6   2.9e+03     199     222 ..     177     200 ..     167     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
                              TnsD 184 GivweerlkeLveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesre 238
                                       G+  ++r+ +L++++   + ei+++lgv++k V+ +++kl++    +++ +++r+
  gi|313125671|ref|YP_004035941.1|  11 GNENRRRILRLLSHKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIESRTDDQRR 65 
                                       6667778778888899999**********************99877777777666 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.6
                              TnsD 199 glslkeiAkelgvdiktVlryakk 222
                                       + +++ +A+el+ +++ V     +
  gi|313125671|ref|YP_004035941.1| 177 EQTVDGVARELNASPEAVEEAVHR 200
                                       557788999999999888766555 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0011      0.38       8      46 ..      21      57 ..      14      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0011
                                      HHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA  8 ylnsikapckTreiAdalglsaYQaRyYLeqLekegkik 46
                                       l s + pc  +ei + lg+s   +   L +Le +g i+
  gi|313125671|ref|YP_004035941.1| 21 LL-S-HKPCYVTEISEYLGVSPKAVIDHLRKLEDAGLIE 57
                                      33.3.69*****************************997 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.018       5.9      11      41 ..      25      55 ..      16      77 .. 0.81
   2 ?    2.1   0.0      0.84   2.8e+02       4      41 ..     168     206 ..     166     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.018
                            HTH_40 11 eglsieeIAkerglkesTIegHLaelieege 41
                                      + + + eI++  g++++ +++HL +l  +g 
  gi|313125671|ref|YP_004035941.1| 25 KPCYVTEISEYLGVSPKAVIDHLRKLEDAGL 55
                                      556789*****************99988874 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.84
                            HTH_40   4 etlell.eeglsieeIAkerglkesTIegHLaelieege 41 
                                       etl  + +  ++++ +A+e + ++  +e+ + +l+e g 
  gi|313125671|ref|YP_004035941.1| 168 ETLAAIaRGEQTVDGVARELNASPEAVEEAVHRLAERGL 206
                                       67777768889******************9999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1370.18
//
Query:       gi|313125672|ref|YP_004035942.1|  [L=163]
Description: hypothetical protein Hbor_09020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.9    8.7  18.1        3.7    7.8  18.1    1.5  1  DUF3792   Protein of unknown function (DUF3792)


Domain annotation for each model (and alignments):
>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  18.1    0.0002       3.7      18     110 ..      48     138 ..      40     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0002
                           DUF3792  18 illlilalllyftslsekvlsililiililsvfigGflagkkakkkgllnGllvGllyflillllslli.kksgsaf 93 
                                       +++++ +ll    ++   +++i+ +i  +l++f+ Gf +g  +++  +++ +l G+l f +l++l++l+ + +++ f
  gi|313125672|ref|YP_004035942.1|  48 VVVFLASLLG---AFLGGSIPIVGFIGRFLGLFAVGFGVGLLSGRSHYVEVGLGGALAFGLLWVLTTLTsGFAFAPF 121
                                       4444444443...333789******************************************999999999999999* PP

                           DUF3792  94 slkllikllllllagai 110
                                       +++ll k+ l+++++  
  gi|313125672|ref|YP_004035942.1| 122 AVELLAKYGLAIAGAGA 138
                                       *****999998844333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 999.73
//
Query:       gi|313125673|ref|YP_004035943.1|  [L=417]
Description: glutamyl-tRNA(gln) amidotransferase subunit d [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-58  197.6   0.9    2.5e-58  196.8   0.7    1.5  2  Asparaginase    Asparaginase, N-terminal
    1.7e-25   89.5   0.0    9.3e-25   87.1   0.0    2.1  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    1.4e-15   56.3   0.1    2.5e-15   55.5   0.1    1.4  1  GatD_N          GatD N-terminal domain
  ------ inclusion threshold ------
      0.058   13.0   0.0      0.089   12.4   0.0    1.4  1  Peripla_BP_4    Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.8   0.7   5.5e-62   2.5e-58       2     188 ..      79     272 ..      78     275 .. 0.95
   2 ?   -3.1   0.0       1.1   4.8e+03     139     165 ..     340     366 ..     336     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 196.8 bits;  conditional E-value: 5.5e-62
                                       EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-S CS
                      Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.yd 77 
                                       v +++tGGTias++d+++ga++ +++ae++l+a+p+l+  a+++ +++ani S+nmtp+ w +laeaie+++e   d
  gi|313125673|ref|YP_004035943.1|  79 VSLISTGGTIASTVDYRTGAVTAQFDAEDVLRAVPDLAGRANYRGRVVANILSENMTPDVWIDLAEAIEAEIEAgTD 155
                                       89**********************************************************************666** PP

                                       EEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE..... CS
                      Asparaginase  78 gfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk..... 149
                                       g+Vv+hGTDT+++tA+a+s+ml++ ++p+v+tGsqr++++++sD ++N + A+ +a ++   a+vlv+++ +     
  gi|313125673|ref|YP_004035943.1| 156 GIVVMHGTDTMQFTAAAMSFMLDT-PVPIVFTGSQRSADRPSSDNVMNAVCAVEAAKAD--CAEVLVCMHASesddv 229
                                       **********************99.*******************************987..9*************** PP

                                       ..EEETTTEEE-BSSSSS-EEETTT--SEEE..ETTEEEESEE CS
                      Asparaginase 150 ..llranrvtKvhtssldaFespnlgplaev..egskvkvnke 188
                                         l+r++rv+K hts++daFe++ ++pl+e+  e+++++++++
  gi|313125673|ref|YP_004035943.1| 230 caLHRGTRVRKNHTSRRDAFETVGAEPLGEIdyETEEITFRRD 272
                                       ******************************9666667776665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
                                       TSECEEEETTEEEETTTEEE-BSSSSS CS
                      Asparaginase 139 iagvlvvfngkllranrvtKvhtssld 165
                                       ++g +v++  ++l+++ + +v  + +d
  gi|313125673|ref|YP_004035943.1| 340 ESGTVVTMTTQCLEGRVCDRVYDTGRD 366
                                       578899999999999988887666555 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.37   1.7e+03      14      30 ..     144     160 ..     119     186 .. 0.83
   2 !   87.1   0.0   2.1e-28   9.3e-25       2     110 ..     291     400 ..     290     403 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.37
                                       HHHHHHHHTT--EEEEE CS
                    Asparaginase_C  14 kvlkallkkgakGvvle 30 
                                       + ++a +++g +G+v+ 
  gi|313125673|ref|YP_004035943.1| 144 EAIEAEIEAGTDGIVVM 160
                                       56677778888888875 PP

  == domain 2  score: 87.1 bits;  conditional E-value: 2.1e-28
                                       EEEEE--TT--HHHHHHHHHT.T--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HH CS
                    Asparaginase_C   2 Vvvlklhpgmdtkvlkallkk.gakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkel 77 
                                       V++lk++pgmd +    +l+   ++G+v+egtG G+++++++++l+e++++g+vv +t+qc++g+v + +y++g++l
  gi|313125673|ref|YP_004035943.1| 291 VDLLKFTPGMDLDAYADFLRGqDLDGLVVEGTGLGHVHTDFIPVLEELVESGTVVTMTTQCLEGRVCDRVYDTGRDL 367
                                       9**********999988887769****************************************************** PP

                                       HHHTEEE-TT--HHHHHHHHHHHCTT---HHHH CS
                    Asparaginase_C  78 erlgvisaddmtpeaarikLmlllgkgldpaev 110
                                        ++gv++a+d  p +a +kLm++ ++ +dp+e 
  gi|313125673|ref|YP_004035943.1| 368 LEAGVVEAGDTLPGTAKVKLMWAVANLEDPEEA 400
                                       ****************************99986 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1   5.6e-19   2.5e-15       1      55 []       1      51 [.       1      51 [. 0.94

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 5.6e-19
                                      --TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                            GatD_N  1 ievGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                      ++ GD+++ve+ g++ eG+lmP+    ++d++v+KLd GYN+Gi+ +e+ ++ +l
  gi|313125673|ref|YP_004035943.1|  1 MNAGDRVRVERAGVTNEGVLMPST---TSDYLVVKLDGGYNVGIERDEA-DVDVL 51
                                      578*********************...*********************9.88775 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05     0.089      40     163 ..     137     268 ..     110     363 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                                       -H.HHHHHHHHHHHHTT-SEEE.E--SSHHHHH.HHHHHHHHTT-EEEEESTT...GCTTT-CEEEEEC-HHHHHHH CS
                      Peripla_BP_4  40 da.aeQvaqiedaiakgvdgii.vapvdstala.palkkakaaGIpVvafdsd...dapsgerlayvgfdneaaGel 110
                                       d+  + +++ie+ i++g dgi+ ++ +d+ + + +a+    +  +p+v+  s+   d ps++ + +     eaa + 
  gi|313125673|ref|YP_004035943.1| 137 DVwIDLAEAIEAEIEAGTDGIVvMHGTDTMQFTaAAMSFMLDTPVPIVFTGSQrsaDRPSSDNVMNAVCAVEAAKAD 213
                                       555666899***********996788899888857777799********9999988888888888888888888888 PP

                                       HHHHHHHHCTTH.EEEEEE.TSCCCHHHHHHHHHHHHHHHHH.-TTCEECCEEES CS
                      Peripla_BP_4 111 qaeylaeklggkkgkvvil.aGspgdpnaeeriegfrkvlke.ypgikivaevag 163
                                       +ae+l+    +++ +v++l +G+   +n++ r ++f+ v +e  ++i + +e ++
  gi|313125673|ref|YP_004035943.1| 214 CAEVLVCMHASESDDVCALhRGTRVRKNHTSRRDAFETVGAEpLGEIDYETEEIT 268
                                       88988887777778888888*****************996664334555553333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2722.32
//
Query:       gi|313125674|ref|YP_004035944.1|  [L=323]
Description: acetyltransferase (gnat) family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-06   26.6   2.3    9.2e-06   26.4   0.0    2.0  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
    9.8e-06   25.8   0.0    2.4e-05   24.5   0.0    1.7  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    9.6e-05   22.4   0.0    0.00023   21.2   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    0.00049   20.5   0.0    0.00094   19.6   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0056   16.8   0.0      0.035   14.2   0.0    2.1  2  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.6e-09   9.2e-06       4     137 ..      17     147 ..      15     148 .. 0.77
   2 ?   -0.9   0.6      0.66   2.4e+03      83      99 ..     255     271 ..     166     294 .. 0.60

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.6e-09
                    Acetyltransf_3   4 LrplteeDlealfelrsdpevmrylpepltleeaeewlerawaeeseeegygwaivl...kdtgviGsv.glrdlee 76 
                                       +r ++++D++a++++ +d    r ++ ++ ++  ++w+++   +++  +  ++++ l    +++++G +  +  l++
  gi|313125674|ref|YP_004035944.1|  17 VRAARPDDYDAVAAFTADTWADR-GGSDYIPDIYHDWIAD--DDGE--TRQTFVVDLgaeTPSDELGAIvQVVMLSP 88 
                                       68999*******99988866666.7889999*******95..3332..22348886575544445555544444444 PP

                    Acetyltransf_3  77 edeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                        +  +  g++++p+++g+G+a+  ++a  ++a +e g++ l+  i   N +S  +++  G+
  gi|313125674|ref|YP_004035944.1|  89 YEA-WGQGIRVNPEYRGRGLAKAITEASFDFA-QEAGATVLRNMIFSWNVKSLGLARDTGY 147
                                       433.667*************************.8888*****************9998886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.66
                    Acetyltransf_3  83 lgymlapsfwgkGyate 99 
                                        +y ++  +w+   a e
  gi|313125674|ref|YP_004035944.1| 255 AEYAVGAWAWRDEDAAE 271
                                       22333333333333333 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   6.7e-09   2.4e-05      58     117 .]      88     147 ..      35     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.7e-09
                                       TTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1  58 ggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYek.lGF 117
                                       + +a+  ++ V+peyrg+Gl++a  ea  ++a e g++ +   ++++n+++ +l  +  G+
  gi|313125674|ref|YP_004035944.1|  88 PYEAWGQGIRVNPEYRGRGLAKAITEASFDFAQEAGATVLRNMIFSWNVKSLGLA-RdTGY 147
                                       34578889*****************************9986669999***99999.54776 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.6e-08   0.00023      30      60 ..      96     126 ..      94     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.6e-08
                   Acetyltransf_CG  30 TeVpeelrGkGiAkkLvkaalddareeglkv 60 
                                       + V++e+rG+G+Ak++++a +d+a+e+g +v
  gi|313125674|ref|YP_004035944.1|  96 IRVNPEYRGRGLAKAITEASFDFAQEAGATV 126
                                       579*************************988 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.6e-07   0.00094       6      49 ..      64     119 ..      48     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.6e-07
                                       EEEEET........TEEEEEEEEEEESTCTEEEEE-GGGTTSSHHHHHHHH....T CS
                    Acetyltransf_7   6 fVaedd........gkivGfialslldaeitrlaVdpeyrgkGiGraLlea....a 49 
                                       fV++ +        g iv  + ls+++a+  ++ V+peyrg+G+++a+ ea    a
  gi|313125674|ref|YP_004035944.1|  64 FVVDLGaetpsdelGAIVQVVMLSPYEAWGQGIRVNPEYRGRGLAKAITEAsfdfA 119
                                       44333366665555666666666666556666****************99744441 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.31   1.1e+03       2      24 ..      17      39 ..      16      59 .. 0.84
   2 !   14.2   0.0   9.8e-06     0.035      78     110 ..      95     127 ..      91     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.31
                                      EEEE-GGGHHHHHHHHHHHTT-- CS
                    Acetyltransf_9  2 irelteedldevlellkyaFqde 24
                                      +r ++++d+d+v+++ +  ++d+
  gi|313125674|ref|YP_004035944.1| 17 VRAARPDDYDAVAAFTADTWADR 39
                                      799***********999998876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.8e-06
                                       EEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EE CS
                    Acetyltransf_9  78 gVavapehrgrgvlskLlaraleemreegqpls 110
                                       g+ v+pe+rgrg+++++++++++ ++e g+++ 
  gi|313125674|ref|YP_004035944.1|  95 GIRVNPEYRGRGLAKAITEASFDFAQEAGATVL 127
                                       5779***********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2212.06
//
Query:       gi|313125675|ref|YP_004035945.1|  [L=340]
Description: histidine kinase with pas domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-10   40.6   0.0    5.2e-10   39.8   0.0    1.4  1  HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like A
    2.5e-08   34.2   0.7    6.8e-08   32.7   0.1    2.0  2  PAS_4      PAS fold


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   5.8e-14   5.2e-10       5     106 ..     240     334 ..     236     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 5.8e-14
                                       HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsi 80 
                                        L+ +++ l +Na+++   +++ ++++     +  + veD+G+Gi++++++++fe   +     +++ ++ G+Gl i
  gi|313125675|ref|YP_004035945.1| 240 LLQLLFDVLFSNALEH--GGDTARIRVG--TTYTGFYVEDDGPGIDPANRERIFEsGVVI----NSTAERAGMGLPI 308
                                       5777888999*****9..4566666666..449**********************54444....567899******* PP

                                       HHHHHHHTTTEEEEEEETTTEEEEEE CS
                         HATPase_c  81 vkklvelmgGeiwvesepgrGttftf 106
                                       + +++el++ +i+ e++  +Gt++ +
  gi|313125675|ref|YP_004035945.1| 309 AARIAELHDWSIHAEQSNLGGTRVEV 334
                                       **************99999***9986 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   7.6e-12   6.8e-08       1     109 [.      11     128 ..      11     129 .. 0.82
   2 ?   -1.1   0.1      0.24   2.2e+03      55      83 ..     190     218 ..     147     221 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.6e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaa...aaelfgappe.ellGktlaellpee.....daarleralrrvlegeepief 68 
                                       +d lp  +a+ld++g ++ +N+a   +a+  g++++ ++ G  + e+  +       aa  ++ +rrvl+ge+  + 
  gi|313125675|ref|YP_004035945.1|  11 FDELPTEVAILDSQGAIVITNRAwrtFASANGYTGDpTFSGVNYLEVCDAVrhdceEAALAADGIRRVLSGEDDMFA 87 
                                       6889999****************555444333333314555555555555577799999999*************** PP

                             PAS_4  69 leelll.pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       l+++ + p e+r++++r++P+r +s + + ++v+  +iT+rr
  gi|313125675|ref|YP_004035945.1|  88 LDYPCHsPTERRWFLMRAVPFRSSSNG-QYAVVMHLEITDRR 128
                                       ****99*******************99.************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.24
                             PAS_4  55 alrrvlegeepiefleelllpgeerhyel 83 
                                         ++++e + +ie++ ++l++++e+ +e 
  gi|313125675|ref|YP_004035945.1| 190 TGTALAEADSTIEQVPVTLREQAEVAWER 218
                                       44455555666666666666777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1861.11
//
Query:       gi|313125676|ref|YP_004035946.1|  [L=355]
Description: carbamoyl-phosphate synthase small subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-38  129.3   0.0    3.6e-37  127.0   0.0    2.1  2  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    1.8e-37  129.0   0.0    2.5e-37  128.5   0.0    1.2  1  GATase           Glutamine amidotransferase class-I
    4.4e-05   23.3   0.8      0.011   15.5   0.3    2.3  2  Peptidase_C26    Peptidase C26


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.0   0.0     6e-41   3.6e-37       2     128 .]       4     121 ..       3     121 .. 0.96
   2 ?   -1.0   0.0      0.24   1.4e+03      22      36 ..     274     288 ..     256     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 6e-41
                   CPSase_sm_chain   2 avLvLedGtvfeGksfgakeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglvv 78 
                                       a+L+LedG+v+e+++ + +++ GE+vf+T+ tGY+e+ltDpsY++q+l+++ypliGnyGv+ee++es++i+ ++ ++
  gi|313125676|ref|YP_004035946.1|   4 AYLALEDGRVIEARGRSPGQTRGELVFTTAYTGYEESLTDPSYEEQVLTFSYPLIGNYGVREERFESDRIHPRAAIA 80 
                                       79**********9999999********************************************************** PP

                   CPSase_sm_chain  79 relseepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgvi 128
                                       +e++e         ++ ewl +e++p+i ++DTR L++ +re+gamk+ i
  gi|313125676|ref|YP_004035946.1|  81 HEFTE---------EVVEWLDSEDVPAIDHIDTRDLVTSIREEGAMKCGI 121
                                       99975.........5779****************************9866 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                   CPSase_sm_chain  22 avGEvvfnTgmtGYq 36 
                                       ++G v+++T   GY+
  gi|313125676|ref|YP_004035946.1| 274 NTGKVIMTTQNHGYT 288
                                       5899*********96 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.5   0.0   4.2e-41   2.5e-37       2     187 ..     170     340 ..     169     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 4.2e-41
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGI 77 
                                       liD++   + ++v++l e+g++v+v+p+d++a e +  + +pd +++s+Gpg+p+  + + ++++e+ + +iP+ GI
  gi|313125676|ref|YP_004035946.1| 170 LIDCG--AKMSIVDSLNERGADVHVLPHDTTAAEVE--ELDPDLLFISNGPGDPAnFGDAQALVEEFVG-EIPLAGI 241
                                       89***..9**************************95..79***************999999999**999.******* PP

                                       THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEE CS
                            GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeel 154
                                       CLG Q++a ++g++++k+  ++h+g +++++d       ++++++ ++++H+y+v++    p +l vt ++ +d++ 
  gi|313125676|ref|YP_004035946.1| 242 CLGQQVIARALGGTTEKMD-FGHRGVNQPVRD------LNTGKVIMTTQNHGYTVDE----PGDLNVTQVNVNDDTA 307
                                       *******************.************......9999**************5....**************** PP

                                       EEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 155 meiiekknpfvgvQFHPEststpegpellfnfl 187
                                       +++ + + +++  Q+HPE++++p+++  +f+ +
  gi|313125676|ref|YP_004035946.1| 308 EGLENAELNVITRQYHPEAHPGPHDSLGFFDDV 340
                                       *******9*****************98888876 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   1.8e-06     0.011     103     127 ..     233     257 ..     222     269 .. 0.84
   2 !    6.0   0.0    0.0015         9     168     216 .]     279     325 ..     269     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
                     Peptidase_C26 103 ergvPilgiCrGlqllnvalGGtly 127
                                         ++P+ giC+G q+++ alGGt+ 
  gi|313125676|ref|YP_004035946.1| 233 VGEIPLAGICLGQQVIARALGGTTE 257
                                       3579******************985 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0015
                     Peptidase_C26 168 ievnslHhqaikelaeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                       i+++  H  +++e ++ l+v+ v   D++ E +e  e +  v+  Q+HPE
  gi|313125676|ref|YP_004035946.1| 279 IMTTQNHGYTVDEPGD-LNVTQVNVnDDTAEGLENAELN--VITRQYHPE 325
                                       5677789999999875.777777766*******999955..9*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2040.99
//
Query:       gi|313125677|ref|YP_004035947.1|  [L=140]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-18   64.5   0.8    5.4e-18   64.5   0.8    1.8  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    8.2e-16   57.3   0.2    1.6e-15   56.4   0.2    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    6.9e-11   42.0   1.3    1.3e-10   41.1   1.3    1.5  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    2.1e-05   24.1   0.1    8.6e-05   22.1   0.0    2.0  2  Sigma70_r4_2    Sigma-70, region 4
    0.00018   21.5   0.0    0.00037   20.5   0.0    1.5  1  HTH_20          Helix-turn-helix domain
    0.00043   19.6   0.2      0.001   18.5   0.0    1.8  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
    0.00055   19.4   0.2     0.0011   18.4   0.2    1.6  1  Sigma70_r4      Sigma-70, region 4
    0.00079   19.1   0.3     0.0016   18.1   0.3    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.001   18.8   0.0     0.0021   17.8   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
     0.0017   18.2   0.1     0.0031   17.4   0.1    1.6  1  HTH_11          HTH domain
     0.0029   17.6   1.4     0.0053   16.8   1.4    1.5  1  NapD            NapD protein
     0.0047   16.5   0.1      0.021   14.5   0.1    2.0  2  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
     0.0074   16.3   0.0      0.013   15.5   0.0    1.4  1  HTH_Mga         M protein trans-acting positive regulator (MG
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.022   14.6   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.011   15.7   0.0      0.029   14.3   0.0    1.7  1  MarR            MarR family
      0.016   15.0   0.0      0.097   12.5   0.0    2.1  2  DUF746          Domain of Unknown Function (DUF746)
      0.016   14.9   0.6      0.039   13.7   0.1    1.9  2  HTH_38          Helix-turn-helix domain
      0.021   14.7   0.2      0.046   13.6   0.0    1.7  2  MarR_2          MarR family
      0.022   14.9   0.0      0.043   14.0   0.0    1.4  1  HTH_28          Helix-turn-helix domain
      0.032   14.2   0.6       0.04   13.9   0.6    1.1  1  Saf-Nte_pilin   Saf-pilin pilus formation protein
      0.034   14.1   0.8       0.09   12.7   0.2    1.9  2  GYD             GYD domain
      0.048   13.0   0.4       0.17   11.2   0.4    1.9  1  DUF4191         Domain of unknown function (DUF4191)
      0.049   13.3   0.0      0.092   12.4   0.0    1.4  1  GntR            Bacterial regulatory proteins, gntR family
      0.051   13.1   0.1       0.24   11.0   0.0    2.1  3  GerE            Bacterial regulatory proteins, luxR family
       0.14   12.3   0.2       0.25   11.5   0.2    1.5  1  MIase           Muconolactone delta-isomerase
       0.14   12.0   0.1       0.79    9.7   0.1    2.0  2  TrmB            Sugar-specific transcriptional regulator TrmB
       0.16   12.4   0.1       0.88   10.0   0.0    2.0  2  FaeA            FaeA-like protein


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.8   8.1e-21   5.4e-18       1      41 [.       1      41 [.       1      42 [. 0.99

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 8.1e-21
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      +D++Dr IL++L++daR++y+e+Ae+vG Se tv++Rv+rL
  gi|313125677|ref|YP_004035947.1|  1 MDDLDREILDILRRDARTPYTEIAEQVGTSEGTVRNRVERL 41
                                      9***************************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.2   2.4e-18   1.6e-15       1      48 []       1      48 [.       1      48 [. 0.98

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.4e-18
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +d++dr+IL +L++++r++++e+Ae++g S +tv+ r++rL+++ +I+
  gi|313125677|ref|YP_004035947.1|  1 MDDLDREILDILRRDARTPYTEIAEQVGTSEGTVRNRVERLTNDNVIE 48
                                      89********************************************97 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   1.3     2e-13   1.3e-10       3      74 ..      65     133 ..      62     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2e-13
                                       EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       vs++ +   +++e+ +++ae+ +V  +++v+G+ d +l v ++d++a ++++ +  ++l++v++t+t ++l 
  gi|313125677|ref|YP_004035947.1|  65 VSVKVDV--DTTEISDQMAEWNQVDFVWQVSGEEDVVLVVDAADTRAVNELITR-ARELDEVKSTKTRLILD 133
                                       5555444..699******************************************.*************9996 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.3e-07   8.6e-05      21      49 ..      12      40 ..       3      41 .. 0.86
   2 ?   -1.2   0.0       2.5   1.6e+03      41      52 ..     108     119 ..     106     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                                      HHHTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrlsR 49
                                      lr+    +y EIAe+ g+segtV++r+ R
  gi|313125677|ref|YP_004035947.1| 12 LRRDARTPYTEIAEQVGTSEGTVRNRVER 40
                                      56666679******************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHH CS
                      Sigma70_r4_2  41 gtVksrlsRArk 52 
                                       ++V+  + RAr+
  gi|313125677|ref|YP_004035947.1| 108 RAVNELITRARE 119
                                       678888999985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   5.6e-07   0.00037      13      55 ..       6      48 ..       2      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.6e-07
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      r+il+ L+r++    +e+ae++++s  t++++++ L     +e
  gi|313125677|ref|YP_004035947.1|  6 REILDILRRDARTPYTEIAEQVGTSEGTVRNRVERLTNDNVIE 48
                                      89*********************************98777776 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.5e-06     0.001      16      51 ..       4      41 ..       2      42 .. 0.83
   2 ?   -2.2   0.0       4.2   2.8e+03      29      45 ..      61      77 ..      48      82 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                      HTH_Tnp_ISL3 16 leayilellles..rsvkavArqlgvSwtTVwrildry 51
                                      l++ il  l+++   + +++A+q+g+S+ TV++++ r+
  gi|313125677|ref|YP_004035947.1|  4 LDREILDILRRDarTPYTEIAEQVGTSEGTVRNRVERL 41
                                      66667777777777899*****************9987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.2
                      HTH_Tnp_ISL3 29 svkavArqlgvSwtTVw 45
                                      ++ +v+  ++v++t + 
  gi|313125677|ref|YP_004035947.1| 61 AMIEVSVKVDVDTTEIS 77
                                      44444444455555444 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.7e-06    0.0011       9      43 ..       5      40 ..       1      42 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
                                      HHHHHH.HHHTTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  9 erevle.lrfgeglTleEIgerlgiSrerVrqiekr 43
                                      +re+l  lr++   ++ EI+e+ g S+++Vr +  r
  gi|313125677|ref|YP_004035947.1|  5 DREILDiLRRDARTPYTEIAEQVGTSEGTVRNRVER 40
                                      67777427889999*****************99766 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.3   2.4e-06    0.0016       4      46 ..       7      49 ..       5      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +il+ l+++     +e++e+ g+Se T+R+  + L+++++++R
  gi|313125677|ref|YP_004035947.1|  7 EILDILRRDARTPYTEIAEQVGTSEGTVRNRVERLTNDNVIER 49
                                      899**************************************99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.2e-06    0.0021       7      46 ..       7      45 ..       7      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.2e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelG 46
                                      +iLd+l++ ++    +e+A++ g +  tv++ +  L++  
  gi|313125677|ref|YP_004035947.1|  7 EILDILRRDART-PYTEIAEQVGTSEGTVRNRVERLTNDN 45
                                      59*********8.9*****************999998765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.6e-06    0.0031       4      43 ..       7      45 ..       5      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.6e-06
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                       il +L + +   +  e+Ae+ + S+ tvr+++++L+   
  gi|313125677|ref|YP_004035947.1|  7 EILDIL-RRDARTPYTEIAEQVGTSEGTVRNRVERLTNDN 45
                                      688899.44445899*********************8776 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.4     8e-06    0.0053      15      67 ..      73     126 ..      53     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8e-06
                              NapD  15 laavkaalaalpgvE.vhasdeegklVvviEaesedeladtieaiealpgVlsa 67 
                                       ++++++++a+  +v+ v ++++e+ +V+v++a++++++ + i++ ++l+ V s+
  gi|313125677|ref|YP_004035947.1|  73 TTEISDQMAEWNQVDfVWQVSGEEDVVLVVDAADTRAVNELITRARELDEVKST 126
                                       6789999********55688999****************************997 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.2e-05     0.021      27      49 ..      21      43 ..       4      58 .. 0.83
   2 ?   -0.5   0.0       1.5     1e+03      28      58 ..      64      94 ..      44      96 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                      HrcA_DNA-bdg 27 eeiAevlkrneGtvRNqlqsLka 49
                                      +eiAe+++  eGtvRN ++ L  
  gi|313125677|ref|YP_004035947.1| 21 TEIAEQVGTSEGTVRNRVERLTN 43
                                      79***************999865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                      HrcA_DNA-bdg 28 eiAevlkrneGtvRNqlqsLkalgLvegvpG 58
                                      e+  +++ +   +  q+     ++ v  v+G
  gi|313125677|ref|YP_004035947.1| 64 EVSVKVDVDTTEISDQMAEWNQVDFVWQVSG 94
                                      6777777777777778877777777766655 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     2e-05     0.013       9      45 ..       7      42 ..       3      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                           HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseLn 45
                                      ++l++L   + +++++e+a++ g+se t++++++ L+
  gi|313125677|ref|YP_004035947.1|  7 EILDILRR-DARTPYTEIAEQVGTSEGTVRNRVERLT 42
                                      79999999.9**********************99986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.3e-05     0.022      13      41 ..      13      41 ..       7      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-05
                            HTH_23 13 llaeGlsvreIAreLgvsrrTvyrwlkry 41
                                        + + +++eIA++ g s+ Tv++ ++r 
  gi|313125677|ref|YP_004035947.1| 13 RRDARTPYTEIAEQVGTSEGTVRNRVERL 41
                                      4455889****************988885 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.4e-05     0.029       8      50 ..       8      50 ..       6      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      iL il++      +e+a+++g+s +tv + + rL  ++ ieR 
  gi|313125677|ref|YP_004035947.1|  8 ILDILRRDARTPYTEIAEQVGTSEGTVRNRVERLTNDNVIERF 50
                                      8999999999999****************************95 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015     0.097      15      36 ..      20      41 ..      17      44 .. 0.88
   2 ?   -1.0   0.0       2.4   1.6e+03      17      37 ..      64      84 ..      58      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                            DUF746 15 laeaadllgtdegiiakwvreF 36
                                       +e+a+++gt+eg+++++v++ 
  gi|313125677|ref|YP_004035947.1| 20 YTEIAEQVGTSEGTVRNRVERL 41
                                      589****************875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                            DUF746 17 eaadllgtdegiiakwvreFr 37
                                      e++  +++d   i+  ++e+ 
  gi|313125677|ref|YP_004035947.1| 64 EVSVKVDVDTTEISDQMAEWN 84
                                      778889999999998888886 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.9e-05     0.039       9      43 ..       5      40 ..       1      41 [. 0.85
   2 ?   -1.6   0.0       3.6   2.4e+03      29      34 ..     135     140 .]     134     140 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                            HTH_38  9 eReeIerll.aeGlslreIArrLgrspsTIsRElkR 43
                                      +Re + +l+ ++   + eIA ++g s +T+ + + R
  gi|313125677|ref|YP_004035947.1|  5 DREILDILRrDARTPYTEIAEQVGTSEGTVRNRVER 40
                                      89999999626778888*************998887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.6
                            HTH_38  29 rLgrsp 34 
                                       rLgrsp
  gi|313125677|ref|YP_004035947.1| 135 RLGRSP 140
                                       8***98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.9e-05     0.046       9      53 ..       7      49 ..       1      55 [. 0.85
   2 ?   -2.6   0.0       8.3   5.5e+03      39      46 ..     107     114 ..     100     119 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.9e-05
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                       +L  L+r  +     +e+a+  g s ++v ++++rL     +er
  gi|313125677|ref|YP_004035947.1|  7 EILDILRRDAR--TPYTEIAEQVGTSEGTVRNRVERLTNDNVIER 49
                                      56777777766..799************************99998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.3
                                       HHHHHHHH CS
                            MarR_2  39 srilkrLv 46 
                                       +r++++L 
  gi|313125677|ref|YP_004035947.1| 107 TRAVNELI 114
                                       55555554 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.4e-05     0.043      12      35 ..      17      40 ..       8      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-05
                            HTH_28 12 GhsvreaArelgisrrtvyrWikr 35
                                        +++e+A+++g+s+ tv+  + r
  gi|313125677|ref|YP_004035947.1| 17 RTPYTEIAEQVGTSEGTVRNRVER 40
                                      459****************98876 PP

>> Saf-Nte_pilin  Saf-pilin pilus formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   6.1e-05      0.04      37     129 ..      16     108 ..       8     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-05
                                       E--TT-EEEEEEEECS.S-SEEEEEEESSEBSSTTSSEEEEE-TTT--EEEEEE-HHHHHTECEEEEETTEEEEEEE CS
                     Saf-Nte_pilin  37 knapsakiaklvvnst.tlkefgvrgisnnvvdstgtawrvagkntgkeigvglssdslrrsdstekwngvnwmtfn 112
                                         +p + ia  v  s  t+++   r   +nv++    a      ++  e+ v +  d+   sd    wn v+++   
  gi|313125677|ref|YP_004035947.1|  16 ARTPYTEIAEQVGTSEgTVRNRVERLTNDNVIERFTVATSTGNIKAMIEVSVKVDVDTTEISDQMAEWNQVDFVWQV 92 
                                       567888999988877526666666777779999999999888889999***********************988665 PP

                                       SSEEEEEEE-SSS-EE- CS
                     Saf-Nte_pilin 113 sndtldivltgpaqnvt 129
                                       s +  d+vl   a +  
  gi|313125677|ref|YP_004035947.1|  93 SGE-EDVVLVVDAADTR 108
                                       554.5777776665554 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.9   1.9e+03      70      85 ..      30      45 ..      21      50 .. 0.75
   2 ?   12.7   0.2   0.00014      0.09      40      82 ..      89     131 ..      72     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.9
                               GYD 70 asGtvrtetlraftee 85
                                      + Gtvr+++ r+++ +
  gi|313125677|ref|YP_004035947.1| 30 SEGTVRNRVERLTNDN 45
                                      6799999888877655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                               GYD  40 lyatlGeyDvvvivEapDdetaaalslalaasGtvrtetlraf 82 
                                       ++ + Ge Dvv +v+a D +++  l  + ++   v+++ +r++
  gi|313125677|ref|YP_004035947.1|  89 VWQVSGEEDVVLVVDAADTRAVNELITRARELDEVKSTKTRLI 131
                                       67789*******************9999999999988777766 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00026      0.17     105     148 ..      80     123 ..       8     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                           DUF4191 105 vavtrqqDvvhrvvGrpGvvLvgEGnkkrvkkllaqekkrikrv 148
                                       +a  +q D v++v G++ vvLv + + +r+ + l +  +++++v
  gi|313125677|ref|YP_004035947.1|  80 MAEWNQVDFVWQVSGEEDVVLVVDAADTRAVNELITRARELDEV 123
                                       4556799*****************99988766666666666655 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.092      28      57 ..      21      50 ..       2      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverr 57
                                       e+a++ g+s  tvR    rL+ ++++er 
  gi|313125677|ref|YP_004035947.1| 21 TEIAEQVGTSEGTVRNRVERLTNDNVIERF 50
                                      69*************************995 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00036      0.24      21      41 ..      21      41 ..       7      43 .. 0.91
   2 ?   -1.5   0.0       2.9   1.9e+03      33      51 ..      51      69 ..      47      74 .. 0.76
   3 ?   -2.1   0.0       4.4   2.9e+03      19      27 ..      72      80 ..      66      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                                      HHHHHHHTS-HHHHHHHHHHH CS
                              GerE 21 keIAeelniSekTVkvhksni 41
                                      +eIAe+ + Se TV++ ++++
  gi|313125677|ref|YP_004035947.1| 21 TEIAEQVGTSEGTVRNRVERL 41
                                      69*************999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                                      HHHHHHHHHHHHHT-SSHH CS
                              GerE 33 TVkvhksnimkKLnvksrv 51
                                      TV +  +ni   ++v  +v
  gi|313125677|ref|YP_004035947.1| 51 TVATSTGNIKAMIEVSVKV 69
                                      8888888988877776655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.4
                                      -HHHHHHHH CS
                              GerE 19 snkeIAeel 27
                                       ++eI++++
  gi|313125677|ref|YP_004035947.1| 72 DTTEISDQM 80
                                      578999997 PP

>> MIase  Muconolactone delta-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00037      0.25      27      69 ..      73     115 ..      49     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                             MIase  27 ekaraqelqrqGklvrlwrvvgeyanisifdvedndeLhelLs 69 
                                         + + ++++  ++  +w+v ge  ++ ++d++d+ +++el++
  gi|313125677|ref|YP_004035947.1|  73 TTEISDQMAEWNQVDFVWQVSGEEDVVLVVDAADTRAVNELIT 115
                                       5667778888888999**********************99986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0012      0.79      26      55 ..      21      50 ..       8      60 .. 0.85
   2 ?    0.2   0.0       1.1   7.2e+02      27      58 ..      64      95 ..      55     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                                      CHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 26 deiaeelgvprskvYevLrsLedkGlVere 55
                                      +eiae++g ++ +v + +++L +  ++er 
  gi|313125677|ref|YP_004035947.1| 21 TEIAEQVGTSEGTVRNRVERLTNDNVIERF 50
                                      69**********************999985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                                      HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 27 eiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      e++ +++v+ + + + + +  + ++V  + g+
  gi|313125677|ref|YP_004035947.1| 64 EVSVKVDVDTTEISDQMAEWNQVDFVWQVSGE 95
                                      89999999999999988888888887766665 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0013      0.88       4      50 ..       7      52 ..       4      57 .. 0.85
   2 ?   -0.3   0.0       2.1   1.4e+03      11      25 ..      66      80 ..      58      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                                      HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE-- CS
                              FaeA  4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspv 50
                                      eIl+ l +  a    +eiA+ +g s   +R   e L     i+r  v
  gi|313125677|ref|YP_004035947.1|  7 EILDILRR-DARTPYTEIAEQVGTSEGTVRNRVERLTNDNVIERFTV 52
                                      57777777.6777779**************************99765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.1
                                      H.S----HHHHHHHH CS
                              FaeA 11 sikapckTreiAdal 25
                                      s+k  + T+ei d +
  gi|313125677|ref|YP_004035947.1| 66 SVKVDVDTTEISDQM 80
                                      4577899****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 759.66
//
Query:       gi|313125678|ref|YP_004035948.1|  [L=200]
Description: isopentenyl-diphosphate delta-isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-15   56.6   1.0    3.8e-15   56.1   1.0    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   1.0   2.1e-19   3.8e-15       2     131 .]      50     185 ..      49     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 2.1e-19
                                       EEEEEEEEEEETTSEEEEEEES..SSSTTT.EE.SSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEE CS
                             NUDIX   2 lrravgvvllnekgevLlvrrs..kkpfpg.We.lPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapy 74 
                                       ++ra+ +++++e+g++Ll++r+  k+ ++  W+ +++ +  +g++ e+A   +leEE+G+++++   l  +++++ y
  gi|313125678|ref|YP_004035948.1|  50 RHRAFTCLVFDEDGRLLLAQRApnKRLWDThWDgTVASHPVQGQSQEDATKQRLEEELGITPDQYSDLR-ITDKFEY 125
                                       8*********************96666666997799************************997775553.5556666 PP

                                       EEEEEE...EEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHHHH CS
                             NUDIX  75 dgpygd...eheilyvfleevegelepndenevsevrwvpleellkeklaaesrkllpwl 131
                                       + +y++   e e++ v+   +e++   +de+e++++ wv++e l +++ + ++ +l pw+
  gi|313125678|ref|YP_004035948.1| 126 KRYYENaglEWEVCAVLKVTLEDTTLDPDEEEIAGLLWVDYEHLHDHPEWYRQLRLCPWF 185
                                       66666676466666666655555555556***************7776666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1104.85
//
Query:       gi|313125679|ref|YP_004035949.1|  [L=173]
Description: metal-dependent protease of the pad1/jab1 superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-15   57.2   0.2    2.3e-15   56.4   0.2    1.4  1  Prok-JAB  Prokaryotic homologs of the JAB domain
    7.8e-07   29.1   0.0    1.7e-06   28.0   0.0    1.5  1  JAB       JAB1/Mov34/MPN/PAD-1 ubiquitin protease
  ------ inclusion threshold ------
      0.088   12.9   0.0       0.11   12.5   0.0    1.1  1  UPF0172   Uncharacterised protein family (UPF0172)


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.2   3.9e-19   2.3e-15       3     107 ..      17     150 ..      15     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 3.9e-19
                          Prok-JAB   3 svlsalvaharra....hpeEtcGlllgke....................seseevivvplvnewsn.......... 45 
                                       ++ +a++ahar+      p E cG+l g++                    s                          
  gi|313125679|ref|YP_004035949.1|  17 EAREAIIAHAREGaattPPSEVCGVLGGYRadtaatnaddasatdsaesaS---------------Addigtgsdtv 78 
                                       56778888888777777*************776665555555555555440...............04555555555 PP

                          Prok-JAB  46 ...............rfeipdpedslarlkfearerglevvgiwHSHpggsarPSetDrrdaaalarvkalliivgd 107
                                                       +++ dpe +  +++  +++rgl+vvg +HSHp++ + PS+tD r a  +   +++++i++ 
  gi|313125679|ref|YP_004035949.1|  79 tvaepvpnvaddprtTYTL-DPETTVETID-TLESRGLDVVGFYHSHPESDPVPSRTDERRATWT---GYVYLICHP 150
                                       5555555667778999999.**********.*******************************876...788888875 PP

>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.9e-10   1.7e-06       8     105 ..      14     134 ..       9     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.9e-10
                                       EEHHHHHHHHHHHHHHHHHT..S--EEEEEEEESSSE..........................EEEEEEEEEESEEE CS
                               JAB   8 leslvllkildhalrtekee..eevmGlliGelnddt..........................tveitnvfalpfee 56 
                                       l +++   i+ ha++++  +  +ev+G+l G   d                            tv + + +    ++
  gi|313125679|ref|YP_004035949.1|  14 LTAEAREAIIAHAREGAATTppSEVCGVLGGYRADTAatnaddasatdsaesasaddigtgsdTVTVAEPVPNVADD 90 
                                       66777788999999999999999*****999988888999999***9999999999999884444444444444444 PP

                                       ESSECEEEEEHHHHHHHHHHHHHHHCTT.SEEEEEEEESSSS-SS--HHH CS
                               JAB  57 tekdvdavsldqeylekksellkklrgr.ervvGWYhshpditvwlsevd 105
                                        +++     ld e   +  e ++ l+ r + vvG+Yhshp+ +  +s+ d
  gi|313125679|ref|YP_004035949.1|  91 PRTT---YTLDPE---TTVETIDTLESRgLDVVGFYHSHPESDPVPSRTD 134
                                       4444...666666...77889999999***************99999987 PP

>> UPF0172  Uncharacterised protein family (UPF0172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05      0.11      17      84 ..      31     124 ..      14     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                           UPF0172  17 aKyptqaVnGvLlgkksssksk.........................vevtDavPLfH..ssltlspmlevAlaqve 66 
                                       a  p ++V+GvL g + ++ ++                         v+v++ vP +     +t +   e  ++ ++
  gi|313125679|ref|YP_004035949.1|  31 ATTPPSEVCGVLGGYRADTAATnaddasatdsaesasaddigtgsdtVTVAEPVPNVAddPRTTYTLDPETTVETID 107
                                       5568899********999888899*******************************9996655666666689999999 PP

                           UPF0172  67 syakekglvivGyYqane 84 
                                       +  +++gl +vG+Y+++ 
  gi|313125679|ref|YP_004035949.1| 108 TL-ESRGLDVVGFYHSHP 124
                                       86.677*********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 990.10
//
Query:       gi|313125680|ref|YP_004035950.1|  [L=237]
Description: hypothetical protein Hbor_09100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-40  137.6   0.0    4.5e-40  137.2   0.0    1.1  1  adh_short       short chain dehydrogenase
    1.1e-35  123.3   0.0    1.6e-35  122.8   0.0    1.2  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    8.6e-06   25.4   0.0      1e-05   25.2   0.0    1.1  1  Epimerase       NAD dependent epimerase/dehydratase family
     0.0023   17.9   0.4      0.032   14.2   0.4    2.0  1  KR              KR domain
     0.0027   17.6   0.0     0.0033   17.3   0.0    1.2  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
       0.02   14.0   0.1      0.022   13.9   0.1    1.1  1  RmlD_sub_bind   RmlD substrate binding domain
       0.13   12.1   0.0        0.2   11.5   0.0    1.2  1  DFP             DNA / pantothenate metabolism flavoprotein


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.0   1.8e-43   4.5e-40       1     190 [.      17     201 ..      17     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 1.8e-43
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       +v+lvtGa +G+Gr+ia++l   Ga+v+++ rs    + + +e         ++ vDvt++ e++++v+++ +  g+
  gi|313125680|ref|YP_004035950.1|  17 QVALVTGANRGLGREIAEQLHDLGATVFAATRSIT--HDIPDE-------WNHLLVDVTQEGEISDAVDDIFASAGR 84 
                                       69***************************888843..334444.......66799********************** PP

                                       ESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG...TSB-TTBHHHH CS
                         adh_short  78 ldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag...kvpvagvaaYs 150
                                       ld+LvnNAGi  g+g++   s +++++++++Nl g++l++++++p +++ ++Gr++nvsS  g   + ++ g ++Y 
  gi|313125680|ref|YP_004035950.1|  85 LDILVNNAGIsGGDGDIVAESVTDIDQTLATNLRGPMLVCKHAVPLLVQDEGGRVINVSSGMGalnEAQSGGSPSYR 161
                                       **********88889999999999***************************************654455667899** PP

                                       HHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 151 AsKaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                        sK +++glt+ l  e+ ++g   n+v+PG v+Tdm  e 
  gi|313125680|ref|YP_004035950.1| 162 ISKTGLNGLTKYLDGEYGDDGLLANSVCPGWVRTDMGGED 201
                                       ************************************8765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   0.0   6.2e-39   1.6e-35       1     183 [.      23     202 ..      23     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 6.2e-39
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnna 77 
                                       Ga +g+Gr+iA++l++ Ga+v ++ ++        ++ +e +   l +DVt+e ++ ++v+++ ++ g+lDilvnna
  gi|313125680|ref|YP_004035950.1|  23 GANRGLGREIAEQLHDLGATVFAATRSITH-----DIPDEWN--HLLVDVTQEGEISDAVDDIFASAGRLDILVNNA 92 
                                       899*******************99777665.....5555433..4999***************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTT...HHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnyn...aygaaKaale 149
                                       gi+   +g+++  s  ++d++l++nl++ +l++k+a+p l++++ g+++n+ss  +    ++      y ++K +l+
  gi|313125680|ref|YP_004035950.1|  93 GISGG-DGDIVAESVTDIDQTLATNLRGPMLVCKHAVPlLVQDEgGRVINVSSGMGALNEAQSGgspSYRISKTGLN 168
                                       ****9.********************************6444335*******987665554444457********** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGST CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgik 183
                                       +lt+yl  e+g++g   N+v+pg+++T++  + +
  gi|313125680|ref|YP_004035950.1| 169 GLTKYLDGEYGDDGLLANSVCPGWVRTDMGGEDA 202
                                       *****************************65543 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.9e-09     1e-05       1     115 [.      19     144 ..      19     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.9e-09
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHH.T-SEEEE--S CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkee.qpdavihlAa 73 
                                       +lVtGa+  +G+ ++++l + g +v + +r  + +   + ++l      e+++ d  a++++f++  + d+ ++ A+
  gi|313125680|ref|YP_004035950.1|  19 ALVTGANRGLGREIAEQLHDLGATVFAATRSITHDIPDEWNHLlvdVTQEGEISD--AVDDIFASAgRLDILVNNAG 93 
                                       59*****************************665555555555666666666665..899****999********** PP

                                       .---....HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT....EEEEEEE CS
                         Epimerase  74 .vgg....vaassedpadfieknlqgtlnlleaarkagvk....rllflsS 115
                                         gg    va+s++d  +++ +nl+g + +++ a    v+    r++++sS
  gi|313125680|ref|YP_004035950.1|  94 iSGGdgdiVAESVTDIDQTLATNLRGPMLVCKHAVPLLVQdeggRVINVSS 144
                                       5555555567999****************9999986555555558888888 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.4   1.2e-05     0.032       3     115 ..      19     119 ..      17     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        l+tG+  gLG+e+a++l + ga+     +Rs   ++d     +       e + + +Dv+++ +++ ++++i a++
  gi|313125680|ref|YP_004035950.1|  19 ALVTGANRGLGREIAEQLHDLGATV-FAATRS--ITHDIP---D-------EWNHLLVDVTQEGEISDAVDDIFASA 82 
                                       59********************975.556677..223322...2.......34456678888888888888888888 PP

                                       S---EEEE------.---TTT--HHHHHHHHTTTTHH CS
                                KR  80 ppikGvihaAgvlr.dklleemtaedleqvlapKvkG 115
                                       +++   ++ Ag++  d+ +   +  d++q la  ++G
  gi|313125680|ref|YP_004035950.1|  83 GRLDILVNNAGISGgDGDIVAESVTDIDQTLATNLRG 119
                                       8888888888887658888888888888888877766 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.3e-06    0.0033       1     133 [.      23     186 ..      23     209 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHT.......T-SEEEES-- CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdvedlaealk.......gadaVvsalg 69 
                                       GA+ + Gr+++++l + g  +v a +R+ ++++++     + + + +dvt++ ++ +a++         d+ v ++g
  gi|313125680|ref|YP_004035950.1|  23 GANRGLGREIAEQLHDLG-ATVFAATRSiTHDIPD-----EWNHLLVDVTQEGEISDAVDdifasagRLDILVNNAG 93 
                                       9****************5.8999999884455554.....3444445555555555555522222226699888886 PP

                                       -TCCHHHH......................HHHHHHHHHHCT--EEEEEEE.TTTTSGCGCHHHHHHH......HCC CS
                    NAD_binding_10  70 gggkdeeg......................aknivdaakeagvkRfvlvsa.igvgdevpgefgewnk......ell 117
                                        +g+d ++                      +k++v  + + +  R++ vs+ +g+ +e+++  ++ ++      + l
  gi|313125680|ref|YP_004035950.1|  94 ISGGDGDIvaesvtdidqtlatnlrgpmlvCKHAVPLLVQDEGGRVINVSSgMGALNEAQSGGSPSYRisktglNGL 170
                                       66663333444455666677999999999999999999999999999998769999877654333222111111355 PP

                                       HHHHHHHHHHHHHHHH CS
                    NAD_binding_10 118 kaylaakraaeellra 133
                                        +yl+  +  + ll +
  gi|313125680|ref|YP_004035950.1| 171 TKYLDGEYGDDGLLAN 186
                                       5555555555555554 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.7e-06     0.022       4      65 ..      20      98 ..      17     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.7e-06
                                      EEESTTSHHHHHHHHHCTTTSEEEEEE-TT............T--TTSHHHHHHHH.....HHH--SEEEE------HH CS
                     RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlaltre............eldltdaeavaell.....keakpdvvvnaAAytavD 65
                                      lvtGan  lG+e+a+ql+  g+ v a tr+             +d+t++ ++ +++     ++ + d++vn A     D
  gi|313125680|ref|YP_004035950.1| 20 LVTGANRGLGREIAEQLHDLGATVFAATRSithdipdewnhlLVDVTQEGEISDAVddifaSAGRLDILVNNAGISGGD 98
                                      8*****************************9999999999987788887777777722223334667777777666555 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.8e-05       0.2      32      93 ..      29      95 ..      22     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.8e-05
                                      HHHHHHHHHHTT-EEEEEE-S-SS---T..T-EEEE--SHHHHHHHHHHHHTT-...SEEEE---S- CS
                               DFP 32 GyalAeaaaarGaeVtlvsgpvsletpe..gvevvkvesaeemleaveealkea...divimaAAva 93
                                      G ++Ae++ + Ga+V   + + + + p+  +  +v+v++  e+ +av++ +++a   di++  A ++
  gi|313125680|ref|YP_004035950.1| 29 GREIAEQLHDLGATVFAATRSITHDIPDewNHLLVDVTQEGEISDAVDDIFASAgrlDILVNNAGIS 95
                                      899**************999965555551155699**************99888888****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1335.61
//
Query:       gi|313125681|ref|YP_004035951.1|  [L=439]
Description: kynureninase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-25   87.5   0.0    1.1e-24   87.1   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    0.00068   18.3   0.0    0.00091   17.9   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0067   16.8   0.6       0.38   11.1   0.8    2.4  2  DUF1651          Protein of unknown function (DUF1651)


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   1.8e-28   1.1e-24      17     335 ..      66     390 ..      59     392 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.8e-28
                                       HHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEE CS
                       Aminotran_5  17 dalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivv 93 
                                       +al+e  +++++ ++r+  ++  e ++  e   +++a l++ae  ee+++  +tt  i + + ++ +  ++g++i+v
  gi|313125681|ref|YP_004035951.1|  66 AALDEAVEQWKTLAIRGWTDADPEWYTYGERLGDRLAPLVGAEP-EEVVVGNSTTVNIHTLVGTF-YDPSRGEKILV 140
                                       57788888999********************************7.****************9999.559******** PP

                                       ET....TSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHH CS
                       Aminotran_5  94 te....aehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklak 166
                                        +    ++h a +   +++ ++   +++v++  ++ +++ d++ ++++e++ +v++  v   +G + ++e+i+++a+
  gi|313125681|ref|YP_004035951.1| 141 NDldfpTDHYAIRAQLRQVGRDPDENLRVVESRDGRTIEEDDIVAAIDEDVGMVFMPSVLYRSGQLLDIERITEAAH 217
                                       9833335799999999************************************************************* PP

                                       HTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EE.EEEEHHHHHTS..SS...STTSEEEEET.TE CS
                       Aminotran_5 167 kkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGv.lyvrkellekleplll..ggemveevsl.ee 238
                                       ++gal   D a ++g  p  +++l+vDf++    K l++ +G  + lyv +++ +  + l +  g e  ++ ++ ++
  gi|313125681|ref|YP_004035951.1| 218 DAGALAGFDLAHSIGAVPHALSDLDVDFAVWCHYKyLNAGPGAAAgLYVNERHFGVTPALAGwwGHEKETQFEMrHT 294
                                       ***********************************95555555444*******999966654334555556667788 PP

                                       EEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCT.STTEEEES.-B-CTCBSEEEE CS
                       Aminotran_5 239 ttfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlks.lpgvrlygpdkaerrasivsf 314
                                       +t a +   f+ GTp++ ++  l  al+ +e+ g++a ++++ +l++ l e +++ lp++++  p++  rr + v  
  gi|313125681|ref|YP_004035951.1| 295 YTPAHSAGAFQIGTPPILAAAPLDGALDVVEDAGIDALREKSLALTDSLIELVDDrLPDCEVGTPRDPTRRGGHV-- 369
                                       888888899********************************************9879*****5565555565555.. PP

                                       EETTCSHHHHHHHHHHTTEEE CS
                       Aminotran_5 315 nfkgvhaedvatlLdeegIav 335
                                       +++  +a  +  +L+++g+ v
  gi|313125681|ref|YP_004035951.1| 370 AVEHPEAYRISEALKDRGVIV 390
                                       556667889999999998877 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.5e-07   0.00091     125     213 ..     178     267 ..      95     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-07
                                       TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GG.GGT-SEEEEETTTTT CS
                   Cys_Met_Meta_PP 125 sdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrpl.klgaDivvhSaTKyl 200
                                        +++++ +ai+e + +v++ ++     +++Die+i+++a++ag+l   D + + +++ ++l +l++D  v    Kyl
  gi|313125681|ref|YP_004035951.1| 178 IEEDDIVAAIDEDVGMVFMPSVLYRSGQLLDIERITEAAHDAGALAGFDLAHSIGAVPHALsDLDVDFAVWCHYKYL 254
                                       4568899*****************************************************966************** PP

                                       TCSSS--EEEEEE CS
                   Cys_Met_Meta_PP 201 gGhsdvvaGvivv 213
                                       +    + aG+ v+
  gi|313125681|ref|YP_004035951.1| 255 NAGPGAAAGLYVN 267
                                       9877777777765 PP

>> DUF1651  Protein of unknown function (DUF1651)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.026   1.6e+02      38      61 ..      18      41 ..      10      43 .. 0.86
   2 !   11.1   0.8   6.3e-05      0.38      52      74 .]      68      90 ..      64      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.026
                           DUF1651 38 ggePpllktrrrltlekArelWke 61
                                      g+ Pp+l + r+++ ++A+  +++
  gi|313125681|ref|YP_004035951.1| 18 GDGPPTLAEAREMDHDDALSHFRD 41
                                      56799*************988875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.3e-05
                           DUF1651 52 lekArelWkellstGWekvepqw 74
                                      l++A e Wk+l   GW+  +p+w
  gi|313125681|ref|YP_004035951.1| 68 LDEAVEQWKTLAIRGWTDADPEW 90
                                      799*****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2529.14
//
Query:       gi|313125682|ref|YP_004035952.1|  [L=167]
Description: hypothetical protein Hbor_09120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.01   15.9   0.9        5.6    7.2   0.1    2.8  3  STT3_PglB_C  STT3/PglB C-terminal beta-barrel domain
        1.3    9.6   8.7       0.82   10.3   1.4    3.1  3  PepSY_like   Putative beta-lactamase-inhibitor-like, PepSY-li


Domain annotation for each model (and alignments):
>> STT3_PglB_C  STT3/PglB C-terminal beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1   0.00062       5.6      23      62 ..      35      74 ..      31      87 .. 0.90
   2 ?    6.4   0.1     0.001       9.3      28      64 ..     105     141 ..      98     146 .. 0.81
   3 ?   -1.6   0.0      0.35   3.1e+03      21      39 ..     146     164 ..     136     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00062
                                      EETTTTEEEETTEEEEEEEEEEEEETTTTEEEE..EE--T CS
                       STT3_PglB_C 23 lskdfkslkiggqkvpvktfveteydkngklkvketeids 62
                                      +++d  ++++g+++++ + + + eyd++++l++  + i+ 
  gi|313125682|ref|YP_004035952.1| 35 FDDDDIEIEFGDKEFEGDDVDDFEYDEDEELEIDGEDIEV 74
                                      6789999*************************98777665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.001
                                       TEEEETTEEEEEEEEEEEEETTTTEEEE..EE--TT- CS
                       STT3_PglB_C  28 kslkiggqkvpvktfveteydkngklkvketeidska 64 
                                        ++  ++ +++++   e+ yd++g ++v+   id ++
  gi|313125682|ref|YP_004035952.1| 105 IEFDRDDIEFEIDDDAEVDYDTDGDFEVEGDDIDIDG 141
                                       5555667788888999************999999776 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.35
                                       EEEETTTTEEEETTEEEEE CS
                       STT3_PglB_C  21 ivlskdfkslkiggqkvpv 39 
                                       i+++ d  ++++ +  +++
  gi|313125682|ref|YP_004035952.1| 146 IEIDGDDAEVEFRDGRIEI 164
                                       6777888888887777766 PP

>> PepSY_like  Putative beta-lactamase-inhibitor-like, PepSY-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.1      0.03   2.7e+02      46      80 ..      47      88 ..      35      94 .. 0.71
   2 ?   10.3   1.4   9.1e-05      0.82      46      81 ..      95     130 ..      65     131 .. 0.79
   3 ?   -0.2   0.1      0.17   1.5e+03      56      69 ..     146     159 ..     134     167 .] 0.50

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.03
                                      HHTTTEEEEEEEECS.SEEEEEETT......SEEEEEETTS- CS
                        PepSY_like 46 nsypdekvtkierkk.keyeielen......eielyfdedGn 80
                                      +++ +++v++ e+++ +e ei+ e+      +++ ++ +dG+
  gi|313125682|ref|YP_004035952.1| 47 KEFEGDDVDDFEYDEdEELEIDGEDievdsdDTDFEIHDDGE 88
                                      347788888888888866666555554444777777777775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.1e-05
                                       HHTTTEEEEEEEECSSEEEEEETTSEEEEEETTS-E CS
                        PepSY_like  46 nsypdekvtkierkkkeyeieleneielyfdedGnl 81 
                                       +s+  e+ + ie+++ ++e+e++++ e+ +d dG++
  gi|313125682|ref|YP_004035952.1|  95 ESFEAESDDGIEFDRDDIEFEIDDDAEVDYDTDGDF 130
                                       4455678889************************86 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.17
                                       EEECSSEEEEEETT CS
                        PepSY_like  56 ierkkkeyeielen 69 
                                       ie +  + e+e+ +
  gi|313125682|ref|YP_004035952.1| 146 IEIDGDDAEVEFRD 159
                                       33333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 930.23
//
Query:       gi|313125683|ref|YP_004035953.1|  [L=339]
Description: hydrogenase maturation factor [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-20   72.7   1.0    4.9e-20   72.2   1.0    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    5.8e-06   26.9   1.6    7.5e-06   26.5   0.2    2.0  2  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   1.0   5.5e-24   4.9e-20       1     153 [.     157     312 ..     157     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 5.5e-24
                                       STTEEEEEEET...SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHH CS
                            AIRS_C   1 kpGdvliltgs...lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlg 74 
                                       ++Gd +++t++     +g ++t+  ++ + +e++    +     l e  +++ +  + a  g+v+a+hD T+ GL g
  gi|313125683|ref|YP_004035953.1| 157 RVGDDVLVTKGpavEATGLLTTLFPDQFDLPETTL---RAAQSRLDEAECVRDAMTASAV-GGVHAMHDATECGLFG 229
                                       68999999999777777777777777777777776...4566666677777777777777.**************** PP

                                       HHHHHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEE CS
                            AIRS_C  75 alaemapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevt 146
                                       al+e+a+++gv++ i+ d++p++  +e     ++++++ + + G l++av+p++ +av+++le+eg p + v G+v 
  gi|313125683|ref|YP_004035953.1| 230 ALNEVADGAGVQLDISTDEIPLRPGVEetcefLGMDPWTATTGGTLVLAVDPDSTAAVVSALESEGTP-VGVAGTVR 305
                                       ******************77776666666699**********************************97.******** PP

                                       ESSSEEE CS
                            AIRS_C 147 akeelsv 153
                                       ++ +++v
  gi|313125683|ref|YP_004035953.1| 306 EGSGVTV 312
                                       9987765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.2   8.4e-10   7.5e-06       4      84 ..      46     134 ..      25     145 .. 0.81
   2 ?   -3.0   0.1       1.4   1.2e+04      20      20 ..     215     215 ..     201     240 .. 0.42

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 8.4e-10
                                       EEEEEEEEEE.EECCTCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT- CS
                              AIRS   4 avvvttdshnrpvlvepvhf...iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgv 71 
                                       av+++td    pv v p  +   +G+ ++  +l D+a+ G  P  l  s++lp       ++ + + ++e ae lgv
  gi|313125683|ref|YP_004035953.1|  46 AVAIATD----PVSVLPDLGlarAGRFTLDFVLADVAVSGLPPSHLAISFTLPpdfedeSFATLWTAMHEEAEDLGV 118
                                       4577777....6666554447899***************************************************** PP

                                       EEEEEEEEEESS...E CS
                              AIRS  72 plvgGdtsfsne...p 84 
                                       ++v+G+t+++++   p
  gi|313125683|ref|YP_004035953.1| 119 SIVTGHTARYSGcsfP 134
                                       ********99765543 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                       C CS
                              AIRS  20 p 20 
                                       +
  gi|313125683|ref|YP_004035953.1| 215 G 215
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1942.42
//
Query:       gi|313125684|ref|YP_004035954.1|  [L=305]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-27   96.2   0.7    2.2e-26   93.0   0.7    2.0  1  Abhydrolase_1   alpha/beta hydrolase fold
      1e-18   68.8  12.0    1.2e-18   68.5  12.0    1.0  1  Abhydrolase_6   Alpha/beta hydrolase family
    6.8e-11   41.9   0.0    1.7e-10   40.6   0.0    1.6  1  Hydrolase_4     Serine aminopeptidase, S33
      0.005   15.6   0.0      0.049   12.3   0.0    2.0  1  Ndr             Ndr family
  ------ inclusion threshold ------
      0.064   12.8   2.1       0.11   12.0   0.4    2.3  2  Transp_inhibit  Transport inhibitor response 1 protein domain


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.7   6.2e-30   2.2e-26       2     257 .]      45     289 ..      44     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 6.2e-30
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v+lhG+p+ ++ w+e  +   La++g++vi++D+rG+  S+++ a   d y+ + +add+  +ldal++   +lv
  gi|313125684|ref|YP_004035954.1|  45 PVVLLHGFPEFWYAWHE--FLGPLADEGYRVIVPDQRGYHLSDKPEAV--DAYHPDELADDVLGLLDALDLSDAHLV 117
                                       8****************..55567777********************8..*************************** PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHH.HHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqa.ksfpdffdgyaadcarnpagplladelaaleqr 154
                                       Gh++G ++a+++ + +p+r + l  l+       +  a r+++ + +   +  ++  +++ p  p +  +++ +++ 
  gi|313125684|ref|YP_004035954.1| 118 GHDWGAFVAWWVGLHAPDRLRTLSVLNV-----PHPTAFRHALsNDWEQRLKSWYVLFFQLPKIPEALAKMGEYRTL 189
                                       ************************9999.....33333333330444556666666666666666666666666666 PP

                                       HHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHH CS
                     Abhydrolase_1 155 hrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkale 231
                                        +l+ +  +p ++  ++ + ++ a s        ++ + + ++a+   + ++   v +ptlv++g++D   + +   
  gi|313125684|ref|YP_004035954.1| 190 CDLMRRSSQPGTFNEADFDCYRAAWSRPGAYRSMVNWYRAIARANPRPKTER---VGVPTLVLWGAKDAFLTRSLAL 263
                                       6666666678888888888888888888888888888888888888888777...888******************* PP

                                       HHHHCHTSEEEEEEETCSSSHHHHSH CS
                     Abhydrolase_1 232 dlaqllpkkrlvvisdagHlaflegp 257
                                       ++ + + ++ lvv++da H+++ e+p
  gi|313125684|ref|YP_004035954.1| 264 QSVEYCENSHLVVLDDATHWIQHEEP 289
                                       **********************9986 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5  12.0   3.3e-22   1.2e-18       1     217 [.      46     292 ..      46     295 .. 0.63

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 3.3e-22
                                       EEEE--GC.....GC..HHHHHHHHCCTCEEEEE--TTS.TS-GGCS.....--HHH.CHHHHHHHCCTT..TTSEE CS
                     Abhydrolase_6   1 vlllHGagssassWl..vapLaallaagvhvlapDlpGh.Grsdppp.....ldled.ladlaalldelaagggpvv 68 
                                       v+llHG++   + W+  + +L +l+ +g++v++pD +G+    +++p     ++ ++ ++d++ lld+l+    +++
  gi|313125684|ref|YP_004035954.1|  46 VVLLHGFP---EFWYawHEFLGPLADEGYRVIVPDQRGYhL--SDKPeavdaYHPDElADDVLGLLDALD--LSDAH 115
                                       8*****99...66754567999999999***********74..333312322333333455588999995..999** PP

                                       EEEETCHHHHHHHHHHCC....EE..EEES-..----TTT.......S----TTHHHHHH........TT-C...CC CS
                     Abhydrolase_6  69 lvGHSlGGalalaaapla..lvvg..vlldppptalpagl.......laaalelllalla........llrl...la 123
                                       lvGH++G+++a+ ++ +a  ++++  vl  p pta++++l       l       + ++         +++l    +
  gi|313125684|ref|YP_004035954.1| 116 LVGHDWGAFVAWWVGLHApdRLRTlsVLNVPHPTAFRHALsndweqrL-------KSWYVlffqlpkiPEALakmGE 185
                                       *********999977777764444779999988777777744444341.......3333332222223222223444 PP

                                       CHCCH......S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHCHTT.......CCHHTT-TTGCEEEC.TT-CHHHHC CS
                     Abhydrolase_6 124 wlsre......plprlfladedadaawrarlarlaallaglgllp.......aaawadlpvpllvlg.geDplvprl 186
                                       +++++      + p +f + +     +ra+++r+ a+++++ +++       ++  +++ vp+lvl+ ++D+ + r 
  gi|313125684|ref|YP_004035954.1| 186 YRTLCdlmrrsSQPGTFNEAD--FDCYRAAWSRPGAYRSMVNWYRaiaranpRPKTERVGVPTLVLWgAKDAFLTRS 260
                                       443335333333333444433..599999999999999988877622222224455555555599975888854433 PP

                                       HH.CCCH.STTEEETCE...SSS-HHHHSHHHH CS
                     Abhydrolase_6 187 le.rlla.qagarlpvvlpgaGHlphleepdev 217
                                       l+ +     +  +l vvl +a H+++ eep +v
  gi|313125684|ref|YP_004035954.1| 261 LAlQSVEyCENSHL-VVLDDATHWIQHEEPVRV 292
                                       22133334488888.**********999*9765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   4.8e-14   1.7e-10       7     237 ..      46     287 ..      41     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.8e-14
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllG 82 
                                       vvl+HG+ e   + +e+   La++G+ v+  D+rG+  s+ ++ ++  + d++ dD+  +++++      +   l+G
  gi|313125684|ref|YP_004035954.1|  46 VVLLHGFPEFWYAWHEFLGPLADEGYRVIVPDQRGYHLSDkPEAVDAYHPDELADDVLGLLDALDL----SDAHLVG 118
                                       9***************************************99999*****************9994....45678** PP

                       Hydrolase_4  83 hSmGGliallyllrypdkva.glilsaP...alkikaklkappllklllkllgkllpklqv........snnlkads 147
                                       h +G+++a  ++l+ pd+++   +l  P   a++ + +   + + + l  +   +++  ++        + ++++d 
  gi|313125684|ref|YP_004035954.1| 119 HDWGAFVAWWVGLHAPDRLRtLSVLNVPhptAFRHALS---NDWEQRLKSWYVLFFQLPKIpealakmgEYRTLCDL 192
                                       *****************999556666662224444433...333333333333333333335555588867777777 PP

                       Hydrolase_4 148 lsrdpevvaayeadplv.hgk.itvrlllelldamkrleeraakit.....lPllllhGeaDkvvdpeasrelyerl 217
                                       + r  +     ead  + + +  + + ++++++   ++ + +++ +     +P+l+l G++D    ++ + + +e +
  gi|313125684|ref|YP_004035954.1| 193 MRRSSQPGTFNEADFDCyRAAwSRPGAYRSMVNWYRAIARANPRPKtervgVPTLVLWGAKDAFLTRSLALQSVEYC 269
                                       777777777777777765433145555556655555555544444444466**************999998888888 PP

                       Hydrolase_4 218 gskdktlklypglyHellnE 237
                                          + +l + + + H + +E
  gi|313125684|ref|YP_004035954.1| 270 E--NSHLVVLDDATHWIQHE 287
                                       8..78999999999999888 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   1.4e-05     0.049      83     272 ..      96     296 ..      87     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                                       HHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES-.--S-..--HHHHHHHHHH........ CS
                               Ndr  83 ddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLini.tska..agwvewakeKlsskl...lk 153
                                       d+lad++l +ld ++l+ +  +G   GA++    +l+ p+r+  l  +n+  ++a  +++ +   ++l s +   ++
  gi|313125684|ref|YP_004035954.1|  96 DELADDVLGLLDALDLSDAHLVGHDWGAFVAWWVGLHAPDRLRTLSVLNVpHPTAfrHALSNDWEQRLKSWYvlfFQ 172
                                       79******************************************977765234332244444444454443311145 PP

                                       ..TTTS-HHHHHHHHHS-HHHHHH......T-HHHHHHHHHHHT-TTHHHHHHHHHHHHT-------TTSSSS-EEE CS
                               Ndr 154 kvgltdllkdlllahkFgkeekse......nsdlvreyrkllkerlnsknlelyleaynkRrdleierkklevkvll 224
                                         ++ ++l  +  ++     ++++      n+     yr   ++    +++ ++ +a+  R +   + + + v++l+
  gi|313125684|ref|YP_004035954.1| 173 LPKIPEALAKMGEYRTLCDLMRRSsqpgtfNEADFDCYRAAWSRPGAYRSMVNWYRAIA-RANPRPKTERVGVPTLV 248
                                       55555666666666666666665555666644445589999999999999999988876.55556677888899999 PP

                                       EEETTSTTHHHHHHHHHHS-TTTEEEEEETT-TT-HHHH-HHHHHHHH CS
                               Ndr 225 vvGdkspfvdevvevnskldkkkttllkvadsgglvleeqPdklaesl 272
                                       + G+k +f+   + ++s    +++ l+ ++d++  +++e+P ++ + l
  gi|313125684|ref|YP_004035954.1| 249 LWGAKDAFLTRSLALQSVEYCENSHLVVLDDATHWIQHEEPVRVQREL 296
                                       999999999999999999999999999999999999999999887765 PP

>> Transp_inhibit  Transport inhibitor response 1 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   3.1e-05      0.11      18      33 ..     115     130 ..     111     144 .. 0.84
   2 ?   -1.3   0.1      0.44   1.6e+03      28      40 ..     223     235 ..     204     237 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                    Transp_inhibit  18 nLvPedWGgyvspWve 33 
                                        Lv +dWG++v+ Wv 
  gi|313125684|ref|YP_004035954.1| 115 HLVGHDWGAFVAWWVG 130
                                       79************96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.44
                    Transp_inhibit  28 vspWvealaeayp 40 
                                       +  W +a+a+a p
  gi|313125684|ref|YP_004035954.1| 223 MVNWYRAIARANP 235
                                       3479999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1840.29
//
Query:       gi|313125685|ref|YP_004035955.1|  [L=747]
Description: amino acid transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-46  158.9  46.7    2.3e-46  158.5  46.7    1.1  1  AA_permease_2   Amino acid permease
    4.2e-33  114.7  43.7    5.9e-33  114.2  43.7    1.2  1  AA_permease     Amino acid permease
    1.6e-20   74.0   7.9    2.1e-10   41.2   0.2    3.5  2  Usp             Universal stress protein family
    1.3e-10   40.6  15.7    1.3e-10   40.6  15.7    2.1  2  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
       0.29   11.8   1.7        0.7   10.6   1.7    1.6  1  DUF4398         Domain of unknown function (DUF4398)


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.5  46.7   6.4e-50   2.3e-46       1     396 [.      10     407 ..      10     433 .. 0.86

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 6.4e-50
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+ l+a+ + +g++ig+gifv +  +aa +gp+++++++++ ++  +  +l   El++a+p+ gG y y  +a g++
  gi|313125685|ref|YP_004035955.1|  10 LGPLAALTIGVGTMIGAGIFVLPgeAAAIAGPVVAVSFVVGGVVS-IFTALSASELGTAMPKAGGSYYYINHALGPL 85 
                                       67889999999************977777***********99998.8899999****99****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgp........dlqgntwltyliaiaililvalinirgikesakiq 144
                                       +++++++ nw++ +++ a+++  ++++++ +++         +l +    t + a +  ++++ +n++g ke++++q
  gi|313125685|ref|YP_004035955.1|  86 FGSIAGMGNWMGLAFASAFYMLGFGGFIIELVNVpsiglgilTLAP----TQVAALLAGATFIGVNYVGAKETGTLQ 158
                                       ********************************96677776554444....44666678889999************* PP

                     AA_permease_2 145 nilgilkillpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdv 219
                                       ni++i+ +  +l+++ ilgl + d ++          f png  ++l g + v+ sf Gf  ++ v+ee+k+  +++
  gi|313125685|ref|YP_004035955.1| 159 NIIVITLV-AILTVFTILGLTMTDLSTLR-------PFAPNGYGSILPGTALVFVSFLGFAKITTVAEEIKNpsRNL 227
                                       ********.699**********8665554.......8999999999999999*****************998879** PP

                     AA_permease_2 220 pkaifigllivlvlyllvniaflgvvpddeianlsn.lgsvaalffeavgg.k.vvaiivvilialsllgaintavi 293
                                       p+a + +++iv+v+y  +++ ++gvv++ e+a++ + +++va+++f ++ g +  + +++ +++ l+ + ++n+ ++
  gi|313125685|ref|YP_004035955.1| 228 PLAVVGSVVIVTVMYAIIMVMLMGVVNWTELAQSTTpVIDVAEVVFSNTLGlGvLGGSLILFGGLLATASSANASIL 304
                                       ******************************9654444*****999999875356888888899999*********** PP

                     AA_permease_2 294 gssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliiga 369
                                       +ssr+++a++rd+ +  ++++++ +f +p+r+i +t ++  +l++++      ++ +l+ ++s++++i+y+l+ i++
  gi|313125685|ref|YP_004035955.1| 305 ASSRINFAMGRDKLITAWLNDIHpRFSTPYRSIAVTGVLI-LLFIAV-----GNVKVLAKAGSVLHLIVYGLMNIAL 375
                                       ***************************************6.443333.....469********************** PP

                     AA_permease_2 370 lilrkkrp.hl.kr...pgkilvaiigalfll 396
                                       ++ r     ++ +    p ++ v i+ga++++
  gi|313125685|ref|YP_004035955.1| 376 IVMRESDVaDYdPDftvPLYPAVPILGAVLSF 407
                                       **996644133333333444556666655554 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2  43.7   1.6e-36   5.9e-33       3     393 ..      16     381 ..      14     413 .. 0.82

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 1.6e-36
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviG 79 
                                       l i +g +iG+g+fv  g +++ aGp+ a ++++++gvv+++++ls +e+ t++pk+gg y+y+ + lgp +G   G
  gi|313125685|ref|YP_004035955.1|  16 LTIGVGTMIGAGIFVLPGEAAAIAGPVVA-VSFVVGGVVSIFTALSASELGTAMPKAGGSYYYINHALGPLFGSIAG 91 
                                       6799**********************766.******************************************99999 PP

                       AA_permease  80 lnylfswitvlaleltaasiliqfwelvtdlpkawvt........gavflvvlliinlvgvkvygeaefilalikii 148
                                       +  ++  +++ a+ + + + +i  + +v+++   +          +++  + ++++n+vg+k  g  + i+ + ++ 
  gi|313125685|ref|YP_004035955.1|  92 MGNWMGLAFASAFYMLGFGGFIIELVNVPSIGLGI-LtlaptqvaALLAGATFIGVNYVGAKETGTLQNIIVITLVA 167
                                       88666666666666555555554444555555333.2588889878888899999***********88887777777 PP

                       AA_permease 149 aiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEv 225
                                       ++  f i+g  ++++  + +                + p+g          +++ + + v+++f G+  ++++a+E+
  gi|313125685|ref|YP_004035955.1| 168 ILTVFTILG-LTMTDLSTLRP---------------FAPNG--------YGSILPGTALVFVSFLGFAKITTVAEEI 220
                                       777777777.34555554444...............56777........899************************* PP

                       AA_permease 226 kdPeksiPkailqvviritifYvlsllligllvprndlg.llndsasaaspfvifikesgvsvl.aplinaviltaa 300
                                       k+P++++P a+   v+++t++Y +++++++ +v+++ l  +++ ++++    v+f + +g+ vl ++li ++ l+a+
  gi|313125685|ref|YP_004035955.1| 221 KNPSRNLPLAVVGSVVIVTVMYAIIMVMLMGVVNWTELAqSTTPVIDV--AEVVFSNTLGLGVLgGSLILFGGLLAT 295
                                       ***********************************9864144555555..66777788888877369********** PP

                       AA_permease 301 lssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisalig 376
                                        ssan+s+ ++sR+ +++ +d+l+  +  + + +   P+r+i+++ ++ ll++  a  n++      +l  +  +  
  gi|313125685|ref|YP_004035955.1| 296 ASSANASILASSRINFAMGRDKLITaWLNDIHPRFSTPYRSIAVTGVLILLFI--AVGNVK------VLAKAGSVLH 364
                                       *************************5555678899************999999..555555......6678888999 PP

                       AA_permease 377 livwlliilsylrfRka 393
                                       liv++l++++++++R +
  gi|313125685|ref|YP_004035955.1| 365 LIVYGLMNIALIVMRES 381
                                       99999999999999975 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.2   5.9e-14   2.1e-10       4     141 .]     476     609 ..     475     609 .. 0.94
   2 !   28.1   3.2   6.7e-10   2.4e-06       4     139 ..     617     730 ..     616     732 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 5.9e-14
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       r++V++ +  + + ++  A +lak+r+++++++h+   ++++a   a+e    ee++  ++++++d    a+   ++
  gi|313125685|ref|YP_004035955.1| 476 RVMVPLANPAHETDLITLASALAKSRDGTVVAVHIEQVPDQTALESARERGDFEEADRLLERARED----AETFDVP 548
                                       89****9999999**************************999999999999999999999999976....7****** PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +++++++++   ee  ++a+ +dad+ V+G+   s+ +     S  + ++ + pc+ lv +
  gi|313125685|ref|YP_004035955.1| 549 IETHTILSHRSFEEVFDAARTYDADITVMGWGPDSHGAPGRAESAIDELASSLPCDFLVLK 609
                                       *********************************888888889****************986 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 6.7e-10
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       ++lV++ g ++s+  +  A+ l +++++++ llhv d +a g+    ++++    ++ e+                 
  gi|313125685|ref|YP_004035955.1| 617 HVLVPTAGGPDSDLSAAVAVTLREQYDSTVSLLHVTDNKAEGEQFLTEWAESHGLSDAELI---------------- 677
                                       79**************************************999999999999888888885................ PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                           v  + ++ e+i ++a++  a ++++G++ r+ lsrl+ G     v+++++c+Vl+
  gi|313125685|ref|YP_004035955.1| 678 ----VEQSVNVEEGIERHARD--ATMLIIGATERGLLSRLVRGTLVLDVVNKVDCSVLL 730
                                       ....55677888889998876..**********************************97 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6  15.7   3.6e-14   1.3e-10       8     253 ..      16     272 ..      10     323 .. 0.86
   2 ?    2.4   1.0     0.016        57     112     160 ..     332     382 ..     317     396 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 3.6e-14
                    Spore_permease   8 fvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpek.tliellkkilgkwLGsllsi 83 
                                       +++ v +++G+gi +lp+ +a+ a+p   +s +++g++ ++ +l +++l   +p+    + ++++ lg + Gs+ ++
  gi|313125685|ref|YP_004035955.1|  16 LTIGVGTMIGAGIFVLPGEAAAIAGPVVAVSFVVGGVVSIFTALSASELGTAMPKAgGSYYYINHALGPLFGSIAGM 92 
                                       6677899*********************************************9986268999*************** PP

                    Spore_permease  84 lfilyFlllaafelRefse.liqvflledtplwiiilllllvilYlvvk...Gieslar.....eflfiivilliil 151
                                          +  ++ +af +  f+  +i+++ ++ + l i++l    v+++l+     G++ +       +  +i++ l++il
  gi|313125685|ref|YP_004035955.1|  93 GNWMGLAFASAFYMLGFGGfIIELVNVPSIGLGILTLAPTQVAALLAGAtfiGVNYVGAketgtLQNIIVITLVAIL 169
                                       *9999*99999999999753778899999999999999998888887551115555533588744455555666777 PP

                    Spore_permease 152 llillfslklaeiknlrPvlgngikpvlkslkttslsflgveillllvpflkdkkkvkkaallg.vlistllylltt 227
                                        ++++  l + ++  lrP + ng+ ++l ++  + +sflg+  ++ + + +k++ + +  a++g v+i+t++y++++
  gi|313125685|ref|YP_004035955.1| 170 TVFTILGLTMTDLSTLRPFAPNGYGSILPGTALVFVSFLGFAKITTVAEEIKNPSRNLPLAVVGsVVIVTVMYAIIM 246
                                       7788999***********************************************99998887763899********* PP

                    Spore_permease 228 livilvlsveqlkkatwptlsllkvi 253
                                       ++ ++v    +l ++t p +++++v+
  gi|313125685|ref|YP_004035955.1| 247 VMLMGVVNWTELAQSTTPVIDVAEVV 272
                                       *********************99886 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.016
                    Spore_permease 112 tplwiiilllllvilYlvvkGieslar..eflfiivilliilllillfslk 160
                                       tp   i ++ +l+ l+++v+ +++la+   +l +iv+ l+ + li++  ++
  gi|313125685|ref|YP_004035955.1| 332 TPYRSIAVTGVLILLFIAVGNVKVLAKagSVLHLIVYGLMNIALIVMRESD 382
                                       77788899999999999*********8555555555555555555444443 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.7    0.0002       0.7      32      61 ..     518     544 ..     516     547 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                           DUF4398  32 aLaqAeaamaekdyeeAdhlaylAerdael 61 
                                       aL+ A++   ++d eeAd+l+++A++dae+
  gi|313125685|ref|YP_004035955.1| 518 ALESARE---RGDFEEADRLLERAREDAET 544
                                       6777776...99****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (747 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 4407.25
//
Query:       gi|313125686|ref|YP_004035956.1|  [L=153]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-08   34.8   0.0    2.6e-08   34.5   0.0    1.1  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   1.4e-12   2.6e-08       6     141 .]      14     144 ..      10     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.4e-12
                                       EEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEE CS
                               Usp   6 lVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkv 82 
                                       l++v + +++ + +   l   +a+g++ + +hvi+    ++ +++ e+ ee ++e     +e     +  +ag++++
  gi|313125686|ref|YP_004035956.1|  14 LIPVANDDDAAATAAAVLPRIAANGGDPVFVHVIEKAGGAPDKASVEQREELAEEMFDFIRE-----ESDDAGVEVE 85 
                                       66776666666666666668888899999*****9988877777777777777777777666.....4579999999 PP

                                       EEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  83 evvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++ + + d+a +i+++a +++a  i    rg ++  +l+ G++ e+++ +++ pV+v +
  gi|313125686|ref|YP_004035956.1|  86 TTLRYGTDVAATIIDTAHDIGATCITFTPRGGKRWWDLFSGDTRESLVTKSDLPVVVLP 144
                                       9999999************************999999*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 911.81
//
Query:       gi|313125687|ref|YP_004035957.1|  [L=132]
Description: hypothetical protein Hbor_09170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.9   0.1       0.15   12.3   0.1    1.3  1  DUF2382   Domain of unknown function (DUF2382)


Domain annotation for each model (and alignments):
>> DUF2382  Domain of unknown function (DUF2382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   8.5e-06      0.15      42      81 ..      33      73 ..      31      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.5e-06
                           DUF2382 42 vvver.epvdrevaaaeaareeeetievplyeErvvvekea 81
                                      v+ve+  +vd e+++a+ +++ ++t++++++eE+++  k++
  gi|313125687|ref|YP_004035957.1| 33 VEVEHdPDVDGEDSPAPWVQFADQTFNMDVTEEELECAKSL 73
                                      8899977899**************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 804.92
//
Query:       gi|313125688|ref|YP_004035958.1|  [L=213]
Description: adenylate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-42  145.0   0.0    2.1e-42  144.8   0.0    1.1  1  ADK              Adenylate kinase
    1.4e-22   80.6   0.1    3.1e-22   79.5   0.0    1.6  2  AAA_17           AAA domain
    1.5e-17   63.2   2.4    1.5e-17   63.2   2.4    1.8  2  ADK_lid          Adenylate kinase, active site lid
    1.3e-09   38.7   0.0    2.2e-09   38.0   0.0    1.3  1  AAA_18           AAA domain
    6.7e-07   29.6   0.0    1.3e-06   28.6   0.0    1.4  1  AAA_33           AAA domain
      0.003   17.7   0.3      0.017   15.2   0.1    2.1  1  SKI              Shikimate kinase
     0.0037   17.0   0.0     0.0069   16.1   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0054   16.9   0.1      0.012   15.8   0.1    1.5  1  PAS_7            PAS fold
  ------ inclusion threshold ------
      0.021   15.2   0.7       0.96    9.9   0.1    2.6  2  zf-IS66          zinc-finger binding domain of transposase IS
      0.035   13.9   0.1        3.3    7.5   0.0    2.4  3  dNK              Deoxynucleoside kinase
      0.055   13.2   0.0        0.1   12.4   0.0    1.4  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.061   13.2   0.0       0.14   12.1   0.0    1.7  2  Ploopntkinase3   P-loop Nucleotide Kinase3
      0.063   13.3   0.0       0.11   12.6   0.0    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.076   12.7   0.3        6.8    6.3   0.0    2.7  3  Thymidylate_kin  Thymidylate kinase
      0.081   12.9   0.0       0.14   12.2   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.091   13.3   0.6        3.5    8.2   0.0    2.6  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.099   12.4   0.3        1.2    9.0   0.0    2.2  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.13   12.3   0.5       0.31   11.1   0.5    1.5  1  DZR              Double zinc ribbon
       0.17   11.4   3.4       0.46   10.0   3.4    1.8  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.18   11.2   0.0       0.24   10.8   0.0    1.2  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.18   11.4   0.0       0.34   10.5   0.0    1.4  1  SRP54            SRP54-type protein, GTPase domain
       0.38   10.9   1.5       0.72   10.0   1.5    1.5  1  Zn-ribbon_8      Zinc ribbon domain
        3.4    7.7   6.3        1.2    9.1   0.4    2.4  2  Prok-RING_1      Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   0.0   2.7e-45   2.1e-42       1     150 [.       7     188 ..       7     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 2.7e-45
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT.-HHH...HHHHHHHHTTSS--HHHHHHHHHHHHHCHGT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksg.telG...keakevmdkgelvpdevvvklvkeelekedk 73 
                                       llGaPgaGKGtq+++l++++ l h++tGd lRa+   + +++     + +e+m+ g+lvpd+vv+++vk +l++   
  gi|313125688|ref|YP_004035958.1|   7 LLGAPGAGKGTQSKRLASEFDLEHVTTGDALRANKDMDiSDMDfeyDTPREYMESGDLVPDDVVNEIVKTALQEA-- 81 
                                       79*******************************986542555511145689*********************977.. PP

                                       TTEEEEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT............................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                               ADK  74 kkgfllDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg............................ 122
                                        +g++lDG+PR++eqae l e     +++ld+vl+ldv+ee lveRltg                            
  gi|313125688|ref|YP_004035958.1|  82 -DGYVLDGYPRNIEQAEYLTE-----ITDLDAVLYLDVSEEELVERLTGrrvcddcganyhvefappeedgvcddcg 152
                                       .9******************9.....89************************************************* PP

                                       ........GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 123 ........DneetvkkRletykkqtkplidyykkkg 150
                                               D+eetv++Rl++y+k+t+p++++y+++g
  gi|313125688|ref|YP_004035958.1| 153 geliqredDTEETVRERLTVYHKNTEPVVNHYRDEG 188
                                       ********************************9876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0     4e-25   3.1e-22       1     123 [.       8     126 ..       8     133 .. 0.86
   2 ?   -2.6   0.0         9     7e+03     127     136 .]     158     167 ..     153     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 4e-25
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT......TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg......glakardemrklpleekkelqkeaaekiaeeakk 71 
                                       lG PG+GKgtq+++l+ +++++h+++Gd lr++   +      + ++ r++m+ ++l++++ + ++++ +++e+   
  gi|313125688|ref|YP_004035958.1|   8 LGAPGAGKGTQSKRLASEFDLEHVTTGDALRANKDMDisdmdfEYDTPREYMESGDLVPDDVVNEIVKTALQEA--- 81 
                                       7******************************9844334333444688899999999999999999999988885... PP

                                       SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  72 kgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                       +g+++dg+pr+ eqa++l +++     +   da+++l++++ee++er+  +r
  gi|313125688|ref|YP_004035958.1|  82 DGYVLDGYPRNIEQAEYLTEIT-----D--LDAVLYLDVSEEELVERLTGRR 126
                                       89**************987554.....4..5****************99875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9
                                       -TS-SHHHHH CS
                            AAA_17 127 rdddneesik 136
                                       r+dd+ee+++
  gi|313125688|ref|YP_004035958.1| 158 REDDTEETVR 167
                                       6666666654 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   2.4     2e-20   1.5e-17       1      36 []     125     160 ..     125     160 .. 0.99
   2 ?   -2.9   0.1       8.9   6.9e+03      10      15 ..     172     176 ..     171     183 .. 0.62

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2e-20
                                       EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                       RrvC +CG+ Yhv+f+pP ++g+CD+CG++L+qR+D
  gi|313125688|ref|YP_004035958.1| 125 RRVCDDCGANYHVEFAPPEEDGVCDDCGGELIQRED 160
                                       9**********************************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.9
                                       EEETTT CS
                           ADK_lid  10 sYhvvf 15 
                                       +Yh + 
  gi|313125688|ref|YP_004035958.1| 172 VYH-KN 176
                                       899.54 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   2.8e-12   2.2e-09       1     114 [.       5     126 ..       5     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.8e-12
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvaken..glllevdpe.aldeskrldedkldklldaleenss 69 
                                       Ill G+pG+GK t +k+L+++  +     g+ lr +   +  ++ +e+d + +   + +  + + d +++++ +   
  gi|313125688|ref|YP_004035958.1|   5 ILLLGAPGAGKGTQSKRLASEFDLehvttGDALRANKDMDisDMDFEYDTPrE---YMESGDLVPDDVVNEIVKT-- 76 
                                       99******************976696676444444433320033333333332...2222222223355555554.. PP

                            AAA_18  70 aleegknlvidghlaeleseaakdikk.....vvLtaspeelleRlekRg 114
                                       al+e++ +v+dg + + e++++    +      +L++s+eel eRl  R+
  gi|313125688|ref|YP_004035958.1|  77 ALQEADGYVLDGYPRNIEQAEYLTEITdldavLYLDVSEEELVERLTGRR 126
                                       4688999***********8877766667*******************997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.7e-09   1.3e-06       2     119 ..       5     126 ..       5     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.7e-09
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg.......tdqqsktdytrvldrlyq.ilnelarkalsag 70 
                                       +ll G+pG+GK t ++rl+ + + +++++ +++r+ +         + +++++y +  d + +  +ne+++ al+++
  gi|313125688|ref|YP_004035958.1|   5 ILLLGAPGAGKGTQSKRLASEFDLEHVTTGDALRANKDmdisdmdFEYDTPREYMESGDLVPDdVVNEIVKTALQEA 81 
                                       6789************************99988887776776655444577799998888654499999******** PP

                            AAA_33  71 rnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRa 119
                                        +++ld   ++ ++ + + ++       +++++++++ee+l eRl  R 
  gi|313125688|ref|YP_004035958.1|  82 DGYVLDGYPRNIEQAEYLTEITD----LDAVLYLDVSEEELVERLTGRR 126
                                       ******76666666666666664....559****************996 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.2e-05     0.017       1     105 [.      11     125 ..      11     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHH.HHHHHHHHHHHHHHHH........HHHHCCCS.SEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaei.feeegeegFrelEsev........lkelleee.glVia 67 
                                       +GaGK t  k+lA + +le + + + +  +  ++i+++ fe ++  ++ e    v        +k  l+e  g+V+ 
  gi|313125688|ref|YP_004035958.1|  11 PGAGKGTQSKRLASEFDLEHVTTGDALRANKDMDISDMdFEYDTPREYMESGDLVpddvvneiVKTALQEAdGYVLD 87 
                                       69**********************************99777667777776654432222222266666666899998 PP

                                       E-TTGGGSHHHHHHHHHHSEEEEEE--HHHHHHHHHHT CS
                               SKI  68 tGGGavlseenrellkekgiviyLdvsleellerlkad 105
                                            ++++e+ + +++   v+yLdvs eel+erl+ +
  gi|313125688|ref|YP_004035958.1|  88 GYPRNIEQAEYLTEITDLDAVLYLDVSEEELVERLTGR 125
                                       88888999998888889*****************9865 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.9e-06    0.0069      34      75 ..       3      43 ..       1      51 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.9e-06
                            RuvB_N 34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdl 75
                                       h+ll G+PG Gk t +k +a+e++ + ++t+g +l  ++d+
  gi|313125688|ref|YP_004035958.1|  3 KHILLLGAPGAGKGTQSKRLASEFDLE-HVTTGDALRANKDM 43
                                      5***********************998.67888898887776 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.5e-05     0.012      56     100 ..     159     203 ..     152     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                             PAS_7  56 agdveaeverrlaaaragkphsfererpdgrvievrgnplpdgGf 100
                                       ++d+e++v++rl+ +++++++ +++ r++g  +e+ g+++pdg f
  gi|313125688|ref|YP_004035958.1| 159 EDDTEETVRERLTVYHKNTEPVVNHYRDEGVLVEIDGEQTPDGVF 203
                                       6899**************************************954 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.16   1.2e+02       2       9 ..     126     133 ..     125     141 .. 0.82
   2 ?    9.9   0.1    0.0012      0.96       2      23 ..     146     170 ..     145     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                           zf-IS66   2 rtCpcCGg 9  
                                       r+C++CG+
  gi|313125688|ref|YP_004035958.1| 126 RVCDDCGA 133
                                       68*****8 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                           zf-IS66   2 rtCpcCGg.l...lkpigedrvreel 23 
                                        +C++CGg l    +  +e+ vre+l
  gi|313125688|ref|YP_004035958.1| 146 GVCDDCGGeLiqrEDDTEET-VRERL 170
                                       68******556654455555.77766 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.041        32       5      49 ..       9      55 ..       5      87 .. 0.75
   2 ?    7.5   0.0    0.0042       3.3     116     144 ..      98     126 ..      75     135 .. 0.84
   3 ?   -2.9   0.0       6.5   5.1e+03     149     168 ..     164     182 ..     149     204 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.041
                                      ESTTSSHHHHHHHHHCCSTCEEEE-..HHHHCCSSSSHHHHHHHHSH CS
                               dNK  5 GnIgaGKstlvklLskklgvkvfeE..pvdkwtnvqknlLekfYkdp 49
                                      G  gaGK t  k+L+ +++ ++++       ++ +    ++  Y+ p
  gi|313125688|ref|YP_004035958.1|  9 GAPGAGKGTQSKRLASEFDLEHVTTgdALRANKDMDISDMDFEYDTP 55
                                      7779***************9888752233444333335555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0042
                                       HHHHCCH-SEEEEEE--HHHHHHHHHHCT CS
                               dNK 116 lleelakpdlliYLkasletclerikkRg 144
                                       +l e+  +d + YL++s e+++er+  R 
  gi|313125688|ref|YP_004035958.1|  98 YLTEITDLDAVLYLDVSEEELVERLTGRR 126
                                       3468888******************9885 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.5
                                       TTS-HHHHHHHHHHHHHHHT CS
                               dNK 149 kkieldYlekLhekyeewlk 168
                                       +++ ++ l   h++ e+ ++
  gi|313125688|ref|YP_004035958.1| 164 ETVRER-LTVYHKNTEPVVN 182
                                       333322.3333333333344 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013       0.1       2      51 ..       3      62 ..       2      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                         PduV-EutP  2 kkilliGkvgsGKttLtqalkg..........eelkYkktqaiefsdeviDtPGeylenr 51
                                      k+ill+G+ g+GK t +++l            ++l+ +k   i  +d   DtP ey+e+ 
  gi|313125688|ref|YP_004035958.1|  3 KHILLLGAPGAGKGTQSKRLASefdlehvttgDALRANKDMDISDMDFEYDTPREYMESG 62
                                      78******************987778777777788888888888888889*******975 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.14       5      36 ..       4      35 ..       1      75 [. 0.85
   2 ?   -2.8   0.0       6.5   5.1e+03      39      58 ..     113     132 ..      98     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                    Ploopntkinase3  5 liylvGqPGaGkstlmaeltkgfdrskveqee 36
                                       i l+G+PGaGk t    l++ fd ++v++ +
  gi|313125688|ref|YP_004035958.1|  4 HILLLGAPGAGKGTQSKRLASEFDLEHVTTGD 35
                                      589***********************999666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.5
                    Ploopntkinase3  39 vphdvlvdrttGevvgaelG 58 
                                       v++++lv+r tG  v  + G
  gi|313125688|ref|YP_004035958.1| 113 VSEEELVERLTGRRVCDDCG 132
                                       77888999999988877666 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014      0.11      64     104 ..     119     163 ..      68     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       EEEE--EEEETTTS-EEECHH...H.HHS-TTTSSS-EEEEESSS CS
                              HypA  64 ieevpvkvrCreCgkefelee...k.alrCpkCgsadveivsGee 104
                                       +e+   +  C++Cg+++++e    + +  C +Cg++ ++  + +e
  gi|313125688|ref|YP_004035958.1| 119 VERLTGRRVCDDCGANYHVEFappEeDGVCDDCGGELIQREDDTE 163
                                       78899999*******99977544324559*****99888776666 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.077        60       3      21 ..       9      27 ..       9      33 .. 0.83
   2 ?    6.3   0.0    0.0088       6.8     119     139 ..     106     126 ..      81     137 .. 0.81
   3 ?   -1.2   0.0       1.7   1.3e+03     137     181 ..     158     202 ..     154     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.077
                                      ESTTSSHHHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlk 21
                                      G  GaGK tq++ l++ ++
  gi|313125688|ref|YP_004035958.1|  9 GAPGAGKGTQSKRLASEFD 27
                                      5569**********99876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0088
                                       SEEEEEESSHHHHHTSCCTTS CS
                   Thymidylate_kin 119 dltflldvdpevalkRlakrd 139
                                       d++++ldv++e+ ++Rl+ r+
  gi|313125688|ref|YP_004035958.1| 106 DAVLYLDVSEEELVERLTGRR 126
                                       99***************9997 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.7
                                       TTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHH CS
                   Thymidylate_kin 137 krdeldeeeeeqldflrkvrerylelakederiliidasksieev 181
                                       ++d  +e++ e+l++++k +e   + +++++ ++ id ++  + v
  gi|313125688|ref|YP_004035958.1| 158 REDDTEETVRERLTVYHKNTEPVVNHYRDEGVLVEIDGEQTPDGV 202
                                       455567888899999888888888888877777888887766655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.14       1      73 [.       4      88 ..       4     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                                      EEEEE--SSSSHHHHHHHGGGGB....S--EEEEE--TT--HHHHH--B--.................--------G-S CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal....nreveyvqltrdtteedlkgrreik........ngttslvdsplvraarege 67
                                      ++lL+G+pG gK + ++rla+ +     ++      ++d+  +d+  ++++               v+ ++++a +e++
  gi|313125688|ref|YP_004035958.1|  4 HILLLGAPGAGKGTQSKRLASEFdlehVTTGDALRANKDMDISDMDFEYDTPreymesgdLVPDDVVNEIVKTALQEAD 82
                                      79*******************9976555555567889999999999888865555332211112233344444444666 PP

                                      EEEEES CS
                             AAA_5 68 ilvlDE 73
                                       +vlD+
  gi|313125688|ref|YP_004035958.1| 83 GYVLDG 88
                                      666665 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0045       3.5       2      17 ..     122     137 ..     121     141 .. 0.91
   2 ?    2.7   0.0      0.23   1.8e+02       7      19 ..     147     159 ..     146     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0045
                   Zn_ribbon_recom   2 LsGllrCgeCGspmtr 17 
                                       L+G  +C +CG+++++
  gi|313125688|ref|YP_004035958.1| 122 LTGRRVCDDCGANYHV 137
                                       89999********987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.23
                   Zn_ribbon_recom   7 rCgeCGspmtrrk 19 
                                       +C +CG+ +++r 
  gi|313125688|ref|YP_004035958.1| 147 VCDDCGGELIQRE 159
                                       79****9998864 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.43   3.4e+02       2      10 ..     126     134 ..     125     137 .. 0.82
   2 ?    9.0   0.0    0.0015       1.2       2      15 ..     146     159 ..     145     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.43
                                       EE-SSS--E CS
                    zf-C4_Topoisom   2 ekCPkCggd 10 
                                       + C+ Cg++
  gi|313125688|ref|YP_004035958.1| 126 RVCDDCGAN 134
                                       57*****86 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
                                       EE-SSS--EEEEEE CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkr 15 
                                       + C+ Cgg+L++++
  gi|313125688|ref|YP_004035958.1| 146 GVCDDCGGELIQRE 159
                                       68**********96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5    0.0004      0.31      11      39 ..     124     156 ..     119     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                               DZR  11 darfCseCgtklkavaa....edrCpsCgekvd 39 
                                       + r+C++Cg++   + a      +C+ Cg ++ 
  gi|313125688|ref|YP_004035958.1| 124 GRRVCDDCGANYHVEFAppeeDGVCDDCGGELI 156
                                       678999999996544445566999999997754 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.4   0.00059      0.46       2      30 ..     127     157 ..     123     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00059
                                       EETTTTCEE.CHEETSTTCEEESSS.SBEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveDpergelvCtdC.GlVle 30 
                                       +C +Cg  + +++ p + + vC dC G++++
  gi|313125688|ref|YP_004035958.1| 127 VCDDCGANYhVEFAPPEEDGVCDDCgGELIQ 157
                                       899****999***************888776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00031      0.24      23      44 ..       3      24 ..       1      57 [. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlps 44
                                       ++ll+G+pG+GK    krl+s
  gi|313125688|ref|YP_004035958.1|  3 KHILLLGAPGAGKGTQSKRLAS 24
                                      468999*************986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00044      0.34       3     112 ..       4     109 ..       2     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00044
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTS.CHHHHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeea.dpaavakeavek 78 
                                        ill+G  GaGK t   +La  +  e+    + + D  Ra     ++ +  +++ p   +++++  p +v++e v++
  gi|313125688|ref|YP_004035958.1|   4 HILLLGAPGAGKGTQSKRLASEFDLEH----VTTGDALRANKDMDISDMDFEYDTPREYMESGDlVPDDVVNEIVKT 76 
                                       69******************9998886....5677888877666666666555555444444444677777777776 PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvv 112
                                       a + ++d  ++D   r+ +++e+++e++++  v+
  gi|313125688|ref|YP_004035958.1|  77 ALQ-EADGYVLDGYPRNIEQAEYLTEITDLDAVL 109
                                       666.446666788888888888888877777665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.5   0.00092      0.72       8      35 ..     128     155 ..     125     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00092
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.e 35 
                                       C++Cg  + v  +   +++ +C +Cg+  
  gi|313125688|ref|YP_004035958.1| 128 CDDCGANYHVEFAPP-EEDGVCDDCGGeL 155
                                       ********9665333.23456*****944 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4    0.0015       1.2      22      32 ..     127     137 ..     126     140 .. 0.91
   2 ?    0.4   0.8      0.83   6.5e+02      22      27 ..     147     152 ..     138     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                       Prok-RING_1  22 vCpeCgtpyHr 32 
                                       vC++Cg+ yH 
  gi|313125688|ref|YP_004035958.1| 127 VCDDCGANYHV 137
                                       8*********5 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.83
                       Prok-RING_1  22 vCpeCg 27 
                                       vC++Cg
  gi|313125688|ref|YP_004035958.1| 147 VCDDCG 152
                                       8****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1282.84
//
Query:       gi|313125689|ref|YP_004035959.1|  [L=839]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-31  109.7   8.8    1.2e-31  109.7   8.8    4.2  3  BAT           GAF and HTH_10 associated domain
    2.1e-28   99.3   6.6    4.5e-15   56.2   0.5    2.7  2  GAF_2         GAF domain
    3.2e-17   62.0   0.0    8.4e-17   60.7   0.0    1.8  1  HTH_10        HTH DNA binding domain
    7.3e-14   52.2   0.3    1.1e-06   29.0   0.0    2.5  2  GAF_3         GAF domain
    4.9e-12   46.6   0.4      6e-05   23.7   0.1    2.7  2  GAF           GAF domain
    0.00015   21.9   0.0    0.00043   20.4   0.0    1.8  1  Response_reg  Response regulator receiver domain
     0.0044   17.1   0.0      0.014   15.5   0.0    1.9  1  HTH_22        HTH domain
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.088   12.3   0.0    2.5  2  Sigma70_r4    Sigma-70, region 4
       0.51   10.6   6.0        4.8    7.5   0.0    5.1  5  PAS_4         PAS fold


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   3.2      0.76   1.5e+03      55      97 ..      36      78 ..      17     117 .. 0.69
   2 ?   -1.9   0.3       1.4   2.7e+03      18      38 ..     134     154 ..     127     169 .. 0.62
   3 !  109.7   8.8     6e-35   1.2e-31       2     154 ..     613     763 ..     613     765 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.76
                               BAT 55 vrdaaedldavedvrvvseeddgtlleltvsgpslastlaehG 97
                                      + +a+e+l +v++v+ v+   dg+        + ++ + +e G
  gi|313125689|ref|YP_004035959.1| 36 ADSAVEELRSVASVQRVESVADGCERLSSGHPDAVVVARSEDG 78
                                      6678888888888888888888875444443444444444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                               BAT  18 valaaeldcrveleglvprsd 38 
                                       v++aae+  rvele+  + s+
  gi|313125689|ref|YP_004035959.1| 134 VEAAAEAAERVELERELRASE 154
                                       445555555555555544444 PP

  == domain 3  score: 109.7 bits;  conditional E-value: 6e-35
                               BAT   2 avveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgt 78 
                                       av+++e ++   +++l+++a+++dc++++   ++++ +  ++f+tv+ga+ ++vr+aa+d+ +++++rvv+ +d + 
  gi|313125689|ref|YP_004035959.1| 613 AVTRVEYAVAGGSFPLARVAERADCTLSVVTGIQQTVEDDALFATVEGASMDAVRAAAADTAGIAEYRVVAGDDAAG 689
                                       699************************************************************************** PP

                               BAT  79 lleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                       ++ +++  p++as+la+hG+++r+aea+++++ l +++P+g+++ s+++ l+ ++++veL+++r+re+p  + +ef
  gi|313125689|ref|YP_004035959.1| 690 TVWFRFVRPVIASRLANHGVVLRRAEATPTETLLEIDIPDGVELHSITQLLSGTFDAVELRSKRHREQP--SGGEF 763
                                       *****99*************************************************************9..55665 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   1.0   3.9e-15   7.7e-12       2     138 .]     283     416 ..     282     416 .. 0.86
   2 !   56.2   0.5   2.3e-18   4.5e-15       3     137 ..     460     600 ..     458     601 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 3.9e-15
                                       HHHHHHHHHHHHHHHHS.S...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B.---TT.HHHHHHHHTS-EEES-G CS
                             GAF_2   2 adleelldlvldelvel.g.aalgyillvdddgglrlaawgeaeeefgaaldr.plgeg.lvgealrtgrpvilndl 74 
                                        +++e++ +v+d + e+ g aa +++ ++ + ++l+ +a + a +++ + l++ +++eg l+g+a+ tg+p++++d+
  gi|313125689|ref|YP_004035959.1| 283 ETVQEIAHRVVDDADEIlGcAASAVFRFDAETNRLEPVAHTPAMDRLYGPLPSfRPSEGnLIGRAFVTGEPLFFDDV 359
                                       689*************66*6667777777778888888888777777777766799********************8 PP

                                       GG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                        e+p+ +     + +lrs +++ l   g  +Gvl+ + +  +afde + e++++la+++  a++
  gi|313125689|ref|YP_004035959.1| 360 HESPALS---NPATDLRSVVVLSL---G-DHGVLVAGVDTVGAFDEVHSEIADLLATTAEAALD 416
                                       8866544...467***********...8.9******99**********************9996 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 2.3e-18
                                       HHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--...-TT.HHHHHHHHTS-EEES- CS
                             GAF_2   3 dleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrpl...geg.lvgealrtgrpvilnd 73 
                                       + e + ++v+++l+  +  ++++++ +d+  + l+ +a+++++++  +    +l    eg ++   ++t +++++++
  gi|313125689|ref|YP_004035959.1| 460 TREAVERAVCERLTAEDrYEFAWVGSIDPTSQtLVPRAASGTGRGYLDDR--SLaldPEGePACSTAATDEETLVSN 534
                                       7789999******77677**********7766333333333333333333..22336688896666666699999** PP

                                       GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +++d  +++++  a +++++s +avPl ++g  +Gvl++ya++p afd   ++++ el+e++a ai
  gi|313125689|ref|YP_004035959.1| 535 VATDLQQQPWRraALERDFQSVVAVPLSYDGVAYGVLTVYADRPAAFDGMVRTVMAELGETVASAI 600
                                       ***9999999999****************************************************9 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   4.2e-20   8.4e-17       1      52 [.     771     822 ..     771     823 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 4.2e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++qlev+++Ay +GYF+ PR  + +e+A+ lG+s+++++ h+r +++kl+
  gi|313125689|ref|YP_004035959.1| 771 LTERQLEVVQTAYYAGYFENPRAHSGDEVADVLGVSPAAFYRHIRTVQRKLF 822
                                       9*************************************************98 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   5.6e-10   1.1e-06       2     127 ..     285     415 ..     284     417 .. 0.87
   2 !   21.0   0.1   1.7e-07   0.00033      22     128 ..     481     601 ..     477     602 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.6e-10
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse...sld.edsalarralssgevvsepsfae 74 
                                       ++e++  +++ + ++lg+ ++a++ +d++ n+l ++a++ + ++l     s++  + +l+ ra+ +ge++++ +++e
  gi|313125689|ref|YP_004035959.1| 285 VQEIAHRVVDDADEILGCAASAVFRFDAETNRLEPVAHTPAMDRLYGplpSFRpSEGNLIGRAFVTGEPLFFDDVHE 361
                                       699999*********************************888888556679989******************99988 PP

                             GAF_3  75 .....edglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                             +++++r++++++L +     Gvl+++ +  +afd+++ e  + lA+ +  a+
  gi|313125689|ref|YP_004035959.1| 362 spalsNPATDLRSVVVLSLGD----HGVLVAGVDTVGAFDEVHSEIADLLATTAEAAL 415
                                       333333558889999999999....9********99**************98765555 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.7e-07
                             GAF_3  22 galllldedgnklqvaagw.dgkpalse...sld.edsalarralssgevvse........psfaeedglp.draal 84 
                                       + ++  d+  ++l+++a++ +g   l     +ld e+++++++a++ +e ++         + ++++   +  ++++
  gi|313125689|ref|YP_004035959.1| 481 AWVGSIDPTSQTLVPRAASgTGRGYLDDrslALDpEGEPACSTAATDEETLVSnvatdlqqQPWRRAALERdFQSVV 557
                                       55666688888888888776777777556669989*******9999999887733333332111223333325999* PP

                             GAF_3  85 avPLvagr.qviGvlalastkprafdaedlelleslArqiataie 128
                                       avPL   +   +Gvl ++ ++p afd   +  + +l+  +a+ai+
  gi|313125689|ref|YP_004035959.1| 558 AVPLSY-DgVAYGVLTVYADRPAAFDGMVRTVMAELGETVASAIS 601
                                       ******.65**********************************96 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1     3e-08     6e-05       2     129 ..     285     411 ..     284     415 .. 0.75
   2 !   20.4   0.0   3.1e-07   0.00061      43     133 .]     512     600 ..     454     600 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3e-08
                                       HHHHHHHHHHHHHHHHTESEEEEEEEEETTEEE....CEEEEECC.....EEEETTSHHHHHHHHHSSSEEESTGGT CS
                               GAF   2 leelldtvveelrellgadrvalylpdydGlhy....dipqasrw.....lfmkngrgicgqvlatgqplvipdstp 69 
                                       ++e++++vv+++ e+lg+   a+++ d++ ++     ++p+ +r      +f++   +++g+++ tg+pl ++d+ +
  gi|313125689|ref|YP_004035959.1| 285 VQEIAHRVVDDADEILGCAASAVFRFDAETNRLepvaHTPAMDRLygplpSFRPSEGNLIGRAFVTGEPLFFDDVHE 361
                                       689*********************94444432233544555555599988888888889***************988 PP

                                       STTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCSHHHHHHHHHHHHHHH CS
                               GAF  70 dprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsppftreelellqvladqv 129
                                       +p  +++       ++  rs++v++l ++g l++ ++ +     f++   e++  la+ +
  gi|313125689|ref|YP_004035959.1| 362 SPALSNP-------ATDLRSVVVLSLGDHGVLVAGVDTVG---AFDEVHSEIADLLATTA 411
                                       8887774.......58999********9998877666655...25555555555555555 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.1e-07
                                       EEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHH CS
                               GAF  43 lfmkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftree 118
                                         +++g++ c ++++  ++lv +      + +q+ +r+ + +  ++s+++vPl  dg  +G+l+++  +p  f+   
  gi|313125689|ref|YP_004035959.1| 512 ALDPEGEPACSTAATDEETLVSN---VATDLQQQPWRRAALERDFQSVVAVPLSYDGVAYGVLTVYADRPaAFDGMV 585
                                       56677999999999988888777...66666666688899999999*********************9998888888 PP

                                       HHHHHHHHHHHHHHH CS
                               GAF 119 lellqvladqvaval 133
                                       + ++ +l++ va a+
  gi|313125689|ref|YP_004035959.1| 586 RTVMAELGETVASAI 600
                                       888888888888776 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.1e-07   0.00043      24      98 ..      47     118 ..      36     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.1e-07
                                       EEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEEE CS
                      Response_reg  24 eevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddfl 98 
                                        +v+ +e+ ++  e l + ++d +++       dG+++++++r++  +lp++++t  ++e++a ++l aga d++
  gi|313125689|ref|YP_004035959.1|  47 ASVQRVESVADGCERLSSGHPDAVVVA---RSEDGVTAVSTLRADAADLPIVFCTDIGSESVARDVLAAGATDYV 118
                                       467777888888888888888888875...469*****************************************8 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.1e-06     0.014      23      63 .]     773     815 ..     765     815 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.1e-06
                            HTH_22  23 eekieivraLdekGiFllkga..vekvAekLgiSraTvYryLr 63 
                                       e+ +e+v+  + +G F+  +a   ++vA+ Lg+S a  Yr++r
  gi|313125689|ref|YP_004035959.1| 773 ERQLEVVQTAYYAGYFENPRAhsGDEVADVLGVSPAAFYRHIR 815
                                       67799999********998762268****************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.6   9.1e+03      23      35 ..     400     412 ..     400     414 .. 0.80
   2 ?   12.3   0.0   4.4e-05     0.088       1      33 [.     767     806 ..     767     823 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.6
                                       HHHHHHHHTS-HH CS
                        Sigma70_r4  23 leEIgerlgiSre 35 
                                       ++EI++ l  + e
  gi|313125689|ref|YP_004035959.1| 400 HSEIADLLATTAE 412
                                       58****9988876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.4e-05
                                       HHHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS- CS
                        Sigma70_r4   1 aLasLpererevlelrf.......geglTleEIgerlgiS 33 
                                       +L++L+er+ ev++  +        + ++  E++++lg+S
  gi|313125689|ref|YP_004035959.1| 767 VLDRLTERQLEVVQTAYyagyfenPRAHSGDEVADVLGVS 806
                                       69***************99998777778889999999999 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0024       4.8       1     108 [.     161     262 ..     161     264 .. 0.63
   2 ?   -1.9   0.0         2   3.9e+03      53     104 ..     341     391 ..     331     393 .. 0.72
   3 ?   -1.1   0.1       1.1   2.3e+03      48      97 ..     456     504 ..     436     506 .. 0.73
   4 ?    0.2   0.0      0.45     9e+02      46      76 ..     534     565 ..     523     590 .. 0.73
   5 ?   -2.5   0.0       3.1   6.2e+03      53      90 ..     663     701 ..     649     717 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0024
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelll.. 74 
                                       l+++ d +++ d++g+++y+ ++ + +fg++ +e+++    + l  + + ++ e     vl+       +e++ +  
  gi|313125689|ref|YP_004035959.1| 161 LNNMTDTVLITDDEGKFTYVCPNVHFIFGYTEAEIRDLGSIDALLGDdLFEESELEKSGVLTN------VECTATdk 231
                                       6889999***************************99877665444332433333333333333......33333333 PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTer 108
                                        gee++++++++ +   +G+   +l  +rD+T r
  gi|313125689|ref|YP_004035959.1| 232 AGEEHTLLVNVREV-SIQGG--TTLYSCRDVTKR 262
                                       56666666666666.45555..566666666666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                             PAS_4  53 eralrrvlegeepiefleelll....pgeerhyelrllPlrdesGevigvlvisrD 104
                                        + + r+  ++ep++f +++      ++++   ++ +l l d     +gvlv ++D
  gi|313125689|ref|YP_004035959.1| 341 GNLIGRAFVTGEPLFFDDVHESpalsNPATDLRSVVVLSLGD-----HGVLVAGVD 391
                                       567788999999999999998877777776666666666655.....777777766 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                             PAS_4  48 daarleralrrvlegeepiefleelllpgeerhyelrllPlrdesGevig 97 
                                        +a+ ++a++r++ ++ ++e+  e    g+  + + +l+P  ++sG+ +g
  gi|313125689|ref|YP_004035959.1| 456 IRAETREAVERAVCERLTAEDRYEFAWVGSIDPTSQTLVPR-AASGTGRG 504
                                       67788888889988887766666666688888888888885.77777555 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.45
                             PAS_4  46 eedaarleralrrvlegeepiefleelll.pg 76 
                                         + +  ++++rr++ ++++++ + ++l  +g
  gi|313125689|ref|YP_004035959.1| 534 NVATDLQQQPWRRAALERDFQSVVAVPLSyDG 565
                                       44666778999999999999999988877555 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 3.1
                             PAS_4  53 eralrrvlegeepiefleelll.pgeerhyelrllPlrd 90 
                                       ++a+r++++  + i +  ++   + ++ ++  +++P+ +
  gi|313125689|ref|YP_004035959.1| 663 MDAVRAAAADTAGIAEYRVVAGdDAAGTVWFRFVRPVIA 701
                                       566666666666666666666666666666666666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (839 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 5265.06
//
Query:       gi|313125690|ref|YP_004035960.1|  [L=50]
Description: hypothetical protein Hbor_09200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-05   23.0   0.8    8.2e-05   22.6   0.8    1.2  1  DUF1272         Protein of unknown function (DUF1272)
    0.00055   19.9   0.6    0.00068   19.6   0.6    1.2  1  DZR             Double zinc ribbon
    0.00069   19.7   2.8     0.0015   18.6   2.8    1.6  1  Zn-ribbon_8     Zinc ribbon domain
     0.0029   17.6   0.2     0.0033   17.4   0.2    1.1  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
     0.0068   15.9   2.3        1.6    8.3   0.2    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0077   15.6   3.0      0.032   13.6   3.0    1.9  1  zf-ribbon_3     zinc-ribbon domain
     0.0081   16.1   0.6       0.01   15.8   0.6    1.1  1  Prok-RING_1     Prokaryotic RING finger family 1
     0.0095   15.6   0.1      0.012   15.3   0.1    1.1  1  TackOD1         Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.012   15.6   0.2      0.014   15.3   0.2    1.1  1  zinc-ribbons_6  zinc-ribbons
      0.021   15.1   2.2      0.051   13.8   2.1    1.7  2  zinc_ribbon_9   zinc-ribbon
      0.022   14.7   1.3       0.05   13.5   1.3    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.031   14.3   0.5      0.034   14.1   0.5    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.046   13.5   2.5        2.4    8.0   0.4    2.4  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.049   13.4   1.2       0.11   12.3   0.1    1.8  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
      0.068   12.9   4.4       0.29   10.9   4.2    2.0  3  zinc_ribbon_2   zinc-ribbon domain
       0.11   13.0   1.8       0.55   10.7   0.3    2.0  2  zf-IS66         zinc-finger binding domain of transposase IS6
       0.14   12.4   1.3       0.17   12.1   1.3    1.1  1  DUF2072         Zn-ribbon containing protein
       0.14   12.6   1.1         14    6.4   0.0    2.1  2  zf-C2H2         Zinc finger, C2H2 type
       0.21   11.2   1.2         13    5.5   0.1    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.32   10.4   3.8          1    8.8   0.4    2.1  2  zf-TFIIB        Transcription factor zinc-finger
       0.63    9.8   2.2        1.8    8.4   0.1    2.0  2  zf-C2H2_11      zinc-finger C2H2-type
       0.71   10.0   5.2        2.2    8.4   0.2    2.1  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres


Domain annotation for each model (and alignments):
>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.8     1e-07   8.2e-05      20      54 ..      10      45 ..       5      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1e-07
                           DUF1272 20 eearicsyEctFCaeCaeevl.envCPncgGelvkR 54
                                      e+a   +yEc  C +   +     +CP+cgGel +R
  gi|313125690|ref|YP_004035960.1| 10 EAAEQSTYECFECGTVLGNDSsLATCPDCGGELRNR 45
                                      5688899***99*998654431579********999 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.6   8.3e-07   0.00068       9      40 ..      13      44 ..       7      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.3e-07
                               DZR  9 ppdarfCseCgtklkavaaedrCpsCgekvdp 40
                                      +++   C+eCgt l + ++  +Cp Cg ++ +
  gi|313125690|ref|YP_004035960.1| 13 EQSTYECFECGTVLGNDSSLATCPDCGGELRN 44
                                      55666799999999998999999999987665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.8   1.9e-06    0.0015       6      37 ..      17      43 ..      16      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsevr 37
                                      Y+C eCg   +vl   +d++l +CP+Cg+e+r
  gi|313125690|ref|YP_004035960.1| 17 YECFECG---TVLG--NDSSLATCPDCGGELR 43
                                      9******...5554..4777999******987 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2     4e-06    0.0033      17      45 ..      16      43 ..      11      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4e-06
                          zf-C2HC5 17 apnClnCGkiiCakeglskpCsfCgspll 45
                                      +  C++CG ++ +   l ++C+ Cg +l 
  gi|313125690|ref|YP_004035960.1| 16 TYECFECGTVLGNDSSL-ATCPDCGGELR 43
                                      567**************.*******9885 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.2    0.0019       1.6      16      33 ..      13      30 ..       9      31 .. 0.82
   2 !    8.0   0.2    0.0025         2       2       9 ..      34      41 ..      33      47 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0019
                                      STTCEEESSSSBEEEECC CS
                      TF_Zn_Ribbon 16 ergelvCtdCGlVledns 33
                                      e+ ++ C +CG+Vl ++s
  gi|313125690|ref|YP_004035960.1| 13 EQSTYECFECGTVLGNDS 30
                                      56677899******9876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                      +CP+Cg++
  gi|313125690|ref|YP_004035960.1| 34 TCPDCGGE 41
                                      68888876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   3.0     4e-05     0.032       1      26 []      15      42 ..      15      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                       zf-ribbon_3  1 stvrCPnCGa.p.lssddnvCpyCGtkl 26
                                      st++C +CG+ +  +s+  +Cp CG++l
  gi|313125690|ref|YP_004035960.1| 15 STYECFECGTvLgNDSSLATCPDCGGEL 42
                                      6899******6666777789*****986 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6   1.2e-05      0.01       4      27 ..      16      39 ..      13      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                       Prok-RING_1  4 gkkCpvCgkelkeedDiVvCpeCg 27
                                        +C  Cg  l +++ + +Cp+Cg
  gi|313125690|ref|YP_004035960.1| 16 TYECFECGTVLGNDSSLATCPDCG 39
                                      579********************9 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.5e-05     0.012      98     137 ..      11      46 ..       7      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                           TackOD1  98 ieeqelihhftCgnvgpeeeflkegkleCpkCktkLrhiG 137
                                         eq++ ++f+Cg+v  +++    +  +Cp C  +Lr+ G
  gi|313125690|ref|YP_004035960.1|  11 AAEQSTYECFECGTVLGNDS----SLATCPDCGGELRNRG 46 
                                       57899999999999987654....5568999999999988 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   1.7e-05     0.014      12      40 ..      12      43 ..       5      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                                      E-SSEEE-TTT--...EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6 12 krgeqyhCeaCqe...dlkkealCpeCeqele 40
                                       ++++y+C +C +   + +  a+Cp+C+ el 
  gi|313125690|ref|YP_004035960.1| 12 AEQSTYECFECGTvlgNDSSLATCPDCGGELR 43
                                      4567899****99777778899*****99985 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.21   1.7e+02      20      28 ..      15      23 ..       7      25 .. 0.61
   2 ?   13.8   2.1   6.2e-05     0.051       3      29 ..      17      40 ..      15      42 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                     zinc_ribbon_9 20 sdvlCPhCg 28
                                      s   C +Cg
  gi|313125690|ref|YP_004035960.1| 15 STYECFECG 23
                                      332388887 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.2e-05
                     zinc_ribbon_9  3 yWChqCdrfVsvspdedsdvlCPhCgg 29
                                      y C +C    +v  +++s ++CP+Cgg
  gi|313125690|ref|YP_004035960.1| 17 YECFECG---TVLGNDSSLATCPDCGG 40
                                      5588888...8888899999******9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.3   6.2e-05      0.05      27      55 ..      15      41 ..       7      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-05
                    OrfB_Zn_ribbon 27 TSktCseCgsknkealsgrtfkCpnCgfe 55
                                      +  +C eCg ++ +  ++ + +Cp+Cg e
  gi|313125690|ref|YP_004035960.1| 15 STYECFECGTVLGN--DSSLATCPDCGGE 41
                                      6679**********..***********87 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   4.2e-05     0.034      68      95 ..      14      41 ..       8      47 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-05
                                      --EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 68 pvkvrCreCgkefeleekalrCpkCgsa 95
                                      + +++C eCg+    +++ ++Cp+Cg++
  gi|313125690|ref|YP_004035960.1| 14 QSTYECFECGTVLGNDSSLATCPDCGGE 41
                                      66789*****99998876668****986 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4     0.003       2.4      17      30 ..      12      25 ..       1      26 [. 0.78
   2 ?    5.5   0.1     0.017        14      20      28 ..      31      39 ..      28      42 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.003
                     A2L_zn_ribbon 17 seqgylvCieCgas 30
                                      +eq+ + C eCg++
  gi|313125690|ref|YP_004035960.1| 12 AEQSTYECFECGTV 25
                                      79**********86 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.017
                     A2L_zn_ribbon 20 gylvCieCg 28
                                      +   C++Cg
  gi|313125690|ref|YP_004035960.1| 31 SLATCPDCG 39
                                      455688887 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.3     1e+03       3       9 ..      18      24 ..      17      27 .. 0.76
   2 ?   12.3   0.1   0.00013      0.11       3      15 ..      34      46 ..      33      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                                      E-SSS-- CS
                    zf-C4_Topoisom  3 kCPkCgg 9 
                                      +C +Cg 
  gi|313125690|ref|YP_004035960.1| 18 ECFECGT 24
                                      6889995 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                                      E-SSS--EEEEEE CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkr 15
                                      +CP Cgg+L  + 
  gi|313125690|ref|YP_004035960.1| 34 TCPDCGGELRNRG 46
                                      8********9885 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0052       4.3      14      22 ..      16      25 ..      10      26 .. 0.75
   2 ?   10.9   4.2   0.00036      0.29       2      22 ..      19      41 ..      18      42 .. 0.91
   3 ?    6.2   0.7     0.011       8.9       2       8 ..      35      41 ..      34      45 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0052
                     zinc_ribbon_2 14 kF.CpyCGtp 22
                                      ++ C +CGt 
  gi|313125690|ref|YP_004035960.1| 16 TYeCFECGTV 25
                                      5569999996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00036
                     zinc_ribbon_2  2 CpnCGaelqdnakF..CpyCGtp 22
                                      C +CG+ l +++    Cp CG +
  gi|313125690|ref|YP_004035960.1| 19 CFECGTVLGNDSSLatCPDCGGE 41
                                      9*******9999999*****976 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.011
                     zinc_ribbon_2  2 CpnCGae 8 
                                      Cp CG e
  gi|313125690|ref|YP_004035960.1| 35 CPDCGGE 41
                                      7777744 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.37     3e+02      40      46 .]      17      23 ..      13      30 .. 0.70
   2 ?   10.7   0.3   0.00067      0.55       3      12 ..      34      43 ..      33      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.37
                           zf-IS66 40 yaCpcCe 46
                                      y+C +C+
  gi|313125690|ref|YP_004035960.1| 17 YECFECG 23
                                      6666664 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00067
                           zf-IS66  3 tCpcCGgllk 12
                                      tCp+CGg+l+
  gi|313125690|ref|YP_004035960.1| 34 TCPDCGGELR 43
                                      8******764 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.3   0.00021      0.17       3      28 ..      18      41 ..      16      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                           DUF2072  3 kCtkCekvfedgskeilkGCpsCGgk 28
                                      +C +C++v+ + s+  l  Cp CGg+
  gi|313125690|ref|YP_004035960.1| 18 ECFECGTVLGNDSS--LATCPDCGGE 41
                                      7********99888..99******96 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.017        14       1      15 [.      17      31 ..      17      33 .. 0.78
   2 ?    5.5   0.2     0.032        26       2       7 ..      34      39 ..      34      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                                      EEETTTTEEESSHHH CS
                           zf-C2H2  1 ykCpdCgksFkrksn 15
                                      y+C +Cg +  + s+
  gi|313125690|ref|YP_004035960.1| 17 YECFECGTVLGNDSS 31
                                      99*****98766555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.032
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      +CpdCg
  gi|313125690|ref|YP_004035960.1| 34 TCPDCG 39
                                      7****9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.016        13       1      11 [.      15      25 ..      15      29 .. 0.87
   2 ?    5.0   0.1     0.022        18       4       9 ..      34      39 ..      31      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                            zf_UBZ  1 dtylCerCgke 11
                                      +ty C +Cg+ 
  gi|313125690|ref|YP_004035960.1| 15 STYECFECGTV 25
                                      59*******86 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.022
                            zf_UBZ  4 lCerCg 9 
                                      +C++Cg
  gi|313125690|ref|YP_004035960.1| 34 TCPDCG 39
                                      8****9 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.067        55      14      26 ..      11      23 ..       7      25 .. 0.75
   2 ?    8.8   0.4    0.0013         1      15      27 ..      28      40 ..      24      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.067
                          zf-TFIIB 14 rggveidyCpqCr 26
                                        +   + C++C+
  gi|313125690|ref|YP_004035960.1| 11 AAEQSTYECFECG 23
                                      5666778999997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                          zf-TFIIB 15 ggveidyCpqCrG 27
                                      ++  + +Cp+C+G
  gi|313125690|ref|YP_004035960.1| 28 NDSSLATCPDCGG 40
                                      5677888999998 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0022       1.8       2      11 ..      14      23 ..      13      25 .. 0.89
   2 ?    1.3   0.2      0.35   2.9e+02       1      11 [.      29      39 ..      28      40 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                        zf-C2H2_11  2 estcqCleCG 11
                                      +st+ C eCG
  gi|313125690|ref|YP_004035960.1| 14 QSTYECFECG 23
                                      79*******9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.35
                        zf-C2H2_11  1 destcqCleCG 11
                                      d+s   C +CG
  gi|313125690|ref|YP_004035960.1| 29 DSSLATCPDCG 39
                                      55666799**9 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0028       2.2      11      25 ..      11      25 ..       4      31 .. 0.82
   2 ?    4.4   0.9     0.048        39      18      23 ..      34      39 ..      27      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0028
                          zf-Mss51 11 apkhvdfeCpdCGip 25
                                      a ++ ++eC +CG +
  gi|313125690|ref|YP_004035960.1| 11 AAEQSTYECFECGTV 25
                                      578999*******75 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.048
                          zf-Mss51 18 eCpdCG 23
                                      +CpdCG
  gi|313125690|ref|YP_004035960.1| 34 TCPDCG 39
                                      8****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 336.46
//
Query:       gi|313125691|ref|YP_004035961.1|  [L=305]
Description: hypothetical protein Hbor_09210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.3e-51  172.1   3.3    1.2e-50  171.6   3.3    1.2  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
    3.8e-06   26.9   0.6    6.8e-06   26.1   0.6    1.4  1  60KD_IMP    60Kd inner membrane protein
  ------ inclusion threshold ------
      0.025   14.8   1.5      0.027   14.7   0.1    1.8  2  DPM3        Dolichol-phosphate mannosyltransferase subunit 3 


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.6   3.3   1.9e-54   1.2e-50       1     169 [.     133     299 ..     133     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.6 bits;  conditional E-value: 1.9e-54
                        EMC3_TMCO1   1 dlvldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrq 77 
                                       +++l+pl++   +lP++ v+++++++tgl+s+llq +l++++km+++q+r+k++qkr +e+qk gd+++l++++++q
  gi|313125691|ref|YP_004035961.1| 133 NVILGPLVE---ILPFYAVVMIIALATGLYSTLLQANLMNMEKMSAYQERMKDIQKRRKEAQKAGDDEALDRIQQEQ 206
                                       6899*****...***************************************************************** PP

                        EMC3_TMCO1  78 eelmedqsemmmdqmkpmivtmipqiliffwlnsffs......gfvvaklpfpltgrfksllqrglesldvrfvssi 148
                                       +e m+dq++m+++q++pm+++m+++i+ f+w+++ +       ++v+ ++++pl+g+++ ++    e++ ++++ +i
  gi|313125691|ref|YP_004035961.1| 207 MEAMGDQMGMFKEQFRPMVWIMFLTIPAFIWMYWAIGvrgsggHIVLQNIVLPLVGKVS-WT----EGVLGPMQAWI 278
                                       ******************************************99999************.**....*********** PP

                        EMC3_TMCO1 149 swYflcsfglsqiirklLgea 169
                                       +wYflcs+g++qiirk L+++
  gi|313125691|ref|YP_004035961.1| 279 VWYFLCSMGFTQIIRKSLDID 299
                                       ******************875 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.6   1.1e-09   6.8e-06       4      92 ..     147     250 ..     145     298 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.1e-09
                          60KD_IMP   4 aIilltiivrlillpltlkqlkssakmqelqPelkeiqekyk......kdk..qklqqemmklYk......kegvnp 66 
                                       a++++  +   +   l +  l++++km++ q ++k+iq++ k      +d+  +++qqe+m+         ke++ p
  gi|313125691|ref|YP_004035961.1| 147 AVVMIIALATGLYSTLLQANLMNMEKMSAYQERMKDIQKRRKeaqkagDDEalDRIQQEQMEAMGdqmgmfKEQFRP 223
                                       667777777778888999999********************999999844346778888887654222222678888 PP

                          60KD_IMP  67 laGclplLiqlpifialyrvlrsla...s 92 
                                       +  ++ +++++p fi +y+++       +
  gi|313125691|ref|YP_004035961.1| 224 M--VWIMFLTIPAFIWMYWAIGVRGsggH 250
                                       8..99**************9977335541 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   4.4e-06     0.027       8      89 ..     110     194 ..     104     196 .. 0.74
   2 ?   -3.2   0.1       1.7     1e+04       7      21 ..     226     240 ..     222     260 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-06
                              DPM3   8 lalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGays...lat.lgygvltfndcpeaakeLqkeike 80 
                                       ++++ l++a w   l+rl+  +++ +   +v +lP++a+v++ a +     t l  ++++++ + +a++e +k+i++
  gi|313125691|ref|YP_004035961.1| 110 VVTVGLFFAYWWQPLQRLIGSTMNVILGPLVEILPFYAVVMIIALAtglYSTlLQANLMNME-KMSAYQERMKDIQK 185
                                       56677888889999999998888888888999999999887644431112331556666665.678*********** PP

                              DPM3  81 AkadLrkkG 89 
                                        +++ +k+G
  gi|313125691|ref|YP_004035961.1| 186 RRKEAQKAG 194
                                       **9999887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                              DPM3   7 tlalallllalwlal 21 
                                       +++++++ + +w++ 
  gi|313125691|ref|YP_004035961.1| 226 WIMFLTIPAFIWMYW 240
                                       444444444455443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1403  (0.0782531); expected 358.6 (0.02)
Passed bias filter:                      855  (0.0476881); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 1816.31
//
Query:       gi|313125692|ref|YP_004035962.1|  [L=192]
Description: cytidylate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-16   59.0   1.9    6.9e-14   52.4   1.9    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    4.6e-15   56.3   0.1    6.2e-15   55.9   0.1    1.2  1  AAA_18           AAA domain
    2.3e-13   50.7   0.2    7.6e-13   49.1   0.2    1.8  1  AAA_17           AAA domain
    6.2e-09   35.9   0.5      6e-05   22.9   0.0    2.1  2  Cytidylate_kin   Cytidylate kinase
    1.8e-08   34.7   0.7    8.1e-07   29.3   0.7    2.2  1  AAA_33           AAA domain
    3.1e-08   33.8   0.1    7.1e-08   32.7   0.1    1.8  1  ADK              Adenylate kinase
    0.00061   19.9   2.6     0.0082   16.3   2.6    2.1  1  SKI              Shikimate kinase
    0.00097   19.4   1.0      0.003   17.8   1.0    1.9  1  AAA_28           AAA domain
     0.0014   19.0   0.9     0.0024   18.3   0.9    1.4  1  AAA_16           AAA ATPase domain
     0.0033   17.2   2.0      0.063   13.0   0.4    2.2  2  AAA_30           AAA domain
     0.0047   17.2   0.0     0.0069   16.7   0.0    1.4  1  AAA_22           AAA domain
     0.0055   17.1   0.0     0.0085   16.5   0.0    1.3  1  AAA              ATPase family associated with various cellul
     0.0057   16.6   0.0     0.0078   16.1   0.0    1.3  1  Rad17            Rad17 P-loop domain
      0.008   16.0   0.4       0.22   11.4   0.0    2.2  2  dNK              Deoxynucleoside kinase
  ------ inclusion threshold ------
      0.052   13.2   0.1        6.2    6.5   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
      0.054   13.4   0.0      0.077   12.9   0.0    1.3  1  Ploopntkinase3   P-loop Nucleotide Kinase3
      0.073   12.8   0.0       0.15   11.8   0.0    1.5  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.081   13.3   0.0       0.12   12.8   0.0    1.3  1  RNA_helicase     RNA helicase
      0.088   13.3   0.0       0.12   12.9   0.0    1.4  1  ABC_tran         ABC transporter
      0.092   12.4   0.0       0.14   11.8   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
       0.12   12.4   0.0       0.22   11.5   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
       0.19   11.2   0.0       0.26   10.7   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
        0.2   11.4   0.1       0.37   10.6   0.1    1.4  1  ATP_bind_1       Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   1.9   8.9e-17   6.9e-14       3     178 ..       4     156 ..       2     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.9e-17
                   Cytidylate_kin2   3 TIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldekld 78 
                                       T+s+  G+g++t    LAe +gl+ ++  +i++++a e  ++  e+ ++ e                         d
  gi|313125692|ref|YP_004035962.1|   4 TVSGPPGAGKSTTVATLAEAFGLEHISGgDIFRQLAAERDMTAVEFNKLAE------------------------KD 56 
                                       778888888888888888888888888778888888888888888877777........................36 PP

                   Cytidylate_kin2  79 delfeaqervirela.aeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrra 154
                                       d++ +   r +r++a + ++v +  R a  +  d    +r +l+apl++r++r+aere+ s + are+ +++++ +a
  gi|313125692|ref|YP_004035962.1|  57 DQIDRDLDRRLRTIAlERDDVLLESRLAGWLAGDAA-DIRLWLDAPLDVRAERIAEREDKSLDVAREETRAREESEA 132
                                       77777788889999988889999******8888866.**************************************** PP

                   Cytidylate_kin2 155 kyykkytgqdwgdaenYdlvlnts 178
                                        +y++y++ d++d   Yd++lnt+
  gi|313125692|ref|YP_004035962.1| 133 LRYEEYYNIDITDLGIYDITLNTA 156
                                       **********************97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.1   7.9e-18   6.2e-15       3     121 ..       5     120 ..       3     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 7.9e-18
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleeg 74 
                                       ++G+pG+GK+t    L++  g+     g++ r++a+e+++   ++++  ++ +++d+d + +l ++  e        
  gi|313125692|ref|YP_004035962.1|   5 VSGPPGAGKSTTVATLAEAFGLehisgGDIFRQLAAERDMTAVEFNKLAEKDDQIDRDLDRRLRTIALER------- 74 
                                       89*****************88899***********************88888899999988888888885....... PP

                            AAA_18  75 knlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik 121
                                       ++++++++la ++  +a di   +L+a+ ++++eR+++R+ ++ + +
  gi|313125692|ref|YP_004035962.1|  75 DDVLLESRLAGWLAGDAADIR-LWLDAPLDVRAERIAEREDKSLDVA 120
                                       679******************.*****************98776555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.2   9.7e-16   7.6e-13       2     132 ..       7     122 ..       6     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 9.7e-16
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea.kkkgvlvd 77 
                                       G+PG+GK+t +++l+e +g++h+s Gd++r+ a+++ +  +  e++kl  e+++++++ + ++++  a ++++vl++
  gi|313125692|ref|YP_004035962.1|   7 GPPGAGKSTTVATLAEAFGLEHISGGDIFRQLAAERDM--TAVEFNKLA-EKDDQIDRDLDRRLRTIAlERDDVLLE 80 
                                       9*********************************9998..667777776.445557777777777777567789997 PP

                                       E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SH CS
                            AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddne 132
                                                    g+ +    ++  d+ + l+a+ ++  er ++++ ++ d   e
  gi|313125692|ref|YP_004035962.1|  81 SRLA---------GWLA---GDA-ADIRLWLDAPLDVRAERIAEREDKSLDVARE 122
                                       7764.........3333...222.3556667777777777766666555555554 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   7.7e-08     6e-05       2      39 ..       4      41 ..       3      57 .. 0.87
   2 !   11.5   0.1   0.00024      0.19      98     162 ..      59     123 ..      51     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.7e-08
                                      EEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHH CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgalYRalala 39
                                      ++ GP g+GKs+   +lae +gl+ ++ g ++R+la  
  gi|313125692|ref|YP_004035962.1|  4 TVSGPPGAGKSTTVATLAEAFGLEHISGGDIFRQLAAE 41
                                      789*******************************9965 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHTT-B.SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHH CS
                    Cytidylate_kin  98 vRailvkklrelvk.karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvslee 162
                                       + + l ++lr+++  +++v++e R  g      a+++++ldA  ++Ra+R ++  ++k+ +v+ ee
  gi|313125692|ref|YP_004035962.1|  59 IDRDLDRRLRTIALeRDDVLLESRLAGWLAGDAADIRLWLDAPLDVRAERIAER-EDKSLDVAREE 123
                                       5667888999988669999*****999999999***************986555.66655555444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.7     1e-09   8.1e-07       2     130 ..       3     124 ..       2     137 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1e-09
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqskt...dytrvldrlyqilnelarkalsagrnvil 75 
                                       + + G+pG+GKst +  l+++ g +++s  +++r+l+++ + +     ++++  d++ + l +++r  + ++ +v+l
  gi|313125692|ref|YP_004035962.1|   3 LTVSGPPGAGKSTTVATLAEAFGLEHISGGDIFRQLAAERDMTAVefnKLAEKDDQIDRDLDRRLRTIALERDDVLL 79 
                                       6678*********************************8655544311122233333555555555444444444444 PP

                            AAA_33  76 datnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaang.ddrsevpe 130
                                              ++ a +l+     ++++  ++++++ ++ +eR+a+R++++ d  ++ ++
  gi|313125692|ref|YP_004035962.1|  80 E------SRLAGWLA----GDAADIRLWLDAPLDVRAERIAEREDKSlD-VAREET 124
                                       3......33344433....3667888*******************9843.333333 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   9.1e-11   7.1e-08       1      58 [.       5      62 ..       5     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 9.1e-11
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpde 58
                                      + G+PgaGK t  ++l++ +gl h+s Gd++R+  ++   +  e +++ +k + +  +
  gi|313125692|ref|YP_004035962.1|  5 VSGPPGAGKSTTVATLAEAFGLEHISGGDIFRQLAAERDMTAVEFNKLAEKDDQIDRD 62
                                      57*******************************9998888888888877777666655 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.6   1.1e-05    0.0082       1     135 [.       9     142 ..       9     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHT...S-HHHH..HHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTG CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtg...ksiaei..feeegeegFrelEsevlkelleeeglViatGGGa 72 
                                       +GaGKst+   lA++ gle i   +++ + +    +++ e+  ++e++ + +r+l++++    le++++ +      
  gi|313125692|ref|YP_004035962.1|   9 PGAGKSTTVATLAEAFGLEHISGGDIFRQLAAerdMTAVEFnkLAEKDDQIDRDLDRRLRTIALERDDVLLES---- 81 
                                       69*******************9977664433322244433322566777778888888777777774444444.... PP

                                       GGSHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSS CS
                               SKI  73 vlseenrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaa 135
                                         + + + +  +  i ++Ld++l++ +er+++++++ l  +++++++++e++a r + y +++
  gi|313125692|ref|YP_004035962.1|  82 --RLAGWLAGDAADIRLWLDAPLDVRAERIAEREDKSLDVAREETRAREESEALRYEEYYNID 142
                                       ..444555555999*********************8777666665566666666666666654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.0   3.8e-06     0.003       4      49 ..       5      55 ..       2     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-06
                            AAA_28  4 itGgestGKTtlleaLaar.gypvv..pEaareileekl..akgedalpwv 49
                                      ++G++++GK+t+++ La+  g +++   +++r++  e+   a ++++l++ 
  gi|313125692|ref|YP_004035962.1|  5 VSGPPGAGKSTTVATLAEAfGLEHIsgGDIFRQLAAERDmtAVEFNKLAEK 55
                                      79***************9989999977888888877776455555555543 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.9     3e-06    0.0024      27     107 ..       3      99 ..       1     138 [. 0.62

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3e-06
                            AAA_16  27 vllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawre 99 
                                       + +sG++G GKs+ v +l++a+  +    g if +  +++  +a+++  la+    +++ r+l++++++ +le+++ 
  gi|313125692|ref|YP_004035962.1|   3 LTVSGPPGAGKSTTVATLAEAFGLEhisgGDIFRQLAAERDMTAVEFNKLAEKD--DQIDRDLDRRLRTIALERDDV 77 
                                       679*****************9988844432333222222222345555555555..366677777777777777777 PP

                            AAA_16 100 kleeala..............a 107
                                        le++la              +
  gi|313125692|ref|YP_004035962.1|  78 LLESRLAgwlagdaadirlwlD 99 
                                       7777766555444444444440 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.4   8.1e-05     0.063      21      42 ..       3      24 ..       1      28 [. 0.88
   2 ?    3.7   0.1     0.058        45     129     171 ..      27      69 ..      25      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.1e-05
                            AAA_30 21 avltGpAGtGKttalkalreaw 42
                                       ++ Gp+G+GK+t++++l+ea+
  gi|313125692|ref|YP_004035962.1|  3 LTVSGPPGAGKSTTVATLAEAF 24
                                      5789**************9985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.058
                            AAA_30 129 asVeaGgvlrdlveaagigtaeLtevvRqkeseeraaalalre 171
                                       + ++ G+++r+l+++++++++e +++   +++  r++ ++lr+
  gi|313125692|ref|YP_004035962.1|  27 EHISGGDIFRQLAAERDMTAVEFNKLAEKDDQIDRDLDRRLRT 69 
                                       56889*******99999********999999999999888886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.9e-06    0.0069       7      32 ..       2      27 ..       1      89 [. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.9e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldee 32
                                      +l+v G++G+GK+t++++l+e +  e
  gi|313125692|ref|YP_004035962.1|  2 LLTVSGPPGAGKSTTVATLAEAFGLE 27
                                      5899****************998543 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-05    0.0085       3      49 ..       5      49 ..       3      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirel 49
                                      ++GppG GK++++  +a+ +g     isg +++ ++  e+ +   e+
  gi|313125692|ref|YP_004035962.1|  5 VSGPPGAGKSTTVATLAEAFGL--EHISGGDIFRQLAAERDMTAVEF 49
                                      79*****************765..67888888876666665555544 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     1e-05    0.0078      47      74 ..       2      29 ..       1      64 [. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                             Rad17 47 iLLisGPsGCgkstvvkvLskelgiklr 74
                                      +L +sGP+G gkst+v  L+  +g + +
  gi|313125692|ref|YP_004035962.1|  2 LLTVSGPPGAGKSTTVATLAEAFGLEHI 29
                                      6889****************99997654 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00028      0.22       1      27 [.       3      29 ..       3      37 .. 0.92
   2 ?    3.3   0.1     0.084        65     123     195 ..      92     163 ..      32     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                                      EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                      ++v+G+ gaGKst v +L++++g +++
  gi|313125692|ref|YP_004035962.1|  3 LTVSGPPGAGKSTTVATLAEAFGLEHI 29
                                      589*******************99987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.084
                                       -SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTHCCHHHHH CS
                               dNK 123 pdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevpvlvidveeldlvaeeekredv 195
                                        d+  +L+a+l++  eri +R+++    + ++  ++ +e+    ++++ ++ ++ + + ++ l ++ +++edv
  gi|313125692|ref|YP_004035962.1|  92 ADIRLWLDAPLDVRAERIAEREDKS-LDVAREETRAREESEALRYEEYYNIDITDLGIYDITLNTARWSEEDV 163
                                       5788899*************99876.45555555555555555555555555555555555556666666555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0079       6.2       3      24 ..       7      28 ..       5      59 .. 0.89
   2 ?    5.2   0.0      0.02        15     118     150 ..      92     124 ..      70     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0079
                                      ESTTSSHHHHHHHHHHHHHHTT CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeeg 24
                                      G  GaGK+t +++l+e++  e+
  gi|313125692|ref|YP_004035962.1|  7 GPPGAGKSTTVATLAEAFGLEH 28
                                      778*************986665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.02
                                       -SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHH CS
                   Thymidylate_kin 118 PdltflldvdpevalkRlakrdeldeeeeeqld 150
                                        d+ + ld + +v+++R+a+r+ +  +++++++
  gi|313125692|ref|YP_004035962.1|  92 ADIRLWLDAPLDVRAERIAEREDKSLDVAREET 124
                                       588999***************994433333333 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.9e-05     0.077       7      36 ..       4      33 ..       1      60 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.9e-05
                    Ploopntkinase3  7 ylvGqPGaGkstlmaeltkgfdrskveqee 36
                                       + G PGaGkst +a+l+++f  +++++ +
  gi|313125692|ref|YP_004035962.1|  4 TVSGPPGAGKSTTVATLAEAFGLEHISGGD 33
                                      56699*****************99998765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.15       3      48 ..       4      44 ..       2      72 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                               PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdl 48
                                       v+g+ GaGk+t+ ++l ++fg e++    i     +r   ae d+
  gi|313125692|ref|YP_004035962.1|  4 TVSGPPGAGKSTTVATLAEAFGLEHISGGDI-----FRQLAAERDM 44
                                      799*******************877774433.....3333333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00015      0.12       2      23 ..       4      25 ..       3      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                      RNA_helicase  2 wlyGpsgeGKStlakeLakall 23
                                       ++Gp+g GKSt++ +La+a+ 
  gi|313125692|ref|YP_004035962.1|  4 TVSGPPGAGKSTTVATLAEAFG 25
                                      589***************9987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00015      0.12      15      42 ..       4      34 ..       1     134 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                                      EEEESTTSSHHHHHHHHT...TSS--SEEEE CS
                                      xxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                          ABC_tran 15 aivGenGaGKStLlklla...gllkpteGei 42
                                       + G+ GaGKSt +++la   gl++   G+i
  gi|313125692|ref|YP_004035962.1|  4 TVSGPPGAGKSTTVATLAeafGLEHISGGDI 34
                                      678*************982224455566666 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.14       5      46 ..       4      41 ..       1      71 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHH CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAve 46
                                       + G+ GaGK tt+a La+ +  e+    +   D+fR  A+e
  gi|313125692|ref|YP_004035962.1|  4 TVSGPPGAGKSTTVATLAEAFGLEH----ISGGDIFRQLAAE 41
                                      56799*************9998886....6678888877766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.22       5      37 ..       6      45 ..       3      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                      E--SSSSHHHHHHHGGGGB.......S--EEEEE--TT-- CS
                             AAA_5  5 vGppGtgKselaerlaaal.......nreveyvqltrdtt 37
                                       GppG gKs+ +  la+a+       ++ +   +  rd+t
  gi|313125692|ref|YP_004035962.1|  6 SGPPGAGKSTTVATLAEAFglehisgGDIFRQLAAERDMT 45
                                      6*****************9666555555555555555555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00033      0.26       3      27 ..       2      26 ..       1      71 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                                      EEEEE--TTSSHHHHHHHHHHHHHH CS
                             KTI12  3 LvvltGlPssGKstrakeLakalee 27
                                      L++++G P +GKst +++La+a+  
  gi|313125692|ref|YP_004035962.1|  2 LLTVSGPPGAGKSTTVATLAEAFGL 26
                                      999*****************99865 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00047      0.37       1      21 [.       5      25 ..       5      30 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                        ATP_bind_1  1 vvGpaGsGKttfvgalseile 21
                                      v Gp+G+GK+t v +l+e + 
  gi|313125692|ref|YP_004035962.1|  5 VSGPPGAGKSTTVATLAEAFG 25
                                      78**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1170.11
//
Query:       gi|313125693|ref|YP_004035963.1|  [L=290]
Description: tRNA pseudouridine synthase b [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-23   84.1   0.1      2e-13   51.0   0.0    3.1  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
    3.4e-22   78.3   0.2    3.4e-22   78.3   0.2    1.8  2  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    1.2e-08   34.9   0.0    2.8e-08   33.7   0.0    1.6  1  DKCLD     DKCLD (NUC011) domain
      4e-08   33.1   0.3    7.2e-08   32.3   0.3    1.5  1  PUA       PUA domain


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   4.4e-17     2e-13       1      52 [.      40      91 ..      40      96 .. 0.93
   2 !   27.5   0.0   7.3e-10   3.3e-06      74     149 .]      94     152 ..      89     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 4.4e-17
                                      HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETE CS
                            TruB_N  1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlga 52
                                      + + +++++ h+GtLDp++tG+L++++g+aT++++++le +KeY+ +++l++
  gi|313125693|ref|YP_004035963.1| 40 RDMAGVERAAHAGTLDPKVTGCLPMLLGDATRMAQVFLEGSKEYVSVLELHK 91
                                      668899*****************************************99986 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 7.3e-10
                                       HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                            TruB_N  74 eekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                        ++le+v+++f+G+++q pp  SAv                  r+ r+ ++y+l+lleve++++ l+++c++GtYi
  gi|313125693|ref|YP_004035963.1|  94 PSDLESVVAEFEGDVYQKPPRKSAVS-----------------RRLRSREVYDLDLLEVEDRQALLRIRCESGTYI 152
                                       57899*******************99.................899*****************************9 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       2.1   9.4e+03      21      38 ..     120     137 ..     120     143 .. 0.69
   2 !   78.3   0.2   7.6e-26   3.4e-22       1      63 [.     153     217 ..     153     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
                                       EEEEETTEGG-..B-HHH CS
                          TruB_C_2  21 RRtrvgpfdeedmvtled 38 
                                       RR+r+ ++ + d++++ed
  gi|313125693|ref|YP_004035963.1| 120 RRLRSREVYDLDLLEVED 137
                                       788888887777676666 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 7.6e-26
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT.--H.HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke.dee.LdrlllPlesal 63 
                                       R+Lc+DiG+a g+gAh+ +LRRt++ pfd++d+vtl dL da++++++ de+ L++++ P e+al
  gi|313125693|ref|YP_004035963.1| 153 RKLCHDIGLAAGTGAHMGHLRRTATDPFDDTDLVTLYDLSDALAFAEQgDESvLRDVVAPAERAL 217
                                       9*******************************************99999999***********98 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   6.3e-12   2.8e-08      30      57 ..       8      35 ..       6      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 6.3e-12
                                      GGG--HHHHHHTEEEEEEE-SSS-HHHH CS
                             DKCLD 30 PlkRpieeyikyGvinLDKPsnPsSHEV 57
                                      P  R++++++++Gv+nLDKP +Ps H+V
  gi|313125693|ref|YP_004035963.1|  8 PDDRSLDDLLSFGVVNLDKPPGPSAHQV 35
                                      899************************9 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.3   1.6e-11   7.2e-08       1      52 [.     221     271 ..     221     283 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.6e-11
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGla 52 
                                       ++v++  +A++ +++ga ++apGv e+++  e+g  Va+v++dg +v++G+ 
  gi|313125693|ref|YP_004035963.1| 221 PHVTIAYSAAEQVAEGAPVYAPGVSEADD-AERGSLVACVTPDGAAVCLGRL 271
                                       6899************************9.********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1761.15
//
Query:       gi|313125694|ref|YP_004035964.1|  [L=363]
Description: deacylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-38  130.8   0.0    6.9e-38  130.4   0.0    1.2  1  AstE_AspA      Succinylglutamate desuccinylase / Aspartoacyla
      0.001   18.6   0.0     0.0014   18.1   0.0    1.1  1  Peptidase_M99  Carboxypeptidase controlling helical cell shap
     0.0073   16.1   0.1      0.017   15.0   0.1    1.6  1  Peptidase_M14  Zinc carboxypeptidase


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.0   1.1e-41   6.9e-38       1     289 [.      41     346 ..      41     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 1.1e-41
                                       SS-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSSTT-S-CTTTTTCCCCCSSTC CS
                         AstE_AspA   1 sgpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyipidredLNRaFpgrslgrsld 77 
                                       +gp++ +++GvHG+E +Gv+++++ +++  ++ i+g++++vp++Np++++++sR ++ ++ d NR Fp  ++     
  gi|313125694|ref|YP_004035964.1|  41 DGPTLWLTGGVHGDEATGVAVAQDAMRADLAERISGTVVCVPVVNPAGLRRNSRQSYYNDDDPNRYFPDPESS---- 113
                                       59*******************************************************************9999.... PP

                                       HHHHHHHHHHHHHHHCHCTCCCGCEEEEEEEESSTB.CCSSEEEE---SSHHHH.........HHHHHHTTTSEEEE CS
                         AstE_AspA  78 ealrateaerladalfaaalpeadivlDLHtgtrgl.khllfaeadiaeaqlqs.........lallkalglpavll 144
                                       +++  ++ er+ ++l +a +++ad  +DLHt+  g+  ++   ++ + e + +s          +l++a+g p++  
  gi|313125694|ref|YP_004035964.1| 114 SSRPPSVQERIDERLYEAFSESADALVDLHTAQIGSmPFVIRDRVLYGERREESeaqalaerlDRLVSAYGFPVLT- 189
                                       555568888888888877779**********999871222222222333333335667755544455555666655. PP

                                       EESS--S.........SHHHHHHHHCTSEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT.-..SCC.CEE CS
                         AstE_AspA 145 ldekesa.........gfletaaeelgalaftlElGgagrlgaedisrtakgvlnvlahigvvagq.e..avepakl 209
                                         e+++          ++  +a++ +g++aft+ElGg  ++++++ +  ++gv  v+ ++g+++++ +   v+++ +
  gi|313125694|ref|YP_004035964.1| 190 --EYPAEeyveqglqrSTAGAALNAAGIPAFTVELGGHSVIEEDTRAAGVAGVYGVMVELGMLDPGdVpdDVDEPGA 264
                                       ..333335669999999*************************************************66994444443 PP

                                       ...EEEEEE.EEGGSCCCSSCSEEECCCCSTTTTETCTEEEETTEEEEECTSTEEEEESSSSEEEESCCTSCCTTTT CS
                         AstE_AspA 210 ...yrvlre.ldeprdiraeeaGlvefkvklgddveagellakalvldslggekvelrapqdgvivfineaalvekg 282
                                            ++++ +++    rae  Glv ++v+ gd v+ g ++  a v++++g++ ++++ + dg++++++e +++ +g
  gi|313125694|ref|YP_004035964.1| 265 gvpDAPVDYpVRRAVHPRAETPGLVRHRVEPGDVVASGNVV--ADVVSPHGEQRATIESEYDGYVIARREGVAAYEG 339
                                       0013333331334445589**********************..********************************** PP

                                       EEEEEEE CS
                         AstE_AspA 283 aalvkva 289
                                       + ++ +a
  gi|313125694|ref|YP_004035964.1| 340 DPVLSMA 346
                                       *998765 PP

>> Peptidase_M99  Carboxypeptidase controlling helical cell shape catalytic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.4e-07    0.0014      31     128 ..      37     143 ..      25     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-07
                                       GGGGSS-EEEEE--SSTT-HHHHHHHHHHHH..HEEE-SSEEEEES-STHHHHHTT-S-TT...S-GGG-SSS--TT CS
                     Peptidase_M99  31 edrdkaphllllagiqgdepggfnaanlflm..hyevkkglvevvpvlnkpsilrnhrgly...ddmnrkfaaldkn 102
                                       e     p l l  g+ gde  g   a+  +     e   g v  vpv+n   + rn r  y   dd nr f   +  
  gi|313125694|ref|YP_004035964.1|  37 EGESDGPTLWLTGGVHGDEATGVAVAQDAMRadLAERISGTVVCVPVVNPAGLRRNSRQSYyndDDPNRYFPDPESS 113
                                       45667899**************98776443211345678*******************8876666889999988888 PP

                                       STTHHHHHH.HHHHHT...-TT--EEEEEE CS
                     Peptidase_M99 103 dpeypiire.ikslia...kpsvdavlhlh 128
                                           p ++e i   +      s da++ lh
  gi|313125694|ref|YP_004035964.1| 114 SSRPPSVQErIDERLYeafSESADALVDLH 143
                                       888887775344333201134666666666 PP

>> Peptidase_M14  Zinc carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.8e-06     0.017      41     137 ..      37     110 ..      17     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-06
                                       STTST-CEEEEEE-SSTT-HHHHHHHHHHHHHHHHHTTTSHHHHHHHHHEEEEEES-STHHHHHHHHHT-TTTTST- CS
                     Peptidase_M14  41 eaeegkpvvlidggiHarEwigsalllylleqLlsaYgedeeikellddtdiyilpvlNPDGyeysstedrlwrknr 117
                                       e e+  p+ +++gg+H++E++g a+++ +++  l      e+i      t ++ +pv+NP G  + s      r  +
  gi|313125694|ref|YP_004035964.1|  37 EGESDGPTLWLTGGVHGDEATGVAVAQDAMRADLA-----ERI----SGT-VVCVPVVNPAGLRRNS------R--Q 95 
                                       5678899*******************999886553.....233....334.6788888888888777......2..3 PP

                                       SBCTTSSSBS--GGGSSSSS CS
                     Peptidase_M14 118 snakessceGvDlnRnFpdl 137
                                       s  +       D+nR Fpd 
  gi|313125694|ref|YP_004035964.1|  96 SYYN-----DDDPNRYFPDP 110
                                       3333.....56888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2283.13
//
Query:       gi|313125695|ref|YP_004035965.1|  [L=275]
Description: methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-07   30.4   0.1    1.3e-06   29.1   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    1.7e-06   28.7   0.1    5.8e-06   27.0   0.0    1.9  2  Methyltransf_12  Methyltransferase domain
    2.1e-06   28.3   0.0    4.4e-06   27.3   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    2.9e-05   23.9   0.0    3.8e-05   23.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    3.2e-05   23.8   0.0    4.7e-05   23.3   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    0.00054   19.2   0.0      0.001   18.3   0.0    1.4  1  Pox_MCEL         mRNA capping enzyme
     0.0049   16.5   0.0     0.0071   16.0   0.0    1.1  1  NodS             Nodulation protein S (NodS)
  ------ inclusion threshold ------
       0.11   12.1   0.1       0.14   11.7   0.1    1.3  1  FmrO             Ribosomal RNA methyltransferase (FmrO)
       0.15   12.4   0.0       0.29   11.5   0.0    1.4  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.9   9.8e+03      82      97 .]      10      25 ..       6      25 .. 0.81
   2 !   29.1   0.0   6.3e-10   1.3e-06       1      89 [.     103     186 ..     103     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.9
                                      HHHHHHHHHHHEEEEE CS
                   Methyltransf_25 82 lekalkeiarvLkpgG 97
                                      ++++l +++ +L++gG
  gi|313125695|ref|YP_004035965.1| 10 ARTLLYRARTLLREGG 25
                                      5778899999999999 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 6.3e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                       v+++GcG Gr ++  a  +  ++++g D+se++++++rer+++ ++  +f++ d  +   +d   D+ +s  + +h+
  gi|313125695|ref|YP_004035965.1| 103 VVEFGCGDGRQVKLGA--Y--ESYVGYDVSESAVKRCRERFAD-DPTKRFETYDPLSD-TPDVNADVALSLEVlFHL 173
                                       899*******998877..4..79******************75.58999*99998553.357789*****9997777 PP

                                       SSHHHHHHHHHHH CS
                   Methyltransf_25  77 lsdedlekalkei 89 
                                       ++d+ +e+ ++++
  gi|313125695|ref|YP_004035965.1| 174 VDDDVYEASMRHL 186
                                       8888888877776 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.9   5.7e+03      82      97 ..      10      25 ..       7      26 .. 0.84
   2 !   27.0   0.0   2.9e-09   5.8e-06       1      82 [.     104     178 ..     104     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.9
                   Methyltransf_12 82 irevldnirklLkpgG 97
                                       r +l ++r lL+ gG
  gi|313125695|ref|YP_004035965.1| 10 ARTLLYRARTLLREGG 25
                                      5788999*******99 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 2.9e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       +e+GcG+G+ ++  + +    +y+g+D+s+sa+++ +e++a+   +     ++e+ d l++ +    D+ ++++vl 
  gi|313125695|ref|YP_004035965.1| 104 VEFGCGDGRQVKLGAYE----SYVGYDVSESAVKRCRERFADDPTK-----RFETYDPLSDTPDVNADVALSLEVLF 171
                                       69******999988888....*********************9964.....455555555555679**********9 PP

                   Methyltransf_12  78 hl...kdi 82 
                                       hl   + +
  gi|313125695|ref|YP_004035965.1| 172 HLvddD-V 178
                                       997742.3 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.2e-09   4.4e-06       2      76 ..     105     177 ..     104     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.2e-09
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES-CCC-..C CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvssevlhhv..e 75 
                                       ++GcG Gr ++  a  ++++vg D+s+ ++k+++e+  +++ k   + ++   l   +d   D+ +s evl+h+  +
  gi|313125695|ref|YP_004035965.1| 105 EFGCGDGRQVKLGA--YESYVGYDVSESAVKRCRERFADDPTK---RFETYDPLsDTPDVNADVALSLEVLFHLvdD 176
                                       79***********9..999*********************974...34444445479999**************653 PP

                                       C CS
                   Methyltransf_11  76 d 76 
                                       d
  gi|313125695|ref|YP_004035965.1| 177 D 177
                                       3 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.9e-08   3.8e-05       5     113 ..     101     199 ..      97     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.9e-08
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlils 80 
                                        +v++ GCG G+ ++  a e      +vG D se a++++re+ ++   +  +Fe  d  +  +    d + D+ ls
  gi|313125695|ref|YP_004035965.1| 101 ESVVEFGCGDGRQVKLGAYE-----SYVGYDVSESAVKRCRERFADDPTK--RFETYDPLSdTP----DVNADVALS 166
                                       5799**********999976.....59**********************9..899988888677....5679***** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedpr 113
                                        evl +l d d +  ++  ++ +  ++++   +
  gi|313125695|ref|YP_004035965.1| 167 LEVLFHLVDDDVYEASMRHLFDSADRFVLILSS 199
                                       9**999999988888888888888777776655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.4e-08   4.7e-05      20     148 ..      97     226 ..      53     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.4e-08
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkfdlIvlrevl 92 
                                       +    +v+++GcG+G+  ++ +++  s++g+D s+ av++ +     +++ +++ +     + p+   d++ + evl
  gi|313125695|ref|YP_004035965.1|  97 EHDVESVVEFGCGDGRQVKLGAYE--SYVGYDVSESAVKRCRerfaDDPTKRFETY-DPLSDTPDVNADVALSLEVL 170
                                       445569*********999977666..9*********99998777763333333333.333445777*********** PP

                   Methyltransf_23  93 ehvpd...ppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsa 148
                                        h+ d   +++ +r++++  + +  +l++ +++++  ++ +l+++     +++ ++f+a
  gi|313125695|ref|YP_004035965.1| 171 FHLVDddvYEASMRHLFD--SADRFVLILSSNRDD-PTSGALHVRHRKFTDDVERWFDA 226
                                       **9966789999*****9..667888888888775.35555555555555555555555 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.1e-07     0.001      58     113 ..      93     145 ..      86     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.1e-07
                          Pox_MCEL  58 tkldesnklkvLdldcgkGgDLeKyekgeIsklvatDiaeesieeckeRYnklrse 113
                                       ++lde +  +v + +cg G   +  + g+ +++v+ D++e ++++c+eR+     +
  gi|313125695|ref|YP_004035965.1|  93 DFLDEHDVESVVEFGCGDG---RQVKLGAYESYVGYDVSESAVKRCRERFADDPTK 145
                                       4567777799******998...56789999*******************9554444 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.6e-06    0.0071      34     149 ..      90     202 ..      80     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.6e-06
                              NodS  34 ilrlslaqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdli 110
                                       +++  l + ++ +++e Gc  G   ++l  y ++    dv e+a++r+rer  + +   + + d      d + d+ 
  gi|313125695|ref|YP_004035965.1|  90 VINDFLDEHDVESVVEFGCGDGRQ-VKLGAY-ESYVGYDVSESAVKRCRERFADDPTKRFETYDPLSDTPDVNADVA 164
                                       5566688999***********985.688887.567789*****************************9********* PP

                              NodS 111 vvaevlyyiedvaelraavrnlvsllapdgqlvfGsard 149
                                       +  evl+++ d     a++r l +  a    l++ s rd
  gi|313125695|ref|YP_004035965.1| 165 LSLEVLFHLVDDDVYEASMRHLFDS-ADRFVLILSSNRD 202
                                       **********999999999988653.3344556666665 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.1e-05      0.14     126     207 ..     115     196 ..      86     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.1e-05
                              FmrO 126 llaadatylasDidsdlv.efldrflalvevegrvevrDlvadvpapraDlaLvLktl.pvLeqrrrGaglr.Lvet 199
                                       +l a   y+++D+    v    +rf +  ++ +r e  D  +d+p  +aD+aL L +l +++++    a++r L ++
  gi|313125695|ref|YP_004035965.1| 115 KLGAYESYVGYDVSESAVkRCRERFAD--DPTKRFETYDPLSDTPDVNADVALSLEVLfHLVDDDVYEASMRhLFDS 189
                                       566667899999975555156788877..899***********************9863777877777776625565 PP

                              FmrO 200 ldapfvvv 207
                                        d +fv++
  gi|313125695|ref|YP_004035965.1| 190 AD-RFVLI 196
                                       54.67665 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.29      57      87 ..      98     128 ..      86     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                      AdoMet_MTase  57 eketsfvdvgcgngllvyvlaaegykgygid 87 
                                       ++  s v+ gcg+g  v + a e y gy + 
  gi|313125695|ref|YP_004035965.1|  98 HDVESVVEFGCGDGRQVKLGAYESYVGYDVS 128
                                       566899*********************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1657.56
//
Query:       gi|313125696|ref|YP_004035966.1|  [L=130]
Description: hypothetical protein Hbor_09270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.31   11.3   6.1        1.7    9.0   0.5    2.2  2  DUF4064   Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5   9.3e-05       1.7      56     101 ..      10      55 ..       3      56 .. 0.84
   2 ?    5.3   0.7    0.0013        23      19      73 ..      84     126 ..      72     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 9.3e-05
                           DUF4064  56 flstllivlgvialiaivlgivgalllkknkkvsGilfiiaailsl 101
                                        l + l+  + +++ a+vl ++++  l     v+G+lf+++ i+++
  gi|313125696|ref|YP_004035966.1|  10 QLKQDLLNNLSVSITAAVLAVLALAALTATDPVGGALFLAVNIAVF 55 
                                       55666677777899**************9999********999877 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0013
                           DUF4064  19 lglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaiv 73 
                                        ++l+++f +l             +++   +  +v++f++t+++ +g+ al a+v
  gi|313125696|ref|YP_004035966.1|  84 TAGLYIGFHVLF------------EQFVSPEFVEVAAFIGTVGVQYGITALYASV 126
                                       344444443333............6677889999*****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 806.72
//
Query:       gi|313125697|ref|YP_004035967.1|  [L=493]
Description: matrixin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-12   45.7   0.0    1.9e-07   31.1   0.0    2.3  2  Peptidase_M10  Matrixin
    0.00058   20.4   0.2     0.0017   18.9   0.1    1.9  2  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
     0.0072   16.5   0.0      0.017   15.3   0.0    1.6  1  Reprolysin_5   Metallo-peptidase family M12
  ------ inclusion threshold ------
      0.092   12.7   0.0       0.18   11.7   0.0    1.4  1  Peptidase_M43  Pregnancy-associated plasma protein-A
       0.13   12.4   2.5       0.25   11.5   2.5    1.5  1  MLTD_N         MltD lipid attachment motif
       0.18   11.8   0.0       0.38   10.7   0.0    1.4  1  Peptidase_M54  Peptidase family M54


Domain annotation for each model (and alignments):
>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   6.4e-11   1.9e-07       2     139 ..      65     337 ..      64     345 .. 0.90
   2 !   12.5   0.0   3.4e-05       0.1       2      60 ..     352     418 ..     351     452 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 6.4e-11
                                       TSSSEEEEEESSSXTTSXHHHHHHHHHHHHHHHHTTS....SSEEEEE.SSSCESEEEEEE.....SSSSSSSSSXB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx.xxxxxxxxxxxx.....xxxxxxxxxxx RF
                     Peptidase_M10   2 wekknltyrilnetpdleeeevrkairrAfkvwsevt....plkFtev.kkgeadikieFg.....rgehgdgypfd 68 
                                       w ++n++ +++ +  +    + +++ir+A++ w++      p++++ + ++ +adi ++ +      +     y+fd
  gi|313125697|ref|YP_004035967.1|  65 WGHENVSVAVSADLGTYGYGTFHEEIRTALEYWNTREntsyPVQYELTnTTYDADIVVNVEprvntCNGRRAAYSFD 141
                                       88999999999999999999*************98775666899988877889*****9997665545566799*** PP

                                       SSSSESEEEBSSSSTTTT..EEEEETTS-EESSTS-......................................... CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx........................................ RF
                     Peptidase_M10  69 gkggvlahafapgeglgg..dihfdddeqWtlgeekv........................................ 103
                                        ++ vl+ +    ++++   + ++d++e+ +++++                                          
  gi|313125697|ref|YP_004035967.1| 142 YCSDVLSAEDSIDSQIDVsmTGRYDENETRQVAKRMFaglsgtkdaeasvepdpngtpwpwqstvtvginasaggnr 218
                                       ******99999877555411567999998888876669*************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M10 104 ............................................................................. 103
                                                                                                                    
  gi|313125697|ref|YP_004035967.1| 219 dykpfvaetiayweknqdeygeyttdfelrpnepspdvevrivesipncgkndnstsdalgcasvlddgahasdtev 295
                                       ***************************************************************************** PP

                                       ......SSSEEHHHHHHHHHHHHTTBESXSSTTSTTSSSCTX CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 104 ......eqgvslflVaaHEiGHalGLeHssdkdalmyplyke 139
                                             ++  s+++   HE+GH+ GLeH + +  lm  +y++
  gi|313125697|ref|YP_004035967.1| 296 vrimydQSDESIVQTMKHEFGHLYGLEHGEGPMPLMDETYRS 337
                                       ****998889999***************************84 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.4e-05
                                       TSSSEEEEEESSSX.TTSXHHHHHHHHHHHHHHHHTTS......SSEEEEE.SSSCESEEEEEESSS CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxx.xxxxxxxxxxxxxxx RF
                     Peptidase_M10   2 wekknltyrilnet.pdleeeevrkairrAfkvwsevt......plkFtev.kkgeadikieFgrge 60 
                                       w++++l+  ++ ++ +d ++e+v+++ir+A + +++ +      +l+F+ v +  eadi+i+F++  
  gi|313125697|ref|YP_004035967.1| 352 WRSNTLSVYVDYSNiTDSDSEQVEREIRDATDYYEAGAegyvpgNLTFEYVsDPAEADITIRFYNTF 418
                                       8888888888877757799***************99999999989******88899*******9654 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.4     1e+04      56      70 ..     110     124 ..      91     132 .. 0.60
   2 !   18.9   0.1   5.7e-07    0.0017      75     123 ..     272     323 ..     255     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.4
                      Reprolysin_3  56 eaergqagyDlvhlf 70 
                                       e    ++++D+v+ +
  gi|313125697|ref|YP_004035967.1| 110 ELTNTTYDADIVVNV 124
                                       322345778887765 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 5.7e-07
                      Reprolysin_3  75 e..sgvgGlAyv...gsvcnsskkagvnsgssvlgkvgadtvaHEiGHnfganH 123
                                       +  s+ +G+A v   g+  + ++ + +++++s   ++ ++t+ HE GH  g++H
  gi|313125697|ref|YP_004035967.1| 272 NstSDALGCASVlddGAHASDTEVVRIMYDQS--DESIVQTMKHEFGHLYGLEH 323
                                       3458899******977777777779******6..88899*************** PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.6e-06     0.017     107     158 ..     276     323 ..     260     337 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.6e-06
                      Reprolysin_5 107 g.vGlAwl...gqlcnsgsagsvstrveksnsvvvstatevqvvaHElGHnfGavH 158
                                         +G+A++   g  ++++++  +  +        +s+ + vq++ HE+GH +G +H
  gi|313125697|ref|YP_004035967.1| 276 DaLGCASVlddGAHASDTEVVRIMYD--------QSDESIVQTMKHEFGHLYGLEH 323
                                       24677777444333333333333333........679999**************** PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     6e-05      0.18      33      84 ..     277     323 ..     256     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6e-05
                     Peptidase_M43  33 nsGvawyPdsGmsadgvarvvfnGaylaadststnksstLthelGhfLgLih 84 
                                       + G a   d+G  a+++  v      ++ d+ ++    t+ he+Gh+ gL+h
  gi|313125697|ref|YP_004035967.1| 277 ALGCASVLDDGAHASDTEVVRI----MY-DQSDESIVQTMKHEFGHLYGLEH 323
                                       4467777777766665554432....45.678899999*************9 PP

>> MLTD_N  MltD lipid attachment motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.5   8.5e-05      0.25      16      32 ..       1      17 [.       1      19 [. 0.96

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-05
                            MLTD_N 16 RavqisalaaaalLaGC 32
                                      ++++i+ +a ++lLaGC
  gi|313125697|ref|YP_004035967.1|  1 MRIRIALVAFLLLLAGC 17
                                      99*************** PP

>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00013      0.38     144     163 ..     306     325 ..     301     334 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHTT----S CS
                     Peptidase_M54 144 rvvkevlhelGhlyGLshCk 163
                                        +v+ + he GhlyGL h +
  gi|313125697|ref|YP_004035967.1| 306 SIVQTMKHEFGHLYGLEHGE 325
                                       689999************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3246.31
//
Query:       gi|313125698|ref|YP_004035968.1|  [L=583]
Description: dihydroxyacid dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-204  680.5   0.5   1.6e-204  680.3   0.5    1.0  1  ILVD_EDD  Dehydratase family
  ------ inclusion threshold ------
      0.085   13.0   0.7        2.1    8.5   0.0    2.4  2  DGC       DGC domain


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  680.3   0.5  1.8e-208  1.6e-204       2     517 .]      55     575 ..      54     575 .. 0.98

  Alignments for each domain:
  == domain 1  score: 680.3 bits;  conditional E-value: 1.8e-208
                          ILVD_EDD   2 piigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaq 78 
                                       p++g+an   +++pc+vhl+++a+a+ eg+ ++gg+p+ef ti++sD+i+mg+egm++sL+sRe+iadsve ++ ++
  gi|313125698|ref|YP_004035968.1|  55 PMVGVANPAADITPCNVHLDDVADAAIEGIDQSGGMPIEFGTITISDAISMGTEGMKASLISREVIADSVELVAFGE 131
                                       99*************************************************************************** PP

                          ILVD_EDD  79 llDalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaac 153
                                       +lDalv+++gCDK++Pg++ma +r+++P++f++gG++++g+++  ++++++vfe vg++a+g++s +el+e+e++ac
  gi|313125698|ref|YP_004035968.1| 132 RLDALVTVAGCDKNLPGMMMASIRTDLPSVFLYGGSIMPGEHEgrDITVQNVFEGVGTYAEGEMSADELDEMERNAC 208
                                       ***************************************88666799999*************************** PP

                          ILVD_EDD 154 pgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvll 230
                                       pgaGsC+gm+TAntma++ ealG++  gsas+pa+s+er ++a++ag+++++ ve+dl+p+diltk++feNAi++++
  gi|313125698|ref|YP_004035968.1| 209 PGAGSCGGMFTANTMASISEALGMAPLGSASAPAESKERYDVARRAGEAVLQAVENDLRPSDILTKKSFENAIAIQV 285
                                       ***************************************************************************** PP

                          ILVD_EDD 231 alGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvlt 307
                                       a+GGStNavlHllA+A ea+v+l++++fde+sr++p +a+l+P g+  m+dlh+ GG+p+v+++Ll+agl hgd++t
  gi|313125698|ref|YP_004035968.1| 286 AVGGSTNAVLHLLALAAEADVDLSIEEFDEISRRTPKIANLQPGGTKVMNDLHEEGGLPVVIRRLLDAGLFHGDAMT 362
                                       ***************************************************************************** PP

                          ILVD_EDD 308 vtgktlaenleeaev.....keqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseee 379
                                       vtg+t+ae+le+ e       +++ i p+++p+++eg +++L+GnLap+Gav+K+++ +   ++++gpArvf+ eee
  gi|313125698|ref|YP_004035968.1| 363 VTGRTIAEELEHLELpddseVSDEFIYPVDDPYQEEGAIKILTGNLAPDGAVLKVTGDD--KFHHTGPARVFEGEEE 437
                                       **********99433455558999*********************************99..7789************ PP

                          ILVD_EDD 380 aveailkgkikagdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGp 456
                                       a++ +++g+i++gdv+ ir+eGPkGgpGm+Eml +t+a++g+g +++val+tDGRfSGa++g+++ghv+PEAa+gGp
  gi|313125698|ref|YP_004035968.1| 438 AMRYVQEGHIESGDVICIRNEGPKGGPGMREMLGVTAAVVGQGHEDDVALLTDGRFSGATRGPMVGHVAPEAAVGGP 514
                                       *****99********************************************************************** PP

                          ILVD_EDD 457 ialvedGDiieidiekrtlelevseeelaaRraawkpekkvktrgllakyaklvssaseGA 517
                                       ial+edGD +++di++r+l++++ ++el+aRr++w+p+  ++++g+lakya+ + sa++GA
  gi|313125698|ref|YP_004035968.1| 515 IALLEDGDEVTVDIPNRELSVDLPDDELDARRDDWEPRDPPYSSGVLAKYANDFGSAANGA 575
                                       *************************************666667*****************8 PP

>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00024       2.1      10      62 ..      93     145 ..      87     157 .. 0.91
   2 ?    2.4   0.2     0.019   1.7e+02       4      52 ..     207     256 ..     206     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00024
                               DGC  10 nvGqlaneaavklakegeakmiclagvgagveelvelaksarkiiaidGCple 62 
                                       + G+++   a+ +  eg  + ++  +v+a++ elv++ ++ + ++++ GC+++
  gi|313125698|ref|YP_004035968.1|  93 EFGTITISDAISMGTEGMKASLISREVIADSVELVAFGERLDALVTVAGCDKN 145
                                       57999999999*****9999999999************************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.019
                               DGC   4 sCsG.asnvGqlaneaavklakegeakmiclagvgagveelvelaksark 52 
                                       +C G +s+ G+ + +++  ++++ +++ +  a++ a+++e +++a++a +
  gi|313125698|ref|YP_004035968.1| 207 ACPGaGSCGGMFTANTMASISEALGMAPLGSASAPAESKERYDVARRAGE 256
                                       7***99***************99777777777788888888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 3349.44
//
Query:       gi|313125699|ref|YP_004035969.1|  [L=229]
Description: molybdenum cofactor synthesis domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.9e-31  106.3   0.7    1.3e-30  106.0   0.7    1.1  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
       0.12   12.9   2.6       0.77   10.4   1.3    2.6  2  ATPgrasp_N     ATP-grasp N-terminal domain
          8    5.6   9.6         10    5.2   9.6    1.1  1  Zip            ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.7   2.1e-34   1.3e-30       1     144 []      78     221 ..      78     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 2.1e-34
                                       EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS..SEEEEESS-SSSTT--HH CS
                     MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea..dviittGGtGptpdDvtp 75 
                                       av+tv++++     eDt g+ l+++++  g+ev  +++v+Dd + +++++ + +++   d+i+t+GGtG+tpdDvt+
  gi|313125699|ref|YP_004035969.1|  78 AVVTVSSSRSID--EDTAGDALVDAFEGDGHEVTVRELVADDFDGVQSTVNRLVDRDdvDAIVTSGGTGVTPDDVTV 152
                                       689999999999..9***********************************555555555****************** PP

                                       HHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE....TTE.EEEE-SSHHHHHHHHHHHHHGGHHH CS
                     MoCF_biosynth  76 ealaklfekelegfeeafrrvslkpgkpvgvapgailsrav....gkt.iigLPGspkavkealeeillpaleh 144
                                       ea+ ++ +k+l+gf+e+frr+s+++     +++ +i  r++    ++t +++LPGs +a++ ++eeil+p+l+h
  gi|313125699|ref|YP_004035969.1| 153 EAVTDIATKTLPGFGELFRRLSYEE-----IGARVIATRSMagivDSTpVFCLPGSENAARLGAEEILVPELPH 221
                                       ************************9.....7777778887788996666***********************97 PP

>> ATPgrasp_N  ATP-grasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3   0.00013      0.77       5      63 ..      73     140 ..      70     159 .. 0.70
   2 ?    0.2   0.0      0.19   1.1e+03       2      16 ..     204     218 ..     203     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                       HHTT-EEEEEEETTS----S-.......TT..EEEEEEE-TTT-H.HHHHHHHHHHHHHS--SEEE-- CS
                        ATPgrasp_N   5 kaLGikvvlvdeedewapeel.......ae.lvekfipldlaqdp.daaleavralsrerpvdGivtf 63 
                                       + LG++vv v+++ + +++ +        e   +++ + +l +d+ d ++ +v++l ++++vd+ivt 
  gi|313125699|ref|YP_004035969.1|  73 ETLGVAVVTVSSSRSIDEDTAgdalvdaFEgDGHEVTVRELVADDfDGVQSTVNRLVDRDDVDAIVTS 140
                                       57999999999996554444420012111122344555555555559*******************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                                       HHHHHTT-EEEEEEE CS
                        ATPgrasp_N   2 eaAkaLGikvvlvde 16 
                                       e A++LG + +lv e
  gi|313125699|ref|YP_004035969.1| 204 ENAARLGAEEILVPE 218
                                       78******9999865 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   9.6    0.0017        10     107     160 ..      20      73 ..       4      99 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0017
                               Zip 107 kektpkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkq 160
                                       +    ++++  + es++ + ++n+ +++++ ++dh++++d++++++++++++++
  gi|313125699|ref|YP_004035969.1|  20 DGHGDSDETGGHGESDDTDGHDNHDSHDNHGDHDHGHGHDGNDSHDHHHAHDVE 73 
                                       333444555556667777777777777777777777777777777776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1452.06
//
Query:       gi|313125700|ref|YP_004035970.1|  [L=262]
Description: hypothetical protein Hbor_09310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00049   19.9   0.2    0.00096   19.0   0.2    1.4  1  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0019   17.9   0.1     0.0041   16.8   0.1    1.5  1  RP-C       Replication protein C N-terminal domain
     0.0021   18.1   0.8     0.0073   16.3   0.8    2.0  1  HTH_20     Helix-turn-helix domain
     0.0083   16.1   0.5      0.021   14.8   0.5    1.7  1  HTH_Crp_2  Crp-like helix-turn-helix domain
     0.0085   15.7   0.4      0.019   14.6   0.4    1.5  1  GntR       Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.034   14.1   0.0    1.4  1  HTH_45     Winged helix-turn-helix
      0.051   13.4   0.2       0.24   11.3   0.2    2.0  2  HTH_5      Bacterial regulatory protein, arsR family
      0.069   13.0   2.3      0.093   12.6   1.2    1.7  2  MarR_2     MarR family
      0.088   12.7   0.0       0.17   11.8   0.0    1.4  1  MarR       MarR family
       0.19   12.1   0.0        0.4   11.0   0.0    1.5  1  HTH_55     RctB helix turn helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   5.3e-07   0.00096      20      59 ..      24      63 ..      16      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.3e-07
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                      l+  + +e+ e ++ +rs+v +++r+L+d GlV+ ++gr+
  gi|313125700|ref|YP_004035970.1| 24 LEAHSKRELTEVVESSRSTVDRAIRELLDVGLVTQRDGRY 63
                                      5666789****************************99986 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.3e-06    0.0041      72     106 ..      27      61 ..      11      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                              RP-C  72 psNaqLsralglsestlrrhlaaLveaGliirrDs 106
                                        s ++L + +  s+st+ r +++L ++Gl++ rD 
  gi|313125700|ref|YP_004035970.1|  27 HSKRELTEVVESSRSTVDRAIRELLDVGLVTQRDG 61 
                                       6889999***************************6 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.8   4.1e-06    0.0073      15      59 ..      18      61 ..      14      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.1e-06
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +lra    e+++  el e ++ s++t+++ +r+L ++gLv++++ 
  gi|313125700|ref|YP_004035970.1| 18 VLRAV-VLEAHSKRELTEVVESSRSTVDRAIRELLDVGLVTQRDG 61
                                      78888.88999999***************************9975 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.5   1.2e-05     0.021      22      55 ..      27      62 ..      11      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E.TE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis.r.gr 55
                                       +++el + + ++r+tv r+++eL + gl++ r gr
  gi|313125700|ref|YP_004035970.1| 27 HSKRELTEVVESSRSTVDRAIRELLDVGLVTqRdGR 62
                                      5899***************************64334 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.4     1e-05     0.019      27      60 ..      29      62 ..      25      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverrqgr 60
                                       reL +  + sr+tv +A+r+L   glv+ r+gr
  gi|313125700|ref|YP_004035970.1| 29 KRELTEVVESSRSTVDRAIRELLDVGLVTQRDGR 62
                                      599**************************99986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.034      21      74 ..      28      81 ..      16      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                            HTH_45 21 kkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkelee 74
                                      +k ++   ++ s +++++ +  L++ gl++++++ Y+ T  G+  le ++ ++e
  gi|313125700|ref|YP_004035970.1| 28 SKRELTEVVESSRSTVDRAIRELLDVGLVTQRDGRYEATLAGECALEAVEAFHE 81
                                      5555555556667788999*****************************999987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00014      0.24       7      46 ..      18      57 ..      14      58 .. 0.84
   2 ?   -0.7   0.0      0.77   1.4e+03      26      37 ..     139     150 ..     135     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                      HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +L+++  + ++  el+e ++ s+stv++  + L + GLV+
  gi|313125700|ref|YP_004035970.1| 18 VLRAVVLEAHSKRELTEVVESSRSTVDRAIRELLDVGLVT 57
                                      56666666667789*************************6 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.77
                                       TS-HHHHHHHHH CS
                             HTH_5  26 glsqstvShHLk 37 
                                       g+ ++ +S HLk
  gi|313125700|ref|YP_004035970.1| 139 GVAPAVLSGHLK 150
                                       688999*****9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.2   5.2e-05     0.093       9      56 ..      17      61 ..      10      63 .. 0.85
   2 ?   -3.0   0.0         4   7.2e+03       9      21 ..     170     183 ..     167     199 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +vL a+  +     + +el++    s+s+v r++++L + GLv++r+g
  gi|313125700|ref|YP_004035970.1| 17 QVLRAVVLEAH---SKRELTEVVESSRSTVDRAIRELLDVGLVTQRDG 61
                                      67777777774...889***************************9954 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                                       HHHHHHHCTTTS.E CS
                            MarR_2   9 rvLaaLgrrpgr.d 21 
                                       +vL  L ++p   d
  gi|313125700|ref|YP_004035970.1| 170 DVLDQLIAAPSTrD 183
                                       78888888875444 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.4e-05      0.17      16      48 ..      25      57 ..      23      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.4e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +++s  eL + ++ s+stv r++++L + Gl++
  gi|313125700|ref|YP_004035970.1| 25 EAHSKRELTEVVESSRSTVDRAIRELLDVGLVT 57
                                      678889*************************98 PP

>> HTH_55  RctB helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00022       0.4      64      99 ..      38      73 ..      20      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                            HTH_55 64 ltraaiqqrlraavsiglfeqlpvrfeeglagktml 99
                                       +r+++++ +r  +++gl +q   r+e  lag   l
  gi|313125700|ref|YP_004035970.1| 38 SSRSTVDRAIRELLDVGLVTQRDGRYEATLAGECAL 73
                                      3588889999**********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1724.07
//
Query:       gi|313125701|ref|YP_004035971.1|  [L=346]
Description: zn-dependent oxidoreductase, NADph:quinone reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-37  128.1   0.2    7.2e-37  126.3   0.1    1.9  2  ADH_zinc_N      Zinc-binding dehydrogenase
      8e-22   78.7   0.0    1.5e-21   77.9   0.0    1.4  1  ADH_zinc_N_2    Zinc-binding dehydrogenase
    8.8e-21   73.8   0.0    1.9e-20   72.8   0.0    1.6  1  ADH_N           Alcohol dehydrogenase GroES-like domain
      7e-05   22.4   1.1    0.00016   21.2   0.8    1.6  2  adh_short       short chain dehydrogenase
    0.00023   20.5   0.2    0.00047   19.5   0.2    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0012   18.9   0.2     0.0027   17.8   0.2    1.5  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.024   15.1   0.2      0.046   14.2   0.2    1.4  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
       0.22   11.7   1.7       0.88    9.8   0.3    2.5  3  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.84   1.9e+03      77     121 ..      77     124 ..      64     129 .. 0.66
   2 !  126.3   0.1   3.2e-40   7.2e-37       1     128 [.     178     304 ..     178     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.84
                                       HCEEEEEEEEECSC.TSSEEE...EEHHHHHHTT-EEEEE-SSCHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGg.gkgeee...fdlrnlllkeksilGsllgslreef 121
                                       +   pg r+++++g   g+++    +  + l ++ +++G ++ +++ e+
  gi|313125701|ref|YP_004035971.1|  77 TRFEPGDRVALIAGvA-GDDTefsRKGDPTLSHDYHLIGEHVRGVHAEY 124
                                       5567888999999953.44433455566678888888888887766665 PP

  == domain 2  score: 126.3 bits;  conditional E-value: 3.2e-40
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG+aavq+A ++Gaev+a++s++ekl++a++ Gad++iny e d+ ++i+e+t+++gvd v++++G ++t++++lk
  gi|313125701|ref|YP_004035971.1| 178 GVGHAAVQIADHAGAEVYATASTDEKLAYAEECGADHTINYAENDFAAEIREMTDKRGVDMVVDHIG-EETYQDSLK 253
                                       9****************************************555***********************.********* PP

                                       CEEEEEEEEECSCTSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  78 llkpgGrlvvvGggkgeee.fdlrnlllkeksilGsllgslreefkealdll 128
                                       +l++gGr+v++G+ +g+++   l++++ k++s++Gs++++ + +  eal+l+
  gi|313125701|ref|YP_004035971.1| 254 SLRKGGRIVTCGATTGPNPdAGLNRIFWKQLSVIGSTMAT-PGQADEALKLV 304
                                       *************7777777********************.99999999987 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   6.5e-25   1.5e-21       2     133 .]     211     340 ..     210     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 6.5e-25
                                       T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EE CS
                      ADH_zinc_N_2   2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsv 73 
                                       GAd+ i+y + df+    + t+++gvD v+d +g e++ ++slk l++gGr+v+ g  +    + + ++ ++k+ sv
  gi|313125701|ref|YP_004035971.1| 211 GADHTINYAENDFAaeirEMTDKRGVDMVVDHIGEETY-QDSLKSLRKGGRIVTCGaTTGPNPDAGLNRIFWKQLSV 286
                                       9*************9**999999*************99.*******888*****99443344444455555666666 PP

                                       EE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  74 kyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                         +++   +++   +  +e ++l+ +G+++p++  v+p++eaa+Ah+ le++  +GK+Vl
  gi|313125701|ref|YP_004035971.1| 287 IGSTMA--TPG---Q-ADEALKLVWDGTFEPRIRDVLPMSEAARAHEMLENREGFGKVVL 340
                                       666665..344...5.56*****************************************8 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.0   8.4e-24   1.9e-20       2     109 .]      28     135 ..      27     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 8.4e-24
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       gev+++vkaa++++ D+++ +g+  l  ++p i+G +++G+v+evg++v++++ GdrV++ + ++  + +  ++g++
  gi|313125701|ref|YP_004035971.1|  28 GEVVVDVKAAALNHLDIWTRRGMPILDLEMPHIPGSDMAGVVHEVGEGVTRFEPGDRVALIAGVAGDDTEFSRKGDP 104
                                       79*************************************************************************** PP

                                       GG-TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                             ADH_N  79 nlCeeakllgvsldGgfaeyvvvpekklvkl 109
                                       +l ++++l+g +++G +aey +vp+++lv++
  gi|313125701|ref|YP_004035971.1| 105 TLSHDYHLIGEHVRGVHAEYACVPASNLVPV 135
                                       ****************************986 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.8   7.1e-08   0.00016       3      59 ..     170     224 ..     168     255 .. 0.76
   2 ?   -1.9   0.0      0.85   1.9e+03     126     144 ..     256     274 ..     246     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.1e-08
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTT CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvt 59 
                                       vlv Gas+G+G+a ++    +Ga+v+++++++ekl + a+e++++  ++ +++ D +
  gi|313125701|ref|YP_004035971.1| 170 VLVLGASGGVGHAAVQIADHAGAEVYATASTDEKL-AYAEECGAD-HTINYAENDFA 224
                                       9*********************************9.899999986.45555555544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.85
                                       CTTEEEEEEEEGGGTSB-T CS
                         adh_short 126 qssGrIvnvsSvagkvpva 144
                                       +++GrIv+ + ++g +p a
  gi|313125701|ref|YP_004035971.1| 256 RKGGRIVTCGATTGPNPDA 274
                                       689*****99999977765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   2.1e-07   0.00047      30      91 ..     169     229 ..     148     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.1e-07
                                       EEEEEST.SHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH CS
                       AlaDh_PNT_C  30 kvlviGg.GvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavke 91 
                                        vlv+G+ G +G +A+++a   ga+V+++    ++l + e++ga   ++++  e+ +a +++e
  gi|313125701|ref|YP_004035971.1| 169 SVLVLGAsGGVGHAAVQIADHAGAEVYATASTDEKLAYAEECGAD--HTINYAENDFAAEIRE 229
                                       699***8799**********************************9..6766666666666655 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   1.2e-06    0.0027       2     101 ..     169     270 ..     168     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                                       EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH..-SEEEE-S- CS
                            DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek..advliDFTt 76 
                                       +v+v+GasG +G++ v+ +++ +++e+ a  +++e+ + +++ g    ++  +  + +++ e+++k  +d+++D   
  gi|313125701|ref|YP_004035971.1| 169 SVLVLGASGGVGHAAVQIADH-AGAEVYATASTDEKLAYAEECGADHTINYAENDFAAEIREMTDKrgVDMVVDHIG 244
                                       599**************9998.9*******99999999999999999999888899999*****9999*******99 PP

                                       HHHHHHHHHHHHHTT-EEEE-.-SS- CS
                            DapB_N  77 peavlenlklalekgvklViG.TTGl 101
                                        e   + lk + + g  + +G TTG 
  gi|313125701|ref|YP_004035971.1| 245 EETYQDSLKSLRKGGRIVTCGaTTGP 270
                                       99888888888877666656546665 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2     2e-05     0.046       2      92 ..     170     261 ..     169     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG..GGTTTECEBEEE..GGGGGCTT-SEEEE-S CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk..aleegkdlkved..vdeeelkevdivflal 74 
                                       v ++Ga+G vG + +++ ++h  +e+ + ++s+  +  ++ae ++  ++ ++++  + +   ++ + ++vd+v+   
  gi|313125701|ref|YP_004035971.1| 170 VLVLGASGGVGHAAVQI-ADHAGAEVYA-TASTD-EKLAYAEECGadHTINYAENDFAAeiREMTDKRGVDMVVDHI 243
                                       88*************97.5667776666.55555.588888888888666666666666447777779********* PP

                                       CHHHHHHHHHHHHHTTSE CS
                    Semialdhyde_dh  75 pagvskelapklaeagvk 92 
                                       ++++ ++  ++l++ g +
  gi|313125701|ref|YP_004035971.1| 244 GEETYQDSLKSLRKGGRI 261
                                       **9999999999888765 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.74   1.7e+03      65      80 ..      78      93 ..      66      95 .. 0.78
   2 ?    9.8   0.3   0.00039      0.88      56      86 ..     154     184 ..     144     187 .. 0.84
   3 ?   -2.3   0.0       2.3   5.1e+03      65      80 ..     254     269 ..     249     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.74
                                      SS-TT-EEEEEEEETT CS
                     ACP_syn_III_C 65 klkpgdlvllvgfGaG 80
                                      +++pgd+v+l++  aG
  gi|313125701|ref|YP_004035971.1| 78 RFEPGDRVALIAGVAG 93
                                      899*****99985555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00039
                                       HHHHHHHTTSS-TT-EEEEEEEETTTEEEEE CS
                     ACP_syn_III_C  56 aLdeaveegklkpgdlvllvgfGaGltwgaa 86 
                                       a   +v++g+l+pg+ vl++g+ +G+  +a+
  gi|313125701|ref|YP_004035971.1| 154 AWRMLVDRGELRPGESVLVLGASGGVGHAAV 184
                                       5567899******************998887 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                                       SS-TT-EEEEEEEETT CS
                     ACP_syn_III_C  65 klkpgdlvllvgfGaG 80 
                                        l++g +++++g+  G
  gi|313125701|ref|YP_004035971.1| 254 SLRKGGRIVTCGATTG 269
                                       689999****999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2241.13
//
Query:       gi|313125702|ref|YP_004035972.1|  [L=103]
Description: hypothetical protein Hbor_09330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 638.12
//
Query:       gi|313125703|ref|YP_004035973.1|  [L=116]
Description: hypothetical protein Hbor_09340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 785.27
//
Query:       gi|313125704|ref|YP_004035974.1|  [L=298]
Description: hypothetical protein Hbor_09350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-30  104.3   6.2    5.6e-30  104.3   6.2    2.2  1  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac
    3.2e-09   37.2   1.9    3.2e-09   37.2   1.9    2.2  2  baeRF_family10   Bacterial archaeo-eukaryotic release factor 
    9.9e-05   22.7   0.0     0.0002   21.7   0.0    1.6  1  eRF1_2           eRF1 domain 2
     0.0063   14.4  12.9       0.01   13.7  12.9    1.2  1  Myosin_tail_1    Myosin tail
  ------ inclusion threshold ------
      0.014   14.9   3.5      0.024   14.2   3.5    1.3  1  Leu_zip          Leucine zipper
      0.037   14.3   4.9        1.5    9.2   0.1    2.6  2  TSC22            TSC-22/dip/bun family
       0.11   12.9  11.2      0.063   13.6   2.3    2.7  2  CLZ              C-terminal leucine zipper domain of cyclic n
        0.2   11.6  10.1       0.79    9.6   4.7    2.4  2  eIF3_subunit     Translation initiation factor eIF3 subunit
       0.21   10.2   2.2       0.33    9.5   2.2    1.2  1  AAA_13           AAA domain
       0.22   11.4   6.3       0.33   10.8   6.3    1.2  1  Mei5             Double-strand recombination repair protein
       0.25   11.1   8.9       0.21   11.4   0.8    2.4  2  DivIC            Septum formation initiator
       0.57    9.0   4.5       0.88    8.4   4.5    1.2  1  Spc7             Spc7 kinetochore protein
        0.7   10.6   6.2        2.1    9.1   3.6    2.1  2  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.79    9.7   5.8        4.7    7.2   0.9    2.7  2  Pox_A_type_inc   Viral A-type inclusion protein repeat
        1.1    9.2   5.5        6.7    6.7   0.5    2.8  2  WD40_alt         Alternative WD40 repeat motif
        1.4    7.9   3.6        2.5    7.1   3.6    1.3  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        1.5    9.1   7.1        5.3    7.3   2.5    2.4  2  MID_pPIWI_RE     MID domain of pPIWI_RE
        1.5    7.5   4.8       0.66    8.8   2.5    1.5  2  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        2.3    7.2   5.2        3.8    6.5   5.2    1.2  1  YdfA_immunity    SigmaW regulon antibacterial
        4.2    7.7  17.4        1.3    9.3  13.2    2.2  3  ABC_tran_CTD     ABC transporter C-terminal domain
        7.9    6.4   9.1         23    4.9   9.0    1.8  1  Ax_dynein_light  Axonemal dynein light chain


Domain annotation for each model (and alignments):
>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   6.2   6.6e-33   5.6e-30       2     129 ..     177     295 ..     176     296 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 6.6e-33
                           acVLRF1   2 rlgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.v 77 
                                       ++ v+lvr+++favgv++g+ ++ + + ++dv++ +++GG+Sq+Rf+Rrr++q++++l+++++a+a+   e++a+ +
  gi|313125704|ref|YP_004035974.1| 177 PVRVALVRSDLFAVGVYDGESVTLVDEVESDVMNAHSKGGFSQARFERRRDEQVENHLDRAKDALAAN--ENAADgL 251
                                       799***************************************************************44..566667* PP

                           acVLRF1  78 vlgGdrslvaevledarlaplatlareelldvpdprravLedavrraravrv 129
                                       v+ G+r+++ ++++ a+    + ++++   + +dp +++L+ avr+++++r+
  gi|313125704|ref|YP_004035974.1| 252 VVLGERTVLGDFRAMAD----HVATVD---ASGDP-EDALRAAVREFWTTRL 295
                                       ***************88....899999...99***.*************996 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.5         2   1.7e+03      50      61 ..      29      40 ..       8      90 .. 0.58
   2 !   37.2   1.9   3.7e-12   3.2e-09      13     106 ..     175     265 ..     172     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2
                    baeRF_family10 50 tktggwksqdrf 61
                                       +++  ++ + +
  gi|313125704|ref|YP_004035974.1| 29 AEAEEERRAAAV 40
                                      222222211111 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 3.7e-12
                    baeRF_family10  13 yerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellaklleergv 89 
                                        e++ v+lv+ + +++ ++ + ++  v+eve++v +++ +gg  sq+rf+rr++eq+e hl+++ ++la  ++e+ +
  gi|313125704|ref|YP_004035974.1| 175 EEPVRVALVRSDLFAVGVYDGESVTLVDEVESDVMNAHSKGGF-SQARFERRRDEQVENHLDRAKDALA--ANENAA 248
                                       57889**************************************.**********************996..79999* PP

                    baeRF_family10  90 erlvlgGdeeetaalld 106
                                       + lv+ G + +   +++
  gi|313125704|ref|YP_004035974.1| 249 DGLVVLGERTVLGDFRA 265
                                       *******9998887765 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.3e-07    0.0002       8      64 ..     184     240 ..     178     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.3e-07
                                       ETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHH CS
                            eRF1_2   8 degeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaea 64 
                                         ++  +g+  g+++++++++e++v   h +Gg s++rfeR r+e++e+ l++  +a
  gi|313125704|ref|YP_004035974.1| 184 RSDLFAVGVYDGESVTLVDEVESDVMNAHSKGGFSQARFERRRDEQVENHLDRAKDA 240
                                       566667899999*************************************99876554 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7  12.9   1.2e-05      0.01      63     119 ..       8      64 ..       4      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                     Myosin_tail_1  63 RaRLaarkqeleeilhdleaRleeeeeraqqlqsekkkmqqniqdleeqldeeeaaR 119
                                       Ra+L+ar +elee  h le R e eeer ++  +++++ +++++ le+++ e e+  
  gi|313125704|ref|YP_004035974.1|   8 RAKLKARIEELEEEKHHLERRAEAEEERRAAAVKDRQEAEAEVNRLEDRITELEDRV 64 
                                       9**************************************************999865 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   3.5   2.8e-05     0.024     129     183 ..       9      63 ..       2      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                           Leu_zip 129 eLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkde 183
                                       + Lk  ie+L+ee ++L+ r +  E++   a++++++ e+++++l+++++e +d+
  gi|313125704|ref|YP_004035974.1|   9 AKLKARIEELEEEKHHLERRAEAEEERRAAAVKDRQEAEAEVNRLEDRITELEDR 63 
                                       56999****************************************9999887765 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.3      0.02        17      18      36 ..      10      28 ..       9      35 .. 0.89
   2 ?    9.2   0.1    0.0018       1.5      15      33 ..      49      67 ..      46      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.02
                             TSC22 18 vLkekIkeLeernseleeE 36
                                       Lk +I eLee+ ++le+ 
  gi|313125704|ref|YP_004035974.1| 10 KLKARIEELEEEKHHLERR 28
                                      59**************985 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0018
                             TSC22 15 eVevLkekIkeLeernsel 33
                                      eV+ L ++I+eLe+r+s+l
  gi|313125704|ref|YP_004035974.1| 49 EVNRLEDRITELEDRVSRL 67
                                      9***************998 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.039        34      59      71 .]       9      21 ..       5      21 .. 0.89
   2 ?   13.6   2.3   7.3e-05     0.063      17      53 ..      34      70 ..      25      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.039
                               CLZ 59 rkLkqRitkLEkk 71
                                      +kLk+Ri++LE++
  gi|313125704|ref|YP_004035974.1|  9 AKLKARIEELEEE 21
                                      7**********85 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.3e-05
                               CLZ 17 eeaakagaeqkeleekverLessLeaLqtrlarLlae 53
                                      e+ a+a ++++e+e  v+rLe ++  L++r+ rL ++
  gi|313125704|ref|YP_004035974.1| 34 ERRAAAVKDRQEAEAEVNRLEDRITELEDRVSRLGGD 70
                                      33566779*************************9765 PP

>> eIF3_subunit  Translation initiation factor eIF3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.7   0.00092      0.79      63     139 ..      19      99 ..       7     110 .. 0.56
   2 ?    4.7   0.2     0.029        25      99     153 ..     219     270 ..     202     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00092
                      eIF3_subunit  63 akkkkskkqkiaeke........errkaeeeeaeeeeeleeedeaarkerlrkaeeesDlknaadlFGgvattketd 131
                                        ++k  ++ + + +e         r++ae+e ++ e+ ++e++++ ++ +    e e D++ ++dlFG   +  ++ 
  gi|313125704|ref|YP_004035974.1|  19 EEEKHHLERRAEAEEerraaavkDRQEAEAEVNRLEDRITELEDRVSR-LGGDDEAELDYRGTEDLFG---ERRDEI 91 
                                       222222222222222233444433334444445555556666555544.455678999**********...447777 PP

                      eIF3_subunit 132 lssldlfn 139
                                       ls l++f 
  gi|313125704|ref|YP_004035974.1|  92 LSRLESFS 99 
                                       77777775 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.029
                      eIF3_subunit  99 aarkerlrkaeeesDlknaadlFGgvattketdlssldlf.npktkedFeelrkal 153
                                       +ar er+r ++ e +l+ a+d++++    +e+++++l  + + +   dF ++++ +
  gi|313125704|ref|YP_004035974.1| 219 QARFERRRDEQVENHLDRAKDALAA----NENAADGLVVLgERTVLGDFRAMADHV 270
                                       67889******************93....555555555543555566666666655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.2   0.00039      0.33     406     468 ..      10      65 ..       4      85 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00039
                            AAA_13 406 eleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLk 468
                                       +l++ ++e+++++  le+ +e  e++ +++ ++ +++e+e++ Le ++++ +  +       +
  gi|313125704|ref|YP_004035974.1|  10 KLKARIEELEEEKHHLERRAEAEEERRAAAVKDRQEAEAEVNRLEDRITELEDRV-------S 65 
                                       5566666666666666666666666666666666666666666666665555444.......3 PP

>> Mei5  Double-strand recombination repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.3   0.00038      0.33     112     167 ..       9      63 ..       3      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                                       ....XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHH CS
                              Mei5 112 ekielekkeLeeekakLekqvrekeelLrrLklvkkyeskndlseLqllikkwrna 167
                                       +k++ +++eLeeek  Le+  +  ee+ r++ +++++e++ +++ L+ +i +++++
  gi|313125704|ref|YP_004035974.1|   9 AKLKARIEELEEEKHHLERRAE-AEEERRAAAVKDRQEAEAEVNRLEDRITELEDR 63 
                                       67888899***********975.5666799********************999875 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.7      0.12     1e+02      34      56 ..       9      30 ..       8      39 .. 0.58
   2 ?   11.4   0.8   0.00025      0.21      25      56 ..      42      72 ..      34      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                                      HHHHHHHHHHHHHHCC-XXXXXX CS
                             DivIC 34 aklkaeneeLeaevkdLksdedy 56
                                      aklka++eeLe+e   L+  ++ 
  gi|313125704|ref|YP_004035974.1|  9 AKLKARIEELEEEKHHLE-RRAE 30
                                      466666666666666663.3333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00025
                                      HHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                             DivIC 25 eiaalqaelaklkaeneeLeaevkdLksdedy 56
                                      ++++ +ae+++l +++ eLe++v++L  ++d 
  gi|313125704|ref|YP_004035974.1| 42 DRQEAEAEVNRLEDRITELEDRVSRL-GGDDE 72
                                      67899*********************.55554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.5     0.001      0.88     231     280 ..      10      62 ..       4      76 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                              Spc7 231 eleekieelkeqkseleeeiaeaervle...eckgwsesevsrlkeevkalee 280
                                       +l+++ieel+e+k++le + +++e+ +    + ++  e ev+rl+++  +le+
  gi|313125704|ref|YP_004035974.1|  10 KLKARIEELEEEKHHLERRAEAEEERRAaavKDRQEAEAEVNRLEDRITELED 62 
                                       45555555555555555544433333321113455555566666666666554 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.6    0.0024       2.1      14      74 ..      10      69 ..       3      73 .. 0.76
   2 ?    1.8   0.0      0.45   3.9e+02      39      92 ..     212     269 ..     179     273 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                           DUF2203 14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGv 74
                                      +lk ++eel + +++le+++ e ee++++a+ ++++e+eae+++le++i el +++++lG 
  gi|313125704|ref|YP_004035974.1| 10 KLKARIEELEEEKHHLERRA-EAEEERRAAAVKDRQEAEAEVNRLEDRITELEDRVSRLGG 69
                                      46777777777777777744.45555555566679999************99999999985 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.45
                           DUF2203  39 akaeaekse.......aaeleaeleeleaeieelve..eieelGvevkdleaglvDFpakldg 92 
                                       +++     +       ++++ +++e+  ++++++++  e  + G +v + + +l DF a  d+
  gi|313125704|ref|YP_004035974.1| 212 HSK-----GgfsqarfERRRDEQVENHLDRAKDALAanENAADGLVVLGERTVLGDFRAMADH 269
                                       222.....1222235677777777777777777665114455688888988999999887776 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.053        45       6      15 ..      11      20 ..       9      21 .. 0.86
   2 ?    7.2   0.9    0.0055       4.7       2      14 ..      49      61 ..      48      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.053
                    Pox_A_type_inc  6 lRsRIsDLEr 15
                                      l+ RI++LE 
  gi|313125704|ref|YP_004035974.1| 11 LKARIEELEE 20
                                      899******6 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0055
                    Pox_A_type_inc  2 EmsrlRsRIsDLE 14
                                      E++rl +RI +LE
  gi|313125704|ref|YP_004035974.1| 49 EVNRLEDRITELE 61
                                      9***********9 PP

>> WD40_alt  Alternative WD40 repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5    0.0078       6.7      10      29 ..       6      24 ..       4      27 .. 0.80
   2 ?    3.8   0.5     0.063        54      14      30 ..      51      67 ..      45      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0078
                          WD40_alt 10 lGdqeqlkvrvseLeeEVrt 29
                                      lG   +lk r+ eLeeE + 
  gi|313125704|ref|YP_004035974.1|  6 LGRA-KLKARIEELEEEKHH 24
                                      5655.8***********665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.063
                          WD40_alt 14 eqlkvrvseLeeEVrtL 30
                                      ++l  r++eLe+ V+ L
  gi|313125704|ref|YP_004035974.1| 51 NRLEDRITELEDRVSRL 67
                                      67888*******99876 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.6    0.0029       2.5      38      97 ..       8      64 ..       3      70 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0029
                             Atg14 38 keslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97
                                      ++ lk +ie+++e+k+    le++++ + ++     +++++ ++++++l+d++++l +++
  gi|313125704|ref|YP_004035974.1|  8 RAKLKARIEELEEEKH---HLERRAEAEEERRAAAVKDRQEAEAEVNRLEDRITELEDRV 64
                                      7789999999999999...56666666666666666666666666777777776666654 PP

>> MID_pPIWI_RE  MID domain of pPIWI_RE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.5    0.0062       5.3      25      62 ..      15      55 ..       2      67 .. 0.74
   2 ?    3.9   0.2     0.072        62      28      93 ..     221     286 ..     199     289 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0062
                      MID_pPIWI_RE 25 l.klpevtrrperllaaikekrr.rvkereealaqllg.ra 62
                                      + +l+e +++ er+++a +e+r  +vk+r+ea a+  + ++
  gi|313125704|ref|YP_004035974.1| 15 IeELEEEKHHLERRAEAEEERRAaAVKDRQEAEAEVNRlED 55
                                      357788888888888888888888******99998877544 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.072
                      MID_pPIWI_RE  28 pevtrrperllaaikekrrrvkereealaqllgraerptl..alveiegkskakkrsdsDPKfalRlg 93 
                                       +  +rr+e+++++++  ++++++ e+a++ l+   er+ l     ++++   a  +++ DP  alR +
  gi|313125704|ref|YP_004035974.1| 221 RFERRRDEQVENHLDRAKDALAANENAADGLVVLGERTVLgdFRAMADHV--ATVDASGDPEDALRAA 286
                                       56788999999999999999999999999999888888888444444444..7788888888888876 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.5   0.00077      0.66     176     236 ..      11      67 ..       4     100 .. 0.72
   2 ?   -2.6   0.0       2.2   1.9e+03     162     199 ..     209     246 ..     204     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00077
                        Fmp27_WPPW 176 leeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledl 236
                                       l+ R+eelee+ ++le++ e  e+++        ++ +e e e+++l+++++ le+ +++l
  gi|313125704|ref|YP_004035974.1|  11 LKARIEELEEEKHHLERRAEAEEERRAAA----VKDRQEAEAEVNRLEDRITELEDRVSRL 67 
                                       78999999999999999999888888874....4444445555555555555555555555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                        Fmp27_WPPW 162 lgkendpervqkelleeRleeleeqiekleekleelel 199
                                       ++++ +    q++  ++R e++e+++++ +++l  +e+
  gi|313125704|ref|YP_004035974.1| 209 MNAHSKGGFSQARFERRRDEQVENHLDRAKDALAANEN 246
                                       55555555667888888899999999888888887776 PP

>> YdfA_immunity  SigmaW regulon antibacterial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.2    0.0044       3.8     239     276 ..      26      64 ..       7      67 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0044
                     YdfA_immunity 239 iaqaka.eerramavakeqemkakvqemrakvveaeaev 276
                                         +a+a eerra+av   qe +a+v++ + ++ e e +v
  gi|313125704|ref|YP_004035974.1|  26 ERRAEAeEERRAAAVKDRQEAEAEVNRLEDRITELEDRV 64 
                                       3466762579*****************999999988776 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  13.2    0.0015       1.3      12      68 ..      10      61 ..       4      63 .. 0.92
   2 ?    6.3   2.1     0.013        12      12      32 ..      45      65 ..      33      75 .. 0.68
   3 ?   -1.6   0.1       3.8   3.2e+03       6      28 ..     223     245 ..     220     249 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                      ABC_tran_CTD 12 eleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeLe 68
                                      +l a+Ie+LEee+  le + +++e     e+ a++ +  +e+eae ++l++r  eLe
  gi|313125704|ref|YP_004035974.1| 10 KLKARIEELEEEKHHLERRAEAEE-----ERRAAAVKDRQEAEAEVNRLEDRITELE 61
                                      799******************998.....8889999999999*********999998 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                      ABC_tran_CTD 12 eleaeIeaLEeeiaeleaela 32
                                      e eae ++LE +i+ele++++
  gi|313125704|ref|YP_004035974.1| 45 EAEAEVNRLEDRITELEDRVS 65
                                      456667777777777776665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.8
                      ABC_tran_CTD   6 eqreleeleaeIeaLEeeiaele 28 
                                       e+r+ e++e+++++    +a+ e
  gi|313125704|ref|YP_004035974.1| 223 ERRRDEQVENHLDRAKDALAANE 245
                                       66666777777777776666655 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   9.0     0.026        23     120     169 ..       7      55 ..       1      68 [. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.026
                   Ax_dynein_light 120 gkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkhee 169
                                       g+++l+++i+eLeeek  le++ +  +++ +a+ k+ +e ++e ++  e+
  gi|313125704|ref|YP_004035974.1|   7 GRAKLKARIEELEEEKHHLERRAEAEEERRAAAVKDRQEAEAEVNRL-ED 55 
                                       67888999999999999999998887777777766666665555443.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1471  (0.0820458); expected 358.6 (0.02)
Passed bias filter:                      867  (0.0483574); expected 358.6 (0.02)
Passed Vit filter:                       194  (0.0108205); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 1653.66
//
Query:       gi|313125705|ref|YP_004035975.1|  [L=356]
Description: hypothetical protein Hbor_09360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-75  252.8   0.1    2.1e-75  252.4   0.1    1.2  1  DUF1611       Domain of unknown function (DUF1611_C) P-loop d
      1e-27   96.1   0.0    3.1e-27   94.6   0.0    1.8  2  DUF1611_N     Domain of unknown function (DUF1611_N) Rossmann
    0.00069   19.5   0.1       0.23   11.3   0.0    2.3  2  AAA_26        AAA domain
  ------ inclusion threshold ------
      0.055   14.3   0.0       0.17   12.7   0.0    1.8  1  GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fol
       0.42   10.9   1.4         27    5.1   0.0    3.2  3  PCP_red       Proto-chlorophyllide reductase 57 kD subunit


Domain annotation for each model (and alignments):
>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.4   0.1   5.9e-79   2.1e-75       2     200 .]     150     350 ..     149     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 252.4 bits;  conditional E-value: 5.9e-79
                           DUF1611   2 vadgkarevkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgiliagegvvldavvvdfvaGavegl 78 
                                       va+gka+ev+a++vl+vGTdc+vGK+t +lel ea++erG++a+f++Tgqtgi+i+g+g ++d+v++df+aGave++
  gi|313125705|ref|YP_004035975.1| 150 VAQGKAAEVDADIVLTVGTDCSVGKMTVSLELVEAARERGIDAGFIPTGQTGIMISGWGNPIDRVISDFTAGAVEEM 226
                                       799************************************************************************** PP

                           DUF1611  79 vkkaaeeeepdlilveGQgsLthpaysgvtlglLlGsqPdalvLchrpgrkhirglpeialppleeeieliealaak 155
                                       ++++ +  + d+++veGQgs+thpays+vt+g+L+G++PdalvLch +gr+hi+g++++++ p++++++l+e+l+++
  gi|313125705|ref|YP_004035975.1| 227 ILEVGD--DYDVLFVEGQGSITHPAYSAVTCGILHGAMPDALVLCHVAGREHIHGYDSFDISPISKYVDLYESLSEP 301
                                       *****6..559****************************************************************** PP

                           DUF1611 156 k...kvvgislNtknls.eeeakealeeleeelglpvvdpvregaeklv 200
                                           +vv+ +lNt++++ + ea++a+e++++elg p++d+vr+ a++++
  gi|313125705|ref|YP_004035975.1| 302 VhesSVVAGALNTSHIDdDSEARAAVESYADELGAPATDIVRFDADEIL 350
                                       999*************95667************************9986 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.0   8.8e-31   3.1e-27       2      94 .]      53     144 ..      52     144 .. 0.98
   2 ?   -3.0   0.0       2.5   8.9e+03      21      32 ..     180     191 ..     163     205 .. 0.58

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 8.8e-31
                         DUF1611_N   2 ekaGkdagelldd.rgipvvssleealaagaevlviGiapeggklpeswreavkeAleaGldvvsGlHerLsddpel 77 
                                       ++ G++a+++ dd  ++p+v+s+++a  ++a++l+iGiap gg ++e+wr +v++A+e+ +dv+sGlH++L+dd+e+
  gi|313125705|ref|YP_004035975.1|  53 DNPGTSAADHRDDlPDVPIVASMDDA--PEADALLIGIAPIGGGFDETWRDDVRTAIERECDVISGLHYFLNDDEEF 127
                                       67899*******************99..************************************************* PP

                         DUF1611_N  78 aalakkkgvkiiDvRkp 94 
                                       aala ++gv++ DvRkp
  gi|313125705|ref|YP_004035975.1| 128 AALASEQGVELNDVRKP 144
                                       ***************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                         DUF1611_N  21 ssleealaagae 32 
                                       + +e+a ++g++
  gi|313125705|ref|YP_004035975.1| 180 ELVEAARERGID 191
                                       334444444444 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   6.4e-05      0.23       5      39 ..     165     199 ..     161     216 .. 0.88
   2 !    6.0   0.0    0.0026       9.3      87     115 ..     222     250 ..     210     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.4e-05
                            AAA_26   5 vtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiq 39 
                                        +gtd +vGK +vsl Lv+a +++g+ +g++   q
  gi|313125705|ref|YP_004035975.1| 165 TVGTDCSVGKMTVSLELVEAARERGIDAGFIPTGQ 199
                                       589**************************975555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0026
                            AAA_26  87 dlekivkelekdadivvVEGagglgvpit 115
                                       ++e+++ e+ +d+d+++VEG g++  p  
  gi|313125705|ref|YP_004035975.1| 222 AVEEMILEVGDDYDVLFVEGQGSITHPAY 250
                                       578888999**************998865 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.7e-05      0.17      25      90 ..      43     114 ..      25     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                                       TEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G......GGHHHHHHHHHHTT-EEE CS
                      GFO_IDH_MocA  25 leevvalldpdaeraeavaesfgveaysdleelladpeidavivatpn......gtheelakaaleagkhvl 90 
                                       ++++va+ld+d++   a+ ++ +++ +  ++ + + pe+da+++++ +      +t ++ ++ a+e+ ++v+
  gi|313125705|ref|YP_004035975.1|  43 DYDIVAVLDRDNPGTSAADHRDDLPDVPIVASMDDAPEADALLIGIAPigggfdETWRDDVRTAIERECDVI 114
                                       569*********************************************999999889999999999999998 PP

>> PCP_red  Proto-chlorophyllide reductase 57 kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.6   5.6e+03      17      26 ..     100     109 ..      99     110 .. 0.83
   2 ?    3.1   0.0      0.03   1.1e+02      32      45 .]     173     186 ..     171     186 .. 0.92
   3 ?    5.1   0.0    0.0074        27      19      34 ..     322     337 ..     321     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                       HHHHHHHHHH CS
                           PCP_red  17 RkkaRraaEk 26 
                                       R  +R+a+E+
  gi|313125705|ref|YP_004035975.1| 100 RDDVRTAIER 109
                                       7789999998 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.03
                                       T-SEE-HHHHHHHH CS
                           PCP_red  32 GleeVtvevveaAk 45 
                                       G+ +V++e+veaA+
  gi|313125705|ref|YP_004035975.1| 173 GKMTVSLELVEAAR 186
                                       899*********97 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHHHHHT-S CS
                           PCP_red  19 kaRraaEklArerGle 34 
                                       +aR+a+E++A e G +
  gi|313125705|ref|YP_004035975.1| 322 EARAAVESYADELGAP 337
                                       79*********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2086.19
//
Query:       gi|313125706|ref|YP_004035976.1|  [L=347]
Description: enolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-41  140.0   0.9    1.2e-40  139.4   0.9    1.2  1  MR_MLE_C  Enolase C-terminal domain-like
    7.4e-12   45.5   0.1    1.3e-11   44.8   0.1    1.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N
     0.0074   15.5   0.0      0.015   14.5   0.0    1.5  1  MAAL_C    Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.4   0.9     2e-44   1.2e-40       2     213 ..     143     342 ..     142     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 2e-44
                                       HHHHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEE CS
                          MR_MLE_C   2 laeearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlE 78 
                                       ++e+ +++v e+g+  +K+k+g    ++d e v+ vr+a+ p+  ++++vDan+aw++++A+r  ++l++++++++E
  gi|313125706|ref|YP_004035976.1| 143 MREKTEDAV-EAGYPVLKIKLGT---DRDEEIVETVRDAA-PD--ATIRVDANEAWTPREAVRKSEMLADYGVEFIE 212
                                       566676655.56********887...6*************.75..5******************************* PP

                                       SSSSTTTHHHHHHHHHHHHSSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEB CS
                          MR_MLE_C  79 EPvppeddleglaelrarasipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapH 155
                                       +Pvp++ d+eg + + +r+ +p+aa+Es+ ++ad+ ++  a+  div+++++++gG+tea+++++ a+a+g++v+++
  gi|313125706|ref|YP_004035976.1| 213 QPVPAS-DPEGVQFVYERSALPVAADESCVTLADVPRV--ADRTDIVNLKLMKCGGLTEAKRMIHTARAHGLEVMLG 286
                                       *****5.6********5559******************..6677********************************* PP

                                       SC.SSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTS..SSBTS CS
                          MR_MLE_C 156 sg.sgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpd..gpGlG 213
                                       ++ ++  + aa++hla  ++ ++          l  e   + +++++G +++ d  + G G
  gi|313125706|ref|YP_004035976.1| 287 CMiESNAAIAAACHLAPLLDYADLDGAL-----LLGEDDYDGVPIKEGEIRLHDlnRSGTG 342
                                       *8459**********9999533322222.....4556666777777777777665555555 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.1   2.1e-15   1.3e-11      12     113 ..      13     118 ..       3     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2.1e-15
                                       EEC.EEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STT...GHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHH CS
                          MR_MLE_N  12 klr.PvqlavttvqkqslvlvkietseGvvGigeatsvgg...raetikaelddhlapllvgkdaanisdlaqllkr 84 
                                       +l+  + ++++t   ++ v+v+++ ++G++G+g a +      +a t++a l + l       d++ + ++ +++  
  gi|313125706|ref|YP_004035976.1|  13 PLAdAFTISRGTQTAAENVIVRVTDDGGMTGVGAAAPSAHygeTADTVEAVLPELLTVVESVGDPHALTEIERKMRE 89 
                                       5555789***************************987654334888888888776655544569999********** PP

                                       HCSSCHHHHHHHHHHHHHHHHHHTTSBHH CS
                          MR_MLE_N  85 avlgnmsAkaaidmAlwDlkakalnlpla 113
                                        v  n +A+ a+ +Al+Dl+ k+l+lpl+
  gi|313125706|ref|YP_004035976.1|  90 RVGRNPAARTAVSIALHDLASKRLGLPLY 118
                                       ***************************97 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.5e-06     0.015     140     200 ..     232     290 ..     224     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-06
                            MAAL_C 140 velvaDeWcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscn 200
                                       + + aDe c tl d+ + +d+  +d+v +k    Gg++++   +  ++ +g++++lG    
  gi|313125706|ref|YP_004035976.1| 232 LPVAADESCVTLADVPRVADR--TDIVNLKLMKCGGLTEAKRMIHTARAHGLEVMLGCMIE 290
                                       5688*************9997..69*******************************97653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2205.48
//
Query:       gi|313125707|ref|YP_004035977.1|  [L=380]
Description: hypothetical protein Hbor_09380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2549.54
//
Query:       gi|313125708|ref|YP_004035978.1|  [L=281]
Description: phage shock protein a (im30), suppresses sigma54-dependent transcription [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-30  106.5  32.3    1.4e-30  106.5  32.3    2.0  2  PspA_IM30       PspA/IM30 family
    0.00072   19.8   6.0    0.00072   19.8   6.0    3.6  3  DUF5082         Domain of unknown function (DUF5082)
     0.0041   17.2   3.6     0.0041   17.2   3.6    3.8  4  DUF1664         Protein of unknown function (DUF1664)
  ------ inclusion threshold ------
      0.029   15.0   4.3      0.029   15.0   4.3    4.1  4  SlyX            SlyX
      0.041   14.1   1.5      0.041   14.1   1.5    4.5  4  Osmo_CC         Osmosensory transporter coiled coil
        0.1   10.5   9.9       0.18    9.8   9.9    1.4  1  Prominin        Prominin
       0.11   13.1  54.1      0.084   13.4  10.4    4.2  3  APG6_N          Apg6 coiled-coil region
       0.24   11.8  33.2        1.5    9.2   0.9    3.3  2  YlqD            YlqD protein
       0.32   11.7  30.3       0.12   13.1   5.3    3.9  3  YabA            Initiation control protein YabA
       0.55   10.1  12.1      0.021   14.7   6.0    1.8  2  ExsD            Antiactivator protein ExsD
       0.66    9.2  36.6          2    7.7   9.8    4.0  5  DUF3450         Protein of unknown function (DUF3450)
       0.71    9.9  15.4       0.44   10.6   6.0    3.3  4  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
        1.1    8.5  11.5       0.11   11.7   7.0    1.6  2  DUF3535         Domain of unknown function (DUF3535)
        1.2    7.9  45.1      0.063   12.2  25.6    2.8  3  Spc7            Spc7 kinetochore protein
        1.3    9.0  44.8        1.1    9.3  22.3    4.3  4  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        2.7    8.4  17.7        9.1    6.7  10.4    2.3  2  DUF2894         Protein of unknown function (DUF2894)
        4.2    7.1  49.8      0.081   12.7  39.0    2.0  2  ERM             Ezrin/radixin/moesin family
        4.5    7.3  45.8        7.6    6.6   7.3    3.9  2  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        4.7    5.3  21.4      0.081   11.1   1.6    2.9  3  COG6            Conserved oligomeric complex COG6
          7    6.0  43.7        6.2    6.2  24.4    2.4  2  Golgin_A5       Golgin subfamily A member 5
        7.4    6.5   7.2        8.1    6.3   0.8    3.8  4  DASH_Dam1       DASH complex subunit Dam1


Domain annotation for each model (and alignments):
>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.5  32.3   1.7e-33   1.4e-30       1     219 [.       2     230 ..       2     232 .. 0.96
   2 ?   -0.2   6.6      0.74   6.3e+02     175     218 ..     235     278 ..     228     280 .. 0.65

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 1.7e-33
                         PspA_IM30   1 gifkrllrllraniselldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaA 77 
                                       gi++r++ ++r++i++ll  aeDP   l+   + m++el++++q +a++ +++k+le + ++ +e ++k  ++A++A
  gi|313125708|ref|YP_004035978.1|   2 GILSRASYVVRSKINSLLNRAEDPTETLDYSYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQARQA 78 
                                       69*************************************************************************** PP

                         PspA_IM30  78 LtkgeeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqeavqks 154
                                        ++ +++LA+ al++++   +q+e+le q a+++++ ++l  + ++l  +iee+++kke++kar +aa a   v+++
  gi|313125708|ref|YP_004035978.1|  79 VRQDRDDLAKRALEKKQAKMNQIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKARYEAAEASSRVSEA 155
                                       ***************************************************************************** PP

                         PspA_IM30 155 lgkls..tesatdslerieeKieerearadaaaelae........saqd.ldakleaagiqkevseqvlarlkaeq 219
                                       + ++    ++ +++ler e+  +e+ear+ a+ el +        s++d  d +le   ++ ev + +l+ lk e 
  gi|313125708|ref|YP_004035978.1| 156 VSGVGdeMGDVSRALERAEDQTDEMEARSAAMDELVDtgafdemmSDKDaIDRELETGRANSEV-DTELETLKTEM 230
                                       ****9999****************************9889888774444699999999999999.99999999875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.74
                         PspA_IM30 175 eerearadaaaelaesaqdldakleaagiqkevseqvlarlkae 218
                                       +e e +a+  + ++  ++dld++l+++   +e  e++l++lk+e
  gi|313125708|ref|YP_004035978.1| 235 AEAESEAESENGSETASADLDEELDEVDVAEEDVEAELEELKNE 278
                                       44444455555555456669999999986655548888888875 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.4     0.035        30       8      53 ..      29      74 ..      23      83 .. 0.80
   2 !   19.8   6.0   8.4e-07   0.00072       7      89 ..      90     173 ..      85     188 .. 0.70
   3 ?    0.5   3.0      0.83   7.1e+02      32     101 ..     215     276 ..     198     281 .] 0.48

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.035
                           DUF5082  8 lqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekp 53
                                      l + ++++r e++++ + I+ L + k++l+ +k +l+++ +k +++
  gi|313125708|ref|YP_004035978.1| 29 LDYSYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQ 74
                                      5667888899999999999999999999999998888887777665 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 8.4e-07
                           DUF5082   7 klqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse.sWkGk.eennydgirsnlessyqt 81 
                                       +l++++a+  ++i++le++I+ L+e+ + l+d+k++l++ +++ +++  +++  +    +++ +++++s + +++  
  gi|313125708|ref|YP_004035978.1|  90 ALEKKQAK-MNQIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKaRYEAAeASSRVSEAVSGVGDEMGD 165
                                       44555544.589************************************99975555554566666666633333333 PP

                           DUF5082  82 yvdkldel 89 
                                       + + l+ +
  gi|313125708|ref|YP_004035978.1| 166 VSRALERA 173
                                       33333333 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.83
                           DUF5082  32 aktklsdekeslkqkkkklekplnsse.sWkGkeennydgirs..nlessyqtyvdkldelidaieeEIerLe 101
                                       a +++++e e+lk++  k++  + s++ s +G+e+++ d +++  +++ + + ++ +l+el           +
  gi|313125708|ref|YP_004035978.1| 215 ANSEVDTELETLKTEMGKSTAEAESEAeSENGSETASADLDEEldEVDVAEEDVEAELEEL-----------K 276
                                       4555555555555544333322222222555554444333333334444444444444444...........3 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.4     0.056        48      82     115 ..      33      66 ..      10      74 .. 0.45
   2 ?    4.4   9.0     0.041        35      44     124 .]      34     115 ..      26     115 .. 0.68
   3 !   17.2   3.6   4.7e-06    0.0041      48     122 ..     109     182 ..      99     184 .. 0.87
   4 ?    0.8   1.2      0.56   4.8e+02      70      93 ..     253     276 ..     208     280 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.056
                           DUF1664  82 skeikeevtevredlseigedvesvkeavegles 115
                                        +++++e+++v+++++++ ++ + ++   + le+
  gi|313125708|ref|YP_004035978.1|  33 YEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEE 66 
                                       3334444444444444444333333333333333 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.041
                           DUF1664  44 esvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk.eaveglesk 116
                                       e++  +l+qv+   ++l+++k++L+ +  r+++++++ +e   + ++ v + r+dl++   + ++ k + +e+les+
  gi|313125708|ref|YP_004035978.1|  34 EKMRDELQQVKqgiADLTTQKKRLEIQKRRLEENVEKHNE---QARQAVRQDRDDLAKRALEKKQAKmNQIEDLESQ 107
                                       6677777777733356667888888777777777777665...5566777788887766555554432578999999 PP

                           DUF1664 117 lerieekQ 124
                                       +++++e+Q
  gi|313125708|ref|YP_004035978.1| 108 IANLQETQ 115
                                       99999988 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 4.7e-06
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                        +l++ +++l + k++L++ri++  +k + +k+  ++ +e  ++v+e +s +g+++  v++a e  e + +++e+
  gi|313125708|ref|YP_004035978.1| 109 ANLQETQDNLVDKKNELQNRIEEFRTKKETMKARYEA-AEASSRVSEAVSGVGDEMGDVSRALERAEDQTDEMEA 182
                                       4688999******************999888876665.667799************************9999996 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.56
                           DUF1664  70 rvdkkldeqkeiskeikeevtevr 93 
                                        +d++lde+  + +++++e++e++
  gi|313125708|ref|YP_004035978.1| 253 DLDEELDEVDVAEEDVEAELEELK 276
                                       344444444444444444444443 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   4.6       0.2   1.7e+02      16      55 ..      37      76 ..      22      85 .. 0.62
   2 ?   15.0   4.3   3.4e-05     0.029       4      57 ..     100     153 ..      98     163 .. 0.92
   3 ?    1.1   0.1      0.72   6.1e+02      40      55 ..     170     185 ..     152     203 .. 0.56
   4 ?   -0.4   0.3       2.2   1.9e+03      32      54 ..     222     244 ..     211     278 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX 16 edtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55
                                       d +++  + +a+   q +rl+ q r+l+e++++ +e+++
  gi|313125708|ref|YP_004035978.1| 37 RDELQQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQAR 76
                                      4555566666666666667777777777777766666544 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXX CS
                              SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgas 57 
                                       ++e+LE+++a +++t + L d   e q +i++ +++ + ++ r +++e+ss+ s
  gi|313125708|ref|YP_004035978.1| 100 QIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKARYEAAEASSRVS 153
                                       79*******************************************999998755 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.72
                                       HHHHHHT-XXXXXXXX CS
                              SlyX  40 lrllaerlkeleessg 55 
                                       l++ +++  e+e++s+
  gi|313125708|ref|YP_004035978.1| 170 LERAEDQTDEMEARSA 185
                                       3333333333333322 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHT-XXXXXXX CS
                              SlyX  32 qidrlqrqlrllaerlkeleess 54 
                                       +++ l++++ + + + ++ +es+
  gi|313125708|ref|YP_004035978.1| 222 ELETLKTEMGKSTAEAESEAESE 244
                                       44444444444444443333332 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.4      0.11        98      10      38 ..      29      57 ..      23      73 .. 0.76
   2 ?   14.1   1.5   4.8e-05     0.041      20      41 ..     100     121 ..      82     139 .. 0.93
   3 ?   -2.5   0.0       7.3   6.3e+03      23      32 ..     218     227 ..     217     230 .. 0.84
   4 ?   -0.7   3.3       2.1   1.8e+03      10      32 ..     254     276 ..     247     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                                      XXXXXTHHHHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC 10 LqehYdnIEqkvedideeIaaLeekRqrL 38
                                      L   Y++   +++++ + Ia+L  +++rL
  gi|313125708|ref|YP_004035978.1| 29 LDYSYEKMRDELQQVKQGIADLTTQKKRL 57
                                      55667777788888888888888877776 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  20 kvedideeIaaLeekRqrLvdq 41 
                                       ++ed++ +Ia+L+e +++Lvd+
  gi|313125708|ref|YP_004035978.1| 100 QIEDLESQIANLQETQDNLVDK 121
                                       7******************997 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7.3
                                       HHHHHHHHHH CS
                           Osmo_CC  23 dideeIaaLe 32 
                                       ++d+e++ L+
  gi|313125708|ref|YP_004035978.1| 218 EVDTELETLK 227
                                       799**99996 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.1
                                       XXXXXTHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  10 LqehYdnIEqkvedideeIaaLe 32 
                                       L e+ d++    ed+++e+++L+
  gi|313125708|ref|YP_004035978.1| 254 LDEELDEVDVAEEDVEAELEELK 276
                                       66777777778899999999997 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   9.9   0.00021      0.18     240     381 ..      32     169 ..       8     202 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
                          Prominin 240 elerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcl.d 315
                                       + e++ ++l+++k+ +  +   +k+L  ++++L+++++++ ++ +qa+ +       + +l+++++ k+++ ++l +
  gi|313125708|ref|YP_004035978.1|  32 SYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQARQAVRQDRD-DLAKRALEKKQA-KMNQIEDLeS 106
                                       56788888888888888888888888888888888888888888888888333.344444444443.6666666666 PP

                          Prominin 316 qlpnvdevlealeevletnlssivkeglarlneipekvk..nqtaevvpdlkkalakgreqikklakk 381
                                       q+ n++e  ++l +  +++l++ ++e    +++ +e++k   + ae  + + +a++  ++++ +++++
  gi|313125708|ref|YP_004035978.1| 107 QIANLQETQDNLVDK-KNELQNRIEE----FRTKKETMKarYEAAEASSRVSEAVSGVGDEMGDVSRA 169
                                       666666666666554.3444444433....22222222200233333334444444444444444443 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  12.0    0.0042       3.6      48     108 ..      25      86 ..      12      98 .. 0.51
   2 ?   13.4  10.4   9.9e-05     0.084      72     130 ..      90     147 ..      86     150 .. 0.90
   3 ?   -1.8  19.4       4.8   4.1e+03      33      77 ..     235     279 ..     148     281 .] 0.62

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0042
                            APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne.l 108
                                        +e l+ ++ek+++e ++  + +++l +++++le + + lee  e+ +e+ ++ +r+ ++ l
  gi|313125708|ref|YP_004035978.1|  25 PTETLDYSYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQARQAVRQDRDdL 86 
                                       33455555555555555555555555555555555555555555555555555555554431 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.9e-05
                            APG6_N  72 elekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyehaq 130
                                       +lek+++++ +++++le++ ++l+e +++ + + nelq   +e+  +++ ++a+ye a+
  gi|313125708|ref|YP_004035978.1|  90 ALEKKQAKM-NQIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKARYEAAE 147
                                       566666666.69*******************************************9886 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.8
                            APG6_N  33 kklkkekkeeekqdeeleeleeeleklekeeeelleeLkeleker 77 
                                       ++ ++e+++e+ +++  ++l+eel++++ +ee+ ++eL+el++e+
  gi|313125708|ref|YP_004035978.1| 235 AEAESEAESENGSETASADLDEELDEVDVAEEDVEAELEELKNED 279
                                       111222222222445566666666666666666666666666665 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1  25.4      0.27   2.3e+02      16      88 ..      35     106 ..      32     202 .. 0.81
   2 ?    9.2   0.9    0.0018       1.5      27      87 ..     214     276 ..     200     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.27
                              YlqD  16 klKeelqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqk 88 
                                       k+++el qq+++ i  l ++ ++Le+q++rl+++++k+++q+ +++++  +   ++ lekk+   +q+e++++
  gi|313125708|ref|YP_004035978.1|  35 KMRDEL-QQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQARQAVRQDRDDLAKRALEKKQAKMNQIEDLES 106
                                       556665.578999************************999966666666665555555555544444444332 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0018
                              YlqD  27 aqieqldkelqqLefqakrlikeikkqsaq..qieeiqeqvekekserlekkkqllqqleqvq 87 
                                       ++ +++d+el+ L++++ +  +e++++ ++    e++ + +++e +e+  + ++++++le+++
  gi|313125708|ref|YP_004035978.1| 214 RANSEVDTELETLKTEMGKSTAEAESEAESenGSETASADLDEELDEVDVAEEDVEAELEELK 276
                                       456889**********99988777665444459999999999999999999999999999887 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.3   0.00014      0.12      11      74 ..      27      87 ..      20      93 .. 0.81
   2 ?    7.1   7.1    0.0095       8.1      14      59 ..      98     143 ..      86     194 .. 0.67
   3 ?    1.5   3.9      0.54   4.6e+02      35      66 ..     213     243 ..     151     278 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA 11 eeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLa 74
                                      e+l+ + e++ +el+++k+ +a+l+ + ++Le+++++l e++e   k++++ ++++++ ++ La
  gi|313125708|ref|YP_004035978.1| 27 ETLDYSYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEENVE---KHNEQARQAVRQDRDDLA 87
                                      67888899**********************************5...444444555555555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0095
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXX CS
                              YabA  14 eeqleelleeleelkeelaelleenaeLeleneklrerleeeekke 59 
                                        +q+e+l +++++l+e+  +l+++ +eL+   e++r++ e+ +++ 
  gi|313125708|ref|YP_004035978.1|  98 MNQIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKARY 143
                                       3466777777777777777777777777777777766652222221 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHHHHHH...XXXXXXXXXXXXXX CS
                              YabA  35 leenaeLeleneklrerl...eeeekkekekkkel 66 
                                          n+e+ +e e+l++++   +   ++++++ + +
  gi|313125708|ref|YP_004035978.1| 213 GRANSEVDTELETLKTEMgksT---AEAESEAE-S 243
                                       3457778888888888884331...22222222.1 PP

>> ExsD  Antiactivator protein ExsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   6.0   2.5e-05     0.021      93     212 ..      41     168 ..      12     190 .. 0.66
   2 ?   -1.8   0.4       2.7   2.3e+03     115     139 ..     232     255 ..     206     278 .. 0.41

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                              ExsD  93 rlldqeiltlsvkveeLeiqinqleikkefWsklaEkessqireqllk.lveslqtklka......qkaelvelesk 162
                                       ++++q i  l ++++ Leiq + le + e  +  a +   q r++l+k  +e+ q+k+++      q+a+l+e +++
  gi|313125708|ref|YP_004035978.1|  41 QQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQARQAVRQDRDDLAKrALEKKQAKMNQiedlesQIANLQETQDN 117
                                       68999*******************98877666667777777777776526899999876411111144555555555 PP

                              ExsD 163 lkeseklvveaWPnfqkslsnlkeladl.tstepvsEaLeelWdalitlen 212
                                       l ++++ ++++   f ++ +++k+  +  ++   vsEa++ + d +  +  
  gi|313125708|ref|YP_004035978.1| 118 LVDKKNELQNRIEEFRTKKETMKARYEAaEASSRVSEAVSGVGDEMGDVSR 168
                                       555555555555555555555554422202223346665555555555444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.7
                              ExsD 115 qleikkefWsklaEkessqireqll 139
                                       +  +++e     +E+ s+ +  +l 
  gi|313125708|ref|YP_004035978.1| 232 KSTAEAESEAE-SENGSETASADLD 255
                                       32222222111.2333333333333 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  12.6    0.0079       6.8      17      98 ..      25     108 ..      11     111 .. 0.59
   2 ?    4.3   9.3     0.024        21      42      91 ..      90     139 ..      74     142 .. 0.62
   3 ?    7.7   9.8    0.0023         2      15      93 ..     105     182 ..      88     193 .. 0.72
   4 ?    5.2   0.4     0.013        11      23      76 ..     140     193 ..     136     208 .. 0.88
   5 ?    2.0   3.4      0.12   1.1e+02      40     101 ..     217     271 ..     199     278 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0079
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvas..qeqeiasleeqieei 91 
                                       + ++++   ek  ++ +q+ + i +l+ +k+ l+ + r+l+e +e+ + + +q  r+ ++  +++ +++ + ++++i
  gi|313125708|ref|YP_004035978.1|  25 PTETLDYSYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQARQAVRQDRDdlAKRALEKKQAKMNQI 101
                                       44444445556666666667777777777777777777777766666666666554443311555666666666666 PP

                           DUF3450  92 eeierel 98 
                                       e +e+++
  gi|313125708|ref|YP_004035978.1| 102 EDLESQI 108
                                       6666666 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.024
                           DUF3450  42 lddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                         ++kq   +++++l++++++l+  +++l +  ++++++i++ ++++e +
  gi|313125708|ref|YP_004035978.1|  90 ALEKKQAKMNQIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETM 139
                                       34566666677777777777777777777777777777777777766655 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0023
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                       +++++++++++ + v+++ + q++i++   +k++++a+y+a+++   + +   + + + + ++ + +++ e q +e+
  gi|313125708|ref|YP_004035978.1| 105 ESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKARYEAAEASS-RVSEAVSGVGDEMGDVSRALERAEDQTDEM 180
                                       6789999999999999999999999999999999999999887654.344444555555555555555555555555 PP

                           DUF3450  92 ee 93 
                                       e+
  gi|313125708|ref|YP_004035978.1| 181 EA 182
                                       55 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.013
                           DUF3450  23 keaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvas 76 
                                       k+  +a +a++++++ ++ + de  ++++ +++++++++++e+  + +++lv++
  gi|313125708|ref|YP_004035978.1| 140 KARYEAAEASSRVSEAVSGVGDEMGDVSRALERAEDQTDEMEARSAAMDELVDT 193
                                       5666788899999999*****************************999999985 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.12
                           DUF3450  40 dklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpl 101
                                       +++d        e+++lk+e  + +++ e  +++ +  e+  a+l+e+++e++  e++++  
  gi|313125708|ref|YP_004035978.1| 217 SEVDT-------ELETLKTEMGKSTAEAESEAESENGSETASADLDEELDEVDVAEEDVEAE 271
                                       44444.......44444444444444444444444444444444444444444444444433 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.065        55      58     100 ..       8      53 ..       4      57 .. 0.83
   2 ?   10.6   6.0   0.00052      0.44      27     118 ..      42     132 ..      26     150 .. 0.74
   3 ?   -0.4   0.0       1.3   1.1e+03      35      76 ..     151     191 ..     124     212 .. 0.64
   4 ?    3.0   1.2      0.11        97      42      91 ..     218     276 ..     204     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.065
                      Baculo_PEP_C  58 laeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlss 100
                                       +  +++++++ll++ +d   +l    +++r eL+ +++ +++L+++
  gi|313125708|ref|YP_004035978.1|   8 SYVVRSKINSLLNRAEDPTETLDysyEKMRDELQQVKQGIADLTTQ 53 
                                       5567788999999999999999999999999999999999999875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00052
                      Baculo_PEP_C  27 lqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtN 103
                                         + q +a+l+t+++ +e q   l+e++++  ++ ++++ +  + L +   + +++  n+++ l+s+++nL+    N
  gi|313125708|ref|YP_004035978.1|  42 QVK-QGIADLTTQKKRLEIQKRRLEENVEKHNEQARQAVRQDRDDLAKRALEKKQAKMNQIEDLESQIANLQETQDN 117
                                       223.3348888888888888888888888888888888888888888877777778888888888888888877777 PP

                      Baculo_PEP_C 104 instLnnllqalnnl 118
                                       +    n l + ++ +
  gi|313125708|ref|YP_004035978.1| 118 LVDKKNELQNRIEEF 132
                                       776666666666655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.3
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdal 76 
                                        +++++  +  +++++s +l++  +++++++++ ++++++ +
  gi|313125708|ref|YP_004035978.1| 151 RVSEAVSGVGDEMGDVSRALER-AEDQTDEMEARSAAMDELV 191
                                       4555555666666666666666.4455555565555555555 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.11
                      Baculo_PEP_C  42 aietqLnalsedlksllaeldt......rldtlltnLtdalnalq...dtlrneLtnln 91 
                                       +++t+L++l++++ ++ ae ++        +t+++ L++ l ++    ++++ eL+ l+
  gi|313125708|ref|YP_004035978.1| 218 EVDTELETLKTEMGKSTAEAESeaesenGSETASADLDEELDEVDvaeEDVEAELEELK 276
                                       56667777777777766666665555557788888899888888888888888888775 PP

>> DUF3535  Domain of unknown function (DUF3535)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   7.0   0.00013      0.11     175     301 ..      30     152 ..       6     159 .. 0.56
   2 ?   -3.5   0.1       5.4   4.6e+03     260     260 ..     235     235 ..     199     271 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                           DUF3535 175 etlqeklleiLeeeepvyYdElalsltrlrqecqdllatlesvgklpklavvvqgeaekaftleqaeklvttdyekl 251
                                       +  +ek+++ L++ ++   ++l+++ +rl  + + l + +e+++++ + av +  +      le+ ++   +++e+l
  gi|313125708|ref|YP_004035978.1|  30 DYSYEKMRDELQQVKQ-GIADLTTQKKRLEIQKRRLEENVEKHNEQARQAVRQDRDDLAKRALEK-KQAKMNQIEDL 104
                                       3333344444442222.234444444444444444444444444444444443333322222222.22222245555 PP

                           DUF3535 252 lkslslkqkllaekqLeerrrrlqaaieeakeeqealhvrvqaalAgAlv 301
                                        +++++ q+ ++  +L +++++lq+ iee+++++e+++ r  aa A+  v
  gi|313125708|ref|YP_004035978.1| 105 ESQIANLQETQD--NLVDKKNELQNRIEEFRTKKETMKARYEAAEASSRV 152
                                       555555555555..888***************************998766 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.4
                           DUF3535 260 k 260
                                       +
  gi|313125708|ref|YP_004035978.1| 235 A 235
                                       1 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  25.6   7.3e-05     0.063     142     259 ..      27     138 ..       9     155 .. 0.62
   2 ?   10.0  12.9   0.00034      0.29     144     242 ..      91     190 ..      84     195 .. 0.82
   3 ?   -2.8  13.5       2.6   2.2e+03     170     254 ..     197     276 ..     170     280 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.3e-05
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieek 218
                                       e+l+  +e+++++ +++++  + l++ +++le +k +lee++ek +e+a++    d+++L+  +++l++ +a+++  
  gi|313125708|ref|YP_004035978.1|  27 ETLDYSYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQARQAVRQDRDDLA--KRALEKKQAKMN-- 99 
                                       4566666667777777777777777777777777777777766666666665555555553..344444444444.. PP

                              Spc7 219 kkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                         ++++l++q+++l+e+ ++l ++k+el+++i+e +  +e 
  gi|313125708|ref|YP_004035978.1| 100 --QIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKET 138
                                       ..777777777777777777777777777777765444443 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00034
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles.id.keeLeelreelaelkaeieek 218
                                       le++ +++ ++ e Le+q ++l+e  ++l+ +k+el++++e+ ++++e +++ ++  e    + e+++ +  e+   
  gi|313125708|ref|YP_004035978.1|  91 LEKKQAKM-NQIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKArYEaAEASSRVSEAVSGVGDEMGDV 166
                                       44444444.567899******************************99999986443667778889999999999999 PP

                              Spc7 219 kkelaelqeqleeleekieelkeq 242
                                       ++ l++ ++q +e e++ ++++e 
  gi|313125708|ref|YP_004035978.1| 167 SRALERAEDQTDEMEARSAAMDEL 190
                                       999999999999999999998875 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.6
                              Spc7 170 peleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksel 246
                                       +e+ + k+++ +ele+ ++ +        +eLe+l+ e+ +  ae e+  +  +  ++  ++l+e+++e++   +++
  gi|313125708|ref|YP_004035978.1| 197 DEMMSDKDAIDRELETGRANS-----EVDTELETLKTEMGKSTAEAESEAESENGSETASADLDEELDEVDVAEEDV 268
                                       455555666666666666622.....236889999999999999999988888899999999999999999999999 PP

                              Spc7 247 eeeiaeae 254
                                       e+e++e +
  gi|313125708|ref|YP_004035978.1| 269 EAELEELK 276
                                       98888876 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  22.3    0.0013       1.1      34     138 ..      27     139 ..      11     141 .. 0.67
   2 ?    7.4  14.7     0.005       4.2      14     110 ..      89     191 ..      80     194 .. 0.71
   3 ?    3.4   9.2     0.085        72      72     137 ..     193     260 ..     165     263 .. 0.68
   4 ?    0.5   8.9      0.65   5.6e+02      17      81 ..     214     278 ..     204     281 .] 0.46

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                    CENP-F_leu_zip  34 emseenqekvileaEtskaevetlkeeieelaeelreleldLvalr........sekeeLek.elqkkqervseLes 101
                                       e+++ + ek+  e  + k+ +  l +++++l+ + r+le ++++          +++++L+k  l+kkq ++++ e 
  gi|313125708|ref|YP_004035978.1|  27 ETLDYSYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEENVEKHNeqarqavrQDRDDLAKrALEKKQAKMNQIED 103
                                       334444445555555555555555555555555555555555433355555555******86369************ PP

                    CENP-F_leu_zip 102 lnsslenlleekEqekvqmkeeskaaveeLqtqlkel 138
                                       l+s++ n l+e  ++ v  k+e ++++ee++t ++ +
  gi|313125708|ref|YP_004035978.1| 104 LESQIAN-LQETQDNLVDKKNELQNRIEEFRTKKETM 139
                                       *****98.6888899***************9998765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.005
                    CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelrelel......dLvalrsekee 84 
                                       ++ +k+    +++e Le+++ +++e q++++  + + ++ +e++++++e+++++ +  e+       ++ +  e  +
  gi|313125708|ref|YP_004035978.1|  89 RALEKKQAKMNQIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKARYEAAEAssrvseAVSGVGDEMGD 165
                                       44455555567899999999999999999999999999999999999999987765554411111145555588888 PP

                    CENP-F_leu_zip  85 LekelqkkqervseLeslnsslenll 110
                                       + + l+   ++ +e+e++   + +l+
  gi|313125708|ref|YP_004035978.1| 166 VSRALERAEDQTDEMEARSAAMDELV 191
                                       88888888888888888877777665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.085
                    CENP-F_leu_zip  72 eldLvalrsekeeLekelqk..kqervs.eLeslnsslenlleekEqekvqmkeeskaaveeLqtqlke 137
                                       +  ++++ s+k+ +++el++   +++v+ eLe+l+ ++ +   e+E e  + ++ s++a   L  +l e
  gi|313125708|ref|YP_004035978.1| 193 TGAFDEMMSDKDAIDRELETgrANSEVDtELETLKTEMGKSTAEAESEA-ESENGSETASADLDEELDE 260
                                       34577888**********972245677559**********999999886.5566788888999988877 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.65
                    CENP-F_leu_zip  17 rkadsLkdkvenLerelemseenqekvileaEtskaevet.lkeeieelaeelreleldLvalrse 81 
                                       r ++ +    e L+ e+  s ++ e+ + e E+  +++++ l ee++e     ++ e++L++l++e
  gi|313125708|ref|YP_004035978.1| 214 RANSEVDTELETLKTEMGKSTAEAES-EAESENGSETASAdLDEELDEVDVAEEDVEAELEELKNE 278
                                       33334444444444444444444333.233333333333236666666666666666666666555 PP

>> DUF2894  Protein of unknown function (DUF2894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  10.4     0.011       9.1      31     127 ..      53     146 ..      37     166 .. 0.72
   2 ?    6.4   0.9     0.013        11      38     120 ..     183     262 ..     145     277 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                           DUF2894  31 sgevrrlleaklaalldayaarleraekaaaealaeaaakapaaspstLaaLlaqiakrasaakeaaaaeeaaaaPa 107
                                       +++  ++++++l++ +++ +++ ++a ++++++la+ a ++++a+ + +++L +qia+  ++++ + ++++ + +  
  gi|313125708|ref|YP_004035978.1|  53 QKKRLEIQKRRLEENVEKHNEQARQAVRQDRDDLAKRALEKKQAKMNQIEDLESQIANL-QETQDNLVDKKNELQN- 127
                                       4445578999**************************999999998899*********99.4444444444444444. PP

                           DUF2894 108 atveateelkaleyfretws 127
                                        ++e+++  k   ++r   +
  gi|313125708|ref|YP_004035978.1| 128 -RIEEFRTKKETMKARYEAA 146
                                       .5555555555554444433 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                           DUF2894  38 leaklaalldayaarleraekaaaealaeaaakapaa...................sp........stLaaLlaqia 87 
                                        +a +++l                                                +         + L++L +++ 
  gi|313125708|ref|YP_004035978.1| 183 RSAAMDEL----------------------------VdtgafdemmsdkdaidrelETgransevdTELETLKTEMG 231
                                       11222222............................13333333333332233333002233334467999999999 PP

                           DUF2894  88 krasaakeaaaaeeaaaaPaatveateelkale 120
                                       k  +a++e++a++e  +++ a+ +  eel+ ++
  gi|313125708|ref|YP_004035978.1| 232 KS-TAEAESEAESENGSET-ASADLDEELDEVD 262
                                       99.5555555555555555.4556666666555 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  39.0   9.4e-05     0.081       4     201 ..      23     233 ..      20     239 .. 0.69
   2 ?   -0.9  16.7       1.4   1.2e+03      17     130 ..     159     276 ..     144     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.4e-05
                               ERM   4 erekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaea.eeeiqrlkesaekeeeekek 79 
                                       e   + l    +++++e ++ ++   + + + ++L+ ++rr+ee+ e+ +++a++a ++  +     a++  e+k++
  gi|313125708|ref|YP_004035978.1|  23 EDPTETLDYSYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEENVEKHNEQARQAvRQDRD---DLAKRALEKKQA 96 
                                       55556666667777777777777777777777777777777777766554444443123333...334455666777 PP

                               ERM  80 lerklreaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstpsks............es.eenve 143
                                        ++++++ e+++a+l+e +++   ++++L++++ee r ++e +k++  +a ++++ s            +s + + +
  gi|313125708|ref|YP_004035978.1|  97 KMNQIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKARYEAAEASSRVSeavsgvgdemgdVSrALERA 173
                                       78899******************************999998888766655555544456999999888733355556 PP

                               ERM 144 eseteeeeenseeesaeletde..veklsleieeeR.vtylekskrlqeqLkeLkseleql 201
                                       e++t+e+e  s+    el   +   e +s++   +R ++  + + ++ + L++Lk+e+ ++
  gi|313125708|ref|YP_004035978.1| 174 EDQTDEMEARSAA-MDELVDTGafDEMMSDKDAIDReLETGRANSEVDTELETLKTEMGKS 233
                                       6666666644443.455654446745577888888845666889*************9765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                               ERM  17 lqeeaekaqeaLreseetaelLaekarraee..eaelLeqkaaeaeeeiqrlkesaek..eeeekeklerklreael 89 
                                       + +e+    +aL+++e++ ++++ ++  + e  +    ++  ++  +  ++l+  +++   + e e l++++ + ++
  gi|313125708|ref|YP_004035978.1| 159 VGDEMGDVSRALERAEDQTDEMEARSAAMDElvDTGAFDEMMSDKDAIDRELETGRANseVDTELETLKTEMGKSTA 235
                                       56788888999999999999998888777773333333344444444444444333330045678888888888888 PP

                               ERM  90 eaarleeeserkeeeaerLkeeleeareaeeeakeklleal 130
                                       ea+  +e ++  e     L eel e+  aee+ +++l e+ 
  gi|313125708|ref|YP_004035978.1| 236 EAESEAESENGSETASADLDEELDEVDVAEEDVEAELEELK 276
                                       88888888888899999999999999999999999888765 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  28.9      0.39   3.4e+02       2      91 ..      53     147 ..      38     192 .. 0.52
   2 ?    6.6   7.3    0.0089       7.6      53     110 ..     217     277 ..     197     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.39
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeakl.qklqedlekqaeiakeaqqkYerelvkhaedvkelqalreel....nelkaei 73 
                                       ++k+le ++ +l+e+ e++++++ q++++d    a++a e +q   +++   ++++ +lq++ + l    nel+++i
  gi|313125708|ref|YP_004035978.1|  53 QKKRLEIQKRRLEENVEKHNEQArQAVRQDRDDLAKRALEKKQAKMNQIEDLESQIANLQETQDNLvdkkNELQNRI 129
                                       23333333333333333333222122233333333333333333333333333333333333333344444444444 PP

                        TPR_MLP1_2  74 aelkaeaesakaeleese 91 
                                       +e++++ e+ ka  e++e
  gi|313125708|ref|YP_004035978.1| 130 EEFRTKKETMKARYEAAE 147
                                       444444444444444444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0089
                        TPR_MLP1_2  53 aedvkelqalreelnelkaei...aelkaeaesakaeleeseesweeqkeelekelselek 110
                                       +e  +el++l++e+ + +ae+   ae ++  e+a+a+l+e+  + +  +e  e el+el++
  gi|313125708|ref|YP_004035978.1| 217 SEVDTELETLKTEMGKSTAEAeseAESENGSETASADLDEELDEVDVAEEDVEAELEELKN 277
                                       5666799999999955555541125678889****************************97 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.6   9.5e-05     0.081      41      93 ..      14      66 ..      11      73 .. 0.94
   2 ?    0.1  10.9       0.2   1.7e+02       9      84 ..      71     146 ..      64     157 .. 0.70
   3 ?   -0.5   0.0      0.31   2.6e+02      37      68 ..     161     192 ..     150     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-05
                              COG6 41 pvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklel 93
                                      +++  L+r e+  e l+ ++++m+++l++ k+  +dl+++ ++L+ +k++le+
  gi|313125708|ref|YP_004035978.1| 14 KINSLLNRAEDPTETLDYSYEKMRDELQQVKQGIADLTTQKKRLEIQKRRLEE 66
                                      78889********************************************9997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                              COG6   9 ytentaeaRrnLrsdiekellkineefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeL 84 
                                       ++e   +a r+ r d+ k++l+ ++  +++ + ++ q+ +++++ ++l +  +e+++++++ +++ +++    e+ 
  gi|313125708|ref|YP_004035978.1|  71 HNEQARQAVRQDRDDLAKRALEKKQAKMNQIEDLESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKARYEAA 146
                                       4455556666667788888888888888888888888888888888888888888888887777666665555544 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.31
                              COG6  37 eefqpvaeqLkriesdveklnelcdemkkkls 68 
                                       +e++ v ++L+r e++ +++++ +  m + ++
  gi|313125708|ref|YP_004035978.1| 161 DEMGDVSRALERAEDQTDEMEARSAAMDELVD 192
                                       68899999999999999999999998887655 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  24.4    0.0073       6.2      44     153 ..      28     141 ..       6     158 .. 0.67
   2 ?    5.6  11.2     0.011       9.1      43     122 ..     190     278 ..     170     281 .] 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0073
                         Golgin_A5  44 alsaeldelkqerdllreelqklnq.....qieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveae 115
                                       +l + ++++++e +++++ +++l++     +i++ r e +++e+++++  + +r+   +l ++  e+++ak +  ++
  gi|313125708|ref|YP_004035978.1|  28 TLDYSYEKMRDELQQVKQGIADLTTqkkrlEIQKRRLE-ENVEKHNEQARQAVRQDRDDLAKRALEKKQAKMNQIED 103
                                       34556666666666666655544440000045555555.56666666666666777777777777888888888889 PP

                         Golgin_A5 116 lerlkeelryleeelvrskatlqsrikdrekeieklrn 153
                                       le++  +l+ ++++lv +k++lq+ri++  ++ e +++
  gi|313125708|ref|YP_004035978.1| 104 LESQIANLQETQDNLVDKKNELQNRIEEFRTKKETMKA 141
                                       99999999999**************9986666555554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                         Golgin_A5  43 talsaeldelkqerdllreelq......klnqqieqlrtel..qdleaqqqaeaeslreq.lqeleeqleeerkake 110
                                        + + ++de+++++d++  el+      ++ +++e+l+te+     ea+ +ae+e+  e   ++l+e+l+e   a+e
  gi|313125708|ref|YP_004035978.1| 190 LVDTGAFDEMMSDKDAIDRELEtgransEVDTELETLKTEMgkSTAEAESEAESENGSETaSADLDEELDEVDVAEE 266
                                       45667889999999999988862222224567899******54455666666666655541679999***999**** PP

                         Golgin_A5 111 eveaelerlkee 122
                                       +veaele+lk+e
  gi|313125708|ref|YP_004035978.1| 267 DVEAELEELKNE 278
                                       ********9987 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.36     3e+02       3      23 ..      38      58 ..      19      73 .. 0.67
   2 ?    6.3   0.8    0.0095       8.1      11      34 ..     100     124 ..      95     126 .. 0.89
   3 ?   -1.3   0.0       2.3     2e+03       6      23 ..     123     140 ..     119     145 .. 0.70
   4 ?   -1.8   0.1       3.4   2.9e+03       6      23 ..     171     188 ..     160     193 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.36
                         DASH_Dam1  3 pafaeLaDsletLdknledLq 23
                                      +++++ +  +++L+++ ++L+
  gi|313125708|ref|YP_004035978.1| 38 DELQQVKQGIADLTTQKKRLE 58
                                      455555666666666655555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0095
                         DASH_Dam1  11 sletLdknledLqqihesLsd.fNe 34 
                                       ++e+L++++ +Lq+++++L+d  Ne
  gi|313125708|ref|YP_004035978.1| 100 QIEDLESQIANLQETQDNLVDkKNE 124
                                       689****************986666 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.3
                         DASH_Dam1   6 aeLaDsletLdknledLq 23 
                                       +eL+  +e+++++ e ++
  gi|313125708|ref|YP_004035978.1| 123 NELQNRIEEFRTKKETMK 140
                                       577777888877777665 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.4
                         DASH_Dam1   6 aeLaDsletLdknledLq 23 
                                       ++ +D+ ++++++   ++
  gi|313125708|ref|YP_004035978.1| 171 ERAEDQTDEMEARSAAMD 188
                                       444555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3186  (0.177701); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                       171  (0.00953762); expected 17.9 (0.001)
Passed Fwd filter:                       101  (0.00563333); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 1.44u 0.40s 00:00:01.84 Elapsed: 00:00:00.59
# Mc/sec: 1432.58
//
Query:       gi|313125709|ref|YP_004035979.1|  [L=209]
Description: alpha/beta hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-07   31.8   0.1    1.4e-07   31.3   0.1    1.1  1  DLH            Dienelactone hydrolase family
    1.3e-05   24.6   1.3      0.036   13.3   0.4    2.8  2  Hydrolase_4    Serine aminopeptidase, S33
    2.1e-05   24.3   0.1    2.9e-05   23.8   0.1    1.3  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    2.2e-05   25.1   9.0     0.0064   17.1   3.3    2.1  2  Abhydrolase_6  Alpha/beta hydrolase family
     0.0013   18.6   0.0     0.0022   17.9   0.0    1.3  1  Abhydrolase_2  Phospholipase/Carboxylesterase
     0.0023   17.8   0.1       0.59   10.0   0.0    2.2  2  VirJ           Bacterial virulence protein (VirJ)
     0.0057   16.3   0.1      0.032   13.9   0.1    1.8  1  FSH1           Serine hydrolase (FSH1)
     0.0087   14.9   0.0      0.011   14.6   0.0    1.1  1  DUF1100        Alpha/beta hydrolase of unknown function (DUF1
  ------ inclusion threshold ------
      0.015   15.4   2.2        3.4    7.7   0.0    2.2  2  Thioesterase   Thioesterase domain
      0.018   14.9   0.0       0.03   14.2   0.0    1.4  1  Lipase_3       Lipase (class 3)
      0.019   14.9   0.0      0.027   14.4   0.0    1.2  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
      0.032   14.2   0.1       0.45   10.4   0.0    2.0  2  UPF0227        Uncharacterised protein family (UPF0227)
      0.045   13.2   0.3      0.098   12.1   0.2    1.6  2  Peptidase_S9   Prolyl oligopeptidase family
      0.056   13.1   0.2      0.084   12.5   0.2    1.4  1  Esterase       Putative esterase
       0.13   11.9   0.2       0.78    9.3   0.1    1.9  2  Abhydrolase_1  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   1.1e-10   1.4e-07      83     183 ..      87     190 ..      73     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.1e-10
                               DLH  83 kaavaylksvpevstkkvgvvGfCmGGalalllaaev...pevdaavafYGlspeke.leeaakikapilalfgeeD 155
                                        +++++++  +e++ ++v++ Gf +GGa+all a e+   ++v a ++ + l  + + +++ ++i +p+++++g++D
  gi|313125709|ref|YP_004035979.1|  87 ADTLRAVEWASEQY-DRVALFGFSFGGAMALLAAVEGadaAAVSALAPAHKLADDLDvVAAFPEIPVPVQVVYGTRD 162
                                       56777777777555.9******************999422344555556664444441567799************* PP

                               DLH 156 efipadevekleealkaanvdlelkvYp 183
                                        + +a+ v   + +++++ v+le + + 
  gi|313125709|ref|YP_004035979.1| 163 DVADAERVAARAREFEQSVVALEADHFF 190
                                       ******9988888888887777766655 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.4     3e-05     0.036      72     117 ..      97     141 ..      47     148 .. 0.80
   2 !    9.4   0.0   0.00049      0.58     184     220 ..     144     180 ..     141     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                       Hydrolase_4  72 ehpelplfllGhSmGGliallyllrypdkvaglilsaPalkikakl 117
                                        ++  ++ l+G S GG++all++ + +d  a++   aPa k++ +l
  gi|313125709|ref|YP_004035979.1|  97 SEQYDRVALFGFSFGGAMALLAAVEGAD-AAAVSALAPAHKLADDL 141
                                       34455899***************99999.77888999999988765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00049
                       Hydrolase_4 184 eeraakitlPllllhGeaDkvvdpeasrelyerlgsk 220
                                       ++  ++i +P+++++G++D v d e  ++ +++  ++
  gi|313125709|ref|YP_004035979.1| 144 VAAFPEIPVPVQVVYGTRDDVADAERVAARAREFEQS 180
                                       66778999***************99998888877765 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   2.5e-08   2.9e-05      73     138 ..      77     137 ..      74     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.5e-08
                                       S---TTTTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-T CS
                     Peptidase_S15  73 GeftvgdsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdl 138
                                       G+++  ++ e +d+  +++W+ +q    ++V+ +G+S++G ++llaa++g +a ++  ++a+ + l
  gi|313125709|ref|YP_004035979.1|  77 GAWDE-GYGERADTLRAVEWASEQY---DRVALFGFSFGGAMALLAAVEGADAAAV-SALAPAHKL 137
                                       77777.999************9985...79******************98876443.333333333 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.3   5.3e-06    0.0064      32      95 ..      46     133 ..       5     142 .. 0.64
   2 !   12.7   2.1   0.00012      0.14     142     219 ..     125     199 ..     120     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.3e-06
                                       E--TTS.TS-..............GGCS--HHH.CHHH...HHHHCCTT.....TTSEEEEEETCHHHHHHHHHHCC CS
                     Abhydrolase_6  32 pDlpGh.Grs..............dpppldled.ladl...aalldelaa...gggpvvlvGHSlGGalalaaapla 86 
                                       p+ +Gh G++              d+  +d+ +  + +   a++l+++     ++++v l+G S+GGa+al+aa   
  gi|313125709|ref|YP_004035979.1|  46 PQHRGHrGDDrlvavseelnrrgiDCLRFDYGAwDEGYgerADTLRAVEWaseQYDRVALFGFSFGGAMALLAAVEG 122
                                       6668888844444444444444444455777663233333233333333355589*****************44433 PP

                                       ...EE.EEES- CS
                     Abhydrolase_6  87 .lvvg.vlldp 95 
                                        + ++  +l+p
  gi|313125709|ref|YP_004035979.1| 123 aDAAAvSALAP 133
                                       33333455555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                                       CCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH..STTEEETCE...SSS-HHHHSHH CS
                     Abhydrolase_6 142 aawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerlla..qagarlpvvlpgaGHlphleepd 215
                                       aa + +la++ +l++ l+   +aa++ +pvp+ v+ g++D++    +er +a  ++ ++  vv   a+H++   +  
  gi|313125709|ref|YP_004035979.1| 125 AAAVSALAPAHKLADDLD--VVAAFPEIPVPVQVVyGTRDDVAD--AERVAAraREFEQS-VVALEADHFFVG-QHG 195
                                       444555566666666666..566*********998679999777..66777732255555.9999****9888.777 PP

                                       HHHH CS
                     Abhydrolase_6 216 evae 219
                                       +vae
  gi|313125709|ref|YP_004035979.1| 196 KVAE 199
                                       7776 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-06    0.0022     104     207 ..     100     202 ..      87     208 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-06
                                       GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-EEEEEEETT-SSS-H.HHHHHHH CS
                     Abhydrolase_2 104 ssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklpilqiHgeeDpvvpl.algkaak 179
                                        +r++++GFS G+a+al +a+     ++ + a+  a  l+  l   a      +p+  ++g+ D v +  +++++a 
  gi|313125709|ref|YP_004035979.1| 100 YDRVALFGFSFGGAMALLAAVEGAD-AAAVSALAPAHKLADDLDVVAAFPEIPVPVQVVYGTRDDVADAeRVAARAR 175
                                       589**************99987654.55566666666665555543332224599999*******999834566677 PP

                                       HHHHTTS-GEEEEEETT--SS--HHHHH CS
                     Abhydrolase_2 180 evlkkllkkvelksyeglaHsideeemq 207
                                       e+ ++++   e + +  ++H  + e + 
  gi|313125709|ref|YP_004035979.1| 176 EFEQSVVA-LEADHFFVGQHGKVAETVS 202
                                       77777666.5555555577776666555 PP

>> VirJ  Bacterial virulence protein (VirJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0089        11      34      80 ..      68     113 ..      50     132 .. 0.69
   2 !   10.0   0.0   0.00049      0.59     133     186 ..     147     203 ..     131     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0089
                              VirJ  34 GvdsLryfWser.tPeevaaDldrlikkyakrwkkkkvvliGysfGaD 80 
                                       G+d Lr+ +    +     aD+ r ++ +++++   +v+l G+sfG  
  gi|313125709|ref|YP_004035979.1|  68 GIDCLRFDYGAWdEGYGERADTLRAVEWASEQY--DRVALFGFSFGGA 113
                                       677777644333033444568888888888886..689*******854 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00049
                              VirJ 133 lakldakrvvCiyGkdek....deacpelkakgvevvklpGghhfdedyealakaile 186
                                         +++   v+ +yG+ ++    + +++  ++ +  vv+l+ +h f ++  ++a+++ +
  gi|313125709|ref|YP_004035979.1| 147 FPEIP-VPVQVVYGTRDDvadaERVAARAREFEQSVVALEADHFFVGQHGKVAETVSD 203
                                       44444.35899***9876331134555556666779*****************98865 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   2.6e-05     0.032      98     201 ..      97     189 ..      74     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                              FSH1  98 kengpfdGiiGFSqGaalaallaslleellkeashpslkfailvsGfkleepkyeeyyeedkiqtptLhvlGelDtv 174
                                       +e+   + + GFS G+a+a l a +               a++ +   ++++++ +++  ++i +p+  v+G++D v
  gi|313125709|ref|YP_004035979.1|  97 SEQYDRVALFGFSFGGAMALLAAVEGADAAA-------VSALAPAHKLADDLDVVAAF--PEIPVPVQVVYGTRDDV 164
                                       4455567899********9888776665432.......22333333344555555666..8999************* PP

                              FSH1 175 vdeerseaLaeafknsskvlkHpggHf 201
                                        d er  a a+ f++   v+  + +Hf
  gi|313125709|ref|YP_004035979.1| 165 ADAERVAARAREFEQ--SVVALEADHF 189
                                       **********99999..6777777776 PP

>> DUF1100  Alpha/beta hydrolase of unknown function (DUF1100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   9.1e-06     0.011     254     316 ..      92     154 ..      86     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.1e-06
                           DUF1100 254 dvpyv..dhtrvgliGfrfGanvavrlaflesekvkavvalGavvhdlltsskklqkvpkmyldv 316
                                        v +    + rv+l+Gf fG+ +++ la +e     av al a+ h+l  + + +++ p++ + v
  gi|313125709|ref|YP_004035979.1|  92 AVEWAseQYDRVALFGFSFGG-AMALLAAVEGADAAAVSAL-APAHKLADDLDVVAAFPEIPVPV 154
                                       5556521467**********9.6888********9999999.568********999999986655 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.3    0.0047       5.6      68      84 ..     103     119 ..      92     121 .. 0.83
   2 ?    7.7   0.0    0.0028       3.4     161     229 ..     134     203 ..     116     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0047
                                       EEEEEETHHHHHHHHHH CS
                      Thioesterase  68 yalfGhSlGgllAfevA 84 
                                       +alfG+S+Gg++A  +A
  gi|313125709|ref|YP_004035979.1| 103 VALFGFSFGGAMALLAA 119
                                       79***********8666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0028
                                       CS-TTSCSE........HHCEEEEEEGSS-CTCCCCCCCHCHCHCTCESCEEEEEESSHCCHHHSHHHHHHHHHHHH CS
                      Thioesterase 161 yslrpeaaq........klratlfngsddklkdldtlelaerweqktsgevsvhvlegdhfylledrleavleiiek 229
                                       +++ +++ +         +++++ +g +d  +d++  + a+   +   +e sv +le+dhf+  +    +v+e++++
  gi|313125709|ref|YP_004035979.1| 134 AHKLADDLDvvaafpeiPVPVQVVYGTRDDVADAE--RVAA---RAREFEQSVVALEADHFFVGQ--HGKVAETVSD 203
                                       44444444466666655677778888888888888..4444...68899999************9..5667776665 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.5e-05      0.03      53      85 ..      91     121 ..      61     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHTT-EEEEEEEETHHHHHHHHHHHH CS
                          Lipase_3  53 kelkrllekypeysivvtGHSLGgalAlLaald 85 
                                       + ++   e+y   ++++ G S+Gga+AlLaa++
  gi|313125709|ref|YP_004035979.1|  91 RAVEWASEQYD--RVALFGFSFGGAMALLAAVE 121
                                       55555667777..999**************986 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.2e-05     0.027      20      95 ..      99     170 ..      91     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                                       --SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-EE-TTS-EE-TT- CS
                            BAAT_C  20 kkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdeskvlpelklsmeklkvnknglldivdv 95 
                                       + d+++l G S+Gg +all a+   +  av ++++++    + +v      ++pe+++  + +  + +++ d+ +v
  gi|313125709|ref|YP_004035979.1|  99 QYDRVALFGFSFGGAMALLAAVEGADAAAVSALAPAHKLADDLDVVA----AFPEIPVPVQVVYGTRDDVADAERV 170
                                       4689********************9*999999999999998888887....6777777777776666666665555 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.14   1.6e+02      57     102 ..      97     142 ..      86     149 .. 0.68
   2 ?   10.4   0.0   0.00038      0.45     133     175 ..     150     193 ..     138     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.14
                           UPF0227  57 gddn..illvGssLGGyyatrlgerfglrqvllnPalkplenlagklg 102
                                       ++++  ++l G s GG +a  l++  g  ++ +  al+p ++la+ l+
  gi|313125709|ref|YP_004035979.1|  97 SEQYdrVALFGFSFGGAMA-LLAAVEGADAAAVS-ALAPAHKLADDLD 142
                                       33334499********987.56777777766654.6777777777666 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00038
                           UPF0227 133 rperilvllskqDevldyrravaefraaaeiveddg.dHafkdv 175
                                        p++++v+ ++ D+v d +r +a  r++ + v + + dH f + 
  gi|313125709|ref|YP_004035979.1| 150 IPVPVQVVYGTRDDVADAERVAARAREFEQSVVALEaDHFFVGQ 193
                                       58999***********************987665444**99765 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   8.2e-05     0.098      41      85 ..      82     122 ..      75     162 .. 0.81
   2 ?   -1.2   0.0      0.95   1.1e+03     133     179 ..     130     187 ..     121     206 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                                       GHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH- CS
                      Peptidase_S9  41 gqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqr 85 
                                       g  e +D + a+e++ +++    +r+a++G S+GG +++ a+ + 
  gi|313125709|ref|YP_004035979.1|  82 GYGERADTLRAVEWASEQY----DRVALFGFSFGGAMALLAAVEG 122
                                       5566678888888886664....8**************9998744 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.95
                                       HH-CGGG--...........---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEE CS
                      Peptidase_S9 133 pyspldnvk...........aypplLlihGlaDdrvppaealklvaaLqkkgknvlll 179
                                       +++p+++++           + +p+ ++ G+ Dd    +  +  +++ ++  + ++  
  gi|313125709|ref|YP_004035979.1| 130 ALAPAHKLAddldvvaafpeIPVPVQVVYGTRDDVADAERVAARAREFEQSVVALEAD 187
                                       5555555555555555666677788888888888777666666665555555555554 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2     7e-05     0.084     114     149 ..     101     134 ..      87     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                                       CCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES-- CS
                          Esterase 114 pdgravaGqSmGGlgALilalkhpdrFgsvssfSpi 149
                                       ++  a++G+S+GG +AL++a++  d    vs+++p 
  gi|313125709|ref|YP_004035979.1| 101 DR-VALFGFSFGGAMALLAAVEGADAA-AVSALAPA 134
                                       33.9****************9987764.67777765 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00066      0.78      72      94 ..     100     122 ..      65     146 .. 0.78
   2 ?    0.8   0.0      0.26   3.1e+02     210     252 ..     150     190 ..     127     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00066
                                       TSSEEEEEETHHHHHHHHHHHHH CS
                     Abhydrolase_1  72 ddkltlvGhSmGGmialayaaey 94 
                                        d+++l G+S+GG++al +a e 
  gi|313125709|ref|YP_004035979.1| 100 YDRVALFGFSFGGAMALLAAVEG 122
                                       68999************999765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.26
                                       HHSEEEEEEETTCSSSCH.HHHHHHHHCHTSEEEEEEETCSSSH CS
                     Abhydrolase_1 210 vlaptlvisgtsDplvpp.kaledlaqllpkkrlvvisdagHla 252
                                       + +p+ v++gt D +++  ++  + ++     + vv   a H+ 
  gi|313125709|ref|YP_004035979.1| 150 IPVPVQVVYGTRDDVADAeRVAARAREF-E--QSVVALEADHFF 190
                                       34499********999996666555544.3..466666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1264.91
//
Query:       gi|313125710|ref|YP_004035980.1|  [L=134]
Description: hypothetical protein Hbor_09410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.3   5.3      0.065   12.9   5.3    1.1  1  PRA1      PRA1 family protein
          9    6.4  12.5         14    5.7   0.0    3.3  3  FixQ      Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   5.3   7.3e-06     0.065      27     126 ..       3     119 ..       1     121 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-06
                              PRA1  27 atsRvkkNllyfrtNYlivvllvlllslltnplslivllllvlawlflyflr...seplv.lfgrelsdr....... 92 
                                       + +R+++ l+ + t  ++v+l+  ++sl  +pl+l+ +l  +++ ++   l+         ++g+ ++ r       
  gi|313125710|ref|YP_004035980.1|   3 LHNRLRNGLHSWNTVVFAVFLAGTAISLHGRPLELLPVLKSIASGVLGAILFqftV---GnVWGYAVEYRntggsvt 76 
                                       67999*******************************99988888877777552442...323455553333555566 PP

                              PRA1  93 ........vvlivllvvsvlllfltg.avlvllwalliglllv 126
                                               vv i+  +v+++   +++ av++ +wa++i ++l 
  gi|313125710|ref|YP_004035980.1|  77 drrflapfVVAIAAGAVTYAYNATLDaAVWTAFWAFTIMMVLL 119
                                       667888779999999999999999998999*******999886 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0016        14      10      25 ..      11      26 ..       4      30 .. 0.82
   2 ?    2.8   0.7     0.013   1.1e+02      15      31 ..      82      98 ..      79      99 .. 0.85
   3 ?    2.2   3.8     0.019   1.7e+02       2      25 ..     100     123 ..      99     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0016
                              FixQ 10 adswgllflvllfygv 25
                                       +sw +++++++++g 
  gi|313125710|ref|YP_004035980.1| 11 LHSWNTVVFAVFLAGT 26
                                      689**********995 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.013
                              FixQ 15 llflvllfygvviyafr 31
                                        f v++ +g+v ya++
  gi|313125710|ref|YP_004035980.1| 82 APFVVAIAAGAVTYAYN 98
                                      56899**********96 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.019
                              FixQ   2 tyealrgfadswgllflvllfygv 25 
                                       t++a ++ a +++++ +vll +g+
  gi|313125710|ref|YP_004035980.1| 100 TLDAAVWTAFWAFTIMMVLLALGI 123
                                       6788899999*********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 885.92
//
Query:       gi|313125711|ref|YP_004035981.1|  [L=118]
Description: hypothetical protein Hbor_09420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.8    8.6  13.8          1    9.4   6.6    2.6  3  DUF1304   Protein of unknown function (DUF1304)
        2.5    8.4  10.2       0.67   10.3   0.8    2.7  3  DUF3382   Domain of unknown function (DUF3382)


Domain annotation for each model (and alignments):
>> DUF1304  Protein of unknown function (DUF1304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4     0.011        98      77     106 ..       2      37 ..       1      41 [. 0.64
   2 ?    4.6   0.2    0.0035        31      53      90 ..      40      78 ..      37      82 .. 0.85
   3 ?    9.4   6.6   0.00011         1      51      90 ..      67     108 ..      63     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.011
                           DUF1304  77 gcvvvaglygaltask...k...illvQglpallAl 106
                                       + v++ag++++l ++         +++ gl a++A+
  gi|313125711|ref|YP_004035981.1|   2 LAVFLAGFALSLQDTPlgrDsafVAVISGLAAVVAF 37 
                                       568999999999996655333445566666666665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0035
                           DUF1304 53 Aagliwglll.gseavglalvlfflgcvvvaglygalta 90
                                       +g iwg+++   +a g++  l fl+  v+a ++ga+t 
  gi|313125711|ref|YP_004035981.1| 40 TVGNIWGYAVeYYNAGGSWTDLPFLTPFVAAIAVGAVTY 78
                                      6899****8855777899999999999999999999996 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00011
                           DUF1304  51 fLAagliwgl.ll.gseavglalvlfflgcvvvaglygalta 90 
                                       f+Aa+++ ++ ++  +++ g+a++++f +++vvag++ ++t+
  gi|313125711|ref|YP_004035981.1|  67 FVAAIAVGAVtYFrIDPVLGAAAWAAFWTFIVVAGIVAVVTQ 108
                                       677777777754467999*********************997 PP

>> DUF3382  Domain of unknown function (DUF3382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.8   7.5e-05      0.67      16      55 ..       2      41 ..       1      50 [. 0.92
   2 ?   -0.9   0.1      0.23   2.1e+03      42      52 ..      70      80 ..      61      82 .. 0.76
   3 ?    3.9   0.4    0.0072        65       3      27 ..      85     110 ..      83     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.5e-05
                           DUF3382 16 lfvpilGlqleldgtrlvleprwglvaiavavvfvgqLlr 55
                                      l+v++ G+ l+l++t l   + +  v+ + a+v ++q+ +
  gi|313125711|ref|YP_004035981.1|  2 LAVFLAGFALSLQDTPLGRDSAFVAVISGLAAVVAFQFTV 41
                                      89999********************************976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.23
                           DUF3382 42 aiavavvfvgq 52
                                      aiav++v  ++
  gi|313125711|ref|YP_004035981.1| 70 AIAVGAVTYFR 80
                                      77888887777 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0072
                           DUF3382   3 LknAliaallalvlfvpilGl.qlel 27 
                                       L  A++aa+ ++++++ i+++ +   
  gi|313125711|ref|YP_004035981.1|  85 LGAAAWAAFWTFIVVAGIVAVvTQFS 110
                                       56799999999999999999855555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 725.75
//
Query:       gi|313125712|ref|YP_004035982.1|  [L=107]
Description: DNA-directed RNA polymerase subunit m [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-17   61.1   2.8    6.7e-17   61.1   2.8    2.9  3  TFIIS_C          Transcription factor S-II (TFIIS)
      1e-08   34.9   2.5      1e-08   34.9   2.5    3.0  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    0.00016   21.5  10.9      0.021   14.7   1.5    2.6  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    0.00039   19.9  14.4       0.18   11.4   3.0    4.0  3  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0004   20.0  14.4       0.49   10.2   0.1    4.4  4  zinc_ribbon_2    zinc-ribbon domain
    0.00044   19.6  16.3     0.0033   16.8   2.7    3.6  3  zf-ribbon_3      zinc-ribbon domain
     0.0016   18.4   1.6     0.0016   18.4   1.6    2.9  2  DZR              Double zinc ribbon
     0.0052   16.8   8.7       0.24   11.4   0.4    2.4  2  HypA             Hydrogenase/urease nickel incorporation, met
  ------ inclusion threshold ------
      0.012   15.6   0.9      0.012   15.6   0.9    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.014   15.6   8.5        8.5    6.7   0.1    4.1  4  zf-RING_7        C4-type zinc ribbon domain
       0.02   14.8   8.9         17    5.5   0.2    4.0  4  ADK_lid          Adenylate kinase, active site lid
      0.022   14.4   7.8       0.13   11.9   2.5    2.3  2  TackOD1          Thaumarchaeal output domain 1
      0.028   14.4   8.0      0.035   14.0   1.5    3.0  3  Prok-RING_1      Prokaryotic RING finger family 1
       0.04   14.0  13.9       0.14   12.2   1.9    4.0  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.05   13.3   1.6       0.05   13.3   1.6    3.9  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.094   13.1  13.4        1.2    9.6   0.1    3.2  3  Lar_restr_allev  Restriction alleviation protein Lar
       0.11   12.6  10.3       0.34   11.0   2.4    3.0  2  DUF2318          Predicted membrane protein (DUF2318)
       0.12   12.0  11.9        2.2    7.9   0.1    4.1  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.13   12.2   0.3       0.13   12.2   0.3    2.8  2  PriA_CRR         PriA DNA helicase Cys-rich region (CRR) doma
       0.14   12.1  10.5       0.12   12.4   2.0    2.4  2  zinc-ribbons_6   zinc-ribbons
       0.37   10.6   0.3       0.37   10.6   0.3    4.1  4  A2L_zn_ribbon    A2L zinc ribbon domain
       0.54   10.6   6.8        3.3    8.1   0.3    2.4  2  Cytochrom_CIII   Class III cytochrome C family
       0.68    9.9  12.8        7.2    6.6   0.1    4.1  4  Nudix_N_2        Nudix N-terminal
       0.78    9.5  12.5        2.9    7.6   0.4    3.5  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        0.8    9.7  13.7        2.4    8.1   0.8    3.7  4  zinc_ribbon_4    zinc-ribbon domain
       0.82    9.9  13.1    1.1e+03   -0.1  13.1    3.1  1  IBR              IBR domain, a half RING-finger domain
          1    9.3  15.0         11    6.0   0.2    4.0  3  zf-trcl          Probable zinc-ribbon domain
        1.2    9.0  19.2        7.1    6.5   1.1    4.3  4  Rubredoxin_2     Rubredoxin metal binding domain
        2.6    8.3  17.6         24    5.1   0.6    3.8  3  Zn-ribbon_8      Zinc ribbon domain
        2.7    8.1   9.9        2.5    8.2   1.0    2.9  2  Zn_Tnp_IS91      Transposase zinc-binding domain
        2.7    8.0  10.6         14    5.7   0.1    4.0  4  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
        3.4    8.2  11.8         44    4.6   0.2    4.0  4  zf-IS66          zinc-finger binding domain of transposase IS
        4.2    7.3  12.5        1.4    8.8   2.6    2.9  2  C1_1             Phorbol esters/diacylglycerol binding domain
        4.8    7.2  14.3        9.1    6.3   1.8    3.2  3  PHD              PHD-finger
        5.1    7.7   6.0         10    6.8   0.3    3.0  3  Trm112p          Trm112p-like protein
        5.5    7.9   9.4          4    8.3   3.6    2.4  2  Ima1_N           Ima1 N-terminal domain
        5.6    6.6  12.7        0.3   10.7   0.9    3.3  4  Sgf11            Sgf11 (transcriptional regulation protein)
          7    6.5   9.7        9.5    6.1   1.9    3.4  4  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        8.8    6.2   7.5        1.9    8.4   0.3    2.4  2  eIF-5_eIF-2B     Domain found in IF2B/IF5


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.86     4e+02       3       8 ..       4       9 ..       2      11 .. 0.71
   2 ?    1.8   0.1      0.48   2.2e+02      30      36 ..      19      25 ..      17      28 .. 0.67
   3 !   61.1   2.8   1.5e-19   6.7e-17       2      39 .]      67     104 ..      66     104 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.86
                           TFIIS_C 3 CpkCgs 8
                                     C +Cgs
  gi|313125712|ref|YP_004035982.1| 4 CDECGS 9
                                     777876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.48
                           TFIIS_C 30 kCtkCgh 36
                                      +C +Cg 
  gi|313125712|ref|YP_004035982.1| 19 VCSSCGA 25
                                      5777765 PP

  == domain 3  score: 61.1 bits;  conditional E-value: 1.5e-19
                           TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                       +C+ Cg+ ea+++ +Qt saDEp+t+f+kC++Cg rWr
  gi|313125712|ref|YP_004035982.1|  67 TCEDCGHGEAWYTIKQTGSADEPPTRFFKCKNCGRRWR 104
                                       8************************************8 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   2.5   2.2e-11     1e-08       1      35 [.       1      31 [.       1      32 [. 0.97
   2 ?    0.6   0.1       1.1   5.3e+02      24      28 ..      68      72 ..      57      74 .. 0.67
   3 ?    2.7   0.1      0.25   1.1e+02      20      28 ..      91     100 ..      85     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.2e-11
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EEESSC CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepadq 35
                                      ++FC +Cg+++ +++++ +    C++Cg+ ++ d+
  gi|313125712|ref|YP_004035982.1|  1 MQFCDECGSMMHNQDGQMV----CSSCGATQEQDS 31
                                      9******************....*********986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                                      ESSSS CS
                    RNA_POL_M_15KD 24 CrqCg 28
                                      C  Cg
  gi|313125712|ref|YP_004035982.1| 68 CEDCG 72
                                      55554 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.25
                                       CE.EEESSSS CS
                    RNA_POL_M_15KD  20 kn.feCrqCg 28 
                                       ++ f C +Cg
  gi|313125712|ref|YP_004035982.1|  91 TRfFKCKNCG 100
                                       4569999997 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.5   4.6e-05     0.021      30      59 ..       3      30 ..       2      36 .. 0.87
   2 !   11.0   2.3   0.00066       0.3      22      55 ..      59     102 ..      50     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-05
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadrD 59
                                       C eCgs + +  ++ +++C++Cg++   D
  gi|313125712|ref|YP_004035982.1|  3 FCDECGSMMHN--QDGQMVCSSCGATQEQD 30
                                      5**********..***********996655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00066
                    OrfB_Zn_ribbon  22 vnpayTSktCseCgsknke..........alsgrtfkCpnCgfe 55 
                                        +p  T  tC  Cg+              ++ +r fkC+nCg +
  gi|313125712|ref|YP_004035982.1|  59 GKPTATDVTCEDCGHGEAWytikqtgsadEPPTRFFKCKNCGRR 102
                                       57888999******976556666789999999*********976 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   3.0   0.00038      0.18       3      31 ..       4      29 ..       2      37 .. 0.78
   2 !    7.4   0.5    0.0067       3.1      15      26 ..      61      72 ..      53      74 .. 0.82
   3 ?    6.4   0.2     0.014       6.2       1       8 [.      94     101 ..      94     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                                      ETTTTCEECHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVled 31
                                      C +Cgs      +  g +vC++CG+  e 
  gi|313125712|ref|YP_004035982.1|  4 CDECGSM--MH-NQDGQMVCSSCGATQEQ 29
                                      9999994..34.577********986555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0067
                                      TSTTCEEESSSS CS
                      TF_Zn_Ribbon 15 pergelvCtdCG 26
                                      p  ++++C+dCG
  gi|313125712|ref|YP_004035982.1| 61 PTATDVTCEDCG 72
                                      67899******9 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.014
                                       EEETTTTC CS
                      TF_Zn_Ribbon   1 ykCPnCgs 8  
                                       +kC+nCg 
  gi|313125712|ref|YP_004035982.1|  94 FKCKNCGR 101
                                       79****97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.03        14      14      21 ..       2       9 ..       1      11 [. 0.83
   2 !   10.2   0.1    0.0011      0.49       9      21 ..      13      25 ..      12      26 .. 0.91
   3 ?    5.8   0.2     0.025        11      12      21 ..      64      73 ..      62      74 .. 0.82
   4 ?    5.0   2.1     0.047        22       1       7 [.      95     101 ..      95     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.03
                     zinc_ribbon_2 14 kFCpyCGt 21
                                      +FC +CG+
  gi|313125712|ref|YP_004035982.1|  2 QFCDECGS 9 
                                      69999996 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                     zinc_ribbon_2  9 lqdnakFCpyCGt 21
                                      +qd++  C+ CG+
  gi|313125712|ref|YP_004035982.1| 13 NQDGQMVCSSCGA 25
                                      89*********97 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.025
                     zinc_ribbon_2 12 nakFCpyCGt 21
                                      +++ C+ CG+
  gi|313125712|ref|YP_004035982.1| 64 TDVTCEDCGH 73
                                      5788999998 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.047
                     zinc_ribbon_2   1 fCpnCGa 7  
                                       +C+nCG+
  gi|313125712|ref|YP_004035982.1|  95 KCKNCGR 101
                                       7*****7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.7   7.3e-06    0.0033       2      24 ..       1      25 [.       1      27 [. 0.92
   2 !    7.2   0.8    0.0074       3.4       9      24 ..      59      73 ..      59      74 .. 0.89
   3 ?    4.0   0.4     0.076        35      18      23 ..      95     100 ..      94     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.3e-06
                       zf-ribbon_3  2 tvrCPnCGa.p.lssddnvCpyCGt 24
                                      +++C +CG+    +++++vC +CG+
  gi|313125712|ref|YP_004035982.1|  1 MQFCDECGSmMhNQDGQMVCSSCGA 25
                                      789*****99679***********6 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0074
                       zf-ribbon_3  9 GaplssddnvCpyCGt 24
                                      G+p ++ d++C  CG+
  gi|313125712|ref|YP_004035982.1| 59 GKP-TATDVTCEDCGH 73
                                      678.999********7 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.076
                       zf-ribbon_3  18 vCpyCG 23 
                                       +C++CG
  gi|313125712|ref|YP_004035982.1|  95 KCKNCG 100
                                       599999 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.6   3.6e-06    0.0016      13      41 ..       2      30 ..       1      36 [. 0.86
   2 ?    2.9   4.1      0.25   1.2e+02      14      36 ..      67     101 ..      54     104 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.6e-06
                               DZR 13 rfCseCgtklkavaaedrCpsCgekvdpe 41
                                      +fC+eCg+ + ++  + +C+sCg+  +++
  gi|313125712|ref|YP_004035982.1|  2 QFCDECGSMMHNQDGQMVCSSCGATQEQD 30
                                      7*********99999********987665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.25
                               DZR  14 fCseCgtk.....lkavaa..........edrCpsCge 36 
                                       +C++Cg+      +k   +            +C +Cg+
  gi|313125712|ref|YP_004035982.1|  67 TCEDCGHGeawytIK---QtgsadepptrFFKCKNCGR 101
                                       677777664433322...12335555555556666665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   2.7     0.003       1.4      72      96 ..       3      27 ..       1      38 [. 0.82
   2 !   11.4   0.4   0.00052      0.24      57      94 ..      52     101 ..      35     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.003
                                      EETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA 72 rCreCgkefeleekalrCpkCgsad 96
                                       C+eCg+ ++ ++ ++ C +Cg+++
  gi|313125712|ref|YP_004035982.1|  3 FCDECGSMMHNQDGQMVCSSCGATQ 27
                                      6*****99997754899*****976 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00052
                                       TTT-EEEEEEE--EEEETTTS-EEECHH.HHH............S-TTTSS CS
                              HypA  57 legaeLeieevpvkvrCreCgkefelee.kal............rCpkCgs 94 
                                        ega++e + +   v+C++Cg+     + k              +C++Cg+
  gi|313125712|ref|YP_004035982.1|  52 EEGANFEGKPTATDVTCEDCGHGEAWYTiK-QtgsadepptrffKCKNCGR 101
                                       468999999999*********655533322.1356788999999*****97 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.19        85      19      26 ..      18      25 ..      11      30 .. 0.72
   2 ?   15.6   0.9   2.6e-05     0.012      19      45 ..      66     101 ..      57     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.19
                     Zn_Tnp_IS1595 19 fvCPhCgs 26
                                       vC  Cg 
  gi|313125712|ref|YP_004035982.1| 18 MVCSSCGA 25
                                      67888885 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.6e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayrikt........rglfqCkeCrk 45 
                                       ++C  Cg+    y+ik+         + f+Ck C++
  gi|313125712|ref|YP_004035982.1|  66 VTCEDCGHGeAWYTIKQtgsadeppTRFFKCKNCGR 101
                                       78******989999999*****************98 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.018       8.5      25      32 ..       3      10 ..       1      11 [. 0.85
   2 ?    1.1   0.2         1   4.6e+02      25      30 ..      19      24 ..      12      25 .. 0.74
   3 ?    4.4   0.2     0.094        43      24      30 ..      66      72 ..      58      72 .. 0.91
   4 ?    6.3   0.0     0.024        11      23      31 ..      93     101 ..      76     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.018
                                      E-TTT--E CS
                         zf-RING_7 25 tCpeCGRI 32
                                      +C+eCG +
  gi|313125712|ref|YP_004035982.1|  3 FCDECGSM 10
                                      8*****87 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1
                                      E-TTT- CS
                         zf-RING_7 25 tCpeCG 30
                                       C +CG
  gi|313125712|ref|YP_004035982.1| 19 VCSSCG 24
                                      588888 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.094
                                      EE-TTT- CS
                         zf-RING_7 24 vtCpeCG 30
                                      vtC+ CG
  gi|313125712|ref|YP_004035982.1| 66 VTCEDCG 72
                                      8*****9 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.024
                                       -EE-TTT-- CS
                         zf-RING_7  23 vvtCpeCGR 31 
                                        ++C +CGR
  gi|313125712|ref|YP_004035982.1|  93 FFKCKNCGR 101
                                       689*****9 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.037        17      23      29 ..       3       9 ..       2      15 .. 0.82
   2 ?    4.8   0.1     0.062        28       2      10 ..      18      26 ..      17      32 .. 0.78
   3 ?    3.9   0.1      0.12        54      16      28 ..      60      72 ..      40      75 .. 0.81
   4 ?    4.4   0.1     0.079        36       4       9 ..      96     101 ..      81     107 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.037
                                      B-TTT-- CS
                           ADK_lid 23 lCDkCGe 29
                                      +CD+CG+
  gi|313125712|ref|YP_004035982.1|  3 FCDECGS 9 
                                      7*****8 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.062
                                      EE-TTT--E CS
                           ADK_lid  2 rvCpkCGrs 10
                                      +vC++CG++
  gi|313125712|ref|YP_004035982.1| 18 MVCSSCGAT 26
                                      478888875 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.12
                                      B--SSTTB-TTT- CS
                           ADK_lid 16 npPkveglCDkCG 28
                                      +p  ++  C +CG
  gi|313125712|ref|YP_004035982.1| 60 KPTATDVTCEDCG 72
                                      5667777788887 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.079
                                       -TTT-- CS
                           ADK_lid   4 CpkCGr 9  
                                       C++CGr
  gi|313125712|ref|YP_004035982.1|  96 CKNCGR 101
                                       778877 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.5   0.00029      0.13     147     176 ..       2      31 ..       1      41 [. 0.75
   2 ?    6.2   0.2     0.017       7.6      65     111 ..      57     101 ..      31     104 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                           TackOD1 147 ykCnsCkslfsepevkarClsCekesesdd 176
                                       + C++C+s++ +++ +++C sC++++e+d+
  gi|313125712|ref|YP_004035982.1|   2 QFCDECGSMMHNQDGQMVCSSCGATQEQDS 31 
                                       568888888888888888888888777654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                           TackOD1  65 leeelvdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCgn 111
                                       +e +   + ++C+ C +g+  ++   ++ +S+d   + ++++ +Cg+
  gi|313125712|ref|YP_004035982.1|  57 FEGKPTATDVTCEDCGHGEAWYT--IKQTGSADEPPTRFFKCKNCGR 101
                                       45666667778888887776554..4677888888888888888875 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.5   7.6e-05     0.035       6      30 ..       3      27 ..       1      31 [. 0.91
   2 ?    2.7   0.1      0.26   1.2e+02      21      27 ..      66      72 ..      56      81 .. 0.86
   3 ?   -0.2   0.1       2.1   9.6e+02       6      12 ..      95     101 ..      93     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.6e-05
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCgtpy 30
                                       C  Cg  ++++d   vC  Cg+ +
  gi|313125712|ref|YP_004035982.1|  3 FCDECGSMMHNQDGQMVCSSCGATQ 27
                                      6*********************986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.26
                       Prok-RING_1 21 VvCpeCg 27
                                      V+C +Cg
  gi|313125712|ref|YP_004035982.1| 66 VTCEDCG 72
                                      8999999 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.1
                       Prok-RING_1   6 kCpvCgk 12 
                                       kC+ Cg+
  gi|313125712|ref|YP_004035982.1|  95 KCKNCGR 101
                                       6777776 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.9   0.00031      0.14       4      26 .]       4      23 ..       4      23 .. 0.90
   2 ?    2.5   0.9      0.35   1.6e+02       4       8 ..      20      24 ..      18      26 .. 0.57
   3 ?    2.8   0.2      0.28   1.3e+02       3       9 ..      67      73 ..      66      74 .. 0.83
   4 ?    4.4   0.6     0.088        41       1       8 [.      93     100 ..      93     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
                            zf-ACC  4 CpsCgemlykkeLernlyVCPkC 26
                                      C++Cg+m+++++     +VC +C
  gi|313125712|ref|YP_004035982.1|  4 CDECGSMMHNQD---GQMVCSSC 23
                                      **********97...59999999 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.35
                            zf-ACC  4 CpsCg 8 
                                      C sCg
  gi|313125712|ref|YP_004035982.1| 20 CSSCG 24
                                      66666 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.28
                            zf-ACC  3 KCpsCge 9 
                                       C+ Cg+
  gi|313125712|ref|YP_004035982.1| 67 TCEDCGH 73
                                      7****96 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.088
                            zf-ACC   1 WtKCpsCg 8  
                                       ++KC  Cg
  gi|313125712|ref|YP_004035982.1|  93 FFKCKNCG 100
                                       79*****8 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.6   0.00011      0.05       7      29 ..       4      25 ..       1      28 [. 0.90
   2 ?    1.0   0.2      0.78   3.6e+02       6      15 ..      67      77 ..      64      79 .. 0.73
   3 ?    1.5   0.3      0.54   2.5e+02       7      12 ..      96     101 ..      93     104 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                           zf-RRN7  7 CgvCgcrsftlddGfyyCrrCht 29
                                      C++Cg+   +  dG+++C +C+ 
  gi|313125712|ref|YP_004035982.1|  4 CDECGS-MMHNQDGQMVCSSCGA 25
                                      999999.9999**********95 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.78
                           zf-RRN7  6 pCgvCgc.rsf 15
                                       C+ Cg    +
  gi|313125712|ref|YP_004035982.1| 67 TCEDCGHgEAW 77
                                      69999965555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.54
                           zf-RRN7   7 CgvCgc 12 
                                       C  Cg 
  gi|313125712|ref|YP_004035982.1|  96 CKNCGR 101
                                       777775 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.2    0.0076       3.5       8      53 ..       3      47 ..       2      53 .. 0.73
   2 ?    9.6   0.1    0.0026       1.2      20      51 ..      54      88 ..      44      92 .. 0.69
   3 ?    3.9   0.2      0.15        69      27      36 ..      89     101 ..      78     106 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0076
                   Lar_restr_allev  8 fCggravlersqrvvaeigqcvyCadCga.....stpwfkiaedeaeaeke 53
                                      fC + + + ++q+++      + C  Cga     s    ++ + ea+++ +
  gi|313125712|ref|YP_004035982.1|  3 FCDECGSMMHNQDGQ------MVCSSCGAtqeqdSDLASEFVSTEAQDDSD 47
                                      999999999999995......7999****8777655555555555555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0026
                   Lar_restr_allev 20 rvvaeigq...cvyCadCgastpwfkiaedeaeae 51
                                      +   e+ +    v+C+dCg ++ w++i +   ++e
  gi|313125712|ref|YP_004035982.1| 54 GANFEGKPtatDVTCEDCGHGEAWYTIKQTGSADE 88
                                      444433336668********999999887766655 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.15
                   Lar_restr_allev  27 q...cvyCadCga 36 
                                       +   ++ C++Cg 
  gi|313125712|ref|YP_004035982.1|  89 PptrFFKCKNCGR 101
                                       134599*****95 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.4   0.00074      0.34      35      62 ..       2      28 ..       1      35 [. 0.80
   2 ?    3.8   1.1      0.14        62      51      61 ..      93     103 ..      59     106 .. 0.44

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00074
                           DUF2318 35 daCevCekkgYvqegeelvCknCgvrfa 62
                                      + C+ C+++ + q + ++vC +Cg + +
  gi|313125712|ref|YP_004035982.1|  2 QFCDECGSMMHNQ-DGQMVCSSCGATQE 28
                                      68****9988765.668******98765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.14
                           DUF2318  51 elvCknCgvrf 61 
                                          CknCg r+
  gi|313125712|ref|YP_004035982.1|  93 FFKCKNCGRRW 103
                                       24566666555 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0048       2.2       3      13 ..       2      12 ..       1      15 [. 0.84
   2 ?    3.1   0.1      0.16        73       3      11 ..      18      26 ..      16      35 .. 0.76
   3 ?    5.1   0.3     0.037        17       2      10 ..      65      73 ..      64      74 .. 0.85
   4 ?    2.2   0.3      0.29   1.3e+02       3      10 ..      94     101 ..      92     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0048
                            zf_UBZ  3 ylCerCgkeip 13
                                      ++C++Cg+++ 
  gi|313125712|ref|YP_004035982.1|  2 QFCDECGSMMH 12
                                      69*****9985 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.16
                            zf_UBZ  3 ylCerCgke 11
                                       +C+ Cg++
  gi|313125712|ref|YP_004035982.1| 18 MVCSSCGAT 26
                                      68*****87 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.037
                            zf_UBZ  2 tylCerCgk 10
                                       ++Ce+Cg+
  gi|313125712|ref|YP_004035982.1| 65 DVTCEDCGH 73
                                      589****96 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.29
                            zf_UBZ   3 ylCerCgk 10 
                                       + C+ Cg+
  gi|313125712|ref|YP_004035982.1|  94 FKCKNCGR 101
                                       89****97 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   0.00029      0.13      11      26 ..      12      27 ..       4      27 .. 0.89
   2 ?    0.4   0.3       1.5   6.8e+02       1       5 [.      96     100 ..      94     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00029
                          PriA_CRR 11 HksrnrLrCHyCgyte 26
                                      H+++++++C  Cg+t+
  gi|313125712|ref|YP_004035982.1| 12 HNQDGQMVCSSCGATQ 27
                                      *************997 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.5
                          PriA_CRR   1 CpnCd 5  
                                       C+nC 
  gi|313125712|ref|YP_004035982.1|  96 CKNCG 100
                                       88885 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.0   0.00026      0.12       3      26 ..       4      27 ..       2      43 .. 0.88
   2 ?    4.7   1.6     0.065        30       2      24 ..      67     101 ..      55     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                                      -SSS-S--EE-SSEEE-TTT--EE CS
                    zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedl 26
                                      C eC + +++++ q+ C++C +  
  gi|313125712|ref|YP_004035982.1|  4 CDECGSMMHNQDGQMVCSSCGATQ 27
                                      *********9999*******8754 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.065
                                       --SSS-S--EE-S............SEEE-TTT-- CS
                    zinc-ribbons_6   2 kCpeCqqelekrg............eqyhCeaCqe 24 
                                       +C++C +   + +            + ++C++C +
  gi|313125712|ref|YP_004035982.1|  67 TCEDCGHGEAWYTikqtgsadepptRFFKCKNCGR 101
                                       57788777777777777777777766677777766 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5      0.24   1.1e+02      23      29 ..       3       9 ..       2      12 .. 0.88
   2 ?   10.6   0.3   0.00081      0.37      18      32 ..      14      28 ..      10      29 .. 0.87
   3 ?    2.3   0.4      0.32   1.5e+02       4      11 ..      66      73 ..      64      74 .. 0.76
   4 ?    2.4   0.5       0.3   1.4e+02       5      10 ..      95     100 ..      94     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.24
                     A2L_zn_ribbon 23 vCieCga 29
                                      +C eCg+
  gi|313125712|ref|YP_004035982.1|  3 FCDECGS 9 
                                      8****97 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00081
                     A2L_zn_ribbon 18 eqgylvCieCgasfp 32
                                       +g +vC  Cga+++
  gi|313125712|ref|YP_004035982.1| 14 QDGQMVCSSCGATQE 28
                                      5899********996 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.32
                     A2L_zn_ribbon  4 kvCsvCgg 11
                                      ++C+ Cg+
  gi|313125712|ref|YP_004035982.1| 66 VTCEDCGH 73
                                      67888887 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.3
                     A2L_zn_ribbon   5 vCsvCg 10 
                                       +C++Cg
  gi|313125712|ref|YP_004035982.1|  95 KCKNCG 100
                                       577776 PP

>> Cytochrom_CIII  Class III cytochrome C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.3     0.041        19      68      90 ..       9      31 ..       2      38 .. 0.69
   2 ?    8.1   0.3    0.0071       3.3       6      41 ..      40      80 ..      34     103 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.041
                                      HHHHCSSTTTCHHHHHHHHHHTS CS
                    Cytochrom_CIII 68 kavHkkkaaksCvgCHkkkkkek 90
                                      + +H+++ ++ C +C  ++++++
  gi|313125712|ref|YP_004035982.1|  9 SMMHNQDGQMVCSSCGATQEQDS 31
                                      56788777788888877776554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0071
                                      ECSSSTCCTCTSSSEEEEEHHHHT.TSHTHHHTSTT.....C CS
                    Cytochrom_CIII  6 kkapkeakkletkkavefnHkaHa.evkeCeeCHhk.....e 41
                                      ++a+++ + +et++ ++f+ k  a +v +Ce+C h       
  gi|313125712|ref|YP_004035982.1| 40 TEAQDDSDVIETEEGANFEGKPTAtDV-TCEDCGHGeawytI 80
                                      455555555699999****99998566.*****998454441 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.016       7.2       2      10 ..       3      11 ..       2      15 .. 0.82
   2 ?    5.2   0.2     0.042        19      24      31 ..      19      26 ..      17      29 .. 0.75
   3 ?    0.2   4.0       1.6   7.2e+02       3       9 ..      68      74 ..      67     101 .. 0.48
   4 ?    2.1   0.3      0.41   1.9e+02       3       8 ..      96     101 ..      92     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.016
                                      B-TTT--B- CS
                         Nudix_N_2  2 FCsqCGtpv 10
                                      FC +CG+ +
  gi|313125712|ref|YP_004035982.1|  3 FCDECGSMM 11
                                      9*****976 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.042
                                      EETTTTEE CS
                         Nudix_N_2 24 vCpaCgti 31
                                      vC++Cg++
  gi|313125712|ref|YP_004035982.1| 19 VCSSCGAT 26
                                      78888865 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.6
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C+ CG+ 
  gi|313125712|ref|YP_004035982.1| 68 CEDCGHG 74
                                      6666665 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.41
                                       -TTT-- CS
                         Nudix_N_2   3 CsqCGt 8  
                                       C++CG 
  gi|313125712|ref|YP_004035982.1|  96 CKNCGR 101
                                       778876 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.1      0.14        63       3      24 ..       4      24 ..       3      26 .. 0.80
   2 ?    4.3   0.1     0.071        32      18      25 ..      66      73 ..      60      74 .. 0.87
   3 ?    7.6   0.4    0.0063       2.9      19      26 ..      95     102 ..      89     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.14
                                      -SSS--B----SSS----SSS- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCG 24
                                      C eCg+ +  + g  + C  CG
  gi|313125712|ref|YP_004035982.1|  4 CDECGSMMHNQDGQMV-CSSCG 24
                                      8899999998888555.99998 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.071
                                      ---SSS-- CS
                    DNA_RNApol_7kD 18 iRCkeCGh 25
                                      + C +CGh
  gi|313125712|ref|YP_004035982.1| 66 VTCEDCGH 73
                                      78*****9 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0063
                                       --SSS--- CS
                    DNA_RNApol_7kD  19 RCkeCGhR 26 
                                       +Ck+CG R
  gi|313125712|ref|YP_004035982.1|  95 KCKNCGRR 102
                                       8*****98 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       4.6   2.1e+03      28      32 ..       4       8 ..       4      12 .. 0.61
   2 ?    3.0   0.1      0.22     1e+02      28      33 ..      20      25 ..      13      28 .. 0.66
   3 ?    6.3   0.2     0.019       8.8      21      33 ..      61      73 ..      60      74 .. 0.84
   4 ?    8.1   0.8    0.0053       2.4      26      36 .]      94     104 ..      88     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.6
                     zinc_ribbon_4 28 CskCg 32
                                      C  Cg
  gi|313125712|ref|YP_004035982.1|  4 CDECG 8 
                                      55555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.22
                     zinc_ribbon_4 28 CskCgh 33
                                      Cs Cg+
  gi|313125712|ref|YP_004035982.1| 20 CSSCGA 25
                                      666654 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.019
                     zinc_ribbon_4 21 akgvkvrCskCgh 33
                                      ++++ v+C  Cgh
  gi|313125712|ref|YP_004035982.1| 61 PTATDVTCEDCGH 73
                                      6778999999999 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0053
                     zinc_ribbon_4  26 vrCskCghvFr 36 
                                        +C++Cg  +r
  gi|313125712|ref|YP_004035982.1|  94 FKCKNCGRRWR 104
                                       69*******97 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1  13.1       2.4   1.1e+03      20      45 ..       3      24 ..       1     106 [. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.4
                               IBR 20 wCprpdCeaiieksegcksvtCskCg 45
                                       C   +C++++++++g  ++ Cs+Cg
  gi|313125712|ref|YP_004035982.1|  3 FCD--ECGSMMHNQDG--QMVCSSCG 24
                                      576..89999999888..44566665 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       2.4   1.1e+03       7      12 ..       4       9 ..       2      11 .. 0.82
   2 ?    6.0   0.2     0.024        11       1      13 [.      14      26 ..      14      28 .. 0.88
   3 ?    4.8   5.0     0.055        25       5      22 ..      66      83 ..      64     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.4
                           zf-trcl  7 CkdCga 12
                                      C +Cg+
  gi|313125712|ref|YP_004035982.1|  4 CDECGS 9 
                                      999997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.024
                           zf-trcl  1 eDktltCkdCgae 13
                                      +D +++C +Cga+
  gi|313125712|ref|YP_004035982.1| 14 QDGQMVCSSCGAT 26
                                      6999*******96 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.055
                           zf-trcl  5 ltCkdCgaefvFtageQe 22
                                      +tC+dCg  + ++   Q 
  gi|313125712|ref|YP_004035982.1| 66 VTCEDCGHGEAWYTIKQT 83
                                      69******9999887774 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.079        36       3       9 ..       4      10 ..       3      17 .. 0.78
   2 ?    6.5   1.1     0.015       7.1       2      11 ..      19      28 ..      19      29 .. 0.85
   3 ?    4.0   0.2     0.088        41       3       9 ..      68      74 ..      67      82 .. 0.81
   4 ?    5.8   1.0     0.024        11       1       8 [.      94     101 ..      94     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.079
                      Rubredoxin_2  3 CsqCGfe 9 
                                      C++CG+ 
  gi|313125712|ref|YP_004035982.1|  4 CDECGSM 10
                                      9999986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.015
                      Rubredoxin_2  2 vCsqCGfesa 11
                                      vCs+CG+++ 
  gi|313125712|ref|YP_004035982.1| 19 VCSSCGATQE 28
                                      7*****9975 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.088
                      Rubredoxin_2  3 CsqCGfe 9 
                                      C++CG+ 
  gi|313125712|ref|YP_004035982.1| 68 CEDCGHG 74
                                      9999986 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.024
                      Rubredoxin_2   1 YvCsqCGf 8  
                                       + C++CG 
  gi|313125712|ref|YP_004035982.1|  94 FKCKNCGR 101
                                       78****96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.4     0.056        26       8      35 ..       4      26 ..       2      30 .. 0.68
   2 ?    5.1   0.6     0.053        24      26      34 ..      65      73 ..      54      77 .. 0.66
   3 ?    3.4   6.1      0.19        85       7      34 ..      67     101 ..      65     104 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.056
                       Zn-ribbon_8  8 CeeCghefevlqsis.dapltaCPeCgse 35
                                      C+eCg        ++ ++ + +C +Cg++
  gi|313125712|ref|YP_004035982.1|  4 CDECG------SMMHnQDGQMVCSSCGAT 26
                                      88888......22343556777****984 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.053
                       Zn-ribbon_8 26 ltaCPeCgs 34
                                      +++C +Cg+
  gi|313125712|ref|YP_004035982.1| 65 DVTCEDCGH 73
                                      455666665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.19
                       Zn-ribbon_8   7 rCeeCghefe...vlqsis.dap...ltaCPeCgs 34 
                                        Ce+Cgh      + q+ s d+p     +C++Cg 
  gi|313125712|ref|YP_004035982.1|  67 TCEDCGHGEAwytIKQTGSaDEPptrFFKCKNCGR 101
                                       58888865546665555555555233334777775 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.0    0.0055       2.5      41      70 ..       3      30 ..       1      40 [. 0.87
   2 ?    2.5   2.3      0.34   1.5e+02      40      52 ..      66      78 ..      59     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0055
                       Zn_Tnp_IS91 41 eCeeCghekivyfsCksrhCpsCqkkatee 70
                                       C+eCg+  +++++ ++  C+sC++ ++++
  gi|313125712|ref|YP_004035982.1|  3 FCDECGS--MMHNQDGQMVCSSCGATQEQD 30
                                      5****95..99999999*******988765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.34
                       Zn_Tnp_IS91 40 yeCeeCghekivy 52
                                      + Ce+Cgh + +y
  gi|313125712|ref|YP_004035982.1| 66 VTCEDCGHGEAWY 78
                                      6788888876665 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3      0.27   1.2e+02      22      27 ..       4       9 ..       3      10 .. 0.86
   2 ?    5.7   0.1     0.031        14      18      26 ..      16      24 ..      12      25 .. 0.85
   3 ?    3.0   0.4      0.21        98      22      27 ..      68      73 ..      66      74 .. 0.88
   4 ?    0.8   0.0       1.1     5e+02      22      26 ..      96     100 ..      90     104 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.27
                    PhnA_Zn_Ribbon 22 CpeCah 27
                                      C+eC++
  gi|313125712|ref|YP_004035982.1|  4 CDECGS 9 
                                      999986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.031
                    PhnA_Zn_Ribbon 18 allvCpeCa 26
                                        +vC+ C+
  gi|313125712|ref|YP_004035982.1| 16 GQMVCSSCG 24
                                      57******7 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.21
                    PhnA_Zn_Ribbon 22 CpeCah 27
                                      C++C+h
  gi|313125712|ref|YP_004035982.1| 68 CEDCGH 73
                                      999998 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.1
                    PhnA_Zn_Ribbon  22 CpeCa 26 
                                       C +C+
  gi|313125712|ref|YP_004035982.1|  96 CKNCG 100
                                       55665 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3       0.1        47       3      12 ..       3      12 ..       2      17 .. 0.84
   2 ?    4.6   0.2     0.095        44       3      22 ..      19      41 ..      17      43 .. 0.80
   3 ?    3.9   0.1      0.16        74       3      10 ..      67      75 ..      65      85 .. 0.82
   4 ?    1.2   0.2       1.1   5.2e+02       4       8 ..      96     100 ..      94     104 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.1
                           zf-IS66  3 tCpcCGgllk 12
                                       C++CG+ ++
  gi|313125712|ref|YP_004035982.1|  3 FCDECGSMMH 12
                                      6*****9887 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.095
                           zf-IS66  3 tCpcCGg.l..lkpigedrvree 22
                                      +C+ CG+ +   + ++ ++v+ e
  gi|313125712|ref|YP_004035982.1| 19 VCSSCGAtQeqDSDLASEFVSTE 41
                                      6*****96688888888888865 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.16
                           zf-IS66  3 tCpcCGg.l 10
                                      tC +CG+ +
  gi|313125712|ref|YP_004035982.1| 67 TCEDCGHgE 75
                                      7*****955 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1.1
                           zf-IS66   4 CpcCG 8  
                                       C++CG
  gi|313125712|ref|YP_004035982.1|  96 CKNCG 100
                                       66666 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.6    0.0031       1.4      12      36 ..       2      25 ..       1      30 [. 0.79
   2 ?    2.5   2.5      0.29   1.3e+02      24      36 ..      89     101 ..      56     103 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0031
                                      -B-TTT-SB--SSSS-EEEETTT-- CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswCkl 36
                                      +fC++Cg+++ +     + Cs C+ 
  gi|313125712|ref|YP_004035982.1|  2 QFCDECGSMM-HNQDGQMVCSSCGA 25
                                      79********.65555678999986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.29
                                       SSS-EEEETTT-- CS
                              C1_1  24 kekqglkCswCkl 36 
                                         ++ +kC++C++
  gi|313125712|ref|YP_004035982.1|  89 PPTRFFKCKNCGR 101
                                       4566789999986 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.7      0.02       9.2      17      27 ..       3      13 ..       1      15 [. 0.87
   2 ?    0.9   0.3      0.97   4.5e+02       2      11 ..      20      29 ..      19      35 .. 0.60
   3 ?    6.3   1.8      0.02       9.1      16      50 ..      66     100 ..      56     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                                      EETTTSCEEET CS
                               PHD 17 qCdgCkrwfHq 27
                                      +Cd+C++ +H+
  gi|313125712|ref|YP_004035982.1|  3 FCDECGSMMHN 13
                                      8*********7 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.97
                                      BTTTTSTTST CS
                               PHD  2 CavCkkksde 11
                                      C+ C++++++
  gi|313125712|ref|YP_004035982.1| 20 CSSCGATQEQ 29
                                      7788773333 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.02
                                       EEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                               PHD  16 vqCdgCkrwfHqkClkppleseekpegewlCekCk 50 
                                       v C++C++    + +k + + +e p++ + C++C 
  gi|313125712|ref|YP_004035982.1|  66 VTCEDCGHGEAWYTIKQTGSADEPPTRFFKCKNCG 100
                                       78999998888888888888888888899999995 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3     0.023        10      47      60 ..      11      24 ..       3      26 .. 0.88
   2 ?    1.9   0.0      0.73   3.4e+02      53      66 ..      65      81 ..      27      83 .. 0.71
   3 ?    0.9   0.2       1.5   6.9e+02      55      62 ..      95     102 ..      91     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.023
                                      EECCCCEEEETTTT CS
                           Trm112p 47 ldieegeLvCpncg 60
                                      ++ ++g++vC++cg
  gi|313125712|ref|YP_004035982.1| 11 MHNQDGQMVCSSCG 24
                                      58899********9 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.73
                                      EEEETTTTE...EEEEE CS
                           Trm112p 53 eLvCpncgr...aYpIk 66
                                        +C++cg+   +Y Ik
  gi|313125712|ref|YP_004035982.1| 65 DVTCEDCGHgeaWYTIK 81
                                      55799997644477766 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.5
                                       EETTTTEE CS
                           Trm112p  55 vCpncgra 62 
                                        C+ncgr 
  gi|313125712|ref|YP_004035982.1|  95 KCKNCGRR 102
                                       7****996 PP

>> Ima1_N  Ima1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.6    0.0087         4      69     119 ..      11      60 ..       2      74 .. 0.57
   2 ?    2.3   0.3      0.64   2.9e+02       4      26 ..      77     100 ..      75     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0087
                            Ima1_N  69 essssssllCskClknqelkvsklaeylpkededdpeyeekeealeeykke 119
                                       +++++ +++Cs+C   qe      +e++++e++dd+++ e+ e+  +++ +
  gi|313125712|ref|YP_004035982.1|  11 MHNQDGQMVCSSCGATQEQDSDLASEFVSTEAQDDSDVIET-EEGANFEGK 60 
                                       45666677788888888888888888877666666653333.333444444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.64
                            Ima1_N   4 ffCnkkskvkyeekns.feCpsCe 26 
                                       ++  k++    e  ++ f+C++C 
  gi|313125712|ref|YP_004035982.1|  77 WYTIKQTGSADEPPTRfFKCKNCG 100
                                       677777777777777789****96 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       4.5   2.1e+03       7      11 ..       4       8 ..       3      12 .. 0.83
   2 ?   -0.8   0.2       2.6   1.2e+03       6      11 ..      19      24 ..      17      25 .. 0.85
   3 ?    3.0   0.1      0.17        77       3      11 ..      64      72 ..      62      73 .. 0.84
   4 ?   10.7   0.9   0.00065       0.3       2      12 ..      91     101 ..      90     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.5
                                      -TTTS CS
                             Sgf11  7 CpnCg 11
                                      C+ Cg
  gi|313125712|ref|YP_004035982.1|  4 CDECG 8 
                                      999*8 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.6
                                      E-TTTS CS
                             Sgf11  6 tCpnCg 11
                                      +C  Cg
  gi|313125712|ref|YP_004035982.1| 19 VCSSCG 24
                                      7****7 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.17
                                      -EEE-TTTS CS
                             Sgf11  3 eyvtCpnCg 11
                                      ++vtC+ Cg
  gi|313125712|ref|YP_004035982.1| 64 TDVTCEDCG 72
                                      689*****8 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00065
                                       C-EEE-TTTSS CS
                             Sgf11   2 seyvtCpnCgR 12 
                                       +++++C+nCgR
  gi|313125712|ref|YP_004035982.1|  91 TRFFKCKNCGR 101
                                       679*******9 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.9     0.021       9.5       4      16 ..       4      16 ..       1      23 [. 0.88
   2 ?   -0.7   0.2       2.9   1.3e+03       3       9 ..      19      25 ..      17      27 .. 0.80
   3 ?    3.5   0.1      0.13        62       2       9 ..      66      74 ..      65      84 .. 0.85
   4 ?   -0.9   0.2       3.1   1.4e+03       3       8 ..      95     100 ..      92     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                                      -SSS--EEEEEE- CS
                    zf-C4_Topoisom  4 CPkCggdLvlkrg 16
                                      C++Cg+ ++ + g
  gi|313125712|ref|YP_004035982.1|  4 CDECGSMMHNQDG 16
                                      ********99877 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.9
                                      E-SSS-- CS
                    zf-C4_Topoisom  3 kCPkCgg 9 
                                       C +Cg+
  gi|313125712|ref|YP_004035982.1| 19 VCSSCGA 25
                                      5999*96 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.13
                                      EE-SSS-.- CS
                    zf-C4_Topoisom  2 ekCPkCg.g 9 
                                      ++C+ Cg g
  gi|313125712|ref|YP_004035982.1| 66 VTCEDCGhG 74
                                      79****955 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.1
                                       E-SSS- CS
                    zf-C4_Topoisom   3 kCPkCg 8  
                                       kC  Cg
  gi|313125712|ref|YP_004035982.1|  95 KCKNCG 100
                                       688887 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.9      0.97   4.5e+02      90     116 ..       4      25 ..       2      26 .. 0.57
   2 ?    8.4   0.3    0.0042       1.9      88     116 ..      66     101 ..      62     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.97
                                       TSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  90 CkeCkspetelekeerllvlkCkaCga 116
                                       C eC+s+   ++  ++ + + C++Cga
  gi|313125712|ref|YP_004035982.1|   4 CDECGSM---MHN-QDGQ-MVCSSCGA 25 
                                       6666654...222.3333.46999997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0042
                                       TSTSSSTSTCEEECC.......SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  88 VlCkeCkspetelek.......eerllvlkCkaCga 116
                                       V+C+ C++ e   ++       e  + ++kCk+Cg+
  gi|313125712|ref|YP_004035982.1|  66 VTCEDCGHGEAWYTIkqtgsadEPPTRFFKCKNCGR 101
                                       89*****9998777656777655778899*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 603.55
//
Query:       gi|313125713|ref|YP_004035983.1|  [L=208]
Description: hypothetical protein Hbor_09440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   11.1   4.1       0.22   10.7   4.1    1.2  1  SMN       Survival motor neuron protein (SMN)


Domain annotation for each model (and alignments):
>> SMN  Survival motor neuron protein (SMN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.1   1.2e-05      0.22     111     181 ..       7      79 ..       1     109 [. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.2e-05
                               SMN 111 eeqnladllteasdededalkeanvnetesstdesdrss..rsakakdksnleiakssqknlrfppvppptpp 181
                                       +++ l+d+    +d d     +++ + +e+s  +sdr s  r++ a+ ++ ++  + s+  +  p +p pt  
  gi|313125713|ref|YP_004035983.1|   7 DDEPLSDIARRVTDDDSAETTNHDAETDEMSGADSDRESddRTTAADRSDATNAVHRSEETNAVPDSPAPTDD 79 
                                       455799**999999766667777888899********99777777777778888899999999*****99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1260.20
//
Query:       gi|313125714|ref|YP_004035984.1|  [L=282]
Description: ribbon-helix-helix protein, copg family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0019   18.5   0.2     0.0077   16.6   0.1    1.9  2  Chlamy_scaf     Chlamydia-phage Chp2 scaffold (Chlamy_scaf)
      0.007   16.3   0.6      0.007   16.3   0.6    2.7  2  RHH_1           Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.021   15.2   0.1      0.049   14.0   0.1    1.6  1  NTS_2           N-terminal segments of P. falciparum erythroc
       0.03   14.6   2.6      0.047   13.9   0.8    2.2  2  DUF948          Bacterial protein of unknown function (DUF948
      0.048   14.4   0.3      0.078   13.7   0.3    1.3  1  zinc_ribbon_15  zinc-ribbon family
       0.06   13.3   0.4      0.099   12.6   0.4    1.3  1  zinc-ribbons_6  zinc-ribbons
      0.071   12.2   0.1        0.1   11.7   0.1    1.2  1  FH2             Formin Homology 2 Domain
       0.14   12.2   1.0        3.2    7.8   0.3    2.2  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
       0.17   12.4   2.3        2.5    8.6   0.2    2.4  2  NPV_P10         Nucleopolyhedrovirus P10 protein
       0.17   10.0   3.1       0.24    9.5   0.6    1.9  2  E3_UbLigase_R4  E3 ubiquitin-protein ligase UBR4
       0.27   10.9   2.8       0.25   11.0   1.3    1.7  2  Mt_ATP-synt_B   Mitochondrial ATP synthase B chain precursor 
       0.38   10.8   2.1        4.2    7.4   0.2    2.9  3  P4Ha_N          Prolyl 4-Hydroxylase alpha-subunit, N-termina
        1.9    8.7   6.6        8.3    6.7   0.2    3.3  3  XhlA            Haemolysin XhlA
        2.1    6.8   4.8        3.2    6.2   4.8    1.2  1  RRN3            RNA polymerase I specific transcription initi
        2.2    8.9   7.7         55    4.4   5.2    2.8  2  YtxH            YtxH-like protein


Domain annotation for each model (and alignments):
>> Chlamy_scaf  Chlamydia-phage Chp2 scaffold (Chlamy_scaf)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   6.4e-06    0.0077      28      99 ..      97     167 ..      78     175 .. 0.84
   2 ?   -1.0   0.0       1.8   2.2e+03      16      35 ..     218     237 ..     212     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.4e-06
                       Chlamy_scaf  28 yGeqssildyqdaleivakaeeafdelPanirkrfanPmellsfledPknrdeveklGlldpekveirkskl 99 
                                       +G+     d  +al+ va  +e+  el  ++   f n  ++l++l d ++  e+ kl  +    v++rk+  
  gi|313125714|ref|YP_004035984.1|  97 HGHPELAADTESALNAVADVRETVSELERRMDAGFENYEDVLEYLTDTADETEA-KLDTVANAIVDLRKRTA 167
                                       56666778999*************************************999887.67777788888888765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                       Chlamy_scaf  16 hlfagdarrqgeyGeqssil 35 
                                         f g   +qg++G  s   
  gi|313125714|ref|YP_004035984.1| 218 ETFDGVREKQGFFGSASLTT 237
                                       568899999*****988655 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   5.8e-06     0.007       5      37 ..       8      40 ..       8      41 .. 0.94
   2 ?   -1.3   0.8         2   2.4e+03       6      20 ..      67      81 ..      65      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.8e-06
                                      EEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  5 rldeellerLdelarrrgrSrSelIReAlreyl 37
                                      +l++el + ++++ +++g  rSel+++Al +y+
  gi|313125714|ref|YP_004035984.1|  8 TLSDELERWVEKKSAESGIDRSELVKRALTAYR 40
                                      5899*************************9996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                      EEHHHHHHHHHHHHH CS
                             RHH_1  6 ldeellerLdelarr 20
                                      l+++l+e++  l++r
  gi|313125714|ref|YP_004035984.1| 67 LEADLDEKVTDLRER 81
                                      788999999888875 PP

>> NTS_2  N-terminal segments of P. falciparum erythrocyte membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.1e-05     0.049       3      27 ..       5      29 ..       3      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                             NTS_2  3 ststigdkiEaYLekksDdSkieqs 27
                                         t++d +E ++ekks +S i++s
  gi|313125714|ref|YP_004035984.1|  5 RVETLSDELERWVEKKSAESGIDRS 29
                                      56799******************87 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.9   2.2e+03      29      51 ..      58      80 ..      52      91 .. 0.52
   2 ?   13.9   0.8   3.9e-05     0.047      27      74 ..     112     159 ..     106     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                            DUF948 29 deaaatieelekqvdpilkeved 51
                                      d +++++ +le ++d+ ++++++
  gi|313125714|ref|YP_004035984.1| 58 DDLEERVIDLEADLDEKVTDLRE 80
                                      55555555555555554444443 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.9e-05
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplt 74 
                                        +  +++t+ ele+++d+  ++ ed+l+   +++++ + kl++v + +
  gi|313125714|ref|YP_004035984.1| 112 AVADVRETVSELERRMDAGFENYEDVLEYLTDTADETEAKLDTVANAI 159
                                       67889************************************9997655 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   6.5e-05     0.078      55      85 ..     183     216 ..     158     217 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                    zinc_ribbon_15  55 keiekkesse...kkeCknCgkeveee...fkyCpkC 85 
                                       k+  ++   +   +  C++C+++v+ +   + yCp+C
  gi|313125714|ref|YP_004035984.1| 183 KREANR---KgisTANCQSCEHTVDISlldVPYCPHC 216
                                       223333...25559**********98644489***** PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   8.3e-05     0.099      15      40 ..     192     221 ..     174     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-05
                                       SEEE-TTT--....EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6  15 eqyhCeaCqe....dlkkealCpeCeqele 40 
                                       ++++C++C++    +l  +++Cp+C++  +
  gi|313125714|ref|YP_004035984.1| 192 STANCQSCEHtvdiSLLDVPYCPHCRETFD 221
                                       7899*****97766677899*****99765 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.6e-05       0.1     280     364 ..      70     159 ..      63     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHT..T-- CS
                               FH2 280 slekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeak...elvkelveYf..ged 351
                                       +l+++v +l++++ ++++e ++++ +++ + ++ + +++ l+  ++  ++++e+++++    e++++++eY+   +d
  gi|313125714|ref|YP_004035984.1|  70 DLDEKVTDLRERVIQVKRESDRKAPEDHGHPELAADTESALNAVADVRETVSELERRMDagfENYEDVLEYLtdTAD 146
                                       6999*********************9999999999999999988887777777777776333788899****76555 PP

                                       TTCCHHHHHHHHH CS
                               FH2 352 kkevspeeffkil 364
                                       ++e++++ + + +
  gi|313125714|ref|YP_004035984.1| 147 ETEAKLDTVANAI 159
                                       5577777766655 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.085     1e+02      47      79 ..      53      85 ..      46      92 .. 0.65
   2 ?    7.8   0.3    0.0027       3.2      44      99 ..     107     164 ..     101     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.085
                      Baculo_PEP_C 47 LnalsedlksllaeldtrldtlltnLtdalnal 79
                                      L+  ++dl++ + +l+++ld+ +t L + + ++
  gi|313125714|ref|YP_004035984.1| 53 LGGRADDLEERVIDLEADLDEKVTDLRERVIQV 85
                                      445556666666777777777777777666665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0027
                      Baculo_PEP_C  44 etqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLls 99 
                                       e+ Lna  +d+++ ++el++r+d+ ++n +d l  l+   d+ + +L+++ + + +L  
  gi|313125714|ref|YP_004035984.1| 107 ESALNA-VADVRETVSELERRMDAGFENYEDVLEYLTdtaDETEAKLDTVANAIVDLRK 164
                                       555666.4568888888888999988888888888886666667778888877777765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1       0.1   1.2e+02      15      34 ..      70      89 ..      60      93 .. 0.85
   2 ?    8.6   0.2    0.0021       2.5      10      60 ..     110     161 ..     108     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                           NPV_P10 15 avddkVdalqqqvddvqenl 34
                                      ++d+kV+ l ++v +v+ ++
  gi|313125714|ref|YP_004035984.1| 70 DLDEKVTDLRERVIQVKRES 89
                                      68999999999999998765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0021
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvte.lnekLdaqsaqLaeletkven 60 
                                       ++++++v + V+ l+ ++d   en +dv e l++  d+  a+L+++ +++ +
  gi|313125714|ref|YP_004035984.1| 110 LNAVADVRETVSELERRMDAGFENYEDVLEyLTDTADETEAKLDTVANAIVD 161
                                       689999999*********9999999998554899999999999999987754 PP

>> E3_UbLigase_R4  E3 ubiquitin-protein ligase UBR4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       0.1   1.2e+02     391     433 ..      47      92 ..      42      98 .. 0.81
   2 ?    9.5   0.6    0.0002      0.24     402     483 ..     135     220 ..     126     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.1
                    E3_UbLigase_R4 391 vsseeeiGslAEnlLeaLkekeekvakkieevRket...keekkrl 433
                                        s++ e+G +A++l e + + e+++ +k++++R++    k+e  r+
  gi|313125714|ref|YP_004035984.1|  47 LSADGELGGRADDLEERVIDLEADLDEKVTDLRERViqvKRESDRK 92 
                                       68999****************************9651115555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0002
                    E3_UbLigase_R4 402 EnlLeaLkekeek.......vakkieevRketkeekkrlAlakRekqLkeLgmktnekgqvivsssileqledleee 471
                                       E++Le L+++ ++       va++i ++Rk+t e+++  A++      +eL  ++n kg  +++ ++ e+  d++  
  gi|313125714|ref|YP_004035984.1| 135 EDVLEYLTDTADEteakldtVANAIVDLRKRTAEAERTAAKRVAA---TELKREANRKGISTANCQSCEHTVDISLL 208
                                       788999988877744445556666666666666555555544443...45556799********************* PP

                    E3_UbLigase_R4 472 dglvCvvCrEgy 483
                                       d   C  CrE +
  gi|313125714|ref|YP_004035984.1| 209 DVPYCPHCRETF 220
                                       **********86 PP

>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         4   4.8e+03     113     135 ..      11      33 ..       8      34 .. 0.76
   2 ?   11.0   1.3   0.00021      0.25      44     123 ..     118     198 ..     107     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_B 113 kkldtlvnaessrrqrlQdelvk 135
                                       + l+ +v+++s++    ++elvk
  gi|313125714|ref|YP_004035984.1|  11 DELERWVEKKSAESGIDRSELVK 33 
                                       67899999999888777777765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC.CHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_B  44 kriekiqeelnqsrnlkeealkerieqekklq.slveltkslfevskeqvaleaeaferelqaklareikkkldtlv 119
                                       + +++ ++ +++ +++ e++l+++ +   ++  +l  + + +++  k ++++e  a++r  +++l+re+++k  +  
  gi|313125714|ref|YP_004035984.1| 118 ETVSELERRMDAGFENYEDVLEYLTDTADETEaKLDTVANAIVDLRKRTAEAERTAAKRVAATELKREANRKGISTA 194
                                       5688899999***************99998886899999*********************************99999 PP

                                       HHHH CS
                     Mt_ATP-synt_B 120 naes 123
                                       n++s
  gi|313125714|ref|YP_004035984.1| 195 NCQS 198
                                       9887 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.54   6.5e+02      34      65 ..      10      42 ..       4      44 .. 0.60
   2 ?    0.1   0.1      0.63   7.6e+02      25      48 ..      70      94 ..      58     113 .. 0.72
   3 ?    7.4   0.2    0.0035       4.2      13      50 ..     135     172 ..     124     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.54
                            P4Ha_N 34 krfleeleeeh.esakedkeeylsnPlnaFkli 65
                                      +  le++ e++  ++  d++e+++  l a++l+
  gi|313125714|ref|YP_004035984.1| 10 SDELERWVEKKsAESGIDRSELVKRALTAYRLV 42
                                      443333333221335678888999999999997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.63
                            P4Ha_N 25 eeekkleklkrfleeleeehes.ak 48
                                      ++ +k+ +l++ + ++++e+++ a+
  gi|313125714|ref|YP_004035984.1| 70 DLDEKVTDLRERVIQVKRESDRkAP 94
                                      5678888888888888888855233 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0035
                            P4Ha_N  13 relveeLesyieeeekkleklkrfleeleeehesaked 50 
                                       ++++e L++ ++e+e+kl+++ +++ +l++++ +a+++
  gi|313125714|ref|YP_004035984.1| 135 EDVLEYLTDTADETEAKLDTVANAIVDLRKRTAEAERT 172
                                       678999************************99775554 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.7     0.081        97      11      31 ..      55      75 ..      51      87 .. 0.74
   2 ?    6.7   0.2     0.007       8.3       8      46 ..     126     164 ..     115     167 .. 0.78
   3 ?    3.3   0.3     0.081        97       8      32 ..     147     171 ..     141     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.081
                              XhlA 11 tkldnleervdkleekaaeae 31
                                      ++ d+leerv +le + +e  
  gi|313125714|ref|YP_004035984.1| 55 GRADDLEERVIDLEADLDEKV 75
                                      577888999999888877654 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.007
                              XhlA   8 rietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                       r+++  +n+e+ ++ l + a+e+e+k++ + + + +l +
  gi|313125714|ref|YP_004035984.1| 126 RMDAGFENYEDVLEYLTDTADETEAKLDTVANAIVDLRK 164
                                       45555679***999***************9999988865 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.081
                              XhlA   8 rietkldnleervdkleekaaeaee 32 
                                       ++e+kld+  + + +l ++ aeae 
  gi|313125714|ref|YP_004035984.1| 147 ETEAKLDTVANAIVDLRKRTAEAER 171
                                       6899999999999999999999885 PP

>> RRN3  RNA polymerase I specific transcription initiation factor RRN3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.8    0.0027       3.2     209     321 ..      49     162 ..      36     175 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0027
                              RRN3 209 iDVeiqveledlddeedeeleeeleededdedddedd.....eesdlddlssdeeaeedee.kdeeeeslkkikelv 279
                                        D e+    +dl++   + +  +l+e+ +d      +     + +++ +  +d++  e ++ ++++ +++ +++e+v
  gi|313125714|ref|YP_004035984.1|  49 ADGELGGRADDLEERVIDLEA-DLDEKVTDL---R-ErviqvKRESDRKAPEDHGHPELAAdTESALNAVADVRETV 120
                                       566777778888888776443.333321111...1.12333322222222222222222222344447889****** PP

                              RRN3 280 ekLDailtllfehlekkfssestkeeeeeeeglelfntLlsl 321
                                       ++L   ++  fe +e+ ++  + +++e+e++ +++ n++++l
  gi|313125714|ref|YP_004035984.1| 121 SELERRMDAGFENYEDVLEYLTDTADETEAKLDTVANAIVDL 162
                                       ****************99999989999999988888888766 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.1   4.9e+03      33      47 ..       5      19 ..       3      39 .. 0.57
   2 ?    4.4   5.2     0.046        55      27      71 ..      68     124 ..      57     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.1
                              YtxH 33 kaddlkekakellee 47
                                      ++++l++ +++++e+
  gi|313125714|ref|YP_004035984.1|  5 RVETLSDELERWVEK 19
                                      455556666555432 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.046
                              YtxH  27 Rkdlkekaddlkekakelleeakeka............kekaedlkekvkekadelk 71 
                                        +dl ek+ dl+e++ +++ e   ka            +e+a +++ +v+e+++el 
  gi|313125714|ref|YP_004035984.1|  68 EADLDEKVTDLRERVIQVKRESDRKApedhghpelaadTESALNAVADVRETVSELE 124
                                       578899999999999999988888889999999999995555555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1288  (0.0718389); expected 358.6 (0.02)
Passed bias filter:                      727  (0.0405488); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1579.62
//
Query:       gi|313125715|ref|YP_004035985.1|  [L=278]
Description: RecA-superfamily ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-08   34.5   0.0      0.001   18.5   0.0    2.2  2  ATPase    KaiC
      7e-05   22.5   0.1    0.00021   20.9   0.1    1.7  1  AAA_25    AAA domain
  ------ inclusion threshold ------
       0.16   11.2   0.0        1.7    7.9   0.0    2.1  2  Rad51     Rad51


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.7e-07     0.001       2      31 ..       5      34 ..       4      49 .. 0.88
   2 !   14.2   0.0   3.5e-06     0.021      99     208 ..     136     248 ..      72     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-07
                            ATPase  2 ktgIeglDeilkgGipegrvvlitGepGtG 31
                                      + g+  lD+i++gG p g+vvl++GepG+G
  gi|313125715|ref|YP_004035985.1|  5 PFGVSRLDRIIDGGAPPGSVVLLVGEPGAG 34
                                      7799************************99 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.5e-06
                            ATPase  99 kdkedleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvl.kkl.gvTailvsekssseeaag 172
                                        ++ + e++++ l ++++e    + vviDsit l    ++++  + +  ++r + k   +   ++ +   ++ ++ +
  gi|313125715|ref|YP_004035985.1| 136 GQRHNRESVLTALGNYLSEHASgNLVVIDSITDLVAAVSDEMSWNDISMVIRGIsKAAhRWGGLILAL--VGRDTLE 210
                                       57888999999999999998887889********7777777777888888888854441445555554..4556666 PP

                            ATPase 173 gygveef..ivdgvivLdlkeieeelvRtleivkmRgt 208
                                       + ++++   +vdg+++ + ++  +++ Rtl +   Rg 
  gi|313125715|ref|YP_004035985.1| 211 RTELAHLmdAVDGTLQFQWETGGSKRARTLVVQEFRGV 248
                                       66666642279***********************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   3.5e-08   0.00021      21     185 ..      10     202 ..       2     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.5e-08
                            AAA_25  21 prrwlvkgllpagelallaGapgtGKt..tlaldlalava.tGkpwlg.......pvapeqgkVlyvsaEdsedelr 87 
                                       +++ +++g  p g+++ll+G pg+G    ++++  + av  t++ +++       +  + ++ V y+s+  + + l 
  gi|313125715|ref|YP_004035985.1|  10 RLDRIIDGGAPPGSVVLLVGEPGAGARefMFTSATMNAVYgTDDDLFDlyygdlhSESSPPAEVHYISFTADKQSLS 86 
                                       6778999999***************75224455555555599999**9****8863345899*************** PP

                            AAA_25  88 rRlravgeal...........rddarllvld...............lagv..eslpLfakdrggtlltadvdaleaa 136
                                       r ++ v+ +            r        d               +ag+  +  +L +  ++    ++++ al + 
  gi|313125715|ref|YP_004035985.1|  87 REMSYVFDESlvdsaterinfR--------DfsatyfrpspiprewYAGEatTLQDLGQRHNR----ESVLTALGNY 151
                                       *******665566555555440........255555566665554422221123344444444....5555667888 PP

                            AAA_25 137 ieevegvrlvviDplsralgg..densnsdvgalvealeriarrtgaavll 185
                                       + e++   lvviD+++ ++++  de s +d+++++  + + a+r g  +l+
  gi|313125715|ref|YP_004035985.1| 152 LSEHASGNLVVIDSITDLVAAvsDEMSWNDISMVIRGISKAAHRWGGLILA 202
                                       88888899*********999999*******************999977665 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00028       1.7      20      58 ..       5      43 ..       1      49 [. 0.86
   2 ?    1.1   0.0     0.032   1.9e+02     117     144 ..     141     169 ..     130     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00028
                                      --S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHH CS
                             Rad51 20 ttGskklDelLgGGietgsiteifGefrsGktqlchtlc 58
                                        G ++lD++++GG + gs+  ++Ge ++G   +  t +
  gi|313125715|ref|YP_004035985.1|  5 PFGVSRLDRIIDGGAPPGSVVLLVGEPGAGAREFMFTSA 43
                                      56899*************************988877655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.032
                                       HHHHHHHTHHHHHHS-E.EEEEEETTTGG CS
                             Rad51 117 qeellqqaaallaedkf.allivDsvtal 144
                                       +e++l+++ + l+e+   +l+++Ds+t l
  gi|313125715|ref|YP_004035985.1| 141 RESVLTALGNYLSEHASgNLVVIDSITDL 169
                                       56677778888877765258888998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1750.92
//
Query:       gi|313125716|ref|YP_004035986.1|  [L=325]
Description: beta-rfap synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-06   28.2   0.8    3.9e-06   27.0   0.8    1.7  1  GHMP_kinases_N  GHMP kinases N terminal domain
    5.3e-05   23.5   0.1    0.00012   22.4   0.1    1.6  1  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.014   14.5   0.1       0.54    9.3   0.0    2.1  2  DUF2625         Protein of unknown function DUF2625


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.8   6.5e-10   3.9e-06       1      66 []      73     134 ..      73     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.5e-10
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                       d++++s +P +aGLGS++ la+a+++A+ ++++ +   +   + a rl   g  sg+ va +  Gg
  gi|313125716|ref|YP_004035986.1|  73 DVTVSSALPRHAGLGSGTQLALAVLVAVGRANDRE---VSVRQLAPRLGR-GGRSGIGVASFETGG 134
                                       689*****************************744...455566665554.666999998887776 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1     2e-08   0.00012       2      79 ..     217     296 ..     216     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2e-08
                    GHMP_kinases_C   2 lealergdlellgellnlsqrs......elkavvgilppeleellealselG.algaklsGaGgGptvfalfkdkde 71 
                                       l+a+  g+++++g+++ +  r+      ++  + g+  p + el+ + +++  ++ga   ++++Gp+v+a++ d ++
  gi|313125716|ref|YP_004035986.1| 217 LPAVADGSASRFGKAVSEIGRLngawyaDE--QGGVYRPPVGELVASVEDNPaCYGA--GQSSWGPAVYAIT-DAEH 288
                                       7788889999*******99999****9888..9***************999956665..59999*******9.**** PP

                    GHMP_kinases_C  72 aeqvaral 79 
                                       a+++++a 
  gi|313125716|ref|YP_004035986.1| 289 ADEARDAG 296
                                       ***99985 PP

>> DUF2625  Protein of unknown function DUF2625
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0     9e-05      0.54      46      67 ..     120     141 ..      95     183 .. 0.79
   2 ?    3.1   0.0     0.007        42      71     122 ..     269     320 ..     267     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 9e-05
                           DUF2625  46 ttrSvlGavvyetGGlliddGw 67 
                                         rS +G   +etGG+l+d G 
  gi|313125716|ref|YP_004035986.1| 120 GGRSGIGVASFETGGVLVDAGH 141
                                       579*****************96 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.007
                           DUF2625  71 lGsgseklerslaslnkvkefaevgekaalLlvadDvlGgvfalnggklged 122
                                       +G+g+++   ++ +++ +++  e+ ++ ++ l a Dv+G v ++ g + g d
  gi|313125716|ref|YP_004035986.1| 269 YGAGQSSWGPAVYAITDAEHADEARDAGEAALAAADVAGEVRVVRGRNTGAD 320
                                       7999999999999999999999999*******************99998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 2050.55
//
Query:       gi|313125717|ref|YP_004035987.1|  [L=107]
Description: hypothetical protein Hbor_09480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.9   0.0       0.03   14.6   0.0    1.3  1  TrkA_N    TrkA-N domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.7e-06      0.03      48     102 ..      30      82 ..       8      96 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-06
                                       -TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEE..EEESSGGGH CS
                            TrkA_N  48 datdeevLeeagiekadaviaatgddeanilavllakelnpkkkii..araqdpeha 102
                                         + ++ + +agi++ad+++ + + d+a+i+   +a+e np+ +i+  +r + pe+a
  gi|313125717|ref|YP_004035987.1|  30 V-ATRDSIVDAGIDSADTLVLT-DMDDASIIP--VAREENPEVRIVtySRDSLPEYA 82 
                                       3.44667779*******98876.455555544..79999***888744566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       163  (0.00909142); expected 358.6 (0.02)
Passed bias filter:                      130  (0.00725082); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 694.70
//
Query:       gi|313125718|ref|YP_004035988.1|  [L=305]
Description: GMP synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-29  100.5   0.1    5.3e-28   96.9   0.1    2.3  2  GMP_synt_C     GMP synthase C terminal domain
    6.4e-08   32.0   0.0    8.1e-05   21.9   0.0    2.2  2  NAD_synthase   NAD synthase
    1.9e-05   23.6   0.0     0.0016   17.3   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
     0.0099   15.4   0.0      0.078   12.5   0.0    2.0  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.023   14.4   0.0    1.3  1  Asn_synthase   Asparagine synthase
      0.055   13.0   0.0       0.23   11.0   0.0    2.0  1  ThiI           Thiamine biosynthesis protein (ThiI)
      0.067   13.2   0.0       0.12   12.4   0.0    1.5  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.17   4.5e+02      31      48 ..      68      85 ..      49     102 .. 0.86
   2 !   96.9   0.1   2.1e-31   5.3e-28      10      92 .]     223     304 ..     214     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                                      ----EEEEEEEEE----- CS
                        GMP_synt_C 31 kRtyeyvvalRaveseDa 48
                                      + t++y+  lR+ve++D 
  gi|313125718|ref|YP_004035988.1| 68 RETFDYMESLRVVEAQDR 85
                                      45899**********996 PP

  == domain 2  score: 96.9 bits;  conditional E-value: 2.1e-31
                                       GGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TT CS
                        GMP_synt_C  10 kkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskP 86 
                                        + wQafa+++  k +Gv+gd+R ++++v +R+ves+D+mta+++el +e+L++i+sri+ + ++v+rvvyd+t+kP
  gi|313125718|ref|YP_004035988.1| 223 YDPWQAFAAVIG-KGTGVKGDNRVHGWIVSVRSVESRDGMTARAQELSWETLQRIQSRITGQNDNVARVVYDVTHKP 298
                                       467*******98.99************************************************************** PP

                                       TS-S-- CS
                        GMP_synt_C  87 patiEw 92 
                                       patiE+
  gi|313125718|ref|YP_004035988.1| 299 PATIEY 304
                                       *****7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   3.1e-08   8.1e-05      14      45 ..      17      48 ..       4      77 .. 0.81
   2 !    8.1   0.0   0.00052       1.3     143     177 ..     153     187 ..     138     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.1e-08
                                      HHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCG CS
                      NAD_synthase 14 kkagakgvvlGlSGGvDSslvaalavkalgke 45
                                      ++ g  ++++ lSGGvDSs++aala +a+g++
  gi|313125718|ref|YP_004035988.1| 17 ETVGDANAIIALSGGVDSSVAAALAYRAIGDQ 48
                                      334557899********************865 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00052
                                       TT--SBETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 143 DgaadlapiaellKtevkeLakelnvPervlkkpP 177
                                       D  + ++p+ +l+K ev+e a+el+    v ++ P
  gi|313125718|ref|YP_004035988.1| 153 DFEGIVEPVRDLYKDEVREVARELGLESVVSERMP 187
                                       6667789******************9888888877 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.2e-07    0.0016       3      36 ..      24      58 ..      22     113 .. 0.71
   2 !    4.2   0.0    0.0059        15     164     186 ..     157     179 ..     152     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.2e-07
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq.gyevigvflklwe 36
                                       ++alSgGVDSsvaaal  ++ g +++ v++ +  
  gi|313125718|ref|YP_004035988.1| 24 AIIALSGGVDSSVAAALAYRAiGDQLTPVYVDTGL 58
                                      589***********999866526777878776654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0059
                     tRNA_Me_trans 164 llfPlgeltKeevrkiAkeagla 186
                                       ++ P+ +l K+evr++A+e gl+
  gi|313125718|ref|YP_004035988.1| 157 IVEPVRDLYKDEVREVARELGLE 179
                                       5669****************998 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   3.1e-05     0.078       2      50 ..      24      73 ..      23     102 .. 0.79
   2 ?    0.6   0.0      0.13   3.3e+02     154     176 ..     157     179 ..     122     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                                      EEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHH CS
                              QueC  2 avvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiake 50
                                      a++ lSGG+DS++++ala +++ ++++ + +d g  +k e+e  ++ ++ 
  gi|313125718|ref|YP_004035988.1| 24 AIIALSGGVDSSVAAALAYRAIgDQLTPVYVDTGLMRKGETEGIRETFDY 73
                                      899**************988743888888888887777777776666555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                                       EE-TTTT--HHHHHHHHHHTTHH CS
                              QueC 154 ieaPlidlsKaeivklgkelgvp 176
                                       i+ P+ dl K e+ +++ elg++
  gi|313125718|ref|YP_004035988.1| 157 IVEPVRDLYKDEVREVARELGLE 179
                                       899*****************964 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.9e-06     0.023      14      40 ..      18      44 ..       8      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.9e-06
                      Asn_synthase 14 lradvpvGalLSGGlDSSliaalaarq 40
                                      +++d    + LSGG+DSS+ aala r 
  gi|313125718|ref|YP_004035988.1| 18 TVGDANAIIALSGGVDSSVAAALAYRA 44
                                      5778888899*************9876 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.8e-05      0.23       6      51 ..      24      70 ..      19     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.8e-05
                              ThiI  6 vlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekvek 51
                                      ++  lSgG+DS Vaa l+ +  G +   v+++  ++ + e+++ +e+
  gi|313125718|ref|YP_004035988.1| 24 AIIALSGGVDSSVAAALAYRAiGDQLTPVYVDTGLMRKGETEGIRET 70
                                      67789**********99987548889999998777777666665554 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05      0.12       2      38 ..      24      61 ..      23      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                                      EEEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-H CS
                       PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpv.pvvfvdtghefp 38
                                       +++ sgG ds+V   La +a  +  + v+vdtg   +
  gi|313125718|ref|YP_004035988.1| 24 AIIALSGGVDSSVAAALAYRAIGDQlTPVYVDTGLMRK 61
                                      57899*****************995489*****97544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2009.69
//
Query:       gi|313125719|ref|YP_004035989.1|  [L=553]
Description: CTP synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.1e-124  412.6   0.1   8.2e-124  412.2   0.1    1.2  1  CTP_synth_N    CTP synthase N-terminus
    7.7e-52  175.8   0.0    1.3e-51  175.1   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    2.2e-06   27.6   0.0    9.8e-06   25.5   0.0    2.0  2  Peptidase_C26  Peptidase C26
     0.0018   18.4   0.0     0.0022   18.1   0.0    1.5  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.059   13.0   0.0       0.16   11.6   0.0    1.6  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.2   0.1  2.3e-127  8.2e-124       1     265 []      16     277 ..      16     277 .. 0.99

  Alignments for each domain:
  == domain 1  score: 412.2 bits;  conditional E-value: 2.3e-127
                                       EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHH CS
                       CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfl 77 
                                       k+i+vtGGv+SglGkGi+aas+g+ll + g++vt++kiDPYlnvdagt++p++hGEv+vl+dG+e+DlDlGnYeRfl
  gi|313125719|ref|YP_004035989.1|  16 KFIFVTGGVMSGLGKGITAASTGRLLSNAGFDVTAVKIDPYLNVDAGTMNPYQHGEVYVLKDGGEVDLDLGNYERFL 92 
                                       8**************************************************************************** PP

                                       T----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHH CS
                       CTP_synth_N  78 dikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfle 154
                                       ++++t+++n+ttGk y++vieker GdylGktvq+iphvtd+ik+ri+++a+   +dv+ive+gGtvgdie++pfle
  gi|313125719|ref|YP_004035989.1|  93 GEDMTSDHNVTTGKTYQHVIEKERAGDYLGKTVQIIPHVTDDIKRRIREAAE--GTDVCIVEVGGTVGDIEGMPFLE 167
                                       ***************************************************8..8********************** PP

                                       HHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--G CS
                       CTP_synth_N 155 airqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvek 231
                                       a+rq+++e +++++l+ hvtlvp+ k +ge+ktkptqhsvkelrs+G+qpdi+v rs ++l++++kekialfc+v++
  gi|313125719|ref|YP_004035989.1| 168 ALRQFAHEEDDDDILFTHVTLVPYSK-NGEQKTKPTQHSVKELRSIGLQPDILVGRSPDKLDASTKEKIALFCDVPT 243
                                       ************************95.9************************************************* PP

                                       GGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                       CTP_synth_N 232 eavisvkdvesiyevpllleeqglaelileklkl 265
                                       eav+s++dve+iy+vpl++ee+gl+e+++e+l+l
  gi|313125719|ref|YP_004035989.1| 244 EAVFSNSDVEDIYHVPLMVEEEGLDEYVMEQLSL 277
                                       ******************************9986 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.1   0.0   3.5e-55   1.3e-51       2     190 .]     313     535 ..     312     535 .. 0.93

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 3.5e-55
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH..THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile..llknpdgilvsgGpgspgvegkieaikearenkiPiLG 76 
                                       l D+y sv+e+l+ha++e++ +v+++++d++    ++   lk++dg++v+gG+g++g+ gkieai+++ren++P+LG
  gi|313125719|ref|YP_004035989.1| 313 LEDAYMSVNEALKHAGIETKTDVNILWVDSDEMLDKHenRLKEADGVVVPGGFGTRGTAGKIEAIRYCRENDVPFLG 389
                                       67***************************86555545656************************************* PP

                                       ETHHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTSEE CS
                            GATase  77 ICLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglknev 122
                                        CLG+Q+++ e +r+v                        ++ e e++ggtmrlg++et        a +yg+  + 
  gi|313125719|ref|YP_004035989.1| 390 LCLGFQMAVVEHARNVLghedahsaeidsdtsdpvidllpEQYETEDMGGTMRLGAHETditedslaAHVYGD-TVC 465
                                       **************9999999999999999999999***988899***********999*******9999999.999 PP

                                       EEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHHH CS
                            GATase 123 ierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflika 190
                                       +erhrHryev p+   +le+  l+++++   +  +mei e+++ p f g+QFHPE++s+p +++++f +++ka
  gi|313125719|ref|YP_004035989.1| 466 TERHRHRYEVAPDyidDLEDGALTFSGRA--G-NRMEILERTDhPyFLGTQFHPEFRSRPDRASPPFVGFVKA 535
                                       ***************77777779999999..3.58********9*************************9986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.41   1.5e+03      48      67 ..     345     364 ..     314     370 .. 0.76
   2 !   25.5   0.0   2.7e-09   9.8e-06      96     216 .]     375     517 ..     368     517 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.41
                     Peptidase_C26  48 deedvkaildkldgllltGg 67 
                                         ++ ++ l++ dg++++Gg
  gi|313125719|ref|YP_004035989.1| 345 MLDKHENRLKEADGVVVPGG 364
                                       335677889999*******9 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 2.7e-09
                     Peptidase_C26  96 aLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..............q....saashavkve 154
                                         ir + e++vP lg C+G+q+  v    ++  + +++s++ d    +                      +h+ +++
  gi|313125719|ref|YP_004035989.1| 375 EAIRYCRENDVPFLGLCLGFQMAVVEHARNVLGHEDAHSAEIDSDTSDpvidllpeqyetedMggtmRLGAHETDIT 451
                                       56788999**************9998888876665555555555444467999988776665055568889****** PP

                     Peptidase_C26 155 kgsllaellgseeievnslHhqaike.....laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       ++sl a+++g++       H+  +       l+++    +  + + +E +e ++++  +lg Q+HPE
  gi|313125719|ref|YP_004035989.1| 452 EDSLAAHVYGDTVCTERHRHRYEVAPdyiddLEDGALTFSGRAGNRMEILERTDHP-YFLGTQFHPE 517
                                       **********7777778888876544444449999999999999**********88.99*******9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.1e-07    0.0022       7      55 ..      25     124 ..      18     431 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.1e-07
                                       STTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                              CbiA   7 kGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................. 54 
                                        +G GK  +aa+ +r+l+++g++V +v+ Dp  n +a   g+ n  +                              
  gi|313125719|ref|YP_004035989.1|  25 MSGLGKGITAASTGRLLSNAGFDVTAVKIDPYLNVDA---GTMNPYQHgevyvlkdggevdldlgnyerflgedmts 98 
                                       69******************************99988...6555555556666666666666666666666666666 PP

                                       .........................C CS
                                       .........................x RF
                              CbiA  55 .........................d 55 
                                                                +
  gi|313125719|ref|YP_004035989.1|  99 dhnvttgktyqhviekeragdylgkT 124
                                       66555555555555555555555551 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.3e-05      0.16      25      87 ..     344     396 ..     324     418 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                          GATase_3  25 vrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqm 87 
                                       + +     ++++l ++ad v++pGg+ t+  +      g  eai+   e+++p lg C G+qm
  gi|313125719|ref|YP_004035989.1| 344 EMLD---KHENRL-KEADGVVVPGGFGTRGTA------GKIEAIRYCRENDVPFLGLCLGFQM 396
                                       2222...234556.56***********99864......77889*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 3314.28
//
Query:       gi|313125720|ref|YP_004035990.1|  [L=466]
Description: hypothetical protein Hbor_09510 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-12   46.3   2.1    6.6e-12   45.8   0.0    2.1  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    1.6e-05   24.8   0.0    1.6e-05   24.8   0.0    1.8  2  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.063   12.7  17.5      0.083   12.3  17.5    1.1  1  SDA1             SDA1
       0.17   11.3   0.0       0.28   10.6   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
       0.95    8.9   0.0       0.95    8.9   0.0    2.2  2  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   1.8e-15   6.6e-12       2     129 ..       8     122 ..       7     123 .. 0.86
   2 ?   -1.6   1.2      0.84     3e+03      29      64 ..     420     454 ..     413     462 .. 0.60

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.8e-15
                                       EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       l+ Ga G++G+ +ae+ a++ d+  ++++a+r++++ + +a   ++ ++  +++d+++ +     +l +  lv+n++
  gi|313125720|ref|YP_004035990.1|   8 LVYGAyGYTGRLIAEEAADR-DL--DVVLAGRDEKRTRDVA---NELDLPYRTFDVSQAAT----MLDDVSLVLNCA 74 
                                       899***************98.56..7**********88887...78888899999988887....89999******* PP

                                       SGG..GHHHHHHHHHHHT-EEEE..SS-BCGCCSCHCCSHHHHHTHHHHHHCTSEE CS
                   Sacchrp_dh_NADP  78 ppi..ssldvlkaCietgvhyvd..tsiskeertnyalreavlklkekakeagvta 129
                                       +p+   +  +++aCiet +hy+d   +          + e++ +  ++a eag+t+
  gi|313125720|ref|YP_004035990.1|  75 GPFdeTADHMVDACIETETHYLDitGE--------IPVFERIKRRSDEADEAGITL 122
                                       ***8777799*************7522........356689999999999999996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.84
                                       EEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHH CS
                   Sacchrp_dh_NADP  29 vadrskeklealaakalgvrfeaialdaenyeavLa 64 
                                       +  r+ e   a+a++a  +++ea+++ ae  e+  +
  gi|313125720|ref|YP_004035990.1| 420 IRRRETEAETAEAETAEAETAEAETVEAEATEE-AE 454
                                       455555555566666666777777777766666.44 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   4.6e-09   1.6e-05       1      90 [.      11      93 ..      11     120 .. 0.84
   2 ?   -3.0   0.8       1.6   5.7e+03      32      50 ..     435     451 ..     415     458 .. 0.44

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.6e-09
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHHHHH CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdeegak 79
                                      GA G +Grl+++e+++r +++v++  R+++++ ++++e  l   + dv+   + a  l++++ V+ ++g+ ++   +a+
  gi|313125720|ref|YP_004035990.1| 11 GAYGYTGRLIAEEAADR-DLDVVLAGRDEKRTRDVANELDLPYRTFDVS---QAATMLDDVSLVLNCAGPFDE---TAD 82
                                      9****************.7****************97777777777776...7788999**********8775...688 PP

                                      HHHHHHHHCT- CS
                    NAD_binding_10 80 nivdaakeagv 90
                                      ++vda+ e+++
  gi|313125720|ref|YP_004035990.1| 83 HMVDACIETET 93
                                      88888877665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                                       CHHHHCTTTCEEEE--TT- CS
                    NAD_binding_10  32 laeleaeeglevvegdvtd 50 
                                       ++   +++++e+ve+++t+
  gi|313125720|ref|YP_004035990.1| 435 AE-A-ETAEAETVEAEATE 451
                                       11.1.23344444444443 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  17.5   2.3e-05     0.083      57     194 ..     328     458 ..     307     466 .] 0.40

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                              SDA1  57 kakkfGeeevaegieGleLlekwkeeekkekreeeeedsddeddeedwevesdddseedseggwidvesdeeeiees 133
                                        a +fG +    +i+G+e ++ +++e  +++   e++   ++ d ed e+e +     d++   id ++de+   +s
  gi|313125720|ref|YP_004035990.1| 328 PAAAFGPDLIL-EIPGVERIDLKDDEIVARETGGESD---EAADGEDAEAEVA----LDDDAVTIDLDDDEQ---SS 393
                                       56778887777.8999996655445444444411222...2233333333321....222233455544433...44 PP

                              SDA1 134 desedeeeeeeeeeekeekeeeeeeee...eeeeeeeeeeeeeekekkkk.kakeaseeekkkek 194
                                       de ed +++e +  + +  ++e+e      e+e+e+ e+e+ e ++++++  ++ea+ee++++++
  gi|313125720|ref|YP_004035990.1| 394 DEAEDAADDEADTPSPRPLSDEAEPVIrrrETEAETAEAETAEAETAEAEtVEAEATEEAEAETT 458
                                       44555554444444444433333332222212222222222111111111112222222222222 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.9e-05      0.28       2      81 ..       8      84 ..       7     114 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.9e-05
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HH.HHHHHHHHH.T-SEEEE--S.---H CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrs.alerlfkee.qpdavihlAa.vggv 77
                                      lV Ga G+ G+ ++++ ++++ +v+   r++++ +          eldl  r+ ++ ++     ++  v+++A+     
  gi|313125720|ref|YP_004035990.1|  8 LVYGAYGYTGRLIAEEAADRDLDVVLAGRDEKRTR-DV-----ANELDLPYRTfDVSQAATMLdDVSLVLNCAGpFDET 80
                                      89*********************988888822222.22.....235555544443333333333788888888755555 PP

                                      HHHH CS
                         Epimerase 78 aass 81
                                      a+ +
  gi|313125720|ref|YP_004035990.1| 81 ADHM 84
                                      4444 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00026      0.95       4      66 ..       8      65 ..       6      92 .. 0.85
   2 ?   -1.9   2.2      0.54   1.9e+03      30      68 ..     420     459 ..     412     465 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00026
                                      EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHH CS
                         adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevea 66
                                      lv Ga +  Gr ia+e a ++ +vv+++r e++ + va+el      + + ++Dv++++ + +
  gi|313125720|ref|YP_004035990.1|  8 LVYGAYGYTGRLIAEEAADRDLDVVLAGRDEKRTRDVANELD-----LPYRTFDVSQAATMLD 65
                                      677888888*******************************99.....6788888887766654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.54
                                       EESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHH CS
                         adh_short  30 vdrseekleevakelkee.gakalaiqvDvtdreevealv 68 
                                       + r+e ++e++ +e  e+  a+a ++++  t+++e+e++ 
  gi|313125720|ref|YP_004035990.1| 420 IRRRETEAETAEAETAEAeTAEAETVEAEATEEAEAETTE 459
                                       5778888888888888877899999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 2915.84
//
Query:       gi|313125721|ref|YP_004035991.1|  [L=266]
Description: aldo/keto reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-50  172.0   0.0      2e-48  165.1   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.026   13.1   0.0      0.037   12.6   0.0    1.1  1  Terminase_1   Phage Terminase


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.1   0.0   2.2e-52     2e-48       1     292 [.       5     249 ..       5     251 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 2.2e-52
                                       .EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTT CS
                      Aldo_ket_red   1 elglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaei 77 
                                       +lg+Gt q+ +     ++e +++++ a+e G++++DtA++Y    +e +++  l +s+ +r+ev++atK+       
  gi|313125721|ref|YP_004035991.1|   5 NLGFGTYQMDD-----RNECVRAIELAMETGYEHVDTAQMY---DNEAFVAAGLDESGIDRDEVFVATKL------D 67 
                                       69********6.....7************************...**************************......9 PP

                                       SSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT CS
                      Aldo_ket_red  78 ksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkk 154
                                        ++l  +++ +  +es ++Lgtd++Dll++H+p  +++   e+l+al+elv+eG i  +G+Snf  +qle a ++  
  gi|313125721|ref|YP_004035991.1|  68 TDNLAYDDVKRTAKESAEKLGTDTIDLLYVHWPINTYD-PVETLSALDELVEEGVIERVGLSNFRPDQLEDAIEHLD 143
                                       ************************************99.************************************** PP

                                       --EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHH CS
                      Aldo_ket_red 155 vkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaee 231
                                        ++ a qve++++  l +e+l el+ +++ +l+ay+p+++G                                 ++e
  gi|313125721|ref|YP_004035991.1| 144 EPLYAHQVEMHPM--LPQEELHELAVEHDHQLVAYCPIARGQVA-----------------------------DVPE 189
                                       *************..************************99887.............................6899 PP

                                       HHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                      Aldo_ket_red 232 lselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                       ++++a++h+ ++aq++l++++  + ++++ip+a +++++++n++a +l+l++ + +++d +
  gi|313125721|ref|YP_004035991.1| 190 IQAVAEKHDATPAQVSLAWLM-GKENVTAIPKAASPDHIRENFAARDLELDDADREKIDGI 249
                                       *********************.6888899*****************************987 PP

>> Terminase_1  Phage Terminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.1e-06     0.037     334     415 ..      38     122 ..      13     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-06
                       Terminase_1 334 rge.deasdagmidekqvvdiivfiaktlavqavaYDP..wnaksfidklektaldiplvevrqsfaklSnslkeve 407
                                       ++  +ea+ a   de ++    vf+a++l+  ++aYD     ak+ ++kl    +d+ +v+   +     ++l ++ 
  gi|313125721|ref|YP_004035991.1|  38 QMYdNEAFVAAGLDESGIDRDEVFVATKLDTDNLAYDDvkRTAKESAEKLGTDTIDLLYVHWPINTYDPVETLSALD 114
                                       44447788888889999988889**************822579********************************** PP

                       Terminase_1 408 klvaeeri 415
                                       +lv+e+ i
  gi|313125721|ref|YP_004035991.1| 115 ELVEEGVI 122
                                       ****9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1438.42
//
Query:       gi|313125722|ref|YP_004035992.1|  [L=49]
Description: hypothetical protein Hbor_09530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 283.73
//
Query:       gi|313125723|ref|YP_004035993.1|  [L=897]
Description: phosphoenolpyruvate carboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.2e-243  810.8   0.0   1.7e-243  810.3   0.0    1.2  1  PEPcase    Phosphoenolpyruvate carboxylase
     0.0036   15.9   0.0     0.0059   15.2   0.0    1.2  1  PEPcase_2  Phosphoenolpyruvate carboxylase
     0.0048   16.7   0.5     0.0081   16.0   0.5    1.3  1  EGL-1      Programmed cell death activator EGL-1


Domain annotation for each model (and alignments):
>> PEPcase  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  810.3   0.0  2.9e-247  1.7e-243       3     795 .]     132     897 .]     130     897 .] 0.95

  Alignments for each domain:
  == domain 1  score: 810.3 bits;  conditional E-value: 2.9e-247
                                       -EEEEE---TT--SSS--HHHHHHHHHHHHHHT-SS--HHHHHHHHHHHHHHHHHHHH---B-SS---HHHHHHHHH CS
                           PEPcase   3 eielVlTAHPteivRrtilkkqrriaelleqldeaelteeereeleeqleeeiallwrtdelrqekptvldEvengl 79 
                                        ie+ +TAHPte++R+t+  k r+ia+ +e++de++lt++er++l +++ +e+++lw+t ++r ++p+++dE++n  
  gi|313125723|ref|YP_004035993.1| 132 LIEPTFTAHPTEARRKTVKAKLRSIASRIEEMDERNLTDRERQQLWREVDAEVTSLWQTSQVRGRRPEPQDEARNVQ 208
                                       5899************************************************************************* PP

                                       HHHHHTHHHHHHHHHHHHHHHHHHHTS.----T---EEEEE-TTTB-TT-TT--HHHHHHHHHHHHHHHHHHHHHHH CS
                           PEPcase  80 syfeevlfeavPellreleealkesfpelelpaasflrfgsWiGgDRDGNpnVtaevtrevlllqrelalekylkev 156
                                       +y+e++lf++v e+++e+e+ l+e++pe+++p+  +++f sW G+DRDGNp+Vt+evt+++l  qr+++leky +++
  gi|313125723|ref|YP_004035993.1| 209 WYLESILFDVVGEVYSEFEDVLAEEYPEVDVPK--LFEFRSWAGSDRDGNPFVTPEVTEDTLARQRSVVLEKYSDAL 283
                                       ***************************777666..****************************************** PP

                                       HHHHHH---....----HHHHHTT-SSS..............TTSHHHHHHHHHHHHHHHHHHHHHHHHHT-.---- CS
                           PEPcase 157 eeLieeLslslelvevseellesleedkekleevyeelaerykeepYRlklaelrkrLentrerleelaekeeeele 233
                                       ++L   Ls   + ++v  e+++sl +d+e+l+ v+ee++ery eepYR kl+ +r+r+++ ++              
  gi|313125723|ref|YP_004035993.1| 284 KRLSGVLSQDGSRIDVGAEFERSLIADRERLPVVAEETEERYPEEPYRQKLKLMRERIRRIED----VRP------- 349
                                       ********************************************************9976543....333....... PP

                                       -TT---SHHHHHHHHHHHHHHHHHTT-HHHHTTHHHHHHHHHHHTTTTSSEEEEEEEHHHHHHHHHHHHHHTTS.-- CS
                           PEPcase 234 eeeayesaeelledLelikesLketgaklladgeledlirqvevfGlhLaklDiRqeserheealaeileylglekd 310
                                         + y++++elledLe+i++sL+++ga+++ad+ ++ l+rqv++fG++La+lD+R++ e+h+ea++e l++ g+  d
  gi|313125723|ref|YP_004035993.1| 350 --DGYAAHHELLEDLEIIDQSLRDNGADVVADEYVSPLMRQVDTFGFTLASLDLRDHRENHTEAVHEALAREGI--D 422
                                       ..358999******************************************************************..9 PP

                                       GGGS-HHHHHHHHHHHHH-SS--..S-TT----HHHHHHHHHHHHHHHS.-...TTSEEEEEEET--SHHHHHHHHH CS
                           PEPcase 311 YaelseeervelLlreLeskrpl..ipkelelseeteevldvlrviaelqeefgkeiietyviSmaeeasdvLevll 385
                                       Y + +e+ rv++L++ + ++ pl  ++++ +ls+++++vl  ++ + e q+e+g  +i+ty iSm+ee+s+vLevl+
  gi|313125723|ref|YP_004035993.1| 423 YYDRDEDGRVAVLTEAILQDEPLvdLSNREDLSDTADRVLTRFEKLGEWQREYGVGAIDTYCISMTEEPSHVLEVLF 499
                                       ***********************33356779********************************************** PP

                                       HHHHTT-..-....S---EEEEE-SHHHHHHHHHHHHHHHHSHHHHHHTTT...EEEEEE-HHHHHHHH-HHHHHHH CS
                           PEPcase 386 LakeaglldkaegaaelrvvPLfEtvedLknapevleellslplyrelvkksgelqevMlGYSDSnKdaGfltsnWe 462
                                       La +ag+++  + ++ l+vvPL+Et + L+ a +++ +l+++++y++++++++ +qe+MlGYSDSnK+ G+l++nW 
  gi|313125723|ref|YP_004035993.1| 500 LADQAGVVSLPD-HCGLDVVPLLETESALNGARRIMGSLFENEAYEQVLAARNGVQEIMLGYSDSNKENGYLAANWD 575
                                       *******77665.9*************************************************************** PP

                                       HHHHHHHHHHHHHHHT-EEEEEE-SSTGGGS-HHHHHHHHHTS-TTTTTT-EEEEE-GGGHHHHHSSHHHHHHHHHH CS
                           PEPcase 463 lykaqealvkvaeeagvklrlFHGrGGsvgRGGgpayeailaqPpgtvngrikiTeQGEviaskyslpelalrnLel 539
                                       lyk q++l++++++++vk+rlFHGrGGs++RGGgp +ea+la P++tv+g+ik+TeQGE ia+ky++p++a rnLe+
  gi|313125723|ref|YP_004035993.1| 576 LYKNQRRLAAICDDFDVKMRLFHGRGGSISRGGGPMNEAMLALPNETVTGQIKFTEQGEAIAEKYANPHIAERNLEQ 652
                                       ***************************************************************************** PP

                                       HHHHHHHHHHS------....HHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHS-HHHHHHSS-SSS------- CS
                           PEPcase 540 vtaavleaslleeaeekk...eeweeimeelsevsreaYrklvyeepdfveyFreaTPieeiskLnigSRPakRkkk 613
                                       +++a ++a   + +e+++   e+w ++m+++++++r++Yr+l+ e+++fv+yF++aTPi+ i++Ln+gSRPa+R+ +
  gi|313125723|ref|YP_004035993.1| 653 MLNAQVRARHEAIQEPEEdvpEAWIDAMDTMAAAARQEYRNLL-ESEGFVSYFEQATPITVIEDLNLGSRPASRSGE 728
                                       ******9986655555555579********************9.9******************************** PP

                                       --GGSS-HHHHHHHHHHTT--GGGTTTHHHHHHHH..HTTTTHHHHHHHHHH-HHHHHHHHHHHHHHHH--HHHHHH CS
                           PEPcase 614 kglesLRAIPWvFsWtqsRlllpaWyGvgtalkevlekeeeklelLremykkwpffrtliskvemvlaKadleiake 690
                                       +++e+LRAIPWvFsWtqsR+++++Wy++gt+l+++l +e +  ++Lremy++wpffrt++++++++la++++ ia++
  gi|313125723|ref|YP_004035993.1| 729 RTVEDLRAIPWVFSWTQSRCIITGWYALGTGLQTYL-DEGGDRATLREMYDEWPFFRTTLDNASLALARTEFGIAEH 804
                                       **********************************96.5567789********************************* PP

                                       HHHHHS-GG.GHHHHHHHHHHHHHHHHHHHHHHT-SSTTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                           PEPcase 691 YvqllvdkelrerlfeeireelertvelvleitgqkelldknpvlqrsvelRnayidPlnllQvelLkrlRqaeeek 767
                                       Y+ l+ d+ lre+++ ++ ee+er+++lvl++ g+++ll+ +++l +s++ Rn+y+dPlnllQ +lL ++ ++e+e 
  gi|313125723|ref|YP_004035993.1| 805 YAALADDD-LREAFYPRLFEEYERAHDLVLDVIGRESLLK-RQWLDESLRRRNPYVDPLNLLQTHLLSQTHRTEDE- 878
                                       *9876655.599************************9997.579***********************987655553. PP

                                       TT----HHHHHHHHHHHHHHHHHH---- CS
                           PEPcase 768 seeeeeellrdallltinGiaaGlrntG 795
                                                +++l lt++GiaaG++ntG
  gi|313125723|ref|YP_004035993.1| 879 ---------ERTLRLTVKGIAAGMKNTG 897
                                       .........68999*************9 PP

>> PEPcase_2  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.9e-07    0.0059     171     323 ..     515     680 ..     493     704 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.9e-07
                                       SEEEEEE-SHHHHHTHHHHHHHHH.....HHT...--SEEEEEEESHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHT CS
                         PEPcase_2 171 ievIPLiEdkesllnideiveeyv.....kek...klkelRvflarSDpAlnyGlisavllvkvAlselykleeelg 239
                                       + v+PL+E++++l  +++i+  ++     +++   +   + ++l+ SD+  + G ++a         +l+++ ++ +
  gi|313125723|ref|YP_004035993.1| 515 LDVVPLLETESALNGARRIMGSLFeneayEQVlaaRNGVQEIMLGYSDSNKENGYLAANWDLYKNQRRLAAICDDFD 591
                                       78*********************965544222554555678************************************ PP

                                       -EEEEEEE-BSSGGGT-..--TTGHHHHHHHTTT-SEEEE-H...HHHHTTHHHHHHHHHHHHHHGGG-------HH CS
                         PEPcase_2 240 vkiyPilGvGslpfRGh..lspenveevleeYagvkTfTvQS...afkYdyeeeevkeairkineaevkkprelsee 311
                                       vk+    G G +  RG+  +++ +++   e+  g   fT Q    a kY  ++ + ++  + +n + + + + ++e 
  gi|313125723|ref|YP_004035993.1| 592 VKMRLFHGRGGSISRGGgpMNEAMLALPNETVTGQIKFTEQGeaiAEKYANPHIAERNLEQMLNAQVRARHEAIQEP 668
                                       **********99999865699999999999999*999**99654577999988888888888888777777788887 PP

                                       HHHHHHHHHHHH CS
                         PEPcase_2 312 eeellleviekl 323
                                       ee++ +++i+ +
  gi|313125723|ref|YP_004035993.1| 669 EEDVPEAWIDAM 680
                                       777777777655 PP

>> EGL-1  Programmed cell death activator EGL-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.5   1.4e-06    0.0081       5      18 ..     581     594 ..     581     594 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHHHHHHH CS
                             EGL-1   5 tKLAaMCDdFDaem 18 
                                       ++LAa CDdFD +m
  gi|313125723|ref|YP_004035993.1| 581 RRLAAICDDFDVKM 594
                                       58*********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (897 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.85u 0.36s 00:00:01.21 Elapsed: 00:00:00.54
# Mc/sec: 4981.87
//
Query:       gi|313125724|ref|YP_004035994.1|  [L=74]
Description: hypothetical protein Hbor_09550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   0.6       0.19   11.6   0.2    1.6  2  UvrD_C_2  UvrD-like helicase C-terminal domain


Domain annotation for each model (and alignments):
>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   1.1e-05      0.19      18      42 ..      21      44 ..      19      44 .. 0.73
   2 ?   -2.4   0.0      0.25   4.5e+03      41      46 ..      55      60 ..      52      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                          UvrD_C_2 18 VivfdpdlaaarmgelrrrlLYtav 42
                                      V+ f++dla+     ++rr++Yta+
  gi|313125724|ref|YP_004035994.1| 21 VVDFWMDLATTGDV-ETRRWVYTAA 44
                                      66678886666544.48******96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.25
                          UvrD_C_2 41 avTRAr 46
                                      a+TR r
  gi|313125724|ref|YP_004035994.1| 55 ALTRGR 60
                                      789977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.36s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 417.71
//
Query:       gi|313125725|ref|YP_004035995.1|  [L=278]
Description: rieske (2fe-2S) domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   18.6   0.1     0.0024   17.8   0.1    1.3  1  Rieske    Rieske [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.3e-07    0.0024      33      72 ..     219     263 ..     186     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-07
                                       TS-EEEEESC-TTTT-BC....GGSEE..ETT.EEE-TTT--EEET CS
                            Rieske  33 dgevyAlsdvCtHrgapl....segki..dekgvleCpcHgwayda 72 
                                       ++ + A  + CtH  + +    + g+   + +  + C+cH+++yd+
  gi|313125725|ref|YP_004035995.1| 219 QDGFMAWLNKCTHFCCVPkyktD-GSAkfNAEDDVYCQCHQSVYDP 263
                                       55677999*********988632.4442356669**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1629.00
//
Query:       gi|313125726|ref|YP_004035996.1|  [L=524]
Description: NAD-dependent aldehyde dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.2e-140  467.7   0.1   3.8e-140  467.4   0.1    1.0  1  Aldedh    Aldehyde dehydrogenase family
    3.3e-05   23.1   0.0    5.4e-05   22.4   0.0    1.2  1  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.4   0.1  4.3e-144  3.8e-140       8     462 .]      29     484 ..      22     484 .. 0.95

  Alignments for each domain:
  == domain 1  score: 467.4 bits;  conditional E-value: 4.3e-144
                                       EEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HH CS
                            Aldedh   8 tievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkpla 84 
                                       ++ v +P++ +++++vpa++a+dv++a+++A+ a+++wa+ p+ eR ++++++++ + +++  l ++ ++etGk+  
  gi|313125726|ref|YP_004035996.1|  29 SLSVESPFDATTLGTVPACNADDVREAFDRARTAQSEWADRPLGERLAVFERFHERVLDEQSSLLDVVQAETGKSRL 105
                                       47899************************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHH.HSEEEEEEC..TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEE CS
                            Aldedh  85 earaeveeaidvlryyaelaek.legevlpss..egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvv 158
                                       +a +e  ++++++ryya+ a+  l+ +  + +    ++++ +r+P+Gvvg+I+PWN+Pl l++  ++pal+aGN+vv
  gi|313125726|ref|YP_004035996.1| 106 DAHEEAVDVASTARYYATNARSfLASRQRTGAvpFVTRTTEHRRPVGVVGIISPWNYPLTLSISDAVPALLAGNAVV 182
                                       **********************7776443322236788999999********************************* PP

                                       EEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEE CS
                            Aldedh 159 lKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlE 235
                                       +KP e tp++al++ el+ e glP++++ vvtg+g+++ge++ve+   d v ftGstevgr +a+aa++nl  ++lE
  gi|313125726|ref|YP_004035996.1| 183 CKPDEGTPFTALRIRELLIESGLPADLFAVVTGRGDDIGETVVEE--SDYVCFTGSTEVGRTVAAAAGRNLIDCSLE 257
                                       *******************************************95..789*************************** PP

                                       E---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---S CS
                            Aldedh 236 lGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPli 312
                                       lGGknp++vl+daD+d+a+e++++++f+naGQ Ci+++r++v +++ ++f++++v ++++l++g + d d dvG+l+
  gi|313125726|ref|YP_004035996.1| 258 LGGKNPMLVLSDADVDAAAENAAQACFSNAGQLCISIERIYVDSDVREDFLDAFVRETQRLTLGAGYDFDYDVGTLA 334
                                       ***************************************************************************** PP

                                       SHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSST.TEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHH CS
                            Aldedh 313 seaqlekvekyveeakeegaklllGgereeaglekg.yfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaie 388
                                       seaqlekv+++ve+a+e+ga + +Gg   +++++ g y +ePtvl++vt++m +a  E+FGPV++v++++ +++a+e
  gi|313125726|ref|YP_004035996.1| 335 SEAQLEKVQSHVEDAVEKGASVQTGG---RRRDDVGpYAYEPTVLTGVTDEMLCADAETFGPVAAVYEVSGIADAVE 408
                                       **************************...44555555**************************************** PP

                                       HHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTT..SEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                            Aldedh 389 iaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaea..lpfgGvkqSglGreggkegleeytevktv 462
                                        aN+ +yGL+a+v++ d +rae+va+r+eaG+v++Nd  ++a  +  +p+gG+++Sg+Gr +g+ g++++te +tv
  gi|313125726|ref|YP_004035996.1| 409 RANEGPYGLNASVWSGDTARAEQVAARIEAGTVNVNDGYAAAWGSvdAPMGGIGDSGIGRRHGEVGMTRFTESQTV 484
                                       *************************************95555444345************************9987 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   6.1e-09   5.4e-05      85     248 ..     146     302 ..     138     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.1e-09
                              LuxC  85 ekaqprglvlhvlsgNvpl.lpvmsilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvyfksgd 160
                                       e+++p g+v  + + N pl l +   + +lL++n+ ++k+  + pf+a ++   l++       ad  +vv   +  
  gi|313125726|ref|YP_004035996.1| 146 EHRRPVGVVGIISPWNYPLtLSISDAVPALLAGNAVVCKPDEGTPFTALRIRELLIESGLP---ADLFAVV--TGRG 217
                                       789999999999999*9973678889*************************9999998886...8899***..9999 PP

                              LuxC 161 tkleeeivqnaDvvvawGgeeaikaiseklkpgkql..ikfGakvSfavvdkealeeealdkaaeraAkDiivfdQq 235
                                       + + e++v+++D v   G+ e  +++++ +  +  +  ++ G k  + v+  +     ++d+aae+aA+   +   q
  gi|313125726|ref|YP_004035996.1| 218 DDIGETVVEESDYVCFTGSTEVGRTVAAAAGRNLIDcsLELGGKNPMLVLSDA-----DVDAAAENAAQACFSNAGQ 289
                                       9*************************997766654313789999999988655.....5***********99999** PP

                              LuxC 236 AClspqvvfvekd 248
                                        C+s   ++v++d
  gi|313125726|ref|YP_004035996.1| 290 LCISIERIYVDSD 302
                                       ***********88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 2892.31
//
Query:       gi|313125727|ref|YP_004035997.1|  [L=102]
Description: moad family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-15   57.9   0.1    1.3e-15   57.7   0.1    1.1  1  ThiS          ThiS family
     0.0077   16.0   0.1      0.013   15.3   0.1    1.3  1  STN           Secretin and TonB N terminus short domain
  ------ inclusion threshold ------
      0.041   13.7   0.1          3    7.8   0.0    2.1  2  Ub-Mut7C      Mut7-C ubiquitin
       0.28    9.8   0.0       0.29    9.7   0.0    1.0  1  Condensation  Condensation domain


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.1     3e-19   1.3e-15       2      77 .]       7      89 ..       6      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 3e-19
                                      EETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG........TTTTEEEEETTEEEGCCTTTSB--TTCEEEE CS
                              ThiS  2 llfaelrelag..eeelelaegstvaelleaLgerypela........lerrvavavNgeivprlwldtelkdgDevai 70
                                      +lfa l e+ag  e+ + +a+++tv+++l+aL  ++++l         l + v++++Ng + +    ++e++dgDe+a+
  gi|313125727|ref|YP_004035997.1|  7 RLFADLAEVAGerETAVTVADDATVEDALDALLDNHDGLRtrvfddgvLADHVNLLRNGADTSL---SEEVSDGDELAL 82
                                      79**********************************9999********99**************...************ PP

                                      EESTTC- CS
                              ThiS 71 lppVaGG 77
                                      +ppV+GG
  gi|313125727|ref|YP_004035997.1| 83 FPPVSGG 89
                                      ******9 PP

>> STN  Secretin and TonB N terminus short domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.9e-06     0.013       7      36 ..      12      42 ..       7      43 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-06
                               STN  7 selvrgnqtvslnign.vtideaLdeLLkgt 36
                                       ++v+g + +++ + + +t+++aLd LL+++
  gi|313125727|ref|YP_004035997.1| 12 LAEVAGERETAVTVADdATVEDALDALLDNH 42
                                      46788866666666555************97 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0082        37      19      42 ..      15      38 ..       1      39 [. 0.77
   2 ?    7.8   0.0   0.00067         3      53      75 ..      62      84 ..      53      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0082
                          Ub-Mut7C 19 arreralavafdeaatvkhviEal 42
                                       + er++av ++  atv +++ al
  gi|313125727|ref|YP_004035997.1| 15 VAGERETAVTVADDATVEDALDAL 38
                                      45567889999*********9997 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00067
                          Ub-Mut7C 53 lvnGesvgfshiledGdrvavyp 75
                                      l nG  +++s+ ++dGd +a  p
  gi|313125727|ref|YP_004035997.1| 62 LRNGADTSLSEEVSDGDELALFP 84
                                      45****************99887 PP

>> Condensation  Condensation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   6.5e-05      0.29      40      64 ..      27      51 ..      20      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.5e-05
                                      -HHHHHHHHHHHHHH-SSCCEEEEE CS
                      Condensation 40 dlerlekalqelierhdaLRtvfle 64
                                      d  ++e+al++l++ hd LRt+   
  gi|313125727|ref|YP_004035997.1| 27 DDATVEDALDALLDNHDGLRTRVFD 51
                                      6779*****************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 617.02
//
Query:       gi|313125728|ref|YP_004035998.1|  [L=412]
Description: trka-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-06   28.2   2.1    2.3e-06   27.4   0.3    2.4  2  TrkA_C    TrkA-C domain


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1     0.094   1.7e+03      49      65 ..     274     290 ..     268     291 .. 0.87
   2 !   27.4   0.3   1.3e-10   2.3e-06       3      67 ..     324     385 ..     322     388 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.094
                                       TT-EEEEEEEHHHHHHH CS
                            TrkA_C  49 eGDvllvvgspsdlael 65 
                                       ++Dv +v+++ sd ++l
  gi|313125728|ref|YP_004035998.1| 274 ADDVATVIVDESDAQQL 290
                                       789*******9999876 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.3e-10
                                       EEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T..-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   3 evtvpagsplvGktlkelnlrargvlvvairRg..geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                        v v  gs lvG tl+   l   +++v+a+r +   + +ips + +L +GD+l++v+ p++++++++
  gi|313125728|ref|YP_004035998.1| 324 TVPVETGSELVGETLRS--L---DATVIAVRPSvgAVETIPSRSRELAAGDILFLVARPETIRRIAR 385
                                       578999***********..9...66999997557689**************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2360.46
//
Query:       gi|313125729|ref|YP_004035999.1|  [L=434]
Description: k+ transporter, NAD-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-12   46.1   0.8    1.1e-11   44.4   0.1    2.4  3  TrkA_C           TrkA-C domain
  ------ inclusion threshold ------
      0.045   13.7   0.0       0.11   12.5   0.0    1.6  1  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       1.4   1.3e+04      49      57 ..     232     240 ..     231     244 .. 0.59
   2 ?   -3.3   0.0       0.9   8.1e+03      43      53 ..     328     338 ..     320     344 .. 0.55
   3 !   44.4   0.1   1.2e-15   1.1e-11       2      68 ..     364     432 ..     363     434 .] 0.95

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.4
                                       TT-EEEEEE CS
                            TrkA_C  49 eGDvllvvg 57 
                                        GD++ v++
  gi|313125729|ref|YP_004035999.1| 232 RGDEVMVLA 240
                                       467777665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.9
                                       TT-B--TT-EE CS
                            TrkA_C  43 gdtvLeeGDvl 53 
                                        + +L ++Dv 
  gi|313125729|ref|YP_004035999.1| 328 ASEILSADDVA 338
                                       34455555555 PP

  == domain 3  score: 44.4 bits;  conditional E-value: 1.2e-15
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       +++t +++  l+G+tl+e+n+r+  +v v+a+rR+  + + p+gd   +++D+l+vvg  sdl +++e+
  gi|313125729|ref|YP_004035999.1| 364 RRLTTREDGVLDGTTLGEANVRETyNVVVLAVRRDgRWTVAPRGDQPVQSDDELIVVGAYSDLTTFTEV 432
                                       6889999999*****************************************************999986 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.2e-05      0.11      39      93 ..     373     426 ..     354     433 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                   Castor_Poll_mid  39 elegkkyedvlla.fqeavviGikvassgkiylnPeddevlqegdkllviaedddt 93 
                                        l+g++ +++ ++   ++vv+ +   ++g+ ++ P+ d+ +q +d+l+v++  +d 
  gi|313125729|ref|YP_004035999.1| 373 VLDGTTLGEANVReTYNVVVLAV--RRDGRWTVAPRGDQPVQSDDELIVVGAYSDL 426
                                       57888888776651446677777..899**********************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.51
# Mc/sec: 2584.22
//
Query:       gi|313125730|ref|YP_004036000.1|  [L=405]
Description: kef-type k+ ransport system, NAD-binding component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-27   93.8   0.4    1.3e-26   93.1   0.4    1.4  1  TrkA_N           TrkA-N domain
    5.5e-13   48.7   2.7    5.5e-13   48.7   2.7    2.2  2  Ion_trans_2      Ion channel
     0.0012   18.1   0.6     0.0021   17.3   0.2    1.7  2  Ion_trans        Ion transport protein
     0.0018   18.2   0.7     0.0018   18.2   0.7    1.6  2  NAD_binding_10   NAD(P)H-binding
     0.0023   18.3   0.1     0.0083   16.5   0.1    2.0  2  NAD_binding_7    Putative NAD(P)-binding
     0.0084   15.9   0.0      0.018   14.8   0.0    1.5  1  IRK              Inward rectifier potassium channel transmemb
  ------ inclusion threshold ------
      0.054   13.8   0.0       0.17   12.1   0.0    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.071   12.7   0.8       0.13   11.8   0.1    1.8  2  NmrA             NmrA-like family
      0.071   13.2   0.0       0.13   12.3   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.13   12.0   0.2       0.22   11.3   0.2    1.3  1  SLS              Mitochondrial inner-membrane-bound regulator


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.4   7.4e-30   1.3e-26       1     116 []     245     359 ..     245     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 7.4e-30
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       ++++G+G++++ ++eeL+++  dv++   deer ++l+++g++v+ +d++de+   +  +++a+av++at++d++ +
  gi|313125730|ref|YP_004036000.1| 245 VLVLGHGDLTEPILEELTQKT-DVLILTPDEERTRRLTDRGYTVLTADPSDEDSQIRGRVKSAQAVVTATNNDAEDA 320
                                       68*****************99.6****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       la+l+a++lnp+ +i+a a ++e++++lk++gad+visp
  gi|313125730|ref|YP_004036000.1| 321 LAILTARQLNPEVTIVAAATHRENVNKLKRAGADTVISP 359
                                       *************************************98 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.5       6.7   1.2e+04      55      72 ..      14      31 ..       8      36 .. 0.54
   2 !   48.7   2.7   3.1e-16   5.5e-13      22      75 ..     164     219 ..     140     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.7
                                      HHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2 55 tivyillGlalfalflav 72
                                      ++++ l+G + +a+ +a+
  gi|313125730|ref|YP_004036000.1| 14 MVLTFLVGALSVATGIAN 31
                                      455555555555555544 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 3.1e-16
                                       ---HHHHHHHHHHHHTTS----SSTT.---.--HHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  22 kwsfldalYfsfvtltTiGYGdivpe.tda.grlftivyillGlalfalflavlgk 75 
                                        +++lda+Yfs+vt +T+GYGdi+p  t a g lft+ +il+ ++ fa++l v+++
  gi|313125730|ref|YP_004036000.1| 164 IHNLLDAFYFSLVTGSTVGYGDITPApTSAvGELFTLSVILVTVSSFAAVLGVVFT 219
                                       5799********************99877779*******************99986 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   1.9e+03     215     237 ..      14      36 ..       4      38 .. 0.80
   2 !   17.3   0.2   1.2e-06    0.0021     175     235 ..     163     219 ..      85     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 215 vifiilgsflllNlliaviadnf 237
                                       +++ +l++ l ++  ia+i+ ++
  gi|313125730|ref|YP_004036000.1|  14 MVLTFLVGALSVATGIANITVTI 36 
                                       78899999999999999999876 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.2e-06
                                       SSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 175 nFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNlliaviad 235
                                         +n+++a+++++++ +t+g+gdi++a++++       +f + +il+++  ++ +++v+ +
  gi|313125730|ref|YP_004036000.1| 163 GIHNLLDAFYFSLVTGSTVGYGDITPAPTSAV----GELFTLSVILVTVSSFAAVLGVVFT 219
                                       34589************************998....4477777777777777777777765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.2   5.7e+03      63     102 ..     115     157 ..      91     168 .. 0.53
   2 !   18.2   0.7   9.8e-07    0.0018       3      85 ..     250     348 ..     249     400 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.2
                                       EEEES---TCCHHHH...HHHHHHHHHHCT--EEEEEEETTTT CS
                    NAD_binding_10  63 aVvsalggggkdeeg...aknivdaakeagvkRfvlvsaigvg 102
                                        Vv+ l+ ++ d+e    + ++++    ag + + +v+a+  +
  gi|313125730|ref|YP_004036000.1| 115 FVVVGLNFRAFDRELqltTTQVAALTALAGAQAYGTVGAFALR 157
                                       3555555555544444434444444444666666666666655 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 9.8e-07
                                       TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-C.CHHHHHHTT-SEEEES---TCCHHHH. CS
                    NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdv.edlaealkgadaVvsalggggkdeeg. 77 
                                       +G     +++el ++  ++v +l+ ++e++ +l  + g +v+++d +d+ ++++  +k a+aVv+a++++++d+ + 
  gi|313125730|ref|YP_004036000.1| 250 HGDLTEPILEELTQK--TDVLILTPDEERTRRLT-DRGYTVLTADPSDEdSQIRGRVKSAQAVVTATNNDAEDALAi 323
                                       677777889999988..599*************8.69***********8356***************9998854445 PP

                                       .................HHHHHHHH CS
                    NAD_binding_10  78 .................aknivdaa 85 
                                                        ++  v+ +
  gi|313125730|ref|YP_004036000.1| 324 ltarqlnpevtivaaatHRENVNKL 348
                                       5555567743333333333334444 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   4.6e-06    0.0083       4      87 ..     239     331 ..     237     360 .. 0.72
   2 ?   -2.3   0.0       3.4   6.1e+03      23      39 ..     345     360 ..     337     373 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.6e-06
                     NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee..............lekdlegadlvi 66 
                                       dl + +vlv G G++ +  ++ l ++  +v +++p+   e e++ +l+++               +++ ++ a+ v+
  gi|313125730|ref|YP_004036000.1| 239 DLLENHVLVLGHGDLTEPILEELTQK-TDVLILTPD---E-ERTRRLTDRGytvltadpsdedsqIRGRVKSAQAVV 310
                                       77789*****************9999.9********...3.3334444444122111112222225666999***** PP

                     NAD_binding_7  67 aatddrelneriaeaakarri 87 
                                       +at+++++ +    +a++ + 
  gi|313125730|ref|YP_004036000.1| 311 TATNNDAEDALAILTARQLNP 331
                                       ****99998877777776554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                     NAD_binding_7  23 vrklleagakvtvvape 39 
                                       v+kl +aga+ tv++p+
  gi|313125730|ref|YP_004036000.1| 345 VNKLKRAGAD-TVISPA 360
                                       7888888888.567776 PP

>> IRK  Inward rectifier potassium channel transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     1e-05     0.018      79     138 ..     161     220 ..     153     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                               IRK  79 vanvksftsallfslEtqttigyGsrvvteeCpeailllviqsivgllidavlvgivlaK 138
                                       +  ++++++a+ fsl t  t+gyG  +++   + + l+ +  ++v++   a+++g+v++ 
  gi|313125730|ref|YP_004036000.1| 161 FDGIHNLLDAFYFSLVTGSTVGYGDITPAPTSAVGELFTLSVILVTVSSFAAVLGVVFTP 220
                                       67899*******************988877766665555555556666667788888875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.6e-05      0.17       1      77 [.     245     313 ..     245     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.6e-05
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       vl++G G   ++++e+l ++ dv     + ++++e+ ++l +       +  + d++++++ +   +k++++vv ++
  gi|313125730|ref|YP_004036000.1| 245 VLVLGHGDLTEPILEELTQKTDV----LILTPDEERTRRLTD----RGYTVLTADPSDEDSQIRGRVKSAQAVVTAT 313
                                       89******************987....9********999975....4567788899999988888888888888665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.5   4.5e+03      44      88 ..      90     138 ..      86     146 .. 0.74
   2 ?   11.8   0.1   7.1e-05      0.13      23      90 ..     263     340 ..     251     348 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                                       TTEEEES-TT-HHHHHHHHTT-SEEEE---GG....S-HHHHHHHHHHH CS
                              NmrA  44 Gvelvkgdlddkeslvealkgvdvvfsvtgfy....skeiedgkklvdA 88 
                                       +v++ +g l++ e    ++  +  +f+v+g++    + e++  ++ v+A
  gi|313125730|ref|YP_004036000.1|  90 PVTVAQGALQSTEQSIPLIGLSTIAFVVVGLNfrafDRELQLTTTQVAA 138
                                       7888899999888888888888888888887777776666655555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.1e-05
                                       -EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SEEEE---GG.........S-HHHHHHHHHHHH CS
                              NmrA  23 hkvralvRdtkselakslkeaGvelv.kgdlddkeslvealkgvdvvfsvtgfy.........skeiedgkklvdAa 89 
                                        k+ +l+  +++e+ + l ++G +++ ++  d+++ ++  +k +++v  +t+             +++  +++v+Aa
  gi|313125730|ref|YP_004036000.1| 263 QKTDVLILTPDEERTRRLTDRGYTVLtADPSDEDSQIRGRVKSAQAVVTATNNDaedalailtARQLNPEVTIVAAA 339
                                       467788888999**************5666888899****************7677777666666666667777776 PP

                                       H CS
                              NmrA  90 k 90 
                                        
  gi|313125730|ref|YP_004036000.1| 340 T 340
                                       5 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.4e-05      0.13       6      85 ..     237     315 ..     232     335 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.4e-05
                                       HHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGC...GHHHHHHT-SEE CS
                      Shikimate_DH   6 kleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkle...elkellaeadvv 79 
                                       +l +l e++vl++G G + e +++ L +   ++v+++  + er ++l ++  ++ ++a + +   +++ ++++a  v
  gi|313125730|ref|YP_004036000.1| 237 QL-DLLENHVLVLGHGDLTEPILEELTQ--KTDVLILTPDEERTRRLTDRGYTV-LTADPSDedsQIRGRVKSAQAV 309
                                       44.47799******************95..578***************998777.6666654111688899999999 PP

                                       EE-SSS CS
                      Shikimate_DH  80 isatas 85 
                                       ++at+ 
  gi|313125730|ref|YP_004036000.1| 310 VTATNN 315
                                       999975 PP

>> SLS  Mitochondrial inner-membrane-bound regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00012      0.22      79     132 ..     221     287 ..     219     354 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                               SLS  79 yieasineilknittetvd.lsellklskvdklkdl.lseelleelgrltntvie................v 132
                                        iea++ ++l ++t e++d l++      v  l    l+e +leel++ t++ i                 v
  gi|313125730|ref|YP_004036000.1| 221 LIEAQLSKALGRMTEEQLDlLENH-----VLVLGHGdLTEPILEELTQKTDVLILtpdeertrrltdrgytV 287
                                       69*****************43333.....455666668****************966666666655555541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 2324.00
//
Query:       gi|313125731|ref|YP_004036001.1|  [L=490]
Description: hypothetical protein Hbor_09620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-13   50.6   3.3    3.5e-13   49.8   3.3    1.4  1  HPP       HPP family
    5.2e-09   36.8   0.5    0.00092   19.7   0.1    3.3  3  Usp       Universal stress protein family
     0.0085   15.6   1.0      0.059   12.8   0.3    2.3  2  SfLAP     Sap, sulfolipid-1-addressing protein


Domain annotation for each model (and alignments):
>> HPP  HPP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   3.3   5.8e-17   3.5e-13       1     116 [.      73     201 ..      73     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 5.8e-17
                               HPP   1 liaslGAsavllfavpesplaqPrnvvgGhlisalvGvaiaklfgl..........sllwlaaalavalaialmllt 67 
                                       l+++l++ ++ lf  pe ++a+P+++vg+ + +a++G+a + + +           ++   +a lav+l+ ++++ +
  gi|313125731|ref|YP_004036001.1|  73 LFPPLASGTYTLFSDPEGQYASPKKFVGSLTTGAVCGLASVGFTEMvygapqttipHP--ESAVLAVFLTGVVTWGA 147
                                       79*************************************5544444556777764333..39*************** PP

                               HPP  68 rtlhPPagAtaliavlgkeikelgwafl....lvpvllgslllvlvalllnn.l 116
                                       ++  P+a +tal+ +++++++el+ +      +v+++l+sl+++ + +++++ +
  gi|313125731|ref|YP_004036001.1| 148 GVEAPSAFSTALLTLVSNPATELSQTQSavayVVNIFLASLIVAGAFVVWREeF 201
                                       *****************9955554332200124459************998755 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.5e-07   0.00092       4     116 ..     218     341 ..     217     364 .. 0.74
   2 ?    1.1   0.0     0.089   5.3e+02       2      43 ..     368     409 ..     367     433 .. 0.76
   3 !   12.3   0.0     3e-05      0.18      96     139 ..     441     484 ..     405     486 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                                       EEEEEE-SSHHHHHHHHHHHHHHHH.CTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH......... CS
                               Usp   4 rIlVavDgseeskkAlewAlelaka.rgaelillhvidprasgavsdadeeaeeeeleleeaeleada......... 70 
                                       ++l+++   e++++ + ++ +la+a + ++++ll ++ ++++g++++ +     + ++   + +   +         
  gi|313125731|ref|YP_004036001.1| 218 HVLIPM-RGEDAERTALFGSRLAAAhDAGKVVLLGIVNESDPGQSPETEAV-DIATSDGDDDDNLPVEademvaele 292
                                       799999.9999999999****999944455555555555555555544444.4444444444444333479999*** PP

                                       ..HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCC.SST CS
                               Usp  71 ..akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrg.rsg 116
                                         a++ +   gv  evvv  gdp  + ++ a++ ++dliV+     r+ 
  gi|313125731|ref|YP_004036001.1| 293 scAADIRTHVGVPCEVVVAAGDPLSTTIQSAQNANCDLIVTPYEEdRGL 341
                                       ****************************************987774444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.089
                                       -SEEEEEE-.SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSH CS
                               Usp   2 ykrIlVavD.gseeskkAlewAlelakargaelillhvidpra 43 
                                       +krIlV v    +++++ +++A +l  ++ + + + ++i ++ 
  gi|313125731|ref|YP_004036001.1| 368 WKRILVLVSrPGDTAHAMIDFATRLTGRN-GVVSVTTCINSEV 409
                                       589*****97778888999***9999996.5667776666555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 3e-05
                                       HHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  96 levaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                        ++a++e++dl+V+Gs++ ++ + +++   +   +r+++c+V v
  gi|313125731|ref|YP_004036001.1| 441 FLTANAESYDLVVLGSSQNRSAASRFVAPPTFERIREVECDVAV 484
                                       5789**************55555555566665667889999988 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.052   3.1e+02      88     115 ..      22      49 ..       9      74 .. 0.60
   2 !   12.8   0.3   9.9e-06     0.059      31      90 ..     135     200 ..     124     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.052
                             SfLAP  88 vrrpkassrselprllsrleslleggal 115
                                       +rr ++++ se++r+l+ + +ll    l
  gi|313125731|ref|YP_004036001.1|  22 LRRIERRELSEFRRWLENTNNLLHLSIL 49 
                                       4444567777777777777755433322 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.9e-06
                             SfLAP  31 llaFlvgwlvvlvalglivlfvlrslls......gasaapssaikalqivlGvlllllaaveavrr 90 
                                       l++Fl g+++ ++++ +   f ++ l+       ++s+++s+++ ++ i+l +l+++ a+v++++ 
  gi|313125731|ref|YP_004036001.1| 135 LAVFLTGVVTWGAGVEAPSAFSTALLTLvsnpatELSQTQSAVAYVVNIFLASLIVAGAFVVWREE 200
                                       667777777777766544333333333322333388888***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2760.20
//
Query:       gi|313125732|ref|YP_004036002.1|  [L=242]
Description: uridine phosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-44  151.0   1.4    3.5e-44  150.8   1.4    1.0  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
      0.099   12.7   0.0       0.22   11.6   0.0    1.6  1  DUF3568    Protein of unknown function (DUF3568)


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.8   1.4     4e-48   3.5e-44       2     228 ..      17     233 ..      16     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 150.8 bits;  conditional E-value: 4e-48
                                       EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEE CS
                         PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGt 78 
                                       ia+i g+pg+v+ +a++  e++++  ++r++k+v  t+ g+p +i+stGiG+p+aa +a  +l    gv+++ir+Gt
  gi|313125732|ref|YP_004036002.1|  17 IALIPGDPGRVDRIAKQ-CENVEEVAQNREYKVVNATYDGVPLTICSTGIGCPSAA-IAIEELSR-VGVETFIRVGT 90 
                                       9****************.**************************************.66555555.77********* PP

                                       EEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS CS
                         PNP_UDP_1  79 aGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfy 155
                                        G+l++++++GD+++++ a   +g+++         y   + +a +d + ++ l+ +aea++ +vh+G++++ d fy
  gi|313125732|ref|YP_004036002.1|  91 IGALQEHVEIGDMIVATGAAKEEGTTR--------RYESKVIPAVPDYDVLTSLVDSAEANDEEVHVGPIVSDDAFY 159
                                       ***************************........6666666777888888888888999***************** PP

                                       -CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH..HCCCHHHHHHHHHHHHH CS
                         PNP_UDP_1 156 aeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeath.eeveefaqeaaknaaal 228
                                       +e++++++++++ g   +eME+a v+ lAr++g++++ai++v  ++++g+ + a+  ee  e a++++++a +l
  gi|313125732|ref|YP_004036002.1| 160 NESDDYVEAWNEAGLLGIEMEAATVFSLARRRGLRAGAICTVDGNLVKGTQKGADSdEELPEKAKNNVERAITL 233
                                       ******************************************87788877777633344444444444444444 PP

>> DUF3568  Protein of unknown function (DUF3568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.4e-05      0.22      55     122 ..      38     104 ..      27     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                           DUF3568  55 lkaiedlnvlsvvekskdsssatieakaaedktvfiklekldknstkvsIrvGslGDeqaSrrlldaI 122
                                       ++++++ + ++vv+ ++d+   ti  +  + +   i +e+l+   ++ +IrvG++G  q   ++ d I
  gi|313125732|ref|YP_004036002.1|  38 EEVAQNRE-YKVVNATYDGVPLTICSTGIGCPSAAIAIEELSRVGVETFIRVGTIGALQEHVEIGDMI 104
                                       44556666.****************9999989999*********************988877776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1260.43
//
Query:       gi|313125733|ref|YP_004036003.1|  [L=166]
Description: hypothetical protein Hbor_09640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 925.73
//
Query:       gi|313125734|ref|YP_004036004.1|  [L=93]
Description: hypothetical protein Hbor_09650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.036   14.0   0.0    1.4  1  Cdc6_C         CDC6, C terminal winged helix domain
      0.035   14.1   0.0      0.047   13.7   0.0    1.2  1  Dimerisation2  Dimerisation domain
      0.036   13.9   0.0       0.49   10.3   0.0    2.1  2  DUF433         Protein of unknown function (DUF433)
      0.067   13.1   0.0      0.086   12.7   0.0    1.2  1  TFIIE_alpha    TFIIE alpha subunit
        0.1   12.6   0.0       0.17   11.9   0.0    1.4  1  HTH_Mga        M protein trans-acting positive regulator (MGA
       0.11   12.6   0.0       0.16   12.1   0.0    1.3  1  DUF2250        Uncharacterized protein conserved in archaea (


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.036      36      60 ..      25      49 ..      17      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                      ---HHHHHHHHHHHHHTTSEEEEEE CS
                            Cdc6_C 36 pltqrevsdllseLemlgileleks 60
                                       l+ re+++++se+++lg lel+ +
  gi|313125734|ref|YP_004036004.1| 25 ELSVREIRSICSEMADLGWLELRAE 49
                                      5899*****************9976 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.047      24      84 ..       6      63 ..       4      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                     Dimerisation2 24 FdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelastyL 84
                                       ++L  +++++ae +a+e ++sv+ ++ ++  ++ Lg Le + +++    +   e a++ L
  gi|313125734|ref|YP_004036004.1|  6 LEALWRRGNVEAESIATEFELSVREIRSICSEMADLGWLELRAESQ---KWVAGESADELL 63
                                      5778888999******************************774444...567777777666 PP

>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.084   2.5e+02      29      51 ..      12      33 ..       3      36 .. 0.74
   2 ?   10.3   0.0   0.00016      0.49      30      46 ..      55      71 ..      51      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.084
                                      HTT--HHHHHHHH.TS-HHHHHH CS
                            DUF433 29 aaGesieeiledyPdLtlediqa 51
                                      +  +  e i+ ++ +L+  +i+ 
  gi|313125734|ref|YP_004036004.1| 12 RGNVEAESIATEF-ELSVREIRS 33
                                      445668999999*.999998875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                                      TT--HHHHHHHH.TS-H CS
                            DUF433 30 aGesieeiledyPdLtl 46
                                      aGes +e+l  yP L++
  gi|313125734|ref|YP_004036004.1| 55 AGESADELLSSYPALKA 71
                                      8**************85 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.9e-05     0.086      17      59 ..       4      46 ..       2      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE CS
                       TFIIE_alpha 17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvky 59
                                       +l++L ++g+v  e +a e ++   e+r++  ++ + +  + 
  gi|313125734|ref|YP_004036004.1|  4 HILEALWRRGNVEAESIATEFELSVREIRSICSEMADLGWLEL 46
                                      69*****************************999988776665 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.7e-05      0.17      11      46 ..       6      40 ..       4      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.7e-05
                           HTH_Mga 11 lelLteneksltldelakeLglseltlqsdiseLne 46
                                      le+L   ++  +   +a+e  ls ++++s++se+ +
  gi|313125734|ref|YP_004036004.1|  6 LEALWR-RGNVEAESIATEFELSVREIRSICSEMAD 40
                                      556666.666666789*****************976 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.4e-05      0.16      24      54 ..      16      46 ..       3      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                           DUF2250 24 YaksiakeleipleevrellkkLeelGLler 54
                                       a sia e+e+++ e+r+++ ++ +lG le 
  gi|313125734|ref|YP_004036004.1| 16 EAESIATEFELSVREIRSICSEMADLGWLEL 46
                                      4899***********************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 545.87
//
Query:       gi|313125735|ref|YP_004036005.1|  [L=169]
Description: hypothetical protein Hbor_09660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.5   3.3      0.014   15.5   3.3    2.1  2  ThiW      Thiamine-precursor transporter protein (ThiW)


Domain annotation for each model (and alignments):
>> ThiW  Thiamine-precursor transporter protein (ThiW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3     0.039     7e+02      84      89 ..      20      25 ..       2      59 .. 0.50
   2 ?   15.5   3.3   8.1e-07     0.014      38      91 ..      75     128 ..      68     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.039
                              ThiW 84 rltrkl 89
                                       +   +
  gi|313125735|ref|YP_004036005.1| 20 VVLSAF 25
                                      322222 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 8.1e-07
                              ThiW  38 aavllGPwyalavalvisliRnllgtgtllalpGsiiGallagllyrltrklll 91 
                                       a+vl G +ya+a + + +l+  l+ +g++l lp ++  ++++g++y +  +l+l
  gi|313125735|ref|YP_004036005.1|  75 AGVLAGILYAVAYTALAALLPPLVSVGSMLVLPHAVATVVVVGFVYSFFAHLVL 128
                                       89********************************************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 914.11
//
Query:       gi|313125736|ref|YP_004036006.1|  [L=287]
Description: sugar kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-51  174.0   0.5    9.9e-51  172.8   0.5    1.5  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8   0.5   5.5e-55   9.9e-51       1     299 [.       1     276 [.       1     279 [. 0.93

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 5.5e-55
                                       EEEEEEEEEEEEEEEEECSSH.TTSEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHT CS
                              PfkB   1 mtkvvviGealidliavsekl.egelv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkke 75 
                                       m +vv+ G+++ d+ + ++++ e +   +v++ +   GG++ NvAv+l++lg dv+++g vGdD++G+  ++el +e
  gi|313125736|ref|YP_004036006.1|   1 MPRVVCAGHVNWDVTLRVDSIpELDGEaTVESRSTAGGGSASNVAVGLSDLGLDVSLLGSVGDDEHGRAARAELVAE 77 
                                       6789******************777777************************************************* PP

                                       TEEETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHH CS
                              PfkB  76 gvdtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleela 152
                                       gvd+d+v+ +++ +t++++ivv+ +ge  ++ ++ga+++++ ++l  +e+ l+ ad+l++ +      + ++ ++la
  gi|313125736|ref|YP_004036006.1|  78 GVDCDHVVTTDELETTTKYIVVQPTGEVMVLGCPGANEAFDAADL--PESVLQDADHLHLTS-----QRPETAKQLA 147
                                       ******************************************988..**************9.....6788888888 PP

                                       HHHHHTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGG CS
                              PfkB 153 eaaknggtfdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGk 229
                                       + a + g  +p+  dp        ++ +++ +d+l++n++E++  +++   d                +t+v ++G 
  gi|313125736|ref|YP_004036006.1| 148 DRAASVG--VPVSFDPGRRIGDRGYEVMISDVDYLFLNDREAALALDAF--DL-------D------GQTLVLKHGP 207
                                       8888888..89999987754678899999**************999999..33.......2......279******* PP

                                       GEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCS CS
                              PfkB 230 eGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiasl 299
                                       +Ga v   dg + +p  +++++vDttGAGD+f++gf+a+ ++g ++e+al+ ana++a++ + +ga++ l
  gi|313125736|ref|YP_004036006.1| 208 DGAEVRRPDGRVAHPG-YPIDAVDTTGAGDAFAAGFIASRVAGDDFERALAVANACGAFISRVPGAREGL 276
                                       ****************.77******************************************999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.37s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1516.84
//
Query:       gi|313125737|ref|YP_004036007.1|  [L=66]
Description: hypothetical protein Hbor_09680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.36s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 374.47
//
Query:       gi|313125738|ref|YP_004036008.1|  [L=272]
Description: hypothetical protein Hbor_09690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-25   90.1   7.6    4.2e-25   89.5   7.6    1.1  1  DUF63     Membrane protein of unknown function DUF63


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   7.6   2.3e-29   4.2e-25      27     267 ..      15     265 ..      11     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 2.3e-29
                             DUF63  27 yaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagllkpplsyllitPliyflvflitlavlli 103
                                       y + L+vav +++ ++ + + ++  + +la +p++ilgs + v+   + l p ++ l  tP +y+ v+++ + + ++
  gi|313125738|ref|YP_004036008.1|  15 YLVGLLVAVGVVVAAVARRRPEVTPQRILAFVPWMILGSAVHVLYVVNALPPVIHPLGGTPAVYLSVGVLGIGTFVA 91 
                                       5566899999999*************************************9999*********************** PP

                             DUF63 104 skklekklkkdykklyaavGvvlvlvvlllLl...lteevvnlevlllvlllaavltalvllllrklk.lellsdkl 176
                                       +       ++    l++ vG+vl++v++++ +   ++e + +++v+++ l++a+v++a  +++l+ +     ++ ++
  gi|313125738|ref|YP_004036008.1|  92 AAEW---AEEALVPLLTGVGTVLSAVAVAAAFlvgASEGTLAPVVPAIGLVVATVVSAGAWVILTRVLpDARITAPV 165
                                       9999...788888999999988776655433324788889999999999999*99999999999888868899**** PP

                             DUF63 177 nlllllahllDasatfvgidllgYvEqHvvpsfLidl.........tGtalvmyplkllvlipvlyildkevkeeee 244
                                        +l++++h lDa +t vgidllg+ E+ ++ +++i+          +Gt + ++ +kl+++  ++ ++  +v+e+ +
  gi|313125738|ref|YP_004036008.1| 166 GILTVFGHALDAVSTAVGIDLLGFSERTPLSRAIIEFaatlptepfFGTVWLFVLVKLVIVSGIVALFADYVREDPT 242
                                       ***********************************9533344444489****************************9 PP

                             DUF63 245 lrnlvklailvlGlaPgiRnllr 267
                                         nl++  + ++Gl+Pg+ nl+ 
  gi|313125738|ref|YP_004036008.1| 243 EGNLLLGFVAAVGLGPGVHNLIL 265
                                       99999999************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1530.56
//
Query:       gi|313125739|ref|YP_004036009.1|  [L=212]
Description: deoxyribose-phosphate aldolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-12   46.6   3.6      4e-12   46.3   3.6    1.1  1  DeoC          DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.019   14.5   0.3      0.093   12.2   0.0    2.0  2  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   3.6   4.5e-16     4e-12       6     232 ..      10     205 ..       6     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 4.5e-16
                                       ECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCT.TSEEEEETECSSCCTTSTTEEEE CS
                              DeoC   6 vDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyak.diallvkldkgtyllkskqrdvd 81 
                                       +D++v+  + t++       d++++ +ea + g +a ++ p ++a as       +a++v++++g++ +  k     
  gi|313125739|ref|YP_004036009.1|  10 IDHTVLGPETTFA-------DVQTVLDEADEYGMNA-CIPPCYVAEASEYAPDvTVATVVGFPHGQHSTAAK----- 73 
                                       6777765555555.......9999999999999999.77888888877655446****************99..... PP

                                       TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEE.EEE-CTTBSSTTCHHHHHHHHH CS
                              DeoC  82 evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplile.lylrdeaikdekvdpdlvaeAa 157
                                          ++  a+++GAd++++v+++  ++++++  +  +i++v +a      ++i+e ++l d++    k       +A 
  gi|313125739|ref|YP_004036009.1|  74 -REEAVDAWENGADELDMVINIGRLKAGADDAVETDIAEVVAA-VPIPVKVIIEtALLTDDE----K------HRAC 138
                                       .89999***********************99999999999865.567889999955555544....4......69** PP

                                       HHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHHH..HHTH..CEEEESH CS
                              DeoC 158 rvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGvseedfletvedAvk..eaga..sGvlsGR 230
                                       +++ae++aD++K++++      +   +e  +++++   +p v+ sGGv         e+A++  +aga  +G++sG 
  gi|313125739|ref|YP_004036009.1| 139 EAAAEADADFVKTSTG---FADGGATVEDVERMAE--YLP-VKASGGV------GSYEEAMAmfDAGAerIGASSGV 203
                                       ****************...3344444444455555..457.99*****......88999998889999999999997 PP

                                       HH CS
                              DeoC 231 ai 232
                                       +i
  gi|313125739|ref|YP_004036009.1| 204 EI 205
                                       65 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1     0.064   5.7e+02      19      78 ..      62     122 ..      53     124 .. 0.67
   2 ?   12.2   0.0     1e-05     0.093      60     101 ..     160     199 ..     148     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.064
                                       TCSTCEEEETTSHHHHHHHHHHHT-SEE.EEEEHHHHCTTHHHHH.HHHHHHHHH-SSEEEE CS
                      His_biosynth  19 Gdrfqelryagdpvelakryeeegadel.hvvDldaakegreanl.dlveeiaeevfipvqv 78 
                                       G    +++ a +  e++ ++ e+gadel +v+ +   k+g +    + ++e++ +v ipv v
  gi|313125739|ref|YP_004036009.1|  62 GFPHGQHSTAAKREEAVDAW-ENGADELdMVINIGRLKAGADDAVeTDIAEVVAAVPIPVKV 122
                                       55555666666666777777.78888885566777777666655525688888888888765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEE CS
                      His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkvii 101
                                       a  + ve++ae   +pv   GG+ s+e++ ++++aga+++  
  gi|313125739|ref|YP_004036009.1| 160 ATVEDVERMAEY--LPVKASGGVGSYEEAMAMFDAGAERIGA 199
                                       567789999999..9**********************99855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1239.69
//
Query:       gi|313125740|ref|YP_004036010.1|  [L=417]
Description: miab-like tRNA modifying enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-23   84.5   0.3      2e-23   83.6   0.1    1.6  2  Radical_SAM  Radical SAM superfamily
      7e-21   74.1   0.3    1.4e-20   73.2   0.3    1.5  1  UPF0004      Uncharacterized protein family UPF0004
    0.00044   20.2   0.1    0.00097   19.1   0.1    1.6  1  TRAM         TRAM domain
  ------ inclusion threshold ------
       0.21   11.6   1.5        5.1    7.1   0.2    3.1  3  Fer2         2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.6   1.6e+04      30      54 ..      53      75 ..      47      89 .. 0.62
   2 !   83.6   0.1   4.4e-27     2e-23       2     165 ..     128     300 ..     127     302 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.6
                                      HHHHHHHHHHHHHHHTTSEEEEEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 30 sveeileevkelkaekgvkevilgg 54
                                      + ++ l+ +kel +e  +  +i++g
  gi|313125740|ref|YP_004036010.1| 53 TERNMLRRAKEL-EEE-TADLIITG 75
                                      555666666666.555.55555555 PP

  == domain 2  score: 83.6 bits;  conditional E-value: 4.4e-27
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS......TTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly......pdfvellerlak 72 
                                       ++ rgC  +Cs+C++++    +gr+ s +vee +e++++l ++ g+ke+ ++g++  +y      +++ ell+r++ 
  gi|313125740|ref|YP_004036010.1| 128 PIARGCMSNCSYCITKF---ATGRVDSPPVEENVEKARAL-VHAGAKEIRITGQDTGVYgwdkgdRKLPELLDRICS 200
                                       689**************...8*******************.9*********************99999999999999 PP

                                       TC..CCTEEEEEEECSSCHG.....HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHT CS
                                       xx..xxxxxxxxxxxxxxxx.....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  73 la..vpgiritvetngtlpd.....eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklrea 140
                                       +   +  +r+ +  +g+ +       e+ +r+       + ++l++++++d  vl+ m+r+h +++++e +e++ e 
  gi|313125740|ref|YP_004036010.1| 201 EIegDFRVRLGMANPGGIHGiheelVEVFDRH---DklYNFIHLPVQSGSDT-VLEAMRRQHRVDKFVEIVETFDET 273
                                       99888889999999999988*95555555555...4555************9.************************ PP

                                       TSET...EEEEEEEBTTTSHHHHHHHHH CS
                                       xxxx...xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 141 gikr...vvdrivglpGendeeleelle 165
                                        ++    ++d+ivg+p e+++++e+ + 
  gi|313125740|ref|YP_004036010.1| 274 -LDYwtlSTDFIVGFPTETEADHEQSMA 300
                                       .999******************998876 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.3   3.1e-24   1.4e-20       1      93 [.       3      92 ..       3      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 3.1e-24
                                      XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHH CS
                           UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCma 79
                                      +++iet+GC+ N+ +s ++ s+L+++g+ +ve++eeAdv ++nTC+v+ek+e++++++ +el+++    + ++++GCma
  gi|313125740|ref|YP_004036010.1|  3 RYHIETYGCTSNRGESRAIESALRDAGHYRVEEPEEADVAIMNTCTVVEKTERNMLRRAKELEEET---ADLIITGCMA 78
                                      789************************************************998776666666655...99******** PP

                                      HS-HHHHHHH-TTS CS
                           UPF0004 80 qrekeellkeepev 93
                                       +++ee+ +e+  +
  gi|313125740|ref|YP_004036010.1| 79 LAQGEEFHEEDVDA 92
                                      ******99987655 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   2.2e-07   0.00097       2      62 .]     355     417 .]     354     417 .] 0.96

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.2e-07
                                       XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT-.....-T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   2 syvGstqeVlveglsksegegiGrtdngkvvfvpgd.....lpgIGdfVeVkItkvkrqyLrGell 62 
                                       s++G+t +V v +++   +    r ++++ ++v+++     +p  Gdf++V++t  +  y++G+++
  gi|313125740|ref|YP_004036010.1| 355 SMIGETHRVMVVREG-TGDSVKCRDEAYRQIIVQNAsehgiEP--GDFLDVEVTSHQTVYAFGKPV 417
                                       899************.999************************..******************976 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.34   1.5e+03      42      76 ..      46      79 ..      45      81 .. 0.45
   2 ?    7.1   0.2    0.0011       5.1      27      63 ..     125     162 ..     108     167 .. 0.75
   3 ?    1.3   0.0     0.076   3.4e+02      10      29 ..     241     260 ..     238     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.34
                                      TTEEEEEESCECTT...SSSSTHHHHHTTEEEEGGGSE CS
                              Fer2 42 tClvevlegevqsd...etelegeeldegklrlaCqti 76
                                      tC+v v+ ++ +++   + ele+e   +   ++ C+++
  gi|313125740|ref|YP_004036010.1| 46 TCTV-VE-KTERNMlrrAKELEEET--ADLIITGCMAL 79
                                      7886.33.33333342233444333..33346777665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0011
                                       TTTTSTTSSSSSSSSTTEEEEEESCECTT..SSSSTHHH CS
                              Fer2  27 ggidipysCggggCgtClvevlegevqsd..etelegee 63 
                                       g ++i  +C  ++C+ C ++   g+v s   e+ +e+++
  gi|313125740|ref|YP_004036010.1| 125 GILPIARGCM-SNCSYCITKFATGRVDSPpvEENVEKAR 162
                                       4789999***.89************95443566666654 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.076
                                       EEEETTTHBHHHHHHHTTTT CS
                              Fer2  10 vevadgettlldaaeenggi 29 
                                       ++v+ g  t+l+a+++++ +
  gi|313125740|ref|YP_004036010.1| 241 LPVQSGSDTVLEAMRRQHRV 260
                                       78999999*******98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2496.39
//
Query:       gi|313125741|ref|YP_004036011.1|  [L=150]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-13   48.4   0.0    1.1e-12   47.9   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    5.1e-11   42.8   0.0      8e-11   42.2   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.2e-11   42.3   0.0    9.2e-11   42.0   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.1e-06   27.8   1.1      3e-06   27.4   0.1    1.7  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0013   18.8   0.1     0.0019   18.3   0.1    1.2  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0016   18.4   0.0      0.025   14.6   0.0    2.2  2  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   3.8e-16   1.1e-12      38     111 ..      55     131 ..      53     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.8e-16
                   Acetyltransf_10  38 eggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkavg 110
                                       +g ++vG++++  dg+   +i+ ++V+pe++g G+g+a+++++ ++++++ ++    vn      +fYe+ GF+++ 
  gi|313125741|ref|YP_004036011.1|  55 DGREVVGMARIvGDGGtvyQITDMVVHPEHQGEGLGTAMMDELVAYLDREAPE-YAYVNLMADVDGFYERWGFEPTA 130
                                       57899******999999*******************************99999.********************996 PP

                   Acetyltransf_10 111 e 111
                                       +
  gi|313125741|ref|YP_004036011.1| 131 P 131
                                       6 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   2.7e-14     8e-11      12      76 .]      57     128 ..      38     128 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.7e-14
                                       TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.......TTSEEEEE.EEEE.THHHHHHHHHHTTEEE CS
                    Acetyltransf_7  12 gkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.......aekgiile.qlel.naekaikfYeklGFee 76 
                                        ++vG+++++ ++   ++it ++V+pe++g G+G+a+++        +      + +++l ++    +fYe+ GFe+
  gi|313125741|ref|YP_004036011.1|  57 REVVGMARIVGDGgtvYQITDMVVHPEHQGEGLGTAMMDElvayldrE---APEYaYVNLmAD--VDGFYERWGFEP 128
                                       577899988888888777888*****************9534333321...112233444333..345*******95 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   3.1e-14   9.2e-11      42     117 .]      57     126 ..      10     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 3.1e-14
                                       TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  42 geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                        e++G++++  +      v+ i +++V+pe++g GlG+a++++l+ ++ +e + + +++v +      ++Ye+ GF
  gi|313125741|ref|YP_004036011.1|  57 REVVGMARIVGDGG---TVYQITDMVVHPEHQGEGLGTAMMDELVAYLDRE-APE-YAYV-NLMADVDGFYERWGF 126
                                       459****8877777...9****************************77777.544.4444.22333489***9999 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   9.9e-10     3e-06      72     127 ..      71     128 ..      62     129 .. 0.88
   2 ?   -1.8   0.1       1.1   3.2e+03     114     124 ..     131     141 ..     130     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9.9e-10
                                       EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--SSHHHHHTTT-EE CS
                    Acetyltransf_9  72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfPssipiYrrfGyei 127
                                       +++++t+  v+peh+g+g+ ++++++++++++ e   +  + l++   ++Y+r G+e+
  gi|313125741|ref|YP_004036011.1|  71 TVYQITDMVVHPEHQGEGLGTAMMDELVAYLDREapEYAYVNLMADVDGFYERWGFEP 128
                                       6899***************************99955566667999999********96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                       -SSHHHHHTTT CS
                    Acetyltransf_9 114 PssipiYrrfG 124
                                       P+s+++Yrr G
  gi|313125741|ref|YP_004036011.1| 131 PASRGMYRRIG 141
                                       999******88 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   6.4e-07    0.0019      10      55 ..      58     103 ..      47     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.4e-07
                   Acetyltransf_CG  10 eevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddare 55 
                                       e v+ ++   +++ v+++t  +V++e++G+G++ +++++ + +  +
  gi|313125741|ref|YP_004036011.1|  58 EVVGMARIVGDGGTVYQITDMVVHPEHQGEGLGTAMMDELVAYLDR 103
                                       56777777767778**************************999765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.2e-06     0.025      24      77 ..      75     126 ..      63     130 .. 0.71
   2 ?    1.5   0.0     0.095   2.8e+02      67      77 ..     132     142 ..     126     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.2e-06
                                       EEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT- CS
                              FR47  24 lgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGf 77 
                                       +  + v+peh+++Glg+ +  +l + + ++     ++v+   +    +ye+ Gf
  gi|313125741|ref|YP_004036011.1|  75 ITDMVVHPEHQGEGLGTAMMDELVAYLDREA-PEYAYVNLMAD-VDGFYERWGF 126
                                       66789**************999998876543.33344443322.3456666666 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.095
                                       HHHHHHHHHT- CS
                              FR47  67 psirlyeklGf 77 
                                       +s+ +y ++G+
  gi|313125741|ref|YP_004036011.1| 132 ASRGMYRRIGG 142
                                       79********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 911.67
//
Query:       gi|313125742|ref|YP_004036012.1|  [L=221]
Description: signal peptidase i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-05   22.2   0.8    0.00021   21.2   0.8    1.6  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.8   1.1e-08   0.00021       2      39 ..      67     127 ..      66     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-08
                                       XXSSTTCCTXXTTXEEEEECTS.......................---TTSEEEEEETTCE CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs.......................epkrGdivvfrlpgee 39 
                                       v+++SMep +  Gd+++V+                             +Gd++v   p+  
  gi|313125742|ref|YP_004036012.1|  67 VESGSMEPHIDTGDMVVVSDAGrfsgasadehgivtyaesdgysrFSGKGDVIVYMPPERT 127
                                       89*****************555666888888888888888888887788888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1242.56
//
Query:       gi|313125743|ref|YP_004036013.1|  [L=302]
Description: cation diffusion facilitator family transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-39  134.3   4.9    5.5e-39  134.0   4.9    1.1  1  Cation_efflux  Cation efflux family
      2e-19   69.5   2.5    3.1e-19   68.9   2.5    1.2  1  ZT_dimer       Dimerisation domain of Zinc Transporter


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.0   4.9   6.2e-43   5.5e-39       3     199 .]       7     199 ..       6     199 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.0 bits;  conditional E-value: 6.2e-43
                     Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllll 79 
                                       + l++n++lal++  v++ t+Sla+ ++a++s sd+v ++++l +l+l+ +ppd ++p G++r+e++++l++++ ++
  gi|313125743|ref|YP_004036013.1|   7 VILAVNVGLALAKAGVWWTTGSLAVGSEAVNSASDAVYSVIVLAGLYLTTQPPDFEHPHGHERIEPFVSLFVAVGVF 83 
                                       6799************************************************************************* PP

                     Cation_efflux  80 glavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvs 156
                                       ++++ +l++a ++++++  +       ++v++vs +v++ l++++ r+g++++s+a+ a al++++D+lt+ ++lv+
  gi|313125743|ref|YP_004036013.1|  84 AAGAGVLWNASTSVLNGTYGGSAGVTGVAVLVVSGGVKYGLYRYCLRVGEQTHSPAIIATALDNRNDILTAGAALVG 160
                                       ***************878888888889999*********************************************** PP

                     Cation_efflux 157 alvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                       +l++  +     p++Dp+a+ +++l i+y++++++++++  L+
  gi|313125743|ref|YP_004036013.1| 161 VLGASAG----VPILDPIAAGVVSLGIIYTGYEIVRDNVNYLV 199
                                       ******8....688*************************9885 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   2.5   3.4e-23   3.1e-19       2      78 ..     204     279 ..     203     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 3.4e-23
                                       ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                          ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                       ++e  +ei + ++++p+vkg hd+ ++++G++i v+lhiev+gd+++ eaH+i  +v ++i  e+p+v dv++H++P
  gi|313125743|ref|YP_004036013.1| 204 PDELTAEILSRALEHPEVKGAHDVVAHYVGPEIDVSLHIEVEGDMTLFEAHDIESKVVESIG-ELPEVDDVFVHIDP 279
                                       78999********************************************************6.89************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1746.99
//
Query:       gi|313125744|ref|YP_004036014.1|  [L=189]
Description: hit family hydrolase, diadenosine tetraphosphate hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-11   44.6   0.0    2.8e-11   44.0   0.0    1.2  1  HIT       HIT domain
    4.8e-05   23.8   0.0    9.8e-05   22.8   0.0    1.5  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    0.00033   20.5   0.0    0.00049   19.9   0.0    1.3  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   4.6e-15   2.8e-11       5      95 ..      40     132 ..      37     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 4.6e-15
                                       -CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEES..G CS
                               HIT   5 pstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinng..a 79 
                                       +++vv + d+++++l++ p  pgh+ vip +h   ++dl++eel ++ ++  + + al++ +  ++ +   n g  a
  gi|313125744|ref|YP_004036014.1|  40 ENRVVARSDHSFVLLNNYPYNPGHVMVIPYRHSGSWSDLSDEELLDHARLKARTVDALNDALGPDAANAGENLGggA 116
                                       57899*********************************************************999999999865215 PP

                                       GGT-SSSS-EEEEEEC CS
                               HIT  80 hagqsvahlHiHvipr 95 
                                       ++g    hlH+H++pr
  gi|313125744|ref|YP_004036014.1| 117 SGGSIEDHLHTHIVPR 132
                                       6666778*******98 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.6e-08   9.8e-05       3     100 ..      28     130 ..      26     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.6e-08
                                       HHHHHHTTSS..-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T- CS
                            DcpS_C   3 vfnilakgke..pervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynev 77 
                                        f+ l +  +  ++rvv ++++  vl   +p ++ h++vip+r+  s  dL+  + +ll + r ka++v   +  ++
  gi|313125744|ref|YP_004036014.1|  28 PFCALPDADDdrENRVVARSDHSFVLLNNYPYNPGHVMVIPYRHSGSWSDLS--DEELLDHARLKARTVDALND-AL 101
                                       56666444433378889999888888899**********************9..66889999999988765544.43 PP

                                       EEEEE--SCCCT-......-S-S--EEEE CS
                            DcpS_C  78 daeelrvgvhyqP......svyhlHlHvi 100
                                        ++  ++g ++          +hlH H++
  gi|313125744|ref|YP_004036014.1| 102 GPDAANAGENLGGgasggsIEDHLHTHIV 130
                                       44444444444333333325578888886 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.3e-08   0.00049       9      68 ..      22      83 ..      14     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.3e-08
                                      HHHHH-S---..-SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHH CS
                          CwfJ_C_1  9 asldsClfCl..snpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevl 68
                                         d C fC   +  +  ++ +v+ +++ ++ l + p + gHv++ip  H  + + l++e+l
  gi|313125744|ref|YP_004036014.1| 22 DGGDACPFCAlpDADDDRENRVVARSDHSFVLLNNYPYNPGHVMVIPYRHSGSWSDLSDEEL 83
                                      56789****644666777889*******************************9999988654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1138.84
//
Query:       gi|313125745|ref|YP_004036015.1|  [L=296]
Description: methionine aminopeptidase, type ii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-43  147.4   0.3    6.3e-43  146.9   0.3    1.2  1  Peptidase_M24  Metallopeptidase family M24
  ------ inclusion threshold ------
      0.043   13.7   0.1       0.22   11.4   0.1    2.0  2  DUF3323        Protein of unknown function N-terminus (DUF332


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9   0.3     7e-47   6.3e-43       1     209 []      12     288 ..      12     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 7e-47
                                       HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TT CS
                     Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkeg 74 
                                       e++r+a++i +++l++++e+++pgvt+ e+a+ +e++  +++ a+g+afp  v +++n+++ h++p   +++++  +
  gi|313125745|ref|YP_004036015.1|  12 EKYREAGQILRQVLDETAEMVEPGVTHLEVAEYAEDR--IYELADGCAFP--VNISVNEEASHASPgrdDETEFG-E 83 
                                       689********************************99..8999*******..77777777779999542344454.5 PP

                                       EEEEEEEEEEETTEEEEEEEEE.ECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBS CS
                     Peptidase_M24  75 dlvlidagaeydgyasDitrTv.lvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffp 150
                                       d+v++d+g+++dgy++D ++Tv l G  ++   el ea++ea++aa++av pGv +++++a +++v++ +g+ +++ 
  gi|313125745|ref|YP_004036015.1|  84 DMVCLDCGVHVDGYIADAAVTVdLSG--NA---ELKEAAEEALDAALDAVAPGVQTGAVGAEIEDVIRGYGY-TPVL 154
                                       **********************7787..44...588************************************.999* PP

                                       SCSEEEESS.SSSEEEEEESS.STT.CSSB--TTBEEEEEE...............EEEEETTT............. CS
                     Peptidase_M24 151 hglGHgvGl.evhdegpsvsr.esn.dgrkleeGmvftiEp...............giyfapge............. 196
                                       ++ GHgv + + h + p+v++     +g + e G+v++iEp               +                    
  gi|313125745|ref|YP_004036015.1| 155 NLSGHGVEQwDAHTG-PNVPNrG-AeRGIEFEVGDVVAIEPfattgsgkvtegakeE------Iyslerdrsvrnrs 223
                                       ********99***98.**97623.3599*************8777665444444444......04555556777778 PP

                                       ...................................................E.EEEEBEEEEEES CS
                     Peptidase_M24 197 ...................................................g.gvriedtvlvte 209
                                                                                            + + e+t++vte
  gi|313125745|ref|YP_004036015.1| 224 arqvleqvkdeyktlpfaarwidapradiaiqrlkqqnvlhgypvlkeddgElVSQAEHTIIVTE 288
                                       88888888999999999999999999999999999999999999999999856999999999997 PP

>> DUF3323  Protein of unknown function N-terminus (DUF3323)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.096   8.6e+02      65     101 ..     107     143 ..      98     167 .. 0.60
   2 ?   11.4   0.1   2.5e-05      0.22      48     124 ..     194     269 ..     175     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.096
                           DUF3323  65 lltrkeeraaeaeawaavfaaleaeaaarpelreWld 101
                                       l  ++e ++a++ea +a+++a+++ +++ ++ +e+ d
  gi|313125745|ref|YP_004036015.1| 107 LSGNAELKEAAEEALDAALDAVAPGVQTGAVGAEIED 143
                                       4556667777777777777777744444444444444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.5e-05
                           DUF3323  48 farsdleevlealfgeplltrkeeraaeaeawaavfaaleaeaaarpelreWldklrgygllrrlykkdeeaarell 124
                                       fa ++  +v e   +e++ + ++ r+ + +  ++v++++++e  + p +++W d++r++  ++rl +++  +  ++l
  gi|313125745|ref|YP_004036015.1| 194 FATTGSGKVTEGA-KEEIYSLERDRSVRNRSARQVLEQVKDEYKTLPFAARWIDAPRADIAIQRLKQQNVLHGYPVL 269
                                       6666666777777.899999999*********************************************987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1738.97
//
Query:       gi|313125746|ref|YP_004036016.1|  [L=229]
Description: calcineurin-like phosphoesterase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-14   53.7   0.1    4.5e-14   53.4   0.1    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    2.3e-07   31.1   0.0    3.5e-07   30.6   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
        0.2   10.4   0.0       0.27   10.0   0.0    1.1  1  Vps16_N        Vps16, N-terminal region


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   7.5e-18   4.5e-14       3     173 ..      23     183 ..      22     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 7.5e-18
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfee 79 
                                       + v+gD+H     g+ ++l++lld+l    + dlv+++GDlv  g+ +  ++ l++   +     ++++GN e    
  gi|313125746|ref|YP_004036016.1|  23 VYVVGDVH-----GCRAELEQLLDELGVT-EDDLVVFVGDLVRKGPDSAGVVSLVRNADN----MFTVRGNNE---- 85 
                                       789*****.....*************777.99*****************9****888888....5********.... PP

                                       HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESE.CEEE...THHHHHHHHHHHSCHHHHCCHHHH CS
                       Metallophos  80 ellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGg.spel...lvsldklgslnleleapepgdewl 151
                                       e l + +  ++  ++      +  nlp+a     s  + l++hGg +p+    ++++d+l+++    +a+ +   w+
  gi|313125746|ref|YP_004036016.1|  86 EKLIRGT--KELDALSGEQLAWIRNLPVAI----SwEDSLVVHGGvDPRKplaDHTIDELENVRALSDADGE-PYWW 155
                                       4444433..2334555555899999**999....5568*******755557885566665555555555554.6699 PP

                                       HHHHHHTTCSEEEEEESSESS..........C CS
                       Metallophos 152 kdlekrekadwvivlgHsply..........r 173
                                       +      +++  +++gH pl+           
  gi|313125746|ref|YP_004036016.1| 156 EV----YQGPSRVFFGHTPLSapvarrhavgL 183
                                       99....999***********988877666663 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   5.8e-11   3.5e-07       4     127 ..      24     169 ..      22     172 .. 0.63

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 5.8e-11
                     Metallophos_2   4 aiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellela.pvlaVrGNnD.....eevveedvlr 72 
                                        ++ D+H+ +++le++l++l  ++ d+++++GDl  ++ +   +  l + a  + +VrGNn+     ++ + ++++ 
  gi|313125746|ref|YP_004036016.1|  24 YVVGDVHGCRAELEQLLDELGVTEDDLVVFVGDLvrKGPDSAGVVSLVRNAdNMFTVRGNNEeklirGTKELDALSG 100
                                       689******************************9665555555555555557**********433332224444444 PP

                     Metallophos_2  73 eaaelgtdlpeeaelelagekvlliHgdpl...................gvkdalaellke.........aeegsdv 121
                                       e+  + ++lp +   e    + l++Hg  +                   +          +          ++g   
  gi|313125746|ref|YP_004036016.1| 101 EQLAWIRNLPVAISWE----DSLVVHGGVDprkpladhtidelenvralS----------DadgepywweVYQGPSR 163
                                       4444444444333333....478999875567776665543333222221..........13333444444666667 PP

                     Metallophos_2 122 vvcGHt 127
                                       v++GHt
  gi|313125746|ref|YP_004036016.1| 164 VFFGHT 169
                                       777776 PP

>> Vps16_N  Vps16, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   4.4e-05      0.27     229     285 ..      66     123 ..      62     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.4e-05
                           Vps16_N 229 rhlalytetgkillisvdlskklleleld.akdipkqiaWvgndaVvvsfesllvlvg 285
                                       + ++l  + +++  +  + ++kl+    + +  + +q+aW+ n  V++s+e+ lv+ g
  gi|313125746|ref|YP_004036016.1|  66 GVVSLVRNADNMFTVRGNNEEKLIRGTKElDALSGEQLAWIRNLPVAISWEDSLVVHG 123
                                       566777777788888888888887655553355679*******************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1329.70
//
Query:       gi|313125747|ref|YP_004036017.1|  [L=254]
Description: hypothetical protein Hbor_09780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-31  110.2  24.4    1.4e-31  109.7  24.4    1.2  1  Sensor    Putative sensor


Domain annotation for each model (and alignments):
>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7  24.4   7.8e-36   1.4e-31       1     162 []      35     240 ..      35     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 7.8e-36
                            Sensor   1 YlllglplgvaafvllvtglslglgllvllvGlplLalalllarglaaveRrrarlllglpvprphrapeppgllar 77 
                                       Yl l++plg+++f++  +g+s+g+ l+++++G+p+L+ +l++a gla+veR++a+lllg+ v++p ++   ++l++r
  gi|313125747|ref|YP_004036017.1|  35 YLSLAFPLGLLYFLFFSIGFSVGVSLTFVVIGIPILLFVLAAALGLASVERKLATLLLGVSVRSPTTSSD-GPLVER 110
                                       9**************************************************************9985554.9***** PP

                            Sensor  78 lrallrdpatwrdllylllhfplglvlfvvavvllalalalltaPlw.............................. 124
                                       +++l+ +++tw+++ yl+ +++lgl++f++++ ll++a+++l++P++                              
  gi|313125747|ref|YP_004036017.1| 111 VKQLVVSQRTWKAVFYLASKLILGLISFTAIMSLLTTAVSFLMIPFVydqpgvyvgivtsepavfrpqmllgwdgll 187
                                       **********************************************6599999999998888888888888877777 PP

                            Sensor 125 ...............tlpeallvavlGlllllvllwvvrglarlqallaraLL 162
                                                      tl eal+va lG++l +v+l +++gla+l+++++  LL
  gi|313125747|ref|YP_004036017.1| 188 vgvrtafrltswqvtTLSEALAVAGLGVILGIVTLNILNGLAWLSGQYTVLLL 240
                                       77777666666555559********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1559.93
//
Query:       gi|313125748|ref|YP_004036018.1|  [L=121]
Description: hypothetical protein Hbor_09790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-08   32.6   1.4      1e-07   31.9   1.4    1.3  1  HTH_20         Helix-turn-helix domain
    0.00076   19.4   0.1     0.0012   18.7   0.1    1.3  1  HTH_11         HTH domain
     0.0018   18.1   0.0     0.0028   17.5   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.003   17.4   1.5     0.0057   16.4   1.5    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0046   17.4   0.3      0.011   16.2   0.3    1.7  1  HTH_27         Winged helix DNA-binding domain
     0.0056   16.6   0.0      0.012   15.5   0.0    1.5  1  PadR           Transcriptional regulator PadR-like family
     0.0075   16.1   0.2      0.012   15.5   0.2    1.3  1  MarR_2         MarR family
  ------ inclusion threshold ------
       0.01   15.4   0.1      0.022   14.3   0.1    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   1.4   4.5e-11     1e-07       3      56 ..      12      64 ..      10      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 4.5e-11
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      + ++L+++  r+il +  r+e+++a +l e++d s +t++++++ L++++L+e+
  gi|313125748|ref|YP_004036018.1| 12 LVSLLDDRYAREILVET-REEPRSADALSEACDASASTIYRRIERLRKHDLLEG 64
                                      66899************.**********************************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   5.5e-07    0.0012       7      41 ..      23      58 ..      19      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.5e-07
                            HTH_11  7 elLleargp.isgeeLAeeLnvSrrtvrrdIkaLee 41
                                      e+L e+r+   s++ L+e  + S +t++r+I++L++
  gi|313125748|ref|YP_004036018.1| 23 EILVETREEpRSADALSEACDASASTIYRRIERLRK 58
                                      6788999999************************86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.3e-06    0.0028      18      58 ..      26      68 ..      23      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                                      H..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 18 l..klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      +  +++p +ad ++e+ + + s++Y+ +++L + +l e +++ 
  gi|313125748|ref|YP_004036018.1| 26 VetREEPRSADALSEACDASASTIYRRIERLRKHDLLEGQQRL 68
                                      5556899****************************99988764 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.5   2.6e-06    0.0057      17      42 .]      32      57 ..       7      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.6e-06
                     HTH_AsnC-type 17 RisyaeLAervGlSestvlrRvrrLe 42
                                       +s  +L+e++  S+st+ rR++rL+
  gi|313125748|ref|YP_004036018.1| 32 PRSADALSEACDASASTIYRRIERLR 57
                                      468999*******************7 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   4.8e-06     0.011      14      68 .]      28      93 ..      21      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre...........krvrlTdkG 68
                                       r+++ ++ +l+++ + ++s+i   +++L +++L+e ++   +++            ++++lT+ G
  gi|313125748|ref|YP_004036018.1| 28 TREEPRSADALSEACDASASTIYRRIERLRKHDLLEGQQRLDPDGHhyevyaarlrkVTIELTPDG 93
                                      3466677799*************************7777766666667777777777777777776 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.6e-06     0.012      24      63 ..      39      78 ..      32      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.6e-06
                                      TT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEE CS
                              PadR 24 egllelseGslYpaLkrLekeglveseweesgegpprkyY 63
                                      +++ ++s++++Y+  +rL+k++l+e++++ + +g    +Y
  gi|313125748|ref|YP_004036018.1| 39 SEACDASASTIYRRIERLRKHDLLEGQQRLDPDGHHYEVY 78
                                      345899*********************9988777777776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   5.5e-06     0.012      10      54 ..      24      65 ..      21      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.5e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +L + + +p+   ++ +l ++++ s s++ r+++rL ++ L+e +
  gi|313125748|ref|YP_004036018.1| 24 ILVETREEPR---SADALSEACDASASTIYRRIERLRKHDLLEGQ 65
                                      7788888885...****************************9865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   9.6e-06     0.022       5      46 ..      21      61 ..      17      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.6e-06
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                       r+IL + +++pr s   L+e+++ S st+ rr++rL +  l
  gi|313125748|ref|YP_004036018.1| 21 AREILVETREEPR-SADALSEACDASASTIYRRIERLRKHDL 61
                                      5666666666555.7789*******************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 726.28
//
Query:       gi|313125749|ref|YP_004036019.1|  [L=101]
Description: hypothetical protein Hbor_09800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.5    8.7  11.6        2.4    8.1   1.4    2.6  2  DUF2474   Protein of unknown function (DUF2474)


Domain annotation for each model (and alignments):
>> DUF2474  Protein of unknown function (DUF2474)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.0     0.001        18      16      33 ..      16      33 ..      15      34 .. 0.88
   2 ?    8.1   1.4   0.00013       2.4      19      38 ..      56      75 ..      48      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.001
                           DUF2474 16 aSVlaLgvvAlllRllMt 33
                                      +SV++L++++l+l +l t
  gi|313125749|ref|YP_004036019.1| 16 LSVFTLFAASLVLSVLVT 33
                                      7************98865 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00013
                           DUF2474 19 laLgvvAlllRllMtaAGlk 38
                                      l L+vv +llR+ +t+AG  
  gi|313125749|ref|YP_004036019.1| 56 LLLAVVPILLRVSLTTAGID 75
                                      669***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 630.04
//
Query:       gi|313125750|ref|YP_004036020.1|  [L=89]
Description: hypothetical protein Hbor_09810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.016   15.3   2.1      0.018   15.1   2.1    1.1  1  ECF_trnsprt  ECF transporter, substrate-specific component
      0.055   13.9   0.4      0.055   13.9   0.4    1.7  2  DUF3262      Protein of unknown function (DUF3262)
      0.057   13.2   4.6      0.067   13.0   4.6    1.2  1  CbtA         Probable cobalt transporter subunit (CbtA)
      0.098   12.7   0.0       0.14   12.2   0.0    1.3  1  Jagunal      Jagunal, ER re-organisation during oogenesis
        1.2    7.5   6.2        1.3    7.3   6.2    1.0  1  ABC_export   Putative ABC exporter
        1.4    8.8   5.7        1.9    8.4   0.0    2.9  3  PetG         Cytochrome B6-F complex subunit 5


Domain annotation for each model (and alignments):
>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.1   6.1e-06     0.018      74     136 ..       9      70 ..       1      87 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.1e-06
                                       HHHHHHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHS...... CS
                       ECF_trnsprt  74 piaflsriligliagllykkgkkknlkeivvsfilagvlgtivatllvlliilplylklktak 136
                                       +  +l+ ++ +++a+l y+++++        ++++++vl+++v  l   ++  ++ ++++++ 
  gi|313125750|ref|YP_004036020.1|   9 VTTALTVVVGVFVASLAYRGYRRNDSE-TMRALVVGIVLIAVVPGLATTGLPAVVEVNDAGVL 70 
                                       78899999999*******999998765.59************999988877766666666554 PP

>> DUF3262  Protein of unknown function (DUF3262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   1.8e-05     0.055      25      67 ..       7      49 ..       1      55 [. 0.77
   2 ?   -1.0   0.0      0.82   2.5e+03      23      35 ..      70      76 ..      59      87 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                           DUF3262 25 agillvvllLwaaWalvsvYkgWaeekiseadllslviRavvl 67
                                        ++ ++ ++ ++++++ +Y+g+ +++ +++++l++ i  +++
  gi|313125750|ref|YP_004036020.1|  7 STVTTALTVVVGVFVASLAYRGYRRNDSETMRALVVGIVLIAV 49
                                      45667888999**************999988887776655554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.82
                           DUF3262 23 liagillvvllLw 35
                                      l       v+lL 
  gi|313125750|ref|YP_004036020.1| 70 L------LVALLS 76
                                      2......222222 PP

>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.6   2.2e-05     0.067     150     203 ..      13      66 ..       8      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                              CbtA 150 atvalsavalalavflarrlaarg.wnavlaaavaflvlvavallalPhvveaPq 203
                                       +tv+++++++ la+ ++rr  +++ ++a+++++v ++v+ ++a + lP vve+ +
  gi|313125750|ref|YP_004036020.1|  13 LTVVVGVFVASLAYRGYRRN-DSEtMRALVVGIVLIAVVPGLATTGLPAVVEVND 66 
                                       68889988888888888877.4445**************************9976 PP

>> Jagunal  Jagunal, ER re-organisation during oogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.8e-05      0.14      87     124 ..      17      54 ..       9      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.8e-05
                           Jagunal  87 lSivpsllgllalkknkikllklyligtlvlgllplly 124
                                       + ++++ l++   ++n++++++  ++g+++++++p l+
  gi|313125750|ref|YP_004036020.1|  17 VGVFVASLAYRGYRRNDSETMRALVVGIVLIAVVPGLA 54 
                                       56788899999***********************9765 PP

>> ABC_export  Putative ABC exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.2   0.00045       1.3     445     514 ..       9      76 ..       1      87 [. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00045
                        ABC_export 445 laylslallflavsvlverllgssaskgletmLrmlvlllallPgiavgllvgvltkgdavlillvtavg 514
                                       ++  +  ++ ++v  l++r    + s++++ ++ + ++l+a++Pg+a  +l +v+  +da++ llv+++ 
  gi|313125750|ref|YP_004036020.1|   9 VTTALTVVVGVFVASLAYRGYRRNDSETMRALV-VGIVLIAVVPGLATTGLPAVVEVNDAGV-LLVALLS 76 
                                       23333334566777788888999999****999.78899************99999999997.5555543 PP

>> PetG  Cytochrome B6-F complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00065       1.9      18      33 ..      16      33 ..       8      35 .. 0.86
   2 ?    1.8   0.7     0.073   2.2e+02       4      11 ..      39      46 ..      37      54 .. 0.77
   3 ?   -0.9   0.2      0.51   1.5e+03      11      16 ..      79      84 ..      68      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00065
                              PetG 18 laGLFva..AYlQYkRgn 33
                                      ++G Fva  AY+ Y+R +
  gi|313125750|ref|YP_004036020.1| 16 VVGVFVAslAYRGYRRND 33
                                      5799**9889******87 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.073
                              PetG  4 pLLlGiVL 11
                                      +L++GiVL
  gi|313125750|ref|YP_004036020.1| 39 ALVVGIVL 46
                                      57889987 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.51
                              PetG 11 LGLvpV 16
                                      LGLv++
  gi|313125750|ref|YP_004036020.1| 79 LGLVAI 84
                                      888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 641.25
//
Query:       gi|313125751|ref|YP_004036021.1|  [L=224]
Description: hypothetical protein Hbor_09820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-29  102.4  22.8      3e-29  102.2  22.8    1.1  1  Sensor    Putative sensor


Domain annotation for each model (and alignments):
>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2  22.8   1.7e-33     3e-29       1     162 []      31     216 ..      31     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1.7e-33
                            Sensor   1 YlllglplgvaafvllvtglslglgllvllvGlplLalalllarglaaveRrrarlllglpvprphrapep...... 71 
                                       Yl+lg+p g+++fv l+ gl++g+gl+v+l+G+p+L+++++++ +la+ve  + r+l g+ +  p+ a+++      
  gi|313125751|ref|YP_004036021.1|  31 YLALGFPFGLVSFVTLTSGLTAGAGLSVTLIGIPILLATIAAGTALASVEAGLTRALVGVNASPPK-AAAAvsngta 106
                                       9**********************************************************9999565.3333579999 PP

                            Sensor  72 ..pgllarlrallrdpatwrdllylllhfplglvlfvvavvllalalalltaPlw.................tlpea 129
                                           ++a +++ l++p+tw++ll ++l f++glv fv++++l +l+l++l aP++                 tl e 
  gi|313125751|ref|YP_004036021.1| 107 sdDDIMAAIKRFLAEPSTWTSLLVAFLWFIFGLVGFVALTTLSSLSLSMLGAPVLhlfapgvdmmvgpyvvdTLSES 183
                                       9999**************************************************76888888888777777769*** PP

                            Sensor 130 llvavlGlllllvllwvvrglarlqallaraLL 162
                                       ++++++G++l+lv+l+ +++la + ++++ +LL
  gi|313125751|ref|YP_004036021.1| 184 AALTAVGIPLTLVSLHALNALAYAFGRITASLL 216
                                       *******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1414.15
//
Query:       gi|313125752|ref|YP_004036022.1|  [L=383]
Description: hypothetical protein Hbor_09830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-16   60.4  30.1    5.2e-12   45.7   8.7    3.2  2  DUF4097    Putative adhesin
  ------ inclusion threshold ------
      0.067   13.1   0.2       0.87    9.4   0.1    2.4  1  KptA_kDCL  KptA in kinetoplastid DICER domain
       0.45   11.0   4.3       0.34   11.4   1.1    2.6  3  HMA        Heavy-metal-associated domain
        3.6    7.9   6.5        5.1    7.4   0.2    3.2  4  Ntox28     Bacterial toxin 28


Domain annotation for each model (and alignments):
>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4  16.9   2.4e-07    0.0011     138     249 ..     161     267 ..      48     273 .. 0.66
   2 !   45.7   8.7   1.2e-15   5.2e-12     130     251 ..     256     382 ..     254     383 .] 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.4e-07
                           DUF4097 138 gseakk.lklqltsGdieleslsletldltsssGdltlsntklegsltitassGdvdlslpeekkaavdassesGdv 213
                                       +s +++ l + +++Gd  +++++++ + +++++Gd t+   k +g  ++++++Gd+ +     ++ +v +++++Gd 
  gi|313125752|ref|YP_004036022.1| 161 DSDSSEsLVVRTEDGDATARETTGN-VVVRTKDGDATAR--KTTGDADVRTEDGDAMAHE---TTGNVVVRTKDGDA 231
                                       3333333666666666666666666.6666666665555..3334466666666654443...45666666666666 PP

                           DUF4097 214 slpkkreeeekesnsisaseknakkkvsvstssGDi 249
                                       ++ k + + +  ++   a++++++++ +v+t++GD 
  gi|313125752|ref|YP_004036022.1| 232 TARKTTGDADVRTKDGDATARKTTGDADVRTEDGDA 267
                                       666666666666666666666666666666666664 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 1.2e-15
                           DUF4097 130 esGdvtiegseakk......lklqltsGdieleslsletldltsssGdltlsntklegsltitassGdvdlslpeek 200
                                       ++ dv++e+  a++      +++++t+Gd + es ++  l + s+ Gd++++   l   + i+++ Gd+++sl e+ 
  gi|313125752|ref|YP_004036022.1| 256 GDADVRTEDGDATAigvkgfVRVHTTDGDARTESCDGI-LGVSSKNGDVDAEVSALRSDTRIETENGDARASLGESL 331
                                       4455555555555555445799****************.************************************** PP

                           DUF4097 201 kaavdassesGdvslpkkreeeekesnsisaseknakkkvsvstssGDitv 251
                                       +a+v  +++ Gdvs++   +++e +++++s++ +++  +++v++++GD+++
  gi|313125752|ref|YP_004036022.1| 332 NARVVGKTAHGDVSVSATLDDSEVSDEHVSGTVGDGGPTLRVQSENGDVKI 382
                                       *****************999******************************9 PP

>> KptA_kDCL  KptA in kinetoplastid DICER domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0002      0.87      89     137 ..     188     235 ..     175     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0002
                         KptA_kDCL  89 tktpatkksdevlsrktfltfaevelralarsgkavvteaaaltlaass 137
                                       ++t ++ + +++++  + ++ ++++++a++  g++vv++ ++  ++a +
  gi|313125752|ref|YP_004036022.1| 188 VRTKDGDATARKTTGDADVRTEDGDAMAHETTGNVVVRTKDGD-ATARK 235
                                       56778888999999************************99995.44444 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   7.5e-05      0.34      21      59 ..      49      86 ..      49      89 .. 0.88
   2 ?   -2.2   0.0       1.4   6.1e+03      33      46 ..     103     116 ..      90     122 .. 0.74
   3 ?   -3.6   0.1       3.7   1.7e+04      34      43 ..     182     192 ..     176     199 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.5e-05
                               HMA 21 selpgVesvkvdlatktvtVegdaestklrkiieaieka 59
                                      ++l++V+sv+v  + + vtV+ +++  + r++++ +ek+
  gi|313125752|ref|YP_004036022.1| 49 KTLTDVQSVVVAADVGNVTVTPNDDL-SERTVRAHVEKK 86
                                      5799******************8886.449999999986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                               HMA  33 latktvtVegdaes 46 
                                        +++++tV++++e+
  gi|313125752|ref|YP_004036022.1| 103 AEEGRATVRTQTED 116
                                       56799999999887 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.7
                               HMA  34 atktvtVeg.d 43 
                                        t+ v+V++ d
  gi|313125752|ref|YP_004036022.1| 182 TTGNVVVRTkD 192
                                       57889998842 PP

>> Ntox28  Bacterial toxin 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   7.4e+03      10      44 ..      83     117 ..      73     118 .. 0.62
   2 ?    7.4   0.2    0.0011       5.1      24      45 ..     173     194 ..     167     198 .. 0.88
   3 ?    2.2   0.1     0.048   2.1e+02      22      44 ..     207     229 ..     202     232 .. 0.84
   4 ?   -1.4   0.1      0.63   2.8e+03      21      44 ..     242     265 ..     230     267 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                            Ntox28  10 iekleniinseltendysaarRelqGevvarkPDG 44 
                                       +ek    i s l    +sa+  e +  v ++  DG
  gi|313125752|ref|YP_004036022.1|  83 VEKKSSSILSSLSAVAFSATAEEGRATVRTQTEDG 117
                                       45555567777888888888888777776666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0011
                            Ntox28  24 ndysaarRelqGevvarkPDGt 45 
                                       +d +a+ Re  G+vv r  DG 
  gi|313125752|ref|YP_004036022.1| 173 EDGDATARETTGNVVVRTKDGD 194
                                       6779*************99995 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.048
                            Ntox28  22 tendysaarRelqGevvarkPDG 44 
                                       + +d +a   e  G+vv r  DG
  gi|313125752|ref|YP_004036022.1| 207 RTEDGDAMAHETTGNVVVRTKDG 229
                                       5667789999*********9999 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.63
                            Ntox28  21 ltendysaarRelqGevvarkPDG 44 
                                       ++ +d +a+ R   G+   r  DG
  gi|313125752|ref|YP_004036022.1| 242 VRTKDGDATARKTTGDADVRTEDG 265
                                       445566677777777666665565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2284.56
//
Query:       gi|313125753|ref|YP_004036023.1|  [L=215]
Description: esterase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-19   69.8   0.0      9e-19   68.1   0.0    1.7  1  Abhydrolase_2  Phospholipase/Carboxylesterase
    1.8e-12   47.0   0.7    8.2e-09   35.1   0.7    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    5.9e-09   35.8   0.0    7.8e-09   35.4   0.0    1.1  1  DLH            Dienelactone hydrolase family
    4.7e-08   32.8   0.2      0.032   13.7   0.0    3.0  3  Peptidase_S9   Prolyl oligopeptidase family
    8.7e-08   32.1   0.0    1.1e-07   31.8   0.0    1.3  1  Abhydrolase_1  alpha/beta hydrolase fold
    1.1e-05   26.1   5.6    4.6e-05   24.1   5.6    1.7  1  Abhydrolase_6  Alpha/beta hydrolase family
    9.8e-05   22.3   0.0    0.00011   22.1   0.0    1.1  1  Palm_thioest   Palmitoyl protein thioesterase
     0.0012   18.6   0.0     0.0015   18.2   0.0    1.2  1  FSH1           Serine hydrolase (FSH1)
     0.0018   17.9   0.0     0.0026   17.3   0.0    1.2  1  PE-PPE         PE-PPE domain
      0.009   15.9   0.1      0.081   12.8   0.1    2.0  2  Abhydrolase_3  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.011   15.3   0.5      0.035   13.6   0.3    2.1  2  Esterase_phd   Esterase PHB depolymerase
       0.02   14.3   0.0       0.11   12.0   0.0    1.8  2  DUF3530        Protein of unknown function (DUF3530)
      0.025   14.2   0.0      0.028   14.1   0.0    1.1  1  Esterase       Putative esterase
      0.071   12.6   0.0       0.34   10.4   0.0    1.9  1  DUF676         Putative serine esterase (DUF676)
      0.089   12.1   0.0       0.13   11.6   0.0    1.1  1  LIP            Secretory lipase
      0.092   11.4   0.0       0.15   10.7   0.0    1.2  1  AXE1           Acetyl xylan esterase (AXE1)
       0.18   11.5   0.0       0.32   10.8   0.0    1.4  1  Abhydrolase_5  Alpha/beta hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.0   8.5e-22     9e-19      12     213 ..      21     210 ..      16     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 8.5e-22
                                       ---EEEEEE--TT--SHHHHHHHH.TT--TTEEEEEE---EEE-GGGTT-EEE-SS-B--SSTTS-B-HHHHHHHHH CS
                     Abhydrolase_2  12 kaqavviflHGlGdsghawaeaakteaalpnikfifphgpelpvtlnggmrmpaWfdlvglspekkedeagikksae 88 
                                        a+avv+++HG G+++ ++   a  e + + ++++ p++ +       g     W++   ++p + +++   + ++ 
  gi|313125753|ref|YP_004036023.1|  21 DAEAVVVLVHGRGATARGMLAFAD-EFHDDGVHYVAPQAQR-------G----TWYPNSFMAPTE-SNQPHYQSALL 84 
                                       5789**************998888.9***********9865.......3....599888888888.55558999999 PP

                                       HHHHHHHHHHH.TT--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-EEEEEEE CS
                     Abhydrolase_2  89 kleelidaelk.kgipssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklpilqiHg 164
                                        l+  +++  +  g++ ++ii++GFSqGa la   + + p ++gg+v +sg ++ ++  +  + ++   +p++++  
  gi|313125753|ref|YP_004036023.1|  85 HLNRAVEQAREtTGLDDEKIIFVGFSQGACLASSYVAQHPSRYGGVVLLSGGFVGPEGAAFDFEGSMAGTPVFLGVS 161
                                       99999998776156*************************************999999888888888889******** PP

                                       TT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--HHHHHHHHHHH CS
                     Abhydrolase_2 165 eeDpvvplalgkaakevlkkllkkvelksyeglaHsideeemqdikefl 213
                                       ++Dp vp + ++++  ++  +  +  ++ yeg +H i +ee++ +++ +
  gi|313125753|ref|YP_004036023.1| 162 DDDPHVPQSRAEETIAAFDRMDADTRFDLYEGRGHGIFPEEIEYLRTLV 210
                                       *****************************************99988765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.7   7.8e-12   8.2e-09       3     112 ..      22     138 ..      20     152 .. 0.90
   2 !   10.3   0.0   0.00028      0.29     191     237 ..     153     201 ..     143     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 7.8e-12
                       Hydrolase_4   3 pkavvvlvHGlaehsgryaelaeaLaaqGfavyalD.hrGhGrse....gkrghvpsfddyvdDlaafvekvkeehp 74 
                                       ++avvvlvHG++ +++ +  +a+++ + G++ +a   +rG         +    +p++++ +  l+ +ve+++e+ +
  gi|313125753|ref|YP_004036023.1|  22 AEAVVVLVHGRGATARGMLAFADEFHDDGVHYVAPQaQRGTWYPNsfmaPTESNQPHYQSALLHLNRAVEQARETTG 98 
                                       789****************************9998648999887788999999********************8887 PP

                       Hydrolase_4  75 el..plfllGhSmGGliallyllrypdkvaglilsaPalk 112
                                           +++ +G S G+ +a +y++++p+++ g++l +  + 
  gi|313125753|ref|YP_004036023.1|  99 LDdeKIIFVGFSQGACLASSYVAQHPSRYGGVVLLSGGFV 138
                                       6667*****************************9987764 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00028
                       Hydrolase_4 191 tlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHellnE 237
                                        +P++l  +++D+ v+++ ++e++++  +   d ++ ly+g  H ++ E
  gi|313125753|ref|YP_004036023.1| 153 GTPVFLGVSDDDPHVPQSRAEETIAAFDRMdaDTRFDLYEGRGHGIFPE 201
                                       59***************9996655555544349*************977 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   7.4e-12   7.8e-09      14     190 ..      23     199 ..      13     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 7.4e-12
                               DLH  14 pvvvviqeifGvn.dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavayl 89 
                                        +vvv+   +G +   +   ++ + + G   +aP+  ++       +++ + a +e  ++   +  l  l+ av+ +
  gi|313125753|ref|YP_004036023.1|  23 EAVVVLVHGRGATaRGMLAFADEFHDDGVHYVAPQAQRGTW-----YPNSFMAPTESNQPH-YQSALLHLNRAVEQA 93 
                                       55555555666665666677777777777777777655554.....566666666777777.55566677799**** PP

                               DLH  90 ksvpevstkkvgvvGfCmGGalalllaaev.pevdaavafYG..lspekele..eaakikapilalfgeeDefipad 161
                                       +++   +++k+  vGf  G+ la  + a+   +  ++v   G  + pe      e   + +p++  + + D+++p++
  gi|313125753|ref|YP_004036023.1|  94 RETTGLDDEKIIFVGFSQGACLASSYVAQHpSRYGGVVLLSGgfVGPEGAAFdfEGSMAGTPVFLGVSDDDPHVPQS 170
                                       ***99******************98777775888999988885533433333113456789**************** PP

                               DLH 162 evekleealkaanvdlelkvYpgagHaFa 190
                                        +e++  a+    +d ++++Y+g gH+ +
  gi|313125753|ref|YP_004036023.1| 171 RAEETIAAFDRMDADTRFDLYEGRGHGIF 199
                                       **************************976 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.07        73      12      30 ..      21      39 ..      16      55 .. 0.81
   2 !   13.7   0.0   3.1e-05     0.032      50      95 ..      88     133 ..      40     138 .. 0.80
   3 !   13.4   0.0   3.9e-05     0.041     143     188 ..     153     198 ..     143     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.07
                                      CCT-EEEEE--TTSSTTHC CS
                      Peptidase_S9 12 drGyvvvvanirGsggyGe 30
                                      d+  vvv +++rG + +G 
  gi|313125753|ref|YP_004036023.1| 21 DAEAVVVLVHGRGATARGM 39
                                      6788***********9994 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEE CS
                      Peptidase_S9  50 aaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavae 95 
                                        a+e + ++   d e+++  G S G  l+   ++q+p++++++v  
  gi|313125753|ref|YP_004036023.1|  88 RAVEQARETTGLDDEKIIFVGFSQGACLASSYVAQHPSRYGGVVLL 133
                                       678888889999*****************************99975 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 3.9e-05
                                       --EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SST CS
                      Peptidase_S9 143 ypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgv 188
                                        +p++l +++ D  vp + a++ +aa ++ + ++++  + + gHg+
  gi|313125753|ref|YP_004036023.1| 153 GTPVFLGVSDDDPHVPQSRAEETIAAFDRMDADTRFDLYEGRGHGI 198
                                       589*****************************************98 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0     1e-10   1.1e-07      34     107 ..      64     138 ..      24     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1e-10
                                       EEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCT..TSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE.. CS
                     Abhydrolase_1  34 llDlrGvgySspapacinddygtasvaddldrildalg..ddkltlvGhSmGGmialayaaeyperVkalvllga.. 106
                                        +++   +  s  p     +  + ++++ ++++++ +g  d+k++ vG+S+G  +a+ y a++p+r  ++vll++  
  gi|313125753|ref|YP_004036023.1|  64 YPNSFMAPTESNQPH---YQSALLHLNRAVEQARETTGldDEKIIFVGFSQGACLASSYVAQHPSRYGGVVLLSGgf 137
                                       333333333333333...33388999*****997765522789******************************9855 PP

                                       C CS
                     Abhydrolase_1 107 i 107
                                       +
  gi|313125753|ref|YP_004036023.1| 138 V 138
                                       4 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   5.6   4.4e-08   4.6e-05       1     126 [.      26     181 ..      26     211 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.4e-08
                                       EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--.TTST.......S-GGCS--HHH.CHHH.HHHHCCTT..... CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDl.pGhG.......rsdpppldled.ladl.aalldelaa.... 62 
                                       v+l+HG g++a++ l   +a  ++++ vh++ap++ +G+        ++++   +++  l++l +a+ ++  +    
  gi|313125753|ref|YP_004036023.1|  26 VVLVHGRGATARGML--AFADEFHDDgVHYVAPQAqRGTWypnsfmaPTESNQPHYQSaLLHLnRAVEQAR-Ettgl 99 
                                       8*******9999997..7766667777999*****445524444443334444555443344432222222.14667 PP

                                       .TTSEEEEEETCHHHHHHHHHHCC....EE.EEES-....................----TTT...S----TTHHHH CS
                     Abhydrolase_6  63 gggpvvlvGHSlGGalalaaapla..lvvg.vlldp..................pptalpagl...laaalelllal 115
                                       ++ +++ vG S+G+ la+ ++++   +  g vll++                  +    p      +++  +++ + 
  gi|313125753|ref|YP_004036023.1| 100 DDEKIIFVGFSQGACLASSYVAQHpsRYGGvVLLSGgfvgpegaafdfegsmagT----P--VflgVSDDDPHVPQS 170
                                       89***********999999444444555557888885554333333332222221....1..122333333333333 PP

                                       HHTT-CCCCHC CS
                     Abhydrolase_6 116 lallrllawls 126
                                       +a ++ +a+++
  gi|313125753|ref|YP_004036023.1| 171 RAEETIAAFDR 181
                                       33333333332 PP

>> Palm_thioest  Palmitoyl protein thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     1e-07   0.00011       2     102 ..      26     136 ..      25     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1e-07
                      Palm_thioest   2 vviwhGldsaesnmqklaeliek.........li.g.tyvknveigeseaedrkasffgnlndqveavckk..lela 65 
                                       vv++hG ++ + +m  +a+++++         +  g  y  + +  +++++ +++s + +ln  ve++ +   l  +
  gi|313125753|ref|YP_004036023.1|  26 VVLVHGRGATARGMLAFADEFHDdgvhyvapqAQrGtWYPNSFMAPTESNQPHYQSALLHLNRAVEQARETtgL-DD 101
                                       89999996666667777777777444444443112434444445556666899**************9888964.67 PP

                      Palm_thioest  66 ngfhaiGfSQGglflRaliercddkknvrnlislggp 102
                                       ++++++GfSQG+ ++  ++ +++++     ++ l+g 
  gi|313125753|ref|YP_004036023.1| 102 EKIIFVGFSQGACLASSYVAQHPSR--YGGVVLLSGG 136
                                       99*****************999543..4666666555 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.4e-06    0.0015      84     190 ..      84     182 ..      40     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                              FSH1  84 egleesldavkdyikengpfdGiiGFSqGaalaallaslleellkeashpslkfailvsGfkleepkyeeyyeedki 160
                                         l+ +++  +++     +    +GFSqGa+la+ ++++            +  ++l+sG  + ++  +  +e +  
  gi|313125753|ref|YP_004036023.1|  84 LHLNRAVEQARETTGLDDEKIIFVGFSQGACLASSYVAQHPSR--------YGGVVLLSGGFVGPEGAAFDFEGSMA 152
                                       344444444444444444445569************9987654........34688999888887766666777777 PP

                              FSH1 161 qtptLhvlGelDtvvdeerseaLaeafkns 190
                                        tp++  + ++D  v+++r+e+ + af++ 
  gi|313125753|ref|YP_004036023.1| 153 GTPVFLGVSDDDPHVPQSRAEETIAAFDRM 182
                                       999999999999999999999999888875 PP

>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.5e-06    0.0026       8      71 ..      62     125 ..      56     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.5e-06
                            PE-PPE   8 vsyPasflpvtglksltvdeSvaeGtenLeaairaelaagekvvvfGySqgalvasnekarlaa 71 
                                         yP+sf+++t+ +++ +++++ +    +e+a ++    +ek++ +G+Sqga  as + a++ +
  gi|313125753|ref|YP_004036023.1|  62 TWYPNSFMAPTESNQPHYQSALLHLNRAVEQARETTGLDDEKIIFVGFSQGACLASSYVAQHPS 125
                                       56****************999999888888888887779999**************99998765 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   7.6e-05     0.081      16      90 ..      46     121 ..      26     148 .. 0.79
   2 ?    1.3   0.0      0.26   2.7e+02     168     210 ..     155     199 ..     143     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.6e-05
                                       TTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHH.HHTETTCEEEEEEETHHHHHHHHHHH CS
                     Abhydrolase_3  16 thdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqaw.elgadpsrivlaGdSaGGnlaaaval 90 
                                        hd+ ++ +a +++     ++  +AP       ++ al  l+ ++eqa  + g+d ++i+++G S G+ la   + 
  gi|313125753|ref|YP_004036023.1|  46 FHDDGVHYVAPQAQRGTWYPNSFMAPTESNQPHYQSALLHLNRAVEQAReTTGLDDEKIIFVGFSQGACLASSYVA 121
                                       45666777777777777777778899999999999999999999999998999*****************987664 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.26
                                       -EEEEEETT-TTH..HHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                     Abhydrolase_3 168 ptlvvvaefDplr..degeayaerlraagvevelieyegmvHgfa 210
                                       p+++ v + Dp    +++e++ +++  +  ++++  yeg  Hg++
  gi|313125753|ref|YP_004036023.1| 155 PVFLGVSDDDPHVpqSRAEETIAAFDRMDADTRFDLYEGRGHGIF 199
                                       677777777776511567788899999***************975 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   3.3e-05     0.035      89     134 ..      94     139 ..      18     155 .. 0.85
   2 ?   -0.7   0.0      0.78   8.2e+02     165     199 ..     149     183 ..     140     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                      Esterase_phd  89 vdehrvdaarvyvaGlsaGaaladllalhypdvfaavalhsGlalG 134
                                        +  ++d  ++   G+s Ga+la+     +p ++  v l sG  +G
  gi|313125753|ref|YP_004036023.1|  94 RETTGLDDEKIIFVGFSQGACLASSYVAQHPSRYGGVVLLSGGFVG 139
                                       345689***********************************97665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.78
                      Esterase_phd 165 gaypglpalvvqGdadtvvavknaeslvvalrrls 199
                                       g++ g p ++   d d  v    ae+ ++a+ r++
  gi|313125753|ref|YP_004036023.1| 149 GSMAGTPVFLGVSDDDPHVPQSRAEETIAAFDRMD 183
                                       67788999998899999999999999999998765 PP

>> DUF3530  Protein of unknown function (DUF3530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.59   6.2e+02     196     209 ..      22      35 ..      17      40 .. 0.66
   2 ?   12.0   0.0    0.0001      0.11     167     222 ..      71     127 ..      54     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.59
                           DUF3530 196 aenivllghgtgAy 209
                                       ae +v+l hg gA 
  gi|313125753|ref|YP_004036023.1|  22 AEAVVVLVHGRGAT 35 
                                       45566666666663 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0001
                           DUF3530 167 ptdaearkahrervrarlqaaiaflnqrgae...nivllghgtgAywaarylaekksak 222
                                       pt++  ++ h ++    l+ a++++++++     +i+++g  +gA +a +y+a+  s+ 
  gi|313125753|ref|YP_004036023.1|  71 PTES--NQPHYQSALLHLNRAVEQARETTGLddeKIIFVGFSQGACLASSYVAQHPSRY 127
                                       4444..67788888999*********99877788********************87765 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.028      72     153 ..      60     141 ..      25     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                                       TSBTTSBB.TTEEETTCCCCCCHCHHHH..THHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEE CS
                          Esterase  72 ysdwdlgarfyenategpgaeayetflt..qeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssf 146
                                          w+     +  a+ ++ +++y+++l   ++ +   +++   ++++   +G+S+G+  A  + ++hp r+g v  +
  gi|313125753|ref|YP_004036023.1|  60 RGTWYPN---SFMAPTESNQPHYQSALLhlNRAVEQARETTGLDDEKIIFVGFSQGACLASSYVAQHPSRYGGVVLL 133
                                       4566655...55677777788888555401444555555555566658889************************** PP

                                       S-.-S-CC CS
                          Esterase 147 Sp.ivnps 153
                                       S+ +v p 
  gi|313125753|ref|YP_004036023.1| 134 SGgFVGPE 141
                                       *5255555 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00033      0.34       5     101 ..      23     124 ..      19     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                            DUF676   5 dhLvVlvHGlqgnsaDlelikeqleki.....keklpeekieflmsennesktfkgidvlgerlaeevlevvkkkkd 76 
                                         +vVlvHG  +    + + +++++        ++ ++   +  ++++  +      +     l   v +  +    
  gi|313125753|ref|YP_004036023.1|  23 EAVVVLVHGRGATARGMLAFADEFHDDgvhyvAPQAQRGTWYPNSFMAPTESNQPHYQSALLHLNRAVEQARETTGL 99 
                                       56788888888888888887777777544444555566666666666666666666666666666666666666666 PP

                            DUF676  77 knkkiSfvghSlGgliaraaiaklk 101
                                       +++ki fvg+S+G   a++ +a+  
  gi|313125753|ref|YP_004036023.1| 100 DDEKIIFVGFSQGACLASSYVAQHP 124
                                       688**************99999765 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.13      50     107 ..      82     139 ..      68     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                               LIP  50 avLdsiraalksekvtgiksdakvalwGYSgGs.lAsawAaelqpeYAPelelvGaalG 107
                                       a L   ra+ ++ + tg  +d k+ + G+S+G+ lAs++ a+  ++Y   + l G  +G
  gi|313125753|ref|YP_004036023.1|  82 ALLHLNRAVEQARETTG-LDDEKIIFVGFSQGAcLASSYVAQHPSRYGGVVLLSGGFVG 139
                                       55666699999999999.6889**********758*******99999999889998888 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014      0.15     146     190 ..      74     118 ..      64     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                       TTT-HHHHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHH CS
                              AXE1 146 keklyyrrvflDavrlveivaslpevDeeRvavlGasqGGalala 190
                                        ++ +y++  l   r+ve +++    D+e++  +G sqG  la  
  gi|313125753|ref|YP_004036023.1|  74 SNQPHYQSALLHLNRAVEQARETTGLDDEKIIFVGFSQGACLASS 118
                                       567789999999***************************999855 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003      0.32      39     141 ..      82     197 ..      76     201 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                     Abhydrolase_5  39 avlgknkaeeiikeapkl..ekfvvgGhslGGvvasrfaaee.ekiegvvflasY...Pekdel....selskkvls 105
                                       a+l  n+a e  +e+ +l  ek +  G s G  +as ++a++ ++  gvv+l+     Pe   +    s ++++v+ 
  gi|313125753|ref|YP_004036023.1|  82 ALLHLNRAVEQARETTGLddEKIIFVGFSQGACLASSYVAQHpSRYGGVVLLSGGfvgPEGAAFdfegSMAGTPVFL 158
                                       8899999998888888663368999***************9966999**9997521224432221111233334444 PP

                     Abhydrolase_5 106 ivgteDgvlnvkslek...akkflpkdtkvvsieGgnha 141
                                        v+++D  ++++++e+   a +++  dt++   eG  h 
  gi|313125753|ref|YP_004036023.1| 159 GVSDDDPHVPQSRAEEtiaAFDRMDADTRFDLYEGRGHG 197
                                       444555555555544411133456666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1299.53
//
Query:       gi|313125754|ref|YP_004036024.1|  [L=323]
Description: lactoylglutathione lyase-like lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-30  105.5   1.0    3.9e-14   52.9   0.1    2.4  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    0.00074   20.3   0.9          1   10.2   0.0    2.5  2  Glyoxalase_6  Glyoxalase-like domain
     0.0023   18.2   0.3        1.1    9.6   0.1    2.8  3  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.1   2.6e-17   1.5e-13       1     127 [.      16     137 ..      16     138 .. 0.71
   2 !   52.9   0.1   6.5e-18   3.9e-14      21     128 .]     180     274 ..     161     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.6e-17
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE...EEST.EEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCT CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdn...teet.eglriaffhaggghielvlneapsgaakhvkkieet 73 
                                       gi+hv+++++d+ ++++FYt+vLG++lvk+t+n      t     +    + g+ ++++ +    +++++       
  gi|313125754|ref|YP_004036024.1|  16 GIHHVTAIADDPNENVRFYTDVLGLRLVKRTVNfddP-HTyHLYYGDETGSPGTALTFFPFGEGRPGRPGR------ 85 
                                       79*******************************9752.221333333444455555566565555555555...... PP

                                       SEEEE.EEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEE CS
                        Glyoxalase  74 vhhva.fialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGille 127
                                       ++ va  +a  +  ++ + +r+++++v v ++ +r + + l    f+D dG  le
  gi|313125754|ref|YP_004036024.1|  86 GQAVAtSFAVPEGSLDYWRERFADHDVTVGEVEDRFGAEVLP---FEDDDGQPLE 137
                                       444441466777788888888888888888888877777777...8888887776 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 6.5e-18
                                       HHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCHHHHHHHHHHHT CS
                        Glyoxalase  21 kvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdvedvgkaldrlkea 97 
                                       + LGf+  ++ d     + +r+ +  +  +++ l+ +e+p g++        tvhhvaf+a d+e + ++ ++l +a
  gi|313125754|ref|YP_004036024.1| 180 ELLGFERGDEAD-----DRVRYVAHGDRATVVDLLKREPPRGRPGTG-----TVHHVAFRAPDTETQMEWREKLTAA 246
                                       568888888888.....888888888888888888888888888777.....8************************ PP

                                       TGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  98 gvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       g  v++  +r+yf+++y   fr+p+G+l+ei
  gi|313125754|ref|YP_004036024.1| 247 GQYVTQQKDRQYFESIY---FREPGGVLFEI 274
                                       *****************...**********8 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00017         1       4      38 ..      22      56 ..      19     134 .. 0.83
   2 !    8.4   0.4   0.00063       3.8      18     106 ..     180     274 ..     156     275 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                      Glyoxalase_6  4 ldaadpaalaaFwaaalgwevereeaaledpegvg 38
                                        a+dp + ++F+ ++lg++++++ +  +dp++ +
  gi|313125754|ref|YP_004036024.1| 22 AIADDPNENVRFYTDVLGLRLVKRTVNFDDPHTYH 56
                                      4489******************9996666665544 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00063
                      Glyoxalase_6  18 aalgwevereeaaledpegvgpaaed.aatllfqrvpe....pakn.rvHldlavedld...aevarlvalGArvlr 85 
                                       ++lg+e+ +e+    d +++  a++d a+ + + +++     p+     H+ ++++d +   +  ++l a+G  v  
  gi|313125754|ref|YP_004036024.1| 180 ELLGFERGDEA----DDRVRYVAHGDrATVVDLLKREPprgrPGTGtVHHVAFRAPDTEtqmEWREKLTAAGQYVT- 251
                                       57888888888....3344444444403344444444456884444247999999888733344445555544444. PP

                      Glyoxalase_6  86 eprdgthgr..vlaDPeGneFcv 106
                                       +++d++  +   ++ P G  F +
  gi|313125754|ref|YP_004036024.1| 252 QQKDRQYFEsiYFREPGGVLFEI 274
                                       44444444479*******99987 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0026        15      60      88 ..       8      36 ..       3      63 .. 0.68
   2 ?   -3.4   0.0         2   1.2e+04      79     101 ..     100     122 ..      91     128 .. 0.63
   3 !    9.6   0.1   0.00018       1.1      65     100 ..     219     257 ..     157     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0026
                                      -THHHTS-EEEEEEEEES-HHHHHHHHCT CS
                      Glyoxalase_4 60 eflaehgeglhhlaywvddldaavarlee 88
                                      +++  + +g+hh+    dd ++ v+ +++
  gi|313125754|ref|YP_004036024.1|  8 SSITMNTTGIHHVTAIADDPNENVRFYTD 36
                                      55666778888888888888877765554 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2
                                       HHHHHHHHCTTTEEEEEEEE-GG CS
                      Glyoxalase_4  79 ldaavarleeqGfevvqkgvrag 101
                                       ld   +r+++++++v + ++r g
  gi|313125754|ref|YP_004036024.1| 100 LDYWRERFADHDVTVGEVEDRFG 122
                                       55566777777777666666655 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00018
                                       TS-EEEEEEEEES-HHHHHHH...HCTTTEEEEEEEE-G CS
                      Glyoxalase_4  65 hgeglhhlaywvddldaavar...leeqGfevvqkgvra 100
                                       + + +hh+a++  d++  +++   l+++G  v+q+++r+
  gi|313125754|ref|YP_004036024.1| 219 GTGTVHHVAFRAPDTETQMEWrekLTAAGQYVTQQKDRQ 257
                                       67789***********99987333566777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2250.18
//
Query:       gi|313125755|ref|YP_004036025.1|  [L=147]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-21   74.9   0.0    4.3e-21   74.6   0.0    1.1  1  HxlR          HxlR-like helix-turn-helix
    4.5e-05   23.5   0.0    6.9e-05   22.9   0.0    1.3  1  HTH_34        Winged helix DNA-binding domain
    6.2e-05   23.4   0.0     0.0001   22.8   0.0    1.3  1  HTH_27        Winged helix DNA-binding domain
     0.0011   18.9   0.0     0.0018   18.1   0.0    1.4  1  MarR_2        MarR family
      0.003   17.4   0.0      0.004   17.0   0.0    1.2  1  HTH_5         Bacterial regulatory protein, arsR family
     0.0047   17.0   0.0     0.0065   16.6   0.0    1.3  1  Replic_Relax  Replication-relaxation
     0.0052   16.7   0.0     0.0085   16.0   0.0    1.4  1  MarR          MarR family
     0.0085   16.0   0.0      0.013   15.4   0.0    1.3  1  PadR          Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.047   13.6   0.0      0.069   13.0   0.0    1.2  1  TrmB          Sugar-specific transcriptional regulator TrmB
       0.08   12.8   0.0       0.12   12.2   0.0    1.3  1  HTH_IclR      IclR helix-turn-helix domain
       0.12   12.3   0.1       0.23   11.5   0.1    1.4  1  HTH_Crp_2     Crp-like helix-turn-helix domain
       0.13   12.4   0.0          9    6.4   0.0    2.3  2  Hol_Tox       Putative Holin-like Toxin (Hol-Tox)
       0.13   12.2   0.0       0.18   11.8   0.0    1.3  1  HTH_43        Winged helix-turn helix
       0.16   11.8   0.0       0.88    9.4   0.0    2.0  1  DUF1495       Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   3.4e-24   4.3e-21       2      89 ..      36     122 ..      35     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 3.4e-24
                                       HHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHH CS
                              HxlR   2 iggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqe 78 
                                       ig++W+l++l+ l +g+kRf+elkr   + s ++L++ L  L++ g+++r+  +  P+   Yslt+kG+sl+pv++e
  gi|313125755|ref|YP_004036025.1|  36 IGSQWRLIVLHDLQDGEKRFNELKRST-GSSSRTLSRVLDDLQELGFVSRRLEEDAPVATYYSLTPKGESLAPVFDE 111
                                       89************************9.67999******************************************** PP

                                       HHHHHHHHHHC CS
                              HxlR  79 lkkwgeeylee 89 
                                       ++ w++e+l e
  gi|313125755|ref|YP_004036025.1| 112 INCWADEWLTE 122
                                       ********976 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.4e-08   6.9e-05       2      67 ..      41     104 ..      40     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.4e-08
                            HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67 
                                       Rl vl+ L  + e  f+elk +++ ++  Ls  l+ L++ g++++++e +     t +++Tp+G +
  gi|313125755|ref|YP_004036025.1|  41 RLIVLHDLQ-DGEKRFNELKRSTGSSSRTLSRVLDDLQELGFVSRRLEEDAP-VATYYSLTPKGES 104
                                       666666664.56779*********************************9999.89*********75 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   7.8e-08    0.0001       7      68 .]      43     102 ..      38     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.8e-08
                            HTH_27   7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre..krvrlTdkG 68 
                                       +vLh ++  +++k+  +l + +  ++ + s +l+ L e G+v r   e    +  + ++lT+kG
  gi|313125755|ref|YP_004036025.1|  43 IVLHDLQ--DGEKRFNELKRSTGSSSRTLSRVLDDLQELGFVSRRLEEDA--PvaTYYSLTPKG 102
                                       57*****..*********************************77777633..336********9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.4e-06    0.0018      10      54 ..      44      85 ..      37      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      vL+ L +++    + +el r +g s  ++sr+l++L++ G+v rr
  gi|313125755|ref|YP_004036025.1| 44 VLHDLQDGEK---RFNELKRSTGSSSRTLSRVLDDLQELGFVSRR 85
                                      6777777776...9****************************998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.1e-06     0.004       4      46 ..      41      83 ..      38      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.1e-06
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      Rl +L+ L++ge+ + el + +g s  t+S+ L  L e+G+V+
  gi|313125755|ref|YP_004036025.1| 41 RLIVLHDLQDGEKRFNELKRSTGSSSRTLSRVLDDLQELGFVS 83
                                      9999**************************************7 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.1e-06    0.0065      19      69 ..      62     106 ..      53     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.1e-06
                      Replic_Relax  19 lfashratarrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarll 69 
                                       +  s r t++r+L +L+elg++sr l++ +         + Y LtpkG+ l 
  gi|313125755|ref|YP_004036025.1|  62 TGSSSR-TLSRVLDDLQELGFVSRrLEEDAPV------ATYYSLTPKGESLA 106
                                       334444.5****************77776333......446*******8877 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.6e-06    0.0085      16      50 ..      51      85 ..      38      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.6e-06
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      g+ +  eL +  g s+ t++rvld L + G+++R+
  gi|313125755|ref|YP_004036025.1| 51 GEKRFNELKRSTGSSSRTLSRVLDDLQELGFVSRR 85
                                      557788999*************************7 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05     0.013      33      70 ..      68     103 ..      46     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCC CS
                              PadR  33 slYpaLkrLekeglveseweesgegpprkyYrlTdaGr 70 
                                       +l ++L++L++ g+v+++ ee  + p   yY lT++G+
  gi|313125755|ref|YP_004036025.1|  68 TLSRVLDDLQELGFVSRRLEE--DAPVATYYSLTPKGE 103
                                       66789*************997..69************8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.4e-05     0.069      18      62 ..      48      96 ..      44     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-05
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEE CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....pklY 62
                                      l+ g+++ +e+ + +g +  +  +vL  L + G+V r+ ++     ++Y
  gi|313125755|ref|YP_004036025.1| 48 LQDGEKRFNELKRSTGSSSRTLSRVLDDLQELGFVSRRLEEdapvATYY 96
                                      56799999*****************************998877543344 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.7e-05      0.12      17      50 ..      51      84 ..      47      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-05
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +e ++ el r tg +  t +R L  L+elG+v +
  gi|313125755|ref|YP_004036025.1| 51 GEKRFNELKRSTGSSSRTLSRVLDDLQELGFVSR 84
                                      555899**************************87 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00018      0.23      31      54 ..      62      85 ..      56      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                      TTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 31 lGltretvsrilseLkreglisrg 54
                                       G++  t+sr+l +L++ g +sr+
  gi|313125755|ref|YP_004036025.1| 62 TGSSSRTLSRVLDDLQELGFVSRR 85
                                      799*****************9965 PP

>> Hol_Tox  Putative Holin-like Toxin (Hol-Tox)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.007         9       9      36 ..       9      36 ..       3      38 .. 0.88
   2 ?    3.4   0.0      0.06        77      20      33 ..      99     112 ..      92     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.007
                           Hol_Tox  9 sevvfktVltdtkkrrallsvsealQli 36
                                       +v ++   +d k  +  +sv +++Q i
  gi|313125755|ref|YP_004036025.1|  9 HQVTRMPPEADDKYNEQACSVIDSIQQI 36
                                      57889999999***************65 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.06
                           Hol_Tox  20 tkkrrallsvseal 33 
                                       t k+++l +v++ +
  gi|313125755|ref|YP_004036025.1|  99 TPKGESLAPVFDEI 112
                                       679*********87 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.18       9      50 ..      41      82 ..      34     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-E CS
                            HTH_43  9 rlylaylideeeanvpklieltgmPRRtlqDtlkalaeldie 50
                                      rl + + ++++e+   +l + tg   Rtl  +l  l+el+  
  gi|313125755|ref|YP_004036025.1| 41 RLIVLHDLQDGEKRFNELKRSTGSSSRTLSRVLDDLQELGFV 82
                                      899************************************964 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00069      0.88      59      87 ..      76     106 ..      29     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00069
                           DUF1495  59 LielGLveeeee..seglklYklteeGieiv 87 
                                       L elG v+++ e   +  ++Y+lt++G+ ++
  gi|313125755|ref|YP_004036025.1|  76 LQELGFVSRRLEedAPVATYYSLTPKGESLA 106
                                       6689***98877323344599******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 975.96
//
Query:       gi|313125756|ref|YP_004036026.1|  [L=612]
Description: protein kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-28   99.3   0.1    8.6e-28   96.9   0.0    2.2  3  ABC1       ABC1 family
    8.5e-06   25.5   0.0    3.8e-05   23.4   0.0    1.9  2  RIO1       RIO1 family
    0.00065   19.7   1.3     0.0032   17.4   0.1    2.7  2  APH        Phosphotransferase enzyme family
  ------ inclusion threshold ------
       0.12   11.7   0.0          1    8.6   0.0    2.0  2  Pkinase    Protein kinase domain
       0.14   11.7   0.0       0.25   10.9   0.0    1.3  1  WaaY       Lipopolysaccharide core biosynthesis protein (WaaY
        4.8    8.0   7.2       0.78   10.5   0.4    3.2  3  TetR_C_15  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   2.9e-31   8.6e-28       3     116 ..     149     261 ..     146     263 .. 0.92
   2 ?   -2.4   0.0       1.8   5.3e+03      72      88 ..     401     420 ..     379     422 .. 0.63
   3 ?   -1.8   0.0       1.1   3.3e+03      74      96 ..     434     456 ..     407     462 .. 0.74

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 2.9e-31
                              ABC1   3 lgkkleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkfl.kelrldlee 78 
                                       lg ++ee+F++fd+ePi  AS++qV++A++ +geeVavK+ rp++++ +++Dl+++++l+ +l  f  +++r  +e+
  gi|313125756|ref|YP_004036026.1| 149 LG-PVEEVFDHFDREPISGASLGQVYTAVV-DGEEVAVKILRPDIRRVVAADLRVVETLMPVLLWFAhPGQRFTFEN 223
                                       44.99***********************86.8****************************99877761555599*** PP

                              ABC1  79 lvdefskslleEldferEAknaekfrenfaklkevkvP 116
                                       l+def++++ eE+d+ +EA+   ++r+nf++ ++++vP
  gi|313125756|ref|YP_004036026.1| 224 LADEFADTIHEEMDYAHEAAMLREIRSNFSDNPKIRVP 261
                                       *************************************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                              ABC1  72 lr...ldleelvdefsksll 88 
                                       ++   +++++lv +f+++l+
  gi|313125756|ref|YP_004036026.1| 401 QDvdqYRIQQLVSQFEETLY 420
                                       33336789999999999886 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                              ABC1  74 ldleelvdefskslleEldferE 96 
                                        ++ ++++ + ++l+ E df  E
  gi|313125756|ref|YP_004036026.1| 434 VRVSTVLEGVCRTLVPEFDFVDE 456
                                       45677788888888888888877 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.39   1.2e+03       2      20 ..     172     189 ..     171     198 .. 0.78
   2 !   23.4   0.0   1.3e-08   3.8e-05      47     149 ..     236     339 ..     221     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.39
                                       EEEEEETTTEEEEEEEE-S CS
                              RIO1   2 VyhavsedgkevaiKiykt 20 
                                       Vy+av  dg+eva+Ki + 
  gi|313125756|ref|YP_004036026.1| 172 VYTAVV-DGEEVAVKILRP 189
                                       888866.899999999875 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHHHHHHHH.HHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHHCG-.HHHHHHHHHHHHHHHHHH CS
                              RIO1  47 prklvklwaekEfr.nLkrleeagvpvPkpielkrhvlvmefigedgvaapklkdvee.eeeaeelyeevleemrkl 121
                                         +  +++  +E+r n +   ++ vpvP+     ++vl me+++  gv++ +++++e+   + eel++ + ++++++
  gi|313125756|ref|YP_004036026.1| 236 MDYAHEAAMLREIRsNFSDNPKIRVPVPREAYSTKNVLTMEYVE--GVKIDRVREIERlGIDREELARRLERAYIQM 310
                                       555556666677653667777888999999999***********..***********5488999999999999999* PP

                                       HHTSTEEESS-STTSEEEETT.EEEE--G CS
                              RIO1 122 ykeaglvHaDLSeyNvlvded.kvviIDv 149
                                       + e g  HaD    N+ v++d  +++ D+
  gi|313125756|ref|YP_004036026.1| 311 ILEDGAFHADPHPGNLAVQSDgTLIFYDF 339
                                       99**************9999977888887 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.4   1.2e+03      88     162 ..      38     120 ..      24     134 .. 0.58
   2 !   17.4   0.1   1.1e-06    0.0032     143     201 ..     292     348 ..     162     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHHHCCHHCH.-STTTB-..........SHHCHTCCHHHHHHCHHHCCCGCCTCCHHHHHHHHHHH CS
                               APH  88 aaqlpellealgeflaalhqvdpaalpla..........dflaqdlellrqlesatarllaselldlleeleeqvla 154
                                       ++ l+  l+ l ++l  +  + p + + a          +++++d +  rq++ + +++l s+ +   ++l + +l 
  gi|313125756|ref|YP_004036026.1|  38 PSGLRVTLRSLWRLLVVIRTFLPLFVGIArdrrrfllfgRRRRPDSATRRQRATYLRDSLISLGPT-FIKLGQ-ILS 112
                                       556666677777777777777555555551111111111344444444455555555555555555.777777.888 PP

                                       HHHHH--S CS
                               APH 155 alaallpg 162
                                       ++++ lpg
  gi|313125756|ref|YP_004036026.1| 113 THPDALPG 120
                                       88887775 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.1e-06
                                       C..HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E.EEEC CS
                               APH 143 d..lleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedag.lgpp 201
                                          ++eel++++ +a  +  +   + +  H D+hpgNl v++d++ +  + Df+++g +gp+
  gi|313125756|ref|YP_004036026.1| 292 LgiDREELARRLERAYIQMIL---EDGAFHADPHPGNLAVQSDGTLI--FYDFGMTGrIGPA 348
                                       245699999999999999999...8****************999999..*****98724444 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.11   3.3e+02      12      34 ..     169     189 ..     164     202 .. 0.87
   2 ?    8.6   0.0   0.00035         1      70     152 ..     268     349 ..     226     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
                                       SEEEEEEEETTTTEEEEEEEEEC CS
                           Pkinase  12 fGkVykaveketgkivAvKkikk 34 
                                        G+Vy av   +g++vAvK+++ 
  gi|313125756|ref|YP_004036026.1| 169 LGQVYTAV--VDGEEVAVKILRP 189
                                       69******..8********9986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00035
                                       SSEEEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTS CS
                           Pkinase  70 kdelylvleyveggeladlle.rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGla 145
                                       +++ +l +eyveg +++++ e ++  ++ ee+ + +++    ++ + + g +H D  p N+ ++++g l   DFG+ 
  gi|313125756|ref|YP_004036026.1| 268 STKNVLTMEYVEGVKIDRVREiERLGIDREELARRLERAY--IQMILEDGAFHADPHPGNLAVQSDGTLIFYDFGMT 342
                                       4566789******999999886556677777666555543..78999*****************************9 PP

                                       EESSSSC CS
                           Pkinase 146 kelesss 152
                                        ++   +
  gi|313125756|ref|YP_004036026.1| 343 GRIGPAT 349
                                       8887655 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.4e-05      0.25     114     176 ..     267     336 ..     261     360 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.4e-05
                              WaaY 114 yvkvyimiieyiegielvdmpeid......devkaki.kqsieklhqlgmvsgdphrgnfivkkdevrii 176
                                       y    ++ +ey+eg+++  + ei+      +e+  ++ ++ i+ + + g    dph gn+ v++d+  i 
  gi|313125756|ref|YP_004036026.1| 267 YSTKNVLTMEYVEGVKIDRVREIErlgidrEELARRLeRAYIQMILEDGAFHADPHPGNLAVQSDGTLIF 336
                                       66778999*******9999888863333335666666246688899999**************9998775 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.2   3.6e+03       3      25 ..     297     319 ..     296     320 .. 0.89
   2 ?   10.5   0.4   0.00026      0.78       5      73 ..     364     436 ..     362     451 .. 0.76
   3 ?   -2.4   0.1       2.8   8.4e+03      82     104 ..     476     498 ..     473     500 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                         TetR_C_15   3 eealdalvdallaahrenpalrr 25 
                                       ee++++l +a++++  e+ a+++
  gi|313125756|ref|YP_004036026.1| 297 EELARRLERAYIQMILEDGAFHA 319
                                       68999999********9999986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                         TetR_C_15   5 aldalvdallaahrenpalrrvlleea..pslgel...elvealeqriaealaalLarrrpelppedlelaafv 73 
                                        +d+++da++a+ + +p   r l++e+   ++++l   + ++   q++++++++ L  ++ +lp +dl+l+++v
  gi|313125756|ref|YP_004036026.1| 364 DIDRVIDAFIAMEALDPTANRELMRETftVAIETLrgqDVDQYRIQQLVSQFEETLYDFPLRLP-QDLALVVRV 436
                                       69*******************9999984433343321044444457888888889999999999.999999987 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.8
                         TetR_C_15  82 lhlaleedpadrealiaelkrll 104
                                        +++++e  +d++a ++e++r +
  gi|313125756|ref|YP_004036026.1| 476 QERFVREYAEDAAAQVQETARTV 498
                                       56777777777777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3642.05
//
Query:       gi|313125757|ref|YP_004036027.1|  [L=63]
Description: hypothetical protein Hbor_09880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 393.68
//
Query:       gi|313125758|ref|YP_004036028.1|  [L=252]
Description: metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-20   73.3   1.2    2.7e-20   72.8   1.2    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
      1e-07   32.2   0.8    1.5e-07   31.7   0.8    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0038   17.1   0.0     0.0061   16.5   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   1.2   4.4e-24   2.7e-20       3     166 ..      44     190 ..      42     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 4.4e-24
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvyla 78 
                                       +L+D  p++r    r+        ++ ++da ++th H DH+ g+++l+   r  ++ply ++  ++  +++ +yl 
  gi|313125758|ref|YP_004036028.1|  44 LLLDVPPEFRDG-IRQA-------DVGSVDAAFVTHWHHDHVGGIDDLALtARFLDIPLYLTATAQDRFAQEKPYLT 112
                                       677777777777.5554.......799**********************9766666****************99988 PP

                                       CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHH..HH CS
                     Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeig..er 153
                                       + ++    ++ l  ge++++g  ++eit++p+ h+ ++       dtl++r+e+g+++++y++D + + +++   ++
  gi|313125758|ref|YP_004036028.1| 113 DSVA----IRNLMHGEPVTVG--DIEITPIPVAHDRPE------CDTLAFRLETGTETMVYAPDFENWCPDMPggKM 177
                                       6666....************9..689************......**********************87755333388 PP

                                       HCT-SEEEEE-S- CS
                     Lactamase_B_2 154 lggadlllldita 166
                                       + +adl++l++t 
  gi|313125758|ref|YP_004036028.1| 178 YTNADLAVLEATP 190
                                       888*******985 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.8   2.5e-11   1.5e-07      10     179 ..      36     211 ..      35     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.5e-11
                                       EEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                       Lactamase_B  10 liegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86 
                                       lie++++++L D   + + +        +  +   vda ++TH+H+DH+Gg ++l+ ++ +  +  +++a a  +++
  gi|313125758|ref|YP_004036028.1|  36 LIETETTTLLLDVPPEFRDGI-------RQADVGSVDAAFVTHWHHDHVGGIDDLALTARFLDIPLYLTATAQDRFA 105
                                       677777777777655555555.......6899999**************************************9999 PP

                                       HHHHHHHCCHH.............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECT CS
                       Lactamase_B  87 addaasrkgll.............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGD 150
                                        ++ +  ++               +++ +++++ +d+ e d+ a+  +++  t   ++     + +++ggk+    D
  gi|313125758|ref|YP_004036028.1| 106 QEKPYLTDSVAirnlmhgepvtvgDIEITPIPVAHDRPECDTLAFRLETGTETMVYAPDFENWCPDMPGGKMYTNAD 182
                                       98888877777888888666666666666666666666666666666666666666666666666666666666666 PP

                                       TTSSHHCCCCCC.TTCEEE-SHCHHHHHH CS
                       Lactamase_B 151 allagetgridltlrgaevrdpsdaekyl 179
                                       +   + t+ i ++l  + v+ p++++k+ 
  gi|313125758|ref|YP_004036028.1| 183 LAVLEATPAIAPELLSSDVPTPDPVTKAA 211
                                       66666666666666666666665555555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     1e-06    0.0061      11     115 ..      36     166 ..      33     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                     Lactamase_B_3  11 lletagarilvDPfka.nlgyeppa.eeaDlvlisqaledHahletlkql........................... 58 
                                       l+et+ +++l+D   +   g ++    ++D+  +++ +  H h+  +  l                           
  gi|313125758|ref|YP_004036028.1|  36 LIETETTTLLLDVPPEfRDGIRQADvGSVDAAFVTHWH--HDHVGGIDDLaltarfldiplyltataqdrfaqekpy 110
                                       78889999999955444555555445789999999999..5566666666669999999999999999999766666 PP

                     Lactamase_B_3  59 ...aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhla 115
                                             ++ l +ge ++vg++ei+ ++ +hd+     +    +f+le +  t+++ ++  
  gi|313125758|ref|YP_004036028.1| 111 ltdSVAIRNLMHGEPVTVGDIEITPIPVAHDRP----ECDTLAFRLETGTETMVYAPDFE 166
                                       666555666666999***************754....55668899999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1675.62
//
Query:       gi|313125759|ref|YP_004036029.1|  [L=214]
Description: dithiol-disulfide isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-36  125.8   0.0      2e-36  125.6   0.0    1.0  1  DSBA           DSBA-like thioredoxin domain
    1.5e-07   31.7   0.3    2.5e-05   24.5   0.0    2.3  2  Thioredoxin_4  Thioredoxin
  ------ inclusion threshold ------
      0.036   14.5   0.6        1.3    9.5   0.0    2.3  2  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.0   3.4e-40     2e-36       1     191 [.      12     210 ..      12     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 3.4e-40
                                       EEEEEEBTTBHHHHHHHHHHHHHHHHCCT.EEEEEEE-SSSCHHHHCT.S.GGG.....SHHHHHHHHHHHHHHHHH CS
                              DSBA   1 tvdeffDvlCPyCylgkerleklaarspd.vkvvlrpfelagakkasgnvgpse.....lpeklkylledlkrlaea 71 
                                       ++ +++D++CP+Cylg e l+++++ ++d +++ ++pf+l+ +k++ +++          +e +++ +e+ +rl+e+
  gi|313125759|ref|YP_004036029.1|  12 QITVYSDYVCPFCYLGRESLRRYQSTREDeLEIDWHPFDLRSQKRNPDGTIDHSvddgkDDEYYEQAKENVRRLQEK 88 
                                       699************************666*************886666544448999989999999********** PP

                                       HT....GGSSHHHHHHHHHHHHHHHHHHH...GHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHT CS
                              DSBA  72 egiplrfpkdklknstraarlllaagaeg...laekvvrelfealwsegqaitddqellevaekaGldaeeldeale 145
                                       +g+++ ++ d   +s+ a+ + ++++++       ++  ++f+alw++g++i+d++ l+++ae+aG+  +e++ al+
  gi|313125759|ref|YP_004036029.1|  89 YGVEMDLDVDTDIDSLPAQMASYYVKQHYdyeTWLDFDVAIFDALWQDGADIGDEELLVKLAEDAGVVGDEIRSALD 165
                                       ********99855*************9995665557889************************************** PP

                                       SHHHHHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHHH CS
                              DSBA 146 seavkeavrentaaaqslgvtGvPtvvvdgkrmvfGadrldtlada 191
                                       ++a  e+vr +  +a + gvtGvPt+  dg   + Ga +++ l++ 
  gi|313125759|ref|YP_004036029.1| 166 DDALREEVRAQFTEAHQQGVTGVPTFAYDGY-GARGAVPPEHLERL 210
                                       ******************************7.9********99876 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   1.3    0.0073        44      17      29 ..      13      25 ..       7      88 .. 0.85
   2 !   24.5   0.0   4.2e-09   2.5e-05      62     165 ..     102     212 ..      90     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0073
                                      EEEEE-TT-HHHH CS
                     Thioredoxin_4 17 vieyedlrCphCa 29
                                      +++y+d+ Cp C 
  gi|313125759|ref|YP_004036029.1| 13 ITVYSDYVCPFCY 25
                                      899*********6 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 4.2e-09
                                       TTTHHHHHHHTT--T.THHHHHHHHHHHHTHHHHTTS-........HHHHH.....HHHHHTS-------HHHHHHH CS
                     Thioredoxin_4  62 eslkaamaarcagee.speaflaikallysqqeewaes........lkelaaealdkdekfeacleeekldalveae 129
                                        sl a ma+  +++  + e +l+++ +++++   w+          l +la++a+    ++ ++l+++ l+++v a+
  gi|313125759|ref|YP_004036029.1| 102 DSLPAQMASYYVKQHyDYETWLDFDVAIFDA--LWQDGadigdeelLVKLAEDAGVVGDEIRSALDDDALREEVRAQ 176
                                       4677777777666664478888888887766..333331133333333355667777889999************** PP

                                       HHHHHHHT--SS-EEEETTEEE-TT--HHHHHHHHT CS
                     Thioredoxin_4 130 skeakkagiestPtfiingekveepqtyeelkalid 165
                                        +ea ++g++++Ptf  +g    ++ ++e l++l++
  gi|313125759|ref|YP_004036029.1| 177 FTEAHQQGVTGVPTFAYDGYGARGAVPPEHLERLVE 212
                                       ********************************9987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.017        99       8      37 ..      12      41 ..       7      94 .. 0.68
   2 ?    9.5   0.0   0.00022       1.3      52     108 ..     159     210 ..     110     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.017
                     Thioredoxin_2  8 vlvvftdpdCpyCkklkkelkelddvtvrv 37
                                       ++v++d  Cp+C + ++ l+ +++ ++  
  gi|313125759|ref|YP_004036029.1| 12 QITVYSDYVCPFCYLGRESLRRYQSTREDE 41
                                      57899999*****99888888886665554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00022
                     Thioredoxin_2  52 aiwcakekkkafkd.ieenvelarkygvrgtPtivfldgkeivarlpGyvpaeeleal 108
                                       +i  a +   a+++ + +++  a++ gv+g+Pt+ +          +G+vp+e le l
  gi|313125759|ref|YP_004036029.1| 159 EIRSALDD-DALREeVRAQFTEAHQQGVTGVPTFAYDGYG-----ARGAVPPEHLERL 210
                                       44444444.24444677888889999*******9875554.....89******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1427.70
//
Query:       gi|313125760|ref|YP_004036030.1|  [L=311]
Description: hypothetical protein Hbor_09910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-26   92.4   0.0    1.5e-25   89.8   0.0    1.9  1  adh_short        short chain dehydrogenase
    3.3e-13   49.7   0.2    4.6e-13   49.3   0.2    1.2  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    4.4e-07   30.0   0.2    1.2e-06   28.6   0.1    1.6  2  KR               KR domain
    0.00012   21.6   0.2    0.00026   20.5   0.2    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.017   15.1   1.7      0.022   14.6   1.7    1.4  1  NAD_binding_10   NAD(P)H-binding
      0.063   13.3   0.0       0.12   12.5   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.082   12.0   0.1       0.11   11.5   0.1    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
       0.99    9.8   5.2        3.6    8.0   5.2    2.1  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0   6.7e-29   1.5e-25       1     189 [.      16     220 ..      16     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 6.7e-29
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHH CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkkl 75 
                                       k+v+vtGa sG+G++  k+la++Ga+vv++ rs+e+ +e+a  ++++   a+++ +++D++d ++v+++ e+  + +
  gi|313125760|ref|YP_004036030.1|  16 KTVVVTGANSGLGYEATKALAAKGAHVVMAVRSPERGREAAHAVQDAvaDADLTLAKLDLADLDSVRRFSEWFHDTF 92 
                                       79********************************************9988899************************ PP

                                       SSESEEEE---SS--SSGGGCSHHH.HHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB........ CS
                         adh_short  76 gkldvLvnNAGitgsgpfselseee.wervievNltgvflltravlpaml.kqssGrIvnvsSvagkvp........ 142
                                       ++l+vL nNAG+    ++ + + e+ +e  + vN  g f lt ++l+ +   + + r+v+ sS + +++        
  gi|313125760|ref|YP_004036030.1|  93 DELHVLANNAGV---MAIPRRETEQgFEMQFGVNHLGHFALTGLLLDRLReTEAETRVVTQSSGIHQNGemdfsdpm 166
                                       ************...34444555555**********************9988899********86444311122222 PP

                                       ....-TTBHHHHHHHHHHHHHHHHHHHHHGGGT...EEEEEEEESSBSSHHHHH CS
                         adh_short 143 ....vagvaaYsAsKaavagltrslakelaptg...irvnavaPGlvdTdmake 189
                                           +  +aaY+ sK a   ++ +l++ l++ g   +  ++++PG+ +T+++++
  gi|313125760|ref|YP_004036030.1| 167 aehsYDKWAAYAQSKLANLLFAYELQRRLERVGeggVLSVGCHPGYAATNLQRR 220
                                       22227789********************99988888*************99875 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.2     2e-16   4.6e-13       1     132 [.      22     156 ..      22     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2e-16
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v..lecDVtdeeqvealveevvekfgklDil 73 
                                       Ga sg+G+++ kala++Ga+vv++ ++ e+ +++++++++++  + +   ++D +d ++v+++ e   ++f++l++l
  gi|313125760|ref|YP_004036030.1|  22 GANSGLGYEATKALAAKGAHVVMAVRSPERgREAAHAVQDAVADAdLtlAKLDLADLDSVRRFSEWFHDTFDELHVL 98 
                                       899*************************998999999999887444446**************************** PP

                                       EE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC...CEEEEEEEGGGT CS
                      adh_short_C2  74 vnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg...gsivnlssvgae 132
                                        nnag++     p    ++++f+  + vn  + f+l+  +l  ++e+    ++v+ ss   +
  gi|313125760|ref|YP_004036030.1|  99 ANNAGVMAI---P-RRETEQGFEMQFGVNHLGHFALTGLLLDRLRETeaeTRVVTQSSGIHQ 156
                                       *******98...3.456899*********************977666576778888775544 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   5.4e-10   1.2e-06       2      93 ..      17     106 ..      16     114 .. 0.86
   2 ?   -2.3   0.0       1.5   3.4e+03      91     113 ..     160     182 ..     134     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.4e-10
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78 
                                       t+++tG+  gLG e ++ la+kga h+v+  Rs++  +++++ ++     +a+ +++++D++d d+v++  e ++++
  gi|313125760|ref|YP_004036030.1|  17 TVVVTGANSGLGYEATKALAAKGA-HVVMAVRSPERGREAAHAVQDAV-ADADLTLAKLDLADLDSVRRFSEWFHDT 91 
                                       689********************8.67888899665555555555443.489************************* PP

                                       SS---EEEE------ CS
                                KR  79 eppikGvihaAgvlr 93 
                                       +++++   + Agv++
  gi|313125760|ref|YP_004036030.1|  92 FDELHVLANNAGVMA 106
                                       *******99999975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                                       ------TTT--HHHHHHHHTTTT CS
                                KR  91 vlrdklleemtaedleqvlapKv 113
                                       +   ++++e++ +++++  ++K+
  gi|313125760|ref|YP_004036030.1| 160 MDFSDPMAEHSYDKWAAYAQSKL 182
                                       33356778888888888888886 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   1.2e-07   0.00026       1     150 [.      18     185 ..      18     196 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHH..T-SE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkee..qpda 67 
                                       ++VtGa+  +G   +kal++kg +v+   r ++++++a+++          +l +ldl d ++++r+ + +   +d+
  gi|313125760|ref|YP_004036030.1|  18 VVVTGANSGLGYEATKALAAKGAHVVMAVRSPERGREAAHAVQdavadadlTLAKLDLADLDSVRRFSEWFhdTFDE 94 
                                       68********************998888888777777766666899****************999997654447788 PP

                                       EEE--S---HHHHHHSHHH.....HHHHHTHHHHHHHHHHH....HHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS- CS
                         Epimerase  68 vihlAavggvaassedpad.....fieknlqgtlnlleaar....kagvkrllflsSsevYGkdaeqpkeettltgp 135
                                          lA  +gv+a   + ++      +  n  g   l   +     +++++  +   Ss +  +++    ++ + + +
  gi|313125760|ref|YP_004036030.1|  95 LHVLANNAGVMAIPRRETEqgfemQFGVNHLGHFALTGLLLdrlrETEAETRVVTQSSGIHQNGEMD-FSDPMAEHS 170
                                       7777777776653333322110112234444443333332222225555544444444444444442.455555555 PP

                                       ---SSHHHHHHHHHH CS
                         Epimerase 136 lkpnspYaaaKlage 150
                                       +    +Ya +Kla  
  gi|313125760|ref|YP_004036030.1| 171 YDKWAAYAQSKLANL 185
                                       677777777777765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.7   9.8e-06     0.022       1      55 [.      22      82 ..      22     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-06
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH.......CTTTCEEEE--TT-CCHHH CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaele.......aeeglevvegdvtdvedla 55
                                      GA+ + G +++k l+a+g  +v++ vR+pe+  e +       a++ l++ ++d+ d ++++
  gi|313125760|ref|YP_004036030.1| 22 GANSGLGYEATKALAAKG-AHVVMAVRSPERGREAAhavqdavADADLTLAKLDLADLDSVR 82
                                      9*************9995.99*******9988744311112224567777777777777766 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.2e-05      0.12       7      66 ..      10      68 ..       5      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                                      HS..TT-EEEEES-SH.HHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEG CS
                      Shikimate_DH  7 leslkekkvlliGaGe.maelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkl 66
                                      ++++++k+v++ Ga   ++ +++k+L+akg++ vv a R+ er +e a+ ++++ +   +l
  gi|313125760|ref|YP_004036030.1| 10 VPDCSGKTVVVTGANSgLGYEATKALAAKGAH-VVMAVRSPERGREAAHAVQDA-VADADL 68
                                      568899*******9653899***********9.9999***********999776.443334 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.1e-05      0.11       2      44 ..      17      82 ..      16     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.1e-05
                                      EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.......................T--TTSHHHHH CS
                     RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeglevlaltre.......................eldltdaeava 44
                                      +++vtGan  lG+e +k+la++g++v+   r+                       +ldl+d ++v+
  gi|313125760|ref|YP_004036030.1| 17 TVVVTGANSGLGYEATKALAAKGAHVVMAVRSpergreaahavqdavadadltlaKLDLADLDSVR 82
                                      589********************9988765655566666666666666666666555555555555 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.2    0.0016       3.6       9      86 ..      30     104 ..      28     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                   Glyco_trans_4_4   9 elaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhahsptag 85 
                                       e  +aLaa G++V++ +++p +g++++++ +  v   ++  +   ladl+++r++ +++   +  +d +h+    ag
  gi|313125760|ref|YP_004036030.1|  30 EATKALAAKGAHVVMAVRSPERGREAAHAVQDAVADADLTLAKLDLADLDSVRRFSEWF---HDTFDELHVLANNAG 103
                                       5679****************999987665555555555443333599***********9...888888887665444 PP

                   Glyco_trans_4_4  86 l 86 
                                        
  gi|313125760|ref|YP_004036030.1| 104 V 104
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1912.69
//
Query:       gi|313125761|ref|YP_004036031.1|  [L=295]
Description: asparaginase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-61  205.7  12.2    9.3e-61  205.5  12.2    1.0  1  Asparaginase_2  Asparaginase


Domain annotation for each model (and alignments):
>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.5  12.2   5.2e-65   9.3e-61       3     295 ..       3     293 ..       1     295 [] 0.90

  Alignments for each domain:
  == domain 1  score: 205.5 bits;  conditional E-value: 5.2e-65
                                       EEEEEEEESE-G-HHHHHHHHHCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCTCCCSSSTTSS-BTTS---EEEE CS
                    Asparaginase_2   3 lvihGGAgsilktkereeavrkalkealeagykvLkeggsaldaVeaavrllEddplfnaGkGsvltedgeveldAs 79 
                                       +++hGGAg +++   + + ++++++ea+e+g+    + ++ +daVeaa+r++E dp fnaG G+++++dg+v+ dA 
  gi|313125761|ref|YP_004036031.1|   3 VIVHGGAGGVPD---EPDPRQQTVDEAAETGA----ARETPIDAVEAAIRVMESDPAFNAGVGGAVQSDGRVRTDAG 72 
                                       89*******999...55667778888888886....5799************************************* PP

                                       EEETTTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHHHHHHTT-----CGGG--HHHHHHHHHHHHCCCH CS
                    Asparaginase_2  80 imdgktlraGaVagvkrvknpislArlvmeksehvlLvgegAeefareqglelvdeesllteerlkelekakkekae 156
                                       +m  ++  +GaVag+  v++++s+Ar+vme+++h++ +g+ A + a++ g+    + +l t e+++++++a   + +
  gi|313125761|ref|YP_004036031.1|  73 VMTSDRE-TGAVAGMDGVEHAVSVARVVMEETPHIFVAGDPAVDVAADFGI--ETDVNLFTPETRERWNDATPPEGT 146
                                       **98765.9******************************************..6788999***********999988 PP

                                       S..B-S-BS-TTT............TT---EEEEEE-TTS-EEEEEEE--STTB-TTEE-STTSTTTSEEEETTTEE CS
                    Asparaginase_2 157 kkeaknvsekelk............aklgTvGaValDsegnlAaaTSTgGltnklvGRvGDspiiGaGtYAdnkvgA 221
                                       ++      +++              +++ TvGaVa+D +  +AaaTSTgG  + l+GRvGD p +G+G YA   +gA
  gi|313125761|ref|YP_004036031.1| 147 SQDHLAWLDDKFGqssatasndadlSDHDTVGAVAFDGR-DFAAATSTGGRWFALAGRVGDVPQVGSGFYA-APAGA 221
                                       77666655554446678877777777777********87.69*****************************.999** PP

                                       EEEEE-HHHHCCTTHHHHHHHHHHTTT--HHHHHHHHHHCHHHHTTT-EEEEEEETTS-EEEEECSCCCEEEEE CS
                    Asparaginase_2 222 vsaTGkGeeiirellaadivalmeykglsleeAaekvieeklkrvkgsgGviavdkkGevaaefnsegmlraya 295
                                       +saTG Ge+i +++l+++ v ++e+ g+++++Aae +iee ++ ++  +Gvi+ d +G v+ + n+egm +++a
  gi|313125761|ref|YP_004036031.1| 222 ASATGAGEDIAKTTLTRRAVRHLER-GEDAQSAAELAIEEFAELTGSGAGVIVADDEG-VGSAYNTEGMQTGVA 293
                                       *************************.**************999988899********9.678899999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1911.26
//
Query:       gi|313125762|ref|YP_004036032.1|  [L=420]
Description: isocitrate dehydrogenase (NADp) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     3e-109  365.3   0.1   5.2e-109  364.6   0.1    1.3  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.6   0.1  2.9e-113  5.2e-109       2     348 .]      33     412 ..      32     412 .. 0.98

  Alignments for each domain:
  == domain 1  score: 364.6 bits;  conditional E-value: 2.9e-113
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkeke 78 
                                       i+++ gdgiG +v +aa kvl+aa+e+ g+++e+  v++G++a+++++e lpe+t++aik+ +v+++g+++tp++++
  gi|313125762|ref|YP_004036032.1|  33 IPIIHGDGIGTDVGPAAQKVLDAAAEATGRSIEWLRVYAGESARKKYDENLPEDTVQAIKDHRVAIKGPLTTPVGAG 109
                                       899************************************************************************** PP

                                       SSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET............ CS
                            Iso_dh  79 vrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg............ 143
                                        r+ n  +aLrk+ldl+an+rp   +   +v+sp+k+  ++ +d+v +Re+t+++Y+g+e e+ +            
  gi|313125762|ref|YP_004036032.1| 110 FRSLN--VALRKKLDLYANVRPTYHL--DGVPSPVKN--PSAMDMVTFRENTEDVYAGIEWEAGTdevqqvkefvee 180
                                       *****..****************999..8*******8..899*******************999999********** PP

                                       ......TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC....... CS
                            Iso_dh 144 ......sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee....... 206
                                             +i ++ v++++k+++e +++r++r a+e+A+++++++vtlv+K+n++k++e ++r++ +e+a+e       
  gi|313125762|ref|YP_004036032.1| 181 emghddVIHDGPVGIGIKPITEFGTKRLVREAIEYAIENDRDSVTLVHKGNIMKFTEgAFRDWGYELAAEefgdvti 257
                                       ****9766899**********************************************************9******* PP

                                       .............TTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-E CS
                            Iso_dh 207 .............eypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkva 270
                                                       +i ++++++D++++ql+++ + +dVi+t+Nl+GD++SD+a a++G+lG++p+a+ g ++++
  gi|313125762|ref|YP_004036032.1| 258 tedelweeydgekPEDKIVVKDRIADNMLQQLLTRTADYDVIATMNLNGDYMSDAAGAQIGGLGIAPGANFG-EGLC 333
                                       *********99766678*******************************************************.68** PP

                                       EEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTS..TCCCHHHHHH CS
                            Iso_dh 271 ifEavHGsapdiagkdkaNpiavilSaalmLryslgleeaAdkiekAvekvleagivTkDlagea..akevstsefg 345
                                       ++E+vHGsap++ag dk+Np+a+ilS  lm +y +g+++a + i +Avek++ +g vT+Dl+++    +++ tsef 
  gi|313125762|ref|YP_004036032.1| 334 LAEPVHGSAPKYAGEDKVNPTAMILSGRLMFEY-MGWKDAGKLIRDAVEKTISEGDVTYDLERQIegGNKLATSEFA 409
                                       *********************************.*****************************9888899******9 PP

                                       HHH CS
                            Iso_dh 346 dav 348
                                       +++
  gi|313125762|ref|YP_004036032.1| 410 EKI 412
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2391.93
//
Query:       gi|313125763|ref|YP_004036033.1|  [L=128]
Description: lactoylglutathione lyase-like lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-10   39.9   0.2    5.3e-10   39.5   0.2    1.1  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    2.3e-07   31.1   1.6    1.8e-06   28.1   1.6    1.9  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
       0.03   14.4   0.6       0.13   12.3   0.6    1.8  1  Glyoxalase_3  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.2   8.9e-14   5.3e-10       1     109 []       3     113 ..       3     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 8.9e-14
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT.-THHHTS-EEEEEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp.eflaehgeglhhlaywv 76 
                                       +++++   Dl+ a++++++ lG    +ry+ ++++ ++++  +    v +e  +p+e++   ++++ +gl+hla++ 
  gi|313125763|ref|YP_004036033.1|   3 HHVELYAADLDSAIEFYEWFLGELGYERYQRWESGQSWKLGPTYL--VVVE--APDEYRdNDFHRRTPGLNHLAFHA 75 
                                       89********************999999*9999998777766655..7888..8888776666899**********9 PP

                                       S...-HHHHHHHHCTTTEEEE..EEEE-GGGTT-EEEE CS
                      Glyoxalase_4  77 d...dldaavarleeqGfevv..qkgvragaagrrfay 109
                                       +    +d+  ++l+e+G++++  +++++ag+++++++y
  gi|313125763|ref|YP_004036033.1|  76 EsraHVDELTRQLRERGVTILyeDAHPYAGGDDHYAVY 113
                                       85557***************955556777777777666 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   1.6   3.1e-10   1.8e-06       2     127 ..       2     123 ..       1     124 [. 0.81

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.1e-10
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC...TSE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee...tvh 75 
                                       ++hv l+++dl+ +++FY+  LG    +++       +  +     g + + +v ++ +  +  ++        + +
  gi|313125763|ref|YP_004036033.1|   2 LHHVELYAADLDSAIEFYEWFLGELGYERYQ-----RWESGQSWKLGPTYLVVVEAPDEYRDNDFH----RrtpGLN 69 
                                       8*******************98855555555.....677888888899999999999998888888....3446899 PP

                                       EEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHC...TEEEEEEEEETTSEEEE CS
                        Glyoxalase  76 hvafialdvedvgkaldrlkeagvkvvaepgrhyf...galysfyfrDpdGille 127
                                       h+af+a +   v++  ++l+e+gv +  e + h++   ++ y +yf+ p   +le
  gi|313125763|ref|YP_004036033.1|  70 HLAFHAESRAHVDELTRQLRERGVTILYE-DAHPYaggDDHYAVYFEGPERLKLE 123
                                       **************************999.5555411134556699999998888 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   2.2e-05      0.13       1     102 [.       2      98 ..       2     120 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                      Glyoxalase_3   1 lDHvvlavpdleeaaarfar...rlGftvtpggehpglgtaNalvmfgdgYlEllavdpeapaperprlfgldrlak 74 
                                       l+Hv l++ dl+ a++ ++    +lG +  ++        + + + +g +Yl +++  +e + ++++r        +
  gi|313125763|ref|YP_004036033.1|   2 LHHVELYAADLDSAIEFYEWflgELGYERYQRW------ESGQSWKLGPTYLVVVEAPDEYRDNDFHR--------R 64 
                                       79999********99988442223333322222......3446899******9999877777665654........4 PP

                      Glyoxalase_3  75 geglhtlalrt...ddidataarlraaGvd...e 102
                                       ++gl +la++    +++d++ ++lr++Gv+   e
  gi|313125763|ref|YP_004036033.1|  65 TPGLNHLAFHAesrAHVDELTRQLRERGVTilyE 98 
                                       6********8844456799999******986553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 806.52
//
Query:       gi|313125764|ref|YP_004036034.1|  [L=176]
Description: hypothetical protein Hbor_09950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0028   17.9   0.4     0.0058   16.9   0.4    1.6  1  DUF1922         Domain of unknown function (DUF1922)
     0.0042   16.6   0.1     0.0048   16.4   0.1    1.1  1  Peptidase_S11   D-alanyl-D-alanine carboxypeptidase
  ------ inclusion threshold ------
      0.013   14.9   0.5      0.048   13.1   0.2    1.8  2  DUF99           Protein of unknown function DUF99
      0.042   14.6   0.8      0.074   13.8   0.3    1.8  2  zf-3CxxC_2      Zinc-binding domain
      0.044   13.3   0.6        0.2   11.2   0.6    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.068   13.0   0.1       0.11   12.4   0.1    1.3  1  DUF728          Protein of unknown function (DUF728)
      0.069   13.2   0.0       0.26   11.3   0.0    2.0  1  EutK_C          Ethanolamine utilization protein EutK C-termi
      0.075   13.1   0.9       0.14   12.2   0.4    1.7  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.078   13.1   0.7       0.12   12.5   0.7    1.4  1  Jiv90           Cleavage inducing molecular chaperone
        0.1   12.5   0.7        0.3   11.0   0.7    1.9  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.13   12.6   0.0       0.21   11.9   0.0    1.4  1  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.18   11.7   0.1       0.18   11.7   0.1    1.9  3  TrmB            Sugar-specific transcriptional regulator TrmB
       0.19   12.4   1.9        1.3    9.8   0.4    2.2  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
       0.21   11.6   0.0        1.6    8.8   0.0    2.0  2  TBPIP           TBPIP/Hop2 winged helix domain
       0.22   11.6   2.8        0.6   10.3   2.8    1.8  1  Zn-ribbon_8     Zinc ribbon domain
       0.26   10.8   1.7        5.5    6.5   0.3    2.3  2  zf-ribbon_3     zinc-ribbon domain
       0.41   11.0   2.4        8.4    6.8   0.1    2.2  2  DUF5403         Family of unknown function (DUF5403)
       0.55   10.9   5.2       0.27   11.9   1.9    2.0  2  FYDLN_acid      Protein of unknown function (FYDLN_acid)
        1.4    8.8   4.9        2.5    7.9   0.8    2.3  2  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   6.1e-06    0.0058       2      61 ..       3      66 ..       2      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.1e-06
                                      EEEEET.TS--..EEEETT-SEEEET.TTEEEE--SSS-BS--SSHHHHHHHHHHHSS---S-T CS
                           DUF1922  2 lifRCd.CGRv..lYakegaktrkCv.CGktikvkerrilkkaedaeeAselVrklqeekyGlt 61
                                       +  C+ CG +  l    ++kt +C+ CG+t + k+ r + ++ed+e+A ++  +l   k+G +
  gi|313125764|ref|YP_004036034.1|  3 AVVGCSeCGSMwlLTDPRQSKTANCPrCGRTHQTKKLRKFLETEDREAARQARAALLAKKHGDS 66
                                      566687799763255567889999*77***********************99999999999965 PP

>> Peptidase_S11  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   5.1e-06    0.0048     110     172 ..      56     122 ..      32     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHSSHHHH.....HHHHHHHHHHTT-TT-B-SSSSSTSHTTCBB-HHHHHHHHHHHHHHHHH CS
                     Peptidase_S11 110 valAekiaGsekaF.....vkmMnkkakelGlkntkfvnptGLdnenqvssArdlailakallkdlpe 172
                                       +al  k  G  +aF     +  M++ ++e G+ ++++ ++ GLd+++ v sA + a+ ++ +  + ++
  gi|313125764|ref|YP_004036034.1|  56 AALLAKKHGDSEAFaktahISEMESLVEESGIDDAEYLEASGLDADE-VASAGEQAMQGQTSSSNRLD 122
                                       5555555555555522222778*************************.88888888877766655444 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.4   3.8e+02     110     157 ..      56     105 ..      35     112 .. 0.59
   2 ?   13.1   0.2     5e-05     0.048     117     170 ..     115     168 ..      99     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.4
                                       HCCT.TSTTHH...HHHHHHHHC.---EEETT....EEEEEESS-HHHHHH CS
                             DUF99 110 kaLrkhfpdee...eRlelieklgerieevektgeelyvravGieleeaak 157
                                       +aL  +  +++    + ++i+++ e+  e +  +   y++a G++++e+a+
  gi|313125764|ref|YP_004036034.1|  56 AALLAKKHGDSeafAKTAHISEM-ESLVEESGIDDAEYLEASGLDADEVAS 105
                                       55554444444011334444444.333333334666788888888888775 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5e-05
                                       TTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHHHHHHHHC-SSSSS-H CS
                             DUF99 117 pdeeeRlelieklgerieevektgeelyvravGieleeaaklvrkltlegriPE 170
                                         +++Rl++++++ +++ + ++++   y + +G+  e a+++++klt++g++ E
  gi|313125764|ref|YP_004036034.1| 115 TSSSNRLDVVREALRKEDRPTEEEVVAYAEEHGVPGEAARNVLEKLTRRGEVSE 168
                                       34589********777777777777789**********************9988 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   7.9e-05     0.074       9      55 ..       6      52 ..       1      77 [. 0.82
   2 ?   -2.2   0.0       7.6   7.2e+03      30      52 ..     116     138 ..     105     147 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.9e-05
                        zf-3CxxC_2  9 kCekCgkeWsSanafaneaQeCkkCkekvepyklrekdkkkgaakke 55
                                       C++Cg  W  +     ++ +C +C+ + +++klr+  ++++++ ++
  gi|313125764|ref|YP_004036034.1|  6 GCSECGSMWLLTDPRQSKTANCPRCGRTHQTKKLRKFLETEDREAAR 52
                                      5**********************************966666554443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.6
                        zf-3CxxC_2  30 CkkCkekvepyklrekdkkkgaa 52 
                                        +  + +v+ + lr++d+  +++
  gi|313125764|ref|YP_004036034.1| 116 SSSNRLDVVREALRKEDRPTEEE 138
                                       44455566666666666555544 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   0.00022       0.2       3      26 ..       7      31 ..       5      33 .. 0.90
   2 ?    5.3   0.2     0.015        14       3      11 ..      27      35 ..      25      49 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                      ETTTTCEECHEETSTTCE.EESSSS CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergel.vCtdCG 26
                                      C +Cgs  l++Dp +  +  C++CG
  gi|313125764|ref|YP_004036034.1|  7 CSECGSMWLLTDPRQSKTaNCPRCG 31
                                      *****966****9999999*****9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                                      ETTTTCEEC CS
                      TF_Zn_Ribbon  3 CPnCgstnl 11
                                      CP Cg t++
  gi|313125764|ref|YP_004036034.1| 27 CPRCGRTHQ 35
                                      *****9985 PP

>> DUF728  Protein of unknown function (DUF728)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00011      0.11      63     106 ..      26      76 ..       4      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            DUF728  63 nc..cgrshl.ekcrkrvetrnreiwkqirrn....qaenmsatakkshns 106
                                       nc  cgr+h  +k rk +et +re  +q r      +  +  a ak +h s
  gi|313125764|ref|YP_004036034.1|  26 NCprCGRTHQtKKLRKFLETEDREAARQARAAllakKHGDSEAFAKTAHIS 76 
                                       55559**9962679**************99752111333445666666655 PP

>> EutK_C  Ethanolamine utilization protein EutK C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.26      26      55 .]     145     174 ..     135     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                            EutK_C  26 hfaWPLekarqvLeqLfsdGaLrkrssrYr 55 
                                         + P e ar+vLe+L   G +     rYr
  gi|313125764|ref|YP_004036034.1| 145 EHGVPGEAARNVLEKLTRRGEVSESRGRYR 174
                                       468899***************999999998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00015      0.14      69      96 ..       3      34 ..       1      43 [. 0.78
   2 ?   -2.0   0.0       3.7   3.5e+03      44      67 ..     103     126 ..      94     160 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      -EEEETTTS-EEECHH..H..HHS-TTTSSS- CS
                              HypA 69 vkvrCreCgkefelee..k..alrCpkCgsad 96
                                      ++v C+eCg+ + l++  +  +++Cp+Cg+++
  gi|313125764|ref|YP_004036034.1|  3 AVVGCSECGSMWLLTDprQskTANCPRCGRTH 34
                                      5688********977655245669*****975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                                       HHHHHHHHHCC.TTTT-EEEEEEE CS
                              HypA  44 LefafellaegtvlegaeLeieev 67 
                                       ++ a e + +g++ ++ +L++ ++
  gi|313125764|ref|YP_004036034.1| 103 VASAGEQAMQGQTSSSNRLDVVRE 126
                                       555555555555555555555444 PP

>> Jiv90  Cleavage inducing molecular chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   0.00013      0.12       5      47 ..       5      45 ..       2      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                             Jiv90  5 iaCtkCgkkHkriaversksaaRfckeCkelhsakegDiWaes 47
                                      + C++Cg+  +++ ++ ++s++  c +C ++h++k+   + e+
  gi|313125764|ref|YP_004036034.1|  5 VGCSECGS--MWLLTDPRQSKTANCPRCGRTHQTKKLRKFLET 45
                                      67999997..699***99****************987666655 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   0.00032       0.3      31      57 ..       7      35 ..       2      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                    OrfB_Zn_ribbon 31 CseCgsknke..alsgrtfkCpnCgfead 57
                                      CseCgs      +++++t +Cp+Cg +++
  gi|313125764|ref|YP_004036034.1|  7 CSECGSMWLLtdPRQSKTANCPRCGRTHQ 35
                                      9999998655568999999*****98875 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.21       2      32 ..      24      54 ..      23      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                           zf-Di19  2 sftCPyCgkeltvkeLveHvedeHrveskev 32
                                      + +CP Cg+++++k+L + +e+e r++++++
  gi|313125764|ref|YP_004036034.1| 24 TANCPRCGRTHQTKKLRKFLETEDREAARQA 54
                                      578*******************999888775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.7   8.2e+03      25      35 ..      78      88 ..      75      91 .. 0.68
   2 ?   -3.4   0.0       9.6   9.1e+03      19      30 ..      94     105 ..      93     106 .. 0.65
   3 ?   11.7   0.1   0.00019      0.18      29      60 ..     143     174 ..     127     176 .] 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.7
                                      HCHHCCCTTSS CS
                              TrmB 25 adeiaeelgvp 35
                                      ++ + ee+g++
  gi|313125764|ref|YP_004036034.1| 78 MESLVEESGID 88
                                      56777888876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.6
                                       HHCCCHHCHHCC CS
                              TrmB  19 klgpatadeiae 30 
                                       +   ++ade+a+
  gi|313125764|ref|YP_004036034.1|  94 EASGLDADEVAS 105
                                       455677888876 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00019
                                       CCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  29 aeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                       aee gvp   + +vL++L ++G V  ++gr++
  gi|313125764|ref|YP_004036034.1| 143 AEEHGVPGEAARNVLEKLTRRGEVSESRGRYR 174
                                       8999***********************99987 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.46   4.3e+02       3      11 ..       5      13 ..       3      21 .. 0.83
   2 ?    9.8   0.4    0.0014       1.3       4      17 ..      26      39 ..      23      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.46
                           zf-ISL3  3 hrCPnCgsk 11
                                        C +Cgs 
  gi|313125764|ref|YP_004036034.1|  5 VGCSECGSM 13
                                      67*****85 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                           zf-ISL3  4 rCPnCgsktvvkhg 17
                                       CP+Cg+++++k+ 
  gi|313125764|ref|YP_004036034.1| 26 NCPRCGRTHQTKKL 39
                                      6*******999985 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.67   6.3e+02      29      52 ..      68      91 ..      57      92 .. 0.81
   2 ?    8.8   0.0    0.0017       1.6       4      48 ..     122     166 ..     119     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.67
                             TBPIP 29 klgKtavqkaLdeLvdegkiieKe 52
                                       + Kta    +++Lv+e  i   e
  gi|313125764|ref|YP_004036034.1| 68 AFAKTAHISEMESLVEESGIDDAE 91
                                      5779999999*****998776655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                             TBPIP   4 elvleylqeqnrPfsvqdvvanlqk.klgKtavqkaLdeLvdegki 48 
                                       ++v e l+++ rP+  ++vva+ ++ ++ ++a+  +L++L   g +
  gi|313125764|ref|YP_004036034.1| 122 DVVREALRKEDRPTE-EEVVAYAEEhGVPGEAARNVLEKLTRRGEV 166
                                       789999*******97.5677777776**************999876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.8   0.00064       0.6       8      35 ..       7      34 ..       1      39 [. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00064
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs.e 35
                                      C eCg     l    + ++ta CP+Cg  +
  gi|313125764|ref|YP_004036034.1|  7 CSECG-SMWLLTDP-RQSKTAnCPRCGRtH 34
                                      99999.44444432.4457888*****853 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.062        58       5      10 ..       7      12 ..       4      19 .. 0.83
   2 ?    6.5   0.3    0.0058       5.5       2       9 ..      24      31 ..      23      37 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.062
                       zf-ribbon_3  5 CPnCGa 10
                                      C++CG+
  gi|313125764|ref|YP_004036034.1|  7 CSECGS 12
                                      999997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0058
                       zf-ribbon_3  2 tvrCPnCG 9 
                                      t +CP+CG
  gi|313125764|ref|YP_004036034.1| 24 TANCPRCG 31
                                      67899999 PP

>> DUF5403  Family of unknown function (DUF5403)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3      0.06        57      27      54 ..      50      77 ..      33      88 .. 0.70
   2 ?    6.8   0.1    0.0089       8.4      13      48 ..     119     154 ..     109     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.06
                           DUF5403 27 erraarvrAvvagHrdtGalaasievet 54
                                      + r+ar+   +++H d+ a+a+  ++ +
  gi|313125764|ref|YP_004036034.1| 50 AARQARAALLAKKHGDSEAFAKTAHISE 77
                                      3345566666789******999888865 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0089
                           DUF5403  13 ahlpgvkaavaeelerraarvrAvvagHrdtGalaa 48 
                                        +l+ v++a+++e + +++ v A ++ H   G+ a 
  gi|313125764|ref|YP_004036034.1| 119 NRLDVVREALRKEDRPTEEEVVAYAEEHGVPGEAAR 154
                                       57999***********************99886554 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.9   0.00029      0.27      27     101 ..      25     104 ..       5     112 .. 0.60
   2 ?   -0.2   0.3       1.7   1.6e+03      67      82 ..     122     137 ..     100     159 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                        FYDLN_acid  27 ivcpkcgeefepeev.....lksraaaaeaeeakkkkeeeedeedeeeeedvsdedadeeeee.dddddvdleeddd 97 
                                       + cp cg + + +++     ++  + aa++++a+  ++++ d+e+ +++ + s+ +   ee+  dd +  + ++ d+
  gi|313125764|ref|YP_004036034.1|  25 ANCPRCGRTHQTKKLrkfleTE-DREAARQARAALLAKKHGDSEAFAKTAHISEMESLVEESGiDDAEYLEASGLDA 100
                                       68***********997776333.333333333344455555555555566666655555554423333344455555 PP

                        FYDLN_acid  98 ddvf 101
                                       d+v+
  gi|313125764|ref|YP_004036034.1| 101 DEVA 104
                                       5555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.7
                        FYDLN_acid  67 eeeeedvsdedadeee 82 
                                       ++  e+ ++ed   ee
  gi|313125764|ref|YP_004036034.1| 122 DVVREALRKEDRPTEE 137
                                       2222222222222222 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.14   1.3e+02      16      20 ..       7      11 ..       4      13 .. 0.70
   2 ?    7.9   0.8    0.0027       2.5       2      10 ..      27      35 ..      26      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.14
                     zinc_ribbon_2 16 CpyCG 20
                                      C++CG
  gi|313125764|ref|YP_004036034.1|  7 CSECG 11
                                      56665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0027
                     zinc_ribbon_2  2 CpnCGaelq 10
                                      Cp+CG+++q
  gi|313125764|ref|YP_004036034.1| 27 CPRCGRTHQ 35
                                      ******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1062.39
//
Query:       gi|313125765|ref|YP_004036035.1|  [L=95]
Description: hypothetical protein Hbor_09960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 548.20
//
Query:       gi|313125766|ref|YP_004036036.1|  [L=37]
Description: hypothetical protein Hbor_09970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       146  (0.00814323); expected 358.6 (0.02)
Passed bias filter:                      133  (0.00741815); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.32s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 235.32
//
Query:       gi|313125767|ref|YP_004036037.1|  [L=121]
Description: hypothetical protein Hbor_09980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.2    7.4  11.1        5.1    7.4   1.7    3.1  3  Ost5      Oligosaccharyltransferase subunit 5


Domain annotation for each model (and alignments):
>> Ost5  Oligosaccharyltransferase subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.7   0.00028       5.1      47      66 ..      11      30 ..       2      32 .. 0.86
   2 ?    0.1   0.4     0.055   9.8e+02      43      43 ..      61      61 ..      30      86 .. 0.51
   3 ?    5.2   0.1    0.0015        26      16      39 ..      94     117 ..      88     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00028
                              Ost5 47 elllalvASlflGfGvvfll 66
                                       ++ alvA++f+G Gvv+ll
  gi|313125767|ref|YP_004036037.1| 11 VMVRALVAACFVGGGVVALL 30
                                      67789*************96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.055
                              Ost5 43 s 43
                                       
  gi|313125767|ref|YP_004036037.1| 61 G 61
                                      1 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0015
                              Ost5  16 afvllligllltalfflyevtstk 39 
                                       ++vll++g +++ + f +e+t t 
  gi|313125767|ref|YP_004036037.1|  94 GVVLLVVGTVIVVWPFGSEMTGTD 117
                                       79**************99999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 741.93
//
Query:       gi|313125768|ref|YP_004036038.1|  [L=87]
Description: hypothetical protein Hbor_09990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-15   55.6   1.7    4.9e-15   55.3   1.7    1.1  1  DUF2892   Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   1.7   2.8e-19   4.9e-15       1      65 [.       8      75 ..       8      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.8e-19
                           DUF2892  1 MkkNvgtldRilrivvGlvllllallglsggw...gwllglvGavllltgltgfCplyallgintcka 65
                                      M++Nvg  dRilr v+G+ l+++a+ +l  g    + ++gl+G++ll+ ++tgfC+  +l+gi+t+++
  gi|313125768|ref|YP_004036038.1|  8 MRQNVGESDRILRGVLGVWLVAVAVSALRVGRrttAAITGLAGLGLLQNAATGFCGGNRLFGIDTTRS 75
                                      99*****************9999999986555889999***************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 521.56
//
Query:       gi|313125769|ref|YP_004036039.1|  [L=218]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-17   62.7   0.0      3e-17   62.1   0.0    1.3  1  HTH_10       HTH DNA binding domain
  ------ inclusion threshold ------
      0.086   12.1   0.0       0.12   11.6   0.0    1.1  1  Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   3.4e-21     3e-17       1      52 [.     161     212 ..     161     213 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.4e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       L+++q+e++++A++ GY+d+PR++t++++A+e G + +t+sehLr+ae++++
  gi|313125769|ref|YP_004036039.1| 161 LSPRQRETVQAALRVGYYDVPREATTAAVADEVGCATATASEHLRRAERRVL 212
                                       789**********************************************997 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.3e-05      0.12     172     246 ..     124     196 ..     111     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.3e-05
                       Pyr_redox_3 172 gknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeyk 246
                                       g + a+ aA+e v +g +Vt+   g+ + +  +dp  sl+p+ ++ ++++++ + ++v  +a++ ++ ++     
  gi|313125769|ref|YP_004036039.1| 124 GTDAAIQAAVEGVPEGVTVTIDAVGTGRVAA-DDPGRSLSPRQRETVQAALRVGYYDVPREATTAAVADEV-GCA 196
                                       5789*****************9999987776.59****************999999999999888888753.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1441.24
//
Query:       gi|313125770|ref|YP_004036040.1|  [L=408]
Description: 3-hydroxy-3-methylglutaryl-CoA reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.1e-129  430.5   3.9   5.9e-129  430.3   3.9    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.3   3.9  3.3e-133  5.9e-129       2     367 .]      36     408 .]      35     408 .] 0.99

  Alignments for each domain:
  == domain 1  score: 430.3 bits;  conditional E-value: 3.3e-133
                                       HHHHHHHHHHS-HHHHHHHTT----HHHHHHHSSS---------EEEEEEEETTE....EEEEEE---STTHHHHHH CS
                       HMG-CoA_red   2 veeRrklleelteeeleelkeesldeevadkmiEnviGyvqlPlGvagpllingk....eylvPmAteEgslvAsas 74 
                                        ++Rr l+ee+++++l+ ++++++++e+ad +iEn++G+vq+P+Gvagp++i g     e ++P+At+Eg+l As++
  gi|313125770|ref|YP_004036040.1|  36 TAARRLLVEEQSDASLDVVGDYGFPAERADPNIENMVGAVQVPMGVAGPVRIRGGrldgERYLPLATTEGALLASVN 112
                                       5789*************************************************988999****************** PP

                                       HHHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHHCCT-EEEEEEEEE-SSEEE CS
                       HMG-CoA_red  75 rgakainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaestsrggglkdievvlagrlvv 151
                                       rg++++n++gG+++++lk+gmtra+v+++++v +a++l +w+  +++ ++l++aae+t+++g+l d++++++g++v+
  gi|313125770|ref|YP_004036040.1| 113 RGCSVLNDAGGANVRILKSGMTRAPVFRVADVVEAEALVEWV--RDNRDALREAAEETTNHGELLDVTPYVVGNSVH 187
                                       ******************************************..********************************* PP

                                       EEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHH CS
                       HMG-CoA_red 152 lrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekil 228
                                       lr+++dt+DAmG+Nmv++at+aa+el+e+e++ ++l+++++Nlctdkk++aina+egrg+sv++++ti++evve+ l
  gi|313125770|ref|YP_004036040.1| 188 LRFRYDTKDAMGMNMVTIATRAACELVEDETD-ASLVALSGNLCTDKKPAAINAVEGRGRSVTTDVTIPREVVEDRL 263
                                       ******************************99.9******************************************* PP

                                       HHHHHHHH-HHHH....HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTTSEEETTTEEEEEEEEE.-- CS
                       HMG-CoA_red 229 kasaealvdlnra.n.igtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaaleevedgdlygsvtlPsle 303
                                       ++++ea+++ln++ n +g+a++ ++gfnah+aN++aA+flAtGqD a+v+e+++ai++ e   dgdly+s++++sle
  gi|313125770|ref|YP_004036040.1| 264 HTTPEAVAELNTRkNlVGSAKAASLGFNAHVANVVAAMFLATGQDEAQVVEGANAITTAEVQ-DGDLYVSISIASLE 339
                                       *********************************************************99987.888*********** PP

                                       --SBSHHHHH-HHHHHHHHTT---HH........HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                       HMG-CoA_red 304 VGtvGGgtklppqaellkllgvkgak.....nakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                       VGtvGGgtklp+qae l++lgv+g +     na++Lae ia   LA+els+l+ALa+++l ++H +l+r
  gi|313125770|ref|YP_004036040.1| 340 VGTVGGGTKLPTQAEGLDVLGVRGGGdpagsNADALAEAIAVGSLAGELSLLSALASRHLSSAHAELGR 408
                                       ******************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2551.84
//
Query:       gi|313125771|ref|YP_004036041.1|  [L=523]
Description: tim-barrel fold metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-89  301.2  13.6      2e-89  301.2  13.6    1.9  2  Amidohydro_3  Amidohydrolase family
    7.4e-17   61.7   1.8    3.8e-12   46.2   0.2    2.6  2  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
        0.1   12.8   0.2       0.37   10.9   0.2    2.0  1  AIRS_C        AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2     0.031   1.9e+02     439     472 ..       4      35 ..       3      36 .. 0.85
   2 !  301.2  13.6   3.4e-93     2e-89       1     473 []      52     519 ..      52     519 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.031
                      Amidohydro_3 439 dADlvvldadpldvdppelaearvrltvvdGrvv 472
                                        ADlv+ld ++ ++++p+  ++   + v dGr+v
  gi|313125771|ref|YP_004036041.1|   4 AADLVLLDGEIHTLTDPDETYE--AMAVRDGRIV 35 
                                       5**************9976664..7889999998 PP

  == domain 2  score: 301.2 bits;  conditional E-value: 3.4e-93
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagtt............pkgrwivgeG 65 
                                       e+iD+ G +vlPGF+D+HtHl+ +g  l +++l++  ++  +++ +++r++  +             + ++wi+g+G
  gi|313125771|ref|YP_004036041.1|  52 ETIDLAGDVVLPGFIDAHTHLDMVGRSLVHADLSG--ASGPDDCVDRLRARGDELasisdagngnedDTDEWILGYG 126
                                       79***********************999*******..****************99********************** PP

                      Amidohydro_3  66 wdeaqfaeerfpyalaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllreg 142
                                       +de+ +++ r+  ++ +ld+v+ d pv + + d H+a +ns+al++ +++       + +  ++a g  +tg++ e+
  gi|313125771|ref|YP_004036041.1| 127 YDESTWDDSRYL-TREDLDAVSTDQPVAAFREDMHVASLNSVALAKHRDA-------MPDADVRAEGGNPTGVIVEE 195
                                       ***********9.********************************94444.......444445555555******** PP

                      Amidohydro_3 143 afhlvldlaplareaeaaavaaalaalasyGitsveagggnvsslddleplfeltaeeklplrvi...ikelldaae 216
                                       a + v++ ++ ++e+ ++ ++aa aa++  G+t+v   ++++  +  + +++el++++ l+lrv     ++ ld++ 
  gi|313125771|ref|YP_004036041.1| 196 AVDVVYEEIQPDEEQTEKLLRAAQAAANERGVTGV---HDMTRTSHKPSVYRELDKADDLTLRVRinyWADHLDSVI 269
                                       ***********************************...***************************9998899***** PP

                      Amidohydro_3 217 rlglplspgseeltigavklfadgvlgsrtalltepyf.....tgwpdfedealaelvaaadergldvaihaigdaa 288
                                         gl++++gse +++ga+k f dg+ g+rta l+epy+     tg+  ++ e+lae+v++ad+++l++  haigd+a
  gi|313125771|ref|YP_004036041.1| 270 DAGLRTNHGSEMVRVGAIKTFTDGSFGGRTAKLSEPYSddeteTGTWVVDPEELAEIVSRADAHDLQLSAHAIGDEA 346
                                       ******************************************99999****************************** PP

                      Amidohydro_3 289 vddvldafeaa.aekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnf...edelldsrlgperargstpvk 361
                                       v +vlda+e   +++++++   r+ehae  +++ i+r+a+ ++ a+vqp f       +l+d rlg+ r++ +++ +
  gi|313125771|ref|YP_004036041.1| 347 VHAVLDAYEDCeNPEKSRH---RVEHAELADDDAIRRFAESGIVASVQPNFLKwaeAGGLYDARLGE-RRTKTNRYA 419
                                       ********99966666666...9*************************8877799*999******85.55667899* PP

                      Amidohydro_3 362 ellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGa 438
                                       + ++a+v++a+gsD  + p+dp+ ++++av+         + ++++l ++eal++yT+g+A+a + edr Gt+e G+
  gi|313125771|ref|YP_004036041.1| 420 AFTEADVPLAFGSD--CMPLDPLLGVHWAVN--------APAEEQRLGVTEALRAYTTGAAYAGFDEDRLGTIETGK 486
                                       **************..**************5........56699********************************* PP

                      Amidohydro_3 439 dADlvvldadpldvdppelaearvrltvvdGrvvy 473
                                       +ADl++l a p + d   ++++ v++t+v+G+vvy
  gi|313125771|ref|YP_004036041.1| 487 KADLTILAASPWESDS--IRDIDVSATIVGGQVVY 519
                                       ***********99995..88999***********9 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   3.5e-06     0.021       1      15 [.      60      74 ..      60      98 .. 0.83
   2 !   46.2   0.2   6.4e-16   3.8e-12      30     344 .]     208     518 ..     194     518 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-06
                                      EEEE-EEEEEEECET CS
                      Amidohydro_1  1 ivlPGlIDaHvHleq 15
                                      +vlPG+IDaH+Hl +
  gi|313125771|ref|YP_004036041.1| 60 VVLPGFIDAHTHLDM 74
                                      69***********53 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 6.4e-16
                                       THHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.HHHHHHHHHHTSSSEEEEEEESSEGGS..........GCCCSHH CS
                      Amidohydro_1  30 petaaealesgiktalksGtttvadmgattst.giealleaaeelplglrilggkvsldr..........gsaetsk 95 
                                       +e+ +  l+ + ++a + G+t v dm  t ++ ++ + l+ a++l l +ri      ld           gs+ ++ 
  gi|313125771|ref|YP_004036041.1| 208 EEQTEKLLRAAQAAANERGVTGVHDMTRTSHKpSVYRELDKADDLTLRVRINYWADHLDSvidaglrtnhGSEMVRV 284
                                       55566666777777778888888888887777777777778888766666665544444477778877777777777 PP

                                       HHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE......TSSCHHHHHHHHHH CS
                      Amidohydro_1  96 asreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHa......letkgevedaeaaf 166
                                         ++++ +g      +k ++  +   ++ + + + +eel+e+++ a+++dl++++Ha      +    ++ed+e+  
  gi|313125771|ref|YP_004036041.1| 285 GAIKTFTDGSFGGRTAKLSEPYSDDETETGTWVVDPEELAEIVSRADAHDLQLSAHAigdeavHAVLDAYEDCENPE 361
                                       7777777776666666666666666677889999999********************54444444444444444444 PP

                                       TTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE..HHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSC CS
                      Amidohydro_1 167 getiehgthlevaeslglldeiklilahgvhlt..pteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvk 241
                                       ++++    h e a++    d i+  ++ g+  +  p+ +++    +   g+ + +  +++ +++r   +   +++v 
  gi|313125771|ref|YP_004036041.1| 362 KSRHRV-EHAELADD----DAIRRFAESGIVASvqPNFLKW----AEAGGLYDARLGERRTKTNRY--AAFTEADVP 427
                                       444333.44444444....7777778888888855553333....335666676777777666664..4444559** PP

                                       EEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEEC CS
                      Amidohydro_1 242 vglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvd 318
                                        ++g+D    +  l+ l ++ +a+      ++  ee+ l + ealr++T+++A a   +d++G+ie Gk+ADl+++ 
  gi|313125771|ref|YP_004036041.1| 428 LAFGSD----CMPLDPLLGVHWAV------NAPAEEQRLGVTEALRAYTTGAAYAGFDEDRLGTIETGKKADLTIL- 493
                                       ******....44555568888888......33357899************9998877789****************. PP

                                       CCTCGGGTTTC.TSEEEEEEEETTEEE CS
                      Amidohydro_1 319 ldilaafvglk.kdgnvkkvivkGklv 344
                                           ++++ ++ +d  v  +iv+G++v
  gi|313125771|ref|YP_004036041.1| 494 --AASPWESDSiRDIDVSATIVGGQVV 518
                                       ..4444443332677789999999887 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   6.2e-05      0.37      38      69 ..     205     235 ..     183     344 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHTTECEEEE--T CS
                            AIRS_C  38 lgdvlleptliyvkralaalkglvkaahDvTg 69 
                                         d++++++l+++++a+a +  +v+++hD+T+
  gi|313125771|ref|YP_004036041.1| 205 QPDEEQTEKLLRAAQAAANE-RGVTGVHDMTR 235
                                       56888888***********8.**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2992.51
//
Query:       gi|313125772|ref|YP_004036042.1|  [L=375]
Description: quinolinate synthetase a [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.1e-102  340.4   0.1   9.3e-102  340.2   0.1    1.0  1  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.2   0.1  5.2e-106  9.3e-102       2     299 .]      39     374 ..      38     374 .. 0.95

  Alignments for each domain:
  == domain 1  score: 340.2 bits;  conditional E-value: 5.2e-106
                                       HHHHHHHH..HTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHS.TTSEEE-SST CS
                              NadA   2 eikelkke..knavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLs.pekkvllpdl 75 
                                       +i+++++e  +++++l+HnYq++ei+e+adf+GDS+eL+++aae++ae++vf+GV+FMae+a+i++ ++++vllp++
  gi|313125772|ref|YP_004036042.1|  39 RIEAAREElgDDVIVLGHNYQRREIVEHADFIGDSYELSKRAAESDAEYVVFAGVTFMAESADIITdDDQTVLLPSM 115
                                       79999999999*******************************************************99********* PP

                                       T---HHHCT--HHHHHHHHHH......STTS-EEEESSS-HHHHTT-....SEEE-TTTHHHHH.HHSS.-SEEEEE CS
                              NadA  76 eagCsladmitaeeveelkee......lpdaavvtYvNssaevKals....divcTSsnavkvv.ealk.ekkilfl 140
                                       ea+C++a m++a +v++++e+        d++ +tY+Ns a++Ka++    ++vcTSsna++ + +a++ ++ +lfl
  gi|313125772|ref|YP_004036042.1| 116 EASCPMAGMAEALQVDAAWEQidaatgDRDVIPITYMNSYADLKAFCaeqgGLVCTSSNAADAFeWAFErGDVVLFL 192
                                       *********************8888763344449**********************************669****** PP

                                       S-HHHHHHHHHHH......................SEEEEESSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-H CS
                              NadA 141 PDqnLgryvakklg.....................ekkiilwkgaCsvHeefkaeeveelkeehpdakvlvHPEcke 196
                                       PD++Lgr++a++lg                     +++++lw+g+C+vHe+f+ae++ee++eeh da+v+vHPEc++
  gi|313125772|ref|YP_004036042.1| 193 PDKHLGRNTAAELGmdsvaewdpwnpeapdatdvaDADVVLWDGYCQVHERFRAEHIEEVREEH-DANVIVHPECRR 268
                                       ***********************************999************************96.89********** PP

                                       HHHHCSSEE--HHHHCCCCGT.TSSSCEEEES-THHHHHHHHH-TTSEEE.....ECSSSSSTTGGG--HHHHHHHH CS
                              NadA 197 evveaadvvgSTsqiikavke.seakefiigTelglverlkkeapekefialsaeaaeeavCetMkkitleklleaL 272
                                       evv aad +gSTsqi++++++ +++++++igTe++lv++l++ +pe +++ l+      + C+ M++i+++ l+++L
  gi|313125772|ref|YP_004036042.1| 269 EVVVAADEAGSTSQICDTIANaDPGETWAIGTEIHLVNHLQRWHPEVNVVPLCGD--ACMDCNAMRQIDPNYLTWLL 343
                                       *******************9989***************************99743..2456**************** PP

                                       HHT-S....B.----HHHHHHHHHHHHHHHH CS
                              NadA 273 eelee...ee.ikvdeevaekAkkalermle 299
                                       e+l+e   ++ ++v e+ +e A +alermle
  gi|313125772|ref|YP_004036042.1| 344 ESLAEdevHNvVEVAEREKELAAVALERMLE 374
                                       *99988884569*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2175.82
//
Query:       gi|313125773|ref|YP_004036043.1|  [L=521]
Description: l-aspartate oxidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-79  267.4   9.4      3e-79  267.1   9.4    1.1  1  FAD_binding_2   FAD binding domain
    7.7e-11   41.8   2.0    4.3e-05   22.9   1.1    3.4  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.1e-07   29.1   1.4    1.7e-05   24.1   2.8    2.2  2  GIDA            Glucose inhibited division protein A
    2.9e-06   26.9   6.3    5.5e-05   22.7   7.0    2.1  2  FAD_oxidored    FAD dependent oxidoreductase
      3e-06   27.1   7.5    0.00011   22.0   7.5    2.5  1  DAO             FAD dependent oxidoreductase
    5.4e-05   22.1   0.2      0.056   12.1   0.5    2.3  2  HI0933_like     HI0933-like protein
    0.00033   20.0   0.5    0.00033   20.0   0.5    1.6  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00067   19.6   0.7     0.0015   18.5   0.7    1.6  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
     0.0059   16.8   1.9      0.016   15.4   1.9    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.013   14.7   0.2      0.027   13.7   0.2    1.5  1  FAD_binding_3   FAD binding domain
      0.068   12.4   0.2      0.099   11.9   0.2    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.15   11.2   0.7       0.28   10.4   0.3    1.6  2  Thi4            Thi4 family


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.1   9.4     2e-82     3e-79       1     417 []      16     384 ..      16     384 .. 0.95

  Alignments for each domain:
  == domain 1  score: 267.1 bits;  conditional E-value: 2e-82
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.GGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT- CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg.atawsqGgidavlspeqkkagikdspelhrtdtlkaldel 76 
                                       Dv+V+GsG+AG+aAAl+aa+ G++v+v +k+ + +  +t w+qGgi++ +         +d pe  r+d+l a+d+ 
  gi|313125773|ref|YP_004036043.1|  16 DVLVVGSGIAGCAAALAAARSGANVLVATKATAPEDaSTDWAQGGIAVTG---------ED-PETFREDVLDASDGT 82 
                                       9*****************************98766669************.........46.*************** PP

                                       S-HHHHHHHHHTHHHHHHHHHHT..T----BCCTS....SB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHH CS
                     FAD_binding_2  77 adqplveafveaapeavdeLeel..gvpfsrtedg....pvdvrelGglsatartlhdaadarretlvtghallarl 147
                                       ad+++v+++v  a++av+       gvpf++++ g     +d  +  ++s++ r+lh + +       tg ++l ++
  gi|313125773|ref|YP_004036043.1|  83 ADPEAVDILVGDARDAVEDVLVDtiGVPFDGAPAGagldDYDHGREAAHSER-RILH-VNAS------TGGHVLRPF 151
                                       *****************98766669******999999***************.****.5555......9******** PP

                                       HHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGT CS
                     FAD_binding_2 148 vesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnap 223
                                       ++++r+++ v+f+e + a+++++++grv+G+ +   ++g+ + + a a+vlatgG+g+           +  ttn+ 
  gi|313125773|ref|YP_004036043.1| 152 LNHLRDHDgVTFLEDAMALDFLTHEGRVHGVHLL--REGSVEPVFAGATVLATGGIGA----------CYGTTTNPD 216
                                       *********************************9..*********************9..........9******** PP

                                       T-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTB.B--THHHHTT-EEE-TTSSBTH......GGGS-HH CS
                     FAD_binding_2 224 avtGdglalalragaalnddrmeevqfhPtslvpirdgsgi.LitealrgeGgilvdkdGrrFm......nelasrd 293
                                       ++tGdg a+a+ aga+++d  m+ vqfhPt+ +    g    L++ea+rgeG++l++ +G+rFm      +ela+rd
  gi|313125773|ref|YP_004036043.1| 217 GATGDGVAMAAFAGARIAD--MQYVQFHPTAYP----GDDPfLVSEAVRGEGAVLRNGEGERFMpgvhddAELAPRD 287
                                       *******************..************....4444479********************************* PP

                                       HHHHHHH.HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEE CS
                     FAD_binding_2 294 vvsrailekeiaeggseanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqh 370
                                       vv+ra+   e++++g+   v ld+s  +++  +++++++  e +++  d      +dp+d  ip       v pa h
  gi|313125773|ref|YP_004036043.1| 288 VVARAVK-DERDRTGE---VRLDVSP-VEP-DFRTEFPDLAELCDE-RD------VDPEDG-IP-------VAPAEH 343
                                       ******9.88887776...78*****.777.8*******9999998.88......9*****.**.......****** PP

                                       EES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 371 ytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                       y +gG+++de+gr+      +++ L+AaGe+a +gvhganrl+++sl
  gi|313125773|ref|YP_004036043.1| 344 YLCGGIAVDERGRT------TLDRLFAAGECARTGVHGANRLASTSL 384
                                       **************......*************************98 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.1   2.9e-08   4.3e-05       2      36 ..      16      49 ..      15     240 .. 0.71
   2 !   15.1   0.0   6.6e-06    0.0099     256     279 ..     347     372 ..     340     386 .. 0.84
   3 ?   -1.4   0.0      0.74   1.1e+03     234     268 ..     440     472 ..     436     477 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.9e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtcl 36
                                      dv+v+G+G+AG+aaal +a++ga+v++   + t +
  gi|313125773|ref|YP_004036043.1| 16 DVLVVGSGIAGCAAALAAARSGANVLVA-TKATAP 49
                                      8************************999.444444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 6.6e-06
                                       TEEE--TTSBESSTTEEE-GGGC..T CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Pyr_redox_2 256 ggivvdeflrtnvpgiyaiGDva..g 279
                                       ggi vde++rt+ + ++a+G +a  g
  gi|313125773|ref|YP_004036043.1| 347 GGIAVDERGRTTLDRLFAAGECArtG 372
                                       89*********************441 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.74
                                       -S-EEES-HHCSHCCT-EEEETTEEE--TTSBESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 234 avGvrpstelleeklglelderggivvdeflrtnv 268
                                       avGv+  ++ l e++  ++ +r + +vd + rt v
  gi|313125773|ref|YP_004036043.1| 440 AVGVERTHADL-EQARSTI-RRLKGEVDAYTRTRV 472
                                       79999999999.9999999.99999******9986 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   2.8   1.2e-08   1.7e-05       1      32 [.      16      47 ..      16      53 .. 0.92
   2 ?    0.9   0.0      0.12   1.9e+02     104     167 ..     154     218 ..     147     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.2e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkl 32
                                      dv V+G G AGc+AAlaaar+Ga+vl  t+ +
  gi|313125773|ref|YP_004036043.1| 16 DVLVVGSGIAGCAAALAAARSGANVLVATKAT 47
                                      79***********************9987765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                                       HHHTSTTEEEEES.-EEEEEECTTEEEEEEETTS-EEEEC...EEEE--TT-BT-EEEETTEEEESSC CS
                              GIDA 104 klenepnleiiee.eveeliveekkvkgvvtedgetikak...avviatGtflkgkihigekelsaGr 167
                                        l++++ ++ +e+ ++ + +++e++v+gv + ++  ++     a+v+atG        +g+++ + G 
  gi|313125773|ref|YP_004036043.1| 154 HLRDHDGVTFLEDaMALDFLTHEGRVHGVHLLREGSVEPVfagATVLATGG---IGACYGTTTNPDGA 218
                                       567777777666515568889999****988776665544444*******9...33445555555555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   7.0   3.7e-08   5.5e-05       1      28 [.      16      43 ..      16      48 .. 0.93
   2 ?    1.0   0.0      0.14   2.1e+02      83     144 ..     138     203 ..     117     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.7e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLv 28
                                      Dv+VvG+g+aG+aAA+aAar+Ga+vl+ 
  gi|313125773|ref|YP_004036043.1| 16 DVLVVGSGIAGCAAALAAARSGANVLVA 43
                                      9************************985 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.14
                      FAD_oxidored  83 tfepevakavleeml....aeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                       +++ ++   vl  +l    + +gvt l ++++ +  + ++r+++v + ++   + + A  ++ ATg
  gi|313125773|ref|YP_004036043.1| 138 HVNASTGGHVLRPFLnhlrDHDGVTFLEDAMALDFLTHEGRVHGVHLLREGSVEPVFAGATVLATG 203
                                       4555555556666666665788***************988*******8655577777777777775 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   7.5     7e-08   0.00011       1      56 [.      16      86 ..      16     373 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH.............H CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeas.............e 56
                                      dv+++G+Gi+G+++A+++ar g  V++  k+  +  +++  ++g ++   ++++                e
  gi|313125773|ref|YP_004036043.1| 16 DVLVVGSGIAGCAAALAAARSGanVLVATKATAPEDASTDWAQGGIAVTGEDPETFRedvldasdgtadpE 86
                                      8*******************99*********7787899999999998877655532244455555555551 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.5   3.8e-05     0.056       2      34 ..      16      48 ..      15      71 .. 0.91
   2 !    7.3   0.0    0.0011       1.6     109     191 ..     145     237 ..     124     251 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      dv+v+G G AG  aA++aa+ g++Vl+  ka++
  gi|313125773|ref|YP_004036043.1| 16 DVLVVGSGIAGCAAALAAARSGANVLVATKATA 48
                                      89*************************988765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHH.HT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE----S..S-GGG....T--SH CS
                       HI0933_like 109 edivdallkelke.agvklrletevksvekeedgkfrvkt.k..seeeleadklvlAtGGl..SiPkl....Gstgk 175
                                        ++++ +l++l++  gv++  +    ++ ++e++++ v++ +  s e + a ++vlAtGG    + ++    G+tg+
  gi|313125773|ref|YP_004036043.1| 145 GHVLRPFLNHLRDhDGVTFLEDAMALDFLTHEGRVHGVHLlRegSVEPVFAGATVLATGGIgaCYGTTtnpdGATGD 221
                                       5677777888776368999999999999999999999998532345678899*******8511344444556***** PP

                                       HHHHHHHTT--EEEEE CS
                       HI0933_like 176 gyklaeqfghtivplr 191
                                       g+ +a+ +g +i++++
  gi|313125773|ref|YP_004036043.1| 222 GVAMAAFAGARIADMQ 237
                                       ************9886 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.5   2.2e-07   0.00033      26      91 ..      12      77 ..       2      81 .. 0.83
   2 ?   -3.4   0.1       3.1   4.7e+03       9      53 ..     359     404 ..     355     413 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.2e-07
                                      B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH CS
                       AlaDh_PNT_C 26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavke 91
                                      +++  vlv+G G+aG +A+ +a++ ga+V v  + +a      ++ +  + v  ++ e+++e v +
  gi|313125773|ref|YP_004036043.1| 12 ARETDVLVVGSGIAGCAAALAAARSGANVLVATKATAPEDASTDWAQGGIAVTGEDPETFREDVLD 77
                                      56789*************************999988888888885555588888888888887765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.1
                                       CSCGCTSEEETTCEETCB--.-EEEEESTSHHHHHHHHHHHHTT-E CS
                       AlaDh_PNT_C   9 lekffggkgtlaGgvpgvep.akvlviGgGvaGlqAiatakglgak 53 
                                       l++ f +   + +gv+g+++ a +  + g v Gl A +ta+  ga+
  gi|313125773|ref|YP_004036043.1| 359 LDRLFAAGECARTGVHGANRlASTSLLEGLVWGLRAGETAADAGAD 404
                                       5566666666777777765437777777778899999999888886 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.7   9.8e-07    0.0015       3      86 ..     432     507 ..     430     521 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.8e-07
                                       HHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BT CS
                    Succ_DH_flav_C   3 eLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrG 79 
                                       +L+++m++ vgv+Rt+++L++a +++++l+ +++  + t  s+         +el+n   +A ++a++A +   S G
  gi|313125773|ref|YP_004036043.1| 432 RLRETMDSAVGVERTHADLEQARSTIRRLKGEVDAYTRTRVSR-------SLYELRNATVCALLVARAASE-APSAG 500
                                       799*****************************99555443333.......467899999999999888876.67888 PP

                                       TBEBTTS CS
                    Succ_DH_flav_C  80 aHaredf 86 
                                       +H+  d 
  gi|313125773|ref|YP_004036043.1| 501 CHHVVDA 507
                                       8887765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.9   1.1e-05     0.016       1      24 [.      19      42 ..      19      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                      EE--SHHHHHHHHHHHCCTEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvll 24
                                      +vG+G++G++aA ++a+ g++vl+
  gi|313125773|ref|YP_004036043.1| 19 VVGSGIAGCAAALAAARSGANVLV 42
                                      8*********************98 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.8e-05     0.027       1      35 [.      14      48 ..      14      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      etdVl+VG+G aG  +al  ++ G +v++ +k + 
  gi|313125773|ref|YP_004036043.1| 14 ETDVLVVGSGIAGCAAALAAARSGANVLVATKATA 48
                                      69*************************99888765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   6.7e-05     0.099     154     205 ..       4      55 ..       1      61 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                       Pyr_redox_3 154 skvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesd 205
                                       s+ +  ++ ++++v+V+G +  ++ aAl  +r ga+V v+t+ +  e+ ++d
  gi|313125773|ref|YP_004036043.1|   4 STTETGADARETDVLVVGSGIAGCAAALAAARSGANVLVATKATAPEDASTD 55 
                                       55667778999*****************************999877766655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00019      0.28      10      51 ..       7      47 ..       1      64 [. 0.79
   2 ?   -3.2   0.0       2.6   3.9e+03     207     233 ..     354     381 ..     348     382 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00019
                                      HHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                              Thi4 10 edllkyaesDvvivGaGssGLtaayylakkpdlkvailersv 51
                                      e   +  e+Dv++vG+G +G +aa   a++ + +v++  +  
  gi|313125773|ref|YP_004036043.1|  7 ETGADARETDVLVVGSGIAGCAAALAAARS-GANVLVATKAT 47
                                      55567789****************999998.77777766655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.6
                                       HECEEETTEEE-T.HHHHHHHT-EB--S CS
                              Thi4 207 ktrevvpnlyvaG.mevaevdganRmGp 233
                                       + r  ++ l++aG  + + v+ganR+ +
  gi|313125773|ref|YP_004036043.1| 354 RGRTTLDRLFAAGeCARTGVHGANRLAS 381
                                       56778899999994466789****9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3277.00
//
Query:       gi|313125774|ref|YP_004036044.1|  [L=270]
Description: nicotinate-nucleotide pyrophosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-53  179.5   0.2    5.9e-53  179.1   0.2    1.2  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
    7.9e-21   73.9   0.1      3e-20   72.1   0.0    1.9  2  QRPTase_N       Quinolinate phosphoribosyl transferase, N-ter
  ------ inclusion threshold ------
       0.15   11.4   0.0       0.24   10.8   0.0    1.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.2   9.8e-57   5.9e-53       1     168 [.     100     265 ..     100     266 .. 0.98

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 9.8e-57
                                       HHHHHHHHHHHHHCT..SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksa..kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvre 75 
                                       +At t+r+veaa++a   +r+++TRkttPglr +ek+Av +GGgd+hrl Ls mv++kdnh+a +g ++ a++++re
  gi|313125774|ref|YP_004036044.1| 100 VATRTRRAVEAAHEAnpDARVAATRKTTPGLRGVEKRAVVAGGGDTHRLTLSGMVMVKDNHVAEMG-LEGAIERFRE 175
                                       8*************9999***********************************************9.********** PP

                                       HHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEE CS
                         QRPTase_C  76 avdkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvi 152
                                         +++ k+eveves e   +++ a+ di+++Dn+s++e+++ ve   +   +vl e+SGg+tl++v++ya +gvdv+
  gi|313125774|ref|YP_004036044.1| 176 RKSFATKLEVEVESPEMGARAADAGTDIVLFDNLSPDEVRDGVE---RLPDSVLAEASGGITLDTVADYAATGVDVV 249
                                       ********************************************...67778************************* PP

                                       EECHHCHTB----EEE CS
                         QRPTase_C 153 svgalthsvkalDisl 168
                                       s+g+lths+++lD+s 
  gi|313125774|ref|YP_004036044.1| 250 SMGSLTHSAPSLDFSF 265
                                       **************96 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0     5e-24     3e-20       2      89 .]      16      98 ..      15      98 .. 0.92
   2 ?   -1.6   0.0      0.48   2.9e+03      52      69 ..     214     231 ..     209     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 5e-24
                                      TT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHH CS
                         QRPTase_N  2 grgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERv 80
                                      g++D+t+   +p+  + +++++ake+gvvaGl++a  vf++l g+++++ v+DG++ve+g+v+le +G+ar+ l++ERv
  gi|313125774|ref|YP_004036044.1| 16 GHRDVTN--DVPG--ETTGRLVAKESGVVAGLDAAVTVFDYL-GVAATPAVDDGASVEPGAVVLETSGPARETLRGERV 89
                                      6778888..4444..45678**********************.************************************ PP

                                      HHHHHHHHH CS
                         QRPTase_N 81 aLnllqrlS 89
                                      a n++ ++S
  gi|313125774|ref|YP_004036044.1| 90 AVNVVGHAS 98
                                      *******98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.48
                                       S-TT-EEETTEEEEEEEE CS
                         QRPTase_N  52 vkDGervekgdvlleieG 69 
                                       v+DG +  +  vl+e++G
  gi|313125774|ref|YP_004036044.1| 214 VRDGVERLPDSVLAEASG 231
                                       799999999*****9999 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     4e-05      0.24     156     195 ..     214     253 ..     206     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4e-05
                                       HHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESH CS
                    Ribul_P_3_epim 156 vrklidekeldlkievDGGvkldnieqiaeagadvlVags 195
                                       vr  +++   ++  e+ GG++ld+++  a+ g+dv+ +gs
  gi|313125774|ref|YP_004036044.1| 214 VRDGVERLPDSVLAEASGGITLDTVADYAATGVDVVSMGS 253
                                       555566656678899***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1722.20
//
Query:       gi|313125775|ref|YP_004036045.1|  [L=270]
Description: orotidine 5''-phosphate decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.9e-32  111.7   0.0    4.6e-32  111.4   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.0   2.6e-36   4.6e-32      17     220 ..      48     246 ..      18     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 2.6e-36
                                       HHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHSTCHHHHTTESEEEEE CS
                         OMPdecase  17 eladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatagsarikewadivtvh 93 
                                       +++d   ++++++K++ +++e+ +  +++ +++a+a+ +++++++D+K+aDIGnt +++a+       +++d++tv+
  gi|313125775|ref|YP_004036045.1|  48 RIIDATHEHAACYKPNAAFYEDADGWRALRETIAYAHGKDVPVLLDAKRADIGNTTRQYAK-----LLDEVDAITVN 119
                                       34555555****************77**********************************8.....899******** PP

                                       GTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH.H....SHHHHHHHHHHHHHHHTTESEEECCCHTH... CS
                         OMPdecase  94 avaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe.k....gytqacveaarehkaedfvmGfvaqetln... 162
                                       +++G +s++++++      ++g++il+++s++g+++lq+ +    +  ++ v a+++  +++  +G+v+++t +   
  gi|313125775|ref|YP_004036045.1| 120 PYMGRDSLQPFLDRG----DKGVFILCRTSNPGGEDLQDlEldsgERVYERVAALADLWNRNDNVGLVVGATAPdel 192
                                       ************987....579*****************94447888899999999999899***********9866 PP

                                       .HHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSS.SHHH CS
                         OMPdecase 163 .ateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkag.dpve 220
                                        +++e+ +d+++l+pgig+ qggd+++  +        + g  +++ +RgI+ ag d  e
  gi|313125775|ref|YP_004036045.1| 193 eSIREQVPDLPFLVPGIGA-QGGDAEAAVEF-----GLADGVGLVNSSRGIIFAGeDNGE 246
                                       5444449***********9.99999999854.....3344788***********944444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1784.23
//
Query:       gi|313125776|ref|YP_004036046.1|  [L=65]
Description: hypothetical protein Hbor_10070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0022   17.8   2.6     0.0022   17.8   2.6    2.0  2  zf-HIT           HIT zinc finger
  ------ inclusion threshold ------
      0.019   15.3   3.7      0.019   15.3   3.7    1.5  1  zf-UBP           Zn-finger in ubiquitin-hydrolases and other 
      0.029   14.5   2.8      0.034   14.2   2.8    1.1  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
      0.062   13.2  10.0       0.18   11.7  10.1    1.7  1  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
       0.55   10.4  11.5       0.19   11.9   5.7    2.1  2  zf-B_box         B-box zinc finger
        1.6    8.7   8.4        1.2    9.1   6.0    2.0  2  DUF2180          Uncharacterized protein conserved in archaea


Domain annotation for each model (and alignments):
>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.6   7.4e-07    0.0022       3      24 ..       5      27 ..       3      27 .. 0.94
   2 ?    1.1   0.2      0.13   3.8e+02      16      21 ..      38      43 ..      34      45 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.4e-07
                                      -B-TTT-S.B-SEE-TTT--EES CS
                            zf-HIT  3 klCgvCgf.pakYkCpkCntryC 24
                                      +lC+vC   +a  +C +C+t  C
  gi|313125776|ref|YP_004036046.1|  5 GLCQVCESrEATHTCVQCGTAAC 27
                                      79******************998 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                                      -TTT-- CS
                            zf-HIT 16 CpkCnt 21
                                      C +C+ 
  gi|313125776|ref|YP_004036046.1| 38 CVRCAD 43
                                      666665 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   3.7   6.5e-06     0.019       1      24 [.       7      29 ..       7      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.5e-06
                                      -TTTH--.SSEEEETTT--EEE-T CS
                            zf-UBP  1 CseCnsenknlWlCLkCghvgCgr 24
                                      C++C+s  +  + C++Cg+  C +
  gi|313125776|ref|YP_004036046.1|  7 CQVCESR-EATHTCVQCGTAACDD 29
                                      *****88.9*************75 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.8   1.2e-05     0.034      52      90 ..       4      45 ..       1      48 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                        zf-RRPl_C4 52 dkLCtkCkeknekekeircetf..ee.ylkklklCkeCkerv 90
                                      + LC++C++++ +++ ++c t   ++ + +  +lC +C  r+
  gi|313125776|ref|YP_004036046.1|  4 SGLCQVCESREATHTCVQCGTAacDDhFDRASNLCVRCADRS 45
                                      57***********999**987533551555678*****9886 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  10.1   5.9e-05      0.18       3      44 ..       5      42 ..       3      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.9e-05
                                      SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT- CS
                        zf-C3HC4_3  3 eeCviClerprnvvllpCgHlvlCeeCaekllkrkkkCpiCr 44
                                       +C++C +r++++++++Cg      +C +++ + ++ C  C 
  gi|313125776|ref|YP_004036046.1|  5 GLCQVCESREATHTCVQCGTA----ACDDHFDRASNLCVRCA 42
                                      58******************9....56666666699999995 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   5.7   6.5e-05      0.19       5      28 ..       6      29 ..       3      29 .. 0.93
   2 ?    1.4   0.2      0.12   3.7e+02      24      29 ..      36      41 ..      34      46 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.5e-05
                          zf-B_box  5 kCpeHknkpatlfCedCqqplCee 28
                                       C+ +++++at  C +C++  C++
  gi|313125776|ref|YP_004036046.1|  6 LCQVCESREATHTCVQCGTAACDD 29
                                      7*********************85 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
                          zf-B_box 24 plCeeC 29
                                       lC  C
  gi|313125776|ref|YP_004036046.1| 36 NLCVRC 41
                                      578888 PP

>> DUF2180  Uncharacterized protein conserved in archaea (DUF2180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.0   0.00041       1.2      12      34 ..      12      34 ..       5      40 .. 0.85
   2 ?   -1.0   0.1       0.6   1.8e+03      58      64 ..      37      43 ..      34      47 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00041
                           DUF2180 12 dtdavaiCivCGkGvCkdHlvre 34
                                       ++a+  C+ CG   C dH  r 
  gi|313125776|ref|YP_004036046.1| 12 SREATHTCVQCGTAACDDHFDRA 34
                                      579999*************9875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.6
                           DUF2180 58 lCkeCle 64
                                      lC +C +
  gi|313125776|ref|YP_004036046.1| 37 LCVRCAD 43
                                      6777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 399.43
//
Query:       gi|313125777|ref|YP_004036047.1|  [L=170]
Description: dnaj-class molecular chaperone with c-terminal zn finger domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-15   55.0   0.1    2.4e-14   53.2   0.0    1.8  2  DnaJ             DnaJ domain
     0.0016   18.7   1.5     0.0021   18.2   1.5    1.2  1  VirB3            Type IV secretory pathway, VirB3-like protei
  ------ inclusion threshold ------
      0.018   15.1   1.1      0.018   15.1   1.1    1.5  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.044   13.7   0.0      0.085   12.8   0.0    1.6  1  RPT              A repeated domain in UCH-protein
      0.057   13.8   0.0       0.09   13.1   0.0    1.4  1  DUF2277          Uncharacterized conserved protein (DUF2277)
        3.8    7.8   6.4         32    4.8   6.4    2.3  1  HemY_N           HemY protein N-terminus


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.13     4e+02      26      43 ..     104     121 ..     100     122 .. 0.81
   2 !   53.2   0.0     8e-18   2.4e-14       2      55 ..     120     170 .]     119     170 .] 0.95

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.13
                                       HHHSTTTSCCHHHHHHHH CS
                              DnaJ  26 lkyHPDknpkdpeaeekF 43 
                                       ++  PD++p+ p+a+e++
  gi|313125777|ref|YP_004036047.1| 104 RRTTPDQSPDRPSAREAY 121
                                       5667********999976 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 8e-18
                                       HHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTS CS
                              DnaJ   2 yYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsd 55 
                                        Y  Lg++++a+++e+k aYr++++++HPD +   + ++e+Fk++n+Aye Lsd
  gi|313125777|ref|YP_004036047.1| 120 AYRTLGLDPSATTEEVKDAYRRMVKEVHPDTE---SGSKEEFKRVNRAYERLSD 170
                                       6*****************************99...77789************98 PP

>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.5   7.1e-07    0.0021      10      78 ..       2      68 ..       1      75 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.1e-07
                             VirB3 10 tRpamllGvplelvllnllvsvilflvglslwillllvplhlvlrliakrDpqmfrvlllrlktrlrlr 78
                                       R+++++G+  +++ +++l++v+ f+   +l++l+++vp++++ +l+  +   +f+  +   +tr+r+r
  gi|313125777|ref|YP_004036047.1|  2 DRDTLVMGLAAVFAGIAMLLIVLGFV--YQLFLLVAAVPFIVTTYLMWDHASGRFQARIRQEQTRRRAR 68
                                      69999999998888877777776666..66666668****************99999988889999888 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.1     6e-06     0.018      38      86 ..       6      48 ..       3      74 .. 0.73
   2 ?   -3.2   0.0       2.8   8.4e+03      98     107 ..     128     137 ..     122     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6e-06
                   Phage_holin_3_6 38 gllgaagvlallalllllvalalalaalwlaalivaavllvlagvlalv 86
                                      +++g+a+v+a +a+ll+++++++ l      +l+vaav ++++  l++ 
  gi|313125777|ref|YP_004036047.1|  6 LVMGLAAVFAGIAMLLIVLGFVYQL------FLLVAAVPFIVTTYLMWD 48
                                      6789999999999999999999888......899998888888777764 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.8
                   Phage_holin_3_6  98 pertieelke 107
                                       p +t ee+k+
  gi|313125777|ref|YP_004036047.1| 128 PSATTEEVKD 137
                                       7899999987 PP

>> RPT  A repeated domain in UCH-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.9e-05     0.085       3      37 ..     118     157 ..     116     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                               RPT   3 eeAyklLgidentdDdviitayqvkled.....dpsqkdk 37 
                                        eAy++Lg+d++++ +++  ay+  + +     ++++k++
  gi|313125777|ref|YP_004036047.1| 118 REAYRTLGLDPSATTEEVKDAYRRMVKEvhpdtESGSKEE 157
                                       58**********99999******99976655543344444 PP

>> DUF2277  Uncharacterized conserved protein (DUF2277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05      0.09       9      48 ..     124     164 ..     117     170 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                           DUF2277   9 rnlePpateeeiraAAlqyVRKvsG.vrkpsaaneeaferA 48 
                                        +l+P at+ee+++A ++ V+ v   +++ s+++ + ++rA
  gi|313125777|ref|YP_004036047.1| 124 LGLDPSATTEEVKDAYRRMVKEVHPdTESGSKEEFKRVNRA 164
                                       47******************999641334455555555555 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   6.4     0.011        32      18      66 ..      31      77 ..       4      83 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.011
                            HemY_N 18 vavlllvllfvllylllrllrlllrlparvrrwrrrrrerkarealseG 66
                                      ++++++v ++v+ yl++   ++ +   ar+r+ + rrr r + +a s+G
  gi|313125777|ref|YP_004036047.1| 31 FLLVAAVPFIVTTYLMWDHASGRF--QARIRQEQTRRRARSGPNAASRG 77
                                      233333444444444444444333..34666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1111.46
//
Query:       gi|313125778|ref|YP_004036048.1|  [L=537]
Description: translation elongation factor 1a GTP binding domain family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-34  117.6   0.0    7.3e-34  117.0   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    6.6e-11   42.4   0.6    2.4e-10   40.6   0.6    2.1  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    4.1e-08   33.5   0.0    2.1e-07   31.2   0.0    2.1  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
     0.0031   17.3   0.7       0.02   14.7   0.0    2.0  2  ATP_bind_1   Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.053   13.6   0.0       0.28   11.3   0.0    2.1  1  MMR_HSR1     50S ribosome-binding GTPase
      0.068   13.1   0.3        1.9    8.4   0.0    2.5  2  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.0   2.4e-37   7.3e-34       2     184 ..     128     339 ..     127     369 .. 0.87

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 2.4e-37
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.............. CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.............. 64 
                                       +++ +g++ghvDhGK+TL+++L++   +  + g++     +lD +++E erg++ + + + +               
  gi|313125778|ref|YP_004036048.1| 128 DHIVVGTAGHVDHGKSTLVGSLVTGQADNGEGGTR----GFLDVQPHEVERGLSADLSYAVYGfdddgpihlhnphr 200
                                       5899*******************888887775543....47******************99999************* PP

                                       .......TTCSSEEEEEEEESSSGGGHHHHHHH..HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESC CS
                          GTP_EFTU  65 .......ketkkylinliDtPGHvdFskevirg..lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKm 132
                                               +++++l++++Dt GH+ + +++irg   + lD+ +lvv+a++G++  t+e+l ++l++++p++v+++K 
  gi|313125778|ref|YP_004036048.1| 201 ksdrarvVQESDRLVSFVDTVGHEPWLRTTIRGlvGQRLDYGLLVVAADDGPTRTTREHLGILLAMELPTVVALTKT 277
                                       ***996549************************77799*************************************** PP

                                       GST.HHHHHHHHHHHHHHHHHH............HHHHHHHHHTTT.......TTEEEEEEBTTTTBTHHHH CS
                          GTP_EFTU 133 Drl.kaelkeiveevkqklsrk............eeklekygekge.......kevpvvfgSalkgegvktl 184
                                       D + ++++ e+ +ev++ l+++            e                    vpvv +Sa++ +g+++l
  gi|313125778|ref|YP_004036048.1| 278 DAVsDERVLEVEREVERLLRDVertplpverhgvE----------AaveeissAVVPVVQTSAVTMDGLDEL 339
                                       ***98999999999998885547777777644322..........03333334689***********99976 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.6   8.1e-14   2.4e-10       1      73 [.     371     441 ..     371     442 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 8.1e-14
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G va g+v sG ++ Gde+ ++++ + +++ +++++s+e++  ++d a  g  +G+ +++++ ++ i++G++l
  gi|313125778|ref|YP_004036048.1| 371 GAVASGTVNSGSVEAGDELLVGPMAD-GSFRQVEVRSIEMHYHRVDRAKSGRIVGIALKGVKESE-IERGMVL 441
                                       89*******************99554.88899*********************************.******9 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0     7e-11   2.1e-07       3     111 ..     449     534 ..     447     535 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7e-11
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEEC.C CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnviveveli.k 78 
                                       +p+++feA v++l++  +t i +gY+pv ++ t+++++ v +         +++       + pGd+  ++ve + +
  gi|313125778|ref|YP_004036048.1| 449 TPVRSFEADVMVLNH--PTRIRDGYEPVVHLETVSEAV-VFHP-------DGGQ-------LLPGDTGHATVEFKfR 508
                                       7899***********..*******************99.3332.......3444.......89*********98758 PP

                                       EEEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  79 pialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       p  +ekg+      rF  Reg +  ++G+vtei
  gi|313125778|ref|YP_004036048.1| 509 PYLVEKGQ------RFVFREGSS-KGVGTVTEI 534
                                       9*******......*****9765.699999998 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.12   3.7e+02       1      17 [.     131     150 ..     131     158 .. 0.73
   2 !   14.7   0.0   6.6e-06      0.02     150     208 ..     261     322 ..     254     349 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                        ATP_bind_1   1 vvGpaG...sGKttfvgals 17 
                                       vvG+aG    GK+t+vg+l+
  gi|313125778|ref|YP_004036048.1| 131 VVGTAGhvdHGKSTLVGSLV 150
                                       5666663336*******997 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.6e-06
                        ATP_bind_1 150 samlrlelPhvvvlnkfDllkeklekeleffedvealslllekee.....ekykklaeaiaell 208
                                        ++l +elP+vv+l+k+D ++  +e+ le+  +ve+l +  e +      + ++   e+i++++
  gi|313125778|ref|YP_004036048.1| 261 GILLAMELPTVVALTKTDAVS--DERVLEVEREVERLLRDVERTPlpverHGVEAAVEEISSAV 322
                                       68899**************99..88899999999888887776666444333333444444433 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.3e-05      0.28       2     114 .]     132     276 ..     131     276 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.3e-05
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE............................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke............................... 47 
                                       v+ +G+   GKStL+ +l+    ++ +  g Tr     + +  + e                               
  gi|313125778|ref|YP_004036048.1| 132 VGTAGHVDHGKSTLVGSLVTG--QADNGEGGTRGFLDVQPH--EVErglsadlsyavygfdddgpihlhnphrksdr 204
                                       7789**************975..446666777655444333..1111223455566666666677777777788888 PP

                                       ..........EEEEECGGCSSHHHHHHHHHHHHHH..HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                          MMR_HSR1  48 ..........ielvDtpGliegaseekglgkafla..leeadlillvvdaseeklkpldeeleelleeakkplilvl 112
                                                 + +vDt+G  e     + l+ +++    ++ d  llvv a  ++ ++  +e   +l   + p++++l
  gi|313125778|ref|YP_004036048.1| 205 arvvqesdrlVSFVDTVG-HE----PW-LRTTIRGlvGQRLDYGLLVVAAD-DGPTRTTREHLGILLAMELPTVVAL 274
                                       88888888889*******.44....66.55555552145589999998766.5566666666666666677777777 PP

                                       ES CS
                          MMR_HSR1 113 nk 114
                                       +k
  gi|313125778|ref|YP_004036048.1| 275 TK 276
                                       65 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.062   1.9e+02     104     122 ..     134     152 ..      90     163 .. 0.76
   2 ?    8.4   0.0   0.00064       1.9      17      77 ..     240     301 ..     237     348 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.062
                                       EECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpe 122
                                        +G+   GKStL+ +l+  
  gi|313125778|ref|YP_004036048.1| 134 TAGHVDHGKSTLVGSLVTG 152
                                       3455557******999875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00064
                                       -EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH......HHHHHHHHHHHTTS CS
                       RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee......eleelkeelealgy 77 
                                       d  l+vv+++  +  +++    L ++ + +++ v++l+K+D +++e+      e   ++  l++++ 
  gi|313125778|ref|YP_004036048.1| 240 DYGLLVVAAD--DGPTRTTREHLGILLAMELPTVVALTKTDAVSDERvleverE---VERLLRDVER 301
                                       5667777777..445566677888899999****************95643332...2222333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 3140.25
//
Query:       gi|313125779|ref|YP_004036049.1|  [L=334]
Description: hypothetical protein Hbor_10100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2093.95
//
Query:       gi|313125780|ref|YP_004036050.1|  [L=243]
Description: haloacid dehalogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-21   77.2   0.0    3.2e-21   76.2   0.0    1.5  1  HAD_2           Haloacid dehalogenase-like hydrolase
    5.3e-13   49.7   0.3    9.3e-13   48.9   0.3    1.4  1  Hydrolase       haloacid dehalogenase-like hydrolase
    6.1e-10   39.0   0.3      1e-09   38.3   0.3    1.4  1  Hydrolase_like  HAD-hyrolase-like
    5.5e-08   33.4   0.5    7.3e-08   33.0   0.5    1.2  1  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.22   11.3   0.0        3.4    7.4   0.0    2.1  1  NIF             NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.0   9.1e-25   3.2e-21       1     178 []      22     211 ..      22     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 9.1e-25
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeygls.elsee.elrkliglslre.llrklgeseeeee...........kie 63 
                                       ++FDlD+Tl+  +    + + e++e +g +  ++ e +++++ ++ +r  ++ +l  +  +             +  
  gi|313125780|ref|YP_004036050.1|  22 VLFDLDDTLVRYRRSPGSLLGEAFEACGTDhLFPVEaYYDRFEEFADRTsSMAELRRE--CFAaicesrgydpeTGR 96 
                                       79**********************9997665343330344444433322022222222..22234556677778777 PP

                             HAD_2  64 ellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpev 140
                                       ++ + + e  ++++v++++g++ +L +  + +y+lg+vT++ ++a+ +k+++ g+ +y +++v + + +  KP+p+ 
  gi|313125780|ref|YP_004036050.1|  97 QVADAFAEARDHRNVEFLPGAEHVLRTF-AGRYRLGVVTNGPQDAQAQKIDASGVGEYVETVVYAGHETATKPAPDA 172
                                       7778888888888***************.9*********************************************** PP

                             HAD_2 141 iekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                       ++ al++l++ +e+++ vG s  +D+ +a +ag+ +++v
  gi|313125780|ref|YP_004036050.1| 173 FALALDRLDVAPENAVHVGNSVeSDVAGANAAGVGSVWV 211
                                       ***********************************9997 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.3   2.6e-16   9.3e-13       2     210 .]      20     205 ..      19     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.6e-16
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH....HHHHHHHHHETTTE.HHHHTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.xxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar....sgaltgfatfigrg.ayaigk 73 
                                       ++v+fD+d TL++ ++s   ++ +a                   + a   ++    +  +++f++f++r    a+ +
  gi|313125780|ref|YP_004036050.1|  20 EAVLFDLDDTLVRYRRSPGSLLGEA-------------------FEACGTDHlfpvEAYYDRFEEFADRTsSMAELR 77 
                                       79**********8886666666666...................444444445643334488888888889999999 PP

                                       HHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  74 pewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaer 150
                                       +e+++a        +  g   + gr va       a+   + + +  p+a+++++++  + ++++++t++ +  +  
  gi|313125780|ref|YP_004036050.1|  78 RECFAAI------CESRGYDPETGRQVADA----FAEARDHRNVEFLPGAEHVLRTFAGR-YRLGVVTNGPQDAQAQ 143
                                       9999999......55555555555555555....5555556677799*********9944.59*****999988886 PP

                                       HHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 151 aanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                        ++  G  +y++ v+ +  et  kp p+++  a+++L + pe+ ++VG +v  D+a++ aAg
  gi|313125780|ref|YP_004036050.1| 144 KIDASGvGEYVETVVYAGHETATKPAPDAFALALDRLDVAPENAVHVGNSVEsDVAGANAAG 205
                                       66666666999**************************************************8 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.3   2.8e-13     1e-09       3      73 ..     166     236 ..     164     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.8e-13
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEE CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddla 73 
                                        KP+p ++  al +l+++pe+ + +G ++++D+agAn+aG+ sv V     + e  ++++ +p+  ++++ 
  gi|313125780|ref|YP_004036050.1| 166 TKPAPDAFALALDRLDVAPENAVHVGNSVESDVAGANAAGVGSVWVSDSSADIEPIPDDAPGPDDRIESVS 236
                                       6**********************************************999999999999999988777775 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.5     2e-11   7.3e-08       1     184 [.      22     218 ..      22     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2e-11
                               HAD   1 alfDfDgTLldg..dslelllrfllrrgaprlwralreklllal....frellrldraglaelleallaglseelaa 71 
                                       +lfD+D TL++   +++ ll +++ ++g  +l+   + + +        +++++l+r+ +a+  e+  +g+++e  +
  gi|313125780|ref|YP_004036050.1|  22 VLFDLDDTLVRYrrSPGSLLGEAFEACGTDHLFPVEAYYDRFEEfadrTSSMAELRRECFAAICES--RGYDPETGR 96 
                                       79*******999545555999999999998885555555333331133555555555555555554..9******** PP

                               HAD  72 elerfvaevirpk..lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.....rltge 141
                                       ++++++ae++  +   + pga  +l+   a  +r+ vv++g++     + ++ g    +++ +e++        t+ 
  gi|313125780|ref|YP_004036050.1|  97 QVADAFAEARDHRnvEFLPGAEHVLR-TFAGRYRLGVVTNGPQDAQAQKIDASG----VGEYVETVVyagheTATKP 168
                                       ******999999986366********.667778*****************9999....4442222211111222222 PP

                               HAD 142 ......lglegkpvrgegkvaalre....wlaaegegidleevvayGDspsDl 184
                                             l l+  +v+ e+ v++ ++     ++a+ +g     +v ++Ds +D+
  gi|313125780|ref|YP_004036050.1| 169 apdafaLALDRLDVAPENAVHVGNSvesdVAGANAAGVG---SVWVSDSSADI 218
                                       222233346666666666664444443333333333333...56667777776 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00095       3.4      32      82 ..     110     159 ..      20     203 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00095
                               NIF  32 svlkRpgldefLkelsklyevvifTasseeyaeavidildpekkllshrly 82 
                                        v   pg+++ L++ +  y +++ T++ ++  ++ id+    + +++ ++y
  gi|313125780|ref|YP_004036050.1| 110 NVEFLPGAEHVLRTFAGRYRLGVVTNGPQDAQAQKIDASGVGE-YVETVVY 159
                                       3333389999999999999999999999988888888765543.4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 1354.56
//
Query:       gi|313125781|ref|YP_004036051.1|  [L=429]
Description: zn-dependent protease with chaperone function [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-37  129.3   1.8    3.4e-37  128.1   0.1    2.2  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra
    2.2e-37  128.7   0.0    3.2e-37  128.2   0.0    1.2  1  Peptidase_M48    Peptidase family M48
     0.0045   16.2   0.0      0.012   14.8   0.0    1.7  1  Peptidase_M56    BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.026   14.1   0.1      0.076   12.6   0.0    1.7  2  DUF2268          Predicted Zn-dependent protease (DUF2268)
       0.15   12.3   0.1       0.31   11.3   0.1    1.6  1  DUF4157          Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1   0.1   9.4e-41   3.4e-37      16     181 ..      43     204 ..      33     205 .. 0.97
   2 ?   -0.2   0.3      0.22   7.9e+02      17      45 ..     220     248 ..     212     335 .. 0.54

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 9.4e-41
                   Peptidase_M48_N  16 adaitkekfdksraYgldksrfglvsslyslilllallllgllpflwklsgkllgldaeseilqslvfllllslist 92 
                                       +++++ ++ d++ aY+++k++++ ++s+++ +l la+++ gl+  +  ++++    +  s++lq++ +l+  +++s 
  gi|313125781|ref|YP_004036051.1|  43 RESLDVDDPDRMLAYQRQKTTLSRIQSWLGVVLVLAVVVSGLFGDVVGMLTE----TGRSTVLQGVGLLIGAVVLSR 115
                                       5677788889999***********************************9999....889****************** PP

                   Peptidase_M48_N  93 lislPfslYstFviEekhGfnkqtlklfikdklkslllalviglpllaallwiiewggeyfylylwlfllvfslllm 169
                                       l++ Pf+lY+tFv+Ee++Gfn+qtl+l++ d++ +l++++++ +++  ++l  +e + + + +  w++++ fsll+m
  gi|313125781|ref|YP_004036051.1| 116 LFGAPFDLYETFVVEERFGFNNQTLGLWLRDFVIGLVISVAFSAVIGGVVLTAVERLPTLWPVAGWAIVVGFSLLMM 192
                                       ***************************************************************************** PP

                   Peptidase_M48_N 170 tiyPtlIaPLFn 181
                                       ++yP +IaPLFn
  gi|313125781|ref|YP_004036051.1| 193 VVYPRFIAPLFN 204
                                       ***********9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                   Peptidase_M48_N  17 daitkekfdksraYgldksrfglvsslys 45 
                                       d+++++ f+  + Y++d sr +  s++y 
  gi|313125781|ref|YP_004036051.1| 220 DVFDRAGFECEQVYEMDASRRSSHSNAYF 248
                                       55666666666666666666665555543 PP

>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.2   0.0   8.8e-41   3.2e-37       3     194 ..     210     412 ..     208     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 8.8e-41
                                       -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT....-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkr....NAFalgggknkrivltdgLlkqllseeelaaVlGHElGHi 75 
                                       + + l++ v++++++ag+  +  +vy++++++r    NA+++g+g++kr+vl+d+L+ + ++++ ++aVl+HEl+H+
  gi|313125781|ref|YP_004036051.1| 210 ESGALRDAVDDVFDRAGF--ECEQVYEMDASRRsshsNAYFVGFGETKRVVLFDTLV-EQMDHDSVQAVLAHELAHW 283
                                       67789999**********..*********99999999********************.******************* PP

                                       HTTHHHHH..HHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT............HHHHHHHH CS
                                       xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxx RF
                     Peptidase_M48  76 khrhsvvs..livsllasillllglallisraeedaagafldalavliglliillfl............alSRkrEy 138
                                       k++h  ++  ++  ++  ++ +l  + + ++  e+    f+  + ++++l i ll +             lS + E+
  gi|313125781|ref|YP_004036051.1| 284 KRGHIWKQlgASAVQMGVVFGFLWWVTTSQWVYEA----FALPTVTYAALAIGLLYAgpmlsllspltnRLSLAHER 356
                                       *****887333333333333333333333333333....3333444444444444445666778************* PP

                                       HHHHHHHHTTT.HHHHHHHHHHHHHHTT--S---HHHHHHS-SS--HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 139 qADeagvellkrakdlvraliklakdlerqdvsaslrsellstHPplleRiqalke 194
                                       +AD ++++++ +++ ++ral +la ++++++  +  +++++++HPp++eRi++l++
  gi|313125781|ref|YP_004036051.1| 357 EADDFAAQTMGESESMTRALTTLAGENLSNPFPHPWYAAFHYSHPPIPERIRRLRD 412
                                       *****************************************************985 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.3e-06     0.012     179     216 ..     255     292 ..     247     311 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-06
                     Peptidase_M56 179 prIvlPadflkklsdeeleyillHElaHlkrkDllvnl 216
                                        r+vl + ++++++ +  + +l+HElaH kr+ ++ +l
  gi|313125781|ref|YP_004036051.1| 255 KRVVLFDTLVEQMDHDSVQAVLAHELAHWKRGHIWKQL 292
                                       478888889**********************9877655 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.1e-05     0.076      31      78 ..     238     285 ..     216     299 .. 0.81
   2 ?   -2.1   0.0      0.68   2.4e+03      98     113 ..     355     370 ..     351     389 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                           DUF2268  31 enrklieekgykgglaipdkiflfl.leneyskerlaallaHEyhHvvr 78 
                                       + r+   +++y  g++  ++++lf  l ++ + ++++a+laHE+ H  r
  gi|313125781|ref|YP_004036051.1| 238 S-RRSSHSNAYFVGFGETKRVVLFDtLVEQMDHDSVQAVLAHELAHWKR 285
                                       3.45666777777888888888887799999999************876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.68
                           DUF2268  98 EGlAesfatelvgeek 113
                                       E  A+ fa++++ge++
  gi|313125781|ref|YP_004036051.1| 355 EREADDFAAQTMGESE 370
                                       5579999999999987 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   8.7e-05      0.31      45      72 ..     256     283 ..     213     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
                           DUF4157  45 ndivfaageyqpesaagrellaHELtHv 72 
                                       + + f     q++  + +++laHEL+H 
  gi|313125781|ref|YP_004036051.1| 256 RVVLFDTLVEQMDHDSVQAVLAHELAHW 283
                                       5677888888999999***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2619.82
//
Query:       gi|313125782|ref|YP_004036052.1|  [L=168]
Description: hypothetical protein Hbor_10130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1066.20
//
Query:       gi|313125783|ref|YP_004036053.1|  [L=313]
Description: methenyltetrahydromethanopterin cyclohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.5e-121  405.4   0.0   1.7e-121  405.3   0.0    1.0  1  MCH       Cyclohydrolase (MCH)


Domain annotation for each model (and alignments):
>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.3   0.0  9.7e-126  1.7e-121       1     311 []       3     309 ..       3     309 .. 0.99

  Alignments for each domain:
  == domain 1  score: 405.3 bits;  conditional E-value: 9.7e-126
                                       -HHHHHHHHHHHHHHTHHHHT-EEEE-TTS-EEEESSSSS---HHHHHHHHHHHTTT-EEEEEEEEEETTEEEEEEE CS
                               MCH   1 SvnelalelveellekaeelrieveelengatviDaGveaeGgleAGlllaeiclggLaevslelsevkgaklpave 77 
                                       S+n++a+elv+e++++a+elr++v+el++gatv+D+Gv+aeGg+eAGlll+ei ++gLa+++ ++++v+ga+ p++e
  gi|313125783|ref|YP_004036053.1|   3 SINRMAIELVDEAIDFADELRVDVYELDTGATVLDFGVNAEGGIEAGLLLSEIETAGLATIQSQMGDVAGAPRPYIE 79 
                                       8**************************************************************************** PP

                                       EEESSHHHHHTTTTS--EEEEET.TEEEEEESTTHHHHTSHHHHHHHT-----S-EEEEEESSS---HHHHHHHHHH CS
                               MCH  78 vstdhPvlacLasqkAgWelsae.kffalgsGPaRalaakeelfeelgyedeadaavlvlesdklPdeevvekvaee 153
                                       v+tdhP+la+L+sqkAgWel+ e +f++lgsGPaRal+a+e+ f++++y de+d +vl +es +lPd+ev+e+vae+
  gi|313125783|ref|YP_004036053.1|  80 VQTDHPALALLCSQKAGWELAFEsGFEGLGSGPARALVAEEDEFHQVEYFDEFDLTVLGVESIELPDDEVAEHVAET 156
                                       *********************9956**************************************************** PP

                                       HTS-GGGEEEEEE-SSSHHHHHHHHTTHHHHHHHHHHHTT--GGGEEEEEEEEE-----SSHHHHHHHHHHHHHHH- CS
                               MCH 154 cgvepenvtllvaptaSlaGsvqvaaRvvevalhkleelgfdlekivsavgtaPiapvakdelkamgrtndailYgg 230
                                       +gvep+ v+l +++t S +Gsv+ aaR++e+a+++l+elg+d++ki sa+g+aP+apv+ de  amgrtnda++Ygg
  gi|313125783|ref|YP_004036053.1| 157 AGVEPSGVFLPTYATGSTVGSVTAAARAAELAVFRLFELGYDPRKILSAFGAAPVAPVSYDEGVAMGRTNDALAYGG 233
                                       ***************************************************************************** PP

                                       EEEEEES...TTHHHHHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-GGGSS-SEEEEEETTT--EEEEE---HHHH CS
                               MCH 231 rvhltveaedeeaedlakklpssaskdygkpFaeifkeaeydfykidkalFspAevtvndletgktfkaGelneell 307
                                       +vhltv+    e  d ++++ps+a ++yg+pF++if+ea++dfy+i++++F+pA+vt+ d+ +g t+++Ge++ee+l
  gi|313125783|ref|YP_004036053.1| 234 EVHLTVT----EDFDDFDEVPSTAGEEYGTPFEQIFEEADWDFYDIPATVFAPAKVTI-DVVNGPTYVHGETDEEIL 305
                                       *******....99999******************************************.****************** PP

                                       HHHT CS
                               MCH 308 aesf 311
                                       aesf
  gi|313125783|ref|YP_004036053.1| 306 AESF 309
                                       ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1978.49
//
Query:       gi|313125784|ref|YP_004036054.1|  [L=105]
Description: hypothetical protein Hbor_10150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-22   79.8   0.4    1.2e-22   79.6   0.4    1.1  1  Thiamine_BP  Thiamine-binding protein
     0.0094   16.2   0.5       0.02   15.2   0.5    1.5  1  HalOD1       Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.4   1.4e-26   1.2e-22       2      92 .]       6      92 ..       5      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1.4e-26
                                      EEEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEESS CS
                       Thiamine_BP  2 eisviPlgtegesvskyVakvvevlkesglkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddrrd 79
                                       +sv+P+   ++s+s  Vak+v++l++ ++ ye++pmgT+ie++ +d+++++v +ah+a+     +Rvst +k+dd+r 
  gi|313125784|ref|YP_004036054.1|  6 MLSVAPVI--EDSMSGEVAKAVAALDDFDVAYETNPMGTVIEADdIDTLLDAVGAAHKAVE---GDRVSTFLKVDDKRT 79
                                      689****6..7*************************************************5...56************* PP

                                      S---HHHHHHHHH CS
                       Thiamine_BP 80 keqtleeKvksve 92
                                      ++q++++Kv++ve
  gi|313125784|ref|YP_004036054.1| 80 TDQRAQDKVDAVE 92
                                      **********996 PP

>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.5   2.2e-06      0.02       3      42 ..      15      55 ..      14      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-06
                            HalOD1  3 espstaVveavaavegvdpt.elepLydaiDpdALdaLfas 42
                                      +s+s +V++avaa+ + d+  e +p+  +i  d +d+L++ 
  gi|313125784|ref|YP_004036054.1| 15 DSMSGEVAKAVAALDDFDVAyETNPMGTVIEADDIDTLLDA 55
                                      78999*************97467***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 690.84
//
Query:       gi|313125785|ref|YP_004036055.1|  [L=355]
Description: hypothetical protein Hbor_10160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-37  128.6  21.0    3.6e-37  128.4  21.0    1.1  1  Virul_fac_BrkB  Virulence factor BrkB
  ------ inclusion threshold ------
       0.23   10.9  12.8      0.064   12.7   8.6    2.0  2  DUF373          Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4  21.0     4e-41   3.6e-37       4     257 ..      30     267 ..      27     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 4e-41
                    Virul_fac_BrkB   4 dlsllAaalayytllSlfPlllvllavlgllglddelqeqlldllaevlpegaaevvedilqrllnqaslgllglav 80 
                                       +l+ +A+++ay+++ Sl Pl+l+lla+++ ++ ++ l + + +l+  vl+eg+ + +    +r+++++ ++l+g av
  gi|313125785|ref|YP_004036055.1|  30 KLTFMAGSIAYHAFVSLLPLFLLLLAIAATFQ-NQTLDDSVRTLAGVVLTEGTRDDFFAEATRATQSTGVSLFGGAV 105
                                       6889************************9777.656666666666666999999999999999999999******** PP

                    Virul_fac_BrkB  81 llwsasggvsalrralnkiygveesrsflrkrllsllllllllvllllslvlsvflqslllasapllglglelsell 157
                                       llw  ++++++l++a+  iy+ e s+ f  ++ + +l+ll l+++l++  v++ +++ ++            + ++ 
  gi|313125785|ref|YP_004036055.1| 106 LLWGTLRIFRGLDTAFSDIYESEASNTFGDQIRDGILVLLTLAIVLVIGSVVNDAVGTVS------------SGTV- 169
                                       **********************99877777777777777777777777777776666622............2244. PP

                    Virul_fac_BrkB 158 llqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYGslgaliill 234
                                       ++ ++r+ +++l l la++ +Y+v+p++ v+l +++pG+l aa++++++  lf+ly + +++       ++++++ll
  gi|313125785|ref|YP_004036055.1| 170 AWLIGRL-FLILGLSLALYPMYYVFPDTDVSLLEVVPGTLTAAVGLTVFESLFQLYTA-VSNTAPNSSVVAGILVLL 244
                                       4778888.6888888****************************************988.578888889********* PP

                    Virul_fac_BrkB 235 lWlylsalilLlGaelnaelqer 257
                                        Wly+s+l++LlGa++na+l++r
  gi|313125785|ref|YP_004036055.1| 245 TWLYFSGLVILLGAAVNAVLSNR 267
                                       ********************998 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.5     0.033   2.9e+02     157     285 ..      43     160 ..      11     163 .. 0.56
   2 ?   12.7   8.6   7.1e-06     0.064     153     292 ..     137     270 ..     131     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.033
                            DUF373 157 iLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallllli 233
                                       ++ +l l+ll++a++++++  + +l   +  l +++l +G + d+    +++++ ++++++ ++++   v ll   +
  gi|313125785|ref|YP_004036055.1|  43 FVSLLPLFLLLLAIAATFQ--NQTLDDSVRTLAGVVLTEGTR-DD----FFAEATRATQSTGVSLFGGAV-LLWGTL 111
                                       4555566666666666553..445555555555566667766.44....233444444444444433322.222344 PP

                            DUF373 234 giisgyislesvssasvssglltlilafiygavewlalailtaslgkiidey 285
                                        i+ g+ +   + s+  +s+  + +   i + + +l+  ++++++g++++ +
  gi|313125785|ref|YP_004036055.1| 112 RIFRGLDT---AFSDIYESEASNTFGDQIRDGILVLLTLAIVLVIGSVVNDA 160
                                       55555444...33333334555555555556666666666667777776655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.1e-06
                            DUF373 153 lrktiLvplGlllliyallll.lglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvval 228
                                       +r  iLv+l l+++++  +++   + ++  ++++ l+G ++l+ G++l          +  ++  + ++++ +v ++
  gi|313125785|ref|YP_004036055.1| 137 IRDGILVLLTLAIVLVIGSVVnDAVGTVSSGTVAWLIGRLFLILGLSLAL------YPMYYVFPDTDVSLLEVVPGT 207
                                       5555666666544333333332556779999****************997......456666677777777666666 PP

                            DUF373 229 lllligiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekd 292
                                       l +++g+   ++sl ++++a +++    +++a i  +++wl++++l+++lg +++++l+++++d
  gi|313125785|ref|YP_004036055.1| 208 LTAAVGLT-VFESLFQLYTAVSNTAPNSSVVAGILVLLTWLYFSGLVILLGAAVNAVLSNRSRD 270
                                       66666653.33555555554444444444555556699********************887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2079.33
//
Query:       gi|313125786|ref|YP_004036056.1|  [L=80]
Description: hypothetical protein Hbor_10170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   13.7   1.1       0.12   12.3   0.1    2.0  2  ACT_3     ACT domain


Domain annotation for each model (and alignments):
>> ACT_3  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.6e-06      0.12      45      66 ..       7      28 ..       6      32 .. 0.90
   2 ?   -0.2   0.1     0.055   9.9e+02       6      16 ..      42      52 ..      38      76 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-06
                                      ETTEEEEEEEHHHHHCTT---- CS
                             ACT_3 45 EaEGlTliltkeeAeaagleye 66
                                      E+E  Tl+++ +eA++  l+  
  gi|313125786|ref|YP_004036056.1|  7 EDETATLVVELDEADQSDLDAA 28
                                      9****************99875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.055
                                      HHHHCST-EEE CS
                             ACT_3  6 LskLLasltpe 16
                                      L  LL ++  +
  gi|313125786|ref|YP_004036056.1| 42 LGSLLVTMPET 52
                                      55666666332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 542.75
//
Query:       gi|313125787|ref|YP_004036057.1|  [L=396]
Description: lycopene cyclase domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-10   41.0  27.1    1.3e-10   41.0  27.1    3.3  3  UbiA          UbiA prenyltransferase family
  ------ inclusion threshold ------
        5.3    6.6   9.4        1.8    8.1   0.1    3.2  3  ABC_membrane  ABC transporter transmembrane region


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.9     0.057   5.1e+02     200     231 ..      30      62 ..       9      70 .. 0.53
   2 !   41.0  27.1   1.5e-14   1.3e-10      68     229 ..      85     247 ..      27     261 .. 0.74
   3 ?   -5.8  10.8         2   1.8e+04     110     149 ..     292     332 ..     256     350 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.057
                              UbiA 200 lla.llllllalllllylllalllaalallraa 231
                                       l++ l+ + la+  ++ ++++++la ++ ++ a
  gi|313125787|ref|YP_004036057.1|  30 LASsLFGAALAGDISFGPAFVHVLAMFFAVYTA 62 
                                       222444444445555555555555554444433 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 1.5e-14
                              UbiA  68 ealifaivllilgllll....alllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgs 140
                                        + ++++v +++g+l+     ++ ++  +a+++l +++++++  +  l   ++ +tv   +  +l++ +g++++tg 
  gi|313125787|ref|YP_004036057.1|  85 RGCVLGLVGAAVGFLCClgylWAAVGIGAAVVTLPTWVIGFLHAP-QLDMNPVTATVGYPVGIALAIAGGYYVQTGA 160
                                       344455555555555556666899********************8.888888888999999999************* PP

                              UbiA 141 lsllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllyll 217
                                       ls+++l++a  +++l +++ ++ d +d++ D+ + ++t +vvlG+++ar+++++l  + l+a  +lll   +l++++
  gi|313125787|ref|YP_004036057.1| 161 LSPEPLAFASVFLVLLTGVKVIDDAKDYDYDASIDKRTVAVVLGPRRARRFAHSLFWAGLIA--VLLLTVDGLFPPF 235
                                       ***********9**************************************955555555555..3555555555555 PP

                              UbiA 218 lalllaalallr 229
                                       ++++++a++l+ 
  gi|313125787|ref|YP_004036057.1| 236 AVVAALAFGLVA 247
                                       555555555544 PP

  == domain 3  score: -5.8 bits;  conditional E-value: 2
                              UbiA 110 rlKrrtllgtvvggiafglppllgwaavtgsl.sllallla 149
                                        l+r+t+l+t v++ a +l++ll + av     +++a+ + 
  gi|313125787|ref|YP_004036057.1| 292 VLGRYTYLATEVLFGAIALALLLRANAVRRAAvTIAAIYPV 332
                                       67777777777777777777777777766665222222222 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1   0.00021       1.8      10      62 ..      49     104 ..      43     118 .. 0.83
   2 ?    3.3   0.2     0.006        54     239     271 ..     145     177 ..     133     179 .. 0.72
   3 ?   -0.9   0.5      0.12   1.1e+03     216     250 ..     214     248 ..     209     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHHHHHHHHHSS...TCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane  10 lagvlsplfplvlgrildtlldk...gdpetealnvysllllllglaqfilallqs 62 
                                       +++vl+++f+++++++ d l+d+   g+++++ +++  ++l l+g+a+++l+ l  
  gi|313125787|ref|YP_004036057.1|  49 FVHVLAMFFAVYTAHVKDGLVDFyvrGEDDDHPMTKRGCVLGLVGAAVGFLCCLGY 104
                                       6789999**************999986666678***************99998854 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHH CS
                      ABC_membrane 239 yalalwfGttlvisgelsvgdlvvflslfailf 271
                                        ++ +  G+++v++g+ls++ l + ++++ +l+
  gi|313125787|ref|YP_004036057.1| 145 GIALAIAGGYYVQTGALSPEPLAFASVFLVLLT 177
                                       4556699**************666666665554 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 216 agikkaianglligitqllgllsyalalwfGttlv 250
                                       + +++ +++ ll ++  l++ +++++al fG +  
  gi|313125787|ref|YP_004036057.1| 214 SLFWAGLIAVLLLTVDGLFPPFAVVAALAFGLVAL 248
                                       56788888999999999999999999999997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2479.32
//
Query:       gi|313125788|ref|YP_004036058.1|  [L=143]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-14   51.7   0.0    1.2e-13   51.3   0.0    1.2  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
  ------ inclusion threshold ------
      0.084   13.0   0.0       0.14   12.3   0.0    1.4  1  Cupredoxin_1  Cupredoxin-like domain
       0.29   11.7   1.0       0.46   11.1   1.0    1.3  1  LPAM_1        Prokaryotic membrane lipoprotein lipid attachme


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0     2e-17   1.2e-13       9      99 .]      53     142 ..      45     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2e-17
                                       TETSEEES...SEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEE CS
                       Copper-bind   9 sgdlqFet...keitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkf 82 
                                       +g+++F +   + +t+ +g++vtfv+ ++  HN+v+ ++   +g ++ + +++de +l  +G +++ tfd +g+Y++
  gi|313125788|ref|YP_004036058.1|  53 DGEFVFTPgtdEPLTITAGTEVTFVW-ESDNHNIVVGNQP--EG-ANWEGTPGDESELYDEGYTYEHTFDVPGEYHY 125
                                       55567765222459************.9999*****8876..44.456677778999******************** PP

                                       EETTTTTTTSEEEEEEE CS
                       Copper-bind  83 fCsPHaaagMkgkvtve 99 
                                        C+PH+++gM + ++ve
  gi|313125788|ref|YP_004036058.1| 126 WCEPHKSVGMIADIVVE 142
                                       **************996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.4e-05      0.14      36     101 ..      65     135 ..      33     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                      Cupredoxin_1  36 kievkagekvklkiknkdkt........peefesedlgeekvlapgktttitiaplkpGeYeftcdmhmdakGk 101
                                        +++ ag++v++ ++ +            +++e ++ +e++  + g t++ t+  + pGeY++ c+ h+   G+
  gi|313125788|ref|YP_004036058.1|  65 PLTITAGTEVTFVWESDNHNivvgnqpeGANWEGTPGDESELYDEGYTYEHTF--DVPGEYHYWCEPHKS-VGM 135
                                       489999**999999998888888888655************************..***********9987.454 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.0   7.6e-05      0.46       3      18 .]      12      27 ..      11      27 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.6e-05
                            LPAM_1  3 KillalgalllLsGCs 18
                                      ++ la++ l+ LsGCs
  gi|313125788|ref|YP_004036058.1| 12 RSALAAVGLVGLSGCS 27
                                      7889***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 983.41
//
Query:       gi|313125789|ref|YP_004036059.1|  [L=278]
Description: hypothetical protein Hbor_10220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-67  226.9   0.0    3.9e-67  226.8   0.0    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase
      0.002   17.9   0.4     0.0047   16.7   0.1    1.8  2  eIF-1a           Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.8   0.0   4.3e-71   3.9e-67       1     286 []       2     274 ..       2     274 .. 0.95

  Alignments for each domain:
  == domain 1  score: 226.8 bits;  conditional E-value: 4.3e-71
                   Methyltrn_RNA_3   1 tvsiaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelF 77 
                                       t+s+++Pss++++a++++++t+++g++ARaa++F+ d+++vf+d+e+e+ ++  + +f++++L+Y++tPpYLrke++
  gi|313125789|ref|YP_004036059.1|   2 TLSVLVPSSLVREAEDKREATRKLGYVARAATVFRADRLIVFPDREGER-RW--GRKFVETVLRYAVTPPYLRKEVW 75 
                                       79********************************************997.56..89********************* PP

                   Methyltrn_RNA_3  78 plhkelkyaglLppldaphhl..rsseegeyreGvvvekskekkskkklVniGlkkevklel..kqevpegtRVtVk 150
                                       + ++el+y+g+Lppl +      +s+++g++++G+v+e+ +++++   +Vn+G++++++l +  ++ v+eg+RV ++
  gi|313125789|ref|YP_004036059.1|  76 GHRDELEYVGVLPPLLVSSTTgsESDDSGSLQQGIVTEVGPDGRV---RVNCGMQHPISLYTpsDMMVKEGERVAIR 149
                                       ***************988887845555****************99...9**********999999************ PP

                   Methyltrn_RNA_3 151 lsseesveakvVspsepreeaglywGYsVrlakslsavftespfeggydlsigtserge.kveeklaelekkkefkh 226
                                       +ss+e+v+a++V+++ p        G++V ++ +l++++ ++    ++ ++i+ts+ ge  +  kla+l+ ++e++ 
  gi|313125789|ref|YP_004036059.1| 150 ISSREPVRARIVDEPVP--------GFDVSRM-DLEEALGRA----DAGITIATSRFGEsLTVPKLADLSPRIEREG 213
                                       *****************........*******.********9....99***********888999****99999*** PP

                   Methyltrn_RNA_3 227 llivfGg.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLalL 286
                                       +++vfG+  rgl+++l  d e+   + +    Fdlwlnt+p+qgs+ +rtEEa++++La+L
  gi|313125789|ref|YP_004036059.1| 214 ATVVFGSpGRGLPDILGIDAEEVTVEPSDGPGFDLWLNTIPRQGSEVVRTEEAMFASLASL 274
                                       ****************9998774446777788**************************997 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       1.6   1.5e+04      29      40 ..      64      75 ..      60      78 .. 0.77
   2 !   16.7   0.1   5.2e-07    0.0047       4      62 ..     108     161 ..     106     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.6
                                      EEE-HHHHCT-- CS
                            eIF-1a 29 aeipgkfRnkiw 40
                                      a +p+ +R+ +w
  gi|313125789|ref|YP_004036059.1| 64 AVTPPYLRKEVW 75
                                      567788899999 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.2e-07
                                       EEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEE CS
                            eIF-1a   4 igkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIv 62 
                                        g+V+e+ +++++rV +   ++ +  ++p  +     +k+G +V + +s  ++ ++rIv
  gi|313125789|ref|YP_004036059.1| 108 QGIVTEVGPDGRVRVNCG-MQHPISLYTPSDMM----VKEGERVAIRISSREPVRARIV 161
                                       69***************7.7************9....**************999****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 1482.00
//
Query:       gi|313125790|ref|YP_004036060.1|  [L=338]
Description: 50S ribosomal protein L3 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.2e-105  352.7   0.0   4.4e-105  351.7   0.0    1.5  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.7   0.0  2.4e-109  4.4e-105       1     369 []       1     338 []       1     338 [] 0.94

  Alignments for each domain:
  == domain 1  score: 351.7 bits;  conditional E-value: 2.4e-109
                                       XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEE CS
                      Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavt 77 
                                       m+++  ++pr+gs+ ++pr+Ra++e+++++s+P dd s    l++f+GyKaGmt++  + d ++s+ +++e +++vt
  gi|313125790|ref|YP_004036060.1|   1 MPQP--SRPRKGSMAYSPRQRAAKEVPRIRSWPDDDGS--PGLQGFAGYKAGMTQVMMVNDEANSPREGMEEAVPVT 73 
                                       7777..99*****************************9..89*********************************** PP

                                       EEEC--EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHH CS
                      Ribosomal_L3  78 vvetppmvivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeik 154
                                       vvetppm++v+v++y++tp+G ++l++vwa +  e+++r+l             +   ++  +++ + + a +e+  
  gi|313125790|ref|YP_004036060.1|  74 VVETPPMRAVAVRAYEDTPYGAKPLTEVWASEFVENLDRTL-------------DLPSEDTFEEDADDLRAAVEA-- 135
                                       *****************************************.............333344445555555554443.. PP

                                       HSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTC..EEECCCCS-TTSEEEEEEEE---EE CS
                      Ribosomal_L3 155 keasvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealek..tvavaavFrqgeliDvigvtkGkGf 229
                                        e   +rvi+htv   +k + +Kk++++E++v+gG++ e+ dfa + +e+   + +++vFr+ge++D++gvtkGkG+
  gi|313125790|ref|YP_004036060.1| 136 GEVDDIRVITHTVPASMKNIPKKKPDVMETRVGGGSLQERSDFALDLVEEggEHSMSDVFRAGEYLDAAGVTKGKGT 212
                                       23345*********************************************99************************* PP

                                       E-HHHHCT----STTTSSS..SSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.S CS
                      Ribosomal_L3 230 eGvvkRWgvkklprkthrg..lRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdlt 304
                                       +G+vkRWgv+k+++k++r+  +R+++++g+w+p+rV+stv++ Gq+Gyh+Rtelnk+++++g+              
  gi|313125790|ref|YP_004036060.1| 213 QGPVKRWGVQKRKGKHARQgwRRRIGNLGPWNPSRVRSTVPQLGQTGYHQRTELNKRLIDLGD-------------- 275
                                       *******************9*******************************************.............. PP

                                       S..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                      Ribosomal_L3 305 ekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                       +++ t +GGfv yGev++++ lvkGs pGp krl+++r++++++ +++ ++ev  +f++tas++g
  gi|313125790|ref|YP_004036060.1| 276 GDDATVDGGFVGYGEVDGPYALVKGSLPGPDKRLLRFRPAIRPNDQPRLDPEV--RFVSTASNQG 338
                                       5667899**********************************************..********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1894.83
//
Query:       gi|313125791|ref|YP_004036061.1|  [L=248]
Description: 50S ribosomal protein L4 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-45  155.5   0.5    1.5e-45  155.3   0.5    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3   0.5   8.1e-50   1.5e-45       3     191 ..      18     247 ..      16     248 .] 0.93

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 8.1e-50
                                       E-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.....STTSTT---S CS
                      Ribosomal_L4   3 LspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.....spiargGgva 73 
                                       L p+vF++ +r+dli+rav+a +anr+q +++++ a++++ +  ++l++  G+G+++ ++ +     +p+a++G++a
  gi|313125791|ref|YP_004036061.1|  18 L-PEVFETAYRPDLIKRAVLAAQANRKQAYGADPyAGMRTPA--ESLGS--GRGMSHDPRENgrarrVPHAVSGRKA 89 
                                       7.9***************************************..6****..********99999999********** PP

                                       S---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES.....---..-S.......S--HHHHHHHHHHTT-... CS
                      Ribosomal_L4  74 hgpkperdystklnkKvrrlAlrsaLsakakqglllvvd.....nle.ple.......esktkelvellkklgl... 134
                                       h+pk+e+d  +++nkK+r+lA+rsaL+a+++++l+  ++     +l+ pl+         ktke+v+ll++lg+   
  gi|313125791|ref|YP_004036061.1|  90 HPPKAEKDQGKEINKKERKLAVRSALAATTDAELVAERGhrfdeDLDlPLVvsddfedLVKTKEVVSLLESLGVhad 166
                                       ***************************************9776655544448888888899**********999999 PP

                                       .......................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHH CS
                      Ribosomal_L4 135 .......................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvitks 184
                                                              ++ks+L+v+se   +  +aarnl+gv+v+++ ++n++dl+++++    +++t+s
  gi|313125791|ref|YP_004036061.1| 167 vehsednkkvragqgkargrkykRPKSILFVTSE---EPSKAARNLAGVDVATASNVNAEDLAPGTHagrlTIFTES 240
                                       99999999999999999999999999******86...99************************************** PP

                                       HHHHHHH CS
                      Ribosomal_L4 185 aveklee 191
                                       ave++++
  gi|313125791|ref|YP_004036061.1| 241 AVEEVAD 247
                                       ***9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1456.71
//
Query:       gi|313125792|ref|YP_004036062.1|  [L=83]
Description: 50S ribosomal protein L23 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-14   53.1   1.6      2e-13   50.5   1.6    1.8  1  Ribosomal_L23  Ribosomal protein L23
  ------ inclusion threshold ------
      0.065   14.0   0.4         12    6.7   0.1    2.0  2  DUF4162        Domain of unknown function (DUF4162)
       0.12   12.7   0.2        0.2   11.9   0.2    1.4  1  DUF4777        Domain of unknown function (DUF4777)


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   1.6   3.3e-17     2e-13       2      77 ..       3      66 ..       2      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 3.3e-17
                                      SEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEEEE CS
                     Ribosomal_L23  2 vilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkaiVt 77
                                      v+  P++tEk+++ ++  nk+ F V++da K+ei + +e+ ++V +ekVnt++ ++ +k+             a+V+
  gi|313125792|ref|YP_004036062.1|  3 VVHHPLVTEKAMNEMDFdNKLQFIVDLDAAKPEIVEEIESRYEVSIEKVNTQVTPKGTKK-------------ATVR 66
                                      7889***********9779**********************************9996665.............3333 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0021        13      35      63 ..      18      46 ..       5      54 .. 0.76
   2 ?    6.7   0.1     0.002        12      31      57 ..      53      80 ..      46      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0021
                                      -TTS-EEEEE-----------------EE CS
                           DUF4162 35 eeggelelkledeeaanellkaltsgvei 63
                                      +++++l++ ++ ++a++e+ ++++s++e+
  gi|313125792|ref|YP_004036062.1| 18 DFDNKLQFIVDLDAAKPEIVEEIESRYEV 46
                                      3458999999999**********877774 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.002
                                      EEEE-TT.S-EEEEE------------- CS
                           DUF4162 31 eeveeeg.gelelkledeeaanellkal 57
                                      ++v+ +g ++++++l+++++a+e+ +++
  gi|313125792|ref|YP_004036062.1| 53 TQVTPKGtKKATVRLSEDDDAQEVASRI 80
                                      5667777788*************99876 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   3.4e-05       0.2      20      45 ..      31      56 ..      23      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                           DUF4777 20 aTldEivervaerydlseeelkkvVk 45
                                      a+ +Eive + +ry++s e+++ +V+
  gi|313125792|ref|YP_004036062.1| 31 AAKPEIVEEIESRYEVSIEKVNTQVT 56
                                      5668********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 485.91
//
Query:       gi|313125793|ref|YP_004036063.1|  [L=242]
Description: 50S ribosomal protein L2 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-46  156.8   3.1    4.6e-46  156.1   3.1    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    5.3e-19   68.0   0.0    2.6e-18   65.8   0.0    2.2  3  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   3.1   5.1e-50   4.6e-46       1     123 [.      90     217 ..      90     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 5.1e-50
                                       SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCT CS
                    Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehk 77 
                                       k+Gn+lpl++ipeG+ v+n+e ++g+ggk+ar++Gt+aq+++++++ ++vklpSgev++++ +crAtiGvv++g+++
  gi|313125793|ref|YP_004036063.1|  90 KPGNTLPLAEIPEGVPVCNVERQVGDGGKFARASGTSAQLLTHDRHVAVVKLPSGEVKRLNPQCRATIGVVAGGGRT 166
                                       68******************************************9******************************** PP

                                       T----STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS--SSSSTEE CS
                    Ribosomal_L2_C  78 ekklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gktksrkapvs 123
                                       ek+++kAg+k+++      ++p+vrGvamn+vdHp+GGG     G    r ++vs
  gi|313125793|ref|YP_004036063.1| 167 EKPFVKAGKKHHKmrargIKWPRVRGVAMNAVDHPFGGGGrqhpG----RPKSVS 217
                                       *************9999889******************9945554....444433 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   2.9e-22   2.6e-18       1      75 [.      11      81 ..      11      83 .. 0.91
   2 ?   -3.1   0.0      0.87   7.8e+03      49      59 ..     135     145 ..     135     161 .. 0.73
   3 ?   -2.5   0.0      0.56     5e+03      43      60 ..     150     168 ..     143     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.9e-22
                                      TB-TT.--BSSTT--------EE-B--S-..--SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE CS
                      Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkr..nkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtv 75
                                      Gr+++ +r+++++++         +++k+  ++++v+g+Vv+ie+Dp+RsAp+A v++edg++r+++apeg+ vGdt+
  gi|313125793|ref|YP_004036063.1| 11 GRGTPtFRAPSHRYKA-------ELSHKKaeSEDTVSGTVVDIEHDPARSAPVAAVEFEDGDQRLVLAPEGVAVGDTI 81
                                      9***************.......566665435677******************************************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.87
                                       -EEEEEETTTE CS
                      Ribosomal_L2  49 piAlvkyedge 59 
                                       ++A vk+ +ge
  gi|313125793|ref|YP_004036063.1| 135 HVAVVKLPSGE 145
                                       57888888765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.56
                                       -TT-SS-EEEEEETT.TEE CS
                      Ribosomal_L2  43 DpgRsApiAlvkyed.gek 60 
                                       +p   A i+ v+ +   ek
  gi|313125793|ref|YP_004036063.1| 150 NPQCRATIGVVAGGGrTEK 168
                                       6777788888887773344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1412.59
//
Query:       gi|313125794|ref|YP_004036064.1|  [L=141]
Description: 30S ribosomal protein s19 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-31  105.8   0.0      1e-30  105.4   0.0    1.1  1  Ribosomal_S19  Ribosomal protein S19
  ------ inclusion threshold ------
      0.066   12.3   0.0      0.068   12.2   0.0    1.1  1  Citrate_synt   Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   1.2e-34     1e-30       1      81 []      42     124 ..      42     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 1.2e-34
                                       .HHHSS.TTCCCHHHHHHHHHH.TS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-S CS
                     Ribosomal_S19   1 rslkkg.pfvqesllkkvrkak.aekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspT 75 
                                       rs+++g +  +e+ll+ vr+a+ +e+++++i+th+Rd+ IlP++v+ t++VynG++f +v+i++emvGh+LgEF++T
  gi|313125794|ref|YP_004036064.1|  42 RSINRGlTLQKEKLLETVREADpEETANSPIRTHLRDMPILPSFVDKTFAVYNGQSFERVRIQPEMVGHYLGEFQLT 118
                                       89****999**********9997778*************************************************** PP

                                       S----S CS
                     Ribosomal_S19  76 rkpvkh 81 
                                       r+ v+h
  gi|313125794|ref|YP_004036064.1| 119 RNSVEH 124
                                       ****99 PP

>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.6e-06     0.068      17      67 ..       8      51 ..       2     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-06
                                      TTTTE.EEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCT CS
                      Citrate_synt 17 gekge.lrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaea 67
                                      g++ge  +YRGy+++eL   + +++ev+ lL     P + + +++++ l+ +
  gi|313125794|ref|YP_004036064.1|  8 GREGEeFTYRGYTLDELQ--EMELDEVVELL-----P-ARQRRSINRGLTLQ 51
                                      5556679*********87..699********.....6.45555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.36s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 800.32
//
Query:       gi|313125795|ref|YP_004036065.1|  [L=153]
Description: 50S ribosomal protein L22 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-17   62.9   0.0    3.5e-17   62.5   0.0    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
       0.16   11.4   0.0        0.2   11.1   0.0    1.1  1  ATP-grasp_5    ATP-grasp domain


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   3.9e-21   3.5e-17       4     102 ..      20     148 ..      18     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3.9e-21
                                       EEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST............................THHHHHHHHHHH CS
                     Ribosomal_L22   4 snlrvsfkklrevarlIrgmkveeAlkyLkf..skkk............................aakfvlklLkna 50 
                                       ++ ++s k+ + + r I+gm+ve+A +yL+   + ++                            a+k +l+lL+n+
  gi|313125795|ref|YP_004036065.1|  20 RDRPISLKHSKAISREIKGMTVEDAEEYLDAviEGERsvpfrqhntgvghrsdiegwdagrypekASKAFLELLQNV 96 
                                       66789**************************9766669*************************************** PP

                                       HHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  51 eanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                        ana++ g d  s+ I ++ ++k  +  +r++rA G ++p++   c +e+++
  gi|313125795|ref|YP_004036065.1|  97 AANADEAGFDGRSMEIMHVAAHKVGERPGRKPRAFGSADPFNTTLCDVELII 148
                                       *************************************************997 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.3e-05       0.2      31     105 ..      40     113 ..      32     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.3e-05
                       ATP-grasp_5  31 lassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkekspeariegvlVqem 105
                                        +++aee ++a+ e +  v  + +  ++ h++d++G     + +e+  +a+ e+l++v++++ ea ++g + + m
  gi|313125795|ref|YP_004036065.1|  40 TVEDAEEYLDAVIEGERSVPFRQHNTGVGHRSDIEGWDA-GRYPEKASKAFLELLQNVAANADEAGFDGRSMEIM 113
                                       67889999999999999999999****************.589**************************998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 866.90
//
Query:       gi|313125796|ref|YP_004036066.1|  [L=310]
Description: 30S ribosomal protein S3 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-20   73.6   0.7    3.3e-20   72.4   0.6    1.7  2  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    7.5e-17   60.9   0.0    1.6e-16   59.8   0.0    1.6  1  KH_2            KH domain
     0.0045   16.8   0.2      0.023   14.5   0.0    2.3  2  KH_1            KH domain
  ------ inclusion threshold ------
        3.4    7.6   7.8       0.66    9.9   0.1    3.0  3  KH_4            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2     9e+03      60      81 ..      14      35 ..      11      36 .. 0.82
   2 !   72.4   0.6   7.3e-24   3.3e-20       1      83 []      99     182 ..      99     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                      HHH-EEEEEEEEETTEEEEEEE CS
                    Ribosomal_S3_C 60 radidyavaeaktkyGiiGvkV 81
                                      r++id+ +ae   + G  G  V
  gi|313125796|ref|YP_004036066.1| 14 RSQIDEFFAEELGRAGYGGMDV 35
                                      7899999999998888888776 PP

  == domain 2  score: 72.4 bits;  conditional E-value: 7.3e-24
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       +a++le+++ fR+a +++i r+m+aga G++i++sG+++ + ++r ek+++G++++  +++++ +d++   a +k G
  gi|313125796|ref|YP_004036066.1|  99 LANALERGWYFRKAGHTTIDRIMDAGALGAEIVLSGKVT-GARSRVEKFNRGYIKHngEPAQEIVDEGQGVAVMKLG 174
                                       689************************************.89*********************************** PP

                                       EEEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVwI 83 
                                       +iGv+V+I
  gi|313125796|ref|YP_004036066.1| 175 TIGVTVKI 182
                                       ******98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   3.7e-20   1.6e-16       2      77 ..      17      89 ..      16      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 3.7e-20
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTG CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpe 77
                                      i+e++a+e+  ag++++++ +t+ ++ iv+++++pg+vIGkgG+ni+k++k+l+ ++ +le+ ++   + +V +p+
  gi|313125796|ref|YP_004036066.1| 17 IDEFFAEELGRAGYGGMDVAKTPMGTQIVLKAEKPGMVIGKGGKNIRKVTKALETRF-NLEDPQID--VQEVDEPD 89
                                      899******************************************************.5******9..78888886 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     5e-06     0.023       4      32 ..      44      72 ..      41      90 .. 0.77
   2 ?   -2.2   0.0      0.87   3.9e+03      29      40 ..     175     186 ..     173     209 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-06
                                      EEEGGGHHHHHHTGGGHHHHHHHHHHT-E CS
                              KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgak 32
                                      i +++++ g +IGkgG+nI++  +   ++
  gi|313125796|ref|YP_004036066.1| 44 IVLKAEKPGMVIGKGGKNIRKVTKALETR 72
                                      5666677799***********98744555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.87
                                       H.T-EEEEESSTT CS
                              KH_1  29 t.gakIkvpksed 40 
                                       t g+ +k+++ + 
  gi|313125796|ref|YP_004036066.1| 175 TiGVTVKIIP-PG 186
                                       5578888874.22 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00015      0.66      33      51 ..      44      62 ..      33      69 .. 0.87
   2 ?    0.3   1.2      0.15   6.6e+02       5      28 ..     247     270 ..     245     284 .. 0.72
   3 ?   -2.6   0.1       1.2   5.2e+03       4      23 ..     285     304 ..     282     309 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00015
                              KH_4 33 lnvegedlGrvIGkrGrtl 51
                                      + ++ e+ G vIGk G+++
  gi|313125796|ref|YP_004036066.1| 44 IVLKAEKPGMVIGKGGKNI 62
                                      5577899**********98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
                              KH_4   5 edilkalvddpeevevteeeeeee 28 
                                       e+i++++v++  +ve ++e++e+e
  gi|313125796|ref|YP_004036066.1| 247 EEIVEEVVEESGDVESDAETDESE 270
                                       567788887777777777744443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                              KH_4   4 vedilkalvddpeevevtee 23 
                                       ve  ++ lv ++e+ + +e+
  gi|313125796|ref|YP_004036066.1| 285 VEAEAEDLVAEMEAADEDED 304
                                       55556677766666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1136  (0.063361); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.38s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 1756.49
//
Query:       gi|313125797|ref|YP_004036067.1|  [L=70]
Description: 50S ribosomal protein L29 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-18   64.1   0.4      1e-17   63.8   0.4    1.0  1  Ribosomal_L29  Ribosomal L29 protein
  ------ inclusion threshold ------
       0.03   14.1   0.7       0.06   13.1   0.7    1.6  1  RPAP1_N        RPAP1-like, N-terminal
        0.3   11.2   3.6          5    7.3   0.7    2.2  2  DUF1192        Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.4   1.7e-21     1e-17       1      56 [.       7      63 ..       7      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.7e-21
                                      HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlre 56
                                      +e+r+++ +e +++++el++eL+n +  +a+g ++enp+ri +++++IARikT+++e
  gi|313125797|ref|YP_004036067.1|  7 AEIRDMTPAEREAEVEELETELLNAKAVQAAGgAPENPGRISELKRTIARIKTIQQE 63
                                      59************************9999999*********************997 PP

>> RPAP1_N  RPAP1-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7     1e-05      0.06      11      30 ..       9      28 ..       6      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                           RPAP1_N 11 LasMspeEIeeereeLlesL 30
                                      +++M+p+E+e+e eeL   L
  gi|313125797|ref|YP_004036067.1|  9 IRDMTPAEREAEVEELETEL 28
                                      789*************8665 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.7   0.00083         5      33      52 ..      18      37 ..       5      40 .. 0.88
   2 ?    5.0   0.1    0.0042        25      28      42 ..      46      60 ..      44      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00083
                           DUF1192 33 eaEIaRleaaiakkkasraA 52
                                      eaE++ le+++ ++ka++aA
  gi|313125797|ref|YP_004036067.1| 18 EAEVEELETELLNAKAVQAA 37
                                      8****************999 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0042
                           DUF1192 28 rIalLeaEIaRleaa 42
                                      rI++L+  IaR+++ 
  gi|313125797|ref|YP_004036067.1| 46 RISELKRTIARIKTI 60
                                      9999**99**99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 420.28
//
Query:       gi|313125798|ref|YP_004036068.1|  [L=158]
Description: rnase p/rnase mrp subunit p29 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-26   90.2   0.0    6.9e-26   90.0   0.0    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   0.0   3.8e-30   6.9e-26       1      84 []       6     151 ..       6     151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 3.8e-30
                                       HHHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTE.....EEEEESTTCEEEEEE........... CS
                           UPF0086   1 ekLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksr.....vktvpKegsvFefev........... 61 
                                       e+L++++l+G++veVv+++np+lvgi+G+Vv Et++tl++  ++++     v +vpK+g++++fe+           
  gi|313125798|ref|YP_004036068.1|   6 ETLTRHELNGLRVEVVDAANPDLVGIAGRVVVETMQTLHVDVSDTSnggtrVCQVPKQGATLQFEIpsrdtrpthtd 82 
                                       58***************************************6543344555************************** PP

                                       ...............................................TTEEEEEECCCCSSXHHHHHCH CS
                           UPF0086  62 ..............................................kdvlevevdGsqlryrpadRaer 84 
                                                                                     ++v++v+vdG++l++rpa R+e+
  gi|313125798|ref|YP_004036068.1|  83 eaadaekasgttsklrsetaggleasqsgrpaedssaasrtssgncEGVAYVTVDGTRLLSRPALRTEK 151
                                       **********************************************999******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 877.58
//
Query:       gi|313125799|ref|YP_004036069.1|  [L=108]
Description: 30S ribosomal protein S17 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-27   94.1   0.5      5e-27   93.8   0.5    1.1  1  Ribosomal_S17    Ribosomal protein S17
  ------ inclusion threshold ------
      0.011   16.1   0.0       0.02   15.3   0.0    1.5  1  Ribosomal_S17_N  Ribosomal_S17 N-terminal
       0.03   14.1   1.2      0.047   13.4   1.2    1.3  1  Toxin_31         Scorpion acidic alpha-KTx toxin family
      0.086   12.8   0.1         13    5.9   0.0    2.5  3  DUF1967          Domain of unknown function (DUF1967)


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.5   1.1e-30     5e-27       1      68 []      34     102 ..      34     102 .. 0.99

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.1e-30
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                       G+V s+ mdkTvvV++e+ v+ pky +y+krr+++ ah +++  +++GD+Vri+e+rPlSktk +vvve
  gi|313125799|ref|YP_004036069.1|  34 GTVASTDMDKTVVVEREYDVRVPKYDRYMKRRSRIPAHAPPCMdLEEGDTVRIAETRPLSKTKAHVVVE 102
                                       99*****************************************************************97 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   4.5e-06      0.02      36      68 ..       3      31 ..       1      32 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.5e-06
                                      --TT----GGGGS-----TTSSSSSS----S-E CS
                   Ribosomal_S17_N 36 vglgfktPkeAiegtYiDkKCPFtGnvsirGri 68
                                      +gl+ + P+eA      D  CPF G   +rG+ 
  gi|313125799|ref|YP_004036069.1|  3 IGLNVEEPEEACS----DENCPFHGSLAVRGQT 31
                                      8999999999998....99************86 PP

>> Toxin_31  Scorpion acidic alpha-KTx toxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.2   1.1e-05     0.047       2      13 ..       8      19 ..       7      23 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                          Toxin_31  2 eePkesCsDemC 13
                                      eeP e+CsDe C
  gi|313125799|ref|YP_004036069.1|  8 EEPEEACSDENC 19
                                      9**********9 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0091        41      13      31 ..      26      44 ..      21      49 .. 0.84
   2 ?   -1.4   0.0      0.51   2.3e+03      10      24 ..      49      63 ..      43      65 .. 0.74
   3 ?    5.9   0.0    0.0028        13      53      65 ..      76      88 ..      75      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0091
                                      EEE-HHHHHHHTTEEE-TG CS
                           DUF1967 13 vVeGekierlvkqtnfene 31
                                       V+G+ ie  v++t++++ 
  gi|313125799|ref|YP_004036069.1| 26 AVRGQTIEGTVASTDMDKT 44
                                      69**************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.51
                                      TEEEEE-HHHHHHHT CS
                           DUF1967 10 gvfvVeGekierlvk 24
                                        + V+ +k +r++k
  gi|313125799|ref|YP_004036069.1| 49 REYDVRVPKYDRYMK 63
                                      358899999999887 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0028
                                      TT--TT-EEEETT CS
                           DUF1967 53 aGakeGdtVrIgd 65
                                      +  +eGdtVrI +
  gi|313125799|ref|YP_004036069.1| 76 MDLEEGDTVRIAE 88
                                      5789*******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 618.86
//
Query:       gi|313125800|ref|YP_004036070.1|  [L=132]
Description: 50S ribosomal protein L14 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-37  126.1   0.5    9.2e-37  125.8   0.5    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.8   0.5   5.2e-41   9.2e-37       4     122 .]      14     132 .]      12     132 .] 0.95

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 5.2e-41
                                       SS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-E CS
                     Ribosomal_L14   4 lktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsv 76 
                                        ++ +++aDN+ga+++++i+v g++    ++++a +Gd+++vsv k++p   +++++v++av+vr++k++rr+dG+ 
  gi|313125800|ref|YP_004036070.1|  14 RGSLITCADNTGARQLKVISVKGYSgtknRHPKAGIGDQVTVSVTKGTP---EMRRQVLEAVIVRQRKSIRRPDGTR 87 
                                       57899*****************8887665669*****************...89*********************** PP

                                       EEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                     Ribosomal_L14  77 irfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                       ++f+dnaaV++++ +ep+Gt+i+gp+are++e+ f  i+s+A++++
  gi|313125800|ref|YP_004036070.1|  88 VKFEDNAAVIIDEMEEPRGTEIKGPIAREVAER-FGSIASTATMIV 132
                                       ********************************9.********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.36s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 749.84
//
Query:       gi|313125801|ref|YP_004036071.1|  [L=119]
Description: 50S ribosomal protein L24 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-22   80.1   0.1    1.5e-22   79.8   0.1    1.1  1  Ribosomal_L26    Ribosomal proteins L26 eukaryotic, L24P arch
    7.6e-05   22.5   0.3    0.00016   21.5   0.3    1.6  1  KOW              KOW motif
  ------ inclusion threshold ------
      0.065   12.6   0.0      0.083   12.2   0.0    1.2  1  Methyltrans_RNA  RNA methyltransferase
       0.13   12.3   0.0       0.18   11.8   0.0    1.3  1  DbpA             DbpA RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.1   3.4e-26   1.5e-22       1      80 [.       2     114 ..       2     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 3.4e-26
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xx RF
                     Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gv 45 
                                       ++++rkqr    nap+h+r+k + a L+++Lre+yg r+++++                                 v
  gi|313125801|ref|YP_004036071.1|   2 TKQPRKQRNETQNAPLHERQKQVRATLTDDLREEYGQRNVRVNagdtvevlrgdaagteaevtdidlkdavvyveDV 78 
                                       79*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                     Ribosomal_L26  46 trekangttvpvgihpSkvvItklkl.DkdrkkiLe 80 
                                       t+ ka+g++vp+++++S++ +t+l+l D++r++ L+
  gi|313125801|ref|YP_004036071.1|  79 TVAKADGEEVPRPLDASNIRVTELDLeDERRESRLK 114
                                       **************************9999998886 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.3   3.6e-08   0.00016       2      32 .]      46      76 ..      45      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.6e-08
                                      TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                      Gd+V+V++G  +G +++V+++d + + V+v+
  gi|313125801|ref|YP_004036071.1| 46 GDTVEVLRGDAAGTEAEVTDIDLKDAVVYVE 76
                                      9****************************97 PP

>> Methyltrans_RNA  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.9e-05     0.083       9      53 ..      35      79 ..      26      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                                      HHHHTTTT--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEEEEE CS
                   Methyltrans_RNA  9 hHlvkVlRlkegdeiklfdgdgkeyeaeieeiskkkvtvkileke 53
                                      ++  + +R+++gd+++++ gd    eae+++i+ k+++v +++ +
  gi|313125801|ref|YP_004036071.1| 35 EYGQRNVRVNAGDTVEVLRGDAAGTEAEVTDIDLKDAVVYVEDVT 79
                                      5667889******************************88776554 PP

>> DbpA  DbpA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.1e-05      0.18       9      54 ..      40      88 ..      37     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.1e-05
                                      GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEE...E-TT-HHHH CS
                              DbpA  9 kdklrpgdivgaiakeaglsgkdIGkIdildkfSfve...vpkekaeev 54
                                      + ++++gd v+ + ++a  +  ++ +Id++d   +ve   v+k++ eev
  gi|313125801|ref|YP_004036071.1| 40 NVRVNAGDTVEVLRGDAAGTEAEVTDIDLKDAVVYVEdvtVAKADGEEV 88
                                      56899************9999**************97444666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 682.66
//
Query:       gi|313125802|ref|YP_004036072.1|  [L=236]
Description: 30S ribosomal protein S4e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-22   78.2   0.0    7.1e-22   77.1   0.0    1.6  1  Ribosomal_S4e  Ribosomal family S4e
      4e-14   52.4   0.1      8e-14   51.5   0.1    1.5  1  RS4NT          RS4NT (NUC023) domain
     0.0027   17.6   1.6     0.0048   16.8   0.2    2.3  2  KOW            KOW motif
      0.006   16.3   0.0       0.01   15.5   0.0    1.4  1  S4             S4 domain
  ------ inclusion threshold ------
       0.01   15.8   0.0       0.19   11.8   0.0    2.6  3  BiPBP_C        Penicillin-Binding Protein C-terminus Family
        4.5    7.2   5.9        1.7    8.5   0.9    2.7  3  Myosin_N       Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.0   2.4e-25   7.1e-22       2      75 .]      91     168 ..      90     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 2.4e-25
                                       TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES.....STT-STTEEEEEETTTT CS
                     Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp.....dpdikvnDtvkidleen 73 
                                       +e++r+++d+ gr++l++I+++ a+ +L K+ +k+ vk+g +ql++hdG+++r++     ++ ++ +D+++id e++
  gi|313125802|ref|YP_004036072.1|  91 EEYFRVFPDEGGRLTLTPIDASAADSRLGKVVGKQSVKGGATQLTLHDGSNVRVEedeepNQ-YSSKDSLVIDNETK 166
                                       79*****************************************************9999777.************** PP

                                       EE CS
                     Ribosomal_S4e  74 kI 75 
                                       +I
  gi|313125802|ref|YP_004036072.1| 167 EI 168
                                       98 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.1   2.7e-17     8e-14       4      34 ..       2      32 ..       1      34 [. 0.96

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 2.7e-17
                                      ---EETTTS-TTS---SSSSSEE----SSSS CS
                             RS4NT  4 kkHLKrlaAPkhWpldkkegvfavkPspGPH 34
                                       +H Krl+AP +Wp+++keg+f+vk s+GPH
  gi|313125802|ref|YP_004036072.1|  2 TRHQKRLSAPNSWPIERKEGTFTVKASAGPH 32
                                      59***************************** PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1         4   1.2e+04      16      20 ..     118     122 ..     117     125 .. 0.72
   2 !   16.8   0.2   1.6e-06    0.0048       2      31 ..     177     210 ..     176     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4
                                       EEEEE CS
                               KOW  16 tGkVv 20 
                                        GkVv
  gi|313125802|ref|YP_004036072.1| 118 LGKVV 122
                                       68888 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.6e-06
                                       TSEEEESSSTTTTCEEEEEEEETTT....TEEEE CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhk....vrVfv 31 
                                       G  V  v+G h+G++G+V+++   +    + V+v
  gi|313125802|ref|YP_004036072.1| 177 GALVTAVDGSHAGEIGTVTEITVTPgsgnNSVTV 210
                                       899******************8777777655665 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.4e-06      0.01       3      46 ..      39      83 ..      37      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.4e-06
                                      HHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                S4  3 Ldkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46
                                      L ++l   lg++  ++eAr + ++ +VlVNG  + d   +++  D
  gi|313125802|ref|YP_004036072.1| 39 LLILLrDVLGYVDNKKEARYALNQDGVLVNGDAISDEQRPIGMFD 83
                                      566666459**********************99999888877655 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.23   6.8e+02      58      80 ..      88     111 ..      83     114 .. 0.80
   2 ?   -2.2   0.0       1.4   4.3e+03      71      79 ..     130     138 ..     125     152 .. 0.60
   3 ?   11.8   0.0   6.3e-05      0.19      49      87 ..     182     220 ..     160     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.23
                           BiPBP_C  58 tkrgrelawqp.epGrhrLtvvDa 80 
                                       t+r++ + + p e Gr +Lt +Da
  gi|313125802|ref|YP_004036072.1|  88 TEREEYFRVFPdEGGRLTLTPIDA 111
                                       667777888889999999999998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                           BiPBP_C  71 GrhrLtvvD 79 
                                       G  +Lt++D
  gi|313125802|ref|YP_004036072.1| 130 GATQLTLHD 138
                                       555555555 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 6.3e-05
                           BiPBP_C  49 lldgeplaetkrgrelawqpepGrhrLtvvDaaGrvddv 87 
                                        +dg+  +e+++  e++++p++G+ ++tv  ++G+ ++v
  gi|313125802|ref|YP_004036072.1| 182 AVDGSHAGEIGTVTEITVTPGSGNNSVTVETEDGEFETV 220
                                       69********************************99887 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.35     1e+03      20      33 ..      17      30 ..      16      31 .. 0.79
   2 ?   -2.6   0.2       1.7   5.1e+03      22      38 ..     128     144 ..     120     146 .. 0.66
   3 ?    8.5   0.9   0.00057       1.7      23      35 ..     205     217 ..     195     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.35
                                      EEESSEEEEEETTS CS
                          Myosin_N 20 eeeGdkvtVetedG 33
                                      e++ +++tV+   G
  gi|313125802|ref|YP_004036072.1| 17 ERKEGTFTVKASAG 30
                                      78899****97655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                       ESSEEEEEETTSEEEEE CS
                          Myosin_N  22 eGdkvtVetedGktvtV 38 
                                       +G+     + dG+ v+V
  gi|313125802|ref|YP_004036072.1| 128 KGGATQLTLHDGSNVRV 144
                                       55555555578887777 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00057
                                       SSEEEEEETTSEE CS
                          Myosin_N  23 GdkvtVetedGkt 35 
                                       +++vtVetedG+ 
  gi|313125802|ref|YP_004036072.1| 205 NNSVTVETEDGEF 217
                                       367********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1404.89
//
Query:       gi|313125803|ref|YP_004036073.1|  [L=175]
Description: 50S ribosomal protein L5 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-21   74.4   0.0    1.1e-20   73.6   0.0    1.5  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    7.9e-17   61.3   0.1    1.5e-16   60.4   0.1    1.5  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   1.2e-24   1.1e-20       1      81 [.      66     141 ..      66     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 1.2e-24
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       piG+kvtLrg+k++efl+++l ++    +        +fd++Gn+sfG++e++ fp  eyd+++gi+G+d+t+ + +
  gi|313125803|ref|YP_004036073.1|  66 PIGAKVTLRGDKAVEFLETALPLADISAK--------QFDETGNFSFGVEEHTEFPSQEYDPQIGIYGLDVTVNLVR 134
                                       8******************9988776555........9*************************************99 PP

                    Ribosomal_L5_C  78 k...tde 81 
                                       +   +++
  gi|313125803|ref|YP_004036073.1| 135 PgyrVKK 141
                                       9776333 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.1   1.7e-20   1.5e-16       2      57 .]      10      62 ..       9      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.7e-20
                                      CTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  2 vMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                       M++P++eK+v++mgvGe g++   l +a+++L+eItGQ+ v+t a ++  +F+ R
  gi|313125803|ref|YP_004036073.1| 10 EMREPQIEKVVVHMGVGEGGRE---LANAEEILEEITGQQSVQTIATRAATQFGAR 62
                                      6*********************...****************************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1050.47
//
Query:       gi|313125804|ref|YP_004036074.1|  [L=58]
Description: 30S ribosomal protein s14 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-11   43.3   3.6    2.6e-11   43.1   3.6    1.1  1  Ribosomal_S14  Ribosomal protein S14p/S29e


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   3.6   1.4e-15   2.6e-11       8      54 .]      13      58 .]       8      58 .] 0.93

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.4e-15
                                      SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                     Ribosomal_S14  8 nssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                       s+ t + n Cr + r +G++ k+ +  +R+cfRe A++   +G+kK++
  gi|313125804|ref|YP_004036074.1| 13 ASRRTGQENECRRCDRKQGLVGKYDInlCRQCFREVARD---MGFKKYR 58
                                      5788999*****************9999***********...*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 346.00
//
Query:       gi|313125805|ref|YP_004036075.1|  [L=130]
Description: 30S ribosomal protein S8 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-24   86.6   0.0    1.6e-24   86.3   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0   8.8e-29   1.6e-24       1     127 []       5     130 .]       5     130 .] 0.88

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 8.8e-29
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCCEEEEE-BSSS-SBSSSEEEE- CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkkikielkynkkkksvikklkrv 75 
                                       Dp++++l+ ++Nae++++ + e+ pas+++ ++l+v+ ++Gyi++fe++ + k  ++++el+   +k++v+k   r+
  gi|313125805|ref|YP_004036075.1|   5 DPLSNALAGVNNAESVGHLSHEIqPASNVIGSVLEVFYDRGYIDGFEFVdDGKAGTFEVELNGAINKCGVVKP--RY 79 
                                       9***********************************************9666667777776666666999883..55 PP

                                       SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  76 skpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                       s ++ + + k ++     + +G++iv+Ts+Gvm++ +Ar++++GG+v+ayv+
  gi|313125805|ref|YP_004036075.1|  80 SAGADE-FEKWEKRYLPARDYGTLIVTTSHGVMSHYDAREQGIGGQVIAYVY 130
                                       555554.7777777778899*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 760.41
//
Query:       gi|313125806|ref|YP_004036076.1|  [L=178]
Description: 50S ribosomal protein L6 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-28   98.3   2.6    1.6e-13   51.1   0.2    2.1  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
       0.58   10.3   5.2          1    9.5   0.2    3.1  3  HSP20         Hsp20/alpha crystallin family


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.2   1.7e-17   1.6e-13       1      76 []       8      80 ..       8      80 .. 0.97
   2 !   47.8   0.2     2e-16   1.8e-12       1      76 []      92     166 ..      92     166 .. 0.99

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.7e-17
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP++v++++k+   ++v Gp+g++t ++++  ++ v ve+++v+ ++ + + k+++  igt+ s+++nm  GVteg
  gi|313125806|ref|YP_004036076.1|  8 IPDDVSAEVKN-LDLTVDGPNGSVTKTLWYP-DISVTVEDGQVVIESEETNAKTNA-TIGTFESHVENMLYGVTEG 80
                                      8*********5.*******************.99999*******************.*****************98 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 2e-16
                                       CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                                       +P+ v+v+++++ ++++lG+k ++ ++++ +++v+v+     +++ v++g dke+v    A+i++ +++++++ +++
  gi|313125806|ref|YP_004036076.1|  92 FPMQVNVQGDEVVIENFLGEKSPRHAKVRGDTDVQVD-----GEELVLTGPDKEDVgqtaADIEQLTRVKDKDTRVF 163
                                       8***********************************9.....*********************************** PP

                                       HTC CS
                      Ribosomal_L6  74 teg 76 
                                       ++g
  gi|313125806|ref|YP_004036076.1| 164 QDG 166
                                       *98 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00012         1      22      48 ..      38      64 ..      29      73 .. 0.81
   2 ?   -0.6   0.0      0.16   1.5e+03      23      35 ..      94     106 ..      78     121 .. 0.72
   3 ?    1.2   0.1     0.045   4.1e+02      22      42 ..     122     141 ..     115     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                                      CEEEEEETTEEEEEEE--..---TT-- CS
                             HSP20 22 elkvkvednrvlvkgeheeeeedekgl 48
                                      ++ v+ved++v++++e+++ + + +  
  gi|313125806|ref|YP_004036076.1| 38 DISVTVEDGQVVIESEETNAKTNATIG 64
                                      99****************777666554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.16
                                       EEEEEETTEEEEE CS
                             HSP20  23 lkvkvednrvlvk 35 
                                       ++v+v++++v+++
  gi|313125806|ref|YP_004036076.1|  94 MQVNVQGDEVVIE 106
                                       5688888888886 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.045
                                       CEEEEEETTEEEEEEE--..- CS
                             HSP20  22 elkvkvednrvlvkgeheeee 42 
                                       + +v+v++++++ +g  + e+
  gi|313125806|ref|YP_004036076.1| 122 DTDVQVDGEELVLTGPDK-ED 141
                                       779999999999999888.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1018.83
//
Query:       gi|313125807|ref|YP_004036077.1|  [L=234]
Description: 50S ribosomal protein L32e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-35  120.8   0.5    1.7e-34  118.5   0.2    2.0  2  Ribosomal_L32e   Ribosomal protein L32
    1.3e-14   54.5   1.6    1.8e-13   50.9   0.4    2.5  2  HHH_5            Helix-hairpin-helix domain
    7.1e-08   31.9   0.7      0.014   15.3   0.1    2.9  3  HHH              Helix-hairpin-helix motif
    4.3e-07   29.7   0.0      2e-06   27.5   0.0    2.1  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    3.6e-05   23.8   0.3    0.00011   22.2   0.3    1.8  1  HHH_2            Helix-hairpin-helix motif
    7.4e-05   22.9   0.1    0.00097   19.3   0.0    2.7  4  Cdd1             Pathogenicity locus
     0.0012   19.0   0.2       0.43   10.9   0.1    2.6  2  HHH_3            Helix-hairpin-helix motif
     0.0045   17.3   0.7        0.7   10.3   0.1    2.9  3  HHH_8            Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.16   13.0   2.2        1.2   10.1   0.5    2.7  3  LytR_C           LytR cell envelope-related transcriptional a


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.51     1e+03      59      88 ..      32      61 ..      14      76 .. 0.72
   2 !  118.5   0.2   8.5e-38   1.7e-34       1     108 []     119     224 ..     119     224 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.51
                                      EEEEESSGGGGTT--TTTE..EEEE-TTS- CS
                    Ribosomal_L32e 59 kkvlVhnvkeLevllmenksyaaeiahsVs 88
                                      ++v   n +eL  +    +  aa+i + V+
  gi|313125807|ref|YP_004036077.1| 32 EDVKAANQSELADVSGIGNALAARIKADVG 61
                                      445566777777777777777888877776 PP

  == domain 2  score: 118.5 bits;  conditional E-value: 8.5e-38
                                       ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE CS
                    Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenk 77 
                                       +++F+r++++++++  +swrkprG  +++rr +kg+   +++G++spk+ rgl+psGf++v Vhnv++Le ++  ++
  gi|313125807|ref|YP_004036077.1| 119 KPQFNRQDYHKKKRTPTSWRKPRGNLSKQRRGIKGKGDTVEAGFRSPKAARGLHPSGFEEVHVHNVDDLEGVDGDTE 195
                                       689************************************************************************** PP

                                       ..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  78 syaaeiahsVsskkrkeiverAaelgikVtN 108
                                         a++ia+sV+++kr+ i+e A+  +i+V+N
  gi|313125807|ref|YP_004036077.1| 196 --AVRIASSVGARKRERIEEAAEDREIRVLN 224
                                       ..****************************9 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.4   9.1e-17   1.8e-13       2      52 ..       7      57 ..       6      60 .. 0.96
   2 ?    2.0   0.0      0.17   3.3e+02      12      56 ..     165     216 ..     164     217 .. 0.64

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 9.1e-17
                                      HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAerii 52
                                      +eL ++sG+Gp+ A al +aG+esved++aa++ eLa++ GiG+ +A ri+
  gi|313125807|ref|YP_004036077.1|  7 QELEDISGVGPSKADALSEAGYESVEDVKAANQSELADVSGIGNALAARIK 57
                                      689***********************************************7 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                                       HHHHHHHHTTT--.....SHHHH..HHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5  12 pktAlallsaGie.....svedl..aaadveeLakipGiGkktAeriilelk 56 
                                       pk A+ l+  G+e      v+dl  ++ d+e++  +  +G+++ eri ++++
  gi|313125807|ref|YP_004036077.1| 165 PKAARGLHPSGFEevhvhNVDDLegVDGDTEAVRIASSVGARKRERIEEAAE 216
                                       7888888888888333334778844455677666666688888888766665 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   6.8e-06     0.014      11      27 ..       7      23 ..       5      26 .. 0.90
   2 !   14.1   0.1   1.6e-05     0.032       1      28 [.      30      57 ..      30      58 .. 0.92
   3 ?   -2.3   0.0       2.5   5.1e+03       9      18 ..     183     192 ..     181     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.8e-06
                                      HHHHTSTT-SHHHHHHH CS
                               HHH 11 eeLlalPGVGpktAeaI 27
                                       eL++++GVGp++A+a 
  gi|313125807|ref|YP_004036077.1|  7 QELEDISGVGPSKADAL 23
                                      69*************96 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.6e-05
                                      SHHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                               HHH  1 sleglipasreeLlalPGVGpktAeaIl 28
                                      s+e +++a+  eL++++G+G + A +I 
  gi|313125807|ref|YP_004036077.1| 30 SVEDVKAANQSELADVSGIGNALAARIK 57
                                      67899*******************9996 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.5
                                       SHHHHHTSTT CS
                               HHH   9 sreeLlalPG 18 
                                       ++++L+ + G
  gi|313125807|ref|YP_004036077.1| 183 NVDDLEGVDG 192
                                       5889998877 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   9.9e-10     2e-06       1      42 [.       7      49 ..       7      52 .. 0.88
   2 ?    0.5   0.0      0.27   5.4e+02       2      15 ..      41      54 ..      40      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 9.9e-10
                   DNA_pol_lambd_f  1 qlFtkvyGVGpktAkkwyakGirtledlra.krakLtreqqiG 42
                                      q++  + GVGp++A  + ++G+ ++ed++a ++++L  +  iG
  gi|313125807|ref|YP_004036077.1|  7 QELEDISGVGPSKADALSEAGYESVEDVKAaNQSELADVSGIG 49
                                      68999*************************8768887766555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.27
                   DNA_pol_lambd_f  2 lFtkvyGVGpktAk 15
                                      ++  v G+G + A 
  gi|313125807|ref|YP_004036077.1| 41 ELADVSGIGNALAA 54
                                      6789*****99986 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   5.5e-08   0.00011       8      52 ..      12      57 ..       2      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.5e-08
                             HHH_2  8 IrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsiv 52
                                      I  VG + A +L ++ ++s++  k+a+  eL+ v +iG+  A+ i+
  gi|313125807|ref|YP_004036077.1| 12 ISGVGPSKADALSEAgYESVEDVKAANQSELADVSGIGNALAARIK 57
                                      778*********9866**************************9996 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.8e-07   0.00097       3      42 ..       4      43 ..       2      47 .. 0.92
   2 ?    2.7   0.0     0.076   1.5e+02       4      30 ..      38      65 ..      35      86 .. 0.74
   3 ?   -3.2   0.0       5.4   1.1e+04      31      46 ..     101     116 ..      97     120 .. 0.76
   4 ?   -2.3   0.0       2.8   5.6e+03      24      35 ..     178     189 ..     152     206 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.8e-07
                              Cdd1  3 kalkelqdiPniGkalaedlvelGirsveelkgedpeely 42
                                      ++++el+di ++G++ a+ l e G++sve++k  +  el 
  gi|313125807|ref|YP_004036077.1|  4 EEIQELEDISGVGPSKADALSEAGYESVEDVKAANQSELA 43
                                      7899****************************99988875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.076
                              Cdd1  4 alkelqdiPniGkalaedlv.elGirsv 30
                                      + +el d+ +iG+ala+ +  ++G  +v
  gi|313125807|ref|YP_004036077.1| 38 NQSELADVSGIGNALAARIKaDVGGLEV 65
                                      56799***********988645665555 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.4
                              Cdd1  31 eelkgedpeelyekle 46 
                                        el +e++++l++k++
  gi|313125807|ref|YP_004036077.1| 101 PELDDETAAALTQKHR 116
                                       5788888999988876 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.8
                              Cdd1  24 elGirsveelkg 35 
                                       e+ +++v++l+g
  gi|313125807|ref|YP_004036077.1| 178 EVHVHNVDDLEG 189
                                       344455555555 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.011        22      14      31 ..       7      24 ..       5      35 .. 0.82
   2 !   10.9   0.1   0.00021      0.43      10      30 ..      36      56 ..      32      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                             HHH_3 14 eeLqklpGlgpklAknIv 31
                                      +eL+ ++G+gp++A+++ 
  gi|313125807|ref|YP_004036077.1|  7 QELEDISGVGPSKADALS 24
                                      799999999999999875 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00021
                             HHH_3 10 tAsaeeLqklpGlgpklAknI 30
                                       A  +eL+ ++G+g +lA +I
  gi|313125807|ref|YP_004036077.1| 36 AANQSELADVSGIGNALAARI 56
                                      6999****************9 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.015        30      44      65 ..       5      25 ..       2      27 .. 0.79
   2 !   10.3   0.1   0.00035       0.7      41      64 ..      30      57 ..      20      58 .. 0.69
   3 ?   -2.2   0.0       2.9   5.7e+03      53      66 ..     201     214 ..     178     216 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                                      HHTTHCTTSTT--HHHHHHHHH CS
                             HHH_8 44 sleeeltklpgiGkkiaakiee 65
                                      +++e l+++ g+G++ a+ + e
  gi|313125807|ref|YP_004036077.1|  5 EIQE-LEDISGVGPSKADALSE 25
                                      3344.99********9998877 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00035
                                      -HHHHTT....HCTTSTT--HHHHHHHH CS
                             HHH_8 41 eitslee....eltklpgiGkkiaakie 64
                                       ++++++    el ++ giG+++aa+i+
  gi|313125807|ref|YP_004036077.1| 30 SVEDVKAanqsELADVSGIGNALAARIK 57
                                      555552223478**************96 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.9
                                       TT--HHHHHHHHHH CS
                             HHH_8  53 pgiGkkiaakieei 66 
                                         +G++ +++iee 
  gi|313125807|ref|YP_004036077.1| 201 SSVGARKRERIEEA 214
                                       45777777777776 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   0.00062       1.2      11      72 ..      11      70 ..       5      88 .. 0.71
   2 ?   -1.3   0.0       2.2   4.5e+03      19      32 ..      87     100 ..      76     133 .. 0.62
   3 ?    1.2   0.0      0.37   7.4e+02      19      66 ..     167     207 ..     159     231 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00062
                            LytR_C 11 gvsGlAarvadaLeerGftvgevgnagnadee...ttivyreaaaaaakalaaalglgelqedsv 72
                                      ++sG+  + adaL+e+G++ +e+ +a+n++e    + i      +a a +++a++g+ e++e+++
  gi|313125807|ref|YP_004036077.1| 11 DISGVGPSKADALSEAGYESVEDVKAANQSELadvSGIG-----NALAARIKADVGGLEVSEETE 70
                                      678999999*********888866666663333332222.....246778888888877666554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                            LytR_C  19 vadaLeerGftvge 32 
                                       v ++L+ rG +  +
  gi|313125807|ref|YP_004036077.1|  87 VETELRPRGLADKT 100
                                       55555555542222 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.37
                            LytR_C  19 vadaLeerGftvgevgnagnadee...ttivyreaaaaaakalaaalglge 66 
                                       +a+ L   Gf+ + v n+++ +     t          +a ++a+++g  +
  gi|313125807|ref|YP_004036077.1| 167 AARGLHPSGFEEVHVHNVDDLEGVdgdT----------EAVRIASSVGARK 207
                                       6777777888888877777762223331..........4445555555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1334.15
//
Query:       gi|313125808|ref|YP_004036078.1|  [L=151]
Description: 50S ribosomal protein L19e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-57  192.8   3.0    3.3e-57  192.6   3.0    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
  ------ inclusion threshold ------
      0.054   12.0   0.0      0.072   11.6   0.0    1.2  1  Tic110          Chloroplast envelope transporter
       0.17   10.3   0.0        0.2   10.1   0.0    1.1  1  Vps35           Vacuolar protein sorting-associated protein 3


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.6   3.0   5.5e-61   3.3e-57       1     142 [.       3     144 ..       3     146 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 5.5e-61
                                       -THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGG CS
                    Ribosomal_L19e   1 dlklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsG 77 
                                       dlk+q+r+aa+vl+vGknrvw+dpe++++iaeAitredir+l++dg+I ++++kgns++rarer+ek+++g+r+g+G
  gi|313125808|ref|YP_004036078.1|   3 DLKAQRRMAADVLDVGKNRVWFDPEAQSDIAEAITREDIRELVDDGTIRAEDAKGNSKGRARERAEKRSYGHRKGPG 79 
                                       589************************************************************************** PP

                                       G--S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT- CS
                    Ribosomal_L19e  78 krkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiek 142
                                       +rkG+++ R ++k++Wi+riRa+Rr Lkelr+++ ++ ++YrelY+ka+Ggef+++ +L++yi++
  gi|313125808|ref|YP_004036078.1|  80 SRKGKSGGRKNSKDEWISRIRAQRRRLKELRDDGPLTPTQYRELYNKASGGEFDSVDRLEAYITN 144
                                       ***************************************************************87 PP

>> Tic110  Chloroplast envelope transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.2e-05     0.072     418     462 ..      12      56 ..       2      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.2e-05
                            Tic110 418 aavLqnlceelrFdpekAselheeiYrqklqqlvedkeLsdedve 462
                                       a+vL+   +++ Fdpe+ s++ e+i r+ +++lv+d+ +  ed +
  gi|313125808|ref|YP_004036078.1|  12 ADVLDVGKNRVWFDPEAQSDIAEAITREDIRELVDDGTIRAEDAK 56 
                                       6677777899*****************************999986 PP

>> Vps35  Vacuolar protein sorting-associated protein 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   3.4e-05       0.2      29      72 ..      99     147 ..      89     151 .] 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.4e-05
                             Vps35  29 LkhasnmlseLrts.sLsPkqYYeLYmav....fdeLrhLssyLkdehk 72 
                                       +++    l+eLr +  L+P qY eLY +     fd++  L++y+++++ 
  gi|313125808|ref|YP_004036078.1|  99 IRAQRRRLKELRDDgPLTPTQYRELYNKAsggeFDSVDRLEAYITNNYD 147
                                       56666779****9857***********9877779**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 866.90
//
Query:       gi|313125809|ref|YP_004036079.1|  [L=184]
Description: 50S ribosomal protein L18 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-30  103.8   0.0    2.6e-18   66.6   0.0    2.2  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
      4e-06   27.2   0.0    5.8e-06   26.7   0.0    1.2  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   2.8e-22   2.6e-18       2      98 ..       6      95 ..       5      99 .. 0.96
   2 !   35.5   0.0     1e-12   9.4e-09     130     163 .]     100     133 ..      95     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 2.8e-22
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvglt 80
                                      r++v +rrrre +tdY++r rl+        + k Rlv rv+nk++ +q+a+   +gd++ aaa+s++l +yg ++   
  gi|313125809|ref|YP_004036079.1|  6 RYKVPMRRRREVRTDYHQRLRLLK-------SGKPRLVARVSNKHVRAQLASPGPNGDNTHAAASSEDLAEYGWEAPTG 77
                                      9*********************85.......5678******************************************** PP

                     Ribosomal_L5e 81 nyaaaYatglllarrllk 98
                                      n  +aY+tg+l ++r+l+
  gi|313125809|ref|YP_004036079.1| 78 NLPSAYLTGYLAGKRALE 95
                                      ***************997 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 1e-12
                     Ribosomal_L5e 130 kaiLdvGLartttgakvfgalkgavdgglsiphs 163
                                       +a+Ld+GL+++t g+kvf++ +ga+d+gl+iph+
  gi|313125809|ref|YP_004036079.1| 100 EAVLDIGLNTATPGNKVFAVQEGAIDAGLEIPHN 133
                                       689******************************7 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   6.5e-10   5.8e-06       7     115 ..      12     129 ..       7     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 6.5e-10
                                       HCHHHHHH..TTT--.TTSSS-EEEEEE-SS-EEEEEE-T..TT--EEEEECS-SCCCT..S-SSSCHHHHHHHHHH CS
                    Ribosomal_L18p   7 rkrRhkRi..rkkls.gtaerprlvvfrsnrhiyaQvidd..vkgktlasastlekelk..lkstknkeaakkvgel 76 
                                       r+rR+ R   +++l+  ++ +prlv   sn+h+ aQ+     + ++t a+as+ + +       t+n  +a   g l
  gi|313125809|ref|YP_004036079.1|  12 RRRREVRTdyHQRLRlLKSGKPRLVARVSNKHVRAQLASPgpNGDNTHAAASSEDLAEYgwEAPTGNLPSAYLTGYL 88 
                                       6666666522345555667799***************9753278899999999887665678899************ PP

                                       HHHHHCHHCHTC-EE--TTSS..S-CHHHHHHHHHHCTSSB CS
                    Ribosomal_L18p  77 iAerakekgiekvvfDrggyk..YhGrvaalAdaaReaGlk 115
                                         +ra+e+g+e++v D g ++     +v a+ ++a +aGl+
  gi|313125809|ref|YP_004036079.1|  89 AGKRALEAGLEEAVLDIGLNTatPGNKVFAVQEGAIDAGLE 129
                                       ****************9865411456899999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1019.09
//
Query:       gi|313125810|ref|YP_004036080.1|  [L=215]
Description: 30S ribosomal protein S5 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-21   76.7   0.1    3.1e-21   75.1   0.1    1.9  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    2.4e-21   74.9   0.1    3.7e-21   74.3   0.1    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.1   3.4e-25   3.1e-21       1      64 [.      50     113 ..      50     114 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 3.4e-25
                                       XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE- CS
                      Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpv 64 
                                       l+++vl+i++vq++t++Grr +f+++v++G+++G +G++++  ++v  Ai+kAi+ Ak+n+++v
  gi|313125810|ref|YP_004036080.1|  50 LEDEVLDINMVQRMTDSGRRVKFRCVVAIGNRDGFLGYAEARDDQVGSAIQKAIDVAKLNIIKV 113
                                       799************************************************************9 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.1   4.2e-25   3.7e-21       1      66 [.     135     201 ..     135     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 4.2e-25
                                       EEEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                    Ribosomal_S5_C   1 tgkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                       +gk g+v+v ++pap+G G+ a+ +vr +lelaG++D +++s+g +r+++n++k+t++ALk+ ++ +
  gi|313125810|ref|YP_004036080.1| 135 EGKAGSVTVEIMPAPQGLGLAAAETVRNILELAGVQDAWTRSNGnTRTTVNLAKGTYNALKNASQSR 201
                                       59***********************************************************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1192.72
//
Query:       gi|313125811|ref|YP_004036081.1|  [L=154]
Description: 50S ribosomal protein L30 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-09   37.4   0.0      3e-09   36.6   0.0    1.3  1  Ribosomal_L30  Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
      0.037   13.9   0.2      0.059   13.3   0.2    1.2  1  DUF3052        Protein of unknown function (DUF3052)
      0.063   13.8   0.0       0.11   13.0   0.0    1.4  1  OHCU_decarbox  OHCU decarboxylase


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0     5e-13     3e-09       3      51 .]       4      52 ..       3      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 5e-13
                                      EEE-S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  3 VtrirsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVkhlV 51
                                      V++ r+ +++++ + +tL++L  + +n +  v++   ++rGm+ kV+++V
  gi|313125811|ref|YP_004036081.1|  4 VVQLRGDVNMSEATHDTLKMLNIHSVNhCALVPES-DTYRGMITKVNDYV 52
                                      99*************************66666666.*************9 PP

>> DUF3052  Protein of unknown function (DUF3052)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   9.8e-06     0.059      29     109 ..      62     145 ..      57     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.8e-06
                           DUF3052  29 iedligeelvdedadevvDvvllWwrddDgdLv...dalvdaltsLadegviwlltpkagreghvepseiaeaakta 102
                                       +e+l+ ++   e+ +++vD+ +l    d +d++   +al+d  t+L ++g+  +l  +  r gh  ++++++   + 
  gi|313125811|ref|YP_004036081.1|  62 VETLLRTRAEPEEGSDTVDAEWLEANTDYDDVTalaEALIDEETTLREQGLSPVLRLHPPRGGHKGQKHVTKEGGQL 138
                                       566677777789999999*99999987777644333***************99999999999999999999888887 PP

                           DUF3052 103 GLvqtss 109
                                       G ++t++
  gi|313125811|ref|YP_004036081.1| 139 GKHTTEQ 145
                                       7777765 PP

>> OHCU_decarbox  OHCU decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.8e-05      0.11      24      94 ..      81     147 ..      56     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                                       HHHH..CGS-SSHHHHHHHHHHHCCCS-HHHHHHHHCTS--TTSCCCHHTHCHHHHHHHCCCTTTTCHHHHHH CS
                     OHCU_decarbox  24 elal..arpfssyeaLiaavaealealseeelleilsaHPrLGekaakkkklsalsrkEqaglglaaseeele 94 
                                       +  l  +  +++++aL +a+ ++ ++l e+ l+ +l+ HP  G++     k +++ +kE  +lg + + e+ +
  gi|313125811|ref|YP_004036081.1|  81 AEWLeaNTDYDDVTALAEALIDEETTLREQGLSPVLRLHPPRGGH-----KGQKHVTKEGGQLG-KHTTEQID 147
                                       33334333899*********************************3.....66899999999999.55555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 868.35
//
Query:       gi|313125812|ref|YP_004036082.1|  [L=165]
Description: 50S ribosomal protein L15 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-16   60.9   0.3      3e-16   60.3   0.3    1.3  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.3   1.7e-20     3e-16       2     126 ..      26     141 ..      25     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.7e-20
                                       GGGTSSTTTTTTTTT-S--......S--.........---.GGG..---EEEEHHHHHHTTTTGTTS.--...---- CS
                    Ribosomal_L27A   2 GktgGrGhkGqkkrsgvkkkpgfeGGqmplyrrlpkrGfk.nskfkkeykvvnlkdLdelideerle.la...deae 73 
                                       G++gGrG++G+ k+++ +  + +  G++         Gfk  +  k    +v++++Lde ++ +  + la   ++a+
  gi|313125812|ref|YP_004036082.1|  26 GHRGGRGRAGRDKHEYHNY-EPI--GKH---------GFKrPEDAKDTVVEVKVQKLDEDAALLAADdLAekdGDAY 90 
                                       9*************98664.338..9**.........***64445666799*******98888888765588789** PP

                                       EEEGGGTTTTSSS....SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EE CS
                    Ribosomal_L27A  74 eidleelaeaglikkkdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkv 126
                                       +id++++ae g     d vKvlg g+++++l+v a++f++ A+e  e aGG++
  gi|313125812|ref|YP_004036082.1|  91 QIDARDVAEDGYE--ADVVKVLGGGQVRQELHVVADAFTAGAVELLEGAGGSA 141
                                       *******777665..5666********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1008.34
//
Query:       gi|313125813|ref|YP_004036083.1|  [L=488]
Description: protein translocase subunit SecY [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-70  237.2  16.4      3e-70  236.9  16.4    1.1  1  SecY             SecY translocase
    7.8e-09   35.2   2.1    7.8e-09   35.2   2.1    2.3  2  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.9  16.4   3.3e-74     3e-70       1     306 []      74     467 ..      74     467 .. 0.85

  Alignments for each domain:
  == domain 1  score: 236.9 bits;  conditional E-value: 3.3e-74
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC........... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg........... 65 
                                       si++LGI+P++tasI+lqLl ++    l  l+ ++++++ ++++++++l+vv++++++l ++++ g           
  gi|313125813|ref|YP_004036083.1|  74 SILQLGIGPIVTASIVLQLLgGA---DLLGLDTDDPRDQILYQGLQKLLVVVMICLTGLPMVFAGGflpadqqvaqs 147
                                       89******************887...78888878**************************99875599********* PP

                                       ......HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHCCHSS.............-HHHH... CS
                              SecY  66 ......lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlpkals.............gliel... 120
                                             ++ ++i++q+++g++l+++++E ++++G+G+G+ l+i+ag++++l++ l              +   +   
  gi|313125813|ref|YP_004036083.1| 148 lgvgvgGVKTIIFAQMFVGGILILFMDEIVSKWGVGSGVGLFIIAGVSQQLVAGLFswqalggtsgffpT---Wfgi 221
                                       ******889*******************************************555536666666644440...2554 PP

                                       ......SS...............THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCS CS
                              SecY 121 ......ale.............gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagv 178
                                             +               g    ll+ll+tl+++ +vvy e++++++p+++++    +g+++++P+kl+ya+v
  gi|313125813|ref|YP_004036083.1| 222 itgaaeI-GsplspgglsdiflG-QGQLLALLTTLFIFGIVVYAESVRIEVPLSHSRV---KGARGRFPVKLIYASV 293
                                       4444440.044445555444432.3899****************************54...59************** PP

                                       CHHHHHHHHHHHHHCCCCS.......................................TCCCS.......THHHHHH CS
                              SecY 179 iPiIfassllalpstiaqfl......................................lalls.......psvlyvv 210
                                       +P+I++++l+a  +++ q+l                                      l           + +l+v+
  gi|313125813|ref|YP_004036083.1| 294 LPMILVRALQANIQFLGQILnnwtglpawlgtysdgavtgglfyylapiqsradwmwfL---GytsqdpaQILLRVL 367
                                       ***********766666666666677777777778888888877777777776553331...15556666667799* PP

                                       HHHHHHHH....HHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecY 211 lyvlliif....Fayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdl 281
                                       + ++++i+    Fa+f++e+t + p+++ae++++sg++ipg+r + + +++++e++++++t+iG+++++l+av++++
  gi|313125813|ref|YP_004036083.1| 368 IDLAFMIVggavFAIFWVETTgMGPESTAEQIQNSGMQIPGFRrNPQIIEQVMERYIPQVTVIGGALVGLLAVMANM 444
                                       *******99**********************************999******************************* PP

                                       HTTS.TT.TTHHHHHHHHHHHHHHH CS
                              SecY 282 lgasligafggtslLivVgvaletv 306
                                       lg+  ig+++gt+lL++V+++++++
  gi|313125813|ref|YP_004036083.1| 445 LGT--IGSVSGTGLLLTVSITYKLY 467
                                       ***..99**************9975 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   2.1   8.7e-13   7.8e-09       1      35 []      38      73 ..      38      73 .. 0.95
   2 ?   -3.1   0.1      0.85   7.6e+03      12      25 ..     192     205 ..     191     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 8.7e-13
                                      HHHHHHCCSB-TT--.SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  1 llYlvlsqiPLyGis.sssssDpfywlRaifAsnrG 35
                                      ++Y++l+++ ++G++ ++ + D+++++R+i+A+++G
  gi|313125813|ref|YP_004036083.1| 38 VMYFFLTNVTMFGLQtQGPGGDFYGQFRSILAGQQG 73
                                      78*************666*****************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.85
                                       TT--SSS-TCCHTT CS
                   Plug_translocon  12 yGissssssDpfyw 25 
                                        G+s++ ++ +f w
  gi|313125813|ref|YP_004036083.1| 192 AGVSQQLVAGLFSW 205
                                       69999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 3109.52
//
Query:       gi|313125814|ref|YP_004036084.1|  [L=293]
Description: hypothetical protein Hbor_10470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-38  130.2  12.0      1e-23   83.5   1.9    2.5  2  DUF4399   Domain of unknown function (DUF4399)
    3.1e-05   23.8   0.4       0.15   11.8   0.1    2.3  2  DUF2436   Domain of unknown function (DUF2436)


Domain annotation for each model (and alignments):
>> DUF4399  Domain of unknown function (DUF4399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   1.9   1.1e-27     1e-23       4      90 ..      95     178 ..      92     179 .. 0.96
   2 !   51.5   2.8   1.1e-17   9.6e-14       4      80 ..     200     285 ..     197     293 .] 0.86

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 1.1e-27
                           DUF4399   4 glegmgvapageetentGhhhllvdeeapeagepipaddqvlHfgkgqtetelelppGkhtLqlqlgdaahvplkps 80 
                                       +++g+++++age  e++Gh+h+lvd++++  ge ip+dd+++H+g gqt+  lel+pG+htL+lq+gd+ h++++  
  gi|313125814|ref|YP_004036084.1|  95 TADGVTIEKAGEVIEGAGHYHILVDTDPVTPGEIIPTDDSHIHYGTGQTDGVLELEPGDHTLHLQVGDGVHKAID-- 169
                                       57899**********************************************************************.. PP

                           DUF4399  81 vlskkitvtV 90 
                                        l ++++vtV
  gi|313125814|ref|YP_004036084.1| 170 -LVDTVEVTV 178
                                       .789999999 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 1.1e-17
                           DUF4399   4 glegmgvapage.etentGhhhllvdeeapeagepipaddqvlHfgkgqtetelel........ppGkhtLqlqlgd 71 
                                       ++e+++++p++e  ++n+Gh h l+d++ ++ ge+ip+d++++Hfg+g+t  +++l        +pG+ht++ q+g 
  gi|313125814|ref|YP_004036084.1| 200 TAENYTIQPVSEgINSNAGHLHALIDTDHVPVGEVIPTDARHMHFGDGSTSGRIDLaeqlgdeyEPGDHTIHFQVGT 276
                                       6899********899***************************************88555555557************ PP

                           DUF4399  72 aahvplkps 80 
                                       ++h++   +
  gi|313125814|ref|YP_004036084.1| 277 GTHRATMVH 285
                                       ****98743 PP

>> DUF2436  Domain of unknown function (DUF2436)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   1.7e-05      0.15      23      73 ..      94     144 ..      84     165 .. 0.86
   2 !   10.0   0.0   5.8e-05      0.52      38      72 ..     215     249 ..     198     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                           DUF2436  23 regeakvvleaadvwgdgsGyqllldadhntygqviPadtgtletgtaspa 73 
                                        +++   + +a +v + ++ y +l+d+d  t g++iP+d   ++ gt +++
  gi|313125814|ref|YP_004036084.1|  94 ATADGVTIEKAGEVIEGAGHYHILVDTDPVTPGEIIPTDDSHIHYGTGQTD 144
                                       455666788999***************************999999988766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 5.8e-05
                           DUF2436  38 gdgsGyqllldadhntygqviPadtgtletgtasp 72 
                                       ++++    l+d+dh   g+viP+d+  +++g+ s+
  gi|313125814|ref|YP_004036084.1| 215 SNAGHLHALIDTDHVPVGEVIPTDARHMHFGDGST 249
                                       44555678******************999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1883.81
//
Query:       gi|313125815|ref|YP_004036085.1|  [L=250]
Description: 3-oxoacyl-ACP reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-68  230.5   5.8    2.3e-68  230.2   5.8    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.3e-59  201.0   0.8    1.6e-59  200.7   0.8    1.1  1  adh_short        short chain dehydrogenase
      2e-19   70.2   0.6    3.2e-19   69.6   0.6    1.2  1  KR               KR domain
    8.1e-06   25.5   0.5    1.6e-05   24.5   0.5    1.7  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0039   16.7   0.0       0.01   15.2   0.0    1.6  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0059   16.5   8.0      0.014   15.3   8.0    1.6  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
       0.02   15.1   0.2      0.039   14.2   0.2    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.021   14.7   0.7      0.038   13.9   0.7    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.032   13.8   1.0      0.054   13.0   1.0    1.3  1  NmrA             NmrA-like family
       0.05   14.0   0.6       0.12   12.8   0.2    1.8  2  Toprim_2         Toprim-like
       0.06   13.6   0.6       0.14   12.5   0.6    1.6  1  TrkA_N           TrkA-N domain
       0.13   13.2   6.3       0.31   12.0   1.4    2.6  2  LytR_C           LytR cell envelope-related transcriptional a
       0.79    9.5   5.5         10    6.0   0.1    3.4  3  Robl_LC7         Roadblock/LC7 domain
        1.2    9.0  10.2       0.19   11.6   4.6    2.2  2  ETF              Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.2   5.8   1.8e-71   2.3e-68       3     233 ..      16     248 ..      12     249 .. 0.93

  Alignments for each domain:
  == domain 1  score: 230.2 bits;  conditional E-value: 1.8e-71
                                       TTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae..vlecDVtdeeqvealveevvekfgklDilvnn 76 
                                        +gIGra+A++lae+Ga+vv+t+ ++++ +++++++ ++l++e  v + DV+d ++v+a++e+v+e++g+  ilvnn
  gi|313125815|ref|YP_004036085.1|  16 TRGIGRAVAEQLAERGATVVATYHDDDEaAEQTAAALAALPTEtaVEQFDVADFDAVAATFETVTERYGHPTILVNN 92 
                                       59**************************9888888888888665469****************************** PP

                                       ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC...CEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                      adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg...gsivnlssvgaervvpnynaygaaKaale 149
                                       ag++++  g +l ++ e ++r++dvnl+++f+++++a++ +++     g+ivn++sv+a+r++++++ y+a+Ka++ 
  gi|313125815|ref|YP_004036085.1|  93 AGVMDN--GLLLRMTPERWQRVIDVNLTGTFYCTREAAKqMLRCDdrgGRIVNVASVAAQRGWAGQSNYAASKAGVL 167
                                       ******..*******************************655533456***************************** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqt 226
                                       +ltr++A+elg k iRvNav+pg+++T++ ++ +g    ++++e  +  gr++tpee+a+++ fLasd+asy++G++
  gi|313125815|ref|YP_004036085.1| 168 GLTRSAARELGGKDIRVNAVAPGYTDTDLLASSSG---HESAVETDTASGRVATPEEIADVIRFLASDAASYVNGEV 241
                                       *****************************888774...567899999****************************** PP

                                       EEESTTG CS
                      adh_short_C2 227 lvvDgGl 233
                                       + vD Gl
  gi|313125815|ref|YP_004036085.1| 242 VRVDDGL 248
                                       ****996 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.7   0.8   1.2e-62   1.6e-59       2     191 ..       9     201 ..       8     205 .. 0.98

  Alignments for each domain:
  == domain 1  score: 200.7 bits;  conditional E-value: 1.2e-62
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       v++vtG+++GIGra+a++la++Ga+vv+ +   +e++e++a+ l ++ ++  + q+Dv+d ++v a++e++ +++g+
  gi|313125815|ref|YP_004036085.1|   9 VAVVTGGTRGIGRAVAEQLAERGATVVAtYHDDDEAAEQTAAALAALPTETAVEQFDVADFDAVAATFETVTERYGH 85 
                                       89**************************9999999****************************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH..HCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml..kqssGrIvnvsSvagkvpvagvaaYsAs 152
                                         +LvnNAG+  +g   +++ e+w+rvi+vNltg+f +tr+++++ml  + ++GrIvnv+Sva++ ++ag++ Y+As
  gi|313125815|ref|YP_004036085.1|  86 PTILVNNAGVMDNGLLLRMTPERWQRVIDVNLTGTFYCTREAAKQMLrcDDRGGRIVNVASVAAQRGWAGQSNYAAS 162
                                       ***********************************************9***************************** PP

                                       HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       Ka+v gltrs+a+el  + irvnavaPG++dTd+ ++++
  gi|313125815|ref|YP_004036085.1| 163 KAGVLGLTRSAARELGGKDIRVNAVAPGYTDTDLLASSS 201
                                       *********************************998765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.6   2.5e-22   3.2e-19       4     154 ..      11     164 ..       9     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 2.5e-22
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tGG+ g+G+++a++lae+ga+ ++    +   de+++++ a+l+al +e  v + Dv+d dav+a++e+++++ +
  gi|313125815|ref|YP_004036085.1|  11 VVTGGTRGIGRAVAEQLAERGATVVATYHDD---DEAAEQTAAALAALPTETAVEQFDVADFDAVAATFETVTERYG 84 
                                       89********************977766555...78888899**********************************8 PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT......S--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled......esldffvlfSSiagllgsagqanYaa 151
                                         +  ++ Agv++++ll +mt e++++v+   ++G+    +  ++      ++   +v ++S+a+  g agq+nYaa
  gi|313125815|ref|YP_004036085.1|  85 HPTILVNNAGVMDNGLLLRMTPERWQRVIDVNLTGTFYCTREAAKqmlrcdDRGGRIVNVASVAAQRGWAGQSNYAA 161
                                       8889********************************99887666635444455567********************9 PP

                                       HHH CS
                                KR 152 aNa 154
                                         a
  gi|313125815|ref|YP_004036085.1| 162 SKA 164
                                       865 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.5   1.3e-08   1.6e-05       2      63 ..      11      79 ..      10     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.3e-08
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHHH CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfkee 63
                                      +VtG+t  iG+a++++l+e+g +v++  ++ ++ +++  + l        + + d+ d +a+++ f+++
  gi|313125815|ref|YP_004036085.1| 11 VVTGGTRGIGRAVAEQLAERGATVVATYHDDDEAAEQTAAALaalptetAVEQFDVADFDAVAATFETV 79
                                      8*****************************8888888888779******99999999999999888754 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.1e-06      0.01       2      74 ..      12      79 ..      11      83 .. 0.88
   2 ?   -2.0   0.0       1.4   1.8e+03     150     166 ..     156     172 ..     150     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.1e-06
                                      EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev 74
                                      +TG++  iG  +ae+L e+g +v+ + +++++ + ++ ++la  p      +  + + D+ D +++   ++ v
  gi|313125815|ref|YP_004036085.1| 12 VTGGTRGIGRAVAEQLAERGATVVATYHDDDEAAEQTAAALAALPT-----ETAVEQFDVADFDAVAATFETV 79
                                      9*******************************99999999997665.....4678999999999998888765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                       -SHHHHHHHHHHHHHHH CS
                     GDP_Man_Dehyd 150 rsPYaaaKlyadwivvn 166
                                       +s Yaa+K+    ++++
  gi|313125815|ref|YP_004036085.1| 156 QSNYAASKAGVLGLTRS 172
                                       799*****988777765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   8.0   1.1e-05     0.014       1     177 [.      14     226 ..      14     233 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH.....HHHCTTTCEEEE.--TT-CCHHHHHHT......T-SEE. CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla.....eleaeeglevve.gdvtdvedlaealk......gadaV. 64 
                                       G+t ++Gr+++++l++rg  +v+a   + +++a     +l+a +  ++ve  dv d +++a++++      g+ ++ 
  gi|313125815|ref|YP_004036085.1|  14 GGTRGIGRAVAEQLAERG-ATVVATYHDDDEAAeqtaaALAALPTETAVEqFDVADFDAVAATFEtvteryGHPTIl 89 
                                       99***************6.9999998886666512222344445555555478888888888887666666555441 PP

                                       EES---TCC....HHHH...................HHHHHHHHHH..CT--EEEEEEETTTTSGCGCHHHHHHHHC CS
                    NAD_binding_10  65 vsalggggk....deeg...................aknivdaake..agvkRfvlvsaigvgdevpgefgewnkel 116
                                       v ++g  ++    +  +                   ++ +++ + +      R+v v ++ +++ ++g+ +  +++ 
  gi|313125815|ref|YP_004036085.1|  90 VNNAGVMDNglllR--MtperwqrvidvnltgtfycTREAAKQMLRcdDRGGRIVNVASVAAQRGWAGQSNYAASK- 163
                                       33343333345440..134445566666777788884444544433223345899999999988777765544333. PP

                                       CHHHHHHHHHHHHHHHHSSSEEEEEEE-CEE-S..T.--SEEEEETTSS----EEEHHHHHHHH CS
                    NAD_binding_10 117 lkaylaakraaeellrasgldwTivrpggLtde..p.ttkyrvvekgepfkggsisradVAdvl 177
                                        + +l   r a+++l  +++    v pg+   +  + +++ + + + ++ +g+  + + +Adv+
  gi|313125815|ref|YP_004036085.1| 164 -AGVLGLTRSAARELGGKDIRVNAVAPGYTDTDllAsSSGHESAVETDTASGRVATPEEIADVI 226
                                       .577788888999999999999999999884443433666677777777777777888888887 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   3.1e-05     0.039       8     101 ..      18     117 ..      11     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHHTTS.......SEEE CS
                   Sacchrp_dh_NADP   8 svGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaallkeg.......dlvv 74 
                                       ++G+avae la+++     ++  + ++e +e++aa a   l ++   +++d+++ +a +aa  +         +++v
  gi|313125815|ref|YP_004036085.1|  18 GIGRAVAEQLAERGAT--VVATYHDDDEAAEQTAA-AlaaLPTETAVEQFDVADFDA-VAATFETVteryghpTILV 90 
                                       8*************87..33333444444444444.2599999999999****9999.5554444334488999999 PP

                                       E-SSGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  75 nlsppissldvlkaCietgvhyvdtsi 101
                                       n ++ + +  +l++  e+  +++d+  
  gi|313125815|ref|YP_004036085.1|  91 NNAGVMDNGLLLRMTPERWQRVIDVNL 117
                                       999999999999998888888888666 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.7     3e-05     0.038       2      71 ..       9      80 ..       8      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                                      EEEE--SC..CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES CS
                           3HCDH_N  2 vaviGaGt..mGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisftt 71
                                      vav+  Gt  +G+ +a+++a++g +Vv +  +++ +++ ++++ + l    + ++++ ++++a++a+ ++ t
  gi|313125815|ref|YP_004036085.1|  9 VAVVTGGTrgIGRAVAEQLAERGATVVATYHDDDEAAEQTAAALAALPTETAVEQFDVADFDAVAATFETVT 80
                                      89999998778999**************99999888888888888888888888888889998888877665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.0   4.3e-05     0.054       2      65 ..      11      79 ..      10      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S...-SHHHHHHHHSTTEEE..ES-TT-HHHHHHHHTT- CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt...kselakslkeaGvelv..kgdlddkeslvealkgv 65
                                      +v+G+T  +G++v++ l+++g +v a  +d     +++a++l++ + e+   + d+ d + +++ +++v
  gi|313125815|ref|YP_004036085.1| 11 VVTGGTRGIGRAVAEQLAERGATVVATYHDDdeaAEQTAAALAALPTETAveQFDVADFDAVAATFETV 79
                                      699***************************9888889999******99875777888888888888776 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   9.4e-05      0.12      22      72 ..       9      60 ..       3      71 .. 0.82
   2 ?   -3.1   0.0       8.8   1.1e+04      22      41 ..     158     179 ..     147     187 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.4e-05
                          Toprim_2 22 nvvalgGt.alteaalkllerypekkvvlalDnDkaGrkaakrlaellreag 72
                                       +v +gGt ++ +a +++l+++ +  v   +D D+a ++ a+ la+l  e+ 
  gi|313125815|ref|YP_004036085.1|  9 VAVVTGGTrGIGRAVAEQLAERGATVVATYHDDDEAAEQTAAALAALPTETA 60
                                      58999***99999*****999944445566*************999876665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.8
                          Toprim_2  22 nvval.gGt.alteaalkller 41 
                                       n+ a+ +G+ +lt+ a+++l  
  gi|313125815|ref|YP_004036085.1| 158 NYAASkAGVlGLTRSAARELGG 179
                                       4444425556677777766655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   0.00011      0.14       6      71 ..      16      77 ..      10      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                      -SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SS CS
                            TrkA_N  6 lGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatg 71
                                         +Gr++ae+L e+g  vv+  +d++ ++e   + + ++ + +t e ++e+ +++++dav a+ +
  gi|313125815|ref|YP_004036085.1| 16 TRGIGRAVAEQLAERGATVVATYHDDDEAAE---QTAAALAALPT-ETAVEQFDVADFDAVAATFE 77
                                      4459**********77457777666655444...44455555555.8899***********99976 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4   0.00024      0.31      10      43 ..      14      54 ..       8      94 .. 0.61
   2 ?    3.2   0.2      0.14   1.7e+02      10      62 ..     164     226 ..     161     244 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                            LytR_C 10 tgvsGlAarvadaLeerGftvgevgnagnadee..........t 43
                                       g++G+ ++va++L+erG tv+++    ++d+e           
  gi|313125815|ref|YP_004036085.1| 14 GGTRGIGRAVAEQLAERGATVVATY---HDDDEaaeqtaaalaA 54
                                      4789***************999833...2222222222222220 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                            LytR_C  10 tgvsGlAarvadaLeerGftvgevgnagnadee...........ttivy.reaaa....aaakalaaal 62 
                                       +gv Gl +++a++L ++  +v +v+     +++           + +       a    a+ +++a+ +
  gi|313125815|ref|YP_004036085.1| 164 AGVLGLTRSAARELGGKDIRVNAVA---PGYTDtdllasssgheSAVETdT---AsgrvATPEEIADVI 226
                                       57889*********99999888844...33233123333334333333211...122334444555555 PP

>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.3     0.046        59      27      48 ..      34      55 ..      27      78 .. 0.81
   2 ?   -2.3   0.0         3   3.8e+03      22      33 ..      97     106 ..      87     112 .. 0.68
   3 ?    6.0   0.1    0.0079        10      40      64 ..     158     182 ..     155     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.046
                                      EEEECCSSSS-HHHHHHHHHHH CS
                          Robl_LC7 27 viatstldnddadqlAalasgl 48
                                      v+at++ d+++a+q+Aa++++l
  gi|313125815|ref|YP_004036085.1| 34 VVATYHDDDEAAEQTAAALAAL 55
                                      77888899***********987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
                                       ETTS-EEEECCS CS
                          Robl_LC7  22 skdGlviatstl 33 
                                       + +Gl++++ t+
  gi|313125815|ref|YP_004036085.1|  97 D-NGLLLRM-TP 106
                                       3.6888888.65 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0079
                                       HHHHHHHHHHHHHHHHHHHCTSSSE CS
                          Robl_LC7  40 qlAalasgllsaakaaarelgegel 64 
                                        +Aa  +g+l+++++aarelg+ ++
  gi|313125815|ref|YP_004036085.1| 158 NYAASKAGVLGLTRSAARELGGKDI 182
                                       59999****************7765 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.6   0.00015      0.19      32      86 ..       6      57 ..       2      84 .. 0.87
   2 ?    0.0   0.3      0.53   6.8e+02      22      85 ..     172     230 ..     170     237 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                      T--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHH CS
                               ETF 32 ggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaalik 86
                                      +gev++v+ G+     a++e+la++Ga+ v    d++ a   ae+ta+alaal  
  gi|313125815|ref|YP_004036085.1|  6 DGEVAVVTGGTRGIGRAVAEQLAERGATVVATYHDDDEA---AEQTAAALAALPT 57
                                      499********999999***********99999999987...9999999999855 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHH CS
                               ETF  22 eaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaali 85 
                                       +aAr+l  k+  +v av  G   +++ l  a +  G + ++  d+++   +++e +a++++ l+
  gi|313125815|ref|YP_004036085.1| 172 SAARELGGKD-IRVNAVAPGY--TDTDLL-ASS-SGHESAVETDTASGRVATPEEIADVIRFLA 230
                                       5899997754.7788888888..333333.333.688888999999999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1721.29
//
Query:       gi|313125816|ref|YP_004036086.1|  [L=315]
Description: ACP S-malonyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-41  141.0   0.2      7e-41  140.8   0.2    1.0  1  Acyl_transf_1  Acyl transferase domain


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.2   3.9e-45     7e-41       2     276 ..      15     293 ..      14     303 .. 0.95

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 3.9e-45
                                       EEE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHHH CS
                     Acyl_transf_1   2 fvfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaellk 78 
                                       f+f+GqGsQ  GMG++ +++ +  +a  +r+d a+    ++ ++++  +  + +l++   +qp+L a  +a +e   
  gi|313125816|ref|YP_004036086.1|  15 FLFPGQGSQTVGMGRAFYDDWPETRALFDRLDSAL----DIDLTELCFEGTTEKLQQPSITQPVLLATGLAVYEGVT 87 
                                       9*******************************886....679**********************************9 PP

                                       HTT.-TTSEEEE-TTHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHT...S-EECCEECS....HHHHHHH..TT.E CS
                     Acyl_transf_1  79 skG.vrpaavvGHSlGElAaavvagalsseeallavvlrsrlmmqla...gpgdmaavel...aeeeeklrcqddvv 148
                                       +   v+p +v+GHSlG   a+++aga+s++e ++ +  r+ +m q+a   gpg m av l   +e+e++ +c +dv 
  gi|313125816|ref|YP_004036086.1|  88 ARFdVEPTLVAGHSLGHFTALGAAGAISPAETAKLTHQRGNCMEQAAaadGPGTMIAVLLatrDEVEKACACREDVG 164
                                       9877****************************************9876789*********98778888888****** PP

                                       EEEEEECCCCECCEEHHHHHHHHHHHHHCC..CCEEECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCC CS
                     Acyl_transf_1 149 gavansprrvvisgsqealrelvervskeg.vgalvenvnvavhspqvdaiadalasaladiaprkpkvakisstsl 224
                                        a +n p++ visg+++ ++++ er+ +++ v+ ++ +v+ a+hsp ++++ d    a+ad+++r++ ++  s +s 
  gi|313125816|ref|YP_004036086.1| 165 IALYNAPKQAVISGTTAGVKAVEERLDERTtVRFHELDVGAAFHSPVMASAVDCVETAMADVTLREADIPVVSDVSG 241
                                       *****************************99********************************************** PP

                                       HHHHHHCHHHHHHHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCCCC CS
                     Acyl_transf_1 225 desserelsaeywvanlrspvrfaeavlsaaetiplvfveispHslllaale 276
                                       +  +++ +  +   + + s+v     v ++++++ + fve +p  +l   +e
  gi|313125816|ref|YP_004036086.1| 242 EVYTKPSVARRDLSNQITSAVDWVRVVEELRAQGIERFVEFPPAGVLSTLVE 293
                                       *******999999******************************888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2289.37
//
Query:       gi|313125817|ref|YP_004036087.1|  [L=156]
Description: phosphopantetheine--protein transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-14   54.0   0.0    1.8e-14   53.8   0.0    1.2  1  ACPS      4'-phosphopantetheinyl transferase superfamily


Domain annotation for each model (and alignments):
>> ACPS  4'-phosphopantetheinyl transferase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0     1e-18   1.8e-14       3      83 ..      19      96 ..      17     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1e-18
                                      EEEEEEHHHHH.HHH-----HHHHHS-HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHT...TS-SSSS--GGG-EEE CS
                              ACPS  3 GiDieklsrlrkrvkrrgakilkrifteeErkllkssdeearaelfarlWaaKEAllKal...gpglrklldfksievl 78
                                      G+D++ ++r+ + + ++g++++ r+ft++E+++++++ ++ +  + a++WaaKEA+lK l   +pg+    +   ie++
  gi|313125817|ref|YP_004036087.1| 19 GVDVVAIDRIADLLAEFGDSFRGRVFTPAEQAYCEAQGDPPQ--HYAARWAAKEAFLKTLagsSPGV----PTAAIEID 91
                                      9***********************************999999..99**************6444444....66666776 PP

                                      E-TTS CS
                              ACPS 79 edstg 83
                                      ++++g
  gi|313125817|ref|YP_004036087.1| 92 RRPDG 96
                                      65554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 990.51
//
Query:       gi|313125818|ref|YP_004036088.1|  [L=407]
Description: 3-oxoacyl-ACP synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-52  178.8  10.5    1.4e-51  175.5   6.5    2.1  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    8.8e-32  109.6   2.9      2e-31  108.4   1.7    2.2  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    1.7e-05   24.3   0.7      9e-05   22.0   0.2    2.1  2  Thiolase_N       Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.5   6.5   2.4e-55   1.4e-51       2     253 .]       3     244 ..       2     244 .. 0.89
   2 !    5.4   0.1    0.0019        11      95     161 ..     280     353 ..     276     390 .. 0.73

  Alignments for each domain:
  == domain 1  score: 175.5 bits;  conditional E-value: 2.4e-55
                                       --EEEEEEEEEBTTBSSHHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..STTEGGTTSTHHH CS
                     ketoacyl-synt   2 epvaivGmgarfPggndveefwelLlegrdaiselpadrwdadklydpparaagkiktklggfldvddfdpeffgis 78 
                                       ++v+++G+g +++ g++++++w  Ll+ r++ +++   r+d+d+  + +a++a +i t       + + d + ++i 
  gi|313125818|ref|YP_004036088.1|   3 RDVVVTGIGLVTALGETADSTWAGLLDERSGAGPIT--RFDPDEA-NVRANVACEIGT-------DPAADTSDDRID 69 
                                       79*******************************999..8***999.477777777777.......69999******* PP

                                       HHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTC..TTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCT.THHHHHSTT CS
                     ketoacyl-synt  79 preaeamdpqqrllleaawealedagltpeel..dgsrvgvfiGvgagdyaalaaldedgsevkasp.kavgavlan 152
                                       +r    m + +++++ aa+ealedag++p +     +r+g  iG+g +  ++++a    g  ++ sp + v a l+n
  gi|313125818|ref|YP_004036088.1|  70 DR---TMGRYTQFAVAAAAEALEDAGFDPVDPawTPERAGTSIGSGLAGLSEIEAAA--G--SRPSPsFLVRA-LTN 138
                                       **...************************5555555569999999999776655544..4..67788567777.*** PP

                                       HHHHHHHHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TT..SGGG CS
                     ketoacyl-synt 153 viagrisyalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllspd..grck 227
                                        +ag++s+a+g++Gp+ ++ tACs++  a++aa + +r+g+adv++aGG+e++++p +v++f+++++ls+   ++  
  gi|313125818|ref|YP_004036088.1| 139 LAAGHVSMAVGAKGPNRAPGTACSAGTHAIAAAADDIRRGRADVVIAGGTEASISPLGVGSFDSMRALSTRaaDPAA 215
                                       **************************99999999********************************66665599988 PP

                                       TTBTTB...-SB-BB-EEEEEEEEECHHH CS
                     ketoacyl-synt 228 afdpka...dGfvlGEGvGavvLkrleda 253
                                       a++p++   dG vl+EG+G+v+L+++++a
  gi|313125818|ref|YP_004036088.1| 216 ASRPFDadrDGLVLAEGCGIVILESRDHA 244
                                       888888888***************99876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHTS-HHTCTTGG...EEEEEEESSTHHHHHHHHHHHTT....GGGSCT.THHHHHSTTHHHHHHHHH CS
                     ketoacyl-synt  95 aawealedagltpeeldgsr...vgvfiGvgagdyaalaaldedgs....evkasp.kavgavlanviagrisya 161
                                       + ++al+dag +p+++d+ +   +   iG + + +a  ++ +e+++    +vk++  +a+ga + ++ a++++++
  gi|313125818|ref|YP_004036088.1| 280 CIERALKDAGRDPAAVDHVNahaTSTPIGDAREAEALNTVFSETDVppttSVKGHLgHALGA-AGAIEAAIVAQT 353
                                       6789************9988666666677666644333333333335556678887788888.888888888876 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.34   2.1e+03      27      43 ..      81      97 ..      62     126 .. 0.78
   2 !  108.4   1.7   3.4e-35     2e-31       1     117 [.     252     365 ..     252     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.34
                                      HHHHHHHHHHHT--GGG CS
                   Ketoacyl-synt_C 27 araiekalaeagvdped 43
                                       +a ++al++ag+dp d
  gi|313125818|ref|YP_004036088.1| 81 VAAAAEALEDAGFDPVD 97
                                      46678899999988855 PP

  == domain 2  score: 108.4 bits;  conditional E-value: 3.4e-35
                                       SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCT CS
                   Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqp 77 
                                       ya ++g++ + d++h + +a++g++++r+ie+al++ag dp+ vd+v+ah+t+tp+gD+ E+eal++vf+e+     
  gi|313125818|ref|YP_004036088.1| 252 YAAVTGAGRSADAHHVTRPAESGDGLRRCIERALKDAGRDPAAVDHVNAHATSTPIGDAREAEALNTVFSETD---V 325
                                       899********************************************************************87...6 PP

                                       SEEE-THHHH-B-GGGHHHHHHHHHHHHHHHTEE--BTT- CS
                   Ketoacyl-synt_C  78 lavgSvKsniGHleaAaGvaelikvvlalkhgvipptlnl 117
                                        + +SvK  +GH+++AaG++e++ v++++ +g+ippt+n+
  gi|313125818|ref|YP_004036088.1| 326 PPTTSVKGHLGHALGAAGAIEAAIVAQTIAEGTIPPTMNY 365
                                       778************************************8 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.5e-08     9e-05      83     114 ..     159     190 ..     136     204 .. 0.88
   2 ?    0.1   0.0      0.07   4.2e+02      27      50 ..     277     300 ..     254     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.5e-08
                                       HGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEE CS
                        Thiolase_N  83 kvcsSglkavalaaqsiaageadvvvagGvEs 114
                                        +cs g +a+a+aa+ i+ g+advv+agG+E 
  gi|313125818|ref|YP_004036088.1| 159 TACSAGTHAIAAAADDIRRGRADVVIAGGTEA 190
                                       68****************************95 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.07
                                       HHHHHHHHHHHHTS-GGGCCEEEE CS
                        Thiolase_N  27 laealkallekagvdpeevdeviv 50 
                                       l++ ++++l++ag dp++vd+v  
  gi|313125818|ref|YP_004036088.1| 277 LRRCIERALKDAGRDPAAVDHVNA 300
                                       56789999*****99999999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 2573.36
//
Query:       gi|313125819|ref|YP_004036089.1|  [L=81]
Description: acyl carrier protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   51.2   1.1    1.4e-13   51.0   1.1    1.1  1  PP-binding     Phosphopantetheine attachment site
  ------ inclusion threshold ------
      0.036   14.2   0.0       0.04   14.0   0.0    1.4  1  Ribosomal_L50  Ribosomal subunit 39S
       0.12   12.6   2.1       0.19   11.9   2.1    1.6  1  PP-binding_2   Acyl-carrier


Domain annotation for each model (and alignments):
>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   1.1   2.3e-17   1.4e-13       3      67 .]      11      77 ..       9      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.3e-17
                        PP-binding  3 lrelvaevlgvpleeidpdtdlf.d.lGlDSllavellaaleeefgveiplsdlfehptlaelaayl 67
                                      +  +v+e l+v++ ++d++t+++ + l  DSl++ve++ a+e+  gv ip++dl e+ t+++l+ay+
  gi|313125819|ref|YP_004036089.1| 11 IEGIVEERLRVDTGDFDAETPFDgEtLDADSLDLVEIAEAIEADVGVHIPDEDLEELETVGDLTAYV 77
                                      6789*******************999****************************99*********97 PP

>> Ribosomal_L50  Ribosomal subunit 39S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.8e-06      0.04      45      76 ..      48      79 ..       6      81 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.8e-06
                     Ribosomal_L50 45 lkrlqqllgheipDykltklhtvkdlveylee 76
                                      +  +    g +ipD  l +l+tv dl  y++e
  gi|313125819|ref|YP_004036089.1| 48 AEAIEADVGVHIPDEDLEELETVGDLTAYVTE 79
                                      56678889*********************965 PP

>> PP-binding_2  Acyl-carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.1   3.3e-05      0.19      47      85 ..      40      78 ..       2      81 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                      PP-binding_2 47 dgldtvefvedveelfdvivsdevadnfetlqeiadlvv 85
                                      d+ld ve+ e +e    v ++de ++++et+ +++ +v 
  gi|313125819|ref|YP_004036089.1| 40 DSLDLVEIAEAIEADVGVHIPDEDLEELETVGDLTAYVT 78
                                      89*****************************99988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 461.28
//
Query:       gi|313125820|ref|YP_004036090.1|  [L=321]
Description: zn-dependent oxidoreductase, NADph:quinone reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-27   94.6   0.7    7.5e-27   93.9   0.7    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
    5.1e-23   82.6   0.8    8.8e-23   81.8   0.8    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    3.9e-08   33.1   0.0    2.4e-07   30.6   0.0    2.3  2  ADH_N         Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
        0.1   12.0   1.4       0.17   11.3   1.4    1.4  1  adh_short     short chain dehydrogenase


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.7   1.7e-30   7.5e-27       1     119 [.     150     266 ..     150     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 1.7e-30
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG++avq+A a+Ga+v a++s++ek+el ++lGad++i+y++ d+ +++ + t  +gvd+v++ vG g ++ a+++
  gi|313125820|ref|YP_004036090.1| 150 GVGSLAVQFADAAGATVLATASTAEKRELTRDLGADHAIDYTDVDVADAVLSRT--DGVDLVVDGVG-GNAFAASVE 223
                                       9****************************************666**********..5**********.********* PP

                                       CEEEEEEEEECSCTSSEEE.EEHHHHHHTT-EEEEE-SSCHHH CS
                        ADH_zinc_N  78 llkpgGrlvvvGggkgeee.fdlrnlllkeksilGsllgslre 119
                                       +l+p Gr+v++G+ +g  + + + +l++ + s++G +l +  +
  gi|313125820|ref|YP_004036090.1| 224 ALAPVGRIVTFGMASGSVPtVATPRLFFANQSVIGYHLEHALD 266
                                       *************666666599999************998333 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.8     2e-26   8.8e-23       1     133 []     182     319 ..     182     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 2e-26
                                       TT-SEEEETTSTTHH....HHH-T.T-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-E CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe....aatgg.egvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrs 72 
                                       lGAd++idy++ d++    +   + +gvD+v+d vgg+a+ +as+++l++ Gr+v+ g+ + s  + + ++    ++
  gi|313125820|ref|YP_004036090.1| 182 LGADHAIDYTDVDVAdavlS---RtDGVDLVVDGVGGNAF-AASVEALAPVGRIVTFGMASGSVPTVATPR-LFFAN 253
                                       8**************85433...3599*************.*******666******96663333333333.44455 PP

                                       EEE--GGG...-........-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  73 vkyeflfsmkas.......aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                        ++  +  +++        + +     + + +++G++++vvdr+ pl+e ++Ah++l+++ ++GK+Vl
  gi|313125820|ref|YP_004036090.1| 254 QSVIGYH-LEHAldhvperVLEA-VPSVIDHLASGQVEVVVDRTVPLSEPQQAHDALANRETVGKVVL 319
                                       5555555.444455544422333.578899*************************************8 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   5.4e-11   2.4e-07       2      76 ..      28     100 ..      27     138 .. 0.75
   2 ?   -1.2   0.0      0.41   1.8e+03      28      48 ..     273     293 ..     259     303 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 5.4e-11
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkeg 76 
                                       gev i+v+a+g++  D++  +g+   + ++p+++G E++G+v  +  + ++l+vGdrV++  ++s g +++ +  
  gi|313125820|ref|YP_004036090.1|  28 GEVSIDVAAVGVNFADIEQRRGNYPDSPSPPFVPGLEVAGTVRTAPAG-SDLAVGDRVAA-LTSSGGYAERATAP 100
                                       79********************99999999************996655.68*******98.45555555555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.41
                                       TSSSSEE---EEEEEEEEEST CS
                             ADH_N  28 evklplilGHEivGeveevgp 48 
                                         + p ++ H ++G+ve v +
  gi|313125820|ref|YP_004036090.1| 273 LEAVPSVIDHLASGQVEVVVD 293
                                       567899999999999988755 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.4   3.9e-05      0.17       3      86 ..     142     214 ..     140     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkld 79 
                                       vlv  +++G+G   ++   ++Ga+v+++++++ek  e+   l+++   + +  vDv+d         ++ ++++++d
  gi|313125820|ref|YP_004036090.1| 142 VLVHAGAGGVGSLAVQFADAAGATVLATASTAEKR-ELTRDLGAD-HAIDYTDVDVAD---------AVLSRTDGVD 207
                                       8999***************************9988.888889985.567777777774.........3334445555 PP

                                       EEEE--- CS
                         adh_short  80 vLvnNAG 86 
                                       ++v ++G
  gi|313125820|ref|YP_004036090.1| 208 LVVDGVG 214
                                       5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2149.94
//
Query:       gi|313125821|ref|YP_004036091.1|  [L=297]
Description: hypothetical protein Hbor_10540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-09   37.1   0.0    2.8e-09   36.8   0.0    1.0  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain
  ------ inclusion threshold ------
      0.045   13.0   5.8       0.65    9.2   0.2    3.0  3  AurF            P-aminobenzoate N-oxygenase AurF


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   3.2e-13   2.8e-09      15     237 ..      27     256 ..      19     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 3.2e-13
                                       HHHHHHCT---GGGS-GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBSSHHHHHHHHHHHHH CS
                    Ribonuc_red_sm  15 lykkleanfWtpeevdlskDlkdwkekLsedekefikkvlaflalldtivnenlverllsevqipearafygfqaam 91 
                                       + + +++ +W p e+dl  D +  ++ L     + +   +a++ + +  v+e lv  l+   +++  + f++  +++
  gi|313125821|ref|YP_004036091.1|  27 YFRHATERHWSPYEIDLAADRAAISD-LGRSAFTQLRATIAMFGAGEENVTEDLV-PLAATTTNKTDQRFVASHIYE 101
                                       6678999***************6663.6666666666677888889999999988.6668888999999******** PP

                                       HHHHHHHHHHHHHHHT...........-HHHHHHHHCHHHH-HHHHHHHHHHHHHHCTTTSCHHHHHHHHHHH.HHH CS
                    Ribonuc_red_sm  92 EniHaesYsllletlvk..........dekekdelfnaieenpalqkkaewikkwyeskkdeekfaerlvafa.lle 157
                                       E+ Ha  +  + + +++          ++ + d+ f a   ++++ ++ e +++ + +++++ + a++   +   +e
  gi|313125821|ref|YP_004036091.1| 102 EAKHAAFFERYWKDVIRpaedargldpTDPTADRWFTA--AYEEIFNRTETAMNQLLDDDTPTNRANAYCHYHlTVE 176
                                       ****************8777777776633334444444..46778999999988888777777888888888889** PP

                                       HCCCHHHHHHH...HHHHHTTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHH CS
                    Ribonuc_red_sm 158 gilfysgFaai...lwlkkrgl.lpglaeiielilrDeglHtdfagllfkelkeenelenkeleeeveelikeavel 230
                                       g++   gF ai   +  +  g  lpgl+e i+ +  Deg H+ ++++   el+++    ++  +++vee+++++ e 
  gi|313125821|ref|YP_004036091.1| 177 GVFGQTGFHAIeatFDPETDGPsLPGLVEGISHVRQDEGRHVGYGMNQLAELLQR----TAVERSFVEETVETLAEP 249
                                       ********987422444466668*****************************999....888888888888888776 PP

                                       HHHHHHH CS
                    Ribonuc_red_sm 231 Ekefitd 237
                                        ++ ++ 
  gi|313125821|ref|YP_004036091.1| 250 VDAVVER 256
                                       6665555 PP

>> AurF  P-aminobenzoate N-oxygenase AurF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0013        12       4      43 ..      20      59 ..      17      67 .. 0.83
   2 ?    9.2   0.2   7.2e-05      0.65     186     213 ..      92     119 ..      58     126 .. 0.81
   3 ?   -0.1   0.1     0.049   4.4e+02     194     224 ..     212     241 ..     204     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0013
                                      X-HHHHHHHHHHHHH-T---........-.----TTS-SS- CS
                              AurF  4 reevlerllessarrsfdplvdiDwdapl.aqedddrwdlp 43
                                       +  +er ++++ +r++ p+ +iD+ a+  a  d +r  ++
  gi|313125821|ref|YP_004036091.1| 20 NRGRAERYFRHATERHWSPY-EIDLAADRaAISDLGRSAFT 59
                                      567899**************.*****999448888887776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 7.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AurF 186 rrvmriHvaEEarHisfareelrrrvpr 213
                                       +r ++ H+ EEa H+ f++ + + +++ 
  gi|313125821|ref|YP_004036091.1|  92 QRFVASHIYEEAKHAAFFERYWKDVIRP 119
                                       6778899999999999999999888765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHHHHHS-HHHHHHHHH CS
                              AurF 194 aEEarHisfareelrrrvprlsraerallrl 224
                                       ++E rH+ +  + l + ++r  ++er ++ +
  gi|313125821|ref|YP_004036091.1| 212 QDEGRHVGYGMNQLAELLQRT-AVERSFVEE 241
                                       699999999999998887764.556665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2160.68
//
Query:       gi|313125822|ref|YP_004036092.1|  [L=255]
Description: transcriptional regulator containing cbs domains [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-17   64.1   0.6    2.9e-08   34.0   0.0    2.4  2  CBS       CBS domain
    8.6e-07   29.2   0.0    2.9e-06   27.5   0.0    1.8  2  ParBc     ParB-like nuclease domain
  ------ inclusion threshold ------
       0.19   11.8   0.1        1.1    9.3   0.1    2.1  1  ParBc_2   Putative ParB-like nuclease


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   3.3e-10     2e-06       1      54 [.      11      65 ..      11      68 .. 0.90
   2 !   34.0   0.0   4.9e-12   2.9e-08       1      53 [.      71     123 ..      71     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.3e-10
                                      HHHHSBSSCEEEETTSBHHHHHHHHH.HHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  1 Vgdimtrdvvtvppdttleealelmr.ekgvsrlPVVdedgklvGivtlrDllra 54
                                      Vg++m +dv +++pd+ +++++e+++  ++ ++lPV d++  ++G+v  +Dll +
  gi|313125822|ref|YP_004036092.1| 11 VGAYMATDVEVARPDDRVADVVETLAgATNDGGLPVCDGERTVLGYVGASDLLAV 65
                                      8999*********************7545589*****9888899********976 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 4.9e-12
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V+ +m+r++v+v pdt++ +a+  + ++g   lPVV++ g+l+G ++  D +r
  gi|313125822|ref|YP_004036092.1|  71 VETVMRRELVVVGPDTSVTDAAHAILRSGQQFLPVVNDAGELLGTFSNGDAVR 123
                                       6789********************88*998677************99888766 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.88   5.3e+03      20      39 ..      85     105 ..      67     109 .. 0.70
   2 !   27.5   0.0   4.9e-10   2.9e-06       4      83 ..     157     231 ..     154     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.88
                             ParBc  20 pekieelvasIkkkGll.qPi 39 
                                       ++++ + +++I  +G++  P+
  gi|313125822|ref|YP_004036092.1|  85 DTSVTDAAHAILRSGQQfLPV 105
                                       567788888899888885565 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 4.9e-10
                             ParBc   4 plseirpnplqprkdspekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivleiddee 80 
                                        +s++ p++  +    ++++e    ++k +Gl +P+iv         +++G++R  Aa rl++++v+++ l i+ +e
  gi|313125822|ref|YP_004036092.1| 157 AVSSLIPTQQEVF---ADELEGRTYELK-NGLAEPLIVVDYG-PETVLVDGHHRALAALRLNVERVDAYALSISPDE 228
                                       5666666666666...889*********.*********9996.999*************************999666 PP

                             ParBc  81 ama 83 
                                         +
  gi|313125822|ref|YP_004036092.1| 229 VGE 231
                                       555 PP

>> ParBc_2  Putative ParB-like nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00018       1.1       3      72 ..     156     214 ..     120     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00018
                                       EEGGGCB-SBSEE-HHHHHHHHHHHHT------.---TT-BEEEEEE-STT-EEE-S-HHHHHHHHHTT- CS
                           ParBc_2   3 veiadLrPTQlavGldeveyklgeleelkekkkldkflekklvpvVigpdgelYliDhHHllrallesgv 72 
                                       v++++L PTQ  v  de+e ++ el++           +     +V+  + e  l+D+HH + a l+ +v
  gi|313125822|ref|YP_004036092.1| 156 VAVSSLIPTQQEVFADELEGRTYELKNGL---------A--EPLIVVDYGPETVLVDGHHRALAALRLNV 214
                                       55666666666666666666655553222.........1..2235666777899******9999887555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1702.46
//
Query:       gi|313125823|ref|YP_004036093.1|  [L=117]
Description: hypothetical protein Hbor_10560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 816.34
//
Query:       gi|313125824|ref|YP_004036094.1|  [L=290]
Description: lysophospholipase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-14   54.1   0.1    2.5e-08   33.9   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
      4e-14   52.5   0.0    5.9e-14   51.9   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
    5.5e-11   43.5   8.0    6.8e-11   43.2   8.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.9e-07   30.9   0.0      6e-05   22.7   0.0    2.5  2  DLH            Dienelactone hydrolase family
    2.1e-06   27.4   0.0      0.018   14.5   0.0    2.1  2  Peptidase_S9   Prolyl oligopeptidase family
    3.5e-06   26.8   0.0    1.2e-05   25.1   0.0    1.7  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    0.00027   19.7   0.0       0.15   10.7   0.0    2.1  2  AXE1           Acetyl xylan esterase (AXE1)
      0.004   17.3   0.0      0.019   15.1   0.0    2.0  2  Abhydrolase_4  TAP-like protein
      0.008   15.9   0.0       0.43   10.3   0.0    2.8  3  Abhydrolase_5  Alpha/beta hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.1   1.3e-11   2.5e-08       1     106 [.      26     132 ..      25     165 .. 0.81
   2 !   18.5   0.0   6.4e-07    0.0013     191     256 ..     200     270 ..     191     271 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.3e-11
                                       SEEEEE-STTT..CGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB..CHHSHHHHHHHHH..HHHHHCTT CS
                     Abhydrolase_1   1 pvlvilhGlpg..ssdvwaerglapaLakdgfdvillDlrGvgySspapacin.ddygtasvaddld..rildalgd 72 
                                       pv+v+  Gl+g  s+++  +   a+ La++g+ v+l+D r++g S   p+  + +  + a+ ++ ++  r +d l+ 
  gi|313125824|ref|YP_004036094.1|  26 PVVVMAGGLAGdrSFGL-PN--YAERLAEAGYAVFLFDYRNHGDSGGDPRNLVsPSRQRADWEAAIEgvRTRDGLDT 99 
                                       56777777777665554.22..35688888***************99999877955556679999997777****** PP

                                       SSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                     Abhydrolase_1  73 dkltlvGhSmGGmialayaaeyperVkalvllga 106
                                        +l+l+G ++GG  +l +aa+ p rV+a+v+  +
  gi|313125824|ref|YP_004036094.1| 100 SNLVLWGTDLGGGHVLDVAADDP-RVRAVVSQTP 132
                                       ********************955.6******999 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 6.4e-07
                                       HHHHCCHHHHHHHHHC......THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 191 qwpttdsaklllrlre......lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                       qw+++  a +ll+l +      l+ v++p+l+++gt D +vp+++  d a+ +++   +v  + gH++ +eg
  gi|313125824|ref|YP_004036094.1| 200 QWTNETPARSLLNLARfsagsdLDSVTCPVLLFGGTRDDVVPIESVADAADEISD-ATFVSLPVGHFDTYEG 270
                                       78888888888898889999999********************************.999999****987765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   2.9e-17   5.9e-14      17     222 ..      39     255 ..      23     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 2.9e-17
                       Hydrolase_4  17 sgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpel..plfllGhSmGGlial 91 
                                       s    + ae+La++G+av+ +D+r hG s+g    + s ++  +D +a++e v+++ +    +l+l+G  +GG  +l
  gi|313125824|ref|YP_004036094.1|  39 SFGLPNYAERLAEAGYAVFLFDYRNHGDSGGDPRNLVSPSRQRADWEAAIEGVRTRDGLDtsNLVLWGTDLGGGHVL 115
                                       55566789**********************************************88876668*************** PP

                       Hydrolase_4  92 lyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqv...........snnlkadslsr...dpev 154
                                        ++++ p+ v++++   P  + +a l ++ +  l+ ++++ +  +lq             n+ +++ +s     +  
  gi|313125824|ref|YP_004036094.1| 116 DVAADDPR-VRAVVSQTPIRSGRAFLTTRGYGFLAKTVFSGIRDRLQSfavgpytvpiaGNPEEFALVSTpgaRRGY 191
                                       ********.999999999988887665777777777788888888887888*******9666666666651115556 PP

                       Hydrolase_4 155 vaayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdk 222
                                       ++ + +d  +++++ +r ll+l +    + ++ +++t P+ll+ G++D vv+ e  ++++++++  d 
  gi|313125824|ref|YP_004036094.1| 192 LDTVPSDAQWTNETPARSLLNLARFS--AGSDLDSVTCPVLLFGGTRDDVVPIESVADAADEIS--DA 255
                                       77888999999999999999999886..678999**********************99999998..44 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   8.0   3.4e-14   6.8e-11       1     208 [.      27     265 ..      27     286 .. 0.55

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3.4e-14
                                       EEEE--GC.....G.CHHHHHHHHCCT.CEEEEE--TTSTS-GGCS--HHHC....HHHHHHHCCTT......TTSE CS
                     Abhydrolase_6   1 vlllHGagssassW.lvapLaallaag.vhvlapDlpGhGrsdpppldledl....adlaalldelaa....gggpv 67 
                                       v+++ G+ ++ +s+ l ++ a++la+  ++v+ +D+++hG+s ++p +l       ad++a+++++++    ++ + 
  gi|313125824|ref|YP_004036094.1|  27 VVVMAGGLAGDRSFgL-PNYAERLAEAgYAVFLFDYRNHGDSGGDPRNLVSPsrqrADWEAAIEGVRTrdglDTSNL 102
                                       6777776666788842.3445555555588899*******9999998885534444666778888877877778888 PP

                                       EEEEETCHHHHHHHHHHCC..EEEEES-...........----TTTS----TTHHHHHHTT-C..CCCHCCH..... CS
                     Abhydrolase_6  68 vlvGHSlGGalalaaaplalvvgvlldppp.........talpagllaaalelllallallrl..lawlsre..... 128
                                       vl+G +lGG  +l +a+  ++v+ +++ +p         t +   l+  +++ ++ +l++++   ++ +        
  gi|313125824|ref|YP_004036094.1| 103 VLWGTDLGGGHVLDVAADDPRVRAVVSQTPirsgrafltTRGYGFLAKTVFSGIRDRLQSFAVgpYTVP--Iagnpe 177
                                       **********99996666655664444434344444333222222233333333333332222111111..011222 PP

                                       ........S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHC.HTTCCHHTT-TTGCEEE.CTT-CHHH.HCHHCCCH.S CS
                     Abhydrolase_6 129 ........plprlfladedadaawrarlarlaallaglg.llpaaawadlpvpllvl.ggeDplvp.rllerlla.q 193
                                                ++r++l+ ++ da w+    + +  l  l  + + +++  +++p+l++ g++D++vp + +++++  +
  gi|313125824|ref|YP_004036094.1| 178 efalvstpGARRGYLDTVPSDAQWTNETPARS--LLNLArFSAGSDLDSVTCPVLLFgGTRDDVVPiESVADAADeI 252
                                       23333333455588885553344444433333..22223244588*********8886699**77742233333354 PP

                                       TTEEETCE...SSS- CS
                     Abhydrolase_6 194 agarlpvvlpgaGHl 208
                                        +a++ v lp  GH+
  gi|313125824|ref|YP_004036094.1| 253 SDATF-VSLP-VGHF 265
                                       44444.4444.4443 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     3e-08     6e-05       3     127 ..      14     129 ..      12     138 .. 0.84
   2 !    5.4   0.0    0.0057        11     141     173 ..     223     255 ..     217     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3e-08
                               DLH   3 aylatpkna.kkpvvvviqeifGvn.dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeek 77 
                                       + l++p+++ + pvvv++  + G +     + +erlae+GY++++ d Y+ ++   ++  + ++++    s+    +
  gi|313125824|ref|YP_004036094.1|  14 GWLYRPDRPaEPPVVVMAGGLAGDRsFGLPNYAERLAEAGYAVFLFD-YRNHG---DSGGDPRNLV----SPS---R 79 
                                       6788999998889999999999*9963456779************99.77777...3333444444....444...5 PP

                               DLH  78 vlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaava 127
                                         +d +aa++ ++++   +t+++++ G  +GG  +l++aa +p+v a+v+
  gi|313125824|ref|YP_004036094.1|  80 QRADWEAAIEGVRTRDGLDTSNLVLWGTDLGGGHVLDVAADDPRVRAVVS 129
                                       557999******************************************97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0057
                               DLH 141 akikapilalfgeeDefipadevekleealkaa 173
                                       + + +p+l + g++D ++p ++v + + ++++a
  gi|313125824|ref|YP_004036094.1| 223 DSVTCPVLLFGGTRDDVVPIESVADAADEISDA 255
                                       6899******************99988888665 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   8.9e-06     0.018      10     107 ..      49     142 ..      41     168 .. 0.85
   2 !   10.8   0.0   0.00012      0.24     114     170 ..     201     253 ..     186     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.9e-06
                                       HHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-G CS
                      Peptidase_S9  10 ladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrp 86 
                                       la++Gy+v+  ++r  g+ G + ++ ++    +++ +D  aa+e + +++  d+++l+++G+  GG  ++ ++++ p
  gi|313125824|ref|YP_004036094.1|  49 LAEAGYAVFLFDYRNHGDSGGDPRNLVSP---SRQRADWEAAIEGVRTRDGLDTSNLVLWGTDLGGGHVLDVAADDP 122
                                       789************99999999996655...56667888999999999*************************666 PP

                                       GG-SEEEEESE---CCCHHCS CS
                      Peptidase_S9  87 dlFkaavaevpvvdvlrydsd 107
                                       +  +a+v++ p+   +++ ++
  gi|313125824|ref|YP_004036094.1| 123 R-VRAVVSQTPIRSGRAFLTT 142
                                       5.599****999887777666 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                                       HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH CS
                      Peptidase_S9 114 eymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLq 170
                                       ++ e  +p ++  +  ++s+ s+ld   +++p+Ll+ G+ Dd vp+++ +  +++  
  gi|313125824|ref|YP_004036094.1| 201 WTNE--TPARSLLNLARFSAGSDLDS--VTCPVLLFGGTRDDVVPIESVADAADEIS 253
                                       3334..44457777889999999999..99*****************9999888765 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     6e-09   1.2e-05      10     248 ..      17     247 ..      13     265 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6e-09
                                       EEE..TTSSSEEEEEEEESS-CCT.CCCCHTTCHHCCHGGGHHHHHTT-EEEEEE-TTSTTS-S---TT..TTTHHH CS
                     Peptidase_S15  10 yrPetkskeklPvlltrtPYgkndelasdkalaleelelqdkvfvarGYavVvqdvrGtggSeGeftvg..dsdeae 84 
                                       yrP  ++ ++ Pv++++     ++  +    +        ++ +++ GYav + d r +g+S G+       s++ +
  gi|313125824|ref|YP_004036094.1|  17 YRP--DRPAEPPVVVMAGGLAGDR-SFGLPNY--------AERLAEAGYAVFLFDYRNHGDSGGDPRNLvsPSRQRA 82 
                                       666..6666666666666655332.2222222........22399********************998877889999 PP

                                       HHHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCCC.CSECTTEEBCCHHHHHHH CS
                     Peptidase_S15  85 dgadvidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlydd.yyregGlvrapgglswed 159
                                       d  ++i+ ++      + +   +G+  +G   l +aa ++p+++a+v++ +i +       r +G++++   +s+  
  gi|313125824|ref|YP_004036094.1|  83 DWEAAIEGVRTRdGLDTSNLVLWGTDLGGGHVLDVAA-DDPRVRAVVSQTPIRSGRAFlTTRGYGFLAKTV-FSGI- 156
                                       ***********9999**********************.99***************9975555555555555.4552. PP

                                       HHCCCCHHTSSS-STTHHHHHHHHHHCHCCCCCCTTHHHTHHHHCCCC--SSSHHHHTT.-HHHHHCT--S-EEEEE CS
                     Peptidase_S15 160 ldllaealtsrradegdalkaaaryeaasdellaeldrqtpveselletgdydafWkdr.nlsedadkvkapvllvg 235
                                        d l+     +   + ++  ++ +  +     ++ ld  +   ++  et++++    +r ++ +d+d v++pvll+g
  gi|313125824|ref|YP_004036094.1| 157 RDRLQSFAVGPYTVPIAGNPEEFALVSTPGARRGYLDTVPSDAQWTNETPARSLLNLARfSAGSDLDSVTCPVLLFG 233
                                       444444444444443434444444456666666666665434455555555544433331344688*********** PP

                                       ECCSSTTC.CHHHH CS
                     Peptidase_S15 236 GwnDwnvk.ngaik 248
                                       G  D+ v  +++ +
  gi|313125824|ref|YP_004036094.1| 234 GTRDDVVPiESVAD 247
                                       ****8887666655 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0   0.00098       1.9      65     129 ..       8      73 ..       3      84 .. 0.79
   2 !   10.7   0.0   7.4e-05      0.15     158     207 ..      84     133 ..      79     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00098
                                       GGEEEEEEEEEES.SSSSEEEEEEEE-TT--..GGGHHHHHHHHHTT-EEEEEE-TTTS..SSB-SS CS
                              AXE1  65 rgarikaklvlPkekeeklPavvefhGYegs..rgeihdllnyaaaGyavvvmdvRGqggesedkvg 129
                                       +++r  ++l +P+ +  + P+vv   G  g+   g ++     a aGyav+  d R  g +  d+++
  gi|313125824|ref|YP_004036094.1|   8 GDERCSGWLYRPD-RPAEPPVVVMAGGLAGDrsFGLPNYAERLAEAGYAVFLFDYRNHGDSGGDPRN 73 
                                       67899********.667779999999998873236677778899************99877666554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEES-S CS
                              AXE1 158 avrlveivaslpevDeeRvavlGasqGGalalavaalekrikavvadyPf 207
                                          ++e v+  +  D + ++  G+  GG+  l vaa ++r++avv++ P 
  gi|313125824|ref|YP_004036094.1|  84 WEAAIEGVRTRDGLDTSNLVLWGTDLGGGHVLDVAADDPRVRAVVSQTPI 133
                                       567899999999***********************************996 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.94   1.9e+03      13      27 ..      10      24 ..       3      32 .. 0.66
   2 !   15.1   0.0   9.4e-06     0.019      32      67 ..     224     259 ..     199     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.94
                     Abhydrolase_4 13 lsCagwpvspqrprd 27
                                        C+gw ++p+rp +
  gi|313125824|ref|YP_004036094.1| 10 ERCSGWLYRPDRPAE 24
                                      45****665555543 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.4e-06
                     Abhydrolase_4  32 kgaapvLllqnerDpaTPyegakklakalggavlvt 67 
                                        ++ pvLl++++rD ++P e+ + +a+++ +a+ v+
  gi|313125824|ref|YP_004036094.1| 224 SVTCPVLLFGGTRDDVVPIESVADAADEISDATFVS 259
                                       3478**************************998886 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.17   3.4e+02      17      32 ..      44      59 ..      27      66 .. 0.82
   2 ?    0.5   0.0      0.23   4.5e+02      55      85 ..      98     128 ..      69     132 .. 0.88
   3 !   10.3   0.0   0.00022      0.43      82     133 ..     208     258 ..     195     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.17
                     Abhydrolase_5 17 elaeklaksGyevvlv 32
                                      ++ae+la++Gy v+l 
  gi|313125824|ref|YP_004036094.1| 44 NYAERLAEAGYAVFLF 59
                                      5799*********986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.23
                     Abhydrolase_5  55 klekfvvgGhslGGvvasrfaaeeekiegvv 85 
                                       +  ++v+ G  lGG  +  +aa++ ++ +vv
  gi|313125824|ref|YP_004036094.1|  98 DTSNLVLWGTDLGGGHVLDVAADDPRVRAVV 128
                                       45789999********99***9999998876 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00022
                     Abhydrolase_5  82 egvvflasYPekdelselskkvlsivgteDgvlnvkslekakkflpkdtkvv 133
                                        +++ la + +  +l + + +vl   gt+D+v++++s+  a++ +++ t +v
  gi|313125824|ref|YP_004036094.1| 208 RSLLNLARFSAGSDLDSVTCPVLLFGGTRDDVVPIESVADAADEISDAT-FV 258
                                       56788999999999*****************************998655.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2047.87
//
Query:       gi|313125825|ref|YP_004036095.1|  [L=447]
Description: hypothetical protein Hbor_10580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-37  127.5   0.1    4.6e-37  126.4   0.1    1.6  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
    0.00033   20.4   0.2      0.027   14.2   0.0    2.4  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
     0.0011   18.2   0.2       0.13   11.5   0.0    2.8  3  DS              Deoxyhypusine synthase
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.29   11.1   0.0    1.5  1  DUF4911         Domain of unknown function (DUF4911)


Domain annotation for each model (and alignments):
>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.1     1e-40   4.6e-37       2     100 .]       5     103 ..       4     103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 1e-40
                                       EEEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCE CS
                    Saccharop_dh_N   2 reveleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeed 78 
                                       r+veleGh+iDsg+l++++ l++++gg+fev+ef+vG++k+dtSy+++ v+ae+e+ L+eil+el+++ga+l+++ d
  gi|313125825|ref|YP_004036095.1|   5 RTVELEGHIIDSGTLQQAFGLVMDLGGDFEVEEFNVGRSKTDTSYCRMDVTAETEDDLQEILHELHQIGANLTDAVD 81 
                                       79*************************************************************************** PP

                                       EEECESSCTTB--TTB----SS CS
                    Saccharop_dh_N  79 vklekaekdgvlpedFYsttnh 100
                                       +++e+a++d+v+p++FYsttnh
  gi|313125825|ref|YP_004036095.1|  82 AHVERAPADQVVPHGFYSTTNH 103
                                       *********************8 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.0    0.0093        41       1      38 [.     189     230 ..     189     261 .. 0.75
   2 !   14.2   0.0     6e-06     0.027      68     135 ..     332     400 ..     313     402 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0093
                                       HHHHHHHHHH-S....SEEEEE-CHHCHTTGHHHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaak....rpvilvGggvarsgaseelrelaekl 38 
                                       ie++ae++++ k    ++++++G   + +ga ++l++l+++ 
  gi|313125825|ref|YP_004036095.1| 189 IEEVAEAVEETKsqggKVLVVAGPALIHAGAGDDLARLVREG 230
                                       567777777777667799********************9875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6e-06
                                       CHHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC....--SEEEECTHHHHHH CS
                      TPP_enzyme_M  68 skaanealeeaDlvlalGarfddirttgsepefapeakiihididpaeigkny....qvdlaivgdvketle 135
                                       + a +e +++aD vl+l + ++ + +++     ++ +k++ +di+pa++ +        ++++v d+++++ 
  gi|313125825|ref|YP_004036095.1| 332 QGAIREQAHKADMVLMLSTLLHSVAVGNC---LPSTTKVVCVDINPATVTQLLdrgsSQAIGMVTDIGTFVP 400
                                       56778999*************99777652...333459*********9988774333467888888888775 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   2.8e-05      0.13      21      82 ..     194     253 ..     183     264 .. 0.75
   2 ?    3.1   0.0      0.01        46     131     163 ..     270     309 ..     257     326 .. 0.70
   3 ?   -1.2   0.0      0.22   9.9e+02     156     177 ..     390     411 ..     370     416 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                                DS  21 dilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkkt 82 
                                       + +++  k++  ++++    +li +G  + +a+lv+e++vd+i +  g  ++D+ + l   t
  gi|313125825|ref|YP_004036095.1| 194 EAVEET-KSQGGKVLVVAGPALIHAGAGDDLARLVREGYVDMISAGNGFATHDIERGLYG-T 253
                                       333343.44555666666669*********************99999999***9888766.4 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.01
                                DS 131 k..vwspselikelG..kein...deeSilywAykndipv 163
                                       k  + ++se+i++ G  ++++    +++i+y + +nd+p 
  gi|313125825|ref|YP_004036095.1| 270 KhhIYTISEVIRAGGiaEAVEeglIQSGIMYECVQNDVPY 309
                                       232459999999877546666555569***********94 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.22
                                DS 156 AykndipvfcpaltDgslGdql 177
                                        +  di  f+p+l D +lG + 
  gi|313125825|ref|YP_004036095.1| 390 GMVTDIGTFVPTLADKVLGENT 411
                                       55679999**********9865 PP

>> DUF4911  Domain of unknown function (DUF4911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.4e-05      0.29      31      54 ..      47      70 ..      43      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.4e-05
                           DUF4911 31 kGlvrirttpdtkeellelLesLk 54
                                      +  +r+ +t++t+++l+e+L++L 
  gi|313125825|ref|YP_004036095.1| 47 TSYCRMDVTAETEDDLQEILHELH 70
                                      5679*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3066.41
//
Query:       gi|313125826|ref|YP_004036096.1|  [L=134]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-12   48.5   0.1    1.4e-12   48.3   0.1    1.2  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.1   7.8e-17   1.4e-12      62     141 .]      52     129 ..       3     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 7.8e-17
                                       HHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEE CS
                               Usp  62 eeaeleadaakaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVl 138
                                       e a ++   + ++   ++v+++  v++ d++e il ++ee dad +V+G r+r+  +++++GS+++++l ++++p+ 
  gi|313125826|ref|YP_004036096.1|  52 EDALNVV--DSRLGGFADVETHQFVRGNDADEDILSYVEEVDADELVIGVRKRNPTAKVVFGSTAQRILLNSNVPMA 126
                                       2222222..24556778999999****************************************************** PP

                                       EEE CS
                               Usp 139 vVr 141
                                       vV+
  gi|313125826|ref|YP_004036096.1| 127 VVP 129
                                       *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 924.72
//
Query:       gi|313125827|ref|YP_004036097.1|  [L=338]
Description: hypothetical protein Hbor_10600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-09   35.5   3.4    6.3e-09   35.5   3.4    2.2  3  PGF-CTERM     PGF-CTERM motif
    4.8e-06   26.8   5.9    1.9e-05   24.8   0.8    2.4  2  CARDB         CARDB
     0.0045   17.7   0.5        1.1   10.1   0.2    2.4  2  GPI-anchored  Ser-Thr-rich glycosyl-phosphatidyl-inositol-anc
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.041   13.7   0.0    1.3  1  DUF4832       Domain of unknown function (DUF4832)
        3.5    8.3   5.7         29    5.3   0.5    3.3  4  YtkA          YtkA-like


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   1.1         5   1.8e+04      12      17 ..       6      11 ..       5      12 .. 0.73
   2 ?   -3.1   0.1       2.4   8.8e+03      14      21 ..     202     209 ..     202     210 .. 0.83
   3 !   35.5   3.4   1.8e-12   6.3e-09       1      23 []     314     336 ..     314     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 5
                         PGF-CTERM 12 GLLaaa 17
                                      +L++aa
  gi|313125827|ref|YP_004036097.1|  6 ALAGAA 11
                                      788887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                         PGF-CTERM  14 LaaalLaR 21 
                                       La+ + +R
  gi|313125827|ref|YP_004036097.1| 202 LAVTFVLR 209
                                       89999988 PP

  == domain 3  score: 35.5 bits;  conditional E-value: 1.8e-12
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       +PGFG+++A+++LLaaalL+RR+
  gi|313125827|ref|YP_004036097.1| 314 QPGFGVAVAVVALLAAALLVRRQ 336
                                       7*********************5 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.014        49      49      84 ..      92     131 ..      43     139 .. 0.66
   2 !   24.8   0.8   5.4e-09   1.9e-05      10      94 ..     174     263 ..     168     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                                       E.....EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEE CS
                             CARDB  49 v.....gtvtvpsLaagesttvsftwtteategevtltvvv 84 
                                             +tv+v  L  +++t v +++t+e  +g ++++ v 
  gi|313125827|ref|YP_004036097.1|  92 GlvkttQTVEVGTLRDDGETAVPTNVTVE-RAGGYHIETVL 131
                                       34455588899*****************9.99999998776 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 5.4e-09
                                       EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE......EEEEESEE-CTEEEEEEEEEE-S-S-CEEEE CS
                             CARDB  10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelv......gtvtvpsLaagesttvsftwtteategevtl 80 
                                       +  ++a++++++ + ++++N+G+a sg+  v+++l +         +t++v ++ +g ++t ++t t++ +  +++l
  gi|313125827|ref|YP_004036097.1| 174 SVSDTASNRTTLDLAASLTNTGDAPSGDLAVTFVLRQADSnvvaarTTSSVGEIRPGRTATTTATATVP-SGYNYYL 249
                                       5667889999***********************97554433469999**********************.99***** PP

                                       EEEESTT-SS--SS CS
                             CARDB  81 tvvvDpdnevaEsn 94 
                                        +v   d+ v ++ 
  gi|313125827|ref|YP_004036097.1| 250 DAVLTRDGVVVDTA 263
                                       ***99999998875 PP

>> GPI-anchored  Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0083        30       6      82 ..      59     135 ..      55     139 .. 0.78
   2 !   10.1   0.2    0.0003       1.1      26      81 ..     201     256 ..     174     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0083
                      GPI-anchored   6 gevvtagkpvtitWkdsgtdpgtvtlvLcagssnn..lksvktiasgiknsdgsytwtvpaslesggaYflqivses 80 
                                       ge+vt g ++ ++ ++  +   +vtl+++a   ++  +k+ +t+  g   +dg++ +  + ++e +g+Y ++ v ++
  gi|313125827|ref|YP_004036097.1|  59 GETVTLGVETRVRHSG--NPTPNVTLLVRAVDAESglVKTTQTVEVGTLRDDGETAVPTNVTVERAGGYHIETVLFQ 133
                                       7888999999999988..5567899988887774433778888866666677*******************998777 PP

                      GPI-anchored  81 ne 82 
                                       ++
  gi|313125827|ref|YP_004036097.1| 134 DN 135
                                       65 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0003
                      GPI-anchored  26 pgtvtlvLcagssnnlksvkti.asgiknsdgsytwtvpaslesggaYflqivsesn 81 
                                       + +vt+vL++  sn +   +t  + +i  +  ++t t  a+++sg +Y+l +v + +
  gi|313125827|ref|YP_004036097.1| 201 DLAVTFVLRQADSNVVAARTTSsVGEIRPG-RTATTTATATVPSGYNYYLDAVLTRD 256
                                       3789*********77666655548888888.999999*9***********9996665 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.041     112     185 ..     173     244 ..     171     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                           DUF4832 112 sslskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklkldadprkwlpgttttitiklklpse 185
                                       +s+s++++++ tl l  +l+N+G A+   +  v +vlr+ ++++ +   ++ ++ ++ pg+t t t+++++ps+
  gi|313125827|ref|YP_004036097.1| 173 VSVSDTASNRTTLDLAASLTNTGDAPS-GDLAVTFVLRQADSNV-VAARTTSSVGEIRPGRTATTTATATVPSG 244
                                       6788888999*************9975.6788999999999999.67889**************9999999965 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1     4e+03      18      43 ..      39      65 ..      33      82 .. 0.60
   2 ?    2.9   0.2     0.047   1.7e+02      24      75 ..      82     131 ..      54     136 .. 0.65
   3 ?    0.2   0.0      0.33   1.2e+03      14      63 ..     194     241 ..     181     258 .. 0.64
   4 ?    5.3   0.5    0.0081        29      23      67 ..     272     316 ..     250     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                              YtkA 18 kagentivvt.vtqggkpVedadvkve 43
                                      + g ++i+ t  ++++++V +++v++ 
  gi|313125827|ref|YP_004036097.1| 39 SPGPTDISETsISYDESAVRGETVTLG 65
                                      556666655556666666666666543 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.047
                              YtkA  24 ivvt.vtqggkpVedad.vkvefwmpameGmeemttkvelkesedGvYeaevnf 75 
                                       + v+ v+++   V+    v+v   +++  G     t+v+++    G Y +e+ +
  gi|313125827|ref|YP_004036097.1|  82 LLVRaVDAESGLVKTTQtVEVGTLRDD--GETAVPTNVTVER--AGGYHIETVL 131
                                       444456666666666644888888884..6666555555555..9999988654 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.33
                              YtkA  14 peepkagentivvtvtqggkpVedadvkvefwmpameGmeemttkvelke 63 
                                       +  +  g+ +++++ +q ++ V +a  + ++ +   +G   + t ++++ 
  gi|313125827|ref|YP_004036097.1| 194 TGDAPSGDLAVTFVLRQADSNVVAARTTSSVGEIR-PGRTAT-TTATATV 241
                                       44456677778888999999999998888888875.667754.4444433 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0081
                              YtkA  23 tivvtvtqggkpVedadvkvefwmpameGmeemttkvelke.sedG 67 
                                       t  + v++++++Ve  + ++e ++++++G++ ++ + e +  s++G
  gi|313125827|ref|YP_004036097.1| 272 TRRISVNETEQAVEFRVEDFEMDDTENAGGQQTEAP-EGTAtSQPG 316
                                       55677999******************9999964444.444336877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2294.21
//
Query:       gi|313125828|ref|YP_004036098.1|  [L=119]
Description: hypothetical protein Hbor_10610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   11.9   1.1       0.12   11.6   1.1    1.1  1  NKAIN     Na,K-Atpase Interacting protein


Domain annotation for each model (and alignments):
>> NKAIN  Na,K-Atpase Interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1   6.7e-06      0.12       9      57 ..      57     106 ..      49     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.7e-06
                             NKAIN   9 tllalcllqlvavlerqvfdflGyqw.apilvnffhiivvilGlfGtiqy 57 
                                       +l +++++ql   + r v  f+ y + ap+l+ f  ++++i  l  ++q 
  gi|313125828|ref|YP_004036098.1|  57 LLAVIAAVQLYLSVSRTVTTFVVYEYrAPVLAAFNLVVFLIAALGISVQV 106
                                       6778999*****************9769******9999999776555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 743.54
//
Query:       gi|313125829|ref|YP_004036099.1|  [L=409]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-15   56.6   0.2    8.7e-15   54.7   0.0    2.1  2  PAS              PAS fold
    6.2e-13   49.2   0.0    1.7e-12   47.8   0.0    1.7  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    2.4e-08   34.2   0.2    7.3e-08   32.6   0.2    1.8  1  PAS_4            PAS fold
    3.5e-08   33.7   0.0    7.1e-07   29.4   0.0    2.5  2  PAS_9            PAS domain
    3.2e-07   30.2   0.0    1.3e-06   28.3   0.0    2.1  1  PAS_8            PAS domain
      7e-05   23.0   0.1     0.0011   19.1   0.0    2.9  2  PAS_7            PAS fold
    7.5e-05   22.7   0.0    0.00016   21.7   0.0    1.5  1  HATPase_c_2      Histidine kinase-like ATPase domain
     0.0015   18.4   0.0     0.0033   17.2   0.0    1.6  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
     0.0064   16.1   0.1      0.013   15.0   0.1    1.5  1  HisKA_4TM        Archaeal 4TM region of histidine kinase
  ------ inclusion threshold ------
      0.023   14.7   1.4        0.1   12.6   0.4    2.6  2  HisKA            His Kinase A (phospho-acceptor) domain
      0.069   13.4   0.0       0.15   12.4   0.0    1.5  1  PAS_3            PAS fold
       0.17   11.8   3.0        5.7    6.9   0.0    3.4  4  Erythro-docking  Erythronolide synthase, docking
       0.22   11.4   0.4         11    6.0   0.0    2.6  2  Myosin_N         Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   6.3e-18   8.7e-15       9     109 ..      85     183 ..      77     187 .. 0.90
   2 ?   -1.9   0.1       2.4   3.3e+03      45      65 ..     221     239 ..     220     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 6.3e-18
                                       HSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSS CS
                               PAS   9 slpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgr 85 
                                         p++i+vvD+ g + ++N+ ae+ +G+s++e+l +s+l+ +++++d  lae ++ +le+ge+  ++e++   +dg+
  gi|313125829|ref|YP_004036099.1|  85 VVPVAIVVVDAAGQVQLWNEGAERTFGWSESEILTQSYLETLSPPTD--LAETVRGRLEAGERLDGVETRHQHQDGS 159
                                       5799*****************************************99..**************************** PP

                                       EEEEEEEEEEEEETTEEEEEEEEE CS
                               PAS  86 pihlevraspvrdaggeilgflgv 109
                                       +  ++++a+p+ ++++   g+ +v
  gi|313125829|ref|YP_004036099.1| 160 ILDVRLWAAPLSHRESGFGGAAFV 183
                                       **************9955555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.4
                                       BGGGGBSTTHHHHHHHHHHHH CS
                               PAS  45 slldliheeddaelaelleql 65 
                                       +l+d+++e+d+  +a+ ++++
  gi|313125829|ref|YP_004036099.1| 221 MLIDSLPENDE--HADVIQRR 239
                                       7999***9996..55555544 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.2e-15   1.7e-12       9     109 ..     308     405 ..     303     408 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.2e-15
                                       HHHHHHHHHHHHHSTTT..EEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHH CS
                         HATPase_c   9 iisnlvdNavkfatkag..eieveika.seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivk 82 
                                       +++n+++Na+k+ +++g  +++v +++ ++d+ +i++eD+G+G+p+ +++ l ++  +       +   G+Gl ++ 
  gi|313125829|ref|YP_004036099.1| 308 ALDNILENALKH-NDSGvpHVTVDVQTeDDDRRTIRIEDDGPGLPETEREVLTTRTET-----PLTHSAGMGLWLAS 378
                                       799*********.655522555555544449*******************77777777.....566899******** PP

                                       HHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  83 klvelmgGeiwvesepgrGttftftlp 109
                                        + ++ gG+++ve+ + +Gt++t++l 
  gi|313125829|ref|YP_004036099.1| 379 WILRHSGGDLTVEDGQSGGTRVTIQLN 405
                                       999999*****************9986 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.2   5.3e-11   7.3e-08       4     110 .]      86     192 ..      84     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.3e-11
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerh 80 
                                       +p+a++v+d+ g+v+ +N+ a++ fg++  e+l +++ e l++   ++l++ +r  le +e+++ +e+++  +++ +
  gi|313125829|ref|YP_004036099.1|  86 VPVAIVVVDAAGQVQLWNEGAERTFGWSESEILTQSYLETLSP--PTDLAETVRGRLEAGERLDGVETRHQHQDGSI 160
                                       799***********************************98887..89************************888888 PP

                             PAS_4  81 yelrl..lPlrdesGevigvlvisrDiTerrr 110
                                       +++rl   Pl +++ +  g+ +++ DiTe+++
  gi|313125829|ref|YP_004036099.1| 161 LDVRLwaAPLSHRESGFGGAAFVVSDITEQKQ 192
                                       8888888**********************985 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   5.2e-10   7.1e-07       1     104 []      87     189 ..      87     189 .. 0.95
   2 ?    1.1   0.0      0.33   4.6e+02      28      51 ..     232     253 ..     209     279 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.2e-10
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       p++i++++  g +  +Ne+a+r +G s+ e+l +s+ ++++++ + +e++r  le+g+     ve+ +++ +g+ + 
  gi|313125829|ref|YP_004036099.1|  87 PVAIVVVDAAGQVQLWNEGAERTFGWSESEILTQSYLETLSPPTDLAETVRGRLEAGE-RLDGVETRHQHQDGSILD 162
                                       68999999***************************999999*****************.99**************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       v+l a+p+   + ++ g+++++ Dite
  gi|313125829|ref|YP_004036099.1| 163 VRLWAAPLSHRESGFGGAAFVVSDITE 189
                                       ********888888999*********8 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.33
                             PAS_9  28 peevlgksitdlfvtdpeanerlr 51 
                                       +++v+++++t+++  + +++ r  
  gi|313125829|ref|YP_004036099.1| 232 HADVIQRRLTNII--ELSDAARYV 253
                                       5677777777777..444444333 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   9.2e-10   1.3e-06       2      61 ..      78     138 ..      77     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.2e-10
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplledaeq 61 
                                       r+ +++  +p++i+vvd +g+ +  +N+ a++ +G+s  +++++   + l   ++l e+ + 
  gi|313125829|ref|YP_004036099.1|  78 RFSTVIGVVPVAIVVVDaAGQ-VQLWNEGAERTFGWSeSEILTQSYLETLSPPTDLAETVRG 138
                                       999**************6666.*************998888887777777777776665544 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   8.1e-07    0.0011       6     115 .]      88     195 ..      83     195 .. 0.80
   2 ?   -2.6   0.0       4.3   5.9e+03      58      71 ..     231     244 ..     198     261 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.1e-07
                             PAS_7   6 qGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsferer 82 
                                        +i+v+Da++++ +wN+   + ++++e+ + ++  le        + +  + d +++v+ rl+a ++ +   + +++
  gi|313125829|ref|YP_004036099.1|  88 VAIVVVDAAGQVQLWNEGAERTFGWSESEILTQSYLE--------TLS-PPTDLAETVRGRLEAGERLDGVETRHQH 155
                                       689***********************99884433333........333.45889999*****99999999999**** PP

                             PAS_7  83 pdgrvievrgnpl.......pdgGfVttytDiTerrraee 115
                                       +dg +++vr  +          gG   + +DiTe+++ e+
  gi|313125829|ref|YP_004036099.1| 156 QDGSILDVRLWAAplshresGFGGAAFVVSDITEQKQREQ 195
                                       ********9655522443323499************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.3
                             PAS_7  58 dveaeverrlaaar 71 
                                       + ++ ++rrl+++ 
  gi|313125829|ref|YP_004036099.1| 231 EHADVIQRRLTNII 244
                                       23333444443333 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.1e-07   0.00016      35     105 ..     308     377 ..     291     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.1e-07
                       HATPase_c_2  35 aveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlali 105
                                       a++ ++ Na +h+  + p+ +v v+ + d+++ t++++D+Gpg  ++e     t +e +    + G+Gl l 
  gi|313125829|ref|YP_004036099.1| 308 ALDNILENALKHNDSGVPHVTVDVQ-TEDDDRRTIRIEDDGPGlPETEREVLTTRTE-TPLTHSAGMGLWLA 377
                                       7777899******************.8888999**********77777766666665.6899999****985 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.4e-06    0.0033       5      54 ..     307     358 ..     302     406 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                       HATPase_c_3   5 kAlaelvdNsld...AdaenvkievnknrgktgeivieDdGkGmseeelknal 54 
                                       +Al  +++N+l    +   +v++ v++++ +  +i+ieDdG G++e e +++l
  gi|313125829|ref|YP_004036099.1| 307 YALDNILENALKhndSGVPHVTVDVQTEDDDRRTIRIEDDGPGLPETE-REVL 358
                                       57888999998644477888********999*************9987.3344 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   9.7e-06     0.013     123     159 ..     183     219 ..     176     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                         HisKA_4TM 123 aradasrakrisdalafvndlirhdlrndlvvirgya 159
                                        ++d +  k+  + la +n ++rh++rnd++v++g+ 
  gi|313125829|ref|YP_004036099.1| 183 VVSDITEQKQREQRLAVLNRVLRHNIRNDVNVVQGHL 219
                                       5778899999999********************9976 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.7   2.4e+03      27      48 ..      16      36 ..       8      62 .. 0.73
   2 ?   12.6   0.4   7.5e-05       0.1       7      51 ..     202     243 ..     197     280 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.7
                                      HHC..T-HSSCHHHHHHHHHHH CS
                             HisKA 27 Lkregklteelkeyletiesea 48
                                      L +e   +e +k++le+ +s a
  gi|313125829|ref|YP_004036099.1| 16 LADE-GHDEVQKRLLESYHSKA 36
                                      5454.45688888998888776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHH CS
                             HisKA   7 agvaHELrtPLsailgnaeaLkregklteelkeyletiesearrl 51 
                                         + H +r+ +++++g +++L ++    +e  e  ++i++    +
  gi|313125829|ref|YP_004036099.1| 202 RVLRHNIRNDVNVVQGHLDMLIDS---LPENDEHADVIQRRLTNI 243
                                       5689*****************994...455555555555544433 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.15       4      75 ..     102     170 ..      99     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy.egeyRirrkdGeyrwveararvi 75 
                                       ++e  e+++G+s++e+l +  s+l+ + p     + e++   l+ ge++  +e R +++dG++  v+  a ++
  gi|313125829|ref|YP_004036099.1| 102 WNEGAERTFGWSESEILTQ--SYLETLSPPT--DLAETVRGRLEAGERLdGVETRHQHQDGSILDVRLWAAPL 170
                                       9******************..8888888765..56666777788999996788*********99888777776 PP

>> Erythro-docking  Erythronolide synthase, docking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.055        76      23      35 ..      16      28 ..       6      37 .. 0.80
   2 ?   -1.9   0.1       2.4   3.3e+03       7      16 ..     141     150 ..     137     154 .. 0.78
   3 ?    6.9   0.0    0.0041       5.7      15      34 ..     219     238 ..     211     245 .. 0.85
   4 ?   -2.8   0.0       4.4   6.1e+03      30      47 ..     268     285 ..     267     293 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.055
                                      TTSS-THHHHHHH CS
                   Erythro-docking 23 sdedGhdDvGaRL 35
                                       +++Ghd+v +RL
  gi|313125829|ref|YP_004036099.1| 16 LADEGHDEVQKRL 28
                                      5789********7 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.4
                                       TTHHHHHHHH CS
                   Erythro-docking   7 dvGdRLDeLe 16 
                                       + G+RLD +e
  gi|313125829|ref|YP_004036099.1| 141 EAGERLDGVE 150
                                       5689999887 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0041
                                       HHHHHHHHTTSS-THHHHHH CS
                   Erythro-docking  15 LekaLeaLsdedGhdDvGaR 34 
                                       L+  ++ L+++d h+Dv +R
  gi|313125829|ref|YP_004036099.1| 219 LDMLIDSLPENDEHADVIQR 238
                                       566689***********997 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 4.4
                                       HHHHHHHHHHHHHHHHHH CS
                   Erythro-docking  30 DvGaRLeaLLRRWnsRRa 47 
                                       D Ga L + L R +s  +
  gi|313125829|ref|YP_004036099.1| 268 DLGALLRTRLDRLDSEYP 285
                                       556666666666666555 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3     0.078   1.1e+02      26      38 ..     329     341 ..     328     343 .. 0.88
   2 ?    6.0   0.0    0.0078        11      13      31 ..     375     395 ..     373     403 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.078
                                       EEEEETTSEEEEE CS
                          Myosin_N  26 vtVetedGktvtV 38 
                                       v V+ted+ ++t+
  gi|313125829|ref|YP_004036099.1| 329 VDVQTEDDDRRTI 341
                                       89********997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0078
                                       -EEEEEEEEESSEEEEEE..T CS
                          Myosin_N  13 yvkGeIkeeeGdkvtVet..e 31 
                                       +++ +I   +G+++tVe    
  gi|313125829|ref|YP_004036099.1| 375 WLASWILRHSGGDLTVEDgqS 395
                                       9999************96644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2722.87
//
Query:       gi|313125830|ref|YP_004036100.1|  [L=301]
Description: hypothetical protein Hbor_10630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-07   29.3   7.3    4.7e-07   29.3   7.3    2.3  2  Zip           ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   1.3   0.00085        15       3      66 ..      55     116 ..      53     142 .. 0.76
   2 !   29.3   7.3   2.6e-11   4.7e-07     193     300 ..     153     253 ..     149     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.00085
                               Zip   3 lkilaiiaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealee 66 
                                       ++ l+ i  +++ +++l  pl v+++      ++l     +a+G ++  a + L+P+a++ + +
  gi|313125830|ref|YP_004036100.1|  55 AWKLLGITWVAFAAMALAAPLGVRHHD--EGANALVWGYGLASGAMVTSAAVFLVPQAINHHPK 116
                                       566667777778888888888888665..55888888999999999999999999999997765 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 2.6e-11
                               Zip 193 lilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfaltaplGiliGilvr 267
                                       l  H f+ GL +G    +  + g +l +A++ H+ p++ +   +L + g + ++ +l + +++++a+l+ +i +   
  gi|313125830|ref|YP_004036100.1| 153 LAAHAFSAGLIIGivYGNMPDLGPTLGLAIVSHKGPAGYAAARRLTSKGRTASSLLLPAAALGIAAILASIIVLP-- 227
                                       568**********9888999************************************9999999999999998766.. PP

                               Zip 268 sisessgaeivsgillalsaGtflYvalvellp 300
                                             g+    g++++++aG+fl+va+ ++lp
  gi|313125830|ref|YP_004036100.1| 228 ------GSGPFRGVVFGFAAGVFLHVAM-DFLP 253
                                       ......9*******************96.5665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1993.50
//
Query:       gi|313125831|ref|YP_004036101.1|  [L=234]
Description: hypothetical protein Hbor_10640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-37  126.5   0.1      1e-36  126.3   0.1    1.0  1  adh_short        short chain dehydrogenase
    1.6e-32  112.9   0.7      2e-32  112.6   0.7    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.1e-08   35.2   0.0    1.4e-08   34.9   0.0    1.1  1  KR               KR domain
    1.5e-05   24.6   0.4    0.00051   19.6   0.1    2.8  2  Epimerase        NAD dependent epimerase/dehydratase family
    0.00036   20.5   1.4    0.00046   20.1   1.4    1.4  1  NAD_binding_10   NAD(P)H-binding
    0.00076   18.7   0.0     0.0011   18.2   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0071   15.7   1.0     0.0076   15.6   0.1    1.5  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
  ------ inclusion threshold ------
       0.03   13.9   0.4      0.052   13.1   0.4    1.4  1  NmrA             NmrA-like family
      0.034   13.9   0.0      0.064   13.0   0.0    1.5  1  DEAD_assoc       DEAD/H associated
      0.048   13.0   0.0       0.26   10.6   0.0    2.0  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.051   12.7   0.0      0.089   11.9   0.0    1.4  1  RmlD_sub_bind    RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.1   6.1e-40     1e-36       1     190 [.       6     196 ..       6     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 6.1e-40
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHH.. CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkkl.. 75 
                                       k+v+vtGas+GIG a+++++a+eGa+vv+++r e++l  v++++ ++  +a a+++Dv+d+ +ve+l+e+a+     
  gi|313125831|ref|YP_004036101.1|   6 KTVVVTGASRGIGVALVRAFAAEGAHVVCCARDEDALSDVVANVADTPGSAEAVRADVRDEYDVERLMETAARSGdd 82 
                                       79*********************************************99**********************998888 PP

                                       SSESEEEE---S....S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHH CS
                         adh_short  76 gkldvLvnNAGi....tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaa 148
                                       +++ vLv NA++     g  p++e s ++++++i +N+ gvf ++r++lp+ + +   r+   s  +++ p +g+ a
  gi|313125831|ref|YP_004036101.1|  83 DGIAVLVPNAAVnhgtPGEMPVHEESYTRFDDTIRTNVRGVFTAVREALPH-V-NDDTRVLVPSGSIAHDPKPGMGA 157
                                       99**********998888899******************************.4.578888888989999******** PP

                                       HHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 149 YsAsKaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                       Y+ sKaav+gl+r++a ++ap    + +v PGlv+T+++  +
  gi|313125831|ref|YP_004036101.1| 158 YAVSKAAVEGLARQFAADVAPV---IGVVDPGLVATGLTDGQ 196
                                       *********************7...9999*******998765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.7   1.2e-35     2e-32       1     184 [.      12     198 ..      12     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.2e-35
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHH..SSEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekf..gklDil 73 
                                       Ga +gIG a+++a+a+eGa+vv++ ++e+a  + v+++a+  g++ ++++DV+de +ve+l+e+++++   +++ +l
  gi|313125831|ref|YP_004036101.1|  12 GASRGIGVALVRAFAAEGAHVVCCARDEDAlSDVVANVADTPGSAeAVRADVRDEYDVERLMETAARSGddDGIAVL 88 
                                       999***************************99999999999997669*******************999889***** PP

                                       EE-----EG..CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHH CS
                      adh_short_C2  74 vnnagiapk..lkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaal 148
                                       v na++ +    + p++e s   fd+++ +n++++f  +++alp++++  +++  s   a+   p+  ay+++Kaa+
  gi|313125831|ref|YP_004036101.1|  89 VPNAAVNHGtpGEMPVHEESYTRFDDTIRTNVRGVFTAVREALPHVNDDTRVLVPSGSIAHDPKPGMGAYAVSKAAV 165
                                       *******99999*************************************9999999999****************** PP

                                       HHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT CS
                      adh_short_C2 149 ealtrylAvelgpkgiRvNavspgpikTlaasgikg 184
                                       e+l+r++A++++p    + +v pg+++T +++g  +
  gi|313125831|ref|YP_004036101.1| 166 EGLARQFAADVAP---VIGVVDPGLVATGLTDGQGR 198
                                       *************...7888*********9998764 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   8.5e-12   1.4e-08       2     171 ..       7     180 ..       6     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 8.5e-12
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78 
                                       t+++tG+  g+G +l+r  a++ga h+v+++R+   +++ ++ +a+++++  + e+v+aDv d+ +ve+l+e++ ++
  gi|313125831|ref|YP_004036101.1|   7 TVVVTGASRGIGVALVRAFAAEGA-HVVCCARD---EDALSDVVANVADTPGSAEAVRADVRDEYDVERLMETAARS 79 
                                       689********************8.899*****...344555999999**99*********************9999 PP

                                       S..S---EEEE------....---TTT--HHHHHHHHTTTTHHH.HHHHHHTTTS--SEEEEEEEHHHHH-.-TT-H CS
                                KR  79 e..ppikGvihaAgvlr....dklleemtaedleqvlapKvkGa.wnLhelledesldffvlfSSiagllg.sagqa 147
                                       +  + i+  +  A v +    + ++ e +  +++  ++  v+G+   + e+l++ + d  vl+ S +     ++g +
  gi|313125831|ref|YP_004036101.1|  80 GddDGIAVLVPNAAVNHgtpgEMPVHEESYTRFDDTIRTNVRGVfTAVREALPHVNDDTRVLVPSGSIAHDpKPGMG 156
                                       88899***9999988873333668999****************84689******99999999988887665379*** PP

                                       HHHHHHHHHHHHHHHHHHHHHTEE CS
                                KR 148 nYaaaNaflDalaeyrrsqglpav 171
                                       +Ya   a +++la++ ++  +p++
  gi|313125831|ref|YP_004036101.1| 157 AYAVSKAAVEGLARQFAADVAPVI 180
                                       **************9988877765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.2e-07   0.00051       1      63 [.       8      76 ..       8     185 .. 0.58
   2 ?   -2.5   0.0       1.7   2.8e+03     215     231 ..     200     216 ..     198     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHH CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkee 63
                                      ++VtGa+  iG alv+a++++g +v++ +r+++a      + +      e v++d++d+ ++erl+++ 
  gi|313125831|ref|YP_004036101.1|  8 VVVTGASRGIGVALVRAFAAEGAHVVCCARDEDALSDVVANVAdtpgsaEAVRADVRDEYDVERLMETA 76
                                      68**********************999999955555444333388999999999999999999998753 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHTT CS
                         Epimerase 215 veDvaeaillvlehvda 231
                                       ++Dva ++++++++ d+
  gi|313125831|ref|YP_004036101.1| 200 ADDVAPMYVWAATEADR 216
                                       79********9999776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.4   2.8e-07   0.00046       1      60 [.      12      75 ..      12     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.8e-07
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH....CT.TTCEEEE--TT-CCHHHHHHTT CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaele....ae.eglevvegdvtdvedlaealkg 60
                                      GA+ ++G +lv+  +a+g  +v+  +R+++ l+++     ++   +e+v +dv d+ d+++ ++ 
  gi|313125831|ref|YP_004036101.1| 12 GASRGIGVALVRAFAAEG-AHVVCCARDEDALSDVVanvaDTpGSAEAVRADVRDEYDVERLMET 75
                                      9****************5.9***********9976533333336899**************9984 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   6.6e-07    0.0011       1     149 [.       8     169 ..       8     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.6e-07
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT... CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel. 76 
                                       v+vtGa+  iG +lvr ++++ + +++   rdE +l ++  ++ ++  +        +v +dvrd+  +e+++e+  
  gi|313125831|ref|YP_004036101.1|   8 VVVTGASRGIGVALVRAFAAEGA-HVVCCARDEDALSDVVANVADTPGS------AEAVRADVRDEYDVERLMETAa 77 
                                       79**************9988765.688899*********9998543333......235669********99999753 PP

                                       ......T-SEEEE------.....HHHHHHSHH...HHHHHHHHHHHHHHHHHHHT..T-SEEEEEEEGGGSS--SH CS
                   Polysacc_synt_2  77 ......kvdvvfhaAAlKh.....VPlveenpl...eaiktNvlgtenvieaaiea..gvkkvvliStDKAvnPtnv 137
                                             ++ v++  AA+ h     +P+ ee  +   ++i+tNv g  + ++ a+ +  + ++v++ S   A +P   
  gi|313125831|ref|YP_004036101.1|  78 rsgdddGIAVLVPNAAVNHgtpgeMPVHEESYTrfdDTIRTNVRGVFTAVREALPHvnDDTRVLVPSGSIAHDPKPG 154
                                       33333367889999999986666679999876522268999999999988888643114456666678888888777 PP

                                       HHH...HHHHHHHHH CS
                   Polysacc_synt_2 138 mGa...tKrlaekll 149
                                       mGa   +K++ e l+
  gi|313125831|ref|YP_004036101.1| 155 MGAyavSKAAVEGLA 169
                                       775333677666665 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.7e-06    0.0076      33      79 ..       2      48 ..       1      64 [. 0.89
   2 ?   -3.9   0.1       4.5   7.4e+03     128     142 ..     171     185 ..     168     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.7e-06
                                      --TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCC CS
                     THF_DHG_CYH_C 33 elegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitre 79
                                      +++gk+vvv G+s+ +g +l   +++++a V +c +  + l++++ +
  gi|313125831|ref|YP_004036101.1|  2 DVSGKTVVVTGASRGIGVALVRAFAAEGAHVVCCARDEDALSDVVAN 48
                                      799********************************999999888764 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.5
                                       TTSSEE--TTTSCHH CS
                     THF_DHG_CYH_C 128 evasaitPvpgGVGp 142
                                       + a+ ++Pv g V p
  gi|313125831|ref|YP_004036101.1| 171 QFAADVAPVIGVVDP 185
                                       667778899988876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   3.2e-05     0.052       1      65 [.       8      76 ..       8      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHST..TEEEES-TT-HHHHHHHHTT- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt..kselakslkeaG..velvkgdlddkeslvealkgv 65
                                      ++v+Ga+  +G ++vra++++g +v    Rd+   s++++++++ +  +e v +d+ d+  ++++++++
  gi|313125831|ref|YP_004036101.1|  8 VVVTGASRGIGVALVRAFAAEGAHVVCCARDEdaLSDVVANVADTPgsAEAVRADVRDEYDVERLMETA 76
                                      68*****************************98889999999998756789999999988888777665 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.9e-05     0.064     133     173 ..      40      80 ..      36     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                        DEAD_assoc 133 aqLldvareypdfpllleavrevledqlDlerlaellrria 173
                                       + L dv++++ d+p   eavr  ++d++D+erl e  +r  
  gi|313125831|ref|YP_004036101.1|  40 DALSDVVANVADTPGSAEAVRADVRDEYDVERLMETAARSG 80 
                                       6799******************************9988765 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.26       2      73 ..      10      75 ..       9      79 .. 0.85
   2 ?   -0.4   0.0      0.36   5.9e+02     152     168 ..     157     173 ..     149     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                      EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHH CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllae 73
                                      +TG +  iG  l++ + ++g +v+   r+++++  + ++++a+ p      + + +++D++D+  +erl++ 
  gi|313125831|ref|YP_004036101.1| 10 VTGASRGIGVALVRAFAAEGAHVVCCARDEDAL-SDVVANVADTPG-----SAEAVRADVRDEYDVERLMET 75
                                      8999999****************9877666665.589999988764.....5789**************986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHH CS
                     GDP_Man_Dehyd 152 PYaaaKlyadwivvnyr 168
                                        Ya++K++ + +++++ 
  gi|313125831|ref|YP_004036101.1| 157 AYAVSKAAVEGLARQFA 173
                                       6*********9999875 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.4e-05     0.089       2      45 ..       7      71 ..       6      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                                      EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.....................T--TTSHHHHHH CS
                     RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeglevlaltre.....................eldltdaeavae 45
                                      +++vtGa+  +G +L++++a+eg++v+ + r+                     ++d++d+  v++
  gi|313125831|ref|YP_004036101.1|  7 TVVVTGASRGIGVALVRAFAAEGAHVVCCARDedalsdvvanvadtpgsaeavRADVRDEYDVER 71
                                      589**************************999666666655555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1548.83
//
Query:       gi|313125832|ref|YP_004036102.1|  [L=500]
Description: four-step phytoene desaturase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-32  112.6   0.1    4.6e-32  111.9   0.1    1.4  1  Amino_oxidase   Flavin containing amine oxidoreductase
    1.8e-17   63.3   0.1    3.8e-17   62.3   0.1    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.9e-11   42.6   4.0    2.3e-09   37.3   4.0    2.8  1  DAO             FAD dependent oxidoreductase
    5.3e-09   35.7   0.6    1.6e-05   24.3   0.4    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.7e-07   31.7   1.8    1.5e-05   25.4   0.3    2.8  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.5e-06   26.4   1.6    5.4e-06   25.7   1.6    1.3  1  FAD_binding_2   FAD binding domain
    6.1e-06   25.9   0.0      8e-06   25.5   0.0    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
      1e-05   24.5   0.0      0.001   17.8   0.4    2.2  2  HI0933_like     HI0933-like protein
    0.00016   21.1   0.5    0.00028   20.2   0.5    1.4  1  FAD_binding_3   FAD binding domain
    0.00093   18.5   0.1     0.0063   15.8   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00096   18.5   0.5     0.0017   17.7   0.5    1.3  1  Thi4            Thi4 family
     0.0093   16.4   0.0      0.016   15.6   0.0    1.4  1  NAD_binding_7   Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.014   14.2   0.0       0.02   13.7   0.0    1.2  1  MCRA            MCRA family
      0.024   13.9   0.3      0.036   13.4   0.3    1.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.027   14.4   0.4       0.53   10.3   0.1    2.5  3  NAD_binding_9   FAD-NAD(P)-binding
      0.033   13.3   1.2      0.049   12.7   1.2    1.2  1  GIDA            Glucose inhibited division protein A
       0.19   10.5   0.5       0.32    9.8   0.5    1.3  1  Trp_halogenase  Tryptophan halogenase
       0.21   11.2   0.5       0.37   10.4   0.5    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.28   11.0   0.3       0.47   10.3   0.3    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.1   4.9e-35   4.6e-32       2     451 ..      23     495 ..      22     496 .. 0.76

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 4.9e-35
                                       HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET..TTHHHHHHHHHTTCCCCEEEESCCGCE CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg..agnpllellkelgledslslpdpgapk 76 
                                        GL++A +L++aG  VtvlE ++++GGR++  ++dG+ +++G++w+ +      ++ ++++   +   +l   ++ +
  gi|313125832|ref|YP_004036102.1|  23 GGLSTACYLADAGATVTVLEKNEQLGGRASRLERDGFRFDMGPSWYLMpdVFEDFFGYFDRTPSD-YYELTRLDPHY 98 
                                       6***********************************************66666777777774444.455788889** PP

                                       EEEETTEECC............TTEECHH.HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH.....HHHCCCCHHH CS
                     Amino_oxidase  77 rvlskggref............pgdlspv.paewealleqgalsaellsleeklrlgleall.....qktldeldld 135
                                       r+ +k+g ++             + ++p   +++e++l+            ek ++   +++              +
  gi|313125832|ref|YP_004036102.1|  99 RIFFKDGDRVdmvpdleqnretFEAYEPGaGKQFEKYLQ----------KAEKNYEVGMEHFvytdrT--------K 157
                                       ********9877666666644444444443333555555..........5555555555555344332........3 PP

                                       HHHHHHCHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETT CS
                     Amino_oxidase 136 skslaesleelgrrepgdvev.....wdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprg 207
                                         ++a++    ++r+++           ++++p+l + +++ + +++g p   + + al+ l+   +f  ++++p+g
  gi|313125832|ref|YP_004036102.1| 158 LSDFADWDVIKNARGLSLIGSmqdhvEKYFDHPKLQQIMQYTLVFLGGAP---NNTPALYNLMSHVDFNMGVYYPDG 231
                                       3333333333333333221111222256666688889999*****99888...************************ PP

                                       HTHHHHHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEES...CC.SHHH CS
                     Amino_oxidase 208 Glsqlpealae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsP...pl.pdek 278
                                       Gl+ +++ + +  e++g+++r++++V ei+  ++   +++edg+++  D+Vv+ ++ ++   + + P   +   ++ 
  gi|313125832|ref|YP_004036102.1| 232 GLGGVVDGMVSlgEELGVEFRVESPVNEIRGREEAFVTRTEDGREFYSDYVVSDADYRHTE-MDLLPegkRQyDEDY 307
                                       *******************************99999999**********************.666665653334466 PP

                                       HHHHHHSEEEEEEEEEEEESSGGSGCSTS.......ECE......CECCCEEETTTEEEEECC...ECCCSTTTEEE CS
                     Amino_oxidase 279 aeairnlgfgsvnkvilefdrkfwednal.......gqg......vlvseltttlgeafissd...fpsrappgkgl 339
                                       +++  +  ++s+  ++l +++ + +++++       +           +  +++ +  +++ +    +  ap+g++ 
  gi|313125832|ref|YP_004036102.1| 308 WQS--RTYAPSAYLLYLGVEGDV-PELEHhtlvlptD-WddhfekIFDDPAWPDDPAYYLCVPsktDDTVAPEGHSN 380
                                       666..557777777888888888.4443223354442.0335668777888888888888888999999******** PP

                                       EEEEEECHHHHHHHTTS-HHHHHHHHHHHHHHHHT....GTSSTCSE....EEEEECCT..ETTTSSSEEE.BTTHH CS
                     Amino_oxidase 340 vllvyvggdaaneleslsdeelvqavlrdLrklfg....eevpepka....tlvtrWht..dplargsysyvsvgpg 406
                                        l+v+v+  a+ + +  ++e   + vl+d++   g    + +         ++v+++++  ++  +++  + ++  +
  gi|313125832|ref|YP_004036102.1| 381 -LFVLVPIAAGLDDTPEQRERYRDLVLDDIAAHTGedlrDRI----VleesFCVDDFSDryNATQGTALGLAHTLRQ 452
                                       .*****955555545669*****************5444333....345559999999755555577888888888* PP

                                       HHHHHHHHCHHCSTTEEE.SGGGCTTTTTS.HHHHHHHHHHHHHHH CS
                     Amino_oxidase 407 hedydplakpegdprlffAGehtsreypgt.vegAilSGlraAari 451
                                       +  ++p++ +e +++l+f+G+ t+   pg  v+ ++ SG  +A+ +
  gi|313125832|ref|YP_004036102.1| 453 TALLRPPHHSEEVSGLYFTGSFTT---PGIgVPMCLISGQLTAEKM 495
                                       ************************...****************876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.1     4e-20   3.8e-17       1      67 [.      17      83 ..      17      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 4e-20
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllre 67
                                      +vG+G++Gl++A++La+ag+ v++lek+++lGGra++ e++g+r+d g++++  ++ ++ ++ ++++
  gi|313125832|ref|YP_004036102.1| 17 VVGGGFGGLSTACYLADAGATVTVLEKNEQLGGRASRLERDGFRFDMGPSWYLMPDVFEDFFGYFDR 83
                                      8***************************************************999999999999986 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   4.0   2.4e-12   2.3e-09       2     198 ..      15     284 ..      14     494 .. 0.58

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.4e-12
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH..................... CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeas..................... 55 
                                       vv++GGG  GlstA +La +g  Vt+lek++++g    gr+s+l + g+r +  +                      
  gi|313125832|ref|YP_004036102.1|  15 VVVVGGGFGGLSTACYLADAGatVTVLEKNEQLG----GRASRLERDGFR-FDMGPswylmpdvfedffgyfdrtps 86 
                                       9*****************99**************....9******99996.44333467777778888888888888 PP

                                       ............................................HHHHHHHHHHHHHHHHHHHHSS...TTSEEEEE CS
                               DAO  56 ............................................elarlslealeelreleeelgi...didyrrtG 85 
                                                                                   +   + +++++  + +e    +   ++ y  ++
  gi|313125832|ref|YP_004036102.1|  87 dyyeltrldphyriffkdgdrvdmvpdleqnretfeayepgagkQ---FEKYLQKAEKNYE----VgmeHFVYTDRT 156
                                       888888888888888888887766666654444444333332211...1111111111111....111134444444 PP

                                       EEEEESS..............HHHHHHHH.....HHHHHH.....HHTTTTEEEEEH..HHHHHHSTT.ST.TTSEE CS
                               DAO  86 llslaad..............eeeleald.....kllall.....leagldaellda..eevrelepa.lp.gllga 134
                                       +ls +ad              +            k ++ +      ++ l   +l +  +++ +l+   ++ ++  +
  gi|313125832|ref|YP_004036102.1| 157 KLSDFADwdviknarglsligS------MqdhveKYFDHPklqqiMQYTL--VFLGGapNNTPALYNLmSHvDFNMG 225
                                       4444443444444444444431......0333333333333211111222..245442334555554432279**** PP

                                       EEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE CS
                               DAO 135 lfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gen.daadavVn 198
                                       ++ypd+g      ++ ++ +  e+lGve++ +++v +++ ++   + v + t+ g++  + d+vV 
  gi|313125832|ref|YP_004036102.1| 226 VYYPDGGL---GGVVDGMVSLGEELGVEFRVESPVNEIRGRE--EAFV-TRTEdGREfYS-DYVVS 284
                                       *****999...99*************************5443..3344.44444887445.77775 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.4   1.6e-08   1.6e-05       2      34 ..      14      45 ..      13      55 .. 0.80
   2 !    9.1   0.0   0.00074       0.7     194     232 ..     245     283 ..     242     289 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.6e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegt 34
                                      +vvv+GgG++Gl++a +la aga vt++e++ +
  gi|313125832|ref|YP_004036102.1| 14 SVVVVGGGFGGLSTACYLADAGATVTVLEKN-E 45
                                      7999999999999999999999999999533.3 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00074
                                       HHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 194 ekeGvevklgtsvkeidgngeklevvledgeeidadlvv 232
                                       e+ Gve+++++ v+ei+g++e   + +edg+e+  d+vv
  gi|313125832|ref|YP_004036102.1| 245 EELGVEFRVESPVNEIRGREEAFVTRTEDGREFYSDYVV 283
                                       577******************7779***********998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.3   1.6e-08   1.5e-05       1      35 [.      14      48 ..      14      56 .. 0.93
   2 ?   -2.4   0.0       7.9   7.4e+03      36      53 ..     122     139 ..     105     145 .. 0.70
   3 ?    4.5   0.0     0.056        53      51      74 ..     245     269 ..     238     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.6e-08
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      +vvvvGgG+ gl  A++la+ g+ Vtv+e +++l 
  gi|313125832|ref|YP_004036102.1| 14 SVVVVGGGFGGLSTACYLADAGATVTVLEKNEQLG 48
                                      69*****************************9997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.9
                                       TTSSHHHHHHHHHHHHHT CS
                         Pyr_redox  36 rllDeeaskilqeklekn 53 
                                        ++++ a+k ++++l+k 
  gi|313125832|ref|YP_004036102.1| 122 EAYEPGAGKQFEKYLQKA 139
                                       678888999999999875 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.056
                                       HHTTEEEECSEEEEEEEEETTS.EE CS
                         Pyr_redox  51 ekngievllntkveeiegsedg.ve 74 
                                       e++g+e++ ++ v+ei+g e+  v+
  gi|313125832|ref|YP_004036102.1| 245 EELGVEFRVESPVNEIRGREEAfVT 269
                                       789****************998665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   1.6   5.8e-09   5.4e-06       2      37 ..      15      50 ..      14      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.8e-09
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                      v+V+G+G++GL+ A  +a+aG++v+v+ek ++ gg 
  gi|313125832|ref|YP_004036102.1| 15 VVVVGGGFGGLSTACYLADAGATVTVLEKNEQLGGR 50
                                      9*******************************9994 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   8.5e-09     8e-06       2      40 ..      15      53 ..      14     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 8.5e-09
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                      vvVvGGg +G+  A   a aGa+v ++e+++ lGG +++
  gi|313125832|ref|YP_004036102.1| 15 VVVVGGGFGGLSTACYLADAGATVTVLEKNEQLGGRASR 53
                                      9**********************************9885 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.4   1.1e-06     0.001       2      36 ..      14      48 ..      13      52 .. 0.95
   2 ?    3.9   0.0     0.018        17     111     159 ..     236     283 ..     224     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +v+v+GgG  Gl +A  +a++g+ V++lek+++lg
  gi|313125832|ref|YP_004036102.1| 14 SVVVVGGGFGGLSTACYLADAGATVTVLEKNEQLG 48
                                      69*******************************98 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEE CS
                       HI0933_like 111 ivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklv 159
                                       +vd +++  +e gv++r+e+ v++++ +e+ +f  +t++++e+ +d++v
  gi|313125832|ref|YP_004036102.1| 236 VVDGMVSLGEELGVEFRVESPVNEIRGREE-AFVTRTEDGREFYSDYVV 283
                                       7888888899***************66555.59999999****999987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.5     3e-07   0.00028       2      35 ..      13      46 ..      12      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      t+V++VG+G  Gl++a  L+ aG  v+++ek ++
  gi|313125832|ref|YP_004036102.1| 13 TSVVVVGGGFGGLSTACYLADAGATVTVLEKNEQ 46
                                      78*****************************875 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.7e-06    0.0063     157     202 ..       5      50 ..       1      57 [. 0.83
   2 ?   -0.2   0.0      0.48   4.6e+02     227     258 ..     249     280 ..     240     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.7e-06
                       Pyr_redox_3 157 kefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseieke 202
                                       ++++ + g+ vvV+Gg+  +  +A+ l+++ga+Vtv+ +++++  +
  gi|313125832|ref|YP_004036102.1|   5 SDLSVLDGTSVVVVGGGFGGLSTACYLADAGATVTVLEKNEQLGGR 50 
                                       5666778999999999999999999999999999999999987765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.48
                       Pyr_redox_3 227 ikvlfnaevkeikekeeeykvktedgkkvevk 258
                                       +++  ++ v+ei+ +ee +  +tedg+++ ++
  gi|313125832|ref|YP_004036102.1| 249 VEFRVESPVNEIRGREEAFVTRTEDGREFYSD 280
                                       56677888999999888888889998886553 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5   1.8e-06    0.0017      10      56 ..       5      50 ..       1      54 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-06
                                      HHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 10 edllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                      +dl  +  + vv+vG+G  GL++a yla + +  v++le++  +GG 
  gi|313125832|ref|YP_004036102.1|  5 SDLSVLDGTSVVVVGGGFGGLSTACYLADA-GATVTVLEKNEQLGGR 50
                                      5566666788********************.**********999995 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05     0.016       5      43 ..      10      46 ..       8     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                     NAD_binding_7  5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkee 43
                                      l+g +v+vvGgG  +++ +  l++aga+vtv+ ++  e+
  gi|313125832|ref|YP_004036102.1| 10 LDGTSVVVVGGGFGGLSTACYLADAGATVTVLEKN--EQ 46
                                      68899***************************998..33 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.1e-05      0.02       3      78 ..      14      86 ..      12     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                      EEEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-----------------CCC----B...-TT-HHHHHHHTTSB- CS
                              MCRA  3 kaylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdpekGyvlrggrel...eehyeclwdLlssipS 78
                                      ++ +vG+G ++L++A+yL       g  +++le+++ +gg   + ++  +G+ +  g         +e +   +++ pS
  gi|313125832|ref|YP_004036102.1| 14 SVVVVGGGFGGLSTACYLADA----GATVTVLEKNEQLGGRASRLER--DGFRFDMGPSWylmPDVFEDFFGYFDRTPS 86
                                      5679**************764....689************9887655..455555544320025555555555555555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   3.8e-05     0.036      28      62 ..      12      46 ..       1      60 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                         v+v+GgG  Gl+ +   +  ga+Vtvl+++++
  gi|313125832|ref|YP_004036102.1| 12 GTSVVVVGGGFGGLSTACYLADAGATVTVLEKNEQ 46
                                      568****************************9987 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00056      0.53       1      43 [.      16      53 ..      16      62 .. 0.85
   2 ?   -3.4   0.0       8.7   8.2e+03      67      78 ..     130     141 ..     112     166 .. 0.56
   3 ?    1.6   0.0      0.26   2.5e+02     117     150 ..     249     283 ..     239     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00056
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwr 43
                                      ++vG+G+ Gl+++  L++        ++t+ +++e  g gr+ r
  gi|313125832|ref|YP_004036102.1| 16 VVVGGGFGGLSTACYLADA-----GATVTVLEKNEQlG-GRASR 53
                                      69**************999.....599******76636.88766 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.7
                     NAD_binding_9  67 ptfaeWlrerga 78 
                                       ++f+++l++ ++
  gi|313125832|ref|YP_004036102.1| 130 KQFEKYLQKAEK 141
                                       445555555543 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.26
                     NAD_binding_9 117 vev.hraevvdleeradgqavlladgaslaadaVv 150
                                       ve+ +++ v +++ r++ +  +++dg+++  d+Vv
  gi|313125832|ref|YP_004036102.1| 249 VEFrVESPVNEIRGREEAFVTRTEDGREFYSDYVV 283
                                       55524778999**********************98 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2   5.2e-05     0.049       2      31 ..      15      44 ..      14      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithk 31
                                      v+V+GgG  G+  A  +a +Ga v+ + ++
  gi|313125832|ref|YP_004036102.1| 15 VVVVGGGFGGLSTACYLADAGATVTVLEKN 44
                                      9***********************998443 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00034      0.32       2      35 ..      15      45 ..      14      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00034
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      +v+vGGG  G  +A++la a+   ++vt++e++e
  gi|313125832|ref|YP_004036102.1| 15 VVVVGGGFGGLSTACYLADAG---ATVTVLEKNE 45
                                      9********************...89****9975 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00039      0.37       3      34 ..      15      46 ..      13      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                                      EEEE--STTHHHHHHHHHHCTSEEEEE-S-HH CS
                    UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDidee 34
                                      ++v+G G+ Gl ta  la +g +v+++ ++e+
  gi|313125832|ref|YP_004036102.1| 15 VVVVGGGFGGLSTACYLADAGATVTVLEKNEQ 46
                                      89************************999985 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3    0.0005      0.47       2      34 ..      15      47 ..      14      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0005
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      v v+G G  G + a  +a ag +V++++ +e+ 
  gi|313125832|ref|YP_004036102.1| 15 VVVVGGGFGGLSTACYLADAGATVTVLEKNEQL 47
                                      89**************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 3379.64
//
Query:       gi|313125833|ref|YP_004036103.1|  [L=298]
Description: lycopene elongase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-26   92.7  21.4    2.9e-26   92.3  21.4    1.2  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3  21.4   1.6e-30   2.9e-26       4     223 ..      43     263 ..      40     293 .. 0.75

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 1.6e-30
                              UbiA   4 palvglalaaggspdl.llllllllgtl..laaaaanalNdyfDreiDadmertpnRPlvsGrispkeali.faivl 76 
                                       p++vg+a+aa+ ++dl + ++l+l+g +    ++  +++Nd fD++ D  ++ + +R     r    ++++ +++++
  gi|313125833|ref|YP_004036103.1|  43 PVAVGVAFAATAVSDLlSPAALVLFGYFllPGNILLYGVNDAFDADVDEANPKKDDR---EARWQGDTVVTaVIVAS 116
                                       899**999999999996444444444446699*************************...77777666666366666 PP

                              UbiA  77 lilgllllalllnpltallgllallly.vvYt.g.lrlKrrtllgtvvggiafglppllgwaavtgslsllalllal 150
                                       ++lgl+l    + p + +  l++++l+ v Y+ + +r+K +++l+ v  g+   lp  +++aav+g+ ++l +l+++
  gi|313125833|ref|YP_004036103.1| 117 GVLGLGLF--AVAPRLTWPYLAGFFLLgVEYSaPpFRFKTTPFLDSVSNGLY-ILPGAAAFAAVAGQHPPLSALVGA 190
                                       77777765..555656666666666666*****99***************95.588999****99996666666666 PP

                              UbiA 151 avflltwaialandlrdregDrkagiktlpvvlGrkaaril.lalllavllla.llllllalllllylllallla 223
                                       +  ++t++++++ +++d+e Dr agi+t+++ lG+++++ + +a++l+++ ++ l+ + l+++l+ y+l++l++a
  gi|313125833|ref|YP_004036103.1| 191 W--AWTMGMHTFSAIPDIEPDRTAGIRTTATFLGERRTYAYcFACWLVAAAAFaLVDWRLGAVLSAYPLAVLAVA 263
                                       6..************************************964332222222222333444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2060.42
//
Query:       gi|313125834|ref|YP_004036104.1|  [L=299]
Description: carotene biosynthesis associated membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-63  214.7  19.5    1.6e-63  214.4  19.5    1.1  1  Caroten_synth  Carotenoid biosynthesis protein


Domain annotation for each model (and alignments):
>> Caroten_synth  Carotenoid biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.4  19.5   8.8e-68   1.6e-63       2     208 ..      65     273 ..      64     274 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.4 bits;  conditional E-value: 8.8e-68
                     Caroten_synth   2 gvvlillgtaalalyav....rllglrralaflllavllslaiEllGvstGfpfGeYsYlsglgpkllglVPltiPl 74 
                                       + ++il+gt++++++++    +++  rr+++ + l++l++++iE+ Gv+tGfp+G+++Y+ +lgp++ g +Pl +P+
  gi|313125834|ref|YP_004036104.1|  65 NGLFILFGTFVMRSPLLvgvlPHTT-RRGATGVGLLTLYAYLIEYTGVHTGFPYGQFAYGVALGPTVGG-IPLGLPV 139
                                       7799************999866655.999****************************************.******* PP

                     Caroten_synth  75 swfplvlaayllarlllesrakrslvrlllaalllvawDlvLDPamvalgfWvweepGafygvPlqNflGWlltglv 151
                                       +++plv++ayll+ lll++ra+++++rl++++++++a+D+vLDP++valgfW+++ pGafygvPl+N++GW+l+++v
  gi|313125834|ref|YP_004036104.1| 140 FFVPLVMNAYLLCLLLLGDRAEHTVIRLCTVIIAVLAMDVVLDPGAVALGFWAYTPPGAFYGVPLSNYAGWVLSATV 216
                                       ***************************************************************************** PP

                     Caroten_synth 152 lvlvlellwrkkaleerreqlelplavllsnfllaavlnllagllipallglllgvl 208
                                       +v++l++ ++++ l +r +++e++l++l+s+++l+++ln+++g+++p+++++l+g++
  gi|313125834|ref|YP_004036104.1| 217 AVILLDWGYDQHILLTRLSECEFMLDDLVSFVILWGGLNAWFGNWLPVAVAALFGLG 273
                                       ******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2383.74
//
Query:       gi|313125835|ref|YP_004036105.1|  [L=338]
Description: phytoene synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-65  219.7  11.7      6e-65  219.4  11.7    1.1  1  SQS_PSY   Squalene/phytoene synthase


Domain annotation for each model (and alignments):
>> SQS_PSY  Squalene/phytoene synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.4  11.7   3.3e-69     6e-65       2     261 ..      15     268 ..      14     270 .. 0.94

  Alignments for each domain:
  == domain 1  score: 219.4 bits;  conditional E-value: 3.3e-69
                                       XHH-HHHHHHHTTS-HHHHHHHHHHHHHHHHHT-.-----..........------------..---------THHH CS
                           SQS_PSY   2 raasksfylaslllppelRdalgalYafcreaddlvDdvs..eplqararldwwrdavdavyaedklkpprepvlra 76 
                                       r+ +k+f+la+++lp+++R+a ++lYaf r+ad++vD ++  ep  +r+rl+++r++  +        + ++pvl a
  gi|313125835|ref|YP_004036105.1|  15 RKTGKTFHLATRVLPERVRHATYVLYAFFRVADEVVDAEEtaEPSAQRERLEQLRAQALGRD------ETDDPVLSA 85 
                                       7899**********************************998888888999*****9988666......467****** PP

                                       HHHHHHHHT--HHHHHHHHHHTS--SS-..--SHHHHHHHHHHHHHHHHHHHHHHH-S.S-HHHHHHHHHHHHHHHH CS
                           SQS_PSY  77 laqlirtyklpkellleliegmeadleftryetlddLeeYcyrvagvVgelclrllgarrsdralaeaarrlGkalQ 153
                                       +a+l ++y++  e +  +i++m++d+++ ryet+d+Le+Y++ +a++Vg+++++++ + +++ +++++a +lG a+Q
  gi|313125835|ref|YP_004036105.1|  86 FAELREQYDIADEDVNVFIDAMRSDITKSRYETYDELETYMDGSAAAVGRMMTDIMQTPNAE-KARPHATALGEAFQ 161
                                       **********************************************************6555.89************ PP

                                       HHHHHT---SH.HHHTT..S-HHHHHHHT--HHHHHHT-.-SHHHHHHHHHHHHHHHHHHHHHHHTGGGS.-HHHHH CS
                           SQS_PSY 154 ltnilRdvpeD.aergrvyLPadvlkefgvseedllrkgvrsaelrallrrlaerArelldearellkqlpdrrarp 229
                                       + n+lRdv+eD +er+rvyLP++ l+++gv+ee+l + +  ++++ra++r++++r+++l++e+  +++ l ++++++
  gi|313125835|ref|YP_004036105.1| 162 MSNFLRDVREDiVERDRVYLPQETLEKHGVTEEQLQSFR-CDENFRAVMREEMRRTEALYREGVHGIQYL-PEDCQF 236
                                       ***********************************7665.6777**************************.999*** PP

                                       HHHHHHHHHHHHHHHHHHTTT-TTT------H CS
                           SQS_PSY 230 alllavalyrailerieaadydvlsrrvklsl 261
                                       a+lla++ly++  ++i+++ ydvls  ++ls+
  gi|313125835|ref|YP_004036105.1| 237 AVLLAAVLYADHHRAIRKRAYDVLSVTPSLST 268
                                       **********************9987777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2416.58
//
Query:       gi|313125836|ref|YP_004036106.1|  [L=94]
Description: hypothetical protein Hbor_10690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.29   11.3   6.5       0.44   10.7   6.5    1.3  1  zf-Mss51       Zinc-finger of mitochondrial splicing suppress
        1.1    9.0   4.7        6.9    6.5   0.1    2.2  2  A2L_zn_ribbon  A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   6.5   4.9e-05      0.44       2      33 ..      64      94 .]      63      94 .] 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.9e-05
                          zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCGiptycseehw 33
                                      CP++ + + a++h ++ Cp  G+ + cs   w
  gi|313125836|ref|YP_004036106.1| 64 CPFCGTSM-AHRHCKYVCPTHGVIYDCSDTFW 94
                                      ****8777.9******************9887 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1   0.00077       6.9      24      31 ..      64      71 ..      61      73 .. 0.83
   2 ?    5.0   0.7    0.0022        20       2      16 ..      72      87 ..      71      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00077
                     A2L_zn_ribbon 24 CieCgasf 31
                                      C++Cg+s 
  gi|313125836|ref|YP_004036106.1| 64 CPFCGTSM 71
                                      *****985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0022
                     A2L_zn_ribbon  2 nlkvCsv.Cggngiln 16
                                        ++C++ C + g+++
  gi|313125836|ref|YP_004036106.1| 72 AHRHCKYvCPTHGVIY 87
                                      569******9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 722.67
//
Query:       gi|313125837|ref|YP_004036107.1|  [L=117]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-08   34.0   0.0    3.6e-08   33.2   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
    3.8e-07   30.1   0.1    6.5e-07   29.3   0.1    1.3  1  HTH_20           Helix-turn-helix domain
    0.00024   21.0   0.0    0.00037   20.4   0.0    1.2  1  HTH_11           HTH domain
     0.0029   17.5   0.0     0.0046   16.9   0.0    1.4  1  HTH_12           Ribonuclease R winged-helix domain
     0.0062   16.5   0.0     0.0089   16.0   0.0    1.3  1  HTH_29           Winged helix-turn helix
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.031   14.3   0.0    1.3  1  HTH_45           Winged helix-turn-helix
      0.055   13.6   0.1       0.19   11.9   0.0    1.8  2  HTH_28           Helix-turn-helix domain
      0.097   12.6   0.0       0.18   11.7   0.0    1.4  1  MarR_2           MarR family
       0.16   11.9   0.0       0.27   11.2   0.0    1.4  2  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.8e-11   3.6e-08       2      46 ..      42      86 ..      41      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.8e-11
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++R++I+++L+++++ + +la el++   t++hH   L+e ++Ve
  gi|313125837|ref|YP_004036107.1| 42 ENRVRIVHALSDRPMNANQLATELNVGYRTIRHHIELLEEHDVVE 86
                                      68**************************************99996 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   3.3e-10   6.5e-07      11      56 ..      43      87 ..      42      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.3e-10
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       R ri  aL +++++ a++la +l +   t+++H++ Lee++ ve+
  gi|313125837|ref|YP_004036107.1| 43 NRVRIVHAL-SDRPMNANQLATELNVGYRTIRHHIELLEEHDVVEG 87
                                      699******.**********************************96 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.9e-07   0.00037       7      41 ..      49      81 ..      44      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                            HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLee 41
                                      + L  ++ p+++++LA eLnv  rt+r +I+ Lee
  gi|313125837|ref|YP_004036107.1| 49 HAL--SDRPMNANQLATELNVGYRTIRHHIELLEE 81
                                      555..44569***********************97 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.3e-06    0.0046      10      49 ..      52      86 ..      45     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                            HTH_12 10 sdkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                                      sd+p+ a+++a+eL+     +g r++R ++  lee++ ++
  gi|313125837|ref|YP_004036107.1| 52 SDRPMNANQLATELN-----VGYRTIRHHIELLEEHDVVE 86
                                      79************6.....67799**********98775 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.5e-06    0.0089       7      40 ..      50      83 ..      44      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.5e-06
                            HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlkrfeegG 40
                                      +l++  ++  q+A  l++ +rt+++++++ ee+ 
  gi|313125837|ref|YP_004036107.1| 50 ALSDRPMNANQLATELNVGYRTIRHHIELLEEHD 83
                                      4444444999*********************987 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.5e-05     0.031      11      74 ..      47     114 ..      44     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                            HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkelee 74 
                                       I +a+s+   +  ++  + n  y++++  ++ L e +++    ++ ++ Y lT++ + + ++++++ e
  gi|313125837|ref|YP_004036107.1|  47 IVHALSDRPMNANQLATELNVGYRTIRHHIELLEEHDVVeggdNDYGKLYFLTDRFETYRDTFEQITE 114
                                       67778888889999999**********************9986678899*****99999998888765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.6e-05      0.19       5      38 ..      47      81 ..      43      83 .. 0.78
   2 ?   -1.4   0.0       1.4   2.7e+03      27      40 ..      93     106 ..      91     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.6e-05
                            HTH_28  5 iikllaaG.hsvreaArelgisrrtvyrWikryee 38
                                      i+ +l +  ++++++A el++++rt++  i  +ee
  gi|313125837|ref|YP_004036107.1| 47 IVHALSDRpMNANQLATELNVGYRTIRHHIELLEE 81
                                      55444433259999**************9999987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                            HTH_28  27 rtvyrWikryeegG 40 
                                         +y +  r+e++ 
  gi|313125837|ref|YP_004036107.1|  93 GKLYFLTDRFETYR 106
                                       56888999999986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.8e-05      0.18       8      53 ..      45      87 ..      43      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.8e-05
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                       r+ +aL +rp   +++++la +l++   ++  +++ L+++  ve 
  gi|313125837|ref|YP_004036107.1| 45 VRIVHALSDRP---MNANQLATELNVGYRTIRHHIELLEEHDVVEG 87
                                      6899*******...9*************************999985 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.5   6.9e+03      57      76 ..      14      33 ..      11      36 .. 0.67
   2 ?   11.2   0.0   0.00014      0.27      52      90 ..      54      92 ..      42     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.5
                   Phage_rep_org_N 57 emlalifnreletvrlaLkv 76
                                      ++++l  +  +++++ aL +
  gi|313125837|ref|YP_004036107.1| 14 QTVSLTNDGRTQSMEKALWY 33
                                      66777777777777777765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00014
                   Phage_rep_org_N 52 ipytaemlalifnreletvrlaLkvlkdlelieisedkv 90
                                       p +a++la+++n    t+r  +++l++  ++e  +++ 
  gi|313125837|ref|YP_004036107.1| 54 RPMNANQLATELNVGYRTIRHHIELLEEHDVVEGGDNDY 92
                                      58899****************************987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 806.10
//
Query:       gi|313125838|ref|YP_004036108.1|  [L=98]
Description: hypothetical protein Hbor_10710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 603.24
//
Query:       gi|313125839|ref|YP_004036109.1|  [L=408]
Description: transposase, is605 orfb family, central region [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-21   76.5   2.2    2.4e-21   76.2   0.5    1.8  2  OrfB_IS605      Probable transposase
    2.5e-18   65.7   0.1    5.7e-18   64.6   0.1    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0037   16.7   0.1      0.007   15.8   0.1    1.4  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.066   12.8   0.5       0.18   11.4   0.1    1.8  2  DUF3445         Protein of unknown function (DUF3445)
      0.087   13.0   1.1       0.82    9.9   1.1    2.5  1  EstA_Ig_like    Esterase Ig-like N-terminal domain
       0.25   11.1   1.8       0.98    9.2   1.9    1.9  1  Rubredoxin_2    Rubredoxin metal binding domain
        5.1    7.3   9.8        1.7    8.9   4.8    2.6  3  DUF3958         Protein of unknown function (DUF3958)


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.7e+03      71      86 ..      71      86 ..      46     106 .. 0.65
   2 !   76.2   0.5   9.3e-25   2.4e-21      12     117 ..     186     287 ..     172     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                        OrfB_IS605 71 kkasrklarlhrkrsr 86
                                      k+ +r ++r ++++s+
  gi|313125839|ref|YP_004036109.1| 71 KALQRTVTRFYQNLSN 86
                                      3344444444444443 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 9.3e-25
                        OrfB_IS605  12 kpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrr 88 
                                         ++++ +giDlGi n + +++++   ++     l  dy++l++e+++l++k k+s+ny+k++ ++a++ r ++r++
  gi|313125839|ref|YP_004036109.1| 186 SLNTSNSVGIDLGILNYIHTSDGK---TVDWL-DLEDDYERLRREQRKLSRKEKGSNNYEKQRVEVAKVKRHIRRKV 258
                                       568999******************...55555.9******************************************* PP

                        OrfB_IS605  89 khllhklathliktlkevgvetLnvgnmk 117
                                       ++++hkl+t l+k++++v ve+Lnv+ m 
  gi|313125839|ref|YP_004036109.1| 259 LDYQHKLTTWLVKEYDAVFVEDLNVQCML 287
                                       *************************9886 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.1   2.2e-21   5.7e-18       1      69 []     301     369 ..     301     369 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2.2e-21
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +r++++ leyk   +G +v++v+ + T k+C+ Cg +  ++   r++ Cp+Cgfe drD nA++N+l+r
  gi|313125839|ref|YP_004036109.1| 301 WRQFITLLEYKGDLHGTHVVQVDARGTTKECASCGVETAKPIWVREHSCPACGFETDRDANASLNVLQR 369
                                       9***************************************9*************************987 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.7e-06     0.007       3      33 ..       2      32 ..       1      33 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-06
                    HTH_OrfB_IS605  3 lkaykyrlyPTpeQeeklartfGcvRfVYNk 33
                                        +++y  yPT+  +e l+ ++++ R +YN+
  gi|313125839|ref|YP_004036109.1|  2 EYSHRYHAYPTQAVAERLEYHIDVHRQAYNY 32
                                      5689**************************8 PP

>> DUF3445  Protein of unknown function (DUF3445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.69   1.8e+03     157     188 ..      11      41 ..       7      58 .. 0.63
   2 ?   11.4   0.1   7.2e-05      0.18       8      68 ..     211     284 ..     205     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.69
                           DUF3445 157 epgkpvkRvnwsiqtddelfwaseeeeeeeld 188
                                       +++ + +R+ + i ++++ ++  ++ e e++d
  gi|313125839|ref|YP_004036109.1|  11 PTQAVAERLEYHIDVHRQAYN-YTRYEYENVD 41 
                                       567889999999999999996.3322333433 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.2e-05
                           DUF3445   8 sewieldktYkerieerrrlle.........ehgekvlavlpeaeaavkElleelveyLparYPqlFel.....s 68 
                                        +w++l+++Y++  +e r+l +         +++ +v +v+++++  v +  + l++ L+++Y  +F +     +
  gi|313125839|ref|YP_004036109.1| 211 VDWLDLEDDYERLRREQRKLSRkekgsnnyeKQRVEVAKVKRHIRRKVLDYQHKLTTWLVKEYDAVF-VedlnvQ 284
                                       68**********99999988887788877767888899999**************************.5244330 PP

>> EstA_Ig_like  Esterase Ig-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.1   0.00032      0.82      33      72 ..      59      97 ..      57     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00032
                                      GGGEEEEEEETTCEEEE-EEEEEEESSSSS--T--ECCEE CS
                      EstA_Ig_like 33 kstFkVagkrseekgsRtvtkvYvndkaekadkskdGkyV 72
                                      k++F+V +++++++ +Rtvt+ Y n ++  ++ +++G+ V
  gi|313125839|ref|YP_004036109.1| 59 KDEFSVFSDVNSKALQRTVTRFYQNLSNLSKK-KQNGNKV 97
                                      689**********************9998666.4888866 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.9   0.00038      0.98       2      21 ..     330     353 ..     330     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00038
                      Rubredoxin_2   2 vCsqCGfesakwfGr....CpsCg 21 
                                       +C +CG e+ak  +     Cp+Cg
  gi|313125839|ref|YP_004036109.1| 330 ECASCGVETAKPIWVrehsCPACG 353
                                       5*************55555****8 PP

>> DUF3958  Protein of unknown function (DUF3958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.4     6e+03      41      55 ..      77      91 ..      68     101 .. 0.53
   2 ?    8.9   4.8   0.00065       1.7      78      98 ..     215     235 ..     209     245 .. 0.84
   3 ?    1.3   0.4      0.15   3.9e+02      54      86 ..     233     265 ..     232     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.4
                           DUF3958 41 skrlfdelletfrkd 55
                                       +r++++l+   +k 
  gi|313125839|ref|YP_004036109.1| 77 VTRFYQNLSNLSKKK 91
                                      334444444433333 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00065
                           DUF3958  78 dLEeeeeeLkrekrqLedqee 98 
                                       dLE+++e+L+re+r+L+++e 
  gi|313125839|ref|YP_004036109.1| 215 DLEDDYERLRREQRKLSRKEK 235
                                       8******************97 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.15
                           DUF3958  54 kdeeshlfeklrdevqrlsrklredLEeeeeeL 86 
                                       k++ s+ +ek+r ev++ +r++r +  + + +L
  gi|313125839|ref|YP_004036109.1| 233 KEKGSNNYEKQRVEVAKVKRHIRRKVLDYQHKL 265
                                       556788899999999999999998887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1285  (0.0716716); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2695.94
//
Query:       gi|313125840|ref|YP_004036110.1|  [L=1044]
Description: ribonucleoside-diphosphate reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-150  502.5   0.0   1.7e-150  502.0   0.0    1.2  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    7.3e-24   83.6   0.2    2.3e-23   82.0   0.1    2.0  2  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
  ------ inclusion threshold ------
        0.2   11.4   4.7       0.38   10.6   4.7    1.5  1  PADR1            PADR1 (NUC008) domain
       0.55   10.2   6.1        1.1    9.2   6.1    1.5  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.0   0.0  3.8e-154  1.7e-150       1     524 []     175     772 ..     175     772 .. 0.94

  Alignments for each domain:
  == domain 1  score: 502.0 bits;  conditional E-value: 3.8e-154
                                       EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRr 77 
                                       s+Cfv s+ d++ +I++t+keaa+++++ggG+G+ ++klR+ g+ v++t+g asGp++fm+++d+++++++qgG+Rr
  gi|313125840|ref|YP_004036110.1| 175 SACFVDSPGDDITDIHQTAKEAAEVFQSGGGMGYAFWKLRPYGDAVGSTGGIASGPITFMRTYDQMCETIAQGGARR 251
                                       79*************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX...........................................XXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................................xxxxxxxx RF
                   Ribonuc_red_lgC  78 GAamvylevwHpDiekfidaKekntgee.........................................enrlsnln 113
                                       GA+m++++v+HpD+++fi+aK+k+++                                           e +lsn+n
  gi|313125840|ref|YP_004036110.1| 252 GAQMGVMRVSHPDVIQFIHAKNKDVSLAhslrlndpddfthnsfadaleeareliddegrvpkhlrnavEGHLSNFN 328
                                       *********************997774478888999999999*********************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX.XXX............................XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 114 isvgvpdlFmeavkedkdwtLfsPrt.vvkleklygeefeeeyeeleekakik...kkevkakeLfeeiaesawetg 186
                                       isvg++d+Fmea+++++++ +++Prt      ++   e +e ye     ++++     +v+a++L+++++  a+e+g
  gi|313125840|ref|YP_004036110.1| 329 ISVGITDDFMEALENGEEFVFTNPRTeE---PHIATPETKEIYEMFGLGEHVEvgeVLSVPAEKLWDQMVDGAYENG 402
                                       *************************732...34555556666665544433332225599***************** PP

                                       XXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX.................... CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                   Ribonuc_red_lgC 187 ePgvlfkDtiNrrnvlekak..ggkIratNlCgEiplleyesvavCnLasinLakfv.................... 241
                                       ePgv++ +++N+++ ++++k   ++I atN+CgE+pl eye+   CnL++inL+++                     
  gi|313125840|ref|YP_004036110.1| 403 EPGVIYLERVNKQHSFDVEKhpEHRILATNPCGEQPLEEYEA---CNLGHINLSTLAdldapdwrvwqaengddyds 476
                                       ****************99998889******************...******************************** PP

                                       ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 242 ...kkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgipydseeal 315
                                          + d+  ++++dw+e+++ i+  +r+L+nv++++++p+++ie++ + +R+iGlGvmgla+++++lgi+y+s+ ++
  gi|313125840|ref|YP_004036110.1| 477 iedAVDAFLEEAIDWEEFDHRIDNGTRFLENVVTMSDFPVEKIEEKVRAMRKIGLGVMGLAQLYIQLGIRYGSDSGN 553
                                       *99889999******************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 316 kfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeekekedweeLreeikkyGlrnamvtalaPT 392
                                       ++ar+++ ++++++  aS+elA+erg+f++++ sk+++ + + ++fe+++  d +e         +rn+++t++aPT
  gi|313125840|ref|YP_004036110.1| 554 EVARQLMTHINHQSKWASHELAEERGTFEDWDDSKFADPTEYREWFEHHTGLDADEWE---DGFPIRNHNTTTIAPT 627
                                       ****************************************999999987755555533...25679*********** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxx RF
                   Ribonuc_red_lgC 393 gsiSliagtssgiePifalvykksvtv.....geflevnpvfeeeLkklglwseellkkiles........vqglee 456
                                       g++S++ +t+ g+ePi++ +y+k+v++     ++++e++++f++ L++++++ ++++++ +e+        v+gle+
  gi|313125840|ref|YP_004036110.1| 628 GTTSMVGNTTGGCEPIYNVAYYKNVSDdvqgdEMLVEFDDYFLRVLEANDIDVDAVKEEAQEQmannefdgVEGLET 704
                                       *************************99888655699***********************9555667899******** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 457 ipeeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                       +p++i ++f+ + d++ +dh  +q a+qk +d++iSkt n+pn+a+ ed+ e+y + ++ G Kgvt+Y
  gi|313125840|ref|YP_004036110.1| 705 VPNAIGELFVVTSDLSGKDHAAVQCACQKGVDSAISKTCNFPNSASKEDMDEVYRYIYNNGGKGVTVY 772
                                       *******************************************************************9 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.1   5.1e-27   2.3e-23       3      83 .]      28     172 ..      26     172 .. 0.97
   2 ?   -4.2   0.0         4   1.8e+04      27      38 ..     236     247 ..     234     252 .. 0.78

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 5.1e-27
                   Ribonuc_red_lgN   3 ltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealyd................................ 47 
                                       + ++++++l++rYl+k+++g++ E+ +++f+RvA+++ +aea y+                                
  gi|313125840|ref|YP_004036110.1|  28 TANAYHNILPARYLRKNADGDLTETQEELFARVAKNISLAEAVYEaerqdveitvtpdqlkpdhprrdelaaevfgk 104
                                       5578899***********************************99999****************************** PP

                   Ribonuc_red_lgN  48 ................................kleedkdlaeefydlmssqkflpasPtlmnaGtelg 83 
                                                                        ++++kd+ e f+d+m s+ f+p+sPtlmnaG+el+
  gi|313125840|ref|YP_004036110.1| 105 gvtaeddaettlsvynvnkfaydtivpelpeeIRTTVKDKRETFQDMMESLSFMPNSPTLMNAGDELQ 172
                                       *******************************999*******************************986 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 4
                   Ribonuc_red_lgN  27 spqqmfmRvAla 38 
                                       +++qm++ +A++
  gi|313125840|ref|YP_004036110.1| 236 TYDQMCETIAQG 247
                                       788999999975 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.7   8.5e-05      0.38       2      34 ..    1005    1037 ..    1004    1044 .] 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.5e-05
                             PADR1    2 drvaDgmlfGalekCpeCkegqlvfdssgYkCt 34  
                                        d++ D+++ G  ++Cp C++ +l++++++ +C+
  gi|313125840|ref|YP_004036110.1| 1005 DAMDDLLAAGESPECPDCGNMTLYYSEGCKTCE 1037
                                        56789*********************9977775 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.1   0.00024       1.1       4      28 ..    1019    1040 ..    1019    1043 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00024
                                        ESTTTSB.EEEEECSCCCEEEESSSS CS
                    RNA_POL_M_15KD    4 CpkCgNl.LlpkedkegknfeCrqCg 28  
                                        Cp+CgN+ L++ e+ ++    C +Cg
  gi|313125840|ref|YP_004036110.1| 1019 CPDCGNMtLYYSEGCKT----CESCG 1040
                                        *******8888999999....****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1044 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.85u 0.30s 00:00:01.14 Elapsed: 00:00:00.49
# Mc/sec: 6387.79
//
Query:       gi|313125841|ref|YP_004036111.1|  [L=75]
Description: hypothetical protein Hbor_10750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.05   13.4   5.4      0.055   13.2   5.4    1.1  1  PAP2             PAP2 superfamily
      0.071   12.7   2.0      0.081   12.5   2.0    1.1  1  Fzo_mitofusin    fzo-like conserved region
          4    6.7   7.7        4.2    6.6   7.7    1.1  1  DUF4191          Domain of unknown function (DUF4191)


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.4   9.3e-06     0.055      87     127 ..      30      70 ..       3      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.3e-06
                              PAP2  87 lalillllavlvalsRlylgvHflsDvlaGlliGialaala 127
                                       +++++++ a++v ++Rl+l+v ++  ++a+++iG++l++ +
  gi|313125841|ref|YP_004036111.1|  30 AFVVVIAIAAVVLIGRLVLRVAWRLVTIAAVVIGLLLLFSF 70 
                                       57889999****************************99865 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.0   1.3e-05     0.081      21      54 ..      36      68 ..      18      71 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                     Fzo_mitofusin 21 tslgvlvvggvvlravgWrvialslalygllYly 54
                                      +  +v+++g +vlr v+Wr+++++++++gll l+
  gi|313125841|ref|YP_004036111.1| 36 AIAAVVLIGRLVLR-VAWRLVTIAAVVIGLLLLF 68
                                      44566666667766.89*************9876 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.7   0.00071       4.2      30      70 ..      30      72 ..      10      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00071
                           DUF4191 30 laaflvvvvvfvvlglllg..slilllilgillgllvalivlt 70
                                      + +++++++++v++g l+    + l++i ++++gll+ + +++
  gi|313125841|ref|YP_004036111.1| 30 AFVVVIAIAAVVLIGRLVLrvAWRLVTIAAVVIGLLLLFSFFG 72
                                      445666777777777776423699999*********9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 455.11
//
Query:       gi|313125842|ref|YP_004036112.1|  [L=208]
Description: anthranilate synthase, component ii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-45  153.2   0.0    7.4e-45  153.1   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    3.5e-08   33.5   0.1    1.1e-07   31.9   0.1    1.7  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
       0.15   11.6   0.0       0.21   11.1   0.0    1.2  1  Peripla_BP_2   Periplasmic binding protein


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1   0.0   1.2e-48   7.4e-45       1     187 [.       6     196 ..       6     199 .. 0.95

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 1.2e-48
                                       EEEESSTSTHHHHHHHHHHTT.....-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHC CS
                            GATase   1 lliDnydsvtenlvhalvelg.....vkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikear 68 
                                       +++Dn ds+t+nlv++l e +     + vev++++as +ei+    +pd+i++s+Gpg+p+    v+ + e+++ + 
  gi|313125842|ref|YP_004036112.1|   6 VVVDNFDSFTYNLVEYLSEQRigddeIAVEVRKNTASLDEIR--DLDPDAIVISPGPGHPKndrdVGVTTEVLTTLS 80 
                                       589****************99999999**************6..69***************8888888888888888 PP

                                       TSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEE CS
                            GATase  69 enkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevt 145
                                       +  iP LG+CLG+ ++++ +g++v ++  ++ hg+  ++++d+++++ gl++++++ ++H++++++   +p+++ev+
  gi|313125842|ref|YP_004036112.1|  81 K-SIPTLGVCLGLEAAVYVYGGSVGHAP-EPIHGKAFPVEHDSHGVFAGLEQQFQAGRYHSLVATE---VPECFEVS 152
                                       8.**************************.9************************************...******** PP

                                       EEEETTE..EEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 146 aksedde..elmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                       a++++ +   +m+++++++p+ +vQFHPEs++t  g+ +++nfl
  gi|313125842|ref|YP_004036112.1| 153 ATTDHFGdeLVMGVRHREYPIEAVQFHPESVLTGVGHDVVRNFL 196
                                       ***9866669********************************96 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   1.8e-11   1.1e-07      84     216 .]      61     181 ..      47     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.8e-11
                     Peptidase_C26  84 eeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgslla 160
                                       ++ +++Rd    + +  +l++++P lg+C+Gl+    ++GG++  + e               ++  v+ ++ +++a
  gi|313125842|ref|YP_004036112.1|  61 GHPKNDRDVGVTTEVLTTLSKSIPTLGVCLGLEAAVYVYGGSVGHAPEP----I-------HGKAFPVEHDSHGVFA 126
                                       567888999988999999*****************99****98765552....2.......2445688999999999 PP

                     Peptidase_C26 161 ellgseeievnslHhqaikelaeelrveAvae...DgviEaieseeakafvlgvQwHPE 216
                                        l +  +++   +H+   +e+ e ++v+A+++   D+++  ++++e  +++ +vQ+HPE
  gi|313125842|ref|YP_004036112.1| 127 GLEQ--QFQAGRYHSLVATEVPECFEVSATTDhfgDELVMGVRHRE--YPIEAVQFHPE 181
                                       9876..9**********************99866677777777666..88********9 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.5e-05      0.21      22      88 ..       6      88 ..       2     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
                                      EEB-GGG--GGGGGGT.........TS-BSBESSSB-HHHHHHH--SEEEE-GGG............GGGHHHHHHHS- CS
                      Peripla_BP_2 22 vgvdtttsdpldadklee.......aivevgadgeidvEklaalkPDlvilskgl.........gltdedeellksgip 84
                                      v vd+++s+ +   + ++       +i++    ++++++++ +l+PD ++ s+g          g+t+e   +l++ ip
  gi|313125842|ref|YP_004036112.1|  6 VVVDNFDSFTYNLVEYLSeqrigddEIAVEVRKNTASLDEIRDLDPDAIVISPGPghpkndrdvGVTTEVLTTLSKSIP 84
                                      55555555555554444456667767777778899*******************9888888877788888888888888 PP

                                      EEE- CS
                      Peripla_BP_2 85 tviv 88
                                      t+ v
  gi|313125842|ref|YP_004036112.1| 85 TLGV 88
                                      8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1295.93
//
Query:       gi|313125843|ref|YP_004036113.1|  [L=543]
Description: anthranilate synthase, component i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-91  303.9   0.0    1.7e-90  303.1   0.0    1.4  1  Chorismate_bind  chorismate binding enzyme
    3.9e-18   66.0   0.0    4.5e-16   59.3   0.0    3.3  2  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.1   0.0   1.9e-94   1.7e-90       2     258 .]     254     511 ..     253     511 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.1 bits;  conditional E-value: 1.9e-94
                                       HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEE CS
                   Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkve 78 
                                       re+Y++av+++k+++ +gd+y+ v+sr  +++   +vdp+ ly+alra np+py++ll+++d++++gaSPE+l++v+
  gi|313125843|ref|YP_004036113.1| 254 REEYEAAVRRTKDHVLDGDIYQGVISRVRELR--GEVDPMGLYEALRAVNPSPYMYLLRHDDRHIVGASPETLVSVH 328
                                       799*****************************..9****************************************** PP

                                       TTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEE CS
                   Chorismate_bind  79 ggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhl 155
                                       g+ r++++piaGT +rg++p ed++l+ e+l+d KeraEh m+vdl+rnd+++v+++gsv+v+e+++v +ys+v+h+
  gi|313125843|ref|YP_004036113.1| 329 GD-RVVSNPIAGTCKRGTSPVEDRRLAGEMLADGKERAEHTMLVDLARNDVRRVSEAGSVRVEEFMNVLKYSHVQHI 404
                                       77.************************************************************************** PP

                                       EEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEET. CS
                   Chorismate_bind 156 vstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkd. 231
                                        st++g+l+++++++d+ +a fP+g++tGaPk rameiid+lE ++RgvY+G vgy + +g+a++a+vIRta v++ 
  gi|313125843|ref|YP_004036113.1| 405 ESTVTGTLADECDSFDATRAAFPAGTLTGAPKVRAMEIIDDLELTPRGVYGGGVGYYSWSGDADFAIVIRTATVERr 481
                                       **************************************************************************666 PP

                                       ...TEEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 232 ...kelrlgaGaGIvadSdpeaEyeEtlaK 258
                                          + ++++aGaG+vadSdp+aEyeEt++K
  gi|313125843|ref|YP_004036113.1| 482 ggeDVISVRAGAGLVADSDPAAEYEETEQK 511
                                       88889***********************99 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0     5e-20   4.5e-16       2     142 .]      40     203 ..      39     203 .. 0.86
   2 ?    0.5   0.0      0.07   6.3e+02      89      99 ..     451     462 ..     357     471 .. 0.79

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 5e-20
                     Anth_synt_I_N   2 dltplsvylklaeee.hkflLeSaenegge................grySfigldpflelkskngevevegpegeel 61 
                                       + tpl++y++l+e++ + flLeSae+  ++                +rySf+g+dp +++++  + ++ve+  g+++
  gi|313125843|ref|YP_004036113.1|  40 TTTPLTAYAALTERSdYGFLLESAEKTASSdpagafapehvttdrhARYSFVGYDPDAVITVGPDGASVETLGGRAA 116
                                       579***********9*********9887778888888889999999***************9999999999777777 PP

                     Anth_synt_I_N  62 eeee.....pldalrellerfrsaedseptelpfvgGlvGylgYDlvreieklp..ksakddlnlpdarlilydtli 131
                                       ++ +     +ld lr  l ++  +  + ++  ++ gGlvG+l+Y++v  +  l     + +++++pda+++l+ +++
  gi|313125843|ref|YP_004036113.1| 117 RYVTpdggdVLDRLRGALPDLPRVGFPDDDRQRLRGGLVGFLAYEAVYDLW-LAevGVERPETDTPDAQFVLTTKTL 192
                                       777777788999999999999966555578888*************98885.332356788899************* PP

                     Anth_synt_I_N 132 vfDhkerrlyl 142
                                        fDh e++ +l
  gi|313125843|ref|YP_004036113.1| 193 SFDHAEETATL 203
                                       *****998876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.07
                     Anth_synt_I_N  89 p.fvgGlvGylg 99 
                                       + ++gG vGy++
  gi|313125843|ref|YP_004036113.1| 451 RgVYGGGVGYYS 462
                                       24899*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 3146.12
//
Query:       gi|313125844|ref|YP_004036114.1|  [L=215]
Description: phosphoribosylanthranilate isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-37  127.3   0.3    6.9e-37  127.1   0.3    1.0  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase
    0.00066   18.8   0.4     0.0036   16.4   0.4    1.8  1  FMN_dh    FMN-dependent dehydrogenase
     0.0029   17.7   0.1     0.0068   16.6   0.1    1.6  1  UPF0180   Uncharacterised protein family (UPF0180)
  ------ inclusion threshold ------
      0.011   15.1   0.7      0.042   13.2   0.3    2.0  2  TMP-TENI  Thiamine monophosphate synthase
      0.033   13.6   3.0      0.077   12.4   0.8    2.2  2  BtpA      BtpA family


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   0.3   1.9e-40   6.9e-37       1     193 [.       4     205 ..       4     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 1.9e-40
                                       TCE----SHHHHHHHHHHTSSEEEEE--T..TBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTEC CS
                              PRAI   1 akicgltrasdvkaavkagadelglifae..sskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgld 73 
                                       +kicg+t+ sd+ a+  agad++g+i ++   ++re s   a+el  ++ +   +  V++ ++++e  ++ + ++ d
  gi|313125844|ref|YP_004036114.1|   4 VKICGVTSESDLRAVERAGADAVGFIADVpvDTPRELSLDRAAELAAAAAPFltTTLVTMPETVSEAIEVGSRVKPD 80 
                                       69************************8752268*******99999888774335899******************** PP

                                       EEEE-CGG.-HHHHHHHHHHS-TTSEEEEEEE-S.SS--S-SSTT-SEEEEE....SSS-SSSXXXXGGGGTTSXX. CS
                              PRAI  74 vvQLHGdedeqeyeellktelpvikalkvaesvd.evkearradhvdllllD....sgaGGtGelldwsliskllks 145
                                       vvQ+HG+  + e+ +++++++  + a +v++  +  + ++  + +vd++++D    +gaGGtG++ dw+  +k  ++
  gi|313125844|ref|YP_004036114.1|  81 VVQIHGEF-DAEQFRAIRAGVDARIAAVVDA--EqPQRACDLDSAVDAIVVDsvsdKGAGGTGKTHDWEQTAKATAE 154
                                       ********.99999****9999999999988..5347777777888*****9999999***************9988 PP

                                       ..TTEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEE.TEEXHHHHHHHHH CS
                              PRAI 146 ..lkviLAGGLtpeNvaeaiklegvlgvDvssGVEtn.GvkDlekirkfvq 193
                                          +v+LAGGLtpeNv+ea+++ ++++vDv+sGVE++ GvkD + +r+fv 
  gi|313125844|ref|YP_004036114.1| 155 ldAPVVLAGGLTPENVTEAVETVNPFAVDVASGVESSgGVKDHDAVRAFVA 205
                                       99***********************************************96 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4     1e-06    0.0036     126     235 ..      12     175 ..       9     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHCTESEEEEESSTSS---BHHHHHCT--BSTT-T.G.TTGGGSTSGSCCTTH................. CS
                            FMN_dh 126 eellkraeaagykalvltvDtpvlgkRerdlrngfslppklklrnllqelakpewaaeal................. 185
                                       e+ l+ +e+ag++a+ +  D+pv+  Re  l+   +l  +  +  ++  ++ pe ++ea                  
  gi|313125844|ref|YP_004036114.1|  12 ESDLRAVERAGADAVGFIADVPVDTPRELSLDRAAELAAAAAPFLTTTLVTMPETVSEAIevgsrvkpdvvqihgef 88 
                                       667999*************************9999999998888888999999999998889999999999999999 PP

                                       ..........................................THHHHHHCCCHB-TC--HHHHHHHHHHHSSEEEEE CS
                            FMN_dh 186 ........................................kkasaaaefvgkqldpsltwddikwlreqtklplvvK 222
                                                                               +++s+++  +g    ++ +w++ ++ +++++ p+v+ 
  gi|313125844|ref|YP_004036114.1|  89 daeqfrairagvdariaavvdaeqpqracdldsavdaivvDSVSDKG--AG-GTGKTHDWEQTAKATAELDAPVVLA 162
                                       99999999999999999999999998888877666554332222222..22.2245669999999999999999999 PP

                                       EE-SHHHHHHHHH CS
                            FMN_dh 223 Gvltaedakrave 235
                                       G lt+e++ +ave
  gi|313125844|ref|YP_004036114.1| 163 GGLTPENVTEAVE 175
                                       9999999999987 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.9e-06    0.0068      24      76 ..     108     176 ..     105     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.9e-06
                           UPF0180  24 vdlet....eedaqsvdaiVv.....tG.....qdtnv..mgiedtetkapvInAsgktaeeIlqevee 76 
                                       vd e+    ++ +  vdaiVv     +G     ++++    +  ++e +apv+ A g+t+e++ + ve+
  gi|313125844|ref|YP_004036114.1| 108 VDAEQpqraCDLDSAVDAIVVdsvsdKGaggtgKTHDWeqTAKATAELDAPVVLAGGLTPENVTEAVET 176
                                       5555544444557789*****555551155555555553244555899*****************9985 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.12   4.3e+02     104     129 ..      10      35 ..       4      63 .. 0.68
   2 ?   13.2   0.3   1.2e-05     0.042     118     170 ..     124     176 ..      38     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.12
                          TMP-TENI 104 hsleeaeeaealgadYigvGpifpTd 129
                                        s+++++++e++gad +g+ +  p d
  gi|313125844|ref|YP_004036114.1|  10 TSESDLRAVERAGADAVGFIADVPVD 35 
                                       45566777888888888875555555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.2e-05
                          TMP-TENI 118 dYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitlenvaevlea 170
                                       d i+v ++         ++ ++e+ +++ ++l  Pvv  GG+t+env e++e+
  gi|313125844|ref|YP_004036114.1| 124 DAIVVDSVSDKGAGGTGKTHDWEQTAKATAELDAPVVLAGGLTPENVTEAVET 176
                                       666666665544444557889999************************99876 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.074   2.6e+02      32      47 ..      12      27 ..       9      52 .. 0.78
   2 ?   12.4   0.8   2.2e-05     0.077     168     251 ..     123     206 ..      87     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.074
                              BtpA 32 vkeakaleegGvDavi 47
                                      +++++a+e +G+Dav 
  gi|313125844|ref|YP_004036114.1| 12 ESDLRAVERAGADAVG 27
                                      68999********994 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.2e-05
                              BtpA 168 vergladavilsGk.atGgevdleelklaketvkvkvlvgsGvseenlekllsiadGvi..vgtsikkdGkianaiD 241
                                       v    +d+v   G   tG++ d e+  +a+  ++ +v+   G + en+++ +++ + +   v++ +   G +    D
  gi|313125844|ref|YP_004036114.1| 123 VDAIVVDSVSDKGAgGTGKTHDWEQTAKATAELDAPVVLAGGLTPENVTEAVETVNPFAvdVASGVESSGGV---KD 196
                                       2223333333344325889999999999999999********************998862357777777763...46 PP

                              BtpA 242 kervrkivel 251
                                       ++ vr++v  
  gi|313125844|ref|YP_004036114.1| 197 HDAVRAFVAN 206
                                       6666766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1377.26
//
Query:       gi|313125845|ref|YP_004036115.1|  [L=345]
Description: anthranilate phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-96  320.2   5.0    1.3e-95  319.8   5.0    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    5.7e-16   58.1   6.6    6.3e-16   58.0   2.6    2.3  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.057   13.1   0.0    1.9  1  DUF2717          Protein of unknown function (DUF2717)


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.8   5.0   2.2e-99   1.3e-95       2     252 ..      73     323 ..      72     324 .. 0.99

  Alignments for each domain:
  == domain 1  score: 319.8 bits;  conditional E-value: 2.2e-99
                                       TTBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEE CS
                   Glycos_transf_3   2 kdlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgf 78 
                                       ++lvD++gTGGd+  t+N+St++aiv+A+aG+ vakhgn svss+sGsaDvLe +g n+e +p  ve+++e++g+gf
  gi|313125845|ref|YP_004036115.1|  73 TPLVDTCGTGGDDYDTINVSTTSAIVAAGAGAAVAKHGNYSVSSSSGSADVLEVAGANVEAEPPAVEEAIERDGIGF 149
                                       579************************************************************************** PP

                                       EEHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHH CS
                   Glycos_transf_3  79 lfapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldev 155
                                       ++ap +h+amk v+++r+elg+rT+fn LGPL+npa +++q++gvy++el++ la +l+++ veralvvhg+G+de+
  gi|313125845|ref|YP_004036115.1| 150 MLAPVFHPAMKAVIGPRKELGMRTIFNALGPLTNPAGAQAQVVGVYDPELVPVLARALSHMSVERALVVHGSGMDEI 226
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTS CS
                   Glycos_transf_3 156 sllakttvaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagk 232
                                       +l+++t vae++ ++i+eyt++ped+gl++a  +a++gg+p+ena+ l+++ +g+ +  krd++l+nagaa++++g 
  gi|313125845|ref|YP_004036115.1| 227 ALHDETVVAEVHGDDIEEYTVTPEDIGLESAPVSAVAGGTPQENAADLRGIVTGEVTGPKRDIILANAGAAIYVSGL 303
                                       ***************************************************************************** PP

                                       SSSHHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 233 adslkegvakaeevidsGkA 252
                                       a+++ eg++ a+++idsG+A
  gi|313125845|ref|YP_004036115.1| 304 AETISEGAEAAANAIDSGAA 323
                                       *******************9 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   2.6     1e-19   6.3e-16       2      63 .]       5      65 ..       4      65 .. 0.96
   2 ?    1.6   0.1     0.043   2.6e+02      19      62 ..     271     320 ..     266     321 .. 0.70

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1e-19
                                      HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N  2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63
                                       +i++  +g +Lt++e+r+a + +++ ++t+aqi+A+L+Alr kGet+ Eia++a+ mr+++
  gi|313125845|ref|YP_004036115.1|  5 TYIERATEGTDLTQDEARNAAQLVFE-DATEAQIGALLTALRSKGETETEIAGFAQGMRDAA 65
                                      6999**********************.89******************************975 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.043
                                       HHHHHHHHTTSS-H....HHHHHHHHHHHHH-..--HHHHHHHHHHHHHH CS
                   Glycos_trans_3N  19 rfaihgilkgevtd....aqiaAfLmAlrlkG..etaeEiaalaeAmres 62 
                                       ++ ++gi++gevt     + +a   +A+++ G  et  E a++a   ++s
  gi|313125845|ref|YP_004036115.1| 271 AADLRGIVTGEVTGpkrdIILANAGAAIYVSGlaETISEGAEAAANAIDS 320
                                       55567888888776555577777778899999888988888888766665 PP

>> DUF2717  Protein of unknown function (DUF2717)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.6e-06     0.057      40      69 ..      40      69 ..       3      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.6e-06
                           DUF2717 40 lidalrkaGysesyiaGfldGlnlasevld 69
                                      l+ alr +G  e+ iaGf +G++ a+++++
  gi|313125845|ref|YP_004036115.1| 40 LLTALRSKGETETEIAGFAQGMRDAARTIE 69
                                      5689**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2213.93
//
Query:       gi|313125846|ref|YP_004036116.1|  [L=302]
Description: hypothetical protein Hbor_10810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2008.37
//
Query:       gi|313125847|ref|YP_004036117.1|  [L=113]
Description: hypothetical protein Hbor_10820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 668.48
//
Query:       gi|313125848|ref|YP_004036118.1|  [L=268]
Description: hypothetical protein Hbor_10830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0025   18.0   0.7     0.0025   18.0   0.7    1.8  3  DUF2104   Predicted membrane protein (DUF2104)


Domain annotation for each model (and alignments):
>> DUF2104  Predicted membrane protein (DUF2104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.61   1.1e+04      55      68 ..      53      66 ..      43      76 .. 0.52
   2 ?   -3.3   0.1      0.64   1.1e+04      64      73 ..     123     132 ..     116     138 .. 0.55
   3 !   18.0   0.7   1.4e-07    0.0025      16      93 ..     154     236 ..     147     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.61
                           DUF2104 55 lvlvpsyilitigl 68
                                      l+     + +++++
  gi|313125848|ref|YP_004036118.1| 53 LEIGTALLGYSVAA 66
                                      33333344444444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.64
                           DUF2104  64 itigllligl 73 
                                       ++ g++++g+
  gi|313125848|ref|YP_004036118.1| 123 LIAGCFILGF 132
                                       3344555554 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.4e-07
                           DUF2104  16 lGLlys..Ykkysepyvekkidkla..lvlaviGwllllnvsllvlvpsyilitiglll.iglvlgmRpGYGrietv 87 
                                       +G+ +s  Y+ y+e ++ek+ + ++  +vl + G +l+ ++s++vl++++ ++t++ +l i+ +   R G+    +v
  gi|313125848|ref|YP_004036118.1| 154 VGMILSdwYRLYREFFREKQYEEMSayMVLEIPGRFLVFAASYVVLLSTVGMLTLASFLmITQTEFARLGFEFEQLV 230
                                       67777666*************987533899******************99998887665155555679999888888 PP

                           DUF2104  88 iGiiva 93 
                                        G +v 
  gi|313125848|ref|YP_004036118.1| 231 AGAMVL 236
                                       888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1713.90
//
Query:       gi|313125849|ref|YP_004036119.1|  [L=94]
Description: hypothetical protein Hbor_10840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.56
# Mc/sec: 503.45
//
Query:       gi|313125850|ref|YP_004036120.1|  [L=665]
Description: histidine kinase/response regulator receiver [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-17   63.4   0.0    5.3e-17   62.3   0.0    1.5  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    3.4e-14   52.9   0.0      1e-13   51.4   0.0    1.8  1  Response_reg  Response regulator receiver domain
    1.5e-13   50.6  10.5    3.3e-13   49.4   1.3    3.3  3  HisKA         His Kinase A (phospho-acceptor) domain
    9.1e-10   39.3   0.0    2.7e-09   37.7   0.0    1.9  1  GAF           GAF domain
    1.9e-08   34.5   2.5    2.1e-08   34.4   0.3    2.2  2  PAS_4         PAS fold
    2.3e-07   31.2   0.6    3.3e-06   27.5   0.0    3.0  3  GAF_2         GAF domain
      2e-06   28.2   0.0    4.2e-06   27.1   0.0    1.6  1  GAF_3         GAF domain
     0.0018   18.2   0.1      0.005   16.8   0.1    1.7  1  HATPase_c_2   Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.038   14.0   0.1       0.12   12.3   0.0    1.9  2  PAS           PAS fold
      0.089   13.1   0.0       0.21   11.8   0.0    1.7  1  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   2.9e-20   5.3e-17       2     107 ..     531     656 ..     530     660 .. 0.80

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.9e-20
                                       HHHHHHHHHHHHHHHHHHH....................HSTTTEE..........EEEEEEEETEEEEEEEESSSS CS
                         HATPase_c   2 dekrLrqiisnlvdNavkf....................atkagei..........eveikaseddlvisveDnGiG 48 
                                       de+rLrq++ nl+ N+v++                    +                +v++++ +++  + veD+G+G
  gi|313125850|ref|YP_004036120.1| 531 DEPRLRQLLENLMRNSVEHgstsnqsnpghaadadaadsQ-----RqskkvergaeSVTVRVGDVEGGFYVEDDGPG 602
                                       89*****************998876666665555544441.....033333444445566655899*********** PP

                                       STTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  49 ipkedlkklfe.kfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrGttftft 107
                                       ip++++  +f+ +++      ++++gtGlGl+iv+++++ +g ++ v++  g+G +f ft
  gi|313125850|ref|YP_004036120.1| 603 IPPDERASVFDsSHT------TKTEGTGLGLAIVERIAKGHGWSVCVTEGTGGGARFEFT 656
                                       **********95444......589***************9*******9999******996 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   5.6e-17     1e-13       1     106 [.      13     120 ..      13     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 5.6e-17
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHH.ESEEEEESSCSSSEHHHHHHHHHHCTTTSEE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeek.vdlillDinmpgmdGlellkeireedpelpv 74 
                                       vl vd d + ++ +r+ l   +  + +v++a d++ ale+l+e++ v++i+   ++p+ +Gl +++++re +++lp 
  gi|313125850|ref|YP_004036120.1|  13 VLYVDGDSDYADRVRSSLVreSLPF-DVQTAPDAECALEHLRESDdVHCIVSEYQLPDTTGLAFYDRVREFSSDLPF 88 
                                       7889999999999999998434445.***************88777******************************* PP

                                       EEEESSTSHHHHHHHHHCTESEEEESSG-HHH CS
                      Response_reg  75 iiltahseeedavealkagaddflsKpfdpee 106
                                       i++ta ++ee a +a++ag+ d+l K    ++
  gi|313125850|ref|YP_004036120.1|  89 ILFTASGSEEIASDAVSAGVTDYLLKREGSDQ 120
                                       **************************977665 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.5      0.01        18      26      66 ..     258     295 ..     249     296 .. 0.84
   2 !   49.4   1.3   1.9e-16   3.3e-13       2      66 ..     433     492 ..     432     493 .. 0.97
   3 ?   -0.2   0.1      0.61   1.1e+03      49      60 ..     525     544 ..     497     549 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.01
                                       HHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA  26 aLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       +L+        l+e+ ++i  +++  +++ve +L+l+r+e 
  gi|313125850|ref|YP_004036120.1| 258 MLES---RERVLREMHDIIAACEKSFTEQVEAVLELGREEL 295
                                       5544...3467899************************985 PP

  == domain 2  score: 49.4 bits;  conditional E-value: 1.9e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       lg+f++ v+H+Lr+PL++ +g +e+ ++     e   e l+ +e+  +r++ l+e+lL+l+r e+
  gi|313125850|ref|YP_004036120.1| 433 LGQFASIVSHDLRNPLNVARGHIELAQN-----ECTNEHLDAVERAHDRMETLIENLLTLARSEE 492
                                       89************************99.....9****************************986 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.61
                                       H........HHHHHHHHHHH CS
                             HisKA  49 r........rldhlvedlLd 60 
                                       +        rl++l+e+l++
  gi|313125850|ref|YP_004036120.1| 525 DrtlladepRLRQLLENLMR 544
                                       14444455577777777754 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   1.5e-12   2.7e-09       5     132 ..     283     416 ..     279     417 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.5e-12
                                       HHHHHHHHHHHHHTESEEEEEEEEETTEEE........CEEEEECCEEEETTSHHHHHHHHHSSSEEESTGG..TST CS
                               GAF   5 lldtvveelrellgadrvalylpdydGlhy........dipqasrwlfmkngrgicgqvlatgqplvipdst..pdp 71 
                                        ++ v+e  re lg ++++l      G +y        d   ++  + ++ +++ c ++++  ++lv+ d++    +
  gi|313125850|ref|YP_004036120.1| 283 QVEAVLELGREELGTEYGTLSE--IRGDDYifevvatdDERIQAGDVVPVSVTN-CERCATAEKTLVLGDISqdSAG 356
                                       5678888889999999999954..566555555544433333444477777999.9**************6624555 PP

                                       THHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHHHHHHH CS
                               GAF  72 rfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvladqvava 132
                                       r  q    d  + +gi  +l++P+++d++++G+++++ ++p   +f+++e+ l+  +++ v+ +
  gi|313125850|ref|YP_004036120.1| 357 RTGQ----DESDDWGIACYLGAPVFVDDDVYGTFCFYGTTPrddQFSEWEVTLVDLMSRWVSYE 416
                                       5666....77899*************************777889**********9999998866 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.3   1.2e-11   2.1e-08       1     110 []     149     254 ..     149     254 .. 0.92
   2 ?   -1.9   0.1       2.2     4e+03      30      75 ..     457     504 ..     449     515 .. 0.48

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.2e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaa....aaelfgappeellGktlaellpeedaarleralrrvlegeepiefleell 73 
                                       +d++ da++++++d +v+ +N++      + +  +  e+ G++l+e lp+ +++ + + + +++e +ep++f+e++ 
  gi|313125850|ref|YP_004036120.1| 149 FDRMADAFFAVNADWHVTVLNEQaktvLTAAMDDDIGEIEGRHLWEELPDAVGTTFYEKYHEAMENQEPVSFEEYYE 225
                                       68899******************777644456678889*******99***************************999 PP

                             PAS_4  74 lpgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +   + ++e+r++P +       g+ v+ rDiTer+r
  gi|313125850|ref|YP_004036120.1| 226 P--LDTWFEVRVYPSET------GLSVYYRDITERYR 254
                                       9..***********966......************86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                             PAS_4  30 appeellGktlaellpee.daarleralrrvlegeepiefleelll.p 75 
                                       +++ e+++++l  +  ++   + l ++l  ++++ee+i ++e ++l +
  gi|313125850|ref|YP_004036120.1| 457 LAQNECTNEHLDAVERAHdRMETLIENLLTLARSEERIGDTELVNLaE 504
                                       444444444444322222244445555555555555555555555544 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.8e-09   3.3e-06       3     130 ..     279     410 ..     277     415 .. 0.81
   2 ?   -1.0   0.0       1.1     2e+03     110     138 .]     487     514 ..     484     514 .. 0.79
   3 ?   -0.8   0.0      0.99   1.8e+03      16      50 ..     585     617 ..     576     636 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-.GGG CS
                             GAF_2   3 dleelldlvldelve.lgaalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilnd.lee 76 
                                       +++e +++vl+  +e lg ++g + ++ +d++ ++++a   ++ + g+ +  p++   +++++   + ++l d +++
  gi|313125850|ref|YP_004036120.1| 279 SFTEQVEAVLELGREeLGTEYGTLSEIRGDDYiFEVVATDDERIQAGDVV--PVSVTNCERCATAEKTLVLGDiSQD 353
                                       66777899*****8879***********9999444555555555555555..66666699*************7777 PP

                                       -S-HHHHH.HHHHTT--EEEEEE-TTS---EEEEES........--HHHHHHHHHHH CS
                             GAF_2  77 dpdkkglp.aghaglrsflavPlisegrvvGvlnlyankppa..fdeedlelLeela 130
                                       ++ + g+   ++ g++  l+ P++ ++ v+G +++y++ p++  f+e +++l+++++
  gi|313125850|ref|YP_004036120.1| 354 SAGRTGQDeSDDWGIACYLGAPVFVDDDVYGTFCFYGTTPRDdqFSEWEVTLVDLMS 410
                                       777777777888888899*****99878*******877777777***9999999886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                       ES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2 110 lyankppafdeedlelLeelaeqiaiaie 138
                                       l a  +++  +++l  L elaeq++  +e
  gi|313125850|ref|YP_004036120.1| 487 L-ARSEERIGDTELVNLAELAEQCWETVE 514
                                       5.56677788999999*********8765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.99
                                       HHSS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S CS
                             GAF_2  16 velg.aalgyillvdddgglrlaawgeaeeefgaal 50 
                                       v++g ++ g+++++d ++g  + +  +a  ++++++
  gi|313125850|ref|YP_004036120.1| 585 VRVGdVEGGFYVEDD-GPG--IPPDERASVFDSSHT 617
                                       567669999988866.454..443333333333333 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   2.3e-09   4.2e-06       3     129 .]     281     419 ..     279     419 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.3e-09
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesld.edsalarralssgevvse......... 69 
                                        e++e++l+l+ + lg+e+g l + ++d   + v+a  d+  +   +++   +++ r a +++  v +         
  gi|313125850|ref|YP_004036120.1| 281 TEQVEAVLELGREELGTEYGTLSEIRGDDYIFEVVATDDERIQAGDVVPvSVTNCERCATAEKTLVLGdisqdsagr 357
                                       5899********************************99888888887777888888888888877666666444443 PP

                             GAF_3  70 psfaeedglpdraalavPLvagrqviGvlalastkpra..fdaedlelleslArqiataier 129
                                       ++ +e d +  +++l +P+ + + v+G+ +++ t pr+  f++ ++ l++ ++r+++ +++r
  gi|313125850|ref|YP_004036120.1| 358 TGQDESDDWGIACYLGAPVFVDDDVYGTFCFYGTTPRDdqFSEWEVTLVDLMSRWVSYELQR 419
                                       222445779************99********999888667*****************99987 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   2.8e-06     0.005      32     110 ..     535     635 ..     499     649 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                       HATPase_c_2  32 irlaveEactNavehayleapegpvevr.............lesdeealtve.........vaDsGpgfdpetlpdp 86 
                                       +r  +e ++ N veh+  ++++ p + +             +e+++e++tv+         v+D+Gpg +p +++  
  gi|313125850|ref|YP_004036120.1| 535 LRQLLENLMRNSVEHGSTSNQSNPGHAAdadaadsqrqskkVERGAESVTVRvgdveggfyVEDDGPGIPPDERASV 611
                                       5566677899***********99998888888888889999999999999998999999999999999888888888 PP

                       HATPase_c_2  87 teeepkeslkegGrGlalikglvD 110
                                          + +++ +  G+Gla++++++ 
  gi|313125850|ref|YP_004036120.1| 612 FDSSHTTKTEGTGLGLAIVERIAK 635
                                       8888899************99875 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     7e-05      0.12       2      93 ..     144     235 ..     143     243 .. 0.90
   2 ?   -3.7   0.0       6.7   1.2e+04      57      80 ..     504     527 ..     484     537 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH....HHHHHHHHHHHHTT-ECC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda....elaelleqlleqgeesra 74 
                                       +++a+++ ++d+ f+v++d  ++  N+ a + l  + ++ +g+   + ++ee ++    +++e++++++e++e+ + 
  gi|313125850|ref|YP_004036120.1| 144 ERQAVFDRMADAFFAVNADWHVTVLNEQAKTVLTAAMDDDIGEIEGRHLWEELPDavgtTFYEKYHEAMENQEPVSF 220
                                       689999***************************************999999999999*****************999 PP

                                       CCEEEECTTSSEEEEEEEE CS
                               PAS  75 geisfklrdgrpihlevra 93 
                                       +e  ++l     +++evr+
  gi|313125850|ref|YP_004036120.1| 221 EEYYEPL----DTWFEVRV 235
                                       9987777....66666665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.7
                                       HHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS  57 elaelleqlleqgeesrageisfk 80 
                                       elae+ ++  e+g+ s ++e++++
  gi|313125850|ref|YP_004036120.1| 504 ELAEQCWETVETGTASLDVETDRT 527
                                       578888888888888888777665 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.21      18     111 .]      37     135 ..      23     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                        OKR_DC_1_N  18 fevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlreidgfie 91 
                                       f+v ++ + + +l+ +++  ++ ++v +++       ++ d +re   dlP  l++ + ++e ++  v + ++ ++ 
  gi|313125850|ref|YP_004036120.1|  37 FDVQTAPDAECALEHLRESDDVHCIVSEYQlpdTTGLAFYDRVREFSSDLPFILFTASGSEEIASDAVSAGVTDYLL 113
                                       667777777778899999***********99999999*******************988999999999999999999 PP

                        OKR_DC_1_N  92 lledtpef..iarqieaaakkY 111
                                         e++ +f  +a +i  a+++Y
  gi|313125850|ref|YP_004036120.1| 114 KREGSDQFevLADRIGDAVCSY 135
                                       8887776633688888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (665 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.81u 0.36s 00:00:01.17 Elapsed: 00:00:00.54
# Mc/sec: 3676.86
//
Query:       gi|313125851|ref|YP_004036121.1|  [L=58]
Description: hypothetical protein Hbor_10860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.074   13.1   0.1      0.084   12.9   0.1    1.0  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.7e-06     0.084      12      50 ..      14      52 ..       5      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-06
                      MMR_HSR1_Xtn 12 ltkldeetvkkilkeykihnaevliredvtvDdlidvie 50
                                      +++ ++++ + i +    h+ +v++++dv++D lid + 
  gi|313125851|ref|YP_004036121.1| 14 QQSNEDDDAEGITTHEHEHEGSVTVESDVSTDALIDRLG 52
                                      444566899999999999******************874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.38s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 334.09
//
Query:       gi|313125852|ref|YP_004036122.1|  [L=372]
Description: DNA modification methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-33  116.3   0.0    2.3e-33  115.9   0.0    1.1  1  N6_N4_Mtase      DNA methylase
      0.005   17.5   0.1        1.2    9.9   0.0    3.2  3  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.086   12.5   0.0        3.5    7.2   0.0    2.2  2  UPF0020          Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.0   3.8e-37   2.3e-33       1     227 [.      23     293 ..      23     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 3.8e-37
                                       EEEEEE--SSSSSCS.................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT.. CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy............endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk.. 63 
                                       v l+vt+pPY +++ +                + ++e  +e++++ l  v++e+ rvL ++g+++in++d + +   
  gi|313125852|ref|YP_004036122.1|  23 VELVVTSPPYPMVEMWddlfseltdeagPALRDGDGEAAFEAMHSALDDVWAEISRVLVPGGIACINVGDATRTVgd 99 
                                       689************999999998877766666777788*********************************999** PP

                                       ........HHHHHHHHHTT-EEEEEEEEEEES.........SSTTTSTCCS-B--EEEEEEEESSTT-..---GGGS CS
                       N6_N4_Mtase  64 ........elkaladeifggffllnvivwkkp.........nsmpesnkdrltsthEyilvfsknkkyllkfnldai 123
                                                ++  a  ++g f  l ++ w+kp         ++m  +n+ ++t +hEy+lvf+ + +          
  gi|313125852|ref|YP_004036122.1| 100 sfrvypnhARVTDAFVELG-FEPLPDVLWRKPtnsaakfmgSGMIPPNA-YVTLEHEYVLVFRNGTDS--------- 165
                                       ******7777777777777.************99999999779999998.******************......... PP

                                       SBSS-HHHHHHHHHHCHHHCC-B--BSEE..........................E-SCCCTTSTTS-CHH----SS CS
                       N6_N4_Mtase 124 kvpyeekdklekrgaytskkkgkkiediW..........................dlseiqsnekkskgdtkkkHpa 174
                                          ++  + +++++ay+ ++++ +++d+W                          d  ++++ + +s  +++++ +a
  gi|313125852|ref|YP_004036122.1| 166 -RAFDPGETRRYESAYFWEERNAWFSDVWtdvagtgqevaartrahtgsgdgeiaDGGNVYDLDAESGDELRER-TA 240
                                       .555555556666669999******************9999999999999999998888888888888888999.** PP

                                       ---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHH CS
                       N6_N4_Mtase 175 qkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyve 227
                                        +P +++ rl+++++  gd+vlDpF+G+GtT  aa+  gr+++G+e e+ +v+
  gi|313125852|ref|YP_004036122.1| 241 AFPFEIPYRLVNMYSVYGDTVLDPFFGTGTTSLAAMVAGRDSVGYELEDAFVD 293
                                       ************************************************99887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.078   4.6e+02      46      83 ..       6      44 ..       2      47 .. 0.81
   2 !    9.9   0.0   0.00019       1.2      74      95 ..      65      87 ..      58      88 .. 0.79
   3 ?    1.8   0.0     0.063   3.7e+02       6      52 ..     267     314 ..     262     344 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.078
                                      EETTEECCCT.SS-TT-EEEEEEES-CCC-CCHHHHHHH CS
                   Methyltransf_11 46 efvvadaekl.pfednsfDlvvssevlhhvedpekalke 83
                                      ++vv+da+++  ++d+ + lvv s     ve ++++++e
  gi|313125852|ref|YP_004036122.1|  6 RVVVGDARTMsDIADDAVELVVTSPPYPMVEMWDDLFSE 44
                                      679******988*********999877777777777776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00019
                                      -.CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11 74 v.edpekalkeiaRvLkpgGllv 95
                                      +   ++++++ei RvL pgG+ +
  gi|313125852|ref|YP_004036122.1| 65 MhSALDDVWAEISRVLVPGGIAC 87
                                      4446899*************986 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.063
                                       TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEEC CS
                   Methyltransf_11   6 GtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvada 52 
                                       GtG  + a + +g++ vg +l ++++++  ++a +++  + e+v+a++
  gi|313125852|ref|YP_004036122.1| 267 GTGTTSLAAMVAGRDSVGYELEDAFVDAFDARATGAPTlSREVVEARL 314
                                       555555555555899999999999999998888888776334444444 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.01        62     107     159 ..       7      56 ..       1      77 [. 0.70
   2 ?    7.2   0.0   0.00059       3.5      29      54 ..     258     283 ..     238     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.01
                                       EEE--GGG--.STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT. CS
                           UPF0020 107 fsqadaakLr.lkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrgg 159
                                       +++ da+ +   +++ v+++vt pPY       ++ ++L+se+ +e+   lr g
  gi|313125852|ref|YP_004036122.1|   7 VVVGDARTMSdIADDAVELVVTSPPYP----MVEMWDDLFSELTDEAGPALRDG 56 
                                       5667788777766779**********5....35666666666666666666664 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00059
                                       TS-EEETT-TTSHHHHHHHHHHTT-- CS
                           UPF0020  29 gepllDPmCGsGtilIEaallgania 54 
                                       g++ lDP+ G+Gt  + a + g++ +
  gi|313125852|ref|YP_004036122.1| 258 GDTVLDPFFGTGTTSLAAMVAGRDSV 283
                                       7899*********9998877777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2129.90
//
Query:       gi|313125853|ref|YP_004036123.1|  [L=435]
Description: cytosine deaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-67  226.5   1.7    6.5e-67  226.3   1.7    1.0  1  Amidohydro_1  Amidohydrolase family
    1.6e-15   57.6   1.0    1.6e-15   57.6   1.0    1.7  2  Amidohydro_3  Amidohydrolase family
    0.00032   20.1   0.0     0.0005   19.5   0.0    1.3  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.3   1.7   1.1e-70   6.5e-67       2     344 .]      51     405 ..      50     405 .. 0.96

  Alignments for each domain:
  == domain 1  score: 226.3 bits;  conditional E-value: 1.1e-70
                                       EEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHH CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgie 64 
                                       ++PGlI  HvH  qsl+rg+     l+dwl          ++ +  ++a+e g  ++l+sGtttv+d+  +   ++e
  gi|313125853|ref|YP_004036123.1|  51 LIPGLIGGHVHSVQSLGRGIaddtALLDWLfdhvlpmeasLDADGMRAAAELGYLELLESGTTTVIDHLSVS--HAE 125
                                       89********************************************************************86..9** PP

                                       HHHHHHHTSSSEEEEEEESSEGGS.......GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHH CS
                      Amidohydro_1  65 alleaaeelplglrilggkvsldr.......gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeel 134
                                         +eaa el  g+r  +gkv++d+       ++++  +a++e+l++      +g +d+++  a++p++a+++s+e l
  gi|313125853|ref|YP_004036123.1| 126 TAFEAAGEL--GIRGRLGKVMMDQrapdgliEDTDEALAETERLLQTY----HGSHDDRIRYAVTPRFAVSCSEECL 196
                                       ********8..********************99999999999999999....************************* PP

                                       HHHHHHHHHH.TTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHH CS
                      Amidohydro_1 135 kealkeakkr.dlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerl 210
                                       + a ++a+ + d+ +++Ha+e+  e+e +e++ g   ++    e+++++gl +e  ++lah+vh t +e ell+e  
  gi|313125853|ref|YP_004036123.1| 197 RGARELADTYdDVTIHTHASENHDEIETVEEDTG---MR--NIEWLHEVGLTGE-DVVLAHCVHTTEAERELLAET- 266
                                       **********************************...55..*************.*********************. PP

                                       HHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHH.HH CS
                      Amidohydro_1 211 keagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslke.al 286
                                        +++v+ cp+sn++l+sg++++ + ld+Gv v+lg Dg  ++n+l+ ++e+r+a +lq++ +    + + ++++ ++
  gi|313125853|ref|YP_004036123.1| 267 -GTNVTYCPSSNMKLASGIAPIVDYLDRGVTVALGNDGPPCNNTLDPFTEMRQASLLQKVEHL---DPKATPAQvIF 339
                                       .******************************************************99998888...56667888799 PP

                                       HHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT.........CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 287 rmaTingAkalglddkvGsievGkdADlvvvdldi.........laafvglkkdgnvkkvivkGklv 344
                                       +maTingAka g++ +vG++ +G +AD+v++d+di         l+++v+ ++   v  ++v+G++v
  gi|313125853|ref|YP_004036123.1| 340 EMATINGAKAAGFE-DVGELREGWKADIVALDTDItratplhdaLSHLVFGAHGDDVEFTMVDGEVV 405
                                       *************5.******************66667779999********************997 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.23   1.4e+03       9      21 ..      50      62 ..      49      74 .. 0.80
   2 !   57.6   1.0   2.6e-19   1.6e-15     278     473 .]     208     406 ..     143     406 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.23
                      Amidohydro_3  9 lvlPGFvDsHtHl 21
                                      l++PG++  H H 
  gi|313125853|ref|YP_004036123.1| 50 LLIPGLIGGHVHS 62
                                      689*********3 PP

  == domain 2  score: 57.6 bits;  conditional E-value: 2.6e-19
                      Amidohydro_3 278 dvaihaigdaavddvldafeaa........aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedell 345
                                       dv ih++  + +d  ++++e+          ++ g+++    l+h+  +te+++e +a+ +     +p +n      
  gi|313125853|ref|YP_004036123.1| 208 DVTIHTHASENHD-EIETVEEDtgmrniewLHEVGLTGEDvVLAHCVHTTEAERELLAETGTNVTYCPSSNM----- 278
                                       6777777777777.4444444445532333233333333367777777799999999999999999999999..... PP

                      Amidohydro_3 346 dsrlgperargstpvkellnagvkvalgsD.apv.gpfdpwprigaavmrktrrggevlrpdeelsleealalyTrg 420
                                             + a+g++p+   l+ gv+valg+D +p+ +++dp+ +++ a  +++++      + +  + + ++ + T +
  gi|313125853|ref|YP_004036123.1| 279 ------KLASGIAPIVDYLDRGVTVALGNDgPPCnNTLDPFTEMRQASLLQKVEHL----DPKATPAQVIFEMATIN 345
                                       ......889*********************97773689**************9775....88899************ PP

                      Amidohydro_3 421 pAkalgledrkGtLevGadADlvvldadpldvdppelaear.........vrltvvdGrvvy 473
                                       +Aka g ed  G L++G +AD+v ld+d+ +++p ++a            v+ t+vdG+vvy
  gi|313125853|ref|YP_004036123.1| 346 GAKAAGFEDV-GELREGWKADIVALDTDITRATPLHDALSHlvfgahgddVEFTMVDGEVVY 406
                                       *********9.**********************97555555********************9 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   8.4e-08    0.0005     220     285 ..     251     310 ..     233     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.4e-08
                                       E-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-S CS
                       A_deaminase 220 HGvrlrkdpvLqyllalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfgtt 285
                                       H v++ ++++  +lla+  + ++ cP+SN++l    +    P+ ++l+rg+ v+l+ D P   +t 
  gi|313125853|ref|YP_004036123.1| 251 HCVHTTEAER--ELLAETGTNVTYCPSSNMKL----ASGIAPIVDYLDRGVTVALGNDGPPCNNTL 310
                                       6666665553..789999**************....77789******************9987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2507.45
//
Query:       gi|313125854|ref|YP_004036124.1|  [L=497]
Description: hypothetical protein Hbor_10890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2953.09
//
Query:       gi|313125855|ref|YP_004036125.1|  [L=92]
Description: hypothetical protein Hbor_10900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0038   17.6   0.4      0.006   17.0   0.4    1.4  1  zf-C2H2       Zinc finger, C2H2 type
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.025   14.5   0.0    1.5  1  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
      0.016   15.1   0.1       0.03   14.2   0.1    1.4  1  zf-C2HC_2     zinc-finger of a C2HC-type
       0.02   15.1   0.0      0.025   14.7   0.0    1.2  1  BRCC36_C      BRCC36 C-terminal helical domain
      0.035   14.1   2.9      0.057   13.4   2.9    1.3  1  DUF1201       Protein of unknown function (DUF1201)
      0.089   12.8   0.3        9.6    6.3   0.0    2.1  2  DUF2116       Uncharacterized protein containing a Zn-ribbon 


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4     2e-06     0.006       1      23 []      19      42 ..      19      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                                      EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2  1 ykCpdCgksFkrksnLkrHirt.H 23
                                      ++C +Cg+ F+ + +L+ H+ + H
  gi|313125855|ref|YP_004036125.1| 19 HTCRVCGRAFPESRLLVLHRGVrH 42
                                      79*****************87766 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   8.4e-06     0.025       5      21 ..      19      36 ..      14      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.4e-06
                      zf-dskA_traR  5 s.CeeCGEpIpeaRlral 21
                                      + C +CG   pe Rl +l
  gi|313125855|ref|YP_004036125.1| 19 HtCRVCGRAFPESRLLVL 36
                                      36************9876 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   9.9e-06      0.03       4      18 ..      20      34 ..      19      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.9e-06
                         zf-C2HC_2  4 pCpkCgRsFnpdrle 18
                                       C+ CgR F ++rl 
  gi|313125855|ref|YP_004036125.1| 20 TCRVCGRAFPESRLL 34
                                      6************95 PP

>> BRCC36_C  BRCC36 C-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   8.5e-06     0.025       3      28 ..      37      62 ..      35      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.5e-06
                          BRCC36_C  3 eslveLpeiLfqEEreayekalrsqe 28
                                       + v+ p++L++EE+eay++a+r++e
  gi|313125855|ref|YP_004036125.1| 37 HRGVRHPSVLTGEEKEAYREAYREEE 62
                                      6668889***************9665 PP

>> DUF1201  Protein of unknown function (DUF1201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.9   1.9e-05     0.057       5      30 ..      65      90 ..      63      92 .] 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                           DUF1201  5 lrsylllafGfliclflfclvvfiwf 30
                                      +rs+ + afG l+ l++  l ++iwf
  gi|313125855|ref|YP_004036125.1| 65 IRSFRIRAFGVLVLLYFGYLFMYIWF 90
                                      69***********************9 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0092        27       6      16 ..      21      31 ..      17      35 .. 0.81
   2 ?    6.3   0.0    0.0032       9.6      25      56 ..      55      86 ..      51      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0092
                           DUF2116  6 CivCGkaIpld 16
                                      C vCG a p+ 
  gi|313125855|ref|YP_004036125.1| 21 CRVCGRAFPES 31
                                      *******9986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0032
                           DUF2116 25 qeeyekkrkkvarsqqilfgililllavvlvl 56
                                      +e+y+++ + ++ +++  fg+l+ll   +l++
  gi|313125855|ref|YP_004036125.1| 55 REAYREEEREIRSFRIRAFGVLVLLYFGYLFM 86
                                      899*******************9976666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 573.74
//
Query:       gi|313125856|ref|YP_004036126.1|  [L=363]
Description: fe2+ transport protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-06   28.0   0.0    9.5e-05   22.6   0.0    2.4  2  Iron_transport  Fe2+ transport protein
  ------ inclusion threshold ------
      0.054   14.0   0.0       0.23   11.9   0.0    2.1  2  MG2             MG2 domain


Domain annotation for each model (and alignments):
>> Iron_transport  Fe2+ transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.1e-08   9.5e-05      69     119 ..     122     172 ..      92     202 .. 0.82
   2 ?    2.9   0.0     0.012   1.1e+02      80     132 ..     300     350 ..     280     360 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-08
                                       EEEEEEETT----EEEE-EEEEETTEEEEEEEE--T-SEEEEEEEEEE--- CS
                    Iron_transport  69 vkykltkkksgeaksgtlmpmvasDgphYganvklkgvgkYkltleieppe 119
                                       v+ ++t+++s  +++     + ++ g hYg+n kl+g g+Y+++++i   +
  gi|313125856|ref|YP_004036126.1| 122 VTIEVTRNGSAVTEEIAYPMLSQKMGLHYGSNYKLDGEGEYEVHVRIGGVS 172
                                       7888898888887777777778899********************996554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.012
                                       --EEEE-EE.EEETTEEEEEEEE--T-SEEEEEEEEEE---TTT-EEE-STTTS CS
                    Iron_transport  80 eaksgtlmp.mvasDgphYganvklkgvgkYkltleieppekkefgrHvdketg 132
                                       ++ + +l++ +  + g hYga v+   +g+ +l+++++ p +  ++rH   et+
  gi|313125856|ref|YP_004036126.1| 300 TVSEMDLTQtLDPELGYHYGATVESVAPGD-ELRVSVATPPQ--IARHDGYETA 350
                                       4445555552455669********888876.88888888877..8899888886 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.6e-05      0.23       6      80 ..      90     166 ..      86     193 .. 0.76
   2 ?   -3.7   0.0         2   1.8e+04       9      18 ..     293     302 ..     290     310 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                                       ES-SEE-TT-EEEEEEEEES.TTCSB---.EEEEEEEE-TTSSEEEEEEE..EE-CTTE.EEEEEE--TT--SEEEE CS
                               MG2   6 tDRglYrPgetVslkallrd.etlqglak.lplkltirdpdgkevkelpl..atdetgg.aesefalpeaaklGeys 77 
                                       + +++ r+ + V+l + l d et++ l++   +++++++ ++ +++e      +++ g+ + s+++l      Gey+
  gi|313125856|ref|YP_004036126.1|  90 FSKTVVRADDSVHLMVTLWDaETGTVLPRdSGVTIEVTRNGSAVTEEIAYpmLSQKMGLhYGSNYKLDG---EGEYE 163
                                       5699**************99888888888899***********99998775455555554555566654...46666 PP

                                       EEE CS
                               MG2  78 vel 80 
                                       v +
  gi|313125856|ref|YP_004036126.1| 164 VHV 166
                                       666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2
                                       SEE-TT-EEE CS
                               MG2   9 glYrPgetVs 18 
                                       +l r getVs
  gi|313125856|ref|YP_004036126.1| 293 TLSRGGETVS 302
                                       6667788886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2416.72
//
Query:       gi|313125857|ref|YP_004036127.1|  [L=277]
Description: hypothetical protein Hbor_10920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.17   10.6   0.0        0.2   10.4   0.0    1.1  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)


Domain annotation for each model (and alignments):
>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   1.1e-05       0.2      51      94 ..      95     140 ..      70     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 1.1e-05
                                       HHHHHHH..HHHHHHHS.TTS-EEEE-SSS-HHHHHHHHHHHHHHT CS
                      Cas_Cas02710  51 llelykk..ikevlekaleeeevivDlTgGtkeMtaglalagillr 94 
                                       + ++y+   + + ++ a+ +++v v++++Gt   ++g+a+a +++ 
  gi|313125857|ref|YP_004036127.1|  95 IHNVYDVmgVTTTIAAAHDDDQVFVNISSGTNVAAVGAAIACMTTA 140
                                       444554300333444447**********************998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2000.86
//
Query:       gi|313125858|ref|YP_004036128.1|  [L=78]
Description: hypothetical protein Hbor_10930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-17   63.2   0.1    2.4e-17   62.9   0.1    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.1   1.4e-21   2.4e-17       8      72 ..       5      65 ..       2      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.4e-21
                            HalOD1  8 aVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeie 72
                                      ++v+ va++e+v +te++pL +aiDpdAL +Lf++    ++ +   ++F+y+gy++++++dg ++
  gi|313125858|ref|YP_004036128.1|  5 SIVSLVAELENVGVTEIPPLASAIDPDALVTLFDK----PNASPSVLEFDYAGYRIVIKGDGNVH 65
                                      699********************************....6677799****************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 500.06
//
Query:       gi|313125859|ref|YP_004036129.1|  [L=751]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-42  144.9  54.2    8.1e-42  143.0  20.6    4.6  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    1.6e-10   41.1  16.2      2e-06   28.0   0.2    5.2  5  HAMP             HAMP domain
    1.2e-06   28.6  25.4    0.00046   20.2   3.4    4.7  4  DUF1664          Protein of unknown function (DUF1664)
    1.7e-05   25.0  33.6      0.039   14.2   1.4    6.6  6  DUF948           Bacterial protein of unknown function (DUF94
    0.00016   21.7  22.4      0.012   15.7   4.3    4.2  4  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    0.00058   20.1  22.5       0.75   10.1   2.9    5.7  4  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0035   17.8   0.5     0.0035   17.8   0.5    4.2  3  DUF1843          Domain of unknown function (DUF1843)
     0.0055   15.7   2.1     0.0055   15.7   2.1    3.3  4  IFT57            Intra-flagellar transport protein 57
     0.0089   14.7  24.5       0.41    9.2   7.8    2.9  2  AAA_13           AAA domain
     0.0098   16.1   0.6     0.0098   16.1   0.6    3.9  3  KxDL             Uncharacterized conserved protein
  ------ inclusion threshold ------
      0.012   15.7   4.2       0.68   10.1   0.5    2.9  2  Importin_rep_6   Importin repeat 6
      0.029   14.4   0.2         14    5.7   0.0    3.3  2  Bcr-Abl_Oligo    Bcr-Abl oncoprotein oligomerisation domain
      0.058   12.7  17.6      0.046   13.0   4.6    3.5  3  CorA             CorA-like Mg2+ transporter protein
      0.068   12.3  10.5       0.36    9.9   0.7    2.6  2  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.072   13.7   8.4       0.16   12.5   1.5    3.4  2  ING              Inhibitor of growth proteins N-terminal hist
      0.094   12.9  16.2        1.1    9.5   0.9    4.2  3  Fib_alpha        Fibrinogen alpha/beta chain family
        0.1   12.3   1.2       0.31   10.8   0.0    2.2  2  TetR             Bacterial transcriptional repressor
       0.17   11.2  36.8      0.031   13.6   7.6    4.7  5  DUF3450          Protein of unknown function (DUF3450)
       0.17   11.3   3.6       0.34   10.3   1.0    2.7  2  IMD              IRSp53/MIM homology domain
       0.21   11.4   1.0        7.6    6.4   0.3    3.6  2  DASH_Dam1        DASH complex subunit Dam1
       0.24   10.5  18.6       0.55    9.3   4.3    4.2  3  RmuC             RmuC family
       0.27   10.8  11.3        4.1    6.9   0.4    4.3  4  Fzo_mitofusin    fzo-like conserved region
       0.28   11.0   4.2        1.3    8.9   0.2    3.3  3  DUF1652          Protein of unknown function (DUF1652)
       0.54    9.9   4.8          1    9.0   1.7    2.4  2  BAR_3            BAR domain of APPL family
       0.78    8.2   5.6       0.22   10.0   0.4    2.4  3  Corona_S2        Coronavirus S2 glycoprotein
       0.84    9.8  11.6        2.9    8.1   0.6    3.9  3  CREPT            Cell-cycle alteration and expression-elevate
        1.4    9.2  29.5      0.042   14.1   1.7    5.0  5  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.6    8.8  36.1       0.45   10.5   5.8    5.1  4  Laminin_II       Laminin Domain II
        2.3    7.7  30.4      0.075   12.6   4.7    3.9  4  Filament         Intermediate filament protein
        3.3    7.9  12.6         22    5.2   0.0    4.3  4  COG5             Golgi transport complex subunit 5
        5.3    7.5  12.3         43    4.6   0.1    4.7  4  Syntaxin_2       Syntaxin-like protein
        5.5    7.6  28.3          2    9.0   0.6    5.0  4  Syntaxin-6_N     Syntaxin 6, N-terminal
        5.6    6.9   5.3        2.6    8.0   0.3    2.9  4  DUF1759          Protein of unknown function (DUF1759)
        8.1    5.9  19.5        2.5    7.5   0.6    4.7  4  DegS             Sensor protein DegS
        8.2    6.2  32.3       0.33   10.7   1.4    4.2  4  ERM              Ezrin/radixin/moesin family
          9    6.2  15.3        2.8    7.8   1.4    4.5  6  Sec34            Sec34-like family
        9.2    6.3  13.3       0.54   10.2   1.1    3.7  3  Serine_rich      Serine rich protein interaction domain
        9.3    6.3  21.3         10    6.1   3.4    4.3  4  GldM_N           GldM N-terminal domain


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.7       0.3   1.4e+02      63     124 ..      36      93 ..      34     128 .. 0.70
   2 !   14.4  10.2   5.1e-05     0.024      75     154 ..     409     488 ..     394     498 .. 0.75
   3 !  143.0  20.6   1.7e-44   8.1e-42       7     171 ..     505     673 ..     489     674 .. 0.90
   4 ?    1.7   1.7      0.41     2e+02     131     168 ..     668     705 ..     662     710 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.3
                                       TCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHH CS
                         MCPsignal  63 AGeqGrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselve 124
                                       AG +G  ++  A+E  + A+   qaa e ea+    +++ ++  + l++++ r ++g++ v+
  gi|313125859|ref|YP_004036129.1|  36 AGVAGVQYSMTASELNEDARANLQAAAEREAIQ---VEQWEQERKRLTSVVAR-DTGVNSVK 93 
                                       8999999*********************88876...34444444444444433.34444332 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                       dEV +  +r+   + ++++l++++ +  +++ e+ +e+ + +++ s+ +++  ++l++++++v++++++++ei++++
  gi|313125859|ref|YP_004036129.1| 409 DEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIEEISSSA 485
                                       67777777787777888888888877777777777777777777777777777888888888888888888888777 PP

                                       HHH CS
                         MCPsignal 152 eeq 154
                                       +e+
  gi|313125859|ref|YP_004036129.1| 486 NEL 488
                                       775 PP

  == domain 3  score: 143.0 bits;  conditional E-value: 1.7e-44
                                       HHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHH CS
                         MCPsignal   7 aseeAeeg....gkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrk 79 
                                       a e+A  g     +e + +v+++++++++  ei +i++Vi+eia+QT +LALNA iEAARAGe+G+GFaVV +EV++
  gi|313125859|ref|YP_004036129.1| 505 AAENALGGiddiREETERTVQEVHKLDEQLGEIGEIVDVITEIAEQTDILALNANIEAARAGEAGEGFAVVSNEVKQ 581
                                       44444444433366777888888888888************************************************ PP

                                       HHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  80 LAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsa 156
                                       LA++++ +a +i+ali+ei+ + +++v s+e  r++v+ g++ v+e+ ++l  ive+v++ a + +ei  a+++q+ 
  gi|313125859|ref|YP_004036129.1| 582 LAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSLGGIVERVEDTAVSAKEIDNATADQAD 658
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHH CS
                         MCPsignal 157 sieevnqaveevakv 171
                                       s++ev +  +e+a +
  gi|313125859|ref|YP_004036129.1| 659 SSQEVLSMTDEIAGI 673
                                       *****9988888765 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 131 keiveavaevadlvqeiaaaseeqsasieevnqaveev 168
                                        ei+   +e +++ q ++aa+e+q+a++ +v++ ++ +
  gi|313125859|ref|YP_004036129.1| 668 DEIAGISEETTAEAQTVSAAAEQQTAAVGDVTNELSTL 705
                                       57788888888899999999999999999888777665 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.2   4.3e-09     2e-06       6      52 ..     317     363 ..     312     364 .. 0.89
   2 !   16.2   0.6   2.1e-05      0.01      15      53 .]     374     413 ..     373     413 .. 0.92
   3 ?    5.1   0.1     0.063        30      12      48 ..     445     482 ..     444     493 .. 0.71
   4 ?   -1.8   0.2       9.1   4.3e+03      10      38 ..     537     569 ..     532     570 .. 0.65
   5 ?   -1.5   0.0       7.2   3.4e+03      39      47 ..     606     614 ..     576     620 .. 0.53

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4.3e-09
                                       THHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   6 ilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                       +++PLr La+++ ++++G+ld++l +++rDE+G++   + +++d L+
  gi|313125859|ref|YP_004036129.1| 317 TVKPLRGLAASVSELRNGNLDVDLATDRRDEFGDVLIGVAHLRDDLQ 363
                                       79*******************************99877777777776 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.1e-05
                                       HHHHHHTTTBTSSTCCT.TSSSHHHHHHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtrlpv.sgrDEiGeLarafNaMldrLre 53 
                                       +++ + a+Gdl++rl+  s    ++++a a+N+M+d++++
  gi|313125859|ref|YP_004036129.1| 374 EVMVQAADGDLTVRLDAdSDSADMRTIATAYNEMMDEVEQ 413
                                       5678889**********9******************9875 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.063
                                       HHHHHHHHHTTT......BTSSTCCT.TSSSHHHHHHHHHHHHH CS
                              HAMP  12 rLaraarriaaG......dldtrlpv.sgrDEiGeLarafNaMl 48 
                                       ++++a+++i++G      +        s  DE+ +L +++++ +
  gi|313125859|ref|YP_004036129.1| 445 EVSSAIQQISDGasqqsdN------LaSVSDEVNDLSASIEEIS 482
                                       6889********5555543......4456888888888877654 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 9.1
                                       HHHHHHHHHHHTTT....BTSSTCCTTSSSHHH CS
                              HAMP  10 LrrLaraarriaaG....dldtrlpvsgrDEiG 38 
                                       + ++++++ +ia+      l++ ++  +  E G
  gi|313125859|ref|YP_004036129.1| 537 IGEIVDVITEIAEQtdilALNANIEAARAGEAG 569
                                       567777778888755555666666666666655 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 7.2
                                       HHHHHHHHH CS
                              HAMP  39 eLarafNaM 47 
                                       e++ ++++M
  gi|313125859|ref|YP_004036129.1| 606 EVVGSIERM 614
                                       344455555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   3.4   9.8e-07   0.00046      37     122 ..     398     483 ..     394     485 .. 0.91
   2 ?    5.0   0.2     0.051        24      75     113 ..     513     551 ..     504     558 .. 0.85
   3 !    9.6   2.1    0.0018      0.87      44     120 ..     573     649 ..     569     653 .. 0.83
   4 ?    6.2   1.0     0.021       9.9      49     102 ..     662     715 ..     646     722 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.8e-07
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       r ++ a +++  ++eq  +  +a   + s+ + r+ ++ de++e+s+e+++ +++++++ s+ ++++ sv++ v++l
  gi|313125859|ref|YP_004036129.1| 398 RTIATAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDL 474
                                       667788888888888888888888899************************************************** PP

                           DUF1664 114 eskleriee 122
                                        +++e+i++
  gi|313125859|ref|YP_004036129.1| 475 SASIEEISS 483
                                       ******986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.051
                           DUF1664  75 ldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       +d+  e ++ + +ev+++ e+l eige v+ + e+ e+ 
  gi|313125859|ref|YP_004036129.1| 513 IDDIREETERTVQEVHKLDEQLGEIGEIVDVITEIAEQT 551
                                       677788889999999999999999999999999988765 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0018
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       + vs++++q+ ++ ++   ++s+ i++++++ de+   ++ ++eev++  + ++e  + +  + e ve+ + + ++i
  gi|313125859|ref|YP_004036129.1| 573 AVVSNEVKQLAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSLGGIVERVEDTAVSAKEI 649
                                       679999999999999999*************************9999888888887777777777777766666555 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.021
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                       ++ ++ +++a   ++ +++ ++v +  ++q+++  ++++e++++++d++++++ 
  gi|313125859|ref|YP_004036129.1| 662 EVLSMTDEIAGISEETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETS 715
                                       444555666666677777777777777777777777777777777777766655 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       7.8   3.7e+03       6      66 ..     299     365 ..     296     379 .. 0.61
   2 !   14.2   1.4   8.3e-05     0.039      32      86 ..     394     448 ..     385     451 .. 0.91
   3 ?    6.8   0.3     0.017       7.8      56      88 ..     450     482 ..     448     483 .. 0.91
   4 ?    4.0   0.1      0.12        59      41      82 ..     512     549 ..     488     560 .. 0.67
   5 !   12.7   0.9   0.00024      0.11      25      84 ..     587     646 ..     571     651 .. 0.61
   6 ?    5.2   4.4     0.055        26      31      87 ..     652     712 ..     642     714 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.8
                            DUF948   6 aAiAFvvLviflivvllklkktldeaaatieele......kqvdpilkevedllakvnelledvnek 66 
                                       + +A++ L  + + + ++  k l+ +aa++ el+      + ++   +e  d+l  v  l +d++++
  gi|313125859|ref|YP_004036129.1| 299 IVLALAGLLGLGVLLHFNTVKPLRGLAASVSELRngnldvDLATDRRDEFGDVLIGVAHLRDDLQDQ 365
                                       5567777777777777777777777777777776555444333344445555555555555555555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.3e-05
                            DUF948  32 aatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       +a ++++    +++++eve++++ +++  +dv++ + ++ +  ++v+++++ vs+
  gi|313125859|ref|YP_004036129.1| 394 SADMRTIATAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSS 448
                                       567888999999***************************************9986 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.017
                            DUF948  56 vnelledvneklekvdplteavadlgesvseln 88 
                                       ++++ ++ +++++++ ++ ++v+dl++s++e++
  gi|313125859|ref|YP_004036129.1| 450 IQQISDGASQQSDNLASVSDEVNDLSASIEEIS 482
                                       5788999**********************9987 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.12
                            DUF948  41 qvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                        +d i +e+e+++++v +    + e+l ++ ++++ + +++e
  gi|313125859|ref|YP_004036129.1| 512 GIDDIREETERTVQEVHK----LDEQLGEIGEIVDVITEIAE 549
                                       467777788888888877....44455555555544444444 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.00024
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       k+ +  ++a iee+e q d+++  +e++ ++v + ++ v e l+++  ++e v+d++ s 
  gi|313125859|ref|YP_004036129.1| 587 KSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSLGGIVERVEDTAVSA 646
                                       444455566666666777777777777777777777777777777777777777666665 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.055
                            DUF948  31 aaatieelekqvdpilkev....edllakvnelledvneklekvdplteavadlgesvsel 87 
                                       a+a  ++  ++v ++++e+    e+++a+++++ +  ++++++v  +t+++ +l + ++ l
  gi|313125859|ref|YP_004036129.1| 652 ATADQADSSQEVLSMTDEIagisEETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIARL 712
                                       4444444444444444444000044555555555577777777777777777777777666 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   4.3   2.5e-05     0.012      32     113 ..     400     490 ..     394     516 .. 0.77
   2 ?   -1.0   0.1       3.4   1.6e+03      39      62 ..     526     548 ..     503     564 .. 0.45
   3 !   11.8   0.4   0.00039      0.18      19      82 ..     576     642 ..     559     658 .. 0.58
   4 ?    3.5   3.0      0.15        70      35     102 ..     652     717 ..     643     722 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                      Baculo_PEP_C  32 ilaqlatlldaietqL...nalsedlksllaeldt...rldtlltnLtdalnalq...dtlrneLtnlnsiltnLls 99 
                                       i+++ ++++d++e+++    a+s+d+++l++ l++   +++++++++++a+++++    + + +L ++  ++++L +
  gi|313125859|ref|YP_004036129.1| 400 IATAYNEMMDEVEQTVqrtRAFSADVSDLVTRLAEradEVNEASQEVSSAIQQISdgaSQQSDNLASVSDEVNDLSA 476
                                       4444444444444444111578889999999888877799***************5554555668888889****** PP

                      Baculo_PEP_C 100 svtNinstLnnllq 113
                                       s+  i s+ n l+ 
  gi|313125859|ref|YP_004036129.1| 477 SIEEISSSANELVM 490
                                       ********999985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                      Baculo_PEP_C  39 lldaietqLnalsedlksllaeld 62 
                                        + ++++qL+++ e + ++++e++
  gi|313125859|ref|YP_004036129.1| 526 EVHKLDEQLGEIGE-IVDVITEIA 548
                                       23333333333333.222233332 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00039
                      Baculo_PEP_C  19 tnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdt 82 
                                       +n ++++   + + +a++++l+++ietq +++  +++++ +e+d+    +d++l+ L   + +++dt
  gi|313125859|ref|YP_004036129.1| 576 SNEVKQLAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDDgadSVDEALQSLGGIVERVEDT 642
                                       5555555444444455666666666666666666666666666555555555555555555555544 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.15
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvt 102
                                       + a + d+ +++L+ +++++   ++e +++ +t++++ +++ +a+  +++neL +l+ +++ L +s++
  gi|313125859|ref|YP_004036129.1| 652 ATADQADSSQEVLS-MTDEIAGISEETTAEAQTVSAAAEQQTAAVG-DVTNELSTLKDDIARLETSLA 717
                                       55556666666555.4778888888888888888888888888887.688999999999999988876 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   2.9    0.0016      0.75       2      84 ..     406     488 ..     405     494 .. 0.72
   2 !    8.2   0.3    0.0062       2.9      34      79 ..     511     556 ..     503     560 .. 0.77
   3 ?    6.5   0.9     0.022        10      40      91 ..     605     656 ..     572     661 .. 0.86
   4 ?    4.9   0.6     0.067        32      33      92 ..     660     720 ..     656     722 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                           BLOC1_2   2 rmfekvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                       +m+++v++ ++ + + +++  +l+++l e+a e  ++ ++v + +++ ++  ++++++l++  ++++++ ++++e+ 
  gi|313125859|ref|YP_004036129.1| 406 EMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIEEIS 482
                                       56777777777777777777777777777777666666666666666666777777788888888888888888888 PP

                           BLOC1_2  79 eavseL 84 
                                       + ++eL
  gi|313125859|ref|YP_004036129.1| 483 SSANEL 488
                                       888876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0062
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                         +++++++++ + ++++kl+e+  e+ + ++ i +i +q++ L  
  gi|313125859|ref|YP_004036129.1| 511 GGIDDIREETERTVQEVHKLDEQLGEIGEIVDVITEIAEQTDILAL 556
                                       5567888888888889999999888999999999999888887765 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.022
                           BLOC1_2  40 kdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                       ++v+ s+e+  e+++   +++++ lq++  i ++v++    ++e+D+ + ++
  gi|313125859|ref|YP_004036129.1| 605 DEVVGSIERMREEVDDGADSVDEALQSLGGIVERVEDTAVSAKEIDNATADQ 656
                                       56788999999999999999************************99998776 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.067
                           BLOC1_2  33 sekykklkdvaaslekkle.klnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       s+++ +++d++a+++++   + +  +++ +++   + ++ +++++L++ +++L++   + E
  gi|313125859|ref|YP_004036129.1| 660 SQEVLSMTDEIAGISEETTaEAQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETSLARFE 720
                                       5666667777777766554134444556677777777777777777777777776665555 PP

>> DUF1843  Domain of unknown function (DUF1843)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       3.7   1.8e+03      21      42 ..     431     452 ..     418     455 .. 0.83
   2 ?   -1.2   0.1       6.3     3e+03      25      50 ..     505     530 ..     504     532 .. 0.89
   3 !   17.8   0.5   7.4e-06    0.0035      20      51 ..     682     713 ..     678     714 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.7
                           DUF1843  21 alaaqaeqqLaeygdiasaleq 42 
                                        la +a++  +  ++++sa++q
  gi|313125859|ref|YP_004036129.1| 431 RLAERADEVNEASQEVSSAIQQ 452
                                       58889999999999*****998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.3
                           DUF1843  25 qaeqqLaeygdiasaleqLkaEIAKl 50 
                                       +ae++L   +di+ + e   +E+ Kl
  gi|313125859|ref|YP_004036129.1| 505 AAENALGGIDDIREETERTVQEVHKL 530
                                       589999999*********99999998 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 7.4e-06
                           DUF1843  20 KalaaqaeqqLaeygdiasaleqLkaEIAKlE 51 
                                        ++ a+aeqq a  gd++++l+ Lk  IA+lE
  gi|313125859|ref|YP_004036129.1| 682 QTVSAAAEQQTAAVGDVTNELSTLKDDIARLE 713
                                       5789***************************9 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.9         3   1.4e+03     181     213 ..      53      85 ..      41     111 .. 0.56
   2 !   15.7   2.1   1.2e-05    0.0055     272     354 ..     397     477 ..     394     485 .. 0.88
   3 ?   -1.9   0.0       2.7   1.3e+03     288     315 ..     515     542 ..     495     558 .. 0.68
   4 !    9.7   4.2    0.0008      0.38     227     353 ..     584     714 ..     574     721 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3
                             IFT57 181 ekekekeeeiieskvdaaeWklEleRvlpqLkv 213
                                       +++ + +++   + +  ++W++E +R ++    
  gi|313125859|ref|YP_004036129.1|  53 DARANLQAAAEREAIQVEQWEQERKRLTSVVAR 85 
                                       345555555666778888888888886554433 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.2e-05
                             IFT57 272 leellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDgsplvkikkaltklkkEi 348
                                       +++  + y+e+ +e++++ ++ +  s+ vs+l + lae  +e+++++qe+ +  ++++Dg++  ++ ++l+++  E+
  gi|313125859|ref|YP_004036129.1| 397 MRTIATAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGAS--QQSDNLASVSDEV 471
                                       56677889999999999999999999999999999999999999999999999999999999..8899999999999 PP

                             IFT57 349 kqmdvr 354
                                       +++   
  gi|313125859|ref|YP_004036129.1| 472 NDLSAS 477
                                       988655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.7
                             IFT57 288 evkekykqlsegvseltrelaeiseele 315
                                       +++e+ +   ++v++l ++l ei e ++
  gi|313125859|ref|YP_004036129.1| 515 DIREETERTVQEVHKLDEQLGEIGEIVD 542
                                       4555555666666666666666655444 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0008
                             IFT57 227 eqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleel......lqeyreaqeelsevkekykqls 297
                                       +++k+    i++ ++e+++q +++   i+++ e++      +++ l++l      +++     +e+++++ +  + s
  gi|313125859|ref|YP_004036129.1| 584 QETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSLggiverVEDTAVSAKEIDNATADQADSS 660
                                       4556666799999999999****************999999999999872222224445555667888888999999 PP

                             IFT57 298 egvseltrelaeiseelekvkqemeergssmtDgsplvkikkaltklkkEikqmdv 353
                                       ++v ++t+e a isee ++  q +    ++ t    +  +++ l++lk +i  ++ 
  gi|313125859|ref|YP_004036129.1| 661 QEVLSMTDEIAGISEETTAEAQTVSAAAEQQTA--AVGDVTNELSTLKDDIARLET 714
                                       999999999999999999888888877777664..455888888888888887765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9  10.0    0.0022         1     312     464 ..     400     545 ..     355     559 .. 0.46
   2 !    9.2   7.8   0.00086      0.41     320     453 ..     576     716 ..     537     727 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                            AAA_13 312 easensafeedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkakiesikklvaeinelia.khNekva 386
                                        a++++++ +++e+  ++++a+++    l  +l ++ +e+ + s e++s+ ++i+ + +++++  ++++ + N  +a
  gi|313125859|ref|YP_004036129.1| 400 IATAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEaSQEVSSAIQQISDGASQQSDNLASVSdEVNDLSA 476
                                       23333344444444444444444444444444444444444422223333333322222222222222202333333 PP

                            AAA_13 387 nleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeei 463
                                       ++ee  ++a++ + l  +e++       k++  + e+a+e++   ++++ +e++   +e+  L +ql ++ +++++i
  gi|313125859|ref|YP_004036129.1| 477 SIEEISSSANELVML--AERA-------KDEGHEGERAAENALGGIDDIREETERTVQEVHKLDEQLGEIGEIVDVI 544
                                       333333333333333..1222.......2233344555555555666666666666666666666666666666666 PP

                            AAA_13 464 n 464
                                       +
  gi|313125859|ref|YP_004036129.1| 545 T 545
                                       5 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00086
                            AAA_13 320 eedkeelkaeaealeeqLkglqraleaKrkepfksve.l.esvkakiesikklvaeineliakhNekvanleeekee 394
                                        +++++l +e++  ++ + +l +++e  r+e++ s+e + e+v++ ++s+ ++++++  ++++      + + +++e
  gi|313125859|ref|YP_004036129.1| 576 SNEVKQLAQETKSSAADISALIEEIETQRDEVVGSIErMrEEVDDGADSVDEALQSLGGIVERVE----DTAVSAKE 648
                                       34456666666666666777777777777777664443233444444444444444443333333....33333322 PP

                            AAA_13 395 akkklel.....hlveeleseld....eykkkykklekaieklekelkeeeaelkkleeeikeLekql 453
                                       + ++        ++v ++++e+     e + + + +++a+e+ ++++ + ++el +l+++i+ Le++l
  gi|313125859|ref|YP_004036129.1| 649 IDNATADqadssQEVLSMTDEIAgiseETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETSL 716
                                       22222220000022333333333111122233333333444444444444555555555555555444 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.5      0.19        88       8      68 ..     394     454 ..     387     487 .. 0.56
   2 ?   -0.2   0.0       2.6   1.2e+03      21      71 ..     589     639 ..     573     641 .. 0.67
   3 !   16.1   0.6   2.1e-05    0.0098       5      79 ..     643     717 ..     641     719 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.19
                              KxDL   8 sedldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesif 68 
                                       s+d+ +i  + ++++++ +++ ++  ++ a ++  +++l +r  +  ++++ev + +++i 
  gi|313125859|ref|YP_004036129.1| 394 SADMRTIATAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQIS 454
                                       5555555555555555555555555555555555555555555555555555555544443 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.6
                              KxDL  21 tsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkki 71 
                                         + + +  +e++++++++    +++r+++ +g+  + e  + L  i +++
  gi|313125859|ref|YP_004036129.1| 589 SAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSLGGIVERV 639
                                       445555556777888888888888888888888888887777777666665 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.1e-05
                              KxDL   5 avdsedldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                       av+ +++d++ a Qa+ s++  + + e+  + +++ ++ + ++a  +q+t ++ +v ++L +++  i +l++ la
  gi|313125859|ref|YP_004036129.1| 643 AVSAKEIDNATADQADSSQEVLSMTDEIAGISEETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETSLA 717
                                       78999*****************************************************************99887 PP

>> Importin_rep_6  Importin repeat 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5    0.0014      0.68      23      67 ..     411     455 ..     394     478 .. 0.84
   2 ?    5.9   0.2     0.029        14      24      84 ..     580     638 ..     569     649 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                    Importin_rep_6  23 edqlakftkgvsanlsdvyervkereneddeynedvdddyddytd 67 
                                        +q+ + t++ sa++sd+  r+ er +e +e +++v   +++ +d
  gi|313125859|ref|YP_004036129.1| 411 VEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISD 455
                                       3799999*********************99999999887777666 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.029
                    Importin_rep_6  24 dqlakftkgvsanlsdvyervkereneddeynedvdddyddytdedlldeinkslaailka 84 
                                       +qla+ tk+ +a++s + e ++ +++e     e + +++dd +d   +de  +sl  i+  
  gi|313125859|ref|YP_004036129.1| 580 KQLAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGAD--SVDEALQSLGGIVER 638
                                       68999999999999999999999999999999999999999876..589999999888765 PP

>> Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.069        32      21      49 ..     508     536 ..     493     550 .. 0.86
   2 ?    5.7   0.0      0.03        14      22      49 ..     691     718 ..     683     722 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.069
                     Bcr-Abl_Oligo  21 meLdsvedieqeLerCkaslrrLekelne 49 
                                         L+ ++di +e er  +++++L+++l e
  gi|313125859|ref|YP_004036129.1| 508 NALGGIDDIREETERTVQEVHKLDEQLGE 536
                                       56899*******************99975 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.03
                     Bcr-Abl_Oligo  22 eLdsvedieqeLerCkaslrrLekelne 49 
                                       +  +v+d+ +eL + k+++ rLe  l++
  gi|313125859|ref|YP_004036129.1| 691 QTAAVGDVTNELSTLKDDIARLETSLAR 718
                                       55789******************99986 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.08        38     182     223 ..     336     377 ..     318     382 .. 0.79
   2 ?   13.0   4.6   9.8e-05     0.046      90     220 ..     407     539 ..     396     551 .. 0.78
   3 ?    2.7   2.0      0.14        67     123     232 ..     593     701 ..     572     715 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.08
                              CorA 182 ddkllddedkeylrdlldelerllemlealrerleslqdtys 223
                                       +d  l  ++++ + d+l+ +++l ++l+ +r+ +es ++ + 
  gi|313125859|ref|YP_004036129.1| 336 LDVDLATDRRDEFGDVLIGVAHLRDDLQDQRDDAESYSEVMV 377
                                       455555566788************************999875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.8e-05
                              CorA  90 aldevikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklr 164
                                        +dev + +++++    ++++l+ rl +  +d+++e+ +++++ +++++d    ++++ ++  +e+ +l  ++ ++ 
  gi|313125859|ref|YP_004036129.1| 407 MMDEVEQTVQRTRAFSADVSDLVTRLAE-RADEVNEASQEVSSAIQQISDGAsqQSDNLASVSDEVNDLSASIEEIS 482
                                       3444444455555888899999988765.58*********************7666666678899999********* PP

                              CorA 165 ralapnrevlkrllakaddkllddedkey.lrdlldelerllemlealrerleslqd 220
                                       ++++++  + +r ++ +++++  +e+++  ++d+++e+er +++++ l e+l  + +
  gi|313125859|ref|YP_004036129.1| 483 SSANELVMLAERAKDEGHEGERAAENALGgIDDIREETERTVQEVHKLDEQLGEIGE 539
                                       **********77777555555555554447**********99999999999887755 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.14
                              CorA 123 lfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdl 197
                                       + +l+e++e+++de+   +  ++++ ++ ++++ +  ++l+ + + + ++    k++ + a +++ d+ +      +
  gi|313125859|ref|YP_004036129.1| 593 ISALIEEIETQRDEVVGSIerMREEVDDGADSVDEALQSLGGIVERVEDTAVSAKEIDN-ATADQADSSQ--EVLSM 666
                                       34444555555555555555555555555555555555555555555555555544444.3333333333..36666 PP

                              CorA 198 ldelerllemlealrerleslqdtyssllserlNr 232
                                        de++ ++e+++a ++ ++   ++  + +   +N+
  gi|313125859|ref|YP_004036129.1| 667 TDEIAGISEETTAEAQTVSAAAEQQTAAVGDVTNE 701
                                       66666666666666666666666666666655555 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   3.2     0.015         7      42     122 ..     408     485 ..     352     529 .. 0.57
   2 ?    9.9   0.7   0.00077      0.36      68     161 ..     582     685 ..     576     708 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                             Atg14  42 kkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsd 117
                                         ++e+ +++++  + + +d + +++++++e    +++ ++ +q+++d  sq+ + ++  + ++  ls+++ +    
  gi|313125859|ref|YP_004036129.1| 408 MDEVEQTVQRTRaFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIEE---- 480
                                       3333444444432222333334444555555555555555555555555555555555555555555555532.... PP

                             Atg14 118 leslq 122
                                       ++s  
  gi|313125859|ref|YP_004036129.1| 481 ISSSA 485
                                       22222 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00077
                             Atg14  68 kleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk..........kRrsdleslqneleerrkkqia 134
                                        ++e+ks  ad+++ ++e+++++++   +ie  ++++    d++           +R +d +   +e+ ++ ++q +
  gi|313125859|ref|YP_004036129.1| 582 LAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDealqslggivERVEDTAVSAKEIDNATADQAD 658
                                       57999**************************************************************9999988887 PP

                             Atg14 135 klqdaikrieqklsslssktlesrssl 161
                                       + q+ +  +++     + +t+e+++++
  gi|313125859|ref|YP_004036129.1| 659 SSQEVLSMTDEIAGISEETTAEAQTVS 685
                                       777766655555444444444443322 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.5   0.00035      0.16       2      83 ..     411     495 ..     410     498 .. 0.82
   2 ?    3.7   0.3       0.2        95       3      98 ..     507     629 ..     505     632 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00035
                                       HHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...TS..S-HHHHHHHHHHHHHHHHHHHHHHHH CS
                               ING   2 LedyldsvenLPlelqrnltelreiDakvqellkeidskiekfl...kngslqknekeeelsriqeelkeaqellde 75 
                                       +e++++   ++ +++++++t+l e   +v+e+ +e++s i++ +   +++s +  + ++e++++  +++e+  +++e
  gi|313125859|ref|YP_004036129.1| 411 VEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISdgaSQQSDNLASVSDEVNDLSASIEEISSSANE 487
                                       7999****************************************665444555555556666888888888888888 PP

                                       HHHHHHHH CS
                               ING  76 Kiqlaqqa 83 
                                        + la+ a
  gi|313125859|ref|YP_004036129.1| 488 LVMLAERA 495
                                       77777766 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.2
                                       HHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHH.........................TS..S-H CS
                               ING   3 edyldsvenLPlelqrnltelreiDakvqellkei..dskiekfl.........................kngslqk 52 
                                       e+ l  ++ + +e++r ++e++++D ++ e+ + +   ++i +                           ++ +   
  gi|313125859|ref|YP_004036129.1| 507 ENALGGIDDIREETERTVQEVHKLDEQLGEIGEIVdvITEIAEQTdilalnanieaarageagegfavvsNEVKQLA 583
                                       56777788899999999999999999998887766332222222244557777777777777777777532222223 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               ING  53 nekeeelsriqeelkeaqelldeKiqlaqqaldlvdkhlrrLdqdl 98 
                                       +e +++ ++i   ++e++   de +  ++ + + vd   +  d++l
  gi|313125859|ref|YP_004036129.1| 584 QETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEAL 629
                                       3333334478888888888888777777777777777777666666 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0     0.037        17      29      86 ..     400     457 ..     392     465 .. 0.80
   2 ?    6.1   0.3     0.024        12      32     116 ..     466     549 ..     461     565 .. 0.81
   3 ?    9.5   0.9    0.0022       1.1      22     124 ..     614     715 ..     598     722 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.037
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskel 86 
                                         + +++ ++++e+++++ +  + ++++lv+++ +   e ++ +++ +++i+++s+  
  gi|313125859|ref|YP_004036129.1| 400 IATAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGA 457
                                       5667778888999999999999999999999999999998888888899998888755 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.024
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLq 108
                                       +v++++++l  ++eeis+s +e   l ++ kd  +e ++ +++    i ++++e e + ++  +++d+q  +i ++ 
  gi|313125859|ref|YP_004036129.1| 466 SVSDEVNDLSASIEEISSSANELVMLAERAKDEGHEGERAAENALGGIDDIREETE-RTVQEVHKLDEQLGEIGEIV 541
                                       7899**********************************999988999999999999.55555567888888888888 PP

                                       HHHHHHHH CS
                         Fib_alpha 109 nvlesneq 116
                                       +v+ +  +
  gi|313125859|ref|YP_004036129.1| 542 DVITEIAE 549
                                       88876543 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0022
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketid 98 
                                       +++ +++   +v++ l++l   +e+++++  +a+e+ +++ d+  + q+  + +d++   +s+e   e +++ +   
  gi|313125859|ref|YP_004036129.1| 614 MREEVDDGADSVDEALQSLGGIVERVEDTAVSAKEIDNATADQADSSQEVLSMTDEIAG-ISEETTAEAQTVSAAAE 689
                                       55566667788999999999999999999999999999999999999999986555554.55555558999999999 PP

                                       CCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqnvlesneqkiqkLeqd 124
                                       +q   +   +n l++++ +i++Le+ 
  gi|313125859|ref|YP_004036129.1| 690 QQTAAVGDVTNELSTLKDDIARLETS 715
                                       99999999999999999999999986 PP

>> TetR  Bacterial transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       3.5   1.6e+03      58      90 ..      43      75 ..      41      85 .. 0.82
   2 ?   10.8   0.0   0.00065      0.31      19     102 ..     400     484 ..     378     508 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.5
                                      HHHHHHHHHHHHHHHHHHHHHTTSB---GHHHH CS
                              TetR 58 yrqlleelqaqlrellqelveagllqaddeele 90
                                      y  +++el++++r+ lq+ +e + +q+++ e e
  gi|313125859|ref|YP_004036129.1| 43 YSMTASELNEDARANLQAAAEREAIQVEQWEQE 75
                                      56678899999**************98887654 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00065
                                       SHHHHHHHHHHHHHHHHHTHHHHHSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHT.TSB---GHHHHHHHH CS
                              TetR  19 sledlwrylealfelmwrYRFlyrDlaellsrnpeLakryrqlleelqaqlrellqelvea.gllqaddeeleaLad 94 
                                        +  + ++++ + ++++r R + +D+++l++r +e a ++++  +e++ +++++ ++  ++ + l+  ++e+++L+ 
  gi|313125859|ref|YP_004036129.1| 400 IATAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQsDNLASVSDEVNDLSA 476
                                       4566999*************************************************997652678888888999998 PP

                                       HHHHHHHC CS
                              TetR  95 niwlvaty 102
                                       +i  ++++
  gi|313125859|ref|YP_004036129.1| 477 SIEEISSS 484
                                       88766665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5      0.24   1.2e+02       4      50 ..      30      80 ..      27     108 .. 0.72
   2 ?   13.6   7.6   6.5e-05     0.031      11     104 ..     401     494 ..     397     500 .. 0.93
   3 ?   -0.2   0.2         1   4.9e+02      20      62 ..     494     536 ..     490     568 .. 0.75
   4 ?    5.9   2.3     0.014       6.7      61     108 ..     570     617 ..     519     622 .. 0.69
   5 ?    4.7   4.3     0.033        16      17      92 ..     645     720 ..     622     726 .. 0.47

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.24
                           DUF3450  4 llalllasgal...aatldqalkeaekavaaaaqsqk.kidklddekqell 50
                                      +++l++a+ a    + t++++++ a++  +aaa+ ++ +++++++e++ l 
  gi|313125859|ref|YP_004036129.1| 30 IVMLVVAGVAGvqySMTASELNEDARANLQAAAEREAiQVEQWEQERKRLT 80
                                      444444444445668888888887777766666655438999999998775 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.5e-05
                           DUF3450  11 sgalaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeq 87 
                                       ++a+++ +d+++++ +++ a +a+++  +++l++ ++e+ +  +++++ +++++   +q+++ +as+  e+++l  +
  gi|313125859|ref|YP_004036129.1| 401 ATAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSAS 477
                                       56678999********************************************************************* PP

                           DUF3450  88 ieeieeierelvpllek 104
                                       ieei+  ++elv l e+
  gi|313125859|ref|YP_004036129.1| 478 IEEISSSANELVMLAER 494
                                       ***********988665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeles 62 
                                        a++e+ +  +aa+ +   id++ +e++  ++e+++l e+l +
  gi|313125859|ref|YP_004036129.1| 494 RAKDEGHEGERAAENALGGIDDIREETERTVQEVHKLDEQLGE 536
                                       5667777777777777788888888888888888888887655 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.014
                           DUF3450  61 eslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidr 108
                                       e  +v  +++++l ++ +++ a++   ieeie  ++e+v  +e+m ++
  gi|313125859|ref|YP_004036129.1| 570 EGFAVVSNEVKQLAQETKSSAADISALIEEIETQRDEVVGSIERMREE 617
                                       555666666667777777777777777777777777777777776554 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.033
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       ++++++++++   ++++++ +  d+++  ++e  ae +++++ +e+ ++    +++ +++++ +ia+le++++++e
  gi|313125859|ref|YP_004036129.1| 645 SAKEIDNATADQADSSQEVLSMTDEIAGISEETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETSLARFE 720
                                       2223333333333333333333444444455555555555555555555555555555555555555555555444 PP

>> IMD  IRSp53/MIM homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0   0.00072      0.34      80     173 ..     402     494 ..     388     496 .. 0.84
   2 ?   -0.8   0.1       1.8   8.4e+02     101     154 ..     576     629 ..     570     651 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00072
                                       HHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHCCCS-CHHHHHHHHHHHHHHHHHH CS
                               IMD  80 alhdsLlnpleekveedkkvlnqldkdyakEykkkraelkKkssellklqkKakkgkddlkvqldelledvndkyll 156
                                       +  +++++++e+ v+   ++ ++   d  +   ++++e++  s e+    ++   g  ++  +l ++ ++vnd+ + 
  gi|313125859|ref|YP_004036129.1| 402 TAYNEMMDEVEQTVQRT-RAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSAS 477
                                       44578889999888765.5566667788999999***********999888888889999***************** PP

                                       HHHHHHHHHHHHHHHHH CS
                               IMD 157 leetvkeavrrAliEEr 173
                                       +ee+ + a    ++ Er
  gi|313125859|ref|YP_004036129.1| 478 IEEISSSANELVMLAER 494
                                       *******9999888888 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHCCCS-CHHHHHHHHHHHHHHHH CS
                               IMD 101 nqldkdyakEykkkraelkKkssellklqkKakkgkddlkvqldelledvndky 154
                                       ++  k+ a+E k+ +a++     e+   +  + ++ + ++ ++d+  ++v++  
  gi|313125859|ref|YP_004036129.1| 576 SNEVKQLAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEAL 629
                                       555566666666666666666666655555555555666666655555555544 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3     0.016       7.6       3      34 ..     462     493 ..     460     494 .. 0.89
   2 ?    0.6   0.0         1   4.9e+02       3      22 ..     700     719 ..     692     725 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLsdfNe 34 
                                       +++a+ +D++++L++ +e++++  ++L+ + e
  gi|313125859|ref|YP_004036129.1| 462 DNLASVSDEVNDLSASIEEISSSANELVMLAE 493
                                       67999*****************9999987765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1
                         DASH_Dam1   3 pafaeLaDsletLdknledL 22 
                                       ++++ L+D ++ L++ l ++
  gi|313125859|ref|YP_004036129.1| 700 NELSTLKDDIARLETSLARF 719
                                       45666666666666665554 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.3    0.0012      0.55       3      81 ..     432     513 ..     430     555 .. 0.74
   2 ?    8.0   0.5    0.0029       1.4     223     285 ..     585     650 ..     573     656 .. 0.77
   3 ?    0.3   0.3      0.65   3.1e+02      25      61 ..     681     717 ..     660     732 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                              RmuC   3 leellkplkeklekfeekveees...keeaeeleslkeqlkelqelneqlgdeaenLtkaLknsktrGnwGEvqLer 76 
                                       l e  ++++e  ++++ ++++ s   ++++++l+s++ +++ l++  e+++++a++L+   +  k  G  GE   e+
  gi|313125859|ref|YP_004036129.1| 432 LAERADEVNEASQEVSSAIQQISdgaSQQSDNLASVSDEVNDLSASIEEISSSANELVMLAERAKDEGHEGERAAEN 508
                                       56667788888888888888888888999999999999999999999999999999998777999999999998888 PP

                              RmuC  77 iless 81 
                                        l  +
  gi|313125859|ref|YP_004036129.1| 509 ALGGI 513
                                       87655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0029
                              RmuC 223 aqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle...gnilrkaeklkelg 285
                                       + +  a++i  l++e+ ++  +++ ++e++++++++  +s+d+a ++l    +++  +a + ke++
  gi|313125859|ref|YP_004036129.1| 585 ETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSLGgivERVEDTAVSAKEID 650
                                       33456889************************************9999766666666666666655 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.65
                              RmuC  25 skeeaeeleslkeqlkelqelneqlgdeaenLtkaLk 61 
                                        ++++ + e+ +++++ +++  + l+d+ ++L++ L 
  gi|313125859|ref|YP_004036129.1| 681 AQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETSLA 717
                                       2222222222222222222222222222222443333 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.9   9.1e+02      98     125 ..     420     447 ..     389     455 .. 0.44
   2 ?    5.5   0.8     0.025        12      90     146 ..     441     496 ..     432     508 .. 0.81
   3 ?    2.4   0.1      0.21     1e+02      97     143 ..     605     651 ..     579     658 .. 0.79
   4 ?    6.9   0.4    0.0088       4.1      96     156 ..     660     720 ..     652     722 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.9
                     Fzo_mitofusin  98 elsstfarlcqqvdetekeleeeikele 125
                                        +s  ++ l ++  e  +e++e  +e++
  gi|313125859|ref|YP_004036129.1| 420 AFSADVSDLVTRLAERADEVNEASQEVS 447
                                       2222233333333333333333333333 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                     Fzo_mitofusin  90 ncshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkas 146
                                       + s+ v + +++  +  +qq+d+  +++++e+++l+++ie++ +  +++ +l ++a+
  gi|313125859|ref|YP_004036129.1| 441 EASQEVSSAIQQISDGASQQSDNL-ASVSDEVNDLSASIEEISSSANELVMLAERAK 496
                                       567777777777777777777765.56899****************99999999987 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.21
                     Fzo_mitofusin  97 qelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrn 143
                                        e+   ++r++++vd   ++++e +++l   +e++e++  +ak + n
  gi|313125859|ref|YP_004036129.1| 605 DEVVGSIERMREEVDDGADSVDEALQSLGGIVERVEDTAVSAKEIDN 651
                                       47777889999999999999999999999999999999999998876 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0088
                     Fzo_mitofusin  96 qqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                        qe+ s+ +++   ++et++e ++  ++ e++ +++ +v++++ +l++   +le++L++fe
  gi|313125859|ref|YP_004036129.1| 660 SQEVLSMTDEIAGISEETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETSLARFE 720
                                       57888888999999999******************************************97 PP

>> DUF1652  Protein of unknown function (DUF1652)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.72   3.4e+02      21      39 ..     379     396 ..     375     402 .. 0.81
   2 ?   -1.1   0.0       3.7   1.8e+03      53      65 ..     422     434 ..     416     435 .. 0.84
   3 ?    8.9   0.2    0.0027       1.3      42      66 ..     579     603 ..     575     604 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.72
                           DUF1652  21 dadgsmtvrlfdpasgevd 39 
                                       +adg +tvrl d +s+  d
  gi|313125859|ref|YP_004036129.1| 379 AADGDLTVRL-DADSDSAD 396
                                       689*******.88877654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.7
                           DUF1652  53 srdisrLieelra 65 
                                       s+d+s+L+ +l +
  gi|313125859|ref|YP_004036129.1| 422 SADVSDLVTRLAE 434
                                       89*******9975 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0027
                           DUF1652  42 vtGiplrelnssrdisrLieelrae 66 
                                       v+ ++ ++ +s++dis+Liee++++
  gi|313125859|ref|YP_004036129.1| 579 VKQLAQETKSSAADISALIEEIETQ 603
                                       5667778889*************98 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.7    0.0021         1      16      99 ..     407     494 ..     402     498 .. 0.82
   2 ?    0.3   0.0      0.97   4.6e+02     100     175 ..     595     671 ..     569     682 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0021
                             BAR_3  16 sleevEaeleelekklkkllKlckrlieagkaysaaqkqfaqsLrelkkes..kgdeetd..esLkkfsellqelen 88 
                                        ++evE+++++++ +  ++  l+ rl e + ++++a +++++ +++++     ++d++ +  +  + +s +++e+++
  gi|313125859|ref|YP_004036129.1| 407 MMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGAsqQSDNLASvsDEVNDLSASIEEISS 483
                                       57899*************************************99999877655555544455888888888888888 PP

                             BAR_3  89 ehtilldqaqr 99 
                                         ++l+  a+r
  gi|313125859|ref|YP_004036129.1| 484 SANELVMLAER 494
                                       88877766655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.97
                             BAR_3 100 sikkpLekFrkedlkevkekkkkFdkesekleaaleknaqlskkkkesele.eadnelkatrkkfhqasldyvlqin 175
                                       ++++++e+ r e +++++  +++ d   ++ ++al++   + ++ ++  +  +   + +a++ +  q+ l++  +i 
  gi|313125859|ref|YP_004036129.1| 595 ALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSLGGIVERVEDTAVSaKEIDNATADQADSSQEVLSMTDEIA 671
                                       45677777777777777888888888888888888877777777666665543333344444445556666666665 PP

>> Corona_S2  Coronavirus S2 glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   0.00046      0.22     248     307 ..     398     488 ..     385     495 .. 0.78
   2 ?   -0.8   0.1      0.83   3.9e+02     264     325 ..     502     565 ..     491     595 .. 0.70
   3 ?   -2.5   0.1       2.7   1.3e+03     477     531 ..     661     717 ..     635     723 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                                       HHHHHHHHHHHHHH............................HHHHHHHHSHHHHHHHHHHHHHHHHHHH...HHHH CS
                         Corona_S2 248 kklaasfnkaigni............................seglatvatalakiqdvvnkqgqalnel...vaql 293
                                       + +a+++n+ + ++                            +e+ + v+ a+++i d  ++q++ l+ +   v++l
  gi|313125859|ref|YP_004036129.1| 398 RTIATAYNEMMDEVeqtvqrtrafsadvsdlvtrlaeradevNEASQEVSSAIQQISDGASQQSDNLASVsdeVNDL 474
                                       5677777777777777777777777777777888888888889999*****************99886552226778 PP

                                       SHHTTSSHSHHHHH CS
                         Corona_S2 294 sknfgaissviqdi 307
                                       s   + iss+ +++
  gi|313125859|ref|YP_004036129.1| 475 SASIEEISSSANEL 488
                                       88899999988876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.83
                                       HHHHHHSHHHHHHHHHHHHHHHHHHHHHHHSH...HTTSSHSHHHHHHHHSCHHHHHHHHHHHHH CS
                         Corona_S2 264 glatvatalakiqdvvnkqgqalnelvaqlsk...nfgaissviqdiydrldkieadaqvdrlit 325
                                       g ++  +al+ i d+ ++  ++++e+ ++l++     g i  vi +i ++ d +  +a ++   +
  gi|313125859|ref|YP_004036129.1| 502 GERAAENALGGIDDIREETERTVQEV-HKLDEqlgEIGEIVDVITEIAEQTDILALNANIEAARA 565
                                       55677788999999877766665543.33444011466788899999999999988888876555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.7
                                       GGCCXXXXXXXXXXXXSX.XXXXHHHH.TTHHHHHHHHHHHHHHHHHHHHHGGGGHH CS
                         Corona_S2 477 peyidvneelqkllenyk.pnvelpdl.dkfnatvlnltseidrlqevidnlneslv 531
                                       +e +++ +e+  + e+++    +++   ++  a+v ++t+e++ l+  i  l  sl 
  gi|313125859|ref|YP_004036129.1| 661 QEVLSMTDEIAGISEETTaEAQTVSAAaEQQTAAVGDVTNELSTLKDDIARLETSLA 717
                                       477788888888888888555666666688888899999999999998888888876 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1       0.1        49      85     125 ..      65     110 ..      44     117 .. 0.73
   2 ?    8.1   0.6    0.0061       2.9      46     126 ..     411     491 ..     393     502 .. 0.83
   3 ?    2.2   1.0       0.4   1.9e+02      34     130 ..     605     703 ..     577     715 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                             CREPT  85 leaqkellakaeekleelkeklekvksvrke.....lkshiqsLPd 125
                                        ++q e+ ++++++l+++  +   v+sv++e     l +h++s+Pd
  gi|313125859|ref|YP_004036129.1|  65 EAIQVEQWEQERKRLTSVVARDTGVNSVKTErsnhaLTQHMESMPD 110
                                       45677788888888888888877777776654444499*******8 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0061
                             CREPT  46 aekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqs 122
                                        e+ ++  +   + +++ ++rL++  +e ++ ++ +++ ++++ + ++++  +l+++ + ++ +++  +e+ s  + 
  gi|313125859|ref|YP_004036129.1| 411 VEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIEEISSSANE 487
                                       45555666666778999999999999999999999999999999999999999999999999999999999998888 PP

                             CREPT 123 LPdL 126
                                       L  L
  gi|313125859|ref|YP_004036129.1| 488 LVML 491
                                       7655 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.4
                             CREPT  34 vsllekik.dkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekv 109
                                        +++ +i+  +ee +  +++v+eal+ l   ++r e+     k++ +  +d   + +e l+ ++e +   +e  ++ 
  gi|313125859|ref|YP_004036129.1| 605 DEVVGSIErMREEVDDGADSVDEALQSLGGIVERVEDTAVSAKEIDNATADQADSSQEVLSMTDEIAGISEETTAEA 681
                                       45566665466777777777777777777777777777777777777777777777777777776666666666666 PP

                             CREPT 110 ksvrkelkshiqsLPdLt.elp 130
                                       ++v +  +++     d+t el+
  gi|313125859|ref|YP_004036129.1| 682 QTVSAAAEQQTAAVGDVTnELS 703
                                       6666666666555555554444 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5       8.5     4e+03      34      53 ..      68      87 ..      46     112 .. 0.59
   2 ?    7.1   2.9     0.013       6.1      27     106 ..     403     483 ..     394     491 .. 0.67
   3 ?   -1.4   0.2       5.7   2.7e+03      57      73 ..     518     534 ..     484     554 .. 0.55
   4 ?   14.1   1.7     9e-05     0.042      31      96 ..     575     641 ..     570     656 .. 0.91
   5 ?    4.2   0.8       0.1        47      67     103 ..     675     711 ..     641     718 .. 0.50

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.5
                       TMF_TATA_bd 34 elerleaerdeareeivklm 53
                                      ++e+ e+er+++++ +++ +
  gi|313125859|ref|YP_004036129.1| 68 QVEQWEQERKRLTSVVARDT 87
                                      34455555555555555444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                       TMF_TATA_bd  27 Elaslkeelerleaerdeareeivklmke.neelkelkkeleelekeleelqeryetlLellGeksEeveELraDva 102
                                        ++++++e+e+  +  ++ ++++ +l+++  e+ +e ++ ++e+++ ++++++  ++    l   s+ev++L a ++
  gi|313125859|ref|YP_004036129.1| 403 AYNEMMDEVEQTVQRTRAFSADVSDLVTRlAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIE 479
                                       56677777777777777777777777644145556666666777777777777777777777888888888888888 PP

                       TMF_TATA_bd 103 DlKe 106
                                       ++  
  gi|313125859|ref|YP_004036129.1| 480 EISS 483
                                       7655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.7
                       TMF_TATA_bd  57 eelkelkkeleelekel 73 
                                       ee++++ +e+ +l ++l
  gi|313125859|ref|YP_004036129.1| 518 EETERTVQEVHKLDEQL 534
                                       22222222222222222 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 9e-05
                       TMF_TATA_bd  31 lkeelerleaerdeareeivklmkeneelkel.kkeleelekeleelqeryetlLellGeksEeveE 96 
                                       + +e+++l++e ++ +++i +l++e e+++++  +++e +++e+++  +  +++L+ lG   E+ve+
  gi|313125859|ref|YP_004036129.1| 575 VSNEVKQLAQETKSSAADISALIEEIETQRDEvVGSIERMREEVDDGADSVDEALQSLGGIVERVED 641
                                       67899**********************987652689***************************9996 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.1
                       TMF_TATA_bd  67 eelekeleelqeryetlLellGeksEeveELraDvaD 103
                                       ee+++e + ++   e+     G  + e   L++D+a 
  gi|313125859|ref|YP_004036129.1| 675 EETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIAR 711
                                       3444444444444444444455555555555555443 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   5.8   0.00095      0.45       2      80 ..     405     483 ..     394     493 .. 0.81
   2 ?    4.4   0.1     0.072        34      10      52 ..     504     546 ..     495     564 .. 0.77
   3 ?    6.9   1.4     0.013       6.1       7      61 ..     578     632 ..     573     651 .. 0.72
   4 ?    4.8   3.8     0.056        27       4      81 ..     653     722 ..     641     734 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00095
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       +e+++e+++t++ + +  a++s  + ++ e + e+n+  +e+   +++ + +  + +++   +  ++++L + ++e+
  gi|313125859|ref|YP_004036129.1| 405 NEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIEEI 481
                                       57888889999988888888888888888888888888888888888888888888888888888888888888877 PP

                                       HH CS
                        Laminin_II  79 kq 80 
                                         
  gi|313125859|ref|YP_004036129.1| 482 SS 483
                                       65 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.072
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdank 52 
                                         a++ l  + ++ +++e+t ++++++++++ e+ e v+  ++
  gi|313125859|ref|YP_004036129.1| 504 RAAENALGGIDDIREETERTVQEVHKLDEQLGEIGEIVDVITE 546
                                       5667777888899999999999999999999888887765554 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsv 61 
                                       e+++ a+e+++  a++s+ +e+++ +  e+ +s+e++ e+v+d    +++A +s 
  gi|313125859|ref|YP_004036129.1| 578 EVKQLAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSL 632
                                       6677788888888888888888888888888888888888877777766665554 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.056
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                       +a++a+ + +evl+ + +++   e+t ++++++ +        +++ + a+ d+ ++ ++L+  + +L+  l + + 
  gi|313125859|ref|YP_004036129.1| 653 TADQAD-SSQEVLSMTDEIAGISEETTAEAQTVSAA-------AEQQTAAVGDVTNELSTLKDDIARLETSLARFEV 721
                                       344443.34666666666666666666666666666.......5556666666666666666666666666555555 PP

                                       H CS
                        Laminin_II  81 l 81 
                                        
  gi|313125859|ref|YP_004036129.1| 722 S 722
                                       5 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.5       6.6   3.1e+03     176     198 ..      56      77 ..      43     110 .. 0.49
   2 ?   12.6   4.7   0.00016     0.075     187     291 ..     440     543 ..     433     551 .. 0.91
   3 ?    9.5   4.1    0.0014      0.64      42     155 ..     576     692 ..     566     709 .. 0.84
   4 ?    2.2   0.2      0.24   1.1e+02     197     235 ..     681     719 ..     673     733 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.6
                                       XXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 176 aqyeelaeknreeaeewykskle 198
                                       a+  + ae++  ++e+w +++ +
  gi|313125859|ref|YP_004036129.1|  56 ANLQAAAEREAIQVEQWEQER-K 77 
                                       333334444444443332222.2 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00016
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 187 eeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqek 263
                                       +ea +  +s ++++++ a+++s++l s+  e+++l  +i++ ++  ++l   ++  +++ +e e   e++l  + ++
  gi|313125859|ref|YP_004036129.1| 440 NEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIEEISSSANELVMLAERAKDEGHEGERAAENALGGIDDI 516
                                       67888889999****************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 264 lseleeelaeireemarqlreYqeLLdv 291
                                        +e e+ ++e+  +++ ql e  e+ dv
  gi|313125859|ref|YP_004036129.1| 517 REETERTVQEVH-KLDEQLGEIGEIVDV 543
                                       **********96.578888888888777 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0014
                                       XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXX CS
                          Filament  42 saevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalr...kdldea 115
                                       s+ev++l +  ++  +++ + ++e++++r+ ++  ++++ree++d   ++++ l++   + + +++     k++d+a
  gi|313125859|ref|YP_004036129.1| 576 SNEVKQLAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSLGGIVERVEDTAvsaKEIDNA 652
                                       5677888888888999999*******************************999888777666666655555****** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 116 tlarvdLekkvesLkeelaflkkvheeEvkelqkqvseqv 155
                                       t  ++d  ++v s+++e+a   +   +E +++ + +++q+
  gi|313125859|ref|YP_004036129.1| 653 TADQADSSQEVLSMTDEIAGISEETTAEAQTVSAAAEQQT 692
                                       *******************999999999988888876443 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.24
                                       XXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHH CS
                          Filament 197 leelqeaaeknsealrsakeeitelrrqiqsleielesl 235
                                        ++++ aae++++a+  + +e++ l+  i +le+ l+  
  gi|313125859|ref|YP_004036129.1| 681 AQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETSLARF 719
                                       566788899999999999999999999999999888765 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.4      0.18        83      43      93 ..     440     483 ..     361     497 .. 0.45
   2 ?   -1.5   0.0       5.4   2.6e+03      15      65 ..     486     535 ..     482     556 .. 0.52
   3 ?    5.2   0.0     0.047        22      55     103 ..     577     626 ..     573     643 .. 0.77
   4 ?    2.4   0.2      0.34   1.6e+02      20      51 ..     687     718 ..     651     736 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX- CS
                              COG5  43 qeldkrlrqlitsnhleLlehlskskslss.vlselksslesLsasyerlks 93 
                                       +        + +++ ++ ++++s+ +s +s  l ++  ++++Lsas+e ++s
  gi|313125859|ref|YP_004036129.1| 440 N--------EASQEVSSAIQQISDGASQQSdNLASVSDEVNDLSASIEEISS 483
                                       1........2222223333344444444444444444444444444444433 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.4
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              COG5  15 nallkatnnnddteldlstplkrlnydiqeldkrlrqlitsnhleLlehls 65 
                                       n+l+  ++ ++d+    + +++    +i++++++ ++ +++ h +L e+l 
  gi|313125859|ref|YP_004036129.1| 486 NELVMLAERAKDEGHEGERAAENALGGIDDIREETERTVQEVH-KLDEQLG 535
                                       5555555555555555555555555555555555444443332.3333333 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.047
                                       XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHH CS
                              COG5  55 snhleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeae 103
                                       ++ ++L +++++s+   s + +e++++ +++  s+er++++v +  ++++
  gi|313125859|ref|YP_004036129.1| 577 NEVKQLAQETKSSAADISaLIEEIETQRDEVVGSIERMREEVDDGADSVD 626
                                       556677777777777767799*******************9976655555 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.34
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              COG5  20 atnnnddteldlstplkrlnydiqeldkrlrq 51 
                                       a+++++ +  d+  +l++l+ di  l++ l +
  gi|313125859|ref|YP_004036129.1| 687 AAEQQTAAVGDVTNELSTLKDDIARLETSLAR 718
                                       55677777888888888888888888777654 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.1      0.13        59      27      66 ..     424     463 ..     388     501 .. 0.59
   2 ?    0.1   0.1       2.3   1.1e+03      35      48 ..     513     526 ..     467     564 .. 0.57
   3 ?    4.6   0.1     0.091        43      33      62 ..     577     606 ..     522     641 .. 0.59
   4 ?    1.7   2.1      0.71   3.4e+02      13      65 ..     591     655 ..     579     719 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                        Syntaxin_2  27 dteelreklhelieeinelikktnellkklsqldnsssds 66 
                                       d  +l  +l e  +e+ne ++++++ ++++s  + ++sd+
  gi|313125859|ref|YP_004036129.1| 424 DVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDN 463
                                       4555555555555555555555555555555555555443 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.3
                        Syntaxin_2  35 lhelieeinelikk 48 
                                       +++++ee+ +++++
  gi|313125859|ref|YP_004036129.1| 513 IDDIREETERTVQE 526
                                       22333333333333 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.091
                        Syntaxin_2  33 eklhelieeinelikktnellkklsqldns 62 
                                       +++++l +e++  + ++++l++++++  + 
  gi|313125859|ref|YP_004036129.1| 577 NEVKQLAQETKSSAADISALIEEIETQRDE 606
                                       666666666666666666666666655444 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.71
                        Syntaxin_2  13 stleklvkqLgtkkd.....teelr.......eklhelieeinelikktnellkklsqldnsssd 65 
                                         +  l++ ++t++d      e++r       ++++e  +++  +++++++   + +++dn + d
  gi|313125859|ref|YP_004036129.1| 591 ADISALIEEIETQRDevvgsIERMReevddgaDSVDEALQSLGGIVERVEDTAVSAKEIDNATAD 655
                                       44555555555555544444222222222333444444444444444444444444444444444 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.6    0.0042         2       3      54 ..     404     454 ..     402     460 .. 0.91
   2 ?    5.9   0.6      0.04        19       4      69 ..     465     529 ..     462     554 .. 0.82
   3 ?    6.0   1.6     0.036        17       3      80 ..     572     653 ..     571     667 .. 0.60
   4 ?    4.5   1.1      0.11        50       8      71 ..     661     723 ..     656     737 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0042
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsie 54 
                                       ++e+ +eV+++++++++  +  ++l +   ++  +e++e+++e+ +a+++i+
  gi|313125859|ref|YP_004036129.1| 404 YNEMMDEVEQTVQRTRAFSADVSDLVTRLAER-ADEVNEASQEVSSAIQQIS 454
                                       8999*******************999998875.9**************9986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.04
                      Syntaxin-6_N   4 fevkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivek 69 
                                        +v +eV++   ++e++ ++ ++l  +++ + ++e +e ++  ++al+ i+   e+ e+tv+ v k
  gi|313125859|ref|YP_004036129.1| 465 ASVSDEVNDLSASIEEISSSANELVMLAERA-KDEGHEGERAAENALGGIDDIREETERTVQEVHK 529
                                       6799999999999999999999999998765.9999999999*********999999999977765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.036
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrwerlledtsss...tseeldetrteLrkalrsiewdledLeetvriveknpsk.fk 75 
                                       F +v +eV++ +++++s  +  + l e+ +++      ++++ r+e+    +s+++ l+ L   v+ ve       +
  gi|313125859|ref|YP_004036129.1| 572 FAVVSNEVKQLAQETKSSAADISALIEEIETQrdeVVGSIERMREEVDDGADSVDEALQSLGGIVERVEDTAVSaKE 648
                                       77788888888888888888886665555553233345666667777777777777777777777666654422244 PP

                      Syntaxin-6_N  76 ideke 80 
                                       id+++
  gi|313125859|ref|YP_004036129.1| 649 IDNAT 653
                                       44433 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.11
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwe.rlledtssstseeldetrteLrkalrsiewdledLeetvriveknp 71 
                                       +eV +  ++++++ ++ + + ++++  +  e+   +  ++ ++l++++ d+  Le + +  e + 
  gi|313125859|ref|YP_004036129.1| 661 QEVLSMTDEIAGISEETTaEAQTVS--AAAEQQTAAVGDVTNELSTLKDDIARLETSLARFEVSG 723
                                       5677777777777777753444443..34788888889999999999999999999886655544 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.4   1.6e+03      90     123 ..     392     425 ..     386     431 .. 0.79
   2 ?    8.0   0.3    0.0055       2.6      58     117 ..     427     486 ..     407     493 .. 0.85
   3 ?   -2.5   0.1       9.2   4.3e+03      90     112 ..     525     547 ..     509     559 .. 0.44
   4 ?   -1.3   0.1         4   1.9e+03      79     116 ..     577     618 ..     572     644 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.4
                           DUF1759  90 edasqlrrivdavneivralealgeeadkydail 123
                                       +d + +r+i  a ne++  +e+  + ++ ++a +
  gi|313125859|ref|YP_004036129.1| 392 SDSADMRTIATAYNEMMDEVEQTVQRTRAFSADV 425
                                       5778899999999999999999999988877655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0055
                           DUF1759  58 aaveaLkkrYdnkrkiirellnelmklpslkeedasqlrrivdavneivralealgeead 117
                                         v++L +r d+ ++  +e   +++++ +  +++ ++l++++d+vn +   +e+++  a+
  gi|313125859|ref|YP_004036129.1| 427 DLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIEEISSSAN 486
                                       46899************************99********************999988776 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 9.2
                           DUF1759  90 edasqlrrivdavneivraleal 112
                                       +++++l +   ++ eiv  + ++
  gi|313125859|ref|YP_004036129.1| 525 QEVHKLDEQLGEIGEIVDVITEI 547
                                       22222333333333333333333 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 4
                           DUF1759  79 nelmklpslkeedasqlrrivdavn....eivralealgeea 116
                                       ne+ +l + ++++a+ + +++++++    e+v  +e++ ee+
  gi|313125859|ref|YP_004036129.1| 577 NEVKQLAQETKSSAADISALIEEIEtqrdEVVGSIERMREEV 618
                                       566666666677777777777777611113344444444444 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4      0.86   4.1e+02      17      55 ..     406     444 ..     393     465 .. 0.48
   2 ?    5.3   1.5     0.027        13       6      56 ..     476     533 ..     469     537 .. 0.76
   3 ?    7.5   0.6    0.0054       2.5       5      59 ..     594     648 ..     592     654 .. 0.92
   4 ?    2.1   0.1      0.25   1.2e+02      15      64 ..     667     716 ..     659     731 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.86
                              DegS  17 eifeIaEsarkeverlkkeleelkeevsevikevdklek 55 
                                       e+++  E++ + ++  + ++++l ++++e  +ev++ ++
  gi|313125859|ref|YP_004036129.1| 406 EMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQ 444
                                       333333333333333333333333333333333333333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.027
                              DegS   6 ktietiekskeeifeIaEsarkeverlkke.......leelkeevsevikevdklekk 56 
                                         ie i +s +e++ +aE+a++e ++ ++        +++++ee++++++ev kl+++
  gi|313125859|ref|YP_004036129.1| 476 ASIEEISSSANELVMLAERAKDEGHEGERAaenalggIDDIREETERTVQEVHKLDEQ 533
                                       57999****************9987666541122222678899999999999888765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0054
                              DegS   5 kktietiekskeeifeIaEsarkeverlkkeleelkeevsevikevdklekkerk 59 
                                       + +ie ie+ ++e++   E+ r+ev++  + ++e  + +  ++++v++++   ++
  gi|313125859|ref|YP_004036129.1| 594 SALIEEIETQRDEVVGSIERMREEVDDGADSVDEALQSLGGIVERVEDTAVSAKE 648
                                       6789*******************************************99887775 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.25
                              DegS  15 keeifeIaEsarkeverlkkeleelkeevsevikevdklekkerkarkrL 64 
                                        +ei  I+E++ +e + ++   e+    v +v +e  +l+ +  +    L
  gi|313125859|ref|YP_004036129.1| 667 TDEIAGISEETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETSL 716
                                       57899999999999999999999999999998888888877766665555 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.14        67      35     132 ..      47      85 ..      39     168 .. 0.51
   2 ?    3.9   2.9     0.086        41      25     116 ..     359     450 ..     355     460 .. 0.85
   3 ?   10.7   1.4   0.00069      0.33      12     101 ..     462     551 ..     455     571 .. 0.82
   4 ?    1.3   8.8      0.53   2.5e+02      57     199 ..     577     710 ..     559     718 .. 0.39

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.14
                               ERM  35 aelLaekarr.aeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLke 110
                                       a +L+e ar  ++ +ae+ + + ++ e+e +rl                                            
  gi|313125859|ref|YP_004036129.1|  47 ASELNEDARAnLQAAAEREAIQVEQWEQERKRLTS------------------------------------------ 81 
                                       34444433321222233333333333444444332.......................................... PP

                               ERM 111 eleeareaeeeakekllealst 132
                                                         ++++
  gi|313125859|ref|YP_004036129.1|  82 ------------------VVAR 85 
                                       ..................2222 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.086
                               ERM  25 qeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserk 101
                                       +++L+++ + ae + e + +a         +a    + ++ ++ + ++ + e e+  +++r++++ +++l+    ++
  gi|313125859|ref|YP_004036129.1| 359 RDDLQDQRDDAESYSEVMVQAADGDLTVRLDADSDSADMRTIATAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAER 435
                                       56788888888888888888888888888888888899999999999999999999999999********9999999 PP

                               ERM 102 eeeaerLkeeleear 116
                                       + e+++  +e+  a 
  gi|313125859|ref|YP_004036129.1| 436 ADEVNEASQEVSSAI 450
                                       999999999998775 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00069
                               ERM  12 erLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreae 88 
                                       + L ++ +e++   +  +e    a++L   a+ra+ e  + e+ a++a   i+ ++e++e++ +e +kl ++l e  
  gi|313125859|ref|YP_004036129.1| 462 DNLASVSDEVNDLSASIEEISSSANELVMLAERAKDEGHEGERAAENALGGIDDIREETERTVQEVHKLDEQLGEIG 538
                                       56778888999999999999999999999999999999999999999999999999999999999999999999999 PP

                               ERM  89 leaarleeeserk 101
                                       + +  ++e  e+ 
  gi|313125859|ref|YP_004036129.1| 539 EIVDVITEIAEQT 551
                                       8888888877764 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.53
                               ERM  57 aeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstp 133
                                       +e+++  q+ k sa++  +  e++e++ +e+   ++r++ee++                 ++  ea + l  ++++ 
  gi|313125859|ref|YP_004036129.1| 577 NEVKQLAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDD--------------GADSVDEALQSLGGIVERV 639
                                       44455555555555555555555555555555555555555554..............4444444444444444444 PP

                               ERM 134 skseseenveeseteeeeenseeesaele..tdeveklsleieeeRvtyleksk.......rlqeqLkeLksele 199
                                       +++     v+++e ++++ +++++s+e+   tde++ +s+e+  e +t+    +        + + L++Lk +++
  gi|313125859|ref|YP_004036129.1| 640 EDT----AVSAKEIDNATADQADSSQEVLsmTDEIAGISEETTAEAQTVSAAAEqqtaavgDVTNELSTLKDDIA 710
                                       322....11111111111111111211110122222222222222222222222000000045555555555554 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.52   2.4e+02      20      59 ..     405     441 ..     391     453 .. 0.36
   2 ?    7.8   1.4    0.0058       2.8       8      63 ..     439     494 ..     428     500 .. 0.79
   3 ?   -1.0   0.0         3   1.4e+03      44      68 ..     517     541 ..     507     559 .. 0.51
   4 ?   -0.7   0.1       2.6   1.2e+03      11      38 ..     578     602 ..     570     631 .. 0.50
   5 ?    4.3   0.1     0.073        34       5      65 ..     611     671 ..     607     676 .. 0.91
   6 ?    2.9   0.4      0.19        91       8      74 ..     656     722 ..     651     736 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.52
                             Sec34  20 dealeqLeeleekfksvsektsslheaceqlleeqkrlee 59 
                                       +e+++++e+  ++ ++ s++ s+l +   +l e  ++++e
  gi|313125859|ref|YP_004036129.1| 405 NEMMDEVEQTVQRTRAFSADVSDLVT---RLAERADEVNE 441
                                       33333333333333333333332222...12222222222 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0058
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                        +e  +e+ + ++++ +  ++ +++  svs++ ++l+++ e++ ++ ++l  lae 
  gi|313125859|ref|YP_004036129.1| 439 VNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIEEISSSANELVMLAER 494
                                       4555667777777777777888899999***************9999999999986 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3
                             Sec34  44 heaceqlleeqkrleelaeeieekL 68 
                                       +e++e+ ++e ++l+e   ei e +
  gi|313125859|ref|YP_004036129.1| 517 REETERTVQEVHKLDEQLGEIGEIV 541
                                       3344444444444444444443333 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.6
                             Sec34  11 ecdelleqtdealeqLeeleekfksvse 38 
                                       e+++l ++t++   +++ l e+   +++
  gi|313125859|ref|YP_004036129.1| 578 EVKQLAQETKSSAADISALIEE---IET 602
                                       3344444444333333333332...222 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.073
                             Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                       +e+ +ee+d+  +++deal++L  + e++++ + + +++++a+ +  ++ +++ ++++ei 
  gi|313125859|ref|YP_004036129.1| 611 IERMREEVDDGADSVDEALQSLGGIVERVEDTAVSAKEIDNATADQADSSQEVLSMTDEIA 671
                                       67788999999999*******************************9999999999999985 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.19
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeel 74 
                                       + ++ +e+l+ tde+    ee + + ++vs+  ++  +a  ++++e + l++    +e+ L  Fe  
  gi|313125859|ref|YP_004036129.1| 656 QADSSQEVLSMTDEIAGISEETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIARLETSLARFEVS 722
                                       5677899999999999999999999999999999999999999999888888888888898888765 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3      0.38   1.8e+02     105     146 ..     392     432 ..     357     437 .. 0.82
   2 ?   10.2   1.1    0.0011      0.54       8      68 ..     437     497 ..     431     553 .. 0.84
   3 ?   -0.2   0.8       1.9   9.1e+02      36      75 ..     609     648 ..     575     718 .. 0.49

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.38
                       Serine_rich 105 sceWslealasdkkqekpddlDrlvmvartvpdDvkqlasfi 146
                                       s + ++ ++a+  ++   d++++ v  +r+ + Dv++l++ +
  gi|313125859|ref|YP_004036129.1| 392 SDSADMRTIATAYNEM-MDEVEQTVQRTRAFSADVSDLVTRL 432
                                       4455666777777554.9******************999866 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                       Serine_rich   8 etlarlqqevesavskLlsfvsskWRskenleanlqeirlavdrlrtslrefleFargala 68 
                                       +++++  qev+sa++++ + +s++    ++++ +++++ ++++++++s +e++ +a++a  
  gi|313125859|ref|YP_004036129.1| 437 DEVNEASQEVSSAIQQISDGASQQSDNLASVSDEVNDLSASIEEISSSANELVMLAERAKD 497
                                       5678899*************************************************99875 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.9
                       Serine_rich  36 enleanlqeirlavdrlrtslrefleFargalanaaklsd 75 
                                        ++e+  +e+   +d++ ++l+++    +++  +a+++++
  gi|313125859|ref|YP_004036129.1| 609 GSIERMREEVDDGADSVDEALQSLGGIVERVEDTAVSAKE 648
                                       4445555555555555555555555555555555544332 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       1.8   8.4e+02      19      53 ..      46      80 ..      41     149 .. 0.81
   2 ?    6.1   3.4     0.022        10      15      78 ..     402     468 ..     397     571 .. 0.72
   3 ?    4.9   0.5     0.052        25      28      79 ..     576     627 ..     556     647 .. 0.81
   4 ?    5.1   1.2     0.046        22      18      72 ..     657     711 ..     646     733 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.8
                            GldM_N 19 nasekNaalyasleakaeenpekakewlekAkevk 53
                                       ase N+++ a+l+a+ae +  ++++w ++ k + 
  gi|313125859|ref|YP_004036129.1| 46 TASELNEDARANLQAAAEREAIQVEQWEQERKRLT 80
                                      67888999999999999999999999998877665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                            GldM_N  15 rsnenasekNaalyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggk...d 78 
                                       ++ ++++++ ++++++ +a  ++  + ++ ++e A+ev+++s+e+ + i+++ +   +++++     
  gi|313125859|ref|YP_004036129.1| 402 TAYNEMMDEVEQTVQRTRAFSADVSDLVTRLAERADEVNEASQEVSSAIQQISDGASQQSDNLasvS 468
                                       5666777888888888888888888888889999999999999999999999998888888653331 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.052
                            GldM_N  28 yasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkde 79 
                                        ++ ++ a+e++  a+++ +  +e++++ de++  ie ++ee+ + a+  de
  gi|313125859|ref|YP_004036129.1| 576 SNEVKQLAQETKSSAADISALIEEIETQRDEVVGSIERMREEVDDGADSVDE 627
                                       5677888888888889999999999999999999999999998888887776 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.046
                            GldM_N  18 enasekNaalyasleakaeenpekakewlekAkevkkksdelynyiealKeeivk 72 
                                       + +s++  ++ ++++   ee+ ++a+ + + A++  ++  +++n + +lK++i++
  gi|313125859|ref|YP_004036129.1| 657 ADSSQEVLSMTDEIAGISEETTAEAQTVSAAAEQQTAAVGDVTNELSTLKDDIAR 711
                                       55667777788889999999999999999999999999999********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (751 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1784  (0.0995036); expected 358.6 (0.02)
Passed bias filter:                      791  (0.0441185); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); expected 17.9 (0.001)
Passed Fwd filter:                        93  (0.00518713); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 1.63u 0.40s 00:00:02.02 Elapsed: 00:00:00.61
# Mc/sec: 3720.51
//
Query:       gi|313125860|ref|YP_004036130.1|  [L=115]
Description: hypothetical protein Hbor_10950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-05   22.4   1.0    0.00012   21.6   1.0    1.4  1  zinc_ribbon_2  zinc-ribbon domain
    0.00032   20.7   0.6    0.00046   20.2   0.6    1.3  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
       0.18   11.4   1.4       0.34   10.6   1.4    1.4  1  zf-tcix        Putative treble-clef, zinc-finger, Zn-binding
       0.79    9.1   3.3       0.47    9.8   0.4    1.9  2  zf-RanBP       Zn-finger in Ran binding protein and others


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.0   2.8e-08   0.00012       2      19 ..      92     109 ..      91     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.8e-08
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyC 19 
                                       C++CGa+++  a FC  C
  gi|313125860|ref|YP_004036130.1|  92 CSRCGAPNPSYAAFCDVC 109
                                       ***************999 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.6     1e-07   0.00046       1      22 [.      92     113 ..      76     115 .] 0.76

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1e-07
                               DZR   1 CpqCgeelppdarfCseCgtkl 22 
                                       C++Cg+++p+ a fC+ C +++
  gi|313125860|ref|YP_004036130.1|  92 CSRCGAPNPSYAAFCDVCLARI 113
                                       7777777777777777776665 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.4   7.6e-05      0.34      13      27 ..      92     106 ..      90     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.6e-05
                           zf-tcix  13 CpkCGtyNGtRglsC 27 
                                       C++CG+ N++ + +C
  gi|313125860|ref|YP_004036130.1|  92 CSRCGAPNPSYAAFC 106
                                       *************99 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4    0.0001      0.47      14      30 .]      85     101 ..      83     101 .. 0.78
   2 ?   -0.7   0.1       0.2     9e+02       7      12 ..     106     111 ..     106     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0001
                                       EESSSSB-TTT--BTSC CS
                          zf-RanBP  14 NfawstkCvaCqapkpd 30 
                                       N ++  +C +C+ap+p+
  gi|313125860|ref|YP_004036130.1|  85 NVPSGATCSRCGAPNPS 101
                                       5566669*******995 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.2
                                       -SSS-- CS
                          zf-RanBP   7 CskClv 12 
                                       C++Cl+
  gi|313125860|ref|YP_004036130.1| 106 CDVCLA 111
                                       999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 669.83
//
Query:       gi|313125861|ref|YP_004036131.1|  [L=87]
Description: hypothetical protein Hbor_10960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 550.57
//
Query:       gi|313125862|ref|YP_004036132.1|  [L=289]
Description: succinyl-CoA synthetase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-25   89.7   2.7      2e-25   89.3   1.2    2.0  2  CoA_binding    CoA binding domain
      1e-12   48.1   1.1    2.2e-12   47.0   1.1    1.5  1  Ligase_CoA     CoA-ligase
    1.8e-09   37.5   0.0    2.8e-09   36.9   0.0    1.3  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.5e-06   28.7   0.1    3.6e-05   24.2   0.1    2.3  2  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   1.2   4.5e-29     2e-25       2      96 .]       7      99 ..       6      99 .. 0.98
   2 ?   -2.0   0.0       1.3     6e+03      34      38 ..     176     180 ..     147     230 .. 0.63

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 4.5e-29
                                      TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding  2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80
                                       dt+v+v+G++g   +g +h++++ +yg+++v+g  p+k+g+ev+g+pvy++v++++e+ ++d++v++vP+++a +av 
  gi|313125862|ref|YP_004036132.1|  7 DDTRVVVQGITGG--EGNFHTQQMVEYGTNVVAGAVPGKGGQEVDGIPVYDTVNQAVEEEDADASVVFVPPAFAGDAVF 83
                                      79*********99..999*****************************************88****************** PP

                                      HHHHTT-SEEEEESST CS
                       CoA_binding 81 elveagikgiviiteg 96
                                      e++++   ++v+iteg
  gi|313125862|ref|YP_004036132.1| 84 EALDTDLDLVVAITEG 99
                                      **************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                       EEC-T CS
                       CoA_binding  34 fgvnp 38 
                                       +g+++
  gi|313125862|ref|YP_004036132.1| 176 IGIGG 180
                                       33333 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   1.1     5e-16   2.2e-12       1     151 [.     151     271 ..     151     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 5e-16
                                       EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEE CS
                        Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvi 77 
                                       ++++GtL+y  +  +++               g +q++ i++G+d            +t++ +al+ + ad+ ++++
  gi|313125862|ref|YP_004036132.1| 151 VSRSGTLTYQVVSNLTDR--------------GIGQTTAIGIGGDPII---------GTSFVDALELFEADKDTDAV 204
                                       689***************..............***************7.........******************** PP

                                       EEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHT.TTSSEEE-SSHHHHHHH CS
                        Ligase_CoA  78 lldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakalee.agveiasskaqalraak 151
                                       ++ +++G g+ e++aa+++++  +        pv  ++aG +a+p++++++a+a+ + +g  +a+sk  al  a+
  gi|313125862|ref|YP_004036132.1| 205 VMCGEIG-GEDEEQAAKYIAENMD-------TPVAGFIAGRTAPPGKRMGHAGAIVSgSGTGTAESKISALNDAG 271
                                       *******.*******999976555.......59******************999877368889999999988776 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   6.2e-13   2.8e-09       2     134 ..     146     284 ..     145     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.2e-13
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsirdgrkflsaar 76 
                                       G+++l+s SG+l  ++++ +++rg+g  +++ +G    + +++ d le +++d++t++++++ E  ++ ++   aa+
  gi|313125862|ref|YP_004036132.1| 146 GNVGLVSRSGTLTYQVVSNLTDRGIGQTTAIGIGGdpIIGTSFVDALELFEADKDTDAVVMCGEIGGEDEEQ--AAK 220
                                       9*********************************94458889**********************88777664..444 PP

                      Succ_CoA_lig  77 raark..kpvvvlksGr....seagaraaashtgalagsdavvdaafrqaGvlrvdsleelfda 134
                                        +a++   pv  + +Gr     ++   a a  +g+ +g  +   +a++ aGv + d+ +e++d 
  gi|313125862|ref|YP_004036132.1| 221 YIAENmdTPVAGFIAGRtappGKRMGHAGAIVSGSGTGTAESKISALNDAGVPVGDTPNEVADH 284
                                       44444449*********43333445556677788888888899999999999999998888775 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1     8e-09   3.6e-05      17     114 ..      22     128 ..      11     130 .. 0.77
   2 ?    1.8   0.0     0.071   3.2e+02       6      61 ..     148     206 ..     148     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8e-09
                                       HHHHHHHHHHT--EEE..ESSS-..SEETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-T CS
                     CoA_binding_2  17 ykvlryllehglpvvp..Vnpke..eeilgekvyaslaed..pepvdlvdvftppeatpeivkealalgakavwlqp 87 
                                       +  +++++e g +vv+  V p +  +e++g +vy +++++  +e+ d+ +vf+pp+ + + v eal+ +   v+   
  gi|313125862|ref|YP_004036132.1|  22 NFHTQQMVEYGTNVVAgaV-PGKggQEVDGIPVYDTVNQAveEEDADASVVFVPPAFAGDAVFEALDTDLDLVVAIT 97 
                                       5556667776666664213.33246*************84489*************************999888777 PP

                                       T....---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  88 g....sedeeaaelaeeagirvvgdrCilve 114
                                       +       +++ +++ e +  +vg++C++++
  gi|313125862|ref|YP_004036132.1|  98 EgiptQDMAKVNKRLSEVDTHLVGPNCPGLI 128
                                       665544445566666668999******9986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.071
                                       ET--S-TTSHHHHHHHHHHHHT.--EEEESSS-SEETTEES----T......T--EEEE CS
                     CoA_binding_2   6 vGasdnpgkfgykvlryllehg.lpvvpVnpkeeeilgekvyaslae.d.pepvdlvdv 61 
                                       vG+ +++g   y+v+++l ++g  + +++   ++ i g   +  l+  + +++ d+v++
  gi|313125862|ref|YP_004036132.1| 148 VGLVSRSGTLTYQVVSNLTDRGiGQTTAIGIGGDPIIGTSFVDALELfEaDKDTDAVVM 206
                                       79999999************885588888888888888776666663223566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1948.43
//
Query:       gi|313125863|ref|YP_004036133.1|  [L=381]
Description: succinyl-CoA synthetase subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-68  228.8   1.2    8.8e-68  227.8   1.2    1.5  1  ATP-grasp_2  ATP-grasp domain
    3.8e-19   69.0   7.5    8.4e-19   67.9   3.8    2.5  2  ATP-grasp_5  ATP-grasp domain
    2.1e-13   50.3   1.5    6.2e-13   48.8   1.5    1.7  1  Ligase_CoA   CoA-ligase
    1.1e-10   41.4   3.6    2.4e-09   37.0   0.8    2.4  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
    1.3e-08   34.6   0.2    2.6e-08   33.6   0.2    1.5  1  ATP-grasp    ATP-grasp domain
    3.2e-07   30.3   0.3    3.2e-07   30.3   0.3    2.2  2  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.8   1.2   2.9e-71   8.8e-68       1     201 [.       2     194 ..       2     195 .. 0.99

  Alignments for each domain:
  == domain 1  score: 227.8 bits;  conditional E-value: 2.9e-71
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTT CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellg 77 
                                       +lhEyqak+i+a+ g++vpe+++a+s +e+ ea++++g  + ++KaQv++GGRGKagG+k++++++ea+eaa+++lg
  gi|313125863|ref|YP_004036133.1|   2 RLHEYQAKDIFAEAGIPVPESRLATSVDEVMEAVEEIGYPA-AIKAQVHVGGRGKAGGIKIATDEDEAREAAEDILG 77 
                                       59*************************************99.*********************************** PP

                                       SEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB- CS
                       ATP-grasp_2  78 kelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakgl 154
                                       ++l+       G +vekvlve  +d++ ElY++i++Dr + k+v+++S+eGGv+iEeva+++Pe+i++ +idpa gl
  gi|313125863|ref|YP_004036133.1|  78 MDLK-------GYTVEKVLVEAGVDFENELYVGITMDRGEGKPVAMVSTEGGVNIEEVAEETPEAIAREHIDPAFGL 147
                                       ****.......****************************************************************** PP

                                       -HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                       ATP-grasp_2 155 keeqareiakklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                       +++qar+++ ++g++++++ ++a i+++ly+l+ ++da+ +EiNP++
  gi|313125863|ref|YP_004036133.1| 148 HPYQARKVVYEAGIPHDVAGDVATILSTLYDLYESKDASDIEINPVM 194
                                       *********************************************86 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   3.8   2.8e-22   8.4e-19       9     222 .]       2     210 ..       1     210 [. 0.83
   2 ?    2.0   0.1     0.039   1.2e+02      30      90 ..     319     378 ..     301     381 .] 0.78

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 2.8e-22
                       ATP-grasp_5   9 lLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeil 85 
                                        L e++ak++++  gipv+e+rla+s++e++ea+eeigyp ++K ++ ++  + ++gG+++  +d++e r+aae+il
  gi|313125863|ref|YP_004036133.1|   2 RLHEYQAKDIFAEAGIPVPESRLATSVDEVMEAVEEIGYPAAIKAQV-HVGGRGKAGGIKI-ATDEDEAREAAEDIL 76 
                                       589*****************************************996.6999*********.89************9 PP

                       ATP-grasp_5  86 ervkekspeariegvlVqemakrggrElivgvteDpvFG.pvilf.GlGGtavevlkdvavalpplnstlarelier 160
                                              ++  +e+vlV+  ++  + El vg+t D   G pv ++  +GG+ +e +++ +   p +  ++  +    
  gi|313125863|ref|YP_004036133.1|  77 GM---DLKGYTVEKVLVEAGVD-FENELYVGITMDRGEGkPVAMVsTEGGVNIEEVAEET---PEAIAREHIDPAFG 146
                                       97...3457899*******999.9***************444444256999999877776...44444444444445 PP

                       ATP-grasp_5 161 tkaskllkg.vrgekkadla.aleellvrlsqLvvdlpeIreldinPllveeeg.vvalDarirl 222
                                       ++ +++ k  ++   ++d+a  ++ +l++l +L ++ +  + ++inP+++++++ vva+Da++++
  gi|313125863|ref|YP_004036133.1| 147 LHPYQARKVvYEAGIPHDVAgDVATILSTLYDLYES-KDASDIEINPVMITSDReVVAADAVMNI 210
                                       666666666455444677543799999999999998.999**********99666********87 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.039
                       ATP-grasp_5  30 rlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervke 90 
                                        +a+  +ea+e ++ei  +vv++++  +     ++    l ++ ++ +++a+++ +e+++e
  gi|313125863|ref|YP_004036133.1| 319 EVAKGINEALESFDEIPKKVVVRLAGTNAEEGMEILNTDL-VEVEKTLEDAVQQAVENAQE 378
                                       6788899****************99988887777766666.66677777777777766655 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   1.5   2.1e-16   6.2e-13       3     150 ..     256     372 ..     252     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.1e-16
                                       SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEE CS
                        Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvill 79 
                                       nG++L + ++dl+                 g+e+++++d+G++a            +++ +al  + +d++v+++++
  gi|313125863|ref|YP_004036133.1| 256 NGAGLVMTTLDLVDYY--------------GGEPANFLDIGGGAK----------AERVANALDMVFSDENVDAVVF 308
                                       6777777777777777..............***************..........7********************* PP

                                       EEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHH CS
                        Ligase_CoA  80 divlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraa 150
                                       +i++G+ + +++a+++ +a+++ +    ++ vv+r+aGt+a+     e+ ++l++  ve+ ++ + a++ a
  gi|313125863|ref|YP_004036133.1| 309 NIFGGITRGDEVAKGINEALESFD--EIPKKVVVRLAGTNAE-----EGMEILNTDLVEVEKTLEDAVQQA 372
                                       ***********************8..999*************.....899999999888888888777665 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.8     8e-13   2.4e-09       4     102 ..       7     107 ..       5     136 .. 0.87
   2 !    4.6   0.1    0.0065        20      20      74 ..     318     372 ..     302     380 .. 0.74

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 8e-13
                                       HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTE....EEESSHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   4 sakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGm....rvarneeelaelvkkalaeaka 76 
                                       +ak++ +++++pv +s  a  ++++e++++++eigyP  ika + +GG+G     ++a++e+e +e+++  l +   
  gi|313125863|ref|YP_004036133.1|   7 QAKDIFAEAGIPVPESRLA--TSVDEVMEAVEEIGYPAAIKAQVHVGGRGKaggiKIATDEDEAREAAEDILGMDLK 81 
                                       689999**********999..***************************97433339********************* PP

                                       HHSTS-EEEEE--SSSEEEEEEEEEE CS
                       CPSase_L_D2  77 afgnkqvlvekslkgpkeiEvevlrD 102
                                        ++ ++vlve  ++   e+ v +  D
  gi|313125863|ref|YP_004036133.1|  82 GYTVEKVLVEAGVDFENELYVGITMD 107
                                       **********9887777766666655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0065
                                       ECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSH.HHHHHHHHHHHHHH CS
                       CPSase_L_D2  20 saapvetleealaiakeigyPviikaafglGGkGmrvarne.eelaelvkkalaea 74 
                                        ++ ++ ++eal+  +ei   v+++ a +   +Gm + +++  e++++++ a+++a
  gi|313125863|ref|YP_004036133.1| 318 DEV-AKGINEALESFDEIPKKVVVRLAGTNAEEGMEILNTDlVEVEKTLEDAVQQA 372
                                       444.788999*************************997654245555555555544 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.2   8.7e-12   2.6e-08       2      96 ..      13     117 ..      12     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 8.7e-12
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS.-CTTT..TEEEECTCCGHHCHHHHC........GTTCEE CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrl.gydGk..Gqsvvrseedleqaleal........keekvi 67 
                                       +++g+pvp+  +++s +e+ ea+ee+g+p+ +Ka+++ g  Gk  G ++  +e+++++a+e +        + ekv+
  gi|313125863|ref|YP_004036133.1|  13 AEAGIPVPESRLATSVDEVMEAVEEIGYPAAIKAQVHvGGRGKagGIKIATDEDEAREAAEDIlgmdlkgyTVEKVL 89 
                                       689******************************6654244554545578899999999999889****99999**** PP

                                       EEE----SEEEEEEEEEETTC-EEE--EE CS
                         ATP-grasp  68 vEefvpfekElsvlvvrsaeGetafypvv 96 
                                       vE  v+fe El v ++   +Ge + +++v
  gi|313125863|ref|YP_004036133.1|  90 VEAGVDFENELYV-GITMDRGEGKPVAMV 117
                                       **********965.555555554444444 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.3   1.1e-10   3.2e-07       6      90 ..       8      95 ..       4     118 .. 0.89
   2 ?    1.2   0.4      0.09   2.7e+02      26      73 ..     324     371 ..     314     379 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.1e-10
                                      HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT....-EEEESSHHHHHHHHHHHCTS-TTCCCC CS
                            GARS_A  6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagK....gvivakseeealkavkeilekkkfGeag 80
                                      akd++++agip +e +  t+++e+ e +ee + +a  +Ka+   +g+    g+++a++e+ea +a+++il     G + 
  gi|313125863|ref|YP_004036133.1|  8 AKDIFAEAGIPVPESRLATSVDEVMEAVEEIGYPA-AIKAQVHVGGRgkagGIKIATDEDEAREAAEDILGMDLKGYTV 85
                                      79*********************************.99999887776334469************************** PP

                                      SSEEEEE--- CS
                            GARS_A 81 ekvviEelle 90
                                      ekv++E  ++
  gi|313125863|ref|YP_004036133.1| 86 EKVLVEAGVD 95
                                      ******8765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.09
                                       HHHHHHHHHHHSSSEEEEEESC-GGGT-EEEE.SSHHHHHHHHHHHCTS CS
                            GARS_A  26 peeakeyieeatakalVvKadglaagKgviva.kseeealkavkeilek 73 
                                        +ea e ++e  +k+ Vv+ +g  a  g+ +  ++  e  k++++ +++
  gi|313125863|ref|YP_004036133.1| 324 INEALESFDEIPKKV-VVRLAGTNAEEGMEILnTDLVEVEKTLEDAVQQ 371
                                       678888899999999.************999844556777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2300.71
//
Query:       gi|313125864|ref|YP_004036134.1|  [L=62]
Description: hypothetical protein Hbor_10990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00077   18.9   3.8      0.086   12.4   0.4    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0055   16.6   3.0       0.19   11.6   0.1    2.2  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.016   14.8   1.4       0.81    9.3   0.1    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.02   14.8   0.3        4.6    7.3   0.0    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.021   14.8   1.2        4.8    7.3   0.1    2.2  2  Rubredoxin      Rubredoxin
      0.022   14.1   0.3        1.3    8.4   0.0    2.2  2  zf-TFIIB        Transcription factor zinc-finger
      0.023   14.9   0.6        2.8    8.2   0.0    2.2  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.026   14.6   1.3       0.24   11.5   1.3    2.0  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.054   12.9   1.3        1.4    8.5   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
       0.11   12.2   3.4        5.7    6.7   0.5    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.14   12.3   3.1        4.2    7.5   0.2    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.15   11.9   0.3        2.9    7.8   0.0    2.1  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
       0.35   10.8   2.6          2    8.4   0.2    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        0.4   10.5   3.6       0.48   10.2   0.2    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
       0.55   10.8   2.7          8    7.1   0.2    2.2  2  zf-C2H2         Zinc finger, C2H2 type
       0.67   10.1   4.5        8.4    6.6   1.7    2.1  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2    0.0018         2       2      16 ..       5      19 ..       4      23 .. 0.87
   2 !   12.4   0.4   7.7e-05     0.086      19      28 ..      48      57 ..      44      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                                      EETTTTCEECHEETS CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpe 16
                                      +CP+C   +++ D++
  gi|313125864|ref|YP_004036134.1|  5 RCPDCDVAMQESDYD 19
                                      7*****999999987 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.7e-05
                                      CEEESSSSBE CS
                      TF_Zn_Ribbon 19 elvCtdCGlV 28
                                      ++vC++CGlV
  gi|313125864|ref|YP_004036134.1| 48 TYVCPECGLV 57
                                      699*****99 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4     0.012        13      13      18 ..       5      10 ..       2      13 .. 0.75
   2 !   11.6   0.1   0.00017      0.19       9      24 ..      46      61 ..      42      62 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                           DUF35_N 13 rCpdCG 18
                                      rCpdC+
  gi|313125864|ref|YP_004036134.1|  5 RCPDCD 10
                                      888887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00017
                           DUF35_N  9 LvgqrCpdCGtvqfPP 24
                                      Lv   Cp CG v+f++
  gi|313125864|ref|YP_004036134.1| 46 LVTYVCPECGLVRFYA 61
                                      78889*********97 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.018        20       4      16 ..       5      17 ..       3      19 .. 0.82
   2 ?    9.3   0.1   0.00072      0.81       2       9 ..      48      55 ..      47      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.018
                            zf_UBZ  4 lCerCgkeipese 16
                                       C++C+  ++es+
  gi|313125864|ref|YP_004036134.1|  5 RCPDCDVAMQESD 17
                                      6*****9998887 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00072
                            zf_UBZ  2 tylCerCg 9 
                                      ty+C++Cg
  gi|313125864|ref|YP_004036134.1| 48 TYVCPECG 55
                                      8******9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0091        10      19      27 ..       4      12 ..       2      28 .. 0.76
   2 ?    7.3   0.0    0.0041       4.6      19      30 ..      49      60 ..      39      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0091
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                      ++CP C ++
  gi|313125864|ref|YP_004036134.1|  4 RRCPDCDVA 12
                                      67****988 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0041
                     Zn_Tnp_IS1595 19 fvCPhCgsrkay 30
                                       vCP Cg  ++y
  gi|313125864|ref|YP_004036134.1| 49 YVCPECGLVRFY 60
                                      59*****76666 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0069       7.8      36      43 ..       5      12 ..       2      18 .. 0.82
   2 ?    7.3   0.1    0.0043       4.8      34      42 ..      48      56 ..      47      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0069
                                      BBTTTB-B CS
                        Rubredoxin 36 vCPdCgve 43
                                      +CPdC+v 
  gi|313125864|ref|YP_004036134.1|  5 RCPDCDVA 12
                                      7****997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0043
                                      T-BBTTTB- CS
                        Rubredoxin 34 dWvCPdCgv 42
                                      ++vCP+Cg+
  gi|313125864|ref|YP_004036134.1| 48 TYVCPECGL 56
                                      699****96 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0012       1.3       2      14 ..       6      18 ..       5      30 .. 0.85
   2 ?    4.3   0.0     0.022        25      20      26 ..      49      55 ..      39      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                          zf-TFIIB  2 CPkCqdeleeser 14
                                      CP C ++++es+ 
  gi|313125864|ref|YP_004036134.1|  6 CPDCDVAMQESDY 18
                                      *********8875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.022
                          zf-TFIIB 20 dyCpqCr 26
                                      ++Cp+C+
  gi|313125864|ref|YP_004036134.1| 49 YVCPECG 55
                                      7899996 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.018        20      15      25 ..       3      13 ..       1      22 [. 0.74
   2 ?    8.2   0.0    0.0025       2.8       4      26 ..      36      59 ..      34      61 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.018
                     Auto_anti-p27 15 aetCpvCgvPL 25
                                      +  Cp+C v +
  gi|313125864|ref|YP_004036134.1|  3 SRRCPDCDVAM 13
                                      678****9866 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                     Auto_anti-p27  4 gelLlkGwt.MLaetCpvCgvPLm 26
                                      gel l+G t +   +Cp+Cg + +
  gi|313125864|ref|YP_004036134.1| 36 GELGLRGSTyLVTYVCPECGLVRF 59
                                      666677777344568****98876 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.3   0.00021      0.24       2      26 ..       6      58 ..       5      62 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                          zf-Mss51  2 CPvpkhkqt............................apkhvdfeCpdCGipt 26
                                      CP ++  ++                            +   v++ Cp+CG++ 
  gi|313125864|ref|YP_004036134.1|  6 CPDCDVAMQesdydvnanrdkvrlkpdgflgelglrgSTYLVTYVCPECGLVR 58
                                      666666665667777777777777778888888887778889********976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.039        43       3       9 ..       4      10 ..       3      17 .. 0.81
   2 ?    8.5   0.1    0.0012       1.4       4       9 ..      50      55 ..      47      57 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.039
                       zf-ribbon_3  3 vrCPnCG 9 
                                      +rCP C+
  gi|313125864|ref|YP_004036134.1|  4 RRCPDCD 10
                                      5899885 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                       zf-ribbon_3  4 rCPnCG 9 
                                       CP+CG
  gi|313125864|ref|YP_004036134.1| 50 VCPECG 55
                                      566665 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5    0.0051       5.7      21      28 ..       3      10 ..       2      13 .. 0.88
   2 ?    6.3   0.1     0.007       7.8      23      29 ..      50      56 ..      49      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0051
                     zf-NADH-PPase 21 arvCpaCg 28
                                      +r+Cp+C+
  gi|313125864|ref|YP_004036134.1|  3 SRRCPDCD 10
                                      79*****7 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.007
                     zf-NADH-PPase 23 vCpaCgl 29
                                      vCp Cgl
  gi|313125864|ref|YP_004036134.1| 50 VCPECGL 56
                                      8****98 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.016        18       2       7 ..       5      10 ..       4      15 .. 0.81
   2 ?    7.5   0.2    0.0038       4.2      16      21 ..      50      55 ..      48      57 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                           UPF0547  2 vCPeCe 7 
                                      +CP C+
  gi|313125864|ref|YP_004036134.1|  5 RCPDCD 10
                                      799998 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0038
                           UPF0547 16 fCphCG 21
                                      +Cp+CG
  gi|313125864|ref|YP_004036134.1| 50 VCPECG 55
                                      455555 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.11   1.2e+02      14      20 ..       4      10 ..       1      19 [. 0.80
   2 ?    7.8   0.0    0.0026       2.9      15      22 ..      48      57 ..      38      61 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                         zf-C2H2_3 14 sqCkeCg 20
                                      ++C+ C+
  gi|313125864|ref|YP_004036134.1|  4 RRCPDCD 10
                                      57****8 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0026
                         zf-C2H2_3 15 q..CkeCgMv 22
                                      +  C+eCg+v
  gi|313125864|ref|YP_004036134.1| 48 TyvCPECGLV 57
                                      235*****97 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.13   1.4e+02       6      11 ..       5      10 ..       5      13 .. 0.87
   2 ?    8.4   0.2    0.0018         2       4      11 ..      48      55 ..      48      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                    Zn_ribbon_SprT  6 rCtgCg 11
                                      rC++C+
  gi|313125864|ref|YP_004036134.1|  5 RCPDCD 10
                                      7****7 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0018
                    Zn_ribbon_SprT  4 vYrCtgCg 11
                                      +Y+C+ Cg
  gi|313125864|ref|YP_004036134.1| 48 TYVCPECG 55
                                      7******9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2      0.35   3.9e+02      24      28 ..       6      10 ..       4      14 .. 0.85
   2 ?   10.2   0.2   0.00043      0.48      22      30 ..      49      57 ..      48      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.35
                     A2L_zn_ribbon 24 CieCg 28
                                      C++C 
  gi|313125864|ref|YP_004036134.1|  6 CPDCD 10
                                      ****5 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00043
                     A2L_zn_ribbon 22 lvCieCgas 30
                                      +vC+eCg++
  gi|313125864|ref|YP_004036134.1| 49 YVCPECGLV 57
                                      8******87 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.069        77       2       7 ..       5      10 ..       5      13 .. 0.88
   2 ?    7.1   0.2    0.0071         8       1       8 [.      49      56 ..      49      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.069
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      +CpdC+
  gi|313125864|ref|YP_004036134.1|  5 RCPDCD 10
                                      7****8 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0071
                                      EEETTTTE CS
                           zf-C2H2  1 ykCpdCgk 8 
                                      y+Cp+Cg 
  gi|313125864|ref|YP_004036134.1| 49 YVCPECGL 56
                                      9*****94 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.031        35       3      14 ..       5      16 ..       4      23 .. 0.71
   2 ?    6.6   1.7    0.0075       8.4      21      26 .]      49      54 ..      48      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.031
                            zf-ACC  3 KCpsCgemlykk 14
                                      +Cp C   +   
  gi|313125864|ref|YP_004036134.1|  5 RCPDCDVAMQES 16
                                      7****8776555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0075
                            zf-ACC 21 yVCPkC 26
                                      yVCP+C
  gi|313125864|ref|YP_004036134.1| 49 YVCPEC 54
                                      9***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 375.96
//
Query:       gi|313125865|ref|YP_004036135.1|  [L=318]
Description: zn-dependent oxidoreductase, NADph:quinone reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-17   62.9   0.1    1.1e-16   62.1   0.1    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
      1e-13   51.4   0.0      2e-13   50.5   0.0    1.5  1  ADH_zinc_N    Zinc-binding dehydrogenase
    7.3e-10   38.7   0.0    1.1e-08   34.9   0.0    2.3  2  ADH_N         Alcohol dehydrogenase GroES-like domain
     0.0037   16.9   0.0     0.0046   16.6   0.0    1.1  1  NIF3          NIF3 (NGG1p interacting factor 3)
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.024   14.5   0.1    1.4  1  ADH_N_2       N-terminal domain of oxidoreductase
      0.024   13.9   0.1       0.04   13.2   0.1    1.3  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   3.6e-20   1.1e-16       1     133 []     185     316 ..     185     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.6e-20
                                       TT-SEEEETTSTTHH.HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----...S-EEE-CHHHCTTT-EEE CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe.aatggegvDvvldtvggealleaslkvlpggGrlvsiggpp..lsaallkpakkrkgrsvk 74 
                                       lGAd v+dy ++d++   t+ +  Dv+ldt   ++l +   ++ ++g+r++ +g++    s++   ++k  k+ + +
  gi|313125865|ref|YP_004036135.1| 185 LGADAVFDYNRDDLKrVITEVGTPDVILDTHMDHYL-QFDADIAADGARIIGVGNDTaeGSFTNIGVTK-SKELRYQ 259
                                       8**************633334789******886766.6666889888*******776565555555555.5556666 PP

                                       E--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  75 yeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                       +  +f  +++ q  +l +l +l+  G ++pv+ r+++leea eA r + +   +GKiVl
  gi|313125865|ref|YP_004036135.1| 260 FMSMF-NTPD-QPAVLSRLSDLLTRGDVEPVIHRTYDLEEAGEAQRNVIHDGFVGKIVL 316
                                       66666.3666.8999*******************************************8 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   6.6e-17     2e-13       1     116 [.     154     265 ..     154     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 6.6e-17
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG+ a+qlA+ +Ga+v++++s +   ++++ lGad+v++y+++dl+  i e      +dv++++    + l+   +
  gi|313125865|ref|YP_004036135.1| 154 GVGHVAIQLANTMGARVFTTSSPDY-HDKLEALGADAVFDYNRDDLKRVITEVG---TPDVILDTHM-DHYLQFDAD 225
                                       9*****************9887775.7**************6658888888888...9*********.********* PP

                                       CEEEEEEEEECSCTSSEEEEEHHHHH.HTT-EEEEE-SSC CS
                        ADH_zinc_N  78 llkpgGrlvvvGggkgeeefdlrnll.lkeksilGsllgs 116
                                       +++ g r+  vG  + e +f+   ++  ke++ +   + +
  gi|313125865|ref|YP_004036135.1| 226 IAADGARIIGVGNDTAEGSFTNIGVTkSKELRYQFMSMFN 265
                                       ************9555444444444447777777666666 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   3.8e-12   1.1e-08       2      60 ..      28      85 ..      27      91 .. 0.93
   2 ?    1.5   0.0     0.091   2.7e+02      87     106 ..      89     108 ..      86     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.8e-12
                                      TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEE CS
                             ADH_N  2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVv 60
                                      gev+++v aag++  D  + +g +     lp+++G +++G+v+ vg++v++++ GdrV+
  gi|313125865|ref|YP_004036135.1| 28 GEVVVEVGAAGVNPVDTYFREG-AYDVPYLPFTPGSDFAGTVVGVGEGVERFSFGDRVF 85
                                      69******************99.6888889****************************7 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.091
                                       TTTSS-SSSBSEEEECGGGE CS
                             ADH_N  87 lgvsldGgfaeyvvvpekkl 106
                                       lg +++G++ae++v p++ l
  gi|313125865|ref|YP_004036135.1|  89 LGNGMSGTYAEQIVSPTELL 108
                                       67779*********998766 PP

>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.5e-06    0.0046     149     215 ..     106     188 ..      39     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                              NIF3 149 elakklkkklglek.............vrvagdldkkvkkvaicaGsGa...slieeakakgaDlliTGelkhheal 209
                                       el+ +l ++++l+                v     ++v++v i +GsG+     i+ a+ +ga ++ T+  ++h+ l
  gi|313125865|ref|YP_004036135.1| 106 ELLTHLPEEVELTDaaafalvgttawqALVHHASVEPVETVLIHGGSGGvghVAIQLANTMGARVFTTSSPDYHDKL 182
                                       444444444444333333333333332333348999************98877899********************* PP

                              NIF3 210 dakekg 215
                                       +a  ++
  gi|313125865|ref|YP_004036135.1| 183 EALGAD 188
                                       997665 PP

>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   8.2e-06     0.024       8      90 ..       5      86 ..       2     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.2e-06
                           ADH_N_2  8 rpegaptesdfeleeeelpelkdGevlvralylSvDPymRgrmndaks.yvepvelgdvmrggavgeVveSknpdfkvG 85
                                      r++ +  ++ +++ e + pe++ Gev+v++   +v P   ++ + a +  + p++ g+  +g++vg  v    ++f+ G
  gi|313125865|ref|YP_004036135.1|  5 RFHEHGGPDVLTVDEIDEPEPGYGEVVVEVGAAGVNPVDTYFREGAYDvPYLPFTPGSDFAGTVVG--VGEGVERFSFG 81
                                      67777778899999*****************999988777665554440445*************9..56677888888 PP

                           ADH_N_2 86 dlVvg 90
                                      d V g
  gi|313125865|ref|YP_004036135.1| 82 DRVFG 86
                                      88876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.4e-05      0.04      26      88 ..     140     204 ..     120     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                       B---EEEEE..STSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCEC.EEHCHHHHHHHHH CS
                       AlaDh_PNT_C  26 vepakvlvi..GgGvaGlqAiatakglgakVtvlDvrparleqleslgakfv.evlksqeellaea 88 
                                       vep +++ i  G G +G  Ai+ a+ +ga+V  +  +p+   +le+lga  v +  + + + +  +
  gi|313125865|ref|YP_004036135.1| 140 VEPVETVLIhgGSGGVGHVAIQLANTMGARVFTT-SSPDYHDKLEALGADAVfDYNRDDLKRVITE 204
                                       456555555445699****************976.6789999999998884313333344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1968.78
//
Query:       gi|313125866|ref|YP_004036136.1|  [L=236]
Description: hypothetical protein Hbor_11010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-41  141.4   0.4    6.5e-41  140.4   0.4    1.4  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.9e-37  128.6   0.0    2.3e-37  128.4   0.0    1.1  1  adh_short     short chain dehydrogenase
    2.5e-05   23.9   0.2    3.3e-05   23.5   0.2    1.4  1  Epimerase     NAD dependent epimerase/dehydratase family
    0.00038   20.4   0.1    0.00071   19.5   0.1    1.4  1  KR            KR domain
  ------ inclusion threshold ------
      0.039   14.4   0.2      0.066   13.7   0.2    1.2  1  CdiI_4        CDI immunity protein
       0.09   12.3   0.1       0.21   11.1   0.1    1.7  1  NmrA          NmrA-like family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.4   0.4   2.2e-44   6.5e-41       1     229 [.      16     232 ..      16     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 2.2e-44
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnn 76 
                                       Ga   +G a+A a+ ++Ga+v+++d+ e + ++++ ++ e  g ++++ + tde++v ++ve vve++g++D+l n 
  gi|313125866|ref|YP_004036136.1|  16 GACGALGSAVAAAFRDAGATVAAADIVEPDdEDSLLDVDE--GVQFYHGNFTDEDDVSHTVESVVEDHGRIDFLANI 90 
                                       677789***********************96666666666..899******************************** PP

                                       ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeg.gsivnlssvgaervvpnynaygaaKaalealt 152
                                       ag  +    p++et+ + fd  +dvnl+ +fl +k+alp+++e+ g+iv +s  ++  + ++  +y a+Ka++  lt
  gi|313125866|ref|YP_004036136.1|  91 AGTWRG-GDPIHETDADTFDLLFDVNLKTMFLASKHALPHLQETeGAIVSVSARSSLEGGEGDGVYRASKAGVRLLT 166
                                       *****9.********************************998888******************************** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                        ++A e     +R Nav p++i+T++++++         ++       +++p e+a+++l L+sd++  ++G+ + v
  gi|313125866|ref|YP_004036136.1| 167 ETIATENLG-TVRANAVMPSVIDTPMNREMM------PDAD----HDAWVDPAEIARTVLALCSDATGVTSGAAVPV 232
                                       *****9888.8***************88775......2222....234699*********************99887 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.0   7.7e-41   2.3e-37       2     191 ..      11     196 ..      10     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 7.7e-41
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       v+lvtGa++ +G a+a ++  +Ga+v+++d+ e + e  +  + e    + +++++ td+++v+ +ve +v+++g++
  gi|313125866|ref|YP_004036136.1|  11 VALVTGACGALGSAVAAAFRDAGATVAAADIVEPDDEDSLLDVDEG---VQFYHGNFTDEDDVSHTVESVVEDHGRI 84 
                                       89*******************************9998888888874...**************************** PP

                                       SEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  79 dvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       d L n AG   g  p++e+++++++ +++vNl+ +fl+++++lp+ l++ +G+Iv vs   ++++ +g  +Y AsKa
  gi|313125866|ref|YP_004036136.1|  85 DFLANIAGTwRGGDPIHETDADTFDLLFDVNLKTMFLASKHALPH-LQETEGAIVSVSARSSLEGGEGDGVYRASKA 160
                                       *********99999*******************************.669**************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       +v+ lt+++a e   t +r nav+P ++dT+m++e  
  gi|313125866|ref|YP_004036136.1| 161 GVRLLTETIATENLGT-VRANAVMPSVIDTPMNREMM 196
                                       *************998.****************9876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   1.1e-08   3.3e-05       1      88 [.      12     108 ..      12     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-08
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HH....HHHHHHHHH.T-SEEE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrs....alerlfkee.qpdavi 69 
                                       +lVtGa G +Gsa++ a+ ++g +v + d  + +++ ++l+     +++++++td++     +e +++++ ++d   
  gi|313125866|ref|YP_004036136.1|  12 ALVTGACGALGSAVAAAFRDAGATVAAADIVEPDDEDSLLDVDegvQFYHGNFTDEDdvshTVESVVEDHgRIDFLA 88 
                                       59**********************9999988665555555544799***********77777888899999999999 PP

                                       E--S.---HHHHHHSHHHHH CS
                         Epimerase  70 hlAa.vggvaassedpadfi 88 
                                       ++A+   g +  +e+ ad++
  gi|313125866|ref|YP_004036136.1|  89 NIAGtWRGGDPIHETDADTF 108
                                       99887555555555556665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   2.4e-07   0.00071       3     153 ..      12     159 ..      11     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.4e-07
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        l+tG++G+LG ++a    + ga+     + +  +++d++   ++l + +  v++++   +d+d+v++++e++ +++
  gi|313125866|ref|YP_004036136.1|  12 ALVTGACGALGSAVAAAFRDAGATVA---AAD-IVEPDDE---DSLLDVDEGVQFYHGNFTDEDDVSHTVESVVEDH 81 
                                       59********************9732...233.4556666...567778889************************* PP

                                       S---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHH.HTTT..S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  80 ppikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhe.lled..esldffvlfSSiagllgsagqanYaaa 152
                                       ++i    + Ag+ r  +++ e++a++++ ++   +k +    + +l++  e+   +v +S  ++l g  g + Y a 
  gi|313125866|ref|YP_004036136.1|  82 GRIDFLANIAGTWRgGDPIHETDADTFDLLFDVNLKTMFLASKhALPHlqETEGAIVSVSARSSLEGGEGDGVYRAS 158
                                       ************995679**********9999988887655441444464566678888888888888888888886 PP

                                       H CS
                                KR 153 N 153
                                        
  gi|313125866|ref|YP_004036136.1| 159 K 159
                                       5 PP

>> CdiI_4  CDI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   2.2e-05     0.066      30      74 ..      28      76 ..      24      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                            CdiI_4 30 gfalegtycifpdenspdeeeyF....egVeFtvgypvdekdvidiVse 74
                                      +f+  g+ +  +d  +pd+e+      egV+F+ g ++de+dv + V+ 
  gi|313125866|ref|YP_004036136.1| 28 AFRDAGATVAAADIVEPDDEDSLldvdEGVQFYHGNFTDEDDVSHTVES 76
                                      6888999999************999**********99999999888864 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   7.1e-05      0.21       2      63 ..      13      75 ..      12      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.1e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEE.ES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHT CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvral.vRdtkselakslkeaGvelvkgdlddkeslvealk 63
                                      lv+Ga G++G++v++a+ +ag +v a  + +++ e +    ++Gv++ +g+  d++ +++ ++
  gi|313125866|ref|YP_004036136.1| 13 LVTGACGALGSAVAAAFRDAGATVAAAdIVEPDDEDSLLDVDEGVQFYHGNFTDEDDVSHTVE 75
                                      79**********************874355565554444457788888888888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1455.16
//
Query:       gi|313125867|ref|YP_004036137.1|  [L=460]
Description: snf family na+-dependent transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-48  164.5  28.6    5.4e-25   88.1  14.2    2.7  2  SNF       Sodium:neurotransmitter symporter family


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   6.4   4.4e-27   7.9e-23       1     114 [.       4     118 ..       4     122 .. 0.96
   2 !   88.1  14.2     3e-29   5.4e-25     182     478 ..     144     441 ..     132     452 .. 0.85

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 4.4e-27
                               SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrkic 77 
                                       Retw ++  fil++vG+avgLgn+W FP+ + + GG +fl+ Yl +++ +G+P +  e+ +G+++++ +i++++++ 
  gi|313125867|ref|YP_004036137.1|   4 RETWATRAGFILAAVGSAVGLGNIWQFPFKTAEFGGATFLVVYLAAVFGIGLPAMLAEFVIGRRSKRNTISAFERLD 80 
                                       9***************************************************************************7 PP

                               SNF  78 .PllkgiGyasivvalyvglyYnvilawalfYlfssft 114
                                         +++ +G   ++  +++  yY v+ +w l Y+  s+t
  gi|313125867|ref|YP_004036137.1|  81 hKKWRFVGAIGLLTGFWILSYYSVVGGWVLRYVGGSIT 118
                                       25799***************************999987 PP

  == domain 2  score: 88.1 bits;  conditional E-value: 3e-29
                               SNF 182 lcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdlekll.....epk.vWi 252
                                       + + +++ +v ++i  G+++++k++  + +   v+l  l v + +LpGa++g  ++l+pdl++l       p+  W+
  gi|313125867|ref|YP_004036137.1| 144 IFMTLVVGIVAFGIEDGIEKATKLMVPSIL---VILGALAVWAFTLPGASEGYGYFLSPDLSQLRltvesAPSfPWV 217
                                       45678899*******************999...*****************************995223222332476 PP

                               SNF 253 d...........aatqiffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgek 318
                                                   a +q ffsl++g+G++i++asY + ++ ++ d+  + + n+l+ +laglvv  +l      qg+ 
  gi|313125867|ref|YP_004036137.1| 218 SfggplaeiipfAVSQAFFSLSLGMGAMITYASYIDGDESLFGDSATIVVFNTLIGILAGLVVIPLLFA----QGV- 289
                                       544444445555899*************************************************99943....232. PP

                               SNF 319 isevaeeGpgLaFiaypealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltlivavl 395
                                         e  + G+g +Fi  + a +++pl+ + +++FFl++++++l s+++ +e++++  +D++ v   +r  + + +  +
  gi|313125867|ref|YP_004036137.1| 290 --EPGSGGAGALFISVAGAFANIPLGRVVGFVFFLVVLVAALSSAISLLEVVVSYAIDNYAV---SRPQMAVGLGGT 361
                                       ..23578*******************************************************...999999****** PP

                               SNF 396 aflvglllvtegGiyvltlldkyaaslsllvvvlleaiavawvyglkkflddikemlgfrpllflklcwkfvsplll 472
                                       +fl+gl    ++   +lt++d+ a +l l + vl  +    wv+g    ++++ + + f  ++ +++ w + s ++l
  gi|313125867|ref|YP_004036137.1| 362 IFLLGLPSAWDT--AWLTWFDNLAYQLLLPASVLGILTFSGWVFGRPA-VEELLRGTNFGDSIGVTWLWLVRSVVFL 435
                                       ******988775..69******99988777777777777789999765.6788888899999999999999998888 PP

                               SNF 473 lvllia 478
                                       +v+l+ 
  gi|313125867|ref|YP_004036137.1| 436 AVILTL 441
                                       888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2722.26
//
Query:       gi|313125868|ref|YP_004036138.1|  [L=472]
Description: snf family na+-dependent transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-40  137.4  32.9    1.2e-20   73.8  12.2    2.7  3  SNF       Sodium:neurotransmitter symporter family


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   8.2   1.9e-24   3.4e-20       1     113 [.       3     117 ..       3     131 .. 0.90
   2 !   73.8  12.2   6.6e-25   1.2e-20     182     396 ..     150     359 ..     136     402 .. 0.85
   3 ?   -0.7   0.1     0.023   4.2e+02     349     380 ..     430     461 ..     420     471 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 1.9e-24
                               SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrkic 77 
                                       Retw ++  fil++vG+avgLgn+WRFP+++ +nGG afl  Yl ++l++G+P +   + +G+++++  +++ r ++
  gi|313125868|ref|YP_004036138.1|   3 RETWATRAGFILAAVGSAVGLGNIWRFPWITAENGGSAFLAVYLGIVLLVGVPGLLGMFVIGRRAKRNPVGALRSLS 79 
                                       9****************************************************99999****************998 PP

                               SNF  78 Pl..lkgiGyasivvalyvglyYnvilawalfYlfssf 113
                                           +   G   i  +l++  +Y v+ +w l Y+ +s+
  gi|313125868|ref|YP_004036138.1|  80 GSnrWGFAGGFLIFSSLVLISFYSVVGGWILRYFGESV 117
                                       751144455556666777788*************9986 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 6.6e-25
                               SNF 182 lcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdlekllep..kvWidaat 256
                                       + l +a v+++ +i  G++ ++k ++ +    + +l+ l + + +  Ga+++  fyl+ d++ l++        aa 
  gi|313125868|ref|YP_004036138.1| 150 VFLALAAVIIVAGIRGGIEIATKWMMPAI---FTLLVGLGIWASTQSGAAEAYAFYLRFDVSTLQNNffGLLGPAAG 223
                                       457788899999***********998754...58999999*************************983346789*** PP

                               SNF 257 qiffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgekisevaeeGpgLaFia 333
                                       q +f+l++g+G++i++asY + +  + +d+  ++++n+++ vlaglvvF +l  +  e g+       +G+g +F+ 
  gi|313125868|ref|YP_004036138.1| 224 QALFTLSLGVGTMITYASYLDEDRSLPFDGATIAVLNTIVGVLAGLVVFPLLFTLGIEPGQT-----GTGAGALFVG 295
                                       ***************************************************98777777764.....68******** PP

                               SNF 334 ypealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrellt.livavla 396
                                        + a ++lp ++l ++ FF ++ l++l s+++++e  ++ +vDe+    rr   l+  +vav+ 
  gi|313125868|ref|YP_004036138.1| 296 LAGAFAQLPGGTLVATAFFAVVALAALSSAISILEISVSFLVDEYGLARRRAAGLVgGLVAVTG 359
                                       **********************************************966644333303444444 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.023
                               SNF 349 vlFFlmlillgldsqfgtvegiitavvDefkv 380
                                       +l F+ l++ g+d ++g+  ++++av+  + +
  gi|313125868|ref|YP_004036138.1| 430 FLVFTLLTTFGVDGKIGFWPTVVAAVAVAIAA 461
                                       47799999999999999999999999866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2730.40
//
Query:       gi|313125869|ref|YP_004036139.1|  [L=47]
Description: hypothetical protein Hbor_11040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       141  (0.00786435); expected 358.6 (0.02)
Passed bias filter:                      138  (0.00769703); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 301.17
//
Query:       gi|313125870|ref|YP_004036140.1|  [L=514]
Description: propionyl-CoA carboxylase carboxyltransferase subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.3e-202  673.8   0.0   1.5e-202  673.7   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain
     0.0042   16.6   0.1      0.019   14.5   0.0    1.9  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.7   0.0  1.6e-206  1.5e-202       2     494 .]      27     512 ..      26     512 .. 0.99

  Alignments for each domain:
  == domain 1  score: 673.7 bits;  conditional E-value: 1.6e-206
                                       SCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGG CS
                    Carboxyl_trans   2 ehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgpa 77 
                                       +h++Gk+tarerid+ ld+g F e++++  hr  ++g+ +k+lp+dgvvtg+G+v+Gr+++v+a+d+tv+ggslg++
  gi|313125870|ref|YP_004036140.1|  27 QHEKGKMTARERIDYFLDDGTFNEFDQFRTHRNHKFGMeEKQLPGDGVVTGYGEVDGRKTFVFAHDFTVFGGSLGEV 103
                                       8*************************************9999*********************************** PP

                                       GCEEECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHT CS
                    Carboxyl_trans  78 kgekllkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalg 154
                                        +ek+ k++++a++ g+p+ig+nds+Ga  riqegv+sl g+G+if++n++asg++pqis ++g+caGg++Y+pa++
  gi|313125870|ref|YP_004036140.1| 104 FAEKVSKVMDKAVEVGAPIIGLNDSAGA--RIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPAIT 178
                                       ****************************..*********************************************** PP

                                       SEEEEETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGS CS
                    Carboxyl_trans 155 drvimveetskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnre 231
                                       d+++mv++ts++f+tGpdvik+v+g eevt eelgGat+h+++sGvah++ e++eeal++ir llsylP   +nn e
  gi|313125870|ref|YP_004036140.1| 179 DFTFMVKDTSHMFITGPDVIKTVTG-EEVTFEELGGATTHASTSGVAHFACESEEEALDQIRLLLSYLP---PNNVE 251
                                       *************************.*******************************************...9*9** PP

                                       S----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SE CS
                    Carboxyl_trans 232 saPivetadepdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrv 305
                                       ++P+ve++d+p+r    l+++vPd+++kpyD ++vi ++ deg+F++++e++Ak++VvGf+rl+G +vGvvAn++rv
  gi|313125870|ref|YP_004036140.1| 252 DPPRVEPWDDPERAdesLNTVVPDEPRKPYDAHDVIDGVLDEGSFFGVHEQFAKNIVVGFGRLDGHSVGVVANQPRV 328
                                       *************999899********************************************************** PP

                                       EETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHH CS
                    Carboxyl_trans 306 eaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGG 382
                                       +aG  l+i++++Kaarf+r+cd +n+P+v+++dv+Gfl+G++qe++gi++hGakl++a++ea+vP +tvi+rkayGG
  gi|313125870|ref|YP_004036140.1| 329 NAG-TLDIEASEKAARFVRFCDSFNIPIVTFVDVPGFLPGTDQEHEGIIRHGAKLLYAYSEATVPLLTVITRKAYGG 404
                                       ***.************************************************************************* PP

                                       HHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Carboxyl_trans 383 ayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfa 459
                                       ay vm sk++gad+++awpta+iaV+gp+gav+il+++e+ aa+    d++a+r + ++ey+ee++npy+aa rgf+
  gi|313125870|ref|YP_004036140.1| 405 AYDVMASKHLGADVNYAWPTAEIAVMGPQGAVNILYSDELDAAD----DPEARRDELIEEYREEFANPYTAADRGFV 477
                                       *******************************************9....9**************************** PP

                                       HTTSSHHHHHHTTSSSEEEHGGGHHHHHHHHHHHH CS
                    Carboxyl_trans 460 Davidpsetraklvialelewkkarklparkrrni 494
                                       Davi+p+etra+lv +le++ +k+++lp +k++ni
  gi|313125870|ref|YP_004036140.1| 478 DAVIEPTETRARLVEDLEMLRSKRKSLPDKKHGNI 512
                                       *********************************97 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.1   9.4e+02      94     111 ..     108     125 ..      74     143 .. 0.66
   2 !   14.5   0.0   2.1e-06     0.019      18     148 ..     308     436 ..     294     446 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHT--EEEE CS
                              MdcE  94 lakalarArlaGhpvigl 111
                                       + k++++A   G+p+igl
  gi|313125870|ref|YP_004036140.1| 108 VSKVMDKAVEVGAPIIGL 125
                                       335555555566666655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.1e-06
                                       EEEEEEETTEEEEEEEE---TTSS-B-HHHHHHHHHHHHHHHTSSS--EEEEEEEE--B--SHHHHHHTHHHHHHHH CS
                              MdcE  18 kvldgsltlesvrfvaVigdankgevGvdealaLaaaVleaieraekrpilvlvDvasQrlgrrdEllGihealahl 94 
                                        v  g+l+++sv+ va  +  n g + ++ a   aa+       + + pi+  vDv++   g  +E  Gi    a l
  gi|313125870|ref|YP_004036140.1| 308 VVGFGRLDGHSVGVVANQPRVNAGTLDIE-ASEKAARFVRFC-DSFNIPIVTFVDVPGFLPGTDQEHEGIIRHGAKL 382
                                       45568888888888888888888888875.555555555566.46689*************************9*99 PP

                                       HHHHHHHHHHT--EEEEEEEEEEHHHH...HHTTTT-SEEEEEET-EEESS-HHHHH CS
                              MdcE  95 akalarArlaGhpvigllvGkavsGaf...lahglqanrlialpgvqvavmdkasaA 148
                                         a+  A +   p+++++  ka  Ga+    +  l a++  a p +++avm+ + a 
  gi|313125870|ref|YP_004036140.1| 383 LYAYSEATV---PLLTVITRKAYGGAYdvmASKHLGADVNYAWPTAEIAVMGPQGAV 436
                                       999999986...9*************7442456799***************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 3244.67
//
Query:       gi|313125871|ref|YP_004036141.1|  [L=87]
Description: hypothetical protein Hbor_11060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.066   12.6   0.0      0.069   12.6   0.0    1.0  1  Glyco_transf_36  Glycosyltransferase family 36
        4.3    8.0   6.5       0.94   10.1   3.0    1.7  2  OAD_gamma        Oxaloacetate decarboxylase, gamma chain


Domain annotation for each model (and alignments):
>> Glyco_transf_36  Glycosyltransferase family 36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.6e-06     0.069     155     208 ..      12      63 ..       2      77 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-06
                   Glyco_transf_36 155 eteietelgegilaarnpyseeekkrvafltlsaevtsfetdreeFiGrngsls 208
                                        t  +++  + ++aa  +  + + ++va++++++e +s++++r +F Gr + +s
  gi|313125871|ref|YP_004036141.1|  12 PTAADEDEAA-AIAAAVAA-HLRDQQVAAAAAEDETDSWDGERWSFAGRMRAVS 63 
                                       5555555544.45555555.3455677777788889*************99886 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.0    0.0001      0.94      60      76 ..      14      30 ..       3      31 .. 0.86
   2 ?   -1.3   0.1      0.39   3.5e+03      52      55 ..      38      41 ..      32      52 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                         OAD_gamma 60 dddeelvAvIaaAiaay 76
                                      + de+ +A+IaaA+aa+
  gi|313125871|ref|YP_004036141.1| 14 AADEDEAAAIAAAVAAH 30
                                      679999**********9 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                         OAD_gamma 52 aaaa 55
                                      aaaa
  gi|313125871|ref|YP_004036141.1| 38 AAAA 41
                                      1111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 543.11
//
Query:       gi|313125872|ref|YP_004036142.1|  [L=94]
Description: hypothetical protein Hbor_11070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 564.07
//
Query:       gi|313125873|ref|YP_004036143.1|  [L=64]
Description: 30S ribosomal protein S17e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-13   48.7   0.3    7.2e-13   48.5   0.3    1.0  1  Ribosomal_S17e  Ribosomal S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.3     4e-17   7.2e-13       4      56 ..       3      55 ..       1      57 [. 0.95

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4e-17
                                      ---HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHH CS
                    Ribosomal_S17e  4 vrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvth 56
                                      ++ k vK+  +v+++ky + +++dF+tnk+ +++ + ++sk +rn+iaGy+t+
  gi|313125873|ref|YP_004036143.1|  3 IKPKYVKQLGKVLLDKYPQAFNTDFETNKESVSKLTNVESKGVRNRIAGYITR 55
                                      56799**********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 400.95
//
Query:       gi|313125874|ref|YP_004036144.1|  [L=211]
Description: hypothetical protein Hbor_11090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-43  149.1   0.0    1.3e-43  148.9   0.0    1.0  1  DUF447    Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   0.0     7e-48   1.3e-43       1     175 [.      27     201 ..      27     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 7e-48
                                       EEEEEEEE-TT.-EEEEEEEEEESSSE...EEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEE CS
                            DUF447   1 yEvivtTksek.rpnaaPiGvivkgdk...vvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfds 73 
                                       +E++vtT++++ r+n+a++G+++ ++    v+++++  +rT +N+ ++g  vi++++Dp++f+ aa+  +ee+d   
  gi|313125874|ref|YP_004036144.1|  27 TESVVTTRGPNdRWNVAALGLHAPDKAtgvVTAKTWGNTRTRRNFHRRGGGVIQFVSDPREFVSAAMTIREEDDP-- 101
                                       69*********************5555567**************************************6666644.. PP

                                       ETTTCTT.EETT-SEEEEEEEEEE....CTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCC..SH CS
                            DUF447  74 etkpakiavlksaeawveveveev....egdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldi..ed 144
                                               vl+ a+awvevev+++    +g +++ ++el+p ++ ++++ ++++nRg+aavi+a+V+a+Rld+   d
  gi|313125874|ref|YP_004036144.1| 102 --------VLDAAHAWVEVEVTRIdggeRGGTRWEKWELRPHDSTVVSKAIPTINRGFAAVIDATVAASRLDVpaYD 170
                                       ........9***************9999999********************************************** PP

                                       HHHHHHHHHHHHHHHHHH--HHHHHHHHHHH CS
                            DUF447 145 keklleeieylssvikktggerekealellk 175
                                       +++ll++++y+ ++++k+gg +ekea++ + 
  gi|313125874|ref|YP_004036144.1| 171 TDELLSRLQYFAETVEKCGGAAEKEAFDTID 201
                                       ***************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1427.45
//
Query:       gi|313125875|ref|YP_004036145.1|  [L=283]
Description: triphosphoribosyl-dephospho-CoA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-60  204.6   3.6    2.7e-60  204.4   3.6    1.0  1  CitG      ATP:dephospho-CoA triphosphoribosyl transferase


Domain annotation for each model (and alignments):
>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.4   3.6   1.5e-64   2.7e-60       1     281 []      12     276 ..      12     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: 204.4 bits;  conditional E-value: 1.5e-64
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHH CS
                              CitG   1 aelavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekaml 77 
                                       ae a+lAlllEv+ tpKPG+Vdr+++   d ++fe+Fla+a+ + + +++aa           + +++G ++e+a+ 
  gi|313125875|ref|YP_004036145.1|  12 AENAQLALLLEVTGTPKPGNVDRERDL--DELRFEHFLAGAVGANRGLRRAA-----------SGAPVGVAFERAIE 75 
                                       689************************..***********************...........678*********** PP

                                       HH..------HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--......--- CS
                              CitG  78 aa..tggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv......eel 145
                                        +  ++g+NT++G+++ll++l+ aa+           +   + + ev++++tv+da++f ra+++++v      e +
  gi|313125875|ref|YP_004036145.1|  76 GMshQSGGNTQFGCLLLLVPLVRAAAAG---------TLSPDGVTEVVESTTVADAADFyRAFEHVAVavadppE-D 142
                                       **************************66.........568899*************************9999872.2 PP

                                       ............HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHH CS
                              CitG 146 ............kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallal 210
                                                   + +l++ +++tl++v+++s g dg ++e++ gF ++f++a   l++     +   d++++a++ l
  gi|313125875|ref|YP_004036145.1| 143 ladldvrrgsdaIPALRD-RETTLYDVMAASEG-DGNAEEWTGGFSRTFDAAETILAD----DGPVPDRVARAFVDL 213
                                       356677777666666777.89*********999.****************88876665....5899*********** PP

                                       HHHS--HHHHHHHHHHHHHHHHHHHH..........H-SHHHHHHHHHHHHHHT---HHHHHHHHHHHHHH CS
                              CitG 211 laelpDtnilrrgGaegaeevqeeArallaaggvaaeaglealeeldrelvernisPGgsADllaatlfla 281
                                       lae +Dt++ + +G+e+a+ev+++A a             e+++el +++v+++i+PG++AD++ a+ f+a
  gi|313125875|ref|YP_004036145.1| 214 LAEGEDTLVRTNHGPEVAAEVRRRADAARGD--------PEKVAELAAAFVDEGINPGTTADIVCAATFVA 276
                                       **************************97776........789***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1726.18
//
Query:       gi|313125876|ref|YP_004036146.1|  [L=257]
Description: tRNA-dihydrouridine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-06   27.9   1.2    1.5e-05   24.2   1.1    2.0  1  Dus       Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.1   8.6e-10   1.5e-05      69     225 ..      93     233 ..      79     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8.6e-10
                                       HHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHH CS
                               Dus  69 aeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalelak 145
                                         aA++ ad    + ++N+ C +++    g G +Llr+ d +++ v+a+ +  +  v+vk+r  i+     +   a+
  gi|313125876|ref|YP_004036146.1|  93 RRAARICAD-RNAILEVNAHCRQDELCAVGCGETLLRDTDRLCEYVAAAADE-GATVSVKVRAEIEGV--SLETTAD 165
                                       5799*****.8889*********************************99887.678*********943..45689** PP

                                       HHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTH CS
                               Dus 146 iveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwl 222
                                       +v +aGa  l v +    +        e I++v  + s+ v+aN +++   ++++ l + Gad+v +gr +  +P +
  gi|313125876|ref|YP_004036146.1| 166 RVADAGASILHVDAM---DS------EEVIADVS-DSSLFVVANNEVRGEASVREYLGY-GADAVSVGRPS-TDPRV 230
                                       ********9988552...22......23455554.457999999999999999999999.99999999975.45666 PP

                                       HHH CS
                               Dus 223 fae 225
                                       +++
  gi|313125876|ref|YP_004036146.1| 231 LRR 233
                                       665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1662.93
//
Query:       gi|313125877|ref|YP_004036147.1|  [L=330]
Description: 2-phospho-l-lactate transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-45  153.7   0.0    7.4e-45  153.4   0.0    1.1  1  UPF0052   Uncharacterised protein family UPF0052
  ------ inclusion threshold ------
      0.031   14.2   0.1      0.049   13.6   0.1    1.3  1  DUF2259   Predicted secreted protein (DUF2259)


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.4   0.0   8.3e-49   7.4e-45       1     263 [.       2     298 ..       2     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 8.3e-49
                                       EEEEE-CHHHHHHHHHHCCSS..CEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S-C........ CS
                           UPF0052   1 vvvlgGGtGlskllrglkevt..aeltavvtvaDdggssGelrrelgllaigDirnvlval...idder........ 64 
                                       v++l+GGtG++kll+g +ev+  +e+t+v +++Dd+++ G       +l+++D+++vl+     +d++r        
  gi|313125877|ref|YP_004036147.1|   2 VTFLAGGTGTPKLLDGSSEVFgpSETTVVANTGDDVELGG-------HLVCPDVDTVLFHGggvLDTDRwwgieddt 71 
                                       789*************************************.......*************99997777777777777 PP

                                       ..HHHHHCH-B-SS......................................SSSSTT-BHHHHHHHHHHHHHS.-H CS
                           UPF0052  65 ..lleeLfqyRfkg......................................dgdlaghslgnllLaalaeltg.sl 100
                                         + +eL ++   +                                      d+d a h+ ++ l+++     g +l
  gi|313125877|ref|YP_004036147.1|  72 ttTDDELHRLA--EaagfdggprylsddaqtggreisrwrrfsgvaefmeigDKDRAVHVTRTSLIDE-----GyTL 141
                                       66333333332..222455555555555555555555555555666666777****************.....99** PP

                                       HHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-EEESTTTGGGG-S....-EEE.EEEESTT----HHHHHHHHH CS
                           UPF0052 101 eeaiealskilkvrgrvlPatddpvelsaeledGeeitgeskiseark.lkapikr.vflepegaeaapevleaike 175
                                       +e++++l+++++++ ++lP++ddpv   +++e G +  +e+++   ++ +++ +++  f ++++ae+++ vl+a+++
  gi|313125877|ref|YP_004036147.1| 142 TEVTRTLADAFDLDIELLPMSDDPVASIVHTEAGAMHFQEYWV---HRrAEPAVEDvEFRGADDAEPTDAVLTALSD 215
                                       ***********************************655*****...66689*****99*****************98 PP

                                       -SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEEEE--SB--TTTSTT-BHHHHHHHHHHCH-.....SS....S CS
                           UPF0052 176 AdlivlgpGslytSiiPiLlvpgiaealreskakkvlvsnimtqkGetdgfsvsdhvkaieravg.....kgvakay 247
                                          +v+gp++++tS++P+L ++ +++al   ++++v+vs++++      +  +s++++ +++ vg     +gva+ay
  gi|313125877|ref|YP_004036147.1| 216 P--VVIGPSNPVTSLGPMLSMDAFRDAL--DRTPVVAVSPFVE------DTVFSGPAADLMAGVGydpstAGVAEAY 282
                                       8..*************************..679*********8......****************999998888888 PP

                                       ..-SEEEEE-S---HHHH CS
                           UPF0052 248 ..vdavlvntsevpeell 263
                                         +da++++t+  + ++l
  gi|313125877|ref|YP_004036147.1| 283 pfADAFVLDTE--DGTAL 298
                                       99******999..44444 PP

>> DUF2259  Predicted secreted protein (DUF2259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.5e-06     0.049      13      52 ..     282     327 ..     275     330 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.5e-06
                           DUF2259  13 fpyAelfviDvntdtfllgaplrsrde......gaslsaareqllr 52 
                                        p A+ fv+D++ +t l + ++r++++       a +++a+e++l+
  gi|313125877|ref|YP_004036147.1| 282 YPFADAFVLDTEDGTALDRPVVRTDTKidgpadAARVARAVESALA 327
                                       699**********************334344447777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2113.69
//
Query:       gi|313125878|ref|YP_004036148.1|  [L=111]
Description: hypothetical protein Hbor_11130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 703.76
//
Query:       gi|313125879|ref|YP_004036149.1|  [L=392]
Description: hd superfamily phosphohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-12   46.4   4.4    9.3e-12   45.2   4.4    1.7  1  HD        HD domain
  ------ inclusion threshold ------
       0.09   12.2   0.2        0.7    9.2   0.0    2.1  2  NMO       Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   4.4     1e-15   9.3e-12       1     121 [.      50     162 ..      50     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1e-15
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH........HHHCTCCHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk........eeefekflaHekvgaeilr 68 
                                       r+eHsl+V++la r  ++l+   +    +++aaLlHDiG+gp g++ e+         ++e +++l+ ++v+a ++ 
  gi|313125879|ref|YP_004036149.1|  50 RFEHSLGVYHLASRALDYLDIgGDRARHVRAAALLHDIGHGPYGHQTEEVirrrtgahHDEIGHLLDETDVAAVLVA 126
                                       79***************99888899999*******************999988887665557787888888888888 PP

                                       HHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  69 evekrlgldledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       + ++++      +a+l+r   e              ql + +++v+++D+l +
  gi|313125879|ref|YP_004036149.1| 127 HDLNPD-----RIAALVRGDGELG------------QLVSGELDVDRMDYLVR 162
                                       888888.....8888888888888............79999999999999965 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.043   3.8e+02      25      55 ..     132     162 ..     119     172 .. 0.86
   2 ?    9.2   0.0   7.8e-05       0.7     231     297 ..     299     379 ..     295     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.043
                               NMO  25 arLaaavsnaGgLGvlasgyltaDrlakeir 55 
                                       +r+aa v  +G LG l sg l  Dr+   +r
  gi|313125879|ref|YP_004036149.1| 132 DRIAALVRGDGELGQLVSGELDVDRMDYLVR 162
                                       789999*****************99986666 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 7.8e-05
                               NMO 231 sdakdahkkklleaklddteltsa..vsGrpaRalatelleeleeakiatlalpeah............elakkira 293
                                       s a+++++k+ +e+ ++ + + s+  ++    R+++++++++leea +  ++l+ a+            e a  +r+
  gi|313125879|ref|YP_004036149.1| 299 SAAREIADKAGVEPDEVLVDVPSRpsFKESRTRVIVNGVVQRLEEASELVAGLRAAErtqwrigvyapaEAADDVRD 375
                                       779999**********999999872244456789***********99999999999988888888888666666888 PP

                               NMO 294 alve 297
                                       a+++
  gi|313125879|ref|YP_004036149.1| 376 AAAD 379
                                       8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2633.31
//
Query:       gi|313125880|ref|YP_004036150.1|  [L=408]
Description: hd superfamily phosphohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-12   46.6   0.8    8.7e-12   45.3   0.8    1.7  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.8   4.8e-16   8.7e-12       1     121 [.      50     162 ..      50     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 4.8e-16
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH........HHHCTCCHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk........eeefekflaHekvgaeilr 68 
                                       r+eHsl+V++la r   +lg      e++++aaLlHD+G+gp ++++e          +++++++ a   vg  +lr
  gi|313125880|ref|YP_004036150.1|  50 RFEHSLGVYHLASRALTHLGIeGVQAERIRAAALLHDVGHGPYSHNIESVtyrytgkyHDDVHELIAEGSVGQ-VLR 125
                                       79******************99999********************9999988776644333666666666666.666 PP

                                       HHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  69 evekrlgldledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       ++ +++      +a+l++   +              ql + +++v+++D+l +
  gi|313125880|ref|YP_004036150.1| 126 DNDLDP----NRIADLVAGEGKYG------------QLVSGELDVDRMDYLVR 162
                                       666666....56999999999999............79999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2958.34
//
Query:       gi|313125881|ref|YP_004036151.1|  [L=337]
Description: cytosine deaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-33  115.6   0.1    3.2e-21   76.0   0.0    2.1  2  Amidohydro_1     Amidohydrolase family
    1.5e-08   34.4   0.0    2.1e-08   33.9   0.0    1.1  1  A_deaminase      Adenosine/AMP deaminase
      7e-06   25.8   5.0    2.7e-05   23.8   0.7    2.2  2  Amidohydro_3     Amidohydrolase family
  ------ inclusion threshold ------
       0.06   13.9   0.6        1.4    9.4   0.2    2.4  2  Usp              Universal stress protein family
      0.095   12.7   0.7         11    6.1   0.0    2.7  2  Molybdopterin_N  Molybdopterin oxidoreductase N-terminal doma


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   4.5e-13   1.6e-09       1      86 [.      40     142 ..      40     164 .. 0.91
   2 !   76.0   0.0   8.8e-25   3.2e-21     162     322 ..     170     316 ..     160     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 4.5e-13
                                       EEEE-EEEEEEECETTECSSS....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSST CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.............vppetaaealesgiktalksGtttvadmgatts 60 
                                       ++lP++++aH+H+ +s  ++a     l++++             +++    ea+++ ++ + + Gt t++++++  +
  gi|313125881|ref|YP_004036151.1|  40 VILPAFVNAHTHIGDSIAKEAgaglSLDELVappdglkhrllraASHAAKVEAMRRSLRLMQSTGTATCLEFREGGV 116
                                       69**************99888***9999999********************************************** PP

                                       HHHHHHHHHHHTSSSEEEEEEESSEG CS
                      Amidohydro_1  61 tgiealleaaeelplglrilggkvsl 86 
                                       +g+ea++eaa+el++++ +lg  +  
  gi|313125881|ref|YP_004036151.1| 117 DGVEAIREAADELAIDPVVLGRETAA 142
                                       *************9999999886554 PP

  == domain 2  score: 76.0 bits;  conditional E-value: 8.8e-25
                                       HHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHH CS
                      Amidohydro_1 162 aeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkalde 238
                                       a + fg ++ +  + +v + +  ld+    ++h+vh++p+ + ++ +   ++ ++ cp+sn++ + g++++r++ld+
  gi|313125881|ref|YP_004036151.1| 170 AGKLFGIHAGERDPHDV-DPALDLDP--EFVVHMVHPEPEHLDRIEAE--DVPIVVCPRSNLVTGVGVPPVRDLLDR 241
                                       55555555555555555.44455555..6789************9999..**************************8 PP

                                       TSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EE CS
                      Amidohydro_1 239 GvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlv 315
                                        + v+lgtD + + ns+++++e+ +  k           ++ s+ e+lrmaT+ngA++ gl  + G ie+ ++A l 
  gi|313125881|ref|YP_004036151.1| 242 -TTVALGTD-NVMLNSPSMFREMEFVSK----------LTDASATEILRMATLNGAEIAGL--NYGVIEPDREAKLL 304
                                       .9*******.*****************4..........4449*******************..************** PP

                                       EECCCT.....C CS
                      Amidohydro_1 316 vvdldi.....l 322
                                       ++d+d+      
  gi|313125881|ref|YP_004036151.1| 305 ILDGDSdnlagA 316
                                       **9954333441 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0     6e-12   2.1e-08     178     317 ..     157     290 ..     137     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 6e-12
                                       G..HHHHHCCCCHTT-EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCS CS
                       A_deaminase 178 l..flklraeagkstllltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllalaqiplevcPlSNvalg 252
                                       +  f +lrae ++++ l+ +HaGE  +++ v  Al+l + e + H v+   +p+ +++   + +p+ vcP SN  + 
  gi|313125881|ref|YP_004036151.1| 157 DseFGDLRAETREAGKLFGIHAGER-DPHDVDPALDL-DPEFVVHMVH--PEPEHLDRIEAEDVPIVVCPRSNLVT- 228
                                       34499*******************7.88999***999.*******876..5788899****************999. PP

                                       ST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-SHHHHHHHHHHHHT--HHHHHHHHH.HHHHCSSS CS
                       A_deaminase 253 afleyaenPlkeflerglnvslntDDPlqfgttLieeYaiaaqvfklseedlaelar.Nsvkqsfl 317
                                           +   P++++l+r   v+l+tD+ ++ + ++  e++ +++    s+ ++ ++a  N+++ ++l
  gi|313125881|ref|YP_004036151.1| 229 ---GVGVPPVRDLLDR-TTVALGTDNVMLNSPSMFREMEFVSKLTDASATEILRMATlNGAEIAGL 290
                                       ...677889***9987.58***************************99999988874377777765 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.5    0.0075        27       9      21 ..      40      52 ..      37      90 .. 0.82
   2 !   23.8   0.7   7.7e-09   2.7e-05     260     455 ..     111     316 ..      55     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0075
                      Amidohydro_3  9 lvlPGFvDsHtHl 21
                                      + lP+Fv +HtH+
  gi|313125881|ref|YP_004036151.1| 40 VILPAFVNAHTHI 52
                                      689*********6 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 7.7e-09
                      Amidohydro_3 260 fedea...laelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegv..........tesqie 323
                                       f+++    ++++ +aade  +d  ++  ++aa+++  d+f a +++ +  +  r+e+ e+           ++++++
  gi|313125881|ref|YP_004036151.1| 111 FREGGvdgVEAIREAADELAIDPVVLGRETAAAMRESDGFGASGARDSEFGDLRAETREAGklfgihagerDPHDVD 187
                                       223334569999*******************************6666555555666666666678899999****** PP

                      Amidohydro_3 324 rvaalqvaagvqpvfnfedelldsrlgperargs.............tpvkellnagvkvalgsDapvgpfdpwpri 387
                                       ++ +l  +  v++v+   +e+l +r+ +e ++ +             +pv+ ll+   +valg+D   +++ + p+ 
  gi|313125881|ref|YP_004036151.1| 188 PALDLDPEFVVHMVHPE-PEHL-DRIEAEDVPIVvcprsnlvtgvgvPPVRDLLDRT-TVALGTD---NVMLNSPS- 257
                                       ************77766.4445.666655555556788888899999*******877.99*****...44444444. PP

                      Amidohydro_3 388 gaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdpp 455
                                         ++ r+     e++    + s +e+l++ T ++A++ gl    G +e+  +A l +ld d + +  +
  gi|313125881|ref|YP_004036151.1| 258 --MF-REM----EFVSKLTDASATEILRMATLNGAEIAGLNY--GVIEPDREAKLLILDGDSDNLAGA 316
                                       ..44.222....9999**************************..***************776666555 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2    0.0004       1.4      70     112 ..      93     139 ..      56     149 .. 0.75
   2 ?    2.4   0.0     0.056     2e+02      80     112 ..     192     224 ..     155     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0004
                                       H....HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESC CS
                               Usp  70 a....akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsr 112
                                       +      ++  +     e+   + d+ e+i e+a+e+ +d +V+G+ 
  gi|313125881|ref|YP_004036151.1|  93 MrrslRLMQSTGTATCLEFREGGVDGVEAIREAADELAIDPVVLGRE 139
                                       123335678899999999999************************86 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.056
                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESC CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsr 112
                                        + e+vv++ +p +e l+  e+ed+ ++V+ ++
  gi|313125881|ref|YP_004036151.1| 192 LDPEFVVHMVHPEPEHLDRIEAEDVPIVVCPRS 224
                                       577899*********************999765 PP

>> Molybdopterin_N  Molybdopterin oxidoreductase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.011        41       9      23 ..      19      33 ..      18      38 .. 0.85
   2 ?    6.1   0.0    0.0031        11       5      29 ..     160     185 ..     158     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.011
                   Molybdopterin_N  9 raevkdGkivgvrPf 23
                                      r++v+dG i++++ +
  gi|313125881|ref|YP_004036151.1| 19 RVVVEDGEITAIEEA 33
                                      79********99865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0031
                   Molybdopterin_N   5 WGafraev.kdGkivgvrPfegDpdP 29 
                                       +G +rae+ ++Gk+ g+++ e Dp+ 
  gi|313125881|ref|YP_004036151.1| 160 FGDLRAETrEAGKLFGIHAGERDPHD 185
                                       5668999967**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2265.13
//
Query:       gi|313125882|ref|YP_004036152.1|  [L=181]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-42  143.3   0.8    6.8e-42  143.3   0.8    1.3  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.16   11.8   2.6          3    7.7   0.4    2.6  2  ETF       Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.3   0.8   7.6e-46   6.8e-42       1     141 []       2     142 ..       2     142 .. 0.99
   2 ?   -3.2   0.1       1.2   1.1e+04      61      67 ..     153     159 ..     144     176 .. 0.43

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 7.6e-46
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+rIlV++Dgs+ s+++le+A+ela  +ga++++l+vi + +++  +++ + ++ +e  +e ae++ +  +a ae 
  gi|313125882|ref|YP_004036152.1|   2 MYQRILVPTDGSPGSERVLEHAVELASVHGATVHALYVINSGSFAGLPMESSWEGLDEMLHEDAEAAIADVRAIAER 78 
                                       9******************************************************************999******* PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                         v+ve+ ++eg p++ei+++ae+ ++dliV+G++gr+g++rlllGSv+e+v+r +++pVl Vr
  gi|313125882|ref|YP_004036152.1|  79 SNVQVETSIVEGTPSREIVRLAERGGCDLIVMGTHGRGGIDRLLLGSVAEKVVRASKVPVLTVR 142
                                       *************************************************************998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                                       HHHHHHH CS
                               Usp  61 leeaele 67 
                                       ++eae++
  gi|313125882|ref|YP_004036152.1| 153 ETEAESK 159
                                       2222221 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4   0.00033         3      14      68 ..      13      67 ..       7     130 .. 0.81
   2 ?    3.3   0.2    0.0075        67     140     170 ..     125     157 ..     109     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00033
                                      -HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GG CS
                               ETF 14 npvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpa 68
                                      +p ++  le A++l+  +g++v+a+ v ++ +   l  + +  G+d+ ++ d +a
  gi|313125882|ref|YP_004036152.1| 13 SPGSERVLEHAVELASVHGATVHALYVINSGSFAGLPMESSWEGLDEMLHEDAEA 67
                                      688999********99899******998866666677777777887777765554 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0075
                                       TEEEEEE-TSSSEEEEE-TTSS--..--S-TT- CS
                               ETF 140 nglaevveadlpavltvrpgafep..aaimaak 170
                                       ++ ++vv a+++ vltvr g  +   +++ +a+
  gi|313125882|ref|YP_004036152.1| 125 SVAEKVVRASKVPVLTVRVGEEDTesENETEAE 157
                                       455689999*********998888553334443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 999.91
//
Query:       gi|313125883|ref|YP_004036153.1|  [L=318]
Description: bira, biotin-(acetyl-CoA-carboxylase) ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-15   55.7   0.0    7.1e-15   55.1   0.0    1.2  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
    5.4e-12   45.5   0.0    1.2e-11   44.4   0.0    1.6  2  HTH_11         HTH domain
    4.3e-08   32.9   0.4    9.4e-08   31.8   0.4    1.6  1  BPL_C          Biotin protein ligase C terminal domain
    2.3e-06   27.1   0.0    4.3e-06   26.2   0.0    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
      7e-05   22.8   0.0    0.00014   21.9   0.0    1.5  1  HTH_20         Helix-turn-helix domain
    0.00047   19.9   0.7     0.0011   18.7   0.1    2.1  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0098   15.8   1.0       0.16   12.0   0.0    2.4  2  HTH_1          Bacterial regulatory helix-turn-helix protein,
  ------ inclusion threshold ------
      0.013   15.4   0.1       0.06   13.2   0.0    2.1  2  MarR_2         MarR family
      0.031   14.1   0.0      0.094   12.5   0.0    1.8  1  HTH_23         Homeodomain-like domain
      0.041   14.2   0.8        1.6    9.1   0.3    2.6  2  Toprim_3       Toprim domain
       0.18   11.7   0.0       0.31   11.0   0.0    1.3  1  HTH_5          Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   4.3e-18   7.1e-15      19     131 .]      95     210 ..      81     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 4.3e-18
                                       GG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-T CS
                     BPL_LplA_LipB  19 selesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegi 91 
                                       +   s+ +v++ +qtg r    + w  p+g++++sl+l+pe    +++ ++ly++  ++av++a        ++ g+
  gi|313125883|ref|YP_004036153.1|  95 AADASDVVVIAAEQTGSRgrlkREWTAPEGGVWMSLVLRPEI---PPAHAPLYTLAAAVAVTRAA-------REAGV 161
                                       44556778888888885577*******************886...9999****************.......9**** PP

                                       TEEEETTTEEEE........TTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  92 pvfikwpnDlyv........ngrKlaGiavtstr.gktlhhivigvgvn 131
                                        ++ikwpnD++v        +grKlaGi+++      ++  +v+g+gvn
  gi|313125883|ref|YP_004036153.1| 162 DASIKWPNDVLVvsdddtdrGGRKLAGILTEMEGeADRVSWVVVGIGVN 210
                                       *******************************999777888999999988 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   7.3e-15   1.2e-11      12      55 .]      13      55 ..       4      55 .. 0.90
   2 ?   -3.4   0.0       6.2     1e+04      19      31 ..     144     156 ..     142     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 7.3e-15
                            HTH_11 12 argpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGYr 55
                                       +gpi+g eLA++L+vSr+++++ ++aL+e g++Ies +  GYr
  gi|313125883|ref|YP_004036153.1| 13 DDGPIPGPELADRLGVSRAAIWKQVEALREDGFEIESGND-GYR 55
                                      4678*********************************999.997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.2
                            HTH_11  19 eeLAeeLnvSrrt 31 
                                        +LA    v+r++
  gi|313125883|ref|YP_004036153.1| 144 YTLAAAVAVTRAA 156
                                       6899999999975 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.4   5.7e-11   9.4e-08       1      47 [.     265     310 ..     265     311 .. 0.97

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 5.7e-11
                                       STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
                             BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                                       ++Gq V++e+  g+veG av++   GaL+++t+dg  + +++Gd+++
  gi|313125883|ref|YP_004036153.1| 265 TLGQYVRVETQSGVVEGEAVDVQVPGALVIQTEDG-ERVVHAGDCEH 310
                                       69*********************************.*********98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   2.7e-09   4.3e-06       1      46 [.       1      45 [.       1      45 [. 0.94

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.7e-09
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                      ++et+r++L++  + + i+  eLA+rlg+S+++++++++ L e+G+
  gi|313125883|ref|YP_004036153.1|  1 MNETRRALLRAFDD-GPIPGPELADRLGVSRAAIWKQVEALREDGF 45
                                      78999999999988.*****************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   8.3e-08   0.00014       9      55 ..       2      48 ..       1      54 [. 0.93

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.3e-08
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTT.EE CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagL.ve 55
                                      +++Rr++lra+ ++++   +ela+rl++s++ + +++++L+e g+ +e
  gi|313125883|ref|YP_004036153.1|  2 NETRRALLRAF-DDGPIPGPELADRLGVSRAAIWKQVEALREDGFeIE 48
                                      79*********.*******************************99777 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   6.9e-07    0.0011       6      42 .]       6      41 ..       1      41 [. 0.85
   2 ?   -2.8   0.1       3.7   6.1e+03      22      33 ..     145     156 ..     140     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.9e-07
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      r++L+a   d+ i+  eLA+r+G+S++++++ v++L+
  gi|313125883|ref|YP_004036153.1|  6 RALLRAFD-DGPIPGPELADRLGVSRAAIWKQVEALR 41
                                      66666664.9*********************999986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                     HTH_AsnC-type  22 eLAervGlSest 33 
                                        LA++v +++++
  gi|313125883|ref|YP_004036153.1| 145 TLAAAVAVTRAA 156
                                       578888887764 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   9.7e-05      0.16      20      39 ..      23      42 ..      23      44 .. 0.95
   2 ?    1.8   0.4      0.15   2.4e+02      13      26 ..     149     162 ..     143     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.7e-05
                                      HHHHTS-HHHHHHHHHHHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEe 39
                                      A++Lg+s +a+++q+ +L+e
  gi|313125883|ref|YP_004036153.1| 23 ADRLGVSRAAIWKQVEALRE 42
                                      89****************98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.15
                                       HSSHHHHHHHHTS- CS
                             HTH_1  13 egsftrAAeeLgls 26 
                                       +  +trAA+e g+ 
  gi|313125883|ref|YP_004036153.1| 149 AVAVTRAAREAGVD 162
                                       5569******9985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.7e-05      0.06       8      49 ..       6      44 ..       1      48 [. 0.83
   2 ?   -1.6   0.0       1.5   2.5e+03      22      35 ..     150     163 ..     137     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaG 49
                                      + +L a  ++p   +   ela+rlg+s++a+ + ++ L + G
  gi|313125883|ref|YP_004036153.1|  6 RALLRAFDDGP---IPGPELADRLGVSRAAIWKQVEALREDG 44
                                      55666666666...8999********************9998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                                       EEHHHHHHHHTSSH CS
                            MarR_2  22 ltvgelarrlglsk 35 
                                       ++v+  ar+ g++ 
  gi|313125883|ref|YP_004036153.1| 150 VAVTRAAREAGVDA 163
                                       68888888888886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.8e-05     0.094      18      47 ..      17      46 ..       3      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-05
                            HTH_23 18 lsvreIAreLgvsrrTvyrwlkryreeGle 47
                                      ++ +e A++Lgvsr  +++ +++ re+G+e
  gi|313125883|ref|YP_004036153.1| 17 IPGPELADRLGVSRAAIWKQVEALREDGFE 46
                                      566899*********************987 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0       0.1   1.7e+02      55      74 ..      19      47 ..       2      49 .. 0.75
   2 ?    9.1   0.3   0.00099       1.6      21      65 ..     147     192 ..     142     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                          Toprim_3 55 d.........Greaaeklaerleaagiea 74
                                                +r+a++k +e+l ++g+e+
  gi|313125883|ref|YP_004036153.1| 19 GpeladrlgvSRAAIWKQVEALREDGFEI 47
                                      344555566699**************986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00099
                          Toprim_3  21 aaviAllsaanlkaiawp.ergkrvviaaDnDaandGreaaeklae 65 
                                       aa++A++ aa+ + ++ + ++ ++v ++ D+D  + Gr+ a  l+e
  gi|313125883|ref|YP_004036153.1| 147 AAAVAVTRAAREAGVDASiKWPNDVLVVSDDDTDRGGRKLAGILTE 192
                                       67899999999999999967**************999998877766 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.31       1      44 [.       2      45 ..       2      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGL 44
                                      ++tR+ +L++  +g+    ela+ lg+s++++  +  +Lre G+
  gi|313125883|ref|YP_004036153.1|  2 NETRRALLRAFDDGPIPGPELADRLGVSRAAIWKQVEALREDGF 45
                                      5899999999999999999**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1980.72
//
Query:       gi|313125884|ref|YP_004036154.1|  [L=185]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-18   66.9   0.2    2.1e-18   66.3   0.2    1.3  1  Mac        Maltose acetyltransferase
    1.8e-11   43.3   7.3    7.4e-10   38.2   2.1    3.3  2  Hexapep    Bacterial transferase hexapeptide (six repeats)
    2.9e-11   42.9   7.2    1.1e-09   37.9   1.5    2.7  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Mac  Maltose acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.2   3.5e-22   2.1e-18       1      53 []       8      59 ..       8      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 3.5e-22
                                      HHHTTS-BETTTSHHHHHHHHHHHHHHHHHHTSTTT-HHHHHHHHHHHSSBES CS
                               Mac  1 KMlaGelYdafsDpeLvaeRlrarelcrryNqtrpsdkdeRrelLrellGsvG 53
                                      KMlaG+ Yd+  Dp L++eRl+ar+l+r+yN+t + + ++R+++LrellGsvG
  gi|313125884|ref|YP_004036154.1|  8 KMLAGDRYDP-TDPTLAEERLAARRLTREYNATWEGEDERREAILRELLGSVG 59
                                      9*********.79*******************99*****************98 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.3    0.0028        17      23      34 ..      99     110 ..      57     112 .. 0.72
   2 !   38.2   2.1   1.2e-13   7.4e-10       2      35 ..     132     165 ..     131     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0028
                                       -TTEEEETTEEE CS
                           Hexapep  23 GdnvkIgagvvi 34 
                                       Gd++ +++gv +
  gi|313125884|ref|YP_004036154.1|  99 GDDCMLAPGVHV 110
                                       455555555543 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 1.2e-13
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++G+ v+Ig +av+ ++V++Gd++++++g+v++
  gi|313125884|ref|YP_004036154.1| 132 VTVGDRVWIGGNAVLNPGVTVGDDSVVASGAVVT 165
                                       789*****************************97 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.93   5.5e+03       2       7 ..      76      81 ..      75      82 .. 0.58
   2 !    7.7   0.1   0.00049       2.9      18      33 ..      96     111 ..      85     112 .. 0.84
   3 !   37.9   1.5   1.8e-13   1.1e-09       1      34 []     131     166 ..     131     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.93
                                      EEE-TT CS
                         Hexapep_2  2 viIGdn 7 
                                      +++Gd+
  gi|313125884|ref|YP_004036154.1| 76 IHVGDD 81
                                      555654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00049
                                       EEE-TT-EE-TT-EE- CS
                         Hexapep_2  18 vslGdncvvgaGvvit 33 
                                       v+ Gd+c +++Gv ++
  gi|313125884|ref|YP_004036154.1|  96 VEFGDDCMLAPGVHVY 111
                                       667**********887 PP

  == domain 3  score: 37.9 bits;  conditional E-value: 1.8e-13
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                       pv++Gd++ iG na+   Gv++Gd++vv++G v+t+
  gi|313125884|ref|YP_004036154.1| 131 PVTVGDRVWIGGNAVLnpGVTVGDDSVVASGAVVTE 166
                                       8**************989****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1177.20
//
Query:       gi|313125885|ref|YP_004036155.1|  [L=597]
Description: acetyl/propionyl-CoA carboxylase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-77  258.5   0.4    6.3e-77  257.8   0.4    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
      9e-46  155.0   0.5    2.8e-45  153.4   0.5    1.9  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    5.7e-34  116.5   0.0    1.2e-33  115.4   0.0    1.6  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    5.6e-17   61.3   6.0    5.6e-17   61.3   6.0    2.5  2  Biotin_lipoyl    Biotin-requiring enzyme
      8e-11   41.9   0.0    1.8e-10   40.7   0.0    1.6  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    3.4e-10   39.8   0.2    6.9e-10   38.8   0.2    1.5  1  ATP-grasp        ATP-grasp domain
    1.7e-08   34.2   3.0     0.0012   18.6   0.1    2.7  2  Biotin_lipoyl_2  Biotin-lipoyl like
    3.4e-05   23.7   0.1      7e-05   22.7   0.1    1.5  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    0.00011   22.3   0.0    0.00024   21.2   0.0    1.5  1  ATP-grasp_3      ATP-grasp domain
     0.0014   18.1   0.1     0.0023   17.4   0.1    1.4  1  ATP-grasp_5      ATP-grasp domain
  ------ inclusion threshold ------
      0.022   15.5   2.5        6.6    7.5   0.0    3.2  3  HlyD_3           HlyD family secretion protein
      0.032   13.5   0.0      0.063   12.5   0.0    1.4  1  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
      0.065   13.0   0.0       0.15   11.8   0.0    1.6  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      0.084   13.4   1.2        0.3   11.6   0.1    2.2  2  CoA_binding_2    CoA binding domain
       0.11   12.4   4.6       0.14   12.1   1.6    2.3  2  GCV_H            Glycine cleavage H-protein
       0.11   11.2   1.3       0.71    8.5   0.6    2.0  2  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
       0.14   12.6   0.1        1.2    9.6   0.0    2.2  2  DUF4019          Protein of unknown function (DUF4019)
        4.2    7.8   6.9       0.74   10.2   1.2    2.5  2  TFIIE-A_C        C-terminal general transcription factor TFII


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.8   0.4   6.4e-80   6.3e-77       2     209 ..     116     321 ..     115     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 257.8 bits;  conditional E-value: 6.4e-80
                                       HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaaf 78 
                                       k++a+++++k++vpvvp+++ pve++ee+ +ia+e+gyPv ika  g+GG+G +v++ne+e+++ +++a++e +a f
  gi|313125885|ref|YP_004036155.1| 116 KTKARALMQKADVPVVPGTTEPVESAEEVKEIADEYGYPVAIKAEGGGGGRGLKVVHNEDEVEDQLETAQREGEAYF 192
                                       7899************************************************************************* PP

                                       STS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-E CS
                       CPSase_L_D2  79 gnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvv 155
                                        n++v+vek+l+ p++iEv++l+D++gnv +++er++slq+r+qkvie+APs++L+d+ r++++eaa + v + +++
  gi|313125885|ref|YP_004036155.1| 193 DNASVYVEKYLEAPRHIEVQILADKHGNVRHLGERDCSLQRRHQKVIEEAPSPALDDDLRERIGEAARRGVDAADYT 269
                                       ***************************************************************************** PP

                                       EEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                       CPSase_L_D2 156 gagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                       +agtvefl++  ++e+y++EvNtR++ve++++e++TG+d+vk+++++a+ge+L 
  gi|313125885|ref|YP_004036155.1| 270 NAGTVEFLVE--DGEFYFMEVNTRIQVEHTVTEQVTGIDVVKWQLRVAAGEELA 321
                                       **********..5**************************************996 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.4   0.5   2.8e-48   2.8e-45       1     110 []       1     110 [.       1     110 [. 0.99

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 2.8e-48
                                       ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SE CS
                     Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgada 77 
                                       +++kvl+anrGeiAvr++ra++elgi+tvavys++d++s hvr+adea+++gpa+a++sYl+ e++++a +++gada
  gi|313125885|ref|YP_004036155.1|   1 MFSKVLVANRGEIAVRVMRACKELGIRTVAVYSDADKHSGHVRYADEAYNIGPARAADSYLDHEAVIEAGEKAGADA 77 
                                       689************************************************************************** PP

                                       EE--SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                     Biotin_carb_N  78 vhpGyGflsEnaefaeaveeagivfiGPsaeal 110
                                       vhpGyGfl+Enaefa++vee++++++GPsa+a+
  gi|313125885|ref|YP_004036155.1|  78 VHPGYGFLAENAEFAAKVEESEMTWVGPSAAAM 110
                                       ******************************998 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.0   1.2e-36   1.2e-33       1     108 []     335     443 ..     335     443 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 1.2e-36
                                       EEEEESEETTTTTEE--.CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-E CS
                     Biotin_carb_C   1 eaRinaEdpeknflpss.GkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelr 76 
                                       e+RinaE+++++f+p++ G+++++++p+g gvR+d+++++g++  ++yDs++aKliv++ +ree++ r +raL+e++
  gi|313125885|ref|YP_004036155.1| 335 EFRINAENAANDFAPATgGTLETYDPPGGIGVRMDDALRQGDDLVTDYDSMIAKLIVTAGDREECIIRSERALEEFD 411
                                       89*************98579********************************************************* PP

                                       EESS-BSHHHHHHHHH-HHHHHT---TTTCCC CS
                     Biotin_carb_C  77 ieGvktnieflrailedeefakgeldtkflee 108
                                       i+G++t i+f+r +l de+f++ge++tk+l+e
  gi|313125885|ref|YP_004036155.1| 412 IDGFHTIIPFHRLMLTDETFRAGEHTTKYLDE 443
                                       ******************************85 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         6   5.9e+03      17      48 ..     310     341 ..     303     343 .. 0.72
   2 !   61.3   6.0   5.7e-20   5.6e-17       7      73 .]     535     596 ..     529     596 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6
                                       CSESSSTTCEE-TTSEEEEEECTTEEEEEEBS CS
                     Biotin_lipoyl  17 vevlvkvGdkVkagqvlaeveamKmemeieap 48 
                                       ++  v++G++ +  q  +e+    me  i+a+
  gi|313125885|ref|YP_004036155.1| 310 WQLRVAAGEELAFSQDDVEIDGHSMEFRINAE 341
                                       67788888888877777777777777777776 PP

  == domain 2  score: 61.3 bits;  conditional E-value: 5.7e-20
                                       SSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl   7 miGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                       m       g +++v v++Gd+V+ g+v++++eamKme+++ a+  G+v++ilv eGd+v+ gd+l+++
  gi|313125885|ref|YP_004036155.1| 535 MQ------GtILSVDVEEGDEVASGDVVCVLEAMKMENDVVAERGGTVSQILVGEGDSVDMGDVLVVL 596
                                       33......44666****************************************************986 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   1.8e-13   1.8e-10      23     174 ..     139     290 ..     122     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.8e-13
                                       -H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHT.....T-.SCEEEEE--.ESEEEEEEEEE CS
                   Dala_Dala_lig_C  23 ekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafk.....yd.ekvlvEeai.egreievavlg 92 
                                       e+ e ++++ +e gypv +K+   G   G++ v++e+e+++ +e+a +     +d ++v vE+++ + r iev +l 
  gi|313125885|ref|YP_004036155.1| 139 ESAEEVKEIADEYGYPVAIKAEGGGGGRGLKVVHNEDEVEDQLETAQRegeayFDnASVYVEKYLeAPRHIEVQILA 215
                                       34456789************************************998733333341579******6669******** PP

                                       TSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEE CS
                   Dala_Dala_lig_C  93 neklevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivl 169
                                       + + +v ++ge+  +  + + ++k +    +     +l+++ +e+i e+a +  +a d +  + v f+++ +ge+++
  gi|313125885|ref|YP_004036155.1| 216 DKHGNVRHLGERDCS--LQRRHQKVI----EEAPSPALDDDLRERIGEAARRGVDAADYTNAGTVEFLVE-DGEFYF 285
                                       ***********9776..456677775....33334569999**************************997.9***** PP

                                       EEEES CS
                   Dala_Dala_lig_C 170 nEvNt 174
                                        EvNt
  gi|313125885|ref|YP_004036155.1| 286 MEVNT 290
                                       ****9 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.2   6.9e-13   6.9e-10      13     159 ..     137     291 ..     123     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 6.9e-13
                                       EECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEE CS
                         ATP-grasp  13 aveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvl 81 
                                        ves+ee++e+a+e g+pv +K + +g  G+G +vv++e+++e+ le++        ++ +v+vE++ +  + + v 
  gi|313125885|ref|YP_004036155.1| 137 PVESAEEVKEIADEYGYPVAIK-AEGGGGGRGLKVVHNEDEVEDQLETAqregeayfDNASVYVEKYLEAPRHIEVQ 212
                                       58999*****************.89999*******************999*************************** PP

                                       EEEETTC-EEE--EEE.EEEE..TTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEE CS
                         ATP-grasp  82 vvrsaeGetafypvve.tvqe..dgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnE 155
                                       +  +++G+++ +      +q+  ++++++   pa ++++  +++ e a++ v++ ++    +vE+ v  dge ++ E
  gi|313125885|ref|YP_004036155.1| 213 ILADKHGNVRHLGERDcSLQRrhQKVIEEAPSPA-LDDDLRERIGEAARRGVDAADYTNAGTVEFLVE-DGEFYFME 287
                                       *******998774432144440045555555555.57779999*********************7666.******** PP

                                       EESS CS
                         ATP-grasp 156 lapR 159
                                       +  R
  gi|313125885|ref|YP_004036155.1| 288 VNTR 291
                                       9988 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.3e-06    0.0012       4      39 ..     530     565 ..     528     572 .. 0.89
   2 !   14.8   1.0   1.9e-05     0.019      10      33 ..     573     596 ..     566     597 .] 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                   Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelDsralq 39 
                                       +Iaa   G++ ++ V++G++V  Gdv  +l+  + +
  gi|313125885|ref|YP_004036155.1| 530 QIAAEMQGTILSVDVEEGDEVASGDVVCVLEAMKME 565
                                       7*************************9888876655 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.9e-05
                   Biotin_lipoyl_2  10 sGrVaqlnVkdGqrVkaGdvLael 33 
                                        G+V+q++V +G+ V  GdvL++l
  gi|313125885|ref|YP_004036155.1| 573 GGTVSQILVGEGDSVDMGDVLVVL 596
                                       58*******************998 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1     7e-08     7e-05       2      92 ..     115     206 ..     114     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7e-08
                                       BHHHHHHHHHHTT--B-..-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TT CS
                            GARS_A   2 sKsfakdllkkagipta..eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkf 76 
                                       +K+ a++l++ka++p    + e ++++ee+ke+ +e + ++  +Ka+g  +g+g +v+++e+e  + ++   ++ + 
  gi|313125885|ref|YP_004036155.1| 115 EKTKARALMQKADVPVVpgTTEPVESAEEVKEIADEYGYPV-AIKAEGGGGGRGLKVVHNEDEVEDQLETAQREGEA 190
                                       68889**********97678999******************.9*********************9999999887776 PP

                                       CCCCSSEEEEE---SE CS
                            GARS_A  77 GeagekvviEelleGe 92 
                                          +++v +E++le  
  gi|313125885|ref|YP_004036155.1| 191 YFDNASVYVEKYLEAP 206
                                       667899******9863 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.4e-07   0.00024      11     159 ..     122     293 ..     114     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.4e-07
                                       HTTT.S---...............-EESS--........SSSEEEEESS-------B--SS--TTE........... CS
                       ATP-grasp_3  11 LkeagvkvP...........tkleaeeleee........ekklvvKprdGaggesvrvveekeeaeaaieeve.... 64 
                                       L+++ + vP            +        e         +++ +K   G+gg +  vv++++e e ++e+ +    
  gi|313125885|ref|YP_004036155.1| 122 LMQK-ADVPvvpgttepvesAE--------EvkeiadeyGYPVAIKAEGGGGGRGLKVVHNEDEVEDQLETAQrege 189
                                       4444.34444445554333222........22223444599*************************999998899** PP

                                       ........EEEE---S.EEEEEEEEE.SSS.EEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTS CS
                       ATP-grasp_3  65 ........lvqefieG.kplSvsllsdgek.vlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekl 131
                                                v +++e  +++ v++l+d++  v+ l   +  +++++++++    +   + +l+e++ e+a++ v + 
  gi|313125885|ref|YP_004036155.1| 190 ayfdnasvYVEKYLEApRHIEVQILADKHGnVRHLGERDCSLQRRHQKVIEEAPSPALDDDLRERIGEAARRGVDAA 266
                                       *******8899999975899******987515667766677776555555555555556667**************9 PP

                                       TT--EEEEEEEEESS.SEEEEEEESS-- CS
                       ATP-grasp_3 132 eglaGyvGvDlvlkdeepyviEvNPRlt 159
                                        +      v+++++d+e y++EvN R++
  gi|313125885|ref|YP_004036155.1| 267 -DYTNAGTVEFLVEDGEFYFMEVNTRIQ 293
                                       .8888888******************98 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.3e-06    0.0023       9      54 ..     113     160 ..     106     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                       ATP-grasp_5   9 lLteaeakelleaygipvvetrl..assaeeaveaaeeigypvvlKiv 54 
                                       l ++ +a++l++  ++pvv+     ++saee+ e+a+e gypv++K  
  gi|313125885|ref|YP_004036155.1| 113 LGEKTKARALMQKADVPVVPGTTepVESAEEVKEIADEYGYPVAIKAE 160
                                       4567899************977777*********************75 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       7.8   7.7e+03      18      36 ..     135     153 ..      91     160 .. 0.74
   2 ?    7.5   0.0    0.0066       6.6       2      29 ..     531     558 ..     530     565 .. 0.89
   3 ?    6.5   0.2     0.013        13       2      29 ..     568     595 ..     567     597 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.8
                            HlyD_3  18 gevvqagdelleiippdtl 36 
                                        e+v++ +e+ ei+++  +
  gi|313125885|ref|YP_004036155.1| 135 TEPVESAEEVKEIADEYGY 153
                                       4567777777777776544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0066
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdelle 29 
                                       + A  +G++ +++veeg+ v++gd++  
  gi|313125885|ref|YP_004036155.1| 531 IAAEMQGTILSVDVEEGDEVASGDVVCV 558
                                       77999*******************9865 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.013
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdelle 29 
                                       + A ++G+v+++ v eg+ v  gd+l+ 
  gi|313125885|ref|YP_004036155.1| 568 VVAERGGTVSQILVGEGDSVDMGDVLVV 595
                                       789*********************9975 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.3e-05     0.063      15      90 ..     109     182 ..     105     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                       ATPgrasp_ST  15 efplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylks 90 
                                       +++ + +K k + l+++a ++v    g+ +  ++++e++++  e+   v+iK+  g gG+G+ v+ ++++ + + +
  gi|313125885|ref|YP_004036155.1| 109 AMERLGEKTKARALMQKADVPVVP--GTTEPVESAEEVKEIADEYGYPVAIKAEGGGGGRGLKVVHNEDEVEDQLE 182
                                       567788899999998888877766..999999*************666****************977555444433 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.15      46     112 ..     252     319 ..     196     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                      ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalklllgle 112
                                       +e++ e+a+r +++   +    v +  ++++ + +E+N+R++    ++  ++G++++++ l+ + g+e
  gi|313125885|ref|YP_004036155.1| 252 RERIGEAARRGVDAADYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTeQVTGIDVVKWQLRVAAGEE 319
                                       4678889999999999999999999999999***********9776662568************9953 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0003       0.3      10     111 ..       8     108 ..       6     112 .. 0.86
   2 ?    1.5   0.2      0.42   4.2e+02      30     113 ..     100     199 ..      89     201 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                                       S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE- CS
                     CoA_binding_2  10 dnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgakavwlq 86 
                                       +n+g  + +v+r ++e g++ v+V+  +++  g+  ya+ a + +p  ++d ++  ea+ e  ++a+a    av   
  gi|313125885|ref|YP_004036155.1|   8 ANRGEIAVRVMRACKELGIRTVAVYSDADKHSGHVRYADEAYNIGPARAADSYLDHEAVIEAGEKAGAD---AV--H 79 
                                       68899999*************************99999999878**********999999888887665...44..4 PP

                                       TT....---HHHHHHHHHTT-EEE.ES-H CS
                     CoA_binding_2  87 pg....sedeeaaelaeeagirvvgdrCi 111
                                       pg    +e++e+a+++ee +++ vg++  
  gi|313125885|ref|YP_004036155.1|  80 PGygflAENAEFAAKVEESEMTWVGPSAA 108
                                       555588999************99998765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.42
                                       EEEESSS-..SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH.--SEEEE-TT.............-- CS
                     CoA_binding_2  30 vvpVnpke..eeilgekvyaslaedpepvdlvdvftppeatpeivkealal.gakavwlqpg.............se 90 
                                       ++ V p +   e lgek  a+   ++ +v +v   t p + +e vke++++ g ++++  +g              e
  gi|313125885|ref|YP_004036155.1| 100 MTWVGPSAaaMERLGEKTKARALMQKADVPVVPGTTEPVESAEEVKEIADEyGYPVAIKAEGggggrglkvvhneDE 176
                                       56666666443444544333333345788888888888888888888855547777777777777777777755544 PP

                                       -HHHHHHHHHTT-EEE.ES-HHH CS
                     CoA_binding_2  91 deeaaelaeeagirvvgdrCilv 113
                                        e+ +e a+++g  +  ++++ v
  gi|313125885|ref|YP_004036155.1| 177 VEDQLETAQREGEAYFDNASVYV 199
                                       45555555556666666666655 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.71   7.1e+02      10      38 ..      93     121 ..      85     153 .. 0.65
   2 ?   12.1   1.6   0.00014      0.14      24      73 ..     530     578 ..     516     581 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.71
                                       EEEETT.EEEEEE-HHHHHHH-SEEEEE- CS
                             GCV_H  10 vkveedgvatvGitdfaqeelgdvvfvel 38 
                                        kvee++++ vG ++ a e+lg+ +  + 
  gi|313125885|ref|YP_004036155.1|  93 AKVEESEMTWVGPSAAAMERLGEKTKARA 121
                                       5788999999*********9998776654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00014
                                       HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                             GCV_H  24 dfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73 
                                       ++a+e+ g +++v++ e+g++v+ g+ + ++E+ K+  +v a+  G+v +
  gi|313125885|ref|YP_004036155.1| 530 QIAAEMQGTILSVDV-EEGDEVASGDVVCVLEAMKMENDVVAERGGTVSQ 578
                                       6899**********9.67****************************9976 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6   0.00072      0.71     274     316 ..       4      46 ..       3     120 .. 0.67
   2 ?    1.1   0.1      0.13   1.3e+02     127     188 ..     108     168 ..      86     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00072
                                       EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHH CS
                    Oxidored_nitro 274 rvaiygdpdrvvalarllkelGmevvaagtetahrddeerlka 316
                                       +v+++  ++++v ++r++kelG+++va+ +   +   + r  +
  gi|313125885|ref|YP_004036155.1|   4 KVLVANRGEIAVRVMRACKELGIRTVAVYSDADKHSGHVRYAD 46 
                                       8999************************998887666543333 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHHCTT-TT---SSEEEEEEETTCGH.GHHHHHHHHHHHHTEEEEEEECTSB-HHHH CS
                    Oxidored_nitro 127 aalealvrklvgkkgekeprkvnilgeynlgp.gdlrelkelleklGlevnavftggtsleel 188
                                       aa+e l +k  ++    ++ +v +++++ ++p + ++e+ke+ +++G+ v   + gg + + l
  gi|313125885|ref|YP_004036155.1| 108 AAMERLGEKT-KARALMQKADVPVVPGT-TEPvESAEEVKEIADEYGYPVAIKAEGGGGGRGL 168
                                       4555555555.324444555999**999.666699*************998888888765555 PP

>> DUF4019  Protein of unknown function (DUF4019)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.1   1.1e+03      20      58 ..      88     127 ..      82     136 .. 0.76
   2 ?    9.6   0.0    0.0012       1.2      40      92 ..     250     305 ..     235     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.1
                           DUF4019  20 easalfkkavteeewekalkavraplGav.ksRklasaee 58 
                                       +a  ++k + +e +w+   +a+ ++lG+  k+R l++   
  gi|313125885|ref|YP_004036155.1|  88 NAEFAAKVEESEMTWVGPSAAAMERLGEKtKARALMQKAD 127
                                       56667888889999*************7515677777655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0012
                           DUF4019  40 avraplGavksRklasaeear...slpgaPdGeYvviqfetefenkkqavEtvtlr 92 
                                       ++r+++G++ +R + +a +++       + dGe+  ++ +t+ + +++++E vt  
  gi|313125885|ref|YP_004036155.1| 250 DLRERIGEAARRGVDAADYTNagtVEFLVEDGEFYFMEVNTRIQVEHTVTEQVTGI 305
                                       689***********99999996533445789**********************965 PP

>> TFIIE-A_C  C-terminal general transcription factor TFIIE alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.2   0.00074      0.74      26      52 ..     460     486 ..     436     491 .. 0.62
   2 ?   -0.6   0.4       1.6   1.6e+03      30      37 ..     514     521 ..     497     572 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00074
                         TFIIE-A_C  26 veeeeeeeeeee..addptvmVaGrpvsl 52 
                                       +e+ ++eee  e  ++d tv V+G+++ +
  gi|313125885|ref|YP_004036155.1| 460 AESGDDEEE--EvtERDFTVEVNGKRFEV 486
                                       333333333..34589*********9976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                         TFIIE-A_C  30 eeeeeeee 37 
                                        e +eeee
  gi|313125885|ref|YP_004036155.1| 514 AESDEEEE 521
                                       33334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 3518.98
//
Query:       gi|313125886|ref|YP_004036156.1|  [L=353]
Description: aspartate semialdehyde dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-33  115.2   0.0    5.3e-33  114.0   0.0    1.6  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    1.6e-30  106.5   0.0    2.5e-30  105.9   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    0.00058   20.0   0.0     0.0012   18.9   0.0    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0014   19.3   0.0     0.0028   18.4   0.0    1.5  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
     0.0059   16.5   0.0      0.011   15.6   0.0    1.4  1  DUF1416          Protein of unknown function (DUF1416)
  ------ inclusion threshold ------
      0.065   12.8   0.0       0.17   11.5   0.0    1.6  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
      0.083   13.7   0.0       0.15   12.9   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0   2.1e-36   5.3e-33       1     119 [.      13     138 ..      13     140 .. 0.98
   2 ?   -3.1   0.0         4     1e+04       8      22 ..     190     205 ..     186     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 2.1e-36
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGC.TT-SEE CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeel.kevdiv 70 
                                       +v+i+GatG+vGq++++lL+ hp +el++l++s+ saGk++aea+k      ++++++++kv+++++e++ ++vd++
  gi|313125886|ref|YP_004036156.1|  13 QVGILGATGAVGQRFIQLLDGHPTFELAALTASEASAGKTYAEAAKwrvntpIPDDVAEMKVTATTPEAVpNDVDLL 89 
                                       69**************************************************************9999999****** PP

                                       EE-SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                    Semialdhyde_dh  71 flalpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                       f++lp+gv+ e++p+++++g +v ++ss+ R+ +d+++ +pe+n+ +++
  gi|313125886|ref|YP_004036156.1|  90 FSSLPSGVATEIEPEFLHEGYVVSSNSSNDRMAPDVPLTIPEINPGHLD 138
                                       *********************************************9986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4
                                       TSHHHHHHHHHHHC.T CS
                    Semialdhyde_dh   8 tGyvGqellrlLee.h 22 
                                        Gy G   ++++++  
  gi|313125886|ref|YP_004036156.1| 190 AGYSGVTSMEIIDNaI 205
                                       6888888888888744 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.0   9.6e-34   2.5e-30       5     183 ..     171     333 ..     168     334 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 9.6e-34
                                       HHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHH CS
                   Semialdhyde_dhC   5 ldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkav 81 
                                       ld+ ++le+v+v+t+qavSGaG+                     gv +++i +N+ip+i++ee k+e+e+r+ l++ 
  gi|313125886|ref|YP_004036156.1| 171 LDQ-FGLESVHVSTLQAVSGAGY--------------------SGVTSMEIIDNAIPHIGGEENKMETESRKLLGEF 226
                                       466.77*****************....................6********************************* PP

                                       HHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCS.....TTEEEEESSHCHHSSHHHH CS
                   Semialdhyde_dhC  82 aetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaa.....pevkvvvneeedrPtpaav 151
                                       + t + l+  + v a+c+r+P l+Gh+e v+++++  ++++e++e++ +++       p++ ++v e + rP+p+++
  gi|313125886|ref|YP_004036156.1| 227 DGTDVSLHEMD-VAASCNRIPTLDGHLENVFAETAedVTPDEAAEAMREYSGVdlhsaPDQLIHVFEDPARPQPRLD 302
                                       ********998.**********************877777777777777766699999******************* PP

                                       TTCSSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                   Semialdhyde_dhC 152 aggtnsvsVGRirkdemgdeglklvvvgDNll 183
                                       +++++ +++     + ++ +glk+ ++++N++
  gi|313125886|ref|YP_004036156.1| 303 RERGDGMQIC-AGGLHETANGLKYNCLAHNTI 333
                                       *997766665.4455566689*********97 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.8e-07    0.0012       1      76 [.      12      78 ..      12      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.8e-07
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S- CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTt 76
                                      ++v+++Ga+G +G++ +++++ ++ +el+a   ++     gk   e+++  +++ ++ dd++e++      +  Tt
  gi|313125886|ref|YP_004036156.1| 12 VQVGILGATGAVGQRFIQLLDGHPTFELAALTASEA--SAGKTYAEAAKW-RVNTPIPDDVAEMK------VTATT 78
                                      589***************************998876..566666665554.67777777766654......34455 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0028       1      50 [.      14      63 ..      14      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                      EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEE.SSTHHHHHHHHHHHT-SE CS
                   DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaa.gsnvellaeqakefkpkl 50
                                      v iLG+TG +G+  ++++  +p +fe++al+a + +  + ++ a+++++++
  gi|313125886|ref|YP_004036156.1| 14 VGILGATGAVGQRFIQLLDGHP-TFELAALTAsEASAGKTYAEAAKWRVNT 63
                                      579*******************.9********7777888888888887765 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.2e-06     0.011      23      95 ..      14      86 ..       4      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                           DUF1416 23 qGkvtrdgepvggayvRLLdssgeFt.aevvtsaeGefrFfaapGeWtvRalarkgngdaeveaesggvaevev 95
                                       G  + +  +vg  ++ LLd++  F  a  ++s++ + + +a   +W+v +  ++  ++++v+a++++    +v
  gi|313125886|ref|YP_004036156.1| 14 VGI-LGATGAVGQRFIQLLDGHPTFElAALTASEASAGKTYAEAAKWRVNTPIPDDVAEMKVTATTPEAVPNDV 86
                                      333.34444799*************54889999999****************************9998876665 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.1   8.1e+03       8      25 ..     171     187 ..     165     189 .. 0.73
   2 ?   11.5   0.0   6.5e-05      0.17      73     111 ..     239     277 ..     233     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.1
                                       HHHHHEEEEEEEEEEEEC CS
                           Gp_dh_C   8 lndkfgikkglmttvhay 25 
                                       l d+fg++++ + t+ a+
  gi|313125886|ref|YP_004036156.1| 171 L-DQFGLESVHVSTLQAV 187
                                       4.6799999999998775 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.5e-05
                                       EEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH CS
                           Gp_dh_C  73 dglAvrVPtpnvsvvdlvvelekevtveevnaalkeaae 111
                                        ++  r+Pt ++++ ++  e++++vt +e  +a++e + 
  gi|313125886|ref|YP_004036156.1| 239 AASCNRIPTLDGHLENVFAETAEDVTPDEAAEAMREYSG 277
                                       56678******************************9885 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.9e-05      0.15       2      71 ..      13      94 ..      12     113 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.9e-05
                                      EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE....EESS...........HHHHHTCTTES CS
                      GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgve....aysd...........leelladpeid 64
                                      +v+i Ga G +g++++ +l + +++ e++al  ++a++ ++ ae+ ++        d            e++++  ++d
  gi|313125886|ref|YP_004036156.1| 13 QVGILGAtGAVGQRFI-QLLDGHPTFELAALTASEASAGKTYAEAAKWRvntpI-PDdvaemkvtattPEAVPN--DVD 87
                                      79*****8889*****.888888*******************776666632532.2244334443333333333..555 PP

                                      EEEE-S- CS
                      GFO_IDH_MocA 65 avivatp 71
                                      +++   p
  gi|313125886|ref|YP_004036156.1| 88 LLFSSLP 94
                                      5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 2183.39
//
Query:       gi|313125887|ref|YP_004036157.1|  [L=322]
Description: phosphoglycerate dehydrogenase-like oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-53  179.4   0.0    5.7e-53  178.9   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.3e-12   47.5   0.0    1.6e-12   47.2   0.0    1.1  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0032   18.0   0.0     0.0084   16.7   0.0    1.7  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.045   13.3   0.0        0.2   11.2   0.0    2.0  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
      0.056   13.6   0.0      0.086   13.0   0.0    1.3  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
       0.17   11.2   0.0       0.32   10.3   0.0    1.4  1  ThiF           ThiF family


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.9   0.0   1.9e-56   5.7e-53       2     177 ..     114     288 ..     113     289 .. 0.97

  Alignments for each domain:
  == domain 1  score: 178.9 bits;  conditional E-value: 1.9e-56
                                       HHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHH CS
                      2-Hacid_dh_C   2 alllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeee 77 
                                       + +l+++rr++ a ++ +++ew   ++++ +el+g+tv+i+GlG+IG+a+ +rl +fg++ i++  +++k   ++e 
  gi|313125887|ref|YP_004036157.1| 114 GSILSFTRRFHVAWRRNEHNEW---RSYPTYELQGSTVAILGLGAIGKATVERLDPFGVETIGVRYTPEKGGpTDEV 187
                                       679*******************...99**************************************999987788889 PP

                                       HTC.EECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES- CS
                      2-Hacid_dh_C  78 lgv.elvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDv 153
                                       +g+ +++ + ++la+sD+v++++plt+ tr+li+a+++++m+++a+l+N++RG++vd++aLl+a++ + i+gaalDv
  gi|313125887|ref|YP_004036157.1| 188 VGFeDKAAFYDALARSDYVVVACPLTETTRGLIDADAFRSMPPEAVLVNVGRGPIVDTDALLDAIRTNDIRGAALDV 264
                                       9997778********************************************************************** PP

                                       -SSSSSGTCHHHHHSTTEEE-SS- CS
                      2-Hacid_dh_C 154 feeeplpedspllelpnviltPHi 177
                                       +++eplp+d++l++++nv++tPH 
  gi|313125887|ref|YP_004036157.1| 265 TDPEPLPDDHELWTFDNVLITPHN 288
                                       ***********************6 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   5.3e-16   1.6e-12      34     131 ..      47     319 ..      11     322 .] 0.91

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 5.3e-16
                                       HHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                        2-Hacid_dh  34 lekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt........ 102
                                        e +k+a +   +    +++++l++++ L + a++ +G+ ++ l+a++e+ i+Vtn+ g++   +AE +        
  gi|313125887|ref|YP_004036157.1|  47 RELLKRASVATGF---TLDENTLAHAEHLDLFACVFAGTGHLPLEAFEEHDIAVTNAAGVHGPNIAEQVigsilsft 120
                                       4444444444444...388********************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|313125887|ref|YP_004036157.1| 121 rrfhvawrrnehnewrsyptyelqgstvailglgaigkatverldpfgvetigvrytpekggptdevvgfedkaafy 197
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|313125887|ref|YP_004036157.1| 198 dalarsdyvvvacpltettrglidadafrsmppeavlvnvgrgpivdtdalldairtndirgaaldvtdpeplpddh 274
                                       ***************************************************************************** PP

                                       ...............T-BHHHHHHHHHHHHHHHHHHHTT.CCGTT CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                        2-Hacid_dh 103 ...............aaTeeaqeniaeeaaenlvaflkg.espan 131
                                                      + T +  e++a+++aen+++  +g e+++n
  gi|313125887|ref|YP_004036157.1| 275 elwtfdnvlitphnsGHTPKYWERMADIVAENVERLSAGeEELQN 319
                                       **************************************9545555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.8e-06    0.0084       1      75 [.     147     216 ..     147     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-06
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedve 75 
                                       +++i+G G +g+a +++l   g    e + + + +pek   + e +g + +a +  +a++++d vv+a++ + ++
  gi|313125887|ref|YP_004036157.1| 147 TVAILGLGAIGKATVERLDPFG---VETI-GVRYTPEKGGPTDEVVGFEDKA-AFYDALARSDYVVVACPLTETT 216
                                       58********************...5655.5699*************99999.999**************98765 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.35     1e+03      93     130 ..      55      92 ..      43     120 .. 0.80
   2 ?   11.2   0.0   6.8e-05       0.2       2      69 ..     143     211 ..     142     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.35
                                       ESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHT CS
                              IlvN  93 fahGfnihfglikppkdvdvvlvAPkgpGhlvreeyee 130
                                        a Gf +  +++   +++d + +   g Ghl  e +ee
  gi|313125887|ref|YP_004036157.1|  55 VATGFTLDENTLAHAEHLDLFACVFAGTGHLPLEAFEE 92 
                                       68899999999999999999999999999988887776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.8e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEE.EHHHHHHT-SEEEE-S- CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevl.tvaeavkkadvvmiliP 69 
                                       l+g ++a++G G+ G+a  + l   g++ +   ++ +k   + +  gfe +    +a +++d v++  P
  gi|313125887|ref|YP_004036157.1| 143 LQGSTVAILGLGAIGKATVERLDPFGVETIGVRYTPEKGGPTDEVVGFEDKaAFYDALARSDYVVVACP 211
                                       8999***********************965444455556677777888765156788889998888887 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.9e-05     0.086       2     109 ..     148     257 ..     147     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.H CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvae.gakaaesieelvasldvvitmvkagkavdevieg.l 76 
                                       ++++GlG +G+  +++l   g +++++  t+ek     +  g++  +   +++a+ d v++  + ++ ++ +i+   
  gi|313125887|ref|YP_004036157.1| 148 VAILGLGAIGKATVERLDPFGVETIGVRYTPEKGGPTDEVvGFEDKAAFYDALARSDYVVVACPLTETTRGLIDAdA 224
                                       899***************************99876655331355555555666666******************99* PP

                                       CCC--TT-EEEE-S---HHHHHHHHHHHHHTT- CS
                     NAD_binding_2  77 lealkkgdilidgstsspedtrelakelkekgl 109
                                       ++++ ++++l++++   + dt  l ++++ +++
  gi|313125887|ref|YP_004036157.1| 225 FRSMPPEAVLVNVGRGPIVDTDALLDAIRTNDI 257
                                       **************9999999988888777665 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011      0.32      15      47 ..     142     174 ..     135     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                                       HHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  15 kLrdskvllvGaGglGsellknLalsGvgkltl 47 
                                       +L+ s+v+++G+G++G   ++ L   Gv+ + +
  gi|313125887|ref|YP_004036157.1| 142 ELQGSTVAILGLGAIGKATVERLDPFGVETIGV 174
                                       6899*******************9999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1889.33
//
Query:       gi|313125888|ref|YP_004036158.1|  [L=463]
Description: flavin-dependent dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-12   45.2   1.5      1e-05   25.3   0.1    2.2  2  DAO             FAD dependent oxidoreductase
    5.9e-10   38.9   0.3    0.00037   19.8   0.5    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.3e-08   33.7   2.3    3.3e-07   29.9   2.3    2.1  1  FAD_binding_3   FAD binding domain
    2.7e-08   33.1   3.6    2.3e-06   26.7   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    1.3e-07   30.7   0.8     0.0013   17.5   2.1    2.3  2  HI0933_like     HI0933-like protein
    2.9e-05   23.3   3.9    5.1e-05   22.5   3.9    1.3  1  FAD_binding_2   FAD binding domain
    7.8e-05   21.9   2.0    0.00063   18.9   1.0    2.3  3  GIDA            Glucose inhibited division protein A
      9e-05   21.7   0.8       0.19   10.7   0.6    2.2  2  Lycopene_cycl   Lycopene cyclase protein
    0.00013   21.5   7.0    0.00013   21.5   7.0    2.1  3  FAD_oxidored    FAD dependent oxidoreductase
    0.00022   21.2   2.8     0.0038   17.2   2.8    2.2  1  NAD_binding_9   FAD-NAD(P)-binding
    0.00024   20.5   1.0     0.0018   17.6   1.3    2.0  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00033   20.8   1.6    0.00087   19.5   0.9    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.017   14.4   0.0    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase
      0.032   13.5   0.1       0.05   12.9   0.1    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.094   11.9   0.2       0.17   11.1   0.2    1.4  1  Thi4            Thi4 family


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   5.8e-07    0.0007       1      31 [.       5      36 ..       5      64 .. 0.92
   2 !   25.3   0.1   8.7e-09     1e-05     141     301 ..     106     282 ..      68     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.8e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                      dv+++GGG +G+++A+++a+ g   ++lekg  
  gi|313125888|ref|YP_004036158.1|  5 DVAVVGGGPAGSAAAHAAAESGasAVVLEKG-V 36
                                      8********************9*******99.4 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 8.7e-09
                                       EEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEE...TCEEEEEEECTEEEEEEEEEEE--GGGHHHHHTT.CT CS
                               DAO 141 gqv.dpakltaalaraaealGveilegtevtgleeed...gkvwgverttpgendaadavVnaaGawsdllgll.ke 212
                                       g + + a++  +l+++ae++G+e + +  v+++e ++      ++v r ++ge  +ad vV+a G++ + ++++  +
  gi|313125888|ref|YP_004036158.1| 106 GFCmHRARFDDFLRNRAETAGAEYRVNVSVRDVESDRdgsP-RHTV-RLASGEDIEADFVVLADGPQRQVTNKVlDR 180
                                       444499***************************66334533.3566.555577645688********6544333333 PP

                                       T.....TSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE.........EEETTTTEEEEEETTSEEEEEESSEEETTC CS
                               DAO 213 l.....dlpispvrgqvlvlkplseklvspaailpvpe.........tdddgrgvyvtprkdgrvlvGgtadeesgd 275
                                       +       ++  ++  ++++++  +    p+a++ + e               ++ ++p  d+  ++G t  + + d
  gi|313125888|ref|YP_004036158.1| 181 FlpfdiTDRLATTKVNHIAYQEHRR---LPEAVARDVEgaikfwwgyMPGHTAYPWIFPNDDNVARIGLTM-PIGMD 253
                                       3444332466889999999944333...333444444455667766644455566666668888999***9.66666 PP

                                       SSTSCSHHHHHHHHHHHHHHSGG....GCG CS
                               DAO 276 ddpevdeedidellealrklfPq....lgd 301
                                        + ++++++  ell++  +++P+    +++
  gi|313125888|ref|YP_004036158.1| 254 LS-DIEAREKYELLRESDERIPNgkeyIRR 282
                                       66.9****************9995333233 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.5   3.1e-07   0.00037       1      30 [.       4      33 ..       4      46 .. 0.87
   2 !   16.6   0.0   2.9e-06    0.0035     180     238 ..     109     170 ..     101     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.1e-07
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve 30
                                      +dv+v+GgGpAG aaa+ +a++ga  +++e
  gi|313125888|ref|YP_004036158.1|  4 FDVAVVGGGPAGSAAAHAAAESGASAVVLE 33
                                      69**********************998885 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.9e-06
                                       TS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE...EEEEEETTSCEEEESEEEE-S-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 180 aldkelsaaleealekeGvevklgtsvkeidgnge...klevvledgeeidadlvvvavGvr 238
                                       ++  ++ ++l+++ e  G e +++ sv +++++ +   +++v l +ge i+ad vv+a G +
  gi|313125888|ref|YP_004036158.1| 109 MHRARFDDFLRNRAETAGAEYRVNVSVRDVESDRDgspRHTVRLASGEDIEADFVVLADGPQ 170
                                       577899**************************999999999*****************9975 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   2.3   2.7e-10   3.3e-07       2     170 ..       4     175 ..       3     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.7e-10
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHS..EECCCCEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaeg..apnelmgeal 76 
                                        dV++VG+GpaG  +a+  +e G + v++ek       prad  +    ++ + +G+ d   +     p e+  +++
  gi|313125888|ref|YP_004036158.1|   4 FDVAVVGGGPAGSAAAHAAAESGASAVVLEKGV-----PRADRPDRLGPDSTDAAGILDYWVDIMdiHPDEMPDDVV 75 
                                       69****************************965.....666666666777778888888765533113566777777 PP

                                       EEECCCC.......CEEEEEHH...CHHCST-CEE-.-HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEE CS
                     FAD_binding_3  77 ynelsdt.......pkaradle...lesspervtvy.pqteleriLvehaeerglqvrfktevesleqdeegvtaev 142
                                         +l++        +   + l     ++s+ +   +    +++  L+++ae +g++ r +  v+ +e d +g +++ 
  gi|313125888|ref|YP_004036158.1|  76 LSTLDRAefigpneS---LILRetgFDTSYDHFGFCmHRARFDDFLRNRAETAGAEYRVNVSVRDVESDRDG-SPRH 148
                                       777666677785443...33333447788888776515789*******************************.6777 PP

                                       EECCTTEEEEEEEEEEEE--GTT-HHHH CS
                     FAD_binding_3 143 rdketgeeetvrakYlvGaDGgrStvrk 170
                                       + + +  e +++a+++v aDG + +v +
  gi|313125888|ref|YP_004036158.1| 149 TVRLASGE-DIEADFVVLADGPQRQVTN 175
                                       76666555.7***********9988765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   2.1    0.0044       5.3       1      22 [.       5      26 ..       5      36 .. 0.82
   2 !   26.7   0.0   1.9e-09   2.3e-06     142     220 ..     100     180 ..      49     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0044
                                      EEEEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                      ++ +vGGG+aG+ aA a a+ +
  gi|313125888|ref|YP_004036158.1|  5 DVAVVGGGPAGSAAAHAAAESG 26
                                      589************9988776 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.9e-09
                                       -B-S--EEEE-HHHHHHHHHHHHHHCT-E.EEE--EEEEEE-TTS-E.EEEEETTS-EEE-SEEEE-SGGG-IIIII CS
                    Trp_halogenase 142 lsalsyAyhldaalyakfLrrvaearGvt.rvegkvvevqldedgrv.eslrledgreveadlfiDcsGfrgllieq 216
                                       +s  ++++ + +a++++fLr+ ae +G + rv+  v +v+ d dg+  + +rl++g+ +ead+++ + G ++ + ++
  gi|313125888|ref|YP_004036158.1| 100 TSYDHFGFCMHRARFDDFLRNRAETAGAEyRVNVSVRDVESDRDGSPrHTVRLASGEDIEADFVVLADGPQRQVTNK 176
                                       455579999*******************93556678899999998862579************************** PP

                                       IT-- CS
                    Trp_halogenase 217 aLkt 220
                                       +L+ 
  gi|313125888|ref|YP_004036158.1| 177 VLDR 180
                                       *975 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.1   1.1e-06    0.0013       1      32 [.       4      35 ..       4      39 .. 0.95
   2 !    9.6   0.0   0.00027      0.33     113     163 ..     116     168 ..     105     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dv+v+GgG+AG  aA +aa+ g++ ++lek+
  gi|313125888|ref|YP_004036158.1|  4 FDVAVVGGGPAGSAAAHAAAESGASAVVLEKG 35
                                      59****************************97 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE...EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedg..kfrvktkseeeleadklvlAtG 163
                                       d+l ++++ ag ++r++ +v++ve+++dg  +++v++ s+e +ead +vlA G
  gi|313125888|ref|YP_004036158.1| 116 DFLRNRAETAGAEYRVNVSVRDVESDRDGspRHTVRLASGEDIEADFVVLADG 168
                                       7899*******************999888224667779*************88 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   3.9   4.3e-08   5.1e-05       1      33 [.       5      37 ..       5      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.3e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      Dv V+G+G AG aAA++aae G++ +v+ek+ +
  gi|313125888|ref|YP_004036158.1|  5 DVAVVGGGPAGSAAAHAAAESGASAVVLEKGVP 37
                                      9*****************************865 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.0   5.3e-07   0.00063       1      28 [.       5      32 ..       5      47 .. 0.87
   2 ?    1.4   0.0      0.11   1.4e+02     128     153 ..     147     172 ..     109     202 .. 0.78
   3 ?   -3.8   0.0       4.3   5.1e+03      78     106 ..     424     452 ..     409     455 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.3e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dv V+GgG AG++AA aaa++Ga+ + +
  gi|313125888|ref|YP_004036158.1|  5 DVAVVGGGPAGSAAAHAAAESGASAVVL 32
                                      79********************998766 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                                       EEEEEETTS-EEEECEEEE--TT-BT CS
                              GIDA 128 vkgvvtedgetikakavviatGtflk 153
                                        + v++++ge i+a+ vv+a G+  +
  gi|313125888|ref|YP_004036158.1| 147 RHTVRLASGEDIEADFVVLADGPQRQ 172
                                       457999*****************333 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 4.3
                                       STTS-CCC-EEEEEE-HHHHHHHHHHHHH CS
                              GIDA  78 NrskGpavralraqvdrelyskevtekle 106
                                         + G +v+  ++q+ + +y+++  ++++
  gi|313125888|ref|YP_004036158.1| 424 TVRAGLSVGRVATQYKKAKYKSRSDKYVQ 452
                                       45678889999999999999988877775 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.6   0.00016      0.19       1      32 [.       5      34 ..       5      44 .. 0.82
   2 !    9.0   0.0   0.00054      0.65      84     145 ..     109     172 ..      93     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      Dv+v+G+GpAg + A+    a+ g + v++e 
  gi|313125888|ref|YP_004036158.1|  5 DVAVVGGGPAGSAAAHAA--AESGASAVVLEK 34
                                      9************99999..777777777764 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00054
                     Lycopene_cycl  84 vsskrlkeellerlvengvkl.leakvesveeeea..geslvvleggrkirarlvvdarglaslk 145
                                       ++++r+   l +r  ++g+++ ++  v  ve + +   + +v l+ g+ i+a +vv a g ++++
  gi|313125888|ref|YP_004036158.1| 109 MHRARFDDFLRNRAETAGAEYrVNVSVRDVESDRDgsPRHTVRLASGEDIEADFVVLADG-PQRQ 172
                                       899************99988636999*******9954468999*****************.6655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   7.0   1.1e-07   0.00013       1      30 [.       5      34 ..       5      36 .. 0.96
   2 ?   -2.1   0.0       1.5   1.8e+03     215     267 ..     199     261 ..     122     289 .. 0.42
   3 ?   -1.2   0.0      0.84     1e+03     188     266 ..     364     446 ..     301     458 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv VvGGgpaG aAA aAa++Ga+ +++e+
  gi|313125888|ref|YP_004036158.1|  5 DVAVVGGGPAGSAAAHAAAESGASAVVLEK 34
                                      9**************************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                      FAD_oxidored 215 gydparyelarvfea.........klskgklpgektdvnwpr......vstdlienldlpeaeyegre 267
                                       +y+++r+      ea         k+ +g++pg+ t++ w         ++ l++ ++++ +++e+re
  gi|313125888|ref|YP_004036158.1| 199 AYQEHRRLP----EAvardvegaiKFWWGYMPGH-TAYPWIFpnddnvARIGLTMPIGMDLSDIEARE 261
                                       111111111....112223455566667777777.555553244444422222233444444444444 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.84
                      FAD_oxidored 188 ekvqaynkrl..cltskpenrvpfekkpegydparyelarvfeaklskgklpgektdvnwpr..vstdli.enldlp 259
                                        ++ +yn+r   ++ ++  ++v+f++  +gy p++ +   + +a+ + ++ +++ +d+n+ +   ++ ++    +++
  gi|313125888|ref|YP_004036158.1| 364 GDLSTYNDRWkaAIGDEVRRNVAFADVVRGYGPDDWDR-GFAAARKMMESSSDKLFDLNMGTvrAGLSVGrVATQYK 439
                                       44444443331133344466677777777777777777.22222223333444457777765554444443355666 PP

                      FAD_oxidored 260 eaeyegr 266
                                       +a+y++r
  gi|313125888|ref|YP_004036158.1| 440 KAKYKSR 446
                                       6666665 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   2.8   3.2e-06    0.0038       1     155 [.       7     169 ..       7     170 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsep...gagrvwrtdqseelllNvpasemslftddp........ 66 
                                       a+vG+Gp+G a++ + +++       +  + ++  p    + r   ++ +++ +l + ++ m +++d+         
  gi|313125888|ref|YP_004036158.1|   7 AVVGGGPAGSAAAHAAAESG-----ASAVVLEKGVPradRPDRLGPDSTDAAGILDYWVDIMDIHPDEMpddvvlst 78 
                                       67888888877777666664.....3333444422201122222222235667788888888888877777777766 PP

                     NAD_binding_9  67 ptfaeWlrerga...lee...aeeldp.ddfvpRalyGrYlrdlfeellarlpegvtvevhraevvdleeradgqav 136
                                        + ae++  ++      e    ++ d  +  + Ra + ++lr+++e++ a++    +v+v   +v++ ++   + +v
  gi|313125888|ref|YP_004036158.1|  79 LDRAEFIGPNESlilR-EtgfDTSYDHfGFCMHRARFDDFLRNRAETAGAEY----RVNVSVRDVESDRDGSPRHTV 150
                                       5556677766666641.22332222220334689999999999999999888....45555556666666666679* PP

                     NAD_binding_9 137 lladgaslaadaVvLAlGh 155
                                       +la+g+ ++ad VvLA G 
  gi|313125888|ref|YP_004036158.1| 151 RLASGEDIEADFVVLADGP 169
                                       ****************885 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.3   1.5e-06    0.0018       2      30 ..       8      35 ..       7      39 .. 0.92
   2 ?   -0.1   0.0      0.37   4.4e+02      85     133 ..     116     168 ..     108     176 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                      ++G+GPaG aaa+++ ++g  + ++lEkg
  gi|313125888|ref|YP_004036158.1|  8 VVGGGPAGSAAAHAAAESGA-SAVVLEKG 35
                                      8*******************.689****9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.37
                       Pyr_redox_3  85 eYlrevaksfelpiklfeeVesvkkedeg...fevetske.tyeAkkviiAtG 133
                                       ++lr+ a++   + + + +V++v+++++g    +v+  ++ ++eA++v++A G
  gi|313125888|ref|YP_004036158.1| 116 DFLRNRAETAGAEYRVNVSVRDVESDRDGsprHTVRLASGeDIEADFVVLADG 168
                                       56666666666666677777777776554344667654433788888888877 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.9   7.3e-07   0.00087       1      28 [.       8      35 ..       8      37 .. 0.97
   2 ?   -2.2   0.0       4.2     5e+03      29      43 ..     103     120 ..      98     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.3e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vG+G +G++aA+++a+ g++ ++lek+
  gi|313125888|ref|YP_004036158.1|  8 VVGGGPAGSAAAHAAAESGASAVVLEKG 35
                                      8*************************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.2
                                       SSSSGGG-EECETT...C CS
                     NAD_binding_8  29 drlGGraasyevpg...v 43 
                                       d++G +++++++++   +
  gi|313125888|ref|YP_004036158.1| 103 DHFGFCMHRARFDDflrN 120
                                       799999999999775443 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-05     0.017     216     259 ..     121     166 ..      60     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                                       HHHTTTTEEEETSEEEEEEEEETTC...EEEEETTSTEEEESEEEE- CS
                     Amino_oxidase 216 laeelrgldirlntrVkeikregdg...vtvtledgevveaDaVvvT 259
                                        ae   g + r+n  V++++ ++dg    tv+l +ge++eaD Vv++
  gi|313125888|ref|YP_004036158.1| 121 RAE-TAGAEYRVNVSVRDVESDRDGsprHTVRLASGEDIEADFVVLA 166
                                       455.889**************8888889*****************98 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.1e-05      0.05      30      66 ..       5      41 ..       1      59 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleq 66
                                       v v+GgG aG +A+++a++ ga+ +vl++   r+ +
  gi|313125888|ref|YP_004036158.1|  5 DVAVVGGGPAGSAAAHAAAESGASAVVLEKGVPRADR 41
                                      699**********************999987776665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00014      0.17      18      51 ..       4      36 ..       1      39 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersv 51
                                       Dv++vG+G++G +aa+  a++ +   ++le+ v
  gi|313125888|ref|YP_004036158.1|  4 FDVAVVGGGPAGSAAAHAAAES-GASAVVLEKGV 36
                                      69***********999999998.99999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2779.97
//
Query:       gi|313125889|ref|YP_004036159.1|  [L=293]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-63  212.9   5.0    5.1e-33  114.5   0.3    2.0  2  Usp             Universal stress protein family
    0.00021   21.4   0.0       0.85    9.9   0.1    2.4  2  MGS             MGS-like domain
  ------ inclusion threshold ------
      0.012   15.6   0.3       0.58   10.1   0.0    2.3  2  Cofac_haem_bdg  Haem-binding uptake, Tiki superfamily, ChaN
      0.027   14.5   0.0       0.43   10.6   0.0    2.3  2  FR47            FR47-like protein


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   0.3   1.1e-36   5.1e-33       1     141 []       1     138 [.       1     138 [. 0.98
   2 !  100.8   0.6   2.1e-32   9.2e-29       2     141 .]     149     287 ..     148     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 1.1e-36
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m++ Il ++Dgs+ +  A+++ l+la +++a+++ll+v d+  s+     d+++e+  +e e++ +ea+     a++
  gi|313125889|ref|YP_004036159.1|   1 MFEQILFPTDGSNGAVVAFDHVLDLAVRHNATVHLLNVADTTQSSVLRRQDDDVETLVQEGERTVREAE---NNAQQ 74 
                                       899*************************************************************99987...5999* PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++v+++++v++g+p +ei+++ e +++dl+V+ ++gr gl+r+l+GS++e+v+r+a++pVl +r
  gi|313125889|ref|YP_004036159.1|  75 RDVDTVTEVTSGEPYREIIDYSETHEIDLVVMPTHGRQGLERFLIGSTTERVVRRANVPVLTIR 138
                                       *************************************************************886 PP

  == domain 2  score: 100.8 bits;  conditional E-value: 2.1e-32
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       y+ +lV++Dgs+++ +Al  +++ a a gael+ll +i   a g     d ++e  e+  ++   +a+a  aa ++ 
  gi|313125889|ref|YP_004036159.1| 149 YQDVLVPTDGSNCANQALSVGVAVADAEGAELHLLSAIAIAALGVDVRVDVQMEMLEESAQQLIDDAAA-FAADAGV 224
                                       899*************************************99999888877777666666665555543.4566666 PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +++ + v  + +  ++il + ee+d+dl+VvG++gr+g++r+llGSv++y++r +p+pVl Vr
  gi|313125889|ref|YP_004036159.1| 225 EPTSKAVEYGPSIHQTILTYIEEQDIDLVVVGTHGRTGFDRYLLGSVTDYLVRTSPIPVLTVR 287
                                       66666666677899**********************************************998 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00019      0.85      50      95 .]      77     136 ..      30     136 .. 0.80
   2 !    9.3   0.0   0.00028       1.2      25      71 ..     218     260 ..     215     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
                                       H.............HHHHHHHTTSCCEEEEE--THHHHHH.CHHHHHHHHHHHTTSHEES CS
                               MGS  50 v.............eildaikngeidlvintlypfkatva.kdgykirraaenidIplpt 95 
                                       v             ei d  + +eidlv++ + +++  ++   g +++r++   ++p+ t
  gi|313125889|ref|YP_004036159.1|  77 VdtvtevtsgepyrEIIDYSETHEIDLVVMPTHGRQGLERfLIGSTTERVVRRANVPVLT 136
                                       044444444444559*********************99999899*************987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00028
                                       HHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--TH CS
                               MGS  25 llkeagipvtevvektgegerlggrveildaikngeidlvintlypf 71 
                                       + ++ag++    ++ ++ g + +  + il  i++++idlv++ + ++
  gi|313125889|ref|YP_004036159.1| 218 FAADAGVE--PTSKAVEYGPSIH--QTILTYIEEQDIDLVVVGTHGR 260
                                       55678888..8899999994555..9***************987765 PP

>> Cofac_haem_bdg  Haem-binding uptake, Tiki superfamily, ChaN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.022        97      85     146 ..      19      76 ..      15      91 .. 0.77
   2 ?   10.1   0.0   0.00013      0.58      22      99 ..     180     252 ..     173     259 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.022
                                       THHHHHHHHTSS--EEEEE--HHHHHHHHTT......------SSSS........-HHHHHH CS
                    Cofac_haem_bdg  85 YrpllefareaglplvalnlprelvrkvareGleslseeeereraslpaeseileseeyraa 146
                                       +  +l +a +++ +++ ln+++   + v r+  + ++++ +++++++ ++     ++++++ 
  gi|313125889|ref|YP_004036159.1|  19 FDHVLDLAVRHNATVHLLNVADTTQSSVLRRQDDDVETLVQEGERTVREAE----NNAQQRD 76 
                                       5678999**********************9989999988888887776443....4444433 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHH.HTT--EEEEEEEEEGGGHHHHHHHHHT...HHH......TT--TTS-..GGGTHHHHHHHHTSS CS
                    Cofac_haem_bdg  22 hhalqlellkaLaaagarlalglEmferdqqpaLdrylag..kideeellealewekrWgydwalYrpllefareag 96 
                                        h l +  ++aL   + r+ + +Em+e   q+++d+ +a   +   e   +a+    ++g   + ++ +l +++e++
  gi|313125889|ref|YP_004036159.1| 180 LHLLSAIAIAALG-VDVRVDVQMEMLEESAQQLIDDAAAFaaDAGVEPTSKAV----EYG--PSIHQTILTYIEEQD 249
                                       4555555566664.356899***************996541122233333333....344..666677777776666 PP

                                       --E CS
                    Cofac_haem_bdg  97 lpl 99 
                                       ++l
  gi|313125889|ref|YP_004036159.1| 250 IDL 252
                                       665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.5e-05      0.43      26      67 ..     102     143 ..      83     147 .. 0.87
   2 ?    1.3   0.0     0.077   3.4e+02      28      66 ..     253     291 ..     237     293 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.5e-05
                                       EEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HH CS
                              FR47  26 alqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtp 67 
                                        l v p+h r+Gl + l+ + ++++++r + ++l ++++++ 
  gi|313125889|ref|YP_004036159.1| 102 DLVVMPTHGRQGLERFLIGSTTERVVRRANVPVLTIRPDDDG 143
                                       57899********************************99975 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.077
                                       EE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-H CS
                              FR47  28 qvlpehrrrGlgsrlvkalakeiaergktvllvvvasNt 66 
                                        v  +h r G+ + l  +++  +++   +++l v+a ++
  gi|313125889|ref|YP_004036159.1| 253 VVVGTHGRTGFDRYLLGSVTDYLVRTSPIPVLTVRAPES 291
                                       5667899*****************999999999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1868.39
//
Query:       gi|313125890|ref|YP_004036160.1|  [L=439]
Description: 2-polyprenyl-6-methoxyphenol 4-hydroxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-23   82.0   1.0    1.8e-22   80.1   1.0    1.8  1  FAD_binding_3   FAD binding domain
    4.1e-08   32.8   0.1    0.00022   20.6   0.0    2.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.6e-07   30.8   3.5    4.2e-06   26.1   0.1    2.5  2  Lycopene_cycl   Lycopene cyclase protein
    4.5e-07   29.8   0.7    4.5e-07   29.8   0.7    1.9  2  DAO             FAD dependent oxidoreductase
    2.9e-06   27.4   0.0      9e-06   25.8   0.0    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.3e-05   24.5   0.9      3e-05   23.3   0.0    2.0  3  FAD_binding_2   FAD binding domain
    1.4e-05   25.6   0.0     0.0002   21.8   0.0    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.5e-05   24.5   0.1       0.02   14.2   0.0    2.2  2  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0069   15.3   0.0        0.1   11.4   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.042   13.8   0.2         13    5.7   0.0    2.6  2  NAD_binding_9   FAD-NAD(P)-binding
      0.053   12.8   0.0       0.13   11.5   0.0    1.6  2  Thi4            Thi4 family
       0.15   12.3   0.0       0.58   10.4   0.0    2.0  2  TrkA_N          TrkA-N domain
       0.17   11.1   0.0        1.8    7.8   0.0    2.0  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.17   10.5   0.0       0.26   10.0   0.0    1.2  1  HI0933_like     HI0933-like protein
       0.18   10.9   0.1       0.68    8.9   0.0    1.8  2  SE              Squalene epoxidase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   1.0   1.5e-25   1.8e-22       3     312 ..       7     297 ..       5     300 .. 0.82

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.5e-25
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyne 79 
                                       dVlIVG+G+aGl+la+ L+++G + ++ve+  +   ++ + gl    + +l++l  ++ ++++++  + ++   +  
  gi|313125890|ref|YP_004036160.1|   7 DVLIVGGGLAGLTLANYLRRQGREPTVVEQAPEWRTTGYGLGLWRDGITVLEELDRAAAVRRRATDPDSFAVRASDG 83 
                                       8***************************************************************8888766666666 PP

                                       CCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEE CS
                     FAD_binding_3  80 lsdtpkaradlelesspervtvypqteleriLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeetvra 155
                                             +  ++++ ++ +   v+   +l  +L+e     +   +r++t  e +e++ +gvt  + d +t++      
  gi|313125890|ref|YP_004036160.1|  84 -----GVLSHVSIPATKTLLLVIHRADLHAALRET---VPdDWIRMGTTPERIEEQRDGVTVAFDDGTTEQF----- 147
                                       .....566666688999999999999999999988...666779999999999**********999987666..... PP

                                       EEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEEEEEECCETEEEEEEEEEC CS
                     FAD_binding_3 156 kYlvGaDGgrStvrktlgiefegeetvyeagvldvlfdadlsdiveplvlilsaesrgvmviPlentlerfyvqvea 232
                                       + +vGaDG++S+vr+    + +  e   +  v ++  ++d++ i +++v +  + s+g+  +  ++      v +++
  gi|313125890|ref|YP_004036160.1| 148 DLVVGADGVHSAVRRLCFDDWTKREF--DTYVWSLWTEQDTD-IGSEMVSVWGPGSEGFVARVGDR------VGFNL 215
                                       9************9977656555553..47777777777777.66778888888888855554444......55666 PP

                                       CE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEE..EEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHH CS
                     FAD_binding_3 233 raekeersekfteeevkarlreivgektldveieevsaw..tvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNta 307
                                        a+ +  +e   ++++++++++i  +     + ++   +  ++++  +e+++ +rv l+GDAaH++ P  G+G  +a
  gi|313125890|ref|YP_004036160.1| 216 AARLDALPETPARDVLRTHAERIGWKLPSLLDATDDDPFfdRIRDVACERWHGDRVVLIGDAAHAVHPISGMGASLA 292
                                       666666777777777777777765544444455555555346889999***************************** PP

                                       HHHHH CS
                     FAD_binding_3 308 iqDav 312
                                       +qDa 
  gi|313125890|ref|YP_004036160.1| 293 LQDAR 297
                                       ***95 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.9e-07   0.00022       2      32 ..       7      37 ..       6      65 .. 0.86
   2 !   10.1   0.0   0.00029      0.34     199     238 ..     118     157 ..      86     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvele 32
                                      dv+++GgG AGl++a +l+++g + t+ve+ 
  gi|313125890|ref|YP_004036160.1|  7 DVLIVGGGLAGLTLANYLRRQGREPTVVEQA 37
                                      89**************************843 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00029
                                       EEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 199 evklgtsvkeidgngeklevvledgeeidadlvvvavGvr 238
                                        +++gt++++i+++ + ++v  +dg++++ dlvv a Gv 
  gi|313125890|ref|YP_004036160.1| 118 WIRMGTTPERIEEQRDGVTVAFDDGTTEQFDLVVGADGVH 157
                                       589*********************************9986 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   3.5e-09   4.2e-06       1     145 [.       7     160 ..       7     168 .. 0.79
   2 !    4.9   0.5    0.0097        12     257     319 ..     270     334 ..     259     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.5e-09
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny...vWsdefedlgaleecvehsWsgt.....ivyl 69 
                                       Dv+++G+G+Agl lA+ l   ++g + +++e +p+  ++  y    W d  + l++l+++   + + t      v++
  gi|313125890|ref|YP_004036160.1|   7 DVLIVGGGLAGLTLANYL--RRQGREPTVVEQAPEW-RTTGYglgLWRDGITVLEELDRAAAVRRRATdpdsfAVRA 80 
                                       9*****************..8888888899999999.6666646678888888888887776655543222227998 PP

                     Lycopene_cycl  70 ddgkkillg......raYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarg 140
                                        dg                 +++++l++ l e ++ +  +++  + e++ee+ +  ++v+ ++g + +  lvv a g
  gi|313125890|ref|YP_004036160.1|  81 SDGGVLSHVsipatkTLLLVIHRADLHAALRETVP-DDWIRMGTTPERIEEQRD-GVTVAFDDGTTEQFDLVVGADG 155
                                       887654333355555567889***********999.88999*************.9********************* PP

                     Lycopene_cycl 141 laslk 145
                                       + s+ 
  gi|313125890|ref|YP_004036160.1| 156 VHSAV 160
                                       76654 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0097
                     Lycopene_cycl 257 kvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsarawatlwp..rerkrqreff 319
                                       +v+ iG aa +vhP  G     +l+ a+  +  + +  r+     r+ +++ p  r++++ r+ f
  gi|313125890|ref|YP_004036160.1| 270 RVVLIGDAAHAVHPISGMGASLALQDARSRTGTLDRSSRRPVVGLRPVRASPPrrRTARQARGAF 334
                                       6899**************99999999998888888888877444444444433004444455555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.7   3.8e-10   4.5e-07       1      55 [.       7      61 ..       7     148 .. 0.82
   2 ?   -2.3   0.1       2.1   2.5e+03     251     299 ..     259     303 ..     216     334 .. 0.53

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.8e-10
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeas 55
                                      dv+i+GGG +Gl+ A +L r+g   t++e++  + + ++g   gl++ g+  l+e  
  gi|313125890|ref|YP_004036160.1|  7 DVLIVGGGLAGLTLANYLRRQGrePTVVEQA--PEWRTTGYGLGLWRDGITVLEELD 61
                                      8*****************88899*******9..7899************97666432 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.1
                                       TTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGG CS
                               DAO 251 rgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPql 299
                                       r+v + ++ ++rv++ g+a   ++  + +++   +   l+ +r +  +l
  gi|313125890|ref|YP_004036160.1| 259 RDVACERWHGDRVVLIGDA---AHAVH-PISGMGASLALQDARSRTGTL 303
                                       3344444444444443322...22222.444444444455555555554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   7.5e-09     9e-06       1      29 [.      10      38 ..      10      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.5e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      IvG+Gl+Gl++A +L+++g++ +++e+++
  gi|313125890|ref|YP_004036160.1| 10 IVGGGLAGLTLANYLRRQGREPTVVEQAP 38
                                      9*************************986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.5e-08     3e-05       1      35 [.       7      41 ..       7      48 .. 0.94
   2 ?   -2.3   0.0       1.5   1.8e+03      65     131 ..     102     169 ..      79     176 .. 0.62
   3 ?   -2.4   0.1       1.6   1.9e+03     109     182 ..     307     379 ..     272     387 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.5e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      Dv+++G+GlAGL+ A  ++++G++ +vve+++e +
  gi|313125890|ref|YP_004036160.1|  7 DVLIVGGGLAGLTLANYLRRQGREPTVVEQAPEWR 41
                                      9*****************************99865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                                       HHHHHHHHTTT-S-HHHHHHHHHTHHHHHHHHHHT.T----BCCTS.....SB-EEE-TT-SSTEEEE-.STT CS
                     FAD_binding_2  65 hrtdtlkaldeladqplveafveaapeavdeLeel.gvpfsrtedg.....pvdvrelGglsatartlhdaad 131
                                       hr d+ +al+e  + ++++++++  pe ++e ++   v f+    g      + v   G +sa +r ++d ++
  gi|313125890|ref|YP_004036160.1| 102 HRADLHAALRETVPDDWIRMGTT--PERIEEQRDGvTVAFDD---GtteqfDLVVGADGVHSAVRRLCFDDWT 169
                                       78888888888888888888765..44443322222233333...2222346666666666666666665555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.6
                                       S...SB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT.EEEEEEEEE CS
                     FAD_binding_2 109 g...pvdvrelGglsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLivedg.rvtGavven 181
                                       +   +v++r++ +  +++rt++  a+      + g++ + r  ++a++ +    ++t+++++  +   rv G+ ++ 
  gi|313125890|ref|YP_004036160.1| 307 SrrpVVGLRPVRASPPRRRTAR-QARG----AFRGRRDVSRITNAAQRTKRGRPPHTPVRDVRETPSsRVIGVCCRS 378
                                       1334666666666666666666.4444....6788888888888888888888888888888444335888887775 PP

                                       T CS
                     FAD_binding_2 182 p 182
                                       +
  gi|313125890|ref|YP_004036160.1| 379 L 379
                                       5 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.7e-07    0.0002       2      35 ..       8      41 ..       7      47 .. 0.92
   2 ?    0.8   0.0      0.61   7.3e+02      57      77 ..     119     138 ..     118     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-07
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v++vGgG+ gl lA++l++ g + tvve +++ +
  gi|313125890|ref|YP_004036160.1|  8 VLIVGGGLAGLTLANYLRRQGREPTVVEQAPEWR 41
                                      89**************************999866 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.61
                                       EECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox  57 vllntkveeiegsedgvesvk 77 
                                       ++++t++e+ie++ dgv+ v 
  gi|313125890|ref|YP_004036160.1| 119 IRMGTTPERIEEQRDGVT-VA 138
                                       6789**********9955.54 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0011       1.4       1      22 [.      15      36 ..      15      39 .. 0.94
   2 !   14.2   0.0   1.7e-05      0.02     212     257 ..     106     151 ..     103     172 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
                                      HHHHHHHHHHHHTTEEEEEEES CS
                     Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEa 22
                                      laGL+ A++L ++G++ tv+E 
  gi|313125890|ref|YP_004036160.1| 15 LAGLTLANYLRRQGREPTVVEQ 36
                                      79*******************6 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEE CS
                     Amino_oxidase 212 lpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVv 257
                                       l  al e+ ++++ir++t   +i+ ++dgvtv + dg++ ++D Vv
  gi|313125890|ref|YP_004036160.1| 106 LHAALRETVPDDWIRMGTTPERIEEQRDGVTVAFDDGTTEQFDLVV 151
                                       7789999**************************************9 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   8.6e-05       0.1       1      32 [.       7      35 ..       7      49 .. 0.81
   2 ?    1.3   0.0       0.1   1.2e+02     314     345 ..     266     298 ..     245     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.6e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                      +++ivGGG aG + A++l++++++    t+ve
  gi|313125890|ref|YP_004036160.1|  7 DVLIVGGGLAGLTLANYLRRQGREP---TVVE 35
                                      699******************9664...4444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                                       EETT.EEE-CCCTEE--CCCS-HHHHHHHHHHH CS
                    Trp_halogenase 314 wvkn.vvalGlasgfvePlestsihliqaalrr 345
                                       w+ + vv++G+a+ +v P+ + +  l+ +++r+
  gi|313125890|ref|YP_004036160.1| 266 WHGDrVVLIGDAAHAVHPISGMGASLALQDARS 298
                                       5543399*************9999999887765 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.013        15       2      20 ..      10      28 ..       9      45 .. 0.80
   2 ?    5.7   0.0     0.011        13     124     154 ..     125     155 ..     102     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                     NAD_binding_9  2 ivGaGprGlavlerLlara 20
                                      ivG+G +Gl++++ L ++ 
  gi|313125890|ref|YP_004036160.1| 10 IVGGGLAGLTLANYLRRQG 28
                                      9************998885 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                     NAD_binding_9 124 vvdleeradgqavlladgaslaadaVvLAlG 154
                                        +++ee++dg++v  +dg++ ++d Vv A G
  gi|313125890|ref|YP_004036160.1| 125 PERIEEQRDGVTVAFDDGTTEQFDLVVGADG 155
                                       56899**********************8866 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.13      18      49 ..       6      36 ..       2      68 .. 0.77
   2 ?   -3.1   0.0       3.1   3.7e+03     123     145 ..     362     384 ..     358     388 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       Dv+ivG+G +GLt a yl ++ + + +++e+
  gi|313125890|ref|YP_004036160.1|  6 PDVLIVGGGLAGLTLANYLRRQ-GREPTVVEQ 36
                                      59*****************998.666666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.1
                                       EEEEETBTEEEEEEEEEHHHHTC CS
                              Thi4 123 DlivregegvaGvvinwtlvela 145
                                       D+   ++++v Gv+  + +v+++
  gi|313125890|ref|YP_004036160.1| 362 DVRETPSSRVIGVCCRSLSVSQK 384
                                       544445799******99999986 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00049      0.58       1      32 [.       8      39 ..       8      43 .. 0.90
   2 ?   -3.2   0.0       8.4     1e+04      31      53 ..     125     146 ..     123     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00049
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdee 32
                                      ++i+G G  G +la++L+++g++ +v+++ +e
  gi|313125890|ref|YP_004036160.1|  8 VLIVGGGLAGLTLANYLRRQGREPTVVEQAPE 39
                                      68*****************77679****9886 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.4
                                       HHHHHHHHHTTSEEEES-TTSHH CS
                            TrkA_N  31 eerveelreeglevvvgdatdee 53 
                                       +er+ee +++g++v   d+t e+
  gi|313125890|ref|YP_004036160.1| 125 PERIEE-QRDGVTVAFDDGTTEQ 146
                                       677777.6688999999999886 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0015       1.8       1      29 [.       9      36 ..       9      43 .. 0.90
   2 ?    1.0   0.0      0.17   2.1e+02     233     274 ..     123     163 ..     101     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEk 29
                                      +I+G+G aGl+ a  l++ g e  +++E+
  gi|313125890|ref|YP_004036160.1|  9 LIVGGGLAGLTLANYLRRQGRE-PTVVEQ 36
                                      6********************6.679987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                       Pyr_redox_3 233 aevkeikekeeeykvktedgkkvevkddvvlatGykpdlsfl 274
                                       ++ ++i+e+   ++v ++dg++ e+ d vv a G ++ ++ l
  gi|313125890|ref|YP_004036160.1| 123 TTPERIEEQRDGVTVAFDDGTT-EQFDLVVGADGVHSAVRRL 163
                                       456899*************965.6678888888988877655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00021      0.26       2      33 ..       7      38 ..       6      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      dv+++GgG AGl  A  ++++g++ +++e+a+
  gi|313125890|ref|YP_004036160.1|  7 DVLIVGGGLAGLTLANYLRRQGREPTVVEQAP 38
                                      89***************************986 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.67     8e+02       4      19 ..     149     164 ..     147     173 .. 0.81
   2 ?    8.9   0.0   0.00056      0.68     132     157 ..     271     296 ..     258     306 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.67
                                SE   4 ltvvcDGifsklRkel 19 
                                       l v +DG++s +R+  
  gi|313125890|ref|YP_004036160.1| 149 LVVGADGVHSAVRRLC 164
                                       77899********965 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00056
                                SE 132 lillGDalnmRHPltggGmtvalnDi 157
                                       ++l+GDa    HP+ g G   al+D+
  gi|313125890|ref|YP_004036160.1| 271 VVLIGDAAHAVHPISGMGASLALQDA 296
                                       89**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2675.07
//
Query:       gi|313125891|ref|YP_004036161.1|  [L=370]
Description: serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-31  110.0   0.0    1.6e-31  109.7   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
       0.11   11.9   0.0        0.2   11.1   0.0    1.3  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.0   1.7e-35   1.6e-31       4     289 ..      17     286 ..      15     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 1.7e-35
                                       BTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHH CS
                       Aminotran_5   4 dsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvals 80 
                                         +++t++ ++V++a+ e           + +h+  ++t+ ++++ e+ +e++++++ + ii t ++te  ++  l+
  gi|313125891|ref|YP_004036161.1|  17 YIPGPTEVREDVIEAMCEP----------MFGHRMDRMTDLYTTIVEDTKEFLGTDN-DVIILTASGTEFWEASTLN 82 
                                       5678888888888888888..........8899***********************7.******************* PP

                                       CCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-...-TTEEEEEEESBETTTTE CS
                       Aminotran_5  81 larslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll...nektklvaithvsnvtGt 154
                                       l      +++i+v + +  +++   +++a+r g +v+ ++ d+++ +++++++++l   ++ +++va  +++++tG+
  gi|313125891|ref|YP_004036161.1|  83 L-----VDENILVATCGSFSER--HANVAERLGKNVDRLEYDWGQAVKPEDVREALersDKHYDVVACVMNESSTGV 152
                                       *.....6799************..999*****************************776799*************** PP

                                       B--HHHHHHHHHHT.T-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS......SS CS
                       Aminotran_5 155 iqpveeigklakkk.galvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekl....epll 225
                                        +p+eeig+++ ++ + +++vDa++++g   +d+++ ++D++++s++K +  P+G+ v  v++++ e+         
  gi|313125891|ref|YP_004036161.1| 153 RNPIEEIGDVIAEYpDTYFVVDAVSSLGGDYVDIDEHNIDVIFASSQKaFAMPPGVAVCAVSNDAYEREletdSASW 229
                                       *************88*********************************9999************9987634433344 PP

                                       .STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH CS
                       Aminotran_5 226 lggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeylle 289
                                       +gg    + sl+++  +++ +   + Tp ++ + + ++ ++++ e   e+  ++++e+aey++e
  gi|313125891|ref|YP_004036161.1| 230 YGGF---QRSLDYYDRKGQTH---S-TPAIPIMLAYRKQMKHMLEESHEERSRRHREMAEYTRE 286
                                       5555...45555555333433...3.*****************999999999999****99986 PP

>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.2e-05       0.2     133     163 ..     203     233 ..     182     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.2e-05
                                       TEEEEEEEESSHHHHHHHHHCCSHHHHTTEE CS
                   AICARFT_IMPCHas 133 anpcGvAvgetlaeAyekAlaaDpvSaFGgi 163
                                       a p GvAv +  ++Aye+ l++D+ S +Gg+
  gi|313125891|ref|YP_004036161.1| 203 AMPPGVAVCAVSNDAYERELETDSASWYGGF 233
                                       6799******99*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2543.52
//
Query:       gi|313125892|ref|YP_004036162.1|  [L=217]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-14   53.9   0.1    2.5e-14   52.8   0.1    1.6  1  HTH_10    HTH DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.1   1.4e-18   2.5e-14       1      52 [.     156     207 ..     156     208 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.4e-18
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT +q ++l +A++ GY+d+PR+ t++++A el+ +kst+ e Lrkaes ++
  gi|313125892|ref|YP_004036162.1| 156 LTTRQQSALEAAVAVGYYDVPRTGTVEAVAAELDCAKSTAGELLRKAESAVV 207
                                       9***********************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1442.06
//
Query:       gi|313125893|ref|YP_004036163.1|  [L=321]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-16   59.6   0.2    3.8e-15   56.2   0.2    2.0  1  Abhydrolase_1    alpha/beta hydrolase fold
    6.1e-11   43.3   9.4    8.2e-11   42.9   9.4    1.1  1  Abhydrolase_6    Alpha/beta hydrolase family
    1.3e-10   41.0   0.0    2.3e-10   40.2   0.0    1.3  1  Hydrolase_4      Serine aminopeptidase, S33
     0.0023   17.6   1.0     0.0033   17.1   1.0    1.4  1  Esterase         Putative esterase
  ------ inclusion threshold ------
       0.01   14.9   0.0      0.014   14.4   0.0    1.1  1  DUF1057          Alpha/beta hydrolase of unknown function (DU
      0.049   13.7   0.0      0.097   12.8   0.0    1.4  1  Abhydrolase_4    TAP-like protein
      0.066   12.8   0.0        4.7    6.7   0.1    2.3  2  DLH              Dienelactone hydrolase family
        7.3    7.0  15.2        3.1    8.2   6.5    2.6  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.2   1.7e-18   3.8e-15       2     251 ..      43     282 ..      42     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.7e-18
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v+lhG pgs  +     + +   +dg ++++lD +G+g+S+p+pa      ++ ++  ++ ++ld  g+ +  +v
  gi|313125893|ref|YP_004036163.1|  43 PVVFLHGTPGSRLLGEI--FDERARRDGVRLLALDRPGYGRSDPWPAR-----TLSDTGSFVTAVLDDAGVSRAGVV 112
                                       8***********99777..78788888********************7.....77889999**************** PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHH.HHHHHHHHHHHHHHCCSCHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgy.aadcarnpagplladelaaleqr 154
                                       G+S GG  ala+aa + erV+++  +++           +  ++s+p +++   + + a +++++ l++ +  l  r
  gi|313125893|ref|YP_004036163.1| 113 GFSGGGPHALAVAATHGERVQRVDVVAG--------AVPPSRRESPPLALRVLeILASATPTLARGLSRLQSVLVAR 181
                                       ***********************99999........34444444444444432144444445555555555555555 PP

                                       HHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC..........THHHHSEEEEEEETT CS
                     Abhydrolase_1 155 hrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre..........lknvlaptlvisgts 221
                                       +++        +++++  s+ ++ +s+a  +l  ++  ++++++ +    +             nv++ + +++g  
  gi|313125893|ref|YP_004036163.1| 182 SDP------SAVVSQYTDSRDADGISSAVSELVKRDFVEALANHRSGFVAETrtlarewdfsTGNVTSAVQLWHGGR 252
                                       554......33333344444444444444444444444444444333333334455555555557999********* PP

                                       CSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                     Abhydrolase_1 222 DplvppkaledlaqllpkkrlvvisdagHl 251
                                       D  vp +   +la++lp+++l v++da Hl
  gi|313125893|ref|YP_004036163.1| 253 DSNVPVEGAQRLAEQLPDATLTVLDDADHL 282
                                       ****************************96 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   9.4   3.6e-14   8.2e-11       1     215 [.      44     290 ..      44     295 .. 0.51

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.6e-14
                                       EEEE--GC.....GCHHHH..HHHHCCTCEEEEE--TTSTS-GGCS--HHH..CHHHHHHHCCTT....TTSEEEEE CS
                     Abhydrolase_6   1 vlllHGagssassWlvapL..aallaagvhvlapDlpGhGrsdpppldled..ladlaalldelaa..gggpvvlvG 71 
                                       v++lHG+++s      +++   +++++gv+ la+D+pG+Grs    + +++  l d   +++++ +  g  ++ +vG
  gi|313125893|ref|YP_004036163.1|  44 VVFLHGTPGS--RL-LGEIfdERARRDGVRLLALDRPGYGRS----DPWPArtLSDTGSFVTAVLDdaGVSRAGVVG 113
                                       8*****7763..32.3466445555555999*********88....77766324444556666665556777799** PP

                                       ETCHHHHHHHHHHCC......EE...EEES-...----TTTS----TTHHHHHHTT-C.....CCCHCCH....... CS
                     Abhydrolase_6  72 HSlGGalalaaapla....lvvg...vlldppp.talpagllaaalelllallallrl.....lawlsre....... 128
                                        S GG  ala+a+      +  +   v+ + pp     ++l+ ++le+l+ +++ l++        l+++       
  gi|313125893|ref|YP_004036163.1| 114 FSGGGPHALAVAATHgervQ--RvdvVAGAVPPsRRESPPLALRVLEILASATPTLARglsrlQSVLVARsdpsavv 188
                                       *****999993333368663..3322444444453333333444444444333322222212211111111222211 PP

                                       ......S-HSCCCCHHHC.....CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGC.....EEECTT-CHHH.HCHH CS
                     Abhydrolase_6 129 ......plprlfladeda.....daawrarlarlaallaglgllpaaawadlpvpl.....lvlggeDplvp.rlle 188
                                              +++++ +   a     +++++++la ++  + +     a++w   +  +     l++gg+D  vp + ++
  gi|313125893|ref|YP_004036163.1| 189 sqytdsRDADGISS---AvselvKRDFVEALANHRSGFVAETRTLAREWDFSTGNVtsavqLWHGGRDSNVPvEGAQ 262
                                       11122211112222...133233466666666666555544433333333333333444544557999977723344 PP

                                       CCCH.STTEEETCE...SSS..-HHHHSHH CS
                     Abhydrolase_6 189 rlla.qagarlpvvlpgaGH..lphleepd 215
                                       rl+  +++a+l +vl +a+H   +++ + d
  gi|313125893|ref|YP_004036163.1| 263 RLAEqLPDATL-TVLDDADHlrTLLQ-SGD 290
                                       55558888888.********654444.555 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0     1e-13   2.3e-10       8     232 ..      45     281 ..      42     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1e-13
                       Hydrolase_4   8 vlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhS 84 
                                       v++HG   +    + + e+  + G+  +alD  G+Grs++  +      + + D  +fv++v ++ + ++  ++G S
  gi|313125893|ref|YP_004036163.1|  45 VFLHGTPGSRLLGEIFDERARRDGVRLLALDRPGYGRSDPWPA------RTLSDTGSFVTAVLDDAGVSRAGVVGFS 115
                                       666665554444444555667899**************97766......789************************* PP

                       Hydrolase_4  85 mGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqv...................... 139
                                        GG  al++++++ ++v+++ ++a a+ +  + + ppl+  +l++l+++ p+l                        
  gi|313125893|ref|YP_004036163.1| 116 GGGPHALAVAATHGERVQRVDVVAGAVPPSRR-ESPPLALRVLEILASATPTLARglsrlqsvlvarsdpsavvsqy 191
                                       **************************988865.488888889**********99999********999988888444 PP

                       Hydrolase_4 140 snnlkadslsrdpevvaayeadplv..hgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrely 214
                                       +++ +ad +s   + v ++ +  +v    + + ++++e  +++ +   ++ ++t  ++l hG++D  v+ e++++l+
  gi|313125893|ref|YP_004036163.1| 192 TDSRDADGIS---SAVSELVKRDFVeaLANHRSGFVAETRTLAREWDFSTGNVTSAVQLWHGGRDSNVPVEGAQRLA 265
                                       4444444444...44444444444436778888999999999999999999999*********************** PP

                       Hydrolase_4 215 erlgskdktlklypglyH 232
                                       e+l+  d tl++ + + H
  gi|313125893|ref|YP_004036163.1| 266 EQLP--DATLTVLDDADH 281
                                       ****..999999999988 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.0   1.5e-06    0.0033     117     154 ..     109     176 ..      95     316 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                                       EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC..............................H CS
                          Esterase 117 ravaGqSmGGlgALilalkhpdrFgsvssfSpivnps..............................n 154
                                         v+G+S GG  AL +a++h +r ++v + ++ v ps                              +
  gi|313125893|ref|YP_004036163.1| 109 AGVVGFSGGGPHALAVAATHGERVQRVDVVAGAVPPSrrespplalrvleilasatptlarglsrlqS 176
                                       579*********************************97777766666666666665555555555550 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.4e-06     0.014      37     125 ..      43     128 ..      21     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.4e-06
                           DUF1057  37 tvvalhGsPGshnDfkYirskleelkiRligvnyPGfefvtgylgqkytnaeRnsyskalleelelkgklillghsR 113
                                        vv lhG+PGs        ++  +  +Rl++++ PG+   +  +  +    +  s+  a+l+++ ++ +  ++g s 
  gi|313125893|ref|YP_004036163.1|  43 PVVFLHGTPGSRLLGEIFDERARRDGVRLLALDRPGYGRSDPWPARTL--SDTGSFVTAVLDDAGVS-RAGVVGFSG 116
                                       4999*******99999999999999***************99998876..5779************7.66789**** PP

                           DUF1057 114 GcenaLqlavtl 125
                                       G+  aL +a+t 
  gi|313125893|ref|YP_004036163.1| 117 GGPHALAVAATH 128
                                       *******99876 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.3e-05     0.097      34      74 ..     242     282 ..     225     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
                     Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalggavlvtvegeGHg 74 
                                       ++ v l  + rD  +P ega++la++l++a+l + ++++H 
  gi|313125893|ref|YP_004036163.1| 242 TSAVQLWHGGRDSNVPVEGAQRLAEQLPDATLTVLDDADHL 282
                                       56666778899*********************999999996 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0021       4.7      95     130 ..     104     140 ..      86     180 .. 0.80
   2 ?    3.6   0.0     0.019        43     142     187 ..     240     281 ..     232     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0021
                               DLH  95 vstkkvgvvGfCmGGalalllaaev.pevdaavafYG 130
                                       + +++ gvvGf  GG  al++aa   ++v+++ +  G
  gi|313125893|ref|YP_004036163.1| 104 AGVSRAGVVGFSGGGPHALAVAATHgERVQRVDVVAG 140
                                       467899**************99987688887755555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.019
                               DLH 142 kikapilalfgeeDefipadevekleealkaanvdlelkvYpgagH 187
                                       ++   ++  +g++D  +p + +++l+e+l    +d+ l v ++a+H
  gi|313125893|ref|YP_004036163.1| 240 NVTSAVQLWHGGRDSNVPVEGAQRLAEQL----PDATLTVLDDADH 281
                                       677889999******************99....5666666666666 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.4     0.035        78      31      67 ..      44     100 ..      12     112 .. 0.60
   2 ?    8.2   6.5    0.0014       3.1       1      82 [.     115     192 ..     115     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.035
                   Glyco_trans_4_4  31 g................apeleedgvrvhrlpvprr....pspladlaalralrrll 67 
                                       +                ++++++dgvr+  l+ p      p+p ++l+ +  +  ++
  gi|313125893|ref|YP_004036163.1|  44 VvflhgtpgsrllgeifDERARRDGVRLLALDRPGYgrsdPWPARTLSDTGSFVTAV 100
                                       033333333556777766679999999999976655222236777777777765555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0014
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       +G+g ++ ++a+   +r  +V+v++ a +p+++e     +rv  + ++++p   + ++ l +l+++l ++r  p  v
  gi|313125893|ref|YP_004036163.1| 115 SGGGPHALAVAATHGERVQRVDVVAGAVPPSRRESPPLALRVLEILASATP---TLARGLSRLQSVL-VARSDPSAV 187
                                       6999999999999999999************99988999999888888775...67788999***99.999999999 PP

                   Glyco_trans_4_4  78 hahsp 82 
                                       ++++ 
  gi|313125893|ref|YP_004036163.1| 188 VSQYT 192
                                       99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2021.63
//
Query:       gi|313125894|ref|YP_004036164.1|  [L=64]
Description: cold-shock DNA-binding protein family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-19   69.6   0.0    1.7e-19   69.4   0.0    1.0  1  CSD           'Cold-shock' DNA-binding domain
  ------ inclusion threshold ------
      0.043   13.5   2.8      0.063   13.0   2.8    1.3  1  OB_RNB        Ribonuclease B OB domain
      0.094   12.6   0.0        0.1   12.5   0.0    1.1  1  Rho_RNA_bind  Rho termination factor, RNA-binding domain
       0.19   11.7   0.6       0.24   11.4   0.6    1.3  1  S1-like       S1-like


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   3.7e-23   1.7e-19       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 3.7e-23
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      +G V  fn+  g+GFI+++d d+dvF+H+ +i g++   L+eg +VeFe+++  kgp+A+n+t+
  gi|313125894|ref|YP_004036164.1|  3 KGNVDFFNDTGGYGFISTDDADDDVFFHMEDIGGED---LEEGTDVEFEIEDAPKGPRATNLTR 63
                                      79*******************************999...**********************986 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.8   1.4e-05     0.063       8      28 ..      13      33 ..       8      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                                      SS-EEEEECT.TEEEEE-HHH CS
                            OB_RNB  8 kGFGFlipdegkeDifippeq 28
                                       G+GF+++d+ ++D+f + e+
  gi|313125894|ref|YP_004036164.1| 13 GGYGFISTDDADDDVFFHMED 33
                                      59**************87766 PP

>> Rho_RNA_bind  Rho termination factor, RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.3e-05       0.1       2      63 ..       3      63 ..       2      64 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                                      EEEEEE-TT..S-EEEE-GTT---TT-EEE-CCCCCCTT--TT-EEEEEEE---SSS-SEEECE CS
                      Rho_RNA_bind  2 eGiLeilpd..gygFlRtsnylpgpedvYVsasqirkfgLrtGDaveGkvrppkerekynaLlr 63
                                      +G +++++d  gygF+ t+     ++dv+ +++ i   +L +G  ve ++  + ++ + ++L+r
  gi|313125894|ref|YP_004036164.1|  3 KGNVDFFNDtgGYGFISTD---DADDDVFFHMEDIGGEDLEEGTDVEFEIEDAPKGPRATNLTR 63
                                      78999999888*****997...789*********************999998877888887776 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   5.4e-05      0.24      14      43 ..      14      48 ..       3      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                           S1-like 14 tfGfv.....DeevfFqrsvvkGrlpkvgdrVlve 43
                                       +Gf+     D++vfF+++ + G   + g  V++e
  gi|313125894|ref|YP_004036164.1| 14 GYGFIstddaDDDVFFHMEDIGGEDLEEGTDVEFE 48
                                      58888777779*********999999999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 461.32
//
Query:       gi|313125895|ref|YP_004036165.1|  [L=416]
Description: flavin-dependent dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-05   22.8   0.2     0.0002   21.5   0.2    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00043   19.6   0.3    0.00094   18.5   0.3    1.5  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0027   17.3   0.2      0.059   12.9   0.1    2.2  2  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.071   13.7   0.3       0.84   10.2   0.1    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.077   12.1   0.7       0.13   11.3   0.7    1.6  1  GIDA           Glucose inhibited division protein A
      0.079   12.2   0.7       0.14   11.5   0.7    1.5  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.095   12.2   0.3       0.55    9.7   0.1    2.0  2  Glu_dehyd_C    Glucose dehydrogenase C-terminus
       0.51   10.1   4.3        1.7    8.4   4.3    1.9  1  HCV_NS4a       Hepatitis C virus non-structural protein NS4a


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   8.8e-08    0.0002       1      30 [.      31      60 ..      31      73 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.8e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                      +vG+ ++Gl+aA++L+  + +v+l+e++++
  gi|313125895|ref|YP_004036165.1| 31 VVGGAMAGLAAAHALRALDWEVVLYERQSY 60
                                      8**************************975 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   4.2e-07   0.00094       3     121 ..      29     181 ..      27     196 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.2e-07
                                       EEEE--SHHHHHHHHHHHHHTS-EEEEE..........TTHCHHHCSHHHHCHHHHHHHHHHHHH............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlve..........legtclnggcllskallgvaedaeias............ 57 
                                        vv+Gg +AGlaaa+ l++   +v+l+e           ++++ + + ++ ++ +         +            
  gi|313125895|ref|YP_004036165.1|  29 AVVVGGAMAGLAAAHALRALDWEVVLYErqsyaekrvnCGEAMTGADAIPLPKTA---------Eygfankppafev 96 
                                       69*************************6666554444433334444333322222.........1233333334567 PP

                                       ............................HHHHCHHHHCCCCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE CS
                                       ............................xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ............................evvkklnqgielllgeevvkidpgk.kkvklekkkegdeekiaydklvl 105
                                                                   +       + ++  ++   ++d  +   v+  +     e++ ++d +v 
  gi|313125895|ref|YP_004036165.1|  97 dvftgdtgsrtlagkgvfpstdayvtdrN-----VVERKWAEQVAEDGVDVREsTGVTKAQ---FREFSEEFDLVVD 165
                                       77887777777777777765554332221.....222222222222333322202222222...4567778888888 PP

                                       ---EEE-BCTCTTC.T CS
                                       xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 106 AtGssprdlgipGvae 121
                                       AtG  +   +++G  +
  gi|313125895|ref|YP_004036165.1| 166 ATGQPSMASKVDGTTD 181
                                       8887777777777744 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   2.6e-05     0.059       2      32 ..      29      61 ..      28      82 .. 0.86
   2 ?    2.2   0.0     0.049   1.1e+02     140     201 ..     118     168 ..      92     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdia 32
                                       v++GG ++Gl++A++L +    V+l+e+++ a
  gi|313125895|ref|YP_004036165.1| 29 AVVVGGAMAGLAAAHALRALDweVVLYERQSYA 61
                                      59***************555689******9543 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.049
                                       EEEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--G CS
                               DAO 140 tgqv.dpakltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaG 201
                                       ++ v d   + +  a+++++ Gv+++e t vt+ +       +       e  ++d vV a+G
  gi|313125895|ref|YP_004036165.1| 118 DAYVtDRNVVERKWAEQVAEDGVDVRESTGVTKAQ-----FREF-----SE--EFDLVVDATG 168
                                       3666233444456788899*********9999873.....3344.....22..2688888887 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00037      0.84       2      32 ..      29      59 ..      28      67 .. 0.92
   2 ?    0.5   0.0      0.42   9.4e+02      43      66 ..     128     151 ..     123     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                      +vvvGg   gl +A al++l  +V + er++
  gi|313125895|ref|YP_004036165.1| 29 AVVVGGAMAGLAAAHALRALDWEVVLYERQS 59
                                      79************************99986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHTTEEEECSEEEEEE CS
                         Pyr_redox  43 skilqeklekngievllntkveei 66 
                                       ++ ++e++ + g++v+ +t v++ 
  gi|313125895|ref|YP_004036165.1| 128 ERKWAEQVAEDGVDVRESTGVTKA 151
                                       5678899999********999875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   5.9e-05      0.13       3      46 ..      30      73 ..      28     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                                      EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE- CS
                              GIDA  3 iViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsigg 46
                                      +V+Gg +AG++AA a+  l  +v+L+  +     ++ C +++ g
  gi|313125895|ref|YP_004036165.1| 30 VVVGGAMAGLAAAHALRALDWEVVLYERQSYAEKRVNCGEAMTG 73
                                      8*************************766666666666666665 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7     6e-05      0.14      29      69 ..      27      67 ..      21     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                      +  +v+Gg +aGl+A+++ ++l+ +V++++ ++ + ++++ 
  gi|313125895|ref|YP_004036165.1| 27 GSAVVVGGAMAGLAAAHALRALDWEVVLYERQSYAEKRVNC 67
                                      6789**************************99988888864 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.24   5.5e+02      24      69 ..      19      61 ..      15      74 .. 0.73
   2 ?    9.7   0.1   0.00024      0.55      59     115 ..     118     174 ..     108     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                       Glu_dehyd_C 24 rsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrp 69
                                      r +++ +  sa+v+G    GL a+ +l+a   ++e v   +r+++ 
  gi|313125895|ref|YP_004036165.1| 19 RRTARKTGGSAVVVGGAMAGLAAAHALRA--LDWE-VVLYERQSYA 61
                                      5566666789******9******999986..4555.4455555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00024
                       Glu_dehyd_C  59 rvyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdlvvEaTGsakhaf 115
                                       + yv++r+  + + ++ v+e G    +s   +  ++ e see+dlvv+aTG++ +a 
  gi|313125895|ref|YP_004036165.1| 118 DAYVTDRNVVERKWAEQVAEDGVDVRESTGVTKAQFREFSEEFDLVVDATGQPSMAS 174
                                       57888888888888888888888888888888889999**************99875 PP

>> HCV_NS4a  Hepatitis C virus non-structural protein NS4a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.3   0.00077       1.7       1      18 [.      27      43 ..      27      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00077
                          HCV_NS4a  1 gpvvlvGlalAglAiyal 18
                                      g +v+vG+a+AglA+ a+
  gi|313125895|ref|YP_004036165.1| 27 GSAVVVGGAMAGLAA-AH 43
                                      5789**********9.76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2626.26
//
Query:       gi|313125896|ref|YP_004036166.1|  [L=283]
Description: metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-16   60.6   3.4    4.2e-16   59.2   3.4    1.7  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   3.4   2.3e-20   4.2e-16       1     233 []      23     273 ..      23     273 .. 0.65

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.3e-20
                                       EEEEESTG...CHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH.................TTCE CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxx RF
                     Exo_endo_phos   1 ltwNvngq...aspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllal.................ggfl 57 
                                       l++Nv  +     p   +++r d++  l++ +++Dv++LQE    +l+ +  +l++                     
  gi|313125896|ref|YP_004036166.1|  23 LSFNVRYDtddDGP-DAWPHRRDDAVRLVRYHRPDVVCLQEPLKHQLDAFRDGLDEyewvavprtggnaadatD--- 95 
                                       68999999996333.68************************999999998888888777666665544444440... PP

                                       EEEECCH................................................ECSSSTTSSEEEEEECSTEEEE CS
                                       xxxxxxx................................................xxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  58 gasstsp................................................tgggggggnggavlsrfpltsl 86 
                                             +                                                                      
  gi|313125896|ref|YP_004036166.1|  96 ------SketddaastgesvpvgydasrfsledsetfwlsetpeepgsvgwdatlP--------------------- 145
                                       ......14433333322223333333333333333333333333333333333330..................... PP

                                       EEEEEEETSSSSGCEEEEEEEEEEEEEEE................CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  87 frrtfiefndlvaalrreplaakleqlni................ashrdhdlvrdlqllalllqvealnadrgapv 147
                                                                                      +   d      +l     + +  a+ ++pv
  gi|313125896|ref|YP_004036166.1| 146 ----------------------------RiltratlqgesgetfhVASVHLDNDGVKARLEGAKLARDRLAQLDGPV 194
                                       ............................255555555555666443333333333344444445567778889**** PP

                                       EEEEE-SSSTSGGGBSCGHHHHHHCTTTHH.SSCESCETTTTTTTTTTTEB-BEEEEEECHHHCCEEEEEEECCHHE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 148 ivaGDfNarpsdddsrvlrtrglalapapv.glyllgggptptyvtraggsrlDrilaspalalfrsgvlppplalv 223
                                       i+aGD Na+p++d++   +++ +++ +  v  +   g++ t ++ t  ++ r+D+++++        + +  +++l 
  gi|313125896|ref|YP_004036166.1| 195 ILAGDCNATPDSDPYEAVTEAFADARH--VaKHGHHGPEKTMHHFTGDPTERIDYVFVRE-------CDVRLSATLA 262
                                       *****************8888777665..479999999*********************9.......6666666666 PP

                                       EC.TSSCSSSB CS
                                       xx.xxxxxxxx RF
                     Exo_endo_phos 224 rr.ealtlSDH 233
                                       +r ++ ++SDH
  gi|313125896|ref|YP_004036166.1| 263 DRtREGYPSDH 273
                                       66666779**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1807.77
//
Query:       gi|313125897|ref|YP_004036167.1|  [L=443]
Description: histidinol dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.9e-155  517.3   4.1   3.7e-155  517.0   4.1    1.0  1  Histidinol_dh  Histidinol dehydrogenase


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  517.0   4.1    2e-159  3.7e-155       8     409 .]      26     440 ..      21     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 517.0 bits;  conditional E-value: 2e-159
                                       -HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC-- CS
                     Histidinol_dh   8 seeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqke 84 
                                       +++v++ v++i+++vr+eGd a++++ ++FD v+ + +l v++ + e+a+e++d++++e++e aa+nir+fhe+q++
  gi|313125897|ref|YP_004036167.1|  26 VTDVQSDVRDIVSRVRNEGDVAIRNFCREFDDVE-VGNLDVTD-DAERAYEEIDDDVRESIEAAAANIREFHERQLP 100
                                       67899**************************774.6799**98.569*****************************9 PP

                                       ..--EEEE...............EECTTE.EEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE- CS
                     Histidinol_dh  85 ..seeevk...............etepgv.vlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtP 143
                                              +               +++ g+  lg+++rp+ervG+Y PgG+aaypS+vlm +vpAkvAgv++++vvtP
  gi|313125897|ref|YP_004036167.1| 101 ddW---REtfdglagdadaasgeQRAAGTrELGRRFRPLERVGVYAPGGTAAYPSSVLMGVVPAKVAGVEHVAVVTP 174
                                       541...33355777888888877555665479********************************************* PP

                                       SSGG.--HHHHHHHHHCT-SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EE CS
                     Histidinol_dh 144 pqdgkvnpavlaaaklagvdeiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEv 220
                                       p  + +np +laaa++ag+d+iy+vGGaqA++alAyGte++++v+k+vGPGn++V+aAK  v+g+v+iD++aGPsE+
  gi|313125897|ref|YP_004036167.1| 175 PG-DPMNPITLAAAHVAGADRIYSVGGAQAVSALAYGTETVKAVQKVVGPGNKWVTAAKAEVRGDVDIDFLAGPSEI 250
                                       *7.589*********************************************************************** PP

                                       EEEE-TTS-HHHHHHHHHHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCC.H-EEEE-SSHH CS
                     Histidinol_dh 221 lviaDetadpefvAaDLlsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslek.qsaiilvedle 296
                                       lv+aDetadp+fvAaDL++qaEHd++a++v vt+++++aea+ ++ve+q++  +r+e++++++e+  s ++++++++
  gi|313125897|ref|YP_004036167.1| 251 LVVADETADPAFVAADLVAQAEHDPNASVVAVTDDADTAEAILAAVERQIAGCEREETIREAFENdASGVLVTRSMS 327
                                       ****************************************************************98999******** PP

                                       HHHHHHHHH--SEEEEESTTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEE CS
                     Histidinol_dh 297 eaielaneyApEHlelqvedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkis 373
                                       ea+ +a+eyA+EHl++q+ed e+ll++i+naG++flG+++p+++gDYa+GtnhvLPTsg A+ ++glsve+Fl++++
  gi|313125897|ref|YP_004036167.1| 328 EAVLFAEEYAAEHLSIQAEDDEALLDRISNAGSVFLGPHTPVAAGDYASGTNHVLPTSGGAKRYGGLSVETFLRSTT 404
                                       ***************************************************************************** PP

                                       EEEE-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                     Histidinol_dh 374 vqelskealkelaeavetlAeaEgLeaHaeavkvRl 409
                                       vq+l++ al++l+e+++tlAeaEgLeaHae+v++Rl
  gi|313125897|ref|YP_004036167.1| 405 VQRLDEGALSDLSETITTLAEAEGLEAHAESVRTRL 440
                                       **********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2832.44
//
Query:       gi|313125898|ref|YP_004036168.1|  [L=258]
Description: methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-10   39.0   0.0    1.8e-09   38.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    3.1e-08   34.2   0.0    6.1e-08   33.2   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    1.1e-07   31.9   0.0    1.7e-07   31.2   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.1e-07   31.7   0.0    4.1e-07   29.9   0.0    1.8  1  Methyltransf_31  Methyltransferase domain
    1.9e-05   25.4   0.0      5e-05   24.0   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    0.00022   20.9   0.0    0.00049   19.7   0.0    1.5  2  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
       0.13   11.5   0.0        2.5    7.3   0.0    2.0  2  CMAS             Mycolic acid cyclopropane synthetase
       0.14   11.7   0.0       0.29   10.6   0.0    1.5  2  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   8.1e-13   1.8e-09       1      97 []      66     150 ..      66     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 8.1e-13
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vL+lGcGtG+l+ +l+++   ++ +g+D  +++l  a++r e        v+gd +d p     fD+v+++   h++
  gi|313125898|ref|YP_004036168.1|  66 VLELGCGTGTLLHRLSDE---YTALGIDRYSDLLSFAAARGE------AAVCGDPTDPPVRP-DFDAVCAF-D-HFV 130
                                       9***************99...69******************5......469********876.8******5.5.568 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                        ++ l ++++ ++  L+pgG
  gi|313125898|ref|YP_004036168.1| 131 ARQSLSAVCEGAYATLRPGG 150
                                       899****************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   2.7e-11   6.1e-08       1      96 []      67     154 ..      67     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.7e-11
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       L++GcGtG l+  l + + + +g+D    +l  a ++++ +      v++d ++ p++   fD+v+++  +   + +
  gi|313125898|ref|YP_004036168.1|  67 LELGCGTGTLLHRLSDEY-TALGIDRYSDLLSFAAARGEAA------VCGDPTDPPVRP-DFDAVCAFDHFVARQSL 135
                                       89*************888.9**************8888776......9******99998.8*****99977777*** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                       +++++ ++  L+pgG++v+
  gi|313125898|ref|YP_004036168.1| 136 SAVCEGAYATLRPGGIFVF 154
                                       *****************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   7.5e-11   1.7e-07      21     163 ..      61     234 ..      36     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7.5e-11
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg........kfdlIvlr 89 
                                           rvL++GcGtG+ll  l+++ ++  g+D ++ + + a+ a+    ++          +         fd ++++
  gi|313125898|ref|YP_004036168.1|  61 ADVERVLELGCGTGTLLHRLSDE-YTALGIDRYSDLLSFAA-ARGEAAVCG---------DptdppvrpDFDAVCAF 126
                                       4667**************99999.9********87666542.222222222.........1222455679******* PP

                   Methyltransf_23  90 evlehvpdppellrqiatllkpgGylllsep.lasl................................kedrllldw 133
                                       + +   +++ ++   +++ l+pgG +++    +a++                                ++  +l+  
  gi|313125898|ref|YP_004036168.1| 127 DHFVARQSLSAVCEGAYATLRPGGIFVFDALsDARAiaasgvetyrgaryvfersvdvardppvvhadYRVTDLRTG 203
                                       ****************************9961444489999999999999999988888888888554444444445 PP

                   Methyltransf_23 134 lylvpag.rhisffsarslkelleeaGlevv 163
                                       +  v+a+ + +++++ +s++e le aG++++
  gi|313125898|ref|YP_004036168.1| 204 ETGVTAErTSFNVYDPESVRESLETAGFSDI 234
                                       55577763666*****************987 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.8e-10   4.1e-07       6     113 ..      65     158 ..      61     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.8e-10
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       rvl+lGCGtG+l+++l +e     +  GiD+  + +++A ++ +           gd ++ +  +    fD +++++
  gi|313125898|ref|YP_004036168.1|  65 RVLELGCGTGTLLHRLSDE----YTALGIDRYSDLLSFAAARGE-------AAVCGDPTDPP--VR-PDFDAVCAFD 127
                                       89***************76....569***************844.......45569999988..55.68******** PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr 113
                                        + a  ++ ++ e++   l+pggi++ +  +
  gi|313125898|ref|YP_004036168.1| 128 HFVARQSLSAVCEGAYATLRPGGIFVFDALS 158
                                       **************************88777 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.2e-08     5e-05       1      99 []      67     152 ..      67     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       Le+GcGtG+ll++l ++    + +g+D  ++ +      +a+ +++ + + + ++  +  ++    fD+v a++ + 
  gi|313125898|ref|YP_004036168.1|  67 LELGCGTGTLLHRLSDE---YTALGIDRYSDLL-----SFAAARGEAAVCGDPTDPPV--RP---DFDAVCAFDHFV 130
                                       8*************999...6666777777666.....55555554444444444443..32...9*********** PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                       + + + +v + +++ L+pgG++
  gi|313125898|ref|YP_004036168.1| 131 ARQSLSAVCEGAYATLRPGGIF 152
                                       ********************85 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.2e-07   0.00049      13      88 ..      62     138 ..      55     144 .. 0.77
   2 ?   -3.4   0.0       2.7     6e+03      29      45 ..     155     171 ..     152     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.2e-07
                              MetW  13 pgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgd.ldkdle.nf.edksfdyvvlsqtlq 86 
                                       +  rvl+lGcG G+ll+ l +  + ++ G++  ++ +  + a+G + + gd  d  +   f +  +fd  v  q+l 
  gi|313125898|ref|YP_004036168.1|  62 DVERVLELGCGTGTLLHRLSD--EYTALGIDRYSDLLSFAAARGEAAVCGDpTDPPVRpDFdAVCAFDHFVARQSLS 136
                                       6689***************88..7899*****************988887724444431230335788888888877 PP

                              MetW  87 at 88 
                                       a+
  gi|313125898|ref|YP_004036168.1| 137 AV 138
                                       76 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.7
                              MetW  29 ellkeekqvdgrGleld 45 
                                       + l + + + + G+e+ 
  gi|313125898|ref|YP_004036168.1| 155 DALSDARAIAASGVETY 171
                                       56888899999999864 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0011       2.5      62      86 ..      62      86 ..      31      90 .. 0.74
   2 ?    2.1   0.0     0.044        98     134     169 ..     123     159 ..     116     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                                      TT-EEEEES-TTSHHHHHHHHHH-- CS
                              CMAS 62 pGmtlLdiGcGWGslvrraverydv 86
                                      + +++L++GcG G+l++r  ++y +
  gi|313125898|ref|YP_004036168.1| 62 DVERVLELGCGTGTLLHRLSDEYTA 86
                                      4579**************9999975 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.044
                                       ES-GGGT.SGGGHHHHHHHHHHHS-TT-EEEEEEEEE CS
                              CMAS 134 vgafehv.gkenydtffkklkkllkedGllllhtits 169
                                       v af+h+   +++ + ++ ++ +l+++G+++  ++  
  gi|313125898|ref|YP_004036168.1| 123 VCAFDHFvARQSLSAVCEGAYATLRPGGIFVFDALSD 159
                                       56788873678899****************9988754 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.29      15      55 ..      47      86 ..      44     102 .. 0.80
   2 ?   -3.9   0.0       3.8   8.6e+03     119     135 ..     136     152 ..     131     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                      S--HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC CS
                               MTS 15 klDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespe 55
                                      k D+  +lL   lp++ + +vl lGcG+G l   l +e+  
  gi|313125898|ref|YP_004036168.1| 47 KTDAWGDLLGARLPADVE-RVLELGCGTGTLLHRLSDEYTA 86
                                      567777899999999766.6**********98888777665 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHEEEEEEE CS
                               MTS 119 eeliaeAkeaLkegGeL 135
                                        ++++ A + L++gG +
  gi|313125898|ref|YP_004036168.1| 136 SAVCEGAYATLRPGGIF 152
                                       56788899999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1688.05
//
Query:       gi|313125899|ref|YP_004036169.1|  [L=121]
Description: iron-sulfur cluster assembly accessory protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-19   68.3   0.0    6.7e-19   68.1   0.0    1.0  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.0   3.8e-23   6.7e-19       3     111 .]      14     117 ..      12     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 3.8e-23
                                       EEE-HHHHHHHHHHHHCTTEC.....EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGG CS
                       Fe-S_biosyn   3 itlteaAaeklkkllaedkke.....lrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksy 74 
                                       +t+te+Aa +  +l+++++ +     lrL+v++gg       C+ g +y +++  e+ e++d+v+++ng++v++++ 
  gi|313125899|ref|YP_004036169.1|  14 VTVTESAASEALRLMESEGMDtdvagLRLFVQQGG-------CA-GLSYGMRFDHEP-EDDDAVIKQNGLRVFIDPA 81 
                                       79******99999999998889*************.......**.************.******************* PP

                                       GHHHS.TTEEEEEEEETTEEEEEEETCCEEEEEEEEE CS
                       Fe-S_biosyn  75 slvfldeglvldfvedlgtlgLksdngilddnvglgk 111
                                       s++++  g +l+f+ +l++ g+  +n+++ +++g+g+
  gi|313125899|ref|YP_004036169.1|  82 SQNYI-GGSTLQFEGGLQGAGFHVENPNVVSECGCGE 117
                                       *****.8****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 759.60
//
Query:       gi|313125900|ref|YP_004036170.1|  [L=83]
Description: hypothetical protein Hbor_11350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.17   11.7   1.1       0.26   11.2   1.1    1.2  1  eIF-5_eIF-2B  Domain found in IF2B/IF5


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.1   1.5e-05      0.26      89     116 ..      47      71 ..      46      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                                       STSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  89 lCkeCkspetelekeerllvlkCkaCga 116
                                        C +C+s +t + + +r+    C+ Cg+
  gi|313125900|ref|YP_004036170.1|  47 FCGNCNSLDTAMDTMGRVE---CNVCGN 71 
                                       5************999998...****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 524.78
//
Query:       gi|313125901|ref|YP_004036171.1|  [L=109]
Description: hypothetical protein Hbor_11360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.7   0.0       0.18   11.4   0.0    1.2  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.9e-06      0.18      27      45 ..      59      77 ..      23      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.9e-06
                                      HSEEEEEEEEEEE..CCEC CS
                           AMMECR1 27 kekaglFVtlkekkgeLRG 45
                                      + +  +FVt+ke++g+LRG
  gi|313125901|ref|YP_004036171.1| 59 EYPFRCFVTWKEGAGDLRG 77
                                      44788*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 670.17
//
Query:       gi|313125902|ref|YP_004036172.1|  [L=223]
Description: hypothetical protein Hbor_11370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.27   11.5   0.1    2.2  1  Sterol_MT_C  Sterol methyltransferase C-terminal
       0.41   11.0   2.4        2.1    8.8   0.3    2.2  2  ERGIC_N      Endoplasmic Reticulum-Golgi Intermediate Compart
        2.7    8.0   9.1       0.37   10.8   1.0    2.3  2  DUF846       Eukaryotic protein of unknown function (DUF846)
        3.2    6.0  11.7          4    5.6  11.7    1.1  1  DUF2070      Predicted membrane protein (DUF2070)
          4    7.2  11.1       0.98    9.2   1.4    2.9  3  DUF5353      Family of unknown function (DUF5353)


Domain annotation for each model (and alignments):
>> Sterol_MT_C  Sterol methyltransferase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.7e-05      0.27      31      57 ..      96     122 ..      93     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.7e-05
                       Sterol_MT_C  31 tqkvaefLekAadsLvaGGkegiFTPm 57 
                                       t +v++ L+ Aa +L+ + + ++FTP+
  gi|313125902|ref|YP_004036172.1|  96 TGRVTTYLAVAAVALIVAVELDVFTPV 122
                                       5689**********************7 PP

>> ERGIC_N  Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.082   2.9e+02      23      48 ..      15      40 ..       7      53 .. 0.86
   2 ?    8.8   0.3   0.00058       2.1      16      54 ..      92     130 ..      86     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.082
                                      XXXXXXXXXXXXXXXXXXXXX.XXX- CS
                           ERGIC_N 23 iislvcillilfLllselteylttev 48
                                      i + ++ ll++fL ++ + ++l++e 
  gi|313125902|ref|YP_004036172.1| 15 INTALAWLLVCFLAIAAVVQFLNGEL 40
                                      67889999**********99999876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00058
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX-EEEEEE CS
                           ERGIC_N  16 qktlsGgiislvcillilfLllselteylttevkeelvv 54 
                                         t++G + + ++++ +++++  el  ++ +++++++ v
  gi|313125902|ref|YP_004036172.1|  92 GMTFTGRVTTYLAVAAVALIVAVELDVFTPVRMNHSFAV 130
                                       579**************************9999999887 PP

>> DUF846  Eukaryotic protein of unknown function (DUF846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.6     0.083     3e+02       5      38 ..      20      53 ..      15      60 .. 0.54
   2 ?   10.8   1.0    0.0001      0.37       7      67 ..     100     165 ..      87     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.083
                            DUF846  5 allfhllfklaailvylfgslfsnsfilkfvvli 38
                                      a+l+++++ +aa++ +l g+l    f++++ ++ 
  gi|313125902|ref|YP_004036172.1| 20 AWLLVCFLAIAAVVQFLNGELQWAGFTVAVAAVA 53
                                      4555555566666666666655445555444443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0001
                            DUF846   7 lfhllfklaailvylfgslf.....snsfilkfvvlilllaldfwvvknisGrlLvgLrwwnevde 67 
                                        ++l++ ++a++v + + +f     ++sf + fvv++ + a+  w v +  +  L g  +  +   
  gi|313125902|ref|YP_004036172.1| 100 TTYLAVAAVALIVAVELDVFtpvrmNHSFAVVFVVITTMAAAGVWAVVRWLSDILLGTAFLLDNRP 165
                                       5677888888888888888878888999***************************99999877544 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  11.7    0.0011         4      20     171 ..      21     191 ..       5     205 .. 0.39

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0011
                           DUF2070  20 liillalli.gllaflssk..lfgillfglpalvaflltlpvlrilggr..ltykrslflalltelivviisllail 91 
                                       +++++ l+i +++ fl+++  + g+ +      va+++  p++ +   +  l+++  ++ al +   ++i      l
  gi|313125902|ref|YP_004036172.1|  21 WLLVCFLAIaAVVQFLNGElqWAGFTVA-----VAAVAIVPAVALRDPTsmLPWEVLFVAALPIIGRALI--AGERL 90 
                                       2222222220222222222222222221.....1111111222121111113443333333333333333..11111 PP

                           DUF2070  92 lsall.qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly................... 148
                                       + + +  +++++  v ++al++a+ l v++ v  ++ + +v++++++ ++a + +v+                    
  gi|313125902|ref|YP_004036172.1|  91 AGMTFtGRVTTYLAVAAVALIVAVELDVFTPVRMNHSFAVVFVVITTMAAAGVWAVVRwlsdillgtaflldnrpne 167
                                       11112234444444444555555555555555555555555444444444444444445555555555555555555 PP

                           DUF2070 149 .fspesfllllllslifalavylf 171
                                        ++++ +  +++++++ + a +lf
  gi|313125902|ref|YP_004036172.1| 168 iIEEALMWDFVAATVAGVFAGILF 191
                                       555555555555555555555555 PP

>> DUF5353  Family of unknown function (DUF5353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.4   0.00027      0.98      10      51 ..      16      57 ..      14      62 .. 0.82
   2 ?   -3.1   0.7       1.9   6.8e+03      41      49 ..     136     144 ..     129     151 .. 0.50
   3 ?    4.1   0.1     0.011        39      31      56 ..     170     195 ..     166     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00027
                           DUF5353 10 NavlvavlsagLGfgAYrkyarGeLtwkvvglwagavGafav 51
                                      N++l+ +l  +L+++A  ++ +GeL+w    ++ +av+++ +
  gi|313125902|ref|YP_004036172.1| 16 NTALAWLLVCFLAIAAVVQFLNGELQWAGFTVAVAAVAIVPA 57
                                      7777888899*****************988877777776644 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.9
                           DUF5353  41 lwagavGaf 49 
                                       ++ +a G+ 
  gi|313125902|ref|YP_004036172.1| 136 TTMAAAGVW 144
                                       333333333 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.011
                           DUF5353  31 rGeLtwkvvglwagavGafavgdyyv 56 
                                       + +L w+ v+++ + v a  + +yy+
  gi|313125902|ref|YP_004036172.1| 170 EEALMWDFVAATVAGVFAGILFEYYF 195
                                       56899*****9999999988999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1357.29
//
Query:       gi|313125903|ref|YP_004036173.1|  [L=229]
Description: hypothetical protein Hbor_11380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0023   17.7   0.3     0.0023   17.7   0.3    1.7  2  DUF2238   Predicted membrane protein (DUF2238)
  ------ inclusion threshold ------
       0.22   12.0   6.1        1.7    9.1   0.1    3.2  3  DUF983    Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.33     3e+03      23      26 ..      38      41 ..      17      72 .. 0.53
   2 !   17.7   0.3   2.6e-07    0.0023      75     139 ..     131     197 ..     100     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.33
                           DUF2238 23 lill 26
                                      l+++
  gi|313125903|ref|YP_004036173.1| 38 LMVV 41
                                      2222 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.6e-07
                           DUF2238  75 vrelllrkkkl...rkwllllavlvvlaisalYEliEwlvalllggeaaeaflGtqGdiWDaqkDmll 139
                                       +r + l++ ++    +++++++++++la++ l+E+iE++++++++  +  + l ++G + D+  D+l+
  gi|313125903|ref|YP_004036173.1| 131 ARAIDLHTDAVdlpPRFMFVFILTFTLAFGVLWEVIEFMISVTSNYLGIGSVLTQYG-LRDTMFDLLF 197
                                       333334444445565699************************999666666666666.8888888775 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00019       1.7      29      68 ..      51      90 ..      47      95 .. 0.93
   2 ?   -0.7   0.1      0.22   1.9e+03      50      70 ..     106     126 ..      93     129 .. 0.79
   3 ?    4.3   0.3    0.0062        55      20      50 ..     137     168 ..     134     187 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00019
                            DUF983 29 yfvilivghlvvplallvevayepplwvhlliwlpltlll 68
                                      +fv  +vg++v++l  ++e    +p+   l++w++ +++l
  gi|313125903|ref|YP_004036173.1| 51 VFVNALVGFVVTFLPGILERDHGIPMDAGLTLWITSAVFL 90
                                      799*******************************998876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                            DUF983  50 yepplwvhlliwlpltlllsl 70 
                                        ++p+w hl+  l   +++++
  gi|313125903|ref|YP_004036173.1| 106 ASIPWWDHLTHALSASIVAAV 126
                                       578999999998888887765 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0062
                            DUF983  20 haraddgPayfvilivghlvvpla.llvevay 50 
                                       h +a d+P+ f++++++ + +++  l+  +++
  gi|313125903|ref|YP_004036173.1| 137 HTDAVDLPPRFMFVFILTFTLAFGvLWEVIEF 168
                                       56777888777666555555555405544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1371.10
//
Query:       gi|313125904|ref|YP_004036174.1|  [L=67]
Description: hypothetical protein Hbor_11390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-23   82.6   1.3    1.9e-23   82.5   1.3    1.0  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   1.3   1.1e-27   1.9e-23       1      64 []       2      65 ..       2      65 .. 0.99

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.1e-27
                                      EEEEEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEEEEECTTCCEEEEEEEEEEEE-S CS
                           Dodecin  1 VyKvielvGsSpkSwedAiqnAiaeAsktlrnirwveVketrahvedgkiaeYqvtlkvgFrle 64
                                      VyK+i+l+G S++S+++A+++A+++A+ tl+n++wveV+e+ ++++  + +eYq++++v+F+le
  gi|313125904|ref|YP_004036174.1|  2 VYKKITLIGRSNESFDAAVDDAVDRAQATLDNVHWVEVQEMGVEIASVENREYQAEVEVAFQLE 65
                                      9************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 435.70
//
Query:       gi|313125905|ref|YP_004036175.1|  [L=467]
Description: 5'-nucleotidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-28  100.2   0.0    2.2e-28   99.5   0.0    1.3  1  5_nucleotid_C  5'-nucleotidase, C-terminal domain
    7.5e-06   26.6   0.1    1.3e-05   25.8   0.1    1.4  1  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
       0.67   10.1   3.8          3    8.0   3.8    2.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> 5_nucleotid_C  5'-nucleotidase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   0.0   3.7e-32   2.2e-28       1     155 [.     271     423 ..     271     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 3.7e-32
                                       EEEEESSB....---HHTS--HHHHHHHHHHTGSTT--EEEEEGGG---.-BTTTEEEHHHHHHHS-S--EEEEEEE CS
                     5_nucleotid_C   1 vigtttveldgrdlalrtgetnlgnliadalraaagadialangggira.dlpaGditvkdlltvlpfgntlvvvel 76 
                                       v++t++++ld+++ ++  ge+++gn++ada+r+++++d++l+n+ggir+    +G++t +dl++v+pf+ ++vv el
  gi|313125905|ref|YP_004036175.1| 271 VVATVNDPLDRTEETVFGGECAIGNFVADAYRWSMETDVGLQNSGGIRNgPPLSGEVTIADLVSVIPFEEHVVVAEL 347
                                       68999999999766776********************************64478*********************** PP

                                       EHHHHHHHHHH.HTTTTTS--TT-E.......EEESEEEEE-TTS-TT--EEEESSS-BEEE--TTSEEEEEEEHHH CS
                     5_nucleotid_C  77 tGaqlkeaLenesvsaskaasgrfl.......qvsGlrytydlskpagervtslsvtvngkpldddktYkvatnsyl 146
                                       tG++l +++ +    a++ +            + sG+++++d +   +e v+s +v   g+p+ +d tY+vat++y+
  gi|313125905|ref|YP_004036175.1| 348 TGEELTAVFRE--CAAATVDF---GephwwqgHLSGVELVWDDD---REAVVSARV--GGEPVAPDSTYTVATSDYV 414
                                       **********4..33333333...3335888999*****99965...789****55..******************9 PP

                                       HTTGGG-HH CS
                     5_nucleotid_C 147 asggdgfsm 155
                                        +   +f++
  gi|313125905|ref|YP_004036175.1| 415 LHTDHEFPT 423
                                       998888876 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   2.1e-09   1.3e-05       5     203 ..       6     199 ..       2     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.1e-09
                                       EEESBTBTTCCTHHHHHHHHHHHH.HHHTTESEEEEE.ST........SSSSSHHHHHHHHHHHHHHHHTSEEEEEC CS
                       Metallophos   5 vigDlHlalgggqlddllkllddl.lreekpdlvlla.GD........lvdrgdlekellellaalvkypipvylll 71 
                                       + +D+     +++ ++   +l+ + ++ ++ d++++  GD        lv+rg  + ++ + ++a ++       + 
  gi|313125905|ref|YP_004036175.1|   6 HYSDIE---NVYDDPERTGCLSGCvQSLSGDDALICGtGDttspgvlaLVERGRQSLDFFRAVDADLD-------TF 72 
                                       444444...33333333333333323337779999999**9999999999999999988888888888.......9* PP

                                       -TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEE..........THHHHHHHHH CS
                       Metallophos  72 GNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspel..........lvsldklgsl 137
                                       GNH+ f+++ +  +g  +  +++w s + + +n   ++      ++v  ++G   ++          l+      ++
  gi|313125905|ref|YP_004036175.1|  73 GNHD-FDYGPEATRGVVADSPQTWVSANVYDDNGDRFAPTHVVpYTVREVNGARVGFtgvtdpatpsLNPMAGELTF 148
                                       ****.999999999999999999999977777777777444446777777777444455565553332333333333 PP

                                       HHSCHHHHCC..HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 138 nleleapepg..dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                       + +  a+  +   + l+d    e++d+v++l+H +         +de +     + ++d++++GH+H 
  gi|313125905|ref|YP_004036175.1| 149 TDPYAAA--EeaIDHLRD----EGVDYVVILSHLGGG-------DDELA----ARVDADVILGGHVHS 199
                                       3333333..245777777....9**************.......44444....5889**********6 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.8    0.0005         3      94     147 ..     171     217 ..       3     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0005
                     Metallophos_2  94 vlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvg 147
                                       v l H    g++d+la+++++     dv++ GH H ++ e  +++l++ PG+ g
  gi|313125905|ref|YP_004036175.1| 171 VILSHLG--GGDDELAARVDA-----DVILGGHVHSERHEYVEETLLLRPGANG 217
                                       3333333..667777777766.....8************************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 3014.07
//
Query:       gi|313125906|ref|YP_004036176.1|  [L=141]
Description: universal stress family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-11   44.8   0.5    6.5e-10   39.7   0.5    2.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.5   3.6e-14   6.5e-10       3     141 .]       4     134 ..       3     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 3.6e-14
                                       SEEEEEE-..SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   3 krIlVavD..gseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                        r++V+v    +++sk+ l  A++ a +r+ael++lhv   +++  v  a+ + + e++  ++              
  gi|313125906|ref|YP_004036176.1|   4 TRVVVPVRypLTKHSKATLSEAIRIATEREAELTVLHVDLYQDNRRVTRAELKRAVEREFGAL-------------- 66 
                                       6899999988999*************************8888777777777777777776666.............. PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCC....SSTTTTCS.SBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrg....rsglsrll.lGSvseyvlrhapcpVlvVr 141
                                        + ++ v++++  + e+ile+a +e+ad++V+Gs++    r+ l+r+l   +   y+ ++ +c V+ Vr
  gi|313125906|ref|YP_004036176.1|  67 -DRTRYVIRRGFLVEETILEEAAAEGADIVVIGSKQasrwRRMLRRFLdDPDIETYLRQKLDCTVITVR 134
                                       .47789999***************************777666666666778899999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 786.55
//
Query:       gi|313125907|ref|YP_004036177.1|  [L=365]
Description: small-conductance mechanosensitive channel [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-34  118.9   0.0    2.7e-34  118.5   0.0    1.1  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.47   10.4  10.5       0.79    9.7  10.5    1.3  1  Colicin_V   Colicin V production protein
        6.9    6.9   0.0        6.9    6.9   0.0    3.2  4  HemY_N      HemY protein N-terminus


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.0   4.5e-38   2.7e-34       2     201 ..     107     314 ..     106     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 4.5e-38
                                       .HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS.SEEEEEE CS
                        MS_channel   2 kilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig.dieGtVe 77 
                                        i++++++++++l++  + g  ++ +  ++G+ ++++g++l  ++ +++ G+++l+++p+++GD++e+  + +G V 
  gi|313125907|ref|YP_004036177.1| 107 RIVRLGVFLIAVLMAGVVAGLRFGDVAISVGVFSAVVGIVLAPIVGSIINGLFILADQPYEVGDMIELDdGRRGFVD 183
                                       5899*****************************************************************8899**** PP

                                       EE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T.. CS
                        MS_channel  78 diglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk.. 152
                                       +i++r tk+ t d++ ++iPns++ +  ++N+s e+ + r+ + +  ty+sd   + k++e l +a++ + +v++  
  gi|313125907|ref|YP_004036177.1| 184 EITIRYTKMFTLDNTFLVIPNSTIRNRLVTNFSAEDERLRLSLGFLATYESD---IPKARELLERAASDSDMVIEgg 257
                                       **********************************99****************...999******************* PP

                                       ..........TS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHH CS
                        MS_channel 153 ..........dkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkilee 201
                                                    +++++de++ds++ +++r+++k+  p + l v+se+  +  + le 
  gi|313125907|ref|YP_004036177.1| 258 pdirigsaryPARPTAYIDEYADSGILITLRYWAKK--PYKLLTVRSEVQTNFSELLED 314
                                       *********99999**********************..***********9988887775 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  10.5   0.00013      0.79      24     117 ..      71     162 ..      68     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                         Colicin_V  24 evlsllgwvvafvvasllypslaellaelilspalaaiiaflllfllvllivsllgallsklvsktglglldrllGa 100
                                        v+ +lg+v++ +v +l + ++a  ++ ++  +++ +i+   + +++vl+++ + g  +++   +   g +  ++G 
  gi|313125907|ref|YP_004036177.1|  71 TVIVILGYVLSGYVVRLVGRPVARRFRRQSVAQVMLRIVRLGVFLIAVLMAGVVAGLRFGD--VAISVGVFSAVVGI 145
                                       6999************************988999999999999999999999999999999..788899******** PP

                         Colicin_V 101 ifGllkglllvvlllll 117
                                       ++  + g ++  l++l+
  gi|313125907|ref|YP_004036177.1| 146 VLAPIVGSIINGLFILA 162
                                       *******9999866554 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.5      0.11   6.4e+02      17      42 ..      68      93 ..      65     113 .. 0.67
   2 ?   -2.4   0.1       0.9   5.4e+03      20      31 ..     113     124 ..     102     132 .. 0.54
   3 ?    0.3   0.5      0.13     8e+02       6      33 ..     128     155 ..     122     164 .. 0.66
   4 ?    6.9   0.0    0.0012       6.9      56      90 ..     217     251 ..     196     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                            HemY_N 17 vvavlllvllfvllylllrllrlllr 42
                                      ++a ++++l++vl   ++rl+++ ++
  gi|313125907|ref|YP_004036177.1| 68 IAATVIVILGYVLSGYVVRLVGRPVA 93
                                      45667777777777777777776654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.9
                            HemY_N  20 vlllvllfvlly 31 
                                       v+l+++l++ ++
  gi|313125907|ref|YP_004036177.1| 113 VFLIAVLMAGVV 124
                                       333333333333 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.13
                            HemY_N   6 awggyrietslvvavlllvllfvllyll 33 
                                       ++g+  i++ +  av+ +vl+ ++  ++
  gi|313125907|ref|YP_004036177.1| 128 RFGDVAISVGVFSAVVGIVLAPIVGSII 155
                                       5666777777777777777765554444 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0012
                            HemY_N  56 erkarealseGlialaeGdfarAekaaakaaklse 90 
                                        +  r +ls G++a  e d  +A++++ +aa++s+
  gi|313125907|ref|YP_004036177.1| 217 AEDERLRLSLGFLATYESDIPKARELLERAASDSD 251
                                       556677899**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2182.54
//
Query:       gi|313125908|ref|YP_004036178.1|  [L=353]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-71  238.2   0.5    9.8e-71  237.6   0.5    1.3  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    1.2e-21   76.4   0.0    2.4e-21   75.4   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    1.3e-07   31.4   0.0    3.7e-07   29.9   0.0    1.7  1  MarR_2          MarR family
    9.7e-07   28.8   0.1      3e-06   27.2   0.1    1.9  1  HTH_20          Helix-turn-helix domain
    2.7e-05   23.9   0.0    6.9e-05   22.6   0.0    1.7  1  HTH_IclR        IclR helix-turn-helix domain
    0.00023   20.7   0.0     0.0011   18.4   0.0    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0014   18.5   0.0     0.0052   16.6   0.0    2.0  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0027   18.0   0.0      0.006   16.9   0.0    1.5  1  Rrf2            Transcriptional regulator
      0.004   16.7   0.0      0.015   14.9   0.0    2.0  1  HTH_CodY        CodY helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.098   13.0   0.0    2.1  2  GCR1_C          Transcriptional activator of glycolytic enzym
       0.03   13.8   0.0       0.23   11.0   0.0    2.5  2  Sigma70_r4      Sigma-70, region 4
      0.057   13.5   0.0       0.12   12.5   0.0    1.5  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.06   13.3   0.0       0.18   11.8   0.0    1.8  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.067   13.3   0.0       0.38   10.9   0.0    2.1  2  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.098   12.6   0.0       0.21   11.5   0.0    1.5  1  MarR            MarR family
       0.13   12.3   0.0       0.41   10.6   0.0    1.8  2  HTH_37          Helix-turn-helix domain
       0.15   11.6   0.0        2.4    7.8   0.0    2.3  2  HTH_47          winged helix-turn-helix


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.6   0.5   9.3e-74   9.8e-71       1     232 [.     110     343 ..     110     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 237.6 bits;  conditional E-value: 9.3e-74
                                       -EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS...----GGGSSSSEEEEE CS
                    Regulator_TrmB   1 avwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp...dedleeldleevatev 74 
                                       av++vksr+t+++++ee+Ie+Ae+el++sl++ lL+++r++l+a+++ gv++ lli+p   ++d++e+d++evat +
  gi|313125908|ref|YP_004036178.1| 110 AVSLVKSRSTILRYVEEIIEDAEYELVLSLTPDLLRRFRDDLAAKIDDGVSIDLLITPasrAPDPAEFDYLEVATIA 186
                                       589************************************************************************** PP

                                       E-S---S..EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEE.EES-TT-EEES- CS
                    Regulator_TrmB  75 rvrrsga.pllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktsevikt.depvekpitfss 149
                                       r+rr+++ p+l+++D++++v+a++++lrd++++y++if++++l +++s++F t+lW+t+e++++  +++++p++++s
  gi|313125908|ref|YP_004036178.1| 187 RARRGITtPVLAVADGEYSVYATQDALRDDRDRYGVIFNRSALGFLVSGFFGTVLWTTAETLAAdGKRRPFPRRYAS 263
                                       ****************************************************************9************ PP

                                       HHHHHHHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTEEEEEE-TT--SSSEEEE CS
                    Regulator_TrmB 150 irlavedikkllraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedgevtVGGlgAvlEDieae 226
                                       ir+av+di+++   + +++a+v Gr +e+g+++++eGrvv +t++++++vas+  ete+g ++VGGl+++lED+ea+
  gi|313125908|ref|YP_004036178.1| 264 IRRAVKDIREI---DGEFYASVSGRHVESGDPTVVEGRVVTTTFEESEEVASFEMETEEGILEVGGLVSALEDVEAQ 337
                                       **********7...66************************************************************* PP

                                       EEEEEE CS
                    Regulator_TrmB 227 eitler 232
                                       ei+l r
  gi|313125908|ref|YP_004036178.1| 338 EIILGR 343
                                       **9975 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   2.3e-24   2.4e-21       4      68 .]      16      80 ..      14      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 2.3e-24
                                      CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                              TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                      ++L eyE+++Yla+l++g++ta+eia ++++p+++vY+++rsL+d+GlVe +++rp++ +avdp+
  gi|313125908|ref|YP_004036178.1| 16 FNLGEYEIDAYLAVLEHGELTASEIADRTDIPQPRVYDTVRSLSDRGLVELRESRPMKIVAVDPD 80
                                      89*************************************************************95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   3.5e-10   3.7e-07      11      56 ..      27      69 ..      24      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.5e-10
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      La+L +++   lt++e+a+r+++++++v  +++ L+++GLve r++
  gi|313125908|ref|YP_004036178.1| 27 LAVLEHGE---LTASEIADRTDIPQPRVYDTVRSLSDRGLVELRES 69
                                      77777777...9******************************9975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   2.8e-09     3e-06      18      60 ..      29      70 ..      26      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.8e-09
                                      HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 18 aLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                       L + ++ltase+a+r d+++  +++ +r L++ gLve+++++
  gi|313125908|ref|YP_004036178.1| 29 VL-EHGELTASEIADRTDIPQPRVYDTVRSLSDRGLVELRESR 70
                                      56.7899*********************************987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   6.5e-08   6.9e-05      17      50 ..      33      66 ..      28      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.5e-08
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +elt se+A+rt++p + v+  +++L  +G+ve 
  gi|313125908|ref|YP_004036178.1| 33 GELTASEIADRTDIPQPRVYDTVRSLSDRGLVEL 66
                                      679*****************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0011      11      48 .]      28      65 ..      20      65 .. 0.92
   2 ?   -0.8   0.0       1.1   1.2e+03      30      40 ..     116     126 ..     115     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++ +++ ++ +e+A+r++++++ v   ++ L + Gl++
  gi|313125908|ref|YP_004036178.1| 28 AVLEHGELTASEIADRTDIPQPRVYDTVRSLSDRGLVE 65
                                      67899*******************************96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                            HTH_24  30 Spstvnrrlkr 40 
                                       S+st++r++++
  gi|313125908|ref|YP_004036178.1| 116 SRSTILRYVEE 126
                                       89******987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.9e-06    0.0052      11      46 ..      30      65 ..      27      65 .. 0.90
   2 ?   -3.5   0.0       9.6     1e+04       3      12 ..     116     125 ..     115     127 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-06
                                      HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 11 LaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      L+ gel+++e+a+ ++++q+ v    + L + GLVe
  gi|313125908|ref|YP_004036178.1| 30 LEHGELTASEIADRTDIPQPRVYDTVRSLSDRGLVE 65
                                      556******************************996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.6
                                       HHHHHHHHHT CS
                             HTH_5   3 tRlkILklLa 12 
                                        R+ IL++++
  gi|313125908|ref|YP_004036178.1| 116 SRSTILRYVE 125
                                       4666777665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.7e-06     0.006      15      57 ..      25      66 ..      21      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.7e-06
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +yLa  e++e ++++eia+r++i+++ +   ++ L+  glv+ 
  gi|313125908|ref|YP_004036178.1| 25 AYLAVLEHGE-LTASEIADRTDIPQPRVYDTVRSLSDRGLVEL 66
                                      6899999998.******************************85 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.4e-05     0.015       2      37 ..      32      67 ..      31      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                          HTH_CodY  2 eGrLtaskiaDriGitrsvivnaLrkLesaGiiesr 37
                                       G Ltas+iaDr  i +  + + +r L   G++e r
  gi|313125908|ref|YP_004036178.1| 32 HGELTASEIADRTDIPQPRVYDTVRSLSDRGLVELR 67
                                      699******************************987 PP

>> GCR1_C  Transcriptional activator of glycolytic enzymes
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.3e-05     0.098      27      66 ..      94     132 ..      83     140 .. 0.85
   2 ?   -0.8   0.0       1.9     2e+03       3      23 ..     264     284 ..     263     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.3e-05
                            GCR1_C  27 ikslekkygkrWrkdskesklfsrRkkiidfierlieeeg 66 
                                       i +le +y +  r+++   +l++ R +i++++e++ie+ +
  gi|313125908|ref|YP_004036178.1|  94 ISELEARYTAPARDTEA-VSLVKSRSTILRYVEEIIEDAE 132
                                       899**********7777.99****************9954 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                            GCR1_C   3 lsreiktVedlwnEykeglng 23 
                                       ++r++k ++++  E++ ++ g
  gi|313125908|ref|YP_004036178.1| 264 IRRAVKDIREIDGEFYASVSG 284
                                       57999*********9998776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.1   2.2e+03      22      33 ..       8      19 ..       6      21 .. 0.86
   2 ?   11.0   0.0   0.00022      0.23      19      50 .]      33      68 ..      25      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.1
                                      -HHHHHHHHTS- CS
                        Sigma70_r4 22 TleEIgerlgiS 33
                                      T+e +g+r+++ 
  gi|313125908|ref|YP_004036178.1|  8 TMESVGDRFNLG 19
                                      8999*****985 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00022
                                      TT--HHHHHHHHTS-HHH....HHHHHHHHHHHHHH CS
                        Sigma70_r4 19 eglTleEIgerlgiSrer....VrqiekrAlrkLRk 50
                                       +lT +EI++r +i++ r    Vr++  r+l  LR+
  gi|313125908|ref|YP_004036178.1| 33 GELTASEIADRTDIPQPRvydtVRSLSDRGLVELRE 68
                                      589*************76222269999999999986 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.12      25      61 ..      37      73 ..      22      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                           DUF2250 25 aksiakeleipleevrellkkLeelGLlervegktik 61
                                      a  ia++++ip+ +v + +++L + GL+e  e++ +k
  gi|313125908|ref|YP_004036178.1| 37 ASEIADRTDIPQPRVYDTVRSLSDRGLVELRESRPMK 73
                                      56799************************99887766 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.3   6.7e+03      27      38 ..       1      12 [.       1      17 [. 0.86
   2 ?   11.8   0.0   0.00017      0.18      21      60 ..      34      75 ..      19      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.3
                                      HHHHTTSSHHHH CS
                         HTH_Crp_2 27 lAsmlGltretv 38
                                      +A+ l +t e+v
  gi|313125908|ref|YP_004036178.1|  1 MADELRTTMESV 12
                                      799999999998 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00017
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgrr.iril 60
                                       lt  e+A++  + +  v  + + L+++gl++ r+ r ++i 
  gi|313125908|ref|YP_004036178.1| 34 ELTASEIADRTDIPQPRVYDTVRSLSDRGLVElRESRpMKIV 75
                                      58999***************************7654554443 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.38      22      57 ..      29      64 ..      25      66 .. 0.91
   2 ?   -1.0   0.0       1.9     2e+03       6      26 ..     232     252 ..     230     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                      HHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 22 LlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                       l++g lt++e++ +t+++   V +++ +L  ++lV
  gi|313125908|ref|YP_004036178.1| 29 VLEHGELTASEIADRTDIPQPRVYDTVRSLSDRGLV 64
                                      589***********************9999888887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.9
                                       HHHHCSTTHHHHHHHHHHHHS CS
                             HTH_9   6 iieehFGevvakVvetLlrkg 26 
                                       +++ +FG+v  + +etL + g
  gi|313125908|ref|YP_004036178.1| 232 LVSGFFGTVLWTTAETLAADG 252
                                       78999****999999998777 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.21      14      48 ..      31      65 ..      27      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                      HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 14 eqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      e+g+l+ se+a++  + ++ v  +++ L ++Gl+e
  gi|313125908|ref|YP_004036178.1| 31 EHGELTASEIADRTDIPQPRVYDTVRSLSDRGLVE 65
                                      89********************************8 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039      0.41      26      49 ..      29      52 ..      27      62 .. 0.90
   2 ?   -2.7   0.0       5.7   6.1e+03      13      31 ..     114     132 ..     108     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                                      HHHHCT--HHHHHHHHT--HHHHH CS
                            HTH_37 26 liekrelsqseaaqllgiaqPkvs 49
                                      ++e+ el+ se+a ++ i+qP+v 
  gi|313125908|ref|YP_004036178.1| 29 VLEHGELTASEIADRTDIPQPRVY 52
                                      68999*****************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.7
                                       HHHHHHHHHHHHHHHHHCT CS
                            HTH_37  13 lkaKaqlalaiaeliekre 31 
                                       +k ++ +++ + e+ie+ e
  gi|313125908|ref|YP_004036178.1| 114 VKSRSTILRYVEEIIEDAE 132
                                       6789999999999999876 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0023       2.4      45      77 ..      33      65 ..      16      66 .. 0.87
   2 ?    1.1   0.0      0.28     3e+02      38      49 ..     195     206 ..     180     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0023
                                      EEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 45 GkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      G+ +  +iA+r+++p  rv++ +r+L + gl++
  gi|313125908|ref|YP_004036178.1| 33 GELTASEIADRTDIPQPRVYDTVRSLSDRGLVE 65
                                      6666679***********************986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.28
                                       HHHHH-EEEEEH CS
                            HTH_47  38 wvLnlaDGkrsL 49 
                                        vL+ aDG+ s+
  gi|313125908|ref|YP_004036178.1| 195 PVLAVADGEYSV 206
                                       69******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2156.20
//
Query:       gi|313125909|ref|YP_004036179.1|  [L=272]
Description: hypothetical protein Hbor_11440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.14   12.3   1.9        5.2    7.2   0.2    2.3  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.23   11.6   1.3        4.1    7.6   0.1    2.5  2  Zn-ribbon_8      Zinc ribbon domain
       0.25   11.3   4.5        5.4    7.0   0.5    2.5  2  Nudix_N_2        Nudix N-terminal
       0.41   10.4   4.5       0.68    9.6   1.6    2.5  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
        2.3    8.7   5.0        9.4    6.7   5.0    2.0  1  Lar_restr_allev  Restriction alleviation protein Lar
        4.8    6.8  11.4        8.6    6.0   8.2    2.7  2  TF_Zn_Ribbon     TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.016        48      20      26 .]     217     223 ..     216     225 .. 0.85
   2 ?    7.2   0.2    0.0017       5.2       4      12 ..     255     263 ..     254     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.016
                            zf-ACC  20 lyVCPkC 26 
                                       l+VCP C
  gi|313125909|ref|YP_004036179.1| 217 LEVCPRC 223
                                       6899998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0017
                            zf-ACC   4 CpsCgemly 12 
                                       C+ Cge+ly
  gi|313125909|ref|YP_004036179.1| 255 CTDCGEILY 263
                                       ********* PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0014       4.1      26      36 ..     217     228 ..     203     230 .. 0.78
   2 ?    2.4   0.1     0.058   1.7e+02       7      13 ..     254     260 ..     237     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                       Zn-ribbon_8  26 ltaCPeCgs.ev 36 
                                       l++CP+Cg+ ++
  gi|313125909|ref|YP_004036179.1| 217 LEVCPRCGGpTA 228
                                       678*****9444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.058
                       Zn-ribbon_8   7 rCeeCgh 13 
                                        C++Cg+
  gi|313125909|ref|YP_004036179.1| 254 ACTDCGE 260
                                       3666664 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.5    0.0061        18       3      14 ..     220     231 ..     219     236 .. 0.78
   2 ?    7.0   0.5    0.0018       5.4      23      33 ..     253     263 ..     235     264 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0061
                                       -TTT--B-EEE- CS
                         Nudix_N_2   3 CsqCGtpvelri 14 
                                       C+ CG+p++  +
  gi|313125909|ref|YP_004036179.1| 220 CPRCGGPTAETT 231
                                       99***9987655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0018
                                       EEETTTTEEE- CS
                         Nudix_N_2  23 lvCpaCgtihY 33 
                                       l C++Cg i Y
  gi|313125909|ref|YP_004036179.1| 253 LACTDCGEILY 263
                                       79*******99 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.6   0.00023      0.68       6      14 ..     220     228 ..     219     230 .. 0.91
   2 ?    0.3   0.1      0.18   5.5e+02      24      32 .]     255     263 ..     253     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00023
                     zf-NADH-PPase   6 CgrCGapte 14 
                                       C+rCG+pt+
  gi|313125909|ref|YP_004036179.1| 220 CPRCGGPTA 228
                                       ********6 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
                     zf-NADH-PPase  24 CpaCglehY 32 
                                       C +Cg++ Y
  gi|313125909|ref|YP_004036179.1| 255 CTDCGEILY 263
                                       9****9877 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.0    0.0031       9.4       3      36 ..     217     260 ..     215     272 .] 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                   Lar_restr_allev   3 LkpCPfCggravlersqrvvaeigq..........cvyCadCga 36 
                                       L+ CP Cgg+    ++ +   + g+          + +C+dCg 
  gi|313125909|ref|YP_004036179.1| 217 LEVCPRCGGPTAETTTASDCCGSGTvgsfdtpeneVLACTDCGE 260
                                       788******9776666655555555899**************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.57   1.7e+03      16      28 ..      12      24 ..       7      24 .. 0.81
   2 ?    6.0   8.2    0.0029       8.6       2      29 ..     219     262 ..     218     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.57
                                      STTCEEESSSSBE CS
                      TF_Zn_Ribbon 16 ergelvCtdCGlV 28
                                       +ge +C  C++V
  gi|313125909|ref|YP_004036179.1| 12 YTGERRCWPCTVV 24
                                      589****999887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0029
                                       EETTTTCEEC...............HEETSTTCE.EESSSSBEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnl...............veDpergel.vCtdCGlVl 29 
                                       +CP Cg+++                 +D+ ++e+  CtdCG++l
  gi|313125909|ref|YP_004036179.1| 219 VCPRCGGPTAetttasdccgsgtvgSFDTPENEVlACTDCGEIL 262
                                       7******875689************9998888887******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1671.68
//
Query:       gi|313125910|ref|YP_004036180.1|  [L=367]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-26   92.3   0.2    1.2e-25   90.7   0.1    1.8  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      4e-08   33.3   0.1    4.3e-07   29.9   0.0    2.2  2  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    7.5e-05   22.2   0.0    0.00021   20.7   0.0    1.7  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00052   20.5   0.0     0.0012   19.4   0.0    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00078   20.1   0.1     0.0058   17.3   0.0    2.2  2  CoA_binding     CoA binding domain
     0.0013   18.9   0.1     0.0047   17.1   0.0    1.9  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.074   12.2   0.5       0.13   11.4   0.5    1.3  1  HIGH_NTase1     HIGH Nucleotidyl Transferase
      0.095   12.3   0.1       0.21   11.2   0.0    1.6  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.1   5.1e-29   1.2e-25       2     120 .]       8     122 ..       7     122 .. 0.98
   2 ?   -1.3   0.0       1.6   3.7e+03      17      67 ..     303     355 ..     286     364 .. 0.57

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 5.1e-29
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78 
                                       +++i+G+G+ig  h+  + e   ++ +++ ld+++e+ +++ e+++ve +++ ++l++   +davi++tpn+ hee+
  gi|313125910|ref|YP_004036180.1|   8 QIGIVGLGNIGHYHADRIVEL--DATLTGGLDIQPEARKRFTEEYDVETFEEKDALFD--TVDAVIITTPNRFHEEY 80 
                                       79*************999999..999********************************..9**************** PP

                                       HHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  79 akaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       a aaleag +vllEKPla ++e a++++++a+ ++ +++vg+
  gi|313125910|ref|YP_004036180.1|  81 AVAALEAGLDVLLEKPLAHSLESAERIAAAAADAEGICMVGF 122
                                       ****************************************96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                                       HHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCT.TESEEE CS
                      GFO_IDH_MocA  17 rplnesqrleevvalldpdaeraeavaesfgve.aysdleelladp.eidavi 67 
                                       +  ++s++++ + a+   ++++  +vae ++v+ + + + + ++++ ++ +++
  gi|313125910|ref|YP_004036180.1| 303 NDTHKSEQKLFLEAVRTGEQPKMNTVAEGLQVQrVIDAIYRSSESEsAVSLAT 355
                                       44444555556677777777777777777777744444444444443444444 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.9e-10   4.3e-07       6      70 ..     139     205 ..     138     229 .. 0.82
   2 ?    0.7   0.0      0.23   5.1e+02      19      51 ..     252     280 ..     243     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.9e-10
                                       TTTTSSEEEEEEEEECBEEECHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEEEEEE..EEE. CS
                    GFO_IDH_MocA_C   6 ngklGevvsvdvwtldtragaeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfGqppsvva..algr 70 
                                       +g++Ge ++v+   +  r+g + + +w  +k + +gG+++d+g+H iDl+ +++  p ++++   +++
  gi|313125910|ref|YP_004036180.1| 139 EGRFGEMKHVE-ANYVRRRGIPGRGSWFTSKdVAGGGSVIDIGVHAIDLALYFLDFPAVEEVsaVTRS 205
                                       799*******9.999999***********************************877766554314443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.23
                                       EECBEEECHHHHCCGGSHHCSTSHHHHTCHHHH CS
                    GFO_IDH_MocA_C  19 tldtragaeakkrwkrrkkksgGvlgdlgiHdi 51 
                                       +  +r++++ +++      +++G+l d g+Hd+
  gi|313125910|ref|YP_004036180.1| 252 WATNRPTNDEFYITG----TDAGALFDRGSHDL 280
                                       555555555555555....789*********97 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.4e-08   0.00021      38     102 ..       8      75 ..       5      86 .. 0.82
   2 ?   -2.1   0.0      0.91     2e+03     148     167 ..      86     103 ..      78     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.4e-08
                                       EEEEES-SHHHHHHHHHHHHTT-EEEE.ESSSHHHHH.CHHHHTC.EECSHHHHHHH-SEEEE-S--S CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkvia.ydrskkkee.eeeelgv.elvsleellaesDivslhlplt 102
                                       ++Gi+GlG+IG+  a+r+ ++++ +++  d ++++++  +ee+ v ++++ ++l+ + D v++++p  
  gi|313125910|ref|YP_004036180.1|   8 QIGIVGLGNIGHYHADRIVELDATLTGgLDIQPEARKrFTEEYDVeTFEEKDALFDTVDAVIITTPNR 75 
                                       69*********************88753788887777644455554889***************9965 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.91
                                       EEEES--SSSSSGTCHHHHH CS
                      2-Hacid_dh_C 148 gaalDvfeeeplpedsplle 167
                                        a+lDv+ e pl   ++l +
  gi|313125910|ref|YP_004036180.1|  86 EAGLDVLLEKPLA--HSLES 103
                                       5899***999999..44544 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.4e-07    0.0012       1      78 [.       8      81 ..       8      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.4e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevl 78
                                      +igi+G Gn+g+  a ++++ +     ++ + + +pe ++ + ee+ v++++ ++  + +  d v+++ + + +ee +
  gi|313125910|ref|YP_004036180.1|  8 QIGIVGLGNIGHYHADRIVELD---ATLTGGLDIQPEARKRFTEEYDVETFE-EKDALFDTVDAVIITTPNRFHEEYA 81
                                      59********************...9999999***************99999.8888889*********998888765 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.6e-06    0.0058       5      89 ..       8      91 ..       5      93 .. 0.73
   2 ?   -0.6   0.0      0.98   2.2e+03      40      75 ..     324     361 ..     299     364 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.6e-06
                                      EEEEETTTSHHHHHHHHHHHHHHE..CEEEEEEC-TT..TTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding  5 kviviGagglgiaglyhfkeklky..gikavfgvnpr..kvgtevlglpvyksvdeleektevdvavitvPaesaqeav 79
                                      +++++G g+ g+   yh ++  +    ++   +++p+  k  te  +++ +++ d l ++  vd+ +it+P+++ +e +
  gi|313125910|ref|YP_004036180.1|  8 QIGIVGLGNIGH---YHADRIVELdaTLTGGLDIQPEarKRFTEEYDVETFEEKDALFDT--VDAVIITTPNRFHEEYA 81
                                      688999999944...555555444005566777888833444555588888888888888..***************** PP

                                      HHHHHTT-SE CS
                       CoA_binding 80 delveagikg 89
                                      ++++eag  +
  gi|313125910|ref|YP_004036180.1| 82 VAALEAGLDV 91
                                      ******9875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.98
                                       TTTCEETTEEEESCHHHHHHHC..TTTEEEEES-HHHH CS
                       CoA_binding  40 kvgtevlglpvyksvdeleekt..evdvavitvPaesa 75 
                                       k+ t  +gl+v+  +d +  +   e  v++ tv+++ a
  gi|313125910|ref|YP_004036180.1| 324 KMNTVAEGLQVQRVIDAIYRSSesESAVSLATVSPPTA 361
                                       56777789999977777766665338888888877765 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.1e-06    0.0047       1      72 [.       8      81 ..       8     121 .. 0.86
   2 ?   -1.2   0.0       0.9     2e+03      59      93 ..     324     357 ..     288     364 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                                      EEEEE--SHHHHHHHHHHHHTT-EEE.EE-SSHHHHHHHHHTT.EEE-SSHHHHHHHCSEEEE-SSSHHHHHHH CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykva.vynrtkekveelvaeg.akaaesieelvasldvvitmvkagkavdev 72
                                      +ig++GlG++G+  a ++++ + +++ + + ++e+ +++ +e  ++++e+  +l++++d+vi+  ++  + +  
  gi|313125910|ref|YP_004036180.1|  8 QIGIVGLGNIGHYHADRIVELDATLTgGLDIQPEARKRFTEEYdVETFEEKDALFDTVDAVIITTPNRFHEEYA 81
                                      69**********************983589**********9966******************998887665555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.9
                                       EEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S--- CS
                     NAD_binding_2  59 vitmvkagkavdeviegllealkkgdilidgstss 93 
                                        +  v +g +v+ vi+ + ++ +++   +  +t+s
  gi|313125910|ref|YP_004036180.1| 324 KMNTVAEGLQVQRVIDAIYRSSESE-SAVSLATVS 357
                                       4667888888888888877665444.444555555 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   5.8e-05      0.13      56      86 ..      81     111 ..      77     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.8e-05
                       HIGH_NTase1  56 aemALenGvDlViElPvvyavqsAelFAkga 86 
                                       a +ALe+G D+ +E P++ +++sAe  A +a
  gi|313125910|ref|YP_004036180.1|  81 AVAALEAGLDVLLEKPLAHSLESAERIAAAA 111
                                       678***********************99887 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.3e-05      0.21       6      78 ..       8      82 ..       5     118 .. 0.82
   2 ?   -3.4   0.0       2.7     6e+03      33      58 ..     316     341 ..     300     345 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.3e-05
                                      -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-H.HHHHHHHTT-EEEEHHHH.HHT-SEEEE-S-HHHHHHHHH CS
                              IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsk.svkkAkeegfevltvaea.vkkadvvmiliPDelqkevye 78
                                      +i ++G G+ Gh +a  + +    ++ gl  + +   +  +e  +e+ + ++a  ++ d v+i +P+++++e   
  gi|313125910|ref|YP_004036180.1|  8 QIGIVGLGNIGHYHADRIVELDATLTGGLDIQPEaRKRFTEEYDVETFEEKDAlFDTVDAVIITTPNRFHEEYAV 82
                                      799*************************998875144445666777777777625789*********99988655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.7
                                       EE-TT-HHHHHHHHTT-EEEEHHHHH CS
                              IlvN  33 glregsksvkkAkeegfevltvaeav 58 
                                       ++r+g++   +  +eg++v++v +a+
  gi|313125910|ref|YP_004036180.1| 316 AVRTGEQPKMNTVAEGLQVQRVIDAI 341
                                       45666666777788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2377.28
//
Query:       gi|313125911|ref|YP_004036181.1|  [L=67]
Description: hypothetical protein Hbor_11460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0087   15.8   0.0     0.0093   15.7   0.0    1.1  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.013   16.3   0.0      0.015   16.1   0.0    1.1  1  YMF19        Plant ATP synthase F0


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     1e-06    0.0093      44      65 ..       8      56 ..       7      67 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-06
                                      IIIIIHHHHHHHHHHHS...........................STTS- CS
                       Oxidored_q3 44 vYvGAilvlflFvimll...........................esaee 65
                                      +Y+G++lvlf F +  +                           ++++e
  gi|313125911|ref|YP_004036181.1|  8 MYLGGMLVLFFFWVYGIvsfvldlkntiipktrqyirgrrrlkeQKEKE 56
                                      8***********9988888888888888888888888888765422222 PP

>> YMF19  Plant ATP synthase F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.0   1.7e-06     0.015      15      58 ..      14      63 ..      12      67 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-06
                             YMF19 15 lclfFitlYivll......knilpkiarilklrkkllsslssevsklkke 58
                                      l+lfF+ +Y ++       ++i+pk+ + ++ r++l +++++e +  ++e
  gi|313125911|ref|YP_004036181.1| 14 LVLFFFWVYGIVSfvldlkNTIIPKTRQYIRGRRRLKEQKEKEEEREERE 63
                                      6899*****9766778**9********************99755544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1303  (0.0726756); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 471.82
//
Query:       gi|313125912|ref|YP_004036182.1|  [L=396]
Description: carbohydrate ABC transporter ATP-binding protein, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-34  118.7   0.0    4.8e-34  117.8   0.0    1.4  1  ABC_tran         ABC transporter
    2.7e-11   44.1   0.0    9.7e-11   42.3   0.0    2.0  1  OB_MalK          MalK OB fold domain
    1.1e-06   28.2   0.2    7.5e-06   25.5   0.2    2.0  1  SMC_N            RecF/RecN/SMC N terminal domain
    1.4e-06   28.4   0.0     0.0059   16.5   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00013   21.8   0.0      0.067   12.9   0.0    2.1  2  AAA_15           AAA ATPase domain
    0.00038   20.4   0.0    0.00056   19.9   0.0    1.3  1  Rad17            Rad17 P-loop domain
     0.0032   17.9   0.0     0.0077   16.6   0.0    1.8  1  AAA_16           AAA ATPase domain
     0.0034   17.1   0.0     0.0073   16.0   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
     0.0067   16.4   0.1      0.016   15.2   0.1    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0071   16.3   0.0      0.024   14.5   0.0    1.8  2  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
       0.01   16.0   0.1        1.5    9.0   0.1    3.3  2  TOBE_2           TOBE domain
      0.011   16.1   0.0      0.093   13.1   0.0    2.3  2  RNA_helicase     RNA helicase
      0.012   15.9   0.4      0.041   14.2   0.1    2.0  2  AAA_22           AAA domain
      0.015   15.7   1.0      0.085   13.3   1.0    2.1  1  AAA              ATPase family associated with various cellul
       0.02   15.4   0.1      0.076   13.6   0.0    2.0  1  CysA_C_terminal  CysA C-terminal regulatory domain
      0.035   13.8   0.0       0.16   11.6   0.0    2.0  2  AAA_30           AAA domain
      0.045   14.2   0.0      0.083   13.4   0.0    1.4  1  AAA_23           AAA domain
      0.051   14.1   0.4       0.48   11.0   0.2    2.6  2  AAA_18           AAA domain
      0.087   13.1   1.3       0.17   12.1   0.5    2.1  1  AAA_28           AAA domain
      0.093   12.3   0.1       0.42   10.2   0.0    2.1  2  AAA_25           AAA domain
        0.1   12.0   0.2        6.6    6.1   0.0    2.2  2  PhoH             PhoH-like protein
       0.12   12.7   0.1         39    4.6   0.0    3.1  3  TOBE             TOBE domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.0     6e-37   4.8e-34       1     136 [.      19     161 ..      19     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 6e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++n++l+++ ge v +vG++G+GKSt ++++agl+ pteGe+ + g+++++  l+  ++ +++++q+  lfp++ v+
  gi|313125912|ref|YP_004036182.1|  19 VDNMNLEINDGEFVCLVGPSGCGKSTTMEMIAGLTMPTEGEVFIGGREVTN--LPPKDRGVAMVFQNIALFPHMDVY 93 
                                       589***********************************************9..9*********************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             e d+++e+a + ++l+++ d+       ++SgGq+qrva+ara++++p+++l+DEp 
  gi|313125912|ref|YP_004036182.1|  94 DNisfglrlrkydkeEIDRRVERASDIVQLEGMLDRMP----DEMSGGQRQRVAIARAIVRNPDVFLMDEPL 161
                                       ***********777777777777777777777777776....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.2e-13   9.7e-11       1      52 [.     235     281 ..     235     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.2e-13
                           OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEh 52 
                                       GSPaMNf +++++e g  + g+ +++++++e     ++ +g++v+lGiRPE+
  gi|313125912|ref|YP_004036182.1| 235 GSPAMNFADGKLTEMG--FVGDRIEVDFDPET---ISASVGDDVTLGIRPED 281
                                       9************999..67899*****9998...9***************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2   9.2e-09   7.5e-06      24     211 ..      29     204 ..      11     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.2e-09
                                       SSEEEEEESTTSSHHHHHHHHH.HHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAil.FvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                        +f ++vGp G+GKs  ++ i   ++ ++    +  +++++l  k +++ ++ + ++++ f + d     ++ ++ +
  gi|313125912|ref|YP_004036182.1|  29 GEFVCLVGPSGCGKSTTMEMIAgLTMPTEGEVFIGGREVTNLPPK-DRGVAMVFQNIAL-FPHMDVY---DNISFGL 100
                                       4799****************9423344444444555555555554.4444444444444.3333333...5555666 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                       + r++ k+e    i+++  + +++ +l  + +  ++++SgG+++ va+a       v+   ++l+De  a+LD+k +
  gi|313125912|ref|YP_004036182.1| 101 RLRKYDKEE----IDRRVERASDIVQLEGMLDRMPDEMSGGQRQRVAIARA----IVRNPDVFLMDEPLANLDAKLR 169
                                       666666665....*******************************9988743....35566689************** PP

                                       HHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 177 kkvaellkeksknaQfivislreemlekadklvgv 211
                                         + + l++ +k+    +i +++++ e +    ++
  gi|313125912|ref|YP_004036182.1| 170 VHMRTELQRLHKELDTTIIYVTHDQAEAMTMSDRI 204
                                       ****9999999997766666666666655444333 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00092      0.75       1      22 [.      31      52 ..      31      74 .. 0.85
   2 !   16.5   0.0   7.3e-06    0.0059     220     298 ..     117     193 ..      90     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00092
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + +l+Gp g+GKS+ ++ + +l
  gi|313125912|ref|YP_004036182.1| 31 FVCLVGPSGCGKSTTMEMIAGL 52
                                      679**************99988 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.3e-06
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                        + ++  ++  ++ ++e+S G+++  a++ a+ r +   +++l DEp ++L+ kl  +  + l +l++  ++ +i +
  gi|313125912|ref|YP_004036182.1| 117 ASDIVQLEGMLDRMPDEMSGGQRQRVAIARAIVRNP---DVFLMDEPLANLDAKLRVHMRTELQRLHKeLDTTIIYV 190
                                       555555555555667899*******9*******999...9********************9996666669******* PP

                            AAA_21 296 THS 298
                                       TH+
  gi|313125912|ref|YP_004036182.1| 191 THD 193
                                       **8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   8.2e-05     0.067      18      44 ..      23      50 ..      18     101 .. 0.89
   2 !    6.9   0.0    0.0053       4.3     315     365 ..     148     193 ..     133     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-05
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsileald 44
                                       +++++  + +l+G+ ++GKS+ +e++ 
  gi|313125912|ref|YP_004036182.1| 23 NLEINDGeFVCLVGPSGCGKSTTMEMIA 50
                                      55555556*****************995 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0053
                            AAA_15 315 ekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       + +     +++++l++EP a+L  ++  ++   l++l ++ +t +i+ TH 
  gi|313125912|ref|YP_004036182.1| 148 IVR-----NPDVFLMDEPLANLDAKLRVHMRTELQRLHKELDTTIIYVTHD 193
                                       444.....8999**************************************7 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   6.9e-07   0.00056      33      76 ..      17      60 ..       7     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.9e-07
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew 76
                                      ++++ + Le +  + + + GPsGCgkst++++++    +   e 
  gi|313125912|ref|YP_004036182.1| 17 TAVDNMNLEINDGEFVCLVGPSGCGKSTTMEMIAGLTMPTEGEV 60
                                      67899999*99999*****************9997776665554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.5e-06    0.0077      22      64 ..      27      74 ..      10     216 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.5e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellr.alekdggiflrgkcdql....e 64
                                      +++e v l+G+sG+GKs+ +++++   + ++g +f+ g+ + +    +
  gi|313125912|ref|YP_004036182.1| 27 NDGEFVCLVGPSGCGKSTTMEMIAGlTMPTEGEVFIGGREVTNlppkD 74
                                      45589****************999534444456667777776655333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     9e-06    0.0073      14      50 ..      21      57 ..      17      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +  +ei+  +++ l+GpsG GKST +  i+ l +p++
  gi|313125912|ref|YP_004036182.1| 21 NMNLEINDGEFVCLVGPSGCGKSTTMEMIAGLTMPTE 57
                                      566788855599*************999998888876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     2e-05     0.016       2      27 ..      32      58 ..      31      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                                      EEEE--SSSSHHHHHHHGGGGB.S--E CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.nrev 27
                                      v+LvGp+G+gKs+ +e +a ++  +e 
  gi|313125912|ref|YP_004036182.1| 32 VCLVGPSGCGKSTTMEMIAGLTmPTEG 58
                                      8*****************999874444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.9e-05     0.024      88     121 ..      17      51 ..       4      61 .. 0.80
   2 ?   -2.4   0.0       4.8   3.9e+03       9      51 ..     157     199 ..     151     217 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +++++++ +++d ++++lvG+SG GKSt ++++++
  gi|313125912|ref|YP_004036182.1|  17 TAVDNMNLEINDgEFVCLVGPSGCGKSTTMEMIAG 51 
                                       56677777788779**************9999876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.8
                                       TTTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEE CS
                       RsgA_GTPase   9 vrpkvaNvdqllivvslkepelslnlldrfLvlaeekgiepvi 51 
                                       ++++ aN+d  l v   +e +  ++ ld  ++ + + ++e + 
  gi|313125912|ref|YP_004036182.1| 157 MDEPLANLDAKLRVHMRTELQRLHKELDTTIIYVTHDQAEAMT 199
                                       5566666666665555554555555566666666555555554 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.38   3.1e+02      60      73 ..     252     265 ..     239     267 .. 0.85
   2 ?    9.0   0.1    0.0018       1.5       1      76 []     275     366 ..     275     366 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.38
                            TOBE_2  60 pGdtVelswdpdda 73 
                                       +Gd++e+ +dp+ +
  gi|313125912|ref|YP_004036182.1| 252 VGDRIEVDFDPETI 265
                                       79********9976 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                            TOBE_2   1 laiRPEklrla.....aagga..n.glsGtVedveylGsstryvvelaggqlvvv..........rqpnadr.dsal 58 
                                       l+iRPE++            a  + +++   + +e +G+++ +++ l + + v +          +   + + ds++
  gi|313125912|ref|YP_004036182.1| 275 LGIRPEDVYTLddassL---AnpTkQVEVITDVLEPMGDEIFVYLLLSEDATVSLdeeargamsdQLLMSVDpDSDI 348
                                       79******997654321...23445999999999*******999998888887776666665555333333334577 PP

                            TOBE_2  59 apGdtVelswdpddavvl 76 
                                       a++ +V + +d  +++++
  gi|313125912|ref|YP_004036182.1| 349 AEDKEVSVVLDRTKVHLF 366
                                       777777777777777776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.093       1      19 [.      32      50 ..      32      69 .. 0.80
   2 ?   -0.2   0.0       1.6   1.3e+03      25      64 ..     255     294 ..     244     306 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                      RNA_helicase  1 iwlyGpsgeGKStlakeLa 19
                                      ++l+Gpsg+GKSt+++ +a
  gi|313125912|ref|YP_004036182.1| 32 VCLVGPSGCGKSTTMEMIA 50
                                      689************9954 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                      RNA_helicase  25 klklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkde 64 
                                       +++ + +++++s ++ dd+  g + ++v   dD ++  + 
  gi|313125912|ref|YP_004036182.1| 255 RIEVDFDPETISASVGDDVTLGIRPEDVYTLDDASSLANP 294
                                       566777788899999999***************9876654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     5e-05     0.041       5      26 ..      29      50 ..      25      59 .. 0.88
   2 ?   -1.5   0.1       3.5   2.8e+03      45     124 ..     157     186 ..     126     214 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrll 26
                                        +++++G+sG+GK+t++++++
  gi|313125912|ref|YP_004036182.1| 29 GEFVCLVGPSGCGKSTTMEMIA 50
                                      67899*************9875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.5
                            AAA_22  45 vtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlrseealeeLrsllnlsrk 121
                                       ++ p  +  ++l+ ++  +l++ +k+                                                   
  gi|313125912|ref|YP_004036182.1| 157 MDEPLANLDAKLRVHMRTELQRLHKE--------------------------------------------------L 183
                                       33333333333333333333332222..................................................2 PP

                            AAA_22 122 gvq 124
                                       +++
  gi|313125912|ref|YP_004036182.1| 184 DTT 186
                                       222 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.0    0.0001     0.085       1      22 [.      32      53 ..      32     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      v+l+Gp G+GK+++++ +a  +
  gi|313125912|ref|YP_004036182.1| 32 VCLVGPSGCGKSTTMEMIAGLT 53
                                      79****************9864 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.3e-05     0.076      23      41 ..     264     282 ..     243     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-05
                   CysA_C_terminal  23 elagadgqevvayVRPhDl 41 
                                          ++ g++v++++RP+D+
  gi|313125912|ref|YP_004036182.1| 264 TISASVGDDVTLGIRPEDV 282
                                       666779************7 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.16      17      46 ..      29      57 ..      20      76 .. 0.81
   2 ?   -1.0   0.0       1.5   1.2e+03      43      68 ..     181     206 ..     171     313 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag 46
                                      g  +++l+Gp G GK+t+++ ++ +    +
  gi|313125912|ref|YP_004036182.1| 29 G-EFVCLVGPSGCGKSTTMEMIAGLTMPTE 57
                                      3.4899**************9988766554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                            AAA_30  43 eaaggrviglAptgkaAkvLaeelgi 68 
                                       ++   ++i +++ ++ A ++++ + +
  gi|313125912|ref|YP_004036182.1| 181 KELDTTIIYVTHDQAEAMTMSDRIAV 206
                                       55555555555555555555554442 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0    0.0001     0.083      20      40 ..      30      50 ..      12      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                            AAA_23 20 gltlItGpNGaGKTTildAik 40
                                       +++++Gp G+GK+T ++ i 
  gi|313125912|ref|YP_004036182.1| 30 EFVCLVGPSGCGKSTTMEMIA 50
                                      5789**************996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00059      0.48       1      44 [.      32      83 ..      32     210 .. 0.80
   2 ?    0.4   0.0       1.1   8.8e+02      52      90 ..     326     369 ..     306     375 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00059
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.........gvnlrdvakenglllevdpe 44
                                      ++l G++G+GK+t  + ++ ++ +         g++++ + ++++ + +v+++
  gi|313125912|ref|YP_004036182.1| 32 VCLVGPSGCGKSTTMEMIAGLT-MptegevfigGREVTNLPPKDRGVAMVFQN 83
                                      79************99987664.445666666666666666666555555555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                            AAA_18  52 ldedkldklldaleenss.....aleegknlvidghlaelesea 90 
                                       lde+ + + +d+l  + +     a++++ ++v+d   ++l++++
  gi|313125912|ref|YP_004036182.1| 326 LDEEARGAMSDQLLMSVDpdsdiAEDKEVSVVLDRTKVHLFDTE 369
                                       45555555555555555566668888999999999999999875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   0.00021      0.17       2      29 ..      32      59 ..      31     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                            AAA_28  2 ivitGgestGKTtlleaLaargypvvpE 29
                                      ++++G++++GK+t++e +a   +p+  E
  gi|313125912|ref|YP_004036182.1| 32 VCLVGPSGCGKSTTMEMIAGLTMPTEGE 59
                                      89**************999766555544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00051      0.42      31      65 ..      27      63 ..      21      81 .. 0.67
   2 ?   -2.1   0.0         3   2.5e+03      97     129 ..     337     378 ..     314     388 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00051
                            AAA_25 31 pagelallaGapgtGKttlaldlalava...tGkpwlg 65
                                        ge++ l+G++g+GK+t    +a  ++   +G+ + g
  gi|313125912|ref|YP_004036182.1| 27 NDGEFVCLVGPSGCGKSTTMEMIAG-LTmptEGEVFIG 63
                                      679**************96543333.333566666666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
                            AAA_25  97 l...........rddarllvldlagveslpLfakdrggtlltad 129
                                       +           ++d+++ v+     ++++Lf++++g++ll + 
  gi|313125912|ref|YP_004036182.1| 337 QllmsvdpdsdiAEDKEVSVVLDR--TKVHLFDTETGEALLHGL 378
                                       444455555554444444444322..357888888888776544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0081       6.6      16      48 ..      26      59 ..      13      68 .. 0.79
   2 ?    3.7   0.1     0.043        35      48     110 ..     143     209 ..     132     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0081
                                      HHH-SEEEEE--TTSST.THHHHHHHHHHHHTTS CS
                              PhoH 16 lkkndivfaiGpaGtGK.tylavalavealkkkk 48
                                      +++ ++v+ +Gp+G+GK t + + +++++ ++++
  gi|313125912|ref|YP_004036182.1| 26 INDGEFVCLVGPSGCGKsTTMEMIAGLTMPTEGE 59
                                      567789***********55677778877766655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.043
                                       S-SEEEEEE-S--T.T----SS---------TTTHHHHHHHTTTS...-TTCHHHHHHTTSEEEEEG CS
                              PhoH  48 kvkriiltrpavea.geelGflpgdleekvdpylrplydaLkdll...gaekvekllekgkievapl 110
                                        + r i+  p v   +e l  l+ +l+  ++  l+ l+ +L++++    +++ e ++ +++i v++ 
  gi|313125912|ref|YP_004036182.1| 143 AIARAIVRNPDVFLmDEPLANLDAKLRVHMRTELQRLHKELDTTIiyvTHDQAEAMTMSDRIAVIDS 209
                                       344555555665336***************************9887778899999999999999875 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.3   1.9e+03      33      60 ..     265     280 ..     249     282 .. 0.57
   2 ?    4.4   0.0     0.056        46       9      44 ..     300     333 ..     293     346 .. 0.80
   3 ?    4.6   0.0     0.048        39      33      64 .]     338     365 ..     331     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.3
                              TOBE  33 LtArvtrrsaeeLgLapGeeVfalikaa 60 
                                       + A+v            G+ V++ i ++
  gi|313125912|ref|YP_004036182.1| 265 ISASV------------GDDVTLGIRPE 280
                                       44444............55555555554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.056
                              TOBE   9 gtVvvveplgseveVrvdlgggatLtArvtrrsaee 44 
                                       +  +v+ep g e +V++ l+  a  t++++++++ +
  gi|313125912|ref|YP_004036182.1| 300 VITDVLEPMGDEIFVYLLLSEDA--TVSLDEEARGA 333
                                       555799*************9999..77777777655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.048
                              TOBE  33 LtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       L  +v+++s  +     ++eV ++++ +kvhl
  gi|313125912|ref|YP_004036182.1| 338 LLMSVDPDSDIA----EDKEVSVVLDRTKVHL 365
                                       677888899888....***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2400.56
//
Query:       gi|313125913|ref|YP_004036183.1|  [L=320]
Description: carbohydrate ABC transporter membrane protein 2, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-10   40.7  19.8    2.1e-10   40.7  19.8    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -8.8  13.7         1   1.8e+04      20      67 ..      45     122 ..      26     125 .. 0.57
   2 !   40.7  19.8   1.2e-14   2.1e-10       3     179 ..     119     309 ..     114     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: -8.8 bits;  conditional E-value: 1
                      BPD_transp_1  20 lrpliivllslPsfvlaillvlvf...............................vilsilghlilp.viillllsa 64 
                                        + ++ v+  +P+++l++l +                                  ++++++  +i   vi+lll s+
  gi|313125913|ref|YP_004036183.1|  45 ATLFFLVTTLFPFYWLLVLAL--TpnrlirdmgllpkgfnpevfitmfervpfhlFMFNSFVLGIATtVIVLLLASL 119
                                       334444555566666555533..144677666777777777777777777776664444444444443555555555 PP

                      BPD_transp_1  65 apy 67 
                                       a+y
  gi|313125913|ref|YP_004036183.1| 120 AGY 122
                                       555 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 1.2e-14
                      BPD_transp_1   3 llGilaalnrnkkldkllrpliivllslPsfvlaillvlvf............vilsilghlilpviillllsaapy 67 
                                       l+G++ + + +++++ +l+  i +++++P+ +++++l+ +f            v + +l ++  p+++ +   ++p+
  gi|313125913|ref|YP_004036183.1| 119 LAGYVFG-RLRFPGRTALMLGILAISYFPPAAFFLPLFELFtggtdivlgpitVSSPDLFNTPAPMVFPFSALFMPL 194
                                       6788888.9999**************************999**********987777888999999*********** PP

                      BPD_transp_1  68 vrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.......l 137
                                        ++i   +  ++p++l+ aar+ G +r   +++v++P+++p ++t  +l+f+++ +++++  ++ ++ +        
  gi|313125913|ref|YP_004036183.1| 195 SIFILTTFYGQIPDGLEDAARVEGTTRLGALFRVIIPLSAPGVATAGVLTFISVYNEFFFSFLMNNGEAsswapivA 271
                                       *********************************************************99866666555454444333 PP

                      BPD_transp_1 138 gtllleailgydyseis....nggvlalviavlllnlvadilqrll 179
                                                +  y+       n +++a ++ vl++ +++ i q+ +
  gi|313125913|ref|YP_004036183.1| 272 --------GILKYQGQFdtpyNLMAAASIVGVLPVAILVIIAQERI 309
                                       ........44444433344555566666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2181.75
//
Query:       gi|313125914|ref|YP_004036184.1|  [L=342]
Description: carbohydrate ABC transporter membrane protein 1, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-18   66.8  17.8      2e-18   66.8  17.8    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   4.5    0.0064   1.2e+02      28      77 ..      39     119 ..      21     122 .. 0.78
   2 !   66.8  17.8   1.1e-22     2e-18       4     174 ..     135     332 ..     132     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0064
                      BPD_transp_1  28 lslPsfvlaillvlvf..................................vilsilghlilp.viillllsaapyvr 69 
                                       l +P ++l+++    +                                  +++s++ + +lp +++ +l s++p+v+
  gi|313125914|ref|YP_004036184.1|  39 LLTPALLLLLV----IavypliqtfgyslyadqltgtarlgqfvgienyvALFSGARDFALPsAFLPGLSSSFPFVT 111
                                       34444443333....1224568888999999999999999999999999999999999999999************* PP

                      BPD_transp_1  70 lirraalr 77 
                                        i+++al 
  gi|313125914|ref|YP_004036184.1| 112 GIYSSALM 119
                                       ***99986 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 1.1e-22
                      BPD_transp_1   4 lGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf........................vilsilghlil 54 
                                       +G+  a  l + +++++++r+ ii+++++P+++ +++++l+f                          l    ++ +
  gi|313125914|ref|YP_004036184.1| 135 IGFAQAliLDQDFRGRRWVRVAIIIPWAVPIVIQGMIWFLMFqpnigfligtqenpailntlglsfTPLRNTSDSLF 211
                                       66666777778899******************************************999999998755556666667 PP

                      BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl 131
                                        +i++ ++ +++++ l++ a+l+s++++l+ +ar+ Gas+wq f+ +++P++lp+++  ++++ ++++  + ++e++
  gi|313125914|ref|YP_004036184.1| 212 LIIVADVWKTTAFMALLILAGLQSIDRSLYDVARVAGASKWQQFKMITFPLILPTVLVAMLFRTIAAMRVYGIIETM 288
                                       799************************************************************************** PP

                      BPD_transp_1 132 gswpG......lgtllleailgydyseisnggvlalviavlllnlvadi 174
                                       +   G      l+ l++++ ++++y   +  +v+++++ ++ ++++++i
  gi|313125914|ref|YP_004036184.1| 289 A---GcttvpsLSCLVVTTFNNSMYGTSA--TVAFVTAGLIGIVVSVYI 332
                                       *...5555888999999999999998555..444444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2030.53
//
Query:       gi|313125915|ref|YP_004036185.1|  [L=487]
Description: sugar ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-13   51.7   0.3    2.2e-13   50.7   0.3    1.4  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    4.2e-11   43.4   0.4    6.3e-11   42.8   0.4    1.2  1  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
        4.8    7.2   6.9         11    6.1   6.9    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.3   3.7e-17   2.2e-13      11     273 ..      74     418 ..      68     424 .. 0.70

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 3.7e-17
                                       TEEEEEEE-..-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG.GS.TTHHH......-HHHHHT CS
                         SBP_bac_8  11 gvkvnvvta..asndleqklkaalaagtapdidvvwanedalatlaeeglladls.dl.dnldd......ltdalaa 77 
                                       +++v+v+     +n  +++++  l++g   ++ ++++++++   +++++ l++ls +l d +++      +++    
  gi|313125915|ref|YP_004036185.1|  74 NITVEVIAGsqVTNNRQNQYQQWLSSGRE-QPTLLMMDSGWTIPFIARNQLQNLSqTLpDSMTSrveenyFEA---- 145
                                       57888877743458889999999999985.567999999****************744344444654444444.... PP

                                       T.....--TS.----EEEEEEE-EEEEEHHHHHHS.....---BH.HHHHHHHH..HHHHH-SEGG---GGGGGGTH CS
                         SBP_bac_8  78 v.....gydgklygvPyasetpyvliynkdlleka....edpktw.dellaaak..klkgkfglpdpasgwlqaall 142
                                             g +g+lyg+P+    p ++ y+kdll  a    +d +tw  e  ++++  k+++ ++ ++p ++++++++ 
  gi|313125915|ref|YP_004036185.1| 146 SvgtakGANGDLYGIPLFPDFP-TMQYRKDLLRNAgygdSDFETWaTESMSWVEfsKITKEAMNANPDTQYGYTFQA 221
                                       23433366999******99988.**********98999988888854556664444665555555555555555555 PP

                                       H...........................ETTEE---H..HHH....................HHHHHHHHHHHHTT- CS
                         SBP_bac_8 143 a...........................kdgksldddggkdgl...................kealellkklkdngk 173
                                                                   +             l                    ++++ l +  d+  
  gi|313125915|ref|YP_004036185.1| 222 SvyeglsccdfnefmtsyggaffgnpaeN-------------LfgpvgdrpvtvdeqpvldsIKMVRTLINGEDDEH 285
                                       55444444444444443333333333330.............25666666666666677666555566666666665 PP

                                       EE..............-S..--SSTTTTTSBSEEEE-T..THHHHHH-T.TTSEEEE.--............S--EE CS
                         SBP_bac_8 174 ty..............dtgadavsefanGevaftings..wdiaaaqka.gkklgai.vp............kqgsf 220
                                        +              +t +   + f+ G++ +  n++   +i+ a++  g++lg++ +p              g++
  gi|313125915|ref|YP_004036185.1| 286 ALdgitgniapeavlqWTEEPSRKPFTGGDAIMHRNWPysININGAEDVfGEDLGVMpIPygvtaeeaqypmTGGPV 362
                                       334556677777788899999***************77336688999999*******65688887776554434555 PP

                                       EEEEEEEE..BTTS-HHHH.HHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHH CS
                         SBP_bac_8 221 aggkglav..pknaknedl.aAldFlkwltspenqaalaektgyipvnksaalspe 273
                                       a   g+ v  + na++ ++ aAl+ +k +++++   + +e +g ip+ +++ +s+ 
  gi|313125915|ref|YP_004036185.1| 363 AALGGWHVtlNPNASQLQKrAALQVMKAMMTEQFKLDIFEIIGWIPPEPDLLDSDR 418
                                       5555555444999**************************************99885 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.4   1.1e-14   6.3e-11      24     311 ..      74     394 ..      60     397 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.1e-14
                                       TEEEEEEEECHHHHHH....HHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHHH CS
                         SBP_bac_1  24 gikVeiesvgsgslaq....kltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkdaadklsss 96 
                                       +i+Ve++ ++  +  +    +++  +++G+ ++ + ++d++w+ +++  ++l+ l+  + + +   v++   +    
  gi|313125915|ref|YP_004036185.1|  74 NITVEVIAGSQVT--NnrqnQYQQWLSSGREQPTLLMMDSGWTIPFIARNQLQNLSQTLPDSMTSRVEE---N---- 141
                                       4666666663333..2336688899*****777*****************************9777653...3.... PP

                                       HTHHHHCE.EE....ES.EEEE.EEEEEEEETTTHHCTTGGG.........SHBHHHHHHHHHHHHHHCTCT..HCC CS
                         SBP_bac_1  97 vlpkilds.kv....ly.vPly.aargliYNkdlfekagldp.........pwtWdelveaakklkekgkkp..igg 155
                                       ++++  ++ k+    ly +Pl      + Y+kdl+ +ag +            +W e+ +  k+++ +++ +  ++ 
  gi|313125915|ref|YP_004036185.1| 142 YFEASVGTaKGangdLYgIPLFpDFPTMQYRKDLLRNAGYGDsdfetwateSMSWVEFSKITKEAMNANPDTqyGYT 218
                                       333333333556789*******88************99999999999999999********************9999 PP

                                       HCCEEHHHHHHHHHHHHHHHHTGGGEECCCT.................HHCSHHHHS.HHHHHHHHHHHHHHHHHHH CS
                         SBP_bac_1 156 arggsasgtayyfalalakslggkvfdkdgg.................gldnpegvt.aatylvklyavanltkelk 214
                                          + ++g    ++++++ s+gg +f++ +                   ld+ + v   ++   + +a +  t + +
  gi|313125915|ref|YP_004036185.1| 219 FQASVYEGLSCCDFNEFMTSYGGAFFGNPAEnlfgpvgdrpvtvdeqpVLDSIKMVRtLINGEDDEHALDGITGNIA 295
                                       999999************************************99999955555555566666666666666666678 PP

                                       TTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE........ CS
                         SBP_bac_1 215 gkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi........ 283
                                       +  ++ ++++  ++ f+ G+a m  +++++           + + + + ++e+lgv p+P+g ++  ++        
  gi|313125915|ref|YP_004036185.1| 296 PEAVLQWTEEPSRKPFTGGDAIMHRNWPYS----------ININGAEDVFGEDLGVMPIPYGVTAEEAQypmtggpv 362
                                       99999999999999999************9..........799999999999**********999999999999999 PP

                                       ..EEEEEEEEBTTCST..HHHHHHHHHHHTSH CS
                         SBP_bac_1 284 ..lgayglaipkgskn..peaAkkFldfllsp 311
                                         lg+++++++ ++++  + aA ++++ + ++
  gi|313125915|ref|YP_004036185.1| 363 aaLGGWHVTLNPNASQlqKRAALQVMKAMMTE 394
                                       99*****9999999997666699988888765 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   6.9    0.0018        11       8      25 ..       1      18 [.       1      19 [. 0.93

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0018
                        TAT_signal  8 LKgsAAaaAAaalggcaa 25
                                      +K+++A + Aa l+gc +
  gi|313125915|ref|YP_004036185.1|  1 MKAAGASGVAASLAGCIS 18
                                      7***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3010.89
//
Query:       gi|313125916|ref|YP_004036186.1|  [L=385]
Description: DNA primase small subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-23   82.4   0.0      6e-23   81.8   0.0    1.2  1  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
      0.047   14.3   0.6       0.45   11.2   0.0    2.7  3  HHH_5          Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   6.7e-27     6e-23       1     172 [.      96     314 ..      96     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 6.7e-27
                                       EEEEEETTT-...TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHH CS
                     DNA_primase_S   1 FDiDmddydd..cseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraaiv 75 
                                       FD+D+d++++   + +++  ++++  ++  ++ld  l+ df+f d+ +vfsg+rG+H++v+d+++r+l++  r++iv
  gi|313125916|ref|YP_004036186.1|  96 FDLDADHLPGvdPETTSYADMLAACKDDLLSLLD-ILENDFDFTDTQVVFSGGRGYHVHVRDENVRELDSDARREIV 171
                                       9*********988888889999999999999998.779*************************************** PP

                                       HH............................................HCHHHHCT--------............... CS
                     DNA_primase_S  76 nylnlyrplhpflsrs.mlkivkpvveeiileeqdpf.........eikkllrllpdkslrekkkw........... 131
                                       +y++ ++  ++ l ++  ++  +++    +l  ++ +         e ++ lr + +++  e  ++           
  gi|313125916|ref|YP_004036186.1| 172 DYVRAIDLDVEGLIGTeSNRGTTRR----VLRRHGGWgarvhdrllELAENLREMEEEAALE--RLqelqgigegra 242
                                       *999885555555555555555555....567789999996665555555555555554444..2244566788888 PP

                                       ............................................-----------------....---.--- CS
                     DNA_primase_S 132 ..............................eakedivlvllyprldeqvtkgikhllkapfcihgktg.nvc 172
                                                                     +a+ ++ ++     +de+vt+++k+l+++p+++hg++g +v+
  gi|313125916|ref|YP_004036186.1| 243 ktilgqihnnfeairegnveaggpgtrilvNALAEEAVTAETAPIDEPVTTDTKRLIRLPGSLHGGSGlRVK 314
                                       88899999999999****************99999999******************************6665 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.28   2.5e+03      24      39 ..     111     126 ..     102     130 .. 0.78
   2 ?   11.2   0.0     5e-05      0.45       2      35 ..     229     262 ..     219     263 .. 0.84
   3 ?   -1.7   0.0       0.5   4.5e+03      32      42 ..     293     303 ..     272     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.28
                                       -SHHHHHHS-HHHHHT CS
                             HHH_5  24 esvedlaaadveeLak 39 
                                       +s++d +aa++++L +
  gi|313125916|ref|YP_004036186.1| 111 TSYADMLAACKDDLLS 126
                                       5788888899988876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5e-05
                                       HHHHTSTT--HHHHHHHHTTT--.SHHHHHHS-HH CS
                             HHH_5   2 eeLlsvsGiGpktAlallsaGie.svedlaaadve 35 
                                       e L++++GiG+ +A+++l + i   +e++ + +ve
  gi|313125916|ref|YP_004036186.1| 229 ERLQELQGIGEGRAKTILGQ-IHnNFEAIREGNVE 262
                                       57899999999999999999.88459999888876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.5
                                       S-HHHHHTSTT CS
                             HHH_5  32 adveeLakipG 42 
                                        d+++L ++pG
  gi|313125916|ref|YP_004036186.1| 293 TDTKRLIRLPG 303
                                       58999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2579.57
//
Query:       gi|313125917|ref|YP_004036187.1|  [L=326]
Description: hypothetical protein Hbor_11520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        1.8    8.8   6.9       0.92    9.8   0.1    2.6  3  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   5.1e-05      0.92      17      64 ..      29      77 ..      24      84 .. 0.80
   2 ?    2.4   0.2    0.0095   1.7e+02      39      93 ..      85     138 ..      78     157 .. 0.86
   3 ?   -2.1   0.2      0.23   4.2e+03      82      82 ..     251     251 ..     214     285 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.1e-05
                                      HHHHHHHHHHC.TTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Acyl-CoA_dh_2 17 efvelarervr.assgekladdpatqlalaeaaarldAAralleraaar 64
                                      ++++++++++   + ++  addp    ++++++ ++++A+ ++e+ ++r
  gi|313125917|ref|YP_004036187.1| 29 DVADYIAQQKAeRKRAADRADDPFSDPEVGRLTDEIETAEDVVEAIYER 77
                                      55556554444366699999************************99988 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.0095
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHH CS
                     Acyl-CoA_dh_2  39 atqlalaeaaarldAAralleraaaraealaaagkevtvedraearraaalavel 93 
                                        + +a a+++a+ + + a  ++ +++    +++++e tv d++ ++r+ ++++++
  gi|313125917|ref|YP_004036187.1|  85 LASFAAADMSADTNGLTAEERDLFDDLVSRIKQNRE-TVLDVLAGKRSGSATTTE 138
                                       678999**********99999999999999999999.799999999887766654 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.23
                                       H CS
                     Acyl-CoA_dh_2  82 e 82 
                                        
  gi|313125917|ref|YP_004036187.1| 251 T 251
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1959.44
//
Query:       gi|313125918|ref|YP_004036188.1|  [L=158]
Description: peroxiredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.3e-39  132.5   0.0    8.7e-39  132.3   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    9.5e-25   87.0   0.0    1.1e-24   86.8   0.0    1.0  1  Redoxin     Redoxin
    3.2e-06   27.1   0.1      4e-06   26.8   0.1    1.2  1  SCO1-SenC   SCO1/SenC
    0.00044   19.9   0.0    0.00046   19.8   0.0    1.1  1  DUF899      Bacterial protein of unknown function (DUF899)
  ------ inclusion threshold ------
      0.057   13.5   0.0      0.073   13.2   0.0    1.2  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   0.0   2.4e-42   8.7e-39       1     123 [.       4     132 ..       4     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 2.4e-42
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       vgd+apdfel+n+dge+vslsd+++++vv++fyp++++p+Ctte+++++++ +ef++++++v+g+s+d+  ++++f+
  gi|313125918|ref|YP_004036188.1|   4 VGDEAPDFELQNQDGEKVSLSDFENEYVVVYFYPRANTPGCTTEACEFRDASNEFEAHDATVLGISDDPISDLEEFA 80 
                                       79*************************************************************************** PP

                                       HH-H.SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  78 ekeslnfpllsDeegkvakaygvlkee......kglalratfvidkegkiry 123
                                       ++++l fpllsDe+g+va ay+ + e+        +  r ++v+ ++g+i++
  gi|313125918|ref|YP_004036188.1|  81 DDHDLSFPLLSDEDGAVASAYDSYGEKnmfgntFDGVFRNSYVVAPDGTIAF 132
                                       *******************************99999*************986 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.0   3.2e-28   1.1e-24       2     138 ..       4     141 ..       3     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 3.2e-28
                                       TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvke 78 
                                       +gd+aPdf+l++  +dg++vsls+f++  vvv+f+p+a +P C++e++++++ ++++++++ +v++++ d  +   e
  gi|313125918|ref|YP_004036188.1|   4 VGDEAPDFELQN--QDGEKVSLSDFENEYVVVYFYPRANTPGCTTEACEFRDASNEFEAHDATVLGISDDPISDLEE 78 
                                       79*******977..**************************************************7776666666*** PP

                                       HHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG....EEE-EEEEEEETTEEEEEEESSSCHT CS
                           Redoxin  79 fwgkeglkfpvlsDgsaaftkalGlrleedaseg....lrtpryavidedgkvvylevepepet 138
                                       f+++++l+fp+lsD+++a+++a++ + e ++  g       + + v+  dg +   + +++pe+
  gi|313125918|ref|YP_004036188.1|  79 FADDHDLSFPLLSDEDGAVASAYDSYGE-KNMFGntfdGVFRNSYVVAPDGTIAFAYEGVSPEG 141
                                       ************************7744.43333688888999999999999999999999954 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   1.1e-09     4e-06       2     104 ..       9     105 ..       8     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.1e-09
                         SCO1-SenC   2 gpFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkey 78 
                                        +Fel +qdge+v+ +d+e+++++v+f     +  C+t+  + +++ +++++   + ++l i+ DP  D    l+e+
  gi|313125918|ref|YP_004036188.1|   9 PDFELQNQDGEKVSLSDFENEYVVVYFYPRANTPGCTTEACEFRDASNEFEAH--DATVLGISDDPISD----LEEF 79 
                                       58*************************9999999****************998..99999999999866....8888 PP

                         SCO1-SenC  79 leafdpriigltGskeeiakaakefr 104
                                       ++ +d ++  l+++  ++a+a+++++
  gi|313125918|ref|YP_004036188.1|  80 ADDHDLSFPLLSDEDGAVASAYDSYG 105
                                       88888888888888888888888875 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.3e-07   0.00046      83     152 ..      39     108 ..      10     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.3e-07
                            DUF899  83 egCpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleee 152
                                       ++ pgC++ a ++  a +++ea+d t+  +s  p+ +le++ ++   ++p+ s+ +  +   +    e++
  gi|313125918|ref|YP_004036188.1|  39 ANTPGCTTEACEFRDASNEFEAHDATVLGISDDPISDLEEFADDHDLSFPLLSDEDGAVASAYDSYGEKN 108
                                       4569***************************************************999999888655544 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05     0.073       3      51 ..      52     101 ..      50     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                        AhpC-TSA_2   3 srdkpeldaagvklvaigigdps.akkFvkltgfpfelyvDpsaklyqal 51 
                                       ++ ++e++a+  ++ +i+ + +s +++F++  + +f+l+ D+++++ +a 
  gi|313125918|ref|YP_004036188.1|  52 RDASNEFEAHDATVLGISDDPISdLEEFADDHDLSFPLLSDEDGAVASAY 101
                                       5568999999********999966******************98765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 965.81
//
Query:       gi|313125919|ref|YP_004036189.1|  [L=33]
Description: hypothetical protein Hbor_11540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      138  (0.00769703); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 218.32
//
Query:       gi|313125920|ref|YP_004036190.1|  [L=754]
Description: ATPase AAA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.7e-100  332.0   0.0    7.1e-49  165.6   0.0    2.5  2  AAA              ATPase family associated with various cellul
      2e-31  107.5   5.3    3.6e-17   61.9   1.0    3.3  2  AAA_lid_3        AAA+ lid domain
    6.4e-24   83.9   0.0    2.8e-23   81.9   0.1    2.2  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.8e-18   67.3   0.1    7.3e-09   36.0   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    4.6e-17   62.2   0.0    2.8e-08   33.7   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      1e-15   58.6   0.1    5.6e-07   30.1   0.0    3.6  2  AAA_16           AAA ATPase domain
    1.2e-15   57.0   0.4    3.1e-15   55.7   0.4    1.8  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    7.6e-12   45.4   0.5    0.00055   20.0   0.0    4.4  2  AAA_5            AAA domain (dynein-related subfamily)
    1.4e-11   44.9   0.1    0.00072   19.8   0.0    3.7  3  AAA_22           AAA domain
    3.6e-11   43.2   0.0    0.00064   19.8   0.0    3.0  3  AAA_14           AAA domain
    1.8e-10   40.6   0.0     0.0002   20.7   0.0    2.4  2  TIP49            TIP49 P-loop domain
    1.7e-09   38.0   0.0     0.0013   18.9   0.0    2.8  2  AAA_33           AAA domain
    7.9e-08   32.2   0.0      0.003   17.3   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    9.9e-08   32.6   0.0     0.0092   16.5   0.0    2.9  2  AAA_18           AAA domain
    1.1e-07   31.5   0.0      0.012   15.1   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    1.5e-07   31.8   0.0      0.028   14.8   0.0    2.8  2  RNA_helicase     RNA helicase
    1.6e-07   31.2   0.0      0.017   15.0   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    2.9e-07   29.9   0.0    0.00034   19.9   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    9.3e-07   28.6   0.2       0.85    9.2   0.0    4.3  4  AAA_25           AAA domain
    9.3e-07   28.4   0.2      0.036   13.5   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.3e-06   28.8   0.0       0.07   13.4   0.0    2.8  2  AAA_28           AAA domain
    1.8e-06   27.9   0.0      0.047   13.7   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    4.3e-06   26.5   0.1      0.097   12.4   0.0    3.1  2  Sigma54_activat  Sigma-54 interaction domain
    1.3e-05   24.5   0.0       0.15   11.2   0.0    2.7  3  NB-ARC           NB-ARC domain
    1.6e-05   24.7   0.0      0.073   12.8   0.0    2.5  2  AAA_24           AAA domain
    1.8e-05   24.2   0.0       0.08   12.2   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    1.9e-05   25.2   0.0        0.2   12.1   0.0    2.7  2  ABC_tran         ABC transporter
    2.9e-05   23.9   0.0       0.26   11.0   0.0    2.7  2  AAA_30           AAA domain
    3.3e-05   23.4   0.1       0.79    9.0   0.0    3.6  3  ATPase           KaiC
    3.4e-05   23.8   0.3       0.21   11.4   0.0    2.6  2  AAA_11           AAA domain
    3.4e-05   23.4   0.1       0.13   11.7   0.0    2.5  2  PhoH             PhoH-like protein
    0.00012   21.2   0.0       0.33   10.0   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00013   22.0   0.1       0.84    9.5   0.0    3.4  3  NACHT            NACHT domain
    0.00016   21.1   0.1       0.64    9.3   0.0    2.7  2  Zeta_toxin       Zeta toxin
     0.0003   20.8   0.3        1.1    9.1   0.0    3.3  2  NTPase_1         NTPase
    0.00032   20.6   0.0       0.22   11.3   0.0    2.9  2  Bac_DnaA         Bacterial dnaA  protein
     0.0004   20.7   0.4        1.9    8.8   0.0    2.8  2  AAA_19           AAA domain
    0.00049   20.5   0.0        1.5    9.3   0.0    3.1  2  AAA_17           AAA domain
    0.00053   19.9   0.2      0.051   13.6   0.0    3.1  2  Vps4_C           Vps4 C terminal oligomerisation domain
    0.00061   19.9   0.0        2.1    8.5   0.0    2.8  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00071   19.6   0.8       0.22   11.4   0.0    3.4  3  ATPase_2         ATPase domain predominantly from Archaea
     0.0028   17.7   0.0        2.7    7.9   0.0    2.6  2  ResIII           Type III restriction enzyme, res subunit
     0.0044   16.1   0.0        1.6    7.7   0.0    2.6  2  T2SSE            Type II/IV secretion system protein
     0.0082   15.6   0.0         10    5.5   0.0    3.3  3  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
      0.011   14.7   0.0        4.6    6.0   0.0    2.9  3  AFG1_ATPase      AFG1-like ATPase
      0.015   15.0   0.4         34    4.1   0.0    4.0  4  Guanylate_kin    Guanylate kinase
      0.016   15.0   0.1        4.9    6.8   0.0    3.0  2  Cytidylate_kin   Cytidylate kinase
      0.019   14.8   0.0        4.5    7.1   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.038   13.9   0.0         12    5.8   0.0    2.4  2  Rad17            Rad17 P-loop domain
      0.039   14.0   0.0       0.14   12.2   0.1    2.0  1  Molydop_binding  Molydopterin dinucleotide binding domain
      0.048   13.8   0.0        3.6    7.7   0.0    2.4  2  Torsin           Torsin
      0.051   13.3   0.0         10    5.9   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.059   13.5   0.0         18    5.4   0.0    2.6  2  SKI              Shikimate kinase
       0.12   11.5   0.0        3.1    6.8   0.0    2.3  2  MCM              MCM P-loop domain
       0.13   11.5   0.1         12    5.0   0.0    2.7  3  KAP_NTPase       KAP family P-loop domain
       0.15   11.2   0.0        5.9    5.9   0.0    2.6  3  PIF1             PIF1-like helicase
       0.17   11.6   0.0         15    5.2   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.17   12.2   0.3        3.3    8.0   0.1    2.6  2  Hydin_ADK        Hydin Adenylate kinase-like domain
        0.2   11.3   0.0        5.2    6.7   0.0    2.7  2  Zot              Zonular occludens toxin (Zot)


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.9   0.0     8e-51   2.4e-48       1     131 [.     227     356 ..     227     357 .. 0.98
   2 !  165.6   0.0   2.3e-51   7.1e-49       1     131 [.     500     631 ..     500     632 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 8e-51
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKTl+akava+e++++f +isg+e++sky gese+++re+f++a+e+a p i+fiDEid++a++r ++
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDASFHTISGPEIMSKYYGESEEQLREIFEDAEENA-PAIVFIDEIDSIAPKRGEA 302
                                       79******************************************************9.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                         ++e+rvv+qLl+ +dg++++ ++v+vigatnr+d +dpal+r gRfdr+iei+
  gi|313125920|ref|YP_004036190.1| 303 GGDVERRVVAQLLSLMDGLDER-GEVVVIGATNRVDAIDPALRRgGRFDREIEIG 356
                                       *********************7.66***************************996 PP

  == domain 2  score: 165.6 bits;  conditional E-value: 2.3e-51
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       vllyGppGtGKTllakava+e++++f++++g+ell+kyvgesek +re+fk+a+e+a p+++f+DEid++a +r  s
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEADSNFISVKGPELLNKYVGESEKGVREIFKKARENA-PTVVFFDEIDSIAIERgqS 575
                                       79******************************************************9.****************988 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       +++s+++ervv+qLlteldg+++ e+ v+vi+++nrpd +d+allr gR+dr+i+++
  gi|313125920|ref|YP_004036190.1| 576 SGDSGVSERVVSQLLTELDGLESLED-VVVIATSNRPDLIDSALLRpGRLDRHIHVP 631
                                       89*********************755.***************************987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.2   1.1e-14   3.3e-12       2      37 ..     380     422 ..     379     440 .. 0.78
   2 !   61.9   1.0   1.2e-19   3.6e-17       1      44 [.     654     711 ..     654     725 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.1e-14
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrr.......gike 37 
                                       vdl+e Ae T+G++GAD+++l +e+a++Alrr       +++e
  gi|313125920|ref|YP_004036190.1| 380 VDLDEYAEITHGFVGADIESLAKESAMNALRRirpqldlDEDE 422
                                       9*******************************55555442333 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 1.2e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr..............gikeitmedfe 44 
                                       dvdl++LA++TeGy+GAD++a+creA+++A r+              g+  +tm++fe
  gi|313125920|ref|YP_004036190.1| 654 DVDLDQLARKTEGYVGADIEAVCREASMAASREfinsvepeeveesiGNVRVTMDHFE 711
                                       9********************************5555555554443333346666665 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.1   9.4e-26   2.8e-23       1      84 [.       2      86 ..       2      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 9.4e-26
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEE.EEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTv.aivwpaepedegkgiIrmdgvtRknagvsiGdkV 78
                                      +L+V+ ++q+d+grg ++id+++ eelgle gd+++ieg+  T+ a vwp++ped+g g++r+dg +R++a+v+i+d+V
  gi|313125920|ref|YP_004036190.1|  2 KLIVKPLKQKDAGRGLAAIDRAAAEELGLEGGDYIRIEGDGGTAiARVWPGYPEDRGSGVVRIDGRLRQQANVGIDDRV 80
                                      58999**********************************777544********************************** PP

                                      EEEEE- CS
                           CDC48_N 79 tVrkae 84
                                      +V++a+
  gi|313125920|ref|YP_004036190.1| 81 QVEPAD 86
                                      ***997 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   2.4e-11   7.3e-09       6     105 ..     227     320 ..     222     325 .. 0.93
   2 !   28.7   0.0   4.1e-09   1.2e-06       6     102 ..     500     592 ..     496     609 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.4e-11
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++aka+a+ +++    ++ ++   e++     + + +++++ ++    aee+   iv++DEid i
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDA----SFHTISGPEIMS----KYYGESEEQLREIFEDAEENApaIVFIDEIDSI 295
                                       6899******************96....************....********************99*********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk +++g dv r  V+  LL +++g
  gi|313125920|ref|YP_004036190.1| 296 APKrGEAGGDVERR-VVAQLLSLMDG 320
                                       ***99******997.66668888886 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 4.1e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  +    +++i +   ell     + + ++++g ++  ++a e+   +v++DEid i
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEAD----SNFISVKGPELLN----KYVGESEKGVREIFKKARENAptVVFFDEIDSI 568
                                       6889******************9....5************....999999**************999********** PP

                                       ---...---------HHHHHHHHHH CS
                             AAA_2  81 hpk...essgadvSregVqrdLLqi 102
                                       + +   +s  + vS+  V+  LL  
  gi|313125920|ref|YP_004036190.1| 569 AIErgqSSGDSGVSER-VVSQLLTE 592
                                       *998744444556655.55555544 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   9.2e-11   2.8e-08      35      99 ..     226     298 ..     216     302 .. 0.82
   2 !   25.5   0.0   3.1e-08   9.3e-06      31      94 ..     495     566 ..     472     572 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 9.2e-11
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsra 99 
                                        vll+GpPG Gkt +ak +a+e+++++++ sgP +      e + +l  ++ + ee+   ++fidei  ++++
  gi|313125920|ref|YP_004036190.1| 226 GVLLHGPPGTGKTLIAKAVANEIDASFHTISGPEImskyygESEEQLREIFEDAEENapAIVFIDEIDSIAPK 298
                                       69*******************************9944444345678999999888763369******988765 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 3.1e-08
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideih 94 
                                       ++   vllyGpPG Gkt lak +a+e ++++ +  gP l      e ++ +  ++++ +e+   v+f dei 
  gi|313125920|ref|YP_004036190.1| 495 QSAKGVLLYGPPGTGKTLLAKAVANEADSNFISVKGPELlnkyvgESEKGVREIFKKARENapTVVFFDEID 566
                                       556679*******************************87322222334456666666555422477777775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.8e-09   5.6e-07      23     139 ..     214     329 ..     194     338 .. 0.71
   2 !   22.9   0.0   3.1e-07   9.3e-05      16      63 ..     489     533 ..     487     605 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.8e-09
                            AAA_16  23 rp.........elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldea 89 
                                       +            vll+G++G+GK+ +++++++++ ++ +++++g    +     y+    +     +l +  +d++
  gi|313125920|ref|YP_004036190.1| 214 ELfkrlgidppKGVLLHGPPGTGKTLIAKAVANEIDAS-FHTISGPEIMS----KYYGeSEE-----QLREIFEDAE 280
                                       335555555559*************************9.77788877777....33222444.....5555555555 PP

                            AAA_16  90 esaeleawrekleealaavpelagaeasrllellkrllallsrderplvl 139
                                       e+a +  + +++++ +   +e+ g+ ++r+ ++l +l++ l ++++ +v+
  gi|313125920|ref|YP_004036190.1| 281 ENAPAIVFIDEIDSIAPKRGEAGGDVERRVVAQLLSLMDGLDERGE-VVV 329
                                       557778888888888888888888888***********88888677.554 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 3.1e-07
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       +e+  +++   vll+G++G+GK+ l++++++++  +   f++ k  +l
  gi|313125920|ref|YP_004036190.1| 489 YEKMDMQSAKGVLLYGPPGTGKTLLAKAVANEADSN---FISVKGPEL 533
                                       66667778899*******************999988...666666555 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.4     1e-17   3.1e-15       1      64 []     102     172 ..     102     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1e-17
                                       ..SCCCCH.HHHCCCTTEEE-TTEEEEECCT.......CCCEEEEEEEECCCCSCEEECTSCCEEESTTCCE CS
                           CDC48_2   1 ridgdema.ylkrqFlgrpvtkGdlvvfefk.......gqeiklvVvstePkgpvgitetTeielgtkpvev 64 
                                       ri g+ +  y+++++ g+pvtkG+ ++ +         +q ++ +++st+P g+v+it++Te+++++kp+e+
  gi|313125920|ref|YP_004036190.1| 102 RIGGN-VGtYIRDKLSGQPVTKGQSIQLPLGfgfmassNQSVPVKIASTQPDGTVVITDSTEVQISQKPAEE 172
                                       67888.888*****************777755566999*******************************985 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.8e-06   0.00055       1      78 [.     226     296 ..     226     346 .. 0.68
   2 !   18.7   0.1   4.4e-06    0.0014       1     134 [.     499     618 ..     499     621 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ +a+ +a  + ++++++ +++ +++    g+ e ++        ++ + a+   ++i+++DE++
  gi|313125920|ref|YP_004036190.1| 226 GVLLHGPPGTGKTLIAKAVANEIDASFHTISGPEIMSKYY--GESE-EQL------REIFEDAEenAPAIVFIDEID 293
                                       59****************************9999777532..2222.122......222222322356666666666 PP

                                       G-- CS
                             AAA_5  76 rae 78 
                                        + 
  gi|313125920|ref|YP_004036190.1| 294 SIA 296
                                       555 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.4e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ la+ +a    +++  v +++      l+ ++   ++ ++ v  +++ +ar   + ++++DE++
  gi|313125920|ref|YP_004036190.1| 499 GVLLYGPPGTGKTLLAKAVANEADSNFISVKGPE------LLNKYV--GESEKGVREIFK-KARenAPTVVFFDEID 566
                                       59*********************99999999987......666666..344455555555.5554778899999999 PP

                                       G--.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  76 rae.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                        +     ++s  s  +er ++   ++el + ++   le++ viat+n++d     +++al
  gi|313125920|ref|YP_004036190.1| 567 SIAiERGQSSGDSGVSERVVS-QLLTELDGLES---LEDVVVIATSNRPD----LIDSAL 618
                                       999888999999999999988.33333333333...45599999999998....555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   7.7e-06    0.0023       8      59 ..     227     278 ..     222     282 .. 0.80
   2 ?    4.3   0.0      0.15        45      72     128 ..     266     330 ..     259     338 .. 0.71
   3 !   19.8   0.0   2.4e-06   0.00072       4      46 ..     496     529 ..     492     559 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.7e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllre 59 
                                       ++++G++GtGKT+ ++ ++++ d+ ++++  +pe++ +++  s++ +++++++
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDA-SFHTISGPEIMsKYYGESEEQLREIFED 278
                                       689******************974.5555567777778888888888888876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.15
                            AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLv 128
                                       + s+e+l+e +e+a +++ +  ++ iDE++ +   +         +++ +L sl++  +    ++++
  gi|313125920|ref|YP_004036190.1| 266 GESEEQLREIFEDAEENAPA--IVFIDEIDSIApkRgeaggdveRRVVAQLLSLMDGLDERGEVVVI 330
                                       46788888888888888877..*********987624556667788888888888764444444445 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 2.4e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvt 46 
                                       +a+ ++++G++GtGKT+l++ +++++d         + +++v+
  gi|313125920|ref|YP_004036190.1| 496 SAKGVLLYGPPGTGKTLLAKAVANEAD---------SNFISVK 529
                                       677789*******************95.........3333332 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       4.3   1.3e+03      89     116 ..     149     176 ..     141     179 .. 0.83
   2 !   19.8   0.0   2.1e-06   0.00064       5     102 ..     227     334 ..     224     351 .. 0.82
   3 !   19.4   0.0   2.8e-06   0.00085       4      76 ..     499     568 ..     496     623 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 4.3
                            AAA_14  89 egknldvivtGSnskllskeiatslagr 116
                                       +++++ v++t S    +s++ a++  g 
  gi|313125920|ref|YP_004036190.1| 149 TQPDGTVVITDSTEVQISQKPAEEIHGA 176
                                       457899*************999998875 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.1e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT ++k +++e      s+  i+  +   k + ++e+ l++i+e ++e+   ++f+DEi  +     
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEID---ASFHTISGPEIMSKYYGESEEQLREIFEDAEENAPAIVFIDEIDSIapkrg 300
                                       7899***********99997766...99****999999988887776677777766667999*********999999 PP

                            AAA_14  77 .......pewekalkslvd..egknldvivtGSns 102
                                              +++   l sl+d  + ++++v+v G  +
  gi|313125920|ref|YP_004036190.1| 301 eaggdveRRVVAQLLSLMDglD-ERGEVVVIGATN 334
                                       9999998888888888888532.578888888766 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 2.8e-06
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                        +++ G+  +GKT l+k +++e     ++++ ++  +  +k   ++ek  ++i++k++e+  t++f+DEi  +
  gi|313125920|ref|YP_004036190.1| 499 GVLLYGPPGTGKTLLAKAVANEAD---SNFISVKGPELLNKYVGESEKGVREIFKKARENAPTVVFFDEIDSI 568
                                       58999**************98888...89998888888887777777677777777666799********887 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   6.6e-07    0.0002      51      97 ..     225     269 ..     217     279 .. 0.86
   2 !   17.3   0.0   7.2e-06    0.0022      49      98 ..     496     543 ..     489     572 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.6e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl Gp+gtGkt +a a+++e+     f ++sg e+ s     +e
  gi|313125920|ref|YP_004036190.1| 225 KGVLLHGPPGTGKTLIAKAVANEID--ASFHTISGPEIMSKYYGESE 269
                                       89**********************7..7899*******998766554 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 7.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  49 aGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev 98 
                                       + ++vLl Gp+gtGkt la a+++e      f++++g e+    v  +e 
  gi|313125920|ref|YP_004036190.1| 496 SAKGVLLYGPPGTGKTLLAKAVANEAD--SNFISVKGPELLNKYVGESEK 543
                                       679*********************965..789*****9998887777764 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.3e-06    0.0013       2      48 ..     227     275 ..     227     336 .. 0.83
   2 !   16.2   0.0   2.9e-05    0.0087       2      43 ..     500     543 ..     500     649 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.3e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdy 48 
                                       vll+G+pG+GK+  a+ ++++ +  + ++s ++++++++g+ ++++++ 
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDasFHTISGPEIMSKYYGESEEQLREI 275
                                       799****************999999999***********9877776643 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.9e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqq 43 
                                       vll G+pG+GK+ la+ ++++ +  ++ +  ++l+++++g+ ++
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEADsnFISVKGPELLNKYVGESEK 543
                                       7899***************9999999999999999999985444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00034       0.1      46      70 ..     223     247 ..     207     256 .. 0.86
   2 !   17.3   0.0   9.9e-06     0.003      45      78 ..     495     528 ..     488     575 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00034
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgve 70 
                                         ++++l Gp+G+GK+ +a a++ e
  gi|313125920|ref|YP_004036190.1| 223 PPKGVLLHGPPGTGKTLIAKAVANE 247
                                       567899***************9876 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 9.9e-06
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsv 78 
                                       +++++++l Gp+G+GK+ la a++ ea  + +sv
  gi|313125920|ref|YP_004036190.1| 495 QSAKGVLLYGPPGTGKTLLAKAVANEADSNFISV 528
                                       567899******************9986665555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00036      0.11       1      44 [.     227     272 ..     227     332 .. 0.71
   2 !   16.5   0.0     3e-05    0.0092       1     105 [.     500     636 ..     500     639 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00036
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.gvnlrdvakenglllevdpe 44 
                                       +ll G+pG+GKt +ak+++++  ++ +++++  +  +++ +++++ 
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIdASfHTISGPEIMSKYYGESEEQL 272
                                       7899**************9996443655555555555444444444 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe.........ald 47 
                                       +ll G+pG+GKt lak+++++   +                    ++++ + a+en +   +++e         + +
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEAdSNfisvkgpellnkyvgesekgVREIFKKARENAPTVVFFDEidsiaiergQSS 576
                                       799***************99874336888888888888999999888888888888888888888888888888888 PP

                            AAA_18  48 eskrldedkldklldaleenss......aleegknlvidghlaeleseaakdikkvvLtaspee 105
                                           + e ++ +ll++l++  s        +++ + +id+ l  +      d++ +++ +++ee
  gi|313125920|ref|YP_004036190.1| 577 GDSGVSERVVSQLLTELDGLESledvvvIATSNRPDLIDSALLRPGRL---DRH-IHVPVPDEE 636
                                       888888888888888888887755555544444444555444333333...344.666666665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00011     0.033      33      62 ..     224     252 ..     213     295 .. 0.84
   2 !   15.1   0.0     4e-05     0.012      30      63 ..     494     526 ..     487     531 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkeky 62 
                                        k vll Gp GtGKt+i+k + +++d  ++
  gi|313125920|ref|YP_004036190.1| 224 PKGVLLHGPPGTGKTLIAKAVANEIDA-SF 252
                                       5789*******************9994.44 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4e-05
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                                       +++ k vll+Gp GtGKt+++k + ++ d ++++
  gi|313125920|ref|YP_004036190.1| 494 MQSAKGVLLYGPPGTGKTLLAKAVANEAD-SNFI 526
                                       788999******************99999.5554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   9.2e-05     0.028       1      36 [.     227     262 ..     227     296 .. 0.79
   2 !   14.3   0.0   0.00014     0.041       1      27 [.     500     529 ..     500     610 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.2e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++l+Gp+g+GK+++ak +a+++  ++ +++ ++++s
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDASFHTISGPEIMS 262
                                       689******************998886666666544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00014
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...k 27 
                                       ++lyGp+g+GK++lak +a++  +++   k
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEADSNFisvK 529
                                       689**************9988876665552 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.4e-05     0.017       2      31 ..     227     256 ..     226     301 .. 0.88
   2 !   13.7   0.0   0.00014     0.043       2     128 ..     500     626 ..     499     629 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.4e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       vll+g PG++ktl++ka+a+ +d++f+ i 
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDASFHTIS 256
                                       89************************9885 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00014
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGte..vfeekekefefkkGpvfanllladeinrapp 76 
                                       vll g PG++ktll+ka+a+  d +f  ++  p+ll   +  +e  v e  +k  e  +  vf + + +  i+r ++
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEADSNFISVK-GPELLNKYVGESEkgVREIFKKARENAPTVVFFDEIDSIAIERGQS 575
                                       7999**********************9997.6889877664433112222233344445555656555556666666 PP

                             AAA_3  77 ktqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldr 128
                                         +s + e +  + +t  +   +l+   +v+at n  +   +  l   +ldr
  gi|313125920|ref|YP_004036190.1| 576 SGDSGVSERVVSQLLTELDGLESLE-DVVVIATSNRPDLIDSALLRPGRLDR 626
                                       6666666666666666666556665.46788888876666666666666666 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0074       2.3      53      81 ..     224     252 ..     187     335 .. 0.77
   2 !   19.9   0.0   1.1e-06   0.00034      47     157 ..     491     616 ..     446     630 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0074
                            DUF815  53 annvLLwGarGtGKSslvkallneyaeeg 81 
                                        + vLL G  GtGK  + ka+ ne+ ++ 
  gi|313125920|ref|YP_004036190.1| 224 PKGVLLHGPPGTGKTLIAKAVANEIDASF 252
                                       5779*******************998765 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.1e-06
                            DUF815  47 fleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlke....lpklvellrerperfilf..vDD 115
                                        ++ ++a+ vLL+G  GtGK  l ka+ ne+ ++   ++  e+ ++ + e    + +++++ re++  ++ f  +D 
  gi|313125920|ref|YP_004036190.1| 491 KMDMQSAKGVLLYGPPGTGKTLLAKAVANEADSNFisVKGPELLNKYVGEsekgVREIFKKARENAPTVVFFdeIDS 567
                                       466789*************************9998444445666666655111155555555555555444455566 PP

                            DUF815 116 LsFeeeeeey.........ksLksvLeGsleakpenvliyaTsNrRhLlpe 157
                                       ++ e+++++           +L + L+G l ++ e+v++ aTsNr +L+  
  gi|313125920|ref|YP_004036190.1| 568 IAIERGQSSGdsgvservvSQLLTELDG-L-ESLEDVVVIATSNRPDLIDS 616
                                       7888877665556666555677778887.3.456889999*****999976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.024       7.4      36      53 ..     227     244 ..     214     249 .. 0.88
   2 ?    7.0   0.0     0.013       3.9     127     177 ..     269     319 ..     252     332 .. 0.87
   3 !    9.2   0.0    0.0028      0.85      36      52 ..     500     516 ..     472     521 .. 0.81
   4 ?   -0.0   0.0       1.8   5.5e+02     129     172 ..     544     589 ..     533     604 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.024
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll G+pgtGKt +a  +
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAV 244
                                       699*********998665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                       +++++++ +++ee + ++ v iD ++++ +   ++  dv +++v++l ++ +
  gi|313125920|ref|YP_004036190.1| 269 EEQLREIFEDAEE-NAPAIVFIDEIDSIAPKRGEAGGDVeRRVVAQLLSLMD 319
                                       4678899999999.77***************999999999******988865 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0028
                            AAA_25  36 allaGapgtGKttlald 52 
                                       +ll+G+pgtGKt la  
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKA 516
                                       79***********9965 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.8
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralgg..densnsdv.galveal 172
                                        v+++ ++++e + + +v +D ++++     ++  +s v +++v++l
  gi|313125920|ref|YP_004036190.1| 544 GVREIFKKARE-NAPTVVFFDEIDSIAIErgQSSGDSGVsERVVSQL 589
                                       57888999999.77**********95544257777777778888776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00027     0.081      25      43 ..     227     245 ..     224     254 .. 0.89
   2 !   13.5   0.0   0.00012     0.036      25      42 ..     500     517 ..     493     521 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00027
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt++ak+++
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVA 245
                                       79*************9975 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00012
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll+GppG+GKt+lak++
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAV 517
                                       89*************987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00023      0.07       2      49 ..     227     279 ..     226     293 .. 0.75
   2 !   12.4   0.0   0.00047      0.14       2      37 ..     500     540 ..     499     572 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00023
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpwv 49 
                                       + + G+++tGKT +++a a++    + ++  pE++ +++ e  ++ +++ +++
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEidaSFHTIsgPEIMSKYYGESEEQLREIFEDA 279
                                       6799***************8876655555688888888877766666555544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00047
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareilee 37 
                                       + + G+++tGKT l++a a++   ++  v  pE   +++ e
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEadsNFISVkgPELLNKYVGE 540
                                       6799***************7656644444478877777754 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00064      0.19      19      59 ..     224     264 ..     199     275 .. 0.75
   2 !   13.7   0.0   0.00016     0.047      18      61 ..     496     539 ..     471     549 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00064
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                        + +lL+G+ G+GKT +++++a++++ +  +++ P   ++++Y
  gi|313125920|ref|YP_004036190.1| 224 PKGVLLHGPPGTGKTLIAKAVANEIDASfhTISGP--EIMSKY 264
                                       3459********************99887667766..455555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00016
                                       HTEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE CS
                              TsaE  18 lgdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYel 61 
                                        ++ +lL+G+ G+GKT l++++a++ + +  +vk P   l+++Y  
  gi|313125920|ref|YP_004036190.1| 496 SAKGVLLYGPPGTGKTLLAKAVANEADSNfiSVKGP--ELLNKYVG 539
                                       24569********************99988888888..57777755 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0012      0.35      23      46 ..     225     248 ..     214     299 .. 0.89
   2 !   12.4   0.0   0.00032     0.097      20      56 ..     495     528 ..     484     574 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0012
                                       S-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheas 46 
                                         vl++G  GtGK+l+a+a+ ++ 
  gi|313125920|ref|YP_004036190.1| 225 KGVLLHGPPGTGKTLIAKAVANEI 248
                                       579****************98765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00032
                                       TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfvav 56 
                                       ++   vl+ G  GtGK+lla+a+ ++    +++f++v
  gi|313125920|ref|YP_004036190.1| 495 QSAKGVLLYGPPGTGKTLLAKAVANEA---DSNFISV 528
                                       55678*****************97654...4556655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0011      0.33      23      45 ..     227     249 ..     214     263 .. 0.84
   2 ?   -2.8   0.0       9.4   2.9e+03      50      91 ..     348     390 ..     344     433 .. 0.61
   3 !   11.2   0.0    0.0005      0.15       8      45 ..     488     522 ..     484     528 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                                       EEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                       v l+G +G GKt +ak + n+ d
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEID 249
                                       789***************99954 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.4
                                       CBTEEEEEEEESXXHHHHHHHXXHHHHHCCC.TTSSSS-STTS CS
                            NB-ARC  50 rFdsvawvvvsktdkseeiletilkeLslse.ddleekeeves 91 
                                       rFd+ + + v ++   +eil+   +++ ++e  dl+e +e  +
  gi|313125920|ref|YP_004036190.1| 348 RFDREIEIGVPDKEGRKEILQVHTRNMPTAEgVDLDEYAEITH 390
                                       6676677777777777777766666665443134555555444 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0005
                                       HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC   8 viekLlekdelqslvvalvGmgGvGKttlakqilnksd 45 
                                       v ek++ +++ +   v l+G +G GKt lak + n+ d
  gi|313125920|ref|YP_004036190.1| 488 VYEKMD-MQSAK--GVLLYGPPGTGKTLLAKAVANEAD 522
                                       556666.56666..799****************99854 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0027      0.83       5      76 ..     227     294 ..     224     301 .. 0.65
   2 !   12.8   0.0   0.00024     0.073       3      22 ..     498     517 ..     496     569 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0027
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie...swedfldevvelaaeladyktlviDtide 76 
                                       +l+ Gp+g+GKT +ak          ++++++ + + ++ +     s e++++ ++  +++ +   +++iD id 
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAV-----ANEIDASFHTISGPEIMSKYygeSEEQLREIFEDAEENAP--AIVFIDEIDS 294
                                       799***********9988.....4456777777776666644355444444444444443333..6777777765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00024
                            AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                       + +l+yGp+g+GKT lak  
  gi|313125920|ref|YP_004036190.1| 498 KGVLLYGPPGTGKTLLAKAV 517
                                       5689*************987 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00026      0.08       4      26 ..     227     251 ..     224     298 .. 0.77
   2 !    9.6   0.0    0.0016      0.48       4      37 ..     500     526 ..     498     566 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                           DUF2075   4 vlVtGvaGtGKtvvllnllael..e 26 
                                       vl +G +GtGKt+++ ++++e+  +
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIdaS 251
                                       6889*****************9430 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0016
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavyl 37 
                                       vl  G +GtGKt+++ ++++e+        ++++
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEA-------DSNFI 526
                                       5778***************999.......33344 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0028      0.86       8      67 ..     221     278 ..     217     328 .. 0.76
   2 !   12.1   0.0   0.00067       0.2       6      71 ..     492     555 ..     490     609 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0028
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       + + + v + G+ G+GK+ ++k++a++ +    +i   g ++ ++   +++++++ ++++
  gi|313125920|ref|YP_004036190.1| 221 IDPPKGVLLHGPPGTGKTLIAKAVANEIDASFHTI--SGPEIMSKYYGESEEQLREIFED 278
                                       66667799*******************99888777..44444444455555555555544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00067
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlf 71 
                                       ++++  + v + G+ G+GK+ L+k++a++ +  +  i ++g +l ++   +++k ++ ++++++ +
  gi|313125920|ref|YP_004036190.1| 492 MDMQSAKGVLLYGPPGTGKTLLAKAVANEAD--SNFISVKGPELLNKYVGESEKGVREIFKKAREN 555
                                       5677788899*****************9986..688888888888888888888888888874444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00084      0.26      21      45 ..     227     251 ..     214     259 .. 0.83
   2 !    9.8   0.0     0.002      0.61      16      42 ..     495     521 ..     487     530 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00084
                            AAA_30  21 avltGpAGtGKttalkalreaweaa 45 
                                       ++l+Gp+GtGKt + ka+++ ++a+
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDAS 251
                                       689**************98877665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.002
                            AAA_30  16 sgdrvavltGpAGtGKttalkalreaw 42 
                                       ++++ ++l Gp+GtGKt + ka+++ +
  gi|313125920|ref|YP_004036190.1| 495 QSAKGVLLYGPPGTGKTLLAKAVANEA 521
                                       455578999************997654 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0042       1.3      14      37 ..     219     242 ..     191     247 .. 0.80
   2 ?    1.0   0.0      0.74   2.2e+02     109     154 ..     270     321 ..     247     324 .. 0.60
   3 !    9.0   0.0    0.0026      0.79      19      37 ..     497     515 ..     490     527 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0042
                            ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                        Gi   + vl+ G pGtGKt++a+
  gi|313125920|ref|YP_004036190.1| 219 LGIDPPKGVLLHGPPGTGKTLIAK 242
                                       577777889************997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.74
                            ATPase 109 eelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                       e+l+e+ ++ ++     v iD i+++     e+  +v R+ + ql++ + +l
  gi|313125920|ref|YP_004036190.1| 270 EQLREIFEDAEEnapAIVFIDEIDSIapkRGEAGGDVERRVVAQLLSLMDGL 321
                                       3344444333332224556666666532156667788999999999999765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0026
                            ATPase  19 grvvlitGepGtGKtifal 37 
                                       ++ vl++G pGtGKt++a+
  gi|313125920|ref|YP_004036190.1| 497 AKGVLLYGPPGTGKTLLAK 515
                                       6679*************97 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00068      0.21      20      41 ..     227     248 ..     208     282 .. 0.80
   2 !    9.7   0.0    0.0022      0.68      19      41 ..     499     521 ..     488     560 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00068
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                       +l++GPPGtgKT    ++ +++
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEI 248
                                       79**********7776666666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0022
                            AAA_11  19 itliqGPPGtgKTktivellsql 41 
                                        +l+ GPPGtgKT    ++ +++
  gi|313125920|ref|YP_004036190.1| 499 GVLLYGPPGTGKTLLAKAVANEA 521
                                       489**********8887777776 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0031      0.95      22      41 ..     227     246 ..     220     255 .. 0.86
   2 !   11.7   0.0   0.00044      0.13      17      42 ..     495     520 ..     486     527 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0031
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   Gp GtGKt++a a+a 
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVAN 246
                                       6788***********99985 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00044
                                       HH-SEEEEE--TTSSTTHHHHHHHHH CS
                              PhoH  17 kkndivfaiGpaGtGKtylavalave 42 
                                       ++ + v   Gp GtGKt+la a+a e
  gi|313125920|ref|YP_004036190.1| 495 QSAKGVLLYGPPGTGKTLLAKAVANE 520
                                       466778999************99966 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0025      0.76     117     138 ..     227     248 ..     221     253 .. 0.90
   2 !   10.0   0.0    0.0011      0.33     117     136 ..     500     519 ..     491     524 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0025
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                       v+++Gp+ tGkt +a+a a+ +
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEI 248
                                       899***************9876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ tGkt la+a a+
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVAN 519
                                       89***************998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0     0.008       2.4       3      24 ..     227     248 ..     225     253 .. 0.89
   2 ?   -1.0   0.0       4.8   1.5e+03      88     111 ..     290     316 ..     259     339 .. 0.55
   3 !    9.5   0.0    0.0028      0.84       3      25 ..     500     522 ..     498     527 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.008
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l+G++G GKT  ++ +a ++
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEI 248
                                       79***************99887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.8
                                       E-STT-SS-TCH.............HHH CS
                             NACHT  88 DglDelvtdlgq....kekqpvrtlLse 111
                                       D +D ++ + g+     e++ v +lL +
  gi|313125920|ref|YP_004036190.1| 290 DEIDSIAPKRGEaggdVERRVVAQLL-S 316
                                       55555555554444422222222222.2 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0028
                                       EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                       v+l G++G GKT L++ +a ++ 
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEAD 522
                                       799**************998865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0021      0.64      15      41 ..     223     249 ..     214     257 .. 0.88
   2 !    8.7   0.0    0.0032      0.98      17      51 ..     498     530 ..     488     543 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdele 41 
                                        Pk +ll G pG GK+ +a+++++e++
  gi|313125920|ref|YP_004036190.1| 223 PPKGVLLHGPPGTGKTLIAKAVANEID 249
                                       5999*******************9985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0032
                        Zeta_toxin  17 klillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       k +ll G pG GK+ la+++++e   ++n++ +++
  gi|313125920|ref|YP_004036190.1| 498 KGVLLYGPPGTGKTLLAKAVANEA--DSNFISVKG 530
                                       669999*****************8..899988865 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0082       2.5       2      32 ..     227     257 ..     226     271 .. 0.87
   2 !    9.1   0.0    0.0037       1.1       2      32 ..     500     530 ..     499     569 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0082
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + k v+++++ s  +++G
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDASFHTISG 257
                                       6789*****************9887666666 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0037
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+++ +s+ ++v+G
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEADSNFISVKG 530
                                       6788******************999999998 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.027       8.1      37      64 ..     227     254 ..     223     379 .. 0.84
   2 !   11.3   0.0   0.00072      0.22      33      66 ..     496     529 ..     487     678 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.027
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenape 64 
                                       ++++g+ G Gkt + ka++ne+ ++++ 
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDASFHT 254
                                       79*******************9988765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00072
                                       .S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                          Bac_DnaA  33 kynPlfiygevGlGktHLlkaignevlenapelr 66 
                                       +   +++yg+ G Gkt L ka++ne+ +n+ + +
  gi|313125920|ref|YP_004036190.1| 496 SAKGVLLYGPPGTGKTLLAKAVANEADSNFISVK 529
                                       56679********************999876544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2    0.0067         2      12      34 ..     226     248 ..     222     286 .. 0.83
   2 !    8.8   0.0    0.0062       1.9      10      33 ..     497     520 ..     491     572 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0067
                            AAA_19  12 vllvtaGpGtGKTrvlkhivall 34 
                                        +l+ ++pGtGKT + k++ +++
  gi|313125920|ref|YP_004036190.1| 226 GVLLHGPPGTGKTLIAKAVANEI 248
                                       5899*********9998877665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0062
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhival 33 
                                       +k +l+ ++pGtGKT + k++ ++
  gi|313125920|ref|YP_004036190.1| 497 AKGVLLYGPPGTGKTLLAKAVANE 520
                                       57799**********988776655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.015       4.6       2      34 ..     231     265 ..     230     306 .. 0.71
   2 !    9.3   0.0    0.0048       1.5       1      34 [.     503     538 ..     503     583 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.015
                                       E-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklveky..gfthlsaGdllreea 34 
                                       G+PG GK+ +++ ++ ++   f+ +s  +++ +  
  gi|313125920|ref|YP_004036190.1| 231 GPPGTGKTLIAKAVANEIdaSFHTISGPEIMSKYY 265
                                       9**************99854677777666665544 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0048
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH..HHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa..Gdllreea 34 
                                       +G+PG GK+ +++ ++ + +  ++s    +ll + +
  gi|313125920|ref|YP_004036190.1| 503 YGPPGTGKTLLAKAVANEADSNFISVkgPELLNKYV 538
                                       7***************99976666644144444444 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.41   1.2e+02      18      44 ..     422     448 ..     416     452 .. 0.87
   2 !   13.6   0.0   0.00017     0.051      22      55 ..     698     731 ..     675     736 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.41
                            Vps4_C  18 dipsdkllePpvtlkDflkalkkarpt 44 
                                       +i++d l   +v+ +Df++a+k   p+
  gi|313125920|ref|YP_004036190.1| 422 EIDTDVLESLEVREDDFKDAMKGIEPS 448
                                       6888888888************99987 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00017
                            Vps4_C  22 dkllePpvtlkDflkalkkarptVskeDLekhee 55 
                                       + + +  vt+++f++al ++ p+V++e  +++ee
  gi|313125920|ref|YP_004036190.1| 698 ESIGNVRVTMDHFEAALDEVNPSVTQETRRRYEE 731
                                       5566678*******************98888887 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0079       2.4      24      80 ..     227     294 ..     222     299 .. 0.57
   2 !    8.5   0.0    0.0068       2.1      19      46 ..     495     522 ..     490     569 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0079
                                       EEEEEETT--HHHHHHCC--T........TS-EE--SSTTHHHH-HHHHHHHT...TTSEEEEEE-TT CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhkn........sgpwleifvverlaklpldlleqa...kggtLylkdiad 80 
                                       v+l G++G+gk+l+A++ +++        sgp +  + + ++ ++  +++e a    +++ ++ +i++
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEidasfhtiSGPEIMSKYYGESEEQLREIFEDAeenAPAIVFIDEIDS 294
                                       9***************9876511110000223222222222333456666666444566777777766 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0068
                                       T-SS-EEEEEETT--HHHHHHCC--TTS CS
                   Sigma54_activ_2  19 qsklpvfltGekGsgkelvArlLhknsg 46 
                                       qs   v+l G++G+gk+l A++ ++++ 
  gi|313125920|ref|YP_004036190.1| 495 QSAKGVLLYGPPGTGKTLLAKAVANEAD 522
                                       66778*****************998765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.11        34      21      68 ..     225     268 ..     214     330 .. 0.60
   2 !   11.4   0.0   0.00072      0.22      11      49 ..     488     525 ..     483     574 .. 0.76
   3 ?   -1.4   0.0       5.7   1.7e+03     111     131 ..     546     569 ..     526     610 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68 
                                       + +++ Gp g GKt + k ++++  d +   +  i+  e+ ++++ e+
  gi|313125920|ref|YP_004036190.1| 225 KGVLLHGPPGTGKTLIAKAVANEI-DAS---FHTISGPEIMSKYYGES 268
                                       557788999999997777777766.333...44455555555555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00072
                          ATPase_2  11 leeilerepneiyfiYGpegsGKtaLlkeiienledkdk 49 
                                       + e +++++++ +++YGp g GKt L k ++++ + +++
  gi|313125920|ref|YP_004036190.1| 488 VYEKMDMQSAKGVLLYGPPGTGKTLLAKAVANEAD-SNF 525
                                       6677788889999***********99999998874.344 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.7
                          ATPase_2 111 ekikkkgkk...iiiiiDelqkli 131
                                       ++i kk+++    ++++De+  + 
  gi|313125920|ref|YP_004036190.1| 546 REIFKKAREnapTVVFFDEIDSIA 569
                                       333334343455677778777665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0     0.009       2.7      22      53 ..     222     253 ..     196     256 .. 0.80
   2 ?    6.9   0.0     0.019       5.9      17      51 ..     490     524 ..     467     565 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.009
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgk 53 
                                       +  k +l++ + GtGKTl+a +++ ++  +++
  gi|313125920|ref|YP_004036190.1| 222 DPPKGVLLHGPPGTGKTLIAKAVANEIDASFH 253
                                       5678899*************999988877665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.019
                                       ......TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                            ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklierllkk 51 
                                       ek++ +  k +l+  + GtGKTl+a +++ +  ++
  gi|313125920|ref|YP_004036190.1| 490 EKMDMQSAKGVLLYGPPGTGKTLLAKAVANEADSN 524
                                       455548888999************98888777664 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0054       1.6      78     156 ..     161     251 ..     136     259 .. 0.62
   2 ?    5.3   0.0     0.028       8.6     127     155 ..     495     523 ..     465     531 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0054
                             T2SSE  78 vrlrvvllPvvagealviR.kksakeltlddlgaeealkekiaevlrkavre...........rglilvsGgTgsGK 142
                                       ++++++  P+ + + +  R  ++  ++t++d+g   +  e+++e+++ ++r+            + +l+ G+ g+GK
  gi|313125920|ref|YP_004036190.1| 161 TEVQISQKPAEEIHGAEGRdTSEGPSVTYEDIGGLDRELEQVREMIELPMRHpelfkrlgidpPKGVLLHGPPGTGK 237
                                       55555555555555555554444555566666665555555555555554431111111111135589********* PP

                             T2SSE 143 ttllyallkeinks 156
                                       t ++ a+ +ei++s
  gi|313125920|ref|YP_004036190.1| 238 TLIAKAVANEIDAS 251
                                       **********9987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                             T2SSE 127 rerglilvsGgTgsGKttllyallkeink 155
                                       ++ + +l+ G+ g+GKt l+ a+ +e ++
  gi|313125920|ref|YP_004036190.1| 495 QSAKGVLLYGPPGTGKTLLAKAVANEADS 523
                                       55678999************999888765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.033        10      26      57 ..     215     246 ..     203     261 .. 0.82
   2 ?   -0.1   0.0       1.8   5.3e+02     117     174 ..     281     344 ..     258     353 .. 0.63
   3 ?    5.3   0.0     0.038        11      27      58 ..     489     520 ..     472     530 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.033
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFar 57 
                                       L+++   + ++ +ll+G++ +GKt i++  a+
  gi|313125920|ref|YP_004036190.1| 215 LFKRLGIDPPKGVLLHGPPGTGKTLIAKAVAN 246
                                       566666667789**************998766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                              TniB 117 elkvrvLiiDEihnll.....agsarkqreflnalksLgnel..kipivlvGteealralrtDpq 174
                                       e  + ++ iDEi+++      ag  +  r+++++l sL++ l  +  +v++G ++ ++a++    
  gi|313125920|ref|YP_004036190.1| 281 ENAPAIVFIDEIDSIApkrgeAG-GDVERRVVAQLLSLMDGLdeRGEVVVIGATNRVDAIDPALR 344
                                       445678999***99973322122.23456677777777777622457888888888888865555 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.038
                              TniB  27 leypkrkrmpnlllvGdsnnGKtmivekFarl 58 
                                       +e+ + +  + +ll+G++ +GKt +++  a++
  gi|313125920|ref|YP_004036190.1| 489 YEKMDMQSAKGVLLYGPPGTGKTLLAKAVANE 520
                                       555556667899************99987765 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.015       4.6      56      79 ..     218     241 ..     193     255 .. 0.81
   2 ?    4.6   0.0     0.041        13      57      80 ..     492     515 ..     471     525 .. 0.85
   3 ?   -0.6   0.0       1.5   4.6e+02     157     168 ..     600     611 ..     582     736 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                       AFG1_ATPase  56 rksvepvrglYlwGgvGrGKtylm 79 
                                       r    p++g+ l+G+ G GKt + 
  gi|313125920|ref|YP_004036190.1| 218 RLGIDPPKGVLLHGPPGTGKTLIA 241
                                       34678****************875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.041
                       AFG1_ATPase  57 ksvepvrglYlwGgvGrGKtylmd 80 
                                        + ++++g+ l+G+ G GKt l  
  gi|313125920|ref|YP_004036190.1| 492 MDMQSAKGVLLYGPPGTGKTLLAK 515
                                       478899**************9865 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.5
                       AFG1_ATPase 157 rgvtlvaTSNia 168
                                         v+++aTSN++
  gi|313125920|ref|YP_004036190.1| 600 EDVVVIATSNRP 611
                                       579999**9985 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.18        55       4      32 ..     226     255 ..     224     260 .. 0.85
   2 ?    2.3   0.0       0.4   1.2e+02      75      95 ..     261     281 ..     255     299 .. 0.78
   3 ?    4.1   0.0      0.11        34       3      30 ..     498     525 ..     496     532 .. 0.87
   4 ?   -1.4   0.0       5.2   1.6e+03      77      95 ..     536     554 ..     532     567 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                                       EEEEESTTTSSHHHHHHHHHHHSTTTEE.E CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg.v 32 
                                        v l gp g+Gk  + ka+ +e   +f  +
  gi|313125920|ref|YP_004036190.1| 226 GVLLHGPPGTGKTLIAKAVANEIDASFHtI 255
                                       68899**************99999998535 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.4
                                       TTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                        +++yg+s e+ +e++e + +
  gi|313125920|ref|YP_004036190.1| 261 MSKYYGESEEQLREIFEDAEE 281
                                       679*************99876 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.11
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       + v l gp g+Gk  l ka+ +e  ++f
  gi|313125920|ref|YP_004036190.1| 498 KGVLLYGPPGTGKTLLAKAVANEADSNF 525
                                       7799****************99999888 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 5.2
                                       EEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  77 nlygtsveaieevlekgki 95 
                                       ++ g+s + ++e+++k+++
  gi|313125920|ref|YP_004036190.1| 536 KYVGESEKGVREIFKKARE 554
                                       6889***********9987 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.016       4.9       3      26 ..     229     252 ..     227     257 .. 0.89
   2 ?    4.8   0.0     0.068        21       4      28 ..     503     527 ..     500     529 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                                       EE-STTSSHHHHHHHHHHHHT-EE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglky 26 
                                       + GP g+GK  +a+a+a+++++++
  gi|313125920|ref|YP_004036190.1| 229 LHGPPGTGKTLIAKAVANEIDASF 252
                                       68*****************99876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.068
                                       E-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                                        GP g+GK  +a+a+a++ + ++++
  gi|313125920|ref|YP_004036190.1| 503 YGPPGTGKTLLAKAVANEADSNFIS 527
                                       6****************99988875 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.015       4.5       4      33 ..     227     256 ..     225     287 .. 0.86
   2 ?    4.9   0.0     0.067        20       4      33 ..     500     529 ..     497     558 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.015
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       +lL+G + +GK+ +a+a+ + +d+++  + 
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDASFHTIS 256
                                       89********************99998775 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.067
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       +lL G + +GK+ la+a+ + +d  ++ ++
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEADSNFISVK 529
                                       9**********************9999876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.048        15      48      81 ..     227     260 ..     215     296 .. 0.78
   2 ?    5.8   0.0     0.039        12      43     107 ..     495     560 ..     473     578 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.048
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvs 81 
                                       +L+ GP+G gk+ + k ++ e   +++  + p  
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDASFHTISGPEI 260
                                       6899***************999988887776654 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.039
                             Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqie 107
                                       +  + +L+ GP+G gk+   k ++ e   +++    p +l++     ++ ++ +++k  +  + + 
  gi|313125920|ref|YP_004036190.1| 495 QSAKGVLLYGPPGTGKTLLAKAVANEADSNFISVKGPELLNKYVGeSEKGVREIFKKARENAPTVV 560
                                       344557899**************9999988888877776654332255555555555555555555 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00046      0.14      28      64 ..      15      50 ..       6      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00046
                                      SS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEE CS
                   Molydop_binding 28 epevveinpedAaalGikdGdlVevesrrGsvevrak 64
                                      ++  + i  + A++lG++ Gd +++e + G++ +r++
  gi|313125920|ref|YP_004036190.1| 15 RG-LAAIDRAAAEELGLEGGDYIRIEGDGGTAIARVW 50
                                      44.788999***********************99987 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.012       3.6      57      77 ..     228     248 ..     221     255 .. 0.88
   2 ?    3.3   0.0      0.27        82      56      76 ..     500     520 ..     488     539 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.012
                                       EEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  57 sfhGwtGtGknfvaeiiaenl 77 
                                        +hG +GtGk  +a+ +a+++
  gi|313125920|ref|YP_004036190.1| 228 LLHGPPGTGKTLIAKAVANEI 248
                                       58***************9976 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.27
                                       EEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaen 76 
                                       + ++G +GtGk  +a+ +a++
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANE 520
                                       4579*************9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.084        25      21      38 ..     224     240 ..     215     247 .. 0.75
   2 ?    5.9   0.0     0.034        10      17      39 ..     492     514 ..     485     519 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.084
                            AAA_29  21 lkgatlltGpsGsGKSTl 38 
                                       +kg +ll Gp G+GK+ +
  gi|313125920|ref|YP_004036190.1| 224 PKG-VLLHGPPGTGKTLI 240
                                       355.9**********866 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.034
                            AAA_29  17 ieidlkgatlltGpsGsGKSTll 39 
                                       ++++ +  +ll Gp G+GK+ l 
  gi|313125920|ref|YP_004036190.1| 492 MDMQSAKGVLLYGPPGTGKTLLA 514
                                       44544446***********8765 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.06        18       1      23 [.     233     255 ..     233     283 .. 0.71
   2 ?    5.3   0.0     0.063        19       1      43 [.     506     553 ..     506     557 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.06
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k++A++++ +f  +
  gi|313125920|ref|YP_004036190.1| 233 PGTGKTLIAKAVANEIDASFHTI 255
                                       69*************99998765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.063
                                       TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHHT...S-HHHHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrtg...ksiaeifeeeg 43 
                                       +G+GK+ ++k++A++ + +fi +   el+ k +g   k ++eif++  
  gi|313125920|ref|YP_004036190.1| 506 PGTGKTLLAKAVANEADSNFISVkgPELLNKYVGeseKGVREIFKKAR 553
                                       69******************9873345677666633344677777655 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.35   1.1e+02      60      87 ..     227     254 ..     223     259 .. 0.87
   2 ?    6.8   0.0      0.01       3.1      50      90 ..     490     529 ..     468     534 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.35
                                       EEEEESSTSTHHHHHHHHHHHSSSEEEE CS
                               MCM  60 vllvgdpgtaKsqlLkyveklapravyt 87 
                                       vll g pgt+K+ + k+v++ ++ +  t
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDASFHT 254
                                       89****************9988777655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
                                       SSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESS CS
                               MCM  50 dktklrgdinvllvgdpgtaKsqlLkyveklapravytsgk 90 
                                       +k+ +++   vll g pgt+K+ l k+v++ a  ++++s k
  gi|313125920|ref|YP_004036190.1| 490 EKMDMQSAKGVLLYGPPGTGKTLLAKAVANEA-DSNFISVK 529
                                       5678889999************9999999655.55666666 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       9.1   2.8e+03      23      46 ..     227     250 ..     221     270 .. 0.84
   2 ?    5.0   0.0     0.041        12     157     189 ..     268     299 ..     251     302 .. 0.75
   3 ?    2.7   0.0      0.19        59      19      48 ..     496     525 ..     487     630 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.1
                        KAP_NTPase  23 vgLygkWGsGKssllnkledelke 46 
                                       v L g+ G+GK+ + + + +e++ 
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDA 250
                                       7889999*****999988888765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.041
                        KAP_NTPase 157 veelladmektLdalqkrlVvviDdLDrcetee 189
                                        ee l ++++  ++ + + +v+iD++D++ +++
  gi|313125920|ref|YP_004036190.1| 268 SEEQLREIFEDAEE-NAPAIVFIDEIDSIAPKR 299
                                       44455555555555.99***********98876 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.19
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledelkefa 48 
                                           v Lyg+ G+GK+ l + + +e +++ 
  gi|313125920|ref|YP_004036190.1| 496 SAKGVLLYGPPGTGKTLLAKAVANEADSNF 525
                                       555688999999999999999888887764 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.35   1.1e+02      23      48 ..     225     250 ..     216     255 .. 0.85
   2 ?    5.9   0.0      0.02       5.9      12      46 ..     487     521 ..     484     528 .. 0.85
   3 ?   -2.4   0.0       6.8   2.1e+03     281     327 ..     653     695 ..     637     702 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.35
                                       S-EEEEESTTSSCHHHHHHHHHHCHC CS
                              PIF1  23 klfFvtGsgGtgKtflwkallkklrs 48 
                                       k + ++G  GtgKt + ka+ + + +
  gi|313125920|ref|YP_004036190.1| 225 KGVLLHGPPGTGKTLIAKAVANEIDA 250
                                       556789*************9999865 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                                       HH......HCTS-EEEEESTTSSCHHHHHHHHHHC CS
                              PIF1  12 aiieavlnekgklfFvtGsgGtgKtflwkallkkl 46 
                                       +++e +  +++k + ++G  GtgKt l ka+ +  
  gi|313125920|ref|YP_004036190.1| 487 EVYEKMDMQSAKGVLLYGPPGTGKTLLAKAVANEA 521
                                       67888889999999**************9998765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.8
                                       HHHHHCCSSS--EEEE-EEE...........ESBSSCHHCHHHCCTT CS
                              PIF1 281 NnyvlsklpgeekeylssDsisksseeieeldalypteflnslkang 327
                                        +  l++l  + + y+ +D     +  ++e+ +  + ef ns++ + 
  gi|313125920|ref|YP_004036190.1| 653 DDVDLDQLARKTEGYVGADI----EAVCREASMAASREFINSVEPEE 695
                                       56668899999999999998....55566678999999999998765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.12        37       2      70 ..     228     291 ..     227     296 .. 0.63
   2 ?    5.2   0.0     0.051        15       5      71 ..     504     565 ..     500     570 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.12
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                       + hG pG GK+ + + ++++   ++ +++   e+ ++   +++ +  + ++++++++       i+++DE
  gi|313125920|ref|YP_004036190.1| 228 LLHGPPGTGKTLIAKAVANEIdASFHTISG-PEIMSKYYGESEEQLREIFEDAEENAP-----AIVFIDE 291
                                       68*********9999999885544444444.455555545555555555555555543.....2566666 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.051
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ l + ++++   ++ +++   ell++ + ++++   + ++++ +++       ++++DE+
  gi|313125920|ref|YP_004036190.1| 504 GPPGTGKTLLAKAVANEAdSNFISVKG-PELLNKYVGESEKGVREIFKKARENAP-----TVVFFDEI 565
                                       78***************9966666666.899999998888877777777777664.....38999997 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1     0.011       3.3       2      30 ..     227     255 ..     226     262 .. 0.91
   2 ?    1.4   0.0       1.1   3.4e+02       2      30 ..     500     528 ..     499     530 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.011
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++hG+P +GKt +a ++a + +a++ ti
  gi|313125920|ref|YP_004036190.1| 227 VLLHGPPGTGKTLIAKAVANEIDASFHTI 255
                                       689******************99998887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.1
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++ G+P +GKt  a ++a + +  ++++
  gi|313125920|ref|YP_004036190.1| 500 VLLYGPPGTGKTLLAKAVANEADSNFISV 528
                                       5789************9999888777766 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.017       5.2       4      62 ..     228     291 ..     227     302 .. 0.81
   2 ?    1.1   0.0      0.85   2.6e+02       4      17 ..     501     514 ..     500     568 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.017
                               Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarliridn 62 
                                       l +G+pG+gKt+  +av +++       +g +i+ +  G   e+++ +++++ + ++ +++id+
  gi|313125920|ref|YP_004036190.1| 228 LLHGPPGTGKTLiaKAVANEIDASFHtiSGPEIMSKYYGESEEQLREIFEDAEEnAPAIVFIDE 291
                                       779********73367999998855534799999999999999999999999888999999983 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.85
                               Zot   4 lvtGapGsgKtsga 17 
                                       l +G+pG+gKt+ a
  gi|313125920|ref|YP_004036190.1| 501 LLYGPPGTGKTLLA 514
                                       679********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (754 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        59  (0.00329076); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              59  [number of targets reported over threshold]
# CPU time: 0.76u 0.36s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 4485.09
//
Query:       gi|313125921|ref|YP_004036191.1|  [L=82]
Description: hypothetical protein Hbor_11560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 550.80
//
Query:       gi|313125922|ref|YP_004036192.1|  [L=423]
Description: transposase, is605 orfb family, central region [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-23   82.9   2.8    1.1e-23   82.9   2.8    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.2e-07   32.0   0.0    3.2e-07   30.6   0.0    1.7  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.043   13.8   0.3      0.095   12.7   0.3    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
        5.5    6.8   8.3         17    5.3   2.3    2.7  2  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       3.4   1.5e+04      55      62 ..     135     142 ..     133     143 .. 0.79
   2 !   82.9   2.8   2.5e-27   1.1e-23       1      67 [.     318     384 ..     318     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.4
                    OrfB_Zn_ribbon  55 eadrDvnA 62 
                                       +++rD+++
  gi|313125922|ref|YP_004036192.1| 135 TFHRDHVS 142
                                       79***986 PP

  == domain 2  score: 82.9 bits;  conditional E-value: 2.5e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       fr+l e++eyka+eyG++ ++v+p++TSk+Cs Cg ++++++sg+ f C++Cg+e ++D+nA+ Ni 
  gi|313125922|ref|YP_004036192.1| 318 FRRLYEYVEYKAEEYGVEAVQVDPRNTSKRCSTCGFTHSDNRSGEAFCCQKCGYENHADYNASKNIG 384
                                       89***************************************************************95 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   7.2e-11   3.2e-07       6     119 ..     199     303 ..     194     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 7.2e-11
                        OrfB_IS605   6 vevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhr 82 
                                        ++++   k  +++g+DlG+nnLa+ +t++    + ++ ++    ++++k++  lq++ +++     a + +  + +
  gi|313125922|ref|YP_004036192.1| 199 SDDPESDSKHRTVLGVDLGVNNLAVASTGR----FWSADEFNHWRREYEKRRGSLQQCGSRH-----AHENIESVGH 266
                                       55668899999*******************....8888999999**************6666.....7999****** PP

                        OrfB_IS605  83 krsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       k + r   +lh++a++li++  e   ++++ ++++ i
  gi|313125922|ref|YP_004036192.1| 267 KETGRFEIYLHSVANELIEEAVEYDCSHIVFEDLTHI 303
                                       ********************99999999999988765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   2.1e-05     0.095      22      96 ..     296     373 ..     276     388 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                       T..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.T.TTT-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS CS
                              HypA  22 aarkvtkvkvevGelsgvepeaLefafellaegtv.legaeLeieevpvkvrCreCgkefeleek..alrCpkCgsa 95 
                                        ++  t+++ ++ + +  +  a++  +e ++ +        ++++  + + rC++Cg + + +++  a+ C+kCg +
  gi|313125922|ref|YP_004036192.1| 296 VFEDLTHIRENIPKATWQHVWAFRRLYEYVEYKAEeYGVEAVQVDPRNTSKRCSTCGFTHSDNRSgeAFCCQKCGYE 372
                                       45566666666666666666667777777765555244456789999999*******999866634689*****987 PP

                                       - CS
                              HypA  96 d 96 
                                       +
  gi|313125922|ref|YP_004036192.1| 373 N 373
                                       5 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   8.4     0.083   3.7e+02       2      22 ..     348     372 ..     347     373 .. 0.60
   2 ?    5.3   2.3    0.0038        17       1       9 [.     365     373 ..     365     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.083
                     zinc_ribbon_2   2 CpnCGaelqd...nakF.CpyCGtp 22 
                                       C+ CG +++d   ++ F C +CG++
  gi|313125922|ref|YP_004036192.1| 348 CSTCGFTHSDnrsGEAFcCQKCGYE 372
                                       7777776654111456688999886 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0038
                     zinc_ribbon_2   1 fCpnCGael 9  
                                       +C +CG+e+
  gi|313125922|ref|YP_004036192.1| 365 CCQKCGYEN 373
                                       7******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2418.52
//
Query:       gi|313125923|ref|YP_004036193.1|  [L=258]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-20   74.1   3.7    2.9e-20   73.8   3.7    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    9.7e-20   70.8   0.0    1.2e-19   70.5   0.0    1.1  1  Hydrolase_4    Serine aminopeptidase, S33
    7.7e-16   58.5   0.1    1.1e-09   38.4   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
       0.02   14.7   0.0        1.8    8.3   0.0    2.2  2  Abhydrolase_5  Alpha/beta hydrolase family
      0.027   14.6   0.0      0.059   13.5   0.0    1.6  1  Abhydrolase_4  TAP-like protein
       0.07   12.9   0.4        4.5    7.0   0.0    2.7  3  Abhydrolase_2  Phospholipase/Carboxylesterase
       0.13   12.0   1.0       0.27   11.0   1.0    1.4  1  DUF3948        Protein of unknown function (DUF3948)
       0.18   11.5   0.1        1.2    8.7   0.0    2.3  2  FSH1           Serine hydrolase (FSH1)


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   3.7   1.3e-23   2.9e-20       1     218 [.      25     246 ..      25     248 .. 0.68

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.3e-23
                                       EEEE--GC.....G...CHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH........CHHHHHHHCCTT..TTS CS
                     Abhydrolase_6   1 vlllHGagssassW...lvapLaallaagvhvlapDlpGhGrsdpppldled........ladlaalldelaagggp 66 
                                       +l++HG+g+++ +W   +  +L    ++ + v ++Dl GhG  ++++ d e+        ++d++a+++e+    ++
  gi|313125923|ref|YP_004036193.1|  25 LLFVHGSGGTHAVWksqF--RL----SDEFPVAVLDLSGHG--ESDDIDAEPgyetcsayVDDVVAVAEEV----DA 89 
                                       79********9***5333..66....888899*********..4455444444112333334445555555....56 PP

                                       EEEEEETCHHHHHHHHHHCC.......EEEEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHH CS
                     Abhydrolase_6  67 vvlvGHSlGGalalaaapla.....lvvgvlldppptalpagllaaalelllallallrllawlsreplprlflade 138
                                        vl+G+SlGGa+ l    ++     +v g++l++  t++ ++ l+++l +l    ++++++  +s    +rlf+++e
  gi|313125923|ref|YP_004036193.1|  90 SVLIGNSLGGAVILT---ALlerevDVDGLILAG--TGAKLAVLDDLLMWLSNDFPRAVSFLHDS----DRLFHDPE 157
                                       6**********9998...6656677878888888..68888888888888888888777766664....33444433 PP

                                       H..C...CCCHCHCCCGHH..HHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH..STTEEETCE...S CS
                     Abhydrolase_6 139 d..a...daawrarlarla..allaglgllpaaawadlpvpllvl.ggeDplvprllerlla..qagarlpvvlpga 205
                                          a   ++a ++  +++   +++++ ++  ++++ ++ vp+l l g+ D+l p+ + ++ +  +++++l  ++++a
  gi|313125923|ref|YP_004036193.1| 158 HeyAmlsQEAMQDVGRAVTerDFRTCHEFDVRDELDAVDVPTLALvGEHDRLTPQSYHEYFCeeMPDCEL-GIVEDA 233
                                       34313322222222222222233333335557788888888854339****99999999999999*****.8***** PP

                                       SS-HHHHSHHHHH CS
                     Abhydrolase_6 206 GHlphleepdeva 218
                                        Hl +le+p++++
  gi|313125923|ref|YP_004036193.1| 234 AHLSMLEQPEAFN 246
                                       **********996 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   5.4e-23   1.2e-19      30     238 ..      46     241 ..      20     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 5.4e-23
                       Hydrolase_4  30 qGfavyalDhrGhGrse...gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvag 103
                                        +f v+ lD  GhG+s+    + g  +  + yvdD+ a+ e+v         +l+G S+GG++ l++ll+++ +v+g
  gi|313125923|ref|YP_004036193.1|  46 DEFPVAVLDLSGHGESDdidAEPG-YETCSAYVDDVVAVAEEVD------ASVLIGNSLGGAVILTALLEREVDVDG 115
                                       5799*************9966666.899***********99998......679************************ PP

                       Hydrolase_4 104 lilsaPalkikaklkappllklllkllgkllpklqvsnnlkadslsrdpevvaayeadplvhgkitvrlllelldam 180
                                       lil+++  k++       l  ll++l + + + +++   +++d l +dpe+  a+ + + +++  ++ + +++ +  
  gi|313125923|ref|YP_004036193.1| 116 LILAGTGAKLA------VLDDLLMWLSNDFPRAVSF--LHDSDRLFHDPEHEYAMLSQEAMQDVGRAVTERDFRTCH 184
                                       *******9877......3456666666666555666..78***************************9999999998 PP

                       Hydrolase_4 181 k.rleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                       + +++++ +++++P+l l Ge+D++++++ ++ + e+++  d++l + + + H  + E+
  gi|313125923|ref|YP_004036193.1| 185 EfDVRDELDAVDVPTLALVGEHDRLTPQSYHEYFCEEMP--DCELGIVEDAAHLSMLEQ 241
                                       84699999*******************************..9***********998886 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.1   4.7e-13   1.1e-09       1     115 [.      23     136 ..      23     158 .. 0.80
   2 !   18.7   0.0   4.9e-07    0.0011     206     256 ..     182     241 ..     141     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.7e-13
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHH.HHHCTTSSEE CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldri.ldalgddklt 76 
                                       p+l+++hG +g++ vw     ++  +  +f v +lDl G+g+S+   a+  + y+t+   +++d +   a  +d  +
  gi|313125923|ref|YP_004036193.1|  23 PTLLFVHGSGGTHAVWKS--QFRLSD--EFPVAVLDLSGHGESDDIDAE--PGYETC--SAYVDDVvAVAEEVDASV 91 
                                       78**************99..885554..8********************..999996..667774434555666667 PP

                                       EEEETHHHHHHHHHHHHHGGGEEEEEEESE......CSSCCHHHH CS
                     Abhydrolase_1  77 lvGhSmGGmialayaaeyperVkalvllga......idpaaslie 115
                                       l+G S+GG++ l++++e    V++l+l g+      +d+  ++ +
  gi|313125923|ref|YP_004036193.1|  92 LIGNSLGGAVILTALLEREVDVDGLILAGTgaklavLDDLLMWLS 136
                                       9*****************999*********666665555555544 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.9e-07
                                       C.........THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 206 e.........lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                                 l++v +ptl + g++D+l+p ++ e++++  p+ +l +++da Hl+ le 
  gi|313125923|ref|YP_004036193.1| 182 TchefdvrdeLDAVDVPTLALVGEHDRLTPQSYHEYFCEEMPDCELGIVEDAAHLSMLEQ 241
                                       0444444455888999************************9999***********99886 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0008       1.8      46      87 ..      77     119 ..      73     131 .. 0.80
   2 ?    4.1   0.0     0.016        37      93     126 ..     189     222 ..     183     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0008
                     Abhydrolase_5  46 aeeiikeapklekfvvgGhslGGvvasr.faaeeekiegvvfl 87 
                                       +++++  a++++  v+ G slGG+v+   + ++e  ++g+++ 
  gi|313125923|ref|YP_004036193.1|  77 VDDVVAVAEEVDASVLIGNSLGGAVILTaLLEREVDVDGLILA 119
                                       6788888999999**********87755055566699*99975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.016
                     Abhydrolase_5  93 kdelselskkvlsivgteDgvlnvkslekakkfl 126
                                       +del +  +++l++vg++D + +++  e   + +
  gi|313125923|ref|YP_004036193.1| 189 RDELDAVDVPTLALVGEHDRLTPQSYHEYFCEEM 222
                                       799*****************98877665555555 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.059      30      92 ..     192     254 ..     171     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                     Abhydrolase_4  30 takgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLl 92 
                                        +++++p+L l +e+D  TP + ++ + +++++ +l +ve++ H ++ ++ ++ + a++++++
  gi|313125923|ref|YP_004036193.1| 192 LDAVDVPTLALVGEHDRLTPQSYHEYFCEEMPDCELGIVEDAAHLSMLEQPEAFNTAIQDFVN 254
                                       344679****************************************************99975 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.002       4.5       8      36 ..      16      44 ..      11      70 .. 0.84
   2 ?    3.0   0.0     0.034        76      88     134 ..      71     117 ..      48     127 .. 0.74
   3 ?   -0.8   0.0      0.48   1.1e+03     155     204 ..     195     240 ..     180     253 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.002
                                      --SS---EEEEEE--TT--SHHHHHHHH. CS
                     Abhydrolase_2  8 spkdkaqavviflHGlGdsghawaeaakt 36
                                      s + +a ++++f+HG G ++  w  +++ 
  gi|313125923|ref|YP_004036193.1| 16 SDRGAAGPTLLFVHGSGGTHAVWKSQFRL 44
                                      55677889************999998874 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHHHT-SS--SEEE CS
                     Abhydrolase_2  88 ekleelidaelkkgipssriiigGFSqGaalalylaltlpkklggiv 134
                                       e+ ++ +d  ++   + ++ +++G S G+a+ l + l  +  + g +
  gi|313125923|ref|YP_004036193.1|  71 ETCSAYVDDVVAVAEEVDASVLIGNSLGGAVILTALLEREVDVDGLI 117
                                       566666776666666777889*************9999888777755 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.48
                                       GG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--HH CS
                     Abhydrolase_2 155 kklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsidee 204
                                       +++p l + ge D + p +     +e++ + + ++el ++e+ aH ++ e
  gi|313125923|ref|YP_004036193.1| 195 VDVPTLALVGEHDRLTPQS----YHEYFCEEMPDCELGIVEDAAHLSMLE 240
                                       5677777777777777644....456666666788888888888876655 PP

>> DUF3948  Protein of unknown function (DUF3948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0   0.00012      0.27      14      27 ..      92     106 ..      87     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                           DUF3948  14 fiG.sasGAvvLTaf 27 
                                       +iG s++GAv+LTa+
  gi|313125923|ref|YP_004036193.1|  92 LIGnSLGGAVILTAL 106
                                       56669*********8 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   2.9e+03       6      24 ..      24      42 ..      22      46 .. 0.85
   2 ?    8.7   0.0   0.00054       1.2     156     188 ..     191     223 ..      55     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                              FSH1  6 kiLcLhGytqsgeiFrakt 24
                                      ++L++hG + +  ++++++
  gi|313125923|ref|YP_004036193.1| 24 TLLFVHGSGGTHAVWKSQF 42
                                      6899***999999999886 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00054
                              FSH1 156 eedkiqtptLhvlGelDtvvdeerseaLaeafk 188
                                       e d + +ptL ++Ge D + +++ +e++ e + 
  gi|313125923|ref|YP_004036193.1| 191 ELDAVDVPTLALVGEHDRLTPQSYHEYFCEEMP 223
                                       567889*****************9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1539.61
//
Query:       gi|313125924|ref|YP_004036194.1|  [L=269]
Description: ketopantoate hydroxymethyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-98  329.4   0.6    1.5e-98  329.3   0.6    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
    0.00012   21.6   2.6      0.033   13.7   0.7    2.6  3  PEP_mutase       Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.3   0.6  1.7e-102   1.5e-98       5     258 ..       5     255 ..       1     256 [. 0.97

  Alignments for each domain:
  == domain 1  score: 329.3 bits;  conditional E-value: 1.7e-102
                   Pantoate_transf   5 kdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvva 81 
                                       +d+r++    ++i+mlTaydattA +++eag+dv+LVGDs+g++ lgy+stlpvt++e++  t+aV+rga++alvva
  gi|313125924|ref|YP_004036194.1|   5 RDVREKA-GTTPITMLTAYDATTAGVANEAGIDVLLVGDSMGNTDLGYDSTLPVTVDEVASRTAAVSRGADDALVVA 80 
                                       5555544.559****************************************************************** PP

                   Pantoate_transf  82 dlPfgsyeaskeqalenAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqgktee 158
                                       d+Pf+s+ +++++++en++r++ke+gadavKle g++++e+ ++lv+ gipVm H+GltPq+v+++ gy+ qg t++
  gi|313125924|ref|YP_004036194.1|  81 DMPFLSVGVDEATSIENCGRMVKEAGADAVKLESGSHTVELTERLVQLGIPVMTHLGLTPQRVKET-GYTQQGTTRD 156
                                       ****************************************************************98.9********* PP

                   Pantoate_transf 159 eaeklledakaleeaGafalvlEavpaelakeiteklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvkkyae 235
                                       e +++l+ a++ eeaGafalvlE++pa+la+++t++lsiptIGIGAG++cdGqvlv++D+lgl+ + +p f k+y +
  gi|313125924|ref|YP_004036194.1| 157 EGHEILDLARKHEEAGAFALVLEHIPANLAAQVTDALSIPTIGIGAGSDCDGQVLVVDDVLGLS-SYSPPFSKQYGN 232
                                       ***************************************************************9.889********* PP

                   Pantoate_transf 236 laesieeavkaYaeevkegsFPa 258
                                       ++e++ +av+aY+e+v++g FPa
  gi|313125924|ref|YP_004036194.1| 233 VREQMLDAVSAYREDVESGGFPA 255
                                       **********************8 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.7   3.6e-06     0.033       7      69 ..      12      74 ..       7      83 .. 0.87
   2 !    6.6   0.0   0.00053       4.7     163     213 ..     100     147 ..      75     156 .. 0.82
   3 ?   -1.0   0.0      0.11     1e+03      85     106 ..     159     180 ..     145     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-06
                        PEP_mutase  7 kgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvs 69
                                      + +p+ ++ a+Da +a ++ eag++ l ++     + lG++ +  ++++e+ + ++a+ +  +
  gi|313125924|ref|YP_004036194.1| 12 GTTPITMLTAYDATTAGVANEAGIDVLLVGDSMGNTDLGYDSTLPVTVDEVASRTAAVSRGAD 74
                                      5579************************************************99999988764 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00053
                        PEP_mutase 163 raYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvplkgtlsvaelaelG 213
                                       r+ +eAGAd+v   +++++ e++e + ++++p++  +    l+ + ++e G
  gi|313125924|ref|YP_004036194.1| 100 RMVKEAGADAVKLESGSHTVELTERLVQLGIPVMTHL---GLTPQRVKETG 147
                                       55689****************999999*****99999...45566665555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.11
                        PEP_mutase  85 eevaetvrrliaaGvvgvniED 106
                                        e+ +  r+ ++aG+ ++++E 
  gi|313125924|ref|YP_004036194.1| 159 HEILDLARKHEEAGAFALVLEH 180
                                       5666778888899999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1682.98
//
Query:       gi|313125925|ref|YP_004036195.1|  [L=91]
Description: hypothetical protein Hbor_11600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.34s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 540.39
//
Query:       gi|313125926|ref|YP_004036196.1|  [L=282]
Description: translation initiation factor 2b subunit ii family (if-2bii) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-43  148.3   1.9    3.3e-43  147.9   1.9    1.1  1  IF-2B      Initiation factor 2 subunit family
     0.0087   16.2   0.4     0.0087   16.2   0.4    2.0  2  CinA_KH    Damage-inducible protein CinA KH domain
  ------ inclusion threshold ------
      0.025   14.8   1.5       0.05   13.8   0.1    2.1  2  THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-ter
      0.034   13.7   0.8      0.059   12.9   0.4    1.6  2  DUF927     Domain of unknown function (DUF927)


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.9   1.9   7.3e-47   3.3e-43       2     279 ..      14     279 ..      13     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 7.3e-47
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       +++s  +a++a ++l e +++ +  +v+e  ++l++++  Lk a+P+  sl na++ +l+  +   + s+v+eak+ 
  gi|313125926|ref|YP_004036196.1|  14 THSSSVVAVKATRALTELLDRDH-ATVEEYERDLERNVGALKRANPSHASLYNAMEGVLT--RVTGEASTVDEAKEL 87 
                                       67889999999999999887776.9***********************************..556999********* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLv 155
                                         +++++++++ie+ +   +++aa+ +kdg+t lT+ +s+tvle ++ aa ++ +++ +v+E rPr  Gr+ta +L+
  gi|313125926|ref|YP_004036196.1|  88 TESAVERVVEDIENGKSRAAANAAKTFKDGETFLTHDYSSTVLEAVEIAAADGNHMTTYVTEARPRYLGRKTARTLS 164
                                       ****************************************************************************9 PP

                                       H.TTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGG CS
                             IF-2B 156 q.agipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlded 231
                                         + i+  li+d a++++++e  d v+vG d i+e+  ++n++GT  +   A + +ipv vv    k++     +  
  gi|313125926|ref|YP_004036196.1| 165 GiDRIEPHLIVDGAAGIFLEE-CDRVVVGMDCIVEDT-LYNRVGTFPIVATAAQLDIPVTVVGSGAKIVDD---GFI 236
                                       6489*****************.**************9.******************************988...333 PP

                                       SSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEE CS
                             IF-2B 232 ifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGv 279
                                         +e r  +e+     e     ++ + npa+D tP el++ +IT++Gv
  gi|313125926|ref|YP_004036196.1| 237 FENEIRSTAEVSLEPVE-----DVFIENPAYDATPTELVDEVITDEGV 279
                                       44677777777654442.....6799*********************8 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.6   7.3e+03      55      65 ..       1      11 [.       1      13 [. 0.85
   2 !   16.2   0.4   1.9e-06    0.0087      14      66 ..      46      98 ..      27     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                                      HHH....HHHH CS
                           CinA_KH 55 liapveeeire 65
                                      +i++++eeire
  gi|313125926|ref|YP_004036196.1|  1 MIDDTIEEIRE 11
                                      79999999997 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.9e-06
                                      HHHHHGGGS-BSSS.EEEEEEETTEEEEEEE...EEHHHHHHHHH....HHHHH CS
                           CinA_KH 14 vaekladlidrenp.tlAiyakegevtvRltakaaneeeaealiapveeeirer 66
                                      ++  ++ l +r np    +y   ++v  R+t +a++ +ea++l + ++e++ e 
  gi|313125926|ref|YP_004036196.1| 46 LERNVGAL-KRANPsHASLYNAMEGVLTRVTGEASTVDEAKELTESAVERVVED 98
                                      55555554.55777577788888*************************999875 PP

>> THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.39   1.7e+03      11      43 ..       7      39 ..       1      57 [. 0.62
   2 ?   13.8   0.1   1.1e-05      0.05      19      46 ..      82     109 ..      63     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.39
                                      HTGGG--SSS--HHHHHHHHHHHHHHHTTSS-S CS
                         THDPS_N_2 11 errdelepetagaearaaveevleaLdaGelRv 43
                                      e+  e+++++++  a +a +++ e+Ld+ ++ v
  gi|313125926|ref|YP_004036196.1|  7 EEIREMQTHSSSVVAVKATRALTELLDRDHATV 39
                                      444555544445555666777777777665554 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.1e-05
                                       SS--HHHHHHHHHHHHHHHTTSS-SEEE CS
                         THDPS_N_2  19 etagaearaaveevleaLdaGelRvAek 46 
                                       ++a++ ++ ave+v+e++++G+ R+A +
  gi|313125926|ref|YP_004036196.1|  82 DEAKELTESAVERVVEDIENGKSRAAAN 109
                                       456677899*****************95 PP

>> DUF927  Domain of unknown function (DUF927)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.47   2.1e+03      64     101 ..      16      52 ..       3      63 .. 0.69
   2 ?   12.9   0.4   1.3e-05     0.059     230     283 ..      62     115 ..      54     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.47
                            DUF927  64 paellsgdgsellkeLldeGltvisknarklLakylqq 101
                                       ++++ + ++++ l+eLld+    +++ + ++L + + +
  gi|313125926|ref|YP_004036196.1|  16 SSSVVAVKATRALTELLDRDHATVEEYE-RDLERNVGA 52 
                                       3445566688899999999999899988.888766555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.3e-05
                            DUF927 230 aTanglEglaaannDllLiLDEiseadprevgelvYmlanGqGkqRanrtgevr 283
                                       +  n++Eg++++ ++     DE +e ++  v+ +v ++ nG++++ an   + +
  gi|313125926|ref|YP_004036196.1|  62 SLYNAMEGVLTRVTGEASTVDEAKELTESAVERVVEDIENGKSRAAANAAKTFK 115
                                       5579*******************************************9877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1779.95
//
Query:       gi|313125927|ref|YP_004036197.1|  [L=634]
Description: multidrug ABC transporter ATPase/permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-31  109.6   0.0    2.6e-31  109.0   0.0    1.3  1  ABC_tran      ABC transporter
    3.9e-11   43.1   5.6    9.9e-11   41.8   5.8    1.5  2  ABC_membrane  ABC transporter transmembrane region
      6e-08   32.4   0.8    4.8e-06   26.2   0.0    2.3  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0001   22.3   0.2      0.077   12.8   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00064   20.2   0.1     0.0026   18.2   0.1    2.1  2  AAA_16        AAA ATPase domain
     0.0012   18.6   0.1     0.0023   17.6   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0021   18.3   0.0      0.006   16.8   0.0    1.8  2  AAA_28        AAA domain
     0.0035   17.6   0.4      0.044   14.1   0.2    2.5  2  AAA_22        AAA domain
     0.0064   15.8   0.4      0.021   14.1   0.0    1.9  2  Zeta_toxin    Zeta toxin
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.045   13.6   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
      0.038   13.7   0.0      0.061   13.0   0.0    1.3  1  AAA_24        AAA domain
      0.052   13.3   6.9      0.035   13.8   2.4    2.6  2  AAA_30        AAA domain
      0.089   12.9   0.1       0.17   11.9   0.1    1.4  1  DUF87         Helicase HerA, central domain
       0.13   12.4   0.0        0.3   11.2   0.0    1.7  1  AAA_33        AAA domain
       0.19   12.3   0.0       0.39   11.3   0.0    1.6  1  AAA_18        AAA domain
       0.64   10.3   3.4       0.89    9.8   0.5    2.7  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.94    9.0   5.4       0.34   10.4   1.1    2.5  2  AAA_25        AAA domain
        3.6    7.8  13.4        3.6    7.8   0.2    2.2  2  EI24          Etoposide-induced protein 2.4 (EI24)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.0   2.6e-34   2.6e-31       2     137 .]     383     531 ..     382     531 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 2.6e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +nvsl  ++ge +aivG +GaGKSt+++lla+l+ p+ G+i+++g+dl++ +   +r +++v+ q+p +f+++ +r+
  gi|313125927|ref|YP_004036197.1| 383 SNVSLRAERGEFIAIVGGSGAGKSTIVSLLARLYAPDTGTIRVNGTDLSTVRVDDWRDRLAVVRQDPYIFDDT-LRN 458
                                       79***********************************************************************.999 PP

                                       H................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n                 +d+ ++++++ l++ +  dtv+++++  LSgGqkqrva+arall++++++++DE+t+
  gi|313125927|ref|YP_004036197.1| 459 NvlasapeasesaferaCADAGVTAFAEGLSDGY--DTVLGEDGVRLSGGQKQRVAIARALLRDADVVVFDEATS 531
                                       9****99866554443333333666666666666..9************************************96 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.1   5.1e+03     180     196 ..      11      27 ..       6      28 .. 0.82
   2 !   41.8   5.8   9.9e-14   9.9e-11      42     268 ..      91     311 ..      36     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.1
                                       HHHHHHHHHTHHHHHHT CS
                      ABC_membrane 180 ssvaeEslsgirtVkaf 196
                                       s+ + E l ++rtV+++
  gi|313125927|ref|YP_004036197.1|  11 SATLGEKLAALRTVISY 27 
                                       5667799*********9 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 9.9e-14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHH CS
                      ABC_membrane  42 vysllllllglaqfilallqsyllnvtgerlskrlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgek 118
                                        ++   +l++ ++f +a++  yl   +    ++ l++ +f+ il +++s+ d++ + ell+ l ++ +   ++l++ 
  gi|313125927|ref|YP_004036197.1|  91 TLLGGAALALGLRFGMATFVRYLQAQLVADYIRSLKTGVFRGILDADLSYVDERGSDELLNTLVTQSNYPATVLSSV 167
                                       56666778888999999999*********************************************999999999888 PP

                                       HHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHH CS
                      ABC_membrane 119 lglffqslltfvgglivmfylgwkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVka 195
                                       l+++ + ll+f   li+++ + + lt ++ a+l +i +    +      +      a+ ++ ++a+  ++gir V++
  gi|313125927|ref|YP_004036197.1| 168 LSVVERTLLVFT-YLILALAVDPLLTTAVAALLGVITVGVRSVVGSAYGAGSSIAAANTEIQAHAQAGVQGIRDVRL 243
                                       887777776666.9999*******999999888777777777777777777888888889***************** PP

                                       TTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHH CS
                      ABC_membrane 196 fgreeyflekfekaleeakkagikkaianglligitqllgllsyalalwfGttlvisgelsvgdlvvflslfa 268
                                       fg  +   +++++al+++  a +   + +++++   ++++ +++++a +++ t+    +ls+g   v l+lfa
  gi|313125927|ref|YP_004036197.1| 244 FGLDDVAATRYTDALDDYIDAVVGLRVNQAIVSNLHRFAAAVVVLVAVYLALTWA---ALSLGA--VGLLLFA 311
                                       ***********************99999999999999999999999999888887...666666..5555555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.026        26      25      41 ..     393     409 ..     383     415 .. 0.86
   2 !   26.2   0.0   4.9e-09   4.8e-06     136     213 ..     502     575 ..     419     581 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.026
                                       SEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnll 41 
                                       +f aivG  G+GKs ++
  gi|313125927|ref|YP_004036197.1| 393 EFIAIVGGSGAGKSTIV 409
                                       699***********998 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 4.9e-09
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                        LSgG+k+ va+a        + a ++++De  ++LD++  + v   ++e++ n  f+v+++r + + +ad+++ v 
  gi|313125927|ref|YP_004036197.1| 502 RLSGGQKQRVAIARA----LLRDADVVVFDEATSNLDARMEESVLGSIREATRNRVFVVVTHRLGSVVDADRIYTVA 574
                                       69******9998754....578999************************************************9997 PP

                                       E CS
                                       x RF
                             SMC_N 213 k 213
                                        
  gi|313125927|ref|YP_004036197.1| 575 D 575
                                       5 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.3    0.0041       4.1       1      24 [.     394     417 ..     394     444 .. 0.77
   2 !   12.8   0.0   7.7e-05     0.077     237     297 ..     503     559 ..     456     562 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0041
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllar 24 
                                       + +++G  g+GKS++  +l  l  
  gi|313125927|ref|YP_004036197.1| 394 FIAIVGGSGAGKSTIVSLLARLYA 417
                                       679****************98854 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.7e-05
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       lS G+k+  a++ allr++   +++++DE  ++L+ ++ +++l+ ++e++r +  ++++TH
  gi|313125927|ref|YP_004036197.1| 503 LSGGQKQRVAIARALLRDA---DVVVFDEATSNLDARMEESVLGSIREATR-NRVFVVVTH 559
                                       599999999**********...9****************************.566699999 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         4   3.9e+03      70     107 ..     118     155 ..      97     190 .. 0.60
   2 !   18.2   0.1   2.6e-06    0.0026      20     107 ..     388     499 ..     383     562 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4
                            AAA_16  70 sa.laqalareellrqlldeaesaeleawrekleealaa 107
                                       +a +++ l++ +++r +ld++ s   e+ +++l+ +l  
  gi|313125927|ref|YP_004036197.1| 118 VAdYIRSLKT-GVFRGILDADLSYVDERGSDELLNTLVT 155
                                       3337777755.8888888886666666666666666653 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.6e-06
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesa............ipy.sa.laqalareell 82 
                                       r+ r+e + ++G sG GKs++v  l+r +  d   ++r + ++l s             + + ++ + +   r+ +l
  gi|313125927|ref|YP_004036197.1| 388 RAERGEFIAIVGGSGAGKSTIVSLLARLYAPD-TGTIRVNGTDL-STvrvddwrdrlavV-RqDPyIFDDTLRNNVL 461
                                       5667799*******************877777.67777777777.331222222222221.0222222222243444 PP

                            AAA_16  83 rqlldeaesaeleawrekleeala.............a 107
                                       +   +++esa  +a +++  +a+a             +
  gi|313125927|ref|YP_004036197.1| 462 ASAPEASESAFERACADAGVTAFAeglsdgydtvlgeD 499
                                       44444444444444444444443355555555555442 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.4e-06    0.0023      17      55 ..     387     426 ..     380     428 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                            AAA_29  17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55 
                                       ++ ++ +++ ++G sG+GKST++  ++ l  p++ ++r N
  gi|313125927|ref|YP_004036197.1| 387 LRAERGEFIAIVGGSGAGKSTIVSLLARLYAPDTgTIRVN 426
                                       555545599**************77777777776666666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     6e-06     0.006       2      64 ..     395     461 ..     394     488 .. 0.81
   2 ?   -2.8   0.0       6.4   6.4e+03      73      80 ..     521     528 ..     495     585 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalpwv.edllafaervleeql 64 
                                       i+i+Gg+++GK+t+++ La+    ++ +++  ++++ + + ++++d l+ v +d+  f + + ++ l
  gi|313125927|ref|YP_004036197.1| 395 IAIVGGSGAGKSTIVSLLARLyapDTGTIRVNGTDLSTVRVDDWRDRLAVVrQDPYIFDDTLRNNVL 461
                                       89*****************875668889999999999999999999999988887777766555554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.4
                            AAA_28  73 nkvlfcDr 80 
                                        +v+++D 
  gi|313125927|ref|YP_004036197.1| 521 ADVVVFDE 528
                                       34444443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.6   5.6e+03     104     118 ..     142     159 ..     116     172 .. 0.72
   2 !   14.1   0.2   4.4e-05     0.044       4      54 ..     391     434 ..     388     547 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.6
                            AAA_22 104 r...seealeeLrsllnl 118
                                       +   s+e+l++L++ +n 
  gi|313125927|ref|YP_004036197.1| 142 DergSDELLNTLVTQSNY 159
                                       343458999999999986 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.4e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstssk 54 
                                       +  +++++G sG+GK+t +  l++ +        ++ ++++v+ + +++ +
  gi|313125927|ref|YP_004036197.1| 391 RGEFIAIVGGSGAGKSTIVSLLARLYA-------PDTGTIRVNGTDLSTVR 434
                                       6789********************995.......36777777777666443 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.2e-05     0.021      13      54 ..     389     430 ..     381     434 .. 0.87
   2 ?   -1.6   0.1       1.4   1.4e+03     123     163 ..     550     588 ..     522     592 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                        Zeta_toxin  13 qerPklillgGqpGAGKselaellkdelerqgnvvrldpDdl 54 
                                        er   i ++G++GAGKs++ +ll++  +++ + +r++++dl
  gi|313125927|ref|YP_004036197.1| 389 AERGEFIAIVGGSGAGKSTIVSLLARLYAPDTGTIRVNGTDL 430
                                       5667789999****************************9987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                        Zeta_toxin 123 evevvvvavkkelSrlgvldRyeeevaegRlvpkeehdeaf 163
                                       +++v+vv +++  S+ ++   y      gR+v+  +h+e +
  gi|313125927|ref|YP_004036197.1| 550 RNRVFVVVTHRLGSVVDADRIYTVA--DGRMVEDGTHEELV 588
                                       6788999999999988875555444..67999999998865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.6e-05     0.045      98     131 ..     391     424 ..     373     431 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevs 131
                                       +++++++vG SG+GKSt++  l+      tg ++
  gi|313125927|ref|YP_004036197.1| 391 RGEFIAIVGGSGAGKSTIVSLLARLYAPDTGTIR 424
                                       358999**************99987777777765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.1e-05     0.061       5      75 ..     395     530 ..     391     542 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-05
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..swedfldevvel.................... 59 
                                       i+i+G sg+GK+t+++ l   + +   + G+ +++++++ +++   w d l  v ++                    
  gi|313125927|ref|YP_004036197.1| 395 IAIVGGSGAGKSTIVSLL---ARLYAPDTGTIRVNGTDLSTVRvdDWRDRLAVVRQDpyifddtlrnnvlasapeas 468
                                       89****************...44455566777777777777755555555555555576666666666666777666 PP

                            AAA_24  60 ..............................................aaeladyktlviDtid 75 
                                                                                     +a l+d +++v+D ++
  gi|313125927|ref|YP_004036197.1| 469 esaferacadagvtafaeglsdgydtvlgedgvrlsggqkqrvaiaRALLRDADVVVFDEAT 530
                                       66666666666777777666666666666666666666666666666666666666666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       6.5   6.5e+03      23      61 ..     209     253 ..     197     266 .. 0.67
   2 ?   13.8   2.4   3.6e-05     0.035      15     121 ..     389     555 ..     378     574 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.5
                            AAA_30  23 ltGpA.GtGKttalkal.reaweaag....grviglAptgkaAkv 61 
                                       ++G A G+G + a +    +a+++ag    ++v ++     aA +
  gi|313125927|ref|YP_004036197.1| 209 VVGSAyGAGSSIAAANTeIQAHAQAGvqgiRDVRLFGLDDVAATR 253
                                       555555777777777765566666666777777777777777666 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.6e-05
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaa.g....................................grviglAp 54 
                                       +++  + +++G+ G+GK+t+++ l+++++ + g                                     +v++ Ap
  gi|313125927|ref|YP_004036197.1| 389 AERGEFIAIVGGSGAGKSTIVSLLARLYAPDtGtirvngtdlstvrvddwrdrlavvrqdpyifddtlrNNVLASAP 465
                                       55667899********************9996675555555544444444444444444444444443333333333 PP

                            AAA_30  55 tgkaAkvLaeelgieastiakllkrlk...............................................gra 84 
                                                                 +                                               +ra
  gi|313125927|ref|YP_004036197.1| 466 --------------------------EasesaferacadagvtafaeglsdgydtvlgedgvrlsggqkqrvaiARA 516
                                       ..........................033333333334444444444444566677777779999999999988777 PP

                            AAA_30  85 rlepgtllivDEa.gmvdtkqlaallkaaekag.akvil 121
                                        l+++++++ DEa + +d+++ +++l ++++a   +v +
  gi|313125927|ref|YP_004036197.1| 517 LLRDADVVVFDEAtSNLDARMEESVLGSIREATrNRVFV 555
                                       888889999999834568888888888888865255544 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00017      0.17      26      46 ..     395     415 ..     380     425 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                             DUF87  26 lAilgsTGsGKSntvavLlee 46 
                                       +Ai+g +G+GKS+ v++L + 
  gi|313125927|ref|YP_004036197.1| 395 IAIVGGSGAGKSTIVSLLARL 415
                                       7**************988653 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031       0.3       3      46 ..     396     451 ..     394     539 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                            AAA_33   3 llvGlpGsGKstlaerl...lkklg............avllssdtlrrrlfgtdqqskt 46 
                                        +vG +G+GKst +  l   +   +              +++ d++r+rl++  q++  
  gi|313125927|ref|YP_004036197.1| 396 AIVGGSGAGKSTIVSLLarlY---ApdtgtirvngtdLSTVRVDDWRDRLAVVRQDPYI 451
                                       689*********998884442...33445555555777788888888888885444332 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00039      0.39       1      44 [.     395     450 ..     395     490 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..............gvnlrdvakenglllevdpe 44 
                                       I++ G +G+GK+t+   L+++  +              +++  d ++++  +  +dp+
  gi|313125927|ref|YP_004036197.1| 395 IAIVGGSGAGKSTIVSLLARL--YapdtgtirvngtdlSTVRVDDWRDRLAVVRQDPY 450
                                       899***************998..33455556556555555666666666666666655 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00089      0.89      32      89 ..     502     546 ..     485     547 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00089
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +lSGG+kq    +a+a   +al+++        ++v++DEA s+lD+++ +++l+ ++
  gi|313125927|ref|YP_004036197.1| 502 RLSGGQKQR---VAIA---RALLRD-------ADVVVFDEATSNLDARMEESVLGSIR 546
                                       566666632...3333...444555.......479**************999998765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       3.8   3.8e+03      49      81 ..      36      70 ..      35      88 .. 0.64
   2 ?   10.4   1.1   0.00034      0.34      31      60 ..     390     421 ..     383     560 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.8
                            AAA_25 49 laldlalava..tGkpwlgpvapeqgkVlyvsaEd 81
                                      +al+l++av    G ++l p++   ++ l v+ ++
  gi|313125927|ref|YP_004036197.1| 36 VALSLVVAVFegVGLSFLLPLVEAGRTSLTVASDQ 70
                                      68888888884444444447755555555555444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00034
                            AAA_25  31 pagelallaGapgtGKttlaldlalava..tG 60 
                                        +ge+++++G +g+GK+t+++ la  +a  tG
  gi|313125927|ref|YP_004036197.1| 390 ERGEFIAIVGGSGAGKSTIVSLLARLYApdTG 421
                                       689*********************99986555 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   8.3      0.14   1.4e+02      19     123 ..      36     201 ..      20     216 .. 0.56
   2 ?    7.8   0.2    0.0036       3.6      20      77 ..     278     340 ..     264     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHH....................-.....TTHHHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                              EI24  19 lllplllnlllfllllvlll....................w.....vllasllvllllllplwlfplvalllaapf. 69 
                                       ++l+l+++++  + +l +ll                    w       + + +++ +ll  + l  ++ + +a ++ 
  gi|313125927|ref|YP_004036197.1|  36 VALSLVVAVFEGV-GLSFLLplveagrtsltvasdqtvvsWfaaayGAVGVPFTFETLLGGAALALGLRFGMATFVr 111
                                       3444444444333.333333677777777666555554444444443333444444444445555555555555554 PP

                                       ...HHHHHHHHHH.HH....................................CCTTSHHHHHHHHHHHHHHHHHHHH CS
                              EI24  70 ...ygllaekvekrhl....................................glvkslaeslkslllllllllvllp 107
                                           +l+a+++++  l                                     +++s+ + + ++ll++++l+++l+
  gi|313125927|ref|YP_004036197.1| 112 ylqAQLVADYIRS--LktgvfrgildadlsyvdergsdellntlvtqsnypaTVLSSVLSVVERTLLVFTYLILALA 186
                                       4445555555532..122333333333344444455555556666677777778888889*************9999 PP

                                       HHHTTHHH....HHHH CS
                              EI24 108 lliPvvglilspllls 123
                                       +  P++ + ++ ll+ 
  gi|313125927|ref|YP_004036197.1| 187 VD-PLLTTAVAALLGV 201
                                       94.5555555554443 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHH CS
                              EI24  20 llplllnlllfllllvlllwvllasllvllllllplwlfplvalllaapf.....ygllaekv 77 
                                       l  ++ +++++++++++l w+ l++ +v lll+++l l p+v+ l ++++     ++ l+e +
  gi|313125927|ref|YP_004036197.1| 278 LHRFAAAVVVLVAVYLALTWAALSLGAVGLLLFAMLRLGPGVSSLQSQLYgldgkLPHLVETL 340
                                       5677888889998888888*99999***************99999887777766666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.52
# Mc/sec: 3671.18
//
Query:       gi|313125928|ref|YP_004036198.1|  [L=35]
Description: hypothetical protein Hbor_11630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); expected 358.6 (0.02)
Passed Vit filter:                         1  (5.57756e-05); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 223.81
//
Query:       gi|313125929|ref|YP_004036199.1|  [L=383]
Description: hypothetical protein Hbor_11640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-11   42.1   0.0    2.7e-10   40.4   0.0    1.8  2  Acetyltransf_9  Acetyltransferase (GNAT) domain
    0.00093   19.4   0.1     0.0024   18.1   0.1    1.7  2  Acetyltransf_1  Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.072   13.5   0.1       0.23   11.9   0.0    1.7  2  Acetyltransf_7  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   4.5e-14   2.7e-10       2     125 ..      19     146 ..      18     148 .. 0.85
   2 ?   -1.5   0.0      0.41   2.4e+03      85     103 ..     293     311 ..     254     338 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.5e-14
                                       EEEE-GGGHHHHHHHHHHHTT----H...HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeesple.eireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvt 77 
                                       +r+ +++d  +   + + + ++++ + + e ++  + l+e++ ++++e +g++vg+l  ++++++v++k+       
  gi|313125929|ref|YP_004036199.1|  19 VRPFQSDDESGLRGVYESVSGRDPGHEWfETMYGSESLFEDAPIVVIEFEGDIVGMLPSVAYRVRVGEKSAIGLLGR 95 
                                       68888888999999999999999999899999**************************************999999* PP

                                       EEEE-CCGTTS-HHHHHHHHHHHHHHHT.T--EEEE--..SSHHHHHTTT- CS
                    Acetyltransf_9  78 gVavapehrgrgvlskLlaraleemree.gqplsllfP..ssipiYrrfGy 125
                                       +V+v+pehr+rgv+++ ++ al+ + +   +++++++    s++  + +G+
  gi|313125929|ref|YP_004036199.1|  96 DVMVHPEHRRRGVFTAATNVALGGYLDYgEATFIFGHMneQSRQACEEMGW 146
                                       ***************999999987766524566666655555566666666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.41
                                       GTTS-HHHHHHHHHHHHHH CS
                    Acetyltransf_9  85 hrgrgvlskLlaraleemr 103
                                       ++++  l +Ll+ral++ +
  gi|313125929|ref|YP_004036199.1| 293 KTRKRALAALLERALTDKK 311
                                       4557777888888877654 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   3.9e-07    0.0024      14      81 ..      44     112 ..      30     146 .. 0.69
   2 ?   -2.7   0.0       1.2   6.9e+03      53      55 ..     274     276 ..     231     315 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.9e-07
                                       HHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEE....EEEESGGGTTSSHHHHH CS
                    Acetyltransf_1  14 ppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayie....slaVspeyrgkGlGsaL 81 
                                        ++ ++++     +   e+  ++v+e++g ++G++    +    g++ +i     +++V+pe+r++G+ +a 
  gi|313125929|ref|YP_004036199.1|  44 HEWFETMYGSESLF---EDAPIVVIEFEGDIVGMLPSVAYRVRVGEKSAIGllgrDVMVHPEHRRRGVFTAA 112
                                       34445555553333...4447888***********65555552334444445557************97665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                       EET CS
                    Acetyltransf_1  53 ipd 55 
                                       +++
  gi|313125929|ref|YP_004036199.1| 274 RWH 276
                                       333 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.8e-05      0.23       3      41 ..      60     108 ..      57     111 .. 0.70
   2 ?   -2.8   0.0       1.5   9.2e+03       5      34 ..     255     288 ..     253     312 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                                       EEEEEEEETTEEEEEEEEEEES.........TCTEE....EEE-GGGTTSSH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld.........aeitr....laVdpeyrgkGi 41 
                                       + + V+e +g ivG++  + +          +        + V+pe+r++G+
  gi|313125929|ref|YP_004036199.1|  60 APIVVIEFEGDIVGMLPSVAYRvrvgeksaiG---LlgrdVMVHPEHRRRGV 108
                                       56788999999998654444437766664433...144589**********7 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.5
                                       EEEEEETTEEEEEEEEEEES...TCTEE....EEE-G CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld...aeitr....laVdp 34 
                                       ++Va ++g +v  +++s++    +   r    + V+p
  gi|313125929|ref|YP_004036199.1| 255 TYVAARGGSDVAALVVSERRwhrT---RwhsiVHVAP 288
                                       577777777777665555543321...1233344555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 2224.40
//
Query:       gi|313125930|ref|YP_004036200.1|  [L=96]
Description: coenzyme pqq synthesis protein d (pqqd) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-16   59.7   0.3    2.6e-16   59.7   0.3    1.3  2  PqqD      Coenzyme PQQ synthesis protein D (PqqD)
  ------ inclusion threshold ------
      0.014   15.5   0.0       0.02   14.9   0.0    1.3  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.4   1.3e+04      46      51 ..      13      18 ..       5      21 .. 0.49
   2 !   59.7   0.3   2.9e-20   2.6e-16       3      66 ..      26      89 ..      24      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                                      -HHHHH CS
                              PqqD 46 deeeae 51
                                      ++++++
  gi|313125930|ref|YP_004036200.1| 13 SADVVA 18
                                      234444 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 2.9e-20
                                      EEE-SS-..EEE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT- CS
                              PqqD  3 vlldpetgkyisLnetgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgl 66
                                       ll+ +tg y+ +n++g+ i++l+d++++ve+++aa+ eeyd++ e+a+adv+++++ L+++gl
  gi|313125930|ref|YP_004036200.1| 26 LLLNLDTGLYHGMNPVGTRIFELIDEPQTVEAVAAAIEEEYDIESEVAAADVREYVETLVDAGL 89
                                      6999**********************************************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.2e-06      0.02       9      58 ..      39      94 ..      38      96 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-06
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHT........S-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerld........lskntlsyHLrvLeeagLvevvr 58
                                      +Pv  ri+ ++  +e++t++++a++++        ++ + ++  +++L++agL ev++
  gi|313125930|ref|YP_004036200.1| 39 NPVGTRIFELI--DEPQTVEAVAAAIEeeydieseVAAADVREYVETLVDAGLAEVTE 94
                                      788889*****..*************445556677*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 555.45
//
Query:       gi|313125931|ref|YP_004036201.1|  [L=419]
Description: hypothetical protein Hbor_11660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-59  199.8   0.0      7e-59  199.5   0.0    1.1  1  NTP_transf_5  Uncharacterised nucleotidyltransferase
  ------ inclusion threshold ------
       0.08   13.0   1.1       0.41   10.7   1.0    2.1  2  TFIIB_C_1     Transcription factor IIB C-terminal module 1


Domain annotation for each model (and alignments):
>> NTP_transf_5  Uncharacterised nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.5   0.0   7.8e-63     7e-59       2     247 ..      46     308 ..      45     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 199.5 bits;  conditional E-value: 7.8e-63
                      NTP_transf_5   2 eadwerllrlarrhrvlpllykslkrlgleqlppeellrrlksayqaiakrnllllaeleellalleeegipvllLK 78 
                                       e++ +++l +a++ +v pl++++l +++    +p+++ +r +++++a+ +rnl++ ael+++l +++++g+++l+ K
  gi|313125931|ref|YP_004036201.1|  46 EVEADEVLTAAHHLGVGPLVASHLTDAD----VPAAFESRARERCRATGVRNLSFVAELHRVLSAFADAGLRCLVYK 118
                                       67899***********************....677****************************************** PP

                      NTP_transf_5  79 Gpala.qlYpdpalRemgDiDllvkredldraeelLeelGyelesd............gsekhevyyre........ 134
                                       Gp+la  +Y+d + R ++D+Dl+v++ d+++a+++Le+lGy + s+              + +++y r         
  gi|313125931|ref|YP_004036201.1| 119 GPVLAvSAYGDLSRRDFSDLDLFVPPGDVPEACAVLESLGYNPWSEngtavtdaeslvSRAAERTYFRPsedtpert 195
                                       *****56************************************9996667554444443333666666688888888 PP

                      NTP_transf_5 135 .......kkgveielhwrllppesprlepdfddlleerarpveiggksilvlspedlllylalHlakhfwnrglgLr 204
                                              + gv++el wrl  +   r +  + + ++er+++v +gg++++++s+ed +l+la H+akh+wnr   L 
  gi|313125931|ref|YP_004036201.1| 196 vatrrppSVGVAVELRWRLGTDL--RPSWLTFETAWERRTEVLVGGRPVPTFSNEDTVLVLARHGAKHYWNR---LG 267
                                       999999999***********984..44566667777889*******************************86...** PP

                      NTP_transf_5 205 wlvDiaallrklkdeldweallararelglrralllaltlake 247
                                       w+vD+aa+l+++  ++dw++l ara++ + rr+l++ l la+e
  gi|313125931|ref|YP_004036201.1| 268 WVVDVAAFLSEN--DIDWDRLRARAARANRRRILHACLLLAAE 308
                                       ***********8..***************************97 PP

>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0   4.6e-05      0.41      38      69 ..     287     317 ..     283     336 .. 0.74
   2 ?   -1.3   0.0      0.26   2.3e+03       4      35 ..     366     397 ..     363     408 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.6e-05
                         TFIIB_C_1  38 rergervekqeevaaaclmlaaerlrqPvPLa 69 
                                       r+r+ r ++   +  acl+laae +  PvP  
  gi|313125931|ref|YP_004036201.1| 287 RARAARANRR-RILHACLLLAAETADAPVPAE 317
                                       7788887765.57899**************54 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.26
                         TFIIB_C_1   4 rmrnalevllklsrrdeavleealelakrfvG 35 
                                       + r+++ +l++l+ ++++  + a+ l     G
  gi|313125931|ref|YP_004036201.1| 366 TRRQQVLTLCRLAFVPQQADYAAVSLPDSLHG 397
                                       56788889999999999999999888776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.38s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2300.29
//
Query:       gi|313125932|ref|YP_004036202.1|  [L=312]
Description: serine kinase of the hpr protein, regulates carbohydrate metabolism [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-06   27.0   0.2    4.7e-06   26.2   0.2    1.3  1  Hpr_kinase_C  HPr Serine kinase C-terminal domain
     0.0051   17.3   0.0     0.0088   16.6   0.0    1.3  1  ABC_tran      ABC transporter
  ------ inclusion threshold ------
      0.016   14.9   0.1      0.029   14.1   0.1    1.3  1  AAA_29        P-loop containing region of AAA domain
      0.019   14.9   0.0       0.76    9.8   0.0    2.3  2  DUF4649       Domain of unknown function (DUF4649)
      0.023   15.1   0.1       0.04   14.3   0.1    1.4  1  AAA_16        AAA ATPase domain
       0.11   12.5   0.0       0.18   11.7   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
       0.15   11.4   0.0       0.22   10.8   0.0    1.2  1  ATPase        KaiC


Domain annotation for each model (and alignments):
>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   1.8e-09   4.7e-06       8      57 ..     121     170 ..     117     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.8e-09
                                       EEESEEEEETTEEEEEEESTCHHHHHHHHHHHTTT-EEEEESSEEEEEET CS
                      Hpr_kinase_C   8 svhGvlvdvygvGvLitGesgvGKselaleLikrghrLvaDDaveikrid 57 
                                        +hG++v v g  v  +Gesg GKs +a  +   ghr + DD+  i+ +d
  gi|313125932|ref|YP_004036202.1| 121 VLHGSVVAVDGRAVAFVGESGAGKSTTAGAFAAAGHRALGDDVAAIRFTD 170
                                       58*****************************************9998665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.4e-06    0.0088      10      32 ..     130     152 ..     125     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.4e-06
                                       TTSEEEEEESTTSSHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlklla 32 
                                        g+ va+vGe+GaGKSt + ++a
  gi|313125932|ref|YP_004036202.1| 130 DGRAVAFVGESGAGKSTTAGAFA 152
                                       5899*************988776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.1e-05     0.029      13      41 ..     123     150 ..     120     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                            AAA_29  13 dghtieidlkg.atlltGpsGsGKSTllDA 41 
                                       +g ++ +d  g a+ ++G+sG+GKST   A
  gi|313125932|ref|YP_004036202.1| 123 HGSVVAVD--GrAVAFVGESGAGKSTTAGA 150
                                       56667777..668*************7655 PP

>> DUF4649  Domain of unknown function (DUF4649)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0003      0.76      15      35 ..      63      84 ..      58      90 .. 0.88
   2 ?    2.5   0.0     0.054   1.4e+02      20      43 ..     268     291 ..     261     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0003
                           DUF4649 15 ltFesyeefiralsgC.vtvpD 35
                                      +tFe  eefi+ + +C +tv  
  gi|313125932|ref|YP_004036202.1| 63 VTFETPEEFILLYDACrITVSQ 84
                                      89*****************975 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.054
                           DUF4649  20 yeefiralsgCvtvpDsypvtklt 43 
                                        +e+i+a   C++v  s pv  lt
  gi|313125932|ref|YP_004036202.1| 268 RDEAILAVDRCLSVVESVPVATLT 291
                                       5799****************9998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.5e-05      0.04      18      49 ..     125     155 ..     117     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellrale 49 
                                       +v + ++++v ++GesG GKs+ + +++ a  
  gi|313125932|ref|YP_004036202.1| 125 SVVAVDGRAVAFVGESGAGKSTTAGAFAAA-G 155
                                       56677789****************999953.2 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     7e-05      0.18      97     116 ..     129     148 ..     114     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7e-05
                                       CTTSEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLi 116
                                       ++++ +++vG+SG+GKSt  
  gi|313125932|ref|YP_004036202.1| 129 VDGRAVAFVGESGAGKSTTA 148
                                       567999***********976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.8e-05      0.22      18      55 ..     130     167 ..     125     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.8e-05
                            ATPase  18 egrvvlitGepGtGKtifalqFlikgaekygepgvfvt 55 
                                       +gr+v  +Ge+G+GK++ a  F+  g +  g+ +  + 
  gi|313125932|ref|YP_004036202.1| 130 DGRAVAFVGESGAGKSTTAGAFAAAGHRALGDDVAAIR 167
                                       6899999*******************999999887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.59
# Mc/sec: 1601.88
//
Query:       gi|313125933|ref|YP_004036203.1|  [L=128]
Description: hypothetical protein Hbor_11680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 713.10
//
Query:       gi|313125934|ref|YP_004036204.1|  [L=369]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-14   54.2   0.0    3.8e-14   53.5   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    1.6e-12   47.5   0.1    4.4e-12   46.0   0.1    1.8  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
      0.011   15.4   0.0       0.04   13.6   0.0    1.8  1  ox_reductase_C  Putative oxidoreductase C terminal domain


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   6.3e-18   3.8e-14       1     116 [.       3     123 ..       3     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 6.3e-18
                                       EEEEEETTSHHHHHHHHHHHHTTTTE......EEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrle......evvalldpdaeraeavaesfgve.aysdleelladpeidavivat 70 
                                       l+va+ G+ ++g+ h ++l +   +       +   l+ +d+e+   +a+++g+e   +d+e +++  e+da +   
  gi|313125934|ref|YP_004036204.1|   3 LNVAVLGYRFMGKAHSNALARLPMFFpdapdvHRHTLIGRDEEALASAADELGFEhTATDWESVVD--EVDAFYNLG 77 
                                       689*****888****999999977779999998899*******************99999******..9******** PP

                                       -GGGHHHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-E CS
                      GFO_IDH_MocA  71 pngtheelakaaleagkhvllEKPlattveeakelvelaekkgklv 116
                                       pn+ h+e  +aal+a   v++EKPla t++ea+++ ++a+ ++ + 
  gi|313125934|ref|YP_004036204.1|  78 PNHIHAEPSIAALKADTPVFCEKPLAPTLDEAEKMRDAAADSDAIA 123
                                       ***************************************9988765 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.1   7.4e-16   4.4e-12       1     113 [.     139     267 ..     139     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 7.4e-16
                                       HHHHHTTTTSSEEEEEEEEECBEEE.CHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEEEEEE....EEE.S CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtrag.aeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfGqppsvva....algrm 71 
                                       K lI++g lGe+++v + + +++ + a+a+++w++++   ++G+lgdlg H+iDl+++L+G +   +     +l+  
  gi|313125934|ref|YP_004036204.1| 139 KGLIDDGTLGEIRHVRGSYMQDWLTdADAPWSWRNDAkLAGSGALGDLGAHTIDLARFLVGDVAGDIErisgNLQ-- 213
                                       789**************888888762678888888889***********************97533332224443.. PP

                                       EEESCTCCSCSEEE.............EEEEEEEETTEEEEEEEECCTSSSEEEE CS
                    GFO_IDH_MocA_C  72 rqnaeaaededaav.............msvlnlekgsgevitlesgvskglsiry 113
                                        + +   ++e++ +             + ++n+++g++e++  + g  + ++ir+
  gi|313125934|ref|YP_004036204.1| 214 -TFVAERPVEGTDEtrpvtvddaysaqATFENGAMGTFEASRVADGHKNDHTIRI 267
                                       .333333344444445777788888888888888888888888777777777776 PP

>> ox_reductase_C  Putative oxidoreductase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.7e-06      0.04       1     137 [.     130     267 ..     130     271 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-06
                    ox_reductase_C   1 rylkvvqkmkkiikennl.kvvatnaryvsayehaakkaw.wek.s..isaGpvveqathfcdlsryfgGdv..dld 70 
                                       r++ ++q +k +i++  l ++      y   + + a   w w + +     G + + ++h  dl+r++ Gdv  d++
  gi|313125934|ref|YP_004036204.1| 130 RFVPAIQYAKGLIDDGTLgEIRHVRGSYMQDWLTDADAPWsWRNdAklAGSGALGDLGAHTIDLARFLVGDVagDIE 206
                                       6788999999999999995677888999999998888877554413113468899****************955566 PP

                    ox_reductase_C  71 tvkaksvewyekaGklskipvdeskipederiprltsaswkyksGavGslehavalqGtkystelev 137
                                        ++ +   +      +++ pv+    +    +  + sa+  +++Ga+G++e + + +G+k + ++ +
  gi|313125934|ref|YP_004036204.1| 207 RISGNLQTF------VAERPVEGTDETRPVTVDDAYSAQATFENGAMGTFEASRVADGHKNDHTIRI 267
                                       665543322......3444555555555666778889999999999999999999999888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 2002.21
//
Query:       gi|313125935|ref|YP_004036205.1|  [L=322]
Description: sugar phosphate isomerase/epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-32  111.7   0.7    4.5e-32  111.2   0.7    1.2  1  AP_endonuc_2    Xylose isomerase-like TIM barrel
    8.7e-20   70.2   0.0    2.3e-19   68.9   0.0    1.8  1  AP_endonuc_2_N  AP endonuclease family 2 C terminus
  ------ inclusion threshold ------
      0.049   13.7   0.0       0.47   10.5   0.0    2.2  2  DUF3122         Protein of unknown function (DUF3122)
       0.12   12.2   0.0       0.17   11.7   0.0    1.2  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.7     1e-35   4.5e-32       4     194 ..      22     248 ..      19     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 1e-35
                                       HHHCT-SEEEEECCTCSHHHHC.......HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHH CS
                      AP_endonuc_2   4 aaeaGfdgvElfgrdlvpvsel.......sdeelrelrkaldelglriaslslftrfgypdederearreesvdalk 73 
                                       + ++G++gvE+   +    ++l       ++++ ++l+ +lde+++++++l +++++ +pde+  e++      +l+
  gi|313125935|ref|YP_004036205.1|  22 LDDIGVQGVEIGVGGFPGDDHLdrraylgDESKQAQLHDLLDEHDMQVSALATHNNPLHPDEETAEEA----DTELR 94 
                                       668999999998766655555567789**********************************9666666....***** PP

                                       HHHHHHHHHTBSEEEEEBCC................GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TT CS
                      AP_endonuc_2  74 raielaaaLGapllvlhpGt................agagpkgseeeawerlaeslneladyaekegvklalEtlag 134
                                       +aielaa+L++ ++++++G                 ++  + +  e +w+ ++e + +la++a+++gv  a+E +++
  gi|313125935|ref|YP_004036205.1|  95 EAIELAAQLDVNTVTCFSGLpaggpndevpnwitapWPTEHADAHEYQWDVAIEYWSALAEFADDHGVDMAIEMHPN 171
                                       **********************************999999999999******************************* PP

                                       TTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGG..EEEEEE.EESS................ CS
                      AP_endonuc_2 135 sgvelgdeelarlldavdspnvgvclDtgHlliaeedvddalraladr..ikhvHikDakg................ 193
                                         v+     +++l +a++++ +g ++D++Hl++++  v da+r l+    i+h+H+kD+k+                
  gi|313125935|ref|YP_004036205.1| 172 MLVYEP-TGMLKLREATNDR-IGANFDPSHLYWQGIEVTDAIRFLGTEdaIHHFHAKDTKVyepksrikgvldttdy 246
                                       ***999.**********975.*************************9999**********97766666665555555 PP

                                       .T CS
                      AP_endonuc_2 194 .d 194
                                        d
  gi|313125935|ref|YP_004036205.1| 247 aD 248
                                       54 PP

>> AP_endonuc_2_N  AP endonuclease family 2 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   5.1e-23   2.3e-19       1      56 []     267     321 ..     267     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 5.1e-23
                    AP_endonuc_2_N   1 dwkdifsaLrqiGYdgplSiEwEDslmsreeGareAvaflkdkllieeseaafdwa 56 
                                       +wkd++s+Lr++GY+g+lSiE+EDsl+s++eG+++Av++l + +++++++++++wa
  gi|313125935|ref|YP_004036205.1| 267 HWKDVVSTLRMVGYEGALSIEHEDSLTSSREGLEKAVDVLGR-AVFDTKPGEAYWA 321
                                       6****************************************6.88**********8 PP

>> DUF3122  Protein of unknown function (DUF3122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.13   5.8e+02      44      83 ..      29      65 ..      23     100 .. 0.77
   2 ?   10.5   0.0    0.0001      0.47      32      66 ..     259     294 ..     241     315 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                           DUF3122 44 eleLrlvgfpgsveldhpqpLeittskgktlkakdvfeee 83
                                       +e+ + gfpg  +ld+   L  ++++    +++d ++e+
  gi|313125935|ref|YP_004036205.1| 29 GVEIGVGGFPGDDHLDRRAYLGDESKQ---AQLHDLLDEH 65
                                      56777889***9999999999766655...4455554443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0001
                           DUF3122  32 vlfkrvkegeeke.leLrlvgfpgsveldhpqpLei 66 
                                       + + + +++ ++    Lr+vg+ g+++++h+++L+ 
  gi|313125935|ref|YP_004036205.1| 259 IGYGHGESHWKDVvSTLRMVGYEGALSIEHEDSLTS 294
                                       5555555544433147****************9974 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.8e-05      0.17      44     129 ..      48     144 ..      40     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                                       EE--TT-CCHHHHHHTT-SEEEES---TCC....HHHH.......HHHHHHHHHHCT--EEEEEEETTTTSGCGCHH CS
                    NAD_binding_10  44 vegdvtdvedlaealkgadaVvsalggggk....deeg.......aknivdaakeagvkRfvlvsaigvgdevpgef 109
                                         gd +++++l + l+ +d  vsal+++++    dee+        + +++ a + +v+ + + s++ +g    +e+
  gi|313125935|ref|YP_004036205.1|  48 YLGDESKQAQLHDLLDEHDMQVSALATHNNplhpDEETaeeadteLREAIELAAQLDVNTVTCFSGLPAGGPN-DEV 123
                                       5689999*******************99999999555557778889999********************9754.445 PP

                                       HHHHH.HCCHHHHHHHHHHHH CS
                    NAD_binding_10 110 gewnk.ellkaylaakraaee 129
                                       ++w +  +  + ++a++++ +
  gi|313125935|ref|YP_004036205.1| 124 PNWITaPWPTEHADAHEYQWD 144
                                       555541455666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1915.19
//
Query:       gi|313125936|ref|YP_004036206.1|  [L=95]
Description: gyd domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-13   47.9   0.0    1.1e-12   47.7   0.0    1.0  1  GYD       GYD domain


Domain annotation for each model (and alignments):
>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0     6e-17   1.1e-12       1      90 [.       4      91 ..       4      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 6e-17
                               GYD  1 YivlvnytdegvkglkdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtetl 79
                                      Yi+ v    +  +++++ ++ + +++e + ++lGg++ + +++lG+yD+ v +E+ Dd +a ++   ++++G ++tet+
  gi|313125936|ref|YP_004036206.1|  4 YITHVDVDGDEYQNPQELASIWGSIREDV-RQLGGEILDTHVVLGPYDFDVRFEVSDDWEAFQVTQVIERHG-LDTETM 80
                                      889999999999*****************.******************************************.****** PP

                               GYD 80 rafteeefdea 90
                                      +a++ e++ e+
  gi|313125936|ref|YP_004036206.1| 81 QALPIERLGEV 91
                                      *****998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 598.38
//
Query:       gi|313125937|ref|YP_004036207.1|  [L=165]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-14   52.3   0.1    6.5e-14   52.0   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.7e-13   49.4   0.1    7.4e-13   48.7   0.1    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.6e-13   49.2   0.4    7.7e-13   48.7   0.4    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.6e-10   40.8   0.0    2.8e-10   40.0   0.0    1.4  1  FR47             FR47-like protein
     0.0078   16.3   0.1      0.032   14.3   0.1    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0085   16.2   0.1      0.016   15.3   0.1    1.7  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.034   14.3   0.0       0.06   13.5   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.096   12.4   0.4        0.3   10.8   0.4    2.0  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
       0.52   10.8   2.0        1.1    9.7   2.0    1.5  1  NTS_2            N-terminal segments of P. falciparum erythro


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.1   3.3e-17   6.5e-14      30     117 ..      55     141 ..      29     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 3.3e-17
                   Acetyltransf_10  30 ealllvaeeggkivGvielrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnasp.yavpfYeklG 105
                                       +a++++++e+++++G+++ r++++i  l+V+pe+rg+G+gk+L+ +v +  +      + +++ ++  a +fYe++G
  gi|313125937|ref|YP_004036207.1|  55 RATTHLYFEDETLMGFAAARRDGYILFLAVAPEARGKGYGKRLVAEVARDHRSV----SCHARTTNeDALSFYEHIG 127
                                       5688999****************************************9997544....7888888889********* PP

                   Acetyltransf_10 106 Fkav..geeqeenG 117
                                       F++    ++ +e+G
  gi|313125937|ref|YP_004036207.1| 128 FEVKrrISNYYEDG 141
                                       **984434445555 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.1   3.7e-16   7.4e-13       6      75 ..      59     129 ..      44     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.7e-16
                                       EEEEETTEEEEEEEEEEESTCTEEEEE-GGGTTSSHHHHHHHHTT...SEEEEE.EEEETHHHHHHHHHHTTEE CS
                    Acetyltransf_7   6 fVaeddgkivGfialslldaeitrlaVdpeyrgkGiGraLleaae...kgiile.qlelnaekaikfYeklGFe 75 
                                       +++ +d+  +Gf+a+ +++ +i +laV+pe+rgkG+G++L++ ++   + +  + ++++++e a++fYe+ GFe
  gi|313125937|ref|YP_004036207.1|  59 HLYFEDETLMGFAAARRDG-YILFLAVAPEARGKGYGKRLVAEVArdhRSV--ScHARTTNEDALSFYEHIGFE 129
                                       4456778889***999887.9999*****************8523233222..23444444489*********9 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.4   3.9e-16   7.7e-13      23     117 .]      46     128 ..      21     128 .. 0.69

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.9e-16
                                       H..HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE CS
                    Acetyltransf_1  23 e..feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikki 97 
                                          f +  ++ + +l++  ed++l Gf+ ++   d     +yi +laV+pe+rgkG+G++L+ ++++  r+  +   
  gi|313125937|ref|YP_004036207.1|  46 HgfFTDAYRRATTHLYF--EDETLMGFAAARR--D-----GYILFLAVAPEARGKGYGKRLVAEVARDHRSVSC--- 110
                                       23222334444445555..9********5544..4.....78********************999998888855... PP

                                       EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  98 vlaveedndaairlYeklGF 117
                                         + + +n+ a  +Ye  GF
  gi|313125937|ref|YP_004036207.1| 111 --HARTTNEDALSFYEHIGF 128
                                       ..55567********99**9 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   1.4e-13   2.8e-10      12      80 ..      67     131 ..      60     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.4e-13
                                       EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  12 laawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       l++   ++ +g++  l v pe+r++G+g+rlv+++a++       v+ +++++N+ + ++ye +Gfe+ 
  gi|313125937|ref|YP_004036207.1|  67 LMGFAAARRDGYILFLAVAPEARGKGYGKRLVAEVARD----HRSVSCHARTTNEDALSFYEHIGFEVK 131
                                       5666677889**********************998775....7789********************986 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.6e-05     0.032      74     126 ..      77     129 ..      20     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                       EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..SSHHHHHTTT-E CS
                    Acetyltransf_9  74 agvtgVavapehrgrgvlskLlaraleemreegqplsllfP..ssipiYrrfGye 126
                                       +++   avape rg+g+ ++L+a++ ++ r+  ++    +    + ++Y++ G+e
  gi|313125937|ref|YP_004036207.1|  77 GYILFLAVAPEARGKGYGKRLVAEVARDHRS--VSCHARTTneDALSFYEHIGFE 129
                                       89999******************99998887..4444444422335666666665 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   8.1e-06     0.016     114     151 ..      97     145 ..      23     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.1e-06
                    Acetyltransf_4 114 llaeiasp...........nensiqfhkalGFelvgifkkcikkngrwi 151
                                       l+ae+a +           ne +  f++++GFe+ ++  ++++++g  +
  gi|313125937|ref|YP_004036207.1|  97 LVAEVARDhrsvscharttNEDALSFYEHIGFEVKRRISNYYEDGGDAY 145
                                       5555555533333333334788*********************999766 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     3e-05      0.06      31      54 ..      83     106 ..      58     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                   Acetyltransf_CG  31 eVpeelrGkGiAkkLvkaalddar 54 
                                        V +e rGkG++k+Lv ++  d r
  gi|313125937|ref|YP_004036207.1|  83 AVAPEARGKGYGKRLVAEVARDHR 106
                                       699***************998877 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   0.00015       0.3      86     143 ..      84     134 ..      16     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                       ESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                    Acetyltransf_8  86 igeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                       +  +eargkg++++l+ ++++      + r+v +  + +Ne a++++e++Gfe ++++
  gi|313125937|ref|YP_004036207.1|  84 V-APEARGKGYGKRLVAEVAR------DHRSVSCHARTTNEDALSFYEHIGFEVKRRI 134
                                       3.4677899999887777664......5899**********************99877 PP

>> NTS_2  N-terminal segments of P. falciparum erythrocyte membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.0   0.00055       1.1      36      48 ..     136     148 ..     133     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00055
                             NTS_2  36 qYYrsGGDGdYLk 48 
                                       +YY+ GGD +YL+
  gi|313125937|ref|YP_004036207.1| 136 NYYEDGGDAYYLR 148
                                       6***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 980.45
//
Query:       gi|313125938|ref|YP_004036208.1|  [L=137]
Description: hypothetical protein Hbor_11730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-35  120.5   0.2    6.8e-35  120.3   0.2    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.2   3.8e-39   6.8e-35       1     138 []       3     137 .]       3     137 .] 0.89

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 3.8e-39
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-.EE.EEEEEESSSHHHHHHHHHHHHHHHHHT-- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepke.ek.eieveaedledlLfdfLdellylfdteyf 75 
                                       +e++dhtADv+++a++++ +++f+++a++l+++ +d  +++++  ++ ++ev+ae++e+lLfd+Ld+l++++d++ +
  gi|313125938|ref|YP_004036208.1|   3 FELRDHTADVAVAASAPTRSALFAAVADGLAAAGCD--EIPETGgDRfDVEVRAENVEALLFDYLDQLIFERDVRAV 77 
                                       89**********************************..4444432235***************************88 PP

                                       S----EEEE.E-SSSEEEEEEEE----.-TT----.----B--S---EEEEETTEEEEEEEEE- CS
                          Archease  76 vfkevkvdeeeeeeeleleaeargekfdkekhevq.tevKAvTyhelrieeeddgweayvvvDi 138
                                       +  + + + ee++ e++l+++arg+++d+     + +e+KAvTy+e+r+ee+d+gweayvv+D+
  gi|313125938|ref|YP_004036208.1|  78 MPVDNEASVEERDGEWVLTGSARGVSLDEI----DaREIKAVTYSEMRVEETDEGWEAYVVLDV 137
                                       87777554458899*************555....449**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 847.17
//
Query:       gi|313125939|ref|YP_004036209.1|  [L=368]
Description: doxx protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.3e-08   34.0   7.7    3.3e-08   34.0   7.7    3.9  5  DoxX        DoxX
  ------ inclusion threshold ------
      0.066   12.0   1.3       0.13   11.1   0.0    2.0  2  VKG_Carbox  Vitamin K-dependent gamma-carboxylase
      0.067   13.1  10.0        8.2    6.3   0.6    3.8  3  DoxD        TQO small subunit DoxD


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.7         1   6.3e+03      68      81 ..       7      20 ..       3      26 .. 0.42
   2 ?   -2.2   0.6       1.1   6.3e+03      45      61 ..      58      74 ..      41      81 .. 0.54
   3 ?   -1.0   0.1      0.46   2.8e+03       4      19 ..     102     117 ..      99     134 .. 0.80
   4 !    8.4   6.7   0.00052       3.1      29      78 ..     116     163 ..     113     168 .. 0.73
   5 !   34.0   7.7   5.6e-12   3.3e-08       3      76 ..     235     312 ..     233     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1
                              DoxX 68 aAlalavtllvatl 81
                                      aA ++ +t +v++ 
  gi|313125939|ref|YP_004036209.1|  7 AAQFVSFTAVVVVA 20
                                      33333333333332 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                              DoxX 45 aylaalvElvgglllll 61
                                      + + +++ + +g l++l
  gi|313125939|ref|YP_004036209.1| 58 LAVLGIGGVTVGALVAL 74
                                      33334444444444444 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.46
                              DoxX   4 llRlllgvlfiahGlq 19 
                                       llRl +g+ ++ +G+ 
  gi|313125939|ref|YP_004036209.1| 102 LLRLSVGLPLVGAGFA 117
                                       7899999999988875 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.00052
                              DoxX  29 taaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllv 78 
                                       +a+++++  +   +    ++ l+ +++g lll+G++tRl+A + ++  lv
  gi|313125939|ref|YP_004036209.1| 116 FAGYFFSPLV--QTAIPTFTRLFGIGVGFLLLFGFGTRLVATVGLLSYLV 163
                                       5666665555..55666677788899*************99877665444 PP

  == domain 5  score: 34.0 bits;  conditional E-value: 5.6e-12
                              DoxX   3 lllRlllgvlfiahG.lqkltgfglegtaaslaalglpp.....pellaylaalvElvgglllllGlltRlaAlala 73 
                                        +lR+ lg+ fi+ G +qkl+  ++ ++ a +a+  l++     pel+ + a+l+E+++g++ll+G +tR aA++ +
  gi|313125939|ref|YP_004036209.1| 235 VVLRVGLGISFIYLGiAQKLM--NPGDALAVVAKYDLTAvvpvaPELWIVGAGLTEVLVGVALLFGAFTRGAAAISF 309
                                       689*********8883699**..788866666655554445555**************************8877544 PP

                              DoxX  74 vtl 76 
                                       ++ 
  gi|313125939|ref|YP_004036209.1| 310 LLF 312
                                       433 PP

>> VKG_Carbox  Vitamin K-dependent gamma-carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.1      0.22   1.3e+03     189     219 ..     127     158 ..     111     187 .. 0.63
   2 ?   11.1   0.0   2.2e-05      0.13      35     128 ..     266     358 ..     244     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.22
                        VKG_Carbox 189 livswfgllfDllivflLllk.ktRilalllv 219
                                        ++  f+ lf + ++flLl+   tR++a++ +
  gi|313125939|ref|YP_004036209.1| 127 TAIPTFTRLFGIGVGFLLLFGfGTRLVATVGL 158
                                       45555666666666666665424555555443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2.2e-05
                        VKG_Carbox  35 kFplfewvkplslewmyllylvmllaalgialGlkYrlsillfvllytyiel.ldktsynNHyYllgllallllflp 110
                                       k+ l  +v + ++ w++   l  +l+++ + +G++ r ++++ +ll+t++ + l     + H  l+gl++ ll+   
  gi|313125939|ref|YP_004036209.1| 266 KYDLTAVVPVAPELWIVGAGLTEVLVGVALLFGAFTRGAAAISFLLFTTTLFgLPDDPVLAHISLFGLVSALLVT-- 340
                                       677888889999999999999999***************999999998765437778889***********9865.. PP

                        VKG_Carbox 111 anryfslDalknkkikkk 128
                                          +fs+Da+++++ +++
  gi|313125939|ref|YP_004036209.1| 341 GSGAFSVDAWLHETDESQ 358
                                       5679******99876554 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.6    0.0014       8.2      75      96 ..     137     158 ..     122     201 .. 0.79
   2 ?    4.6   0.0    0.0046        27       3      26 ..     235     258 ..     233     267 .. 0.91
   3 ?    5.5   1.4    0.0025        15      71     146 ..     284     353 ..     269     363 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0014
                              DoxD  75 EiivGlllliGlltRlsslvaf 96 
                                        i vG lll G+ tRl+++v +
  gi|313125939|ref|YP_004036209.1| 137 GIGVGFLLLFGFGTRLVATVGL 158
                                       4789************997644 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0046
                              DoxD   3 lilRlalgliflsagirkkvlkpa 26 
                                       ++lR+ lg+ f++ gi +k+++p+
  gi|313125939|ref|YP_004036209.1| 235 VVLRVGLGISFIYLGIAQKLMNPG 258
                                       689*******************98 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0025
                              DoxD  71 ftlvEiivGlllliGlltRlsslvafalalgialsayWlgstcedEyqiglllvaael.vliltgsgklslDylllk 146
                                        +l E++vG+ ll G +tR ++     +++ ++ +++  g    d+  ++ +   + +  l++tgsg +s+D+ l +
  gi|313125939|ref|YP_004036209.1| 284 AGLTEVLVGVALLFGAFTRGAAA----ISFLLF-TTTLFGL--PDDPVLAHISLFGLVsALLVTGSGAFSVDAWLHE 353
                                       46789999999999999995544....444444.3333444..3444444444443331578899999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2295.73
//
Query:       gi|313125940|ref|YP_004036210.1|  [L=489]
Description: hypothetical protein Hbor_11750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.1e-155  517.4   0.0   3.5e-155  517.2   0.0    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  517.2   0.0    2e-159  3.5e-155       1     412 []      54     489 .]      54     489 .] 0.98

  Alignments for each domain:
  == domain 1  score: 517.2 bits;  conditional E-value: 2e-159
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvke 73 
                                       ql+n ++lpg++k++++mPD H+G+g+p+G+V at+   g+i+P+ VG+DI CGvr+++tnlt++el+++ +elv++
  gi|313125940|ref|YP_004036210.1|  54 QLRNATHLPGMTKYAICMPDGHQGYGFPVGGVGATDteeGCISPGSVGYDInCGVRMMRTNLTYDELKGNEEELVEA 130
                                       899************************************************************************** PP

                                       HHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  74 lekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlG 150
                                       l++++p+glg  + v+ + +++++vl++g++wa+e+g + e dl+++e+eg   +ad+++vs+kak+r+++qlG+lG
  gi|313125940|ref|YP_004036210.1| 131 LFANIPSGLGGGGIVESDVDTVDQVLSRGVDWALEHGHAVEADLAHCEDEGFRPDADPDAVSQKAKDRGKNQLGSLG 207
                                       **********99****999********************************************************** PP

                                       STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 151 sGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagse 227
                                       sGNHF+Evq v++++ e++a+++glee+q+vv++H+GSRglGhq+++dyl+ ++k+  +   +lpd++La++pags+
  gi|313125940|ref|YP_004036210.1| 208 SGNHFLEVQRVTDVFREDVATEFGLEEDQIVVLIHCGSRGLGHQVCTDYLRRIEKEHGDLLESLPDKELAAAPAGSD 284
                                       ******************************************************99998989*************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxx RF
                              RtcB 228 egqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAt 300
                                        +++Y+ am+aa n+A++NRq+i++r+r+++e+v++++ e++e++l++dvaHNiakkE+h+ +   ++++VhRKGAt
  gi|313125940|ref|YP_004036210.1| 285 LAEEYYGAMCAAINFAWVNRQLIMHRTRRVFERVFGRDWEEMEMDLLYDVAHNIAKKEVHDvGgeeRELFVHRKGAT 361
                                       ************************************9999*********************945779********** PP

                                       E-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTT.CC CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                              RtcB 301 rA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdl.ee 361
                                       rA             +vgqp+iipGsmg++Sy+++G +++   +fgSt+HGAGR+msR++ak+ +++e+v+++l ++
  gi|313125940|ref|YP_004036210.1| 362 RAfpagrpelpsayrDVGQPIIIPGSMGAGSYVLRGGEHSLdlTFGSTAHGAGRTMSRTQAKNDYWGETVQEELrDQ 438
                                       *************************************999889*******************************778 PP

                                       CT-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 362 qgigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       q+i+v+a++ ++++eEap+ YKd+deVv++ +e g+ ++v+r  pv+++kg
  gi|313125940|ref|YP_004036210.1| 439 QKIYVKAQSGATIAEEAPGVYKDVDEVVRVSDELGIGDKVVRTFPVCNIKG 489
                                       899**********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2747.93
//
Query:       gi|313125941|ref|YP_004036211.1|  [L=116]
Description: hypothetical protein Hbor_11760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.03   14.4   0.3       0.17   12.0   0.2    1.9  2  DUF1634          Protein of unknown function (DUF1634)


Domain annotation for each model (and alignments):
>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   9.3e-06      0.17      14      76 ..      18      76 ..      10      83 .. 0.84
   2 ?    0.6   0.0     0.033   5.8e+02      10      30 ..      85     105 ..      74     115 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.3e-06
                           DUF1634 14 avvllGlilllvkhgssesenseltslseilegllelkglaiiqlGllvLiatPvlrVvlsli 76
                                      ++ +lG ++++v+ + + ++++ l++  +     l+ +++a+i+ G lvL+a  ++ V ++l+
  gi|313125941|ref|YP_004036211.1| 18 VLAFLGAVVYIVRLE-H-RTEMALIEAGQY--EQLRTDSRAWILGGGLVLVALGLADVTTTLL 76
                                      67899********99.3.466666666664..458999*******************999886 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.033
                           DUF1634  10 llsaavvllGlilllvkhgss 30 
                                       +++a+v +++l+ +++k +++
  gi|313125941|ref|YP_004036211.1|  85 IAAAFVGFAALAYYFYKRRED 105
                                       456777777777777777743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 766.90
//
Query:       gi|313125942|ref|YP_004036212.1|  [L=115]
Description: hypothetical protein Hbor_11770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.031   14.4   0.4       0.11   12.7   0.1    2.0  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
      0.033   13.6   0.5      0.075   12.5   0.1    1.8  2  zf-ribbon_3      zinc-ribbon domain
       0.11   12.9   0.1       0.17   12.3   0.1    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.13   12.1   0.3       0.35   10.6   0.3    1.7  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.23   11.2   0.1       0.23   11.2   0.1    2.0  3  zinc_ribbon_2    zinc-ribbon domain
        2.6    7.7   5.0       0.32   10.7   0.4    1.8  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain


Domain annotation for each model (and alignments):
>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.5e-05      0.11      14      37 ..       4      27 ..       1      31 [. 0.89
   2 ?   -3.1   0.0       2.9   8.6e+03      15      22 ..      52      59 ..      47      62 .. 0.72
   3 ?   -2.2   0.0       1.5   4.6e+03      22      38 ..      85     101 ..      84     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                          zf-Mss51 14 hvdfeCpdCGiptycseehwedDy 37
                                      +v++ Cp+CG ++   +e + +D+
  gi|313125942|ref|YP_004036212.1|  4 PVSYYCPHCGAVVELQREGYLADK 27
                                      699************999999887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.9
                          zf-Mss51 15 vdfeCpdC 22
                                      ++f C ++
  gi|313125942|ref|YP_004036212.1| 52 INFVCGES 59
                                      67888776 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.5
                          zf-Mss51  22 CGiptycseehwedDye 38 
                                       CG   y s  ++ed  e
  gi|313125942|ref|YP_004036212.1|  85 CGRDFYLSFVRFEDGHE 101
                                       77777777777777665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.5e-05     0.075       3      12 ..       7      16 ..       6      20 .. 0.81
   2 ?   -2.7   0.0       1.5   4.5e+03       8      10 ..      56      58 ..      55      62 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                       zf-ribbon_3  3 vrCPnCGapl 12
                                      ++CP+CGa++
  gi|313125942|ref|YP_004036212.1|  7 YYCPHCGAVV 16
                                      699***9965 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                       zf-ribbon_3  8 CGa 10
                                      CG+
  gi|313125942|ref|YP_004036212.1| 56 CGE 58
                                      776 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.6e-05      0.17       4      24 ..       7      27 ..       5      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
                   Lar_restr_allev  4 kpCPfCggravlersqrvvae 24
                                      + CP+Cg   +l+r+++ + +
  gi|313125942|ref|YP_004036212.1|  7 YYCPHCGAVVELQREGYLADK 27
                                      67************9987765 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00012      0.35      42      53 ..       4      15 ..       2      16 .. 0.87
   2 ?   -2.6   0.0       1.6   4.9e+03      41      48 ..      50      57 ..      47      58 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                    zinc_ribbon_10 42 evkyrCpkCgal 53
                                      +v+y+Cp+Cga+
  gi|313125942|ref|YP_004036212.1|  4 PVSYYCPHCGAV 15
                                      689*******86 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                    zinc_ribbon_10 41 eevkyrCp 48
                                      + ++++C 
  gi|313125942|ref|YP_004036212.1| 50 DGINFVCG 57
                                      56789995 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   7.7e-05      0.23       1       7 [.       8      14 ..       5      18 .. 0.72
   2 ?   -2.6   0.0       1.7   5.1e+03      19      21 ..      56      58 ..      55      59 .. 0.57
   3 ?   -4.1   0.3         5   1.5e+04       5       6 ..      85      86 ..      85      87 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.7e-05
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +Cp+CGa
  gi|313125942|ref|YP_004036212.1|  8 YCPHCGA 14
                                      5777776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                     zinc_ribbon_2 19 CGt 21
                                      CG+
  gi|313125942|ref|YP_004036212.1| 56 CGE 58
                                      554 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 5
                     zinc_ribbon_2  5 CG 6 
                                      CG
  gi|313125942|ref|YP_004036212.1| 85 CG 86
                                      66 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00011      0.32       7      22 ..       7      22 ..       5      23 .. 0.88
   2 ?   -3.9   0.1       3.7   1.1e+04      11      13 ..      55      57 ..      55      58 .. 0.55
   3 ?   -3.1   0.0       2.2   6.5e+03      28      32 ..      84      88 ..      83      90 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                      EE-TTT--EEEECC-- CS
                   Desulfoferrod_N  7 YkCevCGniVeVleaG 22
                                      Y C +CG +Ve   +G
  gi|313125942|ref|YP_004036212.1|  7 YYCPHCGAVVELQREG 22
                                      89*********88777 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.7
                                      TT- CS
                   Desulfoferrod_N 11 vCG 13
                                      vCG
  gi|313125942|ref|YP_004036212.1| 55 VCG 57
                                      566 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.2
                                      ETTEE CS
                   Desulfoferrod_N 28 CCgep 32
                                       Cg +
  gi|313125942|ref|YP_004036212.1| 84 PCGRD 88
                                      58877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 765.49
//
Query:       gi|313125943|ref|YP_004036213.1|  [L=183]
Description: phosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-13   49.8   0.0    1.9e-11   44.4   0.0    2.2  2  HAD_2           Haloacid dehalogenase-like hydrolase
    2.4e-07   31.3   2.7    0.00016   22.0   0.1    2.3  2  Hydrolase       haloacid dehalogenase-like hydrolase
    6.7e-06   26.1   0.1    1.2e-05   25.2   0.1    1.4  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
       0.14   12.6   4.3        4.2    7.7   4.3    2.2  1  HAD             haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.014        64       1      11 [.      12      22 ..      12      79 .. 0.89
   2 !   44.4   0.0   4.3e-15   1.9e-11     102     175 ..     100     173 ..      94     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.014
                             HAD_2  1 iiFDlDgTlld 11
                                      +++DlDgTl+ 
  gi|313125943|ref|YP_004036213.1| 12 VVWDLDGTLVH 22
                                      789******85 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 4.3e-15
                             HAD_2 102 TsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsptDieaakkagikv 175
                                       + + ++a    l+ +++  + d +v+ + v  +KPdpe+++++l+++++ ++++++vGDs +D  +a +ag+ +
  gi|313125943|ref|YP_004036213.1| 100 SLNCEAACHVALDTHDLAGHADAVVGRDSVATRKPDPEPLLETLRRMDAAPDDAVFVGDSRRDKLTAERAGVAF 173
                                       555666677788889999999**************************************************986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.6   0.00033       1.5       2      26 ..      10      34 ..       9      80 .. 0.78
   2 !   22.0   0.1   3.7e-08   0.00016     155     210 .]     117     170 ..     103     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00033
                                      SEEEEESBTTTBCHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  2 ktvvfDkdGTLttgepsvedvivsa 26
                                      ++vv+D+dGTL++       v  +a
  gi|313125943|ref|YP_004036213.1| 10 DAVVWDLDGTLVHLAVDWGAVATEA 34
                                      79**********8764444444444 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 3.7e-08
                                       TTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +G  + dav+++d ++  kp+pe +++++r++ + p + ++VGD+  D   +++Ag
  gi|313125943|ref|YP_004036213.1| 117 AG--HADAVVGRDSVATRKPDPEPLLETLRRMDAAPDDAVFVGDSRRDKLTAERAG 170
                                       44..778999999999********************************99999997 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   2.7e-09   1.2e-05       3      51 ..     132     179 ..     130     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.7e-09
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSS CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltG 51 
                                       +KP pe + + l++++++p++ +++GD+ + D + A +aG+ +  V  G
  gi|313125943|ref|YP_004036213.1| 132 RKPDPEPLLETLRRMDAAPDDAVFVGDS-RRDKLTAERAGVAFRYVGDG 179
                                       8***************************.***********998777766 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.3   0.00094       4.2       1      77 [.      12      85 ..      12     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00094
                               HAD  1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrell.rldraglaelleallaglseelaaelerfv 77
                                      +++D+DgTL++      +    +++ a+ ++ra+   ++   ++ +l   d+++ +e +ea+l+ +++e a++ +r+ 
  gi|313125943|ref|YP_004036213.1| 12 VVWDLDGTLVHLA--VDWGA--VATEAEATFRAAGIDADGTDLWGMLdLADESDMREDIEAILSEHEQEGARRSKRLA 85
                                      79*******9983..23333..44445555666666644444344330445567788888888888877777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1118.45
//
Query:       gi|313125944|ref|YP_004036214.1|  [L=381]
Description: acyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-53  179.9   2.6    4.8e-53  179.4   2.6    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    7.8e-35  119.9   0.1    1.9e-34  118.7   0.1    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    4.7e-24   84.4   0.0    1.2e-23   83.1   0.0    1.7  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    9.5e-24   84.2   3.4    9.5e-24   84.2   3.4    1.8  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.08   12.8   0.0         17    5.3   0.0    2.6  2  HTH_Tnp_Tc3_1  Tc3 transposase


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.4   2.6   1.3e-56   4.8e-53       1     149 [.     231     379 ..     231     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.4 bits;  conditional E-value: 1.3e-56
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       gkG+ +a + l+ +R+++aa+a+gla++a++ea+eya++r++fg+p+ d q+vr+k+ ema++++a+rl+v++aa++
  gi|313125944|ref|YP_004036214.1| 231 GKGLSAAFRILTGGRMGIAAQAVGLAQSAFDEAREYAHDREQFGGPISDIQAVRHKFSEMATQIHASRLMVREAARQ 307
                                       689************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                        dag+++r +asmaK+fase+a++v+++a+q++Gg+Gy+++ +ver+yrd+++++i+eGtseiq+++iar++
  gi|313125944|ref|YP_004036214.1| 308 DDAGEDPRIAASMAKYFASEAAVDVTNEAVQIHGGYGYTTDFEVERMYRDSKITTIYEGTSEIQKEVIARGV 379
                                       **********************************************************************97 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   0.1   5.4e-38   1.9e-34       1     112 [.      11     121 ..      11     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 5.4e-38
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       t+eq+a+rd vrefa ee++p a+e+de++ fp+++w+ lael+l+g+tvpeeygG ++d +++ +v e++a++ ++
  gi|313125944|ref|YP_004036214.1|  11 TDEQRAIRDVVREFAVEEIRPTAREADETESFPEDVWDGLAELDLTGLTVPEEYGGFDADRMTYTVVNEQVAYGQLA 87 
                                       79*************************************************************************** PP

                                       HHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                     Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkrryLpklasg 112
                                       +a++l+vh  l++  i++fG++eqk+ +Lp++a+g
  gi|313125944|ref|YP_004036214.1|  88 VATALSVHC-LATSCIAKFGSDEQKEAWLPEMARG 121
                                       *******96.66689*******************9 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.0   3.3e-27   1.2e-23       2      97 .]     127     219 ..     126     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 3.3e-27
                                       EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE--- CS
                     Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrri 78 
                                       fal+Ep+aGs+ a+++t +a+r+g+eyv+nG+K+witn++  ++++++a+t+ +d   +++ flvp+ + g++v+++
  gi|313125944|ref|YP_004036214.1| 127 FALSEPDAGSNPAEMST-VARREGDEYVINGKKQWITNGQRGDVCILFAKTDPDD-PSSVTQFLVPK-DAGIEVGKK 200
                                       89***************.99999999************************88888.**********5.779****** PP

                                       --BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  79 eeklGlrglptgelvfedv 97 
                                       e+klGlr  +t+ l f+dv
  gi|313125944|ref|YP_004036214.1| 201 EHKLGLRASDTTSLIFDDV 219
                                       *****************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.3   4.5e+03      70      87 ..       5      22 ..       1      35 [. 0.57
   2 !   84.2   3.4   2.7e-27   9.5e-24       2     133 ..     247     368 ..     246     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                                      HTT----HHHHHHHHHHH CS
                     Acyl-CoA_dh_2 70 aagkevtvedraearraa 87
                                      +ag+++t e+ra   +  
  gi|313125944|ref|YP_004036214.1|  5 DAGSALTDEQRAIRDVVR 22
                                      555555555555444444 PP

  == domain 2  score: 84.2 bits;  conditional E-value: 2.7e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       giaa+a+G+A++a++e+ e+a++r +  +g +++d +a+ ++  e+a++++A r+++++aa++     +ag+     
  gi|313125944|ref|YP_004036214.1| 247 GIAAQAVGLAQSAFDEAREYAHDREQ--FGGPISDIQAVRHKFSEMATQIHASRLMVREAARQ----DDAGEDP--- 314
                                       79************************..***********************************....9999998... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                        r  a++a+ +a+e a+++++++++++Gg++++++ +++R++RD ++++++++++
  gi|313125944|ref|YP_004036214.1| 315 -RIAASMAKYFASEAAVDVTNEAVQIHGGYGYTTDFEVERMYRDSKITTIYEGTS 368
                                       .**************************************************9987 PP

>> HTH_Tnp_Tc3_1  Tc3 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0048        17       2      21 ..       7      26 ..       6      33 .. 0.91
   2 ?    4.6   0.0    0.0082        29      19      39 ..     283     303 ..     269     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0048
                                      S----HHHHHHHHHHHHTT- CS
                     HTH_Tnp_Tc3_1  2 GsaLSDtEraillvmkllnv 21
                                      GsaL D  rai +v ++  v
  gi|313125944|ref|YP_004036214.1|  7 GSALTDEQRAIRDVVREFAV 26
                                      9*************999766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0082
                                       TT--HHHHHHHHT--HHHHHH CS
                     HTH_Tnp_Tc3_1  19 lnvklsEiarklsRsRnCIrr 39 
                                          k sE+a+++  sR  +r+
  gi|313125944|ref|YP_004036214.1| 283 VRHKFSEMATQIHASRLMVRE 303
                                       56799*********9987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2378.50
//
Query:       gi|313125945|ref|YP_004036215.1|  [L=400]
Description: alanyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-14   52.3   1.9    1.5e-13   51.3   1.9    1.5  1  DHHA1         DHHA1 domain
    1.3e-11   44.4   0.0    2.2e-11   43.7   0.0    1.4  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
      3e-10   39.2   0.0    4.8e-10   38.6   0.0    1.2  1  tRNA-synt_2c  tRNA synthetases class II (A)


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   1.9   2.6e-17   1.5e-13       2     132 ..     275     398 ..     267     400 .] 0.71

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2.6e-17
                                       HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEE CS
                             DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvake 78 
                                       +s+++er++le el  l e +++  +e+l ++     g +  v  + ++ d ++ g+aa ++    +++ +v++++ 
  gi|313125945|ref|YP_004036215.1| 275 QSIEAERRKLESEL--LTERITE--FETLAKN-----GAQWHVGVI-DGFDSNDAGEAAKDVVRDENETDVVAAVGA 341
                                       34555555555555..4444433..3344443.....888888888.***************995555555555555 PP

                                       ECT.EEEEEEEESSHSS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEE..HCHHHHHHH CS
                             DHHA1  79 egd.kvkvsarskkdgvdagelakeaaaklgggGGGH.dlAaGagip..aekleeale 132
                                       ++     v a+s + gvdag+++++a +++gggGGG   +A+G+g++  + ++  +l+
  gi|313125945|ref|YP_004036215.1| 342 GERpYLVVAAGSDS-GVDAGDVVSRATDEFGGGGGGGaTFAQGGGLDadPADVTSFLK 398
                                       55559999999998.*******************9999********833444555555 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   3.7e-15   2.2e-11       1      44 []     188     231 ..     188     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 3.7e-15
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +r+v+++d++v +CgGtHv+nT eIg + +l  ++ ++gl+R++
  gi|313125945|ref|YP_004036215.1| 188 IRLVTVEDWDVAACGGTHVSNTLEIGPVTVLGRSNPGEGLTRVE 231
                                       79****************************************96 PP

>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0     8e-14   4.8e-10     473     551 ..      12      85 ..       8      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 8e-14
                                       SEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEX CS
                      tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevd 549
                                       +ef + +++++   v Ld+T fYaesGGq +D+G++ +    +   dvqk++g v+h+      ++ +g+++++++d
  gi|313125945|ref|YP_004036215.1|  12 REFDAAATSVDGRDVTLDQTYFYAESGGQPADRGTLGG----IPLDDVQKVDGNVVHTLASA-PDFDEGETITGVID 83 
                                       57888999999999*********************965....6799*************996.9************9 PP

                                       HH CS
                      tRNA-synt_2c 550 ee 551
                                       ++
  gi|313125945|ref|YP_004036215.1|  84 DD 85 
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2399.94
//
Query:       gi|313125946|ref|YP_004036216.1|  [L=172]
Description: XRE family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-06   27.1   1.3    6.2e-06   26.5   0.5    1.8  2  HTH_31          Helix-turn-helix domain
    0.00052   20.0   0.0    0.00078   19.4   0.0    1.3  1  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.023   14.6   0.1      0.053   13.5   0.1    1.5  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.066   13.3   0.4       0.12   12.5   0.0    1.7  2  HTH_3           Helix-turn-helix
      0.092   12.6   0.5       0.23   11.4   0.2    1.7  2  HTH_25          Helix-turn-helix domain
       0.16   11.9   0.1       0.27   11.1   0.1    1.3  1  zf-C4_ClpX      ClpX C4-type zinc finger
       0.16   12.1   0.6       0.32   11.1   0.6    1.5  1  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   4.7e+03      26      33 ..      23      30 ..      17      36 .. 0.52
   2 !   26.5   0.5   2.4e-09   6.2e-06       3      57 ..     112     168 ..     110     172 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
                            HTH_31 26 vsestlsr 33
                                       s  +l+r
  gi|313125946|ref|YP_004036216.1| 23 RSSPKLRR 30
                                      44444443 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 2.4e-09
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrp..spavlealaralgld 57 
                                       G+ ++++R+ aGL+ ee+A+ l   es +  +EqGr +r     + ++a+ + l+++
  gi|313125946|ref|YP_004036216.1| 112 GDVVATARQDAGLTVEELAAELDADESDIDAVEQGRATRAgvGGSLVRAIEEKLDVT 168
                                       9999*********************************86544555777777766665 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     3e-07   0.00078       2      55 ..     113     168 ..     112     172 .] 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3e-07
                            HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEng..kkdvpsaelllkiaealgid 55 
                                       + +  aR  +glt eela +l+ + s i a E g   +   + +l+++i e+l+++
  gi|313125946|ref|YP_004036216.1| 113 DVVATARQDAGLTVEELAAELDADESDIDAVEQGraTRAGVGGSLVRAIEEKLDVT 168
                                       56889*****************************5533355588888888888876 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.1e-05     0.053       5      26 ..      18      45 ..      17      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                    PhnA_Zn_Ribbon  5 CplCa.SeytY.....edgallvCpeCa 26
                                      C+lC+ S+  +     ++  llvCp+Ca
  gi|313125946|ref|YP_004036216.1| 18 CELCGrSSPKLrranvAGANLLVCPDCA 45
                                      99997477777**9999**********8 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       5.1   1.3e+04       4      13 ..      76      85 ..      75      86 .. 0.76
   2 ?   12.5   0.0   4.6e-05      0.12       3      52 ..     117     169 ..     115     171 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.1
                                      HHHHTTHHHH CS
                             HTH_3  4 lRkqlglsqe 13
                                       R++++++q+
  gi|313125946|ref|YP_004036216.1| 76 QRQAKMYDQA 85
                                      6899999985 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.6e-05
                                       HHHHHTTHHHHHHHHHHTSSHHHHHHHHTT...SSCSBHHHHHHHHHHHTSEH CS
                             HTH_3   3 elRkqlglsqeeLAeklGvsrstisriEnG...ernPsletlkklakaLgvsl 52 
                                        +R+ +gl+ eeLA++l+   s i + E G   ++    + + ++++ L+v+l
  gi|313125946|ref|YP_004036216.1| 117 TARQDAGLTVEELAAELDADESDIDAVEQGratRAGVGGSLVRAIEEKLDVTL 169
                                       68****************************99999999999999999999998 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   8.9e-05      0.23       4      34 ..     117     147 ..     115     154 .. 0.90
   2 ?   -1.5   0.0      0.92   2.4e+03      22      32 ..     153     163 ..     147     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.9e-05
                                       HHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                            HTH_25   4 aaRearglsleevaketkIrkdylealEedd 34 
                                        aR+ +gl++ee+a+e+   ++ + a E+++
  gi|313125946|ref|YP_004036216.1| 117 TARQDAGLTVEELAAELDADESDIDAVEQGR 147
                                       59***************99999999999987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.92
                                       --HHHHHHHHC CS
                            HTH_25  22 IrkdylealEe 32 
                                       +  ++++a+Ee
  gi|313125946|ref|YP_004036216.1| 153 VGGSLVRAIEE 163
                                       5557899**98 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00011      0.27       2      29 ..      17      44 ..      16      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                        zf-C4_ClpX  2 rCSFCgksesevkk.lIagpngvyICdeC 29
                                      +C  Cg+s  + ++  +ag n + +C +C
  gi|313125946|ref|YP_004036216.1| 17 SCELCGRSSPKLRRaNVAGAN-LLVCPDC 44
                                      7*******9998772579997.8****** PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   0.00013      0.32       8      33 ..      18      45 ..      16      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                       Zn-ribbon_8  8 CeeCghefevlqsis.daplta.CPeCg 33
                                      Ce Cg+   +l++++   ++   CP+C 
  gi|313125946|ref|YP_004036216.1| 18 CELCGRSSPKLRRANvAGANLLvCPDCA 45
                                      *****9999*****997776666****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1029.28
//
Query:       gi|313125947|ref|YP_004036217.1|  [L=181]
Description: hypothetical protein Hbor_11820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-46  158.8   0.0    1.4e-46  158.6   0.0    1.0  1  GrpB      GrpB protein
  ------ inclusion threshold ------
        0.1   12.8   0.1       0.19   12.0   0.1    1.4  1  MHB       Haemophore, haem-binding


Domain annotation for each model (and alignments):
>> GrpB  GrpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.6   0.0   1.6e-50   1.4e-46       1     160 []       5     165 ..       5     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 158.6 bits;  conditional E-value: 1.6e-50
                                       .X--BS--THHHHHHHHHHHHHHHHH...E.EEEEESGGGSTT--B-S-EEEEEEES-SGGGGGGHHHHHH.TT-EE CS
                              GrpB   1 pvelveydpeWpeqferekarlraal...i.sieHiGSTsvpglaAKpiiDilvvvedledeeelveaLea.agyel 72 
                                       p++++ey+peWp+ fere++rl+++l     +ieHiGSTsvpglaAKpiiDi +vv+d++      ++L a  gyel
  gi|313125947|ref|YP_004036217.1|   5 PITIAEYNPEWPDIFERERQRLASVLdeyTaRIEHIGSTSVPGLAAKPIIDITAVVTDIDGCWGDLDKLSAvFGYEL 81 
                                       699***********************998459*************************99988888899966479998 PP

                                       .-TTTTSTTEEEEEE-SSS..--EEEEEEETT-HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHTT-SS-HHHH--- CS
                              GrpB  73 lrgepgiperrlfvkgedeeertvhlhvveagspelerhllfrdyLrahpearaeYaalKrelaakaeedidaYtea 149
                                            +ip+  lfv+++de+++ ++lh+++a ++++++ llfr+yLr+ p++r+eYa++Kr++a+++++di aYt+ 
  gi|313125947|ref|YP_004036217.1|  82 ----SSIPSDWLFVQRTDESGQLYNLHLISAADDQWKQDLLFREYLRTYPDVRDEYASVKRSAAESNPNDITAYTHS 154
                                       ....479*********9998899****************************************************** PP

                                       -HHHHHHHHHH CS
                              GrpB 150 Keefikeilkr 160
                                       K+ef++++l+r
  gi|313125947|ref|YP_004036217.1| 155 KNEFCQSVLER 165
                                       ******99986 PP

>> MHB  Haemophore, haem-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.2e-05      0.19      20      55 ..     120     155 ..     118     164 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                               MHB  20 saYLdthPdvnqaltslkgqprdqaraavkaYfdan 55 
                                       ++YL t Pdv + + s+k+  ++   ++++aY  ++
  gi|313125947|ref|YP_004036217.1| 120 REYLRTYPDVRDEYASVKRSAAESNPNDITAYTHSK 155
                                       68******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1084.22
//
Query:       gi|313125948|ref|YP_004036218.1|  [L=187]
Description: hypothetical protein Hbor_11840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-34  119.2   9.2    1.4e-34  119.2   9.2    1.3  2  DUF420     Protein of unknown function (DUF420)
    1.9e-06   28.1   7.1    2.2e-05   24.7   1.9    2.4  2  DUF2306    Predicted membrane protein (DUF2306)
     0.0068   16.9   0.2     0.0068   16.9   0.2    2.2  4  DUF1240    Protein of unknown function (DUF1240)
  ------ inclusion threshold ------
       0.11   12.3   3.1       0.23   11.2   3.1    1.5  1  IncD       Inclusion membrane protein D
       0.67    8.7   5.2      0.073   11.9   1.4    1.4  2  Otopetrin  Otopetrin


Domain annotation for each model (and alignments):
>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.5         5   1.8e+04      84      92 ..      16      24 ..      12      29 .. 0.39
   2 !  119.2   9.2   3.8e-38   1.4e-34       1     132 []      48     183 ..      48     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 5
                            DUF420 84 Lavvvvplv 92
                                      L+vv + lv
  gi|313125948|ref|YP_004036218.1| 16 LSVVSLALV 24
                                      233333222 PP

  == domain 2  score: 119.2 bits;  conditional E-value: 3.8e-38
                            DUF420   1 lpalnavlnalaavllllglvaikkgkieaHrklmllafvlsalFlvlYllkhalag.etkfggpeeegvirpvYla 76 
                                       +p++navl+++a+v+++lg++ai++g++++Hr+lml++++l++ FlvlYl++ ++ +  t+f ++    v+++vYl+
  gi|313125948|ref|YP_004036218.1|  48 IPHVNAVLSTTAIVTIVLGVRAIRRGNVARHRALMLSTLGLFIGFLVLYLYRLTILEgPTEFPSQG--VVYQFVYLP 122
                                       69**************************************************887766*****544..69******* PP

                            DUF420  77 iLitHivLavvvvplvlvtlvlalkg.....kfekHrkiaritvpiwlyvavtGvvvYllL 132
                                       +L++Hi+La+v++pl+++ l+la+++     + ++H+ ++r+++ +wl+++v+G vvY+lL
  gi|313125948|ref|YP_004036218.1| 123 TLAVHILLAIVCIPLLYYVLLLAVTRpieeiYETRHKTVGRVAASLWLVSFVLGDVVYTLL 183
                                       *****************************999***************************98 PP

>> DUF2306  Predicted membrane protein (DUF2306)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.9   6.1e-09   2.2e-05      66     146 ..      52     130 ..      47     131 .. 0.88
   2 !    9.3   0.5   0.00034       1.2       2      47 ..     125     174 ..     124     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.1e-09
                           DUF2306  66 flllallwlvftvlalvairrrdfaaHrawmirsYalalaavtlrlvllvlillvgedfetayavlsllawvpnlvv 142
                                       +++l+   +v++vl+ +airr ++a Hra m++   l ++  +l l+   l +l+g++   +  v+  + ++p l+v
  gi|313125948|ref|YP_004036218.1|  52 NAVLSTTAIVTIVLGVRAIRRGNVARHRALMLSTLGLFIGFLVLYLY--RLTILEGPTEFPSQGVVYQFVYLPTLAV 126
                                       6789999**************************99888877666666..777778999999**************99 PP

                           DUF2306 143 aell 146
                                       + ll
  gi|313125948|ref|YP_004036218.1| 127 HILL 130
                                       9776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00034
                           DUF2306   2 vlHialalvalllGalqlvkrlr...ak.rpklHrlaGrvyvlavllaal 47 
                                       ++Hi+la+v ++l    l+ ++    ++     H+++Grv + + l++ +
  gi|313125948|ref|YP_004036218.1| 125 AVHILLAIVCIPLLYYVLLLAVTrpiEEiYETRHKTVGRVAASLWLVSFV 174
                                       79*******998877776655544554458899**********9999866 PP

>> DUF1240  Protein of unknown function (DUF1240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5   8.9e+03      43      58 ..      10      25 ..       4      40 .. 0.60
   2 ?   -1.5   0.1       1.1   3.8e+03      40      56 ..      49      65 ..      14      71 .. 0.60
   3 ?   -1.2   0.1      0.88   3.1e+03      34      59 ..      68      93 ..      53     101 .. 0.53
   4 !   16.9   0.2   1.9e-06    0.0068       6      57 ..     125     176 ..     122     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                           DUF1240 43 vkllaiiailsfvlsl 58
                                       ++ a+++++s+ l +
  gi|313125948|ref|YP_004036218.1| 10 PGVAAALSVVSLALVF 25
                                      5555556666555544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                           DUF1240 40 dklvkllaiiailsfvl 56
                                       +++ +l++ ai+++vl
  gi|313125948|ref|YP_004036218.1| 49 PHVNAVLSTTAIVTIVL 65
                                      34555666666666665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.88
                           DUF1240 34 klakvndklvkllaiiailsfvlslf 59
                                      + ++  +   +   +++ l++++ + 
  gi|313125948|ref|YP_004036218.1| 68 RAIRRGNVARHRALMLSTLGLFIGFL 93
                                      44444444444455555555555554 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 1.9e-06
                           DUF1240   6 sskvvlllfssPlllYfsvlvvlvaitnklakvndklvkllaiiailsfvls 57 
                                       + ++ l+++  Pll+Y+++l+v+  i++ +   +++++++ a + ++sfvl 
  gi|313125948|ref|YP_004036218.1| 125 AVHILLAIVCIPLLYYVLLLAVTRPIEEIYETRHKTVGRVAASLWLVSFVLG 176
                                       5678999******************************************985 PP

>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.1   6.4e-05      0.23      44     112 ..      17      86 ..       5      90 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.4e-05
                              IncD  44 tilavallvvagllf.sgvlcspvsvlaaslffgvgafllggalvggvltteavtrerlhrsqtlmwnnl 112
                                       +++++al+  a l +    l   vs  a  l+  v a+l   a+v  vl   a+ r  + r ++lm   l
  gi|313125948|ref|YP_004036218.1|  17 SVVSLALVFGAVLGYiPASLLPHVSESALDLIPHVNAVLSTTAIVTIVLGVRAIRRGNVARHRALMLSTL 86 
                                       223333333333322134455678999999************************************8776 PP

>> Otopetrin  Otopetrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.4     2e-05     0.073     267     336 ..      34     103 ..      13     164 .. 0.79
   2 ?   -3.6   0.1      0.99   3.6e+03       7      21 ..     171     185 ..     168     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                         Otopetrin 267 lvrkpklsslailladlselvllalaiiaviigfirvrklkfrreeqleLddiLllisafGlfvysvfsi 336
                                        +  p++s+ a+ l+  ++ vl ++ai+++++g+  +r+ ++ r++ l L  + l+i+ + l++y +  +
  gi|313125948|ref|YP_004036218.1|  34 ASLLPHVSESALDLIPHVNAVLSTTAIVTIVLGVRAIRRGNVARHRALMLSTLGLFIGFLVLYLYRLTIL 103
                                       5667899999999****************************************************97644 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.99
                         Otopetrin   7 vaFglgsmvysglef 21 
                                       v F lg +vy+ l++
  gi|313125948|ref|YP_004036218.1| 171 VSFVLGDVVYTLLHL 185
                                       889999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1213.87
//
Query:       gi|313125949|ref|YP_004036219.1|  [L=377]
Description: multicopper oxidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-29  101.0  13.3    2.5e-18   66.2   3.1    3.0  2  Cu-oxidase_2    Multicopper oxidase
    9.3e-22   77.3   6.1    1.1e-17   64.2   1.1    2.5  2  Cu-oxidase_3    Multicopper oxidase
    3.7e-14   53.2   0.1    2.9e-13   50.2   0.0    2.1  2  Cu-oxidase      Multicopper oxidase
    3.4e-05   23.9   0.0       0.15   12.2   0.0    2.7  2  Cupredoxin_1    Cupredoxin-like domain
    0.00043   20.0   1.8    0.00043   20.0   1.8    1.8  2  TAT_signal      TAT (twin-arginine translocation) pathway sig
  ------ inclusion threshold ------
       0.13   12.9   0.0       0.95   10.0   0.0    2.1  2  Self-incomp_S1  Plant self-incompatibility protein S1


Domain annotation for each model (and alignments):
>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   2.3   2.8e-13   8.3e-10      24     136 ..     101     200 ..      83     201 .. 0.85
   2 !   66.2   3.1   8.2e-22   2.5e-18       6     126 ..     237     344 ..     228     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.8e-13
                                       ETCCTTTSSEEEEEETTEEEEEEEEE-SSS.-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTE CS
                      Cu-oxidase_2  24 ngeefsentnvitlpkgevveiviqnntkl.pHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppgg 99 
                                       ++++ s  ++++++ +ge +e+v++n++   pH++H+HG++ +  + g  +                   ++v+pg+
  gi|313125949|ref|YP_004036219.1| 101 DDRPPSVPAPILRTTEGEDMEVVLDNTQGKrPHTVHFHGVQKAWKDDGVPT----------------TTGITVKPGE 161
                                       4556667788999999**********99999*********88886444444................5678999999 PP

                                       EEEEEEES.S-EEEEEEESSH..HHHHTT-EEEEEEECH CS
                      Cu-oxidase_2 100 wvairfkadnpGvwllHCHil..wHldqGmalqfvvrpd 136
                                       + ++ + a+ pG  ++HCH++   H d+Gm++ f v+p+
  gi|313125949|ref|YP_004036219.1| 162 KHTYTIPANVPGTHIYHCHFQthRHIDMGMYGIFRVDPK 200
                                       9999999**************9999**********9986 PP

  == domain 2  score: 66.2 bits;  conditional E-value: 8.2e-22
                                       CCCCCCCEEEEEEEEEEEETC.CTTTSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCS CS
                      Cu-oxidase_2   6 lptllqltsgneeaseitnge.efsentnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpks 81 
                                       +p+++++  g++       ++  ++e+ ++i + +g++v++ + n + + HP+H+H h+fq +++++g+        
  gi|313125949|ref|YP_004036219.1| 237 NPDVFTIN-GKSA------PRtLHPEDGSPIIVSQGDTVRLHLVNGGYMSHPMHIHNHRFQRVEKDGGT-------- 298
                                       45555555.3332......3327789******************************************9........ PP

                                       SGCCGSSCBSEEEE-TTEEEEEEEES..S-EEEEEEESSHHHHHTT CS
                      Cu-oxidase_2  82 ynlenpvrrdtvqvppggwvairfkad.npGvwllHCHilwHldqG 126
                                       +   +    d++++ p ++ +i+f+a+ +pG +l+HCH   H+ +G
  gi|313125949|ref|YP_004036219.1| 299 VPKAARHDMDVTNIAPAERHTIEFTANsDPGIYLMHCHKVNHVMNG 344
                                       333334445*****************77**************9998 PP

>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   1.1   3.5e-21   1.1e-17      23     117 ..     106     200 ..     104     201 .. 0.95
   2 !   15.1   0.3   5.6e-06     0.017      26     107 ..     257     344 ..     227     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 3.5e-21
                                       SSBS-EEEEETT-EEEEEEEE-S.SS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE CS
                      Cu-oxidase_3  23 qfpgptievregdtvvvnvtNkl.dentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhs 98 
                                       ++p+p ++ +eg++++v + N   +++ ++h+hG+q  ++   DGvp  t   ++pge+ ty+++++   gt+ Yh 
  gi|313125949|ref|YP_004036219.1| 106 SVPAPILRTTEGEDMEVVLDNTQgKRPHTVHFHGVQKAWK--DDGVPTTTGITVKPGEKHTYTIPANV-PGTHIYHC 179
                                       589********************9****************..**************************.******** PP

                                       --TT.HHH.TT-EEEEEEE-H CS
                      Cu-oxidase_3  99 hlsl.qqa.aGlaGaiiiedk 117
                                       h+++ ++  +G++G++ +++k
  gi|313125949|ref|YP_004036219.1| 180 HFQThRHIdMGMYGIFRVDPK 200
                                       ****65558*********986 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 5.6e-06
                                       S-EEEEETT-EEEEEEEE-S..SS-B-EEEET--S-GG.......GSC.....SGGG-B-TT-EEEEEEE--S-SEE CS
                      Cu-oxidase_3  26 gptievregdtvvvnvtNkl..dentsihwhGlqqrktswmDG..vpg.....vtqcpiqpgesftyrftvkqqagt 93 
                                       g  i v +gdtv+++++N    ++++ ih h +q  ++   DG  vp      +    i+p e+ t +ft++   g 
  gi|313125949|ref|YP_004036219.1| 257 GSPIIVSQGDTVRLHLVNGGymSHPMHIHNHRFQRVEK---DGgtVPKaarhdMDVTNIAPAERHTIEFTANSDPGI 330
                                       56799*************87446777777776666666...98442221111134468******************* PP

                                       EEEEE--TTHHHTT CS
                      Cu-oxidase_3  94 lwYhshlslqqaaG 107
                                       ++ h h  ++ ++G
  gi|313125949|ref|YP_004036219.1| 331 YLMHCHKVNHVMNG 344
                                       ****9988876666 PP

>> Cu-oxidase  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.2   6.1e+02      36      74 ..     132     167 ..     110     185 .. 0.61
   2 !   50.2   0.0   9.6e-17   2.9e-13       3     144 ..     209     345 ..     207     360 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.2
                                       -SEEEETTBSS.......CTTTTSGGGEEEEETTEEEEE CS
                        Cu-oxidase  36 pdavlingkggfnatladkdgaslatltvepgktyrlri 74 
                                       p +v + g ++     +d++   ++ +tv+pg+++   i
  gi|313125949|ref|YP_004036219.1| 132 PHTVHFHGVQK---AWKDDGVPTTTGITVKPGEKHTYTI 167
                                       45555555222...2222233457789999999987766 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 9.6e-17
                                       EEEEEEEETCBCTTSCBC.HSSCHCHHHHH.....TT--SEEEETTBSS.......CTTTTSGGGEEEEETTEEEEE CS
                        Cu-oxidase   3 yvitlsDwyhkdakelekellasgkapadt.....ppvpdavlingkggfnatladkdgaslatltvepgktyrlri 74 
                                       y++tl++w  + +  ++ e+         +        pd ++ingk+ +  tl +    +   + v +g+t+rl++
  gi|313125949|ref|YP_004036219.1| 209 YFMTLKEWDSRLNRMMAGED---------MsysprNRNPDVFTINGKSAPR-TLHP---EDGSPIIVSQGDTVRLHL 272
                                       66677777333333322222.........122344567********77765.5454...56899************* PP

                                       EEESSS-BEEEEETSB-EEEEEETCETTS...EEEESCEEE-TTEEEEEEEEE-SSSEEEEEEEE.GSSSCHHH CS
                        Cu-oxidase  75 invsaddslnfsIeGHkltVvevDgvyve...pvevdsldIavGqrysvlvtanqapgnYwivas.grsnliea 144
                                       +n++ + s+++ I++H+++ ve Dg  v      ++d  +Ia+++r ++ +tan +pg Y ++++ ++++ + +
  gi|313125949|ref|YP_004036219.1| 273 VNGGYM-SHPMHIHNHRFQRVEKDGGTVPkaaRHDMDVTNIAPAERHTIEFTANSDPGIYLMHCHkVNHVMNGN 345
                                       ***998.69*******************9888899*****************************6655555554 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0     5e-05      0.15      42      96 ..     117     183 ..     111     187 .. 0.74
   2 !    8.5   0.0   0.00069       2.1      22     100 ..     267     344 ..     252     348 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-05
                      Cupredoxin_1  42 gekvklkiknk.dktpeefesed...........lgeekvlapgktttitiaplkpGeYeftcdmhm 96 
                                       ge +++ ++n+ +k+p+++ ++              +  +++pg+++t ti++  pG++ ++c ++ 
  gi|313125949|ref|YP_004036219.1| 117 GEDMEVVLDNTqGKRPHTVHFHGvqkawkddgvpTTTGITVKPGEKHTYTIPANVPGTHIYHCHFQT 183
                                       66666666664155567777766666666666554444589***********************986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00069
                      Cupredoxin_1  22 tveitvkdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitia.plkpGeYeftcdmhmd 97 
                                       tv++ + +gg+    ++++  +    ++++++ t+ +   +d+++ +++ap + +ti+++ + +pG Y ++c   + 
  gi|313125949|ref|YP_004036219.1| 267 TVRLHLVNGGYMSHPMHIHNHR--FQRVEKDGGTVPKAARHDMDV-TNIAPAERHTIEFTaNSDPGIYLMHCHKVNH 340
                                       5666666666666666666655..224666666667777788888.9***********962578********86555 PP

                      Cupredoxin_1  98 .akG 100
                                        + G
  gi|313125949|ref|YP_004036219.1| 341 vMNG 344
                                       4666 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.8   1.4e-07   0.00043       2      25 ..       8      31 ..       7      32 .. 0.90
   2 ?   -2.6   0.4         2   5.8e+03      15      18 ..      44      47 ..      42      56 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      lSRR FLK++++a+  a +g  a+
  gi|313125949|ref|YP_004036219.1|  8 LSRREFLKATGVAGLSASAGCTAP 31
                                      8**************999998776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                        TAT_signal 15 aAAa 18
                                      +AAa
  gi|313125949|ref|YP_004036219.1| 44 TAAA 47
                                      2332 PP

>> Self-incomp_S1  Plant self-incompatibility protein S1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00032      0.95      26      59 ..     153     186 ..     121     237 .. 0.73
   2 ?    0.4   0.0      0.33   9.7e+02      22      53 ..     304     336 ..     301     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00032
                    Self-incomp_S1  26 gvhtlkpgeefsfsfkenffgttlffCefrwgkk 59 
                                          t+kpge+ +++   n+ gt +++C+f+ + +
  gi|313125949|ref|YP_004036219.1| 153 TGITVKPGEKHTYTIPANVPGTHIYHCHFQTHRH 186
                                       55789************************99772 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.33
                    Self-incomp_S1  22 dddlgvhtlkpgeefsfsfkenff.gttlffCe 53 
                                        +d+ v +++p e+ +++f+ n   g  l +C+
  gi|313125949|ref|YP_004036219.1| 304 RHDMDVTNIAPAERHTIEFTANSDpGIYLMHCH 336
                                       578899999999999999999985577788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2457.82
//
Query:       gi|313125950|ref|YP_004036220.1|  [L=59]
Description: hypothetical protein Hbor_11860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 386.87
//
Query:       gi|313125951|ref|YP_004036221.1|  [L=353]
Description: halocyanin domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-33  114.7   6.7    1.5e-16   60.7   0.7    3.3  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    6.3e-09   35.9   0.0     0.0017   18.5   0.0    2.1  2  Cupredoxin_1  Cupredoxin-like domain
      0.004   17.0  13.4      0.023   14.5   0.4    3.3  3  PKD           PKD domain
  ------ inclusion threshold ------
      0.031   14.7   0.2        7.8    6.9   0.0    2.3  2  DUF2924       Protein of unknown function (DUF2924)
       0.31   11.4   2.8         14    6.0   0.4    2.8  2  LRRNT_2       Leucine rich repeat N-terminal domain


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.7   2.4e-18   8.5e-15       5      98 ..      66     148 ..      61     149 .. 0.87
   2 !   60.7   0.7   4.1e-20   1.5e-16       3      98 ..     201     285 ..     197     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2.4e-18
                                       EEETTETSEEESSEEEEETTEEEEEEEE.SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEE CS
                       Copper-bind   5 lgvesgdlqFetkeitvkkgekvtfvnl.avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtY 80 
                                       +++++g++ F +++++v++g++v+++++ ++ +HNvv + ++        k+++     + ++G ++s tf+eag +
  gi|313125951|ref|YP_004036221.1|  66 ASGNGGNFGFGPAAVRVDPGTTVVWKWNgKGSSHNVVAEDGSF-------KSEM-----VGTSGHTFSHTFEEAGVW 130
                                       5667788*******************9999******9988775.......2333.....5568************** PP

                                       EEEETTTTTTTSEEEEEE CS
                       Copper-bind  81 kffCsPHaaagMkgkvtv 98 
                                       k+ C+PH+ +gMkg+v+v
  gi|313125951|ref|YP_004036221.1| 131 KYACTPHKPMGMKGAVVV 148
                                       ****************98 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 4.1e-20
                                       EEEEETTETSEEESSEEEEETTEEEEEEEE.SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSE CS
                       Copper-bind   3 vklgvesgdlqFetkeitvkkgekvtfvnl.avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeag 78 
                                       v +++++++++F +++i+v++g++v++ ++ ++ +HNvv + ++        k+++     ++ +G ++s  f+e+g
  gi|313125951|ref|YP_004036221.1| 201 VGAKGNGASFAFGPAAIRVDPGTTVVWEWNgKGGAHNVVAEDGSF-------KSEM-----VNKSGHSFSHAFEETG 265
                                       444555566*******************998999****9988775.......2233.....5557************ PP

                                       EEEEEETTTTTTTSEEEEEE CS
                       Copper-bind  79 tYkffCsPHaaagMkgkvtv 98 
                                       tYk+ C+PH+++gMkg v v
  gi|313125951|ref|YP_004036221.1| 266 TYKYACTPHKSMGMKGVVLV 285
                                       *****************988 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.9e-06     0.014      17     104 .]      54     148 ..      37     148 .. 0.76
   2 !   18.5   0.0   4.7e-07    0.0017      17     104 .]     191     285 ..     173     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
                      Cupredoxin_1  17 aaaektveitvkdg......gfePskievkagekvklkiknkdktp.eefesed..lgeekvlapgktttitiaplk 84 
                                         ++ +v+itv         gf P+ + v  g+  ++ +k ++k + +++++ed  ++ e v ++g t++ t+  ++
  gi|313125951|ref|YP_004036221.1|  54 RTGQSEVTITVGASgnggnfGFGPAAVRVDPGT--TVVWKWNGKGSsHNVVAEDgsFKSEMVGTSGHTFSHTF--EE 126
                                       45566677777655788999************9..77777777776699999995555666667777777777..** PP

                      Cupredoxin_1  85 pGeYeftcdmhm.d.akGkliV 104
                                       +G ++++c  h+   +kG ++V
  gi|313125951|ref|YP_004036221.1| 127 AGVWKYACTPHKpMgMKGAVVV 148
                                       *********7776789****98 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.7e-07
                      Cupredoxin_1  17 aaaektveitvkdg......gfePskievkagekvklkiknkdktp.eefesedlgeekvlapgktttitiaplkpG 86 
                                         ++++v+++v  +      +f P+ i v  g+  ++ ++ ++k   +++++ed +++ +   ++ +++  a ++ G
  gi|313125951|ref|YP_004036221.1| 191 RTGNDEVTVEVGAKgngasfAFGPAAIRVDPGT--TVVWEWNGKGGaHNVVAEDGSFKSEMVNKSGHSFSHAFEETG 265
                                       455566666666556789999***********9..777887888765*******7766555555555555566**** PP

                      Cupredoxin_1  87 eYeftcdmhm.d.akGkliV 104
                                       +Y+++c  h+   +kG++ V
  gi|313125951|ref|YP_004036221.1| 266 TYKYACTPHKsMgMKGVVLV 285
                                       *******8884589999987 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.9      0.77   2.8e+03      36      49 ..      50      63 ..      10      69 .. 0.47
   2 !   10.4   0.7   0.00012      0.44      19      54 ..      81     128 ..      77     131 .. 0.86
   3 !   14.5   0.4   6.5e-06     0.023      20      56 ..     216     267 ..     201     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.77
                                      --EEEEETTEEEEE CS
                               PKD 36 svvqvlseptvtht 49
                                      +vv  + +++vt+t
  gi|313125951|ref|YP_004036221.1| 50 GVVDRTGQSEVTIT 63
                                      44445555555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00012
                                       ES.-SS-SEEEEE--SS............--EEEEETTEEEEEE-SSE CS
                               PKD  19 avpdganvtysWdfgdg............svvqvlseptvthtYlspG 54 
                                       +v++g+ v + W+                s    +s++t++ht++++G
  gi|313125951|ref|YP_004036221.1|  81 RVDPGTTVVWKWNGKGSshnvvaedgsfkSEMVGTSGHTFSHTFEEAG 128
                                       45899999999995554999999999***99***************99 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 6.5e-06
                                       S....-SS-SEEEEE--SS............--EEEEETTEEEEEE-SSEEE CS
                               PKD  20 v...pdganvtysWdfgdg............svvqvlseptvthtYlspGeY 56 
                                           ++g+ v ++W+   g            s    +s+++++h ++++G+Y
  gi|313125951|ref|YP_004036221.1| 216 AirvDPGTTVVWEWNGKGGahnvvaedgsfkSEMVNKSGHSFSHAFEETGTY 267
                                       44449**********************************************9 PP

>> DUF2924  Protein of unknown function (DUF2924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0046        17      77     104 ..      79     108 ..      55     114 .. 0.77
   2 ?    6.9   0.0    0.0022       7.8      76     105 ..     215     246 ..     156     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0046
                           DUF2924  77 keelkpGtrLvRewkgr..ehevtvledgf 104
                                       + ++ pGt++v +w+g+  +h+v++ +  f
  gi|313125951|ref|YP_004036221.1|  79 AVRVDPGTTVVWKWNGKgsSHNVVAEDGSF 108
                                       56789*********9872145554444445 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0022
                           DUF2924  76 kkeelkpGtrLvRewkgr..ehevtvledgfe 105
                                       ++ ++ pGt++v ew+g+   h+v++ +  f+
  gi|313125951|ref|YP_004036221.1| 215 AAIRVDPGTTVVWEWNGKggAHNVVAEDGSFK 246
                                       556778*********98732566655544464 PP

>> LRRNT_2  Leucine rich repeat N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4     0.004        14      17      31 ..      33      47 ..      21      48 .. 0.76
   2 ?    4.5   0.1     0.012        43      19      31 ..     172     184 ..     161     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.004
                                      .TTTTTTTGTCCCCT CS
                           LRRNT_2 17 dppgaLssWnssstd 31
                                       +++ LssW s++++
  gi|313125951|ref|YP_004036221.1| 33 AQSPTLSSWFSNTSN 47
                                      45899****989887 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                                       TTTTTTGTCCCCT CS
                           LRRNT_2  19 pgaLssWnssstd 31 
                                       p aL+sW s++++
  gi|313125951|ref|YP_004036221.1| 172 PAALKSWFSNTSN 184
                                       678****989887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2322.62
//
Query:       gi|313125952|ref|YP_004036222.1|  [L=517]
Description: amidophosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.2e-21   74.2   0.0    4.6e-20   71.8   0.0    2.1  3  GATase_7      Glutamine amidotransferase domain
    8.2e-20   71.4   0.0    3.3e-19   69.4   0.0    2.0  2  GATase_6      Glutamine amidotransferase domain
    4.2e-07   29.6   0.1    8.1e-07   28.7   0.1    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0021   17.0   0.0     0.0039   16.1   0.0    1.4  1  GATase_4      Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.47   2.1e+03      93     105 ..      40      52 ..      37      58 .. 0.83
   2 !   71.8   0.0     1e-23   4.6e-20      13     122 ..     117     232 ..     111     233 .. 0.95
   3 ?   -3.8   0.0       2.7   1.2e+04      93     106 ..     453     466 ..     447     472 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.47
                          GATase_7  93 aRDrlGikPLyyg 105
                                         Dr   +PLyy 
  gi|313125952|ref|YP_004036222.1|  40 LADRAAARPLYYS 52 
                                       5699*******97 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 1e-23
                          GATase_7  13 aQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeealerlnGmfAf 80 
                                       aQP++   ++g+l +++nG ++N +e+r+eLe+ gh+f++++Dtev+++ l++        + +++++ r++G++++
  gi|313125952|ref|YP_004036222.1| 117 AQPFSVsFKSGSLGLAHNGNLVNADEIRDELEDLGHAFTSDGDTEVIAHDLARnlleedlvRAVKHTMGRIHGSYSL 193
                                       7999986799**************************************9999899*99**999************** PP

                          GATase_7  81 aiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                        i+++e+  +l++RD+ G +PL +g+ + d++++aSe  a+ 
  gi|313125952|ref|YP_004036222.1| 194 TIMHDET--VLAVRDPQGNRPLCIGKLD-DGYVVASESAAID 232
                                       ****999..******************6.7*******99985 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.7
                          GATase_7  93 aRDrlGikPLyyge 106
                                       +RD +G  +L y+ 
  gi|313125952|ref|YP_004036222.1| 453 IRDDIGADSLSYLS 466
                                       69999999999876 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.93   4.2e+03     110     123 ..      40      52 ..      35      58 .. 0.80
   2 !   69.4   0.0   7.4e-23   3.3e-19      10     134 .]      95     227 ..      81     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.93
                          GATase_6 110 lardrlgvkplyya 123
                                       l +dr + +plyy+
  gi|313125952|ref|YP_004036222.1|  40 L-ADRAAARPLYYS 52 
                                       4.599999****97 PP

  == domain 2  score: 69.4 bits;  conditional E-value: 7.4e-23
                          GATase_6  10 vedevalaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevlla.llee 83 
                                        +++++++HvR  ++g  ++  aqPf  + ++g l l+hNG   n++e+r+el++  g+af s+ Dtev+++ l+++
  gi|313125952|ref|YP_004036222.1|  95 LTGTTGIGHVRYPTSGGLDSCCAQPFsvSFKSGSLGLAHNGNLVNADEIRDELED-LGHAFTSDGDTEVIAHdLARN 170
                                       46679************855555***99999************************.****************88855 PP

                          GATase_6  84 lG........eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                       l         ++++ r+ G ++  i+    +t+  +rd  g++pl+++  ++g ++ase
  gi|313125952|ref|YP_004036222.1| 171 LLeedlvravKHTMGRIHGSYSLTIMH--DETVLAVRDPQGNRPLCIGKLDDGYVVASE 227
                                       443334456677777888877776654..6667777**********************8 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   1.8e-10   8.1e-07      16     120 ..     295     420 ..     283     424 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.8e-10
                                       EETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE..................... CS
                      Pribosyltran  16 arlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes............. 79 
                                       ++l +++ ee + + dvv++++  G  fa+ +a + +   +  +   +++d+s e+a+g+++++             
  gi|313125952|ref|YP_004036222.1| 295 RDLGRKLWEESGVESDVVMPVPDSGRAFATGYAEAANE--TTADGDPRESDDSVEFAEGLMKNRyvgrtfimptqde 369
                                       455555666667799*********************84..55678899999999*********9************* PP

                                       ..........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran  80 ..........rlledpagkkVliVDDildtGgTllaalelLkekgpeevri 120
                                                    + ++g++V i+DD +  G+T +  ++l++++g+eev++
  gi|313125952|ref|YP_004036222.1| 370 reravrlklnPIKSTIEGRSVTIIDDSIVRGTTSRQLVQLVRDAGAEEVHV 420
                                       *********999999*********************************985 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.8e-07    0.0039      73     133 ..      99     163 ..      89     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.8e-07
                          GATase_4  73 nvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlke...ykpkl...egrfePvGsTDsEla 133
                                         + H+R  t G      ++pF+ +++  +  +AHnG+l +   ++++l    + f+   + D+E++
  gi|313125952|ref|YP_004036222.1|  99 TGIGHVRYPTSGGLDSCCAQPFSVSFKSGSLGLAHNGNLVNadeIRDELedlGHAFT--SDGDTEVI 163
                                       5689***********************************661225555532222232..33455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 3141.42
//
Query:       gi|313125953|ref|YP_004036223.1|  [L=58]
Description: 50S ribosomal protein L37e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-22   79.9  11.2    1.2e-22   79.8  11.2    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
     0.0022   18.2   2.1      0.003   17.8   2.1    1.3  1  Ribosomal_L32p  Ribosomal L32p protein family
  ------ inclusion threshold ------
      0.011   15.8   2.7      0.014   15.4   2.7    1.1  1  DZR             Double zinc ribbon
      0.014   15.5   3.4      0.043   14.0   3.4    1.7  1  zf-piccolo      Piccolo Zn-finger
      0.081   12.9   1.9       0.09   12.8   1.9    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.09   12.5   6.5       0.61    9.9   0.6    2.1  2  zinc_ribbon_2   zinc-ribbon domain
       0.11   11.9   2.7        5.3    6.6   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
        0.3   10.9   4.9        3.1    7.6   0.5    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.73    9.8   5.3        1.2    9.1   0.5    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
          2    8.5   6.8        3.4    7.7   0.5    2.2  2  YhfH            YhfH-like protein


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8  11.2   6.8e-26   1.2e-22       2      53 ..       4      55 ..       3      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 6.8e-26
                    Ribosomal_L37e  2 kGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKa 53
                                       Gt+s+Gk++k+ tH++CrrCg++syhv+kk+C+scG+ +sak r+y+W++K 
  gi|313125953|ref|YP_004036223.1|  4 AGTPSQGKKNKT-THVKCRRCGEKSYHVNKKVCSSCGFgKSAKRRDYEWQSKT 55
                                      6********666.*************************************995 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.1   1.6e-06     0.003      20      50 ..      11      43 ..       7      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                      ------EEEETTTC..CEECTTC-BTTTTBSSS CS
                    Ribosomal_L32p 20 klkapnlvecpncg..elklpHrvcpscGyYkg 50
                                      k +  + v+c  cg  ++++ + vc+scG+ k 
  gi|313125953|ref|YP_004036223.1| 11 KKNKTTHVKCRRCGekSYHVNKKVCSSCGFGKS 43
                                      55566899******6679***********9875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.7   7.8e-06     0.014      27      49 .]      13      39 ..       4      39 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.8e-06
                               DZR 27 a...edrCpsCgek.vdpearfCpeCG 49
                                      +   + +C +Cgek  + ++++C +CG
  gi|313125953|ref|YP_004036223.1| 13 NkttHVKCRRCGEKsYHVNKKVCSSCG 39
                                      1344899******9999*********9 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.4   2.4e-05     0.043      17      49 ..      14      52 ..       6      56 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                        zf-piccolo 17 ppnyntCteC.......kkqvCnlCGFnptphltekkeWl 49
                                      ++ + +C  C       +k+vC+ CGF  + +     eW 
  gi|313125953|ref|YP_004036223.1| 14 KTTHVKCRRCgeksyhvNKKVCSSCGFGKSAKRR-DYEWQ 52
                                      44555555553323222789*******9966544.47886 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.9     5e-05      0.09      67      94 ..      14      40 ..       9      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                                      E--EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA 67 vpvkvrCreCgkefeleekalrCpkCgs 94
                                      +  +v+Cr+Cg++  + +k   C +Cg 
  gi|313125953|ref|YP_004036223.1| 14 KTTHVKCRRCGEKSYHVNK-KVCSSCGF 40
                                      56789******88875544.57****95 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6   0.00034      0.61       6      22 ..      10      26 ..      10      27 .. 0.88
   2 ?    9.6   5.9   0.00042      0.76       1      21 [.      19      40 ..      19      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                     zinc_ribbon_2  6 GaelqdnakFCpyCGtp 22
                                      G++++ + + C +CG++
  gi|313125953|ref|YP_004036223.1| 10 GKKNKTTHVKCRRCGEK 26
                                      89999999999999986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00042
                     zinc_ribbon_2  1 fCpnCGaelqd.nakFCpyCGt 21
                                      +C +CG++    n k C+ CG+
  gi|313125953|ref|YP_004036223.1| 19 KCRRCGEKSYHvNKKVCSSCGF 40
                                      8********8648888*****7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3    0.0058        10      11      25 ..      13      26 ..      10      27 .. 0.67
   2 ?    6.6   0.2     0.003       5.3       3       9 ..      33      39 ..      30      46 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0058
                       zf-ribbon_3 11 plssddnvCpyCGtk 25
                                      + ++  ++C  CG+k
  gi|313125953|ref|YP_004036223.1| 13 N-KTTHVKCRRCGEK 26
                                      5.6666788888865 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.003
                       zf-ribbon_3  3 vrCPnCG 9 
                                      + C++CG
  gi|313125953|ref|YP_004036223.1| 33 KVCSSCG 39
                                      5566666 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4    0.0091        16       3      10 ..      20      27 ..      19      30 .. 0.76
   2 ?    7.6   0.5    0.0017       3.1       2       9 ..      34      41 ..      34      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0091
                      Rubredoxin_2  3 CsqCGfes 10
                                      C++CG +s
  gi|313125953|ref|YP_004036223.1| 20 CRRCGEKS 27
                                      89999876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0017
                      Rubredoxin_2  2 vCsqCGfe 9 
                                      vCs+CGf 
  gi|313125953|ref|YP_004036223.1| 34 VCSSCGFG 41
                                      7*****96 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.5   0.00066       1.2      14      28 ..       8      24 ..       6      29 .. 0.78
   2 ?    3.5   0.5     0.036        65      17      28 ..      32      39 ..      27      45 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00066
                                      EECSCCCE..EEESSSS CS
                    RNA_POL_M_15KD 14 kedkegkn..feCrqCg 28
                                       ++k++k   + Cr Cg
  gi|313125953|ref|YP_004036223.1|  8 SQGKKNKTthVKCRRCG 24
                                      5566776679******8 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.036
                                      SCCCEEEESSSS CS
                    RNA_POL_M_15KD 17 kegknfeCrqCg 28
                                      k++    C++Cg
  gi|313125953|ref|YP_004036223.1| 32 KKV----CSSCG 39
                                      555....99997 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.0     0.022        39      15      22 ..      19      26 ..      13      29 .. 0.84
   2 ?    7.7   0.5    0.0019       3.4      11      20 ..      30      39 ..      27      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.022
                              YhfH 15 kCteCGke 22
                                      kC  CG++
  gi|313125953|ref|YP_004036223.1| 19 KCRRCGEK 26
                                      8*****96 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0019
                              YhfH 11 LPkKkCteCG 20
                                        kK+C++CG
  gi|313125953|ref|YP_004036223.1| 30 VNKKVCSSCG 39
                                      679******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 368.71
//
Query:       gi|313125954|ref|YP_004036224.1|  [L=77]
Description: small nuclear ribonucleoprotein, lsm family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-15   56.3   0.1    3.3e-15   55.5   0.1    1.4  1  LSM       LSM domain
    2.1e-06   27.7   0.0    2.7e-06   27.4   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1   3.7e-19   3.3e-15       2      66 ..       8      76 ..       7      77 .] 0.80

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3.7e-19
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEE...EEEEEETTET...EEEEEEE.EEEEGGGEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLe...dveetlkdkk...ekrklgl.vliRGnnivlis 66
                                       l+ ++++ vtv+lk+g  + GtL g+Dq+mN+vLe   d ee +       e++ +++ ++iRG+n+v+i 
  gi|313125954|ref|YP_004036224.1|  8 VLEASLEESVTVNLKDGSSYYGTLAGYDQHMNVVLEapaDEEEAI---LgeiEVTPVEDtTIIRGDNVVTIK 76
                                      588899*****************************8332333333...134589999655*********996 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     3e-10   2.7e-06      15      80 ..      16      77 .]       4      77 .] 0.93

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3e-10
                                      EEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS...........-EEEEEEE-GGGEEEEXX CS
                            SM-ATX 15 evevtvknGevyeGifstvslekdfsvvLkmarkvkkanskssspssgeipdtliikakdivdiea 80
                                      +v+v +k+G+ y G + +++    ++vvL+++   ++      ++  ++++dt ii+++++v+i a
  gi|313125954|ref|YP_004036224.1| 16 SVTVNLKDGSSYYGTLAGYDQ--HMNVVLEAPADEEE--AILGEIEVTPVEDTTIIRGDNVVTIKA 77
                                      79*******************..**********9999..7888999999999***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 493.33
//
Query:       gi|313125955|ref|YP_004036225.1|  [L=350]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-15   57.9   0.0    2.3e-15   57.1   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      7e-12   45.5   0.0    2.7e-11   43.6   0.0    2.0  2  PAS_9        PAS domain
      1e-09   38.6   2.4    1.2e-09   38.4   0.8    1.9  2  PAS_4        PAS fold
    3.3e-08   33.5   0.1    6.2e-08   32.7   0.1    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0019   18.2   0.0      0.006   16.6   0.0    1.9  1  PAS_8        PAS domain
     0.0026   17.3   0.2     0.0047   16.5   0.2    1.4  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
     0.0043   17.3   0.1     0.0096   16.2   0.1    1.6  1  PAS_3        PAS fold
     0.0064   16.5   0.8      0.017   15.2   0.8    1.8  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0071   16.3   0.0      0.015   15.3   0.0    1.6  1  PAS          PAS fold
  ------ inclusion threshold ------
      0.079   13.2   0.1        1.1    9.6   0.0    2.5  2  GAF_2        GAF domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   1.3e-18   2.3e-15       3     109 ..     236     340 ..     234     343 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.3e-18
                                       HHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE...TEEEEEEEESSSSSTTHHHT..GTCSTTCHHCSTCHTSTSS CS
                         HATPase_c   3 ekrLrqiisnlvdNavkfatkageieveikase...ddlvisveDnGiGipkedlk..klfekfsqddstkrggggt 74 
                                       ++rL  +i++l++N vk+ t++++ ev+i+as    ++++i v+D G+Gip  ++   +        +++++   g+
  gi|313125955|ref|YP_004036225.1| 236 SSRLSAVIDELCENGVKH-TSCDSPEVRIDASRvdgNWVKICVTDEGPGIPDHERAvlRH-------GEETDLVHGS 304
                                       789***************.99*********9545669***************88882222.......22334568** PP

                                       SHHHHHHHHHHHHTTTEEEEEEET.TTEEEEEEEEE CS
                         HATPase_c  75 GlGlsivkklvelmgGeiwvesep.grGttftftlp 109
                                       GlG+ +v+ +v+++gG+++v + p g G+ +t+++p
  gi|313125955|ref|YP_004036225.1| 305 GLGFWLVRTVVRRIGGHLRVADAPnGSGSVVTVYVP 340
                                       ********************9999899******998 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   1.5e-14   2.7e-11       5     104 .]      23     125 ..      19     125 .. 0.91
   2 ?   -1.6   0.0       1.9   3.3e+03      47      77 ..     285     309 ..     237     325 .. 0.67

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.5e-14
                             PAS_9   5 li..dnpdg.ril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetf 76 
                                       ++   ++dg +++ ++N+ +l+ lGy+ e v+g+++t+++ t+++a++ l+  +e+ r+    ++e ++ + +g+ +
  gi|313125955|ref|YP_004036225.1|  23 VVtrPDEDGvPVIeDCNDRFLERLGYDYESVIGRRVTEFY-TAESAANHLHGGYERARRgDYDREERDFLTADGNVI 98 
                                       44366688899999**************************.**********99999999988999************ PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                        + ++a+p +  dge+vg++++ +D+te
  gi|313125955|ref|YP_004036225.1|  99 STVVRATPRRV-DGEVVGVVAVYVDVTE 125
                                       *********87.58*************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                             PAS_9  47 nerlraaleqgrkkerevevvlirkngetfw 77 
                                        + +ra+l+ g+      e++l++ +g  fw
  gi|313125955|ref|YP_004036225.1| 285 PDHERAVLRHGE------ETDLVHGSGLGFW 309
                                       444444444444......6666676776666 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.8   6.5e-13   1.2e-09       4     109 ..      18     127 ..      15     127 .. 0.92
   2 ?   -1.8   0.0         2   3.5e+03      12      58 ..     162     179 ..     138     205 .. 0.57

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 6.5e-13
                             PAS_4   4 lpdalavl..dpdgr..vlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelllp 75 
                                       lp++++v   d+dg+  ++++N ++ e +g++ e+++G+++ e++++e +a  l+  ++r+ +g+   e+ ++l+ +
  gi|313125955|ref|YP_004036225.1|  18 LPVLVVVTrpDEDGVpvIEDCNDRFLERLGYDYESVIGRRVTEFYTAEsAANHLHGGYERARRGDYDREERDFLTAD 94 
                                       6888888899999954499************************999997888899********************** PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       g      +r++P r  +Gev+gv+++ +D+Te++
  gi|313125955|ref|YP_004036225.1|  95 GNVISTVVRATPRR-VDGEVVGVVAVYVDVTEQK 127
                                       ************86.9****************85 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                             PAS_4  12 dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrr 58 
                                       d++++v+ aN                              + ra++r
  gi|313125955|ref|YP_004036225.1| 162 DDESVVESAN-----------------------------VVGRAVER 179
                                       3333333333.............................33333333 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   3.4e-11   6.2e-08       7     112 ..     203     318 ..     194     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.4e-11
                       HATPase_c_2   7 hvrtvrevaeavlrraglseelld............eirlaveEactNavehayleapegpvevrlesdeealtvev 71 
                                       h++++ + ++ +  + g+++++++            ++  +++E+c N v+h   + pe ++  + ++d+++++++v
  gi|313125955|ref|YP_004036225.1| 203 HLPKLLHEVQTAV-EMGWPDATIQieqqvadvhvssRLSAVIDELCENGVKHTSCDSPEVRIDAS-RVDGNWVKICV 277
                                       5555444444432.46666666666666666777789999***************9997777777.899999***** PP

                       HATPase_c_2  72 aDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvDev 112
                                       +D+Gpg  d e +  +   e ++    +G+G  l++++v  +
  gi|313125955|ref|YP_004036225.1| 278 TDEGPGiPDHERAVLR-HGEETDLVHGSGLGFWLVRTVVRRI 318
                                       ******7777655555.555679**************99877 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.4e-06     0.006      11      45 ..      19      58 ..      15      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.4e-06
                             PAS_8 11 pdgiavvd..lgd..rivdvNqaalellGys.adlkgell 45
                                      p+ ++v+   +++   i d+N+++le lGy+ + ++g  +
  gi|313125955|ref|YP_004036225.1| 19 PVLVVVTRpdEDGvpVIEDCNDRFLERLGYDyESVIGRRV 58
                                      5566655442334788*************99555555444 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   2.6e-06    0.0047     113     163 ..     111     159 ..      92     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-06
                         HisKA_4TM 113 GllaGylaararadasrakrisdalafvndlirhdlrndlvvirgyaeaie 163
                                       G + G  a+    d +  k   + +  +n ++rh++rndl+v++g+ae+++
  gi|313125955|ref|YP_004036225.1| 111 GEVVGVVAV--YVDVTEQKWREQHVNVLNRVMRHNIRNDLNVLHGHAEMLA 159
                                       445554443..34666667777788899*******************9875 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   5.4e-06    0.0096       3      88 ..      37     119 ..      35     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.4e-06
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy.egeyRirrkdGeyrwveararvirde 78 
                                        +++r+ e lGy+ e+++g+  ++ ++   e  ++  +   e +++g  y  +e  ++++dG ++    ra++    
  gi|313125955|ref|YP_004036225.1|  37 DCNDRFLERLGYDYESVIGR--RVTEFYTAESAANHLHGGYERARRGD-YdREERDFLTADGNVISTVVRATPR-RV 109
                                       69******************..**********7777777777776666.8355588*****************8.99 PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g++v v++v
  gi|313125955|ref|YP_004036225.1| 110 DGEVVGVVAV 119
                                       9999999876 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.8   9.3e-06     0.017       7      62 ..     138     191 ..     134     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHC CS
                             HisKA   7 agvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdls 62 
                                         + H +r+ L+++ g ae+L  +   +e++ e  +++ + ++r ++l e   +++
  gi|313125955|ref|YP_004036225.1| 138 RVMRHNIRNDLNVLHGHAEMLAQH--DDESVVESANVVGRAVERWLSLTEKATEIE 191
                                       6799*****************884..789999999999999998888887765555 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.2e-06     0.015      23     109 ..      35     119 ..       9     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.2e-06
                                       EEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEE CS
                               PAS  23 ilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrd 98 
                                       i  +N+ + e lG++ e v+g+ + +++  e+ a  l+  +e++++   +++   ++f + dg +i  +vra+p+r 
  gi|313125955|ref|YP_004036225.1|  35 IEDCNDRFLERLGYDYESVIGRRVTEFYTAESAAnHLHGGYERARRGDYDREE--RDFLTADGNVISTVVRATPRRV 109
                                       5579************************9997666666666666665555554..555668***************9 PP

                                       TTEEEEEEEEE CS
                               PAS  99 aggeilgflgv 109
                                        g+ + g++ v
  gi|313125955|ref|YP_004036225.1| 110 DGE-VVGVVAV 119
                                       865.5588776 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.49   8.7e+02     112     136 ..      77     101 ..      69     103 .. 0.81
   2 ?    9.6   0.0    0.0006       1.1      99     132 ..     108     142 ..     104     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.49
                                       ......--HHHHHHHHHHHHHHHHH CS
                             GAF_2 112 ankppafdeedlelLeelaeqiaia 136
                                       +++++++d+e++++L++ ++ i+++
  gi|313125955|ref|YP_004036225.1|  77 RARRGDYDREERDFLTADGNVISTV 101
                                       568899*********9877777665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0006
                                       -TTS---EEEEE.S......--HHHHHHHHHHHHH CS
                             GAF_2  99 isegrvvGvlnl.yankppafdeedlelLeelaeq 132
                                       + +g+vvGv+++ +   ++++ e+++ +L+ ++++
  gi|313125955|ref|YP_004036225.1| 108 RVDGEVVGVVAVyVDVTEQKWREQHVNVLNRVMRH 142
                                       569*********44778888**********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2147.98
//
Query:       gi|313125956|ref|YP_004036226.1|  [L=450]
Description: hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-08   32.5   2.0    1.6e-06   27.8   0.2    2.6  3  Lactamase_B_2  Beta-lactamase superfamily domain
    9.9e-08   32.2   2.4      3e-07   30.6   2.4    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00082   19.3   0.8      0.033   14.1   0.1    2.9  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.52   3.1e+03     138     167 ..       6      35 ..       4      52 .. 0.75
   2 !   27.8   0.2   2.7e-10   1.6e-06      30     113 ..      73     154 ..      58     181 .. 0.84
   3 !    3.6   0.0     0.007        42     134     200 ..     349     413 ..     320     414 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.52
                                       EEESS-S---HHHHHHHCT-SEEEEE-S-S CS
                     Lactamase_B_2 138 yyigDtgyipeeigerlggadllllditay 167
                                       + ig+ +++  ++ +  +g d++++d+++ 
  gi|313125956|ref|YP_004036226.1|   6 ATIGGYEEVGRQMTAVRAGDDVVVFDMGLN 35 
                                       567888888888888888899999999875 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 2.7e-10
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEE.CSTTEEE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfel.gdgglei 105
                                       +++a++ th+H DH+  +  l+++++  +p++a++ +++ ++++   +++ +  + +++++++ge +++ ++g++e+
  gi|313125956|ref|YP_004036226.1|  73 DVKAIVPTHGHLDHIGAISKLAHRYD--APIVASPFTIELVKQQVEGENKFNV-GNDLVKMEAGEMMSIgDSGNVEL 146
                                       799************99999999554..8***************888888888.9**************64457888 PP

                                       EEEEE-EE CS
                     Lactamase_B_2 106 tatparhk 113
                                       +++ + h+
  gi|313125956|ref|YP_004036226.1| 147 EFVHVTHS 154
                                       88888886 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.007
                                       TEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 134 gkrvyyigDtgyipeeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                       g +v +++ +   p   g+r++   ll +++ +  dd      gHl  e+  +++++l+++ +++ H
  gi|313125956|ref|YP_004036226.1| 349 GDKVIFSARVIPEPTNEGQRYQSERLLKMQGARIYDDIH--VSGHLREEGHYQMLDALQPQHVIPAH 413
                                       555555555555556677888888888888776666553..689*********************99 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   2.4     5e-11     3e-07       9      87 ..      19     116 ..      12     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 5e-11
                                       EEEEETTCEEEES--SCHHHHHHHH...................HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTT CS
                       Lactamase_B   9 yliegdggviLiDtGtsteaaraal...................elaalglkpkdvdavilTHlHlDHiGglgglve 66 
                                       + ++ +++v+++D G+  ++ ++ +                   + +       dv+a++ TH+HlDHiG+  +l++
  gi|313125956|ref|YP_004036226.1|  19 TAVRAGDDVVVFDMGLNLSQVLIHDnvetekmhsldlidmgaipDDRVMSDLEGDVKAIVPTHGHLDHIGAISKLAH 95 
                                       556666666666666666666665566666666666666666555555566678*********************** PP

                                       HHCCEETCCEHHHHCCHCHHH CS
                       Lactamase_B  67 atdvpvgavaeeapalfmeea 87 
                                       ++d+p++a + + +  +   +
  gi|313125956|ref|YP_004036226.1|  96 RYDAPIVASPFTIELVKQQVE 116
                                       ******998776666655555 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.031   1.9e+02      33      53 ..      76      95 ..      73     119 .. 0.84
   2 !   14.1   0.1   5.6e-06     0.033       9      38 ..     384     413 ..     380     418 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.031
                             RMMBL 33 nvilvHGeeeatsalarllke 53
                                       +++ HG+ +++ a  +l+  
  gi|313125956|ref|YP_004036226.1| 76 AIVPTHGHLDHIGAISKLA-H 95
                                      59***********999988.3 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.6e-06
                             RMMBL   9 eeidfSgHadknellelirklkprnvilvH 38 
                                       ++i++SgH   +++ +++  l+p++vi+ H
  gi|313125956|ref|YP_004036226.1| 384 DDIHVSGHLREEGHYQMLDALQPQHVIPAH 413
                                       5799************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2609.75
//
Query:       gi|313125957|ref|YP_004036227.1|  [L=348]
Description: geranylgeranylglyceryl diphosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-66  223.0   0.4    3.8e-66  222.8   0.4    1.1  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
      0.061   13.7   0.6       0.15   12.4   0.6    1.7  1  Endotoxin_C2     Delta endotoxin


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.8   0.4   4.2e-70   3.8e-66       2     228 ..      35     274 ..      34     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 4.2e-70
                                       HHHHHHHHHHHHSSS--HHHHHHHHHHHHHSCG.......H.......HHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                   polyprenyl_synt   2 elleealeylveagGKrlRpllvllaaealkee.......e.......eelekaavlawivellhaasLvhDDimDd 64 
                                       e l+ea++yl+eagGKrlRp+++ll+aeal++        +           ++ ++a+ +e++++++L+hDDimDd
  gi|313125957|ref|YP_004036227.1|  35 ERLYEATRYLLEAGGKRLRPTVTLLTAEALADAeplsedyRsfpaldgA-DIDVMAAAVSIEVIQSFTLIHDDIMDD 110
                                       57999**************************333566555055555543.356999********************* PP

                                       -SEETTEE-HHHCTCHHHHHHHHHHHHHHHHHHHHHHH..STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC. CS
                   polyprenyl_synt  65 setRRGqpcahrlvGnklAindgdfllarafellaklf..eks.lellelfsevllqtveGqlldleeekdddlskf 138
                                       +++RRG p++h+++++++Ai++gd l+a+afe ++++    ++ le+++l+++++++++eGq+ld+e e+++++   
  gi|313125957|ref|YP_004036227.1| 111 DDLRRGVPAVHKEYDTETAILAGDTLYAKAFEFMTQTGadPQNgLEAVRLLATTCTKICEGQALDVEFERRTEVL-- 185
                                       ************************************99964447**********************999999999.. PP

                                       SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT- CS
                   polyprenyl_synt 139 sleeyleivkyKTaylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegk 215
                                         +eyle+v+ KTa+l+ +++a a +l ga+de++eal+++g   G aFQiqDD+lDl+  +e+lgK+ g+D+ e+k
  gi|313125957|ref|YP_004036227.1| 186 -PDEYLEMVELKTAVLYGAAAATAGVLMGADDETVEALYRYGIDSGCAFQIQDDVLDLTVPSEKLGKQRGSDLVENK 261
                                       .*****************************9********************************************** PP

                                       --HHHHHHHHCT- CS
                   polyprenyl_synt 216 ctlpilkalelas 228
                                        tl++l+a ++  
  gi|313125957|ref|YP_004036227.1| 262 ETLITLHARQQGV 274
                                       ********99443 PP

>> Endotoxin_C2  Delta endotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   1.7e-05      0.15      24      61 ..     286     324 ..     277     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                      Endotoxin_C2  24 dtttqaaIdaAqalVdkvtd.stkKaeLqadidkAqelL 61 
                                       +++t+++IdaA a+ +kv +    +++ q+  d+A+ +L
  gi|313125957|ref|YP_004036227.1| 286 EGVTEDDIDAAVAELNKVGSiDYARDKAQELTDRAKRHL 324
                                       589*****************999*************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2194.58
//
Query:       gi|313125958|ref|YP_004036228.1|  [L=577]
Description: glutamyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-59  201.5   0.0    1.9e-59  201.1   0.0    1.1  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    5.8e-18   65.4   0.0    1.7e-17   63.9   0.0    1.8  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.1   0.0   2.1e-63   1.9e-59       1     309 [.     107     412 ..     107     417 .. 0.92

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 2.1e-63
                                       S-EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--H..HHHHHHHHHHHHTT---SSEEEEGG CS
                      tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpereke..eaeesiledlkwlgikwdekptyqs 75 
                                       +Vr R aP+P+G  HiGha+   +   +   ++G+fi+R++DTdpe + +  +a ++iled+++lg+++ +++ ++s
  gi|313125958|ref|YP_004036228.1| 107 EVRMRAAPNPNGPWHIGHARMPAVIGTYKDLYDGSFIVRFDDTDPETKRPdlDAYDAILEDVEYLGFEP-DEVLRAS 182
                                       69******************************************986665226899*************.66***** PP

                                       GGHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBT CS
                      tRNA-synt_1c  76 drfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkide 152
                                       dr +++++ a e+i+ GkAY c c+ e   e++++     +++rd+  e  ++ f e m +g+++++++v+R+k d 
  gi|313125958|ref|YP_004036228.1| 183 DRVETYYDHAREIIEMGKAYTCSCSGEDFSELKNA--GEPCPHRDKDPETTREEF-EAMIDGEYSSGEMVLRIKTDI 256
                                       *********************************99..9999**************.9*******************9 PP

                                       TSS.GGGSSTEEEEEEESGGGSBTT.TBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S. CS
                      tRNA-synt_1c 153 ess.vefrDlvrgriklepqeihdl.vivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglev 227
                                       e++  ++rD v+ r+  +p   h++     ++  P+ df   +dD+l ++th++r+ + +d+ +++  l++++g+e 
  gi|313125958|ref|YP_004036228.1| 257 EHKnPALRDWVAFRMVDTP---HPReEAADYRCWPMLDFQSGVDDHLTGVTHIIRGIDLQDSAKRQGFLYDYFGWEY 330
                                       9999***************...66515678999*******************************************9 PP

                                       -EEE.EEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHH CS
                      tRNA-synt_1c 228 ppfi.heylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresks 303
                                       p+++ +  + + + + k+S   l+  ++  ++++wdd+r ++l+ lrr+G+  +++ + + + + ++s+ ++ ++++
  gi|313125958|ref|YP_004036228.1| 331 PEVVhWGHVQVDAYDVKMSTSTLKEKIEAGELDGWDDPRAPTLKSLRRRGIRGSAIVDAMLELGTSTSD-VDLSMSA 406
                                       8766156778889999***************************************99999999999998.8777777 PP

                                       HHHHHH CS
                      tRNA-synt_1c 304 leafdr 309
                                       + + +r
  gi|313125958|ref|YP_004036228.1| 407 IYSNNR 412
                                       666555 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   1.9e-21   1.7e-17       1     174 []     419     557 ..     419     557 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.9e-21
                    tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveev 77 
                                       A+Ry+ V+d  ++ +e+     ++  + +lhp+++++g r+vp ++ + ie +D+     ge+v Lk+ ++++ e+ 
  gi|313125958|ref|YP_004036228.1| 419 ADRYFLVRDGERFAVEGG----PDAGHPALHPDHEDRGDRTVPATDGVRIESADVPA--SGERVWLKGYGCVRREDD 489
                                       89**************54....5699****************************765..69*************887 PP

                    tRNA-synt_1c_C  78 ekdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepa 153
                                                   l   ++++e  r+ +  +ihW +ae++v +                 + + +++    +g+aep+
  gi|313125958|ref|YP_004036228.1| 490 A-----------LVHTDDTIEAVRSGDVdVIHWAPAEDNVAV----------------RMRTMEGDV---TGVAEPD 536
                                       2...........33344588777888889*************................888888883...7****** PP

                    tRNA-synt_1c_C 154 lanlkkgdivQfeRiGyfrvd 174
                                       +a+ + +d+vQfeRiG++rvd
  gi|313125958|ref|YP_004036228.1| 537 FADTETDDVVQFERIGFVRVD 557
                                       ********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 3276.42
//
Query:       gi|313125959|ref|YP_004036229.1|  [L=218]
Description: kynurenine formamidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-21   74.6   0.2    1.3e-20   74.0   0.2    1.3  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.2   7.2e-25   1.3e-20       1     136 []       5     149 ..       5     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 7.2e-25
                           Cyclase   1 idLshplsedtpvwp.dp...................islsehtGTHlDapgHfae..ktidelpleelvgpavvld 55 
                                       +dL+ p++ ++p++p dp                   ++l++htGTH+Dap+H  +  +t+d+ ++e++ ++a ++d
  gi|313125959|ref|YP_004036229.1|   5 VDLTRPVETGMPTYPgDPdvavtphatqeadgyrvsrLELGTHTGTHIDAPAHTERdgATLDSFDAERFRFDARLVD 81 
                                       7*************65556678889999*************************766888****************** PP

                           Cyclase  56 vsakaaaedyeiitaedleaalakqgveikpgdivlirTgwskrledkeky.rnpglseeaaewlaekgvkavGvDt 131
                                       ++     +  e i  e + ++         + +++++rTgw+++ ++++++ ++p+l +e+ae  a+ g  +vG+D+
  gi|313125959|ref|YP_004036229.1|  82 CRGV---GANEAIGSEAVPET---------DAEMLVFRTGWEAE-WGTDRMtEHPYLAPETAERCADAG-YHVGIDA 144
                                       *776...23335577777443.........6789********99.778999999*************88.589**** PP

                           Cyclase 132 lsvDa 136
                                       ls D+
  gi|313125959|ref|YP_004036229.1| 145 LSPDP 149
                                       **995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       134  (0.00747392); expected 358.6 (0.02)
Passed bias filter:                      122  (0.00680462); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1446.07
//
Query:       gi|313125960|ref|YP_004036230.1|  [L=55]
Description: hypothetical protein Hbor_11960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.13   12.2   0.5       0.21   11.6   0.5    1.4  1  DUF2116    Uncharacterized protein containing a Zn-ribbon (DU
        0.5   10.3   1.9       0.56   10.2   1.9    1.1  1  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   2.4e-05      0.21      37      58 ..       4      25 ..       1      26 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                           DUF2116 37 rsqqilfgililllavvlvlkf 58
                                       +  +lf+il+++ a+++ ++f
  gi|313125960|ref|YP_004036230.1|  4 STDVLLFAILLVVFAIWMATAF 25
                                      57789*************9986 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9   6.3e-05      0.56      75     113 ..      12      49 ..       3      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.3e-05
                         RseC_MucC  75 llllilgallgsallgssellaalgallglvlgflivrl 113
                                       +ll+++++++++a+  +  l++ l+al+gl +g++i+ +
  gi|313125960|ref|YP_004036230.1|  12 ILLVVFAIWMATAF-DAAWLISSLVALAGLSIGIVIMSR 49 
                                       45555555556666.799999*************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 365.90
//
Query:       gi|313125961|ref|YP_004036231.1|  [L=159]
Description: hypothetical protein Hbor_11970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-26   93.9  24.8      1e-26   93.9  24.8    1.4  2  DUF456           Protein of unknown function (DUF456)


Domain annotation for each model (and alignments):
>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   1.6      0.89   1.6e+04      73      79 ..       9      15 ..       4      19 .. 0.34
   2 !   93.9  24.8   5.7e-31     1e-26       1     137 [.      20     155 ..      20     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.89
                            DUF456 73 vGffllp 79
                                      +G+ +++
  gi|313125961|ref|YP_004036231.1|  9 IGLAVVG 15
                                      2222222 PP

  == domain 2  score: 93.9 bits;  conditional E-value: 5.7e-31
                            DUF456   1 vvPvLPGtllilaglllyalltgfaelgwlflavllvlallglvldylapalgakraGaskrgligaivGaivGffl 77 
                                       vvP++PG+l+++ag+lly++ tg++e ++l+la+l+++ l+++++dy+ ++++a++ Gas+ +   ++vGa+vGf+l
  gi|313125961|ref|YP_004036231.1|  20 VVPLVPGALVSVAGVLLYWWSTGYSEPSLLVLAALVLVGLVTVIIDYFGGVIAARAGGASSLT---TAVGALVGFVL 93 
                                       89***********************************************************99...66666666665 PP

                            DUF456  78 lp...plGlllgpflgaflgEllrarkdlreAlkaalgalvGfllgtlvklvlallmlvlflv 137
                                       l+   plG+llg  +++f++E++r+  + +++++ al+++vG+l++t+v+++l+  +lv+ + 
  gi|313125961|ref|YP_004036231.1|  94 LFvtgPLGFLLGLAATVFAVEFYRND-NPEASARIALYTTVGVLASTVVQILLTGSILVVLVG 155
                                       554459***************98888.9******************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1027.62
//
Query:       gi|313125962|ref|YP_004036232.1|  [L=114]
Description: NADH:ubiquinone oxidoreductase subunit I-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   51.4  21.5    5.4e-08   33.3   7.0    2.1  3  Fer4_7    4Fe-4S dicluster domain
    3.5e-13   48.8  13.3    1.3e-07   31.1   4.1    2.5  2  Fer4      4Fe-4S binding domain
    8.3e-09   35.5   4.1    2.2e-08   34.1   4.3    1.6  1  Fer4_9    4Fe-4S dicluster domain
    7.4e-08   32.1  14.1    2.2e-05   24.3   5.3    2.4  2  Fer4_6    4Fe-4S binding domain
    9.9e-08   32.0  11.0      1e-06   28.8  10.8    2.1  2  Fer4_21   4Fe-4S dicluster domain
    1.3e-07   31.6  18.0      1e-05   25.6   7.7    2.1  2  Fer4_10   4Fe-4S dicluster domain
      3e-06   28.1   4.2    0.00035   21.4   1.1    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    1.8e-05   25.2   2.3      0.052   14.1   0.8    2.2  2  Fer4_17   4Fe-4S dicluster domain
      3e-05   23.9  10.3     0.0058   16.7   3.5    2.7  2  Fer4_2    4Fe-4S binding domain
    4.1e-05   23.9   5.3    0.00018   21.9   5.4    1.9  1  Fer4_8    4Fe-4S dicluster domain
     0.0005   20.3   5.0    0.00052   20.2   1.3    2.0  2  Fer4_18   4Fe-4S dicluster domain
     0.0005   20.8  11.1     0.0025   18.6   4.1    2.4  2  Fer4_3    4Fe-4S binding domain
    0.00053   20.3   7.5     0.0015   18.9   2.7    2.4  2  Fer4_4    4Fe-4S binding domain
     0.0014   19.1  13.5      0.019   15.5  13.5    2.4  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.033   14.5   0.0      0.058   13.7   0.0    1.4  1  DUF4969   Domain of unknown function (DUF4969)
      0.065   14.1   3.7        6.1    7.8   0.1    2.1  2  Fer4_22   4Fe-4S dicluster domain
       0.35   11.6  16.8        5.8    7.7  16.8    2.9  1  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   8.1e-06    0.0086      28      52 .]      36      65 ..      11      65 .. 0.69
   2 !   33.3   7.0   5.1e-11   5.4e-08       2      52 .]      51     103 ..      50     103 .. 0.84
   3 !   21.7   2.1   2.1e-07   0.00023       1      21 [.      88     108 ..      88     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.1e-06
                            Fer4_7 28 t.....ekveidpekClgCgaCvavCPtga 52
                                      +      +v++d + C+g gaC + CP+++
  gi|313125962|ref|YP_004036232.1| 36 KlgihgTHVAVDFDICIGDGACLEDCPVDV 65
                                      2333447899*****************986 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 5.1e-11
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidp...ekClgCgaCvavCPtga 52 
                                       Cig gaC + Cpv+++++ +   +++  +v+++p   ++C++C  Cv+vCP++a
  gi|313125962|ref|YP_004036232.1|  51 CIGDGACLEDCPVDVFSWVDTPGHPE-SEVKVQPareDQCIDCMLCVDVCPVDA 103
                                       9******************9977776.666666522278*************97 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2.1e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaielde 21 
                                       +Ci C  Cv++Cpv+ai++d+
  gi|313125962|ref|YP_004036232.1|  88 QCIDCMLCVDVCPVDAIDVDP 108
                                       6****************9986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.8   5.4e-08   5.6e-05       2      23 ..      45      66 ..      44      67 .. 0.91
   2 !   31.1   4.1   1.2e-10   1.3e-07       5      24 .]      86     105 ..      84     105 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.4e-08
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       +d + Cig GaC e CPv++ 
  gi|313125962|ref|YP_004036232.1| 45 AVDFDICIGDGACLEDCPVDVF 66
                                      69*****************985 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.2e-10
                                       TTTSSS-THHHHHSTTTEEE CS
                              Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                       e+ Ci C++Cv+vCPv+AI+
  gi|313125962|ref|YP_004036232.1|  86 EDQCIDCMLCVDVCPVDAID 105
                                       799***************95 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   4.3   2.1e-11   2.2e-08       2      51 .]      51     104 ..      49     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.1e-11
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51 
                                       C+g gaC e Cp +v++  + ++  + + + +    ++Ci+C+ Cv++Cp +ai
  gi|313125962|ref|YP_004036232.1|  51 CIGDGACLEDCPVDVFSWVDTPGHPESEVKVQpareDQCIDCMLCVDVCPVDAI 104
                                       89999******9999977666665555444445555***************987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.5   8.1e-05     0.086       2      23 ..      44      65 ..      43      66 .. 0.88
   2 !   24.3   5.3   2.1e-08   2.2e-05       6      24 .]      86     104 ..      84     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.1e-05
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      v++d d Cig g+C   CP ++
  gi|313125962|ref|YP_004036232.1| 44 VAVDFDICIGDGACLEDCPVDV 65
                                      678889*************876 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2.1e-08
                            Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                       +d Ci+C+ Cv+vCP +ai
  gi|313125962|ref|YP_004036232.1|  86 EDQCIDCMLCVDVCPVDAI 104
                                       799*************998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.5   0.00028       0.3      32      54 ..      42      64 ..      36      68 .. 0.85
   2 !   28.8  10.8   9.5e-10     1e-06       3      58 ..      46     105 ..      45     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                           Fer4_21 32 tvlkvvedeCvGCnlCssvCPve 54
                                      t+++v  d C+G   C++ CPv+
  gi|313125962|ref|YP_004036232.1| 42 THVAVDFDICIGDGACLEDCPVD 64
                                      67888899*************94 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 9.5e-10
                           Fer4_21   3 idedkCigCgkCliaCedtshqai..eidak...tvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +d d Cig g Cl  C+      +   ++++   +v + +ed+C+ C lC++vCPv d+i+
  gi|313125962|ref|YP_004036232.1|  46 VDFDICIGDGACLEDCPVDVFSWVdtPGHPEsevKVQPAREDQCIDCMLCVDVCPV-DAID 105
                                       67899************99999994413334111455667***************9.8886 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   7.7   9.6e-09     1e-05       1      56 []      43     100 ..      43     100 .. 0.81
   2 !   17.8   2.6   2.6e-06    0.0027       6      23 ..      86     103 ..      82     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 9.6e-09
                           Fer4_10   1 kvvidddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +v +d d Ci+ g+C + CP+d+  + +     +se +++    ++C++c  Cv++CP
  gi|313125962|ref|YP_004036232.1|  43 HVAVDFDICIGDGACLEDCPVDVfsWVDTPGHPESEVKVQPAREDQCIDCMLCVDVCP 100
                                       577899****************97644555555555666666889************9 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.6e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadl 23 
                                       +d+Ci C  Cv++CP+d+
  gi|313125962|ref|YP_004036232.1|  86 EDQCIDCMLCVDVCPVDA 103
                                       699************955 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0064       6.7       2      18 ..      51      67 ..      50      85 .. 0.84
   2 !   21.4   1.1   3.4e-07   0.00035       1      20 [.      88     107 ..      88     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0064
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C++ g+C+e CP+++++
  gi|313125962|ref|YP_004036232.1| 51 CIGDGACLEDCPVDVFS 67
                                      89999********9876 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3.4e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++C  C++vCP++ai+ +
  gi|313125962|ref|YP_004036232.1|  88 QCIDCMLCVDVCPVDAIDVD 107
                                       6****************876 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00057       0.6      43      60 ..      48      65 ..      33      66 .. 0.86
   2 !   14.1   0.8   4.9e-05     0.052      44      58 ..      87     101 ..      72     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00057
                           Fer4_17 43 aslCieCgeCerkCPqgl 60
                                      ++ Ci+ g C ++CP ++
  gi|313125962|ref|YP_004036232.1| 48 FDICIGDGACLEDCPVDV 65
                                      578************875 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.9e-05
                           Fer4_17  44 slCieCgeCerkCPq 58 
                                       ++Ci C +C+ +CP 
  gi|313125962|ref|YP_004036232.1|  87 DQCIDCMLCVDVCPV 101
                                       789999999999985 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.6   0.00041      0.44       2      21 ..      43      62 ..      42      63 .. 0.92
   2 !   16.7   3.5   5.5e-06    0.0058       7      21 ..      86     100 ..      83     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      +v+vd d+Cig gaC+  CP
  gi|313125962|ref|YP_004036232.1| 43 HVAVDFDICIGDGACLEDCP 62
                                      799*******999******9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.5e-06
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +d Ci C  Cv++CP
  gi|313125962|ref|YP_004036232.1|  86 EDQCIDCMLCVDVCP 100
                                       688************ PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   5.4   1.7e-07   0.00018       2      64 ..      48     102 ..      47     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                            Fer4_8   2 lekCieCgaCqsaCpv.lrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       ++ Ci+ gaC + Cpv + ++ + + +++ e++   q  ++       ++C  c+ C++vCpv+
  gi|313125962|ref|YP_004036232.1|  48 FDICIGDGACLEDCPVdVFSWVDTPGHPESEVKV--QPARE-------DQCIDCMLCVDVCPVD 102
                                       678************6344555777778887665..33334.......78************96 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.26   2.7e+02      59      75 ..      49      65 ..      33      68 .. 0.81
   2 !   20.2   1.3     5e-07   0.00052      53      79 ..      81     108 ..      69     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.26
                           Fer4_18 59 gdcidcescvkvcPtgi 75
                                        ci  ++c++ cP+++
  gi|313125962|ref|YP_004036232.1| 49 DICIGDGACLEDCPVDV 65
                                      45899999999999876 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5e-07
                           Fer4_18  53 rkekgagdcidcescvkvcPtg.idirk 79 
                                        + + + +cidc  cv+vcP++ id+  
  gi|313125962|ref|YP_004036232.1|  81 VQPAREDQCIDCMLCVDVCPVDaIDVDP 108
                                       45567889************95478755 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6      0.02        21       1      14 [.      51      64 ..      51      65 .. 0.91
   2 !   18.6   4.1   2.4e-06    0.0025       1      15 []      89     103 ..      89     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.02
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+g gaC+e CPv+
  gi|313125962|ref|YP_004036232.1| 51 CIGDGACLEDCPVD 64
                                      9999********96 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.4e-06
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C++Cv+vCPv+A
  gi|313125962|ref|YP_004036232.1|  89 CIDCMLCVDVCPVDA 103
                                       9************98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.13   1.4e+02       4      16 ..      51      63 ..      48      68 .. 0.86
   2 !   18.9   2.7   1.4e-06    0.0015       4      16 ..      89     101 ..      83     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      Cig g+C   CP+
  gi|313125962|ref|YP_004036232.1| 51 CIGDGACLEDCPV 63
                                      9999999999996 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.4e-06
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci+C+ Cv++CP+
  gi|313125962|ref|YP_004036232.1|  89 CIDCMLCVDVCPV 101
                                       ************7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  13.5   1.8e-05     0.019       1      58 []      46     106 ..      46     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                           Fer4_13   1 VDrdtCiacgaCvelaP.dvFeeddegg..asvvaeqptseeekadaeeAadaCPvesIgv 58 
                                       VD d Ci++gaC e +P dvF   d  g   s v+ qp  e++  d++  +d CPv++I v
  gi|313125962|ref|YP_004036232.1|  46 VDFDICIGDGACLEDCPvDVFSWVDTPGhpESEVKVQPAREDQCIDCMLCVDVCPVDAIDV 106
                                       78899************99**987766522699999***********************86 PP

>> DUF4969  Domain of unknown function (DUF4969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.5e-05     0.058      44      78 ..      13      47 ..       3      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-05
                           DUF4969 44 ddpiklvdengeatvevdvdPkskltidGkavkkD 78
                                      +   k+vde +  tv + vdP  kl i G  v  D
  gi|313125962|ref|YP_004036232.1| 13 ETNCKPVDEEDGVTVWGPVDPPEKLGIHGTHVAVD 47
                                      55689*************************99876 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0058       6.1      76      95 ..      45      64 ..      36      65 .. 0.83
   2 ?    7.4   0.6    0.0076       8.1      81      94 ..      88     101 ..      76     103 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0058
                           Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                       ++   C+G g C e cpv+
  gi|313125962|ref|YP_004036232.1| 45 AVDFDICIGDGACLEDCPVD 64
                                      567889************87 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0076
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                       +C+ C  C+++cpv
  gi|313125962|ref|YP_004036232.1|  88 QCIDCMLCVDVCPV 101
                                       55555555555554 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  16.8    0.0055       5.8       1      66 []      44     106 ..      44     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0055
                           Fer4_15   1 VvvDrdaCigcglCvaeap.evfelde.dglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66 
                                       V vD d Cig+g+C++ +p +vf   +  g+++     +e++ ++  +d+  +    +++CPvdAI v
  gi|313125962|ref|YP_004036232.1|  44 VAVDFDICIGDGACLEDCPvDVFSWVDtPGHPE-----SEVKVQPAREDQCIDCMLCVDVCPVDAIDV 106
                                       78****************736666655246663.....4555788888888899999*********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 785.15
//
Query:       gi|313125963|ref|YP_004036233.1|  [L=289]
Description: electron transfer flavoprotein subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-41  139.8   0.2    1.2e-40  139.4   0.2    1.2  1  ETF       Electron transfer flavoprotein domain
  ------ inclusion threshold ------
      0.099   12.5   0.0       0.61   10.0   0.0    2.2  2  Ub-Mut7C  Mut7-C ubiquitin


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.4   0.2   1.3e-44   1.2e-40       3     164 ..      25     196 ..      23     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 1.3e-44
                                       EEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHH CS
                               ETF   3 vlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatak 79 
                                       +l++ +++ ++np+d++al+aA++++ ++gg+v+++++Gpp ++++l+ea+    ad++ l++d+++a++d++ata 
  gi|313125963|ref|YP_004036233.1|  25 HLERGKTPTVMNPNDEHALQAALQTRVQHGGNVAVMSMGPPGYKDVLQEAMESVYADELFLISDREMAAADTWATAI 101
                                       57788899********************************************************************* PP

                                       HHHHHHHHC-.-SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCC..EEEEEECCCCTEEEEEE-TSS CS
                               ETF  80 alaalikked.pdlvlagatai.g..kqvaprlAalLgvplitdvteleveggk..ltvtRpieggnglaevveadl 150
                                       +l+a+i++++ pdl++ag ++  g  ++++p+++++L++plit+v++l+v+++   ++++R +eg+    e+ve+dl
  gi|313125963|ref|YP_004036233.1| 102 TLSAAIEEMGvPDLIFAGFKTAdGetGHTGPQTCWCLDMPLITHVVALDVDEDAgrVRAKRLVEGDISEMETVETDL 178
                                       *********66***********89**************************977799********************* PP

                                       SEEEEE-TTSS--.....- CS
                               ETF 151 pavltvrpgafep.....a 164
                                       pa++  +p  f+p     +
  gi|313125963|ref|YP_004036233.1| 179 PAFIVADP-EFDPsyrtaR 196
                                       ******99.6777454440 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.28   2.5e+03      59      76 ..      45      62 ..      44      64 .. 0.83
   2 ?   10.0   0.0   6.8e-05      0.61      17      45 ..      85     113 ..      80     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.28
                          Ub-Mut7C 59 vgfshiledGdrvavypv 76
                                      + ++ +++ G+ vav+ +
  gi|313125963|ref|YP_004036233.1| 45 AALQTRVQHGGNVAVMSM 62
                                      5678899*******9875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 6.8e-05
                          Ub-Mut7C  17 prarreralavafdeaatvkhviEalGVP 45 
                                         ++re a+a  ++ a t++ +iE +GVP
  gi|313125963|ref|YP_004036233.1|  85 LISDREMAAADTWATAITLSAAIEEMGVP 113
                                       55789999********************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1552.83
//
Query:       gi|313125964|ref|YP_004036234.1|  [L=580]
Description: electron transfer flavoprotein subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-27   93.2   0.5    1.8e-26   92.0   0.5    1.7  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
    3.6e-17   62.8   0.0    1.2e-16   61.1   0.0    1.9  1  ETF        Electron transfer flavoprotein domain
  ------ inclusion threshold ------
      0.024   14.4   1.5       0.14   11.9   0.0    2.1  2  MctB       Copper transport outer membrane protein, MctB


Domain annotation for each model (and alignments):
>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.5     3e-30   1.8e-26       1      84 []     408     503 ..     408     503 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 3e-30
                                       .-TTT-S-EEEE-GGGSS..GGGHHHHHHHHHHHT.-EEEE-HHHHTTT.........SS-CCCB-SSSS-----S- CS
                         ETF_alpha   1 vdLeeakvvvsgGrGlks..kenlelleelaealg.aavgasRavvdag.........wipeerqvGqtGktvaPkl 65 
                                       vdL+ ++vvv++GrG+++  ++++el+ ela+a++ a+vg++R +v+ +         +++eerq+G+tG++vaP+l
  gi|313125964|ref|YP_004036234.1| 408 VDLSGHDVVVAVGRGIGDdpTRGMELALELADAFEdADVGVTRGIVTGSysfdahveqYTQEERQIGETGQVVAPEL 484
                                       699*************998899************99***********95555566666******************* PP

                                       EEEES----HHHHGGGTT- CS
                         ETF_alpha  66 yiavGisGaiqhlaGmkes 84 
                                       y+a+GisGaiqh +Gm+es
  gi|313125964|ref|YP_004036234.1| 485 YVAAGISGAIQHKVGMDES 503
                                       ****************997 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0     2e-20   1.2e-16       2     178 ..     160     386 ..     159     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 2e-20
                                       EEEE-EC.CCCE-HHHHHHHHHHHHHHHH........HT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGS CS
                               ETF   2 lvlaehgvdgklnpvdlealeaArrlkek........aggevtavvvGppeaeealrealaamGadkvilvddpala 70 
                                       +v+ e +  g+l  v +e+l++Ar+l +         ++++v+av+vG++ +  a  + +a  Gad v++ +d++la
  gi|313125964|ref|YP_004036234.1| 160 WVYCETQ-AGELVSVAKEMLGKARQLMDDynaeypdeDDERVVAVLVGDDVKTHA-DDVIA-LGADVVVVHEDERLA 233
                                       8999997.9******************99999999854499********555444.66777.*************** PP

                                       S--CCHHHHHHHHHHHHC.............-.......-SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEET CS
                               ETF  71 gydaeatakalaalikke.............d.......pdlvlagataigkqvaprlAalLgvplitdvteleveg 127
                                        +++ ++++++++++++              +       p  vl++at  g+++ + + a L+ +l++d+++l +++
  gi|313125964|ref|YP_004036234.1| 234 RFQHKPYTEIVSDMARAGathedgeviggrdEewrdydkPRYVLFPATNNGRDLSALVQAELDSGLASDCSGLFIDE 310
                                       *****************9888776666665505555556************************************96 PP

                                       CC...................EEEEEECCCCTEEEEEE-TSS......SEEEEE-TTSS----S-TT---EEEE-- CS
                               ETF 128 gk...................ltvtRpieggnglaevveadl......pavltvrpgafepaaimaakkkeveeve 178
                                       +                    l+++Rp ++g  +++++++d+      p+ ++v pg+fe +++++++++ ++ +e
  gi|313125964|ref|YP_004036234.1| 311 EVisnpvktgaagekrtfervLHMKRPDFSGFEYSTILCLDNprrefhPQGASVIPGSFEVPDPDPEREGLIVDHE 386
                                       669****************************99*****99862333335778888888888888888877776665 PP

>> MctB  Copper transport outer membrane protein, MctB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.3e-05      0.14     149     244 ..     167     265 ..     158     271 .. 0.86
   2 ?    1.1   0.3     0.044   2.6e+02      81     137 ..     410     464 ..     405     509 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                              MctB 149 aadpgekagallgaallt...aeeeasseeraavlaaLreaglvtvedetvapadavvvvteaegstsedaekaaai 222
                                       a++  + a+++lg+a  +    + e  +e+ + v+a L+  ++ t +d+ +a    vvvv e+e  +  +++  ++i
  gi|313125964|ref|YP_004036234.1| 167 AGELVSVAKEMLGKARQLmddYNAEYPDEDDERVVAVLVGDDVKTHADDVIALGADVVVVHEDERLARFQHKPYTEI 243
                                       55566778888988877777866788999*****************999999988888888788899999******* PP

                              MctB 223 larlaaaldergagvVlaGrag 244
                                       + ++a+a +++  g V+ Gr++
  gi|313125964|ref|YP_004036234.1| 244 VSDMARAGATHEDGEVIGGRDE 265
                                       ******************9876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.044
                              MctB  81 LtgrsVavvttpdadeedvdavtelleqAGAtvtgtvtltdkfvdpdeadklrslaa 137
                                       L+g++V+v +  +  ++   +++ +le A+A   + v +t  +v  +   + ++ ++
  gi|313125964|ref|YP_004036234.1| 410 LSGHDVVVAVGRGIGDDPTRGMELALELADAFEDADVGVTRGIVTGS--YSFDAHVE 464
                                       89999999999999999999999999999999999999999888773..33444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.74u 0.35s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 3135.05
//
Query:       gi|313125965|ref|YP_004036235.1|  [L=555]
Description: flavin-dependent dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-12   46.8   2.2    2.3e-11   43.6   2.2    2.2  1  FAD_binding_3   FAD binding domain
    1.5e-07   30.9   2.0    0.00014   21.2   0.2    2.7  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.4e-06   26.7   0.6    5.1e-06   26.1   0.6    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
    6.8e-06   25.9   6.9     0.0024   17.5   3.8    2.3  2  DAO             FAD dependent oxidoreductase
    1.3e-05   25.4   1.9    5.8e-05   23.2   1.9    2.2  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      4e-05   22.9   4.5    0.00013   21.2   1.9    2.3  2  FAD_binding_2   FAD binding domain
    0.00015   21.1   0.4     0.0003   20.1   0.4    1.5  1  Thi4            Thi4 family
     0.0012   17.6   1.9     0.0023   16.7   1.9    1.4  1  HI0933_like     HI0933-like protein
     0.0014   18.8   0.1     0.0023   18.0   0.1    1.4  1  ETF_QO          Electron transfer flavoprotein-ubiquinone oxi
     0.0019   17.5   1.2     0.0036   16.6   1.2    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0026   16.7   0.5       0.16   10.8   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
     0.0094   15.1   2.8      0.064   12.3   4.0    1.7  2  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.013   16.0   2.2       0.79   10.3   0.9    3.1  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
        4.1    7.7   5.7       0.36   11.0   0.6    1.9  2  Fer4_2          4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   2.2   1.8e-14   2.3e-11       3     315 ..       8     339 ..       6     353 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.8e-14
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS.CCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt.vvlpradglnqrtmellrqlGledrilaegapnelmgealyn 78 
                                       + ++VGaGp G+ +a  L+++G++++++e+  ++ +++  ++++  +         l   +++e++ + +++  l n
  gi|313125965|ref|YP_004036235.1|   8 EAVVVGAGPGGAAAAATLARYGIETLVLERGVEAgSKNVSGGIIYGEQSAPVTIDDLFPDFREEAVERPVTRYYLHN 84 
                                       789***************************75551666677777655555555556889999999999999999999 PP

                                       ECCCCCEEEEEHH...CHHCST-CEE--H..HHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEE CS
                     FAD_binding_3  79 elsdtpkaradle...lesspervtvypq..teleriLvehaeerglqvrfktevesleqdeegvtaevrdketgee 150
                                         +d  + +   +    ++++ +  +     + le  + e a+e+g  +  +  v++l++d+ g   e+ + +t+e 
  gi|313125965|ref|YP_004036235.1|  85 VAGDKVETMDLTDlheHDTEWADAVLRRKmdSWLEDRVHEMARETGGGLLTGVHVNGLLRDGHG---EIIGVTTDEL 158
                                       866663333222211222333333322221133666667778999999999999********99...7889999999 PP

                                       EEEEEEEEEE--GTT-HHHHHHTGG.EEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEE............ CS
                     FAD_binding_3 151 etvrakYlvGaDGgrStvrktlgie.fegeetvyeagvldvlfdadlsdiveplvlilsaesrgv............ 214
                                       e ++a+ +++aDG++S  ++++g+     +e+   ++ +++++d + + +v++ +++ ++e                
  gi|313125965|ref|YP_004036235.1| 159 EPLEADVIIAADGVNSELARDAGLMdWDDPEEW--FQGVKAVVDLPPE-TVNDRFALEEDEGAAHlfsgdlfsdvrg 232
                                       9**********************9867777766..7777777777666.6666566666666655788888888888 PP

                                       ...EEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEE.SSSEETTEE CS
                     FAD_binding_3 215 ...mviPlentlerfyvqvearaekeersekfteeevkarlreivgektldveieevsawtvaqrva.ekyrkgrvf 287
                                              +++ ++  +++++    ++ ++ +  ++ ++  l ++  +++ + +   ++ ++ +++va +k   +r++
  gi|313125965|ref|YP_004036235.1| 233 ggfLYTNRDSLSVGTVFHLDSLVAEQAEPHELLDALLTHPLLAQWLDDDYHEREYAAKLVPDSKKVAlRKPYAERLL 309
                                       87444444447788899999998888999999999999999999999999997777777777777662666677*** PP

                                       E-GGGTEEE-STTS..HHHHHHHHHHHHHH CS
                     FAD_binding_3 288 laGDAaHihpPtgG..qGlNtaiqDavnLa 315
                                       l+GDAa  +   g   +G+N a+      a
  gi|313125965|ref|YP_004036235.1| 310 LVGDAAGQMQAQGPiiKGMNHAVTAGALAA 339
                                       *********999865579999997655555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   1.1e-07   0.00014       3      31 ..       9      41 ..       7      71 .. 0.83
   2 !    8.4   0.0   0.00086       1.1     172     239 ..     104     174 ..      90     186 .. 0.83
   3 ?   -2.3   0.0       1.6   2.1e+03     179     203 ..     348     372 ..     336     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-07
                                      EEEE--SHHHHHHHHHHHHHTS-EEEEE....T CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       Pyr_redox_2  3 vvviGgGpAGlaaaltlaqagakvtlve....l 31
                                       vv+G+Gp+G aaa tla++g++++++e    +
  gi|313125965|ref|YP_004036235.1|  9 AVVVGAGPGGAAAAATLARYGIETLVLErgveA 41
                                      69***********************99644332 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00086
                                       ESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.EEEEEETTSCE.EEESEEEE-S-EEE CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       Pyr_redox_2 172 eardrll.raldkelsaaleealekeGvevklgtsvkeidgnge.klevvledgee.idadlvvvavGvrp 239
                                       e +d +l r++d+ l+++++e  ++ G  + +g  v+ + ++g+ ++  v++d+ e ++ad ++ a Gv  
  gi|313125965|ref|YP_004036235.1| 104 EWADAVLrRKMDSWLEDRVHEMARETGGGLLTGVHVNGLLRDGHgEIIGVTTDELEpLEADVIIAADGVNS 174
                                       56788999********************************99998777666666666***********965 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.6
                                       TTS-HHHHHHHHHHHHHTTEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 179 raldkelsaaleealekeGvevklg 203
                                       r+ ++++++ ++++l++eGv  kl+
  gi|313125965|ref|YP_004036235.1| 348 RNKPDQAGKLYAQKLREEGVMSKLR 372
                                       6678899999**********98876 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.6     4e-09   5.1e-06       3     142 ..      10     169 ..       8     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4e-09
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq...rgga... 73 
                                       vVvG+gp+G aAA + ar G ++l++e+    G    sg+   + g +++   +  ++ +f+e+  +   ++++   
  gi|313125965|ref|YP_004036235.1|  10 VVVGAGPGGAAAAATLARYGIETLVLERGVEAGSKNVSGG--IIYGEQSAPVTIDDLFPDFREEAVErpvTRYYlhn 84 
                                       9***************************999999988888..55555555667888888888887774432222432 PP

                      FAD_oxidored  74 ...rlkkrskwn..........tfepevakavleeml............aeagvtvllntrlvevekeg.kriesvt 124
                                          +       +           ++ e a avl   +            +e g  +l++  + +  ++g ++i +vt
  gi|313125965|ref|YP_004036235.1|  85 vagD-------KvetmdltdlhEHDTEWADAVLRRKMdswledrvhemaRETGGGLLTGVHVNGLLRDGhGEIIGVT 154
                                       2220.......122334444443444444444443333333444444447777777777777777777634488888 PP

                      FAD_oxidored 125 veskegrktirAkvfiDA 142
                                       + +    + ++A+v+i A
  gi|313125965|ref|YP_004036235.1| 155 TDE---LEPLEADVIIAA 169
                                       854...788888888765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.8   1.9e-06    0.0024       2      48 ..       9      55 ..       8      75 .. 0.87
   2 !    9.0   0.0   0.00073      0.93     154     268 ..     124     248 ..     114     340 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl 48
                                       v++G+G  G+++A  Lar g  +++le+g   + g+   ++g++++  
  gi|313125965|ref|YP_004036235.1|  9 AVVVGAGPGGAAAAATLARYGieTLVLERG-VEA-GSKNVSGGIIYGEQ 55
                                      69****************************.666.89999999999854 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00073
                                       HHHHHTT-EEEESECEEEEEEEE.TCEEEEEEECTEEE.EEEEEEEE--GGGHHHHHTTCTT...TSEEEEEEEEEE CS
                               DAO 154 raaealGveilegtevtgleeed.gkvwgverttpgen.daadavVnaaGawsdllgllkel...dlpispvrgqvl 225
                                       + a++ G+ +l+g  v gl +++ g + gv  tt++ +  +ad ++ a G+ s l++ ++ l   d p + ++g   
  gi|313125965|ref|YP_004036235.1| 124 EMARETGGGLLTGVHVNGLLRDGhGEIIGV--TTDELEpLEADVIIAADGVNSELARDAG-LmdwDDPEEWFQGVKA 197
                                       458899************855446888888..77666655679999999**998773331.1334334466777777 PP

                                       EEEECCTHSTGSGCSEEEEE...........EEETTTTEEEEEETTSEEEEEES CS
                               DAO 226 vlkplseklvspaailpvpe...........tdddgrgvyvtprkdgrvlvGgt 268
                                       v++ ++e +v  +  l + e           +d + +g +++  + +++ vG+ 
  gi|313125965|ref|YP_004036235.1| 198 VVDLPPE-TVNDRFALEEDEgaahlfsgdlfSDVR-GGGFLYTNR-DSLSVGTV 248
                                       7733333.333322222222444444566633333.333444444.34666664 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   1.9   4.5e-08   5.8e-05       1      32 [.      11      42 ..      11      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.5e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G++aA++La++g++ l+le++   G
  gi|313125965|ref|YP_004036235.1| 11 VVGAGPGGAAAAATLARYGIETLVLERGVEAG 42
                                      8*************************987666 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.9     1e-07   0.00013       2      95 ..       9      92 ..       8     146 .. 0.71
   2 ?    1.6   0.0     0.091   1.2e+02     260     300 ..     352     393 ..     311     401 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1e-07
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S.-H CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela.dq 79
                                      ++V+G+G +G aAA+++a+ G +++v+e + e  g+   s+G i              +s    + d++   +e+a ++
  gi|313125965|ref|YP_004036235.1|  9 AVVVGAGPGGAAAAATLARYGIETLVLERGVE-AGSKNVSGGIIYGE-----------QSAPVTIDDLFPDFREEAvER 75
                                      79*****************************9.44455666665332...........455556667777777777777 PP

                                      HHHHHHHH.THHHHHHH CS
                     FAD_binding_2 80 plveafve.aapeavde 95
                                      p+ +++++  a+++v+ 
  gi|313125965|ref|YP_004036235.1| 76 PVTRYYLHnVAGDKVET 92
                                      77777777556666665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.091
                                       .TTTBB--THHHHTT-EEE-.TTSSBTHGGGS-HHHHHHHHH CS
                     FAD_binding_2 260 dgsgiLitealrgeGgilvd.kdGrrFmnelasrdvvsrail 300
                                       d++g L  ++lr eG++     +G +++ +l +rd+v++ + 
  gi|313125965|ref|YP_004036235.1| 352 DQAGKLYAQKLREEGVMSKLrPRGYDLVRTLGERDDVTNVVD 393
                                       33333999*********9999****************98765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.4   2.3e-07    0.0003      18      64 ..       7      52 ..       1      63 [. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.3e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf 64
                                       + v+vGaG+ G +aa +la+  ++++++ler v  G     GG ++
  gi|313125965|ref|YP_004036235.1|  7 YEAVVVGAGPGGAAAAATLARY-GIETLVLERGVEAGSKNVSGGIIY 52
                                      5679******************.**************9999999876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.9   1.8e-06    0.0023       2      40 ..       8      46 ..       7      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.8e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                      + +v+G+G+ G  aA+++a+ g ++l+le++ ++g+K  
  gi|313125965|ref|YP_004036235.1|  8 EAVVVGAGPGGAAAAATLARYGIETLVLERGVEAGSKNV 46
                                      689*********************************943 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.8e-06    0.0023      56     103 ..     508     552 ..     467     553 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-06
                                       EEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE---STT-C--- CS
                            ETF_QO  56 eivedeeakekklqinaqnCvhCktCdikdpsqniewvvPeGggGPky 103
                                       e+++++ ++e+ + +++q Cv C tC i     + +w+ P Gg+G ++
  gi|313125965|ref|YP_004036235.1| 508 EFIRTNGEQEHVVSLDTQPCVECGTCAIVA---DTDWTHPRGGKGVAF 552
                                       7888888899999***************86...568********9765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.2   2.8e-06    0.0036       1      31 [.      10      40 ..      10      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.8e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.n 31
                                      +++GaGP G aaa +l + g+ + l+lE+g +
  gi|313125965|ref|YP_004036235.1| 10 VVVGAGPGGAAAAATLARYGI-ETLVLERGvE 40
                                      79*******************.589****944 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.9     0.021        28       3      22 ..      10      29 ..       8      40 .. 0.84
   2 !   10.8   0.0   0.00013      0.16      94     234 ..      52     197 ..      46     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.021
                                      EEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase  3 vivGGGtaGwlaAaalakal 22
                                      v+vG+G+ G  aAa+la+++
  gi|313125965|ref|YP_004036235.1| 10 VVVGAGPGGAAAAATLARYG 29
                                      8*****************98 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                                       .--EETTEEHHHHHHHHHHTT--S-HHHHH-SCHHHHHTTB-SB-TTS-B-S--EEEE-HHHHHHHHHH....HHHH CS
                    Trp_halogenase  94 igkqlegvalhhywlkarargaaeeledysleavaakakkfsprekdglsalsyAyhldaalyakfLrr....vaea 166
                                       +g+q   v++ +++ + r++ ++++++ y l++va ++   + +    ++ +++A  + +++++ +L++    +a +
  gi|313125965|ref|YP_004036235.1|  52 YGEQSAPVTIDDLFPDFREEAVERPVTRYYLHNVAGDKVETMDLTDLHEHDTEWADAVLRRKMDSWLEDrvheMARE 128
                                       56677788889999999999999999999999999999999998888999999999999999999997522227888 PP

                                       CT-EEEE--EEEEEE-T.TS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT----EE CS
                    Trp_halogenase 167 rGvtrvegkvvevqlde.dgrveslrledgreveadlfiDcsGfrgllieqaLktgfedwsdvLltdrA 234
                                        G   + g  v+  l++ +g++ ++++++ + +ead +i + G ++ l   a    ++d  +++   +A
  gi|313125965|ref|YP_004036235.1| 129 TGGGLLTGVHVNGLLRDgHGEIIGVTTDELEPLEADVIIAADGVNSELARDAGLMDWDDPEEWFQGVKA 197
                                       899999999999999888*********************************977788888888855555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   4.0     5e-05     0.064       3      28 ..      10      35 ..       8      53 .. 0.88
   2 ?   -2.5   0.0       1.6   2.1e+03     100     167 ..     287     348 ..     252     371 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                                      EEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  3 iViGgGhAGceAAlaaarlGakvlLi 28
                                      +V+G+G  G +AA+++ar G+++l +
  gi|313125965|ref|YP_004036235.1| 10 VVVGAGPGGAAAAATLARYGIETLVL 35
                                      8**********************987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                       HHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSC CS
                              GIDA 100 evteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGr 167
                                       +  + + +++++ +++  +e+l++  +  +g ++++g +ik  +  +++G+ l+++        ++Gr
  gi|313125965|ref|YP_004036235.1| 287 YAAKLVPDSKKVALRKPYAERLLL-VGDAAGQMQAQGPIIKGMNHAVTAGA-LAAEAFA----QAKGR 348
                                       455566677788888888888766.77888888888888888888888888.4444443....33444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   0.00062      0.79       2      31 ..       9      38 ..       8      45 .. 0.92
   2 ?    2.0   0.0      0.24     3e+02      32      78 ..     107     155 ..     103     157 .. 0.85
   3 ?    0.1   0.0      0.96   1.2e+03      37      56 ..     349     368 ..     341     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00062
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      +vvvG+G  g  +A++la++g ++ v+er+
  gi|313125965|ref|YP_004036235.1|  9 AVVVGAGPGGAAAAATLARYGIETLVLERG 38
                                      79************************9997 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.24
                                       SSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEEE CS
                         Pyr_redox  32 dkll.rllDeeaskilqeklekngievllntkveeiegsedg.vesvkl 78 
                                       d +l r++D  ++++++e  ++ g  +l++  v+ +  ++ g + +v++
  gi|313125965|ref|YP_004036235.1| 107 DAVLrRKMDSWLEDRVHEMARETGGGLLTGVHVNGLLRDGHGeIIGVTT 155
                                       67788***********************999999999888887777765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.96
                                       TSSHHHHHHHHHHHHHTTEE CS
                         Pyr_redox  37 llDeeaskilqeklekngie 56 
                                       + +++a+k+ ++kl+++g+ 
  gi|313125965|ref|YP_004036235.1| 349 NKPDQAGKLYAQKLREEGVM 368
                                       567899************95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5         4   5.1e+03      17      21 ..     490     494 ..     490     495 .. 0.82
   2 ?   11.0   0.6   0.00028      0.36       3      17 ..     520     534 ..     517     537 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4
                            Fer4_2  17 vsaCP 21 
                                       v+aCP
  gi|313125965|ref|YP_004036235.1| 490 VTACP 494
                                       69*** PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00028
                            Fer4_2   3 vvvdtdrCigCgaCv 17 
                                       v  dt+ C++Cg+C 
  gi|313125965|ref|YP_004036235.1| 520 VSLDTQPCVECGTCA 534
                                       6789**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.55
# Mc/sec: 3022.61
//
Query:       gi|313125966|ref|YP_004036236.1|  [L=138]
Description: hypothetical protein Hbor_12020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 882.96
//
Query:       gi|313125967|ref|YP_004036237.1|  [L=245]
Description: sortase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-13   49.0   0.1      1e-12   48.3   0.1    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.1e-10   41.0   0.0    3.3e-10   40.3   0.0    1.3  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.8e-07   31.1   0.1    3.3e-07   30.3   0.1    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    5.2e-06   26.8   0.0    1.1e-05   25.8   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00088   20.0   0.1     0.0016   19.1   0.1    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0018   18.5   0.0     0.0042   17.3   0.0    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0028   17.8   0.0     0.0078   16.3   0.0    1.8  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.023   14.5   0.0       0.05   13.4   0.0    1.6  1  LexA_DNA_bind    LexA DNA binding domain
      0.035   14.2   0.2      0.083   13.0   0.0    1.7  2  Adeno_E4         Mastadenovirus early E4 13 kDa protein
       0.04   13.5   0.0      0.059   12.9   0.0    1.2  1  DUF762           Coxiella burnetii protein of unknown functio
       0.04   14.0   0.0       0.11   12.6   0.0    1.8  2  DprA_WH          DprA winged helix domain
      0.082   13.0   0.0       0.18   11.8   0.0    1.7  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.088   13.1   0.2         22    5.5   0.0    3.2  3  Ish1             Putative stress-responsive nuclear envelope 
       0.15   11.8   0.5         19    5.1   0.0    3.2  3  SH3_16           Bacterial dipeptidyl-peptidase Sh3 domain
       0.16   12.2   0.2       0.76   10.1   0.0    2.3  2  ETC_C1_NDUFA4    ETC complex I subunit conserved region


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.1   8.7e-16     1e-12      31     117 .]     132     218 ..      95     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 8.7e-16
                                       TTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHH CS
                    Acetyltransf_1  31 eaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveednda 107
                                       +    +va  ++el+G++ l      k +++++  +  + ++rgkG+Gs+Lle  +e+a+e+g++k++  v ++n+ 
  gi|313125967|ref|YP_004036237.1| 132 QSRMVFVATVEDELAGWVHLDLPETGKLRHTAVLTVGARAKFRGKGIGSRLLERGVEWAEEHGFEKLYNSVPATNEE 208
                                       33366779999**********9999999999999*************************************999*** PP

                                       HHHHHHH.TTE CS
                    Acetyltransf_1 108 airlYek.lGF 117
                                       ai ++ k +G+
  gi|313125967|ref|YP_004036237.1| 209 AISFL-KdHGW 218
                                       *****.65985 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   2.8e-13   3.3e-10       1     155 []      85     239 ..      85     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.8e-13
                    Acetyltransf_4   1 iraateeDakeilaiyaey.vvntaitfeyevssveefekfleal.dsekeyvflvaesdrivGyaylgqfkkrakd 75 
                                       ir+a++ D++++ +  +e  ++ t i+ e  v  +++ e  + ++ + + ++vf +  +d+++G   l  ++    +
  gi|313125967|ref|YP_004036237.1|  85 IRTAQQVDLDALVDAIKEVaEEGTYIEAET-VGDMIDHEEVILRHnKVQSRMVFVATVEDELAGWVHLDLPETGKLR 160
                                       89**********999988524445666665.555555565555553678899999999***********99985556 PP

                    Acetyltransf_4  76 wkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiD 152
                                       + a l+v   + + + +g+g+ l++  ++ + e ++e+l+ ++ ++ne++i f+k +G+e ++  ++++k+  ++ D
  gi|313125967|ref|YP_004036237.1| 161 HTAVLTVGA-RAKFRGKGIGSRLLERGVEWAEEHGFEKLYNSVPATNEEAISFLKDHGWETEAVREDHYKIDDEYVD 236
                                       777777777.6899*************************************************************** PP

                    Acetyltransf_4 153 miw 155
                                       +++
  gi|313125967|ref|YP_004036237.1| 237 EVM 239
                                       987 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1   2.8e-10   3.3e-07       9     109 ..     111     221 ..      99     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.8e-10
                   Acetyltransf_10   9 gietfkefispealreri.eegealllvaeeggkivGvi..elrdgs...hisllfV..dpeyrgqGigkaLleave 77 
                                       ++et+ ++i+ e++  r  + ++ +++va+++++++G +   l +++   h + l V  + ++rg+Gig++Lle+  
  gi|313125967|ref|YP_004036237.1| 111 EAETVGDMIDHEEVILRHnKVQSRMVFVATVEDELAGWVhlDLPETGklrHTAVLTVgaRAKFRGKGIGSRLLERGV 187
                                       337778888887777777467888899**********9944454444477777777755679*************** PP

                   Acetyltransf_10  78 eeaekdgikl.eltvnasp.yavpfYeklGFkav 109
                                       e ae++g ++   +v a++ +a++f + +G+++ 
  gi|313125967|ref|YP_004036237.1| 188 EWAEEHGFEKlYNSVPATNeEAISFLKDHGWETE 221
                                       *******************************986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   8.9e-09   1.1e-05       4      75 ..     135     219 ..     132     220 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 8.9e-09
                                       EEEEEEETTEEEEEEEEEEES...TCTEE.....EEE-GGGTTSSHHHHHHHH.....TTSEEE.EEEEEE..THHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitr.....laVdpeyrgkGiGraLlea.....aekgii.leqlel..naek 64 
                                        vfVa  +++  G + l l +       +     +  + ++rgkGiG++Lle      +e+g++ l+   +  ++e+
  gi|313125967|ref|YP_004036237.1| 135 MVFVATVEDELAGWVHLDLPEtgkL--RHtavltVGARAKFRGKGIGSRLLERgvewaEEHGFEkLY-NSVpaTNEE 208
                                       589**********888777766441..333343355556************9544443336644212.222323339 PP

                                       HHHHHHHTTEE CS
                    Acetyltransf_7  65 aikfYeklGFe 75 
                                       ai+f + +G+e
  gi|313125967|ref|YP_004036237.1| 209 AISFLKDHGWE 219
                                       9*9*9999987 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.4e-06    0.0016       4     137 ..      85     218 ..      82     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
                    Acetyltransf_3   4 LrplteeDlealfelrsdpevmrylpepltleeaeewlera....waeeseeegygwaivlkdtgviGsvglrdlee 76 
                                       +r +++ Dl+al+   + +ev +    ++ ++e+   + ++    ++ ++ ++ + ++ +++d+   G+v l   e 
  gi|313125967|ref|YP_004036237.1|  85 IRTAQQVDLDALVD--AIKEVAE--EGTYIEAETVGDMIDHeeviLRHNKVQSRMVFVATVEDE-LAGWVHLDLPET 156
                                       66676677777763..3345554..334445555444544556555555556667788866777.8*******9998 PP

                    Acetyltransf_3  77 edee..aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                          +  a l    + +f+gkG+++  ++  +e+a ee+g e+l+  + ++Ne  i  l+  G 
  gi|313125967|ref|YP_004036237.1| 157 GKLRhtAVLTVGARAKFRGKGIGSRLLERGVEWA-EEHGFEKLYNSVPATNEEAISFLKDHGW 218
                                       8777888888888899******************.8889***************999998886 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.5e-06    0.0042      12      57 ..      16      61 ..      15      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.5e-06
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                       IY+  e++++v+  ++ ++Ln +p+     l  L++dGy+  +++
  gi|313125967|ref|YP_004036237.1| 16 DIYDYIESHGIVREDEVRRALNFEPAALGAHLTVLRRDGYIRKVGD 61
                                      6***************************************987665 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.5e-06    0.0078      31      58 ..     168     195 ..     136     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.5e-06
                   Acetyltransf_CG  31 eVpeelrGkGiAkkLvkaalddareegl 58 
                                           ++rGkGi+++L ++ +++a+e+g+
  gi|313125967|ref|YP_004036237.1| 168 GARAKFRGKGIGSRLLERGVEWAEEHGF 195
                                       33679*********************97 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.2e-05      0.05      30      59 ..      31      59 ..      16      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.2e-05
                                      HHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 30 eiaralglkSpsaveehLkaLerKGyierd 59
                                      e+ ral+++ p+a   hL  L+r Gyi+  
  gi|313125967|ref|YP_004036237.1| 31 EVRRALNFE-PAALGAHLTVLRRDGYIRKV 59
                                      899******.*****************975 PP

>> Adeno_E4  Mastadenovirus early E4 13 kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         6   7.2e+03      70      75 ..      29      34 ..      12      58 .. 0.57
   2 ?   13.0   0.0   6.9e-05     0.083      23      58 ..      90     125 ..      77     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6
                          Adeno_E4 70 rdrrrr 75
                                       d  rr
  gi|313125967|ref|YP_004036237.1| 29 EDEVRR 34
                                      222222 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.9e-05
                          Adeno_E4  23 gvaysavvdviraaahegvyiepeargrldalrewi 58 
                                        v   a+vd i+  a eg yie e+ g +    e i
  gi|313125967|ref|YP_004036237.1|  90 QVDLDALVDAIKEVAEEGTYIEAETVGDMIDHEEVI 125
                                       577889*******************99876666655 PP

>> DUF762  Coxiella burnetii protein of unknown function (DUF762)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.9e-05     0.059     138     220 ..      18      97 ..       9     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.9e-05
                            DUF762 138 veYierfklvklkldrneigdf.iaqveik.sivskdgeiihvCkkvevevedaklelfkkkfgsqlnlvetikkkl 212
                                        +Yie   +v+ + + +   +f  a      +++ +dg i  v +kv+v+ e+++ ++f  + g++      i+   
  gi|313125967|ref|YP_004036237.1|  18 YDYIESHGIVRED-EVRRALNFePAALGAHlTVLRRDGYIRKVGDKVQVAYEEEDARMFEAEDGTECT----IRTAQ 89 
                                       5789999999888.444444551344444569******************************999995....44433 PP

                            DUF762 213 vellksly 220
                                          l++l+
  gi|313125967|ref|YP_004036237.1|  90 QVDLDALV 97 
                                       33344444 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.5e-05      0.11      12      57 ..      12      58 ..       5      62 .. 0.86
   2 ?   -3.1   0.0       7.4   8.9e+03      50      55 ..     144     149 ..     131     154 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.5e-05
                           DprA_WH 12 dlerrvLaaL.gpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                      ++++ + + + ++  v +D++ r++ +++a++ a+L+ L  +G+++ 
  gi|313125967|ref|YP_004036237.1| 12 ADRKDIYDYIeSHGIVREDEVRRALNFEPAALGAHLTVLRRDGYIRK 58
                                      677778888845689************************99999986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.4
                           DprA_WH  50 ELaGlv 55 
                                       ELaG v
  gi|313125967|ref|YP_004036237.1| 144 ELAGWV 149
                                       455544 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.18       2     126 ..      85     219 ..      84     220 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                       EEEE-GGGHHHHHHHHHHHTT----H...........HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETT. CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespl.........eeireyfrklleesrvlgaedngelvgqlallplelnvpG. 68 
                                       ir++++ dld+ ++  k++ ++ +            +e     ++++++  v++a  ++el+g +     +l +p+ 
  gi|313125967|ref|YP_004036237.1|  85 IRTAQQVDLDALVDAIKEVAEEGTYIEaetvgdmidHEEVILRHNKVQSRMVFVATVEDELAGWV-----HLDLPEt 156
                                       55666666666666665554443332244555556323445667778888888888888888854.....5788888 PP

                                       EEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT.--EEEE--....SSHHHHHTTT-E CS
                    Acetyltransf_9  69 ktlkaagvtgVavapehrgrgvlskLlaraleemreeg.qplsllfP....ssipiYrrfGye 126
                                        +l+  +v  V+  ++ rg+g+ s+Ll+r +e ++e+g ++l   +P     +i++ +  G+e
  gi|313125967|ref|YP_004036237.1| 157 GKLRHTAVLTVGARAKFRGKGIGSRLLERGVEWAEEHGfEKLYNSVPatneEAISFLKDHGWE 219
                                       899999999***********************9999973455555566654446777777776 PP

>> Ish1  Putative stress-responsive nuclear envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.018        22       8      20 ..      16      28 ..      12      35 .. 0.83
   2 ?   -0.6   0.0       1.5   1.8e+03      11      19 ..     188     196 ..     188     197 .. 0.83
   3 ?    3.4   0.0     0.083        99       5      19 ..     205     219 ..     205     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                              Ish1  8 dLkkWLdshGipv 20
                                      d+ ++++shGi++
  gi|313125967|ref|YP_004036237.1| 16 DIYDYIESHGIVR 28
                                      6779*******96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                              Ish1  11 kWLdshGip 19 
                                       +W ++hG+ 
  gi|313125967|ref|YP_004036237.1| 188 EWAEEHGFE 196
                                       6******75 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.083
                              Ish1   5 SdsdLkkWLdshGip 19 
                                       ++++  ++L++hG  
  gi|313125967|ref|YP_004036237.1| 205 TNEEAISFLKDHGWE 219
                                       689999*******76 PP

>> SH3_16  Bacterial dipeptidyl-peptidase Sh3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.08        96      14      28 ..      41      55 ..      41      83 .. 0.79
   2 ?    5.1   0.0     0.016        19      28      45 ..     133     151 ..     122     152 .. 0.79
   3 ?   -1.3   0.0       1.6     2e+03      11      34 ..     219     244 ..     215     245 .] 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.08
                                      E-TT-EEEEEEEEET CS
                            SH3_16 14 alaGrhlrvleeadg 28
                                      a++G hl+vl +++ 
  gi|313125967|ref|YP_004036237.1| 41 AALGAHLTVLRRDGY 55
                                      789999999987754 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                                       T.EEEEEETTT--EEEEEG CS
                            SH3_16  28 g.wawVqlceDgYvGWlpl 45 
                                         +++V + eD   GW+ l
  gi|313125967|ref|YP_004036237.1| 133 SrMVFVATVEDELAGWVHL 151
                                       4479*************87 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.6
                                       EEEE-TT-EEEEEEEE.ET.EEEEEE CS
                            SH3_16  11 aTQalaGrhlrvleea.dg.wawVql 34 
                                        T+a   +h ++ +e  d+ +  V+l
  gi|313125967|ref|YP_004036237.1| 219 ETEAVREDHYKIDDEYvDEvMMAVRL 244
                                       68888888888888777776666665 PP

>> ETC_C1_NDUFA4  ETC complex I subunit conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.9   4.7e+03      57      77 ..      69      89 ..      62      98 .. 0.79
   2 ?   10.1   0.0   0.00064      0.76      55      86 ..     204     234 ..     181     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.9
                                      HHHHHHHHHHCT-EEEEE-SS CS
                     ETC_C1_NDUFA4 57 kedAiayaekqgweyeveepk 77
                                      +edA  +  + g e ++++ +
  gi|313125967|ref|YP_004036237.1| 69 EEDARMFEAEDGTECTIRTAQ 89
                                      689999999999998888764 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00064
                                       SSHHHHHHHHHHCT-EE.EEE-SST-XXXXXXX CS
                     ETC_C1_NDUFA4  55 dskedAiayaekqgwey.eveepkkrkvkpksY 86 
                                       +++e+Ai++ + +gwe   v+e+  +     +Y
  gi|313125967|ref|YP_004036237.1| 204 ATNEEAISFLKDHGWETeAVRED--HYKIDDEY 234
                                       799*************9345555..33333445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1313.16
//
Query:       gi|313125968|ref|YP_004036238.1|  [L=53]
Description: hypothetical protein Hbor_12040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.53
# Mc/sec: 300.20
//
Query:       gi|313125969|ref|YP_004036239.1|  [L=754]
Description: bifunctional p-loop ATPase/acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-46  158.5   0.0    2.4e-46  157.8   0.0    1.4  1  Helicase_RecD    Helicase
    4.4e-44  150.6   0.1    2.1e-27   96.0   0.0    2.2  2  GNAT_acetyltr_2  GNAT acetyltransferase 2
    7.8e-25   86.6   0.0    5.4e-24   84.0   0.0    2.2  2  DUF1726          Domain of unknown function (DUF1726)
    2.7e-05   24.0   0.4    5.7e-05   22.9   0.4    1.6  1  AAA_30           AAA domain
     0.0061   17.0   1.3       0.33   11.3   0.1    3.0  3  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.058   13.7   0.3        0.3   11.4   0.0    2.5  2  zf-HC2           Putative zinc-finger


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.0   8.1e-50   2.4e-46       1     177 []     221     392 ..     221     392 .. 0.91

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 8.1e-50
                     Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvr.kqri 76 
                                       v+ AdRGRGKS+a+Gla+ +l+a+g+ ++lvtap + n++++f+++++ l+++g+     ++++e + +++r + ri
  gi|313125969|ref|YP_004036239.1| 221 VVEADRGRGKSSAAGLAAGSLAADGR-DVLVTAPAYGNAREVFARAIELLRETGTFG---SHDEEAHVVSARgGGRI 293
                                       689*********************98.9***********************999654...33333344555569*** PP

                     Helicase_RecD  77 eyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrelrele 153
                                       ++  p ++++++++ d+l+vDEAAa+p++ll ++  + +   + tTvhGYEG+Grgfs++f ++l +++  ++++++
  gi|313125969|ref|YP_004036239.1| 294 RFTDPPTAATRPDDPDVLLVDEAAAVPVRLLAAFA-DAPSAGFFTTVHGYEGAGRGFSVRFRDRLAESDL-SVTDVQ 368
                                       ***********************************.666778889********************98766.****** PP

                     Helicase_RecD 154 leepiRyaegdplEkwlndlLlLd 177
                                       ++epiRya+ dp+E w +++LlLd
  gi|313125969|ref|YP_004036239.1| 369 MDEPIRYARSDPVETWAFRTLLLD 392
                                       **********************97 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   7.1e-31   2.1e-27       2     127 ..     429     546 ..     428     552 .. 0.92
   2 !   53.1   0.0   9.1e-18   2.7e-14     178     226 ..     551     599 ..     543     600 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 7.1e-31
                   GNAT_acetyltr_2   2 lvallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlip 78 
                                       +++llv +HY+++P+DL+ l DaP+ +  +L+++        +v++v  +a EG +++e+ +++++ g+r +G+++p
  gi|313125969|ref|YP_004036239.1| 429 VFGLLVLAHYRTEPDDLARLLDAPNLECRALMHDG-------HVVSVALLAREGGLDAETRRSMYE-GERVRGNMLP 497
                                       789******************************55.......6***************97766665.56******** PP

                   GNAT_acetyltr_2  79 wtlsqqfqdeefaslsGaRivRiAvhpelqkmGYGsralellekyyegk 127
                                       +++++q +de++a   G R++RiA+h+++++ G Gsr l++++++ e k
  gi|313125969|ref|YP_004036239.1| 498 DVFTSQLRDEDAAAPIGYRVMRIATHHAVRSSGLGSRLLSEIHAEKEAK 546
                                       ******************************************9987765 PP

  == domain 2  score: 53.1 bits;  conditional E-value: 9.1e-18
                   GNAT_acetyltr_2 178 ekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsl 226
                                        ++dylgv++G t+eLl+FW  +g+s+v+ ++t+ne++GE+sa+ml++l
  gi|313125969|ref|YP_004036239.1| 551 ADVDYLGVGYGATPELLSFWDDNGYSTVHFSTTRNETSGEYSALMLNPL 599
                                       689*******************************************987 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.0   1.8e-27   5.4e-24       2      93 .]      67     159 ..      66     159 .. 0.97
   2 ?   -0.6   0.0      0.43   1.3e+03      10      33 ..     428     450 ..     420     451 .. 0.73

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 1.8e-27
                           DUF1726   2 kesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplt.eevkkrfnk 77 
                                       k+++ +LG+t +++v d++e+++Pn+lgrl ++V+GGGl +ll+ppl+e+++++ +f+++l+v+p++ ++v +rf++
  gi|313125969|ref|YP_004036239.1|  67 KHARTLLGTTRTVVVCDAHEEFSPNVLGRLAGVVDGGGLFVLLAPPLDEWPETDGSFEESLAVPPVSvSDVGGRFRT 143
                                       578899*********************************************************************** PP

                           DUF1726  78 rfirklkehegilivd 93 
                                       r++++l++h+g+++v+
  gi|313125969|ref|YP_004036239.1| 144 RLVETLRTHPGVAVVN 159
                                       ************9985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.43
                           DUF1726  10 qtydllvldlfealtPnalgrlve 33 
                                       + ++llvl ++   +P++l+rl +
  gi|313125969|ref|YP_004036239.1| 428 EVFGLLVL-AHYRTEPDDLARLLD 450
                                       55667777.56788*******987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.4   1.9e-08   5.7e-05       8     110 ..     208     329 ..     199     346 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.9e-08
                            AAA_30   8 aavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgi..eastiakllkrlk 81 
                                       aa+e+l + g+  +v+++  G GK+ a + ++  ++a+g++v++ Ap    A++  a+++++  e+ t  +  ++  
  gi|313125969|ref|YP_004036239.1| 208 AALERLRNAGE-AVVVEADRGRGKSSAAGLAAGSLAADGRDVLVTAPAYGNAREvFARAIELlrETGTFGSHDEEAH 283
                                       56777777776.99*********************************987777735655554444444444443333 PP

                            AAA_30  82 .................grarlepgtllivDEagmvdtkqlaallk 110
                                                        +++r ++ ++l+vDEa+ v  + laa+++
  gi|313125969|ref|YP_004036239.1| 284 vvsargggrirftdpptAATRPDDPDVLLVDEAAAVPVRLLAAFAD 329
                                       55566789999****8644555566*************99999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.2   3.6e+03      88     145 ..       9      86 ..       3     107 .. 0.49
   2 !   11.3   0.1   0.00011      0.33       7      82 ..     201     269 ..     197     316 .. 0.80
   3 ?    3.4   0.0      0.03        91      12     123 ..     323     429 ..     318     464 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                            AAA_16  88 eaesaeleawrekleeala.............avpelagaea........srllellkrll.allsrderplvlvlD 142
                                       ++++a+++  +++l+  ++             ++++++++e          r+ ++  +++  ll +  r +v+v+D
  gi|313125969|ref|YP_004036239.1|   9 DLRTAARDTNQRRLLVLAGdrdagidaafdvlDGADVPDDEVafvtaregFRFERVRPKHArTLLGT-TR-TVVVCD 83 
                                       4444444444444444444444445554445422222222223334455555555555555444444.45.666766 PP

                            AAA_16 143 dlq 145
                                         +
  gi|313125969|ref|YP_004036239.1|  84 AHE 86 
                                       555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                            AAA_16   7 eeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggif...lrgkcdqlesaipysalaqalar 78 
                                       +++++ l+aler+r  + e+v++  ++G GKss +  ++ +l +d  ++++   ++g++++         +a+a+  
  gi|313125969|ref|YP_004036239.1| 201 ADQSRTLAALERLRNAG-EAVVVEADRGRGKSSAAGLAAGSLAADgrDVLVtapAYGNAREV--------FARAI-- 266
                                       56677789999998665.9********************99999964466677788888887........77777.. PP

                            AAA_16  79 eell 82 
                                        ell
  gi|313125969|ref|YP_004036239.1| 267 -ELL 269
                                       .344 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.03
                            AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy...salaqalareellrql 85 
                                       Ll+a+ ++ s +   + ++G+ G G    vr  +++l +++   l+ + +q ++ i+y   +++ + +     +r l
  gi|313125969|ref|YP_004036239.1| 323 LLAAFADAPSAG-FFTTVHGYEGAGRGFSVRF-RDRLAESD---LSVTDVQMDEPIRYarsDPVETWA-----FRTL 389
                                       555555444444.37889************55.55566665...555555555558885522233333.....2333 PP

                            AAA_16  86 ldeaes..aeleawrekleealaavpelagaeasrllell 123
                                       l +a+   + l  +++   ++++a ++++ a+ ++ll+++
  gi|313125969|ref|YP_004036239.1| 390 LLDARPavSPLVTDAAPESTEYRALSADELASDEHLLREV 429
                                       3332220023333333333334433333333334444443 PP

>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         5   1.5e+04      14      22 ..     475     483 ..     474     485 .. 0.82
   2 ?   11.4   0.0    0.0001       0.3       4      33 ..     614     643 ..     613     643 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5
                                       CT-SCCCHC CS
                            zf-HC2  14 GeLspeera 22 
                                       G L++e+r+
  gi|313125969|ref|YP_004036239.1| 475 GGLDAETRR 483
                                       89****997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHCCT-SCCCHCCCHHHHCHTCH CS
                            zf-HC2   4 vrelLsaYlDGeLspeerarveaHLaeCpd 33 
                                       ++++++  l ++Ls+++ + v+a + +C++
  gi|313125969|ref|YP_004036239.1| 614 FLDRMPGVLSDPLSDADPDVVRAAIRACDA 643
                                       7899************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (754 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 4120.14
//
Query:       gi|313125970|ref|YP_004036240.1|  [L=123]
Description: 50S ribosomal protein L7ae [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-25   87.3   0.1    4.9e-25   87.1   0.1    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    0.00016   21.5   0.0    0.00024   20.9   0.0    1.3  1  PELOTA_1        PELOTA RNA binding domain
     0.0031   18.0   0.3     0.0044   17.5   0.3    1.4  2  eRF1_3          eRF1 domain 3
     0.0037   17.5   0.9        1.5    9.1   0.1    2.1  2  DUF1269         Protein of unknown function (DUF1269)


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.1   1.1e-28   4.9e-25       4      93 ..      21     110 ..      18     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.1e-28
                                       HHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSEC CS
                    Ribosomal_L7Ae   4 eevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpv 80 
                                        e+l++a+++g++++G++e+tka+erg+a+lv++Aedv+pee++ +l+ ++ ek++py++++ + e G+++g+++ +
  gi|313125970|ref|YP_004036240.1|  21 LEALEVARDTGTVKKGTNETTKAVERGNAELVLVAEDVSPEEIVMHLPEIADEKGIPYIFIETQDEVGHAAGLEVGS 97 
                                       68999************************************************************************ PP

                                       SEEEEEESTTTHH CS
                    Ribosomal_L7Ae  81 salaikdegdskd 93 
                                       +a+ai+d+g++++
  gi|313125970|ref|YP_004036240.1|  98 AAAAIVDAGEAQE 110
                                       *********9987 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.4e-08   0.00024      17      68 ..      28      81 ..      14      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.4e-08
                          PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveev 68
                                      +d+  +K g  E+T+++ R   e vlv+++ +  + + hl ++a+ekg+p+  +
  gi|313125970|ref|YP_004036240.1| 28 RDTGTVKKGTNETTKAVERGNAELVLVAEDVSpeEIVMHLPEIADEKGIPYIFI 81
                                      68899************************888335589***********97654 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   6.4e+03      20      41 ..       3      24 ..       2      24 .. 0.81
   2 !   17.5   0.3   9.8e-07    0.0044      14      59 ..      25     103 ..      14     123 .] 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                                      SSEEESHHHHHHHHHTT-EEEE CS
                            eRF1_3 20 gkavYGveevlkalemgAvetL 41
                                      ++avY + +v + l   A+e L
  gi|313125970|ref|YP_004036240.1|  3 NMAVYVEFDVPADLAEDALEAL 24
                                      5789999999999998888876 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 9.8e-07
                                       HHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS................................ CS
                            eRF1_3  14 elakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv................................ 58 
                                       e+a+dtg++  G +e+ ka+e g  e +Lv e++  ++ ++  ++                                
  gi|313125970|ref|YP_004036240.1|  25 EVARDTGTVKKGTNETTKAVERGNAELVLVAEDVSPEEIVMHLPEiadekgipyifietqdevghaaglevgsaaaa 101
                                       7899*******************************999776555467777777777777766666666444433333 PP

                                       .- CS
                            eRF1_3  59 .k 59 
                                         
  gi|313125970|ref|YP_004036240.1| 102 iV 103
                                       33 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1   0.00034       1.5      36      77 ..      28      69 ..      20      75 .. 0.85
   2 !    7.5   0.1    0.0011         5      20      53 ..      87     120 ..      76     123 .] 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00034
                           DUF1269 36 sdvgidddflkelgeklkpgtsalfllvekatvdkvlealak 77
                                      +d+g  ++  +e  +++++g++ l+l++e++ +++++ +l +
  gi|313125970|ref|YP_004036240.1| 28 RDTGTVKKGTNETTKAVERGNAELVLVAEDVSPEEIVMHLPE 69
                                      56777778889999**********************988865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                           DUF1269  20 lGaavGAaaGAlvgalsdvgidddflkelgeklk 53 
                                       +G a+G  +G++++a+ d+g  ++ ++++++k++
  gi|313125970|ref|YP_004036240.1|  87 VGHAAGLEVGSAAAAIVDAGEAQEQVEDIAAKVE 120
                                       6899**************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 720.88
//
Query:       gi|313125971|ref|YP_004036241.1|  [L=74]
Description: 30S ribosomal protein S28e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-28   96.5   0.8    7.2e-28   96.4   0.8    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.8     4e-32   7.2e-28       3      63 ..      10      70 ..       8      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 4e-32
                                      -EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT- CS
                    Ribosomal_S28e  3 aklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArr 63
                                       + AeVi+++g+tG++Ge++qV++++ eg+++grii+RnV GPvreGDiL L+Et+r A  
  gi|313125971|ref|YP_004036241.1| 10 STSAEVIEIVGKTGMHGEAMQVKCRIREGSNQGRIITRNVLGPVREGDILQLRETQRDADS 70
                                      689******************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 420.95
//
Query:       gi|313125972|ref|YP_004036242.1|  [L=68]
Description: ribosomal protein l24e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-19   67.8   0.0    7.8e-19   67.7   0.0    1.0  1  Ribosomal_L24e  Ribosomal protein L24e


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   4.3e-23   7.8e-19       4      63 ..       5      64 ..       2      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 4.3e-23
                                      -B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXXXXXX CS
                    Ribosomal_L24e  4 ekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrahkkel 63
                                      ++C++sg++i+PG+G+++v+nDg++++F +sK+ek++   r++r+l+WT   + a +  +
  gi|313125972|ref|YP_004036242.1|  5 RTCDYSGEEIEPGTGTMYVKNDGSILHFKDSKAEKNYFLGREARDLEWTAEGQAASGASE 64
                                      79***********************************************99988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.52
# Mc/sec: 396.92
//
Query:       gi|313125973|ref|YP_004036243.1|  [L=153]
Description: nucleoside diphosphate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-57  191.7   0.0    5.7e-57  191.5   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.5   0.0   3.2e-61   5.7e-57       1     134 [.       4     139 ..       4     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 3.2e-61
                                       EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEEST CS
                               NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlege 77 
                                       ert+v++KPd+v+rgligei+sr+e++glk+va k+++++ee+a+ehY ehk+kpff+ lv+f+tsgpv+a+v+eg+
  gi|313125973|ref|YP_004036243.1|   4 ERTFVMVKPDGVQRGLIGEIVSRFEDRGLKMVAGKFMQIDEELAHEHYGEHKDKPFFDGLVDFITSGPVFAMVWEGQ 80 
                                       89*************************************************************************** PP

                                       THHHHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHH..HHHHHHHHHSTGGG CS
                               NDK  78 daiekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdsee..saereiklfFkeee 134
                                       da+++vr+++G+t+pae+apgtiR+d+g++lg+N++HgSd+e+  + erei+lfF+e+e
  gi|313125973|ref|YP_004036243.1|  81 DATRQVRRMMGETDPAESAPGTIRGDYGLDLGRNVIHGSDHEDegANEREISLFFDEDE 139
                                       ****************************************998334789*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 896.26
//
Query:       gi|313125974|ref|YP_004036244.1|  [L=357]
Description: methionine synthase (b12-independent) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-55  189.3   0.0    1.7e-55  188.6   0.0    1.3  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
    4.5e-12   46.1   0.0    7.4e-12   45.4   0.0    1.3  1  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
    3.3e-05   23.2   0.0    4.4e-05   22.8   0.0    1.2  1  URO-D        Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.6   0.0   2.8e-59   1.7e-55       2     323 ..      23     336 ..      22     337 .. 0.92

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 2.8e-59
                                       -BB--SB---SS----..-------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTE CS
                       Meth_synt_2   2 pTttiGSfPqtaevre..araevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgf 76 
                                        Tt++GS+P+ + +++    ae  + ++++e+ e+a+ ++ + + ++ e++g+D +v+ge+ R +mveyf++++ g+
  gi|313125974|ref|YP_004036244.1|  23 LTTVVGSYPKPKWLNRskELAEDDESKFDDEDLEEAYDDAARVITHEHENAGLDTVVDGEMRREEMVEYFAHRIPGY 99 
                                       69*******99866550055677889999***********99999*******************************9 PP

                                       E--SS--EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHH CS
                       Meth_synt_2  77 aftkngwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltdkpvkglltGpvtilnwsfvrddvdraeaaaqia 153
                                        f  ng v+  g  +   p +  +v++ ++  v e    + + +kpvk  +tGp t+ +wsf +     a+ a+++a
  gi|313125974|ref|YP_004036244.1| 100 EF--NGPVKVWGHNYFDKPSVASEVEYDEPWLVDEFEFTSNVAEKPVKVPITGPYTLARWSFNEAYDTEADLAYDLA 174
                                       76..6889999999999999********************************************999999******* PP

                                       HHHHHHHHHHHHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCHHHHH CS
                       Meth_synt_2 154 lalrdevkdLeaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndilsaia 230
                                         + +ev++L +aG+  +QiDepal +  p+ +a   + l+       +d  ++ +++ + +H+Cy ++  i ++i+
  gi|313125974|ref|YP_004036244.1| 175 DLVNEEVEKLVEAGARYVQIDEPALATT-PDDHAIVGECLER-----IVD--GIPEEVRIGLHVCYGDYSRIYPEIN 243
                                       ************************9875.5555333333333.....333..35899******************** PP

                                       TT--SEEEESBSSS-SSGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS-STSB-BB-SS-STTS- CS
                       Meth_synt_2 231 aldvDvitieasrsdeellealeevkygrgvglGvydihsprvpsmeeiaalikkaldvapkerlwvnPdCGLktrk 307
                                       +  +D  ++e  +   e ++++ + +++ ++ lGv+d+h+  v+s+eei++ i + l+v+p e+l v+PdCG+k ++
  gi|313125974|ref|YP_004036244.1| 244 DYPIDEFDVELCNGGYEQIDVFTDPEFEPDLALGVVDVHTAEVESVEEIKENILEGLKVVPPEKLTVSPDCGVKLLP 320
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHH CS
                       Meth_synt_2 308 reearaalknmvdaAk 323
                                       re a ++++nmv aA+
  gi|313125974|ref|YP_004036244.1| 321 REVAYQKMENMVTAAR 336
                                       **************97 PP

>> Meth_synt_1  Cobalamin-independent synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.2e-15   7.4e-12     127     289 ..     120     280 ..     105     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.2e-15
                                       .----S-THHHHHHHHH.HHTTGGEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHHHHHHHHHHHHHTT-SEEEEE CS
                       Meth_synt_1 127 tefklaseklleevkea.kalgieakpvllGpltflkLskakeekveklellekLlpvYkelleeLkeagvewvqid 202
                                       +e+++++ +l++e++   + +   +k  + Gp+t+   s ++  + ++++l  +L ++ +e +e+L eag+++vqid
  gi|313125974|ref|YP_004036244.1| 120 SEVEYDEPWLVDEFEFTsNVAEKPVKVPITGPYTLARWSFNEAYD-TEADLAYDLADLVNEEVEKLVEAGARYVQID 195
                                       468889999******9966677889999**********9999988.8999*************************** PP

                                       -GGGGSSGCHHHHHHHHHHHHHHTC.CTTTSEEEEE--SS-.CCHHHHHTTSSTSEEEEETSS.HCHHHHHHHHCTT CS
                       Meth_synt_1 203 EPalvldlekeelealkeaYeelak.ekkelklllatyFdsvaealellaelpveglglDlvr.aeenlealkkagl 277
                                       EPal++   +++ +++ e  e++     +e+++ l+  +++ ++ + ++ ++p++ + ++l++ + e+++ +++ ++
  gi|313125974|ref|YP_004036244.1| 196 EPALATT--PDDHAIVGECLERIVDgIPEEVRIGLHVCYGDYSRIYPEINDYPIDEFDVELCNgGYEQIDVFTDPEF 270
                                       ****986..5555666666666653137899********************************9999***9999888 PP

                                       .TTSEEEEEEE- CS
                       Meth_synt_1 278 pedkvLsaGvid 289
                                         +  L++Gv+d
  gi|313125974|ref|YP_004036244.1| 271 --EPDLALGVVD 280
                                       ..5568899998 PP

>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   7.4e-09   4.4e-05     178     345 ..     169     337 ..     150     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.4e-09
                                       HHHHHHHHHHHHHHHHHHTT-SEEEEEE.TTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S-EEEEES.SHH.HHH CS
                             URO-D 178 lldkltdvvieylkaqieagAdaiqifD.swagllspedfeefvlpylkrivdevkaegpkvpvilfik.gagaeil 252
                                       l   l+d+v e +++++eagA  +qi + +   + +p+d + +v ++l+rivd++++   +v + l+++ g+++ i+
  gi|313125974|ref|YP_004036244.1| 169 LAYDLADLVNEEVEKLVEAGARYVQIDEpAL--ATTPDD-HAIVGECLERIVDGIPE---EVRIGLHVCyGDYSRIY 239
                                       5556899999****************88444..335555.679**************...579*****9556767** PP

                                       HHHTTS--SEEE--TTS....-HHHHHH..SS....EEE--B-G.GGGGS-HHHHHHHHHHHHT.T---SSSEEB-B CS
                             URO-D 253 edlaelgadvlsldwtv....dlkeaar..evgdkvalqGnldPialLlgspeeiekevkeilekgaggkkgyilnl 323
                                       +++++ ++d + ++  +    ++ +++   e+ +    +G +d +++ ++s eei++++ e l+  + ++++  +++
  gi|313125974|ref|YP_004036244.1| 240 PEINDYPIDEFDVELCNggyeQI-DVFTdpEF-EPDLALGVVDVHTAEVESVEEIKENILEGLK--VVPPEKLTVSP 312
                                       **********9998888555555.55555444.666789*****76666***************..688******** PP

                                       SS-...--TTS-HHHHHHHHHHHHT CS
                             URO-D 324 Ghg...ippetppenvkalveavke 345
                                        +g   +p e+  ++++ +v a++e
  gi|313125974|ref|YP_004036244.1| 313 DCGvklLPREVAYQKMENMVTAARE 337
                                       ***6666889999*******99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2077.50
//
Query:       gi|313125975|ref|YP_004036245.1|  [L=335]
Description: methionine synthase ii (cobalamin-independent) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-12   47.0   0.0    8.1e-12   45.3   0.0    1.7  2  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
    2.3e-08   33.7   0.1    6.4e-08   32.2   0.1    1.6  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain


Domain annotation for each model (and alignments):
>> Meth_synt_1  Cobalamin-independent synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.11   9.7e+02      31      68 ..      40      76 ..      35      88 .. 0.80
   2 !   45.3   0.0   9.1e-16   8.1e-12     107     311 ..      90     291 ..      83     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.11
                                      HHHHHHHHHHHHHHHHHHHCTT-SBEEES---SS-HHH CS
                       Meth_synt_1 31 eeLektakeLrakhwkkqkeagidlipvndfslYDhvL 68
                                      +++ ++ ++ r++ +  q +ag+d +  +++ + D +L
  gi|313125975|ref|YP_004036245.1| 40 DDIVAVYEDAREEVVADQLDAGLDRVVEGQLRW-DDML 76
                                      56677888999999***********99988876.5555 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 9.1e-16
                                       EEEESTTSS-EEEE-BE-SS.----S-THHHHHHHHHHHTTGGEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHHH CS
                       Meth_synt_1 107 emtkwFntnYHYlvPelekdtefklaseklleevkeakalgieakpvllGpltflkLskakeekveklellekLlpv 183
                                        ++++++ n  Y  P++  d +f+ +  + le  +e+    +  ++vl Gp+++  L+  +    +++++l ++ + 
  gi|313125975|ref|YP_004036245.1|  90 GIVRYYDNNNFYRDPQVVGDLSFSGDVAAELEAASEFAG-ETPLQAVLPGPYSLAELATDEYYG-DEADFLAAIGDF 164
                                       5789********************999999998888754.458899************999988.9999*****999 PP

                                       HHHHHHHHHHTT-SEEEEE-GGGGSSGCHHH.HHHHHHHHHHHTCCTTTSEEEEE--SS-.CC.HHHHHTTSSTSEE CS
                       Meth_synt_1 184 YkelleeLkeagvewvqidEPalvldlekee.lealkeaYeelakekkelklllatyFdsvae.alellaelpvegl 258
                                           +e + ++  e++ + +P l++d ++++ +e + ea +++ + +++++++++ty+d+++e +++ l++ ++e++
  gi|313125975|ref|YP_004036245.1| 165 LGGEVEAFPDH--ETLFLLDPSLATDAPDDDiAERVPEAIDAV-AGATDADVVVHTYWDAIDEkTYAHLMDADIEAI 238
                                       99999999988..7788899*******7665167899999999.6999************97626899********* PP

                                       EEETSSHCHHHHHHHHCTT.TTSEEEEEEE-SSS-B---HHHHHHHHHHHHHC CS
                       Meth_synt_1 259 glDlvraeenlealkkaglpedkvLsaGvidGrniWradlekalelleelaek 311
                                       g+D+v+++++    + +++ ++  +++G+ dG+n    d e+  e++e ++++
  gi|313125975|ref|YP_004036245.1| 239 GFDFVAGDRETTLYNINEYGAKDDVALGLADGQNTLVEDPETIRERVEWVNDQ 291
                                       ******665555555555777888999************99999998877765 PP

>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.1   7.1e-12   6.4e-08      31     291 ..      41     293 ..      21     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.1e-12
                                       HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTEE--SS--EEEET.TEEE---EE-SS---SS- CS
                       Meth_synt_2  31 eyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgfaftkngwvqsyg.srcvrppiivgdvsrpaa 106
                                       +  + ++++ e+vv++q ++g+D +v+g+  R d + + +  ++  ++t  g+v  y  + ++r p +vgd+s+  +
  gi|313125975|ref|YP_004036245.1|  41 DIVAVYEDAREEVVADQLDAGLDRVVEGQL-RWDDMLAHPLTIHDNVETG-GIVRYYDnNNFYRDPQVVGDLSFSGD 115
                                       5667788999*******************8.6666666799999999987.677777516789************** PP

                                       SSTHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEE-TTSSTT-- CS
                       Meth_synt_2 107 mtvkesalaqsltdkpvkglltGpvtilnwsfvrddvdraeaaaqialalrdevkdLeaaGikviQiDepalreGlp 183
                                       ++ + +a  +   + p++ +l Gp ++ + +  +   d a+ +a i+  l  ev++  +   + + + +p l + +p
  gi|313125975|ref|YP_004036245.1| 116 VAAELEAASEFAGETPLQAVLPGPYSLAELATDEYYGDEADFLAAIGDFLGGEVEAFPDH--ETLFLLDPSLATDAP 190
                                       *********************************9999********************999..778888899999999 PP

                                       SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCH.HHHHTT--SEEEESB.SSS-SSGGGGTTTT--- CS
                       Meth_synt_2 184 lkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndil.saiaaldvDvitiea.srsdeellealeevkyg 258
                                       +        + + v + ++d++a a+d++v +H   + +++    ++ + d+ +i  ++ ++  e +l  ++e + +
  gi|313125975|ref|YP_004036245.1| 191 DDD------IAERVPE-AIDAVAGATDADVVVHTYWDAIDEKTyAHLMDADIEAIGFDFvAGDRETTLYNINEYGAK 260
                                       988......4444544.588899999**********9999994345555555555555535555689999******* PP

                                       SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS- CS
                       Meth_synt_2 259 rgvglGvydihsprvpsmeeiaalikkaldvap 291
                                        +v lG+ d +   v+  e i+++++ + d ++
  gi|313125975|ref|YP_004036245.1| 261 DDVALGLADGQNTLVEDPETIRERVEWVNDQIH 293
                                       ***********************9998888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2087.77
//
Query:       gi|313125976|ref|YP_004036246.1|  [L=202]
Description: hemk-related methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-11   42.9   0.0      2e-10   40.5   0.0    1.8  2  MTS              Methyltransferase small domain
    3.8e-08   33.9   0.0    1.2e-07   32.4   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    6.3e-08   33.2   0.0    8.9e-07   29.5   0.0    2.1  2  Methyltransf_11  Methyltransferase domain
     0.0003   20.5   0.0     0.0016   18.1   0.0    1.9  1  UPF0020          Putative RNA methylase family UPF0020
    0.00042   21.0   0.0     0.0015   19.2   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
    0.00049   19.9   0.0    0.00064   19.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0022   17.9   0.1     0.0073   16.2   0.1    1.9  1  Methyltransf_23  Methyltransferase domain
     0.0048   16.6   0.0     0.0069   16.0   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0055   16.7   0.0     0.0081   16.1   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0068   16.1   0.0     0.0097   15.6   0.0    1.1  1  NIF3             NIF3 (NGG1p interacting factor 3)
     0.0081   15.6   0.0      0.015   14.7   0.0    1.4  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.036   13.8   0.0      0.064   13.0   0.0    1.4  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.13   11.7   0.0        0.4   10.1   0.0    1.7  2  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   1.4e-13     2e-10      20     107 ..      23     114 ..      17     127 .. 0.94
   2 ?    0.1   0.0      0.38   5.2e+02     116     148 ..     139     171 ..     131     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.4e-13
                                       HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTT CS
                               MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvlee 92 
                                       s+lL+e++ ++++g+ l +G+G G ++ ++a++ +   v++ dv+ +A esa++  e+ ++e    +e+v  ++++ 
  gi|313125976|ref|YP_004036246.1|  23 SALLAEAVVDHARGRFLEVGTGSGWVAEQAARKADVDCVVASDVNPHACESARKRGEKLRAEghlgIEAVRANLVNP 99 
                                       899*****************************999999****************9999998888899********** PP

                                       STTS-EEEEEE---S CS
                               MTS  93 veekkfdlivsNPPf 107
                                       + +++fd++  NPP+
  gi|313125976|ref|YP_004036246.1| 100 FRDGSFDTVAFNPPY 114
                                       **************7 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH CS
                               MTS 116 avaeeliaeAkeaLkegGeLliVanrklgyesl 148
                                       +  + ++ e  ++L++gG+ l+ +++  g +++
  gi|313125976|ref|YP_004036246.1| 139 KFLNPFVDEVGRILTDGGRVLLLVSSLTGFDEV 171
                                       5667789999999*****999988887777666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   8.4e-11   1.2e-07       2      73 ..      39     113 ..      38     132 .. 0.79
   2 ?   -2.2   0.0       5.1   7.1e+03      84      97 .]     143     156 ..     139     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 8.4e-11
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT....TEEEEESBCCGBSSSTTTEEEEEEEST CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl....nvefvqgdaedlpfedgsfDlvvssga 73 
                                       L++G+G+G +++++a++     v++ D+++ ++e ar+r e+ ++     +e v++++ + pf dgsfD v  +  
  gi|313125976|ref|YP_004036246.1|  39 LEVGTGSGWVAEQAARKADVDCVVASDVNPHACESARKRGEKLRAeghlGIEAVRANLVN-PFRDGSFDTVAFNPP 113
                                       9****************8789****************99988555333677777777655.9*********98544 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.1
                                       HHHHHHHHHEEEEE CS
                   Methyltransf_25  84 kalkeiarvLkpgG 97 
                                        +++e+ r+L++gG
  gi|313125976|ref|YP_004036246.1| 143 PFVDEVGRILTDGG 156
                                       578999*****999 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   6.4e-10   8.9e-07       1      66 [.      39     109 ..      39     115 .. 0.89
   2 ?    1.5   0.0      0.35   4.9e+02      78      95 ..     142     159 ..     125     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 6.4e-10
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-....EEEETTEECCCTSS-TT-EEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl....kvefvvadaeklpfednsfDlvv 66 
                                       L+vG+G+G +ae+ a+++    vv+ D+++ + + a++++++ +      +e v+a++ + pf+d+sfD v 
  gi|313125976|ref|YP_004036246.1|  39 LEVGTGSGWVAEQAARKAdvDCVVASDVNPHACESARKRGEKLRAeghlGIEAVRANLVN-PFRDGSFDTVA 109
                                       89*************8888899*******************9999996666667777776.********996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                       + +++e+ R+L  gG+++
  gi|313125976|ref|YP_004036246.1| 142 NPFVDEVGRILTDGGRVL 159
                                       56899**********986 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.2e-06    0.0016      69     132 ..      49     115 ..      21     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                                       HHHHHH.HH--.EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE----- CS
                           UPF0020  69 aeeear.aelk.lygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivtnpPYG 132
                                       ae++ar a++  +++sD ++ + + ar+  ek + ++   +++  a  ++  ++g++d+++ npPY 
  gi|313125976|ref|YP_004036246.1|  49 AEQAARkADVDcVVASDVNPHACESARKRGEKLRAEGHLGIEAVRANLVNpFRDGSFDTVAFNPPYL 115
                                       33444434444799******************99999999999888877777899***********7 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.1e-06    0.0015       1      71 [.      39     109 ..      39     112 .. 0.91
   2 ?   -1.3   0.0       2.8   3.8e+03      84      99 .]     143     158 ..     137     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvv 71 
                                       Le+G+G+G +++  ++k     ++++D++p+a+e a+++  k +++ +  +e    +l + +  +sfD+v 
  gi|313125976|ref|YP_004036246.1|  39 LEVGTGSGWVAEQAARKADVDCVVASDVNPHACESARKRGEKLRAEGHLGIEAVRANLVNPFRDGSFDTVA 109
                                       8****************5555555*********************************9999999****995 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.8
                   Methyltransf_12  84 evldnirklLkpgGrl 99 
                                        ++d++ + L++gGr+
  gi|313125976|ref|YP_004036246.1| 143 PFVDEVGRILTDGGRV 158
                                       5789999*******85 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.6e-07   0.00064       5     122 ..      36     175 ..      32     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.6e-07
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDli 78 
                                        r+l++G+G+G  + ++a++   + + vv  D +++a e+Ar++ +kl  +  +  e+  ++   +  + d +fD +
  gi|313125976|ref|YP_004036246.1|  36 GRFLEVGTGSGWVAEQAARK-A-DVDcVVASDVNPHACESARKRGEKLRAEgHLGIEAVRANLvNP--FRDGSFDTV 108
                                       579***************54.3.33369**********************9755555555555445..999*****9 PP

                   Methyltransf_31  79 lsn.................evlnaladpdkile....eiervlkpggilliedpr..llaelpakv 122
                                         n                  +l    +  k+l+    e+ r l++gg++l+   +  + +e+ + v
  gi|313125976|ref|YP_004036246.1| 109 AFNppylptdpdnewddwmeHALSGGESGRKFLNpfvdEVGRILTDGGRVLLLVSSltGFDEVTERV 175
                                       9997777777777777666655544444444444666699999999999876555433445555555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   5.3e-06    0.0073      16      62 ..      29      95 ..      12     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
                   Methyltransf_23 16 llpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae...................k 62
                                      ++  + a+gr L++G+G+G ++e ++++     v++ D +p+a e a+                   +
  gi|313125976|ref|YP_004036246.1| 29 AV-VDHARGRFLEVGTGSGWVAEQAARKADvdCVVASDVNPHACESARkrgeklraeghlgieavraN 95
                                      33.28899***********999999666433357799****999998877777777766665544440 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     5e-06    0.0069      41     124 ..      34     115 ..      24     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5e-06
                                       CC-EEEETT-TTSHHHHHHHHTT-SE..EEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakk..avlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefd 115
                                        + r+L++  GsG ++ E + R+a+   +v+ + +++a++  ++  e+l++e+    l  +a++a l ++ ++++fd
  gi|313125976|ref|YP_004036246.1|  34 ARGRFLEVGTGSGWVA-EQAARKADVdcVVASDVNPHACESARKRGEKLRAEG---HLGIEAVRANLVNPFRDGSFD 106
                                       5678*********986.777787764227888999***************987...444455555556667899*** PP

                                       EEEE--SSS CS
                     Cons_hypoth95 116 ivflDPPya 124
                                        v ++PPy 
  gi|313125976|ref|YP_004036246.1| 107 TVAFNPPYL 115
                                       ********5 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.9e-06    0.0081      15      85 ..      34     107 ..      24     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.9e-06
                   Methyltransf_18  15 gs.rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled..kievrlsdGleklkeeevdt 85 
                                        + r++ +Gt  g ++  ++++  ++ v+asD+n++++e+a++  ek + e    ie++ ++ +++++++++dt
  gi|313125976|ref|YP_004036246.1|  34 ARgRFLEVGTGSGWVAEQAARKADVDCVVASDVNPHACESARKRGEKLRAEGhlGIEAVRANLVNPFRDGSFDT 107
                                       3348999************************************9999776542245666666666665555555 PP

>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     7e-06    0.0097     178     229 ..      41      92 ..      33      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7e-06
                              NIF3 178 icaGsGaslieeakakgaDlliTGelkhhealdakekgiavidvgHyatErv 229
                                       + +GsG    ++a+++++D+ ++++++ h++ +a+++g ++ + gH  +E v
  gi|313125976|ref|YP_004036246.1|  41 VGTGSGWVAEQAARKADVDCVVASDVNPHACESARKRGEKLRAEGHLGIEAV 92 
                                       557888866668888888*****************************99987 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-05     0.015     161     206 ..      34      80 ..      23     111 .. 0.74
   2 ?   -2.7   0.0       2.2     3e+03     242     284 ..     144     187 ..     140     189 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                              PrmA 161 egeevlDvGtGSGiLa.iaaakLgakkvvavDiDevAvkvakeNael 206
                                       ++ ++l vGtGSG  a  aa k + + vva D+++ A ++a++  e+
  gi|313125976|ref|YP_004036246.1|  34 ARGRFLEVGTGSGWVAeQAARKADVDCVVASDVNPHACESARKRGEK 80 
                                       344899*******8773689999******************986555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                              PrmA 242 laedikklvkeggllilSGilkekaeevaealeq.gfeleevle 284
                                       +++++ +++ +gg+++l     +  +ev e++e+ gf+ e+v++
  gi|313125976|ref|YP_004036246.1| 144 FVDEVGRILTDGGRVLLLVSSLTGFDEVTERVESrGFDYETVVQ 187
                                       56666666666666554333334567888877544888888766 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.7e-05     0.064      73     125 ..      34      91 ..       6     114 .. 0.79
   2 ?   -3.1   0.0       3.8   5.2e+03     163     174 ..     152     163 ..     150     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC......S CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle......n 125
                                       +  r LevG+GsG+ +   ar    ++ vv+ +  ++ +e+a+++ +kl +e       
  gi|313125976|ref|YP_004036246.1|  34 ARGRFLEVGTGSGWVAEQAARKADVDC-VVASDVNPHACESARKRGEKLRAEghlgieA 91 
                                       55699*******************999.9999************999988776555440 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.8
                                       EEEEEEEEEEES CS
                              PCMT 163 LkeGGrlvvPvg 174
                                       L +GGr+++ v 
  gi|313125976|ref|YP_004036246.1| 152 LTDGGRVLLLVS 163
                                       789999998776 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00029       0.4       5      79 ..      38     111 ..      34     119 .. 0.72
   2 ?   -1.2   0.0      0.87   1.2e+03      96     115 ..     141     160 ..     136     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                                       EEEET-TTSHHHHHHHHHSTTSEE.EEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEEE CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknf.lGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifil 79 
                                       +le+G+G+G+ + ++A +++d+++ ++ +++ +  + + k+ e+l+++  + ++      l + ++dgs++ + ++
  gi|313125976|ref|YP_004036246.1|  38 FLEVGTGSGW-VAEQAARKADVDCvVASDVNPHACESARKRGEKLRAEGHLGIEAV-RANLVNPFRDGSFDTVAFN 111
                                       89*****995.678888888887626889999999999999998866542222221.1246777888888877776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.87
                                       SHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_4  96 qpellkelarvLkkgGvlel 115
                                        + +++e+ r+L  gG + l
  gi|313125976|ref|YP_004036246.1| 141 LNPFVDEVGRILTDGGRVLL 160
                                       56799999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1313.06
//
Query:       gi|313125977|ref|YP_004036247.1|  [L=391]
Description: small-conductance mechanosensitive channel [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-50  170.7   0.3    2.9e-50  170.7   0.3    1.7  2  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.21   11.5   2.1        0.3   10.9   2.1    1.3  1  DUF4271     Domain of unknown function (DUF4271)
        3.8    7.0   7.5       0.33   10.5   0.9    2.1  2  DUF1700     Protein of unknown function (DUF1700)
        3.8    5.5   5.2        1.6    6.8   3.0    1.4  1  UPF0182     Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.8       0.7   3.2e+03      16      43 ..      60      87 ..      56     110 .. 0.70
   2 !  170.7   0.3   6.5e-54   2.9e-50       3     206 .]     150     349 ..     148     349 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.7
                                      HHHTTT--SCCHHHHHHHHHHHHHHHHC CS
                        MS_channel 16 vlsllgvnvsallavlGalglalglalk 43
                                      +l++l v++++++ + +a+++ +g   +
  gi|313125977|ref|YP_004036247.1| 60 ALWSLLVSLTTMTLATAAAAVIVGVWGQ 87
                                      6888888888888888888888886555 PP

  == domain 2  score: 170.7 bits;  conditional E-value: 6.5e-54
                                       HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedi 79 
                                       i  + +++++i ivl  + vn+s +l+++G+lg+++g+a+++++  l+aG++l+f++pf+iGD++e+gd+eG+V+di
  gi|313125977|ref|YP_004036247.1| 150 IAQVFLYAFTIAIVLAIWEVNLSGILVGAGFLGIVVGMAARQTLGALLAGFVLMFSRPFEIGDWIEVGDHEGIVTDI 226
                                       77899************************************************************************ PP

                                       -SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-E CS
                        MS_channel  80 glrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkel 156
                                       ++  t+i+tfdg++v++Pn  +++++ +N sr +g+ ri+v++gv+y++d   +e+++e  +ea++e  + l+ +++
  gi|313125977|ref|YP_004036247.1| 227 TIVNTRIQTFDGEYVMVPNDVVSSESLINRSR-KGRLRIEVEVGVDYDAD---PERAAELALEAVEELDDPLNVPTP 299
                                       ********************************.*****************...999999999999999999999*** PP

                                       EEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 157 lvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       +vvl++f+ds++ + +rv++   + ++++++q++++  +k+++e+++i+i
  gi|313125977|ref|YP_004036247.1| 300 QVVLKQFADSAIILGIRVWIDRPSARRKWRTQTAVIAAVKDAFESADIKI 349
                                       ***********************************************986 PP

>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.1   6.8e-05       0.3      82     165 ..      93     185 ..      32     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.8e-05
                           DUF4271  82 a.........ssllllliiflilllylllKlllykllgwlFfdkkkirqwifsylsylsllglllfplvlllvyfpl 149
                                       +         +s+  l++ +l++++ +++  l+ +l+  ++  +  ++q+   + + ++  +l  f ++++l+ ++ 
  gi|313125977|ref|YP_004036247.1|  93 SvfegydlgyDSFVKLGLSVLLVVGAYTMTGLVRRLVDEVTAARPAVSQHQREIAFRIAQVFLYAFTIAIVLAIWEV 169
                                       255666677799****************************************9999999999999999999999999 PP

                           DUF4271 150 ssqillililiillli 165
                                       ++  +l+ + ++ +++
  gi|313125977|ref|YP_004036247.1| 170 NLSGILVGAGFLGIVV 185
                                       9999888888776665 PP

>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.9   7.5e-05      0.33     102     167 ..      60     128 ..      56     134 .. 0.86
   2 ?   -0.2   0.9      0.14   6.4e+02      95     157 ..     158     186 ..     137     214 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.5e-05
                           DUF1700 102 viislvlsllvvalallvsplvllvksllkgfeelsln...vfvsigllglGllllivayylvkilykl 167
                                       +++sl++sl  ++la  ++ +++ v +  +++ ++       + s+  lgl +ll+++ay+++ ++ +l
  gi|313125977|ref|YP_004036247.1|  60 ALWSLLVSLTTMTLATAAAAVIVGVWGQAEAVASVFEGydlGYDSFVKLGLSVLLVVGAYTMTGLVRRL 128
                                       589999****999999999999999888777776665456689*******************9998887 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.14
                           DUF1700  95 lvlipliviislvlsllvvalallvsplvllvksllkgfeelslnvfvsigllglGlllliva 157
                                       + + ++++i+ +                                   +s +l+g G+l ++v 
  gi|313125977|ref|YP_004036247.1| 158 FTIAIVLAIWEV----------------------------------NLSGILVGAGFLGIVVG 186
                                       222222222222..................................22222222222222222 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.0   0.00035       1.6     156     248 ..     111     205 ..      94     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00035
                           UPF0182 156 aliavllvyllsgesl....girlkfaelskaarrhlsvllallllllalsywLdryellyskrgvvtGagYtdvna 228
                                       ++++v+ +y ++g ++    +++   + +s+++r     ++ ++l + +++++L+ +e+ +s  g+++Gag+  + +
  gi|313125977|ref|YP_004036247.1| 111 SVLLVVGAYTMTGLVRrlvdEVTAARPAVSQHQREIAFRIAQVFLYAFTIAIVLAIWEVNLS--GILVGAGFLGIVV 185
                                       333333334334422211124444779999999999999********************999..69*********** PP

                           UPF0182 229 vlpaktilavialvvavlll 248
                                        + a++ l ++++ + +++ 
  gi|313125977|ref|YP_004036247.1| 186 GMAARQTLGALLAGFVLMFS 205
                                       ****9999888655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2488.85
//
Query:       gi|313125978|ref|YP_004036248.1|  [L=289]
Description: dimethyladenosine transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-49  167.2   0.0    4.7e-49  166.8   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
    2.4e-05   24.9   0.0    5.5e-05   23.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
      0.001   19.6   0.0     0.0022   18.6   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
     0.0031   17.1   0.0     0.0053   16.4   0.0    1.3  1  NodS             Nodulation protein S (NodS)
     0.0088   15.5   0.0      0.013   14.9   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.019   14.6   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.017   15.8   0.0      0.041   14.6   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
      0.067   13.5   0.4       0.31   11.3   0.1    2.0  2  TrkA_N           TrkA-N domain
      0.098   12.2   0.0       0.15   11.6   0.0    1.2  1  MTS              Methyltransferase small domain
       0.11   12.2   0.0        0.2   11.4   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.0   2.6e-52   4.7e-49       8     232 ..      34     248 ..      28     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 2.6e-52
                                       CG--EE--HHHHHHHHHHH-GG.TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT...TCCCEEE CS
                            RrnaAD   8 ygqnflknkkvineIldklnle.ekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls...kdeklkv 80 
                                         q+fl++  v+++I + l    ++  vle+g G+G+lT +L+  a+ v+v+E d+rLa++l++++    ++ +l++
  gi|313125978|ref|YP_004036248.1|  34 QDQHFLVDDRVLDRIPSYLPEDtDTSHVLEVGGGTGALTDRLLRVADRVTVVERDTRLAEFLREEFAdaiEADRLTI 110
                                       579************998855459999***************************************99999****** PP

                                       E-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHH CS
                            RrnaAD  81 vhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrl 157
                                       ++ D+l+ ++pe+           ++v+nlPy+is+++ ++ll  +r   v  +l++qkef +r++a+ g  +++rl
  gi|313125978|ref|YP_004036248.1| 111 LEGDALEIDLPEFT----------ACVSNLPYGISSEITFRLL--PRG--VPLVLMFQKEFGERMAAETGTDEYGRL 173
                                       ************65..........8******************..566..78************************* PP

                                       HHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCH CS
                            RrnaAD 158 svlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpgg 232
                                       sv ++ + dv++v++v+k++f P p v+s++v+ +++++d ++ d + +  +v++l++++rkt+++ + ++ + +
  gi|313125978|ref|YP_004036248.1| 174 SVSAQHYGDVEVVETVPKEAFDPAPAVESVVVRVTPRAPDYEVDDEAFFLDFVKALFTQRRKTIRNGIRNTAHIS 248
                                       ********************************************************************9987755 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.1e-08   5.5e-05       1      71 [.      61     129 ..      61     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.1e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvss 71 
                                       vL++G GtG lt +l++     +vt v+ + ++ e  re+++++ +   ++++++gda ++++++  f ++vs+
  gi|313125978|ref|YP_004036248.1|  61 VLEVGGGTGALTDRLLRVA--DRVTVVERDTRLAEFLREEFADA-IeadRLTILEGDALEIDLPE--FTACVSN 129
                                       9***************985..********************883.2357***********99987..8888874 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.2e-06    0.0022       1      67 [.      62     128 ..      62     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvs 67 
                                       L+vG GtG+l+  l + + rv+ v+ ++++ +  +e+  ++ +  +++++++da ++ +++  f ++vs
  gi|313125978|ref|YP_004036248.1|  62 LEVGGGTGALTDRLLRVADRVTVVERDTRLAEFLREEFADAIEadRLTILEGDALEIDLPE--FTACVS 128
                                       89*************999**********************9999*9**********99998..665555 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     3e-06    0.0053      41      73 ..      55      87 ..      44     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                              NodS 41 qgsiadalevGcaaGalterlapyckrltvvdv 73
                                      + + +++levG  +Galt+rl  +++r+tvv+ 
  gi|313125978|ref|YP_004036248.1| 55 DTDTSHVLEVGGGTGALTDRLLRVADRVTVVER 87
                                      567899*************************85 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.3e-06     0.013      17      64 ..      56     101 ..      47     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.3e-06
                                       SST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHH CS
                    Spermine_synth  17 knpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflps 64 
                                       +   +vL +GGg G ++ ++++     ++t+v+ D    +f ++ + +
  gi|313125978|ref|YP_004036248.1|  56 TDTSHVLEVGGGTGALTDRLLRVA--DRVTVVERDTRLAEFLREEFAD 101
                                       56789******************9..**************99987655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     1e-05     0.019      34     100 ..      50     115 ..      40     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                       HHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES- CS
                     Cons_hypoth95  34 nilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkeda 100
                                       + l ++ + ++vL++ +G+Gal    l R a+++++ve+d + ++ l+e+ +     ++ ++l  da
  gi|313125978|ref|YP_004036248.1|  50 SYLPEDTDTSHVLEVGGGTGALT-DRLLRVADRVTVVERDTRLAEFLREEFADAIEADRLTILEGDA 115
                                       5566778999************6.7899*********************988766555666666665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.3e-05     0.041       1      59 [.      62     116 ..      62     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdll 59 
                                       Le+G+GtG+l+++ll+     ++t+v+ +++  e  +e++a+ ++  ++++++ + d+l
  gi|313125978|ref|YP_004036248.1|  62 LEVGGGTGALTDRLLRV--ADRVTVVERDTRLAEFLREEFADAIE--ADRLTILEGDAL 116
                                       8****************..999***********999999999886..445555555554 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00017      0.31      11      48 ..      69     106 ..      62     115 .. 0.87
   2 ?   -0.5   0.1      0.82   1.5e+03      47      70 ..     257     281 ..     241     286 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                       HHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES- CS
                            TrkA_N  11 rslaeeLse.ggkdvvvidkdeerveelreeglevvvgd 48 
                                        +l+++L + +  +v+v+++d + +e lree+++++ +d
  gi|313125978|ref|YP_004036248.1|  69 GALTDRLLRvAD-RVTVVERDTRLAEFLREEFADAIEAD 106
                                       467888888677.6**********************998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.82
                                       S-TTSHHHHHH.TTGGGESEEEE-S CS
                            TrkA_N  47 gdatdeevLee.agiekadaviaat 70 
                                        +a+de+vL++ ag ++ +a+ a+t
  gi|313125978|ref|YP_004036248.1| 257 VEAADEDVLRKrAGNMSPEAFAALT 281
                                       4566777775426777777777766 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.6e-05      0.15      26     107 ..      51     132 ..      46     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.6e-05
                                       HCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EE CS
                               MTS  26 tlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfd 99 
                                       +lp++  + +vl +G G+G+l+  l++  ++  vt+v+ d+r  e+ +e +++   +  +++++ d+le     +f 
  gi|313125978|ref|YP_004036248.1|  51 YLPEDtDTSHVLEVGGGTGALTDRLLRVADR--VTVVERDTRLAEFLREEFADAIEAdrLTILEGDALEIDL-PEFT 124
                                       5777766778*****************9998..999******999999998765443488899999887555.6888 PP

                                       EEEE---S CS
                               MTS 100 livsNPPf 107
                                       + vsN P+
  gi|313125978|ref|YP_004036248.1| 125 ACVSNLPY 132
                                       88888776 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011       0.2      73     132 ..      57     114 ..      50     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHH.HCTTCSEEEEES- CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlk.kldlenvivvvgD 132
                                       + ++vLevG+G+G lt  l r+  +   v  +er  +l+e  +++   + +++++++ +gD
  gi|313125978|ref|YP_004036248.1|  57 DTSHVLEVGGGTGALTDRLLRVADR---VTVVERDTRLAEFLREEFAdAIEADRLTILEGD 114
                                       5689*********888766666555...558999999998777766414455677777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1836.54
//
Query:       gi|313125979|ref|YP_004036249.1|  [L=211]
Description: RNA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-65  219.3   0.3    4.4e-65  219.0   0.3    1.0  1  DUF655    Protein of unknown function (DUF655)
    3.4e-05   24.0   0.0    7.8e-05   22.9   0.0    1.6  1  HHH_3     Helix-hairpin-helix motif
    0.00055   20.1   0.0     0.0018   18.5   0.0    1.8  1  HHH_6     Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.035   13.9   0.2      0.069   12.9   0.2    1.5  1  DUF1473   Protein of unknown function (DUF1473)
       0.11   12.4   0.8       0.58   10.1   0.0    2.6  4  HHH       Helix-hairpin-helix motif
       0.14   12.8   0.6        5.7    7.6   0.0    2.8  3  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   0.3   1.5e-68   4.4e-65       3     180 ..      30     207 ..      28     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 1.5e-68
                                       -EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS- CS
                            DUF655   3 eeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedLt 79 
                                       e a+vLD+lp+G+pdd +  +++ p+++alger++ L+el +  e di + d+v +   ++   v+  re++y+dL+
  gi|313125979|ref|YP_004036249.1|  30 EFAVVLDHLPHGQPDDDRPRYKKSPLAYALGERDFRLFELRLGDESDISIGDRVVVFPSEERDAVEELREVEYDDLS 106
                                       679**************************************************998766555555669********* PP

                                       HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT--- CS
                            DUF655  80 dvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkd 156
                                       ++a +eL++vve+iv+e+E+rfv+f+n+a+pit+RlH+L+lLpg+gkkl+++il+eR+r ++esFed+++rv+gl++
  gi|313125979|ref|YP_004036249.1| 107 NTALSELEYVVEDIVEENERRFVDFYNDAQPITLRLHQLNLLPGIGKKLRNNILDERKRGPYESFEDLEDRVSGLHH 183
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHH-TTSS--SS- CS
                            DUF655 157 paeilverileEiedktekYylFv 180
                                       p ++lveri+eE++d++ kY+ Fv
  gi|313125979|ref|YP_004036249.1| 184 PRDVLVERIMEELRDDDLKYKTFV 207
                                       ***********************8 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.6e-08   7.8e-05      13      52 ..     142     181 ..     139     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.6e-08
                             HHH_3  13 aeeLqklpGlgpklAknIvayReknGpfksreeLl.kvkgl 52 
                                       + +L+ lpG+g+kl +nI++ R k+Gp++s+e+L  +v+gl
  gi|313125979|ref|YP_004036249.1| 142 LHQLNLLPGIGKKLRNNILDER-KRGPYESFEDLEdRVSGL 181
                                       6799******************.***********8667776 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.9e-07    0.0018      29      65 ..     145     180 ..     109     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.9e-07
                             HHH_6  29 LaaikglgeaaaerivaeRekegpfksledlarrvds 65 
                                       L+ + g+g++  ++i++eR+ +gp++s+edl +rv+ 
  gi|313125979|ref|YP_004036249.1| 145 LNLLPGIGKKLRNNILDERK-RGPYESFEDLEDRVSG 180
                                       555679*************9.8************986 PP

>> DUF1473  Protein of unknown function (DUF1473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   2.3e-05     0.069      27      95 ..      81     148 ..      75     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                           DUF1473  27 drvlgfdverdelvlklndlktlkeitklmisr.kfldefyeildkerryielykdalviilflvqyslf 95 
                                       drv+ f  e+ + v  l ++++  ++++  +s+ +++ e   + ++err++++y da +i l l q +l+
  gi|313125979|ref|YP_004036249.1|  81 DRVVVFPSEERDAVEELREVEYD-DLSNTALSElEYVVE-DIVEENERRFVDFYNDAQPITLRLHQLNLL 148
                                       77777765444447777777764.333333333134433.2345789*******************9987 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.6   7.7e+03       3      12 ..      19      28 ..      18      28 .. 0.84
   2 ?   -1.7   0.1       1.1   3.3e+03       6      16 ..      90     100 ..      86     101 .. 0.74
   3 ?   10.1   0.0   0.00019      0.58      12      29 ..     144     161 ..     142     162 .. 0.89
   4 ?   -3.3   0.0       3.4     1e+04       9      17 ..     170     179 ..     170     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                                      HHHHTSSHHH CS
                               HHH  3 eglipasree 12
                                      e+  +a+ e+
  gi|313125979|ref|YP_004036249.1| 19 ENGADATTED 28
                                      7889999997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                       HTSSHHHHHTS CS
                               HHH   6 ipasreeLlal 16 
                                         + +eeL ++
  gi|313125979|ref|YP_004036249.1|  90 ERDAVEELREV 100
                                       56789**9887 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00019
                                       HHHTSTT-SHHHHHHHHH CS
                               HHH  12 eLlalPGVGpktAeaIls 29 
                                       +L  lPG+G+k  + Il+
  gi|313125979|ref|YP_004036249.1| 144 QLNLLPGIGKKLRNNILD 161
                                       5778**********9996 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 3.4
                                       SHHHHHT.ST CS
                               HHH   9 sreeLla.lP 17 
                                       s+e+L++ ++
  gi|313125979|ref|YP_004036249.1| 170 SFEDLEDrVS 179
                                       7899987565 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.9   5.6e+03      26      33 ..     117     124 ..      93     130 .. 0.63
   2 ?    7.6   0.0    0.0019       5.7      40      56 ..     148     164 ..     138     179 .. 0.72
   3 ?    2.3   0.1     0.087   2.6e+02      48      57 .]     189     198 ..     186     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                                       HHHHHHS- CS
                             HHH_5  26 vedlaaad 33 
                                       ved+++++
  gi|313125979|ref|YP_004036249.1| 117 VEDIVEEN 124
                                       56666655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0019
                                       STTS-HHHHHHHHHHHH CS
                             HHH_5  40 ipGiGkktAeriilelk 56 
                                       +pGiGkk+  +i++e k
  gi|313125979|ref|YP_004036249.1| 148 LPGIGKKLRNNILDERK 164
                                       67777777777777665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.087
                                       HHHHHHHHHH CS
                             HHH_5  48 Aeriilelkd 57 
                                       +eri++el+d
  gi|313125979|ref|YP_004036249.1| 189 VERIMEELRD 198
                                       89*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1291.27
//
Query:       gi|313125980|ref|YP_004036250.1|  [L=118]
Description: DNA-directed RNA polymerase subunit f [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-14   53.1   2.5    4.4e-14   52.9   2.5    1.1  1  RNA_pol_Rpb4  RNA polymerase Rpb4
  ------ inclusion threshold ------
      0.058   13.4   2.5      0.071   13.1   2.5    1.1  1  UPF0158       Uncharacterised protein family (UPF0158)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   2.5   4.9e-18   4.4e-14       1     122 [.      12     117 ..      12     118 .] 0.93

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 4.9e-18
                                       EE-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTS CS
                      RNA_pol_Rpb4   1 lLsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfeL 77 
                                       +L+ sEv+++l+ ++e +++ d               +++l+++l +++e++++ f+ l+ ee+++ + +ll+  + 
  gi|313125980|ref|YP_004036250.1|  12 YLTTSEVKELLE-DVEAERAAD--------------EERELRYELARAIEHVNR-FAFLDPEESVELVEDLLELEKV 72 
                                       79**********.777775774..............4689**************.*****9999999999999999* PP

                                       THHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHHHH CS
                      RNA_pol_Rpb4  78 tkaEklqlvnlkPesavelktlieeleerfedeqleeiLdelkev 122
                                       ++  + ++ +l+P+s++el+++ +++++ ++ ++l+eiL+ ++++
  gi|313125980|ref|YP_004036250.1|  73 DEVTAFKIADLLPQSRDELRAVYAQERYALDGDELDEILNVVAKY 117
                                       *******************************************98 PP

>> UPF0158  Uncharacterised protein family (UPF0158)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.5   7.9e-06     0.071      23     103 ..      10      93 ..       3     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-06
                           UPF0158  23 dfylDrieGkvll..idlekqqeeldklekeleeepdRyllipklsvyeskklmesFln.ekvedidakeklldil. 95 
                                       + yl   e k ll  +++e   +e+++l+ el++  +   +   l+  es++l e+ l+ ekv+++ a  k++d l 
  gi|313125980|ref|YP_004036250.1|  10 EEYLTTSEVKELLedVEAERAADEERELRYELARAIEHVNRFAFLDPEESVELVEDLLElEKVDEVTAF-KIADLLp 85 
                                       56777776666652367788899**********************************975999999876.5666655 PP

                           UPF0158  96 qskkalen 103
                                       qs++ l++
  gi|313125980|ref|YP_004036250.1|  86 QSRDELRA 93 
                                       88877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 769.16
//
Query:       gi|313125981|ref|YP_004036251.1|  [L=96]
Description: 50S ribosomal protein L21e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-33  113.4   0.3    4.1e-33  113.2   0.3    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.3   2.3e-37   4.1e-33       1      99 [.       1      95 [.       1      96 [] 0.98

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 2.3e-37
                                      X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEE CS
                    Ribosomal_L21e  1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkk 79
                                      m++s+g+ +gtr ++s+k+r++g++p++++++ey++G+kV++kidpsv kg++h+r++G+tg+v  ++k++++++v+++
  gi|313125981|ref|YP_004036251.1|  1 MPSSNGPLHGTRGKLSNKPRERGTSPPQRAIQEYDEGQKVHLKIDPSVRKGRFHPRFNGHTGEV--IGKQGRAFKVQIN 77
                                      899*************************************************************..************* PP

                                      ETTE..EEEEEE-GGGEEE- CS
                    Ribosomal_L21e 80 vggkileKriivriehlkks 99
                                      +ggk  +K++ivr++hl+ +
  gi|313125981|ref|YP_004036251.1| 78 DGGK--DKTLIVRPAHLRAQ 95
                                      ****..***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 624.84
//
Query:       gi|313125982|ref|YP_004036252.1|  [L=387]
Description: cystathionine gamma-lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.2e-152  506.5   0.0   3.6e-152  506.3   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0017   17.4   0.0     0.0033   16.4   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
     0.0027   17.1   0.1      0.017   14.4   0.1    1.9  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.018   14.3   0.0      0.026   13.7   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
      0.026   13.0   0.0      0.036   12.6   0.0    1.1  1  Met_gamma_lyase  Methionine gamma-lyase


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  506.3   0.0    1e-155  3.6e-152       1     381 [.      10     383 ..      10     384 .. 0.99

  Alignments for each domain:
  == domain 1  score: 506.3 bits;  conditional E-value: 1e-155
                                       HHHHHHTTTTCHTTTTBSS--B---SBBBESSHHHHCTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHH CS
                   Cys_Met_Meta_PP   1 eTllvhagqekdeqtgavavpiyltstykfkdvdeafageekgyeYsRsgnptrsvleeriaaLeggeaalavssGm 77 
                                       eT ++hagq++de+tga ++piy+ sty+++       g ++gyeYsR+gnptrs le+++aaLegge + a+ssGm
  gi|313125982|ref|YP_004036252.1|  10 ETRAIHAGQDPDEETGALMTPIYANSTYVQD-----GPGDHRGYEYSRTGNPTRSDLEDNLAALEGGEFGRAFSSGM 81 
                                       699****************************.....***************************************** PP

                                       HHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT--- CS
                   Cys_Met_Meta_PP  78 aAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvv 154
                                       + i +++l+ll+aGd++v+ dd+Yggt+r++++v+ k  ++++fvdt+d ++++ a++e+t l++ Etptnpl++v 
  gi|313125982|ref|YP_004036252.1|  82 GGI-NTVLNLLEAGDHVVTGDDVYGGTHRIFTQVYDKYDLSFDFVDTTDHDAVADAMREETALLWAETPTNPLMRVN 157
                                       ***.************************************************************************* PP

                                       -HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT CS
                   Cys_Met_Meta_PP 155 DiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalG 231
                                       Di ++a+la++ ++l  vDntfa+p+lqrpl++gaDiv hS TKylgGhsdvvaG++++++ eel++e+ f qn++G
  gi|313125982|ref|YP_004036252.1| 158 DISALADLAHEYDALCAVDNTFATPYLQRPLEHGADIVSHSLTKYLGGHSDVVAGALITDD-EELDEEIGFYQNSVG 233
                                       **********************************************************999.*************** PP

                                       -B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSH CS
                   Cys_Met_Meta_PP 232 avlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelkse 308
                                       a+ spfd++l+lrG kTL++R++rh enA ++A++L+ h++v++vyYpgl+shpqhela++q+ ++gg+lsFe++++
  gi|313125982|ref|YP_004036252.1| 234 ATPSPFDCFLVLRGTKTLGVRMDRHCENASELARWLDDHDAVSDVYYPGLESHPQHELAAEQMDDFGGMLSFEVDGT 310
                                       ***************************************************************************** PP

                                       HHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 309 eekakkfvdnlklfslaeslGgveslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqal 381
                                       +e+a+++v+++ +f+laeslGgveslie+pa mtha+ip+eer +ag+td+l+R+svGiE+vdD++aDl++a+
  gi|313125982|ref|YP_004036252.1| 311 LEQASTVVEETDVFTLAESLGGVESLIEQPAAMTHAAIPREERLEAGLTDGLVRVSVGIEHVDDMKADLDAAF 383
                                       ************************************************************************9 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.3e-07    0.0033      85     204 ..      91     204 ..      74     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.3e-07
                                       -TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHH CS
                       Aminotran_5  85 lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveei 161
                                       l++gd++v+++  + +++    ++ ++  +  +++      + d d+++++++e+t+l+      n +  ++++ ++
  gi|313125982|ref|YP_004036252.1|  91 LEAGDHVVTGDDVYGGTHRIFTQVYDKYDLSFDFVD-----TTDHDAVADAMREETALLWAETPTNPLMRVNDISAL 162
                                       467777777777777777666666655555444444.....47789999**************************** PP

                                       HHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTS CS
                       Aminotran_5 162 gklakkkgalvlvDaaqavghipidvkklgvDflafsghKllg 204
                                       ++la++++al +vD + a +  +  + + g+D+++ s  K+lg
  gi|313125982|ref|YP_004036252.1| 163 ADLAHEYDALCAVDNTFATPYLQRPL-EHGADIVSHSLTKYLG 204
                                       **************999999888777.5699999999999887 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.9e-06     0.017      22     199 ..      55     230 ..      47     240 .. 0.83
   2 ?   -0.7   0.0      0.19     7e+02     280     318 ..     253     289 ..     247     300 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-06
                                       SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHT....T-EEEEE-B-T CS
                   DegT_DnrJ_EryC1  22 gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlel....gakpvfvDvdp 94 
                                       +p+ +++E ++aa  g ++  a+ssG  ++  +L+ l++g  d V++    + +t    +++     +   fvD + 
  gi|313125982|ref|YP_004036252.1|  55 NPTRSDLEDNLAALEGGEFGRAFSSGMGGINTVLNLLEAG--DHVVTGDDVYGGTHRIFTQVydkyDLSFDFVDTT- 128
                                       788899*******************************998..*************998888722113333444444. PP

                                       TTSSB-GGGCGGG--TTE...EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE CS
                   DegT_DnrJ_EryC1  95 dtynidpaaieaaitert...kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfS 168
                                            d +a++ a  e+t    a +p + + +v+d++al ++a++++     D    + + y ++++   +d+ + S
  gi|313125982|ref|YP_004036252.1| 129 -----DHDAVADAMREETallWAETPTNPLMRVNDISALADLAHEYDALCAVDN--TFATPYLQRPLEHGADIVSHS 198
                                       .....8999999999999666677899999999*****************9996..567889999998888887777 PP

                                       -BTTSSS.-SSS..-EEEEESTHHHHHHHHHHHB CS
                   DegT_DnrJ_EryC1 169 FyptKnl.ttGe..GGavvtndeelaekarvlrn 199
                                       +  tK l    +  +Ga++t+deel+e++  ++n
  gi|313125982|ref|YP_004036252.1| 199 L--TKYLgGHSDvvAGALITDDEELDEEIGFYQN 230
                                       6..788875555559************9987776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.19
                                       EEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCH CS
                   DegT_DnrJ_EryC1 280 vlveeeaevkrdelvealkeegigtrvhypnplhrqpvy 318
                                       v+++++ e + +el++ l+++ + ++v+yp  l+++p  
  gi|313125982|ref|YP_004036252.1| 253 VRMDRHCE-NASELARWLDDHDAVSDVYYP-GLESHPQH 289
                                       55565544.8999****************5.66666654 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.2e-06     0.026      46     196 ..      58     185 ..      37     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-06
                                       HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH....HTTSEEE CS
                     Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr....lsggevv 118
                                         +le +la + g         e    ++sG g ++ +l+ l    +gd ++  d +y+  ++i+      +++ + 
  gi|313125982|ref|YP_004036252.1|  58 RSDLEDNLAALEG--------GEFGRAFSSGMGGINTVLNLLE---AGDHVVTGDDVYGGTHRIFTqvydKYDLSFD 123
                                       5566666666666........3334448999998888888877...7999888888877777776511114666677 PP

                                       EEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBS CS
                     Aminotran_1_2 119 ryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvf 195
                                        +        + d +a+ +a +e      +t +++ e+p NP   v +   l +l   a++y +l  vD ++a+ ++
  gi|313125982|ref|YP_004036252.1| 124 FVD-------TTDHDAVADAMRE------ETALLWAETPTNPLMRVNDISALADL---AHEYDALCAVDNTFATPYL 184
                                       777.......8899999999999......999**********8777666666666...**************99887 PP

                                       S CS
                     Aminotran_1_2 196 g 196
                                       +
  gi|313125982|ref|YP_004036252.1| 185 Q 185
                                       7 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.9e-06     0.036     141     242 ..     126     221 ..      94     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-06
                   Met_gamma_lyase 141 gkvdieavkeaikektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncyGefveekePtevGadli 217
                                       ++ d +av++a++e+t l+         + + +++++i+ + +l +e   d ++ vdn +      + P e Gad++
  gi|313125982|ref|YP_004036252.1| 126 DTTDHDAVADAMREETALLWAETP----TNPLMRVNDISALADLAHEY--DALCAVDNTFATP-YLQRPLEHGADIV 195
                                       456777888888888887776554....46788899999999987765..789******9875.4678********* PP

                   Met_gamma_lyase 218 aGsliknpGGgi.aktGGyiaGkeel 242
                                       + sl k  GG   + +G  i+  eel
  gi|313125982|ref|YP_004036252.1| 196 SHSLTKYLGGHSdVVAGALITDDEEL 221
                                       **********7625556666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2534.30
//
Query:       gi|313125983|ref|YP_004036253.1|  [L=93]
Description: hypothetical protein Hbor_12190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   13.8   0.5      0.096   12.6   0.5    1.6  1  MtrG      Tetrahydromethanopterin S-methyltransferase, subuni
      0.044   14.1   2.2      0.054   13.9   2.2    1.1  1  DUF4396   Domain of unknown function (DUF4396)
       0.11   12.4   3.1          2    8.4   2.1    2.1  2  TMEM65    Transmembrane protein 65


Domain annotation for each model (and alignments):
>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.5   1.6e-05     0.096      31      61 ..      34      62 ..      30      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                              MtrG 31 sEiaqriGkkvGRdiGilYGlviGliillvy 61
                                      s +a+r+G  vG   Gil G+viG+ ++ ++
  gi|313125983|ref|YP_004036253.1| 34 SHLAERFG--VGTAAGILLGAVIGVALMWIL 62
                                      56677777..89999************9986 PP

>> DUF4396  Domain of unknown function (DUF4396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.2     9e-06     0.054      13      55 ..      41      83 ..      34      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-06
                           DUF4396 13 laGcaiGdilgmviltslslalglpmaatmilsvvlalllgll 55
                                      ++G a+G++lg+vi+++l ++lg + + t++++v ++++l+ +
  gi|313125983|ref|YP_004036253.1| 41 GVGTAAGILLGAVIGVALMWILGTSSVFTLLVAVGIGFILSPV 83
                                      7899****************99*****************9966 PP

>> TMEM65  Transmembrane protein 65
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4    0.0021        12      87     106 ..      41      60 ..       6      63 .. 0.76
   2 ?    8.4   2.1   0.00033         2      21      56 ..      55      90 ..      48      93 .] 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0021
                            TMEM65  87 algkalGvtiGcllGmlpLl 106
                                        +g+a+G+++G ++G++ + 
  gi|313125983|ref|YP_004036253.1|  41 GVGTAAGILLGAVIGVALMW 60 
                                       36889999999999987654 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00033
                            TMEM65 21 GeaidatlgvtlglstlaaAalGnlvsdvaGvvlgg 56
                                      G a+   lg+   ++ l a ++G ++s v+Gv++++
  gi|313125983|ref|YP_004036253.1| 55 GVALMWILGTSSVFTLLVAVGIGFILSPVVGVLFAE 90
                                      333344566666677899**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 534.64
//
Query:       gi|313125984|ref|YP_004036254.1|  [L=81]
Description: translation elongation factor 1b (aef-1b) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-19   67.4   0.0      1e-18   67.3   0.0    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
      0.081   13.4   0.1       0.41   11.1   0.1    1.9  2  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   1.1e-22     1e-18       4      90 .]       1      81 []       1      81 [] 0.96

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.1e-22
                                      EEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SEE CS
                           EF1_GNE  4 levkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVqs 81
                                      ++v+P++ e dl+el++++++ +l++ ++++  +++ ++afGl +L  +++++dd ++t+++ee+++ ++g     V+s
  gi|313125984|ref|YP_004036254.1|  1 MKVMPNSPEIDLDELQERLED-SLPEgAKING-FERDDVAFGLVALLPTVIVPDDAGGTEAVEEAFSDVDG-----VES 72
                                      79*******************.77777****5.**************************************.....*** PP

                                      EEEEEEEE- CS
                           EF1_GNE 82 veivsfnkl 90
                                      v ++++ ++
  gi|313125984|ref|YP_004036254.1| 73 VSVENVGRI 81
                                      *****9986 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.14   1.2e+03      40      58 ..       3      21 ..       1      23 [. 0.77
   2 ?   11.1   0.1   4.6e-05      0.41      14      34 ..      58      78 ..      48      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.14
                               HMA 40 Vegdaestklrkiieaiek 58
                                      V+ + ++++l +++e +e+
  gi|313125984|ref|YP_004036254.1|  3 VMPNSPEIDLDELQERLED 21
                                      6777777888999999886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.6e-05
                               HMA 14 akvekvLselpgVesvkvdla 34
                                       +ve+++s ++gVesv+v ++
  gi|313125984|ref|YP_004036254.1| 58 EAVEEAFSDVDGVESVSVENV 78
                                      68***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 514.41
//
Query:       gi|313125985|ref|YP_004036255.1|  [L=59]
Description: zn-ribbon RNA-binding protein with a function in translation [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00023   21.1  10.6    0.00091   19.1   4.2    2.3  2  DUF1610         Domain of unknown function (DUF1610)
     0.0036   17.6  10.8       0.27   11.6   2.4    2.1  2  C1_2            C1 domain
     0.0041   17.6  11.1      0.013   16.0   5.9    2.0  2  zf-CHY          CHY zinc finger
     0.0042   17.1  12.4       0.21   11.6  12.4    2.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.013   15.3   1.0      0.013   15.3   1.0    2.9  3  HscB_4_cys      Co-chaperone HscB tetracysteine metal binding
      0.023   14.6   8.2       0.21   11.6   1.7    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.047   14.1  10.1      0.052   13.9  10.1    1.1  1  Rhodanese_C     Rhodanase C-terminal
       0.17   12.0  16.4        1.5    9.0   0.1    3.4  3  UPF0547         Uncharacterised protein family UPF0547
       0.22   11.2  12.1        1.1    8.9   0.0    3.4  3  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
       0.22   11.5  11.7        1.1    9.2  11.7    1.9  1  zinc-ribbons_6  zinc-ribbons
       0.29   10.0   8.1        0.3    9.9   8.1    1.0  1  NMDAR2_C        N-methyl D-aspartate receptor 2B3 C-terminus
       0.31   10.7   0.5       0.31   10.7   0.5    3.8  4  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.34   10.9  11.6       0.47   10.5   1.0    2.0  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.51   10.5  12.8          3    8.0   8.1    2.8  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.54    9.8  12.4          9    5.9   0.3    3.7  3  zf-ribbon_3     zinc-ribbon domain
       0.63    7.8   7.6       0.67    7.7   7.6    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
          1    9.3  10.0       0.69    9.8   0.7    2.2  2  C1_1            Phorbol esters/diacylglycerol binding domain 
        1.2    8.6   9.2        1.2    8.5   9.2    1.0  1  NMD3            NMD3 family
        1.3    9.1  10.4        3.1    7.9  10.4    1.6  1  Zn_Tnp_IS91     Transposase zinc-binding domain
        2.4    8.1  13.8        9.3    6.3   0.1    4.0  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain
          3    8.0  16.4        2.9    8.1   2.9    2.8  3  Zn-ribbon_8     Zinc ribbon domain
        3.7    7.4  13.9        3.8    7.3   0.1    3.9  4  Rubredoxin_2    Rubredoxin metal binding domain
          4    7.3  12.0         10    6.0   8.1    2.4  2  zf-HYPF         HypF finger
        4.8    5.8  10.6        3.6    6.3   6.6    1.9  2  NRDD            Anaerobic ribonucleoside-triphosphate reducta
        8.6    6.6  11.3        4.3    7.5   0.1    2.4  2  DUF2387         Probable metal-binding protein (DUF2387)
        8.8    6.2  15.4         26    4.7   0.2    3.9  5  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   4.2   1.3e-06   0.00091       1      22 [.      12      32 ..      12      32 .. 0.99
   2 ?    5.7   0.4      0.02        14      19      23 ..      51      55 ..      48      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                           DUF1610  1 CtSCGaelaprEravvFpCPNC 22
                                      C+SCG+ + +   a  F+CP+C
  gi|313125985|ref|YP_004036255.1| 12 CVSCGINISGMS-AATFDCPEC 32
                                      ************.********* PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                           DUF1610 19 CPNCG 23
                                      CP CG
  gi|313125985|ref|YP_004036255.1| 51 CPDCG 55
                                      ****9 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   2.4   0.00039      0.27      14      42 ..       5      36 ..       1      40 [. 0.83
   2 !   11.4   3.2   0.00045      0.31      17      41 ..      35      57 ..      33      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00039
                              C1_2 14 dssesfnCsaCgrkidgff...YsCseCdfsl 42
                                      d+   ++C  Cg +i+g+    + C+eCd  +
  gi|313125985|ref|YP_004036255.1|  5 DQRHARQCVSCGINISGMSaatFDCPECDTEI 36
                                      5667799*******9999999*******9765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00045
                              C1_2 17 esfnCsaCgrkidgffYsCseCdfs 41
                                      e  +C  C++++  + Y+C+ C f+
  gi|313125985|ref|YP_004036255.1| 35 EISRCAKCRKQS--NLYECPDCGFM 57
                                      5689******96..66******996 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   1.3    0.0006      0.41      48      74 ..       3      34 ..       1      35 [. 0.83
   2 !   16.0   5.9   1.9e-05     0.013      38      74 ..      23      56 ..      18      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0006
                            zf-CHY 48 eteqekavlCkkCkk.....efaeyfCpiCkl 74
                                      ++ q++a +C +C+      ++a++ Cp C++
  gi|313125985|ref|YP_004036255.1|  3 QSDQRHARQCVSCGInisgmSAATFDCPECDT 34
                                      56789999*****9988887788889****85 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.9e-05
                            zf-CHY 38 evkevlcllCeteqekavlCkkCkkefaeyfCpiCkl 74
                                      ++ ++ c +C+t   + + C kC+k+ + y Cp C +
  gi|313125985|ref|YP_004036255.1| 23 SAATFDCPECDT---EISRCAKCRKQSNLYECPDCGF 56
                                      555666777777...5999****************75 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6  12.4   0.00031      0.21      10      49 .]       7      55 ..       2      58 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                               DZR 10 pdarfCseCgtklkavaa...........edrCpsCgekvdpearfCpeCG 49
                                       +ar C  Cg +++ ++a             rC +C ++ ++    Cp CG
  gi|313125985|ref|YP_004036255.1|  7 RHARQCVSCGINISGMSAatfdcpecdteISRCAKCRKQSNLY--ECPDCG 55
                                      5678888888888877776444444444334666666555554..399998 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.0   1.9e-05     0.013       2      23 ..      11      32 ..      11      33 .. 0.97
   2 ?    1.0   1.6      0.57   3.9e+02      20      24 ..      39      43 ..      37      44 .. 0.93
   3 ?    0.5   0.1      0.78   5.4e+02      20      23 ..      51      54 ..      47      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                                      B-SSS--B--SS-S---B-TTT CS
                        HscB_4_cys  2 rCWnCGgpgapgrgdefFCpqC 23
                                      +C +CG   +++ ++ f Cp C
  gi|313125985|ref|YP_004036255.1| 11 QCVSCGINISGMSAATFDCPEC 32
                                      899******************* PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.57
                                      -TTT- CS
                        HscB_4_cys 20 CpqCR 24
                                      C++CR
  gi|313125985|ref|YP_004036255.1| 39 CAKCR 43
                                      99**9 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.78
                                      -TTT CS
                        HscB_4_cys 20 CpqC 23
                                      Cp C
  gi|313125985|ref|YP_004036255.1| 51 CPDC 54
                                      7777 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.7    0.0003      0.21      30      58 ..      11      38 ..       6      41 .. 0.92
   2 ?   10.7   5.7   0.00054      0.37      30      54 ..      28      56 ..      28      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadr 58
                                      +C  Cg + +   s  tf Cp+C +e+ r
  gi|313125985|ref|YP_004036255.1| 11 QCVSCGINISG-MSAATFDCPECDTEISR 38
                                      8*******999.***********999876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00054
                    OrfB_Zn_ribbon 30 tCseCgsknke....alsgrtfkCpnCgf 54
                                      +C+eC  + ++    ++++++++Cp+Cgf
  gi|313125985|ref|YP_004036255.1| 28 DCPECDTEISRcakcRKQSNLYECPDCGF 56
                                      5***************************8 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  10.1   7.5e-05     0.052      16      63 ..       7      54 ..       1      55 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.5e-05
                       Rhodanese_C 16 evvgkCieCgkpvdelrkrnCanedCnelvlvCeeCaeklkgv.cseeC 63
                                      +   +C+ Cg + + +++    +++C++ +  C++C+++ + + c  +C
  gi|313125985|ref|YP_004036255.1|  7 RHARQCVSCGINISGMSAATFDCPECDTEISRCAKCRKQSNLYeCP-DC 54
                                      46789*********99966666689**************9998565.88 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4      0.84   5.8e+02      14      21 ..       9      16 ..       8      17 .. 0.81
   2 ?    8.8   5.2    0.0024       1.7       3      11 ..      29      37 ..      28      44 .. 0.83
   3 ?    9.0   0.1    0.0022       1.5      16      22 ..      50      56 ..      46      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.84
                           UPF0547 14 aqfCphCG 21
                                      a+ C  CG
  gi|313125985|ref|YP_004036255.1|  9 ARQCVSCG 16
                                      78897798 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0024
                           UPF0547  3 CPeCeakvP 11
                                      CPeC+++++
  gi|313125985|ref|YP_004036255.1| 29 CPECDTEIS 37
                                      ********8 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0022
                           UPF0547 16 fCphCGy 22
                                      +Cp+CG+
  gi|313125985|ref|YP_004036255.1| 50 ECPDCGF 56
                                      8*****9 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0016       1.1       7      19 ..       6      18 ..       2      24 .. 0.86
   2 ?    1.2   4.2      0.41   2.8e+02      13      28 ..      29      43 ..      28      47 .. 0.80
   3 ?    5.2   0.3     0.023        16      12      18 ..      50      56 ..      45      59 .] 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                           zf-tcix  7 lRGvrkCpkCGty 19
                                      +R  r+C +CG++
  gi|313125985|ref|YP_004036255.1|  6 QRHARQCVSCGIN 18
                                      5778*******97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                           zf-tcix 13 CpkCGtyNGtRglsCk 28
                                      Cp+C t+  +R+  C+
  gi|313125985|ref|YP_004036255.1| 29 CPECDTEI-SRCAKCR 43
                                      99999986.7888887 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.023
                           zf-tcix 12 kCpkCGt 18
                                       Cp CG 
  gi|313125985|ref|YP_004036255.1| 50 ECPDCGF 56
                                      7*****6 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  11.7    0.0017       1.1      17      55 ..      10      54 ..       1      57 [. 0.52

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                                      EE-TTT--....EEEEEEE-SSS-S---EEEETTEEE..E--TTT CS
                    zinc-ribbons_6 17 yhCeaCqe....dlkkealCpeCeqelevlkaCgavd..yfCnkc 55
                                       +C +C          +  CpeC+ e++++ +C + +  y C +c
  gi|313125985|ref|YP_004036255.1| 10 RQCVSCGInisgMSAATFDCPECDTEISRCAKCRKQSnlYECPDC 54
                                      556666653332223344566666666666666554433445554 PP

>> NMDAR2_C  N-methyl D-aspartate receptor 2B3 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   8.1   0.00044       0.3     381     422 ..       6      50 ..       1      55 [. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00044
                                       XXXXXXXXXXXXXXXXX.XXXXXXX...XXX.XXXXXXXXXXXXX CS
                          NMDAR2_C 381 keksthCRsClsklsaygagsssvr...spykrCdaCkklgnLYd 422
                                       ++++ +C sC  ++s+++a+++      + + rC  C+k +nLY+
  gi|313125985|ref|YP_004036255.1|   6 QRHARQCVSCGINISGMSAATFDCPecdTEISRCAKCRKQSNLYE 50 
                                       33345688888899999777766446668899************8 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.78   5.4e+02       4      13 ..      11      20 ..      10      21 .. 0.83
   2 ?   10.7   0.5   0.00045      0.31       2      13 ..      26      37 ..      25      38 .. 0.90
   3 ?    2.5   0.6      0.16   1.1e+02       5      11 ..      39      45 ..      37      48 .. 0.85
   4 ?    6.6   0.3    0.0086       5.9       2      10 ..      48      56 ..      47      59 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.78
                            zf_UBZ  4 lCerCgkeip 13
                                      +C  Cg +i+
  gi|313125985|ref|YP_004036255.1| 11 QCVSCGINIS 20
                                      5889**9986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00045
                            zf_UBZ  2 tylCerCgkeip 13
                                      t+ C++C++ei+
  gi|313125985|ref|YP_004036255.1| 26 TFDCPECDTEIS 37
                                      89********97 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.16
                            zf_UBZ  5 CerCgke 11
                                      C++C k+
  gi|313125985|ref|YP_004036255.1| 39 CAKCRKQ 45
                                      ****996 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0086
                            zf_UBZ  2 tylCerCgk 10
                                       y C++Cg 
  gi|313125985|ref|YP_004036255.1| 48 LYECPDCGF 56
                                      599****96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.0   0.00068      0.47      69      94 ..       8      34 ..       1      38 [. 0.77
   2 ?    6.6   3.6     0.011       7.6      71      93 ..      37      55 ..      33      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00068
                                      -EEEETTTS-EEECHHH.HHS-TTTSS CS
                              HypA 69 vkvrCreCgkefeleek.alrCpkCgs 94
                                         +C +Cg +++  ++ ++ Cp+C++
  gi|313125985|ref|YP_004036255.1|  8 HARQCVSCGINISGMSAaTFDCPECDT 34
                                      5568*****99995544489*****87 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                                      EEETTTS-EEECHHHHHS-TTTS CS
                              HypA 71 vrCreCgkefeleekalrCpkCg 93
                                       rC +C+k+ +l     +Cp+Cg
  gi|313125985|ref|YP_004036255.1| 37 SRCAKCRKQSNLY----ECPDCG 55
                                      58*****998865....8****8 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   7.5       3.1   2.2e+03      12      22 ..      22      32 ..       2      42 .. 0.67
   2 ?    8.0   8.1    0.0043         3       2      24 ..      29      56 ..      28      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.1
                          zf-Mss51 12 pkhvdfeCpdC 22
                                       +  +f+Cp+C
  gi|313125985|ref|YP_004036255.1| 22 MSAATFDCPEC 32
                                      45667888888 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0043
                          zf-Mss51  2 CPvpkhkqt.....apkhvdfeCpdCGi 24
                                      CP ++++ +      +++  +eCpdCG+
  gi|313125985|ref|YP_004036255.1| 29 CPECDTEISrcakcRKQSNLYECPDCGF 56
                                      99998887788877778888*******7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.026        18       3      10 ..      10      17 ..       9      22 .. 0.73
   2 ?    4.0   2.6      0.05        34       4      11 ..      28      36 ..      25      45 .. 0.73
   3 ?    5.9   0.3     0.013         9       4       9 ..      50      55 ..      47      56 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.026
                       zf-ribbon_3  3 vrCPnCGa 10
                                      ++C +CG 
  gi|313125985|ref|YP_004036255.1| 10 RQCVSCGI 17
                                      57999985 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.05
                       zf-ribbon_3  4 rCPnCGa.p 11
                                       CP+C++ +
  gi|313125985|ref|YP_004036255.1| 28 DCPECDTeI 36
                                      699999855 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.013
                       zf-ribbon_3  4 rCPnCG 9 
                                      +CP CG
  gi|313125985|ref|YP_004036255.1| 50 ECPDCG 55
                                      566666 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   7.6   0.00098      0.67     618     662 ..       9      55 ..       2      58 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00098
                          PolC_DP2 618 rrkCkkCgk.....etlearCeeCgekteeklvCkkceeeveeekcekce 662
                                       +r+C +Cg      ++ ++ C+eC+++++    C kc+++++  +c+ c+
  gi|313125985|ref|YP_004036255.1|   9 ARQCVSCGInisgmSAATFDCPECDTEISR---CAKCRKQSNLYECPDCG 55 
                                       678888864211114556678888777766...88888888888888886 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.7     0.001      0.69       9      35 ..       7      33 ..       2      37 .. 0.88
   2 ?    5.1   2.2     0.031        21      12      36 ..      37      56 ..      33      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.001
                                      SS--B-TTT-SB--SSSS-EEEETTT- CS
                              C1_1  9 kqptfCkhCgeflwgkekqglkCswCk 35
                                      ++   C  Cg  ++g +   + C +C 
  gi|313125985|ref|YP_004036255.1|  7 RHARQCVSCGINISGMSAATFDCPECD 33
                                      67889********99***********7 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.031
                                      -B-TTT-SB--SSSS-EEEETTT-- CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswCkl 36
                                      ++C++C+++        + C +C++
  gi|313125985|ref|YP_004036255.1| 37 SRCAKCRKQS-----NLYECPDCGF 56
                                      6799998887.....9999999986 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   9.2    0.0018       1.2       1      42 [.      12      55 ..      12      59 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                              NMD3  1 CcrCGkeieeling...lCedCllkevditegiekievevCkeCg 42
                                      C+ CG++i+ + ++    C++C ++  + +++ ++ ++  C++Cg
  gi|313125985|ref|YP_004036255.1| 12 CVSCGINISGM-SAatfDCPECDTEISRCAKCRKQSNLYECPDCG 55
                                      ********755.444789**************************9 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  10.4    0.0045       3.1      17      64 ..       2      55 ..       1      57 [. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0045
                       Zn_Tnp_IS91 17 rpsqrkavekilrCrtaalGf..aryeCeeCghekivyfsCksrh....CpsCq 64
                                      ++s ++  ++  +C+ +  G+  a++ C+eC+ e   + +C++++    Cp C+
  gi|313125985|ref|YP_004036255.1|  2 SQSDQRHARQCVSCGINISGMsaATFDCPECDTEISRCAKCRKQSnlyeCPDCG 55
                                      5677788999999*9988665115667**************9875556799997 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.078        54       6      11 ..      11      16 ..      11      20 .. 0.87
   2 ?   -0.1   5.6       1.3   9.1e+02      25      31 ..      37      43 ..      26      47 .. 0.62
   3 ?    6.3   0.1     0.013       9.3       5      11 ..      49      55 ..      48      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.078
                    Zn_ribbon_SprT  6 rCtgCg 11
                                      +C++Cg
  gi|313125985|ref|YP_004036255.1| 11 QCVSCG 16
                                      7****9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                    Zn_ribbon_SprT 25 YrCrrCk 31
                                       rC +C+
  gi|313125985|ref|YP_004036255.1| 37 SRCAKCR 43
                                      4566666 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.013
                    Zn_ribbon_SprT  5 YrCtgCg 11
                                      Y C++Cg
  gi|313125985|ref|YP_004036255.1| 49 YECPDCG 55
                                      99****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.15     1e+02      25      33 ..       8      16 ..       1      22 [. 0.63
   2 ?    8.1   2.9    0.0042       2.9       7      38 ..      11      38 ..       7      38 .. 0.69
   3 ?    7.0  11.4    0.0089       6.1       6      33 ..      27      55 ..      22      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.15
                       Zn-ribbon_8 25 pltaCPeCg 33
                                         +C +Cg
  gi|313125985|ref|YP_004036255.1|  8 HARQCVSCG 16
                                      344588887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0042
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgsevrr 38
                                      +C +Cg     + +      t  CPeC  e  r
  gi|313125985|ref|YP_004036255.1| 11 QCVSCGINISGMSA-----ATFdCPECDTEISR 38
                                      59999955554442.....4555****887765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0089
                       Zn-ribbon_8  6 YrCeeCghefevlqsis.dapltaCPeCg 33
                                      + C eC++e  + ++   +++l +CP+Cg
  gi|313125985|ref|YP_004036255.1| 27 FDCPECDTEISRCAKCRkQSNLYECPDCG 55
                                      88***************6666666****9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3      0.13        90       2       7 ..      11      16 ..      11      19 .. 0.72
   2 ?    2.9   0.2      0.14        95      17      21 ..      29      33 ..      27      34 .. 0.82
   3 ?    2.1   0.3      0.24   1.6e+02       2      10 ..      38      46 ..      38      48 .. 0.74
   4 ?    7.3   0.1    0.0055       3.8       1       9 [.      49      57 ..      49      59 .] 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.13
                      Rubredoxin_2  2 vCsqCG 7 
                                      +C +CG
  gi|313125985|ref|YP_004036255.1| 11 QCVSCG 16
                                      577777 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                      Rubredoxin_2 17 CpsCg 21
                                      Cp+C 
  gi|313125985|ref|YP_004036255.1| 29 CPECD 33
                                      99996 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.24
                      Rubredoxin_2  2 vCsqCGfes 10
                                      +C +C  +s
  gi|313125985|ref|YP_004036255.1| 38 RCAKCRKQS 46
                                      688887766 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0055
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y+C +CGf 
  gi|313125985|ref|YP_004036255.1| 49 YECPDCGFM 57
                                      899999997 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.14        99      20      28 ..      11      16 ..       2      20 .. 0.63
   2 ?    6.0   8.1     0.015        10       2      28 ..      29      55 ..      29      56 .. 0.99

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                                      TT---TTTS CS
                           zf-HYPF 20 qfisCtnCG 28
                                      q   C +CG
  gi|313125985|ref|YP_004036255.1| 11 Q---CVSCG 16
                                      4...66666 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                                      -HHHHHHHC-TTSTTTT-TT---TTTS CS
                           zf-HYPF  2 CedClrEykdpldRRfhaqfisCtnCG 28
                                      C++C  E+   +  R +     C++CG
  gi|313125985|ref|YP_004036255.1| 29 CPECDTEISRCAKCRKQSNLYECPDCG 55
                                      **************************9 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.7     0.033        23     508     527 ..      10      34 ..       6      37 .. 0.78
   2 ?    6.3   6.6    0.0052       3.6     504     526 ..      33      55 ..      22      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.033
                                       EEETT.--..EESS...SB-TTT-- CS
                              NRDD 508 dvCnecgy..kgei...ekCpkCgs 527
                                         C +cg   +g     ++Cp+C+ 
  gi|313125985|ref|YP_004036255.1|  10 RQCVSCGIniSGMSaatFDCPECDT 34 
                                       57999*9987666688888****93 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0052
                                       E--EEEETT.--EESSSB-TTT- CS
                              NRDD 504 npkidvCnecgykgeiekCpkCg 526
                                        ++i++C +c ++   ++Cp Cg
  gi|313125985|ref|YP_004036255.1|  33 DTEISRCAKCRKQSNLYECPDCG 55 
                                       5799********999999****9 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0063       4.3      24      37 ..       3      16 ..       1      26 [. 0.87
   2 ?    2.3   6.3      0.28   1.9e+02      11      39 ..      29      57 ..      19      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0063
                           DUF2387 24 eedeveyrECvsCg 37
                                      ++d+++ r CvsCg
  gi|313125985|ref|YP_004036255.1|  3 QSDQRHARQCVSCG 16
                                      6789999******9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.28
                           DUF2387 11 CPrCsemDkirmweedeveyrECvsCgft 39
                                      CP C++  +  +    + +  EC +Cgf+
  gi|313125985|ref|YP_004036255.1| 29 CPECDTEISRCAKCRKQSNLYECPDCGFM 57
                                      999998766666666778999******96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.16   1.1e+02      15      20 ..      11      16 ..       7      19 .. 0.64
   2 ?    2.3   4.4      0.21   1.5e+02       2      19 ..      12      32 ..      11      32 .. 0.73
   3 ?    4.7   0.2     0.038        26       2       9 ..      29      36 ..      29      38 .. 0.86
   4 ?    2.6   0.2      0.17   1.2e+02       2       7 ..      39      44 ..      33      46 .. 0.69
   5 ?    1.9   4.7      0.28   1.9e+02      16      20 ..      51      55 ..      38      57 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.16
                     zinc_ribbon_2 15 FCpyCG 20
                                       C  CG
  gi|313125985|ref|YP_004036255.1| 11 QCVSCG 16
                                      555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.21
                     zinc_ribbon_2  2 CpnCGaelq..dnakF.CpyC 19
                                      C +CG  ++    a+F Cp+C
  gi|313125985|ref|YP_004036255.1| 12 CVSCGINISgmSAATFdCPEC 32
                                      888888885444677799999 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.038
                     zinc_ribbon_2  2 CpnCGael 9 
                                      Cp+C +e+
  gi|313125985|ref|YP_004036255.1| 29 CPECDTEI 36
                                      99999998 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.17
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C +C +
  gi|313125985|ref|YP_004036255.1| 39 CAKCRK 44
                                      555544 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.28
                     zinc_ribbon_2 16 CpyCG 20
                                      Cp CG
  gi|313125985|ref|YP_004036255.1| 51 CPDCG 55
                                      66666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 348.95
//
Query:       gi|313125986|ref|YP_004036256.1|  [L=440]
Description: hypothetical protein Hbor_12220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-63  214.6  34.0    2.2e-63  214.4  34.0    1.0  1  TctA      Tripartite tricarboxylate transporter TctA family
  ------ inclusion threshold ------
      0.078   12.8   0.1       0.19   11.5   0.1    1.6  1  DRTGG     DRTGG domain


Domain annotation for each model (and alignments):
>> TctA  Tripartite tricarboxylate transporter TctA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.4  34.0   2.5e-67   2.2e-63       1     409 []      30     431 ..      30     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: 214.4 bits;  conditional E-value: 2.5e-67
                              TctA   1 LllvllGvllGtliGllPGlhatlavalllpltf..gldpeaalilllgiyvgaifggsipaillgvPGtpssvatv 75 
                                       L +++ Gv+lGt++Gl+PGlh+++ + ll+++++  +++p+a+  +++++ v+++f++++pa +lgvP ++++++  
  gi|313125986|ref|YP_004036256.1|  30 LGFAVGGVFLGTVSGLVPGLHVNALALLLAAVAPtiTAPPTAIGTAVIAAGVVHTFLDVVPALVLGVP-DAATAVGS 105
                                       67899******************999999999998888******************************.******** PP

                              TctA  76 ldgyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailse...ksllk 149
                                       l+g++l++ Gr++eA+rl+a+gS++++ ++v+l+l+l+ ++a  + + ++   + lil++++++++ +e   ++++ 
  gi|313125986|ref|YP_004036256.1| 106 LPGHRLVLAGRGREAIRLSAVGSGVAVACAVPLALPLSHFVA--TGREQLYAALPLILAVVIVLLVAAEptwRRRTG 180
                                       ******************************************..5555556666666666666666666789***** PP

                              TctA 150 glialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip.....lslkdlkksl 221
                                       g+++++l+ +lgt++ld  ++ +      +  ++   l p++ GlFg++ l++sl  + +ip     +    l+++l
  gi|313125986|ref|YP_004036256.1| 181 GVACFTLATALGTLTLDLPTAGS-----LVPSSAASMLAPLFAGLFGAPVLIDSLDGRGTIPpqdgtKAALSLRETL 252
                                       *******************9555.....6888999*********************999998665442333344678 PP

                              TctA 222 ptilrgsliGtivGilPgvGasiaaflayavakrlskkpek..fgkgaiegvaapeaannaaaggaliplltlgipg 296
                                        +++ g   G++vG+lPgv+a +a++la +     s+  ++    + ++++++a+++a +a+a++a  +l++ g  +
  gi|313125986|ref|YP_004036256.1| 253 RAAVSGVGGGALVGYLPGVSAGVATVLALGGVGGDSRPGDEsdADRIDRQYIVATSGADTATAVFAAAALVVVGDER 329
                                       8899***************************9998875443125679****************************** PP

                              TctA 297 sgvaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakll.kipkelLlpiilvllvi 372
                                       sgva++l ++        g +     p   ++ la+l++a+ +  +l+ +l++ +  ++ ++p++ L+++il++l +
  gi|313125986|ref|YP_004036256.1| 330 SGVAVALASVG------GGGS-----PFGSVTALAVLVFAAGVGAILVPVLGDRYLTVVrRLPHRPLSATILAVLWV 395
                                       ****9999953......4444.....4455778888888888888888888888888776***************** PP

                              TctA 373 gayalnnslfdvlvmlifgvlGlllrrlgvplaplvl 409
                                       +a ++++  ++++v++++++lGll+ rlgv++++l++
  gi|313125986|ref|YP_004036256.1| 396 LAGVFAGV-TGLCVFAVAALLGLLPPRLGVRRVHLMG 431
                                       ********.**************************95 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.1e-05      0.19      13      66 ..     291     356 ..     283     364 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.1e-05
                                       --..SS--.E-EEEE-SS-HHHHHHHHHTSEEEEEETT.-HHHHHHHTT-T...........EEEEE CS
                             DRTGG  13 ggeeelrr.vekvvvgamsvenmlerlkegdlvivpGD.Rediqlaaleag...........iaali 66 
                                       g+e++ +r  ++++v++  ++ ++  +   +lv+v GD R+ + +a+++ g           +a l+
  gi|313125986|ref|YP_004036256.1| 291 GDESDADRiDRQYIVATSGADTATAVFAAAALVVV-GDeRSGVAVALASVGgggspfgsvtaLAVLV 356
                                       7788899988999999999****************.6616666666555546666666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2608.61
//
Query:       gi|313125987|ref|YP_004036257.1|  [L=110]
Description: 50S ribosomal protein L12ae [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-15   57.6  21.8    2.1e-15   57.1  21.8    1.3  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.015   13.9   3.7      0.017   13.7   3.7    1.0  1  RRN3           RNA polymerase I specific transcription initia
       0.94    8.7   9.6       0.94    8.7   9.6    1.2  1  NOA36          NOA36 protein
        4.4    6.8   7.3        5.4    6.5   7.3    1.1  1  PPP4R2         PPP4R2
        5.5    6.3   6.7          7    6.0   6.7    1.2  1  DUF4746        Domain of unknown function (DUF4746)
        7.1    6.0  11.1        8.4    5.7  11.1    1.1  1  SDA1           SDA1


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1  21.8   7.1e-19   2.1e-15       1      84 [.      16     104 ..      16     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 7.1e-19
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.. CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeee. 76 
                                       e+++en+++vl++agv+ve++rvk+lv+ale++diee+++++aa+  +a+aa+ a+++ +aa ++++++  eeeee 
  gi|313125987|ref|YP_004036257.1|  16 EVNEENVTAVLESAGVDVEESRVKALVAALEDVDIEEAVETAAAA--PAPAAGGAGGEVEAAGDDDDDEGGEEEEEa 90 
                                       689****************************************99..888888877777777777776666666666 PP

                                       ...XX--S...S-- CS
                     Ribosomal_60s  77 ...Eeedd...dmG 84 
                                          Eeed+    +G
  gi|313125987|ref|YP_004036257.1|  91 aeeEEEDEeasGEG 104
                                       75323333434444 PP

>> RRN3  RNA polymerase I specific transcription initiation factor RRN3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.7   5.6e-06     0.017     178     258 ..       1      99 [.       1     107 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-06
                              RRN3 178 vtYirnllklteycpelsedileliverlikiDVe......iqveledlddeedeeleeelee.............d 235
                                       ++Y+   l l e  +e++e+ +++++e +  +DVe      +   led+d ee  e+  ++ +              
  gi|313125987|ref|YP_004036257.1|   1 MEYVYAALILNESDEEVNEENVTAVLESA-GVDVEesrvkaLVAALEDVDIEEAVETAAAAPApaaggaggeveaaG 76 
                                       579***********************975.89**6555555779999999998888776655599999998754431 PP

                              RRN3 236 eddedddedd....eesdlddlssdee 258
                                           ddd+d+    ee+ ++++++dee
  gi|313125987|ref|YP_004036257.1|  77 ----DDDDDEggeeEEEAAEEEEEDEE 99 
                                       ....22222211112222222222222 PP

>> NOA36  NOA36 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   9.6   0.00031      0.94     250     297 ..      50     100 ..      12     107 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00031
                             NOA36 250 deedsdydaylkalasg...ddeddegdedddddddeedddeeeddedeee 297
                                        ee+ + +a   a a+g    + +  gd+ddd+  +ee++  ee++edee+
  gi|313125987|ref|YP_004036257.1|  50 IEEAVETAAAAPAPAAGgagGEVEAAGDDDDDEGGEEEEEAAEEEEEDEEA 100
                                       334444444333333331113444444444444444444444444444443 PP

>> PPP4R2  PPP4R2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   7.3    0.0018       5.4     245     279 ..      30      99 ..       6     104 .. 0.43

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0018
                            PPP4R2 245 svkvee...................................kdddeeddeedtdyveeeeddesedddee 279
                                        v+vee                                   + +   dd++d+  +eeee +e+e++dee
  gi|313125987|ref|YP_004036257.1|  30 GVDVEEsrvkalvaaledvdieeavetaaaapapaaggaggEVEAAGDDDDDEGGEEEEEAAEEEEEDEE 99 
                                       2222223444444444444444477778888888888887522223333333333333333333333333 PP

>> DUF4746  Domain of unknown function (DUF4746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.7    0.0023         7      59     129 ..      27      99 ..       5     106 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0023
                           DUF4746  59 eplevkveveee...eelveevsseeetlekqekekektkakeaeltadepaeeeeaeeeeeeeaveeeeeeee 129
                                       e   v ve ++      + e+v  ee ++e+++ +++ ++  + ++   +  +++++  eeeeea eeeee+ee
  gi|313125987|ref|YP_004036257.1|  27 ESAGVDVEESRVkalVAALEDVDIEE-AVETAAAAPAPAAGGAGGEVEAAGDDDDDEGGEEEEEAAEEEEEDEE 99 
                                       55555555544433333334444444.44444444444443444434334445555555555555555534333 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  11.1    0.0028       8.4      92     158 ..      19     101 ..       6     107 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0028
                              SDA1  92 eedsddeddeedwevesdddseedseggwidvesdee................................eieesde. 135
                                       ee+     ++++                 +dve++                                  e+e + + 
  gi|313125987|ref|YP_004036257.1|  19 EENVTAVLESAG-----------------VDVEESRVkalvaaledvdieeavetaaaapapaaggaggEVEAAGDd 78 
                                       222222223333.................344333334444444444455556677788999999999844444430 PP

                              SDA1 136 sedeeeeeeeeeekeekeeeeee 158
                                       ++de  eeeee+++ee+e+ee++
  gi|313125987|ref|YP_004036257.1|  79 DDDEGGEEEEEAAEEEEEDEEAS 101
                                       44444444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 722.05
//
Query:       gi|313125988|ref|YP_004036258.1|  [L=347]
Description: 50S ribosomal protein L10 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-21   75.7   0.0    4.3e-21   74.9   0.0    1.4  1  Ribosomal_L10    Ribosomal protein L10
      3e-15   56.0   0.0    5.4e-15   55.1   0.0    1.4  1  RL10P_insert     Insertion domain in 60S ribosomal protein L1
      0.001   19.6  13.2      0.001   19.6  13.2    1.9  2  Ribosomal_60s    60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.015   15.5   9.0       0.02   15.1   9.0    1.2  1  RNA_pol_3_Rpc31  DNA-directed RNA polymerase III subunit Rpc3
       0.47   10.1   7.2       0.67    9.6   7.2    1.2  1  Cwf_Cwc_15       Cwf15/Cwc15 cell cycle control protein
        1.2    8.1  16.6        1.8    7.6  16.6    1.1  1  DUF2457          Protein of unknown function (DUF2457)
        8.9    6.8  16.7         17    5.9  16.7    1.4  1  CENP-B_dimeris   Centromere protein B dimerisation domain


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   1.7e-24   4.3e-21       3      97 ..      14     108 ..      12     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.7e-24
                                       CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS..SSCGCCSSS CS
                     Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeee.klkellkgp 78 
                                       +e+K   v el++ l++y+sv vv+++g+++ qlq +R++l ++ ael++ +ntl+ rAle+ ++   +l++++ g+
  gi|313125988|ref|YP_004036258.1|  14 PEWKRIEVGELTDFLEEYQSVGVVSVTGIPSRQLQSMRRDLHGS-AELRMSRNTLVTRALEQVNDGLeELTDYVYGQ 89 
                                       79*****************************************9.****************97765436******** PP

                                       EEEEEESS-TCHHHHCCCC CS
                     Ribosomal_L10  79 valvftnedpvalakvlee 97 
                                       valv tn++p+ l+k le+
  gi|313125988|ref|YP_004036258.1|  90 VALVGTNDNPFGLYKQLEA 108
                                       ***************9987 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   2.1e-18   5.4e-15       3      71 .]     117     185 ..     116     185 .. 0.99

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 2.1e-18
                      RL10P_insert   3 aGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       aG++A++d++ip+g+++  Pg+++ eL+++g  +++ +G i ++ed +v  +Ge+++ e  ++L+ Lgi
  gi|313125988|ref|YP_004036258.1| 117 AGEVAPNDIVIPEGDTGVDPGPFVGELQQVGASARIMEGSIKVTEDSHVLDEGEVVSEELSNVLNELGI 185
                                       8*******************************************************************9 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.2   1.1e+04      17      30 ..     212     225 ..     207     230 .. 0.51
   2 !   19.6  13.2     4e-07     0.001       1      84 [.     236     336 ..     236     346 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.2
                                       XXXXXXXXXXXXXX CS
                     Ribosomal_60s  17 eveaarvkllvkal 30 
                                       +ve++r+++  +a 
  gi|313125988|ref|YP_004036258.1| 212 DVEEYRADIQSAAA 225
                                       44444444444433 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 4e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..................XXXXXXXXXXXX CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaakla..................aaaaaaaaaaaa 59 
                                       +pta++ +++l +a    ea+++ l+++    + + +l+a++ a+l                     a+aaa+a +a
  gi|313125988|ref|YP_004036258.1| 236 YPTAQTAPTMLAKAAG--EAKALGLFAAIEDPELVPDLIAKADAQLRtlaaqiddeealpeelrgVEAPAAAPADEA 310
                                       599********99999..9**************************99***************975343444444444 PP

                                       XXXXXXXXXXXXXXXX...XX--SS-- CS
                     Ribosomal_60s  60 aaaaaaaeekkkeeeee..EeedddmG 84 
                                       ++ +  +ee  + e  +  +++d+d G
  gi|313125988|ref|YP_004036258.1| 311 DEDESTDEEDTEAEA-DdtDDDDEDDG 336
                                       444444444444444.34633333333 PP

>> RNA_pol_3_Rpc31  DNA-directed RNA polymerase III subunit Rpc31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   9.0   7.9e-06      0.02     169     214 ..     274     337 ..     206     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.9e-06
                   RNA_pol_3_Rpc31 169 elleklkelaeeeddee..................ekkekedeeeeeeeeeddefddddedggD 214
                                       +++++l +la ++ddee                  e++e e  +ee+ e e d+ dddded+gD
  gi|313125988|ref|YP_004036258.1| 274 KADAQLRTLAAQIDDEEalpeelrgveapaaapadEADEDESTDEEDTEAEADDTDDDDEDDGD 337
                                       4556666777777777778888888888888776533333333333358889999999998888 PP

>> Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   7.2   0.00026      0.67     110     144 ..     304     337 ..     247     344 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00026
                                       ----------------------------------- CS
                        Cwf_Cwc_15 110 eidaddedseeeeeeeeeesdddsdsdsddddded 144
                                       ++ ad+ d++e+++ee +++ + +d d+dd+dd d
  gi|313125988|ref|YP_004036258.1| 304 AAPADEADEDESTDEE-DTEAEADDTDDDDEDDGD 337
                                       2233333332222222.222222223333333333 PP

>> DUF2457  Protein of unknown function (DUF2457)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  16.6   0.00071       1.8      35      86 ..     275     337 ..     268     344 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00071
                           DUF2457  35 kEnairkLgeea.eeEaeeeeeee..........eddeedeeddddddddedddedddeeded 86 
                                        + ++r L+ ++ +eEa+ ee             e de++++d++d + + dd +ddde+d d
  gi|313125988|ref|YP_004036258.1| 275 ADAQLRTLAAQIdDEEALPEELRGveapaaapadEADEDESTDEEDTEAEADDTDDDDEDDGD 337
                                       567899**9999567787776554889999987656666666666666666666665555554 PP

>> CENP-B_dimeris  Centromere protein B dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  16.7    0.0065        17      11      41 ..     311     341 ..     304     347 .] 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0065
                    CENP-B_dimeris  11 dsesesdeeeeeeeedeededeeddedddev 41 
                                       d +  +dee+ e e d+ d+d+edd d+ e 
  gi|313125988|ref|YP_004036258.1| 311 DEDESTDEEDTEAEADDTDDDDEDDGDGAEG 341
                                       5566779999999999999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2305.44
//
Query:       gi|313125989|ref|YP_004036259.1|  [L=212]
Description: 50S ribosomal protein L1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-44  150.9   0.0    4.7e-44  150.6   0.0    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family
  ------ inclusion threshold ------
        2.3    8.4   5.2         19    5.5   0.2    2.9  3  DUF3168       Protein of unknown function (DUF3168)


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.0   5.2e-48   4.7e-44       6     204 .]      18     206 ..      12     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 5.2e-48
                                       -SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT CS
                      Ribosomal_L1   6 kkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyk 82 
                                       +++f e+v++a+nl++++ + +++r+ ++i+Lp ++g+e+ki++++ +++a    +a+e    ++v+++++l++   
  gi|313125989|ref|YP_004036259.1|  18 ERNFRETVDLAINLRDLDLNDPSKRVDESIVLPAGTGQETKIVVFATGETAL---QAEEVA--DQVMDGDDLEDLGD 89 
                                       789*************************************************...898888..************** PP

                                       -HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEE CS
                      Ribosomal_L1  83 sfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsv 159
                                       +  a + l++e d+f+a+ ++m+ +++ LG v+g+r+kmP+p   +    +dv + v+++++ tv +r+++  +++ 
  gi|313125989|ref|YP_004036259.1|  90 DTDAAKDLADEIDFFVAEANMMQDIGRYLGTVLGPRGKMPTPL--Q--PDDDVVEVVNRMKN-TVQLRSRDRRTFHT 161
                                       *******************************************..4..3789**********.************** PP

                                       EEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                      Ribosomal_L1 160 kvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                       +vG  +++a+e+aeNi+ +v+ l+  ++k+  ni  i++kttm+p
  gi|313125989|ref|YP_004036259.1| 162 RVGAEDMSADEIAENIDVIVRRLEATLEKGPLNIDGIFVKTTMGP 206
                                       ********************************************8 PP

>> DUF3168  Protein of unknown function (DUF3168)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0036        33      69      86 ..       2      19 ..       1      42 [. 0.79
   2 ?    5.5   0.2    0.0021        19      56      78 ..      58      80 ..      36     109 .. 0.84
   3 ?   -1.8   0.1      0.37   3.3e+03      61      61 ..     165     165 ..     139     202 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0036
                           DUF3168 69 akalaaavraaLddaala 86
                                      a+++++av++aLd+a+  
  gi|313125989|ref|YP_004036259.1|  2 ADTIVDAVSRALDEAPER 19
                                      899*********877754 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0021
                           DUF3168 56 qldvwarepgraeakalaaavra 78
                                       + v+a++++  +a+++a++v++
  gi|313125989|ref|YP_004036259.1| 58 KIVVFATGETALQAEEVADQVMD 80
                                      57799999*************97 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.37
                           DUF3168  61 a 61 
                                       a
  gi|313125989|ref|YP_004036259.1| 165 A 165
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.37s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1142.73
//
Query:       gi|313125990|ref|YP_004036260.1|  [L=158]
Description: 50S ribosomal protein L11 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-20   71.6   0.0      8e-20   71.1   0.0    1.2  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
    9.1e-20   70.3   0.0    1.4e-19   69.7   0.0    1.3  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   8.9e-24     8e-20       2      70 .]      68     135 ..      67     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 8.9e-24
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                       +Ppt+ l+k +ag e+gsg+p++++v+++s++qv++IA++K+sdl ++ + ++a+k+++gt+ s+G+++
  gi|313125990|ref|YP_004036260.1|  68 VPPTAELIKDEAGFETGSGEPQENFVADLSFDQVKKIAEQKSSDLLSY-DTKNAAKEVVGTCTSLGVTI 135
                                       6*********************************************99.******************97 PP

>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   1.5e-23   1.4e-19       5      65 .]       2      62 ..       1      62 [. 0.97

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 1.5e-23
                   Ribosomal_L11_N  5 vkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrsf 65
                                      ++++++ vp+G+A+p+PplGp LGp  +n++++++e+n++T+ + g+ +pV+++  +d sf
  gi|313125990|ref|YP_004036260.1|  2 AGTIEVLVPGGEANPGPPLGPELGPTPVNVQDVVQEINDETAAFDGMEVPVTVEYDDDGSF 62
                                      689****************************************************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 929.61
//
Query:       gi|313125991|ref|YP_004036261.1|  [L=354]
Description: peptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-80  267.8   6.4      1e-79  267.6   6.4    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    4.1e-09   35.7   0.1    2.7e-06   26.5   0.1    2.3  2  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.6   6.4   1.2e-83     1e-79       1     292 []      46     336 ..      46     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 267.6 bits;  conditional E-value: 1.2e-83
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGC CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHll 77 
                                       Gn +a+ +g   +p++++++H DeiG++V+++++dGflr++++GG d +v +gq+v+++  +g+++Gvig++++Hl+
  gi|313125991|ref|YP_004036261.1|  46 GNAVAVHEGTGGGPEIAFTGHADEIGYIVRDVTDDGFLRIAAIGGADRTVSKGQHVTVHAADGEVPGVIGQTAIHLR 122
                                       899*************************************************************************9 PP

                                       HHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS- CS
                     Peptidase_M42  78 keeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeel 154
                                       +  ++++  +++e f+Diga++++ea el ++vGd+ +++++++ l++++++++ +D+r+g ++++e+l++  e ++
  gi|313125991|ref|YP_004036261.1| 123 D-VGEEEYDDLEEQFVDIGAADEAEAHEL-VEVGDPLTVETRVRDLHGSRMAARGMDNRVGTWAAAEALRHAVEADV 197
                                       9.56677789*******************.*********************************************** PP

                                       SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS...TTS-CEEEEEETTCCSHHHHHHH CS
                     Peptidase_M42 155 eatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak...lgkGpvirvkDasgiyhpklrkk 228
                                       +atvy+v tvqEE G++Gak++ ++++pd+a+a+Dvt+a+d+p++++k++    lg+Gpvi+     +  hp +++ 
  gi|313125991|ref|YP_004036261.1| 198 DATVYAVSTVQEELGVQGAKMVGYDLNPDAAVAIDVTHATDNPDVESKHKGpveLGEGPVITRG---SANHPAVVEL 271
                                       *********************************************999977899********99...999******* PP

                                       HHHHHHHTT--EEEE.EESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 229 llelAkknnipyqle.vlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                        +++A+++++++ql+ +  ++gtDA+a+ ++++g+p++ i+ip ry+H+pvev++ +dl+a ++L
  gi|313125991|ref|YP_004036261.1| 272 ARNAANDADVDVQLQaAGIRTGTDADAFYTSRSGIPSLNIGIPNRYMHTPVEVVDTEDLDAIATL 336
                                       ***************77889***************************************998776 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0   0.00024       2.1     229     277 ..     171     216 ..     158     223 .. 0.77
   2 !   26.5   0.1     3e-10   2.7e-06     312     428 ..     228     337 ..     221     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00024
                                       EEESSHHHHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-ST CS
                     Peptidase_M18 229 lfaprlDnkvscfaaleallesaedsleeedkvrivalfDnEEvGStsa 277
                                       ++a ++Dn+v+++aa eal ++ e +++    +  +++  +EE+G ++a
  gi|313125991|ref|YP_004036261.1| 171 MAARGMDNRVGTWAAAEALRHAVEADVDA---TVYAVSTVQEELGVQGA 216
                                       78999*****************9994443...34444455788887665 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 3e-10
                                       EEEE--EE--.-TTSGGGS-TTTS--TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HC CS
                     Peptidase_M18 312 liSaDvahai.hPnysskheenhapllnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGsti 387
                                        + +Dv+ha+ +P   skh+     +l++G+vi   +    a + a ++l +++a+ a+v +Q    ++  ++G+  
  gi|313125991|ref|YP_004036261.1| 228 AVAIDVTHATdNPDVESKHKG--PVELGEGPVITRGS----ANHPAVVELARNAANDADVDVQLQ--AAGIRTGTDA 296
                                       6899*****967999999976..579*******8654....455566788999999999999875..456789**** PP

                                       HHHHHHHHT-EEEEEE-EEBSTTSSSEEEECCHHHHHHHHH CS
                     Peptidase_M18 388 gpilaaktGirtiDlGaaqlsmHSireltgskdveeavklf 428
                                        +  +++ Gi  + +G++   mH + e+++++d+    +l+
  gi|313125991|ref|YP_004036261.1| 297 DAFYTSRSGIPSLNIGIPNRYMHTPVEVVDTEDLDAIATLL 337
                                       *********************************98877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2102.57
//
Query:       gi|313125992|ref|YP_004036262.1|  [L=103]
Description: hypothetical protein Hbor_12280 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 597.02
//
Query:       gi|313125993|ref|YP_004036263.1|  [L=345]
Description: mevalonate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-15   54.5   0.3    2.8e-14   53.1   0.3    1.9  1  GHMP_kinases_N   GHMP kinases N terminal domain
      9e-13   48.4   0.9    1.3e-11   44.6   0.2    2.3  2  GHMP_kinases_C   GHMP kinases C terminal
    5.2e-05   22.7   0.0     0.0001   21.8   0.0    1.5  1  GalKase_gal_bdg  Galactokinase galactose-binding signature


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.3   4.7e-18   2.8e-14       1      66 []     111     179 ..      90     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 4.7e-18
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       d++++s+iP+gaGLGSSAA++va + A+ + lg +l  ee a  a++ae ++q g  s  D ++++ Gg
  gi|313125993|ref|YP_004036263.1| 111 DVTVESDIPLGAGLGSSAAVVVASIDAATRELGHPLdpEElAARAYRAEYEVQDGQASRADTFCCAVGG 179
                                       689********************************976446888*********************9998 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.044   2.6e+02      55      81 ..     121     158 ..     120     162 .. 0.67
   2 !   44.6   0.2   2.3e-15   1.3e-11      11      70 ..     259     316 ..     255     329 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.044
                    GHMP_kinases_C  55 GaGgGptvfalf...........kdkdeaeqvaralre 81 
                                       GaG+G++ ++++              d+ e +ara r+
  gi|313125993|ref|YP_004036263.1| 121 GAGLGSSAAVVVasidaatrelgHPLDPEELAARAYRA 158
                                       9**********977777777776444444445555455 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 2.3e-15
                    GHMP_kinases_C  11 ellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkd 70 
                                        +lg+l+   +   l++ +g++++ l++++ a++e+Ga+gakl+GaGgG++++al ++ +
  gi|313125993|ref|YP_004036263.1| 259 AELGRLMDFDHG--LLEALGVSSRTLDNMVWAAREAGAHGAKLTGAGGGGCIVALDETAE 316
                                       689*********..899**************************************74433 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.7e-08    0.0001      12      47 ..       9      44 ..       3      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-08
                                      EEEEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEE CS
                   GalKase_gal_bdg 12 fvasAPGRvnLiGEHtDYngGfVlpmAieqdiyiav 47
                                       v sAPG v L GEH    g    p+Aie++ ++ v
  gi|313125993|ref|YP_004036263.1|  9 TVSSAPGKVYLFGEHAVVYGEPAVPCAIERRATVSV 44
                                      689****************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1989.38
//
Query:       gi|313125994|ref|YP_004036264.1|  [L=245]
Description: isopentenyl phosphate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-38  133.1   4.1    1.4e-38  132.8   4.1    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   4.1     8e-43   1.4e-38       1     228 [.       1     217 [.       1     224 [. 0.94

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 8e-43
                                       TEEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..H CS
                         AA_kinase   1 krvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstle 71 
                                       +++V+KlGGs++tdk++      +sl+++++ +a+   +  +lv+VhGggsf+++ +++ +g+s++  +      ++
  gi|313125994|ref|YP_004036264.1|   1 MTTVLKLGGSVVTDKSTpetvddDSLDAAVAAVADS--DPSRLVIVHGGGSFGHHNAEK-HGVSDSQGT------HD 68 
                                       789*********************************..8889*****************.******996......78 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEE CS
                         AA_kinase  72 eagevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfig 148
                                       +++  + +da+  l+  +v++l++ag++a ++++ +l+a++a+          s+  +  +++l++g+vpvl+g++ 
  gi|313125994|ref|YP_004036264.1|  69 AEAVFEIHDAMRRLNDAVVTRLQDAGIAALPVQPLSLGARDAEA-------AFSLPLDSTATMLDEGFVPVLHGDVI 138
                                       88999999********************************9998.......99999******************997 PP

                                       EETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEE.EHHHCHH....CSSS.TTTHHH CS
                         AA_kinase 149 ldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpei.svdeaee....saselatgGmk 220
                                       +    + +++s+D + + lA  l+Ad++ +++ V+GV+dad+      +++pei +++++++    s+++++tgGm 
  gi|313125994|ref|YP_004036264.1| 139 AHAASGATVVSGDELVTTLARGLDADRVGLCSTVPGVLDADN------EVIPEItAFEDVASvlggSDATDVTGGMA 209
                                       7777779*********************************96......88999967777777999************ PP

                                       HCHHHHHH CS
                         AA_kinase 221 vkhpaala 228
                                       +k++a l+
  gi|313125994|ref|YP_004036264.1| 210 AKVRALLE 217
                                       ****9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1531.84
//
Query:       gi|313125995|ref|YP_004036265.1|  [L=255]
Description: metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-18   65.8   0.5    4.6e-18   65.5   0.5    1.1  1  Lactamase_B_2    Beta-lactamase superfamily domain
    2.6e-09   37.4   3.8    6.2e-09   36.2   3.7    1.9  1  Lactamase_B      Metallo-beta-lactamase superfamily
     0.0062   16.4   0.0      0.011   15.7   0.0    1.4  1  Lactamase_B_3    Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.19   11.2   0.0       0.37   10.2   0.0    1.4  1  Poxvirus_B22R_C  Poxvirus B22R protein C-terminal


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.5     1e-21   4.6e-18       2     200 ..      30     220 ..      29     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1e-21
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE.EEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk.lplyapkgvlavleanf 74 
                                        +L+D+g +++  ++ +          + i  Vllth H DH+ +ll l +   l+++  l++++p g+ + l+  +
  gi|313125995|ref|YP_004036265.1|  30 SLLVDCGSGVLNRLTNTD----V--GYEGIGTVLLTHHHLDHVSDLLALLKarwLAGEThLEVVGPTGTKRLLDGLL 100
                                       689******987733333....2..356***********************988333335****************9 PP

                                       GHHHCHTT.TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE.........CTTEEEEEES CS
                     Lactamase_B_2  75 vylaleee.pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie.........gggkrvyyig 141
                                       + +   ++  +++++e++  +sfe++  g+ei+at+ rh++           l++r+          ++g  ++++g
  gi|313125995|ref|YP_004036265.1| 101 DVHDYLQDrVELRIREVT-AGSFEVA--GFEIEATETRHSKDC---------LAYRFHgdsdagdddRSGGDFVFSG 165
                                       998888886667777776.778***9..899******999886.........99999976666544445555***** PP

                                       S-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 142 DtgyipeeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                       D++ +++ + +  +ga +l +d+ + ++        H tp +  ea+a ++++r++l+H
  gi|313125995|ref|YP_004036265.1| 166 DSEAFEGLA-NFADGAAVLAHDCSFPDEVD---VSNHPTPAQLGEALAGYDIGRVYLTH 220
                                       ******875.599*********99998888...779*********************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   3.7   1.4e-12   6.2e-09      10      90 ..      23      98 ..      15     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.4e-12
                                      EEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHH CS
                       Lactamase_B 10 liegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeead 88
                                      l+e d++ +L+D+G++  + +        +++ + + +v+lTH+HlDH+++l  l +a++ +   + e+     +  + 
  gi|313125995|ref|YP_004036265.1| 23 LVESDERSLLVDCGSGVLNRLTN-----TDVGYEGIGTVLLTHHHLDHVSDLLALLKARWLAGETHLEVVGPTGTKRLL 96
                                      899******************96.....9*******************************9999988877666666655 PP

                                      HH CS
                       Lactamase_B 89 da 90
                                      d+
  gi|313125995|ref|YP_004036265.1| 97 DG 98
                                      54 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.4e-06     0.011      10      86 ..      22     148 ..      19     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                     Lactamase_B_3  10 flletagarilvDPfka....nlgyeppa.....eeaDlvlisqaledHahletlkql..............aenvk 63 
                                       +l+e+++ ++lvD +++     +     +     e +  vl+++++ dH     l+ l                   
  gi|313125995|ref|YP_004036265.1|  22 LLVESDERSLLVDCGSGvlnrLT-----NtdvgyEGIGTVLLTHHHLDHVSDL-LALLkarwlagethlevvG---- 88 
                                       6899999******9965331122.....2234559**************8754.4443456777744444440.... PP

                     Lactamase_B_3  64 vlee.............................geslevggleiravatsh...........d 86 
                                          +                              +s+ev+g+ei+a++t h           d
  gi|313125995|ref|YP_004036265.1|  89 ---PtgtkrlldglldvhdylqdrvelrirevtAGSFEVAGFEIEATETRHskdclayrfhgD 148
                                       ...366666666677777777778877777777899*************99655555555552 PP

>> Poxvirus_B22R_C  Poxvirus B22R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   8.3e-05      0.37     112     157 ..      60     107 ..      55     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.3e-05
                   Poxvirus_B22R_C 112 lefiDtiesvvyYlntsniildakltvaCPiGtLRllel..Dinaytl 157
                                        + +D ++ ++  l++  +  +++l+v+ P Gt Rll++  D++ y+ 
  gi|313125995|ref|YP_004036265.1|  60 HHHLDHVSDLLALLKARWLAGETHLEVVGPTGTKRLLDGllDVHDYLQ 107
                                       68899********************************95449999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1596.80
//
Query:       gi|313125996|ref|YP_004036266.1|  [L=478]
Description: hypothetical protein Hbor_12320 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 3025.01
//
Query:       gi|313125997|ref|YP_004036267.1|  [L=93]
Description: hypothetical protein Hbor_12330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-23   82.4   1.1    2.5e-23   82.1   1.1    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   1.1   1.4e-27   2.5e-23       2      73 ..      15      81 ..      14      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 1.4e-27
                            HalOD1  2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieV 73
                                      +e +s aVveav+ ++++++ el+pLydaiDpd Ld+Lfa      ++a  +++F+y+g+ VtV++d++ie+
  gi|313125997|ref|YP_004036267.1| 15 DEAISLAVVEAVSVAADTPVLELPPLYDAIDPDVLDELFAG-----RQAAERITFRYAGHLVTVHGDRTIEI 81
                                      799**************************************.....77888*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.36s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 523.28
//
Query:       gi|313125998|ref|YP_004036268.1|  [L=921]
Description: ATP dependent helicase, lhr family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-53  181.4   0.8    3.2e-53  180.4   0.8    1.5  1  DEAD_assoc  DEAD/H associated
    4.3e-31  108.0   0.0    4.1e-30  104.9   0.0    2.1  2  DEAD        DEAD/DEAH box helicase
    1.5e-18   67.2   0.1    9.2e-18   64.6   0.0    2.2  2  Helicase_C  Helicase conserved C-terminal domain
    2.4e-09   37.4   0.0    2.9e-08   33.9   0.0    2.2  2  ResIII      Type III restriction enzyme, res subunit
     0.0087   16.3   0.4      0.096   13.0   0.2    2.7  2  AAA_22      AAA domain
  ------ inclusion threshold ------
      0.041   14.2   0.8       0.17   12.2   0.1    2.4  3  AAA_19      AAA domain
      0.049   12.0   0.1       0.14   10.5   0.0    1.7  3  DUF5312     Family of unknown function (DUF5312)


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.4   0.8   1.2e-56   3.2e-53       2     191 .]     691     879 ..     690     879 .. 0.97

  Alignments for each domain:
  == domain 1  score: 180.4 bits;  conditional E-value: 1.2e-56
                        DEAD_assoc   2 PtdrtllvErf..rdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlplllde 76 
                                        t++++ +E+   rde+ ++r++vhs +Grr+n++l++l+a  ++rr + +vqva++D+g+ +++pl+++++  +++
  gi|313125998|ref|YP_004036268.1| 691 ATESRIAIEEQldRDEY-QRRFYVHSNYGRRFNDGLSRLIAFHFARRSNANVQVAVADNGFSISMPLNRKVD--VEA 764
                                       68999*****9988877.99***********************************************99975..899 PP

                        DEAD_assoc  77 llellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavr 153
                                       +++ ++pd ++edl+aal++++l+kr Fr +A+ral++++ry+g +k++ qq++++++Ll++a+++++f +++e++r
  gi|313125998|ref|YP_004036268.1| 765 VIRDIDPDSVDEDLRAALDGTDLLKRYFRINATRALMILKRYKGYEKSAAQQQVSSEMLLSFAQDLDGFAVMEETYR 841
                                       ***************************************************************************** PP

                        DEAD_assoc 154 evledqlDlerlaellrriaageirvvevetprpSpfA 191
                                       e+led+l++++++++lr +++g+++vv++++++p+p A
  gi|313125998|ref|YP_004036268.1| 842 EILEDKLNVAAVKDVLRGVKSGDVEVVARNVDSPTPRA 879
                                       ************************************76 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.0   1.6e-33   4.1e-30       1     170 [.      62     247 ..      62     252 .. 0.91
   2 ?    0.3   0.0       0.2   5.1e+02      45     103 ..     311     374 ..     296     383 .. 0.65

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 1.6e-33
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS......TTSTS-EEEEEESSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet......kgktgpkalivePtreLaeqtlnnlkkfk 71 
                                       t+ Q+ea+pli + ++ l++a+TGsGKTla + ++++ ++++        ++   +l+++P+++La+++++nl++ +
  gi|313125998|ref|YP_004036268.1|  62 TPPQREAVPLIDDSENALICAPTGSGKTLASFTAIINDLFRRdreladGLENSVYCLYISPLKSLANDIHRNLTQPL 138
                                       789************************************99999999779999************************ PP

                                       TTST...........SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHH CS
                                       xxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                              DEAD  72 kyid...........lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlld 135
                                       + i+           lr     g+++ +d ++ l+ +++i+ +tp+ l  ll++ k++  l+ v+++++DE++ l +
  gi|313125998|ref|YP_004036268.1| 139 EGITermdergetvtLRHAIRHGDTDSTDRQKMLETTPHILNTTPETLSILLNSPKFKekLRTVEYVIVDEIHSLAE 215
                                       *866677888888777777777788888999999899***************77777777***************** PP

                                       TTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 136 qgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       ++++ +++  l++l++ ++d +   + i +SAT++
  gi|313125998|ref|YP_004036268.1| 216 NKRGTHLSVSLERLENLCHDSP---TRIGCSATVE 247
                                       **************98888887...48******86 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
                                       STS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET....TSSHHHHHHHHHTT.CSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.xxxxxx RF
                              DEAD  45 ktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig....gvaardqlskldng.vdivvg 103
                                       ++++ +l+ + tr+ ae +l+nl++  + +d + + + +    ++++++  ++l+ g +d+v +
  gi|313125998|ref|YP_004036268.1| 311 QSHTNTLVFTNTRSGAERVLHNLRENYDGYDEQNSGCHHgslsKERRQEIERELKDGnLDVVTT 374
                                       4566899999*************99999888444433331221333344444454444666544 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.84   2.1e+03      40      62 ..     153     175 ..     129     191 .. 0.81
   2 !   64.6   0.0   3.6e-21   9.2e-18       7     108 ..     303     410 ..     298     413 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.84
                                       TSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  40 gikvavlhgelpqnereeileqf 62 
                                        ++ a+ hg++ + +r+++le  
  gi|313125998|ref|YP_004036268.1| 153 TLRHAIRHGDTDSTDRQKMLETT 175
                                       5788999**********999865 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 3.6e-21
                                       HHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                        Helicase_C   7 lell.kleeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatdvae 77 
                                       ++ l +l +++ ++l+f+nt++ +e+ ++ l+e+     + ++ ++hg+l+++ r+ei ++ ++g+ dv+ +++ +e
  gi|313125998|ref|YP_004036268.1| 303 YDRLdELVQSHTNTLVFTNTRSGAERvLHNLRENYdgydEQNSGCHHGSLSKERRQEIERELKDGNLDVVTTSTSLE 379
                                       55555667999***********9984445554444888899************************************ PP

                                       SSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                        Gid+p ++lV++++ p++v+s+ qr+GR+g
  gi|313125998|ref|YP_004036268.1| 380 LGIDMPHIDLVVQVGSPKSVASLLQRVGRAG 410
                                       ******************************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.1e-11   2.9e-08      22     170 ..      73     247 ..      32     248 .. 0.72
   2 ?    0.8   0.0      0.16   4.2e+02      48     111 ..     309     374 ..     301     381 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.1e-11
                                       .TTSEEEEEESTTSTHHHHH.HHHHHHH-S.............-EEEEESSHHHHHHHHHHGGGGTGG.......GE CS
                            ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee........kflflvprkslleqtleefkkflseayke...ig 86 
                                       ++ +++li ++TG+GKTl + +++i  l++  +e          +l + p ksl +   +++++ l+  +++    g
  gi|313125998|ref|YP_004036268.1|  73 DDSENALICAPTGSGKTLASfTAIINDLFRRDRELadglensvYCLYISPLKSLANDIHRNLTQPLEGITERmdeRG 149
                                       678899**************8999999999755559*****999******************999998776667744 PP

                                       EEESSS-B--........-SEEEEEHHHHHHTH.............HHHTTT-SEEEEETGGGTTS.T.......TT CS
                            ResIII  87 kkvsgdkkka.kekdstnkkilvttiqsldadseee.....eeeseellrdrfdviiiDEaHrlgakk.......sw 150
                                       + v+ ++ ++    dst+++ +++t+  + +  +e+     ++ + + +  + +++i+DE H l+++k       s 
  gi|313125998|ref|YP_004036268.1| 150 ETVTLRHAIRhGDTDSTDRQKMLETTPHILNTTPETlsillNSPKFKEKLRTVEYVIVDEIHSLAENKrgthlsvSL 226
                                       444444444453334444444444444444444444333325555555555566************96666666666 PP

                                       HHHHHT-.--SEEEEEESS-S CS
                            ResIII 151 reilekf.keavllglTATpe 170
                                       +++ + + ++ +++g +AT e
  gi|313125998|ref|YP_004036268.1| 227 ERLENLChDSPTRIGCSATVE 247
                                       776444436699******975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                                       H-S.....-EEEEESSHHHHHHHHHHGGGGTGG.........GEEEESSS-B--.......-SEEEEEH CS
                            ResIII  48 llkkgkeekflflvprkslleqtleefkkflseayke.....igkkvsgdkkkakekdstnkkilvtti 111
                                       l +++   ++l++ +++s  e+ l+++++ ++ ++++     +g   +++++++ e++ ++ ++ v+t+
  gi|313125998|ref|YP_004036268.1| 309 LVQSHT--NTLVFTNTRSGAERVLHNLRENYDGYDEQnsgchHGSLSKERRQEI-ERELKDGNLDVVTT 374
                                       455544..9***************999999999988888885555555555555.55555555555444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.2   3.7e-05     0.096       8     114 ..      78     231 ..      73     245 .. 0.65
   2 ?   -3.0   0.0       3.2   8.3e+03      70      91 ..     382     415 ..     347     462 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglelka......... 70 
                                        ++++++G+GKT+   +   ++  +     +++e++     +v++   + +k+l++++ r+l+++l++         
  gi|313125998|ref|YP_004036268.1|  78 ALICAPTGSGKTLASFTAIINDLFR-----RDRELAdglenSVYCLYISPLKSLANDIHRNLTQPLEGitermderg 149
                                       68*********98643333322222.....13333343345666666667778999999999999999999999999 PP

                            AAA_22  71 ..............erlsseellealeqalrarav.................ielliiDEaqhlr...s....eeal 109
                                                        +++ +le+  + l+++                   +e +i+DE++ l    +       l
  gi|313125998|ref|YP_004036268.1| 150 etvtlrhairhgdtDSTDRQKMLETTPHILNTTPEtlsillnspkfkeklrtVEYVIVDEIHSLAenkRgthlSVSL 226
                                       88888888888888444444444544444444444666666677777777788999999999998765145564444 PP

                            AAA_22 110 eeLrs 114
                                       e L +
  gi|313125998|ref|YP_004036268.1| 227 ERLEN 231
                                       44433 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.2
                            AAA_22  70 a............erlsseellealeqalrarav 91 
                                                    +++s   ll+++ +a ++ + 
  gi|313125998|ref|YP_004036268.1| 382 IdmphidlvvqvgSPKSVASLLQRVGRAGHRLGQ 415
                                       0444444444444455555555555555555554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.7e-05      0.17       1     115 [.      65     214 ..      65     222 .. 0.69
   2 ?   -2.3   0.0         2   5.2e+03      45      78 ..     316     369 ..     299     462 .. 0.55
   3 ?   -3.8   0.1       5.8   1.5e+04     105     126 ..     891     912 ..     883     916 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTr.vlkhivallvelggvkp......eeillvaftgrAakelrerlaalgae. 68 
                                       qreav     +++ l+ a+ G+GKT    ++i++ l ++ ++ +        +l +++ +  a+ ++ +l   +++ 
  gi|313125998|ref|YP_004036268.1|  65 QREAVPlIDDSENALICAPTGSGKTLaSFTAIINDLFRRDRELAdglensVYCLYISPLKSLANDIHRNL---TQPl 138
                                       8999987888999************624677777777777654477776677888888888888888888...5555 PP

                            AAA_19  69 ..................................atTiHrlalldfddlltealelleeaeeekklqeeellivDEf 111
                                                                          tT H l   ++++++     ll++ + ++kl+  e++ivDE+
  gi|313125998|ref|YP_004036268.1| 139 egitermdergetvtlrhairhgdtdstdrqkmlETTPHIL---NTTPET--LSILLNSPKFKEKLRTVEYVIVDEI 210
                                       56788888888865555555555555555555544444443...333333..2334557789999*7777******9 PP

                            AAA_19 112 qdvd 115
                                         + 
  gi|313125998|ref|YP_004036268.1| 211 HSLA 214
                                       8765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                            AAA_19  45 illvaftgrAake....lrerlaalgaeatTiHrlal................l 78 
                                        l+ + t+  a++    lre+ ++++++ + +H+ +l                l
  gi|313125998|ref|YP_004036268.1| 316 TLVFTNTRSGAERvlhnLRENYDGYDEQNSGCHHGSLskerrqeierelkdgnL 369
                                       555555555444311115666666666666666443333444444444444330 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 5.8
                            AAA_19 105 llivDEfqdvdelqyrLlkall 126
                                       +l  DE+q ++    r+l+++ 
  gi|313125998|ref|YP_004036268.1| 891 VLAEDESQALKAFHARVLDEIG 912
                                       6666899988888888888775 PP

>> DUF5312  Family of unknown function (DUF5312)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       1.3   3.2e+03     441     479 ..     136     174 ..     132     184 .. 0.86
   2 ?   10.5   0.0   5.4e-05      0.14      78     120 ..     270     312 ..     264     325 .. 0.87
   3 ?   -4.2   0.0       1.5   3.8e+03     182     240 ..     763     822 ..     755     827 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.3
                           DUF5312 441 ekiakleerlspeGeiGkrfakvkkekvatlkkkrklea 479
                                       + ++ + er+ ++Ge+   ++++++  + ++ +++ le+
  gi|313125998|ref|YP_004036268.1| 136 QPLEGITERMDERGETVTLRHAIRHGDTDSTDRQKMLET 174
                                       667888999999****99999999999999999999997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.4e-05
                           DUF5312  78 lyeeellkrlgkkierkapglidikekvltkafYeklkeLkka 120
                                       l +++++++   ++e    +li+++++v++++fY++l eL ++
  gi|313125998|ref|YP_004036268.1| 270 LVDTRFVRDFDLQLECPTDDLINTPRNVVQERFYDRLDELVQS 312
                                       56778899999999999**********************9664 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 1.5
                           DUF5312 182 deifssitddek.aelyeaaraiewlkqfcelpfdrlllaFteisdssatcsasnvksel 240
                                       ++++++i++d+  + l  a    + lk+  ++   r+l+     ++ +++   ++v+se+
  gi|313125998|ref|YP_004036268.1| 763 EAVIRDIDPDSVdEDLRAALDGTDLLKRYFRINATRALMILKRYKGYEKSAAQQQVSSEM 822
                                       678888888775145777778889999999999999999888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (921 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 5649.47
//
Query:       gi|313125999|ref|YP_004036269.1|  [L=61]
Description: hypothetical protein Hbor_12350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0071   16.6   1.2     0.0072   16.6   1.2    1.0  1  DUF3040    Protein of unknown function (DUF3040)
  ------ inclusion threshold ------
       0.13   11.9   0.7       0.13   11.9   0.7    1.1  1  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.2     8e-07    0.0072      36      81 ..       9      56 ..       1      59 [. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8e-07
                           DUF3040 36 arrrslrrlavlavllfvaGllllvlG.vaaaa.vvlgvvGfvvmlag 81
                                      + + + rr ++ a+ +++aG++l +lG  +a   +v ++vG+v+ +a+
  gi|313125999|ref|YP_004036269.1|  9 EESDAFRRGVLGAISGALAGVVLTLLGsNSAGDfLVAIFVGIVTYIAL 56
                                      4566778978888888999********633333699999999999887 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   1.5e-05      0.13     144     194 ..      13      60 ..       2      61 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                         CPP1-like 144 avlltlvgLvvGlllGsllasllqvdvalsglsseellvslvtlvllwlvs 194
                                       a+  +++g + G+l+G +l  l ++   ++g +  + +v +vt++ lwl +
  gi|313125999|ref|YP_004036269.1|  13 AFRRGVLGAISGALAGVVLTLLGSN---SAGDFLVAIFVGIVTYIALWLLT 60 
                                       7778889999999999999887754...455566888************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 414.71
//
Query:       gi|313126000|ref|YP_004036270.1|  [L=120]
Description: hypothetical protein Hbor_12360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.018   15.1   0.0    1.3  1  HTH_3     Helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     1e-06     0.018       2      37 ..      57      93 ..      57     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-06
                                      HHHHHHTTHHHHHHHHHHT.SSHHHHHHHHTTSSCSB CS
                             HTH_3  2 kelRkqlglsqeeLAeklG.vsrstisriEnGernPs 37
                                      + lR ++g++q+ + ++++ + +++is++E+G r+ s
  gi|313126000|ref|YP_004036270.1| 57 RLLRVAAGYDQRSVEREVDdIVQAHISMLESGTRALS 93
                                      5699****************88**********66554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 775.96
//
Query:       gi|313126001|ref|YP_004036271.1|  [L=558]
Description: anion transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-79  267.4  27.7    3.8e-79  266.9  27.7    1.0  1  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
      1e-31  110.3  54.2    9.1e-18   64.5  22.2    3.5  4  CitMHS         Citrate transporter


Domain annotation for each model (and alignments):
>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.9  27.7   4.2e-83   3.8e-79       8     465 ..      17     546 ..       8     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: 266.9 bits;  conditional E-value: 4.2e-83
                     Na_sulph_symp   8 llllvvlliilllPapdgleskawrllaifiaaivglileplplavialialsllavligvlaakalsevlsgfssd 84 
                                        +++v ++ i++ P p gl++k+++ la + +a   +++ +lplav+a+ +  +l++l+ +     l+++l+gf ++
  gi|313126001|ref|YP_004036271.1|  17 AVAVVGTALIAVAPSPGGLTVKGQYALATMFFAGFLWVTGALPLAVTAISIPFVLTALGVYPD---LDTALVGFADH 90 
                                       3455566789999************************************98888878887777...9********** PP

                     Na_sulph_symp  85 ttlLvfaalliaaavektgLgkRiAlvlvkivGkrtliL..gyalvladlllapatpsntAraggivfpvikslssa 159
                                        ++L++a++++a a++k  +++RiAl ++ ++G+++++L    +l +a+l+++++++++tA++ +i++ v+ ++   
  gi|313126001|ref|YP_004036271.1|  91 LIFLFIAGFMLANALQKYDIDRRIALYMMYVMGSSPRRLvgAVMLATAFLSMWVSNTATTAMMTPIALGVLTQVLGR 167
                                       ************************************8883246667899*************************995 PP

                     Na_sulph_symp 160 fgsepekq........................................serkigaylmltvvqsasitsiaflTamA 196
                                        +++ + +                                        s  ++   ++l  +++as++++ +l ++ 
  gi|313126001|ref|YP_004036271.1| 168 EEVKAAADdpsadidssvaadsrsedrdsgtssdvasdggladttrsdSFTNLQISMLLGTAYAASVGGVGTLIGTP 244
                                       55544444456666677777777778899999999999999999999877788899999****************** PP

                     Na_sulph_symp 197 pNllllglinsilgveitwasWflaaiptgvillllvplll.yvlyppeikkkeeakavaktelkelGpltarekal 272
                                       pN++l+g++++ilg ei +++W+l+ +p+ ++ l +v++ll + +ypp+i+ +++a   a + l++ Gpl++r k++
  gi|313126001|ref|YP_004036271.1| 245 PNAILAGQLDKILGYEIGFVQWLLIGLPIVIVTLPIVWYLLtFRIYPPKIDDVDDARDEAGRYLRQEGPLSTRGKRV 321
                                       **********************************9999654389********************************* PP

                     Na_sulph_symp 273 lilfvlllllWifge.............................sln...idattvaivvlvillllrvldWkDivk 317
                                       +i+f     lW+ g+                               +   +   +v++ ++  l+l   ++W+    
  gi|313126001|ref|YP_004036271.1| 322 AIIFTATAGLWVLGGlggffsdylpaawattifggkgatvlgveG-HqglLYYVMVGLAAIPALVLADTMEWD--EL 395
                                       *********************999999999999999998887750.2455888999999999999999*****..45 PP

                     Na_sulph_symp 318 qktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAttaallpilla 394
                                           W+t+ll+gg+iala  l ++g  +w++n++ +sl    p ++++ +++l+++  ++++S+tAt ++++pil+ 
  gi|313126001|ref|YP_004036271.1| 396 ADIDWGTILLFGGGIALADALAATGATNWIANTVFGSLT-GAPILLVVGVVVLLIIFLTEMTSNTATASIIVPILIG 471
                                       6789**********************************9.78999999999999999*******************8 PP

                     Na_sulph_symp 395 va....qaipgappllvalll....alatslagfllpyatgpnpivfgagylkvkdywrlGfilsiigllillllga 463
                                       ++    +++ g   + +a+ l    a+a s+a f lp+at+pn+ivfg+gy++++++ r+G+il+++  ++l +l+ 
  gi|313126001|ref|YP_004036271.1| 472 IGgifaTTL-GLAEVSAAIFLsvsgAVAASFA-FALPVATPPNAIVFGSGYIQQEHMMRAGVILNLVMTAVLTVLI- 545
                                       752221344.5556666655512225677888.********************************99888877776. PP

                     Na_sulph_symp 464 lw 465
                                        w
  gi|313126001|ref|YP_004036271.1| 546 -W 546
                                       .2 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.31   2.8e+03      73      89 ..      13      29 ..       6      44 .. 0.63
   2 !   58.7   9.9   5.8e-20   5.2e-16       3     108 ..      52     163 ..      50     173 .. 0.91
   3 !   64.5  22.2     1e-21   9.1e-18     110     284 ..     218     477 ..     214     495 .. 0.79
   4 ?   -0.5   6.2     0.061   5.5e+02     119     168 ..     494     549 ..     475     557 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.31
                                      x.xxxxxxxxxxxxxxxx RF
                            CitMHS 73 d.llvllvlltallsafv 89
                                        l+++ v++tal+ a++
  gi|313126001|ref|YP_004036271.1| 13 LiLFAVAVVGTALI-AVA 29
                                      34555566666666.333 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 5.8e-20
                                       xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            CitMHS   3 llileklrldvvallvlvll.....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd. 73 
                                       l+++++l+l+v+a+ +  +l       ++++al g+a  +i+l+++++++++al++  + +r+a  ++ ++g++++ 
  gi|313126001|ref|YP_004036271.1|  52 LWVTGALPLAVTAISIPFVLtalgvYPDLDTALVGFADHLIFLFIAGFMLANALQKYDIDRRIALYMMYVMGSSPRr 128
                                       899999*******977777777776666666********************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  74 llvllvlltallsafvsndgvvlimipivlslakr 108
                                       l+ +++l+ta+ls++vsn++++++m+pi+l +  +
  gi|313126001|ref|YP_004036271.1| 129 LVGAVMLATAFLSMWVSNTATTAMMTPIALGVLTQ 163
                                       ******************************98766 PP

  == domain 3  score: 64.5 bits;  conditional E-value: 1e-21
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxx RF
                            CitMHS 110 kklppllliplalaaniggaltpiGtpttraaarpglslpnlll.....................lalllvgllplv 165
                                       ++l++++l+  a+aa++gg+ t+iGtp            pn +l                     l++++v l +++
  gi|313126001|ref|YP_004036271.1| 218 TNLQISMLLGTAYAASVGGVGTLIGTP------------PNAILagqldkilgyeigfvqwlligLPIVIVTLPIVW 282
                                       5678899********************............****************9999999988777777554444 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                            CitMHS 166 llfmfgvalalpvnapkvkkqkaiieaiarsllpv.......................................... 200
                                       +l+   ++   p+++ +v++ ++   +  r+  p                                           
  gi|313126001|ref|YP_004036271.1| 283 YLL---TFRIYPPKIDDVDDARDEAGRYLRQEGPLstrgkrvaiiftataglwvlgglggffsdylpaawattifgg 356
                                       444...77888888888888888888888877777889999777777777777777777777777777777777777 PP

                                       ................xxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 201 ................atillla....................ykkveWsvlllfaGvfllvgaleqtGilealadl 241
                                                             +                    +  ++W+++llf+G + l++al +tG  +++a++
  gi|313126001|ref|YP_004036271.1| 357 kgatvlgveghqgllyY-----VmvglaaipalvladtmewdeLADIDWGTILLFGGGIALADALAATGATNWIANT 428
                                       77666666666666662.....0444447777788999*************************************** PP

                                       x.xx..x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                            CitMHS 242 l.ga..g.gplvalalvlgliallsafisnvavaalmapialgmap..a 284
                                       + g+  g ++l+++ +v++li +l+ ++sn+a+a +++pi++g+    a
  gi|313126001|ref|YP_004036271.1| 429 VfGSltGaPILLVVGVVVLLIIFLTEMTSNTATASIIVPILIGIGGifA 477
                                       *9999855777777888888888*******************9866552 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.061
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxx RF
                            CitMHS 119 plalaaniggaltpiGtpttraaarpglslpnlll...................lalllvgllplvllf 168
                                         a+aa+    ++p+ tp            pn ++                   l++++v+ + ++l+f
  gi|313126001|ref|YP_004036271.1| 494 SGAVAASFAF-ALPVATP------------PNAIVfgsgyiqqehmmragvilnLVMTAVLTVLIWLMF 549
                                       3455666665.89*****............999998888888888888777744444444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 3277.21
//
Query:       gi|313126002|ref|YP_004036272.1|  [L=150]
Description: hypothetical protein Hbor_12380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-09   37.2   0.2    3.8e-09   36.9   0.2    1.3  1  DUF4440   Domain of unknown function (DUF4440)
    1.3e-07   31.6   0.0    1.9e-07   31.0   0.0    1.1  1  S6PP_C    Sucrose-6-phosphate phosphohydrolase C-terminal
    0.00072   20.2   1.7     0.0012   19.4   1.5    1.6  1  SnoaL_2   SnoaL-like domain


Domain annotation for each model (and alignments):
>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.2   6.3e-13   3.8e-09      12      98 ..      28     113 ..      14     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.3e-13
                                       HHCT-HHHHHHCEEEEEEEE-TTS-EEEHHHHHHHHHC..CHCEEEEEEEEEEEEEEE.TTEEEEEEEEEEEECCTT CS
                           DUF4440  12 fvagdaealaallapdavlvgpsgtvldkeellealea..gfaagrslelteeevrvl.gdlAvvtgrytfegrgdg 85 
                                        +  +++++a+ l p +++v+p+g+v+ ++ ll+++++  g+a+g s+++++++vr   gd++v+t+r + +++++ 
  gi|313126002|ref|YP_004036272.1|  28 ETDESFARVADALGPAFEMVTPDGEVRKRDPLLDSIRDghGHAPGLSIDVSDVAVRHEdGDTCVLTYREHQTAPEEA 104
                                       4678999*******************************555577788899999999889**********99998876 PP

                                       EEEEEEEEEEEEE CS
                           DUF4440  86 epvegrgrftsvw 98 
                                        +      ++ v+
  gi|313126002|ref|YP_004036272.1| 105 TT----RVSSVVF 113
                                       22....2234444 PP

>> S6PP_C  Sucrose-6-phosphate phosphohydrolase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   3.1e-11   1.9e-07      22     130 ..       7     113 ..       3     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.1e-11
                            S6PP_C  22 pakevVkfyllyekwrrgeveksdevlqklkailapsgvlvhpsGvekslhesidalrklyGdkkgkkfrvWvDrvl 98 
                                         +e+V    ++e+w rge +++de ++++   l p+  +v p G+ ++    +d++r+ +G+  g  + + v +v 
  gi|313126002|ref|YP_004036272.1|   7 CEREIVGLHDFFERWFRGEAPETDESFARVADALGPAFEMVTPDGEVRKRDPLLDSIRDGHGHAPG--LSIDVSDVA 81 
                                       56899999*******************************************************965..7788999** PP

                            S6PP_C  99 ssqigsdswlvkfdkwelsgeerkcclttvll 130
                                       + +   d+++ ++ ++++  ee ++ + +v++
  gi|313126002|ref|YP_004036272.1|  82 VRHEDGDTCVLTYREHQTAPEEATTRVSSVVF 113
                                       *******************9999999999887 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.5   2.1e-07    0.0012      10     101 ..      30     121 ..      14     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.1e-07
                                       TTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEE...EEETTEEEEEEEEEEEEETTSSE CS
                           SnoaL_2  10 agdldalaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdv...vadgdrvavewtvtgtipatgrg 83 
                                       +  ++++a+ + p +++  p ge+r r+ + + +r  + + p+l +++ dv    +dgd+ ++ ++ +    + +++
  gi|313126002|ref|YP_004036272.1|  30 DESFARVADALGPAFEMVTPDGEVRKRDPLLDSIRDGHGHAPGLSIDVSDVavrHEDGDTCVLTYREHQ---TAPEE 103
                                       345799999999***************************************999999****99998875...67777 PP

                                       EEEEEEEEEEEETTEEEE CS
                           SnoaL_2  84 vtvrgvdvfrvrdGkive 101
                                        t r+ +v  vrd  ++e
  gi|313126002|ref|YP_004036272.1| 104 ATTRVSSVVFVRDSAVTE 121
                                       777888888888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 932.65
//
Query:       gi|313126003|ref|YP_004036273.1|  [L=902]
Description: DNA/RNA helicase, superfamily i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-41  140.6   0.0    7.6e-41  139.9   0.0    1.3  1  AAA_12           AAA domain
    5.4e-38  131.3   0.0    5.2e-19   69.0   0.1    2.9  3  AAA_11           AAA domain
    2.2e-19   69.9   3.6    1.5e-18   67.2   1.1    2.6  2  AAA_30           AAA domain
    1.5e-18   67.3   0.0    3.5e-16   59.6   0.0    2.2  2  Dna2             DNA replication factor Dna2
    2.7e-15   57.0   0.1    4.8e-14   52.9   0.1    2.8  2  AAA_19           AAA domain
    1.2e-12   48.3   0.1    3.5e-12   46.8   0.0    1.8  2  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    4.9e-11   42.8   0.0     0.0033   17.2   0.0    3.2  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    1.4e-05   24.8   0.0    3.5e-05   23.5   0.0    1.5  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    1.6e-05   25.1   0.0    0.00021   21.4   0.0    2.4  2  Cas_Cas4         Domain of unknown function DUF83
    1.7e-05   24.5   0.0    3.8e-05   23.4   0.0    1.7  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    3.2e-05   24.2   0.0    0.00033   20.9   0.0    2.6  3  AAA_22           AAA domain
    0.00015   22.2   1.7     0.0004   20.8   0.3    2.6  1  AAA_16           AAA ATPase domain
    0.00015   21.1   0.2    0.00063   19.1   0.0    2.0  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00019   21.5   0.0    0.00032   20.7   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit
     0.0018   18.2   0.0     0.0048   16.8   0.0    1.7  1  Helicase_RecD    Helicase
     0.0033   17.9   0.0     0.0074   16.7   0.0    1.6  1  AAA              ATPase family associated with various cellul
     0.0083   15.3   0.0       0.27   10.4   0.0    2.1  2  PIF1             PIF1-like helicase
  ------ inclusion threshold ------
      0.015   15.8   0.1       0.14   12.6   0.0    2.6  2  YflT             Heat induced stress protein YflT
      0.017   14.6   0.0       0.13   11.7   0.0    2.2  1  PhoH             PhoH-like protein
      0.025   14.6   0.0       0.25   11.3   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
      0.034   13.9   0.0      0.079   12.7   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.037   13.4   0.0      0.082   12.3   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.05   13.1   0.0      0.094   12.2   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.058   13.1   0.0       0.12   12.1   0.0    1.5  1  AAA_24           AAA domain
      0.061   12.9   0.0       0.42   10.2   0.0    2.4  2  AAA_25           AAA domain
      0.061   13.5   0.0       0.23   11.6   0.0    2.0  1  AAA_33           AAA domain
      0.072   12.7   0.0       0.19   11.3   0.0    1.7  1  SRP54            SRP54-type protein, GTPase domain
      0.077   12.0   0.0       0.15   11.1   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
       0.14   11.9   0.0       0.32   10.7   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.0   1.2e-43   7.6e-41       1     198 [.     701     884 ..     701     885 .. 0.89

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 1.2e-43
                            AAA_12   1 lerSlferllkkekekvvlLdtqYRmhpeIsrfpsklfYkgkLkdae.svkkrele....aqealeeplep.lvfid 71 
                                       l++Slferl+++++e++v+Ld qYRm ++I  f+s +fY+g+L+ a+ +v+ ++l+     ++al+epl+  ++fid
  gi|313126003|ref|YP_004036273.1| 701 LQQSLFERLIDAAPEASVMLDRQYRMSQRIQAFSSAEFYDGALRPATgEVAAQRLSdlgvDESALPEPLRDpVAFID 777
                                       589*****************************************9998666666666777566666665544****9 PP

                            AAA_12  72 vekseeekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntv 148
                                        ++s+          +N+ Eae v++lve+++++g+e   ++igvi+p+raqv  + k+ +          ++v+tv
  gi|313126003|ref|YP_004036273.1| 778 PNGSRVG-------NTNPVEAERVAELVETFVAAGVEP--DDIGVIAPFRAQVAEIGKRTD----------VTVDTV 835
                                       9866544.......469********************9..****************99988..........99**** PP

                            AAA_12 149 dgfQGrekdviilslVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                       d+fQG+ k+v+i+s+V s +     +++d rr+NValTRAk++l++vG++
  gi|313126003|ref|YP_004036273.1| 836 DRFQGSSKEVVIVSFVASGTLDG-PIFEDHRRINVALTRAKKSLVLVGDA 884
                                       ****************9965544.48**********************96 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0     1e-18   6.5e-16       3     111 ..     532     622 ..     530     628 .. 0.95
   2 !   69.0   0.1   8.4e-22   5.2e-19     191     258 ..     631     695 ..     621     698 .. 0.93
   3 ?   -1.3   0.0       2.5   1.5e+03     236     252 ..     869     885 ..     867     889 .. 0.82

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1e-18
                            AAA_11   3 ndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrgll 79 
                                       nd q+ea+k a+  ++++l++GPPGtgKT ti+ ++++l          + ++r+L++a +N AvD+ le l +   
  gi|313126003|ref|YP_004036273.1| 532 NDAQNEAVKLAVDAEDFALVHGPPGTGKTYTIARIVRAL---------VADGNRVLLSAFTNRAVDNALEALRD--- 596
                                       99*************************************.........799********************999... PP

                            AAA_11  80 dsegekykpkivRvgneeeriseavksvslee 111
                                            +   + vRvg e+  i+e++++++l++
  gi|313126003|ref|YP_004036273.1| 597 -----QGFADAVRVGTEN-GIREDMQDLHLKT 622
                                       .....77799********.99***99999886 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 8.4e-22
                            AAA_11 191 evldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpatv 258
                                         l++a +v++T s++gs++++++   fdv ++DEA+q +Ep tl ++ ++  ++vLvGD+ QLp++v
  gi|313126003|ref|YP_004036273.1| 631 AELTDAPVVAATTSSCGSRVMREQ--SFDVALVDEASQLTEPGTLAAINRA-DRFVLVGDHEQLPPVV 695
                                       67999*******************..8*********************999.***************9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.5
                            AAA_11 236 iPlrlgakkvvLvGDpk 252
                                       ++l ++ k +vLvGD +
  gi|313126003|ref|YP_004036273.1| 869 VALTRAKKSLVLVGDAN 885
                                       578888899******86 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   1.1   2.4e-21   1.5e-18       3     177 ..     532     746 ..     530     757 .. 0.78
   2 ?    2.1   0.1      0.22   1.4e+02      47      95 ..     809     849 ..     793     890 .. 0.58

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 2.4e-21
                            AAA_30   3 naeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.La............... 63 
                                       n+ Q +av+ ++  +d +a+++Gp+GtGKt++++ +++a+ a+g rv++ A t++a ++ L+               
  gi|313126003|ref|YP_004036273.1| 532 NDAQNEAVKLAVDAED-FALVHGPPGTGKTYTIARIVRALVADGNRVLLSAFTNRAVDNaLEalrdqgfadavrvgt 607
                                       789*****99999998.*****************************************9666666666666666665 PP

                            AAA_30  64 .............eelgieastiakllkrlk............grarlepg.tllivDEagmvdtkqlaallkaaek 114
                                                    + +g + +++a+l+   +            +r+  e++ ++ +vDEa+ +    + a +++a++
  gi|313126003|ref|YP_004036273.1| 608 engiredmqdlhlKTTGDPNDRVAELT---DapvvaattsscgSRVMREQSfDVALVDEASQLTEPGTLAAINRADR 681
                                       555544444444435555555555555...1455999999998555566668***************9999999977 PP

                            AAA_30 115 agakvilvGDerQlasVeaG......gvlrdlveaagigtaeLtevvRqkeseeraaalalregdaeea 177
                                            +lvGD++Ql++V +       ++++ l++aa   ++ L+  +R+++  ++  + ++ +g  + a
  gi|313126003|ref|YP_004036273.1| 682 ----FVLVGDHEQLPPVVRAendlqqSLFERLIDAAPEASVMLDRQYRMSQRIQAFSSAEFYDGALRPA 746
                                       ....*************875222222689999999999***********99888888888888877644 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.22
                            AAA_30  47 grviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivD 95 
                                        ++ ++Ap  ++ +++++ ++++ +t++++  + k        +++iv 
  gi|313126003|ref|YP_004036273.1| 809 DDIGVIAPFRAQVAEIGKRTDVTVDTVDRFQGSSK--------EVVIVS 849
                                       66778999999999999999999999999996666........233332 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   5.7e-19   3.5e-16       8     157 ..      59     207 ..      52     213 .. 0.88
   2 ?    5.6   0.0      0.02        12     182     199 ..     213     230 ..     208     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 5.7e-19
                              Dna2   8 ktvvLrddWaets..vekgdiihivgkfeeek....iiidnesnllIlhPdlLvsaTsvanslsClRravLqerlkv 78 
                                        +v+L+++W++t    e+g+ + +++  e+e     +  + ++ +++l+Pd+Lv  T + + ++C+R  +L++   +
  gi|313126003|ref|YP_004036273.1|  59 VRVTLWGKWTHTAdlAEPGMDLLVTDAEESEYrgepTYSTAKESYVVLEPDFLVDVTDIRSWVQCPRMYYLNKLSGI 135
                                       6799*****999888999*9999955444333577778888999*****************************9988 PP

                              Dna2  79 sgesskamliGtilHelfqkalleeeldkekleelldklleknleelyalglteeeakeeikekleeiekwakkyvk 155
                                         + + +++ Gti+He+f ++l+      ++l++++++ + +   +l  lg + +e+++e+++++ +ie w+ + + 
  gi|313126003|ref|YP_004036273.1| 136 --PLNYPVVKGTIVHEVFGDLLRG-----RDLDDAIEERVAEAGLQLGLLGYDATEVEDEVRRNAAAIEGWLAQGTL 205
                                       ..68******************87.....89999*************************************998766 PP

                              Dna2 156 ks 157
                                       ++
  gi|313126003|ref|YP_004036273.1| 206 TE 207
                                       55 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
                              Dna2 182 iEEniwspkyGLKGkiDa 199
                                        E +++sp++G+KG+ Da
  gi|313126003|ref|YP_004036273.1| 213 SEYTLISPTFGIKGRADA 230
                                       68889************9 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.1   7.8e-17   4.8e-14       1     145 [.     535     695 ..     535     696 .. 0.70
   2 ?    0.6   0.0       1.1   6.5e+02     124     124 ..     870     870 ..     791     890 .. 0.54

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 7.8e-17
                            AAA_19   1 qreave.alk.ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae....... 68 
                                       q+eav+ a+  e+  lv ++pGtGKT+++  iv+ lv+ g    +++ll aft+rA+++  e+l+  g +       
  gi|313126003|ref|YP_004036273.1| 535 QNEAVKlAVDaEDFALVHGPPGTGKTYTIARIVRALVADG----NRVLLSAFTNRAVDNALEALRDQGFAdavrvgt 607
                                       78999876651678999***********************....89******************7766557777666 PP

                            AAA_19  69 .......atTiHrlal..........ldfddlltealelle.........eaeeekklqeee..llivDEfqdvd.e 116
                                               + +H   l                       l          ++  ++ ++e+   + +vDE+++++ +
  gi|313126003|ref|YP_004036273.1| 608 engiredMQDLH---LkttgdpndrvA-----------ELTdapvvaattSSCGSRVMREQSfdVALVDEASQLTeP 670
                                       666666644444...022233333321...........2224445555552233333433333599*******9945 PP

                            AAA_19 117 lqyrLlkallgekkklllvGDpdQliyvf 145
                                            l a+  ++++++lvGD++Ql++v 
  gi|313126003|ref|YP_004036273.1| 671 G---TLAAIN-RADRFVLVGDHEQLPPVV 695
                                       4...467777.6778***********985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                            AAA_19 124 a 124
                                       a
  gi|313126003|ref|YP_004036273.1| 870 A 870
                                       3 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   5.7e-15   3.5e-12       4     254 ..     114     344 ..     113     345 .. 0.67
   2 ?   -2.4   0.2       5.9   3.7e+03      86     112 ..     376     401 ..     359     429 .. 0.46

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 5.7e-15
                          PDDEXK_1   4 vsrletfleCplrfflryllglreeeeleapdlGtlvHaaleefyewkkldkedleelleeaveelwpellleeeil 80 
                                       v+ ++ + +Cp+ ++l++l g++ ++ + +   Gt+vH+++ ++ +     ++dl++ +ee v+e+    +l+  +l
  gi|313126003|ref|YP_004036273.1| 114 VTDIRSWVQCPRMYYLNKLSGIPLNYPVVK---GTIVHEVFGDLLR-----GRDLDDAIEERVAEA----GLQLGLL 178
                                       6889999***************98999999...********98888.....446666664444444....4444442 PP

                          PDDEXK_1  81 essarlrylaeklkevleklverlaeeleakrg.....frpvalel..efggekvrLkGriDrvddkegelriiDyK 150
                                             +y+a ++++ +++ + +++ +l++ +      +r +   +   fg     +kGr D + +       ++ K
  gi|313126003|ref|YP_004036273.1| 179 ------GYDATEVEDEVRRNAAAIEGWLAQGTLteedeWRSEYTLIspTFG-----IKGRADALRRGMP----VELK 240
                                       ......444444433333333333333333333221136655555544566.....********86666....**** PP

                          PDDEXK_1 151 tgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeel...eallqe 224
                                       tg++ ++++   + ++ +Q ++Y+l+l e      +++ + +ly +   + ++ +e+      +++e+   + ll+ 
  gi|313126003|ref|YP_004036273.1| 241 TGKNLKRDP---RFQDKIQAAAYALVLDER--GV-PANTGTLLYTKN--TALERHEESGDL-SPAKEFsigNGLLEF 308
                                       ***665554...6999************99..33.333777777766..444433333333.444555569999999 PP

                          PDDEXK_1 225 leelaeeilagefparpskk......CeyCpyksvC 254
                                       + ++ +ei+a ef+ +  +       CeyC  ++ C
  gi|313126003|ref|YP_004036273.1| 309 VVRTRNEIAAMEFDTAVPTGfeadanCEYCFEQDTC 344
                                       99999999988887776655677899****777766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                          PDDEXK_1  86 lrylaeklkevleklverlaeeleakr 112
                                       +r + e+ +e+ +++ ++l+e+ +a+r
  gi|313126003|ref|YP_004036273.1| 376 YRAIEEERRETHAEY-RKLWEQSAAER 401
                                       233344444444444.22222222222 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0013      0.78       2      30 ..     550     577 ..     549     602 .. 0.73
   2 !   17.2   0.0   5.3e-06    0.0033      55     118 ..     648     709 ..     617     743 .. 0.79
   3 !   12.3   0.0   0.00016       0.1     174     233 ..     822     881 ..     780     882 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrp 30 
                                       +vhG pG GK+  i +++r  l+   nr 
  gi|313126003|ref|YP_004036273.1| 550 LVHGPPGTGKTYTIARIVRA-LVADGNRV 577
                                       7*****************99.44444444 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.3e-06
                   Viral_helicase1  55 malvkstkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasfllahlpssl 118
                                       +  ++++++++ ++DE+ +l+  +   laa+++a+ ++l+GD++Q p   r+++ l  +l+ +l
  gi|313126003|ref|YP_004036273.1| 648 SRVMREQSFDVALVDEASQLT--EPGTLAAINRADRFVLVGDHEQLPPVVRAENDLQQSLFERL 709
                                       444555789**********99..6888999*****************99998876666666555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00016
                   Viral_helicase1 174 qalkealgvr...evttvhevqGltfdkVtl..vllketdlelisesrenllvAlTRhrkslvil 233
                                       ++     g r    v tv   qG++ ++V++  v + + d  ++ e++    vAlTR++kslv++
  gi|313126003|ref|YP_004036273.1| 822 AE----IGKRtdvTVDTVDRFQGSSKEVVIVsfVASGTLDGPIF-EDHRRINVALTRAKKSLVLV 881
                                       33....3333444499*******999987652155544444444.56999************986 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   5.7e-08   3.5e-05       2     153 ..     532     724 ..     531     756 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.7e-08
                                       SHHHHHHHHS...-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH........ CS
                     UvrD-helicase   2 npeqreaias...lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee........ 67 
                                       n+ q+ea++     +   lv   +G+GKT+++a  +  l++ +    +r+l++ FTn+A +   e ++         
  gi|313126003|ref|YP_004036273.1| 532 NDAQNEAVKLavdAEDFALVHGPPGTGKTYTIARIVRALVADG----NRVLLSAFTNRAVDNALEALRDqgfadavr 604
                                       677888888775456678999***********98888888888....9*************9999999999999888 PP

                                       .........HHHHCCHHCTT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT..................SHTT CS
                     UvrD-helicase  68 .........alkkaeqessdderlrlalqnlseanisTlHsfcqkilkkeanrig..................ldpn 117
                                                +++    ++ +d   r a+ +   +   T  s ++++++++ +++                   +  +
  gi|313126003|ref|YP_004036273.1| 605 vgtengireDMQDLHLKTTGDPNDRVAELTDAPVVAATTSSCGSRVMREQSFDVAlvdeasqltepgtlaainRADR 681
                                       86666555533333333333335566666666777777777778888877777776555555555555555543333 PP

                                       TEEECHHHHH.......HCCHHHHHHHHHSCHSHTTTTHHHHH CS
                     UvrD-helicase 118 frildeedee.......dlkqqellkelleksaddslnldkkk 153
                                       f +  ++++           qq+l+++l+++++++s+ ld + 
  gi|313126003|ref|YP_004036273.1| 682 FVLVGDHEQLppvvraeNDLQQSLFERLIDAAPEASVMLDRQY 724
                                       3333333322555555544466777777776666666666655 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.79   4.9e+02       2      39 ..     114     149 ..     113     175 .. 0.80
   2 !   21.4   0.0   3.4e-07   0.00021      35     115 ..     204     286 ..     183     346 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.79
                          Cas_Cas4   2 gtkiqyyliCkrklwlish.eitleensetvelGkllhe 39 
                                       +t+i++++ C+r  +l +  +i l+     v+ G ++he
  gi|313126003|ref|YP_004036273.1| 114 VTDIRSWVQCPRMYYLNKLsGIPLNYP--VVK-GTIVHE 149
                                       6899***********998867777666..444.999998 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3.4e-07
                          Cas_Cas4  35 kllheesyerekkevelse....sikiDvvekekeklvvvEvKkskkk....eeaaklQllyYlllLekkgveikeG 103
                                        l +e++ + e + ++       +++ D ++    + ++vE+K +k+     + ++k+Q  +Y+l+L+++gv +++G
  gi|313126003|ref|YP_004036273.1| 204 TLTEEDEWRSEYTLIS--PtfgiKGRADALR----RGMPVELKTGKNLkrdpRFQDKIQAAAYALVLDERGVPANTG 274
                                       3333333333333333..2345689999999....89999***999984333445799******************* PP

                          Cas_Cas4 104 vleypkekkree 115
                                        l y k+   e+
  gi|313126003|ref|YP_004036273.1| 275 TLLYTKNTALER 286
                                       *****9887765 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   6.1e-08   3.8e-05       2      52 .]     830     881 ..     829     881 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.1e-08
                          UvrD_C_2   2 ayaltihkaQGsefpaVivfdpdlaaarmgel...rrrlLYtavTRAreklilv 52 
                                       ++++t+ ++QGs  ++Viv  +   + ++       +r + +a+TRA++ l+lv
  gi|313126003|ref|YP_004036273.1| 830 VTVDTVDRFQGSSKEVVIVSFVASGTLDG--PifeDHRRINVALTRAKKSLVLV 881
                                       789****************5444333333..14569****************98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.5   2.8e+03      51      91 ..     366     403 ..     352     410 .. 0.69
   2 !   20.9   0.0   5.4e-07   0.00033       5     112 ..     546     676 ..     543     704 .. 0.74
   3 ?   -2.0   0.0       6.5     4e+03      81     113 ..     866     901 ..     863     902 .] 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.5
                            AAA_22  51 tsskdllrellralglelkaerlsseellealeqalrarav 91 
                                       ++ ++ + ++ ra+++e+ +   +  e++++ eq + +ra+
  gi|313126003|ref|YP_004036273.1| 366 EDEREYFDRIYRAIEEERRE---THAEYRKLWEQSAAERAD 403
                                       45567777888888877777...777777777777666665 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.4e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..................erpevv.fvtlpsstsskdllrellr 62 
                                       + + +v+G++GtGKT++++r+++ l+++ +  +                  ++ +++  v +  +++ ++ +++l  
  gi|313126003|ref|YP_004036273.1| 546 EDFALVHGPPGTGKTYTIARIVRALVADGN--RvllsaftnravdnalealRDQGFAdAVRVGTENGIREDMQDLHL 620
                                       56899********************76544..255888888888888888777777788888888888888888887 PP

                            AAA_22  63 alglelka..erlsseellealeqalrarav....ielliiDEaqhlrseealeeL 112
                                       +++ + ++  ++l+   +++a +  + +r +      + ++DEa  l+++  l  +
  gi|313126003|ref|YP_004036273.1| 621 KTTGDPNDrvAELTDAPVVAATTSSCGSRVMreqsFDVALVDEASQLTEPGTLAAI 676
                                       77777777787777777777777777777777877799999999999524444333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.5
                            AAA_22  81 aleqalraravielliiDEaqhlrs....eealeeLr 113
                                       +++ al ++++ +l+++ +a  l s    +++le+ r
  gi|313126003|ref|YP_004036273.1| 866 RINVALTRAKK-SLVLVGDANALESdpfyARMLEWAR 901
                                       67778888888.9999999999963568888888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.3   6.5e-07    0.0004      26     107 ..     548     635 ..     536     856 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.5e-07
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                         l++G++G+GK+  + ++ ral +dg  +l   ++      + +  ++al r++ +++  +  +++  +++ + l+
  gi|313126003|ref|YP_004036273.1| 548 FALVHGPPGTGKTYTIARIVRALVADGNRVLLSAFTNR----AVDNALEAL-RDQGFADAVRVGTENGIREDMQDLH 619
                                       679***********************877755555555....233378888.7777777777744444444444444 PP

                            AAA_16 103 eala...........a 107
                                         ++           +
  gi|313126003|ref|YP_004036273.1| 620 LKTTgdpndrvaeltD 635
                                       4444355554443430 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     1e-06   0.00063       4     171 ..     549     727 ..     546     737 .. 0.58
   2 ?   -1.8   0.1       2.3   1.4e+03     345     359 ..     866     880 ..     864     882 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                           DUF2075   4 vlVtGvaGtGKtvvllnllael........................eddeeertavylsvNhplvlvlrealakkee 56 
                                        lV+G +GtGKt+   +++ +l                        +d+     + + + N+   +    +l+ +  
  gi|313126003|ref|YP_004036273.1| 549 ALVHGPPGTGKTYTIARIVRALvadgnrvllsaftnravdnalealRDQGFADAVRVGTENGIREDMQDLHLKTTGD 625
                                       69********************6555555555544444333332211111222222222222222222222222222 PP

                           DUF2075  57 kkkkkeafeklssfinnlsef..............kkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkel 119
                                       ++++                               ++  +  +e+ +dv++vDEA  l++          +  l   
  gi|313126003|ref|YP_004036273.1| 626 PNDR----------------VaeltdapvvaattsSCGSRVMREQSFDVALVDEASQLTE----------PGTLA-A 675
                                       2222................0222223333344447999999****************99..........44454.5 PP

                           DUF2075 120 mkrakvvvalvDegQ...elntgeigteeelkklakkleveleekvhLksqfRva 171
                                       ++ra+  v++ D++Q   +++ ++  +++ +++l++  +++    v L++q+R++
  gi|313126003|ref|YP_004036273.1| 676 INRADRFVLVGDHEQlppVVRAENDLQQSLFERLIDAAPEAS---VMLDRQYRMS 727
                                       566777788888888555566666666666777666666665...6799999984 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.3
                           DUF2075 345 ayrVLLtRGrkGlyi 359
                                       +++V LtR+ k l++
  gi|313126003|ref|YP_004036273.1| 866 RINVALTRAKKSLVL 880
                                       68**********998 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   5.2e-07   0.00032      22     153 ..     544     676 ..     523     686 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.2e-07
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG.............GGGTGG....G CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef.............kkflseaykei 85 
                                       + +  +l++ + GtGKT+++a+++++l   g+  ++l+ + ++  ++ +le++             ++ + e+ ++ 
  gi|313126003|ref|YP_004036273.1| 544 DAEDFALVHGPPGTGKTYTIARIVRALVADGN--RVLLSAFTNRAVDNALEALrdqgfadavrvgtENGIREDMQDL 618
                                       4566789999*******************977..9***************999555555555555333333333335 PP

                                       EEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH CS
                            ResIII  86 gkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei 153
                                         k++gd +++   + t++ ++ +t++s  ++          +++++fdv ++DEa  l++  +  +i
  gi|313126003|ref|YP_004036273.1| 619 HLKTTGDPNDR-VAELTDAPVVAATTSSCGSRV---------MREQSFDVALVDEASQLTEPGTLAAI 676
                                       55577777777.999999999999999999999.........89999********9888885455554 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.7e-06    0.0048       2     119 ..     551     684 ..     550     687 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.7e-06
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke...eekkkkaekaelrvr... 72 
                                       + + +G+GK+ +++ ++ al+a+g+ ++l++a ++++v++ +e l+ +  a  ++    +  +++ ++ +l++    
  gi|313126003|ref|YP_004036273.1| 551 VHGPPGTGKTYTIARIVRALVADGN-RVLLSAFTNRAVDNALEALRDQGFADAVRVgteNGIREDMQDLHLKTTgdp 626
                                       67889******************97.9***************99976543333333445333333333334433556 PP

                     Helicase_RecD  73 kqrieyiapdellklkeqa...........dllvvDEAAaiplpllkkllekfkrvvl 119
                                       + r+  ++   ++++++++           d+ +vDEA+++  p   + +++ +r+vl
  gi|313126003|ref|YP_004036273.1| 627 NDRVAELTDAPVVAATTSScgsrvmreqsfDVALVDEASQLTEPGTLAAINRADRFVL 684
                                       333333333333332222245556666666*********9988877777767776665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.2e-05    0.0074       2      39 ..     550     587 ..     549     607 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSST CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyv 39 
                                       l++GppGtGKT+++  +++ l ++  ++ +s +++  v
  gi|313126003|ref|YP_004036273.1| 550 LVHGPPGTGKTYTIARIVRALVADGNRVLLSAFTNRAV 587
                                       89************999999866655555555555555 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00044      0.27      22      59 ..     546     583 ..     531     591 .. 0.82
   2 ?    2.5   0.0       0.1        64     144     163 ..     682     701 ..     679     728 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                                       TS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESS CS
                              PIF1  22 gklfFvtGsgGtgKtflwkallkklrsegkivlavAss 59 
                                         +  v+G  GtgKt+   +++ +l + g+ vl  A +
  gi|313126003|ref|YP_004036273.1| 546 EDFALVHGPPGTGKTYTIARIVRALVADGNRVLLSAFT 583
                                       4567899**************************99987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                                       EEEE--TTS-----SSSSS- CS
                              PIF1 144 vvlgGDfrQilPviekgsra 163
                                        vl GD  Q++Pv++  +  
  gi|313126003|ref|YP_004036273.1| 682 FVLVGDHEQLPPVVRAENDL 701
                                       599***********876654 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       8.3   5.1e+03      33      59 ..     623     649 ..     596     657 .. 0.69
   2 ?   12.6   0.0   0.00023      0.14       8      58 ..     792     843 ..     790     855 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.3
                              YflT  33 dkdrlerlaentdaetettseeglwds 59 
                                         d  +r+ae tda ++ +++++ +++
  gi|313126003|ref|YP_004036273.1| 623 TGDPNDRVAELTDAPVVAATTSSCGSR 649
                                       345588889999988888777655554 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00023
                              YflT   8 eellsaieelkaeGyneddiyvvakdkdrlerlaentdaetettse.eglwd 58 
                                       e + + +e++ a+G++ ddi v+a  ++++ ++ ++td+ ++t    +g+ +
  gi|313126003|ref|YP_004036273.1| 792 ERVAELVETFVAAGVEPDDIGVIAPFRAQVAEIGKRTDVTVDTVDRfQGSSK 843
                                       5678889**********************************99865654444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.13       6      39 ..     532     565 ..     529     723 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                       SHHHHHHHHHHH.H-SEEEEE--TTSSTTHHHHHH CS
                              PhoH   6 tkeQkeylealk.kndivfaiGpaGtGKtylaval 39 
                                       + +Q+e+++    ++d+  + Gp GtGKty   a 
  gi|313126003|ref|YP_004036273.1| 532 NDAQNEAVKLAVdAEDFALVHGPPGTGKTYTI-AR 565
                                       667888887554499***************53.33 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00041      0.25       3      37 ..     550     584 ..     549     597 .. 0.84
   2 ?   -0.0   0.0       1.3   8.1e+02      33      78 ..     612     668 ..     607     708 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                                       EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT-- CS
                             AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtt 37 
                                       l+ GppGtgK+  + r+ +al +  + v+l+++t+
  gi|313126003|ref|YP_004036273.1| 550 LVHGPPGTGKTYTIARIVRALVADGNRVLLSAFTN 584
                                       578******************77777777777665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                                       -TT--HHHHH--B--.........--------...........G-SEEEEESGGG-- CS
                             AAA_5  33 trdtteedlkgrreikngttslvdsplvraar...........egeilvlDEverae 78 
                                       ++d++  +lk   +++++ ++l+d p+v a +           + +++++DE  ++ 
  gi|313126003|ref|YP_004036273.1| 612 REDMQDLHLKTTGDPNDRVAELTDAPVVAATTsscgsrvmreqSFDVALVDEASQLT 668
                                       567777788888888899999999999966668888888777777777777776655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013     0.079      44      82 ..     543     581 ..     515     605 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvr 82 
                                       +++++  ++ Gp+G+GK++  + + ++ v++g +vl   
  gi|313126003|ref|YP_004036273.1| 543 VDAEDFALVHGPPGTGKTYTIARIVRALVADGNRVLLSA 581
                                       6777888999************************98654 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.082       7      48 ..     531     572 ..     526     597 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                      Mg_chelatase   7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpp 48 
                                        ++++++a+++a+  +   l+ GppG+GKt  ++r+   l +
  gi|313126003|ref|YP_004036273.1| 531 NNDAQNEAVKLAVDAEDFALVHGPPGTGKTYTIARIVRALVA 572
                                       5677889***********************988877665554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015     0.094      26      73 ..     539     586 ..     529     597 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                             AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqt 73 
                                       ++l ++++   l+ Gp GtGKt +i +++++l  +   +l   f+++ 
  gi|313126003|ref|YP_004036273.1| 539 VKLAVDAEDFALVHGPPGTGKTYTIARIVRALVADGNRVLLSAFTNRA 586
                                       67888899999*******************999888888777777665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.12       6      35 ..     550     578 ..     548     680 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                            AAA_24   6 liyGpsgiGKTtlakelgpkplfidtekGl 35 
                                       l+ Gp+g+GKT++++++  ++l+ d ++ l
  gi|313126003|ref|YP_004036273.1| 550 LVHGPPGTGKTYTIARI-VRALVADGNRVL 578
                                       789**************.999998766544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.1   1.9e+03      62     119 ..      66     129 ..      56     136 .. 0.79
   2 ?   10.2   0.0   0.00068      0.42      22      63 ..     535     577 ..     519     632 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.1
                            AAA_25  62 pwlg..pvapeqgkVlyvsaEdsedelrrRlravgeal...rddarllvldlagv.eslpLfak 119
                                       +w++  ++a   +  l+ +aE+se + ++ ++ + e +   ++d  ++v+d+ ++ ++ +++++
  gi|313126003|ref|YP_004036273.1|  66 KWTHtaDLAEPGMDLLVTDAEESEYRGEPTYSTAKESYvvlEPDFLVDVTDIRSWvQCPRMYYL 129
                                       3666677777788899999999999999999999999989888888899999998888888876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00068
                            AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpw 63 
                                       ++  vk  + a+++al+ G+pgtGKt     ++ a++  G  +
  gi|313126003|ref|YP_004036273.1| 535 QNEAVKLAVDAEDFALVHGPPGTGKTYTIARIVRALVaDGNRV 577
                                       566777778999**************99988888766566655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00036      0.23       3      25 ..     550     574 ..     549     624 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
                            AAA_33   3 llvGlpGsGKstlaerllkklg..a 25 
                                       l++G+pG+GK++ + r++++l   +
  gi|313126003|ref|YP_004036273.1| 550 LVHGPPGTGKTYTIARIVRALVadG 574
                                       78***************99987664 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.19       4      37 ..     549     582 ..     546     616 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEE CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvllvaa 37 
                                        l+ G+ G+GKT t+a++ + l ++g++vll a 
  gi|313126003|ref|YP_004036273.1| 549 ALVHGPPGTGKTYTIARIVRALVADGNRVLLSAF 582
                                       5889**************************9885 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.15     114     161 ..     531     578 ..     468     581 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                             T2SSE 114 lkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                       ++++++e+++ av ++   lv G+ g+GKt ++  ++  + ++ +r++
  gi|313126003|ref|YP_004036273.1| 531 NNDAQNEAVKLAVDAEDFALVHGPPGTGKTYTIARIVRALVADGNRVL 578
                                       4588999*************************9999999988866665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00052      0.32      24      55 ..     537     569 ..     526     592 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                            RuvB_N  24 eaakkreealdhvllyGpPGlGkt.tlakiiak 55 
                                       ea k   +a d  l++GpPG Gkt t+a+i+ +
  gi|313126003|ref|YP_004036273.1| 537 EAVKLAVDAEDFALVHGPPGTGKTyTIARIVRA 569
                                       5666777899*************9889999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (902 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.84u 0.34s 00:00:01.18 Elapsed: 00:00:00.51
# Mc/sec: 5325.18
//
Query:       gi|313126004|ref|YP_004036274.1|  [L=184]
Description: hypothetical protein Hbor_12400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.2   11.8   0.2         18    5.5   0.1    2.3  2  HHH_2     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0    0.0034        61      39      51 ..      59      71 ..      52      75 .. 0.83
   2 ?    5.5   0.1   0.00098        18      18      44 ..     154     180 ..     153     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0034
                             HHH_2 39 evddiGeeiAqsi 51
                                      ev+++G ++A+ i
  gi|313126004|ref|YP_004036274.1| 59 EVRGVGSRVARRI 71
                                      7889999999888 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.00098
                             HHH_2  18 lLakrFksldaLkkasleeLlevddiG 44 
                                       +L  +F + d+L + +l++L+e d++G
  gi|313126004|ref|YP_004036274.1| 154 DLTDEFSDADELLTEDLDDLIEDDGVG 180
                                       6899*********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1135.52
//
Query:       gi|313126005|ref|YP_004036275.1|  [L=430]
Description: erythromycin esterase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-63  215.8   0.6    1.7e-63  215.6   0.6    1.0  1  Erythro_esteras  Erythromycin esterase
  ------ inclusion threshold ------
      0.077   12.4   0.0       0.12   11.8   0.0    1.2  1  DUF1460          Protein of unknown function (DUF1460)
       0.11   10.8   3.2       0.15   10.3   3.2    1.1  1  Atrophin-1       Atrophin-1 family
       0.45   10.5   4.2       0.79    9.7   4.2    1.3  1  DUF3915          Protein of unknown function (DUF3915)
        2.5    7.7   7.3        6.4    6.5   7.3    1.7  1  BRD4_CDT         C-terminal domain of bromodomain protein 4


Domain annotation for each model (and alignments):
>> Erythro_esteras  Erythromycin esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.6   0.6   4.6e-67   1.7e-63       1     343 [.      65     422 ..      65     423 .. 0.87

  Alignments for each domain:
  == domain 1  score: 215.6 bits;  conditional E-value: 4.6e-67
                                       HHHC---EEEEEEEHHHHHHHHHHHHHS-S-GGGT....S-CCC-CHHHHHHHHHHHHHHHSTT-SS--EEEEEE-S CS
                   Erythro_esteras   1 veehGfrtvalEadwpdalrvdryvrggtgdaeea.krfptwmWrneevlelveWlReyNagrpkkervrfyGlDlq 76 
                                       ve++Gfrt+a+Ea+++++l+ d+yv +g+g+ e+a +++ +w W++++v el++WlR++N+gr+ ++rvr+ G+Dl 
  gi|313126005|ref|YP_004036275.1|  65 VERRGFRTLAIEAGLTATLAADDYVFEGRGTTETAlRELDKWQWQSAAVGELLQWLRSFNEGRSPDDRVRIRGIDLN 141
                                       89**********************************99*************************************** PP

                                       ---HHHHHHHHHHHHCH.CCCCHHHHHHHCCHGGC.S........TSSCCCCCHHHHHHHHHHHH..CCHGGG.... CS
                   Erythro_esteras  77 slresldavldyLakvd.pelagaareryaclapl.adp..raarsaeaaelrscedevvallke..llakreeyaa 147
                                        +++ +d++ +  ++ d p   +++ +++a+la+  + p  ++ r+a ++  r+++d +   ++   + ++++   +
  gi|313126005|ref|YP_004036275.1| 142 DPSKPADRLQSSFERLDlPWVGADDMAAIAALADSpTGPvgEKRREAAVNAVRAVQDGLSDGHAVdsTGEREQ---E 215
                                       ****************878888888888888877753335555555556667777777744433322333222...2 PP

                                       .GG.TSHHHHHHHHHHHHHHHHHHHC...CSSSSSCHHHHHHHHHHHHHHHHHHHH...HHSSEEEEEEHHHHSSS- CS
                   Erythro_esteras 148 edg.eaeeffsaeqnarlvknaeryyra.gdeeswnlrllalRDrhMaenleallehe.argkivvwAHNsHigdar 221
                                       +++ +++e++++++ +r+v++a ++  + + ++   ++ +a+RD++Ma n e+ le   +++ i+ wAH++H+++ +
  gi|313126005|ref|YP_004036275.1| 216 RERtREREQERVRHLCRAVEQACEWAPVrHAHDGPHPEGMAVRDSLMARNAERALE-LdHGEGIIAWAHDGHVQRGT 291
                                       22246799******************99*99999**********************.55779************999 PP

                                       STTTT-S...S-HHHHHHHHHGGGEEEEEEEEEEEEEEEC-..........EEEE----TTSHHHHHHCSS-SEEEE CS
                   Erythro_esteras 222 atdmgkerg.lnaGqllrerlgdeyvaiGftfgtgtvaaas...ewgepmevmtvrppppgslEallhaagppdfll 294
                                       ++d++  ++  ++G++l ++lg++y+ +Gf+f +g+v a +   ++g+ ++ +++++pp++s  a l++ + + +ll
  gi|313126005|ref|YP_004036275.1| 292 FDDGSLWADvETMGEHLTAALGSDYRPVGFDFARGSVCALPsggTAGDGPRAFSIDDPPEESATASLDTLDCAPYLL 368
                                       9999965559**********************************9999***************************** PP

                                       EG-.....CHHHHHHEE...........EEE---SB-BTTSHHHH-SEEEEEEE CS
                   Erythro_esteras 295 dlr....neelrewleeprleraiGv.rpeterqshyveaslaeqfDalifvde 343
                                        ++    +++l+++l++p++ r +G    ++  q++  e++l+e+fD l+fv+e
  gi|313126005|ref|YP_004036275.1| 369 RVAaasdSSRLESLLDRPQRLRYVGSvYDSETPQEAFRETVLSESFDELVFVPE 422
                                       **4456899*****************655555566667788***********98 PP

>> DUF1460  Protein of unknown function (DUF1460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05      0.12      23      67 ..     351     395 ..     343     400 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                                       S-S-SS-SS-B-HHHHHHHHHHHHHBSSHHHHHHHHHHHHBGGG- CS
                           DUF1460  23 keklvirfdglDCftyvetvlalarssseeeFaknLkklRYkdgk 67 
                                       +e+  + +d+lDC  y+  v+a + ss+ e+  ++ ++lRY ++ 
  gi|313126005|ref|YP_004036275.1| 351 EESATASLDTLDCAPYLLRVAAASDSSRLESLLDRPQRLRYVGSV 395
                                       4777889**********************************9765 PP

>> Atrophin-1  Atrophin-1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.2   4.2e-05      0.15     578     621 ..     184     233 ..     173     249 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.2e-05
                        Atrophin-1 578 kreealekakreaeqkareek......erekerekererererereaera 621
                                       kr ea+  a r  +    +++      ere+ere+ rere+er r+  ra
  gi|313126005|ref|YP_004036275.1| 184 KRREAAVNAVRAVQDGLSDGHavdstgEREQERERTREREQERVRHLCRA 233
                                       55555555555555444444400000145555555555555555544444 PP

>> DUF3915  Protein of unknown function (DUF3915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.2   0.00022      0.79      16      42 ..     202     228 ..     192     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00022
                           DUF3915  16 rghccdrdrerererederekerekkk 42 
                                        gh++d   ere+ere+ re+e+e+ +
  gi|313126005|ref|YP_004036275.1| 202 DGHAVDSTGEREQERERTREREQERVR 228
                                       578899888888888777777766533 PP

>> BRD4_CDT  C-terminal domain of bromodomain protein 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   7.3    0.0018       6.4       4      19 ..     213     228 ..     210     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0018
                          BRD4_CDT   4 dqqRelaRkrEqeRRr 19 
                                       +q+Re++R rEqeR r
  gi|313126005|ref|YP_004036275.1| 213 EQERERTREREQERVR 228
                                       79************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2565.72
//
Query:       gi|313126006|ref|YP_004036276.1|  [L=138]
Description: hypothetical protein Hbor_12420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-05   22.7   0.2     0.0003   20.5   0.1    2.0  2  DUF3225   Protein of unknown function (DUF3225)
    7.1e-05   23.1   2.5    0.00025   21.3   2.5    1.7  1  SnoaL_3   SnoaL-like domain


Domain annotation for each model (and alignments):
>> DUF3225  Protein of unknown function (DUF3225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   3.4e-08    0.0003      16      64 ..       7      53 ..       2      86 .. 0.77
   2 ?    0.1   0.0      0.07   6.2e+02     109     123 ..     118     132 ..     113     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.4e-08
                                      HHHHHHHHHTT-HHHHHHHB--STT-EEEETTEEEESHHHHHHHHHHS- CS
                           DUF3225 16 farYeaaLvsndvaaldalfwddpktvRyGvgenLyGieairafRaarp 64
                                      +++Y +aL +   + l  +f ++  +v++Gvge+L+G+++i++  ++++
  gi|313126006|ref|YP_004036276.1|  7 VEDYYEALRRG--EPLYPYFAEEADAVKFGVGETLVGYDDIAEGLREQT 53
                                      56677777655..468899**********************87433333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.07
                                       ETTEEEEEEEEEEE- CS
                           DUF3225 109 lpegWrivaahvsll 123
                                       +++ W  v  hvs+ 
  gi|313126006|ref|YP_004036276.1| 118 TTDEWVFVGMHVSVA 132
                                       5789*********86 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   2.5   2.7e-08   0.00025       2     107 ..       4     109 ..       3     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.7e-08
                           SnoaL_3   2 ealldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakgegisfeltdvrvtesgdvawvt 78 
                                       +a+++++yea+++g    l  ++a+++  +  g +e l g++++ + l+++   ++ ++ e + +rv e ++ a + 
  gi|313126006|ref|YP_004036276.1|   4 RATVEDYYEALRRGE--PLYPYFAEEADAVKFGVGETLVGYDDIAEGLREQTRTTTDWTVESDALRVVERESHAAFS 78 
                                       68899********98..7999999777777777888999****************************8877777777 PP

                           SnoaL_3  79 elldvtaaedgteg...egqlrlTgvlrrtdg 107
                                         +++  ++ ++     +  +r +g l+r+  
  gi|313126006|ref|YP_004036276.1|  79 DSVRMAWTDTEQ-DieyDFDTRWSGTLERRPT 109
                                       765553332222.2335777899999998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.45
# Mc/sec: 911.47
//
Query:       gi|313126007|ref|YP_004036277.1|  [L=78]
Description: hypothetical protein Hbor_12430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 433.23
//
Query:       gi|313126008|ref|YP_004036278.1|  [L=326]
Description: hypothetical protein Hbor_12440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-62  211.2   2.4    1.7e-31  109.7   0.1    2.0  2  Zincin_2  Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> Zincin_2  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.1   9.5e-36   1.7e-31       1     187 [.      23     201 ..      23     208 .. 0.91
   2 !  103.4   0.5     8e-34   1.4e-29     210     332 .]     198     317 ..     195     317 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 9.5e-36
                                       --HHHHHHHHHHHHTGGGS--S-HHHHHHHHHHHHHHHHHHHHHHHT---SS--EEEE--HHHHHHHHHHHHHHTTH CS
                          Zincin_2   1 VdwdlaarvArrlaragevdrseaaaavaelreaarlAelwldevtglpaaagsevevvdraeWveatleswrrlle 77 
                                       +dw ++a+ A++++ +g  d + ++++++ ++  +r+A++ l++v +++ + ++ vev +r  W++a++++++r+++
  gi|313126008|ref|YP_004036278.1|  23 IDWAAVADAAKNVTDPG--DLTLSTEDREGYATDVRDARQRLQSVGDVEFDLPEVVEVQNRHHWIDANIRTFKRVMR 97 
                                       8****************..899999*************************99999********************** PP

                                       HHHHHHH---------------HHHHHHHHHHHHHHHHTT--BTTSSH..---.---EEEE-HHHHHHHHHHTT--H CS
                          Zincin_2  78 pvaeklaealaeelaallrqvggavfgaqvGqalgeLssevlgqtdvg..lplapegrllLvapnvaaverelevdp 152
                                       p+ e+ +          l  v++ v +  ++ +l++L ++vlgq+d+   ++ +++  l++v pn++av+++l+vd 
  gi|313126008|ref|YP_004036278.1|  98 PIEERGR--------VPLPGVTRVVNTGTMAFMLSFLGKNVLGQYDPLllAEGDADHGLYFVHPNIVAVAESLDVDF 166
                                       *977544........5677788889999999****************95455556669******************* PP

                                       HHHHHHHHHHHHHHHHHHHTSTHHHHHHHHHHHHH CS
                          Zincin_2 153 edvrlwvalrEaaharlFaavpWLrehllsaveey 187
                                         +r w+a +E+aha++F a+pWL  hl++++++ 
  gi|313126008|ref|YP_004036278.1| 167 PRFRRWIAFHEVAHAAEFGAAPWLSGHLETRMQDG 201
                                       *****************************999875 PP

  == domain 2  score: 103.4 bits;  conditional E-value: 8e-34
                                       ...--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHHHHHHHHHHHTT---- CS
                          Zincin_2 210 leggllelvqtpeqraaldrLeallaLlEGwvdvVmdavgpevlpsvaalrerfrrrratggpaerllrrllGlelk 286
                                       +++gl +l + + +r+a++ L ++++ +EG+++  md++  +   ++a+lre++++rr++ggp+ rl rrllGl +k
  gi|313126008|ref|YP_004036278.1| 198 MQDGLNSLAHGEFDRRAFSDLDTAMTAVEGYAELLMDRAFDA---EYADLREKLDARRSGGGPIARLARRLLGLGVK 271
                                       56677788888999**************************97...9******************************* PP

                                       ---SSHHHHHHHHHHHHH-HHHHGGGGS-GGGS--HHHHH-HHHHH CS
                          Zincin_2 287 lrqyreaaalvravveavGmegrdavWehPdlLPtaeelddpaawv 332
                                        rqy+++a+++++v++++G+++   vWe+P++LPt ee+++p +w+
  gi|313126008|ref|YP_004036278.1| 272 RRQYERGAKFFETVADERGVAAASVVWENPEHLPTDEEIKNPWKWI 317
                                       *********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.59
# Mc/sec: 1673.39
//
Query:       gi|313126009|ref|YP_004036279.1|  [L=291]
Description: hypothetical protein Hbor_12450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-22   79.8   0.5    2.4e-21   76.6   0.1    2.0  2  Glyoxalase_3  Glyoxalase-like domain
    0.00035   20.8   0.0     0.0017   18.6   0.0    2.1  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.1   2.7e-25   2.4e-21       1     173 [.       4     180 ..       4     182 .. 0.85
   2 ?    1.6   0.1      0.03   2.7e+02      71     116 ..     233     276 ..     206     281 .. 0.69

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 2.7e-25
                      Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdg.YlEllavdpeapaperprlfgldrlakge 76 
                                       +DHv +  ++l+  +    ++ G+  + gg h  + t+ a+v ++dg Y+E++a+ +++ + +++ +   ++la+  
  gi|313126009|ref|YP_004036279.1|   4 IDHVAFGGSELDHLRTAA-ADVGLPSEYGGPHGNGTTHMAVVGLPDGsYIEFIAPTEDTSPDDADFWS--AHLAADA 77 
                                       7************99987.999**********************8777******87777766666554..688999* PP

                      Glyoxalase_3  77 glhtlalrtddidataarlraaGvd....eagrrvrpdggdlrwrllfladealpaegalPfliqwgasdpa..... 144
                                       g  ++++++++++a a+++ + Gv     ++++rv pdg++++w + f       ++g+lPf+i  ++++ +     
  gi|313126009|ref|YP_004036279.1|  78 GPAGWCIEVSNVAASAKTAIDSGVRvdgpHEASRVSPDGTRIEWDMCFEGPT---DDGRLPFVIADRTPRSYrttpn 151
                                       ***********************************************98864...489******8888766566675 PP

                      Glyoxalase_3 145 ..ladhpngalglaelviavsdpeataerla 173
                                         l    +  +g a +v+av+++++ta++l+
  gi|313126009|ref|YP_004036279.1| 152 ldL--VDSPLVGTALVVLAVEKTDRTASLLT 180
                                       333..44445556668888888899988876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.03
                      Glyoxalase_3  71 rlak.geglhtlalrtddidataarlraaGvdeagrrvrpdggd.lrw 116
                                       r+++ geg +++ l+ dd +a+ +++    v    + + pdg + ++w
  gi|313126009|ref|YP_004036279.1| 233 RVDSlGEGPCAYFLAADDFEAATEQFSLTDV----QSFGPDGDRrAAW 276
                                       3332489999999999999999999886664....5555666333555 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.9e-07    0.0017       2      93 ..       6     103 ..       4     119 .. 0.79
   2 ?   -0.9   0.0      0.22   1.9e+03       7      22 ..     248     262 ..     216     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-07
                                       EEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT.....-THHH...TS-EEE CS
                      Glyoxalase_4   2 QigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp.....eflae...hgeglh 70 
                                       ++++   +l+    + ++ +G+  ++  +      ++a++ l +g  +ie+i+p e++     +f+ +     +g  
  gi|313126009|ref|YP_004036279.1|   6 HVAFGGSELDHLRTAAAD-VGLPSEYGGPHGNGTTHMAVVGLPDG-SYIEFIAPTEDTspddaDFWSAhlaADAGPA 80 
                                       666666666666666665.66666666666677789999999998.7*********9977888777778889***** PP

                                       EEEEEES-HHHHHHHHCTTTEEE CS
                      Glyoxalase_4  71 hlaywvddldaavarleeqGfev 93 
                                         +++v+++ a+ +++ + G++v
  gi|313126009|ref|YP_004036279.1|  81 GWCIEVSNVAASAKTAIDSGVRV 103
                                       *********************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.22
                                       -S-HHHHHHHHHH.TT CS
                      Glyoxalase_4   7 VeDleaavarfsallG 22 
                                        +D+eaa ++fs l +
  gi|313126009|ref|YP_004036279.1| 248 ADDFEAATEQFS-LTD 262
                                       456666666666.344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1573.38
//
Query:       gi|313126010|ref|YP_004036280.1|  [L=268]
Description: 30S ribosomal protein S2 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-24   86.1   0.1    1.9e-14   53.4   0.5    2.2  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
        2.8    7.3  10.3          3    7.2  10.3    1.1  1  SDA1          SDA1


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.6e-11   2.3e-07       2      96 ..      87     178 ..      86     184 .. 0.91
   2 !   53.4   0.5   2.1e-18   1.9e-14     148     211 ..     185     248 ..     181     251 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.6e-11
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIygern.gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L agvh+G q++  +++m+++I+ +r+ g +++d+ +t + +r+a++++ +   + ++il  ++++  +   k+ a 
  gi|313126010|ref|YP_004036280.1|  87 LGAGVHIGTQQK--TNDMERFIHRVRDdGLYVLDVSQTDSRIRTAADFLAGY--DPEQILVTSSRQYGRFPAKKFAD 159
                                       679*****6665..899******999549********************975..67899999999999999****** PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTNf 96 
                                        +++   + r+++GtLTN 
  gi|313126010|ref|YP_004036280.1| 160 AVGARARTGRFIPGTLTNP 178
                                       ******************5 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 2.1e-18
                      Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvlada 211
                                        Pd+vvv+dp  ++ avkEa ++gipvia++D+n ++++vd ++p N++  r++++++ +la+ 
  gi|313126010|ref|YP_004036280.1| 185 EPDVVVVTDPIGDSQAVKEAITVGIPVIAMCDSNNQTSNVDLVVPTNNKGRRALSVVYWLLANE 248
                                       59*******************************************************9999875 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.3   0.00034         3     115     176 ..       3      63 ..       1     132 [. 0.55

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00034
                              SDA1 115 dseggwidvesdeeeieesdesedeeeeeeeeeekeekeeeeeeeeeeeeeeeeeeeeeeke 176
                                       d++++ ++v +d+  + e++ s+d+e    e +e+e  e ++++ ++ee+ e+e+++e  +e
  gi|313126010|ref|YP_004036280.1|   3 DNDNEAVEVVDDDVAEAEAA-SDDSETAAAETTEEEVAEATTADAADEEAAEDEADAEAAEE 63 
                                       55566666666655333333.44444333333333333333332222222222222221111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1496  (0.0834402); expected 358.6 (0.02)
Passed bias filter:                      907  (0.0505884); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.39s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 1450.93
//
Query:       gi|313126011|ref|YP_004036281.1|  [L=401]
Description: enolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-78  262.7   0.7    5.2e-78  262.3   0.7    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    3.2e-35  121.2   2.1    4.9e-35  120.6   0.2    2.3  2  Enolase_N  Enolase, N-terminal domain
      3e-10   40.1   0.1    6.5e-10   39.0   0.1    1.6  1  MR_MLE_C   Enolase C-terminal domain-like
    5.3e-05   22.5   1.3    7.2e-05   22.1   0.1    1.7  2  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.3   0.7   1.2e-81   5.2e-78       4     280 ..     133     399 ..     131     401 .] 0.95

  Alignments for each domain:
  == domain 1  score: 262.3 bits;  conditional E-value: 1.2e-81
                                       E-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHH CS
                         Enolase_C   4 lPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnk 80 
                                       +PvP+ nv+ GG+ha ++  +qef+ +Pvga+s++ea+   a v+ ++ ++l ++   + ++ GdeG +aP ++ ++
  gi|313126011|ref|YP_004036281.1| 133 FPVPLGNVVGGGEHAKEATHIQEFLAAPVGAPSVSEAVFANAAVHARVSEILDERD--TPAAKGDEGAWAPPIS-DA 206
                                       7*****************************************************99..88999*********96.57 PP

                                       HHHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEE CS
                         Enolase_C  81 ealdliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsie 155
                                       ea++++ ea+++   +   +v  +ld+a++e+y+++++ y    +        + ++++ +d+  e+v++y +v +e
  gi|313126011|ref|YP_004036281.1| 207 EAFEVVDEAVSDVEDELgfEVRFGLDMAAAELYDDDEDGYVYGDE--------VKSTDEQVDYVAEMVEEYDLVYVE 275
                                       9*********9988776679*************999999976443........57788889**************** PP

                                       S-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEE CS
                         Enolase_C 156 dpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvv 232
                                       dpldedd+e+++ lte++gd+  i Gddl+vtn++rl+++i+ +a+n++l+k nqiG+l+++++av+la ++gy +v
  gi|313126011|ref|YP_004036281.1| 276 DPLDEDDYEGFADLTERVGDQTLICGDDLFVTNVERLQDGIDAGAGNSILIKPNQIGTLSDAFDAVELAVRNGYDAV 352
                                       ***************************************************************************** PP

                                       EE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHH CS
                         Enolase_C 233 vshrsGetedttiadlavglsaGqiktGaparserlakynqllrieee 280
                                       +shrsGetedttia+lav++ a  iktG++ + er ak+n+l+ri ++
  gi|313126011|ref|YP_004036281.1| 353 ISHRSGETEDTTIAHLAVATDAAFIKTGTV-QGERTAKLNELIRIADD 399
                                       ****************************86.79************875 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.2   1.1e-38   4.9e-35       1     131 []       4     124 ..       4     124 .. 0.97
   2 ?   -3.6   0.1       2.6   1.1e+04      45      65 ..     235     256 ..     232     268 .. 0.54

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 1.1e-38
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I++v+ r +ldSrGnpTve++v t++g +graa+psGaStge+ea+el  +           +a+++++++  p+li
  gi|313126011|ref|YP_004036281.1|   4 ITDVRLRRVLDSRGNPTVEADVLTQSGGFGRAAAPSGASTGEYEAIELPPS-----------EAIAAARRHAVPRLI 69 
                                       899*******************************************99986...........899999999999999 PP

                                       .TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 .gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                        ++++ +q+e+D +l ++Dgt+n s++GaN+++a+S+A+aka+A+ ++ ply++l
  gi|313126011|ref|YP_004036281.1|  70 eEVHAGNQREVDGALRAADGTDNFSEIGANSAVAISMAAAKAGADVLGAPLYQHL 124
                                       459**************************************************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.6
                                       -B----SSTTSGG.GT--HHHH CS
                         Enolase_N  45 alelrDgdkkryl.gkgvekav 65 
                                       a el D+d++ y  g  v+   
  gi|313126011|ref|YP_004036281.1| 235 AAELYDDDEDGYVyGDEVKSTD 256
                                       6788887766664244444333 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.1   1.4e-13   6.5e-10      44     176 ..     224     375 ..     177     394 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.4e-13
                                       TSTSEEEEE-TTTS................BHHHHHHHHHHH.GGGTESEEESSSSTTTHHHHHHHHHHHH..SSEE CS
                          MR_MLE_C  44 gddvdlmvDanqaw................dlatAirvarel.eeldllwlEEPvppeddleglaelrara..sipi 101
                                       g +v++ +D+ +a                 ++++ + ++ e+ ee+dl ++E+P+   dd+eg a+l++r   ++ i
  gi|313126011|ref|YP_004036281.1| 224 GFEVRFGLDMAAAElydddedgyvygdevkSTDEQVDYVAEMvEEYDLVYVEDPLDE-DDYEGFADLTERVgdQTLI 299
                                       445566666555523466666666677666555555555555388***********9.78********833567888 PP

                                       EESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCSSHHHHHHHHHHHHTTTTB CS
                          MR_MLE_C 102 aagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgsgglglaaslhlaaaipnl 176
                                       +++    + ++++++ ++aga   + ++++++g ++ a + ++la  +g++ ++ + sg  +    +hla+a++ +
  gi|313126011|ref|YP_004036281.1| 300 CGDDLFVTnVERLQDGIDAGAGNSILIKPNQIGTLSDAFDAVELAVRNGYDAVISHRSGETEDTTIAHLAVATDAA 375
                                       888876555******************************************6666644555555556666665544 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.33   1.5e+03     193     217 ..      85     109 ..      64     119 .. 0.67
   2 !   22.1   0.1   1.6e-08   7.2e-05      91     221 ..     254     377 ..     243     395 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.33
                            MAAL_C 193 aylGGscnetdvsarvsvhvalatr 217
                                           G+ n  +++a+ +v +++a+ 
  gi|313126011|ref|YP_004036281.1|  85 RAADGTDNFSEIGANSAVAISMAAA 109
                                       3456899999999998888888764 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.6e-08
                            MAAL_C  91 rvadylakleeaaapykl.liegPldagskeeqierlaelreklkekgikvelvaDe.Wcntledirefvdaeaadl 165
                                          + ++ ++e ++ y+l ++e+Pld+++     e +a l+e++ ++     +  D+ +  ++e +++ +da+a++ 
  gi|313126011|ref|YP_004036281.1| 254 STDEQVDYVAEMVEEYDLvYVEDPLDEDD----YEGFADLTERVGDQ---TLICGDDlFVTNVERLQDGIDAGAGNS 323
                                       44444444555556676527999999766....45677888776554...4566665278889************** PP

                            MAAL_C 166 vqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvsvhvalatrpaql 221
                                       + ik   +G+++++ +av  + ++g  a +   + et+ +  +++h+a+at++a +
  gi|313126011|ref|YP_004036281.1| 324 ILIKPNQIGTLSDAFDAVELAVRNGYDAVISHRSGETEDT--TIAHLAVATDAAFI 377
                                       *************************************975..689******99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2317.45
//
Query:       gi|313126012|ref|YP_004036282.1|  [L=58]
Description: DNA-directed RNA polymerase subunit k [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-11   43.1   0.0    3.3e-11   42.9   0.0    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.8e-15   3.3e-11       6      49 .]       4      51 ..       1      51 [. 0.82

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.8e-15
                                      S--HHHHHHHHHHHHHHH....HT........SS-SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6  6 vltrYelvriaakRArQieegesl........etqkpvviAlrEiaegkipi 49
                                        +rYe++ri+++RA+Q     s         + + p+ iA +E ++g +p+
  gi|313126012|ref|YP_004036282.1|  4 RYNRYEKARILGARALQV----SYgapvlldtDQSEPILIAAEEYDAGVLPF 51
                                      569***************....65555556542449**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 346.94
//
Query:       gi|313126013|ref|YP_004036283.1|  [L=64]
Description: DNA-directed RNA polymerase subunit n [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.5e-28   96.6   0.3    8.2e-28   96.5   0.3    1.0  1  RNA_pol_N  RNA polymerases N / 8 kDa subunit


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.3   4.6e-32   8.2e-28       1      57 [.       1      58 [.       1      60 [. 0.96

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 4.6e-32
                                      ----SS-TTT--B-STHHHHHHHHHHTT.--HHHHHHHHT--SHHHHHHHHTB--THH CS
                         RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekg.eepkdaLdaLglkryCCrrmllthvdlie 57
                                      M+iPVrCFtCG+v+ge+w+e++++ ++g e+p+++Ld+Lg++r CCrrm+++h dl++
  gi|313126013|ref|YP_004036283.1|  1 MMIPVRCFTCGNVVGEHWDEFKARAREGdENPAKVLDELGVERHCCRRMMVSHKDLVD 58
                                      9************************8876999************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 378.08
//
Query:       gi|313126014|ref|YP_004036284.1|  [L=132]
Description: 30S ribosomal protein S9 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-32  110.4   0.1    8.3e-32  110.3   0.1    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.1   4.6e-36   8.3e-32       1     121 []       7     132 .]       7     132 .] 0.93

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 4.6e-36
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS..SEEEEEEEESS-HHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg..kfdvfvkvkgGGlsgqaeAirlgia 75 
                                       G++K+++Ar++++eg+g++++n++++e   + e+ar k+lep++++g+    ++d+ v+v+gGG+ gqa+A+r++ia
  gi|313126014|ref|YP_004036284.1|   7 GKKKTAIARATVREGEGRVRINSRPVEL-TEPEMARLKMLEPFRIAGEDLrsQVDIDVSVSGGGFAGQADAVRTAIA 82 
                                       89*************************9.877*************98744448************************ PP

                                       HHHHHHHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  76 raLvalekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       r+Lv++ +    eL+      +++ll++D R+ E kK g ++AR++yq+s+R
  gi|313126014|ref|YP_004036284.1|  83 RGLVQYLN--DAELRdaymdfDRSLLVNDVRQSESKKWGGPGARARYQKSYR 132
                                       ******87..578886666788****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 770.30
//
Query:       gi|313126015|ref|YP_004036285.1|  [L=145]
Description: 50S ribosomal protein L13 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-09   36.6   0.4    7.9e-07   29.4   0.4    2.4  1  Ribosomal_L13  Ribosomal protein L13
     0.0023   17.8   1.6        0.7    9.9   0.4    2.3  2  DUF3659        Protein of unknown function (DUF3659)


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.4   8.9e-11   7.9e-07       4     116 ..      11     108 ..      10     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 8.9e-11
                                       EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHH CS
                     Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakell 80 
                                       v+DA++ +lgr+as++a+            ++ +G+ v ++nae+ ++tg++ +    yr+   +g+ +        
  gi|313126015|ref|YP_004036285.1|  11 VVDARNCILGRVASEVAQ------------KALAGEKVAIVNAEDAVITGSEDDVMGVYRKRVEVGSDQG----PYY 71 
                                       788888888888888885............577899***************9999888888888877654....456 PP

                                       CCSHHHHHHHHHHCCS-.SSHHHHHHGCTEEEESSST CS
                     Ribosomal_L13  81 ekkpeeilekaVkgmLp.knklgrrrlkrLkvyagee 116
                                        k+p++i+++aV+gm p k+  gr+ l++++vy g+ 
  gi|313126015|ref|YP_004036285.1|  72 PKRPDRIFKRAVRGMVPyKTDKGREALSNVRVYVGNP 108
                                       789**************667799**********9985 PP

>> DUF3659  Protein of unknown function (DUF3659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.4   7.8e-05       0.7      14      47 ..      11      49 ..       7      58 .. 0.72
   2 !    6.8   0.0   0.00068       6.1      34      47 ..     105     118 ..      97     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.8e-05
                           DUF3659 14 vvdeeGnvvGrvveG.dlkkLaGkk...v.dedGnivde 47
                                      vvd+   ++Grv++    k LaG k   v  ed  i+++
  gi|313126015|ref|YP_004036285.1| 11 VVDARNCILGRVASEvAQKALAGEKvaiVnAEDAVITGS 49
                                      89*************888999999944432334444455 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00068
                           DUF3659  34 aGkkvdedGnivde 47 
                                       +G   dedG+++d+
  gi|313126015|ref|YP_004036285.1| 105 VGNPFDEDGDVLDD 118
                                       68999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 883.56
//
Query:       gi|313126016|ref|YP_004036286.1|  [L=116]
Description: 50S ribosomal protein L18ae [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-11   42.5   0.0    4.7e-11   42.4   0.0    1.0  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    2.5e-07   31.4   0.5    8.6e-07   29.7   0.5    1.7  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   5.3e-15   4.7e-11      20     138 ..       4     115 ..       1     116 [] 0.90

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 5.3e-15
                     Ribosomal_L18  20 envylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPk 96 
                                       +n+ l+ L+   + ++r ++++  + v  rL + r+ ++ + l r+ ++ k+    +++++v g+v+    l +  +
  gi|313126016|ref|YP_004036286.1|   4 TNPRLNSLIAELKAVSRESGANVWQDVADRLEKPRRTHAEVNLGRIERYAKE----DETVIVPGKVLGSGVLEK--N 74 
                                       678888888888999*********************************9995....58999******9887765..7 PP

                     Ribosomal_L18  97 lsvaALrftetararilkaGGeiltlDqLalraPtGkntvLl 138
                                       ++vaA+ f+++ar++i++ G+  +tl+q+a ++P+G+++ ++
  gi|313126016|ref|YP_004036286.1|  75 VTVAAVDFSSSARKKIEQVGD-TVTLEQIAEQNPDGSDVRVI 115
                                       9****************9975.67*************98766 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.5   9.6e-11   8.6e-07      71     127 ..      40      98 ..      27      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 9.6e-11
                                       ---EEEGGGTTTTSSS......SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  71 eaeeidleelaeaglikk..kdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       +++e++l ++  ++ +k+  +  v  Kvlg+g l+k+++v a  fS++A++kIe++G +v+
  gi|313126016|ref|YP_004036286.1|  40 THAEVNLGRI--ERYAKEdeTVIVpgKVLGSGVLEKNVTVAAVDFSSSARKKIEQVGDTVT 98 
                                       4567777777..44444455445556*******************************8886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 716.09
//
Query:       gi|313126017|ref|YP_004036287.1|  [L=260]
Description: DNA-directed RNA polymerase subunit d [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-20   71.2   0.0    4.6e-19   68.9   0.0    1.9  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    2.6e-13   49.2   0.0    3.4e-13   48.8   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   5.1e-23   4.6e-19       1     111 [.      48     143 ..      48     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 5.1e-23
                                       EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCE CS
                     RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadve 77 
                                       V++ en+sv+ DE++  rlgl+pl++  +               ++e+ ++v+l L+v+gp + ++gd++++d+ v+
  gi|313126017|ref|YP_004036287.1|  48 VRFVENSSVMFDEMIGLRLGLVPLTTPLD---------------DFEQGDTVTLALDVEGPATAYSGDIETSDELVK 109
                                       7899*********************5443...............45677889************************* PP

                                       ESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT CS
                     RNA_pol_A_bac  78 ivnpdilIakLrkgqeleleakvkkGiGkehakf 111
                                       +++++++I++L++gq+lelea ++ G Gk hak+
  gi|313126017|ref|YP_004036287.1| 110 PAEDNVPIIELKQGQRLELEADAVLGDGKSHAKH 143
                                       ********************************97 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   3.8e-17   3.4e-13       1      67 [.      18     249 ..      18     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.8e-17
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                         RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea............................................... 30 
                                       +fl+rg++++++N +Rr ++++vp++ i++                                               
  gi|313126017|ref|YP_004036287.1|  18 RFLVRGMTPAVANGIRRAMIADVPTFSIDTvrfvenssvmfdemiglrlglvplttplddfeqgdtvtlaldvegpa 94 
                                       59**************************************************9999999999999999999999999 PP

                                       ............................................................................. RF
                         RNA_pol_L  31 ............................................................................. 30 
                                                                                                                    
  gi|313126017|ref|YP_004036287.1|  95 taysgdietsdelvkpaednvpiielkqgqrleleadavlgdgkshakhqggvavgyrhlhrvevvgdanefeeqep 171
                                       99999999999888888888877777777777777777777777666666666666666666655555555555555 PP

                                       xx.........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  31 pv.........................................vkvntdkdklilevetdgslkPeealkeAlkiLk 66 
                                        +                                         v+v++++  +++ vetdgs ++ e++++A++ + 
  gi|313126017|ref|YP_004036287.1| 172 NIlrgvieeqaaehaadesaedgelvptsefdndltkrypgkeVEVHDVPGAFVFHVETDGSFTVPELVRRAVESIS 248
                                       00555555555555556666666666667777777777777778999**************************9987 PP

                                       x RF
                         RNA_pol_L  67 e 67 
                                       +
  gi|313126017|ref|YP_004036287.1| 249 D 249
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1609.82
//
Query:       gi|313126018|ref|YP_004036288.1|  [L=131]
Description: 30S ribosomal protein S11 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-49  167.3   2.0    1.5e-49  166.9   2.0    1.1  1  Ribosomal_S11   Ribosomal protein S11
      0.004   17.5   0.2     0.0059   17.0   0.2    1.2  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.9   2.0   1.7e-53   1.5e-49       1     110 []      12     130 ..      12     130 .. 0.99

  Alignments for each domain:
  == domain 1  score: 166.9 bits;  conditional E-value: 1.7e-53
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       G+ah++asfnnt+ititd++Gae+++ks+Gg +vk++r ++sPyaa+++aek+ae+v+  Gi+ ++v+v+g      
  gi|313126018|ref|YP_004036288.1|  12 GIAHVHASFNNTLITITDQTGAETIAKSSGGAVVKQNRdEASPYAAMQMAEKVAEEVKAAGIEGLHVRVRGpggnln 88 
                                       9**************************************************************************** PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGpG++a++ralaraGl+igriedvtPiPhdg+r+pk++r
  gi|313126018|ref|YP_004036288.1|  89 ksPGPGAQATIRALARAGLEIGRIEDVTPIPHDGTRAPKNSR 130
                                       ***************************************997 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   6.6e-07    0.0059      28      88 ..      15      75 ..       8      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.6e-07
                                      EEEE-SS-EEEEEE-TTT--EEEEECS-SCCCTS-SSSCHHHHHHHHHHHHHHHCHHCHTC CS
                    Ribosomal_L18p 28 vvfrsnrhiyaQviddvkgktlasastlekelklkstknkeaakkvgeliAerakekgiek 88
                                       v+ s ++  + + d++  +t+a++s+ +   + + + +  aa +++e++Ae+ k++gie 
  gi|313126018|ref|YP_004036288.1| 15 HVHASFNNTLITITDQTGAETIAKSSGGAVVKQNRDEASPYAAMQMAEKVAEEVKAAGIEG 75
                                      588899999999**************998888888999999*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 861.82
//
Query:       gi|313126019|ref|YP_004036289.1|  [L=175]
Description: 30S ribosomal protein S4 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-13   50.3   1.2    2.1e-12   46.5   0.1    2.2  2  S4            S4 domain
     0.0025   18.7   1.2      0.006   17.5   1.0    1.8  1  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.014   1.2e+02      16      23 ..      51      58 ..      47      60 .. 0.92
   2 !   46.5   0.1   2.4e-16   2.1e-12       1      46 [.     105     150 ..     105     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.014
                                      HHHHHHHH CS
                                S4 16 rreArqlI 23
                                      rreAr+lI
  gi|313126019|ref|YP_004036289.1| 51 RREARRLI 58
                                      9******9 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 2.4e-16
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                       rRL++v +r+gl+ +  + rq+I hG+V V+G +v+ ps +V++++
  gi|313126019|ref|YP_004036289.1| 105 RRLQTVAYRKGLGHTPDQSRQFIVHGHVVVDGARVTRPSKMVEVSE 150
                                       8*****************************************9876 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.0   6.7e-07     0.006      38      79 ..      16      58 ..       2     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.7e-07
                                      CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHH CS
                      Ribosomal_S4 38 eYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLl 79
                                      +++  ++ +++ l +rYgl+ +++++r+++e+r++r + +++L+
  gi|313126019|ref|YP_004036289.1| 16 PFQGeRIAQEADLLGRYGLKnKEELWRAQSELRNYR-REARRLI 58
                                      566669999***************************.9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1076.91
//
Query:       gi|313126020|ref|YP_004036290.1|  [L=172]
Description: 30S ribosomal protein S13 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-43  148.5   5.5    1.4e-43  148.3   5.5    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.029   13.1   0.0      0.033   13.0   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
       0.18   12.2   0.0       0.35   11.3   0.0    1.5  1  IMS_HHH        IMS family HHH motif


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.3   5.5   2.4e-47   1.4e-43       1     128 []      22     149 ..      22     149 .. 0.98

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 2.4e-47
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwinrqkdik 77 
                                       Ri +td+dg+k ve +l  +kGiG+r+a+i++ +a+vd++  +g l++++i+ ++++ven+ ++ ++++inr++d+ 
  gi|313126020|ref|YP_004036290.1|  22 RIGQTDLDGTKTVERSLSDMKGIGKRTARIVADAAGVDRTETFGLLDQDDIDAVVDVVENFNDHAPEWMINRRDDFY 98 
                                       99**********************************************************8888888888******* PP

                     Ribosomal_S13  78 dGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                       +G+++h++ +dl++k+r+di+R+k+i+sy+G+RHkrG+kvRGQrTk+tgRt
  gi|313126020|ref|YP_004036290.1|  99 TGETTHKTGSDLEQKRRHDINRMKMINSYKGVRHKRGQKVRGQRTKSTGRT 149
                                       **************************************************8 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.5e-06     0.033     168     263 ..      10      99 ..       3     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-06
                                       XTTSXXH.HHHHHHHHH...S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTX CS
                              FbpA 168 nPleaeeleefkellsk...kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqellee 241
                                        P e e+l+ f  + ++    +k++++ L+  ++G+++ +a+ ++  ag+d++++   l+++d++++ + ++++ ++
  gi|313126020|ref|YP_004036290.1|  10 APEEEEDLQYFVRIGQTdldGTKTVERSLS-DMKGIGKRTARIVADAAGVDRTETFGLLDQDDIDAVVDVVENFNDH 85 
                                       466677766666665556745555666665.568********************************99999988776 PP

                                       XX....XXEE.....XSSSEES CS
                              FbpA 242 leeekfepqlvlkeekpeefsv 263
                                               +++++   +++f+ 
  gi|313126020|ref|YP_004036290.1|  86 AP------EWMINR--RDDFYT 99 
                                       54......333332..344444 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.9e-05      0.35      11      31 ..      36      57 ..      35      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                           IMS_HHH 11 lpitkipGiGgklgek.LeklG 31
                                      ++++++ GiG++++    ++ G
  gi|313126020|ref|YP_004036290.1| 36 RSLSDMKGIGKRTARIvADAAG 57
                                      689**********987666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1098.26
//
Query:       gi|313126021|ref|YP_004036291.1|  [L=120]
Description: thioredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-15   55.0   0.0    6.9e-15   54.9   0.0    1.1  1  Thioredoxin    Thioredoxin
    8.8e-05   22.4   0.0    0.00025   20.9   0.0    1.7  1  TraF           F plasmid transfer operon protein
    0.00014   22.3   0.0     0.0022   18.4   0.0    2.1  1  Thioredoxin_2  Thioredoxin-like domain
    0.00094   19.2   0.0     0.0015   18.6   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
     0.0072   15.7   0.0       0.01   15.2   0.0    1.2  1  OST3_OST6      OST3 / OST6 family, transporter family
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.018   15.5   0.0    1.2  1  DUF836         Glutaredoxin-like domain (DUF836)
      0.015   15.2   0.0      0.019   14.9   0.0    1.3  1  HyaE           Hydrogenase-1 expression protein HyaE
      0.019   15.3   0.0        2.5    8.5   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
      0.026   14.6   0.0      0.029   14.4   0.0    1.3  1  TrbC_Ftype     Type-F conjugative transfer system pilin assem
      0.056   13.2   0.0      0.086   12.6   0.0    1.3  1  KaiB           KaiB domain
       0.15   11.9   0.0       0.18   11.5   0.0    1.1  1  Thioredoxin_9  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   4.2e-18   6.9e-15       6      90 ..      19     101 ..      14     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 4.2e-18
                                       SHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETT CS
                       Thioredoxin   6 tkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkng 82 
                                       ++++ +e +a+ ++lvl++Fy + C+ C++++P+l ++a+++  ++++a ++  e + l ++++++++Ptl+lf++g
  gi|313126021|ref|YP_004036291.1|  19 SEAELDELIAE-NDLVLIDFYTKGCTLCQSIEPVLGNVARAHD-NLTVALCNPREDPPLIERFNIQSVPTLVLFEDG 93 
                                       56778888888.****************************999.********************************* PP

                                       EEEEEEES CS
                       Thioredoxin  83 kevkkyeg 90 
                                       +++ ++  
  gi|313126021|ref|YP_004036291.1|  94 ERAGRLAD 101
                                       *7766543 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.5e-07   0.00025     128     202 ..      29      93 ..       2     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.5e-07
                              TraF 128 akeygLlfFyrgkcpyceaqapilqafadky.glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpk 202
                                       +++  L+ Fy ++c +c+   p+l ++a+ + +l+v   +  + p   l +         r++++++P+lvl++  
  gi|313126021|ref|YP_004036291.1|  29 ENDLVLIDFYTKGCTLCQSIEPVLGNVARAHdNLTVALCNPREDPP--LIE---------RFNIQSVPTLVLFEDG 93 
                                       456899***********************99678888777777766..555.........************9876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.4e-06    0.0022       4      98 ..      29     105 ..      26     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                     Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrg 80 
                                       ++  vl++f++ +C  C+ ++ +l ++            +++     +   c++ +            l +++++++
  gi|313126021|ref|YP_004036291.1|  29 ENDLVLIDFYTKGCTLCQSIEPVLGNV-----------ARAH--DNLTVALCNPRED---------PPLIERFNIQS 83 
                                       567799****************99999...........4444..4444444444433.........46********* PP

                     Thioredoxin_2  81 tPtiv.fldgk...eivarlpG 98 
                                       +Pt+v f dg+   + ++  +G
  gi|313126021|ref|YP_004036291.1|  84 VPTLVlFEDGEragRLADGFQG 105
                                       ***8879999965555555555 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     9e-07    0.0015       6      57 ..      38      91 ..      33     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9e-07
                                      ESSSSTTCHHHHHHHHHHCHCC.TCECEEECC.TTHHHHHHCT-SSSSEEECTT CS
                     Thioredoxin_3  6 lgpgCakCpklekavkeaaaek.gikaevekv.tdfeeiekygVmsvPalvidg 57
                                       ++gC+ C+ +e ++  +a    ++++ + +  +d++ ie+++++svP+lv+ +
  gi|313126021|ref|YP_004036291.1| 38 YTKGCTLCQSIEPVLGNVARAHdNLTVALCNPrEDPPLIERFNIQSVPTLVLFE 91
                                      5899**************999977998777776999999***********9754 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   6.2e-06      0.01      44     105 ..      40      93 ..      35     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.2e-06
                         OST3_OST6  44 fkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppk 105
                                       ++C+lC+ +ep +  va++++        +l  a  +  e + + ++++++s+P l+lf+  
  gi|313126021|ref|YP_004036291.1|  40 KGCTLCQSIEPVLGNVARAHD--------NLTVALCNPREDPPLIERFNIQSVPTLVLFEDG 93 
                                       68**************98754........56899999**********************874 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.1e-05     0.018       5      52 ..      37      86 ..      33      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                      EE-TT-HHHHHHHHHHHHHCCCTT.EEEEEEETTT-CCCHCCCCTT.TTE CS
                            DUF836  5 yskpgChlCeqakekLkelkleeg.leleviDIakdeeleakYgle.ipv 52
                                      + ++gC lC++++ +L +++ +++ l++   +  +d+ l ++++ + +p 
  gi|313126021|ref|YP_004036291.1| 37 FYTKGCTLCQSIEPVLGNVARAHDnLTVALCNPREDPPLIERFNIQsVPT 86
                                      6789**************77666669999999999999999998541555 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.2e-05     0.019      50     100 ..      52     100 ..      16     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                       HHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEE CS
                              HyaE  50 lpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvla 100
                                       l+ + +a  n++ a+   +  ++  l erf+++ +P+l+++ dge  g la
  gi|313126021|ref|YP_004036291.1|  52 LGNVARAHDNLTVALC--NPREDPPLIERFNIQSVPTLVLFEDGERAGRLA 100
                                       5555555555443333..3455667889*****************999886 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.012        19       1      30 [.      30      59 ..      30      72 .. 0.87
   2 ?    8.5   0.0    0.0016       2.5      72      90 ..      73      91 ..      56      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.012
                                      .SEEEEEE--SSSHHHHHHHHHHHHHHHHH CS
                     Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklkelyekl 30
                                      +++vl+ f+++ c  c+ + p l ++ + +
  gi|313126021|ref|YP_004036291.1| 30 NDLVLIDFYTKGCTLCQSIEPVLGNVARAH 59
                                      689******************998877665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
                                      HHHTT-S--TT-SEEEEE- CS
                     Thioredoxin_8 72 nklkkkynvkaiPtlvvld 90
                                        l++++n++++Ptlv+  
  gi|313126021|ref|YP_004036291.1| 73 PPLIERFNIQSVPTLVLFE 91
                                      3799************976 PP

>> TrbC_Ftype  Type-F conjugative transfer system pilin assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-05     0.029      60      84 ..      72      96 ..      20     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                        TrbC_Ftype 60 dPllFrqfkitaVPalvlaeedkas 84
                                      dP l ++f+i++VP+lvl e+ +++
  gi|313126021|ref|YP_004036291.1| 72 DPPLIERFNIQSVPTLVLFEDGERA 96
                                      9*****************9987765 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05     0.086      27      56 ..      59      88 ..      45      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                                      TTTEEEEEEETTTSHCHHCCTCEESCCCCC CS
                              KaiB 27 gfqyeLqvvdvleqPelaeedrlvatPaLi 56
                                      + + ++ + ++ e P l+e + ++ +P+L+
  gi|313126021|ref|YP_004036291.1| 59 HDNLTVALCNPREDPPLIERFNIQSVPTLV 88
                                      56789999*********************8 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.18      50     107 ..      39      93 ..      15     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                       -TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
                     Thioredoxin_9  50 edwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildee 107
                                       ++ C  ++ + Pvl  +a++ +n++v +    e++ l++++     +++Ptl++++++
  gi|313126021|ref|YP_004036291.1|  39 TKGCTLCQSIEPVLGNVARAHDNLTVALCNPREDPPLIERFNI---QSVPTLVLFEDG 93 
                                       55688899*********************************65...9******99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 742.85
//
Query:       gi|313126022|ref|YP_004036292.1|  [L=319]
Description: GTP cyclohydrolase subunit moaa [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-25   89.4   0.0    5.5e-25   88.7   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    6.4e-17   61.7   0.0    1.1e-16   60.9   0.0    1.4  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    1.6e-07   31.6   0.0      3e-07   30.8   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
      3e-05   24.1   0.0    5.6e-05   23.2   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.12   12.7   0.1        2.7    8.4   0.0    2.8  3  Nif11        Nif11 domain
       0.23   12.6   0.4        8.7    7.6   0.0    2.7  3  Cytochrom_C  Cytochrome c


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.0   1.8e-28   5.5e-25       2     165 ..      16     175 ..      15     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.8e-28
                                       EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                       + t  Cn++C++C++       + +e+   ++s++++++ ++ + +e gv+ v ++ggep+l+ d++e+++r  +  
  gi|313126022|ref|YP_004036292.1|  16 SLTDRCNFDCVYCHNEGLgdtrGPMEPSDDEMSTDDVVRFLEVV-EEFGVEKVKFTGGEPMLRQDLAEIIRRTPES- 90 
                                       7899************99**************************.9********************9999999996. PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                          ++ +++tngt + +  +e l+e+g+ rv+++ +a+d+e + +++ + + ++ vle+++++ +ag+++v+ ++v+
  gi|313126022|ref|YP_004036292.1|  91 ---MESSLTTNGTFL-PGRAEDLKEAGLSRVNVSQDALDPEAFAEIT-KSGAYDNVLEGVQAALDAGLDPVKLNMVV 162
                                       ...************.*******************************.88*************************** PP

                                       BTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeeleelle 165
                                       ++  +   +ee+++
  gi|313126022|ref|YP_004036292.1| 163 FE-HTAGYVEEMVD 175
                                       99.67666666665 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   3.7e-20   1.1e-16       2     126 ..     184     298 ..     183     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.7e-20
                                       EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--E CS
                       Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleakketkgpakrykikdgkgeiglIapvsep.FCasCnR 77 
                                       +l++IE+mp  +g+  ++   +  +++ + +e +    e   ++++ ++ry++  g+g +++++pv+++ FCa+C R
  gi|313126022|ref|YP_004036292.1| 184 QLQLIEYMPELTGRPEWN---IDIQRVHDWLEGKADRVEM--REMHHRRRYYV--GQGMVEIVDPVENEdFCANCHR 253
                                       89*******998876555...5555555555555554444..45689999999..6777*********99******* PP

                                       EEE-TTSEEESSSS-SS-EEHHHHHHTT--HHHHHHHHHHHHHT----H CS
                       Mob_synth_C  78 lRltadGklktCLfaeeeidlrdllregaseeeLkelikealarkkekh 126
                                       +R+t +G lk CL +++++  +  + +g    e++e+++e++a++ +++
  gi|313126022|ref|YP_004036292.1| 254 VRVTHEGYLKGCLNRNDDLRPMGQMTRG----EIREAYRETVANRVPYY 298
                                       ***************9986555555555....48999999999987765 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   9.9e-11     3e-07       5      94 ..      12     100 ..       9     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 9.9e-11
                           Fer4_12   5 GvrlslfvsgCnlsCkgCfnketwsfk.....sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelv 76 
                                       Gvr+sl + +Cn+ C +C+n+ + + +     s +e++++   + +e +++  +e++ ++GGEP+l   +++l+e++
  gi|313126022|ref|YP_004036292.1|  12 GVRISL-TDRCNFDCVYCHNEGLGDTRgpmepSDDEMSTDDVVRFLEVVEEFGVEKVKFTGGEPML---RQDLAEII 84 
                                       677765.799*************9998666666777777777888888888888************...99999999 PP

                           Fer4_12  77 kevkeekpekdiwlytgy 94 
                                       ++  e     + + ++g+
  gi|313126022|ref|YP_004036292.1|  85 RRTPESME--SSLTTNGT 100
                                       99888776..45666665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.9e-08   5.6e-05       5      90 ..      18     100 ..      15     123 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.9e-08
                           Fer4_14   5 lsgCnlsCkgCdnketwks..elgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                       + +Cn+ C+ C n+   +    +++ ++e   +++++     +e+  +++ +tGGeP++    ++l ++++r  e++
  gi|313126022|ref|YP_004036292.1|  18 TDRCNFDCVYCHNEGLGDTrgPMEPSDDEMSTDDVVRfLEVVEEFGVEKVKFTGGEPMLR---QDLAEIIRRTPESM 91 
                                       579*********8876555222233333333344444434556777899*********65...77888888877776 PP

                           Fer4_14  79 pekkiwletngt 90 
                                          +  l tngt
  gi|313126022|ref|YP_004036292.1|  92 ---ESSLTTNGT 100
                                       ...555666666 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0009       2.7       1      26 [.      47      83 ..      47      93 .. 0.87
   2 ?    0.2   0.0      0.32   9.7e+02      25      38 ..     122     135 ..     120     139 .. 0.83
   3 ?   -0.8   0.0      0.65   1.9e+03      10      23 ..     174     187 ..     170     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0009
                             Nif11  1 MSeeqlkaFlekvkq...........Dpalreqlkac 26
                                      MS +++ +Fle v++            p lr+ l+ +
  gi|313126022|ref|YP_004036292.1| 47 MSTDDVVRFLEVVEEfgvekvkftggEPMLRQDLAEI 83
                                      ***************9999999999999999999987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.32
                             Nif11  25 acsdheevvalAke 38 
                                       ++ d+e+++++ k+
  gi|313126022|ref|YP_004036292.1| 122 DALDPEAFAEITKS 135
                                       6789*******987 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.65
                             Nif11  10 lekvkqDpalreql 23 
                                       +++v+++p l+ ql
  gi|313126022|ref|YP_004036292.1| 174 VDHVAENPGLQLQL 187
                                       5899******9776 PP

>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11   3.2e+02      11      27 ..      24      39 ..      12     133 .. 0.70
   2 ?   -3.0   0.0       5.9   1.8e+04      29      53 ..     192     216 ..     179     230 .. 0.66
   3 ?    7.6   0.0    0.0029       8.7      11      46 ..     247     287 ..     243     306 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                      TGGGTB-SSSBSSS... CS
                       Cytochrom_C 11 nCaaCHgvegggakqgg 27
                                      +C+ CH  + g +  g+
  gi|313126022|ref|YP_004036292.1| 24 DCVYCHNEGLGDT-RGP 39
                                      6999*96555544.343 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.9
                                       --HHHHHHHTTT-HHHHHHHHTTSS CS
                       Cytochrom_C  29 ptlsgaaerasaasigasvanpaav 53 
                                       p l+g  e++   + +  + +++a+
  gi|313126022|ref|YP_004036292.1| 192 PELTGRPEWNIDIQRVHDWLEGKAD 216
                                       6667766666666666666666554 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0029
                                       TGGGTB-SSSBSSS.........--HHHHHHHTTT-HHHHH CS
                       Cytochrom_C  11 nCaaCHgvegggakqgg.....gptlsgaaerasaasigas 46 
                                        Ca+CH+v+ +  ++ +     + +l+ +++   ++  +a+
  gi|313126022|ref|YP_004036292.1| 247 FCANCHRVRVTHEGYLKgclnrNDDLRPMGQMTRGEIREAY 287
                                       6******9998887776777776666666655555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1928.62
//
Query:       gi|313126023|ref|YP_004036293.1|  [L=353]
Description: chromosome partitioning ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.2e-100  336.0   0.0   1.6e-100  335.7   0.0    1.1  1  ParA            NUBPL iron-transfer P-loop NTPase
    7.2e-14   52.0   0.0    5.8e-13   49.0   0.0    2.1  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    5.2e-11   42.8   0.9    5.3e-09   36.2   0.9    2.1  1  AAA_31          AAA domain
    1.8e-09   37.6   1.0    3.4e-09   36.7   0.4    1.8  2  FeS_assembly_P  Iron-sulfur cluster assembly protein
    2.7e-07   30.2   0.0    3.9e-07   29.6   0.0    1.3  1  MipZ            ATPase MipZ
    3.8e-05   23.3   0.0     0.0096   15.4   0.2    2.3  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
    0.00016   21.1   0.0    0.00024   20.5   0.0    1.2  1  VirC1           VirC1 protein
    0.00019   20.7   3.7     0.0008   18.7   1.1    2.4  2  ArsA_ATPase     Anion-transporting ATPase
    0.00036   20.4   0.0        0.2   11.4   0.0    2.5  2  AAA_26          AAA domain
     0.0041   16.7   0.1      0.012   15.2   0.0    1.8  2  AAA_25          AAA domain
  ------ inclusion threshold ------
      0.031   13.8   0.3       0.31   10.5   0.1    2.0  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
      0.079   12.9   0.2       0.59   10.1   0.1    2.2  2  DUF1610         Domain of unknown function (DUF1610)
       0.13   12.1   0.0       0.17   11.6   0.0    1.3  1  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
       0.14   12.0   0.0       0.23   11.4   0.0    1.2  1  RsgA_GTPase     RsgA GTPase


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.7   0.0  1.2e-103  1.6e-100       2     245 ..      97     338 ..      96     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 335.7 bits;  conditional E-value: 1.2e-103
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSi 78 
                                       vk++iav+SgKGGVGKStvavnlA+ L+k g++vgl+DaDiyGp++pr++ ++e+ + + +++++P e++g+k+mS+
  gi|313126023|ref|YP_004036293.1|  97 VKNIIAVASGKGGVGKSTVAVNLAAGLSKLGARVGLFDADIYGPNVPRMVAADEAPQATGDQTIVPPEKYGMKLMSM 173
                                       9***************************************************99755555989************** PP

                              ParA  79 gfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkk 155
                                       +fl+  ed++v+wrGpm++++++ql++dv+wgelDy+i+DlPPGtgD+qltv+q+lpl+gaviVttpq+va++d++k
  gi|313126023|ref|YP_004036293.1| 174 AFLVG-EDDPVIWRGPMVHQLLTQLVEDVQWGELDYMILDLPPGTGDTQLTVLQTLPLTGAVIVTTPQDVAIDDARK 249
                                       ****9.*********************************************************************** PP

                              ParA 156 aiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepes 232
                                       +++mf k +++vlG+veNms f cp+cg++++ifg ggge++a+e ++p+lg+ipldp++r+ +d g+p+vl++ e 
  gi|313126023|ref|YP_004036293.1| 250 GLQMFGKHDTNVLGIVENMSSFRCPDCGSSHDIFGAGGGEAFAAENDMPFLGAIPLDPDVRTGGDGGRPVVLED-EG 325
                                       *********************************************************************99997.78 PP

                              ParA 233 eaakaleeiaekv 245
                                       e+a+a+++++e+v
  gi|313126023|ref|YP_004036293.1| 326 ETAEAFRRMTESV 338
                                       9999**9999887 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   4.5e-16   5.8e-13       1      82 [.     101     267 ..     101     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.5e-16
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ia+as+kGGvGK+t+a+nLa+ l++ g rV l+DaD  ++n      +  d++p                       
  gi|313126023|ref|YP_004036293.1| 101 IAVASGKGGVGKSTVAVNLAAGLSKLGARVGLFDADIYGPNVP--RMVAADEAPqatgdqtivppekygmklmsmaf 175
                                       89***************************************98..55555555567788888888999888888888 PP

                                       ......................................................................CCHCCCH CS
                                       ......................................................................xxxxxxx RF
                              CbiA  55 ......................................................................dlkrlle 61 
                                                                                                             d+ ++l+
  gi|313126023|ref|YP_004036293.1| 176 lvgeddpviwrgpmvhqlltqlvedvqwgeldymildlppgtgdtqltvlqtlpltgavivttpqdvaidDARKGLQ 252
                                       88888888888888888888888888888888888888888777777777777777777777777776666666666 PP

                                       HHHHHCHCHHHH..EEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  62 llealgkkkalllkiagvvln 82 
                                       ++ + +++      ++g+v n
  gi|313126023|ref|YP_004036293.1| 253 MFGKHDTN------VLGIVEN 267
                                       66555543......5666555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.9   4.1e-12   5.3e-09       2      42 ..      99     139 ..      98     262 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 4.1e-12
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa 42 
                                        +Ia+a  KGGvGK+T +vnlaa l+klg +v l D+D  +
  gi|313126023|ref|YP_004036293.1|  99 NIIAVASGKGGVGKSTVAVNLAAGLSKLGARVGLFDADIYG 139
                                       59************************************755 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.4   2.7e-12   3.4e-09       2      60 ..       4      69 ..       3      80 .. 0.94
   2 ?   -3.1   0.0       7.2   9.3e+03      40      55 ..     234     249 ..     233     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.7e-12
                                      HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.......-EEEEEE--SSTT-TTHHHHHHHHHHH CS
                    FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieg.......gkVsvditltypacslaeairadaeaa 60
                                      eav++ Lr V DP lg d+vs+glv +i++         g+V+++++l+ p  +  ++i+a+++++
  gi|313126023|ref|YP_004036293.1|  4 EAVRDRLRAVEDPDLGDDIVSAGLVNAIEVASddaddgsGVVRISLALGAPYSPHETDIAAQVREQ 69
                                      79**************************9987789999*****************9*****99986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.2
                                       E--SSTT-TTHHHHHH CS
                    FeS_assembly_P  40 itltypacslaeaira 55 
                                       + +t+p+  ++++ r+
  gi|313126023|ref|YP_004036293.1| 234 VIVTTPQDVAIDDARK 249
                                       5678888888888876 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   3.1e-10   3.9e-07       2     110 ..     100     217 ..      99     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.1e-10
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EEE-SSS-HHHHT CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpealalseaeeaev 78 
                                       +i ++  kGG Gkst+av +a  L+k Garv+  d d+    + r +    a ++  + ++  pe + ++  ++a +
  gi|313126023|ref|YP_004036293.1| 100 IIAVASGKGGVGKSTVAVNLAAGLSKLGARVGLFDADIYGPNVPRMVAADEAPQATGDQTIVPPEKYGMKLMSMAFL 176
                                       7999***********************************99999999998888888777777777777776666555 PP

                                       TS-HHH.......HHHHHHHHHHHHH.HH-SEEEEE--.SS CS
                              MipZ  79 eeeeea.......evaeleelvadle.aeldfividtP.Gs 110
                                        +e++          + l++lv+d++  eld++++d P G+
  gi|313126023|ref|YP_004036293.1| 177 VGEDDPviwrgpmVHQLLTQLVEDVQwGELDYMILDLPpGT 217
                                       55444311111112345677777776357899999876344 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   7.5e-06    0.0096       6      33 ..     105     132 ..      99     138 .. 0.85
   2 !    5.5   0.0    0.0075       9.6     194     258 ..     289     352 ..     248     353 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.5e-06
                         Fer4_NifH   6 yGkGGiGksttsqnlsaalaemgkkvli 33 
                                        GkGG+Gkst + nl+a l++ g +v +
  gi|313126023|ref|YP_004036293.1| 105 SGKGGVGKSTVAVNLAAGLSKLGARVGL 132
                                       5**********************99955 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0075
                         Fer4_NifH 194 ekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilenkklviPkplse 258
                                       e+fa+e +++ l ++P+d +vr      + v+  + e e a+ +r + + +++   +v+ +++se
  gi|313126023|ref|YP_004036293.1| 289 EAFAAENDMPFLGAIPLDPDVRTGGDGGRPVVLED-EGETAEAFRRMTESVADMAGVVRRREVSE 352
                                       689*******************9987777766544.45569************999998888876 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.9e-07   0.00024       2      40 ..      99     137 ..      98     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.9e-07
                             VirC1   2 klitfcslkGGaGkttalmglcsalasdgkrvalfeade 40 
                                       ++i+++s kGG Gk+t  + l + l   g rv+lf+ad 
  gi|313126023|ref|YP_004036293.1|  99 NIIAVASGKGGVGKSTVAVNLAAGLSKLGARVGLFDADI 137
                                       6899*********************************95 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.1   6.3e-07    0.0008       5      33 ..     103     131 ..      98     136 .. 0.86
   2 ?    2.0   0.1     0.074        95     114     144 ..     195     227 ..     190     272 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.3e-07
                                       EEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                       ArsA_ATPase   5 lvgGKGGVGKttvsaatavklsekgkkvl 33 
                                       + +GKGGVGK+tv+  +a+ ls+ g +v 
  gi|313126023|ref|YP_004036293.1| 103 VASGKGGVGKSTVAVNLAAGLSKLGARVG 131
                                       469*********************99985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.074
                                       HHHHHHHHCSSSSEEEEESBS.CCHT.CGGGGH CS
                       ArsA_ATPase 114 eellkyvkeeeydvvvlDtaP.TGht.lrllsl 144
                                       ++l++ v+  e d+++lD +P TG+t l +l++
  gi|313126023|ref|YP_004036293.1| 195 TQLVEDVQWGELDYMILDLPPgTGDTqLTVLQT 227
                                       566777788899999999999888875666654 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0055         7       3      35 ..     101     133 ..      99     171 .. 0.91
   2 !   11.4   0.0   0.00016       0.2     132     195 ..     234     310 ..     215     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0055
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyf 35 
                                       i v++   gvGK++v+  L++ l++ g++vg f
  gi|313126023|ref|YP_004036293.1| 101 IAVASGKGGVGKSTVAVNLAAGLSKLGARVGLF 133
                                       568888899********************9977 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00016
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk..vrnpe...........nvetlekksgipvlGvvPylpdle 195
                                       ++V+++++ +i+++   ++++ +++ +vlG++ N   +r p+             e++ + + +p lG++P +pd++
  gi|313126023|ref|YP_004036293.1| 234 VIVTTPQDVAIDDARKGLQMFGKHDTNVLGIVENMssFRCPDcgsshdifgagGGEAFAAENDMPFLGAIPLDPDVR 310
                                       899999999***********************9983333443555666777778899999999***********986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.3e-06     0.012      18      59 ..      86     126 ..      68     155 .. 0.79
   2 ?   -2.5   0.0       2.5   3.2e+03      72      97 ..     316     341 ..     294     349 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.3e-06
                            AAA_25  18 pppprrwlvkgllpagelallaGapgtGKttlaldlalava.t 59 
                                        +   +++++g+  ++ +a+  G +g+GK+t+a++la+ ++ +
  gi|313126023|ref|YP_004036293.1|  86 DLSADEDVLPGV--KNIIAVASGKGGVGKSTVAVNLAAGLSkL 126
                                       555566677777..7889999****************988754 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.5
                            AAA_25  72 gkVlyvsaEdsedelrrRlravgeal 97 
                                       g+ +++  E+  +e  rR+ +  +++
  gi|313126023|ref|YP_004036293.1| 316 GRPVVLEDEGETAEAFRRMTESVADM 341
                                       44455555666656666666555554 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00024      0.31       3      38 ..     100     135 ..      98     144 .. 0.90
   2 ?    1.1   0.0      0.18   2.3e+02     105     138 ..     194     228 ..     186     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                          CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDl 38 
                                       ++a+   +GGvG++++++ La  l +lg +v + D+
  gi|313126023|ref|YP_004036293.1| 100 IIAVASGKGGVGKSTVAVNLAAGLSKLGARVGLFDA 135
                                       67888889***********************88886 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                          CBP_BcsQ 105 llaalkelk.eqyrwillDlpagasaltrellala 138
                                       l++ ++ ++ ++ ++++lDlp g+ +++ ++l++ 
  gi|313126023|ref|YP_004036293.1| 194 LTQLVEDVQwGELDYMILDLPPGTGDTQLTVLQTL 228
                                       455566666788999*******9998887777654 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.86   1.1e+03       8      14 ..     160     166 ..     158     167 .. 0.90
   2 ?   10.1   0.1   0.00046      0.59      12      23 ..     266     277 ..     263     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.86
                           DUF1610   8 laprEra 14 
                                       ++p+E++
  gi|313126023|ref|YP_004036293.1| 160 IVPPEKY 166
                                       9*****9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00046
                           DUF1610  12 EravvFpCPNCG 23 
                                       E+ ++F CP CG
  gi|313126023|ref|YP_004036293.1| 266 ENMSSFRCPDCG 277
                                       6679*******9 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.17       1      45 [.     106     148 ..     106     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtisl 45 
                                       G+  +GKST+a +L+  + + g ++ + D+D+  ++  +P ++++
  gi|313126023|ref|YP_004036293.1| 106 GKGGVGKSTVAVNLAAGLSKLGARVGLFDADIYGPN--VPRMVAA 148
                                       66789**************************98887..5666666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.23      66     120 ..      64     120 ..      55     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHTTSEEEE--TT..THTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  66 eelkeelealgyevllvsak..tkegleelkellkdktsvlvGqSGvGKStLinall 120
                                        +++e++++++yev l+ +   + ++ e++ + +k+ ++v  G+ GvGKSt+  +l+
  gi|313126023|ref|YP_004036293.1|  64 AQVREQFSDTDYEVDLTAKIpsDLSADEDVLPGVKNIIAVASGKGGVGKSTVAVNLA 120
                                       566777788888876664431133555688888999999************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2291.21
//
Query:       gi|313126024|ref|YP_004036294.1|  [L=96]
Description: hypothetical protein Hbor_12620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 573.25
//
Query:       gi|313126025|ref|YP_004036295.1|  [L=211]
Description: uracil-DNA glycosylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-21   77.2   0.0    1.6e-21   76.9   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0   8.8e-26   1.6e-21       2     118 ..      34     163 ..      33     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 8.8e-26
                                       HC-CTT-SEEEEESSTCHHHHHHSSSS.-.STT--HHHHHHHCCCCCCCHHG.....CTEEEEESSS....SECGCT CS
                               UDG   2 gegppdakvvivGeaPgaeedatglpFsg.ragnllrkllneaglkrdlese.....qgvyitnvvkcrppgnrdtp 72 
                                       g+g+   + +++Ge+P    d+tg pF+g +ag++l+++l ++g++r +++      q+v++t + +cr p++r  p
  gi|313126025|ref|YP_004036295.1|  34 GYGDVGGEFLFIGEQPRGGADETGVPFTGdPAGERLQRILGDLGFSRSRPDSdepdlQNVFLTYLTRCRHPERR--P 108
                                       788889999**************************************777669****************99967..* PP

                                       TCCCCTCCHHHHHHHHHHHHSSEEEEESHHHHHH...........HHHHSCESCC CS
                               UDG  73 tsaeikacaplleeeiellkprlivllGktaakall.........geklgklrgk 118
                                        ++ei  c p+l++e++ ++p+++v +G+  +++l           + +++++ +
  gi|313126025|ref|YP_004036295.1| 109 DEEEILTCEPYLNAEVRMINPEILVPIGQRTLESLAidyttrapdSFDIEEAHAT 163
                                       ******************************9999844555555543345555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1259.16
//
Query:       gi|313126026|ref|YP_004036296.1|  [L=77]
Description: hypothetical protein Hbor_12640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0057   16.3   1.9     0.0057   16.3   1.9    1.0  1  DUF5336          Family of unknown function (DUF5336)
  ------ inclusion threshold ------
      0.024   14.5   4.1      0.029   14.3   4.1    1.1  1  DUF3487          Protein of unknown function (DUF3487)
      0.029   13.1   2.7      0.029   13.2   2.7    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
      0.044   13.8  10.3      0.048   13.7  10.3    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.28   10.3   0.9        0.3   10.2   0.9    1.0  1  Herpes_LMP1      Herpesvirus latent membrane protein 1 (LMP1)
       0.29   11.4   5.2       0.36   11.1   5.2    1.2  1  VirB3            Type IV secretory pathway, VirB3-like protei
          1   10.1   7.2        1.5    9.6   7.0    1.4  1  DUF2809          Protein of unknown function (DUF2809)
        1.8    8.7   5.6        2.6    8.2   5.6    1.3  1  SdpI             SdpI/YhfL protein family


Domain annotation for each model (and alignments):
>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.9   2.5e-06    0.0057      65     124 ..       7      66 ..       1      76 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-06
                           DUF5336  65 adleeasatsgglglavvllLlagLlAgvslLPkqksktavaAvlsvlgfLlvlaevina 124
                                       + l ++++t +   l+ v+++l g+ A v  LP ++s++ ++Av+ +++++++++    +
  gi|313126026|ref|YP_004036296.1|   7 DGLAHSRLTRVLCRLGAVAVVLLGIAAVVVFLPAAESWALLVAVFLIAAVVGMVFYGARM 66 
                                       556677778888888888899999****************************99976555 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   4.1   1.3e-05     0.029      27      73 ..      17      67 ..       7      71 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                           DUF3487 27 vlaglglvvglvlglllall....vgslaliptialllvllvvlvggklla 73
                                      vl+ lg+v+ ++lg+ ++++    ++s+al++++ l+++++++++ g  +a
  gi|313126026|ref|YP_004036296.1| 17 VLCRLGAVAVVLLGIAAVVVflpaAESWALLVAVFLIAAVVGMVFYGARMA 67
                                      45567777777777655444223389**********999998887776554 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.7   1.3e-05     0.029     389     438 ..      21      70 ..       5      77 .] 0.51

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                           DUF2207 389 gliilglilillallllvlllvfllilllillliaiivlllfsrllgrrt 438
                                       ++++++++l+++a++++ ++   +++l+ ++l++a++ ++++ +++   t
  gi|313126026|ref|YP_004036296.1|  21 LGAVAVVLLGIAAVVVFLPAAESWALLVAVFLIAAVVGMVFYGARMASKT 70 
                                       22233333333333333333566666666666666666666656665544 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  10.3   2.1e-05     0.048      40      97 ..      21      73 ..      10      77 .] 0.55

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                   Phage_holin_3_6 40 lgaagvlallalllllval..alalaalwlaalivaavllvlagvlalvglkklkkakpl 97
                                      lg a++++ll++++++v+l  a        +al+va++l+++ + +++ g + ++k +++
  gi|313126026|ref|YP_004036296.1| 21 LG-AVAVVLLGIAAVVVFLpaAE------SWALLVAVFLIAAVVGMVFYGARMASKTATP 73
                                      33.33333333333333333132......3466787777777788888888877775554 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.9   0.00013       0.3      76     139 ..      17      76 ..      11      77 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP1  76 llcplgalcllllmitlllialwnlhgqalylgivlfifgcllvlglwiyllellwrlgatiwq 139
                                       +lc lga++++ll i+ +++ l      al + + l+      v+g+  y   +  +  +  wq
  gi|313126026|ref|YP_004036296.1|  17 VLCRLGAVAVVLLGIAAVVVFLPAAESWALLVAVFLI----AAVVGMVFYGARMASKTATPYWQ 76 
                                       79********************999999998765443....45677777777777766666666 PP

>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   5.2   0.00016      0.36      21      59 ..      24      62 ..      12      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                             VirB3 21 elvllnllvsvilflvglslwillllvplhlvlrliakr 59
                                      ++v+l+++++v++fl +   w+ll++v+l+++   ++ +
  gi|313126026|ref|YP_004036296.1| 24 VAVVLLGIAAVVVFLPAAESWALLVAVFLIAAVVGMVFY 62
                                      68999**********999999999999988887777665 PP

>> DUF2809  Protein of unknown function (DUF2809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   7.0   0.00065       1.5      10      47 ..      21      58 ..      14      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00065
                           DUF2809 10 lGdvlvvillyllvrllvpkksplllalavllfavliE 47
                                      lG v vv+l +++v++++p+++ + l++av+l+a ++ 
  gi|313126026|ref|YP_004036296.1| 21 LGAVAVVLLGIAAVVVFLPAAESWALLVAVFLIAAVVG 58
                                      799*******************************9985 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.6    0.0012       2.6      32      65 ..      28      61 ..       9      63 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                              SdpI 32 lwiiaGlillllalgavvlvllvlvlllvivpii 65
                                      l+ ia ++++l+a +++ l++ v+++++v+++++
  gi|313126026|ref|YP_004036296.1| 28 LLGIAAVVVFLPAAESWALLVAVFLIAAVVGMVF 61
                                      2233334444444444445555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1232  (0.0687155); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 465.88
//
Query:       gi|313126027|ref|YP_004036297.1|  [L=254]
Description: hypothetical protein Hbor_12650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-06   26.6   0.0    9.6e-06   25.4   0.0    1.6  2  DUF2064       Uncharacterized protein conserved in bacteria (
     0.0057   15.9   0.0       0.45    9.7   0.0    2.1  2  CofC          Guanylyl transferase CofC like
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.022   14.7   0.0    1.3  1  CTP_transf_3  Cytidylyltransferase


Domain annotation for each model (and alignments):
>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.6e-09   9.6e-06      19     110 ..      76     167 ..      69     181 .. 0.81
   2 ?   -2.3   0.0      0.62   3.7e+03      47      77 ..     184     214 ..     173     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.6e-09
                                       ---TTHHHHHHHH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-S.EEEEE-SS-TT--HHHHHHHHHHTTT-SEEEE CS
                           DUF2064  19 galdkalaeqlalakglevlpQqggdlgeRlarafdrafeagee.pvlliGsDcpqltaalleqAfeaLeeadaVlg 94 
                                       +a+++ +a++l+ + + +++ Q g+++ +R  + + + + ++    + ++  D p +t++ +++++ +L+++++Vlg
  gi|313126027|ref|YP_004036297.1|  76 AAVRTLAADALDDPSEARFEVQVGSSVSARAGNTMMHLLRDEDVrTAAVVRGDAPFFTRSKIDSMAMKLRTNEVVLG 152
                                       4556666777788888888888888888888888888855544449******************************* PP

                                       EBTTSSEEEEEEEG-G CS
                           DUF2064  95 paeDGGYyllGlkkrl 110
                                       p++ G  y+ G++  +
  gi|313126027|ref|YP_004036297.1| 153 PSTAGRSYVAGFSD-P 167
                                       *****999999994.4 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.62
                                       HHHHHHHHHHHHTT-SEEEEE-SS-TT--HH CS
                           DUF2064  47 eRlarafdrafeageepvlliGsDcpqltaa 77 
                                       +R ++a  +++  +++p++  G D+ +l +a
  gi|313126027|ref|YP_004036297.1| 184 ARANDAGHNVAFLEMQPTVRTGVDLLTLVPA 214
                                       5555555555667778888888888888665 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   7.6e-05      0.45      20      63 ..      25      70 ..      17      87 .. 0.86
   2 !    4.1   0.0    0.0038        23      81     126 ..     112     157 ..      92     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7.6e-05
                              CofC 20 ilseeerkellkamlldvidalkr..ldvlvvsedeevleyaldel 63
                                       lse e  +l  aml+d + a++r   d+lv  + e++l+ a+ e+
  gi|313126027|ref|YP_004036297.1| 25 PLSETEAADLYAAMLKDSMVAVSRsgGDLLVNYRSEDLLPEAYREE 70
                                      59*****************999986678************999665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0038
                              CofC  81 kafeeieekeviiipsdiPlikkedvkdllelekradvviaPargG 126
                                       + + + +    +++  d P+ ++ +++ +  + +  +vv+ P+  G
  gi|313126027|ref|YP_004036297.1| 112 HLLRDEDVRTAAVVRGDAPFFTRSKIDSMAMKLRTNEVVLGPSTAG 157
                                       445666777889****************99888889******9988 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.7e-06     0.022      71     160 ..     100     201 ..      97     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-06
                                       SSHHHHHHHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTS.........SEEEEEEETTSHHHHTS CS
                      CTP_transf_3  71 esdterflevvkaflmseneeiivnlqGdnPllqeevikkaietlkenqed.........ylstlvkkvgkeeevln 138
                                       +s+++r  + ++ +l +e+ +++  + Gd P+   + i+ ++ +l+ n+           y++   ++++ ++e+++
  gi|313126027|ref|YP_004036297.1| 100 SSVSARAGNTMMHLLRDEDVRTAAVVRGDAPFFTRSKIDSMAMKLRTNEVVlgpstagrsYVAGFSDPID-FSEAFT 175
                                       57899999999******9999***************************777********77777778888.****** PP

                                       TTSTEEEETTT....SBEEEEESSES CS
                      CTP_transf_3 139 andlkvlldda....gkalyfeesvi 160
                                       ++++++l+ +a     + ++ e++++
  gi|313126027|ref|YP_004036297.1| 176 TPEVETLTARAndagHNVAFLEMQPT 201
                                       ******99998566666677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1585.63
//
Query:       gi|313126028|ref|YP_004036298.1|  [L=107]
Description: hypothetical protein Hbor_12670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 588.30
//
Query:       gi|313126029|ref|YP_004036299.1|  [L=217]
Description: uridine kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-49  167.3   0.0    4.1e-49  167.0   0.0    1.1  1  PRK              Phosphoribulokinase / Uridine kinase family
    8.9e-07   29.0   0.2    1.6e-05   24.8   0.2    2.1  1  dNK              Deoxynucleoside kinase
    8.1e-05   23.2   0.4    0.00018   22.0   0.4    1.6  1  AAA_18           AAA domain
    0.00024   20.8   0.8      0.017   14.8   0.0    2.2  2  CoaE             Dephospho-CoA kinase
    0.00057   19.2   0.0     0.0012   18.1   0.0    1.6  1  Zeta_toxin       Zeta toxin
    0.00081   19.9   0.1     0.0012   19.3   0.1    1.4  1  ABC_tran         ABC transporter
     0.0022   17.8   0.3       0.37   10.6   0.0    2.2  2  AAA_26           AAA domain
     0.0036   17.6   0.0     0.0064   16.8   0.0    1.5  1  AAA_22           AAA domain
     0.0082   16.0   0.0      0.017   15.0   0.0    1.6  1  CPT              Chloramphenicol phosphotransferase-like prot
  ------ inclusion threshold ------
      0.016   15.1   0.6        0.2   11.6   0.2    2.5  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.021   14.8   0.1      0.038   14.0   0.1    1.4  1  T3SS_needle_reg  YopR, type III needle-polymerisation regulat
      0.022   15.0   0.0      0.038   14.2   0.0    1.4  1  AAA_28           AAA domain
      0.023   15.1   3.8        2.5    8.6   0.1    2.5  2  AAA_17           AAA domain
      0.041   14.0   0.0      0.082   13.1   0.0    1.5  1  AAA_33           AAA domain
      0.071   12.8   0.6       0.93    9.2   0.3    2.1  2  AAA_24           AAA domain
      0.097   11.7   0.9       0.15   11.1   0.2    1.6  2  T2SSE            Type II/IV secretion system protein
       0.13   12.8   1.2        0.2   12.1   1.2    1.6  1  AAA_23           AAA domain
       0.14   11.3   0.6       0.33   10.1   0.3    1.7  2  NB-ARC           NB-ARC domain
       0.17   12.0   0.1       0.45   10.6   0.0    1.7  1  Torsin           Torsin
       0.39   10.8   2.9       0.47   10.5   1.1    1.9  2  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   0.0   4.6e-52   4.1e-49       1     192 [.       7     187 ..       7     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 4.6e-52
                               PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyev 77 
                                       vIg+ag  GaGkttvar +++ +g e+        +  + +d+ ++dl+  e ++++  +v+++ p a++++ll  +
  gi|313126029|ref|YP_004036299.1|   7 VIGIAGGTGAGKTTVARLITENVG-ES--------VTRIPIDNYYNDLSHLELSERE--SVNYDHPSAFEWELLHDQ 72 
                                       8**********************9.44........458999*********9999998..899999************ PP

                               PRK  78 lkelkegkkvdkpiYsheteeaapdkeeliegadvlviEGlhalydervaelldlkiyvdisidlelarklqRDiae 154
                                       l +l +g+ ++ p+Y++e ++++  ++e++e++dv++iEG++al+de++ e+ dl+ yv ++ d+++ r++qRD+ e
  gi|313126029|ref|YP_004036299.1|  73 LATLLQGQPIEMPKYDFEVHNRKD-ETETVEPTDVIIIEGILALHDEEINEMFDLRLYVETDADVRILRRIQRDVIE 148
                                       **********************98.**************************************************** PP

                               PRK 155 RGrsleavldsil.rrkpdyvnyikpqfseadliiqrvp 192
                                       RGr+le+v+d++l  +kp  +++i+p++++adlii+ + 
  gi|313126029|ref|YP_004036299.1| 149 RGRDLEGVIDQYLsTVKPMHEQFIEPTKKQADLIIPEGA 187
                                       *************9*********************9865 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.2   1.8e-08   1.6e-05       1     178 [.       8     183 ..       8     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.8e-08
                                       EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSSHHHHHHHHSHHHHH..HHHHHHHHHHHHHHHHCHHSSS CS
                               dNK   1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqknlLekfYkdpsrws..falqtyvllsrlkqqlealatk 75 
                                       i + G  gaGK+t++ l+++++g  v + p+d++ n+ +  Le+  ++  ++    a++ ++l  +l   l+  +  
  gi|313126029|ref|YP_004036299.1|   8 IGIAGGTGAGKTTVARLITENVGESVTRIPIDNYYNDLS-HLELSERESVNYDhpSAFEWELLHDQLATLLQG-QPI 82 
                                       6799******************************88765.566666666665411456666666666666544.333 PP

                                       -EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH.-SEEEEEE--HHH.HHHHHHH....CTTC CS
                               dNK  76 qvvvleRsiysdryiFakalaekgtlseeelkiykelldnlleelak.pdlliYLkaslet.clerikk....Rgre 146
                                       ++   +  +++          e +t++++++ i + +l    ee+++ +dl  Y++++ ++ +l+ri++    Rgr 
  gi|313126029|ref|YP_004036299.1|  83 EMPKYDFEVHNR-------KDETETVEPTDVIIIEGILALHDEEINEmFDLRLYVETDADVrILRRIQRdvieRGRD 152
                                       333344444444.......58899*************999999999999**********96499***9755547887 PP

                                       CCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEE CS
                               dNK 147 eekkieldYlekLhekyeewlkklnevpvlvi 178
                                        e  i  +Yl +++  +e++++ +++   l+i
  gi|313126029|ref|YP_004036299.1| 153 LEGVI-DQYLSTVKPMHEQFIEPTKKQADLII 183
                                       77665.58*************99887764444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.4   2.1e-07   0.00018       1     117 [.       8     148 ..       8     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.1e-07
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf......gvnlrdvakenglllevdpealdeskrldedkldklldaleenss. 69 
                                       I+++G  G+GKtt+a+ + +   ++         ++d+   + ++ e  ++  ++s  + e  +d+l ++l++++  
  gi|313126029|ref|YP_004036299.1|   8 IGIAGGTGAGKTTVARLITENVgESvtripiDNYYNDLSHLELSERESVNY-DHPSAFEWELLHDQLATLLQGQPIe 83 
                                       89****************998744477777433333333333333333332.3334444444455566666665558 PP

                            AAA_18  70 ................aleegknlvidghlaele..seaakdikkvvLtaspeelleRlekRgyee 117
                                                       + e  ++++i+g+la +     +++d+   +++++ ++++ R  +R+  e
  gi|313126029|ref|YP_004036299.1|  84 mpkydfevhnrkdeteTVEPTDVIIIEGILALHDeeINEMFDLR-LYVETDADVRILRRIQRDVIE 148
                                       8888999999999999999**********997751155666666.9******99999988887555 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.9e-05     0.017       2      23 ..       7      29 ..       6      52 .. 0.86
   2 ?    4.7   0.2     0.024        21     104     148 ..     106     150 ..      91     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                      EEEEEESTTSSHHHHHHHHHH.T CS
                              CoaE  2 ivgltGgiasGKstvanlfad.l 23
                                      ++g++Gg ++GK+tva+l+++ +
  gi|313126029|ref|YP_004036299.1|  7 VIGIAGGTGAGKTTVARLITEnV 29
                                      8****************998844 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                                       SEEEEE-TTTTTTTGGGGSSEEEEEE--HHHHHHHHHHCCTSTHH CS
                              CoaE 104 kyvlldvPLLvEkqlekliervlvvdvelelqveRlvardgvsee 148
                                        +++  +  L +++++++++  l v+ + + ++ R ++rd +++ 
  gi|313126029|ref|YP_004036299.1| 106 VIIIEGILALHDEEINEMFDLRLYVETDADVRILRRIQRDVIERG 150
                                       4455556668889999************************98875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.4e-06    0.0012      19      54 ..       8      41 ..       4      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-06
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdl 54
                                      i ++G++GAGK+++a+l+++++  +++v r+  D++
  gi|313126029|ref|YP_004036299.1|  8 IGIAGGTGAGKTTVARLITENV--GESVTRIPIDNY 41
                                      569******************9..899999999887 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.4e-06    0.0012      13      46 ..       7      40 ..       3     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-06
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldg 46
                                      +++i G +GaGK+t+++l+++++     +i +d+
  gi|313126029|ref|YP_004036299.1|  7 VIGIAGGTGAGKTTVARLITENVGESVTRIPIDN 40
                                      789*******************999888887764 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00042      0.37       9     142 ..      13     147 ..       6     150 .. 0.76
   2 ?    5.2   0.0     0.019        17      89     123 ..     169     203 ..     153     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                            AAA_26   9 dtgvGKTvvslgLvralkrkgvkvgyfK.Piqtgieededselikellgldqtyelpeplalsaplspelaarqege 84 
                                       +tg+GKT+v+ ++++         ++ + Pi ++ ++ +  el ++      +y++p+++  +  l ++la  ++g+
  gi|313126029|ref|YP_004036299.1|  13 GTGAGKTTVARLITENV-----GESVTRiPIDNYYNDLSHLELSERES---VNYDHPSAFEWE-LLHDQLATLLQGQ 80 
                                       68999999999999999.....33333338888887666666665554...566666677665.5678899999999 PP

                            AAA_26  85 didlekiv.........kelekdadivvVEGagglgvpiteellnadiaknlgapvilVargglgti 142
                                        i++ k+           e  + +d++++EG+  l +  ++e+++ ++  + +a+v ++ r++++ i
  gi|313126029|ref|YP_004036299.1|  81 PIEMPKYDfevhnrkdeTETVEPTDVIIIEGILALHDEEINEMFDLRLYVETDADVRILRRIQRDVI 147
                                       999999999999997654455567******************************9977777766655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.019
                            AAA_26  89 ekivkelekdadivvVEGagglgvpiteellnadi 123
                                       e++++  +k+ad+++ EGa ++ v+++ee+++a++
  gi|313126029|ref|YP_004036299.1| 169 EQFIEPTKKQADLIIPEGANSVAVNLLEEKVQAEV 203
                                       667788899********************999886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.1e-06    0.0064      10     101 ..      10     113 ..       7     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.1e-06
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee...............erpevvfvtlpsstsskdllrellralglelkae 71 
                                       + G +G+GKTt++r ++e+  e    ++                ++e v ++ ps  +++ l  +l+  l+ +  + 
  gi|313126029|ref|YP_004036299.1|  10 IAGGTGAGKTTVARLITENVGES--VTRipidnyyndlshlelSERESVNYDHPSAFEWELLHDQLATLLQGQPIE- 83 
                                       7799**************98654..444569***********9999999*********************976655. PP

                            AAA_22  72 rlsseellealeqalrarav.....ielliiDEaq 101
                                                 +e + r+  +     + ++ii+ + 
  gi|313126029|ref|YP_004036299.1|  84 -----MPKYDFEVHNRKDETetvepTDVIIIEGIL 113
                                       .....222333333333333333444555555555 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.9e-05     0.017       4      55 ..       8      59 ..       5      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                                      EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGTSTTSEEEE CS
                               CPT  4 ilLnGgsssGKsslaralqevldepwlhlgvDafvealppkrqdeadglefe 55
                                      i + Gg+ +GK+++ar + e + e+   +++D++ + l    ++e + ++++
  gi|313126029|ref|YP_004036299.1|  8 IGIAGGTGAGKTTVARLITENVGESVTRIPIDNYYNDLSHLELSERESVNYD 59
                                      66789*******************************9999888888887776 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00022       0.2       1      99 [.       7     112 ..       7     125 .. 0.78
   2 ?    0.7   0.0      0.49   4.4e+02      78     101 ..     165     189 ..     149     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikel... 74 
                                       v+gi+g  g+GKTt    + + + ++  r+ +    ++  +++  ++ s ++ +  A e  + +++  +l++ +   
  gi|313126029|ref|YP_004036299.1|   7 VIGIAGGTGAGKTTVARLITENVGESVTRIPIDNYYNDLSHLELSERESVNYDHPSAFEWELLHDQLATLLQGQpie 83 
                                       799***********877766777777777777666777777999999999999999999999999999998877665 PP

                              MobB  75 ....eeaelsleellarlsevDlvlvEGf 99 
                                           + +  + ++ +++++++D++++EG 
  gi|313126029|ref|YP_004036299.1|  84 mpkyDFEVHNRKDETETVEPTDVIIIEGI 112
                                       44433334566777888888*******96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.49
                              MobB  78 elsleellarl.sevDlvlvEGfkk 101
                                       ++  e+ ++ + +++Dl++ EG  +
  gi|313126029|ref|YP_004036299.1| 165 KPMHEQFIEPTkKQADLIIPEGANS 189
                                       5666777777745699999999655 PP

>> T3SS_needle_reg  YopR, type III needle-polymerisation regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.2e-05     0.038      41     139 ..     101     198 ..      92     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                                       -SS--HHHHHHHHHHHHHHHHHHHTT--S---HHHHHHHHHHHHHHHS-SSHHHHHHHHHHHHT----H...HHHHH CS
                   T3SS_needle_reg  41 kkpsddavlevLlapvkeeLladfgglqgsvkPplDlpeLrkvlrqfaplGkqkeavLlevleeikplPeneylsdL 117
                                        +p+d  ++e +la   ee+   f  l++ v+   D+  Lr++ r+    G+  e v+ + l+ +kp+   e   + 
  gi|313126029|ref|YP_004036299.1| 101 VEPTDVIIIEGILALHDEEINEMFD-LRLYVETDADVRILRRIQRDVIERGRDLEGVIDQYLSTVKPMH--EQFIEP 174
                                       6789999999888877777777775.59***************************************98..677888 PP

                                       HHHHHHHH-XX..XXXXXXXXXXX CS
                   T3SS_needle_reg 118 irkeLkilipk..namvdnllrns 139
                                        +k   ++ip+  n++  nll++ 
  gi|313126029|ref|YP_004036299.1| 175 TKKQADLIIPEgaNSVAVNLLEEK 198
                                       888888888854488888888765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.3e-05     0.038       2      66 ..       8      75 ..       7      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv..edllafaervleeqlee 66
                                      i i Gg ++GKTt+++ ++++ g +v + +   ++++++  +  + ++v  + + af+ ++l+ ql++
  gi|313126029|ref|YP_004036299.1|  8 IGIAGGTGAGKTTVARLITENvGESVTRIPIDNYYNDLSHLELSERESVnyDHPSAFEWELLHDQLAT 75
                                      5589***************9988888888888888888866666666555467788888888777765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0027       2.5       2      20 ..      12      30 ..      11      37 .. 0.87
   2 ?    7.0   0.6    0.0085       7.6      93     130 ..     117     154 ..     102     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0027
                                      E-TTSSHHHHHHHHHHHHT CS
                            AAA_17  2 GgPGsGKgtqceklvekyg 20
                                      Gg G+GK+t+++ + e++g
  gi|313126029|ref|YP_004036299.1| 12 GGTGAGKTTVARLITENVG 30
                                      99*********99999877 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0085
                                       HHHHHHHH..SEEEEEE--HHHHHHHHHHHT..TST-TS- CS
                            AAA_17  93 pkevleelkpdaiilleadpeeilerrlkdr..trgrddd 130
                                       ++e+ e +  d+ +++e+d+++ + rr++++  +rgrd +
  gi|313126029|ref|YP_004036299.1| 117 DEEINEMF--DLRLYVETDADVRILRRIQRDviERGRDLE 154
                                       44444443..999********9999999985348999865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.1e-05     0.082       4      63 ..      10      73 ..       7      83 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.1e-05
                            AAA_33  4 lvGlpGsGKstlaerllkklg..avllssdtlrrrlfg...tdqqsktdytrvldrlyqilnela 63
                                      + G  G+GK+t+a+ + ++ g  ++++  d++++ l     ++++s ++  + +   ++ l++ +
  gi|313126029|ref|YP_004036299.1| 10 IAGGTGAGKTTVARLITENVGesVTRIPIDNYYNDLSHlelSERESVNY-DHPSAFEWELLHDQL 73
                                      67889************9999*************999976655655544.333333333444443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3     0.001      0.93       4      33 ..       7      40 ..       5     109 .. 0.72
   2 ?    2.2   0.0      0.15   1.3e+02     133     190 ..      93     146 ..      89     153 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                            AAA_24  4 kiliyGpsgiGKTtlakel....gpkplfidtek 33
                                       i i G  g+GKTt+a+ +    g+++  i +++
  gi|313126029|ref|YP_004036299.1|  7 VIGIAGGTGAGKTTVARLItenvGESVTRIPIDN 40
                                      5889************999666666666666665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                            AAA_24 133 trkdedpegeakytrlepklgkktanelkeevDlvlranlkredkvgervlktskses 190
                                        rkde+++ e++ + ++  +     +e++e++Dl l+++ +     + r+l + ++++
  gi|313126029|ref|YP_004036299.1|  93 NRKDETETVEPTDVIIIEGILALHDEEINEMFDLRLYVETD----ADVRILRRIQRDV 146
                                       567777766644344444444555889**********9986....5666666655555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00017      0.15     132     160 ..       8      36 ..       3      41 .. 0.84
   2 ?   -2.2   0.0         2   1.8e+03      19      75 ..     130     185 ..     110     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                             T2SSE 132 ilvsGgTgsGKttllyallkeinksderi 160
                                       i ++GgTg GKtt++  + + + +s  ri
  gi|313126029|ref|YP_004036299.1|   8 IGIAGGTGAGKTTVARLITENVGESVTRI 36 
                                       6699**********999999888876655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                             T2SSE  19 vekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpe 75 
                                       ve++ +v++  r+++ +++  ++l +  + + +s+++ + ++ i+  ++  d  +pe
  gi|313126029|ref|YP_004036299.1| 130 VETDADVRILRRIQRDVIERGRDL-EGVIDQYLSTVKPMHEQFIEPTKKQADLIIPE 185
                                       555555666556655333333333.34555556667777776666666666666664 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   0.00023       0.2      23      54 ..       9      40 ..       6     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                            AAA_23 23 lItGpNGaGKTTildAiklaLygetprlsrks 54
                                       I G +GaGKTT+ + i+   ++ ++r + ++
  gi|313126029|ref|YP_004036299.1|  9 GIAGGTGAGKTTVARLITENVGESVTRIPIDN 40
                                      699***********999977777776666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00036      0.33      20      43 ..       5      28 ..       2      36 .. 0.87
   2 ?   -2.2   0.0         2   1.8e+03      42      83 ..     116     153 ..     112     166 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00036
                                      SEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 20 slvvalvGmgGvGKttlakqilnk 43
                                      s+v+++ G  G GKtt+a+ i ++
  gi|313126029|ref|YP_004036299.1|  5 SFVIGIAGGTGAGKTTVARLITEN 28
                                      69****************999876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                                       CSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTS CS
                            NB-ARC  42 nksdevegrFdsvawvvvsktdkseeiletilkeLslseddl 83 
                                       ++ +e+++ Fd   +v   +td   +il++i +++ ++  dl
  gi|313126029|ref|YP_004036299.1| 116 HD-EEINEMFDLRLYV---ETDADVRILRRIQRDVIERGRDL 153
                                       45.6777777777776...45666667777777666665554 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0005      0.45      54      89 ..       6      41 ..       3      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                                      EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEEE CS
                            Torsin 54 LvlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvkk 89
                                      +v+ + G tG+Gk  va++i en+ ++  r ++ ++
  gi|313126029|ref|YP_004036299.1|  6 FVIGIAGGTGAGKTTVARLITENVGESVTRIPIDNY 41
                                      689999*****************9777666665555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   0.00052      0.47      26      47 ..       8      29 ..       7      41 .. 0.85
   2 ?   -0.6   0.0       1.3   1.2e+03     167     223 ..      81     142 ..      38     146 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00052
                             DUF87 26 lAilgsTGsGKSntvavLleel 47
                                      ++i g TG+GK++ ++++ e++
  gi|313126029|ref|YP_004036299.1|  8 IGIAGGTGAGKTTVARLITENV 29
                                      5899********9999998765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                             DUF87 167 rlldkledllrkggsf...snsstdliallleklekegkitii.dlsgvdelaqql.vvsvi 223
                                        ++++++d+  +++++   + ++td+i     ++ ++++i+ + dl  + e+++++ +   i
  gi|313126029|ref|YP_004036299.1|  81 PIEMPKYDFEVHNRKDeteTVEPTDVIIIEGILALHDEEINEMfDLRLYVETDADVrILRRI 142
                                       56778888888887776666666666655555666666665444777777777666565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1254.91
//
Query:       gi|313126030|ref|YP_004036300.1|  [L=439]
Description: amino acid/amide ABC transporter substrate-binding protein, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-26   91.6   7.7    9.8e-20   71.5   1.3    2.5  2  Peripla_BP_6   Periplasmic binding protein
    1.8e-17   63.5   0.6    1.4e-12   47.4   0.5    2.1  2  ANF_receptor   Receptor family ligand binding region
    0.00056   19.0   0.1     0.0031   16.6   0.1    2.1  2  Peripla_BP_5   Periplasmic binding protein domain
  ------ inclusion threshold ------
      0.089   12.2   3.4       0.32   10.4   3.4    2.0  1  UCR_Fe-S_N     Ubiquitinol-cytochrome C reductase Fe-S subuni
        2.9    7.9  11.6      0.045   13.6   3.0    2.7  2  TAT_signal     TAT (twin-arginine translocation) pathway sign


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   1.1e-08   3.9e-05     190     311 ..      38     153 ..      36     169 .. 0.76
   2 !   71.5   1.3   2.7e-23   9.8e-20       1     186 [.     244     433 ..     244     437 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-08
                                       T-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC.-CHHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHH CS
                      Peripla_BP_6 190 gadavllagtgadlaallkaaaeaGldakrillvsws.gseedlkalggeaaegvlavtpyfpdldnpavrafvaay 265
                                       g++ ++++g++++ ++l++ + ++    + i lv  +  + ++  ++g +++++v++++p   ++ +p ++af + +
  gi|313126030|ref|YP_004036300.1|  38 GPEGLVVIGYPESGIQLFRDYYSQSDGSESI-LVPDGlRDGAMPGQVG-NDMANVTGTAP---AAGGPNQEAFNQLF 109
                                       6777777777777777777775555554444.3333313344334444.46777777755...66899********* PP

                                       HHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHHHHHHHHHS CS
                      Peripla_BP_6 266 eaayggapppsqfaaggyiaadlllealkaagsltreavraalesl 311
                                       ++ y +a  p  f+++ y++++ll+ a  aag++++ a++++++ +
  gi|313126030|ref|YP_004036300.1| 110 QDEYNAA--PGVFTSQSYDSVALLILANAAAGENSGPALKEQMRRI 153
                                       *****98..**********************************975 PP

  == domain 2  score: 71.5 bits;  conditional E-value: 2.7e-23
                                       EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-B CS
                      Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgpl 77 
                                       +i +G l p++G++as+g ++ ++aq  ++++N a    G +++ +++D++ +p+ + +aa+ lv+ +gv ++ g  
  gi|313126030|ref|YP_004036300.1| 244 EISVGILLPETGDLASVGAPMIQAAQIPVKQVNNAN-PAGLTVNAQIEDTQTSPSAGTSAAQALVS-AGVPGVCGSA 318
                                       589*******************************95.58***************************.*********9 PP

                                       SHHHHHHHHHHHHH.HT-EEEESS....-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHH CS
                      Peripla_BP_6  78 ssavaaavaevlak.dgvpvigpa....gltgekcspyvfslgpsysaqasalveylakelggkkvalvyadyafgr 149
                                       ss+v   v++ +   + v+  +p+    + ++ + ++ +f+++ps+  q++ +++ + + l +++v ++ +++ +g+
  gi|313126030|ref|YP_004036300.1| 319 SSGVNVPVSQQAFIpNEVVGCSPSstalSVSNLEDNDFIFRTAPSDFLQGRVMAQVMSERLEASTVSTLFVNNDYGQ 395
                                       999988886644442666666677333345588**********************9888899*************** PP

                                       HHHHHHHHHHHCC.TEEEEEEEEE-TTHHHHHHHHHHH CS
                      Peripla_BP_6 150 egiaalkaaakaa.Ggevvgeepvplgttdfsaqvlqi 186
                                       ++ + ++ +++++ +gev+ ++ + +g++++s+++  +
  gi|313126030|ref|YP_004036300.1| 396 QLSNRFANVFEEQfDGEVYHQTAFNIGESSYSSVIETA 433
                                       ************99999****************99766 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.8e-06     0.017     246     353 ..      54     209 ..      40     210 .. 0.69
   2 !   47.4   0.5   3.9e-16   1.4e-12       4     169 ..     266     433 ..     264     437 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.8e-06
                                       HHHHHHH........................................ST--CCCSSSTCCGSTTCCHHHHH...HHH CS
                      ANF_receptor 246 kfsefld........................................kreklsdekqnyenegkeqisyqaalmYda 282
                                        f++++                                         ++e +++  q+  n+ +  +++q+   Yd+
  gi|313126030|ref|YP_004036300.1|  54 LFRDYYSqsdgsesilvpdglrdgampgqvgndmanvtgtapaaggpNQEAFNQLFQDEYNAAPGVFTSQS---YDS 127
                                       55555555555555555555555666666666666666666666655555555444444444444578788...*** PP

                                       HHHHHHHHHHHHCHH..........SSSHCCB-HHHHCCHHHHHHHHHHHT-EEEETTSCEEB-TTSBBE.-EEEEE CS
                      ANF_receptor 283 VyllaeAlnkllrkk..........kpgralscntlkpweggqkllrylrnvnfeGltGdvkfdengdrv.ptydil 348
                                       V ll  A   ++++           +++  ++    +++ +      +  ++n++G +    f+e+gd + ++y i+
  gi|313126030|ref|YP_004036300.1| 128 VALLILANAAAGENSgpalkeqmrrIANPGGDEYGPEKFVEAVEAAANGDDINYQGASSATNFNEKGDPAsAAYAIW 204
                                       ************99988888665553333334444448888888888999*************************** PP

                                       EEECT CS
                      ANF_receptor 349 nlqgs 353
                                       ++ g+
  gi|313126030|ref|YP_004036300.1| 205 EFEGT 209
                                       *9875 PP

  == domain 2  score: 47.4 bits;  conditional E-value: 3.9e-16
                                       HHHHHHHHHHHT-TTSSTTEEEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHH.CCTT-EEEE CS
                      ANF_receptor   4 eAmklAveeinsdpnllpgiklgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavasla.nlfkiPvis 79 
                                       +A++  v+++n+ +    g +++++i+dt+ ++s++  aa+ ++ + v +v G++ss+v  +v++ a   +++   s
  gi|313126030|ref|YP_004036300.1| 266 QAAQIPVKQVNNAN--PAGLTVNAQIEDTQTSPSAGTSAAQALVSAGVPGVCGSASSGVNVPVSQQAfIPNEVVGCS 340
                                       57778889999773..5678*************************77**********9999998766156889999* PP

                                       SS---GGGG-TTTTTTEEESS--CHHHHHHHHHHHH.HTT--EEEEEEESSHHHHHHHHHHHHHHHHTT.-EEEEEE CS
                      ANF_receptor  80 ygstspelsdknryptflrtvpsdtsqaqAivdilk.hfgWkkvaliysdddygesglqaleeeleerg.icvalke 154
                                       ++st+ ++s+++  ++++rt+psd  q++++++++  +++  +v+++  ++dyg  + + + + +ee    +v +++
  gi|313126030|ref|YP_004036300.1| 341 PSSTALSVSNLEDNDFIFRTAPSDFLQGRVMAQVMSeRLEASTVSTLFVNNDYGQQLSNRFANVFEEQFdGEVYHQT 417
                                       *************9999******************98**************************99998779999998 PP

                                       EEST.CHHHCHHHHHH CS
                      ANF_receptor 155 kipe.ssnddevvrkl 169
                                        ++  +s++++v++  
  gi|313126030|ref|YP_004036300.1| 418 AFNIgESSYSSVIETA 433
                                       8887766677776655 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.2   7.2e+02     255     309 ..     100     152 ..      96     159 .. 0.73
   2 !   16.6   0.1   8.5e-07    0.0031       1      78 [.     245     320 ..     245     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.2
                      Peripla_BP_5 255 penkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekvreallg 309
                                       p+ +af + f++++++       + ++y +v l++ A ++ag+++  +++e++++
  gi|313126030|ref|YP_004036300.1| 100 PNQEAFNQLFQDEYNAAP--GVFTSQSYDSVALLILANAAAGENSGPALKEQMRR 152
                                       556677777777776654..33456789999999999999999999999888864 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 8.5e-07
                      Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlgrkieavvvdpasdwelfaekaeklieedkvevvfGcwt 77 
                                       i vG+L  ++G +a +   +++aa++ ++++n+a   +g +++a ++d +  +++ ++ a++l++  +v  v G+  
  gi|313126030|ref|YP_004036300.1| 245 ISVGILLPETGDLASVGAPMIQAAQIPVKQVNNAN-PAGLTVNAQIEDTQTSPSAGTSAAQALVS-AGVPGVCGSAS 319
                                       68*******************************99.59***************999999999988.78888888766 PP

                      Peripla_BP_5  78 S 78 
                                       S
  gi|313126030|ref|YP_004036300.1| 320 S 320
                                       5 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.4   8.9e-05      0.32       8      29 ..       4      24 ..       2      26 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.9e-05
                        UCR_Fe-S_N  8 eptRRDFLyiATgavgaVGaaa 29
                                      +  RRDFL   +ga+ aVGaa 
  gi|313126030|ref|YP_004036300.1|  4 DIARRDFLKR-AGAASAVGAAG 24
                                      678*****55.58889999986 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.0   1.3e-05     0.045       4      22 ..       7      25 ..       4      31 .. 0.74
   2 ?   -3.8   1.4         4   1.4e+04      14      22 ..      91      99 ..      90     100 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                        TAT_signal  4 RRdFLKgsAAaaAAaalgg 22
                                      RRdFLK ++Aa A +a+g 
  gi|313126030|ref|YP_004036300.1|  7 RRDFLKRAGAASAVGAAGL 25
                                      ******9988887777663 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4
                        TAT_signal 14 aaAAaalgg 22
                                      ++ A a+gg
  gi|313126030|ref|YP_004036300.1| 91 TGTAPAAGG 99
                                      666777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2430.93
//
Query:       gi|313126031|ref|YP_004036301.1|  [L=264]
Description: hypothetical protein Hbor_12700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.003   17.8   0.2     0.0082   16.4   0.2    1.7  1  SdrD_B    SdrD B-like domain
  ------ inclusion threshold ------
      0.017   16.0   0.2       0.09   13.7   0.1    2.1  2  DUF756    Domain of unknown function (DUF756)


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   9.1e-07    0.0082      22      73 ..     180     234 ..     175     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.1e-07
                            SdrD_B  22 kgisgvtVtLkdakgevvatttTd..asGkYkFtnltpGeYkVeftapagy.tvt 73 
                                       ++ ++vt+tL d +++vv+tt T    +G+ +F++   GeY++++++ +g  t+t
  gi|313126031|ref|YP_004036301.1| 180 ETPRDVTLTLSDGNETVVETTQTIqpGNGHLSFDGPIGGEYEMQIETDEGSdTAT 234
                                       55578*************998887446899***************9998874444 PP

>> DUF756  Domain of unknown function (DUF756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     1e-05      0.09      12      67 ..      72     130 ..      58     141 .. 0.80
   2 ?   -0.8   0.0      0.33     3e+03      24      45 ..     183     206 ..     170     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                            DUF756  12 gnlrltlrNt.gk.aaarftVydnaka..pwtytveagdqledhwklassggwYdltVtg 67 
                                       g+ + +lrN+ g+ ++++++V+ + ++    +++++agd++++  +l +s+  Yd+ V  
  gi|313126031|ref|YP_004036301.1|  72 GSAQAKLRNDsGEaTTLTLAVEYEGDRffEESFDLKAGDEVSTD-SLVASHATYDVVVET 130
                                       667889***734447778888766666***************99.688899*****9975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                            DUF756  24 aaarftVydnaka..pwtytveag 45 
                                       + +++t+ d +++   +t t+++g
  gi|313126031|ref|YP_004036301.1| 183 RDVTLTLSDGNETvvETTQTIQPG 206
                                       455666666555566666677666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1533.35
//
Query:       gi|313126032|ref|YP_004036302.1|  [L=251]
Description: branched-chain amino acid ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-32  110.7   0.0    1.1e-31  110.2   0.0    1.3  1  ABC_tran      ABC transporter
    2.4e-10   40.7   0.0    0.00028   20.8   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    8.8e-05   22.0   2.3      0.005   16.3   2.3    2.5  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00055   19.6   0.1     0.0011   18.6   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.002   18.7   0.2     0.0034   17.9   0.0    1.5  1  AAA_23        AAA domain
     0.0052   17.2   0.0     0.0077   16.6   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0065   16.2   0.0       0.13   11.9   0.0    2.0  2  AAA_15        AAA ATPase domain
     0.0077   16.0   0.3     0.0093   15.7   0.3    1.4  1  AAA_30        AAA domain
     0.0082   15.7   0.0      0.015   14.9   0.0    1.4  1  AAA_27        AAA domain
  ------ inclusion threshold ------
      0.012   15.7   0.3      0.017   15.2   0.3    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
      0.015   14.5   0.2      0.023   13.9   0.2    1.2  1  NB-ARC        NB-ARC domain
      0.019   15.2   0.2       0.14   12.4   0.1    2.1  2  AAA_22        AAA domain
       0.02   14.9   0.0      0.066   13.2   0.0    1.8  2  AAA_14        AAA domain
      0.029   14.3   0.1      0.063   13.2   0.0    1.5  2  RsgA_GTPase   RsgA GTPase
      0.043   13.1   0.0       0.09   12.0   0.0    1.5  2  Zeta_toxin    Zeta toxin
      0.056   13.5   0.0      0.088   12.8   0.0    1.4  1  MutS_V        MutS domain V
      0.072   13.5   0.2       0.28   11.6   0.2    2.1  1  AAA           ATPase family associated with various cellular 
      0.097   12.8   0.0       0.16   12.1   0.0    1.5  1  AAA_33        AAA domain
       0.12   11.8   0.1       0.28   10.5   0.0    1.6  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.15   12.3   1.1       0.73   10.1   1.1    2.1  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.15   12.4   0.0       0.24   11.8   0.0    1.4  1  RNA_helicase  RNA helicase
       0.18   11.7   0.0       0.36   10.7   0.0    1.5  1  NACHT         NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.0   1.3e-34   1.1e-31       1     137 []      36     180 ..      36     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 1.3e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l +v+++++ ge v ivG+nGaGKStL+k + gl++   G+++++ +d++  +++e+ +k +g++pq++++f  ltv
  gi|313126032|ref|YP_004036302.1|  36 LTDVDMDVHDGEYVTIVGPNGAGKSTLMKSVFGLTSHMGGTVTFETEDITGlRPEEIIHKGVGYVPQNDNVFAALTV 112
                                       679************************************************9************************* PP

                                       HHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +en            ++ ++ + +++ + e   ++ ++++ ++SgGq+q++a+ ral+ +p+llllDEp+a
  gi|313126032|ref|YP_004036302.1| 113 QENlemgayildeVPQDALDMVFERFPILE---ERKGQKAGTMSGGQQQMLAMGRALMLEPSLLLLDEPSA 180
                                       ****99999554333344555555555544...5556788*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.4e-07   0.00028       4     107 ..      51     143 ..      49     147 .. 0.83
   2 !   18.1   0.0   2.3e-06    0.0019     234     282 ..     149     194 ..     142     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.4e-07
                            AAA_21   4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrler 80 
                                       ++GpNg+GKS+L++   +l            ++ +gg+ +  +  +++  pe+ +  ++   + q+ +    l++ +
  gi|313126032|ref|YP_004036302.1|  51 IVGPNGAGKSTLMKSVFGL------------TSHMGGTVTFETEDITGLRPEEIIHKGVG-YVPQNDNVFAALTVQE 114
                                       9***************999............67888899999999999999999999999.7777777777777777 PP

                            AAA_21  81 sqv..eeklssvetllesgllldkrslee 107
                                       +    +  l +v+++ +++ + +  +lee
  gi|313126032|ref|YP_004036302.1| 115 NLEmgAYILDEVPQDALDMVFERFPILEE 143
                                       77778888888888888888888777776 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.3e-06
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell 282
                                       a  +S G++++la+  al   +   slll+DEp +gL P l+ + ++ +
  gi|313126032|ref|YP_004036302.1| 149 AGTMSGGQQQMLAMGRALMLEP---SLLLLDEPSAGLAPDLVDEMFDKI 194
                                       6679*******99999999988...****************99988655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.3   6.2e-06     0.005      25      50 ..      47      71 ..      36     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.2e-06
                                      SEEEEEESTTSSHHHHHHHHHHHCTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAilFvLGe 50
                                      +   ivGpNG+GKs l+ ++ F L  
  gi|313126032|ref|YP_004036302.1| 47 EYVTIVGPNGAGKSTLMKSV-FGLTS 71
                                      4678***************9.77763 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.4e-06    0.0011      15      39 ..      39      63 ..      33      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       +++++  + + ++Gp+G+GKSTl+
  gi|313126032|ref|YP_004036302.1| 39 VDMDVHDGEYVTIVGPNGAGKSTLM 63
                                      456666444999************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.2e-06    0.0034      23      39 ..      50      66 ..      30     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.2e-06
                            AAA_23 23 lItGpNGaGKTTildAi 39
                                       I+GpNGaGK+T++  +
  gi|313126032|ref|YP_004036302.1| 50 TIVGPNGAGKSTLMKSV 66
                                      6************9865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.4e-06    0.0077      19      62 ..      43      83 ..      32     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.4e-06
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdq 62
                                      v++g  e+v ++G+ G GKs+l+++++  l+ + g +++ ++++
  gi|313126032|ref|YP_004036302.1| 43 VHDG--EYVTIVGPNGAGKSTLMKSVF-GLTSHMGGTVTFETED 83
                                      4444..89******************9.6777766665555555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00016      0.13      16      41 ..      38      64 ..      33      72 .. 0.83
   2 ?    2.2   0.0      0.15   1.2e+02     324     353 ..     170     199 ..     142     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsile 41
                                      dv++d+ +  + +++G+N++GKS++++
  gi|313126032|ref|YP_004036302.1| 38 DVDMDVHDGeYVTIVGPNGAGKSTLMK 64
                                      556666665699*************98 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelan 353
                                       + +ll++EP a L p++  ++++++ e+ +
  gi|313126032|ref|YP_004036302.1| 170 PSLLLLDEPSAGLAPDLVDEMFDKIDEINE 199
                                       5799*********************99855 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   1.1e-05    0.0093      19      50 ..      47      78 ..      40     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                       +++++Gp G+GK+t++k++  +  + gg+v 
  gi|313126032|ref|YP_004036302.1| 47 EYVTIVGPNGAGKSTLMKSVFGLTSHMGGTVT 78
                                      4889****************999999986664 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-05     0.015      16      47 ..      38      67 ..      21      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                            AAA_27 16 drsldfsaeeadlhliyGpNEAGKstalrAis 47
                                      d  +d++ ++ +   i+GpN AGKst+++++ 
  gi|313126032|ref|YP_004036302.1| 38 D--VDMDVHDGEYVTIVGPNGAGKSTLMKSVF 67
                                      3..4555557778889************9875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   2.1e-05     0.017       2      38 ..      49      86 ..      48     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                                      EEEEESTTSSHHHHHHHHHTSTEEE.SSSTTSSSSEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaiv.sdkpgtTrdine 38
                                      v ivG   +GKStL+++ +g ++++ +   + T di+ 
  gi|313126032|ref|YP_004036302.1| 49 VTIVGPNGAGKSTLMKSVFGLTSHMgGTVTFETEDITG 86
                                      78*****************9877664666688887765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.9e-05     0.023      20      47 ..      46      73 ..      34      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                                      SEEEEEEESTTSSHHHHHHHHCCSHCCC CS
                            NB-ARC 20 slvvalvGmgGvGKttlakqilnksdev 47
                                         v++vG  G GK+tl+k+++   +++
  gi|313126032|ref|YP_004036302.1| 46 GEYVTIVGPNGAGKSTLMKSVFGLTSHM 73
                                      4589*****************9765555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00017      0.14       8      26 ..      49      67 ..      43      94 .. 0.89
   2 ?    0.8   0.0      0.68   5.5e+02      79     103 ..     152     182 ..     102     221 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                            AAA_22  8 lvvtGesGtGKTtllrrll 26
                                      ++++G+ G+GK+tl++ ++
  gi|313126032|ref|YP_004036302.1| 49 VTIVGPNGAGKSTLMKSVF 67
                                      689************9886 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.68
                            AAA_22  79 lealeqalrarav.....ielliiDEaqh.l 103
                                       ++  +q++ a ++     ++ll++DE    l
  gi|313126032|ref|YP_004036302.1| 152 MSGGQQQMLAMGRalmlePSLLLLDEPSAgL 182
                                       3444444444444445577788888855555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.1e-05     0.066       3      73 ..      47     126 ..      45     136 .. 0.62
   2 ?   -1.8   0.0       3.7     3e+03      70      85 ..     194     209 ..     183     230 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.1e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe..........kllelilek.lke.ekkty 67 
                                       + ++i+G+  +GK+tl+k ++            +++++e+ + l+ +e          ++++++ ++ ++e  ++  
  gi|313126032|ref|YP_004036302.1|  47 EYVTIVGPNGAGKSTLMKSVFGLTS---HMGGTVTFETEDITGLRPEEiihkgvgyvpQNDNVFAALtVQEnLEMGA 120
                                       6799****************95444...4445566666666544422233334444444445555443222355666 PP

                            AAA_14  68 lflDEi 73 
                                        +lDE+
  gi|313126032|ref|YP_004036302.1| 121 YILDEV 126
                                       777776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                            AAA_14  70 lDEiqevpewekalks 85 
                                       +DEi e+ ++  ++ +
  gi|313126032|ref|YP_004036302.1| 194 IDEINEAGTAILMVEQ 209
                                       5666666544444443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.8e-05     0.063      96     121 ..      42      68 ..      24      84 .. 0.80
   2 ?   -2.9   0.0       6.9   5.6e+03      68      90 ..     193     215 ..     185     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                                       HCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallp 121
                                        ++d + +++vG+ G+GKStL++++ +
  gi|313126032|ref|YP_004036302.1|  42 DVHDgEYVTIVGPNGAGKSTLMKSVFG 68 
                                       45555999*************998765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.9
                                       HHHHHHHTTSEEEE--TTTHTTH CS
                       RsgA_GTPase  68 lkeelealgyevllvsaktkegl 90 
                                         +e++++g+++l+v+++ ke+l
  gi|313126032|ref|YP_004036302.1| 193 KIDEINEAGTAILMVEQNAKEAL 215
                                       44566677777777777766655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.09      19     102 ..      49     137 ..      41     138 .. 0.88
   2 ?   -3.2   0.0       5.2   4.2e+03     126     155 ..     204     233 ..     194     237 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilk.......adpkkaseltqkdaselvekll 88 
                                       + ++G  GAGKs+l++ +   + + g+ v++++ d+  l Pe  ei+        ++++ +++lt ++  e+++ +l
  gi|313126032|ref|YP_004036302.1|  49 VTIVGPNGAGKSTLMKSVFGLTSHMGGTVTFETEDITGLRPE--EIIHkgvgyvpQNDNVFAALTVQENLEMGAYIL 123
                                       6789**************999999*****************9..555547888878899999999999999999999 PP

                        Zeta_toxin  89 qeaiengyniiveg 102
                                       +e+ +   ++++e+
  gi|313126032|ref|YP_004036302.1| 124 DEVPQDALDMVFER 137
                                       99999999999985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.2
                        Zeta_toxin 126 vvvvavkkelSrlgvldRyeeevaegRlvp 155
                                       +++v ++ +++  ++   y   + e+R+++
  gi|313126032|ref|YP_004036302.1| 204 ILMVEQNAKEALRRCDRGYVLANGENRYTD 233
                                       566777777777777777766666677766 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.088       3      39 ..      51      85 ..      49     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                      EE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE CS
                            MutS_V  3 itGpnmaGkstylrqvalivllaqiGsfvpaekaeis 39
                                      i Gpn aGkst++++v    l +++G  v  e+ +i+
  gi|313126032|ref|YP_004036302.1| 51 IVGPNGAGKSTLMKSV--FGLTSHMGGTVTFETEDIT 85
                                      89***********975..6777888888877766654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00035      0.28       2      32 ..      50      85 ..      49     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                                      EEESSTTSSHHHHHHHHHHHHT.....HEEEEEETT CS
                               AAA  2 llyGppGtGKTllakavakelg.....vefleisgs 32
                                       ++Gp G GK++l+k+v   ++     v+f + + +
  gi|313126032|ref|YP_004036302.1| 50 TIVGPNGAGKSTLMKSVFGLTShmggtVTFETEDIT 85
                                      689**************9886322233444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.16       3      20 ..      50      67 ..      49     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                            AAA_33  3 llvGlpGsGKstlaerll 20
                                       +vG++G+GKstl +++ 
  gi|313126032|ref|YP_004036302.1| 50 TIVGPNGAGKSTLMKSVF 67
                                      689***********9985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00035      0.28      25      64 ..      49      88 ..      37     105 .. 0.87
   2 ?   -1.9   0.0       2.3   1.8e+03      48     114 ..     109     177 ..     101     180 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasva 64
                                      + +vGp G+GK+ l k + +l +++  + ++e++ i+ + 
  gi|313126032|ref|YP_004036302.1| 49 VTIVGPNGAGKSTLMKSVFGLTSHMGGTVTFETEDITGLR 88
                                      7799*********************999999999998775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.3
                      Mg_chelatase  48 plseeealevakia.svagkkeeekllkrrpfraphhsaskaalvGggs.kpkpGeislahnGvLfLDE 114
                                       +l+ +e le+ +     + +++ + +++r p  + ++   + ++ Gg++     G   + +  +L+LDE
  gi|313126032|ref|YP_004036302.1| 109 ALTVQENLEMGAYIlDEVPQDALDMVFERFPILEERKGQKAGTMSGGQQqMLAMGRALMLEPSLLLLDE 177
                                       556666666544320222234444555555666666666666666665534455666666666666666 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.1    0.0009      0.73      28      80 ..     147     198 ..     140     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0009
                           SbcCD_C  28 rssgtlSGGekqflay.lalaaalaalyssaegrepalrlvfLDEAFsklDees 80 
                                       +++gt+SGG++q+la+  al++  + l+ ++   +  l++ + DE F+k+De +
  gi|313126032|ref|YP_004036302.1| 147 QKAGTMSGGQQQMLAMgRALMLEPSLLLLDE--PSAGLAPDLVDEMFDKIDEIN 198
                                       6789*******98876235555555555554..367788889999999999865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00029      0.24       2      26 ..      50      73 ..      49     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                       ++Gp+g GKStl+k+ +  l++++
  gi|313126032|ref|YP_004036302.1| 50 TIVGPNGAGKSTLMKS-VFGLTSHM 73
                                      689************9.33333333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00044      0.36       2      20 ..      48      66 ..      47      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00044
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      +v + G++G GK+tL++++
  gi|313126032|ref|YP_004036302.1| 48 YVTIVGPNGAGKSTLMKSV 66
                                      689*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.71u 0.38s 00:00:01.08 Elapsed: 00:00:00.59
# Mc/sec: 1291.86
//
Query:       gi|313126033|ref|YP_004036303.1|  [L=284]
Description: amino acid/amide ABC transporter ATP-binding protein 1, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-31  109.7   0.0      2e-31  109.3   0.0    1.2  1  ABC_tran      ABC transporter
    7.4e-12   45.7   4.5    1.5e-06   28.2   0.3    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.4e-10   40.1   0.1    4.9e-10   39.1   0.1    1.5  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    2.3e-05   25.0   0.0    3.1e-05   24.6   0.0    1.3  1  AAA_23        AAA domain
    5.8e-05   22.8   0.5    0.00012   21.8   0.5    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0007   19.5   0.1     0.0011   18.8   0.1    1.3  1  MukB          MukB N-terminal
     0.0007   19.1   0.4      0.048   13.1   0.4    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0026   17.5   0.1     0.0052   16.5   0.0    1.6  2  AAA_15        AAA ATPase domain
     0.0068   16.8   0.1       0.15   12.5   0.1    2.2  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.022   14.0   0.0    1.5  1  Zeta_toxin    Zeta toxin
       0.07   13.0   0.1       0.15   11.9   0.0    1.6  2  RsgA_GTPase   RsgA GTPase
      0.092   12.5   0.2       0.13   12.0   0.2    1.4  1  AAA_30        AAA domain
        0.1   12.2   0.1       0.17   11.5   0.1    1.3  1  AAA_27        AAA domain
       0.11   12.6   0.5       0.29   11.2   0.5    1.9  1  MMR_HSR1      50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.0   1.6e-34     2e-31       2     137 .]      49     211 ..      48     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 1.6e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++ ++++++g++++++G+nGaGKSt ++l++g+lkp++G+++++g+d++  +++ +++k +   +q ++  +++tv 
  gi|313126033|ref|YP_004036303.1|  49 DDATFQIENGTLTGLIGPNGAGKSTTFNLITGMLKPDKGTVTFNGEDITGmEPHAIANKGLVRTFQIARELEDMTVL 125
                                       7899*********************************************9999************************ PP

                                       HH..............................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHH CS
                                       xx..............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..............................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarall 124
                                       en                              e  e++ ++l+ +++++++++ +     +LSgGq++ +++arall
  gi|313126033|ref|YP_004036303.1| 126 ENmmlapknqrgeklwrsvtpgvrndvieqeeELLERVWEVLEFFEIDHIAEEYA----GNLSGGQRKLLEMARALL 198
                                       ***************9999999999998655444555899999999988888888....****************** PP

                                       HTSSEEEEESTTT CS
                                       xxxxxxxxxxxxx RF
                          ABC_tran 125 kkpkllllDEpta 137
                                       ++p++lllDEp+a
  gi|313126033|ref|YP_004036303.1| 199 TDPDMLLLDEPFA 211
                                       ***********85 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.6   4.8e-07   0.00061       1      37 [.      60      96 ..      60     164 .. 0.65
   2 !   28.2   0.3   1.2e-09   1.5e-06     219     298 ..     156     241 ..     124     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.8e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdels 37
                                      l++liGpNg+GKS+ + ++ ++   d+     + e+ 
  gi|313126033|ref|YP_004036303.1| 60 LTGLIGPNGAGKSTTFNLITGMLKPDKGTVTFNGEDI 96
                                      699****************888654444444444443 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.2e-09
                            AAA_21 219 r.........gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkels 286
                                       +          + f+e ++  e  a +lS G+++ll ++ all ++   + ll+DEp +g +P+l +rll+ + el+
  gi|313126033|ref|YP_004036303.1| 156 EeellervweVLEFFEIDHIAEEYAGNLSGGQRKLLEMARALLTDP---DMLLLDEPFAGVNPSLEKRLLTHIHELR 229
                                       1334445677899*******************************99...9********************9887777 PP

                            AAA_21 287 rngaQviltTHS 298
                                       + g  ++l+ H+
  gi|313126033|ref|YP_004036303.1| 230 EQGYTFLLVEHD 241
                                       777777766555 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.1   3.8e-13   4.9e-10       1      23 []     259     281 ..     259     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 3.8e-13
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                       rv+ eGtPa+++++++VieAYLG
  gi|313126033|ref|YP_004036303.1| 259 RVLTEGTPADIKSNEEVIEAYLG 281
                                       89********************9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.4e-08   3.1e-05      11      78 ..      49     118 ..      33     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.4e-08
                            AAA_23  11 rdqeidF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve.iesegkvkay.velt 78 
                                       +d +++  +  lt ++GpNGaGK+T ++ i+ +L  ++++  + +g+++   +++ i+++g v+++ + ++
  gi|313126033|ref|YP_004036303.1|  49 DDATFQIeNGTLTGLIGPNGAGKSTTFNLITGMLKPDKGT-VTFNGEDITGMEPHaIANKGLVRTFqIARE 118
                                       77788884447********************999877543.444455555555444445555555555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.5   9.1e-08   0.00012      13      55 ..      49      92 ..      46      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.1e-08
                            AAA_29 13 dghtieidlkg.atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      d+ t++i+ +g  t l+Gp+G+GKST +  i+ +L p+k +v+fN
  gi|313126033|ref|YP_004036303.1| 49 DDATFQIE-NGtLTGLIGPNGAGKSTTFNLITGMLKPDKgTVTFN 92
                                      56788888.555999************************9999*9 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   8.9e-07    0.0011      21      76 ..      52     109 ..      45     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.9e-07
                                       EE-HHH.HHHHHHS--SHHHHHHHHHHHHHHS--TTT------------.-------- CS
                              MukB  21 tfdlde.lvttlsGgnGaGksttmaafvtaliPdlsllhfrntteaGat.sgsrdkGl 76 
                                       tf++++  +t l G nGaGkstt   +   l Pd   + f     +G +  +  +kGl
  gi|313126033|ref|YP_004036303.1|  52 TFQIENgTLTGLIGPNGAGKSTTFNLITGMLKPDKGTVTFNGEDITGMEpHAIANKGL 109
                                       78887636899**************9999***********988888865234556666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.4   3.8e-05     0.048      25     200 ..      59     243 ..      47     260 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEE...EETTEE......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx......... RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitf...dnedkk......... 89 
                                        +t ++GpNG+GKs  ++ i  +L  ++       + +d+    + +a ++k+ v  +    +              
  gi|313126033|ref|YP_004036303.1|  59 TLTGLIGPNGAGKSTTFNLITGMLKPDKG--TVTFNGEDITGM-EPHAIANKGLVRTFQiarE----Ledmtvlenm 128
                                       47899*********999999888875443..333344444443.6666667776665323221....2122244444 PP

                                       ..SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS- CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  90 ..lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkp 158
                                         ++ ++   ++ r+v  + +++  i+++e   + v e+le  +i+        +LSgG+++L+ +a  +       
  gi|313126033|ref|YP_004036303.1| 129 mlAPKNQRGEKLWRSVTPGVRND-VIEQEEELLERVWEVLEFFEIDHIaeeyagNLSGGQRKLLEMARAL----LTD 200
                                       43344444455555555555433.4454444444444444444444334447778999999998776432....223 PP

                                       -SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknvkkvaellkekskn.aQfivislree 200
                                         + llDe  a    +  k++ + ++e +++   f+ + ++ +
  gi|313126033|ref|YP_004036303.1| 201 PDMLLLDEPFAGVNPSLEKRLLTHIHELREQgYTFLLVEHDMD 243
                                       3355667766666666666666666666665455666665555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     4e-06    0.0052      20      68 ..      54      99 ..      47     162 .. 0.81
   2 ?   -2.2   0.0       2.1   2.6e+03     323     353 ..     200     230 ..     190     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4e-06
                            AAA_15 20 dlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleif 68
                                      ++++  lt liG+N++GKS+  +++  +l+ +    k +++++ ed+  +
  gi|313126033|ref|YP_004036303.1| 54 QIENGtLTGLIGPNGAGKSTTFNLITGMLKPD----KGTVTFNGEDITGM 99
                                      4444469**********************988....56666666665544 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelan 353
                                       +++ ll++EP a   p++ k l   + el +
  gi|313126033|ref|YP_004036303.1| 200 DPDMLLLDEPFAGVNPSLEKRLLTHIHELRE 230
                                       78999*************9999988887765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00012      0.15       3      66 ..      63     208 ..      61     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       l+Gp G GK+++ + +   l+     ++++g +++ +                                        
  gi|313126033|ref|YP_004036303.1|  63 LIGPNGAGKSTTFNLITGMLKpdKGTVTFNGEDITGMephaiankglvrtfqiareledmtvlenmmlapknqrgek 139
                                       89******************854557888888888666777777777777777777777777777777777777777 PP

                                       .......................................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 .......................................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                                              y g+ +   r+l++ a++   +p  l++DE
  gi|313126033|ref|YP_004036303.1| 140 lwrsvtpgvrndvieqeeellervwevleffeidhiaeeYAGNLSGGQRKLLEMARALLtDPDMLLLDE 208
                                       766666666666666666666666666666666666666666666666666666666665666666666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.8e-05     0.022      21      61 ..      63     103 ..      47     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                        Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPey 61 
                                       l G  GAGKs++ +l++  l+++++ v++++ d+  + P++
  gi|313126033|ref|YP_004036303.1|  63 LIGPNGAGKSTTFNLITGMLKPDKGTVTFNGEDITGMEPHA 103
                                       56889*****************************9999996 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.15      94     125 ..      52      84 ..      16      98 .. 0.83
   2 ?   -3.5   0.0       6.4   8.3e+03      67      85 ..     223     241 ..     215     255 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       HHHCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  94 kellkd.ktsvlvGqSGvGKStLinallpelel 125
                                       + ++++  ++ l+G+ G+GKSt  n +++ l+ 
  gi|313126033|ref|YP_004036303.1|  52 TFQIENgTLTGLIGPNGAGKSTTFNLITGMLKP 84 
                                       55566658899***************9987655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.4
                                       HHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase  67 elkeelealgyevllvsak 85 
                                       +  +el++ gy++llv+ +
  gi|313126033|ref|YP_004036303.1| 223 THIHELREQGYTFLLVEHD 241
                                       4556667777777766544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2    0.0001      0.13      18      62 ..      58     109 ..      49     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkvL 62 
                                         ++ l Gp G+GK+t+ + ++ +++ + g      +++ g+ p + a k L
  gi|313126033|ref|YP_004036303.1|  58 GTLTGLIGPNGAGKSTTFNLITGMLKPDkGtvtfngEDITGMEPHAIANKGL 109
                                       458899*****************99999345555555555555555555554 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00013      0.17      19      49 ..      51      81 ..      39      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                       +f+ e+  l+ ++GpN AGKst+++ i+ +
  gi|313126033|ref|YP_004036303.1| 51 ATFQIENGTLTGLIGPNGAGKSTTFNLITGM 81
                                      4555568889999***********9987765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00023      0.29       3      22 ..      62      81 ..      60     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                      EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                      +++G   +GKSt +n +tg 
  gi|313126033|ref|YP_004036303.1| 62 GLIGPNGAGKSTTFNLITGM 81
                                      799***************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1526.25
//
Query:       gi|313126034|ref|YP_004036304.1|  [L=456]
Description: branched-chain amino acid ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-41  141.7  30.0    2.4e-41  141.7  30.0    1.6  2  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.3       0.2   3.6e+03     140     149 ..      23      32 ..      12      43 .. 0.42
   2 !  141.7  30.0   1.3e-45   2.4e-41       4     252 ..      50     359 ..      47     402 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.2
                      BPD_transp_2 140 llvlavllll 149
                                       llv  + ++l
  gi|313126034|ref|YP_004036304.1|  23 LLVTYAAYVL 32 
                                       1111111111 PP

  == domain 2  score: 141.7 bits;  conditional E-value: 1.3e-45
                      BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl............lllallvallvgaa 68 
                                        l+ +++++a++Al+l+l +g++G++n+g+ gfma+G yv+al ++    +            l+++++++++++a+
  gi|313126034|ref|YP_004036304.1|  50 VLTFYIGVFAMLALALNLHWGYTGLFNIGIVGFMAVGVYVMALFSKPAYTPggaaqvgglglpLIIGIIAGMVAAAL 126
                                       56678899**************************************999999************************* PP

                      BPD_transp_2  69 vglllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.......... 135
                                       +gl+++l+ lrl+ d+l+i+++++s++v++ +  l g  ++ +     ++  g +g +l f     +          
  gi|313126034|ref|YP_004036304.1| 127 LGLVVALPALRLRADYLAIVTIAMSEIVRFSF--LSGDLQQFQLLGNRVGFGGGSGLILDFTDPLQAlfqsvglwga 201
                                       ******************************99..77777777777777777777777766666555566788889** PP

                      BPD_transp_2 136 ..........................llalllvlavllllrrt...rfGralravgeneeaaralGinvkrvklltf 183
                                                                 l++ll+v a ++ll+rt   +fGr l+a++e+e++a  lG++++++k+++f
  gi|313126034|ref|YP_004036304.1| 202 ylgfvdaftvivptnpkpvvdglvygLILLLFVGAYFWLLKRTgesPFGRVLKAIREDEDVANSLGKDTNQFKIKSF 278
                                       **************************888888888888888754449****************************** PP

                      BPD_transp_2 184 visgalAglaGallalllgsipp.nigvglgfnaiaavvlGgagsllgtviGaliigvvksllltllgi........ 251
                                       +++ al glaG++  + +g++ p ++++  +f +++a ++Ggags+ g v+G+ ++++v   +  ++ +        
  gi|313126034|ref|YP_004036304.1| 279 MLGCALMGLAGIFWLMTQGAVTPnFFRPRVTFFVWIALIIGGAGSNTGSVLGGAVFAAVLYQGPRYFKNlidtvlps 355
                                       ***********************9********************************998766766666655555555 PP

                      BPD_transp_2 252 ...p 252
                                          p
  gi|313126034|ref|YP_004036304.1| 356 tdaP 359
                                       5550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2542.52
//
Query:       gi|313126035|ref|YP_004036305.1|  [L=368]
Description: amino acid/amide ABC transporter membrane protein 1, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-34  118.6  45.1    2.7e-34  118.6  45.1    1.8  2  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.2      0.25   4.5e+03      89      98 ..      22      31 ..      12      45 .. 0.42
   2 !  118.6  45.1   1.5e-38   2.7e-34       5     268 .]      55     354 ..      51     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.25
                      BPD_transp_2 89 llllsvlvgl 98
                                      +l+++ +++l
  gi|313126035|ref|YP_004036305.1| 22 ILAFVGVLLL 31
                                      2222222222 PP

  == domain 2  score: 118.6 bits;  conditional E-value: 1.5e-38
                      BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl........................... 54 
                                       +l++++++++a++Gl++++ i++  n++hg f++ Ga++ +   + l  l                           
  gi|313126035|ref|YP_004036305.1|  55 GLMRGLVIGLAGIGLSMTYSILNFANFAHGDFITAGAFSGWATTYVLAGLgradigalvlvgaggsvfggtlgigit 131
                                       788999*******************************9887777776666889************************ PP

                      BPD_transp_2  55 .lllallvallvgaavglllgllvlrlkvdel.........iitllllsvlvgltlllltgitsgvkgqssvkellg 121
                                         +la++++llv++a+  +l l+v r   +++         i+++++ ++l+++++++ +   +g++ q+   ++  
  gi|313126035|ref|YP_004036305.1| 132 gTPLAVIAGLLVAGAFTIVLSLAVDRAIFRPIrdedgitllITSIGVAFALRYMMQFVFGSNVRGTTAQPPSFAVYL 208
                                       *7777777777777777777777777777777777744444444445555555555555555555555555555555 PP

                      BPD_transp_2 122 fagallsflsaviv.....llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAgla 193
                                        +ga ++ +          ++a  l+l v+lll+rt++G a+ra+++ne++ar+ Gi+++rv   ++vi+g+l g+a
  gi|313126035|ref|YP_004036305.1| 209 LDGAVRINM----HdltlvVVAGGLMLGVHLLLQRTKLGKAMRAMADNEDLARVTGIPTERVVRSVWVIGGGLTGVA 281
                                       555554444....15554677788***************************************************** PP

                      BPD_transp_2 194 GallalllgsippnigvglgfnaiaavvlGgagsllgtviGaliigvvksllltllgiptelarvllgallilvl 268
                                       G +++l  g+   n g+ l + ++aav+lGg+gs++g+++G+l+ig+  sl+  ++  p+++ar+  ++++i++l
  gi|313126035|ref|YP_004036305.1| 282 GYMFVLWKGTLGFNDGWLLLLLIFAAVILGGIGSIYGAIAGGLVIGLTASLSVLWI--PSAFARAAAFVVMIVIL 354
                                       **************************************************777777..77************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2015.45
//
Query:       gi|313126036|ref|YP_004036306.1|  [L=168]
Description: GNAT family acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-18   65.8   0.1      5e-18   65.4   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.3e-14   53.0   0.1    4.9e-14   52.5   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.5e-12   47.6   0.2      2e-12   47.1   0.2    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.2e-09   36.6   0.3    1.1e-08   34.9   0.0    1.8  2  FR47             FR47-like protein
    4.9e-06   26.6   0.1    6.9e-06   26.2   0.1    1.3  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0002   21.1   0.1     0.0003   20.5   0.1    1.4  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
    0.00024   21.2   0.0    0.00035   20.7   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00068   19.3   0.0     0.0012   18.6   0.0    1.4  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0011   19.1   0.0      0.002   18.2   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0012   19.6   0.1     0.0014   19.3   0.1    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0036   17.2   0.0     0.0078   16.2   0.0    1.5  1  Acetyltransf_13  ESCO1/2 acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.1     3e-21     5e-18      30     117 .]      57     147 ..      22     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 3e-21
                                       STTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEET CS
                    Acetyltransf_1  30 leaegllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlavee 103
                                         ++g+ va+  +e++Gf++++       +++ +++i+ l+V+p++r +G+Gs+Ll+ +e ++   g++ i l+  +
  gi|313126036|ref|YP_004036306.1|  57 VVTDGIRVARVSDEIVGFVMYSLERGdfeQDETRGVIRNLYVKPAHRSRGIGSRLLKSAEAELAGAGATHICLEAMA 133
                                       234456668888*****************99***************************************9999999 PP

                                       TEHHHHHHHHHTTE CS
                    Acetyltransf_1 104 dndaairlYeklGF 117
                                        n++a+++Ye++G+
  gi|313126036|ref|YP_004036306.1| 134 RNERARKFYERHGY 147
                                       9************8 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.1     3e-17   4.9e-14       7      75 ..      64     148 ..      46     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 3e-17
                                       EEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHH.HTT.....SE...EEEEEEEETHHHH CS
                    Acetyltransf_7   7 VaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLle.aae.....kg...iileqlelnaeka 65 
                                       Va+  ++ivGf+ +sl+          + i +l+V+p++r +GiG++Ll+ a e      g   i le +  ++e+a
  gi|313126036|ref|YP_004036306.1|  64 VARVSDEIVGFVMYSLERgdfeqdetrGVIRNLYVKPAHRSRGIGSRLLKsA-EaelagAGathICLE-AMARNERA 138
                                       677789******99999999998776666666*****************954.224545442222122.2334459* PP

                                       HHHHHHTTEE CS
                    Acetyltransf_7  66 ikfYeklGFe 75 
                                       +kfYe++G++
  gi|313126036|ref|YP_004036306.1| 139 RKFYERHGYT 148
                                       *********7 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.2   1.2e-15     2e-12      34     115 ..      63     156 ..      36     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.2e-15
                   Acetyltransf_10  34 lvaeeggkivGvi..elrdgs........hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yav 98 
                                        va ++++ivG++  +l++g+         i  l+V+p++r++Gig++Ll+ +e+e+  +g  +  l++ a +  a+
  gi|313126036|ref|YP_004036306.1|  63 RVARVSDEIVGFVmySLERGDfeqdetrgVIRNLYVKPAHRSRGIGSRLLKSAEAELAGAGATHiCLEAMARNeRAR 139
                                       589999*******6645444468888888***************************988888889999999999*** PP

                   Acetyltransf_10  99 pfYeklGFkavgeeqee 115
                                       +fYe++G++++  e e+
  gi|313126036|ref|YP_004036306.1| 140 KFYERHGYTVHRVELEK 156
                                       *********99777665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.1   1.8e+03      42      57 ..      49      64 ..      46      68 .. 0.80
   2 !   34.9   0.0     7e-12   1.1e-08      21      81 ..      90     151 ..      82     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHS-S-E CS
                              FR47 42 lvkalakeiaergktv 57
                                      + +a+a+++++ g+ v
  gi|313126036|ref|YP_004036306.1| 49 IREAMARHVVTDGIRV 64
                                      567999**99999876 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 7e-12
                                       TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEEE CS
                              FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfekie 81 
                                        g +  l+v+p hr rG gsrl k+  +e+a +g t + l + a N++++++ye+ G+++ +
  gi|313126036|ref|YP_004036306.1|  90 RGVIRNLYVKPAHRSRGIGSRLLKSAEAELAGAGAThICLEAMARNERARKFYERHGYTVHR 151
                                       49999***************************88652678899***************9875 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   4.3e-09   6.9e-06       6     126 ..      15     148 ..      10     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.3e-09
                                       -GGGHHHHHHHHHHHTT----H...........HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEE CS
                    Acetyltransf_9   6 teedldevlellkyaFqdeespl........e.eireyfrklleesrvlgaedngelvgqlallplelnvpGktlka 73 
                                       +++++d+ ++l+    +d++s++        + +ire+  + +  + + +a+  +e+vg ++ ++le    ++  + 
  gi|313126036|ref|YP_004036306.1|  15 NTAEIDALADLWVSLAADQRSYQshlrsdenRgRIREAMARHVVTDGIRVARVSDEIVGFVM-YSLERGDFEQDETR 90 
                                       667777777777777777777777777777767899999999999999**********9765.66666666666677 PP

                                       EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                    Acetyltransf_9  74 agvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGye 126
                                       + +    v+p hr rg+ s+Ll+ a +e++  g++ ++l +     +++++Y+r Gy 
  gi|313126036|ref|YP_004036306.1|  91 GVIRNLYVKPAHRSRGIGSRLLKSAEAELAGAGATHICLEAmarneRARKFYERHGYT 148
                                       999**************************************88877778********7 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.9e-07    0.0003      56     122 ..      85     149 ..      51     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.9e-07
                              PanZ  56 eledkeaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvkeldlavlqaflealgfaa 122
                                       e++++ + +++l V+   R RG+gs+Ll+ a  ++    ++ +  e+++  +++ +++f e++g++ 
  gi|313126036|ref|YP_004036306.1|  85 EQDETRGVIRNLYVKPAHRSRGIGSRLLKSAEAELAGAGATHICLEAMA--RNERARKFYERHGYTV 149
                                       56778999***************************99999999999976..6678899999999954 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.1e-07   0.00035      56     140 ..      66     153 ..      61     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.1e-07
                    Acetyltransf_4  56 e.sdrivGyaylg....qfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiq 127
                                         sd+ivG   ++     f++  ++  ++   y++  + +++g+g+ l+++ e  l+  + + ++ e ++ ne + +
  gi|313126036|ref|YP_004036306.1|  66 RvSDEIVGFVMYSlergDFEQ-DETRGVIRNLYVK-PAHRSRGIGSRLLKSAEAELAGAGATHICLEAMARNERARK 140
                                       557888887776543223444.7778899999**8.89*************************************** PP

                    Acetyltransf_4 128 fhkalGFelvgif 140
                                       f++++G+++ + +
  gi|313126036|ref|YP_004036306.1| 141 FYERHGYTVHRVE 153
                                       ********98754 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   7.2e-07    0.0012      88     140 ..      99     150 ..      76     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.2e-07
                                       SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEE CS
                    Acetyltransf_8  88 eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfeke 140
                                       ++++r +g++++ll++  + l    +++++++E  +rNera++++e++G++ +
  gi|313126036|ref|YP_004036306.1|  99 KPAHRSRGIGSRLLKSAEAELAGA-GATHICLEAMARNERARKFYERHGYTVH 150
                                       68999**********998887766.9***********************9876 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.3e-06     0.002       9      50 ..      69     116 ..      61     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                   Acetyltransf_CG   9 geevafleYe......vrkegvldfthTeVpeelrGkGiAkkLvkaal 50 
                                       +e v+f+ Y+      +++e + ++   +V++++r +Gi+++L k+a 
  gi|313126036|ref|YP_004036306.1|  69 DEIVGFVMYSlergdfEQDETRGVIRNLYVKPAHRSRGIGSRLLKSAE 116
                                       678999*9997777766666699**********************985 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   8.8e-07    0.0014      12     137 ..      22     147 ..      13     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.8e-07
                    Acetyltransf_3  12 leal.felrsdpe.vmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedee.....a 81 
                                       l++l ++l++d++  + +l+ ++++   +e ++r+  +    +g   a  ++d+ ++G+v++    ++ e+     +
  gi|313126036|ref|YP_004036306.1|  22 LADLwVSLAADQRsYQSHLRSDENRGRIREAMARHVVT----DGIRVAR-VSDE-IVGFVMYSLERGDFEQdetrgV 92 
                                       55564577777775555566677777777777766544....6654333.3555.8****99977777766778866 PP

                    Acetyltransf_3  82 elgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                          ++++p+++ +G+++  ++++   + +  g+++++ ++ ++Ne+ ++ +e+ G+
  gi|313126036|ref|YP_004036306.1|  93 IRNLYVKPAHRSRGIGSRLLKSAEAEL-AGAGATHICLEAMARNERARKFYERHGY 147
                                       667999****************99999.7888**********************97 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.8e-06    0.0078       7      32 ..      93     118 ..      90     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                   Acetyltransf_13   7 isriWvssshRrkgiAtkLldaaren 32 
                                       i+ ++v+++hR++gi ++Ll++a ++
  gi|313126036|ref|YP_004036306.1|  93 IRNLYVKPAHRSRGIGSRLLKSAEAE 118
                                       889*****************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 940.74
//
Query:       gi|313126037|ref|YP_004036307.1|  [L=251]
Description: hypothetical protein Hbor_12770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1412.42
//
Query:       gi|313126038|ref|YP_004036308.1|  [L=74]
Description: hypothetical protein Hbor_12780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-21   75.0   0.0    4.5e-21   74.9   0.0    1.0  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   2.5e-25   4.5e-21       2      73 ..       4      73 ..       3      74 .] 0.93

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 2.5e-25
                            HalOD1  2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieV 73
                                      + ++s+++v+ ++++egv+p el+pL d++D++ Ld+Lf s  +++  + gsvsF y+gyeVtV ++ge e+
  gi|313126038|ref|YP_004036308.1|  4 QAPLSIQIVTEISRLEGVEPFELPPLEDCVDTESLDTLFGS--SDAPFHAGSVSFHYAGYEVTVSHTGEFEI 73
                                      689**************************************..5566789******************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 435.45
//
Query:       gi|313126039|ref|YP_004036309.1|  [L=187]
Description: kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-26   92.1   0.1    3.5e-26   92.1   0.1    1.5  2  AAA_33      AAA domain
    2.9e-07   31.1   0.1    7.4e-07   29.8   0.1    1.7  1  AAA_18      AAA domain
    3.2e-07   29.8   0.8    1.3e-06   27.9   0.8    1.7  1  Zeta_toxin  Zeta toxin
    8.1e-07   28.8   0.0      1e-06   28.4   0.0    1.1  1  KTI12       Chromatin associated protein KTI12
    1.1e-06   29.1   0.1    2.4e-06   28.0   0.1    1.6  1  AAA_17      AAA domain
    1.6e-05   24.3   1.6      0.026   13.8   0.9    2.2  2  6PF2K       6-phosphofructo-2-kinase
     0.0003   21.1   0.0    0.00044   20.5   0.0    1.3  1  AAA_22      AAA domain
     0.0016   18.9   1.2     0.0022   18.4   1.2    1.4  1  AAA_16      AAA ATPase domain
     0.0058   17.0   0.0     0.0099   16.3   0.0    1.5  1  AAA         ATPase family associated with various cellular ac
  ------ inclusion threshold ------
      0.039   13.8   0.1      0.061   13.2   0.1    1.3  1  APS_kinase  Adenylylsulphate kinase
       0.11   12.5   0.0       0.22   11.5   0.0    1.6  1  AAA_5       AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3       4.4   7.1e+03     112     121 ..       9      18 ..       6      25 .. 0.59
   2 !   92.1   0.1   2.1e-29   3.5e-26       1     141 [.      28     161 ..      28     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.4
                            AAA_33 112 keRlakRaan 121
                                       ++R ++Ra++
  gi|313126039|ref|YP_004036309.1|   9 QRRDRQRAKR 18 
                                       5666666664 PP

  == domain 2  score: 92.1 bits;  conditional E-value: 2.1e-29
                            AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvilda 77 
                                       lv ++GlpG+GK+ ++er++ +l++ l+++d++r+ lf++    +++ +  ++++y+ l+ + r+  + g +++lda
  gi|313126039|ref|YP_004036309.1|  28 LVTVCGLPGVGKTLVSERIADRLDGRLIRTDVVRKELFPE----PEYTSAERQSVYDELFSRGRESIQNGTPAVLDA 100
                                       799***********************************75....4555567899*********************** PP

                            AAA_33  78 tnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeealdrqkarfe 141
                                       t+++r++r+r  ++a  ++vp +iv ve+d ++ +eR+a+R+++   +s+++ e   ++++rfe
  gi|313126039|ref|YP_004036309.1| 101 TFRKREDRDRAASVATAADVPLEIVQVECDTQVVRERIAAREDD---ESDADFEIYLKFRDRFE 161
                                       *******************************************6...46799999999999998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   4.5e-10   7.4e-07       1     120 [.      29     148 ..      29     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.5e-10
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdes.krldedkldklldaleenssaleegkn 76 
                                       + ++G pGvGKt +++++++rl      + +++ +  + e +pe  +e+   +++ + d+l++  +e+    ++g +
  gi|313126039|ref|YP_004036309.1|  29 VTVCGLPGVGKTLVSERIADRL-----DGRLIRTDVVRKELFPE--PEYtSAERQSVYDELFSRGRES---IQNGTP 95 
                                       689******************8.....55555555556666666..2220233333334444444444...468999 PP

                            AAA_18  77 lvidghlaeleseaakdikk.........vvLtaspeelleRlekRgyeeaki 120
                                        v+d    + e+ ++   +          v +++++++ +eR+++R+  e + 
  gi|313126039|ref|YP_004036309.1|  96 AVLDATFRKREDRDRAASVAtaadvpleiVQVECDTQVVRERIAAREDDESDA 148
                                       9**********9888877778*************************9887654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.8   7.9e-10   1.3e-06       7     171 ..      16     178 ..      10     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 7.9e-10
                        Zeta_toxin   7 dkk.ypsqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlR.elhPeyeeilkadpkkaseltqkdas 81 
                                       +k+ +p++++  l+ + G pG GK+ ++e ++d+l  +g+ +r  +D +R el+Pe             e+t+++ +
  gi|313126039|ref|YP_004036309.1|  16 AKRtSPESDTGRLVTVCGLPGVGKTLVSERIADRL--DGRLIR--TDVVRkELFPEP------------EYTSAERQ 76 
                                       344468889999***********************..899877..566652788883............34444444 PP

                        Zeta_toxin  82 elvekll...qeaiengyniivegtlrspdvvkklaealkkaGYevevvvvavkkelSrlgvldRyeeevae..... 150
                                        + ++l+    e i+ng   +++ t+r+ ++ +++a  + +a   +e+v v ++ ++ r+++++R+  e+++     
  gi|313126039|ref|YP_004036309.1|  77 SVYDELFsrgRESIQNGTPAVLDATFRKREDRDRAASVATAADVPLEIVQVECDTQVVRERIAAREDDESDAdfeiy 153
                                       444444411146799*****************************************************966667777 PP

                        Zeta_toxin 151 ....gRlvpkeehdeafeglresve 171
                                            R+  +e+  e++++  + +e
  gi|313126039|ref|YP_004036309.1| 154 lkfrDRFEHIEREHETVDNSGDMAE 178
                                       7775577777777777777666555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   6.4e-10     1e-06       3     141 ..      28     164 ..      27     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 6.4e-10
                                       EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE-S- CS
                             KTI12   3 LvvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLskekvVIvDsl 79 
                                       Lv+++GlP +GK+ +++++a+ l  + ++  v+++e +   + +y+ sa+ +++ ++l+s  ++++++ +  ++D++
  gi|313126039|ref|YP_004036309.1|  28 LVTVCGLPGVGKTLVSERIADRLDGRLIRTDVVRKELFP--EPEYT-SAERQSVYDELFSRGRESIQNGTPAVLDAT 101
                                       9***********************************998..55565.67778999********************** PP

                                       --SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-.S..S-HHHHHHHHHH---TT CS
                             KTI12  80 nyikgfRYeLyciakaakttlcvvyvvapldvlvkwneeree.keeyekelldaLiqRyeePd 141
                                          +  R     +a aa+ +l +v+v ++ +v++++   re+ +++ + e++ +   R+e+ +
  gi|313126039|ref|YP_004036309.1| 102 FRKREDRDRAASVATAADVPLEIVQVECDTQVVRERIAAREDdESDADFEIYLKFRDRFEHIE 164
                                       *****************************9999998855554044578899999999999765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.5e-09   2.4e-06       2     128 ..      33     147 ..      32     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-09
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                       G+PG+GK+ ++e+++++++      G l+r  + r++l ++ ++ + + +++ +el  +  e+i++    + +++d 
  gi|313126039|ref|YP_004036309.1|  33 GLPGVGKTLVSERIADRLD------GRLIRTDVVRKELFPEPEYTSAERQSVYDELFSRGRESIQN---GTPAVLDA 100
                                       9****************99......55555555555676777888888888888888888888886...5779**** PP

                                       -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-T CS
                            AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrd 128
                                        +r +e+++  +   + + +++ p  i+ +e+d ++++er + ++  + d
  gi|313126039|ref|YP_004036309.1| 101 TFRKREDRDRAAS--VATAADV-PLEIVQVECDTQVVRERIAAREDDESD 147
                                       **99998885544..4455666.799**************9998544333 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0004      0.66       8      44 ..      22      57 ..      15      86 .. 0.78
   2 !   13.8   0.9   1.6e-05     0.026      96     184 ..      92     175 ..      87     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0004
                                      HT..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                             6PF2K  8 nlknsklvivlvGLpargKtyiskkltrylkwlgvrt 44
                                      + +++  ++ + GLp  gKt++s+++   l    +rt
  gi|313126039|ref|YP_004036309.1| 22 E-SDTGRLVTVCGLPGVGKTLVSERIADRLDGRLIRT 57
                                      4.4444567789*************987776555555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.6e-05
                                       --SEEEEES---SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHHHTTTSGGGTTS-HHHHHHHHHHHHHHH CS
                             6PF2K  96 egqvaifDAtNttrerRklilefveennlkvlflesicsdeeiikeNikevklsspDYkdketeeaikdflkRleny 172
                                       +g  a+ DAt  +re+R+   ++++  ++   ++++ c d ++++e i+      +D +   + e +  f  R e+ 
  gi|313126039|ref|YP_004036309.1|  92 NGTPAVLDATFRKREDRDRAASVATAADVPLEIVQVEC-DTQVVRERIAAR----EDDESDADFEIYLKFRDRFEHI 163
                                       67889***********************9999999999.567888888754....45577778889999******** PP

                                       HTT-----TTTT CS
                             6PF2K 173 ekqyeplddeed 184
                                       e+++e +d++ d
  gi|313126039|ref|YP_004036309.1| 164 EREHETVDNSGD 175
                                       *******97766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.7e-07   0.00044       4      43 ..      25      60 ..      22     125 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.7e-07
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43
                                      t ++++v+G +G+GKT++ +r++++ld +   ++    vv
  gi|313126039|ref|YP_004036309.1| 25 TGRLVTVCGLPGVGKTLVSERIADRLDGRLIRTD----VV 60
                                      67899*********************86544333....33 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.2   1.4e-06    0.0022       5     106 ..       5     103 ..       4     170 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                            AAA_16   5 ReeeleqL.lsalervrsgrp.elvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysa.laq 74 
                                       R+ ++++  ++a ++  ++++ +lv + G +GvGK+ + ++++++l ++    +  ++r +           + +++
  gi|313126039|ref|YP_004036309.1|   5 RGTQQRRDrQRAKRTSPESDTgRLVTVCGLPGVGKTLVSERIADRLDGRlirtD--VVRKELFPE-------PeYTS 72 
                                       5555555524444444444446***********************999933220..122222222.......33555 PP

                            AAA_16  75 alareellrqlldeaesaeleawrekleeala 106
                                       a  r +++ +l ++ +++ ++  ++ l+++++
  gi|313126039|ref|YP_004036309.1|  73 AE-RQSVYDELFSRGRESIQNGTPAVLDATFR 103
                                       55.44666666666555444444444444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.1e-06    0.0099       2      32 ..      30      60 ..      29     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.1e-06
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETT CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgs 32
                                       ++G pG+GKTl+ + +a  l+ +++++++ 
  gi|313126039|ref|YP_004036309.1| 30 TVCGLPGVGKTLVSERIADRLDGRLIRTDVV 60
                                      689******************9999887764 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.7e-05     0.061       4     117 ..      28     137 ..      25     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE CS
                        APS_kinase   4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlva 80 
                                        v + Gl g GK+ ++++++ +L  +     l+  d+vR++L  +  +++++R+     +    ++  ++g+ ++  
  gi|313126039|ref|YP_004036309.1|  28 LVTVCGLPGVGKTLVSERIADRLDGR-----LIRTDVVRKELFPEPEYTSAERQSVYDELFSRGRESIQNGTPAVLD 99 
                                       67889**************9988765.....556699***********************99999999999999999 PP

                                       ----SHHHHHHHHHHHHCH.TEEEEEEEE--HHHHHHH CS
                        APS_kinase  81 fisPyreeReaarelleea.lkfievfvdtplevceer 117
                                       +    re+R++a ++   a + +  v v+++ +v +er
  gi|313126039|ref|YP_004036309.1| 100 ATFRKREDRDRAASVATAAdVPLEIVQVECDTQVVRER 137
                                       99999999*99999998877777788888888888776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.22       4      26 ..      31      53 ..      29     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                      EE--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5  4 LvGppGtgKselaerlaaalnre 26
                                      + G pG+gK+ ++er+a +l  +
  gi|313126039|ref|YP_004036309.1| 31 VCGLPGVGKTLVSERIADRLDGR 53
                                      5799**************99544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.38s 00:00:01.03 Elapsed: 00:00:00.59
# Mc/sec: 947.89
//
Query:       gi|313126040|ref|YP_004036310.1|  [L=140]
Description: hypothetical protein Hbor_12800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 826.02
//
Query:       gi|313126041|ref|YP_004036311.1|  [L=368]
Description: hypothetical protein Hbor_12810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0062   17.0   4.5     0.0062   17.0   4.5    2.0  2  T3SSipB      Type III cell invasion protein SipB
  ------ inclusion threshold ------
      0.024   14.5   2.3      0.031   14.1   2.3    1.2  1  Exo84_C      Exocyst component 84 C-terminal
      0.062   12.7   0.4      0.083   12.3   0.4    1.1  1  Rogdi_lz     Rogdi leucine zipper containing protein
      0.079   12.6   0.2       0.14   11.9   0.2    1.3  1  DUF4972      Domain of unknown function (DUF4972)
       0.38   10.4  13.6       0.13   11.9  10.8    1.6  2  DUF2968      Protein of unknown function (DUF2968)
       0.52   10.7   7.7       0.87   10.0   0.5    2.3  2  Efg1         rRNA-processing protein Efg1
        4.8    7.3   5.9        7.9    6.6   4.7    1.9  2  GvpG         Gas vesicle protein G
        7.6    4.9   6.3        9.4    4.6   6.3    1.1  1  FUSC         Fusaric acid resistance protein family
        8.2    5.7  12.9       0.48    9.7   7.5    1.6  2  DUF3450      Protein of unknown function (DUF3450)


Domain annotation for each model (and alignments):
>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.9       2.2   4.3e+03      50      70 ..      41      60 ..      27      66 .. 0.43
   2 !   17.0   4.5   3.1e-06    0.0062      56     140 ..      88     181 ..      72     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                                      HHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB 50 talseakgatddleaaiekad 70
                                      ta++e++g td+ +a++e ad
  gi|313126041|ref|YP_004036311.1| 41 TATNETAG-TDNETAKAEDAD 60
                                      33333333.222222223333 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.1e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHH.......HHHHH.....HHHHHHHHH CS
                           T3SSipB  56 kgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaa.......eqQagaa...adalqadea 122
                                       + at+ +e++++ a + +s+a+ + ++v++ q+rl++L+ +  e  k+e+        +   +aa   a+  + ++ 
  gi|313126041|ref|YP_004036311.1|  88 EIATRSFEKQVASARSNESKAKVVSQQVNQTQERLESLQTQ-LEVLKAERRegnlsqgRYRSQAArlaAEIRSLQRL 163
                                       5689*********************************9554.33333332201111112222222446888888998 PP

                                       HHHHHHHHHHHHHHHHHH CS
                           T3SSipB 123 lqKkldaasklsekakak 140
                                       l+K  +aa  l  +a++ 
  gi|313126041|ref|YP_004036311.1| 164 LDKSQEAADGLPPEARQA 181
                                       999999999998888764 PP

>> Exo84_C  Exocyst component 84 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.3   1.6e-05     0.031       8      95 ..      83     170 ..      77     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                           Exo84_C   8 deldieiarrkFeeAVdlleklesklkklskklkdeeavlqdlislkveqrreelasklsrellsknevkklksnvs 84 
                                        e+d eia+r Fe+ V++ ++ esk k +s+++++++++l++ ++ ++e +++e  +    + + +++ ++l +++ 
  gi|313126041|ref|YP_004036311.1|  83 TEIDGEIATRSFEKQVASARSNESKAKVVSQQVNQTQERLES-LQTQLEVLKAERREGNLSQGRYRSQAARLAAEIR 158
                                       699******************************998876544.5556666666555555555566666677888888 PP

                           Exo84_C  85 lLirL.gledkA 95 
                                        L rL +++++A
  gi|313126041|ref|YP_004036311.1| 159 SLQRLlDKSQEA 170
                                       888862555555 PP

>> Rogdi_lz  Rogdi leucine zipper containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   4.2e-05     0.083      65     141 ..      89     175 ..      73     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.2e-05
                          Rogdi_lz  65 lrlrtlpk..ltlklnp.tkpivleqLtdlrtlltqaldlLdltlktgdelsks.......aqflssqLrlllesls 131
                                       +  r+++k   + ++n+ ++++v +q++++++ l++  ++L++  ++ +e + s       a+ l++++r+l++ l 
  gi|313126041|ref|YP_004036311.1|  89 IATRSFEKqvASARSNEsKAKVVSQQVNQTQERLESLQTQLEVLKAERREGNLSqgryrsqAARLAAEIRSLQRLLD 165
                                       556677773345555554566*********************76666666665588888889*************** PP

                          Rogdi_lz 132 eAkalLkgpp 141
                                       +++++  g p
  gi|313126041|ref|YP_004036311.1| 166 KSQEAADGLP 175
                                       9998766655 PP

>> DUF4972  Domain of unknown function (DUF4972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2     7e-05      0.14      30     104 ..     103     177 ..      94     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7e-05
                           DUF4972  30 ddesytaveevkteiyieqleelinkltdLrdesqyGek.kgmYPeesraiLedaivklkesiakikegnkaeaee 104
                                        +es   v   ++++  e+le l+++l+ L++e + G+  +g+Y  +  a L  +i +l++ + k +e+    ++e
  gi|313126041|ref|YP_004036311.1| 103 SNESKAKVVSQQVNQTQERLESLQTQLEVLKAERREGNLsQGRY-RSQAARLAAEIRSLQRLLDKSQEAADGLPPE 177
                                       57888899999999***********************9725666.5556889999999999999988887766654 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9  10.8   6.3e-05      0.13     105     174 ..     105     174 ..      89     180 .. 0.89
   2 ?   -3.5   0.0       3.5   6.9e+03      83     100 ..     188     205 ..     185     212 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                           DUF2968 105 eaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqL 174
                                       e++ + + +q++++++r+e+Lq++l+v ++ + + +  Q   r++aa L+a+ +++q+ l++ q+  + L
  gi|313126041|ref|YP_004036311.1| 105 ESKAKVVSQQVNQTQERLESLQTQLEVLKAERREGNLSQGRYRSQAARLAAEIRSLQRLLDKSQEAADGL 174
                                       556667899*****************************************************99876655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.5
                           DUF2968  83 iYadfarqtaelaeveir 100
                                        ++++ + t++l+  e+ 
  gi|313126041|ref|YP_004036311.1| 188 RFDRLRNDTENLSRSEVS 205
                                       566666667777766664 PP

>> Efg1  rRNA-processing protein Efg1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.7     0.032        63      16      51 ..     109     143 ..      90     148 .. 0.70
   2 ?   10.0   0.5   0.00044      0.87       3      44 ..     155     203 ..     153     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.032
                                       S---SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Efg1  16 ekLpaevreekereLkaleaeleeaekkekekklak 51 
                                       + ++++v +++er L++l+ +le  +++++e +l++
  gi|313126041|ref|YP_004036311.1| 109 KVVSQQVNQTQER-LESLQTQLEVLKAERREGNLSQ 143
                                       3367777777777.9999999999888888776653 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00044
                                       HHHHHHHHHHS-SS-....--SHHHHHH...HHHHHHHHHHHHHHHHHH CS
                              Efg1   3 kkiRdlkRlLakkek....Lpaevreek...ereLkaleaeleeaekke 44 
                                       ++iR+l+RlL+k+++    Lp+e+r+++   e++++ l+++ e+ +++e
  gi|313126041|ref|YP_004036311.1| 155 AEIRSLQRLLDKSQEaadgLPPEARQATgldEKRFDRLRNDTENLSRSE 203
                                       68********887767888******985444899999999988776665 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.1   4.1e+03      45      57 ..      85      97 ..      74      99 .. 0.78
   2 ?    6.6   4.7     0.004       7.9      18      77 ..     110     169 ..     104     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                              GvpG 45 daGeIdeeeFdrr 57
                                       +GeI    F+++
  gi|313126041|ref|YP_004036311.1| 85 IDGEIATRSFEKQ 97
                                      4799999999987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.004
                              GvpG  18 qvqeraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLealerleaesee 77 
                                        v +++++  +  e l+++L  L+ e  +G+ ++  +  +  +l   +  l+rl ++s+e
  gi|313126041|ref|YP_004036311.1| 110 VVSQQVNQTQERLESLQTQLEVLKAERREGNLSQGRYRSQAARLAAEIRSLQRLLDKSQE 169
                                       57788888888899********************************99999997666655 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   6.3    0.0047       9.4     170     290 ..      95     182 ..      31     215 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0047
                              FUSC 170 lalaaaalageegaeareaararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlr 246
                                        + +a+a ++e++a++++++  +  +++  l+++++ + +e +++    +++r   s+ ++l a ++sl+rll   +
  gi|313126041|ref|YP_004036311.1|  95 EKQVASARSNESKAKVVSQQVNQTQERLESLQTQLEVLKAERREGNLSQGRYR---SQAARLAAEIRSLQRLLDKSQ 168
                                       34445555555555555566666666666666666666666555555544444...344444455555555555555 PP

                              FUSC 247 aeeaaavpelaallaelaaleaaaaaealeaalaalrarlralr 290
                                       ++ ++ +pe                              +r++ 
  gi|313126041|ref|YP_004036311.1| 169 EAADGLPPE------------------------------ARQAT 182
                                       555544444..............................22222 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       1.6   3.2e+03      17      27 ..      29      39 ..       2      62 .. 0.40
   2 ?    9.7   7.5   0.00024      0.48      20     100 ..      96     176 ..      75     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                           DUF3450 17 tldqalkeaek 27
                                      ++ +a++++e 
  gi|313126041|ref|YP_004036311.1| 29 PAVAAQNATET 39
                                      22222222222 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00024
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeier 96 
                                       +  + a++  ++a+ +++++++ ++  ++l+ +++ lk+e  + ++ + +++++ a + +ei sl++ +++ +e ++
  gi|313126041|ref|YP_004036311.1|  96 KQVASARSNESKAKVVSQQVNQTQERLESLQTQLEVLKAERREGNLSQGRYRSQAARLAAEIRSLQRLLDKSQEAAD 172
                                       4455566667778888999999999999***************************************9999998888 PP

                           DUF3450  97 elvp 100
                                       +l p
  gi|313126041|ref|YP_004036311.1| 173 GLPP 176
                                       7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1556  (0.0867868); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.78u 0.40s 00:00:01.18 Elapsed: 00:00:00.55
# Mc/sec: 2004.01
//
Query:       gi|313126042|ref|YP_004036312.1|  [L=420]
Description: hypothetical protein Hbor_12820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.032   14.1   0.0    1.6  1  MarR_2           MarR family
      0.025   15.0   0.0      0.074   13.5   0.0    1.8  1  HTH_27           Winged helix DNA-binding domain
      0.097   12.2   0.0       0.16   11.6   0.0    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
       0.15   11.9   2.9        1.3    8.8   0.5    2.6  2  DUF4307          Domain of unknown function (DUF4307)
       0.68    9.9   2.7          1    9.4   0.0    2.5  2  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.9e-06     0.032       8      49 ..     354     394 ..     349     395 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.9e-06
                                       HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                            MarR_2   8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaG 49 
                                        rvLa + +++gr l ++e+a +l+ + + +s++++++ + G
  gi|313126042|ref|YP_004036312.1| 354 ERVLALIEHEGGR-LKQQEVAGTLDWTDAKTSQVVRKMRDEG 394
                                       59*********97.************************9877 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.1e-05     0.074       8      46 ..     356     394 ..     351     397 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekG 46 
                                       vL li+h+++r k+ +++g+l+ +d+ +s +++k+   G
  gi|313126042|ref|YP_004036312.1| 356 VLALIEHEGGRLKQQEVAGTLDWTDAKTSQVVRKMRDEG 394
                                       78999*****************************98665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.3e-05      0.16       4      45 ..     352     394 ..     349     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                            HTH_24   4 tdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeG 45 
                                       ++ ++L l++ +++ + q+e+A  l+ + + +++ ++++ +eG
  gi|313126042|ref|YP_004036312.1| 352 NEERVLALIEHEGGrLKQQEVAGTLDWTDAKTSQVVRKMRDEG 394
                                       677999999997777**************************99 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.042   1.5e+02      13      53 ..      11      51 ..       6      58 .. 0.48
   2 ?    8.8   0.5   0.00037       1.3       4      32 ..     243     272 ..     240     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.042
                           DUF4307 13 vvvalalvawigysqgsadvsaevvgfevvddstvevtfeV 53
                                      v+ ++++++++g +  ++  s++ v+ +   ++ v++++++
  gi|313126042|ref|YP_004036312.1| 11 VITVIIFATVLGAATPATAQSTQAVAGTQLAPDDVSLRIDI 51
                                      33334444444444434444444455555555555555555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00037
                           DUF4307   4 llvillvvlvvvalalvawigysq.gsadv 32 
                                       ++++ +++l+vv++++ +w++y++ g + +
  gi|313126042|ref|YP_004036312.1| 243 TWFVGAGLLLVVVAVGGGWVFYRRgGGTAI 272
                                       7999999****************9766665 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.7      0.51   1.8e+03      10      16 ..     213     220 ..     213     228 .. 0.63
   2 ?    9.4   0.0   0.00028         1      13      38 ..     236     266 ..     233     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.51
                                       XXXX.XXX CS
                   Gram_pos_anchor  10 PkTG.eng 16 
                                       P+TG e+g
  gi|313126042|ref|YP_004036312.1| 213 PQTGtETG 220
                                       88885443 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00028
                                       X..XXXXXXXXXXXXXXXXXXXXX...XXXX CS
                   Gram_pos_anchor  13 G..engnifltaaGllallggllL...lvkr 38 
                                       G  +n+++++  aGll+++++++    +++r
  gi|313126042|ref|YP_004036312.1| 236 GdsDNSSTWFVGAGLLLVVVAVGGgwvFYRR 266
                                       5447**********88877777654456555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.55
# Mc/sec: 2310.93
//
Query:       gi|313126043|ref|YP_004036313.1|  [L=52]
Description: hypothetical protein Hbor_12830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00095   19.1   0.5     0.0012   18.8   0.5    1.2  1  DZR          Double zinc ribbon
  ------ inclusion threshold ------
      0.018   14.4   0.6        4.5    6.8   0.1    2.2  2  zf-ribbon_3  zinc-ribbon domain
      0.023   14.6   1.1      0.081   12.9   1.1    1.8  1  Nudix_N_2    Nudix N-terminal
      0.024   14.8   1.9      0.053   13.6   1.9    1.6  1  Zn-ribbon_8  Zinc ribbon domain
       0.11   12.5   2.0        1.8    8.7   0.2    2.2  2  zf-ACC       Acetyl-coA carboxylase zinc finger domain
        0.2   11.3   2.0       0.43   10.2   2.0    1.6  1  RecR         RecR protein


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.5   4.2e-07    0.0012      15      42 ..       4      41 ..       2      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.2e-07
                               DZR 15 CseCgtklkavaa..........edrCpsCgekvdpea 42
                                      C++Cg+ +  + a          +++CpsC+ +v  +a
  gi|313126043|ref|YP_004036313.1|  4 CQNCGSFVTTAYArvfapdgmdhPRVCPSCEDMVRDGA 41
                                      ********977779******************998765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0015       4.5       4      12 ..       3      11 ..       1      16 [. 0.71
   2 ?    6.3   0.1    0.0022       6.5       4       9 ..      29      34 ..      28      43 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                       zf-ribbon_3  4 rCPnCGapl 12
                                      +C nCG+ +
  gi|313126043|ref|YP_004036313.1|  3 ECQNCGSFV 11
                                      588888843 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0022
                       zf-ribbon_3  4 rCPnCG 9 
                                       CP+C 
  gi|313126043|ref|YP_004036313.1| 29 VCPSCE 34
                                      466665 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.1   2.7e-05     0.081       3      29 ..       4      34 ..       4      36 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                                      -TTT--B-E...EE-..-TT-SS-EEEETTTT CS
                         Nudix_N_2  3 CsqCGtpve...lri..pdgDnreRlvCpaCg 29
                                      C++CG+ v+    r+  pdg +++R vCp+C+
  gi|313126043|ref|YP_004036313.1|  4 CQNCGSFVTtayARVfaPDGMDHPR-VCPSCE 34
                                      ******9986653323389999999.9****6 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.9   1.8e-05     0.053       7      34 ..       3      35 ..       3      39 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                       Zn-ribbon_8  7 rCeeCghefe......vlqsis.daplta.CPeCgs 34
                                      +C++Cg  f       v+++   d   +  CP+C  
  gi|313126043|ref|YP_004036313.1|  3 ECQNCG-SFVttayarVFAPDGmD--HPRvCPSCED 35
                                      6*****.55559887666655533..4455****65 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.022        67       4      11 ..       4      11 ..       3      14 .. 0.85
   2 ?    8.7   0.2   0.00061       1.8       4      11 ..      30      37 ..      25      37 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.022
                            zf-ACC  4 CpsCgeml 11
                                      C  Cg+ +
  gi|313126043|ref|YP_004036313.1|  4 CQNCGSFV 11
                                      *****987 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00061
                            zf-ACC  4 CpsCgeml 11
                                      CpsC+ m+
  gi|313126043|ref|YP_004036313.1| 30 CPSCEDMV 37
                                      78888776 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.0   0.00014      0.43      18      40 .]       3      39 ..       1      39 [. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                                      E-TTT--EESSS..............S-CCCCSTTSE CS
                              RecR 18 hCsrCgnlteed..............lCaICsdprRD 40
                                       C++Cg + ++               +C+ C d  RD
  gi|313126043|ref|YP_004036313.1|  3 ECQNCGSFVTTAyarvfapdgmdhprVCPSCEDMVRD 39
                                      6*******77777999*******9999*******999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 300.44
//
Query:       gi|313126044|ref|YP_004036314.1|  [L=78]
Description: sugar-specific transcriptional regulator trmb [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-05   22.9   0.1    7.5e-05   22.5   0.1    1.1  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
        0.1   13.1   0.1       0.12   12.9   0.1    1.1  1  HTH_27    Winged helix DNA-binding domain
       0.11   12.3   0.0       0.15   11.9   0.0    1.2  1  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.3e-08   7.5e-05      13      60 ..      29      76 ..      23      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-08
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      vYl+L  +g+++++e+ e l+  + + Y++L  L ++Gl++   +r++
  gi|313126044|ref|YP_004036314.1| 29 VYLYLSVQGESSITELQEGLEMKKISLYSILGALCKRGLIHQDAERYR 76
                                      9****************************************9988876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     2e-05      0.12      16      52 ..      36      72 ..      27      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                      ++++++++l + l + +++  ++l +L+++GL+++ +
  gi|313126044|ref|YP_004036314.1| 36 QGESSITELQEGLEMKKISLYSILGALCKRGLIHQDA 72
                                      578999***************************6654 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05      0.15      17      51 ..      37      71 ..      32      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +e +++el + + + k + + +L  L ++G++ qd
  gi|313126044|ref|YP_004036314.1| 37 GESSITELQEGLEMKKISLYSILGALCKRGLIHQD 71
                                      4569******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 452.62
//
Query:       gi|313126045|ref|YP_004036315.1|  [L=303]
Description: 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-21   74.9  25.9    5.8e-21   74.9  25.9    1.5  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9  25.9   3.2e-25   5.8e-21       2     236 ..      27     270 ..      26     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 3.2e-25
                              UbiA   2 lipalvg.lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRP....lvsGrispkealifa 73 
                                       l+ a+ g +a++ gg++++ +++l +++++  a+ ++  N+y D+e+D++ +rtp       lv+  + p  +++++
  gi|313126045|ref|YP_004036315.1|  27 LVYAFGGlVAVSVGGTLSPATFALSFVAFVPTAVTVHYANEYDDYETDSRANRTPFSGgsgaLVRTGLPPLFLRRAM 103
                                       566777789*********************************************97733333887777755555555 PP

                              UbiA  74 ivllilgllll....alllnpltallgllallly.vvYt.g.lrlKrrtllgtvvggiafg.lppllgwaavtgsls 142
                                       +++ i+g+l +     + + pl+a+l+ll++ ++ v Y+ + l l   ++ g+ +  i +g l+p  g+++vt+s++
  gi|313126045|ref|YP_004036315.1| 104 LLSSIVGVLAAvvalGAHVLPLSAFLILLTIGIVgVQYSlPpLELVWNGY-GEATNTILGGvLLPAYGFTVVTESVP 179
                                       555555555444434678889*************9*****8788888888.8888888888789999********** PP

                              UbiA 143 llalllalavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllyllla 219
                                       ++a l+++++++l++a +l++++ dr+ D+ +g+ tl+v++  ++ r+ ++l ++++++    l+l++++++ ++++
  gi|313126045|ref|YP_004036315.1| 180 VTATLVFVPFAVLVFANLLTTHWADRKPDASVGKETLAVRWDSHRLRRAYWLSVFAAYAT---LVLLGVGGIVPWVV 253
                                       ************************************************777777777766...66666666666666 PP

                              UbiA 220 lllaalallraarlvrr 236
                                       ++++++a+  +++   r
  gi|313126045|ref|YP_004036315.1| 254 VGAGLFAVPLSVWGGVR 270
                                       66666665555544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1749.90
//
Query:       gi|313126046|ref|YP_004036316.1|  [L=612]
Description: succinate dehydrogenase subunit a [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   7.3e-125  417.3   4.3   7.3e-125  417.3   4.3    1.6  2  FAD_binding_2   FAD binding domain
    3.2e-39  133.8   1.3    5.2e-39  133.2   1.3    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    1.8e-08   34.0   4.5      0.001   18.3   3.7    2.8  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.1e-05   25.2   5.9    0.00033   20.4   5.1    2.5  1  DAO             FAD dependent oxidoreductase
    0.00047   19.0   1.9    0.00047   19.0   1.9    1.9  3  HI0933_like     HI0933-like protein
    0.00057   19.1   3.1    0.00076   18.7   2.1    1.7  2  GIDA            Glucose inhibited division protein A
    0.00073   19.0   4.0    0.00073   19.0   4.0    1.9  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0038   16.5   3.2      0.018   14.3   0.5    2.9  4  Thi4            Thi4 family
     0.0048   16.2   1.8     0.0075   15.6   0.5    1.9  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0095   15.2   1.1     0.0095   15.2   1.1    1.8  2  FAD_binding_3   FAD binding domain
  ------ inclusion threshold ------
      0.021   14.1   1.6      0.028   13.7   0.5    1.7  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.028   14.8   0.5       0.12   12.8   0.0    2.1  2  NAD_binding_7   Putative NAD(P)-binding
      0.041   14.1   0.3       0.21   11.9   0.3    2.3  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.054   14.1   0.9       0.37   11.4   0.6    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.3   4.3  5.7e-128  7.3e-125       1     417 []       5     387 ..       5     387 .. 0.98
   2 ?   -2.4   0.1       1.5   1.9e+03     289     338 ..     471     514 ..     439     532 .. 0.63

  Alignments for each domain:
  == domain 1  score: 417.3 bits;  conditional E-value: 5.7e-128
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                       DviV+G+G+AGL+AA++a+e+G++va+v+k ++++++t +++Ggi+a+l       +++ds+e+h++dt+k++d+l+
  gi|313126046|ref|YP_004036316.1|   5 DVIVVGAGGAGLRAAIAAQEEGADVAIVSKLHPVRSHTGAAEGGINAAL-------REGDSWEQHAYDTMKGSDYLG 74 
                                       9************************************************.......457****************** PP

                                       -HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTC CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarka 154
                                       d+p++e++++ +pe+v +Le++g+ fsr++dg+v +r++Gg+s + rt + a+++      tgh+ll++++e++ k+
  gi|313126046|ref|YP_004036316.1|  75 DAPAIETLCQDSPEEVIQLEHWGLAFSRDDDGRVSQRPFGGMSFP-RTTY-AGAE------TGHQLLHTMYEQLVKR 143
                                       *********************************************.****.9998......**************** PP

                                       TEEEEESEEEEEEEECTT......EEEEEEEEETTTTCEEEEEES.EEEE-----GG..........GSSSBSSGTT CS
                     FAD_binding_2 155 gvdfqerteadeLivedg......rvtGavvenpesgrevrirak.avvlatgGfgrallkellgaaaeaettnapa 224
                                       g+++++++++++L v d+       ++G+v+ + +sg++ +++a+ +v+latgG g+          ++++ttna+a
  gi|313126046|ref|YP_004036316.1| 144 GIEVYDEWYVTRLAVSDEedpedrTCHGVVAYDIKSGEISAFHARnGVILATGGPGQ----------VFDHTTNAVA 210
                                       ***************755566777*********************************..........********** PP

                                       -S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.........GGGS-H CS
                     FAD_binding_2 225 vtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.........nelasr 292
                                       +tGdg a+a+rag++++d  me++qfhPt l+    ++g+Lite++rgeGgil++ dG+rFm         +elasr
  gi|313126046|ref|YP_004036316.1| 211 NTGDGPAMAYRAGVPMED--MEFIQFHPTTLP----STGVLITEGVRGEGGILYNEDGERFMfeygyanndGELASR 281
                                       ******************..************....***************************************** PP

                                       HHHHHHHH.HHHHTTTS..CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEE CS
                     FAD_binding_2 293 dvvsrailekeiaeggs..eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvp 367
                                       dvvsra l +e++eg++  +++v ld++h l++e +  +le+i +  +++++      +dp ++p+p       v+p
  gi|313126046|ref|YP_004036316.1| 282 DVVSRAEL-TEVNEGRGieDEYVHLDMRH-LGEERIIDRLENIVHLSEDFEG------VDPLEEPMP-------VKP 343
                                       ********.999999999999********.**********************......*********.......*** PP

                                       EEEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 368 aqhytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                       +qhy mgG+etdeng++       i+GLYAaGe+a+++vhg nrlgGn l
  gi|313126046|ref|YP_004036316.1| 344 GQHYAMGGIETDENGET------CISGLYAAGECACASVHGSNRLGGNAL 387
                                       *****************......*************************87 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                                       GS-HHHHHHHHH.HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHHHHHHHH CS
                     FAD_binding_2 289 lasrdvvsrailekeiaeggseanvyldashgldaegleatleaineeaa 338
                                       l+++d v++a +++e++++ + ++ + +++    ++gl++ l++ +++a+
  gi|313126046|ref|YP_004036316.1| 471 LEKDDGVQHAEIRAEVQQTMT-QH-VNVFRE---KDGLKEALRD-IRKAR 514
                                       555666666777777776666.55.333333...4666666666.44444 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   1.3     4e-42   5.2e-39       1     128 []     483     612 .]     483     612 .] 0.96

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 4e-42
                                       .HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S- CS
                    Succ_DH_flav_C   1 rkeLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkES 77 
                                       r e +++m+++v+vfR+++gLkeal+++++ re++++v v+dks+++N++l++++e +n+l++Aeai+ +AlaR+E 
  gi|313126046|ref|YP_004036316.1| 483 RAEVQQTMTQHVNVFREKDGLKEALRDIRKAREKYEDVYVADKSRTFNTDLIHTIETRNILDTAEAITLGALARDEF 559
                                       6799************************************************************************* PP

                                       BTTBEBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG-....-S---SS CS
                    Succ_DH_flav_C  78 rGaHaredfperdDenwlkhtlasldaakeeveleyepveletl....kpkeRsY 128
                                       rGaH+r++++er+D++wlkhtl+s   +++e+el y+pv le      +pk RsY
  gi|313126046|ref|YP_004036316.1| 560 RGAHWRKEHQERKDDKWLKHTLLS--WNDGEPELWYRPVVLEGEnktyEPKVRSY 612
                                       ***********************5..5578*********9986677789****99 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.7   8.2e-07     0.001       1      30 [.       4      33 ..       4     215 .. 0.91
   2 !   13.8   0.0     2e-05     0.025     255     279 ..     349     383 ..     331     398 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.2e-07
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve 30
                                      +dv+v+G+G AGl+aa+ +++ ga+v++v+
  gi|313126046|ref|YP_004036316.1|  4 HDVIVVGAGGAGLRAAIAAQEEGADVAIVS 33
                                      59**************************94 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2e-05
                                       TTEEE--TTSBESSTTEEE-GGGC..........T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..........x RF
                       Pyr_redox_2 255 rggivvdeflrtnvpgiyaiGDva..........g 279
                                        ggi++de+++t + g+ya+G +a          g
  gi|313126046|ref|YP_004036316.1| 349 MGGIETDENGETCISGLYAAGECAcasvhgsnrlG 383
                                       59**********************77665554444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   5.1   2.6e-07   0.00033       1     201 [.       5     196 ..       5     209 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.6e-07
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHH...HHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeel...rele 72 
                                       dv+++G+G +Gl +A +++++g  V+++ k + +    +g++ g + ++lr+         + ++a++ +   + l 
  gi|313126046|ref|YP_004036316.1|   5 DVIVVGAGGAGLRAAIAAQEEGadVAIVSKLHPVR-SHTGAAEGGINAALREGD------SWEQHAYDTMkgsDYLG 74 
                                       8*****************9999*********7777.999999999999898666......45555555553304444 PP

                                       HHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTTSTTTSEEEEETTE...EEEEHH CS
                               DAO  73 eelgididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepalpgllgalfypdt...gqvdpa 146
                                       +  +i           l++d+  +e +  +l+    +gl    ++++   +++    +  g++ +p t   g    +
  gi|313126046|ref|YP_004036316.1|  75 DAPAI-------E--TLCQDS-PEEVI--QLE---HWGLA---FSRDDDGRVSQ-R-P-FGGMSFPRTtyaGAETGH 130
                                       33222.......2..333333.13333..222...25553...44542333332.2.2.344444443231333678 PP

                                       HHHHHHHHHHHHTT-EEEESECEEEE...EEEE...TCEEEEE..EECTEEEEEEEE...EEE--G CS
                               DAO 147 kltaalaraaealGveilegtevtgl...eeed...gkvwgve..rttpgendaada...vVnaaG 201
                                       +l++ +++++ ++G+e++ +  vt+l   +eed      +gv   + ++ge++a++a   v++a+G
  gi|313126046|ref|YP_004036316.1| 131 QLLHTMYEQLVKRGIEVYDEWYVTRLavsDEEDpedRTCHGVVayDIKSGEISAFHArngVILATG 196
                                       899999999999999999998888874332222445555555566455555543333448999998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.9   3.7e-07   0.00047       1      32 [.       4      35 ..       4      56 .. 0.86
   2 ?   -4.1   0.0       3.6   4.6e+03      81     105 ..     181     205 ..     169     208 .. 0.70
   3 ?   -4.0   0.0       3.5   4.5e+03     373     384 ..     360     371 ..     348     373 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.7e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dviv+G+G AGl aAi+a+++g++V+++ k 
  gi|313126046|ref|YP_004036316.1|  4 HDVIVVGAGGAGLRAAIAAQEEGADVAIVSKL 35
                                      59**************************9876 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.6
                                       HHHHHHHHTT--EEE-STTEEEETT CS
                       HI0933_like  81 dlialveelgvelkeedsgrlFpvs 105
                                       ++ a+ +++gv l ++  g++F  +
  gi|313126046|ref|YP_004036316.1| 181 EISAFHARNGVILATGGPGQVFDHT 205
                                       4566777777777777777777655 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 3.5
                                       TTSTTEEE-GGG CS
                       HI0933_like 373 kkvpgLffaGEv 384
                                        +++gL+ aGE+
  gi|313126046|ref|YP_004036316.1| 360 TCISGLYAAGEC 371
                                       347999999996 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.1   5.9e-07   0.00076       1      28 [.       5      32 ..       5      60 .. 0.86
   2 ?   -3.1   0.0       2.5   3.2e+03      97     150 ..     137     197 ..     125     214 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.9e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dviV+G+G AG+ AA+aa + Ga+v+++
  gi|313126046|ref|YP_004036316.1|  5 DVIVVGAGGAGLRAAIAAQEEGADVAIV 32
                                      8*************************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHTSTTEEEEES-EEEEE.ECTTEEEEEEETT...S-..EEEEC.EEEE--TT CS
                              GIDA  97 yskevteklenepnleiieeeveeli.veekkvkgvvted...ge..tikak.avviatGt 150
                                       y++ v++ +e +++  + +  v++ + +e+++++gvv  d   ge  +++a+  v++atG 
  gi|313126046|ref|YP_004036316.1| 137 YEQLVKRGIEVYDEWYVTRLAVSDEEdPEDRTCHGVVAYDiksGEisAFHARnGVILATGG 197
                                       6666666666666666666666554314446777776544111221134444579999986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   4.0   5.7e-07   0.00073       1      30 [.       5      34 ..       5      38 .. 0.96
   2 ?   -1.3   0.2       0.8     1e+03     177     246 ..     466     532 ..     406     579 .. 0.50

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.7e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv+VvG+g aG+ AAiaA ++Ga v++v++
  gi|313126046|ref|YP_004036316.1|  5 DVIVVGAGGAGLRAAIAAQEEGADVAIVSK 34
                                      9***************************86 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.8
                      FAD_oxidored 177 rlegveggeedekvqaynkrlcltskpenrvpfekkpegydparyelarvfeaklskgklpgektdvnwp 246
                                       r+e +   e+d+ vq    r   ++   ++v++ ++++g+++a +++ r  + k++  + +++ + +n +
  gi|313126046|ref|YP_004036316.1| 466 RVESL--LEKDDGVQHAEIRAEVQQTMTQHVNVFREKDGLKEALRDI-RKAREKYEDVYVADKSRTFNTD 532
                                       33333..5555556655555555555555555555555555555555.2222223333333333333332 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.5   1.4e-05     0.018      17      49 ..       3      34 ..       1      51 [. 0.76
   2 ?   -2.1   0.0       1.5   1.9e+03     202     224 ..     138     160 ..     133     165 .. 0.86
   3 ?    0.9   0.0      0.18   2.3e+02     208     232 ..     358     383 ..     351     385 .. 0.83
   4 ?   -3.7   0.0       4.5   5.7e+03      76     218 ..     506     523 ..     489     538 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                      e Dv++vGaG +GL aa    ++ +  vai+ +
  gi|313126046|ref|YP_004036316.1|  3 EHDVIVVGAGGAGLRAAIAAQEE-GADVAIVSK 34
                                      89***************887777.888887754 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                       HHHHHHECEEETTEEE-THHHHH CS
                              Thi4 202 daivkktrevvpnlyvaGmevae 224
                                       +++vk+  ev+++ yv+ ++v++
  gi|313126046|ref|YP_004036316.1| 138 EQLVKRGIEVYDEWYVTRLAVSD 160
                                       5799999**********999986 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.18
                                       ECEEETTEEE-T.HHHHHHHT-EB-- CS
                              Thi4 208 trevvpnlyvaG.mevaevdganRmG 232
                                        +  + +ly+aG  + a v+g nR+G
  gi|313126046|ref|YP_004036316.1| 358 GETCISGLYAAGeCACASVHGSNRLG 383
                                       5567899****9558899*******9 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 4.5
                                       HHHHTT---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.- CS
                              Thi4  76 lLdelgikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscv 152
                                        L+++  + e+++d                                                               
  gi|313126046|ref|YP_004036316.1| 506 ALRDIRKAREKYED--------------------------------------------------------------- 519
                                       45555555555555............................................................... PP

                                       B-EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE- CS
                              Thi4 153 DPlvirakvvvdatGhdgeivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyva 218
                                                                                                     +yva
  gi|313126046|ref|YP_004036316.1| 520 --------------------------------------------------------------VYVA 523
                                       ..............................................................4443 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   5.9e-06    0.0075       1      34 [.       7      39 ..       7      42 .. 0.89
   2 ?   -2.6   0.0       1.9   2.5e+03     244     269 ..     174     199 ..     167     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.9e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnign 34
                                      i++GaG aGl aai++++ g  d+ i+ k + + 
  gi|313126046|ref|YP_004036316.1|  7 IVVGAGGAGLRAAIAAQEEGA-DVAIVSKLHPVR 39
                                      89******************9.899999877665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                       Pyr_redox_3 244 eykvktedgkkvevkddvvlatGykp 269
                                        y++k+ + + +++++ v+latG   
  gi|313126046|ref|YP_004036316.1| 174 AYDIKSGEISAFHARNGVILATGGPG 199
                                       67888888888899999999999755 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.1   7.4e-06    0.0095       2      34 ..       4      36 ..       3      49 .. 0.88
   2 ?   -2.3   0.1       1.5     2e+03      57      92 ..     476     523 ..     453     566 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.4e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                       dV++VGaG aGl +a   +e G +v +v k  
  gi|313126046|ref|YP_004036316.1|  4 HDVIVVGAGGAGLRAAIAAQEEGADVAIVSKLH 36
                                      69***************************9975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                                       T-HHHHHHHSEECCCCEEEEEEE........CCCCCEEEEEHH....C CS
                     FAD_binding_3  57 Gledrilaegapnelmgealyne........lsdtpkaradle....l 92 
                                       G+++  ++  +++ ++++++  +        l+d++kar+++e    +
  gi|313126046|ref|YP_004036316.1| 476 GVQHAEIRAEVQQTMTQHVNVFRekdglkeaLRDIRKAREKYEdvyvA 523
                                       444333333323333222222224455555555555555555544443 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   2.2e-05     0.028      30      59 ..       5      34 ..       1      65 [. 0.85
   2 ?   -2.6   0.0       2.1   2.7e+03      13      45 ..     342     374 ..     340     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDv 59
                                       v+v+G+G aGl A+ +a++ ga+V ++ +
  gi|313126046|ref|YP_004036316.1|  5 DVIVVGAGGAGLRAAIAAQEEGADVAIVSK 34
                                      79***********************99865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                                       CTSEEETTCEETCB---EEEEESTSHHHHHHHH CS
                       AlaDh_PNT_C  13 fggkgtlaGgvpgvepakvlviGgGvaGlqAia 45 
                                       ++g+  ++Gg++  e++++ + G   aG  A a
  gi|313126046|ref|YP_004036316.1| 342 KPGQHYAMGGIETDENGETCISGLYAAGECACA 374
                                       689999******999999999998888877765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.3e-05      0.12       6      40 ..       2      36 ..       1     110 [. 0.81
   2 ?   -0.6   0.2       1.4   1.8e+03      46      88 ..     501     543 ..     462     547 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-05
                     NAD_binding_7  6 kgkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                      ++  v+vvG+G  ++r +    e+ga+v +v++  
  gi|313126046|ref|YP_004036316.1|  2 HEHDVIVVGAGGAGLRAAIAAQEEGADVAIVSKLH 36
                                      56789***************************974 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                     NAD_binding_7  46 elvklaeeelekdlegadlviaatddrelneriaeaakarril 88 
                                       + +k a ++++k  e+++ v++a + r  n+ + +++++r+il
  gi|313126046|ref|YP_004036316.1| 501 DGLKEALRDIRKAREKYEDVYVADKSRTFNTDLIHTIETRNIL 543
                                       2222333446666777888888888888888888888888876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00016      0.21       1      27 [.       8      34 ..       8      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                                      EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                      +vGaG +Gl aA +++++g+dv ++ k
  gi|313126046|ref|YP_004036316.1|  8 VVGAGGAGLRAAIAAQEEGADVAIVSK 34
                                      8*********************99876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   0.00029      0.37       2      33 ..       6      37 ..       5      46 .. 0.89
   2 ?   -0.7   0.0       1.7   2.2e+03      45      70 ..     135     160 ..     126     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                      v+vvG+G  gl +A a++e g++V +v     
  gi|313126046|ref|YP_004036316.1|  6 VIVVGAGGAGLRAAIAAQEEGADVAIVSKLHP 37
                                      89************************987665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                       HHHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox  45 ilqeklekngievllntkveeiegse 70 
                                        + e+l k+giev+ +  v+++  s+
  gi|313126046|ref|YP_004036316.1| 135 TMYEQLVKRGIEVYDEWYVTRLAVSD 160
                                       67789999*****9887777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.74u 0.36s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 3365.73
//
Query:       gi|313126047|ref|YP_004036317.1|  [L=292]
Description: succinate dehydrogenase subunit b [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-33  114.0   0.1    1.4e-32  111.9   0.0    2.1  2  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
    3.1e-12   46.8   4.6    3.1e-12   46.8   4.6    2.1  2  Fer4_8    4Fe-4S dicluster domain
    1.4e-08   34.7   4.3    3.3e-08   33.5   4.3    1.7  1  Fer4_10   4Fe-4S dicluster domain
    1.4e-06   28.8   4.0    5.6e-06   26.8   4.0    2.1  1  Fer4_7    4Fe-4S dicluster domain
    0.00011   22.6   4.8    0.00011   22.6   4.8    2.0  2  Fer4_17   4Fe-4S dicluster domain
    0.00062   19.9   9.8     0.0067   16.6   9.7    2.5  2  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.021   14.6   7.5       0.45   10.3   0.4    2.6  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
       0.28   11.2   6.1       0.74    9.8   6.1    1.7  1  DUF3043   Protein of unknown function (DUF3043)
       0.47   11.1   8.7       0.93   10.2   2.4    2.7  2  Fer4_4    4Fe-4S binding domain
       0.96   10.4  16.4       0.35   11.8   8.4    3.2  3  Fer4_16   4Fe-4S double cluster binding domain
        2.2    8.3   9.7        6.1    6.8   3.1    2.5  2  Fer4      4Fe-4S binding domain
        3.8    8.7  11.9          2    9.5   0.4    2.6  2  Fer4_3    4Fe-4S binding domain
        6.3    7.0   7.8        9.6    6.5   2.4    2.5  2  Fer4_6    4Fe-4S binding domain
        6.6    7.0  10.1    1.2e+02    2.9  10.1    2.4  1  Fer4_21   4Fe-4S dicluster domain
        8.9    6.5  14.9        3.2    8.0   0.3    3.0  3  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.0   1.2e-35   1.4e-32       2     108 ..      56     160 ..      55     161 .. 0.95
   2 ?   -0.9   0.1       1.3   1.6e+03      53      65 ..     198     210 ..     182     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 1.2e-35
                            Fer2_3   2 lkvkRfdprrdrg.kqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatik 77 
                                       lkv+R+dp+   + ++++++++v++++++tvldaL++ ++++d++l+fr+sCr++iCGs+a+ +nG ++l C+++++
  gi|313126047|ref|YP_004036317.1|  56 LKVFRYDPEVAGKqEPRFDDFHVPYHKGMTVLDALMYARDHYDSSLTFRHSCRQAICGSDALFVNGSQRLGCKTQLS 132
                                       79******9877679************************************************************** PP

                            Fer2_3  78 dlakqkseieleplpkfpvirDLvvDideml 108
                                       dl++   ++++eplp+ +v++DLvvD+++++
  gi|313126047|ref|YP_004036317.1| 133 DLEE---PVRIEPLPHQEVVKDLVVDMEHFY 160
                                       *986...49*******************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                            Fer2_3  53 regiCGscavain 65 
                                       r   CG+c  ++n
  gi|313126047|ref|YP_004036317.1| 198 RCIWCGACMSSCN 210
                                       4457999987776 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       2.1   2.5e+03      29      39 ..      30      39 ..      13      58 .. 0.50
   2 !   46.8   4.6   2.6e-15   3.1e-12       3      65 .]     197     271 ..     195     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.1
                            Fer4_8 29 rgeaaedvqee 39
                                      + ++ae ++e+
  gi|313126047|ref|YP_004036317.1| 30 KRQKAE-ERER 39
                                      111111.2222 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 2.6e-15
                            Fer4_8   3 ekCieCgaCqsaC...........pvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                        +Ci CgaC+s+C           p++ +++ ++ +d r++   ++++ + le+e+++w+C+t  +CtevCp++i
  gi|313126047|ref|YP_004036317.1| 197 TRCIWCGACMSSCniaagdnkylgPAAINKAyRFTMDEREGEDMKQHRMEILEQEHGVWRCQTQFSCTEVCPKDI 271
                                       69***********77777776666566666668888888776666888888888******************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   4.3   2.8e-11   3.3e-08       5      56 .]     195     268 ..     191     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.8e-11
                           Fer4_10   5 dddtCirCgkCvkaCPadl........................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        + +Ci Cg+C+++C  ++                        ++ + k+ ++e+ +++++v++C++ ++C+e+CP
  gi|313126047|ref|YP_004036317.1| 195 MSTRCIWCGACMSSC--NIaagdnkylgpaainkayrftmderEGEDMKQHRMEILEQEHGVWRCQTQFSCTEVCP 268
                                       5689***********..8889******************************************************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   4.0   4.7e-09   5.6e-06       1      52 []     198     271 ..     198     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.7e-09
                            Fer4_7   1 rCigCgaCvaaC................pvkaieldeeenekgt.ekv.....eidpekClgCgaCvavCPtga 52 
                                       rCi CgaC++ C                +++ +++de+e e+ + +++     e+  ++C++  +C +vCP+++
  gi|313126047|ref|YP_004036317.1| 198 RCIWCGACMSSCniaagdnkylgpaainKAYRFTMDEREGEDMKqHRMeileqEHGVWRCQTQFSCTEVCPKDI 271
                                       8*********************9998877888888888777754233344555666789************985 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2         7   8.4e+03      25      37 ..      21      33 ..      11      46 .. 0.50
   2 !   22.6   4.8   9.4e-08   0.00011       1      60 [.     198     271 ..     198     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7
                           Fer4_17 25 llraaklglleea 37
                                       +++a+++++++ 
  gi|313126047|ref|YP_004036317.1| 21 AAQQARMEKKRQK 33
                                      4555555322222 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 9.4e-08
                           Fer4_17   1 rCiqCgyClpeCpsyeaydne..pk..kllraakl..........glleeaekeekaslCieCgeCerkCPqgl 60 
                                       rCi Cg+C+ +C   +  +++  p+  + ++++++          +++e  e+e+ + +C +   C+++CP+++
  gi|313126047|ref|YP_004036317.1| 198 RCIWCGACMSSCNIAAGDNKYlgPAaiNKAYRFTMderegedmkqHRMEILEQEHGVWRCQTQFSCTEVCPKDI 271
                                       7************999877754455234556666677666655544555566679*****************98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   3.4   0.00017       0.2      17      47 ..     180     210 ..     176     213 .. 0.77
   2 !   16.6   9.7   5.6e-06    0.0067       1      49 [.     198     270 ..     198     271 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                            Fer4_9  17 vvedaaerkarlraaseeaCigCgaCveaCp 47 
                                        +e++++r++r +++  ++Ci CgaC+  C+
  gi|313126047|ref|YP_004036317.1| 180 LEEQRQTRENREKIKMSTRCIWCGACMSSCN 210
                                       5566777777777777799***********6 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.6e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........................eaCigCgaCveaCpkg 49 
                                       +C+ CgaC+++C+  +  ++  +  a ++a++                         ++C +  +C+e+Cpk+
  gi|313126047|ref|YP_004036317.1| 198 RCIWCGACMSSCNIAAGDNKYLGPAAINKAYRFtmderegedmkqhrmeileqehgvWRCQTQFSCTEVCPKD 270
                                       5***********55555555555555555544455555666666788889****99999999999******98 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.6    0.0034         4       6      46 ..     181     219 ..     177     235 .. 0.80
   2 ?   10.3   0.4   0.00037      0.45      20      58 ..     250     289 ..     233     292 .] 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0034
                                       S-SB----HHHHHHHHTT----TT-HHHHCSTT---HHHHH CS
                           Fer4_20   6 kevalglteeealeeAsRClqCkkapcvkgCPveidipefi 46 
                                       +e +++ +++e ++ ++RC+ C    c+++C +    ++++
  gi|313126047|ref|YP_004036317.1| 181 EEQRQTRENREKIKMSTRCIWC--GACMSSCNIAAGDNKYL 219
                                       677778888999**********..789999*9887666665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00037
                                       HHTT----T.T-HHHHCSTT---HHHHHHHHHTT-HHHHH CS
                           Fer4_20  20 eAsRClqCk.kapcvkgCPveidipefikkiaegnleeaa 58 
                                       + +   +C+ +  c++ CP +i   e+i++++++ +++ +
  gi|313126047|ref|YP_004036317.1| 250 QEHGVWRCQtQFSCTEVCPKDIPLTEHIQELKREAVKNNL 289
                                       5555567883456*******************99998765 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.1   0.00062      0.74      10      58 ..       9      57 ..       3      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00062
                           DUF3043 10 keaeaarrrplvapktrkearkrareaarerrerareamraGderylpa 58
                                       e e++  ++++a ++ + ++kr+++++rer++++ e  +aG++ yl++
  gi|313126047|ref|YP_004036317.1|  9 VEDESSADTETSAAQQARMEKKRQKAEERERQAEEAESAAAGEDTYLLK 57
                                      455555555556778888888999999*******************987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.4   0.00078      0.93       2      14 ..     197     209 ..     196     216 .. 0.92
   2 ?    3.7   0.5     0.091   1.1e+02       7      16 ..     257     269 ..     255     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00078
                            Fer4_4   2 erCigCgsCvaaC 14 
                                        rCi Cg+C+++C
  gi|313126047|ref|YP_004036317.1| 197 TRCIWCGACMSSC 209
                                       59*********** PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.091
                            Fer4_4   7 Cg...sCvaaCPq 16 
                                       C    sC+ +CP 
  gi|313126047|ref|YP_004036317.1| 257 CQtqfSCTEVCPK 269
                                       664336******5 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.6       1.5   1.8e+03      30      49 ..      20      39 ..       5      53 .. 0.48
   2 ?   11.7   2.1   0.00033       0.4      34      64 ..     179     209 ..     161     212 .. 0.81
   3 ?   11.8   8.4   0.00029      0.35       1      66 [.     198     269 ..     198     270 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.5
                           Fer4_16 30 cisyntaekkdlaedeekck 49
                                      + +++ +++k+ ++ ee++ 
  gi|313126047|ref|YP_004036317.1| 20 SAAQQARMEKKRQKAEERER 39
                                      33333333333333333332 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00033
                           Fer4_16  34 ntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                       + +e+++ +e++ek k+ ++++ C++C+  C
  gi|313126047|ref|YP_004036317.1| 179 ELEEQRQTRENREKIKMSTRCIWCGACMSSC 209
                                       6788999999999****************** PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00029
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy....ntaekkdlaedeekckkqeai.tgCd...iCqdvCPa 66 
                                       rC+ Cg+C+++C  +a ++k    +++++   y     ++e +d+++++ +  +qe+    C+    C++vCP 
  gi|313126047|ref|YP_004036317.1| 198 RCIWCGACMSSCNIAAGDNKYLGPAAINKA--YrftmDEREGEDMKQHRMEILEQEHGvWRCQtqfSCTEVCPK 269
                                       6***************99884333344443..33355566666666666666655333356665559******5 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.1    0.0051       6.1       6      18 ..     197     209 ..     193     209 .. 0.89
   2 ?    5.0   0.5      0.02        24      14      21 ..     263     270 ..     262     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0051
                                       TTSSS-THHHHHS CS
                              Fer4   6 ekCigCGaCvevC 18 
                                        +Ci CGaC++ C
  gi|313126047|ref|YP_004036317.1| 197 TRCIWCGACMSSC 209
                                       68999******99 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                                       HHHHSTTT CS
                              Fer4  14 CvevCPvg 21 
                                       C evCP +
  gi|313126047|ref|YP_004036317.1| 263 CTEVCPKD 270
                                       ******88 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   5.7      0.35   4.2e+02       1      11 [.     199     209 ..     199     209 .. 0.88
   2 ?    9.5   0.4    0.0017         2       4      14 ..     257     270 ..     253     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.35
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ CgaC+ +C
  gi|313126047|ref|YP_004036317.1| 199 CIWCGACMSSC 209
                                       666******** PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0017
                            Fer4_3   4 Cg...aCvevCPvg 14 
                                       C+    C evCP++
  gi|313126047|ref|YP_004036317.1| 257 CQtqfSCTEVCPKD 270
                                       765456******97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.4     0.008       9.6       8      19 ..     198     209 ..     195     213 .. 0.88
   2 ?    2.7   0.3      0.12   1.5e+02      15      22 ..     263     270 ..     261     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.008
                            Fer4_6   8 kCigCgdCvrvC 19 
                                       +Ci Cg+C++ C
  gi|313126047|ref|YP_004036317.1| 198 RCIWCGACMSSC 209
                                       8**********9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                            Fer4_6  15 CvrvCPeg 22 
                                       C+ vCP +
  gi|313126047|ref|YP_004036317.1| 263 CTEVCPKD 270
                                       ******75 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  10.1       0.1   1.2e+02       6      24 ..     197     215 ..     192     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
                           Fer4_21   6 dkCigCgkCliaCedtshq 24 
                                        +Ci Cg C+ +C+ ++ +
  gi|313126047|ref|YP_004036317.1| 197 TRCIWCGACMSSCNIAAGD 215
                                       68***********976654 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.1       1.3   1.6e+03      30      51 ..      23      42 ..       7      54 .. 0.44
   2 ?    7.4   1.3    0.0039       4.7      47      73 ..     185     211 ..     161     225 .. 0.74
   3 ?    8.0   0.3    0.0027       3.2      43      82 ..     239     278 ..     219     281 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.3
                           Fer4_18 30 dakrGekiagrkkekkalkeke 51
                                      +++r ek++++++e++ +   e
  gi|313126047|ref|YP_004036317.1| 23 QQARMEKKRQKAEERERQ--AE 42
                                      233333332222222222..22 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0039
                           Fer4_18  47 lkekeerkekgagdcidcescvkvcPt 73 
                                       +++++++k k ++ ci c++c++ c +
  gi|313126047|ref|YP_004036317.1| 185 QTRENREKIKMSTRCIWCGACMSSCNI 211
                                       333344455777888888888888865 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0027
                           Fer4_18  43 ekkalkekeerkekgagdcidcescvkvcPtgidirkGlq 82 
                                         k+++ + +++e+g+  c +  sc +vcP +i + + +q
  gi|313126047|ref|YP_004036317.1| 239 DMKQHRMEILEQEHGVWRCQTQFSCTEVCPKDIPLTEHIQ 278
                                       334444455667889999*************998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1802  (0.100508); expected 358.6 (0.02)
Passed bias filter:                      807  (0.0450109); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 1687.47
//
Query:       gi|313126048|ref|YP_004036318.1|  [L=125]
Description: succinate dehydrogenase subunit d [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-08   34.2   8.5    2.7e-08   33.9   8.5    1.1  1  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem
  ------ inclusion threshold ------
       0.22   11.4   9.3      0.085   12.8   5.4    1.9  2  DctQ      Tripartite ATP-independent periplasmic transporters


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   8.5   3.1e-12   2.7e-08      20     119 ..      12     106 ..       3     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.1e-12
                           Sdh_cyt  20 awlsilhritGvallv.glllllvwlllalslsspe.sfarvvallaspiklilllllllallyHllnGiRhllwDl 94 
                                          ++ +rit+++l+v + ++++   ll+ + + ++ +f++ +a ++++ +  l++l+l+ + +H++nG++  l++ 
  gi|313126048|ref|YP_004036318.1|  12 GRRWLWQRITAAFLVVvLAFHFF---LLHFVHHAADvTFQMSAARMQQWTYYSLMVLFLITATFHGVNGVYNALVNQ 85 
                                       557999**********5555555...3344444444488888****998888888999999999***********98 PP

                           Sdh_cyt  95 glglelesarksalavlalavalvl 119
                                       g+    e  rk+a+ ++++a+ + l
  gi|313126048|ref|YP_004036318.1|  86 GI----EGTRKTAVKWTLIAASILL 106
                                       88....7777777666666555444 PP

>> DctQ  Tripartite ATP-independent periplasmic transporters, DctQ component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.4   9.5e-06     0.085      58     129 ..       9      81 ..       4      84 .. 0.68
   2 ?    0.6   0.1     0.055   4.9e+02      67      85 ..      93     111 ..      81     121 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-06
                              DctQ  58 pprvrrlleliadl.lallfaavliwagwlevaaalfeettpvlglplwwvylvlpigaallalvalarllrl 129
                                        +++rr+l   +++ ++++++a+ ++ + ++  aa+ + + ++ ++++w +y++++++++ ++++ +  ++++
  gi|313126048|ref|YP_004036318.1|   9 ERGGRRWLWQRITAaFLVVVLAFHFFLLHFVHHAADVTFQMSAARMQQWTYYSLMVLFLITATFHGVNGVYNA 81 
                                       555666665555551555555544444445666666666677777********************99888776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.055
                              DctQ  67 liadllallfaavliwagw 85 
                                        ++ + +++++++li++g+
  gi|313126048|ref|YP_004036318.1|  93 TAVKWTLIAASILLIVQGI 111
                                       4555666666777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 826.82
//
Query:       gi|313126049|ref|YP_004036319.1|  [L=130]
Description: succinate dehydrogenase subunit c [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-25   89.1   5.8    2.3e-25   89.0   5.8    1.0  1  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   5.8   1.3e-29   2.3e-25       2     120 ..       4     124 ..       3     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 1.3e-29
                           Sdh_cyt   2 rknrplsphlqlyr.lplgawlsilhritGvallvglllllvwlllalslsspesfarvvallas.piklillllll 76 
                                       ++nr l +++++++ + +g+w++i+h++tG++l++ +l+++++ +l+++l++++ + + ++ l s ++  il+++ll
  gi|313126049|ref|YP_004036319.1|   4 SYNRGLIEDFGRWKeFSAGMWAWIFHKFTGWVLVG-YLFTHIA-VLSTALTGQAEYTNTIQTLESlLVVRILEVGLL 78 
                                       689***********889******************.8888876.667778888889999889989999********* PP

                           Sdh_cyt  77 lallyHllnGiRhllwDlglgl.el.esarksalavlalavalvlv 120
                                       +++++H+lnG+R+ll+Dlg+gl  + +s ++s +++ a++va+v +
  gi|313126049|ref|YP_004036319.1|  79 AVAVFHILNGLRLLLVDLGVGLhAQdKSFYASLALTGAIVVASVPT 124
                                       *****************999998777999***99999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 787.88
//
Query:       gi|313126050|ref|YP_004036320.1|  [L=342]
Description: deacylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      7e-66  222.3   0.0    8.5e-66  222.0   0.0    1.0  1  AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase f


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.0   0.0   4.8e-70   8.5e-66       1     288 [.      47     318 ..      47     320 .. 0.99

  Alignments for each domain:
  == domain 1  score: 222.0 bits;  conditional E-value: 4.8e-70
                                       SS-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSSTT-S-CTTTTTCCCCCSSTC CS
                         AstE_AspA   1 sgpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyipidredLNRaFpgrslgrsld 77 
                                       +gp+ ++sA+ HG+El+G+e++r+++++++  d++g+ +++p+ N+p++ a++Ry+pi+++dLNR+Fpgr++     
  gi|313126050|ref|YP_004036320.1|  47 DGPTAFLSAAAHGDELNGIEVVREVAHEWDLSDLAGTLVCMPVLNVPGFLAQQRYLPIYDRDLNRSFPGREDS---- 119
                                       59***********************************************************************.... PP

                                       HHHHHHHHHHHHHHHCHCTCCCGCEEEEEEEESSTBCCSSEEEE---SSHHHHHHHHHHTTTSEEEEEESS--SSHH CS
                         AstE_AspA  78 ealrateaerladalfaaalpeadivlDLHtgtrglkhllfaeadiaeaqlqslallkalglpavllldekesagfl 154
                                            t+a+r+a ++f++ + ++d+ +D+Ht trg++++ +++a+++ +    ++l++a+g  +++  + ++s+g+l
  gi|313126050|ref|YP_004036320.1| 120 -----TSAKRMAARIFDNFIAPCDFGIDFHTSTRGRTNMIHVRANMEHDGS--ARLARAFGSHVII--AGEGSSGML 187
                                       .....*****************************************99988..*************..********* PP

                                       HHHHHHCTSEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT-SCC.CEEEEEEEEEEGGSCCCSSCSEEEC CS
                         AstE_AspA 155 etaaeelgalaftlElGgagrlgaedisrtakgvlnvlahigvvagqeavepaklyrvlreldeprdiraeeaGlve 231
                                       +t+a  +g++++t+E+G+a+r++ e+i+ + +gv++v a++g+ + + av+++ +++v++  +e+++ira+++G+v+
  gi|313126050|ref|YP_004036320.1| 188 RTEATAVGVPTITVEMGEAHRFQRELIDEALAGVESVFAEYGLRDTT-AVRWPGWRTVIDDDSEKTWIRADAGGIVD 263
                                       ***********************************************.9**************************** PP

                                       CCCSTTTTETCTEEEETTEEEEECTSTEEEEESSSSEEEESCCTSCCTTTTEEEEEE CS
                         AstE_AspA 232 fkvklgddveagellakalvldslggekvelrapqdgvivfineaalvekgaalvkv 288
                                       ++ + g+ v  g+ +  ++++ ++++++v+++ap +g++v+  e++ v +g+ l+++
  gi|313126050|ref|YP_004036320.1| 264 MHYDRGALVHEGDRI--CTITNPFKDDNVTIQAPFTGLLVGVLENPVVYPGNPLCHL 318
                                       ***************..**************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2270.61
//
Query:       gi|313126051|ref|YP_004036321.1|  [L=452]
Description: alpha-L-glutamate ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-22   79.8   0.0      3e-22   79.1   0.0    1.3  1  RimK             RimK-like ATP-grasp domain
    3.9e-08   33.3   0.4    2.2e-06   27.6   0.1    2.3  2  Zn_protease      Putative ATP-dependant zinc protease
    1.1e-06   28.2   0.0    2.1e-06   27.2   0.0    1.4  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
    2.2e-05   24.6   0.0    9.7e-05   22.5   0.0    1.9  1  ATP-grasp_3      ATP-grasp domain
    0.00025   21.1   0.2    0.00048   20.2   0.2    1.6  1  R2K_3            ATP-grasp domain, R2K clade family 3
    0.00043   20.8   0.2     0.0012   19.4   0.2    1.7  1  gag-asp_proteas  gag-polyprotein putative aspartyl protease
     0.0024   18.5   0.5     0.0077   16.9   0.5    1.9  1  Asp_protease_2   Aspartyl protease
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.027   14.3   0.1    1.4  1  R2K_2            ATP-grasp domain, R2K clade family 2
      0.017   14.4   0.0      0.052   12.8   0.0    1.7  1  ATPgrasp_YheCD   YheC/D like ATP-grasp
       0.05   13.3   0.0      0.098   12.4   0.0    1.4  1  DUF5488          Family of unknown function (DUF5488)


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   1.7e-25     3e-22       3     175 ..     101     273 ..      99     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.7e-25
                                       -HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--EEE CS
                              RimK   3 dKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeailvq 79 
                                        K+ + + La  +i vp + la +++ ++k  +++  +   v Ks  g+ G +      +++++      + + ++q
  gi|313126051|ref|YP_004036321.1| 101 HKFATAATLANWNIRVPDALLALSNDRLNKDRDRF--GDVGVYKSAIGTHGGGTWKVDLTEAVNPK--VGNRQAFLQ 173
                                       688999999*******************9988887..577799*******9998766666555544..37889999* PP

                                       EE--SS-S..EEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE-..---HHHHHHHHHHHHHCT-SEEEEEEE CS
                              RimK  80 eyieeaen..ediRvlvvddevvaalrrvskeGdFRsnlhrGgvaekl..qlseeekelAikaakamelvvaGvDll 152
                                       + ie  +   +d+Rv +vd+e+++a+ r + +Gd+R+n+ +Gg + ++  ++ ee +e A+ aa++mel+++GvDl+
  gi|313126051|ref|YP_004036321.1| 174 DLIERDDTrhRDLRVYIVDGEIIGAMYRYAPDGDWRTNVALGGDVMNAtdEMPEEARETALYAAEVMELDYVGVDLV 250
                                       ***99988779*******************************9887662258999********************** PP

                                       EETTEEEEEEEESS--SHHHHHH CS
                              RimK 153 rakrgllvlEvnsspglekiekt 175
                                       + ++g +vlEvn   g +++ k 
  gi|313126051|ref|YP_004036321.1| 251 EGEDGWFVLEVNPTAGFKGLYKA 273
                                       ****************9998665 PP

>> Zn_protease  Putative ATP-dependant zinc protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.03        53       3      32 ..     329     360 ..     327     367 .. 0.77
   2 !   27.6   0.1   1.2e-09   2.2e-06      68     132 ..     372     435 ..     361     438 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.03
                       Zn_protease   3 GekEelsLpelkiq..lkakidtgaltsSLsa 32 
                                       G +Ee+ + +   +  + ak dtga+  S++ 
  gi|313126051|ref|YP_004036321.1| 329 GYIEEVVVSGTSGStqAYAKSDTGATRTSIDT 360
                                       7788888877654323899*******999975 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 1.2e-09
                       Zn_protease  68 lrivkirqsagd.aekRpViklqlllgpeiekievtLtdRsavkypvllgvralikakaaVDpsrk 132
                                         ++++++ + +  ++RpV++l + + +   ++  +++dRs++ yp+llg  ++i ++ +VD+ r+
  gi|313126051|ref|YP_004036321.1| 372 KSMTRVKSGSMKsGKARPVVDLVIGIAGTQHTVTASVEDRSHMDYPLLLG--RDILQHYRVDVRRR 435
                                       5667777765554799**********************************..77888899999876 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   1.2e-09   2.1e-06      68     155 ..     166     253 ..     148     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.2e-09
                                       TTS-EEEEE--..GGGGG-EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEE..EEE--HHHHHHHHHHHHHHH CS
                         GSH-S_ATP  68 gkepviaqryl..peikeGDkRillvdGepigyalaRvpaegevRsnlaaggrae..atelterdreiaeelapkLk 140
                                       g+++  +q+ +  ++ ++ D R+ +vdGe ig a+ R + +g+ R+n+a gg +   + e+ e+ re a   a+ ++
  gi|313126051|ref|YP_004036321.1| 166 GNRQAFLQDLIerDDTRHRDLRVYIVDGEIIG-AMYRYAPDGDWRTNVALGGDVMnaTDEMPEEARETALYAAEVME 241
                                       5677778888833478999*************.*******************8751145777777887777777665 PP

                                       HTT--EEEEEEETTE CS
                         GSH-S_ATP 141 ekGllfvGlDvigdk 155
                                          l +vG+D+++++
  gi|313126051|ref|YP_004036321.1| 242 ---LDYVGVDLVEGE 253
                                       ...668999998764 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.4e-08   9.7e-05       4     156 ..     102     263 ..      99     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.4e-08
                                       HHHHHHHHTTT.S---...........-EESS--....SSSEEEEESS-------B--SS--TTE........EEEE CS
                       ATP-grasp_3   4 KlktykkLkeagvkvP.......tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve.lvqe 68 
                                       K++t+  L + +++vP       +    ++l++      +  v K + G  g ++ +v+  e+ + ++ + +  +q+
  gi|313126051|ref|YP_004036321.1| 102 KFATAATLANWNIRVPdallalsN----DRLNKDrdrfGDVGVYKSAIGTHGGGTWKVDLTEAVNPKVGNRQaFLQD 174
                                       888888888888888876644432....3333223334778899999999888898888888877766655458888 PP

                                       ---SEEEEEEEEE.SSSEEEEEEEEEEEET.............TEEEEEEES----HHHHHHHHHHHHHTTSTT--E CS
                       ATP-grasp_3  69 fieGkplSvsllsdgekvlvlavnrqliekaeke.........fvyaGnvtpietelkeevvelaeevvekleglaG 136
                                        ie ++        + + +v  v  ++i+   +          ++  G v+++  e+ ee++e+a  + e + + + 
  gi|313126051|ref|YP_004036321.1| 175 LIERDDTR------HRDLRVYIVDGEIIGAMYRYapdgdwrtnVALGGDVMNATDEMPEEARETALYAAEVM-E-LD 243
                                       88865532......22222333333333222222333333344999999**********************9.5.57 PP

                                       EEEEEEEESS.SEEEEEEES CS
                       ATP-grasp_3 137 yvGvDlvlkdeepyviEvNP 156
                                       yvGvDlv  +++  v+EvNP
  gi|313126051|ref|YP_004036321.1| 244 YVGVDLVEGEDGWFVLEVNP 263
                                       *******************9 PP

>> R2K_3  ATP-grasp domain, R2K clade family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   2.7e-07   0.00048     116     183 ..     183     263 ..      96     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                             R2K_3 116 saEwRvFvvdGevvaas.rYrkanddpdl...............epdlaafaeavralv......gappfyvlDvav 170
                                       +   Rv++vdGe+++a  rY   ++d+ +               +   ++ +e     +       ++  + +D+  
  gi|313126051|ref|YP_004036321.1| 183 HRDLRVYIVDGEIIGAMyRY-APDGDWRTnvalggdvmnatdemP---EEARET----AlyaaevMELDYVGVDLVE 251
                                       6789**********875377.577888887777777755553222...222222....23333566788******** PP

                             R2K_3 171 tadGrwkVVEvnd 183
                                        +dG w V Evn 
  gi|313126051|ref|YP_004036321.1| 252 GEDG-WFVLEVNP 263
                                       ****.*******6 PP

>> gag-asp_proteas  gag-polyprotein putative aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   6.4e-07    0.0012      15      92 .]     350     427 ..     339     427 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.4e-07
                                       ETT-SS-EEEHHHHHHTTGGGGEB..TT--EE-TTST.T-EEEEEEEEEE.EETTEEEEEEEEEESS..SSEEEEHH CS
                   gag-asp_proteas  15 DTGAsstiiseelaerlglsrkedkgkvevktangev.eakrvrldsvkiggielrnvsavvlegel..ddlLLGld 88 
                                       DTGA++t+i ++la ++g  + +     +vk ++ +  +a++v    + i g + + v+a+v + +     lLLG d
  gi|313126051|ref|YP_004036321.1| 350 DTGATRTSIDTSLAAEIGAGPIKS--MTRVKSGSMKSgKARPVVDLVIGIAGTQ-HTVTASVEDRSHmdYPLLLGRD 423
                                       *****************9877763..4455555544324555555567776654.45999999988523456***** PP

                                       HHHH CS
                   gag-asp_proteas  89 fLkr 92 
                                       +L++
  gi|313126051|ref|YP_004036321.1| 424 ILQH 427
                                       *986 PP

>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   4.3e-06    0.0077      15      88 ..     350     422 ..     334     424 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.3e-06
                    Asp_protease_2  15 DTGasttlispelaeklglkvreseltvrvsgaggevkarlvrldslklggltlknvpalvldlgeei.dglLGm 88 
                                       DTGa+ t i+++la+++g  + +s  t++ sg+ ++ kar v+   + ++g t + v+a+v d+  ++  +lLG 
  gi|313126051|ref|YP_004036321.1| 350 DTGATRTSIDTSLAAEIGAGPIKSM-TRVKSGSMKSGKARPVVDLVIGIAG-TQHTVTASVEDRSHMDyPLLLGR 422
                                       ***********************96.6666666666666655544555555.77777787777544442466665 PP

>> R2K_2  ATP-grasp domain, R2K clade family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.5e-05     0.027      68     138 ..     187     273 ..     180     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                             R2K_2  68 Rlfvldgeiit.vsrYagegrldpdp...............evaeeavaalksalpsayvlDvgvtedgetalvEan 128
                                       R++++dgeii+ + rYa +g+ +++                e  e a+ a++      + +D+++ ed ++ + E+n
  gi|313126051|ref|YP_004036321.1| 187 RVYIVDGEIIGaMYRYAPDGDWRTNValggdvmnatdempeEARETALYAAEVMELDYVGVDLVEGED-GWFVLEVN 262
                                       9********96268**9888886666668888988888887555556666665568899999999999.9******* PP

                             R2K_2 129 dgwa.lglygl 138
                                       +  +  gly++
  gi|313126051|ref|YP_004036321.1| 263 PTAGfKGLYKA 273
                                       86641455766 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.9e-05     0.052      95     197 ..     157     240 ..     152     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                    ATPgrasp_YheCD  95 lesllkkllkkkrylvQqgidlatidgrpfDfRvlvqKngkgkWevtgiaaRiagkgsittnlsrGGtalpleellk 171
                                       l ++++ ++++++  +Q  i+  +   r+ D+Rv +  +     e++g++ R a++g+  tn++ GG+++++ + + 
  gi|313126051|ref|YP_004036321.1| 157 LTEAVNPKVGNRQAFLQDLIERDD--TRHRDLRVYIV-D----GEIIGAMYRYAPDGDWRTNVALGGDVMNATDEMP 226
                                       677888899999999999998665..78889999998.2....3699***********************9987777 PP

                    ATPgrasp_YheCD 172 kafgeekaekileeleelalelaeal 197
                                       ++              e+al +ae++
  gi|313126051|ref|YP_004036321.1| 227 EEAR------------ETALYAAEVM 240
                                       6544............4444444444 PP

>> DUF5488  Family of unknown function (DUF5488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.5e-05     0.098       7      60 ..     354     410 ..     349     420 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.5e-05
                           DUF5488   7 srtsiwtvfmlpimyGpiksmieisrssy...nvsvivntpiGvitnaasmaayvnd 60 
                                       +rtsi t +   i  Gpiksm  +   s        +v+  iG+     +++a v+d
  gi|313126051|ref|YP_004036321.1| 354 TRTSIDTSLAAEIGAGPIKSMTRVKSGSMksgKARPVVDLVIGIAGTQHTVTASVED 410
                                       79********************99666551114567888999988888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2696.62
//
Query:       gi|313126052|ref|YP_004036322.1|  [L=187]
Description: DNA-3-methyladenine glycosylase ii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-21   75.0   0.1    7.6e-21   74.6   0.1    1.1  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.1   4.3e-25   7.6e-21       1     108 []      33     173 ..      33     173 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 4.3e-25
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       v +i+ qq+s+++a++i erlf+rf+ +tpe++++ade+ Lr+     G++++K++yi+++A +++           
  gi|313126052|ref|YP_004036322.1|  33 VVSIINQQLSTQSAAAIRERLFDRFE-VTPEAMLNADETALRDV----GLSSQKISYIQNVATAFQtddltragmad 104
                                       568**********************6.*****************....***************************** PP

                                       .............................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHHT CS
                                       .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 .............................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleellep 108
                                                                    g+ dv++v D+++r+++  l+ ++e+  ++ v+ k++e ++p
  gi|313126052|ref|YP_004036322.1| 105 ltdedvlmrlteirgvgdwtakmylmfvlGREDVFPVEDLGIRKAMAELYRMDEN--DRAVMVKRAEAWRP 173
                                       ******************************************************8..66666666688775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1189.57
//
Query:       gi|313126053|ref|YP_004036323.1|  [L=659]
Description: 3-hydroxyacyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-66  223.5   0.5    3.9e-66  222.4   0.5    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      2e-60  204.2   0.0    3.2e-60  203.5   0.0    1.3  1  ECH_1           Enoyl-CoA hydratase/isomerase
    1.7e-47  159.9   2.0    8.3e-33  112.9   0.0    3.4  4  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
    4.4e-36  125.0   0.6      3e-34  119.0   0.1    2.7  3  ECH_2           Enoyl-CoA hydratase/isomerase
    6.7e-07   29.4   0.1    1.6e-06   28.2   0.1    1.6  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    7.5e-05   23.0   0.2    0.00021   21.5   0.2    1.8  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0035   17.9   4.4      0.047   14.3   4.4    2.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0037   16.9   0.1     0.0062   16.1   0.1    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.049   12.9   0.3      0.094   12.0   0.3    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.055   13.3   0.0       0.12   12.1   0.0    1.7  1  DFP             DNA / pantothenate metabolism flavoprotein
       0.21   10.9   1.6        4.4    6.6   0.2    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.25   10.7   2.1        1.2    8.5   0.1    2.6  3  PALP            Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.4   0.5   2.6e-69   3.9e-66       1     179 [.       8     188 ..       8     189 .. 0.99

  Alignments for each domain:
  == domain 1  score: 222.4 bits;  conditional E-value: 2.6e-69
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77 
                                       +++v+GaG mG+gia+v+a ag++V+l di+ee+++++ ++ie sl kl+ek +l++ee++aal+r+ +  dl+e v
  gi|313126053|ref|YP_004036323.1|   8 TITVLGAGNMGHGIAEVAALAGYQVNLRDINEEFVQNGYDQIEWSLGKLAEKDQLSDEEANAALERVATYVDLAESV 84 
                                       69*************************************************************************** PP

                                       .C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-T CS
                           3HCDH_N  78 .dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrge 153
                                        dad+viEav+E++++K++v++ele++a++++i+a+nTSslsisela++++rpe+++g+HFfnPp  m+LvEv++g+
  gi|313126053|ref|YP_004036323.1|  85 sDADVVIEAVPEKMDIKKDVYTELEAAAPDHTIFATNTSSLSISELADVTERPEQFCGMHFFNPPVRMQLVEVISGA 161
                                       ***************************************************************************** PP

                                       T--HHHHHHHHHHHHHTT-EEEEE.CS CS
                           3HCDH_N 154 kTseetvatvvelakkigktpvvv.kd 179
                                       +T+eet++ + +la++++ktpv+v kd
  gi|313126053|ref|YP_004036323.1| 162 ETAEETMDVISDLAEAMDKTPVRVhKD 188
                                       ************************776 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.5   0.0   2.2e-63   3.2e-60       2     250 ..     408     658 ..     407     659 .] 0.97

  Alignments for each domain:
  == domain 1  score: 203.5 bits;  conditional E-value: 2.2e-63
                                       EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHC..HHHHHHHC CS
                             ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeek..akqallke 75 
                                       i + v  i l+rP+ +N++s  l+++l  a+  l  d  vra+ LtG gd+aF+aGad++ ma++       a+l+ 
  gi|313126053|ref|YP_004036323.1| 408 IRDRVGHIELDRPHRMNTISSDLVDDLSGAIDALGADDDVRAILLTGaGDRAFSAGADVQSMAGGAGdpTAGAELSR 484
                                       5677999*******************************************************9986555888999** PP

                                       CHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHH CS
                             ECH_1  76 evlelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeei 152
                                       + +  + kl +++kpviaa+ G+++gGG+el +++D++ia + ++fg++e +lGlipg ggt +l+r+vG  +A+ei
  gi|313126053|ref|YP_004036323.1| 485 KGQRTFGKLEECDKPVIAAIDGYCLGGGMELSMCADLRIATKRSEFGQPEHNLGLIPGWGGTVRLQRIVGTGRAKEI 561
                                       ***************************************************************************** PP

                                       HHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                             ECH_1 153 lllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfs 229
                                       + ++++++a+  ++ G +++ v +++++e+a e a++ a+ +p a r  k a+++  ed+  ++le+ea+ f  +f 
  gi|313126053|ref|YP_004036323.1| 562 IFTADRYEAETMADYGFINELVENDEFEEQAFEYAKQFAQGPPVAQRYTKRAMHNGWEDTD-AGLEVEAQSFGLLFT 637
                                       ********************************************************99875.79************* PP

                                       SHHHHHHHHHHHTCSH----- CS
                             ECH_1 230 kddikeGlqaflEkrkpefed 250
                                       +dd  eG++af+  r+p+f++
  gi|313126053|ref|YP_004036323.1| 638 TDDLMEGMTAFMGDREPDFKG 658
                                       *******************97 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.9   5.9e+03      28      60 ..       5      38 ..       2      67 .. 0.64
   2 !  112.9   0.0   5.6e-36   8.3e-33       1      97 []     191     286 ..     191     286 .. 0.99
   3 !   44.6   0.1   1.1e-14   1.6e-11       4      85 ..     304     385 ..     303     392 .. 0.96
   4 ?   -1.8   0.0       3.4   5.1e+03      44      89 ..     547     591 ..     545     595 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.9
                                      HHHHHHHHHHHHS.SCHHHHHHHHHHHHHHHHHH CS
                             3HCDH 28 diDaamrlglGlp.mGpfelldlvgldvakkile 60
                                      di +++ lg+G    G+ e++ l+g  v+++ ++
  gi|313126053|ref|YP_004036323.1|  5 DINTITVLGAGNMgHGIAEVAALAGYQVNLRDIN 38
                                      6666666666643388999999998888765443 PP

  == domain 2  score: 112.9 bits;  conditional E-value: 5.6e-36
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+vnR+l+pl+nea ++ve g  +++++D+++++++GlpmG fel+d vg+dv++++l++++e+lg+  y+p+pll
  gi|313126053|ref|YP_004036323.1| 191 GFIVNRILVPLMNEAAWAVESGDTTIAEVDSTAKYEIGLPMGSFELADQVGIDVGYHVLQYMHEVLGDA-YEPCPLL 266
                                       9****************************************************************9998.999**** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       e+ ve+++lg+ktgkgfy+y
  gi|313126053|ref|YP_004036323.1| 267 EEKVEEEKLGKKTGKGFYDY 286
                                       ******************99 PP

  == domain 3  score: 44.6 bits;  conditional E-value: 1.1e-14
                                       HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHH CS
                             3HCDH   4 vnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspllekl 80 
                                         R++a + ne+  l+++ va++  iD+a++lg G+p Gp +++d +gl++    l+ l+e++g ++y++ +ll++l
  gi|313126053|ref|YP_004036323.1| 304 SRRLMAVMANEVAGLIQNDVADADAIDRAVMLGGGFPDGPAKMADDAGLETLVETLDELHEKTGAERYEAVDLLREL 380
                                       5799************************************************************************* PP

                                       HHTT- CS
                             3HCDH  81 veagr 85 
                                       +e+g+
  gi|313126053|ref|YP_004036323.1| 381 AESGD 385
                                       *9985 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--BGG CS
                             3HCDH  44 felldlvgldvakkilevlaeelgerayapsplleklveagrlgrk 89 
                                        +l   vg + ak i+   a++++ +  a+  ++++lve+++++++
  gi|313126053|ref|YP_004036323.1| 547 VRLQRIVGTGRAKEII-FTADRYEAETMADYGFINELVENDEFEEQ 591
                                       5666777888888888.47777888877777899999999999876 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.97   1.5e+03     177     245 ..      46     115 ..      16     126 .. 0.49
   2 !  119.0   0.1     2e-37     3e-34       1     179 [.     412     590 ..     412     598 .. 0.95
   3 !    5.7   0.0    0.0061       9.1     243     312 ..     586     653 ..     579     658 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.97
                                       HHHHHHHHHTT...........--------......----SHHHHHHHHHHHT.-S-.TTTHHHHHH.T..-- CS
                             ECH_2 177 lealeeaLaelessd...eeaveevleelaeeaeeeeeeselaekreaidrlfsads.veeiveaLekaeaee 245
                                        +++e +L +l ++d   +e+ +++le++a+ ++    ++++++    i+++ ++ +  ++++++Le+a+ ++
  gi|313126053|ref|YP_004036323.1|  46 YDQIEWSLGKLAEKDqlsDEEANAALERVATYVDL---AESVSDADVVIEAVPEKMDiKKDVYTELEAAAPDH 115
                                       33444444444333333366666666666644444...23444444455555544441456666776544444 PP

  == domain 2  score: 119.0 bits;  conditional E-value: 2e-37
                                       .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHH CS
                             ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeY 77 
                                       vg+i+L+rp+ +N +s ++v++l+ a+++  +dd+v++++l+gag++af+AG Dv++++  a + ++  +e+ r+  
  gi|313126053|ref|YP_004036323.1| 412 VGHIELDRPHRMNTISSDLVDDLSGAIDALGADDDVRAILLTGAGDRAFSAGADVQSMAGGAGDPTAG-AELSRKGQ 487
                                       589********************************************************999987655.79****** PP

                                       HHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH CS
                             ECH_2  78 klnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalT 153
                                       +    ++++ kpv+a +dG+++GgG+ ls+ + +r++t+r+ f  PE ++Gl+P  Gg+  L+r+ g   ++ +  T
  gi|313126053|ref|YP_004036323.1| 488 RTFGKLEECDKPVIAAIDGYCLGGGMELSMCADLRIATKRSEFGQPEHNLGLIPGWGGTVRLQRIVGtGRAKEIIFT 564
                                       ****************************************************************976588999**** PP

                                       ---B-HHHHHHTTS--EE--GGGHHH CS
                             ECH_2 154 Garlkgadalaaglathyvpseklea 179
                                       ++r +++ +   g+ + +v+++++e+
  gi|313126053|ref|YP_004036323.1| 565 ADRYEAETMADYGFINELVENDEFEE 590
                                       ********************999875 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0061
                                       .--SHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-- CS
                             ECH_2 243 aeedewakktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkd 312
                                       +e +e a + ++++++  P++ + t +++++g + +  +  l+ E +    l++++D++eG +a + d++
  gi|313126053|ref|YP_004036323.1| 586 DEFEEQAFEYAKQFAQGPPVAQRYTKRAMHNGWEDT--DAGLEVEAQSFGLLFTTDDLMEGMTAFMGDRE 653
                                       355677888999********************9985..**************************997764 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   1.1e-09   1.6e-06       2     140 ..       9     168 ..       8     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.1e-09
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.......HHHHHHHHHSSBTTTBTT----...TTEEEES-HHHHHT CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree.......elieeineehenvkyLpgiklp...enlvattdlaealk 68 
                                       i+vlGaG+ G  +A v a +g +v l   +e       ++ie    +  +++ L + + +   e +  + dlae+++
  gi|313126053|ref|YP_004036323.1|   9 ITVLGAGNMGHGIAEVAALAGYQVNLRDINEefvqngyDQIEWSLGKLAEKDQLSDEEANaalERVATYVDLAESVS 85 
                                       9*************************99999899977744444444555666666655551114677899******* PP

                                       T--EEEE---HHH..HHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S--.........EEEEESS- CS
                    NAD_Gly3P_dh_N  69 gadiivlvvPsqa..lrevlkklkgllkkkailvsliKGieegtlkllsevieeelkeek.........vavlsGps 134
                                       +ad+++ +vP ++   ++v ++l++  ++++i++  +  ++ ++l  ++e  e++ +++          v v+sG+ 
  gi|313126053|ref|YP_004036323.1|  86 DADVVIEAVPEKMdiKKDVYTELEAAAPDHTIFATNTSSLSISELADVTERPEQFCGMHFfnppvrmqlVEVISGAE 162
                                       **********9864268899*****9999999999999995555555555555555544444446777799999999 PP

                                       -HHHHH CS
                    NAD_Gly3P_dh_N 135 lAeEva 140
                                        AeE +
  gi|313126053|ref|YP_004036323.1| 163 TAEETM 168
                                       999965 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   1.4e-07   0.00021       2     116 ..       9     150 ..       8     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.4e-07
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelva 54 
                                       i ++G G+MG+ +a+  + agy+v + + ++e v++  ++                         + ++ +++e v+
  gi|313126053|ref|YP_004036323.1|   9 ITVLGAGNMGHGIAEVAALAGYQVNLRDINEEFVQNGYDQIewslgklaekdqlsdeeanaalerVATYVDLAESVS 85 
                                       899***************************98888888886799999************999766666666677777 PP

                                       HCSEEEE-SSSHHHHH.HHHHSHCCC--TT-EEEE.-S---HHHHHHHHHHHHH.TT-EEEEEEE CS
                     NAD_binding_2  55 sldvvitmvkagkavd.eviegllealkkgdilid.gstsspedtrelakelke.kglkfldaPV 116
                                       ++dvvi  v+++ +++ +v+++l +a+   +i+   +s+ s+++  +++++ ++  g++f++ PV
  gi|313126053|ref|YP_004036323.1|  86 DADVVIEAVPEKMDIKkDVYTELEAAAPDHTIFATnTSSLSISELADVTERPEQfCGMHFFNPPV 150
                                       77*********999972577777777766666654134445555555555543325666666665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   4.4   3.1e-05     0.047       1      73 [.       8      98 ..       8     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......................-EEECECHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......................vkvtavdnee 57
                                      +i ++GaGnmg+++a+ ++ ag   +++    + n+e ++   ++++                      + +t vd +e
  gi|313126053|ref|YP_004036323.1|  8 TITVLGAGNMGHGIAEVAALAG---YQVN-LRDINEEFVQNGYDQIEwslgklaekdqlsdeeanaaleRVATYVDLAE 82
                                      589*******************...6666.3366666666666666666666666666**********9778888**** PP

                                      HHHH-SEEEE-S-HHH CS
                     F420_oxidored 58 aaeeadvvvlavkped 73
                                       +++advv+ av+ ++
  gi|313126053|ref|YP_004036323.1| 83 SVSDADVVIEAVPEKM 98
                                      ************8665 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   4.1e-06    0.0062       2      86 ..       8      96 ..       7     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.1e-06
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHH....HHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekv....dklnsgkipiyepgLeelvkkavesgrlsfttdvekavee 76
                                      +i+v+G+G +G   a v a +g +v + Di+ee v    d+++ +  ++ e+++ +  +++++ +r+    d+ ++v++
  gi|313126053|ref|YP_004036323.1|  8 TITVLGAGNMGHGIAEVAALAGYQVNLRDINEEFVqngyDQIEWSLGKLAEKDQLSDEEANAALERVATYVDLAESVSD 86
                                      79*******************************99333346777777889999888888888889************** PP

                                      -SEEEE---- CS
                    UDPG_MGDP_dh_N 77 advifiaVgT 86
                                      adv++ aV+ 
  gi|313126053|ref|YP_004036323.1| 87 ADVVIEAVPE 96
                                      *****99974 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   6.3e-05     0.094      30      99 ..       8      94 ..       5      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH....TTTCECEE................HCHHHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles....lgakfvev................lksqeellaea 88
                                      +++v+G+G  G   +++a+  g +V + D++++  ++  +      +k   +                + ++   lae+
  gi|313126053|ref|YP_004036323.1|  8 TITVLGAGNMGHGIAEVAALAGYQVNLRDINEEFVQNGYDqiewSLGK---LaekdqlsdeeanaaleRVATYVDLAES 83
                                      589****************************99887655543333333...2556999********99999999***** PP

                                      HHH-SEEEE-- CS
                       AlaDh_PNT_C 89 vkeadvvigtv 99
                                      v++advvi +v
  gi|313126053|ref|YP_004036323.1| 84 VSDADVVIEAV 94
                                      ********987 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.3e-05      0.12      16      48 ..       2      34 ..       1     111 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-05
                                      ECCTTEEEEE----HHHHHHHHHHHHTT-EEEE CS
                               DFP 16 aiDpVRfisNrSSGkmGyalAeaaaarGaeVtl 48
                                      ++D++ +i+    G mG+ +Ae aa +G +V+l
  gi|313126053|ref|YP_004036323.1|  2 ELDDINTITVLGAGNMGHGIAEVAALAGYQVNL 34
                                      58*****************************98 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2    0.0029       4.4      38      70 ..       8      40 ..       5      60 .. 0.84
   2 ?    2.9   0.1      0.04        60      75     106 ..      70     101 ..      60     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0029
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                      t+ ++G+G++G+ +a++++  g +v   d +++
  gi|313126053|ref|YP_004036323.1|  8 TITVLGAGNMGHGIAEVAALAGYQVNLRDINEE 40
                                      899*********************998887754 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.04
                                       HHHHTCEECSHHHHHHH-SEEEE-S--STTTT CS
                      2-Hacid_dh_C  75 eeelgvelvsleellaesDivslhlpltpetr 106
                                       + e  +++v+l e ++++D+v+ ++p + + +
  gi|313126053|ref|YP_004036323.1|  70 ALERVATYVDLAESVSDADVVIEAVPEKMDIK 101
                                       4455679***************9999876655 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00081       1.2      56      81 ..       7      32 ..       2      34 .. 0.90
   2 ?   -2.6   0.1       1.9   2.9e+03     224     249 ..      65      90 ..      47      93 .. 0.80
   3 ?    0.6   0.0      0.21   3.1e+02     107     155 ..     366     413 ..     347     425 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00081
                                      SEEEEEBSSHHHHHHHHHHHHHT-EE CS
                              PALP 56 ktvveassGNhgralAaaaallGlkv 81
                                       t+++ ++GN+g ++A +aal+G++v
  gi|313126053|ref|YP_004036323.1|  7 NTITVLGAGNMGHGIAEVAALAGYQV 32
                                      689999*****************987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                       CGTTCCHHHHSEEEEEEEEEEHHHHH CS
                              PALP 224 spselafelldrlvdeivtvsdeeal 249
                                       ++++ a+e ++ +vd + +vsd++++
  gi|313126053|ref|YP_004036323.1|  65 EEANAALERVATYVDLAESVSDADVV 90 
                                       57788899999999999999999875 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.21
                                       ECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT CS
                              PALP 107 vggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg 155
                                       +g +  eav++ +ela++ +++++ s++++ +     + i  Ei +++g
  gi|313126053|ref|YP_004036323.1| 366 TGAERYEAVDLLRELAES-GDRFHGSDGGDDADPYEFENISVEIRDRVG 413
                                       46778899999*******.*****9999988877777788888876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 4160.02
//
Query:       gi|313126054|ref|YP_004036324.1|  [L=367]
Description: site-specific recombinase xerd [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-14   53.6   0.1    5.6e-14   52.3   0.1    1.6  2  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.018   15.5   0.0       0.12   12.8   0.0    2.4  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
       0.06   13.7   0.2       0.72   10.2   0.0    2.7  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
      0.063   13.3   0.1       0.21   11.6   0.1    1.9  1  Malate_DH        Malate dehydrogenase enzyme


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.3   5.7e+03      21      41 ..      28      48 ..      20      49 .. 0.79
   2 !   52.3   0.1   1.3e-17   5.6e-14      31     169 ..     211     354 ..     204     356 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHHHHT--HHHHT CS
                   Phage_integrase 21 irdklllellyetGlRisEll 41
                                      +++ ++le+l+  G R  E++
  gi|313126054|ref|YP_004036324.1| 28 AEREAYLEWLLTFGKRPDEAV 48
                                      567899999999999999986 PP

  == domain 2  score: 52.3 bits;  conditional E-value: 1.3e-17
                                       HHHT--HHHHTT-BGGGEECTTTEEEEE.EEECSSSSEEEEECTHHHHHHHHHHHHHH..CHCCTTTSBSSBETTSS CS
                   Phage_integrase  31 yetGlRisEllsLrvkdldlengvilvh.eregKgskeravplseealellkellska..leeaeksellfaskrgk 104
                                       ++ GlR  E+ + +v+ +d++n v++++ e+ +K++   +v l++  +e+l ++l+++  + e +++e + + ++ +
  gi|313126054|ref|YP_004036324.1| 211 LDAGLRPVEVKRSQVGWVDTDNAVLRIPkEESSKNRDHWVVGLQSRTAEALGNWLEEReaYPEYDDTESIWLTRKSN 287
                                       678************************956667777778999****************99888888999999999** PP

                                       B--HHHHHHHHHHHHHHCT-S...SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHHHCC CS
                   Phage_integrase 105 plsrqtvrkafkraveeagie...kpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiYthv 169
                                       p +++t+r  +++++  a+i+    +++  t+Rhs++t + +++ dl + q  l H+s +tt+ Y +v
  gi|313126054|ref|YP_004036324.1| 288 PYNTKTLRYLLHQLCDIADIDtthRQMSWYTIRHSVGTYMTREE-DLAATQAQLRHKSAETTMKYDQV 354
                                       **********************9999******************.********************765 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         1   4.5e+03      46      54 ..      30      38 ..      17      43 .. 0.73
   2 ?   12.8   0.0   2.7e-05      0.12      12      77 ..      48     115 ..      43     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                   Phage_int_SAM_4 46 ieaYlnyLa 54
                                       eaYl++L+
  gi|313126054|ref|YP_004036324.1| 30 REAYLEWLL 38
                                      456666665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.7e-05
                   Phage_int_SAM_4  12 aglserTiksYlsaikrflrflkkk...apeeltkedieaYlnyLanerklsastqknalnalsffykk 77 
                                        g+++ T+ks  +   rf rf++ +     + +t +++ a + +La +    a+  +n+ +a + ++k+
  gi|313126054|ref|YP_004036324.1|  48 VGYAPGTVKSGAYRTDRFYRFVWDQeggYTANVTHDHADAWMKHLA-RGDTGATNKRNCQKAAKRLFKW 115
                                       58********************84466689****************.6666888889999999999998 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00016      0.72      13      83 ..      49     119 ..      40     120 .. 0.85
   2 ?    0.1   0.1      0.23     1e+03      30      58 ..     294     322 ..     279     348 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                                       -S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHH.HHHHHHHHHHHHHHT CS
                   Phage_int_SAM_1  13 glspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslar.rlsalrsFfqflvre 83 
                                       g++p T+ +  ++ +rf +f  ++++   +++t+++  a+ ++l++ + + ++ +r    a +++f++  +e
  gi|313126054|ref|YP_004036324.1|  49 GYAPGTVKSGAYRTDRFYRFVWDQEGGYTANVTHDHADAWMKHLARGD-TGATNKRnCQKAAKRLFKWRHHE 119
                                       689999999999999*******************************87.55555553667888888887766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.23
                                       HHHHHH.TS--TTT--HHHHH.HHHHS--- CS
                   Phage_int_SAM_1  30 lkflaergkesleqlttedvr.aflaelee 58 
                                       l++l + + ++++ ++t +++ ++   +++
  gi|313126054|ref|YP_004036324.1| 294 LRYLLH-QLCDIADIDTTHRQmSWYTIRHS 322
                                       344444.56666666666664344444443 PP

>> Malate_DH  Malate dehydrogenase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.7e-05      0.21      14      28 ..     144     158 ..     136     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                         Malate_DH  14 KeqqraaLRkAALeY 28 
                                         + r a R+AALeY
  gi|313126054|ref|YP_004036324.1| 144 TREERSAVREAALEY 158
                                       5688*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2360.53
//
Query:       gi|313126055|ref|YP_004036325.1|  [L=372]
Description: site-specific recombinase xerd [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-13   48.6   0.1    1.2e-12   48.0   0.1    1.2  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.012   15.7   0.0       0.05   13.7   0.0    1.9  2  AsiA             Anti-Sigma Factor A


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.1   1.3e-16   1.2e-12      27     170 ..     212     361 ..     203     363 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.3e-16
                                       HHHHHHHT--HHHHTT-BGGGEECTTTEEEEE.EEECSSSSEEEEECTHHHHHHHHHHHHHH..CHCCTTTSBSSBE CS
                   Phage_integrase  27 lellyetGlRisEllsLrvkdldlengvilvh.eregKgskeravplseealellkellska..leeaeksellfas 100
                                       + ++ + G R + + +++v   d + ++i+++ e+  K++ e   +l+e+a++ l+ +++++   ++ ++s+ + + 
  gi|313126055|ref|YP_004036325.1| 212 IGTVKAAGWRPALIKRMQVHWYDSDSKTIIIPaEHAVKNNSEWSQALPEKATRPLELWIEQRanISKYDDSDHMWLT 288
                                       666778899999999999999**********977889*************************997888888888889 PP

                                       TTSSB--HHHHHHHHHHHHHHCT-S...SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHHHCCC CS
                   Phage_integrase 101 krgkplsrqtvrkafkraveeagie...kpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiYthva 170
                                       ++g+p s+qt++  ++++ eeagi+    +l   ++Rh+++t  +e+  dl+ v+++l   s s+  +Y+h +
  gi|313126055|ref|YP_004036325.1| 289 RKGNPYSSQTLNYLLNNLIEEAGITergRKLCWYSFRHTLGTYTYEEHKDLKIVAEVLRQNSTSSAARYVHPT 361
                                       99***********************999999****************************************87 PP

>> AsiA  Anti-Sigma Factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.34     3e+03      33      60 ..      90     117 ..      82     120 .. 0.76
   2 ?   13.7   0.0   5.5e-06      0.05      34      69 ..     305     339 ..     298     345 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.34
                                       HHHHHHHT-.ESSSSE--HHHHHHHHHT CS
                              AsiA  33 vellneiGvrtteGkkltqnsfrkivar 60 
                                       +e l    +r  +G +++  s rki   
  gi|313126055|ref|YP_004036325.1|  90 IEALATDEFRRRDGERYSEGSKRKISNA 117
                                       5666666788899999999999998665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.5e-06
                                       HHHHHHT-.ESSSSE--HHHHHHHHHTS-HHHHHHH CS
                              AsiA  34 ellneiGvrtteGkkltqnsfrkivarLtqedkkel 69 
                                       +l+ e+G+ t+ G+kl   sfr+ +   t e+ k+l
  gi|313126055|ref|YP_004036325.1| 305 NLIEEAGI-TERGRKLCWYSFRHTLGTYTYEEHKDL 339
                                       6899****.********************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2230.73
//
Query:       gi|313126056|ref|YP_004036326.1|  [L=64]
Description: hypothetical protein Hbor_12980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.1   0.8        0.1   12.5   0.2    2.0  2  DUF2816   Protein of unknown function (DUF2816)


Domain annotation for each model (and alignments):
>> DUF2816  Protein of unknown function (DUF2816)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   5.7e-06       0.1      27      47 ..       8      28 ..       6      37 .. 0.61
   2 ?    0.4   0.5     0.033     6e+02      18      19 ..      41      42 ..      26      63 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-06
                           DUF2816 27 teYiPqviqekrieYvPvery 47
                                      t+++P+   ++ ieY   e++
  gi|313126056|ref|YP_004036326.1|  8 TDWVPVESIDRAIEYLGFEYV 28
                                      556666666666666555554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.033
                           DUF2816 18 tD 19
                                       +
  gi|313126056|ref|YP_004036326.1| 41 NE 42
                                      23 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 413.12
//
Query:       gi|313126057|ref|YP_004036327.1|  [L=702]
Description: type i restriction-modification system methyltransferase subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-10   40.0   0.0    4.4e-10   39.3   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
    0.00043   20.7   0.0    0.00087   19.8   0.0    1.4  1  Eco57I           Eco57I restriction-modification methylase
     0.0021   17.6   0.0     0.0038   16.8   0.0    1.3  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.052   14.3   0.0       0.14   12.9   0.0    1.7  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   9.8e-14   4.4e-10       5     209 ..     139     338 ..     136     385 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 9.8e-14
                          N6_Mtase   5 llGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiy 81 
                                        +G++YE l+  +   + +  G+  TP e+ +l+   + + +++ v+Dp +G+g l    +      + +t    + 
  gi|313126057|ref|YP_004036327.1| 139 DIGHLYETLIAGN---HRRVLGQHRTPTELAELMRTWAVSGDDT-VLDPGMGAGELSAPFHPDW---EISTDPGRVN 208
                                       579******9766...78889*************9998888885.***********99888865...7889999999 PP

                          N6_Mtase  82 GqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkew.....kektlekderfre 153
                                       G++  + ++ ++++   + g   +    r  d +e +  + ++ +d+++ Npp+  +e      k+k +++ e  +e
  gi|313126057|ref|YP_004036327.1| 209 GVDRSPLAALMGRVAQTISGQRHE---TRRTDFFELDPADLTQDVDAILCNPPYTRHESlssayKDKLNAQAENQTE 282
                                       *********999999888777666...8************9**************9987666544444444444444 PP

                          N6_Mtase 154 avapksnadla.fllhiieslkpkGraavvlangvLfrggkegkIrkalvekdlvea 209
                                          pk++  +a f  h+   l  + raav+ ++  L+rg  e  +++ l+ +  ++a
  gi|313126057|ref|YP_004036327.1| 283 LEIPKTSPLYAyFYYHLGRFLDTGDRAAVLTPHHFLSRGFGE-PLKQFLLREFDIKA 338
                                       47788888888577888888888889*******999998655.45666666666655 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.9e-07   0.00087       3      99 ..     250     361 ..     248     367 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-07
                            Eco57I   3 fdviiGNPPYqeseakkelkaleek.............akdiyqkFvek.alkle.dkylaliiparflasgkglke 64 
                                       +d+i+ NPPY ++e+  +  +++ +             ++++y +F  + +  l+   + a+++p+ fl s   ++ 
  gi|313126057|ref|YP_004036327.1| 250 VDAILCNPPYTRHESLSSAYKDKLNaqaenqteleipkTSPLYAYFYYHlGRFLDtGDRAAVLTPHHFL-SRGFGEP 325
                                       699********99976655543333667789***************86515555565677799******.7778999 PP

                            Eco57I  65 frekllkdkklkklv.efedskevFkdveikggilv 99 
                                       ++++ll++ ++k l  + ++++  F++++++  +++
  gi|313126057|ref|YP_004036327.1| 326 LKQFLLREFDIKALLlDNPKNESKFETAQTTSMVVL 361
                                       ***********9875266777788999998776654 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.5e-07    0.0038      31     127 ..     176     279 ..     164     283 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.5e-07
                                       TCSEEEEET-TTSHHHHHHHHHTT....C.EEEEEESBHHHHHHHHHHHHHTTGC.....EEEEE-STTTTSTTS-E CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakesp....eaevtlvdvdarAlesakenleankle.....vevvasdvleeveekkf 98 
                                        +++vlD G GaG l+a +   ++      +v+ vd +  A  + +   + ++ +     +++++ d  + +  +++
  gi|313126057|ref|YP_004036327.1| 176 GDDTVLDPGMGAGELSAPFHPDWEistdPGRVNGVDRSPLAALMGRVAQTISGQRhetrrTDFFELDPADLT--QDV 250
                                       56789************987654311113469******9998776655554444401334444444444433..69* PP

                                       EEEEE---STTTCHCHHHHHHHHHHHHHH CS
                               MTS  99 dlivsNPPfhagkatelavaeeliaeAke 127
                                       d+i++NPP+ +++  + a  ++l a+A++
  gi|313126057|ref|YP_004036327.1| 251 DAILCNPPYTRHESLSSAYKDKLNAQAEN 279
                                       *************9999999999999976 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.1e-05      0.14       1      71 [.     180     256 ..     180     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                       EEEET-TTSHHHHHHHCTS...T.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSS..STTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl...g.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpf..edgsfDlvvss 71 
                                       vLd G G G+l++ ++  +      ++v gvD s+ +    r     +g + e ++ d+ +l+     + +D+++++
  gi|313126057|ref|YP_004036327.1| 180 VLDPGMGAGELSAPFHPDWeisTdPGRVNGVDRSPLAALMGRVAQTISGQRHETRRTDFFELDPadLTQDVDAILCN 256
                                       8*****************9775258*********9887766665555777888888888888741245689999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (702 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 4443.41
//
Query:       gi|313126058|ref|YP_004036328.1|  [L=104]
Description: hypothetical protein Hbor_13000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 702.36
//
Query:       gi|313126059|ref|YP_004036329.1|  [L=1152]
Description: ATP-dependent exonuclase v subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-55  187.3   0.0    3.5e-26   92.5   0.0    2.3  2  UvrD-helicase  UvrD/REP helicase N-terminal domain
    2.8e-31  108.8   0.0    6.5e-31  107.6   0.0    1.7  1  AAA_19         AAA domain
    6.2e-31  108.0   0.0    1.2e-29  103.8   0.0    2.1  1  UvrD_C         UvrD-like helicase C-terminal domain
    1.2e-21   77.8   2.3    3.8e-21   76.2   2.3    1.9  1  PDDEXK_1       PD-(D/E)XK nuclease superfamily
    8.5e-08   31.9   0.9     0.0032   17.3   0.0    2.9  3  UvrD_C_2       UvrD-like helicase C-terminal domain
    6.3e-06   26.0   0.1     0.0003   20.6   0.0    2.4  2  AAA_30         AAA domain
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.072   13.0   0.0    1.7  1  Gelsolin       Gelsolin repeat
       0.04   13.2   0.0      0.071   12.4   0.0    1.3  1  DUF2800        Protein of unknown function (DUF2800)


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   1.6e-29   3.5e-26       3     138 ..      23     141 ..      21     153 .. 0.93
   2 !   92.3   0.2   1.8e-29     4e-26     211     310 ..     318     414 ..     302     418 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.6e-29
                                       HHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT- CS
                     UvrD-helicase   3 peqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdd 79 
                                       p+q+ +i s   p+ v+A+AG+GKTf+++ ++ +li+ee ++pdril +TFTn Aa  ++e+++++l+ a       
  gi|313126059|ref|YP_004036329.1|  23 PQQETIIDSDAYPMRVLAGAGTGKTFTMVRKVEHLIDEEDVSPDRILTLTFTNNAAGSMREKLNAKLGTAG------ 93 
                                       89999****************************************************************96...... PP

                                       HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHH CS
                     UvrD-helicase  80 erlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkel 138
                                                  +++ +T Hs+c++il  +a+++g+dp+f+++++ + ++++++ +l ++
  gi|313126059|ref|YP_004036329.1|  94 ----------YDIDAYTYHSICNEILTDYAYEAGIDPDFEVATDAE-KYAIVLDVLDDI 141
                                       ..........69*******************************999.688888887776 PP

  == domain 2  score: 92.3 bits;  conditional E-value: 1.8e-29
                                       HHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEE CS
                     UvrD-helicase 211 kkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelf 287
                                       +++ + +  y+++++e+n++Df+ l++++ el+e+   + e++  r++++++DE+QDT++ Q++++k l+++  +lf
  gi|313126059|ref|YP_004036329.1| 318 RDLTAGYAAYERELDERNLIDFDGLVVEAAELMES--PVGEEIAARWDYVFCDEFQDTDRLQFDLVKSLVTDD-NLF 391
                                       56677899************************997..799********************************8.9** PP

                                       EEE-GGG--GGGGTB-THHHHHH CS
                     UvrD-helicase 288 mvGDpkQsIYgFRgAdielflkk 310
                                       +vGD++Q+IY++RgA++ ++  +
  gi|313126059|ref|YP_004036329.1| 392 VVGDDDQAIYEWRGAHVANITDE 414
                                       *****************999765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   0.0   2.9e-34   6.5e-31       2     144 ..      25     402 ..      24     404 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 2.9e-34
                            AAA_19   2 reavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......atTi 72 
                                       +e + ++ + ++ v+aG+GtGKT +++ +v++l+++++v+p++il ++ft+ Aa  +re+l+a ++       a+T+
  gi|313126059|ref|YP_004036329.1|  25 QETIIDSDAYPMRVLAGAGTGKTFTMVRKVEHLIDEEDVSPDRILTLTFTNNAAGSMREKLNAKLGTagydidAYTY 101
                                       4444499999*************************************************99655554899999**** PP

                            AAA_19  73 Hrlal........................................................................ 77 
                                       H++ +                                                                        
  gi|313126059|ref|YP_004036329.1| 102 HSICNeiltdyayeagidpdfevatdaekyaivldvlddieyrsvkpnvygsdgyasgaaskllnfigsmkrsgitp 178
                                       ***98************************************************************************ PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|313126059|ref|YP_004036329.1| 179 ddidaflgpadrvyeladlserveaiasdhlggrsvssvldslpdvradlveerdvlgmdgmeasvrdfldrlvdlc 255
                                       ***************************************************************************** PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|313126059|ref|YP_004036329.1| 256 daleaafeaheagdrdlpdnayklpkyllggyangapkgipgdldleltdhldsflsdcltardltagyaayereld 332
                                       ***************************************************************************** PP

                            AAA_19  78 ....ldfddlltealelleeaeeekklqeee.llivDEfqdvdelqyrLlkallgekkklllvGDpdQliyv 144
                                           +dfd+l+ ea+el+e+    +++ +++ +++ DEfqd+d lq+ L+k l+++++ l++vGD+dQ+iy+
  gi|313126059|ref|YP_004036329.1| 333 ernlIDFDGLVVEAAELMESPVG-EEIAARWdYVFCDEFQDTDRLQFDLVKSLVTDDN-LFVVGDDDQAIYE 402
                                       *****************996444.55568999**********************5555.************7 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.0   5.5e-33   1.2e-29       3     344 ..     427     783 ..     426     785 .. 0.75

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 5.5e-33
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.......x RF
                            UvrD_C   3 LekNyRStksLlkaankflenilnrralekek...ktvekgekivvleaetee..eEaekiaatikall.......e 67 
                                       Le+N+RS + +l++an+ +++  +r+ +++ k   +++ +g+ i + e  +e+  + a++    +++ll       +
  gi|313126059|ref|YP_004036329.1| 427 LEENFRSRQPILDLANEAIQKLDHRERHKTLKrvdEPEYDGDTIATVELSDEDdaDGASQLRTVVQNLLsgaaesfD 503
                                       89***********************5554333468*******99998887665115688888889999999999999 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  68 kneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdkialkrilkrlvlgig 144
                                       ++ +  dia+LvR+n  a  + ++++  gip+ v ++    +   + ++ aylk la+++d+++++r+l   ++ + 
  gi|313126059|ref|YP_004036329.1| 504 EAYDPGDIALLVRKNDHATPVIEEFEDAGIPYQVAGDLA-TESVGVGTVTAYLKALARPEDEVSWNRVLLMRYR-LC 578
                                       99999****************************777655.68899**********************8887665.55 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 145 katveriseelkklglsltDfikedtleygeeFieliraleeknlelllkkiektaeerqalvskyadlfkelaekl 221
                                       ++ ++++    +     l D ++e  l   +eF e  r+ e++++   l  i            +  ++ ++l+++l
  gi|313126059|ref|YP_004036329.1| 579 DTDLRKL----NAGDDPLVDTLRETPL---DEFEEPDRVAEARKHVTELLAI------------RDSASLSHLYREL 636
                                       6678999....3333457788888775...5777555666666654111111............1223334455555 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.....xxxxxxxx RF
                            UvrD_C 222 aelkekseskrkkeeklenlreLysllkelekkeeeeeveeklneileia.tLseseleeskkk.....ekipiiTi 292
                                       +++ +      ++  + + l++L ++++++ + + ++  + ++ + le+  +L +++  + +++     + ++++Ti
  gi|313126059|ref|YP_004036329.1| 637 TDVTNIEWYLSEQ--ERRDLAQLEDVIEQYGDSAVQPPLTPEFIDSLEHYdSLFDESGSSPTSQpdvadDAVNVMTI 711
                                       5555544444422..2356777777777777766665555555555555435544333332222334789******* PP

                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 293 HqAKGlEFdvVflagleegtf.Psyrskk...................ekrleEEkRlfYVaiTRAkkrLfi 344
                                       H++KGl F+vV + +++ g+  Ps+r+ +                   e++  E +R+f V+iTRA + L++
  gi|313126059|ref|YP_004036329.1| 712 HKSKGLDFPVVLIPQVTAGEWaPSSRTYDaletslsdgaeaafaedfvERDARETRRVFHVGITRAEDVLVL 783
                                       *****************99854988888899999999999999999**99****************999875 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   2.3   1.7e-24   3.8e-21       3     251 ..     907    1135 ..     905    1137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 1.7e-24
                          PDDEXK_1    3 SvsrletfleCplrfflryllgl.re..........eeeleapdlGtlvHaaleefyewkkldke.dleelleea 65  
                                        S+++l +++eCp++++l y+ +  ++             ++++++G l+H+++e+  ++  ++++ d  e++   
  gi|313126059|ref|YP_004036329.1|  907 SYTSLAAYEECPRSHYLDYVVNAfPDyqettvrsdsGGGVSQREIGLLFHDTAEQAAKQ-GVKRRgDWYEIC--- 977 
                                        99*********************95555577888877778889*************993.333222555555... PP

                          PDDEXK_1   66 veelwpellleeeilessarlrylaeklkevleklverlaeeleakrgfrpvalelefggekvrLkGriDrvd.d 139 
                                         e+l++ +  e               ++ke + +++e ++   e  +  r+++  l+++g   +L+G iD v  +
  gi|313126059|ref|YP_004036329.1|  978 -ERLASHRRAE-----------DALTAAKECIDRYFELELPNCEIIDAEREFE--LDIDG--HELVGYIDAVYrT 1036
                                        .3444442222...........2223334566666443333222233323333..33334..57*********98 PP

                          PDDEXK_1  140 kegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalt 214 
                                        +++ l +iDyK +     +++  +l+++ Ql++Ylla+     + e+  + +a y  +   +    ++v+  + +
  gi|313126059|ref|YP_004036329.1| 1037 PDDGLLVIDYKATE----RHR--DLEDDKQLPIYLLACCDL--YDEP--VTRAGYAYV--GE--IGPKVETRTFS 1097
                                        8889*******444....555..788999************..6666..555555555..33..45778888899 PP

                          PDDEXK_1  215 eeeleallqeleelaeeilagefparpskk...CeyCpyk 251 
                                        +++lea+++++ e + +i   ef+++ + +   C++C+  
  gi|313126059|ref|YP_004036329.1| 1098 DADLEAVTDDVTESMTRIS--EFSFNRYSAdehCQWCQHN 1135
                                        *******************..999999977789****975 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.3   7.5e+03      15      22 ..     362     369 ..     361     377 .. 0.74
   2 !   17.3   0.0   1.4e-06    0.0032       4      27 ..     708     729 ..     705     736 .. 0.85
   3 !   12.0   0.1   6.4e-05      0.14      21      51 ..     754     783 ..     752     783 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.3
                          UvrD_C_2  15 fpaVivfd 22 
                                       +++V++++
  gi|313126059|ref|YP_004036329.1| 362 WDYVFCDE 369
                                       9****953 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.4e-06
                          UvrD_C_2   4 altihkaQGsefpaVivfdpdlaa 27 
                                       ++tihk++G+ fp+V +  p  +a
  gi|313126059|ref|YP_004036329.1| 708 VMTIHKSKGLDFPVVLI--PQVTA 729
                                       89***************..66555 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 6.4e-05
                          UvrD_C_2  21 fdpdlaaarmgelrrrlLYtavTRAreklil 51 
                                       f+ d+ +++  +++rr +++++TRA + l+l
  gi|313126059|ref|YP_004036329.1| 754 FAEDFVERD-ARETRRVFHVGITRAEDVLVL 783
                                       667888888.667************988876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.4e-07    0.0003      20      77 ..      35     105 ..      23     134 .. 0.71
   2 ?    2.7   0.1     0.039        88      84     143 ..     356     414 ..     323     462 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.4e-07
                            AAA_30  20 vavltGpAGtGKttal.kalreaweaag...grviglAptgkaAkvLaeelg.........ieastiakll 77 
                                        + + ++AGtGKt+++ ++++++++++     r++ l+ t++aA  ++e+l+         i+a+t +++ 
  gi|313126059|ref|YP_004036329.1|  35 PMRVLAGAGTGKTFTMvRKVEHLIDEEDvspDRILTLTFTNNAAGSMREKLNaklgtagydIDAYTYHSIC 105
                                       5567899******8872555666666668999****************86552222222335777777765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.039
                            AAA_30  84 arlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdlvea 143
                                       ++++++ + +  DE   +d  q++ + + +++    + +vGD++Q     +G+ ++ ++++
  gi|313126059|ref|YP_004036329.1| 356 EEIAARwDYVFCDEFQDTDRLQFDLVKSLVTD--DNLFVVGDDDQAIYEWRGAHVANITDE 414
                                       45667778999999999999999888888876..899*******97666667777766554 PP

>> Gelsolin  Gelsolin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.2e-05     0.072      24      64 ..     395     439 ..     379     444 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                                       EESSEEEEEEHTT....SHHHHHHHHHHHHHHHHHCTTTTTSEEE CS
                          Gelsolin  24 dngftiflWiGke....ssqeeknfaadlaaeldseerfplpeli 64 
                                       d  + i+ W+G++     +++ ++faa++ ++l++++r++ p+l+
  gi|313126059|ref|YP_004036329.1| 395 DDDQAIYEWRGAHvaniTDELDRAFAALSDEPLEENFRSRQPILD 439
                                       44459**********999****************99999999987 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.2e-05     0.071      93     223 ..    1004    1134 ..     948    1141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                           DUF2800   93 k..kdalvlvEqrvdfskyvpegfGtaDvviia.ddvLeviDlKyGkgvkVsaekNpQlalYAlGAleefdllyd 164 
                                        +  + +++  E++ +++    e  G  D+v  + dd L viD+K  +  + + e+ +Ql +Y l+ ++ +d    
  gi|313126059|ref|YP_004036329.1| 1004 ElpNCEIIDAEREFELDIDGHELVGYIDAVYRTpDDGLLVIDYKATE-RHRDLEDDKQLPIYLLACCDLYD--EP 1075
                                        333566777788877777788899******988799********987.67899******************..78 PP

                           DUF2800  165 iktVrltIvQPrldnvseweisveeLlewaeevlkpkaekaaegegefvpgehcrFCka 223 
                                        +++   + v     +v++ + s ++L++  ++v ++  +    + ++++++ehc++C+ 
  gi|313126059|ref|YP_004036329.1| 1076 VTRAGYAYVGEIGPKVETRTFSDADLEAVTDDVTESMTRISEFSFNRYSADEHCQWCQH 1134
                                        8999999999888999************999988888888888999***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 6654.87
//
Query:       gi|313126060|ref|YP_004036330.1|  [L=301]
Description: hypothetical protein Hbor_13020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-23   82.2   0.1      7e-23   81.8   0.1    1.1  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.024   13.9   0.0      0.042   13.1   0.0    1.3  1  DUF2800   Protein of unknown function (DUF2800)


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.1   7.8e-27     7e-23       1     254 [.       5     291 ..       5     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 7.8e-27
                          PDDEXK_1   1 rlSvsrletfleCplrfflryllglreeeeleap.dlGtlvHaaleefye..wkkldke..dleelleeaveelwpe 72 
                                       +lS+srl  +++Cp+ + +ry++ ++++ ++e     Gt++H+++e++ +       ++  +  e +++++++ w+e
  gi|313126060|ref|YP_004036330.1|   5 SLSPSRLANYATCPRLYDYRYVQDVNAPDRTELYlNQGTIYHETIEDVCKatN--RGDDpeVIHERAMRIFDAKWDE 79 
                                       59***********************665555554488*************542..33334566677779******** PP

                          PDDEXK_1  73 llleeeilessarlrylaeklkevleklve..rlaeeleakrg.frpvalelefg..gekvrLkGriDrvddkegel 144
                                       +  ++++ es a+++y++++ ++++e+++        ++a+ +  ++  +e+e++  g    L+G+ D v ++++ l
  gi|313126060|ref|YP_004036330.1|  80 HSTPDDY-ESAAHQEYQRAENRAAIESFFApdGGVGIDHARCSiATECWVECEVDgrG----LHGKADNVIRTDDGL 151
                                       9999976.9999999***********99662344555677777877788887777445....*********77777* PP

                          PDDEXK_1 145 riiDyKtgsappkske................laelkeglQlllYllalaegeelkeege.pagalylrlee.pkvk 203
                                        i DyK  +++    +                 +++++ +Q+++Y   ++++  ++  ++ +++  +++l + ++ +
  gi|313126060|ref|YP_004036330.1| 152 HIFDYKR-KTHGMLSDgtaeylgdhldgeahePKRVRNAFQTAAYIEGVKNEPFYE--DGmEIRFSFYGLLNsTSFE 225
                                       ******4.43434334577777777666666555666666************5555..3459999999997756666 PP

                          PDDEXK_1 204 ......deevvkkm..........alteeeleallqeleelaeeilagefparpskk.....CeyCpyksvC 254
                                             d      +          +  e++ + +   ++   + i ++ + ++p +      C  C+y++ C
  gi|313126060|ref|YP_004036330.1| 226 stptgyD------VsargwgrettEIYEDHYDTIWALIRAAHDGITGETYGPEPFDLiseeaCPDCDYREMC 291
                                       5554440......3444555545556677777777888888888887788888887788888********** PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.6e-06     0.042       4     133 ..       6     157 ..       4     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-06
                           DUF2800   4 lSaSsahrWlkCppSar....leeeipdesSeyAeeGtlaHelaelklrkaldakekkgvkselkk........kee 68 
                                       lS+S    +  Cp           + pd++  y ++Gt+ He  e   +      + + +++++ +        +++
  gi|313126060|ref|YP_004036330.1|   6 LSPSRLANYATCPRLYDyryvQDVNAPDRTELYLNQGTIYHETIEDVCKATNRGDDPEVIHERAMRifdakwdeHST 82 
                                       78888888888888665222134578999999**********99988866664444444333322234444432333 PP

                           DUF2800  69 evteemeeavdeyvdfvlekieeak..........kdalvlvEqrvdfskyvpe......gfGtaDvviiaddvLev 129
                                         + e +++ +   +  ++ ie++           +   +  E  v+              +G aD vi +dd L++
  gi|313126060|ref|YP_004036330.1|  83 PDDYESAAHQEYQRAENRAAIESFFapdggvgidhARCSIATECWVE------CevdgrgLHGKADNVIRTDDGLHI 153
                                       33333333333333333444444336333334433333444444444......33444459**************** PP

                           DUF2800 130 iDlK 133
                                        D+K
  gi|313126060|ref|YP_004036330.1| 154 FDYK 157
                                       ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1808.00
//
Query:       gi|313126061|ref|YP_004036331.1|  [L=686]
Description: UvrD/REP helicase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-05   23.7   0.0    7.6e-05   22.2   0.0    1.6  2  UvrD_C       UvrD-like helicase C-terminal domain


Domain annotation for each model (and alignments):
>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.2e-09   7.6e-05      40     126 ..     280     368 ..     256     373 .. 0.88
   2 ?   -3.2   0.0      0.23   4.1e+03     300     314 ..     489     503 ..     487     519 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.2e-09
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  40 gekivvleaeteeeEaekiaatikall.ekneklediavLvRs.nkdadkiskaLkkegipfnvvdeekfFkreeik 114
                                       + ++ vl a++++e   +ia++i++l+ + + +++diav +++  +    + +a+++ gip+     + f + + i+
  gi|313126061|ref|YP_004036331.1| 280 TGSVSVLAADSSDEQLADIANEIEELVaQPDWNYDDIAVATKQsGRSVTDVIEAFERTGIPTESTTVTGFGDDPAIR 356
                                       44789999*******************99999*********997888899*************************** PP

                                       xxxxxxxxxxxx RF
                            UvrD_C 115 dilaylkllank 126
                                       ++la  ++la +
  gi|313126061|ref|YP_004036331.1| 357 ELLAAVRYLAAD 368
                                       ******999765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.23
                                       xxxxxxxxxxxxxxx RF
                            UvrD_C 300 FdvVflagleegtfP 314
                                       F  Vfl++l + ++P
  gi|313126061|ref|YP_004036331.1| 489 FRAVFLVNLVDSEYP 503
                                       889***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4406.69
//
Query:       gi|313126062|ref|YP_004036332.1|  [L=706]
Description: tyrosyl-DNA phosphodiesterase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-09   37.9   0.1      3e-09   36.9   0.1    1.5  1  PLDc_2           PLD-like domain
     0.0002   20.4   0.0    0.00031   19.8   0.0    1.3  1  Tyr-DNA_phospho  Tyrosyl-DNA phosphodiesterase
  ------ inclusion threshold ------
      0.056   13.6   0.0       0.12   12.5   0.0    1.5  1  DAP_epimerase    Diaminopimelate epimerase
      0.077   12.3   0.0       0.13   11.5   0.0    1.4  1  RE_NgoFVII       NgoFVII restriction endonuclease


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   6.6e-13     3e-09      25     132 ..      53     172 ..      32     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.6e-13
                            PLDc_2  25 ildallkaakrgvkvrilldskkd.......dagavdeaslkelkellleagvevrvfetllgslHaKlylidgk.. 92 
                                       i++ + +       +++++++++        +++ ++++ +++l++l + + ++++  +++   lH+Kly+i+++  
  gi|313126062|ref|YP_004036332.1|  53 IYKMFQNRDLAVDSLEVIVGDNQHddyrrslKNTNNAKKIAAQLESLRRDGDLRIHTVDSARVLLHTKLYIIENQdg 129
                                       44444444444456899999988899999998899999999999999888888888766434689*******96666 PP

                            PLDc_2  93 ..tvivGSsNltkrgldlnlElnvviedk.elakeleeeFerl 132
                                         t+i GS+Nl+k+++++   +nv +  + +  + ++e+Ferl
  gi|313126062|ref|YP_004036332.1| 130 srTLICGSANLSKQAWQGSKQTNVNMAWRtDGDTPVDEWFERL 172
                                       66**************555444443332223345788888876 PP

>> Tyr-DNA_phospho  Tyrosyl-DNA phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     7e-08   0.00031     334     380 ..     108     151 ..      38     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7e-08
                                       ..TTTTT--B--EEEEEE--STTSEESEEEEES--BSHHHH--S... CS
                   Tyr-DNA_phospho 334 eeagRkraapHiKtyirfssktlkkidWalltSaNLSkqAWGeleka 380
                                       ++    r++ H+K+yi  +++     +  + +SaNLSkqAW   +++
  gi|313126062|ref|YP_004036332.1| 108 HTVDSARVLLHTKLYIIENQDG---SRTLICGSANLSKQAWQGSKQT 151
                                       3345578888999988885555...6667889999999999655444 PP

>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05      0.12      24      72 ..      81     138 ..      64     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                       H....HHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEE.....EEETTTEEESTTHCC CS
                     DAP_epimerase  24 e....aelvaalcdreagpgadgvlfvkpsgeediklr.....yfnrdgseaemCGnG 72 
                                       +     + +++++ + + + +dg l++ +++++++ l      ++n+dgs +  CG++
  gi|313126062|ref|YP_004036332.1|  81 RslknTNNAKKIAAQLESLRRDGDLRIHTVDSARVLLHtklyiIENQDGSRTLICGSA 138
                                       33333688999***********************999999****************75 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     3e-05      0.13      78     113 ..     111     151 ..      55     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
                                       S....XBXXXEEEEEET.TEEEEEEESXXSXXTTS.XXXSB CS
                        RE_NgoFVII  78 v....kvHsKlYiwkkdgkplsAliGSANlssngl.rtrqr 113
                                              H+KlYi  +++     + GSANls  +   ++q 
  gi|313126062|ref|YP_004036332.1| 111 DsarvLLHTKLYIIENQDGSRTLICGSANLSKQAWqGSKQT 151
                                       3334578**********99************7766444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (706 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 4295.74
//
Query:       gi|313126063|ref|YP_004036333.1|  [L=895]
Description: hypothetical protein Hbor_13050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-20   73.3   0.0    3.6e-20   72.4   0.0    1.4  1  Piwi            Piwi domain
  ------ inclusion threshold ------
      0.032   13.8   0.0       0.36   10.3   0.0    2.1  2  DUF2121         Uncharacterized protein conserved in archaea 
      0.089   13.1   0.0       0.21   11.9   0.0    1.5  1  MID_pPIWI_RE    MID domain of pPIWI_RE
       0.12   12.3   0.0       0.29   11.1   0.0    1.6  1  pPIWI_RE_REase  REase associating with pPIWI_RE


Domain annotation for each model (and alignments):
>> Piwi  Piwi domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0     8e-24   3.6e-20       9     297 ..     612     878 ..     609     882 .. 0.83

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 8e-24
                                       SGHHCHHHHHHHHHHTCCCCEEEEEHHHHCTCCHHHHHHHHHHHHHHHHTT-BS-EEESSSTTSSE....EEEEEEE CS
                              Piwi   9 kkkdkyheikkyletdlgiisqcillktilkrqlkkqtltnvllkinvKlGgknvliveikleldvsptliiGidis 85 
                                       ++ d+y e+k++l  +lg++sq+i+ +++ ++    ++l n+   +  K Gg +  i ++++ +d+    ++G+d++
  gi|313126063|ref|YP_004036333.1| 612 DYDDPYPEFKRRL-GQLGVPSQMITIDNLGND----SYLGNISSSLIGKAGGVPWRIDDVPGDVDA----FVGLDVT 679
                                       5678888888876.567************999....89***************8888889998888....******* PP

                                       EEECCCSCCCEEEEEEEEEETSSEEEEEEEEESSCCCCHHHH.HHHHHHHHHHHHHHTTTT-TTSEEEEEESS.... CS
                              Piwi  86 hgtagtvdnpsvaavvasldkensrylaevstqassqellek.lkeiikellrefkksskkkkperiivyRdGvseG 161
                                        + a +   + ++a + ++  +++ +++e +t+++++   e+ + ++ik++l+ f +++    p++++++RdG    
  gi|313126063|ref|YP_004036333.1| 680 YDHATK---QHLGAAANVIMADGTILASEAVTKQAGETFDEDdVANVIKHVLEIFAEEEGR-PPRHVVIHRDG---- 748
                                       *99988...6677777777789*******************99************999987.***********.... PP

                                       S..S-HHHHHHHHHHHHHHHHHCTTTEEEEEEEECSCS--EEESESTCCCEETT.TCEEETTEEEEEEEECCEEECC CS
                              Piwi 162 qfkqvlnsEvkelkealkklkeqyqpkltvivvqkrhhtrfFasdkaeksqnip.pGtvvdkkitlpeekdfylcsh 237
                                         k  l   +++l++ l+k    +q ++ ++ ++k+ + r+   d+++ ++ i+ +G+   ++   + +  +    +
  gi|313126063|ref|YP_004036333.1| 749 --KFYL--DIESLIKRLDKARDLIQ-RFDLVEIRKSGNPRIAEYDESKSRFDIAdKGVAFHVHNGDHSYLTTT-GGK 819
                                       ..4444..5889999*****99997.***************99999998888862576655444333333333.344 PP

                                       CCEEEEEEEEEEEEEEES..S-CCHHHHHHHHHCTGGTTTT.SS-SS-HHHHHHHHHHHHH CS
                              Piwi 238 aglqgtvkPtkytvlvdeaklsadelqsltyklchmyqrst.rsvsiPapvyyAhklAkrv 297
                                        g  gt +P+++   +++     d l ++ty l+ ++  s+ rs+++P + yyA+k A  +
  gi|313126063|ref|YP_004036333.1| 820 EGSPGTPRPLQIVKRHGS--TDLDTLAEQTYWLSEAHVGSLsRSTRLPITTYYADKCADFA 878
                                       556677777776666666..888**************977659**************9765 PP

>> DUF2121  Uncharacterized protein conserved in archaea (DUF2121)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.1e-05      0.36      84     152 ..     225     296 ..     222     313 .. 0.71
   2 ?    0.6   0.0      0.08   3.6e+02     103     162 ..     676     733 ..     670     751 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.1e-05
                           DUF2121  84 saketkrrRiYatkgayaivelegsevtkkkkgessliv..fGnk.vtkeiankllkkevkkklslkeiekl 152
                                       ++++++rrRiYat++ +  + ++g +v+  ++ge++l    + n+  ++e++++ +k+ v  ++++  i  +
  gi|313126063|ref|YP_004036333.1| 225 TTADASRRRIYATEKLHGTISMHGYTVKPVHQGETTLEArsYTNDgPLQEFVKQDVKRAVAGRFEVSGIDSI 296
                                       67799***********************99999988533113333135555555555555555555555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.08
                           DUF2121 103 velegsevtkkkkgesslivfGnkvtkeiankllkkevkkklslkeiekllkeileevae 162
                                        +++ +++tk++ g+++ +++ + ++  +a +++ k++ ++++  ++++++k++le  ae
  gi|313126063|ref|YP_004036333.1| 676 LDVTYDHATKQHLGAAANVIMADGTI--LASEAVTKQAGETFDEDDVANVIKHVLEIFAE 733
                                       57788888889999888777766655..789999999999999***********998776 PP

>> MID_pPIWI_RE  MID domain of pPIWI_RE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.7e-05      0.21      57     105 ..     587     635 ..     582     645 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                      MID_pPIWI_RE  57 qllgraerptlalveiegkskakkrsdsDPKfalRlglakaGrlsQfil 105
                                       q+++++    +al+ +++k ka++++ +DP++  ++ l + G+ sQ i+
  gi|313126063|ref|YP_004036333.1| 587 QHAQKTSDYDAALIVVPDKDKAAAADYDDPYPEFKRRLGQLGVPSQMIT 635
                                       56666666667*************************************4 PP

>> pPIWI_RE_REase  REase associating with pPIWI_RE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.4e-05      0.29      48      91 ..     575     621 ..     570     641 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.4e-05
                    pPIWI_RE_REase  48 spelLarkl...ekldkgdpadeaflVvPdereeqrpdyravlrral 91 
                                         + L++++   ++++k  ++d+a++VvPd+ +++  dy++ + ++ 
  gi|313126063|ref|YP_004036333.1| 575 ETYELGSEFhysQHAQKTSDYDAALIVVPDKDKAAAADYDDPYPEFK 621
                                       56889999999999*************************98777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (895 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 5593.29
//
Query:       gi|313126064|ref|YP_004036334.1|  [L=558]
Description: hypothetical protein Hbor_13060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-10   40.5   0.0    1.7e-09   37.8   0.0    2.3  2  AAA_14        AAA domain
    8.7e-06   26.1   0.1    2.3e-05   24.7   0.1    1.7  1  AAA_22        AAA domain
    4.7e-05   23.8   0.1    0.00014   22.3   0.1    1.8  1  AAA_16        AAA ATPase domain
     0.0013   19.1   0.1      0.015   15.7   0.0    2.5  2  RNA_helicase  RNA helicase
     0.0013   18.6   0.0     0.0027   17.6   0.0    1.6  1  NACHT         NACHT domain
     0.0022   18.5   0.0     0.0047   17.4   0.0    1.6  1  AAA_23        AAA domain
      0.003   17.2   0.1      0.012   15.2   0.0    2.1  3  AAA_25        AAA domain
     0.0054   15.9   0.0      0.012   14.9   0.0    1.4  1  NB-ARC        NB-ARC domain
      0.006   16.5   0.2      0.059   13.3   0.2    2.1  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0098   15.6   0.0      0.024   14.4   0.0    1.6  1  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.012   16.0   0.0       0.04   14.3   0.0    1.8  2  AAA           ATPase family associated with various cellular 
      0.013   14.8   0.0      0.027   13.8   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.043   14.3   0.0        0.1   13.1   0.0    1.7  1  ABC_tran      ABC transporter
      0.048   12.9   0.0        0.1   11.9   0.0    1.5  1  DUF2075       Uncharacterized conserved protein (DUF2075)
       0.06   13.3   0.0       0.12   12.2   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
       0.16   11.8   0.1       0.35   10.8   0.1    1.5  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.23   11.8   1.6        2.2    8.6   1.6    2.4  1  AAA_19        AAA domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   1.6e-12   1.7e-09       4     125 ..      60     205 ..      57     212 .. 0.79
   2 ?   -0.7   0.0       1.3   1.4e+03      88     123 ..     514     547 ..     501     555 .. 0.71

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.6e-12
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell.................vkkesilyinldderdkkladpe......kllelil 57 
                                       +++i G   +GKTtll+qli  ll                 + +++ilyi l+d  ++ ++  +      +++++++
  gi|313126064|ref|YP_004036334.1|  60 VYAIHGQTGIGKTTLLHQLIAALLnttdlpnqntgleltsaIGPRQILYIPLEDSLYQLERAGDdikrlyQVIDYFQ 136
                                       789********************9******************************88855553332345557888999 PP

                            AAA_14  58 eklke.ekktylflDEiqevpewekalkslvdeg.knldvivtGSnskllskeiatslagrvaeielypl 125
                                        ++ + +++++++lD iq ++  e+   +l+++  ++  +i+tG  ++      +t+ a+ v+++el+p+
  gi|313126064|ref|YP_004036334.1| 137 THVAPrQGQKFILLDDIQALDLNEDRKAQLLNSVdEDTYLILTGNVASQVDL-STTESADTVEKFELWPV 205
                                       98545699************777776666666444568999***87776633.56777777777777764 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                            AAA_14  88 degknldvivtGSnskllskeiatslagrvaeiely 123
                                       d +  +++++t S+ k   +  ++sl+ +  e ++ 
  gi|313126064|ref|YP_004036334.1| 514 DYQAPYRFVITDSLPKSVAE--SESLVTQRGETRIC 547
                                       4456899*******999966..56666555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   2.1e-08   2.3e-05       7     110 ..      60     168 ..      56     183 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.1e-08
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelka..erlsseelle 80 
                                       + +++G++G+GKTtll +l   l +  +    + +    +l+s  +++++ +  l   l +   a    +++ ++++
  gi|313126064|ref|YP_004036334.1|  60 VYAIHGQTGIGKTTLLHQLIAALLNTTDL---PNQNTGLELTSAIGPRQIlYIPLEDSLYQLERAgdDIKRLYQVID 133
                                       679********************865555...555556777777766666666666655544444122555555555 PP

                            AAA_22  81 aleqalraravielliiDEaqhlr....s.eeale 110
                                       +++ ++  r+ ++++++D++q l+    + +++l+
  gi|313126064|ref|YP_004036334.1| 134 YFQTHVAPRQGQKFILLDDIQALDlnedRkAQLLN 168
                                       555555555559***********775331233333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   1.4e-07   0.00014      16     150 ..      45     159 ..      38     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.4e-07
                            AAA_16  16 lervrsgrp.....elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqll 86 
                                       l++++++ +      +  ++G+ G+GK++l+ +l  al  +   + l  +++ l        l++a+  +++l  + 
  gi|313126064|ref|YP_004036334.1|  45 LKTTNTHYTdgvesLVYAIHGQTGIGKTTLLHQLIAALLNT---TdLPNQNTGL-------ELTSAIGPRQILY-IP 110
                                       555555555555557778*************9999877766...1133333333.......59****8855555.55 PP

                            AAA_16  87 deaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadea 150
                                        e++  +le++ + +++ ++            + + ++ ++  ++r + +  ++lDd+q +d  
  gi|313126064|ref|YP_004036334.1| 111 LEDSLYQLERAGDDIKRLYQ------------VIDYFQTHV--APR-QGQKFILLDDIQALDLN 159
                                       56566699999999988887............888888888..444.3336999*****88863 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05     0.015       3      32 ..      63      92 ..      61     102 .. 0.89
   2 ?   -0.2   0.0       1.3   1.3e+03      45      75 ..     140     168 ..     114     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkd 32
                                      ++G++g+GK+tl ++L++all++ +l++++
  gi|313126064|ref|YP_004036334.1| 63 IHGQTGIGKTTLLHQLIAALLNTTDLPNQN 92
                                      89*******************999888765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.3
                      RNA_helicase  45 dgYtgqevvvidDfgqvkdeenpsdlaelir 75 
                                          +gq++++ dD+ +   +  ++  a+l++
  gi|313126064|ref|YP_004036334.1| 140 APRQGQKFILLDDIQALDLN--EDRKAQLLN 168
                                       55579********9998744..334444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.6e-06    0.0027       3      25 ..      61      83 ..      59     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                                      EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                       +++G+ G+GKTtLl++l+ a+ 
  gi|313126064|ref|YP_004036334.1| 61 YAIHGQTGIGKTTLLHQLIAALL 83
                                      689*************9987653 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.5e-06    0.0047      21      59 ..      60      97 ..      53     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.5e-06
                            AAA_23 21 ltlItGpNGaGKTTildAiklaLygetprlsrksgrgfe 59
                                      +++I+G++G GKTT+l  +  aL +  ++l++++ +   
  gi|313126064|ref|YP_004036334.1| 60 VYAIHGQTGIGKTTLLHQLIAALLNT-TDLPNQNTGLEL 97
                                      679********************995.577777654444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.012      35      94 ..      60     126 ..      38     201 .. 0.72
   2 ?   -2.4   0.1       2.8   2.9e+03      86     111 ..     387     412 ..     381     443 .. 0.73
   3 ?   -3.5   0.0       6.1   6.4e+03     125     156 ..     502     532 ..     494     536 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                            AAA_25  35 lallaGapgtGKttlaldlalava..tGkpwlg.......pvap..eqgkVlyvsaEdsedelrrRlravg 94 
                                       + ++ G++g GKttl+ +l +a++  t   ++           +   ++  ly+ +Eds  +l+r    + 
  gi|313126064|ref|YP_004036334.1|  60 VYAIHGQTGIGKTTLLHQLIAALLntT--DLPNqntglelT--SaiGPRQILYIPLEDSLYQLERAGDDIK 126
                                       66899*******************653..444445778442..334999*********9877776444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                            AAA_25  86 lrrRlravgealrddarllvldlagv 111
                                         rR+r+++  lr +++l +l+  ++
  gi|313126064|ref|YP_004036334.1| 387 SLRRYRRTRLYLRNPRHLVLLSQRQE 412
                                       56999999999999999999985443 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.1
                            AAA_25 125 lltadvdaleaaieevegvrlvviDplsralg 156
                                        +++d ++l++   + + +r+v+ D+l + ++
  gi|313126064|ref|YP_004036334.1| 502 HTKSDSEELQELDYQ-APYRFVITDSLPKSVA 532
                                       456777777766666.6699999999877665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.012      15      41 ..      53      79 ..      42      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                      TTTSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 15 kdelqslvvalvGmgGvGKttlakqil 41
                                       d+++slv a++G  G+GKttl++q +
  gi|313126064|ref|YP_004036334.1| 53 TDGVESLVYAIHGQTGIGKTTLLHQLI 79
                                      578999*****************9976 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   5.6e-05     0.059      19      47 ..      57      85 ..      49     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.6e-05
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledk 47
                                      ++ +y i G  g+GKt+Ll ++i  l++ 
  gi|313126064|ref|YP_004036334.1| 57 ESLVYAIHGQTGIGKTTLLHQLIAALLNT 85
                                      57899******************999764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.2e-05     0.024       3      77 ..      59     156 ..      57     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel........................gpkplfidtekGlksldadkfpdieswedflde 55 
                                       l ++i G+ giGKTtl+ +l                        + ++l+i +e++l +l+ +  +di+ + +++d+
  gi|313126064|ref|YP_004036334.1|  59 LVYAIHGQTGIGKTTLLHQLiaallnttdlpnqntgleltsaigPRQILYIPLEDSLYQLERAG-DDIKRLYQVIDY 134
                                       5789****************9999999999999999999999988999999****999998776.679888888888 PP

                            AAA_24  56 vvelaaeladyktlviDtidel 77 
                                       +++  a  ++ k + +D i+ l
  gi|313126064|ref|YP_004036334.1| 135 FQTHVAPRQGQKFILLDDIQAL 156
                                       8888888888888888888765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.8e-05      0.04       3      98 ..      63     175 ..      61     201 .. 0.66
   2 ?   -2.7   0.0       6.9   7.3e+03      93     116 ..     330     352 ..     314     360 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                                       EESSTTSSHHHHHHHHHHHH........THE.............EEEEETTTCSSS...........STTHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel........gve.............fleisgsellsk...........yvgesekkir 47 
                                       ++G  G+GKT+l ++++  l        + +             +l                       g+  k++ 
  gi|313126064|ref|YP_004036334.1|  63 IHGQTGIGKTTLLHQLIAALlnttdlpnQ-NtgleltsaigprqIL---------YipledslyqleRAGDDIKRLY 129
                                       79************999997554433330.1333333333333344.........0444444444557888888888 PP

                                       HHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                               AAA  48 elfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                       ++++  +++     +++ +++D+i al  ++         +  +qLl+ +d+ + 
  gi|313126064|ref|YP_004036334.1| 130 QVIDYFQTHVaprqGQKFILLDDIQALDLNE---------DRKAQLLNSVDEDTY 175
                                       8888876666788667**********97766.........668888888887766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.9
                                       HHHTTTSSSTEEEEEEESSGGGST CS
                               AAA  93 ldgvkkkeskvivigatnrpdkld 116
                                       +++ ++  +++  i+atn  ++l+
  gi|313126064|ref|YP_004036334.1| 330 IQQPEN-LHRLSSIAATNAGEELK 352
                                       445555.46789999999877665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.5e-05     0.027      36      67 ..      56      86 ..      39      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                                      GGS-.SEEEE--TTSSHHHHHHHHHHHHHTT- CS
                      FtsK_SpoIIIE 36 kkmashllvaGatgsGKStalntLilSlatth 67
                                      +++     ++G tg GK+t l+ Li++l+ t+
  gi|313126064|ref|YP_004036334.1| 56 VESL-VYAIHGQTGIGKTTLLHQLIAALLNTT 86
                                      5555.568********************9765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.5e-05       0.1      13      35 ..      60      82 ..      56     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-05
                                      EEEEEESTTSSHHHHHHHHTTSS CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagll 35
                                      ++ai G++G GK+tLl  l+  l
  gi|313126064|ref|YP_004036334.1| 60 VYAIHGQTGIGKTTLLHQLIAAL 82
                                      79**************8776544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.5e-05       0.1       3      98 ..      60     154 ..      58     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.5e-05
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael...eddeeertavylsvNhplvlvlrealakke.ekkkkkeafeklssfinnls 75 
                                       v+ ++G++G GKt +l +l+a+l   +d  +++t   l+     +++l+  l+ +  + ++ ++++++l ++i  ++
  gi|313126064|ref|YP_004036334.1|  60 VYAIHGQTGIGKTTLLHQLIAALlntTDLPNQNTGLELTSAIGPRQILYIPLEDSLyQLERAGDDIKRLYQVIDYFQ 136
                                       788********************98777789999999999999*********9999888999999999999999999 PP

                           DUF2075  76 efkkaeekkeepkedvvivDEAh 98 
                                            ++ ++++  ++++ D  +
  gi|313126064|ref|YP_004036334.1| 137 -----THVAPRQGQKFILLDDIQ 154
                                       .....666666666666666655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.12      99     123 ..      58      82 ..      43      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                       TSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                       + + ++ Gq+G+GK+tL+ +l+  l
  gi|313126064|ref|YP_004036334.1|  58 SLVYAIHGQTGIGKTTLLHQLIAAL 82 
                                       5678899*************99864 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00033      0.35       3      25 ..      62      84 ..      60      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                              MobB  3 givgksgsGKTtLleklipelka 25
                                      +i g+ g GKTtLl++li++l +
  gi|313126064|ref|YP_004036334.1| 62 AIHGQTGIGKTTLLHQLIAALLN 84
                                      6899**************99865 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.6    0.0021       2.2       9      44 ..      57      91 ..      51     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0021
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpee 44
                                      ++ v ++ +  G GKT++l++ +a l+++++++  +
  gi|313126064|ref|YP_004036334.1| 57 ESLVYAIHGQTGIGKTTLLHQLIAALLNTTDLPN-Q 91
                                      566788999******************9998864.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3449.66
//
Query:       gi|313126065|ref|YP_004036335.1|  [L=1674]
Description: hypothetical protein Hbor_13070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00031   20.7   0.0     0.0012   18.9   0.0    1.9  1  DUF3883       Domain of unknown function (DUF3883)
  ------ inclusion threshold ------
      0.088   13.7   0.2       0.25   12.2   0.2    1.7  1  PUD           Bacterial pullanase-associated domain
       0.11   13.0   0.0       0.69   10.4   0.0    2.1  2  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
       0.16   12.1   0.8       0.39   10.9   0.8    1.6  1  DNA_pol3_chi  DNA polymerase III chi subunit, HolC


Domain annotation for each model (and alignments):
>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.6e-07    0.0012      21      83 ..    1552    1619 ..    1530    1630 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.6e-07
                           DUF3883   21 vnedvedglgYDiesvd.kedge...erfIEVKttakgkkdfelsrnElefaq.ekgdkYwlyrVfna 83  
                                        +n  ++d  g+D++ ++ + +g+   +r IE Kt+  ++++  ls nE++ a    +++Y+ly+  n 
  gi|313126065|ref|YP_004036335.1| 1552 ENPLDRDWPGFDVLTIRtDDNGDaviDRCIELKTSGLNTRKPSLSWNEWKAAGgPLSKHYYLYVARNI 1619
                                        455555889******98433444899**********999999**********977899*****98776 PP

>> PUD  Bacterial pullanase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   5.6e-05      0.25       9      50 ..     979    1018 ..     971    1029 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                                        TT---TTEEEEEES.----EEE---EEETTEEEEEEEESS-- CS
                               PUD    9 gdgnydgwgLwlWgdgedgssfpftgtddygayadvelkedd 50  
                                        ++++  gw+Lw+W  +  +ss+ +t +d++  +a+++l ++d
  gi|313126065|ref|YP_004036335.1|  979 DEQSALGWNLWVW--QLRQSSWVPTSFDAVRPTAAWSLPRSD 1018
                                        456889*******..68889999*****99999998887776 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.69      10      77 ..      48     116 ..      45     194 .. 0.78
   2 ?   -0.9   0.0      0.51   2.3e+03       7      30 ..    1324    1343 ..    1319    1413 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..GTCSTTCHHCSTCHTSTSSSH.H CS
                         HATPase_c  10 isnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlk..klfekfsqddstkrggggtGl.G 77 
                                       + +l++Nav++  ++ge +v+ + +  + ++ v +nG   + edl    l ++ +++++t++g++g+G+ +
  gi|313126065|ref|YP_004036335.1|  48 VFELLQNAVDEMDDTGEPRVRFELT--EDSLLVANNGAAFSFEDLYalTLTTRTTKAGETTIGHKGRGFtS 116
                                       7899999999966788888877733..688889************95333335555899999999999852 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.51
                                        HHHHHHHHHHHHHHHSTTTEEEEE CS
                         HATPase_c    7 rqiisnlvdNavkfatkageieve 30  
                                        +++++nl+d+a  +    ++  + 
  gi|313126065|ref|YP_004036335.1| 1324 YEAVNNLIDHAFGN----ETPAIA 1343
                                        44455555555443....222232 PP

>> DNA_pol3_chi  DNA polymerase III chi subunit, HolC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   8.7e-05      0.39      13      66 ..     954    1007 ..     944    1015 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.7e-05
                      DNA_pol3_chi   13 dreelacrllekalragkrvlvlcedeeqlealdelLWtfepdsFlPHglageg 66  
                                        +r++++ +++++ +r  +  +v+++de+ +  ++   W+ +++s++P + ++ +
  gi|313126065|ref|YP_004036335.1|  954 RRHATVAEFTNERWRGSNVSYVFTHDEQSALGWNLWVWQLRQSSWVPTSFDAVR 1007
                                        67889999***************************************8776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1674 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.97u 0.33s 00:00:01.30 Elapsed: 00:00:00.54
# Mc/sec: 9416.17
//
Query:       gi|313126066|ref|YP_004036336.1|  [L=410]
Description: hypothetical protein Hbor_13080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.65   10.0   0.0    2.0  2  DUF1382   Protein of unknown function (DUF1382)


Domain annotation for each model (and alignments):
>> DUF1382  Protein of unknown function (DUF1382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.16   2.9e+03      45      57 ..      74      86 ..      68      87 .. 0.84
   2 ?   10.0   0.0   3.6e-05      0.65       5      44 ..     102     143 ..      99     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.16
                           DUF1382 45 srkLEqleakAea 57
                                      + +LE l a+A+ 
  gi|313126066|ref|YP_004036336.1| 74 MPALEVLNADATT 86
                                      779*******985 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 3.6e-05
                           DUF1382   5 ssveLRaalEaAHa.lAsiGIrFVPiPvat.deefqaLaael 44 
                                       s+ + R+ +  AH+ l ++ I +V  P+++  ++++aLa++l
  gi|313126066|ref|YP_004036336.1| 102 SAADVRTGINQAHGhLSEVNIGYVAAPIQSiTDQARALARDL 143
                                       7889*********8799***********98567899998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2550.89
//
Query:       gi|313126067|ref|YP_004036337.1|  [L=448]
Description: restriction endonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-09   36.1   0.0    9.9e-09   35.2   0.0    1.4  1  Mrr_cat   Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   5.5e-13   9.9e-09       7     115 .]     213     313 ..     208     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5.5e-13
                                       TCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--T.S-B-HHHHHHHHHHCTTS..SEEE CS
                           Mrr_cat   7 keFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryk.nkvgvkeVqeligalkkrgadkgi 82 
                                       +e+e+lva+++ +lG++  +  +++ D +++++a          +v++K ++ ++  +++ ++++g  + + ad++i
  gi|313126067|ref|YP_004036337.1| 213 EELEELVAKAFSRLGFE-ARWIEGGDDTDVEVTAPI------HAVVEVKARSsGTLASPDATRIQGHKERHSADQAI 282
                                       799*************9.999999999999999965......47******9648**********************9 PP

                                       EEESS-B-HHHHHHHHTT--EEEE-HHHHHHHH CS
                           Mrr_cat  83 fvttsdftkaAreeaeelnkieLldgdeLaell 115
                                       +v   +ft+aA+e a++ ++i+Ll  d L  ll
  gi|313126067|ref|YP_004036337.1| 283 VVAP-GFTPAAIEDADR-QGIVLLATDHLKALL 313
                                       9976.59**********.*********998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2570.05
//
Query:       gi|313126068|ref|YP_004036338.1|  [L=255]
Description: hypothetical protein Hbor_13100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1631.94
//
Query:       gi|313126069|ref|YP_004036339.1|  [L=1186]
Description: hypothetical protein Hbor_13110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-08   33.4   4.4    6.3e-08   33.4   4.4    4.5  2  AAA_23        AAA domain
    6.6e-08   32.3   0.0     0.0025   17.3   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    1.2e-07   31.9   0.1    0.00037   20.4   0.0    2.7  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.7e-05   24.8   0.0      0.099   12.3   0.0    2.6  2  AAA_15        AAA ATPase domain
     0.0003   20.4   0.2     0.0022   17.6   0.0    2.5  2  AAA_27        AAA domain
  ------ inclusion threshold ------
      0.013   14.2   0.0      0.013   14.2   0.0    4.4  5  AAA_13        AAA domain
      0.032   14.7   0.2          3    8.3   0.0    3.3  2  ABC_tran      ABC transporter
      0.045   14.2   3.8       0.12   12.8   0.7    3.2  2  Terminase_4   Phage terminase, small subunit
       0.14   12.0   0.0        0.3   10.9   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
        1.6    6.5  12.7      0.072   11.0   6.7    1.7  2  V_ATPase_I    V-type ATPase 116kDa subunit family


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   4.4   3.5e-11   6.3e-08      17     181 ..      49     341 ..      41     357 .. 0.50
   2 ?  -19.5  31.1        10   1.8e+04     115     200 .]     673     770 ..     483     797 .. 0.51

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.5e-11
                            AAA_23  17 FskgltlItGpNGaGKTTildAiklaLygetprlsrks...................grgfeksdveiese...... 68 
                                       Fs+g+++++G N aGK+T+ +Ai++ L+ + ++ s +                    +++f         +      
  gi|313126069|ref|YP_004036339.1|  49 FSPGVNVVYGANAAGKSTLAEAIRWSLWPDEAPSSATVrtdltydgelrrielhggvSEHF---------Rdgepad 116
                                       8***************************876554444456677766665555555552222.........1433333 PP

                            AAA_23  69 ........................gkvkayveltfenkdgry................................... 86 
                                                               +++              +                                   
  gi|313126069|ref|YP_004036339.1| 117 aipvpsldggrryalslhdmlqeeTDDG-------------Efasviqrestggfnidavrsefdltdgaspatrgi 180
                                       3445555433333333333333332222.............123333333333344444445555555555666666 PP

                            AAA_23  87 ..........................trsiererelskkkgkttkkaklelleideleqfisellgskki....... 130
                                                                             +  ++  ++     + +e+ +++++ ++ +++       
  gi|313126069|ref|YP_004036339.1| 181 satkeaaaaidkveelrrdapdleaeR-----------TRLSQLEGDLAAAADASERVDLLETAIQYREAqdaydqr 246
                                       666666666555444333322222220...........222222222222222233333333333333333333333 PP

                            AAA_23 131 .................ilnlilflgqerfeefelkdkke....................................r 154
                                                        +l++++ l+++                                                 
  gi|313126069|ref|YP_004036339.1| 247 vdevtsfpdelasfdgdELDQLDDLDEQI----------AqqkrveqeaavkyreaadklagtelpedgvadgvlqT 313
                                       33333111111211111333332222222..........02222233455556677777778888888999999999 PP

                            AAA_23 155 leelekeleeledekkllekl....eqekek 181
                                       l+ ++++l+++ed ++ l+++    e    k
  gi|313126069|ref|YP_004036339.1| 314 LRGYRDDLDDAEDNRDRLQREvadaE---AK 341
                                       99999999999999999998853321...22 PP

  == domain 2  score: -19.5 bits;  conditional E-value: 10
                            AAA_23 115 deleqfisellgskkiilnlilflgqerfeefelkdkke...................................... 153
                                       +++e++++e                             +                                      
  gi|313126069|ref|YP_004036339.1| 673 ADREELFTERGLEPG-----------------------Drerlatlceqyseyeaaveakgtaettlenrrsdlreh 726
                                       222222222222222.......................022222222222222222223333333333333333322 PP

                            AAA_23 154 ..........rleelekeleeledekkllekleqekekekeleeleeeleeilkele 200
                                                   ++le+el+             ++ e  ++++el +e ++++ke+e
  gi|313126069|ref|YP_004036339.1| 727 dayeeeieerDRDDLERELD-------------EKREIANQYDELLQEKTTLEKEIE 770
                                       22222222222222333333.............333444444455555444444443 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.4e-06    0.0025      22      51 ..      49      78 ..      39     161 .. 0.84
   2 !   13.2   0.1   2.5e-05     0.046      97     200 ..     729     932 ..     205     942 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                                      TTSSEEEEEESTTSSHHHHHHHHHHHCTT. CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 22 fsksftaivGpNGSGKsnlldAilFvLGer 51
                                      fs+++++++G+N +GKs l +Ai++ L  +
  gi|313126069|ref|YP_004036339.1| 49 FSPGVNVVYGANAAGKSTLAEAIRWSLWPD 78
                                      99***********************99654 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.5e-05
                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagiske...................................... 135
                                       ++ + +    ++ e ++++k+   +++ ell+++   ++                                      
  gi|313126069|ref|YP_004036339.1| 729 YEEEIEERDRDDLERELDEKREIANQYDELLQEKTTLEKeiedakasteiadavqergealrgleealeadvadavt 805
                                       33333333333445556666666666666665544333368888888889999999999999999999999999999 PP

                                       ..........................................................CS-HHHHHHHHHHHHHH.. CS
                                       ..........................................................xxxxxxxxxxxxxxxxx.. RF
                             SMC_N 136 ..........................................................lLSgGektLvalaLlfA.. 152
                                                                                                  LS G +  v la+++A  
  gi|313126069|ref|YP_004036339.1| 806 dtllefveaetvssnqepvfqraddllrritdgqfelrlddgtfrafdtgeqrrvdlnDLSSGTRVQVLLAVRVAfv 882
                                       9999999999999999999999999999999999999999999999999999999999********99999999966 PP

                                       .HHCCS--SEEEECTTTTTS-HHHHHHHHHH.HHHHCTTSEEEEE-SSHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                             SMC_N 153 .iqkvkpaplyllDeidaaLDeknvkkvael.lkeksknaQfivislree 200
                                         ++ + ap  llDe  a  D+++ + v +  ++ +++  Q++  + r++
  gi|313126069|ref|YP_004036339.1| 883 eHREQETAPPLLLDETLAPFDDQRAETVLDTvIDLAREGRQVFYFTARHD 932
                                       65677889*****************9998751566777799999988875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.1e-07   0.00037       1      28 [.      53      78 ..      53     114 .. 0.75
   2 !    8.2   0.5    0.0011       1.9     113     242 ..     731     870 ..     665     881 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.1e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrd 28
                                      +nv++G+N++GKS+L +a+++  +  +d
  gi|313126069|ref|YP_004036339.1| 53 VNVVYGANAAGKSTLAEAIRWSLW--PD 78
                                      79*****************99764..33 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                            AAA_21 113 peargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlv 189
                                        e ++ + +  +++l e+  +  + ++  +  t + +++++                                    
  gi|313126069|ref|YP_004036339.1| 731 EEIEERDRDDLERELDEKREIANQYDELLQEKTTLEKEIED------------------------------------ 771
                                       33333333333333333333333333333333333333333.................................... PP

                            AAA_21 190 rslklveielsdlgegeeliasvderlrer............................................... 219
                                                        + +++++++ +er                                               
  gi|313126069|ref|YP_004036339.1| 772 ----------------AKASTEIADAVQERgealrgleealeadvadavtdtllefveaetvssnqepvfqraddll 832
                                       ................2233333333333333333333333333333333333333333333333333333466666 PP

                            AAA_21 220 ...............gvvflengdgqelparelSdGtk 242
                                                      +++ ++ g  + +++++lS+Gt+
  gi|313126069|ref|YP_004036339.1| 833 rritdgqfelrlddgTFRAFDTGEQRRVDLNDLSSGTR 870
                                       667777888888888**********************8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00042      0.75      21      45 ..      49      73 ..      44      85 .. 0.90
   2 !   12.3   0.0   5.5e-05     0.099     207     328 ..     713     894 ..     541     928 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00042
                            AAA_15 21 lseeltvliGkNnsGKSsilealdl 45
                                      +s+ ++v+ G+N++GKS+++ea+ +
  gi|313126069|ref|YP_004036339.1| 49 FSPGVNVVYGANAAGKSTLAEAIRW 73
                                      5666999****************86 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.5e-05
                            AAA_15 207 sdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelk..kilkkkidkik.kfnykgkk 280
                                       ++++++  s+l +   ++        + ee+++++l++ +++ +ei ++++e l+   +l+k i++ k ++++  + 
  gi|313126069|ref|YP_004036339.1| 713 ETTLENRRSDLREHDAYEE-------EIEERDRDDLERELDEKREIANQYDELLQekTTLEKEIEDAKaSTEIADAV 782
                                       3333333333333222222.......225566666666666666666666666655555556666555555555555 PP

                            AAA_15 281 neeieik..................................................................ddee 291
                                       +e +e                                                                    ++ +
  gi|313126069|ref|YP_004036339.1| 783 QERGEALrgleealeadvadavtdtllefveaetvssnqepvfqraddllrritdgqfelrlddgtfrafdtgEQRR 859
                                       5555544566666666666666666666666666666666677778888889999999999999999999999**** PP

                            AAA_15 292 lplnknGsGvqrllllillileaekkdekeeknvill 328
                                       ++ln+ +sG++  +ll++  ++ e ++  +e+   ll
  gi|313126069|ref|YP_004036339.1| 860 VDLNDLSSGTRVQVLLAVRVAFVEHRE--QETAPPLL 894
                                       ************************993..33333333 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-06    0.0022       7      49 ..      32      74 ..      27      87 .. 0.82
   2 ?   -1.9   0.3       1.2   2.1e+03     146     200 ..     652     709 ..     632     716 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                            AAA_27  7 dLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      +L+r   f+   ++++  ++++ ++yG+N AGKst+ +Ai+  
  gi|313126069|ref|YP_004036339.1| 32 TLDRAPGFETAGFSLDGFSPGVNVVYGANAAGKSTLAEAIRWS 74
                                      5556666788888888899********************9755 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                            AAA_27 146 qlLfeasaGlaslrevleaLeaeadelfkprkskk...rainealeeleeakkelrea 200
                                       q L e  +++a  +e l++ +a+++elf++r+ ++   +++++  e+++e +++++++
  gi|313126069|ref|YP_004036339.1| 652 QRLEEVDGSVAVAHEELDRYRADREELFTERGLEPgdrERLATLCEQYSEYEAAVEAK 709
                                       5555566667777888888899999999998876644456666667777766666655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.4e-06     0.013      18      37 ..      53      72 ..      38     109 .. 0.86
   2 ?    4.1   1.9    0.0083        15     315     446 ..     209     349 ..     174     363 .. 0.71
   3 ?    1.3   7.4     0.057     1e+02     316     444 ..     531     659 ..     511     681 .. 0.52
   4 ?    0.3   7.2      0.12   2.1e+02     284     369 ..     737     821 ..     712     837 .. 0.65
   5 ?   -3.8   0.0         2   3.6e+03     283     317 ..    1088    1122 ..    1086    1133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.4e-06
                            AAA_13 18 iNliYGwNGaGKTtLSrllr 37
                                      +N++YG+N aGK+tL++++r
  gi|313126069|ref|YP_004036339.1| 53 VNVVYGANAAGKSTLAEAIR 72
                                      8****************998 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0083
                            AAA_13 315 ensafeed...keelkaeaealeeqLkg..lqraleaKrkepfk.svelesvkakiesikklvaeineliakhNekv 385
                                       + s+ e d    ++++++ + le++++   +q+a +++++e+ + + el s++++     ++++++ e+ia+  +  
  gi|313126069|ref|YP_004036339.1| 209 RLSQLEGDlaaAADASERVDLLETAIQYreAQDAYDQRVDEVTSfPDELASFDGDEL---DQLDDLDEQIAQQKRVE 282
                                       2233333333378888899999999876559999******99998889999999988...899************** PP

                            AAA_13 386 anleeekeeakkklelhlv......eeleseldeykkkykklekaieklekelkeeeaelkkleeei 446
                                       ++ + +  ea++kl   ++        + + l  y ++++++e++   l++e++++ea+  +++e+i
  gi|313126069|ref|YP_004036339.1| 283 QEAAVKYREAADKLAGTELpedgvaDGVLQTLRGYRDDLDDAEDNRDRLQREVADAEAKRSEVREKI 349
                                       **************99999666555444455556666666666666666666666666666666554 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.057
                            AAA_13 316 nsafeedkeelkaeaealeeqLkglqraleaKrk.epfksvelesvkakiesikklvaeineliakhNekvanleee 391
                                       ++a ++d   ++  ++ ++++L++++++l+++ + e+  ++el ++ +++e+ + + +++    a+  e  +++++ 
  gi|313126069|ref|YP_004036339.1| 531 QEAQKRDELRAQFDIDDIRDELETARDRLQNRFDtEVNDDIELAVTVERVERWQAADETVVGKQAALQEANDQVKTY 607
                                       33344444444445577788888888888888652555578887777777755555444444444444444444555 PP

                            AAA_13 392 keeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkklee 444
                                       +e+ +  +e +    +   +++  ++ +++e ++e+ +++ ++++++l+++++
  gi|313126069|ref|YP_004036339.1| 608 REQFCATIEPYTTDAYSYTVETSADATAAVE-SLEQRQRDYENATQRLEEVDG 659
                                       5555555555555444444443333333322.344444444444444444433 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.12
                            AAA_13 284 kqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesv 360
                                       + ++Le+ +++  +  +++ e l++ ++ ++ +++ +++  e+ ++ ++  e+L+gl++alea + + +++  le v
  gi|313126069|ref|YP_004036339.1| 737 DRDDLERELDEKREIANQYDELLQEKTTLEK-EIEDAKASTEIADAVQERGEALRGLEEALEADVADAVTDTLLEFV 812
                                       3344454444444444444444444444443.355666677788888888888999999999999999999999988 PP

                            AAA_13 361 kakiesikk 369
                                       +a+++s ++
  gi|313126069|ref|YP_004036339.1| 813 EAETVSSNQ 821
                                       888876655 PP

  == domain 5  score: -3.8 bits;  conditional E-value: 2
                            AAA_13  283 ekqerLekliekveskkselleklkavsdeasens 317 
                                         ++++ ++l+++v+++ +e+l+ l++vs+  + ++
  gi|313126069|ref|YP_004036339.1| 1088 TFIDKVSELADRVDGDPEEILDALPDVSHFRQDKI 1122
                                        57888999999999999999999999999755433 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0017         3      15      39 ..      55      79 ..      46     110 .. 0.84
   2 ?    2.0   0.4      0.15   2.8e+02      62     121 ..     750     877 ..     692     899 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                                      EEEESTTSSHHHHHHHHTTSS--SE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 15 aivGenGaGKStLlkllagllkpte 39
                                      ++ G n aGKStL++++   l p+e
  gi|313126069|ref|YP_004036339.1| 55 VVYGANAAGKSTLAEAIRWSLWPDE 79
                                      578*************988777755 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                                       EEE-SS--S-TTSBHHHH.......................................................HHHT CS
                                       xxxxxxxxxxxxxxxxxx.......................................................xxxx RF
                          ABC_tran  62 gvlpqepqlfpeltvren.......................................................esde 83 
                                       ++  q ++l +e+t  e+                                                           
  gi|313126069|ref|YP_004036339.1| 750 EIANQYDELLQEKTTLEKeiedakasteiadavqergealrgleealeadvadavtdtllefveaetvssnqeP--- 823
                                       44444444444443333334445445555555555555555555555555555555555555555554333331... PP

                                       C...HHHHHHHSTTGG...............TTCBGESTTSGGS-HHHHHHHHHHH CS
                                       x...xxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  84 e...iekalsklglke...............lkdtvvksspssLSgGqkqrvalar 121
                                           ++++l+++ + +                ++++v  + + LS G ++ v la 
  gi|313126069|ref|YP_004036339.1| 824 VfqrADDLLRRITDGQfelrlddgtfrafdtGEQRRV--DLNDLSSGTRVQVLLAV 877
                                       0222333333333333444444455555432223333..33888888888887775 PP

>> Terminase_4  Phage terminase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.71   1.3e+03      25      63 ..     572     610 ..     557     649 .. 0.64
   2 ?   12.8   0.7   6.8e-05      0.12      14      67 ..     680     737 ..     675     836 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.71
                       Terminase_4  25 aLaayceayaryreaekkiekeGvtittaegegakkknp 63 
                                        La ++e ++r++ a++ +  +   +++a+ + ++ + +
  gi|313126069|ref|YP_004036339.1| 572 ELAVTVERVERWQAADETVVGKQAALQEANDQVKTYREQ 610
                                       567777777777777777755444555444433333333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.8e-05
                       Terminase_4  14 elgilseldseaLaayceayaryreaekkiekeGvtittaegegakkknpavt......i 67 
                                        ++ l++ d+e La +ce y++y+ a +++ ++ +t+++ ++    ++++a+        
  gi|313126069|ref|YP_004036339.1| 680 TERGLEPGDRERLATLCEQYSEYEAAVEAKGTAETTLENRRS--DLREHDAYEeeieerD 737
                                       44558999**********************999999999888..7888887775555551 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00017       0.3      23      50 ..      52      79 ..      39      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                            AAA_29 23 gatlltGpsGsGKSTllDAiqalLvpak 50
                                      g+ ++ G++ +GKSTl  Ai   L p++
  gi|313126069|ref|YP_004036339.1| 52 GVNVVYGANAAGKSTLAEAIRWSLWPDE 79
                                      467899**************99888875 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3      0.93   1.7e+03      29     106 ..     265     342 ..     232     349 .. 0.71
   2 ?   11.0   6.7     4e-05     0.072      17     175 ..     639     827 ..     631     863 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.93
                        V_ATPase_I  29 vrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvel 105
                                       + ++d++++++   ++  ++++ + +++ ++ + +e pe+   d + ++l+ + ++l + ++n ++l++e+ +++ +
  gi|313126069|ref|YP_004036339.1| 265 LDQLDDLDEQIAQQKRVEQEAAVKYREAADKLAGTELPEDGVADGVLQTLRGYRDDLDDAEDNRDRLQREVADAEAK 341
                                       44556666666555544444444444444446777777777888888888888888888888888888888777655 PP

                        V_ATPase_I 106 k 106
                                       +
  gi|313126069|ref|YP_004036339.1| 342 R 342
                                       5 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4e-05
                        V_ATPase_I  17 dvnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenle 93 
                                       ++++ qr++ +  +r++e++ ++ + +ee+++++    +   +e+ le  ++++l +l e+ +++e+ ++   + ++
  gi|313126069|ref|YP_004036339.1| 639 SLEQRQRDYENATQRLEEVDGSVAVAHEELDRYRADREELF-TERGLEPGDRERLATLCEQYSEYEAAVEAKGTAET 714
                                       57789***************************666555554.47888888888899999999999999999999999 PP

                        V_ATPase_I  94 klkkelnelvelkavlekakefleee.eeeeeeeeseeeeeekeeeeeeeseeeeeeelleeeee............ 157
                                       +l++++++l e+ a  e+++e  +++ e+e +e+++ +++ ++  +e+++ e+e e++++++  e            
  gi|313126069|ref|YP_004036339.1| 715 TLENRRSDLREHDAYEEEIEERDRDDlERELDEKREIANQYDELLQEKTTLEKEIEDAKAST--Eiadavqergeal 789
                                       99999999999988888888777666433333322222222221122222222221111111..1223444555555 PP

                        V_ATPase_I 158 ...................lsfv.aGvikrekveafer 175
                                                          l+fv a ++++++ + f+r
  gi|313126069|ref|YP_004036339.1| 790 rgleealeadvadavtdtlLEFVeAETVSSNQEPVFQR 827
                                       55555555556666666655555233555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1370  (0.0764125); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.97u 0.41s 00:00:01.38 Elapsed: 00:00:00.56
# Mc/sec: 6360.98
//
Query:       gi|313126070|ref|YP_004036340.1|  [L=428]
Description: DNA repair exonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-12   47.8   0.6    5.8e-12   46.1   0.2    2.1  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    7.5e-09   36.4   0.3    1.5e-08   35.4   0.3    1.5  1  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.041   14.3   1.2      0.097   13.0   0.5    2.0  2  Toprim_3       Toprim domain
      0.065   13.0   0.0       0.14   12.0   0.0    1.5  1  DUF1317        Protein of unknown function (DUF1317)
       0.11   11.9   0.0       0.18   11.2   0.0    1.3  1  DUF604         Protein of unknown function, DUF604


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.2   1.6e-15   5.8e-12       3     153 ..       6     219 ..       4     233 .. 0.65
   2 ?   -2.2   0.0       1.2   4.2e+03      53      66 ..     288     302 ..     262     337 .. 0.67

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.6e-15
                     Metallophos_2   3 laiiSDlH.................snldaleavlealkevgvdaiihaGDl.eeeep........evleellela. 52 
                                       ++ ++D+H                 s + + ++++e +  +gvda+++aGDl  +e+         e    +  ++ 
  gi|313126070|ref|YP_004036340.1|   6 VLCVADIHigrrpsrlpdrfdpadfSPRTIWANLAESAVTQGVDAVVVAGDLvDQENRyaeafgavE---SVATRLa 79 
                                       6789999988877777777766555555555666999999999********8633333444444332...3333335 PP

                     Metallophos_2  53 ....pvlaVrGNnD...................eevveedvlreaaelgtdl......................... 81 
                                           p++aV GN+D                   +              +t+l                         
  gi|313126070|ref|YP_004036340.1|  80 eagiPLIAVAGNHDadvlpdlaeaiehlqllgrD----------GSWERTALtdadgepclhvdgwsfpgryyhenp 146
                                       557***********88888887544444444330..........333333334444444444455555555444443 PP

                     Metallophos_2  82 .peeaelelagek.vlliHgdplgvkdalaellke..aeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgd 153
                                         +++ ++ +g+  ++++H d  +++d++a+++ +  a++g+   v+GH Hvp++++e +  v++PGs+++   ++
  gi|313126070|ref|YP_004036340.1| 147 lDAYDLVD-EGVPrLGVVHAD-VSGEDRYAPVAVDdlATSGHSAWVLGHLHVPGLRHE-NPPVLYPGSLQPLDPSE 219
                                       22333444.333359999998.588888888888877889999************999.999*******9974444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                     Metallophos_2  53 pvlaVrGNnD.eevv 66 
                                         ++V G++D ++++
  gi|313126070|ref|YP_004036340.1| 288 VTVTVAGRTDaDTDL 302
                                       567888888832222 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.3   4.2e-12   1.5e-08       3     203 ..       6     196 ..       4     197 .. 0.53

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 4.2e-12
                                       EEEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH....T CS
                       Metallophos   3 ilvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky....p 64 
                                       +l+++D+H+           + ++ + +++++ l + +  +++d+v++aGDlvd  +   e    ++ +  +    +
  gi|313126070|ref|YP_004036340.1|   6 VLCVADIHIgrrpsrlpdrfDPADFSPRTIWANLAESAVTQGVDAVVVAGDLVDQENRYAEAFGAVESVATRlaeaG 82 
                                       89******999997777666555555555555555555557**************9555555555555555556668 PP

                                       SEEEEEC-TTS.........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEE.THH CS
                       Metallophos  65 ipvylllGNHe.........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspel.lvs 130
                                       ip+++++GNH+         +                          ++l l +  + +  + l++  g+p l  + 
  gi|313126070|ref|YP_004036340.1|  83 IPLIAVAGNHDadvlpdlaeA-------------------------IEHLQLLGRDGSWeRTALTDADGEPCLhVDG 134
                                       8**********5554443331.........................2333333322222222222222212222234 PP

                                       HHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 131 ldklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                       ++  g++ +e + +   +++  +      + + + + H  ++  +++ +++ a++dl    g  +++ GH Hv
  gi|313126070|ref|YP_004036340.1| 135 WSFPGRYYHENPLDA--YDLVDE------GVPRLGVVHADVS--GEDRYAPVAVDDLAT-SGHSAWVLGHLHV 196
                                       455555555555555..555555......2222333333333..334444444444433.3346666677765 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   2.7e-05     0.097      30      85 ..      37      96 ..      33     105 .. 0.90
   2 ?   -2.6   0.0         2   7.2e+03      59      90 ..     271     303 ..     247     306 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                          Toprim_3 30 anlkaiawpergkrvviaaD.nDaand...GreaaeklaerleaagieavllepaegeDw 85
                                      anl++ a+++++  vv+a D  D++n       a+e +a rl++agi ++++  ++++D+
  gi|313126070|ref|YP_004036340.1| 37 ANLAESAVTQGVDAVVVAGDlVDQENRyaeAFGAVESVATRLAEAGIPLIAVAGNHDADV 96
                                      688889999****************99999999*******************99999886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                          Toprim_3  59 aaeklaerlea.agieavllepaegeDwndvlq 90 
                                       + +++a ++ +   + av++  a  +D++ +l+
  gi|313126070|ref|YP_004036340.1| 271 QLRETATKCGSeTELLAVTVTVAGRTDADTDLR 303
                                       333333333331333344444455556666666 PP

>> DUF1317  Protein of unknown function (DUF1317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     4e-05      0.14      22      45 ..     133     156 ..     129     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                           DUF1317  22 rGWvfPGlkviknPlkAqrlAEEk 45 
                                        GW fPG     nPl A+ l +E 
  gi|313126070|ref|YP_004036340.1| 133 DGWSFPGRYYHENPLDAYDLVDEG 156
                                       6******************99985 PP

>> DUF604  Protein of unknown function, DUF604
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     5e-05      0.18      35      73 ..      62     100 ..      50     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5e-05
                            DUF604  35 erYpklygsddriqaClaelGvpltkekGfHqvDlrgdl 73 
                                       +rY++ +g+ + + + lae G+pl+   G H  D+  dl
  gi|313126070|ref|YP_004036340.1|  62 NRYAEAFGAVESVATRLAEAGIPLIAVAGNHDADVLPDL 100
                                       79********************************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2379.98
//
Query:       gi|313126071|ref|YP_004036341.1|  [L=291]
Description: hypothetical protein Hbor_13130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   14.0   4.3       0.18   12.2   4.3    2.0  1  HalX      HalX domain
      0.068   13.0   0.4      0.068   13.0   0.4    1.6  2  DUF241    Arabidopsis protein of unknown function
      0.087   13.0   0.7        4.7    7.5   0.0    2.7  2  DUF2789   Protein of unknown function (DUF2789)
       0.11   11.3   0.2       0.18   10.6   0.2    1.4  1  ALMT      Aluminium activated malate transporter
       0.19   12.2   3.7       0.66   10.5   1.6    2.5  2  ZapB      Cell division protein ZapB


Domain annotation for each model (and alignments):
>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   4.3   4.9e-05      0.18      35      60 ..     243     268 ..     230     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                              HalX  35 eeYqeLearleelraqldetldeldd 60 
                                       +eY+eL+++++++r+  +e+ +el +
  gi|313126071|ref|YP_004036341.1| 243 DEYEELQEEIDRYRTHCEELSEELVE 268
                                       9*******************999755 PP

>> DUF241  Arabidopsis protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.78   2.8e+03     119     146 ..      42      69 ..      32     101 .. 0.74
   2 ?   13.0   0.4   1.9e-05     0.068     168     233 ..     217     275 ..     191     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.78
                            DUF241 119 ellevvevlreveavtvsvlesLlsfls 146
                                         +++v vl     +t++v  +L + + 
  gi|313126071|ref|YP_004036341.1|  42 VAASLVGVLGTLVLATATVWTALQNQVL 69 
                                       5677888888888888888888877665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.9e-05
                            DUF241 168 keeeeeenelekvdaalesllssskkekvqsalkrleeleecieelEeglekvfRrLIktRVsLLN 233
                                       ++++e+++++++ + +l+++l +        a ++ eel+e i++    +e ++ +L+  RVsL N
  gi|313126071|ref|YP_004036341.1| 217 SDQHEHAEIWSEHQDELCRILDE-------VAADEYEELQEEIDRYRTHCEELSEELVERRVSLQN 275
                                       35666888888888888888877.......79999****************************966 PP

>> DUF2789  Protein of unknown function (DUF2789)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0013       4.7      39      71 ..      54      86 ..      49      90 .. 0.81
   2 ?    3.2   0.2     0.028        99      28      55 ..     213     235 ..     187     254 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                                      -STT-TTS-HHHHHHHHHHHHS--TTHHHHHHH CS
                           DUF2789 39 kladApfWseaQaafLkealeedadWaevvdqL 71
                                       la A++W++ Q++ L ++  ++a+   + ++L
  gi|313126071|ref|YP_004036341.1| 54 VLATATVWTALQNQVLVDERVKEAEKPIIREEL 86
                                      6899**************999999866555555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.028
                                       HHHS.---TTS-STT-TTS-HHHHHHHH CS
                           DUF2789  28 iakhkpleeevkladApfWseaQaafLk 55 
                                       i++ +      + ++A++Wse Q ++ +
  gi|313126071|ref|YP_004036341.1| 213 IDQYS-----DQHEHAEIWSEHQDELCR 235
                                       44444.....2335799******98754 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   4.9e-05      0.18     116     165 ..       1      55 [.       1     102 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.9e-05
                              ALMT 116 ikarYdYgvlvfl..LTFclvvvsgyrtdevielAv.kRfltia..iGalicliv 165
                                       +++r +Y++lvfl  + F+lvvvsgy + +  +l+  +R++  a  +G+l  l++
  gi|313126071|ref|YP_004036341.1|   1 MRNRIQYALLVFLglFIFILVVVSGYLVFQWSNLTLnSRVSVAAslVGVLGTLVL 55 
                                       677889******554999**********999988862465544233666655554 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.17   6.3e+02      15      39 ..     157     181 ..     148     233 .. 0.84
   2 ?   10.5   1.6   0.00018      0.66      16      49 ..     241     274 ..     239     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.17
                              ZapB  15 kaidtitlLqmeieeLkeeneelke 39 
                                       k+i+t + L +ei++L  + ++l e
  gi|313126071|ref|YP_004036341.1| 157 KMIQTHDYLLNEIADLGGQINSLLE 181
                                       7899999999999999888777655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                              ZapB  16 aidtitlLqmeieeLkeeneelkeenreleeene 49 
                                       a d++++Lq+ei++ +   eel+ee  e + +++
  gi|313126071|ref|YP_004036341.1| 241 AADEYEELQEEIDRYRTHCEELSEELVERRVSLQ 274
                                       789*********************9877665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1492  (0.0832171); expected 358.6 (0.02)
Passed bias filter:                      985  (0.0549389); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 1858.80
//
Query:       gi|313126072|ref|YP_004036342.1|  [L=317]
Description: hypothetical protein Hbor_13140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-08   33.8   0.0    8.8e-08   32.2   0.0    1.9  1  HNH_2        HNH endonuclease
     0.0007   19.5   0.0     0.0046   16.9   0.0    2.1  2  HTH_45       Winged helix-turn-helix
     0.0043   16.0   0.4     0.0062   15.5   0.4    1.3  1  DUF3363      Protein of unknown function (DUF3363)
     0.0098   16.4   0.0        1.1    9.8   0.0    2.4  2  AAA_assoc_C  C-terminal AAA-associated domain


Domain annotation for each model (and alignments):
>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0     2e-11   8.8e-08       1      72 []     214     265 ..     214     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2e-11
                             HNH_2   1 CvitgiddpslleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfafe 72 
                                       C i+g+d+p ll++AH++ w          ++r+              + sN+l Ls+++H +Fd+ lf+++
  gi|313126072|ref|YP_004036342.1| 214 CPISGVDHPGLLDVAHVLSWNDY------PEYRA--------------DLSNVLALSKTHHAAFDRELFTID 265
                                       99*******999*******6666......66666..............*********************996 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.25   1.1e+03      40      68 ..      50      78 ..      43      82 .. 0.87
   2 !   16.9   0.0     1e-06    0.0046      34      71 ..     131     168 ..     129     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
                            HTH_45 40 LdmLvekglikkskekYvlTekGlellek 68
                                      +++L++ g++++ ++ ++l   G+e++e+
  gi|313126072|ref|YP_004036342.1| 50 VSYLQQVGFLRQVNDHWELGGAGREYVEQ 78
                                      6789999***********99999999875 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1e-06
                            HTH_45  34 kllnkYLdmLvekglikkskekYvlTekGlelleklke 71 
                                       +++++ ++ L + gl++k++++Y lT+ Gl+++e+  e
  gi|313126072|ref|YP_004036342.1| 131 DMAKQRVNWLRSMGLVEKRGDEYALTDNGLQFVESAVE 168
                                       67889999************************998765 PP

>> DUF3363  Protein of unknown function (DUF3363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   1.4e-06    0.0062     163     286 ..      41     161 ..      22     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-06
                           DUF3363 163 efveahvrRLeaLrragivereedgsWrvpedlleraaaydakrlaepvavevksalslekqvtargatWLDrelvs 239
                                       + +++++rR   L+++g+  r+ +++W+++    e +++ d + l   +++    ++ l +++ a +a  +    vs
  gi|313126072|ref|YP_004036342.1|  41 SSRDSIMRRVSYLQQVGFL-RQVNDHWELGGAGREYVEQGDVATL---LRIMCDRNVGLRSLMYALAAGPMTLAEVS 113
                                       567899***********98.67788*****************999...9999999****************999999 PP

                           DUF3363 240 gekedlada.GFGkevrealarRrqflveqglaeeeqgrvvlrrnlla 286
                                       +++ d++ + G+ +  ++ +++R ++l+++gl e+++++ +l+ n l+
  gi|313126072|ref|YP_004036342.1| 114 EQQLDTHPElGWSRGETDMAKQRVNWLRSMGLVEKRGDEYALTDNGLQ 161
                                       9998877667**********************9999999888777665 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.015        68      12      47 ..      44      79 ..      40      95 .. 0.92
   2 !    9.8   0.0   0.00026       1.1      17      48 ..     136     167 ..     128     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.015
                       AAA_assoc_C 12 ddLlpiveaaelLglveveegdielTelGrkfvead 47
                                      d ++  v  ++  g+++  +++ el  +Gr++ve++
  gi|313126072|ref|YP_004036342.1| 44 DSIMRRVSYLQQVGFLRQVNDHWELGGAGREYVEQG 79
                                      899999***************************975 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00026
                       AAA_assoc_C  17 iveaaelLglveveegdielTelGrkfveadi 48 
                                        v+ ++++glve ++++  lT+ G +fve+ +
  gi|313126072|ref|YP_004036342.1| 136 RVNWLRSMGLVEKRGDEYALTDNGLQFVESAV 167
                                       578899**********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2000.97
//
Query:       gi|313126073|ref|YP_004036343.1|  [L=80]
Description: hypothetical protein Hbor_13150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.014   15.2   0.1      0.022   14.6   0.1    1.4  1  Ribosomal_L21e  Ribosomal protein L21e
      0.033   14.4   0.6       0.62   10.3   0.2    2.0  2  TOBE_2          TOBE domain
      0.081   12.8   0.0       0.12   12.2   0.0    1.5  1  SH3_13          ATP-dependent RecD-like DNA helicase SH3 doma
      0.085   12.8   0.3       0.13   12.2   0.3    1.5  1  DUF4314         Domain of unknown function (DUF4314)


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     5e-06     0.022      31      67 ..       1      35 [.       1      53 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-06
                                      H----TT-EEEE---TT--SS---GGGTT-EEEE..E CS
                    Ribosomal_L21e 31 lreykkGdkVdikidpsvqkgmphkryhGktgrvynv 67
                                      ++ + +Gd+V ++i         h++yhG+ grv++v
  gi|313126073|ref|YP_004036343.1|  1 MQRFSEGDRVRVDIPDET--DPDHQVYHGEHGRVVSV 35
                                      799**********97654..467***********876 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.031   1.4e+02      57      70 ..       3      16 ..       1      18 [. 0.82
   2 ?   10.3   0.2   0.00014      0.62      25      69 ..      22      68 ..      21      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.031
                            TOBE_2 57 alapGdtVelswdp 70
                                      ++ +Gd+V++ ++ 
  gi|313126073|ref|YP_004036343.1|  3 RFSEGDRVRVDIPD 16
                                      6899*****98865 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                            TOBE_2 25 dveylGsstryv.velaggqlvvvrqpnadr.dsalapGdtVelswd 69
                                      + +y G++ r+v v  ++   +++   +++  + a++ G++V  +w+
  gi|313126073|ref|YP_004036343.1| 22 HQVYHGEHGRVVsVLSDDADSLTADERDGQIyRVAFDSGEEVDFRWR 68
                                      678*********777777777777777777667*************6 PP

>> SH3_13  ATP-dependent RecD-like DNA helicase SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.8e-05      0.12      25      61 ..       3      43 ..       1      57 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                            SH3_13 25 vfrvgDkV...mqlkNnydkgvfNGDiGiikei...dkeekkl 61
                                       f++gD+V   +  + ++d++v+ G+ G ++++   d  +++l
  gi|313126073|ref|YP_004036343.1|  3 RFSEGDRVrvdIPDETDPDHQVYHGEHGRVVSVlsdD--ADSL 43
                                      59999999766777899999************97531..2333 PP

>> DUF4314  Domain of unknown function (DUF4314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3     3e-05      0.13      10      48 ..       2      44 ..       1      65 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                           DUF4314 10 eqYpkGtrveLv..smddeqaplppGtkGtVkgV..DDiGtih 48
                                      +++ +G rv++     +d+++++  G++G V +V  DD+ ++ 
  gi|313126073|ref|YP_004036343.1|  2 QRFSEGDRVRVDipDETDPDHQVYHGEHGRVVSVlsDDADSLT 44
                                      57889999888766899***************99888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 500.51
//
Query:       gi|313126074|ref|YP_004036344.1|  [L=270]
Description: DNA repair exonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-11   42.6   0.1    1.5e-10   41.9   0.1    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    7.1e-08   32.8   0.0    2.9e-07   30.8   0.0    1.8  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.1   1.7e-14   1.5e-10       4     203 ..       2     213 ..       1     228 [. 0.63

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.7e-14
                                       EEEESBTB...............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS....HHHHHHHHH.HHHH CS
                       Metallophos   4 lvigDlHl...............algggqlddllkllddllreekpdlvllaGDlvdrg....dlekellel.laal 60 
                                       l+++D+Hl                  + + +d+++ ++ ++ e ++d+v+++GD+ d+         + +e  l+ l
  gi|313126074|ref|YP_004036344.1|   2 LFVSDTHLgyenraetgsgktvpWIDEIDSRDTIRRIRTIAMERDVDAVIHTGDVLDHEvdavT--LDAAESsLRDL 76 
                                       79*********877777777777666677777777777778889**************977443..33333336666 PP

                                       HHHTSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE....EEEEEEESECEEETHHHHH CS
                       Metallophos  61 vkypipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs....lkvlllhGgspellvsldk 133
                                         ++ipvy++lG H+   ++   +y ++  ++  w +d   + n +l++l   +       l ++G s+e  v ld+
  gi|313126074|ref|YP_004036344.1|  77 ALSDIPVYCILGTHD---HNAAIPYYSNSVDGIAWLKD--QVRNEYLIELSASPtsvaGGPLDAYGVSAEN-VGLDD 147
                                       66699**********...56666666666667777777..3344444443333122333444444444444.56666 PP

                                       HHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTT..ESEEEEESSSS CS
                       Metallophos 134 lgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkyg..vdlvisGHtHv 203
                                       +g+++     p   ++ +      +   + ++  H +++ +   + +d  l++ll + +   d v+ G++H+
  gi|313126074|ref|YP_004036344.1| 148 VGKYESLGWRPS--EIAFGA----ASPGPNVLCLHDGVTPYRNRSTADVNLDELLAQSRvsFDCVLVGDEHR 213
                                       666665555554..444444....444444444455555355555555555555444443367788888886 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   3.3e-11   2.9e-07       4     144 ..       2     237 ..       1     255 [. 0.68

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3.3e-11
                     Metallophos_2   4 aiiSDlH.....................snldaleavlealkevgvdaiihaGDl..eeeepevleellela..... 52 
                                       +++SD+H                     +++d ++++ +++ e +vda+ih+GD+   e++  +l+++++ +     
  gi|313126074|ref|YP_004036344.1|   2 LFVSDTHlgyenraetgsgktvpwideiDSRDTIRRIRTIAMERDVDAVIHTGDVldHEVDAVTLDAAESSLrdlal 78 
                                       789***************************************************76644444233333322234457 PP

                     Metallophos_2  53 ...pvlaVrGNnD..........................................eev..veedvlreaaelgtdl. 81 
                                          pv+ + G +D                                          + +   +e v+    +  ++l 
  gi|313126074|ref|YP_004036344.1|  79 sdiPVYCILGTHDhnaaipyysnsvdgiawlkdqvrneylielsasptsvaggplDAYgvSAENVGLDDVGKYESLg 155
                                       779**********9999999888888888887777766666666666666655552222333444444444444444 PP

                     Metallophos_2  82 ..peeaelel....agekvlliHgdpl......gvkdalaellkeaeegsd.vvvcGHtHvp.........evekeg 136
                                         p+e    +    +g +vl +H+          ++ +l+ell + + +s+ +v++G  H+p         + e+e+
  gi|313126074|ref|YP_004036344.1| 156 wrPSEIA--FgaasPGPNVLCLHDGVTpyrnrsTADVNLDELLAQ-SRVSFdCVLVGDEHRPkyddfengySFETED 229
                                       4432222..233457777999998755788887677777777777.4444469999999999655555554444445 PP

                     Metallophos_2 137 gvlvvnPG 144
                                       g+ v++ G
  gi|313126074|ref|YP_004036344.1| 230 GTPVLYTG 237
                                       66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1777.09
//
Query:       gi|313126075|ref|YP_004036345.1|  [L=469]
Description: hypothetical protein Hbor_13170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      0.002   18.0   0.0     0.0057   16.5   0.0    1.8  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


Domain annotation for each model (and alignments):
>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.2e-07    0.0057       6     122 ..      13     121 ..       9     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-07
                       HATPase_c_3   6 AlaelvdNsldAdaen....vkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlk 78 
                                       A  e++ N+ld  a +     +i+ +      g   i+D G G  +e l +    a+++++ ++  +++Gk+G+G+k
  gi|313126075|ref|YP_004036345.1|  13 AAREIIANALDEAALTdtddPDIYSEA-----GAWHIRDYGRGFRYEHLTQ----AEDEEKLNNPDKVIGKFGVGIK 80 
                                       667999999994444323335555555.....689***********98765....677777777899********** PP

                       HATPase_c_3  79 lAslslgkkltvitkkegesstltldvdkidkenekvleeltve 122
                                        A+    ++   it ++    ++t++v+   k++++++e+l+ve
  gi|313126075|ref|YP_004036345.1|  81 DAIATCHRHGIDITIHS---PHNTFTVKEAPKHGFEEIETLHVE 121
                                       ***99999888888887...456677777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3227.69
//
Query:       gi|313126076|ref|YP_004036346.1|  [L=116]
Description: hypothetical protein Hbor_13180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 746.49
//
Query:       gi|313126077|ref|YP_004036347.1|  [L=1168]
Description: DNA/RNA helicase, superfamily ii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.5e-19   68.1   0.0    2.3e-18   66.5   0.0    1.9  1  Helicase_C  Helicase conserved C-terminal domain
    2.3e-12   46.9   0.0    6.2e-12   45.6   0.0    1.7  1  PLDc_2      PLD-like domain
    3.7e-11   42.3   0.2      1e-07   31.0   0.1    2.6  3  SNF2_N      SNF2 family N-terminal domain
      7e-06   26.2   0.3     0.0042   17.1   0.3    2.6  2  ResIII      Type III restriction enzyme, res subunit
     0.0069   15.7   0.0      0.058   12.7   0.0    2.4  2  RE_NgoFVII  NgoFVII restriction endonuclease
  ------ inclusion threshold ------
      0.016   14.4   0.0       0.03   13.6   0.0    1.3  1  DUF2075     Uncharacterized conserved protein (DUF2075)
       0.02   14.7   1.4         15    5.3   0.0    3.8  4  DEAD        DEAD/DEAH box helicase
      0.067   13.5   0.0       0.34   11.3   0.0    2.2  1  DUF5601     Domain of unknown function (DUF5601)
       0.52   10.6   2.8        2.9    8.2   0.1    3.4  3  AAA_22      AAA domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   1.2e-21   2.3e-18       9     111 .]     739     859 ..     720     859 .. 0.79

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.2e-21
                                       HHHHTTTTSEEEEEESSHHHHHH....HHHHHHHT........TSTEEEESTTSTHHHHHHHHHHHH.TTS...... CS
                        Helicase_C   9 llkleeeggkilifvntidrlek....vklllekk........gikvavlhgelpqnereeileqfn.kge...... 66 
                                       +l++  + +k ++f++++d+++     +    e++        +i++a  ++   +++ e+i+++f  +        
  gi|313126077|ref|YP_004036347.1| 739 ILQRGDRAEKLIVFTQFTDTVKYleaaF----EQFqdrgllsdDIRFASATS--DTSNVEKIIQRFApE-Andardk 808
                                       447778899**********995543333....33355668877899999998..5677889*****751.2456677 PP

                                       ......SSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  67 ......sdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                             +dvL atdva++G++++++nlVin+dl +n+ ++iqriGR+ R g
  gi|313126077|ref|YP_004036347.1| 809 idpsdeIDVLFATDVAGEGVNLQDANLVINYDLHWNPLRLIQRIGRVDRLG 859
                                       777777*****************************************9975 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   3.1e-15   6.2e-12      10     133 .]      32     212 ..      23     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3.1e-15
                            PLDc_2  10 ksidiatyyf..vsdreildallkaakrgvkvrilldskkd.................................... 48 
                                       ++i+ia++y+     + +  +l +  + g  +++l+++  +                                    
  gi|313126077|ref|YP_004036347.1|  32 DRIRIAVGYLymSGLKRLRPELDEFLDDGGTLQVLMGNPDQqgldelieahqnlrltgtkfrqsqnvkwserteira 108
                                       78999999994333344577778888999999999997444899999999999999999999999999999999999 PP

                            PLDc_2  49 .............dagavdeaslkelkellleagvevrvfetllgslHaKlylidgk.........tvivGSsNltk 103
                                                    d++a+++a + +l   l ++ ++ +++ +  +++HaK+yl++++         + +vGSsNl+ 
  gi|313126077|ref|YP_004036347.1| 109 etadnyshqllyeDPTAENQAFFTKLIDWLEQGRIQPKLYLQ--ERFHAKAYLFEKNegdiftpkdVGVVGSSNLSL 183
                                       999999999999999999999999999999999***999876..79********966677888888*********** PP

                            PLDc_2 104 rgldlnlElnvviedkelakeleeeFerlw 133
                                       +gl++n+Eln  +++++ +++l+++F+ lw
  gi|313126077|ref|YP_004036347.1| 184 SGLHSNTELNAPVYNEK-VTQLKDWFDDLW 212
                                       ****************9.99*********9 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00033      0.66      53     119 ..     320     379 ..     306     405 .. 0.78
   2 !   31.0   0.1   5.1e-11     1e-07     169     276 ..     397     506 ..     385     543 .. 0.82
   3 ?   -2.9   0.0       1.1   2.2e+03     238     267 ..     705     732 ..     698     743 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00033
                                       HTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  53 qsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhv 119
                                       ++  G + +D  G+GKT   l l+ + +a +       r +  +g +Li++P+ l   We+ +++  
  gi|313126077|ref|YP_004036347.1| 320 NKYDGVLVSDVVGMGKTFVGLGLLEHFHARN-------RLRGNKGKMLIISPKHLQPMWERMVNKQY 379
                                       55678888999**************544433.......345556899*************9998755 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 5.1e-11
                                       ..TTS-S-S-SEEE.ES-GGGT--TTSHHHHHHHH.---S-E.EEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHH CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 169 krsvlkqvewkrvv.lDEghtlknstskaaeavsk.Lstsnr.wiltGTPiqnsledlygLlkfLreepfgekqtfd 242
                                       + + l++ +   v+ +DE+h ++n ++  ++ ++  L t n+ ++lt+TP   s  d+y  +k+ ++e +++     
  gi|313126077|ref|YP_004036347.1| 397 HETLLEEHDDASVClVDEAHHFRNDDTHRYNNLQAfLPTVNQtILLTATPYTKSAWDVYNQIKLFHIEDLTQIPITP 473
                                       5566666666666527*********999999999967776652789**************************99777 PP

                                       HHTHHHHHHHHHHHHHHHHTT-STTEE---GGGT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 243 kllqrpieaqaekgrsrLlqllqrlmlrrakkdv 276
                                         l++ +++ ae+    L +ll+ +m+rr+ +d+
  gi|313126077|ref|YP_004036347.1| 474 PNLYD-FTKMAENDETDLSNLLSHVMVRRTRQDI 506
                                       77764.666899999******************9 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.1
                                       HHHHHHHTHHHHHHHHHHHHHHHHTT-STT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 238 kqtfdkllqrpieaqaekgrsrLlqllqrl 267
                                        + f++ +q++++  +++++++L+qll +l
  gi|313126077|ref|YP_004036347.1| 705 LEPFHQDIQDDYA--MDDKVEQLRQLLGNL 732
                                       5678999999999..***********9865 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0047       9.3       4      62 ..     304     364 ..     285     382 .. 0.80
   2 !   17.1   0.3   2.1e-06    0.0042     123     170 ..     397     447 ..     372     448 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0047
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.........-EEEEES CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee....kflflvp 62 
                                       l+e Q+ a+++ +  +  ++   +l+    G+GKT+v + l e+++  ++ +    k+l++ p
  gi|313126077|ref|YP_004036347.1| 304 LYEFQQWAVNRGI-RIA-NKYDGVLVSDVVGMGKTFVGLGLLEHFHARNRLRgnkgKMLIISP 364
                                       5666777777777.443.77788899999**************99987665566666666655 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.1e-06
                                       ....HHHTTT-SEEEEETGGGTTS...TTTHHHHHT---.SEEEEEESS-S CS
                            ResIII 123 eeseellrdrfdviiiDEaHrlgak..kswreilekfke.avllglTATpe 170
                                        e+   ++d   v ++DEaH+++ +  + ++++   ++  +  + lTATp+
  gi|313126077|ref|YP_004036347.1| 397 HETLLEEHDDASVCLVDEAHHFRNDdtHRYNNLQAFLPTvNQTILLTATPY 447
                                       333344444445************8444888854444436888999****7 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.35   6.9e+02       4      50 ..      28      76 ..      26     105 .. 0.74
   2 !   12.7   0.0   2.9e-05     0.058      78     139 ..     150     215 ..     130     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.35
                                      HHHXSEEEEEESXXXHHHHHHHHHHHHXX..XXSEEEEEEXSHHHHXXX CS
                        RE_NgoFVII  4 leksdelliisGYvspaslselikllkeq..sdikitlivGMyplegls 50
                                      +e+ d++ i++GY+    l++l   l e      ++++++G    +gl+
  gi|313126077|ref|YP_004036347.1| 28 SEGVDRIRIAVGYLYMSGLKRLRPELDEFldDGGTLQVLMGNPDQQGLD 76
                                      67889*********99999998888888754445666666655555555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.9e-05
                                       S.XBXXXEEEEEET.TEEE.....EEEESXXSXXTTSXXXSBXEEEEEE.HHHHHHHHHHHHHHHHH. CS
                        RE_NgoFVII  78 v.kvHsKlYiwkkdgkpls.....AliGSANlssnglrtrqrEtlvdldtedafkeldeyiqsllsks 139
                                         ++H+K Y++ k++ ++      + +GS Nls+ gl+++  E+ + +  ++++++l+  +++l  ++
  gi|313126077|ref|YP_004036347.1| 150 QeRFHAKAYLFEKNEGDIFtpkdvGVVGSSNLSLSGLHSN-TELNAPVY-NEKVTQLKDWFDDLWDDA 215
                                       259**********997553244459************865.47777766.566777888888777665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05      0.03       5     108 ..     326     426 ..     324     442 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                           DUF2075   5 lVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkk 79 
                                       lV+ v G GKt v+l ll     ++  ++++ ++l+ + + ++ + e++ +k+  +++++++  l  + ++ +   +
  gi|313126077|ref|YP_004036347.1| 326 LVSDVVGMGKTFVGLGLLEHFhaRNRLRGNKGKMLIISPKHLQPMWERMVNKQ--YNFNAEVISLGMVSKE-D--FH 397
                                       6777889***********99966666688899999999999999999998888..6666666666544433.2..34 PP

                           DUF2075  80 aeekkeepkedvvivDEAhrlltksdqae 108
                                       ++  +e++++ v +vDEAh  ++  +++ 
  gi|313126077|ref|YP_004036347.1| 398 ETLLEEHDDASVCLVDEAHHFRNDDTHRY 426
                                       677799***************99544432 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0078        15      15      57 ..     323     366 ..     306     403 .. 0.77
   2 ?    3.8   0.0     0.021        43     121     170 ..     406     447 ..     388     452 .. 0.73
   3 ?    1.6   0.1      0.11   2.1e+02     126     156 ..     661     691 ..     630     699 .. 0.80
   4 ?   -2.4   0.0       1.7   3.5e+03     138     176 .]     755     794 ..     748     794 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0078
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtr 57 
                                       + vlv+  +G+GKT +  + +l+++  +   + ++ k+li++P +
  gi|313126077|ref|YP_004036347.1| 323 DGVLVSDVVGMGKTFV-GLGLLEHFHARnrLRGNKGKMLIISPKH 366
                                       5699999********9.77888888766774666669****9964 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.021
                                       TEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 121 qvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       + ++  +DEa+ + ++     +n++ + l       +  +q+i+l+AT+ 
  gi|313126077|ref|YP_004036347.1| 406 DASVCLVDEAHHFRND-DTHRYNNLQAFL-------PTVNQTILLTATPY 447
                                       5567789******998.555556655555.......33346*******85 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.11
                                       EEETHHHHHHTTTHHHHHHHHHHSHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 126 VlDEadrlldqgfsdfinrilnqlpqitcdg 156
                                       +lDE+d++ ++g    +++ + +l++ + d 
  gi|313126077|ref|YP_004036347.1| 661 ILDEIDEMVEEGEYAAYQTEAFHLEELKRDL 691
                                       9**********88888877666666665555 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.7
                                       THHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                              DEAD 138 fsdfinrilnqlpqitcdgklqrqvivlSATlp.kdvkkl 176
                                       f d+++ + ++++q +++g l+  + + SAT   ++v+k+
  gi|313126077|ref|YP_004036347.1| 755 FTDTVKYLEAAFEQFQDRGLLSDDIRFASATSDtSNVEKI 794
                                       77777887777877777777888899******99999985 PP

>> DUF5601  Domain of unknown function (DUF5601)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.34      24      59 ..     616     668 ..     607     670 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                           DUF5601  24 VqdFyqnlaerlnktplyktv.................sseavedlldeiEky 59 
                                       V++Fy++l+  l+++ +++++                 s e+++ +ldei   
  gi|313126077|ref|YP_004036347.1| 616 VHAFYTSLTRMLRSYRMFRDLldegtvavgsdvselinSGEQIDYILDEIDEM 668
                                       99******************99***************************9876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0015       2.9      15     131 ..     332     446 ..     326     450 .. 0.60
   2 ?   -0.7   0.1      0.82   1.6e+03      93     114 ..     658     689 ..     594     700 .. 0.69
   3 ?   -1.0   0.1      0.97   1.9e+03      43     105 ..    1014    1086 ..    1000    1128 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                            AAA_22  15 GtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdl.lrellralglelkaerlsseellealeqalrar 89 
                                       G+GKT++   lle +++++  + ++ + + + ++++   ++ +  ++   + ++   +   s+e++ e+l +     
  gi|313126077|ref|YP_004036347.1| 332 GMGKTFVGLGLLEHFHARNRLRGNKGKMLIISPKHLQpMWERMvNKQYNFNAEVISLG-MVSKEDFHETLLE----E 403
                                       6677777777777766666666666666666666666545444344444444443333.3333333344333....3 PP

                            AAA_22  90 av.ielliiDEaqhlr..seealeeLrsllnlsrkgvqliLvGtp 131
                                       ++  ++ ++DEa+h+r      +++L  +l   + + +++L  tp
  gi|313126077|ref|YP_004036347.1| 404 HDdASVCLVDEAHHFRndDTHRYNNLQAFLP--TVNQTILLTATP 446
                                       3345679********7654777888877776..766667666666 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.82
                            AAA_22  93 elliiDEaqhlr...s.......eealeeLrs 114
                                          i+DE++ +    +       + +leeL++
  gi|313126077|ref|YP_004036347.1| 658 IDYILDEIDEMVeegEyaayqteAFHLEELKR 689
                                       45789999997766514455567888888843 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.97
                            AAA_22   43 v.fvtlpsst.....sskdllrellralglelkaerlsseellealeqalrarav.ielliiDEaqhlr....s 105 
                                        v ++t+p+++     + +++ ++  ra+++ + +  ++    ++++++ +r+ a   +  ++DE   +     +
  gi|313126077|ref|YP_004036347.1| 1014 VeTITCPVDEpvasvDAETFDSRYERAVQVARTE-FGDDMGKRRQFQREARQGASiDRDYVVDELGEVAasveN 1086
                                        3566666666444455666666666666655555.333333335555555555555555667776665543321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.82u 0.31s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 7045.24
//
Query:       gi|313126078|ref|YP_004036348.1|  [L=180]
Description: tata-box binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-28   99.1   0.0    5.6e-17   61.5   0.0    2.1  2  TBP       Transcription factor TFIID (or TATA-binding protein
     0.0031   17.6   0.0     0.0054   16.8   0.0    1.3  1  DUF3378   Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.081   13.5   0.0       0.58   10.7   0.0    2.1  2  NLE       NLE (NUC135) domain


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   8.2e-13   4.9e-09       3      84 ..       2      86 ..       1      87 [. 0.89
   2 !   61.5   0.0   9.4e-21   5.6e-17       7      83 ..     101     177 ..      95     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 8.2e-13
                                      EEEEEEEEEE-SSCE-HHHHHHHCC.TTTEEE-TT.TSSS.EEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP  3 kiqNvvasanlgleldLeklalkae.krnaeYepe.rfpg.lvyrlrepkvtaliFssGkvvitGakseeelreaakki 78
                                      ki+++++s +lg e+dLe+l ++++ + + + e + + pg +++++ +++ +++i+++G+++i Ga  ++ l++a++++
  gi|313126078|ref|YP_004036348.1|  2 KIVSIMGSGSLGKEVDLETLVEELRdEVGESLEANfQSPGiVTVKFGDNSPAFSIYRTGSFQIRGALGHDGLNDAVDQL 80
                                      8*******************988775666666666666667999*********************************** PP

                                      HHHHHH CS
                               TBP 79 apilkk 84
                                      ++il++
  gi|313126078|ref|YP_004036348.1| 81 LEILSN 86
                                      ***987 PP

  == domain 2  score: 61.5 bits;  conditional E-value: 9.4e-21
                                       EEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
                               TBP   7 vvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83 
                                        v+  ++++ l+Le la+++  + +eYepe+fpglvyr  + ++t+liFssGkv ++G+ ++e +r ++k +++ l+
  gi|313126078|ref|YP_004036348.1| 101 AVFMHDVHQGLELEILAVHLGLEYTEYEPEQFPGLVYRPPKHEATLLIFSSGKVLVVGTAKQEVARSVLKSLLDALE 177
                                       578889999**********88*************************************************9999886 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     9e-07    0.0054      17      61 ..     123     166 ..     116     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9e-07
                           DUF3378  17 yyksklrskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61 
                                       +y++++  ++ p+ v++  k ++t  ++ SgKVl+ G+  +++A 
  gi|313126078|ref|YP_004036348.1| 123 EYTEYE-PEQFPGLVYRPPKHEATLLIFSSGKVLVVGTAKQEVAR 166
                                       677775.667*****************************999996 PP

>> NLE  NLE (NUC135) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.22   1.3e+03      30      41 ..      16      27 ..      13      38 .. 0.74
   2 ?   10.7   0.0   9.7e-05      0.58       1      42 [.      43      90 ..      43      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.22
                               NLE 30 kqLselvnkLlk 41
                                       +L++lv +L +
  gi|313126078|ref|YP_004036348.1| 16 VDLETLVEELRD 27
                                      58999*999988 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.7e-05
                               NLE  1 vqvrFvtkded.eslavpgtplsvPasltrkqLselvnkLlk.......e 42
                                      v v+F ++++  + +    +++++ + l+ ++L++ v +Ll+       e
  gi|313126078|ref|YP_004036348.1| 43 VTVKFGDNSPAfSIY--RTGSFQIRGALGHDGLNDAVDQLLEilsnidfE 90
                                      678999998886555..599**********************76544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1190.45
//
Query:       gi|313126079|ref|YP_004036349.1|  [L=1295]
Description: N-6 DNA methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-11   44.2   0.0     0.0003   20.2   0.0    3.6  3  N6_Mtase  N-6 DNA Methylase
    1.7e-11   44.5   0.5    2.7e-10   40.7   0.6    2.8  2  Eco57I    Eco57I restriction-modification methylase
    1.6e-05   24.7   0.0      0.017   14.8   0.0    3.4  3  UPF0020   Putative RNA methylase family UPF0020
    0.00035   20.6   0.0      0.001   19.1   0.0    1.8  1  TaqI_C    TaqI-like C-terminal specificity domain
  ------ inclusion threshold ------
       0.42    9.7   4.7       0.72    8.9   0.1    2.6  2  APG17     Autophagy protein Apg17


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   9.4e-05      0.34       5      42 ..     362     396 ..     358     409 .. 0.85
   2 !   20.2   0.0   8.3e-08    0.0003      49     103 ..     446     512 ..     436     520 .. 0.89
   3 !    9.2   0.0   0.00019      0.67     123     236 ..     660     800 ..     650     851 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.4e-05
                          N6_Mtase   5 llGdvYEyllrkfaeeegksgGeffTPrevsklivell 42 
                                       +lG++YE l+   ae+e  ++G f+TPr  + l+ +++
  gi|313126079|ref|YP_004036349.1| 362 MLGKIYESLI---AEQERGEAGIFYTPRVEVDLMCRMA 396
                                       79******98...66799999*******9999999886 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 8.3e-08
                          N6_Mtase  49 svyDpacGsggllvqaekvlkee............dgktkelsiyGqeknettyrLakmNlllhgie 103
                                        ++DpacGsg++lv +++v++e             ++++ + ++yG+++++ ++r+a+  l l  +e
  gi|313126079|ref|YP_004036349.1| 446 RIVDPACGSGAFLVGMKQVVTELyrklgktpdyhlKEQIINENLYGVDIKDWAVRVAEFRLWLSLVE 512
                                       59*****************9977999********9999******************99888776555 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00019
                          N6_Mtase 123 dkkfdvvvaNppfnqkew.....................kektlekde.rfrea...vapksnadla..fllhiies 172
                                       +  fd+v+ Npp+  +e                       +k+ ++d  ++ e    +   +  d+   f    +e+
  gi|313126079|ref|YP_004036349.1| 660 EGGFDIVIGNPPYVRQEDiidqgihperldkmddgevkkLKKEYKNDLvQYVEEtfdISAYKRSDIYvyFYFKGLEV 736
                                       56799999999998887678889999988888877655422222333224444467744444444333588999*** PP

                          N6_Mtase 173 lkpkGraavvlangvLfrggkegkIrkalvekdlveavi.alpeklFyntsiptcilvlkkekae 236
                                       l+++G+ + +  n  L   g ++++++al+ek  +++v+ ++ ek F    +++ i + +k ++ 
  gi|313126079|ref|YP_004036349.1| 737 LRENGTLSYITSNSWL-DIGYGKRLQQALLEKASLSTVMgNISEKAFEDADVNAYITMANKSQNG 800
                                       **********998887.5678999*************994599****************999864 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.52   1.9e+03      29      60 ..     395     432 ..     383     449 .. 0.70
   2 !   40.7   0.6   7.6e-14   2.7e-10       3     104 ..     663     798 ..     661     800 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.52
                            Eco57I  29 kdiyqkFvekalkle....dkylaliip..arflasgk 60 
                                        ++y++F ++a +l+    ++++ +i +  + + a+ +
  gi|313126079|ref|YP_004036349.1| 395 MALYEQFCDHANDLDaegkQRIVEFIFSepQDWDAESN 432
                                       578***********987777778888753366764444 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 7.6e-14
                            Eco57I   3 fdviiGNPPYqeseakkelkaleek..................................akdiyqkFvekalkle.. 43 
                                       fd++iGNPPY ++e++ ++  + e+                                   +diy++F  k+l++   
  gi|313126079|ref|YP_004036349.1| 663 FDIVIGNPPYVRQEDIIDQGIHPERldkmddgevkklkkeykndlvqyveetfdisaykRSDIYVYFYFKGLEVLre 739
                                       9*************877766555558999*****************************99*************9877 PP

                            Eco57I  44 dkylaliiparflasgkglkefrekllkdkklkklvefedskevFkdveikggilvflkdk 104
                                       +++l+ i+++ +l    ++k++++ ll++ +l++++   ++k +F+d++++  i++  k +
  gi|313126079|ref|YP_004036349.1| 740 NGTLSYITSNSWL-DIGYGKRLQQALLEKASLSTVMGNISEK-AFEDADVNAYITMANKSQ 798
                                       899**********.88899***************99877666.********9999988865 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.7e-06     0.017      27      93 ..     442     503 ..     437     518 .. 0.83
   2 !    5.0   0.0    0.0047        17      93     132 ..     636     673 ..     625     681 .. 0.77
   3 ?   -1.0   0.0      0.32   1.2e+03     129     173 ..     754     799 ..     737     813 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
                                       -TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHH CS
                           UPF0020  27 kpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgar 93 
                                         + +++DP CGsG++l+   +++++ + +l ++  ++lk+++ +e+     lyg+D++  +v+ a+
  gi|313126079|ref|YP_004036349.1| 442 LHELRIVDPACGSGAFLVGMKQVVTELYRKLGKTPDYHLKEQIINEN-----LYGVDIKDWAVRVAE 503
                                       56789*************99999999998888888888888877664.....999999998888876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0047
                                       HHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----- CS
                           UPF0020  93 reNaekagvgdliefsqadaakLrlkegevdvivtnpPYG 132
                                       r+   +ag +++  +   d+ ++   eg +d++++npPY 
  gi|313126079|ref|YP_004036349.1| 636 RNAIDEAGAAGFFMWD-IDFSDVM-VEGGFDIVIGNPPYV 673
                                       5555666666666664.4889998.8889**********6 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.32
                                       ---------HHHH.HHHHHHHHHHHHHH-TT..-EEEEEESSHHHH CS
                           UPF0020 129 pPYGerlgskkal.ekLYseflrelkrvlrgggrlvlltsenkale 173
                                         YG+rl+++     +L   +++  ++ ++    ++++t +nk+ +
  gi|313126079|ref|YP_004036349.1| 754 IGYGKRLQQALLEkASLSTVMGNISEKAFEDADVNAYITMANKSQN 799
                                       569****9997654899999*********99999999999998765 PP

>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.8e-07     0.001      34     120 .]    1102    1190 ..    1071    1190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.8e-07
                            TaqI_C   34 kelfe....ekpKilv.rdiskkldaaydekayyvlntlylliakdelevslkyllgiLNSklikfyykkiystl 103 
                                        + +++    ++p il+ r ++ k ++ ++  a++v  ++y l a +e  ++  yl g+LNS l  +++++i+s++
  gi|313126079|ref|YP_004036349.1| 1102 DPWYKqptvSDPYILLtRYVNAKYQFHFNPCAFPVADNFYYLSASEE--FDPAYLAGYLNSTL-GWFMAEISSRS 1173
                                        5566677776666766377778*********************7775..5***********86.89********* PP

                            TaqI_C  104 rggysrlkrkeleklPi 120 
                                         +   ++ ++e  +lP+
  gi|313126079|ref|YP_004036349.1| 1174 WTNALKFDKTEFMELPV 1190
                                        999*********99997 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0002      0.72     322     346 ..     195     218 ..     158     239 .. 0.71
   2 ?    1.1   1.2     0.047   1.7e+02      74     141 ..     549     611 ..     528     644 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 322 eLrefYegFlsaYdklllEveRRra 346
                                         ++fYe+++sa+d+l +E+ RR+ 
  gi|313126079|ref|YP_004036349.1| 195 VTEDFYENYKSAFDTLSKEL-RRKG 218
                                       4579****************.5554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.047
                                       IHHHHHHHHHHHHHHHHHHHHHTSS-TTS.......STGGGCS--TTTTHHHHHHHHHHHHHHH..HHHH CS
                             APG17  74 kdlikeldaanerLektlekLrktkvepsfrpegeektLlDFvdedsveelkealkesidelqa..aqkk 141
                                       ++l ++ld  ++ L + l++L+  + e    +++        + e++ve lk+ ++ +id+l++   q+ 
  gi|313126079|ref|YP_004036349.1| 549 DTLTRTLDGDTAGLLTELKELKREHFEGEADRTQ-------EIEEKQVELLKNHIDGLIDNLSKdgSQQT 611
                                       5555555555555555555555555554444443.......15566666666666666555554222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.91u 0.31s 00:00:01.22 Elapsed: 00:00:00.49
# Mc/sec: 7972.62
//
Query:       gi|313126080|ref|YP_004036350.1|  [L=77]
Description: hth domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00013   21.9   0.0    0.00015   21.6   0.0    1.2  1  HTH_11         HTH domain
    0.00015   21.6   0.0     0.0002   21.2   0.0    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00038   20.0   0.1    0.00055   19.4   0.1    1.2  1  HTH_CodY       CodY helix-turn-helix domain
    0.00043   20.0   0.0    0.00054   19.7   0.0    1.1  1  HTH_IclR       IclR helix-turn-helix domain
    0.00055   19.9   0.0    0.00062   19.8   0.0    1.1  1  HTH_20         Helix-turn-helix domain
     0.0014   18.7   0.0     0.0018   18.3   0.0    1.2  1  HTH_28         Helix-turn-helix domain
     0.0026   17.6   0.0     0.0039   17.0   0.0    1.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0032   17.2   0.1     0.0041   16.9   0.1    1.2  1  HTH_23         Homeodomain-like domain
     0.0035   17.3   0.0     0.0049   16.8   0.0    1.3  1  HTH_29         Winged helix-turn helix
     0.0045   17.3   0.0     0.0052   17.1   0.0    1.1  1  FaeA           FaeA-like protein
     0.0063   16.1   0.0     0.0092   15.5   0.0    1.2  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.037   14.0   0.1      0.047   13.7   0.1    1.2  1  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.083   13.1   0.0        0.1   12.8   0.0    1.1  1  SgrR_N         Sugar transport-related sRNA regulator N-term
       0.12   12.3   0.0       0.16   11.9   0.0    1.3  1  HTH_36         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.2e-07   0.00015      19      49 ..      36      65 ..      25      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                            HTH_11 19 eeLAeeLnvSrrtvrrdIkaLeelgvpIese 49
                                      +e+Ae  +++rrt + ++++Le+ g +++s+
  gi|313126080|ref|YP_004036350.1| 36 SEIAETVGCTRRTAYTRLQSLESEG-QVTSR 65
                                      79**********************9.77775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.6e-07    0.0002      22      57 ..      32      67 ..      29      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                       a ++eiae +g  r ++Y  L+sLe+ G V+ +k 
  gi|313126080|ref|YP_004036350.1| 32 MAGTSEIAETVGCTRRTAYTRLQSLESEGQVTSRKV 67
                                      57789**************************99874 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   4.3e-07   0.00055       3      40 ..      31      68 ..      29      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.3e-07
                          HTH_CodY  3 GrLtaskiaDriGitrsvivnaLrkLesaGiiesrsLG 40
                                      G    s+ia+ +G tr      L+ Les G + sr +G
  gi|313126080|ref|YP_004036350.1| 31 GMAGTSEIAETVGCTRRTAYTRLQSLESEGQVTSRKVG 68
                                      77778******************************998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.2e-07   0.00054       9      49 ..      23      63 ..      21      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.2e-07
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +da+ + ++  + se+A+  g ++ t++  Lq+L+ +G v+
  gi|313126080|ref|YP_004036350.1| 23 IDAIQTLDGMAGTSEIAETVGCTRRTAYTRLQSLESEGQVT 63
                                      79999999999***************************997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.8e-07   0.00062      27      60 ..      35      68 ..      21      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.8e-07
                                      HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 27 aselaerldlskntlsyHLrvLeeagLvevvreg 60
                                       se+ae++++++ t++ +L+ Le+ g v+++++g
  gi|313126080|ref|YP_004036350.1| 35 TSEIAETVGCTRRTAYTRLQSLESEGQVTSRKVG 68
                                      59*****************************998 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.4e-06    0.0018      10      41 ..      29      61 ..      23      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                            HTH_28 10 aaGh.svreaArelgisrrtvyrWikryeegGi 41
                                      ++G+   +e+A+ +g++rrt y  ++ +e++G 
  gi|313126080|ref|YP_004036350.1| 29 LDGMaGTSEIAETVGCTRRTAYTRLQSLESEGQ 61
                                      6899999***********************995 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.1e-06    0.0039      15      42 .]      30      57 ..      23      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.1e-06
                     HTH_AsnC-type 15 daRisyaeLAervGlSestvlrRvrrLe 42
                                      d+ +  +e+Ae vG+++ t+  R++ Le
  gi|313126080|ref|YP_004036350.1| 30 DGMAGTSEIAETVGCTRRTAYTRLQSLE 57
                                      788999*******************997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   3.2e-06    0.0041      20      45 ..      35      60 ..      25      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.2e-06
                            HTH_23 20 vreIAreLgvsrrTvyrwlkryreeG 45
                                      ++eIA+  g++rrT y  l+  + eG
  gi|313126080|ref|YP_004036350.1| 35 TSEIAETVGCTRRTAYTRLQSLESEG 60
                                      68**************8887765566 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.9e-06    0.0049      11      41 ..      31      61 ..      24      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.9e-06
                            HTH_29 11 GvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      G+  +s+iA+ +g++rrt y+ l   e +G 
  gi|313126080|ref|YP_004036350.1| 31 GMAGTSEIAETVGCTRRTAYTRLQSLESEGQ 61
                                      66669**********************9994 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.1e-06    0.0052       7      60 ..      24      75 ..      19      77 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.1e-06
                                      HHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS-EEEE CS
                              FaeA  7 eylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvstlWel 60
                                      + ++ + + + T+eiA+ +g +   a   L+ Le eg++    v  G s lW +
  gi|313126080|ref|YP_004036350.1| 24 DAIQTLDGMAGTSEIAETVGCTRRTAYTRLQSLESEGQVTSRKV--GNSLLWSV 75
                                      45666688889***************************987665..66778876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.2e-06    0.0092      21      48 .]      36      63 ..      33      63 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.2e-06
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +e+Ae +g ++ t  +rl+ Le+eG ++
  gi|313126080|ref|YP_004036350.1| 36 SEIAETVGCTRRTAYTRLQSLESEGQVT 63
                                      69***********************986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.6e-05     0.047      25      54 ..      36      65 ..      28      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrg 54
                                       e+A+ +G tr t    l+ L+ eg ++ +
  gi|313126080|ref|YP_004036350.1| 36 SEIAETVGCTRRTAYTRLQSLESEGQVTSR 65
                                      69***********************99844 PP

>> SgrR_N  Sugar transport-related sRNA regulator N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.1e-05       0.1      23      48 ..      36      61 ..      24      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                            SgrR_N 23 qelAdvlfCsrRhartlLkkmqeegw 48
                                      +e+A+++ C+rR a t L+ +++eg 
  gi|313126080|ref|YP_004036350.1| 36 SEIAETVGCTRRTAYTRLQSLESEGQ 61
                                      79********************9985 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.16      28      52 ..      35      59 ..      12      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                            HTH_36 28 qetlakrlglsknTvsraikeLeql 52
                                       + +a+  g+ ++T+++ +++Le  
  gi|313126080|ref|YP_004036350.1| 35 TSEIAETVGCTRRTAYTRLQSLESE 59
                                      689*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 515.37
//
Query:       gi|313126081|ref|YP_004036351.1|  [L=118]
Description: hypothetical protein Hbor_13230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 751.84
//
Query:       gi|313126082|ref|YP_004036352.1|  [L=322]
Description: hypothetical protein Hbor_13240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1977.58
//
Query:       gi|313126083|ref|YP_004036353.1|  [L=288]
Description: hypothetical protein Hbor_13250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1751.72
//
Query:       gi|313126084|ref|YP_004036354.1|  [L=317]
Description: hypothetical protein Hbor_13260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   12.5   0.0       0.16   11.8   0.0    1.2  1  RMI1_C    Recq-mediated genome instability protein 1, C-termi


Domain annotation for each model (and alignments):
>> RMI1_C  Recq-mediated genome instability protein 1, C-terminal OB-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.8e-06      0.16      39      68 ..     133     163 ..     128     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.8e-06
                            RMI1_C  39 easkgkwqlkakisDGsaildv.dlssevlt 68 
                                       ++++ +w +++++ DG++  dv  l+++vl 
  gi|313126084|ref|YP_004036354.1| 133 SKRTMTWYVHCYVHDGTGSSDViPLDDDVLD 163
                                       566678***************8358888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2153.38
//
Query:       gi|313126085|ref|YP_004036355.1|  [L=221]
Description: hypothetical protein Hbor_13270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-06   27.1   0.0    0.00017   21.6   0.0    2.6  2  RNase_H_2  RNase_H superfamily


Domain annotation for each model (and alignments):
>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   9.4e-09   0.00017       2     102 ..       7     135 ..       6     154 .. 0.70
   2 ?   -1.1   0.0     0.089   1.6e+03     144     161 ..     180     197 ..     168     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9.4e-09
                         RNase_H_2   2 ffDiEttGlspkknliyliGvldvdekeiekltqllaeepeeekail.......................elf..le 53 
                                        fDiEttG++  ++ +++ G+++  + +   ++q   +  ++ +a+                        e+f    
  gi|313126085|ref|YP_004036355.1|   7 AFDIETTGFEV-RDEVTVAGFAVPMGVR--VFVQTGGRAARDVEAAVrdrveshvqvstheservlleavETFaaER 80 
                                       69*******99.9999*****9976654..34554444444443333355555555556555555554443336567 PP

                         RNase_H_2  54 llekkkalvtfng....ksFDvpflkrlfkkyklde..eefrhiDLlkelrkkkl 102
                                       l+e +  lv+fng    ++FD+pfl++++++ ++++  +e +  DLl ++++  +
  gi|313126085|ref|YP_004036355.1|  81 LIESDVLLVAFNGelwrSGFDLPFLRTRLSRRDVEWpfREMPYADLLPVVTNRFN 135
                                       7777788******555559**********777777766999999**999977655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.089
                         RNase_H_2 144 lekilaYNedDvralatl 161
                                        + ++ +N +Dv+ +  l
  gi|313126085|ref|YP_004036355.1| 180 FTDLVVHNVADVLRTREL 197
                                       5678899999*9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1356.39
//
Query:       gi|313126086|ref|YP_004036356.1|  [L=357]
Description: hnh endonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-11   42.7   2.3    4.7e-11   42.7   2.3    1.7  2  HNH           HNH endonuclease
  ------ inclusion threshold ------
      0.013   15.4   2.4      0.032   14.1   0.1    2.2  2  PHD           PHD-finger
       0.17   12.1   1.5       0.52   10.5   1.5    1.9  1  HNH_2         HNH endonuclease


Domain annotation for each model (and alignments):
>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.1   1.2e+04      38      42 ..      29      33 ..      17      35 .. 0.72
   2 !   42.7   2.3   7.8e-15   4.7e-11       1      42 [.      51      96 ..      51     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.1
                               HNH 38 ksCHn 42
                                      ++CH 
  gi|313126086|ref|YP_004036356.1| 29 RECHE 33
                                      68996 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 7.8e-15
                               HNH  1 CeyCgrkfhks...ealevdHiipisq.ggaddieNlqllCksCHn 42
                                      C+ Cgr + ++     l+v+Hi+   +  g++d+eNl+llC+sCH+
  gi|313126086|ref|YP_004036356.1| 51 CQACGRRGPGKgglATLHVHHIERDPDgMGEHDLENLTLLCRSCHS 96
                                      ***************************9*****************8 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3     0.094   5.6e+02      38      50 ..      42      55 ..      29      58 .. 0.54
   2 ?   14.1   0.1   5.4e-06     0.032       9      28 ..      82     101 ..      78     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.094
                                      SHHSS.TBSSTTTH CS
                               PHD 38 ekpeg.ewlCekCk 50
                                      ++ e+ +  C+ C 
  gi|313126086|ref|YP_004036356.1| 42 DVLEKyKHRCQACG 55
                                      33333578888884 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.4e-06
                                       TSTTSCEEEETTTSCEEETT CS
                               PHD   9 sdeeeelvqCdgCkrwfHqk 28 
                                        d e+ +++C +C++wfHq+
  gi|313126086|ref|YP_004036356.1|  82 HDLENLTLLCRSCHSWFHQQ 101
                                       5678999***********96 PP

>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.5   8.7e-05      0.52      43      67 ..      77     101 ..      51     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.7e-05
                             HNH_2  43 kgstidspsNgllLspdiHklFdqf 67 
                                       +g + ++ +N+ lL++++H +F+q 
  gi|313126086|ref|YP_004036356.1|  77 DGMGEHDLENLTLLCRSCHSWFHQQ 101
                                       5567899***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2276.88
//
Query:       gi|313126087|ref|YP_004036357.1|  [L=69]
Description: hypothetical protein Hbor_13290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        0.2   10.2   0.0        0.2   10.1   0.0    1.0  1  PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isof


Domain annotation for each model (and alignments):
>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   1.1e-05       0.2      31      73 ..      18      56 ..      10      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 1.1e-05
                                      SEEEEEEEEE.S.SSSS-EEESS-SHHHHHHHHHHHTS-HHHH CS
                       PAF-AH_p_II 31 gvflRlyypldkadedredelWlPkkeyaqGlsevlkasrlll 73
                                       +f+Rl+y++ +     + +lW+P++     ++  lk  +++ 
  gi|313126087|ref|YP_004036357.1| 18 DLFMRLFYLSWR----GTRTLWIPSRPNNLRITTALKEASFTR 56
                                      58********55....7899*****998888888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 452.06
//
Query:       gi|313126088|ref|YP_004036358.1|  [L=173]
Description: hypothetical protein Hbor_13300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.034   13.7   0.0      0.064   12.8   0.0    1.5  1  Glycolipid_bind  Putative glycolipid-binding
       0.07   13.0   0.0       0.11   12.3   0.0    1.3  1  GFRP             GTP cyclohydrolase I feedback regulatory pro
       0.15   11.9   0.0       0.27   11.1   0.0    1.4  1  UBA_4            UBA-like domain


Domain annotation for each model (and alignments):
>> Glycolipid_bind  Putative glycolipid-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05     0.064     125     173 ..      96     147 ..      83     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                                       EEEETTTT--EEEEEEEEEEET..TEEEEEE-S..-EEEEEE-TTS-EEEET CS
                   Glycolipid_bind 125 vyvslpdleveraeqrYtrlee.esvyryesed..fsadLtvDedGlVldYp 173
                                        +v++++ + +  + +Y+ l++ ++v+ ++s++    ++L+vD++Gl +  p
  gi|313126088|ref|YP_004036358.1|  96 GFVQVKSGDASLTPAEYSDLTDeGRVFLFSSPSddGGQQLSVDQEGLTVINP 147
                                       589999999999**********99999***99999************98666 PP

>> GFRP  GTP cyclohydrolase I feedback regulatory protein (GFRP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.9e-05      0.11      30      70 ..      32      73 ..      23      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                              GFRP 30 eLgaklrkv.lgnkfkeylvedpprvvLnkLekkGykvvamt 70
                                      +L+ kl+++ +g+ f+    +d+ +vvL+ L+++G+++   +
  gi|313126088|ref|YP_004036358.1| 32 RLETKLESMgSGKLFSILDADDTEEVVLDYLQSNGWRITKYS 73
                                      5677776663466799999******************97654 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.5e-05      0.27       9      29 ..      47      69 ..      45      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.5e-05
                             UBA_4  9 aiTGade..ekArqlLeannWdL 29
                                      +i  ad+  e++ ++L++n+W +
  gi|313126088|ref|YP_004036358.1| 47 SILDADDteEVVLDYLQSNGWRI 69
                                      566774445************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1111.95
//
Query:       gi|313126089|ref|YP_004036359.1|  [L=174]
Description: hypothetical protein Hbor_13310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0049   16.7   0.0     0.0089   15.9   0.0    1.4  1  HHH             Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.03   14.2   0.5      0.044   13.7   0.5    1.2  1  Helicase_IV_N   DNA helicase IV / RNA helicase N terminal
      0.091   13.1   0.0       0.25   11.7   0.0    1.7  2  Transposase_20  Transposase IS116/IS110/IS902 family
       0.17   12.0   0.0       0.42   10.7   0.0    1.6  2  HHH_2           Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     2e-06    0.0089      10      29 ..      90     109 ..      82     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                                       HHHHHTSTT-SHHHHHHHHH CS
                               HHH  10 reeLlalPGVGpktAeaIls 29 
                                       ++ L ++PG+G +tA ++l 
  gi|313126089|ref|YP_004036359.1|  90 LKTLSSIPGIGSATATVVLT 109
                                       789*************9996 PP

>> Helicase_IV_N  DNA helicase IV / RNA helicase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   9.7e-06     0.044      88     128 ..       6      46 ..       3      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.7e-06
                     Helicase_IV_N  88 yqqWskeqvqaladvlqkkeeeieefvqqqkylstsevanl 128
                                       +++W++   +  +++l++ e++++e+ q+q+y+++s+++++
  gi|313126089|ref|YP_004036359.1|   6 ISNWAEAYDESYDEELHEIEQTLHETLQEQRYITQSQLRDV 46 
                                       789**********************************9876 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   6.1e+03      45      66 ..      53      75 ..      51      81 .. 0.63
   2 ?   11.7   0.0   5.5e-05      0.25       2      22 ..      91     111 ..      90     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                    Transposase_20 45 nqSGkkkr.rgriskrGnrrlRr 66
                                      nq G++++   r+++  ++ +Rr
  gi|313126089|ref|YP_004036359.1| 53 NQAGRRSGnIERVNRVPDAFVRR 75
                                      56666666556666666666665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.5e-05
                    Transposase_20   2 elLesipGiGpvtaaallaei 22 
                                       + L+sipGiG  ta+++l   
  gi|313126089|ref|YP_004036359.1|  91 KTLSSIPGIGSATATVVLTFY 111
                                       579***********9998755 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         2   9.1e+03      27      37 ..      22      32 ..      16      40 .. 0.57
   2 ?   10.7   0.0   9.4e-05      0.42      33      58 ..      89     114 ..      86     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2
                             HHH_2 27 daLkkasleeL 37
                                       +++++  e+L
  gi|313126089|ref|YP_004036359.1| 22 HEIEQTLHETL 32
                                      34444444444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.4e-05
                             HHH_2  33 sleeLlevddiGeeiAqsivefFene 58 
                                       +l++L+++++iG  +A+ + +f++ e
  gi|313126089|ref|YP_004036359.1|  89 QLKTLSSIPGIGSATATVVLTFYDPE 114
                                       6889******************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1082.09
//
Query:       gi|313126090|ref|YP_004036360.1|  [L=287]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-05   23.7   0.0      0.017   15.5   0.0    2.7  2  CBS              CBS domain
  ------ inclusion threshold ------
      0.091   11.5   0.0       0.12   11.1   0.0    1.1  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
       0.11   12.5   0.1       0.16   11.9   0.1    1.3  1  HEPN_RiboL-PSP   RiboL-PSP-HEPN


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.9e-06     0.017       2      51 ..      11      59 ..      10      61 .. 0.91
   2 !    5.2   0.0     0.005        30      13      51 ..      82     117 ..      76     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-06
                                      HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51
                                      +++ t+ v  +  dt+ + a+e ++e+g+++ PV  +d+ ++G +++ D+
  gi|313126090|ref|YP_004036360.1| 11 AELATHSVEHLQHDTPPGTAAEWLAENGYDAAPVYANDD-PIGFIHKDDV 59
                                      57889999999*************9999******97688.********98 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.005
                                       ETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS  13 ppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                       + dt+  ++l  ++e+ v  +    + +++ Gi+t+ Dl
  gi|313126090|ref|YP_004036360.1|  82 SGDTSFTDVLSALIENPV-YF-L-GGHNHVTGILTRADL 117
                                       567777788877767334.33.4.67888********98 PP

>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.1e-05      0.12     112     181 ..     131     198 ..      97     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.1e-05
                                       HHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSEEEEEEES--HHHHHHHHHHHHHT CS
                   AdoMet_Synthase 112 eylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtSfgvgyaplseleklvleterlln 181
                                        yl+e+lr+l l+++   +++    +++L d+ +r ++  ++aN +   + ya +s+le++v+++e   +
  gi|313126090|ref|YP_004036360.1| 131 TYLEEHLRELILDTKPDWKTT-PVTADELDDIEDRYED-AQAANVALEEIHYAQFSTLETIVTSVEACWQ 198
                                       577777777766655444433.34578999*9999776.79************************98765 PP

>> HEPN_RiboL-PSP  RiboL-PSP-HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.6e-05      0.16     146     188 ..     202     261 ..     154     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                    HEPN_RiboL-PSP 146 k.......kklnelvkrRNeIAHgnds..........dtdltkdeleeyidfikelveal 188
                                               ++l e  ++RN++AH n            +++ t + l+++++ i++++ +l
  gi|313126090|ref|YP_004036360.1| 202 FstkggadSRLHEVTDLRNDVAHANLLventdsneflSNGRTTENLYNTLETINDVLSNL 261
                                       04555666899************5555555556777888888888888888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1729.33
//
Query:       gi|313126091|ref|YP_004036361.1|  [L=118]
Description: hypothetical protein Hbor_13330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 818.87
//
Query:       gi|313126092|ref|YP_004036362.1|  [L=89]
Description: hypothetical protein Hbor_13340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 577.88
//
Query:       gi|313126093|ref|YP_004036363.1|  [L=302]
Description: ADP-ribosylglycohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-71  240.3   3.1    4.1e-71  240.1   3.1    1.1  1  ADP_ribosyl_GH   ADP-ribosylglycohydrolase
  ------ inclusion threshold ------
      0.023   14.4   3.6      0.063   13.0   2.3    2.1  2  Gly-zipper_YMGG  YMGG-like Gly-zipper
      0.096   12.4   0.1       0.14   11.9   0.1    1.3  1  SurE             Survival protein SurE
       0.36   10.7   7.6      0.052   13.4   3.2    2.0  2  Rick_17kDa_Anti  Glycine zipper 2TM domain


Domain annotation for each model (and alignments):
>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.1   3.1   9.1e-75   4.1e-71       1     291 []       8     280 ..       8     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 240.1 bits;  conditional E-value: 9.1e-75
                                       HHHHHHHHHHHHHGGGTT--HHHHHHHTSS--S-----STTTTTS-TT---HHHHHHHHHHHTEET.TEE-HHHHHH CS
                    ADP_ribosyl_GH   1 GallGaavGDAlGlpvefwsydeirrrygelgetpdktgfghfglkpgewtddtqmalllleslleaggldpedlar 77 
                                       G llG+a GDAlG pvef s +ei+ ++g+l+   ++ g+g++++++g++tddt++al++++sl+e++ +dp+d+ +
  gi|313126093|ref|YP_004036363.1|   8 GILLGLAYGDALGRPVEFTSASEIETEHGRLD---EMVGHGTWNQPAGTITDDTEQALCIARSLVEHQAFDPADISE 81 
                                       88****************************98...9***************************************** PP

                                       HHHH.HHT....T--SS--HHHHHHHHHTTTT-...-S-B.........---BTTTGGG-HHHHHHTSS-HHHHHHH CS
                    ADP_ribosyl_GH  78 rflaeWleepgdteprgignttrealrnlksgepppeagana......ngsagngalmRaaplgllyagdpeeaael 148
                                       rf+a W++    + p++ig+ t+++l++lk+g+++ eag++        + agng++mR++pl++ ya d +++ae+
  gi|313126093|ref|YP_004036363.1|  82 RFVA-WYD----SGPFDIGRMTMRSLSRLKHGDEWDEAGQHVweqsreGQNAGNGSVMRCPPLAIPYATDWDRLAEV 153
                                       ****.***....899*************************99*********************************** PP

                                       HHHHHHTTB--HHHHHHHHHHHHHHHHHHTT-..-STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH...... CS
                    ADP_ribosyl_GH 149 aeeaarlTHnhpeavagaaayaaliaaalrgk..sleealdaaeeelavapaeeelaaalrkalaladsdkdvdvda 223
                                       +++++++TH++p++ ag+a++++++a +l  +  +le+ald           + ++ ++l  a +   +++      
  gi|313126093|ref|YP_004036363.1| 154 SRQSSQITHADPRCTAGCAILNLTVAGLLADAetPLEDALDYV---------STDVPDELLTAFRPLARGE------ 215
                                       ****************************666522466666666.........4455555555666555555...... PP

                                       ..HHHHH--SSBHHHHHHHHHHHHHH.-SSHHHHHHHHHTS-SSHHHHHHHHHHHHHHHH-GGGS-HH CS
                    ADP_ribosyl_GH 224 eeavdelgsggyavealaaalyallhaaddfeeallaavnlGgDtdttgaiaGallGalyGleaiPee 291
                                         + d l ++gy+v++l++al+  l  ad+ e+a+  avn GgDtdt+gaiaGa++Ga++G++++P++
  gi|313126093|ref|YP_004036363.1| 216 --SPDTLETSGYVVHSLQTALHDGLV-ADSAEDAIVTAVNRGGDTDTIGAIAGAVAGARFGASQLPDR 280
                                       ..6777999*****************.99*************************************85 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.27   1.2e+03       8      22 ..       6      20 ..       4      25 .. 0.63
   2 ?   13.0   2.3   1.4e-05     0.063       8      29 ..     259     284 ..     249     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.27
                                      XXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  8 aiGAaaGAvvGaliG 22
                                      a G  +G + G++ G
  gi|313126093|ref|YP_004036363.1|  6 ARGILLGLAYGDALG 20
                                      455566666666655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.4e-05
                                       XXXXXXXXXXXXXXX....XXXXXXX CS
                   Gly-zipper_YMGG   8 aiGAaaGAvvGaliG....sgggkGA 29 
                                        iGA+aGAv+Ga +G     +++ GA
  gi|313126093|ref|YP_004036363.1| 259 TIGAIAGAVAGARFGasqlPDRWLGA 284
                                       58999999999999976666666666 PP

>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.2e-05      0.14      59     118 ..     215     275 ..     151     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                                       TTTCEEEESS-HHHHHHHHHHTTTTTS..SSEEEEEEEES---GGGGGG-HHHHHHHHHHH CS
                              SurE  59 eeeeeyavsGtPadcvklaleellkek.kpdlVvSGiNhGaNlgtdvlySGTvgAaleaal 118
                                       e+ +  ++sG  +   ++al+  l ++ ++d +v+ +N+G  + t     G v++a+ +a 
  gi|313126093|ref|YP_004036363.1| 215 ESPDTLETSGYVVHSLQTALHDGLVADsAEDAIVTAVNRGGDTDTIGAIAGAVAGARFGAS 275
                                       455667789999999999998766655478***************99*********99875 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       2.4   1.1e+04      23      30 ..       5      12 ..       3      20 .. 0.61
   2 ?   13.4   3.2   1.2e-05     0.052      18      39 ..     253     274 ..     246     285 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.4
                   Rick_17kDa_Anti 23 rvlGavvG 30
                                      r++G+++G
  gi|313126093|ref|YP_004036363.1|  5 RARGILLG 12
                                      66666666 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.2e-05
                   Rick_17kDa_Anti  18 gggggrvlGavvGAaaGavaGn 39 
                                       +gg+ +++Ga++GA+aGa  G+
  gi|313126093|ref|YP_004036363.1| 253 RGGDTDTIGAIAGAVAGARFGA 274
                                       5667777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1820.68
//
Query:       gi|313126094|ref|YP_004036364.1|  [L=573]
Description: adaptin n terminal region protein, partial [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-13   48.4  28.7    3.7e-06   27.2   2.5    4.3  4  HEAT_2        HEAT repeats
    3.2e-11   43.5  11.3      6e-05   23.5   0.2    7.2  9  HEAT_EZ       HEAT-like repeat
    1.3e-10   41.6   0.1    7.7e-06   26.0   0.0    3.4  3  Cnd1          non-SMC mitotic condensation complex subunit 1
    3.2e-10   39.2   0.0    1.5e-09   37.0   0.0    1.9  2  Adaptin_N     Adaptin N terminal region
    3.8e-08   32.9  14.6      0.034   14.4   0.0    7.1  8  HEAT          HEAT repeat
    5.5e-07   29.4   9.3     0.0001   22.2   0.0    5.8  6  Arm           Armadillo/beta-catenin-like repeat
    0.00048   19.6   1.7     0.0032   16.9   0.8    2.1  2  DUF5578       Family of unknown function (DUF5578)
     0.0045   16.2   0.0      0.011   15.0   0.0    1.6  1  Cnd3          Nuclear condensing complex subunits, C-term dom
     0.0052   15.7   1.2        1.5    7.6   0.1    2.3  2  API5          Apoptosis inhibitory protein 5 (API5)
  ------ inclusion threshold ------
      0.027   14.1   0.0      0.074   12.6   0.0    1.7  1  CLASP_N       CLASP N terminal
      0.049   13.9   0.3        6.9    7.1   0.1    3.1  3  Cohesin_HEAT  HEAT repeat associated with sister chromatid co
      0.051   13.4   0.2       0.85    9.4   0.1    2.3  2  DUF3088       Protein of unknown function (DUF3088)
      0.052   12.7   0.0        1.7    7.7   0.0    2.6  3  MMS19_C       RNAPII transcription regulator C-terminal


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.7     0.024        34      16      83 ..     271     348 ..     253     353 .. 0.59
   2 !    9.4   6.8     0.001       1.4       6      87 ..     299     389 ..     294     390 .. 0.73
   3 !   27.2   2.5   2.7e-09   3.7e-06       2      84 ..     368     460 ..     367     464 .. 0.74
   4 !   26.5   3.4   4.6e-09   6.3e-06       5      87 ..     482     569 ..     478     570 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.024
                            HEAT_2  16 vrraai.raLg....ri.gnpealpaLvellededpavRraaaeaLgaig..dpeal.paLkelldddd.ddvvRea 82 
                                        rr+a+  a+g    r  + + a++a + ll de +a  raa +aL + +  dp +l ++ +el++  + d+  ++a
  gi|313126094|ref|YP_004036364.1| 271 DRREALrLAMGavkhRAdAREVAVNATFALLGDEPSALDRAALQALHETAadDPTVLkEHVAELAAYASqDSMYQAA 347
                                       46666623444443322123367999999999999999999999998775334554334555544333213444444 PP

                            HEAT_2  83 A 83 
                                       A
  gi|313126094|ref|YP_004036364.1| 348 A 348
                                       4 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.001
                            HEAT_2   6 qalendpdpevrraairaLg..rignpea.lpaLvell..ededpavRraaaeaLgaigdpe......alpaLkell 71 
                                       ++l  d+  ++ raa++aL     ++p++  + + el+   ++d++ ++aa + L ++++ +      a+paL++++
  gi|313126094|ref|YP_004036364.1| 299 ALL-GDEPSALDRAALQALHetAADDPTVlKEHVAELAayASQDSMYQAAATRCLMELAEADpasvldAVPALEAAA 374
                                       566.9***************53345565533334445545579999************853333667799******* PP

                            HEAT_2  72 ddddddvvReaAaeaL 87 
                                       + ++++  +  A+ aL
  gi|313126094|ref|YP_004036364.1| 375 TAETEAT-QSYAVYAL 389
                                       9998876.77777776 PP

  == domain 3  score: 27.2 bits;  conditional E-value: 2.7e-09
                            HEAT_2   2 daLlqalendpdpevrraairaLg...rignp...ealpaLvellededpavRraaaeaLgai......gdpealpa 66 
                                       +aL +a+ + + ++++  a+ aL    +  ++    a++aL+e++++ed+ v+ +a  aLg+i      g +  ++ 
  gi|313126094|ref|YP_004036364.1| 368 PALEAAA-TAETEATQSYAVYALScvaEAYPEevsPAIDALIEAMQSEDETVQTNALAALGKIasnypdGAEPPVDE 443
                                       5666666.89999999999999997763333334456**************************44333333447999 PP

                            HEAT_2  67 LkellddddddvvReaAa 84 
                                       L   ld d + +vR+ A+
  gi|313126094|ref|YP_004036364.1| 444 LVTVLDADAK-RVRNNAV 460
                                       9999987655.5577776 PP

  == domain 4  score: 26.5 bits;  conditional E-value: 4.6e-09
                            HEAT_2   5 lqalendpdpevrraairaLgrignp..ea....lpaLvellededpavRraaaeaLgaigdpealpaLkelldddd 75 
                                        ++l +d + + r +a +aL r g+    a    ++ L ++led++p+vR++++  +g    +  ++ L+e   +d 
  gi|313126094|ref|YP_004036364.1| 482 AARL-EDNNIQARVNASIALHRAGEAspAAiraqQDRLESALEDSSPEVRANVCSLIGNAYVSVPIDMLEEVKENDL 557
                                       5677.89**************9987644225556***************************9999************ PP

                            HEAT_2  76 ddvvReaAaeaL 87 
                                       d+ vRe+A++a+
  gi|313126094|ref|YP_004036364.1| 558 DETVRERAEWAI 569
                                       *********998 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.5     1e+04       8      14 ..      39      47 ..      39      54 .. 0.67
   2 ?   -0.5   1.0       1.4   1.9e+03       4      48 ..     272     312 ..     272     317 .. 0.60
   3 ?   -0.0   1.4      0.98   1.3e+03       6      52 ..     311     352 ..     306     366 .. 0.56
   4 !    7.9   1.1    0.0032       4.4       3      53 ..     344     390 ..     342     392 .. 0.89
   5 !   23.5   0.2   4.3e-08     6e-05       7      55 .]     385     429 ..     379     429 .. 0.91
   6 !   23.4   0.2   4.4e-08   6.1e-05       3      53 ..     418     464 ..     417     466 .. 0.95
   7 !   13.7   0.3   5.1e-05      0.07       2      52 ..     454     500 ..     453     502 .. 0.95
   8 !   12.4   0.1   0.00013      0.17      32      54 ..     517     539 ..     505     540 .. 0.91
   9 ?   -0.9   0.0       1.8   2.5e+03      42      55 .]     559     572 ..     555     572 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.5
                           HEAT_EZ  8 awaLGr..l 14
                                      +wa+G+  l
  gi|313126094|ref|YP_004036364.1| 39 VWAIGNqdL 47
                                      688887664 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                           HEAT_EZ   4 RraAaw.aLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaA 48 
                                       Rr A++ a+G++  +++++ + +v +  ++L+     d++ +   aA
  gi|313126094|ref|YP_004036364.1| 272 RREALRlAMGAVK-HRADAREVAVNATFALLG-----DEPsALDRAA 312
                                       7888888999777.555555555555555555.....5552554444 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.98
                           HEAT_EZ   6 aAawaLGrlaggepellqplvpeilpaLlalLnddsdeV.RaaAagaL 52 
                                       aA+ aL     + + +++++++e +++L+a    ++d+  +aaA ++L
  gi|313126094|ref|YP_004036364.1| 311 AALQAL----HETAADDPTVLKEHVAELAAYA--SQDSMyQAAATRCL 352
                                       666666....4444444444444444444444..55544455555554 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0032
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLg 53 
                                        ++aA ++L++la+  p  +     +++paL a+ + +  +++ +A++aL+
  gi|313126094|ref|YP_004036364.1| 344 YQAAATRCLMELAEADPASVL----DAVPALEAAATAETEATQSYAVYALS 390
                                       6899999**999977777777....*************************8 PP

  == domain 5  score: 23.5 bits;  conditional E-value: 4.3e-08
                           HEAT_EZ   7 AawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       A+ aL+++a+  pe ++p++++++ a+      ++d +V+++A+ aLg++
  gi|313126094|ref|YP_004036364.1| 385 AVYALSCVAEAYPEEVSPAIDALIEAMQ-----SEDeTVQTNALAALGKI 429
                                       999**99**********99999999999.....999788*********97 PP

  == domain 6  score: 23.4 bits;  conditional E-value: 4.4e-08
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLg 53 
                                       v+ +A++aLG +a++ p+  +p v+e++  L       ++ +VR +A+g Lg
  gi|313126094|ref|YP_004036364.1| 418 VQTNALAALGKIASNYPDGAEPPVDELVTVLD-----ADAkRVRNNAVGLLG 464
                                       7999****************************.....9999**********9 PP

  == domain 7  score: 13.7 bits;  conditional E-value: 5.1e-05
                           HEAT_EZ   2 rvRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaL 52 
                                       rvR++A+  LG la++ p  +  + ++i + L      d+    R +A +aL
  gi|313126094|ref|YP_004036364.1| 454 RVRNNAVGLLGDLAQEHPAVVIEYADQIAARLE-----DNNiQARVNASIAL 500
                                       8********************************.....999777*****998 PP

  == domain 8  score: 12.4 bits;  conditional E-value: 0.00013
                           HEAT_EZ  32 aLlalLnddsdeVRaaAagaLgn 54 
                                        L ++L+d+s+eVRa+++  +gn
  gi|313126094|ref|YP_004036364.1| 517 RLESALEDSSPEVRANVCSLIGN 539
                                       68999**************9998 PP

  == domain 9  score: -0.9 bits;  conditional E-value: 1.8
                           HEAT_EZ  42 deVRaaAagaLgnl 55 
                                        +VR+ A +a+++l
  gi|313126094|ref|YP_004036364.1| 559 ETVRERAEWAISRL 572
                                       47888888888886 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.045        62      53     129 ..     324     398 ..     279     401 .. 0.65
   2 !    8.5   0.0    0.0013       1.8      48      88 ..     392     432 ..     366     452 .. 0.69
   3 !   26.0   0.0   5.6e-09   7.7e-06       2      81 ..     455     536 ..     454     542 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.045
                              Cnd1  53 mvkekgflselaklleDenprVvanalaalteiseksenaiynllpdiisklsdalnecsewgqitilefLlsyipk 129
                                           k++++ela     ++++ +a a  +l+e++e ++  ++  +p +      a +e+++   ++ l+++++  p+
  gi|313126094|ref|YP_004036364.1| 324 PTVLKEHVAELAAY-ASQDSMYQAAATRCLMELAEADPASVLDAVPALEAAAT-AETEATQSYAVYALSCVAEAYPE 398
                                       44444455555443.33566777788888888888887777777776655555.66777777777777777776665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
                              Cnd1  48 LilndmvkekgflselaklleDenprVvanalaalteisek 88 
                                       + ++   +++  ++ l ++++ e+++V++nalaal +i+++
  gi|313126094|ref|YP_004036364.1| 392 VAEAYPEEVSPAIDALIEAMQSEDETVQTNALAALGKIASN 432
                                       33334445556677777777777777777777777777765 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 5.6e-09
                              Cnd1   2 iRalairtlg..cirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVva 76 
                                       +R++a+  lg  +   p++v ++ +++ +rL+D++ + R +a i++ +  ++     + + ++l+++leD++p+V+a
  gi|313126094|ref|YP_004036364.1| 455 VRNNAVGLLGdlAQEHPAVVIEYADQIAARLEDNNIQARVNASIALHRAGEASPAAIRAQQDRLESALEDSSPEVRA 531
                                       9**********99************************************888888888999**************** PP

                              Cnd1  77 nalaa 81 
                                       n+ ++
  gi|313126094|ref|YP_004036364.1| 532 NVCSL 536
                                       *8765 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.1e-12   1.5e-09     258     510 ..     283     530 ..     246     536 .. 0.89
   2 !    7.9   0.0   0.00071      0.98      95     209 ..     455     569 ..     452     572 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.1e-12
                                       CCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXXTTTTTTTCCCCSXXTTSXHHHHHHHHHHHCCCX.. CS
                         Adaptin_N 258 lapknelivlavnaLvrllsskdenlryvaLrtllkivkkepkavqhldlkifllktdddvsirlkaldlllklv.. 332
                                       ++ ++++++ avna   ll +++ +l  +aL++l++ +  +p+ ++++  ++     ++d+  +  a  +l++l+  
  gi|313126094|ref|YP_004036364.1| 283 VKHRADAREVAVNATFALLGDEPSALDRAALQALHETAADDPTVLKEHVAELAAYA-SQDSMYQAAATRCLMELAea 358
                                       5556678999*******************************777779999999888.999999***********822 PP

                                       XTTTHHHHHHHHHHHTTSSXXHHHHHHHHHHHHHHHHHSCCHHHHHHHHHHHHHTTXXHHHHHHHHHHHHHHHHHST CS
                         Adaptin_N 333 desNvkeivkeLkkyvkevadedfksklvkaIgrlaekfatdaewvldvllellslsgesvkdeivevirdliqkvp 409
                                       d  +v   v  L   +  + +e   s +v+a++ +ae+++++++  +d l+e +++++e+v+  +++++ ++ +++p
  gi|313126094|ref|YP_004036364.1| 359 DPASVLDAVPALEAAA-TAETEATQSYAVYALSCVAEAYPEEVSPAIDALIEAMQSEDETVQTNALAALGKIASNYP 434
                                       45677778999*9999.665677****************************************************** PP

                                       TTSTTCHHHHCCTCCGXXSHHHHHHHHHHHHHTTTTXTT...HHHHHHCTTTTTTTSXHHHHHHHHHHHHHHHHCXG CS
                         Adaptin_N 410 elheeiiekLaellekieseearaaaiWllGeygelvsntesasdllrslaekfvlesekvklqiltalvKlyltsp 486
                                       +  e  + +L+ +l++ + + +r++a+ llG  +++ +    + ++   +a ++ +++ +++ ++  al + ++ sp
  gi|313126094|ref|YP_004036364.1| 435 DGAEPPVDELVTVLDA-DAKRVRNNAVGLLGDLAQEHPA--VVIEYADQIAARLEDNNIQARVNASIALHRAGEASP 508
                                       ************9986.8889******************..*************************99999999999 PP

                                       CC.THXHHHHHHHHHHHXXSHHHH CS
                         Adaptin_N 487 dketqekliqlvlslatssdlevr 510
                                            +  ++ ++s +++s+ evr
  gi|313126094|ref|YP_004036364.1| 509 A--AIRAQQDRLESALEDSSPEVR 530
                                       4..344667777777778788887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00071
                                       HHHHHHHHHCCC-..-CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHH CS
                         Adaptin_N  95 irglALrvLssir..vpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvv 169
                                       +r++A+  L+++    p ++   a++i + l+d + + r +A +a+ +  +++p ++r q  ++++++l+d++p v 
  gi|313126094|ref|YP_004036364.1| 455 VRNNAVGLLGDLAqeHPAVVIEYADQIAARLEDNNIQARVNASIALHRAGEASPAAIRAQ-QDRLESALEDSSPEVR 530
                                       577888888888866677778889999999999999***********************9.**************** PP

                                       HHHHHHHHHHHCCCCCCCHHHHHH.HCCHHHHHHCS-HHHH CS
                         Adaptin_N 170 laAvalleeikkndrlllkllpkl.vrrLcnllteldpwlq 209
                                       +++ +l+    +     +++l++   + L++ + e  +w++
  gi|313126094|ref|YP_004036364.1| 531 ANVCSLIGNA-YVSVP-IDMLEEVkENDLDETVRERAEWAI 569
                                       *****99888.43333.244444314456667777777766 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         7   9.6e+03       4      12 ..     255     266 ..     254     277 .. 0.67
   2 ?    1.5   0.2      0.33   4.6e+02      13      29 ..     341     357 ..     334     358 .. 0.81
   3 ?   -1.8   0.1         4   5.5e+03       3      29 ..     368     394 ..     367     396 .. 0.77
   4 !   14.4   0.0   2.5e-05     0.034       2      30 ..     404     432 ..     403     433 .. 0.93
   5 !    6.7   0.0    0.0075        10       7      29 ..     446     468 ..     441     470 .. 0.81
   6 ?    0.5   0.0       0.7   9.7e+02       5      25 ..     481     501 ..     479     505 .. 0.86
   7 !   12.6   0.0   9.2e-05      0.13       5      26 ..     518     539 ..     515     541 .. 0.89
   8 ?   -0.2   0.0       1.2   1.7e+03      10      27 ..     555     572 ..     547     572 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7
                                       HHHHHHT-...S CS
                              HEAT   4 lllkllsD...p 12 
                                       +l+++lsD   +
  gi|313126094|ref|YP_004036364.1| 255 TLQTMLSDapaD 266
                                       689999995443 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.33
                                       SHHHHHHHHHHHHHHHH CS
                              HEAT  13 speVReaAakaLgalae 29 
                                       ++   +aA ++L +lae
  gi|313126094|ref|YP_004036364.1| 341 DSMYQAAATRCLMELAE 357
                                       556678*********98 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4
                                       HHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgalae 29 
                                       P+l  + + +     + A++aL  +ae
  gi|313126094|ref|YP_004036364.1| 368 PALEAAATAETEATQSYAVYALSCVAE 394
                                       777777788888888899999987776 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHT-SSHHHHHHHHHHHHHHHHC CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgalaev 30 
                                       +++l++++++++  V  +A+ aLg++a++
  gi|313126094|ref|YP_004036364.1| 404 IDALIEAMQSEDETVQTNALAALGKIASN 432
                                       57899**********************97 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0075
                                       HHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   7 kllsDpspeVReaAakaLgalae 29 
                                       + l  ++ +VR +A+  Lg+la+
  gi|313126094|ref|YP_004036364.1| 446 TVLDADAKRVRNNAVGLLGDLAQ 468
                                       556677788************98 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.7
                                       HHHHHT-SSHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLg 25 
                                       +   l+D++ + R +A  aL 
  gi|313126094|ref|YP_004036364.1| 481 IAARLEDNNIQARVNASIALH 501
                                       66789***********99996 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 9.2e-05
                                       HHHHHT-SSHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLga 26 
                                       l ++l+D+speVR++++  +g+
  gi|313126094|ref|YP_004036364.1| 518 LESALEDSSPEVRANVCSLIGN 539
                                       7889**************9996 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 1.2
                                       T-SSHHHHHHHHHHHHHH CS
                              HEAT  10 sDpspeVReaAakaLgal 27 
                                       +D +  VRe A +a+ +l
  gi|313126094|ref|YP_004036364.1| 555 NDLDETVRERAEWAISRL 572
                                       788999*****9999875 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.51     7e+02      23      36 ..     339     352 ..     331     356 .. 0.83
   2 ?   -0.3   0.1      0.93   1.3e+03      13      37 ..     366     390 ..     362     390 .. 0.87
   3 !   22.2   0.0   7.6e-08    0.0001      12      41 .]     402     431 ..     400     431 .. 0.93
   4 ?    4.3   0.0     0.032        44      14      40 ..     441     467 ..     441     468 .. 0.91
   5 ?    1.5   0.0      0.25   3.5e+02      19      38 ..     520     539 ..     516     540 .. 0.86
   6 ?   -0.1   0.0      0.81   1.1e+03      23      39 ..     556     572 ..     546     572 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.51
                                       TSSHHHHHHHHHHH CS
                               Arm  23 sedeevqeeAawAL 36 
                                       s+d ++q +A+++L
  gi|313126094|ref|YP_004036364.1| 339 SQDSMYQAAATRCL 352
                                       99**********99 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.93
                                       HHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeAawALs 37 
                                       avp+L +  + e e +q  A+ ALs
  gi|313126094|ref|YP_004036364.1| 366 AVPALEAAATAETEATQSYAVYALS 390
                                       6999999999999999*99999997 PP

  == domain 3  score: 22.2 bits;  conditional E-value: 7.6e-08
                                       THHHHHHHHTTTSSHHHHHHHHHHHHHHTT CS
                               Arm  12 GavppLvrLLssedeevqeeAawALsNLaa 41 
                                        a+++L++ ++sede+vq++A++AL+ +a+
  gi|313126094|ref|YP_004036364.1| 402 PAIDALIEAMQSEDETVQTNALAALGKIAS 431
                                       59************************9986 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.032
                                       HHHHHHHTTTSSHHHHHHHHHHHHHHT CS
                               Arm  14 vppLvrLLssedeevqeeAawALsNLa 40 
                                       v+ Lv+ L+ +  +v+ +A++ L+ La
  gi|313126094|ref|YP_004036364.1| 441 VDELVTVLDADAKRVRNNAVGLLGDLA 467
                                       6789******************99776 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.25
                                       HHTTTSSHHHHHHHHHHHHH CS
                               Arm  19 rLLssedeevqeeAawALsN 38 
                                       + L++ ++ev+ ++++ ++N
  gi|313126094|ref|YP_004036364.1| 520 SALEDSSPEVRANVCSLIGN 539
                                       568899************99 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.81
                                       TSSHHHHHHHHHHHHHH CS
                               Arm  23 sedeevqeeAawALsNL 39 
                                       + de+v+e A wA+s L
  gi|313126094|ref|YP_004036364.1| 556 DLDETVRERAEWAISRL 572
                                       6799*********9966 PP

>> DUF5578  Family of unknown function (DUF5578)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.8   2.3e-06    0.0032     152     250 ..     331     430 ..     327     450 .. 0.87
   2 ?    1.4   0.0      0.13   1.7e+02     161     248 ..     452     539 ..     441     553 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                           DUF5578 152 vaeclak.skseetqeeaqklleslaegnPkyqkqvykgliallacsspkaqqlalqtlrvvqeivkeakpsivepl 227
                                       vae+ a  s+ +  q++a + l +lae++P        +l a  ++++  +q +a+ +l +v e+ +e  +  +++l
  gi|313126094|ref|YP_004036364.1| 331 VAELAAYaSQDSMYQAAATRCLMELAEADPASVLDAVPALEAAATAETEATQSYAVYALSCVAEAYPEEVSPAIDAL 407
                                       6777664266677899999********************************************************** PP

                           DUF5578 228 lelLkslhlevqyeaielikelm 250
                                       +e+++s +  vq++a+  + +++
  gi|313126094|ref|YP_004036364.1| 408 IEAMQSEDETVQTNALAALGKIA 430
                                       ***************99887766 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                           DUF5578 161 seetqeeaqklleslaegnPkyqkqvykgliallacsspkaqqlalqtlrvvqeivkeakpsivepllelLkslhle 237
                                        ++++++a  ll  la+  P       +++ a l+ +  +a+  a  +l+ + e+ ++a ++  ++l ++L+    e
  gi|313126094|ref|YP_004036364.1| 452 AKRVRNNAVGLLGDLAQEHPAVVIEYADQIAARLEDNNIQARVNASIALHRAGEASPAAIRAQQDRLESALEDSSPE 528
                                       45677888889999999999999888888999999999999999999999999999999999999999999999999 PP

                           DUF5578 238 vqyeaielike 248
                                       v++++ +li +
  gi|313126094|ref|YP_004036364.1| 529 VRANVCSLIGN 539
                                       99999999865 PP

>> Cnd3  Nuclear condensing complex subunits, C-term domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.7e-06     0.011      31     141 ..     407     534 ..     389     537 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.7e-06
                                       HHHHHC-SSHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHH-CGGGGGGHH... CS
                              Cnd3  31 ilpavrskeaairelglkcLglfclldkklakenlklflqalskgneelkiialkaifDllllhglevldkekkeds 107
                                       ++ a++s+++ ++ ++l +Lg  +  + + a+  ++ ++++l  + ++++  a+  + Dl+  h++ v++ +++   
  gi|313126094|ref|YP_004036364.1| 407 LIEAMQSEDETVQTNALAALGKIASNYPDGAEPPVDELVTVLDADAKRVRNNAVGLLGDLAQEHPAVVIEYADQIAA 483
                                       689****************************************99***********************988888777 PP

                                       .............................HHHHHHHHHHC-TT-HHHHHHHH CS
                              Cnd3 108 d.eeeees.................essksllkllykaLdsednpelqaiaa 141
                                         e+++ +                    +   + l +aL++ ++pe++a ++
  gi|313126094|ref|YP_004036364.1| 484 RlEDNNIQarvnasialhrageaspAAIRAQQDRLESALED-SSPEVRANVC 534
                                       66444433788888888888855554444444445555543.3577777766 PP

>> API5  Apoptosis inhibitory protein 5 (API5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.2    0.0018       2.5      51     135 ..     284     367 ..     278     382 .. 0.88
   2 !    7.6   0.1    0.0011       1.5      52     109 ..     395     452 ..     388     499 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0018
                              API5  51 kfFPslaekaidaqlDLiedddlgirkqAikdLpslckdtkeyvskiadiLaQlLitedaveldavhkallsllkld 127
                                       k+  +  e a++a + L+ d+  +  ++A+++L + + d +  ++  +  La    ++d++ + a  + l++l   d
  gi|313126094|ref|YP_004036364.1| 284 KHRADAREVAVNATFALLGDEPSALDRAALQALHETAADDPTVLKEHVAELAAY-ASQDSMYQAAATRCLMELAEAD 359
                                       666778899**********************************99999999976.56666667777899******** PP

                              API5 128 akasltal 135
                                       +++ l+a+
  gi|313126094|ref|YP_004036364.1| 360 PASVLDAV 367
                                       ***99986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0011
                              API5  52 fFPslaekaidaqlDLiedddlgirkqAikdLpslckdtkeyvskiadiLaQlLited 109
                                        +P+  + aida+++ +  +d +++  A+ +L +++ + ++  +  +d L+ +L ++ 
  gi|313126094|ref|YP_004036364.1| 395 AYPEEVSPAIDALIEAMQSEDETVQTNALAALGKIASNYPDGAEPPVDELVTVLDADA 452
                                       5788999999999999999999999999999999999999998888888888887775 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05     0.074      88     196 ..     437     533 ..     392     565 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                           CLASP_N  88 ldpmveillptLlkllgdtKkiisqnanqalaallsnas.fsprilqvlsvalqdKnvqpReysaiwLkilltrfes 163
                                        +p v    + L+++l +  k++++na   l +l ++ + +  +    + + l+d n q+R  ++i L+ + + ++ 
  gi|313126094|ref|YP_004036364.1| 437 AEPPV----DELVTVLDADAKRVRNNAVGLLGDLAQEHPaVVIEYADQIAARLEDNNIQARVNASIALHRAGEASP- 508
                                       44444....457888999******************999556666999*****************99999999999. PP

                           CLASP_N 164 hkskleasllldliekslkkgleDanptVReta 196
                                               + +++ ++ l ++leD++p+VR + 
  gi|313126094|ref|YP_004036364.1| 509 --------AAIRAQQDRLESALEDSSPEVRANV 533
                                       ........667888999*************876 PP

>> Cohesin_HEAT  HEAT repeat associated with sister chromatid cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       9.9   1.4e+04       1      11 [.     350     360 ..     350     361 .. 0.88
   2 ?    3.4   0.0     0.069        95      21      35 ..     479     493 ..     478     493 .. 0.91
   3 ?    7.1   0.1     0.005       6.9      23      36 ..     518     531 ..     515     537 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.9
                                       HHHHHHHHH-G CS
                      Cohesin_HEAT   1 kalsslvekdp 11 
                                       ++l  l+e+dp
  gi|313126094|ref|YP_004036364.1| 350 RCLMELAEADP 360
                                       789999****9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.069
                                       HHHHHHHHSS-HHHH CS
                      Cohesin_HEAT  21 dtiarrltDsspsVR 35 
                                       d+ia+rl+D+ ++ R
  gi|313126094|ref|YP_004036364.1| 479 DQIAARLEDNNIQAR 493
                                       79********99987 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.005
                                       HHHHHHSS-HHHHH CS
                      Cohesin_HEAT  23 iarrltDsspsVRd 36 
                                       +++ l+Dssp VR+
  gi|313126094|ref|YP_004036364.1| 518 LESALEDSSPEVRA 531
                                       7899*********7 PP

>> DUF3088  Protein of unknown function (DUF3088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00062      0.85      36      84 ..     438     486 ..     436     501 .. 0.81
   2 ?    1.1   0.0      0.23   3.1e+02      54      87 ..     530     563 ..     525     569 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00062
                           DUF3088  36 fPalaekldvervdfarPRkavvallgeenqslPvLvLadgaakaapvk 84 
                                        P + e ++v   d +r R++ v llg+  q  P++v++ +++ aa+ +
  gi|313126094|ref|YP_004036364.1| 438 EPPVDELVTVLDADAKRVRNNAVGLLGDLAQEHPAVVIEYADQIAARLE 486
                                       5788899999999************************998874444444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.23
                           DUF3088  54 RkavvallgeenqslPvLvLadgaakaapvkake 87 
                                       R++v  l+g++  s+P+ +L++ ++++ +++++e
  gi|313126094|ref|YP_004036364.1| 530 RANVCSLIGNAYVSVPIDMLEEVKENDLDETVRE 563
                                       999**************99999987777776655 PP

>> MMS19_C  RNAPII transcription regulator C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.085   1.2e+02     389     416 ..     307     334 ..     299     336 .. 0.89
   2 ?    4.9   0.0    0.0086        12     377     418 ..     405     446 ..     365     448 .. 0.56
   3 ?    7.7   0.0    0.0012       1.7     336     420 ..     406     485 ..     400     485 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.085
                           MMS19_C 389 evkastLetlksileespslvsehlssL 416
                                       ++ +++L+ l++++ ++p++++eh+++L
  gi|313126094|ref|YP_004036364.1| 307 ALDRAALQALHETAADDPTVLKEHVAEL 334
                                       57789********************988 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0086
                           MMS19_C 377 PlLlqaLdlpdaevkastLetlksileespslvsehlssLvp 418
                                         L++a++ +d++v++++L  l  i+ + p+  ++ +++Lv+
  gi|313126094|ref|YP_004036364.1| 405 DALIEAMQSEDETVQTNALAALGKIASNYPDGAEPPVDELVT 446
                                       345666666666666666666666666666666666666665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0012
                           MMS19_C 336 klvegfkssdsetkenyLvALshllkhvPkslllpeLptLlPlLlqaLdlpdaevkastLetlksileespslvseh 412
                                        l+e+++s+d++ ++n L AL  + ++ P     p   +L+ +    Ld + + v++++   l ++++e+p++v e+
  gi|313126094|ref|YP_004036364.1| 406 ALIEAMQSEDETVQTNALAALGKIASNYPDG-AEPPVDELVTV----LDADAKRVRNNAVGLLGDLAQEHPAVVIEY 477
                                       79999999*******************9976.58888887765....799999999999999999999999999999 PP

                           MMS19_C 413 lssLvprL 420
                                       ++++  rL
  gi|313126094|ref|YP_004036364.1| 478 ADQIAARL 485
                                       99987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 3561.94
//
Query:       gi|313126095|ref|YP_004036365.1|  [L=347]
Description: hypothetical protein Hbor_13370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-50  170.3   0.0    3.9e-50  170.0   0.0    1.1  1  RE_AspBHI_N  Restriction endonuclease AspBHI N-terminal
    1.3e-08   34.9   0.1    3.3e-08   33.6   0.1    1.7  1  HNH_2        HNH endonuclease


Domain annotation for each model (and alignments):
>> RE_AspBHI_N  Restriction endonuclease AspBHI N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.0   4.4e-54   3.9e-50       3     184 ..      18     200 ..      16     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 4.4e-54
                                       TCCC-CHHHHT......TS-SS-SEEEECSSS..SECEEEEEE.....-S--TTS--EEETTTTEEEEE-S--STTS CS
                       RE_AspBHI_N   3 nseddelskll......kigntggfrevgksk..epallvlvs.....sqeeedWeDeldeetGeirYyGDnkkpkk 66 
                                       +++dd++ +++      +i+ntgg+r+ g+++  +pa+lvlvs     sq++++WeD+l +++G+i+Y+GD+k+++ 
  gi|313126095|ref|YP_004036365.1|  18 RNSDDQFLRWIrgpldsGIKNTGGIRDLGADRseTPAALVLVSndsgiSQHDDPWEDTLAVNAGYISYWGDAKASNP 94 
                                       578999999995666556**********865445****************************************996 PP

                                       -TT--TT-HHHHHHHHHHHHCCTTCCCS--EEEEEETTCTTEEEEEEEEEES-TTS-CCCSEEEEEEEETTEEEEEE CS
                       RE_AspBHI_N  67 elsdtkrkGNklLkelfdelkeenreeipPilvFekkesgrkvrfkGlavlkavklseeedlvaqwkekegerfqNY 143
                                          d++ ++N+ +k +fd+++ ++re++pP+lvF+k esg  v f+Gl+v+++++       v  +++++g +++NY
  gi|313126095|ref|YP_004036365.1|  95 --YDES-TQNQKIKAAFDNAAAGRRENVPPVLVFRKPESG-VVDFCGLCVPDHFE-------VHAYQADDGTQVPNY 160
                                       ..4444.57*******************************.9*************.......999************ PP

                                       EEEEEEBS-SEE-HHHHHCCCTCGG.-SGGGHHHHHHHHHS CS
                       RE_AspBHI_N 144 raeftiLdvkevsleWiekraeaeetdenapkaWkewvkkg 184
                                       +++f+iL+++ v ++W+++ra++++ d+ ap++W++wv++g
  gi|313126095|ref|YP_004036365.1| 161 QFHFSILNTNAVPVTWLHDRARQND-DSEAPDVWQHWVQTG 200
                                       *************************.*************98 PP

>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.1   3.7e-12   3.3e-08       1      72 []     243     294 ..     243     294 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.7e-12
                             HNH_2   1 CvitgiddpslleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfafe 72 
                                       C +tgi++++ll+ AHI+P          +++r+          +  ++p+N+l L++ +H++Fd+ lf+++
  gi|313126095|ref|YP_004036365.1| 243 CTLTGIREDELLDLAHILP----------RSQRP----------ELAEHPENVLVLNSLHHRAFDAALFTID 294
                                       999**99988*********..........99999..........999**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2294.21
//
Query:       gi|313126096|ref|YP_004036366.1|  [L=161]
Description: hepn domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00024   21.2   0.0    0.00032   20.8   0.0    1.2  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.8e-08   0.00032       5     116 ..      35     146 ..      31     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.8e-08
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--..SSCCHHHHHHCCHHHT...-HHHHHHHHHH CS
                              HEPN   5 lrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkgge.ppkthdlreLleelkkelkeseelreeleeL 80 
                                       l +A + l+a + l ++g+y +++  +  a e ++ A+ l++gg+     hd +    ++  ++  s+   +el+ L
  gi|313126096|ref|YP_004036366.1|  35 LTKACRLLAAVNTLSDQGFYTATIELCFGATERSVEAYALAEGGDnLNDFHDHTTCYDRATALGLLSDTTTRELRDL 111
                                       6789999999999********************************99***********9999999999999999888 PP

                                       HCC.CHHCCCTSS--S--HHHHHHHHHHHHHHHHHHH CS
                              HEPN  81 eka.yiesrYpdakeeyteedaeealkdaeevlelve 116
                                        +  +++s Y+ +++  te++ae++ + a++v e+v 
  gi|313126096|ref|YP_004036366.1| 112 YDTnRTDSYYGGRRP--TERQAETMQQLARSVHEYVT 146
                                       776266677777777..***************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1060.81
//
Query:       gi|313126097|ref|YP_004036367.1|  [L=230]
Description: nucleotidyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.4e-10   38.8   0.1    1.4e-09   37.9   0.1    1.5  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    3.7e-09   36.7   0.3    6.3e-09   36.0   0.3    1.5  1  NTP_transf_2    Nucleotidyltransferase domain
    8.9e-05   22.3   0.0    0.00037   20.3   0.0    2.0  2  MarR_2          MarR family
     0.0016   18.3   0.0      0.004   17.0   0.0    1.7  1  MarR            MarR family
     0.0018   18.5   0.3     0.0039   17.4   0.1    1.6  2  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
       0.01   16.3   0.1      0.036   14.5   0.0    2.0  2  HTH_27          Winged helix DNA-binding domain
      0.016   15.3   0.0      0.043   13.9   0.0    1.7  2  HTH_20          Helix-turn-helix domain
      0.017   14.8   0.1       0.85    9.3   0.0    2.9  3  GntR            Bacterial regulatory proteins, gntR family
      0.026   14.4   0.0      0.041   13.8   0.0    1.3  1  Adenyl_cycl_N   Adenylate cyclase NT domain
      0.099   13.0   0.0       0.17   12.3   0.0    1.3  1  Rrf2            Transcriptional regulator
       0.14   12.0   0.0       0.29   11.0   0.0    1.5  1  DUF1495         Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   8.7e-13   1.4e-09       3      90 ..     117     213 ..     115     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 8.7e-13
                                       TTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS-..--HHHHHHHHHHHHHH......SSSEEEEEETTTS CS
                           Polbeta   3 ikeilekekeielaylFGSrakgkareeSDiDlavllkek..ldleeelelaaeledi.....klgkkvDlvdlnea 72 
                                       + e++e+ + ++ ++l+GS+a+g+a ++SDiDl vl++++   +  +  ++ ++led      +  +++D+  l ++
  gi|313126097|ref|YP_004036367.1| 117 VDELVERLDTVIGIVLYGSVARGDADRRSDIDLWVLVEDDrmANQRTANRVRQDLEDQefdtgRYAYEIDIESLPAV 193
                                       6678888999******************************8877888899999999998887877899999998877 PP

                                       -..HHHHHHHHHS-EEEES- CS
                           Polbeta  73 p..plllyeilkegkllysk 90 
                                       p  ++ l+ +l++g ++y++
  gi|313126097|ref|YP_004036367.1| 194 PnyTDELQDVLSDGLVVYDS 213
                                       63344567788888888876 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.3   3.9e-12   6.3e-09       2      48 ..     114     173 ..     113     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3.9e-12
                                       HHHHHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH..............H CS
                      NTP_transf_2   2 kklleelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsre..............k 48 
                                       +k+ +el e+   v+ +vl+GS+arG+a + SDiDl v+++++  r               +
  gi|313126097|ref|YP_004036367.1| 114 RKAVDELVERLDtVIGIVLYGSVARGDADRRSDIDLWVLVEDD--RManqrtanrvrqdleD 173
                                       5555666666657*****************************9..55446644443333330 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.3e-07   0.00037       5      57 ..      30      82 ..      24      85 .. 0.91
   2 ?   -1.6   0.0       1.6   2.6e+03      32      47 ..     103     118 ..     101     125 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.3e-07
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                       a +++L +L r    +++++el+ + ++s+++++++++ L a  Lv+ r++ 
  gi|313126097|ref|YP_004036367.1| 30 QAVHDILSFLTRYHTDEFSITELTNAVDYSQPTITKAVDILAANDLVTDRRDG 82
                                      57899*********99*******************************999875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                                       TSSHHHHHHHHHHHHH CS
                            MarR_2  32 glsksavsrilkrLva 47 
                                       +++++  +r ++++v+
  gi|313126097|ref|YP_004036367.1| 103 RIPQAEFHRPVRKAVD 118
                                       5666666677776664 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.5e-06     0.004      13      52 ..      42      81 ..      35      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-06
                                      HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      y+ ++ s++eL +++  s++t+t+++d L  ++l++ +++
  gi|313126097|ref|YP_004036367.1| 42 YHTDEFSITELTNAVDYSQPTITKAVDILAANDLVTDRRD 81
                                      5677889****************************97776 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.5   8.9e+03      58      78 ..      58      78 ..      46      81 .. 0.64
   2 !   17.4   0.1   2.4e-06    0.0039       1      75 [.     103     176 ..     103     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.5
                                      --HHHHHHHHHHHHHTTSEEE CS
                    DNA_pol_B_palm 58 klkklleklvkklkkkgfltd 78
                                        ++ ++k v+ l +++++td
  gi|313126097|ref|YP_004036367.1| 58 YSQPTITKAVDILAANDLVTD 78
                                      445666667777777777666 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.4e-06
                                       -EEHHHHHH.HHHHHHHHHHHH-TT-EEEE-HHHHTT-S.EESSEEEEEEBTTBSTTSS--HHHHHHHHHHHHHTTS CS
                    DNA_pol_B_palm   1 riPreEvea.lealvkkaakeldpevevivcGSYRRgae.ssGDvDvlitkkdakseskklkklleklvkklkkkgf 75 
                                       riP++E ++ ++++v + +++ld  + ++  GS  Rg +    D+D+ +  +d + +   +++  +++ + l++++f
  gi|313126097|ref|YP_004036367.1| 103 RIPQAEFHRpVRKAVDELVERLDTVIGIVLYGSVARGDAdRRSDIDLWVLVEDDRMA---NQRTANRVRQDLEDQEF 176
                                       9*****9764899*********************999761579***99999988884...46778888888888877 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.2e-05     0.036      18      61 ..      46      86 ..      29      92 .. 0.80
   2 ?   -2.5   0.0       4.6   7.4e+03      15      34 ..     138     157 ..     131     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                            HTH_27 18 rkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekr 61
                                      + ++++l  ++++++ +i ++++ L +++Lv   +d++d+ +++
  gi|313126097|ref|YP_004036367.1| 46 EFSITELTNAVDYSQPTITKAVDILAANDLV---TDRRDGNTRL 86
                                      55789**************************...4445554455 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.6
                            HTH_27  15 rrrrkkladlcgrlnvedsh 34 
                                       r++ ++ +d+  ++ ved  
  gi|313126097|ref|YP_004036367.1| 138 RGDADRRSDIDLWVLVEDDR 157
                                       66777777777777666665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.7e-05     0.043      14      60 ..      34      82 ..      33      83 .. 0.93
   2 ?   -3.8   0.0       8.9   1.5e+04       7      16 ..     163     172 ..     163     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                      HHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 14 rilraL..araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      +il+ L     ++++ +el  ++d s+ t+ + +++L+  +Lv+ +r g
  gi|313126097|ref|YP_004036367.1| 34 DILSFLtrYHTDEFSITELTNAVDYSQPTITKAVDILAANDLVTDRRDG 82
                                      688888888889**********************************987 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.9
                                       HS-HHHHHHH CS
                            HTH_20   7 LahPvRrril 16 
                                       +a++vR +++
  gi|313126097|ref|YP_004036367.1| 163 TANRVRQDLE 172
                                       5899999876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00052      0.85      27      58 ..      49      80 ..      43      86 .. 0.86
   2 ?    0.5   0.1       0.3   4.9e+02      39      50 ..     111     122 ..     110     124 .. 0.85
   3 ?    0.5   0.0      0.29   4.8e+02       3      21 ..     161     179 ..     159     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00052
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverrq 58
                                        eL  + + s +t+ +A + L+a +lv+ r+
  gi|313126097|ref|YP_004036367.1| 49 ITELTNAVDYSQPTITKAVDILAANDLVTDRR 80
                                      679999999*******************9765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHH CS
                              GntR  39 ttvReALrrLea 50 
                                        +vR+A ++L++
  gi|313126097|ref|YP_004036367.1| 111 RPVRKAVDELVE 122
                                       59*******986 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHTTSS-TT CS
                              GntR   3 eqvyerLredIlsgelrpG 21 
                                       ++ + r+r+d+ + e+  G
  gi|313126097|ref|YP_004036367.1| 161 QRTANRVRQDLEDQEFDTG 179
                                       678899*******999888 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.5e-05     0.041      90     127 ..     125     162 ..     102     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                     Adenyl_cycl_N  90 aaieglylmGStgsiaqsekSDlDiWvchrselsaeel 127
                                        ++ g+ l GS++      +SD+D+Wv ++++  a+++
  gi|313126097|ref|YP_004036367.1| 125 DTVIGIVLYGSVARGDADRRSDIDLWVLVEDDRMANQR 162
                                       5789999********************97665444433 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.17      11      59 ..      33      80 ..      27      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                        +l +L++ +++e +s++e+ + ++ s++ + k +  L+ ++lv+ +r
  gi|313126097|ref|YP_004036367.1| 33 HDILSFLTRYHTDE-FSITELTNAVDYSQPTITKAVDILAANDLVTDRR 80
                                      34899999999998.******************************9876 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.29       5      43 ..      26      64 ..      24      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                           DUF1495  5 lnkSkvRkkvllyLysiypeksnlqeisrrvrskpsnvk 43
                                      + kS++ +++l +L++ +  +  ++e++++v +++  ++
  gi|313126097|ref|YP_004036367.1| 26 IFKSQAVHDILSFLTRYHTDEFSITELTNAVDYSQPTIT 64
                                      6799***************************99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1682.57
//
Query:       gi|313126098|ref|YP_004036368.1|  [L=126]
Description: hypothetical protein Hbor_13400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00081   19.4  13.4       0.18   11.9   0.2    3.8  4  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.002   18.2  16.0      0.089   12.9   3.2    3.3  3  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.028   14.5   0.5      0.028   14.5   0.5    1.7  2  Spt4             Spt4/RpoE2 zinc finger
      0.092   12.9   6.1       0.85    9.8   0.0    3.6  4  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.26   11.4  11.3      0.057   13.5   5.5    2.5  3  DZR              Double zinc ribbon
       0.32   11.3  12.2       0.13   12.5   3.9    3.1  3  zinc_ribbon_9    zinc-ribbon
       0.61   10.2   6.6        2.7    8.1   6.6    2.0  1  Zn_Tnp_IS91      Transposase zinc-binding domain
        1.2    9.2   9.0        2.5    8.1   7.5    2.1  1  HypA             Hydrogenase/urease nickel incorporation, met


Domain annotation for each model (and alignments):
>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0064        14      19      25 ..       8      14 ..       6      15 .. 0.89
   2 ?   -3.6   0.1       5.4   1.2e+04      13      19 ..      57      63 ..      55      63 .. 0.81
   3 !   11.9   0.2   7.9e-05      0.18       2      15 ..      90     103 ..      89     105 .. 0.91
   4 !    9.4   1.1   0.00049       1.1       1      17 [.     108     125 ..     108     126 .] 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0064
                    DNA_ligase_ZBD 19 RCtnlsC 25
                                      +Ctn++C
  gi|313126098|ref|YP_004036368.1|  8 YCTNPDC 14
                                      9****** PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.4
                    DNA_ligase_ZBD 13 egeaiyR 19
                                      ++e ++R
  gi|313126098|ref|YP_004036368.1| 57 QEEIDRR 63
                                      7899988 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 7.9e-05
                    DNA_ligase_ZBD   2 CPvCGsavvReege 15 
                                       CP+C s +v++ +e
  gi|313126098|ref|YP_004036368.1|  90 CPECRSNAVKTIDE 103
                                       ***********998 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00049
                    DNA_ligase_ZBD   1 hCPvCGsavv.Reegeai 17 
                                       hCPvC   +v  e+ +ai
  gi|313126098|ref|YP_004036368.1| 108 HCPVCEEGTVvAEDTGAI 125
                                       9****9888845666776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.4   0.00039      0.88       3      37 ..       4      48 ..       1      51 [. 0.78
   2 !   12.9   3.2     4e-05     0.089       8      39 ..      72     100 ..      68     101 .. 0.76
   3 ?    4.8   0.3     0.014        30      23      36 ..     103     117 ..      98     119 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00039
                       Zn-ribbon_8  3 iYeYrCeeCghefe.......vlqsisdaplta.CPeCgs..evr 37
                                      i+e+ C++ + efe        + +i+d+ +   CP+ g+  ++r
  gi|313126098|ref|YP_004036368.1|  4 IFEFYCTNPDCEFEmpsgwgyYMYAIADDGERIlCPHPGEmgRAR 48
                                      9*******8888**99****98888886666666**988765555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4e-05
                       Zn-ribbon_8   8 CeeCghefevlqsis.dapltaCPeCgsevrrv 39 
                                       C  C ++ +     + d++++aCPeC s++ + 
  gi|313126098|ref|YP_004036368.1|  72 CIHCETQVD----LDfDRDEKACPECRSNAVKT 100
                                       777887877....333777999******88876 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.014
                       Zn-ribbon_8  23 dapltaCPeCgs.ev 36 
                                       +  +++CP C + +v
  gi|313126098|ref|YP_004036368.1| 103 ELVDEHCPVCEEgTV 117
                                       445677****98665 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       3.9   8.8e+03       4       8 ..      72      76 ..      68      86 .. 0.63
   2 ?   14.5   0.5   1.3e-05     0.028       1      25 [.      87     113 ..      87     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                              Spt4  4 CllCk 8 
                                      C++C+
  gi|313126098|ref|YP_004036368.1| 72 CIHCE 76
                                      55554 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.3e-05
                              Spt4   1 lrACllCk..lvktedqFeeegCpnCe 25 
                                       ++AC +C+  +vkt d+  +e Cp+Ce
  gi|313126098|ref|YP_004036368.1|  87 EKACPECRsnAVKTIDELVDEHCPVCE 113
                                       69*****7447***************2 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         4     9e+03      31      37 ..      33      39 ..      31      40 .. 0.71
   2 ?    2.1   0.5       0.1   2.3e+02      32      40 .]      68      76 ..      61      76 .. 0.78
   3 ?    1.7   0.1      0.13     3e+02      16      22 ..      88      94 ..      84     100 .. 0.74
   4 ?    9.8   0.0   0.00038      0.85      13      27 ..     104     120 ..     103     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4
                     Auto_anti-p27 31 ggkvyCv 37
                                      g++++C+
  gi|313126098|ref|YP_004036368.1| 33 GERILCP 39
                                      5678887 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                     Auto_anti-p27 32 gkvyCvaCd 40
                                      + ++C+ C+
  gi|313126098|ref|YP_004036368.1| 68 TYCFCIHCE 76
                                      689*****5 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.13
                     Auto_anti-p27 16 etCpvCg 22
                                      + Cp+C 
  gi|313126098|ref|YP_004036368.1| 88 KACPECR 94
                                      5688884 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00038
                     Auto_anti-p27  13 MLaetCpvC..gvPLmr 27 
                                       + +e+CpvC  g++  +
  gi|313126098|ref|YP_004036368.1| 104 LVDEHCPVCeeGTVVAE 120
                                       679******98888766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.3   5.2e+03       2      10 ..      12      20 ..       8      24 .. 0.61
   2 ?    6.1   0.4    0.0052        12      29      40 ..      70      81 ..      29      85 .. 0.75
   3 ?   13.5   5.5   2.5e-05     0.057       1      37 [.      72     115 ..      72     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                               DZR  2 pqCgeelpp 10
                                      p C+ e+p+
  gi|313126098|ref|YP_004036368.1| 12 PDCEFEMPS 20
                                      455555555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0052
                               DZR 29 drCpsCgekvdp 40
                                       +C +C+++vd+
  gi|313126098|ref|YP_004036368.1| 70 CFCIHCETQVDL 81
                                      456666666665 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 2.5e-05
                               DZR   1 CpqCgee....lppdarfCseCgtk.lkavaa...edrCpsCgek 37 
                                       C +C+++     + d + C+eC+++ +k + +    ++Cp C+e 
  gi|313126098|ref|YP_004036368.1|  72 CIHCETQvdldFDRDEKACPECRSNaVK-TIDelvDEHCPVCEEG 115
                                       99****98888889999******99444.3335989******975 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.34   7.5e+02      20      26 ..      33      40 ..      27      42 .. 0.64
   2 ?   12.5   3.9   5.9e-05      0.13       4      30 ..      71      96 ..      68     101 .. 0.82
   3 ?    2.2   0.3       0.1   2.3e+02      21      30 ..     107     115 ..      96     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.34
                     zinc_ribbon_9 20 sd.vlCPh 26
                                       + +lCPh
  gi|313126098|ref|YP_004036368.1| 33 GErILCPH 40
                                      33257**8 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.9e-05
                     zinc_ribbon_9  4 WChqCdrfVsvspdedsdvlCPhCggg 30
                                      +C +C   V++  d d+ + CP+C++ 
  gi|313126098|ref|YP_004036368.1| 71 FCIHCETQVDLDFDRDEKA-CPECRSN 96
                                      899********87766666.****986 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.1
                     zinc_ribbon_9  21 dvlCPhCggg 30 
                                       +  CP C+ g
  gi|313126098|ref|YP_004036368.1| 107 E-HCPVCEEG 115
                                       3.4****987 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.6    0.0012       2.7      34      79 ..      63     108 ..      58     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                       Zn_Tnp_IS91  34 alGfarye.CeeCghekivyfsCksrhCpsCqkkateewlekqqeel 79 
                                       + Gf++y+ C +C+ +  + f   +++Cp+C ++a +  ++++ +e 
  gi|313126098|ref|YP_004036368.1|  63 RTGFNTYCfCIHCETQVDLDFDRDEKACPECRSNAVKT-IDELVDEH 108
                                       679999988**********************9887654.44555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.5    0.0011       2.5      70     100 ..      69     101 ..      51     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                       EEEETTTS-EEECHHH..HHS-TTTSSS-EEEE CS
                              HypA  70 kvrCreCgkefeleek..alrCpkCgsadveiv 100
                                        + C +C+++++l+ +  +  Cp+C s+ v+++
  gi|313126098|ref|YP_004036368.1|  69 YCFCIHCETQVDLDFDrdEKACPECRSNAVKTI 101
                                       678*********887346889******998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 818.55
//
Query:       gi|313126099|ref|YP_004036369.1|  [L=253]
Description: hypothetical protein Hbor_13420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1565.42
//
Query:       gi|313126100|ref|YP_004036370.1|  [L=590]
Description: hypothetical protein Hbor_13430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.035   13.8   0.0    1.5  1  DDE_Tnp_1  Transposase DDE domain
       0.12   12.6   0.1        1.2    9.4   0.0    2.4  2  SbcCD_C    Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.9e-06     0.035      63     214 .]     370     542 ..     361     542 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-06
                         DDE_Tnp_1  63 kglkqlldelrpr.kgklvlaDaGYasaelldtle.ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltks 137
                                       ++l+ +l++l  + + kl+ aD+G++++e ++ ++    ++++i +               +++ ++ ++n  +++ 
  gi|313126100|ref|YP_004036370.1| 370 RVLENFLRTLTSMvDVKLFMADRGFDGREDIEVCReFVPGKWVICA---------------QDDSNPVGQNSDYRRL 431
                                       45566888888889999**********999999996678*****99...............4444555555555555 PP

                         DDE_Tnp_1 138 qkrrnk.............................................skkekgdvyyvtntnsellsaeevae 169
                                       + + +                                                + + +++++t++n+          
  gi|313126100|ref|YP_004036370.1| 432 RAELEPgstavrpsagygnlnppvkllgysgdnsqadtpdpirafysdmslPGDPDARESLITLINW---------- 498
                                       55555555556666666888999999999**********************9999************.......... PP

                         DDE_Tnp_1 170 lyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                        y++R+ iE+ F+  k+ f   ++++ ++ r   ++++  l +nl
  gi|313126100|ref|YP_004036370.1| 499 QYNQRAKIESMFRMAKNEFD-VATDTDKPPRKSFYFHMSVLFYNL 542
                                       8****************999.677777777777777777777776 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00013       1.2      29      73 ..      35      80 ..      19      92 .. 0.78
   2 ?   -0.4   0.0      0.16   1.4e+03      60      85 ..     279     304 ..     265     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00013
                           SbcCD_C 29 ssgtlSGGekqflaylalaaalaalyssaeg..repalrlvfLDEAF 73
                                      s++  SGG++++ +  +l+ a+a+  +s+++   ++++++ ++DEA 
  gi|313126100|ref|YP_004036370.1| 35 SISHPSGGQRAIEFRKPLLVAMAQKNWSKSSddADRTVDT-VFDEAL 80
                                      56778*********************99985434444554.679996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.16
                           SbcCD_C  60 repalrlvfLDEAFsklDeesiatll 85 
                                       + + lrl  +DE F+++ +  ++ ++
  gi|313126100|ref|YP_004036370.1| 279 HIDELRLWRIDEMFDEVNQALLKYVI 304
                                       456799999******99998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3617.19
//
Query:       gi|313126101|ref|YP_004036371.1|  [L=50]
Description: hypothetical protein Hbor_13440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 321.26
//
Query:       gi|313126102|ref|YP_004036372.1|  [L=74]
Description: hypothetical protein Hbor_13450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.6   0.4      0.042   13.8   0.1    1.5  2  HUN       HPC2 and ubinuclein domain
       0.13   11.3   0.0       0.15   11.1   0.0    1.0  1  COG4      COG4 transport protein


Domain annotation for each model (and alignments):
>> HUN  HPC2 and ubinuclein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.7e-06     0.042      20      40 ..       6      26 ..       5      32 .. 0.83
   2 ?   -3.3   0.0       1.1   9.6e+03      23      29 ..      48      54 ..      46      57 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-06
                               HUN 20 DpFIDDsElydelvpdilktk 40
                                      D FIDDs  +del ++ +++ 
  gi|313126102|ref|YP_004036372.1|  6 DTFIDDSKSVDELRRAKVNRT 26
                                      99*************966654 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                               HUN 23 IDDsEly 29
                                      ID +E +
  gi|313126102|ref|YP_004036372.1| 48 IDPEETD 54
                                      6777754 PP

>> COG4  COG4 transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.7e-05      0.15     137     194 ..       2      57 ..       1      60 [. 0.95

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.7e-05
                              COG4 137 erqldrllsdvksykfsflvrgqfpaksseaaaasaktsnesseeeegvdpreidall 194
                                       +r++d  ++d ks  +  l r++ +++ ++ a + +++ + ++ e++g+dp+e+d++l
  gi|313126102|ref|YP_004036372.1|   2 TRHIDTFIDDSKSVDE--LRRAKVNRTDERGAVGVPVFLTAEELEQQGIDPEETDEVL 57 
                                       699*************..8999**********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 462.47
//
Query:       gi|313126103|ref|YP_004036373.1|  [L=244]
Description: hypothetical protein Hbor_13460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   11.7   0.0       0.64    9.3   0.0    1.9  2  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.034     6e+02     128     155 ..      69      99 ..      63     112 .. 0.78
   2 ?    9.3   0.0   3.6e-05      0.64     107     145 ..     177     218 ..     172     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.034
                                       --HHHHHHHHHTTEEEEE...E-SEEEEE-H CS
                              HEM4 128 arddlaegLeergaevde...vevYetvpae 155
                                       ++d+++++ +e+g+ v++   + vYet+ ++
  gi|313126103|ref|YP_004036373.1|  69 SSDEFKQQAKEQGLPVHDridAAVYETYEMV 99 
                                       5788999999999999853337899996555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 3.6e-05
                                       HGGGS-...---E.EEEEE-SS.S--HHHHHHHHHTTEEEEE CS
                              HEM4 107 Laeelae..slag.krvlllrgeiarddlaegLeergaevde 145
                                       +a e+ +  + ++ ++vl+ +g ++r+ +a++L+  g ev+e
  gi|313126103|ref|YP_004036373.1| 177 MAREIVQitEAKEyDSVLISCGGNHRPGIASYLRDEGWEVTE 218
                                       5666666555555588************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1604.58
//
Query:       gi|313126104|ref|YP_004036374.1|  [L=345]
Description: hypothetical protein Hbor_13470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.3   0.0      0.072   13.4   0.0    1.4  1  PIN_4     PIN domain


Domain annotation for each model (and alignments):
>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     4e-06     0.072      54     129 ..     187     265 ..     151     267 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-06
                             PIN_4  54 nrlldellekesgrlkvqtsaeelpeee.....seseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgi 125
                                        rl ++    + + + +  +  +l   +      e ++ D++I+++  e++++  +++ +L+s+D     +    g+
  gi|313126104|ref|YP_004036374.1| 187 ARLENQPAGANREGFLGLYEYRRLRT-NrtvdiVECDTGDEAIIEAYNEFNQNS-RKQAILFSNDYGFVDRSLDAGV 261
                                       33333333333333333333222222.12223322569**************98.9*********999999999999 PP

                             PIN_4 126 eaed 129
                                       +a+ 
  gi|313126104|ref|YP_004036374.1| 262 PAQH 265
                                       8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2224.48
//
Query:       gi|313126105|ref|YP_004036375.1|  [L=144]
Description: hypothetical protein Hbor_13480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00057   18.8   0.0     0.0013   17.6   0.0    1.5  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
     0.0011   18.9   0.0     0.0014   18.5   0.0    1.2  1  Cas_APE2256   CRISPR-associated protein (Cas_APE2256)
     0.0014   18.4   0.0     0.0015   18.3   0.0    1.1  1  Cas_NE0113    CRISPR-associated protein NE0113 (Cas_NE0113)
     0.0039   16.8   0.1     0.0039   16.8   0.1    1.1  1  Cas_DxTHG     CRISPR-associated (Cas) DxTHG family


Domain annotation for each model (and alignments):
>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     3e-07    0.0013      44      95 ..      60     109 ..      32     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-07
                                       EE--TT-HHHHHHHHHHHHHHS.TTS-EEEE-SSS-HHHHHHHHHHHHHHTE CS
                      Cas_Cas02710  44 ldedandllelykkikevlekaleeeevivDlTgGtkeMtaglalagillrv 95 
                                        + d  d+ e y+   e+++     + ++vD+T G k M+a+++ ag+ + +
  gi|313126105|ref|YP_004036375.1|  60 DETDFPDIIEFYRSTIEAARET--GDTIAVDVTPGRKFMSAIAFQAGFKFDA 109
                                       3456667777888777777776..899********************98865 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.2e-07    0.0014      71     126 ..      62     118 ..      25     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.2e-07
                       Cas_APE2256  71 eglrnLveklarevknkkregekvlinaTgGfKpeiavltlvall.ladevyYihEs 126
                                       + + +++e +++ ++++++ g+++++ +T G K  +a++  ++    ad+v+Y h +
  gi|313126105|ref|YP_004036375.1|  62 TDFPDIIEFYRSTIEAARETGDTIAVDVTPGRKFMSAIAFQAGFKfDADHVFYFHRK 118
                                       47889**************************************9889********86 PP

>> Cas_NE0113  CRISPR-associated protein NE0113 (Cas_NE0113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.4e-07    0.0015      62     133 ..      48     116 ..      14     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.4e-07
                        Cas_NE0113  62 edvsgeelaDirteedneallqlivrlvrelrenegerlhlsiaGGRKtmsillalaaqLygreqDrlyHvl 133
                                        + +++ ++D + e+d   ++++ ++ ++  re  g ++ + +  GRK ms+++  a   +   +D +++ +
  gi|313126105|ref|YP_004036375.1|  48 GGDADVSVHDLDDETDFPDIIEFYRSTIEAARET-GDTIAVDVTPGRKFMSAIAFQAGFKFD--ADHVFYFH 116
                                       44567889**************************.89***************9987765444..88888865 PP

>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   8.8e-07    0.0039      83     166 ..      53     143 ..      16     144 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.8e-07
                         Cas_DxTHG  83 vdveiipgggteeelweifekllekleen.deiilDiThGfrylPvla......llalaylrnvknltikgiyYgaf 152
                                       v+v+ + +  ++ ++ e++   +e+ +e  d+i +D+T G  ++  +a      + a ++++  ++   +g yYg+f
  gi|313126105|ref|YP_004036375.1|  53 VSVHDLDDETDFPDIIEFYRSTIEAARETgDTIAVDVTPGRKFMSAIAfqagfkFDADHVFYFHRK---AGGYYGQF 126
                                       4445577778889999***98888866666**************9999999999889999999886...7889**** PP

                         Cas_DxTHG 153 ...keeeedPildltef 166
                                            ++++ ++d++e+
  gi|313126105|ref|YP_004036375.1| 127 yaeIPRTATDLIDFKEV 143
                                       87766667777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 935.57
//
Query:       gi|313126106|ref|YP_004036376.1|  [L=395]
Description: site-specific recombinase xerd [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-17   62.3   0.0    1.5e-16   60.6   0.0    1.8  2  Phage_integrase  Phage integrase family
    0.00047   20.1   9.3    0.00074   19.5   9.3    1.3  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
       0.82    9.7   4.2         16    5.5   0.2    2.6  2  zf-FCS           MYM-type Zinc finger with FCS sequence motif
       0.96   10.0   7.4          2    8.9   7.4    1.4  1  zf-TAZ           TAZ zinc finger
        1.4    9.1   7.0        3.5    7.8   0.3    2.5  2  Zn-ribbon_8      Zinc ribbon domain
        2.2    9.1   8.7        5.2    7.9   2.5    2.3  2  zinc_ribbon_15   zinc-ribbon family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.6   1.8e+03      74      87 ..      74      87 ..      22     111 .. 0.58
   2 !   60.6   0.0   5.1e-20   1.5e-16       7     170 ..     146     304 ..     143     306 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.6
                                      HHHHHHHHHHHHHH CS
                   Phage_integrase 74 eealellkellska 87
                                      e a++ + +++ ++
  gi|313126106|ref|YP_004036376.1| 74 EDAAKKIVRWIHRT 87
                                      44444444444444 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 5.1e-20
                                       HHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGG.EECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHH CS
                   Phage_integrase   7 everllaaleeslkirdklllellyetGlRisEllsLrvkd.ldlengvilvheregKgskeravplseealellke 82 
                                       +v  l++a+++    rd++l+++ ++ G+R +El++L+v+d  d e+g+ +    +gK++ +r+vpl    ++ l++
  gi|313126106|ref|YP_004036376.1| 146 DVLPLIQATRN---PRDAALIAVGWDAGARSGELRALTVGDiTDYEHGYQIT--VQGKMG-QRTVPLI-PSVPFLQR 215
                                       55667777777...89*************************88999999887..788886.79***96.5689**** PP

                                       HHHHHCHCCTTTSBSSBET..TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT- CS
                   Phage_integrase  83 llskaleeaeksellfask..rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGH 157
                                       +l+ +     + e+ + sk  + +  s +++r+a+k a+ +ag++kp+t+  lR+s a++L+ +g+++  +++  G+
  gi|313126106|ref|YP_004036376.1| 216 WLAAH--PSTDAEAPLWSKltEPEAPSYNALRTAVKDAADRAGVNKPVTFTNLRKSSASHLASRGLNQAHIEDHHGW 290
                                       *****..4444444555553334556889************************************************ PP

                                       SSCCHH.HHHHCCC CS
                   Phage_integrase 158 ssistt.qiYthva 170
                                       +  s + ++Y+ v+
  gi|313126106|ref|YP_004036376.1| 291 TRGSDVaSRYVSVF 304
                                       ******9***9987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   9.3   2.5e-07   0.00074       1      49 []     334     385 ..     334     385 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.5e-07
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa...edrCpsCgekvdpearfCpeCG 49 
                                       Cp+C++++p +   C +C++++++++a   e++C  Cg++++  +   p+C+
  gi|313126106|ref|YP_004036376.1| 334 CPRCHQQTPREMDRCIHCRQAIDKETAiqrEQTCEWCGSSISDYSDHIPNCT 385
                                       ***********************9999***************9999999995 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2    0.0054        16       3      13 ..     345     355 ..     344     364 .. 0.85
   2 ?    5.0   0.5    0.0078        23       5      26 ..     366     388 ..     363     395 .] 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0054
                            zf-FCS   3 kkrCwfCkkyi 13 
                                       ++rC +C++ i
  gi|313126106|ref|YP_004036376.1| 345 MDRCIHCRQAI 355
                                       89*******87 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0078
                            zf-FCS   5 rCwfCkkyikgkpef.tyvlend 26 
                                       +C++C+  i++  ++ ++++ ++
  gi|313126106|ref|YP_004036376.1| 366 TCEWCGSSISDYSDHiPNCTRIN 388
                                       8*******998887777776655 PP

>> zf-TAZ  TAZ zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.4   0.00067         2      13      68 ..     336     386 ..     329     390 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00067
                            zf-TAZ  13 kCkeaekeekCkklpsCkkmkellkHlksckkkkeCkvkvCkslrqllr.haksCke 68 
                                       +C++++      ++ +C ++++ +   ++++++++C+  +C s+ +  + h+ +C++
  gi|313126106|ref|YP_004036376.1| 336 RCHQQT---PR-EMDRCIHCRQAIDKETAIQREQTCE--WCGSSISDYSdHIPNCTR 386
                                       455555...44.699***************97778**..***99998888*****97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0012       3.5      24      38 ..     328     343 ..     317     345 .. 0.75
   2 ?    3.7   1.6     0.022        66       7      34 ..     347     372 ..     347     375 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                       Zn-ribbon_8  24 aplta.CPeCgsevrr 38 
                                       a  ++ CP+C++++ r
  gi|313126106|ref|YP_004036376.1| 328 ATAPVeCPRCHQQTPR 343
                                       446666******8777 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.022
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                       rC  C +  ++  +i +  +++C  Cgs
  gi|313126106|ref|YP_004036376.1| 347 RCIHCRQAIDKETAIQR--EQTCEWCGS 372
                                       79999999997777664..678*****9 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.5    0.0017       5.2      64      85 ..     327     351 ..     302     352 .. 0.77
   2 ?    4.9   0.4     0.015        44      59      85 ..     357     384 ..     352     385 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                    zinc_ribbon_15  64 e...kkeCknCgkeveeefkyCpkC 85 
                                       +     eC++C++++  e++ C +C
  gi|313126106|ref|YP_004036376.1| 327 DataPVECPRCHQQTPREMDRCIHC 351
                                       2344789****************** PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.015
                    zinc_ribbon_15  59 kkesse.kkeCknCgkeveeefkyCpkC 85 
                                       k+++++ +++C+ Cg+++++ +++ p+C
  gi|313126106|ref|YP_004036376.1| 357 KETAIQrEQTCEWCGSSISDYSDHIPNC 384
                                       3333334899****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2413.74
//
Query:       gi|313126107|ref|YP_004036377.1|  [L=358]
Description: hypothetical protein Hbor_13500 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-42  145.9   0.0    1.9e-42  145.7   0.0    1.1  1  DUF4238   Protein of unknown function (DUF4238)


Domain annotation for each model (and alignments):
>> DUF4238  Protein of unknown function (DUF4238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.7   0.0   1.1e-46   1.9e-42       1     271 [.       6     274 ..       6     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 1.1e-46
                           DUF4238   1 khHyvPrfyLknFakdknklvnvydletkkieersvkricgekdmYtiknedsgedpnhiEktlaklEskaakiirk 77 
                                       ++HyvPrfyL+nF++d ++++++y+++++++++ +++r+c+++++Y+        d++++Ek  + +Es ++k + +
  gi|313126107|ref|YP_004036377.1|   6 NQHYVPRFYLRNFSDD-GQKIWLYNMQANREFTEPISRVCARDYFYS--------DETDVEKEIGSIESALSKGLGE 73 
                                       8***************.******************************........4899****************** PP

                           DUF4238  78 ilk.....egkstrtltreerkqlrkflfllkyRtprfreeydtedkeelesymrekkkfekpldelldelkvildt 149
                                       +l+     + +++++l+  +   +++fl+++  Rt    ee++++ +  +e++ r   +  ++  ell+e++  +  
  gi|313126107|ref|YP_004036377.1|  74 LLAiqsvsKFQTEKELK-PDWLRVLQFLTFQEARTALSKEEIEQDGEVMFETFVRAGIEAGELDPELLEEVREGNVW 149
                                       98888895555555555.56777889*********555555555666666666666666666666777777777777 PP

                           DUF4238 150 kvdleetllqeafeddaewfikhleelywalleassdedFitsDnPvflrndestgeeglsaysey....hillPls 222
                                        ++ +    q + +    +++++l++l+ +ll+++++ +++tsD+Pv+ +n+   ge +++ ++      +i++Pl+
  gi|313126107|ref|YP_004036377.1| 150 LEHEQ--SPQLLPMLYQLHCAPLLADLWGTLLVNKTGTELVTSDHPVVRHNPYFLGEGHPQEIGLQsrglQIYCPLT 224
                                       77777..99***********************************************999999988899********* PP

                           DUF4238 223 pkllLvlrsnsleeekedake.iekisreyvkkiNaillqnAkkfiiard 271
                                       ++++L+l +++++e + +++  +e ++++ ++++N++++ n+++++++ +
  gi|313126107|ref|YP_004036377.1| 225 SHHYLLLHDPECYEIECSSEGvREIHDTAVINELNKLQIVNCDNNVFYGT 274
                                       **************888776689999********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 2310.34
//
Query:       gi|313126108|ref|YP_004036378.1|  [L=112]
Description: hypothetical protein Hbor_13510 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 730.95
//
Query:       gi|313126109|ref|YP_004036379.1|  [L=463]
Description: ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-25   88.9   0.0    1.4e-23   84.0   0.0    2.2  1  ATPase_2     ATPase domain predominantly from Archaea
    1.5e-16   60.7   0.0    3.3e-16   59.6   0.0    1.6  1  DUF234       Archaea bacterial proteins of unknown function
    2.9e-07   30.6   0.0      5e-07   29.8   0.0    1.4  1  AAA_14       AAA domain
    2.9e-06   27.8   0.5    3.3e-05   24.3   0.5    2.5  1  AAA_16       AAA ATPase domain
    8.8e-06   26.0   0.0    0.00027   21.2   0.0    2.2  2  AAA_22       AAA domain
     0.0017   18.3   0.0     0.0044   17.0   0.0    1.7  1  HTH_45       Winged helix-turn-helix
     0.0041   17.0   0.0     0.0089   15.9   0.0    1.5  1  TFIIE_alpha  TFIIE alpha subunit
  ------ inclusion threshold ------
       0.09   12.6   0.0       0.21   11.4   0.0    1.7  1  HTH_IclR     IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.0   6.4e-27   1.4e-23       1     233 []       4     202 ..       4     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 6.4e-27
                          ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkk 77 
                                       F++R +el++l  ++e++ +e  +i+G+++ GKtaL+k++i++ ed    v+y  + ++    +l++f         
  gi|313126109|ref|YP_004036379.1|   4 FVNRTEELSRLHALYESSDAELAVIFGRRRLGKTALVKQSIKQYED---AVVYQAK-QKTTALQLRQF--------- 67 
                                       9*****************************************9966...6776544.44455556666......... PP

                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltk 154
                                         +a+++  p ++           + + +e++l  + ++    i+++De+++l+    +++ +l + L+ ++++ + 
  gi|313126109|ref|YP_004036379.1|  68 -IDAAAESYPGVT----------RIREDWENVLGYLAEQD--AIVVLDEFPYLV----EQDPSLPSVLQAMFDHELD 127
                                       .344445556644..........47899*********995..5***********....788**************** PP

                          ATPase_2 155 ekhlcvviclsSeglfie.rvyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyryvGGkPka 229
                                       +  +++v+++sS +++ e  +  +s+l+gr++  ++v+ l ++ a++f+++        + ++  + + ++GG P++
  gi|313126109|ref|YP_004036379.1| 128 DSAATFVLVGSSISMMEEaALLGNSPLYGRSSLkLDVRQLPFDAAMDFFDDA------YTADEQVLTWGVFGGVPYY 198
                                       ******************8899*****************************6......488999************* PP

                          ATPase_2 230 lvel 233
                                       l+e+
  gi|313126109|ref|YP_004036379.1| 199 LEEV 202
                                       *987 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   1.5e-19   3.3e-16       1      91 [.     310     395 ..     310     406 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1.5e-19
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwWkkeeeiDivalde 77 
                                       wf+fvy   +++++  ++++   +++el ++v+  FE+l+  +l++l  ++    ++t+ G+wW+ e+eiD+v+l+ 
  gi|313126109|ref|YP_004036379.1| 310 WFHFVYGTGEQYDQLGENAYDALVEPELADFVSRSFEDLCCSALRSLYPKH----TITETGQWWYGEHEIDVVGLTT 382
                                       ************99876666699**********************887755....588******************* PP

                            DUF234  78 eekkalfgEvKwkn 91 
                                       +e ++++gE+K+++
  gi|313126109|ref|YP_004036379.1| 383 NE-TLIVGECKFQQ 395
                                       *9.5********98 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.2e-10     5e-07       4     107 ..      25     145 ..      22     170 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.2e-10
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.........kllelileklke......... 62 
                                       + vi G Rr GKT l+kq ik++    + ++y + ++ +  +l+++             +       +         
  gi|313126109|ref|YP_004036379.1|  25 LAVIFGRRRLGKTALVKQSIKQYE---DAVVYQAKQKTTALQLRQFIdaaaesypgV--T-------Riredwenvl 89 
                                       679*****************9998...666666666655555554421222112220..2.......1233344466 PP

                            AAA_14  63 ....ekktylflDEiqev....pewekalkslvdeg...knldvivtGSnskllsk 107
                                           e++ +++lDE  ++    p++ ++l+ ++d++   +   +++ GS+ +++ +
  gi|313126109|ref|YP_004036379.1|  90 gylaEQDAIVVLDEFPYLveqdPSLPSVLQAMFDHElddSAATFVLVGSSISMMEE 145
                                       67778999******9888777788999999999955433678********999865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.5   1.5e-08   3.3e-05       1      76 [.       3      71 ..       3     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.5e-08
                            AAA_16  1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76
                                      ++v R eel++L++++e   s++ el ++ G +  GK++lv++  +++e++ ++ +++k++ l     + ++++a+
  gi|313126109|ref|YP_004036379.1|  3 EFVNRTEELSRLHALYE---SSDAELAVIFGRRRLGKTALVKQSIKQYEDAVVYQAKQKTTAL----QLRQFIDAA 71
                                      5999*************...5556999**************9999999999444455555555....444455544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.2e-07   0.00027       4     130 ..      22     138 ..      18     142 .. 0.82
   2 ?    2.4   0.0     0.077   1.7e+02      37      95 ..     220     280 ..     202     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.2e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelle 80 
                                       +a + v++G    GKT l+++  +q+           + v ++++++t+  +l++ +  a ++       + +e +e
  gi|313126109|ref|YP_004036379.1|  22 DAELAVIFGRRRLGKTALVKQSIKQY----------EDAVVYQAKQKTTALQLRQFIDAAAESYPGV--TRIREDWE 86 
                                       67899********************8..........688999***********99999999987666..89****** PP

                            AAA_22  81 aleqalraravielliiDEaqhlr.s.eealeeLrsllnl..srkgvqliLvGt 130
                                        +  +l ++++  ++++DE+ +l  + + + + L  +++   +++  +++LvG 
  gi|313126109|ref|YP_004036379.1|  87 NVLGYLAEQDA--IVVLDEFPYLVeQdPSLPSVLQAMFDHelDDSAATFVLVGS 138
                                       *********99..*********97633323333344444455578888888886 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.077
                            AAA_22  37 e.....erpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraraviell 95 
                                       +     e++ v++++l+++t   ++l++++   +++++   +++   +++l ++l++ ++  l 
  gi|313126109|ref|YP_004036379.1| 220 HgtlhdEPDYVLRMELTEPTRYFSILEAIAGGSTSRNEI-AGTTGIDYNQLSKYLNRLSR--LR 280
                                       244554566666********************9998888.88888888999999998887..44 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     2e-06    0.0044       9      51 ..     242     284 ..     240     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                            HTH_45   9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikk 51 
                                       ++ILeai  g+++  +i     ++y++l+kYL+ L    l+++
  gi|313126109|ref|YP_004036379.1| 242 FSILEAIAGGSTSRNEIAGTTGIDYNQLSKYLNRLSRLRLVDQ 284
                                       78**********************************9999965 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     4e-06    0.0089      14      62 ..     240     287 ..     228     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4e-06
                                       HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                       TFIIE_alpha  14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr 62 
                                         + +l++++  g ++ +++a  ++id n+l k LnrL   rlv+ +  
  gi|313126109|ref|YP_004036379.1| 240 RYFSILEAIA-GGSTSRNEIAGTTGIDYNQLSKYLNRLSRLRLVDQHVP 287
                                       5678999999.9999*****************************98754 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.5e-05      0.21       4      50 ..     240     284 ..     238     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.5e-05
                                       HHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   4 RalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       R ++iL+a+a +       e+A  tg+     + +L+ L +l++v q
  gi|313126109|ref|YP_004036379.1| 240 RYFSILEAIAGGSTS--RNEIAGTTGIDYNQLSKYLNRLSRLRLVDQ 284
                                       889*********996..9***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2697.88
//
Query:       gi|313126110|ref|YP_004036380.1|  [L=649]
Description: penicillin-binding protein, beta-lactamase class c [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-54  184.3   4.5    4.8e-54  183.8   4.5    1.2  1  Beta-lactamase  Beta-lactamase


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.8   4.5   2.7e-58   4.8e-54       1     323 [.      49     376 ..      49     383 .. 0.89

  Alignments for each domain:
  == domain 1  score: 183.8 bits;  conditional E-value: 2.7e-58
                                       HHHHHHHHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEEST.TSBEEEGGGHHHHHHHHHHHHHHTTSSCTT CS
                    Beta-lactamase   1 ldrlvrelmaqggipGvavavvrdgkvvldkggGvadleggrpvta.dtlfriaSvtKtftaaavlqlveeGkldLd 76 
                                       +d+lv+   + +++pG+ vavv+dg + l+kg+Gvad+++   v+a +tlfr +Sv+K++ ++a++q v  G ++ +
  gi|313126110|ref|YP_004036380.1|  49 VDDLVETSLEAHDVPGATVAVVVDGDIALTKGYGVADRNTDTAVDAeQTLFRAGSVSKAVLWTAIMQRVTSGDINPN 125
                                       689999999*************************************9****************************** PP

                                       SBGGGTST..TCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSS..TTSCEE-SHHHH CS
                    Beta-lactamase  77 dpVskylP..efagpgkgkiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkya..pGtkwgYsntgy 149
                                       +pVs yl   ++ +p +++iT+++L+tH++G+ +   ++l ++++ + + l   l+t++p++   pG+  +Ysn+g+
  gi|313126110|ref|YP_004036380.1| 126 APVSTYLDdiQLSTPYDEPITMAHLATHRAGFEAS-NRGLWIRDPTNLRPLSTHLKTAQPACVrpPGEVGSYSNYGA 201
                                       **********99********************999.99999999999999999999999988777************ PP

                                       HHHHHHHHHHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC....TTTBEE CS
                    Beta-lactamase 150 gllgellekvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae....gaggli 222
                                        l+g +l+ vt +++ ++++ ++l+p gm + ++ +p ++  + +++    +p+    +  ++ +++    +ag + 
  gi|313126110|ref|YP_004036380.1| 202 ALAGGVLASVTNTTFTEAIDSQLLTPAGMSSSSFEQPLPDSLASRHATGY-PPGD---VFADGEFPYvglrPAGSMS 274
                                       *************************************9999888888833.2222...2222222335678****** PP

                                       EEHHHHHHHHHHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEECECSSEEEEECCHTEEEEEEE..STEEEEEEE CS
                    Beta-lactamase 223 stardlarflglalegglllsaetlaqltaklssgttrpagiraglglGwvladktgapgtfghtG..ggygtyvfv 297
                                       +ta+d+arf++ +l++g + ++++la  t      ++++  +    +    l+++ g+ +t++h G    +++ + +
  gi|313126110|ref|YP_004036380.1| 275 TTAADMARFMQIHLNDGVVDGERVLASETVDSLHEQWATHHDQLPGMAFGLLEKYYGDVRTLWHNGstIAFHSDLLL 351
                                       **********9999999999999999999998888888888777753333455555559****************** PP

                                       ECGGTEEEEEEESBCSSHHHHHHHHH CS
                    Beta-lactamase 298 dpeanlvvavltnrdppnedaaedar 323
                                       +pe++l+++v  n+ ++ + a++d +
  gi|313126110|ref|YP_004036380.1| 352 VPERGLGLFVSYNGSGG-AAARSDVT 376
                                       ****************8.66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 4185.00
//
Query:       gi|313126111|ref|YP_004036381.1|  [L=197]
Description: hypothetical protein Hbor_13540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.2   0.1      0.048   13.4   0.1    1.4  1  DUF3334   Protein of unknown function (DUF3334)


Domain annotation for each model (and alignments):
>> DUF3334  Protein of unknown function (DUF3334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.7e-06     0.048      51      82 ..     148     180 ..     129     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-06
                           DUF3334  51 fvlf.dGgfsGlvvinfsaeaaleiyrsymlnm 82 
                                       f+l+ d g++Gl+ i f+ +aal +y++y+   
  gi|313126111|ref|YP_004036381.1| 148 FSLVpDLGYAGLIAIGFAVSAALHVYTEYVAVE 180
                                       5554489**********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1201.37
//
Query:       gi|313126112|ref|YP_004036382.1|  [L=141]
Description: disulfide bond formation protein dsbb [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-15   58.1  10.9    4.2e-15   56.5  10.9    1.7  1  DsbB      Disulfide bond formation protein DsbB
  ------ inclusion threshold ------
        3.1    7.3  11.6       0.16   11.5   4.3    2.0  2  BRI3BP    Negative regulator of p53/TP53


Domain annotation for each model (and alignments):
>> DsbB  Disulfide bond formation protein DsbB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5  10.9   4.7e-19   4.2e-15       3     145 ..       7     129 ..       5     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 4.7e-19
                                       HHHHHHHHHHHHHHHHHHHHHCTTTTSXXSHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHHHHHHHH CS
                              DsbB   3 llllllalaslallalAlyfqhvlglePCelCvyqRlallliallallaaiapkrllllllallaalvgaalaarhv 79 
                                        +l++ +l+++++ +++l+f   lgl PCelC+yqR++++ ++++  +a i  +   ++  al +++vg+a++a+hv
  gi|313126112|ref|YP_004036382.1|   7 GVLAVSTLVAVVATVGSLFFSLSLGLVPCELCWYQRILMYPLVVVLAVATIEDR-PGVYRTALPLSVVGMAVSAYHV 82 
                                       5678889999********************************999999997777.5678889999************ PP

                                       HHHHSX-SSTSB-BSXXXTTSXHHHHSSTTTTTXXSSSSSSSXECTT..SEHHHHHHHHHHHHHHHHH CS
                              DsbB  80 gvellpwdpasCgslptfpealpldewlpevfkatgdCgeadwkllg..lsmaqwnllifalllllll 145
                                       +v+  p++  +C                       g C+++++ +lg  l+++  +l++f+l+++l++
  gi|313126112|ref|YP_004036382.1|  83 YVQIAPSA-GTCT--------------------LGGGCSAIQYPMLGglLTIPRLALIAFFLVTVLVA 129
                                       ***88774.6994....................5566************************9999875 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.3   1.7e-05      0.16      74     137 ..      10      73 ..       2      87 .. 0.80
   2 ?   -0.2   0.8      0.07   6.2e+02      76      97 ..     111     132 ..     105     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.7e-05
                            BRI3BP  74 al.llwgllAllayWlLslllgllvallgrvlwllkvvlfllaflyilskeeaeae..taallLlgl 137
                                       a+ +l++++A ++  ++sl lgl+ + l    w  ++ ++ l+ ++ ++  e+++   ++al+L ++
  gi|313126112|ref|YP_004036382.1|  10 AVsTLVAVVATVGSLFFSLSLGLVPCEL---CWYQRILMYPLVVVLAVATIEDRPGvyRTALPLSVV 73 
                                       4437999******************999...899999999999999999999987511567777655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.07
                            BRI3BP  76 llwgllAllayWlLslllgllv 97 
                                       l +  lAl+a++l+ +l+  + 
  gi|313126112|ref|YP_004036382.1| 111 LTIPRLALIAFFLVTVLVAGVC 132
                                       5666789999999988887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 923.93
//
Query:       gi|313126113|ref|YP_004036383.1|  [L=192]
Description: hypothetical protein Hbor_13560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   18.3   1.3     0.0017   18.0   1.3    1.1  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.3   9.6e-08    0.0017      66     113 ..     123     170 ..     103     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.6e-08
                              TauE  66 llllllgsliGallGallllllpsellkllfgvlllllallmllrkkr 113
                                       l ll+l sl+G+ +G+ +l++l+++l+  +f++l++++a++ l+ +++
  gi|313126113|ref|YP_004036383.1| 123 LGLLGLLSLVGSGIGVPVLARLDGALVGGAFSLLVVVSAIYQLVDQRS 170
                                       56899*************************************995553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1200.05
//
Query:       gi|313126114|ref|YP_004036384.1|  [L=668]
Description: hypothetical protein Hbor_13570 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-90  304.0   7.2      9e-76  255.2   1.1    2.1  2  SpoVR           SpoVR like protein
  ------ inclusion threshold ------
      0.044   13.7   0.0       0.51   10.2   0.0    2.3  2  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox


Domain annotation for each model (and alignments):
>> SpoVR  SpoVR like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.2   1.1     1e-79     9e-76       6     327 ..      14     351 ..       9     372 .. 0.83
   2 !   52.3   0.6     4e-18   3.5e-14     330     417 ..     478     563 ..     450     564 .. 0.86

  Alignments for each domain:
  == domain 1  score: 255.2 bits;  conditional E-value: 1e-79
                             SpoVR   6 eleeakeeieeiakelgLdfypnqfeiitaeqmleaaayvgmPlrysHWsfGkeyeklkksykyglsklaYElViNs 82 
                                       elee  +e  ++a++lgL+ yp+++ ++++++m+++ ay+g+  ry+HW++G++y++++k+ ++g+ k  +E+V N 
  gi|313126114|ref|YP_004036384.1|  14 ELEESVREAGNLARKLGLKPYPVNYWVVNYDEMNQLIAYGGFQRRYPHWRWGMTYDRQQKKDQFGMGKA-FEIVNND 89 
                                       7899999999********************************************************998.******* PP

                             SpoVR  83 dPciaylleeNslvqqklviAHvygHndFFknNalFkkttdar..kildslalaaerireyee..ryGeeeVEklld 155
                                       +P+ a+l e+Nsl++qk vi Hv +H+dFF nN +F     ++  +   +l+++ e+i++y++   + +e+VE+++d
  gi|313126114|ref|YP_004036384.1|  90 NPSHAFLQESNSLADQKAVITHVEAHADFFSNNEWFGMFAGDSdlDAAAMLEQHGETIQKYMDdpDIDREDVERFID 166
                                       ************************************98874431156778999*********988899********* PP

                             SpoVR 156 aalaleelvdrykrkekkkleeeekrkkereeyesqvedlwrtle....ekkkkeeeekekeekfpeepeedlllFl 228
                                       a+l le+++d+++++++  + +e+ + ++ ++  ++++   ++ +    e+  +e +e+e+e+    +p++d+l F+
  gi|313126114|ref|YP_004036384.1| 167 AVLCLEDNIDQHRTITDAATGRERVQPEDLRKRLDEMDISQDVRKqvfdEEWLDELAEAEAEAAKLDDPRRDVLAFV 243
                                       **************977777766666666555554433332222211112333344444445678899********* PP

                             SpoVR 229 ekn..........apeLeeWqrdilrivreeaqYFlPQrqtkimNEGwAsywHstilnel.kltdeeileflkshsg 294
                                       +++          a e+e+Wq+d+l i+r+e++YF+PQ++tk+mNEGwA+yw s ++ e     ++e+l +++++s 
  gi|313126114|ref|YP_004036384.1| 244 REHgmyydeeegkAVEMESWQKDVLDILRTESYYFAPQKMTKVMNEGWAAYWESLMMGEErFAGTDEFLTYADHQSR 320
                                       98733333333334579****************************************998355689*********** PP

                             SpoVR 295 vvapsksglNPYalGlklfedierrveepteee 327
                                       v+     glNPY+lG +l+e+ie+++++ +  +
  gi|313126114|ref|YP_004036384.1| 321 VLG--SPGLNPYKLGKELWEYIENTTNRREVAD 351
                                       *95..579****************997665554 PP

  == domain 2  score: 52.3 bits;  conditional E-value: 4e-18
                             SpoVR 330 kfdkkagegreklfevrelekDesfirqyLtkelvrelklfslkkkeeeeeveaiidekgykkvrekLlkqltnagl 406
                                         d   ++g ++++e+re ++D++f++ +Lt+e+v++ + f+++ ++ +   e  + + +y++v++kLl q+tn+g+
  gi|313126114|ref|YP_004036384.1| 478 IADVDRASGWDRMQEIRESHNDVTFLDAFLTQEFVENNHYFTYEFTQATG--EFRVASVDYEDVKKKLLLQFTNFGK 552
                                       334444556679************************************99..999********************** PP

                             SpoVR 407 paiqvedvdle 417
                                       p+i v d++++
  gi|313126114|ref|YP_004036384.1| 553 PTIVVFDGNYD 563
                                       *********97 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   5.7e-05      0.51       6      30 ..      17      41 ..      14      48 .. 0.88
   2 ?    0.3   0.1     0.072   6.5e+02      50      61 ..     190     201 ..     180     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.7e-05
                    YdaS_antitoxin  6 eivGgqkaLAealgvsqqaVsqWlk 30
                                      e+v+++  LA++lg ++  V++W+ 
  gi|313126114|ref|YP_004036384.1| 17 ESVREAGNLARKLGLKPYPVNYWVV 41
                                      579999*****************95 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.072
                    YdaS_antitoxin  50 eVtreeLRpDvd 61 
                                       +V++e+LR+ +d
  gi|313126114|ref|YP_004036384.1| 190 RVQPEDLRKRLD 201
                                       69*******988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 3849.43
//
Query:       gi|313126115|ref|YP_004036385.1|  [L=441]
Description: hypothetical protein Hbor_13580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-130  436.6   0.3   1.2e-130  436.5   0.3    1.0  1  DUF444    Protein of unknown function (DUF444)


Domain annotation for each model (and alignments):
>> DUF444  Protein of unknown function (DUF444)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.5   0.3  6.4e-135  1.2e-130      13     421 .]       3     438 ..       1     438 [. 0.95

  Alignments for each domain:
  == domain 1  score: 436.5 bits;  conditional E-value: 6.4e-135
                            DUF444  13 slenrqRflrrvkeqikeavadavsersikdiskgekikipikdikepefeygkggeregVlpGnkef.keGdkier 88 
                                         e+ +Rf r+++e+++e++++++s++++ + s  ++ikipik +++pef+y+ + +++gV++G++ + + G+++++
  gi|313126115|ref|YP_004036385.1|   3 LREDVERF-REIGEERREDLKEFISYGNLGG-SGPDSIKIPIKVVDLPEFQYD-QLDQGGVGQGKDGTpDVGQPVGQ 76 
                                       6799****.**********************.*********************.***********99989******* PP

                            DUF444  89 peeggggggsgegseaGe.gedefefelsreEfldllfedLeLPdLekkklekveekktkragytrkGspsnldvkr 164
                                       p+ g+g+g+ +e++e+Ge g+d++++e+++eEf+++l+e+L+L dLe+k++e++ee++++++++tr+G++s+ld++r
  gi|313126115|ref|YP_004036385.1|  77 PQPGDGDGDGDEDGEPGEeGADHEYYEMDPEEFAQELDEELGL-DLEPKGKEVIEEIEGDFTDVTRTGPHSTLDFER 152
                                       ****999876666999955************************.********************************* PP

                            DUF444 165 tlrealkRrialkrpkeeelre.......leeelaelea.....................eeeekeseeleeleeei 213
                                       +++e+lkR++a+++ +++ +re         ++++++++                     e+++++s e++e+++e+
  gi|313126115|ref|YP_004036385.1| 153 LFKEGLKRKLAMDF-DDDFVREamkvegeDPQSVYQWCRdqhilvslawiedewkripddERDTWSSYEEMEENVER 228
                                       **************.88888888888888778888888888888888888877777665433479************ PP

                            DUF444 214 eeleerikr.....ipfidelDlRYrrvekepkpesnaVmfclmDvSGSMdetkkdlakrfFilLylFLkrkYekve 285
                                       +++ +ri+r     ipf++e D+RYr++e  +++e+n+V+++++DvSGSM+e+k++l++r+F++L+++L+ kY+++e
  gi|313126115|ref|YP_004036385.1| 229 TTTLQRIRReglrdIPFRRE-DERYRHPEIIEEKEKNVVVVNIRDVSGSMREKKRELVERTFTPLDWYLTGKYDNAE 304
                                       ********************.******************************************************** PP

                            DUF444 286 vvFirHtteAkeVdeeeFFysresGGTvvSsalelmkeiieerYppseWNiYaaqasDgdnwseDsekavellaeki 362
                                       +v+i+H++eA++V+++eFF++r++GGT++Ssa+el+kei+ee+Yp+seWN+Y+++a+D++n+s+D++++v +l+++i
  gi|313126115|ref|YP_004036385.1| 305 FVYIAHDAEAWQVERDEFFGIRSGGGTRISSAYELAKEILEEEYPWSEWNRYVFAAGDSENSSNDTTENVVPLMKEI 381
                                       ***************************************************************************** PP

                            DUF444 363 lplvqyfaYveitpsaseeeqtlweeyekvaeeeenfamakvkekediypvfrellkke 421
                                          ++++aYve++p++++ ++t++ee+e+  ee+ n+++a+v+++ed++++++++l++e
  gi|313126115|ref|YP_004036385.1| 382 --PANLHAYVETQPGGTAINATHAEEVERSLEEQGNVVVAYVSSPEDVVDAIYDILSTE 438
                                       ..9*****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3151.11
//
Query:       gi|313126116|ref|YP_004036386.1|  [L=759]
Description: ser protein kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-41  141.2   1.0      1e-39  136.7   0.1    2.3  2  PrkA      PrkA serine protein kinase C-terminal domain
    5.4e-15   55.2   0.0    1.8e-11   43.6   0.0    3.2  2  AAA_PrkA  PrkA AAA domain


Domain annotation for each model (and alignments):
>> PrkA  PrkA serine protein kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.1    0.0085        76     178     232 ..     396     451 ..     376     462 .. 0.75
   2 !  136.7   0.1   1.2e-43     1e-39       1     252 [.     471     744 ..     471     747 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0085
                              PrkA 178 kelaasalaregkkidytsierlkealekklfedvkdllklisstk.tpdkeqqkk 232
                                       +el ++ l++e    d+++ e+l e + + lf dv++   ++++++  p   +   
  gi|313126116|ref|YP_004036386.1| 396 TELIRRELTNETDVWDVEDREELEERINESLFVDVRSGPGAVKRRElAPHAIEAAA 451
                                       4566888999999999*******************988888774442555555555 PP

  == domain 2  score: 136.7 bits;  conditional E-value: 1.2e-43
                              PrkA   1 leKmklYdgeel.pdsleeedvkeLreeaeereGmsGispRyvikilsealss......seakeekcinpldvleal 70 
                                       ++K+ l+d ++l  + ++e +++e+  ++++ eG +G++++++++i++++l +         ++ ++++p d+l+++
  gi|313126116|ref|YP_004036386.1| 471 VDKALLFDRGYLqVGDTRE-EIDEFGFDSDN-EGTHGVPVTFTRDIIADLLHEdrdrhhPSLEVGTVVMPDDLLDSM 545
                                       5899********6444444.88888878877.*******************997776542567899*********** PP

                              PrkA  71 eeglkeheviseeerekyleflevvreeydervkkevqeAllyseeeqieelvenYldhveayikkekvkdpiTgee 147
                                       +egl +++v+s+ er++y++++ vv+e++ + ++++v  A+l +++ + +e+v++Y++hv+a+  + ++++++   e
  gi|313126116|ref|YP_004036386.1| 546 AEGLHDAPVFSRAERSEYESRVTVVKEYIFDQQEADVLAAVL-ADKHVEQETVAEYVEHVYAWESDGQIETEHGPVE 621
                                       ****************************************77.******************************7775 PP

                              PrkA 148 lepderflrsiEeqig.........iseeakkdFRre.vikelaasalaregkkidyts.....ierlkealekklf 209
                                        ++  ++l+++E+  +          +  + k+FRre vi++l+++a++++++ +++++     i+ ++++le + +
  gi|313126116|ref|YP_004036386.1| 622 PDALLMKLFETEHLGRfaesdytgnEPSADVKEFRREkVITALNRYAWENRDEGFTVEDvelseIPVIRTVLETHEW 698
                                       5555888899999988*******9988899*****************************9***************** PP

                              PrkA 210 edvkdllklisstk....tpdkeqqkkveevverLvekfgYceacAr 252
                                       +dv  l + +  ++      ++e+++ +e++++ +  k+gY++a+A+
  gi|313126116|ref|YP_004036386.1| 699 DDVSRLFEDFDPDQwddpPANTETERVKERTIDHM-VKNGYTPASAE 744
                                       ****7776666444676555***************.666******95 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0     2e-15   1.8e-11       1     318 [.      23     397 ..      23     414 .. 0.76
   2 !    6.5   0.0   0.00037       3.3     331     352 ..     439     460 ..     416     465 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2e-15
                          AAA_PrkA   1 lslaeyleivkedksvaksaaerlldlikdkgl.elvdtaederlsrifsnetikkypafeedffGleetiekivey 76 
                                       +slaey+++  e +s+a +a + ll++i+  g  ++++  e++   r f + +       e+ + G  e++++ v+ 
  gi|313126116|ref|YP_004036386.1|  23 MSLAEYVDAAFESPSIASHASKYLLQAIEAAGTrTVIEEGEEKERYRFFDDPANDG----EHAVLGNTEVLNRFVDD 95 
                                       699******************************66666666666777777665444....34567***********9 PP

                          AAA_PrkA  77 fraaaqrleerkqilyllGPvggGksslverlkklleaa......piyal........................... 120
                                       +r+ a +  +  +i+++ GP ++Gks l   l + l ++        y++                           
  gi|313126116|ref|YP_004036386.1|  96 LRTIAAKRGKGEKIIWFDGPTATGKSELKRCLINGLREYsktlegRRYTVewnvtnvddsrglsyggevsgaehesd 172
                                       999888888888999***************999999988787888667778888999****************9998 PP

                          AAA_PrkA 121 .egsPvfeePlhlipeelrkkleeeygi........rlegllsPlatk...rleeef..gGdiekfkve......k. 176
                                         +sPv+ +Pl+++p e+r++l  e++          l+ +l P++      lee++   G+ + f  +      + 
  gi|313126116|ref|YP_004036386.1| 173 wYESPVQSHPLSVFPAEVRRSLLAELNEnedghipvSLDEELDPFCREaydYLEEKYrrTGKRNLFTAVsdpkhlRv 249
                                       889***************999987776545555677999*****997522257787744466555543211111121 PP

                          AAA_PrkA 177 ilfsilkrigiakvePgdennqdisalvGkv...dirkleeysendpdaysysGalnranrGllefvemfkadikvl 250
                                       +++ ++  +gi++++  d+ +     lvG+     +r+l++  +++p+a+sy+G l+++n Gll  ve      ++l
  gi|313126116|ref|YP_004036386.1| 250 KNYVVDVGQGIGVLHSEDDGSP-KERLVGSWmpsMLRELDSRGRKNPQAFSYDGVLSQGN-GLLTIVEDATQHADLL 324
                                       3455666788999888777654.56888886222589999999***************98.**************** PP

                          AAA_PrkA 251 hplltatqegnyksteklsl.ipfdgiilahsn.esewkkfksnkkn...ealldrivvvkvPyclrvseekk 318
                                         ll +  eg++k  + +++ i  + +i++  + ++e  k+ + +      al  r+ + +  y  +vs e+ 
  gi|313126116|ref|YP_004036386.1| 325 QRLLNVPDEGHVKLDKGIGMdIDTQLLIISNPDlDAELDKYSDRNGRdplKALKRRLDKHEFRYLTNVSLETE 397
                                       **************99999845555556655434678777754333212257777777777777777776655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00037
                          AAA_PrkA 331 dahiaPetlevlarfsiltrlk 352
                                       + ++aP+++e +a++s+++rl 
  gi|313126116|ref|YP_004036386.1| 439 RRELAPHAIEAAAMYSVVSRLD 460
                                       5679****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 4695.16
//
Query:       gi|313126117|ref|YP_004036387.1|  [L=690]
Description: ser protein kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-71  241.1  10.4    1.5e-71  241.1  10.4    2.3  2  PrkA         PrkA serine protein kinase C-terminal domain
    1.6e-65  221.4   0.0    2.6e-65  220.7   0.0    1.3  1  AAA_PrkA     PrkA AAA domain
     0.0035   17.5   0.8       0.18   12.0   0.1    2.6  2  RasGAP_C     RasGAP C-terminus
  ------ inclusion threshold ------
       0.07   13.1   0.2       0.26   11.3   0.2    2.0  1  Mad3_BUB1_I  Mad3/BUB1 homology region 1
       0.21   11.7   0.1        8.2    6.6   0.1    2.7  2  LysM         LysM domain
       0.33   10.9   2.2         23    5.0   1.0    3.3  3  AAA_5        AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> PrkA  PrkA serine protein kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3     0.078   2.3e+02     111     151 ..     220     260 ..     214     270 .. 0.83
   2 !  241.1  10.4     5e-75   1.5e-71       2     257 .]     426     678 ..     425     678 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.078
                              PrkA 111 llyseeeqieelvenYldhveayikkekvkdpiTgeelepd 151
                                       ll ++++  +e v n ++ v     ++k ++  T e ++ +
  gi|313126117|ref|YP_004036387.1| 220 LLAYYDDDLQEVVSNHIEIVRLVASENKRQCIETFEPKDKK 260
                                       56688899***********************9998866655 PP

  == domain 2  score: 241.1 bits;  conditional E-value: 5e-75
                              PrkA   2 eKmklYdgeelpdsleeedvkeLreeaee....reGmsGispRyvikilsealssseakeekcinpldvlealeegl 74 
                                       +K+k Y+ge+  d+ ++ dvk+Lreeae+     eGm+G+s+R++ + ++ea+++s+++++++++pl+v+ ++ee+l
  gi|313126117|ref|YP_004036387.1| 426 QKAKAYNGEI--DEGDDTDVKKLREEAESkmniGEGMEGVSARFIGDEIAEAIMDSTHRDRNYLSPLSVFTHFEENL 500
                                       7********7..788888******9999877777******************************************* PP

                              PrkA  75 keheviseeerekyleflevvreeydervkkevqeAllyseeeqieelvenYldhveayikkekvkdpiTgeelepd 151
                                       ++h++i+e++ e+y+++le+vreey+er+ ++v++Al+y+ +e i+++ e+Y+dhv+ayi++ +v+d+ Tg+e++pd
  gi|313126117|ref|YP_004036387.1| 501 ENHGSIPEDNLERYHRYLEMVREEYKERAIEDVRHALAYDLDE-IQRQGEKYMDHVMAYIDDATVQDELTGREQDPD 576
                                       ************************************9966666.********************************* PP

                              PrkA 152 erflrsiEeqigiseeakkdFRrevikelaasalaregkkidytsierlkealekklfedvk...dllklisstktp 225
                                       e+flrs+Ee+++i+e++k+dFR+ev +++  s+ areg+++d ++++rl++ale+kl+ed+k   ++++l+s+++ +
  gi|313126117|ref|YP_004036387.1| 577 EKFLRSVEEKLDIPEDRKDDFRQEVSNWV--SRRAREGQAFDPQDNDRLRRALERKLWEDKKhniNFSALVSANELD 651
                                       *****************************..*******************************9999******99999 PP

                              PrkA 226 dkeqqkkveevverLvekfgYceacArevleY 257
                                       d+e++ +v+++ve+     gY++++Arevle+
  gi|313126117|ref|YP_004036387.1| 652 DDERNAWVDALVEQ-----GYSREGAREVLEF 678
                                       ********999999.....***********98 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.7   0.0   8.7e-69   2.6e-65       2     355 ..      28     418 ..      27     421 .. 0.87

  Alignments for each domain:
  == domain 1  score: 220.7 bits;  conditional E-value: 8.7e-69
                          AAA_PrkA   2 slaeyleivkedksvaksaaerlldlikdkglelvdtaederlsrifsnetikkypafeedffG..leetiekivey 76 
                                       s+  yl+ v +d+ +a++a++r+ d+    g e    +e++ +      ++   ++  e+ f+G  + e+i+  v+ 
  gi|313126117|ref|YP_004036387.1|  28 SFEWYLDEVYNDPRIARNAHQRVADMFDYYGTEY---DEEAGIVEYLMASEDPIHD-GENTFYGreVHESIHEFVNK 100
                                       6888***********************9999885...4444444433333333333.345899944569******** PP

                          AAA_PrkA  77 fraaaqrleerkqilyllGPvggGksslverlkklleaa......piyal..................egsPvfeeP 129
                                       +++ a++l  +k+i +llGPvg+Gks +  ++++ +e++       +y++                    sP++++P
  gi|313126117|ref|YP_004036387.1| 101 VKSGARGLGPEKRIKLLLGPVGSGKSHFDWMVRRYFEDYtlrdegRMYTFrwtnltdvirdqdpaddvVPSPMHQDP 177
                                       *************************************9989999989999999999999*99999877789****** PP

                          AAA_PrkA 130 lhlipeelrkk........leeeygirlegllsPla...tkrleeefgGdiekf.....kvekilfsilkrigiakv 190
                                       + l+p+e+r++        l+  y ir +  l P +   + +l + ++ d++++     ++++++ s++kr+ i ++
  gi|313126117|ref|YP_004036387.1| 178 IVLLPQEQRDMvierlneaLDAPYTIRNDQALDPASefyMDQLLAYYDDDLQEVvsnhiEIVRLVASENKRQCIETF 254
                                       *****99988721121111334466688888988762114577788999987642222289999************* PP

                          AAA_PrkA 191 ePgdennqdisalvGkvdirkleeysendpdaysysGalnranrGllefvemfkadikvlhplltatqegnykstek 267
                                       eP d++nqd ++l+G v+ +kl+ y e+dp+a+ ysGa+++anrGl+   e++k + ++l+ +l a qe+++k  ++
  gi|313126117|ref|YP_004036387.1| 255 EPKDKKNQDETELTGDVNYSKLAVYGESDPRAFDYSGAFCNANRGLFSGEELLKLQREFLYDFLHASQEQTIKP-KN 330
                                       ************************************************************************97.88 PP

                          AAA_PrkA 268 lslipfdgiilahsnesewkkfksnkknealldrivvvkvPyclrvseekkiyekllkeseladahiaPetlevlar 344
                                          i +d++i+  +n  e+++ k ++k ea+ dr   ++ Py+l+ see  iy k+l+++++ d hi P+tle++  
  gi|313126117|ref|YP_004036387.1| 331 NPRIDIDQVIVGRTNMPEYRDKKGDEKMEAFNDRTKRIDFPYVLEYSEESEIYRKMLRNADVPDMHIEPHTLEMAGL 407
                                       899************************************************************************** PP

                          AAA_PrkA 345 fsiltrlkese 355
                                       f +ltr+ e++
  gi|313126117|ref|YP_004036387.1| 408 FGVLTRIVEPD 418
                                       *******9986 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.032        96      67     122 ..     215     275 ..     206     281 .. 0.70
   2 !   12.0   0.1     6e-05      0.18      32      93 ..     470     531 ..     466     567 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.032
                          RasGAP_C  67 nylesqlesYkayienvleql.........kkkkgklpfskqyfkkrelkksgklpkfgsykysa 122
                                        y+ + l++Y++ +++v+++          + +k++     ++f+ +++k++++++ +g + ys 
  gi|313126117|ref|YP_004036387.1| 215 FYMDQLLAYYDDDLQEVVSNHieivrlvasE-NKRQ---CIETFEPKDKKNQDETELTGDVNYSK 275
                                       466777899***********99999988642.2222...22345556667777777777777775 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6e-05
                          RasGAP_C  32 neIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkkgk 93 
                                       +eIa+ i    ++ ++  + l++ ++  ++L+++ +  e+ le Y++y+e v+e+ k++  +
  gi|313126117|ref|YP_004036387.1| 470 DEIAEAIMDSTHRDRNYLSPLSVFTHFEENLENHGSIPEDNLERYHRYLEMVREEYKERAIE 531
                                       69999999999999999**************************************9998643 PP

>> Mad3_BUB1_I  Mad3/BUB1 homology region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   8.7e-05      0.26       5      50 ..     495     540 ..     492     570 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
                                       HHHHHHHTG.....-THHHHHHHHHHHHHH-TT-T.TT-HHHHHHHH CS
                       Mad3_BUB1_I   5 efeeeleea.eegdDpLelwlryikwieesypqsskesgllellerc 50 
                                       +fee+le++ +  +D Le ++ry++++ e+y++++  +++ + l   
  gi|313126117|ref|YP_004036387.1| 495 HFEENLENHgSIPEDNLERYHRYLEMVREEYKERA-IEDVRHALAYD 540
                                       79******976667*****************9955.33343333333 PP

>> LysM  LysM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.087   2.6e+02       7      18 ..       6      19 ..       3      26 .. 0.75
   2 ?    6.6   0.1    0.0027       8.2      14      33 ..     635     654 ..     635     660 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.087
                                      --HHHHHHHC..TC CS
                              LysM  7 DTLwsIAkry..gi 18
                                      DTL++++k y  ++
  gi|313126117|ref|YP_004036387.1|  6 DTLEDLSKHYkdSV 19
                                      9*********5433 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0027
                                       HHCTCHHHHHHHHCTCSSCG CS
                              LysM  14 krygitveklleaNnlsspd 33 
                                       k+++i++++l +aN+l+++ 
  gi|313126117|ref|YP_004036387.1| 635 KKHNINFSALVSANELDDDE 654
                                       689**************987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.047   1.4e+02       3      14 ..     116     127 ..     115     148 .. 0.86
   2 ?   -0.3   0.0      0.33   9.9e+02      69     109 ..     223     263 ..     186     288 .. 0.79
   3 ?    5.0   1.0    0.0077        23      34     110 ..     504     579 ..     498     662 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.047
                                       EEE--SSSSHHH CS
                             AAA_5   3 lLvGppGtgKse 14 
                                       lL+Gp G+gKs 
  gi|313126117|ref|YP_004036387.1| 116 LLLGPVGSGKSH 127
                                       89********95 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.33
                                       EEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---.. CS
                             AAA_5  69 lvlDEveraesevlnsLlslleerrllleeggelvkakndd 109
                                       +++D+++++ s+ ++++  + +e++++  e +e  ++kn+d
  gi|313126117|ref|YP_004036387.1| 223 YYDDDLQEVVSNHIEIVRLVASENKRQCIETFEPKDKKNQD 263
                                       57788888888888888888888888888888888777755 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0077
                                       TT--HHHHH--B--..........--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---.. CS
                             AAA_5  34 rdtteedlkgrreik.ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeggelvkakndd 109
                                        +++e++l    ++  + ++++++ ++   +r++  + lDE++r   + ++ ++ ++++ +++ +e++++++ + ++
  gi|313126117|ref|YP_004036387.1| 504 GSIPEDNLERYHRYLeMVREEYKERAIE-DVRHALAYDLDEIQRQGEKYMDHVMAYIDDATVQ-DELTGREQDPDEK 578
                                       5667777776666654667777766665.9999999***************************.6666666555544 PP

                                       . CS
                             AAA_5 110 l 110
                                       +
  gi|313126117|ref|YP_004036387.1| 579 F 579
                                       3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 4077.84
//
Query:       gi|313126118|ref|YP_004036388.1|  [L=136]
Description: hypothetical protein Hbor_13610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.2   0.0      0.077   13.2   0.0    1.5  1  DUF2188   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2188  Uncharacterized protein conserved in bacteria (DUF2188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-06     0.077      22      48 ..      86     112 ..      76     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-06
                           DUF2188  22 sktfdTqeeAieaArelAkeqggselv 48 
                                        + +d++e+A++ A+elA++  ++e+ 
  gi|313126118|ref|YP_004036388.1|  86 IEEYDSREAAVDGANELARRFADGEIA 112
                                       5789**************996688876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 872.85
//
Query:       gi|313126119|ref|YP_004036389.1|  [L=149]
Description: hypothetical protein Hbor_13620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-47  160.3   0.0    2.8e-47  160.1   0.0    1.0  1  UPF0179      Uncharacterised protein family (UPF0179)
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.034   14.2   0.0    1.3  1  MelC1        Tyrosinase co-factor MelC1
      0.027   14.7   0.5      0.053   13.7   0.1    1.7  2  DDE_Tnp_1_6  Transposase DDE domain
        0.1   13.2   0.9       0.49   11.0   0.1    2.1  2  Whib         Transcription factor WhiB


Domain annotation for each model (and alignments):
>> UPF0179  Uncharacterised protein family (UPF0179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.1   0.0   6.2e-51   2.8e-47       1     139 [.       3     143 ..       3     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 6.2e-51
                           UPF0179   1 kitLigkklAkeGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekt.eheCavheegvvaveveeapieal 76 
                                       k+tLig++lA++Gt+F+y g++++Ce+C+++k+ClnLe g +Y+++++re++   +Cavh++gv+aveve+ap++a+
  gi|313126119|ref|YP_004036389.1|   3 KVTLIGDRLAEPGTQFVYRGPSSACEGCPYRKQCLNLEVGVRYEVTGIRENAqLLDCAVHDTGVRAVEVEPAPVVAN 79 
                                       69*************************************************8567********************** PP

                           UPF0179  77 ieskkavegskitleseeCdevecesyelcepeglkegekvkivevlgeiee..ckkgrslkkve 139
                                       ++sk a++gsk++l+   C++++c+s+e+c peg++ +e+++i+ev g++++  c  +r+l++ve
  gi|313126119|ref|YP_004036389.1|  80 VPSKGAYAGSKASLA-GPCPHTQCPSHEYCVPEGADFDEEYRIAEVRGDPPHdfCYLDRDLTLVE 143
                                       ***************.***********************************99**********98 PP

>> MelC1  Tyrosinase co-factor MelC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.7e-06     0.034       5      51 ..      84     128 ..      80     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.7e-06
                             MelC1   5 aatagaalaglaaasasaaeapakaegsaepesFDevyrGrRiqGlp 51 
                                       +a ag+  a+la + +++ + p+++   +e+++FDe+yr   ++G p
  gi|313126119|ref|YP_004036389.1|  84 GAYAGSK-ASLAGPCPHT-QCPSHEYCVPEGADFDEEYRIAEVRGDP 128
                                       6667777.8999999999.8*******************99999977 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.2e-05     0.053      25      46 ..      19      40 ..       5      70 .. 0.77
   2 ?   -1.5   0.1      0.62   2.8e+03      34      45 ..     100     111 ..      92     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                       DDE_Tnp_1_6 25 vavyrlkdCrgCplreqCtkkk 46
                                      v +   ++C+gCp+r+qC + +
  gi|313126119|ref|YP_004036389.1| 19 VYRGPSSACEGCPYRKQCLNLE 40
                                      44456799**********8764 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.62
                       DDE_Tnp_1_6  34 rgCplreqCtkk 45 
                                       ++Cp  e C  +
  gi|313126119|ref|YP_004036389.1| 100 TQCPSHEYCVPE 111
                                       579999999765 PP

>> Whib  Transcription factor WhiB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00011      0.49      28      45 ..      25      42 ..      20      53 .. 0.77
   2 ?    0.3   0.1      0.24   1.1e+03      30      49 ..      97     118 ..      81     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                              Whib 28 avCarCpVrreCleeale 45
                                      + C+ Cp r++Cl+  + 
  gi|313126119|ref|YP_004036389.1| 25 SACEGCPYRKQCLNLEVG 42
                                      67**********987663 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.24
                              Whib  30 C..arCpVrreCleealeegee 49 
                                       C   +Cp  + C  e+ + +ee
  gi|313126119|ref|YP_004036389.1|  97 CphTQCPSHEYCVPEGADFDEE 118
                                       5546899999998777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 960.72
//
Query:       gi|313126120|ref|YP_004036390.1|  [L=271]
Description: succinylglutamate desuccinylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-11   42.8   0.0      1e-10   41.2   0.0    1.8  2  AstE_AspA      Succinylglutamate desuccinylase / Aspartoacyla
  ------ inclusion threshold ------
       0.09   12.5   0.0        5.2    6.8   0.0    2.2  2  DUF4166        Domain of unknown function (DUF4166)
       0.18   11.2   0.0       0.25   10.7   0.0    1.2  1  Peptidase_M99  Carboxypeptidase controlling helical cell shap


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   1.7e-14     1e-10       2      81 ..      10      83 ..       9     106 .. 0.80
   2 ?   -0.9   0.0      0.12   7.1e+02     250     250 ..     192     192 ..     129     253 .. 0.57

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.7e-14
                                      S-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSSTT-S-CTTTTTCCCCCSSTCHHH CS
                         AstE_AspA  2 gpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyipidredLNRaFpgrslgrsldeal 80
                                      +p v++++ +HG+E +G  ++++++ +        + + +++aN  A+a   Ryi+   edLNRaFpg+++ ++ + +l
  gi|313126120|ref|YP_004036390.1| 10 TPEVAVVGSIHGDEPCGASAIDRFVAEEPT---VDRPVKLIIANEEALAEDVRYID---EDLNRAFPGDPNAETHERRL 82
                                      589*******************99876555...555678899**************...************93322222 PP

                                      H CS
                         AstE_AspA 81 r 81
                                       
  gi|313126120|ref|YP_004036390.1| 83 A 83
                                      2 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.12
                                       E CS
                         AstE_AspA 250 l 250
                                        
  gi|313126120|ref|YP_004036390.1| 192 D 192
                                       1 PP

>> DUF4166  Domain of unknown function (DUF4166)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0   0.00087       5.2      65     108 ..      80     118 ..      71     132 .. 0.74
   2 ?    3.6   0.0    0.0087        52       7      58 ..     144     191 ..     140     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00087
                           DUF4166  65 desgretltwtRtfefpgktrtfdstmvlaggkglvEylGaglr 108
                                       ++  +e ++  R +++      ++st+++a++  lv+++Ga + 
  gi|313126120|ref|YP_004036390.1|  80 RRLAAEVVREIRGCTTF----SLHSTQSYAKPFALVDSVGA-VA 118
                                       45555555555555555....99*****************9.44 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0087
                           DUF4166   7 erhslragesvvgeGvvdvirgrsllarllaklgglrgalfPeagedvpftv 58 
                                       + h++  + ++ ++G+ d ++ + +l+r++++++g+     P +  + p+++
  gi|313126120|ref|YP_004036390.1| 144 HAHTI--EVECGLQGTPDAEENAYWLIRAFLAATGVVS--APIEAGESPLSL 191
                                       45666..99**************************544..555555555555 PP

>> Peptidase_M99  Carboxypeptidase controlling helical cell shape catalytic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.2e-05      0.25      36      97 ..      10      70 ..       4     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.2e-05
                                      S-EEEEE--SSTT-HHHHHHHHHHHHHEEE-SSEEEEES-STHHHHHTT-S-TTS-GGG-SS CS
                     Peptidase_M99 36 aphllllagiqgdepggfnaanlflmhyevkkglvevvpvlnkpsilrnhrglyddmnrkfa 97
                                      +p + ++  i gdep g  a + f+         v+++ + n +++  + r + +d+nr f 
  gi|313126120|ref|YP_004036390.1| 10 TPEVAVVGSIHGDEPCGASAIDRFVAEEPTVDRPVKLI-IANEEALAEDVRYIDEDLNRAFP 70
                                      68899999******************999999999987.56999***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1731.74
//
Query:       gi|313126121|ref|YP_004036391.1|  [L=161]
Description: hypothetical protein Hbor_13640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-15   54.6   0.3    9.7e-15   54.0   0.3    1.3  1  DUF309    Domain of unknown function (DUF309)


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.3   5.4e-19   9.7e-15       2      59 .]      37      97 ..      36      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 5.4e-19
                            DUF309  2 eeaielfnegeffeaHEvlEelWkeagep..erkllqglIqlAvAlyh.lrrgnvrgakrl 59
                                      e++i+l+n+gef+e H+++E  W ++g++  e  +l+g++q+A++ y+ +  +n +g+++l
  gi|313126121|ref|YP_004036391.1| 37 EHGIRLYNAGEFHESHDCFEVEWYNYGRGtiESAFLHGMVQVAAGAYKhFDFENDDGMRSL 97
                                      689************************9899*************999879999*9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1065.15
//
Query:       gi|313126122|ref|YP_004036392.1|  [L=80]
Description: hypothetical protein Hbor_13650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0011   19.0   0.8     0.0012   18.9   0.8    1.0  1  COPI_assoc  COPI associated protein
  ------ inclusion threshold ------
          1    9.5   5.3        1.3    9.2   5.3    1.2  1  DUF3099     Protein of unknown function (DUF3099)


Domain annotation for each model (and alignments):
>> COPI_assoc  COPI associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.8   1.3e-07    0.0012      65     116 ..      20      72 ..       5      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-07
                        COPI_assoc  65 fsylGRGlfyillg.llvsyggvlsilialllflvGLvyillhlvpsieepen 116
                                         ++GRG+fy+l+  l+v   g+  i +++ll+l+++v  ++++    e p+ 
  gi|313126122|ref|YP_004036392.1|  20 EGAIGRGAFYTLVFlLVVAGIGFAPIGLGILLVLMAVVLPAIGVAVALELPSV 72 
                                       5689**********777777799999999999999999888888666666555 PP

>> DUF3099  Protein of unknown function (DUF3099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   5.3   0.00015       1.3      28      64 ..      30      66 ..      25      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00015
                           DUF3099 28 vvclilavvlvsvengwlalvllvlavvLPwvAVvlA 64
                                      +++++l+v+ +  ++  l ++l+ +avvLP + V +A
  gi|313126122|ref|YP_004036392.1| 30 TLVFLLVVAGIGFAPIGLGILLVLMAVVLPAIGVAVA 66
                                      556666666656666679**************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 509.56
//
Query:       gi|313126123|ref|YP_004036393.1|  [L=95]
Description: hypothetical protein Hbor_13670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 630.18
//
Query:       gi|313126124|ref|YP_004036394.1|  [L=88]
Description: hypothetical protein Hbor_13680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 566.79
//
Query:       gi|313126125|ref|YP_004036395.1|  [L=266]
Description: inositol monophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.9e-47  159.7   3.1    1.3e-46  159.3   3.1    1.0  1  Inositol_P  Inositol monophosphatase family
     0.0021   17.6   0.0     0.0033   16.9   0.0    1.2  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.3   3.1   1.5e-50   1.3e-46       8     270 ..       9     261 ..       3     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 1.5e-50
                                       HHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSS CS
                        Inositol_P   8 aavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekselted 84 
                                       +a ++a++ g+v +++f+ + +++e k   g++d+vt+ad+++++ ++++++e++  ++i+gee+ +  +   ++++
  gi|313126125|ref|YP_004036395.1|   9 VARRAARAGGAVAADRFR-TGIDVERKD--GKTDVVTQADRDAQSRVIDVIREEYAADAIVGEEEDELKQ---VPSE 79 
                                       5789999**********9.888888777..9*********************************999999...9999 PP

                                       SEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEE CS
                        Inositol_P  85 gltwivDPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflngeklplsrappiseallv 161
                                       g  w++DPiDGT nFvr+ + ++++++ +++g+pv+++   P+l+ +y++ +g+ ++ n+e   +s++++ + ++++
  gi|313126125|ref|YP_004036395.1|  80 GAAWVIDPIDGTNNFVRELRVWGTAVAAVEDGTPVAAATRFPALEDTYWT-DGEATYRNSEEVTVSDRDDPEMCVVC 155
                                       9***********************************************95.599999999*********88888877 PP

                                       EEESSSSSSHHHHCHHHHHHHCCCCCH.EEEBESSHHHHHHHHHHTSTSEEEEEC.EBHHHHHHHHHHHHHTTEEEE CS
                        Inositol_P 162 tlfavssrkdtseasllekvesavsae.gvrsvgssalklaavaeGkadaylefgrekkWDhAAGeaileeaGGvvt 237
                                        ++++  +++ + a   +++  +     ++r++g +++ la+va+G++d +l+  r ++WD  AG+  +++aGG+vt
  gi|313126125|ref|YP_004036395.1| 156 PTIWWGFDERDQYARATNAIVDR---FgDMRRFGCAQAVLAMVADGQLDGVLTNVRANPWDSVAGVHMIRAAGGTVT 229
                                       66666555444442333333333...23468*********************9999********************* PP

                                       ESSSCSSSTTSSEEEEESCHHHHHHHHHHHCCH CS
                        Inositol_P 238 dakgegrlllargiiaanqkelaellaaavees 270
                                       d++g+++ + +rg++a+n +++++ +++a++e+
  gi|313126125|ref|YP_004036395.1| 230 DLSGDRWQHDSRGLVASN-GKIHDSVLEAAREI 261
                                       *****9999999999999.99999999998875 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.7e-07    0.0033      59     123 ..      39     100 ..      30     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-07
                            FBPase  59 deqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSnidtnvsv 123
                                       d++ + D  a+  +i++++++ +  ++v EEe+el+ + +++ + +v  +DP+DG  n   ++ v
  gi|313126125|ref|YP_004036395.1|  39 DVVTQADRDAQSRVIDVIREEYAADAIVGEEEDELKQV-PSEGAAWV--IDPIDGTNNFVRELRV 100
                                       67777888899999************************.66666554..6******997666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1697.55
//
Query:       gi|313126126|ref|YP_004036396.1|  [L=149]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-17   63.7   0.6    2.7e-17   62.3   0.8    1.7  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.8e-17   63.1   0.1    2.6e-17   62.5   0.1    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    4.2e-17   61.4   0.0    8.7e-17   60.4   0.0    1.5  2  HTH_24          Winged helix-turn-helix DNA-binding
    5.1e-08   32.9   0.0      1e-07   31.9   0.0    1.5  1  HTH_20          Helix-turn-helix domain
      1e-06   28.5   0.2    4.3e-05   23.3   0.1    2.3  2  MarR_2          MarR family
    7.3e-06   25.8   0.0    1.9e-05   24.5   0.0    1.7  2  MarR            MarR family
    3.3e-05   23.6   0.0    0.00014   21.6   0.0    1.9  2  HTH_IclR        IclR helix-turn-helix domain
    0.00015   21.2   0.6       0.41   10.2   0.1    3.0  3  Sigma70_r4      Sigma-70, region 4
    0.00065   20.2   0.3     0.0059   17.1   0.0    2.3  3  HTH_27          Winged helix DNA-binding domain
    0.00086   19.2   0.0     0.0019   18.1   0.0    1.6  2  HTH_11          HTH domain
     0.0084   16.3   0.0      0.015   15.4   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.031   13.9   0.7       0.13   11.9   0.1    2.4  3  Sigma70_r4_2    Sigma-70, region 4
      0.041   13.9   0.1       0.38   10.7   0.0    2.2  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.053   13.4   0.0        0.1   12.5   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.058   12.8   0.1       0.11   11.9   0.1    1.4  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.062   13.2   0.0       0.15   11.9   0.0    1.7  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.075   13.0   0.1       0.13   12.3   0.1    1.3  1  GYD             GYD domain


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.8   2.6e-20   2.7e-17       1      42 []       3      44 ..       3      44 .. 0.99
   2 ?   -3.3   0.0       8.2   8.7e+03      21      32 ..     121     132 ..     120     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.6e-20
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDe+Dr+IL++Lq daR++++e+A+++ +S +tv+ Rv r+e
  gi|313126126|ref|YP_004036396.1|  3 LDETDRAILRILQSDARTPFSEIARQIDMSSATVHDRVGRME 44
                                      8****************************************8 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.2
                     HTH_AsnC-type  21 aeLAervGlSes 32 
                                       + +Ae+ G S+s
  gi|313126126|ref|YP_004036396.1| 121 ENIAEMEGFSRS 132
                                       679998888877 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.1   2.5e-20   2.6e-17       1      74 [.      69     139 ..      69     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 2.5e-20
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       v++++e+g+    e++ e+l+e++ V+e++ +tG++d +l+v+++d++al++++ e +a+++g+ r++t+++l 
  gi|313126126|ref|YP_004036396.1|  69 VGLRVEQGR---EEDALEQLREIDGVKEVHLTTGEWDVMLRVYAEDTDALRDLMFENIAEMEGFSRSQTMVILG 139
                                       688999999...************************************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   8.3e-20   8.7e-17       1      48 []       3      50 ..       3      50 .. 0.98
   2 ?   -3.4   0.0       7.1   7.5e+03      23      32 ..     123     132 ..     122     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 8.3e-20
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ldetdr+IL++Lq ++r++ +e+A+++++S++tv+ r+ r+e++G+I+
  gi|313126126|ref|YP_004036396.1|  3 LDETDRAILRILQSDARTPFSEIARQIDMSSATVHDRVGRMEDAGVIE 50
                                      7**********************************************7 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.1
                            HTH_24  23 LAerlglSps 32 
                                       +Ae+ g S+s
  gi|313126126|ref|YP_004036396.1| 123 IAEMEGFSRS 132
                                       8999998887 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   9.9e-11     1e-07       9      56 ..       4      51 ..       3      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 9.9e-11
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +++ r+ilr L +++   +se+a+++d+s +t+++++  +e+ag +e+
  gi|313126126|ref|YP_004036396.1|  4 DETDRAILRILQSDARTPFSEIARQIDMSSATVHDRVGRMEDAGVIEG 51
                                      6889******************************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   4.1e-08   4.3e-05       8      52 ..       8      50 ..       2      87 .. 0.81
   2 ?    3.4   0.0     0.068        72       3      41 ..      96     137 ..      95     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.1e-08
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      + +L  L    +     +e+ar  ++s ++v+ ++ r+++aG +e
  gi|313126126|ref|YP_004036396.1|  8 RAILRILQSDAR--TPFSEIARQIDMSSATVHDRVGRMEDAGVIE 50
                                      455555555554..79***************************97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.068
                                       --HHHHHHHHHHHCTTTS...EEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2   3 ltpaqarvLaaLgrrpgr...dltvgelarrlglsksavsri 41 
                                       lt  +++v++ +++++     dl    +a+  g s+s +  i
  gi|313126126|ref|YP_004036396.1|  96 LTTGEWDVMLRVYAEDTDalrDLMFENIAEMEGFSRSQTMVI 137
                                       7889***********988888888888888888888876655 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.8e-08   1.9e-05       6      59 .]       8      61 ..       3      61 .. 0.93
   2 ?   -2.2   0.0         4   4.2e+03       1      15 [.      96     110 ..      96     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.8e-08
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTSE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRev 59
                                        iLril +      se+a+++ +s++tv   + r+e++G ie ++ + D Rev
  gi|313126126|ref|YP_004036396.1|  8 RAILRILQSDARTPFSEIARQIDMSSATVHDRVGRMEDAGVIEGYHAKVDPREV 61
                                      579***********************************************9997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4
                                       --HHHHHHHHHHHHS CS
                              MarR   1 ltltqfviLrilyeq 15 
                                       lt  +++++  +y +
  gi|313126126|ref|YP_004036396.1|  96 LTTGEWDVMLRVYAE 110
                                       688899999988865 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.3e-07   0.00014       7      49 ..       9      50 ..       8      51 .. 0.91
   2 ?   -0.9   0.0       1.4   1.5e+03      17      38 ..     116     137 ..     109     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.3e-07
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      aiL++l + ++   +se+Ar+++++ +tvh  +  ++  G +e
  gi|313126126|ref|YP_004036396.1|  9 AILRILQSDART-PFSEIARQIDMSSATVHDRVGRMEDAGVIE 50
                                      69*********8.9****************9999998888765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                                       SS-BHHHHHHHHTS-HHHHHHH CS
                          HTH_IclR  17 qeltlselArrtglpkStvhRl 38 
                                       ++l +  +A+  g ++S +  +
  gi|313126126|ref|YP_004036396.1| 116 RDLMFENIAEMEGFSRSQTMVI 137
                                       4577888999999999987655 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00038      0.41       4      40 ..       2      39 ..       1      43 [. 0.91
   2 ?    0.8   0.0      0.34   3.6e+02      40      50 .]      77      87 ..      73      87 .. 0.91
   3 !    7.1   0.0    0.0037       3.9       4      36 ..      95     133 ..      94     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00038
                                      HS-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHH CS
                        Sigma70_r4  4 sLpererevlelrf.geglTleEIgerlgiSrerVrqi 40
                                      +L+e +r +l+    +   +++EI+++ ++S  +V+ +
  gi|313126126|ref|YP_004036396.1|  2 ELDETDRAILRILQsDARTPFSEIARQIDMSSATVHDR 39
                                      6999*******999999999**************9876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.34
                                      HHHHHHHHHHH CS
                        Sigma70_r4 40 iekrAlrkLRk 50
                                      +e +Al++LR+
  gi|313126126|ref|YP_004036396.1| 77 REEDALEQLRE 87
                                      7899*****96 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0037
                                       HS-HHHHHHHHHHH......TTT--HHHHHHHHTS-HHH CS
                        Sigma70_r4   4 sLpererevlelrf......geglTleEIgerlgiSrer 36 
                                       +L+  e++v+  ++      +++l +e I+e+ g Sr+ 
  gi|313126126|ref|YP_004036396.1|  95 HLTTGEWDVMLRVYaedtdaLRDLMFENIAEMEGFSRSQ 133
                                       69999*******************************986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.6e-06    0.0059       4      59 ..       6      60 ..       3      67 .. 0.86
   2 ?   -3.0   0.0        10   1.1e+04      16      25 ..      77      86 ..      71      93 .. 0.57
   3 ?    0.6   0.0      0.77   8.1e+02       2      29 ..      97     123 ..      96     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.6e-06
                            HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                       ++++L+ ++  ++r   +++++  ++++++++  + +++ +G++e  + + d re
  gi|313126126|ref|YP_004036396.1|  6 TDRAILRILQ-SDARTPFSEIARQIDMSSATVHDRVGRMEDAGVIEGYHAKVDPRE 60
                                      5889******.99********************************76666555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 10
                            HTH_27 16 rrrkkladlc 25
                                      r++++l++l+
  gi|313126126|ref|YP_004036396.1| 77 REEDALEQLR 86
                                      4455555554 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.77
                            HTH_27   2 trqqalvLhlirhrrrrkkladlcgrln 29 
                                       t+ ++ v+  ++  +++++l+dl++   
  gi|313126126|ref|YP_004036396.1|  97 TTGEWDVMLRVY-AEDTDALRDLMFENI 123
                                       666777766677.799999999998765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.8e-06    0.0019       3      44 ..       8      48 ..       6      63 .. 0.90
   2 ?   -2.6   0.0       5.2   5.5e+03       1      11 [.      77      87 ..      77      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      ++il++L +++   + +e+A+++++S +tv+ ++ ++e++gv
  gi|313126126|ref|YP_004036396.1|  8 RAILRIL-QSDARTPFSEIARQIDMSSATVHDRVGRMEDAGV 48
                                      6899999.99999**************************993 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.2
                            HTH_11  1 RllqilelLle 11
                                      R+++ le+L+e
  gi|313126126|ref|YP_004036396.1| 77 REEDALEQLRE 87
                                      78889999976 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.5e-05     0.015      11      53 ..       8      50 ..       8      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 11 etIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      ++I+++  + +    +++a+ ++ s ++V   + ++e++G +e
  gi|313126126|ref|YP_004036396.1|  8 RAILRILQSDARTPFSEIARQIDMSSATVHDRVGRMEDAGVIE 50
                                      6888888888888899***********************9765 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00012      0.13      28      47 ..      21      40 ..       1      42 [. 0.85
   2 ?   -2.4   0.1       3.7   3.9e+03       6      14 ..      80      88 ..      79      89 .. 0.78
   3 ?   -2.7   0.0       4.7   4.9e+03      30      40 ..     121     131 ..     117     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                      -HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrl 47
                                      +  EIA+++++s++tV  r+
  gi|313126126|ref|YP_004036396.1| 21 PFSEIARQIDMSSATVHDRV 40
                                      678*************8765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.7
                                      HHHTTS-HH CS
                      Sigma70_r4_2  6 ealaeLper 14
                                      +al++L e+
  gi|313126126|ref|YP_004036396.1| 80 DALEQLREI 88
                                      689999887 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.7
                                       HHHHHHHT--H CS
                      Sigma70_r4_2  30 kEIAellgise 40 
                                       + IAe+ g s 
  gi|313126126|ref|YP_004036396.1| 121 ENIAEMEGFSR 131
                                       67999888775 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00036      0.38      25      53 ..      23      51 ..       4      59 .. 0.89
   2 ?    0.5   0.0      0.58   6.1e+02      25      42 ..     121     138 ..     103     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisr 53
                                       e+A+ + ++  tv    ++++++g+i+ 
  gi|313126126|ref|YP_004036396.1| 23 SEIARQIDMSSATVHDRVGRMEDAGVIEG 51
                                      59*************************94 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.58
                                       HHHHHHTTSSHHHHHHHH CS
                         HTH_Crp_2  25 eelAsmlGltretvsril 42 
                                       e +A+m G +r+++  il
  gi|313126126|ref|YP_004036396.1| 121 ENIAEMEGFSRSQTMVIL 138
                                       789999999998876665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.5e-05       0.1       1      45 [.       4      49 ..       4      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.5e-05
                                      SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      d+t + IL++L++   + ++e+a+++++s +tv     ++++aG++
  gi|313126126|ref|YP_004036396.1|  4 DETDRAILRILQSdARTPFSEIARQIDMSSATVHDRVGRMEDAGVI 49
                                      566678*******67789***************9988888888887 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001      0.11      18      47 ..       8      39 ..       5      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                      HTH_Tnp_ISL3 18 ayilellles..rsvkavArqlgvSwtTVwri 47
                                      ++il+ l+++   +++++Arq + S  TV+++
  gi|313126126|ref|YP_004036396.1|  8 RAILRILQSDarTPFSEIARQIDMSSATVHDR 39
                                      5666666666678****************987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.15      16      53 ..      13      50 ..       1      61 [. 0.79
   2 ?   -3.0   0.0       6.8   7.2e+03      40      53 ..      79      92 ..      71      96 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                       L +  +   +eia++++ + ++v + + ++ed+G++e
  gi|313126126|ref|YP_004036396.1| 13 ILQSDARTPFSEIARQIDMSSATVHDRVGRMEDAGVIE 50
                                      45555566679*************************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.8
                                      HHHHHHHHHCTSEE CS
                              TrmB 40 YevLrsLedkGlVe 53
                                       ++L++L + + V+
  gi|313126126|ref|YP_004036396.1| 79 EDALEQLREIDGVK 92
                                      57788887766665 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00012      0.13       9      82 ..      65     138 ..      61     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                               GYD   9 degvkglkdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalsl..alaasGtvrtetlraf 82 
                                       ++++ gl+  + r+e+a e+l ++++g ++++++t+Ge Dv+  v a+D ++   l    + ++ G  r++t+  +
  gi|313126126|ref|YP_004036396.1|  65 TSALVGLRVEQGREEDALEQL-REIDG-VKEVHLTTGEWDVMLRVYAEDTDALRDLMFenIAEMEGFSRSQTMVIL 138
                                       566677777788999999999.88877.789*******************99988765215677888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 823.13
//
Query:       gi|313126127|ref|YP_004036397.1|  [L=379]
Description: hypothetical protein Hbor_13710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-40  140.7  11.4      7e-40  137.9  10.6    2.3  2  DUF63           Membrane protein of unknown function DUF63
  ------ inclusion threshold ------
      0.025   13.0   0.7      0.035   12.5   0.7    1.1  1  SID-1_RNA_chan  dsRNA-gated channel SID-1


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.45     4e+03       3      16 ..      41      54 ..      40      59 .. 0.86
   2 !  137.9  10.6   7.8e-44     7e-40      17     272 .]      87     379 .]      81     379 .] 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.45
                             DUF63  3 eFiykyYidpivyk 16
                                       Fi++y++ p++ +
  gi|313126127|ref|YP_004036397.1| 41 RFIWHYFWGPVQAD 54
                                      69********9876 PP

  == domain 2  score: 137.9 bits;  conditional E-value: 7.8e-44
                             DUF63  17 egYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDag........llkpplsylli 85 
                                        gY++v ++ y + L++a+  ++ l+++l+i  d++f+++++p++++g+ lRvveDa+        +++ pl+ l+i
  gi|313126127|ref|YP_004036397.1|  87 PGYTLVSEVGYMLTLLFALTGVVFLMRRLDIGTDRNFFYSLLPFMFFGGALRVVEDANdtaavaesIITYPLNTLVI 163
                                       69******************************************************6444444444899******** PP

                             DUF63  86 tPliyflvflitlavlliskklekk.lkkdykklyaavGvvlvlvvlllLl......lteevvnlevlllvlllaav 155
                                       +P+iyf+vfl+tl ++ ++++le++ ++++y++ ++a+Gvv++ ++l++L+      ++    +++vl+++l+ a++
  gi|313126127|ref|YP_004036397.1| 164 SPVIYFTVFLVTLGAIAVAVALEHTdVTDSYERPLFAIGVVVLGLTLAYLFslaingAQGVEFHPQVLVVMLAGATL 240
                                       ************************************************99988776555566788999999999999 PP

                             DUF63 156 ltalvllllrklk..lellsdklnlllllahllDasatfvgidl.......lgYvEqHvvpsfLid........... 212
                                       ++a+ ++l++ +   ++  ++++ l+++++h +D+ a ++g+d+        + v +H+v++f +d           
  gi|313126127|ref|YP_004036397.1| 241 SAAATWWLIERFApqINSGTETIGLVIIWGHAVDGVANVIGLDWmtelgagPNLVPKHPVNQFVVDftastlpapih 317
                                       9999999999888678888999**********************777555447899*******99833333333333 PP

                             DUF63 213 .ltGtalvmyplkllvlipvlyildkevkeeee.lrnlvklailvlGlaPgiRnllrmvlgv 272
                                        +tG a+ ++ +kl+    v++++++ + ee+   + l+++a+l++Gl+Pg+R++lr ++gv
  gi|313126127|ref|YP_004036397.1| 318 aITGDAWPFLLVKLVAATFVVWVFEEGIFEESPrYTMLLLIAVLAVGLGPGTRDMLRATFGV 379
                                       34688999*****************98887777699999********************997 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   3.9e-06     0.035     359     479 ..      97     220 ..      86     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-06
                    SID-1_RNA_chan 359 yviavlcmlk..lyqkRhpdinasaysafallavvillgvigvlegkn.kfwilfsii.hllatlllslqiyymgrw 431
                                       y++ +l  l+  ++  R+ di++ ++  + ll ++ + g + v+e++n ++ +  sii + l tl++s  iy+  ++
  gi|313126127|ref|YP_004036397.1|  97 YMLTLLFALTgvVFLMRRLDIGTDRNFFYSLLPFMFFGGALRVVEDANdTAAVAESIItYPLNTLVISPVIYF-TVF 172
                                       6666666664447899999**************************8886555555554278999*****9999.778 PP

                    SID-1_RNA_chan 432 kldvgilrrilevlkkeviqqcsrplyksrmvllvlgnlvnvslavlg 479
                                        +  g +  ++ + +++v+ ++ rpl+   +v+l l  ++ +sla+ g
  gi|313126127|ref|YP_004036397.1| 173 LVTLGAIAVAVALEHTDVTDSYERPLFAIGVVVLGLTLAYLFSLAING 220
                                       88999999999****************999999999999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 2076.43
//
Query:       gi|313126128|ref|YP_004036398.1|  [L=569]
Description: bacteriocin biosynthesis docking scaffold, sagd family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-57  194.7   4.3      4e-57  193.9   4.3    1.4  1  YcaO      YcaO cyclodehydratase, ATP-ad Mg2+-binding


Domain annotation for each model (and alignments):
>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.9   4.3   2.2e-61     4e-57       7     322 ..     236     534 ..     230     535 .. 0.87

  Alignments for each domain:
  == domain 1  score: 193.9 bits;  conditional E-value: 2.2e-61
                              YcaO   7 eeaArasalgEalErysaegffrgdekrvrasyrelegegaldpeelglyseeekdaadfvlepfdpdrpidwvpgw 83 
                                        +aA ++algEalEry+a+ ++r  ++ ++ + +   +++ ++p+++  +++         +++ d+++pi+wv g 
  gi|313126128|ref|YP_004036398.1| 236 WDAAFMKALGEALERYCAG-VYR--ASEFTVAPERT-RARPVSPARFVRPDS---------YRAPDAEEPIPWVDGE 299
                                       57999***********977.433..44444344444.589*******99966.........99************** PP

                              YcaO  84 sltdgeevlvPanlvylyeppegearlfletsnGlAaGntleeAilhGllEliERdafalawyerlplpridlasdp 160
                                       +l++g +v vPa++v++  pp+ ++r+  + ++Gl++Gn+  eA+l Gl+E+iERda  lawy+  ++ ++d+a d+
  gi|313126128|ref|YP_004036398.1| 300 NLATGDTVSVPAEFVHY--PPP-DTRHKPPITTGLGLGNSGTEALLSGLYEVIERDATILAWYSSFDPLKLDVA-DE 372
                                       *****************..444.44888*************************************99999**97.9* PP

                              YcaO 161 eirellerlreagievrlldatldlgipvvaavlvdpk..lllvagaGahldpevAlerAltElaqsrltlisgare 235
                                         r+l++r+r+++++   l +t d+++pv+a+ +++++  +  ++g+Ga+ld + A+++Al E++q+   l+s + e
  gi|313126128|ref|YP_004036398.1| 373 GYRALVKRARSENLTATPLLVTQDVDVPVIAVAVHRDGewPQFAMGSGASLDVADAARSALAEALQNWMELRSMGPE 449
                                       ************************************445644568***********************999888777 PP

                              YcaO 236 dpdfd.eeladvatleradreallwlpeaaakrldfllfaewassgdleedletllerlkaagldvlvvdltrp... 308
                                        ++ +  ++ + a+++  d + +++ ++++a+ +++    + ++ ++ +++l++++er+++agld+++v  t+    
  gi|313126128|ref|YP_004036398.1| 450 RANAEkGAIGEYADFP--DAARRFV-NAGPAVPAASVG--P-DDVPSGKAELDAVVERVADAGLDPYAVRTTTTdva 520
                                       7777668999999998..6666777.888886666644..3.34589********************99999989** PP

                              YcaO 309 dlglpvvkvivPgl 322
                                       +lg+ +v+v++P++
  gi|313126128|ref|YP_004036398.1| 521 SLGFEAVRVLIPEA 534
                                       ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 3078.00
//
Query:       gi|313126129|ref|YP_004036399.1|  [L=274]
Description: hypothetical protein Hbor_13730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1601.56
//
Query:       gi|313126130|ref|YP_004036400.1|  [L=656]
Description: hypothetical protein Hbor_13740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 3901.56
//
Query:       gi|313126131|ref|YP_004036401.1|  [L=415]
Description: serine hydroxymethyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.3e-153  509.4   0.1   6.3e-153  509.1   0.1    1.1  1  SHMT             Serine hydroxymethyltransferase
    2.2e-12   46.8   0.0    4.1e-12   46.0   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II
    1.4e-07   31.2   0.0    7.2e-07   28.8   0.0    2.0  1  Beta_elim_lyase  Beta-eliminating lyase
      0.003   16.9   0.6     0.0047   16.3   0.6    1.5  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.062   13.1   0.6       0.35   10.6   0.1    2.5  2  DUF348           G5-linked-Ubiquitin-like domain
      0.076   13.3   0.2        7.3    7.0   0.0    2.7  2  DUF5403          Family of unknown function (DUF5403)


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  509.1   0.1  2.1e-156  6.3e-153       3     399 .]       8     384 ..       6     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 509.1 bits;  conditional E-value: 2.1e-156
                                       HHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHC CS
                              SHMT   3 esdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelf 79 
                                        +dpe+a++++ e++rq++++ +iasen +s+avl+a+Gs ltnkyaeGyPG ryy Gce+ deveela++rakel+
  gi|313126131|ref|YP_004036401.1|   8 GVDPEIADALEGEEDRQRNTLAMIASENHVSEAVLQAQGSALTNKYAEGYPGSRYYAGCEYADEVEELAIERAKELW 84 
                                       58*************************************************************************** PP

                                       T-STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB CS
                              SHMT  80 kldpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketgli 156
                                       +++    +vnvqp+sG+qan+ vy a+l+pgd+il+l+l++GGhl+hG + ++     +++++e+ +y+vd++tg+i
  gi|313126131|ref|YP_004036401.1|  85 GAE----HVNVQPHSGTQANMGVYLAVLDPGDKILSLELSHGGHLSHGHPANF-----TGQTYEVEQYHVDPDTGYI 152
                                       ***....*********************************************9.....******************* PP

                                       -HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSST CS
                              SHMT 157 dydelekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthkt 233
                                       dyd+l ++a+ef P +iv+G say+r+++++r++++a++v+ay l+d+ahi+Glvaagv+psP+  ad+vt  thkt
  gi|313126131|ref|YP_004036401.1| 153 DYDALAEQAEEFDPDIIVSGYSAYPRVVEWERIQDVAESVDAYHLADIAHITGLVAAGVHPSPVGIADFVTGSTHKT 229
                                       ***************************************************************************** PP

                                       T-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHH CS
                              SHMT 234 lrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknak 310
                                       +r  rgg+i++               ee ++ +++a+fPg qGGPl+h +a+kav++kealepef +y+++ ++nak
  gi|313126131|ref|YP_004036401.1| 230 IRAGRGGIIMTT--------------EEHADDVDKAIFPGAQGGPLMHNVAGKAVGFKEALEPEFEEYAERTVANAK 292
                                       **********99..............7999*********************************************** PP

                                       HHHHHHHHTT-EEGGGS-SSSEEEEEGGGG..TS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHHH CS
                              SHMT 311 alaealkekgyklvsgGtdnhlvlvdlrek..gldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpalts 384
                                       +lae+++e g+++vsgGtdnhlvl dlr+   +++Gk++e++le++ i  n ntvPg+ +sa+ +sG+r Gtp lt+
  gi|313126131|ref|YP_004036401.1| 293 TLAETFEEAGIEVVSGGTDNHLVLADLRPShpDTTGKDVEAALEEAGIVLNANTVPGEtRSAFNPSGIRAGTPGLTT 369
                                       ****************************8733689****************************************** PP

                                       TT--HHHHHHHHHHH CS
                              SHMT 385 rgfkeedlekvakfi 399
                                       rgf+e+ +++v+++i
  gi|313126131|ref|YP_004036401.1| 370 RGFDEAAVREVGELI 384
                                       ***********9876 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   1.4e-15   4.1e-12      40     360 ..      63     376 ..      32     378 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.4e-15
                                       T-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THH.....HHHHH CS
                     Aminotran_1_2  40 ygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasy.....knilr 111
                                       y  ++ ++e+ee  ++ ++  e    ++  +v+  sG++a+  +  ++l+  pgd+il+ +++++ +       ++ 
  gi|313126131|ref|YP_004036401.1|  63 YAGCEYADEVEELAIERAK--ELWGAEHV-NVQPHSGTQANMGVYLAVLD--PGDKILSLELSHGGHlshghPANFT 134
                                       5556666777777776666..55556666.*******************8..************9752222267899 PP

                                       HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                     Aminotran_1_2 112 lsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                         + ev +y+  ++++  +d +al e+ +e+   ++   +i+  +      + +   e+e + d+a++  ++ + D 
  gi|313126131|ref|YP_004036401.1| 135 GQTYEVEQYH-VDPDTGYIDYDALAEQAEEF---DP--DIIV-SGY----SAYPRVVEWERIQDVAESVDAYHLADI 200
                                       9999999999.458999*********88885...44..4444.443....367788888888888999999****** PP

                                       TTTTCBSSSSHTHHHHGGSTTSTT...EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHH CS
                     Aminotran_1_2 189 aYagfvfgsldavatranveeepn...llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaava 261
                                       a+ ++           a+v + p    ++++gs  K    aG R G+i  +++ ++ + k+  p+     l+  ++ 
  gi|313126131|ref|YP_004036401.1| 201 AHITGLVA--------AGVHPSPVgiaDFVTGSTHKTIR-AG-RGGIIMTTEEHADDVDKAIFPGAQgGPLMHNVAG 267
                                       *******8........566666666669******99985.45.67*******************9997777888899 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHH....CHHHHHHHHHHTCTEEEE CS
                     Aminotran_1_2 262 aalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsae....takelskkLleevgvyvt 333
                                       +a+  ++  + e+ee ++r  +++k+l + ++e+g++v++    + ++l dl+++    t k++    lee g+++ 
  gi|313126131|ref|YP_004036401.1| 268 KAVGFKEALEPEFEEYAERTVANAKTLAETFEEAGIEVVSGGtDNHLVLADLRPShpdtTGKDVEA-ALEEAGIVLN 343
                                       99999999999****************************99889999********88855555544.56666***** PP

                                       EGGGGTS......TTEEEEECTTS-HHHHHHHH CS
                     Aminotran_1_2 334 pgtsftv......pgrlRitvAglteeeleelv 360
                                       ++t ++       p+ +R   +glt+   +e++
  gi|313126131|ref|YP_004036401.1| 344 ANTVPGEtrsafnPSGIRAGTPGLTTRGFDEAA 376
                                       ******999999999999999999998888886 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   2.4e-10   7.2e-07      39     242 ..      78     345 ..      40     407 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.4e-10
                                       HHHHHHTT-SEE.EEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--E..EEEE-EBTT...TBE CS
                   Beta_elim_lyase  39 davaelfgkeaa.lfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvk..lrdlknkea...Gkm 109
                                       ++++el g+e++ +  ++Gt+An   + ++l +g++++  e +h+     g +a + g +  + +     +   G++
  gi|313126131|ref|YP_004036401.1|  78 ERAKELWGAEHVnVQPHSGTQANMGVYLAVLDPGDKILSLELSHGGHLSHGHPANFTGQTyeVEQYHV--DpdtGYI 152
                                       688999***98625788************************************999776311333333..1346*** PP

                                       -HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHH CS
                   Beta_elim_lyase 110 dlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemf 186
                                       d ++l++  +e      ++ +i+          +vv+ e ++ va+ +++y +    D A +    ++ g++++  +
  gi|313126131|ref|YP_004036401.1| 153 DYDALAEQAEE--F---DPDIIVSGYSAY---PRVVEWERIQDVAESVDAYHL---ADIAHITG-LVAAGVHPSP-V 216
                                       ******99999..3...334444444444...38******9999999999987...59998875.5588888876.5 PP

                                       TTSSEEEEESSSTT--SS-EEEEE-HH.......................................HHHHHHHHHHH CS
                   Beta_elim_lyase 187 syvDsvtmslkKdllanvGgvlafrddel...................................edylaerveqrky 228
                                         +D vt s  K + a  Gg++++ ++++                                   e+y ++ v+ +k+
  gi|313126131|ref|YP_004036401.1| 217 GIADFVTGSTHKTIRAGRGGIIMTTEEHAddvdkaifpgaqggplmhnvagkavgfkealepefEEYAERTVANAKT 293
                                       79*************************99************************************************ PP

                                       HT---SSTHHHHH....................................... CS
                   Beta_elim_lyase 229 lggglrqagvlaa......................................l 242
                                       l++ +++ag+ ++                                       
  gi|313126131|ref|YP_004036401.1| 294 LAETFEEAGIEVVsggtdnhlvladlrpshpdttgkdveaaleeagivlnaN 345
                                       ************9666666666666666666666666666654444444440 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   1.6e-06    0.0047      90     191 ..     143     246 ..      69     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                                       E-B-TTTSSB-GGGCGGG--TTEEEEEEB-G..GGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT...EECCCS CS
                   DegT_DnrJ_EryC1  90 vDvdpdtynidpaaieaaitertkaIlpVhl..yGqvadmdalkaiaakhglkvieDaAhAlGatykg...kkvGal 161
                                         vdpdt  id +a+++  +e    I++  +  y +v++ ++++++a++ + + + D Ah  G   +g    +vG +
  gi|313126131|ref|YP_004036401.1| 143 YHVDPDTGYIDYDALAEQAEEFDPDIIVSGYsaYPRVVEWERIQDVAESVDAYHLADIAHITGLVAAGvhpSPVG-I 218
                                       569********************999987552277889*************************999995445555.4 PP

                                       SSEEEEE-BTTSSS-SSS-EEEEESTHHHH CS
                   DegT_DnrJ_EryC1 162 gdaavfSFyptKnlttGeGGavvtndeela 191
                                       +d+ + S    K++ +G GG+++t +e  +
  gi|313126131|ref|YP_004036401.1| 219 ADFVTGS--THKTIRAGRGGIIMTTEEHAD 246
                                       4555555..5699***********987654 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       0.6   1.8e+03      15      30 ..     290     305 ..     285     307 .. 0.82
   2 ?   10.6   0.1   0.00012      0.35      14      32 ..     326     344 ..     323     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.6
                                       --SSHHHHHHHTT--- CS
                            DUF348  15 aadTVgdlLeeagitl 30 
                                        a T ++  eeagi++
  gi|313126131|ref|YP_004036401.1| 290 NAKTLAETFEEAGIEV 305
                                       6889999999999985 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                                       ---SSHHHHHHHTT----T CS
                            DUF348  14 TaadTVgdlLeeagitlge 32 
                                       T+  +V+ +Leeagi l++
  gi|313126131|ref|YP_004036401.1| 326 TTGKDVEAALEEAGIVLNA 344
                                       999************9986 PP

>> DUF5403  Family of unknown function (DUF5403)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.036   1.1e+02      13      38 ..       4      29 ..       2      45 .. 0.86
   2 ?    7.0   0.0    0.0024       7.3       9      65 ..     263     318 ..     259     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.036
                           DUF5403 13 ahlpgvkaavaeelerraarvrAvva 38
                                      +h++gv +++a++le +++r r ++a
  gi|313126131|ref|YP_004036401.1|  4 SHVRGVDPEIADALEGEEDRQRNTLA 29
                                      79**************9999887665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0024
                           DUF5403   9 dklvahlpgvkaavaeelerraarvrAvvagHrdtGalaasievetgrvdstvsleD 65 
                                        +++ ++ g k+a++ e e+ a+r  A+++   +t    a iev  g +d +++l+D
  gi|313126131|ref|YP_004036401.1| 263 HNVAGKAVGFKEALEPEFEEYAERTVANAKTLAETF-EEAGIEVVSGGTDNHLVLAD 318
                                       567788889999999999999999999998888887.5788*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.39s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 2336.03
//
Query:       gi|313126132|ref|YP_004036402.1|  [L=297]
Description: 5,10-methylene-tetrahydrofolate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-67  223.6   1.5    1.2e-66  223.0   1.5    1.3  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
    6.6e-38  129.5   0.0      1e-37  128.9   0.0    1.3  1  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.0   1.5   1.3e-70   1.2e-66       1     156 [.     122     286 ..     122     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 223.0 bits;  conditional E-value: 1.3e-70
                                       SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT....T-EEEEE-TTSCCH CS
                     THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLlek....natVtvchsktkdl 73 
                                       hp n+grlv+g++ + pctp+g+ +ll++t++e+eg++v+vvGrsnivgkp+a lL +k    natVtvchs+t++l
  gi|313126132|ref|YP_004036402.1| 122 HPENVGRLVAGHPRFKPCTPHGIQKLLAATDVETEGADVAVVGRSNIVGKPMANLLIQKselgNATVTVCHSRTENL 198
                                       899*******************************************************99999************** PP

                                       HHHHCCSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC.....-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHH CS
                     THF_DHG_CYH_C  74 aeitreadivvvavGkpelikaemvkegavviDvGinrv.....ekgklvGDvdfeevkevasaitPvpgGVGpmTv 145
                                       a++tr adivv+avG pe+i++em++eg +viDvGinrv     ++++lvGDv++e++k++a+aitPvpgGVGpmT 
  gi|313126132|ref|YP_004036402.1| 199 ADKTRAADIVVAAVGIPEFITGEMLSEGVTVIDVGINRVdadteKGYELVGDVEYESAKAKAGAITPVPGGVGPMTR 275
                                       *****************************************9988999***************************** PP

                                       HHHHHHHHHHH CS
                     THF_DHG_CYH_C 146 amllkntleaa 156
                                       amll nt++aa
  gi|313126132|ref|YP_004036402.1| 276 AMLLWNTVKAA 286
                                       ********998 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.0   1.2e-41     1e-37       1     116 []       4     119 ..       4     119 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 1.2e-41
                                       E--HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHH CS
                       THF_DHG_CYH   1 lldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellkl 77 
                                       ++dG+a+a+eir+ l++ +++l + gv+p+La++l+ +dpase+Yv++k+  ceevGie + ++++ ++  eel ++
  gi|313126132|ref|YP_004036402.1|   4 IIDGNAVAAEIRAGLADGIDTLADAGVTPCLATVLMSNDPASETYVSMKHSDCEEVGIEARDFEIDPEAPAEELYDT 80 
                                       79*********************99**************************************************** PP

                                       HHHHHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                       THF_DHG_CYH  78 ieelneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                       i+eln+d+sv+Gilvq+P+p+h+de+++l +i+p+KDVD
  gi|313126132|ref|YP_004036402.1|  81 IDELNADPSVHGILVQMPVPDHVDEREVLRRIDPAKDVD 119
                                       **************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1663.62
//
Query:       gi|313126133|ref|YP_004036403.1|  [L=77]
Description: hypothetical protein Hbor_13770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.059   12.3   0.0      0.078   11.9   0.0    1.2  1  ISN1         IMP-specific 5'-nucleotidase
       0.12   12.3   2.1       0.44   10.5   0.1    2.2  2  Prok-RING_1  Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> ISN1  IMP-specific 5'-nucleotidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.7e-06     0.078     144     161 ..      11      28 ..       2      34 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.7e-06
                              ISN1 144 akklklvtfDGDvtlydD 161
                                        +k+kl+t DGDvtly++
  gi|313126133|ref|YP_004036403.1|  11 RHKMKLLTDDGDVTLYEN 28 
                                       3589************97 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   4.9e-05      0.44      14      32 ..      25      43 ..      17      49 .. 0.84
   2 ?    1.5   0.3     0.033   2.9e+02      16      24 ..      67      75 ..      59      76 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.9e-05
                       Prok-RING_1 14 lkeedDiVvCpeCgtpyHr 32
                                      l e+ D V Cp+Cg p+ r
  gi|313126133|ref|YP_004036403.1| 25 LYENRDDVPCPACGDPFDR 43
                                      567778899****999866 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.033
                       Prok-RING_1 16 eedDiVvCp 24
                                      e+d +VvC+
  gi|313126133|ref|YP_004036403.1| 67 EDDRLVVCT 75
                                      44559***7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 441.22
//
Query:       gi|313126134|ref|YP_004036404.1|  [L=236]
Description: hypothetical protein Hbor_13780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00069   19.6   0.5     0.0013   18.7   0.5    1.4  1  HypA           Hydrogenase/urease nickel incorporation, metal
     0.0039   17.3   0.8     0.0092   16.1   0.8    1.6  1  Zn-ribbon_8    Zinc ribbon domain
     0.0056   16.2   1.8       0.02   14.4   1.7    1.9  1  TF_Zn_Ribbon   TFIIB zinc-binding
     0.0063   16.5   2.1        1.7    8.7   0.0    2.5  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.016   15.3   1.7      0.045   13.8   0.5    2.2  2  DUF1451        Zinc-ribbon containing domain
       0.02   14.3   1.4       0.35   10.3   0.1    2.2  2  zf-ribbon_3    zinc-ribbon domain
      0.039   14.0   0.6      0.067   13.2   0.6    1.3  1  DZR            Double zinc ribbon
       0.13   12.9   0.0       0.27   11.9   0.0    1.6  1  FYDLN_acid     Protein of unknown function (FYDLN_acid)
       0.14   12.2   0.9       0.24   11.5   0.9    1.3  1  Zn_Tnp_IS91    Transposase zinc-binding domain
       0.21   11.3   0.3       0.32   10.8   0.3    1.3  1  A2L_zn_ribbon  A2L zinc ribbon domain
        0.5   10.8   3.5          3    8.3   0.1    2.4  2  zf-IS66        zinc-finger binding domain of transposase IS66
       0.67    9.9   3.2         13    5.8   0.9    2.4  2  zinc_ribbon_4  zinc-ribbon domain
        2.7    7.9   6.1        8.4    6.3   1.3    2.9  3  TFIIS_C        Transcription factor S-II (TFIIS)
        6.6    6.6   6.8         97    2.9   6.8    2.2  1  zinc_ribbon_2  zinc-ribbon domain
        7.5    6.7   6.2        2.9    8.0   0.8    2.2  2  UPF0547        Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.5   1.1e-06    0.0013      67      96 ..       3      33 ..       1      44 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                                      E--EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                              HypA 67 vpvkvrCreCgkefeleek.alrCpkCgsad 96
                                      ++ + rC++Cg+e++  ++ ++ Cp+Cgs +
  gi|313126134|ref|YP_004036404.1|  3 IRGRRRCKSCGHEWSYYDTgEVACPACGSMQ 33
                                      567889*********7665689******976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.8   7.7e-06    0.0092       7      35 ..       8      33 ..       7      35 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.7e-06
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.e 35
                                      rC++Cghe        d  ++aCP+Cgs +
  gi|313126134|ref|YP_004036404.1|  8 RCKSCGHEWSYY----DTGEVACPACGSmQ 33
                                      8*****999955....556889*****954 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.7   1.6e-05      0.02       2      28 ..       8      32 ..       7      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                      EETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlV 28
                                      +C+ Cg++  +  +++ge+ C++CG++
  gi|313126134|ref|YP_004036404.1|  8 RCKSCGHEWSY--YDTGEVACPACGSM 32
                                      7*****97434..66**********98 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.7    0.0057       6.8      35      45 ..       4      14 ..       1      15 [. 0.84
   2 !    8.7   0.0    0.0014       1.7      19      34 ..      24      39 ..      16      44 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0057
                     Zn_Tnp_IS1595 35 rglfqCkeCrk 45
                                      rg+ +Ck+C++
  gi|313126134|ref|YP_004036404.1|  4 RGRRRCKSCGH 14
                                      89*******98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0014
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt 34
                                      + CP+Cgs+++  i +
  gi|313126134|ref|YP_004036404.1| 24 VACPACGSMQSVGIGD 39
                                      66******98877755 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   3.8e-05     0.045     113     140 ..       5      31 ..       1      34 [. 0.89
   2 ?   -0.5   0.0      0.97   1.2e+03      29      53 ..      57      81 ..      44     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                           DUF1451 113 GtlvCekCgkelalkkteeippCpkCga 140
                                       G+ +C++Cg+e +++ t+e+ +Cp+Cg+
  gi|313126134|ref|YP_004036404.1|   5 GRRRCKSCGHEWSYYDTGEV-ACPACGS 31 
                                       8889***************9.6****97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.97
                           DUF1451 29 eeltkeelelvaeylkrDleeaars 53
                                      + l++e l  v++ l+ Dl+++ r+
  gi|313126134|ref|YP_004036404.1| 57 NALDDESLTDVTAGLQSDLRAYLRA 81
                                      6678888999999999999988765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.076        90      19      24 ..       9      14 ..       6      16 .. 0.73
   2 ?   10.3   0.1   0.00029      0.35       2      15 ..      23      38 ..      20      41 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.076
                       zf-ribbon_3 19 CpyCGt 24
                                      C++CG+
  gi|313126134|ref|YP_004036404.1|  9 CKSCGH 14
                                      777776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00029
                       zf-ribbon_3  2 tvrCPnCGa.p.lssd 15
                                      +v CP+CG+ + +  +
  gi|313126134|ref|YP_004036404.1| 23 EVACPACGSmQsVGIG 38
                                      6889999997755555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   5.6e-05     0.067      12      38 ..       6      33 ..       4      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-05
                               DZR 12 arfCseCgtklkavaa.edrCpsCgekv 38
                                       r C+ Cg++ + + + e +Cp+Cg++ 
  gi|313126134|ref|YP_004036404.1|  6 RRRCKSCGHEWSYYDTgEVACPACGSMQ 33
                                      5779999999987776999999999875 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.27       9      62 ..       6      57 ..       2     121 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                        FYDLN_acid  9 KriCpscgak..FYDLnkdPivcpkcgeefepeevlksraaaaeaeeakkkkeeee 62
                                       r C+scg+   +YD +   + cp+cg+++++    + +++ +++e +   + +++
  gi|313126134|ref|YP_004036404.1|  6 RRRCKSCGHEwsYYDTGE--VACPACGSMQSVGIGDRMQHTDSAEELD--LAPHRN 57
                                      589****99644899887..9*******99998884433333333322..222222 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9    0.0002      0.24      40      72 ..       7      38 ..       4      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                       Zn_Tnp_IS91 40 yeCeeCghekivyfsCksrhCpsCqkkateewl 72
                                       +C++Cgh +++y+  ++ +Cp C++ ++    
  gi|313126134|ref|YP_004036404.1|  7 RRCKSCGH-EWSYYDTGEVACPACGSMQSVGIG 38
                                      68*****9.6778888999******99876555 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00027      0.32       6      31 ..       9      33 ..       6      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                     A2L_zn_ribbon  6 CsvCggngilnseqgylvCieCgasf 31
                                      C+ Cg++  +  + g+  C+ Cg+ +
  gi|313126134|ref|YP_004036404.1|  9 CKSCGHEWSY-YDTGEVACPACGSMQ 33
                                      **********.9***********987 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.9      0.16   1.9e+02      36      46 .]       3      13 ..       2      16 .. 0.82
   2 ?    8.3   0.1    0.0025         3       3      27 ..      25      54 ..      23      56 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.16
                           zf-IS66 36 irpkyaCpcCe 46
                                      ir +++C++C+
  gi|313126134|ref|YP_004036404.1|  3 IRGRRRCKSCG 13
                                      68888999986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0025
                           zf-IS66  3 tCpcCGg.llkpigedrvr.....eeldipP 27
                                      +Cp CG+ + + ig++  +     eeld+ P
  gi|313126134|ref|YP_004036404.1| 25 ACPACGSmQSVGIGDR-MQhtdsaEELDLAP 54
                                      6*****9776677766.55666668888766 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.9     0.011        13      27      35 ..       8      16 ..       4      17 .. 0.89
   2 ?    4.0   0.1     0.041        49      24      32 ..      22      30 ..      20      32 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                     zinc_ribbon_4 27 rCskCghvF 35
                                      rC+ Cgh +
  gi|313126134|ref|YP_004036404.1|  8 RCKSCGHEW 16
                                      9******99 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.041
                     zinc_ribbon_4 24 vkvrCskCg 32
                                      ++v C++Cg
  gi|313126134|ref|YP_004036404.1| 22 GEVACPACG 30
                                      567777776 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.3     0.007       8.4      30      38 ..       8      16 ..       6      17 .. 0.90
   2 ?    3.0   0.0     0.078        93       2      10 ..      25      33 ..      24      49 .. 0.79
   3 ?   -3.2   0.0       6.7     8e+03      19      26 ..     218     225 ..     216     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.007
                           TFIIS_C 30 kCtkCghrW 38
                                      +C++Cgh+W
  gi|313126134|ref|YP_004036404.1|  8 RCKSCGHEW 16
                                      7******** PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.078
                           TFIIS_C  2 kCpkCgsre 10
                                       Cp Cgs +
  gi|313126134|ref|YP_004036404.1| 25 ACPACGSMQ 33
                                      6*****976 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.7
                           TFIIS_C  19 RsaDEpmt 26 
                                       R +DE++ 
  gi|313126134|ref|YP_004036404.1| 218 RDGDESAL 225
                                       899**976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   6.8     0.081        97       1      21 [.       8      31 ..       8      32 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.081
                     zinc_ribbon_2  1 fCpnCGae...lqdnakFCpyCGt 21
                                      +C++CG+e    + +++ Cp CG+
  gi|313126134|ref|YP_004036404.1|  8 RCKSCGHEwsyYDTGEVACPACGS 31
                                      699999985545669999****96 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.8    0.0025       2.9      15      25 ..       7      17 ..       7      18 .. 0.87
   2 ?    1.3   0.5      0.31   3.7e+02      16      21 ..      25      30 ..      24      31 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0025
                           UPF0547 15 qfCphCGyvFq 25
                                      ++C  CG++++
  gi|313126134|ref|YP_004036404.1|  7 RRCKSCGHEWS 17
                                      68*99*****7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.31
                           UPF0547 16 fCphCG 21
                                      +Cp CG
  gi|313126134|ref|YP_004036404.1| 25 ACPACG 30
                                      588887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1334.48
//
Query:       gi|313126135|ref|YP_004036405.1|  [L=48]
Description: hypothetical protein Hbor_13790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.1   0.2      0.013   15.9   0.2    1.1  1  MutS_IV   MutS family domain IV


Domain annotation for each model (and alignments):
>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.2     7e-07     0.013      12      49 ..       6      44 ..       1      44 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7e-07
                                      HHHHHHHHHHHHH.CCCCCCCT-TTBEECCCSSSEEEEE CS
                           MutS_IV 12 rleelekeleele.ekereklgikslkveynkvlGyyle 49
                                       ++e  ++lee++ ++e +++g+k l + y ++lG++le
  gi|313126135|ref|YP_004036405.1|  6 EIREQYEFLEEELaSEEMRHSGVKELFTHYKRALGWVLE 44
                                      5666667776655055566999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 280.93
//
Query:       gi|313126136|ref|YP_004036406.1|  [L=98]
Description: transcriptional regulator, padr family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-17   63.3   2.3    1.9e-17   63.0   2.3    1.1  1  PadR      Transcriptional regulator PadR-like family
     0.0018   18.0   0.0     0.0029   17.4   0.0    1.2  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
      0.009   16.0   0.1      0.012   15.6   0.1    1.3  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
       0.01   16.3   0.2      0.015   15.8   0.2    1.4  1  HTH_27    Winged helix DNA-binding domain
       0.03   14.5   0.1      0.037   14.2   0.1    1.2  1  HTH_34    Winged helix DNA-binding domain
      0.048   13.4   0.1       0.06   13.1   0.1    1.3  1  DUF4364   Domain of unknown function (DUF4364)
      0.066   13.1   0.1        1.6    8.7   0.0    2.2  2  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   2.3   7.5e-21   1.9e-17       1      74 [.      11      79 ..      11      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 7.5e-21
                                      HHHHH.CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  1 iLall.eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      +L+++ +  + +G++i++ele+++e   e+++G+lYp+L++L ++gl+e+ +++    ++++yY+lT++Grre++
  gi|313126136|ref|YP_004036406.1| 11 LLYVIaGLDEPHGLAIKEELEDYYEK--EIHHGRLYPNLDTLVEKGLIEKGQRD----RRTNYYTLTRRGRREIK 79
                                      57788444667************986..***********************887....7*************987 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.1e-06    0.0029      53      85 ..      44      76 ..      40      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                           DUF1495 53 ynsessLielGLveeeeeseglklYklteeGie 85
                                      y + + L+e+GL+e+ + ++ +++Y+lt +G++
  gi|313126136|ref|YP_004036406.1| 44 YPNLDTLVEKGLIEKGQRDRRTNYYTLTRRGRR 76
                                      667789*************************97 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.6e-06     0.012      30      67 ..      37      79 ..      24      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.6e-06
                            HTH_45 30 nLsykllnkYLdmLvekgli.....kkskekYvlTekGlelle 67
                                      ++   +l   Ld+Lvekgli     + +++ Y+lT +G++ ++
  gi|313126136|ref|YP_004036406.1| 37 EIHHGRLYPNLDTLVEKGLIekgqrDRRTNYYTLTRRGRREIK 79
                                      56666777789*********88876668899*******98665 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.2   5.7e-06     0.015      14      68 .]      20      74 ..       4      74 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.7e-06
                            HTH_27 14 hrrrrkkladlcgrlnvedshis..yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ++++ +++++l +++  e  h+    +l+ L+ekGL+  ++  +drr+  ++lT  G
  gi|313126136|ref|YP_004036406.1| 20 EPHGLAIKEELEDYYEKEIHHGRlyPNLDTLVEKGLI--EKGQRDRRTNYYTLTRRG 74
                                      5555555666666666666666653489*********..444589*********766 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.5e-05     0.037      26      75 ..      38      84 ..      23      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                            HTH_34 26 atdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvka 75
                                      +  g+L+ +l++L ++g i  +k+ +++ +   +++T+ Gr + k+ +++
  gi|313126136|ref|YP_004036406.1| 38 IHHGRLYPNLDTLVEKGLI--EKGQRDR-RTNYYTLTRRGRREIKARKEW 84
                                      6789*************98..5888888.8889**********9998876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.3e-05      0.06      40      70 ..      47      78 ..      26      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                           DUF4364 40 lseLvesglieee.ekenktlykiTekGketl 70
                                      l+ Lve+glie+  +++ +++y++T +G++ +
  gi|313126136|ref|YP_004036406.1| 47 LDTLVEKGLIEKGqRDRRTNYYTLTRRGRREI 78
                                      899*********9677999*********9865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.05   1.3e+02       2      20 ..       3      21 ..       2      32 .. 0.81
   2 ?    8.7   0.0   0.00063       1.6      42      61 ..      47      64 ..      38      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.05
                                      T--HHHHHHHHHHHCTTTS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgr 20
                                      +lt+ q+++L++++  +++
  gi|313126136|ref|YP_004036406.1|  3 DLTGFQRDLLYVIAGLDEP 21
                                      78999********998876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00063
                                      HHHHHHTTSEEEEESSSSSS CS
                            MarR_2 42 lkrLvaaGLverrpgpeDkR 61
                                      l+ Lv++GL+e+   ++D+R
  gi|313126136|ref|YP_004036406.1| 47 LDTLVEKGLIEKG--QRDRR 64
                                      789*******966..77999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 559.45
//
Query:       gi|313126137|ref|YP_004036407.1|  [L=418]
Description: permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-33  116.9  27.2    1.3e-33  116.5  27.2    1.1  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5  27.2   7.4e-38   1.3e-33       6     324 ..      17     345 ..      12     348 .. 0.80

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 7.4e-38
                   AI-2E_transport   6 vllllllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavll.vlllllvllvllvlllvplliaqltq 81 
                                        l+l ++++y f+s ++ +++++++++y + p+++++k+r  + +la+++ +++l+l +l+l+ ++l+ ++++ l +
  gi|313126137|ref|YP_004036407.1|  17 GLVLAAALAYVFYS-FVGTFVFGIFIYYSTRPIYRRIKRRVRPPSLAAAVaLFALALPALALIAYALA-IVVNELVR 91 
                                       45566666666666.999*******************7666666666665155666666666666666.88888888 PP

                   AI-2E_transport  82 lvkslpayidslqnilnelpslleelen.liqalkqslskilsnilssilnsllsllasllglilslvlvllllffl 157
                                       l+++    ++++     +l +l++ + + l  +l + +++ ls+ilssi +   + la l+ + ++l++++ l f+l
  gi|313126137|ref|YP_004036407.1|  92 LTNNGFFDLSRYPITSDQLARLTDPN-TiLSLELSSLTESELSQILSSIGSA-ADTLAFLGVGGVHLFVMIALAFYL 166
                                       88886644444444444455555555.2357889999999******999865.567777777*************** PP

                   AI-2E_transport 158 lldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilg........vpyalllai 226
                                       l+d +++ + ++  + ++ r  ++a+  ++++ +++++ g++l a+++g ++ i +++l+        +p a l ++
  gi|313126137|ref|YP_004036407.1| 167 LRDDHRFARWVRMNFADD-RGVMEAYCTAVDRDFKNIFFGNILNAVLTGTIGVIAYTVLNmvgpdgvyIPAAALVGL 242
                                       ********9998866666.***************************************984444444469******* PP

                   AI-2E_transport 227 lvglanliPyiGavivlipiaiialltgg...ikevlivlivv....llvqliegnilePklmgkrlglhplvills 296
                                       l+g+a+liP++G  +v+ip+ai+++ +     + ++++v++++    ++v++i + +l+P++ g++  lh  +++++
  gi|313126137|ref|YP_004036407.1| 243 LAGVASLIPVVGMKLVYIPVAIYLAGVSYfsnPGAFWFVIAFIavsfVIVDTIPDLVLRPYVSGRT--LHVGAVMIA 317
                                       ***********************8755443337777777665422227899**************8..6889***** PP

                   AI-2E_transport 297 llaggklfGlvGlilavpltavikaile 324
                                         +g  lfG  G+++a+++++++ ++ +
  gi|313126137|ref|YP_004036407.1| 318 YTFGPLLFGWYGIFFAPMILVLVVNFAK 345
                                       **********************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.76u 0.36s 00:00:01.12 Elapsed: 00:00:00.57
# Mc/sec: 2206.95
//
Query:       gi|313126138|ref|YP_004036408.1|  [L=435]
Description: hypothetical protein Hbor_13820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-49  166.1  26.4    8.1e-49  166.1  26.4    2.5  2  DUF4010   Domain of unknown function (DUF4010)
    7.1e-23   81.3  15.4    7.1e-23   81.3  15.4    3.6  3  MgtC      MgtC family


Domain annotation for each model (and alignments):
>> DUF4010  Domain of unknown function (DUF4010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   5.6     0.027   2.4e+02      66     142 ..      56     128 ..      39     150 .. 0.54
   2 !  166.1  26.4     9e-53   8.1e-49       1     208 [.     198     402 ..     198     403 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.027
                           DUF4010  66 vmllrvllivavvnpallvalalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalillla 142
                                         +  v  +va  + +l  +l l++   a+l+++ ++ll+ +  ++ + + l l++ ++l +A  ++ l+al   l 
  gi|313126138|ref|YP_004036408.1|  56 SLVAAVFTLVAS-KSELGGSL-LAVG--AVLVVVQGILLAVHGLRQRDGTGLSLTTSVSLMAAYGVGTLVALGYALQ 128
                                       333333222222.44555544.3322..2333333333333333333333478899999999999888887755554 PP

  == domain 2  score: 166.1 bits;  conditional E-value: 9e-53
                           DUF4010   1 VlisaisfagYvalrllgarrGllltgllGGlvSStAvtlslarrskeepelarllaagillAnavmllrvllivav 77 
                                       V +++i++++Y++++ +g  rG+++tg++GGl+SS Av+ ++ ++++++pe+ r+ +a++llA a+m +r+l+i+++
  gi|313126138|ref|YP_004036408.1| 198 VTVAGIGIVNYAVVQQYGG-RGIAVTGFFGGLASSAAVVGTMLDHVRQQPEAYRYGVAAVLLADAAMSVRNLFIAIT 273
                                       78*****************.********************************************************* PP

                           DUF4010  78 vnp..allvalalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalilllakaaqeyfGda 152
                                       ++   + l  ++lpl +l++ ++++a++ ++++++ +    + le+P++l++A+ f+++f++il++ ++aq ++G+ 
  gi|313126138|ref|YP_004036408.1| 274 FTAtsRPLLGVVLPLGCLIVGSVAAAWFAADWSQEVT----IPLESPFSLRNAFGFGFVFLVILVVGTMAQGQLGTL 346
                                       9986644556889****99999999999999999999....778********************************* PP

                           DUF4010 153 glyalaalsGladvdAitlslarlaaegtlsaataalaillavlsntlvKavlalv 208
                                       glya +++sG+++++++t++++ l++ gt+s+++a++ailla+++++l+Ka+la++
  gi|313126138|ref|YP_004036408.1| 347 GLYASTFISGFVSSAGATTTAVLLYRGGTISPTAATVAILLATAASVLAKAILAVT 402
                                       *****************************************************974 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3  15.4   7.9e-27   7.1e-23       1     120 [.      26     148 ..      26     149 .. 0.90
   2 ?  -10.5  19.2         2   1.8e+04      54     116 ..     342     403 ..     181     408 .. 0.82
   3 ?   -3.6   1.5       1.6   1.4e+04      90     104 ..     417     431 ..     410     435 .] 0.45

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 7.9e-27
                              MgtC   1 LllAlllGlliGleRelrekaaGlRTfaLvalgaalfvllslelae....srvaaqvvsgigflgagvilkekegak 73 
                                       L+lA+llG+++GleRe++ek+aG+RTfaL +l+aa+f+l++++         v a +v++ g+l a   l++++g +
  gi|313126138|ref|YP_004036408.1|  26 LVLAALLGMFLGLEREWSEKSAGIRTFALTSLVAAVFTLVASKSELggslLAVGAVLVVVQGILLAVHGLRQRDG-T 101
                                       799*************************************66654477666666668888889999999977776.9 PP

                              MgtC  74 vkglTTaaslwvtaaiGllvglglyllavvatvlvllllallreler 120
                                         +lTT++sl++++++G+lv+lg+ l +v+++v++ lll+l+rel+ 
  gi|313126138|ref|YP_004036408.1| 102 GLSLTTSVSLMAAYGVGTLVALGYALQGVTVAVVSSLLLVLKRELHG 148
                                       9*******************************************995 PP

  == domain 2  score: -10.5 bits;  conditional E-value: 2
                              MgtC  54 vsgigflgagvilkekegakvkglTTaaslwvta.aiGllvglglyllavvatvlvllllallr 116
                                        +g   l a +++  +   +  g TT a+l+     i   +++  +lla++a+vl+ ++la+  
  gi|313126138|ref|YP_004036408.1| 342 QLGTLGLYASTFI--SGFVSSAGATTTAVLLYRGgTISPTAATVAILLATAASVLAKAILAVTG 403
                                       2222223355555..3444888888888888765157888888899999999999999998865 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.6
                              MgtC  90 Gllvglglyllavva 104
                                       Gllv++g ++ ++v+
  gi|313126138|ref|YP_004036408.1| 417 GLLVAVGALTGGFVV 431
                                       444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2572.03
//
Query:       gi|313126139|ref|YP_004036409.1|  [L=449]
Description: 4-aminobutyrate aminotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-76  256.2   0.0    2.2e-75  253.9   0.0    1.8  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.9   0.0   1.2e-79   2.2e-75      15     405 ..      45     444 ..      36     445 .. 0.85

  Alignments for each domain:
  == domain 1  score: 253.9 bits;  conditional E-value: 1.2e-79
                                       EEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHH.........HHTT-S---TTTCEEHH...HHHHHHHH CS
                       Aminotran_3  15 kaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavke.........qaaklshvsfgaltnep...alklaekl 79 
                                        aeG + tdvdg+ +lD++s  a+++lG+++Pk+++ ++e         + +++   + +  ++e+    + l++ l
  gi|313126139|ref|YP_004036409.1|  45 DAEGPFCTDVDGNVLLDFTSHVAAAPLGYNNPKIMDRLREfdlvdplkiAGQDFYVSNGERPGEEEfpgPAGLMDRL 121
                                       689*******************************9987763322222213344444444444444422345688888 PP

                                       HHHCT-...SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-T CS
                       Aminotran_3  80 lklapk.gldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflp 155
                                       ++++ + ++d vfl nsG+eAve+A+K++       +++  ++  af+gafHGrtlgals+ +sk+ y+++f+++  
  gi|313126139|ref|YP_004036409.1| 122 TDITSQyDMDTVFLSNSGAEAVENAIKISYD-----ESDGAKYGFAFEGAFHGRTLGALSLNRSKSVYRRKFPEI-S 192
                                       9999764899*******************99.....788888899***************************875.6 PP

                                       SEEEE-TTBGGGTB-HH.........HHHHHHHHHHHHHH.CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHH CS
                       Aminotran_3 156 evvrlkypdeevlkene.........eeeaalleeleale.kkkkdevaAvivEpiqgegGvvvaspeflaklrelc 222
                                       ++v l+y d++++             +  +al ++l   + + + d+va +i+EpiqgegG+ ++s++f+ +l++++
  gi|313126139|ref|YP_004036409.1| 193 GIVDLPYCDKRTCSGGScscgffpdgSDVSALRKKLDPDKgHIHPDDVAYIILEPIQGEGGYRIPSDAFMDELAAVT 269
                                       89999999999987666667777655555555555555458999********************************* PP

                                       HHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTT.T-HHHH CS
                       Aminotran_3 223 kkhdvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfg.Gnplac 298
                                       +++d+ li DE+q G+GrTG++++ +h+ ++pD++t+aKal  G ++s    + +v     ++  +sT+g G+ +a 
  gi|313126139|ref|YP_004036409.1| 270 DEYDITLISDEIQAGVGRTGEMWGSDHFSIEPDVITSAKALRVGATIS----RSDVFPEE-KSRLSSTWGaGDIIAS 341
                                       ****************************************99885555....55555444.44569***75899999 PP

                                       HHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-E CS
                       Aminotran_3 299 avalavleiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlil 375
                                       +  + +l++i++ +l++na e g+++k+  ++++  +  + +vRgkGlm+++e+ ++++++  ++ ++ ++kG+l+l
  gi|313126139|ref|YP_004036409.1| 342 LQGALTLDAIHDYDLMDNAVERGQQFKQFVRDADLGP--VTDVRGKGLMLGVEFDSKERRN--DVQEACLQKGLLTL 414
                                       99******************************99877..********************88..9************* PP

                                       EETTTEEEE---TT--HHHHHHHHHHHHHH CS
                       Aminotran_3 376 saGdnvirllppliitdeeidelleilkka 405
                                        +G +vir+lppl +t+ ei+ + + + +a
  gi|313126139|ref|YP_004036409.1| 415 ACGYDVIRILPPLDVTEREIEIGASLFCDA 444
                                       ********************9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2481.36
//
Query:       gi|313126140|ref|YP_004036410.1|  [L=45]
Description: hypothetical protein Hbor_13840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.34s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 268.43
//
Query:       gi|313126141|ref|YP_004036411.1|  [L=326]
Description: flap endonuclease 1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-23   83.3   0.1    2.1e-23   82.5   0.1    1.5  1  XPG_I         XPG I-region
    1.2e-11   44.9   0.0    2.1e-11   44.2   0.0    1.3  1  XPG_N         XPG N-terminal domain
    3.9e-05   24.2   0.1    9.1e-05   23.0   0.0    1.7  2  5_3_exonuc    5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.071   13.0   0.0       0.11   12.4   0.0    1.4  1  5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like do
      0.079   13.2   0.0       0.14   12.4   0.0    1.3  1  OrfB_IS605    Probable transposase


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.1   5.8e-27   2.1e-23       3      94 .]     144     225 ..     142     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 5.8e-27
                                       HT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHHT- CS
                             XPG_I   3 mgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkkkekekkkvevidlekvlkelgl 79 
                                       + +p+++Ap E+EAq++y++k+g+vd+v seD+D+ll+Gap++lr+l+  + k         +e +dle +l+ l++
  gi|313126141|ref|YP_004036411.1| 144 LDVPVIEAPAEGEAQASYMAKQGDVDYVGSEDYDTLLLGAPYTLRQLT--S-KGD-------PELMDLEATLSDLDV 210
                                       679********************************************8..3.333.......79************* PP

                                       -HHHHHHHHHHHCET CS
                             XPG_I  80 treqlidlaillgcD 94 
                                       t+eqlid+ail+g+D
  gi|313126141|ref|YP_004036411.1| 211 TQEQLIDIAILCGTD 225
                                       **************9 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   5.9e-15   2.1e-11      12     100 ..       8     102 ..       3     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 5.9e-15
                                       HH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS......-HHHHHHHHHHHHHHHTTEEEEEEE--S CS
                             XPG_N  12 evaairsvsiealegkklaiDaslwlyrfliavreqlgnalen......tshlmglfsrllrlldfgikPifVFdgk 82 
                                         a++ +vs   l g ++a+Da  wlyr l++  +  g+++ +         l g+++ l ++ +   +P+fVFdg+
  gi|313126141|ref|YP_004036411.1|   8 SLASLSEVSFDDLAGGVVAVDAHNWLYRYLTTTVKFTGDEVYTttegeeVANLIGIVQGLPKFFEHDLTPVFVFDGG 84 
                                       556778999999*******************999999998887788877678999********************** PP

                                       --GGGHHHHHHHHHHHHH CS
                             XPG_N  83 apdlkkeelekrserrqe 100
                                       +++lk  e + r+++r++
  gi|313126141|ref|YP_004036411.1|  85 VTELKDAEVSERRAQREK 102
                                       *************99987 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       4.6   1.6e+04      58      64 ..     104     110 ..      89     130 .. 0.53
   2 !   23.0   0.0   2.5e-08   9.1e-05       1      52 [.     210     260 ..     210     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.6
                        5_3_exonuc  58 ekLeenk 64 
                                       e+L++++
  gi|313126141|ref|YP_004036411.1| 104 EELKKEA 110
                                       2222222 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 2.5e-08
                        5_3_exonuc   1 vkPeqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenld.elk 52 
                                       v+ eq+id++ L+G   D  +G++g+G+ktA k +ke+g+l ++le+ d  ++
  gi|313126141|ref|YP_004036411.1| 210 VTQEQLIDIAILCGT--DFNEGISGVGPKTALKEVKEHGDLWTVLEARDdYIE 260
                                       6779**********6..5668*************************8773233 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.1e-05      0.11       2      82 ..      24     109 ..      23     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                      5_3_exonuc_N   2 llLiDgsslifRayyal........lttsdgeptnavygflnmllklleeekpthlavvfDakkktfRhelypeYKa 70 
                                       ++ +D+++ ++R    +        +tt++ge+++ + g+++ l k+ e+    + ++vfD + ++ +++ ++e +a
  gi|313126141|ref|YP_004036411.1|  24 VVAVDAHNWLYRYLTTTvkftgdevYTTTEGEEVANLIGIVQGLPKFFEHDL--TPVFVFDGGVTELKDAEVSERRA 98 
                                       5779********88876799999999999*******************9533..5799***977799********** PP

                      5_3_exonuc_N  71 nReetpeelkeq 82 
                                       +Re++ eelk++
  gi|313126141|ref|YP_004036411.1|  99 QREKA-EELKKE 109
                                       **654.455544 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.9e-05      0.14      40     109 ..      80     150 ..      64     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                        OrfB_IS605  40 lykg..rrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhllhklathliktlkevgve 109
                                       +++g   +lk ++ + +++++e +  lkk+   +    + arl + r++r+++++h++++ l+++l+  ++e
  gi|313126141|ref|YP_004036411.1|  80 VFDGgvTELKDAEVSERRAQREKAEELKKEAEERGDDMEAARL-EARTQRLTDVIHETSRGLLERLDVPVIE 150
                                       5555456788889999999999999999999877777888888.668999***************9877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.38s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 1800.01
//
Query:       gi|313126142|ref|YP_004036412.1|  [L=217]
Description: hypothetical protein Hbor_13860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00044   20.2   3.0    0.00073   19.5   3.0    1.3  1  Serglycin       Serglycin
  ------ inclusion threshold ------
      0.063   13.5   0.0       0.17   12.1   0.0    1.7  2  Acetyltransf_1  Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Serglycin  Serglycin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   3.0   8.2e-08   0.00073      92     114 ..     188     210 ..     172     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.2e-08
                         Serglycin  92 sgsgsGsGsGsGsgsgsgfltei 114
                                        gsgsGsGsGsGs+s+s+f+  +
  gi|313126142|ref|YP_004036412.1| 188 VGSGSGSGSGSGSDSDSDFVGVM 210
                                       69*****************8765 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.17      56     117 .]      67     126 ..      27     126 .. 0.84
   2 ?   -1.5   0.0      0.33   2.9e+03      18      43 ..     156     182 ..     138     197 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                                       TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  56 ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                       ++  + +i+ + V+ ++ g  lG +L   +++ a  eg++ + +av  +n  a + + k GF
  gi|313126142|ref|YP_004036412.1|  67 TDASTLWIRYVTVRGDRKGETLGPQLCAFVADAAQGEGYETVKIAV--NNPFAYEALHKAGF 126
                                       5678999*************************99999**9998866..88888888889999 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHSTTC.EEEEEEETTE CS
                    Acetyltransf_1  18 daseeefeesfsleae.gllvaeedge 43 
                                       +a +++++++  +++e  +l ++e+  
  gi|313126142|ref|YP_004036412.1| 156 QAGLDRYRDRDLDDPEsAFLTGRENAD 182
                                       333444666666666634444666643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1236.92
//
Query:       gi|313126143|ref|YP_004036413.1|  [L=202]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-21   76.2   0.1    3.6e-21   75.6   0.1    1.3  1  Methyltransf_11  Methyltransferase domain
    2.3e-18   66.6   0.0    3.1e-18   66.2   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    4.2e-18   65.8   0.1    7.5e-18   65.0   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    3.2e-13   49.6   0.0    5.2e-13   48.9   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.5e-13   49.6   0.0      5e-13   49.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.6e-12   47.3   0.0    4.7e-12   46.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
     0.0039   16.8   0.0     0.0054   16.4   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
     0.0071   16.2   0.0     0.0083   16.0   0.0    1.2  1  Methyltransf_8   Hypothetical methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.1   1.6e-24   3.6e-21       1      96 []      47     136 ..      47     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1.6e-24
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       Ldv+ GtGr ++ala++g + v vD+s  ml +a++ +++       v+ada +lpf d+s+D++++  +lhh++dp
  gi|313126143|ref|YP_004036413.1|  47 LDVAGGTGRATRALARNGLEPVVVDFSRGMLSRARADGRDT------VHADAGTLPFCDDSVDAIIVVDALHHMPDP 117
                                       8******************************9998888776......9***************************** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                       + a++e+aRv+ pgG++v+
  gi|313126143|ref|YP_004036413.1| 118 DGAIREAARVVSPGGVVVV 136
                                       ***************9986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   1.4e-21   3.1e-18      17     161 ..      37     178 ..      18     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.4e-21
                   Methyltransf_23  17 lpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevle 93 
                                       +  +r+  rvLd++ GtG+ ++ l++ng + ++vD s+ + ++a+ a+    + +d+   ++ +++ d I+  + l+
  gi|313126143|ref|YP_004036413.1|  37 SFARRPVERVLDVAGGTGRATRALARNGLEPVVVDFSRGMLSRAR-ADGRDTVHADAGTLPFCDDSVDAIIVVDALH 112
                                       33389999***********************************94.4555555555556788889************ PP

                   Methyltransf_23  94 hvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGle 161
                                       h+pdp  ++r +a+ ++pgG+++++e++ +  + r    +l+++  g  ++f++ ++l+  +e+aGl+
  gi|313126143|ref|YP_004036413.1| 113 HMPDPDGAIREAARVVSPGGVVVVQEFGPDTLRGRG--LVLAERAIGFDSQFWTPDELCAVFENAGLT 178
                                       ***************************976433333..345556555556****************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.1   3.3e-21   7.5e-18       1      97 []      46     132 ..      46     132 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 3.3e-21
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd++ GtGr t+ala+++   + + vD+s +ml +ar+  +      + v++da +lpf d+s+D+++++ alhh+
  gi|313126143|ref|YP_004036413.1|  46 VLDVAGGTGRATRALARNG--LEPVVVDFSRGMLSRARADGR------DTVHADAGTLPFCDDSVDAIIVVDALHHM 114
                                       9*****************5..******************995......78********************999***9 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +d+d   a++e+arv+ pgG
  gi|313126143|ref|YP_004036413.1| 115 PDPD--GAIREAARVVSPGG 132
                                       9777..99***********9 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   2.3e-16   5.2e-13      45     155 ..      40     140 ..      12     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.3e-16
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvt 121
                                        ++ ++vlDvagGtg  + +l++   +  + vv+D++  mL+ +++  +       + ++a+a  Lpf dds D + 
  gi|313126143|ref|YP_004036413.1|  40 RRPVERVLDVAGGTGRATRALAR---NGLEPVVVDFSRGMLSRARADGR-------DTVHADAGTLPFCDDSVDAII 106
                                       455579**********9999875...4567899********97665544.......4589***************** PP

                                       EES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE- CS
                   Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlvvlefs 155
                                       v   l  ++D + a++ea rv+ pGG +vv ef 
  gi|313126143|ref|YP_004036413.1| 107 VVDALHHMPDPDGAIREAARVVSPGGVVVVQEFG 140
                                       *******************************996 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   2.2e-16     5e-13       6     113 ..      45     140 ..      41     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 2.2e-16
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       rvlD++ GtG+ t +la++   + e v +D+s  ++++Ar+             ++d+ +l+  ++d+++D i+  +
  gi|313126143|ref|YP_004036413.1|  45 RVLDVAGGTGRATRALARN---GLEPVVVDFSRGMLSRARAD-------GRDTVHADAGTLP--FCDDSVDAIIVVD 109
                                       89***************54...678999*************5.......3446789******..************* PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr 113
                                       +l++++dpd +++e+ rv++pgg+++++++ 
  gi|313126143|ref|YP_004036413.1| 110 ALHHMPDPDGAIREAARVVSPGGVVVVQEFG 140
                                       ***************************9986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   2.1e-15   4.7e-12       1      98 [.      47     133 ..      47     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.1e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++ +GtG+ +ral+++  ++e ++vD+s+ ++   +++   r+  +++  +l  +d+       s+D++++ ++lh
  gi|313126143|ref|YP_004036413.1|  47 LDVAGGTGRATRALARN--GLEPVVVDFSRGML--SRARADGRDTVHADAGTLPFCDD-------SVDAIIVVDALH 112
                                       8****************..**************..66666666655666666666664.......9*********** PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                       h++d++ ++++++++++pgG+
  gi|313126143|ref|YP_004036413.1| 113 HMPDPDGAIREAARVVSPGGV 133
                                       ********************8 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.4e-06    0.0054      13     113 ..      42     140 ..      34     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-06
                              MetW  13 pgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatr 89 
                                       p  rvld+  G G   + l+  ++++   ++ ++  + ++ a G   ++ d+  +   f d+s d +++  +l  + 
  gi|313126143|ref|YP_004036413.1|  42 PVERVLDVAGGTGRATRALAR-NGLEPVVVDFSRGMLSRARADGRDTVHADA--GTLPFCDDSVDAIIVVDALHHMP 115
                                       6789***************65.9***********************999765..67899****************** PP

                              MetW  90 npkevldellrigr.raivsfPnfG 113
                                       +p+  ++e  r+     +v   +fG
  gi|313126143|ref|YP_004036413.1| 116 DPDGAIREAARVVSpGGVVVVQEFG 140
                                       **********986513455566666 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.7e-06    0.0083     106     180 ..      85     160 ..      46     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.7e-06
                                       TTEEES-TTS-S--TT-EEEEEEES---S.S-HHHHHHHHHHHEEEEEEEEEEEEGGG-S-HHHHHHHHHCTTEEE CS
                    Methyltransf_8 106 ervvacdlakvPledesvdvavfclslmg.tnladflkeanrvlkvGGllkvaevksrfesvklfaraltklGfev 180
                                        + v  d   +P  d+svd +++  +l    +    ++ea rv+ +GG++ v e       ++ ++ a   +Gf+ 
  gi|313126143|ref|YP_004036413.1|  85 RDTVHADAGTLPFCDDSVDAIIVVDALHHmPDPDGAIREAARVVSPGGVVVVQEFGPDTLRGRGLVLAERAIGFDS 160
                                       567788999**********77776666431477899****************998877777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1163.76
//
Query:       gi|313126144|ref|YP_004036414.1|  [L=140]
Description: hypothetical protein Hbor_13880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-19   69.2   8.8    4.4e-19   69.0   8.8    1.0  1  DUF3054   Protein of unknown function (DUF3054)


Domain annotation for each model (and alignments):
>> DUF3054  Protein of unknown function (DUF3054)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   8.8   2.5e-23   4.4e-19       1     110 []      21     135 ..      21     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 2.5e-23
                           DUF3054   1 lvvDvvavlvfaliGrlsH...gesls.llgvletawPFlvglavgWllvapl...yearaaskaaralpagvvvwl 70 
                                       +v+D+++++++++iG ++H   ++ ++ ++g++ t++PFl+    gW ++ +l   y+a aa++a++ +p ++  w+
  gi|313126144|ref|YP_004036414.1|  21 AVGDFLMLAAVLTIGFINHngvDQIFDdPTGWILTLVPFLL----GWGIFGVLigaYSAGAAETAKASIPLTIRGWI 93 
                                       699****************544334446*************....****9998998866666669************ PP

                           DUF3054  71 vavvvGlllR..allkggvalsFvlValvvlavlLlgwRava 110
                                        ++++Gl lR   l++gg+a+ F++V+l++++++L++wR+++
  gi|313126144|ref|YP_004036414.1|  94 PGAILGLGLRasPLFEGGFAWIFAAVILATGMLALVAWRWLF 135
                                       **********999**************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 862.22
//
Query:       gi|313126145|ref|YP_004036415.1|  [L=444]
Description: sugar phosphate permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-26   90.9  60.4    5.6e-19   68.3  28.2    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.015   14.2  20.6      0.033   13.1   1.5    2.3  2  Sugar_tr  Sugar (and other) transporter
        1.1    7.5  20.6       0.11   10.9   5.6    2.9  2  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3  28.2   9.3e-23   5.6e-19      24     241 ..      44     261 ..       7     300 .. 0.75
   2 !   26.0  27.5   6.8e-10   4.1e-06      39     175 ..     295     432 ..     265     443 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 9.3e-23
                             MFS_1  24 aedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgag 100
                                        ++l ++++++g+++t+ + ++++++lp+G+l+dr+G+rr++ l+l+++a +++ll ++++l ++ ++ +  G++a+
  gi|313126145|ref|YP_004036415.1|  44 LTQLDVTAATLGWVVTAGYGLFGIGALPGGVLVDRIGSRRLISLCLFGMAGSFVLLGLSPNLVVVTLALLCWGAAAS 120
                                       345779***********9999*******************************6666675666699999999****** PP

                             MFS_1 101 alfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepp 177
                                       ++ pag+ali++  +  erg ++++ +++ ++G+ lgpll ++l+  l W+ v ++la+ +l+a+  +    ++e  
  gi|313126145|ref|YP_004036415.1| 121 VYHPAGLALISKGMN--ERGTGFAYHGIAGNVGIGLGPLLTAILLVFLDWTTVAMLLAVPALVAGAYATRAKFDESA 195
                                       ************887..6**********************************************8833333333222 PP

                             MFS_1 178 erkrkspkeeekgtgpaplvpawkallkdpvlw......illialllfffgfsglltllplylqevlgls 241
                                       +    ++    ++++ a++ + + ++++    +      ++++++++ ++++ g+lt+lp +l     ++
  gi|313126145|ref|YP_004036415.1| 196 AVDAGAGG---SSKADAGVGS-FAEFVTESKRLiagglaVVFLVVICSGLFYRGVLTFLPDLLSGLDTFD 261
                                       22222222...2336666666.66666666443344456788888888999999******9876666666 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 6.8e-10
                             MFS_1  39 tlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa.sslwlllvlrvlqGlgagalfpagaaliadw 113
                                       ++   + +++++ +G l+dr+   + l+ ++ ++a+ ++l+l ++ ++l +llv+ ++ G++  ++ p  +a +a++
  gi|313126145|ref|YP_004036415.1| 295 SGLLMVGVLGQYAGGKLTDRLPVEWGLVGAFGALAVLAVLFLpVVnAGLAPLLVFGAILGFFLFVIQPFYQATVAEY 371
                                       555667799************999988888888888845555444799999************************** PP

                             MFS_1 114 fpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpee 175
                                       +p   rg+ +g+ ++g+    +lg +l+g +++++  +a+f  la++++ ++++ +++l ++
  gi|313126145|ref|YP_004036415.1| 372 TPAGTRGLSYGYTYLGVFGVGALGGALAGTILTYATPTALFTTLAGIAVAGALF-GFYLARK 432
                                       ***************999999999999999999*****************9885.4444333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.5   5.5e-06     0.033     291     340 ..      57     106 ..      41     123 .. 0.75
   2 ?    6.1  11.7   0.00073       4.4     322     434 ..     319     427 ..     292     431 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH...HHH CS
                          Sugar_tr 291 lvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg.ivall 340
                                       +vt+++g   + a   +  lvdr+G R+l  l+++gma  fv+lg  + l+
  gi|313126145|ref|YP_004036415.1|  57 VVTAGYGLFGIGALPGG-VLVDRIGSRRLISLCLFGMAGSFVLLGlSPNLV 106
                                       55666666666666666.89************************9754444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00073
                                       HHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHH CS
                          Sugar_tr 322 lGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwla 398
                                       +G++g++ ++++l+  +l++v++  + + +++++ +l   +f + + p    +v+E  p ++R++ + +++   + +
  gi|313126145|ref|YP_004036415.1| 319 WGLVGAFGALAVLAVLFLPVVNA--GLAPLLVFGAILG--FFLFVIQPFYQATVAEYTPAGTRGLSYGYTYLGVFGV 391
                                       55555555555555334444444..4555555555554..4444466666677777777777777777777777777 PP

                                       HHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 399 nflisllfpiiteaigggyvflvfaglavlfiifvf 434
                                         l + l  +i+   + +  f   ag+av++++f+f
  gi|313126145|ref|YP_004036415.1| 392 GALGGALAGTILTYATPTALFTTLAGIAVAGALFGF 427
                                       777777776666666667777777777777777666 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.6   1.8e-05      0.11     253     320 ..      51     118 ..      25     187 .. 0.88
   2 ?    4.9   3.4    0.0012       6.9     253     304 ..     378     430 ..     366     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.8e-05
                             MFS_3 253 alvyGillga....lGvGAilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaa 320
                                       a++ G +++a    +G+GA+ g++l+    +r++s rl++l  +++A   + l+l+++l+v++l+ll  Gaa
  gi|313126145|ref|YP_004036415.1|  51 AATLGWVVTAgyglFGIGALPGGVLV----DRIGSRRLISLCLFGMAGSFVLLGLSPNLVVVTLALLCWGAA 118
                                       55555554332222899999998865....6799*********************************99987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0012
                             MFS_3 253 alvyGi.llgalGvGAilgalllsrLRerlsserlvllaavalAlvllslala 304
                                        l yG+  lg +GvGA++gal  ++L     +  +++la +a+A  l+   la
  gi|313126145|ref|YP_004036415.1| 378 GLSYGYtYLGVFGVGALGGALAGTILTYATPTALFTTLAGIAVAGALFGFYLA 430
                                       467996369******************99999999999*99999888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2454.20
//
Query:       gi|313126146|ref|YP_004036416.1|  [L=82]
Description: hypothetical protein Hbor_13900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 546.16
//
Query:       gi|313126147|ref|YP_004036417.1|  [L=332]
Description: ornithine cyclodeaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-68  229.9   0.3    4.2e-68  229.6   0.3    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
      9e-05   22.6   0.0    0.00013   22.0   0.0    1.2  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0011   19.5   0.7      0.003   18.1   0.4    1.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.075   13.5   0.1       0.16   12.4   0.1    1.5  1  NAD_binding_7    Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.6   0.3   9.3e-72   4.2e-68       2     317 ..       3     314 ..       2     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: 229.6 bits;  conditional E-value: 9.3e-72
                                       -EEEE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTC CS
                   OCD_Mu_crystall   2 ekavltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenk 78 
                                       e+ +lt  +v  +   ++ ++av +++r+  +  ++  pr++l+ ++  g +    a l+  +      ++++    
  gi|313126147|ref|YP_004036417.1|   3 ETLFLTSDDVSGLATPAEFVDAVRDGYRQRGE-GAPAEPRTKLPNENPPGFFTTYAAVLPDTG-----AMGGYMYSA 73 
                                       56789999999999999************999.68999*********9999999999999944.....456777777 PP

                                       CCTSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--S CS
                   OCD_Mu_crystall  79 ksglptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldik 155
                                         g +    +  L+d e+G p+al+d+  +   +T+Av+av++  Lar da++lai+G G+qa+ ql+a  av+d++
  gi|313126147|ref|YP_004036417.1|  74 GFGGQDAWFMTPLFDAESGEPMALIDGASMNPFKTGAVGAVGVDALARDDAETLAIVGSGAQARGQLRATAAVRDLE 150
                                       77888999999****************************************************************** PP

                                       EEEEE-SSHHHHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--S CS
                   OCD_Mu_crystall 156 evriydrdeeaaekfaenlqe.fefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkte 231
                                       +v +y  ++e +e fa ++ +  +  v a++s + a+egadiv+t+T a +p++  + ++pG+h++a+g  a +k+e
  gi|313126147|ref|YP_004036417.1| 151 TVWVYSPTKESRESFAGEMDRrLDASVAAVASSAAAIEGADIVITATNASEPVFDGDRLEPGTHVTAMGQYATDKRE 227
                                       *********************78****************************************************** PP

                                       B-HHHHHCCEEEE.SHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHH CS
                   OCD_Mu_crystall 232 Ldddilkradifv.dseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaa 307
                                       Ld   + ra+++       ++  G   +a+ +gv++ed++ aelgeviaGk++GR++deeit+fds+G+++e va a
  gi|313126147|ref|YP_004036417.1| 228 LDATTIERAKYVPdLRDRVTQDAGSFLHALAEGVVDEDHVYAELGEVIAGKVEGREDDEEITVFDSGGTGIETVAGA 304
                                       ************9677889999******************************************************* PP

                                       HHHHHHHCCC CS
                   OCD_Mu_crystall 308 klvyeraeek 317
                                        l ye+a+++
  gi|313126147|ref|YP_004036417.1| 305 YLLYEKAQSE 314
                                       ******9975 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.9e-08   0.00013      13      99 ..     125     213 ..     117     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.9e-08
                                       -EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS CS
                      Shikimate_DH  13 kkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisatasee 87 
                                       ++  ++G G  a+  +++ +a   ++ v v   t e  +++a e+ +  ++++ ++ +  ++++ ad+vi+at+++e
  gi|313126147|ref|YP_004036417.1| 125 ETLAIVGSGAQARGQLRATAAVrDLETVWVYSPTKESRESFAGEMdRRLDASVAAVASSAAAIEGADIVITATNASE 201
                                       567899*99999888887766438999******************666689999*********************** PP

                                       -SB-HHHHHCCH CS
                      Shikimate_DH  88 pilekeeveeal 99 
                                       p+++ +++e   
  gi|313126147|ref|YP_004036417.1| 202 PVFDGDRLEPGT 213
                                       ***999998765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   6.7e-07     0.003       2      69 ..     127     197 ..     126     201 .. 0.86
   2 ?   -1.7   0.0         1   4.7e+03       7      23 ..     250     266 ..     250     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.7e-07
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlav 69 
                                       ++i+G+G ++++ ++  +a  ++ + ++v  s+++e++e++a e+       v + a + + a+e ad+v+ a 
  gi|313126147|ref|YP_004036417.1| 127 LAIVGSGAQARGQLRATAAV-RDLETVWV-YSPTKESRESFAGEMDrrldasVAAVA-SSAAAIEGADIVITAT 197
                                       89**********99977666.48999995.5*************9999998777777.8999999******986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                                       TSHHHHHHHHHHHHTTS CS
                     F420_oxidored   7 aGnmgealasgllaaga 23 
                                       aG++ +ala+g++ ++ 
  gi|313126147|ref|YP_004036417.1| 250 AGSFLHALAEGVVDEDH 266
                                       68889999999999885 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.7e-05      0.16       8      72 ..     125     200 ..     120     202 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleag..akvtvvapev..keele.......elvklaeeel...ekdlegadlviaatd 70 
                                       ++  +vG G  A   +r  ++     +v v++p+       e       ++++++   +    + +egad+vi+at+
  gi|313126147|ref|YP_004036417.1| 125 ETLAIVGSGAQARGQLRATAAVRdlETVWVYSPTKesR---EsfagemdRRLDASVAAVassAAAIEGADIVITATN 198
                                       67789****998876665555443499*******5330...235554445555544444333567***********8 PP

                     NAD_binding_7  71 dr 72 
                                         
  gi|313126147|ref|YP_004036417.1| 199 AS 200
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1949.84
//
Query:       gi|313126148|ref|YP_004036418.1|  [L=355]
Description: cell division protein pelota [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-28   98.7   0.2    3.7e-28   98.1   0.2    1.3  1  eRF1_1    eRF1 domain 1
    2.2e-24   86.1   0.8    6.2e-24   84.7   0.2    2.1  2  eRF1_3    eRF1 domain 3
    3.5e-09   37.1   0.1    6.7e-08   32.9   0.1    2.4  1  eRF1_2    eRF1 domain 2


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.2   6.1e-32   3.7e-28       1     128 [.       1     128 [.       1     129 [. 0.96

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 6.1e-32
                                       HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH........--CEEEEEEEEEEEEEEECT CS
                            eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqr.esstgsreservklkLtikvekvdfdk 76 
                                       m++ +r   ++g++ +tL+pe+ +dlwhl++++++gd v+  t+r++qr + +   +  +r ++  ti+v +v+f  
  gi|313126148|ref|YP_004036418.1|   1 MRISSRGRGEEGRERITLVPENVDDLWHLSHVLESGDLVSGDTTRRIQRdDDQMRDTGGQREHMHVTISVSDVEFAR 77 
                                       99****999****************************************4466777779****************** PP

                                       TSSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                            eRF1_1  77 dagvlrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                        a++lr+ G++++ +++ +lg++htl++e ++++ti+k +++  +l+r++ea
  gi|313126148|ref|YP_004036418.1|  78 FANRLRVGGEIVDCSREDQLGHHHTLNVEEHDEVTIEK-HFKPDQLDRIEEA 128
                                       **************************************.9*********998 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.99   5.9e+03      25      40 ..     231     246 ..     212     247 .. 0.77
   2 !   84.7   0.2     1e-27   6.2e-24       2     113 .]     254     354 ..     253     354 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.99
                                       SHHHHHHHHHTT-EEE CS
                            eRF1_3  25 GveevlkalemgAvet 40 
                                       G + v ++l+ gAv++
  gi|313126148|ref|YP_004036418.1| 231 GDRGVHEVLKRGAVDE 246
                                       6677888899999986 PP

  == domain 2  score: 84.7 bits;  conditional E-value: 1e-27
                                       HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHH CS
                            eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenv 78 
                                       ++e++l+++++e ++++ +k++YG+eev +a+e+gAvetLLv++e  r++++        g+    v+ ++e++++v
  gi|313126148|ref|YP_004036418.1| 254 SKEADLIDDLMEGISTG-EKVAYGIEEVAEAAEFGAVETLLVLDERLREERQ--------GAGEWDVD-VNEVIQTV 320
                                       789************99.9*****************************9732........33333455.99****** PP

                                       HHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  79 eesgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       e +g++v ++sse++ G ql k++gGiaaiLRy++
  gi|313126148|ref|YP_004036418.1| 321 ERQGGDVAVFSSEFDPGRQL-KNLGGIAAILRYRL 354
                                       ********************.************85 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   1.1e-11   6.7e-08      73     127 ..     188     243 ..     136     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.1e-11
                                       HTTTESEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC.C CS
                            eRF1_2  73 dkdklkgiilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek.a 127
                                        + ++++iilagpgf+k++  d++  +++    +i++vd+s+ g+ g++evl+  a
  gi|313126148|ref|YP_004036418.1| 188 SRMDVDAIILAGPGFTKQDARDYIAENHRDVVDKITVVDTSSVGDRGVHEVLKRgA 243
                                       4569************************************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2344.82
//
Query:       gi|313126149|ref|YP_004036419.1|  [L=234]
Description: hypothetical protein Hbor_13930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-34  118.2  27.2    3.2e-34  118.2  27.2    1.5  1  DUF4013        Protein of unknown function (DUF4013)
  ------ inclusion threshold ------
      0.013   14.6   0.4      0.013   14.6   0.4    2.3  3  Man-6-P_recep  Mannose-6-phosphate receptor
        3.9    7.2   5.5        9.6    6.0   5.6    1.6  2  Trp_oprn_chp   Tryptophan-associated transmembrane protein (T


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2  27.2   5.4e-38   3.2e-34       6     167 ..      28     194 ..      24     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 5.4e-38
                           DUF4013   6 liiaivlslvllGYlvrvlrdtirgddelPefddwgkllvdGlkafvvslvYl...liplii.....alltllvala 74 
                                       l+++i+++++++GY+vrvlr +++g++++P f +wg+l+vdGlk++++ +vY+   lip+i      +++ +l+a+a
  gi|313126149|ref|YP_004036419.1|  28 LFVFIIPIFIIQGYMVRVLRGAAKGETAAPSFTNWGELIVDGLKLVIINFVYSlivLIPMIAlsivlGIGNSLSAGA 104
                                       34444444456******************************************777777777655544444444444 PP

                           DUF4013  75 slaagdsaagallvlallglllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialil 151
                                          +   ++ga+ +l+++g+l +l+ + l+ +++++++p+a a+fa +gsl+aaf++++i++ ++    +y++a++l
  gi|313126149|ref|YP_004036419.1| 105 PGPEPGVTVGAAPALGIVGFLGILV-IGLFSIVVSYFIPAAQANFAIEGSLGAAFDISTIVSGAMT--SEYFVAWVL 178
                                       4444444446666666667777666.5555555*****************************7755..6******** PP

                           DUF4013 152 llvigivlsllaillv 167
                                       +lv+g++ls++++ll+
  gi|313126149|ref|YP_004036419.1| 179 VLVVGSILSFIGGLLF 194
                                       **************97 PP

>> Man-6-P_recep  Mannose-6-phosphate receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.4   2.3e-06     0.013     163     220 ..      19      73 ..      11      76 .. 0.89
   2 ?   -3.0   1.0      0.53   3.1e+03     168     182 ..     127     141 ..     122     144 .. 0.87
   3 ?   -4.0   2.5         1   6.1e+03     163     190 ..     180     197 ..     160     210 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-06
                     Man-6-P_recep 163 lsvGsillivllslvavyligGflyqrlvvgakGleqiPnyafWqdlGnlvadGCdfv 220
                                       + +G +l ++++ ++ +++i G++ + l   akG    P ++ W   G+l+ dG  +v
  gi|313126149|ref|YP_004036419.1|  19 ILIGGVLSLLFVFIIPIFIIQGYMVRVLRGAAKGETAAPSFTNW---GELIVDGLKLV 73 
                                       6699********************99999999**********99...67788887766 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.53
                     Man-6-P_recep 168 illivllslvavyli 182
                                       il+i l+s+v  y+i
  gi|313126149|ref|YP_004036419.1| 127 ILVIGLFSIVVSYFI 141
                                       99999********98 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 1
                     Man-6-P_recep 163 lsvGsillivllslvavyligGflyqrl 190
                                       l vGsil           +igG+l+  +
  gi|313126149|ref|YP_004036419.1| 180 LVVGSILS----------FIGGLLFIVI 197
                                       34444444..........3444444332 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.93   5.6e+03     116     131 ..      13      28 ..       7      31 .. 0.79
   2 ?    6.0   5.6    0.0016       9.6      42     138 ..     102     196 ..      93     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.93
                      Trp_oprn_chp 116 tawpvlalaggvllll 131
                                       ++w    l+ggvl ll
  gi|313126149|ref|YP_004036419.1|  13 SDWIPTILIGGVLSLL 28 
                                       6788889999999876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0016
                      Trp_oprn_chp  42 apaltalAlvllAaavAvlavrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaaveltaw 118
                                       a+a+ +   v++ aa A+ +v+ lg  v+g+  ++++  + +a ++ + +++  a+   ++   v++a ++  + aw
  gi|313126149|ref|YP_004036419.1| 102 AGAPGPEPGVTVGAAPALGIVGFLGILVIGLFSIVVSYFIPAAQANFAIEGSLGAAFDIST--IVSGAMTSEYFVAW 176
                                       5566666678888999999999999999999999999999888888877766555544433..5545555555889* PP

                      Trp_oprn_chp 119 pvlalaggvllllagvllll 138
                                       +++ ++g +l +++g+l ++
  gi|313126149|ref|YP_004036419.1| 177 VLVLVVGSILSFIGGLLFIV 196
                                       ****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1479.92
//
Query:       gi|313126150|ref|YP_004036420.1|  [L=238]
Description: hypothetical protein Hbor_13940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-39  134.4  18.4    3.3e-39  134.4  18.4    1.5  2  DUF4013        Protein of unknown function (DUF4013)
  ------ inclusion threshold ------
       0.18   11.8   0.2       0.51   10.4   0.2    1.8  1  SHP            Small hydrophobic protein
       0.22   10.6   0.0       0.47    9.5   0.0    1.5  1  Man-6-P_recep  Mannose-6-phosphate receptor
       0.48   10.0   3.8        1.1    8.8   0.2    2.7  2  PMT_4TMC       C-terminal four TMM region of protein-O-mannos


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4  18.4   7.4e-43   3.3e-39       5     166 ..      27     187 ..      23     189 .. 0.82
   2 ?   -2.6   0.5      0.98   4.4e+03     143     155 ..     198     210 ..     190     218 .. 0.43

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 7.4e-43
                           DUF4013   5 lliiaivlslvllGYlvrvlrdtirgddelPefddwgkllvdGlkafvvslvYlliplii.alltllvalaslaagd 80 
                                       ll ++iv++++++GYlvrv+r+t++g +e+Pefddwg+++vdGlka+v++++Y++ip +i ++l++++++a +a+++
  gi|313126150|ref|YP_004036420.1|  27 LLSVLIVPTILVAGYLVRVIRRTMHGIEEPPEFDDWGDMAVDGLKAMVIAFIYGFIPSLIaGVLVGGSIFAIVAGNA 103
                                       455667777777************************************************84444444555555554 PP

                           DUF4013  81 saagallvlallglllall.lvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllvig 156
                                       +  g+l +++  g+ll ll +++l+l+ +++++p+a+a+fa+t+++++af+++ +++++ +  gky++a++  ++++
  gi|313126150|ref|YP_004036420.1| 104 ARSGGLSIAGGAGVLLGLLvSFVLGLV-AAYIIPAAIANFAETDQFGKAFSVGDLRSVLVS--GKYFTAWVSGFAVI 177
                                       444555555555555555515556666.*****************************9966..7************* PP

                           DUF4013 157 ivlsllaill 166
                                       +v++l+a++l
  gi|313126150|ref|YP_004036420.1| 178 FVAGLVASIL 187
                                       ********98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.98
                           DUF4013 143 gkyiialilllvi 155
                                       g+++ +++++++ 
  gi|313126150|ref|YP_004036420.1| 198 GGFLGFYAAVAAY 210
                                       2333333333332 PP

>> SHP  Small hydrophobic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00011      0.51      15      39 ..      15      39 ..       1      45 [. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                               SHP 15 wpyftlihmiltlislliiitimia 39
                                      w    li  il+l+s+li+ ti++a
  gi|313126150|ref|YP_004036420.1| 15 WVKTVLIGGILSLLSVLIVPTILVA 39
                                      777889*****************98 PP

>> Man-6-P_recep  Mannose-6-phosphate receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0001      0.47     162     209 ..      18      65 ..      12      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0001
                     Man-6-P_recep 162 klsvGsillivllslvavyligGflyqrlvvgakGleqiPnyafWqdl 209
                                       ++ +G il ++ + +v   l++G+l + +     G+e  P++  W d+
  gi|313126150|ref|YP_004036420.1|  18 TVLIGGILSLLSVLIVPTILVAGYLVRVIRRTMHGIEEPPEFDDWGDM 65 
                                       5679*********************99999999*********999776 PP

>> PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2   0.00025       1.1     120     175 ..      76     127 ..       1     150 [. 0.63
   2 ?   -0.9   0.2      0.23     1e+03      51      75 ..     160     184 ..     149     196 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00025
                          PMT_4TMC 120 lflhhYlpAllfailllaalldfllkslkkslkkkklvklivvvvllvlviavFif 175
                                        f++ ++p+l++ +l+ + ++ ++  +  +s      ++++  + +l+ ++++F++
  gi|313126150|ref|YP_004036420.1|  76 AFIYGFIPSLIAGVLVGGSIFAIVAGNAARSG----GLSIAGGAGVLLGLLVSFVL 127
                                       47777777777777777777777764444444....34444444444444444444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.23
                          PMT_4TMC  51 iyllGNpvlwwlstiallvfvllll 75 
                                       + + G  ++ w+s +a++++++l++
  gi|313126150|ref|YP_004036420.1| 160 VLVSGKYFTAWVSGFAVIFVAGLVA 184
                                       5566777777888777776666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1469.85
//
Query:       gi|313126151|ref|YP_004036421.1|  [L=702]
Description: RNA-binding protein, snrnp like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-88  295.3   0.0    9.8e-88  294.9   0.0    1.1  1  FbpA       Fibronectin-binding protein A N-terminus (FbpA)
    2.7e-24   85.9   0.0    4.9e-24   85.1   0.0    1.4  1  NFACT-R_1  NFACT protein RNA binding domain
    4.7e-05   23.5   0.0     0.0006   20.0   0.0    2.4  2  NFACT-R_2  NFACT protein RNA binding domain


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.9   0.0   1.6e-91   9.8e-88       2     431 ..       9     466 ..       8     477 .. 0.92

  Alignments for each domain:
  == domain 1  score: 294.9 bits;  conditional E-value: 1.6e-91
                                       HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXX..XXXXXSSXXHHHHH CS
                              FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltek..pkenpkeppnFcml 75 
                                       +++l a+v EL++ ++g+++dk y+++++ l+l++r ++rgr  L l++  +++r h+ ++    + p +ppnF+m+
  gi|313126151|ref|YP_004036421.1|   9 SVDLSALVTELNR-YEGAKVDKAYLYGDNLLRLRMRdFDRGRVELILEV-GDVKRAHTAKPehVPDAPGRPPNFAMM 83 
                                       789**********.***********************************.*********76557899********** PP

                                       HHHHHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXB CS
                              FbpA  76 LRkyLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvRei 152
                                       LR++L+ga    +eq +fdRi+ +++e+      +e  +++vE++g+ +N+ ++de ++++++++ v+ k    R++
  gi|313126151|ref|YP_004036421.1|  84 LRNRLNGADFAGVEQYEFDRILTFDFERG-----DEDTEIVVELFGQ-GNVAVLDETGEVVRSLETVRLK---SRTV 151
                                       *****************************.....8899*********.**********************...8*** PP

                                       STTXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH............. CS
                              FbpA 153 lpgekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedle 229
                                        pg++Ye+P s  +l P+++++ e fk +++++++d+v++L++++ +l++l+aee ++rag++k+ +++++ +e+++
  gi|313126151|ref|YP_004036421.1| 152 APGAQYEFPSS--RLHPFTVSY-EGFKRRMEDSDTDVVRTLATQV-NLGGLYAEEFCTRAGVEKTMEISDAGDEEYR 224
                                       ***********..*********.*******99*************.******************************* PP

                                       ..HHHHHHHHTXXX....XXEE.....XSSSEESSX..XTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHH..... CS
                              FbpA 230 rlyealqelleeleeekfepqlvlkeekpeefsvvp..lkslselekesfdslsealdeyYakkaerdrveq..... 299
                                       ++y+a+q++ ++l++++f p++++++ + ++ +++p  +++ ++l++es+d+++ealdey+ + +++ + e      
  gi|313126151|ref|YP_004036421.1| 225 AIYDAIQTFHDRLKSGDFDPRVYTEDGNVVDATPFPlkEHEAEGLNSESYDTFNEALDEYFFAFDRSAEDEPeeepg 301
                                       **************************9********986666669*****************9888776655411222 PP

                                       .HHHHHHHH...HHHHHHHHHHHHHHHHHHHHCCGGH.....HHHHCCHH-----------------------..-- CS
                              FbpA 300 .krsdlekr...veneleklekklkklekelekaeka.....enyrligelltaylyaikkgmsevelenyyde.ge 366
                                         r d+e +    ++++e++e  ++ +e+++e+ +++     +ny+l++e+l+++++a+ +   ++e+++++++  e
  gi|313126151|ref|YP_004036421.1| 302 sNRPDFEAEiekKKRIIEQQEGAIEGFEQQAERERERaellyANYELVDEVLSTVRSARDESVPWDEIRQTLEDgAE 378
                                       2556666666667778999999999999999999999************************************9644 PP

                                       ........................---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 367 ........................evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetkeeleylesveaa 419
                                                               +++I+++ ++ + +nA++++k++k+++ ++e++  +ie t+eel+ +++  +a
  gi|313126151|ref|YP_004036421.1| 379 rgipaaeavvdvdgaegtvtieidGTRIEVEVDMGVEKNADRLYKEAKRVEGKKEGAMAAIEDTREELAEVKARRDA 455
                                       8********************99999*************************************************** PP

                                       HHT-.-HHHHHH CS
                              FbpA 420 leqaesledlee 431
                                       +e+  +++d ee
  gi|313126151|ref|YP_004036421.1| 456 WEED-DEDDDEE 466
                                       **33.4444333 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   8.2e-28   4.9e-24       2     109 .]     493     609 ..     492     609 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 8.2e-28
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylr...lsege...le.eipeelleeaaqla 71 
                                       ++wF++sdgylvi+G+++ +nee++kkyl+++d++fh   ++++ ++++   +   +   +e e p+++ +eaaq+a
  gi|313126151|ref|YP_004036421.1| 493 FRWFHTSDGYLVIGGRNADQNEEIVKKYLNKHDLFFHTQAHGGPVTVVKatgP---SepaQEvEFPDSTKREAAQFA 566
                                       89***********************************************5542...3343447************** PP

                         NFACT-R_1  72 kanSia.gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                       +++S+  ++   + d+++v ++++skt++    +++Gs++++g
  gi|313126151|ref|YP_004036421.1| 567 VSYSSIwKEGRYADDAYMVTPDQVSKTPEsgeyIEKGSFVIRG 609
                                       *****9999999***************************9986 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     1e-07    0.0006       2      51 ..     494     545 ..     494     579 .. 0.73
   2 ?    0.4   0.0      0.13   7.6e+02      40     103 ..     627     691 ..     616     692 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-07
                         NFACT-R_2   2 RhfrlsekaklIvgReeeEnkfl.kgll.kkdfvslrakshkGplvlid..gel 51 
                                       R f +s+++ +I gR+++ n+++ k++l k+d++ ++++ h Gp+++++  g +
  gi|313126151|ref|YP_004036421.1| 494 RWFHTSDGYLVIGGRNADQNEEIvKKYLnKHDLF-FHTQAHGGPVTVVKatG-P 545
                                       789999************9998736777777777.*************6343.2 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.13
                         NFACT-R_2  40 hkGplvlidgels..eedlelaariv.arYskgkeeeevevkvkkkegeeekeievkplseeeiekw 103
                                       ++G + ++ g +s  e+++e a ++  +rY++ + ++ v  ++++  + +  ++  k +s ++i+++
  gi|313126151|ref|YP_004036421.1| 627 CEGETRVLGGPPSaiEDHVEAAVSLQpGRYAQNDAAKMVYRRFREMFEDQ--SFVRKVASPDKIQEF 691
                                       55666666665554477888888885489999777776666666655554..466677777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (702 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 4070.88
//
Query:       gi|313126152|ref|YP_004036422.1|  [L=160]
Description: acyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   77.0   0.1    1.3e-21   76.8   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.1e-14   54.7   0.1    1.4e-14   54.4   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    8.6e-11   42.1   0.0    1.5e-10   41.3   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.5e-08   33.6   1.1    2.6e-07   30.8   1.1    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00016   21.9   0.3     0.0012   19.0   0.3    1.9  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00027   21.6   2.2    0.00051   20.7   1.8    1.7  1  Acetyltransf_5   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.12   12.9   0.5       0.45   11.1   0.5    1.9  1  EutN_CcmL        Ethanolamine utilisation protein EutN/carbox
       0.13   12.4   0.3       0.25   11.5   0.3    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.1   5.9e-25   1.3e-21      13     127 .]      39     160 .]      21     160 .] 0.84

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 5.9e-25
                   Acetyltransf_10  13 f.kefispealrerie...egealllvaeeggkivGvielrdgs....hisllfVdpeyrgqGigkaLleaveeeae 81 
                                       f +e+  +e+l+   +   + +a++lva+++g++vG++++r  +    +i++++V+ + r  G g++++ ++e+eae
  gi|313126152|ref|YP_004036422.1|  39 FvEEQDVAEELEWDEHdepDADATHLVAYDDGTVVGAARVRAYDeetaKIERVVVAADRRESGWGRRIMTTAEQEAE 115
                                       4444433344433332346899****************9866666799***************************** PP

                   Acetyltransf_10  82 kdgikleltvnaspyavpfYeklGFkavgeeqeenGirfvpMekel 127
                                       ++g + ++ +na+   +pfYe+lG++a g+e+ ++ i +++M+k+l
  gi|313126152|ref|YP_004036422.1| 116 EMGFS-KVILNAQIRVQPFYESLGYEAFGDEFMDAEIPHISMRKRL 160
                                       ***99.*************************************975 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.1   6.1e-18   1.4e-14       7     117 .]      34     139 ..      24     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 6.1e-18
                                       HHHHHTHHHHHHHHHHHHHHHHHSTTC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHH CS
                    Acetyltransf_1   7 llvesffppnedaseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLl 82 
                                       + +  f ++   a+e e+ e  + +a+ ++lva++dg+++G ++++ +++   ++a ie+++V+ ++r +G G++ +
  gi|313126152|ref|YP_004036422.1|  34 IRRTVFVEEQDVAEELEWDEHDEPDADaTHLVAYDDGTVVGAARVRAYDE---ETAKIERVVVAADRRESGWGRRIM 107
                                       44444444444444444444444445579999******************...9*********************** PP

                                       HHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  83 ealeerareegikkivlaveedndaairlYeklGF 117
                                       +++e++a+e g+ k+ l   + + + +++Ye lG+
  gi|313126152|ref|YP_004036422.1| 108 TTAEQEAEEMGFSKVIL---NAQIRVQPFYESLGY 139
                                       ************99999...889999****99**8 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   6.8e-14   1.5e-10       3      75 ..      61     140 ..      59     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 6.8e-14
                                       EEEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHH.HTT.....SEEEEEEEEETHH.HHHHHH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLle.aae.....kgiileqlelnae.kaikfY 69 
                                       ++++Va+ddg +vG +++  +d   a i+r++V+ + r  G Gr++++ a e      g+   ++ lna+ + ++fY
  gi|313126152|ref|YP_004036422.1|  61 ATHLVAYDDGTVVGAARVRAYDeetAKIERVVVAADRRESGWGRRIMTtA-EqeaeeMGFS--KVILNAQiRVQPFY 134
                                       6789*************9999999999999*****************943.2233344422..234444456688** PP

                                       HHTTEE CS
                    Acetyltransf_7  70 eklGFe 75 
                                       e+lG+e
  gi|313126152|ref|YP_004036422.1| 135 ESLGYE 140
                                       *****8 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   1.1   1.1e-10   2.6e-07       6     126 ..      24     140 ..      21     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.1e-10
                                       -GGGHHHHHHHHHHHTT----H....HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                    Acetyltransf_9   6 teedldevlellkyaFqdeespl.e.eireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVa 80 
                                       te++ ++++++ +++F +e++ + e e + + +++  ++ +l+a+d+g++vg +++ +++        ++a +  V 
  gi|313126152|ref|YP_004036422.1|  24 TETEREDAFSIRRTVFVEEQDVAeElE-WDEHDEPDADATHLVAYDDGTVVGAARVRAYDE-------ETAKIERVV 92 
                                       8999*****************995444.67777777788*************998776653.......57899**** PP

                                       E-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..SSHHHHHTTT-E CS
                    Acetyltransf_9  81 vapehrgrgvlskLlaraleemreegqplsllfP..ssipiYrrfGye 126
                                       va++ r  g  ++++++a +e++e+g + ++l +  +  p+Y+++Gye
  gi|313126152|ref|YP_004036422.1|  93 VAADRRESGWGRRIMTTAEQEAEEMGFSKVILNAqiRVQPFYESLGYE 140
                                       **********************************85446********9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.3   5.5e-07    0.0012      52     139 ..      63     144 ..      24     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.5e-07
                    Acetyltransf_4  52 flvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiq 127
                                        lva+ ++++vG a++++ +   ++ k e  v     d ++ g gr +++  eq + e+++ +    i  +++  + 
  gi|313126152|ref|YP_004036422.1|  63 HLVAYdDGTVVGAARVRAYDE--ETAKIERVVVA--ADRRESGWGRRIMTTAEQEAEEMGFSKV---ILNAQIRVQP 132
                                       466666***********9999..77777765544..578*********************9975...5666788999 PP

                    Acetyltransf_4 128 fhkalGFelvgi 139
                                       f+++lG+e  g+
  gi|313126152|ref|YP_004036422.1| 133 FYESLGYEAFGD 144
                                       *******99887 PP

>> Acetyltransf_5  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.8   2.3e-07   0.00051       1      60 [.      34      91 ..      34     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
                    Acetyltransf_5  1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae.rlegf 60
                                      +R  vF+ee    +e   +  + De Da ++hl+ +d+ + vVG+ R+   de+  ++e++
  gi|313126152|ref|YP_004036422.1| 34 IRRTVFVEEQDVAEEL--EWDEHDEPDADATHLVAYDDGT-VVGAARVRAYDEETaKIERV 91
                                      5899999999988776..336688888*************.*******9999887544544 PP

>> EutN_CcmL  Ethanolamine utilisation protein EutN/carboxysome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5    0.0002      0.45      27      68 ..      78     118 ..      20     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                       EEEE-TTS-EEEEEEEEEESS---TT-EEEEEEGGGGGGSTT CS
                         EutN_CcmL  27 vqpldaegepkgeeiVavDtvgAgvGelVlvveGssarkaag 68 
                                       v+ +d+e+ + ++ +Va+D   +g G  ++++  ++a++ +g
  gi|313126152|ref|YP_004036422.1|  78 VRAYDEETAKIERVVVAADRRESGWGRRIMTTAEQEAEE-MG 118
                                       566688888999*************************87.44 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00011      0.25       7      60 ..      68     122 ..      62     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                   Acetyltransf_CG   7 degeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl.kv 60 
                                       d+g+ v+ ++ ++ +e++ +++ ++V    r  G +++++++a ++a+e g+ kv
  gi|313126152|ref|YP_004036422.1|  68 DDGTVVGAARVRAYDEETAKIERVVVAADRRESGWGRRIMTTAEQEAEEMGFsKV 122
                                       35888999999999999*******************************9998444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.52
# Mc/sec: 920.39
//
Query:       gi|313126153|ref|YP_004036423.1|  [L=508]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-40  138.9  39.7    2.3e-40  138.2  16.0    3.5  4  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
    2.1e-07   31.2   2.6    6.6e-06   26.3   0.1    3.8  3  PAS_4           PAS fold
    2.1e-07   30.9   0.1      2e-06   27.8   0.0    2.8  2  PAS             PAS fold
    7.1e-07   29.4   0.0    1.1e-05   25.6   0.0    2.8  2  PAS_9           PAS domain
    1.3e-05   25.3  28.4     0.0065   16.5   3.5    5.0  6  DUF1664         Protein of unknown function (DUF1664)
    3.3e-05   24.1  31.1    0.00038   20.6   3.8    5.4  5  DUF948          Bacterial protein of unknown function (DUF948
    0.00033   19.7  20.3     0.0017   17.3   4.9    2.6  2  Spc7            Spc7 kinetochore protein
    0.00051   20.5  25.7      0.017   15.6   0.7    4.5  3  Syntaxin-6_N    Syntaxin 6, N-terminal
     0.0016   17.6   5.8       0.16   11.0   0.2    2.3  2  Atg14           Vacuolar sorting 38 and autophagy-related sub
     0.0023   17.1  12.7      0.097   11.8   0.6    4.6  5  RmuC            RmuC family
     0.0046   17.0  29.5      0.092   12.8   1.5    4.7  4  Laminin_II      Laminin Domain II
     0.0072   16.0   3.0     0.0072   16.0   3.0    3.4  3  YkyA            Putative cell-wall binding lipoprotein
  ------ inclusion threshold ------
      0.019   15.1   4.9      0.061   13.5   0.0    3.4  3  MLTR_LBD        MmyB-like transcription regulator ligand bind
      0.026   14.6  26.6        1.1    9.4   1.6    4.5  4  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
      0.028   13.7  19.4       0.14   11.4   2.9    4.0  4  DUF3450         Protein of unknown function (DUF3450)
      0.048   12.9   5.6        2.3    7.4   0.5    2.8  2  TMPIT           TMPIT-like protein
      0.054   13.7  25.8       0.24   11.6   5.1    3.7  3  ATG16           Autophagy protein 16 (ATG16)
      0.077   12.6  12.1       0.28   10.8   4.9    2.6  2  DUF4795         Domain of unknown function (DUF4795)
       0.11   11.7  20.6       0.16   11.1   5.6    3.1  3  ISG65-75        Invariant surface glycoprotein
       0.11   12.6  11.4        3.1    7.9   0.1    3.5  3  Mod_r           Modifier of rudimentary (Mod(r)) protein
       0.12   12.4   4.1        6.3    6.8   0.1    3.4  2  DUF725          Protein of unknown function (DUF725)
       0.12   11.8   9.0      0.094   12.2   0.9    2.8  3  Mce4_CUP1       Cholesterol uptake porter CUP1 of Mce4, putat
       0.12   12.4  14.2       0.69   10.0   0.3    4.5  4  Nup54           Nucleoporin complex subunit 54
       0.37   10.7  12.3      0.045   13.7   1.2    3.4  3  Ferritin        Ferritin-like domain
       0.38   10.8  14.9       0.74    9.8   3.4    3.7  3  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
        0.4    8.6   9.5        1.1    7.1   7.5    2.1  1  Prominin        Prominin
        0.5    9.3  18.0       0.36    9.8   3.0    2.7  2  IFT57           Intra-flagellar transport protein 57
       0.52   10.0  21.2       0.27   10.9   2.4    4.0  4  LXG             LXG domain of WXG superfamily
       0.58   10.2  13.4       0.25   11.4   2.4    2.8  2  Serine_rich     Serine rich protein interaction domain
       0.58   10.7  26.2      0.097   13.1   2.7    6.0  5  NPV_P10         Nucleopolyhedrovirus P10 protein
       0.59    7.9  11.5      0.087   10.6   3.8    2.1  2  Nup88           Nuclear pore component
       0.66    9.7  26.4        1.6    8.4   5.0    3.8  3  DUF745          Protein of unknown function (DUF745)
        1.1    9.0   8.1       0.21   11.4   0.5    2.7  3  DUF1351         Protein of unknown function (DUF1351)
        1.3    9.0   3.6        9.2    6.3   0.3    3.3  4  LOH1CR12        Tumour suppressor protein
        1.5    9.0  16.4        3.2    7.9   0.2    4.5  5  Fib_alpha       Fibrinogen alpha/beta chain family
        1.7    8.9  18.7         10    6.4   2.9    6.2  6  WXG100          Proteins of 100 residues with WXG
        1.9    8.6  27.2       0.48   10.5   4.8    3.5  3  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        2.7    8.5  25.4        3.9    7.9  10.2    3.7  3  T3SSipB         Type III cell invasion protein SipB
        2.8    8.4   6.8        5.1    7.5   0.5    3.7  4  V-SNARE         Vesicle transport v-SNARE protein N-terminus
        3.1    8.1   9.4        8.8    6.7   2.1    2.5  2  PMEI            Plant invertase/pectin methylesterase inhibit
        3.1    8.5  13.0        1.4    9.5   0.3    4.1  3  SlyX            SlyX
        3.4    7.0  15.2          1    8.7   2.6    2.2  2  MafB            Neisseria toxin MafB
        3.7    6.8  20.6        2.4    7.4   4.9    3.2  2  CorA            CorA-like Mg2+ transporter protein
          4    8.2   6.4         61    4.4   0.0    4.3  5  RecG_N          RecG N-terminal helical domain
        4.5    6.9  15.6       0.19   11.4   3.6    2.6  2  DUF4559         Domain of unknown function (DUF4559)
        4.7    6.7  19.3       0.02   14.4   1.6    3.2  3  MscS_porin      Mechanosensitive ion channel porin domain
        4.7    6.6  22.9      0.012   15.1   7.8    2.6  2  LRRFIP          LRRFIP family
        5.3    7.2  25.7       0.33   11.2   4.4    3.2  3  Jnk-SapK_ap_N   JNK_SAPK-associated protein-1
        5.6    7.6  23.0         16    6.2   0.7    5.0  5  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
        5.7    7.4   9.0        1.8    9.0   1.1    3.4  3  Goodbye         fungal STAND N-terminal Goodbye domain
        5.8    6.8  10.0        2.1    8.3   0.4    3.7  4  Cauli_AT        Aphid transmission protein
        7.6    7.1  16.1         24    5.5   1.4    4.7  5  Spectrin        Spectrin repeat
        7.7    6.4   8.6        7.6    6.5   0.1    3.6  4  DUF1759         Protein of unknown function (DUF1759)
        7.9    7.2  21.0        8.4    7.1   0.9    4.4  4  DUF2203         Uncharacterized conserved protein (DUF2203)
        9.9    6.6  19.3         11    6.5   0.5    5.9  5  FlaC_arch       Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       3.6   1.2e+03     112     132 ..     169     189 ..     154     201 .. 0.46
   2 !   11.9   7.5   0.00044      0.14      67     164 ..     202     299 ..     196     307 .. 0.85
   3 !  138.2  16.0   7.1e-43   2.3e-40       8     170 ..     311     473 ..     304     475 .. 0.95
   4 ?    2.1   0.2      0.45   1.5e+02     130     163 ..     468     501 ..     466     507 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHHHHCCHHHH CS
                         MCPsignal 112 trqrveegselveetgealke 132
                                       ++++ e + +lv+e +++l++
  gi|313126153|ref|YP_004036423.1| 169 AQRQQEATHTLVNEVTSTLEQ 189
                                       222222222223333333322 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00044
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH CS
                         MCPsignal  67 GrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadl 143
                                       G    V  dE  ++ ++   +    e+l+ e++ +  d+ ++++ ++  +++  + v e ++al+ + +  a+ ++ 
  gi|313126153|ref|YP_004036423.1| 202 GSETEVLEDELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAA 278
                                       55556777888888888899999999999999999999999999999999999999999999999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 144 vqeiaaaseeqsasieevnqa 164
                                       ++e+aa+s+e  ++++   ++
  gi|313126153|ref|YP_004036423.1| 279 MEEVAASSTEVESAADRARDN 299
                                       999999999998888776655 PP

  == domain 3  score: 138.2 bits;  conditional E-value: 7.1e-43
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHH CS
                         MCPsignal   8 seeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAers 84 
                                       ++  +e ++  ++ ++ ++ +e+  +ei d++  i eiad TN+LALNA iEAARAGe+G+GFaVVA+EV++LA+++
  gi|313126153|ref|YP_004036423.1| 311 RKVTDEVKERSDDLLESVKRLEDDMEEIGDVVGLISEIADRTNILALNANIEAARAGEAGEGFAVVAEEVKSLANET 387
                                       45555556777899999************************************************************ PP

                                       HHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  85 aqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieev 161
                                       +  +++i++ i +iq   +++v+ +eet++ v  + + +++t ++l+e ++av+e ad v+e+++as++q++s+e v
  gi|313126153|ref|YP_004036423.1| 388 QSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELSRASDDQAESVEGV 464
                                       ***************************************************************************** PP

                                       HHHHHHHHH CS
                         MCPsignal 162 nqaveevak 170
                                        +ave v++
  gi|313126153|ref|YP_004036423.1| 465 VSAVEDVSD 473
                                       *****9976 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 130 lkeiveavaevadlvqeiaaaseeqsasieevnq 163
                                       ++++++ +ae++++v++i + ++ q  s+ e  +
  gi|313126153|ref|YP_004036423.1| 468 VEDVSDDAAEIEESVDDIVSVTQTQRDSAGELGT 501
                                       5667788888888888888888888777766655 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1     2e-08   6.6e-06       1     110 []      41     171 ..      41     171 .. 0.87
   2 ?   -1.3   0.1       7.7   2.5e+03      17      69 ..     244     292 ..     236     307 .. 0.65
   3 ?   -0.4   0.0         4   1.3e+03      43      70 ..     383     416 ..     339     442 .. 0.59

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee...................daarleralrr 58 
                                       ld+lp + +v+++ g+ + +N+aa++ fg+p e ++G + ++  +                     d a   ++  +
  gi|313126153|ref|YP_004036423.1|  41 LDALPMPAFVISATGVATGWNEAAERAFGIPKEKIIGASEEDATSMVsydddraektlahkvvdapDTAHENDPSVE 117
                                       79***************************************744444444889999999999997766666666667 PP

                             PAS_4  59 vlegeepiefleelll...pgeerhyelrllPlrdesGe.vigvlvisrDiTerrr 110
                                        ++g   ++f++e+ l   +ge+ ++++r+lP+ d  G+  ++v++++ D Te +r
  gi|313126153|ref|YP_004036423.1| 118 RVRGPSGQFFVDERSLenaDGERMYISFRALPIYD--GDeLVAVVELVEDKTEAQR 171
                                       7999999999999999*****************88..8879***********9875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 7.7
                             PAS_4  17 vlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefl 69 
                                       ++ aN aa +   ++      ++  e + + d a +++a+++v+++ + +e++
  gi|313126153|ref|YP_004036423.1| 244 ITTANDAASQ---IDSRVTEQRKALEAVRD-DLASFSAAMEEVAASSTEVESA 292
                                       5666666444...55555555666665555.7777888888888776666655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 4
                             PAS_4  43 llpee......daarleralrrvlegeepiefle 70 
                                       l++e         +r++r+  r+ e+ + +e+++
  gi|313126153|ref|YP_004036423.1| 383 LANETqshteqITERIDRIQSRADETVTLVEETH 416
                                       3333344333377777777777777754444444 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   6.1e-09     2e-06       5      52 ..      39      86 ..      36     165 .. 0.76
   2 ?   -1.7   0.1       8.6   2.8e+03      18      32 ..     239     253 ..     237     320 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 6.1e-09
                                      HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBST CS
                               PAS  5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldlihe 52
                                       +l++lp p fv+ + g+ +++N+aae+ +G++ e ++g s  d  ++
  gi|313126153|ref|YP_004036423.1| 39 VLLDALPMPAFVISATGVATGWNEAAERAFGIPKEKIIGASEEDATSM 86
                                      689************************************998886554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 8.6
                                       ETTSBEEEECHHHHH CS
                               PAS  18 DedgrilyvNaaaee 32 
                                       D +  i+ +N+aa +
  gi|313126153|ref|YP_004036423.1| 239 DVSNTITTANDAASQ 253
                                       666666666666654 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   3.5e-08   1.1e-05       9     104 .]      53     168 ..      45     168 .. 0.83
   2 ?    0.3   0.0       2.6   8.5e+02       9      23 ..     240     254 ..     234     339 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.5e-08
                             PAS_9   9 pdgril.yaNeaalrllGyspeevlgksitdlf..................vtdpeanerlraaleqgrk...kere 63 
                                         g +   +Neaa+r +G  +e ++g s +d                    v++p+++++ +  +e+ r    +++ 
  gi|313126153|ref|YP_004036423.1|  53 ATG-VAtGWNEAAERAFGIPKEKIIGASEEDATsmvsydddraektlahkvVDAPDTAHENDPSVERVRGpsgQFFV 128
                                       667.4448********************999999999877777777777776666666666666666666999**** PP

                             PAS_9  64 vevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                       +e  l + +ge++++ ++a p++d ++elv+++ +++D te
  gi|313126153|ref|YP_004036423.1| 129 DERSLENADGERMYISFRALPIYD-GDELVAVVELVEDKTE 168
                                       **********************86.67***********987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.6
                             PAS_9   9 pdgrilyaNeaalrl 23 
                                        +++i+ aN+aa ++
  gi|313126153|ref|YP_004036423.1| 240 VSNTITTANDAASQI 254
                                       567789999999988 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.52   1.7e+02      64     101 ..     156     192 ..     154     200 .. 0.73
   2 !    9.5   1.0     0.003      0.98      42     116 ..     179     257 ..     173     260 .. 0.72
   3 !   10.7   1.5    0.0012       0.4      46     121 ..     215     290 ..     198     293 .. 0.70
   4 !    9.7   0.6    0.0025      0.83      38     109 ..     274     348 ..     272     354 .. 0.78
   5 !   16.5   3.5     2e-05    0.0065      44     120 ..     374     450 ..     370     453 .. 0.91
   6 ?    4.9   0.6      0.08        26      69     111 ..     448     490 ..     444     502 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.52
                           DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseige 101
                                       L + ++ v++k ++q + +++++  v+ev + l++ige
  gi|313126153|ref|YP_004036423.1| 156 LVAVVELVEDKTEAQ-RQQEATHTLVNEVTSTLEQIGE 192
                                       555666677776655.5678888889999999988875 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.003
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikee....vtevredlseigedvesvkeavegle 114
                                        v++v++ leq+ e   +++ +L s+ + ++++l +  +  + + +     v+ev+++ +++++ +++ ++a ++++
  gi|313126153|ref|YP_004036423.1| 179 LVNEVTSTLEQIGEGNLDARAELGSETEVLEDELLNIVAEVNRTGDRfeslVDEVESHATDVSNTITTANDAASQID 255
                                       6899**************************99998877777777666111155555555555555555566666666 PP

                           DUF1664 115 sk 116
                                       s+
  gi|313126153|ref|YP_004036423.1| 256 SR 257
                                       55 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0012
                           DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +  ++++  +  ++  ++ +s+   v +++   ++++++i++ vte r+ l+++++d+ s ++a+e+++++ +++e
  gi|313126153|ref|YP_004036423.1| 215 IVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVE 290
                                       3334444444444444555555566777788888888999999999999999999999999999998887777666 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0025
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssrid.rvdkk..ldeqkeiskeikeevtevredlseigedvesvkea 109
                                       s+s a+e+v+ + ++v ++  ++++++ s +d +vd++   de+ke s ++ e v+++++d++eig+ v  ++e+
  gi|313126153|ref|YP_004036423.1| 274 SFSAAMEEVAASSTEVESAADRARDNIGSSLDwTVDTRkvTDEVKERSDDLLESVKRLEDDMEEIGDVVGLISEI 348
                                       678899999999999999999999999999884455433368888888888888888888888888888777665 PP

  == domain 5  score: 16.5 bits;  conditional E-value: 2e-05
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       + v+++++++ ++ ++  +++++ridr++++ de+  + +e++++v ++ + ++++ + +++ ++ave+ +  ++++
  gi|313126153|ref|YP_004036423.1| 374 AVVAEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSEL 450
                                       6789999999*********************************************9999999999999888777766 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.08
                           DUF1664  69 drvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                        ++ +  d+q+e  + + + v++v++d +ei+e v+ + ++ +
  gi|313126153|ref|YP_004036423.1| 448 SELSRASDDQAESVEGVVSAVEDVSDDAAEIEESVDDIVSVTQ 490
                                       6678888999999999999999999999999999998877765 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.8     0.019       6.3      39      84 ..     191     254 ..     156     260 .. 0.74
   2 ?    7.5   2.6     0.015       4.8      28      82 ..     219     277 ..     212     294 .. 0.47
   3 ?    4.1   0.5      0.17        56      48      77 ..     309     338 ..     272     356 .. 0.43
   4 !   20.6   3.8   1.2e-06   0.00038      19      86 ..     375     442 ..     372     445 .. 0.94
   5 ?    7.4   1.0     0.016       5.3      27      76 ..     439     488 ..     436     506 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.019
                            DUF948  39 e..................kqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       +                  +++ +i+ ev+++ +  + l+++v+++  +v + ++ ++d++ ++
  gi|313126153|ref|YP_004036423.1| 191 GegnldaraelgsetevleDELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQI 254
                                       5555555555553333333888888888888888888899999999999999999888887766 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.015
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvne....lledvneklekvdplteavadlge 82 
                                       ++++ ++ e+l ++v++  ++v ++++++n+    + + v+e+ ++++++ + +a  ++
  gi|313126153|ref|YP_004036423.1| 219 VNRTGDRFESLVDEVESHATDVSNTITTANDaasqIDSRVTEQRKALEAVRDDLASFSA 277
                                       34444444445555555555555555555552222333333344444444444444443 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.17
                            DUF948  48 evedllakvnelledvneklekvdplteav 77 
                                       ++++++++v+e  +d+ e +++++  +e++
  gi|313126153|ref|YP_004036423.1| 309 DTRKVTDEVKERSDDLLESVKRLEDDMEEI 338
                                       222223333333333333333333333333 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 1.2e-06
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       vv  ++k++++e++++ e++++++d i   ++++++ v+e+ +dv +  +++d+ ++++++++++v+e
  gi|313126153|ref|YP_004036423.1| 375 VVAEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEE 442
                                       67788999********************************************************9986 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.016
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                        ++eaa+ + el +  d   + ve++++ v+++ +d  e  e+vd +++ 
  gi|313126153|ref|YP_004036423.1| 439 AVEEAADGVSELSRASDDQAESVEGVVSAVEDVSDDAAEIEESVDDIVSV 488
                                       56677777777777777777777777777777777777766666666655 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   4.9   5.3e-06    0.0017     135     264 ..     178     307 ..     176     335 .. 0.86
   2 !    7.8   7.1    0.0042       1.4     163     261 ..     378     493 ..     368     498 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.3e-06
                              Spc7 135 qllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelael 211
                                       +l++++ ++le++ eg  + +++L ++ e l++ l ++++e ++  +++e+l +++e++++  ++ + ++ ++ +++
  gi|313126153|ref|YP_004036423.1| 178 TLVNEVTSTLEQIGEGNLDARAELGSETEVLEDELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQI 254
                                       58899999999999999999999999999999999999999999999999999988887776699999999999999 PP

                              Spc7 212 kaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgws 264
                                       ++ + e++k l+ ++++l++ ++++ee++++ +e+e++  +a++ +    +w+
  gi|313126153|ref|YP_004036423.1| 255 DSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVESAADRARDNIGSSLDWT 307
                                       99999999999999999999999999999999999999998887776666665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0042
                              Spc7 163 eeldellpeleeekaeleeeleklqeaaeeles...............id..keeLeelreelaelkaeieekkkel 222
                                       ee+++l +e++++ ++++e+++++q++a+e  +               id    +L+e+ ++++e+   ++e+++  
  gi|313126153|ref|YP_004036423.1| 378 EEVKSLANETQSHTEQITERIDRIQSRADETVTlveethkdvgraddaIDktVSSLQEASDAVEEAADGVSELSRAS 454
                                       33344444444444444444444444333322222222222221111222114566666666666666666666666 PP

                              Spc7 223 aelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                       ++  e +e + +++e++++  +e+ee +    +v++ ++
  gi|313126153|ref|YP_004036423.1| 455 DDQAESVEGVVSAVEDVSDDAAEIEESVDDIVSVTQTQR 493
                                       666666666666666666666666666666666666655 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.1     0.019       6.3       7      67 ..     216     282 ..     210     287 .. 0.71
   2 !   15.6   0.7   5.4e-05     0.017       8      74 ..     287     352 ..     283     360 .. 0.86
   3 !    9.2   5.7    0.0054       1.8       3      78 ..     373     451 ..     372     495 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.019
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwe.rlledtss.s....tseeldetrteLrkalrsiewdledLeetvriv 67 
                                        +eV+ + ++ esl+++ e +  +++++ +      +++d+  te rkal+ ++ dl  +  +++ v
  gi|313126153|ref|YP_004036423.1| 216 VAEVNRTGDRFESLVDEVEsHATDVSNTiTtandAASQIDSRVTEQRKALEAVRDDLASFSAAMEEV 282
                                       5677777788888888885244444444425666788999999999999999999999999888655 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.4e-05
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskf 74 
                                        eV++++++a+  +++  +   dt++  ++e++e +++L ++++ +e d+e++ ++v+ +++  ++ 
  gi|313126153|ref|YP_004036423.1| 287 TEVESAADRARDNIGSSLDWTVDTRK-VTDEVKERSDDLLESVKRLEDDMEEIGDVVGLISEIADRT 352
                                       69**************9886666665.59****************************9988766555 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0054
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrw.erlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfki 76 
                                       F +v+eeV++ +n+++s  ++  er+ + +s   +t   ++et++++ +a + i+++++ L+e+ ++ve+  + ++ 
  gi|313126153|ref|YP_004036423.1| 373 FAVVAEEVKSLANETQSHTEQItERIDRIQSRadETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSE 449
                                       899**************999994344444443333677889999999999999999999999999999987655333 PP

                      Syntaxin-6_N  77 de 78 
                                        +
  gi|313126153|ref|YP_004036423.1| 450 LS 451
                                       33 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   1.2    0.0028       0.9      28     129 ..     166     293 ..     160     347 .. 0.57
   2 !   11.0   0.2   0.00049      0.16      50     156 ..     386     491 ..     372     503 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0028
                             Atg14  28 rerlaklksekeslkkkiekalegke.......................eaeqledkiknkkakleelksliadlre 81 
                                       +++ ++ +++  +l ++++  le+                          + + ++  ++    ++e  s+  d ++
  gi|313126153|ref|YP_004036423.1| 166 KTEAQRQQEATHTLVNEVTSTLEQIGegnldaraelgsetevledellnIVAEVNRTGDRFESLVDEVESHATDVSN 242
                                       55556666666666666666666666555555555555555555555543334445555555556777777777777 PP

                             Atg14  82 rlqelkdklsqlkkeieekkkklaklsdklk..........kRrsdleslqneleerr 129
                                        + + +d  sq ++++ e++k l++ +d+l+                   ++e+e++ 
  gi|313126153|ref|YP_004036423.1| 243 TITTANDAASQIDSRVTEQRKALEAVRDDLAsfsaameevaA-------SSTEVESAA 293
                                       789999999999999999999999999999877754444442.......222222222 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00049
                             Atg14  50 egkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk..kRrsdleslqne 124
                                       e+++ +eq +++i++ + +++e+ +l++++++ + +  d +++  ++++e++  +++  d ++   R sd    q e
  gi|313126153|ref|YP_004036423.1| 386 ETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSelSRASD---DQAE 459
                                       2222567777888888888888888888888888888888888888888888888888888885555555...7777 PP

                             Atg14 125 leerrkkqiaklqdaikrieqklsslssktle 156
                                         e   + ++ ++d+  +ie+  +++ s t+ 
  gi|313126153|ref|YP_004036423.1| 460 SVEGVVSAVEDVSDDAAEIEESVDDIVSVTQT 491
                                       77777778888887777777776666666655 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.1   1.3e+03     129     158 ..     161     191 ..     155     197 .. 0.55
   2 !    7.8   0.2    0.0047       1.5     219     284 ..     203     268 ..     197     274 .. 0.87
   3 ?    1.8   0.0      0.32     1e+02     225     257 ..     311     343 ..     304     366 .. 0.81
   4 !   11.8   0.6    0.0003     0.097     225     285 ..     388     451 ..     380     457 .. 0.69
   5 ?    1.9   0.1      0.31     1e+02      17      72 ..     447     502 ..     433     503 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.1
                              RmuC 129 rlveaedde.ereealkahaksvkkhikeLs 158
                                       +lve ++++  ++ea   ++++v +  +++ 
  gi|313126153|ref|YP_004036423.1| 161 ELVEDKTEAqRQQEATHTLVNEVTSTLEQIG 191
                                       4555555443555555666666655555554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0047
                              RmuC 219 wrqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklkel 284
                                        ++e +e++  +i+ ++++  d+fe++++++e+  + ++++ ++ ++a+++  ++++++ + l+++
  gi|313126153|ref|YP_004036423.1| 203 SETEVLEDELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAV 268
                                       567778888999999999*****************************9999999999998888765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.32
                              RmuC 225 eknaeeiaellgelydkfekfgedleklgkkle 257
                                       +k ++e+ e++ +l + ++++++d+e++g+ + 
  gi|313126153|ref|YP_004036423.1| 311 RKVTDEVKERSDDLLESVKRLEDDMEEIGDVVG 343
                                       677899999999999999999999999998665 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.0003
                              RmuC 225 eknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle...gnilrkaeklkelg 285
                                       + ++e+i e++ ++ ++  + ++ +e++ k + +a +++dk+v++l+   + + + a+ + el+
  gi|313126153|ref|YP_004036423.1| 388 QSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQeasDAVEEAADGVSELS 451
                                       6677777777777777777777777777777777777777777777766666666666666555 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.31
                              RmuC  17 feekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLk.nsktrGnwGEv 72 
                                       ++e  +  s+++ae+ e +  +++ +++ +++++++ ++++++ + +  + G++G +
  gi|313126153|ref|YP_004036423.1| 447 VSEL-SRASDDQAESVEGVVSAVEDVSDDAAEIEESVDDIVSVTQtQRDSAGELGTM 502
                                       3333.4455777777777888888888888888888888888888788888888766 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.6      0.16        52      16      64 ..     209     254 ..     194     259 .. 0.57
   2 !   12.8   1.5   0.00028     0.092       5      97 ..     258     347 ..     255     365 .. 0.87
   3 !   11.0   3.1     0.001      0.32       4      58 ..     376     430 ..     374     435 .. 0.88
   4 ?    7.4   2.1     0.012       4.1       8      73 ..     422     487 ..     421     506 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.16
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkL 64 
                                       ++ l ++ +++++t +  +++ ++ve    +v   +++i  A+++ +++
  gi|313126153|ref|YP_004036423.1| 209 EDELLNIVAEVNRTGDRFESLVDEVESHATDV---SNTITTANDAASQI 254
                                       34466777777777777777766655555444...44444444444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00028
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       ++e  + +++v ++la  s+ +e++ ++  e+++ +++  +++ ++   ++d r+   ++++  ++Ll+ +k+l+  
  gi|313126153|ref|YP_004036423.1| 258 VTEQRKALEAVRDDLASFSAAMEEVAASSTEVESAADRARDNIGSSLDWTVDTRKVTDEVKERSDDLLESVKRLEDD 334
                                       567778899************************************************************99999988 PP

                                       HHH...HHHHHHHHHH CS
                        Laminin_II  82 eeassslsdniseike 97 
                                        e+   ++d +  i e
  gi|313126153|ref|YP_004036423.1| 335 MEE---IGDVVGLISE 347
                                       887...5555544444 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.001
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdAr 58 
                                       +a+e+++ a+e+++ ++++ ++++++++ + e  + veet+++v  a  ai+   
  gi|313126153|ref|YP_004036423.1| 376 VAEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTV 430
                                       689999999*********************************9999998888655 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG CS
                        Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld 73 
                                       a++ + ++ + l++ s  +e+  + +se+ r  +   e v+    a++d+++   ++e+ ++++++
  gi|313126153|ref|YP_004036423.1| 422 ADDAIDKTVSSLQEASDAVEEAADGVSELSRASDDQAESVEGVVSAVEDVSDDAAEIEESVDDIVS 487
                                       566666777777777777777777777777777777788888888888888888888888887775 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.0       3.3   1.1e+03      66     109 ..     204     246 ..     157     267 .. 0.36
   2 !    8.7   1.5    0.0038       1.3       8      99 ..     246     337 ..     235     356 .. 0.74
   3 !   16.0   3.0   2.2e-05    0.0072      15     116 ..     368     460 ..     357     474 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.3
                              YkyA  66 Reellekekesi.eeakeefekikeeieeiedeelkkeaeeliea 109
                                        +e le e  +i  e +   +  ++ ++e+e     +++++ i++
  gi|313126153|ref|YP_004036423.1| 204 ETEVLEDELLNIvAEVNRTGDRFESLVDEVESH--ATDVSNTITT 246
                                       333333322222011222222222222222211..2333333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0038
                              YkyA   8 ealeeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeef 84 
                                       +a + a ++++ ++eq + L e+ +++   ++  +e       ++++ +d a +n+    +     +++ +e ke  
  gi|313126153|ref|YP_004036423.1| 246 TANDAASQIDSRVTEQRKAL-EAVRDDLASFSAAMEEVAASSTEVESAADRARDNIGSSLDWTVDTRKVTDEVKERS 321
                                       33334444445555555555.555677778888999999999*********************************** PP

                              YkyA  85 ekikeeieeiede.el 99 
                                       +++ e+++ +ed+ e 
  gi|313126153|ref|YP_004036423.1| 322 DDLLESVKRLEDDmEE 337
                                       **********987233 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2.2e-05
                              YkyA  15 elEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeei 91 
                                       e+ ++f+  +e+ ++l ++ q + e+i     ++ d+i++ +de +++vee  + +    ++i+++   ++++++ +
  gi|313126153|ref|YP_004036423.1| 368 EAGEGFAVVAEEVKSLANETQSHTEQIT----ERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAV 440
                                       5558899999*****************6....67888**************99999999999999999999999999 PP

                              YkyA  92 eeiedeelkkeaeelieameeryea 116
                                       ee  d      ++el  a +++ e+
  gi|313126153|ref|YP_004036423.1| 441 EEAADG-----VSELSRASDDQAES 460
                                       998665.....44444444444444 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00019     0.061       8      40 ..      40      71 ..      35     135 .. 0.87
   2 ?   -0.6   0.5         4   1.3e+03      60      64 ..     250     254 ..     207     314 .. 0.51
   3 ?    1.6   0.3      0.84   2.7e+02      59     108 ..     393     443 ..     348     468 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00019
                          MLTR_LBD  8 lLdalepvPAlVldrrwdvlaaNraaraLlgdp 40
                                      lLdal p+PA+V+++      +N+aa++ +g p
  gi|313126153|ref|YP_004036423.1| 40 LLDAL-PMPAFVISATGVATGWNEAAERAFGIP 71
                                      89999.***********************9984 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4
                          MLTR_LBD  60 lrpli 64 
                                       +++ i
  gi|313126153|ref|YP_004036423.1| 250 AASQI 254
                                       22222 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.84
                          MLTR_LBD  59 glrpli...edweevaralvarLraeaarrpddpalaalvaeLsaaspefarl 108
                                       +++++i   + +++   +lv+  + +++r   d+a+++ v  L++as+ +++ 
  gi|313126153|ref|YP_004036423.1| 393 QITERIdriQSRADETVTLVEETHKDVGRA--DDAIDKTVSSLQEASDAVEEA 443
                                       444444333666777777788888888888..999999999999998887765 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.8      0.08        26      91     133 ..     171     213 ..     158     222 .. 0.78
   2 ?    9.4   1.6    0.0033       1.1      32      86 ..     227     284 ..     217     310 .. 0.79
   3 ?    2.6   0.1      0.42   1.4e+02      44      70 ..     312     338 ..     310     360 .. 0.70
   4 ?    7.6   7.2     0.011       3.7      24     116 ..     380     477 ..     372     494 .. 0.47

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.08
                         ApoLp-III  91 kvQsgvqslvkesqklaeslkensqeakeklakaikqayddav 133
                                         Q+++ +lv+e+  + e++ e    a ++l   ++ + d+  
  gi|313126153|ref|YP_004036423.1| 171 RQQEATHTLVNEVTSTLEQIGEGNLDARAELGSETEVLEDELL 213
                                       3499999999999999999999999999999998888877765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0033
                         ApoLp-III  32 enlvdqlkqvikslqeelkkksdel...eealkevkkkieetadklseenPevkkkaq 86 
                                       e+lvd++++ +  +++ +++++d++   ++ ++e +k++e ++d+l + ++++++ a 
  gi|313126153|ref|YP_004036423.1| 227 ESLVDEVESHATDVSNTITTANDAAsqiDSRVTEQRKALEAVRDDLASFSAAMEEVAA 284
                                       78999999999999999999998762225669999***********997776666554 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.42
                         ApoLp-III  44 slqeelkkksdeleealkevkkkieet 70 
                                       ++++e+k+ sd l e++k + +++ee+
  gi|313126153|ref|YP_004036423.1| 312 KVTDEVKERSDDLLESVKRLEDDMEEI 338
                                       456666666666666666666666554 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.011
                         ApoLp-III  24 vetiKensenlvdqlkqvikslqeelkkksdeleealkev...kkkieetadklseenPevkkkaqelqekvQsgvq 97 
                                       v+ + +++++  +q+ + i+ +q+ + ++   +ee+ k+v    ++i +t+ +l+e++ +v+++a+  +e +  +  
  gi|313126153|ref|YP_004036423.1| 380 VKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVgraDDAIDKTVSSLQEASDAVEEAADGVSE-LSRASD 455
                                       4444555555555555555555555555555555555554222455666666666655555554443332.222222 PP

                         ApoLp-III  98 sl...vkesqklaeslkensqe 116
                                            v+ +  ++e+++++++e
  gi|313126153|ref|YP_004036423.1| 456 DQaesVEGVVSAVEDVSDDAAE 477
                                       2200022222233333333333 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1         3   9.9e+02      83     114 ..     161     192 ..     157     203 .. 0.73
   2 ?   11.4   2.9   0.00044      0.14      19     101 ..     210     292 ..     206     337 .. 0.92
   3 ?    3.1   0.5      0.15        49      62     105 ..     372     415 ..     354     422 .. 0.70
   4 ?   10.3   0.6   0.00093       0.3      15     110 ..     413     507 ..     407     508 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3
                           DUF3450  83 sleeqieeieeierelvpllekmidrLeqfve 114
                                       +l e+++e+++ +++   l  ++ ++Leq+ e
  gi|313126153|ref|YP_004036423.1| 161 ELVEDKTEAQRQQEATHTLVNEVTSTLEQIGE 192
                                       56677778888888888888888888887755 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00044
                           DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95 
                                       d++l+  ++ +++  + ++ +d+++  ++++++ ++++++ +++++    ++++ +++++ ++as    +ee+ + +
  gi|313126153|ref|YP_004036423.1| 210 DELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASS 286
                                       5788999999*****************************************************************99 PP

                           DUF3450  96 relvpl 101
                                       +e++  
  gi|313126153|ref|YP_004036423.1| 287 TEVESA 292
                                       999865 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.15
                           DUF3450  62 slevyneqlerlvasqeqeiasleeqieeieeierelvpllekm 105
                                         +v  e++++l ++ ++  ++++e+i++i+  ++e v l e++
  gi|313126153|ref|YP_004036423.1| 372 GFAVVAEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEET 415
                                       55566667777777777777777777777777777777766655 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00093
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                       ++t +++  +  ++ ++ ++ q+  d++++ ++ +++  ra  +++es e   + +e++ +++ +ei++   +i ++
  gi|313126153|ref|YP_004036423.1| 413 EETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELSRASDDQAESVEGVVSAVEDVSDDA-AEIEESVDDIVSV 488
                                       567788888999999999999********99999999999***************99988775.789999999**** PP

                           DUF3450  92 eeierelvpllekmidrLe 110
                                       ++++r+    l +mid+L 
  gi|313126153|ref|YP_004036423.1| 489 TQTQRDSAGELGTMIDGLS 507
                                       ****************996 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5    0.0069       2.3      15      87 ..     220     291 ..     204     341 .. 0.63
   2 ?    7.3   0.4    0.0073       2.4       6      79 ..     386     458 ..     372     503 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0069
                             TMPIT  15 eetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87 
                                       + t +++++ ++e++++ +++s++i++ +  +++++s++++ +k+++   ++ +++ ++ ++e  ++  eves
  gi|313126153|ref|YP_004036423.1| 220 NRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALE-AVRDDLASFSAAMEEVAASSTEVES 291
                                       55555555555555555555555555555555555555555554432.3333333334444433333333333 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0073
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       e +++++++ e+ ++++++ +e+ +l +++ k++ +    + +  ssl++ + +v ee ++ v+el++  +++ 
  gi|313126153|ref|YP_004036423.1| 386 ETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAV-EEAADGVSELSRASDDQA 458
                                       3344444555555555555555555555555555555555555555555555554.344444444444444333 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   4.1      0.13        41      83     165 ..     159     238 ..     156     242 .. 0.85
   2 ?   11.0   1.7    0.0011      0.36     104     177 ..     216     289 ..     208     294 .. 0.84
   3 ?   11.6   5.1   0.00073      0.24      24     161 ..     345     476 ..     332     483 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                             ATG16  83 laqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDE 159
                                       +++l e+ +e++++++ + + ++e++++l++  e    +  + ael +e ++le++l +  +e++      + l DE
  gi|313126153|ref|YP_004036423.1| 159 VVELVEDKTEAQRQQEATHTLVNEVTSTLEQIGE---GNLDARAELGSETEVLEDELLNIVAEVNRTGDRFESLVDE 232
                                       678899*****************99999887665...5556667899999999999999999999999999999999 PP

                             ATG16 160 lsaLql 165
                                       ++++  
  gi|313126153|ref|YP_004036423.1| 233 VESHAT 238
                                       998865 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0011
                             ATG16 104 llelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrkl 177
                                       + e+n + ++ e+   e e+   ++++++++ +++ ++ + ++ e++k++++++D+l++   +++ + + + ++
  gi|313126153|ref|YP_004036423.1| 216 VAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEV 289
                                       5566666777778888889999999**********************************999988776666665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00073
                             ATG16  24 ynrLldrtsaleaenaklek.aaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrge 99 
                                        ++++drt+ l+   a++e+ +a +a +  +  + + +++a+++q      +++++ ++++ ++++   e+    +e
  gi|313126153|ref|YP_004036423.1| 345 ISEIADRTNILALN-ANIEAaRAGEAGEGFAVVAEEVKSLANETQ------SHTEQITERIDRIQSRADETVTLVEE 414
                                       57899999999655.555330333444455555566677777666......778888999999999999999999** PP

                             ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEls 161
                                       + + + ++ ++++k  ++l+e + +++e+ + +++l+++ +d++e +++   +v+d+ D+ +
  gi|313126153|ref|YP_004036423.1| 415 THKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELSRASDDQAESVEGVVSAVEDVSDDAA 476
                                       *********************************************************99865 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.9   0.00086      0.28       5     156 ..     226     394 ..     217     405 .. 0.87
   2 ?    3.8   3.1      0.12        39      10      68 ..     424     482 ..     376     490 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00086
                           DUF4795   5 saellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkv 81 
                                       ++ l+++++++ +++++ +   +++++++++r  +++k lea+++ +     + ++    ++e++ +ad+   ++  
  gi|313126153|ref|YP_004036423.1| 226 FESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVESAADRARDNIGS 302
                                       56789999**************************************9999999999999999999999999999999 PP

                           DUF4795  82 srdq.fDe..akkeLekmleellekleeqeealkkaldtLqeelkekldrlelepLkeqle...............e 140
                                       s d  +D+  +++e ++   +lle+++  e++++++ d +   + e  dr ++  L  ++e               e
  gi|313126153|ref|YP_004036423.1| 303 SLDWtVDTrkVTDEVKERSDDLLESVKRLEDDMEEIGDVVG-LISEIADRTNILALNANIEaarageagegfavvaE 378
                                       99988776115799**********************99999.88888999999999999999999999988888888 PP

                           DUF4795 141 rlkelqkelqeameke 156
                                       ++k+l++e q+ +e++
  gi|313126153|ref|YP_004036423.1| 379 EVKSLANETQSHTEQI 394
                                       8888887777666555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                           DUF4795  10 kklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeel 68 
                                       + + ++++ lqe  + +ee++  +++ +++ +++ e+++  +++ e+v +d  e+ee +
  gi|313126153|ref|YP_004036423.1| 424 DAIDKTVSSLQEASDAVEEAADGVSELSRASDDQAESVEGVVSAVEDVSDDAAEIEESV 482
                                       33446666666666666666666666666666666666666666666666666665554 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.3   1.1e+03      84     127 ..     166     209 ..     156     223 .. 0.66
   2 ?    8.6   3.3     0.003      0.97      51     129 ..     225     303 ..     207     330 .. 0.81
   3 ?   11.1   5.6    0.0005      0.16      49     133 ..     377     461 ..     373     492 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.3
                          ISG65-75  84 leeakekgtltesdaeklkkaceeAkaknkkarekakkalekae 127
                                       ++ea+ ++++t + ++++++++e+  + n +ar++   + e+ e
  gi|313126153|ref|YP_004036423.1| 166 KTEAQRQQEATHTLVNEVTSTLEQIGEGNLDARAELGSETEVLE 209
                                       45556667777777777777777777777777776666666655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.003
                          ISG65-75  51 tadyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekae 127
                                       + + l++e++ +++ + n++   +   +++ s+++e+++  ++  +d      a+ee+ a  ++ ++ a+ a++++ 
  gi|313126153|ref|YP_004036423.1| 225 RFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVESAADRARDNIG 301
                                       45678999999999999999999999999999999998888888888888888888888888888888888888776 PP

                          ISG65-75 128 ka 129
                                       ++
  gi|313126153|ref|YP_004036423.1| 302 SS 303
                                       55 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0005
                          ISG65-75  49 eetadyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalek 125
                                        e+ + l +et+ + ++i + +++++ + ++   l+ee +++    +++++k  + ++eA +++++a + + +  ++
  gi|313126153|ref|YP_004036423.1| 377 AEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELSRA 453
                                       45667889999999999999999999999999999999999999999999999888888888888888888877766 PP

                          ISG65-75 126 aekaskka 133
                                         ++++ +
  gi|313126153|ref|YP_004036423.1| 454 SDDQAESV 461
                                       66655554 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3       0.5   1.6e+02      28      89 ..     169     238 ..     154     248 .. 0.50
   2 ?    7.9   0.1    0.0096       3.1      16      91 ..     252     328 ..     241     335 .. 0.87
   3 ?    7.6   1.5     0.012       3.8      40     117 ..     378     457 ..     374     498 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.5
                             Mod_r  28 vkqlkeekeellaenesla....eknlslep....eleelrselqekleelkelekefeekeqeldellq 89 
                                        ++++e+   l++e  s++    e nl+ +     e e l +el +   e+++  ++fe +  e ++   
  gi|313126153|ref|YP_004036423.1| 169 AQRQQEATHTLVNEVTSTLeqigEGNLDARAelgsETEVLEDELLNIVAEVNRTGDRFESLVDEVESHAT 238
                                       3333333333333333333222233444433233366666666666666666666666666666655554 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0096
                             Mod_r  16 eklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkf 91 
                                       ++++++v++  + ++++++++ +  a+ e++a +  + e   +  r+++ ++l+++   +k  +e +++ d+ll+++
  gi|313126153|ref|YP_004036423.1| 252 SQIDSRVTEQrKALEAVRDDLASFSAAMEEVAASSTEVESAADRARDNIGSSLDWTVDTRKVTDEVKERSDDLLESV 328
                                       7788888877677999999************************************9999999999999999998664 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.012
                             Mod_r  40 aeneslaeknlslepeleelrselqekleelkelekefeekeqeldell..qkfspdallarLqtavaeaeeeSeal 114
                                       +e +sla++  s+ ++++e  +++q++ +e+ +l +e ++   + d+++     s++ + + +++a++   e+S+a 
  gi|313126153|ref|YP_004036423.1| 378 EEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIdkTVSSLQEASDAVEEAADGVSELSRAS 454
                                       56788999999999999999999999999999999999999999999994444466677777777777666666665 PP

                             Mod_r 115 aee 117
                                        ++
  gi|313126153|ref|YP_004036423.1| 455 DDQ 457
                                       444 PP

>> DUF725  Protein of unknown function (DUF725)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2      0.09        29      18      52 ..     234     268 ..     224     276 .. 0.76
   2 ?    6.8   0.1     0.019       6.3      33     111 ..     385     471 ..     374     495 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.09
                            DUF725  18 eqyeaeytkCistaeeekaeidekyeeerqqless 52 
                                       e   +++++ i+ta+++ ++id++++e+r+ le  
  gi|313126153|ref|YP_004036423.1| 234 ESHATDVSNTITTANDAASQIDSRVTEQRKALEAV 268
                                       55667777788899999999999999999988765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.019
                            DUF725  33 eekaeidekyeeerqqlessakeicsalqkC........dsledaldafeCyakagsenskilysisanAtelaakl 101
                                       +e+++ +e+++e ++ ++s+a+e+   +++         d +++++++++ +++a +e+++ ++++s  + ++a+++
  gi|313126153|ref|YP_004036423.1| 385 NETQSHTEQITERIDRIQSRADETVTLVEEThkdvgradDAIDKTVSSLQEASDAVEEAADGVSELSRASDDQAESV 461
                                       44444444444444444444444444444446666776667777777777777777777777777777777777777 PP

                            DUF725 102 seeysaidtt 111
                                       +  +sa+++ 
  gi|313126153|ref|YP_004036423.1| 462 EGVVSAVEDV 471
                                       7777777654 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.7   1.2e+03     181     200 ..     106     125 ..      83     190 .. 0.81
   2 ?   12.2   0.9   0.00029     0.094      38     159 ..     217     338 ..     210     359 .. 0.92
   3 ?    2.7   1.5      0.23        75      52     130 ..     424     494 ..     381     503 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.7
                         Mce4_CUP1 181 pYvypedlPrvnakgGPgga 200
                                       p +  e++P v+  +GP+g+
  gi|313126153|ref|YP_004036423.1| 106 PDTAHENDPSVERVRGPSGQ 125
                                       55678999999999999775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00029
                         Mce4_CUP1  38 tdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadll 114
                                       +++n+  d++++ ++++++  +++ ++ ++ +daa+++ + +++ ++  +++ +  a+ +a++ +++  s+++++  
  gi|313126153|ref|YP_004036423.1| 217 AEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVESAA 293
                                       66778888999999*************************************************************** PP

                         Mce4_CUP1 115 erngdnLirlaadlrptlelLakYspeltCllrnladvepkvaka 159
                                       +r +dn+ + ++ ++ t ++ ++ ++    ll+ ++++e+ +++ 
  gi|313126153|ref|YP_004036423.1| 294 DRARDNIGSSLDWTVDTRKVTDEVKERSDDLLESVKRLEDDMEEI 338
                                       ********************9999999999999999999988876 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.23
                         Mce4_CUP1  52 pqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadllerngdnLirlaadl 128
                                       + + +       +    ++a++ + +a d ++  sr+  +q+++++ +++a+  +s+++a++ e++ d+++++++++
  gi|313126153|ref|YP_004036423.1| 424 DAIDK-------TVSSLQEASDAVEEAADGVSELSRASDDQAESVEGVVSAVEDVSDDAAEI-EESVDDIVSVTQTQ 492
                                       33333.......33344444444555555666667777777777777777777777777764.66666777776666 PP

                         Mce4_CUP1 129 rp 130
                                       r 
  gi|313126153|ref|YP_004036423.1| 493 RD 494
                                       65 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4      0.81   2.7e+02      44      98 ..     168     222 ..     158     249 .. 0.53
   2 ?   10.0   0.3    0.0021      0.69      18      79 ..     238     298 ..     231     300 .. 0.87
   3 ?    2.6   0.8      0.41   1.3e+02      53      82 ..     378     406 ..     314     417 .. 0.73
   4 ?    5.0   0.0     0.073        24      27      67 ..     443     483 ..     428     497 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.81
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  44 evaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleil 98 
                                       e+++++e+ +++ ++++++ ++    ++ + +++ ++   l+  ll +++ ++  
  gi|313126153|ref|YP_004036423.1| 168 EAQRQQEATHTLVNEVTSTLEQIGEGNLDARAELGSETEVLEDELLNIVAEVNRT 222
                                       4445555555555555444444444444444455555555555555555554433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0021
                                       SST.TEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  18 PdpeklvPvpvkGFedLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakk 79 
                                        d ++ + +  +  +++ +Rv+ Q+k++++ r  l + s  +ee++ + ++e+ ++ ++a+ 
  gi|313126153|ref|YP_004036423.1| 238 TDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVA-ASSTEVESAADRARD 298
                                       56677777777888899*****************************.999999999998885 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  53 keisdrleeleqkhqletsvrlekakkrhv 82 
                                       +e+++ ++e++ +h  ++++r++++++r  
  gi|313126153|ref|YP_004036423.1| 378 EEVKSLANETQ-SHTEQITERIDRIQSRAD 406
                                       34444444444.777777777777777654 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.073
                                       EEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  27 pvkGFedLakRvkaQqkevaqhrerlkeisdrleeleqkhq 67 
                                        ++G+++L++  ++Q++ v+   ++++++sd++ e+e++ +
  gi|313126153|ref|YP_004036423.1| 443 AADGVSELSRASDDQAESVEGVVSAVEDVSDDAAEIEESVD 483
                                       589*********************************96654 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.4      0.52   1.7e+02      35     111 ..     224     294 ..     217     342 .. 0.71
   2 ?   13.7   1.2   0.00014     0.045      27     107 ..     370     448 ..     355     460 .. 0.81
   3 ?   -0.4   0.1         3   9.7e+02      73     112 ..     456     495 ..     443     498 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                          Ferritin  35 effdeqaeeerehadklaerilalGgtpvltraeleeieapkefgsveevleaalehekkvteslrelielaeeegD 111
                                         f+  ++e   ha ++ + i + +  +   ++++ e        +++e+++++l++  ++ e++      +e++ D
  gi|313126153|ref|YP_004036423.1| 224 DRFESLVDEVESHATDVSNTITTANDAASQIDSRVTE------QRKALEAVRDDLASFSAAMEEVAASSTEVESAAD 294
                                       5688888888888888888888888733333333333......2477777777777776666666555555555544 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00014
                                       STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCSSHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  27 gpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefgsveevleaalehekkvteslreli 103
                                       g+g+  +ae+ +  a e + h +++ eri  +   ++ t  +l e e+ k++g +++++ + + + ++++++++e++
  gi|313126153|ref|YP_004036423.1| 370 GEGFAVVAEEVKSLANETQSHTEQITERIDRIQSRADETV-TLVE-ETHKDVGRADDAIDKTVSSLQEASDAVEEAA 444
                                       899******************************8333332.3333.23344789***************99999998 PP

                                       HHHH CS
                          Ferritin 104 elae 107
                                       + + 
  gi|313126153|ref|YP_004036423.1| 445 DGVS 448
                                       7655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 3
                                       -SSSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-H CS
                          Ferritin  73 eapkefgsveevleaalehekkvteslrelielaeeegDp 112
                                       ++ ++++ v +++e++ ++  ++ es+ +++ ++++++D 
  gi|313126153|ref|YP_004036423.1| 456 DQAESVEGVVSAVEDVSDDAAEIEESVDDIVSVTQTQRDS 495
                                       3334467899999999999999999999999999999986 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.4    0.0023      0.74      17     118 ..     182     275 ..     173     295 .. 0.69
   2 ?    2.8   2.6      0.34   1.1e+02      23      87 ..     242     304 ..     238     366 .. 0.73
   3 ?    5.3   0.9     0.056        18      32      88 ..     390     441 ..     367     490 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0023
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsi 93 
                                       ++t +L++i   n    a+l +  + +e +L ++ +++++       r++     L d + + +++++n +t+ n  
  gi|313126153|ref|YP_004036423.1| 182 EVTSTLEQIGEGNLDARAELGSETEVLEDELLNIVAEVNRTGD----RFE----SLVDEVESHATDVSNTITTANDA 250
                                       7899999999999999999999999999999999999998443....333....33344444445555666777777 PP

                      Baculo_PEP_C  94 ltnLlssvtNinstLnnllqalnnl 118
                                        +++ s vt   ++L+ +  +l+++
  gi|313126153|ref|YP_004036423.1| 251 ASQIDSRVTEQRKALEAVRDDLASF 275
                                       7777777777777666666666655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.34
                      Baculo_PEP_C  23 nairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneL 87 
                                       n+i + n   ++q+ + +++  + L+a+ +dl s +a+++ ++++++t++++a  +  d++ + L
  gi|313126153|ref|YP_004036423.1| 242 NTITTANDA-ASQIDSRVTEQRKALEAVRDDLASFSAAME-EVAASSTEVESAADRARDNIGSSL 304
                                       455333433.477888888888888888888888666554.455555555555555555555444 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.056
                      Baculo_PEP_C  32 ilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLt 88 
                                        + q+++ +d i+++ ++  +    l++e ++++  + +++++++ +lq   d    + +
  gi|313126153|ref|YP_004036423.1| 390 HTEQITERIDRIQSRADETVT----LVEETHKDVGRADDAIDKTVSSLQeasD----AVE 441
                                       234444444444444444333....3333444555555555555555552222....222 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.5    0.0034       1.1     186     409 ..     216     441 ..     194     472 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0034
                          Prominin 186 rtflkdvpqhidhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnkle 262
                                       +  ++ + + +++++++  e   ++vs++++ a     +d a++++s v++  ++le++ ++l + ++++e+v +++
  gi|313126153|ref|YP_004036423.1| 216 VAEVNRTGDRFESLVDE-VESHATDVSNTITTA-----NDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASS 286
                                       44444444444444444.344444444444433.....345666666666667777777788888888888888888 PP

                          Prominin 263 keLrksgsqLrdglrgvkrdlnqalsn.lCq...seeCskilssleiekldtskcl........dqlpnvdevleal 327
                                       +e+ + +++ rd++ +     + ++   + +   +e+ +++l+s++  + d++           +++ + +++l  l
  gi|313126153|ref|YP_004036423.1| 287 TEVESAADRARDNIGSSL---DWTVDTrKVTdevKERSDDLLESVKRLEDDME--EigdvvgliSEIADRTNILA-L 357
                                       887777777777775543...33333222221112444444444444221111..11122222233333333332.1 PP

                          Prominin 328 eevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkip..realdavisdlenterssk 402
                                       +  +e+  +  + eg a + e  + ++n+t++ ++++++ ++++++  +++ + +   ++ + +  +++++t +s++
  gi|313126153|ref|YP_004036423.1| 358 NANIEAARAGEAGEGFAVVAEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEetHKDVGRADDAIDKTVSSLQ 434
                                       11112222222222222222222222333333333333333333333333333331112222333334444444444 PP

                          Prominin 403 tfddvve 409
                                       +++d ve
  gi|313126153|ref|YP_004036423.1| 435 EASDAVE 441
                                       4444444 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   7.2     0.047        15     202     317 ..     217     338 ..     135     366 .. 0.60
   2 ?    9.8   3.0    0.0011      0.36     238     322 ..     378     462 ..     369     496 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.047
                             IFT57 202 lEleRvlpqLkv...tikadakdWrahleqmkkhkksieeslpetksqlkklhedi...sktlekiesrEkylnsql 272
                                        E++R   +++    ++++ a d  +++ + ++  ++i++ ++e +++l+ + +d+   s ++e++ +  + ++s  
  gi|313126153|ref|YP_004036423.1| 217 AEVNRTGDRFESlvdEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLasfSAAMEEVAASSTEVESAA 293
                                       35555555444455455666667777777777777777777777777777777665222456666666777777777 PP

                             IFT57 273 eellqeyreaqeelsevkekykqlsegvseltrelaeiseelekv 317
                                       +   ++  +  +   ++++  ++++e+  +l +  +++++++e++
  gi|313126153|ref|YP_004036423.1| 294 DRARDNIGSSLDWTVDTRKVTDEVKERSDDLLESVKRLEDDMEEI 338
                                       777777776666666666666666666666666666666666665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                             IFT57 238 eslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseel 314
                                       e+++++ ++ +   e+i++ +++i+sr     + +ee+ ++   a + ++++  +++++s+ v+e  +  +e+s   
  gi|313126153|ref|YP_004036423.1| 378 EEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELSRAS 454
                                       44444444455555555555555555555555555555555555555555555555555555555555555444444 PP

                             IFT57 315 ekvkqeme 322
                                       ++  + +e
  gi|313126153|ref|YP_004036423.1| 455 DDQAESVE 462
                                       44433333 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.4   0.00081      0.27      65     176 ..     175     287 ..     172     302 .. 0.89
   2 ?   -1.2   0.0       4.2   1.4e+03      97     124 ..     310     337 ..     289     352 .. 0.62
   3 ?    6.0   0.7     0.027       8.7       5      43 ..     377     416 ..     374     427 .. 0.79
   4 ?    3.8   1.9      0.13        42      75     140 ..     428     493 ..     419     498 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00081
                               LXG  65 slqdlieqyeefLkkikeales..vepssngfidedfLeqelenglkkakevteelkdeinkilasvsdivslpeld 139
                                       ++++l++++ ++L++i e   +  +e+ s++++ ed L  ++  ++++    +e+l de+++   +vs ++ + +  
  gi|313126153|ref|YP_004036423.1| 175 ATHTLVNEVTSTLEQIGEGNLDarAELGSETEVLEDELL-NIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDA 250
                                       678899999999***9877666589**************.999********************************** PP

                               LXG 140 dsevkdslqkakkkvqetiekledfdqeqksalanle 176
                                        s++ + + +++k ++ + ++l  f + + +  a++ 
  gi|313126153|ref|YP_004036423.1| 251 ASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASST 287
                                       ***********************99888777766655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.2
                               LXG  97 edfLeqelenglkkakevteelkdeink 124
                                         ++ +e++ + + + e+++ l+d +++
  gi|313126153|ref|YP_004036423.1| 310 TRKVTDEVKERSDDLLESVKRLEDDMEE 337
                                       4455555555555555555555555444 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.027
                               LXG   5 vaelieaieqlkseleelkeqleqlkkaiqk.lveledsl 43 
                                       ++e+++++++++s +e+ +e +++++++ ++ ++ +e+ +
  gi|313126153|ref|YP_004036423.1| 377 AEEVKSLANETQSHTEQITERIDRIQSRADEtVTLVEETH 416
                                       7899999999999999999999999999999555555555 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.13
                               LXG  75 efLkkikealesvepssngfidedfLeqelenglkkakevteelkdeinkilasvsdivslpeldd 140
                                       ++ +  +ea  +ve + +g+ + +   ++++  ++ + + +e+  d + +i +sv+divs+++ + 
  gi|313126153|ref|YP_004036423.1| 428 KTVSSLQEASDAVEEAADGVSELSRASDDQAESVEGVVSAVEDVSDDAAEIEESVDDIVSVTQTQR 493
                                       344444555555555788888888888888888888888899999999999999999999887665 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   3.5      0.22        72      49     126 ..     223     305 ..     198     348 .. 0.47
   2 ?   11.4   2.4   0.00075      0.25      36     148 ..     385     505 ..     373     508 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.22
                       Serine_rich  49 vdrlrtslrefleFargalanaaklsd..knlqtkLrkqlqkledsdqilqetsqeLdsc...eWslealasdkkqe 120
                                        dr+++ + e+   a ++  + + ++d  +++  +  +q ++le  ++ l + s ++++    + ++e  a+  +++
  gi|313126153|ref|YP_004036423.1| 223 GDRFESLVDEVESHATDVSNTITTANDaaSQIDSRVTEQRKALEAVRDDLASFSAAMEEVaasSTEVESAADRARDN 299
                                       44444444444444444444444444444344444444433333333333333333332200022222222222222 PP

                       Serine_rich 121 kpddlD 126
                                          +lD
  gi|313126153|ref|YP_004036423.1| 300 IGSSLD 305
                                       233333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00075
                       Serine_rich  36 enleanlqeirlavdrlrtslrefleFargalanaaklsd..knlqtkLrkqlqkledsdqilqetsqeLdsceWsl 110
                                       ++ ++++++i + +dr+++   e + + +++     ++ d   +    L++  +++e++++ ++e s++ d++  s+
  gi|313126153|ref|YP_004036423.1| 385 NETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDaiDKTVSSLQEASDAVEEAADGVSELSRASDDQAESV 461
                                       4568999***********999999999999888877777766566678***************************** PP

                       Serine_rich 111 ealasdkkqek......pddlDrlvmvartvpdDvkqlasfiqg 148
                                       e ++s  ++ +      ++++D +v+v++t  d + +l ++i g
  gi|313126153|ref|YP_004036423.1| 462 EGVVSAVEDVSddaaeiEESVDDIVSVTQTQRDSAGELGTMIDG 505
                                       99999888887788999999*************99999999987 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       4.4   1.4e+03      40      66 ..     163     188 ..     154     200 .. 0.60
   2 ?    5.2   1.0      0.09        29       8      35 ..     246     273 ..     209     305 .. 0.50
   3 ?    3.5   0.4      0.31     1e+02      35      65 ..     312     342 ..     262     351 .. 0.77
   4 ?    0.7   0.3       2.4   7.7e+02      23      58 ..     376     412 ..     373     419 .. 0.66
   5 ?   13.1   2.7    0.0003     0.097      15      63 ..     425     473 ..     418     490 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 4.4
                           NPV_P10  40 lnekLdaqsaqLaeletkvenIqdiLn 66 
                                       +++k +aq +q ++ +t v++++++L 
  gi|313126153|ref|YP_004036423.1| 163 VEDKTEAQRQQ-EATHTLVNEVTSTLE 188
                                       45555665555.344555666666554 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.09
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlp 35 
                                          ++ +++d++V+   ++++ v+++l 
  gi|313126153|ref|YP_004036423.1| 246 TANDAASQIDSRVTEQRKALEAVRDDLA 273
                                       2223333333333333333333333333 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.31
                           NPV_P10  35 pdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                       + ++e++e+ d++ ++++ le+ +e+I d+ 
  gi|313126153|ref|YP_004036423.1| 312 KVTDEVKERSDDLLESVKRLEDDMEEIGDVV 342
                                       3446788888888888888888888887775 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 2.4
                           NPV_P10  23 lqqqvddvqenlpd.vtelnekLdaqsaqLaeletkv 58 
                                       + ++v++++++ +  +++++e++d+++   +e  t v
  gi|313126153|ref|YP_004036423.1| 376 VAEEVKSLANETQShTEQITERIDRIQSRADETVTLV 412
                                       5667777776665414678888888877666655555 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 0.0003
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       a+d+ V++lq++ d v+e    v+el+   d+q+++++ + ++ve+++d
  gi|313126153|ref|YP_004036423.1| 425 AIDKTVSSLQEASDAVEEAADGVSELSRASDDQAESVEGVVSAVEDVSD 473
                                       899*****************************************99976 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.8   0.00027     0.087     567     704 ..     198     333 ..     159     339 .. 0.85
   2 ?    2.1   0.9       0.1        34     586     667 ..     378     456 ..     346     493 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                             Nup88 567 keqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklks 643
                                       +++  +e + le+e  ++  ++++  +++e   d+ e+ +  v++ + ++n+++ ++ +   e +k le+++++l s
  gi|313126153|ref|YP_004036423.1| 198 RAELGSETEVLEDELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLAS 274
                                       5666678889999999999************************************999999999************* PP

                             Nup88 644 lknalkqvkkkldkqrkqiakskeeekksslelsekqkktikeiLkeegeeieelikqvkd 704
                                       + +a+++v     ++++  ++++++   ssl  + + +k +++  ke ++++ e +k+++d
  gi|313126153|ref|YP_004036423.1| 275 FSAAMEEVAASSTEVESAADRARDN-IGSSLDWTVDTRK-VTDEVKERSDDLLESVKRLED 333
                                       ***********99999998888777.6778888776655.666679999999999888765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                             Nup88 586 eraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklkslknalkqvkkkldkqrkqi 662
                                       e++++lA   +e + + e++++r++++ +r+ + +  + e+ +++ +   +i+++++sl++a + v++  d + +  
  gi|313126153|ref|YP_004036423.1| 378 EEVKSLA---NETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELS 451
                                       4444444...3566666667777776666666666666666666666666666666666666555555555444444 PP

                             Nup88 663 akske 667
                                        +s +
  gi|313126153|ref|YP_004036423.1| 452 RASDD 456
                                       33333 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.15        50      99     142 ..     166     209 ..     160     212 .. 0.90
   2 ?    8.4   5.0    0.0049       1.6      63     134 ..     229     300 ..     213     341 .. 0.52
   3 ?    6.3   7.5     0.022         7      47     141 ..     361     454 ..     349     483 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                            DUF745  99 akqaqqqlealkallkaakenlenaeqvaagaqqelaektqlle 142
                                       +++aq+q ea ++l+++++++le++ + +  a +el + t+ le
  gi|313126153|ref|YP_004036423.1| 166 KTEAQRQQEATHTLVNEVTSTLEQIGEGNLDARAELGSETEVLE 209
                                       57899999***************************999999887 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0049
                            DUF745  63 lveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqel 134
                                       lv+++e+  ++ ++ +   +++ ++  + ++  +ka + ++  l++++a+++++ ++ +++e++a+ a  ++
  gi|313126153|ref|YP_004036423.1| 229 LVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVESAADRARDNI 300
                                       444444444444444444444444444444444444444445555555555555555555555444444443 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.022
                            DUF745  47 lqAakAAeAaLaGKqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlena 123
                                       ++Aa+A eA  +G  ++ e++++  +e+++  +++++ + + ++ a+ + + +++ ++ + +  ++++++ ++l++a
  gi|313126153|ref|YP_004036423.1| 361 IEAARAGEAG-EGFAVVAEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEA 436
                                       4666666664.677777777777777777777777777777777777777777777777777777777777777776 PP

                            DUF745 124 eqvaagaqqelaektqll 141
                                        ++ ++a+  ++e +   
  gi|313126153|ref|YP_004036423.1| 437 SDAVEEAADGVSELSRAS 454
                                       666666666665544444 PP

>> DUF1351  Protein of unknown function (DUF1351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00063      0.21      44     167 ..     196     334 ..     182     358 .. 0.65
   2 ?    0.4   1.8       1.4   4.7e+02     143     177 ..     374     407 ..     303     434 .. 0.50
   3 ?    0.8   1.3         1   3.4e+02      75     129 ..     388     419 ..     350     491 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00063
                           DUF1351  44 keraeLnklkkaLddkRkevkkeysePideFeakikelekkikeaidkideqik...efeekekeekk.....kevk 112
                                       + raeL   ++ L+d+  ++  e++   d+Fe+ ++e+e+   ++++ i++      +++ +  e++k     +   
  gi|313126153|ref|YP_004036423.1| 196 DARAELGSETEVLEDELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDaasQIDSRVTEQRKaleavRDDL 272
                                       579**************************************999999997643300033333333332110002333 PP

                           DUF1351 113 aliselaeeaeveleeieiqek........wlnktvslkkieeeieaakaekikkdreeleka 167
                                       a +s  +ee + + +e+e             l  tv ++k++ e+ ++  +++ +  ++le +
  gi|313126153|ref|YP_004036423.1| 273 ASFSAAMEEVAASSTEVESAADrardnigsSLDWTVDTRKVTDEV-KERSDDLLESVKRLEDD 334
                                       444444555555555553222245444444333677777777777.55555555555555554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.4
                           DUF1351 143 kkieeeieaakaekikkdreelekakaeieekaka 177
                                         + ee+ +  a++ +   e++ +++  i++ a++
  gi|313126153|ref|YP_004036423.1| 374 AVVAEEV-KSLANETQSHTEQITERIDRIQSRADE 407
                                       3344444.444444444444444444444444444 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1
                           DUF1351  75 eakikelekkikeaidkideqikefeekekeekkkevkaliselaeeaeveleei 129
                                       +++ +++++ i+ +  + de ++ +ee  k                       ++
  gi|313126153|ref|YP_004036423.1| 388 QSHTEQITERIDRIQSRADETVTLVEETHK-----------------------DV 419
                                       333333333333333333333333333333.......................33 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.3   7.6e+02      53     102 ..     246     295 ..     219     305 .. 0.63
   2 ?   -0.1   0.1       2.6   8.6e+02      79     106 ..     272     299 ..     240     362 .. 0.54
   3 ?    6.3   0.3     0.028       9.2      54     112 ..     376     435 ..     355     445 .. 0.74
   4 ?   -0.4   0.0       3.3   1.1e+03      80     109 ..     459     488 ..     445     493 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.3
                          LOH1CR12  53 klverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqii 102
                                          +   ++d ++++  + l + ++  as+ +a+++v   s ++ +  + 
  gi|313126153|ref|YP_004036423.1| 246 TANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVESAADR 295
                                       33444455666666666667777777777777777777777666665555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.6
                          LOH1CR12  79 yasyaealskvnelsdqlsriqiiledi 106
                                        as+ +a+++v   s ++ +  +   d+
  gi|313126153|ref|YP_004036423.1| 272 LASFSAAMEEVAASSTEVESAADRARDN 299
                                       4444444444444443333333333332 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.028
                          LOH1CR12  54 lverikevdakiitllaelrekqkqyasya.ealskvnelsdqlsriqiiledivpllEt 112
                                       ++e++k++ ++ ++  +++ e+ ++ +s a e+++ v+e ++++ r ++ ++++v +l +
  gi|313126153|ref|YP_004036423.1| 376 VAEEVKSLANETQSHTEQITERIDRIQSRAdETVTLVEETHKDVGRADDAIDKTVSSLQE 435
                                       556777777777777777777777777666356777888888888888888888887765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 3.3
                          LOH1CR12  80 asyaealskvnelsdqlsriqiiledivpl 109
                                       +s    +s v+++sd+ + i+  ++div +
  gi|313126153|ref|YP_004036423.1| 459 ESVEGVVSAVEDVSDDAAEIEESVDDIVSV 488
                                       455556788999999999999999999976 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.4         1   3.4e+02      61      90 ..     162     190 ..     155     221 .. 0.72
   2 ?    5.8   0.3     0.045        15      26      89 ..     212     275 ..     205     301 .. 0.59
   3 ?    4.5   0.4      0.11        36      31     104 ..     266     338 ..     251     366 .. 0.58
   4 ?    6.5   0.9     0.027       8.9      46     130 ..     379     459 ..     373     463 .. 0.71
   5 ?    7.9   0.2    0.0098       3.2      25     105 ..     411     490 ..     407     507 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                         Fib_alpha  61 ikdslrekqkskkdndnvikksskeleeei 90 
                                       + +  +e+q++++ + +++++++++le +i
  gi|313126153|ref|YP_004036423.1| 162 LVEDKTEAQRQQEATHTLVNEVTSTLE-QI 190
                                       444456677777777999999999998.65 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.045
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleee 89 
                                       ll+   +v+++ ++ e+ ++e+++  +++++++++ +d   +  +  +++ ++++ ++++l + 
  gi|313126153|ref|YP_004036423.1| 212 LLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASF 275
                                       5555555566666666666666666666666666666666666666665666666666665532 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.11
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesni 104
                                       + v++dl++    +ee++ s++e+e+   + +d + +    + d+ +v+ +++++ + + l+  +++ + +++i
  gi|313126153|ref|YP_004036423.1| 266 EAVRDDLASFSAAMEEVAASSTEVESAADRARDNIGSSLDWTVDTRKVTDEVKERSD-DLLESVKRLEDDMEEI 338
                                       455666666666666666666666666666666666666666555555555555544.4444444444444444 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.027
                                       CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  46 eisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLe 122
                                       e+++  +e+++++++i++ + + q+ ++++ +++++ +k++     r ++ id+++s++++  + +e+    +++L 
  gi|313126153|ref|YP_004036423.1| 379 EVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVG----RADDAIDKTVSSLQEASDAVEEAADGVSELS 451
                                       455566667777777777777777777665555555555555....8888888888888888888888888888888 PP

                                       HHHHHHHH CS
                         Fib_alpha 123 qdidqker 130
                                        ++d + +
  gi|313126153|ref|YP_004036423.1| 452 RASDDQAE 459
                                       88877765 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0098
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe 101
                                       l+++++kdv +  + + ++++++++ +  +ee    +++  r+   +++  + v++ +++  + + ++++e++d+ +
  gi|313126153|ref|YP_004036423.1| 411 LVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELSRASDDQAESVEGVVSAVEDVSD-DAAEIEESVDDIV 486
                                       566778888888889999999999999999999999999999999999988999999887777.9*******99877 PP

                                       HHHH CS
                         Fib_alpha 102 snir 105
                                       s  +
  gi|313126153|ref|YP_004036423.1| 487 SVTQ 490
                                       6555 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1         4   1.3e+03      15      38 ..     168     191 ..     160     196 .. 0.68
   2 ?    5.0   0.1      0.09        29      46      82 ..     223     259 ..     210     263 .. 0.72
   3 ?    4.2   1.2      0.16        52       8      62 ..     232     281 ..     229     303 .. 0.55
   4 ?   -1.0   0.0       6.8   2.2e+03      12      37 ..     313     338 ..     307     342 .. 0.64
   5 ?    6.4   2.9     0.032        10       4      79 ..     375     456 ..     372     462 .. 0.76
   6 ?   -0.4   0.0       4.1   1.3e+03      11      33 ..     466     488 ..     460     497 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 4
                                       HHHHHHHHHHHHHHHHHHHHHHCG CS
                            WXG100  15 rfqkqaeeledelqrlkaevdalq 38 
                                       ++q+q+e  +++++++ +++++++
  gi|313126153|ref|YP_004036423.1| 168 EAQRQQEATHTLVNEVTSTLEQIG 191
                                       556677777777777777777763 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.09
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  46 adafqaefeewkqaaqklvdaLeeisealkqaanafe 82 
                                       +d+f++  +e+  +a+++ +  ++ ++a  q+ ++++
  gi|313126153|ref|YP_004036423.1| 223 GDRFESLVDEVESHATDVSNTITTANDAASQIDSRVT 259
                                       5667777777777777777777777777776666555 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHH CS
                            WXG100   8 elrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqk 62 
                                       e++++a++++++ ++  d+ +++++ v + +     +a +a ++ ++ + +a+++
  gi|313126153|ref|YP_004036423.1| 232 EVESHATDVSNTITTANDAASQIDSRVTEQR-----KALEAVRDDLASFSAAMEE 281
                                       6667777777777777777777776665533.....2333333333333333333 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 6.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100  12 aaarfqkqaeeledelqrlkaevdal 37 
                                       +  ++++ +++l + ++rl+ +++++
  gi|313126153|ref|YP_004036423.1| 313 VTDEVKERSDDLLESVKRLEDDMEEI 338
                                       55566666677777777777766665 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.032
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...C.GCGCT..HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   4 vdpeelrqaaarfqkqaeeledelqrlkaevda...l.qsgWs..GaaadafqaefeewkqaaqklvdaLeeiseal 74 
                                       v +ee+ + a++ q++ e+++++++r+++  d+   l +++ +  G a da +++   +++a + + +a +++se  
  gi|313126153|ref|YP_004036423.1| 375 VVAEEVKSLANETQSHTEQITERIDRIQSRADEtvtLvEETHKdvGRADDAIDKTVSSLQEASDAVEEAADGVSELS 451
                                       77899**********************99998733344567777788888888888888888888888777777766 PP

                                       HHHHH CS
                            WXG100  75 kqaan 79 
                                       +++ +
  gi|313126153|ref|YP_004036423.1| 452 RASDD 456
                                       66655 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  11 qaaarfqkqaeeledelqrlkae 33 
                                       +a  ++++ a+e+e+ ++++ + 
  gi|313126153|ref|YP_004036423.1| 466 SAVEDVSDDAAEIEESVDDIVSV 488
                                       55566666666666666665554 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.0     0.082        27      48     115 ..     161     229 ..     154     232 .. 0.68
   2 ?   10.5   4.8    0.0015      0.48       4     128 ..     213     337 ..     210     340 .. 0.74
   3 ?    7.1   5.3     0.016       5.3      17     115 ..     377     475 ..     362     484 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.082
                        TPR_MLP1_2  48 elvkhaedvkelqalreel.nelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedl 115
                                       elv+ +++++  q++   l ne++++++++ + + +a+ael  ++e +e +  ++  e++ +  r e l
  gi|313126153|ref|YP_004036423.1| 161 ELVEDKTEAQRQQEATHTLvNEVTSTLEQIGEGNLDARAELGSETEVLEDELLNIVAEVNRTGDRFESL 229
                                       566666666665555544447777777777777777888887777777777777777777777776665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0015
                        TPR_MLP1_2   4 ksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaea 80 
                                        +  +e+++  ++ e++ ++++++ +d+ +    a++a  +  + ++++ ++++++++  + ++ + +e+a   +e+
  gi|313126153|ref|YP_004036423.1| 213 LNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEV 289
                                       56678888999999999999999999999999999999999999999888777776666666666666666666666 PP

                        TPR_MLP1_2  81 esakaeleeseesweeqkeelekelselekriedlneqNklLhdQlEs 128
                                       esa      +  s        +k  +e+++r +dl e  k L d +E+
  gi|313126153|ref|YP_004036423.1| 290 ESAADRARDNIGSSLDWTVDTRKVTDEVKERSDDLLESVKRLEDDMEE 337
                                       666666666666666667777777778888888887776666666665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.016
                        TPR_MLP1_2  17 keeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleesees 93 
                                       +ee ++ +++ q+  e+ +e+  + q +  + +++ +e+ k++ ++ + ++++ + ++e+ +++e+a   ++e   +
  gi|313126153|ref|YP_004036423.1| 377 AEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELSRA 453
                                       566777777788888888888889999999*********************************************** PP

                        TPR_MLP1_2  94 weeqkeelekelselekriedl 115
                                        + q e+ e  +s +e   +d 
  gi|313126153|ref|YP_004036423.1| 454 SDDQAESVEGVVSAVEDVSDDA 475
                                       9999999999999988877776 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       5.8   1.9e+03     103     152 ..     167     220 ..     160     223 .. 0.64
   2 ?    5.1   5.5     0.088        29      46     138 ..     224     315 ..     216     336 .. 0.54
   3 ?    7.9  10.2     0.012       3.9      37     154 ..     387     491 ..     346     508 .] 0.48

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.8
                                       HHHHHHHHH.....HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
                           T3SSipB 103 leaaeqQagaa...adalqadeal.qKkldaasklsekakakekevDdisakvq 152
                                        ea++qQ +      + ++  e++ + +lda   l+ +   +e e+ +i+a v+
  gi|313126153|ref|YP_004036423.1| 167 TEAQRQQEATHtlvNEVTSTLEQIgEGNLDARAELGSETEVLEDELLNIVAEVN 220
                                       444455544443555555555545577888888888888888888888888775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.088
                                       STHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH...HHHH CS
                           T3SSipB  46 delqtalseakgatddl....eaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaa.adal 117
                                       d ++ +++e +  + d+    + a ++a q++s + +  k+++++   l +++ +  e a+   +++ a+++  d  
  gi|313126153|ref|YP_004036423.1| 224 DRFESLVDEVESHATDVsntiTTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVESAADRaRD-- 298
                                       566666666655555550000555555555555556667777777778888866666666666666655544222.. PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB 118 qadealqKkldaasklsekak 138
                                           ++   ld +   ++   
  gi|313126153|ref|YP_004036423.1| 299 ----NIGSSLDWTVDTRKVTD 315
                                       ....22333333333333333 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.012
                                       TTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...........HHTT---------C CS
                           T3SSipB  37 qqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqk...........rlkeLaPdePekak 102
                                       +q + +++ + + +  s a++                         v+e  k            +++L+ ++    +
  gi|313126153|ref|YP_004036423.1| 387 TQSHTEQITERIDRIQSRADETVTL---------------------VEETHKdvgraddaidkTVSSLQEASDAVEE 442
                                       2233333333333333322222222.....................2222223333333333344444222222222 PP

                                       HHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTXXXXXXXX CS
                           T3SSipB 103 leaaeqQagaaadalqadealqKkldaasklsekakakekevDdisakvqgt 154
                                       +   +  +  a  +  + e ++  ++a + +s++a + e+ vDdi++ v++t
  gi|313126153|ref|YP_004036423.1| 443 AADGVSELSRA--SDDQAESVEGVVSAVEDVSDDAAEIEESVDDIVS-VTQT 491
                                       22222233322..2222222355666666666666666666666666.4443 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       5.3   1.7e+03       4      41 ..     179     216 ..     176     220 .. 0.81
   2 ?    1.8   0.4      0.96   3.1e+02       1      72 [.     226     267 ..     196     274 .. 0.59
   3 ?    1.4   0.2       1.3   4.2e+02       1      41 [.     226     265 ..     226     297 .. 0.73
   4 ?    7.5   0.5     0.016       5.1       2      43 ..     388     428 ..     387     444 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 5.3
                           V-SNARE   4 llaeiksklarlsslageerkaalreiekkldeaeell 41 
                                       l++e++s l+++ + + + r ++ +e e   de+ +++
  gi|313126153|ref|YP_004036423.1| 179 LVNEVTSTLEQIGEGNLDARAELGSETEVLEDELLNIV 216
                                       78999999999998877999999998888777777665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.96
                           V-SNARE   1 fkellaeiksklarlsslageerkaalreiekkldeaeelldqMelEvrnlpsserasykaklreykselkk 72 
                                       f++l++e++s+ +++s+    + + a +                             ++ ++++e ++ l+ 
  gi|313126153|ref|YP_004036423.1| 226 FESLVDEVESHATDVSNT-ITTANDAAS-----------------------------QIDSRVTEQRKALEA 267
                                       344444444444444433.234444444.............................445555555555554 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.3
                           V-SNARE   1 fkellaeiksklarlsslageerkaalreiekkldeaeell 41 
                                       f++l++e++s+ +++s+    + + a ++i++++ e ++ l
  gi|313126153|ref|YP_004036423.1| 226 FESLVDEVESHATDVSNT-ITTANDAASQIDSRVTEQRKAL 265
                                       566777777777777755.4467777777777777665555 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.016
                           V-SNARE   2 kellaeiksklarlsslageerkaalreiekkldeaeelldq 43 
                                       ++++++i+++++r++s   +e   ++ e +k++  a++ +d+
  gi|313126153|ref|YP_004036423.1| 388 QSHTEQITERIDRIQSR-ADETVTLVEETHKDVGRADDAIDK 428
                                       6789***********77.5699****************9996 PP

>> PMEI  Plant invertase/pectin methylesterase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.8     0.059        19      40     125 ..     240     310 ..     212     351 .. 0.59
   2 ?    6.7   2.1     0.027       8.8      41     114 ..     385     471 ..     352     499 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHHHHHHHHHS......-HH....HHHHHHHHHHHHHHHHHHHHHHHHH-HH....HHHHHHHHHH CS
                              PMEI  40 lkvalanarsaaaaiskllkkskkkklkkkk....aaledClelyedavdeLedalaalkrskrkvddaqtwlsaal 112
                                       ++ +++ a++aa+ i++  ++         +    +a++d l  ++ a++e+  +  +          +++ +  a 
  gi|313126153|ref|YP_004036423.1| 240 VSNTITTANDAASQIDSRVTE---------QrkalEAVRDDLASFSAAMEEVAASSTE----------VESAADRAR 297
                                       344455555555555443211.........1222356777777777777776655333..........455555555 PP

                                       HHHHHHHHHHTTS CS
                              PMEI 113 tdqdtCedgfkea 125
                                       ++  + +d+  ++
  gi|313126153|ref|YP_004036423.1| 298 DNIGSSLDWTVDT 310
                                       5555555555443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHHS......-HH............HHHHHHHHHHHHHHHHHHHHHHHHH...-HH.... CS
                              PMEI  41 kvalanarsaaaaiskllkkskkkklkkkk............aaledClelyedavdeLedalaalk...rskrk.v 101
                                       + +++++++++++i+++++++ +  +                +a++  ++ +++a d++e+a++ ++   r +++ +
  gi|313126153|ref|YP_004036423.1| 385 NETQSHTEQITERIDRIQSRADETVT---LveethkdvgradDAIDKTVSSLQEASDAVEEAADGVSelsRASDDqA 458
                                       44445555555555555332211111...011123233333345555555555555544444444333333333334 PP

                                       .HHHHHHHHHHHH CS
                              PMEI 102 ddaqtwlsaaltd 114
                                       ++++  +sa+ + 
  gi|313126153|ref|YP_004036423.1| 459 ESVEGVVSAVEDV 471
                                       4444444444332 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       7.6   2.5e+03      27      53 ..     167     193 ..     158     206 .. 0.55
   2 ?    9.5   0.3    0.0044       1.4       3      56 ..     228     281 ..     226     295 .. 0.82
   3 ?    5.3   0.5     0.095        31       2      55 ..     395     448 ..     394     481 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 7.6
                                       HHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  27 aeqqqqidrlqrqlrllaerlkelees 53 
                                       +e q+q ++ ++ +++++  l+++ e 
  gi|313126153|ref|YP_004036423.1| 167 TEAQRQQEATHTLVNEVTSTLEQIGEG 193
                                       344444444444555555444444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56 
                                       + ++e E++ +   +ti + nd+  + + +++++++ l+++++ l++ ++++++
  gi|313126153|ref|YP_004036423.1| 228 SLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEE 281
                                       567899999999999999999999999999999999999999999777776653 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.095
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                        er+++++++   +  ++ee  + v + ++ id+    l++  + ++e+++  +
  gi|313126153|ref|YP_004036423.1| 395 TERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVS 448
                                       69***************************************9999988776654 PP

>> MafB  Neisseria toxin MafB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.6    0.0032         1     151     279 ..     188     318 ..     171     329 .. 0.83
   2 ?    3.7   4.9      0.11        35     161     288 ..     366     492 ..     350     501 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0032
                              MafB 151 rsisqrlldefanagsnlldradeankkifeydpeldrsgnameavnGvadgavnpflaagealGvGdivdgiseav 227
                                         i++  ld  a++gs+     de    + e +   dr    +++v+  a  + n + +a +a    d   + +   
  gi|313126153|ref|YP_004036423.1| 188 EQIGEGNLDARAELGSETEVLEDELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKA 264
                                       456777788899999999999999999999999999**************************988777766666667 PP

                              MafB 228 diaalhnlgllsa..eaklaaitdladaaqlkkdaaeavrdWadenPnaaetve 279
                                         a+  +l+ +sa  e+  a+ t++++aa   +d + +  dW ++   +++ v+
  gi|313126153|ref|YP_004036423.1| 265 LEAVRDDLASFSAamEEVAASSTEVESAADRARDNIGSSLDWTVDTRKVTDEVK 318
                                       779999****99743666777899*******************99999888775 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                              MafB 161 fanagsnlldradeankkifeydpeldrsgnameavnGvadgavnpflaagealG.vGdivdgiseavdiaa..lhn 234
                                         +ag +++  a+e + ++ e +++ ++ +++++ ++  ad +v  +  + + +G + d++d ++++ + a   +++
  gi|313126153|ref|YP_004036423.1| 366 AGEAGEGFAVVAEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGrADDAIDKTVSSLQEASdaVEE 442
                                       55789999999999999***********************************9994567999999999998733333 PP

                              MafB 235 lgllsaeaklaaitdladaaqlkkdaaeavrdWadenPnaaetveavvnvtkaa 288
                                        +     ++l++++  +d a+ ++  + av+d  d+  ++ e+v+ +v+vt++ 
  gi|313126153|ref|YP_004036423.1| 443 AA--DGVSELSRAS--DDQAESVEGVVSAVEDVSDDAAEIEESVDDIVSVTQTQ 492
                                       33..3344455555..47888888899999999999999999999999988765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   9.2      0.41   1.3e+02     121     213 ..     224     340 ..     140     363 .. 0.66
   2 ?    7.4   4.9    0.0072       2.4     109     225 ..     373     492 ..     349     496 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.41
                              CorA 121 drlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlk.................... 175
                                       dr++ l++++e++  ++++++   ++   +i +++++ r+ l  +r+ la   ++++                    
  gi|313126153|ref|YP_004036423.1| 224 DRFESLVDEVESHATDVSNTIttANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEevaasstevesaadrardni 300
                                       66777777777777777777776666666666777777777777777777777777633333333333333333322 PP

                              CorA 176 .rlla.kaddkllddedkeylrdlldelerllemlealre 213
                                        + l+ + d+ +++de ke+ +dll+ ++rl++++e + +
  gi|313126153|ref|YP_004036423.1| 301 gSSLDwTVDTRKVTDEVKERSDDLLESVKRLEDDMEEIGD 340
                                       2222244455555555555555555555555555555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0072
                              CorA 109 gellyrlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kad 182
                                       + ++++ + +++++    +e++ e++d+++++        +e ++++ +    + k  ++l +  +++++  +  ++
  gi|313126153|ref|YP_004036423.1| 373 FAVVAEEVKSLANETQSHTEQITERIDRIQSRAdeTVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADgVSE 449
                                       66777778889999999****************86555678899999999999999999999999999988889899 PP

                              CorA 183 dkllddedkeylrdlldelerllemlealrerleslqdtyssl 225
                                        ++ +d+++e  + + + +e +++++  + e ++ + +  +++
  gi|313126153|ref|YP_004036423.1| 450 LSRASDDQAESVEGVVSAVEDVSDDAAEIEESVDDIVSVTQTQ 492
                                       99999**************************999988776665 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2       1.6   5.2e+02       9      43 ..     163     196 ..     159     216 .. 0.73
   2 ?    4.4   0.0      0.19        61       7      49 ..     224     266 ..     223     288 .. 0.84
   3 ?    1.1   0.0       2.1   6.9e+02      21      63 ..     308     349 ..     289     360 .. 0.69
   4 ?   -0.6   0.0       6.8   2.2e+03      18      38 ..     386     406 ..     371     422 .. 0.47
   5 ?   -0.1   0.1         5   1.6e+03      11      49 ..     396     434 ..     388     459 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.6
                                       HHHHHTS---TTT........HHHHHHH---GGGG CS
                            RecG_N   9 lekllkkvlsgkleteelieeikkkleliddplle 43 
                                       +e + +++ ++   t+ l++e+ ++le+i +  l+
  gi|313126153|ref|YP_004036423.1| 163 VEDKTEAQRQQ-EATHTLVNEVTSTLEQIGEGNLD 196
                                       55555555444.45899999999999998766555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.19
                                       HHHHHHHTS---TTT........HHHHHHH---GGGG-HHHH. CS
                            RecG_N   7 eelekllkkvlsgkleteelieeikkkleliddplleneevlk 49 
                                       +++e l+++v+s+  ++++ i   ++ +++id  + e+ + l+
  gi|313126153|ref|YP_004036423.1| 224 DRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALE 266
                                       78999********************************999883 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 2.1
                                       T........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTSS CS
                            RecG_N  21 leteelieeikkkleliddplleneevlkeklskfldYikpia 63 
                                       ++t ++ +e+k++ + + ++++  e+   e +++ ++ i++ia
  gi|313126153|ref|YP_004036423.1| 308 VDTRKVTDEVKERSDDLLESVKRLEDDM-EEIGDVVGLISEIA 349
                                       5556666666666666666666666666.66666666666665 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 6.8
                                       -TTT........HHHHHHH-- CS
                            RecG_N  18 sgkleteelieeikkklelid 38 
                                       +++ +te++ e i +  +  d
  gi|313126153|ref|YP_004036423.1| 386 ETQSHTEQITERIDRIQSRAD 406
                                       223333333333333333333 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 5
                                       HHHTS---TTT........HHHHHHH---GGGG-HHHH. CS
                            RecG_N  11 kllkkvlsgkleteelieeikkkleliddplleneevlk 49 
                                       + ++ ++s   et  l+ee +k +   dd + +  ++l+
  gi|313126153|ref|YP_004036423.1| 396 ERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQ 434
                                       445555566666666777776666666666555554444 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   4.1       1.1   3.5e+02     175     268 ..     161     252 ..     155     298 .. 0.62
   2 ?   11.4   3.6   0.00058      0.19     171     283 ..     326     439 ..     297     485 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.1
                           DUF4559 175 rLledlk.tvpeleeaeeaieellkilkqefeislkeddevrvltdvllslqklkeleeellkedatkldelvlrae 250
                                       +L+ed      + e++++ ++e++ +l+q  e +l++++e+ ++t+vl+   +l+++  e+ ++ + + ++lv + e
  gi|313126153|ref|YP_004036423.1| 161 ELVEDKTeAQRQQEATHTLVNEVTSTLEQIGEGNLDARAELGSETEVLE--DELLNIVAEVNRT-GDRFESLVDEVE 234
                                       5666654344455666777889999999999999999999999999975..5788887776666.779999999888 PP

                           DUF4559 251 eqkiskeellkelqvlke 268
                                       ++     +++++ +  + 
  gi|313126153|ref|YP_004036423.1| 235 SHATDVSNTITTANDAAS 252
                                       888777777555443332 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00058
                           DUF4559 171 kkilrLledlktvpeleeaeeaieellkilkqefeislkeddevrvltdvllslqklkeleeellkedat.kldelv 246
                                       + ++rL +d++++++++ +  +i ++++il  + +i++ +  e      v+ ++ k +  e++   e++t ++d++ 
  gi|313126153|ref|YP_004036423.1| 326 ESVKRLEDDMEEIGDVVGLISEIADRTNILALNANIEAARAGEAGEGFAVVAEEVKSLANETQSHTEQITeRIDRIQ 402
                                       67889999999**************************9995666666666666655555565555555655****** PP

                           DUF4559 247 lraeeqkiskeellkelqvlkeflnknkd.Lkenlked 283
                                       +ra+e+  + ee+ k++    + ++k    L+e+  + 
  gi|313126153|ref|YP_004036423.1| 403 SRADETVTLVEETHKDVGRADDAIDKTVSsLQEA-SDA 439
                                       *****99999999999999999999876657743.333 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.7       3.7   1.2e+03     204     227 ..     164     189 ..     155     197 .. 0.56
   2 ?   14.4   1.6   6.2e-05      0.02      80     139 ..     230     287 ..     199     332 .. 0.78
   3 ?    2.2   3.1      0.34   1.1e+02      85     139 ..     382     436 ..     375     462 .. 0.46

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.7
                        MscS_porin 204 qellnekRlaeaekav..aqteqlae 227
                                       +    ++R++ea  ++  + t++l++
  gi|313126153|ref|YP_004036423.1| 164 EDKTEAQRQQEATHTLvnEVTSTLEQ 189
                                       44455566666666655444444444 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.2e-05
                        MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnst 139
                                        +e e+  +++s+   +++ + +q++s+++e++ ++e ++  l++ + +++e+ +  +st
  gi|313126153|ref|YP_004036423.1| 230 VDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVAA--SST 287
                                       5789999999999999999999999999999999999999999999999999977..222 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.34
                        MscS_porin  85 qrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnst 139
                                       +  ++t+s+ ++ +e++  ++s++ e+ t  e+ ++    a  ++++  + L++ 
  gi|313126153|ref|YP_004036423.1| 382 SLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEA 436
                                       3334444444444444444444444444444444444444444444443333333 PP

>> LRRFIP  LRRFIP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   7.8   3.7e-05     0.012     117     287 ..     151     320 ..     146     335 .. 0.88
   2 ?   -0.6   1.9       2.3   7.4e+02     224     270 ..     372     418 ..     347     443 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                            LRRFIP 117 YevdlLkdkleeleeslaelqrelrekckelerlkrqlealkleldelkeklkqrdeLiedhglvlveeeatdge.. 191
                                       Y+ d L   +e +e+   e qr+ +  +  +++   +le++ +     +++l    e++ed+ l +v+e +  g+  
  gi|313126153|ref|YP_004036423.1| 151 YDGDELVAVVELVED-KTEAQRQQEATHTLVNEVTSTLEQIGEGNLDARAELGSETEVLEDELLNIVAEVNRTGDrf 226
                                       556666665555555.5799****************************************************99988 PP

                            LRRFIP 192 keeesssssksalvskeaaellesagegtldvrLkklaeekeeLleeveklkqqleeekskksssasseelegeeee 268
                                       ++ +++ +s+++ vs+    + + a  ++ d r  + +++ e +++++   ++ +ee   ++ + +s      ++  
  gi|313126153|ref|YP_004036423.1| 227 ESLVDEVESHATDVSNTITTANDAA--SQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVESAADRARDNIG 301
                                       8888888899999998888777766..9******************************9988888888877777777 PP

                            LRRFIP 269 ndleiqreanklisdyKfk 287
                                       ++l+  ++++k  +++K +
  gi|313126153|ref|YP_004036423.1| 302 SSLDWTVDTRKVTDEVKER 320
                                       77**************988 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.3
                            LRRFIP 224 rLkklaeekeeLleeveklkqqleeekskksssasseelegeeeend 270
                                           +aee ++L +e +   +q+ e+  + +s a+++ +  ee+++d
  gi|313126153|ref|YP_004036423.1| 372 GFAVVAEEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKD 418
                                       55556788888888888888888888777777766666555555554 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   8.6      0.23        73      31     136 ..     156     268 ..     154     298 .. 0.67
   2 ?    1.1   2.1       1.3   4.2e+02      48     107 ..     261     337 ..     253     352 .. 0.70
   3 ?   11.2   4.4     0.001      0.33      43     142 ..     382     480 ..     376     494 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.23
                     Jnk-SapK_ap_N  31 vVkvLElLeslasrneeeeaeleelreeleqLeteyerekelrkrae.........eeleeiedqweeerkelqekv 98 
                                       +V+v El+e  ++ ++++ea+  ++ e +++Le+  e    +  rae         +el++i  ++++    +++ v
  gi|313126153|ref|YP_004036423.1| 156 LVAVVELVEDKTEAQRQQEATHTLVNEVTSTLEQIGEGNLDA--RAElgsetevleDELLNIVAEVNRTGDRFESLV 230
                                       689999999988888888888777777777766633333333..333333333666777777777777777777777 PP

                     Jnk-SapK_ap_N  99 eqleeenrelelkaknaadqlsrleekeaelkkeyskl 136
                                        ++e++   ++  +  a+d +s++ ++ +e++k  ++ 
  gi|313126153|ref|YP_004036423.1| 231 DEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAV 268
                                       77777777777777777777777777777776665554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.3
                     Jnk-SapK_ap_N  48 eeaeleelreeleqLeteyerekelrkrae.................eeleeiedqweeerkelqekveqleeenre 107
                                       +   le +r++l ++    e+ ++ + + e                  +  ++ d+++e+  +l e v++le++++e
  gi|313126153|ref|YP_004036423.1| 261 QRKALEAVRDDLASFSAAMEEVAASSTEVEsaadrardnigssldwtVDTRKVTDEVKERSDDLLESVKRLEDDMEE 337
                                       45556666666666666666666666666666666666666666666777888899999999999999999988776 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.001
                     Jnk-SapK_ap_N  43 srneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadql 119
                                       s  +e ++  e+  e +++++++ ++   l +++ +++ +++d++++  + lqe+   +ee  + ++  +++++dq+
  gi|313126153|ref|YP_004036423.1| 382 SLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELSRASDDQA 458
                                       44567788999*****************************************************99999999999*9 PP

                     Jnk-SapK_ap_N 120 srleekeaelkkeysklherete 142
                                       +++e   + + ++ s    + +e
  gi|313126153|ref|YP_004036423.1| 459 ESVEGVVSAV-EDVSDDAAEIEE 480
                                       9999877766.333333344444 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.4     0.051        17      10      77 ..     161     228 ..     158     249 .. 0.82
   2 ?    6.2   0.7     0.048        16      25      79 ..     233     290 ..     227     305 .. 0.65
   3 ?    1.0   0.0       2.1   6.7e+02      10      39 ..     309     338 ..     306     366 .. 0.75
   4 ?    0.9   0.8       2.1     7e+02      33      61 ..     377     405 ..     374     417 .. 0.74
   5 ?    5.7   0.6      0.07        23      19      90 ..     413     483 ..     405     508 .] 0.59

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.051
                    HIP1_clath_bdg  10 evtkqlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLes 77 
                                       e++   + a+ +qe  ++  +e++ +le++ e +    +e  +e+e L+ el +  ae++r     es
  gi|313126153|ref|YP_004036423.1| 161 ELVEDKTEAQRQQEATHTLVNEVTSTLEQIGEGNLDARAELGSETEVLEDELLNIVAEVNRTGDRFES 228
                                       56777899**********************************************99999876554443 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.048
                    HIP1_clath_bdg  25 verekkeleeelerlk...eeaerkleeqkeelekLkreleakraelarlkssLesse 79 
                                       ve    ++++++  ++   ++ ++++ eq++ le+++ +l++ +a ++++ +s ++ e
  gi|313126153|ref|YP_004036423.1| 233 VESHATDVSNTITTANdaaSQIDSRVTEQRKALEAVRDDLASFSAAMEEVAASSTEVE 290
                                       5555555555554444000455667789999999999999888877777766654444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 2.1
                    HIP1_clath_bdg  10 evtkqlsvarqaqeeverekkeleeelerl 39 
                                       ++ k     ++  +++    k+le+++e++
  gi|313126153|ref|YP_004036423.1| 309 DTRKVTDEVKERSDDLLESVKRLEDDMEEI 338
                                       555666666667777777777777777765 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 2.1
                    HIP1_clath_bdg  33 eeelerlkeeaerkleeqkeelekLkrel 61 
                                       +ee+++l +e+++++e+ +e ++++++  
  gi|313126153|ref|YP_004036423.1| 377 AEEVKSLANETQSHTEQITERIDRIQSRA 405
                                       67888888888888888888888887654 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.07
                    HIP1_clath_bdg  19 rqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqla 90 
                                        +++++v r+ + +++++ +l+e +   +ee +  + +L r   ++ + ++ + s++e+     ++++++++
  gi|313126153|ref|YP_004036423.1| 413 EETHKDVGRADDAIDKTVSSLQEAS-DAVEEAADGVSELSRASDDQAESVEGVVSAVEDVSDDAAEIEESVD 483
                                       5666666666666666666665443.3455555556666666666666666666666665555555554443 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2       1.6   5.3e+02      22      69 ..     232     279 ..     219     296 .. 0.63
   2 ?   -1.2   0.0       8.3   2.7e+03      44      58 ..     324     338 ..     272     354 .. 0.57
   3 ?    9.0   1.1    0.0055       1.8      15     114 ..     382     488 ..     374     494 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.6
                           Goodbye  22 kelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggia 69 
                                       +  s   d+++ i  ++d+ ++ +++  + ++al+ +   +  ++   
  gi|313126153|ref|YP_004036423.1| 232 EVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAM 279
                                       444566788888888888888888666666666666555555554444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 8.3
                           Goodbye  44 frekkeklkealkki 58 
                                         e+ ++l++ +++i
  gi|313126153|ref|YP_004036423.1| 324 LLESVKRLEDDMEEI 338
                                       223333333333333 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0055
                           Goodbye  15 dlkdealkelssvedllkqieaekdkf....eefrekkeklkealkkilspiqllggiaaqgasma...FgPaslcf 84 
                                       +l++e++++ +++ + +++i++++d++    ee +++  ++ +a+ k++s +q  ++ + ++a  +     +++   
  gi|313126153|ref|YP_004036423.1| 382 SLANETQSHTEQITERIDRIQSRADETvtlvEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVselSRASDDQA 458
                                       5667888888899999999999988652222444589999******************9999998844344677777 PP

                           Goodbye  85 nAvsyLikaakkvseiydaieeLfeelsdf 114
                                        +v  ++ a ++vs+   +iee  +++  +
  gi|313126153|ref|YP_004036423.1| 459 ESVEGVVSAVEDVSDDAAEIEESVDDIVSV 488
                                       788888888888888777777766666555 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2       1.1   3.5e+02     118     158 ..     228     272 ..     162     276 .. 0.71
   2 ?    1.4   0.1      0.82   2.7e+02     104     136 ..     305     337 ..     279     356 .. 0.70
   3 ?    2.5   0.2      0.37   1.2e+02     106     150 ..     376     422 ..     366     431 .. 0.71
   4 ?    8.3   0.4    0.0064       2.1      89     162 ..     409     486 ..     394     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.1
                          Cauli_AT 118 nrikkleeetkklaekivte....kllkeevkdlderlseirdsl 158
                                       + ++++e +   +++ i t      ++++ v +  + l+ +rd+l
  gi|313126153|ref|YP_004036423.1| 228 SLVDEVESHATDVSNTITTAndaaSQIDSRVTEQRKALEAVRDDL 272
                                       356666666666666665531111567777778888888888776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.82
                          Cauli_AT 104 ekktklletLkeaqnrikkleeetkklaekivt 136
                                       + +++  ++  e+++r ++l e +k+l+++++ 
  gi|313126153|ref|YP_004036423.1| 305 DWTVDTRKVTDEVKERSDDLLESVKRLEDDMEE 337
                                       445555666667777777777777777776654 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.37
                          Cauli_AT 106 ktklletLk.eaqnrikkleeetkklaek.ivtekllkeevkdlder 150
                                        ++++++L  e+q++ +++ e++ +++++  +t  l++e+ kd+ + 
  gi|313126153|ref|YP_004036423.1| 376 VAEEVKSLAnETQSHTEQITERIDRIQSRaDETVTLVEETHKDVGRA 422
                                       56677777515666889999999999988667888888888887665 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0064
                          Cauli_AT  89 fkklkkifkeggedkekktklletLkeaqn....rikkleeetkklaekivtekllkeevkdlderlseirdslkai 161
                                        + +++  k++g   ++  k +++L+ea++      + ++e ++  +++ ++ + + + v d+ +   ei++s+ +i
  gi|313126153|ref|YP_004036423.1| 409 VTLVEETHKDVGRADDAIDKTVSSLQEASDaveeAADGVSELSRASDDQAESVEGVVSAVEDVSDDAAEIEESVDDI 485
                                       567788899*********************5554455677777777888999999999*****************99 PP

                          Cauli_AT 162 i 162
                                       +
  gi|313126153|ref|YP_004036423.1| 486 V 486
                                       8 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.0      0.23        75      33     104 ..     195     266 ..     167     281 .. 0.76
   2 ?    4.8   1.3      0.12        39      28      93 ..     260     325 ..     224     337 .. 0.47
   3 ?    1.7   0.0       1.1   3.5e+02      36      65 ..     321     350 ..     303     365 .. 0.81
   4 ?    5.5   1.4     0.073        24      34      96 ..     378     444 ..     356     450 .. 0.64
   5 ?   -0.1   0.1       3.9   1.3e+03      27      57 ..     455     485 ..     434     496 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  33 leevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkLe 104
                                       l++  +l  + + le+el +   +v++  +  e+l+de +s + ++++++   n++  ++ +++ e++++Le
  gi|313126153|ref|YP_004036423.1| 195 LDARAELGSETEVLEDELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALE 266
                                       555555666777788888888888888888888888888888888888888888888888888888888887 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.12
                                       SCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  28 dlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLk 93 
                                       +  k le+v++ l  + a ++e+aa  ++v++  + a++ + ++ + + ++++ ++e+ er ++L+
  gi|313126153|ref|YP_004036423.1| 260 EQRKALEAVRDDLASFSAAMEEVAASSTEVESAADRARDNIGSSLDWTVDTRKVTDEVKERSDDLL 325
                                       223445555555555555555555555555555555555544444444444444444444444444 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  36 vqallkkhkaleaelaaqqervkalnelae 65 
                                         +ll+  k+le+++++  + v  + e+a+
  gi|313126153|ref|YP_004036423.1| 321 SDDLLESVKRLEDDMEEIGDVVGLISEIAD 350
                                       567899999999999999998888888776 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.073
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTH....HHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  34 eevqallkkhkaleaelaaqqervkalnelaeklldeghsas....eeieerleelnerWeeLkela 96 
                                       eev++l ++ + + ++++++ +r+++  +    l++e h++     ++i ++++ l+e+ ++++e+a
  gi|313126153|ref|YP_004036423.1| 378 EEVKSLANETQSHTEQITERIDRIQSRADETVTLVEETHKDVgradDAIDKTVSSLQEASDAVEEAA 444
                                       5666666666666666666666666666555555444433333333777777777777766666665 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 3.9
                                       SSCSSSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  27 edlgkdleevqallkkhkaleaelaaqqerv 57 
                                       +d ++++e+v + +++  +  ae+++  + +
  gi|313126153|ref|YP_004036423.1| 455 DDQAESVEGVVSAVEDVSDDAAEIEESVDDI 485
                                       3334444444444444444444444433333 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       4.9   1.6e+03      82     115 ..     160     193 ..     154     201 .. 0.74
   2 ?    2.3   0.6      0.44   1.4e+02      37     120 ..     207     290 ..     204     293 .. 0.87
   3 ?    6.5   0.1     0.023       7.6      57     117 ..     395     455 ..     375     468 .. 0.85
   4 ?   -0.4   0.0       2.9   9.6e+02      73     102 ..     478     506 ..     457     508 .] 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.9
                           DUF1759  82 mklpslkeedasqlrrivdavneivralealgee 115
                                       ++l + k+e ++q +++   vne+  +le++ge 
  gi|313126153|ref|YP_004036423.1| 160 VELVEDKTEAQRQQEATHTLVNEVTSTLEQIGEG 193
                                       4555556677777778888899999999999985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.44
                           DUF1759  37 lLkgeAanvvahlalseenYeaaveaLkkrYdnkrkiirellnelmklpslkeedasqlrrivdavneivralealg 113
                                       +L++e  n+va ++ +++ +e+ v+  ++      + i+   ++  +++s  +e+ + l+++ d +     a+e+++
  gi|313126153|ref|YP_004036423.1| 207 VLEDELLNIVAEVNRTGDRFESLVDEVESHATDVSNTITTANDAASQIDSRVTEQRKALEAVRDDLASFSAAMEEVA 283
                                       68899999999999999999999999999999999999999999999999999999999999999999999999988 PP

                           DUF1759 114 eeadkyd 120
                                           +++
  gi|313126153|ref|YP_004036423.1| 284 ASSTEVE 290
                                       8777666 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.023
                           DUF1759  57 eaaveaLkkrYdnkrkiirellnelmklpslkeedasqlrrivdavneivralealgeead 117
                                          ++++++r d++  +++e ++ + + ++   + +s l++ +dav+e   ++ +l++  d
  gi|313126153|ref|YP_004036423.1| 395 TERIDRIQSRADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSELSRASD 455
                                       5568999*****************************************9999988887766 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.9
                           DUF1759  73 iirellnelmklpslkeedasqlrrivdav 102
                                       i +e ++ ++++ ++++++a +l +++d++
  gi|313126153|ref|YP_004036423.1| 478 I-EESVDDIVSVTQTQRDSAGELGTMIDGL 506
                                       4.5668999999999999999999999986 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.9      0.15        48      10      74 ..     158     224 ..     150     240 .. 0.63
   2 ?    5.7   1.6     0.074        24       6      69 ..     259     331 ..     224     351 .. 0.67
   3 ?    1.9   0.7       1.1   3.4e+02      24      71 ..     349     396 ..     319     404 .. 0.54
   4 ?    7.1   0.9     0.026       8.4       7      71 ..     404     470 ..     401     500 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.15
                           DUF2203  10 alLpllkelleelralrkeleeleeeleeakaeaekse...aaeleaeleeleaeieelveeieelGv 74 
                                       a++ l+++++e+ r +++  ++l++e++++ ++  + +   +ael +e e le+e+ ++v+e++++G 
  gi|313126153|ref|YP_004036423.1| 158 AVVELVEDKTEAQR-QQEATHTLVNEVTSTLEQIGEGNldaRAELGSETEVLEDELLNIVAEVNRTGD 224
                                       45555555555444.33333444444444333333333555889999999999999999999999885 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.074
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekse.........aaeleaeleeleaeieelveei 69 
                                        e ++ L  +++ l+ + a+ +e++  ++e+e+a ++a+ +           ++   e++e ++ + e v+++
  gi|313126153|ref|YP_004036423.1| 259 TEQRKALEAVRDDLASFSAAMEEVAASSTEVESAADRARDNIgssldwtvdTRKVTDEVKERSDDLLESVKRL 331
                                       4556777777777777777777777777777777777654447778887763444444444444444444333 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1.1
                           DUF2203  24 alrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeiee 71 
                                       a r+++  l +++e+a+a ++ +++a  ++e+++l++e ++++e+i+e
  gi|313126153|ref|YP_004036423.1| 349 ADRTNILALNANIEAARAGEAGEGFAVVAEEVKSLANETQSHTEQITE 396
                                       344555555556666666655555555555555555555555555543 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.026
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeiee 71 
                                        A ++++l++e+ +++ ++ + + +++++l+ea+++ e+ +   +el ++ +  ++++e +v+ +e+
  gi|313126153|ref|YP_004036423.1| 404 RADETVTLVEETHKDVGRADDAIDKTVSSLQEASDAVEEAAdgVSELSRASDDQAESVEGVVSAVED 470
                                       58999999999******99999999999999999998776567555555555555666666555554 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.041        13       2      32 ..     230     260 ..     229     272 .. 0.92
   2 ?    0.7   0.7       2.2     7e+02      10      19 ..     322     331 ..     263     347 .. 0.67
   3 ?    0.3   0.3       2.9   9.3e+02      16      37 ..     384     405 ..     378     414 .. 0.74
   4 ?    1.6   0.1       1.1   3.7e+02       3      40 ..     413     450 ..     411     452 .. 0.81
   5 ?    6.5   0.5     0.035        11      15      43 ..     460     488 ..     447     490 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.041
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksvee 32 
                                       +de+E+   ++s +++t+ +  +++ + v+e
  gi|313126153|ref|YP_004036423.1| 230 VDEVESHATDVSNTITTANDAASQIDSRVTE 260
                                       89************************99987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.2
                         FlaC_arch  10 sklsteletv 19 
                                       ++l  +++ +
  gi|313126153|ref|YP_004036423.1| 322 DDLLESVKRL 331
                                       2222233333 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.9
                         FlaC_arch  16 letvkkeneelsksveelkenV 37 
                                        +  ++  e++ + +++++ + 
  gi|313126153|ref|YP_004036423.1| 384 ANETQSHTEQITERIDRIQSRA 405
                                       5667889999999999998765 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 1.1
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       +e  +++++ +  ++   ++++e s+ vee  + V +l
  gi|313126153|ref|YP_004036423.1| 413 EETHKDVGRADDAIDKTVSSLQEASDAVEEAADGVSEL 450
                                       66677888899999999999999999999988877665 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.035
                         FlaC_arch  15 eletvkkeneelsksveelkenVkdllsL 43 
                                       ++e v +  e++s++  e++e+V d++s+
  gi|313126153|ref|YP_004036423.1| 460 SVEGVVSAVEDVSDDAAEIEESVDDIVSV 488
                                       78889999*****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1751  (0.097663); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                        96  (0.00535445); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              55  [number of targets reported over threshold]
# CPU time: 1.43u 0.41s 00:00:01.84 Elapsed: 00:00:00.63
# Mc/sec: 2443.53
//
Query:       gi|313126154|ref|YP_004036424.1|  [L=399]
Description: small-conductance mechanosensitive channel [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-43  148.9   0.1    2.4e-43  148.1   0.1    1.4  1  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.1   1.4e-47   2.4e-43       3     206 .]     164     363 ..     162     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 1.4e-47
                                       HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedi 79 
                                       +l +++++ ++l++l ++  +v++ll+++G+lg+++g+a+++++ +++aG++l+f++pf+iGD+vei + eG+V d+
  gi|313126154|ref|YP_004036424.1| 164 VLQLVMLTAVTLATLAVWDAEVGNLLVGAGFLGIVVGMAARQTLGSFIAGFVLMFSRPFEIGDWVEIDGEEGIVSDV 240
                                       5677888899999**************************************************************** PP

                                       -SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-E CS
                        MS_channel  80 glrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkel 156
                                       ++  t++r+fdg++v+ Pn  +++++i+N +r +++ r+ v++gv+y++d   l+ ++ +   al+    v + +++
  gi|313126154|ref|YP_004036424.1| 241 TIINTRLRNFDGETVVFPNDRVTNATITNRTR-RDQLRLSVDVGVDYETD---LDVAVGVAEAALEDVDVVADVPAP 313
                                       ********************************.*****************...8888888888888888888999** PP

                                       EEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 157 lvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       +v+ ++fgds++ ++vr+++k  +  ++ + ++++++ ik++++  gi+i
  gi|313126154|ref|YP_004036424.1| 314 NVLPTTFGDSAVGLKVRFWIKHPSAPRRAKANAAVVRAIKAAFDGRGIKI 363
                                       **********************9999*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 2135.13
//
Query:       gi|313126155|ref|YP_004036425.1|  [L=125]
Description: hypothetical protein Hbor_13990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-09   35.2   2.1    9.4e-09   34.7   2.1    1.3  1  SHOCT            Short C-terminal domain
    0.00016   21.7   3.5    0.00026   21.0   3.5    1.4  1  DUF1707          Domain of unknown function (DUF1707)
    0.00094   19.8   0.1     0.0013   19.4   0.1    1.2  1  DUF4936          Domain of unknown function (DUF4936)
  ------ inclusion threshold ------
      0.068   13.2   1.7       0.11   12.5   1.7    1.4  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        1.7    9.2   5.6         11    6.5   5.4    2.0  1  DUF202           Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   2.1   2.6e-12   9.4e-09       1      27 [.      70      96 ..      70      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.6e-12
                             SHOCT  1 daLekLkeLyarGeIteEEFeakKakL 27
                                      daL +L+e+yarGe+t++ Feak ++L
  gi|313126155|ref|YP_004036425.1| 70 DALSTLRERYARGELTDAQFEAKLERL 96
                                      89**********************998 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   3.5   7.3e-08   0.00026       4      46 ..      64     106 ..      62     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.3e-08
                           DUF1707   4 sdadReravelLrealaeGrLtldEfdeRleaalaArtrgeLa 46 
                                       sd+d ++a+  Lre +a+G Lt + f+  le+  + +t+++  
  gi|313126155|ref|YP_004036425.1|  64 SDDDSDDALSTLRERYARGELTDAQFEAKLERLVEVETLEDVV 106
                                       9**********************************99999875 PP

>> DUF4936  Domain of unknown function (DUF4936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   3.6e-07    0.0013      39      85 ..      63     111 ..      44     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.6e-07
                           DUF4936  39 lddpesqdglaTwMEvYedvdda.aafaatlaaavaasslaelie.geR 85 
                                       + d++s+d+l+T+ E Y+  +   a+f+a+l+++v+ + l++ +   eR
  gi|313126155|ref|YP_004036425.1|  63 TSDDDSDDALSTLRERYARGELTdAQFEAKLERLVEVETLEDVVVtVER 111
                                       457779***********98665547****************99983344 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.7   3.2e-05      0.11      39      91 ..       4      54 ..       1      66 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.2e-05
                   Phage_holin_3_6 39 llgaagvlallalllllvalalalaalwlaalivaavllvlagvlalvglkkl 91
                                      ++ + g   + a++++l+a+ l++  l+ +a iv++ + vla+ la +++++ 
  gi|313126155|ref|YP_004036425.1|  4 MVSLRGPTWVAAAGFVLIAVGLGF--LATGAPIVGIGFCVLAVGLAGAAVRNH 54
                                      555555666677777777776666..788888999999999999998888865 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.4    0.0031        11      22      65 ..      15      57 ..       8      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0031
                            DUF202 22 alglallrffltgepsalgkilglilivlgiltllvglvrylrr 65
                                      a+g++l+++ l +  +  + i+g+++ vl++ +++ +++++ ++
  gi|313126155|ref|YP_004036425.1| 15 AAGFVLIAVGLGFLATG-APIVGIGFCVLAVGLAGAAVRNHDET 57
                                      55666666544444444.7899**************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 840.23
//
Query:       gi|313126156|ref|YP_004036426.1|  [L=586]
Description: histone acetyltransferase, elp3 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-25   89.0   0.0    1.5e-24   87.3   0.0    1.9  2  Radical_SAM      Radical SAM superfamily
    3.5e-24   84.6   0.1    6.3e-24   83.8   0.1    1.4  1  Radical_SAM_C    Radical_SAM C-terminal domain
    1.6e-09   38.1   0.1    3.5e-09   36.9   0.1    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.6e-05   24.8   0.1    3.7e-05   23.6   0.1    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.045   14.2   0.1      0.089   13.2   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.0   4.2e-28   1.5e-24       5     164 ..     128     347 ..     124     350 .. 0.95
   2 ?   -3.7   0.0       3.9   1.4e+04      29      52 ..     459     482 ..     455     486 .. 0.76

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 4.2e-28
                                       SEESS-.-TTTSCCTT..................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTT CS
                                       xxxxxx.xxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlr.CsfCarpet..................vrregrgrslsveeileevkelkaekgvkevilgggepllypd 62 
                                       + C+++ C +C+ +                    + ++++  + +v   le+++ + +  ++ e+il+gg+ +++++
  gi|313126156|ref|YP_004036426.1| 128 HMCPHGkCLYCPGGPAsefsssqsytghepaaarGVQNDYDPYGQVTLRLEQLRHIGHPVDKVELILMGGTMTARSH 204
                                       6798888***************************999*******************99999***************9 PP

                                       HHHHHHHHHHTC..........................................CCTEEEEEEECSSCHGHHHHHHH CS
                                       xxxxxxxxxxxx..........................................xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  63 fvellerlakla..........................................vpgiritvetngtlpdeeklerl 97 
                                        +++++  ++l+                                          v++i +t+et + + d+e++ r+
  gi|313126156|ref|YP_004036426.1| 205 DYQEWFVKRALEamndydldsdpqpaedqsfkpdpedvefryledviaenetadVRNIGTTFETKPDWCDPEQINRM 281
                                       9999999999999**************************************9999999999999999999******* PP

                                       HHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  98 lelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                                       l+lg + v++g++++ ++ + + m+rgh++++ l+a ++lr++ +k+ +++++g pG ++e+ +e +
  gi|313126156|ref|YP_004036426.1| 282 LDLGATKVEVGVQTTYER-INREMHRGHGVQASLDANRRLRDSAFKVGFHMMPGQPGMTKEMCVEDF 347
                                       ******************.******************************************987765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHHHHHTTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  29 lsveeileevkelkaekgvkevil 52 
                                        ++e+++ +v+ + a  g++++i+
  gi|313126156|ref|YP_004036426.1| 459 PDPERVELQVETYEAAEGTEHFIS 482
                                       578999999999976666888875 PP

>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.1   1.8e-27   6.3e-24       1      80 [.     358     437 ..     358     439 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.8e-27
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd +K+yp+lv+++T  ++++++ ey+pl+ ee+ d+va+++ ++p+ +r++R+++dip + + ag+w++nlr+l+e
  gi|313126156|ref|YP_004036426.1| 358 PDYLKIYPTLVVRDTITYDMWRRDEYEPLNNEEAADVVAEVMGMIPKYTRLQRVQRDIPADFIDAGVWKSNLRQLAE 434
                                       89**************************************************************************9 PP

                     Radical_SAM_C  78 krl 80 
                                       +r 
  gi|313126156|ref|YP_004036426.1| 435 QRA 437
                                       986 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   9.6e-13   3.5e-09      31     117 .]     474     575 ..     443     575 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 9.6e-13
                                       TTC.EEEEEEET.TE..EEEEEEEEEEET....TSTTEEEEEEEEE.........SGGGTTSSHHHHHHHHHHHHHH CS
                    Acetyltransf_1  31 eae.gllvaeed.ge..liGfisllkipd....ekggvayieslaV.........speyrgkGlGsaLlealeerar 90 
                                        ++ ++++  ed  e  liGf++l+   d    e ++ a +++l+V         + ++++kG+G++Lle++ee+ar
  gi|313126156|ref|YP_004036426.1| 474 AEGtEHFISFEDpAEnlLIGFCRLRFPHDpvrrELENAALVRELHVygsevglggDGDWQHKGYGRRLLEHAEEIAR 550
                                       22224444333332246************99996678888888888888888899********************** PP

                                       HTTESEE.EEEEETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1  91 eegikki.vlaveedndaairlYek.lGF 117
                                       + g++k+ v+    +  + +++Y++ lG+
  gi|313126156|ref|YP_004036426.1| 551 DAGYEKMsVI----SGIGVREYYKQkLGY 575
                                       ******9455....89999****644997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1     1e-08   3.7e-05      61     111 ..     530     580 ..     529     585 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1e-08
                   Acetyltransf_10  61 peyrgqGigkaLleaveeeaekdgikleltvnaspyavpfY.eklGFkavge 111
                                        +++++G+g++Lle++ee a+++g++ +++v +    +++Y +klG+++ g+
  gi|313126156|ref|YP_004036426.1| 530 GDWQHKGYGRRLLEHAEEIARDAGYE-KMSVISGIGVREYYkQKLGYHQDGP 580
                                       589**********************9.**************558****9886 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.5e-05     0.089      35      54 ..     531     555 ..     478     577 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                                       GGTTSSHHHHHHHHTT.....SEEE CS
                    Acetyltransf_7  35 eyrgkGiGraLleaae.....kgii 54 
                                       +++ kG+Gr+Lle+ae      g++
  gi|313126156|ref|YP_004036426.1| 531 DWQHKGYGRRLLEHAEeiardAGYE 555
                                       89***********822234444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 3428.25
//
Query:       gi|313126157|ref|YP_004036427.1|  [L=199]
Description: hypothetical protein Hbor_14010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00055   19.7   0.6     0.0038   17.0   0.1    2.4  3  HTH_IclR        IclR helix-turn-helix domain
     0.0057   17.0   0.0     0.0082   16.4   0.0    1.2  1  Pro-kuma_activ  Pro-kumamolisin, activation domain
     0.0099   15.7   0.1     0.0099   15.7   0.1    1.9  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.097   12.7   0.0       0.19   11.8   0.0    1.5  1  HTH_45          Winged helix-turn-helix
       0.17   11.8   0.0       0.31   10.9   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.1e-06    0.0038      23      51 ..      62      90 ..      54      91 .. 0.89
   2 ?    0.2   0.0      0.18   6.6e+02       1      18 [.     116     133 ..     116     146 .. 0.82
   3 ?   -3.7   0.0       3.1   1.1e+04       8      15 ..     159     166 ..     157     167 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 23 elArrtglpkStvhRlLqtLvelGyveqd 51
                                      ++ + +g++++t hRl++ Lve+G+ e+ 
  gi|313126157|ref|YP_004036427.1| 62 DVEDSLGVSRATSHRLTRWLVEEGLAERR 90
                                      666889********************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                                       HHHHHHHHHCT-CTTBSS CS
                          HTH_IclR   1 sldRalaiLdalaeapqe 18 
                                       +++R + +Ld++ e+ +e
  gi|313126157|ref|YP_004036427.1| 116 AAERLAPLLDCICETHRE 133
                                       6799999****9888776 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.1
                                       HHCT-CTT CS
                          HTH_IclR   8 iLdalaea 15 
                                        L++lae 
  gi|313126157|ref|YP_004036427.1| 159 FLELLAES 166
                                       47888875 PP

>> Pro-kuma_activ  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.3e-06    0.0082      43      85 ..      53      93 ..      49     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.3e-06
                    Pro-kuma_activ 43 nygkhltaeevaelfapseeaidaVrnwLessgiaasrhsdtk 85
                                       yg+ l++ +v++ ++ s+++++++++wL+++g+a +r  d+ 
  gi|313126157|ref|YP_004036427.1| 53 LYGQSLDRRDVEDSLGVSRATSHRLTRWLVEEGLAERR--DGT 93
                                      5**********************************999..444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       0.8   2.9e+03      41      59 ..      16      32 ..      12      35 .. 0.67
   2 !   15.7   0.1   2.8e-06    0.0099      10      56 ..      49      92 ..      41      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.8
                                      HHHHHHHTTSEEEEESSSS CS
                            MarR_2 41 ilkrLvaaGLverrpgpeD 59
                                      +l+ + ++ L++++ +  D
  gi|313126157|ref|YP_004036427.1| 16 LLRYAAERRLLREELD--D 32
                                      6777888888887733..4 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.8e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      vL  L+      l  +++++ lg+s+++ +r+ + Lv+ GL err+g
  gi|313126157|ref|YP_004036427.1| 49 VLETLYGQS---LDRRDVEDSLGVSRATSHRLTRWLVEEGLAERRDG 92
                                      666666666...78899***************************976 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.2e-05      0.19      42      74 ..      80     112 ..      70     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                            HTH_45  42 mLvekglikkskekYvlTekGlelleklkelee 74 
                                        Lve+gl + ++++++lT kG+ + ++l +l++
  gi|313126157|ref|YP_004036427.1|  80 WLVEEGLAERRDGTFSLTGKGEVYADELLRLDR 112
                                       699*******************99999887765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.8e-05      0.31      23      58 ..      58      93 ..      53     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.8e-05
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      ++ +++   lgv+r++  +  r L++ Gl er++g+
  gi|313126157|ref|YP_004036427.1| 58 LDRRDVEDSLGVSRATSHRLTRWLVEEGLAERRDGT 93
                                      66799***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1218.44
//
Query:       gi|313126158|ref|YP_004036428.1|  [L=122]
Description: hypothetical protein Hbor_14020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 731.61
//
Query:       gi|313126159|ref|YP_004036429.1|  [L=704]
Description: recj-like exonuclease with dnaj-type zn-finger domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-09   37.2   0.4    4.9e-09   36.1   0.4    1.7  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    3.8e-08   33.5   3.6    1.5e-07   31.7   0.0    3.4  4  S1               S1 RNA binding domain
  ------ inclusion threshold ------
      0.051   13.8   0.0       0.18   12.0   0.0    1.9  2  tRNA_anti_2      OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.4   8.1e-13   4.9e-09       1      73 [.     208     277 ..     208     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 8.1e-13
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveei 73 
                                       V+++G+v+s+  r++g+   +++rD+tg + + +f e+  + + ++ e d+vr  G+v+ r+++ l++  ee+
  gi|313126159|ref|YP_004036429.1| 208 VRIEGEVVST--RQTGGPTIFEIRDETGVVDCAAFVEAGVRAYPEVGESDIVRLDGEVEVRRDE-LQVETEEL 277
                                       89********..*************************************************999.99987776 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.4e-11   1.5e-07       4      72 ..      24      87 ..      21      90 .. 0.92
   2 ?   -3.6   0.0       2.5   1.5e+04      13      25 ..     232     244 ..     232     248 .. 0.79
   3 ?    0.3   0.1      0.15   8.9e+02      43      65 ..     272     294 ..     251     301 .. 0.71
   4 ?   -1.8   0.2      0.69   4.1e+03       5      16 ..     690     701 ..     688     703 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.4e-11
                                      TTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEE CS
                                S1  4 kgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriil 72
                                       g  ++GeV    ++G+fV+l  gv+g++++sel+r+     ++     Gd+v v+v +++++ + i+l
  gi|313126159|ref|YP_004036429.1| 24 PGRYYKGEVDGFAEFGVFVDLASGVTGLLHRSELDRR----LESLDWEAGDTVFVQVKNIRDNGN-IDL 87
                                      57889******************************99....6999***************99988.887 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.5
                                       EEEETTEEEEEET CS
                                S1  13 tsvtkgGafVelg 25 
                                       t v++ +afVe g
  gi|313126159|ref|YP_004036429.1| 232 TGVVDCAAFVEAG 244
                                       5688899***998 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.15
                                       ESCHHHCEETTEEEEEEEEEEET CS
                                S1  43 vedpdevlkvGdevkvkvlkvdk 65 
                                       ve ++ v  +G+e +++v+++d+
  gi|313126159|ref|YP_004036429.1| 272 VETEELVALEGEEADAVVQRLDD 294
                                       55666666677777777777665 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.69
                                       TCEEEEEEEEEE CS
                                S1   5 gevveGeVtsvt 16 
                                       +evv+++Vt  +
  gi|313126159|ref|YP_004036429.1| 690 DEVVDAVVTATV 701
                                       799999999876 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1   6.7e+03      50      77 ..      48      77 ..      24      78 .. 0.61
   2 ?   12.0   0.0   3.1e-05      0.18      13      79 ..     199     264 ..     194     277 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                       tRNA_anti_2 50 isavifrsra.aklk.ftledGmkVlvkgr 77
                                      +   + rs+  ++l+  + e G++V v+++
  gi|313126159|ref|YP_004036429.1| 48 VTGLLHRSELdRRLEsLDWEAGDTVFVQVK 77
                                      555555655533343455899999999875 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.1e-05
                       tRNA_anti_2  13 lleaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledG..mkVlvkgrls 79 
                                        l++++ +av ++Ge+ +  r++ g + f+++De+  ++++ f ++   +++ +e G  + V + g+++
  gi|313126159|ref|YP_004036429.1| 199 NLSDRVGDAVRIEGEVVST-RQTGGPTIFEIRDETGVVDCAAFVEAG--VRAYPEVGesDIVRLDGEVE 264
                                       455677889**********.66799******************8554..34445444004555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 4707.29
//
Query:       gi|313126160|ref|YP_004036430.1|  [L=201]
Description: hypothetical protein Hbor_14040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   47.6  16.7    2.1e-12   47.1  16.7    1.2  1  Yip1      Yip1 domain
  ------ inclusion threshold ------
      0.048   13.5   1.6        2.4    8.1   0.2    2.5  2  DUF2631   Protein of unknown function (DUF2631)


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1  16.7   2.3e-16   2.1e-12       1     170 [.      26     180 ..      26     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.3e-16
                              Yip1   1 llldPrevfrrlkkeppilrapdlallllalltlllgllaslnlgqtlasgeevqgltlssllgaiiggylglllgl 77 
                                       +l++P ++fr     ++  +ap+l +++++++++  +l+a+  ++  +++   + g +ls+++g +++++l+ ++ l
  gi|313126160|ref|YP_004036430.1|  26 VLTRPQRFFRNGVSPGD--QAPGLVFAVVVAVAYTTVLFAF--VPARIPAL--AGGQALSAFVGLAAVALLLAPAVL 96 
                                       799**************..9999999999999999999999..33333333..334455666666666666667777 PP

                              Yip1  78 lllalllhl..iakllggkgsfkqtlsvvgyallPlilgaliaillllllgtllllvgllaliWslvllylglkaah 152
                                        + a+l+++  ia +  ++g + +t++v++ya++P +++++++  l            l+++ +++vl+++gl+++h
  gi|313126160|ref|YP_004036430.1|  97 HITAALQTVflIATVWENRGGISETVQVIAYASAPCAVAGIPSPEL-----------RLVCAGYGAVLMFIGLSEVH 162
                                       77777777688999999*************************9976...........89****************** PP

                              Yip1 153 nlskkkallaalilllll 170
                                       ++s   a++a +++   l
  gi|313126160|ref|YP_004036430.1| 163 DVSIAHAAVAGAVPATFL 180
                                       **********99965544 PP

>> DUF2631  Protein of unknown function (DUF2631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2   0.00026       2.4      30      65 ..      93     128 ..      83     129 .. 0.92
   2 ?    4.1   0.1    0.0045        41      27      51 ..     163     187 ..     162     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00026
                           DUF2631  30 pkttriaGlisvlallamliGnhqGhvedifLigfA 65 
                                       p  ++i++ +  ++l+a + +n  G +e++ +i+ A
  gi|313126160|ref|YP_004036430.1|  93 PAVLHITAALQTVFLIATVWENRGGISETVQVIAYA 128
                                       67899************************9999887 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0045
                           DUF2631  27 gespkttriaGlisvlallamliGn 51 
                                       ++s   + +aG + + +l+++++G 
  gi|313126160|ref|YP_004036430.1| 163 DVSIAHAAVAGAVPATFLFGYVFGG 187
                                       56667789***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1308.89
//
Query:       gi|313126161|ref|YP_004036431.1|  [L=195]
Description: thymidine kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-51  173.0   0.0    5.9e-51  172.8   0.0    1.0  1  TK        Thymidine kinase
  ------ inclusion threshold ------
      0.034   13.9   0.2      0.075   12.8   0.2    1.5  1  AAA_30    AAA domain
       0.23   11.5   1.5       0.48   10.5   1.5    1.5  1  DZR       Double zinc ribbon


Domain annotation for each model (and alignments):
>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8   0.0   9.8e-55   5.9e-51       1     177 []       8     190 ..       8     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 9.8e-55
                                TK   1 gsielilgpmfaGKsteLlrrvkryqlaekkvvvikaakdnRysegkvvthdgisleak..ksktssleeikeelee 75 
                                       g++e+i+g+mf+GK++eLlrr +r+++a ++v v+k+ +d+Ry+e+ v +h g   ea+   s+ +++ ++ ++l+ 
  gi|313126161|ref|YP_004036431.1|   8 GWVEVITGSMFSGKTEELLRRLRRAEIAGQEVAVFKPDIDDRYGETTVGSHAGSEWEAHvvASDGEEMWNLLDKLNG 84 
                                       689*******************************************************9444444455555555554 PP

                                TK  76 edvdvvlvDEaqFfeqdivelseklanegkivivagLdtdFerklFenilkllalaekvkklkavCmkCgkkAsftk 152
                                          dvv++DEa+Ff+ ++v+++e+la  g +v+v g d +F++++F+++ +l+a+ae v kl+a+C++Cg+ As ++
  gi|313126161|ref|YP_004036431.1|  85 --EDVVAIDEANFFSAELVDICEHLAADGRRVLVSGTDQTFRGEPFDPVPQLMAMAEYVDKLQAICSVCGEPASRNQ 159
                                       ..79************************************************************************* PP

                                TK 153 rln......kekeviliGgkekYvsvCrkcy 177
                                       rl       +e+  i++G++e+Y++ Cr+c+
  gi|313126161|ref|YP_004036431.1| 160 RLVdgepahAEGPTIVVGAEESYEARCRNCH 190
                                       **9999*99*********************7 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.2e-05     0.075      12     124 ..       2     119 ..       1     123 [. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                            AAA_30  12 alltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgk..aAkv.Laeelgi..eastiakllkrlk.g 82 
                                       +++t++ +v v+tG   +GKt  l    + +e ag++v+++ p       ++ ++ ++g   ea+ +a+  +++   
  gi|313126161|ref|YP_004036431.1|   2 HAITKSGWVEVITGSMFSGKTEELLRRLRRAEIAGQEVAVFKPDIDdrYGETtVGSHAGSewEAHVVASDGEEMWnL 78 
                                       55666668*************85544444456678899998886540033333444444222555555443332253 PP

                            AAA_30  83 rarlepgtllivDEagmvdtkqlaallkaaekagakvilvGD 124
                                         +l+ ++++ +DEa   +++ ++ + ++++++g +v++ G 
  gi|313126161|ref|YP_004036431.1|  79 LDKLNGEDVVAIDEANFFSAELVD-ICEHLAADGRRVLVSGT 119
                                       3468888***********987665.66666666999999885 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.5   8.1e-05      0.48      12      36 ..     145     191 ..     138     195 .] 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.1e-05
                               DZR  12 arfCseCgtklkavaa......................edrCpsCge 36 
                                       +  Cs Cg++ ++ ++                      e rC +C++
  gi|313126161|ref|YP_004036431.1| 145 QAICSVCGEPASRNQRlvdgepahaegptivvgaeesyEARCRNCHT 191
                                       678*******9877779999999**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1182.28
//
Query:       gi|313126162|ref|YP_004036432.1|  [L=199]
Description: flavoprotein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-32  112.7   0.0    1.6e-32  112.4   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    1.7e-09   37.7   0.0    2.3e-09   37.3   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.055   13.7   0.0      0.078   13.2   0.0    1.3  1  Flavodoxin_5  Flavodoxin domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   0.0   2.7e-36   1.6e-32       3     152 ..       6     143 ..       5     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 2.7e-36
                                       EEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEE CS
                           FMN_red   3 ilvisGSlrkgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliiv 79 
                                       +++++GSlr++s+tr+++e+a+  ++eag + e++dl+ ++lp   +d+d+     ++ d + ++e+i++ada+i++
  gi|313126162|ref|YP_004036432.1|   6 VVAVCGSLRDQSYTRRALEHALVGVREAGGTGEILDLRAYDLP--SLDADE----DEQGDSEVVVERIHEADAVILG 76 
                                       89*****************************************..999998....479999**************** PP

                                       EEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEETS CS
                           FMN_red  80 tPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavgk 152
                                       tP+Y+gsysg+lKn lD+++     +e+ gK v+l+av+gg      a  +lr+v++ l+a+v+p+ +va+++
  gi|313126162|ref|YP_004036432.1|  77 TPVYHGSYSGVLKNTLDYCG----FDEFDGKTVGLLAVAGG-GFPVTALDHLRSVCRALNAWVLPH-QVALPN 143
                                       *******************8....9**************99.55669999****************.999876 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   3.8e-13   2.3e-09       2     102 ..       5      94 ..       4     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3.8e-13
                                       EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTTCHHHHHHH.HHHHHC CS
                      Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeekpadveseq.ieklla 77 
                                       +++ + ++ r  +s +++++++++ ++++ag  + +++dL a  lp l++        +e+     +se  +e++ +
  gi|313126162|ref|YP_004036432.1|   5 HVVAVCGSLRD-QSYTRRALEHALVGVREAG-GTGEILDLRAYDLPSLDA--------DED--EQGDSEVvVERIHE 69 
                                       67888889998.7******************.9***************97........333..455666777***** PP

                                       SSEEEEEEE-BTTB--HHHHHHHHH CS
                      Flavodoxin_2  78 adaivlqfPlwwfgvPailKgwiDr 102
                                       ada++l++P++  +++ +lK+ +D+
  gi|313126162|ref|YP_004036432.1|  70 ADAVILGTPVYHGSYSGVLKNTLDY 94 
                                       ********************98886 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.078      36      63 ..      62      89 ..      34     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                      Flavodoxin_5 36 kesedlesydavvigasvyygkllpela 63
                                      +  e+++++dav++g++vy+g+ ++ l+
  gi|313126162|ref|YP_004036432.1| 62 VVVERIHEADAVILGTPVYHGSYSGVLK 89
                                      4678999***************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 1120.66
//
Query:       gi|313126163|ref|YP_004036433.1|  [L=112]
Description: hypothetical protein Hbor_14070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-09   38.0   0.0    2.1e-09   37.8   0.0    1.1  1  DrsE            DsrE/DsrF-like family
     0.0086   16.2   0.1      0.011   15.9   0.1    1.2  1  DsrH            DsrH like protein
  ------ inclusion threshold ------
       0.06   13.2   0.0      0.066   13.0   0.0    1.2  1  Cyclophil_like  Cyclophilin-like


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   3.4e-13   2.1e-09       3     116 ..       4     110 ..       2     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 3.4e-13
                                       EEEEE-S-TTTBSHHHHHHHHHHHHHTTT......-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-E CS
                              DrsE   3 vfilvtggpygseaarealelalaaaalg......hevsvffygdGvllllkgqtanpadeknlaellkalkeygvk 73 
                                       vf+l +    g+   + ++ la+++++lg       ev++   gd+++l+++     p     l++ ++al+   v+
  gi|313126163|ref|YP_004036433.1|   4 VFHLSS----GDV-DDWQHALANVNNLLGddtvemDEVALLANGDAIYLFVE---RSP-----LSADVRALDGD-VR 66 
                                       666666....555.555678899999999999********************...556.....9*******998.** PP

                                       EEEEHHHHHHTT--GGGE-.T--EEEE-HHHHHHHHHH-SEEEE CS
                              DrsE  74 lyvCgqaakargldededl.gvgvevsglgelaelqnegdrvit 116
                                         +C +++  r++ ++++l  v+ + sg+g+l +lq++g+++++
  gi|313126163|ref|YP_004036433.1|  67 CLACSNSLSGRNIPKSKLLsNVKSVSSGVGALTRLQHDGYAYLK 110
                                       **************88777999********************97 PP

>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.8e-06     0.011      20      73 ..      34      92 ..      14     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-06
                                      -..EEEE-GGGGGGGBTTBTTHHHHHTS..SSEEEEEHHHHHHTT-T.TSB-TTSEEE- CS
                              DsrH 20 D..avlLieDgVyaalkgsrllkalkea..svklyaLkeDleARGlt.eqlsegvkvid 73
                                      D  a+l  +D++y+ +++s+l++ +++    v++ a ++ l  R++  ++l+++vk ++
  gi|313126163|ref|YP_004036433.1| 34 DevALLANGDAIYLFVERSPLSADVRALdgDVRCLACSNSLSGRNIPkSKLLSNVKSVS 92
                                      244677789**************************************888*****9997 PP

>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05     0.066      57      87 ..      28      58 ..      12      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                                      ESSB-TTEEEEECCCTEEEEESS--TT-TTS CS
                    Cyclophil_like 57 kevveagdiaywppGkalclffGktPisdde 87
                                       ++ve+ ++a   +G a+ lf  ++P+s d 
  gi|313126163|ref|YP_004036433.1| 28 DDTVEMDEVALLANGDAIYLFVERSPLSADV 58
                                      689************************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 725.93
//
Query:       gi|313126164|ref|YP_004036434.1|  [L=408]
Description: hypothetical protein Hbor_14080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.1e-133  444.0  18.6   4.7e-133  443.9  18.6    1.0  1  ArsP_2    Putative, 10TM heavy-metal exporter


Domain annotation for each model (and alignments):
>> ArsP_2  Putative, 10TM heavy-metal exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  443.9  18.6  2.6e-137  4.7e-133       2     361 .]       7     397 ..       6     397 .. 0.97

  Alignments for each domain:
  == domain 1  score: 443.9 bits;  conditional E-value: 2.6e-137
                            ArsP_2   2 treilleslsDaflqvsafvavtlliysllslkkdeklvellekseklqvliaallGllPGCGGAivvitlyvrgkv 78 
                                       +++i++ s++D+f+qvsafva+t+l++s++++++ +++v++le++e++q++++allGl+PGCGGAi++++ly+rg+v
  gi|313126164|ref|YP_004036434.1|   7 AIDIFVFSVRDGFVQVSAFVAITVLLFSYIQYRTGGRIVSYLESHERMQPIAGALLGLTPGCGGAIIAMPLYIRGTV 83 
                                       6799************************************************************************* PP

                            ArsP_2  79 sFgavvAvLtatmGDaAFlllalkPkaalivlaialvvgivsGlvvnaih..................dedflrpkv 137
                                       sFg+vvA+L+at+GD+AF++lal+Pkaa +++a+a+v++i++G++++ ++                  d++f++++v
  gi|313126164|ref|YP_004036434.1|  84 SFGTVVAALAATAGDSAFVILALAPKAAAYAYAMAFVAAILFGYAIDIWGlgvgrvdravnrisrpmtDGGFTTTNV 160
                                       ***************************************************************************** PP

                            ArsP_2 138 aeeeee..dassaaaskaeek.......letklsklakvlWllllvpalivall..........lafqvdveallsl 195
                                       a+  ++  ++++ ++++++ +       l t++s+ ++vlW+ ++v++l++++l          l+f+ ++  l+  
  gi|313126164|ref|YP_004036434.1| 161 ADGGPSipNYEMDQSCHDHGHgtgddsgLLTTISHGVHVLWWGVAVAGLVAGVLylvrgapevpLEFAPTFFGLF-- 235
                                       **9999999999999999999999******************************888877666666666666666.. PP

                            ArsP_2 196 eeksiellgavlavlslllwaltreleeekevvsedekiksake.lqkaaqdtsfvtvWvivafllfElvvvltgvd 271
                                            +++g+v++++s++l++++r++ +e+e+ + +++++sa+e +q+aa++ts+vtvWvi+a+l++E+++v++++d
  gi|313126164|ref|YP_004036434.1| 236 -----TIAGLVGTTASFYLHFVGRRFIGEGEAGRIRDDFTSAYEtFQHAAMETSMVTVWVIAAYLIYEYSIVIFSID 307
                                       .....99************************************99******************************** PP

                            ArsP_2 272 laallaalgvlaplvgvliGllPGCgPqilvtslYleGaiPlsaqianaisnDGDALFPaialapkaAlvAtlYsai 348
                                       + a++aa+gvlap++g+l+Gl+PGC+Pqi+++++Y++G iP+sa++anais+DGDALFP++a+++kaA+vAt+Y++i
  gi|313126164|ref|YP_004036434.1| 308 IGAIAAAAGVLAPIGGALLGLIPGCAPQIVFAQVYAQGGIPFSALTANAISQDGDALFPLMAIDMKAAIVATIYTTI 384
                                       ***************************************************************************** PP

                            ArsP_2 349 PAlivgyayyfll 361
                                       PAlivg+++y ++
  gi|313126164|ref|YP_004036434.1| 385 PALIVGIVLYAVW 397
                                       **********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2416.59
//
Query:       gi|313126165|ref|YP_004036435.1|  [L=149]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-37  127.7   1.0    5.1e-37  127.5   1.0    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.026   14.1   0.0    1.2  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
       0.18   11.8   0.0        0.2   11.7   0.0    1.1  1  SIR4_SID  Sir4 SID domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.5   1.0   8.6e-41   5.1e-37       1     140 [.       1     141 [.       1     142 [. 0.87

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 8.6e-41
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaa 75 
                                       my+rIlV++Dgs+ s +A+++A++la++++a++++l+v+++++  +   ++ +++e   el +++++++    ++ a
  gi|313126165|ref|YP_004036435.1|   1 MYERILVPTDGSDLSSAAARHAFDLAQQYDATVHALYVVETDTG-WLTVSKNDVRETLRELGAEASKQAFrdVERIA 76 
                                       9**************************************98764.44444444444444444444444446889999 PP

                                       HCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  76 eaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       +  +++v+++v+eg p e il++ +e+d+dliV+G++g+sgl+r+l+GSv+++v+r a++pV++V
  gi|313126165|ref|YP_004036435.1|  77 ATTQAEVVTDVLEGTPEEQILQYTDENDIDLIVMGTHGHSGLERRLVGSVTNRVVRGADVPVMAV 141
                                       99*************************************************************98 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.4e-06     0.026      34      80 ..      22      68 ..       8      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-06
                          SMC_ScpB 34 leeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkktr 80
                                        +L+++y+++ ++l +ve++ g+  v+k++++e +++l  e +k+ 
  gi|313126165|ref|YP_004036435.1| 22 AFDLAQQYDATVHALYVVETDTGWLTVSKNDVRETLRELGAEASKQA 68
                                      4589**********************************998866665 PP

>> SIR4_SID  Sir4 SID domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.4e-05       0.2      52     126 ..      54     130 ..       3     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                          SIR4_SID  52 eaelvdsesssegseiedpeterkkldrelakevneklakkk..ayskstisdLiesgiaehsplesdpkvSvTNnI 126
                                        + l++  ++   ++  d+e      + e++ +v e + + +   y+ ++ +dLi  g   hs le + + SvTN +
  gi|313126165|ref|YP_004036435.1|  54 RETLRELGAEASKQAFRDVERIAATTQAEVVTDVLEGTPEEQilQYTDENDIDLIVMGTHGHSGLERRLVGSVTNRV 130
                                       444545555555555555555555556666666666665554225999999************************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 897.11
//
Query:       gi|313126166|ref|YP_004036436.1|  [L=219]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-19   69.6   0.0    2.3e-19   68.9   0.0    1.4  1  HTH_10          HTH DNA binding domain
    0.00038   20.1   0.3     0.0024   17.5   0.1    2.2  2  Sigma70_r4_2    Sigma-70, region 4
     0.0025   17.3   0.3      0.018   14.5   0.0    2.1  2  GerE            Bacterial regulatory proteins, luxR family
     0.0026   17.5   0.0     0.0079   15.9   0.0    1.8  1  HTH_38          Helix-turn-helix domain
      0.008   15.7   0.0      0.019   14.5   0.0    1.6  1  Sigma70_r4      Sigma-70, region 4
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.021   14.4   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.028   14.3   0.0      0.051   13.4   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
      0.032   14.1   0.1      0.079   12.9   0.1    1.6  1  MarR_2          MarR family
      0.044   14.0   0.0      0.089   13.0   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.049   13.4   0.0       0.11   12.3   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.052   13.6   0.0       0.11   12.6   0.0    1.6  1  HTH_20          Helix-turn-helix domain
      0.056   13.2   0.1       0.17   11.7   0.1    1.7  1  LexA_DNA_bind   LexA DNA binding domain
      0.079   13.1   0.0       0.15   12.2   0.0    1.5  1  HTH_28          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   1.7e-22   2.3e-19       1      52 [.     162     213 ..     162     214 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1.7e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd+q+ev+k+A+  GY+d PR+v+ +e+A el+ ++st+ ehLrkaes+ +
  gi|313126166|ref|YP_004036436.1| 162 LTDRQREVVKTAVSRGYYDIPRTVSQAEIAAELDCAPSTVAEHLRKAESRMM 213
                                       9************************************************987 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.59   8.2e+02      10      19 ..     161     170 ..     160     176 .. 0.87
   2 !   17.5   0.1   1.7e-06    0.0024      28      53 ..     186     211 ..     184     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.59
                                       TS-HHHHHHH CS
                      Sigma70_r4_2  10 eLperqreif 19 
                                       +L+ rqre++
  gi|313126166|ref|YP_004036436.1| 161 RLTDRQREVV 170
                                       7999****98 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.7e-06
                                       -HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArkk 53 
                                       s++EIA++l++ ++tV  +l++A  +
  gi|313126166|ref|YP_004036436.1| 186 SQAEIAAELDCAPSTVAEHLRKAESR 211
                                       89********************9766 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.43   5.9e+02       3      12 ..     162     171 ..     161     176 .. 0.83
   2 !   14.5   0.0   1.3e-05     0.018      20      45 ..     187     212 ..     184     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.43
                                       S-HHHHHHHH CS
                              GerE   3 LskRErevLr 12 
                                       L++R+rev +
  gi|313126166|ref|YP_004036436.1| 162 LTDRQREVVK 171
                                       9******976 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  20 nkeIAeelniSekTVkvhksnimkKL 45 
                                         eIA+el++++ TV  h++ + +++
  gi|313126166|ref|YP_004036436.1| 187 QAEIAAELDCAPSTVAEHLRKAESRM 212
                                       679****************9988877 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.8e-06    0.0079      22      42 ..     186     206 ..     161     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-06
                            HTH_38  22 slreIArrLgrspsTIsRElk 42 
                                       s++eIA +L+++psT++ +l+
  gi|313126166|ref|YP_004036436.1| 186 SQAEIAAELDCAPSTVAEHLR 206
                                       999*************98877 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.4e-05     0.019       4      44 ..     161     208 ..     160     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrA 44 
                                       +L++r+rev++           +  +++EI+++l+   ++V  ++++A
  gi|313126166|ref|YP_004036436.1| 161 RLTDRQREVVKTAVsrgyydiPRTVSQAEIAAELDCAPSTVAEHLRKA 208
                                       7***********9999998888999****************9999988 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.5e-05     0.021      18      43 ..     185     210 ..     182     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlkrLee 43 
                                        sq+e+A +l+  pstv ++l++ e+
  gi|313126166|ref|YP_004036436.1| 185 VSQAEIAAELDCAPSTVAEHLRKAES 210
                                       79********************9885 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.7e-05     0.051      20      38 ..     189     207 ..     182     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-05
                                       HHHHHHTS-HHHHHHHHHH CS
                             HTH_5  20 elaeelglsqstvShHLkk 38 
                                       e+a+el+  +stv +HL+k
  gi|313126166|ref|YP_004036436.1| 189 EIAAELDCAPSTVAEHLRK 207
                                       8****************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.7e-05     0.079      20      48 ..     183     211 ..     164     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                                       SEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  20 rdltvgelarrlglsksavsrilkrLvaa 48 
                                       r ++++e+a++l+  +s+v  +l++++++
  gi|313126166|ref|YP_004036436.1| 183 RTVSQAEIAAELDCAPSTVAEHLRKAESR 211
                                       4589*********************9985 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.4e-05     0.089      22      45 ..     184     207 ..     180     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.4e-05
                                       SB-HHHHHHHHTS-HHHHHHHHHH CS
                    Fe_dep_repress  22 vvktkdlaerLnvspssVsemlkk 45 
                                        v+++++a +L+ +ps+V e l+k
  gi|313126166|ref|YP_004036436.1| 184 TVSQAEIAAELDCAPSTVAEHLRK 207
                                       5899*****************999 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.3e-05      0.11      19      39 ..     186     206 ..     179     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.3e-05
                            HTH_23  19 svreIAreLgvsrrTvyrwlk 39 
                                       s++eIA+eL++ ++Tv   l+
  gi|313126166|ref|YP_004036436.1| 186 SQAEIAAELDCAPSTVAEHLR 206
                                       899*************84444 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.8e-05      0.11      24      47 ..     184     207 ..     157     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.8e-05
                                       TB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  24 gltaselaerldlskntlsyHLrv 47 
                                        ++ +e+a++ld++++t+  HLr+
  gi|313126166|ref|YP_004036436.1| 184 TVSQAEIAAELDCAPSTVAEHLRK 207
                                       56778*****************97 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012      0.17       3      49 ..     161     207 ..     159     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                       ---HHHHHHHHHHHHHHHHHSS....---HHHHHHHHTS-.HHHHHHHHHH CS
                     LexA_DNA_bind   3 kLTerQrevldlikasieetgy....pPsireiaralglkSpsaveehLka 49 
                                        LT+rQrev++     +++  y      s +eia +l  + ps+v+ehL++
  gi|313126166|ref|YP_004036436.1| 161 RLTDRQREVVKT---AVSRGYYdiprTVSQAEIAAELDCA-PSTVAEHLRK 207
                                       69*****99765...4433322321145779********9.********86 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.15      12      38 ..     184     210 ..     168     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                            HTH_28  12 GhsvreaArelgisrrtvyrWikryee 38 
                                        +s++e+A+el + ++tv   +++ e+
  gi|313126166|ref|YP_004036436.1| 184 TVSQAEIAAELDCAPSTVAEHLRKAES 210
                                       579*******************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1450.15
//
Query:       gi|313126167|ref|YP_004036437.1|  [L=271]
Description: nmra-like family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-21   76.0   1.4    5.4e-21   75.3   1.4    1.3  1  NAD_binding_10   NAD(P)H-binding
    4.2e-20   72.3   0.1    5.1e-20   72.0   0.1    1.1  1  NmrA             NmrA-like family
    8.8e-13   48.3   0.1    1.6e-12   47.4   0.1    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.3e-10   39.4   0.0    4.6e-10   39.0   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.3e-07   30.2   1.2    5.9e-07   28.9   0.7    1.9  2  RmlD_sub_bind    RmlD substrate binding domain
     0.0011   18.2   2.2      0.046   12.8   2.2    2.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
       0.01   15.3   0.5      0.032   13.7   0.5    1.7  1  adh_short        short chain dehydrogenase
      0.012   15.1   0.2      0.053   12.9   0.2    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.012   15.6   0.6      0.032   14.2   0.6    1.8  1  KR               KR domain
      0.034   14.7   0.1      0.092   13.3   0.1    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.05   13.7   0.2      0.084   13.0   0.2    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.14   11.9   0.8       0.22   11.3   0.8    1.4  1  DFP              DNA / pantothenate metabolism flavoprotein
       0.46    9.6   4.9         16    4.6   1.1    2.9  3  NAD_binding_4    Male sterility protein


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   1.4   3.9e-24   5.4e-21       1     146 [.       8     141 ..       8     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 3.9e-24
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                       GAtG  G +l ++l ++ gh+v+a  R+p   +    ++ +e v++d+ + + +++al+++d+V+ a+ + ++    
  gi|313126167|ref|YP_004036437.1|   8 GATGTLGTALQSRLTEA-GHTVRAASRSPPAET----TADVEWVTLDLAEGAGIQSALEDVDVVIHAATAPQGdtka 79 
                                       9****************.5*********98876....478****************************776663444 PP

                                       .HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE-CE CS
                    NAD_binding_10  74 .deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTivrpggL 146
                                        d +g++++v+aa eagv+ fv+ s +g++d            +  +y++ k+ ae+ +++s+l  Tivr + +
  gi|313126167|ref|YP_004036437.1|  80 vDVTGTERLVEAAMEAGVENFVYPSIVGIDD------------IPFSYYEHKHTAEATVETSDLPTTIVRATQF 141
                                       56666*************************5............4569***********************9876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.1   3.7e-23   5.1e-20       2     153 ..       5     150 ..       4     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 3.7e-23
                                       EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG... CS
                              NmrA   2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy... 75 
                                       lv+GaTG +G ++ + l++agh+vra  R +  e+ +      ve v  dl + + +++al++vdvv+ + ++    
  gi|313126167|ref|YP_004036437.1|   5 LVTGATGTLGTALQSRLTEAGHTVRAASRSPPAETTA-----DVEWVTLDLAEGAGIQSALEDVDVVIHAATAPqgd 76 
                                       79*****************************999765.....5899**********************999976898 PP

                                       ..S-HHHHHHHHHHHHHHHS-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEEE-EEGGG-BS CS
                              NmrA  76 ..skeiedgkklvdAakeaGvkhfiySslgddndrsnaeepavphfdsKaeieeyvralgipytfvyagffmenfls 150
                                            +    +lv+Aa eaGv++f+y s++  +d+        + +++K++ e +v+ + +p+t+v+a+ f +++++
  gi|313126167|ref|YP_004036437.1|  77 tkAVDVTGTERLVEAAMEAGVENFVYPSIVGIDDIP------FSYYEHKHTAEATVETSDLPTTIVRATQFHSFVAA 147
                                       7777888899**********************9777......799***************************99988 PP

                                       SS- CS
                              NmrA 151 lla 153
                                       ll 
  gi|313126167|ref|YP_004036437.1| 148 LLD 150
                                       765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.1   1.1e-15   1.6e-12       2     114 ..       5     104 ..       4     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.1e-15
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       lVtGatG +G+al  +l e+g++v + +r + a   +  +d+e+v+ldl +++ ++ +++  ++d+vih+A      
  gi|313126167|ref|YP_004036437.1|   5 LVTGATGTLGTALQSRLTEAGHTVRAASRSPPA---ETTADVEWVTLDLAEGAGIQSALE--DVDVVIHAATA---- 72 
                                       8*****************************555...5556789*****************..89******653.... PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEE CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllfls 114
                                            + d+   ++ gt +l+eaa +agv+++++ s
  gi|313126167|ref|YP_004036437.1|  73 ----PQGDTKAVDVTGTERLVEAAMEAGVENFVYPS 104
                                       ....334555677********************976 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   3.3e-13   4.6e-10       1     117 [.       5     106 ..       5     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.3e-13
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtG++G lG al ++L ++++  +vr++    +++  e++   +v+  ++ D+ + + ++ ale+vdvvih a++ 
  gi|313126167|ref|YP_004036437.1|   5 LVTGATGTLGTALQSRLTEAGH--TVRAAS---RSPPAETT--ADVE-WVTLDLAEGAGIQSALEDVDVVIHAATAP 73 
                                       69*******************5..999864...33332334..4444.7799********************95543 PP

                         3Beta_HSD  78 dvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsa 117
                                              ++    v v GT+ ++ea+++agv+ +vY S +
  gi|313126167|ref|YP_004036437.1|  74 -------QGDTKAVDVTGTERLVEAAMEAGVENFVYPSIV 106
                                       .......3346789**********************9976 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.7   4.3e-10   5.9e-07       2      99 ..       3     103 ..       2     106 .. 0.87
   2 ?   -1.9   0.0         1   1.4e+03     127     149 ..     117     139 ..     111     189 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4.3e-10
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT............T--TTSHHHHHHHHHHH--SEEEE------HHH CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre............eldltdaeavaellkeakpdvvvnaAAytavDk 66 
                                       + lvtGa+G lG++L+ +l+e+g+ v a +r+            +ldl++ + ++++l++   dvv++aA   + D 
  gi|313126167|ref|YP_004036437.1|   3 RTLVTGATGTLGTALQSRLTEAGHTVRAASRSppaettadvewvTLDLAEGAGIQSALED--VDVVIHAATAPQGD- 76 
                                       689**************************999***************************9..899****9755444. PP

                                       HHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEE CS
                     RmlD_sub_bind  67 aEseeeaayavnaeavealAeaaaavgal.Lihv 99 
                                                av+++++e+l eaa ++g+  +++ 
  gi|313126167|ref|YP_004036437.1|  77 -------TKAVDVTGTERLVEAAMEAGVEnFVYP 103
                                       .......567888888888888888887435665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHH-SSEEEEEE- CS
                     RmlD_sub_bind 127 rtKlaGEqavlaagkkalivRts 149
                                       + K+  E +v+ +   ++ivR +
  gi|313126167|ref|YP_004036437.1| 117 EHKHTAEATVETSDLPTTIVRAT 139
                                       56777788888877777887754 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   2.2   3.3e-05     0.046       2     127 ..       5     104 ..       4     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                       lvtGa+G++G +l +++++   ++++  +r+  +  + + e                v  d+++ + +++ale  +v
  gi|313126167|ref|YP_004036437.1|   5 LVTGATGTLGTALQSRLTEA-GHTVRAASRSPPAETTADVE---------------WVTLDLAEGAGIQSALE--DV 63 
                                       78888888888887776654.45677777766554444433...............345699999********..** PP

                                       SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE CS
                   Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliS 127
                                       dvv+haA     P  ++++       v+gte ++eaa+eagv+++v+ S
  gi|313126167|ref|YP_004036437.1|  64 DVVIHAATA---PQGDTKA-----VDVTGTERLVEAAMEAGVENFVYPS 104
                                       *******75...5555444.....469*******************855 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   2.3e-05     0.032       4      86 ..       5      71 ..       3     100 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                                      EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                         adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82
                                      lvtGa++ +G a+  +l ++G +v +++rs+   +e+ +        +  +++D+++ + ++ ++e++       dv++
  gi|313126167|ref|YP_004036437.1|  5 LVTGATGTLGTALQSRLTEAGHTVRAASRSPP--AETTAD-------VEWVTLDLAEGAGIQSALEDV-------DVVI 67
                                      8*************************888854..223222.......556667776666666655554.......5555 PP

                                      E--- CS
                         adh_short 83 nNAG 86
                                      + A+
  gi|313126167|ref|YP_004036437.1| 68 HAAT 71
                                      5555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.9e-05     0.053       1     119 [.       5      98 ..       5     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG +G  G  l  +L e g++v    r   + +               + +++++  Dl + + ++++l++v  d
  gi|313126167|ref|YP_004036437.1|   5 LVTGATGTLGTALQSRLTEAGHTVRAASRSPPAET---------------TADVEWVTLDLAEGAGIQSALEDV--D 64 
                                       8*********************9976544433322...............234568899999999999999998..8 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT.. CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalgle 119
                                        v++ A              t  v+v+Gt rL+ea+ ++g+e
  gi|313126167|ref|YP_004036437.1|  65 VVIHAATAPQ--------GDTKAVDVTGTERLVEAAMEAGVE 98 
                                       8999554322........356678888999999998888876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   2.3e-05     0.032       4      65 ..       5      68 ..       3     108 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                                      EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHH...HHHHHHHTT-EEEE----TT-H CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedska...liaelealgaevevvaaDvsdk 65
                                      l+tG++G LG++l   l e g  ++   sRs++a+ +++    +++  e  g++  + ++Dv  +
  gi|313126167|ref|YP_004036437.1|  5 LVTGATGTLGTALQSRLTEAGH-TVRAASRSPPAETTADVewvTLDLAEGAGIQSALEDVDVVIH 68
                                      9******************996.688999995433332212222222333344444444554443 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.7e-05     0.092       7      68 ..      10      69 ..       6      80 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-05
                                      TSHHHHHHHHHHHHTTS-GGCEEEEEESSCC.CHHHHHHHHC.-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored  7 aGnmgealasgllaagaqpheivvansrnpe.kaeelaeelg.vkvtavdneeaaeeadvvvla 68
                                      +G +g al s+l++ag   h ++ a+sr+p  + ++  e +    +++   + a+e+ dvv+ a
  gi|313126167|ref|YP_004036437.1| 10 TGTLGTALQSRLTEAG---HTVR-AASRSPPaETTADVEWVTlDLAEGAGIQSALEDVDVVIHA 69
                                      8***************...****.5577775033333333334455555667777888888755 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   6.1e-05     0.084       2      79 ..       3      75 ..       2      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-05
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-.S-HHH CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDF.Ttpea 79
                                      + +v+Ga+G++G+++ + ++e +++++ aa  +++      +    ++  +l++a  + ++++le++dv+i   T+p++
  gi|313126167|ref|YP_004036437.1|  3 RTLVTGATGTLGTALQSRLTE-AGHTVRAASRSPP-----AETTADVEWVTLDLAEGAGIQSALEDVDVVIHAaTAPQG 75
                                      678*****************9.8888888888887.....223333444577888889999999999*99975256665 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8   0.00016      0.22      20      91 ..       2      71 ..       1      97 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                      TEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT-SEEEE--- CS
                               DFP 20 VRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealkeadivimaAA 91
                                      VR++   ++G+ G al +++ ++G++V+  s +   et + ve v  + ae   + +++al++ d+vi+aA 
  gi|313126167|ref|YP_004036437.1|  2 VRTLVTGATGTLGTALQSRLTEAGHTVRAASRSPPAETTADVEWVTLDLAEG--AGIQSALEDVDVVIHAAT 71
                                      999***************************9987777777888877777764..6788899999****9985 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.1     0.011        16       1      19 [.       6      24 ..       6      42 .. 0.83
   2 ?    4.2   0.1     0.015        21      81     126 ..      56      96 ..      37     106 .. 0.72
   3 ?    0.6   0.0      0.19   2.6e+02     173     203 ..     112     138 ..     107     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                                      EE-TTSHHHHHHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrt 19
                                      +TGaTG LG+ L  +L + 
  gi|313126167|ref|YP_004036437.1|  6 VTGATGTLGTALQSRLTEA 24
                                      7**********98888655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.015
                                       HHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS CS
                     NAD_binding_4  81 lqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklk 126
                                       +q   e vdv+ih a      +p  + ++v v+Gt++++e a +  
  gi|313126167|ref|YP_004036437.1|  56 IQSALEDVDVVIHAAT-----APQGDTKAVDVTGTERLVEAAMEAG 96 
                                       6677899******885.....5778889999999999999988654 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.19
                                       CCHHHHHHHHHHHHHHHHHHHH---EEEEEE CS
                     NAD_binding_4 173 pntYeqsKalaEklvrearrrsglpvvivRp 203
                                       p  Y   K+ aE  v++      lp++ivR 
  gi|313126167|ref|YP_004036437.1| 112 PFSYYEHKHTAEATVETSD----LPTTIVRA 138
                                       5678889999999998766....9*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1672.60
//
Query:       gi|313126168|ref|YP_004036438.1|  [L=315]
Description: A/G-specific adenine glycosylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-16   59.4   0.0      6e-16   58.8   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.3e-09   37.4   0.0    2.6e-09   36.5   0.0    1.5  1  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.75   10.2   3.2        1.6    9.1   3.2    1.6  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0     1e-19     6e-16       1     101 [.      52     185 ..      52     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1e-19
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTT.HHHHHHHHHHHHHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.......... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGf.yrrKakyikelArilv.......... 66 
                                       vs+++sqqt+  r+ +++e++ +++  pt+ dla+ad +++++ ++++ + y+++aky++e+ r+++          
  gi|313126168|ref|YP_004036438.1|  52 VSEVMSQQTQLGRVVEAWEDFLDEW--PTAADLAAADRSDVVSFWSGHSLgYNNRAKYLHEATRQVIeeydgefprs 126
                                       799*********************8..9*******************655467************************ PP

                                       .......................S-SSS--TTSHHHHHHHHHHTTSSSS...TTHHHHHHH CS
                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                           HhH-GPD  67 .......................gkpdvlivvDvhvrrilkrlrsikek...ktkkkvekk 101
                                                              +  +   vvD++v+r+l+r ++   +   ++++ v+++
  gi|313126168|ref|YP_004036438.1| 127 pdelselmgvgpytanavasfafN--NGDAVVDTNVKRVLHRAFAEIHNaddPDYETVANT 185
                                       *********************663..44599***********9876555334555555554 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   4.3e-13   2.6e-09       1      30 []     118     147 ..     118     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.3e-13
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                       +++g++p+s++eL +l GVGp+tA+a++s+
  gi|313126168|ref|YP_004036438.1| 118 EYDGEFPRSPDELSELMGVGPYTANAVASF 147
                                       599************************997 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.2   0.00027       1.6       4      17 .]     209     224 ..     209     224 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                     EndIII_4Fe-2S   4 RkPkC..eaCPLaDlC 17 
                                       +kP+C    CP++++C
  gi|313126168|ref|YP_004036438.1| 209 KKPRCdeASCPWREWC 224
                                       69************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2003.68
//
Query:       gi|313126169|ref|YP_004036439.1|  [L=437]
Description: 2-polyprenyl-6-methoxyphenol 4-hydroxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-44  151.4   0.0    4.4e-44  151.1   0.0    1.1  1  FAD_binding_3  FAD binding domain
    2.1e-08   33.7   0.2    0.00042   19.5   0.0    2.3  2  FAD_binding_2  FAD binding domain
    0.00029   20.1   0.0      0.001   18.4   0.0    1.9  2  Thi4           Thi4 family
    0.00031   20.9   0.2     0.0017   18.6   0.0    2.2  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00035   19.7   3.9      0.027   13.5   0.1    2.6  3  Lycopene_cycl  Lycopene cyclase protein
    0.00084   18.7   0.0     0.0016   17.7   0.0    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.005   16.0   0.0       0.01   14.9   0.0    1.5  1  GIDA           Glucose inhibited division protein A
     0.0055   16.3   1.8       0.11   12.1   0.2    2.4  2  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.024   13.7   0.0    1.5  2  SE             Squalene epoxidase
      0.014   15.9   0.3      0.038   14.6   0.1    1.8  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.033   13.8   0.0       0.06   13.0   0.0    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.037   12.7   0.0      0.056   12.1   0.0    1.2  1  HI0933_like    HI0933-like protein
      0.058   12.7   0.4        0.1   11.9   0.4    1.4  1  FAD_oxidored   FAD dependent oxidoreductase
      0.081   12.9   0.0       0.15   12.0   0.0    1.4  1  DUF2824        Protein of unknown function (DUF2824)
      0.097   11.9   0.0       0.15   11.3   0.0    1.2  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.12   11.7   0.1       0.21   10.9   0.1    1.2  1  ThiF           ThiF family
        0.2   10.1   0.0       0.41    9.1   0.0    1.4  2  GDI            GDP dissociation inhibitor


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1   0.0   4.2e-47   4.4e-44       2     347 ..      14     358 ..      13     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 4.2e-47
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyn 78 
                                       tdV+IVGaGpaG +l+ lL++ Gv+++l+e+++t  +++r+  +++  +++++q+ + +r+l+    +e ++++  +
  gi|313126169|ref|YP_004036439.1|  14 TDVVIVGAGPAGCVLGGLLARSGVETMLLERHATFDREFRGFAFQPSALRVFDQIDVLERVLDLP--HERISKFKLE 88 
                                       9*************************************************************999..6666655555 PP

                                       ECCCCCEEEEEHH.CHHCST-CEE--HHHHHHHHHHHHHHHT.EEETCSEEEECCE.ECCCCCCCEEEECCTTEEEE CS
                     FAD_binding_3  79 elsdtpkaradle.lesspervtvypqteleriLvehaeerg.lqvrfktevesle.qdeegvtaevrdketgeeet 152
                                         +++    +d + l   +  v  + q+ l+r+Lv++ae+   +++r +t v+ l+ +d++ v  ++ d+e +e+ t
  gi|313126169|ref|YP_004036439.1|  89 LYGRL-YTFVDFTtLSPPHDFVLSIDQPPLLRMLVDDAERFEtFEFRPSTVVRDLLvEDGSVVGVRASDREIDEDLT 164
                                       43555.556666634566777999***************************99875267777788888********* PP

                                       EEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEE..EEEECCETEEEEE CS
                     FAD_binding_3 153 vrakYlvGaDGgrStvrktlgiefegeetvyeagvldvlfdadlsdiveplvlilsaesrgv..mviPlentlerfy 227
                                       +r++ +vGaDG  Stvr+++gi+    +t+ e+ + +v  +a  +     + + ++++ + +   ++P  +    ++
  gi|313126169|ref|YP_004036439.1| 165 IRSRLVVGADGRYSTVRQAAGIDPGLVDTDFEVVWTKVPGSASHE-----IQARINEDGQLLyfGLGPDVQ--LGWL 234
                                       *********************995555555444444444333333.....566666666655667778777..7799 PP

                                       EEEECCE-GGGSCCCHHHHHHHHHHHHH.HTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHH CS
                     FAD_binding_3 228 vqvearaekeersekfteeevkarlrei.vgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqG 303
                                       +   ++++ +er  + ++++++a  +++  + ++  + +++ s ++v+   ++++ ++ + l+GDAaH+ +P gGqG
  gi|313126169|ref|YP_004036439.1| 235 IEKGTYPDLRERGIEAFRDRIAAVDPRLrPALAESLTGFDQCSLLDVSPGFTDEWVRDGLALIGDAAHVASPLGGQG 311
                                       9999********99999988876444431345556679*************************************** PP

                                       HHHHHHHHHHHHHHHHHHHT...TSS-GGGGHHHHHHHHHHHHHHHH CS
                     FAD_binding_3 304 lNtaiqDavnLawkLaavlk...GeAkeelLdtYeeerravaqavvd 347
                                         +aiqDa  L  +   +l+   G  + + L+ Y ++rr+ +++++d
  gi|313126169|ref|YP_004036439.1| 312 NALAIQDAAVLHAAVVPALRresGVLSASSLEPYATRRRPAVRRILD 358
                                       ***************999983334457899************99987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.3   9.2e-05     0.097       1      31 [.      15      45 ..      15      50 .. 0.92
   2 !   19.5   0.0     4e-07   0.00042     138     204 ..     112     179 ..      98     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.2e-05
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                                      Dv+++G+G AG++ +  +a+ G +++++e  
  gi|313126169|ref|YP_004036439.1| 15 DVVIVGAGPAGCVLGGLLARSGVETMLLERH 45
                                      9*************************99976 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4e-07
                                       .HHHHHHHHHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 138 vtghallarlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                       ++ + ll  lv+ a++ +  +f+++t +++L+vedg v+G+ ++++e  ++ +ir++ vv a g ++ 
  gi|313126169|ref|YP_004036439.1| 112 IDQPPLLRMLVDDAERFEtFEFRPSTVVRDLLVEDGSVVGVRASDREIDEDLTIRSRLVVGADGRYST 179
                                       6677899999999999999********************************************99986 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.5e-07     0.001      14      52 ..      10      47 ..       1      54 [. 0.87
   2 ?   -1.8   0.0       1.4   1.5e+03     153     167 ..     161     175 ..     133     187 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.5e-07
                                      HHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS CS
                              Thi4 14 kyaesDvvivGaGssGLtaayylakkpdlkvailersvs 52
                                      +  ++DvvivGaG++G   +  la++ ++++++ler+ +
  gi|313126169|ref|YP_004036439.1| 10 QTFQTDVVIVGAGPAGCVLGGLLARS-GVETMLLERHAT 47
                                      55689*********************.*********976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                                       B-EEEEEEEEEE--G CS
                              Thi4 153 DPlvirakvvvdatG 167
                                       + l+ir+++vv a G
  gi|313126169|ref|YP_004036439.1| 161 EDLTIRSRLVVGADG 175
                                       235666666666665 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.6e-06    0.0017       1      29 [.      18      46 ..      18      66 .. 0.96
   2 ?   -1.3   0.0       2.5   2.6e+03      23      42 ..     142     161 ..     139     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      IvGaG +G+v+  lLa+ g++  lle++ 
  gi|313126169|ref|YP_004036439.1| 18 IVGAGPAGCVLGGLLARSGVETMLLERHA 46
                                      9*************************996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.5
                                       EEE-SSSSSSGGG-EECETT CS
                     NAD_binding_8  23 lllekrdrlGGraasyevpg 42 
                                       ll+e ++ +G ra+++e+++
  gi|313126169|ref|YP_004036439.1| 142 LLVEDGSVVGVRASDREIDE 161
                                       68899999******999976 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   2.5e-05     0.027       1      31 [.      15      43 ..      15      53 .. 0.88
   2 ?   -2.6   0.1         2   2.2e+03     123     143 ..     158     178 ..     143     185 .. 0.73
   3 !    7.0   0.1    0.0025       2.7     260     331 ..     296     366 ..     279     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      Dvv++GaGpAg+ l   l  a+ g++ +l+e
  gi|313126169|ref|YP_004036439.1| 15 DVVIVGAGPAGCVLGGLL--ARSGVETMLLE 43
                                      9**************999..88888888887 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                     Lycopene_cycl 123 vleggrkirarlvvdarglas 143
                                        ++++ +ir+rlvv a g  s
  gi|313126169|ref|YP_004036439.1| 158 EIDEDLTIRSRLVVGADGRYS 178
                                       5678889*******9999555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0025
                     Lycopene_cycl 260 aiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsarawatlwprerkrqreffrllglalllkld 331
                                        iG aa +  P  G   a +++ a +l +a++ alr+ +     + +l p + +r+ ++ r+l+++ll +  
  gi|313126169|ref|YP_004036439.1| 296 LIGDAAHVASPLGGQGNALAIQDAAVLHAAVVPALRR-ESGVLSASSLEPYATRRRPAVRRILDMQLLGQRA 366
                                       5999********************************7.55566677899999999999999******98765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.6e-06    0.0016       2     175 ..      15      46 ..       7      76 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.6e-06
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvki 78 
                                       dvv++G+GpAG+ +   la++g++++l+e                                                
  gi|313126169|ref|YP_004036439.1|  15 DVVIVGAGPAGCVLGGLLARSGVETMLLE------------------------------------------------ 43 
                                       67777777777777777777777777665................................................ PP

                                       EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGv 155
                                                                                                                    
  gi|313126169|ref|YP_004036439.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHT-EEEEEESSS CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 156 ElAaalaklgkevtlveard 175
                                                        +  
  gi|313126169|ref|YP_004036439.1|  44 -----------------RHA 46 
                                       .................322 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   9.9e-06      0.01       1      30 [.      15      44 ..      15      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.9e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                      dv+++G+G AGc     +ar+G++++L+  
  gi|313126169|ref|YP_004036439.1| 15 DVVIVGAGPAGCVLGGLLARSGVETMLLER 44
                                      79*************************943 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.2    0.0001      0.11       1      30 [.      15      46 ..      15      54 .. 0.93
   2 ?    3.2   0.1     0.051        54     152     301 ..     121     264 ..     110     316 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                      dvvi+G+G +G+     Lar g  + lle++ 
  gi|313126169|ref|YP_004036439.1| 15 DVVIVGAGPAGCVLGGLLARSGveTMLLERHA 46
                                      9*******************9*********95 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.051
                                       HHHHHHHTT.-EEEESECEEEEEEEETCEEEEEEECT.EEEE..EEEE..EEE--GGGHH..HHHTTCTTTSEEEEE CS
                               DAO 152 laraaealG.veilegtevtgleeedgkvwgverttp.gend..aada..vVnaaGawsd..llgllkeldlpispv 220
                                       l ++ae+    e++  t v++l  edg v+gv r+++ ++ +  +++   vV a G +s+  ++     +d+ ++ +
  gi|313126169|ref|YP_004036439.1| 121 LVDDAERFEtFEFRPSTVVRDLLVEDGSVVGV-RASDrEIDEdlTIRSrlVVGADGRYSTvrQA---AGIDPGLVDT 193
                                       55555555534777778888877778888888.4444344423533334477777777643222...3344444444 PP

                                       EEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEE..TTSE.EEEEESSE......EETTCSSTSCSHHHHHHH CS
                               DAO 221 rgqvlvlkplseklvspaailpvpetdddgrgvyvtpr..kdgr.vlvGgtad......eesgdddpevdeedidel 288
                                         +v+ +                  ++ ++ ++++ +r  +dg+ +++G  +d       e+g+  p+  e+ i+++
  gi|313126169|ref|YP_004036439.1| 194 DFEVVWT------------------KVPGSASHEIQARinEDGQlLYFGLGPDvqlgwlIEKGTY-PDLRERGIEAF 251
                                       4444444..................2222233333332222332133343333334433222222.35566666666 PP

                                       HHHHHHHSGGGCG CS
                               DAO 289 lealrklfPqlgd 301
                                       +++++++ P+l++
  gi|313126169|ref|YP_004036439.1| 252 RDRIAAVDPRLRP 264
                                       6666666666533 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.7   2.8e+03       3      18 ..     168     183 ..     167     191 .. 0.86
   2 ?   13.7   0.0   2.3e-05     0.024     129     187 ..     291     349 ..     258     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
                                SE   3 kltvvcDGifsklRke 18 
                                       +l v +DG +s +R++
  gi|313126169|ref|YP_004036439.1| 168 RLVVGADGRYSTVRQA 183
                                       58899*******9985 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-05
                                SE 129 kkGlillGDalnmRHPltggGmtvalnDivllskllkpledlsdeekvle..elksfyvkR 187
                                       + Gl l+GDa  +  Pl g G + a++D+++l+  + p   l+ e+ vl+  +l+ + ++R
  gi|313126169|ref|YP_004036439.1| 291 RDGLALIGDAAHVASPLGGQGNALAIQDAAVLHAAVVPA--LRRESGVLSasSLEPYATRR 349
                                       57*******************************999988..55555554311344455555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.6e-05     0.038       2      34 ..      16      48 ..      15      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                      vv+vG+G  g+ l+g la+ g ++ ++er+ ++
  gi|313126169|ref|YP_004036439.1| 16 VVIVGAGPAGCVLGGLLARSGVETMLLERHATF 48
                                      8****************************8765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.7e-05      0.06       1      34 [.      16      49 ..      16      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrle 34
                                      ++i+GaG  G++l++ La+ g +  l+ r + ++
  gi|313126169|ref|YP_004036439.1| 16 VVIVGAGPAGCVLGGLLARSGVETMLLERHATFD 49
                                      68*************************9988554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.3e-05     0.056       2      38 ..      15      51 ..      14      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      dv+++G+G+AG      +a+ g +++lle+  ++ r 
  gi|313126169|ref|YP_004036439.1| 15 DVVIVGAGPAGCVLGGLLARSGVETMLLERHATFDRE 51
                                      8****************************99887765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   9.6e-05       0.1       1      31 [.      15      45 ..      15      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.6e-05
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      Dvv+vG+gpaG++     ar+G +++L+e++
  gi|313126169|ref|YP_004036439.1| 15 DVVIVGAGPAGCVLGGLLARSGVETMLLERH 45
                                      9****************************97 PP

>> DUF2824  Protein of unknown function (DUF2824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.15      43      78 ..      24      58 ..       4      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                           DUF2824 43 eglilvGvvevreienkvvevhavydpgfrGkyale 78
                                       g +l+G+     +e  ++e ha +d +frG +a +
  gi|313126169|ref|YP_004036439.1| 24 AGCVLGGLLARSGVETMLLERHATFDREFRG-FAFQ 58
                                      57899**************************.8865 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.15       1      31 [.      17      46 ..      17      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      +I+GaGPaG   +  l ++g+e  + lE+++
  gi|313126169|ref|YP_004036439.1| 17 VIVGAGPAGCVLGGLLARSGVE-TMLLERHA 46
                                      7********************6.679**985 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0002      0.21      19      44 ..      14      39 ..       5      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                      SEEEEE--SHHHHHHHHHHHHHTTTE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 19 skvllvGaGglGsellknLalsGvgk 44
                                      + v++vGaG  G+ l  +La+sGv+ 
  gi|313126169|ref|YP_004036439.1| 14 TDVVIVGAGPAGCVLGGLLARSGVET 39
                                      789********************985 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00039      0.41       5      39 ..      14      48 ..       9      58 .. 0.89
   2 ?   -3.7   0.0       3.1   3.3e+03     256     272 ..     141     156 ..     137     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00039
                                      ECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                               GDI  5 ydvivlGtGlkecilsGllsvdgkkvlhldrndyy 39
                                       dv+++G+G   c+l Gll+ +g   + l+r+  +
  gi|313126169|ref|YP_004036439.1| 14 TDVVIVGAGPAGCVLGGLLARSGVETMLLERHATF 48
                                      69**********************99999998765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.1
                                       EEEE-TTS-EEEEEETT CS
                               GDI 256 evvldedgkvvGvksee 272
                                       ++++ edg vvGv++ +
  gi|313126169|ref|YP_004036439.1| 141 DLLV-EDGSVVGVRASD 156
                                       5555.99******9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2973.18
//
Query:       gi|313126170|ref|YP_004036440.1|  [L=218]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-18   66.0   0.1    2.7e-18   65.5   0.1    1.2  1  HTH_10        HTH DNA binding domain
    0.00073   19.2   0.1     0.0012   18.4   0.1    1.3  1  Sigma70_r4_2  Sigma-70, region 4
    0.00078   18.9   0.0     0.0091   15.5   0.0    2.0  2  GerE          Bacterial regulatory proteins, luxR family
     0.0026   17.2   0.0     0.0056   16.2   0.0    1.5  1  Sigma70_r4    Sigma-70, region 4
     0.0062   16.4   0.1      0.011   15.6   0.1    1.3  1  HTH_5         Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.025   14.6   0.9      0.052   13.6   0.2    1.9  2  HTH_20        Helix-turn-helix domain
      0.059   13.1   0.0       0.15   11.8   0.0    1.8  1  HTH_38        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.1     1e-21   2.7e-18       1      53 []     159     211 ..     159     211 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LTd+ql+v+++A +mGY++ PR++t  e+A +l+ ++st+sehL +ae kl++
  gi|313126170|ref|YP_004036440.1| 159 LTDRQLTVVRTAAKMGYYEIPRETTHGEIAAALDCAASTVSEHLHRAEAKLVT 211
                                       9*************************************************985 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   4.8e-07    0.0012      28      54 .]     183     209 ..     181     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.8e-07
                                       -HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArkkL 54 
                                       ++ EIA+ l++  +tV  +l+RA +kL
  gi|313126170|ref|YP_004036440.1| 183 THGEIAAALDCAASTVSEHLHRAEAKL 209
                                       799********************9998 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.11   2.9e+02       2      15 ..     158     171 ..     157     175 .. 0.87
   2 !   15.5   0.0   3.6e-06    0.0091      21      46 ..     185     210 ..     177     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                                       SS-HHHHHHHHHHC CS
                              GerE   2 sLskRErevLrlla 15 
                                       +L++R+++v r  a
  gi|313126170|ref|YP_004036440.1| 158 TLTDRQLTVVRTAA 171
                                       7********99877 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.6e-06
                                       HHHHHHHTS-HHHHHHHHHHHHHHHT CS
                              GerE  21 keIAeelniSekTVkvhksnimkKLn 46 
                                        eIA++l++++ TV+ h+ ++  KL 
  gi|313126170|ref|YP_004036440.1| 185 GEIAAALDCAASTVSEHLHRAEAKLV 210
                                       59*******************99995 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.2e-06    0.0056       3      48 ..     157     209 ..     157     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                                       HHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   3 asLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       a+L++r+ +v++           ++ T+ EI++ l+   ++V+ +++rA  kL
  gi|313126170|ref|YP_004036440.1| 157 ATLTDRQLTVVRTAAkmgyyeiPRETTHGEIAAALDCAASTVSEHLHRAEAKL 209
                                       58999999999998888888888999***********************8887 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.3e-06     0.011      14      36 ..     180     202 ..     177     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.3e-06
                                       SSEEHHHHHHHHTS-HHHHHHHH CS
                             HTH_5  14 gelcvcelaeelglsqstvShHL 36 
                                       +e++ +e+a++l+   stvS+HL
  gi|313126170|ref|YP_004036440.1| 180 RETTHGEIAAALDCAASTVSEHL 202
                                       68899*****************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.9   9.9e+03      11      21 ..      14      24 ..      13      31 .. 0.70
   2 ?   13.6   0.2     2e-05     0.052      23      47 ..     180     204 ..     177     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.9
                                      HHHHHHHHHST CS
                            HTH_20 11 vRrrilraLar 21
                                       Rr ++++La+
  gi|313126170|ref|YP_004036440.1| 14 LRRPLFDLLAS 24
                                      58888888844 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                                       TTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  23 egltaselaerldlskntlsyHLrv 47 
                                       ++ t +e+a++ld++ +t+s HL+ 
  gi|313126170|ref|YP_004036440.1| 180 RETTHGEIAAALDCAASTVSEHLHR 204
                                       567889*****************76 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.9e-05      0.15      23      43 ..     184     204 ..     158     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.9e-05
                            HTH_38  23 lreIArrLgrspsTIsRElkR 43 
                                         eIA  L+++ sT+s +l+R
  gi|313126170|ref|YP_004036440.1| 184 HGEIAAALDCAASTVSEHLHR 204
                                       459****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1326.48
//
Query:       gi|313126171|ref|YP_004036441.1|  [L=107]
Description: hypothetical protein Hbor_14160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 666.18
//
Query:       gi|313126172|ref|YP_004036442.1|  [L=140]
Description: hypothetical protein Hbor_14170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 901.74
//
Query:       gi|313126173|ref|YP_004036443.1|  [L=766]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-41  139.6  53.6    4.3e-40  137.3  20.9    5.1  5  MCPsignal      Methyl-accepting chemotaxis protein (MCP) sign
    2.5e-12   47.0  16.7    2.8e-07   30.8   0.1    6.1  5  HAMP           HAMP domain
    1.5e-06   28.2   1.3    1.5e-06   28.2   1.3    3.7  4  dCache_1       Cache domain
    0.00023   19.5   6.4    0.00023   19.5   6.4    2.8  2  EzrA           Septation ring formation regulator, EzrA
      0.007   16.3   2.7      0.025   14.5   0.0    3.1  2  TLP1_add_C     Thiolase-like protein type 1 additional C-term
  ------ inclusion threshold ------
      0.012   15.8   3.3      0.012   15.8   3.3    6.2  4  DUF948         Bacterial protein of unknown function (DUF948)
      0.059   13.4  21.5       0.84    9.7   2.8    5.5  6  DUF1664        Protein of unknown function (DUF1664)
      0.059   13.8  23.6       0.13   12.7   2.3    4.7  5  TBCC_N         Tubulin-specific chaperone C N-terminal domain
      0.066   12.5  13.8        2.7    7.2   0.9    4.0  4  CorA           CorA-like Mg2+ transporter protein
      0.067   12.8   0.1      0.067   12.8   0.1    3.6  4  Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (
       0.08   11.9  11.6       0.72    8.8   0.2    2.9  2  IFT57          Intra-flagellar transport protein 57
        0.1   12.4   7.1        1.9    8.3   0.1    4.8  6  DASH_Dam1      DASH complex subunit Dam1
       0.16   10.8  21.8       0.17   10.8   3.2    2.7  2  Spc7           Spc7 kinetochore protein
       0.22   11.2  21.8        3.5    7.3  10.8    3.3  2  YkyA           Putative cell-wall binding lipoprotein
       0.22   10.6  16.2       0.81    8.8   1.0    3.9  3  RmuC           RmuC family
       0.24    9.2  10.1       0.26    9.0   0.4    2.2  2  Nup88          Nuclear pore component
       0.28   11.4  29.3       0.15   12.3   4.2    6.4  5  WXG100         Proteins of 100 residues with WXG
       0.31   11.2  10.0        1.3    9.2   0.4    4.1  6  Fib_alpha      Fibrinogen alpha/beta chain family
       0.32   10.6   4.6          2    8.0   0.1    3.3  3  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun
       0.54    9.3  15.3       0.22   10.6   2.3    2.5  2  AIP3           Actin interacting protein 3
       0.64    8.3  15.0      0.097   11.0   9.8    2.0  1  MAD            Mitotic checkpoint protein
       0.74    8.9  16.1      0.059   12.5   2.5    2.9  2  BAR_2          Bin/amphiphysin/Rvs domain for vesicular traff
       0.76    9.0  10.6        3.9    6.6   0.1    3.3  3  TMPIT          TMPIT-like protein
       0.88   10.0  21.1        0.3   11.5   2.3    5.0  5  DASH_Dad2      DASH complex subunit Dad2
       0.94    9.8  19.3        4.1    7.8   0.3    5.2  4  BLOC1_2        Biogenesis of lysosome-related organelles comp
       0.97    8.5   4.8        3.5    6.6   1.1    2.4  2  Atg14          Vacuolar sorting 38 and autophagy-related subu
          1    7.2  11.7       0.14   10.1   5.7    2.0  2  V_ATPase_I     V-type ATPase 116kDa subunit family
        1.2    9.0  12.0        4.1    7.3   0.2    4.5  5  Sec34          Sec34-like family
        1.3    9.2  26.3        5.4    7.2   4.7    2.9  2  ATG16          Autophagy protein 16 (ATG16)
        2.1    7.4  20.8    1.7e+02    1.1  20.8    2.6  1  APG17          Autophagy protein Apg17
        2.6    8.1  12.7       0.21   11.6   2.6    3.6  2  DUF725         Protein of unknown function (DUF725)
        3.5    6.7   7.5          2    7.5   4.2    2.1  2  Taxilin        Myosin-like coiled-coil protein
        3.9    6.9  13.4       0.81    9.1   2.6    3.4  3  Flagellar_rod  Paraflagellar rod protein
        4.5    7.1   6.2        1.7    8.4   0.8    3.0  2  Bacillus_HBL   Bacillus haemolytic enterotoxin (HBL)
        4.6    7.1  37.1       0.73    9.7  16.2    3.1  3  PhageMin_Tail  Phage-related minor tail protein
        5.5    6.2  26.7       0.23   10.7   2.6    4.3  4  DUF3450        Protein of unknown function (DUF3450)
        5.8    7.1  31.0       0.39   11.0  10.0    3.6  3  I_LWEQ         I/LWEQ domain
        7.2    5.9  13.1         12    5.2   0.1    3.3  3  GAS            Growth-arrest specific micro-tubule binding
        8.6    6.5   7.0         25    5.0   0.1    3.2  2  COG5           Golgi transport complex subunit 5
        9.8    6.0  15.5        1.2    9.0   3.8    2.9  2  DASH_Spc19     Spc19
        9.9    6.3  19.7        6.1    6.9   1.4    5.1  5  COG2           COG (conserved oligomeric Golgi) complex compo


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4      0.13        59      69     157 ..      41     134 ..      33     143 .. 0.67
   2 ?    6.9   4.0     0.011       4.9     106     164 ..     393     455 ..     367     462 .. 0.56
   3 !    8.8   9.6     0.003       1.3      77     167 ..     396     486 ..     392     499 .. 0.68
   4 !  137.3  20.9   9.9e-43   4.3e-40       2     166 ..     499     667 ..     498     673 .. 0.93
   5 ?    4.7   0.9     0.055        24     137     169 ..     673     705 ..     663     708 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHH..HHHH..............H.HHHHHHHH..HHHHHHHHCCHHHHHHHHHHHH CS
                         MCPsignal  69 GFaVVAdEVrkLAersaqaakei..ealiieiqkeindsvesle.etrqrvee..gselveetgealkeiveavaev 140
                                        +  VA+EV + A+r  q++  +  e+l   +  + +++  +   ++ q +++   s+  ++ + +l + v+ v+ v
  gi|313126173|ref|YP_004036443.1|  41 TYVTVAEEVSDSAQRDLQSTATLqsEQLSGWVSSQKQTARMVSRySVFQTADNpvVSQYLRREKAVLPTAVTDVHYV 117
                                       56789**********99887654114555445444444433333133344443114677888888899999999999 PP

                                       HHHHHHHHHHHHHHHHH CS
                         MCPsignal 141 adlvqeiaaaseeqsas 157
                                       +++ + i a+s+  + +
  gi|313126173|ref|YP_004036443.1| 118 DTENSRIVASSNSDAVG 134
                                       99999999888877766 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                                       ....HHHHHHHHHHHHHHHHHCCHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 106 vesleetrqrveegselveetgealk....eiveavaevadlvqeiaaaseeqsasieevnqa 164
                                        e++       +e +e+ e+t  al     +++++ + va+   e+++as+e+++s+e+++ +
  gi|313126173|ref|YP_004036443.1| 393 SEVMRTIAAAFNEMAEELETTLVALTafgeTVASSSSGVASGAAEVSSASDEIAQSVEQISAG 455
                                       444444444444444444444444431111334444456666666677777777777776655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  77 VrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaasee 153
                                        r++A+   + a+e+e+ ++++++  +++++s + + + ++e s+  +e ++++++i++ + e ad + e++   + 
  gi|313126173|ref|YP_004036443.1| 396 MRTIAAAFNEMAEELETTLVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAGAREQADHLAELSEEMSS 472
                                       48899999999999999999999988888877777766666666666666666666666666666666666666666 PP

                                       HHHHHHHHHHHHHH CS
                         MCPsignal 154 qsasieevnqavee 167
                                       +sas+e+v+ + + 
  gi|313126173|ref|YP_004036443.1| 473 LSASVEQVSATTDD 486
                                       66666666655443 PP

  == domain 4  score: 137.3 bits;  conditional E-value: 9.9e-43
                                       HHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHH CS
                         MCPsignal   2 dlaeeaseeAeeg....gkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVA 74 
                                       d ++ea + A +g    + e  ++v+ +e+++++ + is+++ Vi ++a+QTN+LALNA+iEA RAGe+G GFaVVA
  gi|313126173|ref|YP_004036443.1| 499 DEGREAANGALDGveaiEMETREAVESVEDLDDEIERISNVTGVIADLAEQTNILALNASIEASRAGEAGSGFAVVA 575
                                       56677777788877666788899****************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                       dEV++LAe++a  a+ ie+ +  +q +  ++ve +e+ r++ve g+++v+e+ +++ ei+++v++ +++v+e+aaa+
  gi|313126173|ref|YP_004036443.1| 576 DEVKHLAEETATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAAT 652
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHH CS
                         MCPsignal 152 eeqsasieevnqave 166
                                        eq+++ e+v +  +
  gi|313126173|ref|YP_004036443.1| 653 GEQASTTEDVLSMAD 667
                                       *******99976555 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 137 vaevadlvqeiaaaseeqsasieevnqaveeva 169
                                        +e +++ ++++aa+eeq+a+++ev+++ +++a
  gi|313126173|ref|YP_004036443.1| 673 GEETTAEAENVSAAAEEQTATLSEVSEGAHRLA 705
                                       467788999*****************9988776 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   6.3e-10   2.8e-07       3      52 ..     313     362 ..     311     363 .. 0.94
   2 !   18.1   1.0     6e-06    0.0026      14      52 ..     372     411 ..     369     412 .. 0.92
   3 ?    3.3   0.0      0.25   1.1e+02       4      24 ..     471     493 ..     470     538 .. 0.80
   4 ?    0.9   0.2       1.4     6e+02      32      51 ..     619     638 ..     604     640 .. 0.69
   5 ?   -0.4   0.0       3.4   1.5e+03      11      23 ..     702     714 ..     691     735 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 6.3e-10
                                       HHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   3 arrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                        ++++ PL  La  ++r++ Gdld++lp+ + DE+G ++  ++a++d L+
  gi|313126173|ref|YP_004036443.1| 313 HGTTVTPLSTLAGRVERLRGGDLDVSLPDGRTDEFGSVVDGIDALRDDLK 362
                                       67899******************************************985 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6e-06
                                       HHHHHHHTTTBTSSTCCTTSSSHH.HHHHHHHHHHHHHHH CS
                              HAMP  14 araarriaaGdldtrlpvsgrDEi.GeLarafNaMldrLr 52 
                                       ++++ + a+Gdl++r + +++ E+ +++a+afN+M+++L+
  gi|313126173|ref|YP_004036443.1| 372 RDVMSEAADGDLTVRMDLESDSEVmRTIAAAFNEMAEELE 411
                                       578999*****************66*************97 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.25
                                       HTTHHHHHHHHHHHHHHTTT..B CS
                              HAMP   4 rrilrPLrrLaraarriaaG..d 24 
                                        ++++++++++++++ +a+G   
  gi|313126173|ref|YP_004036443.1| 471 SSLSASVEQVSATTDDLADGsaA 493
                                       58999**************9552 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.4
                                       TSSSHHHHHHHHHHHHHHHH CS
                              HAMP  32 sgrDEiGeLarafNaMldrL 51 
                                        g DE++e   +f++ +d++
  gi|313126173|ref|YP_004036443.1| 619 AGADEVDEALSSFDEIADSV 638
                                       47799999999999998876 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHTTT CS
                              HAMP  11 rrLaraarriaaG 23 
                                       +rLa++a+++++ 
  gi|313126173|ref|YP_004036443.1| 702 HRLADQANELSEL 714
                                       5666666666653 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   1.3   3.4e-09   1.5e-06       5     248 ..      51     276 ..      47     277 .. 0.70
   2 ?   -0.4   0.3       1.8   8.1e+02      12      59 ..     400     444 ..     390     504 .. 0.72
   3 ?    0.3   0.3       1.2   5.1e+02       9      40 ..     611     642 ..     578     672 .. 0.61
   4 ?   -1.1   0.9         3   1.3e+03       9      69 ..     681     746 ..     665     755 .. 0.63

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.4e-09
                          dCache_1   5 eqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallks...ilksnpdisgvy 78 
                                       ++a++ l+++a++ +++++ ++ s++++a+++++  s+++ +++p          + ++l+    +l     + +v 
  gi|313126173|ref|YP_004036443.1|  51 DSAQRDLQSTATLQSEQLSGWVSSQKQTARMVSRY-SVFQTADNP---------VVSQYLRRekaVL--PTAVTDVH 115
                                       6899**********************999999775.566655443.........3444444421132..24457898 PP

                          dCache_1  79 lvdadGqviassdpssppnlegtddpadrdwykealaggg.gkpvisdpyvdqtggkpvitiavpiyddsgkfiGvl 154
                                       +vd ++  i++s+ s+  ++     p  +++++  ++ +   ++ ++ py+  + +k+++++++p+   s +   v+
  gi|313126173|ref|YP_004036443.1| 116 YVDTENSRIVASSNSDAVGT--DPLPEGTSFLTGSINMPVaDQVSYTRPYQ--RDNKTYMAFVSPVQLKSDR---VV 185
                                       88876665555544443344..47888888988877777786677999994..449**********998777...88 PP

                          dCache_1 155 aadldldnlqdllsniklgetgyvfivdsdGniiahpdkdl....lgknlrdelkaqealekalakiesgvssvkln 227
                                       ++  d++++  +l+++ +g  +++ +v+ dG++ ++ + ++           + +a  ++ ++ a   sgv++ + n
  gi|313126173|ref|YP_004036443.1| 186 MVIADMSYVELTLDTAVEG--SFAQVVTTDGKVQFDASGRKnygdY-----GVPNA--TALSEGAAGNSGVYEEGAN 253
                                       8888999999999998744..7*************98743322321.....33322..2222223355666666666 PP

                          dCache_1 228 g...eeylvayapiptglgWylvv 248
                                       +   e++lvayap+ + ++   vv
  gi|313126173|ref|YP_004036443.1| 254 DvlsEDHLVAYAPVSG-TDLVTVV 276
                                       66666*********95.8887776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                          dCache_1  12 lglaeqlanniedvldslenlaetlasnps.lqdlleepnraneasres 59 
                                        +  +++a+++e++l  l+++ et+as++s +++++ e +       ++
  gi|313126173|ref|YP_004036443.1| 400 AAAFNEMAEELETTLVALTAFGETVASSSSgVASGAAEVSS----ASDE 444
                                       44556777778888888888888888887767776665543....2222 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.2
                          dCache_1   9 eqllglaeqlanniedvldslenlaetlasnp 40 
                                       eq+ +++e  a+++++ l s + +a  +++n+
  gi|313126173|ref|YP_004036443.1| 611 EQMREQVEAGADEVDEALSSFDEIADSVSQNS 642
                                       45555555555555555555555555555554 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3
                          dCache_1   9 eqllglaeqlanniedvldslenlaetlasnpslqdlleepnra........neasreslqallksilk 69 
                                       e++++ ae+ ++ +++v + + +la + ++   l +ll+e++           ++ +++++a+l++il+
  gi|313126173|ref|YP_004036443.1| 681 ENVSAAAEEQTATLSEVSEGAHRLADQANE---LSELLSEFDVSaegidfeeELSVDSETAATLENILR 746
                                       455555666666666666666666666654...666677776667777777766666666666666665 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.6     0.045        20     361     443 ..     390     471 ..     383     526 .. 0.58
   2 !   19.5   6.4   5.2e-07   0.00023     100     220 ..     586     708 ..     575     729 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.045
                                       HHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SS-S CS
                              EzrA 361 eeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkieksnLPg 437
                                       e++ e +++  +a+ e++eele++   l+++ e + + +  ++s   + + A +++++  ++++   r+ +  +L  
  gi|313126173|ref|YP_004036443.1| 390 ESDSEVMRTIAAAFNEMAEELETTLVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAGARE-QADHLAE 465
                                       555555555555666666666666666666666666666666666555555555555555555554444.3334444 PP

                                       -TTTHH CS
                              EzrA 438 iPesyl 443
                                       ++e++ 
  gi|313126173|ref|YP_004036443.1| 466 LSEEMS 471
                                       444432 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 5.2e-07
                                       THHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH--- CS
                              EzrA 100 kkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqlenieke 176
                                        +  +++e+ ++++++k +++ e +++++e+ e   +e++++ + ++e+ +++ +n++s +e++++  +q ++ e+ 
  gi|313126173|ref|YP_004036443.1| 586 ATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTTEDV 662
                                       5567899********************************************************************** PP

                                       ------------..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT CS
                              EzrA 177 fsefeeltengd..yveakeilkkleeeideleevieeiPelleel 220
                                       +s  +el   g+    ea+++  ++ee+++ l+ev e    l +++
  gi|313126173|ref|YP_004036443.1| 663 LSMADELAGIGEetTAEAENVSAAAEEQTATLSEVSEGAHRLADQA 708
                                       *******987762267899**************9988776666555 PP

>> TLP1_add_C  Thiolase-like protein type 1 additional C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   5.8e-05     0.025      26      81 ..     158     213 ..     152     215 .. 0.87
   2 ?   -0.0   0.1         2   8.6e+02      29      68 ..     559     597 ..     537     610 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.8e-05
                        TLP1_add_C  26 tyTvefnRdgePekgfvvgRltsdgaRfLAneadeetlealvsedveGakvrV.rqD 81 
                                       +yT +++Rd++   +fv    + + +R++ ++ad + +e++ +++veG   +V + D
  gi|313126173|ref|YP_004036443.1| 158 SYTRPYQRDNKTYMAFVSPV-QLKSDRVVMVIADMSYVELTLDTAVEGSFAQVvTTD 213
                                       8***************9877.77888*********************9877651455 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2
                        TLP1_add_C  29 vefnRdgePekgfvvgRltsdgaRfLAn..eadeetlealvs 68 
                                       +e +R+ge+  gf v+    d+ + LA   ++ +et+e  vs
  gi|313126173|ref|YP_004036443.1| 559 IEASRAGEAGSGFAVVA---DEVKHLAEetATYAETIEDHVS 597
                                       57789999999999998...9999999855455666665554 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.5    0.0082       3.6      40      88 ..     433     481 ..     385     508 .. 0.62
   2 ?    6.8   1.7     0.018         8      24      82 ..     466     548 ..     463     555 .. 0.56
   3 ?   15.8   3.3   2.8e-05     0.012      21      86 ..     575     640 ..     569     661 .. 0.73
   4 ?    3.5   1.5       0.2        86      33      88 ..     657     712 ..     642     717 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0082
                            DUF948  40 kqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       + + +++  ++++ + v+++ ++ +e+ +++ +l e++  l++sv++++
  gi|313126173|ref|YP_004036443.1| 433 SGAAEVSSASDEIAQSVEQISAGAREQADHLAELSEEMSSLSASVEQVS 481
                                       3333334444444444444444555555666555555555555555543 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.018
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvne........................lledvneklekvdpltea 76 
                                       l++ +++++a++e++   +d + + ++++ + + e                         +ed+ +++e++ ++t  
  gi|313126173|ref|YP_004036443.1| 466 LSEEMSSLSASVEQVSATTDDLADGSAAVAERADEgreaangaldgveaiemetreaveSVEDLDDEIERISNVTGV 542
                                       66666777777777776666666666666666666444444444444444444444444444456666666666666 PP

                            DUF948  77 vadlge 82 
                                       +adl+e
  gi|313126173|ref|YP_004036443.1| 543 IADLAE 548
                                       666665 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2.8e-05
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                         ++k++++e+a+  e++e++v  +  + +++++ ++++ e+v+   ++vd+  +++ ++++svs+
  gi|313126173|ref|YP_004036443.1| 575 ADEVKHLAEETATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQ 640
                                       556677777777777777777777777777777777777777777777777777777777777775 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.2
                            DUF948  33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +t e++ + +d++    e+++a+++++ +  +e+++++ ++ e ++ l+++ +el+
  gi|313126173|ref|YP_004036443.1| 657 STTEDVLSMADELAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELS 712
                                       34444444444444444555566666666777888888888888888888877775 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0         2   8.8e+02       7      22 ..      29      44 ..      25      84 .. 0.70
   2 ?   -0.8   0.0       3.4   1.5e+03      90     115 ..     387     412 ..     346     418 .. 0.48
   3 ?    8.5   0.5    0.0046         2      41     121 ..     401     481 ..     395     491 .. 0.55
   4 ?    5.7   2.9     0.032        14      55     121 ..     464     537 ..     438     540 .. 0.52
   5 ?    9.7   2.8    0.0019      0.84      39     107 ..     581     649 ..     572     662 .. 0.56
   6 ?    1.2   0.1      0.83   3.6e+02      65     111 ..     677     716 ..     654     731 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2
                           DUF1664  7 ivpaavvgavgYgyvw 22
                                      iv +avv+  gY yv 
  gi|313126173|ref|YP_004036443.1| 29 IVTVAVVAIGGYTYVT 44
                                      5667777777788875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.4
                           DUF1664  90 tevredlseigedvesvkeavegles 115
                                       +++++d + +++   + +e+ e+le+
  gi|313126173|ref|YP_004036443.1| 387 MDLESDSEVMRTIAAAFNEMAEELET 412
                                       33444444444444444444444444 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0046
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                        a ++++++le+   +l+a  +  +s    v +   e++ +s ei++ v++++ + +e  + + +++e +++l +++
  gi|313126173|ref|YP_004036443.1| 401 AAFNEMAEELETTLVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAGAREQADHLAELSEEMSSLSASV 477
                                       55556666666655555555555555555555555555555555555555555555555555555555555555555 PP

                           DUF1664 118 erie 121
                                       e+++
  gi|313126173|ref|YP_004036443.1| 478 EQVS 481
                                       5543 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.032
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskei.......keevtevredlseigedvesvkeaveglesklerie 121
                                       ++l++    Ls+ +++v ++ d+ ++ s+++       +e  + + +++++i+ + ++  e ve+l+ ++eri+
  gi|313126173|ref|YP_004036443.1| 464 AELSEEMSSLSASVEQVSATTDDLADGSAAVaeradegREAANGALDGVEAIEMETREAVESVEDLDDEIERIS 537
                                       33333344444444444444444444333330000000455566667788888888888888888888888876 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0019
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                       l++  ++ ++ +e+  ++l++ + +  +ri+++ +++++ ++   e  +  +e+ + +s+ +  ve+v 
  gi|313126173|ref|YP_004036443.1| 581 LAEETATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVA 649
                                       444444455555555555555555555555555555555555555555555555555555555555554 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.83
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       +++        ++++++++e ++ ++ev+e+ +++ ++ ++++e+ +
  gi|313126173|ref|YP_004036443.1| 677 TAEA-------ENVSAAAEEQTATLSEVSEGAHRLADQANELSELLS 716
                                       3333.......333333333344444444444444444444444444 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4      0.36   1.6e+02      24      54 ..     389     424 ..     370     451 .. 0.69
   2 ?    7.1   0.7     0.016       6.9      28      81 ..     428     479 ..     421     484 .. 0.84
   3 ?   -1.6   0.0         8   3.5e+03      37      76 ..     497     537 ..     475     542 .. 0.60
   4 ?   12.7   2.3   0.00029      0.13      17      84 ..     578     643 ..     572     647 .. 0.88
   5 ?    4.3   1.6      0.12        53       9      79 ..     675     745 ..     667     749 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.36
                            TBCC_N  24 eaveeekvdsFlkaFteekaaieellesve.....e 54 
                                        ++++e + ++++aF+e ++++e+ l +++      
  gi|313126173|ref|YP_004036443.1| 389 LESDSEVMRTIAAAFNEMAEELETTLVALTafgetV 424
                                       456688889999999999999999998888666552 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.016
                            TBCC_N  28 eekvdsFlkaFteekaaieellesveesadksklkqkldeitaeiqeLqkllae 81 
                                       ++ v+s +++ ++ +++i +++e+++  a + +++++l+e+++e+++L  ++ +
  gi|313126173|ref|YP_004036443.1| 428 SSGVASGAAEVSSASDEIAQSVEQIS--AGAREQADHLAELSEEMSSLSASVEQ 479
                                       555666677888999***********..999*****************988876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 8
                            TBCC_N  37 aFteekaaieellesve.esadksklkqkldeitaeiqeLq 76 
                                       + +e ++a + +l++ve  ++++ +  ++++++  ei+++ 
  gi|313126173|ref|YP_004036443.1| 497 RADEGREAANGALDGVEaIEMETREAVESVEDLDDEIERIS 537
                                       44555555556666666555666666666666666666554 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00029
                            TBCC_N  17 rkeereseaveeekvdsFlkaFteekaaieellesveesadksklkqkldeitaeiqeLqkllaessm 84 
                                        k+ +e++a+  e+++   +++++++a++ e++e+++  ++ ++ ++++de+ ++++e+ ++++++s 
  gi|313126173|ref|YP_004036443.1| 578 VKHLAEETATYAETIEDHVSTLQSKRAEVVERIEQMR--EQVEAGADEVDEALSSFDEIADSVSQNSA 643
                                       5555677777899************************..99999*******************99986 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.12
                            TBCC_N   9 erqeqlekrkeereseaveeekvdsFlkaFteekaaieellesveesadksklkqkldeitaeiqeLqkll 79 
                                       e  +++e+ ++++e+++++ ++v++ + +++++++++ ell++++ sa+  + +++l   ++  ++L+++l
  gi|313126173|ref|YP_004036443.1| 675 ETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSEFDVSAEGIDFEEELSVDSETAATLENIL 745
                                       55556666666666677777777777777777777777777777755555555555555555555555555 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.031        13     181     224 ..     334     377 ..     318     387 .. 0.85
   2 ?    7.2   0.9    0.0061       2.7     124     216 ..     460     548 ..     417     558 .. 0.57
   3 ?    2.1   0.2      0.23     1e+02     181     222 ..     576     617 ..     554     629 .. 0.67
   4 ?    4.6   3.0     0.038        17     121     216 ..     608     716 ..     574     721 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.031
                              CorA 181 addkllddedkeylrdlldelerllemlealrerleslqdtyss 224
                                       ++d  l+d + + +  + d ++ l ++l+++r+ +++ +d +s 
  gi|313126173|ref|YP_004036443.1| 334 DLDVSLPDGRTDEFGSVVDGIDALRDDLKSQRDDARRYRDVMSE 377
                                       5667788888899***************************9986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0061
                              CorA 124 fellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdll 198
                                       ++ l +l+ee+  l+  +   + t++++++  a++ +r+ + r+a++   + + + ++     ++++e+ e  +dl 
  gi|313126173|ref|YP_004036443.1| 460 ADHLAELSEEMSSLSASVeqVSATTDDLADGSAAVAERADEGREAANGALDGV-EAIE-----METREAVESVEDLD 530
                                       22333344444444444455555555555556666666666666666666666.5555.....55555555566666 PP

                              CorA 199 delerllemlealrerle 216
                                       de+er+++ + ++++++e
  gi|313126173|ref|YP_004036443.1| 531 DEIERISNVTGVIADLAE 548
                                       666666666666666665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.23
                              CorA 181 addkllddedkeylrdlldelerllemlealrerleslqdty 222
                                       ++ k+l +e + y ++++d+++ l+ +   + er+e+++++ 
  gi|313126173|ref|YP_004036443.1| 576 DEVKHLAEETATYAETIEDHVSTLQSKRAEVVERIEQMREQV 617
                                       445555666666666666666665555555555555555443 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.038
                              CorA 121 drlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlk...........rllakaddk 184
                                       +r+++  e++e+  de+++ l  +d++ ++  +  a +++ ++   ++++++++vl+           +  + ++ +
  gi|313126173|ref|YP_004036443.1| 608 ERIEQMREQVEAGADEVDEALssFDEIADSVSQNSASVEEVAAATGEQASTTEDVLSmadelagigeeTTAEAENVS 684
                                       33333333333334444444444333333333333334444444444444444444333333335554444466666 PP

                              CorA 185 llddedkeylrdlldelerllemlealrerle 216
                                          +e+   l+++++ ++rl+++++ l+e+l+
  gi|313126173|ref|YP_004036443.1| 685 AAAEEQTATLSEVSEGAHRLADQANELSELLS 716
                                       77777777777777777777777777777765 PP

>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00015     0.067      19      85 ..      23      88 ..      21     112 .. 0.86
   2 ?    1.5   0.1      0.47     2e+02      17      87 ..     413     483 ..     410     505 .. 0.69
   3 ?   -1.0   0.9       2.8   1.2e+03      46      72 ..     592     618 ..     573     661 .. 0.56
   4 ?   -1.0   0.4       2.6   1.2e+03      46     108 ..     631     694 ..     617     718 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH CS
                     Mt_ATP-synt_B 19 valcfigflilvakslgpsikefldkriekiqeelnqsrnlkeealkerieqekklqslveltkslf 85
                                      +al f++++++v+  +g+++   +++  ++ q++l++  +l+ e+l+  + ++k++  +v+ + s+f
  gi|313126173|ref|YP_004036443.1| 23 LALLFVIVTVAVVAIGGYTYVTVAEEVSDSAQRDLQSTATLQSEQLSGWVSSQKQTARMVS-RYSVF 88
                                      5899***************************************************996665.44444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH CS
                     Mt_ATP-synt_B  17 tlvalcfigflilvakslgpsikefldkriekiqeelnqsrnlkeealkerieqekklqslveltkslfev 87 
                                       tlval+ +g ++++  s+  s +++  +  ++i ++ +q  +   e+ + + e  ++++sl++  +++++ 
  gi|313126173|ref|YP_004036443.1| 413 TLVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAGAREQADHLAELSEEMSSLSASVEQVSAT 483
                                       78888888888888888888888777777777777777777766666666666666666666666555544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_B  46 iekiqeelnqsrnlkeealkerieqek 72 
                                       ie   + l++ r++ +e +++  eq++
  gi|313126173|ref|YP_004036443.1| 592 IEDHVSTLQSKRAEVVERIEQMREQVE 618
                                       444444444444444444444444433 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHH.HHHHHHHHHH CS
                     Mt_ATP-synt_B  46 iekiqeelnqsrnlkeealkerieqekklqslveltkslfevskeqvaleaea.ferelqakla 108
                                        ++i ++  q  ++ ee+     eq + +  +++  ++l     e++a   +  +  e q+++ 
  gi|313126173|ref|YP_004036443.1| 631 FDEIADSVSQNSASVEEVAAATGEQASTTEDVLSMADELAGIGEETTAEAENVsAAAEEQTATL 694
                                       5666666666666667777777777777777777777777776666655444312333333333 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0017      0.72     240     326 ..     396     482 ..     386     500 .. 0.74
   2 ?    5.1   5.9     0.021       9.3     227     319 ..     583     681 ..     574     720 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                             IFT57 240 lpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelek 316
                                       + ++  +++++ e+++ tl  +++  + + s+ +   +   e++   +e+ ++++q+s+g  e+ ++lae+see+++
  gi|313126173|ref|YP_004036443.1| 396 MRTIAAAFNEMAEELETTLVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAGAREQADHLAELSEEMSS 472
                                       55666677777777777777777777777777777777778888888888888888888888888888888888888 PP

                             IFT57 317 vkqemeergs 326
                                       ++  +e+ ++
  gi|313126173|ref|YP_004036443.1| 473 LSASVEQVSA 482
                                       8877765433 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                             IFT57 227 eqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqlee......llqeyreaqeelsevkekykqls 297
                                       e++ ++ ++ie+++++++s+ +++ e i+++ e++e+    +++ l++      ++++ ++  ee+++++ +    +
  gi|313126173|ref|YP_004036443.1| 583 EETATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSfdeiadSVSQNSASVEEVAAATGEQASTT 659
                                       66777888888888888888888888888888888888888877665411111134444444444444455555555 PP

                             IFT57 298 egvseltrelaeiseelekvkq 319
                                       e v ++ +ela i ee ++  +
  gi|313126173|ref|YP_004036443.1| 660 EDVLSMADELAGIGEETTAEAE 681
                                       5566666666655555433333 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       6.3   2.8e+03       3      14 ..     401     412 ..     398     426 .. 0.57
   2 ?    8.3   0.1    0.0044       1.9       3      31 ..     461     489 ..     460     495 .. 0.89
   3 ?    3.2   0.0      0.18        77       9      34 ..     523     548 ..     516     550 .. 0.88
   4 ?   -0.6   0.0       2.7   1.2e+03       8      18 ..     592     602 ..     570     633 .. 0.58
   5 ?   -1.6   0.0       5.7   2.5e+03       4      15 ..     630     641 ..     627     649 .. 0.76
   6 ?   -2.0   0.0       7.2   3.1e+03       8      20 ..     704     716 ..     693     727 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.3
                         DASH_Dam1   3 pafaeLaDslet 14 
                                        af+e+a++let
  gi|313126173|ref|YP_004036443.1| 401 AAFNEMAEELET 412
                                       456666666654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0044
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLsd 31 
                                       + +aeL+++++ L++ +e+ + ++++L+d
  gi|313126173|ref|YP_004036443.1| 461 DHLAELSEEMSSLSASVEQVSATTDDLAD 489
                                       579********************999987 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.18
                         DASH_Dam1   9 aDsletLdknledLqqihesLsdfNe 34 
                                        +s+e+Ld+ +e++++++  ++d+ e
  gi|313126173|ref|YP_004036443.1| 523 VESVEDLDDEIERISNVTGVIADLAE 548
                                       589**************999999877 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.7
                         DASH_Dam1   8 LaDsletLdkn 18 
                                       ++D ++tL+++
  gi|313126173|ref|YP_004036443.1| 592 IEDHVSTLQSK 602
                                       44455555443 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 5.7
                         DASH_Dam1   4 afaeLaDsletL 15 
                                       +f e+aDs+++ 
  gi|313126173|ref|YP_004036443.1| 630 SFDEIADSVSQN 641
                                       799****99875 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 7.2
                         DASH_Dam1   8 LaDsletLdknle 20 
                                       LaD+ ++L++ l+
  gi|313126173|ref|YP_004036443.1| 704 LADQANELSELLS 716
                                       4555554444333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.2   0.00038      0.17     141     284 ..     400     542 ..     385     563 .. 0.56
   2 ?    5.4  10.0     0.016       7.2     136     251 ..     595     712 ..     590     745 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                              Spc7 141 kegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkae 214
                                           +e  e+le+    L++  e + +    + +  ae+++  +++ + +e++++    + + L+el ee+++l+a 
  gi|313126173|ref|YP_004036443.1| 400 AAAFNEMAEELETTLVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAgarEQADHLAELSEEMSSLSAS 476
                                       44444455555555555555555555555555555555555555555555555544434677777777777777777 PP

                              Spc7 215 ieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgw 284
                                       +e+ ++ +++l +  ++++e+ +e    ++ ++ ++   e + +e+++   + v+ l +e +++ + tg+
  gi|313126173|ref|YP_004036443.1| 477 VEQVSATTDDLADGSAAVAERADEG---REAANGALDGVEAIEMETREA-VESVEDLDDEIERISNVTGV 542
                                       7755555555555555555555444...333344444444444444443.34466666666666666665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.016
                              Spc7 136 llegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..idkeeLeelreelae 210
                                       ++++L+++  e +e +e+ +e++e+  +e+de+l +++e  ++++++ ++ +e a+   +  ++ e++ ++ +ela 
  gi|313126173|ref|YP_004036443.1| 595 HVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEqaSTTEDVLSMADELAG 671
                                       77888888888899999999999999999999999999999999999888888444332223668888888888888 PP

                              Spc7 211 lkaeieekkkelaelqeqleeleekieelkeqkseleeeia 251
                                       + +e  +  ++++   e+ ++  ++++e + + ++  +e++
  gi|313126173|ref|YP_004036443.1| 672 IGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELS 712
                                       88777755555555544444444444444444443333333 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.5     0.016       6.8      11      97 ..     447     532 ..     436     554 .. 0.68
   2 ?    7.3  10.8     0.008       3.5      11     140 ..     583     717 ..     566     723 .. 0.44

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                              YkyA  11 eeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefeki 87 
                                       ++++++  + +eq++ L el ++   l  ++ + +    d++ + s+ + e ++e +e  +   + +e+ + e  ++
  gi|313126173|ref|YP_004036443.1| 447 QSVEQISAGAREQADHLAELSEEMSSLSASVEQVSATT-DDLADGSAAVAERADEGREAANGALDGVEAIEMETREA 522
                                       33344456777777777777777777777775554444.77788888888888887777777777777777777777 PP

                              YkyA  88 keeieeiede 97 
                                        e++e+++de
  gi|313126173|ref|YP_004036443.1| 523 VESVEDLDDE 532
                                       7777777766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.008
                              YkyA  11 eeavelEkefeeqqekLtelekkeqelyeei...ielgmdefdkikklsdealenveeReellekekesieeakeef 84 
                                       ee++++ +++e+  ++L++  ++  e  e++   +e+g de d+  +  de  ++v++    +e+  ++  e     
  gi|313126173|ref|YP_004036443.1| 583 EETATYAETIEDHVSTLQSKRAEVVERIEQMreqVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTT 659
                                       44444444444444444444444444444431112334444444444444444444444444444444444444444 PP

                              YkyA  85 ekikeeieei..edeelkkeaeelieameeryeaydklykaYkealeldkeLYemLkk 140
                                       e++ +  +e+    ee   eae++  a ee++++ +++ +  + + ++ +eL e+L++
  gi|313126173|ref|YP_004036443.1| 660 EDVLSMADELagIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSE 717
                                       4444444444332333455555555555555555555554444444444444444444 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.4    0.0094       4.1      13      57 ..     444     488 ..     434     511 .. 0.59
   2 ?    8.8   1.0    0.0018      0.81     224     287 ..     585     651 ..     578     655 .. 0.79
   3 ?    4.7   0.3     0.032        14      11      62 ..     666     719 ..     659     726 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0094
                              RmuC  13 klekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLt 57 
                                       ++++  e++++  +e+a++l++l+e++++l++  eq++ ++++L+
  gi|313126173|ref|YP_004036443.1| 444 EIAQSVEQISAGAREQADHLAELSEEMSSLSASVEQVSATTDDLA 488
                                       333333333333355555555555555555555555555555553 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0018
                              RmuC 224 qeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle...gnilrkaeklkelgvk 287
                                        +  ae i +++++l +k ++++e++e++++++e   +++d+a +++    ++++++  +++e+ ++
  gi|313126173|ref|YP_004036443.1| 585 TATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDeiaDSVSQNSASVEEVAAA 651
                                       5667888999999999999999999999999999999999999988887777777777777777665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.032
                              RmuC  11 keklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLk..n 62 
                                        ++l+   e+ ++e ++++ + e+ ++ l+e++e +++l d+a++L++ L+  +
  gi|313126173|ref|YP_004036443.1| 666 ADELAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSefD 719
                                       567778888888888999999999999*********************998544 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4    0.0006      0.26     551     644 ..     440     533 ..     436     564 .. 0.88
   2 ?    3.8   3.7     0.023        10     553     677 ..     589     712 ..     578     717 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0006
                             Nup88 551 lvreeiekrvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseae 627
                                        +++ei++ v++++   ++q + l++l ee  sls ++e++    ++  d   ++++r+++  + +n +l  +  +e
  gi|313126173|ref|YP_004036443.1| 440 SASDEIAQSVEQISAGAREQADHLAELSEEMSSLSASVEQVSATTDDLADGSAAVAERADEGREAANGALDGVEAIE 516
                                       5889******************************************************************9999999 PP

                             Nup88 628 remkkelekikeklksl 644
                                        e ++ +e++++  +++
  gi|313126173|ref|YP_004036443.1| 517 METREAVESVEDLDDEI 533
                                       99999988887644444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.023
                             Nup88 553 reeiekrvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaere 629
                                        e ie +v  l++++++  e +++++e+ +   +++++    ++ei d   +    v++v   + +++ ++ +   +
  gi|313126173|ref|YP_004036443.1| 589 AETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTTEDV-LS 664
                                       578999**********99999999999999999999999999*****999999999999998888887666555.89 PP

                             Nup88 630 mkkelekikeklkslknalkqvkkkldkqrkqiakskeeekksslels 677
                                       m+ el+ i e++   +++++ + + +    +++++++++ + ++ els
  gi|313126173|ref|YP_004036443.1| 665 MADELAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELS 712
                                       9*******9999999999999988888888888877777777776666 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.2   0.00034      0.15       4      82 ..     391     471 ..     388     482 .. 0.77
   2 ?    1.5   0.4      0.83   3.6e+02      44      85 ..     489     530 ..     466     531 .. 0.72
   3 ?    3.5   0.1      0.19        83       4      37 ..     573     606 ..     570     609 .. 0.88
   4 ?    4.4   3.6       0.1        45       7      82 ..     608     684 ..     606     686 .. 0.93
   5 ?    0.9   3.3       1.3   5.5e+02      39      75 ..     680     716 ..     642     723 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00034
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   4 vdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafq..aefeewkqaaqklvdaLeeisealkqaa 78 
                                        d e++r+ aa+f++ aeele+ l +l a  + ++s+ sG a+ a +  ++ +e+ q+++++ ++  e ++ l + +
  gi|313126173|ref|YP_004036443.1| 391 SDSEVMRTIAAAFNEMAEELETTLVALTAFGETVASSSSGVASGAAEvsSASDEIAQSVEQISAGAREQADHLAELS 467
                                       689*******************************9999998766543225555777777777777777777777666 PP

                                       HHHH CS
                            WXG100  79 nafe 82 
                                       ++++
  gi|313126173|ref|YP_004036443.1| 468 EEMS 471
                                       6665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.83
                                       HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  44 aaadafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                       + + a ++  +e ++aa+   d+ e i+ ++++a +++ed D
  gi|313126173|ref|YP_004036443.1| 489 DGSAAVAERADEGREAANGALDGVEAIEMETREAVESVEDLD 530
                                       456777788888899999999999999999999999999988 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.19
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100   4 vdpeelrqaaarfqkqaeeledelqrlkaevdal 37 
                                       v ++e+   a + ++ ae++ed +++l+++ +++
  gi|313126173|ref|YP_004036443.1| 573 VVADEVKHLAEETATYAETIEDHVSTLQSKRAEV 606
                                       67899999********************998776 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdal.qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82 
                                       e+++q+  ++ + a+e+ ++l++ +   d++ q++ s +   a  +e++  ++ +  ++d+L++i+e++++ a++++
  gi|313126173|ref|YP_004036443.1| 608 ERIEQMREQVEAGADEVDEALSSFDEIADSVsQNSASVEEVAAATGEQASTTEDVLSMADELAGIGEETTAEAENVS 684
                                       7899***************************99999999999999************************99999876 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.3
                                       CGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  39 sgWsGaaadafqaefeewkqaaqklvdaLeeisealk 75 
                                       +    aaa++  a++ e+ ++a +l+d+ +e+se l 
  gi|313126173|ref|YP_004036443.1| 680 AENVSAAAEEQTATLSEVSEGAHRLADQANELSELLS 716
                                       3444678888888888888888888888888888775 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.5   4.2e+03      37      63 ..     354     380 ..     348     432 .. 0.51
   2 ?    0.6   0.1       1.4     6e+02      80     117 ..     439     476 ..     384     489 .. 0.55
   3 ?    2.7   0.7       0.3   1.3e+02      34     114 ..     467     546 ..     436     564 .. 0.57
   4 ?    5.5   0.1     0.043        19      29     105 ..     518     600 ..     512     601 .. 0.72
   5 ?    9.2   0.4    0.0029       1.3      25      93 ..     598     665 ..     596     672 .. 0.88
   6 ?   -0.0   0.2       2.1     9e+02      45     114 ..     678     748 ..     655     752 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.5
                                       HCCCCCCCCCCCCHHHHHHHHHHHHHH CS
                         Fib_alpha  37 lekleneleeisnstkeaeelvkeikd 63 
                                       ++ l+++l++ ++  +  +++++e  d
  gi|313126173|ref|YP_004036443.1| 354 IDALRDDLKSQRDDARRYRDVMSEAAD 380
                                       555555555555555555554444333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.4
                                       HHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  80 kksskeleeeilrlketidaqesnirvLqnvlesneqk 117
                                       ++ s+e+ + ++++ +   +q  ++ +L + ++s++ +
  gi|313126173|ref|YP_004036443.1| 439 SSASDEIAQSVEQISAGAREQADHLAELSEEMSSLSAS 476
                                       33333333333333333333333333333333333333 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.3
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                                       ++++++l  ++e++s +t +  + + ++ +   e  + +++    ++ ++ e + e ++  e +d+++++i + ++v
  gi|313126173|ref|YP_004036443.1| 467 SEEMSSLSASVEQVSATTDDLADGSAAVAERADEGREAANGALDGVEAIEMETR-EAVESVEDLDDEIERISNVTGV 542
                                       444555555555555555555555555555555555555554444444444444.3333444445555555555555 PP

                                       HHHH CS
                         Fib_alpha 111 lesn 114
                                       + ++
  gi|313126173|ref|YP_004036443.1| 543 IADL 546
                                       5544 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.043
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn......dnvikksskeleeeilrlketida 99 
                                         ++  +++e+l +e+e+isn t  + +l ++++    ++  +++          v+ +  k+l ee +++ eti +
  gi|313126173|ref|YP_004036443.1| 518 ETREAVESVEDLDDEIERISNVTGVIADLAEQTNILALNASIEASRAgeagsgFAVVADEVKHLAEETATYAETIED 594
                                       56778899***************999999988776544443333332223335566677777788899*******99 PP

                                       CHHHHH CS
                         Fib_alpha 100 qesnir 105
                                       ++s+++
  gi|313126173|ref|YP_004036443.1| 595 HVSTLQ 600
                                       999886 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0029
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrl 93 
                                       +l++++ +v +++e++++++e  +++  ea +   ei ds+ ++ +s ++   ++ + +++ e ++l +
  gi|313126173|ref|YP_004036443.1| 598 TLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTTE-DVLSM 665
                                       6889999****************************************9998888888888777.66555 PP

  == domain 6  score: -0.0 bits;  conditional E-value: 2.1
                                       CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHCCCHHHHHHHCCHHHHHHHHHHHHHH CS
                         Fib_alpha  45 eeisnstkeaeelvkeikdslrekqkskkdndnvikkssk..eleeeilrlketidaqesnirvLqnvlesn 114
                                       +e++n +  aee + +++++ + + + +++  n ++++ +  ++  e ++++e+++   ++   L n+l++ 
  gi|313126173|ref|YP_004036443.1| 678 AEAENVSAAAEEQTATLSEVSEGAHRLADQ-ANELSELLSefDVSAEGIDFEEELSVDSETAATLENILREA 748
                                       456666777777777777777776666664.44444443302344566777888877777777777777765 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0046         2      33     113 ..     396     479 ..     384     489 .. 0.75
   2 ?    1.8   0.2      0.36   1.6e+02      87     117 ..     586     616 ..     521     631 .. 0.77
   3 ?    0.2   1.1       1.1   4.9e+02      13     110 ..     604     707 ..     592     721 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0046
                     PI3K_P85_iSH2  33 ydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskeaq...ehEieklqenleqlksrlkelhsskek 106
                                          +  ++n++ ee+++   al aF+e++      ++  +   + a+    + +e+++   ++  ++l el +++++
  gi|313126173|ref|YP_004036443.1| 396 MRTIAAAFNEMAEELETTLVALTAFGETVASSSSGVASGAAEVSSASdeiAQSVEQISAGAREQADHLAELSEEMSS 472
                                       55667789999999999999999999999888888777665555553334778888888888888899999999999 PP

                     PI3K_P85_iSH2 107 Leedlkq 113
                                       L+ +++q
  gi|313126173|ref|YP_004036443.1| 473 LSASVEQ 479
                                       8888776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.36
                     PI3K_P85_iSH2  87 qenleqlksrlkelhsskekLeedlkqqkee 117
                                        +  e +++++++l+s+++++ e ++q  e+
  gi|313126173|ref|YP_004036443.1| 586 ATYAETIEDHVSTLQSKRAEVVERIEQMREQ 616
                                       3445677788888888888888777776554 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.1
                     PI3K_P85_iSH2  13 eklseklrevskqlqekskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskea.........qe 80 
                                       +++ e+ +++ +q++  + e d+   ++ +i   ++   q     +e+     eq  + e + + a           
  gi|313126173|ref|YP_004036443.1| 604 AEVVERIEQMREQVEAGADEVDEALSSFDEIADSVS---QNSASVEEVAAATGEQASTTEDVLSMAdelagigeeTT 677
                                       456777777777777777777777777777777665...34444556666666777777766666644444444447 PP

                     PI3K_P85_iSH2  81 hEieklqenleqlksrlkelhsskekLeed 110
                                       +E e+++   e+ ++ l+e+ +   +L ++
  gi|313126173|ref|YP_004036443.1| 678 AEAENVSAAAEEQTATLSEVSEGAHRLADQ 707
                                       777777777777777777777766666655 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.3    0.0005      0.22      74     217 ..     392     536 ..     373     540 .. 0.56
   2 ?    4.0   4.9     0.051        22      71     173 ..     596     698 ..     543     720 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXX CS
                              AIP3  74 ldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavlrql 150
                                        +ev + i   ++++++el+ +  +++   ++ +++s+  ++ a+e +s   a++e +++++++++  r+ a     
  gi|313126173|ref|YP_004036443.1| 392 DSEVMRTIAAAFNEMAEELETTLVALTAFGETVASSSSGVASGAAEVSS---ASDEIAQSVEQISAGAREQADHLAE 465
                                       4566666666666666666666555544444444433333333333333...3344555555555554444444444 PP

                                       XXXXXXXXXXXXXXXXXXXXXXX..XXXX.XXXXXXHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 151 ysefkseikeslselrekakkvk..easlastkkssnray...iekgkkkLseesdklvtkvddLqDlvedl 217
                                        se +s++++s+++++++++++   +a++a    +++r+      +g + ++ e+ + v+ v+dL+D +e +
  gi|313126173|ref|YP_004036443.1| 466 LSEEMSSLSASVEQVSATTDDLAdgSAAVA-ERADEGREAangALDGVEAIEMETREAVESVEDLDDEIERI 536
                                       444455555555555555555554433332.222333333011457999*********************86 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.051
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXX CS
                              AIP3  71 iepldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavl 147
                                       +++l++ + ++ e +++++++++   +++++  +s +e++++ ++++++ ++  +a+ e+++ +++v s+  +La +
  gi|313126173|ref|YP_004036443.1| 596 VSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTTEDVLSMADELAGI 672
                                       23444444455555555555555555555666666666666666666666666666666777777777777777776 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3 148 rqlysefkseikeslselrekakkvk 173
                                        +  ++  +++++  +e ++++++v 
  gi|313126173|ref|YP_004036443.1| 673 GEETTAEAENVSAAAEEQTATLSEVS 698
                                       66666666666655555555555554 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   9.8   0.00022     0.097      36     239 ..     522     717 ..     494     733 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                               MAD  36 asalkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalkne 112
                                       a ++ ++l+ e +r  +++  i  l ++   +  al++ iE +r            + e  s  a + +  + l +e
  gi|313126173|ref|YP_004036443.1| 522 AVESVEDLDDEIERISNVTGVIADLAEQT--NILALNASIEASR------------AGEAGSGFAVVADEVKHLAEE 584
                                       55555566666666666666665555443..3345555566555............5566666666667777899** PP

                               MAD 113 laelkrqiekqelelsekesel.eelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqsqeddsli 188
                                       +a +++ ie+  + l++k+ e+ e++++  +  ++ + e+++  +++++  ++ +++ + + e      +q++  + 
  gi|313126173|ref|YP_004036443.1| 585 TATYAETIEDHVSTLQSKRAEVvERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTTED 661
                                       *******************996488999999999******************************************* PP

                               MAD 189 vknskselari.....pelekelerlreenkklnelkenkelLkEevedlkkkLer 239
                                       v ++ +ela i     +e e+  ++ +e+ + l+e++e  + L  ++++l + L+ 
  gi|313126173|ref|YP_004036443.1| 662 VLSMADELAGIgeettAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSE 717
                                       ********988333224566667788999999999999999999999999887765 PP

>> BAR_2  Bin/amphiphysin/Rvs domain for vesicular trafficking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.5   0.00013     0.059      67     167 ..     390     490 ..     387     496 .. 0.93
   2 ?    1.0   5.7      0.44   1.9e+02      67     166 ..     534     647 ..     520     726 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                             BAR_2  67 esisdwwksigaklkelknvssleedeivllgkkkkekskeekesqatsallprtlaqalskaakdsslilqeleek 143
                                       es s++ ++i+a ++e+ +  +++   ++ +g+  + +s+      a+ ++ +  +aq + ++++++ ++ ++l e 
  gi|313126173|ref|YP_004036443.1| 390 ESDSEVMRTIAAAFNEMAEELETTLVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAGAREQADHLAEL 466
                                       5668899*******************************99999999999999************************* PP

                             BAR_2 144 dedlepLikvleqvssaykeiaea 167
                                       +e++++L+   eqvs +  ++a++
  gi|313126173|ref|YP_004036443.1| 467 SEEMSSLSASVEQVSATTDDLADG 490
                                       *****************9998876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                             BAR_2  67 esisdwwksiga...klkelknvssleedeivllgkkkkekskeekesqatsallprtlaqalskaakdsslilqel 140
                                       e is+++ +i++   + + l   +s e ++    g+  +   +e k+  ++ a+   t+  ++s + ++ +++++++
  gi|313126173|ref|YP_004036443.1| 534 ERISNVTGVIADlaeQTNILALNASIEASRAGEAGSGFAVVADEVKHLAEETATYAETIEDHVSTLQSKRAEVVERI 610
                                       45555554443300033333344555556666666666777777777889999999999999999999999999999 PP

                             BAR_2 141 e...........ekdedlepLikvleqvssaykeiae 166
                                       e           e de+l++  ++ ++vs+  ++++e
  gi|313126173|ref|YP_004036443.1| 611 EqmreqveagadEVDEALSSFDEIADSVSQNSASVEE 647
                                       9888888888875555554444444444444333332 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0089       3.9      30      88 ..     426     483 ..     397     556 .. 0.58
   2 ?    5.5   1.4      0.02       8.9       7      81 ..     585     658 ..     571     672 .. 0.47
   3 ?    1.8   0.3      0.27   1.2e+02      14      80 ..     676     750 ..     659     762 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0089
                             TMPIT  30 klqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesl 88 
                                       ++ s +++ +++ +    e+ +s++++++ + +e++++++el+ee+++ ++++++v+++
  gi|313126173|ref|YP_004036443.1| 426 SSSSGVASGAAEVSSASDEIAQSVEQISAGA-REQADHLAELSEEMSSLSASVEQVSAT 483
                                       5555555555555555555555555555443.455555555555555555555544443 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.02
                             TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                        ++ ++++e++ +++++k +e+ + +++++++++    ++ e  ss++++  sv ++++  vee+++ + e+ ++
  gi|313126173|ref|YP_004036443.1| 585 TATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSV-SQNSASVEEVAAATGEQAST 658
                                       222233444444444444444444444444444444444444444444444443.34555555555555554444 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.27
                             TMPIT  14 leetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk........eeeeeeveelkeelkerkk 80 
                                         ++a+++ +  ee ++  s++s+ +++   +++el++ l++++ s++        + ++e++++l++ l+e+++
  gi|313126173|ref|YP_004036443.1| 676 TTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSEFDVSAEgidfeeelSVDSETAATLENILREAEN 750
                                       333334444444444444444444445555555555555555554444555555555566666666666665555 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2       1.7   7.6e+02      17      61 ..     403     451 ..     373     462 .. 0.59
   2 ?    6.8   0.5      0.02       8.7      11      47 ..     460     496 ..     449     498 .. 0.86
   3 ?   -0.9   0.1         5   2.2e+03      15      48 ..     513     546 ..     507     563 .. 0.72
   4 ?   11.5   2.3   0.00069       0.3      23      78 ..     602     657 ..     577     669 .. 0.77
   5 ?    1.2   0.1       1.1   4.9e+02      12      43 ..     692     723 ..     678     753 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.7
                         DASH_Dad2  17 lrdlsdslakqleeLeeklstladgteavas....VlanWqnvlraism 61 
                                       +++++++l++ l +L    +t+a+ ++ vas    V +  +++ +++++
  gi|313126173|ref|YP_004036443.1| 403 FNEMAEELETTLVALTAFGETVASSSSGVASgaaeVSSASDEIAQSVEQ 451
                                       4556666666655555555555555554443111144444444444444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.02
                         DASH_Dad2  11 LeaLkqlrdlsdslakqleeLeeklstladgteavas 47 
                                        ++L +l++  +sl+  +e+++   + ladg++ava+
  gi|313126173|ref|YP_004036443.1| 460 ADHLAELSEEMSSLSASVEQVSATTDDLADGSAAVAE 496
                                       568999999999999*******************985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 5
                         DASH_Dad2  15 kqlrdlsdslakqleeLeeklstladgteavasV 48 
                                       ++++  + +  + +e L+++++ +++ t ++a+ 
  gi|313126173|ref|YP_004036443.1| 513 EAIEMETREAVESVEDLDDEIERISNVTGVIADL 546
                                       5666677777777888888888888777777765 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00069
                         DASH_Dad2  23 slakqleeLeeklstladgteavasVlanWqnvlraismaslkllqkaeeeaeeee 78 
                                       + a+ +e++e+  ++++ g++ v + l++++++  ++s+ s+++ + a+++ e+ +
  gi|313126173|ref|YP_004036443.1| 602 KRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQAS 657
                                       445667888888889999*************************9855554333332 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 1.1
                         DASH_Dad2  12 eaLkqlrdlsdslakqleeLeeklstladgte 43 
                                       ++L ++++ + +la+q +eL+e ls+ +  +e
  gi|313126173|ref|YP_004036443.1| 692 ATLSEVSEGAHRLADQANELSELLSEFDVSAE 723
                                       45777777777777777777777776665555 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0094       4.1      37      78 ..     447     488 ..     435     497 .. 0.80
   2 ?    1.9   0.2      0.64   2.8e+02      49      83 ..     511     542 ..     491     556 .. 0.63
   3 ?    7.4   1.3     0.012       5.3      35      91 ..     599     655 ..     572     660 .. 0.78
   4 ?    2.3   0.6      0.48   2.1e+02      53      90 ..     680     717 ..     656     750 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0094
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                       ++++++ a++++++++l e++ee++++  +++q+ +++++L 
  gi|313126173|ref|YP_004036443.1| 447 QSVEQISAGAREQADHLAELSEEMSSLSASVEQVSATTDDLA 488
                                       567888888999999999999999999999999988888885 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.64
                           BLOC1_2  49 kleklnekyeelqpylqqidqiekqvteLeeavse 83 
                                        +   ++ + e ++ ++++++++++++++ ++  +
  gi|313126173|ref|YP_004036443.1| 511 GV---EAIEMETREAVESVEDLDDEIERISNVTGV 542
                                       33...333347777777777777777777666544 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.012
                           BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                          k ++v++ +e+  e++++  +e+++ l++ d+i ++v++  + v+e+ + + e+
  gi|313126173|ref|YP_004036443.1| 599 LQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQ 655
                                       445667888889999999999999999999999999999999999999888877766 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.48
                           BLOC1_2  53 lnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                        ++ +++ +++   + ++ +   +L + ++eL e  +e
  gi|313126173|ref|YP_004036443.1| 680 AENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSE 717
                                       33333344444444444444444444444444433333 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.17        76      55     112 ..     438     495 ..     402     509 .. 0.51
   2 ?    6.6   1.1     0.008       3.5      59     172 ..     586     698 ..     572     717 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.17
                             Atg14  55 aeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk 112
                                       +++++d+i ++ ++++    ++ad  ++l+e + +ls   +++ ++   la  s++++
  gi|313126173|ref|YP_004036443.1| 438 VSSASDEIAQSVEQISAGAREQADHLAELSEEMSSLSASVEQVSATTDDLADGSAAVA 495
                                       3333444444444444444444444444444444444444444444444455555554 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.008
                             Atg14  59 edkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiak 135
                                       ++ +++  + +++l+s++a+  er+++++++++   +e++e+   + +  d++++  ++ e +     e +++  + 
  gi|313126173|ref|YP_004036443.1| 586 ATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGE-QASTTED 661
                                       455666777888999999999999999999999999999999999999999999888887777665554.5666677 PP

                             Atg14 136 lqdaikrieqklsslssktlesrsslcselaklyglr 172
                                       ++++  + +  +++ + +    ++   ++ a l++++
  gi|313126173|ref|YP_004036443.1| 662 VLSMADELAGIGEETTAEAENVSAAAEEQTATLSEVS 698
                                       7777775555555555555555444444444444444 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.7   0.00032      0.14      27     271 ..     405     658 ..     386     672 .. 0.59
   2 ?   -0.4   7.0      0.46     2e+02      15      93 ..     593     702 ..     575     758 .. 0.41

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00032
                        V_ATPase_I  27 kevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelv 103
                                       +    ++     l+ + e++++ ++ v++   +++s +++ +++++++++  ++  ++l el+e++++l+++++++ 
  gi|313126173|ref|YP_004036443.1| 405 EMAEELETTLVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAGAREQADHLAELSEEMSSLSASVEQVS 481
                                       33334444444444444444444444444444455555555555555555555555555555555555555555555 PP

                        V_ATPase_I 104 elkavlekakefleeeeeeeeeeeseeeeee....keeeeeeeseeeeeeelleeeeelsfvaGvi....krekvea 172
                                        ++  l   ++ ++e+++e +e+ +     +    ++ e+e++++ e+ e+l +e e++s+v+Gvi    +++++ a
  gi|313126173|ref|YP_004036443.1| 482 ATTDDLADGSAAVAERADEGREAANG----AldgvEAIEMETREAVESVEDLDDEIERISNVTGVIadlaEQTNILA 554
                                       55555555555544432222222222....12222333333333333333344444458999999933334678889 PP

                        V_ATPase_I 173 ferilwralrgnlflrqaeieepledp....et.gekveksvfiiffqgeqlkekikkicesfgaklyelpeseeer 244
                                       ++  +     g++   +a + +++++     +t  e++e +v  +  +  ++ e+i+++ e ++a   e++e  ++ 
  gi|313126173|ref|YP_004036443.1| 555 LNASIEASRAGEAGSGFAVVADEVKHLaeetATyAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSF 631
                                       9999877766766555555544444331111444788899999999999*************************999 PP

                        V_ATPase_I 245 eeklkeveeriedlekvleqteealke 271
                                       +e +++v+++ + +e+v  +t e+ ++
  gi|313126173|ref|YP_004036443.1| 632 DEIADSVSQNSASVEEVAAATGEQAST 658
                                       999999999999999999888776554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.46
                        V_ATPase_I  15 nedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeea................................ 59 
                                       +++v+++q k ++ v r+++m ++++   +e++++      e  +                                
  gi|313126173|ref|YP_004036443.1| 593 EDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEAL-SSFDEIADsvsqnsasveevaaatgeqasttedvlsmade 668
                                       333333444444444444444444444333333311.1111111112222222222222222222222222222222 PP

                        V_ATPase_I  60 eesleapeekeldeleeelekleeelkelnenle 93 
                                        +   +++++e +++++  e+ ++ l+e++e ++
  gi|313126173|ref|YP_004036443.1| 669 LAGIGEETTAEAENVSAAAEEQTATLSEVSEGAH 702
                                       2222222222222222222222223333333333 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.065        28      12      57 ..     449     494 ..     436     507 .. 0.57
   2 ?   -0.3   0.0       2.1     9e+02      13      47 ..     513     547 ..     503     554 .. 0.72
   3 ?    4.4   0.2     0.072        31      20      74 ..     590     634 ..     573     641 .. 0.46
   4 ?    7.3   0.2    0.0094       4.1       2      62 ..     614     674 ..     607     682 .. 0.83
   5 ?    2.2   0.3      0.33   1.5e+02      10      72 ..     657     719 ..     652     728 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.065
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrl 57 
                                       ++++ + ++e  ++L+el+e+++s s++ +++++++++l +    +
  gi|313126173|ref|YP_004036443.1| 449 VEQISAGAREQADHLAELSEEMSSLSASVEQVSATTDDLADGSAAV 494
                                       4444555555555555555555555555555555555555544444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.1
                             Sec34  13 delleqtdealeqLeeleekfksvsektsslheac 47 
                                       +++  +t+ea e++e+l ++ +++s+ t  + + +
  gi|313126173|ref|YP_004036443.1| 513 EAIEMETREAVESVEDLDDEIERISNVTGVIADLA 547
                                       55666788888888888888888888776665554 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.072
                             Sec34  20 dealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeel 74 
                                       +++++++++l++k  +v e+ +++          ++++e  a+e++e L+ F+e+
  gi|313126173|ref|YP_004036443.1| 590 ETIEDHVSTLQSKRAEVVERIEQM----------REQVEAGADEVDEALSSFDEI 634
                                       233333333333333333333333..........344455566666666666664 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0094
                             Sec34   2 ldqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelae 62 
                                       ++q+e+  +e+de l++ de+ +++++ + ++++v++ t +  +++e++l+  ++l  + e
  gi|313126173|ref|YP_004036443.1| 614 REQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTTEDVLSMADELAGIGE 674
                                       5678888889999999999999999999999999999999999999999988888876665 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.33
                             Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe 72 
                                       ++++++l+ +de+    ee + + ++vs+  ++  ++  ++ e  +rl + a+e++e L+ F+
  gi|313126173|ref|YP_004036443.1| 657 STTEDVLSMADELAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSEFD 719
                                       556667777777777777777777777777777777777777777777777777777777775 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.7     0.012       5.4      23     161 ..     402     534 ..     385     540 .. 0.65
   2 ?    6.9  13.7     0.015       6.5      22     160 ..     576     718 ..     544     750 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                             ATG16  23 aynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrge 99 
                                       a+n++++  ++      +  +  as++s      +a+  ++ +s+ + + ++++++ ++   ++ + lael  + + 
  gi|313126173|ref|YP_004036443.1| 402 AFNEMAEELETTLVALTAFGETVASSSS-----GVASGAAEVSSA-SDEIAQSVEQISAGAREQADHLAELSEEMSS 472
                                       4444444433322222222222222222.....111111111111.2233445555666666677789999999999 PP

                             ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEls 161
                                       l+ ++ +++++ ++l + + + +er +e ++  +   + ++  e+e re  + v+dl DE++
  gi|313126173|ref|YP_004036443.1| 473 LSASVEQVSATTDDLADGSAAVAERADEGREAANGALDGVEAIEMETREAVESVEDLDDEIE 534
                                       99999999999999999999999999999999999999999999999999999999999986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.015
                             ATG16  22 qaynrLldrtsaleaenaklekaaasaks....sksskksakekeasasq.........snskqsakiqsleqklaq 85 
                                       +  ++L++ t++ ++  + + +  +s+++    +   ++ ++       q         ++ ++ ++i+++ ++ ++
  gi|313126173|ref|YP_004036443.1| 576 DEVKHLAEETATYAETIEDHVSTLQSKRAevveR--IEQMRE-------QveagadevdEALSSFDEIADSVSQNSA 643
                                       4445555555555555555544444444444221..111111.......122334456688889999********** PP

                             ATG16  86 lreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEl 160
                                         ee+a++  +++ +++ +l++ +el+   e++++++e++ ++ +e +a   ++++ +++l+++++ + +l  E 
  gi|313126173|ref|YP_004036443.1| 644 SVEEVAAATGEQASTTEDVLSMADELAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSEF 718
                                       ************************************************************999998888776665 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1  20.8      0.39   1.7e+02     127     331 ..     395     719 ..     350     752 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH..................-------STCCHHHHHHHHHHHHHH CS
                             APG17 127 alkesidelqaaqkkldssllefdtdlrelkkel..................sksksksessslipellkeleslee 185
                                        ++++ + ++++ ++l+++l ++                             s+s++ ++s + i+   +e+ ++  
  gi|313126173|ref|YP_004036443.1| 395 VMRTIAAAFNEMAEELETTLVALTAF-------GetvassssgvasgaaevsSASDEIAQSVEQISAGAREQADHLA 464
                                       23333444445555555544444444.......144455559999999998654555559999999*********** PP

                                       HHHHHHHHHHHHHHHHHHH.......................................................... CS
                             APG17 186 emAslLesLtnHfDqcvkAvkltegggal.rraaae......................................... 220
                                       e+ + ++sL    +q++  ++ + +g+a+  ++a e                                         
  gi|313126173|ref|YP_004036443.1| 465 ELSEEMSSLSASVEQVSATTDDLADGSAAvAERADEgreaangaldgveaiemetreavesvedlddeierisnvtg 541
                                       ***********************99999977777779**************************************** PP

                                       ...............................................................S-CCHHHHHHHHHH CS
                             APG17 221 ...............................................................lseeereelleVle 234
                                                                                                         e  e++ e +e
  gi|313126173|ref|YP_004036443.1| 542 viadlaeqtnilalnasieasrageagsgfavvadevkhlaeetatyaetiedhvstlqskraEVVERIEQMREQVE 618
                                       ************************************************99999999998887633344679****** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHH....HHHHHHHH.. CS
                             APG17 235 kDaaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifk....aeeeflerwe 307
                                         a e+++ + + +e+++++++ +++++e ++++ ++ s++ ++l++ +e+    +e+ a  +    a+ee +++ +
  gi|313126173|ref|YP_004036443.1| 619 AGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTTEDVLSMADELAGIGEETTAEAEnvsaAAEEQTATLS 695
                                       ********************999999999999999999999998888887755555555422200002223333335 PP

                                       .HHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 308 eekekieekleeleeLrefYegFl 331
                                       e  e  ++  ++ +eL+e   +F 
  gi|313126173|ref|YP_004036443.1| 696 EVSEGAHRLADQANELSELLSEFD 719
                                       555555555556666666655555 PP

>> DUF725  Protein of unknown function (DUF725)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4       1.7   7.4e+02      78     103 ..     440     465 ..     432     485 .. 0.76
   2 ?   11.6   2.6   0.00047      0.21      12      99 ..     580     671 ..     575     724 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.7
                            DUF725  78 kagsenskilysisanAtelaaklse 103
                                       +a++e ++++++isa A e+a +l e
  gi|313126173|ref|YP_004036443.1| 440 SASDEIAQSVEQISAGAREQADHLAE 465
                                       56667778888888888888877765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00047
                            DUF725  12 elnevaeqyeaeytkCistaeeekaeidekyeeerqqlessakeicsalqkCdsledalda....feCyakagsens 84 
                                        l+e +++y + +++ +st ++++ae+ e++e+ r+q+e  a+e+ +al++ d++ d++++     e +a+a  e++
  gi|313126173|ref|YP_004036443.1| 580 HLAEETATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQnsasVEEVAAATGEQA 656
                                       67888999*****************************************9997666665431111444555555666 PP

                            DUF725  85 kilysisanAtelaa 99 
                                       ++++++ + A ela 
  gi|313126173|ref|YP_004036443.1| 657 STTEDVLSMADELAG 671
                                       666666666666555 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.3     1e+03     117     148 ..     447     478 ..     435     498 .. 0.50
   2 ?    7.5   4.2    0.0046         2     102     228 ..     593     718 ..     573     721 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.3
                           Taxilin 117 aqieekserneklreenaelteKlkslieqye 148
                                       +++e+ s+   ++++  ael+e ++sl + +e
  gi|313126173|ref|YP_004036443.1| 447 QSVEQISAGAREQADHLAELSEEMSSLSASVE 478
                                       33333333333333333333333333333332 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0046
                           Taxilin 102 kelaekfqakLkdiqaqieekserneklreenaelteKlkslieqyelreehfekllktkelelqlaeaKlqqadal 178
                                       ++  + +q+k +++ ++ie+ +e+ e  ++e  e  + ++++++ + +    +e++  +   +    e  l  ad+ 
  gi|313126173|ref|YP_004036443.1| 593 EDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTTEDVLSMADE- 668
                                       33445678888888889999999999988888888889*********************************77777. PP

                           Taxilin 179 lkeeqekkkrekeyllkeakeltkkvkalketekelkeqlnlYaeKfeef 228
                                       l+   e+ ++e+e + + a+e t+++++++e  + l +q n  +e  +ef
  gi|313126173|ref|YP_004036443.1| 669 LAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSEF 718
                                       6677777888899989***********************99888777776 PP

>> Flagellar_rod  Paraflagellar rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.26   1.1e+02     108     162 ..     402     456 ..     391     475 .. 0.82
   2 ?    9.1   2.6    0.0018      0.81      92     161 ..     557     627 ..     473     634 .. 0.72
   3 ?    1.5   0.3       0.4   1.7e+02      15      74 ..     656     715 ..     638     742 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.26
                     Flagellar_rod 108 vaeqhkqkLrktlenldkaldlarsleelVkegvkklkakqdklqnalselllev 162
                                       + ++ ++ L++tl  l +  + ++s ++ V++g +++ +  d++ + ++++    
  gi|313126173|ref|YP_004036443.1| 402 AFNEMAEELETTLVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAGA 456
                                       45677889999***************************999*9999999987533 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                     Flagellar_rod  92 eerEekRetdy.eeFlkvaeqhkqkLrktlenldkaldlarsleelVkegvkklkakqdklqnalsellle 161
                                       ++ E+ R  ++ + F+ va++ k+  ++t +++++++d +  l++  +e v+++++ +++++  ++e+ ++
  gi|313126173|ref|YP_004036443.1| 557 ASIEASRAGEAgSGFAVVADEVKHLAEETATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEA 627
                                       455777876662569****************************************9999998888887655 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.4
                     Flagellar_rod  15 eaveeDlekikekreeeaaadekqrkrykaqreesdkflqeneeqqeklvreieelereL 74 
                                          +eD+  ++++++ + ++ ++  ++ +a  ee  + l+e++e  + l  + +el + L
  gi|313126173|ref|YP_004036443.1| 656 ASTTEDVLSMADELAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELL 715
                                       445678888888888888888888888888888888888888777666665555554444 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.1   9.4e+02     136     136 ..     446     446 ..     355     487 .. 0.58
   2 ?    8.4   0.8    0.0039       1.7      85     148 ..     586     650 ..     574     713 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.1
                      Bacillus_HBL 136 a 136
                                       a
  gi|313126173|ref|YP_004036443.1| 446 A 446
                                       1 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0039
                      Bacillus_HBL  85 qsyyktlveav..dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvde 148
                                       + y++t++  v   + ++ae++e++e+++e++     ev++ +    + ++++ ++s++ ++ v+ 
  gi|313126173|ref|YP_004036443.1| 586 ATYAETIEDHVstLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEE-VAA 650
                                       67999**9999877899***************************999999999999998764.334 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.2   9.8e+02      54     109 ..     347     405 ..     342     417 .. 0.53
   2 ?    9.7  16.2    0.0017      0.73      33     180 ..     404     549 ..     393     561 .. 0.72
   3 ?    0.6  14.5      0.98   4.3e+02      29     155 ..     558     686 ..     542     756 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.2
                     PhageMin_Tail  54 leeaaeilstalnafglsaadaeeaaDvlaaaanngatsvedla...ealkevgavaka 109
                                        +++++ + ++ + ++ + +da +  Dv+++aa+   t   dl    e++  ++a+++ 
  gi|313126173|ref|YP_004036443.1| 347 FGSVVDGIDALRDDLKSQRDDARRYRDVMSEAADGDLTVRMDLEsdsEVMRTIAAAFNE 405
                                       56666666666666666655777777777777665555444444333444444444444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                     PhageMin_Tail  33 eeilnllegaaklataggaddleeaaeilstalnafglsaadaeeaaDvlaaaanngatsvedlaealkevgavaka 109
                                       +e+ + le+++ + ta+g + + +++ ++s a++   +s +++++ + +++a+a + a+ +++l+e ++ ++a+  +
  gi|313126173|ref|YP_004036443.1| 404 NEMAEELETTLVALTAFGETVASSSSGVASGAAEVSSAS-DEIAQSVEQISAGAREQADHLAELSEEMSSLSASVEQ 479
                                       6888899999********663444444555555555555.7************************************ PP

                     PhageMin_Tail 110 aGlsfeetaaalallaaagikgseAgtalknllsrl...tkeaaealkklGistkdaqgkmksldeiledlsea 180
                                          + ++ a   a+ a+   +g eA+++    + ++   t ea e +++l     d   ++ + ++++ dl+e+
  gi|313126173|ref|YP_004036443.1| 480 VSATTDDLADGSAAVAERADEGREAANGALDGVEAIemeTREAVESVEDLD----DEIERISNVTGVIADLAEQ 549
                                       *******88888888887767777777666666666444456666666652....3334444555555555444 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.98
                     PhageMin_Tail  29 Gvsteeilnllegaaklataggaddleeaaeilstal...nafglsaadaeeaaDvlaaaanngatsvedlaealke 102
                                        +++  + +++ g a +a  ++   +ee+a+++ t+    + ++ + a++ e   ++ + + +ga++v++  +++ e
  gi|313126173|ref|YP_004036443.1| 558 SIEASRAGEAGSGFAVVADEVKHL-AEETATYAETIEdhvSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDE 633
                                       555555666667777777777766.88888888888743345555544999999*********************** PP

                     PhageMin_Tail 103 vgavakaaGlsfeetaaalallaaagikgseAgtalknllsrltkeaaealkk 155
                                       ++ + ++   s ee+aaa + +a+++++    ++ l+ +  + t+ea++   +
  gi|313126173|ref|YP_004036443.1| 634 IADSVSQNSASVEEVAAATGEQASTTEDVLSMADELAGIGEETTAEAENVSAA 686
                                       ************************99998889999999988885544444333 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.8   7.7e+02      65     108 ..      63      84 ..      28     126 .. 0.55
   2 ?   10.7   2.6   0.00053      0.23       4      90 ..     414     500 ..     410     510 .. 0.89
   3 ?    6.8   2.9    0.0082       3.6      12      77 ..     569     634 ..     561     652 .. 0.73
   4 ?    0.3   3.0      0.79   3.5e+02      10      76 ..     651     717 ..     642     743 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                           DUF3450  65 vyneqlerlvasqeqeiasleeqieeieeierelvpllekmidr 108
                                       ++ eql+ +v+sq+q                        +m++r
  gi|313126173|ref|YP_004036443.1|  63 LQSEQLSGWVSSQKQ----------------------TARMVSR 84 
                                       222233333333322......................2334444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00053
                           DUF3450   4 llalllasgalaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqe 80 
                                       l+al++++ ++a++ + + + a++  +a+ ++ + +++++  ++e ++ + +l+ee +sl++  eq+++  +++   
  gi|313126173|ref|YP_004036443.1| 414 LVALTAFGETVASSSSGVASGAAEVSSASDEIAQSVEQISAGAREQADHLAELSEEMSSLSASVEQVSATTDDLADG 490
                                       678888888889999*******************************************************9999998 PP

                           DUF3450  81 iasleeqiee 90 
                                        a + e+ +e
  gi|313126173|ref|YP_004036443.1| 491 SAAVAERADE 500
                                       8888887776 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0082
                           DUF3450  12 galaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasq 77 
                                       +++a  +d++++ ae++ + a+ ++  ++ l+ +++e+++++++++e++e+ + + ++  ++ ++ 
  gi|313126173|ref|YP_004036443.1| 569 SGFAVVADEVKHLAEETATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEI 634
                                       5557789999***********************************999987554444443333333 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.79
                           DUF3450  10 asgalaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvas 76 
                                       a+g  a+t +++l+ a +   + +++ ++ ++++  ++e  a + +++e + +l+ + ++l++l+++
  gi|313126173|ref|YP_004036443.1| 651 ATGEQASTTEDVLSMADELAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSELLSE 717
                                       4445566666666666666666666666666666666666666666666666666666666666554 PP

>> I_LWEQ  I/LWEQ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0  10.0   0.00088      0.39      37     134 ..     433     527 ..     396     569 .. 0.75
   2 ?   -0.5   0.3       3.1   1.3e+03      58     101 ..     555     598 ..     539     619 .. 0.45
   3 ?    2.5   9.4      0.35   1.5e+02      15     111 ..     621     720 ..     615     753 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00088
                            I_LWEQ  37 akeeeLivaakevaastaqLvvasrvKadk...nskslkrLeaaskaVkkatkelvkavkeakekqeeeeseeeeld 110
                                       +   e+ +a++e+a+s+ q+ + +r +ad     s++++ L+a+ ++V+ +t++l     +++e+++e +      +
  gi|313126173|ref|YP_004036443.1| 433 SGAAEVSSASDEIAQSVEQISAGAREQADHlaeLSEEMSSLSASVEQVSATTDDLADGSAAVAERADEGR------E 503
                                       4567899*********************9622257888899999999999*****999999998877763......4 PP

                            I_LWEQ 111 isklslvqakrqemeaqvkilkle 134
                                         +  l +  + eme+++++ + e
  gi|313126173|ref|YP_004036443.1| 504 AANGALDGVEAIEMETREAVESVE 527
                                       677777777777777777765444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.1
                            I_LWEQ  58 vasrvKadknskslkrLeaaskaVkkatkelvkavkeakekqee 101
                                         + + a++ +++ +    ++ +Vk+ ++e    +++++++ ++
  gi|313126173|ref|YP_004036443.1| 555 LNASIEASRAGEAGSGFAVVADEVKHLAEETATYAETIEDHVST 598
                                       44444445555555555555555555555444444444433332 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.35
                            I_LWEQ  15 AkaVaaaanlLveaadavvqgkakeeeLivaakevaastaqLvvasrvKadknskslkrLeaaskaVkkatkelvka 91 
                                       A +V +a ++  e ad+v q+ a+ ee+ +a  e a+ t  ++  +   a    ++ ++ e++s+a +++t+ l + 
  gi|313126173|ref|YP_004036443.1| 621 ADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQASTTEDVLSMADELAGIGEETTAEAENVSAAAEEQTATLSEV 697
                                       788999999***************************************************************99999 PP

                            I_LWEQ  92 vkeakekqeeee...s..eeeeldi 111
                                        + a+  +++++   +  +  e+d+
  gi|313126173|ref|YP_004036443.1| 698 SEGAHRLADQANelsEllS--EFDV 720
                                       9999988888753321221..3333 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.8   3.4e+03      29      55 ..     355     381 ..     352     414 .. 0.54
   2 ?    5.2   0.1     0.026        12      84     133 ..     446     495 ..     437     540 .. 0.86
   3 ?    2.8   6.9      0.15        66      69     194 ..     577     709 ..     571     715 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.8
                               GAS  29 kslKeeieelkkkeernekelseisqe 55 
                                       + l+++++  +  ++r +  +se++  
  gi|313126173|ref|YP_004036443.1| 355 DALRDDLKSQRDDARRYRDVMSEAADG 381
                                       555555555555555555555555443 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.026
                               GAS  84 kqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaai 133
                                        qs +++ a  +e+ ++l +l++e  +l+  +e+v++  d+l +   a+ 
  gi|313126173|ref|YP_004036443.1| 446 AQSVEQISAGAREQADHLAELSEEMSSLSASVEQVSATTDDLADGSAAVA 495
                                       57788888999999999999999999999999999999999988776655 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.15
                               GAS  69 eveeLrkqlknyekdkqsl.knlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaa...iqevqqktg 141
                                       ev++L ++ ++y +  +++   l+++  e+ + +++++++ e   ++++++ +++de+ ++  ++   ++ev   tg
  gi|313126173|ref|YP_004036443.1| 577 EVKHLAEETATYAETIEDHvSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNsasVEEVAAATG 653
                                       66666666666666555431455666667777777777777777777777777666666655443333677777777 PP

                               GAS 142 lknllLekklk...alqeelEkkeaqleevlaaanldpaalsavsekleevlesKn 194
                                        ++   e  l+   +l    E+ +a+ e v aaa+ ++a+ls+vse+ +++ ++ n
  gi|313126173|ref|YP_004036443.1| 654 EQASTTEDVLSmadELAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQAN 709
                                       77776665554111333345666777777777777777777777777666666555 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.058        25      74     115 ..     442     483 ..     431     494 .. 0.57
   2 ?    4.3   0.2     0.096        42      57     107 ..     578     629 ..     572     652 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.058
                                       XXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHH CS
                              COG5  74 lselksslesLsasyerlkskvlepyeeaeklqsalkrlhqt 115
                                        +e+ +s+e++sa  +    ++ e  ee+++l+++ +++  t
  gi|313126173|ref|YP_004036443.1| 442 SDEIAQSVEQISAGAREQADHLAELSEEMSSLSASVEQVSAT 483
                                       555555555555555555555555555555555555555554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.096
                                       XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHH CS
                              COG5  57 hleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeaeklqs 107
                                        ++L e++ + +++ + ++s+l+s+ +++ + +e+++++v    +e+++  s
  gi|313126173|ref|YP_004036443.1| 578 VKHLAEETATYAETIEdHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALS 629
                                       5566666666666555577777777777777777777777665555555444 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.9     0.065        28      57     144 ..     441     530 ..     435     539 .. 0.59
   2 ?    9.0   3.8    0.0028       1.2      50     132 ..     581     670 ..     577     715 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.065
                                       HHHHTTT...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXX CS
                        DASH_Spc19  57 laeeieP...qieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskk 130
                                        ++ei++   qi+   ++  ++l++l+++ ++L a +e+ +   ++ ++ +++ +e++++ +e+ + + +   ++++
  gi|313126173|ref|YP_004036443.1| 441 ASDEIAQsveQISAGAREQADHLAELSEEMSSLSASVEQVSATTDDLADGSAAVAERADEGREAANGALD-GVEAIE 516
                                       4455555000445555666789999999999999999999999999766666666666655544443332.222233 PP

                                       XXXXXXXXXXXXXX CS
                        DASH_Spc19 131 kltkeelerlkkLk 144
                                         t+e  e +++L 
  gi|313126173|ref|YP_004036443.1| 517 METREAVESVEDLD 530
                                       34555555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX... CS
                        DASH_Spc19  50 leaakaslaeeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeee 126
                                       l++  a +ae+ie ++++l +k  + +e+ e+ +e+ +a ++  +  ls+ ++ +++ ++++ s ee   +++++++
  gi|313126173|ref|YP_004036443.1| 581 LAEETATYAETIEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEIADSVSQNSASVEEVAAATGEQAS 657
                                       77888999******************************************999999988888888887777776655 PP

                                       .XXXX.......X CS
                        DASH_Spc19 127 kskkk.......l 132
                                        +++        +
  gi|313126173|ref|YP_004036443.1| 658 TTEDVlsmadelA 670
                                       5444365555550 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.5      0.11        50      70     129 ..     423     480 ..     399     488 .. 0.62
   2 ?    2.9   0.9      0.25   1.1e+02      73     131 ..     468     528 ..     460     539 .. 0.58
   3 ?    1.1   0.1      0.91     4e+02      69     105 ..     510     545 ..     506     559 .. 0.75
   4 ?    6.9   1.4     0.014       6.1      67     109 ..     592     634 ..     586     650 .. 0.84
   5 ?    2.8   0.6      0.26   1.1e+02      56     109 ..     661     714 ..     638     733 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                              COG2  70 eleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevvekl 129
                                        +   +s +a+   +v+s+ +++++  e++++  +e+++     el + + +l++ ve++
  gi|313126173|ref|YP_004036443.1| 423 TVASSSSGVASGAAEVSSASDEIAQSVEQISAGAREQADH--LAELSEEMSSLSASVEQV 480
                                       4444555666666777777777777777777776655442..224444444444444444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.25
                              COG2  73 evesplaaarkkvesvreklsereeeveskleeakeleekr..ellklllkldevveklea 131
                                       e  s+l+a +++v+++++ l++ +++v ++ +e +e+++     +  + +++ e ve++e+
  gi|313126173|ref|YP_004036443.1| 468 EEMSSLSASVEQVSATTDDLADGSAAVAERADEGREAANGAldGVEAIEMETREAVESVED 528
                                       3345566667777777777777777777777777666665554333333444444444444 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.91
                              COG2  69 eeleevesplaaarkkvesvreklsereeevesklee 105
                                       + +e +e +  +a++ ve++ +++++ + +v++ +++
  gi|313126173|ref|YP_004036443.1| 510 DGVEAIEMETREAVESVEDLDDEIERIS-NVTGVIAD 545
                                       567899999999********99998754.45555544 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.014
                              COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeakel 109
                                       +++++++++s+ a++++++e++re++++   ev++ l+   e+
  gi|313126173|ref|YP_004036443.1| 592 IEDHVSTLQSKRAEVVERIEQMREQVEAGADEVDEALSSFDEI 634
                                       6789999999999999999999999999999999988766555 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.26
                              COG2  56 dFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakel 109
                                       d +s+ ++L g+ ee      +++aa ++ +++ +++se  +++ ++ +e +el
  gi|313126173|ref|YP_004036443.1| 661 DVLSMADELAGIGEETTAEAENVSAAAEEQTATLSEVSEGAHRLADQANELSEL 714
                                       456667777777777777777777777777777777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1829  (0.102013); expected 358.6 (0.02)
Passed bias filter:                      920  (0.0513135); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                        78  (0.00435049); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 1.51u 0.37s 00:00:01.88 Elapsed: 00:00:00.66
# Mc/sec: 3478.15
//
Query:       gi|313126174|ref|YP_004036444.1|  [L=35]
Description: hypothetical protein Hbor_14190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 209.30
//
Query:       gi|313126175|ref|YP_004036445.1|  [L=87]
Description: bola protein family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-20   71.5   0.0    5.6e-20   71.4   0.0    1.1  1  BolA      BolA-like protein


Domain annotation for each model (and alignments):
>> BolA  BolA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   3.1e-24   5.6e-20      22      76 .]      27      81 ..      10      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 3.1e-24
                              BolA 22 haeaggetHFkvvivseaFegkslvarhRlvyalLkeelakgiHALslktktpee 76
                                      ++e+++  HF  v+vs+aFegkslv++h++vy++L e ++++iHA++lkt+tpee
  gi|313126175|ref|YP_004036445.1| 27 PDEDHEDAHFAAVVVSPAFEGKSLVQQHQMVYDALGESMTTDIHAMELKTYTPEE 81
                                      44677999*********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 525.54
//
Query:       gi|313126176|ref|YP_004036446.1|  [L=379]
Description: carbohydrate ABC transporter ATP-binding protein, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-32  110.9   0.0    1.2e-31  110.1   0.0    1.4  1  ABC_tran         ABC transporter
      3e-10   40.8   0.0    1.3e-09   38.7   0.0    2.2  1  OB_MalK          MalK OB fold domain
    1.2e-06   28.5   0.2    6.5e-06   26.2   0.1    2.4  2  TOBE_2           TOBE domain
    2.1e-06   27.8   0.0      0.046   13.5   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.5e-05   23.7   0.1    0.00013   22.1   0.0    1.9  1  TOBE             TOBE domain
    0.00025   21.6   0.0     0.0024   18.4   0.0    2.5  2  CysA_C_terminal  CysA C-terminal regulatory domain
    0.00086   19.3   0.0     0.0014   18.5   0.0    1.3  1  Rad17            Rad17 P-loop domain
    0.00086   19.6   0.0     0.0031   17.8   0.0    1.8  2  AAA_22           AAA domain
     0.0012   18.4   0.0      0.043   13.3   0.0    2.2  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0019   18.1   0.2     0.0039   17.1   0.0    1.6  2  RsgA_GTPase      RsgA GTPase
     0.0031   17.1   0.3       0.53    9.8   0.0    3.2  4  AAA_25           AAA domain
     0.0032   17.9   0.0     0.0094   16.3   0.0    1.8  2  AAA_16           AAA ATPase domain
     0.0055   16.5   0.0      0.041   13.6   0.0    1.9  2  AAA_15           AAA ATPase domain
     0.0082   15.9   0.0      0.017   14.9   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.061   13.7   0.0    2.1  2  AAA              ATPase family associated with various cellul
      0.047   13.4   0.1       0.12   12.1   0.1    1.7  1  AAA_30           AAA domain
      0.052   13.7   0.0       0.13   12.4   0.0    1.7  2  AAA_33           AAA domain
       0.14   12.1   0.0       0.36   10.8   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
       0.17   12.4   0.0       0.37   11.2   0.0    1.5  1  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   1.3e-34   1.2e-31       2     136 ..      24     166 ..      23     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 1.3e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + vs+++  ge +++vG++G+GKSt l+++agl++  +Gei+ldg+ ++    +  ++ i++++q   l p++tv+e
  gi|313126176|ref|YP_004036446.1|  24 DGVSVDIDDGEFLVLVGPSGCGKSTTLRMIAGLETVSSGEIRLDGEVVNA--QPPRERDIAMVFQSYALYPHMTVKE 98 
                                       789**********************************************9..888999******************* PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              e ++ +e+ ++ lg+ +l  ++      +LSgGq+qrval ra++++pk++l+DEp 
  gi|313126176|ref|YP_004036446.1|  99 NmsfgleestdmpdsEISSLVEETAEMLGIGDLLGRKP----GELSGGQQQRVALGRAIVRDPKVFLMDEPL 166
                                       ******98887655555555888888888888777776....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   1.4e-12   1.3e-09       1      53 []     240     288 ..     240     288 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.4e-12
                           OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       G P+MNf++ + ++d   ++ + ++ pl+ee   +++l +  +v++GiRPE+i
  gi|313126176|ref|YP_004036446.1| 240 GEPSMNFFEMEMQGDR--LTSDLFDYPLSEET--REALGDTTHVTFGIRPEDI 288
                                       99***********998..999***********..******************8 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.6   6.3e+03      52      64 ..     196     209 ..     185     212 .. 0.53
   2 !   26.2   0.1   6.8e-09   6.5e-06       2      76 .]     282     356 ..     281     356 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.6
                            TOBE_2  52 adr.dsalapGdtV 64 
                                       +++  +a++ Gd++
  gi|313126176|ref|YP_004036446.1| 196 THDqTEAMTMGDRI 209
                                       22223467777766 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 6.8e-09
                            TOBE_2   2 aiRPEklrlaaagg.anglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       +iRPE++++ ++++ ++ ++ +++ ve +G++  ++++ + g +  ++  +    + l++G+ V  +++  +++++
  gi|313126176|ref|YP_004036446.1| 282 GIRPEDIEVVSEAAdDHDFEMVIDVVEPMGNENNVYLSFETGGDADLVATVDG-MRSLDAGQPVVARLPEPAIHLF 356
                                       8********95555256*******************87777777443333333.459****************998 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   4.9e-05     0.046       1      25 [.      35      59 ..      35      82 .. 0.74
   2 !   12.2   0.0   0.00013      0.12     220     298 ..     122     198 ..      89     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.9e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      + vl+Gp g+GKS+ L+ + +l  +
  gi|313126176|ref|YP_004036446.1| 35 FLVLVGPSGCGKSTTLRMIAGLETV 59
                                      579****************999443 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQvilt 295
                                       +   l  gd   + + elS G+++  al  a+ r++   +++l DEp ++L+ +l +   + l ++ ++ g+  + +
  gi|313126176|ref|YP_004036446.1| 122 TAEMLGIGDLLGRKPGELSGGQQQRVALGRAIVRDP---KVFLMDEPLSNLDAQLRSQMRTELqRIQENLGVSTVYV 195
                                       66666667777788999******999********99...9******************9988867777799999999 PP

                            AAA_21 296 THS 298
                                       TH+
  gi|313126176|ref|YP_004036446.1| 196 THD 198
                                       998 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.4e-07   0.00013       6      64 .]     299     355 ..     294     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.4e-07
                              TOBE   6 qlpgtVvvveplg..seveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                        ++  ++vvep g  ++v++  ++gg a+L+A+v++ +  +    +G++V+a++   ++hl
  gi|313126176|ref|YP_004036446.1| 299 DFEMVIDVVEPMGneNNVYLSFETGGDADLVATVDGMRSLD----AGQPVVARLPEPAIHL 355
                                       67889********999999999999999*************....*******998888775 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0         2   1.9e+03       6      21 ..      58      73 ..      58      82 .. 0.78
   2 !   18.4   0.0   2.6e-06    0.0024       1      43 []     245     290 ..     245     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2
                   CysA_C_terminal  6 rvedGklriGglalpv 21
                                      +v+ G +r++g  + +
  gi|313126176|ref|YP_004036446.1| 58 TVSSGEIRLDGEVVNA 73
                                      6899*****9987765 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.6e-06
                   CysA_C_terminal   1 NlFhGrvedGklriGglalpvP...elagadgqevvayVRPhDlei 43 
                                       N+F+   ++ +l+ + ++ p+    ++a  d   v+ ++RP+D+e+
  gi|313126176|ref|YP_004036446.1| 245 NFFEMEMQGDRLTSDLFDYPLSeetREALGDTTHVTFGIRPEDIEV 290
                                       99******99****99****998655555599************98 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.5e-06    0.0014      46      69 ..      34      57 ..      22     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                             Rad17 46 riLLisGPsGCgkstvvkvLskel 69
                                      + L++ GPsGCgkst++++++   
  gi|313126176|ref|YP_004036446.1| 34 EFLVLVGPSGCGKSTTLRMIAGLE 57
                                      5799**************998654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.3e-06    0.0031       4      28 ..      32      56 ..      29      89 .. 0.81
   2 ?   -1.6   0.0       3.2   3.1e+03      39      67 ..     156     184 ..     135     210 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      +  +lv++G+sG+GK+t+lr+++  
  gi|313126176|ref|YP_004036446.1| 32 DGEFLVLVGPSGCGKSTTLRMIAGL 56
                                      5679****************98765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.2
                            AAA_22  39 rpevvfvtlpsstsskdllrellralgle 67 
                                       +p+v++++ p s+  ++l++++  +l++ 
  gi|313126176|ref|YP_004036446.1| 156 DPKVFLMDEPLSNLDAQLRSQMRTELQRI 184
                                       44555555555554444444444444433 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   4.5e-05     0.043      25     206 ..      34     204 ..      24     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       +f ++vGp G+GKs  l  i   L + s+ ++r +   +++++ +  ++ + a v   +    + ++ e+ ++ ++ 
  gi|313126176|ref|YP_004036446.1|  34 EFLVLVGPSGCGKSTTLRMIA-GLETVSSGEIRLD--GEVVNA-QPPRERDIAMVFQSYALYPHMTVKENMSFGLEE 106
                                       577888888888888888773.2332333344433..456665.666666666666666666666666666666666 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                       +    ++    + +++++   + +ll +   ++ +LSgG+++ val    Ai  v+   ++l+De  ++LD++ +++
  gi|313126176|ref|YP_004036446.1| 107 STDMPDSEISSLVEETAEMLGIGDLLGR---KPGELSGGQQQRVALG--RAI--VRDPKVFLMDEPLSNLDAQLRSQ 176
                                       6666666666666666766777777655...5779******977664..455..45556899*************** PP

                                       HHHHHHHHCTTSEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 179 vaellkeksknaQfivislreemlekad 206
                                       + + l++ ++n  +  + ++++++e + 
  gi|313126176|ref|YP_004036446.1| 177 MRTELQRIQENLGVSTVYVTHDQTEAMT 204
                                       *999999999977666665555555554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.2e-06    0.0039      95     131 ..      28      65 ..       6      69 .. 0.82
   2 ?   -3.0   0.0       6.2   5.8e+03      62      88 ..     175     201 ..     166     205 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.2e-06
                                       HHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  95 ellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                         ++d ++ vlvG+SG GKSt + ++++ ++++ ge++
  gi|313126176|ref|YP_004036446.1|  28 VDIDDgEFLVLVGPSGCGKSTTLRMIAGLETVSSGEIR 65 
                                       556666999*******************9999999887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHHHHTTSEEEE--TTTHT CS
                       RsgA_GTPase  62 eeeleelkeelealgyevllvsaktke 88 
                                       ++  +el+   e+lg+++++v  +++e
  gi|313126176|ref|YP_004036446.1| 175 SQMRTELQRIQENLGVSTVYVTHDQTE 201
                                       333456666677777777777665554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00056      0.53      30      50 ..      30      50 ..      24      70 .. 0.90
   2 ?    3.0   0.0     0.071        67     145     188 ..     152     197 ..     144     203 .. 0.81
   3 ?   -1.5   0.0       1.7   1.6e+03     124     147 ..     280     304 ..     250     316 .. 0.74
   4 ?   -1.1   0.0       1.3   1.2e+03      75     135 ..     316     374 ..     307     376 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00056
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +  ge+ +l+G++g+GK+t +
  gi|313126176|ref|YP_004036446.1| 30 IDDGEFLVLVGPSGCGKSTTL 50
                                      5689**************965 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.071
                            AAA_25 145 lvviDplsralgg.densnsdv.galvealeriarrtgaavllvhH 188
                                        +v Dp  ++++   +n +++  +++ + l+ri++++g+ ++ v H
  gi|313126176|ref|YP_004036446.1| 152 AIVRDPKVFLMDEpLSNLDAQLrSQMRTELQRIQENLGVSTVYVTH 197
                                       577788888777776666666669******************9999 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.7
                            AAA_25 124 tl..ltadvdaleaaieevegvrlvv 147
                                       t   +++d++ + +a+++ ++ ++v+
  gi|313126176|ref|YP_004036446.1| 280 TFgiRPEDIEVVSEAADD-HDFEMVI 304
                                       334478999999999999.8999986 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.3
                            AAA_25  75 lyvsaEdsedelrrRlravgeal.rddarllvldlagveslpLfakdrggtlltadvdalea 135
                                       +y+s+E +       l a+   + ++da+ +v+ +  +  ++Lf++++g++l ++ +d+le+
  gi|313126176|ref|YP_004036446.1| 316 VYLSFETGG---DADLVATVDGMrSLDAGQPVVARLPEPAIHLFDTQSGSALKNRSLDELEE 374
                                       566666555...23333333333244555555555445789999999999999999999887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.9e-06    0.0094      22      45 ..      31      54 ..      22      93 .. 0.87
   2 ?   -1.7   0.0       3.5   3.3e+03     106     126 ..     158     184 ..     103     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.9e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrell 45
                                      +++e ++l+G+sG+GKs+ +r+++
  gi|313126176|ref|YP_004036446.1| 31 DDGEFLVLVGPSGCGKSTTLRMIA 54
                                      56799***************9987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.5
                            AAA_16 106 a......avpelagaeasrllellkrl 126
                                       +      + ++l+++++s+++ +l+r+
  gi|313126176|ref|YP_004036446.1| 158 KvflmdePLSNLDAQLRSQMRTELQRI 184
                                       033344444455555555555555554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   4.3e-05     0.041      17      45 ..      26      55 ..      22     115 .. 0.84
   2 ?    0.7   0.0      0.36   3.4e+02     322     365 ..     155     198 ..     144     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdl 45
                                      v++d+++  + vl+G+ ++GKS+ l+++  
  gi|313126176|ref|YP_004036446.1| 26 VSVDIDDGeFLVLVGPSGCGKSTTLRMIAG 55
                                      678888888*****************9965 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.36
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        +++++l++EP  +L  q+ +++   l+++ ++    +++ TH 
  gi|313126176|ref|YP_004036446.1| 155 RDPKVFLMDEPLSNLDAQLRSQMRTELQRIQENLGVSTVYVTHD 198
                                       478999***************************99999999997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-05     0.017      13      39 ..      24      50 ..      21      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      dg +++id  ++ +l+GpsG GKST l
  gi|313126176|ref|YP_004036446.1| 24 DGVSVDIDDGEFLVLVGPSGCGKSTTL 50
                                      77889999666999***********76 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.5e-05     0.061       2      51 ..      37      86 ..      36      95 .. 0.69
   2 ?   -0.6   0.0       1.8   1.7e+03      58      99 ..     156     187 ..     117     206 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfk 51
                                      +l+Gp G+GK+++ + +a    v+  ei +   + + +  +e++i+++f+
  gi|313126176|ref|YP_004036446.1| 37 VLVGPSGCGKSTTLRMIAGLETVSSGEIRLDGEVVNAQPPRERDIAMVFQ 86
                                      79****************87555544444444443455555666666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                       +p+++++DE  +   ++          + +q+ tel++ +++
  gi|313126176|ref|YP_004036446.1| 156 DPKVFLMDEPLSNLDAQ----------LRSQMRTELQRIQEN 187
                                       47777777754444444..........344444444444443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00012      0.12      19      47 ..      34      68 ..      28     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g.....g 47
                                       + vl+Gp G GK+t+l+ ++ + + + g     g
  gi|313126176|ref|YP_004036446.1| 34 EFLVLVGPSGCGKSTTLRMIAGLETVSsGeirldG 68
                                      4789***************9988776644555551 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.13       2      35 ..      36      66 ..      35     108 .. 0.71
   2 ?   -2.5   0.0       5.5   5.2e+03      83     105 ..     176     196 ..     145     211 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrr 35
                                      ++lvG++G+GKst ++ ++   g +++ss ++r 
  gi|313126176|ref|YP_004036446.1| 36 LVLVGPSGCGKSTTLRMIA---GLETVSSGEIRL 66
                                      589************9988...777777777665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.5
                            AAA_33  83 rerarflklarrlgvpvrivvve 105
                                       + r ++ ++ ++lg  v+ v+v+
  gi|313126176|ref|YP_004036446.1| 176 QMRTELQRIQENLG--VSTVYVT 196
                                       22233333333333..3344443 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00038      0.36       2      21 ..      36      55 ..      35      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                                      EEEE--SSSSHHHHHHHGGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaa 21
                                      ++LvGp+G+gKs+  + +a 
  gi|313126176|ref|YP_004036446.1| 36 LVLVGPSGCGKSTTLRMIAG 55
                                      68***********9998876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0004      0.37      14      39 ..      27      53 ..       5      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                            AAA_23 14 eidFsk.gltlItGpNGaGKTTildAi 39
                                      ++d ++  + +++Gp G+GK+T l+ i
  gi|313126176|ref|YP_004036446.1| 27 SVDIDDgEFLVLVGPSGCGKSTTLRMI 53
                                      566655145689***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2479.09
//
Query:       gi|313126177|ref|YP_004036447.1|  [L=298]
Description: carbohydrate ABC transporter membrane protein 2, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-17   62.4  13.9    8.9e-17   61.4  13.9    1.5  1  BPD_transp_1   Binding-protein-dependent transport system inn
  ------ inclusion threshold ------
        2.1    8.3   7.0        7.6    6.5   0.3    3.4  2  Deltameth_res  Deltamethrin resistance


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4  13.9   9.9e-21   8.9e-17       3     177 ..      99     288 ..      97     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 9.9e-21
                      BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf...........vilsilghlilp.viillllsa 64 
                                       l+G++aa   +n n++++  +++l+ +++ +P+  ++++l+  f            i   ++   l  +i++ + + 
  gi|313126177|ref|YP_004036447.1|  99 LIGSIAAyglTNLNWRGQAGVLILFVAGMFVPYQSVLVPLTR-FwtivglhnhlaGIPFLAQRVGLIeLIVTHTAYG 174
                                       79*********************************9999884.44789999999844444555555559999999** PP

                      BPD_transp_1  65 apyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgt 139
                                       +p+ ++++r++  s +++  eaar++Ga+  +i+r++++P+++p+++  li++f+ +++++++++ l s+p   + t
  gi|313126177|ref|YP_004036447.1| 175 IPICTILFRSYYASFDQSMLEAARIDGATFTRIYRRIIFPLSKPMFAVVLIYQFTQVWNDFLFALVLVSSPTseVAT 251
                                       ********************************************************************999666555 PP

                      BPD_transp_1 140 llleailgydyseisnggvlalviavlllnlvadilqr 177
                                         l+ ++g+++++ + + ++a+ ia l+ +lv+ ++ +
  gi|313126177|ref|YP_004036447.1| 252 IALNKLQGSMVQQYN-IQMAAAFIAALPTLLVYVLFGD 288
                                       555555566655555.6666666666666666666655 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.3    0.0097        87       8      18 ..      63      73 ..      62     114 .. 0.85
   2 ?    6.5   0.3   0.00085       7.6      20      43 ..     264     287 ..     260     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0097
                     Deltameth_res  8 Gdwkeqysakq 18
                                      G+w e+++++q
  gi|313126177|ref|YP_004036447.1| 63 GPWNEAWAQMQ 73
                                      9*******999 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00085
                     Deltameth_res  20 kYNavLaaGiviligTialakesg 43 
                                       +YN ++aa+ ++   T+ + + +g
  gi|313126177|ref|YP_004036447.1| 264 QYNIQMAAAFIAALPTLLVYVLFG 287
                                       7***************99987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1710.99
//
Query:       gi|313126178|ref|YP_004036448.1|  [L=335]
Description: carbohydrate ABC transporter membrane protein 1, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-21   74.5  19.5    8.7e-21   74.5  19.5    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   3.3    0.0017        31     117     174 ..      66     134 ..      52     137 .. 0.67
   2 !   74.5  19.5   4.9e-25   8.7e-21       2     176 ..     126     327 ..     125     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0017
                      BPD_transp_1 117 afggllggavlleflgswpGlgtllleailgydyseis............nggvlalviavlllnlvadi 174
                                        + g++g  ++++ l+ w G+g++  + +  ++y++++            +++++++++a l++ lv+ i
  gi|313126178|ref|YP_004036448.1|  66 FVYGAIGWNAIIS-LTDWDGFGNPDYSNLDFSMYAQMLgdptfvaaarntIVLLVVFTVASLIVGLVLAI 134
                                       3334444445555.55599****************999***98888776655555555555555555554 PP

  == domain 2  score: 74.5 bits;  conditional E-value: 4.9e-25
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilp 55 
                                       +++G+++a  + r+ ++ + +r+++ +++sl ++v ai++ ++                       ++s+ ++   +
  gi|313126178|ref|YP_004036448.1| 126 LIVGLVLAilVDRGIRFENTFRTIYLLPMSLSFVVTAIFWAWMYnpqsglvnvvlrniglgfvanDWISDPQTKLGA 202
                                       678999999999***************************99999*******************99999999988888 PP

                      BPD_transp_1  56 viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflg 132
                                       vi++l++++ +y ++++ a+lr++p+d+ eaar++Gas+ +++++v++P++  ++++ +++ ++++l+++ +l  ++
  gi|313126178|ref|YP_004036448.1| 203 VIFALMWQFSGYCMVVYLAGLRAIPSDQFEAARIDGASTVRMYWRVIIPQLRASTMSAAVVLMVFALKAFDFLFVMF 279
                                       ***************************************************************************** PP

                      BPD_transp_1 133 swpGlgtllleailgydyseis....nggvlalviavlllnlvadilq 176
                                       ++++  ++ + a+++y  ++ s    +g+++a+v+++l+l+++   l+
  gi|313126178|ref|YP_004036448.1| 280 GDTPGPSTDILATMMYREAFSStnwaYGAAIATVLFLLALVVIGPYLY 327
                                       **9999999999998888888888877888888888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2118.22
//
Query:       gi|313126179|ref|YP_004036449.1|  [L=459]
Description: sugar ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-28  100.7   1.2    1.7e-28  100.2   1.2    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    3.5e-19   69.9   6.1    4.6e-19   69.5   6.1    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
     0.0011   18.4   0.0        1.5    8.2   0.0    2.2  2  SBP_bac_6   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.015   15.1   5.6      0.029   14.2   5.6    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   1.2   3.8e-32   1.7e-28       2     273 ..      88     398 ..      87     407 .. 0.79

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 3.8e-32
                                       HHHHHHHH-.TEEEEEEE-...-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-HHH CS
                         SBP_bac_8   2 lakefekkt.gvkvnvvta...asndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddltda 74 
                                       l + f++++ +v++n  +a   a+  l + +k+ +   + p+ +++w+ + al +++e ++l+d+ d+ +++++ da
  gi|313126179|ref|YP_004036449.1|  88 LLDGFKEEYpDVELNNNPApggAGSALDTVIKNRVLNRNPPSTFQIWP-GKALTQYVEGDVLQDIGDSVWSQEMRDA 163
                                       56779999999999988875445567888899999999****999999.689**********************998 PP

                                       HHTT.....--TS.----EEEEEEE-EEEEEHHHHHHS.....---BHHHHHHHHHHHHHH-.......SEGG---G CS
                         SBP_bac_8  75 laav.....gydgklygvPyasetpyvliynkdlleka....edpktwdellaaakklkgkf.......glpdpasg 135
                                       +++      +  g++ +vP+++ +   l+yn+++le+a     +  +  +l++a++++   +       ++  p+s+
  gi|313126179|ref|YP_004036449.1| 164 YRQGvqnlsQPAGNYVAVPINIHRLNNLFYNASVLEEAgvdpASLSDPGALNDALDTIASETdavpmahQIKSPWSS 240
                                       888889999999************9************8866657777788888888885444445543333456666 PP

                                       GGGGGTHHETTEE---H..HHH..........HHHHHHHHHHHHTT-EE......-S..--SSTTTTTSBSEEEE-T CS
                         SBP_bac_8 136 wlqaallakdgksldddggkdgl.........kealellkklkdngkty......dtgadavsefanGevaftings 197
                                       + ++  ++ +g++  d++ + ++          ++ e l++lkd+  ++       ++++a+ ++ nG++af+ +g+
  gi|313126179|ref|YP_004036449.1| 241 VQLWETIF-LGYNGADTY-NSAIvegniadheSAVKESLQTLKDYHEHFnqdagsVSWDQANGKVVNGDAAFIHQGD 315
                                       44444444.444443332.233334445556667777777777777766666774589******************* PP

                                       THHHHHH.....-TTTSEEEE.--.S--.EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S CS
                         SBP_bac_8 198 wdiaaaq.....kagkklgai.vp.kqg.sfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnk 266
                                       w++ +++     + + ++g+i +p  +g + + +++++ pkn++ ++ a+ +Fl+++ + ++q+ +    g ip+++
  gi|313126179|ref|YP_004036449.1| 316 WAAGQYKsasefEYDSDWGMIpFPgTSGqYSVVTDSFVFPKNNPSPE-ATRKFLSYCGTVDAQKRFNPIKGSIPPRT 391
                                       *******666655556*****778544436666678***********.6***************9999********* PP

                                       -TTTHHH CS
                         SBP_bac_8 267 saalspe 273
                                       +++++p+
  gi|313126179|ref|YP_004036449.1| 392 DVPTDPF 398
                                       ***9875 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   6.1     1e-22   4.6e-19       3     314 ..      80     377 ..      78     378 .. 0.80

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1e-22
                                       SHHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCH CS
                         SBP_bac_1   3 sltegaalqalvakafekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviav.dndwiarlakaglllpld 75 
                                        +++  alqal+ + f++e+p+++ + ++ ++g++      ++ ++ + ++p   +++  +  +++++++++l++++
  gi|313126179|ref|YP_004036449.1|  80 GEKD--ALQALL-DGFKEEYPDVELNNNPAPGGAGSAldtVIKNRVLNRNPP-STFQIwPGKALTQYVEGDVLQDIG 152
                                       5778..9*****.*****************9999999999999999999977.777775888888***********8 PP

                                       HHHHHT.TECTTCCTEEEEHHHHTHHHHCEEE.ES.EEEE.E.EEEEEEETTTHHCTTGGG.....SHBHHHHHHHH CS
                         SBP_bac_1  76 pyvkay.lapgvkdaadklsssvlpkildskv.ly.vPly.a.argliYNkdlfekagldp.....pwtWdelveaa 142
                                       + v  + + + + ++  +ls+         ++ ++ vP++ +  + l+YN +++e+ag+dp     p   ++ +   
  gi|313126179|ref|YP_004036449.1| 153 DSVWSQeMRDAYRQGVQNLSQP--------AGnYVaVPINiHrLNNLFYNASVLEEAGVDPaslsdPGALNDAL--- 218
                                       7655552777766666666655........345677************************88777777777444... PP

                                       HHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT..HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTE CS
                         SBP_bac_1 143 kklkekgkkpiggarggsasgtayyfalalakslggkvfdkdgg..gldnpegvtaatylvklyavanltkelkgkg 217
                                         +   + + + +a++    +   +++++++++++    ++d +  +++ ++  +   +++++  + ++ +e+++ +
  gi|313126179|ref|YP_004036449.1| 219 DTIASETDA-VPMAHQIKSPWSSVQLWETIFLGYN----GADTYnsAIVEGNIADHESAVKESLQTLKDYHEHFNQD 290
                                       333333333.4799****************99999....44444564455555555555555555555667****** PP

                                       EECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTT CS
                         SBP_bac_1 218 aenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkg 294
                                       a ++++++a + + +G+aa++  g waa        ++   a+  +++ ++g++p+P++ g     ++++ ++ pk+
  gi|313126179|ref|YP_004036449.1| 291 AGSVSWDQANGKVVNGDAAFIHQGDWAA--------GQYKSASEFEYDSDWGMIPFPGTSGQYS--VVTDSFVFPKN 357
                                       ********************99999994........55557777888899*******8766655..69999****** PP

                                       CSTHHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 295 sknpeaAkkFldfllspeaq 314
                                       ++ pea +kFl +  + +aq
  gi|313126179|ref|YP_004036449.1| 358 NPSPEATRKFLSYCGTVDAQ 377
                                       ************98887777 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00034       1.5      13      79 ..     137     210 ..     135     210 .. 0.84
   2 !    8.0   0.0   0.00038       1.7     133     223 ..     297     394 ..     253     401 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00034
                         SBP_bac_6  13 dflekfieeglfqpld.panlpnvnkdfa..eeglkdpdgkyy..pygvgpl.vlavnkdrlkgrpv.PksWaD 79 
                                       ++l++++e +++q++  + +  ++++ ++   ++l++p g+y+  p+++  l  l +n+++l++  v P s +D
  gi|313126179|ref|YP_004036449.1| 137 KALTQYVEGDVLQDIGdSVWSQEMRDAYRqgVQNLSQPAGNYVavPINIHRLnNLFYNASVLEEAGVdPASLSD 210
                                       578999*******9966**************************5555554442478999999999999999887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00038
                         SBP_bac_6 133 vkaagslesgepavsvvpyffadilpekkkgk...nlkvvwPed..Ga.lvspifmlvkkg.kkkelakafidflls 202
                                       ++a g++  g++a+    +++a ++++ ++      + ++ +    G  +v++++ + +k+ + +e +++f+ +++ 
  gi|313126179|ref|YP_004036449.1| 297 DQANGKVVNGDAAFIHQGDWAAGQYKSASEFEydsDWGMIPFPGtsGQySVVTDSFVFPKNnPSPEATRKFLSYCGT 373
                                       5666666666666666666666666666533355544444433222542588899999******************* PP

                         SBP_bac_6 203 pevqailakaggvfPvvtnpa 223
                                        ++q+ ++   g++P+ t+++
  gi|313126179|ref|YP_004036449.1| 374 VDAQKRFNPIKGSIPPRTDVP 394
                                       ********9999999976554 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   5.6   6.4e-06     0.029       2      25 ..      10      34 ..       9      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.4e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaa.lggcaa 25
                                      +SRR+ L+ s+ a+A++a l+gc++
  gi|313126179|ref|YP_004036449.1| 10 FSRRTYLRLSGLAGAGMAgLAGCSG 34
                                      8*********888888888****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2577.75
//
Query:       gi|313126180|ref|YP_004036450.1|  [L=468]
Description: fumarase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   2.8e-107  358.7   0.0   4.1e-107  358.2   0.0    1.2  1  Lyase_1      Lyase
    1.8e-26   92.3   0.4      7e-26   90.4   0.4    2.1  1  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.2   0.0  4.6e-111  4.1e-107       1     312 []      13     342 ..      13     342 .. 0.99

  Alignments for each domain:
  == domain 1  score: 358.2 bits;  conditional E-value: 4.6e-111
                                       CEEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCG CS
                           Lyase_1   1 grftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegkldd 68 
                                       g+++v+ad+++g++t+r+ enf +s+ + +     al+++kk+aa+an dl    +++a+ai++a+dev++ g++dd
  gi|313126180|ref|YP_004036450.1|  13 GEMQVPADAYWGAQTQRAVENFPISGITFSrrfirALGVVKKGAAQANRDLglveENIADAIVEAADEVIA-GEHDD 88 
                                       789**********************8887799999************************************.***** PP

                                       GHHHBSSSSSHHHHHHHHHHHHHH....HHTT.....HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHH CS
                           Lyase_1  69 qfvlkviqegsgtavnmnlnevig....ellg.....ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpale 136
                                       qf+++v+q+gsgt++nmn+nevi+    el+g     ++v+pnd+v++gqSsnD++pTa+++ + +a++++Llpal+
  gi|313126180|ref|YP_004036450.1|  89 QFPVDVFQTGSGTSSNMNANEVIAnraaELMGeeigdRVVHPNDHVNYGQSSNDVIPTAMHVSALEAVEKDLLPALD 165
                                       ****************************999999999**************************************** PP

                                       HHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCT CS
                           Lyase_1 137 qLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpe 213
                                       +L++al++k +ef+ vvk GrThlqdAtPvtlgqe+ +y +++e+ + rl  ++ ++l el+ ggtavgtgln++p 
  gi|313126180|ref|YP_004036450.1| 166 TLREALEAKEEEFAGVVKTGRTHLQDATPVTLGQEFGGYRTQVEKGLGRLDGVR-EHLSELALGGTAVGTGLNTHPD 241
                                       ******************************************************.********************** PP

                                       HHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC- CS
                           Lyase_1 214 faelvakelakvtglp.vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesepGS 288
                                       f ++ a+ +++ tg++   a+n fea +++Da+ e++gal+++a sL k+a+Dlrll+sg+  gl+e++ +e++pGS
  gi|313126180|ref|YP_004036450.1| 242 FPKKAAEYITAETGVEfREADNHFEAQAAHDAMSEAHGALRTVAGSLNKIANDLRLLASGPrNGLGEIEQPENQPGS 318
                                       ***************************************************************************** PP

                                       TTSTTTEBTHHHHHHHHHHHHHHH CS
                           Lyase_1 289 SiMPgKvNPvqlElltgvagrvvG 312
                                       SiMPgK NPv +E++++v  +vvG
  gi|313126180|ref|YP_004036450.1| 319 SIMPGKINPVVAEAVNQVHKQVVG 342
                                       **********************98 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.4   7.8e-30     7e-26       1      54 []     408     461 ..     408     461 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 7.8e-30
                                       GGGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT-HHHHH. CS
                       FumaraseC_C   1 LVTaLnphIGYekAakIAkeAlkegktlreavlelgllteeeldelldpekMtg 54 
                                       L+TaLnp IGY+kA+++Ak+Alkegkt+re+v+e+g+l+eee de+ldpekMt+
  gi|313126180|ref|YP_004036450.1| 408 LATALNPTIGYDKASEVAKTALKEGKTVREVVIEKGYLSEEEADEVLDPEKMTH 461
                                       79***************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2828.83
//
Query:       gi|313126181|ref|YP_004036451.1|  [L=63]
Description: hypothetical protein Hbor_14260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00012   22.0   0.5       0.32   11.1   0.1    2.3  2  zf-C2H2_6       C2H2-type zinc finger
    0.00023   20.9   2.1      0.011   15.6   0.1    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
    0.00065   19.8   1.5    0.00092   19.3   1.5    1.3  1  Zn-ribbon_8     Zinc ribbon domain
     0.0014   18.7   0.1     0.0014   18.6   0.1    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0031   16.9   2.0       0.58    9.7   0.4    2.1  2  zf-ribbon_3     zinc-ribbon domain
     0.0043   17.0   0.8     0.0052   16.8   0.8    1.2  1  DZR             Double zinc ribbon
     0.0059   16.9   0.3     0.0077   16.5   0.3    1.2  1  C1_2            C1 domain
  ------ inclusion threshold ------
      0.012   15.3   0.1      0.012   15.3   0.1    1.1  1  TackOD1         Thaumarchaeal output domain 1
      0.021   14.5   1.3      0.032   14.0   1.3    1.3  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.022   14.7   1.5        1.3    9.0   0.1    2.1  2  zinc_ribbon_4   zinc-ribbon domain
      0.022   15.2   0.5        4.3    7.9   0.1    2.2  2  zf-H2C2_2       Zinc-finger double domain
      0.026   14.1   1.4        3.6    7.3   0.3    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.053   13.7   0.0      0.056   13.6   0.0    1.1  1  Fer4_18         4Fe-4S dicluster domain
      0.075   13.9   1.6         12    7.1   0.1    2.3  2  zf-C2H2_4       C2H2-type zinc finger
       0.14   11.2   0.0       0.15   11.1   0.0    1.1  1  Tmemb_55A       Transmembrane protein 55A
       0.14   12.4   2.1       0.42   10.9   2.2    1.6  2  LIM             LIM domain
       0.15   11.8   2.9        4.1    7.2   0.1    2.1  2  zf-CSL          CSL zinc finger
       0.17   11.7   1.6       0.32   10.8   0.1    1.9  2  zinc_ribbon_12  Probable zinc-ribbon domain
       0.17   11.9   0.9        8.5    6.5   0.1    2.1  2  Elf1            Transcription elongation factor Elf1 like


Domain annotation for each model (and alignments):
>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00034      0.32       3      16 ..      25      38 ..      25      38 .. 0.95
   2 !    9.4   0.0    0.0011       1.1       1       9 [.      44      52 ..      44      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                         zf-C2H2_6  3 eCsvCsksFpslqa 16
                                      eC  C+++Fp +qa
  gi|313126181|ref|YP_004036451.1| 25 ECRSCGATFPEGQA 38
                                      8*********9998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                         zf-C2H2_6  1 vheCsvCsk 9 
                                      ++eC++C++
  gi|313126181|ref|YP_004036451.1| 44 HYECPQCNE 52
                                      7******97 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.1e-05     0.011      19      35 ..      20      37 ..      13      38 .. 0.75
   2 ?    5.5   0.3     0.017        16      19      28 ..      42      51 ..      36      54 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                                      CCE.EEESSSS-EEESSC CS
                    RNA_POL_M_15KD 19 gkn.feCrqCgYeepadq 35
                                      g+  +eCr+Cg+ +p +q
  gi|313126181|ref|YP_004036451.1| 20 GRDmLECRSCGATFPEGQ 37
                                      44459**********876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.017
                                      CCEEEESSSS CS
                    RNA_POL_M_15KD 19 gknfeCrqCg 28
                                      g+ +eC qC 
  gi|313126181|ref|YP_004036451.1| 42 GWHYECPQCN 51
                                      4458888884 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.5   9.8e-07   0.00092       1      34 [.      10      52 ..      10      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.8e-07
                       Zn-ribbon_8  1 MPiYeYr.........CeeCghefevlqsisdapltaCPeCgs 34
                                      MP  +Y+         C++Cg +f + q+ +d    +CP+C++
  gi|313126181|ref|YP_004036451.1| 10 MPSLQYQreqgrdmleCRSCGATFPEGQATNDGWHYECPQCNE 52
                                      6666676777777777************999999999****86 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.5e-06    0.0014      68      96 ..      21      54 ..       2      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                                      --EEEETTTS-EEECHH...H..HHS-TTTSSS- CS
                              HypA 68 pvkvrCreCgkefelee...k..alrCpkCgsad 96
                                      +  ++Cr+Cg++f + +   +  +++Cp+C++a+
  gi|313126181|ref|YP_004036451.1| 21 RDMLECRSCGATFPEGQatnDgwHYECPQCNEAN 54
                                      44689********966544435677*****9875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0043         4       2      17 ..      23      39 ..      22      40 .. 0.75
   2 !    9.7   0.4   0.00061      0.58       2      11 ..      44      54 ..      44      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0043
                       zf-ribbon_3  2 tvrCPnCGa.plssddn 17
                                      + +C +CGa  ++ +++
  gi|313126181|ref|YP_004036451.1| 23 MLECRSCGAtFPEGQAT 39
                                      56799999988777776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00061
                       zf-ribbon_3  2 tvrCPnCGa.p 11
                                      +++CP+C++ +
  gi|313126181|ref|YP_004036451.1| 44 HYECPQCNEaN 54
                                      689****9877 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.8   5.5e-06    0.0052      14      38 ..      25      54 ..      15      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-06
                               DZR 14 fCseCgtklkavaa.....edrCpsCgekv 38
                                       C  Cg++ ++ +a     ++ Cp+C+e++
  gi|313126181|ref|YP_004036451.1| 25 ECRSCGATFPEGQAtndgwHYECPQCNEAN 54
                                      5*******9866669***********9975 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   8.2e-06    0.0077       7      39 ..      13      51 ..       7      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.2e-06
                              C1_2  7 LtlskgedssesfnCsaCgrk.......idgff..YsCseCd 39
                                      L+++ +e+  ++ +C+ Cg +        d     Y+C++C+
  gi|313126181|ref|YP_004036451.1| 13 LQYQ-REQGRDMLECRSCGATfpegqatND--GwhYECPQCN 51
                                      5555.7888999*********998765333..256******8 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   1.3e-05     0.012     101     131 ..      21      52 ..      11      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                           TackOD1 101 qelihhftCgnvgpeeef.lkegkleCpkCkt 131
                                       + ++++ +Cg++ pe +  +++ + eCp+C++
  gi|313126181|ref|YP_004036451.1|  21 RDMLECRSCGATFPEGQAtNDGWHYECPQCNE 52 
                                       5689***********9994556699*****96 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.3   3.4e-05     0.032      19      54 .]      20      54 ..      12      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                    zinc_ribbon_10 19 nryalICskChshnGlapkeeleevkyrCpkCgaln 54
                                       r  l C+ C  ++    + +++ + y Cp+C++ n
  gi|313126181|ref|YP_004036451.1| 20 GRDMLECRSCGATFPEG-QATNDGWHYECPQCNEAN 54
                                      56667799998887444.6699***********987 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0014       1.3      23      35 ..      20      33 ..      16      34 .. 0.76
   2 ?    5.1   0.2     0.024        22       4      10 ..      46      52 ..      45      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                     zinc_ribbon_4 23 gv.kvrCskCghvF 35
                                      g+ ++ C  Cg++F
  gi|313126181|ref|YP_004036451.1| 20 GRdMLECRSCGATF 33
                                      44489999999999 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                     zinc_ribbon_4  4 tCpsCka 10
                                      +Cp+C+ 
  gi|313126181|ref|YP_004036451.1| 46 ECPQCNE 52
                                      7****85 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.022        21      13      24 ..      22      33 ..      14      34 .. 0.84
   2 ?    7.9   0.1    0.0046       4.3      15      22 ..      45      52 ..      39      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.022
                         zf-H2C2_2 13 kpyeCplCdkaF 24
                                        +eC +C+ +F
  gi|313126181|ref|YP_004036451.1| 22 DMLECRSCGATF 33
                                      458******999 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0046
                         zf-H2C2_2 15 yeCplCdk 22
                                      yeCp C+ 
  gi|313126181|ref|YP_004036451.1| 45 YECPQCNE 52
                                      9*****85 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.009       8.5       2      15 ..      23      36 ..      22      39 .. 0.83
   2 ?    7.3   0.3    0.0038       3.6       2      10 ..      44      52 ..      43      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.009
                            zf_UBZ  2 tylCerCgkeipes 15
                                      +  C  Cg+++pe 
  gi|313126181|ref|YP_004036451.1| 23 MLECRSCGATFPEG 36
                                      678*********86 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0038
                            zf_UBZ  2 tylCerCgk 10
                                      +y C++C++
  gi|313126181|ref|YP_004036451.1| 44 HYECPQCNE 52
                                      699****97 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     6e-05     0.056      53      90 ..      15      52 ..       3      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                           Fer4_18 53 rkekgagdcidcescvkvcPtgidirkGlqleciscll 90
                                       ++++  d ++c+sc +  P g    +G  +ec +c +
  gi|313126181|ref|YP_004036451.1| 15 YQREQGRDMLECRSCGATFPEGQATNDGWHYECPQCNE 52
                                      456667799***************************87 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.013        12       2      11 ..      25      34 ..      24      38 .. 0.85
   2 ?    6.1   0.2     0.025        24       1       8 [.      45      52 ..      45      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                         zf-C2H2_4  2 kCpiCgksFs 11
                                      +C+ Cg++F+
  gi|313126181|ref|YP_004036451.1| 25 ECRSCGATFP 34
                                      7********7 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.025
                         zf-C2H2_4  1 fkCpiCgk 8 
                                      ++Cp+C++
  gi|313126181|ref|YP_004036451.1| 45 YECPQCNE 52
                                      89****75 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.15      50      90 ..      16      56 ..       7      62 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                         Tmemb_55A 50 seesgsapvitCrvCqslidv.egkleqhvvkCevCneatpi 90
                                      + e+g + ++ Cr C++     +   +     C +Cnea  i
  gi|313126181|ref|YP_004036451.1| 16 QREQG-RDMLECRSCGATFPEgQATNDGWHYECPQCNEANGI 56
                                      44555.889999999998865144555667899999999877 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.075        71      27      40 ..      24      37 ..      21      42 .. 0.78
   2 ?   10.9   2.2   0.00044      0.42       1      30 [.      26      51 ..      26      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.075
                                      SB-TTT-SB-CTT. CS
                               LIM 27 FtCsdCqkeLkegs 40
                                      + C +C+ ++ eg+
  gi|313126181|ref|YP_004036451.1| 24 LECRSCGATFPEGQ 37
                                      68999999998876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00044
                                      -TTT--BE-TTTEEEEETTEEEETTTSB-T CS
                               LIM  1 CagCnkkiadrelvlkaldkvwHeeCFtCs 30
                                      C +C+ ++ + + +    ++ wH eC +C 
  gi|313126181|ref|YP_004036451.1| 26 CRSCGATFPEGQAT----NDGWHYECPQCN 51
                                      89999999966666....9**********7 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0044       4.1      34      50 ..      13      29 ..       7      33 .. 0.75
   2 ?    5.5   0.3     0.014        14      11      25 ..      37      52 ..      31      56 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0044
                                      HHTT....--EEEETTS CS
                            zf-CSL 34 leegaegaevvvqCssC 50
                                      l+ ++e++ ++++C+sC
  gi|313126181|ref|YP_004036451.1| 13 LQYQREQGRDMLECRSC 29
                                      5555567899******* PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.014
                                      ETTTTEEEEEE.TTSS CS
                            zf-CSL 11 deeeesyyypC.RCgd 25
                                      +++++ ++y+C  C +
  gi|313126181|ref|YP_004036451.1| 37 QATNDGWHYECpQCNE 52
                                      457788*****88975 PP

>> zinc_ribbon_12  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00034      0.32      13      39 ..       5      31 ..       3      34 .. 0.92
   2 ?    0.1   0.2      0.79   7.4e+02       9      14 ..      47      52 ..      44      53 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                    zinc_ribbon_12 13 felLqlPkkflllkkkqqklrCGaCse 39
                                       elL +P+  +++++    l C +C +
  gi|313126181|ref|YP_004036451.1|  5 VELLTMPSLQYQREQGRDMLECRSCGA 31
                                      59***********************86 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.79
                    zinc_ribbon_12  9 CsnCfe 14
                                      C +C+e
  gi|313126181|ref|YP_004036451.1| 47 CPQCNE 52
                                      666665 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.009       8.5      37      55 ..      15      33 ..      10      41 .. 0.83
   2 ?    4.8   0.1     0.031        29      21      33 ..      44      56 ..      37      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.009
                              Elf1 37 ldkkekiaevsCkvCgesf 55
                                       ++++++ +++C++Cg++f
  gi|313126181|ref|YP_004036451.1| 15 YQREQGRDMLECRSCGATF 33
                                      567888999*******976 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.031
                              Elf1 21 kFdCpfCnheksv 33
                                      +++Cp Cn+ + +
  gi|313126181|ref|YP_004036451.1| 44 HYECPQCNEANGI 56
                                      589*****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 405.43
//
Query:       gi|313126182|ref|YP_004036452.1|  [L=622]
Description: glutamyl-tRNA(gln) amidotransferase subunit e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-66  221.9   0.0    1.3e-65  221.5   0.0    1.1  1  GatB_N           GatB/GatE catalytic domain
    1.3e-23   83.5   0.1    2.1e-23   82.9   0.1    1.3  1  GatB_Yqey        GatB domain
    7.9e-15   54.9   0.0    1.7e-14   53.8   0.0    1.6  1  GAD              GAD domain
     0.0016   18.5   0.5     0.0033   17.5   0.5    1.5  1  YqeY             Yqey-like protein
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.34   10.9   0.0    1.8  2  tRNA_synt_1c_R1  Glutaminyl-tRNA synthetase, non-specific RNA


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.5   0.0   3.6e-69   1.3e-65       2     271 ..      12     442 ..      11     444 .. 0.95

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 3.6e-69
                                       EEEEEEEEEB--SB-SSSSSBSS....SSCE..........STTSS--TTTTTS....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....xxxx..........xxxxxxxxxxxxx....................... RF
                            GatB_N   2 viGlEiHaqlktksKlFssaste....eege..........epnsevsevdlal....................... 41 
                                       v GlEiH+ql+t+sKlF++++te    e  +           ++se++e+d a+                       
  gi|313126182|ref|YP_004036452.1|  12 VAGLEIHQQLDTESKLFCGCPTEirepE--DaertftrflhPTKSELGELDEAAleesrverefeylsydttclvee 86 
                                       78*******************8755331..145667777745888899998888*********************** PP

                                       ...TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEE CS
                                       ...xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                            GatB_N  42 ...PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrieri 113
                                          P   P+ l++ea e+++++a  l+++  ++ +++RK ++++++++g+Q+t     +a++G++e+ +  v++e +
  gi|313126182|ref|YP_004036452.1|  87 ddeP---PHrLDEEAREVVMQIASLLDMDAVDQAHLMRKLVIDGSNTSGFQRTT---LVAQDGEIETsDGPVGVEDL 157
                                       9998...999********************************************...677******97789****** PP

                                       EEEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 114 hlEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSv 190
                                        lEe++a+ v+e+++ + ++l+R+G+pL+Ei t+pd++spe+ar+++e++++llr++g++++++  G++R+DvNvS+
  gi|313126182|ref|YP_004036452.1| 158 MLEEESAQRVEETDDGVRFSLDRLGIPLVEIGTRPDISSPEQAREAAERIGMLLRSTGKVKRGL--GTIRQDVNVSI 232
                                       ************999*************************************************..*********** PP

                                       CTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                            GatB_N 191 reeekgeeegtrvEiKnlnslksiekaieyeierqiell...................................... 229
                                       ++       g+rvEiK+++ l++i++++++e+ rq++ll                                      
  gi|313126182|ref|YP_004036452.1| 233 AD-------GARVEIKGVQALDAIDDIVRNEVGRQVKLLdirdelaerdasvgdtqdvtdvfedtdsgviggalssg 302
                                       *4.......49****************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|313126182|ref|YP_004036452.1| 303 gvvqavplfgfdglvgreiqpdrrlgtefsdhakrhgaggifhtdelpaygvteaevtalrdavdadendavaivat 379
                                       ***************************************************************************** PP

                                       ........................-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHH CS
                                       ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 ........................qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseel 271
                                                               +eTr+++ed g+t++lR+ + a   r++pe+d+pp+e++ + 
  gi|313126182|ref|YP_004036452.1| 380 dpetaelaidavkeraetaldgvpEETRGANED-GTTRYLRPLPGA--ARMYPETDVPPVELDPSD 442
                                       *********************************.**********77..5************99765 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.1   5.8e-27   2.1e-23       2     148 .]     478     618 ..     477     618 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 5.8e-27
                                       HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHH CS
                         GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspe 77 
                                       +fe +++eg   ++ a+ ll+ +l+el++ ++++e   +++++l el+ l+++g+++k+ +++vl +++e+ + s+e
  gi|313126182|ref|YP_004036452.1| 478 LFERAIDEG-IDATFAAGLLESTLTELRRDDVAVET--VSDDHLLELMHLVEDGDLAKEGVNDVLSTIAENpSLSAE 551
                                       699999999.5566778899****************..9************************************** PP

                                       HHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  78 eiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       e++ee gL  +s+ +e++++v  v+++n   ++++++  + a+ +l+G+ M +++Gkad+++v+ +l+e++
  gi|313126182|ref|YP_004036452.1| 552 EAVEEAGLSGVSE-DEVRDAVSGVVERN---ADQVEEEGMAAFSALMGEAMGALRGKADGEIVSTVLREEI 618
                                       ************8.**************...777888999****************************986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   4.8e-18   1.7e-14       3      92 ..     297     385 ..     295     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 4.8e-18
                                       HHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TT CS
                               GAD   3 ealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeeg 78 
                                        al+sgg+v+a+ + g +++l+++ei++ +++++e++++++   + +g ++t++++++ +te+ev  l++av+a+e+
  gi|313126182|ref|YP_004036452.1| 297 GALSSGGVVQAVPLFG-FDGLVGREIQPDRRLGTEFSDHAKRH-GAGGIFHTDELPAYgVTEAEVTALRDAVDADEN 371
                                       5899************.8***********************99.********************************* PP

                                       EEEEEEEEEHHHHH CS
                               GAD  79 DillfvAdkkktvn 92 
                                       D++ +vA + +t++
  gi|313126182|ref|YP_004036452.1| 372 DAVAIVATDPETAE 385
                                       *********99987 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   9.3e-07    0.0033      92     142 ..     563     617 ..     560     618 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.3e-07
                                       -HHHHHHHHHHHHH....HTT--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
                              YqeY  92 seeeiealvkeaia....evgaesmkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                                       se+e++++v+ +++    +v++e+m+++  +m+ ++  ++GkaDg+ vs++++e+
  gi|313126182|ref|YP_004036452.1| 563 SEDEVRDAVSGVVErnadQVEEEGMAAFSALMGEAMGALRGKADGEIVSTVLREE 617
                                       67777777666665111167888***************************99986 PP

>> tRNA_synt_1c_R1  Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.5   5.2e+03      41      77 ..      91     127 ..      79     136 .. 0.74
   2 ?   10.9   0.0   9.5e-05      0.34     108     151 ..     556     597 ..     492     604 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.5
                   tRNA_synt_1c_R1  41 ekgldkkkgalLyslatklkkqalekrelivkyIveg 77 
                                        + ld++++++++++a+ l  +a+++ +l+ k +++g
  gi|313126182|ref|YP_004036452.1|  91 PHRLDEEAREVVMQIASLLDMDAVDQAHLMRKLVIDG 127
                                       4467999999999999999977777777777776666 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.5e-05
                   tRNA_synt_1c_R1 108 acGVGvevtpeqieeaVekyieenkeeieekryrknlgkllaev 151
                                       ++G    v+++++++aV+ ++e n++++ee+   +++++l++e+
  gi|313126182|ref|YP_004036452.1| 556 EAGLS-GVSEDEVRDAVSGVVERNADQVEEEGM-AAFSALMGEA 597
                                       55553.489**********************99.8888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 3492.96
//
Query:       gi|313126183|ref|YP_004036453.1|  [L=125]
Description: acyl dehydratase MaoC [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-05   22.3   0.4     0.0011   18.5   0.4    2.0  1  MaoC_dehydratas  MaoC like domain
    7.8e-05   22.8   0.5      0.014   15.5   0.5    2.1  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.18   12.2   0.0    1.5  1  HAMP             HAMP domain


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   1.9e-07    0.0011      12     118 ..       9     105 ..       2     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-07
                                       EEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S- CS
                   MaoC_dehydratas  12 tekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkp 88 
                                       +  e++ t+ad++++a +sgD +p  + p+       g   +hG+lt+ + + +  e +        + +++   +p
  gi|313126183|ref|YP_004036453.1|   9 HVVERSFTPADVRQFADLSGDDQPQYTEPD-----EDGRLLVHGLLTATVPTEVGSELGML-----ARTFTFEAHRP 75 
                                       5678999****************9887776.....4567899***9977666666666655.....6666677788* PP

                                       -BTTCEEEEEEEEEEEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  89 Vlpgdtlkvelevvgkrdvrktkkvevtke 118
                                       V++ +t++   +v++ ++ +++ + +v+++
  gi|313126183|ref|YP_004036453.1|  76 VYTSQTVRCACVVEEIEETEEQYNLTVEVT 105
                                       ***************999998877777665 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   2.3e-06     0.014      10     131 ..      11     115 ..       6     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-06
                   MaoC_dehydrat_N  10 vkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhgeqefeyhe 86 
                                       v+ + +  +vr+fa   g+ +p y++++         l +   +l+++  ++      +g    ++l  + +fe h+
  gi|313126183|ref|YP_004036453.1|  11 VERSFTPADVRQFADLSGDDQPQYTEPDEDG-----RLLV-HGLLTATVPTE------VG-SELGMLARTFTFEAHR 74 
                                       5566677788888888888888888887752.....2222.22222222222......22.23467777889999** PP

                   MaoC_dehydrat_N  87 piraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                       p++ + ++++ + ++++++ +   +   ++ve t+t  +G++v+t
  gi|313126183|ref|YP_004036453.1|  75 PVYTSQTVRCACVVEEIEETE---EQYNLTVEVTCT-CEGDVVMT 115
                                       ******************964...556666666666.78988887 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     3e-05      0.18      25      44 ..      49      68 ..      22      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                                      TSSTCCTTSSSHHHHHHHHH CS
                              HAMP 25 ldtrlpvsgrDEiGeLaraf 44
                                      l++++p++ + E+G+Lar+f
  gi|313126183|ref|YP_004036453.1| 49 LTATVPTEVGSELGMLARTF 68
                                      8889***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 737.97
//
Query:       gi|313126184|ref|YP_004036454.1|  [L=370]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-18   67.5   0.0    2.3e-18   66.4   0.0    1.6  1  Response_reg     Response regulator receiver domain
    1.5e-17   63.7   0.3      5e-17   62.0   0.1    2.0  2  PAS_3            PAS fold
    2.6e-09   37.0   1.7    8.9e-09   35.3   0.5    2.4  2  HisKA            His Kinase A (phospho-acceptor) domain
    0.00018   21.7   0.1    0.00037   20.7   0.1    1.6  1  OKR_DC_1_N       Orn/Lys/Arg decarboxylase, N-terminal domain
    0.00047   20.4   0.3     0.0022   18.3   0.0    2.3  2  PAS_4            PAS fold
     0.0092   17.0   0.9       0.65   11.0   0.0    2.5  2  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
       0.17   12.2   0.9       0.95    9.8   0.3    2.3  2  DUF4061          Domain of unknown function (DUF4061)


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   9.1e-22   2.3e-18       1     106 [.      18     123 ..      18     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 9.1e-22
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl vdDd +++el++ +le  ++ + +v +a++ ++al  l++  +d+i+ D +mp+ +G+e+l+ + e+ p+lp i
  gi|313126184|ref|YP_004036454.1|  18 VLHVDDDAAFAELVAIYLEreSDRI-TVITATSVSDALTELDSG-IDCIVADYEMPDRNGIEFLEVVTERYPDLPFI 92 
                                       789****************844556.899************988.******************************** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpee 106
                                       ++t++++ee a ea++ag+ d+l+K    e+
  gi|313126184|ref|YP_004036454.1|  93 LFTGRGSEEIASEAISAGVTDYLQKSTGTEQ 123
                                       *************************987765 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.6   6.6e+03      23      47 ..      12      36 ..       6      43 .. 0.70
   2 !   62.0   0.1     2e-20     5e-17       3      88 ..     175     260 ..     173     261 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.6
                             PAS_3 23 veswldlvhpeDrervrealqealk 47
                                      v++ + ++h +D + + e ++ +l+
  gi|313126184|ref|YP_004036454.1| 12 VSDPIRVLHVDDDAAFAELVAIYLE 36
                                      5666788999998888777766665 PP

  == domain 2  score: 62.0 bits;  conditional E-value: 2e-20
                             PAS_3   3 yvserveeilGyspeellgk.veswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       yv++ +ee++Gy+++ +++  +    +++hp+D er++e +q al++++ +e  yRi++kd ++ w+++r+++i  e
  gi|313126184|ref|YP_004036454.1| 175 YVEGDCEELTGYTSQAVESGdPVWGEEILHPDDKERAWEVVQSALDDDGTFELTYRIVTKDDQTKWMWERGQAI-CE 250
                                       89999*********************************************************************.99 PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g+ v + g+
  gi|313126184|ref|YP_004036454.1| 251 DGELVALEGF 260
                                       9999998887 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.62   1.6e+03      42      58 ..     142     158 ..     112     159 .. 0.74
   2 !   35.3   0.5   3.5e-12   8.9e-09       2      65 ..     281     339 ..     280     340 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.62
                                       HHHHHHHHHHHHHHHHH CS
                             HisKA  42 etiesearrldhlvedl 58 
                                       +++e+  rrl+ l+++l
  gi|313126184|ref|YP_004036454.1| 142 RVLEERKRRLETLIDNL 158
                                       55666666888888776 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 3.5e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l +f++ v+H++  PL++ +  +e+ +      e+  +yl+t+e+  +rl +l e+lL+lsr +
  gi|313126184|ref|YP_004036454.1| 281 LDEFASIVSHDMQDPLAVAREHVELART-----EDDTDYLDTVEDAHERLKRLTETLLTLSRDG 339
                                       689**********************877.....*****************************86 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   1.5e-07   0.00037      14     111 .]      38     138 ..      24     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                        OKR_DC_1_N  14 ekegfevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlreid 87 
                                       e++ ++v+++ts++D+l+  e +s i+++v +++    +  e+l+ + er +dlP  l++ + ++e ++  + + ++
  gi|313126184|ref|YP_004036454.1|  38 ESDRITVITATSVSDALT--ELDSGIDCIVADYEmpdRNGIEFLEVVTERYPDLPFILFTGRGSEEIASEAISAGVT 112
                                       33678999*****97766..5578***********99999***************9999998888888888888899 PP

                        OKR_DC_1_N  88 gfielledtpef..iarqieaaakkY 111
                                        +++   +t+++  +a++i  a++ Y
  gi|313126184|ref|YP_004036454.1| 113 DYLQKSTGTEQYtlLANRICNAVEGY 138
                                       99998887776522567777776665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.4e-07    0.0022      45      96 ..     176     226 ..     163     235 .. 0.82
   2 ?   -3.5   0.0         5   1.3e+04      91     109 ..     250     268 ..     248     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.4e-07
                             PAS_4  45 peedaarleralrrvlegeepiefleelllpgeerhyelrllPlrdesGevi 96 
                                        e+d ++l  +  +++e+++p++ +e+l+++++er +e+  + l d++G+  
  gi|313126184|ref|YP_004036454.1| 176 VEGDCEELTGYTSQAVESGDPVWGEEILHPDDKERAWEVVQSAL-DDDGTFE 226
                                       34499999************************************.6688744 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5
                             PAS_4  91 esGevigvlvisrDiTerr 109
                                       e+Ge +++ ++++ iT+r+
  gi|313126184|ref|YP_004036454.1| 250 EDGELVALEGFVTGITDRK 268
                                       6899999999999999998 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00025      0.65      25      94 ..      17      85 ..       3      94 .. 0.80
   2 ?    4.2   0.2     0.035        90      18      91 ..     248     331 ..     215     341 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                   Methyltransf_24 25 rlvavdhdpgaeeaaalare..aglddrvrlikads.eealaslaagsiDllfiDgghaaeavledleallpr 94
                                      r++ vd d+   ++a+l++   +  +dr+++i a+s ++al++l+ + iD+++ D +   +  +e+le++ +r
  gi|313126184|ref|YP_004036454.1| 17 RVLHVDDDA---AFAELVAIylERESDRITVITATSvSDALTELD-SGIDCIVADYEMPDRNGIEFLEVVTER 85
                                      677888888...777777766667789999999999788******.88*******999888888888887776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.035
                   Methyltransf_24  18 lrrngagrlvavdhdpg.....aeeaaalare.aglddrvrlikadseealasla......agsiDllfiDgghaae 82 
                                       +++ g+  lva++ + +     +e+++++ r+ ++ld+++ +++ d+++ la  +      + + D  ++D   +a+
  gi|313126184|ref|YP_004036454.1| 248 ICEDGE--LVALEGFVTgitdrKEQQREIERKsHKLDEFASIVSHDMQDPLAVARehvelaRTEDDTDYLDTVEDAH 322
                                       444443..4444443334444445677777778**************998885553333434455555666555555 PP

                   Methyltransf_24  83 avledleal 91 
                                       ++l+ l   
  gi|313126184|ref|YP_004036454.1| 323 ERLKRLTET 331
                                       555555444 PP

>> DUF4061  Domain of unknown function (DUF4061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.5   1.3e+03      61      81 ..     139     159 ..     116     163 .. 0.76
   2 ?    9.8   0.3   0.00037      0.95      39      85 ..     291     337 ..     276     340 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.5
                           DUF4061  61 keedalresdenlkkLvskLe 81 
                                       +++  l+e+++ l++L+++L 
  gi|313126184|ref|YP_004036454.1| 139 RSQRVLEERKRRLETLIDNLP 159
                                       345567799999*****9995 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00037
                           DUF4061  39 eqQekL..arlhfeldaeeeelaekeedalresdenlkkLvskLeqLsk 85 
                                       ++Q+ L  ar h+el  +e+ ++    d+++ ++e lk+L++ L +Ls 
  gi|313126184|ref|YP_004036454.1| 291 DMQDPLavAREHVELARTEDDTD--YLDTVEDAHERLKRLTETLLTLSR 337
                                       67776622689999999988555..6778899**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2248.09
//
Query:       gi|313126185|ref|YP_004036455.1|  [L=321]
Description: zn-dependent protease with chaperone function [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-25   89.1   1.5    9.9e-14   51.6   0.0    2.2  2  Peptidase_M48    Peptidase family M48
    1.6e-05   24.3   0.1    4.7e-05   22.7   0.0    1.9  2  Peptidase_M56    BlaR1 peptidase M56


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   1.1e-17   9.9e-14      10     102 ..      92     182 ..      89     199 .. 0.86
   2 !   36.4   0.3   4.8e-13   4.3e-09     120     194 ..     223     311 ..     209     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.1e-17
                                       HHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  10 vveelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvsliv 86 
                                       v++ la+e++l +++++++v+  ++ NAFal    ++++v+ + L+ + l+++el++ l+HEl+H+ +++s+v+++ 
  gi|313126185|ref|YP_004036455.1|  92 VLDGLAAEMDL-DEPPRLMVASLSTPNAFALDTMGRNTVVVDTVLF-RILDRDELEGLLAHELAHLERKDSLVQTLA 166
                                       567799*****.999*******************999999999999.***************************776 PP

                                       HHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxx RF
                     Peptidase_M48  87 sllasillllglalli 102
                                        +  + +  l+++++ 
  gi|313126185|ref|YP_004036455.1| 167 FSTIQTVVNLAYVVVA 182
                                       6666666666666655 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 4.8e-13
                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHTTT.HHHHHHHHHHHHHHTT-..............-S---HHHHHHS-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxx RF
                     Peptidase_M48 120 liglliillflalSRkrEyqADeagvellkrakdlvraliklakdler..............qdvsaslrsellstH 182
                                       l++ ++ ll  a SRkrEy ADe ++ ++ r+ +l+ral kl +  +               +++++   ++llstH
  gi|313126185|ref|YP_004036455.1| 223 LVMGVMTLLARAHSRKREYAADERAAAVTGRPLALARALEKLERASSAefgilsplwirgevESEEERRLRDLLSTH 299
                                       333445555669*******************************999999*********9865444444444****** PP

                                       --HHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                     Peptidase_M48 183 PplleRiqalke 194
                                       P +++R+++l++
  gi|313126185|ref|YP_004036455.1| 300 PRTEDRVKRLRD 311
                                       **********96 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.19   1.7e+03     108     125 ..      14      31 ..       9      44 .. 0.76
   2 !   22.7   0.0   5.2e-09   4.7e-05     143     219 ..      89     167 ..      37     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.19
                     Peptidase_M56 108 iWivgalilllyliaall 125
                                       ++ vg++++++y + a+ 
  gi|313126185|ref|YP_004036455.1|  14 MVFVGVAVFVFYALLAYA 31 
                                       556788888888888875 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 5.2e-09
                     Peptidase_M56 143 lkeaLkeakeemqlkrnikirlsssidsPavlgl...lkprIvlPadflkklsdeeleyillHElaHlkrkDllvnl 216
                                       +++ L+    em l  +++++++ s+++P  ++l    ++ +v+ + +++ l+ +ele  l+HElaHl rkD lv+ 
  gi|313126185|ref|YP_004036455.1|  89 AYHVLDGLAAEMDLDEPPRLMVA-SLSTPNAFALdtmGRNTVVVDTVLFRILDRDELEGLLAHELAHLERKDSLVQT 164
                                       55677778888889999999886.579998887533389************************************99 PP

                     Peptidase_M56 217 lva 219
                                       l++
  gi|313126185|ref|YP_004036455.1| 165 LAF 167
                                       875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1945.23
//
Query:       gi|313126186|ref|YP_004036456.1|  [L=153]
Description: acyl dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-17   63.1   0.0    2.1e-17   62.8   0.0    1.1  1  MaoC_dehydratas  MaoC like domain
    9.2e-05   22.1   0.0    0.00012   21.7   0.0    1.2  1  FabA             FabA-like domain
    0.00035   20.7   0.0    0.00057   20.0   0.0    1.4  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   3.5e-21   2.1e-17      11     116 ..      15     122 ..       7     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 3.5e-21
                                       EEEEEEEEEHHHHHHHHHHHT---GGGT-HH.HHHHTTTSSSB--HHHHHHHHHHHHHHHHSTT..EGGGEEEEEEE CS
                   MaoC_dehydratas  11 etekeitvteadialyalvsgDlnpiHvdpe.fAkkagfggpIahGmltlaivaklveeelgdn..vvarvgeikvr 84 
                                       e+   + vte++i ++a    D ++ H+dpe + ++++ gg Ia+G++t+a++ +++++e+ ++       g++++r
  gi|313126186|ref|YP_004036456.1|  15 EF-GAYDVTEEEILQFAS-QYDPQWFHTDPErAREESIYGGLIASGWHTTAMMMRMLVDEFLSEtaALGAKGIDELR 89 
                                       55.56889**********.************555689999***********************98777788999*** PP

                                       E-S--BTTCEEEEEEEEEE.EEEEEEEEEEEEE CS
                   MaoC_dehydratas  85 FtkpVlpgdtlkvelevvg.krdvrktkkvevt 116
                                       + +pV+pgdtl  +l+vv+  +++ +   v+++
  gi|313126186|ref|YP_004036456.1|  90 WRRPVRPGDTLSLRLTVVEtEAEGPDRGLVKTR 122
                                       *****************9943334355555555 PP

>> FabA  FabA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     2e-08   0.00012      81     136 ..      78     134 ..      52     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2e-08
                                       -EEEEEEECEEEE-S---TT-.EEEEEEEEEEE..EECCTCEEEEEEEEEETTEEEEE CS
                              FabA  81 klvlfagvdevkfrgqvtPgdkklvleveikkv..seekrviiiadaellvdgklvye 136
                                       + +   g+de ++r++v+Pgd +l+l++++ ++  +   r++++ ++e+l d+++v++
  gi|313126186|ref|YP_004036456.1|  78 AALGAKGIDELRWRRPVRPGD-TLSLRLTVVETeaEGPDRGLVKTRIEVLNDTEVVCS 134
                                       3456789**************.********99964445688***************97 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.5e-08   0.00057      10     105 ..      17     111 ..      10     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.5e-08
                   MaoC_dehydrat_N  10 vkaevereavrefakavgetnpayldeeaaraa.gyrsliaPptflivlatkapelleal.gidlsrllhgeqefey 84 
                                         + v++e++ +fa+   +++  ++d+e ar++  y++lia  + ++++ ++   l  ++ +   +   +g  e+++
  gi|313126186|ref|YP_004036456.1|  17 GAYDVTEEEILQFASQY-DPQWFHTDPERAREEsIYGGLIASGWHTTAMMMRM--LVDEFlSETAALGAKGIDELRW 90 
                                       5689*********9754.57777********9879**********99999977..443331333333345669**** PP

                   MaoC_dehydrat_N  85 hepiraGDelttesriadvyd 105
                                        +p+r+GD+l+ + ++ + + 
  gi|313126186|ref|YP_004036456.1|  91 RRPVRPGDTLSLRLTVVETEA 111
                                       ***********9988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1092.02
//
Query:       gi|313126187|ref|YP_004036457.1|  [L=249]
Description: RNA methyltransferase, trmh family, group 1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-30  104.5   0.0    9.3e-30  103.7   0.0    1.4  2  SpoU_methylase   SpoU rRNA Methylase family
  ------ inclusion threshold ------
      0.013   15.4   0.0       0.37   10.6   0.0    2.8  3  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.0     1e-33   9.3e-30       3     142 .]       8     159 ..       6     159 .. 0.83
   2 ?   -3.6   0.0       1.3   1.2e+04      59      74 ..     186     201 ..     179     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 1e-33
                                       EEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEE CS
                    SpoU_methylase   3 ivvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalv 79 
                                       +vv+ve+e+pgN+G+iaR++k+fg+++l lv+p   +++ +    a++  ++vl+ +   +++e+++e + + ++ +
  gi|313126187|ref|YP_004036457.1|   8 VVVVVEPETPGNVGTIARAMKNFGLTDLKLVNPPPLEPDGEAYGFAGHAREDVLPNADEVTFDEVVEEYHTVATTAI 84 
                                       79*******************************999888877777777779999988888**********9944444 PP

                                       EESTT-SEGC...CSHHH...........TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                    SpoU_methylase  80 atslkgksls...eidlk...........ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                       + + + k+++   ++  +            k+alvfG+E++Gl+n++l+++d++++Ip s +++ LN+ +A+ il+y
  gi|313126187|ref|YP_004036457.1|  85 TNEDSRKHVRfpyKT--PvevresletveTKTALVFGREGRGLNNDELARLDEICSIPASDDYPVLNLGQAATILMY 159
                                       444466666664422..133444455666**********************************************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.3
                                       EEESSHHHHHHHHCCC CS
                    SpoU_methylase  59 kvvdsleealkelkee 74 
                                       + +d++e++l++ +++
  gi|313126187|ref|YP_004036457.1| 186 RFYDNFENFLEHAEHR 201
                                       4678999999887665 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.071   6.4e+02      27      48 ..      19      40 ..       4      44 .. 0.84
   2 ?   10.6   0.0   4.1e-05      0.37     117     177 ..      98     158 ..      65     163 .. 0.74
   3 ?   -0.6   0.0      0.12   1.1e+03      73     106 ..     176     209 ..     169     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.071
                                      HHHHHHHHHHHTT-SEEEEE-- CS
                   Methyltrn_RNA_4 27 DlhDiaRsartygvkkyyvvtp 48
                                      ++  iaR+ + +g++++ +v+p
  gi|313126187|ref|YP_004036457.1| 19 NVGTIARAMKNFGLTDLKLVNP 40
                                      56679*********99999988 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.1e-05
                                       B-HHHHHHHHHH--S-EEEEE--.TT---HHHHTT-SEEB--TTTTSS-----HHHHHHHHH CS
                   Methyltrn_RNA_4 117 vsyeelrelleeeekpvlllfGt.gwGlaeevlekadyiLepirgaseynHLsvrsAvaiil 177
                                        +  e+re le+ e+++ l+fG  g Gl+++ l++ d i  +i + ++y  L    A++i++
  gi|313126187|ref|YP_004036457.1|  98 KTPVEVRESLETVETKTALVFGReGRGLNNDELARLDEIC-SIPASDDYPVLNLGQAATILM 158
                                       234589999*99**********559************975.799*********999999987 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.12
                                       SSSHHHHTTEEEESSHHHHHHHHHHHHSS--EEE CS
                   Methyltrn_RNA_4  73 pdRkealslvkvvesleealeeiekeegkkplvv 106
                                        +R++  ++ ++ +++e+ le+ e++ +k+p+++
  gi|313126187|ref|YP_004036457.1| 176 RERATESEIERFYDNFENFLEHAEHRDHKRPKTM 209
                                       45666667778899999999***99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1522.33
//
Query:       gi|313126188|ref|YP_004036458.1|  [L=205]
Description: hypothetical protein Hbor_14330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1306.65
//
Query:       gi|313126189|ref|YP_004036459.1|  [L=186]
Description: response regulator with chey-like receiver, aaa-type ATPase, and DNA-binding domains [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-17   62.7   0.1    5.3e-17   62.0   0.1    1.3  1  Response_reg  Response regulator receiver domain
    1.4e-13   50.9   5.3    3.9e-13   49.5   5.3    1.8  1  HalX          HalX domain
  ------ inclusion threshold ------
      0.038   13.6   0.0      0.047   13.3   0.0    1.2  1  ThiI          Thiamine biosynthesis protein (ThiI)
      0.046   12.9   0.4        0.1   11.8   0.2    1.6  2  DUF1152       Protein of unknown function (DUF1152)


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.1   1.2e-20   5.3e-17       1     110 [.       8     113 ..       8     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 1.2e-20
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH.HHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealell.keekvdlillDinmpgmdGlellkeireedpelpvii 76 
                                       vl vdD++ + el + +l  + y ev++a+++++al+ +    ++d++llD +mp+m+G ++l+e+r+e  ++pv++
  gi|313126189|ref|YP_004036459.1|   8 VLTVDDERSLTELYAAWLS-DAY-EVRQANSAADALRTVaSGLDPDVVLLDRQMPQMTGDDVLTELRAEGVDCPVVM 82 
                                       899***************9.889.9************9955677********************************* PP

                                       EESSTSHHHHHHHHHCTESEEEESSG-HHHHHHH CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfdpeeLlka 110
                                       +ta +      + +++  dd+l+Kp++ ee+   
  gi|313126189|ref|YP_004036459.1|  83 VTAVDP---GFDIVSMPFDDYLVKPVTNEEVQRT 113
                                       **9887...66677899*********99998765 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   5.3   8.7e-17   3.9e-13       1      58 [.     119     176 ..     119     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 8.7e-17
                              HalX   1 trseYdeelqelfaLasKravLeaekseaeLadseeYqeLearleelraqldetldel 58 
                                       tr +Yde+++++f+La+K+avLe++ +  + +++ + qeL+++le++ +++d+t del
  gi|313126189|ref|YP_004036459.1| 119 TRETYDEQVRRYFTLARKKAVLETSSAVTDVRSNPTSQELRRELEHVSHTADRTRDEL 176
                                       799*****************************************************96 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     1e-05     0.047       9      74 ..      71     138 ..      62     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                              ThiI   9 LlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellae..yqtslevklvvvdfke 74 
                                       L ++G+D pV    ++  G+ +v + ++++++++  ++e+ +++a+ l++  y+ +++  ++    k 
  gi|313126189|ref|YP_004036459.1|  71 LRAEGVDCPVVMVTAVDPGFDIVSMPFDDYLVKPVTNEEVQRTVAASLTRetYDEQVRRYFTLARKKA 138
                                       5689******************************9999999999999976336665554444444443 PP

>> DUF1152  Protein of unknown function (DUF1152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   2.3e-05       0.1      55     144 ..      14     106 ..       4     127 .. 0.82
   2 ?   -0.5   0.0      0.12   5.5e+02      63     113 ..     116     166 ..     105     171 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                           DUF1152  55 veaineavaivnaesrairgarsvlpqlarvakvlneevvlldikkgveglaealeelaeklgid....liigvDvG 127
                                        ++++e  a+  ++++ +r+a+s    l  va+ l+ +vvlld +  +    + l+el +++g+d    ++++vD G
  gi|313126189|ref|YP_004036459.1|  14 ERSLTELYAAWLSDAYEVRQANSAADALRTVASGLDPDVVLLDRQMPQMTGDDVLTEL-RAEGVDcpvvMVTAVDPG 89 
                                       566777778888999****************************999988888888777.44455422326889**** PP

                           DUF1152 128 GDvLAkGdEegLrSPLa 144
                                        D+++ + ++ L+ P  
  gi|313126189|ref|YP_004036459.1|  90 FDIVSMPFDDYLVKPVT 106
                                       **********9999975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.12
                           DUF1152  63 aivnaesrairgarsvlpqlarvakvlneevvlldi..kkgveglaealeela 113
                                       a +++e++    + +   +lar  +vl+++ ++ d+  +  +++l+++le++ 
  gi|313126189|ref|YP_004036459.1| 116 ASLTRETYDE--QVRRYFTLARKKAVLETSSAVTDVrsNPTSQELRRELEHVS 166
                                       4455555543..33344555555556655555555510445677788877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1113.96
//
Query:       gi|313126190|ref|YP_004036460.1|  [L=388]
Description: dihydropteroate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.9e-38  130.7   0.1    1.2e-37  129.9   0.1    1.4  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.1   6.6e-42   1.2e-37       1     244 []      20     252 ..      20     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 6.6e-42
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHH.HHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHC.TSE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqar.kmveeGAdilDiggestrPgaervdeeeelervvpvlealrdea.dvp 75 
                                       mg+lNv+++s ++ + f+d+ +a + +  ++++eGAdi+D+g es++ + e++++eeel+r+   +e l++ + d  
  gi|313126190|ref|YP_004036460.1|  20 MGVLNVSKESPYEPSVFNDAGEAAKYVDtALIDEGADIVDVGLESANKRFEVLSAEEELDRLDTAVEVLESVSgDAV 96 
                                       9****************999999988852799***********************************9999888*** PP

                                       EEEE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCC.CCCSSHHHHHHHHHH CS
                       Pterin_bind  76 isiDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeee.gqyedvveeveafle 151
                                        si t   eva +Al++g d+vNd+ g+  dp+m+ ++ +++aav  m++          + ++   ++eev+   +
  gi|313126190|ref|YP_004036460.1|  97 FSIETRYHEVADEALSRGFDMVNDICGFA-DPEMPTVCTDHDAAVAKMASP---------PdLERPGAIEEVDDIYD 163
                                       *****************************.*********************.........44566778888877665 PP

                                       HHHHHHHHTT--GGGEEEETTTTS...STTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHH.CTTCHGHHHH CS
                       Pterin_bind 152 arveaaeeaGvaperillDpgigf...gkteehnlellrrldelrealevpvllGvSrksflgrll.elgkaeeRda 224
                                           a+++ G+ + + ++Dp +g    +kt eh+ e lrrl e+ +  + p+l+++ rk+fl ++  +  ++ee   
  gi|313126190|ref|YP_004036460.1| 164 ----ALAQNGFTD-KTIVDPAFGGwseAKTLEHDRETLRRLREF-RGYGRPILVSINRKNFLREVAgR--DTEEALP 232
                                       ....88999**88.6678****99899*****************.999****************9732..379**** PP

                                       HHHHHHHHHHHTT-SEEEES CS
                       Pterin_bind 225 gtaaflalaaaaGadivrVh 244
                                       +++a++++a+++Ga+++r+h
  gi|313126190|ref|YP_004036460.1| 233 VSLAATSMAVERGAHVIRTH 252
                                       *******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2672.89
//
Query:       gi|313126191|ref|YP_004036461.1|  [L=226]
Description: hypothetical protein Hbor_14360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-15   57.7   0.0    1.5e-15   57.3   0.0    1.1  1  MAF_flag10  Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   8.3e-20   1.5e-15      23     167 ..      46     181 ..      31     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 8.3e-20
                        MAF_flag10  23 kgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaekkgdiplv 98 
                                        g k + +vga PSL ++++ +    d  v+++a+ta+ +  ++g ++D++v+ lD++  +++     +++g  + +
  gi|313126191|ref|YP_004036461.1|  46 TG-KRVAVVGAAPSLPSEVDAVA---DADVVFTASTATDVVRNAGYEVDLMVTdLDKNPETAR---RRTQNGTPVAA 115
                                       45.99***************996...999****************************555555...55555589999 PP

                        MAF_flag10  99 fasgvnpellkkykgpki.flvtgstqa..lelleeekneilfgGgsvantaldlAvklgfkeIiliGqDla 167
                                       +a+g+n+ +++++ ++     v ++tqa   e      n+ ++gG++++++a +lA  +g+ e+ ++G  + 
  gi|313126191|ref|YP_004036461.1| 116 HAHGDNIPAIREWLPRFDaAHVLATTQAapVE------NVANYGGFTDGDRAAFLADAFGAAELQFVGWEFD 181
                                       ***************98865566666653344......449***************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1416.55
//
Query:       gi|313126192|ref|YP_004036462.1|  [L=272]
Description: hypothetical protein Hbor_14370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1807.31
//
Query:       gi|313126193|ref|YP_004036463.1|  [L=469]
Description: deoxyribodipyrimidine photo-lyase type i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-78  263.0   2.8      2e-78  262.5   2.8    1.2  1  FAD_binding_7   FAD binding domain of DNA photolyase
    1.2e-47  161.9   3.1    1.3e-46  158.6   0.7    2.3  2  DNA_photolyase  DNA photolyase
  ------ inclusion threshold ------
       0.01   15.7   0.1       0.02   14.8   0.1    1.4  1  DUF2726         Protein of unknown function (DUF2726)
      0.093   13.2   0.1      0.093   13.2   0.1    2.6  2  Usp             Universal stress protein family


Domain annotation for each model (and alignments):
>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.5   2.8   4.4e-82     2e-78       1     201 [.     265     460 ..     265     461 .. 0.94

  Alignments for each domain:
  == domain 1  score: 262.5 bits;  conditional E-value: 4.4e-82
                                       HHHHHHHHHHHHHHHHCSTTTTTSSTTGCCTT------HH.HHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHH CS
                     FAD_binding_7   1 flreLlwrefyyallaaepelaeralkekfdripweeseeekleaWkeGrTGfPlvDAamrqLretGwmhnrlRmiv 77 
                                       f+++L+wrefy+++l+ +p++ ++++ke  ++i+w+e+ee +l+aWkeGrTG+P+vDA+mrqLre+ +mhnr+Rmiv
  gi|313126193|ref|YP_004036463.1| 265 FQSQLAWREFYTHVLYFNPDVVTQNYKEYENDIAWREDEE-ALTAWKEGRTGYPIVDAGMRQLREEAYMHNRMRMIV 340
                                       889************************99999***99977.6*********************************** PP

                                       HHHHCTTT-B-HHHHHHHHHHH-TT--CCHHHHHHHHHCT-STTS-STT----CCCCHHHCSTT-HHHHHH-GGGTT CS
                     FAD_binding_7  78 asFltkdLlidWregeevFeellvDadlasnagnwqwlagtgadaapafrifnpvkqgkkfDpegeyirrwvpeLkk 154
                                       asFltkdLlidWreg ++F+ +l D+d+a+++g+wqw+a+tg+da+p+frifnp++qg+++Dp+++yi+++vpeL++
  gi|313126193|ref|YP_004036463.1| 341 ASFLTKDLLIDWREGYAHFRAYLADHDTANDNGGWQWAASTGTDAQPYFRIFNPMTQGERYDPDATYIQQYVPELRD 417
                                       ***************************************************************************** PP

                                       S-HHHHT-GGGSGCHHHHHHT--TTTSS---SS-HHHHHHHHHHHHH CS
                     FAD_binding_7 155 lpakyihepwkapaeeqkkagvvlgkdYpkpivdhkearkraleayk 201
                                         a++ih+ w   +    + + +++ +Yp+piv+h+++r++a++ ++
  gi|313126193|ref|YP_004036463.1| 418 ATADEIHD-WPNLS---PTERETVAPEYPDPIVEHSKRRDQAISMFE 460
                                       *******7.63222...234578999****************98875 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.6   0.7   2.9e-50   1.3e-46       2     160 ..       3     159 ..       2     164 .. 0.94
   2 ?    3.2   0.1     0.018        79      86     138 ..     236     289 ..     228     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: 158.6 bits;  conditional E-value: 2.9e-50
                                       EEEESS---STT-HHHHHHHCTTSEEEEEEEE-HHHHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHH CS
                    DNA_photolyase   2 lvWfrrDlRlhDNpALaaAaasgepvipvfvldpekahklrvgaarvdfllesLadLdeeLrelgirLvvrrgdpad 78 
                                       l+W+rrDlR++DN+ L  Aa++g+ v+pvfv+d++     ++gaarv+f+l  La+L+e++re++++Lvv+rgdp +
  gi|313126193|ref|YP_004036463.1|   3 LHWHRRDLRVSDNHGLVTAADAGD-VVPVFVFDDDVLA--HAGAARVRFMLDALARLRETYRERDSDLVVVRGDPTE 76 
                                       89******************9865.**********434..45*********************************** PP

                                       HHHHHHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHTTTSSSHSSHHHHHHCHHHH CS
                    DNA_photolyase  79 vlpelakelgasavvanreyepdererdeavkealrkagievesfddhtlvepgevktkkgkpykvFtpfrkrwlke 155
                                       +lp+la+e++a+ vv+n++y++ +r rdeav++al++ag++   ++d + +epg++ t+ g+py+v+t f+k+w+++
  gi|313126193|ref|YP_004036463.1|  77 ELPRLAAEYDADGVVWNKDYSRLARTRDEAVRRALDEAGVAHDAVHDAIHHEPGSITTNAGDPYSVYTYFWKKWRNR 153
                                       ***************************************************************************97 PP

                                       HC.S-T CS
                    DNA_photolyase 156 lk.epl 160
                                        k +p+
  gi|313126193|ref|YP_004036463.1| 154 NKaDPF 159
                                       765544 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.018
                                       HCTECEEEEE---SHHHHHHHHHHHHHHH.HCTSEEEEE--SSSS-HHHHHTTT CS
                    DNA_photolyase  86 elgasavvanreyepdererdeavkealr.kagievesfddhtlvepgevktkk 138
                                       ++g+++v+a +e   +  + d++ k++ + +++++ ++f +h+l+   +v t++
  gi|313126193|ref|YP_004036463.1| 236 TIGIREVYAATEEAAENADSDDEAKSVEEfQSQLAWREFYTHVLYFNPDVVTQN 289
                                       6899*************9999999988777789999******887544444554 PP

>> DUF2726  Protein of unknown function (DUF2726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   4.5e-06      0.02      49     108 ..      55     121 ..      46     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.5e-06
                           DUF2726  49 ealnrisakrvDfllc..dkadlkpvavIeldga.....khkqgkarkrDalkraalaaAgipllrv 108
                                       + +++++++  D++++  d++++ p+++ e+d       k +++ ar+rD+ +r+al++Ag+++  v
  gi|313126193|ref|YP_004036463.1|  55 RLRETYRERDSDLVVVrgDPTEELPRLAAEYDADgvvwnKDYSRLARTRDEAVRRALDEAGVAHDAV 121
                                       566778888899999955677789********9877877888********************98666 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.1e-05     0.093      44     108 ..      38      91 ..      16      95 .. 0.71
   2 ?   -0.8   1.1      0.43   1.9e+03      51      51 ..     140     140 ..     100     295 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                                       CCCCCCCHHHHHHHHHHHHHHHHHHHH....HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEE CS
                               Usp  44 sgavsdadeeaeeeeleleeaeleada....akaaaeaggvkvevvveegdpaeeilevaeeedadliV 108
                                        +               +++a++++ +    a+ ++  ++ + ++vv+ gdp ee+ ++a e+dad +V
  gi|313126193|ref|YP_004036463.1|  38 LA---------------HAGAARVRFMldalARLRETYRERDSDLVVVRGDPTEELPRLAAEYDADGVV 91 
                                       33...............33333333334444566667789**************************887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.43
                                       H CS
                               Usp  51 d 51 
                                        
  gi|313126193|ref|YP_004036463.1| 140 Y 140
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3123.98
//
Query:       gi|313126194|ref|YP_004036464.1|  [L=201]
Description: transcriptional regulator containing an amidase domain and an arac-type DNA-binding hth domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.7e-24   84.4   0.0    1.2e-23   83.8   0.0    1.2  1  DJ-1_PfpI  DJ-1/PfpI family
     0.0021   17.7   0.1     0.0057   16.3   0.1    1.5  2  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.021   13.9   0.0      0.026   13.6   0.0    1.2  1  GATase_5   CobB/CobQ-like glutamine amidotransferase domain
      0.091   12.8   0.0       0.15   12.1   0.0    1.3  1  Fer2_2     [2Fe-2S] binding domain


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.0   2.6e-27   1.2e-23       5     164 ..       5     175 ..       4     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 2.6e-27
                                       EEEETTBEHHHHHHHHHHHHH.....TTEEEEEEESS.TSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BH.... CS
                         DJ-1_PfpI   5 vlladgvedvElivpvdvlkr.....agikvdvvsvd.keevkgsrGlkvtvdaslddvkaaeyDalvlpGGr.... 71 
                                       +ll dg+++++++ p++v++      a+++ ++v++d +e+v+ s+Gl+v  d +++  ++++ D+l++pGG     
  gi|313126194|ref|YP_004036464.1|   5 ILLYDGFDELDAVGPYEVFETagafgADCSARLVTLDaRETVTASHGLRVGTDGTFN-PDSSDADVLLVPGGGwsdp 80 
                                       6899****************6677889**********88999**************9.58889********963222 PP

                                       ..HHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTE CS
                         DJ-1_PfpI  72 ..agperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnl 146
                                          g+   +en ++ + +   a++g++va +C+g +lLa agvl+gr + ++ +  d+l++ + ++ d r+v dg++
  gi|313126194|ref|YP_004036464.1|  81 sePGAGMEAENGEIPDAIAAYAQRGGVVAGVCTGGMLLAHAGVLDGRPAVTHATALDDLREMNVDIQDTRFVDDGDV 157
                                       113444556777999************************************************************** PP

                                       EEESSGGGHHHHHHHHHH CS
                         DJ-1_PfpI 147 vTsrgpgaaiefalelle 164
                                       +T+ g+++ +++al l+e
  gi|313126194|ref|YP_004036464.1| 158 LTAGGVTSGLDLALHLVE 175
                                       ***************998 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.3e-06    0.0057      39      90 ..      65     120 ..      44     127 .. 0.77
   2 ?   -1.9   0.0      0.47   2.1e+03      29      69 ..     143     183 ..     129     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
                          GATase_3  39 edadlvilpGg...k.dtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGe 90 
                                       +dad++++pGg     ++  +   +++ ++ +ai+++a++gg v g+C G ++L +
  gi|313126194|ref|YP_004036464.1|  65 SDADVLLVPGGgwsDpSEPGAGMEAENGEIPDAIAAYAQRGGVVAGVCTGGMLLAH 120
                                       5799999999733332334444445556899*********************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.47
                          GATase_3  29 fvplkdeslgedadlvilpGgkdtiqdlallresgldeaik 69 
                                        v+++d+++ +d d++  +G  + ++ + +l e++   +i+
  gi|313126194|ref|YP_004036464.1| 143 NVDIQDTRFVDDGDVLTAGGVTSGLDLALHLVERECGLKIA 183
                                       45566666667888888888777666666666655555555 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.7e-06     0.026      46     111 ..      66     126 ..      21     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-06
                          GATase_5  46 dfqilalp.GGfsygDelgsgkgwakslllneklrealekflnredtlaLGiCnGfqlLvklglvpg 111
                                       d+ +l +p GG s   e+g+g  +      n ++ +a++++ +r ++ + G+C G  lL++ g+++g
  gi|313126194|ref|YP_004036464.1|  66 DADVLLVPgGGWSDPSEPGAGMEAE-----NGEIPDAIAAYAQR-GGVVAGVCTGGMLLAHAGVLDG 126
                                       5555555515677777777776544.....7899**********.******************9987 PP

>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.4e-05      0.15      13      50 ..      95     132 ..      84     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.4e-05
                            Fer2_2  13 hpvqeafveegasqCGyCtpGfvmsaaalleenepkpt 50 
                                        +  +a +++g++  G Ct G++++ a++l+ +++ ++
  gi|313126194|ref|YP_004036464.1|  95 PDAIAAYAQRGGVVAGVCTGGMLLAHAGVLDGRPAVTH 132
                                       5567899**********************998854443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1304.30
//
Query:       gi|313126195|ref|YP_004036465.1|  [L=199]
Description: superoxide dismutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-30  104.8   0.4      4e-30  104.1   0.4    1.3  1  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin
    1.2e-27   96.0   0.0    1.9e-27   95.4   0.0    1.3  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do


Domain annotation for each model (and alignments):
>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.4   4.5e-34     4e-30       1      82 []       2      83 ..       2      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 4.5e-34
                                      S------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sod_Fe_N  1 kyeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlkklekalrnnagghvnHslfwk 79
                                      +yeL++LpY+ydaLePhis+++l++Hhd+Hh++Yvn++N+a+e+le ++++ +  ++ ++ +++++n+ gh++H+lfw+
  gi|313126195|ref|YP_004036465.1|  2 SYELDPLPYEYDALEPHISEQVLTWHHDTHHQGYVNGWNSAEETLESNREEGDFGSSPGAIRNVTHNGCGHILHDLFWN 80
                                      59***************************************************************************** PP

                                      TB- CS
                          Sod_Fe_N 80 nls 82
                                      ++s
  gi|313126195|ref|YP_004036465.1| 81 SMS 83
                                      *96 PP

>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.0   2.1e-31   1.9e-27       1     100 [.      90     188 ..      90     190 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 2.1e-31
                                       --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTH CS
                          Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYy 76 
                                       p+g+la++ieedfgs+e++k ef+aaa +  + Gwa+Lv+d+  ++L+ v ++++d+   ++++p+LalDvweh+Yy
  gi|313126195|ref|YP_004036465.1|  90 PTGSLADRIEEDFGSYEAWKGEFEAAAGN--AGGWALLVYDSFsNQLRNVVVDKHDQGALWGSHPILALDVWEHSYY 164
                                       899**********************9998..89*******986589******************************* PP

                                       HHHTT-HHHHHHHHGGGBBHHHHH CS
                          Sod_Fe_C  77 ldyqnkradYieafwnvvnWkeve 100
                                        dy  +r d+i+af++vv+W+e +
  gi|313126195|ref|YP_004036465.1| 165 HDYGPARGDFIDAFFEVVDWEEPS 188
                                       ********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1301.03
//
Query:       gi|313126196|ref|YP_004036466.1|  [L=172]
Description: hypothetical protein Hbor_14410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1093.47
//
Query:       gi|313126197|ref|YP_004036467.1|  [L=101]
Description: hypothetical protein Hbor_14420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 652.77
//
Query:       gi|313126198|ref|YP_004036468.1|  [L=192]
Description: zn-dependent hydrolase, glyoxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-15   55.1  10.4    2.8e-13   50.3  10.4    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0048   16.4   3.5     0.0097   15.4   3.5    1.7  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3  10.4   3.2e-17   2.8e-13       4     191 ..      12     164 ..       9     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3.2e-17
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       + +n++l+ +++++ L+D G   +          ++   +++d+v +TH H DH+ +++ ++ea+dv ++    +  
  gi|313126198|ref|YP_004036468.1|  12 FTSNVFLV-TGDTTALVDVGANFDVVSR------VRDHVDELDRVYITHTHRDHVDNVAAVREAFDVETWGFDPDQS 81 
                                       57899999.9*****************8......7**************************************9999 PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SHH CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.age 156
                                       +  +  a                        ++++   g+ ++++ ++pgh ++h+++++++++vlf+GD+++ +g+
  gi|313126198|ref|YP_004036468.1|  82 EVDHAIA------------------------DGETVQIGDDDYEALHTPGHKNDHLCFYSRDASVLFAGDLVFaNGS 134
                                       9999999........................99****************************************7777 PP

                                       CCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHS CS
                       Lactamase_B 157 tgridltlrgaevrdpsdaekyldsllklaglkae 191
                                        gr+dl     e +d+    ++ld++++ ++   +
  gi|313126198|ref|YP_004036468.1| 135 FGRTDL-----EEGDRPTLIESLDRVRETIDETLS 164
                                       888888.....999999999999998887766555 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.5   1.1e-06    0.0097      24      53 ..      39      69 ..      23     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-06
                                      SS--..SEEEEE-SS--HHHHGGGGCCCC.C CS
                     Lactamase_B_2 24 lrdelppidaVllthaHyDHlaglltlre.l 53
                                       rd+++++d V +th H DH+ ++  +re +
  gi|313126198|ref|YP_004036468.1| 39 VRDHVDELDRVYITHTHRDHVDNVAAVREaF 69
                                      68999***********************943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1279.36
//
Query:       gi|313126199|ref|YP_004036469.1|  [L=339]
Description: hypothetical protein Hbor_14440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2262.67
//
Query:       gi|313126200|ref|YP_004036470.1|  [L=150]
Description: hypothetical protein Hbor_14450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 879.76
//
Query:       gi|313126201|ref|YP_004036471.1|  [L=332]
Description: thymidylate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-94  314.1   0.0    7.5e-94  313.8   0.0    1.0  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.8   0.0   4.2e-98   7.5e-94       2     267 ..       3     331 ..       2     331 .. 0.97

  Alignments for each domain:
  == domain 1  score: 313.8 bits;  conditional E-value: 4.2e-98
                                       HHHHHHHHHHHH-EEEE-TTSSEEEEEEEEEEEEEGGGCB----SSST-...-HHHHHHHHHHHHTT--BTHHHHTT CS
                   Thymidylat_synt   2 qYldlvrkileeGeekedRtgtgtisvfgaqlrfdlsegefPllTtkkv...flksvieEllWflsgetnvkeLqek 75 
                                       qYldlv+++l++G++k++Rtg++tis f++++++dl+eg fPllTtk +   +++s+i+E++W+lsge+++++L+ +
  gi|313126201|ref|YP_004036471.1|   3 QYLDLVTDVLSNGQHKPNRTGVDTISAFSRHYEVDLQEG-FPLLTTKDLsgfRWNSLIHEFVWYLSGEEHIRTLR-E 77 
                                       9*************************************9.********98889**********************.6 PP

                                       T--TTHHHHHHTTB-SSSHHHHHHHBTST..................TTSSB-HHHHHHHHHHHSTT-ST-EEE--- CS
                   Thymidylat_synt  76 gvkiWdewadeegdlgpvYGkqwrkfkae..................egkkidqlakvidqlkenpdsRriivsawn 134
                                       ++ iWd+wadeeg+l+++YG++wr+f+ +                  ++ ++dq+++v+d+l+enp+sRr++v+aw+
  gi|313126201|ref|YP_004036471.1|  78 ETGIWDAWADEEGRLDTAYGRFWRRFPVPdeglpgeawpedthrwmnDEGTFDQIQYVLDTLRENPNSRRMVVNAWH 154
                                       9************************999999***************99***************************** PP

                                       GGGGGGSSS--SEEEEEEEE..SEETEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEE CS
                   Thymidylat_synt 135 paeldkmaLppChvlfqfyvkdkkegkLslqlyqRSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHi 211
                                       pa+     LppCh++f f+v+ +   kL+l+l+qRS D++lG+pFNia+yalL++ +aq tg+++g+++ht+ daH+
  gi|313126201|ref|YP_004036471.1| 155 PANAAVSTLPPCHYSFVFNVQGD---KLNLHLTQRSGDIALGIPFNIAAYALLATAVAQRTGFEVGKFAHTVVDAHV 228
                                       ***85689************655...5************************************************** PP

                                       E..................................................GGGHHHHHHHHTS---S--EEEE--S CS
                   Thymidylat_synt 212 Y..................................................snhveqvkeqlereprelpklelnke 238
                                       Y                                                   +hv+++ +q++rep + p+++++  
  gi|313126201|ref|YP_004036471.1| 229 YcgegdrgawygdhlsdlqtrladvssrdeyldvrdwlveaapaeaegkerYDHVPGLLKQCAREPGDRPTIDVA-- 303
                                       **************************************************************************7.. PP

                                       STHSGGG--GGGEEEES----SXXXXXXX CS
                   Thymidylat_synt 239 kkvsiedfeledfelenYkphpkikakva 267
                                        +v +++++++d+el++Y+p++ i+++va
  gi|313126201|ref|YP_004036471.1| 304 -DVPLDELTYDDIELHDYDPDEGIRFAVA 331
                                       .3469*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2121.50
//
Query:       gi|313126202|ref|YP_004036472.1|  [L=183]
Description: dihydrofolate reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-46  157.7   0.0    2.3e-46  157.4   0.0    1.0  1  DHFR_1      Dihydrofolate reductase
  ------ inclusion threshold ------
      0.086   11.6   0.0       0.11   11.2   0.0    1.1  1  ABC_ATPase  Predicted ATPase of the ABC class


Domain annotation for each model (and alignments):
>> DHFR_1  Dihydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.4   0.0   2.6e-50   2.3e-46       3     161 .]      22     181 ..      20     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 2.6e-50
                                       EEEEEEETT-EEEBTTB-SS--HHHHHHHHHHHTTCEEEEEHHHHHCC-....S--TTCEEEEE-S-TT---TTEEE CS
                            DHFR_1   3 slivAvaengvIGkdnklpwhlpeDlkrFkklTtgkpvimGrkTfeslg...krpLpnrkniVltrnedlkvegvev 76 
                                       +l++AvaengvIG+d+++pwh++eD+++Fk++T+g+pvi+GrkT+e +     +p+p+r +iVl+++e   +eg+++
  gi|313126202|ref|YP_004036472.1|  22 VLVAAVAENGVIGRDGRMPWHFSEDMAHFKQTTMGHPVILGRKTYENIVdaiGEPFPGRMSIVLSSRELDLPEGAVL 98 
                                       689*******************************************99766678***********99888889**** PP

                                       ESSHHHHC....CCCTTS...SEEEEEE-HHHHHHCGGG-SEEEEEEESS----SEE-----CCCEEEEEEEEE--C CS
                            DHFR_1  77 vssleeal....alakee..keevfviGGaeiYkqalpladklylTeidaefegdtffpeideeewelvereehekd 147
                                       ++s++ea+    ++a+ e   e+v+v+GGa++Y+q+lp a++++lTei+ +++g+t fpe++e+ w +++r+e+e  
  gi|313126202|ref|YP_004036472.1|  99 ANSIKEATeraeSVAE-EmgVETVYVVGGARVYAQFLPRATRMILTEIHDSYDGETEFPEWEEAMWIETDRDERE-- 172
                                       ********66532333.347799************************************************9888.. PP

                                       TTC-S-EEEEEEEE CS
                            DHFR_1 148 eknkyaytfvtyer 161
                                            +++fvtyer
  gi|313126202|ref|YP_004036472.1| 173 -----SFDFVTYER 181
                                       .....788888886 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.2e-05      0.11     372     438 ..     101     170 ..      96     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.2e-05
                                       -B--HHHCHHHHHHHH--EEEEEESS-G...CCTTT-SEEEEEETTEEEE-HHHHHHHHHCHT-----.. CS
                        ABC_ATPase 372 pitplvdrvrelykklgvstilvvggsg...dyldvAdtvilmeeykpkdvtekakeiaeelatkrkeea 438
                                        i+  ++r++++ +++gv t+ vvgg+    ++l+ A ++il e +  +d  ++  e  e +  ++ + +
  gi|313126202|ref|YP_004036472.1| 101 SIKEATERAESVAEEMGVETVYVVGGARvyaQFLPRATRMILTEIHDSYDGETEFPEWEEAMWIETDRDE 170
                                       6888899*******************86222668899999999999999988887777776655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1159.78
//
Query:       gi|313126203|ref|YP_004036473.1|  [L=59]
Description: hypothetical protein Hbor_14480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-24   85.8   0.2    1.5e-24   85.5   0.2    1.1  1  DUF1508   Domain of unknown function (DUF1508)


Domain annotation for each model (and alignments):
>> DUF1508  Domain of unknown function (DUF1508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.2   8.6e-29   1.5e-24       1      48 []      10      58 ..      10      58 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 8.6e-29
                                      ETTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                           DUF1508  1 DknGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeveD 48
                                      D++G+fr+rL+++Ng++Ia+ +egY++k++a+nGI+sV++nap+a++e+
  gi|313126203|ref|YP_004036473.1| 10 DEAGQFRWRLVHDNGNIIADsGEGYATKQNARNGIQSVQENAPEAPIEE 58
                                      789********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 397.06
//
Query:       gi|313126204|ref|YP_004036474.1|  [L=247]
Description: 20S proteasome subunit alpha or beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-51  175.0   0.0    1.4e-51  174.7   0.0    1.1  1  Proteasome      Proteasome subunit
      2e-12   46.6   0.4    5.5e-12   45.1   0.1    1.9  2  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.7   0.0   1.6e-55   1.4e-51       1     173 [.      32     204 ..      32     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 1.6e-55
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vk+G  +vGi++ dgvvl+a++r++  s+l++ +++eKi+k+d ++g+a +G +aDar+lv+ ar+e q  +lryg+
  gi|313126204|ref|YP_004036474.1|  32 VKRGAPSVGIRTADGVVLGAQRRTS--SSLMEAESIEKIHKLDSYLGAASSGHVADARQLVDDAREESQVNHLRYGE 106
                                       799**********************..9999********************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEE.TTT..EEEEEEEETTSEEEEESSEEEESTTHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvd.eeg..gpeLyqidpsGsyieekdavaiGsgseaaktale 151
                                        i ve+l++ +++++q+ tqr+g rpfg+slli+g+d e++  +p+L+q+dpsG+ +e+k avaiGs++  ++++le
  gi|313126204|ref|YP_004036474.1| 107 AIGVETLAKTLSDMIQESTQRGGTRPFGASLLIGGMDgEDDdaQPRLFQTDPSGAPHEWK-AVAIGSNRGDIQEFLE 182
                                       ************************************96443458***************8.**************** PP

                                       HHHSTTBSHHHHHHHHHHHHHH CS
                        Proteasome 152 keykedltleeavelavkalke 173
                                       +e++++l l ++v lav+al  
  gi|313126204|ref|YP_004036474.1| 183 DEWSSELALSDGVSLAVRALAV 204
                                       *******************975 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1   6.1e-16   5.5e-12       1      23 []       9      31 ..       9      31 .. 0.99
   2 ?   -1.9   0.0      0.31   2.8e+03      13      17 ..     152     156 ..     152     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 6.1e-16
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr ++ FSPdGR++QVEYA +A
  gi|313126204|ref|YP_004036474.1|  9 YDRGTSLFSPDGRIYQVEYAREA 31
                                      *********************99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.31
                    Proteasome_A_N  13 RLfQV 17 
                                       RLfQ 
  gi|313126204|ref|YP_004036474.1| 152 RLFQT 156
                                       9***5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1613.15
//
Query:       gi|313126205|ref|YP_004036475.1|  [L=286]
Description: hypothetical protein Hbor_14500 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-12   46.4   0.0    4.8e-12   45.8   0.0    1.3  1  MOSC_N    MOSC N-terminal beta barrel domain
    3.7e-06   27.0   0.0    8.3e-06   25.9   0.0    1.6  1  MOSC      MOSC domain


Domain annotation for each model (and alignments):
>> MOSC_N  MOSC N-terminal beta barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   5.3e-16   4.8e-12       2     113 ..      19     152 ..      18     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 5.3e-16
                            MOSC_N   2 arvssLyvyPiKsckgvslseaevtaaGllalDReflvvdedGkfltqrrePrlalirteldeedglLtltapgr.k 77 
                                       a v +L  +P+Ks++g +++++++ + G l  DRef++ de+G  ++ +re ++++i +++d ++ +L+l + +r +
  gi|313126205|ref|YP_004036475.1|  19 AVVRRLTTFPVKSLDGYDRESVRIVRNGGLDGDREFALFDESGDYVNGKRERAVHRIDADFDPDKRMLRLAVSDRtE 95 
                                       6799*******************77777778****************************************996515 PP

                            MOSC_N  78 dlevslakakasleevsvlelsasgldegd.....................evakwl 113
                                       ++ v+   a+ ++  ++ ++ + s +++ +                     eva w+
  gi|313126205|ref|YP_004036475.1|  96 TFDVDADRAELTAFLSDYFDYEVSLRQNREggfpddteasgptvvstatlrEVASWF 152
                                       667777665555555666666666666666555555656666666666666666665 PP

>> MOSC  MOSC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   9.2e-10   8.3e-06      14     131 .]     139     277 ..     134     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 9.2e-10
                                       EEETHHHHHHHHHS..GGGGG-STTTT--SEEES-...................-TTT-BTT-E.EEETT....... CS
                              MOSC  14 lisresldalneelkegrsveldpgrfreNivvggaaa...........feEd.twkelrigdrrfrlggacsRcqm 78 
                                       ++s++ l++++++++  + + ++ +r+r+N+ +g a +           f+E     e+ igd++++ + +c+Rc +
  gi|313126205|ref|YP_004036475.1| 139 VVSTATLREVASWFDGIDTDGMR-RRLRANVELGAAGDevlpafwedhlFDERgRVVEFSIGDVQLEGVNPCQRCVV 214
                                       56666666666666443333344.89*******66555799**888888777535679999**************** PP

                                       .........EE----THHHHH.....TTHHHHHH..HHT---EEEEEEE-E...EEETTS-EE CS
                              MOSC  79 vnvdqetgarprepcktlakf.....rrvdkrvk..gkgrfGvylrvleeg...tvrvGdeve 131
                                       +  d++tga+ +   +t+ ++     + ++ + +  +  r  v+ rv +e+   t++vGde++
  gi|313126205|ref|YP_004036475.1| 215 PSRDPDTGAEYDGFRETFIRHrgetkPPWSGGDWfnHDFRLMVNTRVPKESwgeTIAVGDEIR 277
                                       *********555555555554122243333322232455555666665555999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1555.08
//
Query:       gi|313126206|ref|YP_004036476.1|  [L=396]
Description: amidohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-48  165.6   3.1    2.2e-48  165.3   3.1    1.0  1  Amidohydro_1  Amidohydrolase family
    8.3e-19   68.4   9.4      4e-13   49.7   5.9    2.2  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   3.1   2.5e-52   2.2e-48       1     325 [.      58     379 ..      58     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 2.5e-52
                                       EEEE-EEEEEEECETTECSSS....GHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHH..HHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwlvppetaaealesgiktalksGtttvadmgattstgiealle..aae 71 
                                       +v PGl+DaHvHl ++   g+    t ++  +  e +++ ++  +++++++G+ttv+d ga    g  a+    a+e
  gi|313126206|ref|YP_004036476.1|  58 VVAPGLVDAHVHLMMD---GRpdvtTINQ--DGRELLSYRAAANLRANIEAGVTTVRDLGAP---GRLAIDAgvAVE 126
                                       589**********877...3342444444..999***************************6...344443356888 PP

                                       T.SSSEEEEEEESSEGGS.............GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHH CS
                      Amidohydro_1  72 e.lplglrilggkvsldr.............gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeel 134
                                       e +  g+r+++++ ++ +             g ae+ ka+re+lk+g a ++k +a+g+v ++ a  +ap++++ el
  gi|313126206|ref|YP_004036476.1| 127 EgVLDGPRVVACGENVVMtgghghwfgreadGAAEVQKAVREQLKRG-AGVVKCMATGGVLTEGAVTGAPELTEREL 202
                                       88777*******99999999***************************.7**************************** PP

                                       HHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHH..HHHHHHHH CS
                      Amidohydro_1 135 kealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpt..eaellker 209
                                       +++++ a+++++p a+Ha+++ g++ +a++a++ ++ehgt+ ++       + + l++  g++  pt   +e + e+
  gi|313126206|ref|YP_004036476.1| 203 SAVVDTASAKGVPTAAHAHGEVGIK-NAVRAGITSVEHGTFMDR-------EAAELMAREGTYWVPTasALEGIVEN 271
                                       ******************9999997.99999999**********.......788***********8888999999** PP

                                       HHHHCEE..HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCG.....GHHHHHHHHHHHHHHCCTTTTHCH CS
                      Amidohydro_1 210 lkeagva..hcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnsl.....nlleelrlalklqrgllyedeegg 279
                                       + eag++   + ++++  +   +a + al++Gv +++gtD   +g  +     n l+e+ l++           e+g
  gi|313126206|ref|YP_004036476.1| 272 GVEAGIPeqAVEKAEDAQDRFERAWEHALEAGVTIAMGTD---AGTPFnfhgeNALREMELMV-----------EYG 334
                                       ****************************************...666664455555888*****...........*** PP

                                       CHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGG CS
                      Amidohydro_1 280 lslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaaf 325
                                       ls++ al++aTin+A+ lg++ +vG+i++G++AD+ v+  d+++++
  gi|313126206|ref|YP_004036476.1| 335 LSAEAALEAATINAAELLGVS-DVGRIAEGYRADMLVLTDDPNENV 379
                                       ********************7.****************44554443 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   3.4e-08   0.00031       1      22 [.      50      71 ..      50      98 .. 0.87
   2 !   49.7   5.9   4.4e-17     4e-13     254     472 ..     187     395 ..     145     396 .] 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.4e-08
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHla 22
                                      e +D +G++v+PG+vD+H Hl 
  gi|313126206|ref|YP_004036476.1| 50 EAVDVSGKVVAPGLVDAHVHLM 71
                                      579*****************75 PP

  == domain 2  score: 49.7 bits;  conditional E-value: 4.4e-17
                      Amidohydro_3 254 f....tgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrr.....rlehaegv.tes 320
                                            tg p++++ +l ++v+ a ++g++ a ha+g+  + ++++a    +e   ++dr+       e + +v t+s
  gi|313126206|ref|YP_004036476.1| 187 TegavTGAPELTERELSAVVDTASAKGVPTAAHAHGEVGIKNAVRAGITSVEHGTFMDREaaelmAREGTYWVpTAS 263
                                       144458999********************************77776666666666666667855555555555**** PP

                      Amidohydro_3 321 qiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrr 397
                                        +e + + +v+ag+  +       ++++  ++  r   ++   l+agv++a+g+D      +p+ + g +  r+   
  gi|313126206|ref|YP_004036476.1| 264 ALEGIVENGVEAGIPEQ-------AVEKAEDAQDRFERAWEHALEAGVTIAMGTD----AGTPFNFHGENALREME- 328
                                       **************922.......333343444444599****************....44555555555555553. PP

                      Amidohydro_3 398 ggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaearvrltvvdGrvv 472
                                           l  +  ls e+al + T ++A++lg +d  G++++G++AD  vl +dp +   +     + ++++ dG+ v
  gi|313126206|ref|YP_004036476.1| 329 ----LMVEYGLSAEAALEAATINAAELLGVSDV-GRIAEGYRADMLVLTDDPNENVSA---WRGSEAVYRDGERV 395
                                       ....56899***********************9.**************9888654443...34466666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2195.95
//
Query:       gi|313126207|ref|YP_004036477.1|  [L=257]
Description: hypothetical protein Hbor_14530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-71  239.7   6.8      2e-71  239.4   6.8    1.1  1  DUF2270      Predicted integral membrane protein (DUF2270)
  ------ inclusion threshold ------
      0.046   13.3   0.1       0.65    9.7   0.0    2.2  2  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
       0.37   10.7   3.5        2.9    7.8   0.6    2.1  2  DUF2975      Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> DUF2270  Predicted integral membrane protein (DUF2270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.4   6.8   3.4e-75     2e-71       1     183 [.      36     213 ..      36     214 .. 0.98

  Alignments for each domain:
  == domain 1  score: 239.4 bits;  conditional E-value: 3.4e-75
                           DUF2270   1 ahlYRgeveratawreRlDrttnWavvvtaallsvalsspeashavlllgmllvlvfLliearryrfydvwrsrvrl 77 
                                       ahlYRge++r++ wreRlDrttnWav+++aa+l++a+s+++++h+v+llg ++v +fL+iearryr+ydvwrsrvr+
  gi|313126207|ref|YP_004036477.1|  36 AHLYRGEIHRMKLWRERLDRTTNWAVILMAAVLTWAFSQATHPHYVILLGNAAVGLFLCIEARRYRAYDVWRSRVRY 112
                                       6**************************************************************************** PP

                           DUF2270  78 leenffaealdpeegaeeeeWreeLaedlrkPtlkislleAlgrRLrrnYlwlllvlllawllkitlfkkeeeslee 154
                                       l+e+++a+ ldpe+  ++e+Wr+eLa+d+r+Ptlki++ eAl++RLrr+Yl+l++vl  awll++t+f+ +      
  gi|313126207|ref|YP_004036477.1| 113 LQEHVWAPGLDPESPLRDEKWRAELARDYRHPTLKITFEEALAHRLRRVYLPLFAVLNGAWLLRVTAFSVDP----- 184
                                       *********************************************************************999..... PP

                           DUF2270 155 llerAavgplpGelvllvvalfylallvl 183
                                       + ++Aavg++pG++v+++v+ +++a++v+
  gi|313126207|ref|YP_004036477.1| 185 WPASAAVGRIPGVVVIAIVISLFAAATVV 213
                                       99****************99998888776 PP

>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.053   3.2e+02      75      95 ..      81     101 ..      80     108 .. 0.79
   2 ?    9.7   0.0   0.00011      0.65      69     104 ..     197     232 ..     160     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.053
                                       HHHHHHHHHHHHHHHHHHHHS CS
                       Oxidored_q2  75 vigaaetavgLallvrlyrey 95 
                                       vi ++ +avgL l++ + r +
  gi|313126207|ref|YP_004036477.1|  81 VILLGNAAVGLFLCIEARRYR 101
                                       677888999999999887765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG-- CS
                       Oxidored_q2  69 lvLtaivigaaetavgLallvrlyreygtddvqelr 104
                                       +v +aivi++  +a ++a   r+++++g++  +elr
  gi|313126207|ref|YP_004036477.1| 197 VVVIAIVISLFAAATVVAYRPRTWHTRGELLSEELR 232
                                       46689*************************999996 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.01        61      69     103 ..      59      91 ..      51      96 .. 0.58
   2 ?    7.8   0.6   0.00048       2.9      50     106 ..     149     211 ..     137     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.01
                           DUF2975  69 aalllaagivalallaelelapgvvllllgvafas 103
                                       +a++l+a+++  a++++  ++p  v+ll+ +a++ 
  gi|313126207|ref|YP_004036477.1|  59 WAVILMAAVLTWAFSQA--THPHYVILLGNAAVGL 91 
                                       34455554444445555..8886666665555544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00048
                           DUF2975  50 vFspanvrrLrriglaliaa.....alllaagivalallae.lelapgvvllllgvafaslvi 106
                                       +F +a + rLrr+ l l+a+      l ++a  v+ +++++ +   pgvv++++++++++++ 
  gi|313126207|ref|YP_004036477.1| 149 TFEEALAHRLRRVYLPLFAVlngawLLRVTAFSVDPWPASAaVGRIPGVVVIAIVISLFAAAT 211
                                       7999999*********99999999888888888999999997777777777776666665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1457.45
//
Query:       gi|313126208|ref|YP_004036478.1|  [L=532]
Description: histidine ammonia-lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   8.2e-186  618.2  12.8   9.3e-186  618.0  12.8    1.0  1  Lyase_aromatic  Aromatic amino acid lyase


Domain annotation for each model (and alignments):
>> Lyase_aromatic  Aromatic amino acid lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.0  12.8  5.2e-190  9.3e-186       1     464 []      20     497 ..      20     497 .. 0.97

  Alignments for each domain:
  == domain 1  score: 618.0 bits;  conditional E-value: 5.2e-190
                                       --HHHHHHHHTCCCEEEE-HHHHHHHHHHHHHHHHHHHCTB--TTTSB-SGGGGGBB--HHHHHHHHHHHHHHC--- CS
                    Lyase_aromatic   1 LtledvvavargkakvelspearerveasravleeilaegepvYGvntGfGaladvripkedleelqrnllrshaaG 77 
                                       Lt+edv avar++akve+++ear++v asr++++ei+++g++vYG+ntGfG+l+d+ri+++++e+lq+nllrsha+G
  gi|313126208|ref|YP_004036478.1|  20 LTPEDVEAVARRGAKVEIDEEARAAVVASRERVAEIVESGQAVYGLNTGFGQLVDTRIEESEIEQLQTNLLRSHASG 96 
                                       89*************************************************************************** PP

                                       EEEE--HHHHHHHHHHHHHHHTTS-S---HHHHHHHHHHHHCTEEE--EEES-------HHHHHHHHHHHTTSSTCC CS
                    Lyase_aromatic  78 vgeplpeevvRaamllrlnslakGysGvrpevverllellnagitPvvperGSvGaSGDLaplahlalvliGegevy 154
                                       +g++l++e+vR ++l+rln+l+kGysGvr  vv++l+++ln++i+Pvv++rGS+GaSGDLaplahlalvliGege++
  gi|313126208|ref|YP_004036478.1|  97 AGRALDTEEVRSLLLTRLNALVKGYSGVREIVVDHLATMLNERIHPVVRSRGSLGASGDLAPLAHLALVLIGEGEAT 173
                                       ***************************************************************************** PP

                                       ET.....TEEEEHHHHHHHTT------TTTHHHHCCSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-BCGG CS
                    Lyase_aromatic 155 yk.....gerlpaaealaeaglepleleakEgLAlinGtalmtalaalaledaerllrladvaaAlslealrGstea 226
                                       +      +erl++aeala a+lepl+l++kEgLAlinGt+l+t++aal ++daerl+++ad+a+Al++e+++G+t++
  gi|313126208|ref|YP_004036478.1| 174 VSgehgeRERLSGAEALATAELEPLTLAPKEGLALINGTQLTTGVAALLVVDAERLAEAADAAGALTTEVTMGTTAN 250
                                       8888888999******************************************************************* PP

                                       G-HHHHCCS--HHHHHHHHHHHHHTTT-SSS...-SB-SS-SS--HHHHTHHHHHHHHHHHHHHHHHHHHHHHTS-- CS
                    Lyase_aromatic 227 fdprihalrphpgqievAarlrallegSelv.shekdeerlvQDayslRcaPqvhGavldalaaarevleiElnsat 302
                                       +dp+ih++rph gq++vA+++++l+++Se+v sh ++++r vQDays Rc+PqvhGav+da++++re++eiElnsat
  gi|313126208|ref|YP_004036478.1| 251 CDPAIHRVRPHGGQAAVAEHIQELTANSEIVeSH-ANCDR-VQDAYSVRCLPQVHGAVRDAIEHLREAVEIELNSAT 325
                                       *******************************888.9****.************************************ PP

                                       SSSEE...........EGCCTCCE---TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHC-TTT.TTT--GGG-SST CS
                    Lyase_aromatic 303 DNPlvd..........deeegavlsgGnFhgepvalalDklaialaelaniserrierLvnpal.segLpafLaaee 368
                                       DNPlv            +++  v+sgGnFhgep+al+lD+l  al+ela+iserr++r+vnp++ +++Lp+fLa e+
  gi|313126208|ref|YP_004036478.1| 326 DNPLVFdaenadnratGTDDAVVISGGNFHGEPLALRLDYLVSALTELAAISERRVDRMVNPNIqEDHLPPFLA-ED 401
                                       *****43444444444267889******************************************5556******.9* PP

                                       CTTB-TTHHHHHHHHHHHHHHHCHCS-SGGG--TCTTTTCSS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Lyase_aromatic 369 pglnsgfmiaqytaaalvsenktlahPasvdsiptsanqeDhvSmgliaarkllevvenlekvlAiellaaaqaldl 445
                                       +glnsgfmi+qytaa+l++e++  ++P s+d++p+s++qeDhvSm++++a  ++ v+en+++v+A+ell+  qa ++
  gi|313126208|ref|YP_004036478.1| 402 SGLNSGFMIPQYTAASLINEIRATGRP-SMDNTPVSGGQEDHVSMSATSAFSAKSVLENARTVVAVELLTGSQASEF 477
                                       ***************************.9************************************************ PP

                                       HHC.TCC-HHHHHHHHHHHC CS
                    Lyase_aromatic 446 rrk.lksspateavyeavre 464
                                        ++ l+++++t+ vye+vre
  gi|313126208|ref|YP_004036478.1| 478 VDDsLAHGRGTSVVYELVRE 497
                                       9877777***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2953.13
//
Query:       gi|313126209|ref|YP_004036479.1|  [L=403]
Description: imidazolonepropionase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-20   74.1   0.3    5.5e-19   68.7   0.3    2.1  1  Amidohydro_1  Amidohydrolase family
    7.2e-12   45.5   8.9    1.3e-06   28.1   4.3    2.5  1  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.3   6.1e-23   5.5e-19       2     343 ..      65     400 ..      64     401 .. 0.73

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 6.1e-23
                                       EEE-EEEEEEECETTECSSS............GHHHHH...............STTHHHHHHHHHHHHHHHHTTEEE CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrga............tledwl...............vppetaaealesgiktalksGttt 51 
                                       ++PG++D H+H+    + g+            t++++l               ++ +++ e l   +  +l +Gttt
  gi|313126209|ref|YP_004036479.1|  65 IVPGFVDPHTHAL---FAGDrsdefeaklrgkTYQEILsegggilrtveavrdASTDELVENLLEQFDVMLAHGTTT 138
                                       89*********93...4444566677777777677777************9999999999999999999******** PP

                                       EEEEEHSSTH......HHHHHHHHHHT..SSSEEEEEEESSEGGS.........GCCCSHHHHHHHHHHHHHHHHHH CS
                      Amidohydro_1  52 vadmgattst......giealleaaee..lplglrilggkvsldr.........gsaetskasreklkagaaetikg 111
                                       +   +    +       +ea+ +aa++  + + + ++g+  +++           + e+ ++ +e+ +a++      
  gi|313126209|ref|YP_004036479.1| 139 AEVKSGYGLDtetelrMLEAIDRAADRhpIRVVPTFMGAHAVPNGtdtddyvesVVSEQIPKAAEQGIAEFC----- 210
                                       975443333346466666666666766898888999999999986888886555444444445555555542..... PP

                                       CTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHC CS
                      Amidohydro_1 112 kadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldei 188
                                                + +++ + +  e+ + +l++ k+++l   +Ha e+++     +aa ++                    
  gi|313126209|ref|YP_004036479.1| 211 -------DVFCEEGVFDV--EQSRRVLEAGKEHGLTPKVHAEELTHLGGTQLAAEVG-------------------- 258
                                       .......44556666666..488999999999*********6666665333333331.................... PP

                                       CEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHH CS
                      Amidohydro_1 189 klilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlal 265
                                        + + h  h t +++  l ++  ++  +++p +   l+ + ++++  l+ G+ v+l+tD    + ++   +++ +a+
  gi|313126209|ref|YP_004036479.1| 259 ATSADHLLHTTGEDIDALVAA--DTTPVLLPGTAFGLGAEYADAEMFLEHGAPVALATD---LNPNC-YSQSMPFAM 329
                                       122456666665555555555..4444466666677***********************...55555.335577777 PP

                                       HHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTE CS
                      Amidohydro_1 266 klqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGk 342
                                        l +     + e+g+++++al ++T n+A+a+ ++ ++G++e G +ADl+v+d  ++ ++ ++   +++++v+++G+
  gi|313126209|ref|YP_004036479.1| 330 TLGC-----V-EMGMTPAQALGASTVNAARAIDRA-EAGRLETGSPADLAVLDAPSYVHLSYNFGVNSIDTVVIDGE 399
                                       3333.....5.677********************7.******************77666666666666********8 PP

                                       E CS
                      Amidohydro_1 343 l 343
                                       +
  gi|313126209|ref|YP_004036479.1| 400 V 400
                                       6 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   4.3   1.5e-10   1.3e-06     147     471 ..     108     400 ..      81     402 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.5e-10
                      Amidohydro_3 147 vldla.plareaeaaavaaalaalasyGitsv.eagggnvsslddleplfeltaee.klplrvi...........ik 209
                                       + +++  ++++++ + +  ++  + ++G t++ ++ g++ + + +l +l ++++++ + p+rv+            +
  gi|313126209|ref|YP_004036479.1| 108 TVEAVrDASTDELVENLLEQFDVMLAHGTTTAeVKSGYGLDTETELRMLEAIDRAAdRHPIRVVptfmgahavpnGT 184
                                       44444333666666666667777778888888888888888888888888887554155888885444333333222 PP

                      Amidohydro_3 210 elldaaerlglplspgseeltigavklfadgvlgsrtalltepyftgwpdfedealaelvaaadergldvaihaigd 286
                                       +  d +e +         +   ++++ f d             +f+ ++ f+ e+ +++++a +e+gl   +ha + 
  gi|313126209|ref|YP_004036479.1| 185 DTDDYVESVVSEQI---PKAAEQGIAEFCD-------------VFCEEGVFDVEQSRRVLEAGKEHGLTPKVHAEEL 245
                                       22222222211111...1222222222222.............3357888889999******************999 PP

                      Amidohydro_3 287 aavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkel 363
                                       + +         ++ +  +    +++h   +t+++i+++ a   ++ + p+++f             +  ++     
  gi|313126209|ref|YP_004036479.1| 246 THLG-------GTQLAAEVGAT-SADHLLHTTGEDIDALVAADTTPVLLPGTAF-----------GLGAEYADAEMF 303
                                       9999.......33333333333.8888888999999999999999999999999...........556677889999 PP

                      Amidohydro_3 364 lnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadA 440
                                       l++g +val++D + +++    ++  ++    +           ++  +al + T ++A+a+   +  G+Le G +A
  gi|313126209|ref|YP_004036479.1| 304 LEHGAPVALATDLNPNCYSQSMPFAMTLGCVEM----------GMTPAQALGASTVNAARAIDRAEA-GRLETGSPA 369
                                       ************777777777777666643333..........489********************8.********* PP

                      Amidohydro_3 441 Dlvvldadpldvdppelaear.vrltvvdGrv 471
                                       Dl+vld +p  v+ + ++ ++ +  +v+dG+v
  gi|313126209|ref|YP_004036479.1| 370 DLAVLD-APSYVHLSYNFGVNsIDTVVIDGEV 400
                                       *****8.5555555555555557777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.57
# Mc/sec: 2145.14
//
Query:       gi|313126210|ref|YP_004036480.1|  [L=316]
Description: formiminoglutamase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-61  208.5   1.0    1.6e-61  208.2   1.0    1.0  1  Arginase  Arginase family
  ------ inclusion threshold ------
       0.14   12.0   0.0        2.9    7.7   0.0    2.1  2  TraB      TraB family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.2   1.0   1.8e-65   1.6e-61       2     276 ..      36     309 ..      35     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 1.8e-65
                                       EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTESCCSEEEEEEEEE--SSCHHHHHHHHHHHHHH CS
                          Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgvleelkivdlgdvavtpvdneevleqieeavae 78 
                                       d++l+G P+d+a+ grpGar GP+air+a+a +++    ++++g     ++ d+gdv+++ ++ ++v +++ e++ae
  gi|313126210|ref|YP_004036480.1|  36 DAVLVGEPYDGAVIGRPGARDGPTAIRDALAGVKS---HHFDAG--PVSSVGDVGDVKLARGSVRDVQDSLRETTAE 107
                                       789**************************999996...455556..7799**********999999*********** PP

                                       HHHTTCEEEEEESSGGGHHHHHHHHHHHH.........STTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTS CS
                          Arginase  79 ilkagklpivlGGDHsialgilralaeky.........gkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegl 146
                                       + ++g++p++lGGD s++++ ++ l             g+ +gv+ fDAH+D+r+     +g s+Gtp r+ +e   
  gi|313126210|ref|YP_004036480.1| 108 LYDSGAFPVFLGGDNSLTYPNVAPLLGGNrdsesdtgnGDSVGVVSFDAHLDCREVR---EGPSSGTPYRQLHE-AG 180
                                       ***********************9977667789999**999*************976...79**********95.55 PP

                                       ECGCEEEEEEE-STCSH..HHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSS CS
                          Arginase 147 lkpkklvqiGirsvdne..eyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGt 221
                                       l+  +l+++G r ++ +    ++++e+g +v+t++ + + g++  +++i++++ ++ d vy+S+D+DvlD++ aPG+
  gi|313126210|ref|YP_004036480.1| 181 LD--TLAVVGARHFETStaYADYLDEQGGTVVTAESVGD-GVDSALDRIRTAL-SDVDTVYVSVDMDVLDATAAPGV 253
                                       54..8***********9976667799***********87.*************.589******************** PP

                                       SS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTT.THHHHHHHHHHHH CS
                          Arginase 222 GtpepgGltlrellallrelaeklnlvgaDvvEvnPaldtea.eqtarlaarlvre 276
                                       ++p pgGlt+rel++l+r +a+  +++g++vvE++P+ld++  ++ta++aar v++
  gi|313126210|ref|YP_004036480.1| 254 SAPTPGGLTSRELFRLVRSIAGDDRIAGFEVVECAPSLDSTPtGRTAATAARTVAH 309
                                       ***************************************96556777777777766 PP

>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00032       2.9     230     261 ..     178     209 ..     173     211 .. 0.86
   2 ?    2.1   0.0     0.017   1.5e+02      27      50 ..     221     244 ..     214     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00032
                              TraB 230 kepgsvfvaVGagHlaGedgvlalLkkkGytv 261
                                       + +  ++++VGa H+   + + ++L ++G tv
  gi|313126210|ref|YP_004036480.1| 178 EAGLDTLAVVGARHFETSTAYADYLDEQGGTV 209
                                       555679***********************887 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.017
                              TraB  27 plspeveealeksdtvvvEldlsd 50 
                                          +++++al+ +dtv+v +d++ 
  gi|313126210|ref|YP_004036480.1| 221 SALDRIRTALSDVDTVYVSVDMDV 244
                                       55689****************943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1644.83
//
Query:       gi|313126211|ref|YP_004036481.1|  [L=587]
Description: urocanate hydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-86  287.9   0.1    4.7e-86  287.2   0.1    1.3  1  Urocanase_C  Urocanase C-terminal domain
    4.8e-85  284.5   0.0    6.3e-85  284.1   0.0    1.1  1  Urocanase    Urocanase Rossmann-like domain
    2.8e-57  191.9   0.0    4.9e-57  191.1   0.0    1.3  1  Urocanase_N  Urocanase N-terminal domain
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.048   14.0   0.0    1.9  1  Ank_5        Ankyrin repeats (many copies)
      0.066   13.4   0.2        0.2   11.8   0.2    1.8  1  DUF2188      Uncharacterized protein conserved in bacteria (D
       0.24   11.6   0.0       0.57   10.4   0.0    1.6  1  PPR_2        PPR repeat family


Domain annotation for each model (and alignments):
>> Urocanase_C  Urocanase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.2   0.1   1.6e-89   4.7e-86       1     195 [.     365     566 ..     365     567 .. 0.99

  Alignments for each domain:
  == domain 1  score: 287.2 bits;  conditional E-value: 1.6e-89
                                       HHHTTT---EEEEETT--HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHH----SS-EEE----T.......THHHHH CS
                       Urocanase_C   1 plFsegkGPFRwvalsgdpeDlaktdeavlellkekedlirWikeAeekvkvqGlpaRilylda.......eeReki 70 
                                       plF++gkGPFRw+alsgdpeD+++td+avlel++e+++l rWi+ A+e+v++qGlp+R+++l++       +eR+++
  gi|313126211|ref|YP_004036481.1| 365 PLFCRGKGPFRWAALSGDPEDIHRTDDAVLELFPEDDRLSRWIELAREQVQYQGLPSRVCWLGYrtdeeglTERARF 441
                                       79*************************************************************999999999***** PP

                                       HHHHHHHHHHSSSSS-EEEEE-S-STTSEE-TTTTTTT-TTS-TTB-HHHHHHHHHHHHHT-SEEEEEESTTT-TTS CS
                       Urocanase_C  71 alafnelvregeikapvvlgRDhlDvgsvasPfretenikDGsdaiaDwavlnallnaargatwvslhnGGgvgiGe 147
                                       al++nelv+egei+apvv++RDhlD+gsvasP rete+++DG+da+aDw++lnalln+a+ga++vs+h+GGgvgiG+
  gi|313126211|ref|YP_004036481.1| 442 ALRINELVAEGEISAPVVVTRDHLDAGSVASPHRETEAMRDGTDAVADWPILNALLNCAAGADIVSVHDGGGVGIGN 518
                                       ***************************************************************************** PP

                                       -EEEEEEEEE-SSHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHH CS
                       Urocanase_C 148 sinagfvvvldGteeaeerlervltaDvalGvvRradagyeealevak 195
                                       +++++ +vvldG++ a+e+++ v+t+D+++Gv+R+adagyeeal++a+
  gi|313126211|ref|YP_004036481.1| 519 ALHTNNHVVLDGSDLAAEKARAVFTTDPGMGVIRHADAGYEEALDEAE 566
                                       *******************************************99886 PP

>> Urocanase  Urocanase Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.1   0.0   2.1e-88   6.3e-85       1     210 []     151     362 ..     151     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 284.1 bits;  conditional E-value: 2.1e-88
                                       TTHHHHHHHHHHHHHHHHHHS.T.T--TT-EEEEE--STTGGGHHHHHHHTT-EEEEEES-HHHHHHHHHTTS-SEE CS
                         Urocanase   1 GpQGivqGTyetllnaarkkl.gkgdlkgklvvtaGlGgMsgaQplAatiagavalvvevdesriekrleqgyvdev 76 
                                       G+QGi+qGTyetl++a+r+++ +++ l+g++vvt+GlGgM+gaQplA+t++ +v++++evde+ri++r+e+gy++e+
  gi|313126211|ref|YP_004036481.1| 151 GTQGILQGTYETLAEAGRRHFpDDEGLRGRIVVTGGLGGMGGAQPLAVTMNRGVCIAAEVDEHRIDRRIETGYCMEK 227
                                       9********************76789*************************************************** PP

                                       ES-HHHHHHHHHHHHHCT--EEEEEES-HHHHHHHHHCTT---SEE---S-TT-TTTS---TT--HHHHHHHHHH-H CS
                         Urocanase  77 addldealalikeakkekealsigllgnvvdvleelveegvlvdlvsdqtsahdplnGYlPegltleeakelrkedp 153
                                       +d++ ea++++++a +e+e+lsi+++gn++dvlee++e+g+++d+v+dqtsahd l+GY+P+g+t+eea+elr+edp
  gi|313126211|ref|YP_004036481.1| 228 TDSVAEAIERAEAAAEEGEPLSIAVHGNAADVLEEMLERGFVPDVVTDQTSAHDELEGYYPSGYTVEEADELREEDP 304
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTT-EE-B-SS-HHHHHHH.TT-TTGGGS-BHHHHT CS
                         Urocanase 154 ekfkeevkeslarhveailklqekGavvfdYGnnlrkeake.agvkeafkypsyvedi 210
                                       +++ ee+ ++++rhv+ il++q++Gav+f+YGnn+r +++e +g ++ f++p++v+++
  gi|313126211|ref|YP_004036481.1| 305 DRYVEESIDTMERHVDGILEMQARGAVAFEYGNNIRGQVEEyKGRDDVFDFPGFVPAY 362
                                       ***************************************985788899********98 PP

>> Urocanase_N  Urocanase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.1   0.0   1.6e-60   4.9e-57       4     126 ..      25     147 ..      23     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 191.1 bits;  conditional E-value: 1.6e-60
                                       --SS--SSSSHHHHHHHHHHHHCT-TTT-SBGGGTEEETTTEESSSSHHHHHHHHHHHHH--TTEEEEEETTEEEEE CS
                       Urocanase_N   4 krgeelkaksweaeailrmleNnLdpevaekpeeLvvYggtgkaarnweqfelivktLkeleedetLlvqsGkpvgl 80 
                                       ++g+++++++w++ea+lrml+NnLdpevae+pe+LvvYggtg+aar+w+++++i+ +L+el++detLlvqsGkpvg 
  gi|313126211|ref|YP_004036481.1|  25 PTGTDIECEGWRQEAALRMLNNNLDPEVAERPEDLVVYGGTGRAARSWDAYDAILGQLRELDDDETLLVQSGKPVGR 101
                                       67899************************************************************************ PP

                                       EE--TTS-SEEEEES-B-GGG-SHHHHHHHHHTT---B-TTTTTTT CS
                       Urocanase_N  81 fksheeaPrvliansnlvpkyateeefeeleakgltmyGqmtAgsw 126
                                       f +he+aPrvliansnlv+k++++++f+elea+g +myGqmtAgsw
  gi|313126211|ref|YP_004036481.1| 102 FTTHERAPRVLIANSNLVGKWDDWDHFHELEAEGKIMYGQMTAGSW 147
                                       ********************************************** PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.6e-05     0.048      16      48 ..     245     276 ..     239     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                             Ank_5  16 gntpLhvAakygaadvvrlLlargadlnltdsr 48 
                                       g +pL +A++++aadv++++l+rg  +++ +++
  gi|313126211|ref|YP_004036481.1| 245 G-EPLSIAVHGNAADVLEEMLERGFVPDVVTDQ 276
                                       4.8*********************999988875 PP

>> DUF2188  Uncharacterized protein conserved in bacteria (DUF2188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   6.6e-05       0.2      25      52 ..     228     255 ..     219     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-05
                           DUF2188  25 fdTqeeAieaArelAkeqggselvihgr 52 
                                        d+ +eAie+A+++A+e+ + ++ +hg 
  gi|313126211|ref|YP_004036481.1| 228 TDSVAEAIERAEAAAEEGEPLSIAVHGN 255
                                       56779***********999*******96 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00019      0.57      22      40 ..     256     274 ..     253     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00019
                             PPR_2  22 AfklfneMkkrglePnsyT 40 
                                       A ++++eM +rg+ P+++T
  gi|313126211|ref|YP_004036481.1| 256 AADVLEEMLERGFVPDVVT 274
                                       889***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 3126.64
//
Query:       gi|313126212|ref|YP_004036482.1|  [L=223]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-19   69.9   0.0    2.1e-19   69.1   0.0    1.4  1  HTH_10         HTH DNA binding domain
    9.9e-06   25.0   0.1    2.5e-05   23.7   0.1    1.7  1  Sigma70_r4     Sigma-70, region 4
    1.1e-05   24.9   0.0    7.9e-05   22.1   0.0    2.2  1  GerE           Bacterial regulatory proteins, luxR family
    0.00016   21.3   0.7     0.0019   17.8   0.2    2.3  2  Sigma70_r4_2   Sigma-70, region 4
     0.0007   19.3   0.0     0.0014   18.4   0.0    1.5  1  HTH_23         Homeodomain-like domain
    0.00078   19.4   0.1     0.0019   18.2   0.1    1.6  1  HTH_29         Winged helix-turn helix
     0.0017   18.2   0.1     0.0033   17.3   0.1    1.4  1  HTH_11         HTH domain
     0.0058   16.2   0.2      0.022   14.3   0.1    2.0  2  HTH_24         Winged helix-turn-helix DNA-binding
     0.0074   16.3   0.1      0.042   13.9   0.0    2.3  2  HTH_20         Helix-turn-helix domain
     0.0083   16.0   0.3       0.44   10.5   0.2    2.5  2  MarR_2         MarR family
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.037   13.8   0.0    1.6  1  TetR_N         Bacterial regulatory proteins, tetR family
      0.045   13.9   0.2       0.11   12.6   0.2    1.7  1  HTH_28         Helix-turn-helix domain
      0.049   13.8   0.0       0.15   12.3   0.0    1.8  1  HTH_17         Helix-turn-helix domain
      0.049   13.6   0.1       0.32   11.0   0.2    2.2  3  HTH_1          Bacterial regulatory helix-turn-helix protein,
       0.13   12.1   0.1       0.47   10.3   0.1    1.9  1  LexA_DNA_bind  LexA DNA binding domain
       0.14   11.9   2.3        0.9    9.4   0.5    2.5  2  HTH_30         PucR C-terminal helix-turn-helix domain
        0.2   11.6   0.0       0.35   10.9   0.0    1.3  1  HTH_36         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   1.9e-22   2.1e-19       1      53 []     156     208 ..     156     208 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.9e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       L+++q+ vl+lA+e GY++ PR +t++++A++lG+s+ t++ehLr+ae+kli+
  gi|313126212|ref|YP_004036482.1| 156 LSPRQYDVLQLAVEDGYYEIPRGTTTEAIADRLGVSRRTAEEHLRRAENKLID 208
                                       789************************************************95 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   2.4e-08   2.5e-05       2      48 ..     153     206 ..     152     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.4e-08
                                       HHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   2 LasLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L  L++r+ +vl+l          +g T e I++rlg+Sr ++  +++rA +kL
  gi|313126212|ref|YP_004036482.1| 153 LPDLSPRQYDVLQLAVedgyyeiPRGTTTEAIADRLGVSRRTAEEHLRRAENKL 206
                                       778***************99998899************************8887 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   7.5e-08   7.9e-05       3      45 ..     156     206 ..     154     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.5e-08
                                       S-HHHHHHHHHHCT........TS-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE   3 LskRErevLrllae........GksnkeIAeelniSekTVkvhksnimkKL 45 
                                       Ls+R+ +vL+l +e        G +++ IA++l++S +T + h++++ +KL
  gi|313126212|ref|YP_004036482.1| 156 LSPRQYDVLQLAVEdgyyeiprGTTTEAIADRLGVSRRTAEEHLRRAENKL 206
                                       999******99886555556669************************9998 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.25   2.6e+02       7      27 ..     152     172 ..     150     174 .. 0.88
   2 !   17.8   0.2   1.8e-06    0.0019      26      54 .]     178     206 ..     177     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.25
                                       HHTTS-HHHHHHHHHHHTS-- CS
                      Sigma70_r4_2   7 alaeLperqreifllrylegl 27 
                                       +l  L++rq  ++ l  ++g+
  gi|313126212|ref|YP_004036482.1| 152 LLPDLSPRQYDVLQLAVEDGY 172
                                       6778***********999986 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.8e-06
                                       ---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  26 glsykEIAellgisegtVksrlsRArkkL 54 
                                       g +++ IA +lg+s +t + +l+RA  kL
  gi|313126212|ref|YP_004036482.1| 178 GTTTEAIADRLGVSRRTAEEHLRRAENKL 206
                                       678999*******************9887 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0014      17      40 ..     178     201 ..     160     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                            HTH_23  17 GlsvreIAreLgvsrrTvyrwlkr 40 
                                       G ++++IA++LgvsrrT    l+r
  gi|313126212|ref|YP_004036482.1| 178 GTTTEAIADRLGVSRRTAEEHLRR 201
                                       8899*************9977777 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.8e-06    0.0019      13      53 ..     173     220 ..     163     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                            HTH_29  13 s......tvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrp 53 
                                       +      t+  iA +lg+srrt   +l+r e++ ++a  +  r++gr+
  gi|313126212|ref|YP_004036482.1| 173 YeiprgtTTEAIADRLGVSRRTAEEHLRRAENKLIDAVFEhLRGRGRG 220
                                       3555555999***************************99977777776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   3.2e-06    0.0033      16      45 ..     179     210 ..     174     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIkaLeelg..vp 45 
                                        + e +A++L+vSrrt   ++++ e ++  + 
  gi|313126212|ref|YP_004036482.1| 179 TTTEAIADRLGVSRRTAEEHLRRAENKLidAV 210
                                       5889*************999999988875544 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.4   2.5e+03      25      45 ..     107     127 ..     104     128 .. 0.80
   2 !   14.3   0.1     2e-05     0.022      17      44 ..     178     205 ..     176     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.4
                            HTH_24  25 erlglSpstvnrrlkrLeeeG 45 
                                       + l l ++ ++   ++L+ +G
  gi|313126212|ref|YP_004036482.1| 107 RVLALDSGSLTDLYRELVADG 127
                                       667888888899999999998 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2e-05
                            HTH_24  17 risqreLAerlglSpstvnrrlkrLeee 44 
                                       +++   +A+rlg+S+ t  ++l+r e++
  gi|313126212|ref|YP_004036482.1| 178 GTTTEAIADRLGVSRRTAEEHLRRAENK 205
                                       478899******************9975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.7   2.8e+03      14      27 ..     118     130 ..     104     152 .. 0.57
   2 !   13.9   0.0     4e-05     0.042      19      46 ..     167     200 ..     156     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
                                       HHHHHHSTCTTB-H CS
                            HTH_20  14 rilraLaraeglta 27 
                                       +++r+L  a+g  +
  gi|313126212|ref|YP_004036482.1| 118 DLYREL-VADGTFV 130
                                       445555.4433333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4e-05
                                       H......STCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  19 L......araegltaselaerldlskntlsyHLr 46 
                                                ++g t +++a+rl++s+ t+  HLr
  gi|313126212|ref|YP_004036482.1| 167 AvedgyyEIPRGTTTEAIADRLGVSRRTAEEHLR 200
                                       455555556899*********************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.099     1e+02      27      49 ..     105     127 ..      95     128 .. 0.92
   2 !   10.5   0.2   0.00042      0.44       2      47 ..     155     204 ..     154     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.099
                                       HHHHHTSSHHHHHHHHHHHHHTT CS
                            MarR_2  27 larrlglsksavsrilkrLvaaG 49 
                                       ++r l l+ ++++ + ++Lva G
  gi|313126212|ref|YP_004036482.1| 105 VCRVLALDSGSLTDLYRELVADG 127
                                       799*****************998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00042
                                       T--HHHHHHHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2   2 gltpaqarvLaaLgrrpgr.....dltvgelarrlglsksavsrilkrLva 47 
                                       +l+p q++vL  L+ ++g+       t  ++a+rlg+s+ ++  +l+r++ 
  gi|313126212|ref|YP_004036482.1| 155 DLSPRQYDVL-QLAVEDGYyeiprGTTTEAIADRLGVSRRTAEEHLRRAEN 204
                                       5777888887.45666667777665599*******************9986 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05     0.037      15      32 ..     177     194 ..     164     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                                       TT--HHHHHHHHTSSHHH CS
                            TetR_N  15 dattvreIAkrAGvskga 32 
                                       ++tt+++IA+r+Gvs+++
  gi|313126212|ref|YP_004036482.1| 177 RGTTTEAIADRLGVSRRT 194
                                       58*************987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00011      0.11      11      38 ..     177     204 ..     160     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            HTH_28  11 aGhsvreaArelgisrrtvyrWikryee 38 
                                       +G +  ++A +lg+srrt    ++r e 
  gi|313126212|ref|YP_004036482.1| 177 RGTTTEAIADRLGVSRRTAEEHLRRAEN 204
                                       4778889******************997 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.15       3      24 ..     180     201 ..     180     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                            HTH_17   3 tveEaAelLgvsrstvyrlirr 24 
                                       t+e +A+ Lgvsr+t+ + +rr
  gi|313126212|ref|YP_004036482.1| 180 TTEAIADRLGVSRRTAEEHLRR 201
                                       8999*************97774 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.9   3.1e+03      23      44 ..      36      57 ..      33      60 .. 0.80
   2 ?   -2.0   0.0       3.5   3.7e+03       6      30 ..     128     152 ..     128     153 .. 0.87
   3 ?   11.0   0.2   0.00031      0.32      20      50 ..     185     216 ..     177     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.9
                                      HTS-HHHHHHHHHHHHHHHTS- CS
                             HTH_1 23 LglsqpavsrqikrLEeelgvp 44
                                      L++  p + + + r E+++gv+
  gi|313126212|ref|YP_004036482.1| 36 LHIRGPDAEAVVDRVEHLVGVR 57
                                      7777788888899999999986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                                       HHHHHHHHSSHHHHHHHHTS-HHHH CS
                             HTH_1   6 lfvavaeegsftrAAeeLglsqpav 30 
                                       +fv v   ++++   e   ls++++
  gi|313126212|ref|YP_004036482.1| 128 TFVDVLSKRHVNVVSEDAPLSPSSL 152
                                       6899999999999999999999986 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00031
                                       HHHHTS-HHHHHHHHHHHHHHHTS-SEE..ESS CS
                             HTH_1  20 AeeLglsqpavsrqikrLEeelgvpLfe..Rtg 50 
                                       A++Lg+s  ++  +++r E+ l +  fe  R g
  gi|313126212|ref|YP_004036482.1| 185 ADRLGVSRRTAEEHLRRAENKLIDAVFEhlR-G 216
                                       99*************************9654.3 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00044      0.47       3      53 ..     155     205 ..     154     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00044
                                       ---HHHHHHHHHHH.HHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind   3 kLTerQrevldlik.asieetgypPsireiaralglkSpsaveehLkaLerK 53 
                                       +L++rQ +vl+l + +   e     +   ia++lg++  +++eehL++ e+K
  gi|313126212|ref|YP_004036482.1| 155 DLSPRQYDVLQLAVeDGYYEIPRGTTTEAIADRLGVS-RRTAEEHLRRAENK 205
                                       58889998888754044555555668889******96.9*********9999 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.33   3.5e+02      28      40 ..      55      67 ..      51      75 .. 0.87
   2 ?    9.4   0.5   0.00086       0.9      16      38 ..     182     204 ..     177     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.33
                                      HHHHHHHHHHHHH CS
                            HTH_30 28 TlryRLrrieell 40
                                       +r RL+r ee+l
  gi|313126212|ref|YP_004036482.1| 55 GVRERLDRPEEVL 67
                                      589******9998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00086
                                       HHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30  16 satAkaLhvHrnTlryRLrriee 38 
                                       +a A++L+v+r T    Lrr+e 
  gi|313126212|ref|YP_004036482.1| 182 EAIADRLGVSRRTAEEHLRRAEN 204
                                       689*****************996 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00033      0.35      24      51 ..     174     204 ..     164     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                            HTH_36  24 cfp...sqetlakrlglsknTvsraikeLeq 51 
                                         p   + e +a rlg+s++T+  +++  e 
  gi|313126212|ref|YP_004036482.1| 174 EIPrgtTTEAIADRLGVSRRTAEEHLRRAEN 204
                                       5564446899*************99998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1266.68
//
Query:       gi|313126213|ref|YP_004036483.1|  [L=114]
Description: hypothetical protein Hbor_14590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 668.85
//
Query:       gi|313126214|ref|YP_004036484.1|  [L=396]
Description: hypothetical protein Hbor_14600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-27   96.9   0.0    1.9e-27   96.0   0.0    1.4  1  MMR_HSR1_C  GTPase of unknown function C-terminal
    1.8e-21   76.3   0.0    1.6e-19   70.0   0.0    3.0  3  MMR_HSR1    50S ribosome-binding GTPase
    1.9e-11   43.8   0.0    4.2e-11   42.7   0.0    1.6  1  TGS         TGS domain
    4.6e-05   23.0   0.0    0.00031   20.3   0.0    2.3  3  FeoB_N      Ferrous iron transport protein B
     0.0065   16.5   0.2       0.54   10.3   0.0    3.1  3  Dynamin_N   Dynamin family
  ------ inclusion threshold ------
      0.063   12.8   0.0       0.15   11.6   0.0    1.6  1  GTP_EFTU    Elongation factor Tu GTP binding domain
        0.1   12.8   0.0       0.78   10.0   0.0    2.3  2  Roc         Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   7.5e-31   1.9e-27       1     109 [.     222     326 ..     222     328 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 7.5e-31
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdk.kvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLek 76 
                                       a+NK+D+p a+en+e+++++ ++d+ ++vp+sA+aE aL++a+++g+++Yepg++df+i +d    ++ +q++ Le+
  gi|313126214|ref|YP_004036484.1| 222 AANKMDKPVAQENFEEITSDPEYDHlTFVPASAHAEKALKNAEEAGIVEYEPGSSDFDIVGD----VSGEQEEGLEQ 294
                                       89******************9988889***********************************....*********** PP

                        MMR_HSR1_C  77 irdlvlkrygsTGVqealnaavfelldlivVYP 109
                                       ir+ +l+ y++ GVq+ l++a+f++++ i+++P
  gi|313126214|ref|YP_004036484.1| 295 IRE-FLNAYDGAGVQASLETALFDVMGAIAIFP 326
                                       ***.****************************9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   6.3e-23   1.6e-19       1      87 [.       4     120 ..       4     150 .. 0.77
   2 ?    2.1   0.0     0.079     2e+02      67     114 .]     174     225 ..     151     225 .. 0.57
   3 ?    0.2   0.0      0.31   7.8e+02      66      88 ..     352     375 ..     258     394 .. 0.64

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 6.3e-23
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.........................EEEEE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.........................ielvD 52 
                                       ++++vG+p vGKS+++na t + +  +++p+tT+d+  g+  ++  +                         ++lvD
  gi|313126214|ref|YP_004036484.1|   4 KIGLVGKPSVGKSSFFNAATMNDVPEGAYPFTTIDPSVGEAYVRV-DcaapefdetctpsvgfcdngtryvpVKLVD 79 
                                       699************************************988441.12333444455555555555555666***** PP

                                       CGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT.....T CS
                          MMR_HSR1  53 tpGliegaseekglgkaflalee.adlillvvdas.....e 87 
                                       ++Gli ga+e+kglg++fl   + ad++++vvd s     e
  gi|313126214|ref|YP_004036484.1|  80 VAGLIPGAHEGKGLGNQFLTDLNeADVLVHVVDFSgetdiE 120
                                       *******************96665*********88543330 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.079
                                       HHHHHHHHC.TSEEEEEEETT..TTCSHHHHHH.HHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  67 gkaflalee.adlillvvdas..eeklkpldee.leelleeakkplilvlnk 114
                                         af+ +++  + ++l + +s   +++++ d+e +++ +++++kp+++++nk
  gi|313126214|ref|YP_004036484.1| 174 MSAFKTNKDeIKQVILSLGLSldPDDWDDADKEaIAREIRKRTKPMLIAANK 225
                                       33444444335555555544455345666665514555566999****9998 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.31
                                       HHHHHHHHHCT.SEEEEEEETTTT CS
                          MMR_HSR1  66 lgkaflaleea.dlillvvdasee 88 
                                       +  a++ + +  d +l+ +d++++
  gi|313126214|ref|YP_004036484.1| 352 EDFAYHLHSDIgDGLLHGIDCRSK 375
                                       233334444534888888888833 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   1.6e-14   4.2e-11      12      60 .]     341     394 ..     330     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.6e-14
                                       E...EETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEEE CS
                               TGS  12 d...lprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIvt 60 
                                       d   lp+g+t eDfAy++h+++++ +++++     ++vg dh+Le+ dv+eIvt
  gi|313126214|ref|YP_004036484.1| 341 DcfiLPEGSTTEDFAYHLHSDIGDGLLHGIDCRskRQVGSDHELEHRDVLEIVT 394
                                       35559**************************99999*****************8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.2e-07   0.00031       2      42 ..       4      44 ..       3      51 .. 0.91
   2 ?   -2.6   0.0       1.4   3.6e+03      72      87 ..      96     112 ..      78     115 .. 0.77
   3 ?   -1.2   0.0       0.5   1.3e+03     101     118 ..     212     229 ..     207     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegkl 42
                                      ++ lvG+p vGk+++fna t  +   g +p +t++ + g+ 
  gi|313126214|ref|YP_004036484.1|  4 KIGLVGKPSVGKSSFFNAATMNDVPEGAYPFTTIDPSVGEA 44
                                      789*******************************9988875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                       HHHHC.TSSSEEEEEEE CS
                            FeoB_N  72 dflle.eepdvvvnvvd 87 
                                       +fl++ +e+dv+v+vvd
  gi|313126214|ref|YP_004036484.1|  96 QFLTDlNEADVLVHVVD 112
                                       55653267899999998 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.5
                                       HHHTTSSEEEEEETHHHH CS
                            FeoB_N 101 llelgvpvvlalnmidea 118
                                       +   ++p+++a n++d+ 
  gi|313126214|ref|YP_004036484.1| 212 IRKRTKPMLIAANKMDKP 229
                                       56677999*******974 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00021      0.54       1      32 [.       5      35 ..       5      37 .. 0.86
   2 ?    1.5   0.0       0.1   2.7e+02     102     139 ..      74     114 ..      63     124 .. 0.84
   3 ?    0.3   0.0      0.25   6.5e+02     139     167 ..     197     225 ..     159     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptT 32
                                      i +vG+ S GKSS+ na +  d  p g+ p T
  gi|313126214|ref|YP_004036484.1|  5 IGLVGKPSVGKSSFFNAATMND-VPEGAYPFT 35
                                      789**************99888.587777766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                                       SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETT CS
                         Dynamin_N 102 gltlvDlPGldsvnkrdq...elvkeyikkadiilavtsan 139
                                        ++lvD+ Gl+  +++ +   +   + +++ad++++v++++
  gi|313126214|ref|YP_004036484.1|  74 PVKLVDVAGLIPGAHEGKglgNQFLTDLNEADVLVHVVDFS 114
                                       689*******9999999978888888889999999999876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.25
                                       TS-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                         Dynamin_N 139 nhdlsnsealflarevdpkgkrtivvltk 167
                                         d+ +++++ +are++++ k +++  +k
  gi|313126214|ref|YP_004036484.1| 197 PDDWDDADKEAIAREIRKRTKPMLIAANK 225
                                       46889999999999999999988876666 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.7e-05      0.15     112     154 ..     206     265 ..     202     344 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.7e-05
                                       HHHHHHHHHTTTEEEEEEESCGST..HHHHHHHHHHHHHHHHHH...............H CS
                          GTP_EFTU 112 eevlrlalkegvpiivfiNKmDrl..kaelkeiveevkqklsrk...............e 154
                                       e ++r ++k+  p+ ++ NKmD++  +++++ei ++ +++  +                e
  gi|313126214|ref|YP_004036484.1| 206 EAIAREIRKRTKPMLIAANKMDKPvaQENFEEITSDPEYDHLTFvpasahaekalknaeE 265
                                       5678889999999***********99999*999988664442224666665444444441 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00031      0.78       1      26 [.       4      29 ..       4      48 .. 0.83
   2 ?   -0.6   0.0      0.59   1.5e+03     106     120 .]     214     228 ..     197     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                                      EEEEESSTTSSHHHHHHCHCT-CCC- CS
                               Roc  1 KvvlvGdsgvGKtsllkrfvedkfse 26
                                      K+ lvG+ +vGK+s+++  + +++ e
  gi|313126214|ref|YP_004036484.1|  4 KIGLVGKPSVGKSSFFNAATMNDVPE 29
                                      899*************9998887765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.59
                                       CSSS-EEEEEE-TTT CS
                               Roc 106 agkspvilvgnkiDl 120
                                        +++p+++ +nk+D+
  gi|313126214|ref|YP_004036484.1| 214 KRTKPMLIAANKMDK 228
                                       3467999*****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2478.21
//
Query:       gi|313126215|ref|YP_004036485.1|  [L=101]
Description: hypothetical protein Hbor_14610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.35s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 634.90
//
Query:       gi|313126216|ref|YP_004036486.1|  [L=141]
Description: hypothetical protein Hbor_14620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 830.96
//
Query:       gi|313126217|ref|YP_004036487.1|  [L=442]
Description: hypothetical protein Hbor_14630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-07   30.8  20.1      0.037   14.0   2.3    3.4  3  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    9.5e-05   22.6  47.2     0.0035   17.6   8.3    5.1  4  Big_6            Bacterial Ig domain
    0.00049   20.2   3.5        0.4   10.9   0.1    4.1  4  DUF1939          Domain of unknown function (DUF1939)
     0.0029   17.7   3.4        7.3    6.7   0.1    3.8  3  Bile_Hydr_Trans  Acyl-CoA thioester hydrolase/BAAT N-terminal
  ------ inclusion threshold ------
      0.011   15.4  29.4       0.28   10.8   4.3    3.2  3  DUF4249          Domain of unknown function (DUF4249)
      0.011   15.7   4.6      0.011   15.7   4.6    7.1  7  Big_1            Bacterial Ig-like domain (group 1)
      0.024   14.8  18.7       0.74   10.0   1.9    4.0  3  MG4              Macroglobulin domain MG4
      0.056   13.5   2.5        9.6    6.3   0.0    3.5  4  DUF5640          Family of unknown function (DUF5640)
       0.18   11.7   4.3          3    7.7   0.1    3.2  3  PUA_3            PUA-like domain
       0.22   11.4   4.1        4.6    7.2   0.2    3.3  4  DBB              Dof, BCAP, and BANK (DBB) motif,
       0.53   10.5  30.3      0.078   13.1   5.4    3.4  3  Calx-beta        Calx-beta domain
        1.3    9.1  19.0         11    6.2   0.4    4.7  5  DUF3244          Domain of unknown function (DUF3244)
        5.1    6.8   9.4         11    5.7   9.4    1.7  1  RR_TM4-6         Ryanodine Receptor TM 4-6


Domain annotation for each model (and alignments):
>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   4.4   3.3e-05     0.045       6      77 ..      31      98 ..      26     125 .. 0.74
   2 !   14.0   2.3   2.7e-05     0.037      15      81 ..     126     187 ..     112     207 .. 0.74
   3 !   12.1   0.7   0.00011      0.15      26      81 ..     219     270 ..     210     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                              bMG3  6 lhaklgrdkllvwvtsLdsgkPvagaeVrlldkkgev.laegtTDaqGvarfaallargkegaapylvsArkd 77
                                      + + + +   +v v   ++g +v++a+V++ ++ g v  ++ +TDa+G +++a+++     +++   v+A++d
  gi|313126217|ref|YP_004036487.1| 31 VNVEQDDATGEVLVDVTNNGTAVENATVNVTSEAGYVgNGTYQTDANGSVTLAQPE-----DTQNITVTATDD 98
                                      556666677789999999**************99987357889************4.....456666666642 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.7e-05
                              bMG3  15 llvwvtsLdsgkPvagaeVrlldkkgevlaegtTDaqGvarfaallargkegaapylvsArkdedla 81 
                                       + + v+  d++ + a ++V++++++ ++ ++ tTD++G ++++a+     e++  + v + +++d++
  gi|313126217|ref|YP_004036487.1| 126 VSIGVERNDTAVANATVNVSVSNDSYAATGNYTTDENGTVELDAP-----EENVSVTVNVSEGDDTT 187
                                       46777777888899999999999**********************.....34455555555555544 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00011
                              bMG3  26 kPvagaeVrlld.kkgevlaegtTDaqGvarfaallargkegaapylvsArkdedla 81 
                                       ++v++a+V++ +  +    ++ +TDa+G ++++a+      ++    v+A+ d+d+ 
  gi|313126217|ref|YP_004036487.1| 219 EAVENATVDVTSdGNYSGTGTYETDADGTVSLPAP-----TENVTITVTATADNDTV 270
                                       79********985777889****************.....57889999999888864 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   8.3   2.5e-06    0.0035      18      80 ..      49     107 ..      39     111 .. 0.88
   2 ?    5.5   7.4     0.014        20      20      82 ..     135     196 ..     112     197 .. 0.76
   3 !   16.0   4.9     8e-06     0.011      21      81 ..     220     278 ..     199     279 .. 0.91
   4 ?    1.7   1.5      0.22   3.1e+02      10      34 ..     411     435 ..     404     442 .] 0.70

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.5e-06
                             Big_6  18 tGkaeagatVtvkdadgtvlgtgtadadGeFsvtlepaqangetlsvvatDaagntSdaatvt 80 
                                       +G+a  +atV+v+ ++g v g+gt + d + svtl++  ++ ++++v+atD   n S+++tv+
  gi|313126217|ref|YP_004036487.1|  49 NGTAVENATVNVTSEAGYV-GNGTYQTDANGSVTLAQ-PEDTQNITVTATDD--NLSAETTVQ 107
                                       69***********999877.***99999999****75.57999*******97..999999987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.014
                             Big_6  20 kaeagatVtvkdadgtvlgtgtadadGeFsvtlepaqangetlsvvatDaagntSdaatvtap 82 
                                       +a a+atV+v+ ++++  +tg  + d + +v+l++++ ++ +++v +++ ++ t ++++++ap
  gi|313126217|ref|YP_004036487.1| 135 TAVANATVNVSVSNDSYAATGNYTTDENGTVELDAPE-ENVSVTVNVSEGDDTTTKTVDLVAP 196
                                       799***************9996666666679998654.4556677777777777777777766 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 8e-06
                             Big_6  21 aeagatVtvkdadgtvlgtgtadadGeFsvtlepaqangetlsvvatDaagntSdaatvta 81 
                                       a  +atV v+ +dg+  gtgt + d   +v+l pa +++ t++v+at  ++ +S+++++t+
  gi|313126217|ref|YP_004036487.1| 220 AVENATVDVT-SDGNYSGTGTYETDADGTVSL-PAPTENVTITVTATADNDTVSETVDLTT 278
                                       7789******.7********998888889999.5788999****************99985 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.22
                             Big_6  10 vsedgttltGkaeagatVtvkdadg 34 
                                        +  g+  +G+a ag +Vtv   ++
  gi|313126217|ref|YP_004036487.1| 411 NAGGGANANGNANAGGSVTVGVDAN 435
                                       556688889**********954333 PP

>> DUF1939  Domain of unknown function (DUF1939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.26   3.6e+02      28      50 ..      66      86 ..      55      93 .. 0.83
   2 ?   -1.7   0.0       2.4   3.3e+03      51      51 ..     133     133 ..      99     154 .. 0.58
   3 !   10.9   0.1   0.00029       0.4      35      55 ..     156     176 ..     138     177 .. 0.89
   4 ?    5.5   0.1     0.014        19      30      53 ..     232     257 ..     224     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.26
                           DUF1939 28 ytGnssvdvtvdedGwvkievpp 50
                                      y Gn     ++d++G v +  p+
  gi|313126217|ref|YP_004036487.1| 66 YVGNGT--YQTDANGSVTLAQPE 86
                                      777766..679*******99987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                           DUF1939  51 k 51 
                                       +
  gi|313126217|ref|YP_004036487.1| 133 N 133
                                       3 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00029
                           DUF1939  35 dvtvdedGwvkievppkgySv 55 
                                       + t+de+G v++++p++ +Sv
  gi|313126217|ref|YP_004036487.1| 156 NYTTDENGTVELDAPEENVSV 176
                                       568****************98 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.014
                           DUF1939  30 Gnss..vdvtvdedGwvkievppkgy 53 
                                       Gn s   +  +d+dG v +++p + +
  gi|313126217|ref|YP_004036487.1| 232 GNYSgtGTYETDADGTVSLPAPTENV 257
                                       66665556789***********8766 PP

>> Bile_Hydr_Trans  Acyl-CoA thioester hydrolase/BAAT N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.037        51      28      49 ..      63      84 ..      37      90 .. 0.79
   2 !    6.7   0.1    0.0053       7.3      27      48 ..     147     168 ..     114     173 .. 0.77
   3 ?    5.7   0.1     0.011        15      21      47 ..     224     250 ..     205     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.037
                   Bile_Hydr_Trans 28 gelfeSfAvykadekGevdlsr 49
                                      +  +   ++y++d++G+v l++
  gi|313126217|ref|YP_004036487.1| 63 EAGYVGNGTYQTDANGSVTLAQ 84
                                      44477889***********987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0053
                   Bile_Hydr_Trans  27 kgelfeSfAvykadekGevdls 48 
                                       +++ + +++ y++de+G+v+l+
  gi|313126217|ref|YP_004036487.1| 147 SNDSYAATGNYTTDENGTVELD 168
                                       3467***************996 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.011
                   Bile_Hydr_Trans  21 asltdekgelfeSfAvykadekGevdl 47 
                                       a+++  + ++++ +++y++d++G+v+l
  gi|313126217|ref|YP_004036487.1| 224 ATVDVTSDGNYSGTGTYETDADGTVSL 250
                                       5555567789***************98 PP

>> DUF4249  Domain of unknown function (DUF4249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.7   0.00044      0.61      58     119 ..      48     107 ..      21     123 .. 0.74
   2 ?    6.6   6.4    0.0037       5.1      58     125 ..     132     200 ..     110     219 .. 0.60
   3 ?   10.8   4.3    0.0002      0.28      47     119 ..     206     277 ..     193     296 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00044
                           DUF4249  58 eevkavtdAtVtlyvnegqey..elsetkagyyssfrlkpgdtyrLeittpdgkeyvsaettvp 119
                                       ++ +av++AtV+++ + g++   +++++ +   s++ ++p dt  +++t++d   + saettv 
  gi|313126217|ref|YP_004036487.1|  48 NNGTAVENATVNVTSEAGYVGngTYQTDAN--GSVTLAQPEDTQNITVTATD--DNLSAETTVQ 107
                                       3357899********754222225553333..23368999999999999988..89******95 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0037
                           DUF4249  58 eevkavtdAtVtlyvnegqey....elsetkagyyssfrlkpgdtyrLeittpdgkeyvsaettvpsppp.ei 125
                                       ++++av +AtV+++v+ + +y    +++++++g++   +++++ +++++++  d   + ++++ +  +p+ ++
  gi|313126217|ref|YP_004036487.1| 132 RNDTAVANATVNVSVS-NDSYaatgNYTTDENGTVELDAPEENVSVTVNVSEGD--DTTTKTVDLV-APEvSL 200
                                       3367899********9.5566555566655555333368899999998888855..4444444443.343223 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0002
                           DUF4249  47 rsvpvsesdsieevkavtdAtVtlyvnegqey....elsetkagyyssfrlkpgdtyrLeittpdgkeyvsaettvp 119
                                       +++ v e + ++ ++av++AtV ++ + g +y    +++++ +g++s  ++ ++ t+++++t+   + +vs+++ + 
  gi|313126217|ref|YP_004036487.1| 206 QTTGV-EVSLERGDEAVENATVDVTSD-G-NYsgtgTYETDADGTVSLPAPTENVTITVTATA--DNDTVSETVDLT 277
                                       44442.222333378999********8.5.222333444333444444456666666666666..589***999876 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   6.9   2.4e-05     0.034       8      49 ..      41      81 ..      35      84 .. 0.90
   2 ?   -1.0   4.9       1.3   1.9e+03       5      35 ..      87     115 ..      85     130 .. 0.70
   3 ?   15.7   4.6   8.2e-06     0.011      16      49 ..     132     166 ..     125     171 .. 0.89
   4 ?   -0.1   0.2      0.68   9.4e+02      20      38 ..     170     188 ..     167     192 .. 0.69
   5 ?    5.6   5.0     0.011        16      19      50 ..     219     250 ..     212     263 .. 0.83
   6 ?    0.9   1.7      0.33   4.6e+02      22      36 ..     255     270 ..     249     279 .. 0.54
   7 ?   -1.6   3.6         2   2.8e+03      15      34 ..     417     436 ..     416     442 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                             Big_1  8 tltatvkDangnpvagatVtfsvsggalsassgtTdanGkat 49
                                      ++ + v+ +ng++v++atV++++ +g + +++ +TdanG +t
  gi|313126217|ref|YP_004036487.1| 41 EVLVDVT-NNGTAVENATVNVTSEAGYVGNGTYQTDANGSVT 81
                                      6778888.69*****************************998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                             Big_1   5 dtntltatvkDangnpvagatVtfsvsggal 35 
                                       dt  +t+t++D   n  a +tV +  +++ +
  gi|313126217|ref|YP_004036487.1|  87 DTQNITVTATD--DNLSAETTVQIVGDNDLT 115
                                       78889999999..567788888777777544 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 8.2e-06
                             Big_1  16 angnpvagatVtfsvsggals.assgtTdanGkat 49 
                                       +n ++va+atV++svs+++ + +++ tTd+nG+++
  gi|313126217|ref|YP_004036487.1| 132 RNDTAVANATVNVSVSNDSYAaTGNYTTDENGTVE 166
                                       6899*************66666**********987 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.68
                             Big_1  20 pvagatVtfsvsggalsas 38 
                                       p ++++Vt++vs g+ +++
  gi|313126217|ref|YP_004036487.1| 170 PEENVSVTVNVSEGDDTTT 188
                                       5679999999999554433 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.011
                             Big_1  19 npvagatVtfsvsggalsassgtTdanGkatv 50 
                                        +v++atV ++++g+   +++  Tda+G+++ 
  gi|313126217|ref|YP_004036487.1| 219 EAVENATVDVTSDGNYSGTGTYETDADGTVSL 250
                                       589***********8888***********986 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.33
                             Big_1  22 agatVtfsvsg.gals 36 
                                       +++t+t+++++ ++++
  gi|313126217|ref|YP_004036487.1| 255 ENVTITVTATAdNDTV 270
                                       5566666666543333 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 2
                             Big_1  15 DangnpvagatVtfsvsgga 34 
                                       +angn+ ag +Vt+ v+++ 
  gi|313126217|ref|YP_004036487.1| 417 NANGNANAGGSVTVGVDANI 436
                                       699*********99999854 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.1    0.0066       9.1      24      85 ..      47     103 ..      39     112 .. 0.68
   2 ?   10.0   1.9   0.00053      0.74      24      75 ..     131     180 ..     123     201 .. 0.78
   3 ?    5.7   2.8     0.012        16      27      84 ..     218     272 ..     174     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0066
                               MG4  24 dpdgspaknvpVkiealkseteekeslttdedGtakfsintpedaksltitvktkdpslpee 85 
                                         +g+ ++n +V ++  + +   + +++td++G + +    ped+++  itv+  d +l++e
  gi|313126217|ref|YP_004036487.1|  47 TNNGTAVENATVNVTS-EAGYVGNGTYQTDANGSVTLA--QPEDTQN--ITVTATDDNLSAE 103
                                       4589***********9.545566777789999977654..4666555..5555556666655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00053
                               MG4  24 dpdgspaknvpVkiealkseteekeslttdedGtakfsintpedaksltitv 75 
                                       + +++ ++n +V +++ + +     ++ttde+Gt+++  + pe++ s+t+ v
  gi|313126217|ref|YP_004036487.1| 131 ERNDTAVANATVNVSVSNDSYAATGNYTTDENGTVEL--DAPEENVSVTVNV 180
                                       578999**********55457788899*******986..4566666666665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.012
                               MG4  27 gspaknvpVkiealkseteekeslttdedGtakfsintpedaksltitvktkdpslpe 84 
                                       ++ ++n +V ++  + + +   +++td+dGt+++   t  ++ ++t+t++ +   ++e
  gi|313126217|ref|YP_004036487.1| 218 DEAVENATVDVTS-DGNYSGTGTYETDADGTVSLPAPT--ENVTITVTATADNDTVSE 272
                                       5679999999999.76778888999******9887644..444555555555555555 PP

>> DUF5640  Family of unknown function (DUF5640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.007       9.6      13      64 ..      67     118 ..      60     124 .. 0.83
   2 ?    1.9   0.1      0.17   2.4e+02      42      83 ..     122     166 ..     120     168 .. 0.74
   3 ?    2.0   0.1      0.16   2.2e+02      16      44 ..     155     183 ..     146     229 .. 0.75
   4 ?    2.3   0.1      0.13   1.7e+02       9      35 ..     231     257 ..     223     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.007
                                       SS-EEEEE-SSS-EEEEEEETTEEEEEE-SSSSEEEEEESS----EEE-EEE CS
                           DUF5640  13 dshktYkFdedGtgelelskaaykftYtieedqLkidfeaekkedceyefsv 64 
                                         + tY+ d++G+++l++++ +++ t t  +d+L+ + + + + d ++++ v
  gi|313126217|ref|YP_004036487.1|  67 VGNGTYQTDANGSVTLAQPEDTQNITVTATDDNLSAETTVQIVGDNDLTVDV 118
                                       56779*****************************997777766666666655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.17
                                       SSSSEEEEEES..S----EEE-EEESSSEEEE-SSTT-...S-EE CS
                           DUF5640  42 eedqLkidfea..ekkedceyefsvngntLtLtggset.eggtyk 83 
                                       ++++++i +e   +++ ++++++sv++++   tg+ +t e+gt +
  gi|313126217|ref|YP_004036487.1| 122 DDGTVSIGVERndTAVANATVNVSVSNDSYAATGNYTTdENGTVE 166
                                       567777755443377888899999999999999998887777766 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.16
                                       EEEEE-SSS-EEEEEEETTEEEEEE-SSS CS
                           DUF5640  16 ktYkFdedGtgelelskaaykftYtieed 44 
                                         Y+ de+Gt+el  ++ +++ t +++e+
  gi|313126217|ref|YP_004036487.1| 155 GNYTTDENGTVELDAPEENVSVTVNVSEG 183
                                       56888999999999999999888777764 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.13
                                       --SSSS-EEEEE-SSS-EEEEEEETTE CS
                           DUF5640   9 tktedshktYkFdedGtgelelskaay 35 
                                       ++ ++   tY+ d+dGt++l  +  ++
  gi|313126217|ref|YP_004036487.1| 231 DGNYSGTGTYETDADGTVSLPAPTENV 257
                                       567788899********9998776665 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.08   1.1e+02      29      59 ..      51      80 ..      33      82 .. 0.82
   2 ?    0.8   0.1      0.31   4.3e+02      29      59 ..     135     165 ..     117     167 .. 0.82
   3 ?    7.7   0.1    0.0022         3      29      58 ..     219     247 ..     203     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.08
                             PUA_3 29 eledGdvVdvfsekgkflGtGyynpqskiav 59
                                      ++ +   V+v+s +  ++G G y  +  ++v
  gi|313126217|ref|YP_004036487.1| 51 TAVENATVNVTS-EAGYVGNGTYQTDANGSV 80
                                      6678899*****.888******998877765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.31
                             PUA_3  29 eledGdvVdvfsekgkflGtGyynpqskiav 59 
                                       ++ +   V+v  +++ + +tG y  +  ++v
  gi|313126217|ref|YP_004036487.1| 135 TAVANATVNVSVSNDSYAATGNYTTDENGTV 165
                                       56788899*************9988877765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0022
                             PUA_3  29 eledGdvVdvfsekgkflGtGyynpqskia 58 
                                       e+ +   Vdv+s +g++ GtG y  +  ++
  gi|313126217|ref|YP_004036487.1| 219 EAVENATVDVTS-DGNYSGTGTYETDADGT 247
                                       4578899*****.**********9887666 PP

>> DBB  Dof, BCAP, and BANK (DBB) motif,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.06        83      50      90 ..      26      67 ..      15      73 .. 0.85
   2 ?    7.2   0.2    0.0033       4.6      26      83 ..      88     144 ..      80     152 .. 0.80
   3 ?    2.0   0.1      0.13   1.8e+02      26      73 ..     139     184 ..     134     194 .. 0.64
   4 ?   -0.1   0.1      0.58     8e+02      52      81 ..     190     226 ..     154     235 .. 0.45

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.06
                               DBB 50 eytlsvkap.dlpsgvvkvtlekggsslgerklkyeskleel 90
                                        tl v++  d   g v v ++++g+ + ++++++ s+ + +
  gi|313126217|ref|YP_004036487.1| 26 ATTLDVNVEqDDATGEVLVDVTNNGTAVENATVNVTSEAGYV 67
                                      57899999988889********************99987765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0033
                               DBB  26 edkvevefskenekakrvkvkleNeytlsvkapdlpsgvvkvtlekggsslgerklky 83 
                                        ++++v+ + +n  + +++v+   ++ l+v++ +  +g+v++ +e++++ ++++++++
  gi|313126217|ref|YP_004036487.1|  88 TQNITVTATDDN-LSAETTVQIVGDNDLTVDVAQADDGTVSIGVERNDTAVANATVNV 144
                                       445777777777.66777777778888889999999*****************99976 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.13
                               DBB  26 edkvevefskenekakrvkvkleNeytlsvkap.dlpsgvvkvtlekgg 73 
                                       +++v+v++s+++  a   + +   + t+ ++ap +  s++v+v  ++g+
  gi|313126217|ref|YP_004036487.1| 139 NATVNVSVSNDS-YAATGNYTTDENGTVELDAPeENVSVTVNV--SEGD 184
                                       456788888888.455556666667899999995555555554..4444 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.58
                               DBB  52 tlsvkapdlp.......sgvvkvtlekggsslgerkl 81 
                                       t+ + ap++         + v+v le+g+  + ++++
  gi|313126217|ref|YP_004036487.1| 190 TVDLVAPEVSldlsveqTTGVEVSLERGDEAVENATV 226
                                       2222222221122222233455555555555555555 PP

>> Calx-beta  Calx-beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.4   5.7e-05     0.078      20      91 ..      31     103 ..      26     110 .. 0.87
   2 ?    6.5   5.7    0.0067       9.2      24      88 ..     121     185 ..     106     195 .. 0.77
   3 ?    1.1   5.6      0.33   4.5e+02      23      88 ..     204     268 ..     183     287 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                                       EEEECCGSEEEEEEEEES.-..SS-EEEEEEEEESSS-TTTSB---EEEEEE-TT--EEEEEEE----TTTT- CS
                         Calx-beta  20 ysvsEsdgvvevcVvrks.gelerevvVsyrteDgtAtagsDYeavegeLvFkpdetekevnvtivdDdvlee 91 
                                       ++v  +d + ev V +++ g++ ++ +V++++e g   +g+  ++++g++++ + e++++++vt +dD++  e
  gi|313126217|ref|YP_004036487.1|  31 VNVEQDDATGEVLVDVTNnGTAVENATVNVTSEAGYVGNGTYQTDANGSVTLAQPEDTQNITVTATDDNLSAE 103
                                       45666666678888888889999*************9999988*************************98765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0067
                                       CCGSEEEEEEEEES-..SS-EEEEEEEEESSS-TTTSB.---EEEEEE-TT--EEEEEEE----TT CS
                         Calx-beta  24 EsdgvvevcVvrksgelerevvVsyrteDgtAtagsDY.eavegeLvFkpdetekevnvtivdDdv 88 
                                        +dg+v++ V+r++++   + +V+++ ++++  a   Y ++ +g++ +++ e+  +v+v++ + d 
  gi|313126217|ref|YP_004036487.1| 121 ADDGTVSIGVERNDTA-VANATVNVSVSNDSYAATGNYtTDENGTVELDAPEENVSVTVNVSEGDD 185
                                       57999*******9765.5788888888887755555676999************999999966443 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.33
                                       ECCGSEEEEEEEEES-..SS-EEEEEEEEESSS-TTTSB.---EEEEEE-TT--EEEEEEE----TT CS
                         Calx-beta  23 sEsdgvvevcVvrksgelerevvVsyrteDgtAtagsDY.eavegeLvFkpdetekevnvtivdDdv 88 
                                       +E+++ vev ++r  +e+ ++ +V++ t+Dg  ++   Y ++++g++ + + ++  +++vt + D+ 
  gi|313126217|ref|YP_004036487.1| 204 VEQTTGVEVSLERG-DEAVENATVDV-TSDGNYSGTGTYeTDADGTVSLPAPTENVTITVTATADND 268
                                       34444455555444.55578889986.78999999889978999*****999999999999654443 PP

>> DUF3244  Domain of unknown function (DUF3244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.039        54      23      65 ..      19      60 ..      15      67 .. 0.70
   2 ?    4.2   0.6     0.032        44      33      91 ..      79     134 ..      71     138 .. 0.69
   3 ?    2.5   2.4      0.11   1.5e+02      25      78 ..      91     149 ..      88     160 .. 0.71
   4 ?    4.9   0.3      0.02        28      31      87 ..     160     214 ..     153     222 .. 0.75
   5 ?    6.2   0.4    0.0078        11      36      65 ..     248     277 ..     242     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.039
                                      -SEEEEE.ETTEEEEEESS--SEEEEEEEETTT--EEEEEEE-G CS
                           DUF3244 23 iPitasi.egnilsiefesplsdvtitikdeetgevvyestivn 65
                                      iP  as+     + +e++++ ++v + ++++  g++v++ t+  
  gi|313126217|ref|YP_004036487.1| 19 IPAAASAaTTLDVNVEQDDATGEVLVDVTNN--GTAVENATVNV 60
                                      7888888555558888888888888888888..88887776644 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.032
                                       EEEEEESS--SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS CS
                           DUF3244  33 ilsiefesplsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskg 91 
                                        +++ + ++ +++t+t +d++    +++ +++   ++  ++d+++ + g+ ++  + ++
  gi|313126217|ref|YP_004036487.1|  79 SVTLAQPEDTQNITVTATDDN--LSAETTVQIVG-DNDLTVDVAQADDGTVSIGVERND 134
                                       578888899999999999993..33344333333.467889999888888777666555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.11
                                       EEEEEETTEEEEEESS--...SEEEEEEEETTT--EEE..EEEE-GGGTTEEEEE-TTS CS
                           DUF3244  25 itasiegnilsiefespl...sdvtitikdeetgevvy..estivnasgstisidlsge 78 
                                       it+++ +++ls e ++++   +d+t+ + +++ g+v    e++++ ++++t+++++s+ 
  gi|313126217|ref|YP_004036487.1|  91 ITVTATDDNLSAETTVQIvgdNDLTVDVAQADDGTVSIgvERNDTAVANATVNVSVSND 149
                                       56666777777777766433378999999999998864337777888899999999875 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.02
                                       TTEEEEEESS--SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEE CS
                           DUF3244  31 gnilsiefesplsdvtitikdeetgevvyestivnasgstisidlsgeesgeYklel 87 
                                       +++ ++e++ p ++v +t+  +e + ++++ +++ a   ++s+dls e++   ++ l
  gi|313126217|ref|YP_004036487.1| 160 DENGTVELDAPEENVSVTVNVSEGDDTTTKTVDLVA--PEVSLDLSVEQTTGVEVSL 214
                                       555577888888888888888888899999999988..7888888888776655555 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.0078
                                       EEESS--SEEEEEEEETTT--EEEEEEE-G CS
                           DUF3244  36 iefesplsdvtitikdeetgevvyestivn 65 
                                       +++  p ++vtit++  + + +v e ++++
  gi|313126217|ref|YP_004036487.1| 248 VSLPAPTENVTITVTATADNDTVSETVDLT 277
                                       6788999***************99998875 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.4    0.0082        11      71     156 ..     312     397 ..     238     413 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0082
                                       XXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX..........XXXXXXXX CS
                          RR_TM4-6  71 gDlseteaeespt..pelkkklaeeeeaeeekeeeeepeaeaeekadaengekeekekekeeeekeseeeeeekkkk 145
                                       +D+ +++   ++   p ++kk+ ++e++e + ++++   +e+ +k    +++k++++k+++ ++++ +++ ++ k +
  gi|313126217|ref|YP_004036487.1| 312 SDFATENNPGNADdaPGQEKKHSDDEANETAADDDKRGPPEHAKKG---KKDKNNEKKAGNGSDNADKNDAKPDKDE 385
                                       4555544444433556666666654444444444444444442222...2222222222111111112122221111 PP

                                       XX.XXXXXXXXX CS
                          RR_TM4-6 146 kk.akskkkeea 156
                                       ++ ++++++ee 
  gi|313126217|ref|YP_004036487.1| 386 SEdESEDSEEER 397
                                       110111222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1601  (0.0892967); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.88u 0.38s 00:00:01.26 Elapsed: 00:00:00.54
# Mc/sec: 2476.71
//
Query:       gi|313126218|ref|YP_004036488.1|  [L=186]
Description: tata binding protein of transcription factor tfiid [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-57  191.8   0.0    1.2e-27   95.7   0.0    2.0  2  TBP         Transcription factor TFIID (or TATA-binding prote
    2.2e-06   27.7   0.0     0.0037   17.4   0.0    2.2  2  DUF3378     Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.024   14.9   0.0        4.2    7.7   0.0    2.6  2  T4bSS_IcmS  Type IVb secretion, IcmS, effector-recruitment


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   4.7e-31   2.8e-27       2      83 ..       8      87 ..       7      89 .. 0.97
   2 !   95.7   0.0   1.9e-31   1.2e-27       2      84 ..      99     181 ..      98     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 4.7e-31
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++iqNvvas+ +g+eldLe+la ++   +a ++p++fpglvyr ++pk++aliF+sGk+v+tGaks ++++ea+  i++
  gi|313126218|ref|YP_004036488.1|  8 IEIQNVVASTGIGQELDLEALADDL--PGADFNPDNFPGLVYRTQDPKAAALIFRSGKIVCTGAKSIDDVHEALGIIFD 84
                                      79*******************9888..**************************************************99 PP

                                      HHH CS
                               TBP 81 ilk 83
                                      +l+
  gi|313126218|ref|YP_004036488.1| 85 KLR 87
                                      997 PP

  == domain 2  score: 95.7 bits;  conditional E-value: 1.9e-31
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       +++qN+v sa+lg++l+L++la  +  +++eYepe+fpglvyr++ep+v++l+F sGk+vitG k+++++++a+++i
  gi|313126218|ref|YP_004036488.1|  99 ITVQNIVSSADLGHNLNLNALAIGLGLEDVEYEPEQFPGLVYRMDEPEVVILLFGSGKIVITGGKQTNDAETAVEEI 175
                                       89********************99779************************************************** PP

                                       HHHHHH CS
                               TBP  79 apilkk 84 
                                       ++ + +
  gi|313126218|ref|YP_004036488.1| 176 VKRIDN 181
                                       **9976 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00044       2.6      25      55 ..      40      70 ..      34      75 .. 0.88
   2 !   17.4   0.0   6.2e-07    0.0037      24      61 ..     132     169 ..     127     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00044
                           DUF3378 25 kkppyavfaakkndttItaYtSgKVlFQGkn 55
                                       + p+ v++ +++++   +++SgK++  G++
  gi|313126218|ref|YP_004036488.1| 40 DNFPGLVYRTQDPKAAALIFRSGKIVCTGAK 70
                                      568***********************98875 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 6.2e-07
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61 
                                        ++ p+ v++ ++++++I ++ SgK+++ G +   +A+
  gi|313126218|ref|YP_004036488.1| 132 PEQFPGLVYRMDEPEVVILLFGSGKIVITGGKQTNDAE 169
                                       5789**************************99888886 PP

>> T4bSS_IcmS  Type IVb secretion, IcmS, effector-recruitment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0057        34      34      61 ..      39      66 ..      11      86 .. 0.83
   2 ?    7.7   0.0    0.0007       4.2      13      60 ..     109     158 ..      98     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0057
                        T4bSS_IcmS 34 tglleqliraadqlaSlaLffglkatve 61
                                       +  ++l+ ++++ + +aL f+ ++ v 
  gi|313126218|ref|YP_004036488.1| 39 PDNFPGLVYRTQDPKAAALIFRSGKIVC 66
                                      578899***************9988765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0007
                        T4bSS_IcmS  13 eadddfdddasai..saeeveedtglleqliraadqlaSlaLffglkatv 60 
                                       +++ + +++a ai    e+ve + ++ ++l+ + d+ + + L fg ++ v
  gi|313126218|ref|YP_004036488.1| 109 DLGHNLNLNALAIglGLEDVEYEPEQFPGLVYRMDEPEVVILLFGSGKIV 158
                                       56666667766652268****************************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1030.17
//
Query:       gi|313126219|ref|YP_004036489.1|  [L=277]
Description: hypothetical protein Hbor_14690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      5e-06   26.3   0.0      1e-05   25.3   0.0    1.5  1  MarR_2     MarR family
     0.0013   18.4   0.0     0.0045   16.6   0.0    1.9  2  Crp        Bacterial regulatory proteins, crp family
     0.0013   18.5   0.0     0.0025   17.6   0.0    1.4  1  HTH_IclR   IclR helix-turn-helix domain
     0.0032   17.5   0.0     0.0082   16.2   0.0    1.7  2  HTH_20     Helix-turn-helix domain
      0.007   16.3   0.0      0.013   15.5   0.0    1.4  1  MarR       MarR family
     0.0072   16.3   0.0      0.012   15.6   0.0    1.3  1  HTH_45     Winged helix-turn-helix
     0.0094   15.8   0.0      0.021   14.7   0.0    1.6  1  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0098   15.9   0.0       0.02   14.9   0.0    1.6  1  HTH_Crp_2  Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.024   14.8   0.0    1.5  1  AbiEi_4    Transcriptional regulator, AbiEi antitoxin
       0.03   14.1   0.1      0.062   13.1   0.1    1.5  1  HTH_23     Homeodomain-like domain
      0.085   12.9   0.0       0.14   12.2   0.0    1.4  1  HTH_29     Winged helix-turn helix


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   6.4e-09     1e-05       9      57 ..      18      63 ..      14      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.4e-09
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                       +L aL  +p    +++ela+++   + +++r++  + ++G+ve++p++
  gi|313126219|ref|YP_004036489.1| 18 AILRALQSSPS---RPSELAAACSCARETAQRTVSAFAEKGWVEKQPDS 63
                                      799*******6...********************************986 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.8e-06    0.0045       7      30 ..      32      55 ..      30      57 .. 0.96
   2 ?   -2.6   0.0       2.8   4.6e+03      19      23 ..     150     154 ..     150     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.8e-06
                                      HHHHHHTS-HHHHHHHHHHHHHTT CS
                               Crp  7 dIAdylGlTrETVSRlLtrLrekG 30
                                      ++A ++ ++rET+ R+++ ++ekG
  gi|313126219|ref|YP_004036489.1| 32 ELAAACSCARETAQRTVSAFAEKG 55
                                      89********************99 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                                       HHHHH CS
                               Crp  19 VSRlL 23 
                                       VSR++
  gi|313126219|ref|YP_004036489.1| 150 VSRVF 154
                                       9**98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.5e-06    0.0025       7      52 .]      18      61 ..      17      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      aiL+al + p +   selA+++  ++ t+ R ++ + e G+ve+++
  gi|313126219|ref|YP_004036489.1| 18 AILRALQSSPSR--PSELAAACSCARETAQRTVSAFAEKGWVEKQP 61
                                      8**********7..9****************************986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     5e-06    0.0082       3      56 ..       7      59 ..       5      63 .. 0.89
   2 ?   -3.7   0.0       7.9   1.3e+04       4      19 ..     197     212 ..     195     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      i  ++++++R +ilraL +  +  +sela+++++++ t+ + + + +e g ve 
  gi|313126219|ref|YP_004036489.1|  7 ISFLVGSESRIAILRAL-QSSPSRPSELAAACSCARETAQRTVSAFAEKGWVEK 59
                                      6667899**********.**********************99999999888776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.9
                                       HHHHS-HHHHHHHHHH CS
                            HTH_20   4 aeALahPvRrrilraL 19 
                                       + ++ + +R+++  +L
  gi|313126219|ref|YP_004036489.1| 197 FQLFVSATRLDFGLML 212
                                       6777888999885555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.7e-06     0.013       5      52 ..      16      62 ..      13      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.7e-06
                                      HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      ++ iLr l +++  + seLa + ++ + t+ r++ +  +kG++e++++
  gi|313126219|ref|YP_004036489.1| 16 RIAILRALQSSP-SRPSELAAACSCARETAQRTVSAFAEKGWVEKQPD 62
                                      566666665554.5899*****************************98 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.1e-06     0.012      10      75 ..      18      85 ..      14      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.1e-06
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikk..skekYvlTekGlelleklkeleel 75
                                      +IL+a++++ ++++++  +     +++++ ++   ekg ++k  ++++Y lT+ G  + ++++e+e +
  gi|313126219|ref|YP_004036489.1| 18 AILRALQSSPSRPSELAAACSCARETAQRTVSAFAEKGWVEKqpDSGTYALTAAGDVVADSYDEFETT 85
                                      7***************************************55479*******************9875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.3e-05     0.021      18      58 ..      23      63 ..      17      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      l++ p++ +e+a +    r +++++++   +kG+Ve+++ +
  gi|313126219|ref|YP_004036489.1| 23 LQSSPSRPSELAAACSCARETAQRTVSAFAEKGWVEKQPDS 63
                                      578999*******************************9976 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.2e-05      0.02      25      53 ..      31      59 ..       7      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisr 53
                                       elA+ +   ret  r+ s++ ++g++++
  gi|313126219|ref|YP_004036489.1| 31 SELAAACSCARETAQRTVSAFAEKGWVEK 59
                                      79*************************95 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-05     0.024      15      49 .]      29      69 ..      16      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                           AbiEi_4 15 ttrelea.aGisp.sa...lrrLvrkGwLvrlr.rGvYali 49
                                      + +el+a +   + +a   ++ + +kGw+++ +  G+Yal+
  gi|313126219|ref|YP_004036489.1| 29 RPSELAAaCSCAReTAqrtVSAFAEKGWVEKQPdSGTYALT 69
                                      67899999*****666***********************85 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.8e-05     0.062       7      45 ..      16      55 ..      14      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                            HTH_23  7 Rlrillllae.GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      R+ il++l+    +++e A+++ + r T +r +++++e+G
  gi|313126219|ref|YP_004036489.1| 16 RIAILRALQSsPSRPSELAAACSCARETAQRTVSAFAEKG 55
                                      6666666666656899*********************999 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.3e-05      0.14       1      41 [.      16      56 ..      16      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      R+++l++l    s++s++A+++ + r t +r++ +f e+G+
  gi|313126219|ref|YP_004036489.1| 16 RIAILRALQSSPSRPSELAAACSCARETAQRTVSAFAEKGW 56
                                      8899999999888***************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1526.18
//
Query:       gi|313126220|ref|YP_004036490.1|  [L=401]
Description: orc complex protein cdc6/orc1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-18   66.6   0.1    3.5e-18   65.3   0.1    1.7  1  Cdc6_C           CDC6, C terminal winged helix domain
      9e-16   58.4   0.2    2.8e-15   56.8   0.0    1.8  2  AAA_22           AAA domain
      2e-10   41.3   2.4    5.2e-10   40.0   0.3    2.5  2  AAA_16           AAA ATPase domain
    6.8e-07   29.8   0.2    2.3e-06   28.1   0.2    1.9  1  AAA              ATPase family associated with various cellul
    2.5e-06   27.5   0.0    8.4e-06   25.8   0.0    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
    7.3e-06   25.8   0.0    1.5e-05   24.8   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
    5.7e-05   23.1   0.0    0.00011   22.1   0.0    1.5  1  NACHT            NACHT domain
    0.00021   21.4   0.1    0.00037   20.7   0.1    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
    0.00028   21.0   0.0     0.0017   18.5   0.0    2.1  1  Sigma54_activ_2  Sigma-54 interaction domain
    0.00096   18.4   0.0     0.0017   17.5   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
     0.0012   18.3   0.0     0.0024   17.3   0.0    1.5  1  TniB             Bacterial TniB protein
     0.0025   18.2   0.0     0.0052   17.2   0.0    1.6  1  RNA_helicase     RNA helicase
     0.0038   17.0   1.8       0.46   10.2   1.8    2.2  1  DEAD             DEAD/DEAH box helicase
      0.009   15.8   0.2      0.017   14.8   0.2    1.5  1  AAA_24           AAA domain
     0.0094   15.5   0.2      0.028   13.9   0.2    1.7  2  AAA_7            P-loop containing dynein motor region
     0.0095   15.2   0.1          1    8.6   0.0    2.2  2  KAP_NTPase       KAP family P-loop domain
  ------ inclusion threshold ------
      0.018   14.2   0.0      0.029   13.5   0.0    1.3  1  NB-ARC           NB-ARC domain
       0.02   14.2   0.0      0.039   13.3   0.0    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.044   13.9   0.2       0.12   12.5   0.1    1.7  2  DUF87            Helicase HerA, central domain
      0.047   13.1   0.0       0.09   12.1   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.05   12.8   0.0       0.06   12.6   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.07   12.6   2.3          9    5.7   0.0    2.9  3  PhoH             PhoH-like protein
       0.11   11.4   0.0       0.18   10.7   0.0    1.3  1  AAA_10           AAA-like domain
       0.11   12.9   1.3        1.2    9.5   0.4    2.7  2  AAA_assoc_2      AAA C-terminal domain
       0.11   12.2   0.3       0.62    9.8   0.1    2.1  2  IstB_IS21        IstB-like ATP binding protein
       0.13   12.7   0.1       0.26   11.8   0.1    1.9  1  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.1   5.1e-21   3.5e-18       2      83 ..     313     393 ..     310     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 5.1e-21
                                       HHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSC CS
                            Cdc6_C   2 calvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdp 78 
                                       +a+++l + ++++ ++t++vyevY+++C  +g d l+ r+v+dll+e ++l i+e  k s+G++eg ++k++L  dp
  gi|313126220|ref|YP_004036490.1| 313 LAMLSLSN-ERQDGFRTSRVYEVYENICTGQGSDSLSLRRVRDLLKEHAFLDIIEQSKHSGGSAEGSYTKHQLLEDP 388
                                       46777777.******************************************************************** PP

                                       HHHHH CS
                            Cdc6_C  79 ddvle 83 
                                       + v++
  gi|313126220|ref|YP_004036490.1| 389 QVVRD 393
                                       *9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   4.1e-18   2.8e-15       6     119 ..      57     179 ..      53     191 .. 0.89
   2 ?   -1.6   0.1       4.3     3e+03      64      64 ..     335     335 ..     272     370 .. 0.48

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 4.1e-18
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlsse 76 
                                       + ++++G +GtGK+++++ + ++l+e a  e+ ++++++v+++++t+ ++  + ++  ++++  +      ++ls++
  gi|313126220|ref|YP_004036490.1|  57 SNVLIYGKTGTGKSLCAKYVSQRLVETAGEEDVKATFAYVDCAQDTTETQAVQTIADSVNQSEVTgikvpdKGLSTS 133
                                       6789********************98888888999999**********************99999************ PP

                            AAA_22  77 ellealeqalraravielliiDEaqhlrs.eealeeLrsllnl...s 119
                                        ++++l++ l+a+++++l+i+DE+++l s +++l +L++  +    +
  gi|313126220|ref|YP_004036490.1| 134 TYYKRLWRILDAQYDVVLIILDEIDKL-SdDDILMQLSRAGEAgkiD 179
                                       ***************************.7699999997765555444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
                            AAA_22  64 l 64 
                                       +
  gi|313126220|ref|YP_004036490.1| 335 Y 335
                                       1 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.3   7.6e-13   5.2e-10       2     150 ..      33     163 ..      32     183 .. 0.64
   2 ?   -0.3   0.1       1.8   1.2e+03      73     103 ..     270     301 ..     216     370 .. 0.57

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 7.6e-13
                            AAA_16   2 lvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysa 71 
                                        vGR++e++ L++a++ ++  ++p++vl++G  G+GKs  ++ + ++l ++      ++ f++ +c q         
  gi|313126220|ref|YP_004036490.1|  33 IVGRDDEISDLATAVNpAIFGQSPSNVLIYGKTGTGKSLCAKYVSQRLVETageedvKATFAYVDCAQD-------- 101
                                       69**************55555555**********************99998444444444444444444........ PP

                            AAA_16  72 laqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwa 147
                                            ++ + ++ ++d  +++e+   +           +++g + s  +  l r+l a++      ++++lD+++++
  gi|313126220|ref|YP_004036490.1| 102 ----TTETQAVQTIADSVNQSEVTGIKV----------PDKGLSTSTYYKRLWRILdAQYDV----VLIILDEIDKL 160
                                       ....333344444444433333333333..........333333366666666666333333....88888888877 PP

                            AAA_16 148 dea 150
                                        ++
  gi|313126220|ref|YP_004036490.1| 161 SDD 163
                                       764 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.8
                            AAA_16  73 aqalareellrqllde.aesaeleawreklee 103
                                       aq  a++++ ++  ++  e ae +++re +++
  gi|313126220|ref|YP_004036490.1| 270 AQSTAASTVREEFVTQaRERAETDRFRELIRG 301
                                       33333333333333331111223333333333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2   3.3e-09   2.3e-06       1     130 [.      59     213 ..      59     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.3e-09
                                       EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS..........................STTHH CS
                               AAA   1 vllyGppGtGKTllakavakel.........gvefleisgsellsk..........................yvges 42 
                                       vl+yG  GtGK+l+ak v + l         +++f  +++++ + +                            +  
  gi|313126220|ref|YP_004036490.1|  59 VLIYGKTGTGKSLCAKYVSQRLvetageedvKATFAYVDCAQDTTEtqavqtiadsvnqsevtgikvpdkglSTSTY 135
                                       79*******************76666666556778888888777556788888887777777766555544333333 PP

                                       HHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GG CS
                               AAA  43 ekkirelfkeakeka...kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pd 113
                                        k++  ++          + + +++DEid+l  ++          ++ qL ++ +  k ++ k+ vig++n+    d
  gi|313126220|ref|YP_004036490.1| 136 YKRLWRIL------DaqyDVVLIILDEIDKLSDDD----------ILMQLSRAGEAGKIDQCKLGVIGISNKiqyKD 196
                                       34444444......1333469999*******7666..........**************************977778 PP

                                       GSTHHHHSTTSSEEEET CS
                               AAA 114 kldpallrgRfdrkiei 130
                                       ++d+ + ++ ++r++ +
  gi|313126220|ref|YP_004036490.1| 197 RMDERVKSSLCEREFVF 213
                                       88887776777777665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.2e-08   8.4e-06       1      96 [.      58     180 ..      58     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.2e-08
                                       EEEEE--SSSSHHHHHHHGGGGB.........S--EEEEE--TT--HHHHH--B--.........--------.... CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.........nreveyvqltrdtteedlkgrreikngttslvdsplvraar.... 64 
                                       +vl+ G++GtgKs  a++++++l         ++++ yv + +dtte++ ++ +       s  +s+++  ++    
  gi|313126220|ref|YP_004036490.1|  58 NVLIYGKTGTGKSLCAKYVSQRLvetageedvKATFAYVDCAQDTTETQAVQTIAD-----SVNQSEVT-GIKvpdk 128
                                       69***************************************************993.....33333333.3334555 PP

                                       ...................G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE. CS
                             AAA_5  65 ...................egeilvlDEverae.sevlnsLlslleerrlll 96 
                                                             +++lDE+++++ +++l+ L +  e  +++ 
  gi|313126220|ref|YP_004036490.1| 129 glststyykrlwrildaqyDVVLIILDEIDKLSdDDILMQLSRAGEAGKIDQ 180
                                       5788888999999999998888999********999**99988777666665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.1e-08   1.5e-05       2      61 ..      34     101 ..      33     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.1e-08
                                       ---SHHHHHHHHHHHHHC..TSSS-EEEECSTTSSHHHHHHHHHH......HSTTTTS-EEEEETTTS CS
                   Sigma54_activat   2 igesealkelleqikkva..ktdlsvlitGesGtGKellaraihe......askrkekpfvavncaai 61 
                                       +g+++++++l + ++ ++  +++++vli G++GtGK+l+a+ + +       ++  ++ f  v+ca+ 
  gi|313126220|ref|YP_004036490.1|  34 VGRDDEISDLATAVNPAIfgQSPSNVLIYGKTGTGKSLCAKYVSQrlvetaGEEDVKATFAYVDCAQD 101
                                       67788888888888877644677********************9977776555556889******954 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.7e-07   0.00011       3      97 ..      59     164 ..      57     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.7e-07
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEE.EEETTTTTTS-....-HCHHHCCCCTS--SSS-C...... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvF.flslrelsrsgna.rsladllfsqlpepaapvse...... 71 
                                       v++ G+ G GK+  ++ + + + e   +++  k  F ++ +++++++++a  ++ad + +     ++ +++      
  gi|313126220|ref|YP_004036490.1|  59 VLIYGKTGTGKSLCAKYVSQRLVETAGEEDV-KATFaYVDCAQDTTETQAvQTIADSVNQSEVTGIKVPDKglstst 134
                                       89********************999999985.555547889888888777555555555554444444444899999 PP

                                       ....CHHHHCCSCCCEEEEEE-STT-SS-T CS
                             NACHT  72 ....vwavllelperlLlilDglDelvtdl 97 
                                            w +l ++ + +L+ilD +D+l++d+
  gi|313126220|ref|YP_004036490.1| 135 yykrLWRILDAQYDVVLIILDEIDKLSDDD 164
                                       **99**********************9976 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   5.4e-07   0.00037       4      86 ..      57     165 ..      54     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.4e-07
                                       --EEEE--TTSSHHHHHHHHHHHTT-.........-EEEEEGGG.-------THHHHHHHHHTTT-HHHHTTS.... CS
                             AAA_2   4 isilllgptgvGktelakalaellfv.....kkekkliradase.lleeeevehlvsrligappgyvgaeegG.... 70 
                                       +++l+ g+tg+Gk++ ak +++ l       + + +++ +d+ +  +e ++v+++ ++  +++   +++ ++G    
  gi|313126220|ref|YP_004036490.1|  57 SNVLIYGKTGTGKSLCAKYVSQRLVEtageeDVKATFAYVDCAQdTTETQAVQTIADSVNQSEVTGIKVPDKGlsts 133
                                       789************99998888844788889999******7651666888999999999999999*********** PP

                                       .................EEEEETGGG------- CS
                             AAA_2  71 .................ivllDEidKihpkess 86 
                                                         + lDEidK +  + +
  gi|313126220|ref|YP_004036490.1| 134 tyykrlwrildaqydvvLIILDEIDKLSD-DDI 165
                                       ***************888889*****998.444 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-06    0.0017       2      44 ..      35      79 ..      34     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                                      ---HHHHHHHHHHHHHH..T-SS-EEEEEETT--HHHHHHCC--T CS
                   Sigma54_activ_2  2 gasaaiqelkerLeqaa..qsklpvfltGekGsgkelvArlLhkn 44
                                      g+   i++l++ ++ a   qs ++v++ G  G+gk+l+A++ ++ 
  gi|313126220|ref|YP_004036490.1| 35 GRDDEISDLATAVNPAIfgQSPSNVLIYGKTGTGKSLCAKYVSQR 79
                                      6667788888888877666999*******************9874 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.5e-06    0.0017      29      79 ..      32      82 ..      18     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.5e-06
                            DUF815 29 dLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyae 79
                                      ++vg d++ ++l + ++  + g++ +nvL++G+ GtGKS + k + +++ e
  gi|313126220|ref|YP_004036490.1| 32 RIVGRDDEISDLATAVNPAIFGQSPSNVLIYGKTGTGKSLCAKYVSQRLVE 82
                                      57899999999*****************************99999887765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.6e-06    0.0024      34     132 ..      55     161 ..      40     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.6e-06
                              TniB  34 rmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara.......r 103
                                        ++n+l++G++ +GK+  ++  +++  ++  e++ k    +v++ +  +e +  + i +++++   +         +
  gi|313126220|ref|YP_004036490.1|  55 SPSNVLIYGKTGTGKSLCAKYVSQRLVETAGEEDVKATFAYVDCAQDTTETQAVQTIADSVNQSEVTGIkvpdkglS 131
                                       5689***********9665555555555566777799********************99999874322234445668 PP

                              TniB 104 vskleqqvlrllr.elkvrvLiiDEihnll 132
                                       +s+ +++  r+l+ +++v ++i+DEi++l 
  gi|313126220|ref|YP_004036490.1| 132 TSTYYKRLWRILDaQYDVVLIILDEIDKLS 161
                                       88999999999973679999999***9875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.6e-06    0.0052       1      44 [.      59     103 ..      59     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.6e-06
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys.rnpeddfw 44 
                                       +++yG++g+GKS++ak+++++l ++ +++  + +++   +++d  
  gi|313126220|ref|YP_004036490.1|  59 VLIYGKTGTGKSLCAKYVSQRLVETAGEEDVKATFAyVDCAQDTT 103
                                       689********************9997666666655577777655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   1.8   0.00066      0.46       9     142 ..      49     169 ..      41     193 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00066
                                       HHHHTT..CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHH..HHHHTTTSTSEEEEE CS
                                       xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                              DEAD   9 plilgg..gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnn..lkkfkkyidlrvlli 81 
                                       p+i g+   +vl+ ++TG+GK+l++   v q+++et g++  ka +       a++t ++  ++++ + ++   ++ 
  gi|313126220|ref|YP_004036490.1|  49 PAIFGQspSNVLIYGKTGTGKSLCA-KYVSQRLVETAGEEDVKATFA--YVDCAQDTTETqaVQTIADSVN---QSE 119
                                       55553323699************96.556778888855555444332..2222222222200111111111...111 PP

                                       ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfi 142
                                       ++g +        d+g+  + +  +rl ++l+ ++    +v +++lDE+d+l+d++   ++
  gi|313126220|ref|YP_004036490.1| 120 VTGIKV------PDKGL-STSTYYKRLWRILDAQY----DVVLIILDEIDKLSDDDILMQL 169
                                       222111......11111.12234455555554444....5666666666666666555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   2.5e-05     0.017       4      79 ..      58     162 ..      55     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.......swedfldevvel.............. 59 
                                       ++liyG+ g+GK+ +ak   ++ +    e+  +      ++d+        +++++ d v++               
  gi|313126220|ref|YP_004036490.1|  58 NVLIYGKTGTGKSLCAKYVSQRLVETAGEE--DVKATFAYVDCAqdttetqAVQTIADSVNQSevtgikvpdkglst 132
                                       79*****************88888887777..334444444444455556666666666666678899999999999 PP

                            AAA_24  60 ........aaeladykt..lviDtidelee 79 
                                               +  +a+y++  +++D id+l +
  gi|313126220|ref|YP_004036490.1| 133 styykrlwRILDAQYDVvlIILDEIDKLSD 162
                                       999999985555555551156788888865 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   4.1e-05     0.028      33      85 ..      56     114 ..      50     129 .. 0.65
   2 ?    0.1   0.0      0.71   4.9e+02      15      66 ..     101     151 ..      85     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkld....ke..kylsltinfsaqtsanqlqdiiesk 85 
                                         +vl++G+tGtGK++++k + ++l     +e  k +++ + + + t+ +q  ++i ++
  gi|313126220|ref|YP_004036490.1|  56 PSNVLIYGKTGTGKSLCAKYVSQRLVetagEEdvKATFAYVDCAQDTTETQAVQTIADS 114
                                       579*************9887666554111133113344455566666666655555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.71
                             AAA_7  15 ptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylslt 66 
                                        t++t  ++++ + + +++   + v ++G + +++ k+l + ld  +y ++ 
  gi|313126220|ref|YP_004036490.1| 101 DTTETQAVQTIADSVNQSEVTGIKVPDKGLSTSTYYKRLWRILD-AQYDVVL 151
                                       69999999999999999999999999999999999999999999.6666554 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0015         1       4      76 ..      39     114 ..      36     119 .. 0.84
   2 ?    4.3   0.2     0.029        20     156     191 ..     131     166 ..     124     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                        KAP_NTPase   4 yasaladilseptl..atpivvgLygkWGsGKssllnkledelkefa..kpvrflfaefnawsfkggddavaellaa 76 
                                        +s la+ ++ p+   + p+ v +ygk G+GKs   + + + l e a  + v+ +fa+++ +  +++ +av+++ ++
  gi|313126220|ref|YP_004036490.1|  39 EISDLATAVN-PAIfgQSPSNVLIYGKTGTGKSLCAKYVSQRLVETAgeEDVKATFAYVDCAQDTTETQAVQTIADS 114
                                       6777888877.66678999**************9999999999999877788999*****99999999999888765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.029
                        KAP_NTPase 156 eveelladmektLdalqkrlVvviDdLDrceteevl 191
                                       + ++ ++++ + Lda+   +++++D++D + ++ +l
  gi|313126220|ref|YP_004036490.1| 131 STSTYYKRLWRILDAQYDVVLIILDEIDKLSDDDIL 166
                                       556667888899***99*************998875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.2e-05     0.029      23     114 ..      59     159 ..      46     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.2e-05
                                       EEEEESTTSSHHHHHHHHCCSHCCCCCCBT...EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS....H CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksdevegrFd...svawvvvsktdkseeiletilkeLslseddleekeeves....l 92 
                                       v ++G+ G GK+  ak + + + e+ g+ d    +a+v  ++  ++ + ++ti+  +++se    + +++       
  gi|313126220|ref|YP_004036490.1|  59 VLIYGKTGTGKSLCAKYVSQRLVETAGEEDvkaTFAYVDCAQDTTETQAVQTIADSVNQSEVTGIKVPDKGLststY 135
                                       789***********************99885556899********************99987654444433237778 PP

                                       HHHHHHHCCCT..TEEEEEEEE-S CS
                            NB-ARC  93 krklvrlLltk..rfllvlDDVwe 114
                                        ++l r+L  +   +l++lD + +
  gi|313126220|ref|YP_004036490.1| 136 YKRLWRILDAQydVVLIILDEIDK 159
                                       899999999998677888888754 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.6e-05     0.039      38      99 ..      55     123 ..      31     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.6e-05
                                       S-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEE..EEEE-TTSS..SCGGGTT-TTBSS....S-B CS
                      FtsK_SpoIIIE  38 mashllvaGatgsGKStalntLilSlatthtPeeVq..liliDykgv..elsalediphlls...vava 99 
                                       ++s++l+ G tg+GKS + +   + l+ t+  e+V+  +  +D++    e +a++ i++ +    v ++
  gi|313126220|ref|YP_004036490.1|  55 SPSNVLIYGKTGTGKSLCAKYVSQRLVETAGEEDVKatFAYVDCAQDttETQAVQTIADSVNqseVTGI 123
                                       459**************9999888888888888885448888887533488888888887773334444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00017      0.12      26      49 ..      59      82 ..      57      92 .. 0.86
   2 ?   -3.0   0.0         9   6.2e+03     112     130 ..     274     292 ..     260     357 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                             DUF87 26 lAilgsTGsGKSntvavLleelle 49
                                      ++i g+TG+GKS  +++  ++l+e
  gi|313126220|ref|YP_004036490.1| 59 VLIYGKTGTGKSLCAKYVSQRLVE 82
                                      689*******************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9
                             DUF87 112 paaavqrsvleealdqaka 130
                                       +a++v ++++ +a ++a+ 
  gi|313126220|ref|YP_004036490.1| 274 AASTVREEFVTQARERAET 292
                                       3333355555555555543 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.09      23      61 ..      57      95 ..      39     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlpsllpplseeealevakia 61
                                       n+l++G  G+GK++ ak +++ l +   ee ++++  +
  gi|313126220|ref|YP_004036490.1| 57 SNVLIYGKTGTGKSLCAKYVSQRLVETAGEEDVKATFAY 95
                                      59*******************999999998888776544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.7e-05      0.06       3      52 ..      58     109 ..      56     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.7e-05
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvlvlreala 52 
                                        vl+ G++GtGK++++  +  +l  +  ee+ +a++++v  ++  +  +a++
  gi|313126220|ref|YP_004036490.1|  58 NVLIYGKTGTGKSLCAKYVSQRLveTAGEEDVKATFAYVDCAQDTTETQAVQ 109
                                       689*************999999977556666677777776655444444443 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.018        12      22      43 ..      59      80 ..      50      89 .. 0.81
   2 ?   -1.5   0.0       2.1   1.4e+03     120     137 ..      91     108 ..      88     112 .. 0.80
   3 ?    5.7   0.0     0.013         9     122     149 ..     151     178 ..     147     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.018
                                      EEEE--TTSSTTHHHHHHHHHH CS
                              PhoH 22 vfaiGpaGtGKtylavalavea 43
                                      v + G++GtGK++ a  +  ++
  gi|313126220|ref|YP_004036490.1| 59 VLIYGKTGTGKSLCAKYVSQRL 80
                                      7899*********997766555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                                       SEEEEE-SGGG--HHHHH CS
                              PhoH 120 dafvilDEAQnttkeqmk 137
                                        +f  +D AQ+tt++q  
  gi|313126220|ref|YP_004036490.1|  91 ATFAYVDCAQDTTETQAV 108
                                       578889*******99875 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.013
                                       EEEE-SGGG--HHHHHHHHTTB-TT-EE CS
                              PhoH 122 fvilDEAQnttkeqmkmfltRlGenskv 149
                                       ++ilDE   ++   + m l+R Ge  k+
  gi|313126220|ref|YP_004036490.1| 151 LIILDEIDKLSDDDILMQLSRAGEAGKI 178
                                       79*********************98775 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00026      0.18      22      60 ..      57     101 ..      45     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                            AAA_10  22 sasliiGdlGnGKSvlakllvlyisllg......gkaliiDpkke 60 
                                       s++li G++G GKS++ak++   ++             ++D  ++
  gi|313126220|ref|YP_004036490.1|  57 SNVLIYGKTGTGKSLCAKYVSQRLVETAgeedvkATFAYVDCAQD 101
                                       567****************98765433335554444556666655 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.5   3.8e+03      21      42 ..      87     107 ..      72     128 .. 0.61
   2 ?    9.5   0.4    0.0017       1.2      14      58 ..     247     290 ..     243     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.5
                                       XXXXXXXXXXXXXXXXXXX.XX CS
                       AAA_assoc_2  21 GDaRkaLnlLElaaeaaeakeg 42 
                                        D+++ + +++ a +++e++  
  gi|313126220|ref|YP_004036490.1|  87 EDVKATFAYVDCAQDTTETQ-A 107
                                       47777777777777777763.2 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0017
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2  14 alaeladGDaRkaLnlLElaaeaaeakegkieitledleealqrk 58 
                                       ala+  +GDaRka+ +L  a e a++ +   ++ +e +++a +r+
  gi|313126220|ref|YP_004036490.1| 247 ALAAREHGDARKAIDILRYAGEIAQS-TAASTVREEFVTQARERA 290
                                       6788889***********99999886.777888888888777665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0009      0.62      45      74 ..      54      83 ..      40     154 .. 0.74
   2 ?    0.4   0.1      0.68   4.7e+02      94     118 ..     134     158 ..     116     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0009
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavra 74
                                      ++  n+++ G +G+GKs  a  ++++ v++
  gi|313126220|ref|YP_004036490.1| 54 QSPSNVLIYGKTGTGKSLCAKYVSQRLVET 83
                                      5668*************9999988888873 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.68
                         IstB_IS21  94 rrdgklaralkrllkvdllilDdlg 118
                                           +l r+l++   v l+ilD++ 
  gi|313126220|ref|YP_004036490.1| 134 TYYKRLWRILDAQYDVVLIILDEID 158
                                       5567788899999999999999986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00038      0.26      13      44 ..      58      89 ..      54     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeill 44
                                       v i G++G+GKS  +k +++ l  t+Ge  +
  gi|313126220|ref|YP_004036490.1| 58 NVLIYGKTGTGKSLCAKYVSQRLVETAGEEDV 89
                                      689********************999998633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 2470.14
//
Query:       gi|313126221|ref|YP_004036491.1|  [L=150]
Description: hypothetical protein Hbor_14710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 891.56
//
Query:       gi|313126222|ref|YP_004036492.1|  [L=643]
Description: DNA/RNA helicase, superfamily ii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-28   98.7   0.0    4.5e-28   98.1   0.0    1.3  1  ERCC3_RAD25_C   ERCC3/RAD25/XPB C-terminal helicase
    3.6e-17   62.9   0.0    9.7e-17   61.5   0.0    1.7  2  ResIII          Type III restriction enzyme, res subunit
    3.6e-14   52.2   0.0    6.8e-14   51.3   0.0    1.4  1  SNF2_N          SNF2 family N-terminal domain
    1.2e-13   51.4   0.0    7.2e-13   48.9   0.0    2.1  2  Helicase_C      Helicase conserved C-terminal domain
    0.00019   21.2   0.0    0.00052   19.8   0.0    1.7  1  DEAD            DEAD/DEAH box helicase
     0.0026   17.6   0.6     0.0071   16.2   0.6    1.8  1  MarR_2          MarR family
     0.0038   17.1   0.0      0.012   15.5   0.0    1.8  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.033   14.1   0.0    1.8  1  MarR            MarR family
      0.015   15.0   0.0      0.036   13.8   0.0    1.7  1  AAA_30          AAA domain
      0.016   15.5   0.4       0.13   12.5   0.4    2.5  1  AAA_22          AAA domain
      0.026   14.1   0.2       0.33   10.5   0.0    2.5  2  AAA_25          AAA domain
      0.037   14.2   0.0       0.14   12.4   0.0    2.0  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.053   13.1   0.1       0.25   10.9   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.054   12.7   0.0      0.097   11.9   0.0    1.5  1  DUF2075         Uncharacterized conserved protein (DUF2075)
      0.081   12.4   0.0       0.15   11.6   0.0    1.3  1  DUF4283         Domain of unknown function (DUF4283)
      0.097   13.1   0.0       0.29   11.5   0.0    1.8  1  AAA             ATPase family associated with various cellula
        0.2   11.6   0.5        7.5    6.5   0.1    2.8  2  AAA_5           AAA domain (dynein-related subfamily)
        0.6    9.5   4.7       0.14   11.5   0.1    2.3  3  DUF3482         Domain of unknown function (DUF3482)


Domain annotation for each model (and alignments):
>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.0   4.6e-31   4.5e-28      25     189 ..     479     633 ..     454     637 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 4.6e-31
                     ERCC3_RAD25_C  25 keylkakskkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkf 101
                                       +e+ +a+ +++++l+ mnp+k+     L++ h k   k +vf D +   +e+a++l  p+i Ge+++++r +++++f
  gi|313126222|ref|YP_004036492.1| 479 NEWSSADGRERRQLASMNPQKIAETRRLLRQHPK--SKALVFVDYLDQGEELAEALDVPFISGEMRHHHRERLFRQF 553
                                       678889999*********************9986..699************************************** PP

                     ERCC3_RAD25_C 102 kknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemays 178
                                       ++  +++t+++s+vgD+ iDlP+a+  i  s   gsrrq aqr Gr +r+  +       a  Y L  + t+e  ++
  gi|313126222|ref|YP_004036492.1| 554 REG-ELRTLVISRVGDEGIDLPNAELAIVASGLGGSRRQGAQRAGRTMRPAGG-------ALVYVLATRGTSEEDFA 622
                                       987.89********************************************999.......9**************** PP

                     ERCC3_RAD25_C 179 tkrqqflvdqG 189
                                       +++ ++l ++G
  gi|313126222|ref|YP_004036492.1| 623 QRQMRHLAEKG 633
                                       *******9998 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   9.8e-20   9.7e-17       3     170 ..     289     430 ..     287     431 .. 0.90
   2 ?   -2.4   0.0       4.3   4.2e+03      45      72 ..     503     530 ..     500     546 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 9.8e-20
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       elreyQ++  +++       ++k g+++ + G+GKT++ + + +++       ++l+lvp+++l  q++ee+ + +s
  gi|313126222|ref|YP_004036492.1| 289 ELREYQQDWTDRFT------EQKSGVLVGPPGAGKTVTGIGILAAVGG-----ETLVLVPSRELAAQWREEILRHTS 354
                                       799****9999995......7899*********************999.....6********************999 PP

                                       G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT CS
                            ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilek 156
                                          ++ig+   g+k+ +         ++++t+q++  d+     ++  +++ +  +i+ DE+H++ +   +r+ ++ 
  gi|313126222|ref|YP_004036492.1| 355 LSEDQIGEYHGGQKQVR--------PVTIATYQTAGMDR-----HRSLFDDREWGLIVYDEVHHVPS-RIYRRSADL 417
                                       99776666666666666........**************.....88999999999************.9****6555 PP

                                       ---SEEEEEESS-S CS
                            ResIII 157 fkeavllglTATpe 170
                                        +++ +lgl+ATp 
  gi|313126222|ref|YP_004036492.1| 418 -QAKHRLGLSATPI 430
                                       .99**********7 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.3
                                       HHHH-S.....-EEEEESSHHHHHHHHH CS
                            ResIII  45 ierllkkgkeekflflvprkslleqtle 72 
                                       ++rll++++++k+l++v+ ++  e + e
  gi|313126222|ref|YP_004036492.1| 503 TRRLLRQHPKSKALVFVDYLDQGEELAE 530
                                       56888999999*****998887766655 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   6.8e-17   6.8e-14      54     227 ..     303     443 ..     292     473 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 6.8e-17
                                       TT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  54 svrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneierhvsssalrvlvy 129
                                       +++ G+L   +G+GKTv+ + +++                 + g tL++vP+ +l+ qW +ei rh+s s+ ++  y
  gi|313126222|ref|YP_004036492.1| 303 EQKSGVLVGPPGAGKTVTGIGILA----------------AVGGETLVLVPSrELAAQWREEILRHTSLSEDQIGEY 363
                                       56789999***************9................244669**********************999988888 PP

                                       SHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 130 ggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLsts 206
                                       +g++              +   v i tY++   +     +rs + ++ew  +v DE h + +   +++    +L+++
  gi|313126222|ref|YP_004036492.1| 364 HGGQ-------------KQVRPVTIATYQTAGMDR----HRSLFDDREWGLIVYDEVHHVPS---RIYRRSADLQAK 420
                                       8874.............34578**********888....9********************86...5666667799** PP

                                       -EEEE-S--SSS..-HHHHHHHH CS
                                       xxxxxxxxxxxx..xxxxxxxxx RF
                            SNF2_N 207 nrwiltGTPiqn..sledlygLl 227
                                       +r+ l++TPi +  + +++++L+
  gi|313126222|ref|YP_004036492.1| 421 HRLGLSATPIREddKEKEIFTLI 443
                                       **********9866777776664 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.7   1.7e+03      13      52 ..     326     369 ..     319     379 .. 0.73
   2 !   48.9   0.0   7.2e-16   7.2e-13       2     109 ..     499     601 ..     498     603 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.7
                                       TTTTSEEEEEESSHHHHHH..HHHHHHHT..TSTEEEESTTSTH CS
                        Helicase_C  13 eeeggkilifvntidrlek..vklllekk..gikvavlhgelpq 52 
                                        ++gg++l+ v++++ + +   ++l++++  + ++  +hg  +q
  gi|313126222|ref|YP_004036492.1| 326 AAVGGETLVLVPSRELAAQwrEEILRHTSlsEDQIGEYHGGQKQ 369
                                       578999*********66556777775555667778888886555 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 7.2e-16
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       k++   +ll +++ ++k+l+fv + d+    + l   +++ v  + ge+ + +re+ ++qf++ge + L+ ++v+ +
  gi|313126222|ref|YP_004036492.1| 499 KIAETRRLL-RQHPKSKALVFVDYLDQG---EEL--AEALDVPFISGEMRHHHRERLFRQFREGELRTLVISRVGDE 569
                                       677778888.899*************99...556..46789999********************************* PP

                                       SSTSTTESEEEES.SSSSSHHHHHHHHTTSSS CS
                        Helicase_C  79 GidipkvnlVinf.dlprnvtsyiqriGRtgR 109
                                       Gid+p+++l i   +l  + ++  qr+GRt+R
  gi|313126222|ref|YP_004036492.1| 570 GIDLPNAELAIVAsGLGGSRRQGAQRAGRTMR 601
                                       ********998651566889***********9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.2e-07   0.00052       2     170 ..     292     430 ..     291     436 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.2e-07
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       ++Q+   + + ++++ ++ ++ G+GKT    i +l++v       g  +l+++P+reLa q  +++ + ++   l++
  gi|313126222|ref|YP_004036492.1| 292 EYQQDWTDRFTEQKSGVLVGPPGAGKTVT-GIGILAAV-------GGETLVLVPSRELAAQWREEILRHTS---LSE 357
                                       578888888999999999*********87.88888777.......6789*****************99888...555 PP

                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                         i + +  ++q++ +     i    +  +d+  ++  ++ ++  ++V DE++ + +  +++  +    q       
  gi|313126222|ref|YP_004036492.1| 358 DQIGEYHGGQKQVRPV----TIATYQTAGMDR--HRSLFDDREWGLIVYDEVHHVPSRIYRRSADL---QA------ 419
                                       5442223333344444....333333333333..244566788999*******9999955555544...22...... PP

                                       STTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxx RF
                              DEAD 156 gklqrqvivlSATlp 170
                                           ++ + lSAT+ 
  gi|313126222|ref|YP_004036492.1| 420 ----KHRLGLSATPI 430
                                       ....12566677665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.6   7.1e-06    0.0071      14      58 ..      53      97 ..      51      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.1e-06
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                      L +++++ +t+++  rrlgls++a+s +l+rL + G ++r++ ++
  gi|313126222|ref|YP_004036492.1| 53 LEAEGRPVMTAQQTGRRLGLSQAAASEALDRLARDGTLQRVEVET 97
                                      666666667***************************999886655 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-05     0.012      22      67 ..      60     107 ..      49     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                                       CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEEE--H CS
                              TrmB  22 patadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYravdp 67 
                                        +ta++  ++lg++++ + e+L +L + G  +r++ +  p +Y ++++
  gi|313126222|ref|YP_004036492.1|  60 VMTAQQTGRRLGLSQAAASEALDRLARDGTLQRVEVEtdPVVYYPAEW 107
                                       689********************************8889*****9987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.3e-05     0.033      18      51 ..      61      94 ..      31      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      ++ ++ +++lg+s+++++++ldrL ++G ++R  
  gi|313126222|ref|YP_004036492.1| 61 MTAQQTGRRLGLSQAAASEALDRLARDGTLQRVE 94
                                      77788899**********************9976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.7e-05     0.036       2      66 ..     290     349 ..     289     409 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
                            AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeel 66 
                                       l++ Q++  +++++++    vl+Gp+G+GKt +  ++ +a+   gg+ ++l p+ + A++ +ee+
  gi|313126222|ref|YP_004036492.1| 290 LREYQQDWTDRFTEQK--SGVLVGPPGAGKTVTGIGILAAV---GGETLVLVPSRELAAQWREEI 349
                                       7788999999998888..59***********9988776655...567788888888888877765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   0.00013      0.13       4     103 ..     303     406 ..     299     429 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.......... 70 
                                       +++++v++G++G+GKT++   +l            + e+ +v +ps +  ++ ++e+lr + l+ +           
  gi|313126222|ref|YP_004036492.1| 303 EQKSGVLVGPPGAGKTVTGIGILAAV---------GGET-LVLVPSRELAAQWREEILRHTSLSEDQigeyhggqkq 369
                                       6899************9977777765.........3332.3444444445666666666666666666665443222 PP

                            AAA_22  71 .erlsseell.ealeqalrarav..........ielliiDEaqhl 103
                                        +      +  ++ + a     +           +l++ DE++h+
  gi|313126222|ref|YP_004036492.1| 370 vR-----PVTiATYQTAGM---DrhrslfddreWGLIVYDEVHHV 406
                                       21.....111111111111...12224444666667777777766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.44   4.4e+02      54      91 ..      76     115 ..      64     160 .. 0.69
   2 ?   10.5   0.0   0.00034      0.33      14      57 ..     285     328 ..     273     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.44
                            AAA_25  54 alavatGkpwlg....pvapeqgkVlyvsaEdsedelrrRlr 91 
                                       a++ a+++   +    +v++e  +V+y+ aE ++  l+ R r
  gi|313126222|ref|YP_004036492.1|  76 AASEALDRLARDgtlqRVEVETDPVVYYPAEWDR--LADRER 115
                                       44444433333344447888***********998..666544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00034
                            AAA_25  14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldlalav 57 
                                       +l+a++++ ++ + +   +++ ++l+G+pg+GKt+  + + +av
  gi|313126222|ref|YP_004036492.1| 285 ELRAELREYQQDWTDRFTEQKSGVLVGPPGAGKTVTGIGILAAV 328
                                       56666666666666677899***************999888877 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.14      14      51 ..      50      89 ..      45      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                      HHHHH.HHSSB-H.HHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 14 Ytlse.ekkvvkt.kdlaerLnvspssVsemlkkLekdGy 51
                                      Y++ e e+ +v t ++  +rL+ s + +se l +L++dG 
  gi|313126222|ref|YP_004036492.1| 50 YDALEaEGRPVMTaQQTGRRLGLSQAAASEALDRLARDGT 89
                                      888888666555516789********************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00025      0.25      18      45 ..      61      88 ..      51      91 .. 0.87
   2 ?   -2.0   0.0       2.8   2.8e+03      26      35 ..     422     431 ..     421     432 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeG 45
                                      ++ ++  +rlglS+++ ++ l+rL ++G
  gi|313126222|ref|YP_004036492.1| 61 MTAQQTGRRLGLSQAAASEALDRLARDG 88
                                      7888999********************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                            HTH_24  26 rlglSpstvn 35 
                                       rlglS ++++
  gi|313126222|ref|YP_004036492.1| 422 RLGLSATPIR 431
                                       89*****986 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.7e-05     0.097       7     102 ..     310     408 ..     254     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.7e-05
                           DUF2075   7 tGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke.......ekkkkkeafeklssfinnlse 76 
                                        G +G+GKtv ++ +la++     + ++ +l+ +++l +  re++ +++        +++ +++  ++ + i ++++
  gi|313126222|ref|YP_004036492.1| 310 VGPPGAGKTVTGIGILAAV-----GGETLVLVPSRELAAQWREEILRHTslsedqiGEYHGGQKQVRPVT-IATYQT 380
                                       599****************.....99999999*******9999999988886555433333333333333.333333 PP

                           DUF2075  77 f..kkaeekkeepkedvvivDEAhrllt 102
                                          +++ +  ++++  ++++DE h + +
  gi|313126222|ref|YP_004036492.1| 381 AgmDRHRSLFDDREWGLIVYDEVHHVPS 408
                                       3467777778888899999999997655 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.15      27      66 ..     193     232 ..     182     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                           DUF4283  27 lrrvlakaWklkggvkikelgdglflfrfsseedlekvle 66 
                                       l+ ++ ++Wk +++++++ ++d++++++ +se  + +v +
  gi|313126222|ref|YP_004036492.1| 193 LETWVENQWKRANQFRLYTHEDDYVVLEAASESLMGNVAR 232
                                       789*****************************99988875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.29       3      70 ..     309     406 ..     308     424 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                                       EESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSS.................................STTHHHHH CS
                               AAA   3 lyGppGtGKTllakavakelg.vefleisgsellsk.................................yvgesekk 45 
                                       l+GppG GKT +   +   +g  +++ +   el  +                                 y+ +++++
  gi|313126222|ref|YP_004036492.1| 309 LVGPPGAGKTVTGIGILAAVGgETLVLVPSRELAAQwreeilrhtslsedqigeyhggqkqvrpvtiatYQTAGMDR 385
                                       89**********99999999734455566666665566667777777777777788888888888888888888888 PP

                                       HHHHHHHHHHTSTSEEEEEETGGGH CS
                               AAA  46 irelfkeakekakpsilfiDEidal 70 
                                        r lf++ +e      ++ DE++ +
  gi|313126222|ref|YP_004036492.1| 386 HRSLFDD-RE---WGLIVYDEVHHV 406
                                       8888877.33...257888888877 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0076       7.5       3      35 ..     308     340 ..     306     413 .. 0.77
   2 ?    2.2   0.0      0.16   1.6e+02      23      56 ..     600     638 ..     586     643 .] 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0076
                                       EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT CS
                             AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrd 35 
                                       +LvGppG gK+     ++aa++ e+++   +r 
  gi|313126222|ref|YP_004036492.1| 308 VLVGPPGAGKTVTGIGILAAVGGETLVLVPSRE 340
                                       69*********9999999988777766655554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.16
                                       B...S--EEEEE--TT--HHHHH--..B--......... CS
                             AAA_5  23 l...nreveyvqltrdtteedlkgr..reikngttslvd 56 
                                       +   +  ++yv+ tr+t+eed+ +r  r++++++ + ++
  gi|313126222|ref|YP_004036492.1| 600 MrpaGGALVYVLATRGTSEEDFAQRqmRHLAEKGVRVTE 638
                                       455567789*************98722333355555555 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00014      0.14       8     174 ..     158     334 ..     151     336 .. 0.74
   2 ?   -2.9   0.1       3.6   3.6e+03     244     272 ..     486     514 ..     472     525 .. 0.66
   3 ?   -2.5   0.1       2.6   2.6e+03      52     103 ..     590     638 ..     588     641 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                           DUF3482   8 nlhavreFDavaaefeeelrLyesLatLleekreaLqrliealeeqrqarreeaae...liaelLidvaayreeade 81 
                                       +l  +r+ D  +a+f++  +L++ ++++l++ +++L++++e+  +++++ r  + e   ++ e+  +++       +
  gi|313126222|ref|YP_004036492.1| 158 YLYKIRQEDVWQAPFDDLDALLSMMRSVLPRRSPHLETWVENQWKRANQFRLYTHEddyVVLEAASESLMGNVA-RQ 233
                                       677778889999****************************9766655555544443122666666666655554.56 PP

                           DUF3482  82 eaeeaakekllerlqekvRqrEqkcveaLl..klYkfreadleea....elpl..legrwqqDlFspetlkelGlsl 150
                                       + +e++  + +++ + +vR   ++  +++l  + Y +++++  e+    + +l  +  ++qqD  +  t ++ G+ +
  gi|313126222|ref|YP_004036492.1| 234 KLDEEHLVAPISDTESWVRDGKEAHIKRILyeAGYPIQDDRDLETgaalDVELraELREYQQDWTDRFTEQKSGVLV 310
                                       677777788889999****9888888888633678888764333211112333113358****************** PP

                           DUF3482 151 gaGaaaGAaaGagiDlavgGltLG 174
                                       g   a   ++G gi +avgG tL 
  gi|313126222|ref|YP_004036492.1| 311 GPPGAGKTVTGIGILAAVGGETLV 334
                                       *999999**************996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.6
                           DUF3482 244 eeakewtseklpeelkklekkarahpews 272
                                        ++++  ++++p+++++  + +r+hp+  
  gi|313126222|ref|YP_004036492.1| 486 GRERRQLASMNPQKIAETRRLLRQHPKSK 514
                                       33333344778888888888888888875 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.6
                           DUF3482  52 eqrqarreeaaeliaelLidvaayreeadeeaeeaakekllerlqekvRqrE 103
                                       +q ++r  ++++    +L+ v+a+r +++e+ +++++++l    ++ vR  E
  gi|313126222|ref|YP_004036492.1| 590 RQGAQRAGRTMRPAGGALVYVLATRGTSEEDFAQRQMRHL---AEKGVRVTE 638
                                       6778888888888999999999999993333333333333...344566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 3887.50
//
Query:       gi|313126223|ref|YP_004036493.1|  [L=40]
Description: hypothetical protein Hbor_14730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        76  (0.00423894); expected 358.6 (0.02)
Passed bias filter:                       69  (0.00384851); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 254.94
//
Query:       gi|313126224|ref|YP_004036494.1|  [L=750]
Description: type i restriction-modification system methyltransferase subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-05   24.9   0.0      3e-05   23.4   0.0    1.7  1  N6_Mtase         N-6 DNA Methylase
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.021   14.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
      0.051   13.6   0.1        2.4    8.2   0.1    2.5  2  Phageshock_PspD  Phage shock protein PspD (Phageshock_PspD)
       0.12   12.1   0.0       0.37   10.4   0.0    1.8  2  UPF0020          Putative RNA methylase family UPF0020
       0.13   12.1   0.0       0.29   11.0   0.0    1.6  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   8.4e-09     3e-05      24     155 ..     170     332 ..     162     388 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.4e-09
                          N6_Mtase  24 sgGeffTPrevsklivell..epksgesvyDpacGsggllvqaekvlkee..........dgktkelsiyGqeknet 88 
                                         G++ TP  + +l ve +   + ++++v+Dp cG+g++l  a++   +           +  + + s+ G ++n+ 
  gi|313126224|ref|YP_004036494.1| 170 AFGRYDTPAGLAELAVESVrnGDFTERVVLDPGCGAGAFLAAAARAKLDSlgrdgetpanSTARIANSVRGFDVNPV 246
                                       5699***************774556779*************99986444479988888655566667788******* PP

                          N6_Mtase  89 tyrLakmNlllh..g.ieykkvk.....irlgdtlekpkfe...kdkkfdvvvaNppfnqkewkektlekderfrea 154
                                       ++r a++ l+l        ++v+     + l+d+ e+   +     +++dv + Npp+ +  w++ t    +r+r++
  gi|313126224|ref|YP_004036494.1| 247 AVRAARLALVLSlrPlLSRDDVSsfaprVVLADAVETTADDaplGGTRADVLLGNPPWLT--WDSLTPRVKDRWRDG 321
                                       ******99987522212233333333565555555444444555999***********64..788888888899998 PP

                          N6_Mtase 155 ..........v 155
                                                  
  gi|313126224|ref|YP_004036494.1| 322 pmanpdldlfA 332
                                       65555555540 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.7e-06     0.021       6      45 ..     197     252 ..     193     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                   Methyltransf_31   6 rvlDlGCGtGeltfelae....elgpkae............vvGiDiseeaielAr 45 
                                       +vlD+GCG+G+++ ++a+     lg ++e            v G+D ++ a++ Ar
  gi|313126224|ref|YP_004036494.1| 197 VVLDPGCGAGAFLAAAARakldSLGRDGEtpanstariansVRGFDVNPVAVRAAR 252
                                       79****************99996666666666777889999***********9997 PP

>> Phageshock_PspD  Phage shock protein PspD (Phageshock_PspD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.046   1.6e+02      21      33 ..     176     188 ..     170     191 .. 0.87
   2 ?    8.2   0.1   0.00068       2.4      25      52 ..     238     265 ..     234     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.046
                   Phageshock_PspD  21 gPaGvAGWAvksv 33 
                                       +PaG+A  Av sv
  gi|313126224|ref|YP_004036494.1| 176 TPAGLAELAVESV 188
                                       6***********9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00068
                   Phageshock_PspD  25 vAGWAvksvArrPLkllLAvALEPlLrr 52 
                                       v G+ v  vA r  +l+L + L PlL+r
  gi|313126224|ref|YP_004036494.1| 238 VRGFDVNPVAVRAARLALVLSLRPLLSR 265
                                       67999*********************98 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0001      0.37      29      94 ..     195     253 ..     173     257 .. 0.78
   2 ?   -2.9   0.0       1.2   4.5e+03     115     132 ..     290     305 ..     277     306 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                                       TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHH CS
                           UPF0020  29 gepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgare 94 
                                       +++ lDP CG G++l  aa  + +      r+  +     a+  ar   +++g+D ++ +v++ar 
  gi|313126224|ref|YP_004036494.1| 195 ERVVLDPGCGAGAFLAAAARAKLDSL---GRDGET----PANSTARIANSVRGFDVNPVAVRAARL 253
                                       6789***********99999999998...455433....3444455555699**********9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                                       --STTS---EEEE----- CS
                           UPF0020 115 LrlkegevdvivtnpPYG 132
                                       L   +   dv+++npP+ 
  gi|313126224|ref|YP_004036494.1| 290 LG-GT-RADVLLGNPPWL 305
                                       44.33.6899******95 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     8e-05      0.29      20      62 ..     192     260 ..     164     315 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8e-05
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlre..................ngf..svtgvDlspeaveiae.......k 62 
                                       +++   vLd GcG G +l  +++                  +    sv g+D +p+av  a+        
  gi|313126224|ref|YP_004036494.1| 192 DFTERVVLDPGCGAGAFLAAAARakldslgrdgetpanstaR-IanSVRGFDVNPVAVRAARlalvlslR 260
                                       68888************9999775666666666666654432.135777888888888777666666551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4866.98
//
Query:       gi|313126225|ref|YP_004036495.1|  [L=92]
Description: hypothetical protein Hbor_14760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 585.05
//
Query:       gi|313126226|ref|YP_004036496.1|  [L=129]
Description: acyl dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-25   86.8   0.0      1e-24   86.5   0.0    1.1  1  MaoC_dehydratas  MaoC like domain
    7.8e-09   35.8   0.0    1.3e-08   35.1   0.0    1.4  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
  ------ inclusion threshold ------
      0.074   13.4   0.0       0.13   12.6   0.0    1.5  1  4HBT             Thioesterase superfamily
        0.1   12.4   0.0       0.15   11.9   0.0    1.2  1  YiiD_C           Putative thioesterase (yiiD_Cterm)


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   2.2e-28     1e-24      14     121 ..       7     110 ..       2     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 2.2e-28
                                       EEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--B CS
                   MaoC_dehydratas  14 keitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVl 90 
                                       +++ vt+++i  +a +sgD npiH+d+++A+++ fgg+IahGm  ++++++++++  gd   + + ++++ F +pV+
  gi|313126226|ref|YP_004036496.1|   7 ASLLVTKSTIDEFASLSGDNNPIHLDDDYAAETMFGGRIAHGMIAASVISAALADLPGD---IIYLSQDFEFENPVR 80 
                                       567799*****************************************************...88************* PP

                                       TTCEEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  91 pgdtlkvelevvgkrdvrktkkvevtkevte 121
                                       pgd + +++evv+ + +++ + v++t +v+e
  gi|313126226|ref|YP_004036496.1|  81 PGDNIVARVEVVE-ELGKDRIRVKTTASVDE 110
                                       *************.55555557777766655 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   2.8e-12   1.3e-08      12     102 ..       9      93 ..       3     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.8e-12
                   MaoC_dehydrat_N  12 aevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhgeqefeyhepi 88 
                                         v+++++ efa+  g+ np++ld+++a+++ +++ ia  + +  +  +a   l +l++d   ++ ++q fe+++p+
  gi|313126226|ref|YP_004036496.1|   9 LLVTKSTIDEFASLSGDNNPIHLDDDYAAETMFGGRIAHGMIAASVISAA---LADLPGD---IIYLSQDFEFENPV 79 
                                       679**********************************9998877776666...7777776...89************ PP

                   MaoC_dehydrat_N  89 raGDelttesriad 102
                                       r+GD +  + ++ +
  gi|313126226|ref|YP_004036496.1|  80 RPGDNIVARVEVVE 93 
                                       ******99888765 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.9e-05      0.13       3      58 ..      39      93 ..      37     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                                      SB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEE CS
                              4HBT  3 vvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlr 58
                                      +++gG++++ +  a  + ++   ++  ++  ++   +f  pvr+gd ++++++v++
  gi|313126226|ref|YP_004036496.1| 39 TMFGGRIAHGMIAASVISAALADLP-GDIIYLSQDFEFENPVRPGDNIVARVEVVE 93
                                      6899999999988888888888887.9999999999****************9974 PP

>> YiiD_C  Putative thioesterase (yiiD_Cterm)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.3e-05      0.15      44     106 ..      38      96 ..      33     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                            YiiD_C  44 gtmFaGSiytlatltgWglvwLqlkeaglkgdiVladakikYlkPvtedptaqvslpeeeale 106
                                       +tmF+G i+  ++ ++    ++    a+l gdi+  + + ++++Pv+    ++++++  e+l 
  gi|313126226|ref|YP_004036496.1|  38 ETMFGGRIAHGMIAAS----VISAALADLPGDIIYLSQDFEFENPVRPGDNIVARVEVVEELG 96 
                                       7**********99774....6677778999****************96655555555334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 841.85
//
Query:       gi|313126227|ref|YP_004036497.1|  [L=276]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-23   82.6   0.1    6.2e-22   78.5   0.1    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    4.8e-23   82.9   6.2    5.6e-23   82.7   6.2    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    2.5e-16   59.7   0.1    8.2e-16   58.0   0.1    1.7  1  Hydrolase_4    Serine aminopeptidase, S33
    0.00011   22.0   0.0        0.4   10.4   0.0    2.2  2  Abhydrolase_5  Alpha/beta hydrolase family
    0.00028   20.4   0.2     0.0079   15.7   0.0    2.5  2  Peptidase_S9   Prolyl oligopeptidase family
    0.00033   20.3   0.1      0.005   16.4   0.1    2.1  2  DLH            Dienelactone hydrolase family
    0.00052   20.1   0.1     0.0012   18.9   0.0    1.7  1  Abhydrolase_4  TAP-like protein
      0.001   18.9   0.0       0.02   14.7   0.0    2.6  3  Abhydrolase_2  Phospholipase/Carboxylesterase
     0.0054   16.9   0.1      0.014   15.5   0.0    1.7  2  Thioesterase   Thioesterase domain
  ------ inclusion threshold ------
      0.054   12.2   0.0      0.083   11.6   0.0    1.2  1  Ndr            Ndr family
       0.12   11.6   0.0       0.23   10.8   0.0    1.4  1  DUF915         Alpha/beta hydrolase of unknown function (DUF9
       0.12   12.3   0.0        1.2    9.1   0.0    2.0  2  UPF0227        Uncharacterised protein family (UPF0227)
        1.5    9.1   4.6         25    5.2   0.2    2.9  4  TetR_C_16      Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.1   4.5e-25   6.2e-22       2     255 ..      27     260 ..      26     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 4.5e-25
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v+l Gl+ + ++w+    a aL+  +++v+llD rG g S+++  +    y++a +a+d+d++l al++d+ ++v
  gi|313126227|ref|YP_004036497.1|  27 TVVFLEGLGYGRWMWRW--QAAALSS-RYEVVLLDNRGTGDSDAPDGP----YSIAQMAADVDAVLSALDVDEAHVV 96 
                                       69*************99..9999999.*******************75....************************* PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCH..HHHHHHHHHHHHHHHCCSCHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdg..yaadcarnpagplladelaaleq 153
                                       G SmGGmia  ya+++ +r  +l ll++   ++   ea ++  ++ +++fd   +a + ++ +  +  a   a+ e+
  gi|313126227|ref|YP_004036497.1|  97 GASMGGMIAQRYALDF-DRTTSLSLLCT---SHGGPEAVPTPPETKQRMFDVpdDADEREVIRYKMRPAMTDAFFES 169
                                       ***************8.45899999999...9999999999999999999961144455556667777777777777 PP

                                       HHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHH CS
                     Abhydrolase_1 154 rhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkal 230
                                       r++l      + +++r+ s+ +  a + +++a+ +       ds+  l  l++      ptl+++gt+D++ p +++
  gi|313126227|ref|YP_004036497.1| 170 RDDLIS----RIVDWRLASDAPEHARTAQAEAVAA------FDSSDELAALDI------PTLILHGTEDRVLPVENG 230
                                       777655....5677777775544444444444333......333333444666......***************999 PP

                                       HHHHHCHTS.....EEEEEEETCSSSHHHH CS
                     Abhydrolase_1 231 edlaqllpk.....krlvvisdagHlafle 255
                                         la+ + +     +  + ++++ Hl f+e
  gi|313126227|ref|YP_004036497.1| 231 QLLADEIAEaadaaVVFEEYDGGSHLFFIE 260
                                       999999877777777778888888888876 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   6.2     4e-26   5.6e-23       1     219 [.      28     267 ..      28     268 .. 0.69

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 4e-26
                                       EEEE--GC.....GCHHHH.HHHHCCTCEEEEE--TTSTS-GGCS--HHH...CHHHHHHHCCTT..TTSEEEEEET CS
                     Abhydrolase_6   1 vlllHGagssassWlvapL.aallaagvhvlapDlpGhGrsdpppldled...ladlaalldelaagggpvvlvGHS 73 
                                       v++l G+g+++++W+   + aa+l+++++v+ +D +G+G+sd p+  ++    +ad++a+l +l  + +++++vG S
  gi|313126227|ref|YP_004036497.1|  28 VVFLEGLGYGRWMWR---WqAAALSSRYEVVLLDNRGTGDSDAPDGPYSIaqmAADVDAVLSAL--DVDEAHVVGAS 99 
                                       79999*********4...448888***************8877776665544557777788888..59999****** PP

                                       CHHHHHHHHHHCC....EE...EEES-................----TTTS----TTHHHHHHTT-CCCCHCCHS-H CS
                     Abhydrolase_6  74 lGGalalaaapla..lvvg...vlldp..........pp....talpagllaaalelllallallrllawlsreplp 131
                                       +GG++a++   +a  ++++    ll++          pp     +++ ++ a+ +e+++  +++++++a++    ++
  gi|313126227|ref|YP_004036497.1| 100 MGGMIAQR---YAldFDRTtslSLLCTshggpeavptPPetkqRMFDVPDDADEREVIRYKMRPAMTDAFFES--RD 171
                                       ********...99873344567777777887666665446666666666688888888888888888888862..33 PP

                                       SCCCCHHHCCCCHCHCCCGHH.....HHCCHHCHTTCCHHTT-TTGCEEE.CTT-C........HHHHCHHCCCHST CS
                     Abhydrolase_6 132 rlfladedadaawrarlarla.....allaglgllpaaawadlpvpllvl.ggeDp........lvprllerllaqa 194
                                        ++++     ++wr + +++      +  a   + + +++a+l  p+l+l g+eD+        l+++ +++++  a
  gi|313126227|ref|YP_004036497.1| 172 -DLIS---RIVDWRLASDAPEhartaQAEAVAAFDSSDELAALDIPTLILhGTEDRvlpvengqLLADEIAEAAD-A 243
                                       .4444...222233333333311111333333355688*********99977****5555444433344555555.7 PP

                                       TEEETCE...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 195 garlpvvlpgaGHlphleepdevae 219
                                        +++ +++ g++Hl+++e++ +v++
  gi|313126227|ref|YP_004036497.1| 244 AVVF-EEYDGGSHLFFIEQAGAVND 267
                                       7777.9999********89899987 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.1   5.9e-19   8.2e-16       6     238 ..      27     261 ..      22     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 5.9e-19
                       Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllG 82 
                                       +vv++ Gl+   +     a+aL    ++v+ lD+rG G s+   g   s+ ++ +D++a+++++  ++      ++G
  gi|313126227|ref|YP_004036497.1|  27 TVVFLEGLGYGRWMWRWQAAALSS-RYEVVLLDNRGTGDSDAPDG-PYSIAQMAADVDAVLSALDVDE----AHVVG 97 
                                       566666655555555555555554.49**************9999.89*************9999554....567** PP

                       Hydrolase_4  83 hSmGGliallyllrypdkvaglilsaPalkikaklk.appllklllkllgkllpklqv.....snnlkadslsrdpe 153
                                        SmGG+ia++y+l+  +  + l l ++  + ++ ++ +p+ ++ +  +   +  +  +     ++ ++a + s    
  gi|313126227|ref|YP_004036497.1|  98 ASMGGMIAQRYALDFDR-TTSLSLLCTSHGGPEAVPtPPETKQRMFDVPDDADEREVIrykmrPAMTDAFFES---- 169
                                       **************999.7899999999999999998888888888888876555555444422222322223.... PP

                       Hydrolase_4 154 vvaayeadplvhgkitvrlllelldamkrleeraakit..........lPllllhGeaDkvvdpeasrelyerlgsk 220
                                             +d l+++ + +rl+ ++ + + +++++a ++           +P+l+lhG++D+v + e+ + l+++++ +
  gi|313126227|ref|YP_004036497.1| 170 ------RDDLISRIVDWRLASDAPEHARTAQAEAVAAFdssdelaaldIPTLILHGTEDRVLPVENGQLLADEIAEA 240
                                       ......344444444444444444444444444433333444444444*******************8888888776 PP

                       Hydrolase_4 221 ...dktlklypglyHellnEp 238
                                           + ++ y+g+ H  + E+
  gi|313126227|ref|YP_004036497.1| 241 adaAVVFEEYDGGSHLFFIEQ 261
                                       544788999******999996 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00058       0.8      41      85 ..      77     119 ..      67     128 .. 0.72
   2 !   10.4   0.0   0.00029       0.4      87     141 ..     198     256 ..     182     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00058
                     Abhydrolase_5  41 lgknkaeeiikeapklekfvvgGhslGGvvasrfaaeeekiegvv 85 
                                       ++ + ++ +++ a ++++  v G s+GG++a r+a + ++  ++ 
  gi|313126227|ref|YP_004036497.1|  77 MAAD-VDAVLS-ALDVDEAHVVGASMGGMIAQRYALDFDRTTSLS 119
                                       4443.445555.44578888999************9877766555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00029
                     Abhydrolase_5  87 lasYPekdelselskkvlsivgteDgvlnvkslekakkflpkdtkvvsi....eGgnha 141
                                       +a++ + del +l +++l + gteD vl+v++ +  ++ +++ +   ++    +Gg h 
  gi|313126227|ref|YP_004036497.1| 198 VAAFDSSDELAALDIPTLILHGTEDRVLPVENGQLLADEIAEAADAAVVfeeyDGGSHL 256
                                       6899999************************9988887777654433221122566665 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2     0.076     1e+02      52      78 ..      81     105 ..      39     114 .. 0.67
   2 !   15.7   0.0   5.7e-06    0.0079     124     190 ..     194     261 ..     166     276 .] 0.71

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.076
                                       HHHHHHTTS--GGGEEEEEETHHHHHH CS
                      Peptidase_S9  52 aealakegyvdserlaitGgSyGGylt 78 
                                       ++a+ +    d ++  + G+S GG+ +
  gi|313126227|ref|YP_004036497.1|  81 VDAVLS--ALDVDEAHVVGASMGGMIA 105
                                       444433..4556677788999999876 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 5.7e-06
                                       CHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEETTS-S..STTS CS
                      Peptidase_S9 124 neegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllifpdegH..gvgk 190
                                       + e   ++ + + l++   + p+L++hG++D   p++++  l+++  ++ +  v +  + +  H   + +
  gi|313126227|ref|YP_004036497.1| 194 QAEAVAAFDSSDELAA--LDIPTLILHGTEDRVLPVENGQLLADEIAEAADAaVVFEEYDGGSHlfFIEQ 261
                                       3333445555555556..99***************************77777799999999999433333 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.12   1.7e+02      86     119 ..      81     112 ..      67     130 .. 0.78
   2 !   16.4   0.1   3.6e-06     0.005     137     197 ..     204     265 ..     179     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                               DLH  86 vaylksvpevstkkvgvvGfCmGGalalllaaev 119
                                       v+++ s    ++++  vvG  mGG +a  +a   
  gi|313126227|ref|YP_004036497.1|  81 VDAVLSA--LDVDEAHVVGASMGGMIAQRYALDF 112
                                       4444444..47778899**********9998765 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.6e-06
                               DLH 137 leeaakikapilalfgeeDefipadevekleealk.aanvdlelkvYpgagHaFandsresy 197
                                        +e a +  p l+l+g+eD + p ++ + l+ +++ aa +++ ++ Y+g  H F+ +++   
  gi|313126227|ref|YP_004036497.1| 204 SDELAALDIPTLILHGTEDRVLPVENGQLLADEIAeAADAAVVFEEYDGGSHLFFIEQAGAV 265
                                       556677889********************9999862567889999**********9887655 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.1e-07    0.0012      31      93 ..     208     275 ..     183     276 .] 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.1e-07
                     Abhydrolase_4  31 akgaapvLllqnerDpaTPyegakklakalgga...vlvtvege.GHgala.agntCvdkavdaYLlt 93 
                                       a+ ++p+L+l ++ D + P e ++ la+++ +a   ++v +e + G + +  ++  +v++ ++++L++
  gi|313126227|ref|YP_004036497.1| 208 AALDIPTLILHGTEDRVLPVENGQLLADEIAEAadaAVVFEEYDgGSHLFFiEQAGAVNDRLATFLNN 275
                                       23369*************************9944556676665535555555*************986 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.42   5.8e+02      12      24 ..      23      35 ..      18      50 .. 0.79
   2 ?   -0.2   0.2      0.54   7.4e+02     102     122 ..      88     108 ..      32     125 .. 0.72
   3 !   14.7   0.0   1.5e-05      0.02     146     205 ..     201     261 ..     194     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.42
                                      ---EEEEEE--TT CS
                     Abhydrolase_2 12 kaqavviflHGlG 24
                                      +++++v+fl GlG
  gi|313126227|ref|YP_004036497.1| 23 RNAETVVFLEGLG 35
                                      678899****999 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.54
                                       --GGGEEEEEETHHHHHHHHH CS
                     Abhydrolase_2 102 ipssriiigGFSqGaalalyl 122
                                       ++ ++  ++G S+G+++a   
  gi|313126227|ref|YP_004036497.1|  88 LDVDEAHVVGASMGGMIAQRY 108
                                       455666678999999998655 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       TTTTS-GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-.GEEEEEETT--SS--HHH CS
                     Abhydrolase_2 146 lessatavtkklpilqiHgeeDpvvplalgkaakevlkkllk.kvelksyeglaHsideee 205
                                       + ss  + + ++p l +Hg+eD v+p+  g++++  + ++    v ++ y g++H    e+
  gi|313126227|ref|YP_004036497.1| 201 FDSSDELAALDIPTLILHGTEDRVLPVENGQLLADEIAEAADaAVVFEEYDGGSHLFFIEQ 261
                                       66677777889*********************999999998889**********9766555 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-05     0.014      10      85 ..      34     110 ..      27     121 .. 0.78
   2 ?   -1.9   0.0       2.2     3e+03     153     187 ..     148     178 ..     111     209 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                       TC.CSGGGHHHHHHCTTCEEEEEEECSTTST..SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHH CS
                      Thioesterase  10 gG.sasvfrslasklsdpvvevlavqlpgre..rdepplesieelaaeyaealrqiqpegPyalfGhSlGgllAfev 83 
                                        G + ++ r+ a++ls++  ev+ +  +g +  +    + si+++aa + + l +    +  +++G S+Gg++A++ 
  gi|313126227|ref|YP_004036497.1|  34 LGyGRWMWRWQAAALSSR-YEVVLLDNRGTGdsDAPDGPYSIAQMAADVDAVLSALD-VDEAHVVGASMGGMIAQRY 108
                                       555678889999999998.89999999999843333347799999999755555555.559*************998 PP

                                       HH CS
                      Thioesterase  84 Ar 85 
                                       A 
  gi|313126227|ref|YP_004036497.1| 109 AL 110
                                       86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                                       HHHHHHTCCS-TTSCSEHHCEEEEEEGSS-CTCCC CS
                      Thioesterase 153 adyraleqyslrpeaaqklratlfngsddklkdld 187
                                       ad+r +++y+ rp  ++    ++f  +dd + +++
  gi|313126227|ref|YP_004036497.1| 148 ADEREVIRYKMRPAMTD----AFFESRDDLISRIV 178
                                       45666666666665555....55555555555554 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     6e-05     0.083      81     122 ..      73     114 ..      62     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6e-05
                                       -HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGG CS
                               Ndr  81 slddladqllavldhfklksviglGvgaGAyilarfalkhpe 122
                                       s+ ++a ++ avl  ++++++  +G+  G  i  r+al ++ 
  gi|313126227|ref|YP_004036497.1|  73 SIAQMAADVDAVLSALDVDEAHVVGASMGGMIAQRYALDFDR 114
                                       899***********************************9864 PP

>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.23      86     129 ..      78     117 ..      65     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                            DUF915  86 akwlkkvlseLkkkYnikkfnavGhSmGglaltsYleeyaddks 129
                                       a+ +++vls L     ++++ +vG SmGg+ + +Y+ +     s
  gi|313126227|ref|YP_004036497.1|  78 AADVDAVLSAL----DVDEAHVVGASMGGMIAQRYALDFDRTTS 117
                                       55555555555....6899****************999876655 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00084       1.2      41      77 ..      73     109 ..      64     117 .. 0.86
   2 ?    0.7   0.0      0.31   4.3e+02     136     151 ..     213     228 ..     188     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00084
                           UPF0227  41 dpqqalkeleklvaelgddnillvGssLGGyyatrlg 77 
                                       + +q+++ +++++++l  d+  +vG s+GG  a+r +
  gi|313126227|ref|YP_004036497.1|  73 SIAQMAADVDAVLSALDVDEAHVVGASMGGMIAQRYA 109
                                       56789999*************************9876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.31
                           UPF0227 136 rilvllskqDevldyr 151
                                       ++l+l++++D vl+++
  gi|313126227|ref|YP_004036497.1| 213 PTLILHGTEDRVLPVE 228
                                       689**********985 PP

>> TetR_C_16  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.024        33      53      96 ..      12      55 ..       9      57 .. 0.85
   2 ?    5.2   0.2     0.018        25      52      91 ..      81     119 ..      73     120 .. 0.74
   3 ?   -2.0   0.2         3   4.2e+03      39      39 ..     169     169 ..     139     201 .. 0.49
   4 ?   -2.7   0.1       4.9   6.8e+03      11      30 ..     181     200 ..     171     210 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.024
                                      TTTS-STTHHHHHHHHHHHHHHHHHHHHTS--TTCCCS-HHHHH CS
                         TetR_C_16 53 aarlggpdaelRaalvasqllGlalaRyvlrleplasasreelv 96
                                      a ++ gp    R a  +  l Gl++ R+++r ++ a  sr e+v
  gi|313126227|ref|YP_004036497.1| 12 AYETRGPATPERNAETVVFLEGLGYGRWMWRWQAAALSSRYEVV 55
                                      5667788888888889999**************99999998887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.018
                                       CTTTS-STTHHHHHHHHHHHHHHHHHHHHTS--TTCCCS- CS
                         TetR_C_16  52 laarlggpdaelRaalvasqllGlalaRyvlrleplasas 91 
                                       + a l++ d +  a++v++ + G++  Ry l ++  +s+s
  gi|313126227|ref|YP_004036497.1|  81 VDAVLSALDVD-EAHVVGASMGGMIAQRYALDFDRTTSLS 119
                                       55555544444.4889***************999888875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3
                                       H CS
                         TetR_C_16  39 l 39 
                                        
  gi|313126227|ref|YP_004036497.1| 169 S 169
                                       1 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 4.9
                                       HHHHHHHHT-HHHHHHHHH- CS
                         TetR_C_16  11 vlevwepearepllallrsa 30 
                                        l+ + pe++++ +a  ++a
  gi|313126227|ref|YP_004036497.1| 181 RLASDAPEHARTAQAEAVAA 200
                                       44444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1680.43
//
Query:       gi|313126228|ref|YP_004036498.1|  [L=556]
Description: acyl-CoA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-90  304.2   0.0    1.7e-90  303.6   0.0    1.2  1  AMP-binding    AMP-binding enzyme
    9.5e-16   58.6   0.2    2.2e-15   57.4   0.2    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.6   0.0   1.9e-94   1.7e-90       2     422 ..      17     461 ..      16     462 .. 0.86

  Alignments for each domain:
  == domain 1  score: 303.6 bits;  conditional E-value: 1.9e-94
                                       HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                       e++a+  p+kv lvd  ++q++TY+eld+r+nr A+ Lr+ Gv+ g+rVa++++n+pe+v +++a++k G+v++pl+
  gi|313126228|ref|YP_004036498.1|  17 ERRAQLSPEKVGLVDATTDQSFTYAELDARANRTARLLRQYGVETGERVAVISRNRPELVDLFFATAKTGGVLAPLS 93 
                                       6899999********999*********************************************************** PP

                                       TTS-HHHHHHHHHHHTESEEE.................ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCC CS
                       AMP-binding  79 ptltaeelayiledseakvli.................atvdselleklleaaakleavklvivldadellkeeelk 138
                                        +l a+e+a +l+ +++k+l+                                   ++  +++vl+ad++ + ++  
  gi|313126228|ref|YP_004036498.1|  94 HRLAAPEIAELLTTVDPKLLViespfvelvadaraadaF-----------------DTGPSILVLSADDAGNDSDDL 153
                                       *********************654444333333333330.................444555555555555444433 PP

                                       HCCCCSCTTS........................................-TSCCCS-BTTSEEEEEEE--SSSS-E CS
                       AMP-binding 139 eeeeseekae........................................kpeeeeelkpddlayiiYTSGTTGkPK 175
                                       +++++ +                                            p e+  ++ dd+ +++ T+G+TG+PK
  gi|313126228|ref|YP_004036498.1| 154 SDAPAFA--AvptfasalpddasdpsddastpsdnastssddasdpsddaSPAEHTDVSMDDPHLFLHTGGSTGTPK 228
                                       3332222..1234556666777777777777777777888888888888866678889******************* PP

                                       EEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHH CS
                       AMP-binding 176 GVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpkllleliekl 252
                                         +l+h+ +++n  +    t ++l ++d+  ++ p++h  g+ + +   ++ G+tvv+++ ++   p+++l+li k+
  gi|313126228|ref|YP_004036498.1| 229 ETVLTHEGILWNSFNT--ITAWGLCPEDTTPMVFPMFHTGGWNVITVPLFHLGGTVVIARDFD---PAAVLRLIPKH 300
                                       ***********97774..55689889****************999999999*******99665...57789****** PP

                                       T-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHC CS
                       AMP-binding 253 kvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpl 329
                                        ++v+ +vP+vl+++ ++++ +    ++dls lr+v +gg+p+++++++++ ++ ++ +++gYGlTE+++  + +p+
  gi|313126228|ref|YP_004036498.1| 301 DASVLIAVPAVLRMMCAHDDWT----ETDLSTLRFVKSGGGPCRESVMQAWWDRDID-LSQGYGLTECGPNNFAMPD 372
                                       ***************9986555....56**************************998.*************966899 PP

                                       TTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEET CS
                       AMP-binding 330 eedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrlde 406
                                        ++++k+ svG p  +v++++vD++ g+++ +ge+Gel ++gp+ ++ Y++ pe+t+e+fd  ++w+ TGDl+r+d+
  gi|313126228|ref|YP_004036498.1| 373 GWPHEKADSVGVPAMHVDARVVDDD-GNEL-QGEVGELELSGPHAARKYWNAPEETRETFD--DGWVSTGDLARVDD 445
                                       9999********************9.7788.7****************************9..57************ PP

                                       TSEEEEEEECCCEEEE CS
                       AMP-binding 407 dGyleivgRkkdlikl 422
                                       dGy++i gRkk+++++
  gi|313126228|ref|YP_004036498.1| 446 DGYVHIEGRKKNMFVS 461
                                       *************986 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.2   2.4e-19   2.2e-15       1      73 [.     470     540 ..     470     543 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2.4e-19
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-T CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktr 73 
                                       evE a+++hp+V++a+V+G+pde++G++  a+V  +d    + eeL a++ ++l+ ++ pk vvfvde+p+  
  gi|313126228|ref|YP_004036498.1| 470 EVEDAVTAHPKVEDAVVIGIPDERWGQVGRAVVQGDDS--VTVEELSAFLDDRLARFKQPKSVVFVDEMPMSG 540
                                       8*******************************997433..367***************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 3296.65
//
Query:       gi|313126229|ref|YP_004036499.1|  [L=234]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-14   51.8   0.0    8.3e-14   51.1   0.0    1.3  1  HTH_10    HTH DNA binding domain
  ------ inclusion threshold ------
      0.035   14.0   0.0      0.078   12.9   0.0    1.6  1  MarR_2    MarR family
      0.097   12.7   0.0       0.26   11.4   0.0    1.7  1  HTH_20    Helix-turn-helix domain
       0.14   12.0   0.0       0.25   11.2   0.0    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
       0.15   12.3   0.0       0.26   11.5   0.0    1.3  1  UPF0122   Putative helix-turn-helix protein, YlxM / p13 like


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   2.3e-17   8.3e-14       1      53 []     171     223 ..     171     223 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 2.3e-17
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       L+d ++++l  A++ GYF  PR +tl +LA+e+++sk+++s+ Lr+ ++k ie
  gi|313126229|ref|YP_004036499.1| 171 LSDVERKTLESAIDGGYFQSPRSATLGSLADEFDVSKPAVSKNLRRGQRKMIE 223
                                       7899**********************************************985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.2e-05     0.078      20      46 ..     192     218 ..     184     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                                       SEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                            MarR_2  20 rdltvgelarrlglsksavsrilkrLv 46 
                                       r  t g la+++++sk+avs+ l+r +
  gi|313126229|ref|YP_004036499.1| 192 RSATLGSLADEFDVSKPAVSKNLRRGQ 218
                                       4579999*****************965 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.2e-05      0.26      11      46 ..     175     215 ..     166     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.2e-05
                                       HHHHHHHHH.....STCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  11 vRrrilraL.....araegltaselaerldlskntlsyHLr 46 
                                        R  +++a+      +++ +t++ la+++d+sk  +s++Lr
  gi|313126229|ref|YP_004036499.1| 175 ERKTLESAIdggyfQSPRSATLGSLADEFDVSKPAVSKNLR 215
                                       566677777777778999**********************8 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     7e-05      0.25      14      37 ..     192     215 ..     188     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7e-05
                                       SSEEHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  14 gelcvcelaeelglsqstvShHLk 37 
                                       ++++ + la+e+++s+++vS  L+
  gi|313126229|ref|YP_004036499.1| 192 RSATLGSLADEFDVSKPAVSKNLR 215
                                       567899**************9887 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.3e-05      0.26      36      63 ..     196     224 ..     187     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.3e-05
                           UPF0122  36 lsEiAeefnvsrqavydnikrte.kllek 63 
                                       l+ +A+ef+vs+ av+ n++r + k++e+
  gi|313126229|ref|YP_004036499.1| 196 LGSLADEFDVSKPAVSKNLRRGQrKMIER 224
                                       7789****************976256665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1500.33
//
Query:       gi|313126230|ref|YP_004036500.1|  [L=479]
Description: amino acid/amide ABC transporter substrate-binding protein, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-62  209.7  15.1    1.2e-61  209.3  15.1    1.1  1  Peripla_BP_6  Periplasmic binding protein
    1.7e-16   60.2   3.8    4.5e-16   58.8   3.8    1.6  1  Peripla_BP_5  Periplasmic binding protein domain
    1.8e-06   27.3   0.3    3.5e-06   26.3   0.3    1.3  1  ANF_receptor  Receptor family ligand binding region
  ------ inclusion threshold ------
        0.1   12.7   0.1       0.22   11.7   0.1    1.5  1  RuvA_N        RuvA N terminal domain


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.3  15.1   2.7e-65   1.2e-61       1     336 [.      67     435 ..      67     439 .. 0.93

  Alignments for each domain:
  == domain 1  score: 209.3 bits;  conditional E-value: 2.7e-65
                                       EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTT...............EETTEEEEEEEEE-TTSHHHHHHHHH CS
                      Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaG...............GinGrkielverDdaydpdraaeaar 62 
                                       ++k+G+++p+s +++++g ++l+g+   +++    G                ++G+  el +rD+++++d+a++ a+
  gi|313126230|ref|YP_004036500.1|  67 TVKLGVIQPMSTDLKYYGMQALWGFFSGMAYK---GdtdpvtgiesgeytvSVGGVDYELYVRDTKFSADTAQTLAT 140
                                       79*****************************8...66679*********99999*********************** PP

                                       HHHHCT--SEEEE-BSHHHHHHH.HHHHHHHT-EEEE.SS.....-HHCCTTSTTEEESS--HHHHHHHHHHHHHHH CS
                      Peripla_BP_6  63 rlvdqdgvdalvgplssavaaav.aevlakdgvpvig.pa.....gltgekcspyvfslgpsysaqasalveylake 132
                                       +lv++++vd+lvg+ ss++a++v ++v+ +++vp++  pa     ++++++c + +f+++++++++a+++++y+a+e
  gi|313126230|ref|YP_004036500.1| 141 DLVQSEDVDMLVGCASSGAASRViTTVAKQANVPYMVgPAasadiTGNSKTCGDMIFRAAENTAMDARSGGKYVAQE 217
                                       ***********************5557888******99663443334468*************************** PP

                                       TTSCEEEEEEESSHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHH CS
                      Peripla_BP_6 133 lggkkvalvyadyafgregiaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallka 209
                                        ++  v+l++ady+fgr+++++++ ++ka+ +e+vg  +v++g+++++ +++++ +aga+ +++++t ++l+al+++
  gi|313126230|ref|YP_004036500.1| 218 TDVQQVYLFGADYSFGRAVVNNYESVLKANNVEIVGKKFVQQGYSEWKGLLDKASEAGAQGIVGGFTVSTLPALFTT 294
                                       ***************************************************************************** PP

                                       HHHTT-SSSCEEEECCC-CHHHHHHHHHHHHT.............TEEEEESCSTCCCSHHHHHHHHHHHHHHTTGG CS
                      Peripla_BP_6 210 aaeaGldakrillvswsgseedlkalggeaae.............gvlavtpyfpdldnpavrafvaayeaayggap 273
                                       +   +++ + + ++++ ++++ + ++  +                g +++ ++++++dn+++ afv+ y +ayg+  
  gi|313126230|ref|YP_004036500.1| 295 YLNGDYNYRVFGGFATEITTSVVGQTLQKVFGkplteqklqgkqfGPFTTRYHWNQYDNDINSAFVDMYSKAYGR-- 369
                                       ********999999888888888777555544566679999999999***************************9.. PP

                                       C--HHHHHHHHHHHHHHHHHHCCTHCCHHHHHHHHHHS-.BECCCTC..CBEECTTSBEE--EEEE CS
                      Peripla_BP_6 274 ppsqfaaggyiaadlllealkaagsltreavraaleslg.fdgllgp..lkftaedhqasrpvyvv 336
                                       +p++f++g ++aa+++++a++++gs++++++++ l++++  +++ g+  ++f + ++qa ++++v+
  gi|313126230|ref|YP_004036500.1| 370 VPDLFTSGMFTAASAIVQAVEESGSTEGADIASSLRGMTvAETPKGTdgYAFQKYNNQARSAMTVA 435
                                       6**************************************99999998668888**********997 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   3.8     1e-19   4.5e-16      37     323 ..     116     423 ..     104     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1e-19
                      Peripla_BP_5  37 vlgrkieavvvdpasdwelfaekaeklieedkvevvfGcwtSasRkavlpvveelnalLfY..p...vqYEGe..Es 106
                                       v g   e  v d +  +++ ++ a++l+++++v++++Gc  S +   v+  v ++ ++ +   p       G+   +
  gi|313126230|ref|YP_004036500.1| 116 VGGVDYELYVRDTKFSADTAQTLATDLVQSEDVDMLVGCASSGAASRVITTVAKQANVPYMvgPaasADITGNskTC 192
                                       668888999**********************************9999*99999999987653331112344541134 PP

                      Peripla_BP_5 107 sknviYtGaapnqqaipavdyllselgakrvflvGsdyvypretnrilkallkakggevvgeeYlplgssdvqkiva 183
                                        + ++ +       a    +y+++e+ +++v+l G+dy + r + +  +++lka+++e+vg+++++ g s+++ +++
  gi|313126230|ref|YP_004036500.1| 193 GDMIFRAAENTAMDARSGGKYVAQETDVQQVYLFGADYSFGRAVVNNYESVLKANNVEIVGKKFVQQGYSEWKGLLD 269
                                       45555555556667777889********************************************************* PP

                      Peripla_BP_5 184 kikkak.............pdvvlstinGdsnvafykelkea....gikaekipvvslsvaeeelaaidaealvGhl 243
                                       k  +a+             p +    +nGd n++ +  ++ +     + ++   v+   ++e++l++ +     G +
  gi|313126230|ref|YP_004036500.1| 270 KASEAGaqgivggftvstlPALFTTYLNGDYNYRVFGGFATEittsVVGQTLQKVFGKPLTEQKLQGKQ----FGPF 342
                                       ***996333333333333344555558999999988777665433355566677888888888888755....5888 PP

                      Peripla_BP_5 244 aawnYfqsvdtpenkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekvreallgqel.kapeGe. 318
                                       +++ +++  d++ n+afv+ +++ +g+  v +  +   +++   ++qAve+ gst+ +++ ++l+g ++ ++p+G+ 
  gi|313126230|ref|YP_004036500.1| 343 TTRYHWNQYDNDINSAFVDMYSKAYGR--VPDLFTSGMFTAASAIVQAVEESGSTEGADIASSLRGMTVaETPKGTd 417
                                       888889999****************96..888899999999*************************99735788874 PP

                      Peripla_BP_5 319 .vkidp 323
                                         ++++
  gi|313126230|ref|YP_004036500.1| 418 gYAFQK 423
                                       445555 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.3   7.9e-10   3.5e-06      22     309 ..     118     408 ..     115     429 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 7.9e-10
                                       TEEEEEEEEE-TT-HHHHHHHHHHHCCC.CEEEEEE-SSH.HHHHHHHHHHCCTT-E.EEESS---GG.GG-TTTTT CS
                      ANF_receptor  22 giklgyeiidtccdfslaleaaldflkg.kvvaviGpsss.svsdavaslanlfkiP.visygstspe.lsdknryp 94 
                                       g++ +++++dt+ +  +a+  a d+++  +v+ ++G +ss ++s+++ ++a+++++P +++++++++   ++k+  +
  gi|313126230|ref|YP_004036500.1| 118 GVDYELYVRDTKFSADTAQTLATDLVQSeDVDMLVGCASSgAASRVITTVAKQANVPyMVGPAASADItGNSKTCGD 194
                                       678899*********************967******99988999*************78899999999555555555 PP

                                       TEEESS--CHHHHHHHHHHHH.HTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEESTCHHHCHHHHHHH CS
                      ANF_receptor  95 tflrtvpsdtsqaqAivdilk.hfgWkkvaliysdddygesglqaleeeleergicvalkekipessnddevvrkll 170
                                        ++r + ++++ a+   + +  +   ++v+l  +d + g+ +++  e  l++++++++ k+ +++     +  + ll
  gi|313126230|ref|YP_004036500.1| 195 MIFRAAENTAMDARSGGKYVAqETDVQQVYLFGADYSFGRAVVNNYESVLKANNVEIVGKKFVQQ---GYSEWKGLL 268
                                       55******99999999887755******************************************4...333344444 PP

                                       HHHTT.T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC............HHHHHTT-EE CS
                      ANF_receptor 171 keiks.karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpe..........ltgleaaegvlg 236
                                        ++++  a+ iv  +  +++  l+ +     ++ + +  +a+++ ts      ++          l+g ++   ++ 
  gi|313126230|ref|YP_004036500.1| 269 DKASEaGAQGIVGGFTVSTLPALFTTYLNGDYNYRVFGGFATEITTSVVGQTLQKvfgkplteqkLQGKQFGPFTTR 345
                                       333445999************99999887777764444445555333333333336677755555555555555555 PP

                                       EEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HHHH CS
                      ANF_receptor 237 frlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscntlk 309
                                          ++ +++  s f+         +  ++ +g+  ++ +   m+ a  ++++A+++ ++++++  a+s++ ++
  gi|313126230|ref|YP_004036500.1| 346 YHWNQYDNDINSAFV---------DMYSKAYGRV-PDLFTSGMFTAASAIVQAVEESGSTEGADIASSLRGMT 408
                                       555888888888888.........5555555555.58888899999999999999999887666655555555 PP

>> RuvA_N  RuvA N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   4.9e-05      0.22       9      55 ..     104     148 ..     103     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-05
                                       EEEESSCEEEEEETTEEEEEEE-HHHHCC..-TTSEEEEEEEEEEETTE CS
                            RuvA_N   9 vvekepdsivvevggvGYevfvplstlss..kegeevklythlivrEda 55 
                                       v+ +e ++ +v vggv Ye++v  + +s+  +     +l t l+ +Ed 
  gi|313126230|ref|YP_004036500.1| 104 VTGIESGEYTVSVGGVDYELYVRDTKFSAdtA----QTLATDLVQSEDV 148
                                       5667778889*************888877541....46*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2840.40
//
Query:       gi|313126231|ref|YP_004036501.1|  [L=288]
Description: amino acid/amide ABC transporter ATP-binding protein 1, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-23   82.3   0.0    6.6e-23   81.7   0.0    1.2  1  ABC_tran      ABC transporter
    4.5e-10   39.2   0.1    1.1e-09   37.9   0.1    1.7  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    1.8e-08   34.6   0.8    0.00062   19.7   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.5e-06   28.9   0.1    1.8e-06   28.6   0.1    1.2  1  AAA_23        AAA domain
     0.0012   18.6   0.5     0.0025   17.6   0.5    1.6  1  AAA_30        AAA domain
     0.0094   15.4   0.1       0.12   11.8   0.1    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0095   15.7   0.2      0.018   14.8   0.2    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0096   15.8   0.1      0.017   15.0   0.1    1.4  1  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.033   14.3   0.4      0.082   13.0   0.1    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
       0.13   12.6   0.1       0.55   10.5   0.0    1.9  2  AAA_22        AAA domain
       0.14   12.0   0.2       0.21   11.4   0.2    1.2  1  MukB          MukB N-terminal
       0.14   11.7   0.1       0.26   10.9   0.1    1.4  1  AAA_27        AAA domain
       0.15   11.7   0.2       0.29   10.8   0.2    1.6  1  AAA_24        AAA domain
       0.18   11.5   0.1       0.38   10.4   0.1    1.4  1  AAA_15        AAA ATPase domain
       0.43   10.1   0.1       0.43   10.1   0.1    2.0  2  FeoB_N        Ferrous iron transport protein B
       0.47   10.4   2.4        1.6    8.7   0.6    2.3  3  TsaE          Threonylcarbamoyl adenosine biosynthesis protei


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   5.9e-26   6.6e-23       2     136 ..      18     189 ..      17     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 5.9e-26
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.................B-HHHCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.................xxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke.................qeleslrke 60 
                                       + v+++l  +e+  ++G+nGaGK+t+++ll+g l+ t+G+i+++ g ++++                  ++e +   
  gi|313126231|ref|YP_004036501.1|  18 DGVDFELGGDELCSLIGPNGAGKTTFFNLLTGALTATAGTIEFRrGSESSRedggsdtdgawqdittaAPHETAAMG 94 
                                       7899*************************************888777777778999999999988877778888888 PP

                                       EEEE-SS--S-TTSBHHHH.......................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  61 igvlpqepqlfpeltvren.......................esdeeiekalsklglkelkdtvvksspssLSgGqk 114
                                       i    q +++fp++tv en                       e++ e+ ++l+++gl+e +  ++    ssLS+G+k
  gi|313126231|ref|YP_004036501.1|  95 IHRSYQITNVFPTSTVFENvriaaqangddattfwrnanhydEYETEARAILERVGLTEHASVPA----SSLSHGEK 167
                                       8888888*******************************999999999************777777....******** PP

                                       HHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 115 qrvalarallkkpkllllDEpt 136
                                       + +++  al+ +p++lllDEp 
  gi|313126231|ref|YP_004036501.1| 168 RQLEVGIALAGDPDVLLLDEPN 189
                                       *********************6 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1     1e-12   1.1e-09       1      23 []     237     259 ..     237     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1e-12
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                       ++IA+G+Pa+vr +++V++AYLG
  gi|313126231|ref|YP_004036501.1| 237 KLIADGSPADVRDNEAVQRAYLG 259
                                       69********************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   5.6e-07   0.00062       4      55 ..      32      79 ..      30      97 .. 0.78
   2 !   13.4   0.0   4.5e-05      0.05     232     292 ..     157     213 ..     109     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.6e-07
                            AAA_21  4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpe 55
                                      liGpNg+GK++++ +l ++      ++ +t+e+++g++ +  ++ +d++   
  gi|313126231|ref|YP_004036501.1| 32 LIGPNGAGKTTFFNLLTGALT----ATAGTIEFRRGSESSREDGGSDTDGAW 79
                                      9***************99876....677777777777777777777666555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.5e-05
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv 292
                                       +pa++lS G kr l +  al+ ++   ++ll+DEp +g   + +  +++l+++ ++ +  v
  gi|313126231|ref|YP_004036501.1| 157 VPASSLSHGEKRQLEVGIALAGDP---DVLLLDEPNAGVSSESVGDIIDLIEDVAT-DHAV 213
                                       899******************999...9***********************87766.4555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   1.6e-09   1.8e-06      12      63 ..      19      71 ..       9     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.6e-09
                            AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdv 63
                                      ++++++ ++ l  ++GpNGaGKTT+++ ++ aL+  +++ + ++g+ + ++d 
  gi|313126231|ref|YP_004036501.1| 19 GVDFELgGDELCSLIGPNGAGKTTFFNLLTGALTATAGTIEFRRGSESSREDG 71
                                      3445558889999**********************998888777666666654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.5   2.2e-06    0.0025      17      75 ..      26     112 ..      21     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-06
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaa.g.......................grviglAptgkaAkvLaeelgi. 68 
                                       gd ++ l Gp G+GKtt  + l+ a++a  g                       +++  +Ap ++aA  + ++ +i 
  gi|313126231|ref|YP_004036501.1|  26 GDELCSLIGPNGAGKTTFFNLLTGALTATaGtiefrrgsessredggsdtdgawQDITTAAPHETAAMGIHRSYQIt 102
                                       5678999*******************99967***************************************9998865 PP

                            AAA_30  69 ...eastiak 75 
                                          ++st+ +
  gi|313126231|ref|YP_004036501.1| 103 nvfPTSTVFE 112
                                       5556666654 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00011      0.12      26     209 ..      29     230 ..      21     239 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk............. 89 
                                       + +++GpNG+GK+ +++ +   L  ++  ++  ++ s+   + + ++ ++ a  +it   + ++             
  gi|313126231|ref|YP_004036501.1|  29 LCSLIGPNGAGKTTFFNLLTGALTATAG-TIEFRRGSESSRE-DGGSDTDGAWQDITTAAPHETaamgihrsyqitn 103
                                       5689*********999877766665443.4444444443343.3344444443333332222222233333333344 PP

                                       ...SSSSSSCEEEEEEEETTSEEEEEETTEEE-H..HHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHC CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  90 ...lkiekeevsisrrvkrkgeseykingkevtk..kevsellesagiske......lLSgGektLvalaLlfAiqk 155
                                          +++  e+v i  ++  ++ ++++ n ++  +  +e + +le++g++++      +LS Gek  + + + +A   
  gi|313126231|ref|YP_004036501.1| 104 vfpTSTVFENVRIAAQANGDDATTFWRNANHYDEyeTEARAILERVGLTEHasvpasSLSHGEKRQLEVGIALAG-- 178
                                       545555667778888887777788887777766544777788888888887777777899999988777777663.. PP

                                       CS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 156 vkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                                        +p  + llDe +a    + v  + +l++   ++  ++ + ++ +++ +++  v
  gi|313126231|ref|YP_004036501.1| 179 -DPD-VLLLDEPNAGVSSESVGDIIDLIEDVATDHAVLLVEHNMDIVMNVSDRV 230
                                       .344.5578888888888888888888888888888888888877777664444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   1.6e-05     0.018      15      50 ..      20      55 ..      12      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                            AAA_29 15 htieidlkg..atlltGpsGsGKSTllDAiqalLvpak 50
                                       ++e+   g   + l+Gp+G+GK+T++  ++  L+++ 
  gi|313126231|ref|YP_004036501.1| 20 VDFELG--GdeLCSLIGPNGAGKTTFFNLLTGALTATA 55
                                      445555..444899************977777777665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.6e-05     0.017      96     131 ..      23      59 ..      10      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                       HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       +l + +++ l+G+ G+GK+t+ n l++ l++  g + 
  gi|313126231|ref|YP_004036501.1|  23 ELGGdELCSLIGPNGAGKTTFFNLLTGALTATAGTIE 59 
                                       555558899******************9888888775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.3e-05     0.082       3      27 ..      31      56 ..      29      64 .. 0.82
   2 ?   -2.2   0.0       3.7   4.2e+03      67      67 ..     200     200 ..     164     237 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-05
                                      EEEESTTSSHHHHHHHHHTS.TEEES CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge.kaivs 27
                                       ++G   +GK+t++n ltg+ +a ++
  gi|313126231|ref|YP_004036501.1| 31 SLIGPNGAGKTTFFNLLTGAlTATAG 56
                                      689****************9655554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.7
                                       H CS
                          MMR_HSR1  67 g 67 
                                        
  gi|313126231|ref|YP_004036501.1| 200 I 200
                                       2 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00049      0.55       6      32 ..      28      54 ..      23     101 .. 0.79
   2 ?   -0.2   0.0      0.99   1.1e+03      57     116 ..     142     204 ..     107     222 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldee 32
                                       ++ ++G+ G+GKTt  + l+  l++ 
  gi|313126231|ref|YP_004036501.1| 28 ELCSLIGPNGAGKTTFFNLLTGALTAT 54
                                      56789************9999888654 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.99
                            AAA_22  57 lrellralglelka..erlsseell.ealeqalraravielliiDEaqh.lrseealeeLrsll 116
                                       +r++l+ +gl  +a  +  s+++   ++le  +  ++++ +l++DE    + s e + ++ +l 
  gi|313126231|ref|YP_004036501.1| 142 ARAILERVGLTEHAsvPASSLSHGEkRQLEVGIALAGDPDVLLLDEPNAgV-SSESVGDIIDLI 204
                                       556666666655555544444444445555555555557888888866666.655555555554 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00019      0.21      28      77 ..      29      79 ..      20     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                      HHHHHS--SHHHHHHHHHHHHHHS--TTT-----------------.---G CS
                              MukB 28 vttlsGgnGaGksttmaafvtaliPdlsllhfrntteaGatsgsrd.kGly 77
                                      + +l G nGaGk+t    +  al      ++fr  +e+  + g  d  G +
  gi|313126231|ref|YP_004036501.1| 29 LCSLIGPNGAGKTTFFNLLTGALTATAGTIEFRRGSESSREDGGSDtDGAW 79
                                      46799*****************************99998776554414555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00023      0.26      11      44 ..      11      45 ..       5      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                            AAA_27 11 yGkftdr.sldfsaeeadlhliyGpNEAGKstalr 44
                                      +G +t    +df+ + ++l  ++GpN AGK+t ++
  gi|313126231|ref|YP_004036501.1| 11 FGGLTAVdGVDFELGGDELCSLIGPNGAGKTTFFN 45
                                      666665426999999*****************986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00026      0.29       7      53 ..      32      83 ..      29     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                            AAA_24  7 iyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdie.swedfl 53
                                      ++Gp+g+GKTt+ + l    + ++  i + +G+ s   d + d   +w+d+ 
  gi|313126231|ref|YP_004036501.1| 32 LIGPNGAGKTTFFNLLtgalTATAGTIEFRRGSESSREDGGSDTDgAWQDIT 83
                                      89***********999777666666778888888888877777777777765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00034      0.38      22      43 ..      27      47 ..      20      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                            AAA_15 22 seeltvliGkNnsGKSsileal 43
                                      +e l  liG+N++GK+++ ++l
  gi|313126231|ref|YP_004036501.1| 27 DE-LCSLIGPNGAGKTTFFNLL 47
                                      44.899************9887 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00038      0.43       4      24 ..      31      51 ..      28      59 .. 0.87
   2 ?   -1.0   0.3         1   1.1e+03      73      88 ..     214     229 ..     200     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00038
                                      EEEESTTSSHHHHHHHHHTTS CS
                            FeoB_N  4 alvGnpnvGkttlfnaltgak 24
                                       l+G   +Gktt+fn ltga 
  gi|313126231|ref|YP_004036501.1| 31 SLIGPNGAGKTTFFNLLTGAL 51
                                      7999999************85 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                                       HHHCTSSSEEEEEEEG CS
                            FeoB_N  73 flleeepdvvvnvvda 88 
                                       +l+e+++d+v+nv d 
  gi|313126231|ref|YP_004036501.1| 214 LLVEHNMDIVMNVSDR 229
                                       4668888999998885 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.6    0.0015       1.6      20      44 ..      28      52 ..       4      59 .. 0.79
   2 ?    0.7   0.0      0.44   4.9e+02      66      89 ..     132     155 ..      90     166 .. 0.75
   3 ?   -3.6   0.0       9.6   1.1e+04      86     103 ..     205     222 ..     201     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                                      EEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE 20 dvilLeGdLGaGKTtlvrglakalg 44
                                      ++  L G+ GaGKTt+   l  al 
  gi|313126231|ref|YP_004036501.1| 28 ELCSLIGPNGAGKTTFFNLLTGALT 52
                                      457899**********999888775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.44
                                       EEEEE-TT-SSTHHHHHCTTCCCC CS
                              TsaE  66 lyHfDlYRledeeeleelgleeyl 89 
                                         H+D Y  e  + le++gl+e  
  gi|313126231|ref|YP_004036501.1| 132 ANHYDEYETEARAILERVGLTEHA 155
                                       78*****99999999999999875 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 9.6
                                       CCCCSTSCEEEEETGGGG CS
                              TsaE  86 eeyleeeavvlvEWpekl 103
                                       e++ +++av+lvE    +
  gi|313126231|ref|YP_004036501.1| 205 EDVATDHAVLLVEHNMDI 222
                                       555556678888876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1820.28
//
Query:       gi|313126232|ref|YP_004036502.1|  [L=234]
Description: amino acid/amide ABC transporter ATP-binding protein 2, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-31  108.4   0.0    5.1e-31  108.0   0.0    1.1  1  ABC_tran     ABC transporter
    6.2e-08   32.8   0.3     0.0026   17.6   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0012   18.5   0.0     0.0027   17.4   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.003   17.8   0.2      0.016   15.5   0.2    2.0  1  AAA_22       AAA domain
     0.0055   17.1   1.0      0.011   16.2   0.9    1.7  1  AAA_16       AAA ATPase domain
     0.0081   13.7   0.5      0.012   13.2   0.5    1.1  1  DUF3584      Protein of unknown function (DUF3584)
     0.0082   15.9   1.4      0.026   14.3   1.4    1.9  1  AAA_30       AAA domain
     0.0094   16.5   0.0      0.011   16.3   0.0    1.3  1  AAA_23       AAA domain
  ------ inclusion threshold ------
       0.01   15.8   0.0       0.02   14.8   0.0    1.4  1  NACHT        NACHT domain
      0.016   15.0   0.0      0.025   14.4   0.0    1.2  1  MukB         MukB N-terminal
      0.022   14.5   0.0      0.027   14.2   0.0    1.2  1  AAA_15       AAA ATPase domain
      0.023   14.6   0.2       0.07   13.0   0.2    1.9  1  NTPase_1     NTPase
      0.026   14.0   0.0        1.1    8.6   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
       0.03   13.9   0.5       0.28   10.7   0.1    2.2  2  AAA_25       AAA domain
       0.03   13.5   0.1       0.05   12.8   0.1    1.3  1  NB-ARC       NB-ARC domain
      0.036   13.7   0.1      0.058   13.0   0.1    1.3  1  SRP54        SRP54-type protein, GTPase domain
      0.082   13.3   0.0       0.11   12.9   0.0    1.5  1  AAA          ATPase family associated with various cellular a
      0.082   13.2   0.4       0.47   10.8   0.1    1.9  2  AAA_19       AAA domain
      0.087   12.9   0.2       0.35   11.0   0.1    2.0  2  MMR_HSR1     50S ribosome-binding GTPase
      0.088   12.7   0.0       0.16   11.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.12   11.9   0.0       0.18   11.3   0.0    1.2  1  AAA_7        P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   0.0     6e-34   5.1e-31       1     136 [.      21     163 ..      21     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 6e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l+ v+l+++ege+va+vG+nG GK+t l+ +++l+ p +G+++++g++l   +++e++++ +g++p++ ++f++ltv
  gi|313126232|ref|YP_004036502.1|  21 LEGVTLDVNEGEVVALVGRNGVGKTTTLRSIMQLTPPRKGSVRYRGTELAGlRTHEVADRGLGWIPEDRRMFSQLTV 97 
                                       6789***********************************************99************************ PP

                                       HHH.........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +en         + ++ +e+a +++++     ++ k+++ sLSgGq+q++a+ar l+ + +lll+DEp+
  gi|313126232|ref|YP_004036502.1|  98 EENirvavpdaeNVSAGLERAFETFSDLR---DHRKQKAGSLSGGQQQMLAIARGLVGENDLLLVDEPS 163
                                       *****999875555555788888777555...3334578*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.1e-05     0.044       2      20 ..      34      52 ..      33      89 .. 0.84
   2 !   17.6   0.0     3e-06    0.0026     229     287 ..     128     183 ..      68     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-05
                            AAA_21  2 nvliGpNgsGKSnLLdald 20
                                       +l+G+Ng+GK++ L+ + 
  gi|313126232|ref|YP_004036502.1| 34 VALVGRNGVGKTTTLRSIM 52
                                      68*************9984 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3e-06
                            AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                        ++  a +lS G++++la++  l   +   +lll+DEp  gL P +++ +++ l ++++
  gi|313126232|ref|YP_004036502.1| 128 HRKQKAGSLSGGQQQMLAIARGLVGEN---DLLLVDEPSEGLAPLIVEAVADALTAAAA 183
                                       34556899********88888888888...9********************99966655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.2e-06    0.0027      12      52 ..      21      62 ..      17      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.2e-06
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kv 52
                                      ++g t+++++ +++ l+G++G+GK+T l +i+ l  p+k +v
  gi|313126232|ref|YP_004036502.1| 21 LEGVTLDVNEGEVVALVGRNGVGKTTTLRSIMQLTPPRKgSV 62
                                      667889999777****************99999877776555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.9e-05     0.016       6      99 ..      32     161 ..      28     164 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee................................erpevvfvtlpss 50 
                                        +++++G  G+GKTt+lr +++  + ++   +                                   e ++v +p  
  gi|313126232|ref|YP_004036502.1|  32 EVVALVGRNGVGKTTTLRSIMQLTPPRKGSVRyrgtelaglrthevadrglgwipedrrmfsqlTVEENIRVAVPDA 108
                                       5789****************999876655544677777777666666666666666655554444444446666666 PP

                            AAA_22  51 tsskdllrellralglelkaerlsseellealeqalrarav.....ielliiDE 99 
                                       ++ +  l++ ++ + + +++ r+++   l+  +q++ a a+       ll++DE
  gi|313126232|ref|YP_004036502.1| 109 ENVSAGLERAFETFSDLRDH-RKQKAGSLSGGQQQMLAIARglvgeNDLLLVDE 161
                                       66666666666666555555.566666666666666666666666666777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.9   1.3e-05     0.011      20      51 ..      29      57 ..       7     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekd 51
                                      ++  +e+v l+G  GvGK++ +r+++ +l+  
  gi|313126232|ref|YP_004036502.1| 29 NE--GEVVALVGRNGVGKTTTLRSIM-QLTPP 57
                                      33..389*******************.56655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.5   1.4e-05     0.012       4      37 ..      17      51 ..      16      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                           DUF3584  4 dsf.lkGrvaeldldghtnieGtNaaGKTtLlrLi 37
                                      ds+ l G++  ++  + + ++G N++GKTt+lr i
  gi|313126232|ref|YP_004036502.1| 17 DSHvLEGVTLDVNEGEVVALVGRNGVGKTTTLRSI 51
                                      899889***777777889**************965 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.4     3e-05     0.026      17      47 ..      30      67 ..      24     190 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag.......g 47
                                      +  v++l+G+ G GKtt+l+++ ++   ++        
  gi|313126232|ref|YP_004036502.1| 30 EGEVVALVGRNGVGKTTTLRSIMQLTPPRKgsvryrgT 67
                                      34599*****************9998877424444433 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.3e-05     0.011      11      41 ..      22      53 ..       6     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                            AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAikl 41
                                      +++++d +   +++++G NG GKTT l+ i  
  gi|313126232|ref|YP_004036502.1| 22 EGVTLDVNEgEVVALVGRNGVGKTTTLRSIMQ 53
                                      7788888552799**************99975 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.3e-05      0.02       2      23 ..      33      54 ..      32      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                                      CEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                      +v+l G++G+GKTt l++++++
  gi|313126232|ref|YP_004036502.1| 33 VVALVGRNGVGKTTTLRSIMQL 54
                                      799****************986 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.9e-05     0.025      27      76 ..      32      82 ..      23     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                                      HHHHHHS--SHHHHHHHHHHHHHHS--TTT-----------.--------- CS
                              MukB 27 lvttlsGgnGaGksttmaafvtaliPdlsllhfrntteaGa.tsgsrdkGl 76
                                       v +l G nG Gk+tt+ +++    P    +++r t  aG  t    d+Gl
  gi|313126232|ref|YP_004036502.1| 32 EVVALVGRNGVGKTTTLRSIMQLTPPRKGSVRYRGTELAGLrTHEVADRGL 82
                                      699******************99999***********9*962455678887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.1e-05     0.027      17      43 ..      24      51 ..      20     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsileal 43
                                      v++d++e  +  l+G+N++GK++ l+ +
  gi|313126232|ref|YP_004036502.1| 24 VTLDVNEGeVVALVGRNGVGKTTTLRSI 51
                                      56777776799**************988 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   8.2e-05      0.07       2      42 ..      34      81 ..      33     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.2e-05
                                      EEEE--TTSSHHHHHHHHHHH.......H...GGGEEEEEEEEE---- CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlel.......lkssgvkvgGfyteevregg 42
                                      v++ G+ GvGKtT ++ +++l       ++ +g +++G+ t+ev ++g
  gi|313126232|ref|YP_004036502.1| 34 VALVGRNGVGKTTTLRSIMQLtpprkgsVRYRGTELAGLRTHEVADRG 81
                                      7899**************986332223367778888899999988765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0013       1.1      24      45 ..      31      52 ..       6      69 .. 0.82
   2 ?    3.6   0.0     0.044        38     136     148 ..     135     147 ..      87     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                                      SSEEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAil 45
                                       ++ a+vG+NG GK+  l +i+
  gi|313126232|ref|YP_004036502.1| 31 GEVVALVGRNGVGKTTTLRSIM 52
                                      45889**********9999984 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.044
                                       CS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvala 148
                                       +LSgG+++++a+a
  gi|313126232|ref|YP_004036502.1| 135 SLSGGQQQMLAIA 147
                                       8********9998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00033      0.28      31      50 ..      29      48 ..      18      55 .. 0.87
   2 ?    1.2   0.1      0.28   2.3e+02      68     108 ..      97     136 ..      67     190 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                            AAA_25 31 pagelallaGapgtGKttla 50
                                       +ge+++l+G+ g+GKtt +
  gi|313126232|ref|YP_004036502.1| 29 NEGEVVALVGRNGVGKTTTL 48
                                      79***************976 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.28
                            AAA_25  68 apeqgkVlyvsaEdsedelrrRlravgealrddarllvldl 108
                                       + e+++V + +aE+  ++l+r ++ ++ +lrd ++  + +l
  gi|313126232|ref|YP_004036502.1|  97 VEENIRVAVPDAENVSAGLERAFE-TFSDLRDHRKQKAGSL 136
                                       348999999999999999998887.6666644444444443 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   5.9e-05      0.05      17      42 ..      30      53 ..      21      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.9e-05
                                      TSCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqiln 42
                                      e +  vvalvG+ GvGKtt +++i++
  gi|313126232|ref|YP_004036502.1| 30 EGE--VVALVGRNGVGKTTTLRSIMQ 53
                                      445..9*************9999976 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   6.8e-05     0.058       3      22 ..      33      52 ..      31      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-05
                                      EEEEEESTTSSHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLa 22
                                      v++lvG +G+GKTttl  + 
  gi|313126232|ref|YP_004036502.1| 33 VVALVGRNGVGKTTTLRSIM 52
                                      899************97665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013      0.11       2      22 ..      35      55 ..      34     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                                      EEESSTTSSHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel 22
                                       l+G  G+GKT++ +++++ +
  gi|313126232|ref|YP_004036502.1| 35 ALVGRNGVGKTTTLRSIMQLT 55
                                      699***************986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00055      0.47       9      34 ..      30      55 ..      23      70 .. 0.86
   2 ?    0.5   0.0       0.8   6.8e+02      99     113 ..     150     164 ..      87     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00055
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivall 34
                                      + +v+++++  G GKT++l+ i++l 
  gi|313126232|ref|YP_004036502.1| 30 EGEVVALVGRNGVGKTTTLRSIMQLT 55
                                      568999****************9876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.8
                            AAA_19  99 klqeeellivDEfqd 113
                                        + e++ll+vDE ++
  gi|313126232|ref|YP_004036502.1| 150 LVGENDLLLVDEPSE 164
                                       344555999999876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00041      0.35       2      21 ..      34      53 ..      33      71 .. 0.85
   2 ?   -1.7   0.0       3.6     3e+03      24      40 ..     177     193 ..     145     230 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00041
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      va+vGr  vGK+t ++++++
  gi|313126232|ref|YP_004036502.1| 34 VALVGRNGVGKTTTLRSIMQ 53
                                      89**************9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.6
                                       EEESSSTTSSSSEEEEE CS
                          MMR_HSR1  24 aivsdkpgtTrdinegr 40 
                                       a +++ + tT+  +e +
  gi|313126232|ref|YP_004036502.1| 177 ALTAAAAETTLLLVEQN 193
                                       34444444444444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.16      98     123 ..      30      55 ..       9      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                       TTSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpel 123
                                       ++++++lvG  GvGK+t + ++++ +
  gi|313126232|ref|YP_004036502.1|  30 EGEVVALVGRNGVGKTTTLRSIMQLT 55 
                                       4599*************999988755 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.18      30      60 ..      28      58 ..      23      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                             AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldke 60
                                      ++++  v lvG  G+GKt++++++++  +++
  gi|313126232|ref|YP_004036502.1| 28 VNEGEVVALVGRNGVGKTTTLRSIMQLTPPR 58
                                      56778899***************99877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1410.63
//
Query:       gi|313126233|ref|YP_004036503.1|  [L=337]
Description: amino acid/amide ABC transporter membrane protein 1, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-40  138.2  43.8    3.4e-40  137.9  43.8    1.0  1  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9  43.8   1.9e-44   3.4e-40       2     268 .]      27     321 ..      26     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 1.9e-44
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl..........lllallvallvgaa 68 
                                       ++n+l++aa+++++A Gl+l+fg++Gv+n++hg++ ++Gay+ +l+++ l  +          +++a++va+++  a
  gi|313126233|ref|YP_004036503.1|  27 LVNGLSKAALYVMLASGLTLIFGLMGVLNFAHGSLTMIGAYLGGLVMVVLAGSaagpgtrflaFFAAVAVAFAALSA 103
                                       789***************************************9998888776679********************** PP

                      BPD_transp_2  69 vglllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.......... 135
                                       +g++l++  +r+ +d++    +ll++ + l+l  l  i    +g + ++++ + + ++   l++++           
  gi|313126233|ref|YP_004036503.1| 104 LGAVLEVGLIRTLYDRPPLYQILLTFGLTLMLDELARIVVSFYGLQPISDWQAAFATKPQILVQQVDlgiisvsgla 180
                                       ***************9977776666666666655666666666666666666666666555555555999******* PP

                      BPD_transp_2 136 ....llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.n 207
                                           l+ +l v+a++ +l+ tr+G+ +ra  e+ e+ +alG++v+rv +++f+i+ ++Ag+aG+lla+    +    
  gi|313126233|ref|YP_004036503.1| 181 lfeiLFGVLTVVAIWAFLTQTRYGLYIRAGSEDAEMIEALGVDVRRVFTFVFAIGVGIAGVAGVLLAWDPSWGASvP 257
                                       *********************************************************************99999889 PP

                      BPD_transp_2 208 igvglgfnaiaavvlGgagsllgtviGaliigvvksllltllgi...ptelarvllgallilvl 268
                                          ++ + a+++v++Gg+g+ +gtv++++i+g+v++ ++ ++++    t l ++ ++++l++vl
  gi|313126233|ref|YP_004036503.1| 258 LAAETLLPAFVVVIVGGLGTFRGTVVAGTIVGLVDATMTWWFQNaiaFTGLPQLTIFLILVVVL 321
                                       99**********************************9999999965559999*******99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2063.22
//
Query:       gi|313126234|ref|YP_004036504.1|  [L=426]
Description: amino acid/amide ABC transporter membrane protein 2, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-34  117.7  22.6    4.8e-34  117.7  22.6    1.6  2  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7  22.6   2.7e-38   4.8e-34       5     235 ..      49     316 ..      46     329 .. 0.89
   2 ?   -3.9   0.1      0.33   5.9e+03     133     144 ..     369     381 ..     347     388 .. 0.49

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 2.7e-38
                      BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl......lllallvallvgaavglllgl 75 
                                       ++  +  ++++A+++ ++ g++G +++gh++f++ Gay++ l+++   +       + ++l+++  v++a+++++g+
  gi|313126234|ref|YP_004036504.1|  49 TMIAVFYFGLFAMSFDFISGYTGYLSFGHAAFYGAGAYLVVLASNGKIPFvpvdtpFVALLVLGGFVALALAVIIGV 125
                                       56778899********************************99999988779****88888899999*********** PP

                      BPD_transp_2  76 lvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv................. 135
                                        + rl   ++++ +l++s +++++        +++ g++  ++++  +++  + ++   v                 
  gi|313126234|ref|YP_004036504.1| 126 VSFRLTGVYFAMITLGFSQVLYVFI-----RDWDYVGSNPRDGIAVLERTAPFNIGVPGVdalnlaigqlagesveg 197
                                       **********999998888888877.....5666666666666666666665555555556669************* PP

                      BPD_transp_2 136 .................llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGa 195
                                                         l+++ ++++l ++++++fGr l a++enee ara+G++++r+kl +f++s+++Ag+aG 
  gi|313126234|ref|YP_004036504.1| 198 flgfltfspaevsyymvGLVVAGCYFALQRIVHSPFGRVLIAIRENEERARAVGYDTFRYKLGAFALSAFFAGVAGG 274
                                       *************99988888889999999*********************************************** PP

                      BPD_transp_2 196 llalllgsipp..nigvglgfnaiaavvlGgagsllgtviGa 235
                                       l+a +  s+ p  ++ +    +a++a+++Gg g+++g+++G 
  gi|313126234|ref|YP_004036504.1| 275 LFAGFRRSVTPenSFYFLVAGDALLAAIIGGFGTIAGPLFGR 316
                                       ***********9999999999******************995 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.33
                      BPD_transp_2 133 viv.llalllvla 144
                                       + + +l +++vl+
  gi|313126234|ref|YP_004036504.1| 369 HAAlYLGIVFVLF 381
                                       2222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2720.44
//
Query:       gi|313126235|ref|YP_004036505.1|  [L=344]
Description: 3-oxoacyl-ACP synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-16   58.4   0.1    7.1e-13   48.6   0.0    2.9  3  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
    6.2e-10   38.8   0.3    1.2e-09   37.9   0.3    1.5  1  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
    0.00048   19.6   0.1      0.001   18.5   0.0    1.6  2  Thiolase_N     Thiolase, N-terminal domain
    0.00055   19.6   2.0       0.85    9.1   0.3    3.3  3  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7   7.8e+03      26      42 ..      22      38 ..      21      45 .. 0.72
   2 !    6.8   0.0    0.0017       7.4       2      77 ..      66     142 ..      65     144 .. 0.87
   3 !   48.6   0.0   1.6e-16   7.1e-13       1      90 []     253     342 ..     253     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                                      HHHHHHT--GGGB--TH CS
                     ACP_syn_III_C 26 avakklglpeekvvvnl 42
                                      ++a++ g+pe  vv ++
  gi|313126235|ref|YP_004036505.1| 22 QIADRSGIPETVVVEKM 38
                                      67788888887776554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0017
                                       HHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH.HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEE CS
                     ACP_syn_III_C   2 ekagltpedidalvphqanlriidavakklglpeekvvvnl.deyGntsaasiplaLdeaveegklkpgdlvllvgf 77 
                                       ++ag +p d+d+++ h    + +  +    +++e   + n  ++  +t  a+ p+a+ +  ++ +  + d++ll+g+
  gi|313126235|ref|YP_004036505.1|  66 ADAGCSPGDLDLVLYHGSEYKDYVVWNAAADVAERIGADNAyAHESYTLCAGAPVAIRHTAAQLRTGDIDTALLLGA 142
                                       6789999999999999999999888999999999977777779999****************999999999999987 PP

  == domain 3  score: 48.6 bits;  conditional E-value: 1.6e-16
                                       HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--THHHH-B-GGGHHHHHHHHHHHTT.SS-TT-EEEEEE CS
                     ACP_syn_III_C   1 LekagltpedidalvphqanlriidavakklglpeekvvvnldeyGntsaasiplaLdeaveeg.klkpgdlvllvg 76 
                                       Le++g++  d+d++ + +++++++++++++lg+      + ld +G+  +a+++la+d a++ g    +gd vl+++
  gi|313126235|ref|YP_004036505.1| 253 LEASGYDRTDLDFVALTHMKRSFHEHLIDELGVGSAGS-YYLDAFGHAQSADQILAIDAALDAGdGPTDGDVVLFLA 328
                                       7999*****************************99987.89***********************44689******** PP

                                       EETTTEEEEEEEE- CS
                     ACP_syn_III_C  77 fGaGltwgaallrw 90 
                                       +G G+tw+a++l+w
  gi|313126235|ref|YP_004036505.1| 329 AGTGYTWAATVLEW 342
                                       ************99 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.3   2.6e-13   1.2e-09       6      65 ..     114     180 ..     111     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.6e-13
                                       GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTT..HHHHTTB-EEEEEEEEEEE.....S CS
                       ACP_syn_III   6 aCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkd..rstavlfGDGAgAvvleas.....e 65 
                                        C+g+ +a+   +a +++g + ++L+ ga +  +++D+++  +s++++fG GA A+vle +     e
  gi|313126235|ref|YP_004036505.1| 114 LCAGAPVAIRHTAAQLRTGDIDTALLLGASREEDLVDYDNdrSSFMFNFGSGASAMVLESTaiegvE 180
                                       5*************************************855688999*************9654431 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.3e-07     0.001      20     112 ..      50     142 ..      33     182 .. 0.91
   2 ?   -3.5   0.0       1.2   5.2e+03     158     179 ..     248     269 ..     218     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-07
                                       TS-HHHHHHHHHHHHHHHHTS-GGGCCEE.EEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHH CS
                        Thiolase_N  20 dlsaeeLlaealkallekagvdpeevdev.ivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavala 95 
                                       d  +++++ +a+++++++ag +p ++d v + G   +    +n a  +a ++g  ++++a+    +c+ +  a+ + 
  gi|313126235|ref|YP_004036505.1|  50 DDHVSDMSVAAAEEAIADAGCSPGDLDLVlYHGSEYKDYVVWNAAADVAERIGA-DNAYAHESYTLCAGAPVAIRHT 125
                                       556899*********************87367888888****************.********************** PP

                                       HHHHHTTSHSEEEEEEE CS
                        Thiolase_N  96 aqsiaageadvvvagGv 112
                                       a ++++g++d +++ G+
  gi|313126235|ref|YP_004036505.1| 126 AAQLRTGDIDTALLLGA 142
                                       **************996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHT--HHHHHHHHHH CS
                        Thiolase_N 158 taenlakkykisReeqdefAvk 179
                                        a+  +++ + +R+++d +A+ 
  gi|313126235|ref|YP_004036505.1| 248 VADDALEASGYDRTDLDFVALT 269
                                       4666677777777777777775 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.1    0.0012       5.3      86     127 ..      51      93 ..      47     111 .. 0.76
   2 !    9.1   0.3   0.00019      0.85     168     203 ..     108     143 ..      88     152 .. 0.78
   3 ?    1.9   0.0      0.03   1.4e+02      92     111 ..     245     264 ..     231     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0012
                                       -HHHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHH....H CS
                     ketoacyl-synt  86 dpqqrllleaawealedagltpeeldgsrvgvfiGvgagdy....a 127
                                       d ++ +++ aa+ea++dag++p +ld      + G++++dy    a
  gi|313126235|ref|YP_004036505.1|  51 DHVSDMSVAAAEEAIADAGCSPGDLD---LVLYHGSEYKDYvvwnA 93 
                                       56678999**************7765...68888888888855541 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00019
                                       EEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE CS
                     ketoacyl-synt 168 svtvdtACsSslvavhaavqslrsgeadvalaGGve 203
                                       ++   t C+ + va+ +   +lr+g++d+al  G++
  gi|313126235|ref|YP_004036505.1| 108 AHESYTLCAGAPVAIRHTAAQLRTGDIDTALLLGAS 143
                                       5666799****88888888************99886 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHTS-HHTCT CS
                     ketoacyl-synt  92 lleaawealedagltpeeld 111
                                       +l++a++ale +g++ ++ld
  gi|313126235|ref|YP_004036505.1| 245 FLTVADDALEASGYDRTDLD 264
                                       799************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2275.66
//
Query:       gi|313126236|ref|YP_004036506.1|  [L=132]
Description: thioesterase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-16   58.7   0.0    9.2e-16   58.4   0.0    1.0  1  4HBT_2       Thioesterase-like superfamily
    6.1e-14   52.1   0.1    8.2e-14   51.7   0.1    1.2  1  4HBT         Thioesterase superfamily
    1.4e-10   40.9   0.1    7.6e-05   22.1   0.2    2.0  2  Acyl-ACP_TE  Acyl-ACP thioesterase


Domain annotation for each model (and alignments):
>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   1.5e-19   9.2e-16       1     121 [.      12     125 ..      12     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.5e-19
                            4HBT_2   1 vrpndvDlnghlnnarylryleearvkflertglksrsiarrgiglilssahvryrrplkfpdrltvefrvididak 77 
                                       vr++d+D+ gh+nna y  y+e+ar+++++ +      ++ + +  +l++ ++ yr+p+    +lt+ + v+++  +
  gi|313126236|ref|YP_004036506.1|  12 VRFRDLDPVGHVNNAVYATYCEQARIDYFQ-D---ALKVEGSDVNTVLANVEINYRKPIEGLGELTIALGVSEVGNT 84 
                                       899**************************5.4...45899999********************************** PP

                            4HBT_2  78 tliiehrflsnadgkkaarveerivvmdygkrskkapvPpellk 121
                                       ++ +e+++    ++  +a++  ++vv+d +++ ++ap+P+e ++
  gi|313126236|ref|YP_004036506.1|  85 SFEMEYELSF--EDEVVATASSVQVVIDPETK-EPAPIPNEWRE 125
                                       ********99..9999***************9.******99876 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.1   1.4e-17   8.2e-14       2      78 ..      21     100 ..      20     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.4e-17
                                       SSB-HHHHHHHHHHHHHHHHHHTTST...TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTS CS
                              4HBT   2 GvvhgGvylallDeaagaalrslggr...gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedg 75 
                                       G+v+++vy++++++a+ +++    +    +   v ++ +i++++p+    elt+   v+++g+ts+++e+e+  ed+
  gi|313126236|ref|YP_004036506.1|  21 GHVNNAVYATYCEQARIDYFQDALKVegsDVNTVLANVEINYRKPIEGLGELTIALGVSEVGNTSFEMEYELSFEDE 97 
                                       9********************99999999******************999**********************99998 PP

                                       CEE CS
                              4HBT  76 rlv 78 
                                       +++
  gi|313126236|ref|YP_004036506.1|  98 VVA 100
                                       775 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   1.3e-08   7.6e-05     156     183 ..       7      34 ..       2      67 .. 0.67
   2 !   18.3   0.0   1.9e-07    0.0011      57     133 ..      54     129 ..      40     132 .] 0.92

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-08
                       Acyl-ACP_TE 156 ekelkvrysDlDlnqHvNNvkYlewile 183
                                       e++l vr+ DlD  +HvNN++Y  + + 
  gi|313126236|ref|YP_004036506.1|   7 ESKLDVRFRDLDPVGHVNNAVYATYCEQ 34 
                                       7899******************876543 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.9e-07
                       Acyl-ACP_TE  57 vvakyeieierlpefgdkveietwaesenklfcyrdfkvrdekgekiieaksvfvlmdqetrrlsrvtdeilaeyee 133
                                       v a++ei+  +++e   +++i+  ++  ++   ++++++   + e++++a+sv v++d et+ ++ +++e ++ +e+
  gi|313126236|ref|YP_004036506.1|  54 VLANVEINYRKPIEGLGELTIALGVSEVGNTSFEMEYELSF-EDEVVATASSVQVVIDPETKEPAPIPNEWRERIEN 129
                                       78999**********************************99.677***************************99955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 869.05
//
Query:       gi|313126237|ref|YP_004036507.1|  [L=160]
Description: queuosine biosynthesis protein qued [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-24   84.1   0.0    8.9e-24   83.8   0.0    1.1  1  PTPS      6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
      0.022   14.7   0.1      0.043   13.8   0.0    1.4  1  GYD       GYD domain


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.0   9.9e-28   8.9e-24       6     120 ..      38     160 .]      34     160 .] 0.94

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 9.9e-28
                                       EEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHHCCS.. CS
                              PTPS   6 feFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkfl.naddpeleell.. 79 
                                       ++++a+Hrl++h+gkc++ HGHny++ v+v+g+ l ++g++vd ge+ +    +++e+Dh+fl +  dp +  +   
  gi|313126237|ref|YP_004036507.1|  38 IRISAGHRLMHHDGKCSRPHGHNYEISVEVTGQ-LTDEGWIVDKGEVTT----VIDEWDHRFLvETGDPLVSAFEas 109
                                       789******************************.*********999988....899*******888888888777** PP

                                       ............--HHHHHHHHHHHHHHHHGCCCGCEEEEEEEEETTEEEEE CS
                              PTPS  80 ...........spTaEnlaklifeelkerlqekevklskvrvwEtpnswaey 120
                                                   pTaE +a l+ ++l++rl +++v+  +v+v Et + +a+y
  gi|313126237|ref|YP_004036507.1| 110 gdadslvvldaPPTAEVMAVLLEDKLRARL-PDSVSDVAVEVRETGELCASY 160
                                       **********999*****************.99999999******9999987 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.8e-06     0.043       4      67 ..      68     132 ..      67     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-06
                               GYD   4 lvnytdegvkgl.kdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalsla 67 
                                       ++++tdeg+     + ++ ++e+ +++  + G  l s + + G+ D +v+++ap  ++++a+ l+
  gi|313126237|ref|YP_004036507.1|  68 TGQLTDEGWIVDkGEVTTVIDEWDHRFLVETGDPLVSAFEASGDADSLVVLDAPPTAEVMAVLLE 132
                                       56888999877767889999****************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1022.59
//
Query:       gi|313126238|ref|YP_004036508.1|  [L=257]
Description: organic radical activating enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-20   73.5   0.1    8.9e-20   71.7   0.1    1.9  1  Radical_SAM   Radical SAM superfamily
    3.6e-14   52.9   0.0    7.7e-14   51.8   0.0    1.5  2  Fer4_14       4Fe-4S single cluster domain
    3.3e-08   33.9   0.0    5.3e-08   33.2   0.0    1.3  1  Fer4_12       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.029   14.3   0.0       0.06   13.3   0.0    1.4  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.1     2e-23   8.9e-20       2      99 ..      42     130 ..      41     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 2e-23
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       v t gCnlrC+fC+ ++t ++e++++ + v+ei+  v +       ++v+l+ggepl +++ + llerla+    g+
  gi|313126238|ref|YP_004036508.1|  42 VRTSGCNLRCWFCDSYHT-SWEPTHAWMGVDEIVSAVTARD----PDHVVLTGGEPLIHDETAPLLERLAEH---GY 110
                                       789**************9.******************7776....9*************************8...** PP

                                       EEEEEECSSCHGHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerlle 99 
                                       ++tvetngtl+ ++    l+ 
  gi|313126238|ref|YP_004036508.1| 111 HVTVETNGTLV-PDAPIDLAS 130
                                       **********9.655444444 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   1.7e-17   7.7e-14       2      92 ..      41     121 ..      40     136 .. 0.82
   2 ?   -3.0   0.0       1.7   7.5e+03      34      57 ..     165     187 ..     154     212 .. 0.59

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.7e-17
                           Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                       fvr+sgCnl C +Cd  +    ++++ ++   +++i++ ++++  +++ +vltGGePL++   +e  +l++rl e++
  gi|313126238|ref|YP_004036508.1|  41 FVRTSGCNLRCWFCDSYH---TSWEPTHAWMGVDEIVSAVTAR--DPDHVVLTGGEPLIH---DETAPLLERLAEHG 109
                                       9*************9543...6677777777777777444444..4588*********99...8999********** PP

                           Fer4_14  79 pekkiwletngtle 92 
                                         +++++etngtl 
  gi|313126238|ref|YP_004036508.1| 110 --YHVTVETNGTLV 121
                                       ..*********986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                           Fer4_14  34 leqilkdlkkseikiqglvltGGe 57 
                                       l++  + ++ +e++ +  v+tG e
  gi|313126238|ref|YP_004036508.1| 165 LDSLATLVERHEFQLK-FVVTGPE 187
                                       4444444555555555.5556655 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.2e-11   5.3e-08       1      96 [.      28     121 ..      28     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.2e-11
                           Fer4_12   1 lnGeGvrl.....slfvsgCnlsCkgCfnket.wsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaea 71 
                                       l+GeG+ +     ++++sgCnl+C +C    t w++++ +       +ei+  +  +  + ++l+GGEPl     ++
  gi|313126238|ref|YP_004036508.1|  28 LQGEGKLVgvpstFVRTSGCNLRCWFCDSYHTsWEPTHAWM----GVDEIVSAVTARDPDHVVLTGGEPLI---HDE 97 
                                       5889965444555999***********86544255555554....36888888888999************...788 PP

                           Fer4_12  72 llelvkevkeekpekdiwlytgytl 96 
                                        ++l++++ e+++  + ++++g+  
  gi|313126238|ref|YP_004036508.1|  98 TAPLLERLAEHGY-HVTVETNGTLV 121
                                       899999*999999.58999999865 PP

>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05      0.06      70     114 ..      72     114 ..      57     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                      TP_methylase  70 ealaealragkdVvllvsGDPlvygtgselvealrareagievev 114
                                       e++ +  +++ d v+l++G Pl+++ ++ l+e+l++  +g++v v
  gi|313126238|ref|YP_004036508.1|  72 EIVSAVTARDPDHVVLTGGEPLIHDETAPLLERLAE--HGYHVTV 114
                                       4553333444578***********************..8888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1525.71
//
Query:       gi|313126239|ref|YP_004036509.1|  [L=236]
Description: preq(0) biosynthesis protein quec [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-72  241.5   0.1    6.9e-72  241.4   0.1    1.0  1  QueC           Queuosine biosynthesis protein QueC
    5.3e-05   22.9   0.0    0.00014   21.5   0.0    1.7  1  ThiI           Thiamine biosynthesis protein (ThiI)
     0.0005   19.0   0.0    0.00064   18.6   0.0    1.1  1  tRNA_Me_trans  tRNA methyl transferase
     0.0064   16.2   0.1     0.0085   15.8   0.1    1.1  1  Asn_synthase   Asparagine synthase
     0.0098   15.0   0.0      0.014   14.5   0.0    1.3  1  NAD_synthase   NAD synthase
  ------ inclusion threshold ------
      0.066   13.7   0.0       0.11   13.0   0.0    1.3  1  Usp            Universal stress protein family


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.4   0.1   2.3e-75   6.9e-72       1     209 [.       9     218 ..       9     219 .. 0.97

  Alignments for each domain:
  == domain 1  score: 241.4 bits;  conditional E-value: 2.3e-75
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG---- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdee 76 
                                       +avvllSGG+DS+t ++ ak++g+ +++l+ +Ygq+ ++ke ++a+++a+el+ ee  ++++d+l+++g s+Ltd+e
  gi|313126239|ref|YP_004036509.1|   9 TAVVLLSGGMDSATTAYEAKARGYDLYCLHTSYGQKtETKEYDCATQLAEELDAEEFLHIETDHLSDIGASSLTDDE 85 
                                       59**********************************99*************************************** PP

                                       -------...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH..HTS- CS
                              QueC  77 ievpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg..edkk 151
                                       i+v++++++ ee+p+++Vp+RN+ +ls+a+s+aea +++a+++G+++ed++gYPDcr+ef++a+++++ +g   +++
  gi|313126239|ref|YP_004036509.1|  86 IDVEDADMDAEEIPTSYVPFRNANLLSMAVSFAEANDCDAVFVGAHSEDYAGYPDCRPEFFEAFEAMVDTGtkPETN 162
                                       ***********************************************************************765689 PP

                                       -EEE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                              QueC 152 ieieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                       i ie P+++ sK++i+++g el+vp+e+t+sCY++ee   aCg+Cd+Ca R ++f+++
  gi|313126239|ref|YP_004036509.1| 163 IDIEVPFVTDSKTDIAQRGRELDVPFEHTWSCYRAEE--PACGTCDSCAYRLQAFRNV 218
                                       ***********************************55..5***************986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.8e-08   0.00014       5      58 ..       9      62 ..       6     132 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.8e-08
                              ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellae 58
                                      ++++LlSgG+DS  +ay +  RG    ++h +    t+ ++ +   +lae l  
  gi|313126239|ref|YP_004036509.1|  9 TAVVLLSGGMDSATTAYEAKARGYDLYCLHTSYGQKTETKEYDCATQLAEELDA 62
                                      789****************************87777788888888888877754 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.1e-07   0.00064       3      48 ..      10      55 ..       8      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-07
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccae 48
                                       vv+lSgG DS+ +a+  k +gy++  ++    +++++++  c ++
  gi|313126239|ref|YP_004036509.1| 10 AVVLLSGGMDSATTAYEAKARGYDLYCLHTSYGQKTETKEYDCATQ 55
                                      689**************************99999988888566543 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.8e-06    0.0085      21      86 ..      11      75 ..       5     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.8e-06
                      Asn_synthase 21 GalLSGGlDSSliaalaarqsksplktFsigf.eekgsdeakyakevaehlgtehtelvlteeelld 86
                                       +lLSGG+DS++ a+ a++    +l + +  + ++ + +e + a ++ae+l  e   l+++ ++l d
  gi|313126239|ref|YP_004036509.1| 11 VVLLSGGMDSATTAYEAKARG-YDLYCLHTSYgQKTETKEYDCATQLAEELDAE-EFLHIETDHLSD 75
                                      589*********999999977.599999999954599***************99.455555555544 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.6e-06     0.014      19      99 ..       8      88 ..       2     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-06
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSE.EEE---HHHHHHHHHHHHHH CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgie.vktidikpivrafeqelkea 95
                                      + +v+ lSGG+DS+++a+ a+          l    +++++ +++  a++lae+l+ e + +i+ ++   +  ++l+++
  gi|313126239|ref|YP_004036509.1|  8 QTAVVLLSGGMDSATTAYEAKARG--YDLYCLHTSyGQKTETKEYDCATQLAEELDAEeFLHIETDHLSDIGASSLTDD 84
                                      667888************987654..44555666559999999999********9865145566555555555555544 PP

                                      H-HH CS
                      NAD_synthase 96 kedl 99
                                      + d+
  gi|313126239|ref|YP_004036509.1| 85 EIDV 88
                                      4444 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.8e-05      0.11      24     113 ..      25     132 ..       8     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                                       HHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..................HHHHHHCTTCEE CS
                               Usp  24 elakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..................akaaaeaggvkv 82 
                                        +akarg +l++lh +  +  ++  +   +   eel+ ee    ++                   ++++ ++++++ 
  gi|313126239|ref|YP_004036509.1|  25 YEAKARGYDLYCLHTSYGQKTETKEYDCATQLAEELDAEEFLHIETDhlsdigassltddeidveDADMDAEEIPTS 101
                                       47999*********99999888888777777777777777777777699999************************* PP

                                       EEEEEESSHHHHHHHHHHHTTSSEEEEESCC CS
                               Usp  83 evvveegdpaeeilevaeeedadliVvGsrg 113
                                        v  ++ +   + + +ae++d+d + vG++ 
  gi|313126239|ref|YP_004036509.1| 102 YVPFRNANLLSMAVSFAEANDCDAVFVGAHS 132
                                       *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1539.63
//
Query:       gi|313126240|ref|YP_004036510.1|  [L=62]
Description: hypothetical protein Hbor_14910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   10.9   0.0       0.18   10.8   0.0    1.0  1  DUF3626   Protein of unknown function (DUF3626)


Domain annotation for each model (and alignments):
>> DUF3626  Protein of unknown function (DUF3626)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     1e-05      0.18     228     258 ..       9      39 ..       4      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1e-05
                           DUF3626 228 kGfklkvdkvpddfRGpampsLakriaaeev 258
                                        Gf++++ +v + fRGp + +La+r + +++
  gi|313126240|ref|YP_004036510.1|   9 DGFSVPALDVLRHFRGPFFLTLAERAHVSGF 39 
                                       79***********************987754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       149  (0.00831056); expected 358.6 (0.02)
Passed bias filter:                      134  (0.00747392); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 383.46
//
Query:       gi|313126241|ref|YP_004036511.1|  [L=484]
Description: hydroxymethylpyrimidine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   3.4e-188  625.7   0.0   3.9e-188  625.5   0.0    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  625.5   0.0  2.2e-192  3.9e-188       1     417 [.       3     422 ..       3     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 625.5 bits;  conditional E-value: 2.2e-192
                      ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkek.pvaiGkglrtkvnaniGtsadasdiee 76 
                                       tq+++ar+g++t++m++vae+env+pefvreeva+G++vipan+nh +  p++iG+ ++tkvnaniG+s+++s+ ee
  gi|313126241|ref|YP_004036511.1|   3 TQFQHARDGETTDAMRRVAERENVSPEFVREEVAAGHAVIPANHNHASLdPMIIGEAFSTKVNANIGNSEETSSREE 79 
                                       899*******************************************6655*************************** PP

                      ThiC_Rad_SAM  77 EveKlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvd 153
                                       E++Kl++a++ gadtvmdLstg+++d++re+ ++ spvpvgtvpiY+a++++  +  ++t+e ll+vi++qae+Gvd
  gi|313126241|ref|YP_004036511.1|  80 ELKKLHMAIHHGADTVMDLSTGQNLDDVREANVRYSPVPVGTVPIYEAVKQV-DDPDDITHELLLDVIRKQAEQGVD 155
                                       *************************************************965.899********************* PP

                      ThiC_Rad_SAM 154 fltiHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaD 230
                                       ++tiHagv +e+l+l++  +R tgivSrgGs+la+wm++n  +nply +f+e++e+++eydvt+SlgdglRpG+iaD
  gi|313126241|ref|YP_004036511.1| 156 YMTIHAGVLMEHLPLTD--GRKTGIVSRGGSILAKWMEENAMQNPLYVHFEEICEVFAEYDVTFSLGDGLRPGCIAD 230
                                       ****************9..********************************************************** PP

                      ThiC_Rad_SAM 231 atdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsai 307
                                       a deaq+ael++lgelv  ar++gvq+mveGPGHvpld ++++v+ ++++c++aPfy+lGplvtDiapgYDhitsai
  gi|313126241|ref|YP_004036511.1| 231 AGDEAQYAELETLGELVGIARDHGVQAMVEGPGHVPLDMVAEQVEREREVCDGAPFYLLGPLVTDIAPGYDHITSAI 307
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 308 GaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelal 384
                                       Ga+ aa aGa++lCyvtp+EHlglPd+edv++G+ a++iaaha+d+a gl++ar++d+als+aR+++dw++qf+lal
  gi|313126241|ref|YP_004036511.1| 308 GATEAARAGAAMLCYVTPKEHLGLPDAEDVRDGLAAYRIAAHAGDVAAGLPGARDWDDALSEARYAFDWRRQFDLAL 384
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 385 dpekareireeklpe....eeeaCsmCgek.Cavkive 417
                                       dpe+a+++++++lp     e+++CsmCg   C+++i +
  gi|313126241|ref|YP_004036511.1| 385 DPERAQDYHDQTLPGdnykEARFCSMCGVEfCSMRIDQ 422
                                       ************987777799*******888****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3301.75
//
Query:       gi|313126242|ref|YP_004036512.1|  [L=360]
Description: cysteine transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-28   99.3  30.4    5.3e-16   59.0  12.7    2.1  2  EamA           EamA-like transporter family
  ------ inclusion threshold ------
          5    7.7   6.2         12    6.4   0.3    2.8  2  GTA_holin_3TM  Holin of 3TMs, for gene-transfer release


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   9.7   4.5e-16     4e-12       7     135 ..      13     139 ..       8     141 .. 0.92
   2 !   59.0  12.7     6e-20   5.3e-16       2     136 ..     182     316 ..     181     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 4.5e-16
                              EamA   7 allaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvlafllf 82 
                                       +++a+l  +++++l ++  ++ ++l  + +r ++   ll ++a+ + +   ++l+++d+l+  + g ++ ++ f  +
  gi|313126242|ref|YP_004036512.1|  13 LVVAVLAVSASAILVRY--SEAPSLVKALYRVVFTVSLLAPVAFARSREElRELPRRDLLWAGVAG-VALAVHFASW 86 
                                       56778888888888877..69999*************************************88888.799******* PP

                              EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       f +l  ts++  + ++  +P+f++i +++ll e++t    +gi+++l+G + +
  gi|313126242|ref|YP_004036512.1|  87 FESLAWTSVAASVTLVQAQPLFVAIGAWALLDERITRGVAVGIAVALFGMATM 139
                                       *************************************************9876 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 6e-20
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                        g+ lal++a++ a+y ++ + l +++s + +++v +++++++ll ++l ++++l  +  ++w l++ +++ ++v++
  gi|313126242|ref|YP_004036512.1| 182 YGDALALVGAVTAAAYVLAGRSLRQRISLIPYVTVVYTVCALVLLGFTLARGHPLFDYAAREWVLFVAMAVGPGVFG 258
                                       6899***************************************************7777778*************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       + ++++al ++++s++s+ ++ eP+ ++ l+ +ll e +t ++++g +++l+G++l++
  gi|313126242|ref|YP_004036512.1| 259 HTVLNWALGYVESSVVSVSLLGEPIGSTALALILLSEIPTPMTIFGGAVVLIGIYLTT 316
                                       *******************************************************986 PP

>> GTA_holin_3TM  Holin of 3TMs, for gene-transfer release
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.2     0.014   1.2e+02      81     117 ..      42      77 ..       9     117 .. 0.69
   2 ?    6.4   0.3    0.0014        12      74     117 ..     266     309 ..     265     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.014
                     GTA_holin_3TM  81 lllwaivldPllaaaialglalvPe.pLwwllggvvgf 117
                                       +++ + +l P+++a   + l+++P  +L+w   gv g+
  gi|313126242|ref|YP_004036512.1|  42 VVFTVSLLAPVAFARSREELRELPRrDLLW--AGVAGV 77 
                                       555555666666666666666666653322..222222 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0014
                     GTA_holin_3TM  74 lgyvtlalllwaivldPllaaaialgl.alvPepLwwllggvvgf 117
                                       lgyv   +++++++ +P+  +a+al l  ++P p ++++gg+v +
  gi|313126242|ref|YP_004036512.1| 266 LGYVESSVVSVSLLGEPIGSTALALILlSEIPTP-MTIFGGAVVL 309
                                       7999999999***************999999999.7788877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2439.67
//
Query:       gi|313126243|ref|YP_004036513.1|  [L=651]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-22   78.5   0.0    9.3e-21   74.1   0.0    2.4  2  Response_reg  Response regulator receiver domain
    1.7e-17   63.9   0.0    4.7e-17   62.5   0.0    1.8  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    8.8e-13   48.1   2.8      3e-12   46.4   0.2    2.8  3  HisKA         His Kinase A (phospho-acceptor) domain
    2.2e-08   34.1   0.0    6.2e-08   32.6   0.0    1.8  1  PAS           PAS fold
    1.7e-06   28.2   1.4    8.4e-06   26.0   0.1    2.7  3  PAS_4         PAS fold
    3.6e-06   27.6   0.0      2e-05   25.2   0.0    2.3  3  GAF           GAF domain
    5.1e-05   23.5   0.0    0.00013   22.2   0.0    1.7  1  PAS_9         PAS domain
    6.6e-05   23.1   0.0    0.00018   21.7   0.0    1.8  1  PAS_3         PAS fold
    0.00012   22.4   0.0    0.00052   20.3   0.0    2.2  1  GAF_2         GAF domain
    0.00046   20.1   0.3     0.0024   17.9   0.1    2.2  2  PAS_8         PAS domain
     0.0034   17.6   0.0      0.021   15.1   0.0    2.4  2  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain
     0.0051   16.8   0.1      0.012   15.5   0.1    1.6  1  HATPase_c_2   Histidine kinase-like ATPase domain
     0.0075   16.1   0.0      0.017   14.9   0.0    1.5  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
     0.0093   16.3   0.0      0.044   14.1   0.0    2.2  2  GAF_3         GAF domain
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.079   13.0   0.0    2.0  2  SpoVT_C       Stage V sporulation protein T C-terminal, trans
       0.18   11.5   0.2       0.48   10.2   0.1    1.8  2  SPOB_a        Sensor_kinase_SpoOB-type, alpha-helical domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0   8.3e-24   9.3e-21       1     105 [.      10     119 ..      10     125 .. 0.90
   2 ?    1.6   0.0      0.26   2.9e+02       5      27 ..     193     215 ..     190     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 8.3e-24
                                       EEEESSSHHHHHHHHHHHH....HTTEEEEEEESSHHHHHHHH..HHHHESEEEEESSCSSSEHHHHHHHHHHCTTT CS
                      Response_reg   1 vlivdDdplvrellrqlle....eegyeevaeaedgkealell..keekvdlillDinmpgmdGlellkeireedpe 71 
                                       vl vdD+p + +l++++le    + ++ +v++a+++++al ll   ++++d+i+ D +mp+m+Glell+ +r++ p+
  gi|313126243|ref|YP_004036513.1|  10 VLYVDDEPELSSLVATYLEreaaDVHL-SVETATNPSDALGLLsdAQDDFDCIVSDYEMPEMNGLELLRAVRATRPN 85 
                                       799****************55433344.999************655566**************************** PP

                                       SEEEEEESSTSHHHHHHHHHCTESEEEESSG-HH CS
                      Response_reg  72 lpviiltahseeedavealkagaddflsKpfdpe 105
                                       lp i++t++++ee+a +a+++ga d+++K    +
  gi|313126243|ref|YP_004036513.1|  86 LPFILYTGKGSEEVARDAFRVGATDYMQKTTGTD 119
                                       *****************************98766 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                                       SSSHHHHHHHHHHHHHTTEEEEE CS
                      Response_reg   5 dDdplvrellrqlleeegyeeva 27 
                                       dD++++r+ l +l+ ++g+e+++
  gi|313126243|ref|YP_004036513.1| 193 DDEQKIRDELDRLFAKDGVETTR 215
                                       9*****************96554 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   4.2e-20   4.7e-17       2     110 ..     539     641 ..     538     643 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 4.2e-20
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlG 77 
                                       d +rL+q++ nlv Nav++   ++++++++ +  ++  + veD+G+Gip++d+  +fe  +++      +  g+G+G
  gi|313126243|ref|YP_004036513.1| 539 DASRLTQVFENLVRNAVEH--GGDDVTISVGPLPQTPGFYVEDDGPGIPEADRSAVFEqGHTT------SEDGSGFG 607
                                       789***************9..7899999999744699********************966666......789***** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEE.EEES CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftf.tlpl 110
                                       lsiv+ +ve +g +i v++ +++G +f + t+p 
  gi|313126243|ref|YP_004036513.1| 608 LSIVEGIVEAHGWTIGVTEGSDGGARFEIiTAPH 641
                                       ***************************9767776 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.1   4.6e+03      20      47 ..     246     272 ..     245     275 .. 0.70
   2 !   46.4   0.2   2.7e-15     3e-12       2      65 ..     440     498 ..     439     500 .. 0.94
   3 ?    0.3   0.0      0.64   7.1e+02      32      58 ..     524     550 ..     512     555 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.1
                                       HHHHHHHHHC..T-HSSCHHHHHHHHHH CS
                             HisKA  20 ilgnaeaLkregklteelkeyletiese 47 
                                       + g+++   ++ +  +e  +yl+++++ 
  gi|313126243|ref|YP_004036513.1| 246 VVGTLHGVTEQ-RGQQERDQYLARLKDA 272
                                       56778887554.3457888899998875 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 2.7e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l++f++ v+H+Lr+P++++ g+ e+ ++           l+++ +  +r+d+lv+d+L+l+r +
  gi|313126243|ref|YP_004036513.1| 440 LEEFASVVSHDLRNPMNVVDGFMELARD-----TGDVSHLDRAMDALDRMDALVNDVLELARQG 498
                                       789***********************99.....778889**********************986 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.64
                                       T-HSSCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  32 klteelkeyletiesearrldhlvedl 58 
                                       ++t el + l+t+   a rl+++ e+l
  gi|313126243|ref|YP_004036513.1| 524 EATLELDDDLATVSADASRLTQVFENL 550
                                       56778899999***********99998 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   5.5e-11   6.2e-08       1     111 [.     142     251 ..     142     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.5e-11
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCC CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrage 76 
                                       e++++++e+l +++ vvDe+g ++ v + + el G++re +lg +++ +++++d++ ++ el +  +++g e + +e
  gi|313126243|ref|YP_004036513.1| 142 ERYDSVFEALETAVYVVDESGQFVSVDDVFVELIGYDRETILGNHVS-SLSPDDEQkIRDELDRLFAKDGVETTRFE 217
                                       6899*******************************************.55566666255555555677888889999 PP

                                       EEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                               PAS  77 isfklrdgrpihlevraspvrdaggeilgflgvlr 111
                                       +++++  ++ ih+  ++s   ++gg    ++g+l+
  gi|313126243|ref|YP_004036513.1| 218 TDVCTASKERIHCIATMSFKSFEGGAQ-RVVGTLH 251
                                       999999999999999999888888865.7777776 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   7.5e-09   8.4e-06       1     109 [.     148     257 ..     148     258 .. 0.75
   2 ?   -1.5   0.0       2.7     3e+03      67     107 ..     428     470 ..     417     472 .. 0.71
   3 ?   -1.1   0.1         2   2.2e+03      37      74 ..     498     535 ..     495     558 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.5e-09
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvleg.eepiefleelll.. 74 
                                       +++l  a++v+d+ g+++ +   + el+g+++e++lG ++ +l p+ d + +++ l+r+ +  +   ++ e+     
  gi|313126243|ref|YP_004036513.1| 148 FEALETAVYVVDESGQFVSVDDVFVELIGYDRETILGNHVSSLSPD-DEQKIRDELDRLFAKdGVETTRFETD-Vct 222
                                       6889999***********************************8888.66666666666555414333333322.246 PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                         +er++ +  + ++  +G+++ v+++++ +Te+r
  gi|313126243|ref|YP_004036513.1| 223 ASKERIHCIATMSFKSFEGGAQRVVGTLHGVTEQR 257
                                       555555556666667789***************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                             PAS_4  67 efleelll..pgeerhyelrllPlrdesGevigvlvisrDiTe 107
                                       +++  l+   ++ e++ ++  + lr++   v+g+++++rD+ +
  gi|313126243|ref|YP_004036513.1| 428 QRERQLRQqnERLEEFASVVSHDLRNPMNVVDGFMELARDTGD 470
                                       4444444454566777777778899999999999999999865 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2
                             PAS_4  37 Gktlaellpeedaarleralrrvlegeepiefleelll 74 
                                       G+t+ e  p ++ + ++ra+ +v +ge+++e  + l +
  gi|313126243|ref|YP_004036513.1| 498 GRTVGETSPVDLTGVVRRAWSAVETGEATLELDDDLAT 535
                                       77888877888889999999999999999988777666 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.3   8.2e+03      15      35 ..     173     193 ..     149     235 .. 0.50
   2 !   25.2   0.0   1.8e-08     2e-05       8     130 ..     294     421 ..     287     424 .. 0.67
   3 ?   -2.1   0.0       4.9   5.4e+03       4      42 ..     545     590 ..     542     640 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.3
                                       HHHTESEEEEEEEEETTEEE.....C CS
                               GAF  15 ellgadrvalylpdydGlhy.....d 35 
                                       el g+dr ++     +G+h+     d
  gi|313126243|ref|YP_004036513.1| 173 ELIGYDRETI-----LGNHVsslspD 193
                                       4444444333.....23232332221 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.8e-08
                                       HHHHHHHHHHTESEEEEEE....EEETT..E.EECEEEEECCEEEETTSHHHH......HHHHHSSSEEESTGGTST CS
                               GAF   8 tvveelrellgadrvalyl....pdydG..l.hydipqasrwlfmkngrgicg......qvlatgqplvipdstpdp 71 
                                        ++++l+e+ ++d +a+y        d     h+  +  ++++ ++++rg  +      + l+  + ++ +d     
  gi|313126243|ref|YP_004036513.1| 294 WTLQSLGEFADVDGAAVYSydsdV--DAlqKtHE-WTIDDQFPLPSTVRG--DdwtwflERLRCFENVRATD----A 361
                                       5899*************9744321..22111133.555555566666888..66655553333333333333....2 PP

                                       THHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE.SSS.CSHHHHHHHHHHHHHHHH CS
                               GAF  72 rfaqynrrdllenmgirsslvvPlvndgelwGllvlhn.psp.pftreelellqvladqva 130
                                         + + +++ l  ++  s+l++P+v++  l+G+++l + +   ++++ e+ l+ + ad+++
  gi|313126243|ref|YP_004036513.1| 362 STLSPSEPEPLCLPENGSFLALPMVSNWSLVGAVTLMStT-SrQWSDKEVSLFGTAADMLS 421
                                       22222345566677999*********************54.459*************9987 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHHHHTESEEEEEE........EEETTEEE......CEEEEECC CS
                               GAF   4 elldtvveelrellgadrvalyl........pdydGlhy......dipqasrw 42 
                                       ++++++v+ + e+ g d v++                 y      +ip+a+r 
  gi|313126243|ref|YP_004036513.1| 545 QVFENLVRNAVEHGG-DDVTISVgplpqtpgF------YveddgpGIPEADRS 590
                                       566667777777666.5556644444322220......122233334444444 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.1e-07   0.00013       3     104 .]     154     255 ..     152     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirknget 75 
                                       ++ +++++g  +++ + + +l+Gy++e +lg +++ l    p++++++r+ l+++      +  ++e++  + + e+
  gi|313126243|ref|YP_004036513.1| 154 AVYVVDESGQFVSVDDVFVELIGYDRETILGNHVSSLS---PDDEQKIRDELDRLFAkdgvETTRFETDVCTASKER 227
                                       566778********************************...777777777777777778889999********9*99 PP

                             PAS_9  76 fwvlltaspvkdd.dgelvgiivilrDite 104
                                       +++ +t+   + + +g+ ++++++l+ +te
  gi|313126243|ref|YP_004036513.1| 228 IHCIATM--SFKSfEGGAQRVVGTLHGVTE 255
                                       9966665..444447777778888887776 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.6e-07   0.00018       2      88 ..     165     249 ..     164     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge..pyegeyRirrkdGeyrwveararvir 76 
                                       ++v++ + e++Gy++e +lg+   + + + p+D +++r++l+++++k++     +e  +++++ e ++  a+++   
  gi|313126243|ref|YP_004036513.1| 165 VSVDDVFVELIGYDRETILGN---HVSSLSPDDEQKIRDELDRLFAKDGveTTRFETDVCTASKERIHCIATMSFK- 237
                                       7899*****************...*********************8888533366677777766666666655543. PP

                             PAS_3  77 dengkpvrvigv 88 
                                       + +g  +rv+g+
  gi|313126243|ref|YP_004036513.1| 238 SFEGGAQRVVGT 249
                                       556666666665 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.7e-07   0.00052       2     138 .]     283     425 ..     282     425 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.7e-07
                                       HHHHHHHHHHHHHHHHSS......EEEEEEE-TTS-..EEEEEEEES-TTSTT-S-B---TT..HHHHHHHHTS-EE CS
                             GAF_2   2 adleelldlvldelvelg.aa...lgyillvdddgg..lrlaawgeaeeefgaaldrplgeg..lvgealrtgrpvi 70 
                                       a+++e+   ++ +l+ lg +a    + ++ +d d +   +++ w+ ++ +   ++ r  g+   ++ e lr  + v 
  gi|313126243|ref|YP_004036513.1| 283 AEVDEIGTKIHWTLQSLGeFAdvdGAAVYSYDSDVDalQKTHEWTIDDQFPLPSTVR--GDDwtWFLERLRCFENVR 357
                                       577888888888888886555466667777775533223366777666666666622..333122334444445788 PP

                                       ES-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  71 lndleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                        +d  +   + ++p+  +  +sfla+P++s+  +vG+++l ++  +++++ +++l+ + a+ ++  +e
  gi|313126243|ref|YP_004036513.1| 358 ATDASTLSPSEPEPLCLPENGSFLALPMVSNWSLVGAVTLMSTTSRQWSDKEVSLFGTAADMLSYTLE 425
                                       88888899999999**********************************************99987775 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   2.1e-06    0.0024       1      60 [.     142     199 ..     142     211 .. 0.72
   2 ?   -1.2   0.0       2.1   2.3e+03      21      58 ..     428     464 ..     411     472 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle.dae 60 
                                       er+ ++fe++  ++ vvd  g+ +v v + + el Gy+ + ++g    + +  l p  e  ++
  gi|313126243|ref|YP_004036513.1| 142 ERYDSVFEALETAVYVVDeSGQ-FVSVDDVFVELIGYDrETILG----NHVSSLSPDDEqKIR 199
                                       79****************6666.*************88554444....444444444443333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                             PAS_8  21 d...rivdvNqaalellGysadlkgellgqllpvlrplled 58 
                                       +   ++++ N++ +e+      +   +l++ ++v+++ +e 
  gi|313126243|ref|YP_004036513.1| 428 QrerQLRQQNERLEEFAS----VVSHDLRNPMNVVDGFMEL 464
                                       233346666777777665....6666666666666666654 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-05     0.021      17      85 ..      35     106 ..      18     134 .. 0.79
   2 ?   -1.7   0.0       3.2   3.5e+03      83     105 ..     455     475 ..     451     480 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                        OKR_DC_1_N  17 gfevvgvtstdDllsvie.qnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlre 85 
                                       + +v ++t+ +D+l +++ ++ + +++v +++    +  ell+++r++ ++lP  l++  + se+v +d++r 
  gi|313126243|ref|YP_004036513.1|  35 HLSVETATNPSDALGLLSdAQDDFDCIVSDYEmpeMNGLELLRAVRATRPNLPFILYTG-KGSEEVARDAFRV 106
                                       56788999999999888626889***********9999***************888876.8999999888875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.2
                        OKR_DC_1_N  83 lreidgfielledtpefiarqie 105
                                       ++ +dgf+el+ dt +   +++ 
  gi|313126243|ref|YP_004036513.1| 455 MNVVDGFMELARDTGD--VSHLD 475
                                       67899********988..55555 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.1e-05     0.012      36     111 ..     547     617 ..     513     632 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                       HATPase_c_2  36 veEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDe 111
                                        e ++ Naveh+      ++v++++   +++  + v+D+Gpg + +++    e++ ++s++ +G+Gl +++g+v+ 
  gi|313126243|ref|YP_004036513.1| 547 FENLVRNAVEHGG-----DDVTISVGPLPQTPGFYVEDDGPGIPEADRSAVFEQGHTTSEDGSGFGLSIVEGIVEA 617
                                       5556789999998.....5899999999**************888888888888999***************9986 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-05     0.017       8      62 ..     548     601 ..     541     611 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                       HATPase_c_3   8 aelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                                         lv+N+++     v+i+v   + +t  + +eDdG G++e++   +++ ++++ e
  gi|313126243|ref|YP_004036513.1| 548 ENLVRNAVEHGGDDVTISVGPLP-QTPGFYVEDDGPGIPEADRSAVFEQGHTTSE 601
                                       579*****************987.79****************9999988877665 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.4   7.2e+03       9      35 ..     140     166 ..     135     168 .. 0.78
   2 !   14.1   0.0     4e-05     0.044       9     129 .]     295     426 ..     289     426 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.4
                             GAF_3   9 llkllvkllgaevgalllldedgnklq 35 
                                       + +++ +++ a   a++++de g+++ 
  gi|313126243|ref|YP_004036513.1| 140 ATERYDSVFEALETAVYVVDESGQFVS 166
                                       56677778888888999***9998876 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4e-05
                             GAF_3   9 llkllvkllgaevgalllldedgnklqvaagwdgkpalse.sldedsalarralssgevvsepsfaeedg....... 77 
                                       +l+ l +  +++ +a++ +d d + lq ++ w+  ++++  s ++++    ++++ +    +  ++++d+       
  gi|313126243|ref|YP_004036513.1| 295 TLQSLGEFADVDGAAVYSYDSDVDALQKTHEWTIDDQFPLpSTVRGDD---WTWFLERLRCFENVRATDAstlspse 368
                                       577788888999999999999999999999994444332223334444...33333333333333333322222222 PP

                             GAF_3  78 ......lpdraalavPLvagr.qviGvlalastkprafdaedlelleslArqiataier 129
                                              + ++ la+P+v+ +  ++G + l+st  r++++++++l+ + A+ ++  +er
  gi|313126243|ref|YP_004036513.1| 369 peplclPENGSFLALPMVS-NwSLVGAVTLMSTTSRQWSDKEVSLFGTAADMLSYTLER 426
                                       223332347999*******.55*****************************99999887 PP

>> SpoVT_C  Stage V sporulation protein T C-terminal, transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.3   2.6e+03       6      27 ..     140     161 ..     137     189 .. 0.83
   2 ?   13.0   0.0     7e-05     0.079      79     126 .]     379     425 ..     358     425 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.3
                           SpoVT_C   6 akeyaeslaetlghivlitDrd 27 
                                       a+e  +s++e+l+ +v ++D+ 
  gi|313126243|ref|YP_004036513.1| 140 ATERYDSVFEALETAVYVVDES 161
                                       6677899999******999975 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7e-05
                           SpoVT_C  79 aqviaPIiaeGdviGaVillskeekkklgelekklaetaAsFLgkqme 126
                                       + ++ P +++   +GaV l+s+++++  ++ e+ l  taA+ L+  +e
  gi|313126243|ref|YP_004036513.1| 379 SFLALPMVSNWSLVGAVTLMSTTSRQ-WSDKEVSLFGTAADMLSYTLE 425
                                       56789***************999776.8***************98776 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       7.2     8e+03      36      54 ..     141     159 ..     139     165 .. 0.74
   2 ?   10.2   0.1   0.00043      0.48      17      60 ..     445     488 ..     428     490 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.2
                            SPOB_a  36 Lgkydkaeeyieevvkelk 54 
                                       +++yd + e +e +v  + 
  gi|313126243|ref|YP_004036513.1| 141 TERYDSVFEALETAVYVVD 159
                                       6899999999988876555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00043
                            SPOB_a  17 rsqRHDflNhLQvIsGylqLgkydkaeeyieevvkelkeeskil 60 
                                       ++  HD  N + v++G+++L + +  ++++++++++l ++  ++
  gi|313126243|ref|YP_004036513.1| 445 SVVSHDLRNPMNVVDGFMELARDTGDVSHLDRAMDALDRMDALV 488
                                       5669***************************9999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 4190.45
//
Query:       gi|313126244|ref|YP_004036514.1|  [L=73]
Description: hypothetical protein Hbor_14950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.24   10.8   2.7       0.28   10.6   2.7    1.0  1  ABC2_membrane  ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.7   1.6e-05      0.28     108     155 ..       9      57 ..       5      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.6e-05
                     ABC2_membrane 108 sllqalifllivyflvgldls.rfflflllllltalaasslgllisala 155
                                        ++ +++++l +y+  + +++  ++ ++  l+l++l+++  gl+ ++ a
  gi|313126244|ref|YP_004036514.1|   9 KVVSGAVLTLPMYLAADSHIQfDGLVLFGGLFLLGLFCMVHGLFTGIAA 57 
                                       5788999999****9999998556********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 465.17
//
Query:       gi|313126245|ref|YP_004036515.1|  [L=159]
Description: hypothetical protein Hbor_14960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-08   32.9   0.0      8e-08   32.6   0.0    1.1  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
     0.0002   21.6   0.1    0.00024   21.4   0.1    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
       0.17   11.6   0.0       0.22   11.3   0.0    1.2  1  LnmK_N_HDF       LnmK N-terminal Hot Dog Fold domain


Domain annotation for each model (and alignments):
>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   1.3e-11     8e-08       1     108 [.      10     130 ..      10     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.3e-11
                                       ESS-HHHHHHHHTTTGGCCSCCCCEE..............EEEE.SSSEE...E......EEECSTTSSCEEEEEEE CS
                    Polyketide_cyc   1 vpapadqvyalvadvesypeflphcs..............svevleeaesglsa......dlevgfggltesftarv 57 
                                       + ap+++++++++d + +  ++p +               + e l+       a      + +   +g  +++t+++
  gi|313126245|ref|YP_004036515.1|  10 IGAPLSTIWEFHSDESGLEALTPDWMgldivsvrgpdgtlDPETLD-------AgskirmSMRPFDVGPAQRWTSHI 79 
                                       689***********************55544444444444444444.......14444448899************* PP

                                       EEEETTT....EEECTTCCCCCEEEEEEEECTECCEEECEEEEEEEEEEEE-SSC CS
                    Polyketide_cyc  58 tldppee....itfklvegdfkslegkWtieslppnsggtrtkvalevdfkfasp 108
                                       +  + ++     + ++++g+fk+ + ++++   ++    t +++ +e++f ++++
  gi|313126245|ref|YP_004036515.1|  80 VARELDDytamFRDEMIGGPFKKWVHTHRFYADGE---KTLMEDHVEYEF-PGGG 130
                                       99999999**********************99999...**********99.4444 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1     4e-08   0.00024       2     143 .]       2     159 .]       1     159 [] 0.75

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4e-08
                                       EEEEEEEEESS-HHHHHHHHTTTTGGGG....T-T.TEEEEECSESTSSS.....TTTEEEEECCCS.........S CS
                   Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwpr....Whp.evarveleggggpa.....rgvegtvrvggr.........g 59 
                                       ++ t+ ++i ap  ++w++ sd +++ +    W+   +++v+++  +g++        ++++r+  r         +
  gi|313126245|ref|YP_004036515.1|   2 ATYTRCTRIGAPLSTIWEFHSDESGLEAltpdWMGlDIVSVRGP--DGTLdpetlDA-GSKIRMSMRpfdvgpaqrW 75 
                                       666777899*************7666652222655555555554..44444455433.3677766668899999988 PP

                                       EEEEEEEEEETTTTEEEEEEE.SSS-TSEEEEEEEEECCETEEEEEEEEEEE..E--TT--HHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  60 tvreelvevdpegrllsyrivkpvpvanyvatwtvtpdgggtrvtwtgefda..gplggpfekpaaakavkgdleag 134
                                       t++ +  e+d+    ++ ++    p+++ v t ++ +dg+ t ++ ++e+++  g++g+ +  p+   +++  +++ 
  gi|313126245|ref|YP_004036515.1|  76 TSHIVARELDDYTAMFRDEMI-GGPFKKWVHTHRFYADGEKTLMEDHVEYEFpgGGVGRAV-SPLGIIGLEPMFRQR 150
                                       899999999986777777775.89*********************9999996668887776.677788999999888 PP

                                       HHHHHHHHH CS
                   Polyketide_cyc2 135 LerLkarle 143
                                        ++ ka+le
  gi|313126245|ref|YP_004036515.1| 151 HAKTKALLE 159
                                       888888776 PP

>> LnmK_N_HDF  LnmK N-terminal Hot Dog Fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.6e-05      0.22      47     102 ..      32      88 ..      23     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
                        LnmK_N_HDF  47 Ptylsfayfrvrg.seelsprgltfGdrldvtskvfdlGsesvltlhrvareggaPa 102
                                       P ++ +  + vrg + +l+p++l  G +++++ + fd+G+    t h vare ++ +
  gi|313126245|ref|YP_004036515.1|  32 PDWMGLDIVSVRGpDGTLDPETLDAGSKIRMSMRPFDVGPAQRWTSHIVARELDDYT 88 
                                       66777778899995568**********************************766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 948.00
//
Query:       gi|313126246|ref|YP_004036516.1|  [L=1509]
Description: glycosyl hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-80  268.7   0.7    1.7e-79  267.1   0.5    1.9  2  Glucodextran_N  Glucodextranase, domain N
    6.6e-32  110.9   0.2    1.1e-22   80.5   0.0    4.3  3  Glyco_hydro_15  Glycosyl hydrolases family 15


Domain annotation for each model (and alignments):
>> Glucodextran_N  Glucodextranase, domain N
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.1   0.5   1.9e-83   1.7e-79       1     262 [.     686     989 ..     686     990 .. 0.98
   2 ?   -2.3   0.0      0.29   2.6e+03      57     109 ..    1446    1497 ..    1442    1504 .. 0.86

  Alignments for each domain:
  == domain 1  score: 267.1 bits;  conditional E-value: 1.9e-83
                    Glucodextran_N   1 ApgaPgaaptWtsaaKdgvGtale....avSrVWFTlaeGiltEvyyPtidtaqlrdlqflv............tdg 61 
                                       Ap++P+++p+Wt+++K+gvGt+++    ++SrVWFTl+eG ltEv++P++d ++lr+l++lv            t++
  gi|313126246|ref|YP_004036516.1| 686 APSGPESRPRWTTGEKYGVGTVADhtedDPSRVWFTLTEGSLTEVRFPRVDLMNLRTLDMLVvdadpessytarTHN 762
                                       899*********************9999************************************************* PP

                    Glucodextran_N  62 etfvdeekrdteskvelldpeslayrvvntd....kegryriekeiftDpdrdvllvrvrfekakeeelrlyalldp 134
                                       et+ d++++++e+++e++++++l +r+v+t+    +++++++++e++tDp++d+ll++++fe+++++e++l+a++d+
  gi|313126246|ref|YP_004036516.1| 763 ETRRDDAADTIERRAEMAEDDALLFRHVITEsgdgRGHEWTLTVEYATDPEHDALLADISFEATDDNEYDLFAVADT 839
                                       *******************************99999***************************************** PP

                    Glucodextran_N 135 hldnsgagdsasvveakggkalvAsd...................g..svalAlaasvpferasvGyvGasDgltdL 190
                                       +l n+g++d++ +  ++g+++lvA+d                   +  sva+A++a+ +f++ +vG++G sD+l++L
  gi|313126246|ref|YP_004036516.1| 840 ALVNTGGEDRGLRLGQMGSYHLVARDagpydqqgktrpllidregNeySVAIAMTAAGRFDWGTVGVAG-SDHLSEL 915
                                       ************************************999999886257*********************.******* PP

                    Glucodextran_N 191 kadgtltweyesasdGnvaltgeldlgtskeftlalGFgesaeeAaa..eaaaslkegfeevlaaYaegWedyl 262
                                        ++g+l++  es++++nv+l+g++ +gt+   t+alGF+e+a++Aaa  eaa++l++g+e+v+++Ya++W ++l
  gi|313126246|ref|YP_004036516.1| 916 FSEGELPNAQESVDNENVVLVGRIGSGTNLGETIALGFAEHADTAAAlgEAAGALTRGYETVRTSYADSWAEFL 989
                                       **********************************************999***********************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.29
                    Glucodextran_N   57 lvtdgetfvdeekrdteskvelldpeslayrvvntdkegryriekeiftDpdr 109 
                                        +v +g+t ++  + +t s++++++pe  +++ v   ++g+ ++++  +tD d 
  gi|313126246|ref|YP_004036516.1| 1446 IV-NGQTNAAVIAVKTPSETTMVEPEGGTFEAVLGIEHGENQVTVAAATDADL 1497
                                        44.88888888899999999999999999999999999999999999999875 PP

>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   5.4e-05      0.48      19     139 ..     298     411 ..     282     425 .. 0.77
   2 !    6.8   0.0   0.00027       2.4     414     446 ..     639     670 ..     554     672 .. 0.89
   3 !   80.5   0.0   1.2e-26   1.1e-22      10     447 ..    1011    1404 ..    1004    1405 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 5.4e-05
                                       TTS-TT-B-S-S-BSSS......B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCHHHHHHHHHHHHHHCTS CS
                    Glyco_hydro_15  19 qnpvtGlliASpstsdp......DYrytWvRDsvyvilavwglgyrdedrakayeleqslvklmrglleamvrqagk 89 
                                         p tG+ iA p+  dp      +Y ytW RD + v   ++       d++   el   l++  r    +  + ++ 
  gi|313126246|ref|YP_004036516.1| 298 TAP-TGAHIAGPE-FDPfythsgGYGYTWFRDEAEVSRYLL-----ASDDRLDLELTDRLATSAR--FFCESQLDDG 365
                                       566.999999999.566688889******************.....7789999999999999888..5666666666 PP

                                       -BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHH CS
                    Glyco_hydro_15  90 vekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmt 139
                                       + +      + g  a+++ +   ++v +      Q D+t+ ++++la+++
  gi|313126246|ref|YP_004036516.1| 366 SWPHRAWAVD-GSLAPGWAH---ARVENSSKPEYQADQTASVVTFLARIL 411
                                       6666665555.445788887...778888888889999999999998874 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00027
                                       -TTS---SEE-TTT--EESSTT-HHHHHHHHHH CS
                    Glyco_hydro_15 414 nslgvLteevdvylgeliraqpllfsealllri 446
                                         +g+L+e+v + +g++++a pl +s+a++l +
  gi|313126246|ref|YP_004036516.1| 639 TAGGYLSEQVFD-DGTTDSAAPLGWSHAMRLHA 670
                                       56899****998.9****************987 PP

  == domain 3  score: 80.5 bits;  conditional E-value: 1.2e-26
                                        CBCSTTSSBTTS-TT-B-S-S-BSSS...........B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCH CS
                    Glyco_hydro_15   10 nvktlilleqnpvtGlliASpstsdp...........DYrytWvRDsvyvilavwglgyrdedrakayeleqslv 73  
                                         +++l + e+++  G+ iASps +++           +Y ++W RD ++v+ ++ ++g            + +++
  gi|313126246|ref|YP_004036516.1| 1011 CLMALRAVEDKTFLGAGIASPSVPWGeavtsdepkgyGYNFVWSRDLYQVFTVFEAVG------------DVETA 1073
                                        55677888999999************************************99999666............22222 PP

                                        HHHHHHHHHHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHHCTTHCHCCC CS
                    Glyco_hydro_15   74 klmrglleamvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmtasglqiist 148 
                                        +   + le +++ +++               ++f  +++   G   wg+ Q+D  s+++ + + + + g ++ + 
  gi|313126246|ref|YP_004036516.1| 1074 A---DALEYIYEYQQD--------------RRGFIPQNTYLNGRTRWGGEQMDNISFPAVMAYMLAERGVTFDDV 1131
                                        2...346667766665..............3567777788889999***********************888876 PP

                                        CHHHHTHHHHHHHHHHHTTS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHH CS
                    Glyco_hydro_15  149 ldevafvqnlvdYieaayktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnk 223 
                                           +  v+   dY++++   + +++WEe+ g s+   s+++ +++l  a+++a + g ++da ++   +d++ + 
  gi|313126246|ref|YP_004036516.1| 1132 GYDYVNVKRSADYVARNGPPTAQERWEEEAGYSPS--SIAAEIAGLASAAAIAIDEGHDADALIWLALADDWTDN 1204
                                        5555599****************************..*************************9999999998888 PP

                                        HHSTTT..GGG...EETTCCECECSCH.............HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TT CS
                    Glyco_hydro_15  224 lqgkygckrgf...wplfntylildgs........faedkeqvqeyrealdasllllpelyfvpaddvdeeyqnp 287 
                                        ++  + ++ g+   +++ +++ i  g           +++    ++re  d+ +l+l++l+  padd        
  gi|313126246|ref|YP_004036516.1| 1205 VESWTATRTGTerhDTVPYYVRITRGGdpdaghlrTLANNGPTLDEREIIDGGFLELVRLGIKPADD-------- 1271
                                        8776666664444344445555555558888888866666777899*********************........ PP

                                        TSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBTT--CG.SSSBSCT--BHHHHHHHHHHHHHHHHHHHHHTE- CS
                    Glyco_hydro_15  288 qsprllaqslyildsllsegflavgeldplvrRysedvkp.dklglsGrpyylctlwtvetlldelyekagkgrl 361 
                                          + + +++++++++++ +++  +g   p ++Ry+ d++  ++  ++G p+               +e +gkgrl
  gi|313126246|ref|YP_004036516.1| 1272 --EVIQNSVTEVDSTIRVDTP--YG---PAFYRYNGDGYGeRERDEEGAPW--------------SIESKGKGRL 1325
                                        ..999****************..44...679*******9646678889999..............789******* PP

                                        EEEECCCHHHHHHHTTTTTGGGSSEEETCHHHHHHHHHHHHHHHHHHHHHH.S-TTS---SEE-T.........T CS
                    Glyco_hydro_15  362 wglvryalglleklveskqltvGlpperesvisaplpveeladliveavee.dnslgvLteevdv.........y 426 
                                        w++++ ++g +e l                  + pl++e+l    +e+++  +ns+++L+e+v++         +
  gi|313126246|ref|YP_004036516.1| 1326 WPIFTGERGEFELLNGT--------------EEGPLAPENL----LETMAGfANSGRMLAEQVWDrehstaynwE 1382
                                        **************999..............6677777765....5666666*******************9999 PP

                                        T--.EESSTT-HHHHHHHHHHH CS
                    Glyco_hydro_15  427 lge.liraqpllfsealllrig 447 
                                         ge + +a+pl++s a+++r++
  gi|313126246|ref|YP_004036516.1| 1383 FGEgTGAATPLAWSMAQFVRLA 1404
                                        999788899**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.48
# Mc/sec: 9491.41
//
Query:       gi|313126247|ref|YP_004036517.1|  [L=805]
Description: hypothetical protein Hbor_14990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.8e-240  800.3   0.0     8e-239  794.8   0.0    2.0  1  GHL5      Hypothetical glycoside hydrolase 5


Domain annotation for each model (and alignments):
>> GHL5  Hypothetical glycoside hydrolase 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  794.8   0.0  4.4e-243    8e-239       2     759 ..      17     754 ..      16     788 .. 0.94

  Alignments for each domain:
  == domain 1  score: 794.8 bits;  conditional E-value: 4.4e-243
                              GHL5   2 llewakeieeseetvfekaqklakklGahyredGlteiGfwtPelaaeviktkeiylevltPleeidfr.akeqeik 77 
                                       ll+w +++ + +++ fe+a  l+ +lGah  ++G  e+GfwtP++ +  +++ +++lev+tP+ +id   ++ ++++
  gi|313126247|ref|YP_004036517.1|  17 LLAWHRDVVSDHDDDFEAATVLTDRLGAHLDAEGRVEVGFWTPDIVEAGVSAADVFLEVFTPTGTIDPAeTDARTVT 93 
                                       99*****************************************************************87256789** PP

                              GHL5  78 frrdrvelkkqgeylwgvvaGlkaGtreqlGslywlryldkeeevkiirdvlayslPyGvfaPaelydleklqrera 154
                                       frr+rv l+++ge++wgvvaG++aGtr++lGsly l y +  +e +++ d+lays+P+G faPaelyd+++l++ ra
  gi|313126247|ref|YP_004036517.1|  94 FRRERVPLRREGEFHWGVVAGMRAGTRDRLGSLYHLTYRE-DGEWRVVTDPLAYSVPFGAFAPAELYDIDRLDETRA 169
                                       *************************************986.5789******************************** PP

                              GHL5 155 dldyfkqtsaaedkk......elprvkapvnilqlhvgtaseeGtleGltkiyqriseklakkepltaaeenyvgyd 225
                                       d +yf++ ++a+++        lpr+++ v++l +h gta+e+G+l+Gl+ +y +i++k ++++pl++ e+n+ gyd
  gi|313126247|ref|YP_004036517.1| 170 DRAYFESLGTADERVstsehdGLPRIDPAVSMLEIHPGTATETGSLAGLADVYAEIGRKKRAGDPLEPWERNFDGYD 246
                                       ******9887766555666669******************************************************* PP

                              GHL5 226 avqllPiePtieyreeeskeseffaiaeeeveeeeseeevkvklkkpntqnwGydvpilgsaatnpavlgslrPdel 302
                                       a+q++P+eP  e    +++++ef+++ +e+      +  ++v+l +p++ nwGyd+++ + +a npa+l++ rPdel
  gi|313126247|ref|YP_004036517.1| 247 AIQVMPVEPLTE----NEETHEFWSVVSES------DGALTVELARPDAINWGYDIVVSAFSAPNPAILETGRPDEL 313
                                       *********865....77899*****9984......46899************************************ PP

                              GHL5 303 vdfiatlhnfstgpiqviydlvyGhadnqaeelinrqflkGpnmyGqdlnhqlPvvraillelqrrkintGadGirv 379
                                       vdfia+ h+++ +pi+v++d+  Ghadn++ el++ +++ Gp myG+ l+   P+ ra++le+q+rk++ GadGirv
  gi|313126247|ref|YP_004036517.1| 314 VDFIAACHDLP-RPIKVVFDVALGHADNRGAELLADRYILGPGMYGKHLDYTEPTARAVFLEMQKRKMDFGADGIRV 389
                                       *********98.7**************************************************************** PP

                              GHL5 380 dGgqdfrffnpltgrveqddayllamsdvvqeiggakrllftifedGrPwPeeGweekstyrdlielkpesyqwgPl 456
                                       dG+qdf  +++ t+++ +dd++l +m  v+q++ g++ + + i+edGrPwP e we  s+yr lie++p+s+qw+P+
  gi|313126247|ref|YP_004036517.1| 390 DGAQDFTSYDEETSEMYHDDDFLAEMDAVTQNVAGTEYRPWMIYEDGRPWPREDWELASSYRALIEQHPHSFQWSPI 466
                                       ***************************************************************************** PP

                              GHL5 457 ifahntPtlkgfwekkwervcevmakGdrwitGcanhdtvrrGnqvdte.....seinwnlGetlpevlknaydnpa 528
                                        fahntP+l  fw +kw rv ev   G +witG+anhdtvrrG+q+d++     s +n +lG+ +pe l++aydnpa
  gi|313126247|ref|YP_004036517.1| 467 TFAHNTPALLTFWATKWWRVREVGEFGGNWITGVANHDTVRRGTQIDPTvefnqSPVNPYLGDDYPETLDAAYDNPA 543
                                       ***********************************************8521212568889***************** PP

                              GHL5 529 vtlwvygfsPGlPmdfinalmrapwgffrntderygvkvvseevGfldwqitpelyekdevfsrlkslGfeeleelr 605
                                        +++ ++f PG+Pmdf+ a+mrapwgf+r+td ++ vkvv++e  fl+wq+ +  ++  e f+r+k+lGf++++el+
  gi|313126247|ref|YP_004036517.1| 544 AAMLFHCFLPGVPMDFVHANMRAPWGFVRDTDPEWNVKVVADESNFLYWQVRETDFSATEHFRRVKDLGFDSVDELH 620
                                       ***************************************************************************** PP

                              GHL5 606 eflkaleealvekdydlekvvevcqacldeekaaceveelkelkeaekveflkeldveklkefalafmedgyevcnv 682
                                        f+ al++a++++dy+++ +++++ a                +++     + ++l  + l ++a a+m d ++++ +
  gi|313126247|ref|YP_004036517.1| 621 SFMDALSAAVEATDYEVDVMADMLSA----------------MDH----PLGTDLVPSDLETYADAWMRDVFDFATL 677
                                       ****************9987766533................333....4556777789****************** PP

                              GHL5 683 shyedkvdseqakfnlalrkfrkakpwlrenlkesdrfnkis.eeektifyGvrtnpeeeeekvvlvahleGepttv 758
                                       s+++d  d+++++  la r+fr+++pwlr++l+e+d f   +  + ++++yG+rt p+ ee +++++a++eG p++v
  gi|313126247|ref|YP_004036517.1| 678 SNWHDAQDEDRTAARLATREFRHDRPWLRDDLREGDYFTYRHpTDGTVLYYGFRTAPNGEE-QLLFAANMEGVPVEV 753
                                       **************************************866615566789*******9876.9**********9998 PP

                              GHL5 759 t 759
                                        
  gi|313126247|ref|YP_004036517.1| 754 S 754
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (805 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 4558.14
//
Query:       gi|313126248|ref|YP_004036518.1|  [L=82]
Description: hypothetical protein Hbor_15000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00024   21.3   3.4      0.088   13.0   0.3    2.1  2  zf-nanos         Nanos RNA binding domain
    0.00027   20.2   2.7       0.16   11.4   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
    0.00055   20.5   1.5       0.58   10.9   0.0    2.2  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
     0.0011   18.9   1.0      0.074   13.0   0.1    2.2  2  YhfH             YhfH-like protein
     0.0014   18.7   3.1     0.0037   17.3   3.1    1.7  1  Zn-ribbon_8      Zinc ribbon domain
     0.0033   17.4   0.8     0.0051   16.8   0.8    1.3  1  DZR              Double zinc ribbon
     0.0035   17.3   5.7      0.052   13.5   5.0    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0059   16.5   3.4      0.042   13.8   0.2    2.2  2  zf_CopZ          Zinc binding domain
     0.0088   15.9   6.5      0.019   14.9   0.7    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
     0.0089   15.7   5.0       0.49   10.2   0.2    2.3  2  zinc_ribbon_2    zinc-ribbon domain
     0.0095   15.5   3.0       0.86    9.3   0.3    2.5  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
  ------ inclusion threshold ------
      0.012   15.7   2.6        1.3    9.1   0.1    2.2  2  CpXC             CpXC protein
      0.012   15.7   3.6       0.37   11.0   0.1    2.6  2  zf-RING_7        C4-type zinc ribbon domain
      0.013   15.5   0.3      0.016   15.2   0.3    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.019   14.9   1.2          2    8.4   0.2    2.3  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.022   14.7   2.7      0.042   13.8   2.7    1.4  1  zf-DNL           DNL zinc finger
      0.025   14.9   2.7      0.078   13.4   2.7    1.8  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.033   13.9   0.6       0.83    9.4   0.1    2.3  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.04   14.2   0.4        3.3    8.1   0.1    2.2  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
      0.041   13.8   3.2        1.9    8.4   0.6    2.3  2  Cys_rich_CPXG    Cysteine-rich CPXCG
      0.046   13.2   6.5       0.49   10.0   6.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.05   13.7   0.7      0.069   13.2   0.7    1.2  1  Ribosomal_L37ae  Ribosomal L37ae protein family
      0.076   12.6   2.3        6.1    6.5   0.1    2.2  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
      0.077   12.9   3.5        3.5    7.6   0.2    2.0  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.091   12.9   6.8        1.2    9.3   0.7    2.2  2  UPF0547          Uncharacterised protein family UPF0547
        0.1   12.6   3.8       0.95    9.4   0.2    2.5  2  Nudix_N_2        Nudix N-terminal
        0.1   12.6   2.0        6.2    6.8   0.1    2.3  2  zinc_ribbon_4    zinc-ribbon domain
       0.11   12.4   3.6        5.5    7.0   0.2    2.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
       0.13   12.0   3.0          1    9.2   0.2    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.13   12.2   4.3          2    8.4   1.0    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.14   12.0   2.2         11    5.9   0.1    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.14   11.5   3.3       0.13   11.6   1.9    1.7  2  zf-TFIIB         Transcription factor zinc-finger
       0.18   11.7   9.1        1.6    8.7   1.6    2.2  2  Prok-RING_1      Prokaryotic RING finger family 1
       0.21   12.1   2.9        4.7    7.9   0.3    2.2  2  zf-C2H2          Zinc finger, C2H2 type
       0.24   11.7   6.3        2.9    8.2   0.5    2.3  2  zinc_ribbon_9    zinc-ribbon
       0.26   11.1   1.6         14    5.5   0.1    2.2  2  zinc_ribbon_5    zinc-ribbon domain
       0.26   11.4   4.4        1.5    8.9   4.4    2.2  1  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.27    9.9   1.1       0.35    9.6   1.1    1.1  1  NRDD             Anaerobic ribonucleoside-triphosphate reduct
       0.29   11.0   3.1        2.2    8.1   0.3    2.2  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.32   11.1   5.2          6    7.0   0.9    2.4  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.33   10.9   6.8        4.2    7.4   2.3    2.4  2  DUF1610          Domain of unknown function (DUF1610)
       0.42   10.4   5.8        1.2    9.0   0.5    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
        0.6   10.2   5.2        1.3    9.1   0.0    2.6  2  Rubredoxin       Rubredoxin
       0.65   10.5   6.3        3.1    8.3   0.1    2.5  2  zf-IS66          zinc-finger binding domain of transposase IS
       0.86    9.9   3.5         17    5.8   0.3    2.2  2  Ribosomal_L32p   Ribosomal L32p protein family
        1.1    9.4   7.8        5.9    7.1   1.4    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        2.1    8.3   4.8        5.9    6.9   0.5    2.3  2  DUF3797          Domain of unknown function (DUF3797)
        2.4    7.9   7.2        1.7    8.4   1.3    2.2  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI


Domain annotation for each model (and alignments):
>> zf-nanos  Nanos RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.3   0.00024     0.088      33      48 ..       4      19 ..       2      23 .. 0.86
   2 !    9.6   0.2    0.0027         1      31      49 ..      22      40 ..      21      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00024
                          zf-nanos 33 kyvCpiCgatgdkAHt 48
                                       yvCp+Cg t+++A  
  gi|313126248|ref|YP_004036518.1|  4 TYVCPHCGTTQERAYR 19
                                      69**********9965 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0027
                          zf-nanos 31 LrkyvCpiCgatgdkAHtt 49
                                      L  ++Cp Cg +g++ H++
  gi|313126248|ref|YP_004036518.1| 22 LIIVTCPECGENGRHVHES 40
                                      6679***********9985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00044      0.16       2      10 ..       4      12 ..       3      17 .. 0.64
   2 !    9.2   0.3    0.0021      0.78       3      11 ..      25      33 ..      24      35 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                       zf-ribbon_3  2 tvrCPnCGa 10
                                      t+ CP+CG+
  gi|313126248|ref|YP_004036518.1|  4 TYVCPHCGT 12
                                      566666665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
                       zf-ribbon_3  3 vrCPnCGap 11
                                      v+CP+CG++
  gi|313126248|ref|YP_004036518.1| 25 VTCPECGEN 33
                                      679999975 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.3    0.0063       2.3       4      13 ..       6      15 ..       3      21 .. 0.79
   2 !   10.9   0.0    0.0015      0.58       4      19 ..      26      41 ..      24      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0063
                           zf-ISL3  4 rCPnCgsktv 13
                                      +CP+Cg +  
  gi|313126248|ref|YP_004036518.1|  6 VCPHCGTTQE 15
                                      7*****9954 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0015
                           zf-ISL3  4 rCPnCgsktvvkhgkk 19
                                      +CP+Cg+  +++h ++
  gi|313126248|ref|YP_004036518.1| 26 TCPECGENGRHVHESY 41
                                      8*******99999765 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.082        31      15      21 ..       6      12 ..       2      18 .. 0.84
   2 !   13.0   0.1    0.0002     0.074      15      31 ..      26      42 ..      25      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.082
                              YhfH 15 kCteCGk 21
                                      +C++CG 
  gi|313126248|ref|YP_004036518.1|  6 VCPHCGT 12
                                      6*****6 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0002
                              YhfH 15 kCteCGkeieEqaecYg 31
                                      +C+eCG++    +e+Y 
  gi|313126248|ref|YP_004036518.1| 26 TCPECGENGRHVHESYV 42
                                      7***************5 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.1     1e-05    0.0037       6      35 ..       5      33 ..       3      37 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsis.dapltaCPeCgse 35
                                      Y C  Cg++ e+  +++     ++CPeCg++
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTTQERAYRVKlI--IVTCPECGEN 33
                                      9**********88777733..556*****86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.8   1.4e-05    0.0051      13      37 ..       5      33 ..       2      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-05
                               DZR 13 rfCseCgtklkavaa....edrCpsCgek 37
                                       +C++Cgt+ +++ +      +Cp+Cge 
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTTQERAYRvkliIVTCPECGEN 33
                                      68*******987777999999*****986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   5.0   0.00014     0.052      19      45 ..       5      32 ..       2      33 .. 0.89
   2 ?    6.3   0.5     0.025       9.3      19      28 ..      25      35 ..      21      40 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                     Zn_Tnp_IS1595 19 fvCPhCgsr..kayriktrglfqCkeCrk 45
                                       vCPhCg +  +ayr+k      C eC++
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTTqeRAYRVKL-IIVTCPECGE 32
                                      69******9********8.9999999986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.025
                     Zn_Tnp_IS1595 19 fvCPhCgsr.k 28
                                      ++CP Cg   +
  gi|313126248|ref|YP_004036518.1| 25 VTCPECGENgR 35
                                      57*****8763 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.4      0.11        42       3      12 ..       6      15 ..       4      26 .. 0.70
   2 !   13.8   0.2   0.00011     0.042       3      20 ..      26      43 ..      24      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                                      B-TTT--B-E CS
                           zf_CopZ  3 kCPvCgkkGk 12
                                       CP+Cg+  +
  gi|313126248|ref|YP_004036518.1|  6 VCPHCGTTQE 15
                                      6****98644 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00011
                                      B-TTT--B-EEE-HHHHH CS
                           zf_CopZ  3 kCPvCgkkGkkVkliTvk 20
                                      +CP Cg++G++V++  v+
  gi|313126248|ref|YP_004036518.1| 26 TCPECGENGRHVHESYVD 43
                                      8***********998775 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.7   5.1e-05     0.019       4      21 ..       4      21 ..       4      23 .. 0.87
   2 ?    4.3   0.6     0.099        37       6      17 ..      26      36 ..      26      37 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.1e-05
                    Zn_ribbon_SprT  4 vYrCtgCgreythhlsir 21
                                      +Y+C++Cg+++++  +++
  gi|313126248|ref|YP_004036518.1|  4 TYVCPHCGTTQERAYRVK 21
                                      7*********99987775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.099
                    Zn_ribbon_SprT  6 rCtgCgreythh 17
                                      +C+ Cg++ ++h
  gi|313126248|ref|YP_004036518.1| 26 TCPECGEN-GRH 36
                                      5*****77.666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2    0.0013      0.49       2      21 ..       7      12 ..       2      15 .. 0.64
   2 !    7.5   0.7    0.0093       3.5      15      21 ..      26      32 ..      25      34 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                      Cp+CG              t
  gi|313126248|ref|YP_004036518.1|  7 CPHCG--------------T 12
                                      55555..............4 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0093
                     zinc_ribbon_2 15 FCpyCGt 21
                                       Cp+CG+
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      5777776 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.3    0.0023      0.86       1      10 [.       3      12 ..       3      16 .. 0.89
   2 ?    6.3   0.2      0.02       7.3       3      10 ..      25      32 ..      24      33 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0023
                            zf_UBZ  1 dtylCerCgk 10
                                      +ty+C+ Cg+
  gi|313126248|ref|YP_004036518.1|  3 ETYVCPHCGT 12
                                      69******97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.02
                            zf_UBZ  3 ylCerCgk 10
                                      ++C++Cg+
  gi|313126248|ref|YP_004036518.1| 25 VTCPECGE 32
                                      59****97 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3    0.0094       3.5      37      51 ..       4      18 ..       2      24 .. 0.77
   2 ?    9.1   0.1    0.0034       1.3      37      52 ..      24      39 ..      14      57 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0094
                              CpXC 37 eatCpkCgataklea 51
                                      +++Cp+Cg+t +  +
  gi|313126248|ref|YP_004036518.1|  4 TYVCPHCGTTQERAY 18
                                      689999999887666 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0034
                              CpXC 37 eatCpkCgatakleap 52
                                       +tCp+Cg++++  ++
  gi|313126248|ref|YP_004036518.1| 24 IVTCPECGENGRHVHE 39
                                      5678888777765554 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.061        23      25      30 ..       6      11 ..       2      12 .. 0.84
   2 ?   11.0   0.1   0.00098      0.37      23      30 ..      24      31 ..      14      31 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.061
                                      E-TTT- CS
                         zf-RING_7 25 tCpeCG 30
                                       Cp+CG
  gi|313126248|ref|YP_004036518.1|  6 VCPHCG 11
                                      5****9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00098
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                      +vtCpeCG
  gi|313126248|ref|YP_004036518.1| 24 IVTCPECG 31
                                      8******9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   4.4e-05     0.016      71      99 ..       5      37 ..       1      46 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.4e-05
                                      EEETTTS-EEECHHH.HH...S-TTTSSS-EEE CS
                              HypA 71 vrCreCgkefeleek.al...rCpkCgsadvei 99
                                      + C +Cg++ e + + +l   +Cp+Cg+++ ++
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTTQERAYRvKLiivTCPECGENGRHV 37
                                      68*****99997764333556******988766 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0054         2      18      26 ..       3      11 ..       1      12 [. 0.83
   2 ?    5.6   0.1     0.042        16      21      27 ..      26      32 ..      15      33 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0054
                    PhnA_Zn_Ribbon 18 allvCpeCa 26
                                      + +vCp+C+
  gi|313126248|ref|YP_004036518.1|  3 ETYVCPHCG 11
                                      679*****7 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.042
                    PhnA_Zn_Ribbon 21 vCpeCah 27
                                       CpeC++
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      5999985 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.7   0.00011     0.042       3      37 ..       4      33 ..       3      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                            zf-DNL  3 tftCkaCetrsskeiskkaYekGvVivqCpgCknr 37
                                      t+ C  C+t +     ++aY+   +iv+Cp+C ++
  gi|313126248|ref|YP_004036518.1|  4 TYVCPHCGTTQ-----ERAYRVKLIIVTCPECGEN 33
                                      57888888765.....579*************764 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.7   0.00021     0.078       2      41 ..       3      37 ..       2      53 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00021
                   Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigqcvyCadCgastpwf 41
                                      e + CP+Cg  ++   + +        v+C +Cg ++ ++
  gi|313126248|ref|YP_004036518.1|  3 ETYVCPHCGTTQERAYRVKLI-----IVTCPECGENGRHV 37
                                      6789*****877655554444.....9*******954444 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0022      0.83      44      53 ..       4      13 ..       1      14 [. 0.85
   2 ?    3.0   0.0      0.23        87      46      52 ..      26      32 ..      15      42 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0022
                    zinc_ribbon_10 44 kyrCpkCgal 53
                                      +y+Cp+Cg++
  gi|313126248|ref|YP_004036518.1|  4 TYVCPHCGTT 13
                                      7******986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.23
                    zinc_ribbon_10 46 rCpkCga 52
                                       Cp+Cg+
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      5666664 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0089       3.3       2      11 ..       4      13 ..       3      23 .. 0.78
   2 ?    4.7   0.0       0.1        37       3      11 ..      25      34 ..      24      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0089
                           zf-Di19  2 sftCPyCgke 11
                                      ++ CP+Cg +
  gi|313126248|ref|YP_004036518.1|  4 TYVCPHCGTT 13
                                      789****974 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.1
                           zf-Di19  3 ftCPyCgk.e 11
                                      +tCP Cg+ +
  gi|313126248|ref|YP_004036518.1| 25 VTCPECGEnG 34
                                      6999999854 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.6    0.0051       1.9       1      11 [.       5      15 ..       5      18 .. 0.85
   2 ?    6.0   0.1     0.029        11       1      10 [.      25      34 ..      25      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0051
                     Cys_rich_CPXG  1 iqCPyCgeeie 11
                                      + CP+Cg ++e
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTTQE 15
                                      67*****9876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.029
                     Cys_rich_CPXG  1 iqCPyCgeei 10
                                      ++CP Cge+ 
  gi|313126248|ref|YP_004036518.1| 25 VTCPECGENG 34
                                      68*****985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   6.1    0.0013      0.49       1      27 [.       5      32 ..       5      33 .. 0.93
   2 ?    5.7   1.2     0.027        10       2       8 ..      26      32 ..      25      39 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                                      EEETTTTCEE.CHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  1 ykCPnCgstn.lveDpergelvCtdCGl 27
                                      y+CP Cg+t+   +  +   ++C++CG+
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTTQeRAYRVKLIIVTCPECGE 32
                                      89*******999999999999*****96 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.027
                                      EETTTTC CS
                      TF_Zn_Ribbon  2 kCPnCgs 8 
                                      +CP+Cg 
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      6888885 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   0.00019     0.069      31      59 ..       2      32 ..       1      36 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00019
                                      HS-BEESSSSSS..EEEEEETTEEEETTTTE CS
                   Ribosomal_L37ae 31 hakytCpfcgkt..kvkRkavgiwkCkkcgk 59
                                       ++y Cp cg+t  +  R+   i +C +cg+
  gi|313126248|ref|YP_004036518.1|  2 TETYVCPHCGTTqeRAYRVKLIIVTCPECGE 32
                                      578*******9966789************97 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3     0.024       8.9      13      18 ..       7      12 ..       6      17 .. 0.90
   2 ?    6.5   0.1     0.016       6.1      12      18 ..      26      32 ..      18      36 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.024
                           zf-tcix 13 CpkCGt 18
                                      Cp CGt
  gi|313126248|ref|YP_004036518.1|  7 CPHCGT 12
                                      *****9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.016
                           zf-tcix 12 kCpkCGt 18
                                       Cp+CG 
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      7*****4 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0093       3.5      45      58 ..       3      16 ..       1      20 [. 0.79
   2 ?    6.1   0.4     0.028        11      30      40 ..      26      36 ..      24      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0093
                    OrfB_Zn_ribbon 45 rtfkCpnCgfeadr 58
                                      +t++Cp+Cg++  r
  gi|313126248|ref|YP_004036518.1|  3 ETYVCPHCGTTQER 16
                                      68899999988776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.028
                    OrfB_Zn_ribbon 30 tCseCgsknke 40
                                      tC+eCg+++++
  gi|313126248|ref|YP_004036518.1| 26 TCPECGENGRH 36
                                      8*****99887 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.7    0.0031       1.2      16      22 ..       6      12 ..       3      13 .. 0.86
   2 ?    6.7   0.8      0.02       7.6       2       7 ..      26      31 ..      25      33 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0031
                           UPF0547 16 fCphCGy 22
                                      +CphCG+
  gi|313126248|ref|YP_004036518.1|  6 VCPHCGT 12
                                      7*****8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.02
                           UPF0547  2 vCPeCe 7 
                                      +CPeC 
  gi|313126248|ref|YP_004036518.1| 26 TCPECG 31
                                      588886 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2    0.0025      0.95      23      31 ..       5      13 ..       3      17 .. 0.84
   2 ?    3.8   0.4      0.15        55       3       8 ..      27      32 ..      26      38 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0025
                                      EEETTTTEE CS
                         Nudix_N_2 23 lvCpaCgti 31
                                      +vCp+Cgt+
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTT 13
                                      699999986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.15
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      C++CG+
  gi|313126248|ref|YP_004036518.1| 27 CPECGE 32
                                      888886 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.051        19       5      10 ..       7      12 ..       5      15 .. 0.75
   2 ?    6.8   0.1     0.017       6.2       2       9 ..      24      31 ..      16      35 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.051
                     zinc_ribbon_4  5 CpsCka 10
                                      Cp+C++
  gi|313126248|ref|YP_004036518.1|  7 CPHCGT 12
                                      888877 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
                     zinc_ribbon_4  2 kitCpsCk 9 
                                      ++tCp+C+
  gi|313126248|ref|YP_004036518.1| 24 IVTCPECG 31
                                      57777776 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.5     0.022       8.3       2       7 ..       7      12 ..       6      16 .. 0.87
   2 ?    7.0   0.2     0.015       5.5       1       9 [.      26      34 ..      26      43 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.022
                         Ogr_Delta  2 CPhCga 7 
                                      CPhCg+
  gi|313126248|ref|YP_004036518.1|  7 CPHCGT 12
                                      *****7 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.015
                         Ogr_Delta  1 rCPhCgapa 9 
                                      +CP+Cg++ 
  gi|313126248|ref|YP_004036518.1| 26 TCPECGENG 34
                                      6*****976 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0027         1      22      31 ..       5      14 ..       3      15 .. 0.89
   2 ?    3.3   0.3      0.18        69      24      28 ..      27      31 ..      23      34 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0027
                     A2L_zn_ribbon 22 lvCieCgasf 31
                                      +vC+ Cg+++
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTTQ 14
                                      9*******98 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.18
                     A2L_zn_ribbon 24 CieCg 28
                                      C+eCg
  gi|313126248|ref|YP_004036518.1| 27 CPECG 31
                                      88887 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.0    0.0054         2      26      34 ..       5      13 ..       3      16 .. 0.78
   2 ?    5.2   0.1     0.053        20       8      18 ..      21      31 ..      14      32 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0054
                           DUF35_N 26 avCphCgsd 34
                                       vCphCg +
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTT 13
                                      589999975 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.053
                           DUF35_N  8 rLvgqrCpdCG 18
                                      +L++  Cp CG
  gi|313126248|ref|YP_004036518.1| 21 KLIIVTCPECG 31
                                      67777788887 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5     0.033        12      25      37 ..       1      13 [.       1      15 [. 0.83
   2 ?    5.9   0.1     0.031        11       2       8 ..      26      32 ..      22      37 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.033
                           TFIIS_C 25 mtvfykCtkCghr 37
                                      mt  y+C  Cg +
  gi|313126248|ref|YP_004036518.1|  1 MTETYVCPHCGTT 13
                                      7889999999975 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.031
                           TFIIS_C  2 kCpkCgs 8 
                                      +Cp+Cg+
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      5777765 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.9   0.00035      0.13       2      26 ..       7      31 ..       6      31 .. 0.98
   2 ?   -2.5   0.0         9   3.4e+03      12      20 ..      70      78 ..      65      79 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                          zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                      CP C+++ e + r ++ i +Cp+C+
  gi|313126248|ref|YP_004036518.1|  7 CPHCGTTQERAYRVKLIIVTCPECG 31
                                      ************************7 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9
                          zf-TFIIB 12 serggveid 20
                                      ++rg v id
  gi|313126248|ref|YP_004036518.1| 70 VKRGLVDID 78
                                      678888887 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.6    0.0043       1.6      22      33 ..       6      17 ..       3      22 .. 0.89
   2 ?    7.7   1.0    0.0091       3.4      20      27 ..      24      31 ..      21      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0043
                       Prok-RING_1 22 vCpeCgtpyHra 33
                                      vCp+Cgt + ra
  gi|313126248|ref|YP_004036518.1|  6 VCPHCGTTQERA 17
                                      9******99886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0091
                       Prok-RING_1 20 iVvCpeCg 27
                                      iV+CpeCg
  gi|313126248|ref|YP_004036518.1| 24 IVTCPECG 31
                                      8******9 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3     0.013       4.7       1       9 [.       5      13 ..       5      19 .. 0.86
   2 ?    4.8   0.1      0.12        45       2       9 ..      26      33 ..      25      39 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.013
                                      EEETTTTEE CS
                           zf-C2H2  1 ykCpdCgks 9 
                                      y+Cp+Cg +
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTT 13
                                      9*****965 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.12
                                      EETTTTEE CS
                           zf-C2H2  2 kCpdCgks 9 
                                      +Cp+Cg+ 
  gi|313126248|ref|YP_004036518.1| 26 TCPECGEN 33
                                      7*****76 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.7     0.021         8      21      28 ..       5      11 ..       1      13 [. 0.72
   2 ?    8.2   0.5    0.0077       2.9      22      29 ..      25      32 ..      12      39 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.021
                     zinc_ribbon_9 21 dvlCPhCg 28
                                       v CPhCg
  gi|313126248|ref|YP_004036518.1|  5 YV-CPHCG 11
                                      45.****8 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0077
                     zinc_ribbon_9 22 vlCPhCgg 29
                                      v+CP+Cg 
  gi|313126248|ref|YP_004036518.1| 25 VTCPECGE 32
                                      69****73 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.069        26       5      11 ..       7      13 ..       5      15 .. 0.90
   2 ?    5.5   0.1     0.037        14       2       9 ..      24      31 ..      23      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.069
                     zinc_ribbon_5  5 CpdCdtk 11
                                      Cp C+t+
  gi|313126248|ref|YP_004036518.1|  7 CPHCGTT 13
                                      *****97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.037
                     zinc_ribbon_5  2 iirCpdCd 9 
                                      i+ Cp+C+
  gi|313126248|ref|YP_004036518.1| 24 IVTCPECG 31
                                      899****8 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.4    0.0041       1.5       2      25 ..       7      33 ..       6      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0041
                          zf-Mss51  2 CPvpkhkqt...apkhvdfeCpdCGip 25
                                      CP++ ++q+     k + ++Cp+CG  
  gi|313126248|ref|YP_004036518.1|  7 CPHCGTTQErayRVKLIIVTCPECGEN 33
                                      ****999996666777778*****965 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.1   0.00094      0.35     508     528 ..       5      33 ..       2      43 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00094
                                       EEETT.--EESS........SB-TTT--B CS
                              NRDD 508 dvCnecgykgei........ekCpkCgse 528
                                        vC++cg+++e+         +Cp+Cg++
  gi|313126248|ref|YP_004036518.1|   5 YVCPHCGTTQERayrvkliiVTCPECGEN 33 
                                       58******8888899*****88*****54 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.19        72       4       8 ..       7      11 ..       5      14 .. 0.83
   2 ?    8.1   0.3    0.0059       2.2       2       9 ..      25      32 ..      24      35 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.19
                                      -SSS- CS
                    zf-C4_Topoisom  4 CPkCg 8 
                                      CP Cg
  gi|313126248|ref|YP_004036518.1|  7 CPHCG 11
                                      ****9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0059
                                      EE-SSS-- CS
                    zf-C4_Topoisom  2 ekCPkCgg 9 
                                      ++CP+Cg+
  gi|313126248|ref|YP_004036518.1| 25 VTCPECGE 32
                                      79*****7 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.034        13       2      11 ..       7      16 ..       6      18 .. 0.83
   2 ?    7.0   0.9     0.016         6       1       7 [.      26      32 ..      26      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.034
                    DNA_ligase_ZBD  2 CPvCGsavvR 11
                                      CP CG+  +R
  gi|313126248|ref|YP_004036518.1|  7 CPHCGTTQER 16
                                      *****97655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.016
                    DNA_ligase_ZBD  1 hCPvCGs 7 
                                      +CP+CG 
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      7*****5 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.044        16      17      23 ..       5      11 ..       4      12 .. 0.86
   2 ?    7.4   2.3     0.011       4.2      19      24 .]      27      32 ..      26      32 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.044
                           DUF1610 17 FpCPNCG 23
                                      + CP CG
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCG 11
                                      57****9 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                           DUF1610 19 CPNCGE 24
                                      CP+CGE
  gi|313126248|ref|YP_004036518.1| 27 CPECGE 32
                                      *****9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5    0.0031       1.2       1      12 [.       5      16 ..       5      18 .. 0.85
   2 ?    4.1   0.6       0.1        37      17      22 ..      27      32 ..      26      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                      Rubredoxin_2  1 YvCsqCGfesak 12
                                      YvC +CG ++ +
  gi|313126248|ref|YP_004036518.1|  5 YVCPHCGTTQER 16
                                      9******99876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.1
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+Cg+
  gi|313126248|ref|YP_004036518.1| 27 CPECGE 32
                                      999996 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0034       1.3      33      45 ..       3      15 ..       1      17 [. 0.84
   2 ?    3.3   0.1      0.23        87      36      42 ..      26      32 ..      25      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0034
                                      TT-BBTTTB-BGG CS
                        Rubredoxin 33 ddWvCPdCgveke 45
                                      +++vCP+Cg ++e
  gi|313126248|ref|YP_004036518.1|  3 ETYVCPHCGTTQE 15
                                      689*****99865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.23
                                      BBTTTB- CS
                        Rubredoxin 36 vCPdCgv 42
                                      +CP+Cg 
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      6****85 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0084       3.1      39      46 .]       4      11 ..       1      22 [. 0.76
   2 ?    4.2   2.3      0.15        57       3       9 ..      26      32 ..      25      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0084
                           zf-IS66 39 kyaCpcCe 46
                                      +y Cp+C+
  gi|313126248|ref|YP_004036518.1|  4 TYVCPHCG 11
                                      67777775 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.15
                           zf-IS66  3 tCpcCGg 9 
                                      tCp+CG 
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      79***97 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.045        17      41      51 ..       6      16 ..       3      21 .. 0.81
   2 ?    5.3   0.3     0.065        24      26      34 ..      24      32 ..      17      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.045
                                      -BTTTTBSSSB CS
                    Ribosomal_L32p 41 vcpscGyYkgr 51
                                      vcp+cG+ + r
  gi|313126248|ref|YP_004036518.1|  6 VCPHCGTTQER 16
                                      99***987776 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.065
                                      EEEETTTCC CS
                    Ribosomal_L32p 26 lvecpncge 34
                                      +v+cp+cge
  gi|313126248|ref|YP_004036518.1| 24 IVTCPECGE 32
                                      799999998 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.4     0.016       5.9      21      26 .]       5      10 ..       3      10 .. 0.93
   2 ?    6.1   0.6     0.032        12       3       9 ..      26      32 ..      25      33 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.016
                            zf-ACC 21 yVCPkC 26
                                      yVCP+C
  gi|313126248|ref|YP_004036518.1|  5 YVCPHC 10
                                      9***** PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.032
                            zf-ACC  3 KCpsCge 9 
                                       Cp+Cge
  gi|313126248|ref|YP_004036518.1| 26 TCPECGE 32
                                      6999998 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.3      0.14        51      13      22 ..       5      13 ..       1      25 [. 0.77
   2 ?    6.9   0.5     0.016       5.9      14      22 ..      25      33 ..      19      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                           DUF3797 13 YvqCPeCgNn 22
                                      Yv CP Cg  
  gi|313126248|ref|YP_004036518.1|  5 YV-CPHCGTT 13
                                      44.****965 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.016
                           DUF3797 14 vqCPeCgNn 22
                                      v CPeCg n
  gi|313126248|ref|YP_004036518.1| 25 VTCPECGEN 33
                                      79****976 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.3    0.0046       1.7      21      29 ..       4      12 ..       4      15 .. 0.87
   2 ?    3.0   0.5      0.23        86       7      12 ..      27      32 ..      25      37 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0046
                           zf-RRN7 21 fyyCrrCht 29
                                      +y+C +C+t
  gi|313126248|ref|YP_004036518.1|  4 TYVCPHCGT 12
                                      69******9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.23
                           zf-RRN7  7 CgvCgc 12
                                      C++Cg 
  gi|313126248|ref|YP_004036518.1| 27 CPECGE 32
                                      999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              48  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 523.55
//
Query:       gi|313126249|ref|YP_004036519.1|  [L=72]
Description: hypothetical protein Hbor_15010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 449.92
//
Query:       gi|313126250|ref|YP_004036520.1|  [L=651]
Description: hypothetical protein Hbor_15020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-12   47.6  10.4      2e-12   47.6  10.4    3.0  3  PMT_2            Dolichyl-phosphate-mannose-protein mannosylt
  ------ inclusion threshold ------
      0.012   14.9   0.4      0.012   14.9   0.4    1.6  2  Glyco_transf_22  Alg9-like mannosyltransferase family


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.53   4.7e+03      57      69 ..      24      36 ..      15      59 .. 0.59
   2 !   47.6  10.4   2.2e-16     2e-12      22     130 ..     114     224 ..      96     235 .. 0.84
   3 !    3.3   0.3    0.0096        86      20      66 ..     397     447 ..     388     460 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.53
                             PMT_2 57 lllavvplfvals 69
                                      +l+a+v l+v+++
  gi|313126250|ref|YP_004036520.1| 24 VLVAAVGLLVFWL 36
                                      2222222233332 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 2.2e-16
                             PMT_2  22 lairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllraleknkl 98 
                                       + i l   l+++  ++++y l    f++r++l+a++ la++plf+ +sa+f  +ap ++l ++++ +++ra+ +++l
  gi|313126250|ref|YP_004036520.1| 114 WNIAL--GLVAAGNAAGVYYLGSAAFDRRVGLVAVVALAASPLFLLTSATFLSYAPATMLNLAFAVAYVRAARTDSL 188
                                       44444..4666677899************************************************************ PP

                             PMT_2  99 kywllagvlfGlgflsK.ytaallliaall...yll 130
                                       ++ +++g+++Gl+f+ + yta+l++i+++l   ++l
  gi|313126250|ref|YP_004036520.1| 189 RWAVASGAAVGLAFFARpYTAVLFAIPFILhtlAVL 224
                                       *****************7788999999998765444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.0096
                             PMT_2  20 selairlvsalagvltilllyllarrlfgkra....allaalllavvplfv 66 
                                         + + l+  ++++ ++++l + +rr + +r+    a +a++ l +++  v
  gi|313126250|ref|YP_004036520.1| 397 YHFDVLLPVSVFAAAGAVALVRFVRRWLAERTtrrrARVAVAVLLLLAAPV 447
                                       667788888888888888888888887764431111333333333332223 PP

>> Glyco_transf_22  Alg9-like mannosyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.4   1.3e-06     0.012      87     220 ..     117     252 ..      53     287 .. 0.75
   2 ?   -2.4   0.1      0.23   2.1e+03     263     305 ..     397     442 ..     394     449 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-06
                   Glyco_transf_22  87 llallsalidyylfravcrkygseiakialllslsswglfvfstrtfsnslemlltsialyllsellsrenksssne 163
                                        l+l++a +   ++ + ++ + +++  +a++++  s   +++s  ++s + +++l  +a+ +           + + 
  gi|313126250|ref|YP_004036520.1| 117 ALGLVAAGNAAGVYYLGSAAFDRRVGLVAVVALAASPLFLLTSATFLSYAPATML-NLAFAVAYV--R--AARTDSL 188
                                       5777777788888888888899999999999998888777776666666555544.444433332..2..3344456 PP

                   Glyco_transf_22 164 kylvavlliavlavliRptsallwlplvlf....lllrlvkkrsktf...lfliialvllvlll 220
                                       +++va+  ++ la++ Rp  a+l++++ +     +l+ + ++  +tf   + +++   + ++++
  gi|313126250|ref|YP_004036520.1| 189 RWAVASGAAVGLAFFARPYTAVLFAIPFILhtlaVLVTGLRTGDDTFdpaFRRVFKRAVAIAVP 252
                                       9*****************8887777766653555566667777777777655555444444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.23
                   Glyco_transf_22 263 fYllqnlpnilgvlllavllgllvl..lsrkvsr.lllllltillt 305
                                       +++ + lp+ +++ + av+l+ +v   l+ + +r    +++++ll 
  gi|313126250|ref|YP_004036520.1| 397 YHFDVLLPVSVFAAAGAVALVRFVRrwLAERTTRrRARVAVAVLLL 442
                                       7777888887777777777777766442223333233344444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4178.03
//
Query:       gi|313126251|ref|YP_004036521.1|  [L=54]
Description: hypothetical protein Hbor_15030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.34s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 317.46
//
Query:       gi|313126252|ref|YP_004036522.1|  [L=376]
Description: spermidine/putrescine ABC transporter ATPase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-34  118.0   0.0    6.4e-34  117.4   0.0    1.3  1  ABC_tran     ABC transporter
    1.9e-07   31.1   0.3    1.9e-07   31.1   0.3    2.2  2  TOBE_2       TOBE domain
    2.1e-06   27.8   0.5      0.015   15.1   0.1    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.2e-05   24.0   0.1    7.8e-05   23.1   0.1    1.4  1  AAA_16       AAA ATPase domain
    6.8e-05   22.9   0.0    0.00014   21.8   0.0    1.4  1  Rad17        Rad17 P-loop domain
     0.0023   18.4   0.0      0.015   15.7   0.0    2.1  1  AAA          ATPase family associated with various cellular a
     0.0039   17.5   0.4       0.01   16.1   0.4    1.8  1  AAA_22       AAA domain
     0.0047   17.1   0.0      0.014   15.6   0.0    1.8  1  AAA_33       AAA domain
     0.0088   16.0   0.0      0.018   15.0   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
       0.01   16.1   0.1      0.076   13.3   0.0    2.1  2  AAA_28       AAA domain
      0.063   13.5   0.3       0.33   11.2   0.3    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.16   11.7   0.0       0.34   10.6   0.0    1.5  1  AAA_30       AAA domain
       0.17   11.9   0.5       0.49   10.4   0.1    1.9  2  AAA_5        AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.0   4.7e-37   6.4e-34       2     136 ..      37     179 ..      36     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 4.7e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       +++sl+++ege++ ++G++G+GK+t l+llagl++p+ G ++l+g+ ++  +  +  ++ +gv++qe  lfp+lt+r
  gi|313126252|ref|YP_004036522.1|  37 HDLSLSVREGEILTLLGPSGCGKTTTLRLLAGLERPDGGAVRLNGRVVSGtEFVPPEERGVGVVFQEFALFPHLTAR 113
                                       799*******************************************9999677888999****************** PP

                                       HH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en           e +++++++l+ ++l+   d+     p +LSgGq+qrvalar+l+ +p++lllDEp+
  gi|313126252|ref|YP_004036522.1| 114 ENiafgladrsdaETEQRVDELLELVDLPRQGDS----YPDELSGGQQQRVALARSLAPEPDILLLDEPF 179
                                       *********8777777777777777777774444....46*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.8   1.1e+04      39      53 ..     152     166 ..     151     171 .. 0.64
   2 !   31.1   0.3   1.4e-10   1.9e-07       1      74 [.     293     363 ..     293     365 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.8
                            TOBE_2  39 laggqlvvvrqpnad 53 
                                       l ggq+++v+ + + 
  gi|313126252|ref|YP_004036522.1| 152 LSGGQQQRVALARSL 166
                                       677888887776654 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.4e-10
                            TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddav 74 
                                       + +RP++++  a ++++  sG+V+ + ylG + +y vel+ g++v +  ++ +   ++  +  V++++d+ + +
  gi|313126252|ref|YP_004036522.1| 293 VLVRPDDVSARACEPGEEPSGRVVARRYLGPTFLYEVELETGERVQCMHNHDE---DVPDDGPVAVEIDAGHEL 363
                                       689*******533335799*************************999888888...8999999***99999875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00022      0.31       3      24 ..      50      71 ..      48      97 .. 0.78
   2 !   15.1   0.1   1.1e-05     0.015     228     298 ..     143     211 ..     104     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                       l Gp g+GK++ L++l +l r
  gi|313126252|ref|YP_004036522.1| 50 TLLGPSGCGKTTTLRLLAGLER 71
                                      699**************99954 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-05
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkll....rrllellkelsrngaQviltTHS 298
                                       + ++  ++elS G+++  al+ +l+  +   ++ll+DEp ++L+  l     +++ ++lke+   g+  i +TH+
  gi|313126252|ref|YP_004036522.1| 143 RQGDSYPDELSGGQQQRVALARSLAPEP---DILLLDEPFSNLDVDLRvqmrEEVRRILKEA---GVTAISVTHD 211
                                       4556678899****99989999999888...**************66622324444555444...7777777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   5.7e-08   7.8e-05      18     107 ..      42     148 ..      32     204 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.7e-08
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd.ggif.lrgkcdqlesaipy..salaqalareellrqlldeae 90 
                                       +vr+g  e++ l G+sG+GK++ +r l+  le+  gg + l+g+ ++ ++ +p     +  ++ +  l+  l ++++
  gi|313126252|ref|YP_004036522.1|  42 SVREG--EILTLLGPSGCGKTTTLRLLA-GLERPdGGAVrLNGRVVSGTEFVPPeeRGVGVVFQEFALFPHLTAREN 115
                                       45555..89*******************.566662444456666666544433354224444444467777777744 PP

                            AAA_16  91 saeleawrekleeala................a 107
                                        a   a+r   e++ +                 
  gi|313126252|ref|YP_004036522.1| 116 IAFGLADRSDAETEQRvdellelvdlprqgdsY 148
                                       433333333333333333333344455544441 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     1e-07   0.00014      33      68 ..      34      69 ..      26     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLske 68
                                      + ++  +L  r+ +iL + GPsGCgk+t+++ L+  
  gi|313126252|ref|YP_004036522.1| 34 TVIHDLSLSVREGEILTLLGPSGCGKTTTLRLLAGL 69
                                      56666788889899******************9864 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.015       2      66 ..      50     177 ..      49     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                       EEESSTTSSHHHHHHHHHHH.......HTHEEEEEETTTCSSS.................................. CS
                               AAA   2 llyGppGtGKTllakavake.......lgvefleisgsellsk.................................. 37 
                                        l Gp G+GKT++ + +a         +  +   +sg+e++                                    
  gi|313126252|ref|YP_004036522.1|  50 TLLGPSGCGKTTTLRLLAGLerpdggaVRLNGRVVSGTEFVPPeergvgvvfqefalfphltareniafgladrsda 126
                                       589***************98554444434555666666666334677777777777777777777777777777777 PP

                                       .....................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 .....................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                            y  e +   ++ ++ a++ a +p il++DE
  gi|313126252|ref|YP_004036522.1| 127 eteqrvdellelvdlprqgdsYPDELSGGQQQRVALARSLApEPDILLLDE 177
                                       777777777777777777777888888888888888888888788888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   7.5e-06      0.01       4      29 ..      45      70 ..      43     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.5e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      +  il++ G+sG+GKTt+lr l+   
  gi|313126252|ref|YP_004036522.1| 45 EGEILTLLGPSGCGKTTTLRLLAGLE 70
                                      56799***************998764 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05     0.014       3     122 ..      50     229 ..      48     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdt........................................... 32 
                                        l G++G+GK+t ++ l+  +     av+l+  +                                           
  gi|313126252|ref|YP_004036522.1|  50 TLLGPSGCGKTTTLRLLAGLERpdggAVRLNGRVvsgtefvppeergvgvvfqefalfphltareniafgladrsda 126
                                       578**********99985433345799****9999999999999999999988888888888888877777777777 PP

                            AAA_33  33 .......lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnls......rrerarflklarrlg 96 
                                              ++  l+   +q ++++ +++    q++ +lar+ + +   ++ld ++ +       + r++++++++++g
  gi|313126252|ref|YP_004036522.1| 127 eteqrvdELLELVDLPRQGDSYPDELSGGQQQRV-ALARSLAPEPDILLLDEPFSNldvdlrVQMREEVRRILKEAG 202
                                       6666655555555566666667777887788887.899988888888999*99777767774577799******999 PP

                            AAA_33  97 vpvrivvvetdeet.lkeRlakRaang 122
                                       v    v+ +  e++ + +R+a+ ++ +
  gi|313126252|ref|YP_004036522.1| 203 VTAISVTHDQEEALsISDRVAVMNDGN 229
                                       887777777666653456666666554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05     0.018      66     122 ..      12      69 ..       2      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  66 eelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       e+ +e  + l+++ l+ s  t++ +++l+  +++ ++ +l+G+SG GK+t +  l++ 
  gi|313126252|ref|YP_004036522.1|  12 ETRSESEAVLELDGLKKSYGTETVIHDLSLSVREgEILTLLGPSGCGKTTTLRLLAGL 69 
                                       555566666777888888999999999*9999988****************9999875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.5e-05     0.076       4      27 ..      51      90 ..      49     134 .. 0.64
   2 ?    0.3   0.0      0.54   7.4e+02     130     161 ..     183     213 ..     159     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.5e-05
                            AAA_28  4 itGgestGKTtlleaLa........ar........gypvv 27
                                      ++G++++GKTt+l+ La        a         g++ v
  gi|313126252|ref|YP_004036522.1| 51 LLGPSGCGKTTTLRLLAglerpdggAVrlngrvvsGTEFV 90
                                      79***************77444443103343445555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.54
                            AAA_28 130 dleereaiderlrealrelgipviivpsgdve 161
                                       d++ r ++ e +r +l+e+g+  i v + d e
  gi|313126252|ref|YP_004036522.1| 183 DVDLRVQMREEVRRILKEAGVTAISV-THDQE 213
                                       67889999999**********99999.66655 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00024      0.33      61      84 ..     167     190 ..     146     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                           SbcCD_C  61 epalrlvfLDEAFsklDeesiatl 84 
                                        p +++++LDE Fs+lD + + ++
  gi|313126252|ref|YP_004036522.1| 167 APEPDILLLDEPFSNLDVDLRVQM 190
                                       5789*************9987666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.34      19      49 ..      47      77 ..      39      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrv 49
                                       + +l Gp G GKtt+l+ l+ + + +gg v
  gi|313126252|ref|YP_004036522.1| 47 EILTLLGPSGCGKTTTLRLLAGLERPDGGAV 77
                                      478899*************999888777666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00036      0.49       3      21 ..      50      68 ..      48      90 .. 0.90
   2 ?   -1.1   0.0       1.2   1.7e+03      65     123 ..     169     228 ..     153     247 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                                      EEE--SSSSHHHHHHHGGG CS
                             AAA_5  3 lLvGppGtgKselaerlaa 21
                                       L+Gp+G+gK++  + la 
  gi|313126252|ref|YP_004036522.1| 50 TLLGPSGCGKTTTLRLLAG 68
                                      69************99986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                       G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---..........-EEEEEESS- CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkakndd.ller...frviatanpl 123
                                       e++il+lDE +  + +v  ++++  e rr+l e g + +++  d+    +      +a +n+ 
  gi|313126252|ref|YP_004036522.1| 169 EPDILLLDEPF-SNLDVDLRVQMREEVRRILKEAGVTAISVTHDQeE--AlsiSDRVAVMNDG 228
                                       67777777766.55555556666666666666667776666665422..13353333344433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2169.82
//
Query:       gi|313126253|ref|YP_004036523.1|  [L=535]
Description: iron ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-24   85.7  36.4    1.4e-13   51.0   3.5    3.8  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.035   14.0   0.0      0.082   12.8   0.0    1.6  1  DUF1952       Domain of unknown function (DUF1952)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   3.5   1.6e-17   1.4e-13       2     131 ..      82     228 ..      81     266 .. 0.81
   2 ?    1.3   3.8     0.028   2.5e+02     112     164 ..     299     353 ..     292     357 .. 0.73
   3 !   46.0  13.0   5.3e-16   4.8e-12       1     168 [.     354     522 ..     350     529 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.6e-17
                      BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf..............vilsilghlilpviilll 61 
                                       illG+ +a   ++   +++++ ++ + ++l +Ps++ a+ +v +f              v +    ++  + +++l+
  gi|313126253|ref|YP_004036523.1|  82 ILLGVPLAyltVRTDLPFRRFWTVAVSLPLVIPSYIGAFAFVSAFgprgdlqrvlaplgVEQLPEIYGLQGTVLVLT 158
                                       67888888555566666666667777777777777777777777789999999999986677777799999****** PP

                      BPD_transp_1  62 lsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl 131
                                       l++ pyv+++ ra l+s+++ l+ aar+l  +rw+ f++v++P++ p +++g +la  ++l ++  ++++
  gi|313126253|ref|YP_004036523.1| 159 LYTYPYVYITARASLKSMDTTLIDAARTLEHGRWEAFKRVTVPQIRPAVAAGSLLAGLYVLSDFGTPSIM 228
                                       *************************************************************999888776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.028
                      BPD_transp_1 112 tglilafggllggavlleflgswpGlgtllleailgydyseis..nggvlalvia 164
                                         ++  +++++   +l+ +lg++++  ++ l ++++y +++is   g++la+++a
  gi|313126253|ref|YP_004036523.1| 299 CAAVAGLALVVPLGILVTWLGTSNAAVNQSLAFEWQYVFNSISvsTGAALAAIVA 353
                                       5556666677777789999999999******************443333333333 PP

  == domain 3  score: 46.0 bits;  conditional E-value: 5.3e-16
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g+++++l+a +++++l+ l+ + ++v++++P +vl++ lv++ +  ++  +  l+ +++++++ ++p ++   ra +
  gi|313126253|ref|YP_004036523.1| 354 GLPVAYLSA-RHSNRLSPLFERATYVGYAVPGVVLGLALVYFGSSVGAPVYPSLYlLVFAYVIRFLPQAVGSLRASF 429
                                       678888888.******************************99999999999999989******************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                         ++ +l eaar+lG + +  fr+v+lP+++p ++ g++l+f   +++  ++++l    + g  +l + ++  y ++
  gi|313126253|ref|YP_004036523.1| 430 LRVDPSLPEAARTLGRTSIGAFRHVTLPLVAPGLFGGAALVFLTTMKELPATLLLR---PSGFKTLVTHIWTAYESG 503
                                       *******************************************************9...345555555566666655 PP

                      BPD_transp_1 154 s....nggvlalviavlll 168
                                       +    ++++l+l+++  l 
  gi|313126253|ref|YP_004036523.1| 504 YfgqaAIPALVLLFVSGLS 522
                                       5322213333333333333 PP

>> DUF1952  Domain of unknown function (DUF1952)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.2e-06     0.082      39      73 .]     418     452 ..     407     452 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.2e-06
                           DUF1952  39 ePlkvGslrisrleveveGeeaerWaeriavaasr 73 
                                        P+ vGslr s l+v+    ea r   r +++a r
  gi|313126253|ref|YP_004036523.1| 418 LPQAVGSLRASFLRVDPSLPEAARTLGRTSIGAFR 452
                                       599*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3228.20
//
Query:       gi|313126254|ref|YP_004036524.1|  [L=394]
Description: iron ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-16   59.4   0.0    4.4e-16   59.0   0.0    1.1  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    5.7e-11   42.6   0.2      1e-10   41.7   0.2    1.5  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    1.1e-08   35.2   0.0    1.6e-08   34.7   0.0    1.2  1  SBP_bac_8   Bacterial extracellular solute-binding protein
     0.0013   18.8   0.0     0.0041   17.1   0.0    1.8  1  SBP_bac_1   Bacterial extracellular solute-binding protein
      0.004   16.5   0.8      0.011   15.1   0.8    1.8  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T
  ------ inclusion threshold ------
      0.037   13.9   1.3      0.037   13.9   1.3    1.9  2  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   1.5e-19   4.4e-16       1     220 [.     134     356 ..     134     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.5e-19
                         SBP_bac_6   1 nplpdlilsfdkdflekfieeglfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpvPksW 77 
                                       n+ +d+++s++  +l+ +++ +  q l+++ l+ v+     + ++d+dg +++ +  + ++ +n+  +k+ ++P + 
  gi|313126254|ref|YP_004036524.1| 134 NSPADVFYSVNAGALGALKQRERTQSLPQEVLEFVP-----KSFRDSDGMWVGSSGRARSVPYNTNTFKESDIPDDI 205
                                       6789********************************.....999******************************999 PP

                         SBP_bac_6  78 aDLl.dPeykgkvalpgnngsdlfealllalykdfgedgvkkllrnlkanlhpaq..mvkaagslesgepavsvvpy 151
                                         +  + +++g+ +   +   ++f+a++ a++  +ged+ +k+l+ + +++ + +    + a +++ ge  +s +++
  gi|313126254|ref|YP_004036524.1| 206 MSFPdQSNFEGELGWAPTY--SSFQAFITAMRILEGEDATRKWLKGIQDLGVSQYgdEFQVARAVADGE--ISAGFT 278
                                       99985789******99977..8*********************************999999********..665554 PP

                         SBP_bac_6 152 ffadilpekkkgk.....nlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvv... 219
                                         + i +   +++     ++ ++    Ga++++  ++v    k  +la  f+  lls+e+q ++a+ ++++P v   
  gi|313126254|ref|YP_004036524.1| 279 NHYYIQRVLARRGlstplRTTFTKGDAGAVFNVAGACVLDTaKDTSLASNFVRHLLSAEAQDYFARTTFEYPLVpei 355
                                       444444444433455755566666666*********************************************97666 PP

                         SBP_bac_6 220 t 220
                                       +
  gi|313126254|ref|YP_004036524.1| 356 E 356
                                       3 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.2   3.5e-14     1e-10      23     229 ..     109     347 ..      87     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 3.5e-14
                                       HH---EEEEESSHHHHHHHH.HHH....-SEEEESSH.HHHHHHHHGGGGG.......GG-EEEEEEEEEEEESTT- CS
                        SBP_bac_11  23 htgvkvevsaggsgklarqi.adga..rpDvwipassawlellaaaglvqa.......esavplassplviavpkgn 89 
                                       +++ +v+  + ++++l++qi ++g+  ++Dv+ + ++++l +l++++++q+         ++++  s   ++   g+
  gi|313126254|ref|YP_004036524.1| 109 YPDFTVRPLYNSAAELVNQIaTEGQnsPADVFYSVNAGALGALKQRERTQSlpqevleFVPKSFRDSDGMWVGSSGR 185
                                       577899999***********5445589****************************9997888888899999999998 PP

                                       ................TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--....HHHHHHHHHTEEEEESS CS
                        SBP_bac_11  90 ................pkkikgwadLlkpglklavadPttspsGlaalalleaaga....qellkalekkvvklges 146
                                                       p++i+++ d  + + +l+ a P t +s +a +++++ +++    +++lk +++  v + ++
  gi|313126254|ref|YP_004036524.1| 186 arsvpyntntfkesdiPDDIMSFPDQSNFEGELGWA-P-TYSSFQAFITAMRILEGedatRKWLKGIQDLGVSQYGD 260
                                       777777777777777778899999988888899999.4.56777777788886666678899********9999999 PP

                                       HHHHHHHHHTTT-SEEEEEHHHH...H.....HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTS CS
                        SBP_bac_11 147 srqlltaveageadagivyesea...kaa...engdkleavylpeglnldpldypaavlkkaakreaAraFlafLrs 217
                                       + q++ av++ge+ ag+++   +   +a+   + + ++++    +g ++   + +a+vl++a++   A  F++ L+s
  gi|313126254|ref|YP_004036524.1| 261 EFQVARAVADGEISAGFTNHYYIqrvLARrglSTPLRTTFTKGDAGAVF--NVAGACVLDTAKDTSLASNFVRHLLS 335
                                       *****************87444433344443334445555556666665..58999********************* PP

                                       HHHHHHHHHTT- CS
                        SBP_bac_11 218 peaqailrkyGf 229
                                       +eaq+ +++  f
  gi|313126254|ref|YP_004036524.1| 336 AEAQDYFARTTF 347
                                       *******99877 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   5.5e-12   1.6e-08       4     267 ..     103     354 ..     100     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.5e-12
                                       HHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-HHHHHTT- CS
                         SBP_bac_8   4 kefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddltdalaavg 79 
                                       +  e+ + +++v+  + + ++l++++ ++ +   a d++  + n++al++l+++  ++ l + + l+ +++ +++  
  gi|313126254|ref|YP_004036524.1| 103 SYIEDLYpDFTVRPLYNSAAELVNQIATEGQNSPA-DVF-YSVNAGALGALKQRERTQSLPQ-EVLEFVPKSFRDS- 175
                                       55666677899***9**9**********9976555.665.7888999*************97.7799999999975. PP

                                       -TS.----EEEEE.EE-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-SEGG---GGGGGGTHHETTEE---H..H CS
                         SBP_bac_8  80 ydgklygvPyase.tpyvliynkdllekaedpktwdellaaakklkgkfglpdpasgwlqaallakdgksldddggk 155
                                        dg    +++ s+ +   + yn+  +++ + p+++  + +    ++g  g++ p+++++qa+ +a            
  gi|313126254|ref|YP_004036524.1| 176 -DG----MWVGSSgRARSVPYNTNTFKESDIPDDIMSFPD-QSNFEGELGWA-PTYSSFQAFITA-MRIL------- 237
                                       .45....3333331345688*******8679999999988.55679****85.666666666666.3222....... PP

                                       HH.HHHHHHHHHHHHTT-.EE-S..--SSTTTTTSBSEEEE...-TTHHHHHH-TTTSEEEE--S-..-EEEEEEEE CS
                         SBP_bac_8 156 dglkealellkklkdngk.tydtgadavsefanGevaftin...gswdiaaaqkagkklgaivpkq..gsfaggkgl 226
                                       +g ++++++lk ++d g+ +y++  ++  ++a+Ge+ ++++   + +++ a +  + +l+ ++ k   g++ +++g 
  gi|313126254|ref|YP_004036524.1| 238 EGEDATRKWLKGIQDLGVsQYGDEFQVARAVADGEISAGFTnhyYIQRVLARRGLSTPLRTTFTKGdaGAVFNVAGA 314
                                       334799**********9779999999999***********74446666667777778*****9854358******** PP

                                       EEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S- CS
                         SBP_bac_8 227 avpknaknedlaAldFlkwltspenqaalaektgyipvnks 267
                                       +v+  ak+  l A  F+++l+s+e+q  +a +t   p  ++
  gi|313126254|ref|YP_004036524.1| 315 CVLDTAKDTSL-ASNFVRHLLSAEAQDYFARTTFEYPLVPE 354
                                       **********9.*****************998887776665 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.4e-06    0.0041      16     314 ..     103     339 ..      91     340 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHT....TSBECCHHHHHHTTECTTC CS
                         SBP_bac_1  16 kafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlaka....glllpldpyvkaylapgvk 87 
                                        + e ++p+ +V+  + +  +l +  ++a+++ + paDv+++ + + ++ l++      l++++ ++v +       
  gi|313126254|ref|YP_004036524.1| 103 SYIEDLYPDFTVRPLYNSAAELVN--QIATEGQNSPADVFYSvNAGALGALKQRertqSLPQEVLEFVPKS------ 171
                                       4567889*****************..99999999999*****66666666655523333333333333333...... PP

                                       CTEEEEHHHHTHHHHC.EEEESEEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHH CS
                         SBP_bac_1  88 daadklsssvlpkild.skvlyvPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsas 162
                                             + + ++ + + s        + ar + YN+  f++++++     d+++         g+ +         +
  gi|313126254|ref|YP_004036524.1| 172 ------FRDSDGMWVGsS--------GrARSVPYNTNTFKESDIP-----DDIMSFPDQSNFEGELG---------W 220
                                       ......333333333311........33888888******99999.....88888888888888887.........2 PP

                                       HHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHH....HHHHHHHTTSC CS
                         SBP_bac_1 163 gtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdga....aalalfeaGea 235
                                         +y  +       +                   +t+++ l++++   k lkg + +++++     +++++++ Ge+
  gi|313126254|ref|YP_004036524.1| 221 APTYSSF------QA------------------FITAMRILEGEDATRKWLKGIQDLGVSQYgdefQVARAVADGEI 273
                                       2222222......22..................44555555555554444444443333322111256777779999 PP

                                       SEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                         SBP_bac_1 236 amaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspe 312
                                        +++  +++++ ++   + +    ++  +++  +v+             ++ g  ++ ++k+   A  F++ lls+e
  gi|313126254|ref|YP_004036524.1| 274 SAGFTNHYYIQRVLARRGLSTPLRTTFTKGDAGAVF-------------NVAGACVLDTAKDTSLASNFVRHLLSAE 337
                                       999999998887776666666666666666666665.............8889999999999888999999999988 PP

                                       HH CS
                         SBP_bac_1 313 aq 314
                                       aq
  gi|313126254|ref|YP_004036524.1| 338 AQ 339
                                       88 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.8   3.7e-06     0.011       4      29 ..       6      30 ..       3      31 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-06
                        UCR_Fe-S_N  4 aesdeptRRDFLyiATgavgaVGaaa 29
                                       e+++ +RR+FL  A++a+g +G+a 
  gi|313126254|ref|YP_004036524.1|  6 GEHRGRSRRRFL-QAAAAAGIIGVAG 30
                                      677889******.899999*****96 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.3   1.2e-05     0.037       3      15 ..      12      24 ..      12      34 .. 0.73
   2 ?   -4.2   1.8         6   1.8e+04      12      16 ..     146     150 ..     145     151 .. 0.36

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                        TAT_signal  3 SRRdFLKgsAAaa 15
                                      SRR FL+++AAa+
  gi|313126254|ref|YP_004036524.1| 12 SRRRFLQAAAAAG 24
                                      9******777776 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 6
                        TAT_signal  12 AAaaA 16 
                                       +A++A
  gi|313126254|ref|YP_004036524.1| 146 GALGA 150
                                       34443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2553.31
//
Query:       gi|313126255|ref|YP_004036525.1|  [L=389]
Description: reversibly glycosylated polypeptide [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-15   57.2   0.0    1.8e-15   56.9   0.0    1.3  1  RGP       Reversibly glycosylated polypeptide


Domain annotation for each model (and alignments):
>> RGP  Reversibly glycosylated polypeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0     1e-19   1.8e-15      94     289 ..     111     322 ..       2     368 .. 0.75

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1e-19
                               RGP  94 sidddcvpak..dekGllvdavaqhiknlktPatPfffntlydPyreGadfvrGyPfs.lreGvet........als 159
                                        iddd +p    d  G +++ ++   +  +  +   + n ly    e   + rGyP+s + e vet        + s
  gi|313126255|ref|YP_004036525.1| 111 FIDDDTLPHDewDFFGRHMENLDYEGELESVRSDERWVNVLYQNADEHGLYPRGYPYSaMDESVETterdvenvVAS 187
                                       56666666542244455555555444434456777899*******************94455665522222222689 PP

                               RGP 160 lGlwlnladydaptqlvk...aeerntryvdavlt....vPkkallpvsGinlafdrelvGpalfealklagegklr 229
                                        Glw n++d+da   l+    +++ +tr   + +t       +  l+v+ +nlaf+re++ +    ++  ++ +  r
  gi|313126255|ref|YP_004036525.1| 188 QGLWTNVPDLDAVRILMDgdlEGQAQTRTEKSDFTgdfvADPGQYLTVCSMNLAFEREVIPAFYQLPMDDNEWSVGR 264
                                       ************99888622223444444444333222134567889***********9965555555555667789 PP

                               RGP 230 yetledlwaGlcvkvicdhlglGvktGlPyvlrkeasn.aleslkkeweGvklmeevvpff 289
                                       ++   d+w+G+ +k  +d l+  v tG P   +++a   +++ l++e  G++l e+v    
  gi|313126255|ref|YP_004036525.1| 265 FD---DIWSGVFLKRAADLLDGEVLTGYPLCEHNKAPRpTFDDLNNEVPGLELNEHVWEVV 322
                                       98...*****************************887625899**********99987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2613.96
//
Query:       gi|313126256|ref|YP_004036526.1|  [L=150]
Description: hpp family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-14   53.1  10.3    3.4e-14   53.1  10.3    1.4  2  HPP           HPP family
  ------ inclusion threshold ------
       0.11   12.4   0.6       0.87    9.5   0.0    2.2  2  DUF1418       Protein of unknown function (DUF1418)
       0.13   12.0   0.0       0.17   11.5   0.0    1.1  1  Peptidase_C5  Adenovirus endoprotease


Domain annotation for each model (and alignments):
>> HPP  HPP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.3   7.7e+03     108     108 ..      16      16 ..       3      26 .. 0.43
   2 !   53.1  10.3   5.7e-18   3.4e-14       1     101 [.      30     141 ..      30     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.3
                               HPP 108 l 108
                                       +
  gi|313126256|ref|YP_004036526.1|  16 T 16 
                                       1 PP

  == domain 2  score: 53.1 bits;  conditional E-value: 5.7e-18
                               HPP   1 liaslGAsavllfavpesplaqPrnvvgGhlisalvGvaiaklfgl.............sllwlaaalavalaialm 64 
                                       l++slG sa++l    + p   Pr+v+gGh ++ ++G++++ +++              + l+l++ +av+l+ + m
  gi|313126256|ref|YP_004036526.1|  30 LFPSLGPSAFVLAVRESGP--TPRTVLGGHAVGVACGLFTYLAVSTflsvpttpldfhpPWLVLSGVVAVGLTSTGM 104
                                       79*********98877777..7*****************87777778889*******7655556************* PP

                               HPP  65 lltrtlhPPagAtaliavlgkeikelgwafllvpvll 101
                                       l+++++hPPa+At+li++lg  ++  ++a++l +v++
  gi|313126256|ref|YP_004036526.1| 105 LAFDAVHPPACATTLIVALGLMSTPAEVALVLPSVAS 141
                                       ********************98666666666554433 PP

>> DUF1418  Protein of unknown function (DUF1418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00015      0.87       5      37 ..      47      79 ..      43      99 .. 0.89
   2 ?    1.0   0.5     0.066   3.9e+02      44      68 ..     116     139 ..      89     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00015
                           DUF1418  5 gklPrsvlilevlGliLLvlayLsvndylsLPg 37
                                      g  Pr+vl    +G+     +yL+v+ +ls+P 
  gi|313126256|ref|YP_004036526.1| 47 GPTPRTVLGGHAVGVACGLFTYLAVSTFLSVPT 79
                                      778****************************96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.066
                           DUF1418  44 aaivmiflGvllllPaavalvwrva 68 
                                       a+++++ lG++   Pa valv+  +
  gi|313126256|ref|YP_004036526.1| 116 ATTLIVALGLM-STPAEVALVLPSV 139
                                       34444444543.3689998887544 PP

>> Peptidase_C5  Adenovirus endoprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.9e-05      0.17      98     139 ..      60     101 ..      52     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
                                       ---HHHHHHHHHHHHHH-TTS-SSSSTTGGGS--EEGGGTTS CS
                      Peptidase_C5  98 saacGlfcilflasfarykqkpldgnpvidlvdGvkpsklns 139
                                         acGlf+ l + +f   +++pld  p    ++Gv    l s
  gi|313126256|ref|YP_004036526.1|  60 GVACGLFTYLAVSTFLSVPTTPLDFHPPWLVLSGVVAVGLTS 101
                                       569*********************999888888887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 978.78
//
Query:       gi|313126257|ref|YP_004036527.1|  [L=800]
Description: helicase with metal-binding cysteine cluster [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.4e-23   81.4   0.0    9.4e-23   80.9   0.0    1.2  1  DEAD        DEAD/DEAH box helicase
      9e-22   77.6   0.1    2.4e-21   76.3   0.1    1.8  1  DUF1998     Domain of unknown function (DUF1998)
    1.4e-09   38.3   0.0    3.8e-09   36.9   0.0    1.7  2  Helicase_C  Helicase conserved C-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.0   1.6e-26   9.4e-23       2     174 ..      54     230 ..      53     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 1.6e-26
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid... 75 
                                       + Qaeai+++ +g++v++a +T+sGK+la+ +p++++      ++g ++l++ P  +L+ ++ ++l+ +  +++   
  gi|313126257|ref|YP_004036527.1|  54 RHQAEAIDAVRDGENVVLATQTASGKSLAYTVPAFERA----MDHGGRTLYLGPQNALIADQDETLSDLAFTLGfgs 126
                                       68*********************************999....57999**********************99866664 PP

                                       .SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH..HCTSSH...CTTEEEEEEETHHHHHHTTTHHHHHHHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 .lrvlliiggvaardqlskldngvdivvgtpgrlddll..stgkln...lsqvrflVlDEadrlldqgfsdfinril 146
                                        ++v+  +g  ++++++++ d+++ +++++p++l+  l  + ++l    +s+++++V+DE++++    f+ ++   l
  gi|313126257|ref|YP_004036527.1| 127 rVSVEQYTGRLSKTEKRDVRDRRPTVLLSNPDMLHYALlpHAHRLWewfFSSLETVVIDEIHGYRGV-FGSHVALTL 202
                                       44444445555555555555688*************6658334433466*****************9.********* PP

                                       HHSHHHCTTSTTTSEEEEEESSBSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 147 nqlpqitcdgklqrqvivlSATlpkdvk 174
                                       ++l++i+++  ++ q +++SAT+ + v+
  gi|313126257|ref|YP_004036527.1| 203 RRLNRICERFDSDPQYVCCSATIGNPVE 230
                                       *******9999999********986665 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.1     4e-25   2.4e-21       1      83 []     685     764 ..     685     764 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 4e-25
                           DUF1998   1 lehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaelleellraalelieecdCeea 77 
                                       +eh +i+++pl + cd++d+g+ +++++  +++++ +i++yd++pgG+G++e++++ +e+llr++ eli++cdCe +
  gi|313126257|ref|YP_004036527.1| 685 AEHGMISLFPLSFLCDRGDIGGLSTPHH--THTDQSTIFVYDGHPGGVGLTENGYDEVETLLRRTHELIRDCDCE-D 758
                                       68**********************9664..489*****************************************8.* PP

                           DUF1998  78 GCpaCl 83 
                                       GCpaC+
  gi|313126257|ref|YP_004036527.1| 759 GCPACV 764
                                       *****8 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.1   1.3e+04      55      77 ..      56      77 ..      53      77 .. 0.78
   2 !   36.9   0.0   6.4e-13   3.8e-09       6     110 ..     289     399 ..     284     400 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.1
                                      HHHHHHHHHTTSSSEEEESGGGT CS
                        Helicase_C 55 reeileqfnkgesdvLiatdvae 77
                                      + e++++ ++ge +v++at+ a+
  gi|313126257|ref|YP_004036527.1| 56 QAEAIDAVRDGE-NVVLATQTAS 77
                                      678889998888.8999998775 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 6.4e-13
                                       HHHHHHHTTTTSEEEEEESSHHHHHH.....HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEES CS
                        Helicase_C   6 llellkleeeggkilifvntidrlek.....vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiat 73 
                                       +++ll   ++g+++l f++ ++ +e+     ++ l+e+     +  v ++++ l++++r++i +   +g+++ + +t
  gi|313126257|ref|YP_004036527.1| 289 FVDLL---SRGHQTLAFTRARQAAERyatesAEDLRERGeseaAAGVSAYQAALKHEKRRKIESGLHDGSVTGVWST 362
                                       45555...99************8875554444555444466667888899999************************ PP

                                       GGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  74 dvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       +++e G+d+ +++ V + ++p +  s+ q++GR+gR+
  gi|313126257|ref|YP_004036527.1| 363 NALELGVDVGGLDAVLIDGYPGTRMSAFQQAGRAGRG 399
                                       ************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (800 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 4729.70
//
Query:       gi|313126258|ref|YP_004036528.1|  [L=141]
Description: hypothetical protein Hbor_15100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-06   28.1   0.0    5.6e-06   27.7   0.0    1.2  1  DUF393    Protein of unknown function, DUF393


Domain annotation for each model (and alignments):
>> DUF393  Protein of unknown function, DUF393
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   3.1e-10   5.6e-06       1      81 [.       8      83 ..       8     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.1e-10
                            DUF393  1 vlyDgeCplCnravqflerrdrkgrirfadlqsasgkallkelgidaeqldslllvieagr.vysgsdAaleiaralpg 78
                                      ++yDgeCp C+ a++ l+++d+ g i++      +++a l e ++  e   ++llv+++++ vy g  Aa+e+a++ + 
  gi|313126258|ref|YP_004036528.1|  8 LVYDGECPYCSIAARALRELDNVGAISWYED---TAQAFL-ERQFG-ETPFAMLLVDRREEcVYAGRSAAAELASRAGT 81
                                      68*******************9999998765...666655.44444.44444555433333799999999999888776 PP

                            DUF393 79 lwr 81
                                        +
  gi|313126258|ref|YP_004036528.1| 82 -PG 83
                                      .33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 831.82
//
Query:       gi|313126259|ref|YP_004036529.1|  [L=147]
Description: hypothetical protein Hbor_15110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-29  102.1   0.0    2.2e-29  101.8   0.0    1.1  1  DUF123    Domain of unknown function DUF123


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.0   1.2e-33   2.2e-29       2      93 ..      30     121 ..      29     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 1.2e-33
                            DUF123   2 elkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvvaseerlEcalaeal.eaeap 77 
                                       e+++g+y+Y+Gsa+gs+gl  Rv rH+++++++++ +hWh+Dy+  ++e+el +v +a ++++Eca+a+al  +++p
  gi|313126259|ref|YP_004036529.1|  30 EFPAGAYAYIGSAFGSNGL-GRVARHCRVAAGEHDVRHWHVDYFGGHSETELVSVAAAPRADAECAVATALgPESSP 105
                                       89*****************.***************************************************55666* PP

                            DUF123  78 vagfGasDckcesHLl 93 
                                       v+gfG+sDc+c++HL+
  gi|313126259|ref|YP_004036529.1| 106 VSGFGSSDCRCHAHLA 121
                                       **************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 862.15
//
Query:       gi|313126260|ref|YP_004036530.1|  [L=263]
Description: MarR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-06   28.3   0.5    3.4e-06   26.8   0.5    1.8  1  MarR_2          MarR family
    1.2e-05   25.1   0.1    2.9e-05   23.9   0.1    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    1.6e-05   24.7   0.0    3.4e-05   23.7   0.0    1.5  1  MarR            MarR family
    3.2e-05   23.5   0.1    8.1e-05   22.2   0.1    1.7  1  GntR            Bacterial regulatory proteins, gntR family
    7.5e-05   22.6   0.1    0.00018   21.4   0.1    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00011   21.7   0.5    0.00049   19.6   0.1    2.3  3  HTH_24          Winged helix-turn-helix DNA-binding
    0.00029   20.6   0.1    0.00075   19.2   0.1    1.8  1  HTH_IclR        IclR helix-turn-helix domain
    0.00075   19.4   0.0     0.0017   18.2   0.0    1.6  1  HTH_11          HTH domain
     0.0011   18.8   0.0     0.0021   18.0   0.0    1.4  1  HTH_36          Helix-turn-helix domain
     0.0012   18.9   0.0     0.0032   17.5   0.0    1.8  1  HTH_20          Helix-turn-helix domain
     0.0013   19.2   0.1     0.0035   17.8   0.1    1.7  1  HTH_27          Winged helix DNA-binding domain
     0.0015   18.4   0.0     0.0029   17.5   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0015   18.7   0.0      0.003   17.7   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0036   17.0   0.1      0.013   15.2   0.0    1.9  2  RP-C            Replication protein C N-terminal domain
      0.008   16.0   0.3      0.008   16.0   0.3    2.6  3  HTH_23          Homeodomain-like domain
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.022   14.4   0.0    1.5  2  DUF4423         Domain of unknown function (DUF4423)
      0.011   15.5   0.1      0.023   14.5   0.1    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.018   15.0   0.0      0.028   14.4   0.0    1.3  1  HTH_45          Winged helix-turn-helix
       0.02   14.9   0.4       0.56   10.3   0.1    2.5  2  HTH_29          Winged helix-turn helix
      0.085   13.0   0.0        9.2    6.4   0.0    2.3  2  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
       0.12   12.7   0.0       0.31   11.4   0.0    1.7  1  Rrf2            Transcriptional regulator


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.5     4e-09   3.4e-06      18      55 ..      17      61 ..       4      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4e-09
                                      TTS.......EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 18 pgr.......dltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +         + + ++l + l +s+s+v r++++Lv+aG+ver +
  gi|313126260|ref|YP_004036530.1| 17 EAVlrrvgpvEQRKRDLSESLSVSRSTVDRAIRELVEAGFVERGE 61
                                      544555554577******************************975 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   3.4e-08   2.9e-05      24      57 ..      29      62 ..      24      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.4e-08
                                      HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      + ++++e l v+rs+v +++r+L+++G+Ver + 
  gi|313126260|ref|YP_004036530.1| 29 RKRDLSESLSVSRSTVDRAIRELVEAGFVERGED 62
                                      5689**************************9876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0     4e-08   3.4e-05      14      49 ..      22      59 ..      18      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4e-08
                                      HSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 14 eqgplsvs..eLakklgvskstvtrvldrLekkGlieR 49
                                      + gp  +   +L + l+vs+stv r++++L+++G++eR
  gi|313126260|ref|YP_004036530.1| 22 RVGPVEQRkrDLSESLSVSRSTVDRAIRELVEAGFVER 59
                                      55666666779**************************9 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   9.5e-08   8.1e-05      28      56 ..      31      59 ..      29      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.5e-08
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglver 56
                                      r+L++ + Vsr+tv +A+r+L+++g ver
  gi|313126260|ref|YP_004036530.1| 31 RDLSESLSVSRSTVDRAIRELVEAGFVER 59
                                      89*************************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   2.1e-07   0.00018      21      55 ..      27      61 ..       8      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.1e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgr 55
                                         +++l++ l ++r+tv r+++eL ++g ++rg 
  gi|313126260|ref|YP_004036530.1| 27 EQRKRDLSESLSVSRSTVDRAIRELVEAGFVERGE 61
                                      55799***************************862 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   5.7e-07   0.00049      21      48 .]      31      58 ..      29      58 .. 0.96
   2 ?   -2.2   0.0       3.7   3.1e+03      32      46 ..     148     162 ..     147     162 .. 0.75
   3 ?   -2.1   0.0       3.4   2.9e+03      36      45 ..     244     253 ..     243     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.7e-07
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                      r+L+e l +S+stv r +++L+e+G+++
  gi|313126260|ref|YP_004036530.1| 31 RDLSESLSVSRSTVDRAIRELVEAGFVE 58
                                      89************************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.7
                            HTH_24  32 stvnrrlkrLeeeGl 46 
                                       s vn++ +r +eeG+
  gi|313126260|ref|YP_004036530.1| 148 SQVNTYHRRIVEEGV 162
                                       678888888888886 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.4
                            HTH_24  36 rrlkrLeeeG 45 
                                       r l rL+e+G
  gi|313126260|ref|YP_004036530.1| 244 RTLSRLWEDG 253
                                       6689999998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   8.8e-07   0.00075      22      50 ..      31      59 ..      13      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.8e-07
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 22 selArrtglpkStvhRlLqtLvelGyveq 50
                                      ++l++ + +++Stv R ++ Lve G+ve+
  gi|313126260|ref|YP_004036530.1| 31 RDLSESLSVSRSTVDRAIRELVEAGFVER 59
                                      79*************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     2e-06    0.0017      20      44 ..      32      56 ..      30      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                            HTH_11 20 eLAeeLnvSrrtvrrdIkaLeelgv 44
                                      +L+e L+vSr+tv r I++L e+g+
  gi|313126260|ref|YP_004036530.1| 32 DLSESLSVSRSTVDRAIRELVEAGF 56
                                      79******************99994 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.4e-06    0.0021      28      54 ..      30      56 ..      24      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-06
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGy 54
                                      +++l++ l +s++Tv rai+eL+++G+
  gi|313126260|ref|YP_004036530.1| 30 KRDLSESLSVSRSTVDRAIRELVEAGF 56
                                      789***********************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.8e-06    0.0032      29      58 ..      32      61 ..      18      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
                                      HHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 29 elaerldlskntlsyHLrvLeeagLvevvr 58
                                      +l e l++s++t+++ +r+L+eag+ve+ +
  gi|313126260|ref|YP_004036530.1| 32 DLSESLSVSRSTVDRAIRELVEAGFVERGE 61
                                      5788899********************865 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   4.1e-06    0.0035       9      53 ..      20      62 ..       9      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.1e-06
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgd 53
                                      L+ ++    +++++dl++ l v+ s++  ++++L+e+G+ver +d
  gi|313126260|ref|YP_004036530.1| 20 LRRVG--PVEQRKRDLSESLSVSRSTVDRAIRELVEAGFVERGED 62
                                      44444..345678***************************88766 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.3e-06    0.0029      19      46 ..      31      58 ..      26      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 19 celaeelglsqstvShHLkkLreaGLVe 46
                                       +l+e l +s+stv++  + L eaG+Ve
  gi|313126260|ref|YP_004036530.1| 31 RDLSESLSVSRSTVDRAIRELVEAGFVE 58
                                      69*************************7 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.5e-06     0.003      25      53 ..      30      58 ..      14      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekdGyve 53
                                      + dl+e L vs s+V   +++L ++G+ve
  gi|313126260|ref|YP_004036530.1| 30 KRDLSESLSVSRSTVDRAIRELVEAGFVE 58
                                      579*************************8 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.5e-05     0.013      75     103 ..      31      59 ..      26      63 .. 0.90
   2 ?   -1.7   0.0       2.3     2e+03     129     146 ..     128     145 ..     127     183 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                              RP-C  75 aqLsralglsestlrrhlaaLveaGliir 103
                                       ++Ls++l++s+st+ r +++LveaG++ r
  gi|313126260|ref|YP_004036530.1|  31 RDLSESLSVSRSTVDRAIRELVEAGFVER 59 
                                       789**********************9865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                              RP-C 129 LsPllaRaeElealaeev 146
                                       L+++++Ra+ ++a a +v
  gi|313126260|ref|YP_004036530.1| 128 LASIIERADRIHAFAPAV 145
                                       566666666666665543 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   9.3e-06     0.008      11      46 ..      19      56 ..      12      59 .. 0.78
   2 ?   -0.5   0.0       1.4   1.2e+03      31      48 ..     147     164 ..     147     166 .. 0.85
   3 ?   -2.8   0.1       7.2   6.2e+03      31      45 ..     243     253 ..     240     255 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.3e-06
                            HTH_23 11 lllla..eGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      +l     + +++r+ ++ L vsr+Tv+r ++  +e G+
  gi|313126260|ref|YP_004036530.1| 19 VLRRVgpVEQRKRDLSESLSVSRSTVDRAIRELVEAGF 56
                                      555553436899*******************9998884 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                            HTH_23  31 rrTvyrwlkryreeGleg 48 
                                       +++v  +++r +eeG+ +
  gi|313126260|ref|YP_004036530.1| 147 PSQVNTYHRRIVEEGVTA 164
                                       5899999***99999865 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.2
                            HTH_23  31 rrTvyrwlkryreeG 45 
                                       rrT++r    + e+G
  gi|313126260|ref|YP_004036530.1| 243 RRTLSRL---W-EDG 253
                                       5666654...3.555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.6e-05     0.022      32      78 ..      23      67 ..      18      76 .. 0.84
   2 ?   -3.5   0.0       8.5   7.2e+03      91     108 ..     147     164 ..     139     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                           DUF4423 32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrq 78
                                      + ++++  + l++ l   +s + v +a++ L+++g++++ edg +r 
  gi|313126260|ref|YP_004036530.1| 23 VGPVEQRKRDLSESLS--VSRSTVDRAIRELVEAGFVERGEDGYVRT 67
                                      56677778899*****..***********************965554 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.5
                           DUF4423  91 seavrsyhkqmlelAiea 108
                                       +  v+ yh+ + e++++a
  gi|313126260|ref|YP_004036530.1| 147 PSQVNTYHRRIVEEGVTA 164
                                       667788888888877655 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.6e-05     0.023      19      52 ..      32      65 ..      29      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                          HTH_DeoR 19 elvellgvSeaTiRRDLneLeeqglltRthGGav 52
                                      +l+e l vS  T+ R ++eL+e+g ++R   G+v
  gi|313126260|ref|YP_004036530.1| 32 DLSESLSVSRSTVDRAIRELVEAGFVERGEDGYV 65
                                      799*************************988876 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.3e-05     0.028      19      74 ..      27      82 ..      17      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                            HTH_45 19 eakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkelee 74
                                      e++k  +  +   s +++++ +  Lve g+++  ++ Yv T  G+ +le ++++ +
  gi|313126260|ref|YP_004036530.1| 27 EQRKRDLSESLSVSRSTVDRAIRELVEAGFVERGEDGYVRTLSGRLVLEAFDRFAN 82
                                      666667777777888899999******************************99976 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00065      0.56      14      46 ..      29      58 ..      10      72 .. 0.78
   2 ?    2.4   0.0      0.19   1.6e+02      26      41 ..     147     162 ..     145     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00065
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGlaalld 46
                                      + +++ + l +sr+tv+r+++  +e G     +
  gi|313126260|ref|YP_004036530.1| 29 RKRDLSESLSVSRSTVDRAIRELVEAG---FVE 58
                                      56888999**************99998...444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.19
                            HTH_29  26 rrtvyrwlkrfeegGl 41 
                                       +++v+++++r +e+G+
  gi|313126260|ref|YP_004036530.1| 147 PSQVNTYHRRIVEEGV 162
                                       689************6 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.037        32      15      30 ..      30      45 ..      25     156 .. 0.82
   2 ?    6.4   0.0     0.011       9.2       2      24 ..     172     195 ..     171     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.037
                                      CHHHHCCTT--HHHHH CS
                     Phage_CI_repr 15 qkeLAdlLgiakssvs 30
                                      +++L++ L++++s+v 
  gi|313126260|ref|YP_004036530.1| 30 KRDLSESLSVSRSTVD 45
                                      679***********96 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                                       HHHHHHHHHT-SSCHHHH.CCTT- CS
                     Phage_CI_repr   2 vleRlmsaygvkmqkeLA.dlLgi 24 
                                       v++Rl+s y +k+q++L+ d+L+i
  gi|313126260|ref|YP_004036530.1| 172 VMNRLVSTYRTKTQEALStDRLEI 195
                                       899**************7366666 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00036      0.31      28      56 ..      30      58 ..      19      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 28 seeiaerqnispsylekilakLrkaglvk 56
                                       ++++e+ ++s+s + + +++L +ag+v+
  gi|313126260|ref|YP_004036530.1| 30 KRDLSESLSVSRSTVDRAIRELVEAGFVE 58
                                      5799***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1560.15
//
Query:       gi|313126261|ref|YP_004036531.1|  [L=374]
Description: aspartate/tyrosine/aromatic aminotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-28   98.0   0.0    4.5e-27   95.2   0.0    1.9  1  Aminotran_1_2   Aminotransferase class I and II
  ------ inclusion threshold ------
      0.058   13.4   0.0       0.22   11.5   0.0    1.9  2  YAcAr           YspA, cpYpsA-related SLOG family
       0.11   13.0   0.0       0.22   12.0   0.0    1.4  1  Deltaretro_Tax  Deltaretrovirus Tax protein


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.0   7.6e-31   4.5e-27      46     363 .]      49     361 ..      38     361 .. 0.77

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 7.6e-31
                                       HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH..........HTTT-EEEEEESS-THHHHHHHH CS
                     Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllk..........lnpgdeilvpdptyasyknilrl 112
                                         +l  +la+ +       + +e +v+v+ Ga++++ +++ ++            +   ++lv +p y +      +
  gi|313126261|ref|YP_004036531.1|  49 DETLCAQLADVYD------VSPE-NVLVTAGATHANLLAESAALtvalddteeaEDSNPQVLVEKPGYQPLVLTPGA 118
                                       5556666666666......7777.77777777777777776665566667766544555577777777777666666 PP

                                       TTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEET CS
                     Aminotran_1_2 113 sggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDea 189
                                         + v r+     +++ l  + + +a  +    +    + ++ + hNPtG + ++e l + ++ +++ + +l+vDe+
  gi|313126261|ref|YP_004036531.1| 119 LSARVDRFLRPARDEYVLSGDRITAAAMD----DF--ALAVTSNRHNPTGRLTSRESLATAAEACREAGGYLLVDEV 189
                                       66666666644446666666666665554....33..6889999********************************* PP

                                       TTTCBSSSS.HTHHH...HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHH CS
                     Aminotran_1_2 190 Yagfvfgsl.davat...ranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaava 261
                                       Ya fv +++ d        ++ +  pn++++gsl K +Gl G+R+G+++++a++v+++r ++ ++    ++  a++ 
  gi|313126261|ref|YP_004036531.1| 190 YAPFVGDATtD---HafgGVTGAGLPNTIVTGSLTKFYGLGGLRIGWLIASAEIVDAARHAAFHVPAvAEPSRALAR 263
                                       ******96653...0334677777888***********************************999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGG CS
                     Aminotran_1_2 262 aalsdallkqseleemrqrlqkrrkelrdeLael..glkvlasqsgmflltdlsaetakelskkLleevgvyvtpgt 336
                                        al++ +    el+++++ + +  +el +++a+   +l+ +  ++  f + + ++ + +el ++ +e+  ++v+pg+
  gi|313126261|ref|YP_004036531.1| 264 RALHNRD----ELSASARDHLQTNHELLASFAAEhdELSGVVYPGSTFAFFEHEHVSGDELVEAAWEQ-DILVVPGR 335
                                       ****999....677776666666667777776667855555555555555555555666*********.******** PP

                                       GGTSTTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 337 sftvpgrlRitvAglteeeleelveal 363
                                        f  +  +R+ + g ++e +e +++al
  gi|313126261|ref|YP_004036531.1| 336 FFDQSDGFRVAL-GRDPEHVEAALDAL 361
                                       ****888*****.**********9986 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.7e-05      0.22      13      50 ..      48      84 ..      41      89 .. 0.87
   2 ?   -2.8   0.0       1.1   6.5e+03      13      24 ..     350     361 ..     348     364 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                             YAcAr 13 dleliwatLdklhaeapidmvlvhGgakGaDrlAarWA 50
                                      d e+++a+L  ++   p + vlv+ ga+ a+ lA++ A
  gi|313126261|ref|YP_004036531.1| 48 DDETLCAQLADVYDVSP-ENVLVTAGATHANLLAESAA 84
                                      4459*************.8***************9977 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                             YAcAr  13 dleliwatLdkl 24 
                                       d e ++a+Ld+l
  gi|313126261|ref|YP_004036531.1| 350 DPEHVEAALDAL 361
                                       6677999**997 PP

>> Deltaretro_Tax  Deltaretrovirus Tax protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.7e-05      0.22      21      58 ..     229     267 ..     218     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                    Deltaretro_Tax  21 lrv.wrlcsrrlvsrlrgalfgppasarpsrhlsrasdh 58 
                                       lr+ w + s  +v   r a f+ pa a psr l+r + h
  gi|313126261|ref|YP_004036531.1| 229 LRIgWLIASAEIVDAARHAAFHVPAVAEPSRALARRALH 267
                                       6665999999***********************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2352.07
//
Query:       gi|313126262|ref|YP_004036532.1|  [L=1040]
Description: fad/fmn-dependent dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-65  221.9   0.3    2.1e-65  220.8   0.1    1.7  2  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    1.9e-41  141.1   0.3    4.6e-41  139.8   0.3    1.7  1  FAD_binding_4  FAD binding domain
    8.9e-09   35.8   3.6    1.8e-08   34.8   3.6    1.6  1  Fer4_17        4Fe-4S dicluster domain
    4.3e-08   33.5   4.3    9.5e-08   32.4   4.3    1.6  1  Fer4_8         4Fe-4S dicluster domain
    6.3e-08   32.7   0.0    2.8e-05   24.2   0.1    2.7  2  CCG            Cysteine-rich domain
    3.8e-05   23.7   3.8    0.00075   19.6   0.4    2.4  2  Fer4_10        4Fe-4S dicluster domain
    0.00028   21.0   1.7      0.014   15.6   0.2    2.4  2  Fer4_9         4Fe-4S dicluster domain
     0.0067   15.9   0.0      0.015   14.7   0.0    1.5  1  Cytokin-bind   Cytokinin dehydrogenase 1, FAD and cytokinin b
  ------ inclusion threshold ------
      0.041   14.0   0.3      0.041   14.0   0.3    2.7  3  Fer4_21        4Fe-4S dicluster domain
      0.052   13.7   0.2       0.19   12.0   0.1    1.9  2  Fer4_18        4Fe-4S dicluster domain
        0.2   11.5  15.1      0.041   13.7   4.2    2.5  2  Fer4           4Fe-4S binding domain
       0.24   12.4   1.5       0.97   10.4   0.1    2.3  2  Fer4_16        4Fe-4S double cluster binding domain
       0.26   11.9   8.3        2.8    8.6   8.7    2.4  2  Fer4_7         4Fe-4S dicluster domain
       0.39   10.9  11.0      0.039   14.0   2.1    2.5  2  Fer4_6         4Fe-4S binding domain
        6.2    7.6  11.7        0.6   10.8   2.5    2.4  2  Fer4_4         4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.8   0.1   1.8e-68   2.1e-65       2     250 .]     308     575 ..     307     575 .. 0.98
   2 ?   -3.7   0.0         6   7.2e+03     189     204 ..     685     700 ..     680     702 .. 0.87

  Alignments for each domain:
  == domain 1  score: 220.8 bits;  conditional E-value: 1.8e-68
                                       -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SS...TTS-TTT-EEEEEEEEE-HHHH CS
                     FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgak...kglpdeeealllvefegddeee 75 
                                       p   aval++++++ +a++ v+ i ++  +paa+e+md++ ldl+++t +++     lp++++++llvef++dd+++
  gi|313126262|ref|YP_004036532.1| 308 PNTAAVALLTYDDVLDAMEDVAPILEH--DPAAVEVMDDVLLDLARETPEFEevvGMLPEGTDSVLLVEFYADDADH 382
                                       78899**********************..*************************9********************** PP

                                       HHHHHHH.HHHHTTT-EEEEE...........................ETGGGGGGGGHHHHHHHHHCTTEEEEEEE CS
                     FAD-oxidase_C  76 aeeelea.lveaileatgaad.................vlvaqdeaeaealwkaRkaalpylrdallkagvavlseD 134
                                        ++++++ ++++  ++++ ad                 ++ a+d+++++++wk+Rk+ lp+l +++ + ++++++eD
  gi|313126262|ref|YP_004036532.1| 383 GRQQVADlVADRVPNGESEADpsagaaetttkphtavtAMEAYDAETRAKFWKMRKSGLPILLSRTTDDKHIAYIED 459
                                       *******88888899999999**************9766************************************** PP

                                       EEEEHHHHHHHHHHHHHHHHHHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-------- CS
                     FAD-oxidase_C 135 tsvPvsrladlvrdikalldkyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHG 211
                                       t++P  +l+++v+d++++ld++++ +++++Hag+g+lh+++l++ +  +  e++e+++dev+dl+v++gGs+sgEHG
  gi|313126262|ref|YP_004036532.1| 460 TAIPAGNLPAFVSDFQDILDDHDTFASYYAHAGPGVLHIRPLVNTKTVEGLETYETIADEVTDLVVKYGGSVSGEHG 536
                                       ***************************************************************************** PP

                                       ---------------THHHHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 212 vGldkkaylerekgeeglalmrriKaalDPkgiLNPgkv 250
                                        G+++ ++ ++ +g+e++a++r +K a+DP+++LNPg++
  gi|313126262|ref|YP_004036532.1| 537 DGRARTQWNRKLYGDELWATFRDLKTAFDPDWLLNPGNI 575
                                       *************************************85 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6
                                       THHHHHHHHHHHHTT- CS
                     FAD-oxidase_C 189 eklvdevvdlavelgG 204
                                        ++v+ev+dl+++++G
  gi|313126262|ref|YP_004036532.1| 685 DEFVEEVTDLCIGCKG 700
                                       5899**********99 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.3   3.9e-44   4.6e-41       1     138 [.      63     200 ..      63     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 3.9e-44
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETT.S--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsr.lnrileideeegtatveaGvtlgd 76 
                                       p +vv pes+e+++a++++++++++pvl+rGgG+sl+gq v +++vvldl + +++++++d ++ tat++aGv+lgd
  gi|313126262|ref|YP_004036532.1|  63 PIGVVMPESTEDIVAVMEYCSKREIPVLPRGGGTSLAGQTV-NEAVVLDLMKhMDGVIDVDTDAATATAQAGVRLGD 138
                                       668*************************************9.********988************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       l+++l+++gl + ++p+ g+ + +GGai +n+ G +s kyG++  +++++evvladG+v ++
  gi|313126262|ref|YP_004036532.1| 139 LNAELEPHGLKFAPDPAWGDKSALGGAIGNNSTGAHSLKYGKTDYYLESVEVVLADGSVTTF 200
                                       ***********************************************************986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   3.6   1.5e-11   1.8e-08       2      61 .]     631     710 ..     630     710 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.5e-11
                           Fer4_17   2 CiqCgyClp........eCpsyeaydne......pkkllraaklglleeaeke......ekaslCieCgeCerkCPq 58 
                                       C++Cg C+         +Cp+++a ++e      + ++lr+a++g+l  +e+       e+ +lCi+C++C ++CP+
  gi|313126262|ref|YP_004036532.1| 631 CHGCGGCRGpqettggvMCPTFRAEEEEilstrgRSNMLRQAMSGDLSPEEQFedefveEVTDLCIGCKGCMKDCPS 707
                                       ************************777544444477899999885444433323456768***************** PP

                           Fer4_17  59 gld 61 
                                       g+d
  gi|313126262|ref|YP_004036532.1| 708 GVD 710
                                       997 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   4.3     8e-11   9.5e-08       3      65 .]     629     709 ..     627     709 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 8e-11
                            Fer4_8   3 ekCieCgaCq........saCpvlrrtkkhlldargeaae........dvqeeqvlee..........eealwsCtt 53 
                                       e C++Cg C+         +Cp++r++ +++l++rg+ +                  +          ee  + C +
  gi|313126262|ref|YP_004036532.1| 629 ELCHGCGGCRgpqettggVMCPTFRAEEEEILSTRGRSNMlrqamsgdL--------SpeeqfedefvEEVTDLCIG 697
                                       67***********************************998555444431........145566667889******** PP

                            Fer4_8  54 cgaCtevCpvgi 65 
                                       c+ C + Cp g+
  gi|313126262|ref|YP_004036532.1| 698 CKGCMKDCPSGV 709
                                       *********986 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.016        20      10      74 ..     814     881 ..     807     886 .. 0.86
   2 !   24.2   0.1   2.4e-08   2.8e-05       2      84 ..     938    1019 ..     937    1020 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                               CCG  10 lraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaee...tgadaiv 74 
                                        ++++pe +ka  + lea+gv++ ++++ +  G +   +g+ ++a++ a++nve++     ++ d++v
  gi|313126262|ref|YP_004036532.1| 814 TNYNHPEAGKAAVRALEAAGVHVRIPDGVTGSGRPPHSKGFIDRAREQARQNVEALAPlvrEEWDVVV 881
                                       67889************************************************998874433455554 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 2.4e-08
                               CCG    2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee...laealakrnvetaeetgadai 73  
                                        +y+  Ch   +++ + ++    +l+++g  +++l +++CCG +g +  + e    ++a+++  ++++e+++ +++
  gi|313126262|ref|YP_004036532.1|  938 TYHGHCH---QKSTKKDHHAVGVLRRAGYRVDPL-DSTCCGMAGSFGYEAEhysMSKAIGEILYDQVENADGEMV 1008
                                        6788884...44445555566778********99.************9988899999****************** PP

                               CCG   74 vtacpgCllql 84  
                                        v++ ++C  ql
  gi|313126262|ref|YP_004036532.1| 1009 VAPGASCRSQL 1019
                                        ********998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.029        34       7      22 ..     629     652 ..     626     681 .. 0.76
   2 !   19.6   0.4   6.3e-07   0.00075       5      32 ..     691     718 ..     687     733 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.029
                           Fer4_10   7 dtCirCgkCvk........aCPad 22 
                                       + C +Cg C+         +CP+ 
  gi|313126262|ref|YP_004036532.1| 629 ELCHGCGGCRGpqettggvMCPTF 652
                                       68*******999999999889993 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 6.3e-07
                           Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgea 32 
                                        +d Ci+C+ C+k CP+ +++ + k+e 
  gi|313126262|ref|YP_004036532.1| 691 VTDLCIGCKGCMKDCPSGVDMAKMKAEV 718
                                       5789*************66444444433 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.043        51      33      43 ..     621     638 ..     575     640 .. 0.75
   2 !   15.6   0.2   1.2e-05     0.014       2      17 ..     695     710 ..     663     726 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.043
                            Fer4_9  33 e.......eaCigCgaCv 43 
                                       e       e C+gCg C 
  gi|313126262|ref|YP_004036532.1| 621 EngfqgmaELCHGCGGCR 638
                                       1455555678*******5 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.2e-05
                            Fer4_9   2 CtgCgaCveaCpagvv 17 
                                       C+gC+ C++ Cp+gv 
  gi|313126262|ref|YP_004036532.1| 695 CIGCKGCMKDCPSGVD 710
                                       6666666666666655 PP

>> Cytokin-bind  Cytokinin dehydrogenase 1, FAD and cytokinin binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.015     245     278 ..     539     574 ..     496     576 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       SSHHHH.HHHHGHH.HHHHHHHHHHH-TT--B-GGG CS
                      Cytokin-bind 245 esqeeW.kkhfGak.WerfverKakyDPkaiLspGq 278
                                       +++++W +k +G++ W++f + K+++DP  +L pG+
  gi|313126262|ref|YP_004036532.1| 539 RARTQWnRKLYGDElWATFRDLKTAFDPDWLLNPGN 574
                                       67899*667799555*******************96 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.23   2.7e+02      27      48 ..     617     638 ..     610     644 .. 0.81
   2 ?   14.0   0.3   3.4e-05     0.041      34      53 ..     688     707 ..     672     724 .. 0.77
   3 ?   -2.9   0.2       6.8   8.1e+03      13      43 ..     942     974 ..     941     975 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.23
                           Fer4_21  27 eidaktvlkvvedeCvGCnlCs 48 
                                       + ++++ ++ +++ C GC  C 
  gi|313126262|ref|YP_004036532.1| 617 NWENENGFQGMAELCHGCGGCR 638
                                       56667777888999****9995 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.4e-05
                           Fer4_21  34 lkvvedeCvGCnlCssvCPv 53 
                                       ++ v+d C+GC+ C++ CP 
  gi|313126262|ref|YP_004036532.1| 688 VEEVTDLCIGCKGCMKDCPS 707
                                       56677888888888888883 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.8
                           Fer4_21  13 kCliaCedtshqaieidaktvlkvv..edeCvG 43 
                                       +C++   ++ h a+ +  ++ ++v   +++C G
  gi|313126262|ref|YP_004036532.1| 942 HCHQKSTKKDHHAVGVLRRAGYRVDplDSTCCG 974
                                       799999999999998877777777533566655 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.8   6.9e+03      14      32 ..     473     491 ..     471     518 .. 0.75
   2 ?   12.0   0.1   0.00016      0.19      51      79 ..     685     713 ..     658     717 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.8
                           Fer4_18  14 rvqsvlydeetllvvydak 32 
                                        +q +l d++t++  y ++
  gi|313126262|ref|YP_004036532.1| 473 DFQDILDDHDTFASYYAHA 491
                                       6899999999998877654 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
                           Fer4_18  51 eerkekgagdcidcescvkvcPtgidirk 79 
                                       +e  e+ +  ci c+ c+k cP g+d+ k
  gi|313126262|ref|YP_004036532.1| 685 DEFVEEVTDLCIGCKGCMKDCPSGVDMAK 713
                                       3334455566****************865 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   3.1     0.088   1.1e+02       5      14 ..     628     637 ..     626     638 .. 0.90
   2 ?   13.7   4.2   3.4e-05     0.041       5      21 ..     692     708 ..     688     709 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.088
                                       TTTSSS-THH CS
                              Fer4   5 eekCigCGaC 14 
                                        e+C gCG C
  gi|313126262|ref|YP_004036532.1| 628 AELCHGCGGC 637
                                       599*****99 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.4e-05
                                       TTTSSS-THHHHHSTTT CS
                              Fer4   5 eekCigCGaCvevCPvg 21 
                                       +++CigC+ C++ CP g
  gi|313126262|ref|YP_004036532.1| 692 TDLCIGCKGCMKDCPSG 708
                                       79*************88 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       1.5   1.7e+03      50      60 ..     627     637 ..     609     640 .. 0.72
   2 ?   10.4   0.1   0.00081      0.97       2      16 ..     695     709 ..     647     740 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.5
                           Fer4_16  50 kqeaitgCdiC 60 
                                       ++e ++gC+ C
  gi|313126262|ref|YP_004036532.1| 627 MAELCHGCGGC 637
                                       45667888877 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00081
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C++C+ C++ CP+++
  gi|313126262|ref|YP_004036532.1| 695 CIGCKGCMKDCPSGV 709
                                       888888888888876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   2.2       3.1   3.7e+03      35      44 ..     628     637 ..     612     651 .. 0.72
   2 ?    8.6   8.7    0.0023       2.8       2      52 .]     631     709 ..     630     709 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.1
                            Fer4_7  35 pekClgCgaC 44 
                                       +e C gCg C
  gi|313126262|ref|YP_004036532.1| 628 AELCHGCGGC 637
                                       5667777777 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0023
                            Fer4_7   2 CigCgaCv........aaCpvkaieldeeenek....................gtekveidpekClgCgaCvavCPt 50 
                                       C gCg C         ++Cp+   e +e  + +                    + e ve + + C+gC+ C++ CP+
  gi|313126262|ref|YP_004036532.1| 631 CHGCGGCRgpqettggVMCPTFRAEEEEILSTRgrsnmlrqamsgdlspeeqfEDEFVEEVTDLCIGCKGCMKDCPS 707
                                       5555555433333333566555444443333331122222222222222211122445788999************9 PP

                            Fer4_7  51 ga 52 
                                       g+
  gi|313126262|ref|YP_004036532.1| 708 GV 709
                                       96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.8      0.36   4.3e+02       7      15 ..     629     637 ..     627     639 .. 0.91
   2 ?   14.0   2.1   3.2e-05     0.039       6      22 ..     692     708 ..     687     711 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.36
                            Fer4_6   7 dkCigCgdC 15 
                                       ++C gCg C
  gi|313126262|ref|YP_004036532.1| 629 ELCHGCGGC 637
                                       89*****99 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.2e-05
                            Fer4_6   6 pdkCigCgdCvrvCPeg 22 
                                        d+CigC  C++ CP g
  gi|313126262|ref|YP_004036532.1| 692 TDLCIGCKGCMKDCPSG 708
                                       59*************87 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.9      0.46   5.6e+02       2      11 ..     629     638 ..     628     639 .. 0.87
   2 ?   10.8   2.5    0.0005       0.6       2      17 .]     693     708 ..     692     710 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.46
                            Fer4_4   2 erCigCgsCv 11 
                                       e C gCg C+
  gi|313126262|ref|YP_004036532.1| 629 ELCHGCGGCR 638
                                       78*******6 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0005
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + CigC+ C+  CP+g
  gi|313126262|ref|YP_004036532.1| 693 DLCIGCKGCMKDCPSG 708
                                       78************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1040 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.46
# Mc/sec: 6816.96
//
Query:       gi|313126263|ref|YP_004036533.1|  [L=590]
Description: l-lactate permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.3e-104  350.8  40.2   4.2e-104  349.1  40.2    1.6  1  Lactate_perm  L-lactate permease


Domain annotation for each model (and alignments):
>> Lactate_perm  L-lactate permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.1  40.2  2.4e-108  4.2e-104       2     521 ..       6     580 ..       5     581 .. 0.92

  Alignments for each domain:
  == domain 1  score: 349.1 bits;  conditional E-value: 2.4e-108
                      Lactate_perm   2 salvalvPIlllllalavlklkgykaallslavsviiallvykmpvekvlaavlkgalsgllpialviiaavflykl 78 
                                       + lval+P+l + ++++ +   +   +++ ++v++   +  + m  ++++aa+++g+++ + +i++++++a++l + 
  gi|313126263|ref|YP_004036533.1|   6 DGLVALLPLLTIAVLMVGFYWPATRTMPVAWLVAIGAGVVGWGMNGTWIAAATINGFIT-AANILYIVFGAILLLYT 81 
                                       789*******************************************************9.889************** PP

                      Lactate_perm  79 svksgafeiirksilsispdrriqvlligfafgaflEGaaGfGtpvAIsaalLvglGfkPlyaaglcLIantapvaf 155
                                        +++gaf++i    +s+s+drr+qv+l+ f++g+f+E aaGfGtp+AI+++lLvglGf+Pl a  ++L  n  +++f
  gi|313126263|ref|YP_004036533.1|  82 LKQTGAFDAINAGFASVSEDRRVQVVLLVFLMGSFIEAAAGFGTPAAIVGPLLVGLGFPPLAAVVIALTGNLMAITF 158
                                       ***************************************************************************** PP

                      Lactate_perm 156 GavGiPitagagatkls........................aleisslvgiilvlislliplllvilldgvkdik.. 206
                                       GavG+P + g+     s                        al+ +s + ++ ++++++   ++ ++ ++ + ik  
  gi|313126263|ref|YP_004036533.1| 159 GAVGTPLIIGMIDIFESvetitadavgngpyadistwvadiALWAASYHVVVGIVLPFIGVAMMTRFFGEERSIKpa 235
                                       ******8776554444457889************9995555555555555555555555555555555544555533 PP

                      Lactate_perm 207 .etfpavlvsglsfaiaqflisnvlGpelpsilgalvslvilalflka..fqpkeifrfagkeeskeksel...... 274
                                        e++p++l +  sf +++fl++ +lGpe+p ++g++v+l++++ +lka  f+p e ++fa +++   +         
  gi|313126263|ref|YP_004036533.1| 236 lEVLPLTLFAWASFSVPYFLTAYFLGPEFPGLIGSMVGLFVTVSALKAgfFHPDEEWDFAPESAWPDHWVGdikpge 312
                                       388999****************************************9888*********998877766665778889 PP

                      Lactate_perm 275 ......................kaakilkAlsPfvllvavivltsipllkalfeeggllatkllsleleelsklilk 329
                                                               +   kA++P+ l+ + +v+t+  +++ + +   ++++ l+ ++   l  l + 
  gi|313126263|ref|YP_004036533.1| 313 sasddvavaadggtvqssmpatAGMPLWKAWTPYALVALLLVVTR--VVDPVKS---FVTMDLFIISWGDLAALPFV 384
                                       9999***************998788999*****************..6666666...99999999999999999999 PP

                      Lactate_perm 330 ikpiveeatalevvfkfkllsspgtiillaavlsiavlklsskdalkvlketlkelklpilaiilvlalanlmnvsG 406
                                        ++i++    + +   f ll+ pg +++++ +++i++  + s + +++  et+++++++++a+ +++a +++m++sG
  gi|313126263|ref|YP_004036533.1| 385 HETILG----TGLTNDFALLYLPGAVFVAVHLVTIPLHGMDSAEIKAAWSETIEKVAPAVIALLFAVATVQIMLQSG 457
                                       999999....78899************************************************************** PP

                      Lactate_perm 407 .......lsktlalalae.tGsaftlfspllGalGvfltGSdtvsNllFgslQletaeqiglsevlllaantvGgvv 475
                                              ++ +l+ ++a  +G ++++f++++Ga G+fl+GS+tvs +lFg++Q  +a+qig +++l+l a++vGg++
  gi|313126263|ref|YP_004036533.1| 458 satntdsMLIVLSEGMAGvAGGIYPFFAAFVGAFGAFLAGSNTVSDILFGTFQYGVADQIGTPRTLMLGAQAVGGAI 534
                                       ***************************************************************************** PP

                      Lactate_perm 476 gkmispqsiaiacaavglvgkEsdllrktviysliyliivgvvall 521
                                       g++i+++++++a a+vglvg E+ ++r  +i+ l+y  ++g+++ll
  gi|313126263|ref|YP_004036533.1| 535 GNLIAVHNVVAALAVVGLVGEEGRVIRLELIPLLYYGTATGLLTLL 580
                                       ******************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3974.92
//
Query:       gi|313126264|ref|YP_004036534.1|  [L=204]
Description: hypothetical protein Hbor_15160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-05   23.8   0.1      6e-05   23.0   0.1    1.4  1  HTH_20    Helix-turn-helix domain
    0.00021   21.2   0.0    0.00036   20.4   0.0    1.3  1  HTH_11    HTH domain
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.032   14.4   0.0    1.4  1  HTH_17    Helix-turn-helix domain
      0.024   14.5   0.0      0.051   13.5   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
       0.05   13.3   0.1      0.078   12.7   0.1    1.3  1  HTH_DeoR  DeoR-like helix-turn-helix domain
      0.071   12.9   0.0       0.14   12.0   0.0    1.5  1  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1     2e-08     6e-05      22      59 ..      36      73 ..      33      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2e-08
                                      CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 22 aegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      a++lta++++e+ld+s+ t+++ L++Lee g + ++++
  gi|313126264|ref|YP_004036534.1| 36 ARPLTATDVMEALDCSRRTAHNKLNELEERGDLATRKV 73
                                      689**************************777777766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.2e-07   0.00036      15      43 ..      38      66 ..      36      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.2e-07
                            HTH_11 15 pisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      p+++ + +e L++Srrt ++ + +Lee g
  gi|313126264|ref|YP_004036534.1| 38 PLTATDVMEALDCSRRTAHNKLNELEERG 66
                                      699************************98 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05     0.032       2      37 ..      39      78 ..      38      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                            HTH_17  2 ltveEaAelLgvsrstvyrlir....rgelpaa.kiGrrwr 37
                                      lt  +++e L++sr+t+++ ++    rg+l a+ k+G r r
  gi|313126264|ref|YP_004036534.1| 39 LTATDVMEALDCSRRTAHNKLNeleeRGDL-ATrKVGARSR 78
                                      899******************66666****.6637888755 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.7e-05     0.051      22      56 ..      38      72 ..      36      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      p+ta+++ e+l+ +r ++ + L++Le++G   ++k
  gi|313126264|ref|YP_004036534.1| 38 PLTATDVMEALDCSRRTAHNKLNELEERGDLATRK 72
                                      89***************************776665 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.6e-05     0.078      15      47 ..      39      72 ..      36      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                          HTH_DeoR 15 lsveelvellgvSeaTiRRDLneLeeqgl.ltRt 47
                                      l+ ++++e l+ S  T+ + LneLee g   tR 
  gi|313126264|ref|YP_004036534.1| 39 LTATDVMEALDCSRRTAHNKLNELEERGDlATRK 72
                                      56789*********************99745554 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.6e-05      0.14      16      46 ..      36      66 ..      22      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelG 46
                                      +++lt +++ ++++ ++ t+h+ L+ L+e+G
  gi|313126264|ref|YP_004036534.1| 36 ARPLTATDVMEALDCSRRTAHNKLNELEERG 66
                                      467**************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1135.26
//
Query:       gi|313126265|ref|YP_004036535.1|  [L=566]
Description: hypothetical protein Hbor_15170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.57
# Mc/sec: 2967.40
//
Query:       gi|313126266|ref|YP_004036536.1|  [L=166]
Description: hypothetical protein Hbor_15180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-11   43.6   0.0    3.4e-11   43.2   0.0    1.1  1  LUD_dom   LUD domain


Domain annotation for each model (and alignments):
>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   1.9e-15   3.4e-11      82     189 .]      64     164 ..      57     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.9e-15
                           LUD_dom  82 fltadvgitganfaiAetGtlvlvdnegnrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyv 158
                                       + ta +g+t a  +iA+ G++vl  ++     +++  + h++v+ ++ i p +  a++ l +    + r     + +
  gi|313126266|ref|YP_004036536.1|  64 LRTAATGVTEAGLGIADYGSVVLQGTPDGIEPVSLFSDRHVAVLRKSDIAPGMGAAFEWLGE----TFR--TGHSSA 134
                                       56899*********************************************************....333..334466 PP

                           LUD_dom 159 sfisgpsrtadielvlvygvhgpkrihvilv 189
                                        + +gps tad    lv+g+hgpk +hv+++
  gi|313126266|ref|YP_004036536.1| 135 IIATGPSATADMG-ALVKGAHGPKAVHVVIL 164
                                       77799******77.999************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 896.18
//
Query:       gi|313126267|ref|YP_004036537.1|  [L=739]
Description: hypothetical protein Hbor_15190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-44  149.8   0.1    1.1e-43  149.1   0.1    1.4  1  LUD_dom   LUD domain
    4.7e-08   33.4   3.6    1.1e-07   32.2   3.6    1.7  1  Fer4_8    4Fe-4S dicluster domain
    9.6e-08   32.0   2.9     0.0005   20.1   0.1    2.5  2  Fer4_10   4Fe-4S dicluster domain
    2.4e-06   27.6   5.1    5.7e-06   26.4   5.1    1.6  1  Fer4_9    4Fe-4S dicluster domain
    2.7e-06   27.8   2.5    5.8e-06   26.8   2.5    1.6  1  Fer4_17   4Fe-4S dicluster domain
    7.7e-06   26.4   4.7    2.2e-05   24.9   4.7    1.8  1  Fer4_7    4Fe-4S dicluster domain
    0.00013   21.6  13.3    0.00017   21.2   3.0    2.4  2  Fer4      4Fe-4S binding domain
    0.00078   19.6   2.0      0.035   14.3   0.2    2.4  2  Fer4_18   4Fe-4S dicluster domain
     0.0011   19.0  10.6     0.0083   16.2  10.6    2.2  1  Fer4_21   4Fe-4S dicluster domain
     0.0012   18.8   2.8     0.0012   18.8   2.8    2.5  2  Fer4_6    4Fe-4S binding domain
     0.0024   17.9  14.8      0.009   16.1   3.9    2.5  2  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   16.7   5.4        0.1   13.6   0.5    2.6  2  Fer4_16   4Fe-4S double cluster binding domain
      0.033   13.9   3.6      0.045   13.5   0.2    2.3  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
      0.038   14.9   5.0      0.038   14.9   5.0    2.5  2  Fer4_3    4Fe-4S binding domain
       0.05   14.4   6.9      0.078   13.8   0.7    2.5  2  Fer4_22   4Fe-4S dicluster domain
      0.073   13.6  13.9      0.037   14.5   3.5    2.4  2  Fer4_4    4Fe-4S binding domain
        1.7    9.5   5.7       0.45   11.3   0.3    2.9  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.1   0.1   1.1e-46   1.1e-43       1     166 [.      66     276 ..      66     303 .. 0.92

  Alignments for each domain:
  == domain 1  score: 149.1 bits;  conditional E-value: 1.1e-46
                           LUD_dom   1 leefienleangaevyyaktaeealelilellkeksv.......................vseggstdlgeigl... 51 
                                       ++++ e +eang++ y+a++a++a+++++e+++ek +                       ++ +++tdlge+ l   
  gi|313126267|ref|YP_004036537.1|  66 IDQLRETVEANGGTLYLADDAADANRYVREVCEEKEAdrvvksksmtseeievneelegaGMDVVETDLGEWVLqva 142
                                       67999******************************99**************************************** PP

                           LUD_dom  52 ........apalhsgreevldlfeekl............treareelrekfltadvgitganfaiAetGtlvlvdne 108
                                               apa+h+ re ++dlf+e++            t++are+l   +++advg+tganf  A+tGt+ lv++e
  gi|313126267|ref|YP_004036537.1| 143 despshivAPAIHKSREAIADLFNERFdpeepletaeelTMFAREQLGALIEDADVGMTGANFITADTGTIALVTSE 219
                                       ***************************************************************************** PP

                           LUD_dom 109 gnrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsr 166
                                       gn+r   ++p++h++v+g++k+ p++ed+  +++++ +++t+ q++t+y+s+ + p  
  gi|313126267|ref|YP_004036537.1| 220 GNARKSAVVPDTHVAVAGVEKVIPTVEDLHPFVELIGKSGTG-QDITSYISLLTPPVE 276
                                       ******************************************.**********55532 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   3.6     1e-10   1.1e-07       3      65 .]     320     387 ..     318     387 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1e-10
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.....dvqeeqvlee....eealwsCttcgaCtevCpvgi 65 
                                        +Ci+C+aC ++C  +++ + h +  +    +     ++  e    +    +e  + Ct+c +C+++Cpv+i
  gi|313126267|ref|YP_004036537.1| 320 LYCIRCSACSNSCANFQHVGGHAFGGETYSGGigtgwEAGVE----GldtaAEFNDLCTGCSRCVNACPVEI 387
                                       68************9999997666555554444444422333....255569999**************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.3   0.00021      0.22       7      31 ..     320     343 ..     315     355 .. 0.78
   2 !   20.1   0.1   4.7e-07    0.0005       7      24 ..     371     392 ..     366     413 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakge 31 
                                         CirC +C ++C a++++vg+ ++
  gi|313126267|ref|YP_004036537.1| 320 LYCIRCSACSNSC-ANFQHVGGHAF 343
                                       57***********.87777776655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 4.7e-07
                           Fer4_10   7 dtCirCgkCvkaCPadl....t 24 
                                       d C++C +Cv+aCP+ +     
  gi|313126267|ref|YP_004036537.1| 371 DLCTGCSRCVNACPVEIdipwI 392
                                       78*************7666652 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   5.1   5.4e-09   5.7e-06       1      49 [.     321     386 ..     321     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5.4e-09
                            Fer4_9   1 kCtgCgaCveaC.pagvvvedaaerkarlraase................eaCigCgaCveaCpkg 49 
                                       +C++C aC ++C ++++v ++a++++      +                 + C+gC +Cv+aCp +
  gi|313126267|ref|YP_004036537.1| 321 YCIRCSACSNSCaNFQHVGGHAFGGETYSGGIGTgweagvegldtaaefnDLCTGCSRCVNACPVE 386
                                       6***********9788888888888888877777888999999999999999************86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   2.5   5.5e-09   5.8e-06       2      61 .]     322     388 ..     321     388 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.5e-09
                           Fer4_17   2 CiqCgyClpeCpsyea.......ydnepkkllraaklglleea.ekeekaslCieCgeCerkCPqgld 61 
                                       Ci+C++C ++C  ++         +++   +   +++g +e+   + e  +lC++C +C+ +CP ++d
  gi|313126267|ref|YP_004036537.1| 322 CIRCSACSNSCANFQHvgghafgGETYSGGIGTGWEAG-VEGLdTAAEFNDLCTGCSRCVNACPVEID 388
                                       ***************95553322222344566666665.55541455899**************9987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   4.7   2.1e-08   2.2e-05       2      51 ..     322     386 ..     321     387 .. 0.62

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.1e-08
                            Fer4_7   2 CigCgaCvaaCp.vkaieldeeenek..............gtekveidpekClgCgaCvavCPtg 51 
                                       Ci C aC + C   + +  + +  e               g ++++   + C+gC +Cv++CP++
  gi|313126267|ref|YP_004036537.1| 322 CIRCSACSNSCAnFQHVGGHAFGGETysggigtgweagveGLDTAAEFNDLCTGCSRCVNACPVE 386
                                       ***********632333333222222333333333222225577788899*************97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.7     0.017        18       7      18 ..     321     332 ..     319     332 .. 0.93
   2 !   21.2   3.0   1.7e-07   0.00017       6      21 ..     371     386 ..     369     387 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                                       TSSS-THHHHHS CS
                              Fer4   7 kCigCGaCvevC 18 
                                        Ci+C aC + C
  gi|313126267|ref|YP_004036537.1| 321 YCIRCSACSNSC 332
                                       5*********99 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.7e-07
                                       TTSSS-THHHHHSTTT CS
                              Fer4   6 ekCigCGaCvevCPvg 21 
                                       ++C+gC +Cv++CPv+
  gi|313126267|ref|YP_004036537.1| 371 DLCTGCSRCVNACPVE 386
                                       99************97 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.04        42      58      97 ..     319     334 ..     299     349 .. 0.70
   2 !   14.3   0.2   3.3e-05     0.035      58      77 ..     370     389 ..     354     393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.04
                           Fer4_18  58 agdcidcescvkvcPtgidirkGlqleciscllcidacdk 97 
                                       +                        l ci c+ c ++c +
  gi|313126267|ref|YP_004036537.1| 319 T------------------------LYCIRCSACSNSCAN 334
                                       3........................446666666666655 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.3e-05
                           Fer4_18  58 agdcidcescvkvcPtgidi 77 
                                       +  c+ c+ cv+ cP++idi
  gi|313126267|ref|YP_004036537.1| 370 NDLCTGCSRCVNACPVEIDI 389
                                       445****************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  10.6   7.8e-06    0.0083       7      54 ..     321     386 ..     317     390 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.8e-06
                           Fer4_21   7 kCigCgkCliaCedtshqai.........eidaktvl.................kvvedeCvGCnlCssvCPve 54 
                                        Ci C  C  +C +   q +                                  +  +d C+GC  C++ CPve
  gi|313126267|ref|YP_004036537.1| 321 YCIRCSACSNSCAN--FQHVgghafggetY------SggigtgweagvegldtaAEFNDLCTGCSRCVNACPVE 386
                                       5***********97..66665564455540......3444444455555555336679**************95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.9     0.093        98       9      19 ..     322     332 ..     321     337 .. 0.91
   2 !   18.8   2.8   1.1e-06    0.0012       7      21 ..     371     385 ..     368     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.093
                            Fer4_6   9 CigCgdCvrvC 19 
                                       Ci C +C + C
  gi|313126267|ref|YP_004036537.1| 322 CIRCSACSNSC 332
                                       *********99 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.1e-06
                            Fer4_6   7 dkCigCgdCvrvCPe 21 
                                       d+C+gC +Cv++CP 
  gi|313126267|ref|YP_004036537.1| 371 DLCTGCSRCVNACPV 385
                                       9*************7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   3.2    0.0067       7.1      10      20 ..     322     332 ..     316     334 .. 0.88
   2 !   16.1   3.9   8.5e-06     0.009       8      21 ..     371     384 ..     366     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0067
                            Fer4_2  10 CigCgaCvsaC 20 
                                       Ci+C+aC ++C
  gi|313126267|ref|YP_004036537.1| 322 CIRCSACSNSC 332
                                       ********99* PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.5e-06
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       d C+gC+ Cv+aCP
  gi|313126267|ref|YP_004036537.1| 371 DLCTGCSRCVNACP 384
                                       68************ PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.5     0.066        70       2      12 ..     322     332 ..     303     337 .. 0.81
   2 ?   13.6   0.5   9.6e-05       0.1       2      15 ..     373     386 ..     366     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.066
                           Fer4_16   2 CgtCgkCaevC 12 
                                       C++C +C ++C
  gi|313126267|ref|YP_004036537.1| 322 CIRCSACSNSC 332
                                       77777777777 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.6e-05
                           Fer4_16   2 CgtCgkCaevCPtn 15 
                                       C++C +C+++CP++
  gi|313126267|ref|YP_004036537.1| 373 CTGCSRCVNACPVE 386
                                       89999999999975 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4      0.49   5.1e+02      12      37 ..     310     333 ..     303     340 .. 0.78
   2 ?   13.5   0.2   4.3e-05     0.045      22      55 ..     371     401 ..     360     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.49
                                       --HHHHHHHHTT----TT-HHHHCST CS
                           Fer4_20  12 lteeealeeAsRClqCkkapcvkgCP 37 
                                       ++e++ l+e   C++C  + c+++C 
  gi|313126267|ref|YP_004036537.1| 310 MREDDQLRETLYCIRC--SACSNSCA 333
                                       6677788899999999..77888885 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.3e-05
                                       TT----TT-HHHHCSTT---HHHHHHHHHTT-HH CS
                           Fer4_20  22 sRClqCkkapcvkgCPveidipefikkiaegnle 55 
                                       + C  C  + cv++CPveidip +i+++ +++++
  gi|313126267|ref|YP_004036537.1| 371 DLCTGC--SRCVNACPVEIDIP-WINTVVRDRIN 401
                                       569999..89***********9.99999888776 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   4.1     0.072        76       1      11 [.     322     332 ..     322     334 .. 0.95
   2 ?   14.9   5.0   3.6e-05     0.038       1      13 [.     373     385 ..     373     387 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.072
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ C+aC ++C
  gi|313126267|ref|YP_004036537.1| 322 CIRCSACSNSC 332
                                       *********** PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.6e-05
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       CtgC++Cv++CPv
  gi|313126267|ref|YP_004036537.1| 373 CTGCSRCVNACPV 385
                                       ************8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.8      0.15   1.6e+02       2      13 ..     322     333 ..     310     337 .. 0.79
   2 ?   13.8   0.7   7.4e-05     0.078      80      96 .]     371     387 ..     363     387 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                           Fer4_22   2 ClsCgaCtlvCp 13 
                                       C++C+aC+  C+
  gi|313126267|ref|YP_004036537.1| 322 CIRCSACSNSCA 333
                                       777777777775 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.4e-05
                           Fer4_22  80 sgCvGCgRCieacpvki 96 
                                         C+GC RC++acpv+i
  gi|313126267|ref|YP_004036537.1| 371 DLCTGCSRCVNACPVEI 387
                                       68************987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.8     0.078        83       4      14 ..     322     332 ..     317     336 .. 0.93
   2 ?   14.5   3.5   3.5e-05     0.037       2      16 ..     371     385 ..     370     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.078
                            Fer4_4   4 CigCgsCvaaC 14 
                                       Ci+C +C ++C
  gi|313126267|ref|YP_004036537.1| 322 CIRCSACSNSC 332
                                       **********9 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.5e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C+gC +Cv+aCP+
  gi|313126267|ref|YP_004036537.1| 371 DLCTGCSRCVNACPV 385
                                       67************7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.0       6.1   6.4e+03       8      20 ..     322     334 ..     318     341 .. 0.83
   2 ?   11.3   0.3   0.00043      0.45       6      33 ..     371     396 ..     370     420 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.1
                           Fer4_15   8 CigcglCvaeape 20 
                                       Ci c +C   + +
  gi|313126267|ref|YP_004036537.1| 322 CIRCSACSNSCAN 334
                                       *******998864 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00043
                           Fer4_15   6 daCigcglCvaeapevfeldedglasvl 33 
                                       d+C+gc +Cv ++p  +e+d   +++v+
  gi|313126267|ref|YP_004036537.1| 371 DLCTGCSRCVNACP--VEIDIPWINTVV 396
                                       89***********9..777776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 4346.83
//
Query:       gi|313126268|ref|YP_004036538.1|  [L=98]
Description: hypothetical protein Hbor_15200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-13   48.6   0.3    7.9e-13   48.3   0.3    1.1  1  PRC       PRC-barrel domain
  ------ inclusion threshold ------
      0.013   15.7   0.1      0.049   13.9   0.1    1.8  1  DUF2171   Uncharacterized protein conserved in bacteria (DUF2
      0.058   13.5   0.0        0.1   12.7   0.0    1.5  1  RcnB      Nickel/cobalt transporter regulator


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.3   1.3e-16   7.9e-13       6      77 ..       8      83 ..       5      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.3e-16
                                      S---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT...........-EEEEEGG.CEECCCTEEEETTS-G CS
                               PRC  6 asdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi......gekevliPfdlavkigkdriivdapke 77
                                      ++ l+G+eVy+++G  +G+V D+ +d + + v++l +s  +  ++       +k vliP++ +v++++d+i+++   e
  gi|313126268|ref|YP_004036538.1|  8 LTTLVGREVYSNNGVFVGEVDDIRLDLNRQAVTGLALSRLND-ELfqsrvePGKGVLIPYR-WVRAVGDVILINDVVE 83
                                      789***********************************9988.555***************.***********98765 PP

>> DUF2171  Uncharacterized protein conserved in bacteria (DUF2171)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.2e-06     0.049       5      52 ..      14      74 ..      12      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.2e-06
                           DUF2171  5 meVvgsdGehvGtVDhvegdrikLtkddseeg................gqhhyiplswVasvdd 52
                                       eV+  +G+ vG VD +   r+ L ++  +                  g+  +ip  wV+ v d
  gi|313126268|ref|YP_004036538.1| 14 REVYSNNGVFVGEVDDI---RLDLNRQAVTGLalsrlndelfqsrvepGKGVLIPYRWVRAVGD 74
                                      59**************9...4444444443224455566688899999************9985 PP

>> RcnB  Nickel/cobalt transporter regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05       0.1      30      44 ..      66      80 ..      62      91 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                              RcnB 30 yrWvriggdyvLvai 44
                                      yrWvr  gd++L+++
  gi|313126268|ref|YP_004036538.1| 66 YRWVRAVGDVILIND 80
                                      9************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 597.25
//
Query:       gi|313126269|ref|YP_004036539.1|  [L=483]
Description: k+ transporter, NAD-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-22   79.6   1.8    4.7e-22   78.4   1.8    1.7  1  TrkA_N           TrkA-N domain
    1.3e-13   51.1   0.4    8.2e-12   45.2   0.1    2.4  2  DHH              DHH family
    2.3e-09   37.8   1.5    3.1e-08   34.1   0.0    2.9  3  DHHA1            DHHA1 domain
    3.3e-09   37.2   0.2    1.1e-08   35.5   0.2    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    3.7e-08   33.7   0.2    9.4e-08   32.4   0.2    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    1.1e-06   28.3   0.2    2.1e-06   27.4   0.2    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    1.2e-06   28.3   0.0    2.2e-06   27.4   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
    5.8e-05   22.7   0.6    0.00027   20.5   0.1    2.0  2  Epimerase        NAD dependent epimerase/dehydratase family
    9.8e-05   22.4   0.1    0.00023   21.2   0.1    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00011   22.4   0.0    0.00019   21.6   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00015   21.4   0.1    0.00038   20.1   0.1    1.7  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00027   21.4   1.9    0.00067   20.1   1.2    2.0  2  NAD_binding_7    Putative NAD(P)-binding
     0.0011   18.4   0.6     0.0025   17.2   0.6    1.6  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0015   17.9   0.0     0.0031   16.9   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0016   18.4   0.0     0.0028   17.6   0.0    1.4  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0029   17.5   0.1     0.0073   16.2   0.1    1.7  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0036   16.6   0.0     0.0058   15.9   0.0    1.3  1  FAD_binding_3    FAD binding domain
  ------ inclusion threshold ------
      0.012   15.0   0.6      0.032   13.7   0.2    2.0  2  adh_short        short chain dehydrogenase
      0.031   13.8   0.7      0.031   13.8   0.7    2.1  3  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.043   14.3   0.8       0.11   13.1   0.8    1.8  1  XdhC_C           XdhC Rossmann domain
      0.044   13.4   0.1      0.089   12.4   0.1    1.4  1  DUF364           Putative heavy-metal chelation
      0.045   14.2   1.3       0.16   12.4   0.7    2.2  2  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
       0.05   13.8   0.0       0.13   12.5   0.0    1.7  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
       0.31   11.7   2.3        1.2    9.8   2.3    2.1  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   1.8   6.3e-25   4.7e-22       1     116 []      13     126 ..      13     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 6.3e-25
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       ++i+G+G vG ++aeeL+e+gkdv++ dkde+rve lr++ l++   d +d+ev e   +++ d+v+++++d ean 
  gi|313126269|ref|YP_004036539.1|  13 YAILGCGSVGHAVAEELTEEGKDVLILDKDESRVEALRDQDLNAQTTDISDPEVSE--AVAERDVVLILASDVEANK 87 
                                       68*****************8779*******************************76..58999************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       +av +++e n+++ i++ra+dp  ++ l +lgadvvi+p
  gi|313126269|ref|YP_004036539.1|  88 AAVSAIRERNSDQFIVVRASDPVSEDELAELGADVVINP 126
                                       *************************************98 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.089        66      23      56 ..      13      46 ..       4      88 .. 0.81
   2 !   45.2   0.1   1.1e-14   8.2e-12       2     101 .]     161     301 ..     160     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.089
                                      HCECS--TCGGCGCCHHCCCSEEEEEEE-S---S CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH 23 nllvDhneksqavegeakeeaedviiiDHHrlge 56
                                      + ++ +++  +av++e+ ee++dv+i+D  ++  
  gi|313126269|ref|YP_004036539.1| 13 YAILGCGSVGHAVAEELTEEGKDVLILDKDESRV 46
                                      4567899999******************988764 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 1.1e-14
                                       EEEE-ECSSSHHHHHHHHHHHHC................................................ECS--T CS
                                       xxxxxxxxxxxxxxxxxxxxxxx................................................xxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialanl................................................lvDhne 30 
                                        +i++h npD Dsi+Sa al+++                                                lvDh +
  gi|313126269|ref|YP_004036539.1| 161 LAILTHDNPDPDSIASAAALQAIaaeydveadilydgemghqenrafvnllgidltplaeapdlreygsvaLVDHMK 237
                                       57999*****************6666666777777777777777777777777777777777777777777****** PP

                                       CGGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  31 ksqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                       + +  +g     ++  i iDH ++ge ++    ++ ++++v+st++i++++++e ++ +s+++a++ll gi
  gi|313126269|ref|YP_004036539.1| 238 SVEPDIG-----TDVDIFIDHFEPGEGIDPV--FIDVRPNVSSTSTILTKYIQEFNISPSEAVATALLYGI 301
                                       *999999.....88999*******9655555..555789******************************98 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.96   7.2e+02      52      87 ..      72      92 ..      23     124 .. 0.61
   2 ?   -0.4   0.0       1.9   1.4e+03      18      60 ..     131     178 ..     115     183 .. 0.75
   3 !   34.1   0.0   4.2e-11   3.1e-08      24     114 ..     346     431 ..     329     434 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.96
                                      HHHHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEE CS
                             DHHA1 52 dagalgiaadklksklkkpvivfvakeegdkvkvsa 87
                                      +++++ i+a+++                 +k++vsa
  gi|313126269|ref|YP_004036539.1| 72 ERDVVLILASDVEA---------------NKAAVSA 92
                                      33334444444444...............3555544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHTCEEEC......TCEEEEEECHCCHHHHHHHHHH CS
                             DHHA1  18 lkealaklkaeellekaeevk......gvkvlvaevgeewdagalgiaa 60 
                                       +  al +l+ +el+ ka+++       + k+++    ++ d++ +++aa
  gi|313126269|ref|YP_004036539.1| 131 ADSALRSLESGELEYKARQLAdllestEGKLAILTH-DNPDPDSIASAA 178
                                       666777777777887777777777777777777777.888888888887 PP

  == domain 3  score: 34.1 bits;  conditional E-value: 4.2e-11
                                       HHHHHHHHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSH.SS-HH CS
                             DHHA1  24 klkaeellekaeevk.gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkd.gvdag 97 
                                       +++ae+++++    + + + lv++ g   d++alg+aa  l++   + ++ ++v++  +d++++sarsk d + ++g
  gi|313126269|ref|YP_004036539.1| 346 DVLAEAIQNR----DvQGSHLVSNAGFIRDRDALGQAAQHLLN--LEgVTTTAVFGIVDDNIYLSARSK-DiRMNIG 415
                                       4444444443....358899999999*****************..777888888888888*********.55***** PP

                                       HHHHHHHHHTTCCEEEE CS
                             DHHA1  98 elakeaaaklgggGGGH 114
                                       +++++a++ +g   GGH
  gi|313126269|ref|YP_004036539.1| 416 NVLQDAFEGIGEA-GGH 431
                                       *****66666555.588 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.2   1.5e-11   1.1e-08       2      92 ..      13     104 ..      12     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.5e-11
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHHH-SEE.EE-S-HHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaaeeadvv.vlavkped 73 
                                        +i+G+G++g+a+a+ l+++g   +++++  +++++++e+l+++       +++  + +ea++e dvv +la   e+
  gi|313126269|ref|YP_004036539.1|  13 YAILGCGSVGHAVAEELTEEG---KDVLIL-DKDESRVEALRDQDLnaqtTDISDPEVSEAVAERDVVlILASDVEA 85 
                                       69*******************...****66.***********655447776777778999***99998468999*** PP

                                       HHHHHHHCGHHHHTTSEEE CS
                     F420_oxidored  74 veevlselakdalkgklvi 92 
                                        ++++s+++++++ + +v+
  gi|313126269|ref|YP_004036539.1|  86 NKAAVSAIRERNSDQFIVV 104
                                       ********88877777777 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.2   1.3e-10   9.4e-08       3      91 ..      15      94 ..      13     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.3e-10
                                      EE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGG CS
                   Sacchrp_dh_NADP  3 iiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppis 81
                                      i+G+GsvG+avae+l ++++    + + d++++++eal    + ++++a++ d++++e   +++++e+d+v+ l+ +++
  gi|313126269|ref|YP_004036539.1| 15 ILGCGSVGHAVAEELTEEGKD---VLILDKDESRVEAL----RDQDLNAQTTDISDPEV--SEAVAERDVVLILASDVE 84
                                      9*****************985...**********8888....6789**********995..999**************6 PP

                                      HHHHHHHHHH CS
                   Sacchrp_dh_NADP 82 sldvlkaCie 91
                                      +++ +  +i+
  gi|313126269|ref|YP_004036539.1| 85 ANKAAVSAIR 94
                                      5554444443 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.2   2.7e-09   2.1e-06       6      82 ..      12      94 ..       9     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.7e-09
                                      -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-......HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregs......ksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78
                                      + a++G+Gs Gha a++l + g dv +  +++s       +  +A+ + ++  +v+eav++ dvv+il+ D   ++   
  gi|313126269|ref|YP_004036539.1| 12 TYAILGCGSVGHAVAEELTEEGKDVLILDKDESrvealrDQDLNAQTTDISDPEVSEAVAERDVVLILASDVEANKAAV 90
                                      569************************999988555443344578888899999*****************88777666 PP

                                      HHTG CS
                              IlvN 79 eeie 82
                                      ++i+
  gi|313126269|ref|YP_004036539.1| 91 SAIR 94
                                      6665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     3e-09   2.2e-06       2      72 ..      14      76 ..      13     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3e-09
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEE CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlv 72
                                      ailG+G++G  +a +L++ g dv ++++++ r+eal++++l+ ++ +    +++pe+ +a+     ++ d+v
  gi|313126269|ref|YP_004036539.1| 14 AILGCGSVGHAVAEELTEEGKDVLILDKDEsRVEALRDQDLNAQTTD----ISDPEVSEAV-----AERDVV 76
                                      8*****************************************99999....4444444444.....333443 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   3.6e-07   0.00027       8      79 ..      19      88 ..      14     107 .. 0.84
   2 ?   -0.1   0.0      0.69   5.2e+02      48      90 ..     151     196 ..     113     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.6e-07
                                      SHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.---HHH CS
                         Epimerase  8 GfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vggvaa 79
                                      G +G a++++l e+g +v+ ld+++s+ +  r++dl+  + d+ d++ + ++++  + d+v+ lA  v   +a
  gi|313126269|ref|YP_004036539.1| 19 GSVGHAVAEELTEEGKDVLILDKDESRVEALRDQDLNAQTTDISDPE-VSEAVA--ERDVVLILASdVEANKA 88
                                      99*******************************************98.666666..46999999776555444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.69
                                       --TT-HH..HHHHHHHHH.T-SEEEE--S---HHHHHHSHHHHHHH CS
                         Epimerase  48 ldltdrs..alerlfkee.qpdavihlAavggvaassedpadfiek 90 
                                       +dl++++  +l+ l +++ +pd +  +Aa + +aa+ +  ad++++
  gi|313126269|ref|YP_004036539.1| 151 ADLLESTegKLAILTHDNpDPDSIASAAALQAIAAEYDVEADILYD 196
                                       56666655577778888889*********99999999888888876 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   3.1e-07   0.00023      13      84 ..      11      81 ..       4     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.1e-07
                                      -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisata 84
                                      ++  ++G G +++ va+ L ++g + v+++  + +r+++l+++  +++++ ++  e++e++ae dvv++  +
  gi|313126269|ref|YP_004036539.1| 11 STYAILGCGSVGHAVAEELTEEGKD-VLILDKDESRVEALRDQDLNAQTTDISDPEVSEAVAERDVVLILAS 81
                                      56789***************99977.****************99888888888899**********986433 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.6e-07   0.00019       2      90 ..      13     107 ..      12     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.6e-07
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT....EEE-S..SHHHHHHHCSEEEE-SSSHHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg....akaae..sieelvasldvvitmvkagkavdev 72 
                                       ++++G G  G+  a++l+++g +v + + ++++ve+l ++      + ++  +++e+va+ dvv+++ ++ +a ++ 
  gi|313126269|ref|YP_004036539.1|  13 YAILGCGSVGHAVAEELTEEGKDVLILDKDESRVEALRDQDlnaqTTDISdpEVSEAVAERDVVLILASDVEANKAA 89 
                                       789*************************************9664422223113457777779999999998888888 PP

                                       HHSHCCC--TT-EEEE-S CS
                     NAD_binding_2  73 iegllealkkgdilidgs 90 
                                       ++ + e+ + + i++  s
  gi|313126269|ref|YP_004036539.1|  90 VSAIRERNSDQFIVVRAS 107
                                       888887766666666554 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   5.1e-07   0.00038       4      56 ..      14      71 ..      11     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.1e-07
                                      EEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-S.....S--TTHHHHHH CS
                    UDPG_MGDP_dh_N  4 sviGlGYvGlvtaavlaeighevigvDideekvdklnsgkip.....iyepgLeelvk 56
                                      +++G G vG   a  l e g++v+++D+de++v++l+ ++++     i +p+ +e v+
  gi|313126269|ref|YP_004036539.1| 14 AILGCGSVGHAVAEELTEEGKDVLILDKDESRVEALRDQDLNaqttdISDPEVSEAVA 71
                                      79*******************************9987665541111155555555554 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.2     9e-07   0.00067      10      86 ..      13      97 ..       8     113 .. 0.78
   2 ?   -2.1   0.0       7.2   5.4e+03      26      68 ..     115     165 ..     112     197 .. 0.51

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9e-07
                     NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapevkeele.........elvklaeeelekdlegadlviaatddrelneria 79
                                        + G G+v+   ++ l e+g++v +++++ ++ +e         ++ ++++ e+++ +++ d+v++  +d e n++ +
  gi|313126269|ref|YP_004036539.1| 13 YAILGCGSVGHAVAEELTEEGKDVLILDKD-ESRVEalrdqdlnaQTTDISDPEVSEAVAERDVVLILASDVEANKAAV 90
                                      6799**************************.44444555655554555566666788899*****************99 PP

                     NAD_binding_7 80 eaakarr 86
                                       a+++r+
  gi|313126269|ref|YP_004036539.1| 91 SAIRERN 97
                                      9998865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.2
                     NAD_binding_7  26 lleagakvtvvapevkeele......elvklaeeelekdlegad..lviaa 68 
                                       l+e ga+v++   ev + +       + ++++ ++l + le ++  l+i +
  gi|313126269|ref|YP_004036539.1| 115 LAELGADVVINPSEVIADSAlrslesGELEYKARQLADLLESTEgkLAILT 165
                                       566677776644443111112222234444444444444444443333333 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.6   3.3e-06    0.0025      27     106 ..       9      88 ..       1      95 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.3e-06
                                       ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEE.EE---BT CS
                       AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvv.igtvlip 102
                                       + ++  ++G G +G + ++  ++ g +V +lD++++r e l++   +  ++   +  +++eav+e dvv i +  + 
  gi|313126269|ref|YP_004036539.1|   9 SMSTYAILGCGSVGHAVAEELTEEGKDVLILDKDESRVEALRDQDLN-AQTTDISDPEVSEAVAERDVVlILASDVE 84 
                                       567889*************************************6666.56888888899999999998735555666 PP

                                       TSS- CS
                       AlaDh_PNT_C 103 Gkka 106
                                       ++ka
  gi|313126269|ref|YP_004036539.1|  85 ANKA 88 
                                       6655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.2e-06    0.0031      37     109 ..      11      90 ..       4      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.2e-06
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.......CHHHHTCEECSHHHHHHH-SEEEE-S--STTTT CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.......eeeelgvelvsleellaesDivslhlpltpetr 106
                                       +t +i+G+G++G+ava+ l++ g +v++ d+ +++ e       +++++ ++  ++ e++ae D+v + +   ++++
  gi|313126269|ref|YP_004036539.1|  11 STYAILGCGSVGHAVAEELTEEGKDVLILDKDESRVEalrdqdlNAQTTDISDPEVSEAVAERDVVLILASDVEANK 87 
                                       799****************************9997776644444444445555578899999999999888777777 PP

                                       TSB CS
                      2-Hacid_dh_C 107 hli 109
                                         +
  gi|313126269|ref|YP_004036539.1|  88 AAV 90 
                                       665 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.8e-06    0.0028       3      47 ..      14      58 ..      12     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.8e-06
                                      EEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTT CS
                    NAD_Gly3P_dh_N  3 avlGaGswGtalAkvlaenghevrlwvreeelieeineehenvky 47
                                      a+lG Gs G a+A  l+e+g++v +  ++e  +e+++++  n + 
  gi|313126269|ref|YP_004036539.1| 14 AILGCGSVGHAVAEELTEEGKDVLILDKDESRVEALRDQDLNAQT 58
                                      89************************************9999874 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   9.8e-06    0.0073       3      60 ..      14      71 ..      12      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.8e-06
                                      EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHH CS
                           3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeev 60
                                      a++G+G +G+ +a+ + ++g +V ++d +e+++e+ +++  +     +++ +++e+ +
  gi|313126269|ref|YP_004036539.1| 14 AILGCGSVGHAVAEELTEEGKDVLILDKDESRVEALRDQDLNAQTTDISDPEVSEAVA 71
                                      89********************************999876665555555555554444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.8e-06    0.0058       5      52 ..      14      61 ..      11      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.8e-06
                                      EEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHH CS
                     FAD_binding_3  5 lIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmel 52
                                      +I G G +G   a +L+e G +v++++k +++v+  r + ln +t ++
  gi|313126269|ref|YP_004036539.1| 14 AILGCGSVGHAVAEELTEEGKDVLILDKDESRVEALRDQDLNAQTTDI 61
                                      699*********************************999999999776 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   4.3e-05     0.032       8      70 ..      18      73 ..      12     104 .. 0.79
   2 ?   -3.5   0.0         8     6e+03      81      93 ..     362     374 ..     345     395 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                                      TTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHH CS
                         adh_short  8 assGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvek 70
                                      + + +G+a+a+el +eG +v+++d+ e+++e++ ++      ++ a ++D++d e  ea+ e+
  gi|313126269|ref|YP_004036539.1| 18 C-GSVGHAVAEELTEEGKDVLILDKDESRVEALRDQ------DLNAQTTDISDPEVSEAVAER 73
                                      3.469***********************99777766......356788888888877777665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8
                                       EEE---SS--SSG CS
                         adh_short  81 LvnNAGitgsgpf 93 
                                       Lv NAG  +++++
  gi|313126269|ref|YP_004036539.1| 362 LVSNAGFIRDRDA 374
                                       7888887544433 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   4.2e-05     0.031       5      80 ..      20      91 ..      15     102 .. 0.85
   2 ?   -3.1   0.1       6.4   4.8e+03       9      50 ..     149     189 ..     147     194 .. 0.51
   3 ?   -2.0   0.0       2.8   2.1e+03      54      92 ..     343     379 ..     340     398 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                                      SHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE----- CS
                      adh_short_C2  5 gIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagia 80
                                      ++G+a+A++l eeG +v++ d +e++   ve+l ++ + ++  +D++d+e  ea++e+ v  +   D+  n a+++
  gi|313126269|ref|YP_004036539.1| 20 SVGHAVAEELTEEGKDVLILDKDESR---VEALRDQ-DLNAQTTDISDPEVSEAVAERDVVLILASDVEANKAAVS 91
                                      89*******************99998...9999885.77799********99999998777777777777777665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.4
                                       HHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--T CS
                      adh_short_C2   9 aiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDV 50 
                                       ++A +l +   ++++   ++ + ++++++a+ l+a + e DV
  gi|313126269|ref|YP_004036539.1| 149 QLADLLESTEGKLAILTHDNPDPDSIASAAA-LQAIAAEYDV 189
                                       5566666666666666666666444444433.3444444444 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-H CS
                      adh_short_C2  54 eqvealveevvekfgklDilvnnagiapklkgpfletsr 92 
                                       e+++ l+e+++++  +   lv nag+ ++   ++l    
  gi|313126269|ref|YP_004036539.1| 343 ETLDVLAEAIQNRDVQGSHLVSNAGFIRD--RDALGQAA 379
                                       66777777888887778889999999998..55444444 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   0.00014      0.11       2      88 ..      14     118 ..      13     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG........-GGG-TT-SE.................-EEEE--S- CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefa........tkerfpeade.................tavvvlthd 53 
                                       +i+G g v++a+a+ + + g +v ++d++e+          +        +                 ++v++l  d
  gi|313126269|ref|YP_004036539.1|  14 AILGCGSVGHAVAEELTEEGKDVLILDKDESRVealrdqdlN--------AqttdisdpevseavaerDVVLILASD 82 
                                       699***************************633355444430........144566667777788889********* PP

                                       HHHHHHHHHHHSSS-.-SEEEESS-HHHHHHHCTTS CS
                            XdhC_C  54 hklDaealeaalrkk.aayigllGSrkkaarrlerl 88 
                                        +  ++a++a+ +++  ++i + +S   ++  l++l
  gi|313126269|ref|YP_004036539.1|  83 VEANKAAVSAIRERNsDQFIVVRASDPVSEDELAEL 118
                                       *********999744255887777776666666665 PP

>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012     0.089      17     132 ..      21     142 ..      18     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            DUF364  17 VGyfapvlkklkekgaeltvlelnpnlleeeegdl........pdeaaeellpeadvviitGstL.vngtlerllel 84 
                                       VG+   v+++l e+g+++ +l+ +++++e  + +         +d++ +e+++e dvv+i +s + +n+     ++ 
  gi|313126269|ref|YP_004036539.1|  21 VGHA--VAEELTEEGKDVLILDKDESRVEALRDQDlnaqttdiSDPEVSEAVAERDVVLILASDVeANKAAVSAIRE 95 
                                       5544..7888889999999999888776654322235566677********************99556666666665 PP

                            DUF364  85 akkaaevvlvGPsapllpevlfdyGvdviagvvvtdpdkllraiaeGg 132
                                        + +++ ++v  s p++++ l+++G+dv+     + +d++lr ++ G 
  gi|313126269|ref|YP_004036539.1|  96 RN-SDQFIVVRASDPVSEDELAELGADVVINPSEVIADSALRSLESGE 142
                                       55.999*********************998777777777777777775 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   0.00021      0.16      20      97 ..      23     103 ..      19     111 .. 0.80
   2 ?   -1.4   0.0       4.2   3.1e+03      25      65 ..     114     158 ..     103     171 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHCTSEEEEE-SSTHHCCCCHHGG..BTCCEEES-C.HHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS CS
                    UDPG_MGDP_dh_C  20 ldiieeLleegaevkiyDPkvkeeaveaele..ekgvevvdsl.eealkgadaiviltehdefkeldlaklkelmkp 93 
                                        +++eeL+eeg++v i D   ++ ++ ++++  +++  + d+  +ea+++ d+++il    e ++ +++ ++e+ ++
  gi|313126269|ref|YP_004036539.1|  23 HAVAEELTEEGKDVLILDKDESRVEALRDQDlnAQTTDISDPEvSEAVAERDVVLILASDVEANKAAVSAIRERNSD 99 
                                       5799***************77777766666665445555544469***************99999999999999866 PP

                                       -EEE CS
                    UDPG_MGDP_dh_C  94 avvf 97 
                                       ++++
  gi|313126269|ref|YP_004036539.1| 100 QFIV 103
                                       6654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.2
                                       HHHHCTSEEEEE-SSTHHCCCCHHGG....BTCCEEES-CHHHHT CS
                    UDPG_MGDP_dh_C  25 eLleegaevkiyDPkvkeeaveaele....ekgvevvdsleealk 65 
                                       eL+e ga+v+i    v ++ + ++le    e++++ +++l e  +
  gi|313126269|ref|YP_004036539.1| 114 ELAELGADVVINPSEVIADSALRSLEsgelEYKARQLADLLESTE 158
                                       566667777666666666666555555555555555555555555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017      0.13       1      29 [.      15      43 ..      15      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      I+G G  G + A +L+++g+dvl+l+k +
  gi|313126269|ref|YP_004036539.1| 15 ILGCGSVGHAVAEELTEEGKDVLILDKDE 43
                                      89************************975 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.3    0.0016       1.2       1      82 [.      17      95 ..      17     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                                      --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TTHHHHHT--CB---HHHHHHHH.S-EEEEE-S--HHHHTTHH CS
                     NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskdrkallasealtldlddliahl.dpdvvVEcasseavaelvl 77
                                      G+G +G av+e+l+++ ++     v+++d+d s++++ r ++l+++++  + +++ + + + dvv+ +as+  + + ++
  gi|313126269|ref|YP_004036539.1| 17 GCGSVGHAVAEELTEEGKD-----VLILDKDeSRVEALRDQDLNAQTTDISDPEVSEAVaERDVVLILASDVEANKAAV 90
                                      9****************97.....8999999677777666666655555544555554457999998888888888887 PP

                                      HHHHT CS
                     NAD_binding_3 78 kaLka 82
                                      +a+++
  gi|313126269|ref|YP_004036539.1| 91 SAIRE 95
                                      77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2700.22
//
Query:       gi|313126270|ref|YP_004036540.1|  [L=97]
Description: hypothetical protein Hbor_15230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 609.45
//
Query:       gi|313126271|ref|YP_004036541.1|  [L=161]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-09   37.8   0.6    2.7e-09   36.9   0.6    1.5  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    6.8e-07   28.8   0.3    2.2e-06   27.1   0.3    1.9  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.4e-05   23.8   0.3    9.8e-05   22.3   0.0    1.9  2  HTH_20          Helix-turn-helix domain
    7.9e-05   22.4   0.0    0.00012   21.8   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
     0.0003   20.6   0.0    0.00052   19.8   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0061   16.4   0.1      0.017   15.0   0.0    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.025   14.5   0.0    1.6  1  MarR_2          MarR family
      0.058   12.8   0.2        1.6    8.1   0.0    2.1  2  DUF99           Protein of unknown function DUF99
      0.083   13.1   0.0       0.16   12.2   0.0    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.12   12.3   0.1        0.2   11.6   0.1    1.4  1  GYD             GYD domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.6   1.5e-12   2.7e-09      11      74 ..      75     137 ..      65     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.5e-12
                                       THHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  11 eqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                        ++++f+e++ +++ V+++y + G+ d+++ ++    e  er++ + + ++++v rt++++v++
  gi|313126271|ref|YP_004036541.1|  75 GSHHDFKEKILDVEGVTQAYFTMGETDFIVVAHLSGREMVERLITD-FETIDEVDRTNSTFVIS 137
                                       3589******************************************.***************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.3   1.2e-09   2.2e-06       1      48 []       1      48 [.       1      48 [. 0.95

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.2e-09
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +de d+++L+++ +    s  +L e++g+++st+++rl++L e+G+Ik
  gi|313126271|ref|YP_004036541.1|  1 MDERDIRLLKAISDLETGSPEQLHEETGIPVSTIHYRLNNLREAGVIK 48
                                      79999999999999999999***************************8 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.5e-08   9.8e-05      14      55 ..       7      48 ..       4      50 .. 0.91
   2 ?   -2.3   0.2       2.6   4.7e+03      48      58 ..      56      67 ..      56      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.5e-08
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      r+l+a+++ e  ++++l+e+ +++ +t++y+L+ L+eag ++
  gi|313126271|ref|YP_004036541.1|  7 RLLKAISDLETGSPEQLHEETGIPVSTIHYRLNNLREAGVIK 48
                                      677788888999***************************996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.6
                                      HHHCTT.EEEEC CS
                            HTH_20 48 LeeagL.vevvr 58
                                      Le++gL v+vv 
  gi|313126271|ref|YP_004036541.1| 56 LEKVGLgVTVVV 67
                                      899***999985 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   6.8e-08   0.00012       6      51 ..       6      50 ..       3      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.8e-08
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +++L+a++    + +  +l+++tg+p St h  L+ L e G ++ d
  gi|313126271|ref|YP_004036541.1|  6 IRLLKAISDLETG-SPEQLHEETGIPVSTIHYRLNNLREAGVIKND 50
                                      799*********8.9**************************99876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.9e-07   0.00052       6      46 ..       7      48 ..       2      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.9e-07
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++Lk+ ++ +  +  +l ee+g++ st+ + L+ LreaG+++
  gi|313126271|ref|YP_004036541.1|  7 RLLKAISDlETGSPEQLHEETGIPVSTIHYRLNNLREAGVIK 48
                                      778888886668889************************996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   9.4e-06     0.017       8      53 ..       3      48 ..       1      51 [. 0.91
   2 ?   -2.8   0.0       3.5   6.3e+03      42      54 ..     104     116 ..     104     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.4e-06
                                      HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      e +++  +a+  l+  + ++++ee+g+p s++   L++L ++G+++
  gi|313126271|ref|YP_004036541.1|  3 ERDIRLLKAISDLETGSPEQLHEETGIPVSTIHYRLNNLREAGVIK 48
                                      77889999999999999**************************997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.5
                                       HHHHHHHCTSEEE CS
                              TrmB  42 vLrsLedkGlVer 54 
                                       v+  L+ + +Ver
  gi|313126271|ref|YP_004036541.1| 104 VVAHLSGREMVER 116
                                       5678899999987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-05     0.025       8      51 ..       6      47 ..       1      58 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                       r+L a+ + + +  ++ +l +++g++ s+++++l+ L +aG +
  gi|313126271|ref|YP_004036541.1|  6 IRLLKAISDLETG--SPEQLHEETGIPVSTIHYRLNNLREAGVI 47
                                      6888888888874..99*************************98 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0009       1.6      83     105 ..      19      41 ..      11      55 .. 0.85
   2 ?    2.9   0.1     0.036        65       5      55 ..      87     134 ..      83     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0009
                                       -HHHHHHHH---EEEEESS---H CS
                             DUF99  83 DlerlheetglPviavtreepdl 105
                                        +e+lheetg+Pv ++ ++  +l
  gi|313126271|ref|YP_004036541.1|  19 SPEQLHEETGIPVSTIHYRLNNL 41 
                                       589*************9998875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.036
                                       EEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHH CS
                             DUF99   5 vlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaii 55 
                                       v G+  ++f+   ++++ ++v + + ++++v+ ++    t+d  D t++ +
  gi|313126271|ref|YP_004036541.1|  87 VEGVTQAYFT---MGETDFIVVAHLSGREMVERLITDFETIDEVDRTNSTF 134
                                       5688999988...46666677777799999***999988888888777643 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.9e-05      0.16      23      50 ..      22      49 ..      20      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-05
                    B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvk 50
                                      +L+ e+++ ++ ++yrl+ L + g I+ 
  gi|313126271|ref|YP_004036541.1| 22 QLHEETGIPVSTIHYRLNNLREAGVIKN 49
                                      7999********************9985 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00011       0.2      37      63 ..      90     116 ..      67     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                               GYD  37 leslyatlGeyDvvvivEapDdetaaa 63 
                                       + + y+t+Ge D++v+  +  +e +++
  gi|313126271|ref|YP_004036541.1|  90 VTQAYFTMGETDFIVVAHLSGREMVER 116
                                       6799***********998777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1085.90
//
Query:       gi|313126272|ref|YP_004036542.1|  [L=319]
Description: dmt(drug/metabolite transporter) superfamily permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-45  153.1  38.2    9.8e-25   87.3  13.6    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.41   10.4   4.4        3.5    7.4   0.1    3.5  2  DUF3188   Protein of unknown function (DUF3188)
          2    8.4   3.1        7.9    6.5   0.1    2.9  3  COX4      Cytochrome c oxidase subunit IV


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3  13.6   1.6e-28   9.8e-25       2     135 ..      12     145 ..      11     147 .. 0.96
   2 !   72.1  16.5     8e-24   4.8e-20       2     135 ..     159     294 ..     158     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 1.6e-28
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkd.wllllllgllgtvl 77 
                                       + +ll+++ ++fw+++fv++ ++l++++pl ++++r+ iag++ l +a+ +  ++  +s +d wl+ ++ g++ +++
  gi|313126272|ref|YP_004036542.1|  12 WNALLFIALSCFWGTSFVAIEAGLEYFPPLLFAGIRYGIAGLAILSYAVATTDRW-HPSGRDeWLSAAVAGVFIIAA 87 
                                       668999*************************************************.7777777************** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       ++ l++++  ++sas+a++++sl+Pv+t+++++ +lg++l ++  +g++l+++Gv+++
  gi|313126272|ref|YP_004036542.1|  88 YHALLYIGEMYVSASVAAVVVSLAPVLTAVFAAGILGQPLDKIAGVGFLLGIVGVVIV 145
                                       *******************************************************998 PP

  == domain 2  score: 72.1 bits;  conditional E-value: 8e-24
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtv 76 
                                       lgi+l+ll++ ++ai++vl+  l ++++  ++ ++ +li++ +l++ a+ +++++   +++ +++++l++l ++++v
  gi|313126272|ref|YP_004036542.1| 159 LGIVLVLLSTASFAIGGVLTEPLRTSLPAESMQAWAMLIGAGVLFVGAVARGESPatIEWTSTAIISLMYLTFVSGV 235
                                       79*****************************************************999999999************* PP

                              EamA  77 lafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       ++fl++f + ++++a+++ l+++lePv++ + +++llg  +++++l+g+v +++G +l+
  gi|313126272|ref|YP_004036542.1| 236 VGFLIYFALHERVGATEINLVSYLEPVVASLAGWVLLGHVVSSTTLVGFVTVFIGFALV 294
                                       *******************************************************9997 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.5     0.039   2.3e+02       7      45 ..     136     172 ..     133     174 .. 0.80
   2 ?    7.4   0.1   0.00058       3.5      24      45 ..     190     210 ..     184     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.039
                           DUF3188   7 llgllillysqrqgsdrlqslPallvGlgLivsgavgrg 45 
                                       llg++++    +++  +l s    l G++L++++ +++ 
  gi|313126272|ref|YP_004036542.1| 136 LLGIVGVVIVANPDPANLLST--NLLGIVLVLLSTASFA 172
                                       677887777789999999998..8999999999888775 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00058
                           DUF3188  24 lqslPallvGlgLivsgavgrg 45 
                                       +q+  a+l+G+g++++gav rg
  gi|313126272|ref|YP_004036542.1| 190 MQAW-AMLIGAGVLFVGAVARG 210
                                       5666.88************997 PP

>> COX4  Cytochrome c oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.085   5.1e+02      67      96 ..      71     100 ..      61     106 .. 0.79
   2 ?   -1.3   0.1      0.33     2e+03      61      88 ..     208     236 ..     186     248 .. 0.65
   3 ?    6.5   0.1    0.0013       7.9      71     104 ..     279     312 ..     274     317 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.085
                              COX4  67 tkewkkvlggvlillglslllfllirlfva 96 
                                        +ew + +++ ++++++  +l+++ +++v 
  gi|313126272|ref|YP_004036542.1|  71 RDEWLSAAVAGVFIIAAYHALLYIGEMYVS 100
                                       459999999999999999988888888875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.33
                              COX4  61 pemkaptk.ewkkvlggvlillglslllf 88 
                                       ++ + p   ew++++ + l+ l +   ++
  gi|313126272|ref|YP_004036542.1| 208 ARGESPATiEWTSTAIISLMYLTFVSGVV 236
                                       55555555677777666666666555554 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0013
                              COX4  71 kkvlggvlillglslllfllirlfvagpvpkTls 104
                                       ++ +g+v +++g++l+   +ir+ + g+vp+T +
  gi|313126272|ref|YP_004036542.1| 279 TTLVGFVTVFIGFALVKRHAIRARILGDVPTTAT 312
                                       6889***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 1977.06
//
Query:       gi|313126273|ref|YP_004036543.1|  [L=191]
Description: hypothetical protein Hbor_15260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.17   11.6   0.0    1.1  1  CAP59_mtransfer  Cryptococcal mannosyltransferase 1


Domain annotation for each model (and alignments):
>> CAP59_mtransfer  Cryptococcal mannosyltransferase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.3e-06      0.17      83     128 ..     113     158 ..      76     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.3e-06
                   CAP59_mtransfer  83 gkkelkRIeyLaelRNkaLepLeelakegkekfdkvlFlnDvvfta 128
                                       ++ + +R e+L ++R +a + L++      e+ ++v FlnDv  t+
  gi|313126273|ref|YP_004036543.1| 113 PNFRRRRAERLFTTRSAAFDHLKRAGGVAPEDLERVWFLNDVWATQ 158
                                       66799*****************997666667899********8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1243.87
//
Query:       gi|313126274|ref|YP_004036544.1|  [L=485]
Description: hypothetical protein Hbor_15270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-09   35.6   0.0    1.8e-07   30.6   0.0    2.1  2  DUF2048        Abhydrolase domain containing 18
  ------ inclusion threshold ------
      0.036   13.3   0.0       0.14   11.4   0.0    1.8  2  Hydrolase_4    Serine aminopeptidase, S33
      0.055   13.1   0.0       0.25   11.0   0.0    2.1  1  Abhydrolase_1  alpha/beta hydrolase fold
       0.12   11.9   0.0       0.25   10.9   0.0    1.5  1  DLH            Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0     4e-11   1.8e-07     102     194 ..     237     333 ..     208     353 .. 0.82
   2 ?    2.8   0.0     0.011        49     302     352 .]     412     466 ..     400     466 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4e-11
                           DUF2048 102 TGDh.sywrRrnllakpllkenigsiilenpfYglrkPkeQvrss..l.knVsdlfvmgsalilEslvllhwlereG 174
                                        GD   yw   + +++ l +++  +++++ p+ g r P  Q+  +  l +  + +f +++a ++E+ v + w  +eG
  gi|313126274|ref|YP_004036544.1| 237 YGDRlGYWPEEEAIGRRLARDGYRAVLPDAPWHGRREPLGQFSGEpyLaRMPVSAFELLGAAVQETGVFVDWARTEG 313
                                       4664259999999****************************9875334244456777777889************** PP

                           DUF2048 175 yGplgltGlSmGGhmaslaa 194
                                          +++ GlS+GG  a  +a
  gi|313126274|ref|YP_004036544.1| 314 APAVAVGGLSLGGSIAFAVA 333
                                       *************9996555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.011
                           DUF2048 302 kdDayvpresvaslqeiw..pgsevryldgGHvs..ayllkkklfrkaivealer 352
                                        +D   p+e+ a+l + w  p  +vr  d+GH+   a l + + f+++++ al+r
  gi|313126274|ref|YP_004036544.1| 412 SHDDVAPTETTATLVRQWdvPRRNVRTWDSGHLGtaARLYRGDEFQRTLTAALDR 466
                                       56777788888888777766899*********96336799**********99997 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.1e-05      0.14      21      97 ..     248     336 ..     225     360 .. 0.78
   2 ?   -1.3   0.0      0.23     1e+03     194     224 ..     406     436 ..     393     442 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                       Hydrolase_4  21 aelaeaLaaqGfavyalDhrGhGrse..........gkrghvpsfddy...vdDlaafvekvkeehpelplfllGhS 84 
                                       + ++++La+ G+  +  D+  hGr e           +r+ v+ f+ +   v+    fv+ +++e     + + G S
  gi|313126274|ref|YP_004036544.1| 248 EAIGRRLARDGYRAVLPDAPWHGRREplgqfsgepyLARMPVSAFELLgaaVQETGVFVDWARTEG-APAVAVGGLS 323
                                       45899***************************9999889999999876222666666777666443.3469999*** PP

                       Hydrolase_4  85 mGGliallyllry 97 
                                       +GG ia++++ r+
  gi|313126274|ref|YP_004036544.1| 324 LGGSIAFAVAGRC 336
                                       ********99654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.23
                       Hydrolase_4 194 llllhGeaDkvvdpeasrelyerlgskdktl 224
                                       ++  +G++D v + e ++ l+++    + ++
  gi|313126274|ref|YP_004036544.1| 406 IFCWYGSHDDVAPTETTATLVRQWDVPRRNV 436
                                       67789************99999877766655 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.6e-05      0.25       1     137 [.     226     391 ..     226     402 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.6e-05
                                       SEEEEE-STTTCGGG....GTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB...........CHH.....SHHH CS
                     Abhydrolase_1   1 pvlvilhGlpgssdv....waerglapaLakdgfdvillDlrGvgySspapacin..........ddy.....gtas 58 
                                       p+l+++ Gl+  +d     + e ++++ La+dg++ +l+D + +g+ +p     +          + +         
  gi|313126274|ref|YP_004036544.1| 226 PTLIFFSGLGSYGDRlgywPEEEAIGRRLARDGYRAVLPDAPWHGRREPLGQ-FSgepylarmpvSAFellgaAVQE 301
                                       679999999995555555555668**********************988884.556666655555444555553333 PP

                                       HHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHH........GGGEEEEEEESE....CSSCCHHHHHHHHHHHH CS
                     Abhydrolase_1  59 vaddldrildalgddkltlvGhSmGGmialayaaey........perVkalvllga....idpaaslieaqrqqaks 123
                                       +  ++d+++   g   +++ G S+GG ia+a+a +         p+ V  +++ g+    ++++   + +++  a s
  gi|313126274|ref|YP_004036544.1| 302 TGVFVDWARTE-GAPAVAVGGLSLGGSIAFAVAGRCgewpesmrPDLVGTVAAPGSlmqtLSESKLVSLLDLDDALS 377
                                       44555555544.788888***************99888877777777777777666666666666666666666666 PP

                                       HHCHHCHHHHHHHH CS
                     Abhydrolase_1 124 fpdffdgyaadcar 137
                                         ++ d + +++a+
  gi|313126274|ref|YP_004036544.1| 378 AAGWTDEDLNEFAP 391
                                       66666666666655 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.5e-05      0.25      24     118 ..     242     335 ..     213     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.5e-05
                               DLH  24 GvndnikdiserlaeeGYvalaPdlYarqaldpn.deaeaaraldelvskva.eekvlddlkaavaylksvpevstk 98 
                                       G+  + + i +rla+ GY a++Pd  + +  +p  +   +  + ++ vs+ +   + +++    v+++++ +     
  gi|313126274|ref|YP_004036544.1| 242 GYWPEEEAIGRRLARDGYRAVLPDAPWHGRREPLgQFSGEPYLARMPVSAFElLGAAVQETGVFVDWARTEG---AP 315
                                       555566789***************987777344303333334444444444202344444456677777777...78 PP

                               DLH  99 kvgvvGfCmGGalalllaae 118
                                        v+v G  +GG +a+++a +
  gi|313126274|ref|YP_004036544.1| 316 AVAVGGLSLGGSIAFAVAGR 335
                                       99*************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3157.70
//
Query:       gi|313126275|ref|YP_004036545.1|  [L=641]
Description: ser-tRNA(thr) hydrolase; threonyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-34  117.9   0.0    8.7e-34  117.0   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.7e-18   66.6   0.4    8.8e-18   64.3   0.2    2.3  2  HGTP_anticodon  Anticodon binding domain
    1.1e-12   47.8   0.3    2.3e-12   46.8   0.3    1.6  1  TGS             TGS domain
    1.6e-11   44.1   0.0      3e-11   43.2   0.0    1.5  1  tRNA_SAD        Threonyl and Alanyl tRNA synthetase second ad
     0.0012   19.5   3.9      0.018   15.7   0.2    3.2  3  ThiS            ThiS family


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.0   2.4e-37   8.7e-34       5     178 ..     321     527 ..     315     528 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 2.4e-37
                                       ETTSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   5 drndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeasldds 79 
                                       d nd+ey LkP+n+++++ ++ ++   s+r LP+++++ + +yR+E++ +++GL Rv  F+ +dg+ f+ +++++++
  gi|313126275|ref|YP_004036545.1| 321 DVNDEEYGLKPMNCPGHATIFDQN-SWSYRdLPVRYFEDGKVYRKEQRgELSGLSRVWSFTIDDGHLFCRPEQIEQE 396
                                       679******************988.777555*****************99*************************** PP

                                       HHHHHHHHHHHHHHTT.SCEEEEEEGTTSC.................................BTTSEEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxx RF
                      tRNA-synt_2b  80 lrdlikaisriferlglefraiielmsaks.................................adykdkkefeavse 123
                                       +r++++ i++++ ++gle ++ +   + ++                                 a+y++k +f   + 
  gi|313126275|ref|YP_004036545.1| 397 IRQVMNSIYEVLDTFGLEAHVALAT-RPEKsvgsdeiweqsesqlrsvlenqnidydlepgdgAFYGPKIDFSFEDA 472
                                       ******************8765555.3333477899**************************************999 PP

                                       TTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                      tRNA-synt_2b 124 sltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                        l+++++  t+q + ++++er+++t+  e+n+e++++mi++a  g  eR+  +++e+
  gi|313126275|ref|YP_004036545.1| 473 -LGRKWDGPTVQVD-FNMPERFDLTYTGEDNEEHRPVMIHRAlYGsYERFFMVLIEH 527
                                       .*************.***************************9999********997 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.76   2.7e+03      12      35 ..     395     418 ..     390     425 .. 0.83
   2 !   64.3   0.2   2.5e-21   8.8e-18       1      92 [.     540     626 ..     540     628 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.76
                                       HHHHHHHHHHHHHHHTTTSEEEEE CS
                    HGTP_anticodon  12 eeleeyakklaeeLraagirveld 35 
                                       +e+ +++++++e L   g+++++ 
  gi|313126275|ref|YP_004036545.1| 395 QEIRQVMNSIYEVLDTFGLEAHVA 418
                                       48999***********99999886 PP

  == domain 2  score: 64.3 bits;  conditional E-value: 2.5e-21
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       qv ++p+++   + + ya ++++eL   ++rv + d++ ++g+kire ++ ++p++++vGe+e e+gt++vrdr++r
  gi|313126275|ref|YP_004036545.1| 540 QVRILPISD---DQLGYAHRVKNELG--DFRVSVEDRSWTLGRKIREGQEDNVPYMLIVGENEEESGTISVRDRQER 611
                                       89*******...89***********8..678********************************************** PP

                                       EEEEEETTHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklk 92 
                                       e++ vs+d + e l+
  gi|313126275|ref|YP_004036545.1| 612 EEQDVSIDAFREHLE 626
                                       ********9988775 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.3   6.4e-16   2.3e-12       3      60 .]       6      63 ..       4      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 6.4e-16
                                      EEETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECSEEEETTSBB-SSEEEEEEE CS
                               TGS  3 vytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnGqrvgldhvLedgdvveIvt 60
                                      v +PdG++  + +gatveD+Ay I+ +l+++++++ V+G++v+   ++ dg+ v Ivt
  gi|313126275|ref|YP_004036545.1|  6 VNLPDGSELSVEEGATVEDVAYEIGPGLGEDTVAGVVDGELVDKAAPVHDGAQVVIVT 63
                                      557*****************************************************98 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   8.4e-15     3e-11       2      44 .]     170     218 ..     169     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.4e-15
                                       EEEEETT.EEEEESS---SBGGGC-SEEEE.......CCECCCTCEEEEE CS
                          tRNA_SAD   2 rvvsiGdisvelCgGtHvpnTgeIgafkil.......seesiakglrRIy 44 
                                       +++ +G+ + +lC G+Hv++Tg+Iga+ +l       ++++ +++l+R+y
  gi|313126275|ref|YP_004036545.1| 170 SFYVQGE-FEDLCKGPHVESTGKIGAVELLnissaywRGDEENETLTRVY 218
                                       67889*8.*****************************************9 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   4.9e-06     0.018      13      72 ..      11      63 ..       3      63 .. 0.91
   2 ?   -2.2   0.0       1.8   6.6e+03      11      35 ..     427     451 ..     419     456 .. 0.79
   3 ?    3.4   0.1     0.035   1.3e+02      12      38 ..     601     632 ..     590     640 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.9e-06
                                      CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEE CS
                              ThiS 13 eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailp 72
                                       +el ++eg+tv+++  ++g        e+ va  v+ge+v++    +++ dg +v+i++
  gi|313126275|ref|YP_004036545.1| 11 GSELSVEEGATVEDVAYEIGPGL----GEDTVAGVVDGELVDK---AAPVHDGAQVVIVT 63
                                      478899**************999....569*************...************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                                       HTCEEEEESSTSBHHHHHHHHHHHT CS
                              ThiS  11 ageeelelaegstvaelleaLgery 35 
                                       +g+ e+ ++++s ++ +le+ + +y
  gi|313126275|ref|YP_004036545.1| 427 VGSDEIWEQSESQLRSVLENQNIDY 451
                                       4478899999999999999988777 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.035
                                       T.....CEEEEESSTSBHHHHHHHHHHHTCHH CS
                              ThiS  12 g.....eeelelaegstvaelleaLgerypel 38 
                                       g     ++++ ++++ ++++ +e+L+++y+e 
  gi|313126275|ref|YP_004036545.1| 601 GtisvrDRQEREEQDVSIDAFREHLEAEYDEK 632
                                       5555567889999****************654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3889.25
//
Query:       gi|313126276|ref|YP_004036546.1|  [L=495]
Description: (1-_4)-alpha-d-glucan branching protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   7.5e-150  499.8   0.5   9.3e-150  499.5   0.5    1.0  1  Glyco_hydro_77  4-alpha-glucanotransferase


Domain annotation for each model (and alignments):
>> Glyco_hydro_77  4-alpha-glucanotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  499.5   0.5  5.2e-154  9.3e-150       2     465 ..      12     474 ..      11     477 .. 0.94

  Alignments for each domain:
  == domain 1  score: 499.5 bits;  conditional E-value: 5.2e-154
                                       -GGGSB-SSSSSS--SS.HHHHHHHHHHHTT--EEEES--SE...ST.--TTS-SESSSE-GGGS-CHG.HHHHHHH CS
                    Glyco_hydro_77   2 plsSLrskksyGiGdlg.dlkefvdflakagqklwqilPlndt..epdtsPYsslSafalnplyidlealpelaela 75 
                                       ++ SL+++  +GiGdlg  ++ f+d+la+a+q+lwq  Pl++t   +  sPY+s+Safa+npl++dl+      +l+
  gi|313126276|ref|YP_004036546.1|  12 HVPSLPGP--HGIGDLGdGARAFIDWLASAEQSLWQFCPLGPTasIHGHSPYQSYSAFAGNPLLVDLD------QLR 80 
                                       899*****..*******99***********************8533355*******************......99* PP

                                       HTTSSHGGGSS........B--HHHHHHHHHHHHHHHHHTHHH.HHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                    Glyco_hydro_77  76 eegllakeele........rvdyekvielklkllrkaferfkekkkakeskefeeFveenaewledyalFmalkekf 144
                                       e+g+l++++le        +++y++v+e+k++ lr+a+erf+++++++++++f++F e++++wl+ yalFmal++++
  gi|313126276|ref|YP_004036546.1|  81 EDGYLTDDDLEpvpafsdhEIEYDRVAEYKREQLRTAHERFQSEATTEDREAFDAFREHESSWLDGYALFMALRTRY 157
                                       *********9556667777********************************************************98 PP

                                       T-SSGGGS-HHHHTTTHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEEEESS--SSSHHHHHC CS
                    Glyco_hydro_77 145 egaswseWpeelrkrkeealekakkelaeeiefykflQylfdkqlkelkeyanekgieligDlpigvardSadvWan 221
                                       +  +w++Wp+e+r+++e+a+++ ++ela+ei++ +f Q++fd+q++elk+yan++g++l+gDlpi+va dSadvWa 
  gi|313126276|ref|YP_004036546.1| 158 D-GAWTTWPQEIRTHDEAAINRHREELADEISYREFAQFVFDTQWRELKAYANDHGVKLVGDLPIYVALDSADVWAA 233
                                       8.58************************************************************************* PP

                                       GGGB-BTTTS......EESSBSSSTT-EEEEEE-B-HHHHHHTTTHHHHHHHHHHHTT-SEEEETTGGGGTEEEEEE CS
                    Glyco_hydro_77 222 pelFkldesa......GaPPDafsatGQnWgnPlynweelekdgyawwikrlraalklfdalRIDHvlGffrlWeip 292
                                       pe F+l e+       G+PP   +++GQ+WgnPly+w++l++++y+ww++rl++ ++l+d++RIDH+ Gf+++W+ip
  gi|313126276|ref|YP_004036546.1| 234 PEAFDLTEENepvavaGVPPNP-NDDGQRWGNPLYDWDYLRENDYDWWMDRLERLFELVDVTRIDHFKGFDEYWAIP 309
                                       ********************87.899*************************************************** PP

                                       TT-SSCTC-EEEE--HHHHHHHHHHHHHHCT-EEEE---SS--HHHHHHHHHTT-BEEEEGGGTTSTTTT.TTSGGG CS
                    Glyco_hydro_77 293 aeektalngeyvkypgeelfevlkeelqkgkllviaEDLGvvpdevrelleelgilgmkvlqfafedeenefylphn 369
                                       a++++   ge+ ++pg+++fe++++++  g+l++i EDLG++ + +++l++++g++gm+v q+a+  +e + y+p +
  gi|313126276|ref|YP_004036546.1| 310 ADAHSPAAGEWRDAPGHDFFETVEDQF--GDLPFIVEDLGFLDQRMTDLRDRFGFPGMRVPQYANWCQEGDMYQPMH 384
                                       ***************************..************************************555448****** PP

                                       S-SSEEEES--TTS--HHHHHTHHHHHHHHHHHHHHHHTTCCS-GGGHHHHHHHHHHHSSSSEEEEEHHHHT.TTGG CS
                    Glyco_hydro_77 370 ypensvvytgtHDndtlrgwweeerakekealleylkeegpeeaeeeivealirlalasvaklailplqDll.lgee 445
                                       +pensv yt+tHD++t++g++++  a++k+ l+  ++++g     +ei++++i+++++s+a +a +++qD+l lg+e
  gi|313126276|ref|YP_004036546.1| 385 FPENSVGYTSTHDTNTFVGYYRDLPADQKDCLHYNIGADG-----SEIHWSIIDAVWRSNAVIAFTTIQDILgLGAE 456
                                       *********************5555556655555554444.....89****************************** PP

                                       G-S--TT-SSSSTTS-B--S CS
                    Glyco_hydro_77 446 eriNvPgtveeepnWrwrlk 465
                                       +r+NvPgt+++  nWrwr++
  gi|313126276|ref|YP_004036546.1| 457 ARFNVPGTTDG--NWRWRCT 474
                                       *********88..*****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 3001.50
//
Query:       gi|313126277|ref|YP_004036547.1|  [L=153]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-13   48.8   0.6    5.6e-13   48.2   0.6    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    5.6e-11   42.1   2.1    1.3e-10   41.0   2.1    1.6  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    3.4e-07   30.1   0.0    5.6e-07   29.4   0.0    1.4  1  HTH_11           HTH domain
    6.7e-07   29.1   0.1    1.4e-05   24.9   0.1    2.2  2  MarR_2           MarR family
    8.3e-06   25.9   0.0    1.5e-05   25.1   0.0    1.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      8e-05   22.6   0.1    0.00015   21.8   0.1    1.4  1  HTH_20           Helix-turn-helix domain
    8.6e-05   22.2   0.3    0.00018   21.2   0.1    1.7  1  HTH_DeoR         DeoR-like helix-turn-helix domain
    0.00028   20.8   0.0    0.00044   20.1   0.0    1.3  1  MarR             MarR family
    0.00029   20.4   0.2     0.0011   18.6   0.0    2.0  2  GntR             Bacterial regulatory proteins, gntR family
    0.00042   20.1   0.0    0.00066   19.5   0.0    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0015   18.5   0.3     0.0045   16.9   0.0    1.8  2  AsnC_trans_reg   Lrp/AsnC ligand binding domain
     0.0016   18.8   0.0     0.0026   18.1   0.0    1.4  1  Rrf2             Transcriptional regulator
     0.0031   17.3   0.0     0.0063   16.3   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
     0.0035   17.3   0.2      0.012   15.6   0.1    2.0  2  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0039   16.8   0.1     0.0074   15.9   0.1    1.4  1  Sigma70_r4_2     Sigma-70, region 4
     0.0044   16.8   0.1     0.0087   15.8   0.1    1.5  1  HTH_23           Homeodomain-like domain
     0.0054   16.5   0.2      0.011   15.6   0.2    1.4  1  HTH_10           HTH DNA binding domain
     0.0065   16.6   0.1      0.013   15.6   0.1    1.5  1  HTH_28           Helix-turn-helix domain
     0.0074   16.3   0.1       0.13   12.3   0.0    2.1  2  HTH_29           Winged helix-turn helix
     0.0075   15.9   0.0      0.013   15.2   0.0    1.3  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
     0.0093   16.0   0.2      0.019   15.0   0.2    1.5  1  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
  ------ inclusion threshold ------
       0.01   15.6   0.1      0.024   14.4   0.1    1.7  1  HTH_30           PucR C-terminal helix-turn-helix domain
      0.011   15.4   0.2      0.016   14.8   0.2    1.3  1  HTH_50           Helix-turn-helix domain
      0.011   15.2   0.0      0.018   14.6   0.0    1.4  1  GerE             Bacterial regulatory proteins, luxR family
      0.018   15.2   0.3      0.039   14.2   0.1    1.6  1  HTH_Tnp_Tc3_2    Transposase
      0.026   14.1   0.3       0.12   11.9   0.1    2.0  2  Sigma70_r4       Sigma-70, region 4
      0.035   13.5   0.3      0.064   12.7   0.3    1.5  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.047   13.9   0.0      0.099   12.9   0.0    1.7  1  PaaX             PaaX-like protein
      0.049   13.2   0.0      0.078   12.6   0.0    1.3  1  DDRGK            DDRGK domain
      0.054   13.4   0.3       0.12   12.4   0.3    1.5  1  HTH_1            Bacterial regulatory helix-turn-helix protei
       0.07   13.1   0.0       0.12   12.4   0.0    1.3  1  HTH_6            Helix-turn-helix domain, rpiR family
      0.091   13.4   0.1       0.59   10.8   0.0    2.0  2  RPA_C            Replication protein A C terminal
       0.15   11.8   1.3       0.19   11.5   0.5    1.7  1  HTH_38           Helix-turn-helix domain
       0.15   11.9   0.0       0.31   11.0   0.0    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm
       0.16   12.0   0.0       0.29   11.2   0.0    1.4  1  Phage_terminase  Phage terminase small subunit


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.6   1.1e-15   5.6e-13       1      48 []       6      54 ..       6      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.1e-15
                            HTH_24  1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ld +dr+IL  Lq+++r +s +++A  l++S stv+ r++rLe++G+I+
  gi|313126277|ref|YP_004036547.1|  6 LDSLDRRILYSLQAEARhTSSNDIAASLDVSASTVRNRIQRLESDGIIR 54
                                      7999********************************************7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   2.1   2.4e-13   1.3e-10       1      42 []       6      48 ..       6      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.4e-13
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaR.isyaeLAervGlSestvlrRvrrLe 42
                                      LD +Dr+IL  Lq+ aR +s  ++A+ + +S+stv++R++rLe
  gi|313126277|ref|YP_004036547.1|  6 LDSLDRRILYSLQAEARhTSSNDIAASLDVSASTVRNRIQRLE 48
                                      8**************9857889********************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.1e-09   5.6e-07       4      44 ..      12      52 ..      10      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.1e-09
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                       il  L ++  + s++++A  L+vS +tvr++I++Le+ g+
  gi|313126277|ref|YP_004036547.1| 12 RILYSLQAEARHTSSNDIAASLDVSASTVRNRIQRLESDGI 52
                                      688889666666***************************93 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   2.7e-08   1.4e-05       3      52 ..       6      54 ..       4      62 .. 0.90
   2 ?    1.9   0.0      0.42   2.2e+02      25      50 ..     107     132 ..     102     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.7e-08
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      l+  ++r+L+ L ++ +   + +++a+ l++s s+v ++++rL++ G ++
  gi|313126277|ref|YP_004036547.1|  6 LDSLDRRILYSLQAEARH-TSSNDIAASLDVSASTVRNRIQRLESDGIIR 54
                                      566789*********985.5***************************997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.42
                                       HHHHHHHTSSHHHHHHHHHHHHHTTS CS
                            MarR_2  25 gelarrlglsksavsrilkrLvaaGL 50 
                                       + l+r+ g++   +sri ++L + GL
  gi|313126277|ref|YP_004036547.1| 107 NVLVRAIGVDGDDLSRIGEELDELGL 132
                                       67999************999999997 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     3e-08   1.5e-05      12      51 ..      13      52 ..      12      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3e-08
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGy 51
                                       +Y+l+ e    +  d+a  L+vs+s+V   +++Le+dG 
  gi|313126277|ref|YP_004036547.1| 13 ILYSLQAEARHTSSNDIAASLDVSASTVRNRIQRLESDGI 52
                                      68************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   2.8e-07   0.00015      13      56 ..      11      55 ..       6      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.8e-07
                                      HHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      rril  L a+a+  + +++a+ ld+s +t++++++ Le+ g++++
  gi|313126277|ref|YP_004036547.1| 11 RRILYSLqAEARHTSSNDIAASLDVSASTVRNRIQRLESDGIIRG 55
                                      7888888888899999**************************986 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   3.4e-07   0.00018      11      47 ..      20      56 ..      10      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.4e-07
                          HTH_DeoR 11 qqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      + ++ s +++++ l+vS  T+R+ ++ Le +g+++  
  gi|313126277|ref|YP_004036547.1| 20 EARHTSSNDIAASLDVSASTVRNRIQRLESDGIIRGY 56
                                      56788999*************************7655 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.7e-07   0.00044       7      50 ..      12      56 ..      10      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.7e-07
                                      HHHHHHHHSTTEEHH.HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  7 viLrilyeqgplsvs.eLakklgvskstvtrvldrLekkGlieRs 50
                                      +iL++l  +  ++ s ++a  l vs stv + + rLe +G i+ +
  gi|313126277|ref|YP_004036547.1| 12 RILYSLQAEARHTSSnDIAASLDVSASTVRNRIQRLESDGIIRGY 56
                                      6999999999999999**************************855 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.1e-06    0.0011      27      54 ..      26      53 ..       7      56 .. 0.90
   2 ?   -1.4   0.0       3.7   1.9e+03      22      33 ..      77      88 ..      73      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglv 54
                                       +++aa ++Vs++tvR  ++rLe++g++
  gi|313126277|ref|YP_004036547.1| 26 SNDIAASLDVSASTVRNRIQRLESDGII 53
                                      578***********************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.7
                                      SB---HHHHHHH CS
                              GntR 22 dkLPsereLaae 33
                                      +++P+ +eLaa+
  gi|313126277|ref|YP_004036547.1| 77 APIPEREELAAA 88
                                      5799999**986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.3e-06   0.00066       5      45 ..      11      53 ..       7      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  5 lkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      ++IL++L+   + +++ ++a+ l++s stv+    +L+  G++
  gi|313126277|ref|YP_004036547.1| 11 RRILYSLQAeaRHTSSNDIAASLDVSASTVRNRIQRLESDGII 53
                                      68*****998888**************************9998 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       6.1   3.1e+03      45      55 ..       4      14 ..       2      26 .. 0.64
   2 !   16.9   0.0   8.7e-06    0.0045      14      59 ..      83     128 ..      79     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.1
                                      SSHHHHHHHHH CS
                    AsnC_trans_reg 45 rdlealerflr 55
                                      rdl++l+r + 
  gi|313126277|ref|YP_004036547.1|  4 RDLDSLDRRIL 14
                                      77888877654 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.7e-06
                                       HHHHHHHHTSTTEEEEE.EESSSSSEEEEEEESSHHHHHHHHHHTTT CS
                    AsnC_trans_reg  14 eefeealaelpeVvecy.rvtGdydyllkvvvrdlealerflrekla 59 
                                       ee+++a a++p Vve+  ++tG+++ l+++   d ++l+r+ +e l+
  gi|313126277|ref|YP_004036547.1|  83 EELAAAAADVPGVVEVQeVMTGEANVLVRAIGVDGDDLSRIGEE-LD 128
                                       7899************7368*******************99555.55 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     5e-06    0.0026      13      56 ..      13      54 ..       1      57 [. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5e-06
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +l+ L++e++  + ss++ia++ ++s+s ++  +++L+  g+++
  gi|313126277|ref|YP_004036547.1| 13 ILYSLQAEAR--HTSSNDIAASLDVSASTVRNRIQRLESDGIIR 54
                                      6666666666..57****************************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05    0.0063       8      49 ..      13      54 ..      11      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      iL  l ++++  +  ++A+ ++++ Stv++ +q L+  G+++
  gi|313126277|ref|YP_004036547.1| 13 ILYSLQAEARHTSSNDIAASLDVSASTVRNRIQRLESDGIIR 54
                                      77778888888899***********************99886 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.4e-05     0.012      21      53 ..      23      55 ..       3      65 .. 0.85
   2 ?   -1.6   0.0       5.3   2.7e+03      38      50 ..     120     132 ..     109     145 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisr 53
                                      + +  ++A+ l ++ +tv   +++L+ +g+i+ 
  gi|313126277|ref|YP_004036547.1| 23 HTSSNDIAASLDVSASTVRNRIQRLESDGIIRG 55
                                      56889**************************94 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHTTS CS
                         HTH_Crp_2  38 vsrilseLkregl 50 
                                       +sri  eL + gl
  gi|313126277|ref|YP_004036547.1| 120 LSRIGEELDELGL 132
                                       4555555555554 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.5e-05    0.0074      28      49 ..      25      46 ..      17      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                                      -HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrlsR 49
                                      s  +IA+ l++s +tV++r++R
  gi|313126277|ref|YP_004036547.1| 25 SSNDIAASLDVSASTVRNRIQR 46
                                      6679*****************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.7e-05    0.0087      22      46 ..      28      52 ..      11      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                            HTH_23 22 eIAreLgvsrrTvyrwlkryreeGl 46
                                      +IA+ L+vs +Tv++ ++r + +G+
  gi|313126277|ref|YP_004036547.1| 28 DIAASLDVSASTVRNRIQRLESDGI 52
                                      8******************866886 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   2.1e-05     0.011      21      49 ..      21      49 ..      19      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                            HTH_10 21 PRrvtlkeLAkelGIskstlsehLrkaes 49
                                       R ++++++A  l++s+st+ +++++ es
  gi|313126277|ref|YP_004036547.1| 21 ARHTSSNDIAASLDVSASTVRNRIQRLES 49
                                      6999*********************9886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.5e-05     0.013      11      41 ..      22      52 ..      11      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-05
                            HTH_28 11 aGhsvreaArelgisrrtvyrWikryeegGi 41
                                      ++ s +++A+ l +s +tv+  i+r+e+ Gi
  gi|313126277|ref|YP_004036547.1| 22 RHTSSNDIAASLDVSASTVRNRIQRLESDGI 52
                                      4559999*********************997 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00025      0.13      15      41 ..      26      52 ..      16      58 .. 0.85
   2 ?    1.9   0.0      0.44   2.2e+02      18      56 ..     109     150 ..      99     153 .] 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00025
                            HTH_29 15 vsqiAkllglsrrtvyrwlkrfeegGl 41
                                        +iA+ l++s +tv++ + r e +G+
  gi|313126277|ref|YP_004036547.1| 26 SNDIAASLDVSASTVRNRIQRLESDGI 52
                                      678***********************7 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.44
                            HTH_29  18 iAkllglsrrtvyrwlkrfeegGlaa....lldrrrsgrprnr 56 
                                       ++++ g++ +   r+ +  +e Gl+     l++   ++rp+ r
  gi|313126277|ref|YP_004036547.1| 109 LVRAIGVDGDDLSRIGEELDELGLRVsdedLIR-NTHRRPYSR 150
                                       688899999999999999999999887777665.334556555 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-05     0.013      19      55 ..      19      55 ..       5      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                      HrcA_DNA-bdg 19 kkkravKgeeiAevlkrneGtvRNqlqsLkalgLveg 55
                                       + r   +++iA+ l+    tvRN +q L + g++ g
  gi|313126277|ref|YP_004036547.1| 19 AEARHTSSNDIAASLDVSASTVRNRIQRLESDGIIRG 55
                                      45677889**********************9999887 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   3.7e-05     0.019      15      45 ..      12      41 ..      11      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHHTT--EE-HHHHHHHCTS-HHHHH CS
                    Put_DNA-bind_N 15 ryLeelkeegveriSSteLaealgvtaaqvR 45
                                      r+L +l++e   ++SS+++a+ l+v+a++vR
  gi|313126277|ref|YP_004036547.1| 12 RILYSLQAE-ARHTSSNDIAASLDVSASTVR 41
                                      788888887.799*****************9 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.7e-05     0.024      14      37 ..      25      48 ..      13      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHH CS
                            HTH_30 14 nisatAkaLhvHrnTlryRLrrie 37
                                      + ++ A++L v+  T+r+R++r+e
  gi|313126277|ref|YP_004036547.1| 25 SSNDIAASLDVSASTVRNRIQRLE 48
                                      66889*****************98 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   3.1e-05     0.016       9      46 ..       7      46 ..       1      48 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                            HTH_50  9 eefErelik..kayekYpStRklAkrLGvShtaianklrk 46
                                      ++ +r ++   +a ++++S+  +A+ L vS +++ n++++
  gi|313126277|ref|YP_004036547.1|  7 DSLDRRILYslQAEARHTSSNDIAASLDVSASTVRNRIQR 46
                                      6778888861145679*********************987 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.5e-05     0.018       3      41 ..       9      47 ..       7      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
                                      S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH CS
                              GerE  3 LskRErevLrllaeGksnkeIAeelniSekTVkvhksni 41
                                      L++R +  L+  a   s+++IA++l++S+ TV++ ++++
  gi|313126277|ref|YP_004036547.1|  9 LDRRILYSLQAEARHTSSNDIAASLDVSASTVRNRIQRL 47
                                      555555566666777899***************998875 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   7.5e-05     0.039       2      41 ..      12      46 ..      10      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.5e-05
                     HTH_Tnp_Tc3_2  2 rrIvrlvrkdPritlreLanelkeeGksvsreTirrrLrk 41
                                      r +++l ++ +++++ ++a++l      vs++T+r+r+++
  gi|313126277|ref|YP_004036547.1| 12 RILYSLQAEARHTSSNDIAASL-----DVSASTVRNRIQR 46
                                      4456677889************.....**********985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00024      0.12       5      43 ..       6      46 ..       3      47 .. 0.75
   2 ?   -0.6   0.0       1.9   9.7e+02      15      31 ..     111     128 ..     104     129 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                                      S-HHHHHHHHHHH..TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  5 Lpererevlelrf..geglTleEIgerlgiSrerVrqiekr 43
                                      L+  +r++l+      +  +  +I++ l++S ++Vr ++ r
  gi|313126277|ref|YP_004036547.1|  6 LDSLDRRILYSLQaeARHTSSNDIAASLDVSASTVRNRIQR 46
                                      55556666666666555556779**************9876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                                       HHH.TTT--HHHHHHHHT CS
                        Sigma70_r4  15 lrf.geglTleEIgerlg 31 
                                           ++g  l+ Ige+l+
  gi|313126277|ref|YP_004036547.1| 111 RAIgVDGDDLSRIGEELD 128
                                       555544455899999986 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   0.00012     0.064      21      51 ..      18      47 ..      11      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                      HTH_Tnp_ISL3 21 lelllesrsvkavArqlgvSwtTVwrildry 51
                                       ++++++ s  ++A+ l+vS++TV++++ r+
  gi|313126277|ref|YP_004036547.1| 18 QAEARHT-SSNDIAASLDVSASTVRNRIQRL 47
                                      5677888.999****************9985 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00019     0.099      29      57 ..      29      57 ..      11      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                              PaaX 29 llaelGiseslvRaalsRlakaGwlvrek 57
                                      + a+l++s+s+vR  + Rl+ +G +++  
  gi|313126277|ref|YP_004036547.1| 29 IAASLDVSASTVRNRIQRLESDGIIRGYH 57
                                      7899*******************998754 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015     0.078     117     145 ..      27      55 ..      16      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                       HHHHHHH-S-HHHHHHHHHHHHHHSSS-E CS
                             DDRGK 117 eelavkfklktqevierikeLeeqgsltG 145
                                       +++a+ ++++++ v++ri+ Le++g + G
  gi|313126277|ref|YP_004036547.1|  27 NDIAASLDVSASTVRNRIQRLESDGIIRG 55 
                                       79*************************98 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00023      0.12       4      39 ..      14      49 ..      12      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                                      HHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1  4 lrlfvavaeegsftrAAeeLglsqpavsrqikrLEe 39
                                      l  ++a a++ s +  A  L +s ++v  +i+rLE+
  gi|313126277|ref|YP_004036547.1| 14 LYSLQAEARHTSSNDIAASLDVSASTVRNRIQRLES 49
                                      5678888999999999*******************7 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00024      0.12      29      57 ..      18      46 ..       5      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                                      S---TT--HHHHHHHTT--HHHHHHHH-- CS
                             HTH_6 29 pdkaielsikalAkaaavSeativrfakk 57
                                      + +a++ s++++A+ + vS +t+    + 
  gi|313126277|ref|YP_004036547.1| 18 QAEARHTSSNDIAASLDVSASTVRNRIQR 46
                                      45799*****************9655555 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0012      0.59      71      97 ..      27      53 ..       7      58 .. 0.92
   2 ?    0.2   0.0       2.4   1.2e+03      71      95 ..     107     131 ..     102     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0012
                                      HHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 71 deiaqklrlsvndvkqavdeLsneGii 97
                                      + ia++l +s ++v++ ++ L+++Gii
  gi|313126277|ref|YP_004036547.1| 27 NDIAASLDVSASTVRNRIQRLESDGII 53
                                      68************************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.4
                                       HHHHHHSTSXHHHHHHHHHHHHHTT CS
                             RPA_C  71 deiaqklrlsvndvkqavdeLsneG 95 
                                       +++ ++++++  d+ ++ +eL + G
  gi|313126277|ref|YP_004036547.1| 107 NVLVRAIGVDGDDLSRIGEELDELG 131
                                       578899999***********99888 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   0.00037      0.19       9      43 ..      10      46 ..       2      47 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                            HTH_38  9 eReeIerlla..eGlslreIArrLgrspsTIsRElkR 43
                                      +R+ ++ l a  +  s  +IA  L++s sT+ + ++R
  gi|313126277|ref|YP_004036547.1| 10 DRRILYSLQAeaRHTSSNDIAASLDVSASTVRNRIQR 46
                                      555555553211335667**************99988 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0006      0.31      23      53 ..      24      54 ..       2      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0006
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVe 53
                                       + ++ia  l+v+ s+v + +++Le+ G+++
  gi|313126277|ref|YP_004036547.1| 24 TSSNDIAASLDVSASTVRNRIQRLESDGIIR 54
                                      55689***********************986 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00057      0.29      24      41 ..      25      42 ..      10      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00057
                   Phage_terminase 24 klkdIAkvLdvsestvrk 41
                                         dIA  Ldvs stvr+
  gi|313126277|ref|YP_004036547.1| 25 SSNDIAASLDVSASTVRN 42
                                      567**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 926.30
//
Query:       gi|313126278|ref|YP_004036548.1|  [L=359]
Description: cbs domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-28   98.3   0.5    5.7e-28   97.8   0.5    1.1  1  DUF21     Cyclin M transmembrane N-terminal domain
    1.4e-11   44.6   2.1    4.5e-07   30.2   0.0    2.4  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.5   6.4e-32   5.7e-28       4     173 ..      14     203 ..      11     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 6.4e-32
                             DUF21   4 vlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvella 80 
                                       vll+l+++ff++ E+Al++++++  +e ++ g+++ +r++ +++++e +L+t+++g+t ++i+ +++a+++++ l++
  gi|313126278|ref|YP_004036548.1|  14 VLLILANGFFVAIEFALTRARQFSESEFVD-GDSRLERAWAMTQDLELYLTTCQVGITASSIAVGIVAEPALAALFE 89 
                                       899*********************888887.678******************************************* PP

                             DUF21  81 e.........galavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil.. 146
                                       +          +++++ia  i+ l++l  gE +P  l+++++  ++++ a pl++++ +++Pl+ l + ++++ l  
  gi|313126278|ref|YP_004036548.1|  90 PlfagttlatVGAGAIIAYGIINLVHLTHGEQAPTYLGVERSRLVCRYGAAPLYWFYLIISPLISLGDSVAKWTLql 166
                                       9*******99779999************************************************************* PP

                             DUF21 147 ..........esesepavseeelkklveeseeegvie 173
                                                 e+e++   s+++l++ +++  e+g+++
  gi|313126278|ref|YP_004036548.1| 167 fgiemtgawlEAEEDAIESRAQLRSRLSSLLERGELS 203
                                       **********999999********9999998888875 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.5   7.3e-06     0.065       1      47 [.     221     270 ..     221     280 .. 0.80
   2 !   30.2   0.0     5e-11   4.5e-07       7      55 ..     293     340 ..     288     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-06
                                       HHHH..SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT.B.EEEEEE CS
                               CBS   1 Vgdi..mtrdvvtvppdttleealelmrekgvsrlPVVdedg.k.lvGivt 47 
                                       V+++  + +d+v ++ d++++e l++ +e+ ++r+P V +++ + + Giv 
  gi|313126278|ref|YP_004036548.1| 221 VREVmvPKSDIVALSTDASVAENLDRVTETPHTRYPLV-GSNlEtVEGIVY 270
                                       6787335559*****************888899*****.45555266**96 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 5e-11
                                       SSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   7 rdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                        +++tv+ dt++++a++++  ++   l VV edg +vG++t +D l+ +
  gi|313126278|ref|YP_004036548.1| 293 APPMTVSADTSVSDAIDRFQAERQ-ELAVVFEDGDVVGLLTATDALETV 340
                                       5889***************75554.7766637888*********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2256.03
//
Query:       gi|313126279|ref|YP_004036549.1|  [L=186]
Description: transcriptional regulator containing an amidase domain and an arac-type DNA-binding hth domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.3e-24   84.1   0.0    1.1e-23   83.8   0.0    1.1  1  DJ-1_PfpI  DJ-1/PfpI family
     0.0056   16.4   0.0      0.016   14.9   0.0    1.6  1  ThiJ_like  ThiJ/PfpI family-like


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.0   1.3e-27   1.1e-23       2     164 ..       2     165 ..       1     166 [. 0.87

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.3e-27
                                       EEEEEEETTBEHHHHHHHHHHHHH......TTEEEEEEESS........TSEEEETTSEEEE-SEEGGGCTCCG-SE CS
                         DJ-1_PfpI   2 kvlvlladgvedvElivpvdvlkr......agikvdvvsvd........keevkgsrGlkvtvdaslddvkaaeyDa 64 
                                       + +++ +d++  ++++  +d l r      a +                +e+v+++  l++ +d + +  +  eyD+
  gi|313126279|ref|YP_004036549.1|   2 RTAFVAFDDMTALDFVGAFDPLTRldtmdlAPF-------PfewnicarAETVTTTANLQFGADSVGE--SLTEYDI 69 
                                       667899999999999999999998444333222.......2334455559**************9666..6889*** PP

                                       EEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEE CS
                         DJ-1_PfpI  65 lvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvv 141
                                       +v+pGG     +lre++ ++++++++  +  l+a++C+g +lL aag l+g+++T++pa +d+l +a  ++ d+rvv
  gi|313126279|ref|YP_004036549.1|  70 VVIPGGAG-TRTLREDDHFLSWLRTA--DPDLLASVCTGSLLLGAAGFLDGQTATTHPAATDEL-AAYCEVADDRVV 142
                                       ******88.***************86..6789********************************.9999******** PP

                                       EETTEEEESSGGGHHHHHHHHHH CS
                         DJ-1_PfpI 142 vdgnlvTsrgpgaaiefalelle 164
                                        +g++vT+rg+ +a++++l l+e
  gi|313126279|ref|YP_004036549.1| 143 DEGEIVTARGVSSALDLGLYLVE 165
                                       *****************999987 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-06     0.016      81     163 ..      63     134 ..      44     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
                         ThiJ_like  81 sleeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlwme 157
                                       sl+eyd+v +pGG++     l e+    ++   +l    r+ ++  +l+++c g l l +a       +tt P+ ++
  gi|313126279|ref|YP_004036549.1|  63 SLTEYDIVVIPGGAGTRT--LRED----DHFLSWL----RT-ADPDLLASVCTGSLLLGAAGFLDGQTATTHPAATD 128
                                       89************9866..4333....5666677....44.356799*******9999999955566688899999 PP

                         ThiJ_like 158 rtsill 163
                                       + + ++
  gi|313126279|ref|YP_004036549.1| 129 ELAAYC 134
                                       887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1073.76
//
Query:       gi|313126280|ref|YP_004036550.1|  [L=306]
Description: 3-methyladenine DNA glycosylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-12   46.0   0.0      1e-11   45.2   0.0    1.3  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    1.1e-07   31.9   0.0    4.2e-07   30.1   0.0    1.8  1  OGG_N     8-oxoguanine DNA glycosylase, N-terminal domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   1.1e-15     1e-11       1      96 [.     134     275 ..     134     285 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.1e-15
                                       HHHHHHTTS-HHHHHHHHHHHHHHHS............HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfg............fptpedladadeekLrelirelGfyrrKakyikelAril 65 
                                       +s+i+s+q +++r+  +  rl++++g            fpt+++la  +e++Lr+l     ++ ++a+y++ +A+++
  gi|313126280|ref|YP_004036550.1| 134 ISFICSAQMRVSRIHGMQMRLAREYGdtvtvagetyhaFPTADQLAVRTEDELRDL----SLG-YRAPYVQRTAEMV 205
                                       79******************************************************....999.************* PP

                                       H........................................S-SSS--TTSHHHHHHHHHHTTSSSSTTHH CS
                                       x........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  66 v........................................gkpdvlivvDvhvrrilkrlrsikekktkk 96 
                                       +                                        g+ + +++ D++++ ++  +++  e  ++ 
  gi|313126280|ref|YP_004036550.1| 206 AngdahpndavglpyedardsltqfvgvgdkvsdcvllfslGFLE-AVPLDTWIQTAIADHYPDCEAGNYT 275
                                       *****************************************9988.7778*****9999888765555555 PP

>> OGG_N  8-oxoguanine DNA glycosylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   4.7e-11   4.2e-07       9     121 .]      17     133 ..       8     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.7e-11
                                       --HHHHHCSSS-SSEEE-TTS..-EEEEETT.........EEEEEEEETTEEEEET--.............HHHHHH CS
                             OGG_N   9 ldlkktLkcGQsFrWkktekt..eyvgvlgd.........rvveLkqeeddllyrtlesesstkasseeakeeetee 74 
                                       +dl++tL++GQs+ W + ++   e + v g+          +  ++ e+  + +r +          e + + +   
  gi|313126280|ref|YP_004036550.1|  17 FDLQATLESGQSYLWDRADGRmyESMDVYGGdawyetvvpPIDGVSDEQAVVRVRQT------DGRLEWEATTDAVP 87 
                                       99**************88877442444444422222211144444433333333333......35666667778899 PP

                                       THHHHTTTTS-HHHHHHHHTT.SHHHHHHHCCTTT-------HHHHH CS
                             OGG_N  75 ilrdYfnLdvdleelykewskkdplfkksadkftGiRllrqdpwEcL 121
                                       il++ ++Ld dl+ +  + + +d+l+++++d + G+Rl+r  p+ cL
  gi|313126280|ref|YP_004036550.1|  88 ILTHLLRLDDDLDAIL-DATPDDSLLERAYDAYEGMRLVRDPPFPCL 133
                                       ***************9.88999**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.62
# Mc/sec: 1484.09
//
Query:       gi|313126281|ref|YP_004036551.1|  [L=138]
Description: hypothetical protein Hbor_15340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-37  127.4   0.5    2.3e-37  127.4   0.5    1.6  2  DUF555    Protein of unknown function (DUF555)


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.5   1.3e-41   2.3e-37       1     101 []       2     101 ..       2     101 .. 0.99
   2 ?   -1.8   0.2      0.22     4e+03      71      85 ..     104     118 ..     103     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 1.3e-41
                            DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpeldfveievgetecPkcgeelesalvvadtalvglllemkvf 77 
                                       d++vv+eaa+ v+dv+++d+Ai+iAi+++g+ lnp+l++vei++g+ ++P+ geel +a+v+ad+alv+l+lem+vf
  gi|313126281|ref|YP_004036551.1|   2 DCRVVVEAAVPVYDVETADEAIRIAIAKTGELLNPDLNYVEINMGSRTSPS-GEELLPAFVAADEALVALELEMTVF 77 
                                       89************************************************9.999********************** PP

                            DUF555  78 naeseEhaeriakseigkaledvP 101
                                       n+e+eEha+ria++eig++le+vP
  gi|313126281|ref|YP_004036551.1|  78 NVEQEEHAARIARKEIGQRLENVP 101
                                       ***********************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.22
                            DUF555  71 llemkvfnaeseEha 85 
                                       +le++v+  e+eE+ 
  gi|313126281|ref|YP_004036551.1| 104 VLEVEVLPSEEEEEE 118
                                       589999998888864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 818.96
//
Query:       gi|313126282|ref|YP_004036552.1|  [L=78]
Description: metal-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-20   71.3   0.2    6.5e-20   71.2   0.2    1.0  1  UPF0058   Uncharacterised protein family UPF0058


Domain annotation for each model (and alignments):
>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.2   3.6e-24   6.5e-20       1      71 [.       1      71 [.       1      77 [. 0.95

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 3.6e-24
                                      --HHHHHHHHHHHHHHHHHHTSTT--TTTTHHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHC CS
                           UPF0058  1 MhKdeLieLHqllvevkkeleeeevekeefkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekees 71
                                      M+K+eLi+LH ll+ev+ ++ee e+++  +++Y+eL ++P+ ih+sK++hkaA+f L + i + l e e++
  gi|313126282|ref|YP_004036552.1|  1 MKKQELIHLHGLLAEVHTQIEEWENDEVPLTAYNELGVRPTSIHKSKTDHKAAVFKLVKGITSSLDEPEQE 71
                                      9****************************************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 520.78
//
Query:       gi|313126283|ref|YP_004036553.1|  [L=135]
Description: translation initiation factor 2 subunit beta (aeif-2b) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-37  127.4   0.0    2.8e-37  127.2   0.0    1.0  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
  ------ inclusion threshold ------
      0.039   13.7   0.1       0.17   11.6   0.1    2.0  2  OxoDH_E1alpha_N  2-oxoisovalerate dehydrogenase E1 alpha subu
        2.9    8.0   7.5        1.1    9.4   2.2    2.8  3  YyzF             YyzF-like protein


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   0.0   4.7e-41   2.8e-37       4     116 ..      17     128 ..      14     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 4.7e-41
                                       CCSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHH CS
                      eIF-5_eIF-2B   4 kedkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakklekll 80 
                                       ++d+ +r+++p++ v+ eg+  tv++Nf+e++++L r+p+h++k l++elgt+++ide+gr+ l+g+f++++++++l
  gi|313126283|ref|YP_004036553.1|  17 VTDRGSRFQVPEPVVRPEGN-ATVYENFDETCDRLAREPSHLMKALQSELGTSAQIDEKGRVRLTGDFSQRRVQDAL 92 
                                       568899**************.******************************************************** PP

                                       HHHHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  81 dkyieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                       d+y+++yVlC+eC+sp+t+l++e+  +vlkC+aCga
  gi|313126283|ref|YP_004036553.1|  93 DSYVDDYVLCSECDSPDTRLVTEQGAMVLKCDACGA 128
                                       ***********************************7 PP

>> OxoDH_E1alpha_N  2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.9e-05      0.17       4      20 ..      23      40 ..      22      44 .. 0.78
   2 ?   -1.3   0.0      0.33   1.9e+03      18      28 ..      81      91 ..      80      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                   OxoDH_E1alpha_N  4 rLhVPEPkvRP.GdtpDF 20
                                      r+ VPEP vRP G ++ +
  gi|313126283|ref|YP_004036553.1| 23 RFQVPEPVVRPeGNATVY 40
                                      89*********6666655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.33
                   OxoDH_E1alpha_N 18 pDFsdleipeA 28
                                       DFs+ ++++A
  gi|313126283|ref|YP_004036553.1| 81 GDFSQRRVQDA 91
                                      59**9998876 PP

>> YyzF  YyzF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.19   1.1e+03       6      15 ..       7      16 ..       4      20 .. 0.62
   2 ?   -1.9   0.0       0.6   3.6e+03      32      42 ..      43      53 ..      36      58 .. 0.65
   3 ?    9.4   2.2   0.00018       1.1       6      40 ..      88     127 ..      86     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.19
                              YyzF  6 vElAlDefVd 15
                                      +++AlDe  d
  gi|313126283|ref|YP_004036553.1|  7 LDKALDESPD 16
                                      5677776544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.6
                              YyzF 32 lsktCefCekp 42
                                       ++tC+   ++
  gi|313126283|ref|YP_004036553.1| 43 FDETCDRLARE 53
                                      56788765555 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00018
                              YyzF   6 vElAlDefVdeye.....qaPdiekleeveklsktCefCe 40 
                                       v +AlD +Vd+y      ++Pd++ ++e+     +C+ C 
  gi|313126283|ref|YP_004036553.1|  88 VQDALDSYVDDYVlcsecDSPDTRLVTEQGAMVLKCDACG 127
                                       678********953333479*********99999****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 915.68
//
Query:       gi|313126284|ref|YP_004036554.1|  [L=59]
Description: hypothetical protein Hbor_15370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00085   19.2   0.1     0.0012   18.7   0.1    1.2  1  zinc_ribbon_4   zinc-ribbon domain
     0.0065   16.4   1.3      0.021   14.8   1.0    1.8  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.7   1.0        0.1   12.7   1.6    1.9  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.012   15.2   0.7        4.4    7.0   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.015   15.3   0.2       0.81    9.8   0.0    2.1  2  DUF2752         Protein of unknown function (DUF2752)
      0.015   14.8   0.6        3.6    7.2   0.0    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.015   15.2   1.0       0.13   12.2   0.2    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.019   15.5   0.9       0.03   14.9   0.9    1.4  1  Stc1            Stc1 domain
      0.031   14.3   0.1      0.031   14.3   0.1    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.035   13.5   1.8        2.1    7.9   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.036   14.4   1.2      0.066   13.6   1.3    1.4  1  DUF4379         Probable Zinc-ribbon domain
      0.042   13.8   0.9        3.2    7.7   0.1    2.2  2  Nudix_N_2       Nudix N-terminal
      0.042   13.8   0.6      0.068   13.1   0.6    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.055   13.3   0.3        1.6    8.6   0.1    2.1  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
      0.055   13.5   0.9        5.2    7.1   0.1    2.1  2  CpXC            CpXC protein
      0.056   13.2   1.7        2.8    7.8   0.1    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.056   13.5   1.3       0.12   12.5   1.3    1.5  1  DZR             Double zinc ribbon
      0.057   13.5   0.9       0.16   12.0   0.1    1.9  2  Elf1            Transcription elongation factor Elf1 like
      0.076   13.5   0.9        8.8    7.0   0.1    2.2  2  zf-H2C2_2       Zinc-finger double domain
       0.12   11.6   0.7       0.14   11.4   0.7    1.1  1  DUF2310         Zn-ribbon-containing, possibly nucleic-acid-b
       0.28   11.4   3.5        5.8    7.2   0.4    2.3  2  zf-RING_7       C4-type zinc ribbon domain
       0.39   10.9   3.2        4.9    7.4   0.3    2.1  2  Zn-ribbon_8     Zinc ribbon domain
       0.41   10.7   0.2       0.41   10.7   0.2    2.2  2  DUF1610         Domain of unknown function (DUF1610)
        0.5   10.8   1.5         12    6.3   0.1    2.1  2  DUF983          Protein of unknown function (DUF983)
        0.7    9.7   4.1        7.3    6.4   0.2    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.7e-06    0.0012       5      32 ..      10      37 ..       7      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                     zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCg 32
                                      Cp+C++  e +++ lp  +++ +Cs+Cg
  gi|313126284|ref|YP_004036554.1| 10 CPECGKDWEASPSSLPSLKKNFTCSACG 37
                                      ***************************8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.0   2.9e-05     0.021      20      44 ..       9      37 ..       6      39 .. 0.78
   2 !    8.8   0.2    0.0022       1.6      17      31 ..      29      44 ..      25      59 .] 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
                     Zn_Tnp_IS1595 20 vCPhCgsr...kayrikt...rglfqCkeCr 44
                                       CP Cg++   ++ +       + f C++C+
  gi|313126284|ref|YP_004036554.1|  9 LCPECGKDweaSPSS--LpslKKNFTCSACG 37
                                      5******99554445..45599********7 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr.kayr 31
                                       +f+C +Cg + ++ +
  gi|313126284|ref|YP_004036554.1| 29 KNFTCSACGMSrRLSE 44
                                      5799****98874443 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.045        33      15      23 ..       6      14 ..       2      22 .. 0.81
   2 ?   12.7   1.6   0.00014       0.1       1      30 [.       9      44 ..       9      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.045
                          zf-Mss51 15 vdfeCpdCG 23
                                      v++ Cp+CG
  gi|313126284|ref|YP_004036554.1|  6 VRLLCPECG 14
                                      7889****9 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                          zf-Mss51  1 lCPvpkhkqt......apkhvdfeCpdCGiptycse 30
                                      lCP + ++ +      ++ + +f+C  CG++   se
  gi|313126284|ref|YP_004036554.1|  9 LCPECGKDWEaspsslPSLKKNFTCSACGMSRRLSE 44
                                      5999988888999999999***********988887 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0062       4.4       4      10 ..       9      15 ..       7      20 .. 0.86
   2 ?    6.9   0.1    0.0067       4.8       2      11 ..      30      39 ..      29      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0062
                            zf_UBZ  4 lCerCgk 10
                                      lC++Cgk
  gi|313126284|ref|YP_004036554.1|  9 LCPECGK 15
                                      7*****9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0067
                            zf_UBZ  2 tylCerCgke 11
                                      +++C+ Cg +
  gi|313126284|ref|YP_004036554.1| 30 NFTCSACGMS 39
                                      79*****986 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.077        55       5      15 ..       4      14 ..       1      15 [. 0.81
   2 ?    9.8   0.0    0.0011      0.81       9      25 ..      31      47 ..      29      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.077
                           DUF2752  5 altGipCPGCG 15
                                      a+  + CP CG
  gi|313126284|ref|YP_004036554.1|  4 AFVRLLCPECG 14
                                      667899****9 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                           DUF2752  9 ipCPGCGltRavhallh 25
                                      + C +CG+ R +  +++
  gi|313126284|ref|YP_004036554.1| 31 FTCSACGMSRRLSEFMR 47
                                      78********9888775 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0097         7       3       8 ..      10      15 ..       8      22 .. 0.73
   2 ?    7.2   0.0    0.0051       3.6      19      26 ..      30      37 ..      27      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0097
                                      ETTTTC CS
                      TF_Zn_Ribbon  3 CPnCgs 8 
                                      CP+Cg 
  gi|313126284|ref|YP_004036554.1| 10 CPECGK 15
                                      677764 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0051
                                      CEEESSSS CS
                      TF_Zn_Ribbon 19 elvCtdCG 26
                                      +++C++CG
  gi|313126284|ref|YP_004036554.1| 30 NFTCSACG 37
                                      68888887 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00019      0.13      20      30 .]       8      18 ..       7      18 .. 0.93
   2 ?    1.8   0.0      0.34   2.4e+02      19      26 ..      30      37 ..      26      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                    PhnA_Zn_Ribbon 20 lvCpeCahEwe 30
                                      l+CpeC+  we
  gi|313126284|ref|YP_004036554.1|  8 LLCPECGKDWE 18
                                      79********7 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.34
                    PhnA_Zn_Ribbon 19 llvCpeCa 26
                                      ++ C+ C+
  gi|313126284|ref|YP_004036554.1| 30 NFTCSACG 37
                                      56788886 PP

>> Stc1  Stc1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.9   4.1e-05      0.03      41      74 ..       9      52 ..       2      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.1e-05
                                      --TTTS-----E..........EE-SSS--EEESTTS-HHHHHS CS
                              Stc1 41 kCkectakqate..........leCsaCqktkpldeFsksqrrk 74
                                       C ec ++   +           +CsaC+ ++ l+eF +++r  
  gi|313126284|ref|YP_004036554.1|  9 LCPECGKDWEASpsslpslkknFTCSACGMSRRLSEFMRTERDL 52
                                      57777776555567777777779*****************9975 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.3e-05     0.031      69      95 ..       6      39 ..       1      56 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-05
                                      -EEEETTTS-EEECHHHHH.......S-TTTSSS CS
                              HypA 69 vkvrCreCgkefeleekal.......rCpkCgsa 95
                                      v++ C eCgk++e + ++l       +C +Cg +
  gi|313126284|ref|YP_004036554.1|  6 VRLLCPECGKDWEASPSSLpslkknfTCSACGMS 39
                                      7899*********6653223445566*****976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.003       2.1      19      24 ..      10      15 ..       8      18 .. 0.69
   2 ?    5.2   0.2      0.02        14       4       9 ..      32      37 ..      29      40 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.003
                       zf-ribbon_3 19 CpyCGt 24
                                      Cp CG+
  gi|313126284|ref|YP_004036554.1| 10 CPECGK 15
                                      666665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.02
                       zf-ribbon_3  4 rCPnCG 9 
                                      +C++CG
  gi|313126284|ref|YP_004036554.1| 32 TCSACG 37
                                      688888 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.3   9.2e-05     0.066      32      56 .]      10      36 ..       6      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-05
                           DUF4379 32 CakCgheWeasvsnrtkgssk..CpkC 56
                                      C++Cg+ Weas+s+  + +++  C  C
  gi|313126284|ref|YP_004036554.1| 10 CPECGKDWEASPSSLPSLKKNftCSAC 36
                                      *************99766655679998 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0045       3.2      21      29 ..       6      14 ..       3      16 .. 0.84
   2 ?    4.8   0.1     0.038        28       3       8 ..      33      38 ..      31      44 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0045
                                      -EEEETTTT CS
                         Nudix_N_2 21 eRlvCpaCg 29
                                       Rl Cp Cg
  gi|313126284|ref|YP_004036554.1|  6 VRLLCPECG 14
                                      699999998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.038
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      Cs+CG 
  gi|313126284|ref|YP_004036554.1| 33 CSACGM 38
                                      666664 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   9.5e-05     0.068      31      54 ..      10      38 ..       8      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-05
                    OrfB_Zn_ribbon 31 CseCgsknke.....alsgrtfkCpnCgf 54
                                      C+eCg+  +      +  +++f+C++Cg+
  gi|313126284|ref|YP_004036554.1| 10 CPECGKDWEAspsslPSLKKNFTCSACGM 38
                                      ******9999999998899*********8 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.11        77      16      20 ..      10      14 ..       2      17 .. 0.80
   2 ?    8.6   0.1    0.0022       1.6      14      22 ..      31      39 ..      19      43 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.11
                         zf-C2H2_3 16 CkeCg 20
                                      C+eCg
  gi|313126284|ref|YP_004036554.1| 10 CPECG 14
                                      ****8 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0022
                         zf-C2H2_3 14 sqCkeCgMv 22
                                       +C+ CgM+
  gi|313126284|ref|YP_004036554.1| 31 FTCSACGMS 39
                                      46******7 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.017        12      36      48 ..       6      18 ..       1      29 [. 0.73
   2 ?    7.1   0.1    0.0072       5.2      37      51 ..      30      44 ..      26      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                              CpXC 36 featCpkCgatak 48
                                       +  Cp+Cg++ +
  gi|313126284|ref|YP_004036554.1|  6 VRLLCPECGKDWE 18
                                      5667888887654 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0072
                              CpXC 37 eatCpkCgataklea 51
                                      ++tC +Cg +++l+ 
  gi|313126284|ref|YP_004036554.1| 30 NFTCSACGMSRRLSE 44
                                      79********99976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0039       2.8       2       7 ..      10      15 ..       8      16 .. 0.68
   2 ?    4.8   0.1     0.033        24      15      20 ..      31      37 ..      26      39 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0039
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp+CG+
  gi|313126284|ref|YP_004036554.1| 10 CPECGK 15
                                      666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.033
                     zinc_ribbon_2 15 F.CpyCG 20
                                      F C+ CG
  gi|313126284|ref|YP_004036554.1| 31 FtCSACG 37
                                      5599998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.3   0.00016      0.12      14      37 ..       9      39 ..       7      45 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                               DZR 14 fCseCgtklkavaa.......edrCpsCgek 37
                                       C+eCg++ +a ++       + +C++Cg +
  gi|313126284|ref|YP_004036554.1|  9 LCPECGKDWEASPSslpslkkNFTCSACGMS 39
                                      5888888877666677778778888888865 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.1   7.6e+02      24      29 ..      10      15 ..       3      18 .. 0.68
   2 ?   12.0   0.1   0.00023      0.16      13      40 ..      22      49 ..      15      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                              Elf1 24 CpfCnh 29
                                      Cp C++
  gi|313126284|ref|YP_004036554.1| 10 CPECGK 15
                                      777765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00023
                              Elf1 13 kkkkklptkFdCpfCnheksvevkldkk 40
                                       + ++l+++F+C  C++++ ++  + ++
  gi|313126284|ref|YP_004036554.1| 22 SSLPSLKKNFTCSACGMSRRLSEFMRTE 49
                                      567889***********98877666655 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.043        31      16      22 ..       9      15 ..       3      16 .. 0.86
   2 ?    7.0   0.1     0.012       8.8      12      21 ..      28      37 ..      27      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.043
                         zf-H2C2_2 16 eCplCdk 22
                                       Cp+C+k
  gi|313126284|ref|YP_004036554.1|  9 LCPECGK 15
                                      5****99 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                         zf-H2C2_2 12 ekpyeCplCd 21
                                      +k ++C++C+
  gi|313126284|ref|YP_004036554.1| 28 KKNFTCSACG 37
                                      577******8 PP

>> DUF2310  Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.7    0.0002      0.14     220     249 ..       9      40 ..       4      45 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                           DUF2310 220 kCPscggeWklkeplhd..lfdfkCdecrLvs 249
                                        CP+cg++W+ + +       +f C  c +  
  gi|313126284|ref|YP_004036554.1|   9 LCPECGKDWEASPSSLPslKKNFTCSACGMSR 40 
                                       5********98876655234579999997655 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.035        25      26      30 ..      10      14 ..       8      15 .. 0.90
   2 ?    7.2   0.4    0.0081       5.8       1       8 [.      32      39 ..      32      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.035
                                      -TTT- CS
                         zf-RING_7 26 CpeCG 30
                                      CpeCG
  gi|313126284|ref|YP_004036554.1| 10 CPECG 14
                                      ****9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0081
                                      EETTT--B CS
                         zf-RING_7  1 tCgGChme 8 
                                      tC++C+m 
  gi|313126284|ref|YP_004036554.1| 32 TCSACGMS 39
                                      8*****95 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3    0.0068       4.9      29      35 ..      10      16 ..       2      21 .. 0.76
   2 ?    4.2   0.3     0.065        46       6      12 ..      31      37 ..      29      54 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0068
                       Zn-ribbon_8 29 CPeCgse 35
                                      CPeCg++
  gi|313126284|ref|YP_004036554.1| 10 CPECGKD 16
                                      9999874 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.065
                       Zn-ribbon_8  6 YrCeeCg 12
                                      + C +Cg
  gi|313126284|ref|YP_004036554.1| 31 FTCSACG 37
                                      7799998 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00057      0.41      18      24 .]       9      15 ..       5      15 .. 0.88
   2 ?    2.0   1.5       0.3   2.2e+02       1       6 [.      33      38 ..      33      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00057
                           DUF1610 18 pCPNCGE 24
                                      +CP+CG+
  gi|313126284|ref|YP_004036554.1|  9 LCPECGK 15
                                      7*****8 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.3
                           DUF1610  1 CtSCGa 6 
                                      C++CG 
  gi|313126284|ref|YP_004036554.1| 33 CSACGM 38
                                      ****95 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.017        12      10      22 ..       9      21 ..       5      26 .. 0.83
   2 ?    4.1   0.2     0.089        64       5      17 ..      27      39 ..      25      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.017
                            DUF983 10 aCeaCgldlshar 22
                                       C++Cg+d+++ +
  gi|313126284|ref|YP_004036554.1|  9 LCPECGKDWEASP 21
                                      5********9876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.089
                            DUF983  5 LkvadaCeaCgld 17
                                      Lk + +C+aCg++
  gi|313126284|ref|YP_004036554.1| 27 LKKNFTCSACGMS 39
                                      677889*****85 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5     0.033        24      17      22 ..      10      15 ..       9      19 .. 0.77
   2 ?    6.4   0.2      0.01       7.3       1       9 [.      31      39 ..      31      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.033
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+Cg 
  gi|313126284|ref|YP_004036554.1| 10 CPECGK 15
                                      9***84 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      + Cs+CG +
  gi|313126284|ref|YP_004036554.1| 31 FTCSACGMS 39
                                      78*****75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 374.26
//
Query:       gi|313126285|ref|YP_004036555.1|  [L=330]
Description: transcription initiation factor iib (tfiib) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-38  130.8   0.2    3.8e-18   65.3   0.2    2.2  2  TFIIB           Transcription factor TFIIB repeat
    3.6e-17   61.6   1.9    7.9e-17   60.5   1.9    1.6  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.011   15.7   0.3      0.019   15.0   0.3    1.3  1  DZR             Double zinc ribbon
      0.011   15.2   2.5      0.042   13.4   0.1    2.9  3  Sigma70_r4      Sigma-70, region 4
      0.024   14.6   0.5      0.049   13.6   0.5    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.025   14.6   0.0        2.2    8.4   0.0    2.2  2  Cyclin_C        Cyclin, C-terminal domain
      0.057   12.9   3.2       0.23   10.9   3.2    1.9  1  zf-ribbon_3     zinc-ribbon domain
      0.069   13.0   0.1       0.12   12.2   0.1    1.4  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.16   12.1   0.9        0.8    9.8   0.1    2.3  3  DUF1272         Protein of unknown function (DUF1272)
        0.4   10.4   1.2       0.93    9.3   1.2    1.6  1  A2L_zn_ribbon   A2L zinc ribbon domain
        1.7    8.9   4.9        1.7    8.8   0.9    2.3  3  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   8.1e-21   1.3e-17       1      71 []     149     219 ..     149     219 .. 0.97
   2 !   65.3   0.2   2.3e-21   3.8e-18       1      71 []     243     313 ..     243     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 8.1e-21
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+a+al+Lpe V++ A  ++++al++++l Grs +g+a ++ly A+r++++ r++ e   v++V + ++
  gi|313126285|ref|YP_004036555.1| 149 IDRMASALGLPENVRETASVIYRRALDDDLLPGRSIEGVATSALYAAARQAGTPRSLDELETVSRVDKMEL 219
                                       789***************************************************************99875 PP

  == domain 2  score: 65.3 bits;  conditional E-value: 2.3e-21
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rfa++l+L+++ +++A  l+++a++ ++++G+sp g+aAA++y A+++ ++k tq+e+s+v+ +se+ti
  gi|313126285|ref|YP_004036555.1| 243 VPRFASELDLSDEAERQARDLLRNAKKAGIHSGKSPVGLAAAAVYAAALLTNEKVTQSEVSEVASISEVTI 313
                                       689******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   1.9   4.8e-20   7.9e-17       2      43 .]      34      74 ..      33      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 4.8e-20
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+Cg++ l++D++rge+vC+dCGlV+e + +d gpewr+f
  gi|313126285|ref|YP_004036555.1| 34 VCPECGGS-LITDEARGETVCGDCGLVVETDAVDRGPEWRAF 74
                                      8******7.8******************************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   1.2e-05     0.019       7      40 ..      27      62 ..      25      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                               DZR  7 elppdarfCseCgtklkavaa..edrCpsCgekvdp 40
                                      e++++ ++C+eCg +l   +a  e++C  Cg  v+ 
  gi|313126285|ref|YP_004036555.1| 27 ETEEETQVCPECGGSLITDEArgETVCGDCGLVVET 62
                                      6788999********99777799*******987765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       2.7   4.3e+03       5      11 ..     114     120 ..     112     126 .. 0.64
   2 ?    0.6   0.0      0.26   4.2e+02      34      46 ..     163     175 ..     153     176 .. 0.89
   3 ?   13.4   0.1   2.6e-05     0.042      18      45 ..     294     321 ..     285     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.7
                                       S-HHHHH CS
                        Sigma70_r4   5 Lperere 11 
                                       L++r+re
  gi|313126285|ref|YP_004036555.1| 114 LSARQRE 120
                                       6777775 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAlr 46 
                                       re+++ i +rAl+
  gi|313126285|ref|YP_004036555.1| 163 RETASVIYRRALD 175
                                       89*********96 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 2.6e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAl 45 
                                        e+ T++E++e+  iS+ ++r + k+ l
  gi|313126285|ref|YP_004036555.1| 294 NEKVTQSEVSEVASISEVTIRNRYKELL 321
                                       6899*******************99877 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5     3e-05     0.049      29      60 ..      33      64 ..      18      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                    OrfB_Zn_ribbon 29 ktCseCgsknkealsgrtfkCpnCgfeadrDv 60
                                      + C+eCg  + ++ ++ + +C +Cg++   D 
  gi|313126285|ref|YP_004036555.1| 33 QVCPECGGSLITDEARGETVCGDCGLVVETDA 64
                                      89**********9*************988885 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.036        59      47      84 ..     187     224 ..     183     234 .. 0.90
   2 ?    8.4   0.0    0.0013       2.2      47      89 ..     281     323 ..     275     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.036
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcve 84 
                                       +A++al++a ++ ++p   ++le +++++k +l   ++
  gi|313126285|ref|YP_004036555.1| 187 VATSALYAAARQAGTPRSLDELETVSRVDKMELTRTYR 224
                                       79****************************99987765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                                       +Aaaa+++a    n++  ++++ ++  +s+  +++ ++ +le+
  gi|313126285|ref|YP_004036555.1| 281 LAAAAVYAAALLTNEKVTQSEVSEVASISEVTIRNRYKELLEV 323
                                       8**********99**********************99999886 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.2   0.00014      0.23       1      25 [.      31      59 ..      31      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                       zf-ribbon_3  1 stvrCPnCGa.plss...ddnvCpyCGtk 25
                                      +t+ CP+CG  ++++   + +vC  CG +
  gi|313126285|ref|YP_004036555.1| 31 ETQVCPECGGsLITDearGETVCGDCGLV 59
                                      5889******99987233568******75 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.6e-05      0.12       4      34 ..      35      63 ..      33      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-05
                                      ESTTTSBEEEEECSCCCEEEESSSS-EEESS CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYeepad 34
                                      Cp+Cg  L+ +e++  ++  C  Cg + ++d
  gi|313126285|ref|YP_004036555.1| 35 CPECGGSLITDEARGETV--CGDCGLVVETD 63
                                      ***************999..*****999887 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00049       0.8      41      53 ..      32      44 ..      24      48 .. 0.80
   2 ?   -3.9   0.1       9.4   1.5e+04      42      48 ..      51      57 ..      50      59 .. 0.63
   3 ?   -0.1   0.0      0.63     1e+03       2      26 ..     250     274 ..     249     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00049
                           DUF1272 41 envCPncgGelvk 53
                                      ++vCP+cgG l++
  gi|313126285|ref|YP_004036555.1| 32 TQVCPECGGSLIT 44
                                      69********975 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9.4
                           DUF1272 42 nvCPncg 48
                                       vC +cg
  gi|313126285|ref|YP_004036555.1| 51 TVCGDCG 57
                                      4566665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.63
                           DUF1272   2 LelrpnCecCdkdlppdseearics 26 
                                       L+l ++ e+  +dl +++++a i s
  gi|313126285|ref|YP_004036555.1| 250 LDLSDEAERQARDLLRNAKKAGIHS 274
                                       7899999999**********99875 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.2   0.00057      0.93       5      30 ..      34      59 ..      31      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00057
                     A2L_zn_ribbon  5 vCsvCggngilnseqgylvCieCgas 30
                                      vC  Cgg  i   ++g+ vC +Cg++
  gi|313126285|ref|YP_004036555.1| 34 VCPECGGSLITDEARGETVCGDCGLV 59
                                      8999********************87 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.9    0.0011       1.7      24      35 ..      29      41 ..      19      45 .. 0.76
   2 ?   -0.0   4.1       0.6   9.7e+02      29      35 ..      35      41 ..      35      64 .. 0.63
   3 ?    0.3   0.2      0.47   7.7e+02       7      16 ..      52      61 ..      50      69 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                       Zn-ribbon_8 24 aplta.CPeCgse 35
                                      +++t+ CPeCg+ 
  gi|313126285|ref|YP_004036555.1| 29 EEETQvCPECGGS 41
                                      457788*****84 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.6
                       Zn-ribbon_8 29 CPeCgse 35
                                      CPeCg+ 
  gi|313126285|ref|YP_004036555.1| 35 CPECGGS 41
                                      6666653 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.47
                       Zn-ribbon_8  7 rCeeCghefe 16
                                       C +Cg + e
  gi|313126285|ref|YP_004036555.1| 52 VCGDCGLVVE 61
                                      4777775555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      810  (0.0451782); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2013.24
//
Query:       gi|313126286|ref|YP_004036556.1|  [L=224]
Description: hypothetical protein Hbor_15400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.041   13.5   0.6       0.94    9.0   0.1    2.0  2  Alpha-amylase  Alpha amylase, catalytic domain


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1    0.0031        56     201     250 ..      51     100 ..      32     125 .. 0.79
   2 ?    9.0   0.1   5.2e-05      0.94     135     184 ..     133     182 ..     115     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0031
                                       HTCCGTT-EEEEE-TT-SCCCHCCCC-CGG-SICECCITTCGGGCC-CTS CS
                     Alpha-amylase 201 tvasrkevmtvgEvssdasedlrvyttearlelemvldfphldvaqkaki 250
                                       ++++  +++ v+E+   a ++  v ++++++ +e++ld++ ++++ ++++
  gi|313126286|ref|YP_004036556.1|  51 YATDGPQTVEVNETVTVAGQERHVVAKNQVTTYEKTLDLTIFEAKLGMFT 100
                                       455677888899******************************99998875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 5.2e-05
                                       SSS-TTS-BB-TTTCCCCCCCCCCCCCCCTTT-SEEEETTCCCTTTCCCC CS
                     Alpha-amylase 135 hlflkklpdLnteneevrkelkdvvkfwlekgidGfRlDvvkhvskveal 184
                                       +++l++  +  ++  +v+ +  +v kf  +  i+G R+Dv  hv k ++ 
  gi|313126286|ref|YP_004036556.1| 133 YQGLSDVNKVSSQTITVQGQETEVTKFAAKATINGERVDVYVHVMKYKDG 182
                                       45555555666666668899999*********************995443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1344.69
//
Query:       gi|313126287|ref|YP_004036557.1|  [L=132]
Description: hypothetical protein Hbor_15410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 848.43
//
Query:       gi|313126288|ref|YP_004036558.1|  [L=154]
Description: hypothetical protein Hbor_15420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   13.6   0.3      0.069   12.8   0.3    1.4  1  HTH_33    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   3.8e-06     0.069      42      58 ..     111     127 ..     109     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-06
                            HTH_33  42 rprapkqdpeaqeafkk 58 
                                       r r++k+ +ea+ea+++
  gi|313126288|ref|YP_004036558.1| 111 RDRHHKRHAEAVEAWRE 127
                                       88*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 982.03
//
Query:       gi|313126289|ref|YP_004036559.1|  [L=284]
Description: rRNA biogenesis protein nop56/nop58 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-41  140.7   0.0    7.9e-41  140.0   0.0    1.3  1  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   0.0   4.4e-45   7.9e-41      86     229 ..     135     275 ..      78     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 4.4e-45
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCC CS
                               Nop  86 knikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfra 162
                                       +++ ++++rv +l++ r++l  ++esr  a+APNl+++ G+ +aarLi+ aGgL++LakmP+ t+q+lGae alf +
  gi|313126289|ref|YP_004036559.1| 135 DRVVSYARRVADLADERDDLRAFVESRAPALAPNLAEMAGPVLAARLIALAGGLERLAKMPSGTVQVLGAEDALFAH 211
                                       578999*********************************************************************** PP

                                       HH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                               Nop 163 lk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                       l+ ++++pk+G+iy +e+v+  t p++++ +aR+ a K+a+aaRiD++   +g++  +++ee+ ++++
  gi|313126289|ref|YP_004036559.1| 212 LEgRGSSPKHGVIYVHEYVR-GTHPEHRGSAARAFAGKLAIAARIDHY---SGEFKSEIHEELAERME 275
                                       **6669*************9.66***********************87...48888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1515.88
//
Query:       gi|313126290|ref|YP_004036560.1|  [L=211]
Description: rRNA 2'-o-methyltransferase fibrillarin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-54  184.6   0.0    1.6e-54  184.4   0.0    1.0  1  Fibrillarin    Fibrillarin
  ------ inclusion threshold ------
       0.12   11.4   0.1       0.15   11.0   0.1    1.1  1  Histidinol_dh  Histidinol dehydrogenase
       0.17   11.9   0.0       0.33   10.9   0.0    1.5  1  TIR-like       Predicted nucleotide-binding protein containin


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   0.0   2.7e-58   1.6e-54      27     223 ..      21     209 ..      14     211 .] 0.94

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 2.7e-58
                                       STT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEES CS
                       Fibrillarin  27 vpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavef 103
                                       ++ge+vYgE +   +e+ +R W++ rsKl+a+   g++ + +  ++ vLYlGaasGttvsHv+D  g     yavef
  gi|313126290|ref|YP_004036560.1|  21 THGETVYGEPR---DEDGWRAWDAGRSKLGAMFEYGMD-TGLVGDETVLYLGAASGTTVSHVADFAG---PTYAVEF 90 
                                       68999***976...7889*******************9.56778999*****************987...78***** PP

                                       SHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS-.-EEEEEEESSSTTHHHHHHHHHHHHEEEEEEEEEEEEHHH CS
                       Fibrillarin 104 sprvlrelievakkRknivPileDArkPekYralve.kvDvifaDvaqpdqarilaknaklflkeggyllisikars 179
                                       + r +r+l+ va+ R n++P+l+DArkPe+Y+++ve   D+i +Dva   qa ++ +n + fl+++g ll +ikars
  gi|313126290|ref|YP_004036560.1|  91 AARPVRDLLGVAEARDNLFPLLKDARKPETYAHIVEaDLDCIVQDVATRGQATVANRN-RQFLRDDGRLLAVIKARS 166
                                       ***********************************988**************998888.569*************** PP

                                       HHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEE CS
                       Fibrillarin 180 idvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgk 223
                                        dvt++p++vf++  ++l+e+ +++le+ +l+ ++ dh+ vv++
  gi|313126290|ref|YP_004036560.1| 167 EDVTADPDDVFEDVLTELREA-YEILETTRLDRFHDDHLGVVAR 209
                                       ******************986.9******************986 PP

>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   2.5e-05      0.15       5      77 ..     119     193 ..     115     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.5e-05
                                       ----HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSS.SSG.GCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHH CS
                     Histidinol_dh   5 eedseeveetvkeiledvreeGdealleytekFDkv.kkl.eslrvseeeieealekldeelkealeeaaenirk 77 
                                       e+ ++ ve+  + i++dv ++G++ + + +++F +   +l + ++  +e++++  +++ e++ + l+ea+e +++
  gi|313126290|ref|YP_004036560.1| 119 ETYAHIVEADLDCIVQDVATRGQATVANRNRQFLRDdGRLlAVIKARSEDVTADPDDVFEDVLTELREAYEILET 193
                                       4555567888999********************64433334889999999*******************986554 PP

>> TIR-like  Predicted nucleotide-binding protein containing TIR-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.5e-05      0.33      79     114 ..      49      87 ..      28      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.5e-05
                          TIR-like  79 ifElGlflgklgrenviilk...kgevelpsDlaGilyi 114
                                       +fE+G+  g++g e+v++l      +v+ ++D+aG +y+
  gi|313126290|ref|YP_004036560.1|  49 MFEYGMDTGLVGDETVLYLGaasGTTVSHVADFAGPTYA 87 
                                       8*****************94455889999******9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1161.62
//
Query:       gi|313126291|ref|YP_004036561.1|  [L=358]
Description: hypothetical protein Hbor_15450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-73  248.2   0.1    1.2e-73  248.0   0.1    1.0  1  GCS2           Glutamate-cysteine ligase family 2(GCS2)
     0.0088   15.7   0.1        6.1    6.4   0.0    2.8  3  Amidoligase_2  Putative amidoligase enzyme


Domain annotation for each model (and alignments):
>> GCS2  Glutamate-cysteine ligase family 2(GCS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.0   0.1   1.4e-77   1.2e-73       1     291 []      15     295 ..      15     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: 248.0 bits;  conditional E-value: 1.4e-77
                                       EEEEEEEEEEETTTTEE-S-HHHHHCCCTTT-S.SSEEEE-SSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHH CS
                              GCS2   1 lgvEeeflvvdlatgdlrgwseiledeaiiglseggsvvkelpegqvElstapleslaeaaeeisadleelrsvade 77 
                                       lgvEeef++vd+ ++  +g s+   d+  +gl  g+++++el++ +vE++t+ +e+ +ea e ++a +e+l s+a++
  gi|313126291|ref|YP_004036561.1|  15 LGVEEEFYIVDSDGYPASGISDLIYDDPPEGLL-GDRIDHELFKFTVETQTPLIENPSEADELVRAVREALVSHAAD 90 
                                       69*************************999999.******************************************* PP

                                       TT-EEE--SB-SS---------------THHHHHGG..G.G-S--B-EEEEEEE-SSHHHHH.HHHHHHHTTHHHHH CS
                              GCS2  78 lGlellglGthPfalrsedevtpkaryrrmleymdrvGvlgrqmmvaglhvqvnidssseedVevlrlvrallPvll 154
                                       +G++++++G+hP a+++e  ++ k+ry+++l+++++  + ++++++aglhv+v++d+ +++  ++ + +r++lP ll
  gi|313126291|ref|YP_004036561.1|  91 HGYRIAAAGLHPAAKWRELDHATKPRYKSQLDRIQY--P-QHRNTTAGLHVHVGVDDPDKAT-WIANELRWYLPPLL 163
                                       ************************************..7.*****************55555.************** PP

                                       HHH--B-EETTEE-S-SB-GGGCCTTSTT-CS----SSHHH.HHHHHHHHTTSTT-SSGG.G--BSEEEETTTT.EE CS
                              GCS2 155 AlsAnSPfleGrdtgyaStRariftqtpqagelplafedgaaferyaryaldvpvidvrrfrlwldirpsslpgttl 231
                                       AlsAnSPf++G dtg++S+Ra+if+++p+ +++p  fed  a++r+ r++ +++ i++r+ +lw+d+rp++ +g t+
  gi|313126291|ref|YP_004036561.1| 164 ALSANSPFWNGFDTGLSSARAKIFENLPN-TGMPSRFEDFEAYQRFERRMVEHGSIEDRG-ELWYDVRPHTGHG-TV 237
                                       *****************************.******************************.9************.** PP

                                       EEEEEE--...SSHHHHHHHHHHHHHHHHHHHHH------GGGGTT.HHHHHHHHHHHGG CS
                              GCS2 232 elrihdttlfPevrlrallearlldaqpadrldalpaavlvallddeaeenawdavrsgl 291
                                       e+r  d++++Pe  l+ ++++++l  + a r+ + +  ++  ++++  +en+w+a r+g+
  gi|313126291|ref|YP_004036561.1| 238 EVRTPDAQSDPEKTLAFVEYVHALVLDLAARYEDGESGTTIRRELL--DENKWRATRHGH 295
                                       ********************************99998887776666..*********985 PP

>> Amidoligase_2  Putative amidoligase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.11     1e+03      76     118 ..      58     101 ..      31     115 .. 0.73
   2 !    6.4   0.0   0.00068       6.1     107     133 ..     128     153 ..     119     160 .. 0.76
   3 !    5.9   0.0   0.00098       8.8     224     252 ..     233     261 ..     197     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.11
                     Amidoligase_2  76 vpvElvsPplelsedlealeelvraLreagavgtnas....cglhvH 118
                                        +vE  +P +e     ++ +elvra rea   +  +     ++ ++H
  gi|313126291|ref|YP_004036561.1|  58 FTVETQTPLIEN---PSEADELVRAVREALVSHAADHgyriAAAGLH 101
                                       567888888883...56777888888887777755556666777777 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00068
                     Amidoligase_2 107 vgtnascglhvHldaevpdleaetlrn 133
                                       ++ n ++glhvH++ ++pd +a+ + n
  gi|313126291|ref|YP_004036561.1| 128 QHRNTTAGLHVHVGVDDPD-KATWIAN 153
                                       565777***********99.4655555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.00098
                     Amidoligase_2 224 erpTvEfRlpngtldaeeikawirlclal 252
                                       +++TvE R p+++ d e++ a ++   al
  gi|313126291|ref|YP_004036561.1| 233 GHGTVEVRTPDAQSDPEKTLAFVEYVHAL 261
                                       567****************9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2061.07
//
Query:       gi|313126292|ref|YP_004036562.1|  [L=156]
Description: sugar-specific transcriptional regulator trmb [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-06   26.7   0.0    5.9e-06   26.1   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
    5.7e-06   25.8   0.0    9.4e-06   25.1   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
    0.00021   21.1   0.0    0.00029   20.7   0.0    1.3  1  TFIIE_alpha    TFIIE alpha subunit
    0.00061   19.6   0.0    0.00094   19.0   0.0    1.3  1  HTH_5          Bacterial regulatory protein, arsR family
      0.001   18.7   0.0     0.0019   17.8   0.0    1.4  1  GntR           Bacterial regulatory proteins, gntR family
     0.0014   18.5   0.1     0.0045   16.8   0.0    1.8  2  MarR_2         MarR family
     0.0014   18.5   0.1      0.003   17.5   0.1    1.4  1  HTH_Crp_2      Crp-like helix-turn-helix domain
     0.0015   18.3   0.0     0.0027   17.5   0.0    1.4  1  HTH_IclR       IclR helix-turn-helix domain
     0.0017   18.4   0.1     0.0032   17.5   0.1    1.5  1  HTH_20         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.025   14.8   0.0    1.5  1  DUF3369        Domain of unknown function (DUF3369)
      0.016   15.3   0.0      0.028   14.5   0.0    1.3  1  Replic_Relax   Replication-relaxation
      0.018   15.0   0.0      0.034   14.1   0.0    1.4  1  MarR           MarR family
      0.065   13.6   0.0       0.11   12.9   0.0    1.3  1  Rrf2           Transcriptional regulator
      0.079   12.8   1.2       0.25   11.2   0.0    2.4  3  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.12   12.7   0.0       0.87    9.9   0.0    2.1  2  HTH_Tnp_Tc3_2  Transposase


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   4.9e-09   5.9e-06       8      67 ..      43     109 ..      42     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.9e-09
                                       HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE--H CS
                              TrmB   8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYravdp 67 
                                       e+ a++++ L ++  at +e+a+ +g+  s+v e+L +L d  +V r+k++       p+ Y+a+ p
  gi|313126292|ref|YP_004036562.1|  43 ETRARIFVFLRQNPHATSEEVANGTGLYPSTVREALAELHDEEMVSRRKRKnsgagnnPYEYEAIAP 109
                                       566889999999*************************************999************988 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   7.8e-09   9.4e-06       4      47 ..      44      87 ..      41      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.8e-09
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      t+ +I   L++np+ +  e+A  +gl pstv++ l +L +e+ +
  gi|313126292|ref|YP_004036562.1| 44 TRARIFVFLRQNPHATSEEVANGTGLYPSTVREALAELHDEEMV 87
                                      66677778******************************999876 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.4e-07   0.00029      15      75 ..      45     105 ..      31     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.4e-07
                                       HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEE CS
                       TFIIE_alpha  15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywr 75 
                                        + +   L ++   t e++a+ +++ +  +r++L++L ++ +v+ ++r++ + +   y + 
  gi|313126292|ref|YP_004036562.1|  45 RARIFVFLRQNPHATSEEVANGTGLYPSTVREALAELHDEEMVSRRKRKNSGAGNNPYEYE 105
                                       5677788999999*************************************88887777664 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.8e-07   0.00094       2      46 ..      43      88 ..      42      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.8e-07
                                      HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +tR +I  +L++++ +++ e a+ +gl +stv++ L+ L+++ +V+
  gi|313126292|ref|YP_004036562.1| 43 ETRARIFVFLRQNPhATSEEVANGTGLYPSTVREALAELHDEEMVS 88
                                      89************99***************************997 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.6e-06    0.0019      30      60 ..      63      93 ..      59      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                      HHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR 30 LaaefgVsrttvReALrrLeaeglverrqgr 60
                                      +a   g   +tvReAL +L  e +v rr+++
  gi|313126292|ref|YP_004036562.1| 63 VANGTGLYPSTVREALAELHDEEMVSRRKRK 93
                                      5556666789******************996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.8e-06    0.0045       6      55 ..      44      91 ..      40      98 .. 0.89
   2 ?   -2.1   0.0       3.1   3.8e+03       7      17 ..     123     133 ..     121     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.8e-06
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      + ar+  +L+ +p    t  e+a  +gl +s+v  +l++L +  +v rr+
  gi|313126292|ref|YP_004036562.1| 44 TRARIFVFLRQNPH--ATSEEVANGTGLYPSTVREALAELHDEEMVSRRK 91
                                      7899*********9..9*****************************9884 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                                       HHHHHHHHHCT CS
                            MarR_2   7 qarvLaaLgrr 17 
                                       q+  L++L rr
  gi|313126292|ref|YP_004036562.1| 123 QLNTLFNLDRR 133
                                       77789999887 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.5e-06     0.003       4      55 ..      36      91 ..      35      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.5e-06
                                      HHHHHHHHCTTTC....EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2  4 ArfLlrlaeragg....eielpltqeelAsmlGltretvsrilseLkreglisrgr 55
                                       ++Ll+ + ra+     + + + t ee A+  Gl ++tv  +l+eL +e ++sr++
  gi|313126292|ref|YP_004036562.1| 36 LAWLLDTETRARIfvflRQNPHATSEEVANGTGLYPSTVREALAELHDEEMVSRRK 91
                                      5789887666432333334679*******************************763 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.2e-06    0.0027      12      50 ..      51      89 ..      46      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      + ++++  t  e+A+ tgl +Stv+  L+ L+ + +v +
  gi|313126292|ref|YP_004036562.1| 51 FLRQNPHATSEEVANGTGLYPSTVREALAELHDEEMVSR 89
                                      4455555699***********************999987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.7e-06    0.0032       6      59 ..      39      92 ..      31      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-06
                                      HHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  6 ALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +L+ ++R+ri+  L+++  +t +e+a   +l ++t++  L++L + + v +++ 
  gi|313126292|ref|YP_004036562.1| 39 LLDTETRARIFVFLRQNPHATSEEVANGTGLYPSTVREALAELHDEEMVSRRKR 92
                                      4666*******************************************9999985 PP

>> DUF3369  Domain of unknown function (DUF3369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.1e-05     0.025      35     101 ..      23      89 ..      20     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                           DUF3369  35 rsleefaegvltqlasllnlkkdg..lvcaskakaaaskelkvlaatgkfesligkpleeladeelrel 101
                                       r ++ef e+v+  la ll+ ++ +  +v+ +++ +a s   +v ++tg + s++++ l+el+dee++++
  gi|313126292|ref|YP_004036562.1|  23 RAVAEFDENVVDLLAWLLDTETRAriFVFLRQNPHATS--EEVANGTGLYPSTVREALAELHDEEMVSR 89 
                                       67899*************99877776666666666555..79********************9998655 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.3e-05     0.028       5      60 ..      53     105 ..      49     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                      Replic_Relax   5 aehrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYa 60 
                                       ++  ++T++ +a+ +    ++ +r +La+L++++++sr +++  + ++g +py Y 
  gi|313126292|ref|YP_004036562.1|  53 RQNPHATSEEVANGTGLYPST-VREALAELHDEEMVSRRKRK--NSGAGNNPYEYE 105
                                       555566666666665555556.****************4444..6777789**995 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-05     0.034       2      54 ..      42      94 ..      42      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspe 54
                                      t+t+ +i + l++++ ++  e a+  g+ +stv ++l +L ++++++R+k ++
  gi|313126292|ref|YP_004036562.1| 42 TETRARIFVFLRQNPHATSEEVANGTGLYPSTVREALAELHDEEMVSRRKRKN 94
                                      67888899999**************************************9987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     9e-05      0.11      12      63 ..      47      95 ..      41      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-05
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-T CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgG 63
                                      ++ ++L ++++   ++see+a+ +++ ps ++  la+L  +++v  ++ k+ 
  gi|313126292|ref|YP_004036562.1| 47 RIFVFLRQNPH---ATSEEVANGTGLYPSTVREALAELHDEEMVSRRKRKNS 95
                                      66667777666...79****************************98775555 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.7   3.3e+03      30      39 ..       9      18 ..       8      19 .. 0.81
   2 ?   11.2   0.0   0.00021      0.25      10      41 ..      50      81 ..      43      82 .. 0.89
   3 ?   -1.3   0.1       1.7   2.1e+03       4       9 ..     130     135 ..     129     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
                     HTH_AsnC-type 30 SestvlrRvr 39
                                      +e+t ++R++
  gi|313126292|ref|YP_004036562.1|  9 TEQTTRERLE 18
                                      6899999985 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00021
                     HTH_AsnC-type 10 eaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                        L++++ ++ +e+A  +Gl +stv++ ++ L
  gi|313126292|ref|YP_004036562.1| 50 VFLRQNPHATSEEVANGTGLYPSTVREALAEL 81
                                      569***********************988877 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.7
                     HTH_AsnC-type   4 iDrkIL 9  
                                       +Dr++L
  gi|313126292|ref|YP_004036562.1| 130 LDRRLL 135
                                       8***99 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.74   8.9e+02      27      41 ..       5      19 ..       1      21 [. 0.80
   2 ?    9.9   0.0   0.00073      0.87       2      51 ..      46      93 ..      45      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.74
                     HTH_Tnp_Tc3_2 27 GksvsreTirrrLrk 41
                                      G +   +T r rL +
  gi|313126292|ref|YP_004036562.1|  5 GDESTEQTTRERLEA 19
                                      888999******976 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00073
                     HTH_Tnp_Tc3_2  2 rrIvrlvrkdPritlreLanelkeeGksvsreTirrrL...rkaglkkrkprk 51
                                      +rI    r++P++t++e+an +         +T+r  L   +++ + +r+ rk
  gi|313126292|ref|YP_004036562.1| 46 ARIFVFLRQNPHATSEEVANGT-----GLYPSTVREALaelHDEEMVSRRKRK 93
                                      6788889************988.....667789*9865111666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.59u 0.37s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 831.90
//
Query:       gi|313126293|ref|YP_004036563.1|  [L=168]
Description: cytidyltransferase-related enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-12   45.6   0.0      1e-11   45.2   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like
     0.0042   17.0   0.2      0.023   14.6   0.1    2.1  2  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   1.1e-15     1e-11       2     142 ..       5     142 ..       4     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.1e-15
                                       EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST.-..SCSSTHHHHHHHH.HHHTTCTTEEEEEEESEHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkk.k..kplasaeeRleml.elakevdevisvdpweltr 74 
                                       +gGtFDp+H GHl+l+ +a++l++  + vg++sde + k+ +  + + + eeR + l  +++   e  +++++e+  
  gi|313126293|ref|YP_004036563.1|   5 LGGTFDPVHDGHLALFARAFELGD--VTVGLTSDELAPKTrHvdRYVRPFEERKRDLlDELEPLAE-EHDREFEIRT 78 
                                       69**********************..79*******888884488*********9865133333333.4444444444 PP

                                       .....HHHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  75 .....evlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                             + ++ + d  +l+++ ++ +   + +e++e  g  +l +++++         ++++ + iSst+i +
  gi|313126293|ref|YP_004036563.1|  79 lteptGIATEPGFD--VLIVSPETKDGGARINEIREERGLPPLDIEVVD-------HVPAEDGKRISSTRIVR 142
                                       6667789999999*..********9999888899999999999999888.......9999**********975 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.5e-06     0.023      13      33 ..       7      27 ..       1     103 [. 0.69
   2 ?    0.1   0.0     0.072   6.5e+02     139     158 .]     119     139 ..      98     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-06
                           FAD_syn 13 GnFDGvHlGHqallkkaveaa 33
                                      G FD vH GH al+++a e+ 
  gi|313126293|ref|YP_004036563.1|  7 GTFDPVHDGHLALFARAFELG 27
                                      79***************9987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.072
                           FAD_syn 139 fevevvpkv.eleeekissta 158
                                       +++evv++v  +++++isst+
  gi|313126293|ref|YP_004036563.1| 119 LDIEVVDHVpAEDGKRISSTR 139
                                       56789999988999*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 983.14
//
Query:       gi|313126294|ref|YP_004036564.1|  [L=102]
Description: transcription initiation factor tfiiib, brf1 subunit/transcription initiation factor tfiib [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-05   24.4   0.5    4.3e-05   23.5   0.5    1.5  1  TFIIB       Transcription factor TFIIB repeat
  ------ inclusion threshold ------
      0.052   13.1   1.0      0.065   12.8   0.1    1.7  2  Sigma70_r4  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.5   4.7e-09   4.3e-05       5      70 ..      21      83 ..      17      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.7e-09
                                      HHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
                             TFIIB  5 adaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70
                                      ad+leL  + ++ A  ++   + +   + rs+ ++aAA+ly +++ ++++r+q+++++ + V+  +
  gi|313126294|ref|YP_004036564.1| 21 ADRLELGSEARSYASDMFLSQVPD---ADRSKRAVAAASLYAGALIAGEERSQSRVANAMDVTRLS 83
                                      556666655555555544333333...459******************************999766 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.29   2.6e+03      24      34 ..      18      28 ..      17      30 .. 0.76
   2 ?   12.8   0.1   7.2e-06     0.065      18      46 ..      65      93 ..      46      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.29
                                      HHHHHHHTS-H CS
                        Sigma70_r4 24 eEIgerlgiSr 34
                                      eE ++rl +  
  gi|313126294|ref|YP_004036564.1| 18 EEAADRLELGS 28
                                      79999998765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.2e-06
                                      TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4 18 geglTleEIgerlgiSrerVrqiekrAlr 46
                                      ge+++++ +++ ++++r  + q+ k+ l+
  gi|313126294|ref|YP_004036564.1| 65 GEERSQSRVANAMDVTRLSIQQRWKEILE 93
                                      8*********************9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 614.30
//
Query:       gi|313126295|ref|YP_004036565.1|  [L=1250]
Description: type i restriction-modification system methyltransferase subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-16   60.2   0.0    3.9e-16   59.2   0.0    1.5  1  TaqI_C           TaqI-like C-terminal specificity domain
      2e-16   60.2   0.0    3.8e-09   36.3   0.0    2.3  2  N6_Mtase         N-6 DNA Methylase
    4.4e-14   52.9   0.0    8.9e-14   51.9   0.0    1.5  1  Eco57I           Eco57I restriction-modification methylase
    5.2e-06   26.4   0.0    1.5e-05   24.9   0.0    1.8  1  HSDR_N_2         Type I restriction enzyme R protein N termin
    3.9e-05   23.4   0.0     0.0019   17.9   0.0    2.3  2  UPF0020          Putative RNA methylase family UPF0020
    0.00016   21.7   0.0    0.00038   20.5   0.0    1.6  1  HSDR_N           Type I restriction enzyme R protein N termin
  ------ inclusion threshold ------
      0.018   14.7   0.0        1.2    8.7   0.0    2.5  2  Cons_hypoth95    Conserved hypothetical protein 95
      0.022   14.9   0.0       0.18   11.9   0.0    2.2  2  Cas_Cas4         Domain of unknown function DUF83
       0.03   14.1   0.0       0.31   10.8   0.0    2.4  2  Methyltransf_31  Methyltransferase domain
       0.11   12.8   0.0       0.33   11.3   0.0    1.7  1  Tox-REase-9      Restriction endonuclease fold toxin 9


Domain annotation for each model (and alignments):
>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   2.2e-19   3.9e-16       2     120 .]     921    1078 ..     920    1078 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.2e-19
                            TaqI_C    2 pllkGkdikrysieik.................gnYldlikkklknek........................a.. 33  
                                        pl++G++++r  ++++                 +      +    +++                        +  
  gi|313126295|ref|YP_004036565.1|  921 PLIRGENVRRWIVDWEeevaiypydddgelvdfS------EYPSVKSHledhreyledrycvkkggkgiyeyDgp 989 
                                        899*************999999999996666663......33333333333334555555666565555555155 PP

                            TaqI_C   34 ..kelfeekpKilvrdiskkldaaydekayyvlntlylliakdelevslkyllgiLNSklikfyykkiystlrgg 106 
                                          k++fe + +i v+d++ ++++ y +    ++nt+y+l+ +de+++s+  llg+LNS + +fy+k+ ++ l+++
  gi|313126295|ref|YP_004036565.1|  990 rcKSVFEGDFRIPVPDMATENQFSYADGYNCFKNTAYVLTFNDEQPYSELELLGLLNSAVSEFYIKQKSPFLNDQ 1064
                                        6799999******************************************************************** PP

                            TaqI_C  107 ysrlkrkeleklPi 120 
                                        y r+k ++++++P+
  gi|313126295|ref|YP_004036565.1| 1065 YFRYKSQYIDPIPL 1078
                                        *************6 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   2.1e-12   3.8e-09       3      70 ..     391     459 ..     389     502 .. 0.79
   2 !   21.4   0.0   6.8e-08   0.00012     109     241 ..     685     816 ..     646     840 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.1e-12
                          N6_Mtase   3 kdllGdvYEyllrkfaeeegksgGeffTPrevsklivell...epksgesvyDpacGsggllvqa.ekvlke 70 
                                        dllGd+Y    r+f  e+ k  Gef+TP+ v+  i++ +      s+e  +Dp cGsg +lv+a e+++++
  gi|313126295|ref|YP_004036565.1| 391 GDLLGDLYQ---RYFDPETRKALGEFYTPQPVIDYIMDGVgyeRGVSNERLIDPSCGSGTFLVEAvERYITD 459
                                       699****98...78999**********************98887778889*************982456654 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 6.8e-08
                          N6_Mtase 109 irlgdtlekpkfekdkkfdvvvaNppfnqkew.kektlekderfreavapksnadlafllhiieslkpkGraavvla 184
                                       +  +dt      ++ ++ d+vv Npp+ + ++ +++  e+  r+ +    +    + f+   +e+l ++G  + +  
  gi|313126295|ref|YP_004036565.1| 685 KMFEDTVLALVVKNYMEYDYVVGNPPYVNIKYiSDTAQERYTRLYDSAFGRFDLYVLFIERGLEMLTEDGELGYITS 761
                                       4567777777788999***********888895666666666777777777777788****************9976 PP

                          N6_Mtase 185 ngvLfrggkegkIrkalvekdlveavialp.eklFyntsiptcilvlkkekaerkgkv 241
                                       n  + r   + +Ir+ +  +  +   i +  +++F   +   cil++++++++  ++v
  gi|313126295|ref|YP_004036565.1| 762 N-KFARAEYGREIRRLISSEYSLAEYIDFGdTEVFKDATNYPCILFVDRDRNR--KTV 816
                                       5.6889999*******************97368****99999********964..443 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0     5e-17   8.9e-14       1     105 [.     700     812 ..     700     813 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 5e-17
                            Eco57I   1 mkfdviiGNPPYqeseakkelkaleek........akdiyqkFvekalkle..dkylaliiparflasgkglkefre 67 
                                       m +d ++GNPPY +++ + ++++++ +          d+y+ F+e++l++   d+ l+ i++++f  ++++++e+r+
  gi|313126295|ref|YP_004036565.1| 700 MEYDYVVGNPPYVNIKYISDTAQERYTrlydsafgRFDLYVLFIERGLEMLteDGELGYITSNKFA-RAEYGREIRR 775
                                       899*************988888444449******999*************98899**********9.9********* PP

                            Eco57I  68 kllkdkklkklvefedskevFkdveikggilvflkdkk 105
                                        + ++ +l+++++f d + vFkd++ + +il++ +d++
  gi|313126295|ref|YP_004036565.1| 776 LISSEYSLAEYIDFGDTE-VFKDATNYPCILFVDRDRN 812
                                       ****************99.**************99986 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   8.6e-09   1.5e-05      35     100 ..      57     121 ..      36     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 8.6e-09
                          HSDR_N_2  35 kkkraDivvykkdkkpllivecKapsvkiseevleqlksYlealkaeylvvtNglehivykvdkkk 100
                                         +r+D++  ++++ +  + e K+   ++   + +ql+ Y+  l+aey+v+tNg++  +y+  +++
  gi|313126295|ref|YP_004036565.1|  57 DDRRPDYITLDSNEAVTAVYEFKTTGRSLPP-HESQLFHYMDYLRAEYGVLTNGEQLRLYRRGEDR 121
                                       4679*********9************99965.88*************************9976654 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-06    0.0019      29      90 ..     435     493 ..     431     510 .. 0.67
   2 ?    2.8   0.0     0.045        80     118     132 ..     698     712 ..     677     737 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                       TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHH...HH--EEEEES-HHHHH CS
                           UPF0020  29 gepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeear...aelklygsDldrrvvq 90 
                                       +e+l+DP CGsGt+l+Ea     + +      + +e    +ee+ r   ++ +++g+D+ + +v 
  gi|313126295|ref|YP_004036565.1| 435 NERLIDPSCGSGTFLVEAVERYITDV------ENFEDNPDWEEHLRdlcTRPRIVGLDIHPFAVL 493
                                       689**************965444444......234455556666663323333666666665555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.045
                                       TTS---EEEE----- CS
                           UPF0020 118 kegevdvivtnpPYG 132
                                       +  e+d +v+npPY 
  gi|313126295|ref|YP_004036565.1| 698 NYMEYDYVVGNPPYV 712
                                       4459**********6 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.1e-07   0.00038     118     190 ..      55     119 ..      22     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                                       SSS---EEEEEEE.TTEEEEEEEE--TT-HHHHHHHHTSS---.---S..SSGGGGG-.....-EEEEE-SS-EEEE CS
                            HSDR_N 118 gnqkrrpDivlfv.nglplvviElKrpgtieeAinQikryrkeksdvs..ipqlfrYl.....qfgvisngketrfy 186
                                        ++ rrpD++ +  n+   +v E+K                 + ++++  + qlf+Y+     ++gv++ng+++r+y
  gi|313126295|ref|YP_004036565.1|  55 LPDDRRPDYITLDsNEAVTAVYEFKT----------------TGRSLPphESQLFHYMdylraEYGVLTNGEQLRLY 115
                                       56889***9988638***********................55556668**************************9 PP

                                       E--S CS
                            HSDR_N 187 aktk 190
                                        + +
  gi|313126295|ref|YP_004036565.1| 116 RRGE 119
                                       8765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00069       1.2      40      80 ..     433     473 ..     422     484 .. 0.87
   2 ?    2.9   0.1      0.04        72      80     133 ..     667     721 ..     661     730 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00069
                                       HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHH CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkil 80 
                                       + ++r++D  +GsG+  +EA+ R++  +  +e ++   + l
  gi|313126295|ref|YP_004036565.1| 433 VSNERLIDPSCGSGTFLVEAVERYITDVENFEDNPDWEEHL 473
                                       78899**********************99999988766655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.04
                                       HHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH.HHHH CS
                     Cons_hypoth95  80 lkenleelklee.etaelkedaleallklakkkeefdivflDPPyakellieevl 133
                                       + en++ lk e+   + +k+ +   l   +k+  e+d+v  +PPy + ++i ++ 
  gi|313126295|ref|YP_004036565.1| 667 MLENVRYLKEEHnDGRLFKMFEDTVLALVVKNYMEYDYVVGNPPYVNIKYISDTA 721
                                       56888888877664455555554555555668899**********9988777665 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.8e-05      0.18      48     103 ..      52     109 ..      24     145 .. 0.81
   2 ?   -0.3   0.0      0.57     1e+03      89     132 ..     739     783 ..     735     792 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.8e-05
                          Cas_Cas4  48 evelsesikiDvve..kekeklvvvEvKkskkkeeaaklQllyYlllLe.kkgveikeG 103
                                       e++l +  + D+++  +++  + v+E+K   +  + ++ Ql +Y+ +L+ + gv  + G
  gi|313126295|ref|YP_004036565.1|  52 EFTLPDDRRPDYITldSNEAVTAVYEFKTTGRSLPPHESQLFHYMDYLRaEYGVLTN-G 109
                                       566656778999997556666778*************************999*9887.4 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.57
                          Cas_Cas4  89 YlllLe.kkgveikeGvleypkekkreevelteelreelekaike 132
                                       Y+l++e    +  + G+l y++++k  + e+ +e r+ + + ++ 
  gi|313126295|ref|YP_004036565.1| 739 YVLFIErGLEMLTEDGELGYITSNKFARAEYGREIRRLISSEYSL 783
                                       556666555556688****************99999999887765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.31       3      47 ..     434     498 ..     433     500 .. 0.81
   2 ?   -0.5   0.2      0.55   9.8e+02      50      77 ..    1205    1232 ..    1202    1242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelae.........elgpkae...........vvGiDiseeaielAren 47 
                                       ++ r++D+ CG+G+++ e+ e         e +p+ e           +vG+Di ++a+  A+ +
  gi|313126295|ref|YP_004036565.1| 434 SNERLIDPSCGSGTFLVEAVEryitdvenfEDNPDWEehlrdlctrprIVGLDIHPFAVLMAQIR 498
                                       6889*****************888888877444444466777777777**********9988865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.55
                   Methyltransf_31   50 klgldnveFeqgdieeleklledekfDl 77  
                                        +l+ d+ e++q die+le  + d+ +Dl
  gi|313126295|ref|YP_004036565.1| 1205 RLEADREEVRQTDIEDLEAEIDDAVYDL 1232
                                        677788899*******995588877776 PP

>> Tox-REase-9  Restriction endonuclease fold toxin 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.33      21      78 ..      44     104 ..      33     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                       Tox-REase-9  21 vlgvgrekEfklpsgkRiDfvdfet....kiiyELKPnnpraikrGlkqlevYkqeleseyG 78 
                                       ++g+    Ef+lp  +R+D++ ++       +yE K  + r++   + ql +Y   l+ eyG
  gi|313126295|ref|YP_004036565.1|  44 GTGTDLRSEFTLPDDRRPDYITLDSneavTAVYEFKT-TGRSLPPHESQLFHYMDYLRAEYG 104
                                       55566789***********8876654466789***96.556788888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.87u 0.33s 00:00:01.20 Elapsed: 00:00:00.51
# Mc/sec: 7443.09
//
Query:       gi|313126296|ref|YP_004036566.1|  [L=394]
Description: hypothetical protein Hbor_15510 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-11   43.1   0.0    6.3e-11   42.2   0.0    1.4  1  HSDR_N_2   Type I restriction enzyme R protein N terminus (HS
    1.2e-06   28.6   3.3    1.7e-05   24.9   0.0    3.3  5  HSDR_N     Type I restriction enzyme R protein N terminus (HS
  ------ inclusion threshold ------
       0.06   12.6   5.4      0.095   12.0   5.4    1.2  1  DUF1978    Domain of unknown function (DUF1978)
      0.096   12.8   0.1       0.21   11.7   0.1    1.5  1  TetR_C_29  Tetracyclin repressor-like, C-terminal domain
        3.5    8.5   8.5         11    6.9   1.4    3.3  4  FliT       Flagellar protein FliT


Domain annotation for each model (and alignments):
>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   1.8e-14   6.3e-11      21     106 ..      46     131 ..      24     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.8e-14
                          HSDR_N_2  21 keliavekelqlgskkkraDivvykkdkkpllivecKapsvkiseevleqlksYlea.lkaeylvvtNglehivykv 96 
                                        +++a+e+++ + s +  +D+++   d +p+++ve+K  + ++++++++ql sY++  l ++++++tNg+++ v+ +
  gi|313126296|ref|YP_004036566.1|  46 STEVALEYTIPMASGSTHVDYALLVGD-SPVVFVEAKPVRSTLTDDEVQQLRSYMRQeLDVDWGILTNGKSFEVLTK 121
                                       57899********************99.***************************9769****************99 PP

                          HSDR_N_2  97 dkkkkkfeel 106
                                       +  ++  ee+
  gi|313126296|ref|YP_004036566.1| 122 NRHRNGGEEV 131
                                       8888777766 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.035   1.3e+02       3      24 ..      24      45 ..      22      49 .. 0.84
   2 !   24.9   0.0   4.7e-09   1.7e-05     110     192 ..      49     125 ..      46     127 .. 0.82
   3 ?   -1.2   0.2      0.45   1.6e+03      76     112 ..     185     220 ..     145     234 .. 0.48
   4 ?   -1.5   0.1      0.58   2.1e+03       8      59 ..     212     264 ..     203     289 .. 0.69
   5 ?   -3.1   0.0       1.7   6.1e+03     169     189 ..     301     321 ..     299     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.035
                                      SHHHHHH.HHHHHHHHTT-EE. CS
                            HSDR_N  3 sEaeleqelidellrelGyqvl 24
                                       E+ ++ +l+ ++l+ lG++  
  gi|313126296|ref|YP_004036566.1| 24 DEENTKVKLVQPFLELLGWNLY 45
                                      68888889***********975 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 4.7e-09
                                       EEE----S.SSS---EEEEEEETTEEEEEEEE--TT.-HHHHHHHHTSS---.---SSSGGGGG-......-EEEEE CS
                            HSDR_N 110 vvnQvtvt.gnqkrrpDivlfvnglplvviElKrpg.tieeAinQikryrkeksdvsipqlfrYl......qfgvis 178
                                       v+ ++t+   ++   +D+ l+v+  p+v++E+K  + t            +++    ++ql+ Y+       +g+++
  gi|313126296|ref|YP_004036566.1|  49 VALEYTIPmASGSTHVDYALLVGDSPVVFVEAKPVRsT----------LTDDE----VQQLRSYMrqeldvDWGILT 111
                                       677777778889999*******************4211..........11233....99999999999999****** PP

                                       -SS-EEEEE--SSS CS
                            HSDR_N 179 ngketrfyaktkrr 192
                                       ngk + + +k++ r
  gi|313126296|ref|YP_004036566.1| 112 NGKSFEVLTKNRHR 125
                                       ****9999998766 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.45
                                       HHHHHHTS-EEEE......TS-EEEEES.S-SSSGGGS-EEEEE CS
                            HSDR_N  76 fyellkegkvkfk......egrkknikL.iDkknlenNrfqvvn 112
                                       ++e         +      e ++ +i+L    ++  +N ++v++
  gi|313126296|ref|YP_004036566.1| 185 VTES--------VtetvenEVGDLTIDLeEQSREFVQNLVSVLR 220
                                       1111........11111233444444443334455556665555 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.58
                                       HH.HHHHHHHHTT-EE................----SHHHHHHHHHHHHHHHH CS
                            HSDR_N   8 eqelidellrelGyqvlskkdveiegrrpe.vrkskaevaleknlreqlgaln 59 
                                       +q+l+  l ++  +  +++ ++  e ++pe   ++ + ++le+++ +++++++
  gi|313126296|ref|YP_004036566.1| 212 VQNLVSVLREQRHFVSEEPPGESEEDDEPEsDDAADEIEPLENRVAGTIARKE 264
                                       45566666666666666677777777777766666667888888888888766 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 1.7
                                       GGG--EEEEE-SS-EEEEE-- CS
                            HSDR_N 169 frYlqfgvisngketrfyakt 189
                                       f Y++++v  + +e++++ak 
  gi|313126296|ref|YP_004036566.1| 301 FDYVAMYVTGDVREVKYFAKV 321
                                       889999***********9985 PP

>> DUF1978  Domain of unknown function (DUF1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   5.4   2.7e-05     0.095      83     212 ..     134     257 ..     110     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                           DUF1978  83 eelekesskkNqkeleeaekellkalkd.lkdqeierveeRlkelealYpevseskeeteaqekvelevdLetalgs 158
                                       ++++ +   +N   le ++ke +++ k     +++ + +  +++l+     v es+ et  +e  +l++dLe+   +
  gi|313126296|ref|YP_004036566.1| 134 VQFDLDDLAENPDVLELLTKESIRSGKSdEVAEQVAQTNRAIRHLQENEDSVTESVTETVENEVGDLTIDLEEQSRE 210
                                       566666677888999999999999866504455556666779*********************************** PP

                           DUF1978 159 iEeeyrevvrdQedywKeeekkelersaElrekgtkvkseEleeqlesleellk 212
                                         +++++v+r+Q  ++ ee   e        e++ +  s+++++++e le+++ 
  gi|313126296|ref|YP_004036566.1| 211 FVQNLVSVLREQRHFVSEEPPGE-------SEEDDEPESDDAADEIEPLENRVA 257
                                       *******************9999.......666777777999999999998875 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.8e-05      0.21       8      55 ..     133     179 ..     131     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.8e-05
                                       HHHHHHHHHHH-HHHHHHHHHHHHS-TT--TTS--SS-.THHHHHHHH CS
                         TetR_C_29   8 lveftfdyhaanpefvrLvsiEnlhrgrhlkksesirelnspliekle 55 
                                       +v+f  d +a+np+++ L++ E++ +g++ +  e++++  +++i++l+
  gi|313126296|ref|YP_004036566.1| 133 VVQFDLDDLAENPDVLELLTKESIRSGKSDEVAEQVAQ-TNRAIRHLQ 179
                                       68889999******************************.556666665 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.019        68       9      31 ..       2      24 ..       1      40 [. 0.78
   2 ?   -1.8   0.0       1.6   5.9e+03      34      52 ..      86     104 ..      79     111 .. 0.68
   3 ?    6.9   1.4    0.0031        11       3      69 ..     154     220 ..     153     228 .. 0.70
   4 ?   -0.5   0.2      0.62   2.2e+03      16      32 ..     207     228 ..     191     256 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.019
                                      -HHHHHHHHHHHHHHHHHHHCS- CS
                              FliT  9 dWdelaaleaerqqlverlreld 31
                                      d de+ + ++++qql+e+  ++d
  gi|313126296|ref|YP_004036566.1|  2 DRDEIDEHVQRCQQLIESSPQMD 24
                                      67999************988888 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                       T--HHHHHHHHHHHHHHHH CS
                              FliT  34 plspaereekrellrrila 52 
                                        l+++e +++r  +r+ l+
  gi|313126296|ref|YP_004036566.1|  86 TLTDDEVQQLRSYMRQELD 104
                                       5677777777777776555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0031
                                       HHHHCT-HHHHHHHHHHHHHHHHHHHCS--ST--HHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHH CS
                              FliT   3 eaAragdWdelaaleaerqqlverlreldaaplspaereekrellr.....rilandaeirallqprldelq 69 
                                       e +r+g+ de+a+++a+  +++ +l+e++     ++ +e  +e  +       ++++++ r+ +q   + l+
  gi|313126296|ref|YP_004036566.1| 154 ESIRSGKSDEVAEQVAQTNRAIRHLQENE-----DSVTESVTETVEnevgdLTIDLEEQSREFVQNLVSVLR 220
                                       6799*************************.....33333333333333334556666666666666655555 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.62
                                       HHHH.HHHHHHHHHCS-....- CS
                              FliT  16 leae.rqqlverlreld....a 32 
                                       + +e  q+lv  lre++    +
  gi|313126296|ref|YP_004036566.1| 207 QSREfVQNLVSVLREQRhfvsE 228
                                       2233234444444444466551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2295.59
//
Query:       gi|313126297|ref|YP_004036567.1|  [L=271]
Description: hypothetical protein Hbor_15520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-21   76.4   0.0    2.9e-21   75.2   0.0    1.6  2  DisA_N    DisA bacterial checkpoint controller nucleotide-bin


Domain annotation for each model (and alignments):
>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.35   6.2e+03      99     108 ..      38      47 ..      32      60 .. 0.59
   2 !   75.2   0.0   1.6e-25   2.9e-21       6     118 ..     142     261 ..     137     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.35
                                       SEEEEE-TTT CS
                            DisA_N  99 alvivVSeet 108
                                         v+vV +e+
  gi|313126297|ref|YP_004036567.1|  38 TPVVVVASEN 47 
                                       4444444442 PP

  == domain 2  score: 75.2 bits;  conditional E-value: 1.6e-25
                                       HHHHHT--EEEEEESSSC.........CCTTCCTSEEEEEE--HHHHHHHTSTTSTTCSSEEEE.ETTEEEEEEEEE CS
                            DisA_N   6 elskkkiGaliviereee.........lkeiietgvkldaevskellkeifekksplhDGAvii.rdgrivaagviL 72 
                                       + ++k +Gal+v++++ +          + + ++ v++ +++ + +lke+     + +DGA+ii ++g+iv+a ++L
  gi|313126297|ref|YP_004036567.1| 142 GQKGKPVGALFVVGDAGKvmnksrplsYNPFEKSHVHVGDPIVNVMLKEF-----SRLDGAFIIsDSGKIVSAYRYL 213
                                       567899***********9666666643357778999**************.....*********88*********** PP

                                       --.TT-TTS.ST-SHHHHHHHHHHHHSSSEEEEE-TTTS-EEEEETTE CS
                            DisA_N  73 pl.senkel.kelGtRHraAlgiseetdalvivVSeetgkislakdgk 118
                                       ++ +e  ++ k+lG+RH a+++i+++t+a++iv Se++g ++ +k+g+
  gi|313126297|ref|YP_004036567.1| 214 EPaAEGVDIpKGLGARHMAGAAITRDTNATTIVLSESDGLVRAFKGGQ 261
                                       **777778988***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1784.61
//
Query:       gi|313126298|ref|YP_004036568.1|  [L=283]
Description: small-conductance mechanosensitive channel [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-15   55.8   1.4    4.5e-15   55.8   1.4    2.8  4  MS_channel  Mechanosensitive ion channel
    7.5e-08   32.2   3.2    1.2e-06   28.3   0.3    4.0  5  TM_helix    Conserved TM helix
  ------ inclusion threshold ------
        1.3    8.7   9.3       0.14   11.9   4.5    1.7  2  DUF443      Protein of unknown function (DUF443)
        8.9    5.9   5.7         29    4.3   1.1    2.5  2  TMEM100     Transmembrane protein 100
        9.4    5.8  10.6        2.4    7.8   1.3    2.6  2  CPP1-like   Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.14   4.9e+02       7      33 ..      45      71 ..      40      90 .. 0.74
   2 ?   -0.8   0.3      0.25   9.1e+02       2      24 ..      97     119 ..      96     128 .. 0.83
   3 ?   -3.2   0.1       1.4     5e+03       7      28 ..     134     155 ..     129     156 .. 0.63
   4 !   55.8   1.4   1.3e-18   4.5e-15       4     105 ..     174     278 ..     172     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHHHTTT--SCCHHHHHHH CS
                        MS_channel  7 liivvgilivlsllgvnvsallavlGa 33
                                      li++v+ ++v   lg  +  +l++lG+
  gi|313126298|ref|YP_004036568.1| 45 LIVLVAGVAVALILGTLTRRVLTGLGV 71
                                      677777777777888888888888886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.25
                                       .HHHHHHHHHHHHHHHHTTT--S CS
                        MS_channel   2 kilkiliivvgilivlsllgvnv 24 
                                       +++++ ++ ++il++ls  +vn 
  gi|313126298|ref|YP_004036568.1|  97 WLVRYFVVGIAILAALSIANVNY 119
                                       57899999999999999998885 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHTTT--SCCHH CS
                        MS_channel   7 liivvgilivlsllgvnvsall 28 
                                       l ++v+iliv  ++g +v  l+
  gi|313126298|ref|YP_004036568.1| 134 LFFAVVILIVGIVVGDKVELLV 155
                                       5566677776666666665555 PP

  == domain 4  score: 55.8 bits;  conditional E-value: 1.3e-18
                                       HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHH....HHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEE CS
                        MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglal....glalkdlisnlvaGiillfekpfkiGDlveigdieGtV 76 
                                        k++++ ++ li+ls+lgv + al+  l+a  +a+    g+a+ d++++ +aG  ll+++p+ iGD +++gd  G+V
  gi|313126298|ref|YP_004036568.1| 174 AKFTVFYLASLIALSQLGVATMALVIFLAAYLFAIvflgGIAFADMLKSGAAGTYLLLTQPYAIGDEIRVGDTGGIV 250
                                       6899******************************96666779*********************************** PP

                                       EEE-SSEEEEEETTSEEEEEEHHHHHTS- CS
                        MS_channel  77 ediglrttkirtfdgrivtiPnsslvtsn 105
                                       +++ l++t++++ dg++ ++Pn++++++ 
  gi|313126298|ref|YP_004036568.1| 251 QEVDLFVTHVED-DGEEYIVPNRKVFEEG 278
                                       **********75.899********99875 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2   4.8e-05      0.17      19      47 ..      43      71 ..      25      73 .. 0.91
   2 ?   -2.9   1.0         2   7.1e+03      18      19 ..     102     103 ..      93     117 .. 0.44
   3 !   28.3   0.3   3.5e-10   1.2e-06       2      40 ..     119     157 ..     118     164 .. 0.87
   4 ?   -2.5   3.5       1.4   5.2e+03      20      31 ..     196     207 ..     194     214 .. 0.86
   5 ?    0.2   0.3      0.21   7.7e+02      20      37 ..     206     223 ..     204     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.8e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                          TM_helix 19 gAilILlvGwiiAkfvsrlvtkllaktgi 47
                                       A+++L+ G  +A ++  l++++l+ +g+
  gi|313126298|ref|YP_004036568.1| 43 FALIVLVAGVAVALILGTLTRRVLTGLGV 71
                                      69***********************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2
                                       HH CS
                          TM_helix  18 vg 19 
                                       ++
  gi|313126298|ref|YP_004036568.1| 102 FV 103
                                       33 PP

  == domain 3  score: 28.3 bits;  conditional E-value: 3.5e-10
                                       XXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix   2 plnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtk 40 
                                       ++  ++++++ flP L+ A++IL+vG +++  v  lv  
  gi|313126298|ref|YP_004036568.1| 119 YADRFWSQVVEFLPMLFFAVVILIVGIVVGDKVELLVAE 157
                                       56789**************************99998865 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHH CS
                          TM_helix  20 AilILlvGwiiA 31 
                                       A++I+l +++ A
  gi|313126298|ref|YP_004036568.1| 196 ALVIFLAAYLFA 207
                                       999**9999988 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHH CS
                          TM_helix  20 AilILlvGwiiAkfvsrl 37 
                                       +++++l G   A +++ +
  gi|313126298|ref|YP_004036568.1| 206 FAIVFLGGIAFADMLKSG 223
                                       7899*********99876 PP

>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2      0.55     2e+03      67      83 ..      50      66 ..      44      73 .. 0.70
   2 ?   11.9   4.5     4e-05      0.14      68     181 ..     103     216 ..      74     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.55
                            DUF443 67 lalGsavllgnllrkli 83
                                       ++++a++lg+l+r+++
  gi|313126298|ref|YP_004036568.1| 50 AGVAVALILGTLTRRVL 66
                                      45566889999999876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4e-05
                            DUF443  68 alGsavllgnllrklidvfniqlsklvnliillivlllvlvlriyiskklkkklynevelekkskekiilipkslkn 144
                                       ++G+  +l++l  + +++ +   s++v ++ +l   +++l++ i++  k+++ + +++  +  +  +i +ip   k+
  gi|313126298|ref|YP_004036568.1| 103 VVGI-AILAALSIANVNYADRFWSQVVEFLPMLFFAVVILIVGIVVGDKVELLVAERL--RGVKLPQIGIIPAAAKF 176
                                       3343.4577777788888888899999999999999999***********99999987..57888899999*99999 PP

                            DUF443 145 fllllfaylfflglvi..lalvali.etqniiilivllll 181
                                        +++l   + +  l +  +alv ++  +   i+++  + +
  gi|313126298|ref|YP_004036568.1| 177 TVFYLASLIALSQLGVatMALVIFLaAYLFAIVFLGGIAF 216
                                       9999998887766655005555555444444555544444 PP

>> TMEM100  Transmembrane protein 100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.017        62      59      73 ..      42      56 ..      36      66 .. 0.85
   2 ?    4.3   1.1     0.008        29      59      71 ..     135     147 ..     130     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.017
                           TMEM100 59 PfgvvvLvaGvvvta 73
                                       f+ +vLvaGv+v+ 
  gi|313126298|ref|YP_004036568.1| 42 WFALIVLVAGVAVAL 56
                                      699********9975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.008
                           TMEM100  59 PfgvvvLvaGvvv 71 
                                        f+vv+L++G+vv
  gi|313126298|ref|YP_004036568.1| 135 FFAVVILIVGIVV 147
                                       59*********98 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.0     0.011        38     143     168 ..      39      64 ..       6     103 .. 0.68
   2 ?    7.8   1.3   0.00067       2.4     141     194 ..     130     183 ..     103     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                         CPP1-like 143 ravlltlvgLvvGlllGsllasllqv 168
                                       r v ++l++Lv+G++++ +l +l + 
  gi|313126298|ref|YP_004036568.1|  39 RDVWFALIVLVAGVAVALILGTLTRR 64 
                                       44556666666666666666665544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00067
                         CPP1-like 141 lgravlltlvgLvvGlllGsllasllqvd...valsglsseellvslvtlvllwlvs 194
                                       ++  + +++v L+vG+++G  ++ l+ +    v l+   +   + ++  + +++l+s
  gi|313126298|ref|YP_004036568.1| 130 FLPMLFFAVVILIVGIVVGDKVELLVAERlrgVKLP---QIGIIPAAAKFTVFYLAS 183
                                       6666889****************9998877665444...444555666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1978.99
//
Query:       gi|313126299|ref|YP_004036569.1|  [L=345]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-13   49.9   0.0    9.8e-13   48.6   0.0    1.7  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    1.1e-08   35.3   0.0    3.9e-08   33.5   0.0    1.9  2  PAS_9            PAS domain
    2.8e-05   24.3   0.1    8.5e-05   22.8   0.0    1.9  2  PAS_4            PAS fold
    0.00058   19.8   0.1     0.0011   18.9   0.1    1.5  1  HATPase_c_2      Histidine kinase-like ATPase domain
     0.0018   18.3   0.0     0.0066   16.4   0.0    2.0  1  PAS_8            PAS domain
     0.0023   18.2   0.0      0.027   14.7   0.0    2.3  2  PAS_3            PAS fold
     0.0025   17.7   0.0     0.0064   16.4   0.0    1.6  1  HATPase_c_5      GHKL domain
     0.0043   17.0   1.1     0.0089   16.0   1.1    1.6  1  HisKA            His Kinase A (phospho-acceptor) domain
     0.0062   16.1   0.0      0.011   15.4   0.0    1.4  1  HisKA_4TM        Archaeal 4TM region of histidine kinase
  ------ inclusion threshold ------
      0.019   14.6   0.9      0.042   13.6   0.9    1.6  1  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
      0.021   13.9   0.5      0.026   13.6   0.5    1.1  1  Pox_F11          Poxvirus F11 protein
      0.023   14.7   0.1      0.088   12.8   0.0    2.0  2  PAS              PAS fold
      0.035   12.9   0.2      0.035   12.9   0.2    1.6  2  FA_desaturase_2  Fatty acid desaturase
        0.1   12.1   0.1       0.14   11.6   0.1    1.2  1  ECH_2            Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.8   7.4e+03      71      86 ..      97     113 ..      80     162 .. 0.65
   2 !   48.6   0.0   7.7e-16   9.8e-13       6     109 ..     243     343 ..     239     345 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.8
                                       STSSSHHHHHHHH.HHH CS
                         HATPase_c  71 gggtGlGlsivkk.lve 86 
                                        +g+G+ + i     ve
  gi|313126299|ref|YP_004036569.1|  97 VFGRGFAAPIIADsTVE 113
                                       56666666655433333 PP

  == domain 2  score: 48.6 bits;  conditional E-value: 7.7e-16
                                       HHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS..TTCHHCSTCHTSTSSSHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfe..kfsqddstkrggggtGlGls 79 
                                       L  +i  +++Nav ++  +++ ++v++++++d++ + + DnG+G+p+++++++f+   ++q       + gtG++l 
  gi|313126299|ref|YP_004036569.1| 243 LATAIEAVLENAVTHNDaDDPVVRVSVEVHDDHVILAIADNGPGVPESQRDLIFGreEYDQ------LHHGTGISLF 313
                                       67788999*******44355566777777789**********************9666666......889******* PP

                                       HHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlp 109
                                        ++++ + ++Geiwve+++ rG  f ++l 
  gi|313126299|ref|YP_004036569.1| 314 FADSVFDSYDGEIWVEDNDPRGAIFKMRLE 343
                                       ****9999*****************99885 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0     3e-11   3.9e-08       5     102 ..      29     122 ..      25     124 .. 0.93
   2 ?   -1.7   0.0       2.7   3.5e+03      41      57 ..     181     197 ..     164     241 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3e-11
                             PAS_9   5 lidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                       li +p++ ++ ++N++ l+llGy + e++g s  ++  +d++  e++ + l +g+   +++  + ++k g  ++ + 
  gi|313126299|ref|YP_004036569.1|  29 LIADPNF-VIrDVNPGCLDLLGYESGELVGESAATIA-GDDRIYEDVVEHLSRGE--TWTGRFIAQTKAGANVFGRG 101
                                       6788***.999**************************.*****************..******************** PP

                             PAS_9  81 taspvkdddgelvgiivilrDi 102
                                        a+p++ d+ ++ g+i+i++D 
  gi|313126299|ref|YP_004036569.1| 102 FAAPIIADS-TVEGVIAIFVDT 122
                                       *****9775.89999*****95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.7
                             PAS_9  41 vtdpeanerlraaleqg 57 
                                       v+++e++++lr++le+ 
  gi|313126299|ref|YP_004036569.1| 181 VHKSERARDLRNLLERS 197
                                       47777777777777765 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   6.6e-08   8.5e-05       2     108 ..      22     125 ..      21     127 .. 0.88
   2 ?   -2.2   0.0       3.8   4.9e+03      42      70 ..     230     261 ..     220     269 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.6e-08
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                        s+ ++ ++ dp+++++++N+   +l+g++  el+G++ a ++ +   +r+ +++ + l+ +e+++   +  +  g+
  gi|313126299|ref|YP_004036569.1|  22 RSTEAPALIADPNFVIRDVNPGCLDLLGYESGELVGESAATIAGD---DRIYEDVVEHLSRGETWTGRFIAQTkAGA 95 
                                       67889999********************************99887...78888888888888888888888888999 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTer 108
                                        ++   ++ P+  ++ +v gv++i++D+  +
  gi|313126299|ref|YP_004036569.1|  96 NVFGRGFAAPI-IADSTVEGVIAIFVDTAKQ 125
                                       99999999**9.578889*******998765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.8
                             PAS_4  42 ellpee...daarleralrrvlegeepiefle 70 
                                       +++pe    + + l++a+++vle   ++ +++
  gi|313126299|ref|YP_004036569.1| 230 QVFPEVivrADDLLATAIEAVLENAVTHNDAD 261
                                       46666666566677888888888888777665 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     9e-07    0.0011      35     121 ..     246     338 ..     230     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9e-07
                       HATPase_c_2  35 aveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvD 110
                                       a+e ++ Nav+h+  ++p   v+v++e+ ++ + + +aD+Gpg  + +     + ee+++     G+ l++  +++D
  gi|313126299|ref|YP_004036569.1| 246 AIEAVLENAVTHNDADDP--VVRVSVEVHDDHVILAIADNGPGvPESQRDLIFGREEYDQLHHGTGISLFFADSVFD 320
                                       4555677********999..88888889***************6555555556677778888888888888888888 PP

                       HATPase_c_2 111 ev..ey.....dgegnvv 121
                                       ++  e+     d++g + 
  gi|313126299|ref|YP_004036569.1| 321 SYdgEIwvednDPRGAIF 338
                                       875544565555555555 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.2e-06    0.0066       3      45 ..      17      60 ..      16      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.2e-06
                             PAS_8  3 lralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell 45
                                      +r +f s   + +++d +   i+dvN+  l+llGy+  +l ge  
  gi|313126299|ref|YP_004036569.1| 17 YREAFRSTEAPALIADpNFV-IRDVNPGCLDLLGYEsGELVGESA 60
                                      78899999999999*96655.***************666655544 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.1e-05     0.027       3      75 ..      39     106 ..      37     119 .. 0.85
   2 ?    0.6   0.0      0.55     7e+02      17      42 ..     168     193 ..     164     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvi 75 
                                        v++ + ++lGy++ el g     +  +  +D  r++e++ e+l++ge ++g +  ++k G  +  +  a +i
  gi|313126299|ref|YP_004036569.1|  39 DVNPGCLDLLGYESGELVGE---SAATIAGDD--RIYEDVVEHLSRGETWTGRFIAQTKAGANVFGRGFAAPI 106
                                       589*****************...788888888..9*******************9999999877776666666 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.55
                             PAS_3  17 eellgkveswldlvhpeDrervreal 42 
                                       e+l++  +++l++vh  +r+r  ++l
  gi|313126299|ref|YP_004036569.1| 168 ESLEKAQDKILEIVHKSERARDLRNL 193
                                       455555899********999877765 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     5e-06    0.0064       9      92 ..     246     333 ..     239     342 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5e-06
                       HATPase_c_5   9 ilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ekkkle..sskskkeehGiGlk..sireiv 78 
                                        +  +L+NA+   ++   +++++r++v+ +++++i+ i  +  g   +++ l    ++ ++ +hG+G++    +++ 
  gi|313126299|ref|YP_004036569.1| 246 AIEAVLENAVTHNDA---DDPVVRVSVEVHDDHVILAIADNGPGvpeSQRDLIfgREEYDQLHHGTGISlfFADSVF 319
                                       444556666654333...58****************99988666443333332456677888999997622579*** PP

                       HATPase_c_5  79 kkykgnlsieaedg 92 
                                       ++y+g++++e +d 
  gi|313126299|ref|YP_004036569.1| 320 DSYDGEIWVEDNDP 333
                                       ********998875 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.1     7e-06    0.0089       9      56 ..     139     195 ..     133     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7e-06
                                       HHHHHHHHHHHHHHHHHHHHC.........T-HSSCHHHHHHHHHHHH..HHHHHHH CS
                             HisKA   9 vaHELrtPLsailgnaeaLkre.......gklteelkeyletiesear..rldhlve 56 
                                       + H+Lr+ L++++g ++  + e       ++l   + + le++++++r   l++l+e
  gi|313126299|ref|YP_004036569.1| 139 LRHDLRNELNVMYGHIQRAQSEssidevtESLEKAQDKILEIVHKSERarDLRNLLE 195
                                       78*****************99888866665555666668888888877665555554 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.3e-06     0.011     125     159 ..     120     154 ..     101     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.3e-06
                         HisKA_4TM 125 adasrakrisdalafvndlirhdlrndlvvirgya 159
                                        d+++ ++  +a   +n l+rhdlrn+l+v+ g+ 
  gi|313126299|ref|YP_004036569.1| 120 VDTAKQQQYENASEVLNRLLRHDLRNELNVMYGHI 154
                                       477788888999999***************98865 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.9   3.2e-05     0.042       4      55 ..     126     172 ..     122     180 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                            SPOB_a   4 eeikelkeliklL.rsqRHDflNhLQvIsGylqLgkydkaeeyieevvkelke 55 
                                       +   + ++  ++L r +RHD  N+L v +G +q  +    e+ i+ev++ l++
  gi|313126299|ref|YP_004036569.1| 126 Q---QYENASEVLnRLLRHDLRNELNVMYGHIQRAQ---SESSIDEVTESLEK 172
                                       3...4455555555669**************98544...44556666666655 PP

>> Pox_F11  Poxvirus F11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5     2e-05     0.026     220     294 ..     112     190 ..     107     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                           Pox_F11 220 vedivkarveLE.ksrfeitkel..rtllkelneryndvyadmikl.seeivdeilkrlekaadsaladvkavrkak 292
                                       ve ++   v+   + ++e + e+  r l + l+++ n +y  + ++ se ++de+   leka+d++l  v++ ++a+
  gi|313126299|ref|YP_004036569.1| 112 VEGVIAIFVDTAkQQQYENASEVlnRLLRHDLRNELNVMYGHIQRAqSESSIDEVTESLEKAQDKILEIVHKSERAR 188
                                       666666677766235677777776777888888899999998876626889****************9999999988 PP

                           Pox_F11 293 sk 294
                                       + 
  gi|313126299|ref|YP_004036569.1| 189 DL 190
                                       63 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.9e-05     0.088       3      73 ..      17      84 ..      16     121 .. 0.83
   2 ?   -1.9   0.1       2.5   3.3e+03      40      79 ..     133     168 ..     128     203 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-05
                                      HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-EC CS
                               PAS  3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesr 73
                                      +r+ + s+ +p ++ D + +i  vN+   +llG++  e++g+s    i  +d+   +e + ++l+ ge ++
  gi|313126299|ref|YP_004036569.1| 17 YREAFRSTEAPALIADPNFVIRDVNPGCLDLLGYESGELVGESAA-TIAGDDR--IYEDVVEHLSRGETWT 84
                                      6778889999*********************************99.9999988..7777777766666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                                       HCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS  40 evlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       evl++ l +++ +e    l+  +    ++++es++ e+++
  gi|313126299|ref|YP_004036569.1| 133 EVLNRLLRHDLRNE----LNVMYGHIQRAQSESSIDEVTE 168
                                       56666665555555....4444444444444444444433 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   2.8e-05     0.035     237     307 ..     120     191 ..     112     210 .. 0.86
   2 ?   -2.7   0.4       1.5     2e+03     181     222 ..     240     281 ..     236     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                   FA_desaturase_2 237 rdgkdeelFeefsavaqrlgvYtardyldileelikkWkieel.eglsgegrrardyvcalperlrrvaera 307
                                        d+ +++++e+ s+v +rl  ++ r+ l+++   i++ + e+  ++++++ ++a+d+++++ ++ +r+ +  
  gi|313126299|ref|YP_004036569.1| 120 VDTAKQQQYENASEVLNRLLRHDLRNELNVMYGHIQRAQSESSiDEVTESLEKAQDKILEIVHKSERARDLR 191
                                       489999*************************9999999888655********************99998865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                   FA_desaturase_2 181 dellakicgaiaadEkrHeaaYtrvvekllevdpdeavlala 222
                                       d+lla+ ++a+ ++   H+ a   vv+  +ev  d+++la+a
  gi|313126299|ref|YP_004036569.1| 240 DDLLATAIEAVLENAVTHNDADDPVVRVSVEVHDDHVILAIA 281
                                       788999999999999999999999999999999999999987 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00011      0.14     139     244 ..      77     176 ..      73     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                       HHCSSTTHHHHHHHH---B-HHHHHHTTS--EE--GGGHHHHHHHHHTT.........--------......----S CS
                             ECH_2 139 LsrlpgelGlylalTGarlkgadalaaglathyvpseklealeeaLaelessd.eeaveevleelaeeaeeeeeese 214
                                       Lsr +  +G+++a T     ga+++  g+a  ++ ++ +e + + + ++ +++  e+ +evl++l ++  +    +e
  gi|313126299|ref|YP_004036569.1|  77 LSRGETWTGRFIAQTK---AGANVFGRGFAAPIIADSTVEGVIAIFVDTAKQQqYENASEVLNRLLRHDLR----NE 146
                                       6666677777777665...4899999***************999999887766689999999999865554....67 PP

                                       HHHHHHHHHHHT.-S-TTTHHHHHH.T..- CS
                             ECH_2 215 laekreaidrlfsadsveeiveaLekaeae 244
                                       l+    +i+r+ s++s++e+ e+Leka+++
  gi|313126299|ref|YP_004036569.1| 147 LNVMYGHIQRAQSESSIDEVTESLEKAQDK 176
                                       877899*******************74433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2195.11
//
Query:       gi|313126300|ref|YP_004036570.1|  [L=180]
Description: acyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-10   40.4   6.9    5.9e-09   35.3   0.2    3.0  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
    3.4e-10   39.5   5.4    4.2e-09   36.0   0.1    2.8  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.11   9.5e+02      19      26 ..      67      74 ..      67      75 .. 0.63
   2 !    7.6   0.1   0.00035       3.2      20      34 ..      90     104 ..      90     106 .. 0.89
   3 !   35.3   0.2   6.6e-13   5.9e-09       2      36 .]     119     153 ..     118     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.11
                                      TEEE-TTE CS
                           Hexapep 19 nVkIGdnv 26
                                      +V++G++v
  gi|313126300|ref|YP_004036570.1| 67 GVTVGSGV 74
                                      56777666 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00035
                                       EEE-TTEEEETTEEE CS
                           Hexapep  20 VkIGdnvkIgagvvi 34 
                                       V++Gd+v++g  +vi
  gi|313126300|ref|YP_004036570.1|  90 VTLGDDVIVGYDSVI 104
                                       899*******99998 PP

  == domain 3  score: 35.3 bits;  conditional E-value: 6.6e-13
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       +vIG+ ++Ig+ avi+++V+IG+++ ++a++ +++
  gi|313126300|ref|YP_004036570.1| 119 VVIGDRAMIGAKAVILPGVHIGEDAQVAANSLVTR 153
                                       79*****************************9985 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.15   1.3e+03      23      30 ..      67      74 ..      66      75 .. 0.57
   2 !    5.1   0.1    0.0022        19      18      27 ..      90      99 ..      89     105 .. 0.57
   3 !   36.0   0.1   4.7e-13   4.2e-09       2      34 .]     119     153 ..     118     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                                      T-EE-TT- CS
                         Hexapep_2 23 ncvvgaGv 30
                                      +++vg+Gv
  gi|313126300|ref|YP_004036570.1| 67 GVTVGSGV 74
                                      35566665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0022
                                      EEE-TT-EE- CS
                         Hexapep_2 18 vslGdncvvg 27
                                      v+lGd+++vg
  gi|313126300|ref|YP_004036570.1| 90 VTLGDDVIVG 99
                                      4566666655 PP

  == domain 3  score: 36.0 bits;  conditional E-value: 4.7e-13
                                       EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                       v IGd+ +iGa a+i  Gv++G+++ v+a++ +t+
  gi|313126300|ref|YP_004036570.1| 119 VVIGDRAMIGAKAVIlpGVHIGEDAQVAANSLVTR 153
                                       89*****************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1187.39
//
Query:       gi|313126301|ref|YP_004036571.1|  [L=430]
Description: phosphoribosylamine--glycine ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-54  184.4   0.2    2.7e-54  183.9   0.2    1.2  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
    9.8e-22   77.6   0.2    2.2e-21   76.4   0.1    1.6  2  GARS_N       Phosphoribosylglycinamide synthetase, N domain
      1e-14   54.6   0.1    6.1e-14   52.1   0.1    2.2  2  GARS_C       Phosphoribosylglycinamide synthetase, C domain
     0.0003   20.9   0.0    0.00059   19.9   0.0    1.4  1  ATP-grasp_3  ATP-grasp domain
  ------ inclusion threshold ------
       0.04   13.4   0.0       0.13   11.7   0.0    1.8  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
      0.077   12.2   0.0       0.16   11.2   0.0    1.5  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp
       0.17   11.5   0.4       0.58    9.7   0.4    2.0  1  ATP-grasp_4  ATP-grasp domain


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.2   1.1e-57   2.7e-54       1     194 []     105     292 ..     105     292 .. 0.94

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 1.1e-57
                                       HBHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TT CS
                            GARS_A   1 asKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkf 76 
                                       ++K+f ++++++ gip+  ++++f+d+e+a+eyi+e + +   vK++gl++gKgv+v+ ++  + + +ke l++  +
  gi|313126301|ref|YP_004036571.1| 105 TDKAFQREFMAEEGIPGCpDFSVFEDTEAACEYIDEYDGDL-AVKPAGLTGGKGVKVTGDQ-VTKAEAKEYLRESDY 179
                                       69**************987*********************9.9**************9765.455567888886555 PP

                                       CCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHHHHHH CS
                            GARS_A  77 GeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteellekikee 149
                                           e+vv+Ee+l GeE++++a+v + +v+p+p++qdhkr++egD+gpnTGGmG+ys     +p++t e++++++e 
  gi|313126301|ref|YP_004036571.1| 180 ----EEVVLEERLVGEEFTVQAFVANGDVRPTPAVQDHKRAYEGDEGPNTGGMGSYSdsvaELPFMTFEDYTEAVE- 251
                                       ....69**************************************************9888899************9. PP

                                       THHHHHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
                            GARS_A 150 ileptveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                                       +le tv++l++    +kGvLy+++ml++dg kv+efn+RfgDpe+
  gi|313126301|ref|YP_004036571.1| 252 VLEATVDALDD----YKGVLYGQFMLTADGVKVIEFNARFGDPEA 292
                                       *********74....8***************************97 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.1   8.8e-25   2.2e-21       4      90 .]       6     104 ..       4     104 .. 0.89
   2 ?   -3.8   0.0         7   1.8e+04      54      64 ..     378     388 ..     372     396 .. 0.63

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 8.8e-25
                                       EEEESSHHHHHHHHHHTTSTTESEEEEEE.--CGG............TTHHHHHHHHHHCTESEEEE-SHHHHHTTH CS
                            GARS_N   4 LvvGsGGRehalawklaqspkvekvyvap.gNagt............edlealvefakeekidlvvvGpeapLvaGv 67 
                                       L+vG+GGReha+a++l+ sp++e   +a  +N+g+            + ++++v++a+e ++d++v+Gpe+ L aGv
  gi|313126301|ref|YP_004036571.1|   6 LLVGGGGREHAIARALTASPDCELYACASnRNPGIaslsagfrqvseTAADDIVAYATEVGADVAVIGPESALEAGV 82 
                                       99********************955555579999999998888776544567************************* PP

                                       HHHHHHHHT-EEES--CCCCHHH CS
                            GARS_N  68 adaleeekgikvfGpskeaAqlE 90 
                                       adal+++ g+ +fGp++e A++E
  gi|313126301|ref|YP_004036571.1|  83 ADALDDA-GVYTFGPQAEDARIE 104
                                       ****777.**************9 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7
                                       EEEE-SHHHHH CS
                            GARS_N  54 lvvvGpeapLv 64 
                                       ++vvG e+ ++
  gi|313126301|ref|YP_004036571.1| 378 FAVVGVEDTIA 388
                                       55666665554 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.79     2e+03      38      59 ..     153     172 ..     119     182 .. 0.74
   2 !   52.1   0.1   2.4e-17   6.1e-14       1      79 [.     326     413 ..     326     414 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.79
                                       -SSEEEEEEEEESSHHHHHHHH CS
                            GARS_C  38 sGGRvlavvavgetleeAraka 59 
                                       +GG+ + v++ +  +++A+ak 
  gi|313126301|ref|YP_004036571.1| 153 TGGKGVKVTGDQ--VTKAEAKE 172
                                       677776666655..55554444 PP

  == domain 2  score: 52.1 bits;  conditional E-value: 2.4e-17
                                       EEEEEEEETTTTSS--ST-EEBS.....TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB CS
                            GARS_C   1 avgvvlaskGYPgsyekgkeitg.....egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkik 67 
                                       +v+ +++++GYP+++  g++i+      +++ +f+a++      l+t+ +R +avv+v++t++eA+++a++++++  
  gi|313126301|ref|YP_004036571.1| 326 TVCKYAVPDGYPTDPDDGAQIEVdeenvGDALLFYASVDarddgLYTTTSRSFAVVGVEDTIAEAEKAAEAGLSAA- 401
                                       69*******************87999998889*****9899999******************************87. PP

                                       -TTEE--STTTH CS
                            GARS_C  68 feglfyRkDIGa 79 
                                        egl +R+DIG+
  gi|313126301|ref|YP_004036571.1| 402 GEGLRIRHDIGK 413
                                       69*********7 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.3e-07   0.00059       3     159 ..     106     288 ..     105     290 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-07
                                       SHHHHHHHHTTT.S-.--...........-EESS--SSSEEEEESS-------B--SS--TTE.............. CS
                       ATP-grasp_3   3 dKlktykkLkeagvk.vP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve....... 64 
                                       dK +  +++ e+g++ +P       t++  e ++e +  l vKp+   gg++v v  ++ ++ +a e++        
  gi|313126301|ref|YP_004036571.1| 106 DKAFQREFMAEEGIPgCPdfsvfedTEAACEYIDEYDGDLAVKPAGLTGGKGVKVTGDQVTKAEAKEYLResdyeev 182
                                       666667777777665466776665555556666667889999***999**999999888888777777778889999 PP

                                       EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET.............TEEEEEEES----H...HHHHHHHHHHHHT CS
                       ATP-grasp_3  65 lvqefieGkplSvsllsdgekvlvlavnrqliekaeke.........fvyaGnvtpietel...keevvelaeevve 129
                                       ++ e + G++++v++ + + +v++    + +    e +          +y+ +v++ +        e+ve+ e +v 
  gi|313126301|ref|YP_004036571.1| 183 VLEERLVGEEFTVQAFVANGDVRPTPAVQDHKRAYE-GdegpntggmGSYSDSVAELPFMTfedYTEAVEVLEATVD 258
                                       **************9998889988654444433322.1357887777666666655443222237788888888888 PP

                                       TSTT--EEEEEEEEESS.SEEEEEEESS-- CS
                       ATP-grasp_3 130 kleglaGyvGvDlvlkdeepyviEvNPRlt 159
                                       +l + +G++   ++l+ ++  viE N+R+ 
  gi|313126301|ref|YP_004036571.1| 259 ALDDYKGVLYGQFMLTADGVKVIEFNARFG 288
                                       888888888889****************95 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.2e-05      0.13       1      63 [.     106     167 ..     106     192 .. 0.81
   2 ?   -1.8   0.0      0.73   1.9e+03     154     180 ..     263     287 ..     232     293 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeel 63 
                                       Dk   +e +++ ++p  p +++  e++e a +  +e+     +k+a   GGkG +v  ++ + 
  gi|313126301|ref|YP_004036571.1| 106 DKAFQREFMAEEGIPGCPDFSV-FEDTEAACEYIDEYDGDLAVKPAGLTGGKGVKVTGDQVTK 167
                                       78888999***********999.9*******************************98775433 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.73
                                       -EEEEEEEEEEETTTTEEEEEEEESS- CS
                       CPSase_L_D2 154 vvgagtveflldpkskeyyviEvNtRl 180
                                       ++g    +f+l +  +   viE N+R 
  gi|313126301|ref|YP_004036571.1| 263 YKGVLYGQFMLTA--DGVKVIEFNARF 287
                                       5555556788875..778899999996 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.4e-05      0.16      47      99 ..     129     181 ..      97     199 .. 0.69
   2 ?   -3.8   0.0       2.3   5.8e+03     250     266 ..     272     287 ..     265     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.4e-05
                       ATPgrasp_ST  47 aeiseleafvkeleegvviKpakgsgGkGilviteredqdylkssgksallde 99 
                                       ++ +++ +++ e++ ++++Kpa   gGkG+ v  ++ ++   k+  ++ +++e
  gi|313126301|ref|YP_004036571.1| 129 EDTEAACEYIDEYDGDLAVKPAGLTGGKGVKVTGDQVTKAEAKEYLRESDYEE 181
                                       6677888999999888***************9966555555555444444444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.3
                       ATPgrasp_ST 250 vldeekgplllElNarp 266
                                        l++++ + ++E Nar 
  gi|313126301|ref|YP_004036571.1| 272 MLTADG-VKVIEFNARF 287
                                       677777.99*****985 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00023      0.58      43      78 ..     171     204 ..     156     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00023
                       ATP-grasp_4  43 eeykeevveeesflvEeyieGeEfavdayfdeeGep 78 
                                       +ey +   + e++++Ee + GeEf v a++  +G  
  gi|313126301|ref|YP_004036571.1| 171 KEYLR-ESDYEEVVLEERLVGEEFTVQAFV-ANGDV 204
                                       33443.3578999****************9.77754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2649.97
//
Query:       gi|313126302|ref|YP_004036572.1|  [L=711]
Description: prolyl oligopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-62  209.3   0.0    7.8e-62  208.5   0.0    1.3  1  Peptidase_S9    Prolyl oligopeptidase family
      9e-59  199.3   0.0    1.1e-58  199.0   0.0    1.1  1  Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propel
     0.0012   18.2   0.1     0.0046   16.3   0.0    1.8  2  Hydrolase_4     Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.5   0.0   1.3e-65   7.8e-62       9     209 ..     505     708 ..     498     710 .. 0.97

  Alignments for each domain:
  == domain 1  score: 208.5 bits;  conditional E-value: 1.3e-65
                                       HHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH- CS
                      Peptidase_S9   9 lladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqr 85 
                                       +l + G v +van+rG+g++Ge++h+ag+r+++q+ fdDf+aaae+l+++gy+++erla++GgS+GG+l+ga ++qr
  gi|313126302|ref|YP_004036572.1| 505 FL-ESGGVLAVANLRGGGEFGESWHHAGRREHKQRVFDDFFAAAEHLVENGYTSTERLACFGGSNGGLLVGASITQR 580
                                       45.89************************************************************************ PP

                                       GGG-SEEEEESE---CCCHHCSTTSTHH.HCCCC--TTTCHHHHHHHHHH-CGGG--..---EEEEEEETT-SSS-T CS
                      Peptidase_S9  86 pdlFkaavaevpvvdvlrydsdtdllte.eymewgnpeeneegykelspyspldnvk..aypplLlihGlaDdrvpp 159
                                       pdlF+aav++vp +d+lr++++  ll+e +++e+g p +++e y+++ +ysp++nv+  ayp++L+++G+ D+rv p
  gi|313126302|ref|YP_004036572.1| 581 PDLFAAAVCKVPLLDMLRFHTS--LLGEtWTTEYGSP-DDPEAYEYIREYSPYHNVEerAYPAVLFTTGESDSRVDP 654
                                       **********************..59999********.99999********************************** PP

                                       HHHHHHHHHHH..--S-S.EEEEEETTS-SSTTSSHHHH.HHHHHHHHHHHHHC CS
                      Peptidase_S9 160 aealklvaaLq..kkgkn.vlllifpdegHgvgkprakv.eelarllaFlkeal 209
                                        +a k++a++q  + g + +ll++  + gHg+gkp +kv ee  ++++Fl ++l
  gi|313126302|ref|YP_004036572.1| 655 FHARKMAARMQaaQSGADpILLKTRSQTGHGSGKPVSKVvEENLDEWSFLGDQL 708
                                       ***********99899999*******************************9887 PP

>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.0   0.0   1.8e-62   1.1e-58       1     413 [.      34     440 ..      33     441 .. 0.90

  Alignments for each domain:
  == domain 1  score: 199.0 bits;  conditional E-value: 1.8e-62
                                       ------TT.EEEETTEEEE-TTGGGGSTTSHHHHHHHHHHHHHHHHHHCTST.CHHHHHHHHHHHT-S-EE---EEE CS
                    Peptidase_S9_N   1 PetardesvvdelhgdkvsDpYrWLeDddspetkayleaenkyteevlaqlkelrekikeeitklikeddisapfrk 77 
                                       Pet ++++   +lh+d + DpY WLe+ d +++ a+  a+n+y++++l++l  +re ++ ++++l  ++ +    ++
  gi|313126302|ref|YP_004036572.1|  34 PETDQRDT-GYTLHDDDIDDPYLWLEETD-DDVSAWTAAQNDYADDYLDSLD-IRESLRPRFEDLARTTTYMPVKAR 107
                                       45555555.679**************976.79********************.**************9999777667 PP

                                       TTEEEEEEE-SS-SS-EEEEECSTS-TTS-EEEEE-GGGGSTTS-.EEEEEEEE-TTSSEEEEEEEETTSSEEEEEE CS
                    Peptidase_S9_N  78 gkyyyysrneggknqsvlyrqdalskegeeeevlLDpNtlsedgtfvalgefavsedgkllAyslsksGsdwytirv 154
                                       ++ y+    + + +++vl  ++ l    e+ +vl DpN++s+dg+ v+++ +  ++dg+l+Ay++ ++G+++y +rv
  gi|313126302|ref|YP_004036572.1| 108 QNGYFQRVRDADADHPVLTFRPGL---NEDRRVLGDPNEMSDDGS-VSVDWYVPNPDGSLVAYGVAEGGDEQYDVRV 180
                                       777777778999*********877...3467**************.******************************* PP

                                       EETTTTEEEEEEEEEEESEE...EEECTTSSEEEEEESS-SSS-TSTSB-S-BEEEEEETTS-GGG-EEEES-TTGT CS
                    Peptidase_S9_N 155 kdietgedlpdeledvkfsg...ivWaadekgffYtrydkedersdtdtnlnqkvyrhkLGtaqseDelvfeeeeep 228
                                        + e+ge +++el+dv  +g   + W++d  gf+Y +      + +    l+++v++h++Gt+  +D  ++ e   +
  gi|313126302|ref|YP_004036572.1| 181 LETESGE-TAEELTDVGRTGpwcFGWTDD--GFYYLTTGSVGDGGQ----LEKEVCFHEIGTDPADDWTLADEFSTQ 250
                                       ******9.89999999988765589**99..******885555555....9*********************999** PP

                                       TBEEEEEE-TTSSEEEEEEESSSS--EEEEEEGGGTSS--EEEEESSSSS-EEEEEEETTEEEEEE-TT-TT-EEEE CS
                    Peptidase_S9_N 229 kwllgaersedgkylfissasgtdtnelyvldlekeskkvlklvdnrfdaeysvehnegdrfliltndgapnfrlvs 305
                                       +w l +e ++   y+++   +g++ ++ly+++l +++    +lv + +da ++     g++ ++ t  +a n+r+vs
  gi|313126302|ref|YP_004036572.1| 251 TWPL-VETDAESDYVILGHTEGWERTDLYYAELGSDE--LHPLVVG-EDALFEPTLD-GNDVYVNTSLDASNYRVVS 322
                                       **99.88888888***********************5..9******.9999999888.9****************** PP

                                       EETT..SSSGG...............GEEEEE--.SSCEEEEEEECTTEEEEEEEETTEEEEEEEETTTS-.EEEEE CS
                    Peptidase_S9_N 306 vdln..dpsps...............ewkelvperekvvleeitvfknylvvsyrkdvlsrvqvvdlkngkvllfev 365
                                       v l+  d  ps                ++++v+er++ +++e +v ++++vv y++d+ +++ v+d  +g+    +v
  gi|313126302|ref|YP_004036572.1| 323 VSLDavD--PSasptdvgesstdpnkPFETVVAERDDAIAQELDVIGDRIVVKYLRDAVHELVVFD-ADGE-QDETV 395
                                       ****554..444588999999999988999************************************.6677.79*** PP

                                       B-SSSSEEEEEE--TT-SEEEEEEEETTCEEEEEEEETTTTCEEEEEE CS
                    Peptidase_S9_N 366 plpgvgsvssasgekedselfysfsSfltPstiykldlatgelellke 413
                                       plpg gsv s+ ge+   +lf+ ++Sf++P++i ++ +  +e++++ +
  gi|313126302|ref|YP_004036572.1| 396 PLPGRGSVASFGGED---DLFFTYESFTEPPSIRRYAFGADETTVVDQ 440
                                       ***********9664...48****************999999998865 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.6e-07    0.0046      42     112 ..     523     595 ..     497     608 .. 0.86
   2 ?   -1.3   0.0      0.18   1.1e+03     193     220 ..     639     667 ..     629     670 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.6e-07
                       Hydrolase_4  42 hGrsegkrghvpsfddyvdDlaafvekvkeehpel..plfllGhSmGGliallyllrypdkvaglilsaPalk 112
                                       +G+s  + g+ ++ +++ dD+ a+ e+++e+  ++  +l ++G S GGl++ + ++++pd +a++++  P+l+
  gi|313126302|ref|YP_004036572.1| 523 FGESWHHAGRREHKQRVFDDFFAAAEHLVENGYTSteRLACFGGSNGGLLVGASITQRPDLFAAAVCKVPLLD 595
                                       566779999999*****************87776668***********************999*999888876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.18
                       Hydrolase_4 193 P.llllhGeaDkvvdpeasrelyerlgsk 220
                                       P +l+  Ge+D  vdp  +r++++r++++
  gi|313126302|ref|YP_004036572.1| 639 PaVLFTTGESDSRVDPFHARKMAARMQAA 667
                                       4389999***************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 4400.43
//
Query:       gi|313126303|ref|YP_004036573.1|  [L=475]
Description: hypothetical protein Hbor_15580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-10   40.2  25.5    1.9e-06   27.6   8.5    3.5  3  PQQ_2       PQQ-like domain
      7e-08   32.0  11.5      0.077   13.0   0.0    5.4  6  PQQ         PQQ enzyme repeat
     0.0011   19.3  28.9        4.2    8.0   0.3    9.0  7  PQQ_3       PQQ-like domain
  ------ inclusion threshold ------
        0.1   12.9   0.1       0.24   11.7   0.1    1.6  1  PH_6        Pleckstrin homology domain


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   8.5   4.3e-10   1.9e-06      32     150 ..      97     251 ..      71     253 .. 0.78
   2 !   16.6   3.3     1e-06    0.0045       4     146 ..     234     357 ..     231     360 .. 0.70
   3 !   14.2   5.1   5.5e-06     0.024       3     138 ..     344     474 ..     342     475 .] 0.70

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.3e-10
                             PQQ_2  32 avlsggtlfva....tgggrlvaldaatGkvlWettlegpvvga..............plvaegrvvvva..sdg.. 86 
                                        + ++g lf++    +g   ++a+d+++ +v+W+t+ +g++v+                +++ + v+ va  +d+  
  gi|313126303|ref|YP_004036573.1|  97 NT-GDGILFTTlrrdGGNSAVAAVDPSDASVRWRTKMDGEAVSGshaafqriargqwgATLTAETVYSVAgnADEre 172
                                       34.678888888887789999****************9999988899**********99*******99998877788 PP

                             PQQ_2  87 ..qlialdaedGkrlWstqqrseepaelrssaspava.........gdtvvvges.....sgklvaldpkdGkvlWe 147
                                         +l+ald  +G+r Ws ++++ + a +++s+   va          +t v +++        +++ld++dG v+W 
  gi|313126303|ref|YP_004036573.1| 173 wtELYALDRSNGERRWSLKRDR-KLAVAGVSDGLLVAtgleffpppNETPVSHQTpeeplTTVVYGLDVTDGAVRWT 248
                                       99***************66666.44444555555555667777777555555555799999999************9 PP

                             PQQ_2 148 rel 150
                                       re 
  gi|313126303|ref|YP_004036573.1| 249 REF 251
                                       975 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1e-06
                             PQQ_2   4 vvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvv 80 
                                       vv+ ld ++Ga+ W+ +    +++ ++ av +   ++va  g+rl +l   +G+  ++++ +gp++ + +va++r++
  gi|313126303|ref|YP_004036573.1| 234 VVYGLDVTDGAVRWTRE----FTAVRDVAV-GPEGIYVA-AGDRLLGLG-RDGETQFTVD-DGPAKWI-EVADERLF 301
                                       6899************5....788888888.55556666.899999997.9999999999.9998888.99999999 PP

                             PQQ_2  81 vvasdg...qlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlW 146
                                       + a++g   +l ++   +G+  W  ++          + +  ++gd++++g+    + a+d +dG v W
  gi|313126303|ref|YP_004036573.1| 302 FLAGEGdgaTLHGVA-PNGDGDWK-HDVP--------VEELLLDGDRLYAGG--DSVLAVD-ADGTVAW 357
                                       999555336666666.99999999.5555........334444455555554..3444444.4444444 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5.5e-06
                             PQQ_2   3 gvvsaldaatGaelWrvdlarplgggvsravlsggtlfvat..gggrlvaldaatGkvlWettlegpvvgaplvaeg 77 
                                       ++v a+da +G++ Wr d     ++ +    ++g+tl++++  + +  +a++ + G+ +W++++++ +  + + a  
  gi|313126303|ref|YP_004036573.1| 344 DSVLAVDA-DGTVAWRDDN--YGQWLL--LDPDGDTLYTRSgvRADAATAYS-TAGEKRWTFDPPSNNAWP-EAATA 413
                                       6788***8.8*******97..345666..4459*******633556677776.89*********9985555.55555 PP

                             PQQ_2  78 rvvvvasdgqlialdaedG.krlWstqqrse.epaelrssaspava.gdtvvvgessgklvald 138
                                        ++v++   +++a d++d  k+++ +++++e   a  r +  +av+ +dtv++++  ++l al 
  gi|313126303|ref|YP_004036573.1| 414 DAMVAT---AITADDSDDLfKTVYAVDSAGEaTAAFGRDTVFDAVGrDDTVYLADGQSNLLALT 474
                                       554554...4555555554355666566665344447778888888999999999999999986 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         2   8.8e+03      22      34 ..     126     138 ..     125     140 .. 0.78
   2 !   13.0   0.0   1.7e-05     0.077       9      25 ..     173     189 ..     171     191 .. 0.90
   3 !   10.9   0.1     8e-05      0.36       9      25 ..     232     248 ..     228     254 .. 0.88
   4 !    5.2   0.4    0.0048        21       4      28 ..     340     361 ..     337     363 .. 0.78
   5 !    6.6   0.1    0.0018       8.1      19      35 ..     392     408 ..     388     411 .. 0.84
   6 ?   -2.5   0.0       1.4   6.2e+03      11      17 ..     432     438 ..     431     441 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                                       EEEEEESSSCGSS CS
                               PQQ  22 vlWrfktggpvls 34 
                                       v+Wr+k +g+ +s
  gi|313126303|ref|YP_004036573.1| 126 VRWRTKMDGEAVS 138
                                       79*9998888776 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.7e-05
                                       TSEEEEEETTTCCEEEE CS
                               PQQ   9 dGylyAlDadTGkvlWr 25 
                                       ++ lyAlD+++G+ +W+
  gi|313126303|ref|YP_004036573.1| 173 WTELYALDRSNGERRWS 189
                                       678*************8 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 8e-05
                                       TSEEEEEETTTCCEEEE CS
                               PQQ   9 dGylyAlDadTGkvlWr 25 
                                        +++y lD+++G v+W+
  gi|313126303|ref|YP_004036573.1| 232 TTVVYGLDVTDGAVRWT 248
                                       678*************8 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.0048
                                       EEEETTSEEEEEETTTCCEEEEEES CS
                               PQQ   4 ylgsadGylyAlDadTGkvlWrfkt 28 
                                       y+g  +  ++A+D ++G+v Wr ++
  gi|313126303|ref|YP_004036573.1| 340 YAG--GDSVLAVD-ADGTVAWRDDN 361
                                       555..33699***.*******9875 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0018
                                       TCCEEEEEESSSCGSSE CS
                               PQQ  19 TGkvlWrfktggpvlsl 35 
                                        G+++W+f+++++  + 
  gi|313126303|ref|YP_004036573.1| 392 AGEKRWTFDPPSNNAWP 408
                                       4**********999886 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 1.4
                                       EEEEEET CS
                               PQQ  11 ylyAlDa 17 
                                       ++yA+D 
  gi|313126303|ref|YP_004036573.1| 432 TVYAVDS 438
                                       6899993 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.7      0.16   7.1e+02      14      39 ..      93     122 ..      76     123 .. 0.78
   2 ?    4.7   0.0      0.01        46       3      38 ..     126     181 ..     125     183 .. 0.73
   3 ?    3.0   0.0     0.035   1.6e+02       1      28 [.     184     210 ..     184     220 .. 0.85
   4 !    5.7   0.4    0.0047        21       1      30 [.     243     270 ..     243     315 .. 0.82
   5 !    8.0   0.3   0.00093       4.2       5      39 ..     323     352 ..     319     356 .. 0.76
   6 ?   -1.2   0.2      0.73   3.3e+03      20      29 ..     371     380 ..     353     390 .. 0.61
   7 !    5.7   1.7    0.0049        22      18      36 ..     455     473 ..     393     475 .] 0.65

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.16
                             PQQ_3  14 nsspavdgglvyvgtg....dGtlyAlDae 39 
                                       + ++ +++g+++++      +  + A+D+ 
  gi|313126303|ref|YP_004036573.1|  93 TNATNTGDGILFTTLRrdggNSAVAAVDPS 122
                                       455578999999998898889999999986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                             PQQ_3   3 vlWsvqlpgpvnssp..............avdgglvyvgtg......dGtlyAlDa 38 
                                       v+W+++ +g+++s+               ++   +vy ++g         lyAlD 
  gi|313126303|ref|YP_004036573.1| 126 VRWRTKMDGEAVSGShaafqriargqwgaTLTAETVYSVAGnadereWTELYALDR 181
                                       79***999955554447788766666665555668999999888888889999986 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.035
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgt 28 
                                       Ge++Ws + + ++ + + v++gl+++++
  gi|313126303|ref|YP_004036573.1| 184 GERRWSLKRDRKL-AVAGVSDGLLVATG 210
                                       8999999999776.77888999998765 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0047
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgd 30 
                                       G v+W++++ + v + +av+   +yv++gd
  gi|313126303|ref|YP_004036573.1| 243 GAVRWTREFTA-V-RDVAVGPEGIYVAAGD 270
                                       899*******6.3.5566666666666663 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.00093
                             PQQ_3   5 WsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       W++++p +    +++dg+++y+g++  ++ A+Da+
  gi|313126303|ref|YP_004036573.1| 323 WKHDVPVE---ELLLDGDRLYAGGD--SVLAVDAD 352
                                       66666633...4799********95..77777774 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 0.73
                             PQQ_3  20 dgglvyvgtg 29 
                                       dg+++y+ +g
  gi|313126303|ref|YP_004036573.1| 371 DGDTLYTRSG 380
                                       5677776655 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.0049
                             PQQ_3  18 avdgglvyvgtgdGtlyAl 36 
                                       +  +++vy ++g+ +l Al
  gi|313126303|ref|YP_004036573.1| 455 VGRDDTVYLADGQSNLLAL 473
                                       3347888888888888887 PP

>> PH_6  Pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.4e-05      0.24      32      73 ..      82     125 ..      71     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                              PH_6  32 esaed.aheviawAsetGkGLLffskkedka.spsgvinLadas 73 
                                       +s+e  +  +++ A++tG+G+Lf +  +d   s++++++ +das
  gi|313126303|ref|YP_004036573.1|  82 DSTEVaTATNTTNATNTGDGILFTTLRRDGGnSAVAAVDPSDAS 125
                                       4555446678999**********998666544777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2985.20
//
Query:       gi|313126304|ref|YP_004036574.1|  [L=725]
Description: hypothetical protein Hbor_15590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-74  247.6   0.1    7.5e-74  247.1   0.1    1.2  1  Thioredox_DsbH  Protein of unknown function, DUF255
    9.2e-10   38.6   0.0    1.8e-09   37.7   0.0    1.5  1  Thioredoxin_7   Thioredoxin-like
    0.00066   19.0   0.0       0.44    9.7   0.0    2.3  2  GlcNAc_2-epim   N-acylglucosamine 2-epimerase (GlcNAc 2-epime
  ------ inclusion threshold ------
      0.038   13.1   0.0       0.22   10.5   0.0    2.0  2  Glyco_hydro_88  Glycosyl Hydrolase Family 88


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.1   0.1   1.7e-77   7.5e-74       1     162 [.       7     171 ..       7     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 247.1 bits;  conditional E-value: 1.7e-77
                    Thioredox_DsbH   1 knrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvk 77 
                                       +nrla+e+spYl+qha+npv+W+pw+e a+e+a+e+d+pi+ls+GysachWChvm++esfed++vaa+lnesfv+vk
  gi|313126304|ref|YP_004036574.1|   7 RNRLADEQSPYLQQHADNPVNWQPWDETAIEAAREKDRPIFLSVGYSACHWCHVMADESFEDDDVAAVLNESFVPVK 83 
                                       69*************************************************************************** PP

                    Thioredox_DsbH  78 vDreerPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregr...pgflevlekiaelweeereel 151
                                       vDreerPdld+iy++++q++tg ggWPl+v+ltp++kpf+ gtYfpkeer +r   pgfl+++++ ae+we++ree+
  gi|313126304|ref|YP_004036574.1|  84 VDREERPDLDRIYQTICQLVTGGGGWPLSVWLTPQGKPFYVGTYFPKEERRDRgnvPGFLDLCRSFAEAWENDREEI 160
                                       **********************************************99877544449******************** PP

                    Thioredox_DsbH 152 eeeaeelleal 162
                                       e++a+++++a+
  gi|313126304|ref|YP_004036574.1| 161 ENRAQQWTAAI 171
                                       ******99887 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   3.9e-13   1.8e-09       2      65 ..      28      91 ..      27     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.9e-13
                                      --SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-G CS
                     Thioredoxin_7  2 wlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterda 65
                                      w+ + ++a ++a+e+ +p+++ +g s c+ C++++++  +d++v+a+l+e fv ++vd +er +
  gi|313126304|ref|YP_004036574.1| 28 WQPWDETAIEAAREKDRPIFLSVGYSACHWCHVMADESFEDDDVAAVLNESFVPVKVDREERPD 91
                                      99999*****************************99999999****9************99875 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   9.9e-05      0.44      39     125 ..     235     325 ..     228     337 .. 0.54
   2 !    6.8   0.0   0.00078       3.5      90     183 ..     437     531 ..     430     540 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.9e-05
                                       TTHHHHHHHHHHHTTTTTB.-TTTSSB-SEEETTEEEE-..-EEHHHHH...HHHHHHHHHHTTT-TTHHHHHHHHH CS
                     GlcNAc_2-epim  39 pgwldlvehGlkflekvlr.daehggyfsalrdggvlda..skdaYdha...Fvllalasalaageeeakdlldetl 109
                                       ++ l+++ + l+++++ +  d+  gg+ + ++d++   +  +k +Yd a    v la+     +g+ +++++++et+
  gi|313126304|ref|YP_004036574.1| 235 DEPLTVAMETLDAMAGGGMyDHVGGGFHRYATDRQWTVPhfEKMLYDNAeipRVYLAAHR--LTGRADYAEVARETF 309
                                       455555666666666554434444455555555543333114556666654444444433..466666666666666 PP

                                       HHHHHHTEETTTTEE- CS
                     GlcNAc_2-epim 110 avlekhlweekaglvk 125
                                       +++ ++l++++ g++ 
  gi|313126304|ref|YP_004036574.1| 310 DFVARELRHPDGGFFS 325
                                       6666666666666554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00078
                                       HHHHHTTT-TTHHHHHHHHHHHHHHHTEETTTTEE--EE-T.TSS-BEEHHHHHHHHHHHHHHHHTT-BTHHHHHHH CS
                     GlcNAc_2-epim  90 lasalaageeeakdlldetlavlekhlweekaglvkeesdk.efsklrgsnpnMhlleAmLalaeatgdkeylerae 165
                                       la+ + ++ +e+++l++++l +  +hlw+e +g +   ++  +++ +   +    l      l++atgd  +l+ a 
  gi|313126304|ref|YP_004036574.1| 437 LAQGALVLGDEYAELAADALGFAREHLWDESEGRLSRRFKDgDVKGEGYLEDYAFLARGAFDLYQATGDVDHLAFAV 513
                                       68888899999********************998877765504444433344455666677799************* PP

                                       HHHHHHTTTTGGGGTT-- CS
                     GlcNAc_2-epim 166 eiaelvisefadaesglv 183
                                       e+a+ +++ f+d   g++
  gi|313126304|ref|YP_004036574.1| 514 ELAREIVASFYDDAAGTL 531
                                       ********9999887765 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     5e-05      0.22      57     118 ..     264     325 ..     220     341 .. 0.71
   2 ?   -0.9   0.0      0.15   6.6e+02      33     162 ..     491     520 ..     482     537 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5e-05
                                       HHHHCCCTTS-.CTTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B.TTS.B.S CS
                    Glyco_hydro_88  57 wadslideggk.telelDdidigllllllyeltkderykeaaeeladyvlakpprtseGgfwh 118
                                       +a + ++++ + +++  D+++i  ++l+ ++lt++ +y e a+e +d  +a++ r  +Ggf+ 
  gi|313126304|ref|YP_004036574.1| 264 YATDRQWTVPHfEKMLYDNAEIPRVYLAAHRLTGRADYAEVARETFD-FVARELRHPDGGFFS 325
                                       55555666655888999******************************.6667777799**986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-CTTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS- CS
                    Glyco_hydro_88  33 vflsglleayeatgdkeyldyakawadslideggktelelDdidigllllllyeltkderykeaaeeladyvlakpp 109
                                       ++ +g  ++y+atgd + l++a + a++                                                 
  gi|313126304|ref|YP_004036574.1| 491 FLARGAFDLYQATGDVDHLAFAVELAREI------------------------------------------------ 519
                                       55666677777777777666655544433................................................ PP

                                       B.TTS.B.SBTTSTTEEETHHHHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHH CS
                    Glyco_hydro_88 110 rtseGgfwhkkkepeqlWlDgLfMaipllaklskvtgepkyldeaikqfllta 162
                                                                                            
  gi|313126304|ref|YP_004036574.1| 520 ----------------------------------------------------V 520
                                       ....................................................2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (725 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4889.99
//
Query:       gi|313126305|ref|YP_004036575.1|  [L=271]
Description: hypothetical protein Hbor_15600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1736.88
//
Query:       gi|313126306|ref|YP_004036576.1|  [L=166]
Description: thioredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-05   23.0   0.0    9.4e-05   22.3   0.0    1.3  1  Thioredoxin      Thioredoxin
    0.00042   20.2   0.0    0.00058   19.8   0.0    1.4  1  AhpC-TSA         AhpC/TSA family
  ------ inclusion threshold ------
       0.13   12.2   3.3        1.8    8.5   0.2    2.3  2  DUF2816          Protein of unknown function (DUF2816)
       0.14   12.6   0.1       0.28   11.7   0.1    1.5  1  Peptidase_M15_4  D-alanyl-D-alanine carboxypeptidase
       0.16   12.3   0.1        3.3    8.1   0.0    2.2  2  Thioredoxin_8    Thioredoxin-like


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.6e-08   9.4e-05       8      91 ..      59     151 ..      54     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.6e-08
                                       HHHHHHHTT.TSSEEEEEEE.-TTSHHHHCHHHHHHHHHHHCTT...TSEEEEEETT....TSHHHHHHTT-SSSSE CS
                       Thioredoxin   8 enFeeevak.ekklvlveFy.ApwCghCkalaPeleklaeelkd...kvklakvdvd....enedlakkyevegiPt 75 
                                       +++e++v+  +++ ++ + +  +wC  C++  P ++++ ++ +    +v  + v+ +    +   l+++y++e+iPt
  gi|313126306|ref|YP_004036576.1|  59 DSYEDTVETlSEDGLVFKVWgGDWCKDCRNQLPDFAAALDAAEVpdeRVEHYPVEKEddgsKTGPLVEEYDIEYIPT 135
                                       66788887764555555666269*************9977666555877777775541111566799********** PP

                                       EEEEETTEEEEEEESS CS
                       Thioredoxin  76 lklfkngkevkkyega 91 
                                       +++ ++g+ev+++++ 
  gi|313126306|ref|YP_004036576.1| 136 VVVERDGEEVARFVED 151
                                       ********99998765 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.6e-07   0.00058      20      56 ..      65     101 ..      50     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.6e-07
                                       CHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCC CS
                          AhpC-TSA  20 lsdykgkpvvlffypkdwcpvCttelpalaklyeefk 56 
                                       +++++ + +v+ ++ +dwc+ C+++lp++a+++++ +
  gi|313126306|ref|YP_004036576.1|  65 VETLSEDGLVFKVWGGDWCKDCRNQLPDFAAALDAAE 101
                                       45677789***********************987654 PP

>> DUF2816  Protein of unknown function (DUF2816)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.011        39      48      59 ..     104     115 ..     100     117 .. 0.81
   2 ?    8.5   0.2    0.0005       1.8      24      38 ..     127     141 ..     125     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.011
                           DUF2816  48 derveYqpvers 59 
                                       derve +pve++
  gi|313126306|ref|YP_004036576.1| 104 DERVEHYPVEKE 115
                                       799999999986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0005
                           DUF2816  24 eyqteYiPqviqekr 38 
                                       ey+ eYiP v++e+ 
  gi|313126306|ref|YP_004036576.1| 127 EYDIEYIPTVVVERD 141
                                       8***********986 PP

>> Peptidase_M15_4  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.7e-05      0.28      30      61 ..      54      85 ..      32      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.7e-05
                   Peptidase_M15_4 30 kpengeayadevvkifkklGf...eWGgdWksfkD 61
                                      + ++++ y ++ v+ + + G+    WGgdW   kD
  gi|313126306|ref|YP_004036576.1| 54 PAWDADSY-EDTVETLSEDGLvfkVWGGDW--CKD 85
                                      44555555.688888899997779******..666 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.066   2.4e+02       9      24 ..      79      94 ..      73     108 .. 0.81
   2 ?    8.1   0.0   0.00091       3.3      65      91 ..     111     140 ..     101     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.066
                                      --SSSHHHHHHHHHHH CS
                     Thioredoxin_8  9 gaswcppckaftpklk 24
                                      g +wc++c++ +p   
  gi|313126306|ref|YP_004036576.1| 79 GGDWCKDCRNQLPDFA 94
                                      568******9988765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00091
                                       EE-TT-....HHHHTT-S--TT-SEEEEE-T CS
                     Thioredoxin_8  65 pfddkk....rnklkkkynvkaiPtlvvldk 91 
                                       p+++++    +  l ++y+++ iPt+vv  +
  gi|313126306|ref|YP_004036576.1| 111 PVEKEDdgskTGPLVEEYDIEYIPTVVV-ER 140
                                       554443333356889**********665.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1061.65
//
Query:       gi|313126307|ref|YP_004036577.1|  [L=340]
Description: cysteine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-61  208.2   0.4    2.2e-61  207.8   0.4    1.0  1  PALP        Pyridoxal-phosphate dependent enzyme
    7.7e-05   22.7   0.0    0.00017   21.5   0.0    1.5  1  ADH_zinc_N  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.8   0.4   2.5e-65   2.2e-61       7     282 ..      10     272 ..       6     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 207.8 bits;  conditional E-value: 2.5e-65
                                       S--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   7 pTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaallGlk 80 
                                       ++Plv++ + +   g+ + +K Es np+gS KdR a  ++++++++    +++ +ve +sGN+g++l+++aa+ G++
  gi|313126307|ref|YP_004036577.1|  10 GSPLVEVSSPE---GATVAAKVESKNPGGSAKDRPALAMIEAAERAgeiSPGDELVEPTSGNTGIGLSMVAAAKGYD 83 
                                       57888887765...888*************************999999***************************** PP

                                       EEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHTT. CS
                              PALP  81 vtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEileqlg. 155
                                        ti +p++ spe+++ +r++Ga++++v+gd  +a+++a el+ae  g++ + qf+n+++  + y t++ Eileq+g 
  gi|313126307|ref|YP_004036577.1|  84 MTIIMPSSQSPERRDIMRAYGATIELVDGDISDAKDRADELEAE--GMTQLRQFENEANPRAhYRTTAEEILEQIGd 158
                                       ********************************************..******************************* PP

                                       TTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHH CS
                              PALP 156 gkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafel 232
                                       + +da+v++vG+Gg+i+Gi+  l+e++p+ ++++vep++++ l ++          +++   +g++   p+     l
  gi|313126307|ref|YP_004036577.1| 159 RTVDALVAGVGTGGTISGIGSRLREEFPEMEIVAVEPAENAVLSTGE---------SGSDDYQGMG---PGFVSPNL 223
                                       **************************************999999999.........3445555555...55777777 PP

                                       HSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCC CS
                              PALP 233 ldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagel 282
                                        ++l+d+++ v+ e+a + +r+lar+egi+v+ ss+a+  a+  r a++l
  gi|313126307|ref|YP_004036577.1| 224 DRDLLDDVIPVPLEDAEAECRRLAREEGILVGQSSGASNLAA-RRVAERL 272
                                       7888888889***********************777776666.4655555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     2e-08   0.00017       1      91 [.      70     181 ..      70     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2e-08
                                       HHHHHHHHHHHHTT-EEEE.EESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHT...................TT CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaevia.vdsseeklelakklGadevinykea.dlverikelt...................gg 56 
                                       g+Gl  v++Ak + +++i+  + s+e++++++ +Ga+  +   +  d ++r  el                      
  gi|313126307|ref|YP_004036577.1|  70 GIGLSMVAAAKGYDMTIIMpSSQSPERRDIMRAYGATIELVDGDIsDAKDRADELEaegmtqlrqfeneanprahYR 146
                                       8**************99999***************885555535556666666666666889999998888777645 PP

                                       SSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC.T CS
                        ADH_zinc_N  57 egvdvvfecvGsgatleaalkllkpgGrlvvvGg.g 91 
                                         +  ++e +G  +t++a ++ +  gG++  +G  +
  gi|313126307|ref|YP_004036577.1| 147 TTAEEILEQIG-DRTVDALVAGVGTGGTISGIGSrL 181
                                       57888******.*********************732 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2297.23
//
Query:       gi|313126308|ref|YP_004036578.1|  [L=290]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-27   95.3   0.1    2.7e-20   73.1   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    1.2e-24   88.2   5.4    1.4e-24   87.9   5.4    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.9e-15   56.8   0.0    4.2e-15   55.7   0.0    1.6  1  Hydrolase_4    Serine aminopeptidase, S33
      0.003   17.5   0.1          1    9.2   0.1    2.5  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
     0.0032   16.2   0.0      0.015   14.0   0.0    1.8  2  Ndr            Ndr family
     0.0066   16.1   0.0     0.0098   15.6   0.0    1.3  1  FSH1           Serine hydrolase (FSH1)
  ------ inclusion threshold ------
      0.012   15.3   0.1       0.02   14.5   0.1    1.3  1  Esterase       Putative esterase
      0.017   15.0   0.0        2.5    7.8   0.0    2.9  3  Abhydrolase_2  Phospholipase/Carboxylesterase
      0.019   14.7   0.0        2.7    7.7   0.0    2.2  2  Abhydrolase_5  Alpha/beta hydrolase family
       0.16   12.1   0.0       0.35   11.0   0.0    1.5  1  Abhydrolase_4  TAP-like protein


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.1   1.5e-23   2.7e-20       1     106 [.      30     130 ..      30     145 .. 0.90
   2 !   20.3   0.0   1.9e-07   0.00034     206     251 ..     206     265 ..     174     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.5e-23
                                       SEEEEE-STTTCGGG..GTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSE CS
                     Abhydrolase_1   1 pvlvilhGlpgssdv..waerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkl 75 
                                       p++v++hG++  s    w+e  l+paL + +++v+++Dl+G+g+S+ + + +    +t+ + ++l+r+l+a  +d +
  gi|313126308|ref|YP_004036578.1|  30 PPVVLIHGGGLDSAElsWCE--LIPALTD-DYRVYAIDLPGYGHSDEPERVP----TTDYYVRVLERFLEAEEIDAP 99 
                                       68888888888665558999..******9.*******************964....577788*************** PP

                                       EEEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                     Abhydrolase_1  76 tlvGhSmGGmialayaaeyperVkalvllga 106
                                       +lvG S+GG +al ya+ +pe V+a+v++++
  gi|313126308|ref|YP_004036578.1| 100 ALVGVSLGGGVALGYALGHPEDVSAVVAINS 130
                                       *****************************98 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.9e-07
                                       C..............THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                     Abhydrolase_1 206 e..............lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHl 251
                                                      l n + ptl+i+g++D+lvp + +++ ++l p++++++++ +gH+
  gi|313126308|ref|YP_004036578.1| 206 AeigftglrtnyvddLPNLSMPTLFIHGEDDKLVPSSWSVRAESLVPNSEVRILPECGHW 265
                                       244555555667666667777**************************************9 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   5.4   7.9e-28   1.4e-24       1     218 [.      32     275 ..      32     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 7.9e-28
                                       EEEE--GC.......GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS....--HHHCHHHHHHHCCTT..TTSEEEEE CS
                     Abhydrolase_6   1 vlllHGagss..assWlvapLaallaagvhvlapDlpGhGrsdppp....ldledladlaalldelaagggpvvlvG 71 
                                       v+l+HG+g++    sW   +L ++l+++++v+a+DlpG+G+sd p     +d+  ++ l+++l+++    +++ lvG
  gi|313126308|ref|YP_004036578.1|  32 VVLIHGGGLDsaELSWC--ELIPALTDDYRVYAIDLPGYGHSDEPErvptTDYY-VRVLERFLEAEE--IDAPALVG 103
                                       8*******988899999..*********************77555533334442.355588888886..9999**** PP

                                       ETCHHHHHHHHHHCC.......EE.EEES-.......----TTTS----TTHH....HHHHTT-CCCCH.CCH.... CS
                     Abhydrolase_6  72 HSlGGalalaaapla.....lvvg.vlldppp.....talpagllaaalelll....allallrllawl.sre.... 128
                                        SlGG +al    +a     +v++ v++++++     +++p+g l  ++++l     +++a+ r+ a++ +r+    
  gi|313126308|ref|YP_004036578.1| 104 VSLGGGVALG---YAlghpeDVSAvVAINSYGlgdsvPGGPLGALFVRVPYLSelswRAIARSRTVAYFaVRAivay 177
                                       **********...666667655558*****77665444555555555555555543433334444444422224444 PP

                                       ..S-HSCCCCHHH..C...CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH..STT CS
                     Abhydrolase_6 129 ..plprlfladed..a...daawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerlla..qag 195
                                           +++ ++++   a   d +  ++++r+   ++gl ++ +++++ l +p+l + g++D+lvp  +  ++   ++ 
  gi|313126308|ref|YP_004036578.1| 178 gnV-RPHVVDQVYeeAqrnDGSAWRTFQRAEIGFTGLRTNYVDDLPNLSMPTLFIhGEDDKLVPSSWSVRAEslVPN 253
                                       432.334444222211233333333333333444455566699*********88845777788866665555566** PP

                                       EEETCE...SSS-HHHHSHHHHH CS
                     Abhydrolase_6 196 arlpvvlpgaGHlphleepdeva 218
                                        ++  +lp +GH+p  e+p++v+
  gi|313126308|ref|YP_004036578.1| 254 SEV-RILPECGHWPPREQPQRVN 275
                                       ***.***************9997 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   2.3e-18   4.2e-15       7     237 ..      32     269 ..      26     271 .. 0.75

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.3e-18
                       Hydrolase_4   7 vvlvHGlaehsgrya..elaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfll 81 
                                       vvl+HG +  s   +  el+ aL++ ++ vya+D  G+G+s+ +  +vp +d yv+ l+ f+   ++e+ ++p  l+
  gi|313126308|ref|YP_004036578.1|  32 VVLIHGGGLDSAELSwcELIPALTD-DYRVYAIDLPGYGHSD-EPERVPTTDYYVRVLERFL---EAEEIDAP-ALV 102
                                       8999999988877642279999985.8**************6.45558********999996...45555555.89* PP

                       Hydrolase_4  82 GhSmGGliallyllrypdkvaglilsaPalkikakl..........kappllklllkllgkllpklqv......... 139
                                       G S+GG +al y+l +p++v++++ +++   +  ++          ++p l +l  +                    
  gi|313126308|ref|YP_004036578.1| 103 GVSLGGGVALGYALGHPEDVSAVVAINSYG-LGDSVpggplgalfvRVPYLSELSWR----------Aiarsrtvay 168
                                       ***************************995.55577445444444323333333222..........2333333455 PP

                       Hydrolase_4 140 .snnlkadslsrdpevvaayeadplvhgkitvrlll....elldamkrleeraakitlPllllhGeaDkvvdpeasr 211
                                          +   ++    p+vv+++ ++    ++  +r+++    +++ +  + +++ +++++P+l++hGe+Dk+v+ + s 
  gi|313126308|ref|YP_004036578.1| 169 fAVRAIVAYGNVRPHVVDQVYEEAQRNDGSAWRTFQraeiGFTGLRTNYVDDLPNLSMPTLFIHGEDDKLVPSSWSV 245
                                       577788888888888888888888877777776665222267888899999*********************98888 PP

                       Hydrolase_4 212 elyerlgskdktlklypglyHellnE 237
                                       ++   ++  + ++++ p++ H   +E
  gi|313126308|ref|YP_004036578.1| 246 RAESLVP--NSEVRILPECGHWPPRE 269
                                       8777777..78999999999976666 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   0.00057         1      25      54 ..     100     130 ..      81     137 .. 0.90
   2 !    6.0   0.0    0.0054       9.7     116     135 ..     226     245 ..     165     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00057
                                       EEEEETHHHHHHHHHHHHSS.SEEEEEEES- CS
                            BAAT_C  25 gllGiSkGgelalllasflk.kisavvling 54 
                                       +l+G+S Gg +al  a  ++ ++savv+in 
  gi|313126308|ref|YP_004036578.1| 100 ALVGVSLGGGVALGYALGHPeDVSAVVAINS 130
                                       79******************9********95 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0054
                                       SEEEEEEETT-SSS-HHHHH CS
                            BAAT_C 116 gpillvvgedDknwpSkesa 135
                                        p l++ gedDk++pS+ s 
  gi|313126308|ref|YP_004036578.1| 226 MPTLFIHGEDDKLVPSSWSV 245
                                       689*************9776 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   8.3e-06     0.015      12     135 ..      20     133 ..      15     139 .. 0.86
   2 ?   -0.3   0.0       0.2   3.5e+02     253     277 ..     259     283 ..     209     285 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.3e-06
                                       EEEEESS--TTS-EEEEE--TT--HHHHTHHHHHSHHHHHHHTTSEEEEEE-TT-STT-----TT-----HHHHHTT CS
                               Ndr  12 svtvqGdqeekkpvllTyhDlglnhkscFqelfnsesmaeilekfvilhvdaPGqeegaaslpedyqfpslddladq 88 
                                       s  v Gd+    p+++  h  gl++      l  +e +  +++   ++ +d PG  +  +     + +p+ d     
  gi|313126308|ref|YP_004036578.1|  20 SALVAGDPA--SPPVVLIHGGGLDSAE----LSWCELIPALTDDYRVYAIDLPGYGHSDE----PERVPTTDYYVRV 86 
                                       567888888..7888888888888766....88899999**************9876544....35699999999** PP

                                       HHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S CS
                               Ndr  89 llavldhfklksviglGvgaGAyilarfalkhperveglvLinitsk 135
                                       l+  l+  ++++   +Gv  G  + + +al hpe v+++v in  + 
  gi|313126308|ref|YP_004036578.1|  87 LERFLEAEEIDAPALVGVSLGGGVALGYALGHPEDVSAVVAINSYGL 133
                                       ******************************************98765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.2
                                       ETT-TT-HHHH-HHHHHHHHHHHHH CS
                               Ndr 253 vadsgglvleeqPdklaeslklflk 277
                                       + ++g  +  eqP+++   + lfl+
  gi|313126308|ref|YP_004036578.1| 259 LPECGHWPPREQPQRVNSLVRLFLQ 283
                                       56899999*********99999998 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.5e-06    0.0098     154     206 ..     216     270 ..     169     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
                              FSH1 154 yy..eedkiqtptLhvlGelDtvvdeerseaLaeafknsskvlkHpggHfvPnkk 206
                                        y  + +++++ptL+++Ge+D++v+++ s +    + ns+  +  + gH  P+++
  gi|313126308|ref|YP_004036578.1| 216 NYvdDLPNLSMPTLFIHGEDDKLVPSSWSVRAESLVPNSEVRILPECGHWPPREQ 270
                                       343567889****************997776666666644445555667666665 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.1e-05      0.02     117     145 ..      99     127 ..      85     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                       EEEEEETHHHHHHHHHHHCSTTTCCEEEE CS
                          Esterase 117 ravaGqSmGGlgALilalkhpdrFgsvss 145
                                        a++G S+GG +AL +al hp+  + v +
  gi|313126308|ref|YP_004036578.1|  99 PALVGVSLGGGVALGYALGHPEDVSAVVA 127
                                       69********************9988876 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.25   4.6e+02      10      30 ..      25      47 ..      21      54 .. 0.76
   2 ?    2.5   0.0      0.06   1.1e+02     108     138 ..     100     130 ..      85     136 .. 0.90
   3 ?    7.8   0.0    0.0014       2.5     156     183 ..     225     252 ..     209     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.25
                                      SS---EEEEEE--TT.--S.HHH CS
                     Abhydrolase_2 10 kdkaqavviflHGlG.dsg.haw 30
                                      +d+a++ v+++HG G ds+  +w
  gi|313126308|ref|YP_004036578.1| 25 GDPASPPVVLIHGGGlDSAeLSW 47
                                      6899999******9944444555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.06
                                       EEEEETHHHHHHHHHHHT-SS--SEEEEES- CS
                     Abhydrolase_2 108 iigGFSqGaalalylaltlpkklggivafsg 138
                                       +++G S G+ +al  al  p+ ++ +va+++
  gi|313126308|ref|YP_004036578.1| 100 ALVGVSLGGGVALGYALGHPEDVSAVVAINS 130
                                       789************************9986 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0014
                                       G-EEEEEEETT-SSS-HHHHHHHHHHHH CS
                     Abhydrolase_2 156 klpilqiHgeeDpvvplalgkaakevlk 183
                                        +p l iHge+D++vp++ + +a+ +  
  gi|313126308|ref|YP_004036578.1| 225 SMPTLFIHGEDDKLVPSSWSVRAESLVP 252
                                       479999*************999986544 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0015       2.7      55      95 ..      95     136 ..      85     147 .. 0.84
   2 ?    4.7   0.0     0.013        24      94     127 ..     219     252 ..     209     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                     Abhydrolase_5  55 klekfvvgGhslGGvvasrfaaee.ekiegvvflasYPekde 95 
                                       +++   + G slGG va  +a  + e + +vv + sY   d+
  gi|313126308|ref|YP_004036578.1|  95 EIDAPALVGVSLGGGVALGYALGHpEDVSAVVAINSYGLGDS 136
                                       556667889*************8868***********88776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.013
                     Abhydrolase_5  94 delselskkvlsivgteDgvlnvkslekakkflp 127
                                       d+l +ls+++l i g++D +++ +   +a+  +p
  gi|313126308|ref|YP_004036578.1| 219 DDLPNLSMPTLFIHGEDDKLVPSSWSVRAESLVP 252
                                       789******************9887777666655 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.35      34      93 ..     225     284 ..     201     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                     Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLlt 93 
                                       + p+L++ +e D  +P ++  ++ +  +++++ +  + GH   +++ + v+++v+ +L++
  gi|313126308|ref|YP_004036578.1| 225 SMPTLFIHGEDDKLVPSSWSVRAESLVPNSEVRILPECGHWPPREQPQRVNSLVRLFLQS 284
                                       489*****************************999*****99999999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1773.78
//
Query:       gi|313126309|ref|YP_004036579.1|  [L=349]
Description: transposase, is605 orfb family, central region [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-22   78.7   2.0    1.1e-21   76.5   0.7    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00098   19.3   0.2     0.0026   18.0   0.0    1.8  2  OrfB_IS605      Probable transposase
     0.0028   17.9   0.8     0.0055   17.0   0.8    1.5  1  C1_2            C1 domain
  ------ inclusion threshold ------
      0.067   13.1   0.6       0.12   12.3   0.6    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.069   13.2   0.1       0.14   12.2   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.17   11.8   3.8      0.097   12.6   1.3    1.9  2  PHD             PHD-finger
       0.87    9.2   2.7       0.91    9.2   0.8    2.0  2  PikAIV_N        Narbonolide/10-deoxymethynolide synthase PikA
        7.2    6.5   6.7        6.2    6.7   4.1    2.3  3  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.26   5.8e+02      42      62 ..     146     165 ..     135     169 .. 0.82
   2 !   76.5   0.7   4.8e-25   1.1e-21       1      69 []     276     342 ..     276     342 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.26
                    OrfB_Zn_ribbon  42 lsgrtfkCpnCgfeadrDvnA 62 
                                       + g+ ++C+  + e+d+D+ +
  gi|313126309|ref|YP_004036579.1| 146 RRGDDWYCT-FNIEYDADTSG 165
                                       468899**9.9999****876 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 4.8e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l++++ yka+++Gi ve v+ ++TS++Cs Cgs +++  +g+ f C++Cg   ++D+nA+ Ni++r
  gi|313126309|ref|YP_004036579.1| 276 FHQLQQFITYKAERAGIRVEAVDAYHTSQRCSACGSMGNR--DGDHFSCSECGRGRHADLNASENIAQR 342
                                       899*************************************..************************987 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       3.8   8.5e+03      70      85 ..      17      32 ..       7      36 .. 0.67
   2 !   18.0   0.0   1.2e-06    0.0026      12     101 ..     162     244 ..     142     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.8
                        OrfB_IS605 70 ykkasrklarlhrkrs 85
                                      ++k  +  arl+r  +
  gi|313126309|ref|YP_004036579.1| 17 RRKEWQHAARLYRDTK 32
                                      5677777788888766 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.2e-06
                        OrfB_IS605  12 kpkgnkaagiDlGinnLatv.vtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrr 87 
                                        + g++ +g+D+G +++++v + ++ ++ l +g ++k    y++++ + l   l++++    a r   r+ +k +rr
  gi|313126309|ref|YP_004036579.1| 162 DTSGETPIGVDIGERHILAVtAYGEDESMLVSGGEAK----YVRRKYRSLRDSLSEAG----ALRARNRVGDKEQRR 230
                                       56778889******99776625666677999996665....55555566666666665....777888999999999 PP

                        OrfB_IS605  88 rkhllhklathlik 101
                                       +k+l hkl+++li 
  gi|313126309|ref|YP_004036579.1| 231 IKDLNHKLSRRLIT 244
                                       99999999999885 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.8   2.5e-06    0.0055       2      39 ..     274     326 ..     273     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-06
                              C1_2   2 sHpHpLtls.............kgedssesfnCsaCgrkidgff..YsCseCd 39 
                                       +H H+L+ +               + ++ s +CsaCg  ++ +   +sCseC 
  gi|313126309|ref|YP_004036579.1| 274 WHFHQLQQFitykaeragirveAVDAYHTSQRCSACGSMGNRDGdhFSCSECG 326
                                       566777777777777777777666678889*********6555566******6 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   5.5e-05      0.12       3      31 ..     302     330 ..     300     335 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                       Prok-RING_1   3 tgkkCpvCgkelkeedDiVvCpeCgtpyH 31 
                                       t ++C++Cg   + + D   C eCg   H
  gi|313126309|ref|YP_004036579.1| 302 TSQRCSACGSMGNRDGDHFSCSECGRGRH 330
                                       6799*********************9888 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.2e-05      0.14      64      96 ..     297     329 ..     267     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                                       EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       ++  + + rC+ Cg+ ++ + ++++C +Cg+ +
  gi|313126309|ref|YP_004036579.1| 297 VDAYHTSQRCSACGSMGNRDGDHFSCSECGRGR 329
                                       445567889*****9999888899*****9865 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         2   4.5e+03      42      47 ..     149     154 ..     139     155 .. 0.71
   2 ?   12.6   1.3   4.3e-05     0.097       1      27 [.     305     331 ..     305     341 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2
                                       STBSST CS
                               PHD  42 gewlCe 47 
                                       ++w+C+
  gi|313126309|ref|YP_004036579.1| 149 DDWYCT 154
                                       48***6 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.3e-05
                                       SBTTTTSTTSTTSCEEEETTTSCEEET CS
                               PHD   1 rCavCkkksdeeeelvqCdgCkrwfHq 27 
                                       rC++C++  + +++  +C +C+r  H 
  gi|313126309|ref|YP_004036579.1| 305 RCSACGSMGNRDGDHFSCSECGRGRHA 331
                                       6******8889***************7 PP

>> PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.3   5.3e+03       2       8 ..     128     134 ..     127     134 .. 0.85
   2 ?    9.2   0.8   0.00041      0.91      10      25 ..     207     222 ..     207     222 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                          PikAIV_N   2 sdeklVe 8  
                                       ++++lVe
  gi|313126309|ref|YP_004036579.1| 128 PVDRLVE 134
                                       7999998 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00041
                          PikAIV_N  10 LRaSLkEnERLRqqNr 25 
                                       LR SL E+  LR +Nr
  gi|313126309|ref|YP_004036579.1| 207 LRDSLSEAGALRARNR 222
                                       9**************9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.2   9.4e+03      11      16 ..      30      35 ..      29      36 .. 0.75
   2 ?    1.8   0.2     0.093   2.1e+02      15      21 ..     305     311 ..     302     313 .. 0.71
   3 ?    6.7   4.1    0.0028       6.2       1      21 [.     305     327 ..     305     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.2
                     zinc_ribbon_2 11 dnakFC 16
                                      d+ +FC
  gi|313126309|ref|YP_004036579.1| 30 DTKQFC 35
                                      677899 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.093
                     zinc_ribbon_2  15 FCpyCGt 21 
                                        C+ CG+
  gi|313126309|ref|YP_004036579.1| 305 RCSACGS 311
                                       5888885 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0028
                     zinc_ribbon_2   1 fCpnCGael.qdnakF.CpyCGt 21 
                                       +C+ CG     d++ F C++CG 
  gi|313126309|ref|YP_004036579.1| 305 RCSACGSMGnRDGDHFsCSECGR 327
                                       69999999846***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2307.99
//
Query:       gi|313126310|ref|YP_004036580.1|  [L=154]
Description: hypothetical protein Hbor_15650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.8   0.0      0.098   13.0   0.0    1.4  1  C6_DPF    Cysteine-rich domain


Domain annotation for each model (and alignments):
>> C6_DPF  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.5e-06     0.098      27      58 ..      29      60 ..       6      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-06
                            C6_DPF 27 lkeeayvmkDPfseekeekilvlGakCslCek 58
                                          +y + DPf+++   +++ +Ga  slC+ 
  gi|313126310|ref|YP_004036580.1| 29 AALSTYQIYDPFENSLAVDTVSVGAAVSLCND 60
                                      345689************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1155.57
//
Query:       gi|313126311|ref|YP_004036581.1|  [L=90]
Description: hypothetical protein Hbor_15660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 535.74
//
Query:       gi|313126312|ref|YP_004036582.1|  [L=387]
Description: thiamine biosynthesis ATP pyrophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-44  149.5   0.0    1.3e-43  148.9   0.0    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
    1.1e-16   61.2   0.0      2e-16   60.4   0.0    1.4  1  THUMP          THUMP domain
     0.0063   16.0   0.0        2.1    7.8   0.0    2.5  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.017   14.0   0.0      0.027   13.3   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase
      0.068   12.9   0.0        1.3    8.7   0.0    2.2  2  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   0.0   3.7e-47   1.3e-43       1     192 [.     176     366 ..     176     370 .. 0.91

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 3.7e-47
                              ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlk 77 
                                       gtqg+v +L+SgGiDSpVaa++l++RGc    v+++   + +++ + +  ++ + la    + +++ +vvd  +v++
  gi|313126312|ref|YP_004036582.1| 176 GTQGRVAVLVSGGIDSPVAAWRLMRRGCIPIPVYVDLGEYGGADHRARAFEVIRTLAARAPGEDLRPRVVDGSDVVD 252
                                       89**************************99888888777777776666666666666666679************** PP

                              ThiI  78 eilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiik 154
                                        ++ +v e  +++ l+r ml +Ae va++ ga+++ tGe+Lgq +Sqt  Nl v++++  ++i rPL++ dK +i++
  gi|313126312|ref|YP_004036582.1| 253 RLIAEVSET-RMLSLRRAMLVMAEAVARRDGAHSVATGEALGQKSSQTGANLAVTDEAATMPIHRPLLTTDKSDIVA 328
                                       *****9875.77899************************************************************** PP

                              ThiI 155 lAkeigtyeisiekedkCsvlakhPttkakleevekae 192
                                        A++igty+ s+ +  +  v + hP+t+a +e+v + e
  gi|313126312|ref|YP_004036582.1| 329 EARRIGTYDDSTLPVGCERVAPSHPETNAAVEDVAAVE 366
                                       *************998777777************8765 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   5.5e-20     2e-16       2     140 ..      32     162 ..      31     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 5.5e-20
                                       HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHH CS
                             THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkk 78 
                                       ++++ll e + +   ve+++ r+vv + +++ + ++ +    + +ar      pv  v+ea+++ + +  + + +++
  gi|313126312|ref|YP_004036582.1|  32 NVRALLRERDSDGD-VERRWSRLVVHTARPHSVAEAVATLPGVAFAR------PV-VVTEATIDAVRDVLQTLARDH 100
                                       78999999999866.66669*******98876666666666666666......88.********************* PP

                                       HHHCT-EEEEEEEESSSTS..SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEE CS
                             THUMP  79 feeeketFaVrvkrrgkhf..eftsreinrevGkaivektglkVdlenPdivvrveiikdkayi 140
                                          e  tFaV ++r+g +   +f+sre+  e G++i e+tg++Vdl+nPd + r+e+++d a++
  gi|313126312|ref|YP_004036582.1| 101 ESSE--TFAVDSRRVGPKDrhDFSSRELDIEGGRLIEEQTGATVDLDNPDRTYRIEVREDDAFV 162
                                       9998..********9986677***************************************9998 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0025       8.9       3      23 ..     182     202 ..     180     236 .. 0.81
   2 !    7.8   0.0    0.0006       2.1     143     178 ..     300     338 ..     267     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0025
                                       EEE--SSHHHHHHHHHHHHH- CS
                              QueC   3 vvllSGGlDSttvlalakkeg 23 
                                        vl+SGG+DS ++++  +++g
  gi|313126312|ref|YP_004036582.1| 182 AVLVSGGIDSPVAAWRLMRRG 202
                                       699*********999988876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0006
                                       HHHHH...HTS--EEE-TTTT--HHHHHHHHHHTTHHHH CS
                              QueC 143 alnlg...edkkieieaPlidlsKaeivklgkelgvple 178
                                        +nl+   e+ ++ i+ Pl++ +K++iv+ + ++g   +
  gi|313126312|ref|YP_004036582.1| 300 GANLAvtdEAATMPIHRPLLTTDKSDIVAEARRIGTYDD 338
                                       4555566677889******************99996544 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.5e-06     0.027       2      33 ..     180     211 ..     179     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-06
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflk 33 
                                       +v+v++SgG+DS vaa +l ++g   i v++ 
  gi|313126312|ref|YP_004036582.1| 180 RVAVLVSGGIDSPVAAWRLMRRGCIPIPVYVD 211
                                       79*******************99877777765 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.047   1.7e+02       2      19 ..     181     198 ..     180     234 .. 0.83
   2 ?    8.7   0.0   0.00037       1.3     127     166 ..     301     338 ..     261     340 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.047
                                       EEEE--SCHHHHHHHHHH CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllll 19 
                                       v+v vSgG+DS +  + l
  gi|313126312|ref|YP_004036582.1| 181 VAVLVSGGIDSPVAAWRL 198
                                       67889******8766655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00037
                                       H-S-SEEEETTCCEE-CCCT--HHHHHHHHHHTT---B-- CS
                        ATP_bind_3 127 agikeaseiasirlvRPlLkvskeeleeylkekkikwveD 166
                                       a ++   e a++ + RPlL++ k+++ + +  ++i  ++D
  gi|313126312|ref|YP_004036582.1| 301 ANLAVTDEAATMPIHRPLLTTDKSDIVAEA--RRIGTYDD 338
                                       33555666789***************8744..44555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2353.81
//
Query:       gi|313126313|ref|YP_004036583.1|  [L=376]
Description: glycine/d-amino acid oxidase, deaminating [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-53  180.7   0.5    6.7e-53  180.5   0.5    1.0  1  DAO            FAD dependent oxidoreductase
     0.0022   17.3   0.3     0.0038   16.5   0.3    1.3  1  FAD_binding_3  FAD binding domain
     0.0042   16.4   0.0      0.015   14.6   0.0    1.8  2  Amino_oxidase  Flavin containing amine oxidoreductase
     0.0075   15.6   0.0        0.4    9.9   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.018   14.7   0.1    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.013   14.8   0.1       0.15   11.2   0.1    2.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.029   13.1   0.0        3.3    6.3   0.0    2.1  2  HI0933_like    HI0933-like protein
      0.037   13.9   0.2      0.062   13.2   0.2    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.12   12.7   1.9       0.15   12.3   0.0    2.2  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.17   11.2   0.0       0.23   10.8   0.0    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
       0.21   10.8   0.1       0.54    9.5   0.0    1.6  2  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.5   0.5   4.1e-56   6.7e-53       1     351 [.       6     357 ..       6     358 .. 0.85

  Alignments for each domain:
  == domain 1  score: 180.5 bits;  conditional E-value: 4.1e-56
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgllhsglrylpeaselarlslealeelreleee 74 
                                       dv+++G G +G++tAy+La rg  V+ le+ d ++  g+S++ +++++ + ++ p    +++l+++a++++rel+e+
  gi|313126313|ref|YP_004036583.1|   6 DVIVVGVGGMGSATAYHLANRGadVLGLERYDVPHDmGSSHGVTRIIRKAQYEHP---SYVPLVRRAYDLWRELAEK 79 
                                       8******************************999966************877666...679**************** PP

                                       HSSTTSEEEEEEEEEES.SHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHH CS
                               DAO  75 lgididyrrtGllslaa.deeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpakl 148
                                       +g d+ +  tG +  +  d    + +d + ++++++++d+ell+a+ev++++p+  lp+ + a++ pd+g + p++ 
  gi|313126313|ref|YP_004036583.1|  80 TGRDL-LTITGGIDAGPpD---SQVFDGSRRSCEAHDIDHELLSAAEVNDRFPGydLPEDHRAVYQPDGGFLVPEQC 152
                                       **876.6779999998644...4455555556667*******************876666899************** PP

                                       HHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEE CS
                               DAO 149 taalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgllkeldlpispvrgq 223
                                       + a  +aa+a+G+ei+ +++ +++    +++++v  ttp g+  +ad +V++aGaw+  l+   +el+   +p r  
  gi|313126313|ref|YP_004036583.1| 153 IIAHTEAAQAAGGEIRAREPMRDFTPLADGGVRV--TTPkGTY-EADRLVVTAGAWTPkLV---PELEGLAVPERQV 223
                                       ************************5544455777..9999986.5699*********9777...7776667999999 PP

                                       EEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTS.EEEEEESSE.....EETTCSS..TSCSHHHHHHHHHHH CS
                               DAO 224 vlvlkplseklvspaailpvpetdddgrgvyvtprkdg.rvlvGgtad.....eesgddd..pevdeedidelleal 292
                                          l+p +    + a  +pv++  d+++++y +pr d  ++++G   +     +   +d+   ++ ++d ++l+ ++
  gi|313126313|ref|YP_004036583.1| 224 LAWLQPSDS-AAFDAENFPVFVHADEDGHYYGFPRHDVpGFKFGKFNHfeetvD---PDEmdRQPRPADERALRAYA 296
                                       999977655.56677999999999999*******94323499999888774433...333556999999999***** PP

                                       HHHSGG.GCGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                               DAO 293 rklfPq.lgdvlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                       +++fP+  g+ ++  ++l + +pd+ ++++ +p+++ + + +G+sghG+++a ++G++la+
  gi|313126313|ref|YP_004036583.1| 297 ERCFPKgAGPTVKLATCLFTnTPDEHFILDTHPEHPQITIGAGFSGHGFKFASVVGEILAD 357
                                       ******44555555559888469********99**************************98 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   2.3e-06    0.0038       2      45 ..       5      48 ..       4      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EE CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradgl 45
                                      +dV++VG G  G  +a  L+++G +v+ +e+++  ++ + ++g+
  gi|313126313|ref|YP_004036583.1|  5 YDVIVVGVGGMGSATAYHLANRGADVLGLERYDVPHDMGSSHGV 48
                                      79*******************************99999988886 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.53   8.6e+02       5      22 ..      18      35 ..      17      39 .. 0.85
   2 !   14.6   0.0   9.4e-06     0.015     205     272 ..     139     211 ..      60     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.53
                                      HHHHHHHHTTEEEEEEES CS
                     Amino_oxidase  5 aaArqLlsaGfdVtvlEa 22
                                      a+A++L+++G dV+ lE 
  gi|313126313|ref|YP_004036583.1| 18 ATAYHLANRGADVLGLER 35
                                      79***********97776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.4e-06
                                       E...TTHTHHHHHHHHH.....TTTTEEEETSEEEEEEEE.ETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEES CS
                     Amino_oxidase 205 p...rgGlsqlpealae.....elrgldirlntrVkeikr.egdgvtvtledgevveaDaVvvTvplgvlkailfsP 272
                                       +   +gG+  + + + +     ++ g++ir +++ ++ +   ++gv+vt+  g+  eaD+ vvT+  ++ k   ++P
  gi|313126313|ref|YP_004036583.1| 139 VyqpDGGFLVPEQCIIAhteaaQAAGGEIRAREPMRDFTPlADGGVRVTTPKGTY-EADRLVVTAGAWTPK---LVP 211
                                       144455544444444444444899****************77777****999996.*********999877...555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.026        42     166     195 ..       6      35 ..       3      52 .. 0.70
   2 !    9.9   0.0   0.00024       0.4      97     143 ..     166     213 ..     151     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.026
                       Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtr 195
                                       +v+V+G +  +  +A++l+++ga+V  + r
  gi|313126313|ref|YP_004036583.1|   6 DVIVVGVGGMGSATAYHLANRGADVLGLER 35 
                                       567776666666677777777777755554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00024
                       Pyr_redox_3  97 piklfeeVesvkk.edegfevetsketyeAkkviiAtGefdkPnklni 143
                                       +i++ e  ++ ++ +d+g +v+t k+tyeA+++++ +G +    +++ 
  gi|313126313|ref|YP_004036583.1| 166 EIRAREPMRDFTPlADGGVRVTTPKGTYEADRLVVTAGAWTPKLVPEL 213
                                       677777777888867899********************9875555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.1e-05     0.018       1      31 [.       7      37 ..       7      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      + ++G G++Gs  a++La+ gadv  + r +
  gi|313126313|ref|YP_004036583.1|  7 VIVVGVGGMGSATAYHLANRGADVLGLERYD 37
                                      579*********************9888765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   9.4e-05      0.15       1     114 [.       5     209 ..       5     235 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.4e-05
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.................... 57 
                                       +dv+v+G G  G a+a +la+ ga+v+ + ++   + +++  s+ ++++ ++a+ ++                    
  gi|313126313|ref|YP_004036583.1|   5 YDVIVVGVGGMGSATAYHLANRGADVLGL-ERY-DVPHDMGSSHGVTRIIRKAQYEHpsyvplvrraydlwrelaek 79 
                                       69************************999.333.3334466666666666666666666666777777777766666 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                       Pyr_redox_2  58 ............................................................................. 57 
                                                                                                                    
  gi|313126313|ref|YP_004036583.1|  80 tgrdlltitggidagppdsqvfdgsrrsceahdidhellsaaevndrfpgydlpedhravyqpdggflvpeqciiah 156
                                       66666666666666666666666666666666666666666666666666666666666666666666666666644 PP

                                       .HHHHCHHHHCCCCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE-BC CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .evvkklnqgielllgeevvkidpgk.kkvklekkkegdeekiaydklvlAtGssprdl 114
                                        e  +    g e +++e+  ++ p + + v +++ k     ++++d+lv+  G+++ +l
  gi|313126313|ref|YP_004036583.1| 157 tEAAQAA--GGEIRAREPMRDFTPLAdGGVRVTTPK----GTYEADRLVVTAGAWTPKL 209
                                       3221111..233344444444443332445554333....3667777777777655555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0066        11       1      31 [.       5      35 ..       5      40 .. 0.91
   2 ?    6.3   0.0     0.002       3.3     115     164 ..     156     204 ..     149     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0066
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllek 31
                                      +dviv+G G  G  +A ++a+rg++Vl le+
  gi|313126313|ref|YP_004036583.1|  5 YDVIVVGVGGMGSATAYHLANRGADVLGLER 35
                                      59************************98776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.002
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                        ++++++ag ++r ++ +++++  +dg +rv+t  ++++ead+lv++ G 
  gi|313126313|ref|YP_004036583.1| 156 HTEAAQAAGGEIRAREPMRDFTPLADGGVRVTT-PKGTYEADRLVVTAGA 204
                                       56778999*************************.9************885 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   3.8e-05     0.062       2      30 ..       7      35 ..       6      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      v v+G G mG+  a+ +a++g +V  +++
  gi|313126313|ref|YP_004036583.1|  7 VIVVGVGGMGSATAYHLANRGADVLGLER 35
                                      78**********************87765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     9e-05      0.15       1      28 [.       9      36 ..       9      71 .. 0.91
   2 ?   -1.9   0.4       2.5   4.1e+03       2       8 ..     336     342 ..     335     345 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vG G  G+++Ay+La++g+dvl le+ 
  gi|313126313|ref|YP_004036583.1|  9 VVGVGGMGSATAYHLANRGADVLGLERY 36
                                      8999*******************99975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                                       E--SHHH CS
                     NAD_binding_8   2 vGaGlsG 8  
                                       +GaG+sG
  gi|313126313|ref|YP_004036583.1| 336 IGAGFSG 342
                                       8*****9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.23       1      54 [.       6      64 ..       6     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.....q 54
                                      Dv+VvG g  G a A+  a++Ga vl +e+++v   + +s +v+ +i + + e      
  gi|313126313|ref|YP_004036583.1|  6 DVIVVGVGGMGSATAYHLANRGADVLGLERYDVPHDMGSSHGVTRIIRKAQYEhpsyvP 64
                                      9******************************9998888888888888754333345552 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00033      0.54      18      49 ..       5      35 ..       3      47 .. 0.88
   2 ?   -2.4   0.0       1.4   2.2e+03      50      71 ..     333     354 ..     303     362 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00033
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       Dv++vG G  G ++ay la++ +  v+ ler
  gi|313126313|ref|YP_004036583.1|  5 YDVIVVGVGGMGSATAYHLANR-GADVLGLER 35
                                      69******************99.777777765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                       SSS--TTTTTTSTTBSEEEEET CS
                              Thi4  50 svspGGGawlGGqlfsaivvrk 71 
                                       ++++G G  + G  f  +v + 
  gi|313126313|ref|YP_004036583.1| 333 QITIGAGFSGHGFKFASVVGEI 354
                                       5778888888888888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2331.50
//
Query:       gi|313126314|ref|YP_004036584.1|  [L=857]
Description: polyphosphate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-71  238.8   0.1    5.8e-71  237.4   0.0    1.8  2  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
    1.5e-65  219.9   0.8    3.8e-62  208.8   0.1    3.7  3  PP_kinase_C    Polyphosphate kinase C-terminal domain 2
    8.2e-64  214.9   3.4    1.3e-63  214.3   3.4    1.3  1  PP_kinase      Polyphosphate kinase middle domain
    8.5e-36  122.5   0.1    3.9e-35  120.4   0.1    2.3  1  PP_kinase_N    Polyphosphate kinase N-terminal domain
    1.1e-10   41.5   0.0      4e-05   23.5   0.1    2.6  2  PLDc_2         PLD-like domain
  ------ inclusion threshold ------
      0.024   14.2   0.3      0.052   13.1   0.3    1.5  1  MR_MLE_C       Enolase C-terminal domain-like


Domain annotation for each model (and alignments):
>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.7   5.2e+03      34      53 ..     227     246 ..     226     263 .. 0.84
   2 !  237.4   0.0   1.9e-74   5.8e-71       1     164 [.     351     515 ..     351     518 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                                       TTEEEEEEEES-S-S--HHH CS
                     PP_kinase_C_1  34 pkvlaikitlYrvakdskiv 53 
                                       p+v+ +++t++r+++++++ 
  gi|313126314|ref|YP_004036584.1| 227 PNVEIVNTTVFRLTRNAEVR 246
                                       78999999999999998875 PP

  == domain 2  score: 237.4 bits;  conditional E-value: 1.9e-74
                                       SHHHHHHHS-EEEECTTB-S.CHHHHHHHHHHC-TTEEEEEEEES-S-S--HHHHHHHHHHHTT-EEEEEES--SSS CS
                     PP_kinase_C_1   1 sifeairkkdillhhPyesf.esvvelleeAaedpkvlaikitlYrvakdskivkaLieAaengkqvtvlvElkArf 76 
                                       sif++ir+ dillhhPy+sf ++v+++l+eAa+dp+vlaik ++Yr+a+ds+++++LieAaengkqv+v+vElkArf
  gi|313126314|ref|YP_004036584.1| 351 SIFSEIRRDDILLHHPYHSFdDTVQRFLDEAASDPDVLAIKAAIYRTASDSQVIQSLIEAAENGKQVAVMVELKARF 427
                                       69******************889****************************************************** PP

                                       --HHHHHHHHHHHHHT-EEEE--TT--B--EEEEEEE---S---EEEEEESS-SS---SS-EEEEEEEE--HHHHHH CS
                     PP_kinase_C_1  77 deenNiewakkleeagvkvvygvvglkvhaklllvvrreeeklrryvhlgtGnynektaklYtDlslltadeelged 153
                                       de+nN+ew ++lee+g++v+yg+ glk+h+k++lvvr+ee++++ y h++tGny+++tak Y Dl+lltad+++g+d
  gi|313126314|ref|YP_004036584.1| 428 DEQNNLEWVRRLEEEGIHVAYGTIGLKTHTKTALVVREEEDGVQLYSHVATGNYHSETAKGYVDLGLLTADRDIGQD 504
                                       ***************************************************************************** PP

                                       HHHHHHHHTT- CS
                     PP_kinase_C_1 154 veklfnvltgk 164
                                       + k+fn++tg 
  gi|313126314|ref|YP_004036584.1| 505 LVKVFNFFTGP 515
                                       *******9986 PP

>> PP_kinase_C  Polyphosphate kinase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.1    0.0058        17      39      61 ..     399     421 ..     380     429 .. 0.90
   2 !  208.8   0.1   1.3e-65   3.8e-62       1     172 []     524     711 ..     524     711 .. 0.91
   3 ?   -1.9   0.0      0.66     2e+03     128     163 ..     799     834 ..     796     841 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0058
                       PP_kinase_C  39 edkeiidkLyeAsqaGVkikliv 61 
                                       +d+++i++L+eA++ G ++ ++v
  gi|313126314|ref|YP_004036584.1| 399 SDSQVIQSLIEAAENGKQVAVMV 421
                                       799****************9998 PP

  == domain 2  score: 208.8 bits;  conditional E-value: 1.3e-65
                       PP_kinase_C   1 LlvaplnlrekllelidreieaakagkkakiilklNsledkeiidkLyeAsqaGVkiklivrgicclrpgvkglsen 77 
                                       Ll+ap+++re++++ i+re+++a++g++a+i++k+N led +++++Ly+As aGV+i+livr+ic+lrpg +++sen
  gi|313126314|ref|YP_004036584.1| 524 LLIAPVTMREEFTKCIRREARHAQNGEDARIVAKVNGLEDPQMVEALYRASMAGVEIDLIVRDICRLRPGLADVSEN 600
                                       89*************************************************************************** PP

                       PP_kinase_C  78 ikvisivdrfLEhaRiyifeng...............geeevyisSaDlmtRnldrRvevlvpvedeklkkelkeil 139
                                       i+v+sivdrfLEh+Ri++feng               g +e yi+SaD+m+Rnld+Rve+++pved++++++l+ il
  gi|313126314|ref|YP_004036584.1| 601 ITVHSIVDRFLEHSRIFYFENGasadssqalgaaddaGGPEWYIGSADWMERNLDKRVEAVAPVEDRDIREQLRFIL 677
                                       *******************99633322222222222245789*********************************** PP

                       PP_kinase_C 140 elqlkDnvkareldedgeykkvke.keekkvraQ 172
                                       el ++Dn k +++++dg+y++ ++ ++e+ v++Q
  gi|313126314|ref|YP_004036584.1| 678 ELAMNDNRKRWTMNADGTYEQRHPpDGEPVVNMQ 711
                                       **********************997888888877 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.66
                       PP_kinase_C 128 deklkkelkeilelqlkDnvkareldedgeykkvke 163
                                       d ++ + l++ l  +++Dn   + +  + +y++v +
  gi|313126314|ref|YP_004036584.1| 799 DDNCDDALDDDLPQVMRDNPDRWYVPDSDHYRYVVR 834
                                       66778889999999************9999999875 PP

>> PP_kinase  Polyphosphate kinase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.3   3.4   4.3e-67   1.3e-63       2     202 .]     140     333 ..     139     333 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 4.3e-67
                                       HHHHHHHHHHHTTGGG---EE--TTTS-----TT-EEEEEEEESST-SS-..EEEEEE--TTS-SEEEE-T.TSS-. CS
                         PP_kinase   2 qkefleeyFeeevfpvLtplavdpshpfpflsnkslnlavelrkkekeekekefalvkvPsvlpRfielppeeegke 78 
                                       q+e++++yFee v+p Ltpla+dp+hpfpf+sn+sl+lav  r++  +++e +f +vk+P++ pR++el   ++g  
  gi|313126314|ref|YP_004036584.1| 140 QREQMRQYFEESVLPTLTPLAFDPAHPFPFISNLSLSLAVMTRRD--SDDEPTFTRVKIPQNRPRLVEL---DDG-- 209
                                       99****************************************996..555579****************...455.. PP

                                       EEEEHHHHHHCCHHHH-TTSEEEEEEEEEEE-SSS----.---.-------------------EEEEETT--HHHHC CS
                         PP_kinase  79 rfilledvIeanldelFpgyevleaylfrvtRnadleidedeaedlleeiekeLkkRrrgevvRLeveaempeellk 155
                                       ++ille+vI+ nld lFp++e++++++fr+tRna++  +e+ aedl+++i++ +++Rr++ vvRLevea++p+ +++
  gi|313126314|ref|YP_004036584.1| 210 EYILLEEVIRSNLDLLFPNVEIVNTTVFRLTRNAEVRRNEEVAEDLIDMIQEVIEQRRFATVVRLEVEADAPDAVVS 286
                                       5**************************************************************************** PP

                                       CHTTTT---TTT.EEEE-S--GGGGGCS...--TTTSSS----B--H CS
                         PP_kinase 156 fLlkeleldeedvyeidgpldltdlmklvgkdrpeLkyppftpqtpp 202
                                       +L+++l++ +++v++++gpld + l +l++ drp Lk +++tpq +p
  gi|313126314|ref|YP_004036584.1| 287 LLQEQLDIADDEVFRLPGPLDYRELLSLTDLDRPALKLDSWTPQLHP 333
                                       ****************************99**************986 PP

>> PP_kinase_N  Polyphosphate kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.1   1.3e-38   3.9e-35       1     106 [.      25     130 ..      25     131 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 1.3e-38
                                       XXXHHHHHHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHHHHHHHCCHHHHH.HTT-..-----------HHHHHH CS
                       PP_kinase_N   1 ylnRelSwLkFneRVLeeAedervplleRlkFlaIfssNlDEFfmvRvaslkrqleakvekksedgltpeeqlkais 77 
                                       ylnRelS ++F++RVL+eA d+r+plleR++Fl+If++N+DEFfm Rv++lk+q++a+v++++ dg+tp++ql+++ 
  gi|313126314|ref|YP_004036584.1|  25 YLNRELSEMEFQRRVLHEALDDRQPLLERVRFLSIFTKNMDEFFMKRVGGLKQQIDADVTEQTVDGRTPTQQLTEVL 101
                                       89*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHTHHHHHHHTTEEE CS
                       PP_kinase_N  78 eeveelveeqekileeellpeLaeegikl 106
                                       e+++ ++++q +++ +e++ +La+egi++
  gi|313126314|ref|YP_004036584.1| 102 EKARPMFRAQARCFLDEIRGALADEGIHI 130
                                       ***************************98 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   1.3e-08     4e-05      15     130 ..     393     510 ..     380     512 .. 0.86
   2 !   15.0   0.0   5.6e-06     0.017      21     126 ..     562     674 ..     545     679 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.3e-08
                            PLDc_2  15 atyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlylidg 91 
                                       a+y   sd++++++l++aa++g++v +++     +a++ ++ +l + ++l  e+g+ v   +      H+K++l+ +
  gi|313126314|ref|YP_004036584.1| 393 AIYRTASDSQVIQSLIEAAENGKQVAVMVEL---KARFDEQNNLEWVRRL-EEEGIHVAYGTI-GLKTHTKTALVVR 464
                                       566678999*********************9...7788777888888888.******997543.3568******964 PP

                            PLDc_2  92 k.......tvivGSsNltkrgldlnlElnvviedkelakeleeeFe 130
                                       +       +  v + N+  +  ++  +l++ + d+++ + l + F+
  gi|313126314|ref|YP_004036584.1| 465 EeedgvqlYSHVATGNYHSETAKGYVDLGLLTADRDIGQDLVKVFN 510
                                       447899888889999*****99*************99999999986 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.6e-06
                            PLDc_2  21 sdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlylidgk..... 92 
                                        d+++++al++a+  gv++ +++++      ++ ++ l+  +e ++ + +  r+   l+   H+ ++ +++      
  gi|313126314|ref|YP_004036584.1| 562 EDPQMVEALYRASMAGVEIDLIVRD-----ICRLRPGLADVSENITVHSIVDRF---LE---HSRIFYFENGasads 627
                                       67899*******************9.....677788888888886666666333...34...889998874456677 PP

                            PLDc_2  93 .............tvivGSsNltkrgldlnlElnvviedkelakele 126
                                                      ++GS+ + +r+ld++ E+   +ed+++ ++l+
  gi|313126314|ref|YP_004036584.1| 628 sqalgaaddaggpEWYIGSADWMERNLDKRVEAVAPVEDRDIREQLR 674
                                       789999999999999**************************999986 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   1.7e-05     0.052      17      72 ..     389     442 ..     373     447 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                                       EEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGG CS
                          MR_MLE_C  17 avKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleel 72 
                                       a+K  + +   a d ++++ + ea+++g++v +mv+  +++d +  ++++r+lee 
  gi|313126314|ref|YP_004036584.1| 389 AIKAAIYR--TASDSQVIQSLIEAAENGKQVAVMVELKARFDEQNNLEWVRRLEEE 442
                                       66666555..699****************************************874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (857 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 5387.72
//
Query:       gi|313126315|ref|YP_004036585.1|  [L=401]
Description: methionine adenosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.8e-176  585.7   4.8   4.3e-176  585.5   4.8    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.5   4.8  2.4e-180  4.3e-176       1     396 []       4     397 ..       4     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 585.5 bits;  conditional E-value: 2.4e-180
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       rni++e++++ +ve+q+vEivErKGiGHPDsiaDgiae+vsrals+ yl+++g++lh+n+D+++lvaGes+p+fgGG
  gi|313126315|ref|YP_004036585.1|   4 RNIKIEAVERLAVEDQSVEIVERKGIGHPDSIADGIAESVSRALSNLYLDRVGKVLHYNTDETQLVAGESAPAFGGG 80 
                                       79*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BE CS
                   AdoMet_Synthase  78 eviepieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevpla 154
                                       eviep++ill+gratk+++gek+pv+++aleaa++yl+en+++l++ +dvivdvklg+gs dL+dvf +++ evp++
  gi|313126315|ref|YP_004036585.1|  81 EVIEPMYILLVGRATKKYDGEKLPVDSVALEAARDYLRENIPELEFGTDVIVDVKLGEGSGDLQDVFGEDNVEVPMS 157
                                       **********************************************************************99***** PP

                                       SSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHH CS
                   AdoMet_Synthase 155 NDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevke 231
                                       NDtSfgvg+apl+e+e++vl++er+ln   + +++p +G D+Kvmg Re++ i++Tva+a+vd +++d+++Y+++ e
  gi|313126315|ref|YP_004036585.1| 158 NDTSFGVGHAPLTETENIVLNVERQLNG-PYAERHPYLGPDVKVMGKREGDYIDITVAAAMVDAHIDDMADYKDAVE 233
                                       ***************************7.78********************************************** PP

                                       HHHHHHHHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-T CS
                   AdoMet_Synthase 232 eikeeveelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNP 308
                                       +++e+v+++a+++t+ rev+v+vNtaD+++e+s+yltvtGtsaE+gDdGsvGRGNR+nGlitpnrpms+EA++GKNP
  gi|313126315|ref|YP_004036585.1| 234 HVREYVSDVATDYTD-REVNVDVNTADNYDEGSIYLTVTGTSAEMGDDGSVGRGNRANGLITPNRPMSMEATSGKNP 309
                                       ***************.************************************************************* PP

                                       TT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-H CS
                   AdoMet_Synthase 309 vsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideeleki 385
                                       v+H+GKiYn+l++ ia+ +v++v+g+++++vrllsqiG+pideP+va+++vi+e+gv+l+++e++v++iide+l+++
  gi|313126315|ref|YP_004036585.1| 310 VNHIGKIYNLLSTDIAEAVVADVDGIRDLQVRLLSQIGRPIDEPHVADAKVITEDGVELSDIEADVQAIIDERLADV 386
                                       ***************************************************************************** PP

                                       HHHHHHHTTT- CS
                   AdoMet_Synthase 386 eeiteeliegk 396
                                       +++t+++i+g+
  gi|313126315|ref|YP_004036585.1| 387 TNVTRRVIDGE 397
                                       ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2399.65
//
Query:       gi|313126316|ref|YP_004036586.1|  [L=196]
Description: adenylate cyclase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-42  144.3   2.3    4.1e-42  144.1   2.3    1.0  1  CYTH          CYTH domain
     0.0006   18.3   0.1      0.079   11.3   0.0    2.0  2  Peptidase_M6  Immune inhibitor A peptidase M6


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.1   2.3   4.6e-46   4.1e-42       1     179 []       1     189 [.       1     189 [. 0.96

  Alignments for each domain:
  == domain 1  score: 144.1 bits;  conditional E-value: 4.6e-46
                                       EEEEEEEEEE-HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEE...................E CS
                              CYTH   1 miEvEvKflvsaaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiR...................r 58 
                                       m+EvEvK++    ++e+++  l++++a +e +v+q dtYy +p+rd+a+tdeaLRiR                   +
  gi|313126316|ref|YP_004036586.1|   1 MYEVEVKLPT---DHETVRSQLTDAGAVHEASVTQIDTYYGAPHRDFAETDEALRIRretrvsdgtnqsdgegetaE 74 
                                       89*******9...78876544*****************************************************996 PP

                                       ETTTEEE.EEEEEECSSST...EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEE CS
                              CYTH  59 aegdgee.ltlKgpgvdge...reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalD 131
                                       a++   + +t+Kgp+vd++   r e+e  vs         da+ a  +l+glg+ pv +v+k+R+ y+l+g +v+lD
  gi|313126316|ref|YP_004036586.1|  75 ADKATTTkMTYKGPLVDSAsktRTEHEMVVS---------DAESAEGILSGLGFSPVETVEKEREFYHLDGYTVTLD 142
                                       66667777**********9999999999999.........************************************* PP

                                       EETTTTEEEEEEEEEESSHHHHHHHHHHHHHHHHHTTEEGGGBSCSHH CS
                              CYTH 132 aveflegeevEiElevedeeevkeaaekllallrelglssaskirrsy 179
                                       av +l ge+vEiE+e++ eee ++++e ++++lr lgl++ ++ir+sy
  gi|313126316|ref|YP_004036586.1| 143 AVSDL-GEFVEIEAETATEEEIDAVREGAFDVLRDLGLDPDDQIRTSY 189
                                       *****.****************************************99 PP

>> Peptidase_M6  Immune inhibitor A peptidase M6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   8.8e-06     0.079     477     524 ..       8      55 ..       3      68 .. 0.87
   2 !    5.2   0.0   0.00061       5.5     452     509 ..      78     135 ..      70     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.8e-06
                      Peptidase_M6 477 fsDdaegatskftlnGftkkggtkekaqyyllelrnyvgvDkgLktlk 524
                                       +  d e+  s++t  G +++ ++ + + yy + +r+++++D++L+ ++
  gi|313126316|ref|YP_004036586.1|   8 LPTDHETVRSQLTDAGAVHEASVTQIDTYYGAPHRDFAETDEALRIRR 55 
                                       55689***************************************6543 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.00061
                      Peptidase_M6 452 ltDgglamkGfavDdlavtvdGeqvfsDdaegatskftlnGftkkggtkekaqyylle 509
                                        t + +++kG  vD  + t   +++++ dae+a+  ++  Gf   ++++++ ++y l+
  gi|313126316|ref|YP_004036586.1|  78 ATTTKMTYKGPLVDSASKTRTEHEMVVSDAESAEGILSGLGFSPVETVEKEREFYHLD 135
                                       6778899*********999999999999*********************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1118.52
//
Query:       gi|313126317|ref|YP_004036587.1|  [L=176]
Description: hypothetical protein Hbor_15720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1226.87
//
Query:       gi|313126318|ref|YP_004036588.1|  [L=241]
Description: cytochrome C oxidase subunit II [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-19   69.9   1.0    6.8e-19   67.9   0.0    2.2  3  COX2          Cytochrome C oxidase subunit II, periplasmic do
    0.00025   21.1   0.0    0.00036   20.6   0.0    1.4  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.088   13.2   2.3       0.16   12.4   2.3    1.5  1  CopD          Copper resistance protein D
       0.09   13.1   3.4        2.2    8.7   0.0    3.1  3  Sigma_reg_N   Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       2.8   1.2e+04       4      16 ..      46      58 ..      44      60 .. 0.79
   2 ?    0.2   0.1      0.15   6.6e+02       1      18 [.     121     138 ..     121     143 .. 0.85
   3 !   67.9   0.0   1.5e-22   6.8e-19      45     117 ..     143     215 ..     139     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.8
                              COX2  4 kaiGhqwywsyey 16
                                        iG+  y +y+y
  gi|313126318|ref|YP_004036588.1| 46 IVIGYMLYNAYKY 58
                                      5689999999998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                              COX2   1 ltikaiGhqwywsyeytd 18 
                                       + ++  G+q+ w + y++
  gi|313126318|ref|YP_004036588.1| 121 MEVRVEGYQFGWRFVYPN 138
                                       568899********9987 PP

  == domain 3  score: 67.9 bits;  conditional E-value: 1.5e-22
                              COX2  45 dnrvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssmpivv 117
                                       d  + +p ++++rl+vt++dv h+f vp l vk+da+pG+ + +++ ++ +G +  qc elcG  hs+m   v
  gi|313126318|ref|YP_004036588.1| 143 DGVLRVPQNESVRLVVTSDDVYHNFGVPELRVKTDAIPGQQTDTWFRATETGNYSAQCYELCGSGHSFMTATV 215
                                       556779***************************************************************8655 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   8.1e-08   0.00036      36      93 ..     145     201 ..      99     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.1e-08
                      Cupredoxin_1  36 kievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeftcd 93 
                                       ++ v+++e+v+l ++  d+  ++f +++l+++++  pg++t  ++++ + G Y+  c 
  gi|313126318|ref|YP_004036588.1| 145 VLRVPQNESVRLVVT-SDDVYHNFGVPELRVKTDAIPGQQTDTWFRATETGNYSAQCY 201
                                       689*****9999886.56678*********************************9995 PP

>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.3   3.6e-05      0.16       9      69 ..       5      62 ..       4     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                              CopD  9 rlalaavavvlvtGvvnallrvglagllttayGrlllaKlalllvllalaalnrfrlvprl 69
                                      +++++ava+++ +G+v+   r   a  +++ y + l++ ++++++++++ ++n +  +   
  gi|313126318|ref|YP_004036588.1|  5 TIVWVAVAAIIQSGLVPRGTR---AYVFQSIYDVFLILGVLVGVIVIGYMLYNAYKYRAGG 62
                                      589**************7777...9999999**********************99655444 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.023     1e+02      16      38 ..      35      57 ..      26      65 .. 0.80
   2 ?    8.7   0.0   0.00048       2.2      16      67 ..      88     146 ..      84     150 .. 0.80
   3 ?   -1.3   0.1      0.64   2.8e+03      50      62 ..     224     236 ..     220     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.023
                       Sigma_reg_N 16 vlislivlllifvilvvtllyla 38
                                      v+++l+vl+ ++vi ++++++++
  gi|313126318|ref|YP_004036588.1| 35 VFLILGVLVGVIVIGYMLYNAYK 57
                                      56788899999999988888875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00048
                       Sigma_reg_N  16 vlislivlllifvil..vvtllyl....aekegnkl.revlelaveitsPNvyvdsgsv 67 
                                       ++++l+++++i++i+  + tll++    +++e+++   e ++  +++ +PN y ++g++
  gi|313126318|ref|YP_004036588.1|  88 TSFILSMIIVISLISwtYGTLLFVeegpQPEETMEVrVEGYQFGWRFVYPNGYTQDGVL 146
                                       456667777777777768888888*9999999999988999999*********988775 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.64
                       Sigma_reg_N  50 elaveitsPNvyv 62 
                                       e+  e t+PN++ 
  gi|313126318|ref|YP_004036588.1| 224 ESWYESTQPNTTT 236
                                       5667889***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1424.35
//
Query:       gi|313126319|ref|YP_004036589.1|  [L=873]
Description: heme/copper-type cytochrome/quinol oxidase subunit 1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.9e-129  430.1  72.0   8.9e-129  430.1  72.0    2.9  3  COX1      Cytochrome C and Quinol oxidase polypeptide I
    7.4e-19   68.6  13.3    7.4e-19   68.6  13.3    2.9  3  COX3      Cytochrome c oxidase subunit III


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.1  72.0  9.9e-133  8.9e-129       2     432 .]      78     521 ..      77     521 .. 0.97
   2 ?    1.7  13.8      0.01        93      43     181 ..     617     771 ..     615     798 .. 0.52
   3 ?   -6.0  15.7         2   1.8e+04      80     181 ..     699     796 ..     689     873 .] 0.49

  Alignments for each domain:
  == domain 1  score: 430.1 bits;  conditional E-value: 9.9e-133
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT........-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCT CS
                              COX1   2 igllylilalvlllvggllgllirlqlafp........dletynqlrtlHgnlmiflfatpfilgfgnylvplllga 70 
                                       +g+ly++++l++l++gg+l+ l+r+ql++p         +  ynq++++Hg +m+f+f+ pf++gf+ny+vpl++ga
  gi|313126319|ref|YP_004036589.1|  78 VGILYIVTSLFFLVLGGVLAWLLRIQLWAPrtptttvlGPMAYNQAVSAHGLIMVFWFLSPFAFGFANYIVPLQIGA 154
                                       89*************************9987777777777************************************* PP

                                       SS-S-HHHHHHHHHHHHHHHHHHHHHHH..CSS-STTTTTTTC.........SHHHHHHHHHHHHHHHHHHHHHHHH CS
                              COX1  71 rdlafprlnalsfwlvvlgvvllllsll..gaattgwteYapls........evdlwllglllvvvssllgainfiv 137
                                       +dlafprlnals+wl++++++l+ +s++  g+++ gwt+Yapl+        +  +++l+l+l+v+s+++ ++nf++
  gi|313126319|ref|YP_004036589.1| 155 KDLAFPRLNALSYWLYLFSGILFGVSFFqgGTFSGGWTMYAPLNvptftpdvGASTAVLALVLFVASVTVSSVNFLT 231
                                       ****************************9888********************8888********************* PP

                                       HHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SS...SCE-HHHHHHHHHHHHTHHH CS
                              COX1 138 tilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslg.kff...spgdplldqhlfWffgHpeV 210
                                       t++k+ra+g+t+ +lplf+w++l t++++l+a+++l +al++l+ dr lg ++f   sp   +l++hlfWffgHpeV
  gi|313126319|ref|YP_004036589.1| 232 TMHKMRAEGLTLRRLPLFTWSILLTVWMMLFAFAALLAALIILSSDRLLGtTYFaleSPAGSMLWAHLFWFFGHPEV 308
                                       **************************************************999965555999*************** PP

                                       HHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCCC CS
                              COX1 211 yililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglkvf 287
                                       yi+++palg++++++ +f+gr++++ k++++a++l+++ sf+vw+HH+f t ++  +k+l++++++ i +P+ l vf
  gi|313126319|ref|YP_004036589.1| 309 YIVFFPALGVMAEVFQTFTGRRIVGRKWFIAAMVLVALQSFVVWMHHMFLTTINLEIKTLFMITTIGISLPFDLMVF 385
                                       ***************************************************************************** PP

                                       HHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
                              COX1 288 nwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllp 364
                                        +++tl +g+irf+tp+lf++g+++lfiigG+tGv+l++  ++y + +tywvvaHfH+v++g+v+ +l++++yy++p
  gi|313126319|ref|YP_004036589.1| 386 ALIYTLLKGKIRFTTPFLFVFGALLLFIIGGITGVFLGAIVLDYEFRGTYWVVAHFHYVMVGGVT-ALIGGLYYWFP 461
                                       ***************************************************************99.99********* PP

                                       HHHSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
                              COX1 365 kltgrmlserlaklhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                                       k+tgrm++e l+klhf ++f+G++l+++p+++++    prr++dy       + lq +++l+t+gg++
  gi|313126319|ref|YP_004036589.1| 462 KITGRMYDEFLGKLHFGIYFVGFNLLYFPLFVAW--ETPRRVFDY------SAGLQIWHQLATVGGFV 521
                                       *********************************9..99*******......3699***********96 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S-HHHHHHHHH...HHHHHHHHHHHHHH.......CS...S-STTT CS
                              COX1  43 Hgnlmiflfatpfilgfgnylvplllgardlafprlnalsfw...lvvlgvvllllsll.......ga...attgwt 106
                                       H++ + f+ ++ ++++f+++l  l +g rd afp  ++ +f+   ++++g+v+l++ ++       g    a + w 
  gi|313126319|ref|YP_004036589.1| 617 HASHASFWPFVVGLGVFFLFL-GL-SGLRDAAFPEGMTGGFYlgfTLLGGTVTLASLVFmalepfhGPedvAGEAW- 690
                                       777777777766644444444.33.378**************9964444444444444456655543344444444. PP

                                       TTTTC.SHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHTT-CC.GS-HH..HHHHHHHHHHHHHHCHHHH CS
                              COX1 107 eYaplsevdlwllglllvvvssllgainfivtilk......rrapgmtva.klplf..vwavlatailillalpvla 174
                                          p+++ ++  +g++++ +s ++ +  fi +++       + a+++  +  +p +  ++ +l+ +++++lal++  
  gi|313126319|ref|YP_004036589.1| 691 ---PFEGLEYGKIGMWIFLTSDVVLFGGFIGAYVFtrvafgWTAWEPIPSdPIPGLmnTYLLLTSSFTVVLALVAAE 764
                                       ...66677777777777766666655555555554222222444443333533333124455555666666666555 PP

                                       HHHHHCH CS
                              COX1 175 lalllll 181
                                           + l
  gi|313126319|ref|YP_004036589.1| 765 KKSRWGL 771
                                       5555544 PP

  == domain 3  score: -6.0 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHHHHHCS.....S-STTTTTTTC..............................SHHHHHHHHH CS
                              COX1  80 alsfwlvvlgvvllllsllga.....attgwteYapls.............................evdlwllgll 122
                                       ++++w+++ + v+l+ +++ga     ++ gwt++ p+                              +     +gl+
  gi|313126319|ref|YP_004036589.1| 699 KIGMWIFLTSDVVLFGGFIGAyvftrVAFGWTAWEPIPsdpipglmntyllltssftvvlalvaaekK---SRWGLV 772
                                       68899999999999999984445555**********98665555444444444444444444443221...222222 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCH CS
                              COX1 123 lvvvssllgainfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllll 181
                                                                          a l+t++++ + ++v+ +  + +l
  gi|313126319|ref|YP_004036589.1| 773 -----------------------------------ASLVTTFVLGVGFLVNKAIEWDHL 796
                                       ...................................333333333333333333332222 PP

>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   1.6      0.77   6.9e+03     128     170 ..     217     259 ..     165     289 .. 0.51
   2 ?   -4.3   4.9       1.5   1.3e+04     131     170 ..     340     380 ..     293     461 .. 0.59
   3 !   68.6  13.3   8.3e-23   7.4e-19      77     255 ..     699     872 ..     667     873 .] 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.77
                                       HHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHHH CS
                              COX3 128 llntiillssGvtvtyahhsliegnrkkalkgllltillavlf 170
                                       l+ + + +ss   +t  h+   eg   + l   + +ill+v +
  gi|313126319|ref|YP_004036589.1| 217 LFVASVTVSSVNFLTTMHKMRAEGLTLRRLPLFTWSILLTVWM 259
                                       3333333333333333333333333333333333333333333 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHHHTT.BHHHHHHHHHHHHHHHHHH CS
                              COX3 131 tiillssGvtvtyahhslieg.nrkkalkgllltillavlf 170
                                       +++l++    v + hh +++  n +  +  ++ ti +++ f
  gi|313126319|ref|YP_004036589.1| 340 AMVLVALQSFVVWMHHMFLTTiNLEIKTLFMITTIGISLPF 380
                                       45566666666677766555312222233333344343333 PP

  == domain 3  score: 68.6 bits;  conditional E-value: 8.3e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHS--GGGTSSSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHTTBH CS
                              COX3  77 klGlilfiisevllflalfwaffhsalsPtvelGatwpPvGikavnPlevPllntiillssGvtvtyahhsliegnr 153
                                       k+G+ +f++s+v+lf ++  a+  + ++      ++w P+  +++      l+nt +ll+s  tv  a  +  ++ r
  gi|313126319|ref|YP_004036589.1| 699 KIGMWIFLTSDVVLFGGFIGAYVFTRVAFGW---TAWEPIPSDPIP----GLMNTYLLLTSSFTVVLALVAAEKKSR 768
                                       6799****************99877665443...57***9776654....599************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH...HH-SS-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--BS CS
                              COX3 154 kkalkgllltillavlftllqavey...leasftisdgvyGsvfylatGlhglhviigtillavallrllk.yhltk 226
                                          + +l+ t++l+v f++ +a+e+    +  + +s  v  s+f+l+tGlh  hvi g ++ +  + r  +  +l +
  gi|313126319|ref|YP_004036589.1| 769 WGLVASLVTTFVLGVGFLVNKAIEWdhlFHEGLWLSTNVRASTFFLTTGLHAAHVIAGLVVTLYLIARAWRgAYLED 845
                                       ************************8332356788*********************9886554444444433145666 PP

                                       SB-HHHHHHHHHHHHHHHHHHHHHHHTTT CS
                              COX3 227 nhhlGfeaailywhfvdvvwlflyvsvyw 255
                                       n     e   lywhfvd+vwlfl+  +y+
  gi|313126319|ref|YP_004036589.1| 846 NSS--VEYFGLYWHFVDIVWLFLFPLFYI 872
                                       655..566789*************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (873 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 5121.36
//
Query:       gi|313126320|ref|YP_004036590.1|  [L=86]
Description: hypothetical protein Hbor_15750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-11   42.5  10.5    8.5e-11   42.1  10.5    1.2  1  COX4_pro  Prokaryotic Cytochrome C oxidase subunit IV
  ------ inclusion threshold ------
       0.32   11.3   4.2       0.33   11.3   3.5    1.4  1  2TM       2TM domain


Domain annotation for each model (and alignments):
>> COX4_pro  Prokaryotic Cytochrome C oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1  10.5   9.5e-15   8.5e-11       1      71 [.       8      78 ..       8      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 9.5e-15
                          COX4_pro  1 livfvlllilTaiefalviiklgkllaiiiilvlalvKavlillyFMHLkeekkglrllaliflvflilll 71
                                      +i++v+l++  ++++++ +++  +++a+ +i+vl +vKavl+++yF HL++e+++l++l+ i l+  ++l+
  gi|313126320|ref|YP_004036590.1|  8 TIIYVVLFASATVQVLVEFAGVAYWTAFGLIIVLSAVKAVLVAAYFQHLRWEPRSLTYLVGIGLAAALALT 78
                                      589***************99999**************************************9999888775 PP

>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.5   3.7e-05      0.33      19      71 ..       6      63 ..       2      68 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                               2TM 19 vYlivniflilinl......gsswflwpilfWgiglllhalkvFgtekffgk.eWeerki 71
                                      +Y i+ ++l++  +      +   ++w++   g++++l a+k+ ++ ++f+  +We r +
  gi|313126320|ref|YP_004036590.1|  6 LYTIIYVVLFASATvqvlveFAGVAYWTA--FGLIIVLSAVKAVLVAAYFQHlRWEPRSL 63
                                      45555555555533344444444446666..5888899999999999999999***8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 551.96
//
Query:       gi|313126321|ref|YP_004036591.1|  [L=75]
Description: hypothetical protein Hbor_15760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 483.74
//
Query:       gi|313126322|ref|YP_004036592.1|  [L=188]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-14   52.5   0.0    7.3e-14   52.0   0.0    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.5e-10   40.6   0.0    3.9e-10   40.0   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.6e-10   39.5   0.0      1e-09   38.4   0.0    1.6  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.3e-07   29.8   0.0    8.4e-07   28.9   0.0    1.5  1  FR47             FR47-like protein
    5.2e-05   23.3   0.0    0.00012   22.1   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      6e-05   23.7   0.0    8.3e-05   23.3   0.0    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0015   18.2   0.2     0.0031   17.2   0.0    1.6  2  Acetyltransf_8   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.01   16.3   0.6       0.14   12.6   0.1    2.2  2  MycE_N           MycE methyltransferase N-terminal
      0.014   15.5   0.0      0.032   14.3   0.0    1.6  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.064   13.4   0.7      0.096   12.9   0.7    1.7  1  FGase            N-formylglutamate amidohydrolase
        0.2   11.2   0.0       0.29   10.7   0.0    1.2  1  GNAT_acetyltran  GNAT acetyltransferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   4.5e-17   7.3e-14      41     117 .]      92     174 ..      14     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 4.5e-17
                                       T.TE.EEEEE.....EEEEEET....TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEH CS
                    Acetyltransf_1  41 d.ge.liGfi.....sllkipd....ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveednd 106
                                       d ++ ++Gf+                 ++++  + +++V + yrg Gl+ +L++ ++e are+g+ ++ l+v++dn 
  gi|313126322|ref|YP_004036592.1|  92 DpETvPVGFVttecsE-----ApsvfDRTDRLCVGDIFVCEPYRGTGLANELVRRAAEDARERGCSELALDVDVDNG 163
                                       2322499999553330.....233666667999******************************************** PP

                                       HHHHHHHHTTE CS
                    Acetyltransf_1 107 aairlYeklGF 117
                                       +a+++Ye lGF
  gi|313126322|ref|YP_004036592.1| 164 RAVAFYESLGF 174
                                       ******99**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   2.4e-13   3.9e-10       2      75 ..      59     175 ..      58     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.4e-13
                                       TEEEEEEEET..........................TEEEEEEEEEEES..........TCTEE...EEE-GGGTTS CS
                    Acetyltransf_7   2 kgevfVaedd..........................gkivGfialslld..........aeitr...laVdpeyrgk 39 
                                       +++v+Va d+                            +vGf+  ++++              +   ++V + yrg 
  gi|313126322|ref|YP_004036592.1|  59 GHRVWVAFDEsnttdanetvndhvpdadtgafsdpeTVPVGFVTTECSEapsvfdrtdrL---CvgdIFVCEPYRGT 132
                                       578999988888888866665555555555555555555599998888899998765333...2567********** PP

                                       SHHHHHHH.HTT....SEEEEE...EEEETHHHHHHHHHHTTEE CS
                    Acetyltransf_7  40 GiGraLle.aae....kgiile...qlelnaekaikfYeklGFe 75 
                                       G++ +L++ aae    +g+  e    + +++ +a++fYe+lGFe
  gi|313126322|ref|YP_004036592.1| 133 GLANELVRrAAEdareRGCS-ElalDVDVDNGRAVAFYESLGFE 175
                                       *******9642245568886.32123333444***********8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.2   5.3e+03      26      40 ..      55      69 ..      46      72 .. 0.78
   2 !   38.4   0.0   6.4e-13     1e-09      53     112 ..     119     180 ..      87     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.2
                   Acetyltransf_10 26 ieegealllvaeegg 40
                                      ++ + + ++va+++ 
  gi|313126322|ref|YP_004036592.1| 55 LNREGHRVWVAFDES 69
                                      567889999999885 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 6.4e-13
                   Acetyltransf_10  53 hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgee 112
                                        ++ +fV + yrg+G++++L+ ++ e a+++g ++ +l v+ ++  av+fYe+lGF+++ ++
  gi|313126322|ref|YP_004036592.1| 119 CVGDIFVCEPYRGTGLANELVRRAAEDARERGCSElALDVDVDNgRAVAFYESLGFETTRRQ 180
                                       57789*****************************************************9776 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   5.1e-10   8.4e-07       3      81 ..      99     178 ..      97     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.1e-10
                                       EEEETTT--EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEE.EETT-HHHHHHHHHHT-E CS
                              FR47   3 GlyrkelgelaawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllv.vvasNtpsirlyeklGfe 78 
                                       G++  e +e+     r d   +g + v +  r+ Gl+  lv+  a++ +erg   l++ v  +N ++ ++ye+lGfe
  gi|313126322|ref|YP_004036592.1|  99 GFVTTECSEAPSVFDRTDRLCVGDIFVCEPYRGTGLANELVRRAAEDARERGCSELALdVDVDNGRAVAFYESLGFE 175
                                       55666666666666666666778899999***********************8766654999**************9 PP

                                       EEE CS
                              FR47  79 kie 81 
                                         +
  gi|313126322|ref|YP_004036592.1| 176 TTR 178
                                       875 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   7.7e-08   0.00012      22      57 ..     115     150 ..      97     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.7e-08
                   Acetyltransf_CG  22 egvldfthTeVpeelrGkGiAkkLvkaalddareeg 57 
                                       +++l +  ++V e +rG G+A +Lv++a +dare+g
  gi|313126322|ref|YP_004036592.1| 115 TDRLCVGDIFVCEPYRGTGLANELVRRAAEDARERG 150
                                       5577777899************************98 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.1e-08   8.3e-05      61     138 .]      93     175 ..       8     175 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.1e-08
                    Acetyltransf_3  61 kdtgv.iGsvglrdleeedee.....aelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSir 130
                                       ++t v +G+v     e  + +     + +g + + ++++g G+a e vr + e a +e g ++l   +d +N + ++
  gi|313126322|ref|YP_004036592.1|  93 PET-VpVGFVTTECSEAPSVFdrtdrLCVGdIFVCEPYRGTGLANELVRRAAEDA-RERGCSELALDVDVDNGRAVA 167
                                       333.668888777444443335567755662666699******************.7777***************** PP

                    Acetyltransf_3 131 vleklGfe 138
                                        +e+lGfe
  gi|313126322|ref|YP_004036592.1| 168 FYESLGFE 175
                                       *******7 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.5   4.1e+03      11      27 ..      53      69 ..      48      89 .. 0.64
   2 !   17.2   0.0   1.9e-06    0.0031      90     141 ..     128     178 ..     100     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                                      HHCTSCCCHHHH----- CS
                    Acetyltransf_8 11 rWmnrprvaewweeagt 27
                                      +W+nr+  + w   +++
  gi|313126322|ref|YP_004036592.1| 53 DWLNREGHRVWVAFDES 69
                                      57777776666644443 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.9e-06
                                       HHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  90 eargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                        +rg gl+++l+r+ ++ + ++ +++   ++ dv+N ra++++e++Gfe  +
  gi|313126322|ref|YP_004036592.1| 128 PYRGTGLANELVRRAAEDARER-GCSELALDVDVDNGRAVAFYESLGFETTR 178
                                       3678888888888888877665.*************************9876 PP

>> MycE_N  MycE methyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.8e-05      0.14      12      54 ..      25      67 ..      23     106 .. 0.85
   2 ?    2.0   0.0      0.18   2.9e+02      31      58 ..     134     163 ..     132     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.8e-05
                            MycE_N 12 dadiaaavaelGlervarvLvdElvfRadleelpvdevsvqla 54
                                      +++++a+v+ ++l++ ++++ +E++fR+d  + +   v v ++
  gi|313126322|ref|YP_004036592.1| 25 HRELEATVETHALADDVDIVTEEVAFRLDWLNREGHRVWVAFD 67
                                      6799*************************99988877777665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.18
                            MycE_N  31 LvdElvfRadleelpv..devsvqlalsag 58 
                                       L++Elv Ra  ++ +    e+ + +++  g
  gi|313126322|ref|YP_004036592.1| 134 LANELVRRAAEDARERgcSELALDVDVDNG 163
                                       789******988888733444444444444 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-05     0.032      76     127 ..     120     176 ..     114     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                       EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                       v+++ v   +rg g++++L++ra e++re+g +   l       +++++Y+++G+e+
  gi|313126322|ref|YP_004036592.1| 120 VGDIFVCEPYRGTGLANELVRRAAEDARERGCSELALDVdvdngRAVAFYESLGFET 176
                                       788899999*********************977666655577779999999999986 PP

>> FGase  N-formylglutamate amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   5.9e-05     0.096      94     122 ..       7      35 ..       2     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.9e-05
                                       T--HHHHHHHHHHTHHHHHHHHHHHHHHH CS
                             FGase  94 pldaaeveerieryyrpYhaalaellarl 122
                                       p ++ +v++ +e+++ pYh++l++++++ 
  gi|313126322|ref|YP_004036592.1|   7 PANESAVRRYVEELWLPYHRELEATVETH 35 
                                       55788899*****************9864 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018      0.29     170     238 ..     106     178 ..     102     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                   GNAT_acetyltran 170 sgasSysvyekgiei.eidTkedyrrkgLAtivaaalileclkrg...lyPsWDaaneaSvaLaekLGYefek 238
                                       s+a S++  ++ +++ +i   e yr+ gLA+ +  +  +++ +rg   l    D +n  +va +e+LG+e ++
  gi|313126322|ref|YP_004036592.1| 106 SEAPSVFDRTDRLCVgDIFVCEPYRGTGLANELVRRAAEDARERGcseLALDVDVDNGRAVAFYESLGFETTR 178
                                       788888888888888689999***********************833345667777*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1172.70
//
Query:       gi|313126323|ref|YP_004036593.1|  [L=66]
Description: hypothetical protein Hbor_15780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.52   10.8   4.7       0.67   10.4   4.7    1.2  1  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.7   3.8e-05      0.67      16      58 ..      10      54 ..       8      57 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.8e-05
                            DUF202 16 tslalialglallrffltgepsalgkilg..lilivlgiltllvg 58
                                      ts+ali++gl+ l      + + + ++ g  ++l+++gilt+ ++
  gi|313126323|ref|YP_004036593.1| 10 TSMALIFAGLLALLYGEYAGLTVTFVPTGgvVVLVGIGILTAYIA 54
                                      9************96554444444444443355999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 437.18
//
Query:       gi|313126324|ref|YP_004036594.1|  [L=102]
Description: hypothetical protein Hbor_15790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0051   17.1   0.0     0.0085   16.4   0.0    1.3  1  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.021   14.9   0.1    1.3  1  zf-CHCC        Zinc-finger domain
      0.023   14.9   0.3      0.041   14.2   0.3    1.4  1  zinc_ribbon_9  zinc-ribbon
      0.036   14.0   0.4      0.056   13.4   0.4    1.3  1  zf-C2HC_2      zinc-finger of a C2HC-type
      0.039   14.4   0.2      0.062   13.8   0.2    1.4  1  zf-C2H2        Zinc finger, C2H2 type
       0.05   14.5   0.3       0.12   13.3   0.1    1.7  2  zf-C2H2_4      C2H2-type zinc finger
      0.092   12.9   0.1       0.14   12.3   0.1    1.2  1  DUF678         Protein of unknown function (DUF678)
       0.13   12.4   0.1       0.19   11.9   0.1    1.2  1  DUF2256        Uncharacterized protein conserved in bacteria 
       0.15   12.2   0.2       0.28   11.4   0.2    1.4  1  zf-RING_7      C4-type zinc ribbon domain
       0.31   10.9   1.2        0.4   10.6   0.3    1.6  2  Rad50_zn_hook  Rad50 zinc hook motif


Domain annotation for each model (and alignments):
>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.8e-06    0.0085       4      29 ..      27      53 ..      25      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.8e-06
                           zf-Di19  4 tCPyCgkeltvkeL.veHvedeHrves 29
                                      tCPyC + + +++L v Hv + H +e 
  gi|313126324|ref|YP_004036594.1| 27 TCPYCDRPFRTDRLrVLHVGEAHADEW 53
                                      9******9999999678******9875 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.2e-05     0.021      20      37 .]      18      35 ..      14      35 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                      EE--TTSEEEETTTTEEE CS
                           zf-CHCC 20 ieldkkgpvdCgYCglrF 37
                                      ie d++   +C+YC++ F
  gi|313126324|ref|YP_004036594.1| 18 IEPDETPVTTCPYCDRPF 35
                                      5556788899******98 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   2.3e-05     0.041      13      31 ..      17      35 ..      11      35 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                     zinc_ribbon_9 13 svspdedsdvlCPhCgggF 31
                                      +++pde++ ++CP+C+  F
  gi|313126324|ref|YP_004036594.1| 17 NIEPDETPVTTCPYCDRPF 35
                                      5788899999******988 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   3.1e-05     0.056       4      18 ..      27      41 ..      26      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                         zf-C2HC_2  4 pCpkCgRsFnpdrle 18
                                       Cp+C R F +drl 
  gi|313126324|ref|YP_004036594.1| 27 TCPYCDRPFRTDRLR 41
                                      6************96 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   3.5e-05     0.062       2      19 ..      27      44 ..      26      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                                      EETTTTEEESSHHHHHHH CS
                           zf-C2H2  2 kCpdCgksFkrksnLkrH 19
                                      +Cp+C+++F++  + + H
  gi|313126324|ref|YP_004036594.1| 27 TCPYCDRPFRTDRLRVLH 44
                                      8********986666666 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.6e-05      0.12       2      20 ..      27      45 ..      26      49 .. 0.80
   2 ?   -2.0   0.0       5.4   9.6e+03      16      21 ..      73      78 ..      68      80 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-05
                         zf-C2H2_4  2 kCpiCgksFsskkaLlr.Hl 20
                                      +Cp+C+++F + ++L+  H+
  gi|313126324|ref|YP_004036594.1| 27 TCPYCDRPF-RTDRLRVlHV 45
                                      7********.7887787787 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.4
                         zf-C2H2_4 16 LlrHlk 21
                                      +l Hlk
  gi|313126324|ref|YP_004036594.1| 73 FLYHLK 78
                                      578998 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.8e-05      0.14       7      32 ..       6      32 ..       2      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.8e-05
                            DUF678  7 kkkrrkrkpkttvede.ddctTCSlCq 32
                                       +k+ + +p+t +e++ + +tTC  C+
  gi|313126324|ref|YP_004036594.1|  6 SQKQNQIRPETNIEPDeTPVTTCPYCD 32
                                      57778999******876999******7 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00011      0.19       4      18 ..      22      36 ..      19      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                           DUF2256  4 elpsKiCavCgrpft 18
                                      e p  +C++C rpf 
  gi|313126324|ref|YP_004036594.1| 22 ETPVTTCPYCDRPFR 36
                                      678899********6 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00016      0.28      10      31 ..       5      33 ..       2      33 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                      -CCHHHHHCCS.....TB..-EE-TTT-- CS
                         zf-RING_7 10 ppqvlselrag.....de..vvtCpeCGR 31
                                      ++q ++++r       de  v tCp+C R
  gi|313126324|ref|YP_004036594.1|  5 SSQKQNQIRPEtniepDEtpVTTCPYCDR 33
                                      566667775554444433669******98 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00022       0.4      21      33 ..      27      39 ..      18      42 .. 0.87
   2 ?   -3.5   0.0       5.7     1e+04      10      11 ..      67      68 ..      61      73 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                                      E-TTT--EE-HHH CS
                     Rad50_zn_hook 21 cCPlCgReldeeh 33
                                       CP C+R++ +++
  gi|313126324|ref|YP_004036594.1| 27 TCPYCDRPFRTDR 39
                                      7********9997 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.7
                                      HH CS
                     Rad50_zn_hook 10 kk 11
                                      + 
  gi|313126324|ref|YP_004036594.1| 67 EE 68
                                      22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 598.23
//
Query:       gi|313126325|ref|YP_004036595.1|  [L=481]
Description: hypothetical protein Hbor_15800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.014   15.4   0.0       0.94    9.6   0.0    2.9  3  Sulf_coat_C  Sulfolobus virus coat protein C terminal
       0.16   11.7   0.4       0.71    9.6   0.1    2.2  2  SpoVS        Stage V sporulation protein S (SpoVS)


Domain annotation for each model (and alignments):
>> Sulf_coat_C  Sulfolobus virus coat protein C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.024   2.2e+02      47      65 ..      69      87 ..      61      89 .. 0.91
   2 ?   -2.5   0.0      0.63   5.6e+03       3      14 ..     116     127 ..     114     130 .. 0.74
   3 ?    9.6   0.0   0.00011      0.94      30      63 ..     189     222 ..     178     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.024
                       Sulf_coat_C 47 syyisafnanpqvldavvn 65
                                      s+  s+f ++ ++ldav n
  gi|313126325|ref|YP_004036595.1| 69 SFLFSSFVTDTEILDAVAN 87
                                      7889*************98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.63
                       Sulf_coat_C   3 avlsqyGitGpn 14 
                                       a +  +G+tGp 
  gi|313126325|ref|YP_004036595.1| 116 AAVVWFGVTGPA 127
                                       555679999995 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00011
                       Sulf_coat_C  30 nriGsGpalvnminGlksyyisafnanpqvldav 63 
                                       +r+Gs pa+v +i  +    +s   +npq l   
  gi|313126325|ref|YP_004036595.1| 189 ERVGSWPAVVGLITLVWVEVVSPVASNPQTLAVA 222
                                       69***************************99754 PP

>> SpoVS  Stage V sporulation protein S (SpoVS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   7.9e-05      0.71      13      44 ..       8      39 ..       3      44 .. 0.88
   2 ?   -2.1   0.0      0.37   3.3e+03       8      20 ..     213     225 ..     210     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 7.9e-05
                                      HHHHHHHHHHHHTSEEEEEE-SHHHHHHHHHH CS
                             SpoVS 13 kvagAiagvlrekgkvevqaiGagAvnqavkA 44
                                      ++  A+a++lr+ g+ +v+++G++A++  v A
  gi|313126325|ref|YP_004036595.1|  8 HLRPAVAACLRQFGSLAVTVVGVAALSRPVLA 39
                                      56679*********************998877 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.37
                                       T--HHHHHHHHHH CS
                             SpoVS   8 ksnpnkvagAiag 20 
                                       +snp+++a A+ g
  gi|313126325|ref|YP_004036595.1| 213 ASNPQTLAVAVLG 225
                                       5999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2798.31
//
Query:       gi|313126326|ref|YP_004036596.1|  [L=146]
Description: hypothetical protein Hbor_15810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 919.95
//
Query:       gi|313126327|ref|YP_004036597.1|  [L=327]
Description: FKBP-type peptidylprolyl isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-06   28.8   0.2    3.1e-06   27.4   0.1    1.8  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   1.7e-10   3.1e-06       6      74 ..      30     123 ..      26     173 .. 0.78
   2 ?   -2.7   0.0      0.43   7.8e+03      60      74 ..     224     238 ..     219     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.7e-10
                                       -TTCEEEEEEEEEET.TSSEEEEH...........CC..HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGG CS
                            FKBP_C   6 kegdtVtvhykgkle.dgkvfdss...........rs..rakplefkvGsgqvikGfeealegmkvGekrtltippe 68 
                                       +++d+V++ y+ +   d++v+d++            +  + +p ++ vG+g++ +  ++ l g +vG+  t++ip  
  gi|313126327|ref|YP_004036597.1|  30 QDDDFVRLAYTVRTVeDDTVVDTTdeavaeeaeidTDeyEFEPRTIIVGAGHIFESVDDELIGSEVGDSGTVEIPAA 106
                                       7899*********9769******999999888866224588999********************************* PP

                                       GTTTT...........T CS
                            FKBP_C  69 laYge...........k 74 
                                       +a+ge           +
  gi|313126327|ref|YP_004036597.1| 107 EAFGEfdddevrtvsaN 123
                                       *****554444444440 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.43
                                       EEEEEEEGGGTTTTT CS
                            FKBP_C  60 krtltippelaYgek 74 
                                       + t+t+ +e  Y e 
  gi|313126327|ref|YP_004036597.1| 224 TETVTVDKETLYIEA 238
                                       567777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2001.27
//
Query:       gi|313126328|ref|YP_004036598.1|  [L=91]
Description: hypothetical protein Hbor_15830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 596.57
//
Query:       gi|313126329|ref|YP_004036599.1|  [L=207]
Description: RecA-superfamily ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-06   28.1   0.0    0.00061   19.2   0.0    2.1  2  ATPase     KaiC
     0.0081   15.3   0.1      0.015   14.4   0.1    1.4  1  PAXNEB     PAXNEB protein
  ------ inclusion threshold ------
      0.066   13.5   0.0       0.11   12.8   0.0    1.4  1  Trigger_N  Bacterial trigger factor protein (TF)


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0   0.00056       3.4       2      25 ..       6      29 ..       5      40 .. 0.89
   2 !   19.2   0.0     1e-07   0.00061     113     219 ..      91     194 ..      81     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00056
                            ATPase  2 ktgIeglDeilkgGipegrvvlit 25
                                      +tgI  lD+ l gG+p g++v + 
  gi|313126329|ref|YP_004036599.1|  6 STGITVLDRELGGGLPAGSTVFLN 29
                                      7******************99775 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1e-07
                            ATPase 113 eaikeika.krvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLd 188
                                       + i+++ +  +++iD +++l + +++   R+ l +l + + ++g  ail     ++++ a++   ++ ++d v+ L+
  gi|313126329|ref|YP_004036599.1|  91 KLIHDLPErANLIIDVVDVL-EATDPVRYRTFLNELQTHMVNTGGLAILHGM--KGDDPANRKYTKH-MADVVFDLQ 163
                                       667777775789********.*******************999999999877..5889999999999.********* PP

                            ATPase 189 lkeieeelvRtleivkmRgtkhskkehpfeI 219
                                        +   +e++  l + k Rg +   +++ +  
  gi|313126329|ref|YP_004036599.1| 164 TTVDGTEIENRLAVPKFRGGRAPDETIKLRL 194
                                       *******************988877776655 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   2.5e-06     0.015      19      46 ..       5      32 ..       3      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-06
                            PAXNEB 19 tStGtpsLDklLgGGLplGsillieEdg 46
                                       StG++ LD+ LgGGLp Gs + + +d 
  gi|313126329|ref|YP_004036599.1|  5 LSTGITVLDRELGGGLPAGSTVFLNADP 32
                                      6*******************99988775 PP

>> Trigger_N  Bacterial trigger factor protein (TF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05      0.11      34      66 ..     170     202 ..     144     207 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                       HHHTTS-BTTC-TT---CCCHHHHCTCCCHHHH CS
                         Trigger_N  34 klakkvkipGFRkGkvPrsiiekrygkevleea 66 
                                       ++ +++ +p FR G++P + i+ r+ +ev  + 
  gi|313126329|ref|YP_004036599.1| 170 EIENRLAVPKFRGGRAPDETIKLRLAEEVAVDT 202
                                       6788999******************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1333.10
//
Query:       gi|313126330|ref|YP_004036600.1|  [L=210]
Description: chromosome partitioning ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-12   45.7   0.0    8.5e-12   45.2   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    9.2e-11   41.7   1.0    8.4e-06   25.4   0.1    2.1  2  ParA         NUBPL iron-transfer P-loop NTPase
    9.3e-05   22.3   2.6      0.017   14.9   0.0    2.1  2  AAA_26       AAA domain
    0.00018   21.5   0.5     0.0049   16.8   0.5    2.1  1  AAA_31       AAA domain
     0.0037   16.8   0.2       0.84    9.1   0.3    2.1  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
  ------ inclusion threshold ------
      0.015   14.6   0.7      0.037   13.3   0.7    1.6  1  MipZ         ATPase MipZ
       0.29   10.3   0.9       0.44    9.7   0.9    1.2  1  ArsA_ATPase  Anion-transporting ATPase


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   3.3e-15   8.5e-12       1     113 [.       2     181 ..       2     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 3.3e-15
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       +a+a++kGG GKTt++++La+al      + +vDaD++++nl++l g+  +  +                       
  gi|313126330|ref|YP_004036600.1|   2 LAVAGGKGGCGKTTTTLGLATALDG---PTTVVDADTDMPNLHSLAGVPREPPQnhvghvhprddtvtvypaptdst 75 
                                       69***********************...***************8777766666689999999999999999999999 PP

                                       ..............................................................CCHCCCHHHHHHCHC CS
                                       ..............................................................xxxxxxxxxxxxxxx RF
                              CbiA  55 ..............................................................dlkrllellealgkk 69 
                                                                                                     d  +   ++ alg++
  gi|313126330|ref|YP_004036600.1|  76 gaheergdrtddgksrlrrvrdtadgqvlidcpagagpdaatplreadevllvtppctpalrDTVKTAAMADALGTN 152
                                       99999999999999999999999999999999999999999999999999999999888888666667777777755 PP

                                       HHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  70 kalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgvip 113
                                             ++g vl r +         +++e l+   g pvlg +p
  gi|313126330|ref|YP_004036600.1| 153 ------VLGAVLVRAR------VVPSGVESLL---GCPVLGTVP 181
                                       ......6777777643......4455666666...666666665 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   3.3e-09   8.4e-06       6      67 ..       2      60 ..       1      72 [. 0.86
   2 !   15.2   0.1   4.4e-06     0.011     115     171 ..     103     157 ..      93     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.3e-09
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliP 67
                                      +av+ gKGG GK+t++  lA+aL      + ++DaD   p++ +l gv +e p+++  +++P
  gi|313126330|ref|YP_004036600.1|  2 LAVAGGKGGCGKTTTTLGLATALD---GPTTVVDADTDMPNLHSLAGVPREPPQNHVGHVHP 60
                                      79********************95...567899***************99877776555666 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.4e-06
                              ParA 115 LiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvv 171
                                       ++iD+P G g  + t + +   +++++Vt p + al d+ k+++m++ + ++vlG v
  gi|313126330|ref|YP_004036600.1| 103 VLIDCPAGAGPDAATPLREA--DEVLLVTPPCTPALRDTVKTAAMADALGTNVLGAV 157
                                       68********9998888877..79*******************************87 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.7    0.0015       3.9       5      28 ..       4      27 ..       1      32 [. 0.83
   2 !   14.9   0.0   6.8e-06     0.017     130     190 ..     124     182 ..     121     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
                            AAA_26  5 vtgtdtgvGKTvvslgLvralkrk 28
                                      v+g   g GKT+++lgL+ al+  
  gi|313126330|ref|YP_004036600.1|  4 VAGGKGGCGKTTTTLGLATALDGP 27
                                      78888899************9765 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.8e-06
                            AAA_26 130 pvilVargglgtinqllltiealrqknvrvlGvilNkvrnpenvetlekksgipvlGvvPy 190
                                       +v+lV+++ + ++ +++ t++++   + +vlG +l +  +      +e+  g pvlG+vP 
  gi|313126330|ref|YP_004036600.1| 124 EVLLVTPPCTPALRDTVKTAAMADALGTNVLGAVLVR--ARVVPSGVESLLGCPVLGTVPP 182
                                       79*********************************98..677899999************7 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5   1.9e-06    0.0049       4      40 ..       2      35 ..       1     146 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                      +a+a  KGG GKTTt++ la al      + +vD+D+
  gi|313126330|ref|YP_004036600.1|  2 LAVAGGKGGCGKTTTTLGLATALDGP---TTVVDADT 35
                                      588899**************998543...44566665 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.3   0.00033      0.84       4      28 ..       2      26 ..       1      43 [. 0.85
   2 !    5.8   0.0    0.0033       8.4     107     147 ..      90     131 ..      71     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00033
                          CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhe 28
                                      la+ G +GG+G+t+ + +La+al+ 
  gi|313126330|ref|YP_004036600.1|  2 LAVAGGKGGCGKTTTTLGLATALDG 26
                                      8999******************975 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0033
                          CBP_BcsQ 107 aalkelk.eqyrwillDlpagasaltrellaladlvllvvep 147
                                       ++l++++ + +  +l+D+paga + + + l+ ad vllv+ p
  gi|313126330|ref|YP_004036600.1|  90 SRLRRVRdTADGQVLIDCPAGAGPDAATPLREADEVLLVTPP 131
                                       5566666556678************************99866 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   1.4e-05     0.037       4     128 ..       3     130 ..       1     138 [. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                                       EE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHH.HHHHHHHHT------EEE-SSS-HHH..H CS
                              MipZ   4 vlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylen.raataerkglsLplpealalseaeea..e 77 
                                        ++  kGG Gk+tt++ +a+aL       +++d d+    l+   +  r   +++ g   p  +++++  a +    
  gi|313126330|ref|YP_004036600.1|   3 AVAGGKGGCGKTTTTLGLATALDGPT---TVVDADTDMPNLHSLAGVpREPPQNHVGHVHPRDDTVTVYPAPTDstG 76 
                                       57889****************97544...445666666667766664245555556666666666666544333003 PP

                                       TTS-HHHHHHHHHHHHHHHHHH-S.EEEEE--SS--HHHHHHHHT-SE..EEEE CS
                              MipZ  78 veeeeeaevaeleelvadleaeld.fividtPGsdsalsrlahsladt..lvtP 128
                                       ++ee   ++ + +  ++++  ++d  ++id+P    + + +   +ad   lvtP
  gi|313126330|ref|YP_004036600.1|  77 AHEERGDRTDDGKSRLRRVRDTADgQVLIDCPAGAGPDAATPLREADEvlLVTP 130
                                       333333344455556666666666458888888888888888888885225666 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.9   0.00017      0.44       6      25 ..       5      24 ..       2      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00017
                                      EEESTTSSHHHHHHHHHHHH CS
                       ArsA_ATPase  6 vgGKGGVGKttvsaatavkl 25
                                       gGKGG GKtt    +a+ l
  gi|313126330|ref|YP_004036600.1|  5 AGGKGGCGKTTTTLGLATAL 24
                                      69*********998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1263.59
//
Query:       gi|313126331|ref|YP_004036601.1|  [L=138]
Description: hypothetical protein Hbor_15860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-27   93.6  11.1    1.2e-26   93.4  11.1    1.1  1  Com_YlbF      Control of competence regulator ComK, YlbF/YmcA
     0.0015   17.8   2.0     0.0018   17.6   2.0    1.1  1  DUF3080       Protein of unknown function (DUF3080)
     0.0049   17.2  11.9     0.0068   16.8  11.9    1.2  1  OmpH          Outer membrane protein (OmpH-like)
      0.007   17.1   4.2      0.031   15.0   3.9    1.8  2  Occludin_ELL  Occludin homology domain
  ------ inclusion threshold ------
      0.059   11.3   1.0       0.27    9.1   0.4    1.8  2  Prominin      Prominin
      0.072   11.3   0.1        0.1   10.8   0.1    1.2  1  Adeno_100     Late 100kD protein
       0.12   12.2   7.3       0.21   11.4   7.3    1.5  1  Nsp1_C        Nsp1-like C-terminal region
       0.23   10.0   1.9       0.24    9.9   1.9    1.0  1  FUSC          Fusaric acid resistance protein family
        9.3    6.7  12.6         13    6.3   3.3    1.9  2  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4  11.1   5.9e-30   1.2e-26       3     104 ..      24     124 ..      22     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 5.9e-30
                                       HHHHHHHHHHHHSHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHTSHHH CS
                          Com_YlbF   3 dkareLaeaIkeseeykeykeaeealeedeelqklikefkklqkelqekqmkgeelkeeekkelqelkeeldknplv 79 
                                       +  +eL+e+I+e++eyk+++ea++a+e+dee+q+ i+ef++l++e+++++++g++ +e+ + ++q++++el++ p++
  gi|313126331|ref|YP_004036601.1|  24 ELGHELGEEIAETPEYKAFEEAKAAVENDEEIQTEIREFQQLREEFMMARQTGNATQEALQ-KVQSAQRELHSKPVM 99 
                                       6679*************************************************87777777.*************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  80 keyleaeqelnellqevnkiiaeai 104
                                       +eylea++el++ l+ +nk+i++++
  gi|313126331|ref|YP_004036601.1| 100 AEYLEAQEELQDRLEAINKAISDPL 124
                                       **********************987 PP

>> DUF3080  Protein of unknown function (DUF3080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.0   8.9e-07    0.0018     140     211 ..      49     121 ..      19     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.9e-07
                           DUF3080 140 lelseakae.elkealsqLnelke.....aslqqesainseeleqalqrleksrllgqllrslallsarLnaatelL 210
                                       +     +++ e++++++++++l+e     +++ + ++ + +++++a+++l+++++++++l ++++l++rL+a+++++
  gi|313126331|ref|YP_004036601.1|  49 V-----ENDeEIQTEIREFQQLREefmmaRQTGNATQEALQKVQSAQRELHSKPVMAEYLEAQEELQDRLEAINKAI 120
                                       2.....222488999999999999998877778888899999********************************998 PP

                           DUF3080 211 e 211
                                       +
  gi|313126331|ref|YP_004036601.1| 121 S 121
                                       7 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  11.9   3.4e-06    0.0068      11     103 ..      33     121 ..      29     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.4e-06
                                       HHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  11 leespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqelqkk 86 
                                       ++e+pe+ka +e  +k + + ++e++++ +e+q+l+ee+  + +++ +++e+ q++q  ++el   +     e+ ++
  gi|313126331|ref|YP_004036601.1|  33 IAETPEYKAFEE--AKAAVENDEEIQTEIREFQQLREEFMMARQTGnATQEALQKVQSAQRELHS-KPVM-AEYLEA 105
                                       578999999999..67778999*****************97777765566666667777777777.3333.555555 PP

                                       HHHHHHHHHHHHHHHHH CS
                              OmpH  87 qqellkpildkinkaik 103
                                       q+el++  l+ inkai+
  gi|313126331|ref|YP_004036601.1| 106 QEELQD-RLEAINKAIS 121
                                       556555.4888888886 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.32   6.3e+02      49      78 ..      16      45 ..       1      54 [. 0.48
   2 !   15.0   3.9   1.5e-05     0.031      28      98 ..      52     122 ..      35     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.32
                      Occludin_ELL 49 kegskeykkieeeilqeykklkkdpeyqek 78
                                      + ++++ +++ +e+ +e ++  + +++ e+
  gi|313126331|ref|YP_004036601.1| 16 SIQTDRLEELGHELGEEIAETPEYKAFEEA 45
                                      444444444444444444444444444444 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.5e-05
                      Occludin_ELL  28 haeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklike 98 
                                        +e+++  ++f++L++e   ++++ + ++++ +++++  ++l+++p   e  +  e+L+++L+ i k i++
  gi|313126331|ref|YP_004036601.1|  52 DEEIQTEIREFQQLREEFMMARQTGNATQEALQKVQSAQRELHSKPVMAEYLEAQEELQDRLEAINKAISD 122
                                       567888999********************************************************999975 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4   0.00013      0.27     212     281 ..      19      88 ..      11      98 .. 0.85
   2 ?    2.8   0.4     0.011        22     195     227 ..      94     125 ..      63     131 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00013
                          Prominin 212 sddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeL...rksgsqLrdglrgvkr 281
                                       +d L++ g++lg+++a+t e +   a++e ++ +en +e+++++++ ++l +e    r++g+  +++l++v+ 
  gi|313126331|ref|YP_004036601.1|  19 TDRLEELGHELGEEIAETPEYK---AFEEAKAAVENDEEIQTEIREFQQLREEFmmaRQTGNATQEALQKVQS 88 
                                       57899*************9999...*****************9999999988864447778888888888765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.011
                          Prominin 195 hidhvlvqnyeelekhvsddLddagkhlgldla 227
                                       h + v+ + y e+++++ d L+ ++k + + la
  gi|313126331|ref|YP_004036601.1|  94 HSKPVMAE-YLEAQEELQDRLEAINKAISDPLA 125
                                       33457777.888888888888888888877765 PP

>> Adeno_100  Late 100kD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.1e-05       0.1     548     582 ..      43      77 ..      33      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.1e-05
                         Adeno_100 548 aeltavvlqkpkvlskireiqksrekfllkkGkGv 582
                                       +e +a v +++++ + ire q+ re+f++ +  G+
  gi|313126331|ref|YP_004036601.1|  43 EEAKAAVENDEEIQTEIREFQQLREEFMMARQTGN 77 
                                       5679*************************998887 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   7.3    0.0001      0.21      11     106 ..      13     111 ..       4     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                            Nsp1_C  11 saaslknktldelinkWtteLeeq..ekeFeeqakkvneWDrvLvengekIskLysevleaeqeqnkidqeLeyies 85 
                                       + +s++   l+el ++  +e+ e+   k Fee  + v e D+ +     + ++L++e + a+q+ n+  + L+ ++s
  gi|313126331|ref|YP_004036601.1|  13 VDMSIQTDRLEELGHELGEEIAETpeYKAFEEAKAAV-ENDEEIQTEIREFQQLREEFMMARQTGNATQEALQKVQS 88 
                                       5566888888888888888888762246677655555.558999999999*************************** PP

                            Nsp1_C  86 qqdeLes..lLdnyEkeleells 106
                                        q+eL+s  ++++y +  eel+ 
  gi|313126331|ref|YP_004036601.1|  89 AQRELHSkpVMAEYLEAQEELQD 111
                                       *****874456666555555554 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.9   0.00012      0.24     207     285 ..      48     119 ..      14     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                              FUSC 207 aayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalr 283
                                       a+  +++i+ ++r  ++l+ +++++ ++ +++++ l+ +++++++ +   ++++ae  +     a+e+l+++l+a+ 
  gi|313126331|ref|YP_004036601.1|  48 AVENDEEIQTEIREFQQLREEFMMARQTGNATQEALQKVQSAQRELH--SKPVMAEYLE-----AQEELQDRLEAIN 117
                                       44457789999*****************************9999998..5677777776.....3555555555555 PP

                              FUSC 284 ar 285
                                       ++
  gi|313126331|ref|YP_004036601.1| 118 KA 119
                                       44 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.3    0.0064        13     149     197 ..      16      64 ..       4      69 .. 0.83
   2 ?    4.9   3.7     0.016        32     148     192 ..      79     120 ..      62     124 .. 0.47

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0064
                            AAA_23 149 kdkkerleelekeleeledekkllekleqekekekeleeleeeleeilk 197
                                       + + +rleel  el e+ +e  + ++ e++k   ++ ee++ e+ e ++
  gi|313126331|ref|YP_004036601.1|  16 SIQTDRLEELGHELGEEIAETPEYKAFEEAKAAVENDEEIQTEIREFQQ 64 
                                       567789****************999999999999988888888887765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.016
                            AAA_23 148 lkdkkerleelekeleeledekkllekleqekekekeleeleeel 192
                                       +++ +++++++++el  +  +++ le++e   e +++le++++++
  gi|313126331|ref|YP_004036601.1|  79 TQEALQKVQSAQRELHSKPVMAEYLEAQE---ELQDRLEAINKAI 120
                                       13333445555555555555555555544...5566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1799  (0.10034); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 798.50
//
Query:       gi|313126332|ref|YP_004036602.1|  [L=508]
Description: hypothetical protein Hbor_15870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.23   11.5   0.1       0.23   11.5   0.1    2.4  2  OppC_N          N-terminal TM domain of oligopeptide transpor
        0.3   10.6   7.6        0.6    9.6   7.6    1.4  1  Pneumo_att_G    Pneumovirinae attachment membrane glycoprotei
        2.1    9.0   6.7       0.63   10.7   3.6    1.6  2  NAM-associated  No apical meristem-associated C-terminal doma


Domain annotation for each model (and alignments):
>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.8e-05      0.23      15      35 ..     148     168 ..     140     187 .. 0.81
   2 ?    0.1   1.5      0.14   8.3e+02       2       9 ..     248     255 ..     247     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                            OppC_N  15 lAvvglvilllllliaifaPl 35 
                                       lA ++ v+l+ l+++a+f+P+
  gi|313126332|ref|YP_004036602.1| 148 LATIAAVVLIGLVVAAVFGPF 168
                                       899***************876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                            OppC_N   2 lwqdawrr 9  
                                       +wqdaw++
  gi|313126332|ref|YP_004036602.1| 248 RWQDAWHQ 255
                                       7*****87 PP

>> Pneumo_att_G  Pneumovirinae attachment membrane glycoprotein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   7.6    0.0001       0.6     182     242 ..     435     495 ..     429     505 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0001
                      Pneumo_att_G 182 aevstPaypsqrasksdpasqgeqtataklllastesvltedtatskssepqleprpsqrG 242
                                        +++ P+  s++ +++ +++ +e+tat++    st +  t+ tat + ++   +prps r 
  gi|313126332|ref|YP_004036602.1| 435 VNATVPPSLSDEPTRESNETTTETTATTTEATDSTATRITDSTATASAGNTGRKPRPSGRY 495
                                       56689**************************99**999********************543 PP

>> NAM-associated  No apical meristem-associated C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.2   1.3e+04      29      41 ..     273     285 ..     248     294 .. 0.39
   2 ?   10.7   3.6   0.00011      0.63      34      86 ..     448     500 ..     428     503 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.2
                    NAM-associated  29 rkpkssassspat 41 
                                       ++++s++ +  +t
  gi|313126332|ref|YP_004036602.1| 273 QSTDSTPTAPTPT 285
                                       2222222222222 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                    NAM-associated  34 sassspatsssestdee.dssesssesseesaadsestsssrlkRPiGkkk.aKe 86 
                                       +++s+++t+++++t  + ++++s+ +  ++s a+++  +++r++RP G+ + aK+
  gi|313126332|ref|YP_004036602.1| 448 TRESNETTTETTAT--TtEATDSTATRITDSTATASAGNTGRKPRPSGRYQnAKR 500
                                       22233333333222..33455555555567778888889999*******887887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3298.03
//
Query:       gi|313126333|ref|YP_004036603.1|  [L=143]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-30  106.2   0.1    1.4e-28   99.5   0.0    2.0  2  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0014        25       2      13 ..      10      21 ..       9      23 .. 0.89
   2 !   99.5   0.0   7.6e-33   1.4e-28      12     121 .]      37     138 ..      36     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0014
                            Y1_Tnp  2 snlkyhivlvtk 13
                                      ++l+yhiv+v+k
  gi|313126333|ref|YP_004036603.1| 10 YELYYHIVFVPK 21
                                      789*******99 PP

  == domain 2  score: 99.5 bits;  conditional E-value: 7.6e-33
                            Y1_Tnp  12 tkyRrkvltgeveerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassrlinkefpelkk 88 
                                        +yRr++ltg+ +erl++i++ei+e+k+ ++ e e+mpDHvHl++  ppk+++s iv+++kg s+r++n+++ +   
  gi|313126333|ref|YP_004036603.1|  37 AQYRRSHLTGKTKERLETIFAEICEDKGLELAESEVMPDHVHLFIGSPPKNAPSLIVNWVKGISARKYNQRYDD--- 110
                                       58*******************************************************************55544... PP

                            Y1_Tnp  89 kklkkeslWqrgYfvstvgeasletvkrYIenq 121
                                        ++k    W+r+Y+v t+g+as+ +v++YI +q
  gi|313126333|ref|YP_004036603.1| 111 -RVK----WTRSYYVGTAGSASKGAVEQYIAEQ 138
                                       .345....**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 912.64
//
Query:       gi|313126334|ref|YP_004036604.1|  [L=460]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-29  100.9   0.1    1.2e-28   99.8   0.1    1.6  1  OrfB_IS605      Probable transposase
    2.3e-17   62.6   0.8    4.7e-17   61.7   0.8    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.068   13.2   0.5       0.13   12.3   0.5    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.1     2e-32   1.2e-28       9     119 ..     196     328 ..     176     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 2e-32
                        OrfB_IS605   9 e.......lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn......... 69 
                                       e        + p  ++ a++D+G+nnL++++t++g+ +ly+gr+l+ ++++++ eia+lqskl++ +          
  gi|313126334|ref|YP_004036604.1| 196 EvenasrfRNSPLASEEAALDVGANNLVACSTTTGNLYLYDGRELFGRFRETTDEIARLQSKLPERRSlsesrktss 272
                                       055556667889999***************************************************99********* PP

                        OrfB_IS605  70 ......ykkasrklarlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                              ++ s++++rl+r+r++rr+h++++l+++l+++l+++gv t++vg+++d+
  gi|313126334|ref|YP_004036604.1| 273 sgrlreGRYSSKRIRRLYRQRTKRRDHAQNALVRDLVERLYDEGVATVYVGDLTDV 328
                                       ****99899********************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.8   7.9e-21   4.7e-17       1      67 [.     347     412 ..     347     414 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 7.9e-21
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f+k++++l++ ++eyGi++e  ++a+TS+tC+eCg   ++ ++g+t++C+ Cgfe ++D+ A+   l
  gi|313126334|ref|YP_004036604.1| 347 FKKFIHRLACVCEEYGISLEAESEAWTSQTCPECGDHEETVRHGDTLTCS-CGFEGHADLTASETFL 412
                                       89************************************************.***********98766 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   2.2e-05      0.13      42     105 ..     327     393 ..     318     396 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHH.H..HHS-TTTSSS-EEEEESSSE CS
                              HypA  42 eaLefafellaegtvlegaeLeieevpvkvrCreCgkefelee.k..alrCpkCgsadveivsGeel 105
                                       ++Le+ +++  ++++ +   ++    ++ + C+e g + e e+ +  + +Cp+Cg ++ ++ +G+ l
  gi|313126334|ref|YP_004036604.1| 327 DVLETHWSVRVNEKTHNFWAFKKFIHRLACVCEEYGISLEAESeAwtSQTCPECGDHEETVRHGDTL 393
                                       55677777777776666667777778888999999999886654246779*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 2486.77
//
Query:       gi|313126335|ref|YP_004036605.1|  [L=329]
Description: protein with diphthamide biosynthesis protein 2-related domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-77  260.8   0.0    2.2e-77  260.5   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
     0.0082   16.8   0.0       0.34   11.6   0.0    2.3  2  GTP-bdg_N        GTP-binding GTPase N-terminal
  ------ inclusion threshold ------
      0.021   14.9   0.0       0.94    9.6   0.0    2.3  2  Peptidase_S66    LD-carboxypeptidase N-terminal domain
       0.13   11.5   0.0       0.26   10.6   0.0    1.4  1  CCB1             Cofactor assembly of complex C subunit B
       0.16   11.9   0.0       0.33   10.9   0.0    1.5  1  DUF4224          Domain of unknown function (DUF4224)


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.5   0.0   6.3e-81   2.2e-77       1     295 [.      32     314 ..      32     320 .. 0.94

  Alignments for each domain:
  == domain 1  score: 260.5 bits;  conditional E-value: 6.3e-81
                   Diphthamide_syn   1 fPegllpdsaeiadil.eef..gaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvdrlpvlYvfveiel 74 
                                       fPegl++  +++ad l e++  +++++++g ++YGaC++d++ +++   d+ vH+Ghs++++  + +++Yv+  +++
  gi|313126335|ref|YP_004036605.1|  32 FPEGLKRRGPAVADDLrERCddDVTFMLSGQPCYGACDLDTYLMRR--TDVFVHFGHSPMKE--SDKIIYVPLFSNV 104
                                       9***************8887778889********************..9************9..889********** PP

                   Diphthamide_syn  75 dvehlvetlkknfkekkkivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklkeeeeevda 151
                                       d   ++e   +++ ++++++lv+t+q+ + +e++++ lee+gy+v +    ++ + +g+vlgc+++++   + ++d+
  gi|313126335|ref|YP_004036605.1| 105 DPFPILEDSLAEL-DGDEVGLVTTAQHMNRFEDMCDWLEERGYDVHTRRGDDRLTFEGQVLGCNYASA---DIDADQ 177
                                       *************.7999*********************99**99944445599**************...5689** PP

                   Diphthamide_syn 152 ilyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelve 228
                                       +ly+g+g+fh+l+l++++p+++v+ +dp+++ +t  +  ++k++++Rya ++ka+da+k+G+i++t+ +qgr+e++e
  gi|313126335|ref|YP_004036605.1| 178 VLYVGGGKFHPLGLAMEHPDKKVVIADPVNNVVTIAD--TEKFMKQRYASVHKAMDAEKWGVIFCTKIGQGRMEIAE 252
                                       *******************************888765..9************************************9 PP

                   Diphthamide_syn 229 rlkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalge 295
                                       ++ ++ +    ++yl++++e++p++L+nf ++dafV+++Cpr+++ddg +F+kP+ltp+E+ +a+g+
  gi|313126335|ref|YP_004036605.1| 253 KIIEDND----NAYLITMDEVTPDRLRNF-DMDAFVNTGCPRITTDDGPRFHKPMLTPQEYRIAVGD 314
                                       9988776....78****************.**********************************984 PP

>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.055     2e+02      29      58 ..     175     204 ..     158     208 .. 0.87
   2 !   11.6   0.0   9.6e-05      0.34      33      70 ..     241     278 ..     211     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.055
                         GTP-bdg_N  29 pdpatyiGkGkveeikelveeeeadlvifd 58 
                                        d+  y+G Gk++ +  ++e+ + ++vi d
  gi|313126335|ref|YP_004036605.1| 175 ADQVLYVGGGKFHPLGLAMEHPDKKVVIAD 204
                                       67889***************9999999977 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.6e-05
                         GTP-bdg_N  33 tyiGkGkveeikelveeeeadlvifddeLspsqqrnLe 70 
                                       t iG+G++e  ++++e+++  ++i+ de++p   rn  
  gi|313126335|ref|YP_004036605.1| 241 TKIGQGRMEIAEKIIEDNDNAYLITMDEVTPDRLRNFD 278
                                       789********************************975 PP

>> Peptidase_S66  LD-carboxypeptidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.028     1e+02       2      37 ..     123     152 ..     122     187 .. 0.72
   2 ?    9.6   0.0   0.00026      0.94      47      87 ..     216     256 ..     189     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.028
                                       EEE-SSS-GGGSSH.HHHHHHHHHHHHCTEEEEEGC CS
                     Peptidase_S66   2 aivapSsglkkeeekeeleraievleelglevvlgk 37 
                                       ++v+ +++       +++e ++++lee+g++v+  +
  gi|313126335|ref|YP_004036605.1| 123 GLVTTAQH------MNRFEDMCDWLEERGYDVHTRR 152
                                       56666633......349***************9665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00026
                                       SS-HHHHHHHHHHHHC-TTECEEEES--SS-CHHCHHHH-H CS
                     Peptidase_S66  47 agtdeeRaadLnealadpeikaiicarGGygaarllpyldf 87 
                                        +  ++R a+ ++a++ ++  +i+c++ G+g +++ +++  
  gi|313126335|ref|YP_004036605.1| 216 EKFMKQRYASVHKAMDAEKWGVIFCTKIGQGRMEIAEKIIE 256
                                       456789*****************************999944 PP

>> CCB1  Cofactor assembly of complex C subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.3e-05      0.26      35      74 ..     125     163 ..     119     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.3e-05
                              CCB1  35 eseeseeelleelkeyleqraYrvaevdaeketvtfeGlv 74 
                                       ++++++ + +e++ ++le+r+Y+v++  +  +++tfeG+v
  gi|313126335|ref|YP_004036605.1| 125 VTTAQHMNRFEDMCDWLEERGYDVHT-RRGDDRLTFEGQV 163
                                       556677788999************99.777799*****98 PP

>> DUF4224  Domain of unknown function (DUF4224)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.2e-05      0.33      17      35 ..     135     153 ..     117     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.2e-05
                           DUF4224  17 saQakwLranGipfvvrad 35 
                                       + +++wL ++G+++++r++
  gi|313126335|ref|YP_004036605.1| 135 EDMCDWLEERGYDVHTRRG 153
                                       679*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.39s 00:00:01.05 Elapsed: 00:00:00.58
# Mc/sec: 1716.36
//
Query:       gi|313126336|ref|YP_004036606.1|  [L=146]
Description: hypothetical protein Hbor_15910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-36  122.8   6.4      1e-35  122.7   6.4    1.0  1  LDcluster4       SLOG cluster4 family
      6e-05   23.2   0.1    0.00013   22.1   0.1    1.5  1  Lysine_decarbox  Possible lysine decarboxylase
    0.00019   20.7   5.5    0.00038   19.8   4.8    1.7  2  DNA_processg_A   DNA recombination-mediator protein A


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   6.4   1.7e-39     1e-35       3     145 ..       2     137 ..       1     146 [] 0.88

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.7e-39
                        LDcluster4   3 kigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdii 79 
                                        ++++G ++  ++++++e+a ++Gr++A++g+++++Gg +Gvme a++Gak agG t+Gilp  +++ ++n+yvd +
  gi|313126336|ref|YP_004036606.1|   2 RVSIIGGSS--VTDTVRETAAATGRIVAQRGHTVVCGGLGGVMESACRGAKAAGGETIGILPT-DRRADANEYVDTP 75 
                                       6999**999..89999***********************************************.888889999**** PP

                        LDcluster4  80 iyTGlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgtdellseiiekkekder 145
                                       i+TGlg+  Rn ++v   d+viai+g  GTlsEi l+l +++p+  l  t  ++ + ie  e++e+
  gi|313126336|ref|YP_004036606.1|  76 IATGLGHG-RNALVVMNGDAVIAIDGAGGTLSEIGLSLVYDRPIAGLG-T--HEVDGIEACETPEE 137
                                       ******77.**************************************9.3..33444444444444 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.2e-08   0.00013       1      69 [.      42     108 ..      42     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHH CS
                   Lysine_decarbox   1 meavakgaleaggrviGiipkillaeeapneevnelvivedmeeRkealveladafvilPGGiGTleEl 69 
                                       me + +ga  agg++iGi p    ++  +ne+v++ + +   + R++  v+ +da++++ G  GTl E+
  gi|313126336|ref|YP_004036606.1|  42 MESACRGAKAAGGETIGILPTD--RRADANEYVDTPIATGLGHGRNALVVMNGDAVIAIDGAGGTLSEI 108
                                       89999*************6654..455679************************************997 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   4.8   6.4e-08   0.00038      45     105 ..       3      63 ..       1      77 [. 0.95
   2 ?   -0.6   0.0      0.11   6.3e+02     146     183 ..      84     119 ..      70     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.4e-08
                    DNA_processg_A  45 vaiVGtRkaseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlgtg 105
                                       v+i+G  ++++  +e+a+ + + +a++g+t+v G+  G+ + a r+a +agg+t+++l+t 
  gi|313126336|ref|YP_004036606.1|   3 VSIIGGSSVTDTVRETAAATGRIVAQRGHTVVCGGLGGVMESACRGAKAAGGETIGILPTD 63 
                                       89********************************************************986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.11
                    DNA_processg_A 146 RnriiaglseavlvveaaekSGalitaelAlelgrevf 183
                                       Rn +++   +av+ +     +G+l  + l l ++r++ 
  gi|313126336|ref|YP_004036606.1|  84 RNALVVMNGDAVIAID--GAGGTLSEIGLSLVYDRPIA 119
                                       7777777777766654..56899988888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 782.50
//
Query:       gi|313126337|ref|YP_004036607.1|  [L=277]
Description: zn-dependent hydrolase of beta-lactamase fold family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-19   70.1   1.0    2.3e-19   69.7   1.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.3e-11   44.6   0.1      2e-11   44.0   0.1    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.39   10.7  11.4        1.4    8.9  11.4    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   1.0   3.8e-23   2.3e-19       2     201 .]      41     240 ..      40     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 3.8e-23
                                       EEEES--TTHHHH..HTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH.HCCTT CS
                     Lactamase_B_2   2 riLiDagpdlrqq..alralqPve.lrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla.vlean 73 
                                        + iD+  +l  +    r   Pv+   +++++ daVl th+H DH++g ++ ++ l+ + ++ yap++ l+  le++
  gi|313126337|ref|YP_004036607.1|  41 TLAIDPYVGLGDPprTVRM-IPVPfDPHDVAEMDAVLATHEHTDHVHG-PSQAPiLESTGAQYYAPDDSLDvALEDE 115
                                       6789*****9999633333.6**************************9.6666657777899**9965555245655 PP

                                       CGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---..H CS
                     Lactamase_B_2  74 fvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip..e 148
                                          +  +   +++++e++ g++fe+g    e+t++ ++h+  +    +a+  ++++ie +  +++++gDt+  +  e
  gi|313126337|ref|YP_004036607.1| 116 AWVDDYDIS-EEQFTEVTDGDTFEVG----EFTIH-VEHSYDP----DATHPVSYVIEHESGTFFHGGDTKPDEefE 182
                                       555555555.78*************9....36664.5666666....899*********************777666 PP

                                       HHHHHHCT-SEEEEE...-S-SSTTHHHH...HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 149 eigerlggadlllld...itayeddemir...hmgHltpeeaveaaadlgakrlvliHi 201
                                       ++ge+++ +dl +l    i+  +d+e  +   + + +t +eav+aa dl+  r+++ H+
  gi|313126337|ref|YP_004036607.1| 183 ALGEKYD-IDLGVLAfgsIGNIDDKETGEpvrTKWYSTENEAVKAASDLQFDRFLPSHW 240
                                       6665555.8876665333677777776645555555555*******************9 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.1   3.4e-15     2e-11       2     161 ..      24     237 ..      23     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3.4e-15
                     Lactamase_B_3   2 ltwlghnsflleta.garilvDPfkanlgyeppa...............eeaDlvlisqaledHahletlkql.... 58 
                                       + +lg n f l+++ g+++++DP+    g++ p+                e+D+vl +++++dH h +  +++    
  gi|313126337|ref|YP_004036607.1|  24 IWYLGCNGFFLKGSdGTTLAIDPYV---GLGDPPrtvrmipvpfdphdvAEMDAVLATHEHTDHVHGPSQAPIlest 97 
                                       77***********549*******95...444444457788888999999******************9999999*** PP

                     Lactamase_B_3  59 ...........................aenvkvleegeslevggleiravatshdavggsergenngflleqdglti 108
                                                                  +e+++ +++g+++evg++ i   +++  +   +     + +++e +  t+
  gi|313126337|ref|YP_004036607.1|  98 gaqyyapddsldvaledeawvddydisEEQFTEVTDGDTFEVGEFTIHVEHSYD-PDATH----PVSYVIEHESGTF 169
                                       **************************999****************998777776.33333....367********** PP

                     Lactamase_B_3 109 yhlGhlahelsseelkelgrvDvvltPvgg...............pltlgqeealelakrLkpklvlP 161
                                       +h G++  + ++e l e  ++D+ ++  g                +  +  +ea+++a+ L+ +  lP
  gi|313126337|ref|YP_004036607.1| 170 FHGGDTKPDEEFEALGEKYDIDLGVLAFGSigniddketgepvrtKWYSTENEAVKAASDLQFDRFLP 237
                                       *******9888888888888887655555555677777777777434444556777777776666555 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  11.4   0.00023       1.4      45     162 ..      72     186 ..      67     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
                                       EEEEE-SBSSHHHHTT..GGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCT CS
                       Lactamase_B  45 vdavilTHlHlDHiGg..lgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnagg 119
                                        dav+ TH H+DH+ g   + + e t++  +a  + + + +++ea+ +    +     +  +  ++d +  +++++ 
  gi|313126337|ref|YP_004036607.1|  72 MDAVLATHEHTDHVHGpsQAPILESTGAQYYAPDDSLDVALEDEAWVDDYDIS-----EEQFTEVTDGDTFEVGEFT 143
                                       59*************94447799999999999999999999999977655543.....5666666666667777777 PP

                                       EEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 120 rralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                       ++  + +   +++++++v+e ++g++   GD+ + +e + +++
  gi|313126337|ref|YP_004036607.1| 144 IHVEHSYDPDATHPVSYVIEHESGTFFHGGDTKPDEEFEALGE 186
                                       77777778889*********************99887776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1550.49
//
Query:       gi|313126338|ref|YP_004036608.1|  [L=610]
Description: hypothetical protein Hbor_15930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-06   28.7   7.9     0.0083   16.2   0.6    3.5  3  DUF1664         Protein of unknown function (DUF1664)
    1.4e-06   27.4  11.5     0.0061   15.5   0.5    2.4  2  Spc7            Spc7 kinetochore protein
    8.7e-06   25.8  11.1     0.0037   17.3   0.7    3.1  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
    2.3e-05   25.0   4.2    2.3e-05   25.0   4.2    3.4  2  APG6_N          Apg6 coiled-coil region
    7.1e-05   22.6   0.1      0.059   13.1   0.0    2.4  2  DUF4201         Domain of unknown function (DUF4201)
    0.00018   21.2  13.3     0.0088   15.7   2.6    3.3  3  Filament        Intermediate filament protein
    0.00023   20.3   0.8    0.00023   20.3   0.8    3.3  4  IFT57           Intra-flagellar transport protein 57
    0.00024   21.3   7.1      0.049   13.9   0.1    3.7  2  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
    0.00028   19.7   1.7    0.00028   19.7   1.7    1.5  2  AAA_13          AAA domain
    0.00029   20.9   7.6       0.13   12.4   0.8    3.4  3  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
    0.00039   20.5   7.9       0.41   10.7   0.1    4.0  3  COG2            COG (conserved oligomeric Golgi) complex comp
    0.00057   19.6   2.1    0.00096   18.9   0.3    2.1  2  Lebercilin      Ciliary protein causing Leber congenital amau
    0.00066   19.7   6.6       0.29   11.2   2.8    3.4  3  Laminin_II      Laminin Domain II
    0.00085   19.2   2.3        0.2   11.5   0.1    2.3  2  DUF724          Protein of unknown function (DUF724)
    0.00092   19.6   6.7       0.61   10.6   0.0    4.1  4  ZapB            Cell division protein ZapB
     0.0011   19.2  21.6       0.92    9.8   0.4    5.8  5  ABC_tran_CTD    ABC transporter C-terminal domain
     0.0018   18.5   5.5       0.28   11.5   1.1    3.7  3  DUF5082         Domain of unknown function (DUF5082)
     0.0019   17.8   4.9     0.0027   17.3   2.4    2.2  2  Leu_zip         Leucine zipper
     0.0019   18.3   2.2     0.0019   18.3   2.2    3.3  2  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
      0.002   18.4  11.6       0.33   11.3   0.9    3.8  4  BLOC1_2         Biogenesis of lysosome-related organelles com
     0.0023   17.3   2.5      0.072   12.4   1.0    2.4  2  GAS             Growth-arrest specific micro-tubule binding
     0.0026   17.3   3.0     0.0026   17.3   3.0    2.1  2  HMMR_N          Hyaluronan mediated motility receptor N-termi
     0.0039   17.4   0.8      0.036   14.3   0.1    2.5  2  Fib_alpha       Fibrinogen alpha/beta chain family
     0.0045   17.3   8.4       0.61   10.4   0.3    3.6  2  Tup_N           Tup N-terminal
     0.0051   16.9   4.4       0.13   12.3   3.2    2.3  2  DUF1640         Protein of unknown function (DUF1640)
     0.0068   14.6   6.7       0.07   11.3   6.9    2.0  1  EzrA            Septation ring formation regulator, EzrA
     0.0069   15.8  11.7       0.11   11.8   3.1    2.9  3  Rab5-bind       Rabaptin-like protein
     0.0075   16.5  15.5          1    9.6   0.2    4.8  4  XhlA            Haemolysin XhlA
     0.0075   16.7   2.4       0.84   10.0   1.0    3.4  3  DUF4200         Domain of unknown function (DUF4200)
     0.0087   15.5  16.2       0.02   14.3  16.2    1.6  1  Tropomyosin     Tropomyosin
     0.0097   15.7   0.1       0.21   11.3   0.0    2.3  2  DUF713          Protein of unknown function (DUF713)
  ------ inclusion threshold ------
       0.01   13.9   0.6      0.023   12.7   0.6    1.5  1  Prominin        Prominin
       0.01   16.0  12.7       0.31   11.2   5.2    3.8  4  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
      0.013   14.3   4.0      0.017   13.9   0.7    2.1  2  HAUS5           HAUS augmin-like complex subunit 5
      0.014   14.6   2.2       0.83    8.8   0.1    2.3  2  DLP_helical     Dynamin-like helical domain
      0.016   15.6  18.8        6.9    7.2   2.5    4.9  3  NPV_P10         Nucleopolyhedrovirus P10 protein
      0.021   15.3  11.7       0.81   10.2   0.2    3.5  3  Spectrin        Spectrin repeat
      0.025   13.9  18.0       0.14   11.4   9.4    3.0  3  CorA            CorA-like Mg2+ transporter protein
      0.055   13.3   6.8      0.027   14.3   3.2    2.0  2  KASH_CCD        Coiled-coil region of CCDC155 or KASH
      0.069   11.3  12.5       0.34    9.0  12.6    1.8  1  HOOK            HOOK protein
       0.07   13.4   0.8         22    5.3   0.1    2.9  2  FliJ            Flagellar FliJ protein
      0.075   13.5   7.8       0.61   10.5   4.9    2.8  2  Fez1            Fez1
      0.081   11.7   6.7       0.58    8.8   3.9    3.1  2  Tektin          Tektin family
      0.082   13.6   0.9        4.5    8.0   0.4    3.1  2  YabA            Initiation control protein YabA
      0.082   12.9   6.6         13    5.8   0.0    4.1  4  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
      0.085   13.2   8.5       0.77   10.0   2.2    2.8  2  zf-C4H2         Zinc finger-containing protein
      0.087   11.9   0.1       0.34   10.0   0.1    1.8  2  Atg14           Vacuolar sorting 38 and autophagy-related sub
      0.087   12.7   5.8        2.1    8.1   0.5    2.9  3  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
      0.093   11.1   6.2       0.17   10.2   2.4    2.0  2  MAD             Mitotic checkpoint protein
       0.11   12.0   8.9       0.59    9.6   6.1    2.2  2  Golgin_A5       Golgin subfamily A member 5
       0.11   12.6   3.6       0.86    9.7   1.3    2.9  2  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
       0.15   11.2   3.0       0.77    8.8   0.9    2.4  3  FH2             Formin Homology 2 Domain
       0.16   11.6   0.1       0.99    9.0   0.0    2.3  2  PI3K_P85_iSH2   Phosphatidylinositol 3-kinase regulatory subu
        0.2   11.2   4.4        2.7    7.5   0.1    3.1  4  Fzo_mitofusin   fzo-like conserved region
       0.21   12.1   4.1        1.2    9.7   0.5    3.3  2  TBCC_N          Tubulin-specific chaperone C N-terminal domai
       0.24   11.6   4.8        5.4    7.2   0.1    2.9  2  GCN5L1          GCN5-like protein 1 (GCN5L1)
       0.27   10.4   2.8          3    6.9   0.8    2.6  4  RmuC            RmuC family
       0.27   11.3   4.0        2.8    8.0   0.1    3.2  3  ADIP            Afadin- and alpha -actinin-Binding
       0.28   11.1   9.5         32    4.5   0.1    4.8  6  Prefoldin       Prefoldin subunit
       0.29   11.5  10.5         33    5.0   0.7    4.9  3  FlaC_arch       Flagella accessory protein C (FlaC)
        0.3   11.2  22.4      0.049   13.8   3.8    2.7  2  Tropomyosin_1   Tropomyosin like
       0.31   10.7   1.7        3.8    7.2   0.1    2.8  3  RPW8            Arabidopsis broad-spectrum mildew resistance 
       0.32    8.8   0.8       0.45    8.3   0.8    1.1  1  Nup88           Nuclear pore component
       0.34   11.4   7.0         12    6.5   1.4    3.2  3  DUF16           Protein of unknown function DUF16
       0.35   10.7   7.5        2.1    8.2   1.6    2.4  2  Nsp1_C          Nsp1-like C-terminal region
       0.35   11.3  15.8       0.62   10.5   0.5    5.1  5  CLZ             C-terminal leucine zipper domain of cyclic nu
       0.36   10.8  12.3        2.9    7.9   0.4    4.5  3  Prefoldin_2     Prefoldin subunit
       0.38   10.0  13.1        1.4    8.1   1.2    3.7  3  DUF3450         Protein of unknown function (DUF3450)
        0.4   11.0   8.6        1.2    9.4   4.8    3.2  2  THOC7           Tho complex subunit 7
        0.4   10.4   3.7          3    7.5   0.1    2.2  2  SHE3            SWI5-dependent HO expression protein 3
       0.43   10.4   3.3         13    5.6   0.2    3.4  4  SKA2            Spindle and kinetochore-associated protein 2
       0.43   10.2  18.5       0.03   13.9  10.4    2.7  1  DUF4795         Domain of unknown function (DUF4795)
       0.71   10.1   6.4         19    5.5   0.0    4.0  4  JIP_LZII        JNK-interacting protein  leucine zipper II
        0.9    8.9   5.1    1.3e+02    1.8   0.1    2.7  1  DUF4618         Domain of unknown function (DUF4618)
        0.9    9.2   5.8        1.3    8.7   4.0    2.2  1  GrpE            GrpE
          1    9.2   4.8         39    4.1   0.0    3.0  3  Sec34           Sec34-like family
        1.8    7.4   5.9       0.95    8.4   3.0    1.9  2  Vps53_N         Vps53-like, N-terminal
        1.9    8.9  11.6         13    6.2   2.4    4.5  5  Csm1_N          Csm1 N-terminal domain
        2.4    7.5   7.3        6.7    6.0   5.1    2.4  2  Cluap1          Clusterin-associated protein-1
        2.9    8.8   5.3         22    6.0   1.1    3.3  2  PRKG1_interact  cGMP-dependent protein kinase interacting dom
        3.2    7.9  21.3        5.3    7.2   7.0    3.3  3  ATG16           Autophagy protein 16 (ATG16)
        3.3    7.7   8.5        6.7    6.7   5.3    2.8  2  Rootletin       Ciliary rootlet component, centrosome cohesio
        4.3    8.0   9.4         18    6.0   0.1    3.6  3  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
        6.4    7.0  11.4        1.6    8.9   5.4    2.4  2  Jnk-SapK_ap_N   JNK_SAPK-associated protein-1
        6.7    6.0  10.8        5.4    6.3   7.4    2.1  1  DUF2353         Uncharacterized coiled-coil protein (DUF2353)


Domain annotation for each model (and alignments):
>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.4   0.00025     0.052      64     119 ..     430     485 ..     422     496 .. 0.83
   2 !   16.2   0.6   3.9e-05    0.0083      51     120 ..     477     546 ..     474     550 .. 0.89
   3 ?    4.6   0.1      0.15        31      34      66 ..     559     590 ..     550     604 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00025
                           DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       L ++++ +d++ld+  + ++ +++e+t++  d ++i++d+++++     l++++e+
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVED 485
                                       78999999999999999999999999999999999999988888888888888765 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.9e-05
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                         + e +++t ++L++  d+  + +  ++e+ + ++eev++v+ed++e+++d+++  +a  gl+++l ++
  gi|313126338|ref|YP_004036608.1| 477 GALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDV 546
                                       56778899999999999999999999999***********************************999877 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.15
                           DUF1664  34 vTkrslsdavesvskqleqvseslaatkrhLss 66 
                                        T+ sl+d v+sv ++l+++  ++++  + L++
  gi|313126338|ref|YP_004036608.1| 559 LTRESLEDDVASVRSDLDELD-DVQTRIESLED 590
                                       567777777777777666653.23333333444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   2.9e-05    0.0061     170     258 ..     397     484 ..     382     495 .. 0.73
   2 !   15.1   3.6   3.8e-05     0.008     137     219 ..     504     596 ..     501     606 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-05
                              Spc7 170 peleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksel 246
                                        +l+++ ++l++  + l e+ +e e   ++ +  lr+e+++l++e++++ +++a+++++l++ +++ e++++  s+l
  gi|313126338|ref|YP_004036608.1| 397 RRLQAQMNDLQAYSDALAEFIDE-EGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTL 472
                                       45666666666666666666666.66778888889999999999999999999999999988888888888888888 PP

                              Spc7 247 eeeiaeaervle 258
                                       e ++ + ++ +e
  gi|313126338|ref|YP_004036608.1| 473 EGDLGALDERVE 484
                                       877766555444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.8e-05
                              Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqe....aaeeles......idkeeLee 203
                                       +e+L ++l+e++e++ ed e+L+++ ++  ++   l+ee  +++e +++l       +e+le+      +d +eL  
  gi|313126338|ref|YP_004036608.1| 504 VEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGeivlTRESLEDdvasvrSDLDELDD 580
                                       68999999999999999999999999999999999999999999999999994444222222233334455555555 PP

                              Spc7 204 lreelaelkaeieekk 219
                                       ++ ++++l+ +ie ++
  gi|313126338|ref|YP_004036608.1| 581 VQTRIESLEDDIEVLM 596
                                       5555555555555443 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.7   1.7e-05    0.0037      23      98 ..     424     499 ..     408     500 .. 0.92
   2 !   11.2   3.6    0.0014      0.29      55     134 ..     509     591 ..     502     597 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-05
                    CENP-F_leu_zip  23 kdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervse 98 
                                       +d v++L +e+e ++e++++   +  t  ae+ +  +  e ++  l+ le dL al +  e+ +++l +  ++ se
  gi|313126338|ref|YP_004036608.1| 424 QDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASE 499
                                       78899************************************************************99998877665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0014
                    CENP-F_leu_zip  55 etlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqe...kvqmkeeskaav 128
                                        tl ee+e   e  +el+ dL+++ s    L++el + +e + +L+   + +++ le+  +    +  + ++ ++++
  gi|313126338|ref|YP_004036608.1| 509 TTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESLEDDVASvrsDLDELDDVQTRI 585
                                       46999999999999999999999999999999999999999999999999999999887666555666666777777 PP

                    CENP-F_leu_zip 129 eeLqtq 134
                                       e+L+ +
  gi|313126338|ref|YP_004036608.1| 586 ESLEDD 591
                                       777665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   4.2   1.1e-07   2.3e-05       9     119 ..     394     504 ..     392     512 .. 0.85
   2 ?    8.0   4.7     0.019       3.9      45     125 ..     511     591 ..     498     603 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.1e-07
                            APG6_N   9 lLleeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaela 85 
                                       + + +l+ q++++++  da+ ef ++  + ++  +  ++e+e+l+eel++  ++ ++ ++eL ++++ re+++++l+
  gi|313126338|ref|YP_004036608.1| 394 VRIRRLQAQMNDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLS 470
                                       5577888888888888888888888877776666669**************************************** PP

                            APG6_N  86 aleeelealeeeeerfwreynelqlelleleeel 119
                                       +le  l al+e  e   ++  e + + +e     
  gi|313126338|ref|YP_004036608.1| 471 TLEGDLGALDERVEDTAQQLTEVDDKASEAVAGV 504
                                       ****************999999888777766555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.019
                            APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeelds 121
                                        dee+e+ +e++e+l+++ ++  +  + l++e  ++++++a+l  e     e  e  + + ++   el + + + +s
  gi|313126338|ref|YP_004036608.1| 511 LDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELDDVQTRIES 587
                                       46677777788888888888888888888888888888888877777777777777777777766777777777777 PP

                            APG6_N 122 leaq 125
                                       le  
  gi|313126338|ref|YP_004036608.1| 588 LEDD 591
                                       6655 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0051       1.1      89     138 ..     430     479 ..     424     480 .. 0.92
   2 !   13.1   0.0   0.00028     0.059      64     166 ..     475     580 ..     469     594 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0051
                           DUF4201  89 leselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggll 138
                                       l++e+++l +el+   +++a +++el+ + ++r+ +r++ + l+ ++g l
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGAL 479
                                       7899************************************9999887765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00028
                           DUF4201  64 eLkrlkkkttktvhalthlkeklh....mleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg 136
                                       +L +l +++ +t ++lt++ +k++     +e+ + +l +e +  +e++++l + l+++    + l+++  +++++ +
  gi|313126338|ref|YP_004036608.1| 475 DLGALDERVEDTAQQLTEVDDKASeavaGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIA 551
                                       788999******************666667777777888888899******************************** PP

                           DUF4201 137 llrvPaLlkDYdktkekveekrksvkkLrr 166
                                       +l+ + +l+  +  +++v++ r+ +++L  
  gi|313126338|ref|YP_004036608.1| 552 DLDGEIVLT-RESLEDDVASVRSDLDELDD 580
                                       **9999998.66666777766666666643 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.35        74     223     279 ..     394     449 ..     390     454 .. 0.85
   2 !   11.1   1.4    0.0011      0.22     207     279 ..     451     523 ..     445     524 .. 0.92
   3 !   15.7   2.6   4.1e-05    0.0088      53     138 ..     519     597 ..     516     601 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 223 rqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireema 279
                                        +i +l++++++l++ +++l + + e e + +  ++ l++++++l+eel    +++a
  gi|313126338|ref|YP_004036608.1| 394 VRIRRLQAQMNDLQAYSDALAEFIDE-EGTGQDLVDGLRQEVEALDEELDAFGDDIA 449
                                       57899999999999999999887766.89999999*************998877776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0011
                                       XXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 207 nsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireema 279
                                        +++l +a  + +++r  + +le +l +l +  + + +ql+e++++ +++++ ++e  + l+ee++ + e+++
  gi|313126338|ref|YP_004036608.1| 451 VEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIE 523
                                       56778888899999*****************************************************999986 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 4.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  53 ekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatlarvdLekkvesL 129
                                       ++ +eel + l +++++ a l+ el+++re+++dl   +   +  re++E++++++r dlde+     d+++++esL
  gi|313126338|ref|YP_004036608.1| 519 HEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEI---VLTRESLEDDVASVRSDLDELD----DVQTRIESL 588
                                       5789******************************98655...679****************985....9******** PP

                                       XXXXXXXXX CS
                          Filament 130 keelaflkk 138
                                       ++++++l +
  gi|313126338|ref|YP_004036608.1| 589 EDDIEVLMQ 597
                                       ****99865 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.1       8.5   1.8e+03     110     183 ..     146     219 ..     144     257 .. 0.62
   2 ?   -1.7   5.3       5.3   1.1e+03     127     177 ..     270     319 ..     258     356 .. 0.43
   3 ?    5.9   0.0     0.026       5.4     271     355 ..     398     483 ..     397     484 .. 0.90
   4 !   20.3   0.8   1.1e-06   0.00023     202     350 ..     432     594 ..     428     599 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.5
                             IFT57 110 LadeaLkkkkfkfkkpkypkeeeeeeeeev.eddaelelekveeeelikseeededeedeeeelklesekkeeke 183
                                       L+  aL+ +  ++++p  +    e+ +e v e +a+  ++ + +  +++++++   ++ +++++ +e+ +++ ++
  gi|313126338|ref|YP_004036608.1| 146 LVRDALQGN-GSLSDPASDAAAAEDAAESVlEAEADAGADPLADPLAADDTDAAVGSDTDSDNVPVETVDETATD 219
                                       566666664.66777777755555555555677888888888888887766666444444444444444444333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.3
                             IFT57 127 ypkeeeeeeeeeveddaelelekveeeelikseeededeedeeeelklese 177
                                       ++++e +e+ +e  d a++ +++ ++e++ +++ +d d++ +++++  +++
  gi|313126338|ref|YP_004036608.1| 270 ITRSEASEDRTE-ADAADVAADATTDEAADTDDVADADQTADTDDVADADQ 319
                                       443333222222.33344444444444333333333332222222222222 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.026
                             IFT57 271 qleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDg.splvkikkaltklkk 346
                                       +l+ +++++++ ++ l+e+ ++  + ++ v  l++e + ++eel++   ++   ++++t + +    i++ l++l+ 
  gi|313126338|ref|YP_004036608.1| 398 RLQAQMNDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAAdADREDIRDDLSTLEG 474
                                       57889999*******************************************9999998866234578********** PP

                             IFT57 347 Eikqmdvri 355
                                       ++  +d r+
  gi|313126338|ref|YP_004036608.1| 475 DLGALDERV 483
                                       **9999886 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 1.1e-06
                             IFT57 202 lEleRvlpqLkv............ti.kadakdWrahleqmkkhkksieeslpetksqlkklhedisktlekiesrE 265
                                       +E+e    +L +            t   ad +d r +l +++    +++e +++t +ql+++ ++ s+++  +e+  
  gi|313126338|ref|YP_004036608.1| 432 QEVEALDEELDAfgddiatveaelTAaDADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELN 508
                                       5666666666666666666666554437888899999999999999******************************* PP

                             IFT57 266 kylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssm.tDgsplvkikkal 341
                                       + l++++e   ++ +e+++ ls++      l e++ + +++ a+++ e+  + + +e+  +s+ +D + l  +++ +
  gi|313126338|ref|YP_004036608.1| 509 TTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESLEDDVASVrSDLDELDDVQTRI 585
                                       *******************************************************998876654999********** PP

                             IFT57 342 tklkkEikq 350
                                       ++l+ +i+ 
  gi|313126338|ref|YP_004036608.1| 586 ESLEDDIEV 594
                                       ****99975 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   0.00023     0.049      33      97 ..     391     462 ..     380     472 .. 0.73
   2 ?    7.2   2.4     0.027       5.6      31     102 ..     476     548 ..     463     566 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.......S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  33 eldekrrelqveleelqaerNelskeIgkakkkk.......edaeeliaevkelkeelkaleaelkeleael 97 
                                       ++d + r+lq+++++lqa + +l++ I +    +       ++ e+l +e ++ +++++++eael++++a+ 
  gi|313126338|ref|YP_004036608.1| 391 SADVRIRRLQAQMNDLQAYSDALAEFIDEEGTGQdlvdglrQEVEALDEELDAFGDDIATVEAELTAADADR 462
                                       678899*********************998877745555666666666666666666666666666666655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  31 lleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       l +lde+ + + ++l e+  +  e+ + ++++     e+ e++ ++++el+++l+++  + + l++el ++  
  gi|313126338|ref|YP_004036608.1| 476 LGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLdEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVRE 548
                                       5567777777777777777777777777777766667888888888888888888888888888877766554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1         5   1.1e+03      90     189 ..     240     337 ..     238     388 .. 0.48
   2 !   19.7   1.7   1.3e-06   0.00028     285     454 ..     396     558 ..     378     578 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5
                            AAA_13  90 esiekqekieklkkeikkleekleaaea.qlqkaekekkklekeledeawkkivkkknsalsealkglkyeekfker 165
                                       + +++++ i+   +++++  +kl+a++   ++ +e+ ++  e++++d a+   +   ++a + +     ++++++  
  gi|313126338|ref|YP_004036608.1| 240 SAADIEAAIDDDSDDVDAGPRKLTAETTpAITRSEASEDRTEADAADVAADATT---DEAAD-TDDVADADQTADTD 312
                                       566777777777777777766655444313344444444555555555544332...22222.22233445555555 PP

                            AAA_13 166 llkelkkk.nrkaaellsdeelkak 189
                                       ++++++++ ++++ +   d+ ++++
  gi|313126338|ref|YP_004036608.1| 313 DVADADQTaDTDDYVDIGDSVADDA 337
                                       5554444412333333333333333 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.3e-06
                            AAA_13 285 qerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfk.svelesv 360
                                       ++rL+  +++++  +    + l++ +de+      ++ ++ l++e eal+e+L++  + +     e+ + +++ e++
  gi|313126338|ref|YP_004036608.1| 396 IRRLQAQMNDLQAYS----DALAEFIDEEG---TGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAaDADREDI 465
                                       334444444333332....33444444332...34455888888999999999988888877777776658889999 PP

                            AAA_13 361 kakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeea 437
                                        ++++ ++ ++ ++ e +++  ++ ++++++++ea   +e  l   l++e+++ ++++++l+++++++  +++   +
  gi|313126338|ref|YP_004036608.1| 466 RDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEE-LNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDE 541
                                       99999999999999999999999999999999999999999.66669999999999999999999999999999999 PP

                            AAA_13 438 elkkleeeikeLekqlr 454
                                       el  ++e+i++L  ++ 
  gi|313126338|ref|YP_004036608.1| 542 ELGDVREDIADLDGEIV 558
                                       99999999999987775 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.4    0.0033      0.71      26     108 ..     397     490 ..     393     493 .. 0.72
   2 !   12.4   0.8   0.00059      0.13      38     102 ..     467     530 ..     462     539 .. 0.54
   3 !    8.8   4.0    0.0074       1.6      22      97 ..     490     578 ..     485     597 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0033
                      Baculo_PEP_C  26 rlqnvqilaqlatlldaietqL......nalsedlksllaeldtrldtlltnLtdalnalq......dtlrneLtnl 90 
                                       r +++q+ ++l++  da+++ +      ++l + l++ +++ld++ld++ + + +  ++l+      +++r +L +l
  gi|313126338|ref|YP_004036608.1| 397 RRLQAQM-NDLQAYSDALAEFIdeegtgQDLVDGLRQEVEALDEELDAFGDDIATVEAELTaadadrEDIRDDLSTL 472
                                       5555555.5666666655555511111146777777788888889999999999888888899999999******** PP

                      Baculo_PEP_C  91 nsiltnLlssvtNinstL 108
                                       + +l  L   v  + + L
  gi|313126338|ref|YP_004036608.1| 473 EGDLGALDERVEDTAQQL 490
                                       ****99998888777766 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00059
                      Baculo_PEP_C  38 tlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvt 102
                                        +l ++e+ L+al+e++++   ++ t++d+ +++  + + +l++tl++e +++  ++ +L  ++ 
  gi|313126338|ref|YP_004036608.1| 467 DDLSTLEGDLGALDERVEDTA-QQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLS 530
                                       455556666666666666633.3334455555555555555566666666666666666655444 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0074
                      Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq.......dtlrn 85 
                                       L+ +  + ++ +a +++l ++++++++a+ ed+++l+ +l++       ld+ l  + + ++ l        ++l+ 
  gi|313126338|ref|YP_004036608.1| 490 LTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQtasaaaGLDEELGDVREDIADLDgeivltrESLED 566
                                       55555666666788888888888888888888888888888888888877777777777777777433333344444 PP

                      Baculo_PEP_C  86 eLtnlnsiltnL 97 
                                       +  ++ s+l +L
  gi|313126338|ref|YP_004036608.1| 567 DVASVRSDLDEL 578
                                       444444444444 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1      0.14        30      68     112 ..     424     468 ..     395     485 .. 0.78
   2 ?    6.6   1.2     0.037       7.8      66     108 ..     485     527 ..     478     537 .. 0.81
   3 !   10.7   0.1    0.0019      0.41      66     119 ..     538     591 ..     533     603 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.14
                              COG2  68 qeeleevesplaaarkkvesvreklsereeeveskleeakeleek 112
                                       q+ ++ ++++++a+ ++++++ + ++  e+e+++  ++++++++ 
  gi|313126338|ref|YP_004036608.1| 424 QDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDD 468
                                       666777777788888888888888888887777777777777765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.037
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeake 108
                                       +  ++l ev+ + ++a+  ve+++  l+e  e+v++ +ee ++
  gi|313126338|ref|YP_004036608.1| 485 DTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSD 527
                                       5668889999999999999999999999999999999988765 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0019
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellkll 119
                                       gl+eel  v+ ++a +  ++  +re+l++  + v+s l+e  +++   e+l++ 
  gi|313126338|ref|YP_004036608.1| 538 GLDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELDDVQTRIESLEDD 591
                                       99*******************************************999888765 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   4.5e-06   0.00096      46     190 ..     411     554 ..     392     557 .. 0.92
   2 ?   -0.5   0.1         4   8.3e+02      19      36 ..     577     594 ..     559     604 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.5e-06
                        Lebercilin  46 kaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkk.LsedknLaer.e 120
                                        aL  + d+e   ++l++  ++Ev++l e+l    +   ++e +l  ++a+ + ++d+l++l+  L     L+er e
  gi|313126338|ref|YP_004036608.1| 411 DALAEFIDEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGdLG---ALDERvE 484
                                       688899999999999************************************************8565...9*99955 PP

                        Lebercilin 121 eLqkkLeeleakleekeekikeLerkleleeksfrrqlaaekkktkeaqeevkalqeeierlkqklkeKe 190
                                       + +++L+e+ +k+ e+   ++eL+  l+ e ++ +  ++  +   +++ +  + l ee+ ++++++++ +
  gi|313126338|ref|YP_004036608.1| 485 DTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLD 554
                                       67899******************************************************99999988765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 4
                        Lebercilin  19 elaelqskleelrkEnkl 36 
                                       el+++q ++e l+ + ++
  gi|313126338|ref|YP_004036608.1| 577 ELDDVQTRIESLEDDIEV 594
                                       333444444444444444 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2     0.019       4.1      17      82 ..     425     490 ..     413     498 .. 0.71
   2 !    9.4   1.8    0.0049         1      15      91 ..     451     528 ..     439     531 .. 0.41
   3 !   11.2   2.8    0.0014      0.29       8      67 ..     497     556 ..     491     604 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.019
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       + + +l q++e + e+l  + ++++ +++++ +a    +d r+  ++Le  +  L ++++   q+ 
  gi|313126338|ref|YP_004036608.1| 425 DLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQL 490
                                       567777777777777777777777777777777777777777777777777777777666555543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0049
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXX--TTTTTGGGHHHHHHHHHH... CS
                        Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankai....rdArrsvkkLeklapqLldklkelkqleeasss 87 
                                       v++ l++ +++ e ++++ls++++++   +e v+d  +++    + A+++v  +e+l   L + ++ + +  e+   
  gi|313126338|ref|YP_004036608.1| 451 VEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLtevdDKASEAVAGVEELNTTLDEEVEAVHEDIEE--- 524
                                       55555555555555555555555555444444443333330000333333333333333333333333332222... PP

                                       HHHH CS
                        Laminin_II  88 lsdn 91 
                                       lsd+
  gi|313126338|ref|YP_004036608.1| 525 LSDD 528
                                       4444 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--T CS
                        Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekl 67 
                                       a+e ++ v+e  + l++++e + e+++e+ +++ +t   +  + + + d+r+ + +L+ +
  gi|313126338|ref|YP_004036608.1| 497 ASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGE 556
                                       666666666666666666666666666666666666666666666666666666666543 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00094       0.2      87     184 ..     396     493 ..     394     497 .. 0.95
   2 ?    7.2   0.4     0.019         4     100     182 ..     511     593 ..     504     597 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00094
                            DUF724  87 VkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarl 163
                                       ++ lq+++n+L +  d  ++  +e+   +  +   ++e + l+ee+d +   i+++e +l+++ +++e+   ++++l
  gi|313126338|ref|YP_004036608.1| 396 IRRLQAQMNDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTL 472
                                       67899999999999999999999999999999999****************************************** PP

                            DUF724 164 kseaekleeeledveqeFeav 184
                                       + +  +l+e++ed+ q+  +v
  gi|313126338|ref|YP_004036608.1| 473 EGDLGALDERVEDTAQQLTEV 493
                                       ***************998776 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.019
                            DUF724 100 lkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeled 176
                                       l +e + ++e +++l  ++++ +s+ + l+ee+ ++ + i++l  + +l++e  e++ +++ +   e +++++++e+
  gi|313126338|ref|YP_004036608.1| 511 LDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELDDVQTRIES 587
                                       55677888999999*************************************99999999999999999999999999 PP

                            DUF724 177 veqeFe 182
                                        e++ e
  gi|313126338|ref|YP_004036608.1| 588 LEDDIE 593
                                       998876 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       3.5   7.3e+02      20      39 ..     396     415 ..     394     421 .. 0.75
   2 !   10.6   0.0    0.0029      0.61      21      65 ..     428     472 ..     425     481 .. 0.90
   3 ?    6.7   1.0     0.046       9.8       4      51 ..     488     539 ..     475     557 .. 0.55
   4 ?    1.0   0.1       2.9   6.1e+02       3      25 ..     575     597 ..     569     604 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 3.5
                              ZapB  20 itlLqmeieeLkeeneelke 39 
                                       i++Lq ++ +L++ + +l+e
  gi|313126338|ref|YP_004036608.1| 396 IRRLQAQMNDLQAYSDALAE 415
                                       78888888888888888777 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0029
                              ZapB  21 tlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                       + L++e+e+L ee  +  + ++ +e+e+ +  ++re +++ l++L
  gi|313126338|ref|YP_004036608.1| 428 DGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTL 472
                                       669***********************************9999887 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.046
                              ZapB   4 elLeqLEskiqkaidtitlL....qmeieeLkeeneelkeenreleeeneql 51 
                                       ++L +   k ++a+  +++L     +e+e++ e+ eel++   +  +    l
  gi|313126338|ref|YP_004036608.1| 488 QQLTEVDDKASEAVAGVEELnttlDEEVEAVHEDIEELSDDLSQTASAAAGL 539
                                       5666666666666655554400003444444444455554444444444444 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 2.9
                              ZapB   3 lelLeqLEskiqkaidtitlLqm 25 
                                       l+ L+  +++i+++ d i+ L +
  gi|313126338|ref|YP_004036608.1| 575 LDELDDVQTRIESLEDDIEVLMQ 597
                                       67788889999999888888755 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.49     1e+02      23      41 ..     395     414 ..     391     420 .. 0.80
   2 ?    7.0   0.5     0.032       6.8       7      41 ..     431     463 ..     429     468 .. 0.86
   3 ?    7.1   3.5     0.031       6.6       9      60 ..     468     514 ..     462     527 .. 0.62
   4 ?    4.8   2.6      0.15        33      12      58 ..     510     551 ..     505     557 .. 0.72
   5 !    9.8   0.4    0.0044      0.92       9      61 ..     542     596 ..     538     598 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.49
                      ABC_tran_CTD  23 eiaeleaeladpelysdp.e 41 
                                       +i  l+a+++d + ysd  +
  gi|313126338|ref|YP_004036608.1| 395 RIRRLQAQMNDLQAYSDAlA 414
                                       788999****9999998744 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.032
                      ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpe 41 
                                       ++e e+l++e++a   +ia++eael +++  +d e
  gi|313126338|ref|YP_004036608.1| 431 RQEVEALDEELDAFGDDIATVEAELTAAD--ADRE 463
                                       6899*********************9998..6655 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.031
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60 
                                        l +le ++ aL+e+ ++  ++l + +     +k +e+ a  eel++ L+e 
  gi|313126338|ref|YP_004036608.1| 468 DLSTLEGDLGALDERVEDTAQQLTEVD-----DKASEAVAGVEELNTTLDEE 514
                                       467788888888888888888888777.....44555555555555555543 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.15
                      ABC_tran_CTD  12 eleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLe 58 
                                       +l++e ea  e+i+el + l++ +      + a l +el +++++++
  gi|313126338|ref|YP_004036608.1| 510 TLDEEVEAVHEDIEELSDDLSQTAS-----AAAGLDEELGDVREDIA 551
                                       6999*****************9984.....45555555555555544 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.0044
                      ABC_tran_CTD   9 eleeleaeIeaLEeei....aeleaeladpelysdpeklaelsaeleeleaeLeely 61 
                                       el  + ++I+ L+ ei    ++le+ +a+    sd ++l ++++++e le+++e l+
  gi|313126338|ref|YP_004036608.1| 542 ELGDVREDIADLDGEIvltrESLEDDVASVR--SDLDELDDVQTRIESLEDDIEVLM 596
                                       5666777888888887333345555555444..888*****************9988 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       2.9   6.2e+02       4      24 ..     395     415 ..     392     420 .. 0.72
   2 !   11.5   1.1    0.0013      0.28      13     117 ..     428     535 ..     421     541 .. 0.82
   3 ?    5.7   0.0     0.083        18      11      38 ..     577     604 ..     568     606 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.9
                           DUF5082   4 kisklqaqiaelrseiaalee 24 
                                       +i++lqaq+ +l++  +al e
  gi|313126338|ref|YP_004036608.1| 395 RIRRLQAQMNDLQAYSDALAE 415
                                       578888888888877776665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0013
                           DUF5082  13 aelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirs...nlessyqtyvdkl 86 
                                       + lr+e++al+e +        ++++e  +++++++++++ l + e   G  ++ +++ ++   +++++ ++ v  +
  gi|313126338|ref|YP_004036608.1| 428 DGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQqltEVDDKASEAVAGV 504
                                       56788888888888888877778888888888888888888888887777766666666666889************ PP

                           DUF5082  87 delidaieeEIerLenqiseaqgvldtlqsq 117
                                       +el   ++eE+e   ++i+e++ +l+++ s+
  gi|313126338|ref|YP_004036608.1| 505 EELNTTLDEEVEAVHEDIEELSDDLSQTASA 535
                                       **************************99876 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.083
                           DUF5082  11 qiaelrseiaaleekIerLkeaktklsd 38 
                                       + ++ + +i++le++Ie L + +++l d
  gi|313126338|ref|YP_004036608.1| 577 ELDDVQTRIESLEDDIEVLMQFRDRLND 604
                                       67899****************9999987 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.4   1.3e-05    0.0027     129     230 ..     428     530 ..     401     550 .. 0.81
   2 !    7.9   2.2    0.0093         2     137     243 ..     489     592 ..     487     600 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-05
                           Leu_zip 129 eLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldl 204
                                       + L++e+e L+ee +   + + ++E+++t a  +++ ++ +l+ l+ +lg+ +++ e ++++++++++k +e  + +
  gi|313126338|ref|YP_004036608.1| 428 DGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEdTAQQLTEVDDKASEAVAGV 504
                                       4489**********************************************997766647889999999998888888 PP

                           Leu_zip 205 ektleektasaksleedlastkhelL 230
                                       e+  ++  ++ ++++ed+ +   +l 
  gi|313126338|ref|YP_004036608.1| 505 EELNTTLDEEVEAVHEDIEELSDDLS 530
                                       88777777777777777777666654 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0093
                           Leu_zip 137 rLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldlektleekt 212
                                       +L e ++k +e +  +E+  t++ ee ++++++++el ++l+++ ++++  ++e+ +++e +a+l  ++  t e+ +
  gi|313126338|ref|YP_004036608.1| 489 QLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAgLDEELGDVREDIADLDGEIVLTRESLE 565
                                       44555555555555555555555555555555555555555555444433444555555555555555555555555 PP

                           Leu_zip 213 asaksleedlastkhelLkvqeqLelaekeL 243
                                       ++ +s+++dl +    l  vq ++e  e ++
  gi|313126338|ref|YP_004036608.1| 566 DDVASVRSDLDE----LDDVQTRIESLEDDI 592
                                       555555555432....334555555555555 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.6     0.026       5.5      59     127 ..     448     516 ..     395     518 .. 0.77
   2 !   18.3   2.2     9e-06    0.0019       3     117 ..     469     580 ..     467     588 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.026
                        TPR_MLP1_2  59 lqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNklLhdQlE 127
                                       ++++ +el  + a+++++++++ +++ +l +  e  e + ++l +  +++ + +  ++e N++L +  E
  gi|313126338|ref|YP_004036608.1| 448 IATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVE 516
                                       566667777777777777777777777777777777777777777777777777777777777766665 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 9e-06
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       l++le ++ +l+e+ e+ +++l+++ ++  +  + ++e +    +e+    ed++el+   ++l+++ + +a l +e
  gi|313126338|ref|YP_004036608.1| 469 LSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELS---DDLSQTASAAAGLDEE 542
                                       78999999***************************************99999998776...7*************** PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelselekriedlne 117
                                       + +++++++    ++  ++e+le++++++++ +++l++
  gi|313126338|ref|YP_004036608.1| 543 LGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELDD 580
                                       ***********************************986 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.91   1.9e+02      44      86 ..     397     439 ..     391     449 .. 0.76
   2 ?    8.1   1.0     0.016       3.3       9      86 ..     435     513 ..     430     517 .. 0.86
   3 !   11.3   0.9    0.0016      0.33      11      86 ..     465     541 ..     457     551 .. 0.89
   4 !    9.0   0.7    0.0082       1.7      49      92 ..     560     603 ..     548     606 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.91
                           BLOC1_2  44 aslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                         l++++++l++ +++l++++++    ++ v+ L + v++LDe
  gi|313126338|ref|YP_004036608.1| 397 RRLQAQMNDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDE 439
                                       4577778888887778888888877778888888888888887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.016
                           BLOC1_2   9 kyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidq.iekqvteLeeavseL 84 
                                       + l++el+a  +d+ ++e+  +aa +  ++++d ++ le +l +l+e+ e  +++l+++d+   + v+  ee+   L
  gi|313126338|ref|YP_004036608.1| 435 EALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDkASEAVAGVEELNTTL 511
                                       56899******************************************999999999999752566777777777777 PP

                           BLOC1_2  85 De 86 
                                       De
  gi|313126338|ref|YP_004036608.1| 512 DE 513
                                       76 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0016
                           BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnek.yeelqpylqqidqiekqvteLeeavseLDe 86 
                                       ++ +l+    d+  L +  e ++++ ++++d+a+++ + +e+ln + +ee++   + i+++ +++++  +a++ LDe
  gi|313126338|ref|YP_004036608.1| 465 IRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTlDEEVEAVHEDIEELSDDLSQTASAAAGLDE 541
                                       67788999999999999999***********************98625699999************99999999998 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0082
                           BLOC1_2  49 kleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       + e l+   +++++ l+++d++++++++Le+ +++L ++  +L 
  gi|313126338|ref|YP_004036608.1| 560 TRESLEDDVASVRSDLDELDDVQTRIESLEDDIEVLMQFRDRLN 603
                                       567788888999*********************99988888776 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   1.0   0.00034     0.072      66     186 ..     430     550 ..     395     554 .. 0.61
   2 !   10.1   0.3    0.0017      0.37      28     128 ..     508     605 ..     505     607 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00034
                               GAS  66 aeeeveeLrkqlknyekd....kqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqq 138
                                       +++eve L ++l  +  d     ++l+++ a  ++  + l++l+ +   l +r+e   ++  e+ +k  +a+  v +
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEALDEELDAFGDDiatvEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEE 506
                                       45555555555555555411112356666667777777777777777777777777777777777776666666654 PP

                               GAS 139 ktglknllLekklkalqeelEkkeaqleevlaaanldpaalsavsekl 186
                                            n+ L   ++a++e++E+    l+++ +aa   +++l  v+e +
  gi|313126338|ref|YP_004036608.1| 507 ----LNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDI 550
                                       ....46777777777777777777777777666544446666666665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0017
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                        ++l ee+e   +  e+ + +ls++++    l e+L  ++e+++ L  ++   ++   sl+   a +++  +el d+
  gi|313126338|ref|YP_004036608.1| 508 NTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRE---SLEDDVASVRSDLDELDDV 581
                                       578999***************************************9998876544...6666666666677777777 PP

                               GAS 105 kwehevleqrfekvekerdelykk 128
                                       +   e+le+ +e + + rd+l++ 
  gi|313126338|ref|YP_004036608.1| 582 QTRIESLEDDIEVLMQFRDRLNDA 605
                                       777777777777777777777665 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.0   1.2e-05    0.0026     218     328 ..     415     529 ..     390     535 .. 0.80
   2 ?    2.2   0.4      0.48     1e+02     246     297 ..     539     593 ..     521     604 .. 0.49

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-05
                            HMMR_N 218 ekieekseteklley.ieelsnvseqlekykldiaqleellkekndeiesLkssLeeke...qelskqvkdlnekck 290
                                       e i+e    + l++   +e++++ e+l+ +  dia +e  l +++ + e+++ +L+  e    +l+++v+d  +++ 
  gi|313126338|ref|YP_004036608.1| 415 EFIDEEGTGQDLVDGlRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEgdlGALDERVEDTAQQLT 491
                                       445666666667664157999*******************************98876551115789*********** PP

                            HMMR_N 291 llekekeelvreeeekeqtlsaEleelkeklklkeqea 328
                                       +++ +  e v   ee + tl  E+e ++e ++  +++ 
  gi|313126338|ref|YP_004036608.1| 492 EVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDL 529
                                       *****************************999877775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.48
                            HMMR_N 246 ykldiaqleellkekndeiesLkssLeekeqelskqvkdl...nekckllekeke 297
                                         +++  ++e ++  + ei+  ++sLe+    +    ++l   +++++ le + e
  gi|313126338|ref|YP_004036608.1| 539 LDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELddvQTRIESLEDDIE 593
                                       3555555555555556666655666655555555444333000334444444444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   0.00017     0.036      30     126 ..     462     558 ..     456     565 .. 0.93
   2 !    9.1   0.2    0.0065       1.4      22     110 ..     507     598 ..     506     605 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00017
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                                       ++d+++dl++le +l  + ++ +++ +  +e++d+  e+ +  ++ ++++ +  + + e+i++l + ++++ s    
  gi|313126338|ref|YP_004036608.1| 462 REDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAG 538
                                       67899***************************************99******************************* PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 107 LqnvlesneqkiqkLeqdid 126
                                       L + l + +++i++L  +i 
  gi|313126338|ref|YP_004036608.1| 539 LDEELGDVREDIADLDGEIV 558
                                       ***************98876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0065
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH...HHHH.HHHHHHHHHHHHHCCCHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqks...kkdn.dnvikksskeleeeilrlk 94 
                                       l+++l++  + v++d+e+l ++l++ ++     +e   ++++ +++   +   ++++ +  + +++++l+ e  +++
  gi|313126338|ref|YP_004036608.1| 507 LNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEivlTRESlEDDVASVRSDLD-ELDDVQ 582
                                       7889999999999999999999999999988888877777665554332200022234888888899999.888899 PP

                                       HHHHCCHHHHHHHHHH CS
                         Fib_alpha  95 etidaqesnirvLqnv 110
                                        +i + e  i+vL + 
  gi|313126338|ref|YP_004036608.1| 583 TRIESLEDDIEVLMQF 598
                                       9998888888888665 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.3    0.0048         1       3      69 ..     424     490 ..     424     496 .. 0.93
   2 !   10.4   0.3    0.0029      0.61       2      76 ..     511     578 ..     510     579 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0048
                             Tup_N   3 nelLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYEeeiarL 69 
                                       ++l d ++qE +al +e+  +      +e+ +++  ++ + ir  l  Le    ++ ++ E+  ++L
  gi|313126338|ref|YP_004036608.1| 424 QDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQL 490
                                       699***********************************************99999999998888887 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0029
                             Tup_N   2 lnelLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYEeeiarLkaeLesr 76 
                                       l+e  +av +++++ls ++s++ +    ++        El  +r+ + +L+ +    +++ E+++a  +++L++ 
  gi|313126338|ref|YP_004036608.1| 511 LDEEVEAVHEDIEELSDDLSQTASAAAGLDE-------ELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDEL 578
                                       6777889999999999999999988888886.......9*********************************975 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2      0.13        28      75     142 ..     428     490 ..     394     493 .. 0.71
   2 !   12.3   3.2   0.00063      0.13      70     148 ..     488     577 ..     450     585 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.13
                           DUF1640  75 aalrseteklqreleklkqkLreeidklkadirldlnleKgrireelakleakiqelnnkidrevsal 142
                                         lr+e e+l +el++       +i +++a+     +  +++ir++l+ le  +  l+++++   ++l
  gi|313126338|ref|YP_004036608.1| 428 DGLRQEVEALDEELDAFGD----DIATVEAE-LTAADADREDIRDDLSTLEGDLGALDERVEDTAQQL 490
                                       4455555555555555554....55555555.234499999*******99999999999988776665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00063
                           DUF1640  70 e.........rsefaalrseteklqreleklkqkLreeidkl..kadirldlnleKgrireelakleakiqelnnki 135
                                       +          + +a +++ ++ l +e+e+++++++e  d+l  +a+    l++e g++re+ a l+ +i  + + +
  gi|313126338|ref|YP_004036608.1| 488 QqltevddkaSEAVAGVEELNTTLDEEVEAVHEDIEELSDDLsqTASAAAGLDEELGDVREDIADLDGEIVLTRESL 564
                                       04555555448899999999************9999999988445677899************************** PP

                           DUF1640 136 drevsalrteiEs 148
                                       + +v+++r+ +++
  gi|313126338|ref|YP_004036608.1| 565 EDDVASVRSDLDE 577
                                       ********99986 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   6.9   0.00033      0.07     198     361 ..     429     593 ..     399     600 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                       HHHHHHHHHHHHHHHHHHHHTTTTTTSHH...HHHHHHHHHHHSTTS--SGGGS..SSSSHHHHHHHHHHHHHHHHT CS
                              EzrA 198 kleeeideleevieeiPelleelkkelpk...qleelkegykemkeegYaleel..niekeieelekkieeilerlk 269
                                        l++e+++l+e ++ + + +++++ el +     e++++   +++ +  al+e   +  ++++e+++k +e+++ ++
  gi|313126338|ref|YP_004036608.1| 429 GLRQEVEALDEELDAFGDDIATVEAELTAadaDREDIRDDLSTLEGDLGALDERveDTAQQLTEVDDKASEAVAGVE 505
                                       33333333333333333333333333332111344555555555555555555444566666666666666666666 PP

                                       T--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTH CS
                              EzrA 270 eleledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeelekl 346
                                       el+     ee++ ++e+i++L ddl +   A    +++l  ++e +  l+ ++  ++e+l++   s     ++l++l
  gi|313126338|ref|YP_004036608.1| 506 ELNT-TLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESLEDDVASV---RSDLDEL 578
                                       6664.45666666666666666666666666666666666666666666666666666665544442...4556666 PP

                                       HHHHHHHHHHHHHHH CS
                              EzrA 347 relekelkelekdye 361
                                       +++++++++le+d+e
  gi|313126338|ref|YP_004036608.1| 579 DDVQTRIESLEDDIE 593
                                       666666666666655 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   3.1   0.00054      0.11      39     148 ..     399     507 ..     395     515 .. 0.77
   2 ?    7.4   4.1     0.012       2.6      53     146 ..     479     579 ..     477     585 .. 0.72
   3 ?    4.7   0.3     0.077        16     198     255 ..     542     596 ..     536     606 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00054
                         Rab5-bind  39 LekerkdkkeLedslkelseetskqvselakrvkksEllleeLqqafskakrniqeqlavlvksreqvedelvrLqk 115
                                       L+++++d +   d l e  +e  +    +    +++E+l eeL+ af +++++++ +l+ + + re + d+l++L+ 
  gi|313126338|ref|YP_004036608.1| 399 LQAQMNDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEELD-AFGDDIATVEAELTAADADREDIRDDLSTLEG 474
                                       66667777777777777766666655555567799999999997.6999**************************** PP

                         Rab5-bind 116 dyesLlGkhrkhvslleeEkidlPddveeLqel 148
                                       d   L  +    +++l e + +  + v  + el
  gi|313126338|ref|YP_004036608.1| 475 DLGALDERVEDTAQQLTEVDDKASEAVAGVEEL 507
                                       *****9999999999987666555555555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.012
                         Rab5-bind  53 lkelseetskqvselakrvkksEllleeLqqafskakrniqeqlavlvksreq.......vedelvrLqkdyesLlG 122
                                       l e  e+t++q++e+ +++ ++ +  eeL+ + +++ + ++e++++l + + q       +++el  + +d   L G
  gi|313126338|ref|YP_004036608.1| 479 LDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQtasaaagLDEELGDVREDIADLDG 555
                                       56778899999999998888888888888888888888888888888877777222222246677777777777777 PP

                         Rab5-bind 123 khrkhvslleeEkidlPddveeLq 146
                                       +  +  + le++  ++  d++eL 
  gi|313126338|ref|YP_004036608.1| 556 EIVLTRESLEDDVASVRSDLDELD 579
                                       777777777777777777777775 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.077
                         Rab5-bind 198 eierlkeelasisslkvele.eikvekesle...kslaektrqldklqtikselEeqlkele 255
                                       e+ +++e++a        l+ ei + +esle   +s +    +ld+ qt++++lE++++ l 
  gi|313126338|ref|YP_004036608.1| 542 ELGDVREDIAD-------LDgEIVLTRESLEddvASVRSDLDELDDVQTRIESLEDDIEVLM 596
                                       33344444444.......4325666677776222456677778889999999**99987665 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2     0.005         1       3      47 ..     431     475 ..     430     479 .. 0.94
   2 !    9.2   0.8    0.0067       1.4       1      44 [.     464     507 ..     464     513 .. 0.80
   3 ?    7.4   0.3     0.024         5       3      46 ..     512     555 ..     510     557 .. 0.93
   4 ?    3.7   0.4      0.34        72       3      29 ..     565     594 ..     563     604 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.005
                              XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkklesn 47 
                                       ++++e ++++ld  ++++ ++e   + a++  + + +dl+ le  
  gi|313126338|ref|YP_004036608.1| 431 RQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGD 475
                                       68999***********************************99975 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0067
                              XhlA   1 eikerlerietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                       +i+++l ++e++l  l+erv++  +  +e++ k+ ++   +++l
  gi|313126338|ref|YP_004036608.1| 464 DIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEEL 507
                                       68999999999999999999999999999999988776655555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.024
                              XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                       +e++e +++++++l++++++    aa  +e++  + ed+++l  
  gi|313126338|ref|YP_004036608.1| 512 DEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDG 555
                                       7999************************************9975 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.34
                              XhlA   3 kerlerietkldnlee...rvdkleekaae 29 
                                       +++++ + ++ld+l++   r++ le++ + 
  gi|313126338|ref|YP_004036608.1| 565 EDDVASVRSDLDELDDvqtRIESLEDDIEV 594
                                       566777777777777776677777766554 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       1.5   3.1e+02      95     116 ..     395     416 ..     379     419 .. 0.69
   2 !   10.0   1.0     0.004      0.84       5      99 ..     431     532 ..     430     565 .. 0.82
   3 ?    1.5   0.0       1.8   3.7e+02      88     113 ..     577     602 ..     559     606 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.5
                           DUF4200  95 eiekleekleeykkYeefLekv 116
                                       +i++l++++++++ Y + L ++
  gi|313126338|ref|YP_004036608.1| 395 RIRRLQAQMNDLQAYSDALAEF 416
                                       5666666666666666666555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.004
                           DUF4200   5 kremfevqealeakkeeiqrleeal...kqreeelekkeqeleedllkfdkflkendakraralkkaeee....rkl 74 
                                       ++e++ ++e+l+a  ++i++ e +l   +  +e++++  + le dl  +d+ +++  ++ ++   ka e     ++l
  gi|313126338|ref|YP_004036608.1| 431 RQEVEALDEELDAFGDDIATVEAELtaaDADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAvagvEEL 507
                                       78999999999999999999777661114567888899999999999999999999999998888887763333677 PP

                           DUF4200  75 kkekeaeikklkaeietlkseiekl 99 
                                       +   ++e++  +++ie+l  +++++
  gi|313126338|ref|YP_004036608.1| 508 NTTLDEEVEAVHEDIEELSDDLSQT 532
                                       8888888999999999888776665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.8
                           DUF4200  88 eietlkseiekleekleeykkYeefL 113
                                       e+++++++ie le+ +e ++++++ L
  gi|313126338|ref|YP_004036608.1| 577 ELDDVQTRIESLEDDIEVLMQFRDRL 602
                                       45555566666666665555555544 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3  16.2   9.5e-05      0.02       6     162 ..     430     590 ..     395     606 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.5e-05
                       Tropomyosin   6 veeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaades....er 78 
                                       +++e++   e+l+++ + ++  e++ + a+a+ + ++  +++le +l   +er+e++ ++L+e+  +a+e     e+
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAvagvEE 506
                                       56677777777777777777777777777777777777777777777777777777777777777777777666666 PP

                       Tropomyosin  79 arKvlEnrelkdeekleeleaqlkeakeiaeeadrkyeEvarklvvvesdLeraeeraeaaeskiveLeeeLkvvgn 155
                                       +  +l +   +  e +eel + l++  + a   d+ +  v + ++ +++++  ++e  e   + +++  +eL  v++
  gi|313126338|ref|YP_004036608.1| 507 LNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELDDVQT 583
                                       66667667777777777777777777777777777777777777777777777777777777777777777777777 PP

                       Tropomyosin 156 nlksLev 162
                                        + sLe 
  gi|313126338|ref|YP_004036608.1| 584 RIESLED 590
                                       7777764 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00099      0.21      25     111 ..     415     500 ..     396     501 .. 0.88
   2 ?    1.9   0.1      0.79   1.7e+02      44     102 ..     515     572 ..     505     605 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00099
                            DUF713  25 rFeekEqewsdwlkklrepivklknrfsdfeeeikksdkeekklekedleelqselsnLakkvlsaynkLeeafekl 101
                                        F  +E   +d++ +lr+++  l ++   f ++i++ + e    +  d+e+++ +ls L++ +  + +++e+  ++l
  gi|313126338|ref|YP_004036608.1| 415 EFIDEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADA-DREDIRDDLSTLEGDLGALDERVEDTAQQL 490
                                       6888899999****************************77777665.99****************999999999999 PP

                            DUF713 102 kelsekfedk 111
                                       +e+++k +++
  gi|313126338|ref|YP_004036608.1| 491 TEVDDKASEA 500
                                       9999988765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.79
                            DUF713  44 ivklknrfsdfeeeikksdkeekklekedleelqselsnLakkvlsaynkLeeafeklk 102
                                       +  +++  +++ +++ ++ +    l+ e+l ++++++  L +++  + ++Le++  +++
  gi|313126338|ref|YP_004036608.1| 515 VEAVHEDIEELSDDLSQTASAAAGLD-EELGDVREDIADLDGEIVLTRESLEDDVASVR 572
                                       55555555666666666665544444.48888888888888888888888888766655 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   0.00011     0.023     222     395 ..     422     593 ..     399     605 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                          Prominin 222 lgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCq.seeCs 297
                                        g+dl d l+++v    +el+++++++ +++++L + ++  +++r   s+L+  l +  +++++++++l + + + s
  gi|313126338|ref|YP_004036608.1| 422 TGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEvDDKAS 498
                                       5899999999995555578*************************************************666224444 PP

                          Prominin 298 kilssleiekldtskcldqlpnvdevlealeevletnlssivkeglarlneipekvkn...qtaevvpdlkkalakg 371
                                       ++   +e   l+t  + ++++ v e +e+l + l +  s ++    ++l +++e +++   ++  + ++l  ++a+ 
  gi|313126338|ref|YP_004036608.1| 499 EAVAGVEE--LNTTLD-EEVEAVHEDIEELSDDLSQTASAAA-GLDEELGDVREDIADldgEIVLTRESLEDDVASV 571
                                       44444433..444444.3555555555555444333332222.2233444444444332223444444455555555 PP

                          Prominin 372 reqikklakkiprealdavisdle 395
                                       r+ +++l  ++ +++++++ +d+e
  gi|313126338|ref|YP_004036608.1| 572 RSDLDELD-DV-QTRIESLEDDIE 593
                                       55544443.33.444444444444 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1       1.4   2.9e+02      65     102 ..     395     435 ..     389     443 .. 0.53
   2 ?    2.9   0.0      0.58   1.2e+02       8      46 ..     421     459 ..     416     462 .. 0.86
   3 ?   11.2   5.2    0.0015      0.31      19     104 ..     467     553 ..     462     557 .. 0.93
   4 ?    3.5   0.1      0.37        77      41      77 ..     560     596 ..     555     607 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.4
                       TMF_TATA_bd  65 eleelekeleelqeryetlLellGek...sEeveELraDva 102
                                       +++ l++++++lq   ++l e + e    ++ v+ Lr++v+
  gi|313126338|ref|YP_004036608.1| 395 RIRRLQAQMNDLQAYSDALAEFIDEEgtgQDLVDGLRQEVE 435
                                       55666666666666666666666553222444555555444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.58
                       TMF_TATA_bd   8 gpsvqlverlsseirrlEgElaslkeelerleaerdear 46 
                                       g+ + lv+ l +e+  l+ El ++ ++++++eae  +a 
  gi|313126338|ref|YP_004036608.1| 421 GTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAAD 459
                                       667889999********************9999877765 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0015
                       TMF_TATA_bd  19 seirrlEgElaslkeelerleaerdeareeivklmkeneelke.lkkeleelekeleelqeryetlLellGeksEev 94 
                                         +  lEg+l +l e++e  +++  e+ +   + ++ +eel++ l++e+e + + +eel++ ++++       +Ee 
  gi|313126338|ref|YP_004036608.1| 467 DDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTtLDEEVEAVHEDIEELSDDLSQTASAAAGLDEEL 543
                                       56889*******************************999987527899***************************** PP

                       TMF_TATA_bd  95 eELraDvaDl 104
                                        + r+D+aDl
  gi|313126338|ref|YP_004036608.1| 544 GDVREDIADL 553
                                       *********8 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.37
                       TMF_TATA_bd  41 erdeareeivklmkeneelkelkkeleelekeleelq 77 
                                        r++++++++++ ++ +el++ ++++e+le  +e l 
  gi|313126338|ref|YP_004036608.1| 560 TRESLEDDVASVRSDLDELDDVQTRIESLEDDIEVLM 596
                                       6899999999999999999999999999999988765 PP

>> HAUS5  HAUS augmin-like complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.7   8.2e-05     0.017      86     183 ..     424     527 ..     399     539 .. 0.85
   2 ?    1.1   0.1      0.61   1.3e+02      85     130 ..     539     584 ..     526     589 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.2e-05
                             HAUS5  86 ekeverLraeirrldkeleareeelsreeaevkraldeisdsrhrqvlLe....aydqqceeaakilaedtkrlqeq 158
                                       +  v+ Lr+e++ ld+el a  +++++ eae+ +a ++++d r     Le    a d+++e++a+ l e   + +e 
  gi|313126338|ref|YP_004036608.1| 424 QDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEgdlgALDERVEDTAQQLTEVDDKASEA 500
                                       5668999999999999999999999999999999999999999876666544449********************** PP

                             HAUS5 159 vqqlrdaer..kaekevvfgtskssks 183
                                       v+  ++++    +e+e+v ++ ++ ++
  gi|313126338|ref|YP_004036608.1| 501 VAGVEELNTtlDEEVEAVHEDIEELSD 527
                                       *******99888899999988877553 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.61
                             HAUS5  85 lekeverLraeirrldkeleareeelsreeaevkraldeisdsrhr 130
                                       l +e    r+ i+ ld e+  + e+l+ + a+v   lde  d+++r
  gi|313126338|ref|YP_004036608.1| 539 LDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELDDVQTR 584
                                       77888999*********************************99988 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.051        11      45     124 ..     412     489 ..     401     496 .. 0.57
   2 ?    8.8   0.1    0.0039      0.83      72     129 ..     518     575 ..     511     593 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.051
                       DLP_helical  45 ateekikknggelalieetkksvirdvlerqlpeaeerleelekevekleesakriekelaelkkeieearielree 121
                                       a +e i+++g  + l++  ++ v  + l+++l    + +  +e+e++ ++ + ++i+++l++l+ ++    + +++ 
  gi|313126338|ref|YP_004036608.1| 412 ALAEFIDEEGTGQDLVDGLRQEV--EALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDT 486
                                       56666666666666666666666..4555555555555555555555555555555555555555555544444444 PP

                       DLP_helical 122 lka 124
                                        ++
  gi|313126338|ref|YP_004036608.1| 487 AQQ 489
                                       443 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0039
                       DLP_helical  72 lerqlpeaeerleelekevekleesakriekelaelkkeieearielreelkayfsdL 129
                                       +++ ++e  + l+++ + ++ l+e++ + ++++a l  ei  +r+ l++ +++ +sdL
  gi|313126338|ref|YP_004036608.1| 518 VHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDL 575
                                       67889999999********************************************999 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3       0.2        41       9      56 ..     430     453 ..     390     460 .. 0.59
   2 ?    6.3   6.5     0.064        13      10      66 ..     431     491 ..     422     543 .. 0.64
   3 ?    7.2   2.5     0.033       6.9       8      54 ..     545     595 ..     542     605 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.2
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                        r++++a                        l e+Lda  + +a++e+
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEA------------------------LDEELDAFGDDIATVEA 453
                                       2333333........................44444444444444443 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.064
                           NPV_P10  10 radikavddkVdalqqqvddvqenlp....dvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       r++++a+d+ +da  + ++ v+++l     d +++ + L  +   L +l++ ve+  + L+
  gi|313126338|ref|YP_004036608.1| 431 RQEVEALDEELDAFGDDIATVEAELTaadaDREDIRDDLSTLEGDLGALDERVEDTAQQLT 491
                                       5666666666666666665555554311113345666666666666666666655555554 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.033
                           NPV_P10   8 vIradikavddkV....dalqqqvddvqenlpdvtelnekLdaqsaqLael 54 
                                        +r+di+++d  +    ++l++ v++v+++l ++++++++++++ + ++ l
  gi|313126338|ref|YP_004036608.1| 545 DVREDIADLDGEIvltrESLEDDVASVRSDLDELDDVQTRIESLEDDIEVL 595
                                       589999999999844445899999*********999999999988877655 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.7    0.0088       1.9       3     105 .]     396     492 ..     394     492 .. 0.80
   2 ?    1.4   0.5         2   4.3e+02       8      52 ..     509     552 ..     493     565 .. 0.54
   3 ?   10.2   0.2    0.0039      0.81      23      69 ..     558     604 ..     553     609 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHH CS
                          Spectrin   3 lqqfaqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeie 79 
                                       +++++ ++++l++  +   e++ +e  g+dl  v  l ++ +al +el+a  + + ++++  ++     + + e+i+
  gi|313126338|ref|YP_004036608.1| 396 IRRLQAQMNDLQAYSDALAEFIDEEGTGQDL--VDGLRQEVEALDEELDAFGDDIATVEAELTAA----DADREDIR 466
                                       5778888888888888888888555556665..78899999999999999998888777554433....5677**** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  80 erleelnerWeeLkelaaerkqkLee 105
                                       + l+ l+    +L e+++++ q+L e
  gi|313126338|ref|YP_004036608.1| 467 DDLSTLEGDLGALDERVEDTAQQLTE 492
                                       ***********************975 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin   8 qdadeleeWieekeellssedlgkdleevqallkkhkaleaelaa 52 
                                         +de  e   e  e+l s+dl+++ +++  l +++ ++++++a+
  gi|313126338|ref|YP_004036608.1| 509 TTLDEEVEAVHEDIEEL-SDDLSQTASAAAGLDEELGDVREDIAD 552
                                       33344444444444444.444444444444444444444444444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0039
                                       HHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  23 llssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklld 69 
                                        l+ e l+ d+++v++ l+++++++  +++ ++ ++ l+++ ++l d
  gi|313126338|ref|YP_004036608.1| 558 VLTRESLEDDVASVRSDLDELDDVQTRIESLEDDIEVLMQFRDRLND 604
                                       6788999**********************************999976 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       3.1   6.5e+02     176     214 ..     378     416 ..     322     419 .. 0.74
   2 ?    6.7   2.4     0.019         4     112     174 ..     426     490 ..     396     500 .. 0.78
   3 ?   11.4   9.4   0.00067      0.14      94     222 ..     482     606 ..     475     607 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.1
                              CorA 176 rllakaddkllddedkeylrdlldelerllemlealrer 214
                                       +ll++++d  l++ +  ++r+l+ +++ l+ +++al+e 
  gi|313126338|ref|YP_004036608.1| 378 KLLRSELDFGLPRSADVRIRRLQAQMNDLQAYSDALAEF 416
                                       688889999999999999999999999999999998875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                              CorA 112 lyrlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevl 174
                                       l   l++ v+ l+e+l++  +++  +e el   d  +++i+++l++l+ +l+ l + + ++ + l
  gi|313126338|ref|YP_004036608.1| 426 LVDGLRQEVEALDEELDAFGDDIATVEAELtaADADREDIRDDLSTLEGDLGALDERVEDTAQQL 490
                                       445566667777777777777777777777*99******************99988887777766 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00067
                              CorA  94 vikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrrala 168
                                        ++++ ++  +++++++   + ++e++ +l+e++e+++e+++el+d l    s  +++ +el ++r++++ l   + 
  gi|313126338|ref|YP_004036608.1| 482 RVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLsqTASAAAGLDEELGDVREDIADLDGEIV 558
                                       44455556667888888888999*************************9888889999999***********99999 PP

                              CorA 169 pnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdty 222
                                        +re l++ +a     + d    + l+d++ ++e+l++++e+l +  ++l+d++
  gi|313126338|ref|YP_004036608.1| 559 LTRESLEDDVA---SVRSDL---DELDDVQTRIESLEDDIEVLMQFRDRLNDAF 606
                                       99999955555...333333...45999**********9999999888888876 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       3.7   7.8e+02      53      94 ..     425     466 ..     394     488 .. 0.52
   2 ?   14.3   3.2   0.00013     0.027      16     116 ..     486     587 ..     480     602 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.7
                          KASH_CCD  53 kstQqalqkaklleeEleelkalvkeleEkrarlkaqnkqle 94 
                                         +  + q+ ++l+eEl+     + ++e +   + a ++ + 
  gi|313126338|ref|YP_004036608.1| 425 DLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIR 466
                                       444444555566666666555555555555555555555555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00013
                          KASH_CCD  16 nNkkLaeenskLkkavetaeetnakLteeieeLkkklks....tQqalqkaklleeEleelkalvkeleEkrarlka 88 
                                         ++L e   k  +av  +ee+n  L ee+e+  + +      + q++  a  l+eEl ++++ + +l+    ++  
  gi|313126338|ref|YP_004036608.1| 486 TAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEElsddLSQTASAAAGLDEELGDVREDIADLDG---EIVL 559
                                       569999***************************99987622224678888899**********9999875...5778 PP

                          KASH_CCD  89 qnkqlekenqsLiakiesLqeeniklla 116
                                        ++ le +  s ++ +++L++  +++ +
  gi|313126338|ref|YP_004036608.1| 560 TRESLEDDVASVRSDLDELDDVQTRIES 587
                                       8888999999999999999988887765 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  12.6    0.0016      0.34     390     590 ..     399     594 ..     390     603 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                              HOOK 390 leeklealqkekerl...laerdaLketneELkc.aqlqqkelsqadalaskss.ssgenlaaellpaevreklirL 461
                                       l+++++ lq   + l   + e  + +++++ L+   ++ ++   + da  ++ +  ++e +aa+    ++r+ l  L
  gi|313126338|ref|YP_004036608.1| 399 LQAQMNDLQAYSDALaefIDEEGTGQDLVDGLRQeVEALDE---ELDAFGDDIAtVEAELTAADADREDIRDDLSTL 472
                                       33333333333332211144555555555555551122222...23333333332345666667777889999**** PP

                              HOOK 462 qhENKmLklkqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkk 538
                                       + +  +L +++e +  ++lte+ ++   a + +  +e+ n +  + ++ +++ +eel  +l++  s a     l ++
  gi|313126338|ref|YP_004036608.1| 473 EGDLGALDERVEDT-AQQLTEVDDK---ASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAG---LDEE 542
                                       ***99998888887.6666666555...55555556666678899999999**********999888886...9*** PP

                              HOOK 539 leehleklkevqeelqkkkeqleelepklssnkqkieeleeaLkkkdedlka 590
                                       l    e + +++ e+   +e le+  ++++s     +++++ ++  ++d+++
  gi|313126338|ref|YP_004036608.1| 543 LGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELDDVQTRIESLEDDIEV 594
                                       ************************99***************99999999876 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1      0.11        22      13      91 ..     395     464 ..     390     471 .. 0.79
   2 ?    5.2   0.0      0.11        24       2      82 ..     485     564 ..     484     573 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.11
                              FliJ  13 elqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqer 89 
                                       ++++ +++++ l+ y + +++ + +e+         + q   + l+++++ + +el+    ++ + ++e+ +a   r
  gi|313126338|ref|YP_004036608.1| 395 RIRRLQAQMNDLQAYSDALAEFIDEEG---------TGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADR 462
                                       678889999999999999988888888.........77888888888888888888888888888888888877777 PP

                              FliJ  90 kk 91 
                                       + 
  gi|313126338|ref|YP_004036608.1| 463 ED 464
                                       65 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.11
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqveka 78 
                                       + a++L e+  +  +a + +eel+ +++e  +   ++ +     +l ++ +  + lde++   ++++a++  ++   
  gi|313126338|ref|YP_004036608.1| 485 DTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIE-ELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLT 560
                                       679999999999999999999999999999998888884.4458899999999999999999999999999888887 PP

                              FliJ  79 reew 82 
                                       re +
  gi|313126338|ref|YP_004036608.1| 561 RESL 564
                                       7776 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.1    0.0061       1.3      45     143 ..     432     528 ..     390     537 .. 0.39
   2 ?   10.5   4.9    0.0029      0.61      31     156 ..     453     604 ..     433     607 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0061
                              Fez1  45 akleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeak 121
                                       +       e++ l+e+l+   +++ ++e+el  + ++ e +r+ +++le +l  l e++++++++ +e   +++ea 
  gi|313126338|ref|YP_004036608.1| 432 Q-------EVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAV 501
                                       2.......233333333333333444444444444444444444444444443333333332222222221111111 PP

                              Fez1 122 aqrqe.....aeeleelkreverlrae 143
                                       a  +e      ee+e+ ++++e+l   
  gi|313126338|ref|YP_004036608.1| 502 AGVEElnttlDEEVEAVHEDIEELSDD 528
                                       111111111123344444444444444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0029
                              Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk....kseaellrekvekleeelkelreel 103
                                        e+ a  a+  ++r +l++ e  +  l+e++e+ +++l +++++ +++    ++ +++l+e+ve+++e+++el ++l
  gi|313126338|ref|YP_004036608.1| 453 AELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAvagvEELNTTLDEEVEAVHEDIEELSDDL 529
                                       55555555566666666666666666666666666666666666665555555555666666666666666666666 PP

                              Fez1 104 selsleeeeaa......................lesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqas 156
                                       s++++ ++                         +  d++   r++ +el++ + ++e l+  ++   q +++ ++
  gi|313126338|ref|YP_004036608.1| 530 SQTASAAAGLDeelgdvrediadldgeivltreSLEDDVASVRSDLDELDDVQTRIESLEDDIEVLMQFRDRLND 604
                                       664443333334444444444444444444444223333444555677777777777777777776666666655 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.9    0.0028      0.58     249     363 ..     430     552 ..     424     562 .. 0.66
   2 ?    0.2   0.1       1.2   2.5e+02     334     359 ..     562     587 ..     545     603 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                            Tektin 249 lrkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtqR.pnvElcr.......De 317
                                       lr+ +e + +  +   ++ + v+ e+++++ + e++++++   e+ l     R+e  +q   +v+          +e
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQlTEVDDKAseavagvEE 506
                                       55555555555556666666666666666666666666666666666666666655444312222222111112244 PP

                            Tektin 318 aqyrLveEvkeleetieaLkeklaeaeaslkaLertrleleediav 363
                                           L eEv+ + e+ie+L + l+++ ++   L+++  ++ edia+
  gi|313126338|ref|YP_004036608.1| 507 LNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIAD 552
                                       567899*************************************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                            Tektin 334 eaLkeklaeaeaslkaLertrlelee 359
                                       e+L++ +a +++ l++L++ ++++e+
  gi|313126338|ref|YP_004036608.1| 562 ESLEDDVASVRSDLDELDDVQTRIES 587
                                       44444444444444444444444332 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.27        56      13      53 ..     430     484 ..     417     509 .. 0.54
   2 ?    8.0   0.4     0.021       4.5       4      64 ..     463     523 ..     460     595 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............X CS
                              YabA  13 leeqleelleeleelkeelaelleenaeLeleneklrerl..............e 53 
                                       l +++e+l eel++  +++a++  e ++  ++ e +r+ l              e
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLstlegdlgaldervE 484
                                       5566666666666666666666666666666666666666444444444422221 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXX CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkk 64 
                                       +++ d l++le +l++l e++e+  ++l+e+ ++ +e  +  e+l ++l+ee ++ +e+ +
  gi|313126338|ref|YP_004036608.1| 463 EDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIE 523
                                       5566666666666666666666666666666666655555555555555333333222222 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.064        13      35      65 ..     427     457 ..     418     464 .. 0.89
   2 ?    2.9   0.1      0.53   1.1e+02      39      73 ..     466     500 ..     463     501 .. 0.90
   3 ?    2.9   3.2      0.51   1.1e+02      27      72 ..     486     531 ..     481     533 .. 0.81
   4 ?    2.2   1.8      0.84   1.8e+02      11      60 ..     512     565 ..     511     600 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.064
                        TMF_DNA_bd  35 ikkLrkknkelekeikelkkkleklekelee 65 
                                       ++ Lr++++ l++e++   + ++++e el+ 
  gi|313126338|ref|YP_004036608.1| 427 VDGLRQEVEALDEELDAFGDDIATVEAELTA 457
                                       678************************9976 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.53
                        TMF_DNA_bd  39 rkknkelekeikelkkkleklekeleeleerlkea 73 
                                       r +++ le ++  l++++e+  ++l+e  ++++ea
  gi|313126338|ref|YP_004036608.1| 466 RDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEA 500
                                       6778899999*****************99999886 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.51
                        TMF_DNA_bd  27 kelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                       + ++l +  +k  + ++  e+  ++l++++e + +++eel++ l++
  gi|313126338|ref|YP_004036608.1| 486 TAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQ 531
                                       555666666788888889999999999***************9987 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.84
                        TMF_DNA_bd  11 DeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelk....kklekle 60 
                                       De+++++ e  e+Ls+   +   +   L++++ +  ++i++l+       e+le
  gi|313126338|ref|YP_004036608.1| 512 DEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDgeivLTRESLE 565
                                       777888888888888888888888777887777777777777744442223333 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.2    0.0037      0.77      30     123 ..     424     522 ..     393     540 .. 0.49
   2 ?    4.4   3.4      0.19        40      13     105 ..     505     595 ..     496     605 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0037
                           zf-C4H2  30 ekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrse.... 102
                                       +         ++ L qE +a  eeL    +Di ++E  +  a+ ++e   +  + l  ++ +l e+v+++ ++    
  gi|313126338|ref|YP_004036608.1| 424 QD-------LVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQltev 493
                                       33.......34455566666666666666666666666666666666666666665555555555555444431000 PP

                           zf-C4H2 103 ........lglekledleeeeeellkeei 123
                                                g+e+l+++ +ee e+++e+i
  gi|313126338|ref|YP_004036608.1| 494 ddkaseavAGVEELNTTLDEEVEAVHEDI 522
                                       00000033444444444444444444444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.19
                           zf-C4H2  13 eklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeey 89 
                                       e+l++ l +evea+++    +ee +  l++  +      eeL  +++Di +l+  i  ++e+ e  ++++++ ++e+
  gi|313126338|ref|YP_004036608.1| 505 EELNTTLDEEVEAVHE---DIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDEL 578
                                       5555666666665544...355555566666666666679999********************************** PP

                           zf-C4H2  90 kklkeevnelrse.lgl 105
                                       + +++++++l  +   l
  gi|313126338|ref|YP_004036608.1| 579 DDVQTRIESLEDDiEVL 595
                                       *******9998884444 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0       0.4        85      66     130 ..     424     488 ..     390     508 .. 0.55
   2 ?   10.0   0.1    0.0016      0.34      23     119 ..     475     576 ..     431     595 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.4
                             Atg14  66 kakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrk 130
                                       ++ ++ l+++++ l e+l    d++ +  +e+ ++ +  +  +d+l++   dl +l +++e   +
  gi|313126338|ref|YP_004036608.1| 424 QDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQ 488
                                       33445555555555555555555555555555555555555555555555555555555544333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0016
                             Atg14  23 rlyelrerlaklksekeslkkkiekalegke........eaeqledkiknkkakleelksliadlrerlqelkdkls 91 
                                       +l  l er+ ++  +  ++  k ++a++g e        e+e   ++i+ ++++l+++ s  a l e+l  +++++ 
  gi|313126338|ref|YP_004036608.1| 475 DLGALDERVEDTAQQLTEVDDKASEAVAGVEelnttldeEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIA 551
                                       45556666666666667777777777777667777777788888889999999999999999999999999999999 PP

                             Atg14  92 qlkkeieekkkklaklsdklkkRrsdle 119
                                        l+ ei  +++ l+   +++   rsdl+
  gi|313126338|ref|YP_004036608.1| 552 DLDGEIVLTRESLEDDVASV---RSDLD 576
                                       99999999998888777777...44444 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.5    0.0099       2.1      85     175 ..     407     498 ..     399     500 .. 0.85
   2 ?    7.8   1.9     0.013       2.7      98     173 ..     460     535 ..     438     559 .. 0.79
   3 ?    0.5   0.0       2.3   4.8e+02     101     136 ..     569     603 ..     558     605 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0099
                      Bacillus_HBL  85 qsyyktlveav.dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvi 160
                                       q+y + l e++ +++++++l+++l +  e + +   +  ++i+ +++  ++ ++d ++   d+++l+  l++ +  +
  gi|313126338|ref|YP_004036608.1| 407 QAYSDALAEFIdEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERV 483
                                       88999999999666789999999988888888888888899999999999999999999999999999999999999 PP

                      Bacillus_HBL 161 sqlqneiedlqgkik 175
                                       ++  ++++++++k +
  gi|313126338|ref|YP_004036608.1| 484 EDTAQQLTEVDDKAS 498
                                       999999999888765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.013
                      Bacillus_HBL  98 kdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgk 173
                                        d++++ ++l+ L+ ++    + v++++++L++  +k  + ++  ++   +l++ +++   +i++l  +++++ ++
  gi|313126338|ref|YP_004036608.1| 460 ADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASA 535
                                       6778888888888888888888888888888888888888888888888888888888888888888887777654 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 2.3
                      Bacillus_HBL 101 aellellekLqeeiqqnqkevkqlikeLkklklkla 136
                                       a++ ++l +L  ++q+  ++ +++i+ L++++++l+
  gi|313126338|ref|YP_004036608.1| 569 ASVRSDLDELD-DVQTRIESLEDDIEVLMQFRDRLN 603
                                       55566666664.588888889999999999998886 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.28        59     434     472 ..     418     456 ..     393     473 .. 0.72
   2 ?   10.2   2.4   0.00083      0.17      37     196 ..     484     602 ..     475     606 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.28
                               MAD 434 adassskeevdslkkkleeLelerqrLreqkeelElele 472
                                       +++++ ++ vd l++++e L  e +   + + + E+el 
  gi|313126338|ref|YP_004036608.1| 418 DEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELT 456
                                       456666777888888888888888888888888888886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00083
                               MAD  37 salkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknel 113
                                       ++ ++ql+e  d+  e  +                                              ++e++++l +e+
  gi|313126338|ref|YP_004036608.1| 484 EDTAQQLTEVDDKASEAVAG---------------------------------------------VEELNTTLDEEV 515
                                       34444444444444444444.............................................455555555555 PP

                               MAD 114 aelkrqiekqelelsekeseleelqerldllkkklseleqli....qqlekkqkelaeaeqrikeLefeiqsqedds 186
                                       ++ ++ ie+   +ls++ s    l e+l   ++ +++l+  i    ++le    +     + + + + +i+s edd 
  gi|313126338|ref|YP_004036608.1| 516 EAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIvltrESLEDDVASVRSDLDELDDVQTRIESLEDDI 592
                                       55555555555555555555555555555555555555555445555555555555555555555555555555555 PP

                               MAD 187 livknsksel 196
                                       +++ + +++l
  gi|313126338|ref|YP_004036608.1| 593 EVLMQFRDRL 602
                                       5555555554 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.14        29      81     146 ..     400     464 ..     371     473 .. 0.72
   2 ?    9.6   6.1    0.0028      0.59      60     190 ..     459     589 ..     446     604 .. 0.41

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.14
                         Golgin_A5  81 eaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatlqsrikdrek 146
                                       +aq+ ++ + + + l+e+ ++  + +     +++e+e l+eel++  ++   + a+l +   dre+
  gi|313126338|ref|YP_004036608.1| 400 QAQM-NDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADRED 464
                                       4433.5666666666666666666666777778888888888888888888888877777777775 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0028
                         Golgin_A5  60 reelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskat 136
                                        ++ ++ +  +++l  +l  l+++++  a++l e   ++ e+++  ++ + ++++e+e ++e+++ l ++l+++ + 
  gi|313126338|ref|YP_004036608.1| 459 DADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTAS- 534
                                       3344444444444444555555555444455444444555555544445555555555555555555555543322. PP

                         Golgin_A5 137 lqsrikdrekeieklrnqlttkslsss.sesele...sRlkqLtesLiqKQtvlEals 190
                                               ++e+ ++r++++    +   +++ le   + +++  + L   Qt +E+l+
  gi|313126338|ref|YP_004036608.1| 535 ---AAAGLDEELGDVREDIADLDGEIVlTRESLEddvASVRSDLDELDDVQTRIESLE 589
                                       ...2222233333333333222111111122222000223333444444444444444 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.3    0.0041      0.86      56     117 ..     472     536 ..     461     552 .. 0.69
   2 ?    6.6   0.4     0.037       7.7      19      99 ..     510     588 ..     505     595 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0041
                         ApoLp-III  56 leealkevkkkieetadklse...enPevkkkaqelqekvQsgvqslvkesqklaeslkensqea 117
                                       le  l  + + +e ta++l+e   + +e++  ++el++++ + v+++ ++ ++l  +l++ +++a
  gi|313126338|ref|YP_004036608.1| 472 LEGDLGALDERVEDTAQQLTEvddKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAA 536
                                       55555555666666666666666667778888888888888888888888888888888776654 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.037
                         ApoLp-III  19 sqeevvetiKensenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsg 95 
                                         +e ve++ e  e+l d l+q+++ +   l ++ + + e + ++  +i+ t+++l+   + v   ++el   vQ++
  gi|313126338|ref|YP_004036608.1| 510 TLDEEVEAVHEDIEELSDDLSQTASAA-AGLDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELD-DVQTR 584
                                       345667888888888888888876554.4577777888899999999999999999999999999999996.69999 PP

                         ApoLp-III  96 vqsl 99 
                                       ++sl
  gi|313126338|ref|YP_004036608.1| 585 IESL 588
                                       9988 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.58   1.2e+02     270     339 ..     388     453 ..     375     458 .. 0.73
   2 ?    8.8   0.9    0.0037      0.77     244     342 ..     425     530 ..     417     535 .. 0.75
   3 ?    4.6   0.3     0.071        15     249     339 ..     511     597 ..     507     609 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.58
                                       HHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 270 vkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeake 339
                                       ++++a v +  l++++++l+   ++l + ++++ +     + +++ l++ ++  +e+l+ + ++  ++++
  gi|313126338|ref|YP_004036608.1| 388 LPRSADVRIRRLQAQMNDLQAYSDALAEFIDEEGT----GQDLVDGLRQEVEALDEELDAFGDDIATVEA 453
                                       78899999999999999999999999999999999....6666666666666666666666666665555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0037
                                       BHHHHHHHHHHTTSGGGGGHHHHTTTHHH...CCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCT....TSSTT-THH CS
                               FH2 244 tLLHylvkiireklpevldfsseLknvkk...aakvnleslekevkklekglkklekelessek....keepsdkfl 313
                                        L++ l ++++   +e++ f +++ +v+    aa  + e++++++++le +l +l + +e+ ++     +++  + +
  gi|313126338|ref|YP_004036608.1| 425 DLVDGLRQEVEALDEELDAFGDDIATVEAeltAADADREDIRDDLSTLEGDLGALDERVEDTAQqlteVDDKASEAV 501
                                       5888999999999999**********995444999999999999999999999999999999997555444455555 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 314 evlkeflkeaeeklkkleeelkeakelvk 342
                                       + ++e  ++ +e+++ + e+ +e+ + + 
  gi|313126338|ref|YP_004036608.1| 502 AGVEELNTTLDEEVEAVHEDIEELSDDLS 530
                                       55666666666666666666666665555 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.071
                                       HHHHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHH CS
                               FH2 249 lvkiireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaee 325
                                       l+++++  +++++++s++L++  +aa+     l++e+ ++++++++l  e+   +++ e++ + + +  + l++ ++
  gi|313126338|ref|YP_004036608.1| 511 LDEEVEAVHEDIEELSDDLSQTASAAA----GLDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELDDVQT 583
                                       778899999999999999999999765....7888888888888888888888888777777777777777888888 PP

                                       HHHHHHHHHHHHHH CS
                               FH2 326 klkkleeelkeake 339
                                       ++++le++ + +++
  gi|313126338|ref|YP_004036608.1| 584 RIESLEDDIEVLMQ 597
                                       88888888877766 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0047      0.99      43     135 ..     430     553 ..     392     564 .. 0.62
   2 ?   -1.1   0.0       5.8   1.2e+03      82     107 ..     577     602 ..     559     606 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0047
                     PI3K_P85_iSH2  43 iseeiqlkrqaleaFneaikmFeeqiklqekfskeaq...............................ehEieklqe 88 
                                       +++e++     l+aF++ i   e +++  +   ++                                 ++ +  ++e
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEALDEELDAFGDDIATVEAELTAADADREDIRddlstlegdlgaldervedtaqqltevddkaSEAVAGVEE 506
                                       45555555555555555555555555555544444424444445555555555555555666666665455557777 PP

                     PI3K_P85_iSH2  89 nleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqL 135
                                        +  l + ++ +h+  e+L++dl q+++    l+ e+  ++ ++  L
  gi|313126338|ref|YP_004036608.1| 507 LNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADL 553
                                       77778888888888888888888888888888888887777777766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.8
                     PI3K_P85_iSH2  82 EieklqenleqlksrlkelhsskekL 107
                                       E +++q+ +e l++ ++ l + +++L
  gi|313126338|ref|YP_004036608.1| 577 ELDDVQTRIESLEDDIEVLMQFRDRL 602
                                       44444555555555555555555555 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       5.6   1.2e+03     115     156 ..     404     445 ..     396     450 .. 0.71
   2 ?   -0.1   0.0       2.9   6.1e+02     103     153 ..     427     477 ..     408     490 .. 0.69
   3 ?    2.9   0.5      0.34        72      98     134 ..     492     528 ..     482     548 .. 0.69
   4 ?    7.5   0.1     0.013       2.7     104     149 ..     551     596 ..     531     606 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.6
                     Fzo_mitofusin 115 keleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                       ++l++  ++l + i++  + q     lr++ + l++eL++f 
  gi|313126338|ref|YP_004036608.1| 404 NDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEELDAFG 445
                                       566666666666677766777777788888888888888885 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.9
                     Fzo_mitofusin 103 farlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLe 153
                                       ++ l+q+v+  ++el++  +++ +  ++l ++    + +r+  s+le +L 
  gi|313126338|ref|YP_004036608.1| 427 VDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLG 477
                                       566777777777777765555555555555555666666666666665554 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.34
                     Fzo_mitofusin  98 elsstfarlcqqvdetekeleeeikelekeiekleev 134
                                       e++   ++  + v+e +++l+ee+++++++ie+l + 
  gi|313126338|ref|YP_004036608.1| 492 EVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDD 528
                                       4444455555667888888899999888888888654 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.013
                     Fzo_mitofusin 104 arlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslle 149
                                       a l  ++  t+++le++++++++++++l++vq++ + l +  + l 
  gi|313126338|ref|YP_004036608.1| 551 ADLDGEIVLTRESLEDDVASVRSDLDELDDVQTRIESLEDDIEVLM 596
                                       5667777788999999999999999999999999999987766654 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.5    0.0055       1.2      29     108 ..     435     514 ..     398     519 .. 0.86
   2 ?    2.4   0.5      0.97   2.1e+02      11      76 ..     512     579 ..     504     593 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0055
                            TBCC_N  29 ekvdsFlkaFteekaaieellesveesadksklkqkldeitaeiqeLqkllaessmfLpsYdlrsaq..ealskLke 103
                                       e  d+ l+aF +  a +e++l++++  ad+++ +++l  ++ ++ +L++ + ++   L++ d + +   + +++L++
  gi|313126338|ref|YP_004036608.1| 435 EALDEELDAFGDDIATVEAELTAAD--ADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEavAGVEELNT 509
                                       5666678899999999999999999..*********************************99887651156888888 PP

                            TBCC_N 104 sleea 108
                                       +l+e 
  gi|313126338|ref|YP_004036608.1| 510 TLDEE 514
                                       88875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.97
                            TBCC_N  11 qeqlekrkeereseaveeekvdsFlkaFteekaaieellesve..esadksklkqkldeitaeiqeLq 76 
                                        e++e+ +e+ e+ +++ ++++s ++ ++ee  +++e +++++    + +++l+++++ + ++++eL+
  gi|313126338|ref|YP_004036608.1| 512 DEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDgeIVLTRESLEDDVASVRSDLDELD 579
                                       44555555555555555555555555555555555555555555533444444444444444444443 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4       0.1        21      29      98 ..     489     554 ..     477     566 .. 0.74
   2 ?    7.2   0.1     0.025       5.4      76     105 ..     567     596 ..     559     598 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.1
                            GCN5L1  29 altealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlalvesfnsalkeiGDvenWaktie 98 
                                       +  +++ dk  + va + + +  l++e+ a+++ +++++   +q ++++  +++   e+GDv++ ++ ++
  gi|313126338|ref|YP_004036608.1| 489 Q-LTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDE---ELGDVREDIADLD 554
                                       3.34578888888888888899999*******9999999999999999999886...6788876555555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.025
                            GCN5L1  76 lvesfnsalkeiGDvenWaktienDlksit 105
                                        v s++s+l+e++Dv+  ++++e D+++++
  gi|313126338|ref|YP_004036608.1| 567 DVASVRSDLDELDDVQTRIESLEDDIEVLM 596
                                       678999*******************99876 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.06        13       2      59 ..     436     493 ..     423     500 .. 0.66
   2 ?    6.9   0.8     0.014         3       7      62 ..     476     531 ..     470     538 .. 0.77
   3 ?    4.1   0.1       0.1        21       4      50 ..     505     554 ..     502     570 .. 0.83
   4 ?   -0.4   0.0       2.3   4.9e+02       5      51 ..     541     587 ..     537     603 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.06
                              RmuC   2 qleellkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtka 59 
                                       +l+e l+ + + ++++e ++++ + ++++ +  l++  + l +l e+++d+a++Lt++
  gi|313126338|ref|YP_004036608.1| 436 ALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEV 493
                                       4555566666666666666666666666666666666666777777777777777654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                              RmuC   7 lkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLkn 62 
                                       l  l+e++e++ ++++e++++ +e+ + ++e  ++l e  e ++++ e+L++ L++
  gi|313126338|ref|YP_004036608.1| 476 LGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQ 531
                                       56688888888888888888888888888888888888888888888888877765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.1
                              RmuC   4 eellkplkeklekfeekveees...keeaeeleslkeqlkelqelneqlg 50 
                                       eel ++l+e++e+++e +ee s   ++ a++ + l+e+l+ ++e  ++l+
  gi|313126338|ref|YP_004036608.1| 505 EELNTTLDEEVEAVHEDIEELSddlSQTASAAAGLDEELGDVREDIADLD 554
                                       78889999999999999999998888888888999999999888766665 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.3
                              RmuC   5 ellkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgd 51 
                                       e l  ++e +++++ ++  + ++ +++ +s++  l el + ++++++
  gi|313126338|ref|YP_004036608.1| 541 EELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDELDDVQTRIES 587
                                       55555666666666666666666666666666666666666666654 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3         1   2.2e+02      73     131 ..     431     489 ..     396     499 .. 0.64
   2 ?    8.0   0.1     0.013       2.8      58     118 ..     504     564 ..     493     566 .. 0.88
   3 ?    0.4   0.0       2.9   6.2e+02      54      82 ..     560     591 ..     555     604 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 1
                              ADIP  73 qskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktq 131
                                       ++++e l+++l ++   +a+v+a+++ + ++ ++  + l ++  +l  l   ++++++q
  gi|313126338|ref|YP_004036608.1| 431 RQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQ 489
                                       44455555555555555555555555555555555555555555555444444444444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.013
                              ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeel 118
                                       ++e + +l+ e e  + +ie l++ l+q+++ +a + +++ + + ++++l+  +  ++e+l
  gi|313126338|ref|YP_004036608.1| 504 VEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESL 564
                                       567788999**************************************99998888777765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.9
                              ADIP  54 qreslnetirkleaeierl...qskierlktq 82 
                                       +resl++++ + +++++ l   q++ie+l++ 
  gi|313126338|ref|YP_004036608.1| 560 TRESLEDDVASVRSDLDELddvQTRIESLEDD 591
                                       67888888888887777642224444444443 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.61   1.3e+02      10      35 ..     394     420 ..     390     427 .. 0.78
   2 ?   -0.1   0.0       3.8     8e+02      89     114 ..     430     455 ..     422     461 .. 0.66
   3 ?    1.5   0.2       1.2   2.6e+02      80     116 ..     463     499 ..     449     503 .. 0.65
   4 ?    3.4   0.3      0.32        67      82     117 ..     479     514 ..     476     517 .. 0.91
   5 ?    4.3   0.3      0.17        35      76     116 ..     498     538 ..     493     542 .. 0.81
   6 ?    4.5   0.1      0.15        32       6      47 ..     562     600 ..     559     603 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHHHHHHHHHHHTT.. CS
                         Prefoldin  10 aelaqlkeaieelektletlktlkk.e 35 
                                        ++++l++++++l++  ++l ++++ e
  gi|313126338|ref|YP_004036608.1| 394 VRIRRLQAQMNDLQAYSDALAEFIDeE 420
                                       678999999999999999999999843 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  89 lekqlekleeeleklkdqittleanl 114
                                       l++ +e l eel+   d i t+ea+l
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEALDEELDAFGDDIATVEAEL 455
                                       55666666777777777777766665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanlaq 116
                                       e + + l++le  l  l e +e+ ++q+t++ +++++
  gi|313126338|ref|YP_004036608.1| 463 EDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASE 499
                                       5566667777777777777777777777777666665 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaql 117
                                       l++++e+  +ql+++ +++ ++ + +++l+ +l++ 
  gi|313126338|ref|YP_004036608.1| 479 LDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEE 514
                                       89*************************999999876 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  76 eeAiellkkkleelekqlekleeeleklkdqittleanlaq 116
                                        eA++ +++  ++l++ +e + e++e+l+d + ++  ++a 
  gi|313126338|ref|YP_004036608.1| 498 SEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAG 538
                                       57777777777899999999999999999999999888775 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEET CS
                         Prefoldin   6 eslqaelaqlkeaieelektletlktlkkedegkevlvplga 47 
                                       esl++++a++++ ++el+++  ++++l++   ++evl+++ +
  gi|313126338|ref|YP_004036608.1| 562 ESLEDDVASVRSDLDELDDVQTRIESLED---DIEVLMQFRD 600
                                       78999999999999999999999999999...7777776665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.2      0.67   1.4e+02      16      16 ..     490     490 ..     427     525 .. 0.59
   2 ?    3.0   0.0      0.64   1.3e+02       2      36 ..     522     556 ..     521     561 .. 0.92
   3 ?    5.0   0.7      0.16        33       5      41 ..     564     596 ..     559     600 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.67
                         FlaC_arch  16 l 16 
                                       l
  gi|313126338|ref|YP_004036608.1| 490 L 490
                                       2 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.64
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelken 36 
                                       i+el  +ls++ +  + + +e+ ++++++ +l+ +
  gi|313126338|ref|YP_004036608.1| 522 IEELSDDLSQTASAAAGLDEELGDVREDIADLDGE 556
                                       7999*************************999866 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.16
                         FlaC_arch   5 lEnklsklst...eletvkkeneelsksveelkenVkdll 41 
                                       lE ++ ++ +   el       +++++ +e l+++++ l+
  gi|313126338|ref|YP_004036608.1| 564 LEDDVASVRSdldEL-------DDVQTRIESLEDDIEVLM 596
                                       455555555533444.......444555666666665555 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.8   0.00023     0.049      43     141 ..     395     493 ..     390     495 .. 0.89
   2 ?    1.2  11.1       1.7   3.6e+02      41     127 ..     505     602 ..     494     606 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00023
                     Tropomyosin_1  43 knqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeeleesdkkLkettekLretdvkaeelERkvka 119
                                       +++ l+++++ l++      e  +e+ + +   + l + ++ L eel+    ++++    L+ +d+  e++      
  gi|313126338|ref|YP_004036608.1| 395 RIRRLQAQMNDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLST 471
                                       6777888888888888888888888889999999******************************************* PP

                     Tropomyosin_1 120 Leqerdewekkyeeleekykea 141
                                       Le    + ++++e++++++ e+
  gi|313126338|ref|YP_004036608.1| 472 LEGDLGALDERVEDTAQQLTEV 493
                                       ****************999876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.7
                     Tropomyosin_1  41 tkknqqleeevekleeklkeakekaeesekkktnne...........altrkiqlLEeeleesdkkLkettekLret 106
                                       ++ n +l+eeve + e+++e  + +++++++++  +            l   i l  e le+  +++++ ++ L ++
  gi|313126338|ref|YP_004036608.1| 505 EELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDeelgdvrediaDLDGEIVLTRESLEDDVASVRSDLDELDDV 581
                                       455667777777777777777777777666666554557777778889999999999999999999*********** PP

                     Tropomyosin_1 107 dvkaeelERkvkaLeqerdew 127
                                       + + e lE  +++L q rd  
  gi|313126338|ref|YP_004036608.1| 582 QTRIESLEDDIEVLMQFRDRL 602
                                       *******99999999988865 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       5.1   1.1e+03      47      74 ..     430     457 ..     396     460 .. 0.74
   2 ?    7.2   0.1     0.018       3.8      10      72 ..     480     543 ..     477     551 .. 0.84
   3 ?    1.1   0.1       1.4   2.9e+02      27      57 ..     568     598 ..     556     606 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 5.1
                              RPW8  47 vvkeieklnkeldrpreeieeLkklLek 74 
                                       +++e+e l +eld + ++i   + +L+ 
  gi|313126338|ref|YP_004036608.1| 430 LRQEVEALDEELDAFGDDIATVEAELTA 457
                                       4567777777777777777776666665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.018
                              RPW8  10 gaalgellkaileakkksldfksilkrLestl.eritPvvkeieklnkeldrpreeieeLkklL 72 
                                       +  +++ ++ ++e+ +k+++    +++L+ tl e+++ v ++ie+l+++l +  +    L ++L
  gi|313126338|ref|YP_004036608.1| 480 DERVEDTAQQLTEVDDKASEAVAGVEELNTTLdEEVEAVHEDIEELSDDLSQTASAAAGLDEEL 543
                                       556677788899999999999999********66899*************99888888888777 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.4
                              RPW8  27 sldfksilkrLestleritPvvkeieklnke 57 
                                       +++++s l++L++  +ri+ + ++ie l + 
  gi|313126338|ref|YP_004036608.1| 568 VASVRSDLDELDDVQTRIESLEDDIEVLMQF 598
                                       4455566666666666666666666665544 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.8    0.0021      0.45     566     668 ..     461     563 ..     449     606 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                             Nup88 566 qkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklk 642
                                        +e   ++l++le +   l er+e  A+++ e+ dk  + v  v+++  +l +++  + e   e++  l+++ ++  
  gi|313126338|ref|YP_004036608.1| 461 DREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAA 537
                                       5777889*********************************************9999999999999************ PP

                             Nup88 643 slknalkqvkkkldkqrkqiakskee 668
                                        l+++l +v++ +     +i  ++e+
  gi|313126338|ref|YP_004036608.1| 538 GLDEELGDVREDIADLDGEIVLTRES 563
                                       *******9999887776666555554 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.15        32      31      92 ..     391     455 ..     377     474 .. 0.71
   2 ?    6.5   1.4     0.055        12      25      74 ..     479     532 ..     477     557 .. 0.69
   3 ?    1.0   0.1       2.9   6.1e+02      32      58 ..     574     600 ..     554     605 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.15
                                       .BHHHHHHHHHHHH...HHHHHHHHHHHHHHH...HHHHHHHHHHHHHH.......HHHHHHHHH CS
                             DUF16  31 snkqrLkkieakvdklgeqinkleqkvekqge...kikelkveqkaqgeelnkvdetleliletL 92 
                                       s + r+++++a+++ l+   ++l++ +++ g     ++ l++e++a +eel++ ++ +  +   L
  gi|313126338|ref|YP_004036608.1| 391 SADVRIRRLQAQMNDLQAYSDALAEFIDEEGTgqdLVDGLRQEVEALDEELDAFGDDIATVEAEL 455
                                       56778888888888888888888888887764222477888888888888876655555554444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.055
                                       HHHB-..BHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  25 lnefkdsnkqrLkkieakvd....klgeqinkleqkvekqgekikelkveqkaq 74 
                                       l+e  +++ q+L+++++k +      +e    l ++ve+  e i+el+ +  + 
  gi|313126338|ref|YP_004036608.1| 479 LDERVEDTAQQLTEVDDKASeavaGVEELNTTLDEEVEAVHEDIEELSDDLSQT 532
                                       7888899******99998773332455555667777778888888777665544 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 2.9
                                       BHHHHHHHHHHHH...HHHHHHHHHHH CS
                             DUF16  32 nkqrLkkieakvdklgeqinkleqkve 58 
                                          +L ++++++++l+  i++l q  +
  gi|313126338|ref|YP_004036608.1| 574 DLDELDDVQTRIESLEDDIEVLMQFRD 600
                                       456788888888888888888877655 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4     0.064        14      43     107 ..     432     496 ..     427     505 .. 0.86
   2 ?    8.2   1.6      0.01       2.1      17     100 ..     508     588 ..     497     601 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.064
                            Nsp1_C  43 kkvneWDrvLvengekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsk 107
                                       ++v++ D+ L   g+ I+ +  e+ +a+++ + i + L+ +e +   L++ +++  ++l e+  k
  gi|313126338|ref|YP_004036608.1| 432 QEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDK 496
                                       5788889999999*****************************99999999888888888877655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.01
                            Nsp1_C  17 nktldelinkWtteLeeqekeFeeqakkvneWDrvLvengekIskLysevleaeqeqnkidqeLeyiesqqdeLesl 93 
                                       n tlde ++  ++++ee ++  ++ a+  +  D+ L +  e I++L  e++ +    + +++    + s+ deL+++
  gi|313126338|ref|YP_004036608.1| 508 NTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLT---RESLEDDVASVRSDLDELDDV 581
                                       789********************************************999865...568999999999999999998 PP

                            Nsp1_C  94 LdnyEke 100
                                        +++E+ 
  gi|313126338|ref|YP_004036608.1| 582 QTRIESL 588
                                       7777653 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       1.6   3.3e+02      27      46 ..     390     409 ..     385     415 .. 0.83
   2 ?    4.4   0.2      0.23        49      15      57 ..     417     458 ..     414     460 .. 0.84
   3 ?   10.5   0.5    0.0029      0.62      19      69 ..     455     505 ..     451     507 .. 0.88
   4 ?    0.7   0.1       3.2   6.7e+02      24      49 ..     506     531 ..     493     544 .. 0.61
   5 ?    3.8   0.5      0.35        74       9      43 ..     559     595 ..     547     605 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.6
                               CLZ  27 keleekverLessLeaLqtr 46 
                                       ++++ +++rL+++++ Lq  
  gi|313126338|ref|YP_004036608.1| 390 RSADVRIRRLQAQMNDLQAY 409
                                       678899***********975 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.23
                               CLZ  15 LDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyess 57 
                                       +Dee    ++  + l + ve L+++L+a+ + +a + ae++++
  gi|313126338|ref|YP_004036608.1| 417 IDEE-GTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAA 458
                                       7777.5677788889999**********999999999999876 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0029
                               CLZ  19 aakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqRitkLE 69 
                                         +a a+++++ + ++ Le+ L aL+ r++ + +++++++ k  + ++ +E
  gi|313126338|ref|YP_004036608.1| 455 LTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVE 505
                                       567789********************************9999888887776 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 3.2
                               CLZ  24 aeqkeleekverLessLeaLqtrlar 49 
                                       + + +l+e ve + + +e L + l +
  gi|313126338|ref|YP_004036608.1| 506 ELNTTLDEEVEAVHEDIEELSDDLSQ 531
                                       44455666666666666666555544 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.35
                               CLZ   9 LlKdglLDee..aakag..aeqkeleekverLessLeaL 43 
                                       L+++ l D    ++  +  +e +++++++e+Le  +e+L
  gi|313126338|ref|YP_004036608.1| 559 LTRESLEDDVasVR--SdlDELDDVQTRIESLEDDIEVL 595
                                       44444444442222..13366667777777777777766 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5      0.66   1.4e+02      74      80 ..     451     457 ..     395     503 .. 0.56
   2 ?    4.4   0.8      0.17        37      60      95 ..     504     539 ..     496     548 .. 0.82
   3 ?    7.9   0.4     0.014       2.9      15      47 ..     562     594 ..     559     598 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.66
                                       HHHHHHH CS
                       Prefoldin_2  74 lekeikt 80 
                                       +e+e+++
  gi|313126338|ref|YP_004036608.1| 451 VEAELTA 457
                                       2222222 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleel 95 
                                       +ee++++L+e+ e + + i++l++ l++     + l
  gi|313126338|ref|YP_004036608.1| 504 VEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGL 539
                                       689999999999999999999999988876665555 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--E CS
                       Prefoldin_2  15 qqlaqqikqletqlkelelvleelelldedtkv 47 
                                       + l+ ++++++ +l+el++v++ +e+l++d +v
  gi|313126338|ref|YP_004036608.1| 562 ESLEDDVASVRSDLDELDDVQTRIESLEDDIEV 594
                                       67899999*********************9655 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5      0.25        52      52      98 ..     395     441 ..     390     476 .. 0.69
   2 ?    8.1   1.2    0.0069       1.4      20      92 ..     482     554 ..     469     558 .. 0.82
   3 ?    4.7   0.1     0.076        16      66     103 ..     560     597 ..     554     603 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.25
                           DUF3450  52 eyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel 98 
                                       ++r+l+++ ++l++y + l++ +++  +  + ++   +e+e++ +el
  gi|313126338|ref|YP_004036608.1| 395 RIRRLQAQMNDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEEL 441
                                       67788888888888888888777776555555555555555555544 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0069
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                        ++++a++ ++ + ++++ +  +++  ++l +e++a++e +e+l+   +q ++  a +++e+ +++e+i++++
  gi|313126338|ref|YP_004036608.1| 482 RVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLD 554
                                       6788888888888888888888888888888888888888888888888888888888888888888887765 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.076
                           DUF3450  66 yneqlerlvasqeqeiasleeqieeieeierelvplle 103
                                        +e le+ vas+++++++l+  +++ie +e++++ l++
  gi|313126338|ref|YP_004036608.1| 560 TRESLEDDVASVRSDLDELDDVQTRIESLEDDIEVLMQ 597
                                       57889999****************************96 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.8    0.0057       1.2      31     100 ..     414     531 ..     379     537 .. 0.68
   2 ?    0.7   0.1       2.9   6.1e+02      77     116 ..     554     593 ..     533     603 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0057
                             THOC7  31 a.....................................esteeeleqlkedllldfaafelsie...........rl 59 
                                       a                                     e++  + ++++ed+  d++++e  +            +l
  gi|313126338|ref|YP_004036608.1| 414 AefideegtgqdlvdglrqevealdeeldafgddiatvEAELTAADADREDIRDDLSTLEGDLGaldervedtaqQL 490
                                       25555555665566666666666666666666666777444555555555555555555555554455555977777 PP

                             THOC7  60 qllakanerereryeaekeeieseieavreeieelkaqLee 100
                                         +++  ++ ++ +e+++ ++++e eav+e+ieel ++L++
  gi|313126338|ref|YP_004036608.1| 491 TEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQ 531
                                       7778888889999999999999***************9987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.9
                             THOC7  77 keeieseieavreeieelkaqLeearatranrkeydelae 116
                                         ei  + e+++++ ++ +++L+e   ++ + +  +   e
  gi|313126338|ref|YP_004036608.1| 554 DGEIVLTRESLEDDVASVRSDLDELDDVQTRIESLEDDIE 593
                                       4444444455555555555555555544444444444444 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1     0.014         3     106     199 ..     399     497 ..     374     507 .. 0.75
   2 ?    3.4   0.8      0.25        53     137     225 ..     510     601 ..     502     603 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHH...HH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXXX.XXXXXXXXXXX CS
                              SHE3 106 leeelerlkvqYdal...vd...sqkeYkehYqqeieeLkesleklklenekqleelqerissndkdidtkldsynn 176
                                       l+++++ l++  dal   +d   + +   +  +qe+e L e+l+++  +   ++e   +    + +di   l+ +++
  gi|313126338|ref|YP_004036608.1| 399 LQAQMNDLQAYSDALaefIDeegTGQDLVDGLRQEVEALDEELDAFGDDIA-TVEAELTAADADREDIRDDLSTLEG 474
                                       6677777777777772223322222344566789*************9999.56666666777778*********** PP

                                       XXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 177 kkknlesieeeknkkllkklesl 199
                                          +l++  e+  ++l++  +++
  gi|313126338|ref|YP_004036608.1| 475 DLGALDERVEDTAQQLTEVDDKA 497
                                       *******9999999988765555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHSSSXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXX CS
                              SHE3 137 eLkesleklklenekqleelqerissndkdidtkldsynnkkknlesieeeknkkllkkleslaseld....leswl 209
                                       +L e++e+ +++ e +l +  +++ s +  +d++l +  +  ++l+   +   + l+  + s++s+ld    +++ +
  gi|313126338|ref|YP_004036608.1| 510 TLDEEVEAVHEDIE-ELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLTRESLEDDVASVRSDLDelddVQTRI 585
                                       46667777777766.56666666777777999999999999999999999999999999999999998877766666 PP

                                       XXXXXXXXXXXXXXXX CS
                              SHE3 210 elykelkelileyaek 225
                                       e  ++  e+ +++ ++
  gi|313126338|ref|YP_004036608.1| 586 ESLEDDIEVLMQFRDR 601
                                       6666666666666655 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       3.1   6.6e+02      46      66 ..     395     415 ..     374     464 .. 0.72
   2 ?    5.3   0.3     0.076        16      45      99 ..     467     521 ..     432     533 .. 0.76
   3 ?    5.6   0.2     0.061        13      47      99 ..     469     521 ..     461     573 .. 0.66
   4 ?    2.9   0.0      0.44        92      44      73 ..     575     604 ..     559     607 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.1
                              SKA2  46 rlkkvkeelqaLkeqceella 66 
                                       r+++++++++ L++  ++l++
  gi|313126338|ref|YP_004036608.1| 395 RIRRLQAQMNDLQAYSDALAE 415
                                       566666666666666555543 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.076
                              SKA2  45 erlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasaelppls 99 
                                        +l+ +  +l aL e++e+ +++  e+ dk++  +++  el + L +++e+  ++
  gi|313126338|ref|YP_004036608.1| 467 DDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHED 521
                                       5677777777888888888888888888888888877777777777776554444 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.061
                              SKA2  47 lkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasaelppls 99 
                                       l+ +  +l aL e++e+ +++  e+ dk++  +++  el + L +++e+  ++
  gi|313126338|ref|YP_004036608.1| 469 LSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHED 521
                                       55555555566666666666666666666666655555555555555433332 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.44
                              SKA2  44 lerlkkvkeelqaLkeqceellaekkelid 73 
                                       l +l +v++++++L++++e l + + +l d
  gi|313126338|ref|YP_004036608.1| 575 LDELDDVQTRIESLEDDIEVLMQFRDRLND 604
                                       67899**************99998887766 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  10.4   0.00014      0.03       9     140 ..     396     534 ..     382     603 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                           DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvk....adkeeveeel.aekadkeaLatk 80 
                                       +  lq+++ +lq++     ++ +e  +++ + ++ +++l++++e+l+++     +d  +ve el a  ad+e+++  
  gi|313126338|ref|YP_004036608.1| 396 IRRLQAQMNDLQAYS----DALAEFIDEEGTGQDLVDGLRQEVEALDEELdafgDDIATVEAELtAADADREDIRDD 468
                                       677888888888776....889999**********************9987787999999999934569******99 PP

                           DUF4795  81 vsrdqfDeakkeLekmleellekleeqeealkkaldtLqeelkekld......rlelepLkeqle...e 140
                                        s   ++  + +L++ +e+  ++l+e++++  +a+  ++ el++ ld      + ++e+L++ l    +
  gi|313126338|ref|YP_004036608.1| 469 LST--LEGDLGALDERVEDTAQQLTEVDDKASEAVAGVE-ELNTTLDeeveavHEDIEELSDDLSqtaS 534
                                       965..5555555555555555555555555555555554.55555552222335566666666653330 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0      0.09        19      35      67 ..     427     459 ..     425     462 .. 0.78
   2 ?   -0.2   0.0       5.6   1.2e+03      42      70 ..     462     490 ..     458     497 .. 0.76
   3 ?    2.4   0.2      0.87   1.8e+02      38      67 ..     511     540 ..     500     544 .. 0.57
   4 ?    2.1   0.1         1   2.1e+02      33      59 ..     576     602 ..     555     606 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.09
                          JIP_LZII  35 vdeLtsereiLreEleslqkakerlesrikelE 67 
                                       vd L +e e+L eEl++  +  +++e ++++++
  gi|313126338|ref|YP_004036608.1| 427 VDGLRQEVEALDEELDAFGDDIATVEAELTAAD 459
                                       788888888888888888888888887777665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 5.6
                          JIP_LZII  42 reiLreEleslqkakerlesrikelEeel 70 
                                       re +r++l++l+  + +l +r++++ ++l
  gi|313126338|ref|YP_004036608.1| 462 REDIRDDLSTLEGDLGALDERVEDTAQQL 490
                                       66677788888888888888888877766 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.87
                          JIP_LZII  38 LtsereiLreEleslqkakerlesrikelE 67 
                                       L +e e+++e++e+l + +++  s  + l+
  gi|313126338|ref|YP_004036608.1| 511 LDEEVEAVHEDIEELSDDLSQTASAAAGLD 540
                                       445555666666666666555555555555 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 1
                          JIP_LZII  33 arvdeLtsereiLreEleslqkakerl 59 
                                        ++d+ +++ e+L++++e l++ ++rl
  gi|313126338|ref|YP_004036608.1| 576 DELDDVQTRIESLEDDIEVLMQFRDRL 602
                                       456666666666666666666666666 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.63   1.3e+02      77     112 ..     562     600 ..     547     603 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.63
                           DUF4618  77 ekeekklekLeq...qleqlnakvqklqeelnvLstYkD 112
                                       e +e ++++ +    +l+ +++++++l+++++vL  ++D
  gi|313126338|ref|YP_004036608.1| 562 ESLEDDVASVRSdldELDDVQTRIESLEDDIEVLMQFRD 600
                                       444455554444011555667889999999999888877 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.0    0.0062       1.3      11     104 ..     431     531 ..     427     539 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0062
                                       HHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHC.... CS
                              GrpE  11 edeeeeleeeleelekevkelkekllrllaefenlrkrtekeke..eakkfaiekfakdLLpvlDnleralksak.. 83 
                                       ++e e+l+eel+++ + ++ ++ +l  + a+ e +r  + +      a ++ +e+ a++L +v D+ + a++ ++  
  gi|313126338|ref|YP_004036608.1| 431 RQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGdlGALDERVEDTAQQLTEVDDKASEAVAGVEel 507
                                       68999*******************************99865554136899*********************988777 PP

                                       ...HHH-HHHHHHHHHHHHHHHHH CS
                              GrpE  84 ...eneeekslleGvemtlkqllk 104
                                           +ee+++++e +e   + l +
  gi|313126338|ref|YP_004036608.1| 508 nttLDEEVEAVHEDIEELSDDLSQ 531
                                       666666666888888877777766 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.19        39       3      69 ..     404     470 ..     402     474 .. 0.90
   2 ?    4.0   0.8       0.2        41       9      68 ..     484     543 ..     475     545 .. 0.75
   3 ?    0.7   0.1         2   4.3e+02      37      67 ..     565     595 ..     548     605 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.19
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       + L+++++ + e++++  + +++++ l++++++ +e+  ++ ++  ++ +e +  +   e+i+++L+
  gi|313126338|ref|YP_004036608.1| 404 NDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLS 470
                                       7899999999999999999999999999999999999999999999999999999999999999887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.2
                             Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                       e++ ++l e  d+a e ++ +ee  ++ +e+ +++he+ e+l ++ ++  + a  ++e+L
  gi|313126338|ref|YP_004036608.1| 484 EDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEEL 543
                                       455666666677788888888888888888888888888888888888888887777766 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2
                             Sec34  37 sektsslheaceqlleeqkrleelaeeieek 67 
                                       +++  s++++ ++l + q+r+e+l ++ie  
  gi|313126338|ref|YP_004036608.1| 565 EDDVASVRSDLDELDDVQTRIESLEDDIEVL 595
                                       4444455555555555555555555555433 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.57   1.2e+02      26      89 ..     426     492 ..     424     496 .. 0.73
   2 ?    8.4   3.0    0.0045      0.95      18      98 ..     474     554 ..     457     556 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.57
                           Vps53_N  26 likklqeeikklddeiksvvraqanvg...ekgkealeeaqkaieelfqkikeikdkaekseemvke 89 
                                       l++ l++e++ ld+e+    ++ a v    + +  + e++ + ++ l+ ++  + ++ e + + + e
  gi|313126338|ref|YP_004036608.1| 426 LVDGLRQEVEALDEELDAFGDDIATVEaelTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTE 492
                                       556677777777777777666655554111346678899999***************9999988776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0045
                           Vps53_N  18 qslanidelikklqeeikklddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdI 94 
                                         l  +de ++   +++ ++dd+  ++v +  +  +   e++e +++ ieel+++++++ + a+  +e + ++ +dI
  gi|313126338|ref|YP_004036608.1| 474 GDLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDI 550
                                       567789999999999***************999999999************************************** PP

                           Vps53_N  95 kqLD 98 
                                         LD
  gi|313126338|ref|YP_004036608.1| 551 ADLD 554
                                       ***9 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       2.9   6.1e+02      39      59 ..     392     412 ..     389     421 .. 0.82
   2 ?    3.9   0.1      0.33        69      21      62 ..     426     467 ..     403     475 .. 0.65
   3 ?    0.1   0.0       4.9     1e+03      38      64 ..     471     497 ..     456     503 .. 0.62
   4 ?    6.2   2.4     0.062        13      16      66 ..     495     545 ..     487     549 .. 0.80
   5 ?    0.7   0.1       3.2   6.8e+02      42      58 ..     577     593 ..     561     604 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2.9
                            Csm1_N  39 kdqeiesLkeqlaeleekvke 59 
                                        d +i +L++q++ l++ ++ 
  gi|313126338|ref|YP_004036608.1| 392 ADVRIRRLQAQMNDLQAYSDA 412
                                       578999******999987765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.33
                            Csm1_N  21 lvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkelee 62 
                                       lv  l +E   L+++l+   + i +++++l +++++++++ +
  gi|313126338|ref|YP_004036608.1| 426 LVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRD 467
                                       666667777777777777777777777777777777666655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 4.9
                            Csm1_N  38 tkdqeiesLkeqlaeleekvkeleerr 64 
                                       t +  + +L e+++   +++ e ++++
  gi|313126338|ref|YP_004036608.1| 471 TLEGDLGALDERVEDTAQQLTEVDDKA 497
                                       444444555555555555555555554 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.062
                            Csm1_N  16 dsAdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkk 66 
                                       d+A  +v+ + + N++L++++e  ++ ie+L   l +  +  + l+e+  +
  gi|313126338|ref|YP_004036608.1| 495 DKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGD 545
                                       677778888888899999999999999999999999988888888777665 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 3.2
                            Csm1_N  42 eiesLkeqlaeleekvk 58 
                                       e+  ++ ++++le +++
  gi|313126338|ref|YP_004036608.1| 577 ELDDVQTRIESLEDDIE 593
                                       44444444444444443 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.1     0.032       6.7     114     217 ..     398     530 ..     389     551 .. 0.76
   2 ?    2.2   3.5      0.47     1e+02     148     203 ..     489     544 ..     481     598 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.032
                            Cluap1 114 dlssklsdlkaarqlaseite...kgasLydlLekeve..........................lreartkalsrql 161
                                        l+++++dl+a+  + +e ++   +g+ L d L++eve                          + + r++  + + 
  gi|313126338|ref|YP_004036608.1| 398 RLQAQMNDLQAYSDALAEFIDeegTGQDLVDGLRQEVEaldeeldafgddiatveaeltaadadREDIRDDLSTLEG 474
                                       5789999999987766555542335789*********9888888888888888888888888777777777777778 PP

                            Cluap1 162 eleeiekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLq 217
                                       +l  ++++++++ ++++e  +k ++a++ +e+ +++L++ +e  ++++e  ++ L+
  gi|313126338|ref|YP_004036608.1| 475 DLGALDERVEDTAQQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLS 530
                                       88888888888888877777778888888888888888888877777777666665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.47
                            Cluap1 148 elreartkalsrqleleeiekalkeaikkvkeelektkkalenlesdeanLeakie 203
                                       +l e  +ka ++   +ee++++l e++++v+e++e+++++l++++s  a L++ + 
  gi|313126338|ref|YP_004036608.1| 489 QLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELG 544
                                       34455555555666666666666666666666666666666666666666665543 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.1      0.11        22      11      77 ..     432     494 ..     424     535 .. 0.40
   2 ?    3.2   0.7      0.81   1.7e+02      14      89 ..     537     591 ..     504     604 .. 0.43

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.11
                    PRKG1_interact  11 eenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkele 77 
                                       +e e L +eL+    +++++++el+ ++  r++ + +  s+le    +  +l++++ ++ ++l+e++
  gi|313126338|ref|YP_004036608.1| 432 QEVEALDEELDAFGDDIATVEAELTAADADRED-IRDDLSTLEG---DLGALDERVEDTAQQLTEVD 494
                                       555666666666666666666665555544322.2222221111...11122222222222221111 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.81
                    PRKG1_interact  14 erLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkeleeLraenqrLkdE 89 
                                         L +eL ++++++++l  e+                        r+sle  ++ + ++l el+++++  + L d 
  gi|313126338|ref|YP_004036608.1| 537 AGLDEELGDVREDIADLDGEIV---------------------LTRESLEDDVASVRSDLDELDDVQTRIESLEDD 591
                                       2222333333333333333222.....................244555555555555555555555555555543 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   7.7      0.48     1e+02      10     147 ..     316     470 ..     259     486 .. 0.74
   2 ?    5.9   8.5     0.064        13      80     163 ..     445     532 ..     398     553 .. 0.44
   3 ?    7.2   7.0     0.025       5.3      59     163 ..     487     588 ..     480     603 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.48
                             ATG16  10 darqekafaeliqaynrLldrtsaleaenaklekaaasaks....sksskksakekeasasq............... 67 
                                       da q++   ++++     +d ++  e+ +a++ +a+++a s         + a e +    +               
  gi|313126338|ref|YP_004036608.1| 316 DADQTADTDDYVDIGDSVADDADDTESTTASATAASTTAASgslaA----ALAAELR----Agdvpeddlkllrsel 384
                                       5555555666666666666666666666666655544444433221....1111111....1223355667777777 PP

                             ATG16  68 ......snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletk 138
                                             s+ ++  ++q++ + l++  + lae   + g+ ++ +  l +e+++l+e+l +    +a +eae +a    
  gi|313126338|ref|YP_004036608.1| 385 dfglprSADVRIRRLQAQMNDLQAYSDALAEFIDEEGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADAD 461
                                       78888877777788888888888888888888888888888888888888888888888888888888888888777 PP

                             ATG16 139 lkdreeelr 147
                                       ++d ++ l 
  gi|313126338|ref|YP_004036608.1| 462 REDIRDDLS 470
                                       777666654 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.064
                             ATG16  80 eqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkd....reeelrekekl 152
                                        + +a++ +el+++   r++  + l +l+  l +l+e+ +  +++l e+ ++ ++    +++    ++ee++   + 
  gi|313126338|ref|YP_004036608.1| 445 GDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASEAVAGVEElnttLDEEVEAVHED 521
                                       33444444444444444444444444444444444444444444444443333333222222000022333333333 PP

                             ATG16 153 vqdlqDElsaL 163
                                       +++l D+ls+ 
  gi|313126338|ref|YP_004036608.1| 522 IEELSDDLSQT 532
                                       33444444444 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.025
                             ATG16  59 kekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraal 135
                                        +++++ ++   k s+ ++  e++ ++l ee+++++   +el++ l ++ ++ + l+e+l   +e +a+l  e+   
  gi|313126338|ref|YP_004036608.1| 487 AQQLTEVDD---KASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEIVLT 560
                                       334444333...67778888888888888888888888888888888888888888888888888888888888888 PP

                             ATG16 136 etklkdreeelrekeklvqdlqDElsaL 163
                                       ++ l+d  + +r     ++d+q  +++L
  gi|313126338|ref|YP_004036608.1| 561 RESLEDDVASVRSDLDELDDVQTRIESL 588
                                       8888888888887777777777666665 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.3     0.032       6.7      69     127 ..     472     545 ..     397     557 .. 0.61
   2 ?   -0.8   0.1       6.3   1.3e+03     105     125 ..     562     582 ..     555     599 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.032
                         Rootletin  69 l...........eealakLeeErqrsek....laqvnslLreqleearqaneaLtedlqkltkdwerlreeleq 127
                                       l           e + ++L e   ++++    ++++n++L e++e+ ++  e+L++dl ++ +    l eel +
  gi|313126338|ref|YP_004036608.1| 472 LegdlgaldervEDTAQQLTEVDDKASEavagVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEELGD 545
                                       12222333333366677777666665542222678999999999999999999999999988888888888755 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 6.3
                         Rootletin 105 eaLtedlqkltkdwerlreel 125
                                       e+L++d+  +++d+++l + +
  gi|313126338|ref|YP_004036608.1| 562 ESLEDDVASVRSDLDELDDVQ 582
                                       566666666666666554433 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       9.2   1.9e+03      22      62 ..     374     414 ..     363     424 .. 0.79
   2 ?    6.0   0.1     0.087        18      21      93 ..     402     473 ..     388     479 .. 0.78
   3 ?    2.1   4.1       1.4     3e+02      34      89 ..     488     543 ..     475     595 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 9.2
                    HIP1_clath_bdg  22 qeeverekkeleeelerlkeeaerkleeqkeelekLkrele 62 
                                        ++++  ++el++ l r  + + r+l+ q   l++    l+
  gi|313126338|ref|YP_004036608.1| 374 EDDLKLLRSELDFGLPRSADVRIRRLQAQMNDLQAYSDALA 414
                                       57888888888888888888888888888888887666655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.087
                    HIP1_clath_bdg  21 aqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93 
                                       + +++++  + l+e +++ +   +  ++  ++e+e+L +el a  +++a++++ L+      e++   l++L+
  gi|313126338|ref|YP_004036608.1| 402 QMNDLQAYSDALAEFIDE-EGTGQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLE 473
                                       445666666666665555.44556667788899*************************999999999999997 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 1.4
                    HIP1_clath_bdg  34 eelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssql 89 
                                       ++l ++ ++a++ ++  +e   +L +e+ea ++++++l   L++++ + + l ++l
  gi|313126338|ref|YP_004036608.1| 488 QQLTEVDDKASEAVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTASAAAGLDEEL 543
                                       33333334444444443344444444444444444444444444444433333333 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.4    0.0076       1.6      20     131 ..     423     534 ..     414     553 .. 0.67
   2 ?    0.7   0.3       2.7   5.7e+02      31      73 ..     557     599 ..     546     606 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0076
                     Jnk-SapK_ap_N  20 geevvkgLmPkvVkvLElLeslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqe 96 
                                       g++ v+gL   v ++ E+L+++  + +  eael    +++e+++ +++    +  + +e++e + +q+ e   + +e
  gi|313126338|ref|YP_004036608.1| 423 GQDLVDGLRQEVEALDEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDERVEDTAQQLTEVDDKASE 499
                                       67777777777777778888888888888888777777777777777777777777777777777777777777777 PP

                     Jnk-SapK_ap_N  97 kveqleeenrelelkaknaadqlsrleekeaelkk 131
                                       +v+ +ee n  l+  ++++++ +++l++  ++  +
  gi|313126338|ref|YP_004036608.1| 500 AVAGVEELNTTLDEEVEAVHEDIEELSDDLSQTAS 534
                                       77777777777776666666666655555444433 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.7
                     Jnk-SapK_ap_N  31 vVkvLElLeslasrneeeeaeleelreeleqLeteyerekelr 73 
                                       +V + E+Le  ++  ++   el++++  +e+Le + e   ++r
  gi|313126338|ref|YP_004036608.1| 557 IVLTRESLEDDVASVRSDLDELDDVQTRIESLEDDIEVLMQFR 599
                                       5556677777777777777777777777777776666555544 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   7.4     0.025       5.4      60     177 ..     438     557 ..     374     578 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.025
                           DUF2353  60 kekekklsqlleesreenkalkleveeLrqklkeaqgDiklLR..eqlarqrlglkdedlletrhssaeereelvkq 134
                                       +e+  +  + ++ +  e  a   + e++r+ l+ ++gD  +L    + + q+l+  d++++e+    +e    l ++
  gi|313126338|ref|YP_004036608.1| 438 DEELDAFGDDIATVEAELTAADADREDIRDDLSTLEGDLGALDerVEDTAQQLTEVDDKASEAVAGVEELNTTLDEE 514
                                       66666667777777888888899999999999999999999963355566666666666667766668888899999 PP

                           DUF2353 135 lEklkekiqqlerdlkavldekeelvterdaykeKaerLnqeL 177
                                       +E ++e i++l  dl ++      l  e    +e ++ L+ e+
  gi|313126338|ref|YP_004036608.1| 515 VEAVHEDIEELSDDLSQTASAAAGLDEELGDVREDIADLDGEI 557
                                       9999999999999999988887777777776666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1415  (0.0789224); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); expected 358.6 (0.02)
Passed Vit filter:                       168  (0.00937029); expected 17.9 (0.001)
Passed Fwd filter:                       111  (0.00619109); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              85  [number of targets reported over threshold]
# CPU time: 1.74u 0.43s 00:00:02.17 Elapsed: 00:00:00.65
# Mc/sec: 2847.30
//
Query:       gi|313126339|ref|YP_004036609.1|  [L=298]
Description: hypothetical protein Hbor_15940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.5   0.0      0.068   13.1   0.0    1.3  1  HisG      ATP phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.8e-06     0.068      70     159 ..     200     288 ..     119     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-06
                                       EEES-HHHHHHHHHHTT-E.EEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHH CS
                              HisG  70 iaTsypnlakkyfeekglk.veiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankksl 145
                                       i   y++l++  +  + l+ ++  + + svE   a+  + + v l+ tG+T r+ gL   e+++ s++vL+ n +++
  gi|313126339|ref|YP_004036609.1| 200 ISPRYERLVEAVLGTRPLEnISFAYPEESVEEESAIADVGLGVYLTMTGSTARDYGLVLGEHLFPSETVLMENVAET 276
                                       666677777777766666657777777788888888777778899**************************777666 PP

                                       HSHHHHHHHHHHHH CS
                              HisG 146 kkkekieellerlr 159
                                       +  + +e++++ + 
  gi|313126339|ref|YP_004036609.1| 277 T--AAVEHVAQAIT 288
                                       5..67777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1684.52
//
Query:       gi|313126340|ref|YP_004036610.1|  [L=79]
Description: hypothetical protein Hbor_15950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.33s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 481.51
//
Query:       gi|313126341|ref|YP_004036611.1|  [L=389]
Description: tryptophanyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-25   90.0   0.0      1e-24   87.4   0.0    1.8  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
       0.13   12.4   5.1       0.54   10.4   0.4    3.3  2  DUF1707       Domain of unknown function (DUF1707)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   1.1e-28     1e-24       5     292 ..      69     347 ..      65     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 1.1e-28
                                       --EEEEEEETSSS-BGGGHHHHHHHHHHHH.TTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTC CS
                      tRNA-synt_1b   5 plrvysGidPTgklHlGylvplkklvelqk.aghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgl 80 
                                         +v++G  P+g++HlG+++p+    +lq+  g  v++ + D + +  + +  + +++ +++++       +la+g+
  gi|313126341|ref|YP_004036611.1|  69 TCSVVTGRGPSGPMHLGHVLPFYFAKYLQEqTGAYVYVPLSDDEKYFAKDR--QFEDISAHVRENLRD---LLAVGF 140
                                       5789*************************9899*************99999..899999988888888...****** PP

                                       HTTTEEEEETHHHHTTH..HHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS... CS
                      tRNA-synt_1b  81 dpekaevvlqsewlehl..elaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad... 152
                                       dpe++++v+ ++  +      a + +dl++         +   +  + e++  ++g+  Yp  qaa  ll +     
  gi|313126341|ref|YP_004036611.1| 141 DPERTRFVIDTADADVVypLAAAFANDLTP---------ATV-EAVYGEQP--NVGLTFYPAVQAAHLLLPQLVhgr 205
                                       *********987555443223334444444.........333.33444434..89**************99988899 PP

                                       ...EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCH CS
                      tRNA-synt_1b 153 ...lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkav 226
                                          lvp+  DQ+ ++++ rd+a + ++    +kp  l+ ++l++l G  KmS+S++   I L+d+ ++v++ki +  
  gi|313126341|ref|YP_004036611.1| 206 hptLVPVAVDQDPHVRVCRDIAAKERYD--VDKPGDLLSRFLPSLGGPGKMSSSDDAPSIELTDDRATVEEKIHRYA 280
                                       999************************9..9******************************************9888 PP

                                       CSTTC...SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 227 tdsde...evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                        + ++     ++   + + ++   +++l  + ++++ r++e l+ +++ + ++ g++k ++ae++  +l
  gi|313126341|ref|YP_004036611.1| 281 HSGGRdslAAHREHGGDPAVDV-AYQYLHFFFESDD-RTVERLARDYRAGDLTSGEMKARAAEQIVDFL 347
                                       8888878889999999******.9999999999998.****************************9998 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4     6e-05      0.54       9      34 ..     315     340 ..     314     344 .. 0.93
   2 ?    2.2   0.5     0.021   1.9e+02       2      13 ..     368     379 ..     367     388 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6e-05
                           DUF1707   9 eravelLrealaeGrLtldEfdeRle 34 
                                       +r+ve+L++ + +G Lt  E+  R +
  gi|313126341|ref|YP_004036611.1| 315 DRTVERLARDYRAGDLTSGEMKARAA 340
                                       799*******************9976 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.021
                           DUF1707   2 RasdadRerave 13 
                                       R++d++Rera +
  gi|313126341|ref|YP_004036611.1| 368 RLTDDERERARR 379
                                       99*******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 2122.99
//
Query:       gi|313126342|ref|YP_004036612.1|  [L=283]
Description: hypothetical protein Hbor_15970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1661.19
//
Query:       gi|313126343|ref|YP_004036613.1|  [L=402]
Description: ferrichrome ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-19   69.8   0.1    3.8e-19   69.2   0.1    1.3  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.1   2.1e-23   3.8e-19       2     237 ..      89     361 ..      89     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 2.1e-23
                                       EE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT........TS-BSBESSSB-HHHHHHH--SEEEE-GGG... CS
                      Peripla_BP_2   2 aslspsvteillalGatdkvvgvdtttsdpldadklee......aivevgadgeidvEklaalkPDlvilskgl... 69 
                                       a++ ++++++ +alG++d + +v+ +++ ++  ++++       +     + g id E    ++ D+ + ++++   
  gi|313126343|ref|YP_004036613.1|  89 ATYCQGYADMGIALGQADGLLSVGYKPRLHTHWYEELDgvsvdkESLQELYQGGIDKELFYTMDADIHVIDPNWiin 165
                                       5777899***************************99855655554455556667777*****************999 PP

                                       ..........GGGHHHHHHHS-EEE----TTS......HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH.HHHHTS CS
                      Peripla_BP_2  70 .......gltdedeellksgiptvivessntg......eslkeqiralgellgledeaeklvaeidskla.aaksai 132
                                              ++ de+ e  ++ i  +i++ + t       +  +e ++ ++e++++++++e++ + +d+ ++ ++ + +
  gi|313126343|ref|YP_004036613.1| 166 nfkgweqADIDEITEGVAPFIGNLIFRHTDTWhedyqyYTMYEAFEKVAEIFQEQERYEAFKSLHDEYVRgRVAEQL 242
                                       99984333333344444444445788888888*************************************95678888 PP

                                       -TT...-EEEEEEEETTE......EEEE-TTSTTTHHHHTS--EESTTT--.....STT-EEE-HHHHHHH--SEEE CS
                      Peripla_BP_2 133 dse..kpkpvlvfggade....ggyvvagsnsyigdlldalgieniaaesk.....kseyeeisaEqilasdpdvif 198
                                       + e   ++++l+++ ++e    ++y +++ ++ i+ l d l+++++++        + ++ +i+ Eq+l+ dpd ++
  gi|313126343|ref|YP_004036613.1| 243 PAEseAASAALIYAAGNEpekfSPYRLNTGGTSIKHLRD-LKVKDAFEGTDvkgisSTNRTKIDYEQLLEVDPDTLL 318
                                       888877888888888888899888888888888887766.*********99************************** PP

                                       EEEH....HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-HH CS
                      Peripla_BP_2 199 vsgr....aeadnktgleflkenpllaelpAvkngrVyaldss 237
                                         g+    ++++++t ++++k++++ ++l+Avkn rV++ +++
  gi|313126343|ref|YP_004036613.1| 319 LKGHetktEAEFQNTLVKHMKNHDIGSQLTAVKNDRVFRGGPT 361
                                       **************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2561.63
//
Query:       gi|313126344|ref|YP_004036614.1|  [L=143]
Description: hypothetical protein Hbor_15990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-05   23.1  13.7    7.4e-05   23.1  13.7    1.7  2  CopD      Copper resistance protein D
  ------ inclusion threshold ------
       0.37   10.8   4.3        1.4    8.9   4.3    2.2  1  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3      0.35   3.2e+03      12      22 ..      15      25 ..       5      37 .. 0.55
   2 !   23.1  13.7   8.2e-09   7.4e-05       4     105 .]      45     143 .]      43     143 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.35
                              CopD 12 laavavvlvtG 22
                                      l+  ++++v G
  gi|313126344|ref|YP_004036614.1| 15 LWTGGTLVVAG 25
                                      33333333333 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 8.2e-09
                              CopD   4 lrrFsrlalaavavvlvtGvvnallrvglagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqal 80 
                                        rrF  l +a++ ++l +G  +a  +++ + l t+++G l+la+++l+lvl+++    ++ l+  l    ++ + a+
  gi|313126344|ref|YP_004036614.1|  45 ARRFWYLTVASTLLLLFSGGHLAGTIYTAETLQTMGRGNLVLAMVGLWLVLAIVLFFGYRQLTNSLS---EKSAVAA 118
                                       799*9*********************999**********************999999999******3...3444555 PP

                              CopD  81 rhrlrrsaalelvlalvvlllaaal 105
                                       + + r ++    +++++ l++a++l
  gi|313126344|ref|YP_004036614.1| 119 ATKARPWFLGASAVSIALLVVAGVL 143
                                       559999**99*******99999987 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.3   0.00016       1.4      15      29 ..      86     100 ..      85     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00016
                            OppC_N  15 lAvvglvilllllli 29 
                                       lA+vgl+++l+++l+
  gi|313126344|ref|YP_004036614.1|  86 LAMVGLWLVLAIVLF 100
                                       8*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 789.39
//
Query:       gi|313126345|ref|YP_004036615.1|  [L=125]
Description: bacterial regulatory protein, arsr family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-09   35.7   0.1    9.4e-09   35.2   0.1    1.2  1  HTH_20    Helix-turn-helix domain
    0.00011   22.0   0.2    0.00016   21.4   0.2    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
    0.00012   22.0   0.0     0.0002   21.3   0.0    1.3  1  HTH_7     Helix-turn-helix domain of resolvase
    0.00094   19.0   0.0     0.0015   18.4   0.0    1.3  1  MarR_2    MarR family
     0.0035   17.1   0.0     0.0054   16.5   0.0    1.3  1  HTH_IclR  IclR helix-turn-helix domain
     0.0062   16.4   0.0     0.0082   16.0   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0075   16.2   0.0      0.011   15.7   0.0    1.2  1  HTH_11    HTH domain
  ------ inclusion threshold ------
      0.075   13.2   0.0       0.11   12.6   0.0    1.3  1  FUR       Ferric uptake regulator family
      0.076   13.0   0.0       0.15   12.0   0.0    1.4  2  PadR      Transcriptional regulator PadR-like family
       0.13   12.1   0.0       0.18   11.6   0.0    1.3  1  DUF742    Protein of unknown function (DUF742)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   5.2e-12   9.4e-09       2      59 ..      16      71 ..      15      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5.2e-12
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      ++++ L++   r il +L  + + +asel+e++dl+ +t+++ L+ L+e  Lv+  +e
  gi|313126345|ref|YP_004036615.1| 16 TVLKSLDDDKCRTILTLL--DNPKSASELCEECDLPSSTVYRKLELLRESMLVREYTE 71
                                      58999*************..*********************************98776 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   9.1e-08   0.00016       5      45 ..      26      66 ..      22      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.1e-08
                                      HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      ++ +  L +++++++el+ee +l+ stv + L  Lre+ LV
  gi|313126345|ref|YP_004036615.1| 26 CRTILTLLDNPKSASELCEECDLPSSTVYRKLELLRESMLV 66
                                      55567799*****************************8777 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.1e-07    0.0002       4      43 ..      19      58 ..      18      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                                      -SS-HHHHGGGGSSTTTT--STTTSSSS---SSSS--SS- CS
                             HTH_7  4 sklskndinrvvkLleeGisiskIAkevnisRsTvYRyla 43
                                      ++l++++  ++++Ll+++ s+s++++e ++  sTvYR+l+
  gi|313126345|ref|YP_004036615.1| 19 KSLDDDKCRTILTLLDNPKSASELCEECDLPSSTVYRKLE 58
                                      577888899*****************************95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.5e-07    0.0015       9      55 ..      27      70 ..      21      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.5e-07
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      r ++ L ++p    +++el+++++l+ s+v r l+ L +  Lv++ +
  gi|313126345|ref|YP_004036615.1| 27 RTILTLLDNPK---SASELCEECDLPSSTVYRKLELLRESMLVREYT 70
                                      67788999998...*****************************6654 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     3e-06    0.0054      20      49 ..      38      67 ..      28      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3e-06
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyve 49
                                      + sel+++++lp Stv+R L  L e  +v+
  gi|313126345|ref|YP_004036615.1| 38 SASELCEECDLPSSTVYRKLELLRESMLVR 67
                                      789***************999998876665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.6e-06    0.0082      15      53 ..      30      67 ..      20      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.6e-06
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      l+Ll   p++a+e+ ee ++p s+vY+ L+ L +  lV+
  gi|313126345|ref|YP_004036615.1| 30 LTLL-DNPKSASELCEECDLPSSTVYRKLELLRESMLVR 67
                                      5566.67999********************999877775 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.1e-06     0.011       3      43 ..      27      64 ..      25      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.1e-06
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      ++il+lL ++ +  s++eL ee ++  +tv+r ++ L+e++
  gi|313126345|ref|YP_004036615.1| 27 RTILTLL-DNPK--SASELCEECDLPSSTVYRKLELLRESM 64
                                      5788888.6665..***********************9976 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.1e-05      0.11      39      61 ..      47      69 ..      37      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.1e-05
                                      T--HHHHHHHHHHHHHTTSEEEE CS
                               FUR 39 eislaTVYrtLklleeaglvkel 61
                                      ++  +TVYr L+ll+e+ lv+e 
  gi|313126345|ref|YP_004036615.1| 47 DLPSSTVYRKLELLRESMLVREY 69
                                      56679**************9986 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       6.8   1.2e+04      36      45 ..      16      25 ..       7      26 .. 0.73
   2 ?   12.0   0.0   8.5e-05      0.15      22      64 ..      42      83 ..      36      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.8
                                      HHHHHHHHTT CS
                              PadR 36 paLkrLekeg 45
                                      ++Lk+L +++
  gi|313126345|ref|YP_004036615.1| 16 TVLKSLDDDK 25
                                      6788888776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.5e-05
                                      CSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEE CS
                              PadR 22 lsegllelseGslYpaLkrLekeglveseweesgegpprkyYr 64
                                      l e+  +l  +++Y+ L+ L+++ lv ++ e  ++gp+  +Y+
  gi|313126345|ref|YP_004036615.1| 42 LCEE-CDLPSSTVYRKLELLRESMLVREYTEVRRDGPNATLYE 83
                                      4443.788899********************9999*9999886 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.9e-05      0.18      42      85 ..      23      66 ..       7      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.9e-05
                            DUF742 42 qpehrailrLcreplsVaelaAelklPvgvvrvLlsdLldagll 85
                                       +++r+il L  +p+s  el  e +lP ++v   l  L ++ l+
  gi|313126345|ref|YP_004036615.1| 23 DDKCRTILTLLDNPKSASELCEECDLPSSTVYRKLELLRESMLV 66
                                      57899************************997666555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 768.88
//
Query:       gi|313126346|ref|YP_004036616.1|  [L=91]
Description: hypothetical protein Hbor_16010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.076   13.1   1.6      0.073   13.1   0.9    1.5  1  Jagunal          Jagunal, ER re-organisation during oogenesis
       0.34   11.0   7.4       0.42   10.7   7.4    1.1  1  TspO_MBR         TspO/MBR family
       0.34   11.5   5.2       0.18   12.3   3.2    1.5  2  DUF1218          Protein of unknown function (DUF1218)
       0.46    8.9   2.7       0.43    9.0   2.7    1.2  1  Phlebovirus_G2   Phlebovirus glycoprotein G2
        3.8    7.7  13.7        2.4    8.4   1.3    2.3  2  YtpI             YtpI-like protein


Domain annotation for each model (and alignments):
>> Jagunal  Jagunal, ER re-organisation during oogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.9     2e-05     0.073      87     132 ..      18      63 ..      12      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                           Jagunal  87 lSivpsllgllalkknkikllklyligtlvlgllpllygaveylke 132
                                       l  ++sl+++ a ++ +i  l+++ ig  v+ l++ l+g+++ l  
  gi|313126346|ref|YP_004036616.1|  18 LGGIVSLMAYRAYNRTRIAGLQFFAIGLAVITLGTFLVGVFHHLGG 63 
                                       56799***********************************998765 PP

>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   7.4   0.00012      0.42      38     102 ..      10      79 ..       4      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                       HHTTHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHH CS
                          TspO_MBR  38 vfppvWtvlyilmgvaaylvwka.....lalyavqlvlnllwsplffglkspvlalvdivallglvvali 102
                                       v  +v +vl +++ ++ay+++++     l+++a+ l++  l ++l+  ++ ++ a + i +ll +v++ i
  gi|313126346|ref|YP_004036616.1|  10 VVKIVALVLGGIVSLMAYRAYNRtriagLQFFAIGLAVITLGTFLVGVFHHLGGASATIGMLLESVIISI 79 
                                       55677777777777777777777999**99*******************************998888765 PP

>> DUF1218  Protein of unknown function (DUF1218)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.2   5.1e-05      0.18       2      59 ..       5      66 ..       4      72 .. 0.79
   2 ?   -0.9   0.1      0.67   2.4e+03      39      56 ..      70      87 ..      63      89 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                           DUF1218  2 avllllaqiiasvasgcl...ccrkekspssa....krtlavvlfvlswivfaiAvalllvGaav 59
                                      ++ll++  i+a v++g++   + r+ +   ++     +++a+ l+v+++ +f+++v+  l Ga+ 
  gi|313126346|ref|YP_004036616.1|  5 IILLVVVKIVALVLGGIVslmAYRAYN---RTriagLQFFAIGLAVITLGTFLVGVFHHLGGASA 66
                                      78999*********9999542223333...22235799*******************99999975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.67
                           DUF1218 39 fvlswivfaiAvalllvG 56
                                      ++l  ++  i+++++++G
  gi|313126346|ref|YP_004036616.1| 70 MLLESVIISIGFVVMIYG 87
                                      455556666777777776 PP

>> Phlebovirus_G2  Phlebovirus glycoprotein G2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.7   0.00012      0.43     450     488 ..      48      86 ..       4      91 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00012
                    Phlebovirus_G2 450 wdlsdwvsGlldwlGGplktilvilgyialaivllvlli 488
                                       + l  ++ G+   lGG   ti+++l  ++++i ++v++ 
  gi|313126346|ref|YP_004036616.1|  48 ITLGTFLVGVFHHLGGASATIGMLLESVIISIGFVVMIY 86 
                                       56677899****************************986 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.3   0.00067       2.4      58      82 ..       8      32 ..       2      36 .. 0.89
   2 ?    4.9   5.2    0.0083        30      34      79 ..      46      90 ..      32      91 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00067
                              YtpI 58 alvvgavflvlGlanlfaGiraykh 82
                                       +vv +v lvlG +  + ++ray++
  gi|313126346|ref|YP_004036616.1|  8 LVVVKIVALVLGGIVSLMAYRAYNR 32
                                      589*******************975 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0083
                              YtpI 34 asialGlflilfgin.qllllestvalvvgavflvlGlanlfaGira 79
                                      a i+lG+fl+  g+   l   + t+++  + v++ +G++ +++G+++
  gi|313126346|ref|YP_004036616.1| 46 AVITLGTFLV--GVFhHLGGASATIGMLLESVIISIGFVVMIYGLKQ 90
                                      5577777764..67745556899*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 535.88
//
Query:       gi|313126347|ref|YP_004036617.1|  [L=868]
Description: rnd superfamily exporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-31  109.4  39.6    2.1e-17   63.0  13.9    3.1  3  MMPL            MMPL family
    3.2e-11   43.3   6.4    5.7e-07   29.5   0.3    2.6  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
    4.4e-09   35.0  12.2    1.1e-07   30.4   3.2    2.1  2  Patched         Patched family
  ------ inclusion threshold ------
      0.021   14.2  18.4      0.042   13.2   8.4    2.6  2  SecD_SecF       Protein export membrane protein
       0.16   12.9   0.2       0.16   12.9   0.2    4.8  5  Pilin_N         Archaeal Type IV pilin, N-terminal
       0.26   11.2   0.6       0.65    9.8   0.0    1.8  2  HPIH            N-terminal domain with HPIH motif


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.9      0.33   9.7e+02     167     187 ..      19      39 ..       7      42 .. 0.77
   2 !   58.4   9.8   1.8e-19   5.4e-16      71     305 ..     199     436 ..      49     474 .. 0.79
   3 !   63.0  13.9   7.2e-21   2.1e-17      86     301 ..     648     859 ..     560     866 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.33
                              MMPL 167 lvaallplltvvvsllaalgl 187
                                       l++all+++++vv+ +a lg+
  gi|313126347|ref|YP_004036617.1|  19 LIIALLLVVSAVVGAGAVLGT 39 
                                       677888888888888887775 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 1.8e-19
                              MMPL  71 lsdpdvaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlkl 147
                                       +  +d++ +++S+D +++ +  +    ++s  + ++v++ + +++++++ + +++ v G++++ ++ ++a      +
  gi|313126347|ref|YP_004036617.1| 199 FLPTDYEPGTTSADARTTLVFQKSP--SSSATTTQTVNDAQVTINSLVEKRFADAFVFGQGIIDEESSQAIGDTFII 273
                                       334559999*****99965555444..566667789***************************************** PP

                              MMPL 148 ievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvs 224
                                       i+ v++v++lv+L i+yr lv +l+ +  v++ ++   g+    +  lg+  +++ ++    lli+ ++DY l +v 
  gi|313126347|ref|YP_004036617.1| 274 ITPVAVVLLLVVLTIAYRDLVDVLVSVFGVGIVMVWYAGV----QGWLGIPSNSTLIAV-PFLLIGLSIDYSLHVVM 345
                                       ******************************9998888887....888888866665555.5689************* PP

                              MMPL 225 Ryreelaagedree..........aviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvliv 291
                                       Ryre+++   d++           a+   +a++  + + a++  a+ +++  ++ l++++ +++  ++G++  + + 
  gi|313126347|ref|YP_004036617.1| 346 RYREAREGTLDTDGesvgrrdpatAMRLGIAGVVLALATAAFSTAVGFFSNYISPLGSIQDFAILSGVGIVAIFVVF 422
                                       ******999888656666666655666666666666666777777778888899*********************** PP

                              MMPL 292 lTllPAllvllGra 305
                                        +l+PA+   l ++
  gi|313126347|ref|YP_004036617.1| 423 AALVPAVKLELEQF 436
                                       ******97766665 PP

  == domain 3  score: 63.0 bits;  conditional E-value: 7.2e-21
                              MMPL  86 kaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLli 162
                                       ++ar++v ++g+++ +  ++ v+ + +a+e      ++++  tG ++++a ++ a  + l    ++tl vil++L+ 
  gi|313126347|ref|YP_004036617.1| 648 QSARLTVGVQGNASAQSVASDVRGVSSAIEGDA---PVRATATGGPVITAVVQGALFETLVEGFAITLGVILTLLIG 721
                                       579999999999999999999999999999888...9**************************************** PP

                              MMPL 163 vy....rSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaaged 235
                                       +y    r++   ++ l+ v++ l+  lg+      +l +  ++ ++ + + l+i+ G+DY +    R+ +e+a+  +
  gi|313126347|ref|YP_004036617.1| 722 LYwwrhRAPGLGVVTLVPVLIALAWLLGT----MAALDIPFNSETVVI-TSLAIGLGVDYSIHASERFVDERARSDS 793
                                       *9766677777777777777777777766....556778888888776.5699************************ PP

                              MMPL 236 reeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvl 301
                                        ++++ ra+++tg++ +++++t a+ +  L++a  p l+ +G++ +l+++ ++ + +T+lP llv+
  gi|313126347|ref|YP_004036617.1| 794 LADSLSRALTGTGGALLGSAVTTAAGFGVLALALSPPLQRFGIVTGLSIIYAFVACVTVLPCLLVI 859
                                       ***************************************************************997 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.4   3.9e-06     0.012      11     125 ..     298     422 ..     294     433 .. 0.79
   2 !   29.5   0.3   1.9e-10   5.7e-07       6     138 ..     730     862 ..     726     866 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
                                       HHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH...........HHHHHH CS
                    Sterol-sensing  11 agviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde...........seriae 76 
                                       ++v+ v++ ++   g+  +lg++++   +  +Pfl++  ++d ++ +v  +++  + + +              +  
  gi|313126347|ref|YP_004036617.1| 298 VSVFGVGIVMVWYAGVQGWLGIPSNSTLI-AVPFLLIGLSIDYSLHVVMRYREAREGTLDtdgesvgrrdpATAMRL 373
                                       67788888889999**********99999.89****************99998877554446667776643444444 PP

                                       HHHHHCCCCHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                    Sterol-sensing  77 algevgpsilltsltellalllgaltdvpavqeFclfaavavlvdFllq 125
                                       ++  v  ++   +++ ++ ++  +++ +  +q F++ + v+++  F++ 
  gi|313126347|ref|YP_004036617.1| 374 GIAGVVLALATAAFSTAVGFFSNYISPLGSIQDFAILSGVGIVAIFVVF 422
                                       44445555556677788888888999999*************9999865 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 1.9e-10
                                       HHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHH CS
                    Sterol-sensing   6 fgLglagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgev 81 
                                        gLg++ ++ vl+++a  lg +a+l+++++  ++ v+  l++  gvd +    + +++   ++d   + + +al+ +
  gi|313126347|ref|YP_004036617.1| 730 PGLGVVTLVPVLIALAWLLGTMAALDIPFNSETV-VITSLAIGLGVDYSIHASERFVDERARSDSlADSLSRALTGT 805
                                       589*******************************.************9999999999888887777*********** PP

                                       CCCCHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHH CS
                    Sterol-sensing  82 gpsilltsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldir 138
                                       g ++l +++t ++ + + al   p +q F + + ++++  F+  +t+   +L + +r
  gi|313126347|ref|YP_004036617.1| 806 GGALLGSAVTTAAGFGVLALALSPPLQRFGIVTGLSIIYAFVACVTVLPCLLVIRER 862
                                       ****************888****************************9999998876 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   1.7   6.8e-05       0.2     247     370 ..     291     420 ..     186     435 .. 0.58
   2 !   30.4   3.2   3.7e-11   1.1e-07     249     384 ..     725     861 ..     700     865 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.8e-05
                           Patched 247 idwvrskpilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdmflmvaawkrteakls....... 316
                                        d+v      ++++v+   + +v   G+  wlG+++ns +  +PFL +++ +D +  +v ++++ +  +        
  gi|313126347|ref|YP_004036617.1| 291 RDLVD-----VLVSVFGVGIVMVWYAGVQGWLGIPSNSTLIAVPFLLIGLSIDYSLHVVMRYREAREGTLdtdgesv 362
                                       33333.....3334444444455556777899999999999999999999999776555555554443335778885 PP

                           Patched 317 ....vkkrigealseagvaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfi 370
                                               +   ++ +  a++   +  ++ F    i++l  iq F+i  +v i+  f+
  gi|313126347|ref|YP_004036617.1| 363 grrdPATAMRLGIAGVVLALATAAFSTAVGFFSNYISPLGSIQDFAILSGVGIVAIFV 420
                                       5544444444444444444444445555555555678888999999999998888776 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 3.7e-11
                           Patched 249 wvrskpilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdmflmvaa.wkrteaklsvkkrigea 324
                                       w   +p l ++ ++  ++A    lG++ +l ++fns + v+  L++++GvD +  + ++ +++  +++s+   +++a
  gi|313126347|ref|YP_004036617.1| 725 WRHRAPGLGVVTLVPVLIALAWLLGTMAALDIPFNSETVVITSLAIGLGVDYSIHASERfVDERARSDSLADSLSRA 801
                                       77788999999999999**********************************876666651566667778******** PP

                           Patched 325 lseagvaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavlaiaa 384
                                       l  +g a++   +T ++ Fg+ a++  p +q F i+t+++i+++f+  +t++  +l+i +
  gi|313126347|ref|YP_004036617.1| 802 LTGTGGALLGSAVTTAAGFGVLALALSPPLQRFGIVTGLSIIYAFVACVTVLPCLLVIRE 861
                                       ****************************************************99999876 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   8.4   1.4e-05     0.042      19     170 ..     257     417 ..     239     426 .. 0.74
   2 ?    5.8   2.3    0.0026       7.8      23     131 ..     698     805 ..     684     857 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                       EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHH.HHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHT CS
                         SecD_SecF  19 etvgpsvskelaekavlallialvliliyvalrFewrvala.aiialvhDviitvgvlsllgievdlatvaalLtii 94 
                                         ++++ s+ +  + ++   +a+vl+l+++++++++ v +  ++  +   ++  +gv  +lgi+ +++ +a    +i
  gi|313126347|ref|YP_004036617.1| 257 GIIDEESSQAIGDTFIIITPVAVVLLLVVLTIAYRDLVDVLvSVFGVGIVMVWYAGVQGWLGIPSNSTLIAVPFLLI 333
                                       56888899999999999999****************9987514555777777789********************** PP

                                       TSSSHHHHHHHHHHHHHHHH--SS-HHHHHHH....HHHHHHHHHHHTTHH....HHHHHHHHHHHHTTTTHHHHHH CS
                         SecD_SecF  95 GYSvndtvvvfdrvrenlrkkkratlkeiinl....slnqtLtrtiltslt....tllvvvallllggdslkdfala 163
                                       G S++ ++ v  r re ++ + +++ + +  +    ++   +   +l+ +t    t++  ++ ++ + +s++dfa+ 
  gi|313126347|ref|YP_004036617.1| 334 GLSIDYSLHVVMRYREAREGTLDTDGESVGRRdpatAMRLGIAGVVLALATaafsTAVGFFSNYISPLGSIQDFAIL 410
                                       *****************6666665555554431101333333333333333322366666666777779*****999 PP

                                       HHHHTST CS
                         SecD_SecF 164 llvGliv 170
                                         vG+++
  gi|313126347|ref|YP_004036617.1| 411 SGVGIVA 417
                                       9999875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HH.HHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSS CS
                         SecD_SecF  23 psvskelaekavlallialvliliyvalrFewr.valaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSv 98 
                                       + + ++l+e  ++ l++ l l++   + r + + +++  ++ ++  +  ++g +++l i+++++tv+     iG  v
  gi|313126347|ref|YP_004036617.1| 698 GALFETLVEGFAITLGVILTLLIGLYWWRHRAPgLGVVTLVPVLIALAWLLGTMAALDIPFNSETVVITSLAIGLGV 774
                                       333344444444444443333222223333322245555555777888899**************998888899999 PP

                                       HHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHH CS
                         SecD_SecF  99 ndtvvvfdrvrenlrkkkratlkeiinlslnqt 131
                                       + ++   +r  +++   +  +l++ + ++l+ t
  gi|313126347|ref|YP_004036617.1| 775 DYSIHASERFVDERA--RSDSLADSLSRALTGT 805
                                       999999988766633..3455555555555554 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   5.3e-05      0.16      11      72 ..      19      90 ..      18      98 .. 0.73
   2 ?   -3.7   5.5         6   1.8e+04       3      18 ..     274     289 ..     274     306 .. 0.78
   3 ?   -2.1   0.6       2.5   7.5e+03      12      26 ..     415     429 ..     413     436 .. 0.80
   4 ?   -2.2   0.1       2.7   8.2e+03      15      30 ..     472     487 ..     471     506 .. 0.64
   5 ?    2.0   0.0      0.14   4.1e+02      27      76 ..     575     624 ..     572     627 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.3e-05
                           Pilin_N 11 LmvaitvIlaAviaa.fvlglasneekapqasievk.......idssastgkna.....vslehkgGdsidtkdl 72
                                      L++a+ +++ Av++a  vlg+   ee+  qasi+ +       i+++++t+        v+++ +gGd+++ ++l
  gi|313126347|ref|YP_004036617.1| 19 LIIALLLVVSAVVGAgAVLGT-TGEEQIGQASIDSTeqaaldrIEATYETD--DavvaqVVVRDEGGDVLTRESL 90
                                      889999999999965278888.89999999999555445544433333332..134668**********998765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6
                           Pilin_N   3 VSpViGviLmvaitvI 18 
                                       ++pV  v+L+v++t+ 
  gi|313126347|ref|YP_004036617.1| 274 ITPVAVVLLLVVLTIA 289
                                       5799999999999985 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.5
                           Pilin_N  12 mvaitvIlaAviaaf 26 
                                       +vai v+ aA++ a+
  gi|313126347|ref|YP_004036617.1| 415 IVAIFVVFAALVPAV 429
                                       699999999999776 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2.7
                           Pilin_N  15 itvIlaAviaafvlgl 30 
                                       i+vI+++++ a+++ +
  gi|313126347|ref|YP_004036617.1| 472 IVVIVISLLLASAGAY 487
                                       6777777776666655 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.14
                           Pilin_N  27 vlglasneekapqasievkidssastgknavslehkgGdsidtkdlkivl 76 
                                       v+g ++ +  +  +s+  ++ ++++t  na++ +  +Gd +++kd++ v+
  gi|313126347|ref|YP_004036617.1| 575 VVGSDGRAAIEGPVSVLRTVAAENQTVANAIETRDTDGDGLPDKDVATVY 624
                                       555555666666677766677888888888**************998776 PP

>> HPIH  N-terminal domain with HPIH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.1   3.2e+03     100     122 ..     215     237 ..     212     245 .. 0.66
   2 ?    9.8   0.0   0.00022      0.65       5      30 ..     459     484 ..     456     496 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                              HPIH 100 ltLvFpdsnstssataPelenvp 122
                                       +tLvF++s s+s++t  ++++  
  gi|313126347|ref|YP_004036617.1| 215 TTLVFQKSPSSSATTTQTVNDAQ 237
                                       7999*998775544555555544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00022
                              HPIH   5 llaslskfaakhPIhtIvvvallast 30 
                                       ll  ++++a + PI +Iv+++llas+
  gi|313126347|ref|YP_004036617.1| 459 LLSGTASLARRAPIVVIVISLLLASA 484
                                       5667899999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (868 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.83u 0.34s 00:00:01.17 Elapsed: 00:00:00.53
# Mc/sec: 4894.22
//
Query:       gi|313126348|ref|YP_004036618.1|  [L=351]
Description: site-specific recombinase xerd [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-17   61.3   0.0    1.9e-16   60.3   0.0    1.4  1  Phage_integrase  Phage integrase family
      4e-08   33.6   3.8    9.9e-07   29.1   0.9    2.2  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    7.2e-08   32.6   0.6    3.4e-07   30.4   0.5    2.2  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.021   14.7   0.0       0.33   10.9   0.0    2.2  2  Phage_integr_3   Archaeal phage integrase


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   4.2e-20   1.9e-16      23     169 ..     147     334 ..     132     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 4.2e-20
                                       HHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE...............................EEECSSSSEE CS
                   Phage_integrase  23 dklllellyetGlRisEllsLrvkdldlengvilvh...............................eregKgsker 68 
                                       d +++ +l++tG+R++El++L+  d++l++ + l +                               ++  K+++++
  gi|313126348|ref|YP_004036618.1| 147 DHAVMVTLLKTGMRVGELCNLDCRDVSLADDTPLGDvsnraqldgrgpslyvsaepaaggttngerrTASNKRKRST 223
                                       56788899*************************99999***************************999999****** PP

                                       EEECTHHHHHHHHHHHHHHCHCCTTTSBSSBET...TSSB--HHHHHHHHHHHHHHCT-S.......SC--TTHHHH CS
                   Phage_integrase  69 avplseealellkellskaleeaeksellfask...rgkplsrqtvrkafkraveeagie.......kpltpHtlRh 135
                                       +vp+ ee+  +l+++l+++ +  ++ e lf+s+    g++l++  v + ++r + e g         +++tpH +Rh
  gi|313126348|ref|YP_004036618.1| 224 VVPVDEELEAVLTRWLAVRPDVTSPAEPLFVSTsgsWGNRLTTDMVHHLVERHAAERGWHraggdaeENVTPHYFRH 300
                                       *******************999***********999788888888888888888885655666668899******** PP

                                       HHHHHHHHHCTSHHHHHHHHT-SSCCHHHHHHCC CS
                   Phage_integrase 136 sfataLleagvdlrvvqkllGHssisttqiYthv 169
                                        f t+L  +  d   v++l G     ++ +Yth+
  gi|313126348|ref|YP_004036618.1| 301 FFTTHLRDRTGDRGIVKYLRGDVGGDIIDTYTHN 334
                                       *******999999999999998888888888885 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.9   2.2e-10   9.9e-07       5      78 ..      18      99 ..      15     104 .. 0.87
   2 !   12.9   0.1   2.6e-05      0.11       4      34 ..      70     100 ..      68     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.2e-10
                   Phage_int_SAM_4  5 frealrlaglserTiksYlsaikrflrflkkk..........apeeltkedieaYlnyLanerklsastqknalnalsf 73
                                      f++ ++++g++erT+++Y + ++rf +fl+ +          +++e + +d +a +++L+ +  ++ st+ ++ + l  
  gi|313126348|ref|YP_004036618.1| 18 FLQDMTYHGKTERTRDAYERVLRRFEAFLT-DpeanpmdaekRVSEASHRDCMAWIHSLR-RADAADSTIATYASYLHR 94
                                      8899*************************5.33445555555******************.6667************** PP

                   Phage_int_SAM_4 74 fykkv 78
                                      fy  +
  gi|313126348|ref|YP_004036618.1| 95 FYAYM 99
                                      **875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.6e-05
                   Phage_int_SAM_4   4 rfrealrlaglserTiksYlsaikrflrflk 34 
                                       ++++ lr a+ +++Ti +Y s++ rf ++++
  gi|313126348|ref|YP_004036618.1|  70 AWIHSLRRADAADSTIATYASYLHRFYAYMT 100
                                       68999***********************998 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.5   7.7e-11   3.4e-07      13      81 ..      26     100 ..      15     103 .. 0.88
   2 ?   -2.2   0.0       1.2   5.4e+03      14      25 ..     130     141 ..     119     150 .. 0.52

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 7.7e-11
                                       -S-HHHHHHHHHHHHHHHHHHHH.......TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  13 glspnTlraYrrdLrrflkflae......rgkesleqlttedvraflaeleeeglsatslarrlsalrsFfqflv 81 
                                       g ++ T+ aY+r Lrrf+ fl++      + ++ + +++++d+ a++  l++++ + +++a + s l++F+++ +
  gi|313126348|ref|YP_004036618.1|  26 GKTERTRDAYERVLRRFEAFLTDpeanpmDAEKRVSEASHRDCMAWIHSLRRADAADSTIATYASYLHRFYAYMT 100
                                       55789*****************998878888999999***********************************976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                       S-HHHHHHHHHH CS
                   Phage_int_SAM_1  14 lspnTlraYrrd 25 
                                       +s   +ra++r 
  gi|313126348|ref|YP_004036618.1| 130 ISISGMRAFLRE 141
                                       333333333333 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.058   2.6e+02      63     114 ..      85     140 ..      74     160 .. 0.73
   2 ?   10.9   0.0   7.3e-05      0.33     100     156 ..     289     345 ..     264     348 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.058
                                       EEE-SSS-EEEEEEESS---....--B--HHHHHHHHHT-T....--GHHHHHHHH CS
                    Phage_integr_3  63 ialekgeKkafyiylptelakelerlelseeavkefeakkk....vkakyiRkwva 114
                                       ia+   + + fy+y+ +  a e + ++l  e+++e+   +     ++++ +R +  
  gi|313126348|ref|YP_004036618.1|  85 IATYASYLHRFYAYMTQVGAFEANPMTLVMEEMDEQIDANPsrreISISGMRAFLR 140
                                       55555566789999998877778888887777765554433445599999998865 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.3e-05
                                       HT-T--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CCTTSCHHCHHHHHHHHHHHH CS
                    Phage_integr_3 100 akkkvkakyiRkwvatklaelgvpeevidFiqGrkpssvlekhYlnllvlAdeaYkk 156
                                       a+++v+ +y+R++++t l ++  + +++ ++ G     +  ++  n   +  e+Y++
  gi|313126348|ref|YP_004036618.1| 289 AEENVTPHYFRHFFTTHLRDRTGDRGIVKYLRGDVGGDIIDTYTHNWGDRVRETYEQ 345
                                       4556*******************************9999999887777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2100.90
//
Query:       gi|313126349|ref|YP_004036619.1|  [L=141]
Description: hypothetical protein Hbor_16040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.8   1.2       0.25   11.3   0.0    2.2  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.4e-05      0.25      17      34 ..      28      45 ..      17      49 .. 0.88
   2 ?    0.8   0.5      0.03   5.4e+02       6      17 ..      98     109 ..      92     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.4e-05
                                      HHHHHTSSHHHHHHHHHH CS
                             RHH_1 17 larrrgrSrSelIReAlr 34
                                      +a+++g+S+Se++R ++ 
  gi|313126349|ref|YP_004036619.1| 28 HAEELGMSQSEFVRTMVQ 45
                                      79************8876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.03
                                       EEHHHHHHHHHH CS
                             RHH_1   6 ldeellerLdel 17 
                                       l +++ +rLde 
  gi|313126349|ref|YP_004036619.1|  98 LTDDIEDRLDET 109
                                       678888999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 908.69
//
Query:       gi|313126350|ref|YP_004036620.1|  [L=236]
Description: hypothetical protein Hbor_16050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-67  227.3   0.0    1.7e-67  227.2   0.0    1.0  1  SRAP      SOS response associated peptidase (SRAP)


Domain annotation for each model (and alignments):
>> SRAP  SOS response associated peptidase (SRAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.2   0.0   9.7e-72   1.7e-67       1     218 [.       1     222 [.       1     223 [. 0.92

  Alignments for each domain:
  == domain 1  score: 227.2 bits;  conditional E-value: 9.7e-72
                              SRAP   1 MCgRyaltlapeelaeeleaeeedkelrpsynvaptqkvpvvvaeeeeeeeeeeerklqamkwGlvPswakdpkklg 77 
                                       MCgRy+l + +eelae+++a+ e+  ++p+yn+ap+q+ pvv+++++e         ++ +kwGlvP+wa+d+ ++g
  gi|313126350|ref|YP_004036620.1|   1 MCGRYSLFTPQEELAERFDATFETP-PEPRYNCAPGQRLPVVTDDDPE--------AFRFLKWGLVPQWADDQ-SVG 67 
                                       *******************854444.8****************77777........89************999.99* PP

                              SRAP  78 lktiNaRsetlaekplfrsalkkkRcvvpadGFYEWkkkgkekqPyfikrkdgkllalAGLydvwe........... 143
                                        ++iNaR+et+ ekp+fr+a++++Rc+vpadGFYEW + ++ kqPy +  +d++++a+AGL+++w+           
  gi|313126350|ref|YP_004036620.1|  68 NTLINARAETVREKPSFRDAFERRRCLVPADGFYEWVSADNGKQPYRVAFEDDRPFAMAGLWERWKppqtqtglgdf 144
                                       ************************************878899***********************989888888887 PP

                              SRAP 144 ......eegeeeklytytiiTteankqlaelHdRmPviLeeeelraWLdprkedskelqellkpaeeeelevypVsk 214
                                             ++ e e l t+t++T+e+n+ +++lHdRm viL ++e ++WL+    d++++++ll++ +++e+++ypVs+
  gi|313126350|ref|YP_004036620.1| 145 agdgdaTDAEPEILETFTVVTAEPNELVSDLHDRMSVILAPDEEETWLHG---DAADAESLLDTHPDTEMRAYPVST 218
                                       7666553337899***********************************99...777778899999999********* PP

                              SRAP 215 eVnk 218
                                       +Vn+
  gi|313126350|ref|YP_004036620.1| 219 RVNS 222
                                       **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1573.64
//
Query:       gi|313126351|ref|YP_004036621.1|  [L=251]
Description: exonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-37  129.6   0.0    1.4e-37  129.2   0.0    1.2  1  RNase_H_2       RNase_H superfamily
     0.0023   17.6   0.0      0.003   17.3   0.0    1.2  1  DNA_pol_A_exo1  3'-5' exonuclease


Domain annotation for each model (and alignments):
>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.0   1.6e-41   1.4e-37       1     164 [.      87     236 ..      87     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 1.6e-41
                         RNase_H_2   1 lffDiEttGlspkknliyliGvldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrl 77 
                                       +ffDiEttGl++ +n ++++++++ d+++++ +   + ++ ++e+  ++     +++   + +fngk+FDvpfl++ 
  gi|313126351|ref|YP_004036621.1|  87 CFFDIETTGLDSAQNDVTTVSFHR-DGETTTLV---RGHDLTAEALREQ-----FTDAALVASFNGKRFDVPFLEDN 154
                                       6**********************5.77766533...4688888888888.....89********************* PP

                         RNase_H_2  78 fkkykldeeefrhiDLlkelrkkklesysLksvekelgierreedlsGsqavklyqeylrtgdeellekilaYNedD 154
                                       f ++ +d    +hiDL++++r+ +l++ +Lks+ek++gi+r+++dlsG++av+l+++y r gde++l+++++YN+dD
  gi|313126351|ref|YP_004036621.1| 155 F-DISIDT---PHIDLMYPCRRLDLTG-GLKSIEKAVGIDRDRPDLSGRDAVRLWHQYERDGDEDALDTLVSYNRDD 226
                                       *.777775...****************.************************************************* PP

                         RNase_H_2 155 vralatlyek 164
                                       +++l +l++ 
  gi|313126351|ref|YP_004036621.1| 227 TANLSNLMDV 236
                                       *******986 PP

>> DNA_pol_A_exo1  3'-5' exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.4e-07     0.003      25     117 ..      89     177 ..      79     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-07
                                       EEEEEE-SSSTTSSEEEEEEEEECSSEEEEEECTTTTTT-HGHHHHHHHT-TTSEEEESSHHHHHHHHHHHHTS--S CS
                    DNA_pol_A_exo1  25 vDtEttsldlisatlvliliqlgekeeayiidplelgddvalealkrlledenitkvghnakfDlevlardfgiele 101
                                       +D Ett+ld+  a++ ++ +++ ++ e+  ++  +  +   +eal++ ++d+ +   + + +fD+ +l  +f+i + 
  gi|313126351|ref|YP_004036621.1|  89 FDIETTGLDS--AQNDVTTVSFHRDGETTTLVRGHDLT---AEALREQFTDAALVASFNGKRFDVPFLEDNFDISID 160
                                       8*********..98888888888885555544444444...48**********9999999*************9986 PP

                                       .SEEEHHHHHHHTTHST CS
                    DNA_pol_A_exo1 102 .nlfdtmlaayvldyer 117
                                        + +d+m+  + ld++ 
  gi|313126351|ref|YP_004036621.1| 161 tPHIDLMYPCRRLDLTG 177
                                       14445577776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1623.99
//
Query:       gi|313126352|ref|YP_004036622.1|  [L=109]
Description: hypothetical protein Hbor_16070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.19   11.9   0.0    1.2  1  DUF520    Protein of unknown function (DUF520)


Domain annotation for each model (and alignments):
>> DUF520  Protein of unknown function (DUF520)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     1e-05      0.19     120     147 ..      59      86 ..      38      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1e-05
                            DUF520 120 vqasiqgdevRvtgkkrDdLQaviallk 147
                                       v+  + + +vRv+g++ DdLQ+v    k
  gi|313126352|ref|YP_004036622.1|  59 VELGLYQLSVRVSGRSEDDLQSVEDSAK 86 
                                       555556668*************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 701.39
//
Query:       gi|313126353|ref|YP_004036623.1|  [L=228]
Description: glycosyl transferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-17   61.5   0.0    1.1e-16   61.1   0.0    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
    2.4e-06   27.6   0.2      3e-06   27.3   0.2    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   1.2e-20   1.1e-16       2     168 ..      12     165 ..      11     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.2e-20
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                       vv+ tyNee+ + ++l+ + ++ ++ + e+++vD ++ D+t+ei+++      + +vi +e  +G++ a+++++   
  gi|313126353|ref|YP_004036623.1|  12 VVMGTYNEEQAIGAVLADIDRI-TDGRAEVVCVDGSD-DRTPEIARQM-----GATVIEQE-PQGYGVAVREAVLTP 80 
                                       899*******************.*********98666.**********.....9*******.88************* PP

                                       -SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCS CS
                   Glycos_transf_2  79 tgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfei 155
                                       +  ++++ D Dd+++ + l+ +++++++ g+dvv g r   +    +   ++     +  +        ++ +++ +
  gi|313126353|ref|YP_004036623.1|  81 DRPVVVTTDCDDTYPMEMLPTFLDRIND-GYDVVSGDRLSPGATAMPTLNRY----GNAAFALLASLLMGRRVHDTT 152
                                       ****************************.************99999999986....599999*************** PP

                                       TCCCEEEEHHHHH CS
                   Glycos_transf_2 156 gsaallrrealee 168
                                        +++++rre+l +
  gi|313126353|ref|YP_004036623.1| 153 TGMRAYRRELLHD 165
                                       *********9976 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.2   3.3e-10     3e-06       3     181 ..       9     172 ..       7     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.3e-10
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       d+av+  t+nee+ +g+vl+++ +++ +r ev v+vd+sd+ t e a++       ++ +v+  ++  g ++++r  
  gi|313126353|ref|YP_004036623.1|   9 DVAVVMGTYNEEQAIGAVLADIDRITDGRAEV-VCVDGSDDRTPEIARQ-------MGATVI-EQEPQGYGVAVR-- 74 
                                       59**********************98899886.799************9.......465766.545345555555.. PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralg 156
                                        ea+ + ++ +v+  D D+    + l+ +l  +  +++++v ++++   + t+++ l++  ++   +  la  ++++
  gi|313126353|ref|YP_004036623.1|  75 -EAVLTPDRPVVVTTDCDDTYPMEMLPTFLDRI-NDGYDVVSGDRL-SPGATAMPTLNR--YGNAAFALLASLLMGR 146
                                       .9999999************************9.9*******9976.588899998998..8888888888889987 PP

                   Glyco_tranf_2_3 157 .vltlnGsgslirrevlkelegldp.l 181
                                        v   ++ + ++rre+l ++ ++++  
  gi|313126353|ref|YP_004036623.1| 147 rVHDTTTGMRAYRRELLHDI-DWTEnT 172
                                       6877788899**********.777644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1396.85
//
Query:       gi|313126354|ref|YP_004036624.1|  [L=378]
Description: hypothetical protein Hbor_16090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.5e-101  338.8   0.0   2.9e-101  338.6   0.0    1.0  1  DUF3179         Protein of unknown function (DUF3179)
  ------ inclusion threshold ------
      0.066   13.1   0.0       0.13   12.2   0.0    1.5  1  Nudix_N_2       Nudix N-terminal
       0.19   11.7   0.2        0.4   10.7   0.2    1.5  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


Domain annotation for each model (and alignments):
>> DUF3179  Protein of unknown function (DUF3179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.6   0.0  4.8e-105  2.9e-101       1     285 []      67     372 ..      67     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 338.6 bits;  conditional E-value: 4.8e-105
                           DUF3179   1 kDgIPaidnPefas.aeeasksldddepVigvelngearaYPlrilvwheiVNdtlggepvavTYCpLcgtalafer 76 
                                       kD+IPai +P+f s  ++ +++ldd e Vigvel+gearaYPl +l+wheiVNd+++ +pv vTYCpLcg+a++ er
  gi|313126354|ref|YP_004036624.1|  67 KDAIPAIVSPKFGSdWSDVDATLDDGELVIGVELDGEARAYPLAVLNWHEIVNDQFD-RPVLVTYCPLCGSAVVAER 142
                                       7***********987899999***********************************8.9****************** PP

                           DUF3179  77 ridggelefgvsGkLvnsnlvmyDreteslwqQllgeaiaGklegteLeelpvvtttwekwkeahpdtkVl...... 147
                                       +++g++ +fgvsG L++s+lvmyDre+eslw+Q+l++ai G+l+g++L+ lp++tt+w++w+e+hpdt+Vl      
  gi|313126354|ref|YP_004036624.1| 143 TVAGDTRTFGVSGYLWQSDLVMYDRESESLWSQVLATAIRGSLTGSQLDLLPSTTTSWGEWRESHPDTSVLlpppvs 219
                                       ****************************************************************************9 PP

                           DUF3179 148 .seetgssrdYgrdPygsyepasdr.plfpvekrddrlppkerVvgvevgddavaypkaelkeegvvedtvgdkevv 222
                                        + +++++rdY+r+Py +ye +s+r  +   ++ ddrl+pk+rV+gv +gd+avayp+++l+e+ vv+d+vg+ +vv
  gi|313126354|ref|YP_004036624.1| 220 dTVTGRQTRDYDRNPYLGYE-TSSRvGIGFNDDVDDRLHPKARVIGVAHGDKAVAYPLSTLSETPVVNDEVGGLPVV 295
                                       88899999************.7777567777799******************************************* PP

                           DUF3179 223 vvldadaesaldakrv.....vldees........gtlwdlangealdgklkgarlerv.aaaeafWFawaaFhpet 285
                                       ++++ d++ ++ ++rv     ++d+es        g++wdl++g+aldg+++ga+l r   ++ +fWFawa F+pet
  gi|313126354|ref|YP_004036624.1| 296 AAATVDGTLVAYDRRVdgsaiTFDRESgtdvltgdGSRWDLHTGRALDGPHEGAALARAnDRSLMFWFAWADFFPET 372
                                       ********99999988*****888888888888999**********************9667889**********98 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05      0.13       2      20 ..     130     149 ..     129     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                       B-TTT--B.-EEE--TT-SS CS
                         Nudix_N_2   2 FCsqCGtp.velripdgDnr 20 
                                       +C+ CG++ v+ r+ +gD+r
  gi|313126354|ref|YP_004036624.1| 130 YCPLCGSAvVAERTVAGDTR 149
                                       9*******6669999***99 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   6.7e-05       0.4       2      12 ..     131     141 ..     130     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.7e-05
                    DNA_ligase_ZBD   2 CPvCGsavvRe 12 
                                       CP CGsavv e
  gi|313126354|ref|YP_004036624.1| 131 CPLCGSAVVAE 141
                                       ********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2321.57
//
Query:       gi|313126355|ref|YP_004036625.1|  [L=66]
Description: hypothetical protein Hbor_16100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 394.80
//
Query:       gi|313126356|ref|YP_004036626.1|  [L=283]
Description: acyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-14   51.7   9.1    3.3e-10   40.1   0.4    3.2  3  Bactofilin   Polymer-forming cytoskeletal
      0.002   17.8  17.5       0.19   11.5   0.2    5.9  7  Hexapep      Bacterial transferase hexapeptide (six repeats)
  ------ inclusion threshold ------
      0.035   13.7   0.4       0.48   10.0   0.6    2.4  4  DUF3494      Protein of unknown function (DUF3494)
      0.045   13.5   0.1      0.045   13.5   0.1    4.2  4  Hexapep_2    Hexapeptide repeat of succinyl-transferase
        0.5   10.3   2.8         20    5.1   0.0    2.9  3  DUF3672      Fibronectin type III protein
        4.9    7.3   5.4        6.5    6.9   1.1    3.1  3  Phage_spike  Phage spike trimer


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.8   3.6e-05      0.11      22      83 ..      15      80 ..       8      83 .. 0.85
   2 !   10.7   0.1   0.00016      0.49       4      64 ..      50     109 ..      45     123 .. 0.53
   3 !   40.1   0.4   1.1e-13   3.3e-10      15      97 ..     178     265 ..     163     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                        Bactofilin 22 dG.kv.eGdieakgklvvgeggkvegnikaeevvvaGt.vk..GnveaeekvelkktakveGdikak 83
                                      dG +v e+d+ ++g+++vg +++ve  ++ ++v   G+ v+  G++eae+  +l+  + v G++ ++
  gi|313126356|ref|YP_004036626.1| 15 DGtTVeEHDLVTDGDVIVGGQSTVEFGVRGRNVFA-GErVQfgGDIEAEGDCRLDVWCDVAGNVLVG 80
                                      5644568999**********************987.6545566********************9765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                        Bactofilin   4 gegtkikGelevegdlridGkveGdi..eakgklvvgeggkvegnika.eevvvaGtvk..Gnvea 64 
                                       ge +++ G++e egd+r+      d+  + +g++ vg+++ +  ++++ +++ v+G ++  ++v++
  gi|313126356|ref|YP_004036626.1|  50 GERVQFGGDIEAEGDCRL------DVwcDVAGNVLVGQDAYLGERVHVgGRLMVSGDLDigDDVDI 109
                                       344555555555555554......444444555566666655555555444555555333244444 PP

  == domain 3  score: 40.1 bits;  conditional E-value: 1.1e-13
                        Bactofilin  15 vegdlri..dGkveGdieakgklvvgeggkvegnika.eevvva.Gt.vkGnveaee.kvelkktakveGdikaksl 85 
                                       +++  +i  d +++G+++a+ +++vg++ +v g+++a ++++v  Gt ++G+v+ ++ +v ++++a++ Gd+++++l
  gi|313126356|ref|YP_004036626.1| 178 TSAPAHIgdDCRLHGNVRAE-SITVGSDNNVFGSLRArGDITVGsGTrIHGDVTTRNgTVAIEGDARILGDVSCAEL 253
                                       55555665577999***998.9***************7779996688899*****999******************* PP

                        Bactofilin  86 eieegavfeGkl 97 
                                       e++e+a ++G++
  gi|313126356|ref|YP_004036626.1| 254 ELNENAAVDGTM 265
                                       *********986 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.44   1.3e+03      19      29 ..      29      39 ..      27      43 .. 0.56
   2 ?   -0.8   0.0      0.49   1.5e+03       5      20 ..      44      59 ..      44      60 .. 0.87
   3 !   11.5   0.2   6.5e-05      0.19       7      36 .]      64      93 ..      62      93 .. 0.92
   4 !    6.6   0.3    0.0023       6.8       5      31 ..      86     112 ..      85     112 .. 0.92
   5 !    6.6   0.2    0.0023       6.9       2      23 ..     182     202 ..     181     207 .. 0.58
   6 ?    4.0   1.2     0.015        45      18      33 ..     215     230 ..     198     236 .. 0.76
   7 ?    3.3   0.3     0.024        72       3      16 ..     218     231 ..     216     248 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.44
                                      TEEE-TTEEEE CS
                           Hexapep 19 nVkIGdnvkIg 29
                                      +V++G  ++++
  gi|313126356|ref|YP_004036626.1| 29 DVIVGGQSTVE 39
                                      55665555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.49
                                      ETTEEE-TTEEEETTE CS
                           Hexapep  5 GsnvlIgpfaviggnV 20
                                      G nv+ g  +++gg++
  gi|313126356|ref|YP_004036626.1| 44 GRNVFAGERVQFGGDI 59
                                      7899999999999986 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 6.5e-05
                                      TEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  7 nvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                      ++ ++ ++ ++gnV +G ++++g+ v +gg
  gi|313126356|ref|YP_004036626.1| 64 DCRLDVWCDVAGNVLVGQDAYLGERVHVGG 93
                                      79999999****************999986 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0023
                                       ETTEEE-TTEEEETTEEE-TTEEEETT CS
                           Hexapep   5 GsnvlIgpfaviggnVkIGdnvkIgag 31 
                                       G+ v++g   ++ g+  IGd+v I++g
  gi|313126356|ref|YP_004036626.1|  86 GERVHVGGRLMVSGDLDIGDDVDIEEG 112
                                       8999999999**************986 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0023
                                       EEEETTEEE-TTEEEETTEEE- CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIG 23 
                                       ++IG+++ ++ ++   + +++G
  gi|313126356|ref|YP_004036626.1| 182 AHIGDDCRLHGNVRA-ESITVG 202
                                       566666666666655.555555 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.015
                                       TTEEE-TTEEEETTEE CS
                           Hexapep  18 gnVkIGdnvkIgagvv 33 
                                       g++++G++++I+  v+
  gi|313126356|ref|YP_004036626.1| 215 GDITVGSGTRIHGDVT 230
                                       7788888888887766 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.024
                                       EEETTEEE-TTEEE CS
                           Hexapep   3 vIGsnvlIgpfavi 16 
                                       ++Gs++ I+  ++ 
  gi|313126356|ref|YP_004036626.1| 218 TVGSGTRIHGDVTT 231
                                       34444444444433 PP

>> DUF3494  Protein of unknown function (DUF3494)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.6   1.8e+03     171     196 ..      72      97 ..      61     105 .. 0.80
   2 ?    6.6   0.0    0.0017       5.2     158     203 ..     176     219 ..     164     221 .. 0.89
   3 ?   10.0   0.6   0.00016      0.48     162     205 ..     197     240 ..     193     244 .. 0.92
   4 ?    5.2   0.2    0.0047        14       7      35 ..     217     245 ..     211     280 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.6
                                       EEEEEEEESS-EEE-TT-EEEEEEEE CS
                           DUF3494 171 tfeGtilaqtsitlstgatvnGrlla 196
                                       +++G++l  +   l +   v Grl+ 
  gi|313126356|ref|YP_004036626.1|  72 DVAGNVLVGQDAYLGERVHVGGRLMV 97 
                                       67899999999999999999999886 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                                       EEESS-EEE-TT-EEEEEEEESS-EEE-TT-EEEEEEEESSSEEEE CS
                           DUF3494 158 WqvggsatlgtgstfeGtilaqtsitlstgatvnGrllaqtgaVtL 203
                                       Wq ++ a +g +  ++G++ a +sit+ ++ +v G+l a+ g++t 
  gi|313126356|ref|YP_004036626.1| 176 WQTSAPAHIGDDCRLHGNVRA-ESITVGSDNNVFGSLRAR-GDITV 219
                                       ******************976.68*************997.68885 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00016
                                       S-EEE-TT-EEEEEEEESS-EEE-TT-EEEEEEEESSSEEEESS CS
                           DUF3494 162 gsatlgtgstfeGtilaqtsitlstgatvnGrllaqtgaVtLdn 205
                                       +s+t+g ++++ G   a+  it+ +g+ ++G +  ++g+V+++ 
  gi|313126356|ref|YP_004036626.1| 197 ESITVGSDNNVFGSLRARGDITVGSGTRIHGDVTTRNGTVAIEG 240
                                       6889************************************9975 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.0047
                                       EE-TT-EEESSEEEESSS-GGEES--B-S CS
                           DUF3494   7 vtntGstvitGdiGvspastaitGfadel 35 
                                       +t  + t i+Gd+ + +++ ai G a  l
  gi|313126356|ref|YP_004036626.1| 217 ITVGSGTRIHGDVTTRNGTVAIEGDARIL 245
                                       44444477777777777777777777555 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.84   2.5e+03       7      18 ..      29      42 ..      29      43 .. 0.68
   2 ?    3.2   0.5     0.026        77       5      27 ..      86     110 ..      75     113 .. 0.59
   3 ?   13.5   0.1   1.5e-05     0.045       1      22 [.     181     203 ..     181     207 .. 0.87
   4 ?   -0.8   0.2      0.45   1.3e+03       2      18 ..     217     236 ..     216     244 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.84
                                      T-EE-TT-EE..SE CS
                         Hexapep_2  7 nCliGanagi..Gv 18
                                      ++++G  +++  Gv
  gi|313126356|ref|YP_004036626.1| 29 DVIVGGQSTVefGV 42
                                      57788888765676 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.026
                                       -TT-EE-TT-EE.S.EEE-TT-EE- CS
                         Hexapep_2   5 GdnCliGanagi.G.vslGdncvvg 27 
                                       G+++ +G +  + G  ++Gd++ ++
  gi|313126356|ref|YP_004036626.1|  86 GERVHVGGRLMVsGdLDIGDDVDIE 110
                                       4444444444445358888888876 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.5e-05
                                       .EEE-TT-EE-TT-E.ESEEE-T CS
                         Hexapep_2   1 pviIGdnCliGanag.iGvslGd 22 
                                       p +IGd+C ++ n     +++G 
  gi|313126356|ref|YP_004036626.1| 181 PAHIGDDCRLHGNVRaESITVGS 203
                                       789**********9955999996 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.45
                                       EEE-TT-EE-TT-EE..S.E CS
                         Hexapep_2   2 viIGdnCliGanagi..G.v 18 
                                       +++G  + i+ + ++  G v
  gi|313126356|ref|YP_004036626.1| 217 ITVGSGTRIHGDVTTrnGtV 236
                                       67899999998887666645 PP

>> DUF3672  Fibronectin type III protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.7   5.1e+03      26      43 ..      45      62 ..      41      64 .. 0.84
   2 ?    5.1   0.0    0.0068        20      30      46 ..     184     200 ..     178     204 .. 0.89
   3 ?    3.8   0.8     0.016        48      14      52 ..     213     251 ..     202     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.7
                           DUF3672 26 nnvviaenctisGtlrAe 43
                                      +nv  +e  ++ G + Ae
  gi|313126356|ref|YP_004036626.1| 45 RNVFAGERVQFGGDIEAE 62
                                      688889999999999887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0068
                           DUF3672  30 iaenctisGtlrAekil 46 
                                       i+++c ++G++rAe i 
  gi|313126356|ref|YP_004036626.1| 184 IGDDCRLHGNVRAESIT 200
                                       99************995 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.016
                           DUF3672  14 irGsinAnsGt.lnnvviaenctisGtlrAekilGDivka 52 
                                        rG+i   sGt ++++v++ n t+     A +ilGD+  a
  gi|313126356|ref|YP_004036626.1| 213 ARGDITVGSGTrIHGDVTTRNGTVAIEGDA-RILGDVSCA 251
                                       589999999986789999999887655444.899998766 PP

>> Phage_spike  Phage spike trimer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.21   6.3e+02      21      45 ..      25      61 ..      22      66 .. 0.59
   2 ?   -2.2   0.0       1.5   4.6e+03      24      43 ..      75     101 ..      72     111 .. 0.56
   3 ?    6.9   1.1    0.0022       6.5      30      54 .]     216     240 ..     192     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.21
                                      EEEEEEEEE.EEEESSE........EEEE.....S-EEE CS
                       Phage_spike 21 ecTgnLtvg.tltvqgG........Gtik.....Gdith 45
                                      ++ g+++vg + tv+ G        G        Gdi++
  gi|313126356|ref|YP_004036626.1| 25 VTDGDVIVGgQSTVEFGvrgrnvfaG--ErvqfgGDIEA 61
                                      68899999987777777443333332..03334477765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                       EEEEEEEEEESSE.....E..EEES-E CS
                       Phage_spike  24 gnLtvgtltvqgG.....G..tikGdi 43 
                                       gn+ vg+ ++ g+     G   ++Gd+
  gi|313126356|ref|YP_004036626.1|  75 GNVLVGQDAYLGErvhvgGrlMVSGDL 101
                                       566666555555433332344445554 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0022
                                       EEEESSEEEEES-EEEESS-EEETT CS
                       Phage_spike  30 tltvqgGGtikGdithsgGnlssnG 54 
                                        +tv  G  i+Gd+t  +G++   G
  gi|313126356|ref|YP_004036626.1| 216 DITVGSGTRIHGDVTTRNGTVAIEG 240
                                       68888888999***99999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1668.73
//
Query:       gi|313126357|ref|YP_004036627.1|  [L=305]
Description: hypothetical protein Hbor_16120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-62  210.5   4.1    2.7e-62  210.0   4.1    1.2  1  DUF4349          Domain of unknown function (DUF4349)
    0.00013   22.0   7.1     0.0023   18.0   7.4    2.2  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0012   17.8   1.7     0.0015   17.5   1.7    1.2  1  Spc7             Spc7 kinetochore protein
     0.0013   18.4   0.9      0.076   12.6   0.0    2.1  2  Filament         Intermediate filament protein
     0.0015   18.7   5.0     0.0058   16.9   0.3    2.4  2  ABC_tran_CTD     ABC transporter C-terminal domain
     0.0028   15.9   0.4     0.0038   15.5   0.4    1.1  1  EzrA             Septation ring formation regulator, EzrA
     0.0033   15.9   3.2     0.0045   15.4   3.2    1.1  1  MAD              Mitotic checkpoint protein
     0.0038   17.8   1.0      0.019   15.5   0.1    2.0  2  DUF2408          Protein of unknown function (DUF2408)
     0.0069   15.0   1.0     0.0091   14.6   1.0    1.0  1  Macoilin         Macoilin family
  ------ inclusion threshold ------
      0.016   15.4   2.5      0.049   13.9   2.7    1.6  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.019   14.5   0.5      0.027   14.1   0.5    1.2  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.022   14.1   1.6       0.03   13.7   1.6    1.1  1  DUF2353          Uncharacterized coiled-coil protein (DUF2353
      0.028   14.5   1.2      0.069   13.2   1.2    1.7  1  PilJ             Type IV pili methyl-accepting chemotaxis tra
      0.035   14.3   4.4        1.8    8.8   0.4    2.5  2  Spc24            Spc24 subunit of Ndc80
      0.049   13.7   2.8      0.094   12.8   2.8    1.4  1  COG2             COG (conserved oligomeric Golgi) complex com
      0.071   13.3   3.8        3.2    7.9   0.2    2.2  2  IFT20            Intraflagellar transport complex B, subunit 
      0.072   13.0   0.3      0.072   13.0   0.3    1.6  1  DUF4017          Protein of unknown function (DUF4017)
      0.077   13.4   4.4       0.17   12.3   4.4    1.5  1  Snapin_Pallidin  Snapin/Pallidin
      0.078   11.6   0.3        0.1   11.2   0.3    1.1  1  FapA             Flagellar Assembly Protein A
      0.097   12.0   9.2        2.1    7.6   6.8    2.9  2  DUF3450          Protein of unknown function (DUF3450)
        0.1   12.4   3.7        1.1    8.9   4.0    1.9  2  DUF4201          Domain of unknown function (DUF4201)
       0.15   12.2   3.3        2.4    8.3   3.3    2.2  1  DUF2730          Protein of unknown function (DUF2730)
       0.17   10.6   2.6       0.18   10.6   0.2    2.0  2  DUF3573          Protein of unknown function (DUF3573)
       0.22   11.3   3.0        1.1    9.0   0.5    2.2  2  SKA2             Spindle and kinetochore-associated protein 2
       0.25   11.1   8.8        1.4    8.8   1.5    2.5  2  DivIC            Septum formation initiator
       0.28   11.7   1.9        0.9   10.2   1.9    1.9  1  LPAM_1           Prokaryotic membrane lipoprotein lipid attac
       0.28   10.5   4.3       0.43    9.9   4.3    1.2  1  GAS              Growth-arrest specific micro-tubule binding
        0.3   11.0   3.6        0.5   10.2   3.1    1.6  1  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or
       0.36   11.4   7.8        1.5    9.4   7.9    1.8  1  APG6_N           Apg6 coiled-coil region
        0.4   11.2   3.7       0.57   10.7   3.7    1.2  1  AAA_23           AAA domain
       0.44   10.5   5.9        7.7    6.5   0.8    2.6  2  Prefoldin_2      Prefoldin subunit
       0.45   10.9   9.2         15    6.0   1.1    3.3  3  HalX             HalX domain
       0.52   10.4   3.8       0.43   10.6   1.8    1.8  2  DUF1664          Protein of unknown function (DUF1664)
       0.57   10.7   5.7        3.8    8.1   3.3    2.4  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.72    9.7   5.8        7.9    6.3   0.4    2.0  2  SPX              SPX domain
          1    8.6   3.9        1.8    7.8   3.9    1.3  1  CorA             CorA-like Mg2+ transporter protein
        1.2    9.1   6.0          2    8.4   4.5    2.0  2  Laminin_II       Laminin Domain II
        1.3    9.2   5.4         14    5.9   1.1    2.3  2  bZIP_2           Basic region leucine zipper
        1.6    9.0   6.1        1.5    9.1   1.0    2.3  2  Osmo_CC          Osmosensory transporter coiled coil
        2.8    8.4  13.2        2.6    8.5   1.9    2.9  3  DUF4140          N-terminal domain of unknown function (DUF41
        2.8    8.1   9.7         48    4.1   9.4    2.2  2  TolA_bind_tri    TolA binding protein trimerisation
        5.6    7.2   8.2        1.7    8.8   1.2    2.5  2  Cnn_1N           Centrosomin N-terminal motif 1


Domain annotation for each model (and alignments):
>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.0   4.1   6.4e-65   2.7e-62       1     210 [.      75     289 ..      75     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 6.4e-65
                           DUF4349   1 rkliytasltlevedvdaavaairelveeagGyvesss..ersgtegdersasltlRvPaarldafldelaelgkvt 75 
                                       r+li+t+++++ev+d++a+ ++++++v+ +gG+v+++s  ++s ++++  +++++lRvPaa++da++++ ++ g+v+
  gi|313126357|ref|YP_004036627.1|  75 RALIKTGTVRVEVDDFQASKSNLTAAVQGYGGFVSDTSqeRHSVDNETYLTGQVVLRVPAADFDALVEDAKAEGEVE 151
                                       78************************************66666677888899************************* PP

                           DUF4349  76 srstsaeDVTeqyvDleaRlkaleasedrllallekaksvedlleiereLsevqaeieslegqlryLdnqvaystvt 152
                                        ++t++eDVT+++vDleaRl++l+a++d+l++l+++a+++ed+l+++reLs+vq eie+le+q ++L+++va+st+t
  gi|313126357|ref|YP_004036627.1| 152 VVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANTTEDVLAVQRELSDVQGEIERLEAQKQSLQDRVAFSTLT 228
                                       ***************************************************************************** PP

                           DUF4349 153 vtlrepeaeteaeeee...gegflealsggwnalveflagllvvlgallPwllvlalvlal 210
                                       v+l+ep++++++ +++   ++++l+a+ ++++++++++++l+v l+++lP++lv+++ ++l
  gi|313126357|ref|YP_004036627.1| 229 VRLEEPRPTPDRVAPDrwyDTPVLSAFFQSVDGVATVARALVVGLAYALPYFLVFVFPFVL 289
                                       **************99***9************************************55544 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.1   4.5e+02      40      88 ..      73     121 ..      67     125 .. 0.82
   2 !   18.0   7.4   5.4e-06    0.0023      47     124 ..     143     222 ..     136     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.1
                    CENP-F_leu_zip  40 qekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLeke 88 
                                       q+++ +   t + ev  +++ + +l++  +     ++++++e+ ++++e
  gi|313126357|ref|YP_004036627.1|  73 QNRALIKTGTVRVEVDDFQASKSNLTAAVQGYGGFVSDTSQERHSVDNE 121
                                       5566677778899999999999999999999999999999999887765 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5.4e-06
                    CENP-F_leu_zip  47 aEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkq..ervseLeslnsslenlleekEqekvqmk 121
                                         ++  eve +k++ e  + +l +le+ L++lr ++++L k   + +  e v   ++  s+++  +e++E++k  ++
  gi|313126357|ref|YP_004036627.1| 143 DAKAEGEVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANttEDVLAVQRELSDVQGEIERLEAQKQSLQ 219
                                       3344557999*****************************88887765225688888999*************99998 PP

                    CENP-F_leu_zip 122 ees 124
                                       ++ 
  gi|313126357|ref|YP_004036627.1| 220 DRV 222
                                       875 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.7   3.6e-06    0.0015     153     230 ..     148     223 ..      82     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.6e-06
                              Spc7 153 edkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                        + e+++ + e +++ l +le++ ++l+++ ++l++ ++e  + + e++ ++++el++++ eie+++++ ++lq+++
  gi|313126357|ref|YP_004036627.1| 148 GEVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDE--ANTTEDVLAVQRELSDVQGEIERLEAQKQSLQDRV 222
                                       4567777788888888888888888888888888888877..44577777888888888888888888888888776 PP

                              Spc7 230 e 230
                                       +
  gi|313126357|ref|YP_004036627.1| 223 A 223
                                       5 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00018     0.076      67     142 ..      70     187 ..      63     190 .. 0.85
   2 ?    4.1   0.5     0.066        28     214     247 ..     190     223 ..     188     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX..........................................XXXXXXX CS
                          Filament  67 tkerarlqleldnlreeledlrkkyeke..........................................lnkreev 101
                                       ++ ++r+ +  +++r e++d++++ ++                                           l +  ++
  gi|313126357|ref|YP_004036627.1|  70 ANVQNRALIKTGTVRVEVDDFQASKSNLtaavqgyggfvsdtsqerhsvdnetyltgqvvlrvpaadfdaLVEDAKA 146
                                       5566777778888888888888777766778888888888888888888888888888888888888888889999* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 102 EaelkalrkdldeatlarvdLekkvesLkeelaflkkvhee 142
                                       E e++ ++ + ++ t + vdLe+++e L+ + + l+k+++e
  gi|313126357|ref|YP_004036627.1| 147 EGEVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDE 187
                                       ***************************************98 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.066
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 214 akeeitelrrqiqsleieleslkkqkasleaqla 247
                                       + e++  ++r++   + e+e l++qk+sl++++a
  gi|313126357|ref|YP_004036627.1| 190 TTEDVLAVQRELSDVQGEIERLEAQKQSLQDRVA 223
                                       5677778888888888888888888888888765 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.6      0.21        89      39      60 ..     159     181 ..     140     192 .. 0.64
   2 !   16.9   0.3   1.3e-05    0.0058       7      32 ..     198     223 ..     196     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.21
                      ABC_tran_CTD  39 dp.eklaelsaeleeleaeLeel 60 
                                       d  ++l +l a+le+l+a+ ++l
  gi|313126357|ref|YP_004036627.1| 159 DVtDRLVDLEARLENLRAQRDQL 181
                                       33466777777777777766654 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.3e-05
                      ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaela 32 
                                       qrel  +  eIe+LE+++++l++++a
  gi|313126357|ref|YP_004036627.1| 198 QRELSDVQGEIERLEAQKQSLQDRVA 223
                                       9*********************9987 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   8.8e-06    0.0038     286     383 ..     136     233 ..     113     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.8e-06
                                       HHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHH CS
                              EzrA 286 eidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyee 362
                                       ++d+L++d ++E e  + v++n++ ++++l  le+ +++l+++ d+l++ Y+ + + +e +  +++el++++ ++e+
  gi|313126357|ref|YP_004036627.1| 136 DFDALVEDAKAEGEV-EVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYD-EANTTEDVLAVQRELSDVQGEIER 210
                                       677777777777775.589*********************************.5999******************98 PP

                                       HH..HHHS-SS---STTGGGTHH CS
                              EzrA 363 le..ekleekkvaYSelqeelee 383
                                       le  ++  ++ va+S+l+ +lee
  gi|313126357|ref|YP_004036627.1| 211 LEaqKQSLQDRVAFSTLTVRLEE 233
                                       86226677899******999987 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.2     1e-05    0.0045     389     472 ..     141     223 ..     121     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                               MAD 389 vqkvqahneeveaqlevaeeevggykqqastlerelqalrqqesladass....skeevdslkkkleeLelerqrLr 461
                                       v++ +      e ++ev++ +     ++   le+ l+ lr q ++  + +    ++e+v +++++l +++ e +rL+
  gi|313126357|ref|YP_004036627.1| 141 VEDAK-----AEGEVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYdeanTTEDVLAVQRELSDVQGEIERLE 212
                                       44555.....45555666666666678888888888888866655433333444*********************** PP

                               MAD 462 eqkeelElele 472
                                        qk++l  +++
  gi|313126357|ref|YP_004036627.1| 213 AQKQSLQDRVA 223
                                       *****987776 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   4.5e-05     0.019      39     126 ..      71     175 ..      47     182 .. 0.80
   2 ?    0.9   0.2       1.5   6.4e+02      35      60 ..     192     217 ..     176     233 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.5e-05
                           DUF2408  39 e...........vkeelkelkeeLkkieskrdeegkFkseegke.......vvekgqavlngLlddcfdlvedlkaq 97 
                                       +           v+ e+++++++ +++ +  +  g F+s+ ++e          +gq vl+   +d   lved ka+
  gi|313126357|ref|YP_004036627.1|  71 NvqnraliktgtVRVEVDDFQASKSNLTAAVQGYGGFVSDTSQErhsvdneTYLTGQVVLRVPAADFDALVEDAKAE 147
                                       13344677777799999999999999999999999999887766665444444455********************* PP

                           DUF2408  98 dgeekkvasslqpiYdrLleikttLenLl 126
                                        ge + v+++ +++ drL+++   LenL 
  gi|313126357|ref|YP_004036627.1| 148 -GEVEVVKTNTEDVTDRLVDLEARLENLR 175
                                       .68899*********************95 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.5
                           DUF2408  35 kesee...vkeelkelkeeLkkieskrde 60 
                                       +   +   v+ el++++ e++++e+++++
  gi|313126357|ref|YP_004036627.1| 192 E---DvlaVQRELSDVQGEIERLEAQKQS 217
                                       2...1333778888888888888877665 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.0   2.1e-05    0.0091     336     454 ..      44     222 ..      22     237 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                          Macoilin 336 agsagssnssskkhsessksvtsssssknskkqklpaGkssaalkdaaen........................... 385
                                       a  +  ++ss ++  ++s+s +ss++++ +++  + +G ++ +  d                               
  gi|313126357|ref|YP_004036627.1|  44 AAPTVETTSSGASGGANSDSAASSKTANVQNRALIKTGTVRVEVDDFQASksnltaavqgyggfvsdtsqerhsvdn 120
                                       22333344555555555555555555555555533333333222221111122333333333333333333333333 PP

                          Macoilin 386 ...............................slpnnqlskkdalvrLeadikkLkaeLqasrqteqelrskisslts 431
                                                                      ++  n+    d lv Lea ++ L+a+ ++ r+  +e +   + l+ 
  gi|313126357|ref|YP_004036627.1| 121 etyltgqvvlrvpaadfdalvedakaegeveVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANTTEDVLAV 197
                                       66666666665555555555555544444444444444556667777777777777777777777776666665554 PP

                          Macoilin 432 eer...slkselqqlkkendllqtkl 454
                                        +r    ++ e++ l+ ++++lq ++
  gi|313126357|ref|YP_004036627.1| 198 -QRelsDVQGEIERLEAQKQSLQDRV 222
                                       .2201134556666666666666654 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.7   0.00011     0.049      10      97 ..     136     222 ..     129     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00011
                                       -HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHH CS
                      Seryl_tRNA_N  10 npeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkal 86 
                                       +++a+ e  k+ ge +       ++ ++   l+++le+l+a+r +l k   +a    ed  ++  e ++++ e+++l
  gi|313126357|ref|YP_004036627.1| 136 DFDALVEDAKAEGEVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANTT-EDVLAVQRELSDVQGEIERL 211
                                       6777888888777666666777788899999**********************997.7******************* PP

                                       HHHHHHHHHHH CS
                      Seryl_tRNA_N  87 eaelkeleael 97 
                                       ea+ + l++++
  gi|313126357|ref|YP_004036627.1| 212 EAQKQSLQDRV 222
                                       *****999876 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   6.3e-05     0.027      80     145 ..     154     221 ..     112     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-05
                     PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedl..kqqkeeereleReinalkpellqLqkrkdkylew 145
                                       +++ e++++ l +l++rl++l++++++L +     +++e+ + ++Re++ ++ e+ +L+ +k  ++ +
  gi|313126357|ref|YP_004036627.1| 154 KTNTEDVTDRLVDLEARLENLRAQRDQLRKLYdeANTTEDVLAVQRELSDVQGEIERLEAQKQSLQDR 221
                                       67788999999*****************98551157789999********************988776 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.6   7.1e-05      0.03      21     148 ..      83     221 ..      78     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-05
                           DUF2353  21 crqerdqyklmaeqLqerlsalkkqleeekakaadlkee.........kekekklsqlleesree..nkalklevee 86 
                                       +r e d +++   +L   ++++    +++++ +++ ++e         +   ++  +l+e+++ e   +  k++ e+
  gi|313126357|ref|YP_004036627.1|  83 VRVEVDDFQASKSNLTAAVQGYGGFVSDTSQERHSVDNEtyltgqvvlRVPAADFDALVEDAKAEgeVEVVKTNTED 159
                                       56777777777777777777777766666666666655567777888777788889999999986224678999999 PP

                           DUF2353  87 LrqklkeaqgDiklLReqlarqrlglkdedlletrhssaeereelvkqlEklkekiqqlerd 148
                                       + ++l +++   + LR+q  + r+ +++ ++ e+    ++e +++  ++E+l++++q+l+  
  gi|313126357|ref|YP_004036627.1| 160 VTDRLVDLEARLENLRAQRDQLRKLYDEANTTEDVLAVQRELSDVQGEIERLEAQKQSLQDR 221
                                       *********9999***9999999999999999998888999999999999999999999865 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.2   0.00016     0.069      42      94 ..     155     214 ..     144     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                              PilJ  42 earaqlretiaqfdrtlaalrlg.dpapgllvpae......avraqleaveqlWqelkkp 94 
                                       ++ +++++++ +++++l++lr + d+ + l++ a+      av+++l++v+ + ++l+ +
  gi|313126357|ref|YP_004036627.1| 155 TNTEDVTDRLVDLEARLENLRAQrDQLRKLYDEANttedvlAVQRELSDVQGEIERLEAQ 214
                                       6789*****************998889999999989999999999999999988888766 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.7     0.017       7.2       8      40 ..     159     191 ..     149     199 .. 0.73
   2 ?    8.8   0.4    0.0043       1.8       6      34 ..     194     222 ..     189     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.017
                             Spc24   8 riakelsdleselesleselaelkeeleeleee 40 
                                       +++  l dle+ le+l+++ ++l++ ++e ++ 
  gi|313126357|ref|YP_004036627.1| 159 DVTDRLVDLEARLENLRAQRDQLRKLYDEANTT 191
                                       456667788888888888888888877777654 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0043
                             Spc24   6 kfriakelsdleselesleselaelkeel 34 
                                        ++++ elsd++ e+e+le+++++l++++
  gi|313126357|ref|YP_004036627.1| 194 VLAVQRELSDVQGEIERLEAQKQSLQDRV 222
                                       567899********************997 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.8   0.00022     0.094      56     131 ..     159     233 ..     134     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                              COG2  56 dFvslSghLvglqeeleevesplaaarkkves..vreklsereeeveskleeakeleekrellklllkldevvekle 130
                                       d   + ++Lv+l+++le+++ +  ++rk  ++  ++e + + ++e+++   e ++le+++++l++ + +++++++le
  gi|313126357|ref|YP_004036627.1| 159 D---VTDRLVDLEARLENLRAQRDQLRKLYDEanTTEDVLAVQRELSDVQGEIERLEAQKQSLQDRVAFSTLTVRLE 232
                                       3...7788888888888888888888887665114577888888888888888899999999999999999988888 PP

                              COG2 131 a 131
                                       +
  gi|313126357|ref|YP_004036627.1| 233 E 233
                                       5 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0075       3.2      28     113 ..     104     189 ..      79     195 .. 0.79
   2 ?    6.7   0.8     0.019         8      81     107 ..     194     220 ..     186     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0075
                             IFT20  28 ckeFvkkinefqklvkelievleelakkvekeKlkAigarnllkseakqreaeqqqlqaliaekkaeleRlrveles 104
                                          Fv+++++ +  v++ + ++ ++  +v  +   A+    + + e +  +++ +++  ++ + +a le+lr++ + 
  gi|313126357|ref|YP_004036627.1| 104 YGGFVSDTSQERHSVDNETYLTGQVVLRVPAADFDALVEDAKAEGEVEVVKTNTEDVTDRLVDLEARLENLRAQRDQ 180
                                       446788888888888888888888888999999999999999999999999999*********************** PP

                             IFT20 105 Lqkveqeqk 113
                                       L+k+  e +
  gi|313126357|ref|YP_004036627.1| 181 LRKLYDEAN 189
                                       **9987765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                             IFT20  81 qqqlqaliaekkaeleRlrvelesLqk 107
                                         ++q ++++ + e+eRl+++ +sLq 
  gi|313126357|ref|YP_004036627.1| 194 VLAVQRELSDVQGEIERLEAQKQSLQD 220
                                       5578999******************95 PP

>> DUF4017  Protein of unknown function (DUF4017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   0.00017     0.072      18      48 ..     253     283 ..     249     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                           DUF4017  18 avilPaseGYntvgWkLfvGqiYalPillit 48 
                                       +    + +G  tv+  L+vG +YalP +l+ 
  gi|313126357|ref|YP_004036627.1| 253 SAFFQSVDGVATVARALVVGLAYALPYFLVF 283
                                       55667889******************99874 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.4   0.00039      0.17      14      86 ..     149     222 ..     145     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00039
                   Snapin_Pallidin  14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklkkRa 86 
                                       +++ ++++ +++++   +L ++l++l+++ ++l+++ + a++ +d+   ++ L+ ++ ++++l+ + q+l++R+
  gi|313126357|ref|YP_004036627.1| 149 EVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDeANTTEDVLAVQRELSDVQGEIERLEAQKQSLQDRV 222
                                       566677888888888889999999999999999999999999999****************************8 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00023       0.1     328     411 ..     152     225 ..     115     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                              FapA 328 v.gldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelke 403
                                       v   +        +++ ++l +le++le+l+++ ++l+kl      e++  e++  +++++   + e+e le+++++
  gi|313126357|ref|YP_004036627.1| 152 VvKTNT-------EDVTDRLVDLEARLENLRAQRDQLRKLYD----EANTTEDVLAVQRELSDVQGEIERLEAQKQS 217
                                       334444.......45555555555555555555444444332....33457999999******************** PP

                              FapA 404 lkeelesk 411
                                       l+++++ +
  gi|313126357|ref|YP_004036627.1| 218 LQDRVAFS 225
                                       **999877 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.26   1.1e+02      12      86 ..      46     120 ..      40     123 .. 0.81
   2 ?    7.6   6.8     0.005       2.1      31      87 ..     142     198 ..     132     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.26
                           DUF3450  12 galaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                       +++++t + a   a++  aa++++ + +++   ++ ++  e+ + ++ +++l++  + +   v++  qe++s+++
  gi|313126357|ref|YP_004036627.1|  46 PTVETTSSGASGGANSDSAASSKTANVQNRALIKTGTVRVEVDDFQASKSNLTAAVQGYGGFVSDTSQERHSVDN 120
                                       444666677777777888888888888888888999999999999**********99999999999999999876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.005
                           DUF3450  31 aaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeq 87 
                                       ++a+++ +++ ++ +++++ +++ +l+++le+l+++++ql++l ++++++ + l  q
  gi|313126357|ref|YP_004036627.1| 142 EDAKAEGEVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANTTEDVLAVQ 198
                                       567788888889999999999999999999999999999999988765543322222 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.0    0.0027       1.1      92     158 ..     149     215 ..     144     219 .. 0.81
   2 ?    3.4   0.2      0.14        58      83     114 ..     191     222 ..     187     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0027
                           DUF4201  92 elselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekr 158
                                       e++  k+++++ ++rl +l+++l++++++rd+lrk +++ ++    l v   l D   + e++e  +
  gi|313126357|ref|YP_004036627.1| 149 EVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANTTEDVLAVQRELSDVQGEIERLEAQK 215
                                       678899********************************99988877777666666666666666555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                           DUF4201  83 keklhmleselselkkelkekeerlaklrkel 114
                                        e   ++++els+ + e++++e+++++l++++
  gi|313126357|ref|YP_004036627.1| 191 TEDVLAVQRELSDVQGEIERLEAQKQSLQDRV 222
                                       56667889999999999999999999999886 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.3    0.0057       2.4      37      91 ..     159     220 ..     143     224 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0057
                           DUF2730  37 klaekveendkrlteletkvenL.......PtakdlekLkllladlrgelkaleaevrqlsh 91 
                                        +++ + + + rl++l ++ ++L        t++d+ +++ +l+d++ge++ lea+ ++l+ 
  gi|313126357|ref|YP_004036627.1| 159 DVTDRLVDLEARLENLRAQRDQLrklydeaNTTEDVLAVQRELSDVQGEIERLEAQKQSLQD 220
                                       44444445555555554444443222222268889999999999999999999988888775 PP

>> DUF3573  Protein of unknown function (DUF3573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.98   4.2e+02      37      93 ..      63     120 ..       8     142 .. 0.63
   2 ?   10.6   0.2   0.00042      0.18      38      83 ..     187     233 ..     140     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.98
                           DUF3573  37 snlidkelilklqkqik..elqaeinhlketknsnesaqfttysskvedsklprslldn 93 
                                       s +  k + ++ +  ik   ++ e++++++ k  n +a    y   v+d+ + r   dn
  gi|313126357|ref|YP_004036627.1|  63 SAASSKTANVQNRALIKtgTVRVEVDDFQASKS-NLTAAVQGYGGFVSDTSQERHSVDN 120
                                       222233333333333331146667777777766.7777777777777777777666666 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00042
                           DUF3573  38 nlidkelilklqkqikelqaeinhlketkns.nesaqfttysskved 83 
                                       +++  e +l +q+++ ++q+ei++l+++k+s  + + f+t + ++e+
  gi|313126357|ref|YP_004036627.1| 187 EANTTEDVLAVQRELSDVQGEIERLEAQKQSlQDRVAFSTLTVRLEE 233
                                       45678899*********************997788899998887766 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1       0.3   1.3e+02      46      71 ..     156     181 ..     135     191 .. 0.58
   2 ?    9.0   0.5    0.0026       1.1      45      76 ..     192     223 ..     182     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.3
                              SKA2  46 rlkkvkeelqaLkeqceellaekkel 71 
                                       + ++v+++l  L++++e+l a++ +l
  gi|313126357|ref|YP_004036627.1| 156 NTEDVTDRLVDLEARLENLRAQRDQL 181
                                       44556666666666666666665543 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0026
                              SKA2  45 erlkkvkeelqaLkeqceellaekkelidkir 76 
                                       e++ +v++el+ ++ ++e l a+k+ l d++ 
  gi|313126357|ref|YP_004036627.1| 192 EDVLAVQRELSDVQGEIERLEAQKQSLQDRVA 223
                                       678899*******************9999875 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.3    0.0088       3.8      21      55 ..     159     193 ..     150     197 .. 0.81
   2 ?    8.8   1.5    0.0032       1.4      17      47 ..     192     222 ..     188     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                             DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLksded 55 
                                       ++   +++l+a l++l+a++++L +  ++ + +ed
  gi|313126357|ref|YP_004036627.1| 159 DVTDRLVDLEARLENLRAQRDQLRKLYDEANTTED 193
                                       556678899***************99999965665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0032
                                       XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  17 laykqlkqeiaalqaelaklkaeneeLeaev 47 
                                        ++ ++++e+ + q e+++l a++++L+++v
  gi|313126357|ref|YP_004036627.1| 192 EDVLAVQRELSDVQGEIERLEAQKQSLQDRV 222
                                       677889999999999*********9999998 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9    0.0021       0.9       5      18 .]       9      22 ..       4      22 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0021
                            LPAM_1  5 llalgalllLsGCs 18
                                      l++ +al++L+GCs
  gi|313126357|ref|YP_004036627.1|  9 LVVVVALAALAGCS 22
                                      77889********9 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.3     0.001      0.43      44     120 ..     145     220 ..     141     232 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                               GAS  44 rnekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvek 120
                                       ++e e++ ++++ ++ ++ L  +e+ +e+Lr+q  + +k   + +n+ + +  +++el+d++ e e le + +++++
  gi|313126357|ref|YP_004036627.1| 145 KAEGEVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDE-ANTTEDVLAVQRELSDVQGEIERLEAQKQSLQD 220
                                       5566666666677777777777777777777666666665444.344444555556666666666666666665554 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.1    0.0012       0.5      93     184 ..     119     208 ..      91     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                              FTA4  93 vnedltkeelIkeLPeswe...veekeaeeepleallerYaelrarLielserrqqlqarlarlrklkallepflgs 166
                                        ne +   +++ + P++     ve+  + e + e  +++ +++  rL++l++r+++l+a+ ++lrkl  + + ++++
  gi|313126357|ref|YP_004036627.1| 119 DNETYLTGQVVLRVPAADFdalVED-AKAEGEVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANTTEDV 194
                                       6677777777777777766444333.333344588899999***************************999999665 PP

                              FTA4 167 ...edpqesvqenlvtrdgel 184
                                          +       ++l   +ge+
  gi|313126357|ref|YP_004036627.1| 195 lavQ-------RELSDVQGEI 208
                                       4441.......4444444443 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.9    0.0035       1.5      14      82 ..     153     220 ..      87     223 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0035
                            APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereelea 82 
                                       +++  e++++   ++e+ l++l++++++ + +  +++++ e++ ++++e ++ + e+++le+++++l++
  gi|313126357|ref|YP_004036627.1| 153 VKTNTEDVTDRLVDLEARLENLRAQRDQLR-KLYDEANTTEDVLAVQRELSDVQGEIERLEAQKQSLQD 220
                                       344455555555555666666666655555.34455566666666666666666666666666666654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.7    0.0013      0.57     105     193 ..     144     232 ..      43     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0013
                            AAA_23 105 kkaklellei.deleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkllekleqeke 180
                                        ka+  ++e+ +++++ +++ l   +++l+++  + ++  +  +++++ e + ++++el + + e++ le+++q ++
  gi|313126357|ref|YP_004036627.1| 144 AKAE-GEVEVvKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANTTEDVLAVQRELSDVQGEIERLEAQKQSLQ 219
                                       3333.444444888999999999999999999999999999999999999999999999999999999999999999 PP

                            AAA_23 181 kekeleeleeele 193
                                        + ++++l  +le
  gi|313126357|ref|YP_004036627.1| 220 DRVAFSTLTVRLE 232
                                       9988888777766 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.8     0.018       7.7      69      97 ..     155     183 ..     110     192 .. 0.66
   2 ?    5.2   0.4     0.046        20      67      91 ..     197     221 ..     194     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  69 erketlekeiktlekqleklekeleelke 97 
                                       ++ e+++ ++  le +le+l+++ ++l++
  gi|313126357|ref|YP_004036627.1| 155 TNTEDVTDRLVDLEARLENLRAQRDQLRK 183
                                       44444444444444444444444444443 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  67 Leerketlekeiktlekqlekleke 91 
                                       ++ ++ +++ ei++le q+++l+ +
  gi|313126357|ref|YP_004036627.1| 197 VQRELSDVQGEIERLEAQKQSLQDR 221
                                       4566677788888888888888766 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.1     0.053        22      35      55 ..     162     182 ..     158     188 .. 0.81
   2 ?    6.0   1.1     0.036        15      23      50 ..     187     214 ..     187     222 .. 0.89
   3 ?    3.8   0.1      0.18        75      22      57 ..     211     244 ..     210     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.053
                              HalX  35 eeYqeLearleelraqldetl 55 
                                       ++  +Learle lraq d++ 
  gi|313126357|ref|YP_004036627.1| 162 DRLVDLEARLENLRAQRDQLR 182
                                       67789**********988765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.036
                              HalX  23 eaekseaeLadseeYqeLearleelraq 50 
                                       ea+ +e+ La   e ++ ++++e+l+aq
  gi|313126357|ref|YP_004036627.1| 187 EANTTEDVLAVQRELSDVQGEIERLEAQ 214
                                       78999*********************99 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.18
                              HalX  22 LeaekseaeLadseeYqeLearleelraqldetlde 57 
                                       Lea+k    L+d  +++ L+ rlee r + d+++++
  gi|313126357|ref|YP_004036627.1| 211 LEAQKQ--SLQDRVAFSTLTVRLEEPRPTPDRVAPD 244
                                       677776..499999*************999999998 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       7.6   3.2e+03      91     113 ..      82     104 ..      66     120 .. 0.58
   2 ?   10.6   1.8     0.001      0.43      55     117 ..     158     222 ..     144     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.6
                           DUF1664  91 evredlseigedvesvkeavegl 113
                                       +vr ++++++   +++ +av+g 
  gi|313126357|ref|YP_004036627.1|  82 TVRVEVDDFQASKSNLTAAVQGY 104
                                       44445555555555555555444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.001
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeis..keikeevtevredlseigedvesvkeavegleskl 117
                                       e++++   +L++r++++ ++ d+  ++   ++++e+v +v+++ls+++ ++e +++  ++l+ ++
  gi|313126357|ref|YP_004036627.1| 158 EDVTDRLVDLEARLENLRAQRDQLRKLYdeANTTEDVLAVQRELSDVQGEIERLEAQKQSLQDRV 222
                                       45555556799999999999999999862257899*******************99999988776 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.3    0.0088       3.8      19      67 ..     149     197 ..     141     205 .. 0.87
   2 ?    5.2   0.7     0.069        29      26      53 ..     193     220 ..     186     233 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0088
                           NPV_P10  19 kVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnp 67 
                                        V++++++ +dv++ l d++   e+L aq +qL +l ++ ++ +d+L  
  gi|313126357|ref|YP_004036627.1| 149 EVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANTTEDVLAV 197
                                       6899999999999999999999999*************99999999984 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.069
                           NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLae 53 
                                        v  vq +l dv+   e+L+aq ++L++
  gi|313126357|ref|YP_004036627.1| 193 DVLAVQRELSDVQGEIERLEAQKQSLQD 220
                                       3444555555555555558888777764 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.7     0.021       8.9      42     127 ..      26     121 ..      14     127 .. 0.66
   2 ?    6.3   0.4     0.018       7.9     203     273 ..     155     221 ..     151     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                               SPX  42 eaetlrellnrpedskkkssertepstsaaadesgnsaadasssepkdeae...........slprrsplsrssrss 107
                                       + ++ r  l+r++d  ++++  t ++ts+ a+ ++ns + ass++ + + +             + + + s+ +   
  gi|313126357|ref|YP_004036627.1|  26 DDDSGRAELHRSDDGAATAAP-TVETTSSGASGGANSDSAASSKTANVQNRaliktgtvrveVDDFQASKSNLTAAV 101
                                       555666666666666666654.445555555544444444444444444446777888988755566666778999* PP

                               SPX 108 ssygglvssppsansssssd 127
                                       + ygg+vs+ +++++s +++
  gi|313126357|ref|YP_004036627.1| 102 QGYGGFVSDTSQERHSVDNE 121
                                       ************99998876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
                               SPX 203 akeeefterlesLrkqlealrprrikeaeerksdlyrwreifglk.sveaqvfessreldrgelseeardke 273
                                        + e++t+rl +L+  le+lr++r +      ++ly++ +  ++  +v+++ ++ + e +r e ++++ +++
  gi|313126357|ref|YP_004036627.1| 155 TNTEDVTDRLVDLEARLENLRAQRDQ-----LRKLYDEANTTEDVlAVQRELSDVQGEIERLEAQKQSLQDR 221
                                       567899****************9999.....66667776655555556666666666666665544444444 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.9    0.0043       1.8     138     215 ..     149     222 ..     134     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0043
                              CorA 138 edeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrer 214
                                       e e+ + ++++  ++l++l+ rl +lr +  ++r+++++  + ++d l  + +   l+d++ e+erl+ + ++l++r
  gi|313126357|ref|YP_004036627.1| 149 EVEVVKTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANT-TEDVLAVQRE---LSDVQGEIERLEAQKQSLQDR 221
                                       5566899999***************************77776.6777777777...9******************99 PP

                              CorA 215 l 215
                                       +
  gi|313126357|ref|YP_004036627.1| 222 V 222
                                       8 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.2     0.046        19      56      98 ..     145     184 ..      63     190 .. 0.66
   2 ?    8.4   4.5    0.0048         2       9      74 ..     154     221 ..     139     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.046
                                       XXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHH CS
                        Laminin_II  56 dArrsvkkLeklapqLldklkelkqleeassslsdniseikel 98 
                                        A+ +v  ++ + +++ d+l  l+ + e+   l ++ +++++l
  gi|313126357|ref|YP_004036627.1| 145 KAEGEVEVVKTNTEDVTDRLVDLEARLEN---LRAQRDQLRKL 184
                                       34556777777777777777777777766...66666666655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0048
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGG CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsv..eetnekvkdankairdArrsvkkLeklapqLldk 74 
                                       +  ++ v + l +l+++len++++  ++++    ++t+e+v + ++ + d++ ++  Le + + L d+
  gi|313126357|ref|YP_004036627.1| 154 KTNTEDVTDRLVDLEARLENLRAQRDQLRKLYdeANTTEDVLAVQRELSDVQGEIERLEAQKQSLQDR 221
                                       45566777777778877777766555544433005577778888888888888888888888777776 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.1     0.032        14      24      53 ..     154     183 ..     153     184 .. 0.88
   2 ?    4.9   0.2     0.063        27      30      49 ..     204     223 ..     196     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  24 kakeeeleervkeLeeeNaqLrqkveqLek 53 
                                       k ++e+  +r+ +Le++ + Lr++ +qL+k
  gi|313126357|ref|YP_004036627.1| 154 KTNTEDVTDRLVDLEARLENLRAQRDQLRK 183
                                       6678999999************99999986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.063
                                       HHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  30 leervkeLeeeNaqLrqkve 49 
                                        + ++++Le++++ L+++v+
  gi|313126357|ref|YP_004036627.1| 204 VQGEIERLEAQKQSLQDRVA 223
                                       57789999999999999985 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.55   2.4e+02      20      38 ..     163     181 ..     151     184 .. 0.72
   2 ?    9.1   1.0    0.0036       1.5      20      41 ..     200     221 ..     196     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.55
                                       HHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  20 kvedideeIaaLeekRqrL 38 
                                       ++ d+++ +++L ++R++L
  gi|313126357|ref|YP_004036627.1| 163 RLVDLEARLENLRAQRDQL 181
                                       4457777788888888887 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  20 kvedideeIaaLeekRqrLvdq 41 
                                       ++ d+  eI++Le+++q+L d+
  gi|313126357|ref|YP_004036627.1| 200 ELSDVQGEIERLEAQKQSLQDR 221
                                       5789***************886 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       7.1     3e+03      12      12 ..      74      74 ..      20     103 .. 0.62
   2 ?    5.3   5.1     0.064        27      57      96 ..     154     193 ..      61     195 .. 0.78
   3 ?    8.5   1.9    0.0061       2.6      58      97 ..     185     224 ..     180     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 7.1
                           DUF4140 12 r 12
                                       
  gi|313126357|ref|YP_004036627.1| 74 N 74
                                      1 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.064
                           DUF4140  57 vpnreaeeeelkalraeleeledelaaledelaaaearla 96 
                                       ++n+e ++++l  l+a+le+l++++++l++  + a+++ +
  gi|313126357|ref|YP_004036627.1| 154 KTNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEANTTED 193
                                       2455555557999999999999999999988777777665 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0061
                           DUF4140  58 pnreaeeeelkalraeleeledelaaledelaaaearlaf 97 
                                       + + + +e++ a+++el  ++ e+++le++++++++r af
  gi|313126357|ref|YP_004036627.1| 185 YDEANTTEDVLAVQRELSDVQGEIERLEAQKQSLQDRVAF 224
                                       5555555569999999999999999999999999999887 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.9      0.15        64      18      38 ..     162     182 ..     146     191 .. 0.65
   2 ?    4.1   9.4      0.11        48       3      54 ..     161     221 ..     159     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.15
                     TolA_bind_tri  18 qlllelqqqlealqqelreLR 38 
                                         l++l  +le+l+++ ++LR
  gi|313126357|ref|YP_004036627.1| 162 DRLVDLEARLENLRAQRDQLR 182
                                       456666666666666666666 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                     TolA_bind_tri   3 edrvarLErilears.........qlllelqqqlealqqelreLRGqiEelqyqleqleer 54 
                                        dr+  LE  le+               +  + + a q+el++ +G+iE+l+ q ++l+ r
  gi|313126357|ref|YP_004036627.1| 161 TDRLVDLEARLENLRaqrdqlrklYDEANTTEDVLAVQRELSDVQGEIERLEAQKQSLQDR 221
                                       5666666666666433444443332233445566789999999999999999999999987 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.2    0.0041       1.7      36      70 ..     155     189 ..     140     192 .. 0.86
   2 ?    3.1   0.6      0.25   1.1e+02      34      66 ..     190     222 ..     186     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0041
                            Cnn_1N  36 eqkeellkenielkveveslqkelkekkkllreae 70 
                                       ++ e++ + +++l+ ++e+l+ + ++++kl +ea+
  gi|313126357|ref|YP_004036627.1| 155 TNTEDVTDRLVDLEARLENLRAQRDQLRKLYDEAN 189
                                       57899************************999987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.25
                            Cnn_1N  34 seeqkeellkenielkveveslqkelkekkkll 66 
                                       ++e++ ++ +e+ +++ e+e l+ +++++++++
  gi|313126357|ref|YP_004036627.1| 190 TTEDVLAVQRELSDVQGEIERLEAQKQSLQDRV 222
                                       55777788999999***********99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1428  (0.0796475); expected 358.6 (0.02)
Passed bias filter:                      836  (0.0466284); expected 358.6 (0.02)
Passed Vit filter:                       159  (0.00886831); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 1845.44
//
Query:       gi|313126358|ref|YP_004036628.1|  [L=391]
Description: hypothetical protein Hbor_16130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.7e-32  110.6   0.0    8.9e-32  110.0   0.0    1.3  1  MMR_HSR1_C  GTPase of unknown function C-terminal
    9.4e-21   74.0   0.0    7.5e-20   71.1   0.0    2.2  2  MMR_HSR1    50S ribosome-binding GTPase
    2.3e-11   43.6   0.0    1.6e-10   40.8   0.0    2.2  2  TGS         TGS domain
    3.8e-08   33.0   0.0    2.4e-07   30.4   0.0    2.3  3  FeoB_N      Ferrous iron transport protein B
  ------ inclusion threshold ------
       0.13   12.0   0.0       0.94    9.3   0.0    2.2  2  NOG1        Nucleolar GTP-binding protein 1 (NOG1)


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.0   2.5e-35   8.9e-32       1     112 []     219     321 ..     219     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 2.5e-35
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLeki 77 
                                       ++NKaD+ a+ en+e+l+e ++    vv ++A+ ElaLr+aa++g+i+Y pgd+df+i +d    ++++q++ Leki
  gi|313126358|ref|YP_004036628.1| 219 VANKADV-APPENLERLREVDK---PVVAATADGELALRRAADAGIIDYLPGDDDFDIVGD----VSDAQQSGLEKI 287
                                       79*****.************88...7***********************************....************ PP

                        MMR_HSR1_C  78 rdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       r+ v+++ g+TGVqea+n+av+++ld+++ YPV++
  gi|313126358|ref|YP_004036628.1| 288 RE-VVETNGGTGVQEAINTAVYDVLDMVTAYPVQN 321
                                       **.99****************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   2.1e-23   7.5e-20       2      87 ..       4     121 ..       3     155 .. 0.78
   2 ?   -0.1   0.0      0.27   9.5e+02      92     114 .]     200     222 ..     170     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.1e-23
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.....................EEEEECGGCS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.....................ielvDtpGli 57 
                                       +a++G+pN+GKSt+ +a t + + v+++p+tT+d+n+g     +++                     +el+D++Gl+
  gi|313126358|ref|YP_004036628.1|   4 IALAGKPNAGKSTFYKAATMADVDVGNYPFTTIDPNRGVSY-ARTRcpcldrdercgncedgvryvgVELLDVAGLV 79 
                                       89************************************665.3222556666677888888888888********99 PP

                                       SHHHHHHHHHHHHHHHHC.TSEEEEEEETT...........T CS
                          MMR_HSR1  58 egaseekglgkaflalee.adlillvvdas...........e 87 
                                        ga+e++glg++fl+    ad+il vvdas            
  gi|313126358|ref|YP_004036628.1|  80 PGAHEGRGLGNQFLDALTnADVILAVVDASggtneegepveV 121
                                       9*************977769********99777655555441 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  92 pldeeleelleeakkplilvlnk 114
                                       + +e l++  + ++kp++lv+nk
  gi|313126358|ref|YP_004036628.1| 200 EHQEALASDVRARTKPIVLVANK 222
                                       233445555556899*****998 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.34   1.2e+03      28      42 ..      86     104 ..      84     134 .. 0.69
   2 !   40.8   0.0   4.6e-14   1.6e-10       6      59 ..     334     387 ..     330     388 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.34
                                       TTHHHHEEEEEECS....E CS
                               TGS  28 rslakkfiyAlVnG....q 42 
                                       r+l+++f+ Al n      
  gi|313126358|ref|YP_004036628.1|  86 RGLGNQFLDALTNAdvilA 104
                                       7899999999988655552 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 4.6e-14
                                       TTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS   6 PdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       Pd+ +  l rg+t++D+Ay++h+++++  ++A      +r   d++L++gdv++Iv
  gi|313126358|ref|YP_004036628.1| 334 PDAFL--LERGSTPKDLAYAVHSDIGEGYLHAVNARsdRRIAEDYELDEGDVIKIV 387
                                       55555..9**************************9999*****************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   6.7e-11   2.4e-07       2      42 ..       3      43 ..       2      53 .. 0.90
   2 ?   -1.5   0.0      0.44   1.6e+03      77      89 ..      97     109 ..      88     110 .. 0.82
   3 ?   -2.8   0.0       1.1     4e+03     101     120 ..     209     228 ..     204     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.7e-11
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegkl 42
                                      ++al+G+pn+Gk+t+  a t a+ +vgN+p +t++ ++g  
  gi|313126358|ref|YP_004036628.1|  3 SIALAGKPNAGKSTFYKAATMADVDVGNYPFTTIDPNRGVS 43
                                      69*********************************998875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.44
                                       TSSSEEEEEEEGG CS
                            FeoB_N  77 eepdvvvnvvdat 89 
                                       +++dv++ vvda+
  gi|313126358|ref|YP_004036628.1|  97 TNADVILAVVDAS 109
                                       5789*******96 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.1
                                       HHHTTSSEEEEEETHHHHHH CS
                            FeoB_N 101 llelgvpvvlalnmideaek 120
                                       +   ++p+vl+ n+ d+a  
  gi|313126358|ref|YP_004036628.1| 209 VRARTKPIVLVANKADVAPP 228
                                       55667899999999999865 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.31   1.1e+03      14      25 ..      99     110 ..      95     114 .. 0.87
   2 ?    9.3   0.0   0.00026      0.94      32      58 .]     200     224 ..     193     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.31
                              NOG1  14 adavlFllDpse 25 
                                       ad++l ++D+s+
  gi|313126358|ref|YP_004036628.1|  99 ADVILAVVDASG 110
                                       699*******97 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00026
                              NOG1  32 eeQlsLleeikelfankpvivvlnKiD 58 
                                       e Q +L  +++++  +kp++ v+nK+D
  gi|313126358|ref|YP_004036628.1| 200 EHQEALASDVRAR--TKPIVLVANKAD 224
                                       78***********..47********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2527.02
//
Query:       gi|313126359|ref|YP_004036629.1|  [L=99]
Description: hypothetical protein Hbor_16140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 547.21
//
Query:       gi|313126360|ref|YP_004036630.1|  [L=373]
Description: aspartate/tyrosine/aromatic aminotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-64  216.0   0.0    9.4e-64  215.8   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.1e-13   51.2   0.1    1.7e-13   50.6   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.2e-08   32.3   0.0      1e-07   31.6   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    4.4e-07   28.8   0.0    6.2e-07   28.3   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    8.1e-07   28.3   0.0    1.1e-06   27.9   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.011   14.5   0.0      0.019   13.7   0.0    1.3  1  Aminotran_3      Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.8   0.0   3.1e-67   9.4e-64       2     361 ..      26     363 ..      25     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 215.8 bits;  conditional E-value: 3.1e-67
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d inLg+++++++     ++++++a++e a + g +  y+ ++g  +l+ea+a  + r+++++  +++ + + +G+ 
  gi|313126360|ref|YP_004036630.1|  26 DAINLGIGQPDFA----APEHARRAAIE-AIKDGRADAYTENKGIRSLREAIAAKHERDQGIERHPDDIIATAGGSE 97 
                                       679**********....***********.**************************************6666666666 PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       al  a ++      gde+++pdp + sy+   +l++g+ v++pl+  +d +ld  a+eea+++       t  ++v+
  gi|313126360|ref|YP_004036630.1|  98 ALHIAMEAHVG--SGDEVIIPDPGFVSYDALTKLADGTPVPVPLR--DDLTLDPAAVEEAITD------DTAAFIVN 164
                                       66666666665..******************************99..****************......889***** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       sp NPtG+v ++e++++ +++a+++ +l ++De+Y+ +vf+  ++ +  a+++e +n+++v+s sK ++++G+R+G+
  gi|313126360|ref|YP_004036630.1| 165 SPGNPTGAVSPPEDIREFARIADEHDVLCISDEVYEYTVFDG-EFRS-PAEFAETDNVVVVNSASKLYSMTGWRLGW 239
                                       ****************************************95.5767.9**************************** PP

                                       EEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmf 307
                                       + g+++ ++ + ++++ +    s+++q a+ aal  ++ +   ++em + +q+rr+ ++d+L+++gl+v +++++++
  gi|313126360|ref|YP_004036630.1| 240 VHGSSRRIERMVRAHQYVQAcaSAPAQFAAEAALTGPQGI---VDEMTDSFQRRRDIVVDGLEDIGLTVPTPKGAFY 313
                                       *****99999999999776677****************96...********************************** PP

                                       EEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                     Aminotran_1_2 308 lltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                        + +++      + +++le+ gv+v+pg+ f++   g  R+++ +++e+ l e+++
  gi|313126360|ref|YP_004036630.1| 314 AMPEVPDG----FVDECLER-GVIVVPGEAFGAngDGYARLSY-ATDEASLHEALD 363
                                       ******99....********.************99999*****.999999999986 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.1   5.6e-17   1.7e-13      41     144 ..      89     196 ..      43     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 5.6e-17
                                       EEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE. CS
                   DegT_DnrJ_EryC1  41 aiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl. 116
                                        ia++ G++Alh+a++a  vg gdeVI+p  +Fv+  +    +  +pv+v    d++++dpaa+e+ait  t+a + 
  gi|313126360|ref|YP_004036630.1|  89 IIATAGGSEALHIAMEA-HVGSGDEVIIPDPGFVSYDALTKLADGTPVPVPLR-DDLTLDPAAVEEAITDDTAAFIv 163
                                       69**************9.68899***************************998.9*****************88662 PP

                                       .....EB-GGGB---HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 117 .....pVhlyGqvadmdalkaiaakhglkvieD 144
                                            p  +++ + d+ +  +ia++h++  i+D
  gi|313126360|ref|YP_004036630.1| 164 nspgnPTGAVSPPEDIREFARIADEHDVLCISD 196
                                       442222334444569**************9999 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   3.4e-11     1e-07      12     166 ..      42     195 ..      36     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.4e-11
                                       HHHHHHHHCS----C.CCT--HHHHHHHHHHHHHTT-SEEEE........ES-HHHHHHHHHHHH--TTEEEEEETT CS
                   Beta_elim_lyase  12 eamsdaqaaamlGde.sYgedktvnrLedavaelfgkeaalf........vpqGtaAnsillkillqrgeevivtep 79 
                                        a ++a+ a+  G + +Y e+k+++ L +a+a+  + ++++         ++ G  A +i++++++ +g+evi+ +p
  gi|313126360|ref|YP_004036630.1|  42 HARRAAIEAIKDGRAdAYTENKGIRSLREAIAAKHERDQGIErhpddiiaTAGGSEALHIAMEAHVGSGDEVIIPDP 118
                                       45566667788888549*********************99977789999999************************* PP

                                       -HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHH CS
                   Beta_elim_lyase  80 ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaai 156
                                       + +  d   a+  la+ ++++++ +++ ++d++++e+ai++     +  ++i+    n t  G v ++e +re a i
  gi|313126360|ref|YP_004036630.1| 119 GFVSYD---ALTKLADGTPVPVPLRDDLTLDPAAVEEAITD-----DTAAFIVNSPGNPT--GAVSPPEDIREFARI 185
                                       988877...6677788889999999999*************.....46699999999998..*************** PP

                                       HHHCT-EEEE CS
                   Beta_elim_lyase 157 akkygiplhl 166
                                       a+++++  + 
  gi|313126360|ref|YP_004036630.1| 186 ADEHDVLCIS 195
                                       ****987665 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   2.1e-10   6.2e-07      69     177 ..      88     200 ..      74     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.1e-10
                                       EEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST..TSHHHHHHHCCTTEEEEEE CS
                   Cys_Met_Meta_PP  69 aalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt..sdleelekaikentklvyl 143
                                         +a++ G  A++ a+ a + +Gde+++ d  +  +++ l+k++  + + v   d    d++++e+ai++ t ++ +
  gi|313126360|ref|YP_004036630.1|  88 DIIATAGGSEALHIAMEAHVGSGDEVIIPDPGFV-SYDALTKLADGTPVPVPLRDDltLDPAAVEEAITDDTAAFIV 163
                                       56899***************************96.688889999999999998886447999*************** PP

                                       ESS-TTTT---...-HHHHHHHHHHTT-EEEEEGTTT CS
                   Cys_Met_Meta_PP 144 Etptnpllkvv...DiekiaklakkagvlvvvDntfa 177
                                        +p+np+  v    Di++ a++a +++vl + D ++ 
  gi|313126360|ref|YP_004036630.1| 164 NSPGNPTGAVSppeDIREFARIADEHDVLCISDEVYE 200
                                       ********995556***************99998654 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   3.6e-10   1.1e-06      61     177 ..      86     198 ..      60     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.6e-10
                                       GGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-- CS
                       Aminotran_5  61 eeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln 137
                                        ++ii t G++ea+ +++ +    +  gde+++ + +  +   +  +la   g  v  +pl ++ +ld+ ++e++++
  gi|313126360|ref|YP_004036630.1|  86 PDDIIATAGGSEALHIAMEAH---VGSGDEVIIPDPGFVSYD-ALTKLA--DGTPV-PVPLRDDLTLDPAAVEEAIT 155
                                       489**************9999...*************99999.667776..45555.88****************** PP

                                       TTEEEEEEESBETTTTEB--HHHHHH...HHHHTT-EEEEE-T CS
                       Aminotran_5 138 ektklvaithvsnvtGtiqpveeigk...lakkkgalvlvDaa 177
                                       ++t++ +++   n tG + p e+i +   +a ++++l + D +
  gi|313126360|ref|YP_004036630.1| 156 DDTAAFIVNSPGNPTGAVSPPEDIREfarIADEHDVLCISDEV 198
                                       *****************98866665500055567888887776 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.3e-06     0.019     184     234 ..     149     198 ..     140     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-06
                                       HHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-T CS
                       Aminotran_3 184 alekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEv 234
                                       a+e++++d++aA+iv       G  v++pe +++ + ++++hdvl i DEv
  gi|313126360|ref|YP_004036630.1| 149 AVEEAITDDTAAFIVNSPGNPTGA-VSPPEDIREFARIADEHDVLCISDEV 198
                                       688999*********975555555.55666699*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2027.95
//
Query:       gi|313126361|ref|YP_004036631.1|  [L=50]
Description: hypothetical protein Hbor_16160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 306.17
//
Query:       gi|313126362|ref|YP_004036632.1|  [L=449]
Description: DNA repair helicase rad25 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-22   80.9   0.0    2.8e-22   79.5   0.0    1.7  2  ResIII         Type III restriction enzyme, res subunit
      1e-17   63.7   2.1    3.9e-17   61.9   2.1    2.1  1  XPB_DRD        Xeroderma pigmentosum group B helicase damage 
    2.5e-17   62.9   0.0    3.3e-17   62.5   0.0    1.1  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    9.1e-14   51.8   0.0    1.8e-12   47.6   0.0    2.4  2  Helicase_C     Helicase conserved C-terminal domain
    3.1e-08   33.6   0.1      2e-07   30.9   0.0    2.2  2  DEAD           DEAD/DEAH box helicase
     0.0022   18.2   0.0        1.3    9.2   0.0    2.8  3  Helicase_C_2   Helicase C-terminal domain
     0.0031   16.3   0.1      0.016   13.9   0.1    2.2  2  SNF2_N         SNF2 family N-terminal domain
  ------ inclusion threshold ------
       0.12   11.6   0.0       0.19   11.0   0.0    1.3  1  SecA_DEAD      SecA DEAD-like domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0   1.2e-25   2.8e-22       2     171 .]      75     214 ..      74     214 .. 0.94
   2 ?   -2.5   0.0       1.9   4.3e+03      53      77 ..     332     356 ..     321     381 .. 0.72

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 1.2e-25
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       ++lr+yQ  a++++       +d+rg+++++TG+GKT+va+++i++l        +l++vp+ +ll+q+++e++  +
  gi|313126362|ref|YP_004036632.1|  75 YDLRDYQRGALDAWH-----ANDERGVLELPTGAGKTVVAVAAIAALGG-----STLIVVPTVDLLNQWRRELETEF 141
                                       579***********8.....899*************************9.....5*******************999 PP

                                       GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHH CS
                            ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreile 155
                                       +     +g++  g++ ++         i+v+t++s++ +         +   + f+++++DE+H+lg+ + +r +++
  gi|313126362|ref|YP_004036632.1| 142 DIS---VGQFGGGEQTQE--------AITVSTYDSAYLRA--------DDVGGDFEFVVFDEVHHLGG-EGYRDVAR 198
                                       988...677777777777........************99........999*****************.******** PP

                                       T---SEEEEEESS-S- CS
                            ResIII 156 kfkeavllglTATper 171
                                        + +  +lglTAT+er
  gi|313126362|ref|YP_004036632.1| 199 LLTAPARLGLTATFER 214
                                       *************985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                                       ...-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII  53 keekflflvprkslleqtleefkkf 77 
                                         ++++++   ++l+ ++ e++   
  gi|313126362|ref|YP_004036632.1| 332 CDDRVIVFTAHTDLVYRLSERYLLP 356
                                       4568899999999999998888544 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   2.1   1.8e-20   3.9e-17       1      57 []       4      63 ..       4      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.8e-20
                                      EEEETTEEEECSSSTT......-CT.EEETTTTEEEEEGGGHHHHHHHHHCTT--EEEES CS
                           XPB_DRD  1 LrYdrGTllidgdprgkas...lpfvewDeRvekyRapAlrYrdlveaLraagiefeDrv 57
                                      L++++GT+++ g+++++ s   lp+v wD+R    RapA+rY+dl++ L+++g+++eDr+
  gi|313126362|ref|YP_004036632.1|  4 LTFEDGTVRVGGLAESDVSaadLPGVAWDDRGLVARAPAYRYADLRASLDERGLDYEDRI 63
                                      89*************9663456************************************95 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   1.5e-20   3.3e-17      36     182 ..     310     449 .]     300     449 .] 0.84

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.5e-20
                     ERCC3_RAD25_C  36 kllyvmnp.nkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntif 111
                                       +  ++mn+ +k++++  +++ h   +D++ivf+ +   + +++++   p i+ et+ ++r ++l++f+  + ++ ++
  gi|313126362|ref|YP_004036632.1| 310 ARRIMMNAdQKVETLGRILDRHC--DDRVIVFTAHTDLVYRLSERYLLPAITSETAASDRRELLERFRDGT-YSRVV 383
                                       33444554257777777776664..79*****9888888888899999********************885.66677 PP

                     ERCC3_RAD25_C 112 lskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrq 182
                                        ++v D+ +D+P+anv + ++   gs r   qrlGr+Lr+k++    +  a  Y Lvs +t e   +++r+
  gi|313126362|ref|YP_004036632.1| 384 TANVLDEGVDVPDANVAVLLA-GSGSEREFTQRLGRVLRPKTD----GGAAILYELVSAETAEERVAQRRR 449
                                       899*************99876.579****************99....889***************999985 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.19   4.3e+02      15      48 ..     116     150 ..     106     166 .. 0.75
   2 !   47.6   0.0     8e-16   1.8e-12       2     109 ..     320     421 ..     319     423 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.19
                                       TTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEEST CS
                        Helicase_C  15 eggkilifvntidrlek.vklllekkgikvavlhg 48 
                                        gg +li+v+t+d l++  + l+++++i+v  + g
  gi|313126362|ref|YP_004036632.1| 116 LGGSTLIVVPTVDLLNQwRRELETEFDISVGQFGG 150
                                       5899*********9987777776666777766655 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 8e-16
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       k+e+l ++l  ++ ++++++f+  +d ++  +l    + +   ++++e+ +++r+e le+f++g++  +++ +v+ +
  gi|313126362|ref|YP_004036632.1| 320 KVETLGRIL-DRHCDDRVIVFTAHTDLVY--RLS---ERYLLPAITSETAASDRRELLERFRDGTYSRVVTANVLDE 390
                                       778888999.8999************996..555...5577888********************************* PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       G+d+p++n+ + +    + +++ qr GR+ R
  gi|313126362|ref|YP_004036632.1| 391 GVDVPDANVAVLLAGSGSEREFTQRLGRVLR 421
                                       *****************************99 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0     9e-11     2e-07       2     145 ..      79     200 ..      78     216 .. 0.71
   2 ?   -3.2   0.0       2.7     6e+03      97     164 ..     316     338 ..     305     343 .. 0.50

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9e-11
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       d+Q+ a+++   +++  +++ +TG+GKT +++ ++  +        g  +liv+Pt  L +q  ++l++ ++   ++
  gi|313126362|ref|YP_004036632.1|  79 DYQRGALDAWHaNDERGVLELPTGAGKTVVAVAAIA-A-------LGGSTLIVVPTVDLLNQWRRELETEFD---IS 144
                                       56777777777445678899**********988888.3.......46799******************9999...45 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinri 145
                                       v  + gg+++    ++      i+v+t +      ++      +++f+V+DE++ l  +g++d  + +
  gi|313126362|ref|YP_004036632.1| 145 VGQFGGGEQT----QEA-----ITVSTYDSAYLRADD---VGGDFEFVVFDEVHHLGGEGYRDVARLL 200
                                       6544444333....333.....444444433332221...23689*****************988764 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.7
                                       TCSEEEEEHHHHHH.HHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEE CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  97 gvdivvgtpgrldd.llstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqviv 164
                                       ++d  v t gr++d +++++                                              viv
  gi|313126362|ref|YP_004036632.1| 316 NADQKVETLGRILDrHCDDR----------------------------------------------VIV 338
                                       44444555555554333322..............................................444 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1   2.5e+03       7      33 ..     115     141 ..     110     166 .. 0.74
   2 !    5.6   0.0    0.0075        17      39      87 ..     357     401 ..     324     405 .. 0.74
   3 !    9.2   0.0   0.00058       1.3     129     151 ..     410     432 ..     408     443 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                      Helicase_C_2   7 vvpggvlvffpSyklleevverlkeel 33 
                                       +  g +l+++p  +ll++ +++l++e 
  gi|313126362|ref|YP_004036632.1| 115 ALGGSTLIVVPTVDLLNQWRRELETEF 141
                                       567889999999999999999999875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0075
                      Helicase_C_2  39 eifveekeesrekvleeykekkkkgaillavcrGklsEGidfsddllra 87 
                                        i  e+ +++r+++le++++      ++ a +   l EG+d++d+++ +
  gi|313126362|ref|YP_004036632.1| 357 AITSETAASDRRELLERFRD-GTYSRVVTANV---LDEGVDVPDANVAV 401
                                       3555658889**********.55556666665...9*******998765 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00058
                      Helicase_C_2 129 ravnQaiGRliRhkdDygaivll 151
                                       r++ Q +GR++R k+D ga +l 
  gi|313126362|ref|YP_004036632.1| 410 REFTQRLGRVLRPKTDGGAAILY 432
                                       6789****************996 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   7.2e-06     0.016      63     117 ..     100     139 ..      87     211 .. 0.83
   2 ?   -1.3   0.0       0.3   6.8e+02     279     330 ..     242     288 ..     220     321 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.2e-06
                                       -TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                            SNF2_N  63 emGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneier 117
                                        +G+GKTv ++a i+                 l g tLivvP+ +ll+qW +e+e+
  gi|313126362|ref|YP_004036632.1| 100 PTGAGKTVVAVAAIA----------------ALGGSTLIVVPTvDLLNQWRRELET 139
                                       579999999999999................36689*****************986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.3
                                       S---EEEEEEEEE--HHHHHHHH....................HHHHHH-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 279 nlPpkteeiiflklskverksYnrllevlrkkalakllkrseaalksssksk 330
                                        l++ +++ i ++l++ er+ Y+     +++ +    lk s+ ++ s+s+ +
  gi|313126362|ref|YP_004036632.1| 242 HLAEYEVRRIEVDLTPAERERYE-----EAQGTFVDYLKTSNLSFRSGSDYQ 288
                                       577788888999999*****999.....444444444555556666555433 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.4e-05      0.19      93     132 ..      95     132 ..      70     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.4e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SecA_DEAD  93 kiaemkTGEGKtlvatlpaylnaltgkgvhvvtvndYLak 132
                                        + e+ TG GKt+va+   +++al g++  vv + d L +
  gi|313126362|ref|YP_004036632.1|  95 GVLELPTGAGKTVVAVA--AIAALGGSTLIVVPTVDLLNQ 132
                                       5889*********9985..678**********99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2508.30
//
Query:       gi|313126363|ref|YP_004036633.1|  [L=143]
Description: hypothetical protein Hbor_16180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   14.1   0.3      0.057   13.7   0.3    1.1  1  CARDB     CARDB


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   3.2e-06     0.057       1      72 [.      58     128 ..      58     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-06
                                       S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelvgtvtvpsLaagesttvsftwtte 72 
                                       +pDL v +t+  +e++ + ++++   v N G+ +   +++v+++ +g++ ++ t   +a+g++++ s+t+ ++
  gi|313126363|ref|YP_004036633.1|  58 KPDLYV-KTFDFDETE-NGNLRVFGDVGNRGDVErVATVQVRVTRNGKEYTQETTVTVASGTTASFSVTFGIS 128
                                       599999.777777665.55789999*******9979999**********966666699**********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 810.96
//
Query:       gi|313126364|ref|YP_004036634.1|  [L=514]
Description: hypothetical protein Hbor_16190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   8.8e-138  459.2   0.0     4e-137  457.1   0.0    1.8  2  DUF790     Protein of unknown function (DUF790)
     0.0099   15.8   0.7      0.033   14.1   0.0    2.2  3  GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
  ------ inclusion threshold ------
      0.073   12.9   2.4        5.8    6.9   0.0    3.4  3  DUF433     Protein of unknown function (DUF433)
       0.23   11.8   9.5      0.061   13.6   1.7    2.9  3  DUF2267    Uncharacterized conserved protein (DUF2267)


Domain annotation for each model (and alignments):
>> DUF790  Protein of unknown function (DUF790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.1   0.0    9e-141    4e-137       1     387 []       1     398 [.       1     398 [. 0.98
   2 ?   -0.2   0.0     0.069   3.1e+02     101     162 ..     417     493 ..     404     498 .. 0.81

  Alignments for each domain:
  == domain 1  score: 457.1 bits;  conditional E-value: 9e-141
                            DUF790   1 MLpsdllrvrrrggkivpkflkeenlelaaelielfeehvGekrgeleeelkeleeeatdyklvrGLakllereaef 77 
                                       ML++dl rv+r+gg ++p+f+ +e+++laa++i++f+ hvGe+r++l+++l++le+ea+d+klvrGLa+ll+rea+f
  gi|313126364|ref|YP_004036634.1|   1 MLTKDLRRVSRAGGGYHPQFVGRESRPLAARVIGVFQGHVGEPRHRLDDALSSLEDEADDFKLVRGLAALLDREATF 77 
                                       ***************************************************************************** PP

                            DUF790  78 etespldpeelReevFeaaaea..vvseeereevleevaeelgvspeeveealyadleenkiLtef.eeitpeeLlk 151
                                       e+++pl+p+++R++ Fe+a++a   +++e r++vl++va++lg+++e++ee+lyad+  n++Ltef  +++p++Ll+
  gi|313126364|ref|YP_004036634.1|  78 EVVAPLPPTRVRRATFEEAETAgvPTTTEARTAVLKRVADRLGTDTEAIEESLYADRAVNEVLTEFdARWSPDSLLE 154
                                       ********************9997888899************************************568******** PP

                            DUF790 152 rYNlslvqtlLfkatelrirvsdaeykelfravkllgLmyeieedaeegleitvdGPaslfkaterYGlalAkllpa 228
                                       +YNlsl+qt+Lf+ate+r+r+sd+  k+l++avk+lgLmyei++d e+ +e++v+GP +lf++t+rYG+a+A+ll++
  gi|313126364|ref|YP_004036634.1| 155 QYNLSLAQTALFDATEVRVRSSDP--KRLVSAVKRLGLMYEIRRDGET-RELVVTGPDALFRRTRRYGTAFARLLRT 228
                                       ***********************8..********************65.**************************** PP

                            DUF790 229 llkvekWeleAeikdrdkkkrelrfeldsedsglvshyeeeke..fdssveeefaerfeklktdwelerepellkig 303
                                       ++ +++W+++A+i+dr+   +e++++l+++d   v+++e+++e  +ds ve++fa+rfe l+ dwel+repe+l++g
  gi|313126364|ref|YP_004036634.1| 229 VAGTAEWTMTATIDDRG---TEREMTLSDAD-LSVPNVEPVTEptYDSGVEADFAARFEGLDLDWELVREPEPLAAG 301
                                       ****************9...9********77.999******999********************************* PP

                            DUF790 304 gsvmiPDFale.............ekdgrrvyleIvGfwtpeylkkKleklrka.erkelivavserlklekagvka 366
                                       +++miPDFa++             +  ++rv++e++Gfwtpey++kKl++++++ +++el+va++e+l++ ++ v++
  gi|313126364|ref|YP_004036634.1| 302 ARAMIPDFAFVyrpggdaagensgDDPEFRVFFEVMGFWTPEYVEKKLDQFATVsDDVELVVAADESLAVAED-VAE 377
                                       ********************99988889*************************9778**************96.*** PP

                            DUF790 367 kdlrvilfkdklrvkdVlevl 387
                                        d+rv++++++++vkdV+++l
  gi|313126364|ref|YP_004036634.1| 378 LDHRVVTYSGSVHVKDVVDLL 398
                                       ******************986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.069
                            DUF790 101 vseeereevleevaeelgvspeeveealyadlee.nkiLtef..............eeitpeeLlkrYNlslvqtlL 162
                                       +s++   + l+e+a+++ v ++++e++ + d e+  + L++               +  ++e++l++Y ls + ++L
  gi|313126364|ref|YP_004036634.1| 417 LSPDADVASLAELADSYAVAEDALESVSFPDHEQvGRALVRPavvdalgdeleagmSLSDAEAILEEYGLSDASAVL 493
                                       56667778899999999999999999999999872467887788899999998888888899999999999998887 PP

>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.56   2.5e+03     221     239 ..      66      85 ..      41     135 .. 0.68
   2 !   14.1   0.0   7.4e-06     0.033      83     148 ..     204     269 ..     202     311 .. 0.83
   3 ?   -2.5   0.1      0.88     4e+03     154     154 ..     397     397 ..     345     454 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.56
                         GvpL_GvpF 221 elaarldg.levrltGPwpP 239
                                        laa ld   +++++ P+pP
  gi|313126364|ref|YP_004036634.1|  66 GLAALLDReATFEVVAPLPP 85 
                                       44444333355666666655 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.4e-06
                         GvpL_GvpF  83 vlkdeeavrelLeeeadelreaLerlagkvEygvkvlwdeealleelleedpelrelreeieaase 148
                                       v+++ +a+ +  +++ + ++++L+++ag++E+  +++ d++  ++e++ +d +l+  + e  +++ 
  gi|313126364|ref|YP_004036634.1| 204 VVTGPDALFRRTRRYGTAFARLLRTVAGTAEWTMTATIDDRGTEREMTLSDADLSVPNVEPVTEPT 269
                                       788899998889999************************************999988887776665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.88
                         GvpL_GvpF 154 l 154
                                       l
  gi|313126364|ref|YP_004036634.1| 397 L 397
                                       2 PP

>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0013       5.8      21      48 ..     136     162 ..     134     164 .. 0.92
   2 ?   -1.0   0.1      0.37   1.7e+03      19      42 ..     389     414 ..     388     417 .. 0.67
   3 ?    3.6   0.1     0.013        60      21      47 ..     461     489 ..     460     495 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0013
                                       THHHHHHHHTT--HHHHHHHH.TS-HHH CS
                            DUF433  21 VetilellaaGesieeiledyPdLtled 48 
                                       V  +l  ++a +s++ +le+y +L+l++
  gi|313126364|ref|YP_004036634.1| 136 VNEVLTEFDARWSPDSLLEQY-NLSLAQ 162
                                       8899*****************.999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.37
                                       -BTHHHHHHHHTT--..HHHHHHHH. CS
                            DUF433  19 ipVetilellaaGes..ieeiledyP 42 
                                       + V+++++ll+  e+  i+e ++d P
  gi|313126364|ref|YP_004036634.1| 389 VHVKDVVDLLRIYEDelIAEAADDLP 414
                                       57999999999855433555555555 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.013
                                       THHHHHHHHTT--...HHHHHHHH.TS-HH CS
                            DUF433  21 VetilellaaGes...ieeiledyPdLtle 47 
                                       V+ + + l+aG+s    e ile+y +L+ +
  gi|313126364|ref|YP_004036634.1| 461 VDALGDELEAGMSlsdAEAILEEY-GLSDA 489
                                       6777889999999666688*****.88866 PP

>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.7   1.4e-05     0.061      29     105 ..      65     149 ..      62     154 .. 0.84
   2 ?    1.9   0.2     0.056   2.5e+02      88     119 ..     387     417 ..     356     419 .. 0.79
   3 ?   -2.9   0.0       1.7   7.6e+03      92     105 ..     457     470 ..     424     473 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                                       HHHHTTS-HHHHHHHHTTS.-HHHHHHHHTT--TTS.-----SHHHHHHHHHHTS.....E......HHHHHHHHHH CS
                           DUF2267  29 rtLrdrlteeeaadlaaqL.Peelrgllrdgwppve.pgkrfdreeflervaeelgvdped......aeqaaraVfa 97 
                                       r L+ +l++e+  ++ a L P  +r++ +++ + ++ p     r++ l+rva++lg+d e+      a++a+  V++
  gi|313126364|ref|YP_004036634.1|  65 RGLAALLDREATFEVVAPLpPTRVRRATFEEAETAGvPTTTEARTAVLKRVADRLGTDTEAieeslyADRAVNEVLT 141
                                       568999*************66679988888887777888899*************9999889998888888888888 PP

                                       HHHHHS-H CS
                           DUF2267  98 alkealse 105
                                         +++ s+
  gi|313126364|ref|YP_004036634.1| 142 EFDARWSP 149
                                       77666665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHS-HHHHHHHHHTS-HHH CS
                           DUF2267  88 aeqaaraVfaalkealsegeiedvaaqLPkdl 119
                                          +++ V+++l+   +++ i++ a+ LP++l
  gi|313126364|ref|YP_004036634.1| 387 GSVHVKDVVDLLRIY-EDELIAEAADDLPDEL 417
                                       5679999***99977.88999********997 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHS-H CS
                           DUF2267  92 araVfaalkealse 105
                                         aV++al ++l++
  gi|313126364|ref|YP_004036634.1| 457 RPAVVDALGDELEA 470
                                       34677777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2884.60
//
Query:       gi|313126365|ref|YP_004036635.1|  [L=182]
Description: hypothetical protein Hbor_16200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-09   35.6   0.0    1.2e-08   34.8   0.0    1.3  1  Methyltranf_PUA  RNA-binding PUA-like domain of methyltransfe


Domain annotation for each model (and alignments):
>> Methyltranf_PUA  RNA-binding PUA-like domain of methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   6.6e-13   1.2e-08       1      48 [.     125     177 ..     125     178 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 6.6e-13
                   Methyltranf_PUA   1 alrYlkGetielep.dlkkGwvlVcyd....gyplGwgKlvggrlKNkyPkgl 48 
                                       a r+++Ge+ el+  d+++G+++ +++     +p+G+g +++g+l++ +Pkg+
  gi|313126365|ref|YP_004036635.1| 125 ADRFVRGEDQELDRwDGDWGYLVAAHEfegeREPIGVGLYLHGELRSTVPKGR 177
                                       78***********87**************99*********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 991.41
//
Query:       gi|313126366|ref|YP_004036636.1|  [L=312]
Description: nol1/nop2/sun family RNA methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-52  177.1   0.0    5.8e-52  176.3   0.0    1.4  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.3e-05   25.6   0.0    3.2e-05   24.3   0.0    1.6  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    0.00037   20.3   0.0    0.00058   19.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.053   13.6   0.0       0.09   12.9   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.98   4.4e+03     183     197 ..       6      20 ..       4      21 .. 0.87
   2 !  176.3   0.0   1.3e-55   5.8e-52       2     199 ..      92     308 ..      91     309 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.98
                                       EE-TTTTSS-SEEEE CS
                   Methyltr_RsmB-F 183 rllPhtenkdgffia 197
                                       r+ P  +++d+ff+a
  gi|313126366|ref|YP_004036636.1|   6 RYAPLVDDEDAFFAA 20 
                                       7889999******98 PP

  == domain 2  score: 176.3 bits;  conditional E-value: 1.3e-55
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg. 77 
                                       l+L+p+++e + D+caaPG+KTt +a+lm+++g+++ +d+n  Rl+++ +n +rLgv n+ v++ Dar+++    g 
  gi|313126366|ref|YP_004036636.1|  92 LALDPEPGEIVWDACAAPGSKTTQLADLMDDTGVLIGNDNNLGRLSALRHNAERLGVSNLVVTNQDARNYSLKPFGe 168
                                       79********************************************************************9887777 PP

                                       ..........EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTT CS
                   Methyltr_RsmB-F  78 ........elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEn 146
                                               + fD++L+DaPCs  g+ir++pd+  r + + + ++a  qk +l  a++ +++gG++vYsTC+ ++eEn
  gi|313126366|ref|YP_004036636.1| 169 dtddsaaiDAFDKALVDAPCSCEGTIRKNPDALDRWTMNHVHSVAGIQKGILRRAVQATRPGGTVVYSTCTFAPEEN 245
                                       9999999999**********************99999**************************************** PP

                                       HHHHHHHHHH-TTEEEESSBSTTSTTSSECEEC...........TSEEE-TTTTSS-SEEEEEE CS
                   Methyltr_RsmB-F 147 eevieeaLkkredvelvetelsepkglklgeea...........gtlrllPhtenkdgffiakl 199
                                       e+v++++L ++ d +lv+ ++ +  +++ g+++            + r++Ph++++ gff akl
  gi|313126366|ref|YP_004036636.1| 246 EAVLDHVLGEE-DCKLVPWDAPDNFETAPGVTEwedeeydpsveLAHRVYPHHNDTGGFFCAKL 308
                                       ********987.9*****************9999*********999*****************9 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   7.1e-09   3.2e-05      15      87 ..      12      85 ..       4      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 7.1e-09
                                      GGHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---...TTSHHHHTTS-EE--T CS
                   Methyltr_RsmF_N 15 eeaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerpgkhplheaGlyYiQEp 87
                                      ++ +af+aa+++p ++ +RvNt+K++v++ +++ +  ++  ep +w +    l+e+  pg++  +  G+ + QE 
  gi|313126366|ref|YP_004036636.1| 12 DDEDAFFAACDRPLPSVVRVNTIKTTVDRARSALDaeNVGYEPTDWHPGILKLDER-GPGTTWPYFHGWLHGQEE 85
                                      56799*********************99999877768999******9988888888.889888889999999985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-07   0.00058       6     114 ..     101     244 ..      96     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-07
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.led........e 73 
                                        v D+ ++ G +t +la+++ + + ++G D++   ++  r na++lg++n+ +  +d+ + + + + +        +
  gi|313126366|ref|YP_004036636.1| 101 IVWDACAAPGSKTTQLADLMDDTGVLIGNDNNLGRLSALRHNAERLGVSNLVVTNQDARNYSLKpFGEdtddsaaiD 177
                                       57899999**********9999**************************************88666666799999999 PP

                   Methyltransf_31  74 kfDlilsnevl......................naladpdkileeiervlkpggilliedpr....l 114
                                        fD  l ++++                           ++ il+++ ++ +pgg ++ +++      
  gi|313126366|ref|YP_004036636.1| 178 AFDKALVDAPCscegtirknpdaldrwtmnhvhSVAGIQKGILRRAVQATRPGGTVVYSTCTfapeE 244
                                       99997777444444444444444466665443233344566777999**********9999954431 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05      0.09      21     145 ..      98     249 ..      80     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS........HHHTTEEEECS-CCCSSHHHHHCHCHHH.... CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm........aplpgvttiqgditdpetiekikealse.... 85 
                                       pg+ v D +aaPG+ +  l+  +  +g++++ D + +        a  +++ + +  +t++++++  ++ ++e    
  gi|313126366|ref|YP_004036636.1|  98 PGEIVWDACAAPGSKTTQLADLMDDTGVLIGNDNNLGrlsalrhnA--ERLGVSNLVVTNQDARNYSLKPFGEdtdd 172
                                       7888*******************88999999998777666443221..44444455556666666666555555666 PP

                                       ....SSEEEEEE--S-SS-CH..HHHHHHHH.........CCCCHHHHCCHCCCCECCCEEEECCCH..CCCHHHHH CS
                              FtsJ  86 ....rkvdlvvsDgapdvsgv..hdldeylq.........sqLllaalelalkllkpggtfvlkifr..geeteall 145
                                             +d  + D   +++g+  ++ d++ +         + + +  l+ a++  +pggt+v  +++   ee ea+l
  gi|313126366|ref|YP_004036636.1| 173 saaiDAFDKALVDAPCSCEGTirKNPDALDRwtmnhvhsvAGIQKGILRRAVQATRPGGTVVYSTCTfaPEENEAVL 249
                                       67777788888888777777552333443337766666655777888888888889999999888774344444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1719.98
//
Query:       gi|313126367|ref|YP_004036637.1|  [L=246]
Description: ATP-grasp superfamily enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-38  133.3   0.1    1.3e-38  133.1   0.1    1.0  1  PAC2          PAC2 family
  ------ inclusion threshold ------
      0.033   14.5   0.4       0.08   13.3   0.4    1.5  1  kleA_kleC     Uncharacterized KorC regulated protein A
       0.18   11.9   1.0        1.6    8.8   1.0    2.4  1  Sigma70_r1_2  Sigma-70 factor, region 1.2


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.1   2.2e-42   1.3e-38       2     212 ..      19     225 ..      18     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 2.2e-42
                                       EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEE.TTT.SEEEEEEEE CS
                              PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyak.dsgsrdllvlqgr 75 
                                       ++G+pg+G+Vg++a+d+L+e ++++++g +++d+ +p      v++++eg  +  +p+rlya+ +   rdllvlq+ 
  gi|313126367|ref|YP_004036637.1|  19 VEGLPGVGLVGKIAADHLVEAFDMVHYGNLHCDG-IP-----KVAVYHEGdpELSTPVRLYADaE---RDLLVLQSD 86 
                                       89********************************.**.....999999999**********9955...********8 PP

                                       -HSCHHH..HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT......-CEEEE CS
                              PAC2  76 epilqye..efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees......eyggiv 144
                                        pi+++   e+a++l +w+++++   ++ L+gl+ ++++d     p  ++++a  e  +  +ee+      e+g i+
  gi|313126367|ref|YP_004036637.1|  87 VPIVPQAatEVANCLSSWFDDIESMPIF-LSGLPQEKSED----VP-ALYAVAAGEGAA-MVEEAgidfpnEMGLIS 156
                                       8888888888*************99999.*****887754....44.556666444433.33333445667****** PP

                                       HHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHH.T---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 145 gitglLlsaakergipavgllaevphylpdPkaaaalleflskll.glevdtedLeedaeeleeqleel 212
                                       g+tg+Ll+ a +++  avgl +e+++++pdP+a+++++++  + l g+ev++++L  +aee++++ ++l
  gi|313126367|ref|YP_004036637.1| 157 GPTGALLHDALKNDRTAVGLIVESDPQFPDPEASRVIIKKGIEPLaGIEVPVDNLVDRAEEIRNAKKQL 225
                                       **********************************999999866665*****************998776 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   1.3e-05      0.08       9      45 ..     208     244 ..     205     245 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                         kleA_kleC   9 iDeLpevatdlvarRdkiAaklaeAeeLvrqaeeLRa 45 
                                       +D+L + a+++++ + ++A+++++ +e   qa+ LR+
  gi|313126367|ref|YP_004036637.1| 208 VDNLVDRAEEIRNAKKQLAQRMQQGDEESTQAQPLRM 244
                                       8999999****************************96 PP

>> Sigma70_r1_2  Sigma-70 factor, region 1.2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0   0.00027       1.6      23      34 .]     224     235 ..     210     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00027
                                       HHHHHHHCCHHH CS
                      Sigma70_r1_2  23 eLAkrieaGdea 34 
                                       +LA+r+++Gde+
  gi|313126367|ref|YP_004036637.1| 224 QLAQRMQQGDEE 235
                                       7*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1406.00
//
Query:       gi|313126368|ref|YP_004036638.1|  [L=256]
Description: molecular chaperone grpe (heat shock protein) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-39  134.9   6.7      2e-39  134.9   6.7    2.0  2  GrpE           GrpE
    9.8e-05   20.9  12.3    0.00011   20.7  12.3    1.1  1  MAD            Mitotic checkpoint protein
     0.0072   16.6  19.3      0.011   16.0  19.3    1.2  1  ATG16          Autophagy protein 16 (ATG16)
  ------ inclusion threshold ------
      0.011   15.3   4.7      0.012   15.2   4.7    1.1  1  Exonuc_VII_L   Exonuclease VII, large subunit
      0.015   15.5   2.3      0.027   14.7   2.3    1.4  1  Fib_alpha      Fibrinogen alpha/beta chain family
      0.028   15.1   3.0        1.6    9.5   2.7    2.6  1  CHASE6_C       C-terminal domain of two-partite extracellular
      0.041   14.3   2.3        0.1   13.1   0.6    2.2  2  Cep57_MT_bd    Centrosome microtubule-binding domain of Cep57
      0.059   12.6   1.3      0.095   11.9   1.3    1.3  1  TMPIT          TMPIT-like protein
      0.082   11.4   2.6       0.11   11.0   2.6    1.1  1  Het-C          Heterokaryon incompatibility protein Het-C
       0.15   11.6   2.0       0.25   10.9   2.0    1.4  1  Fzo_mitofusin  fzo-like conserved region
       0.16   12.7   3.5       0.35   11.6   3.5    1.6  1  Occludin_ELL   Occludin homology domain
       0.21   11.6   1.8       0.45   10.6   1.8    1.7  1  DUF1664        Protein of unknown function (DUF1664)
       0.21   11.0   7.6       0.28   10.6   7.6    1.2  1  MIIP           Migration and invasion-inhibitory
       0.31   10.4   7.6       0.39   10.0   7.6    1.1  1  FAM76          FAM76 protein
       0.34   10.7   1.4       0.55   10.0   1.4    1.3  1  PSI_PsaF       Photosystem I reaction centre subunit III
       0.69   10.3   4.4        2.8    8.3   1.1    2.6  2  GAT            GAT domain
        1.3    8.6  15.6       0.65    9.6   9.2    2.2  2  Lebercilin     Ciliary protein causing Leber congenital amaur
        1.4    9.0  13.5        2.4    8.2  13.5    1.4  1  UPF0242        Uncharacterised protein family (UPF0242) N-ter
        2.3    7.2   6.8        3.2    6.8   6.8    1.1  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
        2.5    8.3   8.4        3.3    7.8   0.5    2.4  2  IFP_35_N       Interferon-induced 35 kDa protein (IFP 35) N-t
        3.8    8.2  11.3       0.24   12.0   5.2    2.2  2  SlyX           SlyX
        4.5    5.7  10.3        5.4    5.5  10.3    1.1  1  Macoilin       Macoilin family
        5.3    6.3   6.2        7.1    5.9   5.8    1.4  1  CorA           CorA-like Mg2+ transporter protein
        6.9    5.8   6.9         10    5.2   6.9    1.4  1  Tho2           Transcription factor/nuclear export subunit pr
        9.3    5.6  14.7         13    5.1  14.7    1.2  1  Golgin_A5      Golgin subfamily A member 5


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   7.0       1.9   1.3e+03       4      55 ..      41      93 ..      34      99 .. 0.76
   2 !  134.9   6.7   2.8e-42     2e-39       6     166 .]      97     253 ..      91     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                                      ...CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTT.THHHHHHHHHHH CS
                              GrpE  4 eeeeeeeedeeeeleeeleelekevkelkekllrllaefe.nlrkrtekekee 55
                                       e e++e+++ +e e+e e++e+e +e++   + ++ae    +  r+++  +e
  gi|313126368|ref|YP_004036638.1| 41 GEAEAAETETAAEKEAEAETAETETAEAEAVGDAANAETTgDVAARVAEYDDE 93
                                      56788888888888999999999999999888888888876777776665555 PP

  == domain 2  score: 134.9 bits;  conditional E-value: 2.8e-42
                                       .CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC. CS
                              GrpE   6 eeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksa 82 
                                       e +++e + ++le++l++  +e++el+e+l+r++a+f+n++kr++k++++++++a e+f++  + v+Dnl ral+  
  gi|313126368|ref|YP_004036638.1|  97 EVAALERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIRETATEDFVERVVTVRDNLLRALD-- 171
                                       567788899999999999999*****************************************************9.. PP

                                       .HHH-HHHHHHHHHHHHHHHHHHHHHTT-EE---T.TSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE CS
                              GrpE  83 keneeekslleGvemtlkqllkiLekhgvekiepk.gepFDpnlheavstveddekeegtvvevvqkGYklkdrvlR 158
                                         ++e  ++  G+e tl++++ iL+ + v  i+p+ ge+ Dp+ he++++ve+d+ +egtv +v+q GY + ++v+R
  gi|313126368|ref|YP_004036638.1| 172 --QDEDADIRPGIESTLEEFDRILADEDVSTIDPEpGEEVDPTRHEVMMRVESDQ-PEGTVADVYQPGYEMAEKVIR 245
                                       ..478889***********************************************.********************* PP

                                       -EEEEEEE CS
                              GrpE 159 pAmVkVsk 166
                                        A+ +Vsk
  gi|313126368|ref|YP_004036638.1| 246 EAQITVSK 253
                                       ******97 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  12.3   1.6e-07   0.00011      62     168 ..      45     153 ..      12     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.6e-07
                               MAD  62 kreeekeealreqiElarlkkknlealnkkekeke..sklaearevisalknelaelkrqiekqelelsekeselee 136
                                         e+e +++ ++++E a + +   ea+  +++  +  +  a + e  ++l +e+a+l+r ++k e +l +k +e  e
  gi|313126368|ref|YP_004036638.1|  45 AAETETAAEKEAEAETAETETAEAEAVGDAANAETtgDVAARVAEYDDELADEVAALERRVQKLETKLATKAEEADE 121
                                       233333333344444444445555566555554440145667789******************************** PP

                               MAD 137 lqerldllkkklseleqliqqlekkqkelaea 168
                                       l erl+  ++ +++++++ ++ + + +e a++
  gi|313126368|ref|YP_004036638.1| 122 LTERLKRTQADFQNYKKRAKKRQDQIRETATE 153
                                       *******************9999999888776 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  19.3   1.5e-05     0.011      30     150 ..      33     151 ..      25     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                             ATG16  30 rtsaleaenaklekaaasakssksskksakekeasasq.snskqsakiqsleqklaqlreelaelyksrgelaqrll 105
                                        t+a e+  ++  +++++a ++++++++a++++a+a++  ++++++++ + ++++a+  +ela+   + + l+ r++
  gi|313126368|ref|YP_004036638.1|  33 ATAAAEQNGEAEAAETETAAEKEAEAETAETETAEAEAvGDAANAETTGDVAARVAEYDDELAD---EVAALERRVQ 106
                                       4444443333332232333323333333333333333345777888888888888888888887...5899****** PP

                             ATG16 106 elneelqkleeklkedeerlaeleaeraaletklkdreeelreke 150
                                       +l+++l+++ e++ e +erl++ +a+ ++ +++ k+r++++re +
  gi|313126368|ref|YP_004036638.1| 107 KLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIRETA 151
                                       ******************************************976 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   4.7   1.6e-05     0.012     151     239 ..      62     166 ..      27     249 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                      Exonuc_VII_L 151 elerrlekaikrll................eekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkr 211
                                       e+e    +a+  +                 +e + ++ +l++r+++ e++l++k+++ del+erl+r ++  +++ +
  gi|313126368|ref|YP_004036638.1|  62 ETETAEAEAVGDAAnaettgdvaarvaeydDELADEVAALERRVQKLETKLATKAEEADELTERLKR-TQADFQNYK 137
                                       3333222222221122333333333344435555666677777777777777777777777777777.666677777 PP

                      Exonuc_VII_L 212 erleelkerl.kekleekkerlkklkerl 239
                                       +r ++ ++++ ++ +e+  er+ +++++l
  gi|313126368|ref|YP_004036638.1| 138 KRAKKRQDQIrETATEDFVERVVTVRDNL 166
                                       77777776664444444444443333333 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.3   3.7e-05     0.027      19     107 ..      80     170 ..      78     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                                       CCHHHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC.HHH CS
                         Fib_alpha  19 gCglqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeil.rlk 94 
                                       +  ++  + +y+ ++ ++++ le+++++++ +  +  e   e+++ l+++q+  ++ ++  kk +++++e  + ++ 
  gi|313126368|ref|YP_004036638.1|  80 TGDVAARVAEYDDELADEVAALERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIRETATeDFV 156
                                       5567788899*********************************************9999999999999965431455 PP

                                       HHHHCCH.HHHHHH CS
                         Fib_alpha  95 etidaqe.snirvL 107
                                       e++++   + +r+L
  gi|313126368|ref|YP_004036638.1| 157 ERVVTVRdNLLRAL 170
                                       55555443555555 PP

>> CHASE6_C  C-terminal domain of two-partite extracellular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.7    0.0022       1.6      28      71 ..      86     161 ..      65     164 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                          CHASE6_C  28 rilkYrpeLaekleqakqkill................................keeaaeksekedldpfvqRlVt 71 
                                       r+++Y+ eLa+++++ +++++                                 +++ +++ +++ ++ fv+R+Vt
  gi|313126368|ref|YP_004036638.1|  86 RVAEYDDELADEVAALERRVQKletklatkaeeadelterlkrtqadfqnykkrAKKRQDQIRETATEDFVERVVT 161
                                       5666666666666555555544444555555555555555666666666687664555556666777779999997 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.4     1e+03      19      37 ..      93     111 ..      90     115 .. 0.70
   2 ?   13.1   0.6   0.00014       0.1       6      42 ..     115     151 ..     111     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                       Cep57_MT_bd  19 eLedEfehlklelqelaaq 37 
                                       eL dE++ l  + q+l+ +
  gi|313126368|ref|YP_004036638.1|  93 ELADEVAALERRVQKLETK 111
                                       5677777777777777665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                       Cep57_MT_bd   6 sqspkeaLaevlkeLedEfehlklelqelaaqynald 42 
                                       +++ +++L e lk  + +f+ +k++ ++ ++q++++ 
  gi|313126368|ref|YP_004036638.1| 115 KAEEADELTERLKRTQADFQNYKKRAKKRQDQIRETA 151
                                       567899***************************9986 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.3   0.00013     0.095       2      59 ..      96     153 ..      91     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkks 59 
                                       +e++ le+++++le++  +  ++ +el++  ++++ + ++ kkr+k+ +++++++ ++
  gi|313126368|ref|YP_004036638.1|  96 DEVAALERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIRETATE 153
                                       5788899999999999999999999999999999999999999999999999888776 PP

>> Het-C  Heterokaryon incompatibility protein Het-C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.6   0.00015      0.11     285     404 ..      55     193 ..      39     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                             Het-C 285 qsevdeldaaleeaekssssssksalksllsklpgtgddlaeeaeelkakseaqeaena..............sase 347
                                       ++e +  +++ +eae+  +++++++  ++ +++   +d+la+e+  l++++++ e++ a              ++++
  gi|313126368|ref|YP_004036638.1|  55 EAEAETAETETAEAEAVGDAANAETTGDVAARVAEYDDELADEVAALERRVQKLETKLAtkaeeadelterlkRTQA 131
                                       44555556666666666677788888888888888888888888888888887776666445555555544442222 PP

                             Het-C 348 skanavpgvspnfdpee..............vakkiypilefrDkvvksiseai..ekipglekliekisetl 404
                                       + +n            +              +   +  +++ rD++++++++    +  pg+e+ +e++   l
  gi|313126368|ref|YP_004036638.1| 132 DFQNY-----------KkrakkrqdqiretaTEDFVERVVTVRDNLLRALDQDEdaDIRPGIESTLEEFDRIL 193
                                       22222...........12222233333344467778889999********87642267799999999987665 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.0   0.00034      0.25      97     153 ..      92     148 ..      75     157 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                     Fzo_mitofusin  97 qelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLe 153
                                        el+  +a l+++v++ e++l ++ +e ++  e+l+++q   +  +++a++ + +++
  gi|313126368|ref|YP_004036638.1|  92 DELADEVAALERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIR 148
                                       477777777777888888888777777777777777777777777777777666665 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.5   0.00049      0.35      25      81 ..      92     148 ..      84     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00049
                      Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkr 81 
                                        el +e++++++++++Le++l + +e+ +e +++ ++ + +++++kk ++ ++++ r
  gi|313126368|ref|YP_004036638.1|  92 DELADEVAALERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIR 148
                                       37999************************99999999999****9998777776655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.8   0.00063      0.45      45     110 ..      82     147 ..      73     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00063
                           DUF1664  45 svskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       +v+ ++ +  ++la+    L++r++++++kl   +e + e++e +++ + d ++ ++  ++ ++ +
  gi|313126368|ref|YP_004036638.1|  82 DVAARVAEYDDELADEVAALERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQI 147
                                       566777777788888888888888888888888888888888888888888888887776665555 PP

>> MIIP  Migration and invasion-inhibitory
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   7.6   0.00039      0.28      12     135 ..      44     168 ..      28     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                              MIIP  12 evplsqetlsvksraslpkdarsad.arqgdscdvawgaavssrvaslppakvqhqeelgrpRphsapllatsdlkd 87 
                                       e+  ++   +++  a++ ++ ++a+   +gd+ + +++++v+ rva+   + ++++++l+r  ++    lat+  + 
  gi|313126368|ref|YP_004036638.1|  44 EAAETETAAEKEAEAETAET-ETAEaEAVGDAANAETTGDVAARVAEYDDELADEVAALERRVQKLETKLATKAEEA 119
                                       33333333333333333333.33334789********************************666777789******* PP

                              MIIP  88 pelsagesdlgpqeaqllrseearqskesktprvtf.keeskvpdsslr 135
                                       +el+ ++++ + + ++ ++ +++rq++  +t+  +f +   +v d+ lr
  gi|313126368|ref|YP_004036638.1| 120 DELTERLKRTQADFQNYKKRAKKRQDQIRETATEDFvERVVTVRDNLLR 168
                                       ***9999999988899999999999999999988884444566666665 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.6   0.00054      0.39     159     277 ..      38     154 ..       9     172 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                             FAM76 159 skkskekskekkaskkkskkhkkrssrlevskleeeklaeekesnetskksldsnssdhlv.avtqLkeeiaslkkq 234
                                       +++ + ++ e+++  +k+ + +++  ++e++++e  + a ++e++++ ++   +++ d+l  +v+ L+ ++++l+ +
  gi|313126368|ref|YP_004036638.1|  38 EQNGEAEAAETETAAEKEAEAETA--ETETAEAEAVGDAANAETTGDVAAR-VAEYDDELAdEVAALERRVQKLETK 111
                                       222222221222222222222222..2222222222222223333333332.3344444442577888899999999 PP

                             FAM76 235 leqkdqellekdkkitelkaellekekelreklkelekeakek 277
                                       l++k +e  e    +   +a+ ++ +k+ +++  +++++a+e 
  gi|313126368|ref|YP_004036638.1| 112 LATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIRETATED 154
                                       9999999999999999999999999888888888887776654 PP

>> PSI_PsaF  Photosystem I reaction centre subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.4   0.00077      0.55      27      77 ..      84     138 ..      55     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00077
                          PSI_PsaF  27 CseskafakrlkkevkklekrlkkyeadsaP....alalkakiektkkrfekysk 77 
                                          ++ +++ l +ev+ le+r++k e + a     a  l +++++t++ f++y k
  gi|313126368|ref|YP_004036638.1|  84 AARVAEYDDELADEVAALERRVQKLETKLATkaeeADELTERLKRTQADFQNYKK 138
                                       334566999999999******99998876652112567999************87 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.1    0.0038       2.8      27      73 ..      92     135 ..      84     139 .. 0.69
   2 ?    3.7   1.4       0.1        74      24      68 ..     117     170 ..     114     176 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0038
                               GAT  27 keLyetckamqpriqklieetadeedllaelLqlNDeLnnvlerYer 73 
                                       +eL++++ a+++r+qkl +++a + +   e  +l + L ++ + +++
  gi|313126368|ref|YP_004036638.1|  92 DELADEVAALERRVQKLETKLATKAE---EADELTERLKRTQADFQN 135
                                       6999999*********9999955554...444444444444444444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                               GAT  24 ellkeLyetckamqpriqklieet..........adeedllaelLqlNDeLnnvl 68 
                                       e  +eL e++k+ q  +q++  +           a e+  +++   + D+L ++l
  gi|313126368|ref|YP_004036638.1| 117 EEADELTERLKRTQADFQNYKKRAkkrqdqiretATED-FVERVVTVRDNLLRAL 170
                                       67778888888888888888777522222222214444.6666666666666655 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.4     0.076        55      86     186 ..      47     112 ..      32     115 .. 0.55
   2 ?    9.6   9.2   0.00091      0.65      51     102 ..     101     152 ..      97     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.076
                        Lebercilin  86 lekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerkleleeksfrrqlaaek 162
                                         +   ekeae + +++++ + +++ ++ n +   +++ +++e  ++l                             
  gi|313126368|ref|YP_004036638.1|  47 ETETAAEKEAEAETAETETAEAEAVGDAANAETTGDVAARVAEYDDELA---------------------------- 95 
                                       4455556666666666666666666666666666666666655444444............................ PP

                        Lebercilin 163 kktkeaqeevkalqeeierlkqkl 186
                                              +ev+al++++++l++kl
  gi|313126368|ref|YP_004036638.1|  96 -------DEVAALERRVQKLETKL 112
                                       .......34444444444444443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00091
                        Lebercilin  51 yedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkd 102
                                       +e++ ++L   la   eE   l erl+++q+  ++ +k+ k+++++++++ +
  gi|313126368|ref|YP_004036638.1| 101 LERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIRETAT 152
                                       4566667777778888888888888888888888888888888888877654 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  13.5    0.0033       2.4      91     149 ..      91     150 ..      35     179 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0033
                           UPF0242  91 leelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLae.kqe 149
                                         el +e   L++++++ e++l+   ee  +L e+l+ +++df+++k+ ++++ ++ +++
  gi|313126368|ref|YP_004036638.1|  91 DDELADEVAALERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQiRET 150
                                       34667778888888**********************************999876652333 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.8    0.0044       3.2      62     127 ..      84     149 ..      34     165 .. 0.41

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0044
                             Atg14  62 iknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqnelee 127
                                       + + +++ +el  ++a l++r+q+l++kl +  +e +e  ++l++ +++    ++++++ q++++e
  gi|313126368|ref|YP_004036638.1|  84 AARVAEYDDELADEVAALERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIRE 149
                                       222223333333334444444444444444444444444444444433333222222233333333 PP

>> IFP_35_N  Interferon-induced 35 kDa protein (IFP 35) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.5    0.0046       3.3       4      29 ..      93     118 ..      92     120 .. 0.87
   2 ?    4.1   3.1     0.068        49       7      36 ..     117     151 ..     113     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0046
                          IFP_35_N   4 eitkeniqLkeeiqkLeaELQettre 29 
                                       e+++e   L++++qkLe+ L  ++ e
  gi|313126368|ref|YP_004036638.1|  93 ELADEVAALERRVQKLETKLATKAEE 118
                                       899999*************9887765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.068
                          IFP_35_N   7 keniqLkeeiqkLeaELQettref.....qikedi 36 
                                       +e  +L e++++  a+ Q+ ++       qi+e +
  gi|313126368|ref|YP_004036638.1| 117 EEADELTERLKRTQADFQNYKKRAkkrqdQIRETA 151
                                       78899*************97655411111666655 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.4       8.5   6.1e+03      37      46 ..      47      54 ..      32      71 .. 0.46
   2 ?   12.0   5.2   0.00033      0.24       1      53 [.     101     153 ..     101     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.5
                                      HHHHHHHHHT CS
                              SlyX 37 qrqlrllaer 46
                                      +++ ++  e+
  gi|313126368|ref|YP_004036638.1| 47 ETETAA--EK 54
                                      333222..22 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00033
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX   1 leerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                       le r+++LE+kla   +  +eL + + + q + +  +++ ++ +++++e +++
  gi|313126368|ref|YP_004036638.1| 101 LERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKKRQDQIRETATE 153
                                       689*******************************************9988765 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  10.3    0.0075       5.4     480     563 ..      47     140 ..       5     177 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0075
                          Macoilin 480 earaslekqLaeekkrkkeeeetaaravala.....aasr.secteslkskkreleaeikkLekelklkeeqirele 550
                                       e+ +++ek  + e     ++e++a   +a a     +a+r  e  + l  +   le  ++kLe++l  k e+++el 
  gi|313126368|ref|YP_004036638.1|  47 ETETAAEKEAEAETAETETAEAEAVGDAANAettgdVAARvAEYDDELADEVAALERRVQKLETKLATKAEEADELT 123
                                       33344445444454444444444433333331111234566777788888888888888888888877777777766 PP

                          Macoilin 551 lkvq....elrkykese 563
                                        + +    ++++yk+ +
  gi|313126368|ref|YP_004036638.1| 124 ERLKrtqaDFQNYKKRA 140
                                       44431111445554443 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.8    0.0099       7.1     149     223 ..      76     148 ..      49     175 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0099
                              CorA 149 ilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtys 223
                                        ++++ ++  r++++ + la+  ++l+r+++k ++kl ++++    ++l ++l+r + + +++++r+ + qd++ 
  gi|313126368|ref|YP_004036638.1|  76 NAETTGDVAARVAEYDDELADEVAALERRVQKLETKLATKAE--EADELTERLKRTQADFQNYKKRAKKRQDQIR 148
                                       444445555555555555555555555555533333333333..4555555555555555555555555555443 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.9     0.014        10      22     115 ..      85     161 ..      26     173 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                              Tho2  22 vpkeqYekeieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekkswfknd 98 
                                         +++Y++e++    e+++l+++ ++ + + + k +e+++l+e+ ++ ++++++ +++ +k              ++
  gi|313126368|ref|YP_004036638.1|  85 ARVAEYDDELAD---EVAALERRVQKLETKLATKAEEADELTERLKRTQADFQNYKKRAKK--------------RQ 144
                                       444444443322...2222211122223333444444444444444444444444444444..............44 PP

                              Tho2  99 ekkkkeitdallqrcil 115
                                       ++ ++++t+ +++r++ 
  gi|313126368|ref|YP_004036638.1| 145 DQIRETATEDFVERVVT 161
                                       45555555555555554 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  14.7     0.019        13      36     142 ..      43     152 ..      34     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.019
                         Golgin_A5  36 eeglesstalsaeldelkqerdllreel...qklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkak 109
                                       +e++e++ta+++e ++ ++e +++++e    +++ ++  ++ + +++ +++   e+  l+ ++q+le++l+++ ++ 
  gi|313126368|ref|YP_004036638.1|  43 AEAAETETAAEKEAEAETAETETAEAEAvgdAANAETTGDVAARVAEYDDELADEVAALERRVQKLETKLATKAEEA 119
                                       566777888888888888888888777622223445566899999******************************** PP

                         Golgin_A5 110 eeveaelerlkeelryleeelvrskatlqsrik 142
                                        e+ + l+r++ +++  ++  ++ + ++++  +
  gi|313126368|ref|YP_004036638.1| 120 DELTERLKRTQADFQNYKKRAKKRQDQIRETAT 152
                                       ***************999988877776665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3039  (0.169502); expected 358.6 (0.02)
Passed bias filter:                     1019  (0.0568353); expected 358.6 (0.02)
Passed Vit filter:                       200  (0.0111551); expected 17.9 (0.001)
Passed Fwd filter:                        56  (0.00312343); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 1.01u 0.41s 00:00:01.42 Elapsed: 00:00:00.58
# Mc/sec: 1337.71
//
Query:       gi|313126369|ref|YP_004036639.1|  [L=251]
Description: hypothetical protein Hbor_16240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-07   31.5   2.4    3.3e-07   31.1   2.4    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   2.4   1.9e-11   3.3e-07       1     218 [.      13     220 ..       5     222 .. 0.57

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.9e-11
                                       EEEE--GC.....G.......CHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH.CHHHHHHHCCTT..TTSEEE CS
                     Abhydrolase_6   1 vlllHGagssassW.......lvapLaallaagvhvlapDlpGhGrsdpppldled.ladlaalldelaagggpvvl 69 
                                       +l++ G       W       +v+ L+ +l++ ++v+a+ lp +G  ++ ++ +   ++++ +  d         v+
  gi|313126369|ref|YP_004036639.1|  13 LLFVLG-------WgnepddkHVSWLLDRLTEEYCVHAVTLPMNG--WDFDDQYLSpVRTYYEDHDFD-------VV 73 
                                       455555.......77766543477889999************889..777777722255555555555.......9* PP

                                       EEETCHHHHHHHHHHCC..EE.....EEES-...----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHC CS
                     Abhydrolase_6  70 vGHSlGGalalaaaplalvvg.....vlldppp.talpagllaaalelllallallrllawlsreplprlfladeda 140
                                       + HS GG++a++   la+vv      v+l+p + ta+ +g+ + +l+++l+ ++ +   +++s e +++ + +    
  gi|313126369|ref|YP_004036639.1|  74 LSHSTGGLIAAH---LADVVDnaprnVFLSPWWgTAPNDGFESVVLPYYLQIPTTR---RLFSPERDTPVIGD---- 140
                                       ************...77433344667*****3344445555555555555555533...33333334434444.... PP

                                       CCCHCHCCCGHHHHCCHHC....HTTCCHHTT-TTGCEEEC.TT-CHHHHCHHCCCH.STTEEETCE...SSS-HHH CS
                     Abhydrolase_6 141 daawrarlarlaallaglg....llpaaawadlpvpllvlg.geDplvprllerlla.qagarlpvvlpgaGHlphl 211
                                            + ++++++  ++ +      + a+++  +++ +v++  +D++v   +++++   + +       ++GH ++ 
  gi|313126369|ref|YP_004036639.1| 141 -LKSEDEYDEAPQGISPAFlrtiMDAQARLPYFREQDVVFCsLSDRMVS--VRAIGDrTPTEN--LRPYDGGHEFFS 212
                                       .444444444444444333000022233333333333555658888888..777776323333..345578886666 PP

                                       HSH.HHHH CS
                     Abhydrolase_6 212 eep.deva 218
                                       ++  ++v+
  gi|313126369|ref|YP_004036639.1| 213 SSGrEAVV 220
                                       56666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1421.86
//
Query:       gi|313126370|ref|YP_004036640.1|  [L=635]
Description: molecular chaperone DnaK [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   6.6e-242  804.0  17.7   6.7e-240  797.4  17.7    2.0  1  HSP70      Hsp70 protein
    2.9e-20   72.4   0.2    2.9e-20   72.4   0.2    2.1  2  MreB_Mbl   MreB/Mbl protein
  ------ inclusion threshold ------
       0.01   15.1   0.1      0.053   12.8   0.0    2.1  3  StbA       StbA protein
      0.046   13.4   0.0       0.14   11.9   0.0    1.9  1  FGGY_C     FGGY family of carbohydrate kinases, C-terminal do
       0.18   12.0   4.4       0.32   11.2   1.7    2.2  2  PhyH       Phytanoyl-CoA dioxygenase (PhyH)


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  797.4  17.7  1.9e-243  6.7e-240       1     599 []       6     580 ..       6     580 .. 0.99

  Alignments for each domain:
  == domain 1  score: 797.4 bits;  conditional E-value: 1.9e-243
                                       EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTSH CS
                             HSP70   1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkfsdp 76 
                                       ++GiDLGttns++avmegg++e+i+n+eg+rttPsvvaFt++ erlvG++Ak+qa++np+ t+ s+Kr++G+  +d 
  gi|313126370|ref|YP_004036640.1|   6 ILGIDLGTTNSAFAVMEGGDPEIIVNAEGDRTTPSVVAFTDDdERLVGKPAKNQAIQNPDHTIRSIKRHMGE--ED- 79 
                                       68***************************************99****************************9..66. PP

                                       HHHHHHTTXSSEEEEETTSBEEEEEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHH CS
                             HSP70  77 evqkeikelpykvvkkengkavveveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatk 153
                                                 y+v+ +            +e++tpeqisam L+k+k++ae+ylg++v++avitvPaYfnd qRqatk
  gi|313126370|ref|YP_004036640.1|  80 ----------YTVEID------------DEEYTPEQISAMTLQKIKRDAEDYLGDEVEKAVITVPAYFNDRQRQATK 134
                                       ..........666555............89*********************************************** PP

                                       HHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHH CS
                             HSP70 154 dAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDeal 230
                                       dAg+iAG++v Ri+NepTAa++aYGld+++ +++vlvyDlGggtfdvS+l+l+ Gv+ev+aT+gD++lGG+d+D+a+
  gi|313126370|ref|YP_004036640.1| 135 DAGEIAGFEVERIINEPTAASMAYGLDDDS-DQTVLVYDLGGGTFDVSVLDLGGGVYEVVATNGDNDLGGDDWDQAI 210
                                       ***************************998.********************************************** PP

                                       HHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHHHHHH CS
                             HSP70 231 vehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg.kdlseklsRakfeelvedll 306
                                       +++l+eef++++gidl++d++alqrlk+aae+aK+eLSs+k+t+inl+++t++++g ++l+ekl+Rakfe+l++dl+
  gi|313126370|ref|YP_004036640.1| 211 IDWLAEEFENNHGIDLREDRQALQRLKDAAEEAKIELSSRKETTINLPFITATDSGpVHLEEKLTRAKFESLTSDLI 287
                                       ***************************************************************************** PP

                                       HHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHC CS
                             HSP70 307 ertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkd 383
                                       +rt+ p+e+al+da+++ke+id+v+lvGGstR+P+v+e+v+e++g ep+k+vnpDeava+GAA+q+gvl g  ev+d
  gi|313126370|ref|YP_004036640.1| 288 DRTVGPTEQALEDAGYTKEDIDDVILVGGSTRMPQVHEKVEEMLGIEPKKNVNPDEAVALGAAIQGGVLGG--EVDD 362
                                       ***********************************************************************..**** PP

                                       CEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSC CS
                             HSP70 384 llllDvtpLslgietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippa 460
                                       ++llDvtpLslgie++gg++++lie+nttipt++s++f+taadnqt+v+++v+qgere++++n+llg+f+l+gippa
  gi|313126370|ref|YP_004036640.1| 363 IVLLDVTPLSLGIEVKGGLFERLIEKNTTIPTEESKIFTTAADNQTSVQVRVFQGEREIAEENELLGEFQLTGIPPA 439
                                       ***************************************************************************** PP

                                       STTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 461 prGvpqieVtfdidanGiltvsakdketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeel 537
                                       p+G+pqieVtf+id+nGi++v+a+dk++g+ e+itie   gls+eeie+m+++ae++aeed++++e+iea+neae+ 
  gi|313126370|ref|YP_004036640.1| 440 PAGTPQIEVTFNIDENGIVNVEAEDKGSGNAESITIEGGAGLSDEEIEQMQEEAEQHAEEDEQRRERIEARNEAESA 516
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSC..HHHHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 538 vyslekkleeeaekvseaekekvesaieeLkeeleeee..keeieakteelkkvvekiaeklye 599
                                       v+++e+ lee++e+v+++ ++++e+a+++++++le+e+  kee+e++te+l+k++++i++++y+
  gi|313126370|ref|YP_004036640.1| 517 VQRAETLLEENEEQVDDDLRADIEAAMDDVEATLEDEDatKEELEDATEALSKELQEIGKQMYQ 580
                                       **********************************9998889*********************96 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.2     8e-24   2.9e-20       3     316 ..       6     350 ..       4     354 .. 0.76
   2 ?   -0.8   0.9      0.14   5.1e+02     199     263 ..     484     552 ..     478     563 .. 0.73

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 8e-24
                                       EEEEEE-SSEEEEEETTTE...EEEEE......ES-EEEETTT--EEEESHHHHTTTTS-GT.TEEEE.-SEET..T CS
                          MreB_Mbl   3 dlgiDLGtantlvyvkgkg...ivlne......psvvAikkktkkvlavGeeAkkmlgktpg.nikav.rPlkd..G 66 
                                        lgiDLGt+n    v + g   i++n       psvvA++ +++++  vG+ Ak+   + p+ +i+ + r + +   
  gi|313126370|ref|YP_004036640.1|   6 ILGIDLGTTNSAFAVMEGGdpeIIVNAegdrttPSVVAFTDDDERL--VGKPAKNQAIQNPDhTIRSIkRHMGEedY 80 
                                       68********98877665545577763344444*******999987..8****987766665157655256643223 PP

                                       E..ESSHHHHHHHHHHH.HHHHHT..SS-S..S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHH CS
                          MreB_Mbl  67 v..iadlevaeellkyf.ikkvkk..kksl..skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiG 136
                                       +  i d e++ e +  + ++k+k+  ++ l  + ++ vi+vP   ++ +r+A k+a + aG +   +i+ep aA + 
  gi|313126370|ref|YP_004036640.1|  81 TveIDDEEYTPEQISAMtLQKIKRdaEDYLgdEVEKAVITVPAYFNDRQRQATKDAGEIAGFEVERIINEPTAASMA 157
                                       3247899999888876525666665333344467899**************************************** PP

                                       TT--TTSSS-EEEEEE-SS-EEEEEEETTEEEEEE.....EES-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH CS
                          MreB_Mbl 137 aglpveepsgnmvvdiGggttevavislggivtsk.....svrvaGdeldeaiikyirkkynlliGertaekikiei 208
                                        gl+ +  +  +v d+Gggt +v+v+ lgg v+          ++Gd++d+aii+++ ++++   G    e+ ++++
  gi|313126370|ref|YP_004036640.1| 158 YGLDDDSDQTVLVYDLGGGTFDVSVLDLGGGVYEVvatngDNDLGGDDWDQAIIDWLAEEFENNHGIDLRED-RQAL 233
                                       *****************************9776541111145799*******************99998887.6678 PP

                                       -BSS--HHHHEEEEEEEETTT.TCEEEEEEEHHHH..HHHH.HHHHHHHH.HHHHHHHHTS-HHHHHHHHHH....- CS
                          MreB_Mbl 209 gsavkeeeeekmeikGrdlvt.glpkevevsseev..real.kepvsaiv.eavkevLektppeLaadivdr....g 276
                                         ++  +ee k+e++ r+ +t +lp  +  +s  v  +e l + ++++++ + + ++   t   L    + +     
  gi|313126370|ref|YP_004036640.1| 234 QRLKDAAEEAKIELSSRKETTiNLPFITATDSGPVhlEEKLtRAKFESLTsDLIDRTVGPTEQALEDAGYTKedidD 310
                                       89999999999999988654438888777777655223444144566655245677777776666533322211224 PP

                                       EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHH CS
                          MreB_Mbl 277 ivltGGgallkgldkllseetglpvkvaedpltcvakGtg 316
                                       ++l+GG++ + ++++ ++e++g++ k   +p ++va G++
  gi|313126370|ref|YP_004036640.1| 311 VILVGGSTRMPQVHEKVEEMLGIEPKKNVNPDEAVALGAA 350
                                       8999**********************************87 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.14
                                       HHHHHHHHHH-BSS--HHHHEEEEEEEETTTTCE.EEEEE...EHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          MreB_Mbl 199 rtaekikieigsavkeeeeekmeikGrdlvtglp.kevev...sseevrealkepvsaiveavkevLek 263
                                       ++ e+++ e  + ++e+e+++ +i+ r+ ++    +  ++   ++e+v + l+  ++a ++ v+++Le+
  gi|313126370|ref|YP_004036640.1| 484 EEIEQMQEEAEQHAEEDEQRRERIEARNEAESAVqRAETLleeNEEQVDDDLRADIEAAMDDVEATLED 552
                                       566788888888888888888888888876554404433333367889999999999999999999997 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       1.9   6.7e+03      43      65 ..      78     100 ..      72     103 .. 0.76
   2 ?   12.8   0.0   1.5e-05     0.053     159     247 ..     162     245 ..     134     256 .. 0.80
   3 ?   -1.8   0.0      0.39   1.4e+03     248     299 ..     284     337 ..     267     349 .. 0.71

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.9
                              StbA  43 kpanYlidgekysfdslssdave 65 
                                       + +  +id+e y+ +++s+ +++
  gi|313126370|ref|YP_004036640.1|  78 EDYTVEIDDEEYTPEQISAMTLQ 100
                                       56677899999999999987765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.5e-05
                              StbA 159 ldeleslLiiDlGGttLDvakv..rgklegiskvkgdskiGvslitdavkealetaktrtssfladeliknrkdeey 233
                                        d+ + +L+ DlGG t Dv+ +   g + ++  + gd+++G     +a+ + l++      +f  ++ i+ r+d+++
  gi|313126370|ref|YP_004036640.1| 162 DDSDQTVLVYDLGGGTFDVSVLdlGGGVYEVVATNGDNDLGGDDWDQAIIDWLAE------EFENNHGIDLREDRQA 232
                                       4567889************975226999***********************9986......4666788999999999 PP

                              StbA 234 Lkrrindedkresv 247
                                       L+ r++d+++ +++
  gi|313126370|ref|YP_004036640.1| 233 LQ-RLKDAAEEAKI 245
                                       99.67777776665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.39
                              StbA 248 levinekvkkLkerviravsefsgythvmvvGGGael..iaeaikkatevsdek 299
                                       ++ i++ v   ++ + +a  + +++  v++vGG + +  ++e++ ++ +++ +k
  gi|313126370|ref|YP_004036640.1| 284 SDLIDRTVGPTEQALEDAGYTKEDIDDVILVGGSTRMpqVHEKVEEMLGIEPKK 337
                                       566777777777777777788889999999999998755777888877776555 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.8e-05      0.14     124     196 ..     275     355 ..     208     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                            FGGY_C 124 arAaleavalqlrailealekd.......sgkpldrlavdGGgskndllmqllAdilg.vpVerpktaeatalGaAi 192
                                       +rA +e++   l +++   +++       ++ ++d ++++GG ++ + + +   ++lg  p + + ++ea+alGaAi
  gi|313126370|ref|YP_004036640.1| 275 TRAKFESLTSDLIDRTVGPTEQaledagyTKEDIDDVILVGGSTRMPQVHEKVEEMLGiEPKKNVNPDEAVALGAAI 351
                                       555555555555555555544466666767888*************************777777888********** PP

                            FGGY_C 193 lAav 196
                                        ++v
  gi|313126370|ref|YP_004036640.1| 352 QGGV 355
                                       9986 PP

>> PhyH  Phytanoyl-CoA dioxygenase (PhyH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.16   5.9e+02      28      84 ..      78     138 ..      39     164 .. 0.75
   2 ?   11.2   1.7   8.9e-05      0.32      12      93 ..     480     571 ..     453     595 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.16
                                       H.....HHHCHTTCCSEEEEECEEESTTCCCEECCCHHCHHHHTTHHHHHHHHHHHHTSCEE CS
                              PhyH  28 l.....ldralesgdkidfffeekaaadedglleksinkvghflhprkvadlvrailgqdvy 84 
                                             +d++ +++++i+++  +k ++d+++ l  ++++ +++  p +++d+ r++ +++  
  gi|313126370|ref|YP_004036640.1|  78 EdytveIDDEEYTPEQISAMTLQKIKRDAEDYL-GDEVEKAVITVPAYFNDRQRQATKDAGE 138
                                       244445588899999999999999999999999.8888888888888999998888877664 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.9e-05
                                       SS-HHHHHHHHHHHHHHHHHCHTTCCSEEEEECEEESTTCCCEE.CCCHHCHHHHTTH..HHHHHHHHHHHTSCEEE CS
                              PhyH  12 flsaeevealraeiealldralesgdkidfffeekaaadedgll.eksinkvghflhp..rkvadlvrailgqdvyv 85 
                                        ls+ee+e++++e+e+++++  +++++i++  e++ a ++++ l e++++ v++ l    +  +d+v+a l ++++ 
  gi|313126370|ref|YP_004036640.1| 480 GLSDEEIEQMQEEAEQHAEEDEQRRERIEARNEAESAVQRAETLlEENEEQVDDDLRAdiEAAMDDVEATLEDEDAT 556
                                       799**************999999999999999888888888888777777777777777977888888888777766 PP

                                       E.......EEEEEEE CS
                              PhyH  86 a.......avlqsmy 93 
                                       +       + l++++
  gi|313126370|ref|YP_004036640.1| 557 KeeledatEALSKEL 571
                                       666666563333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2450  (0.13665); expected 358.6 (0.02)
Passed bias filter:                     1056  (0.058899); expected 358.6 (0.02)
Passed Vit filter:                       169  (0.00942607); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.11u 0.43s 00:00:01.54 Elapsed: 00:00:00.57
# Mc/sec: 3341.20
//
Query:       gi|313126371|ref|YP_004036641.1|  [L=388]
Description: molecular chaperone DnaJ [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-43  148.5   0.0    1.9e-43  148.1   0.0    1.2  1  DnaJ_C         DnaJ C terminal domain
    6.7e-26   90.2   4.8    1.2e-25   89.3   4.8    1.5  1  DnaJ           DnaJ domain
    7.5e-13   48.6  18.5    1.9e-12   47.4  18.5    1.7  1  DnaJ_CXXCXGXG  DnaJ central domain
    3.2e-05   23.8  11.4       0.03   14.3   2.6    2.7  2  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
  ------ inclusion threshold ------
      0.014   15.1   6.6      0.074   12.7   0.5    2.5  2  TackOD1        Thaumarchaeal output domain 1
      0.017   15.8   0.7        5.2    7.8   0.0    2.5  2  LTXXQ          LTXXQ motif family protein
      0.088   12.7   0.1       0.19   11.7   0.1    1.6  1  RPT            A repeated domain in UCH-protein
       0.15   12.3  21.0        3.9    7.8   1.0    4.5  4  DUF5351        Family of unknown function (DUF5351)
       0.18   12.3   5.2       0.39   11.2   5.2    1.6  1  zf-CHY         CHY zinc finger
       0.29   11.3   3.9       0.54   10.4   3.3    1.8  1  zf-RING_10     zinc RING finger of MSL2
        2.7    8.1  15.9        4.9    7.2   3.9    2.1  2  DZR            Double zinc ribbon


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.0   1.2e-46   1.9e-43       2     148 .]     136     352 ..     135     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 1.2e-46
                                       EEEEEE-HHHHHH-.EEE.EEEE...................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                            DnaJ_C   2 eveleisleelykGktkkikikrnvi................................................... 27 
                                       +++++++lee+y+G++k+++++r ++                                                   
  gi|313126371|ref|YP_004036641.1| 136 RTRVSLDLEEAYEGVEKQFSVERPERcpecdgdghpadaevhtcpqcngqgqtttvrdtplgrvqqtqtcrqcngeg 212
                                       67899******************999*************************************************** PP

                                       ...................TEEEEEE-TT--TT-EEEETT-SS..SS..S---EEEEEEE---SS-EEETTEEEEEE CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  28 ...............kkekktlevkipaGikdgqkirlegeGd..eeggepGDlivtikvkphpvFkrkgndlyvev 87 
                                                      ++e+ tlev+ipaGi+dgq++r+e eG   e+gg++GDl+++++ ++h+ F+r+g+dl++++
  gi|313126371|ref|YP_004036641.1| 213 qtysercsqcngdgvVREEATLEVTIPAGIRDGQTLRMEREGApgENGGPNGDLLIEVSIREHEDFERDGDDLHHRL 289
                                       **************665666***********************98888***************************** PP

                                       EEEHHHHHHTEEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  88 eislaeallGgklevptldgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                        is+ +a++G+++evpt++g+++l+i   tq+ge +ri+++Gmp+l+ ++++Gdl+v+v+v++P
  gi|313126371|ref|YP_004036641.1| 290 AISFPQAVFGATVEVPTVNGTTELEIpkgTQSGESFRIRNEGMPHLR-GRGNGDLHVQVQVVTP 352
                                       **********************************************8.**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   4.8   7.6e-29   1.2e-25       1      63 []       4      65 ..       4      65 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 7.6e-29
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      d+Y++Lgvs+dasedeIk+aYrk+a +yHPD + ++p+aeekFk++++A evL+d++kR+qYD
  gi|313126371|ref|YP_004036641.1|  4 DFYDVLGVSRDASEDEIKQAYRKKAAQYHPDVS-DEPDAEEKFKKVKKAKEVLTDEQKRRQYD 65
                                      79*******************************.9***************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4  18.5   1.1e-15   1.9e-12       1      67 []     162     226 ..     162     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.1e-15
                     DnaJ_CXXCXGXG   1 CkkCkGsgakk.gkkktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                       C++C+G+g  + ++++tC++C+G+G++++ ++t lg ++  +++tC++C+G+G+++  +++C++C+G+g
  gi|313126371|ref|YP_004036641.1| 162 CPECDGDGHPAdAEVHTCPQCNGQGQTTTVRDTpLGRVQ--QTQTCRQCNGEGQTY--SERCSQCNGDG 226
                                       ********86535699*********87777765576644..578***********9..778******86 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.6   1.9e-05      0.03      11      44 ..     160     190 ..     156     196 .. 0.84
   2 !   13.8   1.7   2.6e-05     0.043      11      43 ..     203     229 ..     200     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                       EE-TTTTTTSEETTE......E-TTTTTSSEEE- CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkglipT 44 
                                       + C++C+g G+ + +       CP+C+G+g   T
  gi|313126371|ref|YP_004036641.1| 160 ERCPECDGDGHPADA---EVHTCPQCNGQGQTTT 190
                                       68********98888...4568*******98777 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.6e-05
                                       EE-TTTTTTSEETTE......E-TTTTTSSEEE CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkglip 43 
                                       ++C +Cng G+  +e       C +C+G g++ 
  gi|313126371|ref|YP_004036641.1| 203 QTCRQCNGEGQTYSE------RCSQCNGDGVVR 229
                                       58*************......*********986 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.9     0.013        22      66      94 ..     152     183 ..     132     191 .. 0.67
   2 ?   12.7   0.5   4.5e-05     0.074      70      97 ..     199     226 ..     196     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.013
                           TackOD1  66 eeelvdrirlCpsCksghlnv...revCpkCk 94 
                                       ++  v+r   Cp+C++         ++Cp+C+
  gi|313126371|ref|YP_004036641.1| 152 KQFSVERPERCPECDGDGHPAdaeVHTCPQCN 183
                                       36677888889999876554311146788886 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.5e-05
                           TackOD1  70 vdrirlCpsCksghlnvrevCpkCkSid 97 
                                       v+++++C++C++   ++ e C++C+   
  gi|313126371|ref|YP_004036641.1| 199 VQQTQTCRQCNGEGQTYSERCSQCNGDG 226
                                       67899*******************9765 PP

>> LTXXQ  LTXXQ motif family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.015        24      82      99 ..      45      62 ..      17      68 .. 0.86
   2 ?    7.8   0.0    0.0032       5.2      14      30 ..     354     370 ..     354     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                                      HHHHHHHHHTS-HHHHHH CS
                             LTXXQ 82 aealkqfyavLtpEQkak 99
                                       +++k+  +vLt+EQk++
  gi|313126371|ref|YP_004036641.1| 45 FKKVKKAKEVLTDEQKRR 62
                                      67899999*******964 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0032
                                       ---HHHHHHHHHHHHHH CS
                             LTXXQ  14 kLtdaQkaalkalaeaa 30 
                                       +L+d+Q++al+a+aea 
  gi|313126371|ref|YP_004036641.1| 354 NLNDEQREALEAFAEAG 370
                                       79************996 PP

>> RPT  A repeated domain in UCH-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012      0.19       6      35 ..       6      38 ..       3      53 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                               RPT  6 yklLgidentdDdviitayqvkled...dpsqk 35
                                      y++Lg+++++++d+i  ay+ k +    d s++
  gi|313126371|ref|YP_004036641.1|  6 YDVLGVSRDASEDEIKQAYRKKAAQyhpDVSDE 38
                                      99********************95543322333 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.032        53      18      27 ..     160     169 ..     159     171 .. 0.86
   2 ?    7.8   1.0    0.0024       3.9      19      28 ..     178     187 ..     176     188 .. 0.90
   3 ?    5.5   2.6     0.012        20      18      28 ..     203     213 ..     202     214 .. 0.88
   4 ?    6.2   0.2    0.0073        12      17      28 ..     216     227 ..     216     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.032
                           DUF5351  18 ETCesCeGtg 27 
                                       E C++C G g
  gi|313126371|ref|YP_004036641.1| 160 ERCPECDGDG 169
                                       77******98 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0024
                           DUF5351  19 TCesCeGtgk 28 
                                       TC++C+G+g+
  gi|313126371|ref|YP_004036641.1| 178 TCPQCNGQGQ 187
                                       9*******97 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.012
                           DUF5351  18 ETCesCeGtgk 28 
                                        TC +C+G+g+
  gi|313126371|ref|YP_004036641.1| 203 QTCRQCNGEGQ 213
                                       5********97 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0073
                           DUF5351  17 SETCesCeGtgk 28 
                                       SE C +C+G g+
  gi|313126371|ref|YP_004036641.1| 216 SERCSQCNGDGV 227
                                       899******995 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   5.2   0.00024      0.39      18      62 ..     175     224 ..     155     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                            zf-CHY  18 klyaCreCH.....eeledhelerlevkevlcllCete.qekavlCkkCkk 62 
                                       ++++C +C      ++++d +l r++++++ c +C+ e q+ ++ C++C+ 
  gi|313126371|ref|YP_004036641.1| 175 EVHTCPQCNgqgqtTTVRDTPLGRVQQTQT-CRQCNGEgQTYSERCSQCNG 224
                                       6899*****888665577889999999976.99998762577888999974 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.3   0.00033      0.54      19      57 ..     198     236 ..     179     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                        zf-RING_10  19 keCqHyvCrlCvgkkkklkpsCsqCkdyekyeenkqlrl 57 
                                       +  q + Cr+C g+ +    +CsqC+     +e+ +l++
  gi|313126371|ref|YP_004036641.1| 198 RVQQTQTCRQCNGEGQTYSERCSQCNGDGVVREEATLEV 236
                                       5557789*******************8888888877776 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.9     0.003       4.9      28      48 ..     159     182 ..     132     190 .. 0.71
   2 ?    5.2  16.3     0.014        22       1      48 [.     162     222 ..     162     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.003
                               DZR  28 edrCpsC...gekvdpearfCpeC 48 
                                       ++rCp+C   g+++d+e  +Cp+C
  gi|313126371|ref|YP_004036641.1| 159 PERCPECdgdGHPADAEVHTCPQC 182
                                       778888844445566666678888 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
                               DZR   1 CpqC...geelppdarfCseCgtklkavaa..........edrCpsCgekvdpearfCpeC 48 
                                       Cp+C   g++ +++ ++C++C+ + + ++            ++C +C+ + +  ++ C +C
  gi|313126371|ref|YP_004036641.1| 162 CPECdgdGHPADAEVHTCPQCNGQGQTTTVrdtplgrvqqTQTCRQCNGEGQTYSERCSQC 222
                                       9999433455777788******996533336778888888********************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.72u 0.38s 00:00:01.10 Elapsed: 00:00:00.57
# Mc/sec: 2037.19
//
Query:       gi|313126372|ref|YP_004036642.1|  [L=316]
Description: zn-dependent protease with chaperone function [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-27   96.7   0.6    1.8e-27   96.4   0.0    1.4  2  Peptidase_M48  Peptidase family M48
    2.1e-05   24.3   0.0    3.1e-05   23.8   0.0    1.2  1  SprT-like      SprT-like family
    3.4e-05   23.2   0.1      8e-05   22.0   0.0    1.7  2  Peptidase_M56  BlaR1 peptidase M56
    0.00061   19.6   0.0    0.00082   19.2   0.0    1.2  1  BSP            Peptidase of plants and bacteria


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       1.8   8.2e+03      86     110 ..      11      35 ..       3      55 .. 0.53
   2 !   96.4   0.0     4e-31   1.8e-27       2     194 ..      81     305 ..      80     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHTT-SHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  86 vsllasillllglallisraeedaa 110
                                       ++l   +ll+l+++++++ ++ +aa
  gi|313126372|ref|YP_004036642.1|  11 MGLTVFVLLGLLVVAVLAITGFFAA 35 
                                       4455555555555555555554444 PP

  == domain 2  score: 96.4 bits;  conditional E-value: 4e-31
                                       --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikh 77 
                                        + +el ++v+ la+++g+  p+++++ v+ ++  A ++g ++++ +ivl++g+l + l+ +el+aVl+HE++Hi++
  gi|313126372|ref|YP_004036642.1|  81 EQRPELSRTVSALASQVGI--PMPTIALVDTDEPIALTTGLSQSNaTIVLSQGIL-DRLDGDELRAVLAHEVAHIAN 154
                                       67899**************..99999999999999********************.********************* PP

                                       THHHHH.HHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT.HHH CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  78 rhsvvs.livsllasillllglallisraeedaagafldalavliglliillflalSRkrEyqADeagvellkrakd 153
                                        +++v+ +  + +    +   l+   ++ ++  ag ++  la+ + l   + + +lSR+rE+ AD+ +v ++ +a++
  gi|313126372|ref|YP_004036642.1| 155 SDAAVMtVALAPVVLADHIQSLSTPQQSSDQHPAGSVIYGLATTFELGARIAVGNLSRAREFAADRGAVTITGDAAA 231
                                       ***887422222222222223333344444444555555666666666666666*********************** PP

                                       HHHHHHHHHHHTT--S---HHHH.................................HHS-SS--HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 154 lvraliklakdlerqdvsaslrs.................................ellstHPplleRiqalke 194
                                       l++al +l  +   +++  +  +                                 +l++tHPp +eR+++l++
  gi|313126372|ref|YP_004036642.1| 232 LASALRTLEGTEIPETDLRERTDvaalsvvagqrgvtadlsglrrgyfgsvfryleDLTRTHPPVKERLERLTA 305
                                       *******98765554444444446899999*****************************************986 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   6.9e-09   3.1e-05      43      77 ..     120     154 ..      61     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.9e-09
                         SprT-like  43 vrhhasIeLseklldsrsedrllntLaHElcHlal 77 
                                       ++ +a+I Ls+ +ld  + d+l+ +LaHE++H+a+
  gi|313126372|ref|YP_004036642.1| 120 SQSNATIVLSQGILDRLDGDELRAVLAHEVAHIAN 154
                                       56789****************************98 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.44     2e+03     105     125 ..      13      33 ..       2      43 .. 0.53
   2 !   22.0   0.0   1.8e-08     8e-05     177     218 ..     122     163 ..      42     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.44
                     Peptidase_M56 105 llliWivgalilllyliaall 125
                                       l++ +++g l++++  i++++
  gi|313126372|ref|YP_004036642.1|  13 LTVFVLLGLLVVAVLAITGFF 33 
                                       444444444444444444433 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.8e-08
                     Peptidase_M56 177 lkprIvlPadflkklsdeeleyillHElaHlkrkDllvnllv 218
                                           Ivl++ +l +l+++el  +l+HE aH+++ D+ v  ++
  gi|313126372|ref|YP_004036642.1| 122 SNATIVLSQGILDRLDGDELRAVLAHEVAHIANSDAAVMTVA 163
                                       3468*******************************9987665 PP

>> BSP  Peptidase of plants and bacteria
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.8e-07   0.00082      58     127 ..     106     196 ..      74     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-07
                               BSP  58 llrdidgvaytsGldddhkeIhlslsyiekasaekdakaevtgvLthelvhvyqwea.................... 114
                                       l++  + +a t+Gl++ + +I+ls   + +        +e++ vL he++h+ + +a                    
  gi|313126372|ref|YP_004036642.1| 106 LVDTDEPIALTTGLSQSNATIVLSQGILDRLDG-----DELRAVLAHEVAHIANSDAavmtvalapvvladhiqsls 177
                                       6788999*******************9999664.....7************98888866666666666666666666 PP

                               BSP 115 ......egrapggliEGiA 127
                                              +++ g++i G+A
  gi|313126372|ref|YP_004036642.1| 178 tpqqssDQHPAGSVIYGLA 196
                                       5555544455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 1709.65
//
Query:       gi|313126373|ref|YP_004036643.1|  [L=96]
Description: cupin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-10   38.6   0.7    7.7e-10   38.4   0.7    1.2  1  Cupin_2         Cupin domain
    9.7e-06   25.4   0.1    1.2e-05   25.1   0.1    1.0  1  AraC_binding_2  AraC-binding-like domain
    1.9e-05   24.2   0.1    2.5e-05   23.9   0.1    1.2  1  Cupin_3         Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.026   14.4   0.0       0.03   14.2   0.0    1.1  1  AraC_binding    AraC-like ligand binding domain
      0.055   13.7   0.2      0.083   13.1   0.2    1.4  1  Multi_ubiq      Multiubiquitin
       0.06   13.1   0.3        1.3    8.8   0.3    2.3  1  CDC48_2         Cell division protein 48 (CDC48), domain 2
      0.084   13.1   0.0      0.086   13.0   0.0    1.1  1  Ectoine_synth   Ectoine synthase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.7     3e-13   7.7e-10       3      59 ..      25      83 ..      23      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3e-13
                                      EEEETTEEEEEECSSSEE..EEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE CS
                           Cupin_2  3 velppGesapshrHpged..effyVleGegeltvdgeeveleaGdsvyfpagtpHrfrN 59
                                      ve +p  ++ +h H +ed  e+++ +eGe+ l v+g evel++Gd+v + +  + ++rN
  gi|313126373|ref|YP_004036643.1| 25 VEADPDWTGMEHDHADEDheEVYFLVEGEASLVVEGDEVELNPGDAVRVSPDAERQIRN 83
                                      56667777777888777777***********************************9999 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   4.6e-09   1.2e-05      19      98 ..       5      85 ..       2      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.6e-09
                    AraC_binding_2 19 adrfdarlrsarlgdlslgrlrygaav...sirpselddfylvqlplsGraeveqggrevvlgpgdavvldpgrpyrlr 94
                                      ad++++  + ++  +l+++ +++++++   ++++ + +d+  v + ++G+a++ + g ev+l+pgdav ++p+   ++r
  gi|313126373|ref|YP_004036643.1|  5 ADALHFMREELDTENLGFTVVEADPDWtgmEHDHAD-EDHEEVYFLVEGEASLVVEGDEVELNPGDAVRVSPDAERQIR 82
                                      567777777888899999999999666322555555.88**********************************999998 PP

                    AraC_binding_2 95 wsad 98
                                       + +
  gi|313126373|ref|YP_004036643.1| 83 NG-P 85
                                      77.4 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   9.9e-09   2.5e-05      23      61 ..      41      78 ..      33      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9.9e-09
                                      ESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                           Cupin_3 23 yeedEfcyileGevkvtpeggetvelraGDlvvlpkgls 61
                                       + +E  +++eGe ++++ +g +vel +GD+v++ ++ +
  gi|313126373|ref|YP_004036643.1| 41 EDHEEVYFLVEGEASLVV-EGDEVELNPGDAVRVSPDAE 78
                                      4568999***********.***************99875 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.2e-05      0.03       2      56 ..      20      76 ..      19      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                      EEEEEEETTSTT-SEEE..ETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TT CS
                      AraC_binding  2 pdiegieagypdhsfpp..hvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppg 56
                                      +++++ ea+ ++ +++   +  d+ ++   +eG+++l ++g +++l+pGd + + p+
  gi|313126373|ref|YP_004036643.1| 20 LGFTVVEADPDWTGMEHdhADEDHEEVYFLVEGEASLVVEGDEVELNPGDAVRVSPD 76
                                      56677777777777632113344999************************9888776 PP

>> Multi_ubiq  Multiubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   3.3e-05     0.083      29      64 ..      40      80 ..      33      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                        Multi_ubiq 29 dpaddpvvleivty......gedgeirdgesVdLkakGverf 64
                                      d+++++v++ + ++      g++ e+ +g+ V++  + +er 
  gi|313126373|ref|YP_004036643.1| 40 DEDHEEVYFLVEGEaslvveGDEVELNPGDAVRVS-PDAERQ 80
                                      66555555555555999999999999999999999.888885 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00051       1.3      39      63 ..      63      87 ..       6      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00051
                                      EEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2 39 vstePkgpvgitetTeielgtkpve 63
                                      v+  P ++v+++++ e +++ +pve
  gi|313126373|ref|YP_004036643.1| 63 VELNPGDAVRVSPDAERQIRNGPVE 87
                                      6788999999999999999999997 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.3e-05     0.086      25      88 ..      12      74 ..       2      96 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.3e-05
                                      EEE-GGGSSSSEEEEEEE-.TT--EEEE-TT-EEEEEEEE--EEEEETTT--EEEE-TTEEEEET CS
                     Ectoine_synth 25 RlllkddgmGfslhettik.agtetelkYknHleavycieGegeveeledgevyeikpgtlYlld 88
                                      R  l  +++Gf++ e     +g e++   ++H e  +++eGe+++    +g++ e++pg+   + 
  gi|313126373|ref|YP_004036643.1| 12 REELDTENLGFTVVEADPDwTGMEHDHADEDHEEVYFLVEGEASLVV--EGDEVELNPGDAVRVS 74
                                      6668899*****99987653799999999**************9987..5888999998765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 566.50
//
Query:       gi|313126374|ref|YP_004036644.1|  [L=363]
Description: GTPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-51  174.4   0.0      2e-51  174.1   0.0    1.1  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
    9.7e-26   89.5   0.0    1.6e-25   88.8   0.0    1.4  1  CobW_C       Cobalamin synthesis protein cobW C-terminal doma
    0.00086   18.4   0.1        1.8    7.4   0.0    3.1  3  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0014   17.8   0.1     0.0021   17.2   0.1    1.2  1  T2SSE        Type II/IV secretion system protein
     0.0022   17.9   0.0       0.21   11.5   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
     0.0065   16.5   0.1      0.018   15.1   0.0    1.7  2  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
     0.0066   16.0   0.0        2.7    7.5   0.0    2.2  2  GTP_EFTU     Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.026   14.9   0.0    1.7  1  AAA_16       AAA ATPase domain
      0.016   15.0   0.0      0.026   14.4   0.0    1.2  1  dNK          Deoxynucleoside kinase
      0.045   13.9   0.0      0.088   13.0   0.0    1.6  1  AAA_33       AAA domain
      0.051   13.5   0.0      0.077   12.9   0.0    1.2  1  ATPase_2     ATPase domain predominantly from Archaea
      0.081   12.2   0.0       0.15   11.3   0.0    1.4  1  Zeta_toxin   Zeta toxin
      0.097   12.6   0.0       0.18   11.7   0.0    1.4  1  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.099   12.9   0.0        0.2   11.9   0.0    1.5  1  AAA_22       AAA domain
       0.13   12.6   0.1       0.33   11.2   0.0    2.0  2  AAA_28       AAA domain
       0.17   11.6   0.1       0.39   10.5   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
       0.17   11.9   0.0       0.37   10.8   0.0    1.6  1  AAA_14       AAA domain


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.1   0.0   1.9e-54     2e-51       1     175 [.      10     200 ..      10     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 1.9e-54
                                       EEEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCC.CT.EEEETTTTECCHCTT-HHHHHHHH CS
                              cobW   1 pvtvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellret.gveivelenGciCctlredllkeleal 76 
                                       pvt+++G lG+GKTtL+n++l+n+ag+++av+vN++ge+++Dael++ + ++ +++l+nGciCc lr+dl+ e+ +l
  gi|313126374|ref|YP_004036644.1|  10 PVTLVSGTLGAGKTTLVNRILQNQAGYDVAVLVNDMGEINVDAELVAGStDEDVIDLTNGCICCRLRDDLTDEVVRL 86 
                                       79********************************************9984555************************ PP

                                       HHHHTT-SEEEEEECTTTTHHHH..HTT.SHHHHHCCCECEEEEEEETTTH...............CCHCCHHHHHH CS
                              cobW  77 eereerldviliEttGlaePapv..aft.eeelksdltldavvavvDaknl..............eaeeekieekae 136
                                       ++++  +d++l+E++G++eP p+  +f  e+e++++++ld++v v+Da  +              +  +++ ++ + 
  gi|313126374|ref|YP_004036644.1|  87 ADER-AFDCLLVEASGVSEPFPIakTFLeEDEVTDRYRLDTMVSVLDAYGFwkefdpettrpdgrHPGGRELANVLV 162
                                       ****.9*****************77555899*****************888*************9999********* PP

                                       HHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-E CS
                              cobW 137 dqlaaadllvlnKtDlldeeallekleerlrqlnpeakv 175
                                       dq++++d+l+lnK+Dl++++a  +++e+++r+l+p+a++
  gi|313126374|ref|YP_004036644.1| 163 DQVEFCDVLLLNKCDLVPDDAI-DEVEAVARELQPRASL 200
                                       ********************65.************9875 PP

>> CobW_C  Cobalamin synthesis protein cobW C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.0   1.5e-28   1.6e-25       1      94 []     253     344 ..     253     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 1.5e-28
                            CobW_C   1 issfvfrarrpfdperleelleeelpegilRaKGivwlagkpd.alvlqgvggrlrlepagawwaaededrrseLVf 76 
                                       +ssf++++ rpf+per++ +++e +p g++RaKG++ l+++++ ++ l+ +g++++ +p g+w a+  +++ ++LVf
  gi|313126374|ref|YP_004036644.1| 253 VSSFCYESTRPFHPERFNTWIDE-WPSGVYRAKGFFLLPTRSEtVMGLNRAGPSVTAGPIGEWRAD--DEPATRLVF 326
                                       68*********************.*****************999*******************999..********* PP

                            CobW_C  77 IGrdldkealeeaLdacl 94 
                                       IG+d+d++a++e+L++cl
  gi|313126374|ref|YP_004036644.1| 327 IGTDVDEAAIREQLADCL 344
                                       *****************7 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0018       1.8      34      66 ..      14      44 ..       5      52 .. 0.87
   2 ?    4.5   0.0     0.014        15     110     133 ..      80     103 ..      76     106 .. 0.92
   3 ?    2.4   0.0     0.062        66     156     205 ..     155     210 ..     151     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                                      EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                      + G+ GaGk tlv+++ ++  ++G+ vavl  D
  gi|313126374|ref|YP_004036644.1| 14 VSGTLGAGKTTLVNRILQN--QAGYDVAVLVND 44
                                      68999**********9875..89******9766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHTT-SEEEEEEESST CS
                              MeaB 110 trevvllleaaGfDvvlietvGvG 133
                                       t evv+l +   fD +l+e  Gv 
  gi|313126374|ref|YP_004036644.1|  80 TDEVVRLADERAFDCLLVEASGVS 103
                                       789*****************9995 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.062
                                       TTTTT--CCCHHH-SEEEEE---......HHHHHHHHHHHHHHHHHCSTTBTTB-- CS
                              MeaB 156 DelqgikkGileiaDiivvnkaD......kkeaekaarelraaleleeekekeWrp 205
                                        el  +    +e  D++ +nk D        e+e +arel+   +l ++++++ +p
  gi|313126374|ref|YP_004036644.1| 155 RELANVLVDQVEFCDVLLLNKCDlvpddaIDEVEAVARELQPRASLYRTTYADVSP 210
                                       5555555566899**********987776678888999998888877777666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     2e-06    0.0021     131     174 ..      11      53 ..       6      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
                             T2SSE 131 lilvsGgTgsGKttllyallkeinksderivtvEDpvEiqlega 174
                                       + lvsG+ g GKttl++ +l+  + + +  v+v D  Ei+++++
  gi|313126374|ref|YP_004036644.1|  11 VTLVSGTLGAGKTTLVNRILQNQAGY-DVAVLVNDMGEINVDAE 53 
                                       679*******************9999.88999*******99876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0    0.0002      0.21     101     123 ..      11      33 ..       6      60 .. 0.86
   2 ?    4.2   0.0     0.035        37      48      76 ..     168     195 ..     155     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                       EEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpel 123
                                       ++++ G  G+GK+tL+n++l+++
  gi|313126374|ref|YP_004036644.1|  11 VTLVSGTLGAGKTTLVNRILQNQ 33 
                                       68899*************99874 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.035
                                       EEEEEEE-GGG--HHHHHHHHHHHHHHTT CS
                       RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealg 76 
                                         v++lnK+Dl+ ++  ++e+++  ++l+
  gi|313126374|ref|YP_004036644.1| 168 CDVLLLNKCDLVPDDA-IDEVEAVARELQ 195
                                       4589**********99.777777777665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.7e-05     0.018      21      42 ..      11      32 ..       3      41 .. 0.83
   2 ?   -3.1   0.0       7.3   7.7e+03      69      79 ..     119     129 ..     102     143 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                      EEEEEESTTSSHHHHHHHHHHH CS
                              TsaE 21 vilLeGdLGaGKTtlvrglaka 42
                                      v l +G LGaGKTtlv  ++++
  gi|313126374|ref|YP_004036644.1| 11 VTLVSGTLGAGKTTLVNRILQN 32
                                      56789************99986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.3
                                       EE-TT-SSTHH CS
                              TsaE  69 fDlYRledeee 79 
                                        D YRl++  +
  gi|313126374|ref|YP_004036644.1| 119 TDRYRLDTMVS 129
                                       58899875444 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0025       2.7       7      28 ..      13      34 ..       8      53 .. 0.83
   2 !    6.5   0.0     0.005       5.2     119     153 ..     163     197 ..     116     286 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0025
                                      EEEESTTSSHHHHHHHHHHHTT CS
                          GTP_EFTU  7 giighvDhGKtTLtdrLlyktg 28
                                       + g + +GKtTL+ r+l++  
  gi|313126374|ref|YP_004036644.1| 13 LVSGTLGAGKTTLVNRILQNQA 34
                                      5789999***********8765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.005
                                       HHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU 119 lkegvpiivfiNKmDrlkaelkeiveevkqklsrk 153
                                        +++   ++++NK+D + ++    ve+v ++l+ +
  gi|313126374|ref|YP_004036644.1| 163 DQVEFCDVLLLNKCDLVPDDAIDEVEAVARELQPR 197
                                       45555589*********666666666666676444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.5e-05     0.026      23      48 ..       7      34 ..       2      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                            AAA_16 23 rp.elvllsGesGvGKsslvrellr.al 48
                                      ++ +++l+sG  G GK++lv+++l+ ++
  gi|313126374|ref|YP_004036644.1|  7 DTrPVTLVSGTLGAGKTTLVNRILQnQA 34
                                      44589***************99986233 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.4e-05     0.026       3      27 ..      14      39 ..      12      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                                      EEESTTSSHHHHHH.HHHCCSTCEEE CS
                               dNK  3 veGnIgaGKstlvk.lLskklgvkvf 27
                                      v+G++gaGK+tlv+ +L++++g+ v+
  gi|313126374|ref|YP_004036644.1| 14 VSGTLGAGKTTLVNrILQNQAGYDVA 39
                                      89************99****998764 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.3e-05     0.088       1      28 [.      11      42 ..      11      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.3e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg....avll 28
                                      ++l+ G  G+GK+tl+ r+l++++    avl+
  gi|313126374|ref|YP_004036644.1| 11 VTLVSGTLGAGKTTLVNRILQNQAgydvAVLV 42
                                      67899***************998877655555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.3e-05     0.077      18      60 ..       7      48 ..       3      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-05
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialree 60
                                      +++++ ++ G  g GKt+L+++i++n+  +d   + ++++ e+
  gi|313126374|ref|YP_004036644.1|  7 DTRPVTLVSGTLGAGKTTLVNRILQNQAGYDV-AVLVNDMGEI 48
                                      688999*********************88775.5556666665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.15      16      50 ..      10      42 ..       2      47 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                        Zeta_toxin 16 PklillgGqpGAGKselaellkdelerqgnvvrld 50
                                      P + l++G  GAGK++l + + ++ + + +v +l 
  gi|313126374|ref|YP_004036644.1| 10 P-VTLVSGTLGAGKTTLVNRILQNQA-GYDVAVLV 42
                                      4.5799*************9999964.44444444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.18       4      44 ..      14      52 ..      11      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                              MobB  4 ivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdk 44
                                      + g+ g+GKTtL++++++  ++ g+ v+++  +  +++vd 
  gi|313126374|ref|YP_004036644.1| 14 VSGTLGAGKTTLVNRILQ--NQAGYDVAVLVNDMGEINVDA 52
                                      56899***********98..5899****9999999998886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019       0.2       4      29 ..       8      33 ..       5      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      t+ +++v G  G+GKTtl++r+l++ 
  gi|313126374|ref|YP_004036644.1|  8 TRPVTLVSGTLGAGKTTLVNRILQNQ 33
                                      77899****************99875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031      0.33       4      26 ..      14      38 ..      11     149 .. 0.85
   2 ?   -3.2   0.1       8.2   8.6e+03      65      86 ..     332     354 ..     312     358 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                            AAA_28  4 itGgestGKTtlleaLaar..gypv 26
                                      ++G+ ++GKTtl++++ ++  gy v
  gi|313126374|ref|YP_004036644.1| 14 VSGTLGAGKTTLVNRILQNqaGYDV 38
                                      89***********998865577774 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.2
                            AAA_28  65 eeeaaa.aankvlfcDrglldtl 86 
                                        e+a + +  ++l+ D ++ d  
  gi|313126374|ref|YP_004036644.1| 332 DEAAIReQLADCLLTDEEMADAD 354
                                       33333334456666666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00037      0.39      24      39 ..      11      26 ..       3      31 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00037
                            AAA_29 24 atlltGpsGsGKSTll 39
                                      +tl++G+ G+GK+Tl+
  gi|313126374|ref|YP_004036644.1| 11 VTLVSGTLGAGKTTLV 26
                                      79*************8 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00035      0.37       2      49 ..       9      61 ..       8      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikell.....vkkesilyinldderdkkladp 49
                                      r++ +++G   +GKTtl++++++++      v  +++ +in+d e  + ++d+
  gi|313126374|ref|YP_004036644.1|  9 RPVTLVSGTLGAGKTTLVNRILQNQAgydvaVLVNDMGEINVDAELVAGSTDE 61
                                      678999****************9999888887778888888888776665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1965.03
//
Query:       gi|313126375|ref|YP_004036645.1|  [L=50]
Description: hypothetical protein Hbor_16300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 290.07
//
Query:       gi|313126376|ref|YP_004036646.1|  [L=44]
Description: hypothetical protein Hbor_16310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.6   0.4      0.031   14.5   0.4    1.1  1  DUF1059   Protein of unknown function (DUF1059)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   1.7e-06     0.031      12      38 ..      12      38 ..       9      44 .] 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-06
                           DUF1059 12 dCgfeitaeteeEvlrkvaeHakaaHg 38
                                       C++++ a++  E ++   +H + +H 
  gi|313126376|ref|YP_004036646.1| 12 HCEWKAIATSYPEMVEMYHDHLRGDHP 38
                                      6*************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.34s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 264.73
//
Query:       gi|313126377|ref|YP_004036647.1|  [L=388]
Description: theronine dehydrogenase-like zn-dependent dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-28   96.4   0.5    1.7e-27   95.4   0.5    1.4  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    1.1e-10   41.3   0.8    2.5e-10   40.1   0.8    1.7  1  ADH_N_assoc   Alcohol dehydrogenase GroES-associated
    9.2e-09   35.4   0.2    3.3e-08   33.6   0.2    1.9  2  ADH_zinc_N    Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.012   14.3   0.1       0.09   11.5   0.1    1.9  2  HI0933_like   HI0933-like protein
      0.018   14.5   0.2      0.047   13.2   0.0    1.7  2  Glu_dehyd_C   Glucose dehydrogenase C-terminus
       0.02   14.2   0.1      0.033   13.5   0.1    1.3  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain
      0.098   11.9   0.0       0.14   11.3   0.0    1.3  1  Pyr_redox_2   Pyridine nucleotide-disulphide oxidoreductase
       0.14   11.4   0.0       0.22   10.7   0.0    1.2  1  Pyr_redox_3   Pyridine nucleotide-disulphide oxidoreductase
       0.19   11.1   0.4        0.3   10.4   0.4    1.3  1  FAD_oxidored  FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.5   8.6e-31   1.7e-27       1     103 [.      25     135 ..      25     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 8.6e-31
                                       TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT- CS
                             ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkege 77 
                                       p++v+i++++++iCgsDlh+++g  ++ +++++++GHE +G+v evg++v++lk Gdr+v++++++cg C++C+eg+
  gi|313126377|ref|YP_004036647.1|  25 PNDVIIDITTTAICGSDLHMYEG--RTAAEPGIVFGHENMGVVTEVGEGVSTLKEGDRIVAPFNVACGFCKNCEEGY 99 
                                       589*******************9..699************************************************* PP

                                       GGG-.........TTBEETTTS........S-SSSBSEEEECG CS
                             ADH_N  78 enlC.........eeakllgvs........ldGgfaeyvvvpe 103
                                       + +C                          ++Gg+ae++ +p 
  gi|313126377|ref|YP_004036647.1| 100 TGFCtnvnpgfagG-------AygyvamgpYKGGQAEKLRIPY 135
                                       ****7766664442.......1233355689******999884 PP

>> ADH_N_assoc  Alcohol dehydrogenase GroES-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.8   1.3e-13   2.5e-10       1      23 []       1      23 [.       1      23 [. 0.98

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.3e-13
                       ADH_N_assoc  1 MKAVTyqGpkdVrVeeVPDPkIe 23
                                      MKAV+yqGp++V+Ve+V++P++e
  gi|313126377|ref|YP_004036647.1|  1 MKAVVYQGPNEVAVEDVDEPELE 23
                                      ********************997 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.2   1.7e-11   3.3e-08       1      70 [.     185     254 ..     185     260 .. 0.87
   2 ?   -1.4   0.0         1   2.1e+03      70      93 ..     277     302 ..     257     347 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.7e-11
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsga 70 
                                       +vGl+a   Ak+ Ga e+++vd+ +++lela+k     +in  e+ ++ve+i ++ gg  vd  +++vG++a
  gi|313126377|ref|YP_004036647.1| 185 PVGLMAAYSAKIKGAsEIFVVDRVPSRLELAEKHCDATAINF-EDgNPVEQITDAHGG-EVDRGVDAVGYQA 254
                                       7********************************655556666.444**********55.**********665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                                       HHHHHHHHCEEEEEEEEECSC..TSS CS
                        ADH_zinc_N  70 atleaalkllkpgGrlvvvGg..gkg 93 
                                        +l++ ++ ++p G+l + G+  +++
  gi|313126377|ref|YP_004036647.1| 277 VVLNQLIRTVRPTGQLGIPGLyvPSD 302
                                       67899999999999999988766333 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.5e-05      0.09       2      31 ..     177     207 ..     176     213 .. 0.78
   2 ?    0.4   0.0       0.1     2e+02      41      61 ..     328     348 ..     318     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                                       SEEEE--SHHHHHHHHHHHHTT-.-EEEE-S CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgk.rVlllek 31 
                                       ++++ G+G+ GlmaA sa+ +g+ ++ ++++
  gi|313126377|ref|YP_004036647.1| 177 SIAIYGAGPVGLMAAYSAKIKGAsEIFVVDR 207
                                       58999*************7666515777776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.1
                                       HCGGGT-EEEETT-SGGGEEE CS
                       HI0933_like  41 isGgGrcNvTnlseepeells 61 
                                         G G+cNv ++++e+++l+ 
  gi|313126377|ref|YP_004036647.1| 328 RLGTGQCNVKDHNRELRDLII 348
                                       569********9999998875 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       3.8   7.5e+03      90     110 ..      13      35 ..       5      41 .. 0.67
   2 ?   13.2   0.0   2.4e-05     0.047      32     112 ..     176     254 ..     168     263 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.8
                       Glu_dehyd_C  90 pvdei..peaseemdlvvEaTGs 110
                                        v+++  pe +++ d++++ T +
  gi|313126377|ref|YP_004036647.1|  13 AVEDVdePELEHPNDVIIDITTT 35 
                                       45544225778888999988865 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.4e-05
                       Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlv.eelGatYvd.sretpvdeipeas.eemdlvv 105
                                       es  + GaG++GL+a+   +   +g ++++v++r +    +++l  ++ +at ++ ++ +pv++i++a+  e+d  v
  gi|313126377|ref|YP_004036647.1| 176 ESIAIYGAGPVGLMAAYSAKI--KGASEIFVVDRVPS---RLELAeKHCDATAINfEDGNPVEQITDAHgGEVDRGV 247
                                       6889***********766665..89999*****8554...4445514578888873346899999998834788888 PP

                       Glu_dehyd_C 106 EaTGsak 112
                                       +a G+ +
  gi|313126377|ref|YP_004036647.1| 248 DAVGYQA 254
                                       8888865 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.7e-05     0.033      25      77 ..     171     226 ..     161     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                                       CB---.EEEEESTSHHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHH.TTTCECEE CS
                       AlaDh_PNT_C  25 gvepa.kvlviGgGvaGlqAiatakglga.kVtvlDvrparleqles.lgakfvev 77 
                                       g +p+  + + G+G +Gl A+  ak  ga ++ v+D  p+rle  e+ + a+ ++ 
  gi|313126377|ref|YP_004036647.1| 171 GLKPGeSIAIYGAGPVGLMAAYSAKIKGAsEIFVVDRVPSRLELAEKhCDATAINF 226
                                       44466257899*****************9569***********9999777776655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.3e-05      0.14     142     189 ..     174     223 ..     128     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                                       T.SEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSSTTS-HHHHHHH CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 142 p.krivvvGgGyiGvElAaalaklgke.vtlveardrllraldkelsaal 189
                                       p ++i++ G+G++G+  A  ++  g+  + +v++ +  l+  +k + a++
  gi|313126377|ref|YP_004036647.1| 174 PgESIAIYGAGPVGLMAAYSAKIKGASeIFVVDRVPSRLELAEKHCDATA 223
                                       2689***********9999998886644*******999966666655554 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.22       2      29 ..     180     207 ..     179     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEk 29 
                                       I GaGP Gl aa+ +k +g +++ ++++
  gi|313126377|ref|YP_004036647.1| 180 IYGAGPVGLMAAYSAKIKGASEIFVVDR 207
                                       78***********************997 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00015       0.3       2      28 ..     178     204 ..     177     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLv 28 
                                       + ++G+gp G++AA++A+ +Ga+ + v
  gi|313126377|ref|YP_004036647.1| 178 IAIYGAGPVGLMAAYSAKIKGASEIFV 204
                                       78*******************986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2310.96
//
Query:       gi|313126378|ref|YP_004036648.1|  [L=236]
Description: hypothetical protein Hbor_16330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-08   32.5   0.1    3.9e-07   29.0   0.0    2.3  3  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.2e-11   3.9e-07       7      76 ..      15      84 ..      10     105 .. 0.91
   2 ?   -1.2   0.0     0.033   5.9e+02     281     307 ..     106     133 ..      86     145 .. 0.76
   3 ?   -0.6   0.0     0.021   3.7e+02     179     237 ..     158     214 ..     152     220 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.2e-11
                                      HSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEE CS
                       AMP-binding  7 ktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvp 76
                                      ++  ++al  +++g++++Y ++   + +++++Lr lGv+ gd Va++ +  pe ++++++++++Gav+v 
  gi|313126378|ref|YP_004036648.1| 15 RRTSAPALRADASGRSYSYYDFVTTSYKAGNVLRYLGVRGGDEVAVAPDFLPEPLLTFYGAAQLGAVTVF 84
                                      5568899977999*********************99*******************************996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.033
                                       CGTT.-SEEEEESS-EBHHHHHHHHHHH CS
                       AMP-binding 281 dlss.lrlvllggeplspellrffralf 307
                                       dl+  ++l++ gg+p +p+++++ +++ 
  gi|313126378|ref|YP_004036648.1| 106 DLPPgHKLAVYGGAPERPDTTHWEKEVW 133
                                       6666689999999999999999877775 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.021
                                       EEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTC CS
                       AMP-binding 179 lshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkd 237
                                       ++h+ l+ ++ ++ ++++  ++ +d+v++  ++a    ++++ll+++l+G+ +v+++++
  gi|313126378|ref|YP_004036648.1| 158 YTHADLLDAAVAV-VDEYG-IGVGDEVVVRDSFARPSVVVSGLLAPILAGSVLVFPDEE 214
                                       5677777776665.44442.234555655555555555667788888888888887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1380.01
//
Query:       gi|313126379|ref|YP_004036649.1|  [L=351]
Description: spermidine/putrescine ABC transporter ATPase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-35  122.0   0.0    4.3e-35  121.2   0.0    1.4  1  ABC_tran  ABC transporter
    3.8e-11   43.0   0.3    1.1e-10   41.5   0.3    1.9  1  TOBE_2    TOBE domain
    9.3e-05   22.4   0.0        0.5   10.1   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0023   17.4   0.0       0.14   11.6   0.0    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
     0.0048   17.2   0.1      0.048   13.9   0.0    2.1  2  AAA_22    AAA domain
     0.0071   16.3   0.0      0.011   15.7   0.0    1.3  1  Rad17     Rad17 P-loop domain
  ------ inclusion threshold ------
      0.016   15.6   0.9       0.16   12.4   0.9    2.2  1  AAA       ATPase family associated with various cellular acti
       0.02   15.2   0.1      0.073   13.4   0.0    1.8  2  AAA_16    AAA ATPase domain
      0.063   13.8   0.0       0.15   12.6   0.0    1.6  2  AAA_23    AAA domain
       0.18   11.6   0.0       0.37   10.6   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   0.0   2.4e-38   4.3e-35       2     136 ..      23     164 ..      22     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 2.4e-38
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++v++++++ge   +vG++G+GK+t l++++g ++pt+G++++dg+++ +   +   +    ++q+ +lfp++tv+e
  gi|313126379|ref|YP_004036649.1|  23 DRVDFSVRRGEFFSLVGPSGCGKTTTLRMISGFETPTKGDVRIDGRSMVD--VPPEARDTNLVFQHLSLFPHMTVGE 97 
                                       789**********************************************9..888999999**************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e++e++ ++l+ ++l++++d+      +++SgGq+qrva+aral+++pk+lllDEp 
  gi|313126379|ref|YP_004036649.1|  98 NvgyglkkagvdagERSERVRNFLELVDLEGFADRDP----TEISGGQQQRVAIARALVNEPKVLLLDEPL 164
                                       ***********88888888999999999999888887....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.3   6.2e-14   1.1e-10       1      76 []     278     349 ..     278     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 6.2e-14
                            TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelag.gqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       ++iRPE+l +   ++++ +sGtV+++ ++G++t yv+e a+  + + v+++ ++   +++ Gd++++ ++p + vv+
  gi|313126379|ref|YP_004036649.1| 278 VSIRPEDLIV---ADDGDISGTVVERYFQGDQTNYVIESANdLPPLSVVTQGRR--GNIERGDELRVDVRPGAPVVF 349
                                       79********...66679********************9995444444444444..4****************9998 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00028       0.5       2      22 ..      35      55 ..      34      77 .. 0.79
   2 !   10.1   0.0   0.00028       0.5     208     298 ..     109     196 ..      92     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00028
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                        l+Gp g+GK++ L+ ++++
  gi|313126379|ref|YP_004036649.1| 35 FSLVGPSGCGKTTTLRMISGF 55
                                      569***************887 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00028
                            AAA_21 208 liasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.k 283
                                       +  +++er r  ++ +++ ++  +++++e+S G+++  a++ al   +   ++ll+DEp + L+ kl +     l k
  gi|313126379|ref|YP_004036649.1| 109 DAGERSERVRN-FLELVDLEGFADRDPTEISGGQQQRVAIARALVNEP---KVLLLDEPLSALDRKLRKQMQVELrK 181
                                       55555555555.7777888888899999*******9999999999988...9***********98777665533335 PP

                            AAA_21 284 elsrngaQviltTHS 298
                                       ++++  + ++ +TH+
  gi|313126379|ref|YP_004036649.1| 182 IHEKVQGAFFYVTHD 196
                                       555555566777776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.02        35      25      41 ..      33      49 ..      21      55 .. 0.82
   2 !   11.6   0.0   7.9e-05      0.14     135     213 ..     135     211 ..      85     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.02
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      +f ++vGp G+GK+  l
  gi|313126379|ref|YP_004036649.1| 33 EFFSLVGPSGCGKTTTL 49
                                      5889*********9866 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.9e-05
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSE..EEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQ..fivislreemlekadklv 209
                                       +++SgG+++ va+a       v+   + llDe  +aLD k +k++   l++ ++++Q  f+ +++++e+    +  v
  gi|313126379|ref|YP_004036649.1| 135 TEISGGQQQRVAIARA----LVNEPKVLLLDEPLSALDRKLRKQMQVELRKIHEKVQgaFFYVTHDQEVAMTLSDRV 207
                                       47999*9999988755....345555779*********************99999988899*****99988877666 PP

                                       EEEE CS
                                       xxxx RF
                             SMC_N 210 gvtk 213
                                        v+ 
  gi|313126379|ref|YP_004036649.1| 208 AVMN 211
                                       6655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.7e-05     0.048       5      25 ..      32      52 ..      29      82 .. 0.89
   2 ?    0.9   0.0      0.29   5.1e+02      57     116 ..     117     183 ..     104     199 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrl 25
                                        +  ++G+sG+GKTt+lr++
  gi|313126379|ref|YP_004036649.1| 32 GEFFSLVGPSGCGKTTTLRMI 52
                                      567889************986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.29
                            AAA_22  57 lrellralglelkaerlsseellealeqalrarav...ielliiDEaqh.lr...seealeeLrsll 116
                                        r++l+ ++le+ a r+ +e    + ++ + ara    +++l++DE    l+   ++++  eLr+++
  gi|313126379|ref|YP_004036649.1| 117 VRNFLELVDLEGFADRDPTEISGGQQQRVAIARALvnePKVLLLDEPLSaLDrklRKQMQVELRKIH 183
                                       5666777777777755555555544444444444457777999998444344333355555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.1e-06     0.011      47      68 ..      34      55 ..      13      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.1e-06
                             Rad17 47 iLLisGPsGCgkstvvkvLske 68
                                         + GPsGCgk+t+++++s  
  gi|313126379|ref|YP_004036649.1| 34 FFSLVGPSGCGKTTTLRMISGF 55
                                      56689************99864 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9     9e-05      0.16       3      20 ..      37      54 ..      35     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9e-05
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      l+Gp G+GKT++ + +  
  gi|313126379|ref|YP_004036649.1| 37 LVGPSGCGKTTTLRMISG 54
                                      89************9976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.1e-05     0.073      20      44 ..      30      52 ..      20      70 .. 0.84
   2 ?   -1.2   0.0       1.3   2.3e+03      70     106 ..     145     180 ..     122     228 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrel 44
                                      r+g  e   l+G+sG+GK++ +r++
  gi|313126379|ref|YP_004036649.1| 30 RRG--EFFSLVGPSGCGKTTTLRMI 52
                                      444..7899*************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                            AAA_16  70 salaqalareellrqlldeaesaeleawrekleeala 106
                                       +a+a+al + e    llde+ sa+ +  r++ + +l+
  gi|313126379|ref|YP_004036649.1| 145 VAIARALVN-EPKVLLLDEPLSALDRKLRKQMQVELR 180
                                       446666644.555555666555555555555555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.3e-05      0.15      15      39 ..      25      52 ..      14      81 .. 0.83
   2 ?   -3.2   0.0       5.7     1e+04     176     190 ..     170     184 ..     126     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-05
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                      +dF      ++ ++Gp G+GKTT l+ i
  gi|313126379|ref|YP_004036649.1| 25 VDFsvrRGEFFSLVGPSGCGKTTTLRMI 52
                                      566665557999************9988 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.7
                            AAA_23 176 eqekekekeleelee 190
                                       + +k+ + el ++ e
  gi|313126379|ref|YP_004036649.1| 170 KLRKQMQVELRKIHE 184
                                       222333334444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.37      14      39 ..      24      49 ..      19      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                      + ++++++ +++ l+GpsG GK+T l
  gi|313126379|ref|YP_004036649.1| 24 RVDFSVRRGEFFSLVGPSGCGKTTTL 49
                                      466777766699***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2107.33
//
Query:       gi|313126380|ref|YP_004036650.1|  [L=382]
Description: spermidine/putrescine ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-22   80.9   9.9    1.9e-22   80.4   9.9    1.1  1  SBP_bac_8      Bacterial extracellular solute-binding protein
    4.5e-16   59.0   1.2    5.6e-16   58.7   1.2    1.1  1  SBP_bac_6      Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.01   15.1   1.1       0.02   14.2   1.1    1.4  1  UCR_Fe-S_N     Ubiquitinol-cytochrome C reductase Fe-S subuni
      0.016   15.4   0.0      0.036   14.3   0.0    1.5  1  IreB           IreB regulatory phosphoprotein
          3    8.4   6.5        5.9    7.4   6.5    1.4  1  K_channel_TID  Potassium channel Kv1.4 tandem inactivation do


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   9.9   5.2e-26   1.9e-22       5     270 ..      64     339 ..      55     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 5.2e-26
                                       HHHHH-TEEEEEEE-.-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG..GSTTHHH-HHHHHTT CS
                         SBP_bac_8   5 efekktgvkvnvvta.asndleqklkaalaagtapdidvvwanedalatlaeeglladls..dldnlddltdalaav 78 
                                       + e + +v+vn++++ +s ++ +  k+    g+  + d++++n+++++++++++l+a++    + n+d++ d+++++
  gi|313126380|ref|YP_004036650.1|  64 DIESRLDVTVNFTKStSSSKMFSGWKS----GQDAQYDIAVPNNNYVPKMVDADLVAPVPsdAVSNYDSTYDKFQSF 136
                                       455555899999888666666666666....55446799******************99885669999999988888 PP

                                       .....--TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHH.....HHH-SEGG---GGG.GGGTHHE CS
                         SBP_bac_8  79 .....gydgklygvPyasetpyvliynkdllekaedpktwdellaaakkl.....kgkfglpdpasgwl.qaallak 144
                                            + dg+ ygvP+  +  y+  y+  +++     k++d l++  + +      g+++++d+    +  aal+  
  gi|313126380|ref|YP_004036650.1| 137 aesqfTKDGTMYGVPIRFGW-YGYSYDSRKIPTD-HEKSYDVLFS--DSYegtdlSGQIIMYDNHFKAMsAAALYL- 208
                                       8888999************6.9**********86.99*******9..55522222788899988876550444444. PP

                                       TTEE-.--H.....HHH.HHHHHHHHHHHHTT-EE.-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEE.EE-- CS
                         SBP_bac_8 145 dgksl.dddg...gkdglkealellkklkdngkty.dtgadavsefanGevaftingswdiaaaqkagkklg.aivp 215
                                       ++ +  ++ +   ++++++e+ + +k+ k   + y  +++++++ f++G+++++++g+ +i   +++g +++ +++p
  gi|313126380|ref|YP_004036650.1| 209 GYRDAfTGSKitlSEKQIDEVKQTMKEQKSLLQGYiAADPTYIKSFKQGNFVIGQSGRNEIVEMKANGTDWAeMAAP 285
                                       44443255557777888899999999999888866699******************************9987588** PP

                                       S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH--.-BS-S-TTT CS
                         SBP_bac_8 216 kqgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgy.ipvnksaal 270
                                       k+gs+a++++ +v+k+++n+d+ A++ ++ +  p   a+l +  gy ++vn++ ++
  gi|313126380|ref|YP_004036650.1| 286 KEGSLAWFESAVVSKKSDNKDM-AWKVINEFIAPKLGAKLGK-VGYsPSVNPKIQE 339
                                       *********************9.***************9999.7773668888775 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   1.2   1.6e-19   5.6e-16       3     230 ..      95     343 ..      93     359 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.6e-19
                         SBP_bac_6   3 lpdlilsfdkdflekfieeglfqpldpanlpnvnkdfa.....eeglkdpdgkyy..pygvgplvlavnkdrlkgrp 72 
                                        +d+ +  +++++ k+++++l++p++++ + n++  ++     +e    +dg+ y  p++ g+++  +++ +++  +
  gi|313126380|ref|YP_004036650.1|  95 QYDIAV-PNNNYVPKMVDADLVAPVPSDAVSNYDSTYDkfqsfAESQFTKDGTMYgvPIRFGWYGYSYDSRKIPTDH 170
                                       589999.*******************9999999999999889855555556777778****************8776 PP

                         SBP_bac_6  73 vPksWaDLldPeykg.....kvalpgnngsdlfealllalyk............dfgedgvkkllrnlkanlhpaq. 131
                                         ks++ L+++ y+g     ++ + +n    +  a++l+l +            ++ +d+vk+ +++ k +l+ +  
  gi|313126380|ref|YP_004036650.1| 171 E-KSYDVLFSDSYEGtdlsgQIIMYDNHF-KAMSAAALYLGYrdaftgskitlsEKQIDEVKQTMKEQKSLLQGYIa 245
                                       4.************999988999999999.66666666666679*******88555588888888888888877768 PP

                         SBP_bac_6 132 .mvkaagslesgepavsvvpyffadilpekkkgk.nlkvvwPedGalvspifmlvkkg.kkkelakafidfllspev 205
                                          ++++s ++g+  + ++    + i+  k  g    ++  P++G+l++ ++++v k+  +k+ a+++i+ +  p++
  gi|313126380|ref|YP_004036650.1| 246 aDPTYIKSFKQGN--FVIGQSGRNEIVEMKANGTdWAEMAAPKEGSLAWFESAVVSKKsDNKDMAWKVINEFIAPKL 320
                                       8************..777777777777777766667899************************************** PP

                         SBP_bac_6 206 qailakaggvfPvvtnpavlnelpe 230
                                       +a l k g+ +P+ +np+  ++l +
  gi|313126380|ref|YP_004036650.1| 321 GAKLGKVGY-SPS-VNPKIQEHLSD 343
                                       ********9.***.99998887754 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.1   5.7e-06      0.02       5      29 ..      11      34 ..       9      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.7e-06
                        UCR_Fe-S_N  5 esdeptRRDFLyiATgavgaVGaaa 29
                                      +s ++tRR FL +A+ga+g+ G+a 
  gi|313126380|ref|YP_004036650.1| 11 QSSSTTRRAFL-TAAGAAGVTGTAG 34
                                      57899******.999*******997 PP

>> IreB  IreB regulatory phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05     0.036      37      70 ..     239     271 ..     214     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                              IreB  37 QivGYllsgdptYitsyknARslirkleRdelle 70 
                                        + GY+ + dptYi s+k+   +i +  R+e++e
  gi|313126380|ref|YP_004036650.1| 239 LLQGYI-AADPTYIKSFKQGNFVIGQSGRNEIVE 271
                                       456896.67***********************98 PP

>> K_channel_TID  Potassium channel Kv1.4 tandem inactivation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.5    0.0016       5.9      32      62 ..      17      47 ..      10      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0016
                     K_channel_TID 32 rlahsraaaaaavaaaaaaaeGeGGggGGsh 62
                                      r+a   aa aa v+++a++ +G  G+gGGs 
  gi|313126380|ref|YP_004036650.1| 17 RRAFLTAAGAAGVTGTAGCLGGITGSGGGSA 47
                                      77888899999999999************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2477.94
//
Query:       gi|313126381|ref|YP_004036651.1|  [L=308]
Description: spermidine/putrescine ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-14   52.4  21.0    5.2e-14   52.4  21.0    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   8.3      0.82   1.5e+04      30      62 ..      36     105 ..      13     123 .. 0.56
   2 !   52.4  21.0   2.9e-18   5.2e-14       2     175 ..     108     295 ..     104     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 0.82
                      BPD_transp_1  30 lPsfvlaillvlvf...................................vilsilghlilp..viillll 62 
                                       l +++la+l ++v                                    +++s l +++++    +l+l+
  gi|313126381|ref|YP_004036651.1|  36 LFFLLLAPLTFMVTvsfmtvnesyaivweptlanysallsgdgafwqtsFFKSLLLSYFIAavTTVLCLT 105
                                       3334444444444466666777777777777777777775555544444333333333333122333333 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 2.9e-18
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................vilsilghlilpviilll 61 
                                       ++l++l+a +r++++ k++ +l+ +++ + ++v a  ++l+f                   l+ + +++ ++i+ l+
  gi|313126381|ref|YP_004036651.1| 108 LPLAYLLA-RRGGRTFKVVIFLVLLPFFTMYLVRAYSWFLMFgpsgvindtlltigvvsEPLGLFNFGVPAIIVGLT 183
                                       67777777.77777666666666655555555555558888899999999999999998777788999999****** PP

                      BPD_transp_1  62 lsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlg 138
                                         ++py++l  +a l+ ++ +lvea+r lGa+r++ f+ vvlP++lp +i+g +++f+ +lg+++ + flg+++   
  gi|313126381|ref|YP_004036651.1| 184 HAYFPYMLLSLYASLDGVDFSLVEASRDLGAGRFEAFKDVVLPLILPGMISGSLFVFVPSLGAFITPRFLGQGK--V 258
                                       ***********************************************************************665..5 PP

                      BPD_transp_1 139 tllleailgydyseisnggvlalviavlllnlvadil 175
                                       +++ + i+++  s+ ++g+  a+  ++++ ++va++l
  gi|313126381|ref|YP_004036651.1| 259 LMIGQLIESRINSLYAIGYGSAASMFIIVSIVVAFAL 295
                                       5555555555555555333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2003.90
//
Query:       gi|313126382|ref|YP_004036652.1|  [L=298]
Description: spermidine/putrescine ABC transporter permease ii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-16   60.2  13.7    2.1e-16   60.2  13.7    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   8.8      0.22     4e+03      26      69 ..      47     109 ..      37     116 .. 0.58
   2 !   60.2  13.7   1.2e-20   2.1e-16       2     174 ..     111     282 ..     106     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.22
                      BPD_transp_1  26 vllslPsfvlaillvlvf.........................vilsilghlilpviillllsaapyvr 69 
                                       v+l++P +v++      f                         +     g+l+++v i+++  ++++v+
  gi|313126382|ref|YP_004036652.1|  47 VFLWVPLLVMM------FlsvaqnastlfpfegftlshyaatfADTALMGSLWTSVQIATVSAIIATVL 109
                                       45555555555......4444455889999999888888888733333444444444444444444443 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 1.2e-20
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp..viillllsaapyvrlirraal 76 
                                       + +++ +  ++ ++l+++ r+  i+++ +P ++l+i l+   + +++lg+++    ++++  ++ +p+v+li+ a l
  gi|313126382|ref|YP_004036652.1| 111 VAASFAL-ARHDFPLKEVYRTSAILPMVVPGIILGIALLI--FYQTVLGFTMGFgtIVLTHSVYGLPFVVLIVTARL 184
                                       3334444.5************************8888774..577899977777446677789************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydyse 152
                                       +s +++l+eaar lGa + ++fr v+lP ++p + +g+++a+++++ +++ + f+ + +  l+t +++ i +   + 
  gi|313126382|ref|YP_004036652.1| 185 YSFDESLEEAARDLGADPVETFRDVTLPIVAPAVGAGFLFAWIRSFEDFIRAFFVRGTTDvLTTSMFSMIKYGTAPK 261
                                       ********************************************************555454444444444444444 PP

                      BPD_transp_1 153 isnggvlalviavlllnlvadi 174
                                       ++ +++ ++v++++++++va+ 
  gi|313126382|ref|YP_004036652.1| 262 MN-AISSFIVFVIAIVLAVAMN 282
                                       44.6777777777666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1850.10
//
Query:       gi|313126383|ref|YP_004036653.1|  [L=668]
Description: acyl-CoA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-73  245.5   0.0      1e-72  245.1   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    3.9e-22   79.0   0.5    7.8e-22   78.0   0.5    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    8.6e-10   38.4   0.1    8.6e-10   38.4   0.1    3.6  4  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.1   0.0   1.7e-76     1e-72       7     422 ..     110     547 ..     103     548 .. 0.88

  Alignments for each domain:
  == domain 1  score: 245.1 bits;  conditional E-value: 1.7e-76
                                       HSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                       AMP-binding   7 ktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                       +t++ val++    g+ +++TY++l++++nr+A++L+s G++ gd+V++++p+ pe v +l+++lk+Ga++vp+ ++
  gi|313126383|ref|YP_004036653.1| 110 ETRNNVALIWegePGDERKITYHDLHRESNRVANVLESYGIETGDTVGLYMPMVPEVVSILYGCLKVGAIAVPIFSG 186
                                       67899*******9899************************************************************* PP

                                       S-HHHHHHHHHHHTESEEE.......E..TCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS CS
                       AMP-binding  81 ltaeelayiledseakvli.......a..tvdselleklleaaakleavklvivldadellkeeelkeeeeseekae 148
                                       ++ ++ a  +edse++vl+       +  +   +l +++++a a+  +v++++v+d+ +++k e+  ++  +++++ 
  gi|313126383|ref|YP_004036653.1| 187 FGVDATATRIEDSECSVLFtadgfyrRggE--VTLKDAADDAIAEAGHVEHTVVYDRLGFEKREDRSIKWRTRDEWW 261
                                       ********************9999862443..344444555555668999*********999987777766666652 PP

                                       ........-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS-TTSCH CS
                       AMP-binding 149 ........kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr..fklkeddvvlsilplahif 215
                                                  e++el++++  +++Y+SGTTG+PKG++++h+ ++ ++a+ +   +  f+ k++d+++++ ++ +++
  gi|313126383|ref|YP_004036653.1| 262 hetvaeadSTYETKELDSSQESMLLYSSGTTGEPKGIVHTHAGVLMQCAK-E--IYfgFDHKPEDRFFWVSDIGWMM 335
                                       4678889955577799*******************************999.4..443366678************** PP

                                       HHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEE CS
                       AMP-binding 216 glilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllg 291
                                       g  + l++  + G+tv ++++ ++ ++p++++++ie+++ t++   P++++al + g+ +  ++++dls lrl+ + 
  gi|313126383|ref|YP_004036653.1| 336 GP-WTLIGNHAFGGTVFMYEGAPDhPEPDRFWDMIERHGLTTFGISPTAIRALRKYGDGY--VEQHDLSTLRLLGST 409
                                       *7.*********************777**************************9988888..6788*********** PP

                                       SS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEE CS
                       AMP-binding 292 geplspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeG 365
                                       gep  pe + +f++ +g+   +++++ G TE +g++  +p + +  k+ s G p  g+ + ivD ++     ++e G
  gi|313126383|ref|YP_004036653.1| 410 GEPWDPESWMWFYENVGGgdtPIINISGGTEICGCFL-MPMPSQPLKPCSLGGPGLGMNIDIVDSAGDSIADTHERG 485
                                       **************99999*****************8.5555555677899***************6666667777* PP

                                       EEEEEET..TS-SEBTT-HHHHHHHEEE..TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 366 ellvrgp..gvmkgYlkkpeataeafds..egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                        l+ r    +++k  +  +e+  + ++s  e+  +   GD +  dedG  ++ gR++d +++
  gi|313126383|ref|YP_004036653.1| 486 FLVARDScpSMTKSLWSGDERYLKEYWSsfEDPpLWDHGDWAQKDEDGFWFLHGRADDALNV 547
                                       *****76458*******99**99999986742349999********************9876 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.5   1.3e-25   7.8e-22       1      76 []     556     634 ..     556     634 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 1.3e-25
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       e+E +l++h+aV++aa+vGv+d+++G a+va+Vvl+d++e+   l+eeL++ v +e g+  +p++++fv+e+pkt+s
  gi|313126383|ref|YP_004036653.1| 556 EIEGVLIEHDAVNQAAAVGVDDDTTGTAVVAYVVLEDDVEPtdeLREELRELVGEEQGKPFRPRELKFVSEFPKTQS 632
                                       8**********************************987433346********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|313126383|ref|YP_004036653.1| 633 GK 634
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.1   1.4e-13   8.6e-10       2      55 .]      36     100 ..      35     100 .. 0.82
   2 ?   -2.8   0.5       1.1   6.5e+03      11      21 ..     256     266 ..     244     274 .. 0.66
   3 ?   -0.1   0.0      0.15   9.1e+02      11      23 ..     361     374 ..     352     388 .. 0.79
   4 ?   -1.5   0.2      0.41   2.4e+03       7      16 ..     526     535 ..     523     540 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.4e-13
                                       HHHHHHHHH-H........HHHHHHHHCC..S--SB--S-SECSTTTC.T-EESTT-EE-HHHHH CS
                            ACAS_N   2 kelykeSiedp........eaFWaeqake..ldWekpfdkvldgskgp.fikWFeGGklNicyNc 55 
                                       +el ++ ++d         e+FW+e  +   +d+++++d v d+++gp f +W++GG +N+++N+
  gi|313126383|ref|YP_004036653.1|  36 DELIRRTCTDVdgvaesgvEWFWDELVEYldIDFYEDYDAVRDDTDGPqFSEWYPGGSINVAHNV 100
                                       55555555555555555559********6569*******************************96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                                       -HHHHHHHHHC CS
                            ACAS_N  11 dpeaFWaeqak 21 
                                         +++W e  +
  gi|313126383|ref|YP_004036653.1| 256 TRDEWWHETVA 266
                                       55788877655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.15
                                       -HHHHHHHHHCC.S CS
                            ACAS_N  11 dpeaFWaeqake.l 23 
                                       +p++FW+ + ++ l
  gi|313126383|ref|YP_004036653.1| 361 EPDRFWDMIERHgL 374
                                       579***98877654 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.41
                                       HHHH-HHHHH CS
                            ACAS_N   7 eSiedpeaFW 16 
                                       ++ +d ++FW
  gi|313126383|ref|YP_004036653.1| 526 WAQKDEDGFW 535
                                       7889999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 4119.51
//
Query:       gi|313126384|ref|YP_004036654.1|  [L=460]
Description: short chain fatty acids transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.1e-127  425.8  23.1   2.5e-127  425.6  23.1    1.1  1  SCFA_trans     Short chain fatty acid transporter
    8.3e-06   24.3   5.2    8.3e-06   24.3   5.2    2.2  3  ABG_transport  AbgT putative transporter family
     0.0018   16.8   7.0     0.0018   16.8   7.0    2.3  3  DcuC           C4-dicarboxylate anaerobic carrier


Domain annotation for each model (and alignments):
>> SCFA_trans  Short chain fatty acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.6  23.1  4.2e-131  2.5e-127       9     453 .]       1     458 [.       1     458 [. 0.93

  Alignments for each domain:
  == domain 1  score: 425.6 bits;  conditional E-value: 4.2e-131
                        SCFA_trans   9 lvalvskylPdplifallltlvtfvlvlvltkqtavslvdvwgnGfwnllsfamqmalilvtGqalassklvkkllk 85 
                                       ++ +v++++P p++fa+ll++v+f   +v+ ++t+ s+v  w+nGfw ll famqm+lilvtG+ala+++ v++ ++
  gi|313126384|ref|YP_004036654.1|   1 MASVVERVMPSPFLFAILLSYVVFAGGIVVEGTTPASMVTYWYNGFWVLLDFAMQMVLILVTGYALAYHPFVQRGIE 77 
                                       56789************************************************************************ PP

                        SCFA_trans  86 kiaslakdtksavvlvtllaliaavinwGlGlvvgailakevarrvk....gldyalliaaayigl.ltwhgGlsgs 157
                                       +++s++++ k+avvlv l++++ a++ wGlGl+vga++a+e+ r+       ++y+ll  a+y+g+ ltwh+G++gs
  gi|313126384|ref|YP_004036654.1|  78 RLTSIPNNGKQAVVLVGLISMVIAWVHWGLGLIVGAVMAREMGRQAAtrdiQVHYPLLCLAGYMGMgLTWHWGIAGS 154
                                       ****************************************99887652222589*********************** PP

                        SCFA_trans 158 iPllvatpneplkkiavelvgreiiPvsetlfssynliilailivvlplitamlaPkkeevksidk........... 223
                                       +Pll++tp++   +     ++ ++iP s+t+f++y+l  +++ i  ++l++++laP++ ++ +i             
  gi|313126384|ref|YP_004036654.1| 155 APLLMNTPGNVFVEQ---GIISDLIPTSQTVFHPYTLTLVVTGILYTALVLYLLAPEPADTEGITAyipesklfdsa 228
                                       *********965432...35689*****************************************9999999666555 PP

                        SCFA_trans 224 ....kllkeekeeekklkskkdatiaekleeskllallisilGiaylgvyfyekGfn.ltlnsvnlifllvGlllhk 295
                                           + + + +  +      + +t++e +++s+l   +i++ G+a+  + f  +G   l+ln vn++fl++Gl l++
  gi|313126384|ref|YP_004036654.1| 229 vdggEDVSSVEMPSDTSGVTEPTTLSEMINQSRLTGGIIALSGVAFALYTFATQGLSaLNLNLVNFLFLFLGLALYT 305
                                       544433333222333333467899*********************9999999***988******************* PP

                        SCFA_trans 296 tPlaymraitraarsvaGilvqfPfyaGimgmmessalGGpslatliaeafinvankktfplltlfsaalinifiPs 372
                                       +P ay      a  s+ Gi++qfP+yaGi gmm+ s+l        +ae++++++++ tfp++++++aa++n+f+Ps
  gi|313126384|ref|YP_004036654.1| 306 QPKAYQEQFYDAITSTGGIVLQFPLYAGIIGMMNRSGLSA-----TMAETLVSLSTEATFPAVAWITAAVVNVFVPS 377
                                       ************************************9887.....899***************************** PP

                        SCFA_trans 373 GGGewaiqgpilipaaqalGvdlGksvlaiayGdawtnliqPfwalPalaiaGlgardilGycitalilaglilvig 449
                                       GGGew++ g  +++aa+ lGv+ G++++a+a+Gda tnl+qPfwalP+l+i+G++ard++Gy +t+++l    l++g
  gi|313126384|ref|YP_004036654.1| 378 GGGEWTVIGTTVLQAANELGVPAGQATVAYAVGDAHTNLLQPFWALPLLGITGIRARDMFGYGVTMMLLLIPFLAVG 454
                                       ***************************************************************************** PP

                        SCFA_trans 450 lvll 453
                                       l++l
  gi|313126384|ref|YP_004036654.1| 455 LIFL 458
                                       *996 PP

>> ABG_transport  AbgT putative transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.7      0.18   1.1e+03     474     495 ..      89     112 ..      52     117 .. 0.63
   2 ?   -2.1   0.1      0.14   8.2e+02      13      44 ..     176     207 ..     167     219 .. 0.57
   3 !   24.3   5.2   1.4e-09   8.3e-06     329     473 ..     312     451 ..     294     458 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.18
                     ABG_transport 474 iaflvvwvllllvwvl..lglplG 495
                                        ++lv+ + ++++wv   lgl +G
  gi|313126384|ref|YP_004036654.1|  89 AVVLVGLISMVIAWVHwgLGLIVG 112
                                       455666677888887733444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.14
                     ABG_transport  13 lPdPvllfiilivvllvasailsalglsvknp 44 
                                       +P   ++f    + l+v+  + +al l +  p
  gi|313126384|ref|YP_004036654.1| 176 IPTSQTVFHPYTLTLVVTGILYTALVLYLLAP 207
                                       55555555555555555555555555544444 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 1.4e-09
                     ABG_transport 329 kalaesmssmgayivlvff.aaqfvalfnwsnlGkilavkgaelLkeigltgillllglil.lsalinlligsasak 403
                                       +++ ++++s g  ivl f   a ++ ++n+s l   +a    e+L ++  +  +++ ++    +a++n+++ s+  +
  gi|313126384|ref|YP_004036654.1| 312 EQFYDAITSTGG-IVLQFPlYAGIIGMMNRSGLSATMA----ETLVSL--STEATFPAVAWiTAAVVNVFVPSGGGE 381
                                       566677777666.78888626999******99988775....566544..44444444443046899********** PP

                     ABG_transport 404 WavlaPifvPmlmllgisPeltqaayRigDsvtniitPlmsyfplvlalaqkykkklgiG.tllslllPYs 473
                                       W+v++  +      lg+    +++ay +gD+ tn++ P+ + +pl+ ++  + +  +g G t++ ll+P+ 
  gi|313126384|ref|YP_004036654.1| 382 WTVIGTTVLQAANELGVPAGQATVAYAVGDAHTNLLQPFWA-LPLLGITGIRARDMFGYGvTMMLLLIPFL 451
                                       **************************************986.89999999999999999955666667764 PP

>> DcuC  C4-dicarboxylate anaerobic carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.6      0.18   1.1e+03     129     143 ..      27      41 ..       7     115 .. 0.59
   2 ?    1.4   0.1     0.014        84      62     109 ..     306     353 ..     299     363 .. 0.80
   3 !   16.8   7.0     3e-07    0.0018     350     461 ..     346     456 ..     330     459 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.18
                              DcuC 129 ggtvlgiseetvafy 143
                                       g++v g++ ++++ y
  gi|313126384|ref|YP_004036654.1|  27 GIVVEGTTPASMVTY 41 
                                       333333333333222 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.014
                              DcuC  62 dleiielvkveltsravdvglfilvvGGfagvvnrtGaidagvkalvk 109
                                       + +++++  ++  + +++++l+  +  G++g++nr+G + ++ + lv 
  gi|313126384|ref|YP_004036654.1| 306 QPKAYQEQFYDAITSTGGIVLQFPLYAGIIGMMNRSGLSATMAETLVS 353
                                       556667777888888999999999999**********99999888875 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 3e-07
                              DcuC 350 lisnalsglsg.ivfilvmlliqallafvvpSgsglavltmplmapLAdlvgvpralvvlafqlasgllniisPtsg 425
                                        +++ l +ls  + f  v+ ++ a+++++vpSg g   +    + + A+ +gvp+  +++a+ +++  +n++ P   
  gi|313126384|ref|YP_004036654.1| 346 TMAETLVSLSTeATFPAVAWITAAVVNVFVPSGGGEWTVIGTTVLQAANELGVPAGQATVAYAVGDAHTNLLQPF-- 420
                                       444445555554999999*********************************************************.. PP

                              DcuC 426 vvvatlglarvsfgtwvkfvakllavllvvsillli 461
                                         +  lg+  ++ ++++ + ++++++l+ + ++ li
  gi|313126384|ref|YP_004036654.1| 421 WALPLLGITGIRARDMFGYGVTMMLLLIPFLAVGLI 456
                                       77889************9999999888766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2897.91
//
Query:       gi|313126385|ref|YP_004036655.1|  [L=195]
Description: acetyltransferase, n-acetylglutamate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-07   30.6   0.0    5.9e-07   29.7   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00034   21.3   0.2    0.00092   19.9   0.0    1.7  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00078   19.4   0.0     0.0013   18.7   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0018   18.7   0.0     0.0026   18.1   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.3e-10   5.9e-07      34     103 ..      32     104 ..       3     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.3e-10
                                       EEEEEEET..TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEE.EEET CS
                    Acetyltransf_1  34 gllvaeed..geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivl.avee 103
                                        +++a+++  ++ +Gf +++   de ++ +++ +++  p++r +G+G + +e l+ +a +e++++++  +ve+
  gi|313126385|ref|YP_004036655.1|  32 DYVIALDEgtNTKAGFGRIRVHKDEGEEWCELAFVFTLPAWRDQGVGAHVVERLLTKASDEEFDRVYTfTVEP 104
                                       455677774455*****************************************************97735544 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.1e-07   0.00092      52     120 ..      31     100 ..       2     106 .. 0.68
   2 ?   -1.1   0.0       0.6   2.7e+03       6      18 ..     114     128 ..     109     184 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.1e-07
                    Acetyltransf_3  52 egygwaivl...kdtgv.iGsvglrdleeedeeaelgymla.psfwgkGyateavralleyafeelglerlvav 120
                                       +   ++i l    +t++  G +++++ e+e e++el +++  p+++ +G++  +v+ ll+ a +e+  +r++  
  gi|313126385|ref|YP_004036655.1|  31 R--DYVIALdegTNTKAgFGRIRVHKDEGE-EWCELAFVFTlPAWRDQGVGAHVVERLLTKASDEE-FDRVYTF 100
                                       3..355654435445577899999876665.67********7777788**************7666.7777655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.6
                    Acetyltransf_3   6 plteeDlealfe..l 18 
                                       p+ ++Dl+++++  l
  gi|313126385|ref|YP_004036655.1| 114 PVDSDDLPEILQerL 128
                                       666667777642122 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.9e-07    0.0013      28     110 ..      30     116 ..       3     120 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.9e-07
                   Acetyltransf_10  28 egealllvaeeg.gkivGvielrdgs.......hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspy 96 
                                       + ++ +++++eg ++ +G++++r ++       +++ +f  p++r qG+g+  +e+++++a++++      v   + 
  gi|313126385|ref|YP_004036655.1|  30 SRDY-VIALDEGtNTKAGFGRIRVHKdegeewcELAFVFTLPAWRDQGVGAHVVERLLTKASDEEFD---RVYTFTV 102
                                       4444.444444415555666655555556*******************************9888766...3444444 PP

                   Acetyltransf_10  97 avpfYeklGFkavg 110
                                         +++ ++GF++v+
  gi|313126385|ref|YP_004036655.1| 103 EPDYFLTFGFQPVD 116
                                       44566666776665 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.8e-07    0.0026       5      75 ..      33     113 ..       9     114 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.8e-07
                                       EEEEEET..TEEEEEEEEEEES......TCTEEEEE-GGGTTSSHHHHHHH.H..TT..SEEEEE.EEEETHHHHHH CS
                    Acetyltransf_7   5 vfVaedd..gkivGfialslld......aeitrlaVdpeyrgkGiGraLle.a..ae..kgiile.qlelnaekaik 67 
                                       + +a d+  +   Gf ++ +++      +e+ +++++p++r +G+G   +e +  ++  +    + ++++ +    +
  gi|313126385|ref|YP_004036655.1|  33 YVIALDEgtNTKAGFGRIRVHKdegeewCELAFVFTLPAWRDQGVGAHVVErLltKAsdEE---FdRVYTFT-VEPD 105
                                       445666666555677777777777776666666***************9994233112211...23334422.2244 PP

                                       HHHHTTEE CS
                    Acetyltransf_7  68 fYeklGFe 75 
                                       ++  +GF+
  gi|313126385|ref|YP_004036655.1| 106 YFLTFGFQ 113
                                       77777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1273.21
//
Query:       gi|313126386|ref|YP_004036656.1|  [L=95]
Description: hypothetical protein Hbor_16410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.35s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 551.31
//
Query:       gi|313126387|ref|YP_004036657.1|  [L=98]
Description: hypothetical protein Hbor_16420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.1    7.9   7.3    4.1e+02    1.8   8.2    2.0  1  DUF4282   Domain of unknown function (DUF4282)


Domain annotation for each model (and alignments):
>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   8.2     0.023   4.1e+02      19      62 ..      23      71 ..      21      93 .. 0.49

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.023
                           DUF4282 19 lgivlialvllslivgafaal.....seslsagggllllllaviafllm 62
                                      l++v + +v+ s+i+g f+        ++ +++ggl+ l ++++ + l+
  gi|313126387|ref|YP_004036657.1| 23 LIAVGASVVATSGIIGFFIGNngsevVSEIPLFGGLIVLPTTPVSMTLY 71
                                      5566666666677777777777766644444444444444444444222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 550.11
//
Query:       gi|313126388|ref|YP_004036658.1|  [L=137]
Description: cytidine deaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-16   59.7   0.3    2.5e-16   59.4   0.3    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    3.1e-11   43.6   0.1    4.8e-11   43.0   0.1    1.2  1  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.3   2.8e-20   2.5e-16       5     100 ..       3     103 ..       1     104 [. 0.89

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 2.8e-20
                                       HHHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE... CS
                   dCMP_cyt_deam_1   5 ekllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv... 77 
                                       e+l++ a ++ ++a+ ++s+ +VGa++ + +  +++g+n e+a++s+ +HAE +A+++a kng+ ++ +  l+v   
  gi|313126388|ref|YP_004036658.1|   3 ESLVTRAREMLEQAHvPYSEYRVGAALRTADGEVFVGCNIENANYSNSLHAEEVAVAEAIKNGHREF-DR-LAVtsg 77 
                                       6788999999999999*************88*******************************76577.44.444479 PP

                                       ...EE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  78 ...tlePCsmCakaiiqsgikkvvvg 100
                                           ++PC+mC++ ++++  +++vv+
  gi|313126388|ref|YP_004036658.1|  78 ardGVTPCGMCRQTLAEFCDEDLVVV 103
                                       9999**************99999876 PP

>> dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.1   5.4e-15   4.8e-11      46     109 ..       4      67 ..       2      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 5.4e-15
                                       HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHHTT-- CS
                   dCMP_cyt_deam_2  46 elkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvlggke 109
                                       +l+ +A ++ +++++pys+   G aL t+dg+v+ G  iE+a +  sL++ ++A+ +++ +g++
  gi|313126388|ref|YP_004036658.1|   4 SLVTRAREMLEQAHVPYSEYRVGAALRTADGEVFVGCNIENANYSNSLHAEEVAVAEAIKNGHR 67 
                                       588999***************************************************9996553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 779.78
//
Query:       gi|313126389|ref|YP_004036659.1|  [L=272]
Description: uridine phosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-45  155.1   1.9    2.1e-45  154.8   1.9    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.8   1.9   1.2e-49   2.1e-45       2     225 ..      25     243 ..      24     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 154.8 bits;  conditional E-value: 1.2e-49
                                       EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEE CS
                         PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGt 78 
                                        +++ g+p++v+ + +   ++ +++  +r+++++tGt++g+p++++stGiG p+aa +a  +l    ++ ++ir+G+
  gi|313126389|ref|YP_004036659.1|  25 AVLLPGNPERVDKVTAL-WDDAEEKAYHREYRTATGTYEGTPISVTSTGIGSPSAA-IAIEELAR-VEAQTLIRVGS 98 
                                       68999************.**************************************.44444444.66********* PP

                                       EEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS CS
                         PNP_UDP_1  79 aGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfy 155
                                       +G+++p++ vGD+vi++ a++++g+s+        +y++  y+a ad+e +++l++aae+lg+++h+G++++ad+fy
  gi|313126389|ref|YP_004036659.1|  99 CGAIQPEMDVGDLVITSGAVRQEGTSK--------EYVREDYPAVADHEVVSALVAAAERLGYDYHVGLTMSADSFY 167
                                       ***************************........9***************************************** PP

                                       -CH.............HHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHH CS
                         PNP_UDP_1 156 aet.............eaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaq 219
                                       a +             +  ++ l++ +++++eME++a++++A+ +g++++a+++v   +a++  +    e+ +e   
  gi|313126389|ref|YP_004036659.1| 168 AGQgrpgfdgfraagsDSLVEELQDANVKNIEMEASALLTIANVYGLRAGAVCSV---YANRVTG----EFRTEGES 237
                                       ***********8776655555999999****************************...3332322....34444444 PP

                                       HHHHHH CS
                         PNP_UDP_1 220 eaakna 225
                                       +aa++a
  gi|313126389|ref|YP_004036659.1| 238 RAAETA 243
                                       444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1600.64
//
Query:       gi|313126390|ref|YP_004036660.1|  [L=396]
Description: NADH dehydrogenase, fad-containing subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-39  134.8   0.2    4.6e-39  134.4   0.2    1.1  1  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
      2e-08   34.6   0.2    7.2e-07   29.7   0.0    2.5  2  Pyr_redox    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.047   12.9   0.0      0.075   12.3   0.0    1.5  1  Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
      0.068   12.4   0.3        9.7    5.4   0.0    2.3  2  AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4   0.2     1e-42   4.6e-39       2     294 .]       4     311 ..       3     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 1e-42
                                       SEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..HHHHCHHHH.CCCCHC CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx.xxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeias..evvkklnqg.ielllg 72 
                                       +vvv+G+G AG+ a ++l +     a+ t v +e+  +++   ++  +++ +++ ++a   +   ++++   e+++g
  gi|313126390|ref|YP_004036660.1|   4 QVVVLGSGYAGTGAVKRLEEelgPDAELTWV-SENDYHLVLHEVHRCIREPSAESNVAIpiD---EIKEPqTEFVKG 76 
                                       8*******************87669******.888888775556666666666666555663...444443778888 PP

                                       CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp....... 142
                                        +v +id + + v+l   ++g   +++yd+l+++ Gs +   gi+G++e  ++l ++ld+a++++++ +        
  gi|313126390|ref|YP_004036660.1|  77 -HVENIDVEDRVVEL---EDG---DVEYDYLLVCLGSATAFYGIEGLQEFSHEL-KSLDDAREIHSDIKAaaedasr 145
                                       .9********89999...334...59**********999999*****9999988.********************** PP

                                       ...SEEEEES-SHHHHHHHHHHHHHT-......EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEE CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ...krivvvGgGyiGvElAaalaklgk......evtlveardrllraldkelsaaleealekeGvevklgtsvkeid 210
                                          ++++v G+G+ G+ +A+++a + +      ++tlve +d++ ++ d+el+ al+++le+++ve+ +g  + ++d
  gi|313126390|ref|YP_004036660.1| 146 ddpAKVIVGGAGLSGIQTAGEIAGYRDehrapiDITLVEGLDEVFPGNDPELQGALRKRLEARDVEILTGDFISKVD 222
                                       *********************9888767788889******************************************* PP

                                       ETTEEEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE.EETTEEE--TTSBESSTTEEE-GGGC.....TE CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.....xx RF
                       Pyr_redox_2 211 gngekle.vvledgeeidadlvvvavGvrpstelleeklglel.derggivvdeflrtnvpgiyaiGDva.....gg 280
                                       +++  l   ++ed ee+d+d +++  G++ + e +  ++ +e  ++ ++i +d   +t+++ ++aiGD a      +
  gi|313126390|ref|YP_004036660.1| 223 EENVYLGgGEDEDPEELDYDVLIWTGGITGQEEVA--DADIEKdERSNRIFTDADFQTSDERVFAIGDSAlieqgTD 297
                                       9999555899*********************9996..77888834679**************************999 PP

                                       CCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Pyr_redox_2 281 kggpelaqaAvqqG 294
                                          p +aqaA+q++
  gi|313126390|ref|YP_004036660.1| 298 SVAPPTAQAAWQAA 311
                                       99*********987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.055   2.4e+02       2      19 ..       5      22 ..       4      51 .. 0.76
   2 !   29.7   0.0   1.6e-10   7.2e-07       1      70 [.     150     225 ..     150     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.055
                                      EEEECSSHHHHHHHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgala 19
                                      vvv+G+Gy g  + + l 
  gi|313126390|ref|YP_004036660.1|  5 VVVLGSGYAGTGAVKRLE 22
                                      8********987776664 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.6e-10
                                       EEEEECSSHHHHHHHHHHHHTT......SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelg......kkVtvversdkllrllDeeaskilqeklekngievllntkveeiegse 70 
                                       kv+v G+G++g+  Ag++a ++       ++t+ve  d++ ++ D+e++ +l+++le++ +e+l++  + ++++++
  gi|313126390|ref|YP_004036660.1| 150 KVIVGGAGLSGIQTAGEIAGYRdehrapIDITLVEGLDEVFPGNDPELQGALRKRLEARDVEILTGDFISKVDEEN 225
                                       689999************88886666667*************************************9999999765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.7e-05     0.075     165     305 .]     149     287 ..      75     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrk......gaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaev 235
                                        kv+V G++ S++ +A e++ +        ++t+v   +e+   + dp  +l+   ++rle+    + +++l+   +
  gi|313126390|ref|YP_004036660.1| 149 AKVIVGGAGLSGIQTAGEIAGYrdehraPIDITLVEGLDEVFPGN-DP--ELQGALRKRLEA----RDVEILTGDFI 218
                                       566777777888888888876622111123344444444444432.33..355555555554....569******** PP

                       Pyr_redox_3 236 keikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                        +++e+ + y    ed++  e + dv++ tG     + ++++ +e+de +   +t+++ +t  + +f +G
  gi|313126390|ref|YP_004036660.1| 219 SKVDEE-NVYLGGGEDEDPEELDYDVLIWTGGITGQEEVADADIEKDERSNRIFTDADFQTSDERVFAIG 287
                                       ****97.5577778888888999999999**************************************998 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0022       9.7      29      46 ..       3      20 ..       1      46 [. 0.88
   2 ?    4.7   0.1    0.0036        16      27      45 ..     147     165 ..     136     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0022
                                      -EEEEESTSHHHHHHHHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiat 46
                                       +v+v+G G aG+ A++ 
  gi|313126390|ref|YP_004036660.1|  3 TQVVVLGSGYAGTGAVKR 20
                                      58*************985 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0036
                                       ---EEEEESTSHHHHHHHH CS
                       AlaDh_PNT_C  27 epakvlviGgGvaGlqAia 45 
                                       +pakv+v G+G  G+q + 
  gi|313126390|ref|YP_004036660.1| 147 DPAKVIVGGAGLSGIQTAG 165
                                       59*************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2335.42
//
Query:       gi|313126391|ref|YP_004036661.1|  [L=51]
Description: hypothetical protein Hbor_16470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-06   27.6   0.0    2.1e-06   27.3   0.0    1.1  1  DUF2080   Putative transposon-encoded protein (DUF2080)


Domain annotation for each model (and alignments):
>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.2e-10   2.1e-06      19      45 ..      14      40 ..       9      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.2e-10
                           DUF2080 19 egkVkpfGnSAkvsiPkeylGkkvylv 45
                                       g+VkpfGnSA v++Pk + G  v +v
  gi|313126391|ref|YP_004036661.1| 14 DGEVKPFGNSAHVTVPKRWRGADVKVV 40
                                      79***************9988887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       140  (0.00780858); expected 358.6 (0.02)
Passed bias filter:                      106  (0.00591221); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.53
# Mc/sec: 291.71
//
Query:       gi|313126392|ref|YP_004036662.1|  [L=177]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-38  130.7   0.1    1.5e-38  130.3   0.1    1.2  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
      2e-09   37.7   0.0    3.3e-09   36.9   0.0    1.3  1  Rrf2          Transcriptional regulator
    7.1e-08   32.3   0.0    1.1e-07   31.7   0.0    1.3  1  HTH_11        HTH domain
     0.0034   17.2   0.0     0.0063   16.4   0.0    1.5  1  TrmB          Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.099   12.5   0.0       0.17   11.8   0.0    1.4  1  MarR_2        MarR family


Domain annotation for each model (and alignments):
>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.1   4.3e-42   1.5e-38       1      78 [.       5      82 ..       5      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 4.3e-42
                      HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiqtl 78
                                      eLts+qk+il+aLi+lyr+ + avKge+iAe ++rn+Gt+RNq+qsLkal+LvegvpGPkGGYkPt++ayeal+++++
  gi|313126392|ref|YP_004036662.1|  5 ELTSSQKTILTALINLYRQTEDAVKGEDIAEEVNRNPGTIRNQMQSLKALQLVEGVPGPKGGYKPTANAYEALDVEQM 82
                                      69************************************************************************9986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   9.3e-13   3.3e-09       3      66 ..       6      68 ..       4      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 9.3e-13
                                      --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE CS
                              Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr 66
                                      l+s+ +  l+al+ L ++ e+  v+ e+iae++n +p  ++  ++ L+   lv+ v G++GGy+
  gi|313126392|ref|YP_004036662.1|  6 LTSSQKTILTALINLYRQTEDA-VKGEDIAEEVNRNPGTIRNQMQSLKALQLVEGVPGPKGGYK 68
                                      677888899***********98.****************************************6 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0     3e-11   1.1e-07       4      55 .]      16      68 ..      11      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3e-11
                            HTH_11  4 qilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GYr 55
                                      +++  L++++++ + ge++Aee n+   t+r+ +++L++l   +e++pg+  GY+
  gi|313126392|ref|YP_004036662.1| 16 ALIN-LYRQTEDaVKGEDIAEEVNRNPGTIRNQMQSLKALQ-LVEGVPGPkgGYK 68
                                      3444.55555555***************************9.*********9996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.8e-06    0.0063       5      59 ..       5      71 ..       1      80 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-06
                                      HHHHHCCCHCHHHH.....HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......T CS
                              TrmB  5 GLseyEakvYlaLl.....klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......p 59
                                       L++    + +aL+     +++  + ++iaee+++   ++ + ++sL+   lVe ++g         
  gi|313126392|ref|YP_004036662.1|  5 ELTSSQKTILTALInlyrqTEDAVKGEDIAEEVNRNPGTIRNQMQSLKALQLVEGVPGPkggykptA 71
                                      666666666677765555566778899*******************************955555333 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.8e-05      0.17       7      58 ..      13      64 ..      10      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                      ++ +L +L+r  +  +   ++a++ +  ++++ +  + L a  Lve +pgp 
  gi|313126392|ref|YP_004036662.1| 13 ILTALINLYRQTEDAVKGEDIAEEVNRNPGTIRNQMQSLKALQLVEGVPGPK 64
                                      567899999999988999******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.36s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1010.16
//
Query:       gi|313126393|ref|YP_004036663.1|  [L=306]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-45  153.7   0.3    6.6e-45  153.4   0.3    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.9e-43  149.2   1.0    1.3e-42  146.4   1.0    2.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.3e-17   63.0   0.1    2.8e-17   62.7   0.1    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.6e-12   47.0   0.1    2.1e-12   46.6   0.1    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.4e-09   37.6   0.4    1.1e-07   31.3   0.4    2.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.2e-07   29.4   0.0    0.00016   20.9   0.0    2.2  2  NAD_binding_4    Male sterility protein
     0.0075   15.7   0.4       0.96    8.9   0.0    2.7  2  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.042   13.7   0.1       0.71    9.8   0.0    2.2  2  KR               KR domain
      0.064   13.3   0.1      0.095   12.7   0.1    1.2  1  DUF3558          Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.4   0.3   3.3e-48   6.6e-45       1     241 []       6     235 ..       6     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 3.3e-48
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       +lVtG++GfiGs+l+++l++ + evi++d l  + ++++   +e+v++ ++d++     + +e++d+ +hlAa++++
  gi|313126393|ref|YP_004036663.1|   6 VLVTGGAGFIGSNLANHLADSN-EVIAVDDLHLGTPENLSSAVEFVDASVLDDD-----LPTEGIDVLFHLAAYSSY 76 
                                       79*****************987.9*******99999999888899999999988.....45569*********6666 PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                           e++ +  + n++g +n +e ar+ g++ ++++s+s++YG  +e p  e++   p++ ++ Y a+Kla e++ e
  gi|313126393|ref|YP_004036663.1|  77 TMAEENKRAATRVNVEGFVNAVEQAREDGCETVVYASTSSIYGSRTE-PSPEDM---PVEARTCYEASKLAREQYGE 149
                                       666666677789***********************************.999***...******************** PP

                                       HHHHHHT-EEEEEEESEEE.STT....S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHH CS
                         Epimerase 155 ayaaqyglnaiilrlfnly.Gpr....ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvl 226
                                       ++++ y++    lr f++y G +    +++ge ++ +++++ ki++g+    l+gdg++ Rdf +v+D++++i l++
  gi|313126393|ref|YP_004036663.1| 150 YFHHHYDMTLAGLRFFSVYqG-YggaeEHKGEYANTVAQFAHKIANGE-RPELFGDGSQTRDFTHVNDIVRGIELAA 224
                                       ******************954.4488899999****************.**************************** PP

                                       HHHTT-STTEEEEES CS
                         Epimerase 227 ehvdagdkgeiyniG 241
                                       +h    + ++iyn+G
  gi|313126393|ref|YP_004036663.1| 225 DH----RLQGIYNLG 235
                                       **....556799998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.4   1.0   6.8e-46   1.3e-42       1     331 [.       7     298 ..       7     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 6.8e-46
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+la++L +   ev+ ++++    ++g+ e+l +         ++++ + + D +     l    +d
  gi|313126393|ref|YP_004036663.1|   7 LVTGGAGFIGSNLANHLADS-NEVIAVDDL----HLGTPENLSS--------AVEFVDASVLDDD-----LPTEGID 65 
                                       9*****************98.778777544....5566777764........3556666666655.....7778899 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                         ++LAA s      e+  + ++vnv G ++ +e +r+ g+e    ++ aSts +YG+ +  p  E+ p+++r +Y 
  gi|313126393|ref|YP_004036663.1|  66 VLFHLAAYSSYTMAEENKRAATRVNVEGFVNAVEQAREDGCE---TVVYASTSSIYGSRT-EPSPEDMPVEARTCYE 138
                                       9*************************************9997...6889*********97.6899************ PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT....SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrget....fvtrkitravarialgkqevlylGnldakRdwghvk 227
                                       a+Kl+ ++  + +++ y++     ++f  +  + g++       +++ +++++ia+g+++ l +G+++++Rd++hv+
  gi|313126393|ref|YP_004036663.1| 139 ASKLAREQYGEYFHHHYDMTLAGLRFFSVYQGYGGAEehkgEYANTVAQFAHKIANGERPEL-FGDGSQTRDFTHVN 214
                                       ****************************99999887533334678999**********9999.8************* PP

                                       HHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--S CS
                     GDP_Man_Dehyd 228 Dyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevd 304
                                       D+v+++ l+  +  +  y+++tge++  +++v+l ++elg ++e +               ++ ++d        v+
  gi|313126393|ref|YP_004036663.1| 215 DIVRGIELAADHRLQGIYNLGTGESYDFNTMVRLINEELGTDVEPK--------------YIENPLD------VYVH 271
                                       ****************************************876543..............2222333......2356 PP

                                       B--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 305 lllgdaskakeeLgWkpkvsfeelvre 331
                                        +++d++k++e  gW+pk+sfee+v++
  gi|313126393|ref|YP_004036663.1| 272 DTMADTTKIREATGWEPKISFEEGVQR 298
                                       789*********************986 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.1   1.4e-20   2.8e-17       2     235 ..       5     257 ..       4     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.4e-20
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..........eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                       ++lvtG+ G +Gs+La+ la ++ ev+a++            ++++ da+ +++ l     dv+ ++AAy     aE
  gi|313126393|ref|YP_004036663.1|   5 RVLVTGGAGFIGSNLANHLADSN-EVIAVDDLhlgtpenlssAVEFVDASVLDDDLPTEGIDVLFHLAAYSSYTMAE 80 
                                       79******************999.9****766799999999999999999999999********************* PP

                                       HSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH....H- CS
                     RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla....ag 140
                                       ++++aa +vn+e+  +  e+a++ g  ++++ St  ++ G++++p  ed +++ ++ Y ++Kla Eq  +     + 
  gi|313126393|ref|YP_004036663.1|  81 ENKRAATRVNVEGFVNAVEQAREDGCeTVVYASTSSIY-GSRTEPSPEDMPVEARTCYEASKLAREQYGEYfhhhYD 156
                                       *************************84699*******9.6669999******************8887655332255 PP

                                       SSEEEEEE-SEESS.........SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG CS
                     RmlD_sub_bind 141 kkalivRtswvyge.........kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekel 206
                                        + + +R+  vy           +  n v+++ ++ ++ e+ +++ D  q++  T+++d+ + +  +++++++    
  gi|313126393|ref|YP_004036663.1| 157 MTLAGLRFFSVYQGyggaeehkgEYANTVAQFAHKIANGERPELFGDgsQTRDFTHVNDIVRGIELAADHRLQ---- 229
                                       566779******6646667743333466666666666555555555444999***********9888888885.... PP

                                       -EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 207 agvyHlanegetswlefArailkeagads 235
                                        g+y l+  ++     + r i +e+g+d 
  gi|313126393|ref|YP_004036663.1| 230 -GIYNLGTGESYDFNTMVRLINEELGTDV 257
                                       .9999999999999999999988888865 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   1.1e-15   2.1e-12       1     128 [.       7     124 ..       7     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.1e-15
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G++l ++L + +e   + v Dl+ +++      ++ v+ ++ + v+d d     +eg+dv++hla+++
  gi|313126393|ref|YP_004036663.1|   7 LVTGGAGFIGSNLANHLADSNE--VIAVDDLHLGTPE---NLSSAVE-FVDASVLDDDL---PTEGIDVLFHLAAYS 74 
                                       69****************9996..4445555555544...4445555.77888888754...689***********9 PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgee 128
                                         +  + ++    +vnv+G  n +e +++ g +++vY S+ ++ g   + e+
  gi|313126393|ref|YP_004036663.1|  75 SYTMaEENKRAATRVNVEGFVNAVEQAREDGCETVVYASTSSIYGS--RTEP 124
                                       9876477778899***************************999888..4443 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.4   5.4e-11   1.1e-07       1     128 [.       6     114 ..       6     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5.4e-11
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG++G iGs+l +++++++  ++i ++   l+l + e+ l    + + +         +  d++ l++ l + +
  gi|313126393|ref|YP_004036663.1|   6 VLVTGGAGFIGSNLANHLADSN--EVIAVDD--LHLGTPEN-L----S-SAV---------EFVDASVLDDDLPTEG 63 
                                       7999999999999999987654..5555443..33322222.2....1.122.........3457777888888899 PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                       +dv+fh AA+    ++een   a + Nv g  n +e a e g ++vv+ St
  gi|313126393|ref|YP_004036663.1|  64 IDVLFHLAAYSSYTMAEENKRAATRVNVEGFVNAVEQAREDGCETVVYAST 114
                                       99************************************************9 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0     0.002         4       1      22 [.       8      29 ..       8      35 .. 0.87
   2 !   20.9   0.0   8.1e-08   0.00016      85     167 ..      61     145 ..      56     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.002
                                      EE-TTSHHHHHHHHHHHHHS-. CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpe 22
                                      +TG+ GF+G+ L + L ++++ 
  gi|313126393|ref|YP_004036663.1|  8 VTGGAGFIGSNLANHLADSNEV 29
                                      7***************999873 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 8.1e-08
                                       HHH--EEEE--SS-S....STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H..... CS
                     NAD_binding_4  85 aeevdviihsaAtvnf...depykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegeke 158
                                       +e +dv +h aA  ++   +e+ + + rvNveG ++ +e a++     ++++ ST+ ++g r++   e++  e ++ 
  gi|313126393|ref|YP_004036663.1|  61 TEGIDVLFHLAAYSSYtmaEENKRAATRVNVEGFVNAVEQAREDGCE-TVVYASTSSIYGSRTEPSPEDMPVEARTC 136
                                       5779********655411145666799***************98888.*******9999999977666554444433 PP

                                       .HHH--EEE CS
                     NAD_binding_4 159 ekldedera 167
                                        ++++++r+
  gi|313126393|ref|YP_004036663.1| 137 YEASKLARE 145
                                       333333333 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00048      0.96       1      31 [.       4      33 ..       4      58 .. 0.79
   2 ?    4.4   0.1     0.012        23      76     159 ..      62     147 ..      37     171 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00048
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEE CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvd 31
                                      k vlvtG+++ IG ++a++la ++  v++vd
  gi|313126393|ref|YP_004036663.1|  4 KRVLVTGGAGFIGSNLANHLADSNE-VIAVD 33
                                      679******************9854.44443 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.012
                                       SSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGT........SB-T CS
                         adh_short  76 gkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagk........vpva 144
                                       +++dvL + A+     +   + ee+ ++   vN+ g +++++++ +     +      +sS+ g         +pv+
  gi|313126393|ref|YP_004036663.1|  62 EGIDVLFHLAAY----SSYTMAEENKRAATRVNVEGFVNAVEQARED--GCETVVYASTSSIYGSrtepspedMPVE 132
                                       567888888877....4566667777777888888888888776554..2233333344444443222222226677 PP

                                       TBHHHHHHHHHHHHH CS
                         adh_short 145 gvaaYsAsKaavagl 159
                                         ++Y AsK a +++
  gi|313126393|ref|YP_004036663.1| 133 ARTCYEASKLAREQY 147
                                       778888888776665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00035      0.71       3      23 ..       6      26 ..       5      32 .. 0.91
   2 ?    1.7   0.0      0.11   2.2e+02      99     145 ..      77     122 ..      45     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00035
                                      EEEETTTSHHHHHHHHHHHHH CS
                                KR  3 ylitGGlGgLGlelarwlaek 23
                                      +l+tGG+G +G  la++la++
  gi|313126393|ref|YP_004036663.1|  6 VLVTGGAGFIGSNLANHLADS 26
                                      69****************986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                                       T--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT CS
                                KR  99 emtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsag 145
                                       +m +e+ +++++  v+G  n  e  +++  +  v+++S ++++gs++
  gi|313126393|ref|YP_004036663.1|  77 TMAEENKRAATRVNVEGFVNAVEQAREDGCET-VVYASTSSIYGSRT 122
                                       46667777788888999999999998877776.56789999999875 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.8e-05     0.095      89     169 ..      66     144 ..      50     147 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                           DUF3558  89 vsvsfswyegspirrerateerlditieGrp.aviardpgdeasCevavgvadgqvvvvsvs.esrgkaagadpCea 163
                                       v + ++ y + ++ +e +++ +  +++eG+  av+  +++    Ce++v ++  +++ + ++ ++++ + +a  C +
  gi|313126393|ref|YP_004036663.1|  66 VLFHLAAYSSYTMAEENKRAAT-RVNVEGFVnAVEQARED---GCETVVYASTSSIYGSRTEpSPEDMPVEARTCYE 138
                                       5555555555555555444433.89999998344444444...5******************999999999999*** PP

                           DUF3558 164 arklae 169
                                       a kla+
  gi|313126393|ref|YP_004036663.1| 139 ASKLAR 144
                                       ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1938.56
//
Query:       gi|313126394|ref|YP_004036664.1|  [L=299]
Description: arginase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-74  249.8   5.5      4e-74  249.6   5.5    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.6   5.5   2.2e-78     4e-74       3     276 ..       5     292 ..       3     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: 249.6 bits;  conditional E-value: 2.2e-78
                                       EEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTESCCSEEEEEEEEE--................SS CS
                          Arginase   3 vallGvPfdaagsgrpGarfGPraireasarleealeynlelgvleelkivdlgdvavt................pv 63 
                                         ++GvP+d  g++r+G+++GP+a+r a   ++e l  + ++g    ++++d+gd+av+                + 
  gi|313126394|ref|YP_004036664.1|   5 TRIIGVPTDY-GANRRGVDMGPSALRYAG-LVDE-L--S-SAG----VSTEDAGDLAVPhhaihdadaggenakhIN 71 
                                       579*******.*****************2.2222.2..2.346....9**********999******9999998755 PP

                                       CHHHHHHHHHHHHHHHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHH CS
                          Arginase  64 dneevleqieeavaeilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrr 140
                                       + eev+ ++++ava++l+++ +p+vlGGDHsia+g++ + a+   +++gv++fDAH D++tpet++sgn hG+p++ 
  gi|313126394|ref|YP_004036664.1|  72 EVEEVTTALADAVADALSDEVTPLVLGGDHSIAIGSMVGSARD--ADIGVVWFDAHGDFNTPETSPSGNVHGMPLAA 146
                                       77779*************************************7..57****************************** PP

                                       ...........HHHHTSECGCEEEEEEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEE CS
                          Arginase 141 ...........aaeegllkpkklvqiGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvyl 206
                                                  +a+   lk+++++++G+r+vd++e   ++++ ++++tm +ide+g+++v + +l++ ++++d v++
  gi|313126394|ref|YP_004036664.1| 147 algigdfegveWANAPRLKEENVAIVGLRDVDENETTAIQDSDVTAYTMSDIDERGITEVTQDALDVATNGTDGVHV 223
                                       ***********9999*****************************************************999****** PP

                                       EEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHH CS
                          Arginase 207 SfDiDvlDpavaPGtGtpepgGltlrellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvre 276
                                       S+D+D+lDp  aPG+Gtp++gG+t+re++a+++ +ae++ ++++++vEvnP ld++ ++ta++a +l+++
  gi|313126394|ref|YP_004036664.1| 224 SLDLDWLDPREAPGVGTPVRGGVTYREAHAAMELVAESGAMRSLELVEVNPILDEH-NETAAVATELAAS 292
                                       *******************************************************5.5********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1878.05
//
Query:       gi|313126395|ref|YP_004036665.1|  [L=861]
Description: DNA gyrase subunit a [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.4e-157  525.0   0.0   2.1e-157  524.4   0.0    1.3  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    1.9e-81  267.3   8.3    7.2e-16   57.4   0.1    6.4  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.4   0.0  2.4e-161  2.1e-157       1     425 [.      43     490 ..      43     491 .. 0.98

  Alignments for each domain:
  == domain 1  score: 524.4 bits;  conditional E-value: 2.4e-161
                     DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGn 76 
                                       Ra+P+vrDGlKPv+RriLyam++   +++++++K++ +vGe++g+YhPHGd+++yda+ r+aqdf++++pl+d+qGn
  gi|313126395|ref|YP_004036665.1|  43 RALPDVRDGLKPVHRRILYAMNEAgVSARSSHRKSSSIVGETMGDYHPHGDSAIYDALARMAQDFSMRYPLVDGQGN 119
                                       9**************************************************************************** PP

                     DNA_topoisoIV  77 fGsildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipp 153
                                       fGs+ dgd++Aa+RY+e+r+++ia+ell++idk+tvd+q+nyD++++EP+vlp+ +PnlLvnG++GIavGm+t+ipp
  gi|313126395|ref|YP_004036665.1| 120 FGSV-DGDPPAAMRYTEARMAPIAEELLEDIDKDTVDFQSNYDDRKQEPVVLPSSFPNLLVNGSSGIAVGMSTNIPP 195
                                       ****.************************************************************************ PP

                     DNA_topoisoIV 154 hnlkeiidaliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie.e.ktivitElP 225
                                       hnl+e+ida+ +l++++++   +l+e+v+gPdfptg+ i+gk+ +++ay+tgrG+i+vra++e++ + ++ivitElP
  gi|313126395|ref|YP_004036665.1| 196 HNLGEVIDATTHLIENPDCtveDLMEYVKGPDFPTGANIVGKNAVHKAYKTGRGRIRVRAEFEVDeDgDNIVITELP 272
                                       ***************************************************************99758********* PP

                     DNA_topoisoIV 226 igvntskliekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdkkp 300
                                       ++ n+++lie+i++ v+++ki+ i+d+rdesdr g+r+v+elkrga++++v+++l+++ +Les++ v nl+l+d++p
  gi|313126395|ref|YP_004036665.1| 273 YQENKARLIERIADDVNDGKIEgIRDLRDESDRdGIRVVVELKRGANPDVVKNQLLEH-HLESTFGVINLALVDGQP 348
                                       ********************************99*******************99986.8***************** PP

                     DNA_topoisoIV 301 kylslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLieelse... 374
                                       ++l+lke lke+l++r+ev++rr+ey+l+++e+r++ileg lkal++id+v+e+ir+s+++++ak++L  e++    
  gi|313126395|ref|YP_004036665.1| 349 RVLTLKETLKEYLDHRREVVRRRSEYELGEAEDRAHILEGRLKALENIDDVVETIRNSESRDDAKAALRGEMTVevd 425
                                       ***********************************************************************877789 PP

                     DNA_topoisoIV 375 ...........eqaeyllemrlrrLtkeeveklekeieelekeikelekllak...lkklikeel 425
                                                  +qa++++ m+l +Lt++e+ ++++e+ee++++i++l+++l++   l ++ik+el
  gi|313126395|ref|YP_004036665.1| 426 geplptfdfseDQANHIVAMQLGSLTSMEAAEIKDEYEEVQDRIDRLNEILNNpdeLDAVIKSEL 490
                                       9***************************************************9888888888776 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.2   3.1e-17   2.8e-13       1      48 []     522     569 ..     522     569 .. 0.96
   2 !   39.6   0.0   2.8e-14   2.5e-10       1      45 [.     572     619 ..     572     622 .. 0.96
   3 !   36.9   0.0     2e-13   1.8e-09       2      47 ..     631     674 ..     630     675 .. 0.95
   4 !   57.4   0.1   8.1e-20   7.2e-16       2      47 ..     679     724 ..     678     725 .. 0.96
   5 !   38.1   0.0   8.7e-14   7.8e-10       2      38 ..     731     767 ..     730     776 .. 0.94
   6 !   45.9   0.0   3.1e-16   2.8e-12       1      46 [.     781     826 ..     781     828 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 3.1e-17
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                       d ++++T+  y+kr+pl+++++q+Rg+kG++g +lkegd++ sv+v+s
  gi|313126395|ref|YP_004036665.1| 522 DVVVVVTEDDYIKRMPLDTFRAQHRGGKGIIGTDLKEGDRVSSVFVAS 569
                                       6799*****************************************975 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 2.8e-14
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklvsvl 45 
                                       d+ll +T++G+v++++ +++pe++R+a+G+ ++    l++g+++++v+
  gi|313126395|ref|YP_004036665.1| 572 DYLLYFTNHGQVYKLKTYQIPEMSRTARGKSAVnllELDDGEEITAVV 619
                                       899******************************************997 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 2e-13
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       +l ++T+nGyvkr++++++ ++   ++G+++ kl+e+d+l +v+v+
  gi|313126395|ref|YP_004036665.1| 631 YLTMATQNGYVKRTSVEKFQNIL--TTGIIATKLDEDDELADVEVT 674
                                       7889*******************..99****************997 PP

  == domain 4  score: 57.4 bits;  conditional E-value: 8.1e-20
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       +l+l+++ G+++rf++s+++++gR a+Gv+g+kl+ +d+lv+v+ v
  gi|313126395|ref|YP_004036665.1| 679 DLVLASRDGMAIRFDESDVRAMGRSARGVRGMKLEGDDELVGVAAV 724
                                       89*****************************************988 PP

  == domain 5  score: 38.1 bits;  conditional E-value: 8.7e-14
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkeg 38 
                                       ++l++T+nGy+kr +++ +++q+R++kG + ik++++
  gi|313126395|ref|YP_004036665.1| 731 WVLTVTQNGYGKRSDIERYRRQSRNGKGLIDIKTNDR 767
                                       79*******************************9997 PP

  == domain 6  score: 45.9 bits;  conditional E-value: 3.1e-16
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlv 46 
                                       d+l+++++ G+++r+p+++++  gR+++Gv++++++egd++ sv v
  gi|313126395|ref|YP_004036665.1| 781 DHLFVMSESGQILRTPVEDISTVGRNTMGVTVMDMDEGDHVASVDV 826
                                       89*****************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (861 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5719.04
//
Query:       gi|313126396|ref|YP_004036666.1|  [L=637]
Description: DNA gyrase subunit b [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-61  206.6   0.4    3.6e-61  205.7   0.4    1.5  1  DNA_gyraseB    DNA gyrase B
    1.5e-29  102.0   0.0    3.4e-29  100.8   0.0    1.7  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    1.1e-24   87.0   0.1    7.4e-24   84.4   0.1    2.1  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    5.1e-17   62.0   0.0    1.1e-16   60.9   0.0    1.6  1  Toprim         Toprim domain
    0.00023   21.0   0.0    0.00054   19.8   0.0    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.7   0.4     1e-64   3.6e-61       1     173 [.     225     393 ..     225     394 .. 0.98

  Alignments for each domain:
  == domain 1  score: 205.7 bits;  conditional E-value: 1e-64
                       DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktln 77 
                                       G+++fv++ln+ k++l+++v+++++e+  e  ieveva+q t++ + +i+ F+Nni+t+eGGtH++gfk+alt+++n
  gi|313126396|ref|YP_004036666.1| 225 GIREFVRYLNETKSTLHDDVIYYDDED--EG-IEVEVAMQATEELQGSIHAFANNINTREGGTHLTGFKTALTRVVN 298
                                       9**************************..88.***********9999****************************** PP

                       DNA_gyraseB  78 eyakkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakki 154
                                       +ya++++ll++ + +++gediregltav+s+k+p+pqFeGQTK+kLgnsev++ive+v+ e+l  ++een+ +a++i
  gi|313126396|ref|YP_004036666.1| 299 DYARSNNLLDDLD-SLKGEDIREGLTAVISIKHPDPQFEGQTKTKLGNSEVRGIVESVTHEQLGTYFEENPGTAQAI 374
                                       ***********98.*************************************************************** PP

                       DNA_gyraseB 155 lekaveaakareaarkare 173
                                       + kaveaakar+aa+ka+e
  gi|313126396|ref|YP_004036666.1| 375 VMKAVEAAKARRAAKKAEE 393
                                       ****************987 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.0   9.5e-33   3.4e-29       4      63 .]     567     626 ..     564     626 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 9.5e-33
                     DNA_gyraseB_C   4 veiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefie 63 
                                       +++qRfKGLGEmnpeqLw+TTm+p++R L +++ieda++ad++f++LmG+ vepR++fi+
  gi|313126396|ref|YP_004036666.1| 567 TQVQRFKGLGEMNPEQLWDTTMNPDNRVLKRINIEDAAAADRMFNVLMGDAVEPRKQFIK 626
                                       69********************************************************96 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.1   2.1e-27   7.4e-24       1     110 [.      32     178 ..      32     180 .. 0.93
   2 ?   -0.2   0.0       0.4   1.4e+03      43      80 ..     250     291 ..     226     322 .. 0.64

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.1e-27
                                       EHHHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..............GTCSTT CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk..............klfekf 61 
                                       +d+++L++++ ++vdN++++  a++++ei v+++  e d ++sv+DnG+Gip++ ++              + ++kf
  gi|313126396|ref|YP_004036666.1|  32 TDSRGLHHLVYEVVDNSIDEalAGYCDEIGVSVH--E-DGSVSVTDNGRGIPVDTHEqydrpavevimtvlHAGGKF 105
                                       699*****************7777**********..7.*******************************877777** PP

                                       CHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEE.........................EEETTTEEEEEEEEES CS
                         HATPase_c  62 sqddstkrggggtGlGlsivkklvelmgGeiwv.........................esepgrGttftftlpl 110
                                       ++ +s++++gg +G+G+s+v++l+e ++ ei++                         es+++ Gtt++f+++ 
  gi|313126396|ref|YP_004036666.1| 106 DN-KSYQVSGGLHGVGVSVVNALSEWLEVEIKRdgalwrhrfdqgepdqeafervrdlESDEDTGTTIRFKPDG 178
                                       **.**********************99988888999999****999999999999999888899******9985 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.4
                                       EESSSSSTTHHHT........GTCSTTCHHCSTCHTSTSSSH.HHHH CS
                         HATPase_c  43 eDnGiGipkedlk........klfekfsqddstkrggggtGl.Glsi 80 
                                       eD Gi + ++++         +   +f +  + +++ ggt+l G++ 
  gi|313126396|ref|YP_004036666.1| 250 EDEGIEVEVAMQAteelqgsiH---AFAN--NINTREGGTHLtGFKT 291
                                       4555555555544554332222...3333..2333334444435554 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   3.2e-20   1.1e-16       1     100 [.     422     531 ..     422     534 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.2e-20
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEE CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiila 69 
                                       el++vEg+s+ +++++ ++++fqa+++ +G+il++e+ ++++++e  e++  +++++a     ++    r+++iil+
  gi|313126396|ref|YP_004036666.1| 422 ELFVVEGDSAGGSAKQGRDRKFQAILPIKGKILNVEKhRLDRILEnnEVRALITAIGAgigeeFDIDDVRYERIILM 498
                                       69***********************************9888888899999999999999999999999********* PP

                                       CSSSHHHHHHHHHHHHHHT....HHHTTTEEEEEE CS
                            Toprim  70 tDpDreGeaiawellevlk....ellenkigrvef 100
                                       tD+D++G +i+++ll++l+    +l+e+  g+v+ 
  gi|313126396|ref|YP_004036666.1| 499 TDADVDGAHIRTLLLTLLYrhmrPLIEA--GYVYA 531
                                       ****************999777777776..66665 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.5e-07   0.00054       7     123 ..      41     166 ..      36     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-07
                       HATPase_c_3   7 laelvdNsld....AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeak.r.........ksts 69 
                                       + e+vdNs+d    + + ++ ++v+++    g+++++D+G G++ ++ +++ r+a +   +  +          + s
  gi|313126396|ref|YP_004036666.1|  41 VYEVVDNSIDealaGYCDEIGVSVHED----GSVSVTDNGRGIPVDTHEQYDRPAVEVIMTVlHaggkfdnksYQVS 113
                                       88********95544455699999996....69**********9887666555554444332112222322113444 PP

                       HATPase_c_3  70 lGkkGiGlklAslslgkkltvitkkegesstltldvdkidkenekvleeltvee 123
                                        G +G+G  + +  l++ l+v+ k +g  +  ++d    d+e ++ +++l+++e
  gi|313126396|ref|YP_004036666.1| 114 GGLHGVG-VSVVNALSEWLEVEIKRDGALWRHRFDQGEPDQEAFERVRDLESDE 166
                                       7789999.6666777777889999999999999998888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 4324.88
//
Query:       gi|313126397|ref|YP_004036667.1|  [L=800]
Description: DNA topoisomerase vi, b subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-62  207.6   0.0    1.7e-61  206.7   0.0    1.5  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    5.3e-37  126.5   4.7    7.8e-37  125.9   1.7    2.5  2  Top6b_C         Type 2 DNA topoisomerase 6 subunit B C-termin
    8.4e-15   55.3   0.0    2.2e-14   53.9   0.0    1.8  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    2.5e-11   43.6   0.0    6.3e-11   42.3   0.0    1.7  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
     0.0028   17.6   1.5      0.012   15.6   0.0    2.6  2  HATPase_c_2     Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.078   13.3   1.1       0.39   11.0   0.5    2.4  2  DUF11           Domain of unknown function DUF11
       0.11   13.2   0.1       0.52   11.0   0.0    2.1  2  LAMTOR          Late endosomal/lysosomal adaptor and MAPK and


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.7   0.0   6.7e-65   1.7e-61       1     159 []     506     670 ..     506     670 .. 0.99

  Alignments for each domain:
  == domain 1  score: 206.7 bits;  conditional E-value: 6.7e-65
                    Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydega 77 
                                       P+t+clspi++el+e+gl+ke++++f+aa tr+++v+ g+pfivE+giayGG+l++e ++++lRfaNrvPL+y++ga
  gi|313126397|ref|YP_004036667.1| 506 PPTNCLSPITDELVEAGLRKEYDADFYAAATRDAEVHGGDPFIVEAGIAYGGDLQSEGSVDLLRFANRVPLVYQRGA 582
                                       99*************************************************************************** PP

                    Topo-VIb_trans  78 dvitkavksinwkrYkleq......pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkyls 148
                                       +++t++vk+i w++Y+l+q      p++p+v++vhvast+vPf+se+K+a+a+++eie+ei+la++e+ r+Lk+yl+
  gi|313126397|ref|YP_004036667.1| 583 CATTDVVKRIGWRNYGLDQpggsgmPKGPAVIMVHVASTNVPFTSESKDALANIPEIEDEIELAIREASRELKSYLN 659
                                       ***************************************************************************** PP

                    Topo-VIb_trans 149 kkekekeekek 159
                                       k+++ +++++k
  gi|313126397|ref|YP_004036667.1| 660 KRRSMQKRRKK 670
                                       ***99998876 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.34   8.6e+02      42      89 ..     346     396 ..     336     420 .. 0.61
   2 !  125.9   1.7     3e-40   7.8e-37       2     114 .]     691     797 ..     690     797 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.34
                                       -----EEE--EES-----------EE....E-SSSEEE-EEE---TT-EEEE CS
                           Top6b_C  42 dkkeefelheilpaeieeaspeakvv....emdneydlkWelsvsageskvl 89 
                                       +++++fel +i+++ +++++ e  v+      +n     W++ v+ + ++ l
  gi|313126397|ref|YP_004036667.1| 346 ERTTHFELGDIVDTVANDIESEFDVTfgdtVRENAVEAAWDILVT-DRTADL 396
                                       577899999999999999998777651111234556667777664.344444 PP

  == domain 2  score: 125.9 bits;  conditional E-value: 3e-40
                                       SS---SHHHHHHHTT-EEEEEEE--SSS-EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EE CS
                           Top6b_C   2 reepdidpvvArimgnvlvereveengdgvevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWe 78 
                                       +++p+id ++Arim+nv+verev ++    +v+l v+N+sd++e++++++i++ae++++ ++a+vv++d+e+++kW+
  gi|313126397|ref|YP_004036667.1| 691 QDRPNIDGALARIMNNVSVEREVADD----TVTLAVENHSDRTEQPDITDIVTAEPTDVPDDATVVDLDGEWFVKWN 763
                                       79************************....*********************************************** PP

                                       E---TT-EEEE----SS-GGGS--B----------- CS
                           Top6b_C  79 lsvsageskvleYsvdseaeeelsliveGveeekvT 114
                                       +svsage+++l+Y+v+s+a+++++  v+Gve+ek+T
  gi|313126397|ref|YP_004036667.1| 764 PSVSAGETAELTYTVTSDASFDIN--VDGVETEKLT 797
                                       ************************..*********9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   8.4e-18   2.2e-14       4      97 ..      45     145 ..      42     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 8.4e-18
                                       HHHHHHHHHHHHHHHHH...HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCH.....HCSTCHTS CS
                         HATPase_c   4 krLrqiisnlvdNavkf...atkageieveikaseddlvisveDnGiGipkedlkklfe.kfsq.....ddstkrgg 71 
                                       ++L  +++++vdNa+++   a+ +++i+vei+ s d++++ veDnG+Gi+ke+++k+f+          +++++rg+
  gi|313126397|ref|YP_004036667.1|  45 RGLVTAVKEAVDNALDAteeAGIKPDISVEIRESGDYYTLIVEDNGPGITKEQIPKVFGkL-LYgsrfhAREQSRGQ 120
                                       78999***********94443355699999996669*******************999953.433698889999999 PP

                                       TSSSHHHHHHHH.HHHHTTTEEEEEEE CS
                         HATPase_c  72 ggtGlGlsivkk.lvelmgGeiwvese 97 
                                       +g G+++++  + l++  g   +v+s+
  gi|313126397|ref|YP_004036667.1| 121 QGIGISAAVLYSqLTS--GKPAKVTSR 145
                                       9999999998664554..434444333 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   2.5e-14   6.3e-11       5     109 ..      49     163 ..      46     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.5e-14
                       HATPase_c_3   5 kAlaelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGi 75 
                                       +A+ e vdN+ldA  e      +++e+ +  g+  ++ +eD+G G+++e++ +++ +l   s+  +  ++s+G+ Gi
  gi|313126397|ref|YP_004036667.1|  49 TAVKEAVDNALDATEEAgikpdISVEIRES-GDYYTLIVEDNGPGITKEQIPKVFgKLLYGSRF-HAREQSRGQQGI 123
                                       79*************999999999999886.7899******************77589999999.57899******* PP

                       HATPase_c_3  76 GlklAsl....slgkkltvitkkegess..tltldvdkid 109
                                       G+  A+l     +gk ++v+++++g+s    ++l +d   
  gi|313126397|ref|YP_004036667.1| 124 GISAAVLysqlTSGKPAKVTSRTQGDSAaqYFELIIDTDT 163
                                       *988875222268999*********999433444444333 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.6e-06     0.012      29     102 ..      44     125 ..      14     128 .. 0.75
   2 ?   -0.4   0.5      0.41   1.1e+03      29      41 ..     640     652 ..     625     744 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.6e-06
                       HATPase_c_2  29 ldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........keslke 97 
                                       +  +  av+Ea+ Na  +  + + + +++v+++ +++  t+ v+D+Gpg + e++p+   + +        ++s+  
  gi|313126397|ref|YP_004036667.1|  44 ARGLVTAVKEAVDNALDATEEAGIKPDISVEIRESGDYYTLIVEDNGPGITKEQIPKVFGKLLygsrfharEQSRGQ 120
                                       456788*****************9*************************9999888755444466666666666666 PP

                       HATPase_c_2  98 gGrGl 102
                                       +G+G+
  gi|313126397|ref|YP_004036667.1| 121 QGIGI 125
                                       66665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.41
                       HATPase_c_2  29 ldeirlaveEact 41 
                                        dei+la+ Ea  
  gi|313126397|ref|YP_004036667.1| 640 EDEIELAIREASR 652
                                       5688888888854 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.7   4.4e+03      61      84 ..     174     201 ..     140     207 .. 0.62
   2 ?   11.0   0.5   0.00015      0.39      17      80 ..     717     782 ..     713     788 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.7
                             DUF11  61 v....gsLeagesatlsftvrvtrtaas 84 
                                             +L + + ++++++++++ +a++
  gi|313126397|ref|YP_004036667.1| 174 LapgeSDLSPTHGTRIEVEMEANMRARQ 201
                                       1333345666666677777777766665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00015
                             DUF11  17 tytltvtNtgpasangvvvtDtlPaglayvsvsas....qgtasaltsv...gsLeagesatlsftvrvtr 80 
                                       t+tl v N + ++  +  +tD++ a  + v+  a+     g     + v   +s+ age+a l++tv+  +
  gi|313126397|ref|YP_004036667.1| 717 TVTLAVENHSDRTE-QPDITDIVTAEPTDVPDDATvvdlDGE----WFVkwnPSVSAGETAELTYTVTSDA 782
                                       89***********9.9*******9999999999995544444....4445569**************9765 PP

>> LAMTOR  Late endosomal/lysosomal adaptor and MAPK and MTOR activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.2   5.6e+03      40      54 ..     276     290 ..     276     292 .. 0.91
   2 ?   11.0   0.0    0.0002      0.52      29      65 ..     660     696 ..     649     699 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                            LAMTOR  40 qeaLnkIvqetsdnl 54 
                                       qe+++++ ++t+d++
  gi|313126397|ref|YP_004036667.1| 276 QEEFTRVGAKTADKI 290
                                       8999**********8 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                            LAMTOR  29 eqespekltdeqeaLnkIvqetsdnlIDISaidssgi 65 
                                       ++ s +k+++ q+ L +I+ e +d+l +++ +d+++i
  gi|313126397|ref|YP_004036667.1| 660 KRRSMQKRRKKQDVLGRILPEMADKLAEVTKQDRPNI 696
                                       678899***************************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (800 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 4958.90
//
Query:       gi|313126398|ref|YP_004036668.1|  [L=364]
Description: DNA topoisomerase vi subunit a [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-15   54.4   0.3    1.5e-14   53.7   0.3    1.4  1  TP6A_N    Type IIB DNA topoisomerase


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.3   8.4e-19   1.5e-14       1      61 [.      70     136 ..      70     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 8.4e-19
                                       HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH......GGGS-SSHHHHHHHHHHHHHHHTS-GGGGT CS
                            TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr......dvelFksQaesdrliddievllgvsReeLn 61 
                                       rk+ + ++ +e++ ++leeg+++T+R++YY       +++ F +Q+es++li+d+e + +v+Re+++
  gi|313126398|ref|YP_004036668.1|  70 RKLLKATYAIEFLVNQLEEGRSSTLRELYYLseswdtEEAQFNDQDESNQLIEDLEIVSNVTREDFH 136
                                       68889999*************************99888****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2199.16
//
Query:       gi|313126399|ref|YP_004036669.1|  [L=273]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   51.3   0.0    2.8e-07   30.5   0.0    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold
    1.3e-10   42.2   9.0    1.6e-10   41.9   9.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    7.1e-10   38.6   0.0    3.3e-09   36.4   0.0    1.9  1  Hydrolase_4    Serine aminopeptidase, S33
    1.6e-05   24.9   0.0    3.8e-05   23.7   0.0    1.6  2  Abhydrolase_4  TAP-like protein
     0.0018   18.0   0.6     0.0082   15.8   0.3    1.9  2  Esterase       Putative esterase
     0.0021   17.8   0.0       0.58    9.9   0.0    2.1  2  Abhydrolase_5  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.047   13.8   0.0      0.075   13.1   0.0    1.3  1  Thioesterase   Thioesterase domain


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.1e-10   2.8e-07      52     117 ..      76     147 ..      29     160 .. 0.78
   2 !   18.7   0.0   4.1e-07    0.0011     201     252 ..     207     252 ..     189     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.1e-10
                                       CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE........CSSCCHHHHHH CS
                     Abhydrolase_1  52 ddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllga........idpaaslieaq 117
                                       +d +t  +a +   +ld lg +++  +G+SmGG++a ++aa+ype V +lvl ++         +   +++ ++
  gi|313126399|ref|YP_004036669.1|  76 PDATTREIAGSAATALDELGGGHV--LGYSMGGFVAQHLAADYPELVERLVLGSTaarvgdagRTVLEDWETWA 147
                                       455677777777788999999999..**************************9995555444444444444444 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.1e-07
                                       HHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSH CS
                     Abhydrolase_1 201 llrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHla 252
                                       l++      v  ptlv++g++D+l+pp+ l++ ++ lp+++l  + ++gH a
  gi|313126399|ref|YP_004036669.1| 207 LGD------VRMPTLVVGGDEDRLFPPELLRETKEMLPDATLALLRGTGHAA 252
                                       344......555**************************************87 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   9.0   6.4e-14   1.6e-10       1     218 [.      29     261 ..      29     263 .. 0.57

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6.4e-14
                                       EEEE--GC.....G......C.HHHHHHHHCCT.....CEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT..T CS
                     Abhydrolase_6   1 vlllHGagssassW......l.vapLaallaag.....vhvlapDlpGhGrsdpppldledladl.aalldelaagg 64 
                                       +++l+G++   +++      + +  La+    +     ++v+++ +p      +p+ + +++a   a +ldel    
  gi|313126399|ref|YP_004036669.1|  29 LVVLPGLS---DAFaggptkAtAEYLARVTY-RgltddFTVWTVRRPRA---LDPDATTREIAGSaATALDEL---- 94 
                                       57778855...44433332211222222222.235556999*****944...555555555333357788888.... PP

                                       TSEEEEEETCHHHHHHH.HHHCC...EE.EEES-..----TTTS----TTHHHHHHTT-CCCCHCCH.......... CS
                     Abhydrolase_6  65 gpvvlvGHSlGGalala.aapla.lvvg.vlldppptalpagllaaalelllallallrllawlsre.......... 128
                                       g  +++G+S+GG++a++ aa+++ lv++ vl ++      a+ ++a +++l+ + +++ + aw +++          
  gi|313126399|ref|YP_004036669.1|  95 GGGHVLGYSMGGFVAQHlAADYPeLVERlVLGST-----AARVGDAGRTVLEDWETWAKTGAWGNLYassaresytg 166
                                       56678************66666655555444444.....45555555555555555555555553333321222222 PP

                                       ...........S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-C.HHHHCHHCCCH CS
                     Abhydrolase_6 129 ...........plprlfladedadaawrarlarlaallaglgllpaaawadlpvpllvl.ggeDp.lvprllerlla 192
                                                  +l++l+ +     ++  + ++  +a+l ++g    +++ d+++p+lv+ g+eD+   p+ll++   
  gi|313126399|ref|YP_004036669.1| 167 wrhhvypaamcLLGPLLTP-----PYPEDVVTSIRACLEHDG---TDRLGDVRMPTLVVgGDEDRlFPPELLRETKE 235
                                       2222122222334434444.....666666666666666666...889********999669999655566776666 PP

                                       .STTEEETCE...SSS-HHHHSHHHHH CS
                     Abhydrolase_6 193 .qagarlpvvlpgaGHlphleepdeva 218
                                        +++a+l  +l+g+GH+   e+ ++++
  gi|313126399|ref|YP_004036669.1| 236 mLPDATL-ALLRGTGHAAATEQTTAFN 261
                                       88*****.********87775657766 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.3e-12   3.3e-09      80     238 ..      99     256 ..      87     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.3e-12
                       Hydrolase_4  80 llGhSmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqvsnnlkadslsrdpevva 156
                                       +lG SmGG++a++++++yp+ v++l+l ++a ++      + l  +  +    ++ +l+   ++  +s + ++++v 
  gi|313126399|ref|YP_004036669.1|  99 VLGYSMGGFVAQHLAADYPELVERLVLGSTAARVGDAG-RTVLEDWETWAKTGAWGNLYA--SSARESYTGWRHHVY 172
                                       89*********************************874.334555666777778888888..445555555555554 PP

                       Hydrolase_4 157 ayeadplv.hgkitvrlllelldamkrleeraakit.....lPllllhGeaDkvvdpeasrelyerlgskdktlkly 227
                                          a  ++ +  +t     ++++ + +++e++   +     +P+l++ G++D++ +pe  re+ e l+  d tl+l 
  gi|313126399|ref|YP_004036669.1| 173 --PAAMCLlGPLLTPPYPEDVVTSIRACLEHDGTDRlgdvrMPTLVVGGDEDRLFPPELLRETKEMLP--DATLALL 245
                                       ..333333366666666666666666666555444444444***************************..9****** PP

                       Hydrolase_4 228 pglyHellnEp 238
                                        g  H   +E+
  gi|313126399|ref|YP_004036669.1| 246 RGTGHAAATEQ 256
                                       *****988886 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         4     1e+04      53      66 ..      87     100 ..      77     106 .. 0.55
   2 !   23.7   0.0   1.5e-08   3.8e-05      34      93 ..     211     270 ..     197     273 .] 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4
                     Abhydrolase_4  53 akklakalggavlv 66 
                                       a+++ ++lgg++++
  gi|313126399|ref|YP_004036669.1|  87 AATALDELGGGHVL 100
                                       34444555555555 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.5e-08
                     Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLlt 93 
                                         p+L++++  D   P+e  +++++ l++a+l   +g+GH a +++ t+ ++ v ++L++
  gi|313126399|ref|YP_004036669.1| 211 RMPTLVVGGDEDRLFPPELLRETKEMLPDATLALLRGTGHAAATEQTTAFNRVVGRFLRE 270
                                       589*******************************************************97 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.24     6e+02      17      51 ..      19      53 ..      14      56 .. 0.87
   2 !   15.8   0.3   3.2e-06    0.0082     118     176 ..      98     157 ..      77     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                                      C.GGTTTEEEEEEE--TTHHCCHHHHHCHHCCCCH CS
                          Esterase 17 dyspgrkypvvylldGltgwdqnfrakelleslar 51
                                      +y++g ++ ++++l Gl++ +  +++k++ e lar
  gi|313126399|ref|YP_004036669.1| 19 YYRAGDGPETLVVLPGLSDAFAGGPTKATAEYLAR 53
                                      4599999*******************999887665 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.2e-06
                                       EEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CCHCHHHC......TTCCHHHCC-CCCCHCH CS
                          Esterase 118 avaGqSmGGlgALilalkhpdrFgsvssfSpivnpsnamWgq......eekeawqendpvllake 176
                                        v+G SmGG++A +la+++p++  +    S      +a  g       e+ e+w++ +++ +  +
  gi|313126399|ref|YP_004036669.1|  98 HVLGYSMGGFVAQHLAADYPELVERLVLGST-----AARVGDagrtvlEDWETWAKTGAWGNLYA 157
                                       689********************99999883.....33333344455555555666666655554 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0     0.004        10      46      86 ..      84     125 ..      44     140 .. 0.69
   2 !    9.9   0.0   0.00023      0.58      94     142 ..     205     252 ..     198     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.004
                     Abhydrolase_5  46 aeeiikeapklekfvvgGhslGGvvasrfaaee.ekiegvvf 86 
                                       a ++  + ++l    v G+s+GG va ++aa+  e +e +v+
  gi|313126399|ref|YP_004036669.1|  84 AGSAATALDELGGGHVLGYSMGGFVAQHLAADYpELVERLVL 125
                                       555555555666667889************998456666553 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00023
                     Abhydrolase_5  94 delselskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGgnhag 142
                                       d l +  +++l + g+eD + + + l+++k++lp+ +++  ++G  ha 
  gi|313126399|ref|YP_004036669.1| 205 DRLGDVRMPTLVVGGDEDRLFPPELLRETKEMLPD-ATLALLRGTGHAA 252
                                       77889999*************************95.6788899999985 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.9e-05     0.075      64      86 ..      96     115 ..      59     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                                       SSSSEEEEEETHHHHHHHHHHHH CS
                      Thioesterase  64 pegPyalfGhSlGgllAfevArq 86 
                                            ++ G+S+Gg++A+ +A+ 
  gi|313126399|ref|YP_004036669.1|  96 GG---HVLGYSMGGFVAQHLAAD 115
                                       44...89************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1649.27
//
Query:       gi|313126400|ref|YP_004036670.1|  [L=238]
Description: zn-dependent hydrolase of beta-lactamase fold family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-31  109.8   0.0    1.6e-31  109.4   0.0    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.012   15.1   0.1       0.02   14.4   0.1    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.0   1.8e-35   1.6e-31       2     163 .]      10     203 ..       9     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 1.8e-35
                     Lactamase_B_3   2 ltwlghnsfllet.agarilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql................... 58 
                                       + wlg++++++e+ ag ++++DP+++++  ++ a++ Dlv++++++  H++ ++++++                   
  gi|313126400|ref|YP_004036670.1|  10 VAWLGYATVRIESeAGYVVYLDPGRYGVLDDYYARDGDLVCVTHDH--HYDSDAIRSVakedatvvvfegvdasnid 84 
                                       78***********55*******************************..**********9887777777777777774 PP

                     Lactamase_B_3  59 ......aenvkvlee..........geslevggleiravatshdavggser.........genngflleqdgltiyh 110
                                             +       +          +e+l++g +++++ a++++a g+++r         g ++gfll++dg+++++
  gi|313126400|ref|YP_004036670.1|  85 rdvaavE-------DlpyevirvgeEEHLTAGPVDLWTLAAYNEADGPHTRddgslvhppGFGCGFLLSVDGIKVFW 154
                                       4444440.......35555555555777999************6666555545555555599*************** PP

                     Lactamase_B_3 111 lGhlahelsseelkelgrvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                       +G+ +     + +++l  vD++l+++gg+++++++ea++la +L+p lvlP+h
  gi|313126400|ref|YP_004036670.1| 155 PGDSDV---LAGFEQL-SVDLFLANIGGSIVMDRHEAADLAAALNPGLVLPIH 203
                                       *****9...7888888.***********************************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.2e-06      0.02      30     201 .]      45     204 ..      38     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-06
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleit 106
                                       + d+V +th+H  H+ + + +r  +++++++++ +gv a   ++ v+++ + +   +v  +  +e ++ g+++l  t
  gi|313126400|ref|YP_004036670.1|  45 DGDLVCVTHDH--HY-DSDAIRSVAKEDATVVVFEGVDASNIDRDVAAVEDLP--YEVIRVGEEEHLTAGPVDL-WT 115
                                       5699999**98..88.99999998888899**999999987777666666655..6777777777788888887.66 PP

                                       EEEE-EE--C......TCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT CS
                     Lactamase_B_2 107 atparhksgr......rldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirhmg 177
                                       + + + + g+       l   +g  +G+++  +g +v++ gD+  + +   e+l  +dl l +i+         + +
  gi|313126400|ref|YP_004036670.1| 116 LAAYNEADGPhtrddgSLVHPPGFGCGFLLSVDGIKVFWPGDSDVLAGF--EQLS-VDLFLANIG---------GSI 180
                                       6666666666666666666667799*******************88844..4555.999999999.........899 PP

                                       ---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 178 HltpeeaveaaadlgakrlvliHi 201
                                        ++  ea+++aa+l+++ +++iH+
  gi|313126400|ref|YP_004036670.1| 181 VMDRHEAADLAAALNPGLVLPIHY 204
                                       9**********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1428.17
//
Query:       gi|313126401|ref|YP_004036671.1|  [L=472]
Description: hypothetical protein Hbor_16580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-49  170.0   1.7    1.3e-49  169.8   1.7    1.0  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
    0.00052   19.5   0.1      0.067   12.6   0.0    2.7  3  Sulfatase     Sulfatase
     0.0037   16.4   0.0     0.0079   15.3   0.0    1.4  1  DUF1501       Protein of unknown function (DUF1501)


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.8   1.7   2.1e-53   1.3e-49       1     357 []      13     382 ..      13     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 169.8 bits;  conditional E-value: 2.1e-53
                                       EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEE CS
                      Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyv 77 
                                       v+v+ + Gl +d +    e +p+l++L++ g +   l p fP++T+p++++l TG++P+ HG v+N  ydrkt+ + 
  gi|313126401|ref|YP_004036671.1|  13 VIVLDVVGLQPDHVTS--ESMPHLSELFDDGATTG-LVPPFPAVTIPAQTTLSTGRSPATHGDVSNAEYDRKTDTV- 85 
                                       79**************..*****************.**************************************97. PP

                                       EEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESE.....TTTTSEBTTCT.SC............TBHHSBTCT.C CS
                      Phosphodiest  78 vfvtededaprwwqgepiwdtaakarglkaaalfw.....pgsevdystyyylvs...........etppryleddf 138
                                       + + +d+      +  +iw+    +  l+++alf+     + ++v+++ +                 t p+ ++d+ 
  gi|313126401|ref|YP_004036671.1|  86 ELWGRDSG-----DRRRIWELQSDC-ELTTGALFFqhlygTSADVAVTPKPI--EdenngliemncWTNPDDFYDEL 154
                                       55555554.....469999999999.99999999977743334444443333..25578888887744444444777 PP

                                       STTS......CHHHHHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHH CS
                      Phosphodiest 139 nakv......pledkvdkavlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaig 209
                                       ++++       +++ +++a ++tw+  a++++  +   ++pd+l vyl+++D+ g+++Gp+s e+e+al++vD+ +g
  gi|313126401|ref|YP_004036671.1| 155 REEYghfplhNYWGPAANAESSTWILSAAREATER---YDPDMLWVYLPHLDYTGQSHGPNSDEFEAALSEVDELVG 228
                                       777799999*****99977888**99888774444...*************************************** PP

                                       HHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGHGEEEEECBHHS.SSEEEEEESTEEE.CCCTTHH CS
                      Phosphodiest 210 dLlealderglsaetniilvSDHGmadvsddkvielndlleekgllhlkdegkggakaliainpkarelnrvaeaea 286
                                       + ++al+++  ++et++++vS++G+ +v  ++ ++ n+ l+++gll+++d++       +   + a+ +++va++++
  gi|313126401|ref|YP_004036671.1| 229 EYIDALRKTDRWSETAVVVVSEYGFHEV--STPVFPNRALRDAGLLQTQDAE-----GGAIPDLAASAAFAVADHQV 298
                                       ****************************..99*****************999.....4433334333458******* PP

                                       HHHHHHHHTCHHCCHST.HTT..TEEEEEGG.GS-GGGCH.STTS-SEEEEE-TTEEEESSTTCS...........S CS
                      Phosphodiest 287 eevyaelkakleelrkk.ege..alavylke.aipkrlhy.kkrapdlvlvadpgwsitskdkpd...........e 347
                                       ++vy + +a  e  r+  e +  + ++ + + +   +  + ++ a++lvl+ad + +++++++++           +
  gi|313126401|ref|YP_004036671.1| 299 AHVYCDHDAV-ERAREAlEDRpgIERILDGDdQAAYG--IdHENAGELVLLADADAWFAYYWWHEdeteamppyadS 372
                                       ******9999.55553434443455555555233333..346********************999888888888888 PP

                                       BS-SEE--SS CS
                      Phosphodiest 348 yeikgthGyd 357
                                       ++i++++Gyd
  gi|313126401|ref|YP_004036671.1| 373 VDIHEKPGYD 382
                                       8888888886 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.0    0.0054        32      26      75 ..      31      80 ..      13      97 .. 0.74
   2 !   12.6   0.0   1.1e-05     0.067     209     247 ..     211     249 ..     140     265 .. 0.80
   3 ?   -1.6   0.0      0.23   1.4e+03     298     309 .]     436     447 ..     428     447 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0054
                                      SHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT CS
                         Sulfatase 26 tpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg 75
                                      +p+l++l + g +   +    +++ p+  +l tgr+p+++g +sn e+  
  gi|313126401|ref|YP_004036671.1| 31 MPHLSELFDDGATTGLVPPFPAVTIPAQTTLSTGRSPATHGDVSNAEYDR 80
                                      77777777666654444333349******************999998864 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEE CS
                         Sulfatase 209 qlleaylnsveyvDdligrvlaaLeenglldntlvvftS 247
                                        + +++ +++++vD+l+g+ ++aL+++  + +t vv++S
  gi|313126401|ref|YP_004036671.1| 211 PNSDEFEAALSEVDELVGEYIDALRKTDRWSETAVVVVS 249
                                       566778899***************************998 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.23
                                       GHHHHHHHHTTE CS
                         Sulfatase 298 Dlfptildlagi 309
                                        ++ptildl+g+
  gi|313126401|ref|YP_004036671.1| 436 QVAPTILDLLGV 447
                                       699*******96 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-06    0.0079     258     302 ..     208     252 ..     197     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-06
                           DUF1501 258 tHsnlekahkklakelDqalaaLlkdLkqrGllddTlVvwagEFG 302
                                       +H+ ++++ +  + e+D+ + +++++L ++ ++ +T+Vv+++E+G
  gi|313126401|ref|YP_004036671.1| 208 SHGPNSDEFEAALSEVDELVGEYIDALRKTDRWSETAVVVVSEYG 252
                                       689999999999*******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2683.82
//
Query:       gi|313126402|ref|YP_004036672.1|  [L=432]
Description: myo-inositol-1-phosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-47  160.6   0.0    9.8e-45  153.3   0.0    2.1  1  NAD_binding_5   Myo-inositol-1-phosphate synthase
      1e-27   96.5   0.0    1.6e-27   95.9   0.0    1.3  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.0   1.1e-48   9.8e-45       1     320 [.       6     392 ..       6     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 1.1e-48
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5   1 lGvllvGlgGnngtTlvagvlankkglswetkeglkkanylGsvtqsstirlGkdeeegedvyvpikdllplvnpnd 77 
                                       +Gv+ vG++Gn++tT++ag   +++g + et          G vt+ + ++l                 l+l+++++
  gi|313126402|ref|YP_004036672.1|   6 TGVWFVGARGNVATTAIAGARGIARGTTDET----------GMVTAREPCTL-----------------LDLPAVSE 55 
                                       69*****************************..........99999887766.................99****** PP

                                       xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5  78 lvfgGwDisslnlaeamer...akvldkdlqeqlkpeleki.kplksvydkdfiaanqeeradnvlkgkskleqleq 150
                                       +vfgG+Di + +l +++++   ++++d++ +e ++++l++i   +++   ++  +a +    d++ ++++  e++eq
  gi|313126402|ref|YP_004036672.1|  56 FVFGGHDIADRPLIHTATElsdSNIVDRETLEIVSDDLREIdDRIETGTAQNCGSAVSLADGDTLDSNHTVSEIVEQ 132
                                       ************98877766669******************5555555666666666666677777777899***** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 151 irkdireFkkknkldkvivlwtanTEryievipgvndtlenllkaikeneeeispstiyavAailegvpyingsPqn 227
                                       ir+d ++F +++++d+++v++ a+ E  +   +   +tl+++++a+++++ ++++s++ya+Aa+ +g py+n++P++
  gi|313126402|ref|YP_004036672.1| 133 IRSDYSDFVAETGVDRLVVVNLASSEPPVTDPDR-YETLAAFEEAVEADDADLPASSLYAYAALDDGHPYVNFTPST 208
                                       ****************************988777.99**************************************** PP

                                       xx.xxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                     NAD_binding_5 228 tl.vpglvelAekkgvfiaGdDfKt.................................................... 251
                                       +  + gl elAe+k+v++aG D Kt                                                    
  gi|313126402|ref|YP_004036672.1| 209 GSdLGGLRELAETKNVPHAGRDAKTgetllksalgpmfagrnldvlswdgfnilgngdgkvleddenkagklqskgg 285
                                       ***************************************************************************** PP

                                       .....................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 252 .....................................................lLAaPlilDLvllveLaqrvevkk 275
                                                                                             LAaPl+lDLv+lv+ a   +   
  gi|313126402|ref|YP_004036672.1| 286 vlsnilgsnmhnrvridytpslgdwktawdhvhfrgfmgttmslqftwqgadsTLAAPLVLDLVRLVAYADDHDEG- 361
                                       ********************************************************************99999988. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 276 ekkkefkklesvlsllsyflKaPlvskgtkvvnalfkQraaleni 320
                                                 +v++ ls f+K P++      +++l++Q+a+le +
  gi|313126402|ref|YP_004036672.1| 362 ----------GVQTHLSSFFKEPMDV----SEHDLSRQFAMLESY 392
                                       ..........***************9....89*********9976 PP

>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0   1.8e-31   1.6e-27       1     109 []     234     338 ..     234     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.8e-31
                                       SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEEEE-GG CS
                    Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvikYvpy 77 
                                       G+T+lks+L ++++ r+l v s+  +NilGn Dgk+l+++e+++ K +sK  v+++i+++n ++     v+i+Y+p+
  gi|313126402|ref|YP_004036672.1| 234 GETLLKSALGPMFAGRNLDVLSWDGFNILGNGDGKVLEDDENKAGKLQSKGGVLSNILGSNMHNR----VRIDYTPS 306
                                       99**********************************************************88765....9******* PP

                                       GTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                    Inos-1-P_synth  78 lgDsKvaldeieseiflggkntielkleceDS 109
                                       lgD+K+a+d++++++f+g++++++++++  DS
  gi|313126402|ref|YP_004036672.1| 307 LGDWKTAWDHVHFRGFMGTTMSLQFTWQGADS 338
                                       *******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2677.72
//
Query:       gi|313126403|ref|YP_004036673.1|  [L=284]
Description: metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-17   62.4   0.0    5.3e-17   62.0   0.0    1.3  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0     3e-21   5.3e-17       1     178 [.       4     189 ..       4     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 3e-21
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG...............GGHHHHHHHHTT..TTTEEEEE-- CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtss...............kdskavlelakk.ypnkvyavlGi 61 
                                       iD+H+H++s+       +  ++++++g++ v+ ++  s               + ++  +e a + +  + y+++ i
  gi|313126403|ref|YP_004036673.1|   4 IDSHAHMTSR-----TTDDYREMRRSGIECVIEPSFWSgsdklypesffdyfeHIIDFETERADRvAGMEHYVTVSI 75 
                                       8********3.....567889999999**999888888888899999998875233333444444577789****** PP

                                       -GGGGGCC.CCHHHHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HH. CS
                        TatD_DNase  62 HPnevdeasedlleelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaee. 136
                                        P e+ +++++ ++ +++l +++++++vv++GeiG ++ ++     ++ e +F+eqlrlA+e++ p++iHl ++e+ 
  gi|313126403|ref|YP_004036673.1|  76 NPKEAVDREMS-EAVIDRLpEYLERDRVVGVGEIGFNL-QT-----DEEEWAFREQLRLAEEHEQPVIIHLPHTEKp 145
                                       **999875333.3456666666****************.44.....456778***********************99 PP

                                       ....HHHHHHHHCGGCCSEEEETT--S-HHHHHHHHHTTEEEEE-G CS
                        TatD_DNase 137 ....dlleilkeaaeakakvvlHsfsgsaeeakkflklgyyislsg 178
                                            ++ei++e + ++ ++++ + + +  e +++  ++++++++ 
  gi|313126403|ref|YP_004036673.1| 146 kgavRTVEIIEEMGVTQERIIIDHNEPETMETTAA--TDCWLGFTL 189
                                       9999*********9777677775534444444444..466666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1496.87
//
Query:       gi|313126404|ref|YP_004036674.1|  [L=278]
Description: sugar phosphate isomerase/epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-38  130.9   0.6    5.7e-38  130.5   0.2    1.4  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.044   13.5   0.0       0.18   11.6   0.0    1.9  2  PheRS_DBD1    PheRS DNA binding domain 1


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.5   0.2   6.4e-42   5.7e-38       1     208 [.      21     230 ..      21     232 .. 0.94
   2 ?   -2.7   0.0      0.36   3.2e+03       9      22 ..     249     262 ..     238     276 .. 0.48

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 6.4e-42
                                       HHHHHHCT-SEEEEECCTCSHHHHC.HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC.....HTTCS.HHHHHH CS
                      AP_endonuc_2   1 laaaaeaGfdgvElfgrdlvpvsel.sdeelrelrkaldelglriaslslftrfgypded.....erear.reesvd 70 
                                       ++a+a+aG+dg+El ++++  + ++ +dee +e+r+al+++gl i+  ++f+     d +     e +++ r++ v+
  gi|313126404|ref|YP_004036674.1|  21 IDAVADAGYDGIELLFDQPFLYPPAaTDEEYDEVRAALERTGLDISNCNAFMLTAIEDFHhpsfiEVDENyRRRRVE 97 
                                       589********************99*******************9988888766665555666667777799999** PP

                                       HHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHH CS
                      AP_endonuc_2  71 alkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeelarl 147
                                       ++ + +++aa+LG++++ + pG  + ++++s+e a e+++ +l+ela +ae +gv +++E+ +   +e+   +++++
  gi|313126404|ref|YP_004036674.1|  98 YTLDSLDAAAELGCDHISIEPG-GPLPDGKSREWAMETFVGGLEELAVKAENVGVDVLVEPEPDLLIETS-MQFLDV 172
                                       **********************.55788899999************************************.****** PP

                                       HHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSS CS
                      AP_endonuc_2 148 ldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeG 208
                                       +++vds+++  ++D gHl+  +ed+++++++l +++kh H+ D+      ++++h ++g+G
  gi|313126404|ref|YP_004036674.1| 173 IERVDSDRIACNFDAGHLYCVGEDPAELVETLSPYTKHYHLEDIPE---VREHDHTQLGDG 230
                                       **********************************************...9**********9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.36
                                       -SEEEEECCTCSHH CS
                      AP_endonuc_2   9 fdgvElfgrdlvpv 22 
                                       + +vEl++++   +
  gi|313126404|ref|YP_004036674.1| 249 YITVELYPYQETAA 262
                                       33355555554444 PP

>> PheRS_DBD1  PheRS DNA binding domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     2e-05      0.18      18      32 ..      99     113 ..      94     117 .. 0.87
   2 ?   -1.4   0.0      0.22     2e+03      11      37 ..     168     194 ..     163     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                        PheRS_DBD1  18 evdslelAaelgvdH 32 
                                       ++dsl++Aaelg+dH
  gi|313126404|ref|YP_004036674.1|  99 TLDSLDAAAELGCDH 113
                                       58************* PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.22
                        PheRS_DBD1  11 qrLekkgevdslelAaelgvdHqkvVG 37 
                                       q L+  + vds  +A ++   H   VG
  gi|313126404|ref|YP_004036674.1| 168 QFLDVIERVDSDRIACNFDAGHLYCVG 194
                                       566666788888888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1536.55
//
Query:       gi|313126405|ref|YP_004036675.1|  [L=311]
Description: 4-hydroxybenzoate polyprenyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-18   67.6  25.6      1e-18   67.6  25.6    2.2  2  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6  25.6   5.6e-23     1e-18       5     233 ..      39     251 ..      37     257 .. 0.83
   2 ?   -1.4   3.6     0.063   1.1e+03      74     102 ..     268     299 ..     264     308 .. 0.65

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 5.6e-23
                              UbiA   5 alvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgl 81 
                                       a v+la+a g +++ ++++ l+l+ +l+ aa+ +lNd++D+++Da+   +p+RP++sGr+ + eal ++i+ll+ g+
  gi|313126405|ref|YP_004036675.1|  39 AGVALAVALGATVSVPTIVGLCLASALIYAAGTTLNDVADVDEDAK--ERPDRPIPSGRVGRSEALSVGIILLVGGV 113
                                       446699999999999*******************************..88*************************** PP

                              UbiA  82 lllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgsl.sllalllalavfllt 156
                                       +++   ++ l  +l+++al+l+  +Y g  lK +++ g +  g a gl + lg  +++    + lall+ + v +++
  gi|313126405|ref|YP_004036675.1| 114 VVA-TVVGGLGPGLTAVALALAvALYDG-LLKGTPA-GFFAMGSARGLNVALGLSIAGVAAfDGLALLFPASVVVYV 187
                                       ***.9999999999999999999****8.9999999.*******************877654555666556666666 PP

                              UbiA 157 waialandlrdregDrkagiktlpvvl.Grkaarillalllavlllallllllalllllylllalllaalallraar 232
                                       +a+  +      e    +g    +v l G+ a++   a  ++v+     ++++   ++ + l+a+l+aa +l++ +r
  gi|313126405|ref|YP_004036675.1| 188 AALTRM-----AEAETGGGGDGSAVALtGAGATLA--A--MVVA-----VVVTVRGTPTAGLAATLVAAGFLAWDWR 250
                                       666666.....778866665556666637777776..4..2222.....3457899999999999999999999988 PP

                              UbiA 233 l 233
                                        
  gi|313126405|ref|YP_004036675.1| 251 A 251
                                       6 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.063
                              UbiA  74 ivllilgllll...alllnpltallgllalll 102
                                       + +++lg++ll   ++ +  +t++l+++a+++
  gi|313126405|ref|YP_004036675.1| 268 VGTCVLGIVLLdaaVAVIAGPTFVLAAAAFAI 299
                                       55666676666666555666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1777.20
//
Query:       gi|313126406|ref|YP_004036676.1|  [L=281]
Description: sugar phosphate isomerase/epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-41  140.7   0.4    1.2e-40  139.2   0.1    1.7  2  AP_endonuc_2    Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.061   13.1   0.1       0.54   10.0   0.0    2.6  3  AP_endonuc_2_N  AP endonuclease family 2 C terminus


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.1   1.3e-44   1.2e-40       2     210 .]      20     237 ..      19     237 .. 0.97
   2 ?   -0.7   0.0     0.086   7.7e+02       1      33 [.     243     274 ..     243     278 .. 0.64

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 1.3e-44
                                       HHHHHCT-SEEEEECCTCSHHHHC.HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC...........HTTCS.H CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel.sdeelrelrkaldelglriaslslftrfgypded...........erear.r 65 
                                       +++a++G++gvEl g++++ + +    +++++l+ al e++l ++ ++++t  gy d+              +++ r
  gi|313126406|ref|YP_004036676.1|  20 RRIAAHGYEGVELLGDTPHAYFPEfGADDAAALADALTETDLAVSNINANTATGYYDDAppssffepsviNPDPDlR 96 
                                       789*******************99*9*******************************99999988888776666699 PP

                                       HHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCH CS
                      AP_endonuc_2  66 eesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgde 142
                                       ++ v+++krai+la   Gap + l +G    +p+  ++ea+++l++sl +++dyae++gv +++E  ++  +e+  +
  gi|313126406|ref|YP_004036676.1|  97 AWRVEYIKRAIDLATSTGAPAVCLATG--RPLPGTLPDEAYQLLRDSLHDILDYAEPRGVDVGIEFEPELLIECT-D 170
                                       999************************..9*********************************************.* PP

                                       HHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 143 elarlldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGei 210
                                       e++ l+d+v+++n+gv+lD+gH+  ++ed+++ +++ a +i  vH+ D+ g + +g+++h+ +g+G++
  gi|313126406|ref|YP_004036676.1| 171 EVLTLIDDVGRDNLGVNLDIGHAAVYGEDLRESIEQSAGHITGVHLEDIAG-GIRGKHYHLVPGDGDL 237
                                       ***************************************************.899***********85 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.086
                                       HHHHHHCT-SEE...EEECCTCSHHHHCHHHHHHHH CS
                      AP_endonuc_2   1 laaaaeaGfdgv...Elfgrdlvpvselsdeelrel 33 
                                       ++a+ ++G+dg+   El++++++p      +++r++
  gi|313126406|ref|YP_004036676.1| 243 FDALDSIGYDGFvtlELYTYPDRPDE----AAARAF 274
                                       56777888887644488888888775....455555 PP

>> AP_endonuc_2_N  AP endonuclease family 2 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.21   1.9e+03       5      17 ..      18      30 ..      16      30 .. 0.83
   2 ?   -2.5   0.0      0.49   4.4e+03      30      41 ..      43      54 ..      42      60 .. 0.77
   3 ?   10.0   0.0     6e-05      0.54       1      21 [.     238     258 ..     238     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.21
                    AP_endonuc_2_N  5 ifsaLrqiGYdgp 17
                                       +++ ++ GY+g+
  gi|313126406|ref|YP_004036676.1| 18 AVRRIAAHGYEGV 30
                                      68899999**996 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.49
                    AP_endonuc_2_N 30 eeGareAvaflk 41
                                      e Ga +A+a+ +
  gi|313126406|ref|YP_004036676.1| 43 EFGADDAAALAD 54
                                      789999998755 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 6e-05
                    AP_endonuc_2_N   1 dwkdifsaLrqiGYdgplSiE 21 
                                       d++ +f aL +iGYdg + +E
  gi|313126406|ref|YP_004036676.1| 238 DFDVVFDALDSIGYDGFVTLE 258
                                       7999*************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1672.20
//
Query:       gi|313126407|ref|YP_004036677.1|  [L=618]
Description: ATP-dependent DNA ligase i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-47  162.2   0.0    1.8e-47  161.6   0.0    1.2  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    1.3e-35  123.3   0.0    2.3e-35  122.5   0.0    1.4  1  DNA_ligase_A_N  DNA ligase N terminus
    1.6e-17   63.9   0.0    5.2e-17   62.3   0.0    2.0  1  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
    2.1e-06   28.2   0.0    3.2e-06   27.6   0.0    1.3  1  RNA_ligase      RNA ligase
  ------ inclusion threshold ------
       0.88    7.7   6.3        1.2    7.2   6.3    1.1  1  Nop14           Nop14-like family


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.6   0.0     5e-51   1.8e-47       2     204 .]     287     487 ..     286     487 .. 0.93

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 5e-51
                                       EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEE........EETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTT CS
                    DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvh........kegdkvklfSRrlkditaakpelvkalkeafkkd 70 
                                       mLA+  + + +al++   +++ vE K+DG+R+qvh         +g++v+l+SR++ d+t+a+pe+v++++  ++  
  gi|313126407|ref|YP_004036677.1| 287 MLAQAGT-VTDALDEW--DEAAVERKFDGARVQVHvapddasaDDGEDVSLYSRNMDDVTDALPEIVEFVEDHVDV- 359
                                       8999888.899****8..45559************9888887558999**********************998876. PP

                                       ESEEEEEEEEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB- CS
                    DNA_ligase_A_M  71 eksvilDGElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilk 147
                                          vilDGE+vavd + g++lpfq++ +r+++k++v ++ +e+++ l +FD+L+ d e+l+d p+ eR + L e+l 
  gi|313126407|ref|YP_004036677.1| 360 --PVILDGEVVAVDDD-GAPLPFQEVLRRFRRKHDVGRMREEVRVELHAFDCLHADSEDLLDAPVTERHARLAEVL- 432
                                       ..49********9877.***********************************************************. PP

                                       -BTTTEEE--EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 148 esedrvelaeslevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                          d+  +++ l+ +d++e++++ e ++++g+EG+++Knpds+Y pg+r+knwlK K
  gi|313126407|ref|YP_004036677.1| 433 --ADTNAVSDLLVSEDADEIAAFEEASLDAGHEGIMLKNPDSTYSPGNRGKNWLKRK 487
                                       ..555567999********************************************88 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.5   0.0   6.4e-39   2.3e-35       2     173 .]       3     182 ..       2     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 6.4e-39
                                       CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT. CS
                    DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealg. 73 
                                       Fae+a+  ++ie+ ++++l+ +a+++++f     ag+ dl  ++r+    ++P++d+++++ig++ll++a+a+a+g 
  gi|313126407|ref|YP_004036677.1|   3 FAEFAARASEIEA-EPADLATVALVRDLF---CDAGD-DLPVVTRFvqgrVFPAWDSTTLDIGPRLLREAIARAAGq 74 
                                       9************.999************...44567.9*************************************6 PP

                                       .--HHHHHHHHHHHS-HHHHHHHHH...CCHHHH......------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHH CS
                    DNA_ligase_A_N  74 .lskkkikdalakvgDlgevaeevl...skrstl......akkspltieevnelLdklaaa.gkgsedekkkilkkl 139
                                        ++ ++++d+la++g++g+va+++    + +          +++ lt++ev+e+L++laaa g gsed+k ++l +l
  gi|313126407|ref|YP_004036677.1|  75 nVTADDVEDRLADAGEIGSVAAAYDfggQ-Q--GlaafsgGTNDGLTVNEVDETLRDLAAAsGPGSEDRKLNTLFGL 148
                                       666779**************888875332.2..235798888999*************9889*************** PP

                                       HHHS-HHHHHHHHHHHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 140 lkraspeEakyliriilkdlriglsektvldala 173
                                       ++ras++Eakyl+r++l+++rig++++tv+da a
  gi|313126407|ref|YP_004036677.1| 149 FNRASSSEAKYLARLVLGEMRIGVGAGTVRDAVA 182
                                       *******************************986 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   1.5e-20   5.2e-17       2      99 .]     508     600 ..     507     600 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.5e-20
                                       GGSEEEEEEEEEE...TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEES CS
                    DNA_ligase_A_C   2 gglvgslllgvyd...dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfa 75 
                                       ++++g++ll ++d   dg++ ++gkv+tG++d+el+el + l++   +      +  ++    v ++P++v+eV ++
  gi|313126407|ref|YP_004036677.1| 508 ANHLGTFLLSARDesgDGDYATIGKVATGITDEELAELSDLLEPEIVS------EDGQT----VELNPSVVFEVGYE 574
                                       6789**********99999***********************622222......22222....2289********** PP

                                       EEECTSSSTT..EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  76 eitasgkyka..slRfPrfkrlReDk 99 
                                       ei++s++y++  +lRfPrf+ +ReDk
  gi|313126407|ref|YP_004036677.1| 575 EIQRSPTYSSgyALRFPRFIAVREDK 600
                                       *************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   8.8e-10   3.2e-06       3     161 .]     304     487 ..     302     487 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 8.8e-10
                                       EEEEEE-SSEEEEEEEETT.........EEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES. CS
                        RNA_ligase   3 vvvtEKlDGtnfriylvke.........vgvasRsqilpfgeekfkefkrwaaalrkklkeklaneelilyGElig. 69 
                                         v+ K DG+++++++ ++         v + sR+ +           +    +  + ++++ +   +il GE++  
  gi|313126407|ref|YP_004036677.1| 304 AAVERKFDGARVQVHVAPDdasaddgedVSLYSRNMDD---------VTDALPEIVEFVEDHVD-VPVILDGEVVAv 370
                                       57999***********9753334444444444444333.........33333344445555555.58*********7 PP

                                       ..........SS..TTSS.....................EEEEEEEEEEECTTBECE--HHHHHHHHHCCTB..EEE CS
                        RNA_ligase  70 .........hsikygglpk....................efyvFdifdirdkeeqrylspdevealakglgtvpvly 117
                                                +        +                    e+ +Fd+++ +   +++ l+   +e +a+    + vl 
  gi|313126407|ref|YP_004036677.1| 371 dddgaplpfQ--------EvlrrfrrkhdvgrmreevrvELHAFDCLHAD---SEDLLDAPVTERHAR---LAEVLA 433
                                       7655444331........022334444577778888888********887...889999999999999...356665 PP

                                       EE.SS....HHHHHCCC....H.HHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                        RNA_ligase 118 egkfl....aaeellel..l.l.skgnkrEGlVikpeselyk.nkg.raifKvk 161
                                        +++      +e++ e+  + + s +   EG+ +k+++++y+  ++ ++++K k
  gi|313126407|ref|YP_004036677.1| 434 DTNAVsdllVSEDADEIaaFeEaSLDAGHEGIMLKNPDSTYSpGNRgKNWLKRK 487
                                       5555544444555555587334577889***************9999*****76 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.3   0.00034       1.2     361     402 ..     191     235 ..     139     277 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00034
                             Nop14 361 lveseseeee...eeeeedeeeeedeeeeeeeeededdlsdlese 402
                                          +ese++e   ++++ ++ +++d+ e+  +++d++d  d+ +e
  gi|313126407|ref|YP_004036677.1| 191 SATEESEDDEggpKDDDAEDRSKDDDAEDRPKDDDTEDTADDADE 235
                                       111122211111111111111112222221111111111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.38s 00:00:01.18 Elapsed: 00:00:00.55
# Mc/sec: 3409.25
//
Query:       gi|313126408|ref|YP_004036678.1|  [L=510]
Description: hypothetical protein Hbor_16650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 2758.35
//
Query:       gi|313126409|ref|YP_004036679.1|  [L=243]
Description: proteasome subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.7e-52  175.2   0.6    1.1e-51  175.0   0.6    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0   0.6   6.3e-56   1.1e-51       2     190 .]      47     226 ..      46     226 .. 0.96

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 6.3e-56
                                       HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                        Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                       k+Gtt+vG+k++dgvvla+d+ra+ g+++ s+++v+K+ +i+++ ++++aG+++ a+ l+r +rae++ly+ r g++
  gi|313126409|ref|YP_004036679.1|  47 KTGTTTVGLKTEDGVVLATDMRASLGHMV-SSKNVQKVEEIHPTGALTIAGSVSAAQSLIRSIRAEVRLYESRRGED 122
                                       89***************************.6666******************************************* PP

                                       TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHS CS
                        Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyk 155
                                       ++++     + ++l+++ +rsg   ++v+ +++g+d+eg  ++y+idp+Gs++ee+ ++++Gsgs++a ++le+ey+
  gi|313126409|ref|YP_004036679.1| 123 MSMQ-----ALSTLLGNFLRSGA-FYIVQPILGGFDDEG-AHIYSIDPAGSILEEE-YTVTGSGSQYALGVLEQEYS 191
                                       ****.....99999999999966.799*********998.7**************6.******************** PP

                                       TTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 156 edltleeavelavkalkealerdklsgknievavi 190
                                        dl+ eea+++a +a+k+a+erd +sg++i+v+v+
  gi|313126409|ref|YP_004036679.1| 192 NDLSIEEAKTTAARAIKSAVERDLASGNGINVCVV 226
                                       *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1448.80
//
Query:       gi|313126410|ref|YP_004036680.1|  [L=61]
Description: hypothetical protein Hbor_16670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 386.57
//
Query:       gi|313126411|ref|YP_004036681.1|  [L=122]
Description: hypothetical protein Hbor_16680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-44  150.2   0.1    2.2e-44  149.9   0.1    1.1  1  DUF555    Protein of unknown function (DUF555)


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.9   0.1   1.2e-48   2.2e-44       1     101 []       3     104 ..       3     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 149.9 bits;  conditional E-value: 1.2e-48
                            DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpe.ldfveievgetecPkcgeelesalvvadtalvglllemkv 76 
                                       +y v++eaaw+vrdv+++ddAig+A+seagkrln++  ++ve+evg t cP+cge+++sa+++adtalvgllle++v
  gi|313126411|ref|YP_004036681.1|   3 NYLVAMEAAWLVRDVEDIDDAIGVAVSEAGKRLNEKdKEYVEVEVGVTGCPACGEPFDSAFIAADTALVGLLLEIDV 79 
                                       79*********************************99**************************************** PP

                            DUF555  77 fnaeseEhaeriakseigkaledvP 101
                                       fna+ e ha+riakse+g al+dvP
  gi|313126411|ref|YP_004036681.1|  80 FNADGEKHASRIAKSEVGGALRDVP 104
                                       ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 743.19
//
Query:       gi|313126412|ref|YP_004036682.1|  [L=179]
Description: XRE family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-23   83.0   4.1    7.3e-15   55.2   0.3    2.4  2  CBS             CBS domain
    1.1e-11   44.7   0.1    1.7e-11   44.0   0.1    1.3  1  HTH_3           Helix-turn-helix
    1.7e-10   41.1   0.8    3.3e-10   40.2   0.8    1.4  1  HTH_31          Helix-turn-helix domain
    1.1e-06   28.6   0.0      2e-06   27.7   0.0    1.4  1  HTH_19          Helix-turn-helix domain
    6.8e-05   22.7   0.0    0.00014   21.7   0.0    1.5  1  HTH_37          Helix-turn-helix domain
      0.005   16.7   0.1      0.012   15.5   0.1    1.6  1  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.022   15.2   0.0    1.4  1  HTH_26          Cro/C1-type HTH DNA-binding domain
      0.017   15.2   0.0      0.029   14.5   0.0    1.3  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.04   13.9   0.0       0.12   12.3   0.0    1.8  1  HTH_Crp_2       Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.3   3.7e-18   7.3e-15       2      55 ..      67     119 ..      66     121 .. 0.95
   2 !   29.1   0.4   5.1e-10     1e-06       1      53 [.     128     177 ..     123     179 .] 0.91

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3.7e-18
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                        d+m+++vv+v+pd+++++a ++m ++g+s+lPV+  dg++vGi++  D+ r+ 
  gi|313126412|ref|YP_004036682.1|  67 DDLMNTNVVSVSPDDSVRDARDRMLDEGFSQLPVI-RDGRPVGIISNGDIRRVQ 119
                                       59*********************************.8*************9986 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 5.1e-10
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V+++m++ + tv p +tlee+   + ++ +s++++V e g+ vGi+t+ D++ 
  gi|313126412|ref|YP_004036682.1| 128 VAEVMREAITTVEPAATLEEIDSSL-DH-HSAVLIV-EGGQTVGIITEADIAA 177
                                       7889*********************.54.58999**.899***********85 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.1   8.5e-15   1.7e-11       1      49 [.       9      57 ..       9      61 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 8.5e-15
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49
                                      l+e+Rk+l+l+q  LAe++Gvs+  i+riE G+  P+l+tl ++ +aL+
  gi|313126412|ref|YP_004036682.1|  9 LRERRKELDLTQSTLAEMAGVSQPLIARIEGGDVDPRLSTLRRIVNALD 57
                                      89*********************************************97 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.8   1.7e-13   3.3e-10       6      56 ..       9      58 ..       7      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.7e-13
                            HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56
                                      Lr++R++  L+q  +Ae +gvs+  + r+E G  + p++++l+++++al+ 
  gi|313126412|ref|YP_004036682.1|  9 LRERRKELDLTQSTLAEMAGVSQPLIARIEGGDVD-PRLSTLRRIVNALDE 58
                                      9*********************************7.*************94 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     1e-09     2e-06       4      53 ..       9      57 ..       8      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1e-09
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53
                                      L+e R+el ltq  lae++g+s+  i+ iE+g   +p  ++l++i++al+
  gi|313126412|ref|YP_004036682.1|  9 LRERRKELDLTQSTLAEMAGVSQPLIARIEGGDV-DPRLSTLRRIVNALD 57
                                      8999****************************99.************997 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.2e-08   0.00014      23      72 ..       9      57 ..       6      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.2e-08
                                      HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHHHHHTT CS
                            HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnlltalG 72
                                      ++e +++++l+qs +a++ g++qP + r++ g+++  +l++L+++++al+
  gi|313126412|ref|YP_004036682.1|  9 LRERRKELDLTQSTLAEMAGVSQPLIARIEGGDVD-PRLSTLRRIVNALD 57
                                      68899*************************88887.59**********97 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.9e-06     0.012       2      36 ..       9      43 ..       8      46 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.9e-06
                                      HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  2 LraaRearglsleevaketkIrkdylealEeddfd 36
                                      Lr++R+++ l+   +a+   +++ ++ ++E +d+d
  gi|313126412|ref|YP_004036682.1|  9 LRERRKELDLTQSTLAEMAGVSQPLIARIEGGDVD 43
                                      9******************************9986 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.1e-05     0.022       2      51 ..       9      57 ..       8      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLg 51
                                      Lre  ++ ++t+s La+++g+s++ ++r+  g +  ++l+tL +i +aL+
  gi|313126412|ref|YP_004036682.1|  9 LRERRKELDLTQSTLAEMAGVSQPLIARIEGGDV-DPRLSTLRRIVNALD 57
                                      889999999************************6.***********9997 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-05     0.029      71     115 ..       6      50 ..       2      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                    MqsA_antitoxin  71 pafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvk 115
                                       p+++++ rk+l+l+q+ +ae+ G+     +r e G v p l++++
  gi|313126412|ref|YP_004036682.1|   6 PHDLRERRKELDLTQSTLAEMAGVSQPLIARIEGGDVDPRLSTLR 50 
                                       7788899*********************************99875 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.2e-05      0.12      17      40 ..      13      36 ..       2      38 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
                                      EEEEEHHHHHHHHHTTSSHHHHHH CS
                         HTH_Crp_2 17 eielpltqeelAsmlGltretvsr 40
                                      + el+ltq  lA+m G+++  + r
  gi|313126412|ref|YP_004036682.1| 13 RKELDLTQSTLAEMAGVSQPLIAR 36
                                      458***************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.35s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1091.70
//
Query:       gi|313126413|ref|YP_004036683.1|  [L=95]
Description: hypothetical protein Hbor_16700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.02   14.8   2.8       0.02   14.8   2.8    1.8  2  DUF3084    Protein of unknown function (DUF3084)
        2.9    6.6   8.3        3.4    6.4   8.3    1.0  1  LptF_LptG  Lipopolysaccharide export system permease LptF/Lpt
        7.5    6.2   9.1        2.8    7.6   6.5    1.4  1  Wzy_C      O-Antigen ligase


Domain annotation for each model (and alignments):
>> DUF3084  Protein of unknown function (DUF3084)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   2.8   3.4e-06      0.02      32      71 ..      21      60 ..       8      66 .. 0.88
   2 ?    0.4   0.2      0.11   6.4e+02      43      72 ..      58      86 ..      54      90 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-06
                           DUF3084 32 slFgLRPkkTavlvtiltGvliaaltlavllllseelrea 71
                                       l  +RP + a l+t l G+ +a++t+  l++   ++r +
  gi|313126413|ref|YP_004036683.1| 21 ALLFIRPNRAASLLTFLVGIGVAVVTFLYLTTGVATARVV 60
                                      56779*************************9988888865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                           DUF3084 43 vlvtiltGvliaaltlavl.lllseelreal 72
                                       +v++  G+ i+ +   +l ++ s++lr+a+
  gi|313126413|ref|YP_004036683.1| 58 RVVAV--GLWITGIGGLLLaAAGSSSLRSAV 86
                                      44444..555554443333034456666665 PP

>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   8.3   0.00057       3.4     282     349 ..      13      76 ..       3      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00057
                         LptF_LptG 282 clvfaliaaplglvkrrggrglrlliaillfvlyyvllslgkalaengvlppilaawlpnilflllgl 349
                                       + +++ + a l ++++r    l +l++i+++v+ ++ l++g a a+   +  +++ w+  i  lll++
  gi|313126413|ref|YP_004036683.1|  13 VPLAVAVVALLFIRPNRAASLLTFLVGIGVAVVTFLYLTTGVATARV--V--AVGLWITGIGGLLLAA 76 
                                       34444455557777788888888888888888888888888888887..3..6799999998888876 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.5   0.00047       2.8      14      60 ..       5      51 ..       3      64 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00047
                             Wzy_C 14 tsRsgiigllvalivlliifykrripfllllgilvgvilli.ilfvls 60
                                      +s + ++ +++a+ v+ ++f+++ ++  ll  +lvg+ +++ ++++l 
  gi|313126413|ref|YP_004036683.1|  5 YSAVDLVLVPLAVAVVALLFIRPNRAASLLT-FLVGIGVAVvTFLYLT 51
                                      56777889999**************333333.4444443330333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 598.47
//
Query:       gi|313126414|ref|YP_004036684.1|  [L=432]
Description: cytochrome p450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-78  263.2   0.0    5.4e-78  262.8   0.0    1.1  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.8   0.0     3e-82   5.4e-78       1     445 [.       6     412 ..       6     426 .. 0.89

  Alignments for each domain:
  == domain 1  score: 262.8 bits;  conditional E-value: 3e-82
                                       --SESEHHCCHCHHHHTTTCCHHHHHHHHHHHH-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHH CS
                              p450   1 Ppgptplplvgnllqlgrkeelhevlrklqkkygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallat 77 
                                       Pp p  lp++gn + ++  + ++++++++  ++g++ rl + +++  ++ +p++++++l++++++f+++ +++ la 
  gi|313126414|ref|YP_004036684.1|   6 PPTPGGLPVLGNTVAFA--RDPFSFIDSAVTTHGDVIRLSMLGRDRYIVAHPDLFERALVTDRDAFVKT-EDFRLA- 78 
                                       88899************..78*****************************************9999886.555555. PP

                                       HHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHH CS
                              p450  78 srkpfkgkgvlfangekwkklRrfltptltsfgklsleelveeeaedlveklrkkagesselditellskaaldvig 154
                                             g +vl  +g++w+++R++l p +++ ++  + + + ++a++  e + + ++ s     +e +   ++d++g
  gi|313126414|ref|YP_004036684.1|  79 -----FGDSVLAVDGDEWREQRDLLDPFFFFRQITDYIPKMRKQADRRAESWTPGQTYS----AVEEMKGLTFDILG 146
                                       .....79**********************999666899999999999999998877777....9************* PP

                                       HHHHSSHHHTTTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCH CS
                              p450 155 silFgarfdlledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerretl 231
                                       s+l+g   +  ++  + +l +a ++l+  ++ +s   + l+     lpt+ +r++++av +l + +d       + l
  gi|313126414|ref|YP_004036684.1| 147 STLLGQDPG-KRSG-DDSLRRAADDLNAYFAPTS---WALPG---SLPTPSRRRFNRAVTTLREEVD-------RLL 208
                                       ******988.5555.559********99997766...33333...258**********666665555.......555 PP

                                       CHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCC CS
                              p450 232 dsakksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlg 308
                                         + +s  d+l++l +a+  ++g    s++ +  ++  ++faG++Tt+ +l+++ y+L ++P+v e++ +Eidev+g
  gi|313126414|ref|YP_004036684.1| 209 AAD-HSGDDLLSVLAEAR-GEEGY-PRSETAVSDQLVGIIFAGHETTALALTYTWYLLSEHPSVRERVEHEIDEVVG 282
                                       555.5788*********8.55555.889************************************************* PP

                                       TTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--G CS
                              p450 309 dkreptyddlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdp 385
                                       d +++  ++l++l++l+ vikE+LR +p+++ +lpR +t++++++gy+ip+G+ev++++  +hrd+ +f++P++Fdp
  gi|313126414|ref|YP_004036684.1| 283 D-DPVGAEHLSDLTVLERVIKESLRVYPPIH-TLPRTTTREIELGGYSIPEGSEVLLSVRNVHRDERFFEHPDQFDP 357
                                       *.59***************************.********************************************* PP

                                       GGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSGGE CS
                              p450 386 eRFldekgnskrksfaflPFGaGpRnCiGerlArmelklflatlLqnFevelqpetdppp 445
                                       +R++++++    +++a++PFGaGpR CiG+ +A+ e k +l+ l++++++e   ++ + +
  gi|313126414|ref|YP_004036684.1| 358 DRWERNDA----PEYAYVPFGAGPRRCIGQSFAMIEAKTALTELMKRYRLEW-AGNGELD 412
                                       ******76....89************************************97.4455444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3054.85
//
Query:       gi|313126415|ref|YP_004036685.1|  [L=334]
Description: phosphoribosylformylglycinamidine cyclo-ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-23   83.5   0.0    2.9e-23   82.7   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    2.7e-14   53.6   2.7    5.3e-14   52.7   2.7    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.0   3.3e-27   2.9e-23       2     153 ..     174     329 ..     173     331 .. 0.91

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 3.3e-27
                                       TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT......TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHH CS
                            AIRS_C   2 pGdvliltgslGlggagtslkrkileeegldds......avqlgdvlleptliyvkralaalkglvkaahDvTgGGL 72 
                                        Gd+l++  s+G++++g+ l+r+  +++++  +       + +g++llept+iy +++ ++++++v+aa++vTgGG 
  gi|313126415|ref|YP_004036685.1| 174 SGDALVGFRSSGIHSNGLTLARTATTRDHEYTDdcpfegYETIGEALLEPTRIYTNLLDPMREHGVNAAAHVTGGGW 250
                                       7**************************9998779****6666********************************886 PP

                                       HHHHHHHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEE CS
                            AIRS_C  73 lgalaemapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGe 144
                                         +l +m + +   +e  +d  p+f+ ++     s++em++++n+G ++va+ +++++++la ++     + +vIG+
  gi|313126415|ref|YP_004036685.1| 251 -TNLERMGDFH-YVVEDAFDPHPVFEFVQsegnvSDEEMHRTFNMGTGFVAALAPDDAEALADAT-----DGRVIGH 320
                                       .68****9997.77777777999999999999*************************99999999.....4789*** PP

                                       EEESSSEEE CS
                            AIRS_C 145 vtakeelsv 153
                                       v+++ ++s+
  gi|313126415|ref|YP_004036685.1| 321 VEDGSGVSI 329
                                       ***998876 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   2.7   5.9e-18   5.3e-14       5      93 ..      60     161 ..      22     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 5.9e-18
                                       EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvp 72 
                                       ++++td+++++++v++  +    +G  ++a+n++Dl+a G rP+a++++la+       +e+v +gl+ +ae+++++
  gi|313126415|ref|YP_004036685.1|  60 LALATDGVGTKLIVAEALGdystVGIDCIAMNANDLVAAGVRPVAFVDYLAVDepderFAEQVGEGLSVGAERADIE 136
                                       599***********887777888***********************************9****************** PP

                                       EEEEEEEEESS....EEEEEEEEEE CS
                              AIRS  73 lvgGdtsfsne....ptisvtavGl 93 
                                       lvgG+t++++e    + ++ t+ Gl
  gi|313126415|ref|YP_004036685.1| 137 LVGGETAVMPEvikgLDLAGTCAGL 161
                                       *********9999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2169.09
//
Query:       gi|313126416|ref|YP_004036686.1|  [L=82]
Description: hypothetical protein Hbor_16730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 518.75
//
Query:       gi|313126417|ref|YP_004036687.1|  [L=212]
Description: peptidase m50 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-05   22.4  12.3       0.02   14.2   0.3    3.0  2  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
      0.035   13.8   1.6      0.045   13.4   0.2    1.8  2  Tmemb_185A     Transmembrane Fragile-X-F protein


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   6.7     5e-05      0.45       6     106 ..      59     139 ..      52     159 .. 0.82
   2 !   14.2   0.3   2.2e-06      0.02     197     219 ..     162     184 ..     150     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   6 lgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkk 82 
                                        gi  ++HEl+H +vA ++g  v ef   +G   l++   ++  +i + p G  V  +g+  ++e            
  gi|313126417|ref|YP_004036687.1|  59 AGIGFLLHELAHKVVAVRFGQ-VAEFRADYGMLFLAVM-SSLAGFIFAAP-G-AVYHRGMLTDRE------------ 119
                                       5777899*************6.7799999977666655.55666688899.5.599999996655............ PP

                                       XXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  83 spwqrllivlAGplanfilailvf 106
                                             li+lAGp++n+ la l++
  gi|313126417|ref|YP_004036687.1| 120 ----HGLIALAGPVTNLALAALFL 139
                                       ....99**************9986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 197 lisvnLgilNLlPipvLDGghll 219
                                        i++ L+ +N+lP+ +LDG  ++
  gi|313126417|ref|YP_004036687.1| 162 TINLFLAAFNMLPFGALDGKTVI 184
                                       79*****************8875 PP

>> Tmemb_185A  Transmembrane Fragile-X-F protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.18   1.6e+03     233     249 ..     127     143 ..      88     146 .. 0.67
   2 ?   13.4   0.2   5.1e-06     0.045      50     101 ..     156     207 ..     150     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.18
                        Tmemb_185A 233 aaakeipiavvfiPLfl 249
                                        ++ ++++a++f+P++l
  gi|313126417|ref|YP_004036687.1| 127 GPVTNLALAALFLPVLL 143
                                       55777777777777765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.1e-06
                        Tmemb_185A  50 apfkavlitllllafelLlciklestyvklsaalswkivflPllalevvslv 101
                                       + f+ v+i l+l af +L +  l+ ++v  +++  +++vf+P+l+l ++ ++
  gi|313126417|ref|YP_004036687.1| 156 VGFRGVTINLFLAAFNMLPFGALDGKTVISWSKGVFAVVFIPSLLLTLALVF 207
                                       67899***********************8899999*********99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1329.58
//
Query:       gi|313126418|ref|YP_004036688.1|  [L=555]
Description: hypothetical protein Hbor_16750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-29  101.5   0.0    6.8e-16   58.9   0.0    2.2  2  TraB      TraB family
  ------ inclusion threshold ------
       0.12   12.6   0.2          4    7.6   0.0    2.5  2  DUF2371   Uncharacterised conserved protein (DUF2371)
       0.18   12.1   0.5          2    8.7   0.1    2.7  2  COX7C     Cytochrome c oxidase subunit VIIc


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   1.1e-19   6.8e-16       9     155 ..       9     143 ..       2     152 .. 0.88
   2 !   40.2   0.0   5.8e-14   3.5e-10     159     253 ..     277     356 ..     265     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.1e-19
                              TraB   9 gttsyLfGTiHvskksvyplspeveealeksdtvvvEldlsdd..tdeatqkelaklkllpdgktlsdllseelyar 83 
                                       g+ + ++GT+Hvs++sv +++++v e  e++d+v+vEld+ ++   +  + +++   +ll  g+t+ +++   +++ 
  gi|313126418|ref|YP_004036688.1|   9 GR-VRVVGTAHVSEDSVREVEDVVAE--ERPDVVAVELDEGRYrqMKGGAPDDIEPGDLLR-GNTVFQFIAYWMLSY 81 
                                       44.689********************..9***********999755555667777788887.*************** PP

                              TraB  84 lqkalakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlsll 155
                                       +q+ l + ++++      +P  +a +l++ e  ++k g+d +lvDr++++t++r + +++ +E+++ + +l 
  gi|313126418|ref|YP_004036688.1|  82 VQAQLGE-KFDV------EP--GADMLAAVET-AEKFGIDVALVDRDINETMRRFWSQMSLIEKLKMVGGLA 143
                                       *******.9***......**..*********8.69******************************9876665 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 5.8e-14
                              TraB 159 pdeeqlealeetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieallkepgsv 235
                                       pd++++e+ e ++d + +++d ++ ++e              e++e +p   ++l+deR+++ a+++ al +++ +v
  gi|313126418|ref|YP_004036688.1| 277 PDDDVEEMEELDIDSM-TDTDVVSAMME--------------EFREFSPGGAQALIDERDAYIAHRLVALRQSGHHV 338
                                       4555555555555333.35666777777..............9*************************988999*** PP

                              TraB 236 fvaVGagHlaGedgvlal 253
                                       +++VGagH  G++ +l++
  gi|313126418|ref|YP_004036688.1| 339 VAVVGAGHREGIERYLKY 356
                                       ***********9998876 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00067         4      82     115 ..     114     147 ..      69     159 .. 0.75
   2 ?    2.3   0.1     0.028   1.7e+02      99     124 ..     241     266 ..     231     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00067
                           DUF2371  82 essseklgllarfleqylysdklkvlGPlimGiG 115
                                        ++++   ++ rf +q    +klk++G l  G+G
  gi|313126418|ref|YP_004036688.1| 114 LVDRDINETMRRFWSQMSLIEKLKMVGGLAFGLG 147
                                       45566678899*********************98 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.028
                           DUF2371  99 lysdklkvlGPlimGiGiflfiCana 124
                                       l s  ++ +G l++G+G+ l++ + a
  gi|313126418|ref|YP_004036688.1| 241 LSSFAVRTVGSLTLGVGVGLLLAGLA 266
                                       567778999*********99987765 PP

>> COX7C  Cytochrome c oxidase subunit VIIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00034         2      40      58 ..     222     240 ..     203     255 .. 0.81
   2 ?    0.2   0.0      0.15   9.1e+02      24      49 ..     369     394 ..     359     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHHHHHHHHHH CS
                             COX7C  40 avkywgflgvgFalPFlav 58 
                                       a+ ++g +g+g+a+PF+a+
  gi|313126418|ref|YP_004036688.1| 222 AAGIIGGFGLGLAAPFIAS 240
                                       45899************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                                       STTTSSSS--SSHHHHHHHHHHHHHH CS
                             COX7C  24 gpysnLPFsknnKipfavkywgflgv 49 
                                       +p s LP+ k   ++ ++ +++f+g+
  gi|313126418|ref|YP_004036688.1| 369 TPSSGLPWAKIVGTGISAAVVVFFGL 394
                                       49999***777788888888999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3865.29
//
Query:       gi|313126419|ref|YP_004036689.1|  [L=454]
Description: glycerate 2-kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-76  254.7   0.7    1.2e-75  254.0   0.7    1.3  1  DUF4147   Domain of unknown function (DUF4147)
    6.4e-31  106.8   3.0    1.5e-30  105.5   3.0    1.7  1  MOFRL     MOFRL family


Domain annotation for each model (and alignments):
>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.0   0.7   1.4e-79   1.2e-75       2     229 .]      18     251 ..      17     251 .. 0.95

  Alignments for each domain:
  == domain 1  score: 254.0 bits;  conditional E-value: 1.4e-79
                                       HHHHHHHHHHTTSHHHHHHTTHHHH--..............-SEEEEEESTTHHHHHHHHH....HHHGEEEEEEET CS
                           DUF4147   2 lraifeaaveavdpeklvkralslkee.......eldlskkkrvvvvgaGKAaaamaaalee...ealksgvvvvkk 68 
                                       + ++++ +v+av p+++v++a+sl+++       ++dls+++r++v+g GKA  ++a ale+   +++++g vv+++
  gi|313126419|ref|YP_004036689.1|  18 ALKCLSDGVNAVLPDRIVRDAVSLNDNtlsvaeaTYDLSAFDRILVIGGGKAGDGVADALETvlgDRIDGGAVVTPE 94 
                                       578999****************9955556667779**************************99998999******85 PP

                                       T-----TT-EEEEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHC CS
                           DUF4147  69 ghaeekerievleaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlas 145
                                          ++ +ri+ l +ahp+P+e +ve+a +i++l++++++++lvl++++GG+SA+++ Pa+gi+l+d+q++t+aLl+s
  gi|313126419|ref|YP_004036689.1|  95 P--TSGDRIDRLPGAHPVPSETGVESAARIVDLLSETDDRTLVLAVVTGGASAVIPTPADGISLADLQTTTDALLRS 169
                                       5..57899********************************************************************* PP

                                       T--HHHHHHHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT---..-H CS
                           DUF4147 146 GasIqelNtVRkhlsaikGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalailekykleeklpe 222
                                       Ga+I elN+VRkhls++kGG+Lar+aapa+v+ L+ SDVvg+dl+vIASGPt+pd++t++dal++l++y+l+  +pe
  gi|313126419|ref|YP_004036689.1| 170 GAHIGELNAVRKHLSTLKGGGLARLAAPATVIGLVFSDVVGNDLSVIASGPTAPDETTYDDALSVLDRYGLD--VPE 244
                                       ***********************************************************************9..9** PP

                                       HHHHHH. CS
                           DUF4147 223 svrelLe 229
                                       svr+ Le
  gi|313126419|ref|YP_004036689.1| 245 SVRSRLE 251
                                       ***9986 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   3.0   1.7e-34   1.5e-30       2     109 .]     335     436 ..     334     436 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 1.7e-34
                                       EEEEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT--H CS
                             MOFRL   2 vllsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaaglda 78 
                                       v+l+gGE+tvtv+g+G GG+n e++l++a+el+     +++v++++++DG DG t++aGaivd++t+++a++ + +a
  gi|313126419|ref|YP_004036689.1| 335 VILTGGECTVTVRGDGDGGPNLEYCLSAARELD-----TDAVVAAIDSDGEDGGTTVAGAIVDSRTVDDASD-ESEA 405
                                       89****************************544.....6799***************************998.699* PP

                                       HHHHHTT-HHHHHHHTT-EE-----S----E CS
                             MOFRL  79 keaLanndsyeffeklgallktgpTgtNVnD 109
                                       ++ La+nds +f+++ + l++tgpTgtNVnD
  gi|313126419|ref|YP_004036689.1| 406 AASLAENDSLSFLRDRKCLIRTGPTGTNVND 436
                                       ******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.66
# Mc/sec: 2081.32
//
Query:       gi|313126420|ref|YP_004036690.1|  [L=202]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-14   52.0   0.8    9.7e-14   51.2   0.8    1.4  1  HTH_20    Helix-turn-helix domain
      2e-05   24.4   0.1    4.1e-05   23.4   0.1    1.5  1  MarR_2    MarR family
    8.8e-05   22.0   0.0    0.00046   19.7   0.0    2.1  1  HTH_24    Winged helix-turn-helix DNA-binding
     0.0073   16.2   0.0      0.018   14.9   0.0    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.037   13.9   0.0      0.062   13.2   0.0    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
      0.056   13.9   0.2       0.85   10.2   0.0    2.2  2  HTH_27    Winged helix DNA-binding domain
        1.1    9.4   7.9       0.34   11.1   2.8    2.6  3  DprA_WH   DprA winged helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.8   3.8e-17   9.7e-14       1      58 [.      28      84 ..      28      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 3.8e-17
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      d++++AL++ + rril+ L  ++++ a++la+++d+s +++ yHL  Leeag+vevv+
  gi|313126420|ref|YP_004036690.1| 28 DDLLSALSSGTARRILADL-HEDPANAAALADTVDTSLQNVQYHLGRLEEAGAVEVVD 84
                                      6899***************.************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.6e-08   4.1e-05       4      54 ..      36      83 ..      32      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +++ +r+La L+  p    ++++la++ + s ++v+++l rL++aG ve +
  gi|313126420|ref|YP_004036690.1| 36 SGTARRILADLHEDP---ANAAALADTVDTSLQNVQYHLGRLEEAGAVEVV 83
                                      5899*******9998...6*****************************987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.8e-07   0.00046       6      47 ..      40      80 ..      35      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
                            HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      r+IL  L ++   + + LA+ ++ S+++v ++l rLee+G +
  gi|313126420|ref|YP_004036690.1| 40 RRILADLHED-PANAAALADTVDTSLQNVQYHLGRLEEAGAV 80
                                      5666666664.478899***********************77 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   6.9e-06     0.018      18      58 ..      46      86 ..      41     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.9e-06
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      l ++pa+a  +a  ++ + ++v+  L +Le++G Ve+++  
  gi|313126420|ref|YP_004036690.1| 46 LHEDPANAAALADTVDTSLQNVQYHLGRLEEAGAVEVVDTV 86
                                      5689********************************98644 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.062       3      46 ..      38      81 ..      36      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      t ++IL  L e ++ +  la+ ++ s  +v +HL +L+eaG Ve
  gi|313126420|ref|YP_004036690.1| 38 TARRILADLHEDPANAAALADTVDTSLQNVQYHLGRLEEAGAVE 81
                                      67899999*********************************886 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00033      0.85      16      48 ..      48      80 ..      39     102 .. 0.77
   2 ?    1.5   0.0      0.16   4.2e+02      28      48 ..     109     131 ..     104     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00033
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                      ++++ +a+l+++++++ +++ y l +L+e+G v
  gi|313126420|ref|YP_004036690.1| 48 EDPANAAALADTVDTSLQNVQYHLGRLEEAGAV 80
                                      689999************************766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                            HTH_27  28 lnvedshis.yslkkLtek.GLv 48 
                                        ++e +++  ++l++L ++ G+v
  gi|313126420|ref|YP_004036690.1| 109 ADREGTTGLmSALRRLLAAvGVV 131
                                       6889999999******9987777 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.8   0.00013      0.34       9      56 ..      34      81 ..      10      83 .. 0.91
   2 ?   -2.7   0.0       2.6   6.8e+03      13      22 ..     120     129 ..     111     132 .. 0.76
   3 ?   -2.8   0.1       2.8   7.2e+03      27      40 ..     166     179 ..     162     181 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                           DprA_WH  9 plddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                       +++++rr+La L  +P    +L+  +  + + v+ +L  LE aG ve
  gi|313126420|ref|YP_004036690.1| 34 LSSGTARRILADLHEDPANAAALADTVDTSLQNVQYHLGRLEEAGAVE 81
                                      45899*************************************999886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                           DprA_WH  13 lerrvLaaLg 22 
                                         rr+Laa+g
  gi|313126420|ref|YP_004036690.1| 120 ALRRLLAAVG 129
                                       5688888876 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.8
                           DprA_WH  27 hvDqLvrrtglpaa 40 
                                       + D+ + ++glp++
  gi|313126420|ref|YP_004036690.1| 166 ASDTAATAAGLPPG 179
                                       55666677788776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1220.50
//
Query:       gi|313126421|ref|YP_004036691.1|  [L=155]
Description: hypothetical protein Hbor_16780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-38  129.7   0.0    5.3e-38  129.6   0.0    1.0  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   0.0   2.9e-42   5.3e-38       5     127 ..      12     137 ..       6     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 2.9e-42
                                       EEEETTT.TEEEEEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETTE CS
                       DNase-RNase   5 ialdass.qspvvlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdledgt 80 
                                       + +da+  + p+v+L+ +++  +lpI+i + +aqai+lal ge+++RPlthDLl+++++++g+ +++++I+dl dgt
  gi|313126421|ref|YP_004036691.1|  12 VGVDAEGgSVPAVILEVRQE--FLPIVITSDQAQAIQLALTGEPFERPLTHDLLVDMITEFGGAIDSIRIDDLTDGT 86 
                                       4477777569*****99985..6****************************************************** PP

                                       EEEEEEEEET.---....EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH-EE CS
                       DNase-RNase  81 fyAelvlrke.eee....leidaRpSDaiaLAlrtgapIyveeevleeasie 127
                                       f+A++  ++  +      + +daRpSD++aLA+r+++pI+v++evl+ea+ +
  gi|313126421|ref|YP_004036691.1|  87 FFAKIDAERYeN-GepkkFVFDARPSDSVALAVRVDCPILVSDEVLDEAGQP 137
                                       ********9753.24778*******************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 939.38
//
Query:       gi|313126422|ref|YP_004036692.1|  [L=153]
Description: hypothetical protein Hbor_16790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 934.05
//
Query:       gi|313126423|ref|YP_004036693.1|  [L=198]
Description: hypothetical protein Hbor_16800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1273.12
//
Query:       gi|313126424|ref|YP_004036694.1|  [L=1044]
Description: isoleucyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.6e-184  613.4   0.1   4.9e-184  612.9   0.1    1.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.1e-28  100.2   0.4      2e-28   99.2   0.4    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
    4.1e-28   98.2   0.0    2.1e-10   39.9   0.0    4.0  3  tRNA-synt_1g   tRNA synthetases class I (M)
    0.00073   18.5   0.0      0.025   13.5   0.0    2.6  2  tRNA-synt_1f   tRNA synthetases class I (K)
     0.0017   17.7   0.0     0.0057   16.0   0.0    1.9  1  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
     0.0036   16.8   0.0      0.015   14.9   0.0    2.0  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
      0.033   14.1   0.3       0.09   12.7   0.3    1.8  1  zf-FPG_IleRS   Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  612.9   0.1  1.9e-187  4.9e-184       4     600 ..      19     635 ..      17     637 .. 0.96

  Alignments for each domain:
  == domain 1  score: 612.9 bits;  conditional E-value: 1.9e-187
                       tRNA-synt_1   4 ekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv 80 
                                       + W+ee+++++++e++ + + f +vdgPPy  G++H+G a++ktlkd +irykrm+G++v+ +pG+D++Gl+ie kv
  gi|313126424|ref|YP_004036694.1|  19 DYWDEENAYEATKEAHADDPAFFFVDGPPYTSGQMHLGTAWNKTLKDAIIRYKRMTGHRVTDRPGYDMHGLPIEVKV 95 
                                       57*************************************************************************** PP

                       tRNA-synt_1  81 ekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliy 157
                                       e++lg + k++ +++g+e f++++++++++  e + ++++ +Gv++D+d++y+Tl++e++ea +++f ++ad+gl+ 
  gi|313126424|ref|YP_004036694.1|  96 EEELGFETKRDIEEYGMESFIDECKSFAERNREAMDDDFQSIGVWMDWDDPYKTLSPEYMEAAWWAFDQVADRGLVE 172
                                       ***************************************************************************** PP

                       tRNA-synt_1 158 rgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv....... 227
                                       rgk+ vn++++++ta++  Evey + ++++i+v+fpl+d e  +lvi+TTtP+T++++t vav+ e+ y        
  gi|313126424|ref|YP_004036694.1| 173 RGKRSVNYCPRCQTAIAANEVEYDEIDSPSIYVKFPLEDREG-SLVIWTTTPWTIPANTFVAVDGEMTYQavraekg 248
                                       ******************************************.**************************99999877 PP

                       tRNA-synt_1 228 itkeklilaeallkslvkke..sekkiledergkeLegkevelpl.........vnrkipiiaddyvdkeaGtGvVk 293
                                        + e l lae  ++ ++kk   ++++++e+  g+e++g e+ +pl          + +  + + +yv+++  tG+V+
  gi|313126424|ref|YP_004036694.1| 249 GESEVLYLAEPCVEDVLKKGryEDYEVVEELSGEEMVGWEYDNPLaghlneyadFEGAGEVYTAEYVEADR-TGLVH 324
                                       7788999***********9986667*************************9988888999********997.***** PP

                       tRNA-synt_1 294 iaPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskk 370
                                        aP+h+++D++ g++ +l+v +++d  g++te+a++++g  v da+  ++e+l++ g ll++ +++h +++c+r ++
  gi|313126424|ref|YP_004036694.1| 325 SAPGHGQEDFARGQDLGLDVFVPVDGRGEFTEQAGDYAGTFVRDANPDIIEDLEADGSLLHSGEHSHRYGHCWRCDT 401
                                       ***************************************************************************** PP

                       tRNA-synt_1 371 piiyrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvre 446
                                        ii+ at+qWf+ v++++d++l+++e+ ++ p++ +++r+ +++++++dW+iSRqr+WG ++p++ s++ e+ +v+ 
  gi|313126424|ref|YP_004036694.1| 402 DIIFLATDQWFITVTDVKDELLDNIEDSEWHPQWaRDNRFRDFVADAPDWNISRQRYWGIPLPIWESEDGEDFIVVG 478
                                       **********************************999**************************************99 PP

                       tRNA-synt_1 447 elkelvagreeeea.ekkalekeakdkl..kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadml 520
                                         +el++   ++ +  + +l++ ++d l   ++  ++e+++dv+DvW +S+  + +tl+yp + ++++++ +pad++
  gi|313126424|ref|YP_004036694.1| 479 TREELAERADQDVDpGELDLHRPSVDPLtiTEDGTTYERVPDVFDVWIDSSVATWGTLDYPGN-ETDFEELWPADLI 554
                                       888887765555441577899999**9977778889**************************9.99*********** PP

                       tRNA-synt_1 521 leGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvg 596
                                       +e  D++rgW+ + + +++a +g+ P++evl+hg+  de+GrKmSKslgN++ p++ i++ g d lR +l+   ++g
  gi|313126424|ref|YP_004036694.1| 555 VEAHDQTRGWFWSQLGMGTAARGEIPYEEVLMHGFANDENGRKMSKSLGNIVTPEEAIDRAGRDPLRAYLLsHDQQG 631
                                       **********************************************************************9566666 PP

                       tRNA-synt_1 597 rdin 600
                                        d++
  gi|313126424|ref|YP_004036694.1| 632 VDLS 635
                                       6666 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.4   7.9e-32     2e-28       1     150 [.     683     830 ..     683     833 .. 0.92

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 7.9e-32
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       d w+ls+l+ + ++v +a ++y+ ++a++a+ +f+++d++++y++++++r++ e+++++++ a+++l++vl++ ++l
  gi|313126424|ref|YP_004036694.1| 683 DEWVLSRLQTVKADVADAWDDYEVHDALNAILDFVTEDVSRFYVKAIRERMWEEEDSESKRgAYATLATVLNETVQL 759
                                       89***************************************************999888888*************** PP

                       Anticodon_1  77 laPfmPfitEelwqreeeel.gkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsselkv 150
                                       +aPf+P+++E ++q    +l g++++++  ++p  +e + ++el e+ +++l+++ +a+ ++r++ + k +++++ 
  gi|313126424|ref|YP_004036694.1| 760 IAPFTPYVAERMYQ----HLdGSETTVHALDYPTVDEAWrDEEL-ERNMAVLRNVEEAAANARQQGERKLRWPVQR 830
                                       *************5....4447789999999**96667888888.99******************99999999654 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   8.3e-14   2.1e-10       8     136 ..      47     194 ..      42     196 .. 0.82
   2 !   17.2   0.0   6.7e-07    0.0017     168     239 ..     395     468 ..     375     477 .. 0.86
   3 !   34.9   0.0   2.7e-12     7e-09     244     373 ..     521     643 ..     501     649 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 8.3e-14
                                       B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT............TS.....-HHHHH CS
                      tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke............gv.....tpeelv 67 
                                       pY++g++HlG + +    D+++Rykr++g+ v+   g D+hG pie+k e+e            g+     + + ++
  gi|313126424|ref|YP_004036694.1|  47 PYTSGQMHLGTAWNKTLKDAIIRYKRMTGHRVTDRPGYDMHGLPIEVKVEEElgfetkrdieeyGMesfidECKSFA 123
                                       8************99999******************************98754332222222112222222346678 PP

                                       HHHHHHHHHHHHHTT-..--SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                      tRNA-synt_1g  68 ekvheeikelfkklni..sfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                       e+++e+++++f+++++   +d+ ++t s e  e++   f ++ ++gl+++++ ++ ycp++++ ++  +ve
  gi|313126424|ref|YP_004036694.1| 124 ERNREAMDDDFQSIGVwmDWDDPYKTLSPEYMEAAWWAFDQVADRGLVERGKRSVNYCPRCQTAIAANEVE 194
                                       88999999*****99733678999**************************************998877775 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6.7e-07
                                       .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET...T CS
                      tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP...g 239
                                       ++  +++  ++  t+++f  + +++++l + ie +e + +    +  ++++ +   d++isr+  wGip+P    
  gi|313126424|ref|YP_004036694.1| 395 HCWRCDTDIIFLATDQWFITVTDVKDELLDNIEDSEWHPQWARDNRFRDFVAD-APDWNISRQRYWGIPLPiweS 468
                                       788999999999********************888877888888999999988.9****************7742 PP

  == domain 3  score: 34.9 bits;  conditional E-value: 2.7e-12
                                       EE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH...TT----S-EEE CS
                      tRNA-synt_1g 244 vlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg...aelklpkkvva 317
                                       v+ VW+d  +    ++ +     g+e +++e W +        +i     +    fw  + +g    +    ++v  
  gi|313126424|ref|YP_004036694.1| 521 VFDVWIDSSVATWGTLDYP----GNETDFEELWPA-------DLIVEAHDQTRGWFWSQLGMGtaaRGEIPYEEVLM 586
                                       7779999888777777765....578899999944.......45555555566899999999965333335689*** PP

                                       E--EEE.--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1g 318 heyltv.egkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfve 373
                                       h++ +  +g+K+SkS g++v+++ea++r   d lR yl+++ ++  Dl+f w+ + +
  gi|313126424|ref|YP_004036694.1| 587 HGFANDeNGRKMSKSLGNIVTPEEAIDRAGRDPLRAYLLSHDQQGVDLSFDWDGLAD 643
                                       ***9962689******************************************98765 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.03        78       3      62 ..      21      78 ..      19     149 .. 0.76
   2 !   13.5   0.0   9.7e-06     0.025     269     322 ..     585     637 ..     577     645 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.03
                      tRNA-synt_1f  3 WadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeev 62
                                      W ++ a + ++e +   ++     v+    +SG++H+G++ +    d++ r  r  g++v
  gi|313126424|ref|YP_004036694.1| 21 WDEENAYEATKEAHA--DDPAFFFVDGPPYTSGQMHLGTAWNKTLKDAIIRYKRMTGHRV 78
                                      666777776644422..244445555556789******9999888888888777777764 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.7e-06
                      tRNA-synt_1f 269 vvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldld 322
                                       ++  +  +++g+kms+S Gn++t+e++++ a ++ lr ++l+ + ++ ++l++d
  gi|313126424|ref|YP_004036694.1| 585 LMHGFANDENGRKMSKSLGNIVTPEEAIDRAGRDPLRAYLLS-HDQQGVDLSFD 637
                                       456677899999*************************99998.78888888887 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-06    0.0057     235     285 ..     579     629 ..     568     646 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                                       S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-T CS
                      tRNA-synt_1e 235 kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahy 285
                                        ++ +  +h      +g+kmsksL+n++t ++++ +     lR +lls++ 
  gi|313126424|ref|YP_004036694.1| 579 IPYEEVLMHGFANDENGRKMSKSLGNIVTPEEAIDRAGRDPLRAYLLSHDQ 629
                                       556666677666667899*************************99998653 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.7e-06     0.015      10     138 ..     203     346 ..     199     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.7e-06
                     tRNA-synt_1_2  10 leiefkveeseeklevfttrpdtlfGvtfvalapehplvekl..aekkkel....aafieevkkksesereletkek 80 
                                       + ++f++e++e +l ++tt p t+   tfva+  e         +  ++e+    +  +e+v kk + e     +e 
  gi|313126424|ref|YP_004036694.1| 203 IYVKFPLEDREGSLVIWTTTPWTIPANTFVAVDGEMTYQAVRaeKGGESEVlylaEPCVEDVLKKGRYEDYEVVEEL 279
                                       6799**************************99877665444433333444411224456777888888888888899 PP

                     tRNA-synt_1_2  81 eGv.ftglkaihPitgek.........ipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikq 138
                                       +G  + g +  +P+ g+           ++++a+yv ++  tg v + P+h q+Df+  +  +l++  
  gi|313126424|ref|YP_004036694.1| 280 SGEeMVGWEYDNPLAGHLneyadfegaGEVYTAEYVEAD-RTGLVHSAPGHGQEDFARGQDLGLDVFV 346
                                       9987889*******987667889988889*******987.69*************9877777776654 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   3.5e-05      0.09      16      29 ..     173     186 ..     170     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                       CTTEEEEE-TTTT. CS
                      zf-FPG_IleRS  16 qagrstyfCprCqk 29 
                                        + rs ++CprCq+
  gi|313126424|ref|YP_004036694.1| 173 RGKRSVNYCPRCQT 186
                                       578**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1044 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.81u 0.35s 00:00:01.16 Elapsed: 00:00:00.53
# Mc/sec: 5897.52
//
Query:       gi|313126425|ref|YP_004036695.1|  [L=346]
Description: hypothetical protein Hbor_16820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2228.37
//
Query:       gi|313126426|ref|YP_004036696.1|  [L=513]
Description: glycerol kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-74  251.2   0.0    1.3e-74  250.8   0.0    1.2  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    3.1e-61  206.6   0.4    5.5e-61  205.8   0.4    1.4  1  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
    0.00013   21.6   0.3     0.0072   15.8   0.1    2.2  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.8   0.0   2.2e-78   1.3e-74       1     245 []       6     263 ..       6     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 250.8 bits;  conditional E-value: 2.2e-78
                                       EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE CS
                            FGGY_N   1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisg 77 
                                       +i ++D+Gtt+t+++v+d+ gkvvasa++++e+++p++gw+e+ p+eiw+ +++++  +le+ag++++q +aIgi++
  gi|313126426|ref|YP_004036696.1|   6 YIGAVDQGTTGTRFMVFDHSGKVVASAYQKHEQIYPEPGWVEHAPAEIWENTQAVMLTALEEAGLDAEQLEAIGITN 82 
                                       7899************************************************************************* PP

                                       -SS-EEEEETTT.EESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHS.CCHHCCHC. CS
                            FGGY_N  78 qreglvllDknd.kpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkene.pevfekie. 151
                                       qre++ ++Dk   + + nai+w+drrt   ve l+ eg+e+ ++ektgl  +++f+++k +Wl++n  p ++++++ 
  gi|313126426|ref|YP_004036696.1|  83 QRETTLIWDKASgRAIANAIVWQDRRTTDRVETLQDEGKEEWVREKTGLEPDAYFSATKAEWLLDNAdPIKLARMRp 159
                                       **********999***************************************************9963778899999 PP

                                       ............EEEEHHHHHHHHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCC..EEE CS
                            FGGY_N 152 ............kflliddyLiwrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesse..iig 214
                                                   +f++id++++++Ltg++vtdvtnas++mlfni++ +wd+ell+ + +p elLP++++ss    +g
  gi|313126426|ref|YP_004036696.1| 160 ddvreraeqgelMFGTIDSWVTYKLTGAHVTDVTNASRTMLFNIHDMDWDDELLEEFNVPAELLPEVRPSSDedLYG 236
                                       99999999*************************************************************98622688 PP

                                       EEECCCCCCTT.S-EEEEEEEEEHHHHHHHH CS
                            FGGY_N 215 elkpelaaklGlkegvpvvggggDqqaaalG 245
                                       ++ p     +    ++pv+g++gDqqaa++G
  gi|313126426|ref|YP_004036696.1| 237 TTDPDGFLGA----EIPVAGALGDQQAALFG 263
                                       8888777666....8***************9 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.8   0.4   9.2e-65   5.5e-61       1     197 [.     272     461 ..     272     462 .. 0.97

  Alignments for each domain:
  == domain 1  score: 205.8 bits;  conditional E-value: 9.2e-65
                            FGGY_C   1 akvslGTssflll.vgtkpvisehglltpva..gedgkpeyalegsiavagslvawlldnlglreeirdageveesl 74 
                                       ak+++GT+sf+l+ +g++ v sehgllt+v+   + ++ +yalegsi+++g++++wl d   l   i+da+e+ e l
  gi|313126426|ref|YP_004036696.1| 272 AKNTYGTGSFMLMnTGDEAVMSEHGLLTTVGfqRSGEPVQYALEGSIFITGAAIEWLEDV-SL---IDDAAET-EEL 343
                                       79*****************************886669*********************98.55...9*****9.*** PP

                            FGGY_C  75 aelaaaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpld 151
                                       a     ++v ++ gv+fvpaf+gl ap+wd++argti+g++++t  +h++rA+le++a+q+r++ ea+e+dsg++l+
  gi|313126426|ref|YP_004036696.1| 344 A-----RSVDSTDGVYFVPAFTGLGAPHWDQRARGTILGMTRGTRREHVVRATLESIAFQTRDVAEAMEEDSGIDLS 415
                                       *.....99999****************************************************************** PP

                            FGGY_C 152 rlavdGGgskndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                       +l+vdGG++kn++l+ql+ +i+g++++rp  +e+talGaA++A++a
  gi|313126426|ref|YP_004036696.1| 416 TLRVDGGAVKNNFLCQLQSNIVGTDIVRPMVDETTALGAAYAAGLA 461
                                       ********************************************98 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.2e-06    0.0072       3      66 ..      10      79 ..       8     115 .. 0.84
   2 !    3.8   0.0    0.0057        34     188     267 .]     381     458 ..     378     458 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-06
                                      EEE-SSEEEEEEEETTTEEEEEEEE--.......TTS-HHH.........HHHHHHHHHHT--GGGECEE. CS
                       BcrAD_BadFG  3 iDgGsTttkavlmdekgevlgrgitns.......anlesvrfeaaekvleealtealerageeeadieety 66
                                      +D G+T t+++++d +g+v++ ++ +          +e +  ++ +++ + ++ +ale+ag++++++e + 
  gi|313126426|ref|YP_004036696.1| 10 VDQGTTGTRFMVFDHSGKVVASAYQKHeqiypepGWVE-HAPAEIWENTQAVMLTALEEAGLDAEQLEAIG 79
                                      8************************9944444422233.445778999******************99873 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0057
                                       T--HHHHHHHHHHHHHHHHHHHHHTT---SS.....EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHH CS
                       BcrAD_BadFG 188 gekaedIlaglhraialrvialisrsggvtde....vtltGGvakneaavkelrklvkenygevkininpdsiytga 260
                                       g+ +e +++ + ++ia +   +++  ++        + + GG  kn +++      +++n+ + +  + p+ + t a
  gi|313126426|ref|YP_004036696.1| 381 GTRREHVVRATLESIAFQTRDVAEAMEEDSGIdlstLRVDGGAVKN-NFL----CQLQSNIVGTD-IVRPMVDETTA 451
                                       666677777666666655555554444444434444999*******.444....44589999965.588999999** PP

                                       HHHHHHH CS
                       BcrAD_BadFG 261 lGAalfA 267
                                       lGAa  A
  gi|313126426|ref|YP_004036696.1| 452 LGAAYAA 458
                                       ***9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3350.29
//
Query:       gi|313126427|ref|YP_004036697.1|  [L=407]
Description: glycerol-3-phosphate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-58  197.0   6.9    8.1e-58  196.7   6.9    1.0  1  DAO            FAD dependent oxidoreductase
    1.4e-10   40.8   7.3      2e-10   40.3   7.3    1.2  1  FAD_binding_2  FAD binding domain
    1.1e-08   34.7   1.9    1.9e-07   30.6   1.8    2.6  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.2e-05   23.9   3.0    3.9e-05   23.1   3.0    1.5  1  FAD_binding_3  FAD binding domain
    0.00055   20.5   2.4       0.17   12.4   2.2    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0051   17.2   0.1       0.25   11.8   0.0    2.9  3  NAD_binding_7  Putative NAD(P)-binding
      0.009   15.3   5.5       0.93    8.7   1.3    2.7  3  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.022   14.7   0.6      0.051   13.5   0.6    1.6  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.03   13.7  11.0       0.17   11.2  11.0    1.9  1  FAD_oxidored   FAD dependent oxidoreductase
       0.07   12.2   3.7        2.5    7.1   0.1    2.1  2  GIDA           Glucose inhibited division protein A
      0.095   11.4   3.9        1.7    7.3   1.8    2.1  2  HI0933_like    HI0933-like protein
       0.17   11.5   1.2       0.36   10.5   1.2    1.5  1  ApbA           Ketopantoate reductase PanE/ApbA
       0.18   12.0   4.7       0.39   11.0   3.7    2.1  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.32   10.0   6.6        2.6    7.0   1.2    2.3  2  Lycopene_cycl  Lycopene cyclase protein
       0.44    9.8   1.6       0.65    9.2   0.3    1.7  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.7   6.9   6.8e-61   8.1e-58       1     351 [.       6     350 ..       6     351 .. 0.83

  Alignments for each domain:
  == domain 1  score: 196.7 bits;  conditional E-value: 6.8e-61
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHH.HHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeasela.rlslealeelreleee 74 
                                       dvv+iGGG +G+++ ++La rg  Vtl+e+g  ++ g+Sgr+ gllhsg ry++   e+  r + + ++ lr++++e
  gi|313126427|ref|YP_004036697.1|   6 DVVVIGGGATGAGIVRDLALRGvdVTLVERG-GLSAGTSGRSHGLLHSGARYAEAD-EVGaRECIAENRILRDIAGE 80 
                                       9******************************.7777***************88866.43226666666666666666 PP

                                       HSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHHHH CS
                               DAO  75 lgididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lpgllgalfypdtgqvdpaklta 150
                                           + +r tG l+l   e++ e+++++  ++++ g++ e l+++evr   ++ ++ +  a+ +pd ++v p +l+a
  gi|313126427|ref|YP_004036697.1|  81 ----C-VRDTGGLFLQLAEDDPEYFEAKRTACEDIGIPIETLSGDEVRNEISGlSEAVERAMKVPD-AVVSPSRLVA 151
                                       ....4.7899999997656679999999999999***********9**66666466899*******.********** PP

                                       HHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECT.EEEEEEEEEEE--GGGHHHH.HTT.CTTTSEEEEEEE CS
                               DAO 151 alaraaealGveilegtevtgleeedgkvwgve..rttp.gendaadavVnaaGawsdll.gll.keldlpispvrg 222
                                       a a++a+++G++il++++v++l  edg+++gv+     + ge+ aa++vVnaaGaw+  + +++  e+   ++p++g
  gi|313126427|ref|YP_004036697.1| 152 ANAADARDHGATILTNAPVEDLHVEDGRITGVKvgG--SvGETIAAKQVVNAAGAWAEDVgRMAgVEV--AMRPTKG 224
                                       *********************98999******9642..3377667899**********8867776555..88***** PP

                                       EEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGG CS
                               DAO 223 qvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPql 299
                                        ++ ++   + +v ++        +d+++g +v+p  dg+v++G+t  e +++dd + d+++++++ e+++k++P  
  gi|313126427|ref|YP_004036697.1| 225 VMVSVQYDGLGPVLNR-------ARDPADGDIVVPH-DGEVVLGTTSIEVDDPDDYPEDAQEVERMVEECSKMLPPA 293
                                       *****88777666665.......9***********8.7*********999999999******************986 PP

                                       CGEE..EEEEEEEEE..TTSSEEEEEEETEEEEEEEEECTTTHHH...HHHHHHHHHHH CS
                               DAO 300 gdvl..rkwaGlrpl..pdglpligetpgvkglylatGhsghGlt...lapatGkllae 351
                                       ++ +  r+w G+rpl  pd++   g   +++g++ +  h+  G+    +  + Gkl+++
  gi|313126427|ref|YP_004036697.1| 294 REAErvRTWWGVRPLyaPDEDSREGARGISRGFFCV-DHGDDGVEnftSIVG-GKLTTY 350
                                       5544227*******5579**9999995566666666.776666541104444.777776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   7.3   1.7e-13     2e-10       1     204 [.       6     207 ..       6     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.7e-13
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                       Dv+ViG+G+ G      +a +G +v++ve ++   g++  s G +   + + +++++++  +  + +  l   ++++
  gi|313126427|ref|YP_004036697.1|   6 DVVVIGGGATGAGIVRDLALRGVDVTLVERGGLSAGTSGRSHGLLHSGA-RYAEADEVGARECIAENRILRDIAGEC 81 
                                       9**********99999****************************98766.66667888888889999999******* PP

                                       -HHHHHHHHHTHHHHHHHHHHT.......T----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHH CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeel.......gvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarl 147
                                        ++   +f++ a++  +++e++       g+p+ +  + +v+    G   a  r +++++da    +v+  +l+a+ 
  gi|313126427|ref|YP_004036697.1|  82 VRDTGGLFLQLAEDDPEYFEAKrtacediGIPIETLSGDEVRNEISGLSEAVER-AMKVPDA----VVSPSRLVAAN 153
                                       **********************99999999999995555555544444444444.4448887....99********* PP

                                       HHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 148 vesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                       ++ ar++g ++++++++++L vedgr+tG+ v    ++  ++i+ak+vv a+g++  
  gi|313126427|ref|YP_004036697.1| 154 AADARDHGATILTNAPVEDLHVEDGRITGVKVG---GSVGETIAAKQVVNAAGAWAE 207
                                       *********************************...55556799**********986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   1.8   1.6e-10   1.9e-07       2     119 ..       6     215 ..       5     232 .. 0.92
   2 ?   -0.5   0.0      0.48   5.7e+02     180     220 ..     349     392 ..     340     402 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.6e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                       dvvviGgG+ G    ++la  g++vtlv ++g +  g+   s+ ll++++++ +a                      
  gi|313126427|ref|YP_004036697.1|   6 DVVVIGGGATGAGIVRDLALRGVDVTLV-ERGGLSAGTSGRSHGLLHSGARYAEADevgareciaenrilrdiagec 81 
                                       9***************************.77778888888888888888888888789999**************** PP

                                       .......................................................................HHHHCH CS
                                       .......................................................................xxxxxx RF
                       Pyr_redox_2  58 .......................................................................evvkkl 63 
                                                                                                              +  +  
  gi|313126427|ref|YP_004036697.1|  82 vrdtgglflqlaeddpeyfeakrtacedigipietlsgdevrneisglseaveramkvpdavvspsrlvaaNAADAR 158
                                       **********************************************************************9778888 PP

                                       HHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                       Pyr_redox_2  64 nqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGv 119
                                        +g + l++++v ++  + ++++  k  ++ +e+ia++++v A G+++ d   + Gv
  gi|313126427|ref|YP_004036697.1| 159 DHGATILTNAPVEDLHVEDGRITGVKVGGSVGETIAAKQVVNAAGAWAEDVgRMAGV 215
                                       88999999999****99999****8888899******************99766676 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.48
                                       TS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE..EEE.EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx.xxx RF
                       Pyr_redox_2 180 aldkelsaaleealekeGvevklgtsvkeidgnge..kle.vvl 220
                                       ++ ++++a+  ++ ek Gv+  ++t +k++ g ++  +l+ +v+
  gi|313126427|ref|YP_004036697.1| 349 TYRQMAEATTDRVCEKLGVAADCRTAAKRLPGADDpeQLDaYVT 392
                                       67788899999999999**********99988887665555555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   3.0   3.2e-08   3.9e-05       1     180 [.       4     221 ..       4     318 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.2e-08
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHH..HHTT-HHHHHHHSEECCCCEE CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmell..rqlGledrilaegapnelmge 74 
                                       +tdV+++G+G +G+   + L+ +Gv+v+lve+    + ++ r++gl     +    +++G  + i+++   +++ ge
  gi|313126427|ref|YP_004036697.1|   4 DTDVVVIGGGATGAGIVRDLALRGVDVTLVERGGLSAGTSgRSHGLLHSGARYAeaDEVGARECIAENRILRDIAGE 80 
                                       69*******************************99999888****98877776422789999999999999999999 PP

                                       EEEEE.....................................CCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHH CS
                     FAD_binding_3  75 alyne.....................................lsdtpkaradlelesspervtvypqteleriLveh 114
                                        ++ +                                      ++++  ++ +e   + ++  v p   +    +++
  gi|313126427|ref|YP_004036697.1|  81 CVRDTgglflqlaeddpeyfeakrtacedigipietlsgdevRNEISGLSEAVERAMKVPDAVVSPSRLVAAN-AAD 156
                                       9999999999999999999999999977777775554333322222333444444445555555554444444.445 PP

                                       HHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-H.HHHHHTGGEEEEE CS
                     FAD_binding_3 115 aeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrSt.vrktlgiefegee 180
                                       a+ +g+++  ++ ve l+ ++  +t +  + + ge  t+ ak +v a G++   v + +g+e+    
  gi|313126427|ref|YP_004036697.1| 157 ARDHGATILTNAPVEDLHVEDGRITGVKVGGSVGE--TIAAKQVVNAAGAWAEdVGRMAGVEVAMRP 221
                                       58899999999999988888888888877776555..5***********998547777777744433 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.2   0.00014      0.17       2      31 ..       7      36 ..       6      40 .. 0.95
   2 ?    5.4   0.0     0.023        28      49      78 ..     156     185 ..     146     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      vvv+GgG +g      la  g +Vt+ver+
  gi|313126427|ref|YP_004036697.1|  7 VVVIGGGATGAGIVRDLALRGVDVTLVERG 36
                                      8***************************97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.023
                                       HHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  49 klekngievllntkveeiegsedgvesvkl 78 
                                         +++g ++l+n+ ve ++ ++  +++vk+
  gi|313126427|ref|YP_004036697.1| 156 DARDHGATILTNAPVEDLHVEDGRITGVKV 185
                                       56899**************88866999987 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00021      0.25       7      40 ..       4      37 ..       2     131 .. 0.68
   2 ?   -1.5   0.0         3   3.6e+03      88     103 ..     237     252 ..     227     253 .. 0.88
   3 ?    2.0   0.0      0.23   2.7e+02      64     102 ..     353     391 ..     276     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                      +  v+v+GgG  +a  vr l+  g +vt+v    
  gi|313126427|ref|YP_004036697.1|  4 DTDVVVIGGGATGAGIVRDLALRGVDVTLVERGG 37
                                      778**************************97763 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3
                     NAD_binding_7  88 lvnvadkpelcdfifp 103
                                       ++n+a +p+++d+++p
  gi|313126427|ref|YP_004036697.1| 237 VLNRARDPADGDIVVP 252
                                       689***********99 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.23
                     NAD_binding_7  64 lviaatddrelneriaeaakarrilvnvadkpelcdfif 102
                                       ++ a+td+  ++  +a++++++ + +  ad+pe+ d ++
  gi|313126427|ref|YP_004036697.1| 353 MAEATTDRVCEKLGVAADCRTAAKRLPGADDPEQLDAYV 391
                                       555667667777789******************999987 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   1.3   0.00078      0.93      17      54 ..       4      41 ..       2      55 .. 0.84
   2 !    7.5   0.1    0.0018       2.2      75     137 ..     121     185 ..     115     202 .. 0.77
   3 ?   -1.9   0.0       1.3   1.6e+03      67     108 ..     249     290 ..     247     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00078
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS.SS-- CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailers.vspG 54
                                      ++Dvv++G+G++G    + la + ++ v+++er  +s G
  gi|313126427|ref|YP_004036697.1|  4 DTDVVVIGGGATGAGIVRDLALR-GVDVTLVERGgLSAG 41
                                      58*********************.********9425555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0018
                                       HHHHHTT---EEESSEEEESEHHHHHHHHHHHHHTST...TEEEEESEEEEEEEEETBTEEEEEEE CS
                              Thi4  75 elLdelgikyedegdyvvvkdaalftstllskvlqla...nvkllnavaveDlivregegvaGvvi 137
                                       e+ +e+   +e  +  + v da+   s+l+++  + a   ++ +l+   veDl v +  +++Gv +
  gi|313126427|ref|YP_004036697.1| 121 EVRNEISGLSEAVERAMKVPDAVVSPSRLVAANAADArdhGATILTNAPVEDLHVED-GRITGVKV 185
                                       55566666677777889999****999998765543323389*************99.78888865 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                                       EEEETTTHHHHHHTT---EEESSEEEESEHHHHHHHHHHHHH CS
                              Thi4  67 ivvrkpakelLdelgikyedegdyvvvkdaalftstllskvl 108
                                       ivv ++++ +L    i+ +d +dy   ++ ++ + + +sk+l
  gi|313126427|ref|YP_004036697.1| 249 IVVPHDGEVVLGTTSIEVDDPDDYPEDAQEVERMVEECSKML 290
                                       899999999999999999999999888888888777777766 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   4.3e-05     0.051       2      30 ..       7      35 ..       6      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      v viG G  Gagi   +a +g++V+lv++
  gi|313126427|ref|YP_004036697.1|  7 VVVIGGGATGAGIVRDLALRGVDVTLVER 35
                                      89************************997 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  11.0   0.00014      0.17       1     158 [.       6     219 ..       6     320 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.........qvvtgiareflerlr 68 
                                       DvvV+GGg+ G       a +G  v Lve+ g   G++ +  +    g + +e          + ++i r++  ++ 
  gi|313126427|ref|YP_004036697.1|   6 DVVVIGGGATGAGIVRDLALRGVDVTLVERGGLSAGTSGRSHGLLHSGARYAEadevgarecIAENRILRDIAGECV 82 
                                       9**********99999****************999999888877777766565678999999666666666666555 PP

                      FAD_oxidored  69 q.rgga.........rlkkrskwn...........................................tfepevakav 92 
                                       + +gg          +                                                   ++ p+ + a+
  gi|313126427|ref|YP_004036697.1|  83 RdTGGLflqlaeddpE-------YfeakrtacedigipietlsgdevrneisglseaveramkvpdaVVSPSRLVAA 152
                                       5334445544333221.......012233445678888889999999999999966666666666655666655555 PP

                      FAD_oxidored  93 leemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATgd..GdlaalaGvpyrv 158
                                         +  +++g t+l+n+ +++ ++e++ri++v+v   + ++ti+Ak ++ A g    d++ +aGv++ +
  gi|313126427|ref|YP_004036697.1| 153 NAADARDHGATILTNAPVEDLHVEDGRITGVKVG-GSVGETIAAKQVVNAAGAwaEDVGRMAGVEVAM 219
                                       55555999****************99*******4.4459***********996325999999999876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.0    0.0054       6.4       1      28 [.       6      33 ..       6      77 .. 0.80
   2 ?    7.1   0.1    0.0021       2.5     114     155 ..     166     209 ..     148     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0054
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dv+ViGgG  G      +a +G++v+L+
  gi|313126427|ref|YP_004036697.1|  6 DVVVIGGGATGAGIVRDLALRGVDVTLV 33
                                      79*************************9 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0021
                                       EES-EEEEEECTTEEEEEEE..TTS-EEEECEEEE--TT-BT-E CS
                              GIDA 114 ieeeveeliveekkvkgvvt..edgetikakavviatGtflkgk 155
                                        ++ ve+l ve+++++gv+   + geti ak+vv a+G++ +  
  gi|313126427|ref|YP_004036697.1| 166 TNAPVEDLHVEDGRITGVKVggSVGETIAAKQVVNAAGAWAEDV 209
                                       56779************6642289**************977655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.8    0.0014       1.7       2      32 ..       6      36 ..       5      41 .. 0.92
   2 ?    4.1   0.0     0.013        16     109     164 ..     147     204 ..     128     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      dv+viGgGa G      +a rg +V+l+e++
  gi|313126427|ref|YP_004036697.1|  6 DVVVIGGGATGAGIVRDLALRGVDVTLVERG 36
                                      8***********99999***********986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE...TTEEEEESEEEE---- CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvkt..kseeeleadklvlAtGG 164
                                       +++v a  + +++ g ++ ++  v++++ e++++  vk+  + +e+++a+++v A G 
  gi|313126427|ref|YP_004036697.1| 147 SRLVAANAADARDHGATILTNAPVEDLHVEDGRITGVKVggSVGETIAAKQVVNAAGA 204
                                       567788888999***************************7667899*******99986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.2    0.0003      0.36       1      31 [.       7      37 ..       7      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      ++++G Ga G  +   La  g dvtl+ r+ 
  gi|313126427|ref|YP_004036697.1|  7 VVVIGGGATGAGIVRDLALRGVDVTLVERGG 37
                                      689*************************998 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.7   0.00032      0.39       1      29 [.       9      37 ..       9      59 .. 0.84
   2 ?   -2.7   0.0       5.9   7.1e+03      31      40 ..     343     352 ..     341     366 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      ++G+G++G+ + + La +g+dv+l+e++ 
  gi|313126427|ref|YP_004036697.1|  9 VIGGGATGAGIVRDLALRGVDVTLVERGG 37
                                      8*************************984 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.9
                                       SSGGG-EECE CS
                     NAD_binding_8  31 lGGraasyev 40 
                                       +GG++++y+ 
  gi|313126427|ref|YP_004036697.1| 343 VGGKLTTYRQ 352
                                       7999999986 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.2    0.0022       2.6       1      33 [.       6      36 ..       6      46 .. 0.92
   2 ?    5.7   0.3    0.0054       6.4     101     165 ..     162     232 ..     131     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0022
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieas 33
                                      DvvviG+G+ g  +   l  a  g+ v+l+e +
  gi|313126427|ref|YP_004036697.1|  6 DVVVIGGGATGAGIVRDL--ALRGVDVTLVERG 36
                                      9*****************..99********977 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0054
                     Lycopene_cycl 101 gvklleakvesveeeea..geslvvleggrkirarlvvdarglaslk....karrlglQtfyGvevevdnp 165
                                       + +l++a ve  + e+   + + v  + g++i a+ vv a g+ +++    ++ ++ +    Gv+v v+ +
  gi|313126427|ref|YP_004036697.1| 162 ATILTNAPVEDLHVEDGriTGVKVGGSVGETIAAKQVVNAAGAWAEDvgrmAGVEVAMRPTKGVMVSVQYD 232
                                       556788888865544443477778888899************88888676677777777778999988766 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3   0.00054      0.65     164     197 ..       4      37 ..       1      47 [. 0.85
   2 ?   -1.1   0.0      0.75     9e+02      98     135 ..     164     205 ..     154     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00054
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgs 197
                                       +++vvViGg+ +++ +  +l+ +g +Vt+v rg 
  gi|313126427|ref|YP_004036697.1|   4 DTDVVVIGGGATGAGIVRDLALRGVDVTLVERGG 37 
                                       7899999999999999999999999999999875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.75
                       Pyr_redox_3  98 iklfeeVesvkked...egfevetske.tyeAkkviiAtGef 135
                                       i ++  Ve+++ ed   +g +v  s + t+ Ak+v+ A+G +
  gi|313126427|ref|YP_004036697.1| 164 ILTNAPVEDLHVEDgriTGVKVGGSVGeTIAAKQVVNAAGAW 205
                                       5566666666655422245666666644999******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2292.20
//
Query:       gi|313126428|ref|YP_004036698.1|  [L=63]
Description: hypothetical protein Hbor_16850 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 402.05
//
Query:       gi|313126429|ref|YP_004036699.1|  [L=408]
Description: transposase, is605 orfb family, central region [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-21   76.5   2.2    2.4e-21   76.2   0.5    1.8  2  OrfB_IS605      Probable transposase
    2.5e-18   65.7   0.1    5.7e-18   64.6   0.1    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0037   16.7   0.1      0.007   15.8   0.1    1.4  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.066   12.8   0.5       0.18   11.4   0.1    1.8  2  DUF3445         Protein of unknown function (DUF3445)
      0.087   13.0   1.1       0.82    9.9   1.1    2.5  1  EstA_Ig_like    Esterase Ig-like N-terminal domain
       0.25   11.1   1.8       0.98    9.2   1.9    1.9  1  Rubredoxin_2    Rubredoxin metal binding domain
        5.1    7.3   9.8        1.7    8.9   4.8    2.6  3  DUF3958         Protein of unknown function (DUF3958)


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.7e+03      71      86 ..      71      86 ..      46     106 .. 0.65
   2 !   76.2   0.5   9.3e-25   2.4e-21      12     117 ..     186     287 ..     172     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                        OrfB_IS605 71 kkasrklarlhrkrsr 86
                                      k+ +r ++r ++++s+
  gi|313126429|ref|YP_004036699.1| 71 KALQRTVTRFYQNLSN 86
                                      3344444444444443 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 9.3e-25
                        OrfB_IS605  12 kpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrr 88 
                                         ++++ +giDlGi n + +++++   ++     l  dy++l++e+++l++k k+s+ny+k++ ++a++ r ++r++
  gi|313126429|ref|YP_004036699.1| 186 SLNTSNSVGIDLGILNYIHTSDGK---TVDWL-DLEDDYERLRREQRKLSRKEKGSNNYEKQRVEVAKVKRHIRRKV 258
                                       568999******************...55555.9******************************************* PP

                        OrfB_IS605  89 khllhklathliktlkevgvetLnvgnmk 117
                                       ++++hkl+t l+k++++v ve+Lnv+ m 
  gi|313126429|ref|YP_004036699.1| 259 LDYQHKLTTWLVKEYDAVFVEDLNVQCML 287
                                       *************************9886 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.1   2.2e-21   5.7e-18       1      69 []     301     369 ..     301     369 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2.2e-21
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       +r++++ leyk   +G +v++v+ + T k+C+ Cg +  ++   r++ Cp+Cgfe drD nA++N+l+r
  gi|313126429|ref|YP_004036699.1| 301 WRQFITLLEYKGDLHGTHVVQVDARGTTKECASCGVETAKPIWVREHSCPACGFETDRDANASLNVLQR 369
                                       9***************************************9*************************987 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.7e-06     0.007       3      33 ..       2      32 ..       1      33 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-06
                    HTH_OrfB_IS605  3 lkaykyrlyPTpeQeeklartfGcvRfVYNk 33
                                        +++y  yPT+  +e l+ ++++ R +YN+
  gi|313126429|ref|YP_004036699.1|  2 EYSHRYHAYPTQAVAERLEYHIDVHRQAYNY 32
                                      5689**************************8 PP

>> DUF3445  Protein of unknown function (DUF3445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.69   1.8e+03     157     188 ..      11      41 ..       7      58 .. 0.63
   2 ?   11.4   0.1   7.2e-05      0.18       8      68 ..     211     284 ..     205     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.69
                           DUF3445 157 epgkpvkRvnwsiqtddelfwaseeeeeeeld 188
                                       +++ + +R+ + i ++++ ++  ++ e e++d
  gi|313126429|ref|YP_004036699.1|  11 PTQAVAERLEYHIDVHRQAYN-YTRYEYENVD 41 
                                       567889999999999999996.3322333433 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.2e-05
                           DUF3445   8 sewieldktYkerieerrrlle.........ehgekvlavlpeaeaavkElleelveyLparYPqlFel.....s 68 
                                        +w++l+++Y++  +e r+l +         +++ +v +v+++++  v +  + l++ L+++Y  +F +     +
  gi|313126429|ref|YP_004036699.1| 211 VDWLDLEDDYERLRREQRKLSRkekgsnnyeKQRVEVAKVKRHIRRKVLDYQHKLTTWLVKEYDAVF-VedlnvQ 284
                                       68**********99999988887788877767888899999**************************.5244330 PP

>> EstA_Ig_like  Esterase Ig-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.1   0.00032      0.82      33      72 ..      59      97 ..      57     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00032
                                      GGGEEEEEEETTCEEEE-EEEEEEESSSSS--T--ECCEE CS
                      EstA_Ig_like 33 kstFkVagkrseekgsRtvtkvYvndkaekadkskdGkyV 72
                                      k++F+V +++++++ +Rtvt+ Y n ++  ++ +++G+ V
  gi|313126429|ref|YP_004036699.1| 59 KDEFSVFSDVNSKALQRTVTRFYQNLSNLSKK-KQNGNKV 97
                                      689**********************9998666.4888866 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.9   0.00038      0.98       2      21 ..     330     353 ..     330     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00038
                      Rubredoxin_2   2 vCsqCGfesakwfGr....CpsCg 21 
                                       +C +CG e+ak  +     Cp+Cg
  gi|313126429|ref|YP_004036699.1| 330 ECASCGVETAKPIWVrehsCPACG 353
                                       5*************55555****8 PP

>> DUF3958  Protein of unknown function (DUF3958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.4     6e+03      41      55 ..      77      91 ..      68     101 .. 0.53
   2 ?    8.9   4.8   0.00065       1.7      78      98 ..     215     235 ..     209     245 .. 0.84
   3 ?    1.3   0.4      0.15   3.9e+02      54      86 ..     233     265 ..     232     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.4
                           DUF3958 41 skrlfdelletfrkd 55
                                       +r++++l+   +k 
  gi|313126429|ref|YP_004036699.1| 77 VTRFYQNLSNLSKKK 91
                                      334444444433333 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00065
                           DUF3958  78 dLEeeeeeLkrekrqLedqee 98 
                                       dLE+++e+L+re+r+L+++e 
  gi|313126429|ref|YP_004036699.1| 215 DLEDDYERLRREQRKLSRKEK 235
                                       8******************97 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.15
                           DUF3958  54 kdeeshlfeklrdevqrlsrklredLEeeeeeL 86 
                                       k++ s+ +ek+r ev++ +r++r +  + + +L
  gi|313126429|ref|YP_004036699.1| 233 KEKGSNNYEKQRVEVAKVKRHIRRKVLDYQHKL 265
                                       556788899999999999999998887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1285  (0.0716716); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2679.83
//
Query:       gi|313126430|ref|YP_004036700.1|  [L=40]
Description: hypothetical protein Hbor_16870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       117  (0.00652574); expected 358.6 (0.02)
Passed bias filter:                      101  (0.00563333); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.46
# Mc/sec: 264.10
//
Query:       gi|313126431|ref|YP_004036701.1|  [L=46]
Description: hypothetical protein Hbor_16880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 324.80
//
Query:       gi|313126432|ref|YP_004036702.1|  [L=433]
Description: glycerol 3-phosphate dehydrogenase (quinone) subunit c [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-22   79.8   0.6    2.9e-11   43.4   0.0    2.6  2  CCG              Cysteine-rich domain
    3.9e-09   36.8  13.8    4.4e-09   36.7   7.1    3.1  3  Fer4_8           4Fe-4S dicluster domain
    2.6e-06   27.9   8.8    2.6e-06   27.9   8.8    3.2  3  Fer4_17          4Fe-4S dicluster domain
    2.3e-05   24.9  12.3      0.013   16.1   0.2    3.5  4  Fer4_7           4Fe-4S dicluster domain
    8.6e-05   22.6  16.6     0.0038   17.3  13.5    3.8  4  Fer4_10          4Fe-4S dicluster domain
    0.00068   19.8  10.2    0.00068   19.8  10.2    3.2  3  Fer4_9           4Fe-4S dicluster domain
     0.0014   18.3   7.8      0.071   12.8   0.0    4.7  5  zf-CSL           CSL zinc finger
  ------ inclusion threshold ------
      0.021   15.0   3.8        8.4    6.6   0.5    3.4  3  Fer4_18          4Fe-4S dicluster domain
      0.022   13.8   0.0      0.036   13.1   0.0    1.2  1  DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
      0.031   14.6   0.0      0.065   13.6   0.0    1.5  1  DUF3390          Domain of unknown function (DUF3390)
       0.14   11.4   0.1       0.23   10.7   0.1    1.2  1  DUF1385          Protein of unknown function (DUF1385)
       0.18   12.8  15.8       0.36   11.8  11.9    3.3  4  Fer4_16          4Fe-4S double cluster binding domain
        2.8    8.1  15.8       0.27   11.4   0.8    3.2  3  Fer4_21          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   2.1e-14   2.9e-11       1      85 []     200     284 ..     200     284 .. 0.94
   2 !   34.2   0.1   1.6e-11   2.1e-08       2      84 ..     331     413 ..     330     414 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.1e-14
                               CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaee..tgadaivt 75 
                                       +ayf+gC + +++ pev kal ++ e+ g e+ ++ ++ C G + + +g+ + a + ak nv+++++  ++   iv+
  gi|313126432|ref|YP_004036702.1| 200 IAYFHGC-YSNYNTPEVAKALVRVYEEFGYEIAVP-RQRCSGTPMFANGMLDDAGRAAKTNVSEFNDllEEGYDIVA 274
                                       69*****.9************************99.******************************96646667*** PP

                               CCG  76 acpgCllqlk 85 
                                        c +C+++l+
  gi|313126432|ref|YP_004036702.1| 275 SCTSCSMSLR 284
                                       *******985 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 1.6e-11
                               CCG   2 ayfdgChllraa.ypevrkalkkllealgveleelekesCCGagggrsgkee...laealakrnvetaeetgadaiv 74 
                                       ay+ +Ch+ ++   ++  +++++l   +gv++e+  ++sC G +g++ +kee   +++++++++++++  ++ ++ +
  gi|313126432|ref|YP_004036702.1| 331 AYHAPCHARNQGlDRQAVELFREL---DGVTIEDV-GDSCSGISGTYGWKEEkyeTSMKIGEEMFDHMSHAEGNVGM 403
                                       8*****754444444444445555...88888888.9*************99899999******************* PP

                               CCG  75 tacpgCllql 84 
                                       t+cp+C++q+
  gi|313126432|ref|YP_004036702.1| 404 TECPTCSMQM 413
                                       ********98 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   7.1   3.2e-12   4.4e-09       2      65 .]      36     100 ..      35     100 .. 0.84
   2 ?    2.9   0.0      0.11   1.5e+02      31      55 ..     253     280 ..     232     281 .. 0.61
   3 ?   -1.1   0.1         2   2.7e+03      45      54 ..     400     409 ..     360     415 .. 0.60

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 3.2e-12
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.dvqeeqvlee...eealwsCttcgaCtevCpvgi 65 
                                       +++C +C  C ++Cpv++  ++++  + ++ ++ +  +++   +   ++++ sC++c++C+++Cp ++
  gi|313126432|ref|YP_004036702.1|  36 ADNCYKCTSCDTSCPVAEVNDDFPGPKFQGPEQwRLKRKD---DadiDDSIMSCSNCMRCDNACPSSV 100
                                       689***************************9995222222...234699****************875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                            Fer4_8  31 eaae...dvqeeqvlee....eealwsCttcg 55 
                                       +aa+    + ++         ++++ sCt+c 
  gi|313126432|ref|YP_004036702.1| 253 RAAKtnvSEFND----LleegYDIVASCTSCS 280
                                       333322212222....13345999*******6 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2
                            Fer4_8  45 eealwsCttc 54 
                                       + ++ +C tc
  gi|313126432|ref|YP_004036702.1| 400 NVGMTECPTC 409
                                       5566677666 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   8.8   1.9e-09   2.6e-06       1      60 [.      38     100 ..      38     101 .. 0.87
   2 ?   -0.5   0.0       1.3   1.8e+03      43      50 ..     273     280 ..     241     308 .. 0.78
   3 ?   -0.8   0.1       1.7   2.3e+03      37      50 ..     397     410 ..     364     414 .. 0.51

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.9e-09
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepk...kllraaklglleeaekeekaslCieCgeCerkCPqgl 60 
                                       +C +C  C  +Cp  e +d+ p    +  ++++l+++++a  ++ + +C++C +C+ +CP+++
  gi|313126432|ref|YP_004036702.1|  38 NCYKCTSCDTSCPVAEVNDDFPGpkfQGPEQWRLKRKDDADIDDSIMSCSNCMRCDNACPSSV 100
                                       6****************99965543578888888999999999*****************987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                           Fer4_17  43 aslCieCg 50 
                                       + +C++C 
  gi|313126432|ref|YP_004036702.1| 273 VASCTSCS 280
                                       45566664 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.7
                           Fer4_17  37 aekeekaslCieCg 50 
                                       ae +  + +C +C 
  gi|313126432|ref|YP_004036702.1| 397 AEGNVGMTECPTCS 410
                                       23334667776664 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.5   2.5e-05     0.034      25      50 ..      26      51 ..       9      54 .. 0.67
   2 !   16.1   0.2   9.3e-06     0.013      36      51 ..      84      99 ..      55     120 .. 0.70
   3 ?   -2.0   0.0       4.3   5.9e+03      37      41 ..     275     279 ..     254     282 .. 0.74
   4 ?   -1.3   0.1       2.6   3.5e+03      31      41 ..     399     409 ..     364     411 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                            Fer4_7 25 ekgtekveidpekClgCgaCvavCPt 50
                                      +++ ++++  +++C+ C++C + CP+
  gi|313126432|ref|YP_004036702.1| 26 DETEMDLRPGADNCYKCTSCDTSCPV 51
                                      223344555679*************8 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.3e-06
                            Fer4_7 36 ekClgCgaCvavCPtg 51
                                      ++C++C +C ++CP+ 
  gi|313126432|ref|YP_004036702.1| 84 MSCSNCMRCDNACPSS 99
                                      5666666666666654 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.3
                            Fer4_7  37 kClgC 41 
                                       +C++C
  gi|313126432|ref|YP_004036702.1| 275 SCTSC 279
                                       45555 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.6
                            Fer4_7  31 veidpekClgC 41 
                                        ++ +++C +C
  gi|313126432|ref|YP_004036702.1| 399 GNVGMTECPTC 409
                                       35556666665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3  13.5   2.8e-06    0.0038       6      56 .]      36      97 ..      32      97 .. 0.93
   2 !   14.6   2.0   1.9e-05     0.026       8      30 ..      85     111 ..      76     124 .. 0.69
   3 ?    0.2   0.0      0.63   8.6e+02      28      49 ..     259     280 ..     241     285 .. 0.77
   4 ?    0.7   0.1      0.41   5.7e+02      35      49 ..     396     410 ..     389     415 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.8e-06
                           Fer4_10  6 ddtCirCgkCvkaCPadl...........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +d C +C+ C ++CP+                + + ++++++ +++ + +C +c  C  aCP
  gi|313126432|ref|YP_004036702.1| 36 ADNCYKCTSCDTSCPVAEvnddfpgpkfqGPEQWRLKRKDDADIDDSIMSCSNCMRCDNACP 97
                                      589*************66*********9988888999999999999***************9 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.9e-05
                           Fer4_10   8 tCirCgkCvkaCPadl....tsvgakg 30 
                                       +C +C +C +aCP+++     ++ a+g
  gi|313126432|ref|YP_004036702.1|  85 SCSNCMRCDNACPSSVplsqMHNTARG 111
                                       6*************7777653333333 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.63
                           Fer4_10  28 akgeaseeeavrkkvekCtgcg 49 
                                       ++++++  e+  + v +Ct c 
  gi|313126432|ref|YP_004036702.1| 259 VSEFNDLLEEGYDIVASCTSCS 280
                                       5566666777778888999986 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.41
                           Fer4_10  35 eeavrkkvekCtgcg 49 
                                       +++ ++++ +C++c 
  gi|313126432|ref|YP_004036702.1| 396 HAEGNVGMTECPTCS 410
                                       567788999999996 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  10.2   4.9e-07   0.00068       1      49 [.      38      99 ..      38     101 .. 0.81
   2 ?   -0.2   0.1      0.83   1.1e+03      33      40 ..     264     280 ..     235     282 .. 0.65
   3 ?   -0.6   0.0       1.1   1.5e+03      10      20 ..     404     414 ..     378     424 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.9e-07
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..............eaCigCgaCveaCpkg 49
                                      +C++C++C ++Cp   v++d  + k +  + ++               +C  C++C +aCp+ 
  gi|313126432|ref|YP_004036702.1| 38 NCYKCTSCDTSCPVAEVNDDFPGPKFQGPE-QWrlkrkddadiddsiMSCSNCMRCDNACPSS 99
                                      6***********988877776666655432.334699999*******99************86 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.83
                            Fer4_9  33 e.........eaCigCg 40 
                                       +          +C++C 
  gi|313126432|ref|YP_004036702.1| 264 DlleegydivASCTSCS 280
                                       14445556666788775 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.1
                            Fer4_9  10 eaCpagvvved 20 
                                       + Cp++ ++++
  gi|313126432|ref|YP_004036702.1| 404 TECPTCSMQME 414
                                       34666555555 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       1.7   2.3e+03      40      50 ..      35      45 ..      23      48 .. 0.68
   2 ?    0.3   0.2      0.42   5.8e+02      42      50 ..      81      89 ..      66     114 .. 0.65
   3 !   12.8   0.0   5.2e-05     0.071      32      55 ..     264     284 ..     247     287 .. 0.83
   4 ?    0.9   0.0      0.29   3.9e+02       2      21 ..     317     336 ..     316     349 .. 0.74
   5 ?    4.1   0.0     0.027        37      40      53 ..     399     412 ..     376     414 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                                      ..--EEEETTS CS
                            zf-CSL 40 gaevvvqCssC 50
                                      ga+   +C+sC
  gi|313126432|ref|YP_004036702.1| 35 GADNCYKCTSC 45
                                      46777788888 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.42
                                      --EEEETTS CS
                            zf-CSL 42 evvvqCssC 50
                                      + ++ Cs C
  gi|313126432|ref|YP_004036702.1| 81 DSIMSCSNC 89
                                      445555555 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 5.2e-05
                                       HHHHTT....--EEEETTSSEEEE CS
                            zf-CSL  32 edleegaegaevvvqCssCSLwik 55 
                                       + lee   g+++v+ C+sCS+ ++
  gi|313126432|ref|YP_004036702.1| 264 DLLEE---GYDIVASCTSCSMSLR 284
                                       34455...5***********9876 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.29
                                       EEEGGGSEEETTTTEEEEEE CS
                            zf-CSL   2 eveledfefdeeeesyyypC 21 
                                       e el+d +++e+   y+ pC
  gi|313126432|ref|YP_004036702.1| 317 ESELKDASVSEQSFAYHAPC 336
                                       67899999877555555555 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.027
                                       ..--EEEETTSSEE CS
                            zf-CSL  40 gaevvvqCssCSLw 53 
                                       g   +++C++CS+ 
  gi|313126432|ref|YP_004036702.1| 399 GNVGMTECPTCSMQ 412
                                       556689******86 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.5    0.0061       8.4      45      73 ..      23      51 ..      11      58 .. 0.78
   2 ?    6.5   0.1    0.0069       9.5      50      75 ..      75     100 ..      60     121 .. 0.75
   3 ?    0.5   0.0       0.5   6.9e+02      51      83 ..     396     427 ..     369     429 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0061
                           Fer4_18 45 kalkekeerkekgagdcidcescvkvcPt 73
                                      +   e+e   + ga +c +c sc + cP+
  gi|313126432|ref|YP_004036702.1| 23 VFDDETEMDLRPGADNCYKCTSCDTSCPV 51
                                      5556666677788999***********97 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0069
                           Fer4_18  50 keerkekgagdcidcescvkvcPtgi 75 
                                        +   +++   c +c  c + cP  +
  gi|313126432|ref|YP_004036702.1|  75 DDADIDDSIMSCSNCMRCDNACPSSV 100
                                       44445666778888888888888876 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.5
                           Fer4_18  51 eerkekgagdcidcescvkvcPtgidirkGlql 83 
                                       + + + g+++c +c++ ++   tg di++ lql
  gi|313126432|ref|YP_004036702.1| 396 HAEGNVGMTECPTCSMQME-HGTGYDIKHPLQL 427
                                       2233445556666655544.4688999998886 PP

>> DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.6e-05     0.036     144     216 ..     160     231 ..     155     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                   DDE_Tnp_ISAZ013 144 enegwvsvgtdkdtaefavesirrwWqevgkarypkakrllitaDaggsnssrsrlwkkelqkladelgleiq 216
                                        ne ++ ++++++  efa +++r+wW e+g a+ ++ ++  i    g  +++++    k l++  +e g ei 
  gi|313126432|ref|YP_004036702.1| 160 INEKVLGITSEREFPEFAQQTFREWWAERGGAKVSSDEK-KIAYFHGCYSNYNTPEVAKALVRVYEEFGYEIA 231
                                       5888999***********************998876555.344445555556666666666666666666665 PP

>> DUF3390  Domain of unknown function (DUF3390)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.7e-05     0.065      66      87 ..     168     189 ..     162     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.7e-05
                           DUF3390  66 tsvRtlPkpakkslrdlakerg 87 
                                       ts R++P++a++++r++++erg
  gi|313126432|ref|YP_004036702.1| 168 TSEREFPEFAQQTFREWWAERG 189
                                       678*****************97 PP

>> DUF1385  Protein of unknown function (DUF1385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00016      0.23      92     123 ..     282     313 ..     274     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                           DUF1385  92 slmkdikrvfqYHGAEHktincyeageeltve 123
                                       sl ++   +f+YHG E  + n+yea e l ++
  gi|313126432|ref|YP_004036702.1| 282 SLRQEYPELFEYHGTEEVAANTYEAMEYLRIH 313
                                       555666789****************9999865 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  11.9   0.00026      0.36       1      65 [.      38      97 ..      38      99 .. 0.77
   2 ?    8.7   2.8    0.0025       3.4       2      20 ..      86     104 ..      85     135 .. 0.75
   3 ?   -2.5   0.0       7.4     1e+04      55      60 ..     274     279 ..     253     281 .. 0.64
   4 ?   -2.5   0.0       7.5     1e+04      55      60 ..     404     409 ..     377     418 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                           Fer4_16  1 rCgtCgkCaevCPtnaikek.kekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      +C +C+ C  +CP++ ++ +   ++++ +e+   + +++ d+ +++ +      +  C +C ++CP
  gi|313126432|ref|YP_004036702.1| 38 NCYKCTSCDTSCPVAEVNDDfPGPKFQGPEQWRLKRKDDADIDDSIMS------CSNCMRCDNACP 97
                                      6*****************996677788777776655555555555555......559********9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0025
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C +C +C ++CP+++  ++
  gi|313126432|ref|YP_004036702.1|  86 CSNCMRCDNACPSSVPLSQ 104
                                       ************9874444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7.4
                           Fer4_16  55 tgCdiC 60 
                                       + C  C
  gi|313126432|ref|YP_004036702.1| 274 ASCTSC 279
                                       566666 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 7.5
                           Fer4_16  55 tgCdiC 60 
                                       t C +C
  gi|313126432|ref|YP_004036702.1| 404 TECPTC 409
                                       444444 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   0.00019      0.27      34      55 ..      30      53 ..      15      55 .. 0.74
   2 ?    7.0   0.7    0.0046       6.4       7      22 ..      85      99 ..      77     117 .. 0.70
   3 ?   -2.2   0.1       3.4   4.7e+03      11      16 ..     276     281 ..     272     286 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                           Fer4_21 34 lkvv..edeCvGCnlCssvCPved 55
                                      + ++  +d+C  C+ C + CPv +
  gi|313126432|ref|YP_004036702.1| 30 MDLRpgADNCYKCTSCDTSCPVAE 53
                                      444333799999999999999965 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0046
                           Fer4_21  7 kCigCgkCliaCedts 22
                                      +C +C +C  aC+  s
  gi|313126432|ref|YP_004036702.1| 85 SCSNCMRCDNACPS-S 99
                                      58888888888883.4 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.4
                           Fer4_21  11 CgkCli 16 
                                       C++C +
  gi|313126432|ref|YP_004036702.1| 276 CTSCSM 281
                                       444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2649.52
//
Query:       gi|313126433|ref|YP_004036703.1|  [L=420]
Description: glycerol 3-phosphate dehydrogenase (quinone) subunit b [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-29  102.7   3.0    2.9e-29  102.4   3.0    1.0  1  FAD_binding_2  FAD binding domain
    1.5e-08   34.4   0.5    0.00011   21.7   2.0    2.2  2  FAD_oxidored   FAD dependent oxidoreductase
    1.1e-06   28.5   1.3     0.0066   16.1   0.0    2.2  2  DAO            FAD dependent oxidoreductase
    3.9e-05   23.0   0.0      0.015   14.6   0.0    2.3  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00016   20.9   1.3    0.00037   19.7   1.3    1.6  1  GIDA           Glucose inhibited division protein A
    0.00033   21.1   0.1      0.067   13.8   0.2    2.7  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00063   18.6   0.2       0.21   10.2   0.5    2.1  2  HI0933_like    HI0933-like protein
     0.0032   16.8   0.6       0.37   10.0   0.5    2.1  2  FAD_binding_3  FAD binding domain
     0.0092   16.4   0.6       0.03   14.8   0.0    2.0  2  NAD_binding_7  Putative NAD(P)-binding
     0.0094   16.3   2.3       0.11   12.8   0.0    2.2  2  Senescence     Senescence-associated protein
  ------ inclusion threshold ------
      0.051   14.2   0.8        0.1   13.3   0.8    1.4  1  Hemerythrin    Hemerythrin HHE cation binding domain
       0.18   11.0   0.1       0.36   10.0   0.1    1.4  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   3.0     2e-32   2.9e-29       1     415 [.       6     402 ..       6     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 2e-32
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                       Dv+V+G+GlA  ++Al+aae G++v +v  +++   ++  ++G id+++        ++d p + ++ +++ l+++ 
  gi|313126433|ref|YP_004036703.1|   6 DVLVVGGGLAAATSALAAAESGKTVRLVAHKKS---TLRQASGLIDVLG------YTDGDGPHADPYAAISDLPDD- 72 
                                       9*******************************9...*************......44579*************966. PP

                                       -HHHHHHHHHTHHHHHHHHHHT.T----B..CCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHH CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeel.gvpfsr..tedgpvdvrelGglsatartlhdaadarretlvtghallarlvesa 151
                                        +p+  ++ +  +e ++ + e  g ++ +  t+++++  +  G++++tar++     +       g   l +++e+ 
  gi|313126433|ref|YP_004036703.1|  73 -HPYKLVGEDGIKEGLRIFDEAvGEMYAGghTDTNALVPTYGGTVKPTARYPK-SVEP--GLASVGEPTLFVGFEGT 145
                                       .77777888888888888888888888883334449************99999.5555..68889999999999999 PP

                                       HTCTEEEEESEEEEEEEECTT...EEEEEEEEETTTTCEEEEEES..EEEE-----GG...............GSSS CS
                     FAD_binding_2 152 rkagvdfqerteadeLivedg...rvtGavvenpesgrevrirak..avvlatgGfgr.....allkellgaaaeae 218
                                           +df ++  ad++    g   + +G+ v +p++ r+ +   +  + ++  + +gr     +l++++ +++  +e
  gi|313126433|ref|YP_004036703.1| 146 ----TDFAPQVVADHVAA-AGvpfETRGVRVPFPKTFRDDARLTRlaKALDKDESAGRvgvrrSLAETVKAHLEGEE 217
                                       ....9***********88.55699**********666666444444577888888888999**************** PP

                                       BSSGTT-S-HHHHHHHCTTSS.EES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTHGGGS-HHH CS
                     FAD_binding_2 219 ttnapavtGdglalalragaa.lnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFmnelasrdv 294
                                        ++ pa  Gd+++ ++ra+++   +  ++ev+++P+sl++++++ ++    al   G+ +  ++G+  ++  a+ d+
  gi|313126433|ref|YP_004036703.1| 218 RVGFPAMLGDAHGEEVRAELEdRLGVSVFEVPTGPPSLLGLQLEDRL--FDALDEAGVRI--STGNPAVGYEADGDR 290
                                       **********************9999*********************..77888888766..566665655556666 PP

                                       HHHH.HH.HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEE CS
                     FAD_binding_2 295 vsra.ilekeiaeggseanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqh 370
                                       + +  + +++ + + + a  +++a++gl  +g+++++e+  +e+ +g++ +     +p dr    ++ + + + ++ 
  gi|313126433|ref|YP_004036703.1| 291 IEAVyVDRRGNRVPYH-AEEFVLATGGLVGKGIDSDRER-VTEPVFGCHIP-----HPDDR---YDWSDEEAFGGHE 357
                                       6555055555566666.999*******************.99*******88.....99999...9************ PP

                                       EES-EEEBETTSBESTTEEESS.BTEEE-STCEESSSSTTS--TTH CS
                     FAD_binding_2 371 ytmgGvetdengrvldadgqpi.pGLYAaGevaaggvhganrlgGn 415
                                       +  +Gv+ de++r++ a+g+p+ ++L AaG v  gg + a++ +++
  gi|313126433|ref|YP_004036703.1| 358 FARFGVVPDEEMRPTTASGEPHfENLRAAGSVV-GGADVAREKSAS 402
                                       **************888777644**********.999888877665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.0   7.5e-08   0.00011       1      31 [.       6      36 ..       6      39 .. 0.94
   2 !    9.0   0.0   0.00054      0.81      93     144 ..     264     315 ..     241     316 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.5e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      Dv+VvGGg+a  + A+aAa++G++v Lv  +
  gi|313126433|ref|YP_004036703.1|  6 DVLVVGGGLAAATSALAAAESGKTVRLVAHK 36
                                      9**************************9865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00054
                      FAD_oxidored  93 leemlaeagvtvllntrlvevekegkriesvtveskeg.rktirAkvfiDATg 144
                                       l + l+eagv++ ++  +v+ e +g+rie+v v +++g r  ++A+ f+ ATg
  gi|313126433|ref|YP_004036703.1| 264 LFDALDEAGVRISTGNPAVGYEADGDRIEAVYV-DRRGnRVPYHAEEFVLATG 315
                                       457789***************************.56655*********99997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.5   0.00013       0.2       1      29 [.       6      36 ..       6      68 .. 0.85
   2 !   16.1   0.0   4.4e-06    0.0066     152     232 ..     264     344 ..     228     401 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      dv+++GGG + ++ A+++a+ g  V l+  +
  gi|313126433|ref|YP_004036703.1|  6 DVLVVGGGLAAATSALAAAESGktVRLVAHK 36
                                      8*******************99988777655 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.4e-06
                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEE..EEEEEEE--GGGHH.HHHTTCTTT.SEEEEEEEEE CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttpgend..aadavVnaaGawsd.llgllkeld.lpispvrgqv 224
                                       l +a+ ++Gv+i +g +++g e++++++  v+++ +g+++  +a+  V+a+G  ++  ++ +   + + ++pv g++
  gi|313126433|ref|YP_004036703.1| 264 LFDALDEAGVRISTGNPAVGYEADGDRIEAVYVDRRGNRVpyHAEEFVLATGGLVGkGIDSD---ReRVTEPVFGCH 337
                                       788999***************9988888888634446554235566******9877333222...213459999999 PP

                                       EEEEECCT CS
                               DAO 225 lvlkplse 232
                                       +   p ++
  gi|313126433|ref|YP_004036703.1| 338 IPH-PDDR 344
                                       977.5444 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   9.8e-06     0.015       2      33 ..       6      37 ..       5      88 .. 0.85
   2 !    6.2   0.0    0.0035       5.2     181     236 ..     256     315 ..     228     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-06
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      dv+v+GgG A+ + al +a++g  v lv  ++
  gi|313126433|ref|YP_004036703.1|  6 DVLVVGGGLAAATSALAAAESGKTVRLVAHKK 37
                                      89*************************94333 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0035
                                       S-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE..EEETTSCE..EEESEEEE-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx..xxxxxxxxxxx RF
                       Pyr_redox_2 181 ldkelsaaleealekeGvevklgtsvkeidgngekle..vvledgee..idadlvvvavG 236
                                       l+ +l+++l +al + Gv++ +g+ ++  +++g+++e  +v+  g++  + a+  v+a+G
  gi|313126433|ref|YP_004036703.1| 256 LGLQLEDRLFDALDEAGVRISTGNPAVGYEADGDRIEavYVDRRGNRvpYHAEEFVLATG 315
                                       6778999999*****************999999977777999999996666777777776 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.3   2.5e-07   0.00037       1      38 [.       6      43 ..       6      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.5e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiael 38
                                      dv V+GgG+A    Alaaa++G  v L++hk +t+ + 
  gi|313126433|ref|YP_004036703.1|  6 DVLVVGGGLAAATSALAAAESGKTVRLVAHKKSTLRQA 43
                                      79*****************************9998765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.2   4.5e-05     0.067       2      36 ..       7      41 ..       6      46 .. 0.90
   2 ?    4.4   0.0     0.038        57      21      77 ..     241     295 ..     226     299 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSST CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllr 36
                                      v+vvGgG+ +   A a+ae gk V +v  ++  lr
  gi|313126433|ref|YP_004036703.1|  7 VLVVGGGLAAATSALAAAESGKTVRLVAHKKSTLR 41
                                      89***********************9999988774 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.038
                                       TTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox  21 lgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       lg +V  v  ++  l  l+ +++++l + l + g+++ +++ ++  e ++d +e+v 
  gi|313126433|ref|YP_004036703.1| 241 LGVSVFEVPTGPPSL--LGLQLEDRLFDALDEAGVRISTGNPAVGYEADGDRIEAVY 295
                                       665555555555555..899999*********************9999999877775 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.5   0.00014      0.21       2      37 ..       6      41 ..       5      45 .. 0.94
   2 !    5.9   0.0    0.0029       4.3     113     166 ..     262     318 ..     256     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                      dv+v+GgG A    A++aa+ gk V l+ ++k+++r
  gi|313126433|ref|YP_004036703.1|  6 DVLVVGGGLAAATSALAAAESGKTVRLVAHKKSTLR 41
                                      89*****************************99887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE----SS CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvktk...seeeleadklvlAtGGlS 166
                                       d l  +l+eagv++ + +   + e++ d++  v ++   ++  ++a++ vlAtGGl 
  gi|313126433|ref|YP_004036703.1| 262 DRLFDALDEAGVRISTGNPAVGYEADGDRIEAVYVDrrgNRVPYHAEEFVLATGGLV 318
                                       568899*******************99998888884333555789**********85 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.5   0.00025      0.37       3      39 ..       6      42 ..       4      47 .. 0.89
   2 !    4.9   0.0    0.0089        13     105     149 ..     258     301 ..     194     319 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                      dVl+VG+G+a +++al  +e G  v+lv   ++t ++
  gi|313126433|ref|YP_004036703.1|  6 DVLVVGGGLAAATSALAAAESGKTVRLVAHKKSTLRQ 42
                                      8***************************998888765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0089
                                       HHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTE CS
                     FAD_binding_3 105 teleriLvehaeerglqvrfktevesleqdeegvtaevrdketge 149
                                        +le  L +++ e+g+++  ++  ++ e+d++ ++a++ d++ g+
  gi|313126433|ref|YP_004036703.1| 258 LQLEDRLFDALDEAGVRISTGNPAVGYEADGDRIEAVYVDRR-GN 301
                                       5789999********************************997.44 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     2e-05      0.03       8      41 ..       5      38 ..       3      81 .. 0.85
   2 ?   -1.5   0.3       2.3   3.4e+03      12      22 ..     389     399 ..     385     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                     NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtvvapevk 41
                                      + vlvvGgG  Aa+ +   +e+g++v +va + +
  gi|313126433|ref|YP_004036703.1|  5 EDVLVVGGGLAAATSALAAAESGKTVRLVAHKKS 38
                                      679***************************9952 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                     NAD_binding_7  12 vvGgGevAark 22 
                                       vvGg +vA +k
  gi|313126433|ref|YP_004036703.1| 389 VVGGADVAREK 399
                                       9*******998 PP

>> Senescence  Senescence-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.6     0.071   1.1e+02     124     150 ..      10      36 ..       7      37 .. 0.94
   2 !   12.8   0.0   7.5e-05      0.11     111     155 ..     376     420 .]     311     420 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.071
                        Senescence 124 vldgleeaakqllsatsdattkvvehk 150
                                       v+ gl +a+++l+ a s  t++ v hk
  gi|313126433|ref|YP_004036703.1|  10 VGGGLAAATSALAAAESGKTVRLVAHK 36 
                                       899***********************9 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.5e-05
                        Senescence 111 gevlnasldafstvldgleeaakqllsatsdattkvvehkYGeeA 155
                                       ge   + l+a+  v+ g++ a  + +s +s at++v++ + GeeA
  gi|313126433|ref|YP_004036703.1| 376 GEPHFENLRAAGSVVGGADVAREKSASGVSLATGAVAGSRAGEEA 420
                                       555556799***********************************9 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.8   6.7e-05       0.1      18      77 ..     182     238 ..     175     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHHHCCC.HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHH CS
                       Hemerythrin  18 erlraladaaaevhga.lrklaelldelvdeleaHhaaEEellfPlledrpggravldvle 77 
                                       + l +la a+++++ a +  +++ l+e v+   aH++ EE++ fP++ ++++g++v ++le
  gi|313126433|ref|YP_004036703.1| 182 R-LTRLAKALDKDESAgRVGVRRSLAETVK---AHLEGEERVGFPAMLGDAHGEEVRAELE 238
                                       3.5566666555554446666666666666...6**************7777777777665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00024      0.36     165     200 ..       5      40 ..       2      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseie 200
                                       ++v+V+Gg+  a+  Al  ++ g++V++v ++++  
  gi|313126433|ref|YP_004036703.1|   5 EDVLVVGGGLAAATSALAAAESGKTVRLVAHKKSTL 40 
                                       79***************************9988654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2761.92
//
Query:       gi|313126434|ref|YP_004036704.1|  [L=594]
Description: glycerol 3-phosphate dehydrogenase (quinone) subunit a [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-53  180.6   1.2      9e-53  180.1   1.2    1.2  1  DAO            FAD dependent oxidoreductase
    4.1e-10   39.8   3.4    5.1e-10   39.5   1.6    2.2  2  Fer2_BFD       BFD-like [2Fe-2S] binding domain
    1.6e-08   34.1   0.0    7.5e-08   32.0   0.0    1.9  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.7e-06   27.4   2.7    1.2e-05   24.6   2.7    2.0  1  FAD_binding_2  FAD binding domain
    0.00059   19.2   6.3      0.013   14.8   6.3    2.2  1  FAD_binding_3  FAD binding domain
     0.0071   16.6   0.4      0.031   14.5   0.3    2.1  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.067   13.8   0.5      0.067   13.8   0.5    2.0  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
       0.14   11.3   0.1         13    4.8   0.0    2.1  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
       0.15   12.0   0.0       0.32   10.9   0.0    1.6  1  DAO_C          C-terminal domain of alpha-glycerophosphate ox


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.1   1.2   4.5e-56     9e-53       2     351 ..       7     363 ..       6     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 180.1 bits;  conditional E-value: 4.5e-56
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelg 76 
                                       v++iGGG +G+++ ++La rg  Vtl+ekg  + +g++gr  gllhsg ry+ +  +  + + e++ee r l +  +
  gi|313126434|ref|YP_004036704.1|   7 VLVIGGGSTGCGIVRDLAMRGldVTLVEKG-NLTHGTTGRMHGLLHSGGRYAVSD-Q--PSATECIEENRVLRRI-A 78 
                                       99****************************.6666**************977754.3..9999999999999998.5 PP

                                       STTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHHHHHH CS
                               DAO  77 ididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lpgllgalfypdtgqvdpakltaal 152
                                        ++ +++tG l++ + e++ ++++++l+ ++e g++ae+l+aee+re+ep   ++++ a+ +pd g +dp++l+ a 
  gi|313126434|ref|YP_004036704.1|  79 SHC-VEMTGGLFVQRPEDSDDYFEEKLEGCRECGIPAEVLSAEEAREMEPYlAEDIKRAIRVPD-GAIDPFRLCVAN 153
                                       555.8*********98888999******99********************9655**********.999********* PP

                                       HHHHHHTT-EEEESECEEEEEEEETCEEEEE..........EECTEEEE.........EEEEEEE--GGGHHHH.HT CS
                               DAO 153 araaealGveilegtevtgleeedgkvwgve..........rttpgend.........aadavVnaaGawsdll.gl 209
                                       a++a ++G+++ +++ev+++  edg v+gve                 +          ad+vVna+Gaw++++ ++
  gi|313126434|ref|YP_004036704.1| 154 AADAIDHGARVETHAEVVDVLIEDGEVVGVEvehgeadlgiA------EgepgtreklYADYVVNATGAWAGQIgDM 224
                                       *******************988899*****888755444441......24556666786699**********99566 PP

                                       T.CTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHH CS
                               DAO 210 l.keldlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedi 285
                                       +    d+ ++p +g +  ++ ++  +v ++        +  g+  +v+p +  + ++G+t++e ++++d + +  ++
  gi|313126434|ref|YP_004036704.1| 225 AgV--DVAVRPSKGVMTIMNVRQVDTVVNR-------CRPKGDADIVVPHE-TTCILGTTDEEVDDPEDYPEEGWEV 291
                                       644..5699**********55444555554.......88999999999*86.76888****877777777777779* PP

                                       HHHHHHHHHHSGGG..CGEEEEEEEEEEE..TTSSEEEEEEETEEEEEEEEEC...TTTHHHHHHHHHHHHHH CS
                               DAO 286 dellealrklfPql..gdvlrkwaGlrpl..pdglpligetpgvkglylatGh...sghGltlapatGkllae 351
                                       d +++ l++l+P l  ++  r++ G+rpl  p+g    ++t ++++++l+  +     +G+++  + Gkl+++
  gi|313126434|ref|YP_004036704.1| 292 DLMIDTLSELVPMLseARTIRSFWGVRPLyePPGTGTEDPTDITRDFFLLDHAdrdDLPGMSSIVG-GKLTTY 363
                                       *************844445589999***55789988888887888888876666656678877777.888876 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.4   1.1e+04      11      33 ..     131     138 ..     130     142 .. 0.59
   2 !   39.5   1.6   2.6e-13   5.1e-10       1      47 [.     438     486 ..     438     490 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.4
                          Fer2_BFD  11 geIrdairraglttveevkrrtk 33 
                                       ++I++ai               +
  gi|313126434|ref|YP_004036704.1| 131 EDIKRAI---------------R 138
                                       4667776...............3 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 2.6e-13
                          Fer2_BFD   1 iVCrCegvtegeIrdairraglttveevkrrtkagtg.Cgg..Crpaiee 47 
                                       +VC+Cegvt+ eI da+ ++  t++++v+ rt+a++g C+g  C +++++
  gi|313126434|ref|YP_004036704.1| 438 VVCECEGVTRAEIHDAM-NHAGTDLNAVRIRTRASMGnCQGafCSHRMAN 486
                                       6****************.54479*********************988764 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   3.7e-11   7.5e-08       2     119 ..       6     227 ..       5     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3.7e-11
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                       +v+viGgG  G+   ++la  g++vtlve +g++ +g+    + ll++++++ +                       
  gi|313126434|ref|YP_004036704.1|   6 SVLVIGGGSTGCGIVRDLAMRGLDVTLVE-KGNLTHGTTGRMHGLLHSGGRYAVSDqpsatecieenrvlrriashc 81 
                                       79**************************5.555555555555666666666666557888889999999999999** PP

                                       .......................................................................HHHHCH CS
                                       .......................................................................xxxxxx RF
                       Pyr_redox_2  58 .......................................................................evvkkl 63 
                                                                                                              +  + +
  gi|313126434|ref|YP_004036704.1|  82 vemtgglfvqrpedsddyfeeklegcrecgipaevlsaeearemepylaedikrairvpdgaidpfrlcvaNAADAI 158
                                       ***********************************************************************777888 PP

                                       HHHCCCCHCCTCEEEEESCEEEEETEEEC............TCEEEEEESEEEE---EEE-BC.TCTTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                       Pyr_redox_2  64 nqgielllgeevvkidpgkkkvklekkke............gdeekiaydklvlAtGssprdl.gipGv 119
                                        +g ++ + +evv++  + ++v+  + +             g  ek+ +d++v AtG+++  + ++ Gv
  gi|313126434|ref|YP_004036704.1| 159 DHGARVETHAEVVDVLIEDGEVVGVEVEHgeadlgiaegepGTREKLYADYVVNATGAWAGQIgDMAGV 227
                                       88888888888999988888888866555889999999999999***************9999888887 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   2.7   5.8e-09   1.2e-05       2     204 ..       7     219 ..       6     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.8e-09
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S- CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldelad 78 
                                       v+ViG+G  G+     +a +Gl+v++vek++ + g+t    G +   + + + +++   ++    + +l   + ++ 
  gi|313126434|ref|YP_004036704.1|   7 VLVIGGGSTGCGIVRDLAMRGLDVTLVEKGNLTHGTTGRMHGLLHSGG-RYAVSDQPSATECIEENRVLRRIASHCV 82 
                                       9********************************997776655555555.3332232323333445667888999*** PP

                                       HHHHHHHHHTHHHHHHHHHHT.......T----B.CCTSSB-EEE-TT-SST..EEEE-.STT-......HHHHHHH CS
                     FAD_binding_2  79 qplveafveaapeavdeLeel.......gvpfsr.tedgpvdvrelGglsat..artlhdaadarretlvtghalla 145
                                       +    +fv++ ++  d++ee+       g+p    +   +  +re+    a+  +r  + ++d      ++ ++l++
  gi|313126434|ref|YP_004036704.1|  83 EMTGGLFVQRPEDSDDYFEEKlegcrecGIPAEVlS---AEEAREMEPYLAEdiKRAIR-VPDG----AIDPFRLCV 151
                                       *********************996665555554421...22333333333334423344.4443....555588888 PP

                                       HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET.........TTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenp.........esgrevrirakavvlatgGfgr 204
                                       + ++ a ++g ++ +++e++++++edg+v+G++ve           e g+++++ a+ vv atg++ +
  gi|313126434|ref|YP_004036704.1| 152 ANAADAIDHGARVETHAEVVDVLIEDGEVVGVEVEHGeadlgiaegEPGTREKLYADYVVNATGAWAG 219
                                       8899999****************************8899******9999999*************987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   6.3   6.5e-06     0.013       3     198 ..       6     248 ..       4     287 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.5e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EE...........EHHHHHHHHHTT-HHHHHHHSE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radgl...........nqrtmellrqlGledrilaega 67 
                                       +Vl++G+G +G    + L+++G +v+lvek + t+ ++ r +gl           ++   e +++  + +ri+++  
  gi|313126434|ref|YP_004036704.1|   6 SVLVIGGGSTGCGIVRDLAMRGLDVTLVEKGNLTHGTTgRMHGLlhsggryavsdQPSATECIEENRVLRRIASHC- 81 
                                       69*****************************999988776665533333333333677899999999999999999. PP

                                       ECCCCEEEEEEE.......................CCCCCEEEEEHH..CHHCST-CEE--HHHHHHH...HHHH.. CS
                     FAD_binding_3  68 pnelmgealyne.......................lsdtpkaradle..lesspervtvypqteleri...Lveh.. 114
                                       ++ + g +++ +                       ls   +   ++e  l    +r   +p   +++    ++++  
  gi|313126434|ref|YP_004036704.1|  82 VEMTGGLFVQRPedsddyfeeklegcrecgipaevLS--AEEAREMEpyLAEDIKRAIRVPDGAIDPFrlcVANAad 156
                                       4444577777778988888888777666665555422..22223333334455666666666665553211333300 PP

                                       HHHHTEEETCSEE.EECCEECCCCCCCEEE.........ECCTTEEEEEEEEEEEE--GTT.-HHHHHHTGGEEEEE CS
                     FAD_binding_3 115 aeerglqvrfkte.vesleqdeegvtaevr.........dketgeeetvrakYlvGaDGgr.Stvrktlgiefegee 180
                                       a  +g++v+ ++e v  l +d+e v  ev          + e g++e++ a+Y+v a G++ +++ + +g+++    
  gi|313126434|ref|YP_004036704.1| 157 AIDHGARVETHAEvVDVLIEDGEVVGVEVEhgeadlgiaEGEPGTREKLYADYVVNATGAWaGQIGDMAGVDVAVRP 233
                                       3456788888888433445666666666666666666669999999*************985689999999877766 PP

                                       EEEEEEEEEEEEEC-SCC CS
                     FAD_binding_3 181 tvyeagvldvlfdadlsd 198
                                       ++   gv+ +++  +++ 
  gi|313126434|ref|YP_004036704.1| 234 SK---GVMTIMNVRQVDT 248
                                       66...4444443334333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   1.6e-05     0.031       1      42 [.       9      48 ..       9      80 .. 0.75
   2 ?   -2.0   0.0       2.2   4.4e+03      29      40 ..     354     365 ..     352     380 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETT CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpg 42
                                      ++G+G +G+ + + La +g+dv+l+ek++ +  + ++ +++g
  gi|313126434|ref|YP_004036704.1|  9 VIGGGSTGCGIVRDLAMRGLDVTLVEKGNLT--HGTTGRMHG 48
                                      8**************************9866..445555544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                       SSSSGGG-EECE CS
                     NAD_binding_8  29 drlGGraasyev 40 
                                       + +GG++++y++
  gi|313126434|ref|YP_004036704.1| 354 SIVGGKLTTYRM 365
                                       5689****9998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   3.4e-05     0.067       1      31 [.       6      36 ..       6      42 .. 0.94
   2 ?   -2.8   0.2         5   9.9e+03      53      79 ..     160     186 ..     157     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                      +v+v+GgG +g+     la  g +Vt+ve +
  gi|313126434|ref|YP_004036704.1|  6 SVLVIGGGSTGCGIVRDLAMRGLDVTLVEKG 36
                                      699*************************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5
                                       TTEEEECSEEEEEEEEETTSEEEEEEE CS
                         Pyr_redox  53 ngievllntkveeiegsedgvesvklk 79 
                                       +g +v ++++v+ +  ++ +v +v+++
  gi|313126434|ref|YP_004036704.1| 160 HGARVETHAEVVDVLIEDGEVVGVEVE 186
                                       577788888888888555558888875 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0065        13     191     215 ..       4      28 ..       1      38 [. 0.82
   2 ?    4.4   0.0    0.0086        17     297     339 ..     174     215 ..     162     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0065
                       K_oxygenase 191 kkriaVvGsGqSaaeifedllrrqk 215
                                         +++V+G+G ++  i++dl+ r  
  gi|313126434|ref|YP_004036704.1|   4 TPSVLVIGGGSTGCGIVRDLAMRGL 28 
                                       568*****************98754 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0086
                       K_oxygenase 297 llpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                       l+++ ev ++e e+ ge +l + + e g++e+l +d+vv ATG
  gi|313126434|ref|YP_004036704.1| 174 LIEDGEVVGVEVEH-GEADLGIAEGEPGTREKLYADYVVNATG 215
                                       56677888888887.69*************************9 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.32       1     100 [.     384     474 ..     384     494 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                       --TTS---TT--.......TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH...HHHHHTTS-HHHHHHHHHH CS
                             DAO_C   1 crTkklpLvGaenwsknlaaelaqeygldeevaehLaerYGsraeevlelakedekpelaerlspelpyieaevvYa 77 
                                       crT++ pL+G+e+   ++ ++ ++e+g+ +   ++ a+r Gsr+++vl   + d+       +++ + +++ae+  a
  gi|313126434|ref|YP_004036704.1| 384 CRTAEEPLPGSED--FSVLRDWMDEFGIRSPIGRRSAQRLGSRTDDVL--GEWDG---PNPVVCECEGVTRAEIHDA 453
                                       9***********6..57789***************************9..76666...4556667777888888877 PP

                                       HHHS---SHHHHHHTTS-HHHH- CS
                             DAO_C  78 vrhEmartlvDvlaRRtrlafld 100
                                       ++  +a t    +  Rtr+++ +
  gi|313126434|ref|YP_004036704.1| 454 MN--HAGTDLNAVRIRTRASMGN 474
                                       77..4556566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 3289.27
//
Query:       gi|313126435|ref|YP_004036705.1|  [L=393]
Description: cdc6-related protein, aaa superfamily ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.5e-14   52.1   1.2    9.5e-14   52.1   1.2    1.9  2  AAA_16     AAA ATPase domain
    2.6e-05   24.5   0.0    4.8e-05   23.6   0.0    1.5  1  AAA_22     AAA domain
     0.0069   16.3   1.0      0.021   14.7   0.4    2.2  2  MarR_2     MarR family
  ------ inclusion threshold ------
      0.018   15.3   0.0       0.03   14.7   0.0    1.4  1  AAA_19     AAA domain
       0.02   15.0   0.2      0.084   12.9   0.2    2.1  1  HTH_20     Helix-turn-helix domain
      0.034   14.2   0.0       0.06   13.4   0.0    1.5  1  MMR_HSR1   50S ribosome-binding GTPase
      0.083   13.4   0.0       0.13   12.8   0.0    1.3  1  ABC_tran   ABC transporter
      0.086   13.0   0.1       0.18   11.9   0.1    1.6  1  AAA_33     AAA domain
       0.17   11.9   0.0       0.41   10.6   0.0    1.7  1  AAA_5      AAA domain (dynein-related subfamily)
        1.2    9.8  14.6        1.4    9.6   1.4    3.8  4  SnoaL_2    SnoaL-like domain


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   1.2   5.3e-17   9.5e-14       2     164 ..      36     186 ..      35     194 .. 0.80
   2 ?   -0.6   0.0      0.82   1.5e+03      74     159 ..     221     256 ..     194     317 .. 0.60

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 5.3e-17
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                        vGR+  le+Ll+ l+++ +gr  e+  ++G++G GKs++v +l+++l ++    + ++    ++     a ++a +
  gi|313126435|ref|YP_004036705.1|  36 PVGRGPTLERLLDRLDPAFDGRLpESFCVVGPKGAGKSAVVAALFEHLAAT----APTQHGAIQTT--TRAATSAVT 106
                                       79********************************************99999....44444444222..223555664 PP

                            AAA_16  78 reellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslql 154
                                       +   +++++++a+++e++  r+ l +++ ++ + +g +  +l++ l++ l++ +r    lv+ +D++   ++ +l+ 
  gi|313126435|ref|YP_004036705.1| 107 E---FAAVDARAADSEFALLRAVLAAVADDAVPERGVGTAALRDRLRDELDRFRR----LVVAVDHVGESKTVTLET 176
                                       5...555555555577777777777777788899999999**********99999....****************** PP

                            AAA_16 155 laaLlrlles 164
                                       l++++++++ 
  gi|313126435|ref|YP_004036705.1| 177 LDSTFEEMSP 186
                                       *999998775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.82
                            AAA_16  74 qalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadea 150
                                       + +  ++l+r+  d+++ +e++aw                                                 ad +
  gi|313126435|ref|YP_004036705.1| 221 RRA-SDGLVRDGIDHETVSEVAAW-------------------------------------------------ADGD 247
                                       333.22344444444333344444.................................................4333 PP

                            AAA_16 151 slqllaaLl 159
                                        ++ laaL+
  gi|313126435|ref|YP_004036705.1| 248 AHDGLAALF 256
                                       333333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.7e-08   4.8e-05       8     101 ..      62     167 ..      57     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.7e-08
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralglelka 70 
                                        +v+G++G+GK+ +++ l+e l + a   +              +  e++ v++ +  s   llr++l a+ +++  
  gi|313126435|ref|YP_004036705.1|  62 FCVVGPKGAGKSAVVAALFEHLAATAP--TqhgaiqtttraatsAVTEFAAVDARAADSEFALLRAVLAAVADDAVP 136
                                       689******************954444..2469******98888888888**********************99988 PP

                            AAA_22  71 .erlsseellealeqalraravielliiDEaq 101
                                        ++  + +l+++l++ l++ ++  ++ +D + 
  gi|313126435|ref|YP_004036705.1| 137 eRGVGTAALRDRLRDELDRFRR-LVVAVDHVG 167
                                       7888999999*********999.999999665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.8   8.6e+03      35      52 ..     212     229 ..     210     238 .. 0.71
   2 !   14.7   0.4   1.2e-05     0.021       2      58 ..     294     358 ..     293     360 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHHHHTTSEE CS
                            MarR_2  35 ksavsrilkrLvaaGLve 52 
                                       ++a+  +l r  + GLv+
  gi|313126435|ref|YP_004036705.1| 212 RHALVDVLTRRASDGLVR 229
                                       566666677777778876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       T--HHHHHHHHHHHCTTTS.....EEEHHHHHH..HHTSSHHHHHHHHHHHHHTTSEEEE.ESSS CS
                            MarR_2   2 gltpaqarvLaaLgrrpgr.....dltvgelar..rlglsksavsrilkrLvaaGLverr.pgpe 58 
                                       +l+ + +rvLa+L+  ++       +++ ++a+    +ls ++v r+l +L + G v+r+ +g++
  gi|313126435|ref|YP_004036705.1| 294 ALPASRRRVLAVLASLDPAdcssvTVAADAIAAhpSVDLSAATVKRVLYELADDGIVRRVdTGLG 358
                                       578899***********9988877779999999999***********************966655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.7e-05      0.03      13      68 ..      62     114 ..      53     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                            AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae 68 
                                       ++v+++ G GK+ v+ +  ++l ++   + ++ ++ + t+ A++ ++e   a++a+
  gi|313126435|ref|YP_004036705.1|  62 FCVVGPKGAGKSAVVAALFEHLAATA--PTQHGAIQTTTRAATSAVTEFA-AVDAR 114
                                       6899********************99..4467777777888888888766.44444 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   4.7e-05     0.084      11      60 ..     298     356 ..     294     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHH...STCTTB-HHHHHHHH......TS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  11 vRrrilraL...araegltaselaerl......dlskntlsyHLrvLeeagLvevvreg 60 
                                       +Rrr+l+ L    +a++ +++  a+++      dls +t+ + L +L++ g+v++v++g
  gi|313126435|ref|YP_004036705.1| 298 SRRRVLAVLaslDPADCSSVTVAADAIaahpsvDLSAATVKRVLYELADDGIVRRVDTG 356
                                       5999999998889999999999999999888888*********************9876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.3e-05      0.06       2      52 ..      62     112 ..      61     193 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvD 52 
                                       +++vG   +GKS ++ al++  a ++ ++   ++++++  +   +e+  vD
  gi|313126435|ref|YP_004036705.1|  62 FCVVGPKGAGKSAVVAALFEHLAATAPTQHGAIQTTTRAATSAVTEFAAVD 112
                                       589****************98555555543333333333332223444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     7e-05      0.13      14      51 ..      62     103 ..      54     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7e-05
                                       EEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkp....teGeilldgkdlke 51 
                                         +vG+ GaGKS ++++l ++l      + G i+   +  ++
  gi|313126435|ref|YP_004036705.1|  62 FCVVGPKGAGKSAVVAALFEHLAAtaptQHGAIQTTTRAATS 103
                                       578***********9999988877566678888666555554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001      0.18       4      72 ..      64     132 ..      62     184 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                            AAA_33   4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrn 72 
                                       +vG++G+GKs ++  l ++l+a+  ++  ++++ +       t+ + v  r+ +  ++l+r +l+a ++
  gi|313126435|ref|YP_004036705.1|  64 VVGPKGAGKSAVVAALFEHLAATAPTQHGAIQTTTRAATSAVTEFAAVDARAADSEFALLRAVLAAVAD 132
                                       79******************9988888887777776656666666666666665555555555544444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00023      0.41       2      31 ..      62      93 ..      61     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                                      EEEE--SSSSHHHHHHHGGGGB..S--EEEEE CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal..nreveyvq 31
                                      +++vGp+G gKs ++  l + l  +++++  +
  gi|313126435|ref|YP_004036705.1| 62 FCVVGPKGAGKSAVVAALFEHLaaTAPTQHGA 93
                                      79**************9999996655554443 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3     0.075   1.3e+02      33      74 ..      69     111 ..      41     123 .. 0.79
   2 ?    4.2   0.8     0.038        68      15      62 ..     125     168 ..     109     187 .. 0.71
   3 ?   -1.8   0.0       2.8     5e+03      45      69 ..     192     216 ..     187     231 .. 0.71
   4 ?    9.6   1.4   0.00076       1.4       5      48 ..     240     284 ..     238     352 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.075
                                       EESHHHHHH.HHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEE CS
                           SnoaL_2  33 lrGreaira.ffralfaafpdlrfeihdvvadgdrvavewtvt 74 
                                         G+ a+ a  f++l a+ p+ +  i+  +     +++e+ + 
  gi|313126435|ref|YP_004036705.1|  69 GAGKSAVVAaLFEHLAATAPTQHGAIQTTTRAATSAVTEFAAV 111
                                       56888777779999999***********999999999998664 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.038
                                       HHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEE CS
                           SnoaL_2  15 alaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdvva 62 
                                       a++a +a+d+v e  +g+   r+++r+ + ++     +l + +++v +
  gi|313126435|ref|YP_004036705.1| 125 AVLAAVADDAVPERGVGTAALRDRLRDELDRF----RRLVVAVDHVGE 168
                                       66677777777777776666666666666666....567777777644 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.8
                                       HHHHHEEEEEEEEEEEEEETTEEEE CS
                           SnoaL_2  45 alfaafpdlrfeihdvvadgdrvav 69 
                                       a+ +afpd ++e  +v   +++++v
  gi|313126435|ref|YP_004036705.1| 192 AVGRAFPDAHVESVEVPRYERHALV 216
                                       4566789999998888666666665 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00076
                                       HHHHHTTCH.HHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHH CS
                           SnoaL_2   5 laalnagdl.dalaalfapdvvwedpggelrGreairaffralfa 48 
                                       +aa+++gd+ d+laalf++ vv +d g+++ G   ++a   a+ +
  gi|313126435|ref|YP_004036705.1| 240 VAAWADGDAhDGLAALFSAAVVATDDGATRIGSSHVAAGCDAVPE 284
                                       58******889******************9999999997766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.67u 0.41s 00:00:01.08 Elapsed: 00:00:00.58
# Mc/sec: 2054.18
//
Query:       gi|313126436|ref|YP_004036706.1|  [L=225]
Description: phosphoglycolate phosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-26   91.9   0.0    1.7e-15   57.5   0.1    2.1  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    2.8e-05   23.8   0.0    0.00025   20.6   0.0    2.0  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
    4.1e-05   24.0   0.0      0.057   13.7   0.0    2.3  2  Hydrolase        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.043   12.9   0.2       0.17   11.0   0.0    1.9  2  Trehalose_PPase  Trehalose-phosphatase
       0.13   12.3   0.7       0.58   10.2   0.0    2.2  2  HAD_2            Haloacid dehalogenase-like hydrolase
       0.47   10.8   2.7         44    4.4   0.6    3.1  3  HAD              haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.6e-11   4.6e-08       1      76 [.       8      79 ..       8     124 .. 0.88
   2 !   57.5   0.1   5.7e-19   1.7e-15     174     252 ..     139     217 ..     102     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.6e-11
                                      EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilyk 76
                                      ++lD+DGTL ++ +++++++ +++  +      vv+ATG s+    ++ + lgl+  v+a NG+++  ++g++ y+
  gi|313126436|ref|YP_004036706.1|  8 LVLDIDGTLTDEPGRLDPRAFDVLPSWD---APVVLATGKSFPYPVSLCHYLGLERNVVAENGGVV-LANGEVTYT 79
                                      589****************999999976...9**********************************.999999965 PP

  == domain 2  score: 57.5 bits;  conditional E-value: 5.7e-19
                                       ESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTH CS
                       Hydrolase_3 174 sskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedG 250
                                        +++ + +  +gv Kg + k+l+++l+++++e +a+GD+ ND + + ++g ++A++na+e +k+aAd v      dG
  gi|313126436|ref|YP_004036706.1| 139 DTGYAYHVKTPGVEKGIGFKRLCETLSMDPDEFVAVGDSTNDTSTFGVVGQSYAVANADEAAKAAADEVLSASYMDG 215
                                       4567788999***********************************************************99988888 PP

                                       HH CS
                       Hydrolase_3 251 Va 252
                                        +
  gi|313126436|ref|YP_004036706.1| 216 TL 217
                                       65 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.077   2.3e+02       5      47 ..       8      47 ..       7      92 .. 0.68
   2 !   20.6   0.0   8.5e-08   0.00025     162     218 ..     149     200 ..     108     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.077
                                      EEE-TBTTTB..S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HH CS
                              S6PP  5 lvsdLDntlv.dgdnealarlnelleaeerkdvllvfaTGRsld 47
                                      lv d+D+tl+ ++ + + +++  l     + d  +v+aTG+s+ 
  gi|313126436|ref|YP_004036706.1|  8 LVLDIDGTLTdEPGRLDPRAFDVLP----SWDAPVVLATGKSFP 47
                                      7999****99433344444443333....467777777777765 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 8.5e-08
                                       TT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHHHH CS
                              S6PP 162 kraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqwll 218
                                        + +kg   + L++ l +++++++ +Gds nD++ +    ++  V+na+e+     +
  gi|313126436|ref|YP_004036706.1| 149 PGVEKGIGFKRLCETLSMDPDEFVAVGDSTNDTSTFGVVGQSYAVANADEA-----A 200
                                       5678999999**************************888888899999988.....2 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00098       2.9       4      38 ..       8      44 ..       7      98 .. 0.73
   2 !   13.7   0.0   1.9e-05     0.057     145     204 ..     123     182 ..     107     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00098
                                      EEEESBTTTBCHH....HHHHHHHHHHCHHHHHHHHHHH CS
                                      xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  4 vvfDkdGTLttge....psvedvivsaalalaaaletgs 38
                                      +v+D+dGTLt+      p+  dv++s   +  ++l+tg 
  gi|313126436|ref|YP_004036706.1|  8 LVLDIDGTLTDEPgrldPRAFDVLPSW--DAPVVLATGK 44
                                      699*******65566888888888888..6666666663 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 145 petaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaa 204
                                       ++  +++a ++ +d +d  +a+ ++t +  +  g++++++ L  +p e ++VGD+ nD +
  gi|313126436|ref|YP_004036706.1| 123 EKLLREVATEYEMDVIDTGYAYHVKTPGVEKGIGFKRLCETLSMDPDEFVAVGDSTNDTS 182
                                       44455555555555556666666666666699**************************76 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.19   5.7e+02       2      10 ..      10      18 ..       9      24 .. 0.88
   2 ?   11.0   0.0   5.7e-05      0.17     127     204 ..     117     190 ..     108     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.19
                                      EETBTTTB- CS
                   Trehalose_PPase  2 lDydGTlsp 10
                                      lD+dGTl++
  gi|313126436|ref|YP_004036706.1| 10 LDIDGTLTD 18
                                      8******97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.7e-05
                                       .THHHHHHHHHHHHHHH.--EEEE-SSEEEEE-S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-T CS
                   Trehalose_PPase 127 lqakelaehlesvltdkpdlevtqgkkvvevrpqgvsKGkaverlleslgsadseddfvlciGDdrtDedmFsvlrk 203
                                       ++  + ++ l++v t++ +++v +      v+  gv KG   +rl e+l  +   +d  +++GD   D + F v+ +
  gi|313126436|ref|YP_004036706.1| 117 VSLAADEKLLREVATEY-EMDVIDTGYAYHVKTPGVEKGIGFKRLCETLSMD---PDEFVAVGDSTNDTSTFGVVGQ 189
                                       56677788899988888.99999999999*********************99...77777************99987 PP

                                       T CS
                   Trehalose_PPase 204 t 204
                                        
  gi|313126436|ref|YP_004036706.1| 190 S 190
                                       6 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.35     1e+03       2      12 ..       9      19 ..       8      20 .. 0.85
   2 ?   10.2   0.0   0.00019      0.58     140     166 ..     156     182 ..     121     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.35
                             HAD_2  2 iFDlDgTlldt 12
                                      + D+DgTl d+
  gi|313126436|ref|YP_004036706.1|  9 VLDIDGTLTDE 19
                                      67******996 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                             HAD_2 140 viekaleklklkkeeviyvGDsptDie 166
                                        +++++e l ++++e + vGDs++D  
  gi|313126436|ref|YP_004036706.1| 156 GFKRLCETLSMDPDEFVAVGDSTNDTS 182
                                       568899*******************75 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.6     0.015        44       2      12 ..       9      19 ..       8      30 .. 0.83
   2 ?    2.2   0.0      0.07   2.1e+02      86     169 ..      23      99 ..      19     104 .. 0.69
   3 ?    3.1   0.0     0.038   1.1e+02     167     184 ..     164     181 ..     120     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.015
                               HAD  2 lfDfDgTLldg 12
                                      ++D+DgTL+d+
  gi|313126436|ref|YP_004036706.1|  9 VLDIDGTLTDE 19
                                      89*******98 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.07
                               HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelg.adevlatelevdd..rltgelglegkpvrgegkvaalr 159
                                       ldp a ++l    +   +vv+ +g   p+   l+  lg   +v+a+     +  ++ +   +e + + ++++++a++
  gi|313126436|ref|YP_004036706.1|  23 LDPRAFDVLP---SWDAPVVLATGKSFPYPVSLCHYLGlERNVVAE-----NggVVLAN--GEVTYTGDKERAQAVA 89 
                                       5677777777...445699*******************55555555.....33666666..6666666666778887 PP

                               HAD 160 ewlaaegegi 169
                                       +   a+g ++
  gi|313126436|ref|YP_004036706.1|  90 DEFVARGGDL 99 
                                       7666666555 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.038
                               HAD 167 egidleevvayGDspsDl 184
                                          d++e va+GDs +D 
  gi|313126436|ref|YP_004036706.1| 164 LSMDPDEFVAVGDSTNDT 181
                                       45677789*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1232.54
//
Query:       gi|313126437|ref|YP_004036707.1|  [L=110]
Description: hypothetical protein Hbor_16940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-31  107.3   0.0    3.1e-31  107.1   0.0    1.0  1  CutA1            CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
      0.053   13.5   0.0       0.21   11.6   0.0    1.8  2  Phage_term_smal  Phage small terminase subunit


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.0   3.5e-35   3.1e-31       3      97 ..       4      96 ..       2      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 3.5e-35
                                      EEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEE CS
                             CutA1  3 vlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeii 81
                                      v+vtap +++a+++a++lvee+laACvn +  +eSvYrW+g++ +++Ev ll+kt++e++ el kr++elhpy+vp+i 
  gi|313126437|ref|YP_004036707.1|  4 VYVTAP-SDHAEDIAHTLVEERLAACVNRVA-CESVYRWDGEVFDESEVILLAKTTAERYGELRKRITELHPYDVPCIE 80
                                      89****.578********************9.*********************************************** PP

                                      EEEESEEEHHHHHHHH CS
                             CutA1 82 alpieagseaYlkWie 97
                                       ++ +++ +aY++W+e
  gi|313126437|ref|YP_004036707.1| 81 RFDEDDVLPAYAAWVE 96
                                      **************97 PP

>> Phage_term_smal  Phage small terminase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.13   1.2e+03      80     102 ..       8      30 ..       5      57 .. 0.71
   2 ?   11.6   0.0   2.4e-05      0.21      26      48 ..      86     108 ..      81     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.13
                   Phage_term_smal  80 lPdrfkrtlatvvaeeiadaalk 102
                                        P+ +  ++a++++ee ++a  +
  gi|313126437|ref|YP_004036707.1|   8 APSDHAEDIAHTLVEERLAACVN 30 
                                       57777777777777776665544 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.4e-05
                   Phage_term_smal  26 elLpkYqpwvegvlaagsgaqde 48 
                                       ++Lp+Y++wveg+ a+g+++ d 
  gi|313126437|ref|YP_004036707.1|  86 DVLPAYAAWVEGATADGEDEGDG 108
                                       68***************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 630.65
//
Query:       gi|313126438|ref|YP_004036708.1|  [L=66]
Description: hypothetical protein Hbor_16950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 375.39
//
Query:       gi|313126439|ref|YP_004036709.1|  [L=185]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-20   71.8   0.1    1.4e-19   70.5   0.1    1.6  2  Methyltransf_11  Methyltransferase domain
    9.4e-17   61.5   0.0    2.3e-16   60.3   0.0    1.6  2  Methyltransf_25  Methyltransferase domain
    2.9e-09   36.9   0.0    4.1e-09   36.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    4.6e-07   29.4   0.0    6.3e-07   29.0   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    4.8e-06   26.5   0.0      6e-06   26.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0015   19.2   0.0     0.0032   18.2   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.059   13.2   0.0       0.13   12.1   0.0    1.6  1  Methyltransf_8   Hypothetical methyltransferase
      0.089   11.9   0.0       0.34   10.0   0.0    1.7  2  DREV             DREV methyltransferase
       0.27   11.7   1.3         32    5.1   0.0    3.1  3  DUF4350          Domain of unknown function (DUF4350)


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.1   7.2e-23   1.4e-19       2      95 ..      42     132 ..      41     133 .. 0.97
   2 ?   -2.2   0.0       3.3   6.6e+03      49      65 ..     154     169 ..     140     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 7.2e-23
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                       d+G+GtG ++ ++a +++++++vD+  em++  ++k+ ++   v+fv ad+++lpf+d+  D+ +s+++ h ++  +
  gi|313126439|ref|YP_004036709.1|  42 DFGSGTGFYTDDVAPHVGTCYAVDVQSEMHEFYRQKGAPDT--VTFVTADVSSLPFADDELDAAFSTMTYHEFA-SD 115
                                       89************999**********************99..9*****************************5.99 PP

                                       HHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  79 kalkeiaRvLkpgGllv 95 
                                       +a++e+aRv+kpgG++v
  gi|313126439|ref|YP_004036709.1| 116 DAVAELARVVKPGGRVV 132
                                       **************987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.3
                                       TEECCCTSS-TT-EEEE CS
                   Methyltransf_11  49 vadaeklpfednsfDlv 65 
                                        +da +  fe + fD++
  gi|313126439|ref|YP_004036709.1| 154 LGDAVT-AFEAHGFDVI 169
                                       455553.6777788877 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   1.1e-19   2.3e-16       1      97 []      40     129 ..      40     129 .. 0.93
   2 ?   -2.7   0.0       4.9   9.8e+03      59      70 ..     160     171 ..     150     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.1e-19
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       v d+G GtG +t ++a ++  ++ ++vD+++em e  r++ + +   v+fv++d+++lpf+d++ D+ +s++++h +
  gi|313126439|ref|YP_004036709.1|  40 VADFGSGTGFYTDDVAPHV--GTCYAVDVQSEMHEFYRQKGAPD--TVTFVTADVSSLPFADDELDAAFSTMTYHEF 112
                                       78****************9..8*******************544..8***********************8888878 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                         +   +a++e+arv+kpgG
  gi|313126439|ref|YP_004036709.1| 113 ASD---DAVAELARVVKPGG 129
                                       744...699**********9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.9
                                       SSSTTTEEEEEE CS
                   Methyltransf_25  59 pfedgsfDlvvs 70 
                                        fe++ fD++ +
  gi|313126439|ref|YP_004036709.1| 160 AFEAHGFDVIRA 171
                                       466777777755 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0     2e-12   4.1e-09       4     111 ..      37     135 ..      34     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2e-12
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       + +v D G+GtG++t   a  +g+    + +D + e+ e+ r+   k   d v+F  +d+ +l+  ++d+  D  +s
  gi|313126439|ref|YP_004036709.1|  37 DAVVADFGSGTGFYTDDVAPHVGT---CYAVDVQSEMHEFYRQ---KGAPDTVTFVTADVSSLP--FADDELDAAFS 105
                                       67899**************98876...*************999...78899*************..********999 PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggillied 111
                                         + ++  ++d++  e+ rv+kpgg++++ d
  gi|313126439|ref|YP_004036709.1| 106 TMT-YHEFASDDAVAELARVVKPGGRVVTVD 135
                                       655.5777777778888**********9866 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   3.1e-10   6.3e-07      49     156 ..      38     138 ..      22     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.1e-10
                                       TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES- CS
                   Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfG 125
                                       a v D  +Gtg ++ +++ +vg   +   +D++++m +  ++k    +   + f++a+   Lpf dd  D    +  
  gi|313126439|ref|YP_004036709.1|  38 AVVADFGSGTGFYTDDVAPHVG---TCYAVDVQSEMHEFYRQKG---APDTVTFVTADVSSLPFADDELDAAFSTMT 108
                                       5677999999999988888875...6678899****99998874...455899*****************9887777 PP

                                       GGG-S-HHHHHHHHHHHEEEEEEEEEEEE-- CS
                   Ubie_methyltran 126 lrnvtDklkaLkeayrvlkpGGrlvvlefsk 156
                                          ++  + a+ e+ rv+kpGGr+v ++ +k
  gi|313126439|ref|YP_004036709.1| 109 YHEFAS-DDAVAELARVVKPGGRVVTVDWTK 138
                                       788875.568899************998766 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0     3e-09     6e-06       9     123 ..      23     139 ..      14     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3e-09
                   Methyltransf_23   9 ls.dklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...kakkaqkdqfdeqeaaepqg 81 
                                       +s ++l+ ll + ++++ v d+G GtG  ++  ++++ ++++vD  +e++e ++    +++  ++ +d ++ ++ ++
  gi|313126439|ref|YP_004036709.1|  23 CSrEELLSLL-RPNPDAVVADFGSGTGFYTDDVAPHVGTCYAVDVQSEMHEFYRqkgAPDTVTFVTADVSSLPFADD 98 
                                       3335566666.589*************99999999999****************9999999999999999******* PP

                   Methyltransf_23  82 kfdlIvlrevlehvpdppellrqiatllkpgGylllseplas 123
                                         d + ++++ + + +   +++ +a+ +kpgG+++  ++++ 
  gi|313126439|ref|YP_004036709.1|  99 ELDAAFSTMTYHEFAS-DDAVAELARVVKPGGRVVTVDWTKA 139
                                       ***************8.899***************9999765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-06    0.0032       2      99 .]      42     131 ..      41     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       ++G+GtG +++ ++++    + ++vD+++++ e  ++k a      +++v+ ++ +l   d  +  D+ ++  + h 
  gi|313126439|ref|YP_004036709.1|  42 DFGSGTGFYTDDVAPH--VGTCYAVDVQSEMHEFYRQKGAPDT---VTFVTADVSSLPFAD--DELDAAFSTMTYHE 111
                                       8***************..99999*********77766655544...444555544444444..59*********999 PP

                   Methyltransf_12  79 lkdirevldnirklLkpgGrl 99 
                                       +   +++++++++++kpgGr+
  gi|313126439|ref|YP_004036709.1| 112 F-ASDDAVAELARVVKPGGRV 131
                                       7.778999***********85 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.3e-05      0.13     107     154 ..      84     131 ..      26     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.3e-05
                                       TEEES-TTS-S--TT-EEEEEEES---SS-HHHHHHHHHHHEEEEEEE CS
                    Methyltransf_8 107 rvvacdlakvPledesvdvavfclslmgtnladflkeanrvlkvGGll 154
                                         v+ d++ +P +d+  d a   ++       d + e  rv+k+GG +
  gi|313126439|ref|YP_004036709.1|  84 TFVTADVSSLPFADDELDAAFSTMTYHEFASDDAVAELARVVKPGGRV 131
                                       45789*****************999999999***************76 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00017      0.34      95     135 ..      37      77 ..      26      93 .. 0.88
   2 ?   -0.5   0.0      0.26   5.2e+02     218     260 ..     115     158 ..      96     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                              DREV  95 dkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk 135
                                       d  + d+G+G G  t  vap++   ya ++ ++m +  ++k
  gi|313126439|ref|YP_004036709.1|  37 DAVVADFGSGTGFYTDDVAPHVGTCYAVDVQSEMHEFYRQK 77 
                                       56789*****************************9866655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.26
                              DREV 218 eeevarlievlkkagfeve.aftrlPylceGdlnnsfyylddai 260
                                       ++ va+l  v+k+ g +v   +t++     G   ++ y l da+
  gi|313126439|ref|YP_004036709.1| 115 DDAVAELARVVKPGGRVVTvDWTKAGDGESGPPTDERYGLGDAV 158
                                       57889999999999988753699988777777777777777776 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.066   1.3e+02      25      53 ..      70     101 ..      63     109 .. 0.71
   2 ?    5.1   0.0     0.016        32      48      68 ..     114     134 ..     107     135 .. 0.83
   3 ?    0.5   0.0      0.42   8.4e+02       4      27 ..     151     174 ..     149     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.066
                           DUF4350  25 rkpfdalegedgtllvvapdlrlte...eela 53 
                                        + f+++ g+++t+ +v+ d++  +   +el+
  gi|313126439|ref|YP_004036709.1|  70 MHEFYRQKGAPDTVTFVTADVSSLPfadDELD 101
                                       56789999999999888888765544446665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                           DUF4350  48 teeelaallewvarGntlvla 68 
                                       +++ +a+l + v++G+++v +
  gi|313126439|ref|YP_004036709.1| 114 SDDAVAELARVVKPGGRVVTV 134
                                       4477999************87 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.42
                           DUF4350   4 pnGtralaelLeaqGvevrrvrkp 27 
                                       ++G+  +++  ea+G +v+r+++ 
  gi|313126439|ref|YP_004036709.1| 151 RYGLGDAVTAFEAHGFDVIRATTR 174
                                       78999999999*******999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1062.09
//
Query:       gi|313126440|ref|YP_004036710.1|  [L=51]
Description: hypothetical protein Hbor_16970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0013   18.3   0.1          1    9.2   0.0    2.1  2  A2L_zn_ribbon   A2L zinc ribbon domain
  ------ inclusion threshold ------
      0.011   15.6   0.9        2.4    8.1   0.1    2.1  2  zf-trcl         Probable zinc-ribbon domain
      0.011   15.7   0.4      0.012   15.7   0.4    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.013   15.7   0.4      0.016   15.4   0.4    1.2  1  zf-UBR          Putative zinc finger in N-recognin (UBR box)
      0.016   15.0   1.0        1.6    8.7   0.1    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.017   15.1   0.5       0.26   11.3   0.1    2.1  2  Ogr_Delta       Ogr/Delta-like zinc finger
      0.018   15.1   5.5      0.056   13.6   5.5    1.7  1  Zn-ribbon_8     Zinc ribbon domain
      0.021   14.2   0.1      0.022   14.2   0.1    1.0  1  Mcm10           Mcm10 replication factor
      0.023   14.4   3.6       0.56   10.0   0.4    2.1  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.044   13.6   0.1      0.046   13.6   0.1    1.0  1  MCM_OB          MCM OB domain
      0.081   12.6   1.2       0.14   11.8   1.2    1.3  1  TackOD1         Thaumarchaeal output domain 1
        0.1   12.3   3.6       0.57    9.9   3.6    1.9  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.13   12.1   3.2       0.37   10.7   3.2    1.7  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.32   11.1   0.2       0.32   11.1   0.2    2.0  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.56    9.8   3.3         15    5.3   0.2    2.4  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00085         1      18      29 ..      14      25 ..       6      28 .. 0.89
   2 !    7.7   0.0    0.0024       2.8       4      16 ..      33      45 ..      30      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00085
                     A2L_zn_ribbon 18 eqgylvCieCga 29
                                      + +y+ C +Cga
  gi|313126440|ref|YP_004036710.1| 14 TESYYECRDCGA 25
                                      679********8 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0024
                     A2L_zn_ribbon  4 kvCsvCggngiln 16
                                       +C+ Cg++ ++n
  gi|313126440|ref|YP_004036710.1| 33 TTCEECGSDALFN 45
                                      589*****99997 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0054       6.5       5      13 ..      18      26 ..      14      28 .. 0.80
   2 ?    8.1   0.1     0.002       2.4       5      16 ..      33      44 ..      30      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0054
                           zf-trcl  5 ltCkdCgae 13
                                      + C+dCga 
  gi|313126440|ref|YP_004036710.1| 18 YECRDCGAR 26
                                      78*****86 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.002
                           zf-trcl  5 ltCkdCgaefvF 16
                                       tC++Cg++  F
  gi|313126440|ref|YP_004036710.1| 33 TTCEECGSDALF 44
                                      58*******999 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.4   9.8e-06     0.012      68      96 ..      15      42 ..       4      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.8e-06
                                      --EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA 68 pvkvrCreCgkefeleekalrCpkCgsad 96
                                      +  ++Cr+Cg++++ +   ++C++Cgs  
  gi|313126440|ref|YP_004036710.1| 15 ESYYECRDCGARTTGKP-ITTCEECGSDA 42
                                      56689*****9999664.468*****975 PP

>> zf-UBR  Putative zinc finger in N-recognin (UBR box)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.4   1.3e-05     0.016       9      31 ..      14      39 ..       5      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                            zf-UBR  9 gevvyrCltCsld...etsviCeeCf 31
                                       e++y+C++C+     +    CeeC 
  gi|313126440|ref|YP_004036710.1| 14 TESYYECRDCGARttgKPITTCEECG 39
                                      589*********976644799***96 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0013       1.6      24      37 ..      13      26 ..      12      28 .. 0.82
   2 ?    5.6   0.1     0.012        15       2       9 ..      34      41 ..      33      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                           TFIIS_C 24 pmtvfykCtkCghr 37
                                      p+  +y+C +Cg r
  gi|313126440|ref|YP_004036710.1| 13 PTESYYECRDCGAR 26
                                      56679******987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                           TFIIS_C  2 kCpkCgsr 9 
                                      +C++Cgs+
  gi|313126440|ref|YP_004036710.1| 34 TCEECGSD 41
                                      79999987 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00022      0.26      22      37 ..      14      27 ..       4      30 .. 0.89
   2 ?    2.6   0.0      0.11   1.4e+02       1       9 [.      34      42 ..      34      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                         Ogr_Delta 22 reryyqCsnfeCgatf 37
                                      +e yy+C++  Cga+ 
  gi|313126440|ref|YP_004036710.1| 14 TESYYECRD--CGART 27
                                      79*******..**986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                         Ogr_Delta  1 rCPhCgapa 9 
                                      +C +Cg+ a
  gi|313126440|ref|YP_004036710.1| 34 TCEECGSDA 42
                                      699***987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.5   4.7e-05     0.056       6      36 ..      18      42 ..      17      43 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.7e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsev 36
                                      Y+C++Cg + +       +p t+C eCgs++
  gi|313126440|ref|YP_004036710.1| 18 YECRDCGARTT------GKPITTCEECGSDA 42
                                      9******7766......457888*****954 PP

>> Mcm10  Mcm10 replication factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.9e-05     0.022     291     319 ..      16      41 ..       7      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                             Mcm10 291 rFFkCakCgkRtvsldrlPskhCsnCges 319
                                        +++C++Cg Rt      P ++C++Cg+ 
  gi|313126440|ref|YP_004036710.1|  16 SYYECRDCGART---TGKPITTCEECGSD 41 
                                       69**********...679********985 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   0.00047      0.56       1      10 [.      18      27 ..      18      29 .. 0.90
   2 ?    5.8   0.2    0.0098        12       3      10 ..      35      42 ..      34      43 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00047
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y+C++CG+++
  gi|313126440|ref|YP_004036710.1| 18 YECRDCGART 27
                                      9******987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0098
                      Rubredoxin_2  3 CsqCGfes 10
                                      C++CG+++
  gi|313126440|ref|YP_004036710.1| 35 CEECGSDA 42
                                      99999875 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.9e-05     0.046      20      68 ..       2      47 ..       1      50 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                                      EEEE---EE.EEEEEEEEETTT-.-EEES----S.B-..TTT-HHH-EEE- CS
                            MCM_OB 20 vtrasevkp.klkkavfeckkcgktveveleePr.kCeekeCeskdpfkle 68
                                      v + ++v p + +++++ec++cg+ ++    +P  +C  +eC+s   f+l+
  gi|313126440|ref|YP_004036710.1|  2 VLTHTDVDPySPTESYYECRDCGARTT---GKPItTC--EECGSDALFNLS 47
                                      566667766356899********9555...6775489..89*987777765 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.2   0.00012      0.14     133     170 ..       3      40 ..       1      45 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                           TackOD1 133 LrhiGvD.YdrplevykCnsCkslfsepevkarClsCek 170
                                       L+h +vD Y+  ++ y+C++C+  ++ +    +C +C++
  gi|313126440|ref|YP_004036710.1|   3 LTHTDVDpYSPTESYYECRDCGARTTGK-PITTCEECGS 40 
                                       88999996777777899*****998765.4578999987 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.6   0.00048      0.57       1      25 [.      18      40 ..      18      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00048
                                      -B-SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevslkkgdpiRCkeCGh 25
                                      Y C +Cga+++ k+     C eCG+
  gi|313126440|ref|YP_004036710.1| 18 YECRDCGARTTGKPI--TTCEECGS 40
                                      99*******987775..68****97 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.2   0.00031      0.37      14      36 ..      20      43 ..      17      43 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                           DUF35_N 14 CpdCGtvqfPPr.avCphCgsddl 36
                                      C+dCG+    +    C  Cgsd+l
  gi|313126440|ref|YP_004036710.1| 20 CRDCGARTTGKPiTTCEECGSDAL 43
                                      *********************987 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00026      0.32       4      24 ..       5      25 ..       3      30 .. 0.78
   2 ?    1.3   0.5      0.32   3.9e+02      17      23 ..      33      39 ..      27      42 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                          zf-Mss51  4 vpkhkqtapkhvdfeCpdCGi 24
                                      +++ +  +p +  +eC dCG 
  gi|313126440|ref|YP_004036710.1|  5 HTDVDPYSPTESYYECRDCGA 25
                                      455555689999********7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.32
                          zf-Mss51 17 feCpdCG 23
                                       +C +CG
  gi|313126440|ref|YP_004036710.1| 33 TTCEECG 39
                                      58****9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.4     0.016        19       2      10 ..      17      25 ..      16      27 .. 0.85
   2 ?    5.3   0.2     0.012        15       4      10 ..      34      40 ..      33      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                            zf_UBZ  2 tylCerCgk 10
                                      +y C +Cg+
  gi|313126440|ref|YP_004036710.1| 17 YYECRDCGA 25
                                      79*****97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                            zf_UBZ  4 lCerCgk 10
                                      +Ce+Cg+
  gi|313126440|ref|YP_004036710.1| 34 TCEECGS 40
                                      8****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 296.58
//
Query:       gi|313126441|ref|YP_004036711.1|  [L=370]
Description: hypothetical protein Hbor_16980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-64  216.4  21.9    6.1e-64  216.0  21.9    1.1  1  DUF368    Domain of unknown function (DUF368)
  ------ inclusion threshold ------
       0.37   10.6   0.0       0.37   10.6   0.0    4.8  6  LapA_dom  Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> DUF368  Domain of unknown function (DUF368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.0  21.9   6.8e-68   6.1e-64       1     230 [.      52     306 ..      52     316 .. 0.94

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 6.8e-68
                            DUF368   1 mGaAdvvPGvSGGtiAlitGiYeelieslksinlealklllra.......rlkaalkkinlkfLlalvlGivvsilv 70 
                                       mGaAd+vPGvSGGtiAlitGiYe+li+++++i++ ++ ++l +       ++ aalkk+++ fL+al +Gi+vs+ +
  gi|313126441|ref|YP_004036711.1|  52 MGAADAVPGVSGGTIALITGIYERLIAAVTAISPGRIMAVLGGvvperrgDAIAALKKMDVGFLIALGAGIAVSVTS 128
                                       9*********************************999999887788888899999********************** PP

                            DUF368  71 lakllsyllekypillwslffGlilasvvvlikevkkwsvkkiialllglaiallltvlepveteeslvfvflaGai 147
                                       + +++++ +++yp+l++++ffGli+as++vl++ev+ ++  +i a+++g+++a++ +  + ++  ++l +++laGai
  gi|313126441|ref|YP_004036711.1| 129 ITRVMHIGINTYPVLTFGFFFGLIAASAWVLFTEVEVNTPGRIGAAIAGFVFAFVASGQAGTSLGTGLPVTVLAGAI 205
                                       ***************************************************************************** PP

                            DUF368 148 aicAmilPGiSGSfiLlllGlYelllealkeld..................vkvllvfllGavvGllsfsrvlsall 206
                                       a++AmilPGiSGS++L+llG+Ye++  alk+++                    +++ f+lGav+Gl+++++ ++++l
  gi|313126441|ref|YP_004036711.1| 206 AVSAMILPGISGSLLLILLGQYEYMSGALKSFVdgllglvvggsttpvtesGLIVVAFMLGAVIGLFTIAHAVRWAL 282
                                       *********************************999888777776665444245999******************** PP

                            DUF368 207 kkyrsltlavliGlmlGslrkvwp 230
                                       +++r+ tla+l++l++G+lr+ + 
  gi|313126441|ref|YP_004036711.1| 283 EHHRKPTLAFLVALIVGALRAPVA 306
                                       *******************98765 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.6      0.56     5e+03      27      37 ..     116     126 ..     112     136 .. 0.52
   2 ?   -1.2   0.3       0.2   1.8e+03      23      38 ..     143     158 ..     137     164 .. 0.63
   3 ?   -4.1   5.7       1.6   1.5e+04      26      39 ..     173     186 ..     171     216 .. 0.66
   4 ?   10.6   0.0   4.1e-05      0.37      22      50 ..     258     283 ..     249     288 .. 0.80
   5 ?   -2.2   0.3      0.41   3.7e+03      23      32 ..     292     301 ..     289     304 .. 0.69
   6 ?   -3.1   0.9      0.78     7e+03      19      33 ..     325     339 ..     318     341 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.56
                          LapA_dom  27 fgiGallgwll 37 
                                       +++Ga +++ +
  gi|313126441|ref|YP_004036711.1| 116 IALGAGIAVSV 126
                                       34455333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.2
                          LapA_dom  23 llvafgiGallgwlls 38 
                                       l + f++G++++  + 
  gi|313126441|ref|YP_004036711.1| 143 LTFGFFFGLIAASAWV 158
                                       5555666666655444 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 1.6
                          LapA_dom  26 afgiGallgwllsl 39 
                                       a+++G+++++++s 
  gi|313126441|ref|YP_004036711.1| 173 AAIAGFVFAFVASG 186
                                       56666666666654 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 4.1e-05
                          LapA_dom  22 lllvafgiGallgwllslwsylrlrrelr 50 
                                       l++vaf +Ga++g+++ +      r++l 
  gi|313126441|ref|YP_004036711.1| 258 LIVVAFMLGAVIGLFTIAH---AVRWALE 283
                                       89************99985...5555554 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 0.41
                          LapA_dom  23 llvafgiGal 32 
                                        lva+++Gal
  gi|313126441|ref|YP_004036711.1| 292 FLVALIVGAL 301
                                       5777777776 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 0.78
                          LapA_dom  19 LsllllvafgiGall 33 
                                        ++   + +g+Ga+l
  gi|313126441|ref|YP_004036711.1| 325 AIFAAMAIVGAGAVL 339
                                       555556677788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2135.71
//
Query:       gi|313126442|ref|YP_004036712.1|  [L=430]
Description: nucleotide sugar dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-55  185.8   0.2    8.4e-55  185.2   0.2    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    5.6e-36  122.6   0.1    1.1e-35  121.7   0.1    1.5  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    1.3e-28   99.4   0.3    5.7e-28   97.4   0.2    2.1  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    3.8e-07   30.2   0.0    8.4e-07   29.0   0.0    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    3.3e-05   23.9   0.0     0.0003   20.8   0.0    2.3  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00014   22.4   0.2       0.11   13.1   0.0    3.8  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00054   19.6   0.2     0.0044   16.7   0.2    2.2  1  ApbA            Ketopantoate reductase PanE/ApbA
     0.0043   16.3   0.0     0.0078   15.5   0.0    1.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0088   16.3   0.6      0.044   14.0   0.1    2.5  2  TrkA_N          TrkA-N domain
  ------ inclusion threshold ------
      0.027   14.3   0.0      0.085   12.7   0.0    1.8  2  Rossmann-like   Rossmann-like domain
      0.047   13.9   0.0        1.2    9.3   0.0    2.7  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.053   14.1   0.0        0.2   12.2   0.0    2.1  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.072   13.3   0.1       0.95    9.7   0.1    2.2  2  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
        0.1   11.9   0.0       0.81    9.0   0.0    2.2  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.2   0.2   6.6e-58   8.4e-55       1     184 [.       1     185 [.       1     188 [. 0.96

  Alignments for each domain:
  == domain 1  score: 185.2 bits;  conditional E-value: 6.6e-58
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77 
                                       m+is+iG+GYvG + aa++a +gh+v+ vDidee v++lnsg++pi ep L+e +++++  +rl++ttd++  + ++
  gi|313126442|ref|YP_004036712.1|   1 MEISIIGSGYVGTTIAACFADVGHNVVNVDIDEEIVETLNSGNSPIHEPSLDERIEEHA-GDRLRATTDYDA-ILDT 75 
                                       89********************************************************9.8*********98.9*** PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHC...EEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEE CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkk...gkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvv 150
                                       dv+f+a  TPs + + ++Dl+ +e+ a+s++ +l +   +++vv+kSTv++ t+ee++ +ilee+s k+ g+dfdv 
  gi|313126442|ref|YP_004036712.1|  76 DVTFLALSTPSTD-DGHIDLSVMEAGAKSLGATLAEkddYHLVVTKSTVVPTTTEEVIAPILEEHSGKTvGEDFDVG 151
                                       *************.7777***************9888889**************************9999******* PP

                                       E------TTSHHHHHHS-S-EEEEESSCHHHHHH CS
                    UDPG_MGDP_dh_N 151 snPEflregsavkdllnpdrvviGveekkaeaal 184
                                       +nPEflregsav d+l pd+vv+G + ++a+++l
  gi|313126442|ref|YP_004036712.1| 152 MNPEFLREGSAVDDFLDPDKVVLGSHTDRAAERL 185
                                       ************************9999888766 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.7   0.1   8.8e-39   1.1e-35       1      93 [.     207     299 ..     207     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 8.8e-39
                      UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaee 77 
                                       ++AE+iK+a+Nafla kIs++N+lan+c+++++d++eV++a+gld+rig++fl +g+G+GGsc+pkDv+a+va+a++
  gi|313126442|ref|YP_004036712.1| 207 REAEMIKYANNAFLAAKISLVNDLANICKEYEVDTDEVLDAIGLDSRIGSEFLGAGVGWGGSCFPKDVAAIVAAARD 283
                                       68*************************************************************************** PP

                      UDPG_MGDP_dh  78 lgleaelleavrevNe 93 
                                       +g+e+ +l+a++evN+
  gi|313126442|ref|YP_004036712.1| 284 VGYEPAMLDAAVEVND 299
                                       ***************8 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.4   4.3e+03      36      67 ..     202     237 ..     184     239 .. 0.48
   2 !   97.4   0.2   4.5e-31   5.7e-28       1     104 [.     321     419 ..     321     420 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.4
                                       E-SSTHHCCCCHHGG....BTCCEEES-CHHHHTT- CS
                    UDPG_MGDP_dh_C  36 yDPkvkeeaveaele....ekgvevvdsleealkga 67 
                                       ++  ++e+++ ++++    + ++++v++l++ +k++
  gi|313126442|ref|YP_004036712.1| 202 VETGIREAEMIKYANnaflAAKISLVNDLANICKEY 237
                                       333333333333333555555666666666666655 PP

  == domain 2  score: 97.4 bits;  conditional E-value: 4.5e-31
                                       EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--G CS
                    UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehd 77 
                                       a+lGlafK++tdD+R+S+a+ +i+ Ll++ga+v+ yDP+++e+ + +     ++ ++ds+e+al+gada++++t++d
  gi|313126442|ref|YP_004036712.1| 321 AVLGLAFKPGTDDVRNSRAIPLIDALLDAGADVVGYDPVATENFRDK---FPDLDYADSAESALDGADAALVVTDWD 394
                                       89*******************************************99...678************************ PP

                                       GGGGS-HHHHHHCCSS-EEEESSS-CC CS
                    UDPG_MGDP_dh_C  78 efkeldlaklkelmkpavvfDgrnvld 104
                                       ef  l  ++  + m++avv+Dgrn+++
  gi|313126442|ref|YP_004036712.1| 395 EFAAL--DDEFDAMADAVVVDGRNIVT 419
                                       ****7..567899************96 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   6.5e-10   8.4e-07       2      82 ..       3      78 ..       2      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 6.5e-10
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavdad 80
                                      + +iG+G +G+ iaa fa  g++Vv vdi+ee++e+ ++  +      +++ +l+e   e+a +r+++ttd++++ d+d
  gi|313126442|ref|YP_004036712.1|  3 ISIIGSGYVGTTIAACFADVGHNVVNVDIDEEIVETLNSGNSP-----IHEPSLDERIEEHAGDRLRATTDYDAILDTD 76
                                      78*******************************9988777665.....45556666666888999********999999 PP

                                      EE CS
                           3HCDH_N 81 lv 82
                                      + 
  gi|313126442|ref|YP_004036712.1| 77 VT 78
                                      75 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.4e-07    0.0003       1      43 [.       2      44 ..       2      89 .. 0.80
   2 ?    0.1   0.0      0.55     7e+02      41      70 ..     208     237 ..     196     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.4e-07
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSS CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehe 43
                                      +i+++G+G  Gt++A+ +a+ gh+v+    +ee +e++n+ + 
  gi|313126442|ref|YP_004036712.1|  2 EISIIGSGYVGTTIAACFADVGHNVVNVDIDEEIVETLNSGNS 44
                                      599***********************************98664 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.55
                                       HSSBTTTBTT----TTEEEES-HHHHHTT- CS
                    NAD_Gly3P_dh_N  41 ehenvkyLpgiklpenlvattdlaealkga 70 
                                       e e  ky ++  l +++  ++dla+ +k+ 
  gi|313126442|ref|YP_004036712.1| 208 EAEMIKYANNAFLAAKISLVNDLANICKEY 237
                                       567789******************999976 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   8.5e-05      0.11       2      72 ..       3      85 ..       2      95 .. 0.77
   2 ?    0.2   0.0      0.87   1.1e+03      25      78 ..     169     231 ..     155     246 .. 0.59
   3 ?    3.6   0.0     0.077        99      18      93 ..     346     413 ..     340     416 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.5e-05
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.................-EEECECHHHHHHH-S CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.................vkvtavdneeaaeead 63
                                      i iiG+G +g ++a  ++  g   h++v + + ++e + e+ ++ +                  ++ a++  +a+ ++d
  gi|313126442|ref|YP_004036712.1|  3 ISIIGSGYVGTTIAACFADVG---HNVVNV-DIDEE-IVETLNSGNspihepslderieehagDRLRATTDYDAILDTD 76
                                      89*******************...****33.55555.555555544589999999999999994444445888888899 PP

                                      EEEE-S-HH CS
                     F420_oxidored 64 vvvlavkpe 72
                                      v +la+ + 
  gi|313126442|ref|YP_004036712.1| 77 VTFLALSTP 85
                                      999998665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.87
                                       GGCEEEEEESSCCCHHHHHHHHC...........-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                     F420_oxidored  25 pheivvansrnpekaeelaeelg...........vkvtavdneeaaeeadvvvlavkpedveevl 78 
                                       p ++v++ s +   ae l+  +            v++ +   +e+++ a+  +la k + v +++
  gi|313126442|ref|YP_004036712.1| 169 PDKVVLG-SHTDRAAERLRGVFDpllerapdaslVET-GIREAEMIKYANNAFLAAKISLVNDLA 231
                                       5555544.44444444444444444455555543332.336788888888888888887777665 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.077
                                       HHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                     F420_oxidored  18 llaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                       ll ag    ++v +   +p   e +++++     a ++e a++ ad  ++   +  ++++ +e   da ++ +v++
  gi|313126442|ref|YP_004036712.1| 346 LLDAG---ADVV-G--YDPVATENFRDKFPDLDYADSAESALDGADAALVVTDWDEFAALDDEF--DAMADAVVVD 413
                                       56666...6666.4..566666777777765555668999************************..999****998 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   3.4e-06    0.0044       1      48 [.       3      55 ..       3     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.4e-06
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT....C CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg....g 48
                                      i i+G+G +G+++aa+ a  g++v+ ++ ++  +e+l++ ++ +++++     
  gi|313126442|ref|YP_004036712.1|  3 ISIIGSGYVGTTIAACFADVGHNVVNVDIDEeIVETLNSGNSPIHEPSlderI 55
                                      78*****************************9999999999999999953322 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.1e-06    0.0078     145     195 ..       3      53 ..       1     120 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.1e-06
                                       EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealek 195
                                       i ++G+Gy+G+ +Aa +a++g++v+ v+  ++++++l++  s + e  l +
  gi|313126442|ref|YP_004036712.1|   3 ISIIGSGYVGTTIAACFADVGHNVVNVDIDEEIVETLNSGNSPIHEPSLDE 53 
                                       679********************9999999998888887766665544444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   3.4e-05     0.044       2      39 ..       4      41 ..       3      59 .. 0.90
   2 ?   -1.7   0.1       2.5   3.3e+03      59      75 ..     380     396 ..     347     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                                      EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHH CS
                            TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelre 39
                                       iiG G vG+++a  + + g+ +vv +d dee ve+l  
  gi|313126442|ref|YP_004036712.1|  4 SIIGSGYVGTTIAACFADvGH-NVVNVDIDEEIVETLNS 41
                                      69****************889.6************9975 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                                       TGGGESEEEE-SSSHHH CS
                            TrkA_N  59 giekadaviaatgddea 75 
                                        ++ ada +++t+ de+
  gi|313126442|ref|YP_004036712.1| 380 ALDGADAALVVTDWDEF 396
                                       56778888888886665 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.6e-05     0.085      12      40 ..       2      30 ..       1      56 [. 0.89
   2 ?   -3.0   0.0       4.8   6.1e+03       4      32 ..      85     111 ..      82     129 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.6e-05
                     Rossmann-like 12 svGiisaGrvGtalgaaleraghvvvgis 40
                                      ++ ii++G vGt+++a ++ +gh vv + 
  gi|313126442|ref|YP_004036712.1|  2 EISIIGSGYVGTTIAACFADVGHNVVNVD 30
                                      688**********************9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.8
                     Rossmann-like   4 pdersarlsvGiisaGrvGtalgaalera 32 
                                       p++ ++ +++ ++ aG    +lga+l+  
  gi|313126442|ref|YP_004036712.1|  85 PSTDDGHIDLSVMEAGA--KSLGATLAEK 111
                                       66666667777777764..3455555443 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0009       1.2       2      42 ..       3      43 ..       2     144 .. 0.73
   2 ?    1.6   0.0      0.22   2.8e+02      13      61 ..     341     389 ..     340     420 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0009
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg 42
                                      i +iG G  G+ +a  +++ g++v+ ++ ++e ve+l + +
  gi|313126442|ref|YP_004036712.1|  3 ISIIGSGYVGTTIAACFADVGHNVVNVDIDEEIVETLNSGN 43
                                      899***************************99998887655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
                                       HHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..EEE-SSHHHHHHHCSEEEE CS
                     NAD_binding_2  13 nmalnllkagykvavynrtkekveelvaeg..akaaesieelvasldvvit 61 
                                       +++  ll+ag +v++y+  + ++e++ ++   ++ a+s+e++++++d+ ++
  gi|313126442|ref|YP_004036712.1| 341 PLIDALLDAGADVVGYD--PVATENFRDKFpdLDYADSAESALDGADAALV 389
                                       57788999********9..45788888875558888888888888876544 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016       0.2       2      37 ..       3      38 ..       2      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTT CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrl 37
                                      + ++G+Gy+g   A+ +a+ g++V  v+  +++   
  gi|313126442|ref|YP_004036712.1|  3 ISIIGSGYVGTTIAACFADVGHNVVNVDIDEEIVET 38
                                      679*********************999988888755 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00074      0.95       4      42 ..     210     248 ..     208     254 .. 0.94
   2 ?    0.8   0.0      0.43   5.5e+02      74     100 ..     270     296 ..     264     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00074
                    NAD_binding_11   4 qavKlvnnlllainlaaasEalvlaekaGldpekvlevi 42 
                                       + +K +nn+ la+++  + +   +++ + +d ++vl++i
  gi|313126442|ref|YP_004036712.1| 210 EMIKYANNAFLAAKISLVNDLANICKEYEVDTDEVLDAI 248
                                       679**********************************98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.43
                    NAD_binding_11  74 mlKDlglalelareagaplpllalaeq 100
                                       + KD++ ++++ar++g++  +l +a +
  gi|313126442|ref|YP_004036712.1| 270 FPKDVAAIVAAARDVGYEPAMLDAAVE 296
                                       56**************99888887755 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00063      0.81      38      71 ..       2      35 ..       1      57 [. 0.82
   2 ?    0.0   0.0      0.36   4.6e+02      56      94 ..     347     386 ..     342     395 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00063
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkk 71
                                      ++ iiG G +G+++a +++ +g +v+ +d  ++ 
  gi|313126442|ref|YP_004036712.1|  2 EISIIGSGYVGTTIAACFADVGHNVVNVDIDEEI 35
                                      578***********************99988664 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.36
                                       HHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SE CS
                      2-Hacid_dh_C  56 kafgmkviaydrskkkeeeeeelgvelv.sleellaesDi 94 
                                          g++v++yd+  +++ +++   ++++ s e +l  +D 
  gi|313126442|ref|YP_004036712.1| 347 LDAGADVVGYDPVATENFRDKFPDLDYAdSAESALDGADA 386
                                       567999******9998777777777444378888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2675.93
//
Query:       gi|313126443|ref|YP_004036713.1|  [L=1081]
Description: hypothetical protein Hbor_17000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-26   90.8  29.3    6.4e-23   81.4  13.1    2.8  2  STT3            Oligosaccharyl transferase STT3 subunit
    7.5e-23   80.6   5.3      2e-22   79.3   5.3    1.7  1  AglB_L1         Archaeal glycosylation protein B long periphe
  ------ inclusion threshold ------
        5.4    6.8  12.8      0.096   12.5   4.9    2.0  2  DUF5373         Family of unknown function (DUF5373)
        5.6    6.6  14.0       0.12   12.1   3.1    2.6  2  HlyIII          Haemolysin-III related


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4  13.1   1.4e-26   6.4e-23      16     300 ..      45     339 ..      29     383 .. 0.79
   2 !   13.6   8.2   5.1e-06     0.023     342     461 ..     490     613 ..     398     661 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 1.4e-26
                                       HCC.CCCCCCT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEE.STTCCHCCC.CHHHHHH CS
                              STT3  16 asrdlFtdedglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrv.dygplivlLamlasaii 91 
                                       +++    + +g+  +  +D +Y +R + +++ +        + +++fd+ + +P+G  v ++g+l+  +  +a+ +i
  gi|313126443|ref|YP_004036713.1|  45 SKF----IRNGEVFFDGNDAWYHLREVSYTVRH-------WPSTIPFDPWTHFPYGTSVgQFGTLYDQIVATAALVI 110
                                       333....6789999*******************.......8***************98868********45555555 PP

                                       CCHHC..HHHHHHHHCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CC.CCCTTSTT--STCCCCHHHHHH CS
                              STT3  92 nhsld..vsirevclwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPg.YlsrtvaGfyDtdmfeivlllf 165
                                        +  +    i ++ l+ pa++g L+aIp+y + ++l++  +G++AA+ll++ Pg +l+rt  G  D+++ e +++ +
  gi|313126443|ref|YP_004036713.1| 111 GLGSPsqELIAKTLLVTPAVFGALTAIPAYIIGKRLAGRGPGVFAAILLGLMPGlFLQRTLVGVSDHNGVEPFFQAI 187
                                       55544866688899999******************************************************887765 PP

                                       HHHHHHHHHHCCS..................TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTT... CS
                              STT3 166 vlffflkaiktks..................nkislaviaaliiflivlaWggyailiyallllfilalLiigr... 221
                                        +  +l a +  +                      +avia+++ +l+   W    +li+ +l +f+l+ + +     
  gi|313126443|ref|YP_004036713.1| 188 SVAALLIAFAVAEkempiweivaerdfdairSSTKWAVIAGVATALYMWVWPPG-VLIVGVLGAFVLVKMASDVang 263
                                       544444443333336***************99999******************9.**************99988777 PP

                                       ..S-CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCC..... CS
                              STT3 222 ..felklkiavtfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfis..... 291
                                          e  + +a     ++a+l+  +i++  +gf+        +  ++++ll l++ g+ v l  +    qf+s     
  gi|313126443|ref|YP_004036713.1| 264 ksPEPTAFVAAVSMGVTAVLM--VIQIEEFGFSA------TSFSLVQPLLALIVAGGAVFL--AWFARQFESrdvsp 330
                                       777788888889999999999..**********6......666777888888887777777..44445555555555 PP

                                       CHHTT.HHH CS
                              STT3 292 lfqpgilse 300
                                        f+p+ ++ 
  gi|313126443|ref|YP_004036713.1| 331 SFYPAAVFG 339
                                       555554333 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.1e-06
                                       HHHS---S--CCHHHCCSSST..TTTCCCHH..HCHHCCHHCTCHHHHHHHHHHHHHCCC-SCHCCCCCHHHHHHHC CS
                              STT3 342 ilvsvwlpvgllaltkglrfl..iftvPlgi..ifvgllleflavfvkiysvsqilfsgvvvillmltllpvlalla 414
                                        +v vw +   +a++  lrf   ++++ + +  +++  +l+fl v+ +++ v+ + +  vv+i+++++l+++  ll 
  gi|313126443|ref|YP_004036713.1| 490 LFVIVWAVFMTSAAFTQLRFHyyLAVIVVVVnaYLLSEVLSFLDVRATMSTVTDLELYQVVSIAMVVLLIAAPVLLV 566
                                       5788899999999999999986344444444889******************************************* PP

                                       CCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCT.TTTTHHH.TTHHHCH CS
                              STT3 415 avkiskifstykdekeakikvaakavaptksnglkeslew.kantnrd 461
                                        + + ++     d+  + +  +++   p +  +++ s ew k+nt+++
  gi|313126443|ref|YP_004036713.1| 567 PLNVRNTETAALDKSNTAWETSQGH-SPSEVLKWESSFEWtKENTPKE 613
                                       *****99999999999999986666.7999999999999999999987 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   5.3   4.5e-26     2e-22       1      88 [.     898    1002 ..     898    1006 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 4.5e-26
                                        -EEEEEEBS.SSSEEEEEEEEE-.TTS-EEEEEEEEE.-BTTEEEEEE---SS...........-SSSSEESS-E CS
                           AglB_L1    1 GAtitGsae.agatvtasvelet.nqgrtftYrqeaeadedGefeltvPYstegee.....dgetnssveaagpY 68  
                                        GAt++Gs++ a+ tvtasve+e+ +++ tf+Y+q+a+++edGef++t+PYst+g++     +g+tn+sv+a+gpY
  gi|313126443|ref|YP_004036713.1|  898 GATVQGSGApANSTVTASVEMEIpTENSTFEYTQQAQTNEDGEFTMTLPYSTTGYSeygpdNGYTNVSVRATGPY 972 
                                        9*****975156***********77799***************************99****************** PP

                                        EEEETT..........EEEEE---HHHHHH CS
                           AglB_L1   69 evtagn..........vtaeveVpEeaVls 88  
                                        ++++g+          ++ +++V+E +V  
  gi|313126443|ref|YP_004036713.1|  973 TISSGAslnesgyivgYQSNLSVSEGQVNG 1002
                                        ****988888999999999999*9999975 PP

>> DUF5373  Family of unknown function (DUF5373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.0      0.87   3.9e+03      81     123 ..     290     333 ..     268     355 .. 0.41
   2 ?   12.5   4.9   2.1e-05     0.096      65     133 ..     492     561 ..     467     583 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.87
                           DUF5373  81 ahyysalifllv.plavlvlliilaflkilflnleaielksvls 123
                                          +sa+ f lv pl  l++    +fl  ++ ++e+  +++ ++
  gi|313126443|ref|YP_004036713.1| 290 EFGFSATSFSLVqPLLALIVAGGAVFLAWFARQFESRDVSPSFY 333
                                       23345544433314444444444555555555544444444333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
                           DUF5373  65 aftvavfivenk.iLmrahyysalifllvplavlvlliilaflkilfln..leaielksvlslvvaliilcv 133
                                       + + avf+       +r+hyy+a+i+++v    ++l+++l+fl++ +    ++++el +v+s++++++++ +
  gi|313126443|ref|YP_004036713.1| 492 VIVWAVFMTSAAfTQLRFHYYLAVIVVVVNA--YLLSEVLSFLDVRATMstVTDLELYQVVSIAMVVLLIAA 561
                                       4455677766541569*******99877653..799999999999887734566666666655555555544 PP

>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.1   2.6e-05      0.12      93     192 ..     221     319 ..     170     368 .. 0.87
   2 ?   -0.8   3.2      0.22     1e+03     109     187 ..     489     563 ..     460     583 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                            HlyIII  93 lplilyalakapkagllylslilalgvlgiisklvplfsrpearplravlfillgllgvipllhlllvltqlgeaae 169
                                       + ++++a   +  +++++   +l++gvlg ++ + ++ + ++ +  +  +f+++ ++gv ++l  ++ ++++g +a+
  gi|313126443|ref|YP_004036713.1| 221 TKWAVIAGVATALYMWVWPPGVLIVGVLGAFVLVKMASDVANGKSPEPTAFVAAVSMGVTAVLM-VIQIEEFGFSAT 296
                                       455555556667789999999****************999999999999999999999999999.888899998889 PP

                            HlyIII 170 lalvllvlggvlylvGavfYalr 192
                                        ++ +  l ++++  Gavf+a++
  gi|313126443|ref|YP_004036713.1| 297 SFSLVQPLLALIVAGGAVFLAWF 319
                                       99999999999**********98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.22
                            HlyIII 109 lylslilalgvlgiisklvplfsrpearplravlfillgllgvipllhlllvltqlgeaaelalvllvlggvlylvG 185
                                       +++++++a+ +++  ++ + ++   ++ ++ +++     l+ v+++l++  +++ +    el  v+ ++++vl +++
  gi|313126443|ref|YP_004036713.1| 489 HLFVIVWAVFMTSAAFTQLRFHYYLAVIVVVVNA---YLLSEVLSFLDVRATMS-TVTDLELYQVVSIAMVVLLIAA 561
                                       5667777776666666666662222222222223...33455556655333333.3323356667777777776666 PP

                            HlyIII 186 av 187
                                        v
  gi|313126443|ref|YP_004036713.1| 562 PV 563
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1081 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1583  (0.0882927); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 1.08u 0.32s 00:00:01.40 Elapsed: 00:00:00.54
# Mc/sec: 5975.33
//
Query:       gi|313126444|ref|YP_004036714.1|  [L=351]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-49  169.8   0.4    6.2e-49  167.2   0.4    2.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.3e-49  166.4   0.2    2.3e-48  164.8   0.2    1.7  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.6e-19   68.8   0.0    6.2e-18   64.8   0.0    2.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.4e-16   59.7   0.0    3.4e-16   59.2   0.0    1.2  1  NAD_binding_4    Male sterility protein
    9.4e-10   38.1   2.0    4.1e-09   35.9   2.0    1.9  1  RmlD_sub_bind    RmlD substrate binding domain
    1.7e-09   37.2   0.0    2.1e-08   33.7   0.1    2.0  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    8.6e-08   32.3   1.0    9.4e-07   28.9   1.0    2.1  1  NAD_binding_10   NAD(P)H-binding
    1.8e-06   28.0   0.0      3e-06   27.3   0.0    1.2  1  KR               KR domain
    0.00075   19.8   0.1      0.002   18.4   0.0    1.7  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0011   18.5   0.2      0.002   17.6   0.2    1.4  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.011   15.2   0.1       0.28   10.7   0.2    2.6  2  NmrA             NmrA-like family
      0.067   12.5   0.1       0.11   11.7   0.1    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.2   0.4   4.1e-52   6.2e-49       1     331 [.       8     343 ..       8     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: 167.2 bits;  conditional E-value: 4.1e-52
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT......TTGC...CEEEEE--TT-HHHHHHHH CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakd...pkeelee...nlklhkgDltDssslerll 71 
                                       L+TG+aGf+Gs+ +e+  e+g +v+ ++++s + ++++ ++ ++    + + +ee   +++l+++D++D + le+++
  gi|313126444|ref|YP_004036714.1|   8 LVTGGAGFVGSHAVEYYAERGSDVTALDNLSRTETLEKADESRNTaayNWNYIEEnypDVELVEADIRDFETLESIV 84 
                                       9****************************99988887777554431112333333223789**************** PP

                                       HHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-.SSSSB-TT... CS
                     GDP_Man_Dehyd  72 aevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkv.qevpqtEt... 144
                                       + +  d++++ A+q +V  s+++P + +evn+ Gt+++Lea+r++    +  ++ aSt  vYG+  +e+p++E+   
  gi|313126444|ref|YP_004036714.1|  85 EGH--DAIVHTAGQVAVTASLTDPRTDFEVNAEGTFNVLEAARKADS--DPAVVVASTNKVYGNNvNEIPVREEenr 157
                                       ***..9**************************************986..567899********97379**9876444 PP

                                       ........S----............-SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHH CS
                     GDP_Man_Dehyd 145 ........tpfyP............rsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitrav 201
                                                                + PY+++Kl+ad  v++y e   + a   +++  ++ r+  +  +  + +++
  gi|313126444|ref|YP_004036714.1| 158 ywyddsdfE---NgipetlsidgceHTPYGVSKLTADLYVQDYAERGAVDAAAFRMSCIYGTRQFGNEDQGWVAHFA 231
                                       444443330...1455666666677***************************************9999999999999 PP

                                       HHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC..SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH... CS
                     GDP_Man_Dehyd 202 arialgkqevlylGnldakRdwghvkDyveamwlmlqq..dkpedyviatgethsvrefvelaflelgktiewegkg 276
                                         +++++ + +++G+++++Rd ++vkD ++a++++l    dkp  y+i+ g + +  +++  +fl++ +        
  gi|313126444|ref|YP_004036714.1| 232 ISTLRDE-PLTIFGDGKQVRDVLYVKDLIRAYDAFLSDpeDKPAVYNIGGGAENTT-SLL--EFLDILE-------- 296
                                       9988876.88899***********************97324555555554443332.222..2444432........ PP

                                       .........TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 277 eeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                                               ++  ++  +++   r+g+++ ++ d+s+a+e L+W+++vsfee++++
  gi|313126444|ref|YP_004036714.1| 297 --------SKTGTRTDISYDEWREGDQKVYVSDTSRAREHLDWEAQVSFEEGIER 343
                                       ........1223467788889*******************************986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.2   1.6e-51   2.3e-48       1     241 []       7     279 ..       7     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 1.6e-51
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..................EEEE--TT-HHHHHHH CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl..................elveldltdrsalerl 59 
                                       +lVtG++Gf+Gs+ v++ +e+g +v++ld+ls+++  ++ ++                   elve+d++d + le +
  gi|313126444|ref|YP_004036714.1|   7 VLVTGGAGFVGSHAVEYYAERGSDVTALDNLSRTETLEKADESrntaaynwnyieenypdvELVEADIRDFETLESI 83 
                                       79*****************************9999888888889********************************* PP

                                       HHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGT............... CS
                         Epimerase  60 fkeeqpdavihlAavggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYG............... 120
                                       ++  + da++h A++  v as +dp   +e n++gt n+leaarka+ +  ++ +s+  vYG               
  gi|313126444|ref|YP_004036714.1|  84 VE--GHDAIVHTAGQVAVTASLTDPRTDFEVNAEGTFNVLEAARKADSDpAVVVASTNKVYGnnvneipvreeenry 158
                                       **..89****************************************9998************999999888888888 PP

                                       ..SCSS.SSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHH CS
                         Epimerase 121 ..kdae.qpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkil 194
                                         +d +      +tl+     ++pY+++Kl+++ +v++ya+ + ++a ++r++ +yG r++ +e+++ +++++ + l
  gi|313126444|ref|YP_004036714.1| 159 wyDDSDfENGIPETLSIDGCEHTPYGVSKLTADLYVQDYAERGAVDAAAFRMSCIYGTRQFGNEDQGWVAHFAISTL 235
                                       773333212333333444489******************************************************** PP

                                       TTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
                         Epimerase 195 egkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                                       + + ++t++gdg+++Rd lyv+D+++a+ ++l  ++++  + +yniG
  gi|313126444|ref|YP_004036714.1| 236 RDE-PLTIFGDGKQVRDVLYVKDLIRAYDAFLSDPEDK--PAVYNIG 279
                                       **9.******************************9886..66****9 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0   4.2e-21   6.2e-18       1     221 [.       8     258 ..       8     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 4.2e-21
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...............viegDvtdkdklee 62 
                                       +vtGgaGF+G++ v+   ++++  +v +lD   ++e+le++ +++++                ++e+D++d ++le 
  gi|313126444|ref|YP_004036714.1|   8 LVTGGAGFVGSHAVEYYAERGS--DVTALDNLSRTETLEKADESRNTAaynwnyieenypdveLVEADIRDFETLES 82 
                                       69***************99995..******77777777777666555445667777889998899************ PP

                         3Beta_HSD  63 alegvdvvihlaslvdvagkltedei.mkvnvkGTrnvleacvkagv.rvlvYtSsaevvgpnslgeeilngd.... 133
                                        +eg d+++h+a+ v v+  lt+ +   +vn +GT nvlea++ka+  +++v  S+ +v g+n+++ ++++ +    
  gi|313126444|ref|YP_004036714.1|  83 IVEGHDAIVHTAGQVAVTASLTDPRTdFEVNAEGTFNVLEAARKADSdPAVVVASTNKVYGNNVNEIPVREEEnryw 159
                                       ******************97776655169**************9976268888899999999988777764331111 PP

                         3Beta_HSD 134 ...........EeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlakl 199
                                                  E+l ++ + + +y  sK  a+ +v    +r   + + +   ++  +  +G+ d+  v+ +  ++  
  gi|313126444|ref|YP_004036714.1| 160 yddsdfengipETLSIDGCEHTPYGVSKLTADLYVQDYAERGAVDAAAFRMSCIYGTRQFGNEDQGWVAHFAISTLR 236
                                       11111111112444444456677888888888888877777777777777777777777777777777666666666 PP

                         3Beta_HSD 200 glalfkigdeevlsdrvYvgNv 221
                                        + l   gd +++ d  Yv  +
  gi|313126444|ref|YP_004036714.1| 237 DEPLTIFGDGKQVRDVLYVKDL 258
                                       6677778888888888887765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   2.3e-19   3.4e-16       1     225 [.       9     231 ..       9     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.3e-19
                                       EE-TTSHHHHHHHHHHHHHS-.T.EEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpev.kiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGL 76 
                                       +TG+ GF+G++ +e   ++ ++v  +  l R+++ e+a e  +++ ++ +  ++ +      ++ ve+D+ +     
  gi|313126444|ref|YP_004036714.1|   9 VTGGAGFVGSHAVEYYAERGSDVtALDNLSRTETLEKADESRNTAAYNWNYIEENY----PDVELVEADIRDF---- 77 
                                       7*********************9999999**9999999998888888888888885....99********975.... PP

                                       -HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SS CS
                     NAD_binding_4  77 seedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveek 150
                                         e+l+ ++e  d+i+h a++v +++++ +    ++vN eGt +vle a+k  +  +++  ST  v+g++ +e+   
  gi|313126444|ref|YP_004036714.1|  78 --ETLESIVEGHDAIVHTAGQVAVTASLTDprtDFEVNAEGTFNVLEAARKADSDPAVVVASTNKVYGNNVNEI--- 149
                                       ..69**********************9998333468****************99999******88888888777... PP

                                       S-H.............HHH--EEEETTTCCC.HHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.....-SSST- CS
                     NAD_binding_4 151 vyeege.......keekldederaklkglpn.tYeqsKalaEklvrearrrsglpvvivRpsiitg.....esktGw 214
                                       +++e+e       ++ +    e  + +g+++  Y  sK  a+  v+++++r+ + ++ +R s+i+g     +  +Gw
  gi|313126444|ref|YP_004036714.1| 150 PVREEEnrywyddSDFENGIPETLSIDGCEHtPYGVSKLTADLYVQDYAERGAVDAAAFRMSCIYGtrqfgNEDQGW 226
                                       333444467888444444445555677888768*********************************55555555555 PP

                                       --TTSHHHHHH CS
                     NAD_binding_4 215 ingsdlgirgl 225
                                       +        + 
  gi|313126444|ref|YP_004036714.1| 227 VAH------FA 231
                                       544......33 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   2.0   2.8e-12   4.1e-09       3     176 ..       7     243 ..       5     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 2.8e-12
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.................................T--TTSHHHHHHH CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre.................................eldltdaeavael 46 
                                       +lvtG+ G +Gs+ ++  ae+g +v+al++                                  e+d++d e+++++
  gi|313126444|ref|YP_004036714.1|   7 VLVTGGAGFVGSHAVEYYAERGSDVTALDNLsrtetlekadesrntaaynwnyieenypdvelvEADIRDFETLESI 83 
                                       89**************************766789******************************************* PP

                                       HHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-..EEEEEEEGGGS-S-.........TTS- CS
                     RmlD_sub_bind  47 lkeakpdvvvnaAAytavDkaEseeeaayavnaeavealAeaaaavga..lLihvStDyVFdGe.........kkrp 112
                                       ++    d++v++A   av +  ++++ +++vnae++ ++ eaa+++++   ++  St  V+  +         ++r 
  gi|313126444|ref|YP_004036714.1|  84 VEG--HDAIVHTAGQVAVTASLTDPRTDFEVNAEGTFNVLEAARKADSdpAVVVASTNKVYGNNvneipvreeENRY 158
                                       *99..788***********************************998764379*********9999899998852232 PP

                                       .B-TTS---..-SSH.........HHHHHHHHHHHHHHH-S....SEEEEEE-SEESS.....SSS-HHHHHHHHHH CS
                     RmlD_sub_bind 113 .Yeeddets..Plnv.........YGrtKlaGEqavlaagk....kalivRtswvyge.....kgknfvktmlrlak 168
                                        Y  +d  +  P ++         YG +Kl     v+++ +    +a+ +R+s +yg      +++ +v+ +     
  gi|313126444|ref|YP_004036714.1| 159 wYDDSDFENgiPETLsidgcehtpYGVSKLTADLYVQDYAErgavDAAAFRMSCIYGTrqfgnEDQGWVAHFAISTL 235
                                       23333322222433223333444488888888888888665111245558888888774444445555555555555 PP

                                       H-SEEEEE CS
                     RmlD_sub_bind 169 ereelkvv 176
                                       ++e+l+++
  gi|313126444|ref|YP_004036714.1| 236 RDEPLTIF 243
                                       55555555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   1.4e-11   2.1e-08       1     131 [.       7     141 ..       7     150 .. 0.81
   2 ?    1.2   0.0      0.11   1.6e+02     138     163 ..     183     208 ..     179     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.4e-11
                                       EEEETTTSHHHHHHHHHHHHH..B-SEEEEEES-HHHHHHHHHH......-TTEEEE.......E--TT-HHHHHHH CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk..kpkkiillerdElklyeiekeleeelkkkklkve...ivpvigdvrdkerleka 72 
                                       vlvtG++G +Gs+ v+  +++  +++ +  l+r+E+   + e+++++ ++ + ++ +   +  v +d+rd e+le++
  gi|313126444|ref|YP_004036714.1|   7 VLVTGGAGFVGSHAVEYYAERgsDVTALDNLSRTETLEKADESRNTAAYNWNYIEENypdVELVEADIRDFETLESI 83 
                                       89*****************99777788888999997655555554444444444433111455679*********** PP

                                       TT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-S.EEEEEEEGGG CS
                   Polysacc_synt_2  73 leelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvk.kvvliStDKA 131
                                       +e  + d+++h+A    V +  + p   ++ N  gt nv+eaa +a+ + +vv+ St K 
  gi|313126444|ref|YP_004036714.1|  84 VE--GHDAIVHTAGQVAVTASLTDPRTDFEVNAEGTFNVLEAARKADSDpAVVVASTNKV 141
                                       **..9****************************************998736777789885 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHGGG--SSS--EE CS
                   Polysacc_synt_2 138 mGatKrlaekllqalakeseekktkf 163
                                       +G++K++a++++q +a++ + +  +f
  gi|313126444|ref|YP_004036714.1| 183 YGVSKLTADLYVQDYAERGAVDAAAF 208
                                       8*************999876555443 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   1.0   6.3e-10   9.4e-07       1      99 [.      11     138 ..      11     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.3e-10
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH.................HHHCT.TTCEEEE--TT-CCHHHHHHT CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla.................eleae.eglevvegdvtdvedlaealk 59 
                                       G+ G vG+++v+  ++rg  +vtal  n ++++                  +e++ + +e+ve+d+ d e+l++ ++
  gi|313126444|ref|YP_004036714.1|  11 GGAGFVGSHAVEYYAERG-SDVTAL-DNLSRTEtlekadesrntaaynwnYIEENyPDVELVEADIRDFETLESIVE 85 
                                       899**************5.999998.4433333333555778888887765666668******************** PP

                                       T-SEEEES---TCC.............HHHHHHHHHHHHHHCT--EEEEEEET CS
                    NAD_binding_10  60 gadaVvsalggggk.............deegaknivdaakeagvkRfvlvsai 99 
                                       g+da+v ++g+ +              ++eg+ n+++aa++a+    v+v + 
  gi|313126444|ref|YP_004036714.1|  86 GHDAIVHTAGQVAVtasltdprtdfevNAEGTFNVLEAARKADSDPAVVVAST 138
                                       *****99997666655566554555555555***********99887777664 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0     2e-09     3e-06       3     144 ..       7     145 ..       6     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2e-09
                                       EEEETTTSHHHHHHHHHHHHHH..S-EEEEE-SS........--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekg..arhlvllsRsa......aadedskaliaelealgaevevvaaDvsdkdaveal 71 
                                       +l+tGG+G +G + ++  ae+g   + l  lsR++      +++++++ + + +e++  +ve+v+aD+ d + +e++
  gi|313126444|ref|YP_004036714.1|   7 VLVTGGAGFVGSHAVEYYAERGsdVTALDNLSRTEtlekadESRNTAAYNWNYIEENYPDVELVEADIRDFETLESI 83 
                                       79********************66667778****8666555445555558889999999****************** PP

                                       HHHHHHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--T CS
                                KR  72 leeikaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsa 144
                                       +e  +        ++h+Ag ++ ++    +  d ++ ++   +G+ n+ e+ ++ + d  v+++S   ++g++
  gi|313126444|ref|YP_004036714.1|  84 VEGHD-------AIVHTAGQVAVTA----SLTDPRTDFEVNAEGTFNVLEAARKADSDPAVVVASTNKVYGNN 145
                                       **997.......8******887654....44455666778889**************************9986 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.4e-06     0.002       3      80 ..       9      97 ..       7     104 .. 0.76
   2 ?   -2.7   0.0       4.4   6.6e+03      16      34 ..     122     140 ..     116     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                                      EE--.SHHHHHHHHHHHCTCCT-GEEEEEE.....SSHHHHHHHHCHH............TTTCEEEEE--TTTHHHHH CS
                   Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvad.....rskeklealaaka............lgvrfeaialdaenyeavL 63
                                      + G+ G+vG+ ++e++a++++    +t  d      ++ek+++                 + +++e ++ d+ + e  L
  gi|313126444|ref|YP_004036714.1|  9 VTGGaGFVGSHAVEYYAERGSD---VTALDnlsrtETLEKADES---RntaaynwnyieeNYPDVELVEADIRDFET-L 80
                                      55555***********999875...5655511111344444444...155699***********************9.* PP

                                      HHHHTTSSEEEE-SSGG CS
                   Sacchrp_dh_NADP 64 aallkegdlvvnlsppi 80
                                      +++++++d++v+ ++++
  gi|313126444|ref|YP_004036714.1| 81 ESIVEGHDAIVHTAGQV 97
                                      *************9987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.4
                                       HHHCTCCT-GEEEEEESSH CS
                   Sacchrp_dh_NADP  16 llarhfdvdaeitvadrsk 34 
                                       + ar+ d d+ ++va+ +k
  gi|313126444|ref|YP_004036714.1| 122 EAARKADSDPAVVVASTNK 140
                                       5677888888999988775 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   1.3e-06     0.002       3     122 ..       7     127 ..       5     147 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEES..CHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHH...HHHHHHH CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdr..seekleevakelkeegakalaiqvDvtdreeveal...vekavkk 74 
                                       vlvtG+++ +G   ++ +a++G +v+++d+  + e+le++ ++ + ++ +  +i+ +  d e vea    +e+ ++ 
  gi|313126444|ref|YP_004036714.1|   7 VLVTGGAGFVGSHAVEYYAERGSDVTALDNlsRTETLEKADESRNTAAYNWNYIEENYPDVELVEADirdFETLESI 83 
                                       9**************************87621445555554444444555555554444444444330114555566 PP

                                       HSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHH CS
                         adh_short  75 lgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpa 122
                                       +++ d++v+ AG   ++     s ++ +  +evN  g+f++ +a+ +a
  gi|313126444|ref|YP_004036714.1|  84 VEGHDAIVHTAGQ--VAV--TASLTDPRTDFEVNAEGTFNVLEAARKA 127
                                       6777999999999..344..44555566669**********9998666 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00018      0.28       1      72 [.       7      94 ..       7     106 .. 0.69
   2 ?    1.0   0.0      0.17   2.5e+02     152     228 ..     226     302 ..     181     338 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S..............-SHHHHHHHHS..TTEEEES-TT-HHHHHHHHT CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt..............kselakslkea..Gvelvkgdlddkeslvealk 63
                                      +lv+G++G  G++ v++ +++g +v al   +                 + + ++e+   velv++d+ d e l+++++
  gi|313126444|ref|YP_004036714.1|  7 VLVTGGAGFVGSHAVEYYAERGSDVTALDNLSrtetlekadesrntAAYNWNYIEENypDVELVEADIRDFETLESIVE 85
                                      79*************************9655544466666655444222223333322246777777778888888888 PP

                                      T-SEEEE-- CS
                              NmrA 64 gvdvvfsvt 72
                                      g d++  + 
  gi|313126444|ref|YP_004036714.1| 86 GHDAIVHTA 94
                                      887776655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                                       S-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHH.TTEEE.EE-SEEE-HHHHHHHHHHHHT CS
                              NmrA 152 laqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprkl.kgkri.klagntlsgneivelfekkig 226
                                       ++  +  +t  +e  +t+ g+g+    +l  ++D  ++  + l+dp++   +  i   a+nt s+ e ++++e k+g
  gi|313126444|ref|YP_004036714.1| 226 WVAHFAISTLRDE-PLTIFGDGKQVRDVL-YVKDLIRAYDAFLSDPEDKpAVYNIgGGAENTTSLLEFLDILESKTG 300
                                       4444555555554.788888988666666.8899999999999998888544444257999999*********9999 PP

                                       S- CS
                              NmrA 227 kt 228
                                        +
  gi|313126444|ref|YP_004036714.1| 301 TR 302
                                       75 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.6e-05      0.11      32      93 ..       8      88 ..       4     102 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.6e-05
                                      EEE.STSHHHHHHHHHHHHTT-EEEEEES..SHHHHHHHHHTTTCECEE....................HCHHHHHHHH CS
                       AlaDh_PNT_C 32 lvi.GgGvaGlqAiatakglgakVtvlDv..rparleqleslgakfvev....................lksqeellae 87
                                      lv  G+G +G +A++  ++ g +Vt+lD   r+++le+ ++      ++                      ++ e+l++
  gi|313126444|ref|YP_004036714.1|  8 LVTgGAGFVGSHAVEYYAERGSDVTALDNlsRTETLEKADESR----NTaaynwnyieenypdvelveaDIRDFETLES 82
                                      555268**********************422455555555533....23122344455555555555554445555555 PP

                                      HHHH-S CS
                       AlaDh_PNT_C 88 avkead 93
                                       v+  d
  gi|313126444|ref|YP_004036714.1| 83 IVEGHD 88
                                      555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2180.45
//
Query:       gi|313126445|ref|YP_004036715.1|  [L=375]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-46  158.7   0.1    1.9e-23   83.2   0.1    2.1  2  Epimerase        NAD dependent epimerase/dehydratase family
    7.2e-46  157.1   0.0    4.7e-23   82.1   0.0    2.2  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.4e-19   70.2   0.1    2.9e-17   62.6   0.1    2.2  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.3e-15   57.4   0.0    1.1e-06   28.0   0.0    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.7e-08   33.3   0.0    0.00064   19.0   0.0    2.2  2  NAD_binding_4    Male sterility protein
      9e-07   29.0   0.0    1.5e-06   28.2   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
    1.1e-06   28.3   0.9    4.3e-06   26.3   0.3    2.0  2  adh_short        short chain dehydrogenase
    0.00061   19.4   0.1     0.0011   18.5   0.1    1.5  1  NmrA             NmrA-like family
    0.00071   19.8   0.3     0.0015   18.8   0.3    1.5  1  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.011   15.7   0.1       0.16   11.9   0.1    2.5  2  KR               KR domain
      0.021   14.0   0.7      0.049   12.7   0.1    2.0  3  RmlD_sub_bind    RmlD substrate binding domain
      0.047   14.0   0.0      0.094   13.0   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.092   12.6   0.0       0.14   12.0   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.13   11.7   0.1       0.39   10.3   0.1    1.7  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.17   11.6   1.7       0.24   11.1   0.2    2.0  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.1   1.6e-26   1.9e-23       1     134 [.       4     142 ..       4     150 .. 0.93
   2 !   73.5   0.0   1.4e-23   1.7e-20     130     240 ..     171     279 ..     157     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 1.6e-26
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAa 73 
                                       +lVtG++Gf+Gs++v++l + gy+v+++d+l+++ +  + + l    e v +d++dr+ +++l++  ++d+  h A 
  gi|313126445|ref|YP_004036715.1|   4 VLVTGGAGFVGSHIVDELVASGYDVTVVDNLTEQVHDDEPDYLndeaEYVWGDVRDRELMTELLE--EADVLNHQAS 78 
                                       79*****************************999999888888**********************..89******** PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT..EEEEEEEGGGGTSCSSS.SBSTCSTTS CS
                         Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvk..rllflsSsevYGkdaeq.pkeettltg 134
                                         gv++s+ + ++++e n+  t ++l+ +   ++   +++ +sS ++YG++a   p+e+t+++ 
  gi|313126445|ref|YP_004036715.1|  79 AVGVGQSMYEIEKYVEVNTLATARILDIIVNEDISleKIVVASSMSIYGEGAYHcPEEDTLHYP 142
                                       ******************************9977777****************76888877554 PP

  == domain 2  score: 73.5 bits;  conditional E-value: 1.4e-23
                                       CSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTS.TTSHHHHHHHHHHTTSSSEEEETT CS
                         Epimerase 130 ttltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngege.vsrvipalirkilegkqevtllgd 205
                                       t++++p +++s Ya++K   e+l+ ++a++y+++a++lr+fn+yG r+  g+  ++v + + ++i++   + +++ d
  gi|313126445|ref|YP_004036715.1| 171 TSEKKPRESTSVYAISKKDQEELTLSVARSYDIPAVALRYFNIYGSRQALGNpYTGVCAIFSSRIKNDN-PPLIFED 246
                                       4445577999*************************************888888***************9.******* PP

                                       ST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
                         Epimerase 206 gtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                                       g++ Rdf++++D+a+a+ l++e+ +a d   ++n+
  gi|313126445|ref|YP_004036715.1| 247 GEQTRDFIHISDIARANRLAMERDEAEDV--ALNL 279
                                       ***********************554433..6665 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.1   2.8e-23   3.4e-20       1     149 [.       5     142 ..       5     147 .. 0.91
   2 !   82.1   0.0     4e-26   4.7e-23     139     331 ..     169     345 ..     163     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 2.8e-23
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGf+Gs++++ L++ gy+v+++++++++++ ++ + l         ++ + + gD++D++ +++ll+e+  d
  gi|313126445|ref|YP_004036715.1|   5 LVTGGAGFVGSHIVDELVASGYDVTVVDNLTEQVHDDEPDYLN--------DEAEYVWGDVRDRELMTELLEEA--D 71 
                                       9***************************999998877777665........445789****************9..7 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS---- CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyP 149
                                          + A    V++s+ + e+++evn l+t+r+L++i +  + +  +++ aS+  +YG+ + +  +E+t  yP
  gi|313126445|ref|YP_004036715.1|  72 VLNHQASAVGVGQSMYEIEKYVEVNTLATARILDIIVNEDI-SLEKIVVASSMSIYGEGAYHCPEEDTLHYP 142
                                       88899999****************************98865.4679************99999999998888 PP

  == domain 2  score: 82.1 bits;  conditional E-value: 4e-26
                                       SSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECT CS
                     GDP_Man_Dehyd 139 vpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylG 215
                                       +  +E++p + +s Ya++K  ++ ++ +  ++y+++av  ++fn ++ r+    +   ++ + +   ++ ++ l++ 
  gi|313126445|ref|YP_004036715.1| 169 IATSEKKPRESTSVYAISKKDQEELTLSVARSYDIPAVALRYFNIYGSRQALGNPYTGVCAIFSSRIKNDNPPLIFE 245
                                       5579**********************************************9987777777776666666779999** PP

                                       TTT-EEEEEEHHHHHHHHHHHHHCSS---EE..E-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGC CS
                     GDP_Man_Dehyd 216 nldakRdwghvkDyveamwlmlqqdkpedyv..iatgethsvrefvelaflelgktiewegkgeeevgrakesgkvv 290
                                       +++++Rd+ h++D+++a +l++++d++ed+   ++tg+  ++ e++e  +   gk         +e        + +
  gi|313126445|ref|YP_004036715.1| 246 DGEQTRDFIHISDIARANRLAMERDEAEDVAlnLGTGNPKTITEIAETLIDLYGK--------SDE-------LEPE 307
                                       **************************99976114555666666655543333332........122.......2333 PP

                                       CCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 291 vevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                                       +    + fr+g+ + +++d+s+a e L++kp+v+fee++re
  gi|313126445|ref|YP_004036715.1| 308 I---ANDFRQGDIRHCYADTSRAAELLDFKPSVTFEEGMRE 345
                                       3...4679*******************************98 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   2.4e-20   2.9e-17       1     123 [.       5     129 ..       5     146 .. 0.90
   2 !    5.5   0.0    0.0062       7.4     134     225 ..     173     263 ..     161     274 .. 0.66

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.4e-20
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleealegvdvvihlasl 76 
                                       +vtGgaGF+G+++v eLv  +   +v v+D  +++   +e   +n +  ++ gDv+d + ++e le++dv+ h as+
  gi|313126445|ref|YP_004036715.1|   5 LVTGGAGFVGSHIVDELVASG--YDVTVVDNLTEQVHDDEPDYLNDEAeYVWGDVRDRELMTELLEEADVLNHQASA 79 
                                       69*******************..6******9999988888888887777**************************** PP

                         3Beta_HSD  77 vdvag.kltedeimkvnvkGTrnvleacvkagv..rvlvYtSsaevvgpn 123
                                       v v + +++ +++ +vn   T  +l+  v+ ++  +++v  Ss+++ g+ 
  gi|313126445|ref|YP_004036715.1|  80 VGVGQsMYEIEKYVEVNTLATARILDIIVNEDIslEKIVVASSMSIYGEG 129
                                       ***9879999******************998763368********99984 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0062
                         3Beta_HSD 134 EeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvp......llkqlaklglalf 204
                                       E++++e   +++y+ sK+  E+l l+          ++  +aLR   iyG ++ l  p       +   +k+ +  +
  gi|313126445|ref|YP_004036715.1| 173 EKKPRE--STSVYAISKKDQEELTLSVAR-----SYDIPAVALRYFNIYGSRQALGNPytgvcaIFSSRIKNDNPPL 242
                                       444444..4689***********999877.....45899***********998764441100003334445555555 PP

                         3Beta_HSD 205 kigdeevlsdrvYvgNvawah 225
                                          d e++ d++    +a a 
  gi|313126445|ref|YP_004036715.1| 243 IFEDGEQTRDFIHISDIARAN 263
                                       555555666666666666555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   1.6e-09   1.9e-06       1     127 [.       4     121 ..       4     124 .. 0.81
   2 !   28.0   0.0   9.3e-10   1.1e-06     124     259 ..     169     310 ..     155     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.6e-09
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG++G +Gs++v++++++     ++ + +E+  ++  + l     +++       v gdvrd+e ++++le  +
  gi|313126445|ref|YP_004036715.1|   4 VLVTGGAGFVGSHIVDELVASGYDVTVVDNLTEQVHDDEPDYL-----NDEA----EYVWGDVRDRELMTELLE--E 69 
                                       89*****************998876666555555444333333.....2233....3569**************..9 PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-..SEEEEEE CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagv..kkvvliS 127
                                        dv+ h A    V    +++ + ++ N l+t  ++++ ++ ++  +k+v+ S
  gi|313126445|ref|YP_004036715.1|  70 ADVLNHQASAVGVGQSMYEIEKYVEVNTLATARILDIIVNEDIslEKIVVAS 121
                                       ************************************9988776336777766 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 9.3e-10
                                       EEEEEGGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT...TS....SHHHHHHHHHTT.SSE CS
                   Polysacc_synt_2 124 vliStDKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgSr...GS....viplFkkqikeg.gpv 192
                                       ++ S  K  ++t+v+ ++K+ +e l+ ++a++    +   v+ R+ N+ gSr   G     v  +F ++ik++  p+
  gi|313126445|ref|YP_004036715.1| 169 IATSEKKPRESTSVYAISKKDQEELTLSVARSY---DIPAVALRYFNIYGSRqalGNpytgVCAIFSSRIKNDnPPL 242
                                       7788899999*******************9999...8999***********955521444499*********95578 PP

                                       EES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEE.E--.-EEEHHHHHHHH..........SSSS-E CS
                   Polysacc_synt_2 193 tvTdpemtRyfmtieeavqLvlqalalakggeifv.ldmGepvkivdlakalielsgleekkeediei 259
                                          d e tR f+ i++ ++    a+++ +  ++ + l  G+p +i+++a++li+l+g++ + e++i+ 
  gi|313126445|ref|YP_004036715.1| 243 IFEDGEQTRDFIHISDIARANRLAMERDEAEDVALnLGTGNPKTITEIAETLIDLYGKSDELEPEIAN 310
                                       8899**************************999774789******************99988777765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   5.9e-05     0.071       1      25 [.       6      30 ..       6      52 .. 0.90
   2 !   19.0   0.0   5.3e-07   0.00064      79     218 ..      61     231 ..      53     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                                      EE-TTSHHHHHHHHHHHHHS-.TEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevki 25
                                      +TG+ GF+G++++ +L+ +  +v++
  gi|313126445|ref|YP_004036715.1|  6 VTGGAGFVGSHIVDELVASGYDVTV 30
                                      7****************99988755 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 5.3e-07
                                       HHHHHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHT..SSS--.-EEEEEE.GGGTTS-TTT--S CS
                     NAD_binding_4  79 edlqelaeevdviihsaAtvnfde...pykellrvNveGtrevlelak..klkklkvllhvST.ayvngeregevee 149
                                       e + el ee dv  h a  v + +   ++++ ++vN+++t ++l++     ++  + ++  S+ ++  +  ++  ee
  gi|313126445|ref|YP_004036715.1|  61 ELMTELLEEADVLNHQASAVGVGQsmyEIEKYVEVNTLATARILDIIVneDISL-EKIVVASSmSIYGEGAYHCPEE 136
                                       67889**************9775533377889*************987323444.5666667745555555545566 PP

                                       SS-H..........................HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EE CS
                     NAD_binding_4 150 kvyeege....................keekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsii 206
                                       ++++ +                     +e +   ++++k ++ +  Y  sK   E+l  + +r+ ++p+v +R  +i
  gi|313126445|ref|YP_004036715.1| 137 DTLHYPSlrgsetmaegqwehvcpdcgTELEPIATSEKKPRESTSVYAISKKDQEELTLSVARSYDIPAVALRYFNI 213
                                       666555588999************999888888888889999999******************************** PP

                                       E-......-SSST---TT CS
                     NAD_binding_4 207 tg......esktGwings 218
                                       +g      ++ tG++  +
  gi|313126445|ref|YP_004036715.1| 214 YGsrqalgNPYTGVCAIF 231
                                       **9999999999988765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.3e-09   1.5e-06       1     104 [.       8     128 ..       8     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH...CTTTCEEEE--TT-CCHHHHHHTT-SEE...EES---T CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele...aeeglevvegdvtdvedlaealkgadaV...vsalggg 71 
                                       G+ G vG+++v+el+a+ g++vt++   +e++++ e    ++++e v gdv d e ++e l+ ad+     sa+g g
  gi|313126445|ref|YP_004036715.1|   8 GGAGFVGSHIVDELVAS-GYDVTVVDNLTEQVHDDEpdyLNDEAEYVWGDVRDRELMTELLEEADVLnhqASAVGVG 83 
                                       99***************.5***988777999985443333689***********************94434444555 PP

                                       CC..HHHH..........HHHHHHHHHHCT-..-EEEEEEETTTTSG CS
                    NAD_binding_10  72 gk..deeg..........aknivdaakeagv..kRfvlvsaigvgde 104
                                       ++  +  +          +++i+d   ++++  +++v+ s++ ++ e
  gi|313126445|ref|YP_004036715.1|  84 QSmyE--IekyvevntlaTARILDIIVNEDIslEKIVVASSMSIYGE 128
                                       55440..3555666777899999988777643389******999965 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.3   3.6e-09   4.3e-06       2     121 ..       3     109 ..       2     130 .. 0.77
   2 ?   -0.3   0.0      0.51   6.1e+02     140     167 ..     174     201 ..     170     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.6e-09
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                        vlvtG+++ +G  i++el+++G++v+vvd+  e++    +e   ++++a ++ +Dv+dre + +l+e+a       
  gi|313126445|ref|YP_004036715.1|   3 NVLVTGGAGFVGSHIVDELVASGYDVTVVDNLTEQV--HDDEPDYLNDEAEYVWGDVRDRELMTELLEEA------- 70 
                                       69****************************999888..44555555899*******************99....... PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHH CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlp 121
                                       dvL + A+  g+g     s  e+e+++evN  ++  +   +++
  gi|313126445|ref|YP_004036715.1|  71 DVLNHQASAVGVG----QSMYEIEKYVEVNTLATARILDIIVN 109
                                       7776666663333....34566777777777777666655555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.51
                                       TSB-TTBHHHHHHHHHHHHHHHHHHHHH CS
                         adh_short 140 kvpvagvaaYsAsKaavagltrslakel 167
                                       k+p +++++Y+ sK   + lt s+a+ +
  gi|313126445|ref|YP_004036715.1| 174 KKPRESTSVYAISKKDQEELTLSVARSY 201
                                       6889999********9999999999876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   9.4e-07    0.0011       1      68 [.       4      73 ..       4      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.4e-07
                                      EEESSTTSHHHHHHHHHHHHHT-EEEE...EES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEE CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvra...lvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvv 68
                                      +lv+G++G  G+++v+ l+++g++v +   l+ +++ ++ + l+++ +e v gd+ d+e++ e+l+++dv 
  gi|313126445|ref|YP_004036715.1|  4 VLVTGGAGFVGSHIVDELVASGYDVTVvdnLTEQVHDDEPDYLNDE-AEYVWGDVRDRELMTELLEEADVL 73
                                      79**********************9873334555566777777665.89********************96 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   1.2e-06    0.0015       5      58 ..       9      66 ..       5     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                                      S-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE....EEES-TTSHHHHHHT CS
                            TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkdeerveelreegle....vvvgdatdeevLeea 58
                                      G+G vG+++++eL + g+ dv+v+d+  e+v+  + + l+    +v gd+ d+e++ e+
  gi|313126445|ref|YP_004036715.1|  9 GAGFVGSHIVDELVAsGY-DVTVVDNLTEQVHDDEPDYLNdeaeYVWGDVRDRELMTEL 66
                                      89*************777.7**********99988777444455********9987664 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00013      0.16       3      77 ..       4      72 ..       2     127 .. 0.80
   2 ?    0.9   0.0      0.31   3.7e+02      22      52 ..     340     370 ..     336     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                      EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                                KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77
                                      +l+tGG+G +G ++++ l+++g    v+   ++++++d+    + l+    e e+v  Dv d++ +++llee++ 
  gi|313126445|ref|YP_004036715.1|  4 VLVTGGAGFVGSHIVDELVASGYDVTVVDNLTEQVHDDEP---DYLN---DEAEYVWGDVRDRELMTELLEEADV 72
                                      79********************776666555533333333...3343...4778888888888888888888765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.31
                                       HHHS-EEEEE-SS..--HHHHHHHHHHHHTT CS
                                KR  22 ekgarhlvllsRsaaadedskaliaelealg 52 
                                       e+g r+lv  +R++ a+++ ++  aele++g
  gi|313126445|ref|YP_004036715.1| 340 EEGMRELVEWGREQDAQDNFEEAHAELEDKG 370
                                       799**********999999999999999987 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.1e-05     0.049       2      85 ..       3     103 ..       1     126 [. 0.81
   2 ?   -2.8   0.0       2.2   2.6e+03     115     141 ..     173     199 ..     167     218 .. 0.66
   3 ?   -3.2   0.0       2.9   3.5e+03     167     199 ..     266     300 ..     261     306 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...................T--TTSHHHHHHHHHHH--SEEEE-- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...................eldltdaeavaellkeakpdvvvnaA 59 
                                       ++lvtG+ G +Gs+++++l ++g++v+ +++                      d++d+e ++ell+e   dv+ + A
  gi|313126445|ref|YP_004036715.1|   3 NVLVTGGAGFVGSHIVDELVASGYDVTVVDNLteqvhddepdylndeaeyvWGDVRDRELMTELLEE--ADVLNHQA 77 
                                       69**************************977667788888888888887777788888888888887..67788888 PP

                                       ----HHHHHHSHHHHHHHHTHHHHHH CS
                     RmlD_sub_bind  60 AytavDkaEseeeaayavnaeaveal 85 
                                           v +   e e+  +vn  a++++
  gi|313126445|ref|YP_004036715.1|  78 SAVGVGQSMYEIEKYVEVNTLATARI 103
                                       87888887777777888887777776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                                       TTS----SSHHHHHHHHHHHHHHHH-S CS
                     RmlD_sub_bind 115 eddetsPlnvYGrtKlaGEqavlaagk 141
                                       e+ + +  +vY+ +K + E+  l+   
  gi|313126445|ref|YP_004036715.1| 173 EKKPRESTSVYAISKKDQEELTLSVAR 199
                                       455556678999999999988776444 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.9
                                       HHH-SEEEEESS-..EE--EEHHHHHHHHHHHHHH CS
                     RmlD_sub_bind 167 akereelkvvaDq..lgsPTsardlAevllqllek 199
                                       a er+e + va    +g+P    ++Ae l++l  k
  gi|313126445|ref|YP_004036715.1| 266 AMERDEAEDVALNlgTGNPKTITEIAETLIDLYGK 300
                                       55555555444431156788888888888888766 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.9e-05     0.094       3      73 ..       6      73 ..       4      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                                      EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEE CS
                   Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlv 73
                                      + G+ G+vG+ ++++l++++ +  ++tv+d   e+++    + l+ ++e +  d+ ++e  +++ll+e+d++
  gi|313126445|ref|YP_004036715.1|  6 VTGGaGFVGSHIVDELVASG-Y--DVTVVDNLTEQVHDDEPDYLNDEAEYVWGDVRDREL-MTELLEEADVL 73
                                      55555*************98.5..7**********9999999999999999999999998.99999999986 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.14       6      38 ..       9      41 ..       3      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      --SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N  6 GaGtmGagiaavfasagleVvlvdiseealeka 38
                                      GaG +G+ i   ++++g++V++vd  +e++++ 
  gi|313126445|ref|YP_004036715.1|  9 GAGFVGSHIVDELVASGYDVTVVDNLTEQVHDD 41
                                      89**********************977776544 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00032      0.39      19      31 ..     156     168 ..     152     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00032
                                       CEEESSSSBEEEE CS
                      TF_Zn_Ribbon  19 elvCtdCGlVled 31 
                                       e+vC+dCG+ le 
  gi|313126445|ref|YP_004036715.1| 156 EHVCPDCGTELEP 168
                                       89******99984 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.8   2.2e+03      22      32 .]     131     141 ..     127     141 .. 0.82
   2 ?   11.1   0.2    0.0002      0.24      15      30 ..     150     165 ..     149     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                     zf-NADH-PPase  22 rvCpaCglehY 32 
                                        +Cp  ++ hY
  gi|313126445|ref|YP_004036715.1| 131 YHCPEEDTLHY 141
                                       59**9999998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                     zf-NADH-PPase  15 paeggwarvCpaCgle 30 
                                       +aeg+w  vCp+Cg+e
  gi|313126445|ref|YP_004036715.1| 150 MAEGQWEHVCPDCGTE 165
                                       799***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2275.54
//
Query:       gi|313126446|ref|YP_004036716.1|  [L=313]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-52  179.1   0.0    1.2e-52  178.8   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.1e-52  177.3   0.0    6.2e-52  177.0   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.3e-14   53.9   0.0    1.6e-14   53.6   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.8e-12   45.3   0.0    7.2e-12   45.0   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    9.8e-12   44.6   0.0    3.4e-06   26.4   0.0    2.2  2  NAD_binding_4    Male sterility protein
    4.3e-08   32.6   0.0    0.00057   19.1   0.0    2.8  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0021   17.6   0.0     0.0072   15.8   0.0    1.9  2  adh_short        short chain dehydrogenase
     0.0034   17.3   0.0     0.0068   16.3   0.0    1.5  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
       0.02   14.2   0.1      0.057   12.7   0.1    1.6  1  Hydrolase_4      Serine aminopeptidase, S33
       0.12   12.3   0.0       0.75    9.7   0.0    2.0  2  KR               KR domain
       0.14   11.1   0.0       0.23   10.4   0.0    1.2  1  DUF3182          Protein of unknown function (DUF3182)
       0.15   11.6   0.0       0.61    9.6   0.0    1.9  2  NmrA             NmrA-like family
       0.16   12.0   0.4       0.71    9.9   0.4    2.1  1  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.8   0.0   8.4e-56   1.2e-52       2     241 .]       7     244 ..       6     244 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 8.4e-56
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       +VtG++Gf+Gs+lv+ ll+ gy+v++ld+  s+++ ++le+++  + +  +++  e + + +++ +v+h+A  ++++
  gi|313126446|ref|YP_004036716.1|   7 VVTGGAGFLGSHLVDSLLNDGYQVTVLDNFGSGRP-ENLEHVDAERFETINHDVSEPFPSLNNVGVVYHFASRASPK 82 
                                       8*****************************66665.66788899999999999999999999*************** PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS.BSTCSTTS--.--SSHHHHHHHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp.keettltgpl.kpnspYaaaKlageklv 153
                                       +  +++ +++ +n +gt n l+ a+++++ r++ +s+sevYG+++e p  ee+  + ++  p+ pY  +K+ +e l+
  gi|313126446|ref|YP_004036716.1|  83 DFDSHAVEIALANGMGTHNALQFASEHEA-RVVLASTSEVYGDPEEHPqHEEYRGNVNVrGPRAPYDESKRFAEALA 158
                                       *****************************.****************9968888877788****************** PP

                                       HHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                         Epimerase 154 eayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                        ay aq+ l++ ++r+fn yGpr   +++ rvip +++++legk ++t++gdg++ R f+yv+D++ +i +++++++
  gi|313126446|ref|YP_004036716.1| 159 VAYEAQHSLDIRTVRIFNTYGPR-MRQDDGRVIPNFLTQALEGK-DLTVYGDGSQTRSFCYVSDLIAGIRAFADAPS 233
                                       **********************9.8888****************.******************************** PP

                                       T-STTEEEEES CS
                         Epimerase 231 agdkgeiyniG 241
                                       + +kge++n+G
  gi|313126446|ref|YP_004036716.1| 234 EVAKGEVVNVG 244
                                       **********9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.0   0.0   4.5e-55   6.2e-52       2     332 .]       8     307 ..       7     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 177.0 bits;  conditional E-value: 4.5e-55
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       +TG+aGf Gs+l++ Ll+ gy+v+++++  s  + +++eh+         e+++ +++D+++        +  ++  
  gi|313126446|ref|YP_004036716.1|   8 VTGGAGFLGSHLVDSLLNDGYQVTVLDNFGSG-RPENLEHVD-------AERFETINHDVSEPF-----PSLNNVGV 71 
                                       9**********************999876654.557777764.......35899******9964.....34455689 PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.....S----- CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.....tpfyPr 150
                                       vy++A     +   +++ + a +n++Gt++ L+ + ++    ++r++ aStsEvYG+++e+pq+E+     +   Pr
  gi|313126446|ref|YP_004036716.1|  72 VYHFASRASPKDFDSHAVEIALANGMGTHNALQFASEH----EARVVLASTSEVYGDPEEHPQHEEyrgnvNVRGPR 144
                                       ************999********************886....58*********************8666555667** PP

                                       SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHH CS
                     GDP_Man_Dehyd 151 sPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvk 227
                                        PY  +K +a+ ++v+y+ ++ l + + ++fn+++pr+ ++   r i+++++++++gk + +++G+++++R++ +v+
  gi|313126446|ref|YP_004036716.1| 145 APYDESKRFAEALAVAYEAQHSLDIRTVRIFNTYGPRMRQD-DGRVIPNFLTQALEGK-DLTVYGDGSQTRSFCYVS 219
                                       *************************************9887.99*************9.8899************** PP

                                       HHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--S CS
                     GDP_Man_Dehyd 228 Dyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevd 304
                                       D + +++++  + +     +a+ge+++v++  e+++ el + i                 ++   +++++  + + +
  gi|313126446|ref|YP_004036716.1| 220 DLIAGIRAFADAPS----EVAKGEVVNVGNTDEVTIFELAELILEIV-------------DTDSDITYEPLPEDDPK 279
                                       *******9888765....49*******************98665432.............22334555566667778 PP

                                       B--B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 305 lllgdaskakeeLgWkpkvsfeelvrem 332
                                        +  d+ska   L+W+p++++e++++++
  gi|313126446|ref|YP_004036716.1| 280 IRRPDISKATGMLDWEPTIGLEKGLKRT 307
                                       8899********************9975 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   1.2e-17   1.6e-14       1     255 [.       7     250 ..       7     271 .. 0.73

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.2e-17
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlas 75 
                                       vvtGgaGFlG++lv +L++ +   +v vlD   s +  e+l++v+ +   +i+ Dv +       l++v vv h as
  gi|313126446|ref|YP_004036716.1|   7 VVTGGAGFLGSHLVDSLLNDG--YQVTVLDNFGSGRP-ENLEHVDAERfeTINHDVSEPF---PSLNNVGVVYHFAS 77 
                                       8*****************999..6******6555444.5566665555449999998874...578999******99 PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyesl...hqdaype 148
                                           +    +  ei  +n  GT+n l+ + +++ r +v  S+ ev g+    ee    +Ee + + +   + ++y e
  gi|313126446|ref|YP_004036716.1|  78 RASPKDfDSHAVEIALANGMGTHNALQFASEHEAR-VVLASTSEVYGD---PEEHP-QHEEYRGNVNvrgPRAPYDE 149
                                       887777567778999******************87.578*********...33322.466666555546799***** PP

                         3Beta_HSD 149 sKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkl....lvpllkqlaklglalfkigdeevlsdrvYvgNv 221
                                       sK+ aE+l ++      +    l    +R    yG++ ++    + p + + a  g+ l  +gd +++ ++ Yv  +
  gi|313126446|ref|YP_004036716.1| 150 SKRFAEALAVAYEA---QH--SLDIRTVRIFNTYGPRMRQddgrVIPNFLTQALEGKDLTVYGDGSQTRSFCYVSDL 221
                                       *******9887766...33..344455789999***8764222245555555566779***************9876 PP

                         3Beta_HSD 222 awahilAaralqdpkkkssvagqayfisddsPve 255
                                           i   ra+ d  ++++++g++  + ++  v+
  gi|313126446|ref|YP_004036716.1| 222 ----IAGIRAFADA-PSEVAKGEVVNVGNTDEVT 250
                                       ....4444555555.5566666666665555555 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   5.2e-15   7.2e-12       3     254 ..       6     284 ..       4     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 5.2e-15
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.........T--TTSHHHHHHHHHHH--S.....EEEE------HH CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre.........eldltdaeavaellkeakpd.....vvvnaAAytavD 65 
                                        +vtG+ G lGs+L+++l ++g++v+ l++          ++d ++ e++++ ++e  p+     vv++ A      
  gi|313126446|ref|YP_004036716.1|   6 AVVTGGAGFLGSHLVDSLLNDGYQVTVLDNFgsgrpenleHVDAERFETINHDVSEPFPSlnnvgVVYHFASRASPK 82 
                                       589*************************87789999*99999999999999999876666555569*********** PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-....TTS-B-TT.S----SSHHHHHHHHHHHHHH CS
                     RmlD_sub_bind  66 kaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGe....kkrpYeed.detsPlnvYGrtKlaGEqavl 137
                                          s+  + + +n  ++++  + a++++a ++  St  V+       ++++Y+ + +  +P+  Y ++K   E    
  gi|313126446|ref|YP_004036716.1|  83 DFDSHAVEIALANGMGTHNALQFASEHEARVVLASTSEVYGDPeehpQHEEYRGNvNVRGPRAPYDESKRFAEALAV 159
                                       ****************************************76645555555765425678*************9666 PP

                                       H.H-SSEEEEEE-SEESS.......SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.G CS
                     RmlD_sub_bind 138 a.agkkalivRtswvyge.......kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeek 204
                                       a + ++ l +Rt  ++          +   + ++l  a e + l+v  D  q++s  ++ dl + + + +++  e  
  gi|313126446|ref|YP_004036716.1| 160 AyEAQHSLDIRTVRIFNTygprmrqDDGRVIPNFLTQALEGKDLTVYGDgsQTRSFCYVSDLIAGIRAFADAPSE-V 235
                                       615555566899998887333443333446778999***********998899999**************99997.7 PP

                                       GG-EEEE---BS-EEHHHHHHHHHHHHCHTT.SEEEEE-CCCS--SS---S CS
                     RmlD_sub_bind 205 elagvyHlanegetswlefArailkeagads.eevkpistaeyptpAkRPa 254
                                       ++ +v  ++n++e++ +e+A+ il+ +++ds    +p    e   + +RP 
  gi|313126446|ref|YP_004036716.1| 236 AKGEVVNVGNTDEVTIFELAELILEIVDTDSdITYEPL--PEDDPKIRRPD 284
                                       779***********************999884333444..33334556665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.4e-06    0.0046       1      27 [.       8      32 ..       8      46 .. 0.88
   2 !   26.4   0.0   2.5e-09   3.4e-06      86     205 ..      67     176 ..      59     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.4e-06
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyl 27
                                      +TG+ GFLG++L+  LL++  +  +++
  gi|313126446|ref|YP_004036716.1|  8 VTGGAGFLGSHLVDSLLNDGYQ--VTV 32
                                      7****************99874..444 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 2.5e-09
                                       HH--EEEE--SS-...S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H...... CS
                     NAD_binding_4  86 eevdviihsaAtv...nfdepykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekee 159
                                       ++v v++h a +    +fd++  e+  +N +Gt++ l++a++ ++   ++  ST+ v+g+ e++ +           
  gi|313126446|ref|YP_004036716.1|  67 NNVGVVYHFASRAspkDFDSHAVEIALANGMGTHNALQFASEHEAR--VVLASTSEVYGDPEEHPQH---------- 131
                                       799*****997763337999*********************88666..9999**9999999977533.......... PP

                                       HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-E CS
                     NAD_binding_4 160 kldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsi 205
                                        ++     + +g    Y  sK  aE l  ++  ++ l +  vR+ +
  gi|313126446|ref|YP_004036716.1| 132 -EEYRGNVNVRGPRAPYDESKRFAEALAVAYEAQHSLDIRTVRIFN 176
                                       .55566777889999***********************99999755 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.4   0.00056      0.77       2     128 ..       7     118 ..       6     123 .. 0.68
   2 !   19.1   0.0   4.2e-07   0.00057     138     250 ..     147     265 ..     139     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00056
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                       +vtG++G +Gs+lv+ +l+   +  +l +    +  ++e+       ++++  e  ++  dv +       l+  +v
  gi|313126446|ref|YP_004036716.1|   7 VVTGGAGFLGSHLVDSLLNDGYQVTVLDNFGSGRPENLEHVD-----AERF--E--TINHDVSEP---FPSLN--NV 69 
                                       699999999999999999877654444333333444444433.....3322..2..222344433...33444..78 PP

                                       SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                        vv+h A        +++++e    N +gt+n ++ a e++  +vvl St
  gi|313126446|ref|YP_004036716.1|  70 GVVYHFASRASPKDFDSHAVEIALANGMGTHNALQFASEHEA-RVVLAST 118
                                       899999988888889999999999999999999999999886.5777777 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHHHHHHHGGG--S.SS--EEEEEEE-EETT.GTTSSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHH... CS
                   Polysacc_synt_2 138 mGatKrlaekllqalakese.ekktkfvvvRfGNVlg.SrGSviplFkkqikeggpvtv.TdpemtRyfmtiee... 208
                                       +  +Kr+ae l++a++++++ + +t  ++  +G  +    G vip F  q  eg+++tv  d + tR f  +++   
  gi|313126446|ref|YP_004036716.1| 147 YDESKRFAEALAVAYEAQHSlDIRTVRIFNTYGPRMRqDDGRVIPNFLTQALEGKDLTVyGDGSQTRSFCYVSDlia 223
                                       5679**********99888313334445555666554257*******************558899998888877332 PP

                                       HHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH....... CS
                   Polysacc_synt_2 209 avqLvlqalalakggeifvldmGepvkivdlakalielsgle 250
                                       +++    a ++  +ge+  +   + v+i +la+ ++e+++++
  gi|313126446|ref|YP_004036716.1| 224 GIRAFADAPSEVAKGEVVNVGNTDEVTIFELAELILEIVDTD 265
                                       566777888888899987666669*********999998754 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.2e-06    0.0072       1      60 [.       4      61 ..       4      70 .. 0.91
   2 ?   -2.0   0.0       1.5   2.1e+03       8      33 ..      93     118 ..      87     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.2e-06
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTS CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtd 60
                                      ++++vtG+++ +G  +++ l+++G++v+v+d+  +   e ++++ +e  ++ +i+ Dv++
  gi|313126446|ref|YP_004036716.1|  4 QHAVVTGGAGFLGSHLVDSLLNDGYQVTVLDNFGSGRPENLEHVDAE--RFETINHDVSE 61
                                      589*****************************999999999999985..79999999875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                       TTSHHHHHHHHHHHHTT-EEEEEESC CS
                         adh_short   8 assGIGraiakelakeGakvvvvdrs 33 
                                        ++G+G   a ++a+e    vv++++
  gi|313126446|ref|YP_004036716.1|  93 LANGMGTHNALQFASEHEARVVLAST 118
                                       57899999999999875444444443 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     5e-06    0.0068       1     126 [.      10     152 ..      10     174 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.....HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.....peklaeleaeeglevvegdvtdvedlaealkgadaVvsalgggg 72 
                                       G+ G  G++lv+ ll++ g++vt+l  n     pe l+++ ++e+ e++  dv+   +    l+++ +V+  +++ +
  gi|313126446|ref|YP_004036716.1|  10 GGAGFLGSHLVDSLLND-GYQVTVLD-NfgsgrPENLEHV-DAERFETINHDVS---EPFPSLNNVGVVYHFASR-A 79 
                                       999**************.5***9983.3232336666655.3566666666665...445566777777555532.2 PP

                                       C....HHHH..........HHHHHHHHHHCT--EEEEEEETTTTSGCGCH......HHHHHHHCCHHHHHHHHH CS
                    NAD_binding_10  73 k....deeg..........aknivdaakeagvkRfvlvsaigvgdevpge......fgewnkellkaylaakra 126
                                       +    d+++          + n+++ a e++  R+vl s+  v+ + +++       g++n +  +a +++ ++
  gi|313126446|ref|YP_004036716.1|  80 SpkdfDSHAveialangmgTHNALQFASEHEA-RVVLASTSEVYGDPEEHpqheeyRGNVNVRGPRAPYDESKR 152
                                       22345444477788888889999999988887.89999999998532221111222334444555555655444 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.1e-05     0.057      21      66 ..      17      63 ..      14     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                       Hydrolase_4 21 aelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafv 66
                                      ++l++ L + G++v  lD+ G Gr e  ++++ ++f+++  D+++ +
  gi|313126446|ref|YP_004036716.1| 17 SHLVDSLLNDGYQVTVLDNFGSGRPEnLEHVDAERFETINHDVSEPF 63
                                      589**********************9778889999999999998755 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00054      0.75       4      28 ..       7      31 ..       5      62 .. 0.86
   2 ?    0.0   0.0       0.5   6.9e+02      11      38 ..      96     122 ..      93     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00054
                                      EEETTTSHHHHHHHHHHHHHHS-EE CS
                                KR  4 litGGlGgLGlelarwlaekgarhl 28
                                      ++tGG+G LG +l++ l+++g +  
  gi|313126446|ref|YP_004036716.1|  7 VVTGGAGFLGSHLVDSLLNDGYQVT 31
                                      79******************97654 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHHS-EEEEE-SS..-- CS
                                KR  11 gLGlelarwlaekgarhlvllsRsaaad 38 
                                       g+G++ a + a+++++++vl s s+ + 
  gi|313126446|ref|YP_004036716.1|  96 GMGTHNALQFASEHEARVVLASTSE-VY 122
                                       7888889999999999999999885.22 PP

>> DUF3182  Protein of unknown function (DUF3182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.23     307     344 ..     104     139 ..      99     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                           DUF3182 307 afaedpalravrastvEvygedeavpadalvlyrgede 344
                                       +fa++ ++r+v ast Evyg+ e++p++    yrg+ +
  gi|313126446|ref|YP_004036716.1| 104 QFASEHEARVVLASTSEVYGDPEEHPQHEE--YRGNVN 139
                                       59999*********************9874..666655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00044      0.61       2      28 ..       7      33 ..       6     105 .. 0.90
   2 ?   -0.5   0.0      0.53   7.3e+02     164     221 ..     200     258 ..     188     271 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00044
                                      EESSTTSHHHHHHHHHHHHHT-EEEEE CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvral 28
                                      +v+G++G +G+++v+ ll++g++v +l
  gi|313126446|ref|YP_004036716.1|  7 VVTGGAGFLGSHLVDSLLNDGYQVTVL 33
                                      69**********************987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.53
                                       S.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHH.TTEEEEE-S.EEE-HHHHHHHH CS
                              NmrA 164 edkvtllgpgnpkavlldaeeDiGafvikilkdprkl.kgkriklag.ntlsgneivelf 221
                                       ++ +t+ g+g+    +   + D  a + + ++ p+++ kg+++++ + ++++  e++el+
  gi|313126446|ref|YP_004036716.1| 200 GKDLTVYGDGSQTRSFC-YVSDLIAGIRAFADAPSEVaKGEVVNVGNtDEVTIFELAELI 258
                                       44677788888766666.778887777777788999888888887542677887877776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4   0.00051      0.71       2      99 ..      10     113 ..       9     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00051
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev.......elvvrvprvplpllkrllrsl.aflrrlrrllkr 70 
                                       GG++    +L+  L  +G++Vtv+   ++g++e+ +       e++   ++ p+p+l++ +  +  ++r+  + ++ 
  gi|313126446|ref|YP_004036716.1|  10 GGAGFLGSHLVDSLLNDGYQVTVLDNFGSGRPENLEhvdaerfETINHDVSEPFPSLNNVGVVYhFASRASPKDFDS 86 
                                       888888899***************44444444444445789995555555555566666555550555667788888 PP

                    Glyco_transf_4  71 ekpDvvHahspaalgaallalrrrlgipl 99 
                                       + + +  a++ +++   +l  + ++ +++
  gi|313126446|ref|YP_004036716.1|  87 HAVEIALANGMGTH--NALQFASEHEARV 113
                                       88888888887776..4444444445554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1784.23
//
Query:       gi|313126447|ref|YP_004036717.1|  [L=336]
Description: dtdp-glucose pyrophosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-35  122.3   0.0      3e-35  122.0   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    1.8e-14   54.4   0.0    2.3e-14   54.1   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    7.4e-07   29.1   0.1    1.3e-06   28.3   0.1    1.5  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0012   18.4   4.7       0.35   10.7   0.1    3.2  3  Hexapep          Bacterial transferase hexapeptide (six repea
  ------ inclusion threshold ------
       0.13   12.0   2.3        3.8    7.3   0.4    3.2  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.0   0.0   8.3e-39     3e-35       1     245 [.       2     241 ..       2     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 122.0 bits;  conditional E-value: 8.3e-39
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTT..SGGGTSEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlke..gskfgvev 75 
                                       kavI a G+GtRL+P t+t +k +v  +g  +++ + l  l+n +iee+++v+  + ++ + ++ ++  g++   ++
  gi|313126447|ref|YP_004036717.1|   2 KAVIPAAGQGTRLYPQTHTKPKAMVRLAGR-PILGHILVSLSNTRIEEVVIVVGGQMKAQIIDYSTAmfGDR--FDI 75 
                                       799***************************.******************99999888887777666511445..55* PP

                                       EEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEE CS
                   NTP_transferase  76 lialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvie 152
                                       +++ +++ +g+ +++++a+e+ + ++    +l+  gD+l+++ ye++++ + + +  ++ ++g+++vee++ yGv+e
  gi|313126447|ref|YP_004036717.1|  76 TFVEQEQAEGLGHSIYQAEEVCRGDS----LLIALGDMLFEKGYEKFLQAHNQLDD-VDGSIGVKQVEEPQHYGVVE 147
                                       ***********************999....89999*******************99.9******************* PP

                                       ECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHH.HH.CCHHHTT...SSCHHHHHHHHHHHTTEEEEEECST CS
                   NTP_transferase 153 adeegrverfvEKPkeakaselassGiYvfnsevllfl.ak.dleelkr...gedeitdilpkaleegkvalaflfk 224
                                       +++e+r+e++vEKP++++ s+la sGiY+ + + llf  ++  +e+ +r   ge ++td+l+++++ + +     f+
  gi|313126447|ref|YP_004036717.1| 148 VNGEERIEQLVEKPDNPP-SDLAISGIYLIEDSDLLFDsLAeLVENDERgagGEYQLTDALQRMIDFEADLGT--FE 221
                                       ******************.**********98775555412224444433111678889999999888655554..44 PP

                                       TEE-EEEXSSHHHHHHHHHHH CS
                   NTP_transferase 225 daeyWsDvGtldslleanekl 245
                                        + +W D G +  llean+ l
  gi|313126447|ref|YP_004036717.1| 222 VY-NWYDCGRPGTLLEANRVL 241
                                       44.5*************9866 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   6.4e-18   2.3e-14       1     115 [.       3     126 ..       3     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 6.4e-18
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHH........TTCTS-EEE CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggdeevlaal........arlgvrvve 64 
                                       avi A+G+++R+      ++Ka+++l+g+p+l ++l +l+   ++evv+v+g +  ++ +        +r+++++ve
  gi|313126447|ref|YP_004036717.1|   3 AVIPAAGQGTRLypqthTKPKAMVRLAGRPILGHILVSLSNTRIEEVVIVVGGQMKAQIIdystamfgDRFDITFVE 79 
                                       7899********6554334********************************99755542233344444778999999 PP

                                       -TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHT CS
                      NTP_transf_3  65 dedpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasg 115
                                       +e+  +g ++s++ a + + + d +l++++Dm +  ++ +e++l+a+ + +
  gi|313126447|ref|YP_004036717.1|  80 QEQ-AEGLGHSIYQAEEVC-RGDSLLIALGDMLF--EKGYEKFLQAHNQLD 126
                                       985.89*************.9***********99..788899888885443 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   3.7e-10   1.3e-06       2      57 ..       2      59 ..       1      93 [. 0.82

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.7e-10
                                      EEEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHH CS
                              IspD  2 vvvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvseddte 57
                                       +vipAAG+G+R+      +pK+ + l+g+++l h + +l + ++++++v+vv  +   
  gi|313126447|ref|YP_004036717.1|  2 KAVIPAAGQGTRLypqTHTKPKAMVRLAGRPILGHILVSLSN-TRIEEVVIVVGGQMKA 59
                                      69**********94434678***************9877665.9999999998766544 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   9.6e-05      0.35      14      30 ..     256     272 ..     250     274 .. 0.90
   2 !    9.5   0.5   0.00023      0.81       1      20 [.     272     291 ..     272     305 .. 0.75
   3 ?   -2.1   0.0         1   3.8e+03      25      35 ..     310     320 ..     309     321 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.6e-05
                                       EEEETTEEE-TTEEEET CS
                           Hexapep  14 aviggnVkIGdnvkIga 30 
                                       avi ++V IGd+v++++
  gi|313126447|ref|YP_004036717.1| 256 AVIVPPVDIGDDVTLES 272
                                       9*************998 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00023
                                       TEEEETTEEE-TTEEEETTE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnV 20 
                                       s+vIG nv I++++ i++ +
  gi|313126447|ref|YP_004036717.1| 272 SSVIGPNVSIDSGTSIRNSI 291
                                       57888888888877776654 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1
                                       TEEEETTEEEE CS
                           Hexapep  25 nvkIgagvvig 35 
                                       ++++g+ ++++
  gi|313126447|ref|YP_004036717.1| 310 HSIVGSSARVH 320
                                       67788777776 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4    0.0011       3.8      14      28 ..     256     272 ..     251     283 .. 0.78
   2 ?    3.7   0.1     0.015        53       8      21 ..     273     288 ..     271     292 .. 0.76
   3 ?   -1.6   0.0      0.66   2.4e+03       6      15 ..     293     302 ..     289     306 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                                       -EE..SEEE-TT-EE-T CS
                         Hexapep_2  14 agi..GvslGdncvvga 28 
                                       a+i  +v++Gd++++++
  gi|313126447|ref|YP_004036717.1| 256 AVIvpPVDIGDDVTLES 272
                                       676788******98875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.015
                                       -EE-TT-EE..SEEE- CS
                         Hexapep_2   8 CliGanagi..GvslG 21 
                                       ++iG+n  i  G+s++
  gi|313126447|ref|YP_004036717.1| 273 SVIGPNVSIdsGTSIR 288
                                       5788998888888886 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.66
                                       TT-EE-TT-E CS
                         Hexapep_2   6 dnCliGanag 15 
                                       ++++iG  a+
  gi|313126447|ref|YP_004036717.1| 293 KDSIIGGEAT 302
                                       6888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2087.20
//
Query:       gi|313126448|ref|YP_004036718.1|  [L=586]
Description: hypothetical protein Hbor_17050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-49  169.4  40.6    1.6e-49  169.1  40.6    1.1  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
    3.7e-30  105.0   0.0    5.7e-30  104.4   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    9.9e-12   45.2   0.0    1.8e-11   44.4   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
        3.1    8.1  13.3        9.3    6.6   0.6    4.2  4  BacteriocIIc_cy  Bacteriocin class IIc cyclic gassericin A-li


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1  40.6   3.6e-53   1.6e-49       3     301 .]     263     550 ..     256     550 .. 0.88

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 3.6e-53
                   LPG_synthase_TM   3 lglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglf 79 
                                        g+a++++l+      ++++ ++++l+ ++p w+l+a +++  ++ +r++r+r+llr++g+  s + +lr +++g+f
  gi|313126448|ref|YP_004036718.1| 263 FGIAILVGLFS----LTGFEGVFQTLSDAQPAWILAAAGMYGSTFAFRTWRFRVLLRTAGHMASRGGVLRSIFTGWF 335
                                       34455555555....55**********************9999999******************************* PP

                   LPG_synthase_TM  80 vnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallll 156
                                       vn ++P+++ G+v+r + lk +e+v+++   + vvver+ld+l+l+ll++++ l++++ ++ +  +l++++lal+ll
  gi|313126448|ref|YP_004036718.1| 336 VNFLIPARA-GDVARGLALKSTEDVPFGVTSGLVVVERILDMLMLGLLMGIVTLMFLSNSQGRFLALAAFGLALVLL 411
                                       ********9.**************************************99999888887766643555555555554 PP

                   LPG_synthase_TM 157 avlalllllllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwllealtlylllralg 233
                                       ++l+ +l+ l  r + r   +++r++  la ++    s     +l +p +l+la++lsl +wllea+tl+l +ralg
  gi|313126448|ref|YP_004036718.1| 412 VGLV-VLVQLDERIADRFESRFPRIREGLAGLRHAVGS-----LLDNPYALALALFLSLPVWLLEASTLFLSARALG 482
                                       4444.466677777777777777777777777766665.....689******************************* PP

                   LPG_synthase_TM 234 vdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                       v+++l + l++ +a+ l +a+p++PgGlG++Eaa a +l+l+ +s+++++++ l+++++ l ++++lG
  gi|313126448|ref|YP_004036718.1| 483 VSLDLIVGLTASVAAFLTQAVPVTPGGLGTYEAAIAGVLSLFSISTTLGTSIGLIDHFMRLAFVYILG 550
                                       *****************************************************************998 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   1.3e-33   5.7e-30       1     170 []       4     174 ..       4     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 1.3e-33
                                       EEEEEESS-TTTHHHHHHHHHHH....GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq....dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalna 73 
                                       s v+p++Ne  +l+++++s+ +       + ++ei++vDD+StDet+ ++++l +e+  v+v++r  n G+++a+ +
  gi|313126448|ref|YP_004036718.1|   4 SLVVPAHNEVGNLERLVDSVTSElsppRFDHELEILLVDDNSTDETPGLCDQLEREYSSVTVVHRHDNPGFGNAVKE 80 
                                       78***********************999999********************************************** PP

                                       HHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCC CS
                   Glycos_transf_2  74 glraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgn 150
                                       gl+ a+gd+i+ +  D+  +p +++klvea+e+ g+dv++g+r+  +g+ d +++ k     +r ++   +   ++ 
  gi|313126448|ref|YP_004036718.1|  81 GLSTASGDIIIPFMGDLSDSPSDVPKLVEAIED-GYDVAYGSRFTEGGSVDGYPPVKL--LYNRSFNNLIRLLFGIR 154
                                       *********************************.***********************9..89999999999****** PP

                                       STTCSTCCCEEEEHHHHHCH CS
                   Glycos_transf_2 151 lsfeigsaallrrealeell 170
                                       + +++  ++++rre++ee++
  gi|313126448|ref|YP_004036718.1| 155 SKDVTNAFTAYRREVIEEIG 174
                                       ****************9985 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   3.9e-15   1.8e-11       4     188 ..       3     185 ..       2     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 3.9e-15
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaq..e.y..prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       ++++Vp+ ne   l+++++s+ +   + +  +++e+ +v+d+s++et   +++l+++++   v+vv++ +n+g+   
  gi|313126448|ref|YP_004036718.1|   3 VSLVVPAHNEVGNLERLVDSVTSElsPpRfdHELEILLVDDNSTDETPGLCDQLEREYSS--VTVVHRHDNPGF--- 74 
                                       799*********999999998865222234666*************************98..59******9997... PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaar 152
                                        +a++e+l+++++d+++ + +D   +P  +++l+ ++  ++++++++++f++ +s    +  +l +++ + +  ++ 
  gi|313126448|ref|YP_004036718.1|  75 GNAVKEGLSTASGDIIIPFMGDLSDSPSDVPKLVEAI-EDGYDVAYGSRFTEGGSVDGYPPVKLLYNRSFNNLIRLL 150
                                       55668*******************************9.**************9886655556655555555444444 PP

                   Glyco_tranf_2_3 153 ralgvltlnGsgslirrevlkelegldplflltdDy 188
                                         ++   ++ +++++rrev +e++  +   +   D+
  gi|313126448|ref|YP_004036718.1| 151 FGIRSKDVTNAFTAYRREVIEEIGVETL-DSDSFDI 185
                                       4445555566*************95444.3333444 PP

>> BacteriocIIc_cy  Bacteriocin class IIc cyclic gassericin A-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2      0.02        88      50      75 ..     242     267 ..     235     280 .. 0.90
   2 ?    6.6   0.6    0.0021       9.3      74      90 ..     287     303 ..     273     304 .. 0.83
   3 ?    4.9   0.2    0.0068        31      16      86 ..     403     475 ..     391     484 .. 0.65
   4 ?   -2.2   0.1       1.1   5.1e+03      59      73 ..     506     520 ..     483     533 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHH---SSTTTTTSSSSS CS
                   BacteriocIIc_cy  50 arklldavasGaslgtafaiilGvtl 75 
                                        r+ll a++sG+ l    a++ G+++
  gi|313126448|ref|YP_004036718.1| 242 LRDLLSAITSGGPLRIVGAAVFGIAI 267
                                       599******************99976 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0021
                                       SS-STHHHHTSSSS-S- CS
                   BacteriocIIc_cy  74 tlPawilaaaaalGita 90 
                                       + Pawilaaa+ +G t 
  gi|313126448|ref|YP_004036718.1| 287 AQPAWILAAAGMYGSTF 303
                                       56************985 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0068
                                       XXXXXXXXXXXXXXXXXX-TTHHHHT--S---SSHHHHHHHH.HHH---SS..TTTTTSSSSS-STHHHHTSSS CS
                   BacteriocIIc_cy  16 lfaisivlvvalllataniyfiadklGiqlatatarklldav.asGaslgt..afaiilGvtlPawilaaaaal 86 
                                        f +  vl+v l++       iad++  ++     + l     a G+ l    a+a  l ++lP w l+a++ +
  gi|313126448|ref|YP_004036718.1| 403 AFGLALVLLVGLVVLVQLDERIADRFESRFPR-IREGLAGLRhAVGSLLDNpyALALALFLSLPVWLLEASTLF 475
                                       56777788888887777778889998877643.333333333133444444116667778899******98765 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.1
                                       HH---SSTTTTTSSS CS
                   BacteriocIIc_cy  59 sGaslgtafaiilGv 73 
                                       + + lgt  a+i Gv
  gi|313126448|ref|YP_004036718.1| 506 TPGGLGTYEAAIAGV 520
                                       345677777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3514.46
//
Query:       gi|313126449|ref|YP_004036719.1|  [L=231]
Description: glycosyl transferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-16   59.2   0.1    5.6e-16   58.8   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    9.2e-06   25.7   0.0      1e-05   25.6   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00013   22.4   0.1    0.00022   21.7   0.1    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.028   14.8   0.0      0.037   14.4   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
       0.11   13.0   0.2       0.18   12.4   0.2    1.3  1  YflT             Heat induced stress protein YflT
       0.12   11.7   0.1       0.18   11.2   0.1    1.1  1  NAD_binding_5    Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.1   1.9e-19   5.6e-16       2     168 ..       2     162 ..       1     164 [. 0.84

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.9e-19
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                       v +p+yNe+++++ ++e  laq     +e++vvD++S+D+t+e++ee+     + +v+  ++  G++ a  +++++ 
  gi|313126449|ref|YP_004036719.1|   2 VGMPAYNEAENIATAVENFLAQ--NTVDEVVVVDNNSSDNTAELAEEA-----GATVVSETRQ-GYGYACQRAFQEM 70 
                                       679*******************..************************.....9999999955.***********97 PP

                                       -SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.EEEECCHCCCCHCCCCCCS CS
                   Glycos_transf_2  79 tgd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv.generlyfkerkrslkgnl 151
                                             +++++  D ++  d++ekl+ +  +   d v+g+r   +  +   +   +  + n+ + +  +    + nl
  gi|313126449|ref|YP_004036719.1|  71 YEHdsdLLVLVEPDGTFVADDIEKLLSYSSD--FDFVVGTRTSPQLIWEGANMDPFLrWGNWFVGKLVEVLHNTSNL 145
                                       544466************************9..66799999888777776666655566666677777777777788 PP

                                       TTCSTCCCEEEEHHHHH CS
                   Glycos_transf_2 152 sfeigsaallrrealee 168
                                       +++ ++++l++ +a+e+
  gi|313126449|ref|YP_004036719.1| 146 TDVGCTFRLIKADAYED 162
                                       88888888888887776 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   3.4e-09     1e-05       6     115 ..       2     100 ..       1     168 [. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.4e-09
                   Glyco_tranf_2_3   6 vlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                       v  p++ne++ +   +e++laq +  +evvvv+++s++ t+e aee       ++ +vv  +r+    g+ +a ++a
  gi|313126449|ref|YP_004036719.1|   2 VGMPAYNEAENIATAVENFLAQ-NTVDEVVVVDNNSSDNTAELAEE-------AGATVVSETRQ----GYGYACQRA 66 
                                       677******************8.999****************9999.......36789988884....555566666 PP

                   Glyco_tranf_2_3  83 lr.avk..sdlvllvDdDtvvePdtlkrllqffltp 115
                                       ++ +++  sdl++lv+ D     d +++ll +   +
  gi|313126449|ref|YP_004036719.1|  67 FQeMYEhdSDLLVLVEPDGTFVADDIEKLLSYS--S 100
                                       663333447777777766655555557777775..4 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   7.4e-08   0.00022       2      87 ..       8      90 ..       7      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.4e-08
                   Glyco_tranf_2_4  2 neadiLpefla.hhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvD 79
                                      nea+ +   ++  + ++ +d+++v+dn+s+D+t+++ +e  +  + ++++ y   +   ++ +++ ++  ++d ++ v 
  gi|313126449|ref|YP_004036719.1|  8 NEAENIATAVEnFLAQNTVDEVVVVDNNSSDNTAELAEEAGATVVSETRQGYG--YACQRAFQEMYEH--DSDLLVLVE 82
                                      6666666666623445679********************99999999999885..3334455555543..567777666 PP

                   Glyco_tranf_2_4 80 aDEflvvp 87
                                       D  +v +
  gi|313126449|ref|YP_004036719.1| 83 PDGTFVAD 90
                                      66666655 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.037      28     109 ..      14      97 ..       6     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHCTT..-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHH.H..SSSCEEEEETT-TT- CS
                      NTP_transf_3  28 ervldalraa.gvdevvvvggd..eevlaalarlgvrvvededpgkgplaslaaalra.aa.dadavlvlacDmPll 99 
                                       + +++++ a+ +vdevvvv ++  ++ ++ +++ g++vv+++   +g +++ + a ++  + d+d ++++  D  ++
  gi|313126449|ref|YP_004036719.1|  14 ATAVENFLAQnTVDEVVVVDNNssDNTAELAEEAGATVVSET--RQGYGYACQRAFQEmYEhDSDLLVLVEPDGTFV 88 
                                       5566666666369******9986667888889999*****98..799999999999996444777777777787775 PP

                                       -HHHHHHHHH CS
                      NTP_transf_3 100 tpelverlla 109
                                        ++ +e+ll 
  gi|313126449|ref|YP_004036719.1|  89 -ADDIEKLLS 97 
                                       .566777766 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   5.9e-05      0.18       4      66 ..       7      69 ..       5      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                              YflT  4 yeneeellsaieelkaeGyneddiyvvakdkdrlerlaentdaetettseeglwdsiknlfrs 66
                                      y+  e    a+e + a+   ++  +v  +  d++ +lae+++a +++++ +g + +  ++f+ 
  gi|313126449|ref|YP_004036719.1|  7 YNEAENIATAVENFLAQNTVDEVVVVDNNSSDNTAELAEEAGATVVSETRQGYGYACQRAFQE 69
                                      778889999*******************************************99999999986 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1     6e-05      0.18     145     186 ..       7      48 ..       2      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 145 leqleqirkdireFkkknkldkvivlwtanTEryievipgvn 186
                                       ++++e+i + +++F ++n +d+v+v+   + ++ +e  ++  
  gi|313126449|ref|YP_004036719.1|   7 YNEAENIATAVENFLAQNTVDEVVVVDNNSSDNTAELAEEAG 48 
                                       57899************************9999999888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 1292.62
//
Query:       gi|313126450|ref|YP_004036720.1|  [L=589]
Description: hypothetical protein Hbor_17070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   14.7   0.0      0.016   14.1   0.0    1.2  1  DUF4438   Domain of unknown function (DUF4438)
       0.12   11.5   0.1        1.7    7.7   0.1    2.2  2  DUF608    Glycosyl-hydrolase family 116, catalytic region
          3    6.0   5.2       0.97    7.6   0.1    2.3  3  YfhO      Bacterial membrane protein YfhO


Domain annotation for each model (and alignments):
>> DUF4438  Domain of unknown function (DUF4438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-06     0.016       5     127 ..     411     531 ..     407     536 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-06
                                       TTSBEEE---EESEESS--TTSBSSS-BSSS---EEEE..E-SSGGGHHHHHHH--BT-EEEE-SSTTTT.-EEEEE CS
                           DUF4438   5 kdGkarllpgvggitynvkvGdsavglagDhvepgvsitakkedekenkalqllsCvGneakvvsGeakg.akGvvt 80 
                                       ++G+  +l   gg ++ ++vG  +v    Dhve gv +   ++++ +  al +l    n   +++ +++g ++ + +
  gi|313126450|ref|YP_004036720.1| 411 NKGTMAVLLRAGGTVLAYSVGFASVYALFDHVETGVEL---NRSSIAAVALVVLLVGTNGGLILTQATAGySTHYDY 484
                                       579999********************************...567788888888877777777777666662456778 PP

                                       EEETTTTEEEEE--HHHHTT--TT-EEEEEE--TT-BBTT.-TTSEE- CS
                           DUF4438  81 GkhggiehvlvdfdeevleklaigdkilvkalGqGLklld.ypdvkvl 127
                                       G++ g ++vl +++e  ++  a +++ +v  +  GLkl + y d +++
  gi|313126450|ref|YP_004036720.1| 485 GQK-GNDEVLSYVKETYADLPADEQSEVVVPFDIGLKLREpYHDTELY 531
                                       888.78999999988776666666667788899999997646666555 PP

>> DUF608  Glycosyl-hydrolase family 116, catalytic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.029   1.8e+02     161     201 ..     284     324 ..     280     330 .. 0.89
   2 ?    7.7   0.1   0.00029       1.7      55     117 ..     497     556 ..     476     578 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.029
                            DUF608 161 vkGvsaycgglwlaaLeaaiemaellgdkkdaeeykellek 201
                                       ++G  +y + lwl+   +++++ +l++++++a+ + e+l++
  gi|313126450|ref|YP_004036720.1| 284 LSGWAGYASLLWLSPFLVLLAVGSLVSNQETARPTLEWLQN 324
                                       68999***********************9999988888875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00029
                            DUF608  55 kiladgkvlprkvknavpHdlgdpeeepweevnayllhdtseWkDlnlkfvLqvYRdyvited 117
                                       k ++    +  +++ +vp d+g    ep++ +  y + d     D ++ +v+  +R y++++ 
  gi|313126450|ref|YP_004036720.1| 497 KETYADLPADEQSEVVVPFDIGLKLREPYHDTELYSVSDL---EDSQPPLVIVKHRKYYAVNS 556
                                       5555555567788999*****************9887776...69*************99876 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.6     0.046   2.7e+02     366     434 ..      67     142 ..      46     156 .. 0.67
   2 ?   -2.8   0.0      0.23   1.4e+03     278     300 ..     324     347 ..     311     358 .. 0.84
   3 ?    7.6   0.1   0.00016      0.97     346     461 ..     363     487 ..     358     502 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.046
                              YfhO 366 klkllaailllvlllliilllknkksynfltssqlllgllllllalllllllll.........kkkkkklvllllll 433
                                       +++++   + + ++++ i+ +  +++  +++   ++++ll l l++ l+ +l+          ++++++++++l+l 
  gi|313126450|ref|YP_004036720.1|  67 QWGMWHPPTYVYSVAAAIVAFGTNTI--VIRGATFVATLLTLPLLVALVNTLVDrdavsvrksWRSPSWQLAALVLA 141
                                       66777777777777777777776666..7777777777777777777777655589999977655555544444443 PP

                              YfhO 434 v 434
                                       +
  gi|313126450|ref|YP_004036720.1| 142 L 142
                                       3 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.23
                              YfhO 278 s.lpniyvgllpllllilyFvlkk 300
                                       + +p+++vg++++l+ + y vl k
  gi|313126450|ref|YP_004036720.1| 324 NrAPVLFVGAVAVLTYVQYTVLAK 347
                                       3699**********9999998876 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00016
                              YfhO 346 lsflllllaaealkelkqlkklkllaailllvlllliilllknkksynfltssqlll..........gllllllall 412
                                       ++ l ++ +a +l+   +  ++ +  + +l+ +++++++l+ ++++ +f + + ++l          ++ +  +++ 
  gi|313126450|ref|YP_004036720.1| 363 FAVLAAVCVAHFLDAPLET-RRLWRFGAVLAGVVAAVTFLAPDPFYVSFNKGTMAVLlraggtvlaySVGFASVYA- 437
                                       5666666677777644444.44444455555555558888888888888877666666665544444444444444. PP

                              YfhO 413 lllllll.......kkkkkklvllllllvlvlelggnaylslnkisyssrseyaea 461
                                             l       ++ +++ ++++ l+vl++  +g ++l++ + +ys++++y+++
  gi|313126450|ref|YP_004036720.1| 438 ------LfdhvetgVELNRSSIAAVALVVLLVGTNGGLILTQATAGYSTHYDYGQK 487
                                       ......25566666777777777777777667777777777777789999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 3335.40
//
Query:       gi|313126451|ref|YP_004036721.1|  [L=455]
Description: arylsulfotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-11   44.8   0.3    9.4e-10   38.3   0.2    2.7  1  Arylsulfotran_2  Arylsulfotransferase (ASST)
    1.1e-09   37.7   2.4    2.7e-08   33.1   0.5    3.1  4  Arylsulfotrans   Arylsulfotransferase (ASST)
    7.2e-06   25.7   0.5       0.56   10.2   0.0    3.7  3  PQQ              PQQ enzyme repeat
    0.00023   20.9   5.8    0.00039   20.1   2.6    2.4  2  PQQ_2            PQQ-like domain
  ------ inclusion threshold ------
       0.06   13.4   4.0       0.31   11.2   0.1    3.3  3  NHL              NHL repeat


Domain annotation for each model (and alignments):
>> Arylsulfotran_2  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.2   2.6e-13   9.4e-10     137     297 ..     202     342 ..     169     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.6e-13
                   Arylsulfotran_2 137 eskpedyfHlNsvekfedgdyLiSlrelsslflirpkegkvlWqlqGpkggdfeldnstf.srQHdariveetedki 212
                                          p+d  H+N+ve  +dg  + Slr+++ +++++ +  +  W+l G+       d++++   QH++++ ++   + 
  gi|313126451|ref|YP_004036721.1| 202 GAYPYDWTHINDVELLDDGRIMASLRNQDQVVFLNRSGLEESWTLGGE-------DEFETiYEQHNPDYIPTKMGGP 271
                                       468*******************************9788899*******.......66655156******98887777 PP

                   Arylsulfotran_2 213 vislfnNentdtnerepttglildv.dlqnkevtllrklkdaedeissvsqGsyqllpnghvlveegsigrveeyda 288
                                        + + + en+   e ++++g+ ++   +q+++++                   ++ lpng+ lv++++ grv+  ++
  gi|313126451|ref|YP_004036721.1| 272 AVIVADSENNRIVEFQRSEGEWVESwTWQDRTMSW---------------PRDADRLPNGNTLVTDTAAGRVIDLNT 333
                                       77787776555555555555544430233444444...............44566********************** PP

                   Arylsulfotran_2 289 ngkivlear 297
                                       +g+iv++++
  gi|313126451|ref|YP_004036721.1| 334 DGEIVWSYE 342
                                       ******986 PP

>> Arylsulfotrans  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.5   7.7e-12   2.7e-08     121     222 ..     170     256 ..     156     260 .. 0.88
   2 ?    1.9   0.0     0.023        83     241     259 ..     249     267 ..     248     292 .. 0.81
   3 ?   -1.4   0.0      0.24   8.6e+02     121     142 ..     277     299 ..     266     309 .. 0.86
   4 ?    2.2   0.1     0.018        66      98     143 ..     313     344 ..     277     365 .. 0.66

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 7.7e-12
                    Arylsulfotrans 121 ktveDtiievd.ktGkvvkewdlakiLdpyrdallkaakapfgdiagvgagrdWlHiNsveydekddsiivSsRhqs 196
                                       +  +D +  ++ +tG +v++w++ + + p++               g +   dW+HiN ve    d+ i++S+R+q+
  gi|313126451|ref|YP_004036721.1| 170 DIARDNVHLLNiETGTIVWKWRAEQSF-PRNG--------------GGAYPYDWTHINDVELLD-DGRIMASLRNQD 230
                                       6789***********************.5544..............566789*********999.************ PP

                    Arylsulfotrans 197 avvkidyrtkkvkWilgdkegwekel 222
                                        vv ++++  + +W lg ++ +e  +
  gi|313126451|ref|YP_004036721.1| 231 QVVFLNRSGLEESWTLGGEDEFETIY 256
                                       ******999999*****999998765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.023
                    Arylsulfotrans 241 egdfdwtwgqHtavlipng 259
                                       e++f++ ++qH++ +ip +
  gi|313126451|ref|YP_004036721.1| 249 EDEFETIYEQHNPDYIPTK 267
                                       689**************98 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.24
                    Arylsulfotrans 121 ktveDtiievd.ktGkvvkewdl 142
                                       ++ +  i+e++ ++G+ v++w  
  gi|313126451|ref|YP_004036721.1| 277 DSENNRIVEFQrSEGEWVESWTW 299
                                       5667899****9********976 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.018
                    Arylsulfotrans  98 lpngnllvlvaeenykrkdgkkvktveDtiievdktGkvvkewdla 143
                                       lpngn+lv+ +                  +i ++++G++v++++++
  gi|313126451|ref|YP_004036721.1| 313 LPNGNTLVTDT--------------AAGRVIDLNTDGEIVWSYEIQ 344
                                       44444444444..............445566677777777766654 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.02        73       7      23 ..     116     132 ..     113     135 .. 0.83
   2 !    7.7   0.0     0.001       3.6      11      29 ..     175     193 ..     172     197 .. 0.82
   3 !   10.2   0.0   0.00016      0.56      14      29 ..     328     344 ..     317     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.02
                                       ETTSEEEEEETTTCCEE CS
                               PQQ   7 sadGylyAlDadTGkvl 23 
                                       ++ + ++ ++++TG+v+
  gi|313126451|ref|YP_004036721.1| 116 CRKNLIRTVNLTTGEVK 132
                                       66778999*******98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.001
                                       EEEEEETTTCCEEEEEESS CS
                               PQQ  11 ylyAlDadTGkvlWrfktg 29 
                                       ++  l+++TG+++W+ +++
  gi|313126451|ref|YP_004036721.1| 175 NVHLLNIETGTIVWKWRAE 193
                                       57779*********96665 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00016
                                       EEETTT.CCEEEEEESS CS
                               PQQ  14 AlDadT.GkvlWrfktg 29 
                                        +D++T G+++W+++++
  gi|313126451|ref|YP_004036721.1| 328 VIDLNTdGEIVWSYEIQ 344
                                       4566666*******986 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.3   4.8e+03     190     219 ..      39      70 ..      16      79 .. 0.47
   2 !   20.1   2.6   1.1e-07   0.00039       3     159 ..     174     352 ..     141     360 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                             PQQ_2 190 latgrrlwskeiss..inglpildgdllyvvs 219
                                       +at +++ s+e+++  +  +p++++++++v+ 
  gi|313126451|ref|YP_004036721.1|  39 TATYSPNVSQELTAitVADSPHATAKFVVVGA 70 
                                       33333333222222224444666666666655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.1e-07
                             PQQ_2   3 gvvsaldaatGaelWrvdlar......p......lgggvsravlsggtlfva.tgggrlvaldaatGkvlWettleg 66 
                                       + v+ l+ +tG+++W+ + ++      +      ++++ +  +l++g++ +     +++v l+++  ++ W+   e 
  gi|313126451|ref|YP_004036721.1| 174 DNVHLLNIETGTIVWKWRAEQsfprngGgaypydWTHINDVELLDDGRIMASlRNQDQVVFLNRSGLEESWTLGGED 250
                                       56788888999999999775545555404555558888888889999988887899999999999999999999999 PP

                             PQQ_2  67 pvvga.........plvaegrvvvva.sdg.qlialdaedGkr..lWstqqrseepaelrssaspavagdtvvvges 130
                                       ++ ++         p+  +g +v va s++ +++++    G+   +W+ q+r+   ++  ++a++   g+t+v  ++
  gi|313126451|ref|YP_004036721.1| 251 EFETIyeqhnpdyiPTKMGGPAVIVAdSENnRIVEFQRSEGEWveSWTWQDRT---MSWPRDADRLPNGNTLVTDTA 324
                                       99998999999999876666665555444459999999999855599977777...443355666666********* PP

                             PQQ_2 131 sgklvaldpkdGkvlWerelaaprgtsel 159
                                        g++  l+ +dG+ +W++e+ ++ ++ +l
  gi|313126451|ref|YP_004036721.1| 325 AGRVIDLN-TDGEIVWSYEIQMAYEAERL 352
                                       ********.99*********987755544 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       1.2   4.4e+03       6      22 ..     157     175 ..     156     178 .. 0.68
   2 ?   11.2   0.1   8.5e-05      0.31      15      28 .]     273     286 ..     272     286 .. 0.92
   3 ?    2.0   0.0     0.069   2.5e+02       3      25 ..     306     328 ..     304     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                                       EEEEETTTEEEEEE..CCC CS
                               NHL   6 GvavdsnGdiyVaD..sen 22 
                                       +v  ++  + +VaD  + n
  gi|313126451|ref|YP_004036721.1| 157 DVDRVNETHYLVADiaRDN 175
                                       55555666899**976655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.5e-05
                                       EEEEECCCTEEEEE CS
                               NHL  15 iyVaDsenhrvqvF 28 
                                       ++VaDsen+r++ F
  gi|313126451|ref|YP_004036721.1| 273 VIVADSENNRIVEF 286
                                       89*********977 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.069
                                       SEEEEEEETTTEEEEEECCCTEE CS
                               NHL   3 yPhGvavdsnGdiyVaDsenhrv 25 
                                       +P++   ++nG+ +V+D+   rv
  gi|313126451|ref|YP_004036721.1| 306 WPRDADRLPNGNTLVTDTAAGRV 328
                                       68899999*********988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2684.39
//
Query:       gi|313126452|ref|YP_004036722.1|  [L=241]
Description: methyltransferase, fkbm family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-17   62.0   0.0    8.7e-17   61.7   0.0    1.1  1  Methyltransf_21  Methyltransferase FkbM domain
    8.5e-05   22.4   0.0    0.00011   22.0   0.0    1.3  1  Met_10           Met-10+ like-protein
     0.0013   18.1   0.0     0.0025   17.2   0.0    1.3  1  V_cholerae_RfbT  Vibrio cholerae RfbT protein
     0.0016   18.0   0.0     0.0024   17.4   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0086   15.9   0.0      0.019   14.7   0.0    1.6  1  SAM_3            SAM domain (Sterile alpha motif)


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   2.4e-20   8.7e-17       1     172 [.      58     219 ..      58     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.4e-20
                   Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndv.....glyelivegksg..gky 70 
                                       d+Ganig ++ f+    +  +  + v+a+EP         +lr n   + +++ +     ++ +       +  g  
  gi|313126452|ref|YP_004036722.1|  58 DIGANIGLYACFVG---TASDDID-VVAFEPSHR---ASSELRKN---IELNRLDvqirsEALS-------DecG-T 116
                                       9******4444442...3344555.57****999...88999888...6666553222212222.......2222.3 PP

                   Methyltransf_21  71 fpfavgdtngfstssvlggedaryievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvE 147
                                       + f + + ++ + +s  +   a+ +evp vt ds+ +++  +++++ kiDvEGaE++vL+G +  l+r  ++ +++E
  gi|313126452|ref|YP_004036722.1| 117 ASFVDEGLTQNHLQSRAETGTADATEVPIVTGDSLVDDGETPHPTVAKIDVEGAEMQVLQGLDAELSRPEFRTVFCE 193
                                       5555666666666666667999**********************************************99999**** PP

                   Methyltransf_21 148 vhkfk.efetelfdeirqflrecgyr 172
                                       vh  k  +  ++++e+ qflre+g+ 
  gi|313126452|ref|YP_004036722.1| 194 VHPRKlPEYDSSPEEVEQFLRERGFS 219
                                       *****88888**************97 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.2e-08   0.00011      94     155 ..      46     107 ..      14     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.2e-08
                                       HHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEE CS
                            Met_10  94 laklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkp 155
                                       +   ve g+v  d+ A iG +a  ++  s++  v+a +   ++   l++ni+lN+++  +++
  gi|313126452|ref|YP_004036722.1|  46 VLDAVEGGDVFYDIGANIGLYACFVGTASDDIDVVAFEPSHRASSELRKNIELNRLDVQIRS 107
                                       4567999*************************************************998875 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     7e-07    0.0025      82     208 ..      55     176 ..      44     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7e-07
                   V_cholerae_RfbT  82 tyidiganvgtfcgiaarhitqgkiiaiepltemensirmnvqlnnplvefhhfgcaigenegenifevyefdnrvs 158
                                        + digan+g ++        +  ++a ep       +r n++ln   v+++    a+ ++ g   f    +    +
  gi|313126452|ref|YP_004036722.1|  55 VFYDIGANIGLYACFVGTASDDIDVVAFEPSHRASSELRKNIELNRLDVQIR--SEALSDECGTASFVDEGLT--QN 127
                                       688*******99888888888999*********************9888876..5688888898887443332..34 PP

                   V_cholerae_RfbT 159 slyfkkntdiadkvknsqvlvrklssldisptnsvvikidaegaeieiln 208
                                        l  + +t  ad  +   v    l     +p    v kid egae+++l+
  gi|313126452|ref|YP_004036722.1| 128 HLQSRAETGTADATEVPIVTGDSLVDDGETP-HPTVAKIDVEGAEMQVLQ 176
                                       5666788899998877666665555444444.56789*********9997 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.7e-07    0.0024      26      93 ..      46     114 ..      26     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.7e-07
                                       HCHCCTCSE.EEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTS CS
                               MTS  26 tlpkelsgk.vlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleev 93 
                                        l++ + g+   D+G+ +G+ ++ +  +s++++v++++ ++rA    ++n+e n+l+v+++ + + +e 
  gi|313126452|ref|YP_004036722.1|  46 VLDAVEGGDvFYDIGANIGLYACFVGTASDDIDVVAFEPSHRASSELRKNIELNRLDVQIRSEALSDEC 114
                                       555554555147***********************************************9988877766 PP

>> SAM_3  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   5.4e-06     0.019       9      29 ..     203     223 ..     201     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.4e-06
                             SAM_3   9 kStpeeVkaWLtakgFskktv 29 
                                        S+peeV+++L+++gFs +t+
  gi|313126452|ref|YP_004036722.1| 203 DSSPEEVEQFLRERGFSLETL 223
                                       79***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1597.69
//
Query:       gi|313126453|ref|YP_004036723.1|  [L=418]
Description: hypothetical protein Hbor_17100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-12   47.9  29.3    1.3e-12   47.9  29.3    1.9  2  GT87           Glycosyltransferase family 87
  ------ inclusion threshold ------
       0.77    9.7   6.1        0.3   11.0   2.2    2.3  2  Phage_holin_8  Putative phage holin


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.2       1.3   1.1e+04     135     148 ..      26      39 ..      21      52 .. 0.60
   2 !   47.9  29.3   1.5e-16   1.3e-12       1     239 []      84     324 ..      84     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 1.3
                              GT87 135 talvltalpllllp 148
                                       + ++++al+l ++p
  gi|313126453|ref|YP_004036723.1|  26 VPVLIVALSLFVVP 39 
                                       44444444444444 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 1.5e-16
                              GT87   1 FtYPPfaallfaplallpyglalalwallnlaalllalrlllrrlgralasavalalllaalalepvlstlgfGqin 77 
                                       ++YPP+++ll +p+ ++++ la+++w ++ l +l++++  ll   +++l + + + ll+a++ + p   +l  Gq++
  gi|313126453|ref|YP_004036723.1|  84 YIYPPLTLLLWLPFVVFDPLLAGVVWDIVVLGVLYASVLFLLSSRNVSLNARWRFGLLAALVGFYPTILWLKAGQVS 160
                                       89*****************************************999999**************************** PP

                              GT87  78 llllllvlldllllrrrrpl.....laGlliGlaaaiKltPalfllylllrrrwralaaaaatalvltalpllllp. 148
                                       +ll++l+ ++  l   +++      l G+++++  + K  P   +++  + r+  +l+ ++++++v+++++l++++ 
  gi|313126453|ref|YP_004036723.1| 161 GLLAALLCVAAGLSG-GDEGprhgiLTGAILAVVSLFK--PFYAVAATPVPRKNARLVGGFLGVAVVILAGLIIFGi 234
                                       *****9999955544.4333223346777777777777..77777777889999999999****************9 PP

                              GT87 149 ...pssleyfletlfdtseriaedvgnqsllslagllaralalglsavtllwlvlvllvvalaavaawrlrrrerll 222
                                           ++++y l+ l    e  ++  g +s   +  ++ r++ + +    +l++ ++ +++++++ +a r+ +  +l 
  gi|313126453|ref|YP_004036723.1| 235 dmqLAQFDYLLTGLGWG-ETAEAGGGGSSPTNWGPYYFRPFIVFG--GFALYVKFAFVALLAVVSIASRWMDSTELD 308
                                       99999999999955444.333566688999999999999886666..678888889999999999999*99665555 PP

                              GT87 223 alaaallvall.alLvsP 239
                                       ++   ++ +++ + L+sP
  gi|313126453|ref|YP_004036723.1| 309 ERL--FVLGFTaVPLLSP 324
                                       555..2555554688887 PP

>> Phage_holin_8  Putative phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.2   3.4e-05       0.3      23      73 ..     103     154 ..      97     174 .. 0.83
   2 ?   -1.9   0.1      0.34     3e+03      21      45 ..     170     194 ..     156     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                     Phage_holin_8  23 llpgidad.vvlGAfaGavlfVvsakdltlltrlayflvSfiaGvlaaglaa 73 
                                       ll+g+  d vvlG +  +vlf +s++++ l +r  + l++ ++G++   l +
  gi|313126453|ref|YP_004036723.1| 103 LLAGVVWDiVVLGVLYASVLFLLSSRNVSLNARWRFGLLAALVGFYPTILWL 154
                                       67777755389*********************************99777655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.34
                     Phage_holin_8  21 agllpgidadvvlGAfaGavlfVvs 45 
                                       a  l+g d +   G + Ga+l Vvs
  gi|313126453|ref|YP_004036723.1| 170 AAGLSGGDEGPRHGILTGAILAVVS 194
                                       4446666666666778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2455.46
//
Query:       gi|313126454|ref|YP_004036724.1|  [L=414]
Description: hypothetical protein Hbor_17110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-18   64.9  22.9    8.5e-18   64.9  22.9    2.7  3  GT87      Glycosyltransferase family 87


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.6     0.039     7e+02     212     239 .]       7      32 ..       3      45 .. 0.60
   2 !   64.9  22.9   4.8e-22   8.5e-18       1     239 []      77     320 ..      77     320 .. 0.76
   3 ?   -3.0   3.4      0.27   4.8e+03      68     132 ..     341     400 ..     323     406 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.039
                              GT87 212 awrlrrrerllalaaallvallalLvsP 239
                                       ++r rr ++ l++   ++v l +lLv+P
  gi|313126454|ref|YP_004036724.1|   7 FRRTRRSRPRLFWL--SAVTLASLLVFP 32 
                                       33344444444444..333334777776 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 4.8e-22
                              GT87   1 FtYPPfaallfaplallpyglalalwallnlaalllalrlllrrlgralasavalalllaalalepvlstlgfGqin 77 
                                       ++YPP  +llfap++++++++a++lw +++la+l + l  l+r +g++l+   +  ll+a++ + p   +l  Gq++
  gi|313126454|ref|YP_004036724.1|  77 YVYPPVVVLLFAPFTVVSPWMAGLLWNVFSLAVLGAGLFALVRSFGVRLSIPSKAVLLWALVGFFPTILWLKAGQVS 153
                                       89***********************************************656666666679**************** PP

                              GT87  78 llllllvlldllllrrrrpl..........laGlliGlaaaiKltPalfllylllrrrwralaaaaatalvltalpl 144
                                       ++l+ l+ +++++ r  r +          ++G+l+ +    K + a  ++ ll  r+ ++++ a+a ++++++l+ 
  gi|313126454|ref|YP_004036724.1| 154 GFLTGLFCFAVAAHR--RSWqdddsttlalASGALTTISSSFKPFYAPSGAHLL--RDKKRFVGAVAAVVGIVGLS- 225
                                       **********99988..557777888888779***********66666666555..99999999999999999996. PP

                              GT87 145 lllppssleyfletlfdtseri..aedvgnqsllslagllaralalgl...sa....vtllwlvlvllvvalaavaa 212
                                       l+++ ++++++l++l+   +    a     +   ++++ ++    +g    ++     +++  + ++l++++a++++
  gi|313126454|ref|YP_004036724.1| 226 LFFGVETFTDYLGVLTHGKG-WgqA-----TEPGGISTDITN---WGPfffRPlyffGSAALYIRLALTFGVAGLVL 293
                                       56788********9999955.2242.....232344444444...33322111222222333333555566666677 PP

                              GT87 213 wrlr...rrerllalaaallvallalLvsP 239
                                       +  r   +r++++ala   l+ ++  L+sP
  gi|313126454|ref|YP_004036724.1| 294 YSRRddsARSEYAALA---LGLTTIPLASP 320
                                       7776566667777777...88888899998 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.27
                              GT87  68 lstlgfGqinllllllvlldllllrrrrpllaGlliGlaaa.iKltPalfllylllrrrwralaaa 132
                                          l+ G   + +l ++l+ ++++        G++ G++a+ i+ + al +l+++l+   +ala +
  gi|313126454|ref|YP_004036724.1| 341 ELQLDDGLPEIPVLSVLLFHVHAYT------LGFFAGFGATiIPAVSALEPLLPFLQAGMWALALM 400
                                       5555555555555555555555555......66666665541344444444455555444555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2337.51
//
Query:       gi|313126455|ref|YP_004036725.1|  [L=242]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-06   26.5   0.1    1.2e-05   25.2   0.1    1.6  1  Glycos_transf_2  Glycosyl transferase family 2
    7.7e-06   26.0   1.1      0.077   12.9   0.2    2.5  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00021   20.8   0.0       0.21   11.0   0.0    2.1  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00028   20.9   1.0    0.00071   19.5   0.7    1.7  2  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0032   17.0   0.0       0.99    8.9   0.0    2.2  2  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.033   13.8   0.0      0.053   13.2   0.0    1.3  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1     4e-09   1.2e-05      58     104 ..      62     107 ..      40     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4e-09
                                       EEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHH CS
                   Glycos_transf_2  58 virreenvGkagalnaglraatgdyilflDaDdepdpdwleklveal 104
                                       v+ r+   G + a+n+g+++atg++i++ D+D +++      lv+ +
  gi|313126455|ref|YP_004036725.1|  62 VVVRTD-DGRSVARNRGVEEATGEWIVLADDDITFPTTLTAMLVDSM 107
                                       455553.499************************9998888888776 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   2.6e-05     0.077      57     100 ..      57      95 ..      32     119 .. 0.81
   2 !   11.7   0.1   5.7e-05      0.17     159     219 ..     123     184 ..      97     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                   Glyco_tranf_2_3  57 pdvrvrvvvnarnlgstgksralnealravksdlvllvDdDtvv 100
                                       pd  + vvv++++    g+s a n++++ +++++++l DdD   
  gi|313126455|ref|YP_004036725.1|  57 PD-WLEVVVRTDD----GRSVARNRGVEEATGEWIVLADDDITF 95 
                                       56.3789999885....5667779****************9754 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.7e-05
                   Glyco_tranf_2_3 159 tlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfp.sslka 219
                                       tl ++ +++ r+++++ +g+d++   ++D +  +r+  ag ++  +p+ +v + +  ++++a
  gi|313126455|ref|YP_004036725.1| 123 TLLTRYMVFHRSLWDAVGGFDESREHGEDSDFVYRCADAGAKIRPLPRNIVPHHDAdTEFSA 184
                                       566799*************************************9999999888765233544 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00066         2      68      92 ..      69      93 ..      59     112 .. 0.81
   2 !   11.0   0.0   7.1e-05      0.21     168     214 ..     129     173 ..     116     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00066
                   Glyco_tranf_2_2 68 slaaarNrGaskaesdlvlFlDaDc 92
                                      + + arNrG+++a ++ ++  D D 
  gi|313126455|ref|YP_004036725.1| 69 GRSVARNRGVEEATGEWIVLADDDI 93
                                      56789***************99764 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.1e-05
                   Glyco_tranf_2_2 168 ilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvell 214
                                       ++ +r     vGG+DE+   hg ED d++ R a a  ++ + p ++ 
  gi|313126455|ref|YP_004036725.1| 129 MVFHRSLWDAVGGFDESR-EHG-EDSDFVYRCADAGAKIRPLPRNIV 173
                                       5667788889*******8.555.9*******************9997 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.7   2.4e-07   0.00071      71     119 ..     123     170 ..      82     185 .. 0.78
   2 ?   -0.9   0.0      0.45   1.3e+03       2      15 ..     173     186 ..     172     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.4e-07
                   Glyco_trans_2_3  71 psvGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpe 119
                                       ++ +++++++rs++++vgg+d  ++  +ED d+  r++ +G ++r  p 
  gi|313126455|ref|YP_004036725.1| 123 TLLTRYMVFHRSLWDAVGGFD-ESREHGEDSDFVYRCADAGAKIRPLPR 170
                                       47799****************.7799***************99987765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.45
                   Glyco_trans_2_3   2 illlDaDtvlppdc 15 
                                       + ++DaDt  ++ +
  gi|313126455|ref|YP_004036725.1| 173 VPHHDADTEFSALE 186
                                       56999999887755 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00033      0.99      23      53 ..      75     104 ..      70     115 .. 0.78
   2 !    6.0   0.0    0.0025       7.5     105     153 ..     128     175 ..     118     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00033
                   Glyco_transf_21  23 lqaleaakydllvisDsdvrvkpdyLeella 53 
                                       ++++e+a  +++v++D+d++++++ L+ +l 
  gi|313126455|ref|YP_004036725.1|  75 NRGVEEATGEWIVLADDDITFPTT-LTAMLV 104
                                       57899***************9765.555544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0025
                   Glyco_transf_21 105 smalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqt 153
                                        m+++r+  +a+GGf + ++e  eD  +  + ++aG k++  p+ i+ +
  gi|313126455|ref|YP_004036725.1| 128 YMVFHRSLWDAVGGFDE-SREHGEDSDFVYRCADAGAKIRPLPRNIVPH 175
                                       599**************.9999****************99988887733 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.053      11      67 ..     116     170 ..     107     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                   Glyco_transf_7C  11 gyklpyekyfgGvlalrkedfekiNGfsntfwgWGgEDdelyaRlakkgleierpek 67 
                                       +   p +++ +  +++ ++ + +++Gf++      gED++++ R a++g +i  ++ 
  gi|313126455|ref|YP_004036725.1| 116 EDFWPMDTLLTRYMVFHRSLWDAVGGFDESREH--GEDSDFVYRCADAGAKIRPLPR 170
                                       555666777777899***************998..9*************99876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1480.89
//
Query:       gi|313126456|ref|YP_004036726.1|  [L=396]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-38  131.2   0.0      4e-38  130.6   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    2.1e-31  109.1   0.2    6.3e-31  107.6   0.2    1.8  1  Glyco_trans_1_4  Glycosyl transferases group 1
    4.5e-30  104.9   4.6    8.7e-30  103.9   1.9    2.5  3  Glyco_transf_4   Glycosyltransferase Family 4
    1.5e-27   97.0  11.0    9.5e-27   94.4   8.3    2.7  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      1e-05   25.6   0.0      2e-05   24.6   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    0.00045   20.0   0.4      0.005   16.6   0.4    2.2  1  Glyco_transf_5   Starch synthase catalytic domain
     0.0011   19.3   0.1      0.004   17.5   0.0    1.9  2  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.046   14.3   5.0         17    6.1   0.0    3.3  3  DUF4398          Domain of unknown function (DUF4398)
       0.14   11.8   0.1       0.31   10.7   0.0    1.5  2  DUF3492          Domain of unknown function (DUF3492)


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.0     2e-41     4e-38      13     159 ..     207     362 ..     197     378 .. 0.94

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 2e-41
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...........STTHHHHHHHHHHHCTTCGGGEEE CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..........ngeeekelkklaeelelsdnviflg 79 
                                       +++k++l+vgrl + Kgvd+l+ka++++ + +n++v++v++G           +++  e+++l +el+++d+  f g
  gi|313126456|ref|YP_004036726.1| 207 DGRKTVLFVGRLARAKGVDVLVKAARDVLDSSNDPVRFVLVGpdkhmfggsaAESYPTEIRRLLDELGVRDDFVFAG 283
                                       789************************************************************************** PP

                                       CCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  80 evsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                       +vs+e+l +l+++ad+fvlps++E+ G+vllEA+a+g+pv+ +++gg++evv++ + G +v+p+ + +laea+  +l
  gi|313126456|ref|YP_004036726.1| 284 QVSDEELVSLYTAADAFVLPSRYEAQGMVLLEALASGTPVVGTDVGGISEVVTSDV-GRVVPPEAPVQLAEALLAVL 359
                                       ********************************************************.****************9999 PP

                                       HSH CS
                   Glycos_transf_1 157 ede 159
                                       + +
  gi|313126456|ref|YP_004036726.1| 360 DAD 362
                                       865 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   0.2   3.2e-34   6.3e-31       1     133 [.     209     360 ..     209     361 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 3.2e-34
                                       SEEEEEES---GG.GTHHHHHHHHHHHH.H.H..EEEEEES---.............HHHHHHHT..T-T.TEEEE- CS
                   Glyco_trans_1_4   1 rpvilfvGrleenvkgvdllleavpllrkk.d..vrlvivGdgprp...........eeleelaa..gleerveftG 61 
                                       r+++lfvGrl ++ kgvd+l++a+  ++++ +  vr+v+vG + ++            e+++l++  g++++++f+G
  gi|313126456|ref|YP_004036726.1| 209 RKTVLFVGRL-ARAKGVDVLVKAARDVLDSsNdpVRFVLVGPD-KHmfggsaaesypTEIRRLLDelGVRDDFVFAG 283
                                       589*******.677**********8888665358*******43.12233334445558888877669999******* PP

                                       --..THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  62 fv..edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrLle 133
                                       +v  e+l +l+ aad fv+Ps  e  g++llEa+a+g+pvV tdvggi+evv  + g +vpp+ p +laea+l++l+
  gi|313126456|ref|YP_004036726.1| 284 QVsdEELVSLYTAADAFVLPSryEAQGMVLLEALASGTPVVGTDVGGISEVVtSDVGRVVPPEAPVQLAEALLAVLD 360
                                       **8777***************999****************************9999****************99986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   1.9   4.4e-33   8.7e-30       2     169 ..      19     189 ..      18     190 .. 0.78
   2 ?   -0.5   0.0      0.53   1.1e+03     130     146 ..     293     309 ..     287     314 .. 0.86
   3 ?   -0.8   0.0      0.67   1.3e+03     130     166 ..     357     395 ..     301     396 .] 0.55

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 4.4e-33
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev........elvvrvprvplpllkrllrslaflrrlrrllkr 70 
                                       GGverh++ ++ +La+r h+Vtvv +++d + +              +  ++    +l   l+   ++  lrr+ +r
  gi|313126456|ref|YP_004036726.1|  19 GGVERHIRAVTTGLAARDHNVTVVDRRHDVDDPLSIdgvdvlrlAAPRVQTGLLDGWLDHVLNECLYSAGLRRAQER 95 
                                       9***********************77777777666545443332111111111122333444556667788888888 PP

                    Glyco_transf_4  71 e.kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatad 146
                                         + DvvHah+ +a++aa + +r + ++p+V+t+H+ +  +     +  +++++r++e  l+r ad+ iavSea+ad
  gi|313126456|ref|YP_004036726.1|  96 IaEADVVHAHNMYAGLAARRLAR-KARVPFVYTCHNGM--WCTDDVNTYEQQVVRRFEGSLMRDADASIAVSEAVAD 169
                                       89*********999866655555.6*************..788889999999************************* PP

                    Glyco_transf_4 147 elrerygvppekitVipnGvDle 169
                                         r+ yg + ++ tVipnGvD+e
  gi|313126456|ref|YP_004036726.1| 170 GART-YG-D-ADPTVIPNGVDTE 189
                                       ****.*9.5.688********98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.53
                    Glyco_transf_4 130 llrradrviavSeatad 146
                                       l+ +ad+++ +S+++a+
  gi|313126456|ref|YP_004036726.1| 293 LYTAADAFVLPSRYEAQ 309
                                       6899**********997 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.67
                    Glyco_transf_4 130 llrradrviavSeatadelrerygvpp..ekitVipnGv 166
                                       ++  adr  a S +++d+ ++ y  p+  ++i+ ++ Gv
  gi|313126456|ref|YP_004036726.1| 357 AVLDADRNGAMSVTARDYAERTYAWPRivSRIESVYEGV 395
                                       244677777777777777777777666666777777666 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   8.3   4.8e-30   9.5e-27       1     160 []      19     185 ..      19     185 .. 0.85
   2 ?    2.4   0.0     0.097   1.9e+02     125     144 ..     292     311 ..     208     326 .. 0.56

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 4.8e-30
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpsplad.........laalralrrllr 68 
                                       gG++r+++++  +Laar h Vtv+ ++ + ++p l  dgv v rl +pr + +l d           ++++lrr+  
  gi|313126456|ref|YP_004036726.1|  19 GGVERHIRAVTTGLAARDHNVTVVDRRHDVDDP-LSIDGVDVLRLAAPRVQTGLLDgwldhvlneCLYSAGLRRAQ- 93 
                                       8**********************9887777777.****************96565544333333344669999994. PP

                   Glyco_trans_4_4  69 qrrerpdvvhahsptaglaarlarrrrgiplvvtlhg.lllrrg.sgavrrlyralerrllrradavlvvseaeaee 143
                                        r    dvvhah+ +aglaar+++r++++p+v+t+h+  ++++  ++ +++++r++e  l+r ada ++vsea+a+ 
  gi|313126456|ref|YP_004036726.1|  94 ERIAEADVVHAHNMYAGLAARRLARKARVPFVYTCHNgMWCTDDvNTYEQQVVRRFEGSLMRDADASIAVSEAVADG 170
                                       7999**************99888879**********745555446999***************************** PP

                   Glyco_trans_4_4 144 lralgvpadrvvvvpng 160
                                       +r +g ++   +v+png
  gi|313126456|ref|YP_004036726.1| 171 ARTYGDADP--TVIPNG 185
                                       ****96633..69**98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.097
                   Glyco_trans_4_4 125 rllrradavlvvseaeaeel 144
                                        l++ ada++ +s++ea+ +
  gi|313126456|ref|YP_004036726.1| 292 SLYTAADAFVLPSRYEAQGM 311
                                       67788888888888888766 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     1e-08     2e-05      12     107 ..      24     129 ..      17     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1e-08
                   Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd...........rkgpleylkafklkklikki.kPD 76 
                                       h + +  +La+r+++V+v+ ++ + +d l  +g+ v rl  +            ++  e l  + l++  ++i + D
  gi|313126456|ref|YP_004036726.1|  24 HIRAVTTGLAARDHNVTVVDRRHDVDDPLSIDGVDVLRLAAPrvqtglldgwlDHVLNECLYSAGLRRAQERIaEAD 100
                                       77778899*************9999999***********6666667787765444477777789999999998468* PP

                   Glyco_trans_4_2  77 vvhahyakpygllgslaarlsgvipvvlsvw 107
                                       vvhah++   gl+++ +ar+++ +p+v++ +
  gi|313126456|ref|YP_004036726.1| 101 VVHAHNMYA-GLAARRLARKAR-VPFVYTCH 129
                                       ******986.99*********9.******99 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4   2.5e-06     0.005       2     171 ..       3     130 ..       2     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.5e-06
                    Glyco_transf_5   2 ilfvasEvapl..aktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkv 76 
                                       i+++++   p+     GG+ ++++a    La++ h+v+v+  r++  +                             
  gi|313126456|ref|YP_004036726.1|   3 IVHITAGLVPIhgEFGGGVERHIRAVTTGLAARDHNVTVVDRRHDVDDP---------------------------- 51 
                                       6666666666644445777777888888888888888888777722222............................ PP

                    Glyco_transf_5  77 aklkkdgvdvyfldnpeffdreglYgdkgedyednaerfalfsraalelleklgwkpdvihahDWhtalvpallkel 153
                                         l+ dgvdv+ l +p+++  +gl      ++ d+  +  l+s++  ++ e++  + dv+hah  +++l++  l+  
  gi|313126456|ref|YP_004036726.1|  52 --LSIDGVDVLRLAAPRVQ--TGLL----DGWLDHVLNECLYSAGLRRAQERI-AEADVVHAHNMYAGLAARRLARK 119
                                       ..23369999999999965..4566....589999999999999988888884.579*************7777776 PP

                    Glyco_transf_5 154 ykerglfkkiktvftiHN 171
                                               ++++v+t HN
  gi|313126456|ref|YP_004036726.1| 120 A-------RVPFVYTCHN 130
                                       4.......4********9 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.8   5.5e+03      56      82 ..      80     106 ..      76     113 .. 0.71
   2 !   17.5   0.0     2e-06     0.004       3      61 ..     301     360 ..     299     390 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                   Glyco_trans_1_2  56 iryllanpeerraiaeaarervlaeht 82 
                                       ++++l + ++rra  + a ++v   h+
  gi|313126456|ref|YP_004036726.1|  80 LNECLYSAGLRRAQERIAEADVVHAHN 106
                                       667777778888877777777766665 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2e-06
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekirylla 61 
                                       + psr+e   ++l+Ea+a+G++++ +d  g+ e +t +   ++    + +lae++ ++l+
  gi|313126456|ref|YP_004036726.1| 301 VLPSRYEAQGMVLLEALASGTPVVGTDVGGISEVVTSDVGRVVPPeAPVQLAEALLAVLD 360
                                       5799*****************************999885433333577777777777765 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0087        17      26      56 ..      89     121 ..      84     137 .. 0.83
   2 ?    2.5   0.5      0.11   2.3e+02       4      22 ..     157     175 ..     156     179 .. 0.88
   3 ?    5.8   0.0     0.011        22      21      56 ..     346     379 ..     343     388 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0087
                           DUF4398  26 leeAreaLaqAeaamaekdyee..AdhlaylAe 56 
                                       l++A+e +a+A+   a + y    A++la+ A+
  gi|313126456|ref|YP_004036726.1|  89 LRRAQERIAEADVVHAHNMYAGlaARRLARKAR 121
                                       999**********55555565566999999997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                           DUF4398   4 adAraaleaAraagaeeyA 22 
                                       adA+ a+++A a+ga+ y 
  gi|313126456|ref|YP_004036726.1| 157 ADASIAVSEAVADGARTYG 175
                                       699************9986 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.011
                           DUF4398  21 yApaeleeAreaLaqAeaamaekdyeeAdhlaylAe 56 
                                       +Ap++l+eA  a+  A++   + +   A+++a+++ 
  gi|313126456|ref|YP_004036726.1| 346 EAPVQLAEALLAVLDADRNG-AMSVT-ARDYAERTY 379
                                       6999*************966.55665.999999876 PP

>> DUF3492  Domain of unknown function (DUF3492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.31     166     205 ..      92     130 ..      78     151 .. 0.87
   2 ?   -3.0   0.0       2.3   4.6e+03      42      64 ..     370     392 ..     366     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                           DUF3492 166 laeelpkadvyHavstGyAgllgallkerkgtpllltEHG 205
                                        +e++ +adv+Ha++  yAgl +  l+++ ++p++ t H+
  gi|313126456|ref|YP_004036726.1|  92 AQERIAEADVVHAHNM-YAGLAARRLARKARVPFVYTCHN 130
                                       688999********98.********************994 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                           DUF3492  42 deeeygelkyelPenVveveevy 64 
                                       + ++y+e +y+ P  V+++e+vy
  gi|313126456|ref|YP_004036726.1| 370 TARDYAERTYAWPRIVSRIESVY 392
                                       56788999********9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2377.58
//
Query:       gi|313126457|ref|YP_004036727.1|  [L=410]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-37  126.5   0.0    1.1e-36  126.0   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    7.6e-26   91.1   0.0    1.9e-25   89.8   0.0    1.7  1  Glyco_trans_1_4  Glycosyl transferases group 1
    5.3e-14   52.6   3.3    8.3e-14   51.9   3.3    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    3.5e-12   46.6   0.0    8.5e-12   45.3   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
    1.1e-10   42.2   5.2    2.1e-10   41.3   5.2    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0034   17.4   0.0     0.0056   16.7   0.0    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.0   3.5e-40   1.1e-36      13     172 .]     212     386 ..     202     386 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 3.5e-40
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....................STTHHHHHHHHHHHC CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...................ngeeekelkklaeele 70 
                                        + k++l+ gr +++Kg+++++ a+ +     + ++ lv+ G                    ++++ ++ + a++ +
  gi|313126457|ref|YP_004036727.1| 212 PDGKTVLYAGRKVPHKGLHRAVSAISKM----ETDATLVVLGplgsgfsdvdsldgvnpddLEPYLGSVIEDAQNSG 284
                                       46789*********************75....79**************************999************** PP

                                       TTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHH CS
                   Glycos_transf_1  71 lsdnviflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaea 147
                                       + d++ f g+v + dl++++ +ad++ +ps  E+fG+v++E+ma+g+pv+a++++++ e+v dgetG+l  +++a a
  gi|313126457|ref|YP_004036727.1| 285 VTDQISFPGYVADADLPAYYAAADVTTFPSVLESFGMVPVESMACGTPVVAHDVPPIDETVLDGETGFLTNEVSASA 361
                                       ***************************************************************************** PP

                                       HHHHHHHHHHSHHHHHHHHHHHHHH CS
                   Glycos_transf_1 148 laeairklledeelrerlgenarkr 172
                                       la+a+++ll+d+ lr ++ e++r+r
  gi|313126457|ref|YP_004036727.1| 362 LAAALDRLLTDDSLRSQFAERGRNR 386
                                       **********************986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0   6.4e-29   1.9e-25       2     134 .]     215     372 ..     214     372 .. 0.82

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 6.4e-29
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES...--...........-.........HHHHHHHT.T-T.T CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivG...dg...........prp.......eeleelaa.gleer 56 
                                       +++l+ Gr +++ kg++  + a+ ++   d++lv+ G   +g           p +       + +e+  + g++++
  gi|313126457|ref|YP_004036727.1| 215 KTVLYAGRKVPH-KGLHRAVSAISKME-TDATLVVLGplgSGfsdvdsldgvnP-DdlepylgSVIEDAQNsGVTDQ 288
                                       689*****9655.*************9.669******55511333333333331.13333443444433337999** PP

                                       EEEE---..THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHH CS
                   Glyco_trans_1_4  57 veftGfv..edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaea 127
                                       ++f G+v  +dl++++aaadv+ +Ps  e+fg++ +E+ma+g+pvVa dv+ i e+v  ge+g+l ++ +++ala+a
  gi|313126457|ref|YP_004036727.1| 289 ISFPGYVadADLPAYYAAADVTTFPSvlESFGMVPVESMACGTPVVAHDVPPIDETVldGETGFLTNEVSASALAAA 365
                                       *******8778****************************************99**999********9999******* PP

                                       HHHHHH- CS
                   Glyco_trans_1_4 128 ilrLled 134
                                       + rLl+d
  gi|313126457|ref|YP_004036727.1| 366 LDRLLTD 372
                                       *****97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   3.3   2.8e-17   8.3e-14       4     169 ..      20     197 ..      17     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 2.8e-17
                    Glyco_transf_4   4 verhvleLaraLarrGheVtvvtpgddgpleeev....elvvrvprvplpllkrllrslaflrrlrrllkre.kpDv 75 
                                       +e  +++La  La  Gh+ tv+t g +g+ + ++    + +++++ +p+ +  +     + +rr++ +++re  +Dv
  gi|313126457|ref|YP_004036727.1|  20 IEKLTFDLASTLASEGHDATVLTVGESGRRYTAEgvqlVEITEPITRPPSHVTPVVEFGRKARRVADRIHREnPVDV 96 
                                       68889************************999999666666666666655555555555566666666666689*** PP

                    Glyco_transf_4  76 vHahspaalgaallalrrrlgiplVltvHglye..........krllkarlkplsrllralerrl.lrradrviavS 141
                                       vHa +++ l ++    r   ++plV+  H+  +           ++ ++ ++ ++ ++r  e+++ +  a rv+ vS
  gi|313126457|ref|YP_004036727.1|  97 VHAVYYPNL-LG---FRPPGDAPLVVAEHNAHPwrkehrfieeLTITHRLRWEADTYIRLAEAHAaFFGAERVLSVS 169
                                       ****96665.33...34458*********************998888999999999999999999999********* PP

                    Glyco_transf_4 142 eatadelrerygvppekitVipnGvDle 169
                                       +a  +++ +  + +++k ++ +n vD++
  gi|313126457|ref|YP_004036727.1| 170 DAHGEWIDRAIPEARSKRETMYNFVDTD 197
                                       *********999999************8 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   2.8e-15   8.5e-12       3      88 ..     311     398 ..     309     401 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.8e-15
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarerv 77 
                                        +ps  es+ ++ +E +acG+++++ d + ++e + +g++++l    +   la+++++ll+++ +r++ ae++r+r+
  gi|313126457|ref|YP_004036727.1| 311 TFPSVLESFGMVPVESMACGTPVVAHDVPPIDETVLDGETGFLTNevSASALAAALDRLLTDDSLRSQFAERGRNRA 387
                                       5789999********************************9999999******************************* PP

                   Glyco_trans_1_2  78 laehtydhrae 88 
                                        ++++ + +++
  gi|313126457|ref|YP_004036727.1| 388 VERFDIETAVQ 398
                                       ***99888776 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   5.2     7e-14   2.1e-10       3     144 ..      20     176 ..      18     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 7e-14
                   Glyco_trans_4_4   3 igryvaelaraLaarGheVtvltpapapgapeleedgvrvhrl..pvprrps.pladlaalralrrll..rqrrerp 74 
                                       i++ + +la+ La +Gh+ tvlt ++ ++++  +++gv+++ +  p+ r ps  ++ +++ r +rr+    +r+ ++
  gi|313126457|ref|YP_004036727.1|  20 IEKLTFDLASTLASEGHDATVLTVGESGRRY--TAEGVQLVEItePITRPPShVTPVVEFGRKARRVAdrIHRENPV 94 
                                       6667789****************97777766..77788888774455555551445577888888888755699999 PP

                   Glyco_trans_4_4  75 dvvhahsptaglaarlarrrrgiplvvtlh.............glllrrgsgavrrly.ral.errllrradavlvv 136
                                       dvvha +++  l  r    + ++plvv  h             +l+ +++ ++++  y r +  ++++ +a +vl+v
  gi|313126457|ref|YP_004036727.1|  95 DVVHAVYYPNLLGFR-P--PGDAPLVVAEHnahpwrkehrfieELTITHRLRWEADTYiRLAeAHAAFFGAERVLSV 168
                                       *******96555332.2..349********7666666555554344556678888888444455699999******* PP

                   Glyco_trans_4_4 137 seaeaeel 144
                                       s+a+ e +
  gi|313126457|ref|YP_004036727.1| 169 SDAHGEWI 176
                                       **998876 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.9e-06    0.0056      12      90 ..      23     107 ..      17     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-06
                   Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd.....rkg.pleyl..kafkl.kklikkikPDvvh 79 
                                        t  la+ La++g++ +v+t +++  +++ aeg+++ +++ +     +++ p+ ++  ka+++  ++ +++  Dvvh
  gi|313126457|ref|YP_004036727.1|  23 LTFDLASTLASEGHDATVLTVGESGRRYT-AEGVQLVEITEPitrppSHVtPVVEFgrKARRVaDRIHRENPVDVVH 98 
                                       5778999**************99967777.99*******7666666677787777765599994556666666**** PP

                   Glyco_trans_4_2  80 ahyakpygllg 90 
                                       a+y +  +llg
  gi|313126457|ref|YP_004036727.1|  99 AVYYP--NLLG 107
                                       ***65..4555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2633.20
//
Query:       gi|313126458|ref|YP_004036728.1|  [L=465]
Description: arylsulfatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-42  145.8   0.1    2.4e-42  145.4   0.1    1.2  1  Sulfatase     Sulfatase
    1.2e-08   34.9   0.0    8.8e-07   28.8   0.0    2.6  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
    2.7e-05   24.0   0.6      0.023   14.6   0.0    2.9  3  DUF4994       Domain of unknown function
    0.00011   22.3   0.0    0.00031   21.0   0.0    1.8  1  DUF4976       Domain of unknown function (DUF4976)
     0.0018   17.0   0.0      0.003   16.2   0.0    1.4  1  DUF229        Protein of unknown function (DUF229)
     0.0035   16.5   0.0     0.0053   15.9   0.0    1.2  1  DUF1501       Protein of unknown function (DUF1501)
     0.0046   17.7   0.3      0.029   15.1   0.1    2.3  2  Sulfatase_C   C-terminal region of aryl-sulfatase


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.1   9.5e-46   2.4e-42       1     309 []       8     348 ..       8     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 9.5e-46
                                       EEEEEEEESSE-TTGSGGGTTTSCS...SHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTT CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktat...tpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevg 74 
                                       p+vv++++d+l+++d+g+yg    +   tp++d la+eg rf  ++s +p++  s  a  t+ yp ++         
  gi|313126458|ref|YP_004036728.1|   8 PHVVFLTVDSLRRDDVGCYGQLDIEydlTPQIDTLADEGARFDAAISNGPSTLYSFLASQTSTYPLEDE-------- 76 
                                       89******************98866688**************************************965........ PP

                                       THHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC.CTTTSEEEETSSSCHHTCCCC.CCCCCECTCCC... CS
                         Sulfatase  75 ggglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk.nrgfdrflgfptgsaalkdpe.kseyngevlrv... 146
                                         +  ++ ++L+e l + GY+taa+       +         rgfd+f +f + +a++++      ++++   +   
  gi|313126458|ref|YP_004036728.1|  77 --EHTRNRPFLAEELSKGGYETAAFVTNPFLTTHY----GfDRGFDHFRDFTGSEADDEGTAgLKRDFMD---Klnr 144
                                       ..7899****************8887544443333....3489*******98888887764313344444...3445 PP

                                       ..................TTTTCSHHHHHHHHHHHHHHCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCC CS
                         Sulfatase 147 ..................ppeggysddrlldealefllarn.dkpfflylatlapHappeapdeyakkyatffddgs 204
                                                         + +++    ++ de++++l  ++ d+p fl+ +++ pH+p+  ++ey +    f +++s
  gi|313126458|ref|YP_004036728.1| 145 alrrspflyeiakgvknfSSAPFPRAGQVNDEVVTYLESTDgDDPLFLWAHYMDPHHPYLPEPEYRDL--PFVPSLS 219
                                       8999**************999999999999999****99999**************977777777555..7888888 PP

                                       CCCH..........................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCG CS
                         Sulfatase 205 eaar..........................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgaslee 255
                                       +++                           +l++ y + ++++Dd+i+rv+  L+engl+d+tl+++ SDhg++  e
  gi|313126458|ref|YP_004036728.1| 220 KWEIirlsakidlikrddydrtnitdetlsNLRALYRAQIKRTDDAIKRVVRSLKENGLYDDTLLIIASDHGDEFFE 296
                                       887788888899999999999******************************************************77 PP

                                       HHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC.EEECSEEEGGGHHHHHHHHTTE CS
                         Sulfatase 256 sngplrggkganayeggtrvPllvwwpgekap.rvseelvshiDlfptildlagi 309
                                         +   g+   + y++ ++vP++v  p   ++ + +e+l+   D+ pt+ld agi
  gi|313126458|ref|YP_004036728.1| 297 --HGSLGHSP-QLYDELIHVPFVVKTPADHETiESVEGLMAYLDIPPTVLDFAGI 348
                                       ..55555555.8*****************************************97 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   3.4e-10   8.8e-07     142     233 ..     146     291 ..      10     299 .. 0.62
   2 ?   -2.5   0.0       1.1   2.8e+03     282     307 ..     418     443 ..     359     460 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.4e-10
                                       S...CHHHHHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-T.T..SHH................ CS
                      Phosphodiest 142 v...pledkvdkavlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGp.d..spe................ 196
                                       +   p+   ++k v+ ++ +a+f +  ++   +  d +++yle+tD     f + +  +p                 
  gi|313126458|ref|YP_004036728.1| 146 LrrsPFLYEIAKGVK-NFSSAPFPR--AG---QVNDEVVTYLESTDGDDPLFLWaHymDPHhpylpepeyrdlpfvp 216
                                       344444444444344.555555543..22...555667777777777776666533444445556666677777777 PP

                                       ......................................HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 197 ......................................vedalrrvDkaigdLlealderglsaetniilvSDHG 233
                                                                              +++++r D+ai++ +++l+e+gl+++t +i++SDHG
  gi|313126458|ref|YP_004036728.1| 217 slskweiirlsakidlikrddydrtnitdetlsnlralYRAQIKRTDDAIKRVVRSLKENGLYDDTLLIIASDHG 291
                                       77777777777777777777777777777778888888899*********************************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                       CTTHHHHHHHHHHTCHHCCHSTHTTT CS
                      Phosphodiest 282 aeaeaeevyaelkakleelrkkegea 307
                                       +  +  +v+ael++ + ++++ ege+
  gi|313126458|ref|YP_004036728.1| 418 VLSDTPDVAAELREIVRTHLDAEGEH 443
                                       33344455555555555555445554 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.6   6.7e+03      43      73 ..     221     251 ..     219     263 .. 0.60
   2 !    6.4   0.1    0.0032       8.1      21      47 ..     367     396 ..     362     398 .. 0.81
   3 !   14.6   0.0   8.9e-06     0.023      67      97 ..     402     432 ..     399     433 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                           DUF4994  43 WkyiePskgpalikltkielGnskepqLydl 73 
                                       W  i+ s++  lik  + +  n +++ L +l
  gi|313126458|ref|YP_004036728.1| 221 WEIIRLSAKIDLIKRDDYDRTNITDETLSNL 251
                                       6666666666666555555555555555544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0032
                           DUF4994  21 kkdReyvieqaa...nktlsvrkkkWkyie 47 
                                       ++dRe+vi++ +   ++  s+r+ +Wkyi 
  gi|313126458|ref|YP_004036728.1| 367 ATDREHVISEYTywdDRITSLRTPEWKYIV 396
                                       589*****98752325789*********95 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 8.9e-06
                           DUF4994  67 epqLydlkkdegekenvaekhpekvkelkel 97 
                                       ++ L+d+++d++e++nv ++ p++  el+e+
  gi|313126458|ref|YP_004036728.1| 402 REELFDINTDPTEQTNVLSDTPDVAAELREI 432
                                       689*************************987 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.2e-07   0.00031       2      88 ..     351     427 ..     350     460 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-07
                           DUF4976   2 padmqGksllpllkgkkkkewrkalyYhyyeyPaehavkrhygvrteryklihfykdidewelyDlkkDpkelknly 78 
                                       p++m+G+s+++ ++  ++++ +    Y+y++        r  ++rt ++k i  y  +d  el+D+++Dp+e  n++
  gi|313126458|ref|YP_004036728.1| 351 PSSMRGESVRESFETGATDREHVISEYTYWDD-------RITSLRTPEWKYIVDYL-HDREELFDINTDPTEQTNVL 419
                                       88999999999999555555555555555554.......8899*******998885.5889***************9 PP

                           DUF4976  79 ddpeyeevvk 88 
                                        d+   +v++
  gi|313126458|ref|YP_004036728.1| 420 SDTP--DVAA 427
                                       8742..3333 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-06     0.003     309     346 ..     257     294 ..     241     389 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                            DUF229 309 nllealDedllkylkklekkgllentlvlllsDHGlrf 346
                                       + ++++D+ + ++ ++l+++gl ++tl+++ sDHG  f
  gi|313126458|ref|YP_004036728.1| 257 AQIKRTDDAIKRVVRSLKENGLYDDTLLIIASDHGDEF 294
                                       567889*****************************655 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-06    0.0053     261     310 ..     250     299 ..     247     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                           DUF1501 261 nlekahkklakelDqalaaLlkdLkqrGllddTlVvwagEFGRtpkingn 310
                                       nl +  + ++k +D+a++  ++ Lk++Gl ddTl + a++ G  + ++g+
  gi|313126458|ref|YP_004036728.1| 250 NLRALYRAQIKRTDDAIKRVVRSLKENGLYDDTLLIIASDHGDEFFEHGS 299
                                       5666678899******************************9977766665 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   3.3e+03      60      96 ..     234     275 ..     233     281 .. 0.74
   2 !   15.1   0.1   1.1e-05     0.029      50      92 ..     399     438 ..     378     456 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                                       TT-TT--S-TTSTT.....CCHHHHHHHHHHHHHHHCCC--- CS
                       Sulfatase_C  60 erDpsEkyplsaes.....peykevlkeikkaveehkktlkp 96 
                                       +rD +++++++ e+     + y++ +k++ +a++++ ++lk+
  gi|313126458|ref|YP_004036728.1| 234 KRDDYDRTNITDETlsnlrALYRAQIKRTDDAIKRVVRSLKE 275
                                       677777788887777666677888888888888888887764 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-05
                                       EECCEEEEETTT-TT--S-TTSTTCCHHHHHHHHHHHHHHHCC CS
                       Sulfatase_C  50 ehdpPllFdlerDpsEkyplsaespeykevlkeikkaveehkk 92 
                                        hd   lFd+++Dp+E++++ +++   ++v +e++++v++h +
  gi|313126458|ref|YP_004036728.1| 399 LHDREELFDINTDPTEQTNVLSDT---PDVAAELREIVRTHLD 438
                                       589999***************766...4444444544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2700.38
//
Query:       gi|313126459|ref|YP_004036729.1|  [L=283]
Description: arylsulfatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-20   74.4   0.1    1.4e-20   73.9   0.1    1.2  1  Sulfatase  Sulfatase


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.1   7.7e-25   1.4e-20       2     237 ..       9     282 ..       8     283 .] 0.78

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 7.7e-25
                                       EEEEEEESSE-TTGSGGGTTTSCS...SHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT CS
                         Sulfatase   2 nvvliladdlgagdlglyggktat...tpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg 75 
                                        +v++++d+l+++ +g+yg+       tp++d+la+ g+rf  ++s ap +  s  a+lt+ yp             
  gi|313126459|ref|YP_004036729.1|   9 PIVFLTIDSLRRDEVGCYGDRGVDydlTPEIDSLAADGVRFDTAISNAPNTLFSFLATLTSTYPLAK---------- 75 
                                       59******************9866777************************************9994.......... PP

                                       HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC.CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC..... CS
                         Sulfatase  76 gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk.nrgfdrflgfptgsaalkdpekseyngevlrv..... 146
                                       +g     ++++e l +aGY+ta ++  ++ + sr      +rgfd + +f  gs + +d + s+ +++ + v     
  gi|313126459|ref|YP_004036729.1|  76 KGNTAGRPAVAEELSDAGYRTAGFH--SNPFLSRHY--GfHRGFDVYHDFTDGSGDGDDDGESSLTNRFFEVlnrtl 148
                                       69999****************5555..444444444..3478999777777776666666666666666666777** PP

                                       ................TTTTCSHHHHHHHHHHHHHHCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCC CS
                         Sulfatase 147 ................ppeggysddrlldealefllarn.dkpfflylatlapHappeapdeyakkyatffddgsea 206
                                                        + +++    + d a e l++ + d+p+f++++++  H+p+  + +y +    f +d s  
  gi|313126459|ref|YP_004036729.1| 149 hrspllheyaketknyFTPPYTRAGPINDAATEHLRNVDfDDPQFVWVHYMDAHHPYLPTGKYREL--PFLPDIS-- 221
                                       **********999988555555566666777777777899**************954333333222..1222222.. PP

                                       CH...............................HHHHHHHHHHHHHHHHHHHHHHHHHHTTT CS
                         Sulfatase 207 ar...............................qlleaylnsveyvDdligrvlaaLeengl 237
                                                                         l++ y + v+++Dd++g+++a+L++ g 
  gi|313126459|ref|YP_004036729.1| 222 -PvrtvdlaakidlvkhpeydgarasvserdvaDLRALYRAQVKRTDDAVGEIVAELKRPGN 282
                                       .13345666677777778888888888999999************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1925.71
//
Query:       gi|313126460|ref|YP_004036730.1|  [L=161]
Description: arylsulfatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00028   20.7   0.1       0.27   11.2   0.0    2.2  2  DUF4994      Domain of unknown function
     0.0052   17.0   0.1      0.011   16.0   0.1    1.6  1  DUF4976      Domain of unknown function (DUF4976)
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.021   14.3   0.0    1.4  1  Sulfatase    Sulfatase
       0.03   15.1   0.1       0.04   14.7   0.1    1.3  1  Sulfatase_C  C-terminal region of aryl-sulfatase


Domain annotation for each model (and alignments):
>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1   0.00073       3.3      17      46 ..      58      90 ..      42      96 .. 0.73
   2 !   11.2   0.0   6.1e-05      0.27      65      94 ..      95     124 ..      93     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00073
                           DUF4994 17 lGkdkkdReyvieqaank...tlsvrkkkWkyi 46
                                      l + k++Re vi++ an+     s r+ +Wkyi
  gi|313126460|ref|YP_004036730.1| 58 LENGKTEREAVISEYANSgkrITSRRTLEWKYI 90
                                      4567899*****98776522256778899***9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.1e-05
                           DUF4994  65 skepqLydlkkdegekenvaekhpekvkel 94 
                                       + ++ L+dl++d +e++++ +++pe+++ +
  gi|313126460|ref|YP_004036730.1|  95 HDREELFDLTTDSTEQTDCSTDRPEVLESF 124
                                       56899********************98765 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.4e-06     0.011       2      80 ..      46     116 ..      45     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
                           DUF4976   2 padmqGksllpllkgkkkkewrkalyYhyyeyPaehavkrhygvrteryklihfykdidewelyDlkkDpkelknly 78 
                                       p++m+G+s+l+ l+  + k+ r+a+  +y +       kr  + rt ++k i   + +d  el+Dl +D +e  +  
  gi|313126460|ref|YP_004036730.1|  46 PDEMEGQSFLDALE--NGKTEREAVISEYANS-----GKRITSRRTLEWKYILD-DYHDREELFDLTTDSTEQTDCS 114
                                       99***********9..6778899999998665.....56666778999998853.345889**********988775 PP

                           DUF4976  79 dd 80 
                                        d
  gi|313126460|ref|YP_004036730.1| 115 TD 116
                                       54 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.6e-06     0.021     269     308 ..       2      42 ..       1      43 [. 0.96

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-06
                                       SHHHHBEEEEEEETTTSHC.EEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 269 yeggtrvPllvwwpgekap.rvseelvshiDlfptildlag 308
                                       y++ ++vP++v  p e  +    e l+   D+ pt+ldlag
  gi|313126460|ref|YP_004036730.1|   2 YDELIHVPFIVKPPAEYDTvDAIEDLTAYLDIGPTFLDLAG 42 
                                       8999************************************9 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   8.8e-06      0.04      49      87 ..      93     131 ..      66     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.8e-06
                                       EEECCEEEEETTT-TT--S-TTSTTCCHHHHHHHHHHHH CS
                       Sulfatase_C  49 tehdpPllFdlerDpsEkyplsaespeykevlkeikkav 87 
                                        +hd   lFdl++D +E+++ s++ pe+ e ++++ +++
  gi|313126460|ref|YP_004036730.1|  93 DYHDREELFDLTTDSTEQTDCSTDRPEVLESFRDAVRER 131
                                       79********************76665555554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 999.00
//
Query:       gi|313126461|ref|YP_004036731.1|  [L=491]
Description: o- antigen and teichoic acid export membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-13   48.3   7.4      8e-13   48.3   7.4    2.7  3  Polysacc_synt_3  Polysaccharide biosynthesis protein
    1.9e-12   47.4  13.9    1.9e-12   47.4  13.9    4.1  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
      2e-06   27.4  14.1      2e-06   27.4  14.1    2.3  2  Polysacc_synt    Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.044   14.2   0.8      0.044   14.2   0.8    4.9  6  MrpF_PhaF        Multiple resistance and pH regulation protei


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.047   2.1e+02     183     234 ..      17      71 ..      15      72 .. 0.81
   2 !   48.3   7.4   1.8e-16     8e-13       2     291 ..      36     323 ..      35     325 .. 0.84
   3 ?    1.7   4.3     0.028   1.2e+02     116     165 ..     356     406 ..     353     474 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.047
                   Polysacc_synt_3 183 klllsnllnylarnldnlliGkvlssaaLGlYs...vakrlaslpvaeitsviak 234
                                       k+ l ++++ l+  + +++ ++ l+s +LG Y    +a  l++ pv+ + ++i+k
  gi|313126461|ref|YP_004036731.1|  17 KAALGKFIMALIGFVGTIIFARWLGSDSLGGYYlllTAAALSNRPVQGLAEAIQK 71 
                                       56677889999999999************98853336888999999999888875 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 1.8e-16
                   Polysacc_synt_3   2 LARLLspedFGvvaialvvislanlfvdmGlssaliqkedltee....dlstvftfnlvlgllialvlfllaplias 74 
                                        AR L  +  G + ++l+  +l+n  v+ Gl +a+ ++ + +       ls+   + +   +l+al+ ++l+ +++s
  gi|313126461|ref|YP_004036731.1|  36 FARWLGSDSLGGYYLLLTAAALSNRPVQ-GLAEAIQKRGSESGFeleqTLSVGTLVVIGWTALAALIAYALRGYLQS 111
                                       6777777777777777777777776664.777775444343322222256666777778889999999********* PP

                   Polysacc_synt_3  75 fynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssl 151
                                       f++ p  v    ++al   lsg++ +q+ l++   + ++ + ++ v s +++ + +   +lg+g+  ++ig++++ l
  gi|313126461|ref|YP_004036731.1| 112 FFGFPGSVS--AFVALLASLSGFFILQSQLVAL-GRISRNQWFDTVRSYLTFPAQLGFLILGWGAAGVAIGEVVATL 185
                                       *****8765..5788888899999888887765.4666677778889999999************************ PP

                   Polysacc_synt_3 152 lslvllwlaskwr.prlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvae 227
                                       l  v ++ +      r+   ++++++l ++ ++ + ++ l   +++ld ll G +++++a G Y va rl ++p a 
  gi|313126461|ref|YP_004036731.1| 186 LLYVPMYRSFGTGfARP--TVETMRSLWEYAKYSIPNEYLTHTYSQLDMLLLGFLVGKSATGEYGVALRL-TVPAAF 259
                                       *9999988777662455..5679**********************************************8.69**** PP

                   Polysacc_synt_3 228 itsviakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWlea 291
                                       ++ v ++ lf+ +S+l++  +++   ++++l++ +++++P++vg +++ e lv + ++ ++++a
  gi|313126461|ref|YP_004036731.1| 260 VSMVATQGLFSRVSNLRSKGERVDIDVQNTLSFASIVAIPMLVGGVLLDEQLVVTAYSAEYKSA 323
                                       ************************************************************9987 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.028
                   Polysacc_synt_3 116 kitlvssvvgvivaivlAll.glgvwALvigtllssllslvllwlaskwrp 165
                                       k+++ s++++v v + +Al+  +g+  +vi t+++++++  +l +++k+ +
  gi|313126461|ref|YP_004036731.1| 356 KVKVNSVLLAVNVIVGVALTvAYGAIGVVIATVIAEAVRYGFLAWYVKQSI 406
                                       5666667777666666665415799999***************99999874 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3      0.47   2.1e+03      32      54 ..      19      41 ..      10      58 .. 0.51
   2 ?   -0.8   2.1      0.33   1.5e+03      94     130 ..      95     131 ..      77     144 .. 0.41
   3 ?    1.6   5.6     0.057   2.6e+02       6      80 ..     121     194 ..     118     218 .. 0.63
   4 ?   -1.0   0.4      0.38   1.7e+03      90     134 ..     289     333 ..     253     338 .. 0.53
   5 !   47.4  13.9   4.3e-16   1.9e-12       8     141 ..     333     463 ..     326     465 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.47
                   Polysacc_synt_C 32 lkalvigalvklilnllliplfg 54
                                      ++  +i al+ ++ ++++  ++g
  gi|313126461|ref|YP_004036731.1| 19 ALGKFIMALIGFVGTIIFARWLG 41
                                      33444444444444444444443 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                   Polysacc_synt_C  94 pllaalvmgivvylllllllglllla....alalllavlvg 130
                                       ++laal+ +++      +l +++  +    a++ lla l g
  gi|313126461|ref|YP_004036731.1|  95 TALAALIAYAL----RGYLQSFFGFPgsvsAFVALLASLSG 131
                                       22223333222....22222222211111122333333333 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.057
                   Polysacc_synt_C   6 alsiiflsls..tvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrr 79 
                                       a++++++sls   +l+s L +lgr  +  ++  +   + +  +l ++   +g+ G+ai+ v+a l+  v +++    
  gi|313126461|ref|YP_004036731.1| 121 AFVALLASLSgfFILQSQLVALGRISRNQWFDTVRSYLTFPAQLGFLiLGWGAAGVAIGEVVATLLLYVPMYR---- 193
                                       5566666665445666777777777777777777777777777644437788777776666666666555554.... PP

                   Polysacc_synt_C  80 l 80 
                                        
  gi|313126461|ref|YP_004036731.1| 194 S 194
                                       3 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.38
                   Polysacc_synt_C  90 rllkpllaalvmgivvylllllllgllllaalalllavlvgalvY 134
                                       +l    ++a+ m +  +ll  +l+ +  +a    ++ +lvg lv+
  gi|313126461|ref|YP_004036731.1| 289 TLSFASIVAIPMLVGGVLLDEQLVVTAYSAEYKSAATLLVGLLVF 333
                                       333333344444444333444444444444345555566666665 PP

  == domain 5  score: 47.4 bits;  conditional E-value: 4.3e-16
                   Polysacc_synt_C   8 siiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgik 84 
                                         ++ + s+vl ++  gl+r+   +k++ + ++v++i+ + l+  +g++G++iatv+a++v   ++ +++++ +   
  gi|313126461|ref|YP_004036731.1| 333 FQLLRTQSQVLDGVVAGLDRPNVKVKVNSVLLAVNVIVGVALTVAYGAIGVVIATVIAEAVRYGFLAWYVKQSIPSV 409
                                       5556666899**************************************************************99988 PP

                   Polysacc_synt_C  85 lellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllll 141
                                         + r++   +++a++mgivvy  l+++l + ++   +l++ +++ga++Y ++l+ l
  gi|313126461|ref|YP_004036731.1| 410 SLFPRSMAEQAASAVGMGIVVY-GLRQTLAIDSWL--ILGVVLGAGAVAYTGILFTL 463
                                       86677888************99.666666666665..89999999********9987 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4  14.1   4.5e-10     2e-06       9     266 ..      19     268 ..      14     276 .. 0.77
   2 ?   -3.4  15.8       1.1   4.8e+03     101     251 ..     315     464 ..     258     479 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.5e-10
                     Polysacc_synt   9 llsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.kelvslillnvllv 84 
                                       +l+++i +l++fv ++++ar lg    G ++l+l+ +  l++    Gl  a+ ++ +++  + +++ s+++l v+  
  gi|313126461|ref|YP_004036731.1|  19 ALGKFIMALIGFVGTIIFARWLGSDSLGGYYLLLTAA-ALSNRPVQGLAEAIQKRGSESGFElEQTLSVGTLVVIGW 94 
                                       6899***************************999876.56777888**************95445555555444444 PP

                     Polysacc_synt  85 llvlvllfllllliaa.....flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilv 156
                                       + +++l++   + + +     f+g p  ++  ++l ++l    g+ +++++l+   +  + +  ++v ++l++ + +
  gi|313126461|ref|YP_004036731.1|  95 TALAALIA---YAL-RgylqsFFGFPGSVSAFVALLASLS---GFFILQSQLVALGRISRNQWFDTVRSYLTFPAQL 164
                                       44444444...444.3133347777777777777777666...4444444444444444444568999999999999 PP

                     Polysacc_synt 157 liavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsillg 233
                                       ++++++++     ++g +++ +v+ +++++ +++ f+  f+ ++ +++r l  ++ + + +++++  y ++d++llg
  gi|313126461|ref|YP_004036731.1| 165 GFLILGWG-----AAGVAIGEVVATLLLYVPMYRSFGTGFARPTVETMRSLWEYAKYSIPNEYLTHTYSQLDMLLLG 236
                                       99999999.....556666666666778888899******************************************* PP

                     Polysacc_synt 234 lllgaeavGiYnaayqllvaisgllapivtaal 266
                                       +l g +a G+Y +a +l+ ++  ++++ +t+ l
  gi|313126461|ref|YP_004036731.1| 237 FLVGKSATGEYGVALRLT-VPAAFVSMVATQGL 268
                                       ***********9999875.46666666666555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                     Polysacc_synt 101 flglpelavlylilalmll.llvgvasfrrglfqglermky.aavsqvveqlsrvilvliavflfldivaavlgavl 175
                                        +++++++   l+  l +  ll + +++  g + gl r +  + v++v+  + +++ v++ v ++    ++v+++v+
  gi|313126461|ref|YP_004036731.1| 315 AYSAEYKSAATLLVGLLVFqLLRTQSQVLDGVVAGLDRPNVkVKVNSVLLAVNVIVGVALTVAYGA--IGVVIATVI 389
                                       455554444444444444467888888888888888887652456666666666666666666666..555555555 PP

                     Polysacc_synt 176 aalvg.givslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsi.llglllgaeavGiYnaayql 250
                                       a  v+ g+++++v      p+ + +  + + e    ++ + i+ ++   +  ids  +lg  lga+av++     +l
  gi|313126461|ref|YP_004036731.1| 390 AEAVRyGFLAWYVKQ--SIPSVSLF-PRSMAEQAASAVGMGIVVYGLRQTLAIDSWlILGVVLGAGAVAYTGILFTL 463
                                       555550444444444..56777777.99***************************************9976555555 PP

                     Polysacc_synt 251 l 251
                                       +
  gi|313126461|ref|YP_004036731.1| 464 S 464
                                       4 PP

>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   9.7e-06     0.044      36      52 ..      24      40 ..      23      41 .. 0.90
   2 ?   -1.9   0.3         1   4.7e+03      31      39 ..      97     105 ..      84     112 .. 0.57
   3 ?   -3.8   0.3         4   1.8e+04      33      40 ..     123     130 ..     119     133 .. 0.51
   4 ?   -2.7   0.1       1.8   8.2e+03      11      27 ..     324     340 ..     322     344 .. 0.66
   5 ?   -2.4   1.8       1.5   6.8e+03      16      24 ..     370     378 ..     363     396 .. 0.51
   6 ?   -2.4   3.5       1.5   6.8e+03      16      48 ..     424     456 ..     420     460 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.7e-06
                         MrpF_PhaF 36 vlAllgFvgtvafarfl 52
                                      ++Al+gFvgt++far l
  gi|313126461|ref|YP_004036731.1| 24 IMALIGFVGTIIFARWL 40
                                      78*************65 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                         MrpF_PhaF  31 ldvalvlAl 39 
                                       l + +++Al
  gi|313126461|ref|YP_004036731.1|  97 LAALIAYAL 105
                                       233344444 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 4
                         MrpF_PhaF  33 valvlAll 40 
                                       val+ +l 
  gi|313126461|ref|YP_004036731.1| 123 VALLASLS 130
                                       34444444 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.8
                         MrpF_PhaF  11 gtllvallallailtgr 27 
                                       +tllv+ll+   ++t++
  gi|313126461|ref|YP_004036731.1| 324 ATLLVGLLVFQLLRTQS 340
                                       46777777766666665 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 1.5
                         MrpF_PhaF  16 allallail 24 
                                       + +al  ++
  gi|313126461|ref|YP_004036731.1| 370 VGVALTVAY 378
                                       333333332 PP

  == domain 6  score: -2.4 bits;  conditional E-value: 1.5
                         MrpF_PhaF  16 allallailtgrpayldvalvlAllgFvgtvaf 48 
                                       + ++++   +++++ +d  l+l+++   g+va+
  gi|313126461|ref|YP_004036731.1| 424 VGMGIVVYGLRQTLAIDSWLILGVVLGAGAVAY 456
                                       567777778889999999999999988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2841.78
//
Query:       gi|313126462|ref|YP_004036732.1|  [L=358]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-32  110.7   5.1    1.4e-31  109.8   5.1    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.9e-27   96.1  10.2    2.9e-27   96.1  10.2    2.4  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      1e-26   93.5   0.0    1.6e-26   92.8   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    3.9e-21   75.9   0.0    7.6e-21   75.0   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.6e-08   34.7   0.0    2.5e-08   34.0   0.0    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    8.8e-06   25.6   0.4      0.002   17.8   0.0    2.8  2  Glyco_transf_5   Starch synthase catalytic domain


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   5.1   4.6e-35   1.4e-31       2     170 .]      21     181 ..      20     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 4.6e-35
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgd.dgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvH 77 
                                       GGve+hv+e++++L +rGh+Vtv+t +  dg ++ e    ++++ v+++ +  ++  +   ++l+++++r + DvvH
  gi|313126462|ref|YP_004036732.1|  21 GGVETHVREISERLVERGHDVTVLTADAgDGGFRAE---RRNGVHVRRFRSIAPGGAMHVCPQLAAAVRRTDADVVH 94 
                                       9***********************665504555555...4555555555566677777788999************* PP

                    Glyco_transf_4  78 ahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygv 154
                                       ah+++++ +  +al    + ++V+t H +   +   + + +l  ++r + r+++rrad+v+avS++++++l++ ++v
  gi|313126462|ref|YP_004036732.1|  95 AHNYHSFPLFFAALGI-GDRRFVVTPHYHG--GSADSTRDKLLSAYRPVGRWAVRRADAVVAVSKWERKQLATDFDV 168
                                       ******9999888887.9*********999..78999999999999******************************* PP

                    Glyco_transf_4 155 ppekitVipnGvDler 170
                                       ++   tVipnG D++r
  gi|313126462|ref|YP_004036732.1| 169 DA---TVIPNGLDVDR 181
                                       *8...*********97 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1  10.2   9.7e-31   2.9e-27       1     160 []      21     176 ..      21     176 .. 0.84
   2 ?    1.0   0.1      0.18   5.3e+02     121     141 ..     273     293 ..     188     311 .. 0.54
   3 ?    0.1   0.1      0.32   9.4e+02      85     110 ..     278     302 ..     263     328 .. 0.66

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 9.7e-31
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgap.eleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdv 76 
                                       gG++++v+e++++L++rGh+Vtvlt+++  g + +++++gv+v+r++  + +   + +  +++l++++  rr   dv
  gi|313126462|ref|YP_004036732.1|  21 GGVETHVREISERLVERGHDVTVLTADAGDGGFrAERRNGVHVRRFRSIAPG---GAMHVCPQLAAAV--RRTDADV 92 
                                       8************************6655555516899*******9854333...57999********..******* PP

                   Glyco_trans_4_4  77 vhahsptaglaarlarrrrgiplvvtlhglllrrg..sgavrrlyralerrllrradavlvvseaeaeelra.lgvp 150
                                       vhah++++ ++  +a    + ++vvt+h + +        + ++yr++ r+++rradav++vs +e+++l+  + v+
  gi|313126462|ref|YP_004036732.1|  93 VHAHNYHSFPLFFAALGIGDRRFVVTPHYHGGSADstRDKLLSAYRPVGRWAVRRADAVVAVSKWERKQLATdFDVD 169
                                       ******9888888887456999******65544331244577889**************************989999 PP

                   Glyco_trans_4_4 151 adrvvvvpng 160
                                           +v+png
  gi|313126462|ref|YP_004036732.1| 170 ---ATVIPNG 176
                                       ...589**98 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.18
                   Glyco_trans_4_4 121 alerrllrradavlvvseaea 141
                                        +e + ++ a a+ + ++ ++
  gi|313126462|ref|YP_004036732.1| 273 KFEAYGMTVAEALAAGTPCVV 293
                                       333333333333333333333 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.32
                   Glyco_trans_4_4  85 glaarlarrrrgiplvvtlhglllrr 110
                                       g+ ++ a  ++g+p+vv   g+l+++
  gi|313126462|ref|YP_004036732.1| 278 GMTVAEAL-AAGTPCVVREAGALVDW 302
                                       45555555.77999999888655443 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   5.5e-30   1.6e-26      13     132 ..     190     304 ..     180     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 5.5e-30
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                        ++++il+vgrle++Kgv+++i+a+ +l     p++ l++aG+g++ +el++ a +  ++d+v+flg+v+ e+l+ l
  gi|313126462|ref|YP_004036732.1| 190 RDRPYILTVGRLEEYKGVQHAIRALSEL-----PEYDLLVAGSGPYHDELERTARQEDVEDRVEFLGYVDGEELPGL 261
                                       5899**********************77.....89****************************************** PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvk 132
                                       +  ad++v  s  E+ G+++ EA+aag+p+++  ag + + v 
  gi|313126462|ref|YP_004036732.1| 262 YAGADAYVTLSKFEAYGMTVAEALAAGTPCVVREAGALVDWVS 304
                                       *********************************9998877765 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.0   2.5e-24   7.6e-21       1     115 [.     192     310 ..     192     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 2.5e-24
                                       SEEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH CS
                   Glyco_trans_1_4   1 rpvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaa 72 
                                       rp il+vGrl e++kgv+  ++a+ +l   ++ l+++G+gp   +ele+ a+  ++e+rvef+G+v  e+l+ l+a 
  gi|313126462|ref|YP_004036732.1| 192 RPYILTVGRL-EEYKGVQHAIRALSELP--EYDLLVAGSGPyH-DELERTARqeDVEDRVEFLGYVdgEELPGLYAG 264
                                       689*******.777**************..57*********65.69*9877568999*********9999******* PP

                                       -SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE CS
                   Glyco_trans_1_4  73 advfvaPs..egfglkllEamaaglpvVatdvggiaevv.gengll 115
                                       ad +v  s  e  g+++ Ea+aag+p+V+ ++g++ + v  en + 
  gi|313126462|ref|YP_004036732.1| 265 ADAYVTLSkfEAYGMTVAEALAAGTPCVVREAGALVDWVsRENCVG 310
                                       ********999*********************98899886555444 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   8.4e-12   2.5e-08      10     138 ..      24     154 ..      19     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 8.4e-12
                   Glyco_trans_4_2  10 svhtlrlakeLakrgyeVhvitpkkga..kdeleaegihvhrlkvdrkgpleylkaf.klkklikkikPDvvhahya 83 
                                       ++h++++ + L +rg++V+v+t + g    + ++++g+hv r++  +  p + + +  +l++ +++   Dvvhah+ 
  gi|313126462|ref|YP_004036732.1|  24 ETHVREISERLVERGHDVTVLTADAGDggFRAERRNGVHVRRFR--SIAPGGAMHVCpQLAAAVRRTDADVVHAHNY 98 
                                       689********************777756788899********9..555*****9777******************* PP

                   Glyco_trans_4_2  84 kpygllgslaarlsgvipvvlsvwGldv...lkfpkksklkklllklalkkatkvist 138
                                        +  l+   aa+  g  ++v++ +  +     + +k   ++++  ++a+++a++v + 
  gi|313126462|ref|YP_004036732.1|  99 HSFPLFF--AALGIGDRRFVVTPHYHGGsadSTRDKLLSAYRPVGRWAVRRADAVVAV 154
                                       9975533..5566677****88763333213444444449999**********99875 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.8e-07     0.002       1      59 [.       8      66 ..       8      82 .. 0.80
   2 !    4.4   0.2    0.0084        25     125     170 ..      84     120 ..      72     172 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.8e-07
                    Glyco_transf_5  1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPry..gaikeekkeleevael 59
                                      kil v++ ++p  + GG+  +v+++++ L ++ghdv+v++ +   g +++e+++  +v ++
  gi|313126462|ref|YP_004036732.1|  8 KILQVTPRYPP--QSGGVETHVREISERLVERGHDVTVLTADAgdGGFRAERRNGVHVRRF 66
                                      89*********..***************************998545555555555555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0084
                    Glyco_transf_5 125 lleklgwkpdvihahDWhtalvpallkelykerglfkkiktvftiH 170
                                       ++++     dv+hah +h+  + + +  +        + ++v+t H
  gi|313126462|ref|YP_004036732.1|  84 AVRR--TDADVVHAHNYHSFPLFFAALGIG-------DRRFVVTPH 120
                                       3333..359999999999987744444333.......356666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2156.74
//
Query:       gi|313126463|ref|YP_004036733.1|  [L=384]
Description: glycosyl transferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-18   66.9   0.0    3.9e-18   66.2   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.7e-17   62.7   1.6    7.1e-17   61.7   1.0    1.7  2  Glycos_transf_2  Glycosyl transferase family 2
      2e-14   54.0   0.0    3.4e-14   53.2   0.0    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    3.9e-11   42.7   0.0    6.5e-11   42.0   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
    0.00091   18.8   0.0     0.0014   18.1   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.026   13.9   0.0    1.3  1  Anp1             Anp1
       0.18   12.4   0.5       0.43   11.1   0.2    1.8  2  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   1.5e-21   3.9e-18       1     230 []      47     266 ..      46     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.5e-21
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnlgstgks 76 
                                       p+ ++++ pt+nee+ +++ l+++++ +yp  +v +vv d sd+et+e ++ + a+ ++  ++++  +   +++g +
  gi|313126463|ref|YP_004036733.1|  47 PT-VSIVLPTYNEERIIENKLRDIVSLDYPMEKVELVVvDSSDDETREIIRNFFADREAPTLNLIEED---ERRGLA 119
                                       45.9*************************76555444438999*********9999999899*99443...457888 PP

                   Glyco_tranf_2_3  77 ralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavg.tpvfllnrstlvsalgalefaerhlrflaar 152
                                        aln+a+ a++ ++v+  D D+ v  d+l+ +++ +++p+vgav+  +v +l +s +   +  ++    ++++l  +
  gi|313126463|ref|YP_004036733.1| 120 PALNDAYAAAENEMVVKTDCDSKVAADALREAAANLADPDVGAVTgRNVDVLGGSEVEEGYRGIQ---AKIQTLESH 193
                                       99***************************99999999********77889999999977665544...344444444 PP

                   Glyco_tranf_2_3 153 ralgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvy 229
                                          ++l+++G +s+++ +    +   dp  +++dD el+l +rr+g r+++ p++   e+++s++++ + q+ R ++
  gi|313126463|ref|YP_004036733.1| 194 -LDSTLIFHGPFSAFENDDIVSI---DP-DSIADDTELALLIRRNGKRVVFDPDVRYKEASHSEFSKRRTQKDRRAM 265
                                       .4456668********9988888...99.99******************************************9877 PP

                   Glyco_tranf_2_3 230 g 230
                                       g
  gi|313126463|ref|YP_004036733.1| 266 G 266
                                       5 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   1.0   2.8e-20   7.1e-17       1     130 [.      50     181 ..      50     234 .. 0.85
   2 ?   -0.7   0.0      0.42   1.1e+03      83     121 ..     212     247 ..     200     285 .. 0.60

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.8e-20
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagalnag 74 
                                       s+v ptyNee  +++ l+ +++  +p +++e++vvD ++ Det+ei++++ +  e p + +i  +e++G+a aln +
  gi|313126463|ref|YP_004036733.1|  50 SIVLPTYNEERIIENKLRDIVSLdYPMEKVELVVVDSSD-DETREIIRNFFAdrEAPTLNLIEEDERRGLAPALNDA 125
                                       8**********************8899999999998877.************************************* PP

                                       HHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC- CS
                   Glycos_transf_2  75 lraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernk 130
                                        +aa  + ++  D D+ ++ d l++ ++ l ++++++v g  +   g++   e  +
  gi|313126463|ref|YP_004036733.1| 126 YAAAENEMVVKTDCDSKVAADALREAAANLADPDVGAVTGRNVDVLGGSEVEEGYR 181
                                       ********************************999999888777776666666554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.42
                                       EEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEEC CS
                   Glycos_transf_2  83 ilflDaDdepdpdwleklvealekdgadvvlgqrprifg 121
                                       i+ +D D++ d+  l  l   + ++g+ vv+   +r++ 
  gi|313126463|ref|YP_004036733.1| 212 IVSIDPDSIADDTELALL---IRRNGKRVVFDPDVRYKE 247
                                       777888888888544444...444444445444433333 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   1.3e-17   3.4e-14       4     192 ..     136     317 ..     133     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.3e-17
                   Glyco_trans_2_3   4 llDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflr 80 
                                         D+D+ + +d lre+aa la+p+v++v+g  + + +++ +ee +        +k++   + l +++ ++G  +++ 
  gi|313126463|ref|YP_004036733.1| 136 KTDCDSKVAADALREAAANLADPDVGAVTGRNVDVLGGSEVEEGYRG----IQAKIQTLESHLDSTLIFHGPFSAFE 208
                                       56*****************************9987555555555553....2358888999999************* PP

                   Glyco_trans_2_3  81 rsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGceleklillvrll. 156
                                        +   +++ +d  ++s+++D++++l ++r+G rv+f p++  ke s +++  ++ Q+ R a+G     l+ll++++ 
  gi|313126463|ref|YP_004036733.1| 209 ND---DIVSID--PDSIADDTELALLIRRNGKRVVFDPDVRYKEASHSEFSKRRTQKDRRAMGL----LRLLFQHRd 276
                                       77...666668..99************************************************4....444555554 PP

                   Glyco_trans_2_3 157 gylgsllwsa..lplhlallllfslla...lalvlllllll 192
                                       ++ ++ l  +  lp+ + +++++++l     +l++l+ ll+
  gi|313126463|ref|YP_004036733.1| 277 ALGRHGLYGGivLPFNWWFMVVSPWLLagaVSLATLFGLLV 317
                                       34455554443356666666666665545433333444444 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   2.5e-14   6.5e-11      22     153 ..     122     246 ..     105     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.5e-14
                   Glyco_transf_21  22 llqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqa..kls 96 
                                       l+ a++aa+++++v  D+d  v++d+L+e +a+l+dp+vg Vt+  v +      +++e  + ++ a++ +   +l 
  gi|313126463|ref|YP_004036733.1| 122 LNDAYAAAENEMVVKTDCDSKVAADALREAAANLADPDVGAVTGRNVDVLGG---SEVEEGYRGIQAKIQTLesHLD 195
                                       57899***************************************99877654...5666666654444444444799 PP

                   Glyco_transf_21  97 glgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqt 153
                                        + +  G + a+  +++ +i    +  d +A+D++l+ l+r++G++vv+ p++ + +
  gi|313126463|ref|YP_004036733.1| 196 STLIFHGPFSAFENDDIVSI---DP--DSIADDTELALLIRRNGKRVVFDPDV-RYK 246
                                       9**************99998...88..9**********************996.333 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.5e-07    0.0014       1     102 [.      50     151 ..      50     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.5e-07
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkaky.y.deeielivvddgSsekfleevssiidlnllvylkde.ddkayslaaarN 74 
                                       s+v+p +++e+   ie++++ + +  y  e++el+vvd  S +++ e ++++ + +    l+   +d+  +la a N
  gi|313126463|ref|YP_004036733.1|  50 SIVLPTYNEERI--IENKLRDIVSLdYpMEKVELVVVD-SSDDETREIIRNFFADREAPTLNLIeEDERRGLAPALN 123
                                       789999998888..*****9998862346778888876.688999*********9998866544045589******* PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfeki 102
                                            ae ++v+  D D  ++ D +   
  gi|313126463|ref|YP_004036733.1| 124 DAYAAAENEMVVKTDCDSKVAADALREA 151
                                       ***********************99654 PP

>> Anp1  Anp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     1e-05     0.026      13      72 ..      39      98 ..      31     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                              Anp1 13 tadaaenkekvLiltplrdaekflpeyfenllkltyphelidLaflvsdtsegdktleal 72
                                       a++++++ +v i+ p  ++e+++++ ++ + +l+yp e+++L ++ s+ +e  ++ +++
  gi|313126463|ref|YP_004036733.1| 39 PANKQRAEPTVSIVLPTYNEERIIENKLRDIVSLDYPMEKVELVVVDSSDDETREIIRNF 98
                                      567888999**********************************88877777666655544 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00017      0.43       1      81 [.      56     140 ..      56     152 .. 0.75
   2 ?   -1.9   0.0       1.9   4.8e+03      42      63 ..     247     269 ..     207     280 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                   Glyco_tranf_2_4   1 rneadiLpeflahhlalgf...drilvydndstDgtrailkel.pevkllhvdksyederrqve.llkallaryaea 72 
                                       +ne+ i+++ l+ + +l++   +  lv+ + s+D+tr+i+++  ++ +  +     ederr+ + +l+ + a  ae+
  gi|313126463|ref|YP_004036733.1|  56 YNEERIIENKLRDIVSLDYpmeKVELVVVDSSDDETREIIRNFfADREAPTLNLIEEDERRGLApALNDAYAA-AEN 131
                                       69999*******999999755334789999**********996577777777777777777765566666644.466 PP

                   Glyco_tranf_2_4  73 dwvlvvDaD 81 
                                       + v+  D+D
  gi|313126463|ref|YP_004036733.1| 132 EMVVKTDCD 140
                                       667777776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                   Glyco_tranf_2_4  42 evkllhvdksy.ederrqvellk 63 
                                       e+++ ++ k   ++ rr++ ll+
  gi|313126463|ref|YP_004036733.1| 247 EASHSEFSKRRtQKDRRAMGLLR 269
                                       22333333322122444454544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2437.33
//
Query:       gi|313126464|ref|YP_004036734.1|  [L=346]
Description: glycosyl transferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-13   49.5   0.1    6.3e-13   48.9   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    4.1e-06   26.9   0.0    6.3e-06   26.2   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00026   21.4   0.0    0.00054   20.4   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.028   14.8   0.0    1.5  1  NTP_transf_3     MobA-like NTP transferase domain
       0.11   12.0   0.1       0.27   10.7   0.1    1.6  2  gpUL132          Glycoprotein UL132
       0.13   12.7   0.0       0.35   11.4   0.0    1.7  2  CoA_binding_2    CoA binding domain


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1   2.1e-16   6.3e-13       1     119 [.       7     116 ..       7     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.1e-16
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       ++ iptyNe++t+  ++    +        i+v+D gS Detv+i+e+      + rv+ ++ + Gk+ a+++++++
  gi|313126464|ref|YP_004036734.1|   7 CILIPTYNEAETIGGVVSDYHSE---GFENILVIDGGSDDETVDIAEDR-----GARVVMQS-GSGKGQAIREAVEY 74 
                                       699***************99998...555566667779***********.....9*******.66***********8 PP

                                       .--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEE CS
                   Glycos_transf_2  78 .atgdyilflDaDdepdpdwleklvealekdgadvvlgqrpri 119
                                            y+l lD D ++  ++   ++e+l++ g+  v+g r++ 
  gi|313126464|ref|YP_004036734.1|  75 hIEAPYVLMLDGDATYCAKDADTMLEPLDE-GYEHVIGDRFAD 116
                                       46666*************************.999999998865 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   2.1e-09   6.3e-06       3     137 ..       5     129 ..       4     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.1e-09
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeypr.vevvvvvde.sdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       d+ +l+pt+ne     e++  ++++ +++ +e ++v d+ sd+et++ ae         + rvv ++   gs gk +
  gi|313126464|ref|YP_004036734.1|   5 DVCILIPTYNE----AETIGGVVSDYHSEgFENILVIDGgSDDETVDIAED-------RGARVVMQS---GS-GKGQ 66 
                                       4899*******....566666665534335777766654499*****9975.......366888554...55.9*** PP

                   Glyco_tranf_2_3  78 alnealr.avksdlvllvDdDtvv.ePdtlkrllqffltpkvgavgtpvfll.nrstl..vsalg 137
                                       a+ ea++ +++  +vl++D+D+    +d+ + +l  + ++++++v +++f++ ++ ++  +++lg
  gi|313126464|ref|YP_004036734.1|  67 AIREAVEyHIEAPYVLMLDGDATYcAKDA-DTMLEPL-DEGYEHVIGDRFADmHDGAMtrFNQLG 129
                                       *******88************99978888.7778888.99********99975777775533333 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.8e-07   0.00054       1      88 [.      13      94 ..      13     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvD 79
                                      +nea++++ ++  + + gf++ilv+d +s+D+t +i +    ++++   +s +    + ++++a+   + ea +vl++D
  gi|313126464|ref|YP_004036734.1| 13 YNEAETIGGVVSDYHSEGFENILVIDGGSDDETVDIAEDRG-ARVVMQSGSGK----GQAIREAVE-YHIEAPYVLMLD 85
                                      69**********99999*******************98853.33333333333....344555555.445889999999 PP

                   Glyco_tranf_2_4 80 aDEflvvpd 88
                                       D  ++ +d
  gi|313126464|ref|YP_004036734.1| 86 GDATYCAKD 94
                                      987777666 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   9.3e-06     0.028      30     102 ..      22      94 ..       9     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.3e-06
                                       HHHHHCTT.-CEEEEE..CSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HH CS
                      NTP_transf_3  30 vldalraagvdevvvv..ggdeevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpe 102
                                       v+   ++ g+++++v+  g d+e  + ++++g+rvv ++  g g +++++ a++   +a +vl+l +D  +  ++
  gi|313126464|ref|YP_004036734.1|  22 VVSDYHSEGFENILVIdgGSDDETVDIAEDRGARVVMQS--GSGKGQAIREAVEYHIEAPYVLMLDGDATYCAKD 94 
                                       566667778999999963344899999***********8..89999********9779**********9876544 PP

>> gpUL132  Glycoprotein UL132
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.94   2.8e+03      96     120 ..      46      70 ..      41     110 .. 0.75
   2 ?   10.7   0.1   9.1e-05      0.27      39     117 ..     251     327 ..     228     337 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.94
                           gpUL132  96 lddtddsggsspfgsgsrrgsqipa 120
                                       +d ++d g    + sgs +g  i  
  gi|313126464|ref|YP_004036734.1|  46 VDIAEDRGARVVMQSGSGKGQAIRE 70 
                                       4556788888889999999888753 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.1e-05
                           gpUL132  39 vhnvrnneimkvlailfyivtgtsifsfiavlvavvyssc..ckhpgrfrfadeeavnllddtddsggsspfgsgsr 113
                                       +  v  n    vla+    v+ ++i+  + +l+  v s      h   +r  dee+    d+t dsg  s  gs   
  gi|313126464|ref|YP_004036734.1| 251 IEWVTVNTSHEVLAV----VAAAAILFGVQLLMFGVLSDLilSLHRDTLRKIDEETGTNADQTPDSGSNSNSGSTRP 323
                                       555555555555554....44455555555555555554311469999**************************999 PP

                           gpUL132 114 rgsq 117
                                       rg +
  gi|313126464|ref|YP_004036734.1| 324 RGVR 327
                                       9976 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.35      64     108 ..      15      59 ..       4      63 .. 0.89
   2 ?   -3.5   0.1       4.8   1.4e+04      57      81 ..     252     276 ..     249     281 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                       -HHHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHHTT-EEE.E CS
                     CoA_binding_2  64 ppeatpeivkealalgakavwlqpgsedeeaaelaeeagirvvgd 108
                                        +e++  +v + +++g + + +  g  d+e++++ae++g rvv++
  gi|313126464|ref|YP_004036734.1|  15 EAETIGGVVSDYHSEGFENILVIDGGSDDETVDIAEDRGARVVMQ 59 
                                       578888999**********************************86 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.8
                                       -EEEE-S-HHHHGGGHHHHHHH--S CS
                     CoA_binding_2  57 dlvdvftppeatpeivkealalgak 81 
                                       + v+v t  e+++ ++ +a+  g++
  gi|313126464|ref|YP_004036734.1| 252 EWVTVNTSHEVLAVVAAAAILFGVQ 276
                                       5566666555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2261.01
//
Query:       gi|313126465|ref|YP_004036735.1|  [L=108]
Description: hypothetical protein Hbor_17220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0052   17.0   0.2       0.27   11.5   0.2    2.9  2  DUF2795   Protein of unknown function (DUF2795)


Domain annotation for each model (and alignments):
>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.2   1.5e-05      0.27       3      43 ..      31      78 ..      30      79 .. 0.81
   2 ?   -0.2   0.0     0.065   1.2e+03      20      33 ..      92     105 ..      90     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.5e-05
                           DUF2795  3 gadyPatKdeLveyArrngA.......pdevleaLeaLPdreYespae 43
                                      ++ yP+t deLv+++ +  +         ++ eaLe  P  +Y+s ae
  gi|313126465|ref|YP_004036735.1| 31 DITYPVTDDELVRALDDVAVpynaaggTVRLSEALESVPQSQYTSKAE 78
                                      899***********9976655555666888889999999999999887 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.065
                           DUF2795  20 ngApdevleaLeaL 33 
                                         A++ +l  L+aL
  gi|313126465|ref|YP_004036735.1|  92 RSASNNILGQLRAL 105
                                       67999******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 726.56
//
Query:       gi|313126466|ref|YP_004036736.1|  [L=70]
Description: hypothetical protein Hbor_17230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0046   16.8   0.3     0.0076   16.2   0.0    1.5  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.2e-07    0.0076       2      34 ..       5      38 ..       5      43 .. 0.94
   2 ?   -3.4   0.1      0.59   1.1e+04       9      14 ..      57      62 ..      56      64 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-07
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlr 34
                                      ++++++++l+er++  ++ +  +S S+l+R +lr
  gi|313126466|ref|YP_004036736.1|  5 TTVSIPKDLAERVETTIEGTSfSSTSDLVRFLLR 38
                                      69****************************8887 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.59
                                      HHHHHH CS
                             RHH_1  9 ellerL 14
                                      +++e+L
  gi|313126466|ref|YP_004036736.1| 57 DIAEQL 62
                                      556655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 419.10
//
Query:       gi|313126467|ref|YP_004036737.1|  [L=139]
Description: hypothetical protein Hbor_17240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.039   13.7   0.0    1.6  1  CobS_N    Cobaltochelatase CobS subunit N terminal


Domain annotation for each model (and alignments):
>> CobS_N  Cobaltochelatase CobS subunit N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.2e-06     0.039       5      20 ..      54      69 ..      52      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-06
                            CobS_N  5 lPDtkvsvRevFGIDs 20
                                      lPD   svR+vFG+D 
  gi|313126467|ref|YP_004036737.1| 54 LPDAGKSVRAVFGVDL 69
                                      79*************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 853.15
//
Query:       gi|313126468|ref|YP_004036738.1|  [L=226]
Description: hypothetical protein Hbor_17250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   11.0   0.0        1.4    8.1   0.0    1.9  2  DUF4336   Domain of unknown function (DUF4336)


Domain annotation for each model (and alignments):
>> DUF4336  Domain of unknown function (DUF4336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.012   2.2e+02      29      64 ..      40      70 ..      36      97 .. 0.77
   2 ?    8.1   0.0   7.7e-05       1.4     135     161 ..     124     150 ..     100     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.012
                           DUF4336 29 kggLlvyaPvapTkellelvkeleaehgevkyivlp 64
                                      +gg ++++Pv +       ++el ae+g+v+ iv++
  gi|313126468|ref|YP_004036738.1| 40 DGGVWLFDPVDAP-----NLDELLAEYGDVSGIVVG 70
                                      7899999999653.....478888889999999986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 7.7e-05
                           DUF4336 135 lelglgkfaevaffhkasktllvtDav 161
                                       l+ +  +++ev f+h++s tllv  +v
  gi|313126468|ref|YP_004036738.1| 124 LDSSIPPWQEVGFYHESSGTLLVPETV 150
                                       45566679***************8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1268.61
//
Query:       gi|313126469|ref|YP_004036739.1|  [L=247]
Description: hypothetical protein Hbor_17260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.6e-06   25.8   0.4     0.0035   17.6   0.1    3.0  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    2.5e-05   24.5   0.6      0.038   14.1   0.3    3.2  2  Glyoxalase_3  Glyoxalase-like domain
    0.00016   21.8   0.0       0.11   12.7   0.0    2.7  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.011   15.6   0.3        2.7    7.9   0.0    3.4  3  Glyoxalase_2  Glyoxalase-like domain
      0.051   14.4   7.2        3.7    8.4   0.0    2.9  3  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.7e-05      0.06      35     100 ..      93     172 ..       7     178 .. 0.50
   2 !   17.6   0.1   9.7e-07    0.0035       4      84 ..     145     215 ..     143     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                                       TTTEEEEEEEETT.EEEEEEEESSTT-THHH..............TS-EEEEEEEEES-HHHHHHHHCTTTEEEEEE CS
                      Glyoxalase_4  35 evdlafallgsgs.vqieLieplegpeflae..............hgeglhhlaywvddldaavarleeqGfevvqk 96 
                                       +++l++ ++ + + v+i  i    g++  ++                +g+  + ++v+dl++a a++++ Gfevv++
  gi|313126469|ref|YP_004036739.1|  93 SHSLYVYDADG-NcVEIGGIDEAGGKSEDDRegvsgdgeqtpanlPLTGIFEVVLEVTDLERAEAQFRALGFEVVDR 168
                                       34444444433.4477766666665533333344444444444478999999999********************99 PP

                                       EE-G CS
                      Glyoxalase_4  97 gvra 100
                                       g++ 
  gi|313126469|ref|YP_004036739.1| 169 GDER 172
                                       9775 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 9.7e-07
                                       EEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEE.EEEEEES-H CS
                      Glyoxalase_4   4 givVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflaehgeglh.hlaywvddl 79 
                                        + V+Dle+a a+f a lG+++ +r  ++  +v+l      sg+v +eL ep  g   +a+ ++glh  la+++dd 
  gi|313126469|ref|YP_004036739.1| 145 VLEVTDLERAEAQFRA-LGFEVVDRGDER-PRVRL------SGPVDLELWEPQLG---IADARGGLHvELAFRTDDP 210
                                       5679***********7.***999998644.55644......45799********9...999999999457******* PP

                                       HHHHH CS
                      Glyoxalase_4  80 daava 84 
                                       +aav+
  gi|313126469|ref|YP_004036739.1| 211 HAAVE 215
                                       *9997 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.013        48       6      29 ..      10      33 ..       8      84 .. 0.82
   2 !   14.1   0.3     1e-05     0.038       4      32 ..     144     171 ..     144     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.013
                      Glyoxalase_3  6 lavpdleeaaarfarrlGftvtpg 29
                                      l v+ le+a++ +++rlG+ +t+ 
  gi|313126469|ref|YP_004036739.1| 10 LEVKYLEAAREFYETRLGLVPTNE 33
                                      67899**************99954 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1e-05
                      Glyoxalase_3   4 vvlavpdleeaaarfarrlGftvtpggeh 32 
                                       vvl v dle+a a+f r+lGf+v+++g  
  gi|313126469|ref|YP_004036739.1| 144 VVLEVTDLERAEAQF-RALGFEVVDRGDE 171
                                       7999***********.********99976 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   3.1e-05      0.11       9     128 .]      12     108 ..       7     108 .. 0.72
   2 !    6.2   0.0    0.0031        11       3      67 ..     142     216 ..     140     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                                       ESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHC CS
                        Glyoxalase   9 vgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdve 85 
                                       v+ le++ +FY+  LG+  + ++d        + a+     g+ ++vl+++ s ++ +v      + h af ++ + 
  gi|313126469|ref|YP_004036739.1|  12 VKYLEAAREFYETRLGLVPTNESD-------TTVAYD---VGQTTVVLRRPVSVPRGGV------HTHYAFSTTREA 72 
                                       67799*******************.......233333...3344444444444444444......125777776666 PP

                                       HHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  86 dvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                         +++  +l++ +      p    fg++ s y++D dG+ +ei
  gi|313126469|ref|YP_004036739.1|  73 Y-DDWMTELSDLD------PAEFTFGSSHSLYVYDADGNCVEI 108
                                       6.**********9......666678888888899999999997 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0031
                                       EEEEEEESHHHHHHHHHHHHHTSEEEEEEEE...........EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHH CS
                        Glyoxalase   3 dhvallvgdleksldFYtkvLGfklvkktdn...........teeteglriaffhaggghielvlneapsgaakhv 67 
                                         v+l v+dle++ + ++  LGf++v++ d             e  e + +++   gg h+el+ +  +++aa+  
  gi|313126469|ref|YP_004036739.1| 142 FEVVLEVTDLERAEAQFRA-LGFEVVDRGDErprvrlsgpvdLELWEPQLGIADARGGLHVELAFRTDDPHAAVEA 216
                                       5677889999999999998.**********9999999988763333555556667788899999999888888776 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00076       2.7       8     114 ..      12     109 ..       5     111 .. 0.53
   2 ?   -3.2   0.0       2.2   7.8e+03      64      81 ..     143     160 ..     141     168 .. 0.60
   3 ?    0.1   0.0       0.2   7.3e+02     101     113 ..     231     243 ..     228     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00076
                                       ES-HHHHHHHHHHTT---EEEE-SSEEEETTS-EEEEHHHHHH-------S--SS-EEEEEES-HHHHHHHH..GGG CS
                      Glyoxalase_2   8 vkdieeskkFYedvlelkikldfGenvsfetgfalkedlkelinldesiaeqsnnfeLyFevedvdaflqklkeaen 84 
                                       vk +e +++FYe +l l  + +  + v ++ g +    l++ +++++       ++      e  d+++ +l + + 
  gi|313126469|ref|YP_004036739.1|  12 VKYLEAAREFYETRLGLVPTNESDTTVAYDVGQTTV-VLRRPVSVPRG--GVHTHYAFSTTREAYDDWMTELSDLDP 85 
                                       778888888888888888888888888888775421.12222222221..122223333334444555555544443 PP

                                       S-EEEEEEE-TTS-EEEEEE-TT--EEEEE CS
                      Glyoxalase_2  85 iellhelkekpWgqrvirfyDpDkhiiEig 114
                                        e+             +++yD D++ +Eig
  gi|313126469|ref|YP_004036739.1|  86 AEFTFGS------SHSLYVYDADGNCVEIG 109
                                       3333222......23456666666666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.2
                                       EEEEEES-HHHHHHHH.. CS
                      Glyoxalase_2  64 eLyFevedvdaflqklke 81 
                                       e+  ev d++ +  +++ 
  gi|313126469|ref|YP_004036739.1| 143 EVVLEVTDLERAEAQFRA 160
                                       555666666666666654 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.2
                                       EEEE-TT--EEEE CS
                      Glyoxalase_2 101 irfyDpDkhiiEi 113
                                       +r+ D D+h+iE 
  gi|313126469|ref|YP_004036739.1| 231 LRVRDADGHVIEF 243
                                       5899*******95 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0     0.001       3.7       4      72 ..      10      72 ..       7      89 .. 0.71
   2 ?    3.6   0.2     0.032   1.1e+02      64      92 ..     146     174 ..     112     184 .. 0.86
   3 ?    5.5   4.3    0.0084        30      13     104 ..     156     241 ..     143     244 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                      Glyoxalase_6  4 ldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe..paknrvHldlavedldae 72
                                      l ++  +a+ +F+++ lg++ + e+    d  +   a + ++t ++ r+p+  p +  vH++ a +  +++
  gi|313126469|ref|YP_004036739.1| 10 LEVKYLEAAREFYETRLGLVPTNES----DTTV---AYDVGQTTVVLRRPVsvP-RGGVHTHYAFSTTREA 72
                                      5667889999*************99....2222...223445666666666433.4479999887666655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.032
                      Glyoxalase_6  64 lavedldaevarlvalGArvlreprdgth 92 
                                       l+v+dl+++ a+  alG +v+++ +++ +
  gi|313126469|ref|YP_004036739.1| 146 LEVTDLERAEAQFRALGFEVVDRGDERPR 174
                                       7899*************999999988764 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0084
                      Glyoxalase_6  13 aaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe...paknrvHldlav..edldaevarlvalGArvl 84 
                                       a+F  +alg+ev+++    e+p+++     + + l + + +     a+  +H++la   +d++a+    v++G+   
  gi|313126469|ref|YP_004036739.1| 156 AQF--RALGFEVVDRG--DERPRVRLS---GPVDLELWEPQLgiaDARGGLHVELAFrtDDPHAA----VEAGGPWA 221
                                       333..57889988888..333333222...44444444444466645556887775533888555....59999998 PP

                      Glyoxalase_6  85 reprdgthgrvlaDPeGneF 104
                                         p++ ++g  ++D +G++ 
  gi|313126469|ref|YP_004036739.1| 222 VGPEEIENGLRVRDADGHVI 241
                                       88888876669999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1343.35
//
Query:       gi|313126470|ref|YP_004036740.1|  [L=99]
Description: hypothetical protein Hbor_17270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 575.75
//
Query:       gi|313126471|ref|YP_004036741.1|  [L=349]
Description: 2-isopropylmalate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-64  217.7  10.5    2.1e-64  217.7  10.5    1.5  2  HMGL-like     HMGL-like
  ------ inclusion threshold ------
      0.016   14.6   2.0      0.022   14.2   0.7    1.9  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.17   11.8   0.0       0.45   10.4   0.0    1.7  1  HlyD_D4       Long alpha hairpin domain of cation efflux syst


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.7  10.5   3.4e-68   2.1e-64      35     264 .]       1     224 [.       1     224 [. 0.98
   2 ?   -2.6   0.0      0.54   3.2e+03      73      99 ..     300     326 ..     296     338 .. 0.71

  Alignments for each domain:
  == domain 1  score: 217.7 bits;  conditional E-value: 3.4e-68
                                       HT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSST CS
                         HMGL-like  35 agvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkd 111
                                       +g ++iE+gfp+ s  +fe+v  ia+a  ++ +++l+r ++ d++aa +    ag+++vhvf++ts+++l  +++ +
  gi|313126471|ref|YP_004036741.1|   1 MGTHVIEAGFPVNSDAEFEAVSDIAAATDTT-VCGLARVVDTDVEAALD----AGVEMVHVFVSTSDVQLADSMHAS 72 
                                       7999**********************99666.*****************....************************ PP

                                       HHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS CS
                         HMGL-like 112 reevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkerv 188
                                       +ee++++a+e v++++++g +v +s++da+rtd+ flae++ a+++aG++ +ni+Dt Gv+tP  +a+li+++++++
  gi|313126471|ref|YP_004036741.1|  73 KEEAVERAVESVERVKDAGVEVMFSPMDATRTDMTFLAEILSAVDDAGVDWVNIPDTCGVATPTRFANLIREVRQHT 149
                                       ***************************************************************************** PP

                                       -.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 189 kdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaalealg.vdtgldlqklrsiaalv 264
                                       +  + + vH+H+d+GlA+an++a+ eaGa +  ++vnG+GeraGnaa ee+v+ ++ l  vdtg+d++++++++++v
  gi|313126471|ref|YP_004036741.1| 150 D--AHIDVHAHDDFGLATANAMAGFEAGAAQAQVSVNGIGERAGNAAYEEVVMSAKSLYdVDTGIDTERITELSRIV 224
                                       *..******************************************************989*************9987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.54
                                       SSHHHHHHHHH....TT-SEEEEEEES CS
                         HMGL-like  73 arekdikaavealkgagakrvhvfiat 99 
                                       ++++ ++a  +++k +ga++ +v++a+
  gi|313126471|ref|YP_004036741.1| 300 PDDSEVRAVTRRVKDTGAEKERVTTAV 326
                                       566677777777777777776666665 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   3.6e-06     0.022      74     190 ..      41     159 ..      12     183 .. 0.74
   2 ?   -2.1   0.0      0.35   2.1e+03      33      58 ..     289     302 ..     275     336 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-06
                                       HHHHHHHHHTBSEEEEEBCC....GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHH CS
                      AP_endonuc_2  74 raielaaaLGapllvlhpGt....agagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeelar 146
                                         +e+a + G+++++++++t      +    s+eea+er++es++++ d     gv++ + +++ + + +    la+
  gi|313126471|ref|YP_004036741.1|  41 TDVEAALDAGVEMVHVFVSTsdvqLADSMHASKEEAVERAVESVERVKDA----GVEVMFSPMDATRTDMT--FLAE 111
                                       567899999**********9866633555566668888888888888888....9************8666..8888 PP

                                       HHHHHTTTTEEE..EEEHHHHHHH..TTTHHHHHHHHHGGEEEEEE.E CS
                      AP_endonuc_2 147 lldavdspnvgv..clDtgHllia..eedvddalraladrikhvHikD 190
                                       +l+avd+  v      Dt+        +++++++r++ d    vH++D
  gi|313126471|ref|YP_004036741.1| 112 ILSAVDDAGVDWvnIPDTCGVATPtrFANLIREVRQHTDAHIDVHAHD 159
                                       888888765322113566655544445555555555555566666666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.35
                                       HHHHHHHTTSEEEEEEECCCHSTCTH CS
                      AP_endonuc_2  33 lrkaldelglriaslslftrfgypde 58 
                                       +rk+l+++g+r            pd+
  gi|313126471|ref|YP_004036741.1| 289 VRKRLEDAGFR------------PDD 302
                                       55555555555............222 PP

>> HlyD_D4  Long alpha hairpin domain of cation efflux system protein, CusB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.6e-05      0.45       6      54 ..     268     313 ..     265     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.6e-05
                                       -TTHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCT-..-HHHHHHHHHHTS CS
                           HlyD_D4   6 iPeWvaaQeEYLalkelgdlaslldaareRlrLaGM..pdadIrrleasgK 54 
                                        Pe v aQ E+ + k++g        +r+Rl  aG    d+++r++ ++ K
  gi|313126471|ref|YP_004036741.1| 268 TPEMVGAQREFVLGKHTGS-----HSVRKRLEDAGFrpDDSEVRAVTRRVK 313
                                       69**********9999998.....89*********85347999*9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2067.97
//
Query:       gi|313126472|ref|YP_004036742.1|  [L=35]
Description: hypothetical protein Hbor_17290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       126  (0.00702772); expected 358.6 (0.02)
Passed bias filter:                       82  (0.0045736); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 249.12
//
Query:       gi|313126473|ref|YP_004036743.1|  [L=582]
Description: acetolactate synthase large subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-52  175.6   1.7    6.4e-52  175.4   0.0    2.1  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.2e-48  163.2   0.4    4.1e-47  160.0   0.4    2.5  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    7.8e-46  155.2   0.2    1.9e-45  154.0   0.1    1.8  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
     0.0054   16.5   0.0     0.0088   15.8   0.0    1.3  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.35   10.6   0.0    1.7  1  DUF5612       Domain of unknown function (DUF5612)


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.1   7.6e+03      27      43 ..      63      82 ..      55      98 .. 0.65
   2 ?   -4.1   0.0       3.4   1.2e+04     100     121 ..     198     217 ..     186     223 .. 0.60
   3 !  175.4   0.0   1.8e-55   6.4e-52       1     153 []     405     554 ..     405     554 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.1
                                      TS-TTTHHHHHHHHHH...H CS
                      TPP_enzyme_C 27 lgtmGyglpaAiGakl...a 43
                                      + tm  + +aA++a +    
  gi|313126473|ref|YP_004036743.1| 63 HITMAHEQGAAHAADAfgvV 82
                                      78888888888888765431 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.4
                                       TTTSBB.BS----HHHHHHHTT CS
                      TPP_enzyme_C 100 ksgpagkdlkpvdfaklaealG 121
                                         +++   ++++d a++a a+ 
  gi|313126473|ref|YP_004036743.1| 198 PKTTT--PQTEPDEAAVANAAR 217
                                       33333..256667777777764 PP

  == domain 3  score: 175.4 bits;  conditional E-value: 1.8e-55
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHST.TSEEEEEEEHHHHHHTGGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakp.drevvaivGDGgflmilqelatavrrnlpit 76 
                                       ++G++++waa+++ +++p+++++s glgtmGyglpaAiGa la++ d+evv+i GDG+flm++qel+ avr+ l+it
  gi|313126473|ref|YP_004036743.1| 405 GVGQHQMWAAQYWTFTEPQTWVSSHGLGTMGYGLPAAIGARLAAEdDQEVVCIDGDGSFLMTIQELSVAVREELDIT 481
                                       69****************************************755389***************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       v vlnNe+ gm++++q+ f+++r+++ ++     + f klaea+Ga+g rv+++  +e+++a++ea+e +gp++i++
  gi|313126473|ref|YP_004036743.1| 482 VAVLNNEYIGMVRQWQDAFFEGRRMAAQY--NWCPEFDKLAEAFGARGWRVDDY--DEVADAIEEAIEYDGPSVIDF 554
                                       **************************886..66668******************..*******************95 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.0   0.4   1.1e-50   4.1e-47       2     170 ..      24     190 ..      23     192 .. 0.98
   2 ?   -0.4   0.0      0.21   7.4e+02     119     159 ..     519     554 ..     498     560 .. 0.68

  Alignments for each domain:
  == domain 1  score: 160.0 bits;  conditional E-value: 1.1e-50
                                       EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHH CS
                      TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatn 78 
                                       t+a a+vraL+++gve +fgv G+ i+p++dal +++ ir++++ hEqgaa+aAd++  + ++pgv+l+tsgpGatn
  gi|313126473|ref|YP_004036743.1|  24 TGASAVVRALENAGVEAAFGVQGGAIMPVYDALYDSD-IRHITMAHEQGAAHAADAFGVVRNEPGVCLATSGPGATN 99 
                                       899*********************************6.*************************************** PP

                                       CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EE CS
                      TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPv 155
                                       ++t++a+A+ d+  +l+l+g++p+ ++g +++q e+d  ++  p+tk++++ ++++++  ++ +A++ a++grpgP+
  gi|313126473|ref|YP_004036743.1| 100 LVTGIADANMDSDGILALTGQVPSNMVGSDAFQ-ETDTIGVTTPITKHNYFAADSDSVGDTVGEALALADEGRPGPT 175
                                       *********************************.******************************************* PP

                                       EEEEEHHHCC-EEEH CS
                      TPP_enzyme_N 156 ylelpkdvlleevde 170
                                       +++lpkdv l e+d 
  gi|313126473|ref|YP_004036743.1| 176 LVDLPKDVTLGETDR 190
                                       **********99986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.21
                                       HHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEE CS
                      TPP_enzyme_N 119 lfrpvtkyaervtspeelpealrrAirtalsgrpgPvylel 159
                                       l++ +    +rv++ +e++ a+++Ai+       gP ++++
  gi|313126473|ref|YP_004036743.1| 519 LAEAFGARGWRVDDYDEVADAIEEAIE-----YDGPSVIDF 554
                                       555666667777777777777777665.....346666655 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.0   0.1   5.3e-49   1.9e-45       1     137 []     212     347 ..     212     347 .. 0.98
   2 ?   -3.9   0.0         3   1.1e+04      99     115 ..     543     560 ..     527     560 .. 0.55

  Alignments for each domain:
  == domain 1  score: 154.0 bits;  conditional E-value: 5.3e-49
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       ++ aa +++ a+rp++l+Gggv+ ++a+ee+r++a ++giPvvtt+ g g++ped++l+l  +g+hg+ +an+a+ +
  gi|313126473|ref|YP_004036743.1| 212 VANAARAIEMAERPLLLLGGGVIKADATEEARAFAHEYGIPVVTTMPGIGSFPEDDDLCLSWAGMHGTGYANMAITH 288
                                       5789************************************************************************* PP

                                       -SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                       +Dl++a+G+rfdd r tg  ++fapea++ihididpaei+kn ++d+++vgd++++l++L
  gi|313126473|ref|YP_004036743.1| 289 TDLLIAVGTRFDD-RLTGGIDTFAPEAEVIHIDIDPAEISKNIHADYPVVGDAATALRQL 347
                                       *************.77888999************************************98 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3
                                       TTTTT-.EEEEEESSCCC CS
                      TPP_enzyme_M  99 efapea.kiihididpae 115
                                       ++  ++  +i ++idpae
  gi|313126473|ref|YP_004036743.1| 543 AIEYDGpSVIDFHIDPAE 560
                                       333334578999999886 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.5e-06    0.0088      21      70 ..     208     257 ..     189     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-06
                                       EE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEET CS
                             CO_dh  21 leealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvata 70 
                                        e a+  +a++i  a+rPll++G+ v ka   e+      e  ++vv t 
  gi|313126473|ref|YP_004036743.1| 208 DEAAVANAARAIEMAERPLLLLGGGVIKADATEEARAFAHEYGIPVVTTM 257
                                       45667789**********************999999999999****9996 PP

>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.9e-05      0.35      52     131 ..     209     289 ..     201     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.9e-05
                                       HHHHHHHHHHGGGSTTEEEEEEESSB--THHHHHHHHHHHT.T-EEEE.ES-BSSHHHHSSEEESSHHHHHH.HHHH CS
                           DUF5612  52 eeelaeaveavsrlprvkvlvlaGslmGGkiteavkklkeekdiivis.lnmaGsvtevadlvvtdpvqaGv.lavm 126
                                       e ++a+a +a++  +r  +l+l G+++  + te+ +   +e +i+v++ +  +Gs +e  dl ++   + G+  a m
  gi|313126473|ref|YP_004036743.1| 209 EAAVANAARAIEMAERP-LLLLGGGVIKADATEEARAFAHEYGIPVVTtMPGIGSFPEDDDLCLSWAGMHGTgYANM 284
                                       78899******999985.7889**********************9986256689********998765555436777 PP

                                       HH-TT CS
                           DUF5612 127 avadt 131
                                       a+++t
  gi|313126473|ref|YP_004036743.1| 285 AITHT 289
                                       77665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 3365.66
//
Query:       gi|313126474|ref|YP_004036744.1|  [L=226]
Description: acetolactate synthase small subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-21   75.5   0.0    5.2e-21   74.6   0.0    1.5  1  ALS_ss_C  Small subunit of acetolactate synthase
    1.8e-15   56.5   0.0    5.3e-15   55.0   0.0    1.8  2  ACT_5     ACT domain
    3.7e-11   42.6   0.1      1e-10   41.2   0.0    1.8  2  ACT       ACT domain
     0.0014   19.2   0.0     0.0026   18.3   0.0    1.4  1  ACT_4     ACT domain
     0.0055   16.7   0.0       0.01   15.8   0.0    1.4  1  ACT_6     ACT domain
  ------ inclusion threshold ------
        0.2   11.5   0.0       0.38   10.6   0.0    1.4  1  WIYLD     Ubiquitin-binding WIYLD domain


Domain annotation for each model (and alignments):
>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   1.8e-24   5.2e-21       2      74 .]     132     202 ..     131     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.8e-24
                                       EEEEEEEE.-SCHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                          ALS_ss_C   2 ElaLiKVkaekeerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                       El+L+KV+ ++   +++ +i+e++++k++d +p +++++ltg+e+kid+ i+++++fgi+e++RtG++Al+RG
  gi|313126474|ref|YP_004036744.1| 132 ELVLLKVRGDE--PDKVHAITEMYEGKTLDAGPRTITVQLTGNEQKIDDAIDAFRQFGIIEIARTGQTALARG 202
                                       9********77..667********************************************************8 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   1.8e-18   5.3e-15       2      62 .]      60     121 ..      59     121 .. 0.95
   2 ?   -2.0   0.0       1.1   3.3e+03      27      44 ..     156     174 ..     148     180 .. 0.59

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.8e-18
                             ACT_5   2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62 
                                       +pgvL Rv ++v+rr F+++sl++ +t+ +g++ri+++Ve+  + ++++ +Ql+KL  V++V
  gi|313126474|ref|YP_004036744.1|  60 DPGVLSRVSGLVSRRQFNIESLTVGPTTVDGHSRITMVVEEpAPGIDQIEKQLSKLKPVISV 121
                                       8*******************************************************877765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                             ACT_5  27 ttedggtvrieltVes.er 44 
                                       +t d+g+ +i+++ ++ e 
  gi|313126474|ref|YP_004036744.1| 156 KTLDAGPRTITVQLTGnEQ 174
                                       5556666667776666444 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   3.4e-14     1e-10       2      65 ..      52     115 ..      51     117 .. 0.96
   2 ?   -3.4   0.0       2.9   8.8e+03      46      64 ..     167     185 ..     162     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 3.4e-14
                                       EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                       v++ +v++ PG+L+rv+g++++r++Ni+s++++++   + +++++v+++ + ++++++++l kl
  gi|313126474|ref|YP_004036744.1|  52 VISALVENDPGVLSRVSGLVSRRQFNIESLTVGPTTVDGHSRITMVVEEPAPGIDQIEKQLSKL 115
                                       78999********************************************************998 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.9
                                       EEEEEEHHHHHHHHHHHHT CS
                               ACT  46 vvivvdeedleevlealkk 64 
                                       v ++++e+ ++++++a+++
  gi|313126474|ref|YP_004036744.1| 167 VQLTGNEQKIDDAIDAFRQ 185
                                       5566778888888887765 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.7e-07    0.0026       7      78 ..      51     121 ..      47     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.7e-07
                             ACT_4   7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78 
                                       + ++  +e+++g+L++++ ++s  + ni+s+++  +  dg  +i++ ve + +  ++++ ++L +++ VisV
  gi|313126474|ref|YP_004036744.1|  51 AVISALVENDPGVLSRVSGLVSRRQFNIESLTVGPTTVDGHSRITMVVE-EPAPGIDQIEKQLSKLKPVISV 121
                                       679999*****************************999****9999998.4555666666666666666666 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.4e-06      0.01       3      65 ..      51     115 ..      49     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-06
                             ACT_6   3 llitvtGpdrpGltasLtsvlaefgvni..lDieqavihgrlsLgllvsgpedalarlekaLlfl 65 
                                        +i+++ ++ pG+++++++++++ + ni  l+++  ++ g+  ++++v+ p+  + ++ek+L++l
  gi|313126474|ref|YP_004036744.1|  51 AVISALVENDPGVLSRVSGLVSRRQFNIesLTVGPTTVDGHSRITMVVEEPAPGIDQIEKQLSKL 115
                                       6899999**************98666664478999***************************986 PP

>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.38       4      20 ..     172     188 ..     170     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                             WIYLD   4 gkeRidaAidamkelGf 20 
                                       ++++id Aida++++G+
  gi|313126474|ref|YP_004036744.1| 172 NEQKIDDAIDAFRQFGI 188
                                       5799************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1363.88
//
Query:       gi|313126475|ref|YP_004036745.1|  [L=347]
Description: ketol-acid reductoisomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-71  236.8   0.1    1.2e-70  236.4   0.1    1.2  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    7.8e-64  214.3   0.2    1.1e-63  213.8   0.2    1.2  1  IlvC            Acetohydroxy acid isomeroreductase, catalytic
    3.7e-09   37.0   0.1    7.3e-09   36.1   0.1    1.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    7.3e-08   32.0   0.0    1.3e-07   31.1   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    5.3e-06   26.7   0.0      1e-05   25.7   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0023   17.6   0.0      0.004   16.8   0.0    1.5  1  ApbA            Ketopantoate reductase PanE/ApbA
     0.0073   16.4   0.0      0.014   15.4   0.0    1.4  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
  ------ inclusion threshold ------
      0.011   16.0   0.3      0.029   14.7   0.3    1.6  1  Mur_ligase      Mur ligase family, catalytic domain
      0.015   15.7   0.4       0.25   11.8   0.1    2.7  3  NAD_binding_7   Putative NAD(P)-binding
       0.03   14.8   1.3       0.28   11.7   0.5    2.5  2  CoA_binding_2   CoA binding domain
       0.05   14.4   0.1      0.092   13.6   0.1    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
       0.05   13.6   0.3       0.94    9.4   0.3    2.3  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.085   12.7   0.5       0.14   12.0   0.5    1.3  1  Rossmann-like   Rossmann-like domain
      0.091   12.6   1.5       0.15   11.9   0.5    1.9  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.13   11.0   0.4       0.15   10.8   0.4    1.3  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.4   0.1     1e-73   1.2e-70       2     165 .]      21     183 ..      20     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: 236.4 bits;  conditional E-value: 1e-73
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       +++k++av+GyGsqGha+a+nl dsg+dvvvglre+s+s + Ak++g++v+t  ea+++ad+v +l+PD++q +v+ 
  gi|313126475|ref|YP_004036745.1|  21 IDDKTVAVLGYGSQGHAHAQNLADSGVDVVVGLRESSSSRAAAKDDGLRVATPVEAAAEADIVSVLVPDTVQPAVF- 96 
                                       789*************************************************************************. PP

                                       HHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHH CS
                              IlvN  79 eeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalay 155
                                       eei+++l++g++l+fahGfnih+++i+pp+dvdv++vAPk+pGhlvr++y++ +G+p liav+qd++g+a++ alay
  gi|313126475|ref|YP_004036745.1|  97 EEIRDELDAGDTLQFAHGFNIHYNQIRPPEDVDVTMVAPKSPGHLVRRNYQSDEGTPGLIAVYQDETGDARDEALAY 173
                                       99*************************************************************************** PP

                                       HHHTTHHHH- CS
                              IlvN 156 akgiGatraG 165
                                       a++iG+traG
  gi|313126475|ref|YP_004036745.1| 174 AHAIGCTRAG 183
                                       *********9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.8   0.2   9.2e-67   1.1e-63       1     144 []     189     332 ..     189     332 .. 0.99

  Alignments for each domain:
  == domain 1  score: 213.8 bits;  conditional E-value: 9.2e-67
                                       HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                              IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                       F+eEtetDlfgEqavLcGgv++lv+ g+etlv+aGyspe+Ayfecl+elklivdl+yegG+ +m++s+Sdtaeyg+l
  gi|313126475|ref|YP_004036745.1| 189 FQEETETDLFGEQAVLCGGVTSLVKQGYETLVDAGYSPEMAYFECLNELKLIVDLMYEGGLGEMWHSVSDTAEYGGL 265
                                       99*************************************************************************** PP

                                       HHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCHTT CS
                              IlvC  78 tagprviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralmpw 144
                                       t+g+rv++e+++e+m+eilee+q+G+fa+e+i+en+agrp++++l+++e++h+ie+vg+ lr+l+ w
  gi|313126475|ref|YP_004036745.1| 266 TRGDRVVDEHARENMEEILEEVQNGTFAREWIAENQAGRPSYTQLKDREENHHIEQVGEPLRDLFAW 332
                                       ***************************************************************9987 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   6.1e-12   7.3e-09       2      88 ..      26     106 ..      25     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 6.1e-12
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevl 78 
                                       ++++G+G++g+a a++l+ +g    ++vv+  r+ ++ +++a++ g +v +    eaa+ead+v + v+ ++ ++v 
  gi|313126475|ref|YP_004036745.1|  26 VAVLGYGSQGHAHAQNLADSG---VDVVVG-LRESSSSRAAAKDDGLRVAT--PVEAAAEADIVSVLVPDTVQPAVF 96 
                                       89*******************...****88.88888899999999988888..8999999***************** PP

                                       HHCGHHHHTT CS
                     F420_oxidored  79 selakdalkg 88 
                                       +e+++++++g
  gi|313126475|ref|YP_004036745.1|  97 EEIRDELDAG 106
                                       ***8877766 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.1e-10   1.3e-07      27     102 ..      14      90 ..       2      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.1e-10
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S--S CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlplt 102
                                       ++   + + +ktv+++G+G+ G+a a+ l+  g++v++  r  ++++ ++++ g+++++  e+ ae+Divs+ +p t
  gi|313126475|ref|YP_004036745.1|  14 EDADRTHIDDKTVAVLGYGSQGHAHAQNLADSGVDVVVGLRESSSSRaAAKDDGLRVATPVEAAAEADIVSVLVPDT 90 
                                       556677899*************************98877776665555899999********************977 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   8.7e-09     1e-05       2      86 ..      26     109 ..      25     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.7e-09
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglle 78 
                                       ++++G G  G+  a+nl+++g +v+v  r++++ ++++++    ++++ e++a++d+v ++v+++ +  +v e++ +
  gi|313126475|ref|YP_004036745.1|  26 VAVLGYGSQGHAHAQNLADSGVDVVVGLRESSSSRAAAKDDGLRVATPVEAAAEADIVSVLVPDTVQ-PAVFEEIRD 101
                                       89*******************************99999999999999999*************9544.567777999 PP

                                       C--TT-EE CS
                     NAD_binding_2  79 alkkgdil 86 
                                       +l++gd+l
  gi|313126475|ref|YP_004036745.1| 102 ELDAGDTL 109
                                       99999875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.3e-06     0.004       1      48 [.      26      78 ..      26     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.3e-06
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEEETT...C CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrltseg...g 48
                                      +a+lG G++G   a +La  g dv++ lr+     a  k++Glr+ ++     
  gi|313126475|ref|YP_004036745.1| 26 VAVLGYGSQGHAHAQNLADSGVDVVVGLRESsSSRAaAKDDGLRVATPVeaaA 78
                                      69***************************999888889*******99985542 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.014      21      83 ..      21      84 ..      14     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                      -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHH.CTT-EE--HHHCTTT-SEEE CS
                     AdoHcyase_NAD 21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaa.meGfevvtleevvkkadivv 83
                                      +  k++ v GyG  G   a+ l   G  v+v   +  ++  aa  +G++v+t  e++++adiv 
  gi|313126475|ref|YP_004036745.1| 21 IDDKTVAVLGYGSQGHAHAQNLADSGVDVVVGLRESSSSRAAAkDDGLRVATPVEAAAEADIVS 84
                                      7789**************************9988777766555168***************974 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   2.5e-05     0.029      18      81 ..      25      78 ..      22      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                                      HHHHTTSEEEEEESSHCHHHTT-EEEES-HGGGGEE-TS-TTCHHHHHHHHTTEEEEEHHHHHH CS
                        Mur_ligase 18 flalkGykvdGsdfieslialGaaavvghdaanivvssiskdnpeleaakepgipvesraeaLa 81
                                       +a  Gy  +G+ ++++l ++G+ +vvg +++              +aak+ g++v  + ea a
  gi|313126475|ref|YP_004036745.1| 25 TVAVLGYGSQGHAHAQNLADSGVDVVVGLRES----------SSSRAAAKDDGLRVATPVEAAA 78
                                      57999***************************..........7888888888888876666655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00021      0.25       4      54 ..      20      67 ..      18     110 .. 0.65
   2 ?   -0.5   0.0       1.4   1.7e+03      30      50 ..     127     158 ..     123     205 .. 0.60
   3 ?    0.2   0.0      0.86     1e+03      66      94 ..     307     335 ..     269     345 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                     NAD_binding_7  4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee 54
                                      ++++k+v v G G+ +   +++l+++g +v+v   e    ++++  ++++ 
  gi|313126475|ref|YP_004036745.1| 20 HIDDKTVAVLGYGSQGHAHAQNLADSGVDVVVGLRE---SSSSRAAAKDDG 67
                                      789****************************96555...333323333222 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                     NAD_binding_7  30 gakvtvvapev.......keele......elvkl 50 
                                       + +vt+vap++       ++  +      +l+ +
  gi|313126475|ref|YP_004036745.1| 127 DVDVTMVAPKSpghlvrrNY--QsdegtpGLIAV 158
                                       67899999996544443311..022344444444 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.86
                     NAD_binding_7  66 iaatddrelneriaeaakarrilvnvadk 94 
                                       ++  +dre+n++i +  +  r l+  ad+
  gi|313126475|ref|YP_004036745.1| 307 YTQLKDREENHHIEQVGEPLRDLFAWADE 335
                                       56778999999999988777777777775 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   0.00024      0.28       1      77 [.      24     101 ..      24     108 .. 0.74
   2 ?    0.8   0.0      0.55   6.6e+02      27      62 ..     127     159 ..     107     202 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                       --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-.......SEETTEES----T....T--EEEE-S-HHHHGG CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpke.......eeilgekvyaslaedpepvdlvdvftppeatpe 70 
                                       +t+aV+G     g+ g+  +++l ++g++vv V  +e        + +g +v   +++   + d+v+v++p +++p+
  gi|313126475|ref|YP_004036745.1|  24 KTVAVLG----YGSQGHAHAQNLADSGVDVV-VGLREssssraaAKDDGLRVATPVEA-AAEADIVSVLVPDTVQPA 94 
                                       6899999....6777999999****997765.55665445444444455557777774.689*************** PP

                                       GHHHHHH CS
                     CoA_binding_2  71 ivkeala 77 
                                       + +e+ +
  gi|313126475|ref|YP_004036745.1|  95 VFEEIRD 101
                                       ****954 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.55
                                       T--EEEESSS-SEETTEES----T....T--EEEE- CS
                     CoA_binding_2  27 glpvvpVnpkeeeilgekvyaslaedpepvdlvdvf 62 
                                       +++v++V pk++  l +++y+s +   +++ l+ v+
  gi|313126475|ref|YP_004036745.1| 127 DVDVTMVAPKSPGHLVRRNYQSDE---GTPGLIAVY 159
                                       567777888877777777777766...455555554 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.7e-05     0.092       2      77 ..      25      94 ..      24     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.7e-05
                                      EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngthee 77
                                       va+ G+G  g  h+++l +s     vv+l +++++ra   a+  g+ + + +e+ ++   +d+v+v +p + + +
  gi|313126475|ref|YP_004036745.1| 25 TVAVLGYGSQGHAHAQNLADS-GVDVVVGLRESSSSRAA--AKDDGLRVATPVEAAAE---ADIVSVLVPDTVQPA 94
                                      599************999999.77788888888887766..89*****9999999998...9********976655 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3   0.00079      0.94       2      32 ..      26      56 ..      25     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00079
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-H CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvree 32
                                      +avlG Gs G a A+ la+ g +v++  re+
  gi|313126475|ref|YP_004036745.1| 26 VAVLGYGSQGHAHAQNLADSGVDVVVGLRES 56
                                      9********************9998866665 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   0.00012      0.14      12      90 ..      25     101 ..      15     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                     Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdaelpglvkgl 88 
                                       +v +++ G  G a ++ l+ +g  v  +  + ++s  ra ++  +  v++  + aa+a+++ + vPd+  p + +++
  gi|313126475|ref|YP_004036745.1|  25 TVAVLGYGSQGHAHAQNLADSGVDV--VVGLRESSSSRAAAKDDGLRVATPVEAAAEADIVSVLVPDTVQPAVFEEI 99 
                                       5788899999999999998777554..4556667777788888999999999****************999999887 PP

                     Rossmann-like  89 aa 90 
                                         
  gi|313126475|ref|YP_004036745.1| 100 RD 101
                                       65 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   0.00013      0.15       1      33 [.      25      57 ..      25      83 .. 0.81
   2 ?   -1.3   0.0       1.5   1.8e+03      65      90 ..      66      91 ..      52     104 .. 0.68
   3 ?   -3.6   0.0       7.2   8.6e+03      38      49 ..     276     287 ..     260     319 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdisee 33
                                      +vav+G G  G+  a+ +a +g++Vv+  ++++
  gi|313126475|ref|YP_004036745.1| 25 TVAVLGYGSQGHAHAQNLADSGVDVVVGLRESS 57
                                      69***********************98655444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                                      HCEEEES-HHHHHC-SEEEE-S-SSH CS
                           3HCDH_N 65 arisfttdleeavdadlviEavvEnl 90
                                      + ++++t +e+a++ad+v   v++ +
  gi|313126475|ref|YP_004036745.1| 66 DGLRVATPVEAAAEADIVSVLVPDTV 91
                                      55677788888888888877776654 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 7.2
                                       HHHHHHHHHHCC CS
                           3HCDH_N  38 alekiekslekl 49 
                                       a+e++e+ le++
  gi|313126475|ref|YP_004036745.1| 276 ARENMEEILEEV 287
                                       333333333332 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   0.00012      0.15     265     311 ..      17      62 ..       9     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                       HHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHH CS
                    Oxidored_nitro 265 dyheylagkrvaiygdpdrvvalarllkelGmevvaagtetahrdde 311
                                       d + ++  k+va+ g++++ +a a+ l++ G++vv+ + e+++++  
  gi|313126475|ref|YP_004036745.1|  17 D-RTHIDDKTVAVLGYGSQGHAHAQNLADSGVDVVVGLRESSSSRAA 62 
                                       4.678899***************************988877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2137.00
//
Query:       gi|313126476|ref|YP_004036746.1|  [L=94]
Description: hypothetical protein Hbor_17330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 604.29
//
Query:       gi|313126477|ref|YP_004036747.1|  [L=473]
Description: 3-isopropylmalate dehydratase large subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   5.3e-147  490.5   0.0     6e-147  490.4   0.0    1.0  1  Aconitase  Aconitase family (aconitate hydratase)
    0.00023   20.0   0.0    0.00038   19.3   0.0    1.3  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  490.4   0.0  6.7e-151    6e-147       1     461 []       8     459 ..       8     459 .. 0.94

  Alignments for each domain:
  == domain 1  score: 490.4 bits;  conditional E-value: 6.7e-151
                         Aconitase   1 ekiwdahlvee..eg..iayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeeale 73 
                                       +k+wd+h+v++   g  +++v   +l+++vt++qa+  l++++ +v+ +++t at+dh vp++   d+s        
  gi|313126477|ref|YP_004036747.1|   8 DKVWDNHTVTQlpTGqtQLFV-GLHLIHEVTSPQAFGMLRERGMDVAFPDRTHATVDHIVPTS---DQSR------- 73 
                                       69*****99777734335666.*****************************************...6665....... PP

                         Aconitase  74 knledefernkeryefLksaakafgirvvppg...qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGg 147
                                          +d  ++  e+++ L+++ ++ gi++ +p    qGIvH++++E+g+++pg+t+v++DSHT+++g++G+la+G+G+
  gi|313126477|ref|YP_004036747.1|  74 -PYTDDAAE--EMMSELEENVRDAGIDFSDPTtgdQGIVHVIGPEQGITQPGTTIVCGDSHTSTHGAFGALAFGIGT 147
                                       .56666666..99******************9999****************************************** PP

                         Aconitase 148 ieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMa 224
                                       +++ +vl++ ++ +++ kv ++++tG+l+egv+akD++l++i++l+++g+vg+v E++Ge++e+L +e+r++i+NM+
  gi|313126477|ref|YP_004036747.1| 148 SQIRDVLATGCIAMEKQKVRKIEVTGELGEGVEAKDVILEIIRRLGTDGGVGYVYEYAGEAIENLGMEGRMSICNMS 224
                                       ***************************************************************************** PP

                         Aconitase 225 aEvGAttglfpvdektleYLkatgreeaavlveaydkaqalf.elaadedaeydkvleldlstlepsvagpkrPqda 300
                                       +E GA++g++++de+t+e+L+ t+  ++    e++++ + ++ ++++dedaeyd+v+++d ++lep v+++++P + 
  gi|313126477|ref|YP_004036747.1| 225 IEGGARAGYVNPDETTFEWLEETDEFADD--PEKFERLKPYWeSVQSDEDAEYDDVVTIDGDELEPVVTWGTTPGQG 299
                                       *********************77764444..6**********7799******************************* PP

                         Aconitase 301 vplselvk.k.efkeelekeaaekaley.klkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkp 374
                                       v ++e ++ + e+ e+  +++a++a e+ + ++g +++  ++d+a++gSCTN+++ d+r+aa+l++     g++v++
  gi|313126477|ref|YP_004036747.1| 300 VGITEPIPaPeELPEDK-QDTARRAQEHmRVTPGETMEGYPIDVAFLGSCTNARLADLRRAARLVK-----GRQVHE 370
                                       *******9754566655.55556666656999**********************************.....****** PP

                         Aconitase 375 gvktsvaPGSevvkayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLa 449
                                       +v+++v+PGS++v+  +e+eGl +i+e+aGfe+++agCs+C+g n+d+le +ea++sssNRNF gRqg +++r+ L+
  gi|313126477|ref|YP_004036747.1| 371 DVRAMVVPGSQRVQTAAEEEGLKDIFEEAGFEWRNAGCSMCLGmNEDQLEGDEACASSSNRNFVGRQGsKDGRTVLM 447
                                       *******************************************************************879******* PP

                         Aconitase 450 SPelvvaaAlaG 461
                                        P +v+aaA++G
  gi|313126477|ref|YP_004036747.1| 448 NPRMVAAAAING 459
                                       **********98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.2e-08   0.00038     283     360 ..     330     411 ..     293     432 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.2e-08
                            DUF521 283 l..skakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvtt.srevkeeaerlglveklekaGvkvlsd 355
                                       +  ++ +  ++d+ +lG c  + l +lr+ a+l+kg++++++v+ +v+  s+ v+ +ae++gl ++ e+aG +  + 
  gi|313126477|ref|YP_004036747.1| 330 TpgETMEGYPIDVAFLGsCTNARLADLRRAARLVKGRQVHEDVRAMVVPgSQRVQTAAEEEGLKDIFEEAGFEWRNA 406
                                       13445788899****997899********************9987777615669******************99988 PP

                            DUF521 356 tCmvv 360
                                        C ++
  gi|313126477|ref|YP_004036747.1| 407 GCSMC 411
                                       88655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3528.50
//
Query:       gi|313126478|ref|YP_004036748.1|  [L=204]
Description: 3-isopropylmalate dehydratase small subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.4e-19   68.0   0.0    1.3e-18   67.5   0.0    1.2  1  Aconitase_C  Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0   7.5e-23   1.3e-18      14     128 ..      18     124 ..       6     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 7.5e-23
                                       HHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--SSBTBS--- CS
                       Aconitase_C  14 deksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagknfGeGSSR 90 
                                          + +dtd++ip  f + ++  glg+  + + r++++++      +d + ++ r+k  +++++v+   nfG+GSSR
  gi|313126478|ref|YP_004036748.1|  18 IRGNDIDTDQIIPARFMKVVTFDGLGQFAFFDLRFDDDDEP-----KDHPMNEDRFK--DSSVMVVN-ANFGCGSSR 86 
                                       55667899999999999999999999999998888877664.....47788******..66777776.7******** PP

                                       THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEE CS
                       Aconitase_C  91 ehAAkalrllGikaviaeSFerIfennliknglLplef 128
                                       ehA+ al   Gi a+i eSF++If  n +  g+ +++ 
  gi|313126478|ref|YP_004036748.1|  87 EHAPQALMRWGIDAIIGESFAEIFAGNCLALGIPTVTA 124
                                       ****************************9999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1291.43
//
Query:       gi|313126479|ref|YP_004036749.1|  [L=325]
Description: 3-isopropylmalate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-85  287.5   0.0    1.6e-85  287.3   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.3   0.0   8.8e-90   1.6e-85       1     344 [.       4     320 ..       4     324 .. 0.94

  Alignments for each domain:
  == domain 1  score: 287.3 bits;  conditional E-value: 8.8e-90
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSS CS
                            Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkek 77 
                                       +i+++egdgiG evv+aa++vlka+      ++ef e+d+G a+  etge+lp+et +a+ +ad+ l+ga g     
  gi|313126479|ref|YP_004036749.1|   4 QIVVVEGDGIGAEVVPAAVDVLKAVG-----DFEFVEADAGDAVKAETGEALPQETYDAVADADATLFGAAGETA-- 73 
                                       599**********************9.....79*************************************98877.. PP

                                       SSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEE CS
                            Iso_dh  78 evrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdt 154
                                              +l Lr+ +d f+n+rp+k ++       l++    e+dlv +Re+t+g+Y+g+e   ++          t
  gi|313126479|ref|YP_004036749.1|  74 ----ADVILPLREAVDSFVNVRPAKAYPG---VDALRP----ETDLVFLRENTEGVYSGHEDRLSDD-----LSTLT 134
                                       ....55699******************53...445665....58*****************999997.....68899 PP

                                       EEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGG CS
                            Iso_dh 155 klyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvkspk 230
                                        +++++++e++a++a++    +   +  + +Kanv++ ++ ++r+++  va+    ++e+e++l+D++a ++  +p+
  gi|313126479|ref|YP_004036749.1| 135 RVVTTSASEQLAEYACDFVGGE-GGSFQIAHKANVMRETDgRFRDTIVSVAD--KRGVEVEEVLMDAFATRVCLDPT 208
                                       *******************999.99*************************99..789******************** PP

                                       GGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT- CS
                            Iso_dh 231 qfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgl 307
                                       qfd iv++Nl GD+lSD+aa lvG+lGllpSa++g+   a+fE+vHG+apdiag ++aNp+a+ilSaa++L++ lg 
  gi|313126479|ref|YP_004036749.1| 209 QFDTIVCPNLAGDVLSDLAAGLVGGLGLLPSANIGP-DNALFEPVHGTAPDIAGEGIANPSATILSAAMLLEH-LGY 283
                                       ***********************************7.59**********************************.*** PP

                                       HHHHHHHHHHHHHHHHHTSCCHHHCTTSTCCCHHHHH CS
                            Iso_dh 308 eeaAdkiekAvekvleagivTkDlageaakevstsef 344
                                       +++ +++ +Ave++l++g +T Dl+g aa+e  t+++
  gi|313126479|ref|YP_004036749.1| 284 DDEGAAVREAVESTLAEGPCTPDLGGDAATEDVTKAI 320
                                       ****************************666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2210.81
//
Query:       gi|313126480|ref|YP_004036750.1|  [L=255]
Description: transcriptional regulator, deor family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-51  171.9   0.1    1.2e-50  171.5   0.1    1.1  1  DeoRC           DeoR C terminal sensor domain
    1.6e-15   56.6   0.2    2.8e-15   55.8   0.2    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    3.5e-07   30.2   0.2    8.7e-07   28.9   0.2    1.6  1  HTH_20          Helix-turn-helix domain
      9e-07   28.4   1.4    3.1e-06   26.6   0.3    2.4  2  HTH_24          Winged helix-turn-helix DNA-binding
      1e-06   28.5   0.3    2.3e-06   27.4   0.3    1.5  1  MarR_2          MarR family
    1.4e-06   28.2   0.0    2.5e-06   27.3   0.0    1.4  1  HTH_11          HTH domain
    3.4e-06   26.8   0.0    5.2e-06   26.2   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
    1.5e-05   24.5   0.1    3.2e-05   23.5   0.1    1.5  1  GntR            Bacterial regulatory proteins, gntR family
    0.00011   22.1   0.0     0.0002   21.2   0.0    1.4  1  MarR            MarR family
     0.0003   20.5   0.1    0.00055   19.7   0.1    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    0.00033   20.5   0.0    0.00076   19.3   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00065   19.6   0.0     0.0013   18.7   0.0    1.5  1  HTH_36          Helix-turn-helix domain
    0.00071   19.5   0.0     0.0014   18.6   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0022   17.5   1.5      0.033   13.7   0.2    2.5  2  Sigma70_r4      Sigma-70, region 4
     0.0032   17.2   0.4     0.0078   16.0   0.1    1.8  2  HTH_23          Homeodomain-like domain
      0.004   17.1   0.1      0.017   15.0   0.0    2.1  2  HTH_12          Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.021   13.2   0.0       0.03   12.7   0.0    1.1  1  DUF505          Protein of unknown function (DUF505)
      0.022   14.5   0.0      0.033   13.9   0.0    1.3  1  DUF4423         Domain of unknown function (DUF4423)
      0.043   13.9   0.3      0.076   13.1   0.3    1.4  1  DprA_WH         DprA winged helix domain
      0.044   13.6   0.1       0.11   12.2   0.0    1.7  1  HTH_38          Helix-turn-helix domain
       0.05   13.9   0.1       0.27   11.6   0.0    2.1  2  HTH_Tnp_1       Transposase
      0.055   13.3   2.3       0.17   11.7   0.3    2.5  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.066   13.3   0.2       0.15   12.2   0.2    1.7  1  HTH_28          Helix-turn-helix domain
      0.086   13.0   0.0       0.15   12.2   0.0    1.3  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.11   12.0   0.1       0.21   11.2   0.1    1.4  1  HTH_CodY        CodY helix-turn-helix domain
       0.13   12.5   0.0       0.24   11.6   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.22   11.6   0.0        0.4   10.8   0.0    1.4  1  BRCT_3          BRCA1 C Terminus (BRCT) domain
       0.34   10.6   1.3         17    5.2   0.1    2.7  2  Sigma70_r4_2    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.5   0.1   1.9e-53   1.2e-50       2     159 ..      75     231 ..      74     232 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.5 bits;  conditional E-value: 1.9e-53
                             DeoRC   2 naeeKrrIAkaAaeliedgdtifldaGtTtlelaraLaekknltvvTnslnvaeeLsekedikvillGGevrkkses 78 
                                       n++ Kr IA++A+e i +g+++f+daGtTt+e+a++ + + ++  vTns ++a eL ++ + +v l+GG++r+++++
  gi|313126480|ref|YP_004036750.1|  75 NIDGKRSIAERAVEEITPGQVVFFDAGTTTMEVAKQAPTDGSVLSVTNSPRLAVELGKE-ENDVKLTGGTLRSRTRA 150
                                       8899*****************************************************98.99*************** PP

                             DeoRC  79 lvgplaeealrqfnvdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKfgkrafvriaaleeida 155
                                       lvgp+ae+++++ n+d++flg+n+ida+ggltt++e+ea++k+ + e+a+rv+l+aD +K+gkr+fv++a+l ++d+
  gi|313126480|ref|YP_004036750.1| 151 LVGPTAESFMERTNFDLLFLGTNAIDADGGLTTPNEDEARMKELMTEKAARVVLVADATKVGKRSFVKFADLGDVDV 227
                                       ***************************************************************************** PP

                             DeoRC 156 litD 159
                                       ++tD
  gi|313126480|ref|YP_004036750.1| 228 FVTD 231
                                       ***9 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.2   4.4e-18   2.8e-15       1      54 [.       6      59 ..       6      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 4.4e-18
                          HTH_DeoR  1 RieqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGavsi 54
                                      R   i+el+  ++  sve l+++lg+S+aTiRRDL+eLe  gl++R hGGav +
  gi|313126480|ref|YP_004036750.1|  6 RKRRIVELVSADDGRSVEGLADELGYSKATIRRDLRELEDRGLIERSHGGAVPV 59
                                      7889***********************************************865 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.2   1.4e-09   8.7e-07      13      57 ..       8      52 ..       5      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.4e-09
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      rri  + + ++g++++ la++l+ sk+t+++ Lr+Le+ gL+e+ 
  gi|313126480|ref|YP_004036750.1|  8 RRIVELVSADDGRSVEGLADELGYSKATIRRDLRELEDRGLIERS 52
                                      8999999************************************85 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.3   4.8e-09   3.1e-06       4      48 .]       6      50 ..       4      50 .. 0.96
   2 ?   -1.0   0.0         2   1.3e+03      27      42 ..     137     152 ..     136     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.8e-09
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       +r+I el+ ++ + s   LA++lg S++t++r l++Le+ GlI+
  gi|313126480|ref|YP_004036750.1|  6 RKRRIVELVSADDGRSVEGLADELGYSKATIRRDLRELEDRGLIE 50
                                      689*****************************************7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2
                            HTH_24  27 lglSpstvnrrlkrLe 42 
                                       + l+ +t++ r + L+
  gi|313126480|ref|YP_004036750.1| 137 VKLTGGTLRSRTRALV 152
                                       68999*******9995 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.3   3.7e-09   2.3e-06       9      56 ..       9      54 ..       6      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.7e-09
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      r+   + + +g   +v  la++lg+sk+++ r l++L+++GL+er+ g
  gi|313126480|ref|YP_004036750.1|  9 RIVELVSADDG--RSVEGLADELGYSKATIRRDLRELEDRGLIERSHG 54
                                      55556667777..5*******************************955 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   3.9e-09   2.5e-06       1      45 [.       6      48 ..       6      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.9e-09
                            HTH_11  1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                      R++ i+el+ +a++  s e LA+eL+ S++t+rrd+++Le+ g  
  gi|313126480|ref|YP_004036750.1|  6 RKRRIVELV-SADDGRSVEGLADELGYSKATIRRDLRELEDRG-L 48
                                      8899*****.555559************************999.3 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   8.2e-09   5.2e-06       3      46 ..       6      50 ..       4      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.2e-09
                                      HHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       +++I+ l++    ++v  la+elg s++t+++ L+ L++ GL+e
  gi|313126480|ref|YP_004036750.1|  6 RKRRIVELVSADDgRSVEGLADELGYSKATIRRDLRELEDRGLIE 50
                                      6899*******666*****************************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1     5e-08   3.2e-05      27      62 ..      22      57 ..      20      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5e-08
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                      ++ La+e+g s+ t+R+ Lr+Le +gl+er +g+++
  gi|313126480|ref|YP_004036750.1| 22 VEGLADELGYSKATIRRDLRELEDRGLIERSHGGAV 57
                                      788******************************987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.1e-07    0.0002      16      51 ..      18      53 ..       7      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.1e-07
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      ++ sv  La+ lg sk+t+ r l++Le++GlieRs+
  gi|313126480|ref|YP_004036750.1| 18 DGRSVEGLADELGYSKATIRRDLRELEDRGLIERSH 53
                                      5668889***************************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   8.6e-07   0.00055       7      50 ..       9      51 ..       4      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.6e-07
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +i +++++ +++ ++  lA+++g +k+t +R L+ L+ +G++e+
  gi|313126480|ref|YP_004036750.1|  9 RIVELVSADDGR-SVEGLADELGYSKATIRRDLRELEDRGLIER 51
                                      677888888888.9999*************************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-06   0.00076      20      58 ..      17      55 ..      11      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       +  +++ +a elg +++++ + Lr+Led+Gl+er++g 
  gi|313126480|ref|YP_004036750.1| 17 DDGRSVEGLADELGYSKATIRRDLRELEDRGLIERSHGG 55
                                      56778999***************************9986 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     2e-06    0.0013      27      55 .]      21      49 ..      12      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-06
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s+e la  lg sk T++r ++eLe+ G+i
  gi|313126480|ref|YP_004036750.1| 21 SVEGLADELGYSKATIRRDLRELEDRGLI 49
                                      8999***********************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.2e-06    0.0014      25      54 ..      23      52 ..      10      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrg 54
                                      e lA+ lG +  t+ r l+eL+++gli+r+
  gi|313126480|ref|YP_004036750.1| 23 EGLADELGYSKATIRRDLRELEDRGLIERS 52
                                      679*************************74 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   5.2e-05     0.033       7      39 ..       5      38 ..       4      43 .. 0.94
   2 ?    2.3   0.1      0.19   1.2e+02       3      13 ..     232     242 ..     232     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-05
                                      HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4  7 ererevlelrf.geglTleEIgerlgiSrerVrq 39
                                      er r+++el+  ++g++ e ++++lg S+ ++r+
  gi|313126480|ref|YP_004036750.1|  5 ERKRRIVELVSaDDGRSVEGLADELGYSKATIRR 38
                                      89*******************************8 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                                       HHS-HHHHHHH CS
                        Sigma70_r4   3 asLpererevl 13 
                                       a+Lp+rer+ +
  gi|313126480|ref|YP_004036750.1| 232 AELPQRERQAF 242
                                       589*****987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.2e-05    0.0078       3      36 ..       3      38 ..       1      50 [. 0.86
   2 ?   -2.5   0.0       7.6   4.9e+03      35      46 ..     236     247 ..     236     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                            HTH_23  3 sereRlrillllae..GlsvreIAreLgvsrrTvyr 36
                                       ++++ ri+ l+    G sv+  A+eLg s+ T++r
  gi|313126480|ref|YP_004036750.1|  3 PAERKRRIVELVSAddGRSVEGLADELGYSKATIRR 38
                                      5789999******778*******************8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.6
                            HTH_23  35 yrwlkryreeGl 46 
                                       +r ++++++eG+
  gi|313126480|ref|YP_004036750.1| 236 QRERQAFENEGV 247
                                       588999988997 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.7e-05     0.017      30      54 ..      31      55 ..      16      66 .. 0.79
   2 ?   -2.2   0.0       6.5   4.1e+03      18      42 ..     125     151 ..     121     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                            HTH_12 30 igeravRyrLrkleergltrrvgya 54
                                      +++ ++R+ Lr le+rgl++r   +
  gi|313126480|ref|YP_004036750.1| 31 YSKATIRRDLRELEDRGLIERSHGG 55
                                      56689***************97655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.5
                            HTH_12  18 eiaeeLkkr..gydigeravRyrLrkl 42 
                                       ++a eL k   + ++   ++R r r+l
  gi|313126480|ref|YP_004036750.1| 125 RLAVELGKEenDVKLTGGTLRSRTRAL 151
                                       567777666234555666777776665 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.6e-05      0.03     481     530 ..      17      65 ..       6      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                            DUF505 481 krgvsveelveevdeleeeevrealeklearglvevlpdgnvvlTeaGel 530
                                       + g sve l +e+ ++ +  +r+ l++le rgl+e    g+v +T +G++
  gi|313126480|ref|YP_004036750.1|  17 DDGRSVEGLADEL-GYSKATIRRDLRELEDRGLIERSHGGAVPVTTVGKE 65 
                                       5688899999999.99********************************96 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.2e-05     0.033      26      81 ..      10      62 ..       8     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                           DUF4423 26 irellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtek 81
                                      i el+++ d+ +++e la+ l+   s++ +++ l+ L++ gl++++  g + +t+ 
  gi|313126480|ref|YP_004036750.1| 10 IVELVSADDG-RSVEGLADELG--YSKATIRRDLRELEDRGLIERSHGGAVPVTTV 62
                                      889*******.***********..**********************9988777764 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   0.00012     0.076      12      61 .]       5      55 ..       2      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                           DprA_WH 12 dlerrvLaaLgp.ePvhvDqLvrrtglpaaevsaaLleLELaGlverlpGg 61
                                      + +rr+++++++ + ++v+ L+ ++g + a++ + L eLE  Gl+er  Gg
  gi|313126480|ref|YP_004036750.1|  5 ERKRRIVELVSAdDGRSVEGLADELGYSKATIRRDLRELEDRGLIERSHGG 55
                                      6789******9856**********************************998 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.11      19      42 ..      18      41 ..       6      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                            HTH_38 19 eGlslreIArrLgrspsTIsRElk 42
                                       G s+   A +Lg+s+ TI R l+
  gi|313126480|ref|YP_004036750.1| 18 DGRSVEGLADELGYSKATIRRDLR 41
                                      68899999*************877 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00041      0.27       8      48 ..       3      44 ..       3      76 .. 0.80
   2 ?   -1.1   0.0       3.8   2.5e+03      20      32 ..      98     110 ..      84     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                         HTH_Tnp_1  8 sdefKariVres.lepgksvsevArrhgvspnqLykWrrqyr 48
                                      ++e K riV+++  + g+sv  +A ++g s+++ ++  r+ +
  gi|313126480|ref|YP_004036750.1|  3 PAERKRRIVELVsADDGRSVEGLADELGYSKATIRRDLRELE 44
                                      6899*******9999******************998666655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.8
                         HTH_Tnp_1  20 lepgksvsevArr 32 
                                       +++g+++ evA++
  gi|313126480|ref|YP_004036750.1|  98 FDAGTTTMEVAKQ 110
                                       6788888888887 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00026      0.17       6      42 .]       8      44 ..       8      44 .. 0.94
   2 ?    0.2   0.1       1.1   6.8e+02      26      41 ..     136     151 ..     123     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      r+I+e+  +d  +s++ LA+++G S +t++r +r Le
  gi|313126480|ref|YP_004036750.1|  8 RRIVELVSADDGRSVEGLADELGYSKATIRRDLRELE 44
                                      89****************************9888776 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                     HTH_AsnC-type  26 rvGlSestvlrRvrrL 41 
                                        v l+  t + R r+L
  gi|313126480|ref|YP_004036750.1| 136 DVKLTGGTLRSRTRAL 151
                                       6899999*****9988 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00024      0.15       1      40 [.       6      47 ..       6      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                            HTH_28  1 qRleiiklla..aGhsvreaArelgisrrtvyrWikryeegG 40
                                      ++++i++l+   +G+sv  +A elg s  t++r ++ +e  G
  gi|313126480|ref|YP_004036750.1|  6 RKRRIVELVSadDGRSVEGLADELGYSKATIRRDLRELEDRG 47
                                      6999****8855589*****************9888877766 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00023      0.15      28      62 ..      25      59 ..       8      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                           DUF2250 28 iakeleipleevrellkkLeelGLlervegktikr 62
                                      +a+el  ++  +r+ l++Le+ GL+er +g ++  
  gi|313126480|ref|YP_004036750.1| 25 LADELGYSKATIRRDLRELEDRGLIERSHGGAVPV 59
                                      578899999*******************9988755 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00033      0.21      10      38 ..      25      52 ..      18      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                          HTH_CodY 10 iaDriGitrsvivnaLrkLesaGiiesrs 38
                                      +aD++G  ++ i   Lr Le  G+ie rs
  gi|313126480|ref|YP_004036750.1| 25 LADELGYSKATIRRDLRELEDRGLIE-RS 52
                                      7************************9.44 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00037      0.24      25      57 ..      22      54 ..      16      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00037
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                      +  la +L+ s++++   l++Le+ G++e ++ 
  gi|313126480|ref|YP_004036750.1| 22 VEGLADELGYSKATIRRDLRELEDRGLIERSHG 54
                                      5679***********************998775 PP

>> BRCT_3  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00063       0.4      24      74 ..     202     251 ..     188     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00063
                            BRCT_3  24 ilklaGaavvkkekseaeeislgkldvvvtdsscpeevlkkaeqlkipvvS 74 
                                       ++ +a a+ v k +  +  ++lg +dv+vtd ++p+  ++  e+ ++ vv+
  gi|313126480|ref|YP_004036750.1| 202 VVLVADATKVGKRSFVKF-ADLGDVDVFVTDAELPQRERQAFENEGVSVVA 251
                                       444444444444333333.58999*************************97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.026        17      13      47 ..       5      40 ..       4      42 .. 0.82
   2 ?    3.4   0.2     0.093        59       9      20 ..     232     243 ..     232     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.026
                                      HHHHHHHHH.HHTS---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 13 erqreifll.ryleglsykEIAellgisegtVksrl 47
                                      er r+i++l ++ +g s +  A +lg s +t+++ l
  gi|313126480|ref|YP_004036750.1|  5 ERKRRIVELvSADDGRSVEGLADELGYSKATIRRDL 40
                                      567777777356689*****************9876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.093
                                       TTS-HHHHHHHH CS
                      Sigma70_r4_2   9 aeLperqreifl 20 
                                       aeLp+r+r++f+
  gi|313126480|ref|YP_004036750.1| 232 AELPQRERQAFE 243
                                       69********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1390.21
//
Query:       gi|313126481|ref|YP_004036751.1|  [L=330]
Description: fructose-bisphosphate aldolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-76  256.5   0.0    3.5e-76  256.4   0.0    1.0  1  F_bP_aldolase  Fructose-bisphosphate aldolase class-II


Domain annotation for each model (and alignments):
>> F_bP_aldolase  Fructose-bisphosphate aldolase class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.4   0.0   1.9e-80   3.5e-76       2     280 .]       8     326 ..       7     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 256.4 bits;  conditional E-value: 1.9e-80
                                       HHHHHHHHHHHHT--EEEEE--SHHHHHHHHHHHHHHTS-EEEEE-HHHHHHHH-......HHHHHHHHHHHHHHHH CS
                     F_bP_aldolase   2 nlkellkkAkeegyavgafnvtnletvkavleaaeeaksPvIlqlsegaaakyag......gaealaelvraaaeay 72 
                                       +l +++++A +eg+++ a n+ + + +++++e+a++++s+++lqls gaa+++ g      g++a+  +++++ae+y
  gi|313126481|ref|YP_004036751.1|   8 ELAKVYDDALDEGFGLIASNIAEPNVMMGLMEGAARENSDLLLQLSGGAATFA-GnedpvsGLKAMGTYIESIAEQY 83 
                                       67899********************************************9666.56*******************66 PP

                                       T...-EEEEEE----GHHHHHHHHHHS-.SEEEE--TTS-HHHHHHHHHHHHHHHHHTT..-EEEEE---------- CS
                     F_bP_aldolase  73 kkasvpvalhlDHgakleglkkaieagf.sSvMiDgSelpleeNialtkevverahalg..vsvEaElGriggeedg 146
                                       +   + v l++DH ++++ +++ ++ g  sS+MiD+S++p+eeN+++++evv++ ++ g  v++EaElG+i+g ed+
  gi|313126481|ref|YP_004036751.1|  84 D---IGVFLNMDHQTDMDFIEAQMDLGIpSSIMIDASHEPFEENVERSREVVQMKEDKGadVLIEAELGQIKGVEDE 157
                                       6...**********************85389************************9977669*************** PP

                                       -TT-TTTS--HHHHHHHHHHHH-EEEE--SS---SS--SS...--THHHHHHHHHH......--SEE-SGTTS-HHH CS
                     F_bP_aldolase 147 vvaeeklyTdpeeaeefveetgvdalAvaiGnvHGvykpk.pkLdferlkeiqkav......vplVlHGgsgvpdee 216
                                       ++aee++yTdpe+a+efv++tg+d+lA+++G+ HGv k k  +L++++ ++i+ a+      +plVlHG+sgv++++
  gi|313126481|ref|YP_004036751.1| 158 IEAEEAFYTDPEQAVEFVDRTGCDLLAISVGTQHGVAKGKdLELRPDLARDIRVALrdhgldTPLVLHGSSGVQPDQ 234
                                       **9**********************************999555********************************** PP

                                       HHHHHHTTEEEEEE-HHHHHHHHHHH....HHG......G.................E-HH.H-HHHHHHHHHHHHH CS
                     F_bP_aldolase 217 irkaiklGvvKiNidtdlrlaytkav....kke......k.................enkk.ydprkllkeaeeamk 265
                                       ++++ ++G++K+N dt+++++yt+++    +++      +                 +nk+ +dpr++ ++ +e+++
  gi|313126481|ref|YP_004036751.1| 235 LQEMLQHGICKVNKDTRYQYEYTRTAfdhyREDpeaivpPegvedardtffnetewsPNKDvFDPRVVGRKIRERIA 311
                                       **************************755433355555505555666667777777799999*************** PP

                                       HHHHHHHHHTT-SS- CS
                     F_bP_aldolase 266 evvkekiellgsagk 280
                                       +v ++  ++ gsa++
  gi|313126481|ref|YP_004036751.1| 312 DVHADLTHVSGSANQ 326
                                       ************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1797.67
//
Query:       gi|313126482|ref|YP_004036752.1|  [L=49]
Description: hypothetical protein Hbor_17390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0011   18.9   1.4      0.014   15.3   0.2    2.1  2  RHH_1         Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.015   16.0   0.3      0.018   15.8   0.3    1.1  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.6e-06     0.014       3      19 ..       3      19 ..       3      20 .. 0.91
   2 ?    2.9   0.1     0.013   1.2e+02       7      18 ..      21      32 ..      21      33 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-06
                                      EEEEEHHHHHHHHHHHH CS
                             RHH_1  3 sirldeellerLdelar 19
                                      +i+ldee+++rLd l+ 
  gi|313126482|ref|YP_004036752.1|  3 QIHLDEETVARLDSLRQ 19
                                      69************986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.013
                                      EHHHHHHHHHHH CS
                             RHH_1  7 deellerLdela 18
                                      de+++e + el+
  gi|313126482|ref|YP_004036752.1| 21 DEDYDEIVTELI 32
                                      89********97 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.3     2e-06     0.018       2      34 ..       3      35 ..       3      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-06
                      VAPB_antitox  2 tIsIsdevYekLkklKregeSFsdvIerLlekk 34
                                      +I +++e+  +L++l++e+e +++++ +L++  
  gi|313126482|ref|YP_004036752.1|  3 QIHLDEETVARLDSLRQEDEDYDEIVTELINIY 35
                                      5999*************************9844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 282.72
//
Query:       gi|313126483|ref|YP_004036753.1|  [L=149]
Description: hypothetical protein Hbor_17400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.14   12.1   0.1         12    6.0   0.0    2.4  3  DASH_Dad4  DASH complex subunit Dad4


Domain annotation for each model (and alignments):
>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.33   5.9e+03      42      66 ..      24      48 ..      17      50 .. 0.64
   2 ?    3.6   0.0    0.0037        66      14      32 ..      53      71 ..      52      79 .. 0.86
   3 ?    6.0   0.0   0.00066        12      42      69 ..     114     141 ..     111     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.33
                         DASH_Dad4 42 knvelvsqlwenYqrnvqfnLeatg 66
                                      +  e++sq w      ++f++e++g
  gi|313126483|ref|YP_004036753.1| 24 AASEFTSQEWGLIMTATEFEIEHAG 48
                                      5556667777767777788777665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0037
                         DASH_Dad4 14 sRIiknvekLnesvvelnk 32
                                      +RI++  ekL + + el++
  gi|313126483|ref|YP_004036753.1| 53 ARIVADTEKLPQIMPELEN 71
                                      6*************99986 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.00066
                         DASH_Dad4  42 knvelvsqlwenYqrnvqfnLeatgelk 69 
                                       ++++ + +l+++Y+  +q +Le+ g+ +
  gi|313126483|ref|YP_004036753.1| 114 EQLAEAEKLVQEYADELQRHLESKGKWE 141
                                       6788899***************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.58
# Mc/sec: 780.13
//
Query:       gi|313126484|ref|YP_004036754.1|  [L=415]
Description: had superfamily hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-11   42.6   0.0    0.00023   21.0   0.0    2.1  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
     0.0059   16.9   1.2       0.48   10.7   0.1    2.7  2  Hydrolase    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.037   14.4   1.6        9.1    6.6   0.2    2.9  2  HAD          haloacid dehalogenase-like hydrolase
       0.16   11.4   0.0       0.35   10.3   0.0    1.5  2  CutC         CutC family


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.4e-07   0.00064       1      47 [.      94     143 ..      94     157 .. 0.90
   2 !   21.0   0.0   5.1e-08   0.00023     165     236 ..     308     383 ..     278     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                                       EEEEIIIIIS-...TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHH CS
                       Hydrolase_3   1 ialDlDGTLln...sdkkisektkeaikklkekgikvviATGRslravlp 47 
                                       ++lD+D TL +    d++i+  t + + +++e+g+ +vi+TG  l++v+ 
  gi|313126484|ref|YP_004036754.1|  94 LVLDVDETLRSagrTDNEIPRDTLHLLTEFHEAGVPIVICTGQTLENVKG 143
                                       589******876768999************************99999875 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 5.1e-08
                                       CTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHS.....SEEEEETTS-HHHH CS
                       Hydrolase_3 165 lnklltitssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaa.....glgvAmgnaseevk 236
                                       + + +++  ++    ei + + +K +++++ +  l+++   v+++GD++ D+  +e+a     g++ A + as+ v 
  gi|313126484|ref|YP_004036754.1| 308 F-DRIDVAYYHADAAEIGSLELNKPNGVQAALDVLGVDDPFVLVMGDSKSDLRVMEWAaeadaGIAAAPKHASQDVL 383
                                       3.4569999999*********************************************97775566666666666665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00011      0.48     120     158 ..     113     152 ..      58     172 .. 0.71
   2 ?    3.9   0.2     0.012        56     171     207 ..     326     362 ..     279     365 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                       HTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TTGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                         Hydrolase 120 kpeaaeavasLkaagievvlltgdnpetaeraanq.lGdd 158
                                         ++ +++ ++++ag+++v++tg+  e+++    q lG++
  gi|313126484|ref|YP_004036754.1| 113 PRDTLHLLTEFHEAGVPIVICTGQTLENVKGFTIQgLGNE 152
                                       3455599999********************6666669922 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.012
                                       STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 171 vakpspegkvaaireLqgkpeevamVGDgvnDaaala 207
                                           +p+g++aa++ L+++   v++ GD+  D+  ++
  gi|313126484|ref|YP_004036754.1| 326 LELNKPNGVQAALDVLGVDDPFVLVMGDSKSDLRVME 362
                                       44459************99778*******99987665 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0039        18      90     128 ..     116     154 ..      86     180 .. 0.71
   2 ?    6.6   0.2     0.002       9.1     145     188 .]     321     362 ..     263     362 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0039
                               HAD  90 alellaahraaGdrvvvvSgglrplvepll.aelgadevl 128
                                        l ll + ++aG+++v+++g   ++v+ +  + lg  e++
  gi|313126484|ref|YP_004036754.1| 116 TLHLLTEFHEAGVPIVICTGQTLENVKGFTiQGLG-NELV 154
                                       455566556*****************999977777.3333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.002
                               HAD 145 egkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                        +  + + +k++ +++  a    g d + v + GDs sDl  ++
  gi|313126484|ref|YP_004036754.1| 321 AEIGSLELNKPNGVQA--ALDVLGVDDPFVLVMGDSKSDLRVME 362
                                       5555666689999999..5555555555599*********9885 PP

>> CutC  CutC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.8e-05      0.35     121     198 ..      79     156 ..      68     160 .. 0.87
   2 ?   -3.9   0.0       1.7   7.8e+03     112     133 ..     217     238 ..     210     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.8e-05
                              CutC 121 rAfDvvadpeealeqlielgvervLtsGqkssalegleklaeLveqaaerieimagaGvnaenvaela.kktGvaev 196
                                        A+D  ++  +a+++l+ l v+  L s ++++     ++l+ L e  ++ + i++++G + env+ ++ +  G + v
  gi|313126484|ref|YP_004036754.1|  79 TALDLHSKYGRAVNALV-LDVDETLRSAGRTDNEIPRDTLHLLTEFHEAGVPIVICTGQTLENVKGFTiQGLGNELV 154
                                       6999999999***9998.99********************************************9986244566666 PP

                              CutC 197 Hl 198
                                       H+
  gi|313126484|ref|YP_004036754.1| 155 HS 156
                                       65 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.7
                              CutC 112 aegLgvtfHrAfDvvadpeeal 133
                                        +  ++t+   fD  +dp+ea+
  gi|313126484|ref|YP_004036754.1| 217 GNEFNITLKPNFDIGSDPAEAV 238
                                       5678999999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2386.62
//
Query:       gi|313126485|ref|YP_004036755.1|  [L=412]
Description: gluconate dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-55  186.1   0.8    8.8e-55  185.6   0.8    1.2  1  MR_MLE_C      Enolase C-terminal domain-like
    4.8e-14   52.6   0.1    1.7e-13   50.8   0.0    1.9  2  MR_MLE_N      Mandelate racemase / muconate lactonizing enzym
  ------ inclusion threshold ------
      0.029   14.1   0.1      0.049   13.4   0.1    1.4  1  SBP_bac_11    Bacterial extracellular solute-binding protein
      0.056   13.2   0.8       0.13   12.0   0.2    1.8  2  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.6   0.8     2e-58   8.8e-55       2     218 ..     168     396 ..     167     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 185.6 bits;  conditional E-value: 2e-58
                                       HHHHHHHHHHHHT-SEEEEETSSS...............HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHH CS
                          MR_MLE_C   2 laeearelvaeqgfravKlkvggd...............dvaedvervravreavgpgddvdlmvDanqawdlatAi 63 
                                        a+ea++ v+e g++a+K+++  +               ++++ +e v+av e+v  +d++d+++D+++ ++   A 
  gi|313126485|ref|YP_004036755.1| 168 CADEAERVVEELGYDALKFDLDVPsgfekdranrhlrpgEIRHKAEIVEAVTERV--KDRADVAFDCHWTFSGGSAK 242
                                       5799*999************9999*******************************..6678**************** PP

                                       HHHHHHGGGTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHH CS
                          MR_MLE_C  64 rvareleeldllwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitear 139
                                       r+a ++e++d++wlE+Pvppe+ l+   e++ ++  +pi +gE+ y++ + r+l+e++avdi+ pd+ +vgG+ e+r
  gi|313126485|ref|YP_004036755.1| 243 RLAAAIEDYDVWWLEDPVPPEN-LAVQEEVT-KStVTPITVGENRYRVTEERRLIENQAVDIIAPDLPKVGGMRETR 317
                                       ******99************76.********.66699**************************************** PP

                                       HHHHHHHHTT-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB CS
                          MR_MLE_C 140 kvaalaeafgvpvapHsgsgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGvel 216
                                       k+a++a ++ +pva+H++s++++++as+h+ +aipn+l +ey+ ++    +e l e++++edG++++p++pGlG++l
  gi|313126485|ref|YP_004036755.1| 318 KIADVANQYYIPVAMHNVSSPVATMASAHVGTAIPNSLAVEYHSYEL-GWWEDLVEETVIEDGYIEIPEKPGLGLTL 393
                                       *****************989*************************98.555556677899***************** PP

                                       -.H CS
                          MR_MLE_C 217 d.e 218
                                       d +
  gi|313126485|ref|YP_004036755.1| 394 DmD 396
                                       *44 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   3.9e-17   1.7e-13      27     117 .]      52     144 ..      38     144 .. 0.90
   2 ?   -2.1   0.0      0.94   4.2e+03      53      86 ..     265     299 ..     259     304 .. 0.69

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 3.9e-17
                                       EEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS.......CHHHHHHH CS
                          MR_MLE_N  27 slvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg.......nmsAkaai 96 
                                       +  lv+i+t++G+vG+gea    g++e     ++  + p +vg+++  i  l + l +++ g       + +A+++i
  gi|313126485|ref|YP_004036755.1|  52 PWTLVRIYTDAGIVGTGEAYWGAGVPEL----IE-RMKPFVVGENPLDIDRLFEHLVQKMSGegsvegvTVTAISGI 123
                                       5679***************998865554....44.59******************999999999************* PP

                                       HHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  97 dmAlwDlkakalnlpladLlG 117
                                       ++Al+Dl++k l++p ++LlG
  gi|313126485|ref|YP_004036755.1| 124 EIALHDLAGKILEIPAYQLLG 144
                                       ********************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.94
                                       HHHHHHHH.HHHHHHHTTSBTTHHHHHHHHHHHHC CS
                          MR_MLE_N  53 etikaeld.dhlapllvgkdaanisdlaqllkrav 86 
                                       ++++ e+    + p  vg++  ++ ++++l++ ++
  gi|313126485|ref|YP_004036755.1| 265 LAVQEEVTkSTVTPITVGENRYRVTEERRLIENQA 299
                                       55555554145888999999999999888877655 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05     0.049      26      78 ..     232     281 ..     210     380 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                       --EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEE CS
                        SBP_bac_11  26 vkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplas 78 
                                       ++ ++s+g++ +la++i+   ++Dvw+++++  +e+la ++ v++++ +p++ 
  gi|313126485|ref|YP_004036755.1| 232 CHWTFSGGSAKRLAAAIE---DYDVWWLEDPVPPENLAVQEEVTKSTVTPITV 281
                                       344445555555555555...56**************9998888766666554 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2     3e-05      0.13      94     164 ..     164     243 ..     161     264 .. 0.76
   2 ?   -1.5   0.0      0.37   1.7e+03     129     153 ..     314     343 ..     303     373 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                       SHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH..........HHHHHHHHHH.....T-EEEEE....CHH CS
                      Amidohydro_2  94 dpedaaaeleraveelgfkGvrlnphvggddllgdrld..........rpifealeel.....glpvdihtGpspew 155
                                       dpe++a+e+er veelg  +++++++v+ +  +++++            +i+ea  e+     ++ +d h      w
  gi|313126485|ref|YP_004036755.1| 164 DPEACADEAERVVEELGYDALKFDLDVPSGFEKDRANRhlrpgeirhkAEIVEAVTERvkdraDVAFDCH------W 234
                                       89*************************9888888887777788888886666655554333346666666......5 PP

                                       HCHHHHHHH CS
                      Amidohydro_2 156 lfggpqett 164
                                       +f g +++ 
  gi|313126485|ref|YP_004036755.1| 235 TFSGGSAKR 243
                                       566555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.37
                                       GGHHHHHHHHHHHT-EEEEE...........C CS
                      Amidohydro_2 129 rldrpifealeelglpvdihtGps.......p 153
                                       r  r+i  +++ + +pv +h           +
  gi|313126485|ref|YP_004036755.1| 314 RETRKIADVANQYYIPVAMH--NVsspvatmA 343
                                       34488999999999999999..2212233332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2362.08
//
Query:       gi|313126486|ref|YP_004036756.1|  [L=177]
Description: hypothetical protein Hbor_17430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-09   35.7   0.1    1.2e-08   35.0   0.1    1.3  1  MOSC      MOSC domain


Domain annotation for each model (and alignments):
>> MOSC  MOSC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1     7e-13   1.2e-08      12     131 .]      54     153 ..      50     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 7e-13
                                       EEEEETHHHHHHHHHS..GGGGG-STTTT--SEEES-.......-TTT-BTT-E.EEETT................E CS
                              MOSC  12 vllisresldalneelkegrsveldpgrfreNivvggaaafeEdtwkelrigdrrfrlggacsRcqmvnvdqetgar 88 
                                       v  +++e l+ ++ee +     +l  gr r Nivv g a+ ++  ++++r+gd++fr +                 r
  gi|313126486|ref|YP_004036756.1|  54 VTFVAAEALETIREETGI----DLTDGRHRRNIVVRG-ATLHDLLETTFRVGDATFRGT-----------------R 108
                                       677889999999999944....5888*********77.5789999*********99988.................6 PP

                                       E----THHHH.H.TTHHHHHHHHT---EEEEEEE-EEEETTS-EE CS
                              MOSC  89 prepcktlak.f.rrvdkrvkgkgrfGvylrvleegtvrvGdeve 131
                                       pr pc+ +++   ++ ++r+ ++ r G+ + v+++gtv+vGde+e
  gi|313126486|ref|YP_004036756.1| 109 PRPPCAHVEAvAgEEGVARALKRKRGGICANVVTGGTVAVGDELE 153
                                       **********55966666777889******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1012.16
//
Query:       gi|313126487|ref|YP_004036757.1|  [L=211]
Description: hypothetical protein Hbor_17440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0019   18.6   0.5     0.0066   16.9   0.2    1.8  2  Rubrerythrin  Rubrerythrin


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   3.7e-07    0.0066       2      55 ..      40      91 ..      38     116 .. 0.83
   2 ?   -0.7   0.0     0.099   1.8e+03      58     105 ..     151     198 ..     130     207 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-07
                                      HHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  2 iLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnkllek 55
                                      +Le A a+E  ar+ ++  a+  +   +  + +F  +Ae+E  H +++ + l+k
  gi|313126487|ref|YP_004036757.1| 40 VLEVAAASEHAARETFRKWADDEE--SETAQGAFTTVAEQEDTHLRRVTNELDK 91
                                      6999999******99999999999..8999999***********9888777766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.099
                                       TTHH.B.SSBBS-------TTGGHHHHHHHHHHHHHHHHHCHHHHHHH CS
                      Rubrerythrin  58 pelelevkekvreyaeakpkflttaknLeeaiegayaeeeemyrfyee 105
                                        +l+ e +e     +   +++  t+++ e+a   a +  + +y  y++
  gi|313126487|ref|YP_004036757.1| 151 RDLKAETNETLEAGLDLLEEVCATEDDWETAQMVAGYTIQLAYDDYAD 198
                                       333333333334444444444444444455555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1202.23
//
Query:       gi|313126488|ref|YP_004036758.1|  [L=562]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-43  146.3  54.9    3.7e-41  140.8  30.2    3.3  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    1.1e-26   93.7   0.2    4.4e-26   91.7   0.0    2.2  2  Protoglobin      Protoglobin
     0.0014   18.9  33.1       0.15   12.3   2.5    4.8  4  DUF948           Bacterial protein of unknown function (DUF94
  ------ inclusion threshold ------
      0.019   15.0  41.6       0.86    9.6   4.0    4.9  5  Laminin_II       Laminin Domain II
      0.047   13.7  32.3        1.1    9.3   3.4    4.3  4  DUF1664          Protein of unknown function (DUF1664)
      0.058   13.7   0.1       0.14   12.4   0.1    1.6  1  DUF1842          Domain of unknown function (DUF1842)
      0.066   13.2   0.3      0.066   13.2   0.3    3.7  3  ApoO             Apolipoprotein O
      0.067   12.1  33.9       0.41    9.5  17.2    2.3  2  Spc7             Spc7 kinetochore protein
        0.5   10.9  27.3        1.3    9.5   0.3    5.3  4  HisKA_3          Histidine kinase
        1.3    8.7  30.8       0.22   11.2  14.0    3.1  3  TMP_2            Prophage tail length tape measure protein
        1.7    9.0  31.8        1.1    9.5   4.5    4.7  4  BLOC1_2          Biogenesis of lysosome-related organelles co
        1.9    7.3  29.2        1.2    8.0   9.2    3.0  3  DUF677           Protein of unknown function (DUF677)
        8.4    6.9  24.3        2.8    8.5   1.6    5.9  6  NPV_P10          Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4  11.2    0.0003      0.41      75     160 ..     213     295 ..     206     302 .. 0.59
   2 !  140.8  30.2   2.7e-44   3.7e-41       4     168 ..     293     471 ..     290     475 .. 0.95
   3 !    5.5   1.5    0.0099        14     135     169 ..     473     507 ..     470     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                       +E r+ Aer  q + ++++ +    + i+++ +s   +++r+e   +++ e  e+++ ++ ++++++++v+eiaa++
  gi|313126488|ref|YP_004036758.1| 213 QEAREQAERRRQLTTQVQREL---REPIDEVHQSSLTVTERAEDIRDIATEQVEDMEAVAGEISQMSATVEEIAATA 286
                                       444555555555555544444...44445555555555566666666666777777777777777777777777777 PP

                                       HHHHHHHHH CS
                         MCPsignal 152 eeqsasiee 160
                                       ee  +++ e
  gi|313126488|ref|YP_004036758.1| 287 EEVENTSLE 295
                                       777666554 PP

  == domain 2  score: 140.8 bits;  conditional E-value: 2.7e-44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCC CS
                         MCPsignal   4 aeeaseeAeeggkevanvvkqmeeieks..............skeisdiieVideiadQTNlLALNAaiEAARAGeq 66 
                                       + ea e+A++g++  +++++ m+e+++                +e+ ++ie i++ia+QTNlLALNA+iEAARAGe+
  gi|313126488|ref|YP_004036758.1| 293 SLEAAERASKGETAANEAIEVMQEVSQAateasedvrrlqtkIDEVDEVIETINDIAEQTNLLALNASIEAARAGEA 369
                                       567888999999999999999999999899999999999888999******************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH CS
                         MCPsignal  67 GrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadl 143
                                       G+GFaVVA+EV++LAe+s+++a e+e+ +  +q e  ++vesl+et+++ +eg el  e+ ++l+eiveav++ ++ 
  gi|313126488|ref|YP_004036758.1| 370 GEGFAVVAEEVKSLAEQSQEQASEVEQTVNSVQSEAGETVESLTETTEKLHEGIELGGEAMSSLSEIVEAVERTTEG 446
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 144 vqeiaaaseeqsasieevnqaveev 168
                                       + e+a a+++q+ s+e+v+ ave+ 
  gi|313126488|ref|YP_004036758.1| 447 IAEVADATDNQAMSAEQVTGAVENT 471
                                       **********************986 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0099
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 135 eavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                       e++++va++v+e+a as eq++ i+ + ++ ++++
  gi|313126488|ref|YP_004036758.1| 473 EQAKNVASQVDEVADASREQTNQIKAIRESSKRLD 507
                                       567899*********************99998865 PP

>> Protoglobin  Protoglobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0   3.2e-29   4.4e-26       2     156 ..      29     211 ..      28     213 .. 0.96
   2 ?   -2.7   0.1       3.4   4.7e+03      28      28 ..     320     320 ..     275     362 .. 0.58

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 3.2e-29
                                       GHHHHHHHHHTT-SHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSHHHHHHHCH.HCHHHHHHHHHHHHHHHCCCS CS
                       Protoglobin   2 earlayllsflglteedlaaLralapliealipavvdafYekllsfpetarifet.ssqierlkdflksyllklfsg 77 
                                       ++++a ++sf ++ +ed+++L +l+pl +   ++vvd+fY++l s ++  +i+ + s+ ++ lk+ + +yl++l sg
  gi|313126488|ref|YP_004036758.1|  29 DEEIAWRKSFNRFGAEDVERLESLSPLFDGIAEDVVDDFYDQLTSDENSNEIIGRsSKGLDALKRDQIAYLKSLGSG 105
                                       789**************************************************9967789***************** PP

                                       SCCHHHHHHHHHHHHHHCHCT--HHHHHHCHHHHHHHHHHHHCCCS............................-SH CS
                       Protoglobin  78 pfdsayveyldkvGkmhtrlgleprwyiaalglvqevllealleke...........................klsa 127
                                       ++  +y+e++ +vGk+h  l++ p+ y++a++ + e l+ea+ ++                            +   
  gi|313126488|ref|YP_004036758.1| 106 EYGKQYFERRARVGKIHDMLDVGPKFYLGAYSIYYENLIEAIGADVkqefsgssddtdglfaqlrsstadgdvDDAV 182
                                       ******************************************999999********************988888888 PP

                                       HHHHHHHHHHHHHHHHHHHHHCGGGBXTT CS
                       Protoglobin 128 aektalvkalnKliwldndlaleaYvreg 156
                                       + + +   +l Kl++ld++ a+e+Y++ +
  gi|313126488|ref|YP_004036758.1| 183 DAVVDRSISLLKLFLLDQQVAMETYIHSY 211
                                       888888899*****************987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.4
                                       H CS
                       Protoglobin  28 l 28 
                                        
  gi|313126488|ref|YP_004036758.1| 320 A 320
                                       2 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   2.7    0.0026       3.6      33      87 ..     224     282 ..     208     292 .. 0.66
   2 !    9.6   5.9   0.00076       1.1      29      85 ..     280     353 ..     278     356 .. 0.78
   3 !   12.3   2.5   0.00011      0.15      25      87 ..     388     450 ..     372     452 .. 0.76
   4 ?    5.8   3.9     0.012        16      24      80 ..     433     488 ..     427     507 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0026
                            DUF948  33 atieelekqvdpilkevedllakvnelledvne....klekvdplteavadlgesvsel 87 
                                       +  +++++++++ ++ev++   +v e +ed+++    ++e+++++  ++ +++++v+e+
  gi|313126488|ref|YP_004036758.1| 224 QLTTQVQRELREPIDEVHQSSLTVTERAEDIRDiateQVEDMEAVAGEISQMSATVEEI 282
                                       55556666666666666666666666666665555557777777777777777777665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00076
                            DUF948  29 deaaatieele.................kqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       +e+aat ee+e                 +++ ++++ev ++ +++ e +  ++ k+++vd+++e ++d++e+ +
  gi|313126488|ref|YP_004036758.1| 280 EEIAATAEEVEntsleaaeraskgetaaNEAIEVMQEVSQAATEASEDVRRLQTKIDEVDEVIETINDIAEQTN 353
                                       555555555555556666666666667788889999*****9999999999999***************99865 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00011
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       ++ ++e+++t+++++++++++++ ++++++k  e  e   e + ++ +++eav+ ++e ++e+
  gi|313126488|ref|YP_004036758.1| 388 QEQASEVEQTVNSVQSEAGETVESLTETTEKLHEGIELGGEAMSSLSEIVEAVERTTEGIAEV 450
                                       556678888888888888888888888888888855555569999999999999999888776 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.012
                            DUF948  24 lkktldeaaatieele...kqvdpi...lkevedllakvnelledvneklekvdplteavadl 80 
                                       l+++++++++t e++    + +d+     ++v++++++++e       + ++v + +++vad+
  gi|313126488|ref|YP_004036758.1| 433 LSEIVEAVERTTEGIAevaDATDNQamsAEQVTGAVENTRE-------QAKNVASQVDEVADA 488
                                       33444444444444432222222220002333333333333.......333333333333333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.047        65      20      71 ..     202     254 ..     197     256 .. 0.72
   2 ?    6.4   2.4    0.0059       8.2       3      46 ..     249     292 ..     247     309 .. 0.81
   3 ?    9.6   4.0   0.00062      0.86       5      56 ..     307     358 ..     303     369 .. 0.74
   4 ?    7.2   6.3    0.0036       4.9       5      81 ..     377     453 ..     375     462 .. 0.62
   5 ?    9.4   6.6   0.00075         1       5      78 ..     433     506 ..     428     515 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.047
                                       XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II  20 aplsqnlentkeklse.inrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                        ++++ ++  ++++ e ++r  + t+++ +++ + i+++ +s+ ++++ a+++
  gi|313126488|ref|YP_004036758.1| 202 VAMETYIHSYSQEAREqAERRRQLTTQVQRELREPIDEVHQSSLTVTERAEDI 254
                                       56777777777776551445555666666699999999999999999999998 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0059
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnek 46 
                                       e a+++ ++a+e  e++++++ +++++++ ++ei++++ee+++ 
  gi|313126488|ref|YP_004036758.1| 249 ERAEDIRDIATEQVEDMEAVAGEISQMSATVEEIAATAEEVENT 292
                                       678999*******************************9998654 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00062
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankaird 56 
                                       a+ea e ++ev +  ++ s+++ +++ k+ e+++ +e +n+ +++ n     
  gi|313126488|ref|YP_004036758.1| 307 ANEAIEVMQEVSQAATEASEDVRRLQTKIDEVDEVIETINDIAEQTNLLALN 358
                                       6788888888888888888888888888888888888888877776654444 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0036
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       a+e+++ a++ +eq  +++q ++ +++++ e  +s+ et+ek+++  +   +A +s +++ + +++  + + e+   
  gi|313126488|ref|YP_004036758.1| 377 AEEVKSLAEQSQEQASEVEQTVNSVQSEAGETVESLTETTEKLHEGIELGGEAMSSLSEIVEAVERTTEGIAEVADA 453
                                       66777777777777777777777777777777777777777777665555555555555555555555555555544 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.00075
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       ++e+ e ++ + e +a+++  ++n   +++++ + ve+t e++k+   +++++ +++++ ++++  + +  k+l
  gi|313126488|ref|YP_004036758.1| 433 LSEIVEAVERTTEGIAEVADATDNQAMSAEQVTGAVENTREQAKNVASQVDEVADASREQTNQIKAIRESSKRL 506
                                       56666666777777777777888888888888888888888888888888888888887777777666554444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.4   0.00082       1.1      58     122 ..     227     291 ..     213     293 .. 0.86
   2 ?    7.7   3.3    0.0025       3.5      60     114 ..     292     346 ..     285     354 .. 0.75
   3 ?    5.4   2.1     0.013        17      48     115 ..     378     442 ..     369     447 .. 0.56
   4 ?    9.2   3.9   0.00087       1.2      46     121 ..     426     500 ..     415     505 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00082
                           DUF1664  58 aatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       ++++r+L + id+v ++   ++e +++i++  te  ed++++  ++++++++ve+++++ e++e+
  gi|313126488|ref|YP_004036758.1| 227 TQVQRELREPIDEVHQSSLTVTERAEDIRDIATEQVEDMEAVAGEISQMSATVEEIAATAEEVEN 291
                                       57789999999999999999999999999999999999999999999999999999999988886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0025
                           DUF1664  60 tkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       t  + ++r  + ++  +e +e+ +e+++  te++ed++++++++++v+e++e+++
  gi|313126488|ref|YP_004036758.1| 292 TSLEAAERASKGETAANEAIEVMQEVSQAATEASEDVRRLQTKIDEVDEVIETIN 346
                                       5555566666667777888899999999999999999999999999999988875 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.013
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       ++++++ e+ +++  + ++ +++v+++     e+ ++++e  ++++e+++  ge ++s++e+ve +e 
  gi|313126488|ref|YP_004036758.1| 378 EEVKSLAEQSQEQASEVEQTVNSVQSE---AGETVESLTETTEKLHEGIELGGEAMSSLSEIVEAVER 442
                                       444444444444444555444444444...44444444455555677777777777777777777665 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00087
                           DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                        ++ + ++se ++a+ ++ ++ i++v +  d+q+  +++++  v++ re+ +++ ++v++v +a ++  ++++ i 
  gi|313126488|ref|YP_004036758.1| 426 GGEAMSSLSEIVEAV-ERTTEGIAEVADATDNQAMSAEQVTGAVENTREQAKNVASQVDEVADASREQTNQIKAIR 500
                                       556666666655554.566899****************************************99999999999886 PP

>> DUF1842  Domain of unknown function (DUF1842)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0001      0.14      18      70 ..     429     481 ..     418     509 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                           DUF1842  18 pvlslsLlvntpakkvsGtaqitQavspplnfeadVtGkysalkveppseaki 70 
                                        + sls +v++++++ +G+a+++ a++ +   + +VtG  ++++ + ++ a++
  gi|313126488|ref|YP_004036758.1| 429 AMSSLSEIVEAVERTTEGIAEVADATDNQAMSAEQVTGAVENTREQAKNVASQ 481
                                       45578899*********************************988766444444 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   2.3       1.7   2.4e+03      33      33 ..     295     295 ..     203     354 .. 0.60
   2 ?   13.2   0.3   4.8e-05     0.066      16      61 ..     376     421 ..     370     425 .. 0.94
   3 ?    1.2   0.5      0.23   3.2e+02      13      46 ..     461     494 ..     434     505 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                              ApoO  33 a 33 
                                       +
  gi|313126488|ref|YP_004036758.1| 295 E 295
                                       0 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.8e-05
                              ApoO  16 LeegvrslRkslepytsavqdelnkvkskvetaeqsvtdtiasLke 61 
                                       ++e v+sl ++ ++++s+v++++n+v+s + ++++s+t+t + L+e
  gi|313126488|ref|YP_004036758.1| 376 VAEEVKSLAEQSQEQASEVEQTVNSVQSEAGETVESLTETTEKLHE 421
                                       688999**************************************97 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.23
                              ApoO  13 tdrLeegvrslRkslepytsavqdelnkvkskve 46 
                                       ++++   v+++R+++++ +s+v++  +  +++ +
  gi|313126488|ref|YP_004036758.1| 461 AEQVTGAVENTREQAKNVASQVDEVADASREQTN 494
                                       4455555555555555555555555444443333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  17.2    0.0003      0.41     106     259 ..     200     351 ..     198     362 .. 0.77
   2 ?    8.2   8.7   0.00074         1     151     269 ..     384     497 ..     370     516 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0003
                              Spc7 106 vkalmdnqfklvKtnarlqakkdWYeWRmqllegLkegleenlegleedkelLekqeeeldellpeleeekaeleee 182
                                       ++++m+  ++   + ar qa++     R ql  +++ +l+e ++++ + + +++++ e + ++  e +e  +++  e
  gi|313126488|ref|YP_004036758.1| 200 QQVAMETYIHSYSQEAREQAER-----RRQLTTQVQRELREPIDEVHQSSLTVTERAEDIRDIATEQVEDMEAVAGE 271
                                       5666777777777777777765.....9********************************************99999 PP

                              Spc7 183 leklqeaaeeles....idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                                       + ++ + +ee+++    +++++Le++ +  ++ ++  +e  + ++e+ +  +e +e++  l+++++e+ e i+  ++
  gi|313126488|ref|YP_004036758.1| 272 ISQMSATVEEIAAtaeeVENTSLEAAER-ASKGETAANEAIEVMQEVSQAATEASEDVRRLQTKIDEVDEVIETIND 347
                                       9999998888776333366666666543.344445555566677777777788888888888888888888888777 PP

                              Spc7 256 vlee 259
                                       + e+
  gi|313126488|ref|YP_004036758.1| 348 IAEQ 351
                                       7776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00074
                              Spc7 151 leedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqe 227
                                        e+ +e+ ++ e+ ++++  e  e  ++l+e+ ekl e   el      +L e+ e++++  + i+e  + +++   
  gi|313126488|ref|YP_004036758.1| 384 AEQSQEQASEVEQTVNSVQSEAGETVESLTETTEKLHEGI-ELGGEAMSSLSEIVEAVERTTEGIAEVADATDNQAM 459
                                       4455555555555666666666666666666666666633.344455555555555555555555555555555555 PP

                              Spc7 228 qleeleekieelkeqkseleeeiaeaervleeckgwsesevs 269
                                         e+++ ++e+++eq +++ +++ e  +  +e+    +++++
  gi|313126488|ref|YP_004036758.1| 460 SAEQVTGAVENTREQAKNVASQVDEVADASREQ----TNQIK 497
                                       555555555555555555555555332222221....22222 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.0     0.045        62      32      65 ..     209     242 ..     192     245 .. 0.75
   2 ?    5.9   5.2     0.013        18      23      62 ..     293     334 ..     238     340 .. 0.90
   3 ?    9.5   0.3   0.00098       1.3      27      66 ..     376     415 ..     353     417 .. 0.89
   4 ?    3.3   0.8     0.089   1.2e+02      23      58 ..     463     498 ..     429     505 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.045
                                       TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                           HisKA_3  32 ekdpekaaeqlreieelarealqevRrllhnLrp 65 
                                       ++  ++a+eq+++ ++l  + ++e+R+ + + ++
  gi|313126488|ref|YP_004036758.1| 209 HSYSQEAREQAERRRQLTTQVQRELREPIDEVHQ 242
                                       4445699999999999999999999998877665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                                       HHHHHHHHT..TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           HisKA_3  23 qlelakrll..ekdpekaaeqlreieelarealqevRrllhn 62 
                                        le+a+r+   e+++++a e ++e+ ++a ea ++vRrl ++
  gi|313126488|ref|YP_004036758.1| 293 SLEAAERASkgETAANEAIEVMQEVSQAATEASEDVRRLQTK 334
                                       6888888885555666**********************9665 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00098
                                       HHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTH CS
                           HisKA_3  27 akrllekdpekaaeqlreieelarealqevRrllhnLrpa 66 
                                       +++++++ +e+ +eq+ e+e+++++ ++e+ ++++ L ++
  gi|313126488|ref|YP_004036758.1| 376 VAEEVKSLAEQSQEQASEVEQTVNSVQSEAGETVESLTET 415
                                       5567888999***********************9999865 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.089
                                       HHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHH CS
                           HisKA_3  23 qlelakrllekdpekaaeqlreieelarealqevRr 58 
                                       q+  a ++++++++ +a q++e+++++re  +++++
  gi|313126488|ref|YP_004036758.1| 463 QVTGAVENTREQAKNVASQVDEVADASREQTNQIKA 498
                                       444555566777778888899999988888887766 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   9.2      0.17   2.3e+02     112     176 ..     276     329 ..     255     363 .. 0.59
   2 ?   11.2  14.0   0.00016      0.22      87     195 ..     384     495 ..     355     501 .. 0.83
   3 ?    3.5   2.8     0.037        50      89     136 ..     456     503 ..     450     515 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
                             TMP_2 112 asqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatGqsvdetakela 176
                                       ++ +e++a++++e+ +t  +aae +++   +++ + e +++v++aa+e ++ +            
  gi|313126488|ref|YP_004036758.1| 276 SATVEEIAATAEEVENTSLEAAERASKGETAANEAIEVMQEVSQAATEASEDV-----------R 329
                                       23456666666666666666666666666666666666777776666666543...........2 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00016
                             TMP_2  87 yykgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaa....ae 159
                                       + + +++a+e++++++     aG T+++L++ +e+++e  +  ++a ++l++++++ + ++e +++va a+    ++
  gi|313126488|ref|YP_004036758.1| 384 AEQSQEQASEVEQTVNSVQSEAGETVESLTETTEKLHEGIELGGEAMSSLSEIVEAVERTTEGIAEVADATdnqaMS 460
                                       578999************************************************************99886222134 PP

                             TMP_2 160 lekatGqsvdetakelaklakdPvkaaeklneqlhf 195
                                        e++tG +v++t ++ +++a++  + a++  eq + 
  gi|313126488|ref|YP_004036758.1| 461 AEQVTG-AVENTREQAKNVASQVDEVADASREQTNQ 495
                                       444454.79999999999998888888888888775 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.037
                             TMP_2  89 kgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaeal 136
                                       + a +a++++ a+ +t ++a   asq++++a++  e++++++a++e+ 
  gi|313126488|ref|YP_004036758.1| 456 NQAMSAEQVTGAVENTREQAKNVASQVDEVADASREQTNQIKAIRESS 503
                                       556778888899999999999999999999999999999999998875 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.8    0.0049       6.7      30      92 ..     217     280 ..     197     293 .. 0.79
   2 ?    9.5   4.5   0.00083       1.1      11      79 ..     289     357 ..     281     361 .. 0.82
   3 ?    3.0   1.7     0.091   1.2e+02      42      85 ..     376     420 ..     368     425 .. 0.59
   4 ?    2.6   3.3      0.12   1.6e+02      33      71 ..     462     500 ..     413     508 .. 0.41

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0049
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqie.kqvteLeeavseLDeyskeLE 92 
                                       e+a+++ +  ++v  +l++ ++++ + + ++ +  + i +i  +qv+++e+++ e+ ++s   E
  gi|313126488|ref|YP_004036758.1| 217 EQAERRRQLTTQVQRELREPIDEVHQSSLTVTERAEDIRDIAtEQVEDMEAVAGEISQMSATVE 280
                                       4444444445566678999999999999999999999999963699999999999999998877 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00083
                           BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       +e++   ++e  +  e+  ++a+e  ++++++a ++++++ +l+ k +e+++ ++ i++i +q++ L  
  gi|313126488|ref|YP_004036758.1| 289 VENTSLEAAERASKGETAANEAIEVMQEVSQAATEASEDVRRLQTKIDEVDEVIETINDIAEQTNLLAL 357
                                       5555555566666677788899999**************************************988765 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.091
                           BLOC1_2  42 vaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLD 85 
                                       va+++++ +e+ +e+  e+++ +++++ +  ++v++L+e+ ++L 
  gi|313126488|ref|YP_004036758.1| 376 VAEEVKSLAEQSQEQASEVEQTVNSVQsEAGETVESLTETTEKLH 420
                                       445555555555666666666666665245566666666666654 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.12
                           BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqie 71 
                                       ++   ++++  +++++ +++++e  ++ +++ +qi++i 
  gi|313126488|ref|YP_004036758.1| 462 EQVTGAVENTREQAKNVASQVDEVADASREQTNQIKAIR 500
                                       222222222222223333333333334444444444444 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   3.4      0.18   2.5e+02     226     327 ..     207     302 ..     202     311 .. 0.54
   2 ?    4.8  10.1     0.008        11     252     334 ..     282     358 ..     248     359 .. 0.65
   3 ?    8.0   9.2   0.00085       1.2     223     326 ..     394     497 ..     373     503 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.18
                            DUF677 226 wvasawkkyeealkrqkeivssmekgievakkdvenisilverleseiksilktvefAvekeeneaavklaleeikk 302
                                       ++ s  ++  e   r +++ +++++ +     +v++ s  v +    i+ i   + + ve+    +av   +++++ 
  gi|313126488|ref|YP_004036758.1| 207 YIHSYSQEAREQAERRRQLTTQVQRELREPIDEVHQSSLTVTERAEDIRDI---ATEQVED---MEAVAGEISQMSA 277
                                       555555555666666666666666666555555555555555544444443...2333333...3366666666666 PP

                            DUF677 303 kvekltekieevgeeaakcskliak 327
                                        ve++  + eev++   + ++ ++k
  gi|313126488|ref|YP_004036758.1| 278 TVEEIAATAEEVENTSLEAAERASK 302
                                       6666666666666655555555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.008
                            DUF677 252 ievakkdvenisilverleseiksilktvefAvekeeneaavklaleeikkkvekltekieevgeeaakcskliaka 328
                                       i +  ++ven s +  +     +    ++++A+e  +   +v +a +e +++v +l+ ki ev+e ++  + +++++
  gi|313126488|ref|YP_004036758.1| 282 IAATAEEVENTSLEAAERA---SKGETAANEAIEVMQ---EVSQAATEASEDVRRLQTKIDEVDEVIETINDIAEQT 352
                                       2233333333333222222...222345666777655...8999999999*************************** PP

                            DUF677 329 rlvvLq 334
                                        l +L+
  gi|313126488|ref|YP_004036758.1| 353 NLLALN 358
                                       999885 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00085
                            DUF677 223 vgkwvasawkkyeealkrqkeivssmekgievakkdvenisilverleseiksilktvefAvekeeneaavklalee 299
                                       v + v+s+  +  e++    e  +++++gie   +++ ++s  ve++e   ++i + ++   ++    ++v  a+e+
  gi|313126488|ref|YP_004036758.1| 394 VEQTVNSVQSEAGETVESLTETTEKLHEGIELGGEAMSSLSEIVEAVERTTEGIAEVADATDNQAMSAEQVTGAVEN 470
                                       555678888899999999999*********************************98776555555556778888888 PP

                            DUF677 300 ikkkvekltekieevgeeaakcsklia 326
                                        +++ +++ +++ ev +   + ++ i+
  gi|313126488|ref|YP_004036758.1| 471 TREQAKNVASQVDEVADASREQTNQIK 497
                                       888888999999998887777766665 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         2   2.8e+03      52      66 ..      89     126 ..      50     130 .. 0.60
   2 ?    3.7   1.0     0.063        87      32      61 ..     260     282 ..     198     296 .. 0.55
   3 ?    8.5   1.6     0.002       2.8       7      43 ..     315     351 ..     306     365 .. 0.64
   4 ?    3.7   0.5     0.063        87      14      62 ..     392     441 ..     375     452 .. 0.69
   5 ?    1.7   0.0      0.27   3.7e+02      21      60 ..     431     470 ..     427     473 .. 0.85
   6 ?    2.4   1.1      0.16   2.2e+02      13      44 ..     468     496 ..     459     510 .. 0.47

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2
                           NPV_P10  52 aelet.......................kvenIqdiLn 66 
                                       ++l+                         v +I+d+L 
  gi|313126488|ref|YP_004036758.1|  89 DALKRdqiaylkslgsgeygkqyferraRVGKIHDMLD 126
                                       33333333333335557777777777778888888886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.063
                           NPV_P10  32 enlpdvtelnekLdaqsaqLaeletkvenI 61 
                                       e+++        ++a + ++ +++++ve+I
  gi|313126488|ref|YP_004036758.1| 260 EQVE-------DMEAVAGEISQMSATVEEI 282
                                       1222.......2222222222222244443 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.002
                           NPV_P10   7 lvIradikavddkVdalqqqvddvqenlpdvtelnek 43 
                                         + ++ ++ ++ V  lq+++d+v+e +++++++ e+
  gi|313126488|ref|YP_004036758.1| 315 QEVSQAATEASEDVRRLQTKIDEVDEVIETINDIAEQ 351
                                       4455666666777777777777777777776666554 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.063
                           NPV_P10  14 kavddkVdalqqqv.ddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                       ++v++ V+++q++  + v++  +++++l+e ++   +++ +l++ ve+++
  gi|313126488|ref|YP_004036758.1| 392 SEVEQTVNSVQSEAgETVESLTETTEKLHEGIELGGEAMSSLSEIVEAVE 441
                                       56777777777776334444444555677777777777777777777665 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.27
                           NPV_P10  21 dalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       ++l++ v+ v+   + + e+ +  d+q+ + +++  +ven
  gi|313126488|ref|YP_004036758.1| 431 SSLSEIVEAVERTTEGIAEVADATDNQAMSAEQVTGAVEN 470
                                       6788899999999999999999999999999998888876 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.16
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekL 44 
                                       ++++ ++ + + +qvd+v++ +++ t   +++
  gi|313126488|ref|YP_004036758.1| 468 VENTREQAKNVASQVDEVADASREQT---NQI 496
                                       44444555555555555544433311...222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2327  (0.12979); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        72  (0.00401584); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.60u 0.41s 00:00:02.01 Elapsed: 00:00:00.67
# Mc/sec: 2529.53
//
Query:       gi|313126489|ref|YP_004036759.1|  [L=382]
Description: zn-dependent hydrolase, glyoxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-13   51.0   3.8    2.7e-13   50.4   3.8    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.3e-12   47.4   0.0    4.4e-12   46.5   0.0    1.5  1  Rhodanese      Rhodanese-like domain
    0.00015   21.3   1.0    0.00032   20.3   1.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.019   14.9   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
      0.054   13.6   0.0       0.11   12.6   0.0    1.5  1  T2SSG          Type II secretion system (T2SS), protein G


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   3.8   7.5e-17   2.7e-13       5     179 ..     131     275 ..     127     329 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 7.5e-17
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       ++ +y ++  g++ +iD++       aa+    ++  + d+  vi TH H+DH++g+++l++a d+ +++ a++++ 
  gi|313126489|ref|YP_004036759.1| 131 GCLAYMLVSSGEAAVIDPLRQFVDRYAAD----AREYGADIVSVIDTHVHADHVSGVRELADAVDATPVYPAAAEAR 203
                                       6789***********************96....******************************************** PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                       ++                        +++++ dg++ +++++  t  +++gh++    +++++ +f+GD l+  + +
  gi|313126489|ref|YP_004036759.1| 204 GLVADS--------------------ATKLVSDGDEIHVGDVTLTAVHTPGHTSEMTAFQIDDSCFSGDGLFLDSVA 260
                                       ******....................************************************************999 PP

                                       CCCC.TTCEEE-SHCHHHHHH CS
                       Lactamase_B 159 ridltlrgaevrdpsdaekyl 179
                                       r dl       + + +ae++ 
  gi|313126489|ref|YP_004036759.1| 261 RPDL------EHGDEGAEDAA 275
                                       9999......33333333333 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   1.2e-15   4.4e-12       1     105 [.       2     106 ..       2     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.2e-15
                         Rhodanese   1 sakelkellekgkva.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel.gidnkktvvvycdg 75 
                                       +++el+++le+g+ + llDvR++eeY+++hI g      +  +++k+  a+ + ++ee +++ g+d+++ vv +c  
  gi|313126489|ref|YP_004036759.1|   2 TPEELHDRLERGESVtLLDVRNREEYDAWHIDGDSVT-TTLVPYSKFMTAEVQGTVEETARKaGLDPDELVVAVCGR 77 
                                       799******8888778***************885555.5999*********************************** PP

                         Rhodanese  76 ggraaaaaallkklGyknvsvldGGfkawk 105
                                       g+ +  +a ll+  G +n  +l+ G+++w+
  gi|313126489|ref|YP_004036759.1|  78 GEASDYVAELLRDVG-YNAENLEDGMRGWA 106
                                       ***9999********.8************7 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.0     9e-08   0.00032       5     110 ..     146     244 ..     144     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9e-08
                                       ES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEE.EEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   5 iDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklply.apkgvlavleanfvylal 79 
                                       iD+   ++     +    + +r+  ++i  V+ th H+DH+ g+  l+    +  p+y a ++ +  ++++   l++
  gi|313126489|ref|YP_004036759.1| 146 IDPLRQFVDR---YA---AdAREYGADIVSVIDTHVHADHVSGVRELADAV-DATPVYpAAAEARGLVADSATKLVS 215
                                       4444444444...33...12556667999********************43.3489**9999999999999988888 PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatpa 110
                                       + + +++v ++++   +++g    e+ta+++
  gi|313126489|ref|YP_004036759.1| 216 DGD-EIHVGDVTLTAVHTPGH-TSEMTAFQI 244
                                       888.78888888888777774.457777765 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.3e-06     0.019      11      85 ..     136     234 ..     131     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.3e-06
                     Lactamase_B_3  11 lletagarilvDPfka.nlgyeppa..eeaDlvlisqaledHahletlkql........................ae 60 
                                       +l ++g   ++DP ++    y+++a    aD+v +     +H h++ + ++                        ++
  gi|313126489|ref|YP_004036759.1| 136 MLVSSGEAAVIDPLRQfVDRYAADAreYGADIVSVID---THVHADHVSGVreladavdatpvypaaaearglvaDS 209
                                       566789999*****88644444444336677776633...334444444444448889*****************99 PP

                     Lactamase_B_3  61 nvkvleegeslevggleiravatsh 85 
                                        +k++++g+++ vg++ ++av+t  
  gi|313126489|ref|YP_004036759.1| 210 ATKLVSDGDEIHVGDVTLTAVHTPG 234
                                       *********************9975 PP

>> T2SSG  Type II secretion system (T2SS), protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     3e-05      0.11      53      92 ..     102     142 ..      93     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                                       SS--STTT-.-S----STT---EEE---SSS.S-EEEE--T CS
                             T2SSG  53 pknwegpYlkkklpkDpWgnpyvyrspgehg.efdllslGa 92 
                                        + w+  Y+++++p+D+  + ++yr p++   ++ l+s G+
  gi|313126489|ref|YP_004036759.1| 102 MRGWAHVYVSETVPTDADATVFQYRRPSSGClAYMLVSSGE 142
                                       578*9***********************98569****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2145.30
//
Query:       gi|313126490|ref|YP_004036760.1|  [L=108]
Description: ferredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-11   44.3   2.6    1.6e-11   44.0   2.6    1.2  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.036   14.1   0.2      0.038   14.0   0.2    1.2  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   2.6   1.8e-15   1.6e-11       5      77 ..      10      79 ..       6      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.8e-15
                                      TEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTTSSSSTHHHHHTTEEEEGGGSEE CS
                              Fer2  5 gkevevevadgettlldaaeenggidipysCggggCgtClvevlegev.qsdetelegeeldegklrlaCqtiv 77
                                      g++ +++v d +t +l+a+ e  gi+ +ysC+ g C +C +e+leg+v q+ ++ l++ee++e  ++l+C++++
  gi|313126490|ref|YP_004036760.1| 10 GTGESIQVSDKQT-ILKACIEE-GIAQEYSCRVGMCLACSAEILEGDVvQPAARGLTEEEREE--YALTCMARP 79
                                      88999***99999.******99.*************************987766666666433..56*****98 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   4.2e-06     0.038      27      66 ..      13      53 ..       1      87 [. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-06
                            Fer2_3 27 eedtvldaLlkikeevdptlafrasCregiCGscavai.nG 66
                                      e+ +v d  + +k  +++ +a ++sCr g+C +c+++i +G
  gi|313126490|ref|YP_004036760.1| 13 ESIQVSDKQTILKACIEEGIAQEYSCRVGMCLACSAEIlEG 53
                                      445555666667888899****************9988344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 647.31
//
Query:       gi|313126491|ref|YP_004036761.1|  [L=688]
Description: hypothetical protein Hbor_17480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-24   85.7  16.5    8.6e-21   74.7   9.2    3.4  3  DUF839      Bacterial protein of unknown function (DUF839)
  ------ inclusion threshold ------
        2.9    7.9   6.6          6    6.9   6.6    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> DUF839  Bacterial protein of unknown function (DUF839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   2.3e-05      0.21     485     524 .]      36      74 ..      10      74 .. 0.79
   2 !    3.2   0.1    0.0044        39      21      82 ..     121     192 ..     105     213 .. 0.72
   3 !   74.7   9.2   9.6e-25   8.6e-21     149     457 ..     214     642 ..     203     672 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.3e-05
                            DUF839 485 sdaargevkrfltepegsEvtGvtfsPdgktlfvnvqhPg 524
                                       +   +ge+ rf+t + g+EvtG+ ++ ++ tl+ ++qhP+
  gi|313126491|ref|YP_004036761.1|  36 APMVKGELTRFATTAFGAEVTGPFVT-QSGTLIFSLQHPS 74 
                                       4456899******************9.999*********5 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0044
                            DUF839  21 eakvlvrwGdklfagapefd...........qsaeaqekqvgynhDgmaffplsrsadeglLvvNhEytseei 82 
                                       e+  l++ Gd++ ++ +              q    + + +gy  D  +f+p ++  ++g+L  N E +  ++
  gi|313126491|ref|YP_004036761.1| 121 EYVLLAQEGDNIGDDEDL-GipttpdgvnisQFDGTRYSDFGYTPDMNQFVPTNEDGTKGVLFTNFEASPGNV 192
                                       566677777777776542.135555576665556677789*************99999********9876555 PP

  == domain 3  score: 74.7 bits;  conditional E-value: 9.6e-25
                            DUF839 149 ktsadaegvkilGTanNCagGtTpWGtyLtcEEnfng..yfggeea..vkadqkryGitgttgy............. 208
                                       ++++++  +++ GT  NC g  +pWGt L++EE   +   +g+  +  + + +  +G++g++++             
  gi|313126491|ref|YP_004036761.1| 214 NLANTEAMRELGGTRINCYGDRSPWGTPLSAEEEYAHprLAGTATTsdIMDAGSGVGYRGASQFwnrpnptevgsse 290
                                       5567788999*************************999744444223599999************************ PP

                            DUF839 209 .......................................erFdvanepkkfGyvvEv.dpvdprstpvkrtalGrfk 245
                                                                              +++    +  + Gy+v    p+ ++ +pvk    Gr +
  gi|313126491|ref|YP_004036761.1| 291 wydeyndgvypqgafalaglelhayylgadpvgdetpigDTY---PNVYRTGYIVDFrKPEWAEPKPVKYYVFGRAA 364
                                       ***********9888888888877777776666554333333...555899****98346667************** PP

                            DUF839 246 HEaaavvveddkrvvvYlgdDerkeylYkFvsndrvgtgnskansaLldeGtLyvakfned............gtve 310
                                        Ea  v   +     vYl+ D   + lYkFv+ +++          +   GtLy+ak+ ++             +++
  gi|313126491|ref|YP_004036761.1| 365 WEAPDV---QSDEKTVYLTSDGDTKGLYKFVADEPIPSY----DDPMDVAGTLYAAKVTNEdaaknkppanvdLELD 434
                                       ******...6667789*******************8866....6899***********9999**********999** PP

                            DUF839 311 Wvplveg.............................................................qgglta.en 325
                                       W+pl+++                                                              +++t+  n
  gi|313126491|ref|YP_004036761.1| 435 WLPLSHAtnrevaswiaeyddvtqvdylethaetdwqedfeaalaeadkavakngnqdfitdeeiqawANKWTDdPN 511
                                       ****************************************************************9999777777645 PP

                            DUF839 326 g...fadqaevl.vktrlaadkvGat.kmdrpEdievnPttg.evyvvltnnkkrdeskidsanpraknkyGqivrl 396
                                            ++  +v  ++tr+aa+++Gat ++++ E+i    ++    y+ l   + ++++  ++++ r +   G +v  
  gi|313126491|ref|YP_004036761.1| 512 AvvdDESLRKVPfLETRAAAKAIGATvEFRKSEGIDSVEDAQpGDYIYLGISELNGGMSDQHGDLRMDRVDGGLVYR 588
                                       43335555666526788888*****856999****966665575666666666668888899*******99999988 PP

                            DUF839 397 ieesrdvaatkftwdlfllaGdpedakaasaessegndlespDnlafdpaGrlwiatDgsg 457
                                        e ++d   +  t++ +++ +d +d      +  +++ + + Dn+ + + Gr++ ++D ++
  gi|313126491|ref|YP_004036761.1| 589 AEIEAD--YNISTLEPVIVGSDASDP-----ADVANDSVLNIDNVFVMDDGRVLCCEDADK 642
                                       888775..5677999****9996666.....44566667789****************876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.6   0.00066         6       1      26 []       3      28 ..       3      28 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00066
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalggcaaa 26
                                      +++RR ++ +s Aaa +a ++g aaa
  gi|313126491|ref|YP_004036761.1|  3 EFTRRKLMATSVAAALGASVAGTAAA 28
                                      59********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 3896.74
//
Query:       gi|313126492|ref|YP_004036762.1|  [L=147]
Description: hypothetical protein Hbor_17490 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 982.46
//
Query:       gi|313126493|ref|YP_004036763.1|  [L=144]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-39  135.6   0.7    1.8e-39  135.5   0.7    1.0  1  Usp       Universal stress protein family
     0.0082   15.8   0.1      0.031   13.9   0.0    1.8  2  SRP54     SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
       0.11   13.3   0.1       0.24   12.2   0.1    1.8  1  GARS_N    Phosphoribosylglycinamide synthetase, N domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.7     3e-43   1.8e-39       1     141 []       1     139 [.       1     139 [. 0.98

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 3e-43
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+rIlV++Dgs++s+ A+++A++ ak+++a++++l+v+d+ ++++  ++   ++e+   + e++ e+     aa++
  gi|313126493|ref|YP_004036763.1|   1 MYERILVPTDGSKASQGAIKHAIDIAKQYDATIHALYVVDSGTYSSLEAGSNIVAEALRGEGEKAVEQVV--SAADD 75 
                                       9**************************************************************9999885..***** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +gv+v++ v +g + + il + ee+d+dl+V+G++grsgl+r+llGSv+e+++r++++pVl Vr
  gi|313126493|ref|YP_004036763.1|  76 AGVEVTTSVQNGTAHRDILNYTEENDCDLVVMGTHGRSGLDRYLLGSVTEKIVRSSDVPVLTVR 139
                                       *************************************************************998 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.086   5.2e+02      84     125 ..       2      43 ..       1      63 [. 0.76
   2 !   13.9   0.0   5.2e-06     0.031      44     104 ..      65     122 ..      53     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.086
                                       SSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTB CS
                             SRP54  84 idvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldatt 125
                                       ++ +lv T G  +++ ++ + ++  k+  ++++ l+v+d+ t
  gi|313126493|ref|YP_004036763.1|   2 YERILVPTDGSKASQGAIKHAIDIAKQYDATIHALYVVDSGT 43 
                                       567888888888888777777777777778889999999866 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.2e-06
                                       HHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHH CS
                             SRP54  44 AveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndkelmee 104
                                       AveQ+   a+ +gv+v+++ +     +  ++ ++  +e+++d+v++ T Gr+  d+ l+  
  gi|313126493|ref|YP_004036763.1|  65 AVEQVVSAADDAGVEVTTSVQ---NGTAHRDILNYTEENDCDLVVMGTHGRSGLDRYLLGS 122
                                       9************99986554...457889999999****************999888765 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     4e-05      0.24      21      59 ..      62     109 ..      15     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                                       TSTTESEEEEEE--CGG.........TTHHHHHHHHHHCTESEEEE-S CS
                            GARS_N  21 qspkvekvyvapgNagt.........edlealvefakeekidlvvvGp 59 
                                        ++ ve+v+ a  +ag+         + +++++++ +e+++dlvv+G 
  gi|313126493|ref|YP_004036763.1|  62 GEKAVEQVVSAADDAGVevttsvqngTAHRDILNYTEENDCDLVVMGT 109
                                       4578999999999999988776665544567***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 954.15
//
Query:       gi|313126494|ref|YP_004036764.1|  [L=97]
Description: hypothetical protein Hbor_17510 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 655.10
//
Query:       gi|313126495|ref|YP_004036765.1|  [L=566]
Description: membrane-bound mannosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-12   46.5   5.1    4.5e-12   46.5   5.1    3.3  5  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
    0.00028   20.5   4.4    0.00028   20.5   4.4    2.5  2  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.23     2e+03      69      90 ..      16      37 ..      11      45 .. 0.68
   2 !   46.5   5.1     5e-16   4.5e-12       4     130 ..      77     204 ..      74     212 .. 0.91
   3 ?   -0.7   0.5      0.17   1.5e+03     128     139 ..     331     341 ..     271     364 .. 0.57
   4 ?   -0.7   0.8      0.16   1.5e+03      50      66 ..     342     358 ..     296     388 .. 0.63
   5 ?   -2.6   1.8      0.61   5.5e+03      50      50 ..     398     398 ..     343     425 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.23
                             PMT_2 69 salftpdaplvllwalalylll 90
                                      +++f++d + ++++ala+++ll
  gi|313126495|ref|YP_004036765.1| 16 GLEFRTDRVTLAVVALAALALL 37
                                      5667777777777777776665 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 5e-16
                             PMT_2   4 Pliawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvl 80 
                                       Pl + l +l+++++g s++ +rl+ a++g+   l+  ll+r++f+   +l+ a++la+ plfv++s+ ++ d+pl +
  gi|313126495|ref|YP_004036765.1|  77 PLLYHLDRLVFAVLGVSDMTARLPVAVLGAALPLC-ALLFRDRFDDAESLVFAAFLAFNPLFVYYSRFLRGDVPLAF 152
                                       8888899**********************988876.5899999********************************** PP

                             PMT_2  81 lwalalylllraleknklkywllagvlfGlgflsKytaallliaall..yll 130
                                       + ++++ ++lra ++++ ++ ++  ++++l+f s  +aa +++  ++  +ll
  gi|313126495|ref|YP_004036765.1| 153 FALAFAGFTLRAYDRRSRRDAYAGSIALALAFASSGFAAAYVLCGVVvvILL 204
                                       ***********************************99999988766644444 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.17
                             PMT_2 128 yllisarrilke 139
                                       y+  + rr l +
  gi|313126495|ref|YP_004036765.1| 331 YVSSE-RRPLLD 341
                                       33333.332222 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.16
                             PMT_2  50 raallaalllavvplfv 66 
                                         a+++a+  a++p+ +
  gi|313126495|ref|YP_004036765.1| 342 AFAYWSAAAFAIFPVAT 358
                                       34455555555555444 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 0.61
                             PMT_2  50 r 50 
                                        
  gi|313126495|ref|YP_004036765.1| 398 D 398
                                       1 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   4.4   3.2e-08   0.00028      74     201 ..      87     205 ..      29     243 .. 0.82
   2 ?   -2.8   0.3      0.42   3.8e+03     124     226 ..     328     354 ..     310     371 .. 0.46

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.2e-08
                               PMT  74 eyypenvpyvslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyc 150
                                       + +++ v+ +++Rl  a+lg+ ++ l+  +l++  f+   +l++a+++++ ++++  sr+   d+pL+ff l+   +
  gi|313126495|ref|YP_004036765.1|  87 FAVLG-VSDMTARLPVAVLGAALP-LCA-LLFRDRFDDAESLVFAAFLAFNPLFVYYSRFLRGDVPLAFFALAFAGF 160
                                       66777.999999*******99765.554.556778999*******************************97655555 PP

                               PMT 151 lvkferkapfsrswwlwllltgvalglavsvKwvglftvllvgllliwelw 201
                                        ++++      r+ +  +++  +al+la  + ++++ +++l g+++++ l+
  gi|313126495|ref|YP_004036765.1| 161 TLRAY-----DRRSRRDAYAGSIALALAFASSGFAA-AYVLCGVVVVILLV 205
                                       55554.....56777788999999999999988777.44466666666555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.42
                               PMT 124 enslitlsryilldspLlfftllsmyclvkferkapfsrswwlwllltgvalglavsvKwvglftvllvgllliwel 200
                                        n+++ + r  lld+                                                              
  gi|313126495|ref|YP_004036765.1| 328 WNRYVSSERRPLLDA-------------------------------------------------------------- 342
                                       333344444444443.............................................................. PP

                               PMT 201 wqllgdkslllksivkhllaralali 226
                                                     + ++ a a+a +
  gi|313126495|ref|YP_004036765.1| 343 --------------FAYWSAAAFAIF 354
                                       ..............444444444332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3468.81
//
Query:       gi|313126496|ref|YP_004036766.1|  [L=146]
Description: hypothetical protein Hbor_17530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   12.0   0.0       0.29   11.3   0.0    1.4  1  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.6e-05      0.29      23      50 ..      25      52 ..       9      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.6e-05
                                      ---B--EETTEEEEEEESSTTCCSB--T CS
                           Flg_new 23 tlpanptkeGYtFaGWytdsdgttaydf 50
                                        p++ tk  Y+F GW  d+ +tt  +f
  gi|313126496|ref|YP_004036766.1| 25 VHPPDVTKLHYEFHGWLGDDLLTTVSNF 52
                                      35899***********998777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 840.31
//
Query:       gi|313126497|ref|YP_004036767.1|  [L=439]
Description: hypothetical protein Hbor_17540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-31  106.6   0.9    1.3e-30  105.4   0.9    1.7  1  DUF4157        Domain of unknown function (DUF4157)
  ------ inclusion threshold ------
      0.017   15.5   0.5      0.032   14.6   0.5    1.5  1  Peptidase_M91  Effector protein
       0.11   12.5   0.0       0.22   11.6   0.0    1.5  1  HTH_35         Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.9   2.2e-34   1.3e-30       2      78 ..     175     251 ..     174     252 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 2.2e-34
                           DUF4157   2 lpeavraemerafgadlsdVrvhtgsaaaraaralgAqAfTlgndivfaageyqpesaagrellaHELtHvvqqreg 78 
                                       l++++++ me ++g+ l+dVr+htg++aa+a+++++A+AfT+gn+i+f++gey+p+sa+g+++laHEL+Hv qq++g
  gi|313126497|ref|YP_004036767.1| 175 LDSSIQRAMEDRMGDTLGDVRIHTGPSAAKACEDINARAFTVGNHIAFNHGEYDPSSAEGQHILAHELAHVRQQTGG 251
                                       89************************************************************************986 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   5.3e-06     0.032      68     135 ..     212     274 ..     149     279 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.3e-06
                     Peptidase_M91  68 kgegtdaeinynpafsseeegkegrPsavLyHElaHaydalngtlddgeydgkdeedssgvpneErqA 135
                                       + ++ +++i +n         +  + +++L+HElaH+++++ g +   +++g+ e d +   + Er+A
  gi|313126497|ref|YP_004036767.1| 212 RAFTVGNHIAFNHGEYDP---SSAEGQHILAHELAHVRQQTGGAVSMLPQTGEIEIDPDE--RLEREA 274
                                       455556666666653333...5556669***************99988888877777665..555554 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.7e-05      0.22      38      61 ..     347     370 ..     329     382 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.7e-05
                            HTH_35  38 rpwpkgEalIAeaLgvppeeiwPs 61 
                                        pw +gE +I +a++ +++++wP+
  gi|313126497|ref|YP_004036767.1| 347 YPWLEGEVVIHHAVEQQVQQLWPE 370
                                       49*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2447.27
//
Query:       gi|313126498|ref|YP_004036768.1|  [L=317]
Description: transcription initiation factor iib (tfiib) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-44  147.9   1.4    9.1e-24   83.3   0.2    2.3  2  TFIIB           Transcription factor TFIIB repeat
      1e-18   66.6   1.1    1.6e-18   65.9   1.1    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0063   16.2   0.2      0.012   15.3   0.2    1.4  1  Ribosomal_S27e  Ribosomal protein S27
  ------ inclusion threshold ------
      0.013   15.2   1.7      0.044   13.5   1.6    1.9  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.015   14.8   1.0       0.36   10.4   0.1    3.4  3  Sigma70_r4      Sigma-70, region 4
      0.042   14.0   1.3        2.5    8.3   0.3    2.5  2  Zn-ribbon_8     Zinc ribbon domain
      0.071   13.0   0.3        0.2   11.6   0.2    1.8  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.075   12.9   0.4       0.74    9.7   0.1    2.8  3  HTH_23          Homeodomain-like domain
      0.078   13.2   0.5       0.15   12.3   0.5    1.4  1  IBR             IBR domain, a half RING-finger domain
        0.1   12.6   0.1        7.4    6.7   0.0    3.3  3  HTH_3           Helix-turn-helix
       0.11   12.6   0.0       0.84    9.7   0.0    2.1  2  Cyclin_C        Cyclin, C-terminal domain
       0.14   12.7   0.4       0.46   11.1   0.4    1.9  1  Trm112p         Trm112p-like protein
       0.16   11.9   2.3          5    7.1   0.5    2.5  2  Nudix_N_2       Nudix N-terminal
       0.42   10.6   2.4       0.89    9.6   2.4    1.5  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.1     9e-21   1.2e-17       1      71 []     139     209 ..     139     209 .. 0.98
   2 !   83.3   0.2   7.1e-27   9.1e-24       1      71 []     233     303 ..     233     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 9e-21
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+a+al+ p  V++ A  ++++al+e+++ Grs +g+a ++ly Acr+e+  r++ e+++v++V +k+i
  gi|313126498|ref|YP_004036768.1| 139 IDRMASALGVPRSVREVASVIYRRALNEDLIRGRSIEGVATSALYAACRQEGIPRSLDEVAEVSRVPQKEI 209
                                       789***************************************************************99997 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 7.1e-27
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rfa+al+L+e+V+ +A+e+++ ++e+++l+G+sp+g aAA++y A++++++k+tq+e+++v+qV+e+ti
  gi|313126498|ref|YP_004036768.1| 233 VPRFASALGLSEEVQAKATEIIDVSAEQGLLSGKSPTGFAAAAIYAASLLCNEKKTQREVADVAQVTEVTI 303
                                       689******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   1.1   1.3e-21   1.6e-18       2      43 .]      23      64 ..      22      64 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.3e-21
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                       CP+C stn+++D+++gelvC dCGlVl++++id gpewr+f
  gi|313126498|ref|YP_004036768.1| 23 ACPECESTNIITDADQGELVCDDCGLVLDERQIDRGPEWRAF 64
                                      5***************************************98 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   9.2e-06     0.012       7      36 ..      21      50 ..      20      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.2e-06
                                      EEE-TTTS-EEEEESS-SS-EEESSSTCEE CS
                    Ribosomal_S27e  7 dvkCpdCenetvvFshaatvvkCisCgkvL 36
                                      ++ Cp+Ce + ++ +  +    C  Cg vL
  gi|313126498|ref|YP_004036768.1| 21 RIACPECESTNIITDADQGELVCDDCGLVL 50
                                      689************************998 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1       0.1   1.3e+02      24      30 ..      24      30 ..      13      33 .. 0.82
   2 ?   13.5   1.6   3.4e-05     0.044       6      30 ..      24      49 ..      19      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
                     A2L_zn_ribbon 24 CieCgas 30
                                      C+eC+++
  gi|313126498|ref|YP_004036768.1| 24 CPECEST 30
                                      *****97 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.4e-05
                     A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                                      C  C + +i+  ++qg+lvC +Cg++
  gi|313126498|ref|YP_004036768.1| 24 CPECESTNIITdADQGELVCDDCGLV 49
                                      8889999999999***********86 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2   2.9e+03      34      45 ..     153     164 ..     143     166 .. 0.61
   2 ?    0.7   0.0       0.3   3.8e+02      20      35 ..     192     207 ..     185     220 .. 0.70
   3 ?   10.4   0.1   0.00028      0.36      18      42 ..     284     308 ..     275     314 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAl 45 
                                       re ++ i +rAl
  gi|313126498|ref|YP_004036768.1| 153 REVASVIYRRAL 164
                                       355666777776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.3
                                       T--HHHHHHHHTS-HH CS
                        Sigma70_r4  20 glTleEIgerlgiSre 35 
                                       +++l E++e+  +++ 
  gi|313126498|ref|YP_004036768.1| 192 PRSLDEVAEVSRVPQK 207
                                       5677777777666654 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00028
                                       TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiek 42 
                                        e+ T+ E++++ ++++ ++r +  
  gi|313126498|ref|YP_004036768.1| 284 NEKKTQREVADVAQVTEVTIRNRYQ 308
                                       5899*****************9976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3     0.002       2.5      15      34 ..      12      29 ..       6      32 .. 0.65
   2 ?    3.9   0.0     0.046        59       5      22 ..      40      56 ..      39      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                       Zn-ribbon_8 15 fevlqsisdapltaCPeCgs 34
                                       ev q ++  + +aCPeC s
  gi|313126498|ref|YP_004036768.1| 12 QEVEQDSD--ERIACPECES 29
                                      45566444..3666****98 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.046
                       Zn-ribbon_8  5 eYrCeeCghefevlqsis 22
                                      e  C++Cg + +++q i+
  gi|313126498|ref|YP_004036768.1| 40 ELVCDDCGLVLDERQ-ID 56
                                      568999999999888.55 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00016       0.2      30      57 ..      23      51 ..      18      56 .. 0.90
   2 ?   -3.8   0.0       9.9   1.3e+04      10      24 ..     215     229 ..     211     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                    OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCgfead 57
                                       C+eC s+n   + ++ +++C++Cg+++d
  gi|313126498|ref|YP_004036768.1| 23 ACPECESTNIItDADQGELVCDDCGLVLD 51
                                      5********99899***********9966 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.9
                    OrfB_Zn_ribbon  10 ykakeyGikveevnp 24 
                                       y  +e G +++ v+p
  gi|313126498|ref|YP_004036768.1| 215 YISQELGLELKPVDP 229
                                       778999999999988 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.8   1.1e+04      24      32 ..     143     151 ..     143     151 .. 0.84
   2 ?   -1.4   0.0       1.7   2.2e+03      17      26 ..     210     219 ..     195     222 .. 0.55
   3 ?    9.7   0.1   0.00058      0.74      12      47 ..     281     312 ..     274     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.8
                            HTH_23  24 AreLgvsrr 32 
                                       A +Lgv+r+
  gi|313126498|ref|YP_004036768.1| 143 ASALGVPRS 151
                                       679***997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                            HTH_23  17 GlsvreIAre 26 
                                       G ++r I++e
  gi|313126498|ref|YP_004036768.1| 210 GRTYRYISQE 219
                                       4444445555 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00058
                            HTH_23  12 lllaeGlsvreIAreLgvsrrTvyrwlkryreeGle 47 
                                       ll+ e++++re+A+   v++ T++   +ry +e++e
  gi|313126498|ref|YP_004036768.1| 281 LLCNEKKTQREVADVAQVTEVTIR---NRY-QEQIE 312
                                       56667******************9...667.56665 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   0.00012      0.15       5      45 ..       7      47 ..       4      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                               IBR  5 klklkksles.dpnlkwCprpdCe.aiieksegcksvtCskCg 45
                                      ++++++++e+ + +++ Cp  +Ce + i  +++++++ C +Cg
  gi|313126498|ref|YP_004036768.1|  7 QRQREQEVEQdSDERIACP--ECEsTNIITDADQGELVCDDCG 47
                                      67788999*96666*****..9*965566677789999****7 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.58   7.4e+02      39      51 ..     137     149 ..     130     152 .. 0.76
   2 ?    0.7   0.0      0.42   5.4e+02       5      27 ..     186     210 ..     182     219 .. 0.77
   3 ?    6.7   0.0    0.0058       7.4       7      27 ..     284     304 ..     279     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHTSE CS
                             HTH_3  39 etlkklakaLgvs 51 
                                       + + ++a aLgv+
  gi|313126498|ref|YP_004036768.1| 137 SEIDRMASALGVP 149
                                       5677888888887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.42
                                       HHHTTHHH..HHHHHHHTSSHHHHH CS
                             HTH_3   5 Rkqlglsq..eeLAeklGvsrstis 27 
                                         q g+ +   e+Ae++ v++  i 
  gi|313126498|ref|YP_004036768.1| 186 CRQEGIPRslDEVAEVSRVPQKEIG 210
                                       5566666666999999999998776 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0058
                                       HTTHHHHHHHHHHTSSHHHHH CS
                             HTH_3   7 qlglsqeeLAeklGvsrstis 27 
                                         + +q+e+A+++ v+  ti+
  gi|313126498|ref|YP_004036768.1| 284 NEKKTQREVADVAQVTEVTIR 304
                                       6789*************9997 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.6   7.6e+02      47      84 ..     177     214 ..     175     223 .. 0.78
   2 ?    9.7   0.0   0.00066      0.84       3      86 ..     229     310 ..     227     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.6
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcve 84 
                                       +A++al++a+++ + p   +++ +++++ ++++   ++
  gi|313126498|ref|YP_004036768.1| 177 VATSALYAACRQEGIPRSLDEVAEVSRVPQKEIGRTYR 214
                                       79*******99987788888888888877777766665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00066
                                       HHHHHHHHHCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHH CS
                          Cyclin_C   3 plsFlrrflkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedl 79 
                                       p +F+ rf  a +  ++ e+++ a  ++++++ +  + + +p   Aaaa+++a+   n+++ ++++  + ++++  +
  gi|313126498|ref|YP_004036768.1| 229 PKQFVPRFASALGL-SE-EVQAKATEIIDVSAEQGLLSGKSPTGFAAAAIYAASLLCNEKKTQREVADVAQVTEVTI 303
                                       77888899666443.35.89999999999999999999999999**************************9999999 PP

                                       HHHHHHH CS
                          Cyclin_C  80 kpcveli 86 
                                       ++ ++  
  gi|313126498|ref|YP_004036768.1| 304 RNRYQEQ 310
                                       8877765 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00036      0.46      33      62 ..      20      49 ..       5      50 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
                                      S-SS----SCHHTTEECCCCEEEETTTTEE CS
                           Trm112p 33 lpkekpedyellleldieegeLvCpncgra 62
                                       + + pe+ ++ + +d ++geLvC +cg++
  gi|313126498|ref|YP_004036768.1| 20 ERIACPECESTNIITDADQGELVCDDCGLV 49
                                      333344444667889*************86 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.5    0.0039         5      16      30 ..      15      29 ..       8      31 .. 0.84
   2 ?    3.9   0.1     0.041        53      23      31 ..      41      49 ..      33      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0039
                                      TT-SS-EEEETTTTE CS
                         Nudix_N_2 16 dgDnreRlvCpaCgt 30
                                      + D+ eR  Cp C+ 
  gi|313126498|ref|YP_004036768.1| 15 EQDSDERIACPECES 29
                                      789**********85 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.041
                                      EEETTTTEE CS
                         Nudix_N_2 23 lvCpaCgti 31
                                      lvC++Cg +
  gi|313126498|ref|YP_004036768.1| 41 LVCDDCGLV 49
                                      79*****87 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.4    0.0007      0.89       4      26 ..      23      47 ..      23      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0007
                    PhnA_Zn_Ribbon  4 kCplCaSeytY..edgallvCpeCa 26
                                      +Cp+C S +    +d   lvC++C+
  gi|313126498|ref|YP_004036768.1| 23 ACPECESTNIItdADQGELVCDDCG 47
                                      5******999999***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1733.30
//
Query:       gi|313126499|ref|YP_004036769.1|  [L=315]
Description: nuclease-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-26   90.7   1.3    7.5e-26   90.7   1.3    2.0  2  LTD       Lamin Tail Domain
    4.4e-21   75.4   0.0    6.2e-21   74.9   0.0    1.2  1  SNase     Staphylococcal nuclease homologue


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.21   1.9e+03      41      41 ..      73      73 ..      36     135 .. 0.55
   2 !   90.7   1.3   8.4e-30   7.5e-26       5     109 ..     206     314 ..     203     315 .] 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.21
                               LTD 41 w 41
                                       
  gi|313126499|ref|YP_004036769.1| 73 V 73
                                      1 PP

  == domain 2  score: 90.7 bits;  conditional E-value: 8.4e-30
                               LTD   5 agdvvIsevmedgagnnan....efvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsa 76 
                                       + ++ I +v++d++gn+++    e+v + N +++ +dLsgw+++da+++ ytfp+gt tl++ + +++ sg+gt+  
  gi|313126499|ref|YP_004036769.1| 206 NTTIEIVRVHPDADGNDNEnpngEYVVFRNEGEQVIDLSGWSVADAADNeYTFPSGT-TLEPDAELTLKSGTGTDRE 281
                                       56899********999999****************************99********.******************* PP

                               LTD  77 sngskasssavwnnggdavaLydasgevvdsvg 109
                                        + +++++savwnnggd+++L+da+g+vv +  
  gi|313126499|ref|YP_004036769.1| 282 GTVYWGRNSAVWNNGGDTITLRDADGTVVRERR 314
                                       ****************************98765 PP

>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   6.9e-25   6.2e-21       1     107 [.      67     187 ..      67     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 6.9e-25
                                       EEEETTEE-STSSBTTT...............TTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEE CS
                             SNase   1 kvrLvgidaPetakpkk...............tvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvyl 60 
                                       +vrL+g+d+Pe    ++               +++  g++A++++k ++++++v ++ +++  ++++ygrll+yvy+
  gi|313126499|ref|YP_004036769.1|  67 TVRLLGVDTPEVYGSNTpdefegvpdteagaaCLETAGENASAYAKARLSGQEVSLVFDETadRRGYYGRLLGYVYV 143
                                       69***********888899*******************************88888777777999************* PP

                                       TTEEHHHHHHHTTSSEE---BTTSTTTHHHHHHHHHHHHHTT-GGGC CS
                             SNase  61 nkknineeLvkeGlArvyevyekneekkkellkaeeeAkkkrkglWs 107
                                       +++++n  L++ G Ar   vy++ ++++++++ ae++A+ + +glWs
  gi|313126499|ref|YP_004036769.1| 144 DGQSFNYDLIETGHAR---VYDSTFTERERYQTAEKDARTAGRGLWS 187
                                       ****************...7778899********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1645.00
//
Query:       gi|313126500|ref|YP_004036770.1|  [L=133]
Description: hypothetical protein Hbor_17570 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0017   18.1   0.0     0.0078   15.9   0.0    1.8  2  CAP59_mtransfer  Cryptococcal mannosyltransferase 1


Domain annotation for each model (and alignments):
>> CAP59_mtransfer  Cryptococcal mannosyltransferase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.031   5.6e+02      36      67 ..      26      57 ..      11      65 .. 0.83
   2 !   15.9   0.0   4.3e-07    0.0078      19      67 ..      79     127 ..      70     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.031
                   CAP59_mtransfer 36 vSiyesgskdgtkeaLraleaelealgversi 67
                                      +S+  s+ + +++e Lr+l+++l+a g + ++
  gi|313126500|ref|YP_004036770.1| 26 ISLSASNLDSTAPEYLRDLKSDLAADGYHPTV 57
                                      7888899999999******9999998877666 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.3e-07
                   CAP59_mtransfer  19 leallelirfLgpenvfvSiyesgskdgtkeaLraleaelealgversi 67 
                                       l++ +++++fLg +++ + + e   +d+ ++aLral+++ ++ gv+ s+
  gi|313126500|ref|YP_004036770.1|  79 LREFVRAASFLGAARLELTVTEVADEDTVETALRALDERAHREGVHFSV 127
                                       5688999*************************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 736.38
//
Query:       gi|313126501|ref|YP_004036771.1|  [L=207]
Description: methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-12   47.1   0.1    2.7e-12   46.6   0.1    1.2  1  MTS              Methyltransferase small domain
    3.5e-10   39.8   0.3    4.9e-10   39.3   0.3    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      7e-10   39.5   0.0    1.4e-09   38.5   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    3.3e-09   36.7   0.0    9.9e-09   35.2   0.0    1.7  1  UPF0020          Putative RNA methylase family UPF0020
    2.7e-08   33.8   0.0    3.9e-08   33.2   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    8.8e-08   32.0   0.0    1.2e-07   31.6   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
    4.4e-07   30.5   0.0    8.4e-07   29.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    4.9e-05   22.8   0.0    8.3e-05   22.0   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00026   21.0   0.0    0.00031   20.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00091   19.1   0.0      0.001   18.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0095   16.7   0.0      0.018   15.8   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.043   13.8   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.037   13.3   0.0      0.049   12.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
       0.12   12.4   0.1       0.18   11.9   0.1    1.3  1  FtsJ             FtsJ-like methyltransferase
       0.15   11.7   0.0       0.23   11.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.17   11.6   0.0       0.21   11.3   0.0    1.3  1  Met_10           Met-10+ like-protein
       0.24   11.0   0.0       0.31   10.6   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   2.5e-15   2.7e-12      30     127 ..      46     145 ..      35     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2.5e-15
                                       C.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST.TS-EEEEE CS
                               MTS  30 e.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve.ekkfdliv 102
                                       + + ++v+DlG+G+G+l++ +a + p  +v+ vd+da Al+ a+en  + +    ++ v  d++++    ++  +++
  gi|313126501|ref|YP_004036771.1|  46 DvEGKTVVDLGTGTGMLALGAALRGPA-RVVGVDIDADALDTARENRIRVGTTtpIHWVRADATQAPLcIDEPTTVL 121
                                       445678*****************9998.8******************9999995666666777666543577789** PP

                                       E---STTTCHCHHHHHHHHHHHHHH CS
                               MTS 103 sNPPfhagkatelavaeeliaeAke 127
                                       +NPPf a++  ++++ ++++++A++
  gi|313126501|ref|YP_004036771.1| 122 MNPPFGAQHG-HEHADRAFLQTAAS 145
                                       *******998.77788888888875 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.3   4.6e-13   4.9e-10     161     207 ..      48      94 ..      40     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 4.6e-13
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelN 207
                                       eg++v+D+GtG+G+La++aa+ g ++vv+vDiD  A++ a+eN  + 
  gi|313126501|ref|YP_004036771.1|  48 EGKTVVDLGTGTGMLALGAALRGPARVVGVDIDADALDTARENRIRV 94 
                                       689****************************************8655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   1.3e-12   1.4e-09       1      88 [.      52     142 ..      52     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.3e-12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEE..EST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvs..sga 73 
                                       v+dlG+GtG l+l +a r g a+v+gvDi++++l++are+  + g    +++v++da++ p+  ++   v++   ++
  gi|313126501|ref|YP_004036771.1|  52 VVDLGTGTGMLALGAALR-GPARVVGVDIDADALDTARENRIRVGTttPIHWVRADATQAPLCIDEPTTVLMnpPFG 127
                                       89**************99.57******************998866677***********997555555555523222 PP

                                       GGGSSHHHHHHHHHH CS
                   Methyltransf_25  74 lhhlsdedlekalke 88 
                                        +h +++  +++l+ 
  gi|313126501|ref|YP_004036771.1| 128 AQHGHEHADRAFLQT 142
                                       345444444555555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   9.4e-12   9.9e-09      77     193 ..      72     183 ..      21     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 9.4e-12
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHH CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelk 153
                                       ++++g+D+d+ ++++areN  + g +  i+++ ada++ +l  +e  +++ npP+G   g+++a +    +fl++++
  gi|313126501|ref|YP_004036771.1|  72 ARVVGVDIDADALDTARENRIRVGTTTPIHWVRADATQAPLCIDEPTTVLMNPPFGAQHGHEHADR----AFLQTAA 144
                                       4579************************************8888999*************999975....5666666 PP

                                       HH-TT..-EEEEEESSHHHHHCC---ESEEEEEEETTEEE CS
                           UPF0020 154 rvlrgggrlvlltsenkalekaleeralrkvkeknvklgl 193
                                       + l++ + +v  t +++ +e++++++  + +++++  ++l
  gi|313126501|ref|YP_004036771.1| 145 S-LSNVSYSVHNTGSQEFVEAFAADEGGEVTHAFRATFSL 183
                                       6.33336677777777777777777788888888777666 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   3.7e-11   3.9e-08       3      54 ..      48      97 ..      46     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.7e-11
                   Methyltransf_31  3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld 54
                                      +g++v+DlG+GtG l++ +a  l+  a+vvG+Di+++a+  Aren+ + g +
  gi|313126501|ref|YP_004036771.1| 48 EGKTVVDLGTGTGMLALGAA--LRGPARVVGVDIDADALDTARENRIRVGTT 97
                                      5789****************..5667******************98766655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.1e-10   1.2e-07      38     129 ..      45     132 ..      39     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.1e-10
                                       CCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EE CS
                     Cons_hypoth95  38 aeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeef 114
                                        ++eg++v+Dl  G+G l+l A+ Rg +++v v+ d+ a+ + +en  +++++  ++ ++ da++a l       e 
  gi|313126501|ref|YP_004036771.1|  45 GDVEGKTVVDLGTGTGMLALGAALRGPARVVGVDIDADALDTARENRIRVGTTTPIHWVRADATQAPLCI--D--EP 117
                                       56999**********************************************9999********9999888..2..33 PP

                                       EEEEE--SSSTTCH. CS
                     Cons_hypoth95 115 divflDPPyakelli 129
                                         v ++PP+ +++  
  gi|313126501|ref|YP_004036771.1| 118 TTVLMNPPFGAQHGH 132
                                       69*******999873 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0     8e-10   8.4e-07       1      57 [.      53     112 ..      53     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 8e-10
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpf 57 
                                       +d+G+GtG la   a rg arvvgvD+++ +l++a+e+  + g    + +v+ada++ p+
  gi|313126501|ref|YP_004036771.1|  53 VDLGTGTGMLALGAALRGpARVVGVDIDADALDTARENRIRVGTttPIHWVRADATQAPL 112
                                       59*************99*********************99999999999*******9886 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   7.9e-08   8.3e-05      39     112 ..      40     112 ..      35     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.9e-08
                                       HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHH.HHHHHTSSTEEEEE--TTT-TT CS
                   Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgek.klkeegkinieflqanaeeLpf 112
                                       v +l+++ +g++v+D+ +Gtg la  l  +++   +vv++Di+++ L+++++ +++  +++ i+++ a+a + p 
  gi|313126501|ref|YP_004036771.1|  40 VADLNGDVEGKTVVDLGTGTGMLA--LGAALRGPARVVGVDIDADALDTAREnRIRVGTTTPIHWVRADATQAPL 112
                                       778999***************887..567789999*************99872555556669*******998775 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.9e-07   0.00031      21      78 ..      44      98 ..      32     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-07
                   Methyltransf_32 21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78
                                      + + + +tvvD+G G g L+   al   + + +vvg+d+ ++  ++a++ + ++g + 
  gi|313126501|ref|YP_004036771.1| 44 NGDVEGKTVVDLGTGTGMLALGAAL---RGPARVVGVDIDADALDTARENRIRVGTTT 98
                                      5567789******************...88******************9999988544 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.8e-07     0.001      22      62 ..      48     123 ..      24     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.8e-07
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae..................................k 62 
                                       +g+ v+d+G+GtG l+  ++ +g   v+gvD++  a + a+                                  +
  gi|313126501|ref|YP_004036771.1|  48 EGKTVVDLGTGTGMLALGAALRGPaRVVGVDIDADALDTARenrirvgtttpihwvradatqaplcidepttvlmN 123
                                       6789******************9989*******9999998877777777666666665555555555555555551 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-05     0.018       1      42 [.      53      93 ..      53     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklak 42
                                      +++G+GtG l+   + +  +++++gvDi+++a++ a+e   +
  gi|313126501|ref|YP_004036771.1| 53 VDLGTGTGMLALGAALR-GPARVVGVDIDADALDTARENRIR 93
                                      599*****998887777.9**************555554333 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.1e-05     0.043      14      74 ..      48     107 ..      39     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdG 74 
                                       +g++v+D Gt  g+l++ ++ +g a +v+ +Di + +l++a+en  + g+++ i+ + +d 
  gi|313126501|ref|YP_004036771.1|  48 EGKTVVDLGTGTGMLALGAALRGPA-RVVGVDIDADALDTARENRIRVGTTTPIHWVRADA 107
                                       4899****************99998.99****************99999988888777665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.7e-05     0.049      62     108 ..      48      94 ..      12     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                                       TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS CS
                              CMAS  62 pGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdel 108
                                       +G+t++d+G+G G l+  a+ r  ++vvg+ + ++   +a+++  ++
  gi|313126501|ref|YP_004036771.1|  48 EGKTVVDLGTGTGMLALGAALRGPARVVGVDIDADALDTARENRIRV 94 
                                       7*********************9*********999999988865555 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00017      0.18      21      58 ..      48      83 ..      34     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                      TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSH CS
                              FtsJ 21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpma 58
                                      +gktvvDlg ++G  +  ++ r g+ ++vv+vD+   a
  gi|313126501|ref|YP_004036771.1| 48 EGKTVVDLGTGTGMLALGAALR-GP-ARVVGVDIDADA 83
                                      689*******************.87.9*******8773 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.23      53     132 ..      25     106 ..      13     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                       TEEE--HHHHHHHHHHTT--...TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHH.HHHCTTCS CS
                              PCMT  53 natiSaphmvalalellelk...kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrn.lkkldlen 125
                                       +++   p + a ++   +l+   +g+ v+++G+G+G l+  l   ++  +rvv+++  ++  ++a++n ++   ++ 
  gi|313126501|ref|YP_004036771.1|  25 EQYPTPPGLAAHVVHVADLNgdvEGKTVVDLGTGTGMLA--LGAALRGPARVVGVDIDADALDTARENrIRVGTTTP 99 
                                       555566666777766666543337999**********97..4566788889*****988877777665155555556 PP

                                       EEEEES- CS
                              PCMT 126 vivvvgD 132
                                       ++ v +D
  gi|313126501|ref|YP_004036771.1| 100 IHWVRAD 106
                                       6666666 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.21     100     160 ..      48     107 ..      36     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                       TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-G CS
                            Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDg 160
                                       eg++Vvd+  G G +a+ +a    + rv+++d++ ++    +en  +      ++ + +D+
  gi|313126501|ref|YP_004036771.1|  48 EGKTVVDLGTGTGMLALGAAL-RGPARVVGVDIDADALDTARENRIRVGTTTPIHWVRADA 107
                                       799*****************7.55667*********9998888855555555555555555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00029      0.31       3      83 ..      51     128 ..      49     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflS 78 
                                       +++Dl +G+G  +   al    +v++++i+ + l  a +N    g    i +v +d +++   + + ++    v++ 
  gi|313126501|ref|YP_004036771.1|  51 TVVDLGTGTGMLALGAALRgPARVVGVDIDADALDTARENRIRVGTTTPIHWVRADATQAPLCIDEPTT----VLMN 123
                                       78999999999999999994469******************999*************998777766666....8888 PP

                   Methyltransf_15  79 pPwGG 83 
                                       pP G 
  gi|313126501|ref|YP_004036771.1| 124 PPFGA 128
                                       88884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1204.96
//
Query:       gi|313126502|ref|YP_004036772.1|  [L=550]
Description: hypothetical protein Hbor_17590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-08   35.0  14.1    1.3e-08   35.0  14.1    2.7  3  Rhomboid    Rhomboid family
  ------ inclusion threshold ------
        8.1    6.4   7.7        1.1    9.2   2.0    2.6  2  Herpes_US9  Alphaherpesvirus tegument protein US9


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3      0.65   5.9e+03     103     120 ..      40      59 ..      12      70 .. 0.45
   2 !   35.0  14.1   1.5e-12   1.3e-08       9     148 ..      90     250 ..      80     252 .. 0.76
   3 ?   -1.9   0.3      0.33   2.9e+03      84     116 ..     277     306 ..     268     324 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.65
                                       C.....CCCCCCCCCCHHHC CS
                          Rhomboid 103 a..llllllfillnlvlgll 120
                                           +l +++ +l +++g+l
  gi|313126502|ref|YP_004036772.1|  40 RrrFVLGVPWGSLITLVGVL 59 
                                       13434444444444444443 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 1.5e-12
                                       HHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHH............HHHHHHHHHHH......HHHHHHHHHHHHH-S CS
                          Rhomboid   9 rlltsmflHagwlHllfNmlallvfGsplerrl............Gslrflllyll......sglagsllsllfsae 67 
                                        ++t++f+H g  Hl++N+ a  +f++ +e  +            Gs+r   +  +      +++++++l+++f   
  gi|313126502|ref|YP_004036772.1|  90 GVVTAAFSHNGPGHLIGNLTATAMFAPVAEYAWghfprergstsfGSWRTNPYVRAflivplVVFVAAILTAAFALG 166
                                       589*****************************9999****8888877765444333111222444455555555554 PP

                                       ...-EESSHHHHHHHHHHHHHHHHCCCCGS----HC...CCCCCCCCCCHHHCTSS........STTTHHHHHHHHH CS
                          Rhomboid  68 sesplvGaSGaifgllgallvlvprnrkllrkliiallllllfillnlvlgllpra........ggvsnlAHlgGll 136
                                          p++G+SGa+f++ g++lv+ p     + +   a  + +++ +l++     +++        + ++ ++H  Gl 
  gi|313126502|ref|YP_004036772.1| 167 ---PIIGFSGAVFAFAGFALVNYPLVTVIALVGSRA--TRVVYNALQTPQLTASGHpayitpwwADIAIQGHALGLF 238
                                       ...**********************99999888888..44444444444444444444466666************* PP

                                       HHHHHHHHHCCH CS
                          Rhomboid 137 aGlllgllllrr 148
                                       +G++lgl+++r+
  gi|313126502|ref|YP_004036772.1| 239 IGVFLGLVVVRN 250
                                       *******99986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.33
                                       HHHHHHHHCCCCGS----HC...CCCCCCCCCC CS
                          Rhomboid  84 gallvlvprnrkllrkliiallllllfillnlv 116
                                       +++++++ +++ l+r + +a   l++ +++ ++
  gi|313126502|ref|YP_004036772.1| 277 AVYWFRGGETYVLYRAVGVA---LVVTVAVIIA 306
                                       45555555555555544444...2222222222 PP

>> Herpes_US9  Alphaherpesvirus tegument protein US9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.0   0.00012       1.1      37      57 ..     149     169 ..     142     171 .. 0.83
   2 ?   -2.2   0.3      0.44     4e+03      35      45 ..     301     311 ..     291     327 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00012
                        Herpes_US9  37 tliivllvAvlsaaFalGall 57 
                                       + ++v++ A+l+aaFalG ++
  gi|313126502|ref|YP_004036772.1| 149 VPLVVFVAAILTAAFALGPII 169
                                       44689*************886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.44
                        Herpes_US9  35 vitliivllvA 45 
                                       v ++i+v +vA
  gi|313126502|ref|YP_004036772.1| 301 VAVIIAVTVVA 311
                                       44555565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 3129.92
//
Query:       gi|313126503|ref|YP_004036773.1|  [L=92]
Description: metal-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-34  116.1   1.9      7e-34  116.0   1.9    1.0  1  UPF0058        Uncharacterised protein family UPF0058
  ------ inclusion threshold ------
      0.033   14.7   0.1      0.048   14.1   0.1    1.3  1  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   1.9   7.8e-38     7e-34       1      86 [.       1      87 [.       1      88 [. 0.97

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 7.8e-38
                                      --HHHHHHHHHHHHHHHHHH.TSTT--TTTTHHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH CS
                           UPF0058  1 MhKdeLieLHqllvevkkel.eeeevekeefkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekeessaervsk 78
                                      MhKdeL+eLH+++v++k+++  +e+v++e f+ Ye+L ++P+h+h+sK+ehk+A+fvLgna+a a+se+e+s+a+rv k
  gi|313126503|ref|YP_004036773.1|  1 MHKDELLELHEQMVTIKDYFaSQEHVNSELFEPYEQLAVDPSHVHKSKSEHKHAVFVLGNALAAAMSEDEFSNAGRVGK 79
                                      ********************667799999************************************************** PP

                                      HHHHHHHH CS
                           UPF0058 79 rlkelaek 86
                                      r++ela++
  gi|313126503|ref|YP_004036773.1| 80 RMEELAKD 87
                                      *****986 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.4e-06     0.048       3      49 ..      35      79 ..      33      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.4e-06
                     T7SS_ESX_EspC  3 dnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpica 49
                                      ++L Vdp+h+ +  ++h+ ++  + +a+aaa   s++  ++ G ++ 
  gi|313126503|ref|YP_004036773.1| 35 EQLAVDPSHVHKSKSEHKHAVFVLGNALAAA--MSEDEFSNAGRVGK 79
                                      689**************************99..33333333455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.36s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 524.60
//
Query:       gi|313126504|ref|YP_004036774.1|  [L=69]
Description: hypothetical protein Hbor_17610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00022   21.0   0.1    0.00029   20.6   0.1    1.2  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.048   13.5   0.0       0.06   13.2   0.0    1.1  1  IclR      Bacterial transcriptional regulator
      0.081   12.8   0.1       0.28   11.1   0.1    1.9  1  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   4.9e-08   0.00029       2      35 ..       4      38 ..       3      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.9e-08
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlre 35
                                      v+i+++e l  ++ +l++ ++ +Sr e+I+e+l  
  gi|313126504|ref|YP_004036774.1|  4 VNISVPEHLEMQIAQLVEQGEfVSREEAIEELLST 38
                                      89******************************976 PP

>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     1e-05      0.06      51      90 ..       7      46 ..       3      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                                      -SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEEEE-TT CS
                              IclR 51 tdpeeLleeLakvReqGyavdreEeeegvrciAapifdas 90
                                        pe+L+ ++a+  eqG  v+reE  e++ + +   f  s
  gi|313126504|ref|YP_004036774.1|  7 SVPEHLEMQIAQLVEQGEFVSREEAIEELLSTGLRAFKTS 46
                                      5689*************************99998877765 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.8e-05      0.28       1      19 [.       1      19 [.       1      22 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                             RHH_5  1 SkRvnvtLPeelleeLeew 19
                                      +++vn+++Pe+l  +++++
  gi|313126504|ref|YP_004036774.1|  1 MPKVNISVPEHLEMQIAQL 19
                                      79**********9888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 415.11
//
Query:       gi|313126505|ref|YP_004036775.1|  [L=197]
Description: sulfite oxidase-like oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-36  123.7   0.0    7.2e-36  123.4   0.0    1.1  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.4   0.0     4e-40   7.2e-36       3     172 .]      34     179 ..      32     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 4e-40
                                       ----.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHH CS
                    Oxidored_molyb   3 avpkvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlr 79 
                                        +p+ dp++w ++v+g ve++l++s+++++++pa+++  +++C++              +w   + +++e+tGv + 
  gi|313126505|ref|YP_004036775.1|  34 GTPSWDPQSWAFDVWGAVEEELTFSYEEFQDIPAETQRQDFHCVT--------------GW---SKFDCEFTGVTFP 93 
                                       568889***************************************..............8*...9************ PP

                                       HHHHHTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBT CS
                    Oxidored_molyb  80 dvLekagvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvK 156
                                       ++ e agv+ ++a hv+f+++d      +y++++ple++++++v+++ e++gepLp dhG PlR+v p+ ++++ +K
  gi|313126505|ref|YP_004036775.1|  94 TLAELAGVR-DDAIHVMFHALD------GYTTNLPLEDCMREEVMFVSEYDGEPLPSDHGGPLRVVTPHKYAYKGAK 163
                                       ********7.9**********9......5***********99*********************************** PP

                                       TEEEEEEESS---SHH CS
                    Oxidored_molyb 157 wlkrievsdeesegyw 172
                                       w++ +e+ +e+++gyw
  gi|313126505|ref|YP_004036775.1| 164 WVSGVEFLTEPERGYW 179
                                       ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1136.74
//
Query:       gi|313126506|ref|YP_004036776.1|  [L=440]
Description: isochorismate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-74  250.7   0.0    2.1e-74  250.3   0.0    1.1  1  Chorismate_bind  chorismate binding enzyme


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.3   0.0   1.2e-78   2.1e-74       2     258 .]     172     430 ..     171     430 .. 0.96

  Alignments for each domain:
  == domain 1  score: 250.3 bits;  conditional E-value: 1.2e-78
                                       HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEE......EETTEEEEEEESS CS
                   Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysfll......eledsellgaSPE 72 
                                       ++d+++ v++++e+i+agdl+kvvl+++l a l+++++  +++++l   +p++y fl+      + ++ +++ga+PE
  gi|313126506|ref|YP_004036776.1| 172 KDDWNAGVNAAVERISAGDLRKVVLAQALAADLASDLSVPDILDRLGDSYPDCYRFLVepepdaDRPQASFFGATPE 248
                                       689*******************************************************776655444489******* PP

                                       EEEEEETTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEE CS
                   Chorismate_bind  73 lllkveggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkvery 149
                                       +l++++g+ ++et ++aGT+ rg+tp+ede l++ell+deK+ +Eh+++ + ir++L+++  ++sv++   + v+r+
  gi|313126506|ref|YP_004036776.1| 249 RLVSLRGR-TVETGALAGTTGRGETPAEDEWLARELLDDEKNVHEHELVAETIRDQLAPF--ASSVNTG-DRCVKRL 321
                                       ******65.***************************************************..7****95.567**** PP

                                       TTEEEEEEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SE CS
                   Chorismate_bind 150 sevlhlvstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRt 226
                                       ++v+hl + i+++l+++ ++l+l++al+Pt+av+G+P ++a+e i++ E+++Rg+Ya++vg++da g + +av++R+
  gi|313126506|ref|YP_004036776.1| 322 ATVQHLWTPITATLATSEHVLSLVEALHPTPAVGGLPPEKALETIRDTEPFDRGWYAAPVGWIDAAGYGSFAVALRS 398
                                       ***************************************************************************** PP

                                       EEEETTEEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 227 avvkdkelrlgaGaGIvadSdpeaEyeEtlaK 258
                                       av +d++ +l+aG G+v dSdp++E++E++ K
  gi|313126506|ref|YP_004036776.1| 399 AVSRDDTTTLFAGVGVVEDSDPDREWDEVQLK 430
                                       *****99**********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2460.37
//
Query:       gi|313126507|ref|YP_004036777.1|  [L=583]
Description: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-38  131.4   0.0    5.7e-38  130.2   0.0    1.6  2  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
    9.5e-11   41.8   0.0    1.3e-10   41.3   0.0    1.1  1  TPP_enzyme_M_2  Middle domain of thiamine pyrophosphate
    4.8e-10   39.4   0.0    1.7e-09   37.7   0.0    1.8  2  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
     0.0041   16.9   0.0      0.011   15.5   0.0    1.7  1  GRDA            Glycine reductase complex selenoprotein A
  ------ inclusion threshold ------
       0.13   12.6   0.0         25    5.2   0.0    2.6  2  PucR            Purine catabolism regulatory protein-like fam


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.2   0.0   1.6e-41   5.7e-38       4     169 ..      11     182 ..       9     185 .. 0.97
   2 ?   -3.8   0.0       2.3   8.2e+03     140     163 ..     541     563 ..     540     569 .. 0.74

  Alignments for each domain:
  == domain 1  score: 130.2 bits;  conditional E-value: 1.6e-41
                                       HHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCH CS
                      TPP_enzyme_N   4 aealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnal 80 
                                       a+ lv+ L+++gv+ v++ pGsr++pl++a++++++i+v  +++E++ af+A g ar+tg +  +++tsg++a+n+ 
  gi|313126507|ref|YP_004036777.1|  11 ARTLVDELAKAGVDAVCITPGSRSTPLTEAFDRHDDIHVFSHLDERSSAFFALGRARRTGDVTPLVCTSGTAAANYH 87 
                                       7789************************************************************************* PP

                                       HHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHH.......HHHHHHHSS CS
                      TPP_enzyme_N  81 talaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealr.......rAirtalsg 150
                                       +a++eA+++r+P+lvl++drp + r+ g+ q ++dq++l+ + +++   +++pe++p+ lr       rA+++a+ +
  gi|313126507|ref|YP_004036777.1|  88 PAIIEAAQSRVPMLVLTADRPPEIRDSGANQ-TIDQEKLYGDAVRWYKDLAEPEATPRKLRslrttaaRALTKATGT 163
                                       *******************************.********************************************* PP

                                       S--EEEEEEEHHHCC-EEE CS
                      TPP_enzyme_N 151 rpgPvylelpkdvlleevd 169
                                       + gPv+l++p   +le+v+
  gi|313126507|ref|YP_004036777.1| 164 PAGPVHLNVPFRKPLEPVT 182
                                       **********999999887 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.3
                                       HHHHHHHHHSSS--EEEEEEEHHH CS
                      TPP_enzyme_N 140 lrrAirtalsgrpgPvylelpkdv 163
                                       +r+A++ta ++  g  ++e+  d 
  gi|313126507|ref|YP_004036777.1| 541 FRKAYETA-TQSEGTHVIEVVTDA 563
                                       57888888.888888888877665 PP

>> TPP_enzyme_M_2  Middle domain of thiamine pyrophosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   3.7e-14   1.3e-10      34     208 .]     223     407 ..     213     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.7e-14
                                       HHHTTSSEEEEE-B--..HHHHHHHHHHHHHHT--EEE-TTT-S........--SSTTHHHHTTSHHHHHHHTT-SE CS
                    TPP_enzyme_M_2  34 drwrqkrGvvvaGrls..aeegkqvaawaeklGWplltDvqsql........gqalpyaDlwLanpkvkeeLaqadi 100
                                       +r+ + rG+vvaG  +    ++++vaa+a+  G p+l+D +s++           ++  D +L + +v++   + di
  gi|313126507|ref|YP_004036777.1| 223 ERLSTPRGLVVAGPADapGIDSEAVAAFAHATGFPILADPLSGVrfgghvrvAPVIGGYDSFLDE-QVTQSWPDPDI 298
                                       578899*******998435699*********************9999998878889999*99975.688999***** PP

                                       EEEESB---SHHHHHHHHH---SEEEEEESS-SB--TT--SEEEEES-HHHHHHHS-------....--SHHHHHHH CS
                    TPP_enzyme_M_2 101 viqfGsrlvsKrllqflaelkpeeyWlvdesqgrldpahhrkrrfvakveewlrahpaesqkp....Walellalse 173
                                       v  fG++ +sK l ++la+++  e  +vd+ +g  +++  +   +va+ ++ +         p    W ++ ++ + 
  gi|313126507|ref|YP_004036777.1| 299 VFRFGASPTSKPLRKYLARVDA-EQLVVDPAAGWREAEFTATDLVVADPSRLMVRLSRLLAGPggpeWRKRWENADA 374
                                       **********************.778**********************9987655444433333344*999888888 PP

                                       HHHHHHHTT.TTSSSHHHHHHTGGGGS-TT-EEEE CS
                    TPP_enzyme_M_2 174 klaelveqqldeefgEaqlahqlaellpeqgqLFl 208
                                       + ++++e+  ++ef E  +   + el p+  ++F+
  gi|313126507|ref|YP_004036777.1| 375 THESVLET--SDEFCEGRVLADVVELAPDPATIFV 407
                                       88887775..589***************9999997 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.52   1.9e+03      56      78 ..      80     103 ..      61     106 .. 0.74
   2 !   37.7   0.0   4.6e-13   1.7e-09      25     153 .]     433     559 ..     413     559 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.52
                                       HHHHHT.GGGHHHHHHTT-SEEEE CS
                      TPP_enzyme_C  56 Ggflmi.lqelatavrrnlpitvv 78 
                                       G+ + + +++++ a++ ++p++v+
  gi|313126507|ref|YP_004036777.1|  80 GTAAANyHPAIIEAAQSRVPMLVL 103
                                       566777789999999999999987 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 4.6e-13
                                       TTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTT CS
                      TPP_enzyme_C  25 gglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggkrks 101
                                        g + +   ++ A+Ga  a  d +   ++GD ++++ ++ l  + r +++ t+vv+nN g g   + +  +++  ++
  gi|313126507|ref|YP_004036777.1| 433 RGASGIDGIVSTALGAGSATTD-DLTLVTGDLAYYHDMNGLLAIGRSDVDATIVVVNNDGGGIFHMLPIEQFDPPFT 508
                                       5555555667899999998655.999*****************************************9999988888 PP

                                       TSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C 102 gpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       ++  k+ + +d++  a  +G + arve  d + +++a ++a +++g+ +iev
  gi|313126507|ref|YP_004036777.1| 509 SQF-KTPHGLDLEPSADLYGLSFARVEGGDSDGFRKAYETATQSEGTHVIEV 559
                                       866.68999*****************************************97 PP

>> GRDA  Glycine reductase complex selenoprotein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.2e-06     0.011      37     106 ..     201     272 ..     193     282 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.2e-06
                              GRDA  37 ecfvctaaGamdlenqkrvkelaekfgaenvvvllGaaea...eaaglaaetvtaGdptfaGplagvqlGlkv 106
                                       + fv t++G  +l++   +++lae+ ++   +v+ G a+a   ++  +aa + ++G p  a pl+gv++G +v
  gi|313126507|ref|YP_004036777.1| 201 DAFVGTTTGVPELDDD-ALRDLAERLSTPRGLVVAGPADApgiDSEAVAAFAHATGFPILADPLSGVRFGGHV 272
                                       68***********976.69*******************98444566788888999*************99665 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.007        25      60      89 ..      12      40 ..       4      48 .. 0.77
   2 ?    4.5   0.0     0.012        42      33     101 ..     192     262 ..     181     270 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.007
                              PucR 60 aelvrelaeagvaaLviklg.reipeeliea 89
                                      + lv+ela+agv a++i  g r  +  l ea
  gi|313126507|ref|YP_004036777.1| 12 RTLVDELAKAGVDAVCITPGsR--STPLTEA 40
                                      689***************9843..3444444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                              PucR  33 pdiaellrggeLllttglalkddpealaelvrelaeagvaaLviklgr...eip.eelieaadelglPlielp 101
                                       p+ia+  r++ ++ tt    + d++al++l ++l+     +Lv+   +    i+ e++ ++a + g+P+++ p
  gi|313126507|ref|YP_004036777.1| 192 PEIAAEGREDAFVGTTTGVPELDDDALRDLAERLSTP--RGLVVAGPAdapGIDsEAVAAFAHATGFPILADP 262
                                       5555555555555554444466889999999999765..4777776421235534888999********9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3568.25
//
Query:       gi|313126508|ref|YP_004036778.1|  [L=158]
Description: hypothetical protein Hbor_17650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1001.15
//
Query:       gi|313126509|ref|YP_004036779.1|  [L=159]
Description: hypothetical protein Hbor_17660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 941.69
//
Query:       gi|313126510|ref|YP_004036780.1|  [L=305]
Description: 1,4-dihydroxy-2-naphthoate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-52  178.9   0.0    1.8e-51  174.9   0.0    1.9  1  ECH_1     Enoyl-CoA hydratase/isomerase
    1.1e-16   61.3   0.0    2.3e-16   60.2   0.0    1.5  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.9   0.0     2e-55   1.8e-51       8     250 ..      35     300 ..      32     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: 174.9 bits;  conditional E-value: 2e-55
                                       EEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTS......EEEEEB-HHHHHHHHC..HHHHHH.. CS
                             ECH_1   8 viklnrPeavNalsaelltEliqalekleddksvravvLtG.gdk......aFaaGadlkemaeeek..akqall.. 73 
                                        i ++rPe+ Na+ + +++El +al +++++  v+ v LtG g+       aF+aG+d+  + + ++  +++++   
  gi|313126510|ref|YP_004036780.1|  35 RIAFDRPEKRNAFRPGTVDELYAALDHARKQADVGCVLLTGnGPSekdggwAFCAGGDQSVRGGSGYeyRDDDEAdd 111
                                       699**************************************87754566669********99988776644433311 PP

                                       ............HCCHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETT.TEEE-GGGGGTS--CTTCH CS
                             ECH_1  74 ............keevlelwtklytvpkpviaavnGaaigGGlelalacDiviaadn.asfglnelklGlipgaggt 137
                                                   + ++le +++++ +pkpv+a v G a+gGG+ l+++cD++ a+d+ a+f ++   + ++++ +g+
  gi|313126510|ref|YP_004036780.1| 112 addplvreakagRLHILEVQRLIRFMPKPVVAVVPGWAVGGGHSLHVVCDLTLASDEhAKFLQTDPDVASFDAGFGS 188
                                       1111111111114456778889999*****************************886377***************** PP

                                       HHHHHHHHHHHHHHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHH.HHH CS
                             ECH_1 138 qilarkvGkskAeeilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakle.dal 213
                                        +la++vG++kA+e+   gk +sa+ea ++G+ ++++p+e+l+  ale+a ++ +ksp a+r+lk a+n + +    
  gi|313126510|ref|YP_004036780.1| 189 AYLAKQVGQKKAREVFFRGKTYSAEEAVDMGMANEAIPHEKLETVALEWADEMTNKSPMAMRMLKYAFNMTDDgLVG 265
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH----- CS
                             ECH_1 214 aeqleaeaklfestfskddikeGlqaflEkrkpefed 250
                                       +++++ ea+ + ++++++  +eG++aflEkr+p+f d
  gi|313126510|ref|YP_004036780.1| 266 QQVFAGEATRLGYMTDEA--QEGRDAFLEKRDPNFSD 300
                                       **************9995..5**************86 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0   2.6e-20   2.3e-16       3     189 ..      35     242 ..      33     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 2.6e-20
                                       EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSS......ECE--B-..-HHHHHHHHCS...... CS
                             ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagek......afCAGgD..vralyeaakeg...... 65 
                                       +i ++rp++ Na     v++l +al++ +k+ +v +v+l+g+g+       afCAGgD  vr    +  e       
  gi|313126510|ref|YP_004036780.1|  35 RIAFDRPEKRNAFRPGTVDELYAALDHARKQADVGCVLLTGNGPSekdggwAFCAGGDqsVRG--GSGYEYrdddea 109
                                       6889*************************************9766668888*******44443..222222223344 PP

                                       ..-TH.....H.HHHHHHHHHHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT.-EEE--GGGGT--.-- CS
                             ECH_2  66 ..kke.....e.eeffreeYklnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvter.tvfAmPEtaIGlf.PD 132
                                         + +     e ++   +  +++ li  +pkpvva++ G ++GgG +l v + +  ++++ ++f   +  +  f   
  gi|313126510|ref|YP_004036780.1| 110 ddA-DdplvrEaKAGRLHILEVQRLIRFMPKPVVAVVPGWAVGGGHSLHVVCDLTLASDEhAKFLQTDPDVASFdAG 185
                                       431.13333222334445678999*********************************96516787777777666267 PP

                                       TTHHHHHHCSSTTHHHHHHHH---B-HHHHHHTTS--EE--GGGHHHHHHHHHTT.. CS
                             ECH_2 133 vGgsyfLsrlpgelGlylalTGarlkgadalaaglathyvpseklealeeaLaeles 189
                                        G  y+ +++ ++ ++ +   G++ ++++a+ +g+a+  +p+ekle+++ + a+  +
  gi|313126510|ref|YP_004036780.1| 186 FGSAYLAKQVGQKKAREVFFRGKTYSAEEAVDMGMANEAIPHEKLETVALEWADEMT 242
                                       7888888999999********************************999766555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1912.66
//
Query:       gi|313126511|ref|YP_004036781.1|  [L=648]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-36  124.0   0.2    6.1e-21   74.6   0.0    3.1  3  PAS_9            PAS domain
    1.5e-23   83.0   0.1    1.3e-10   41.3   0.0    2.6  2  PAS              PAS fold
    6.8e-23   81.0   3.0    1.4e-13   51.1   0.1    3.1  3  PAS_4            PAS fold
    1.9e-18   66.5   0.0    1.3e-08   35.0   0.0    2.6  2  PAS_3            PAS fold
    9.1e-16   58.4   0.1      1e-14   55.0   0.1    2.3  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
      5e-09   36.2   1.2    1.6e-08   34.6   0.0    2.2  2  HATPase_c_2      Histidine kinase-like ATPase domain
    1.3e-07   31.4   0.1      0.016   15.2   0.0    3.4  3  PAS_8            PAS domain
    7.2e-07   29.6   0.0    1.5e-06   28.6   0.0    1.6  1  GAF_3            GAF domain
    9.8e-07   29.5   0.0      1e-05   26.2   0.0    2.4  2  GAF              GAF domain
    3.8e-05   24.0   0.1     0.0006   20.1   0.0    2.7  3  GAF_2            GAF domain
    0.00023   21.0   0.0    0.00048   20.0   0.0    1.5  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
  ------ inclusion threshold ------
      0.031   13.9   0.2      0.075   12.6   0.0    1.7  2  HisKA_4TM        Archaeal 4TM region of histidine kinase
      0.059   12.9   0.8        9.6    5.7   0.1    2.4  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      0.066   11.7   1.8       0.11   11.1   1.8    1.2  1  FUSC             Fusaric acid resistance protein family
       0.17   12.0   0.8       0.41   10.8   0.8    1.7  1  DUF5132          Protein of unknown function (DUF5132)


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   4.1e-15     5e-12      10     104 .]     195     288 ..     187     288 .. 0.91
   2 !   74.6   0.0   5.1e-24   6.1e-21       7     104 .]     316     413 ..     307     413 .. 0.94
   3 ?   -3.3   0.0       9.2   1.1e+04      45      71 ..     458     482 ..     433     499 .. 0.63

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 4.1e-15
                             PAS_9  10 dgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltasp 84 
                                        g  +ya+ a++r+lGysp+e+ g ++td+   + ++ a+e  +++l++    +++ e+++ +++g+ +  +++a+p
  gi|313126511|ref|YP_004036781.1| 195 TGQFTYASSAVKRILGYSPAELTGEQFTDFTteAAAEVAAEAYARVLDNQN--VQNLELDFLDDTGSVVVLEVNATP 269
                                       68889**************************88888888999999999999..************************ PP

                             PAS_9  85 vkdddgelvgiivilrDite 104
                                       v++ dg +vg+ ++ rD+t+
  gi|313126511|ref|YP_004036781.1| 270 VIE-DGDVVGVQGVGRDVTD 288
                                       *85.67899999******96 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 5.1e-24
                             PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                         p+ +++y+Ne+++r++Gys+ee lg+++  l+   tdpe+ +rl+ a+++g+  +  ve++++r++g++fw+++ 
  gi|313126511|ref|YP_004036781.1| 316 REPNEPLIYVNEGFERVTGYSAEETLGRNLCFLQgeQTDPERSQRLETAIDAGE--PVVVELINYRRDGTPFWNQIY 390
                                       56888999*********************99999********************..********************* PP

                             PAS_9  82 aspvkdddgelvgiivilrDite 104
                                       ++pv d+ g +++++++++D+te
  gi|313126511|ref|YP_004036781.1| 391 LAPVDDKTGAITHYVGFQQDVTE 413
                                       *****99***************8 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9.2
                             PAS_9  45 eanerlraaleqgrkkerevevvlirk 71 
                                       ++ er+++ l +++  er++e++ + +
  gi|313126511|ref|YP_004036781.1| 458 RRVERIAQDLLSMS--ERARELEQYAR 482
                                       33334444444444..66666665544 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   5.2e-13   6.2e-10       2     113 .]     177     286 ..     176     286 .. 0.95
   2 !   41.3   0.0   1.1e-13   1.3e-10       7     113 .]     303     411 ..     299     411 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 5.2e-13
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +++ai e++ d  f v   g ++y+++a  ++lG+s+ e+ g+ + d+  e   ae+a++   + +++++ ++ e +
  gi|313126511|ref|YP_004036781.1| 177 RFEAIAETSFDILFRVGLTGQFTYASSAVKRILGYSPAELTGEQFTDFTTEA-AAEVAAEAYARVLDNQNVQNLELD 252
                                       7999******************************************999776.569********************* PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       f    g+++ lev+a+pv++ g+ + g+ gv+rd+
  gi|313126511|ref|YP_004036781.1| 253 FLDDTGSVVVLEVNATPVIEDGDVV-GVQGVGRDV 286
                                       *********************9976.********7 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 1.1e-13
                                       HHHSSSEEEEEE...TTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   7 leslpdpifvvD...edgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisf 79 
                                       ++ + ++i + D    +   +yvN+ +e+ +G+s+ee lg++l  l   e+ + e+ ++le+++ +ge+   + i+ 
  gi|313126511|ref|YP_004036781.1| 303 MDEAQVGISISDirePNEPLIYVNEGFERVTGYSAEETLGRNLCFLQ-GEQTDpERSQRLETAIDAGEPVVVELINY 378
                                       566677777777666777889***********************555.555556*********************** PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++ dg+p++ ++  +pv d+ g i++++g+ +d+
  gi|313126511|ref|YP_004036781.1| 379 RR-DGTPFWNQIYLAPVDDKTGAITHYVGFQQDV 411
                                       **.*****************************97 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.1   9.6e+03      38      63 ..     136     162 ..     118     176 .. 0.60
   2 !   51.1   0.1   1.2e-16   1.4e-13       6     110 .]     187     291 ..     182     291 .. 0.95
   3 !   29.3   0.1   6.7e-10     8e-07      17     110 .]     322     416 ..     315     416 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.1
                             PAS_4  38 ktla.ellpeedaarleralrrvlege 63 
                                        t+  e++ e ++  ++r l+r + ++
  gi|313126511|ref|YP_004036781.1| 136 FTDSeEMFLELLGKLVSRELERRAHEQ 162
                                       344456777777777777766655554 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 1.2e-16
                             PAS_4   6 dalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhy 81 
                                       d+l+ ++  g+++ya+ a  +++g++p+el+G+ + ++ +e +a+  ++a++rvl+ + ++  +   l+  g+ +++
  gi|313126511|ref|YP_004036781.1| 187 DILFRVGLTGQFTYASSAVKRILGYSPAELTGEQFTDFTTEAAAEVAAEAYARVLDNQNVQNLELDFLDdTGSVVVL 263
                                       7899999*********************************999********************9999999******* PP

                             PAS_4  82 elrllPlrdesGevigvlvisrDiTerrr 110
                                       e++++P+  e+G+v+gv +++rD+T+r++
  gi|313126511|ref|YP_004036781.1| 264 EVNATPV-IEDGDVVGVQGVGRDVTDRKE 291
                                       *******.68*****************85 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 6.7e-10
                             PAS_4  17 vlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeep.iefleelllpgeerhyelrllPlrde 91 
                                        +y+N+ ++++ g+++ee lG+ l  +l  e   ++ ++ l+ +++ +ep + +l+ ++++g + + ++ l P++d 
  gi|313126511|ref|YP_004036781.1| 322 LIYVNEGFERVTGYSAEETLGRNLC-FLQGEqTDPERSQRLETAIDAGEPvVVELINYRRDGTPFWNQIYLAPVDDK 397
                                       68***********************.5555544444555566666555550555666666***************** PP

                             PAS_4  92 sGevigvlvisrDiTerrr 110
                                        G + +++++ +D+Ter+r
  gi|313126511|ref|YP_004036781.1| 398 TGAITHYVGFQQDVTERKR 416
                                       *****************97 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.1e-11   1.3e-08       2      88 ..     199     282 ..     198     283 .. 0.98
   2 !   28.9   0.0   8.5e-10     1e-06       2      88 ..     323     407 ..     322     408 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.1e-11
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +y+s +v++ilGysp+el+g   ++ d+      e + ea++++l+++ + + e  ++   G+++ +e  a+++  e
  gi|313126511|ref|YP_004036781.1| 199 TYASSAVKRILGYSPAELTGE--QFTDFTTEAAAEVAAEAYARVLDNQNVQNLELDFLDDTGSVVVLEVNATPV-IE 272
                                       79*******************..**************************99***********************.** PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g +v v+gv
  gi|313126511|ref|YP_004036781.1| 273 DGDVVGVQGV 282
                                       ********97 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 8.5e-10
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvird 77 
                                       iyv+e +e+++Gys+ee lg+    l ++  e   ++  + l++a++ gep+ +e    r+dG+ +w + +  ++ d
  gi|313126511|ref|YP_004036781.1| 323 IYVNEGFERVTGYSAEETLGR---NLCFLQGEQtDPERSQRLETAIDAGEPVVVELINYRRDGTPFWNQIYLAPVDD 396
                                       8********************...5666666664677778899999******************************* PP

                             PAS_3  78 engkpvrvigv 88 
                                       + g +++++g+
  gi|313126511|ref|YP_004036781.1| 397 KTGAITHYVGF 407
                                       ********997 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.83   9.9e+02      71     105 ..     101     137 ..      85     143 .. 0.78
   2 !   55.0   0.1   8.5e-18     1e-14       5     109 ..     527     628 ..     524     630 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.83
                                       STSSSHHHHHHHH.HHH.HTTTEEEEEEETTTEEEEE CS
                         HATPase_c  71 gggtGlGlsivkk.lve.lmgGeiwvesepgrGttft 105
                                          +GlG +i  k +v+    G++ + ++++rGt ft
  gi|313126511|ref|YP_004036781.1| 101 IDTFGLGTYIGTKiVVQnETYGTVCFADTDERGTPFT 137
                                       4567888888888777766669999999999999886 PP

  == domain 2  score: 55.0 bits;  conditional E-value: 8.5e-18
                                       HHHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsi 80 
                                        L+q++ +l++Na+k++  +++++ +e++ + +++ i v+DnG+Gi++ + k + e   +       +  +GlGl +
  gi|313126511|ref|YP_004036781.1| 527 ELKQMVTELIENAIKHNLsNDPHVVIEVNNNGEWIDIVVSDNGPGIDEMEAKVVSEGGET-----PLQHSSGLGLWL 598
                                       79**************44588888888885559***************999966654444.....6788******** PP

                                       HHHHHHHTTTEEEEEEET.TTEEEEEEEEE CS
                         HATPase_c  81 vkklvelmgGeiwvesep.grGttftftlp 109
                                       v+  v+++gG+++++ ++ g Gtt t++lp
  gi|313126511|ref|YP_004036781.1| 599 VNWAVTRYGGSFRISATEqGDGTTATIRLP 628
                                       ***8888*******5555599******998 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.91   1.1e+03      37     114 ..     230     308 ..     215     316 .. 0.68
   2 !   34.6   0.0   1.3e-11   1.6e-08      20     112 ..     503     606 ..     484     627 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.91
                       HATPase_c_2  37 eEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvDev 112
                                       +E+ + a+    ++++ + +e+ + +d+++++v   +  p   d      +++  + +++ke+ r l++ ++ +De 
  gi|313126511|ref|YP_004036781.1| 230 AEVAAEAYARVLDNQNVQNLELDFLDDTGSVVVLEVNATPViEDGDVVGVQGVGRDVTDRKERQRELHIKNRAMDEA 306
                                       45555555555555555667777777777766655555555566666666667777788999999999999999987 PP

                       HATPase_c_2 113 ey 114
                                       ++
  gi|313126511|ref|YP_004036781.1| 307 QV 308
                                       76 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 1.3e-11
                       HATPase_c_2  20 rraglseelld.............eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetl 83 
                                       +r +++ ++++             e++  v+E++ Na++h+  ++p  +v +++  ++e++ ++v+D+Gpg d  ++
  gi|313126511|ref|YP_004036781.1| 503 QREQWPNATIQlaiqtdrdicagsELKQMVTELIENAIKHNLSNDP--HVVIEVNNNGEWIDIVVSDNGPGIDEMEA 577
                                       4466666666666666666777779999***************999..88888889***************888877 PP

                       HATPase_c_2  84 pdpteeepkeslkegGrGlalikglvDev 112
                                       +   e + +  + ++G+Gl l++  v  +
  gi|313126511|ref|YP_004036781.1| 578 KVVSEGGETPLQHSSGLGLWLVNWAVTRY 606
                                       7777888899***********98777666 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.3   7.6e+03      30      37 ..     143     152 ..     141     172 .. 0.61
   2 !   12.2   0.0   0.00012      0.15       1      48 [.     176     224 ..     176     245 .. 0.77
   3 !   15.2   0.0   1.3e-05     0.016       7      60 ..     303     356 ..     298     366 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.3
                             PAS_8  30 alellG..ys 37 
                                       +lellG  +s
  gi|313126511|ref|YP_004036781.1| 143 FLELLGklVS 152
                                       8889983333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgql 48 
                                       +r++a+ e+s d ++ v  +g +++++  a  ++lGys a+l ge + ++
  gi|313126511|ref|YP_004036781.1| 176 QRFEAIAETSFDILFRVGlTG-QFTYASSAVKRILGYSpAELTGEQFTDF 224
                                       688888888888888775444.5***************999999988444 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.3e-05
                             PAS_8   7 fesspdgiavvd....lgdrivdvNqaalellGysadlkgellgqllpvlrplledae 60 
                                       ++ +++gi + d    +   +++vN+ +++ +Gys    +e+lg+ l+ l+++  d e
  gi|313126511|ref|YP_004036781.1| 303 MDEAQVGISISDirepNEP-LIYVNEGFERVTGYS---AEETLGRNLCFLQGEQTDPE 356
                                       6778999999776445555.*************99...33566666666666655444 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.2e-09   1.5e-06       2     129 .]      21     157 ..      20     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.2e-09
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvsepsfaeedgl 78 
                                        +  ++ +l+l+++ +++ +g+l   d++ ++++   g ++  ++ e+++ dsa +r++++ + +++++++a+ d +
  gi|313126511|ref|YP_004036781.1|  21 TEAKIARALDLGAEFFDLPIGFLTRIDDGIQEIVQSTGGHELIQPGETCPLDSAYCRLTVELDSPLAVQDAAASDIS 97 
                                       5778999********************99889977788788888899*********************999885554 PP

                             GAF_3  79 pd.......raalavPLvagrqviGvlalastkpra..fdaedlelleslArqiataier 129
                                       ++       + ++   +v++++++G++++a t++r   f+++++ +le l+ +++ ++er
  gi|313126511|ref|YP_004036781.1|  98 QQaidtfglGTYIGTKIVVQNETYGTVCFADTDERGtpFTDSEEMFLELLGKLVSRELER 157
                                       4444444449999999***99************99889*****************99997 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   8.4e-09     1e-05      14     133 .]      33     155 ..      20     155 .. 0.73
   2 ?    0.0   0.0         1   1.2e+03      79     109 ..     251     284 ..     204     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.4e-09
                                       HHHHTESEEEEEEEEETTEEECEEEEECC.EEEETTSHHHH.......HHHHHSSSEEESTGGTSTTHHTTHHHHHH CS
                               GAF  14 rellgadrvalylpdydGlhydipqasrw.lfmkngrgicg.......qvlatgqplvipdstpdprfaqynrrdll 82 
                                       +e++++  + l +   dG+++ i q+      +++g++ c         +++ + pl ++d+++++  +q      +
  gi|313126511|ref|YP_004036781.1|  33 AEFFDLPIGFLTR-IDDGIQE-IVQSTGGhELIQPGET-CPldsaycrLTVELDSPLAVQDAAASDISQQ-----AI 101
                                       5566666666655.3666555.5555555544444444.333355444777779******9866666666.....78 PP

                                       HHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  83 enmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvladqvaval 133
                                       + +g  ++++  +v+++e++G++++ ++++   pft++e+ +l+ l+ +v+ +l
  gi|313126511|ref|YP_004036781.1| 102 DTFGLGTYIGTKIVVQNETYGTVCFADTDErgtPFTDSEEMFLELLGKLVSREL 155
                                       89*************************766788***************999876 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1
                                       HHHHHHTTES...EEEEEEEEETTEEEEEEEEEE CS
                               GAF  79 rdllenmgir...sslvvPlvndgelwGllvlhn 109
                                       +d+l+ +g++    + + P++ dg+++G+  + +
  gi|313126511|ref|YP_004036781.1| 251 LDFLDDTGSVvvlEVNATPVIEDGDVVGVQGVGR 284
                                       5566666666555666889999****99966665 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     5e-07    0.0006       9     135 ..      26     153 ..      18     156 .. 0.79
   2 ?    0.1   0.0      0.76   9.1e+02      95     111 ..     267     283 ..     197     299 .. 0.79
   3 ?   -1.9   0.0       3.1   3.7e+03      48      72 ..     351     374 ..     328     390 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5e-07
                                       HHHHHHHHHS.S..EEEEEEE-TT.S-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG-S-HHHH CS
                             GAF_2   9 dlvldelvel.gaalgyillvddd.gglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleedpdkkgl 83 
                                        ++ld  +e+ +  +g++  +dd+ ++++ ++ g++  + g+ +  pl+++ +   ++   p+ ++d ++  d +++
  gi|313126511|ref|YP_004036781.1|  26 ARALDLGAEFfDLPIGFLTRIDDGiQEIVQSTGGHELIQPGETC--PLDSAYCRLTVELDSPLAVQDAAA-SDISQQ 99 
                                       57889999966999******995423333336666666666666..8888899999999********444.466666 PP

                                       HHHHHTT--EEEEEE-TTS---EEEEES........--HHHHHHHHHHHHHHHH CS
                             GAF_2  84 paghaglrsflavPlisegrvvGvlnlyankppa..fdeedlelLeelaeqiai 135
                                       + +  gl++ ++  ++ +++++G ++++ +++++  f++++  +Le+l+ ++++
  gi|313126511|ref|YP_004036781.1| 100 AIDTFGLGTYIGTKIVVQNETYGTVCFADTDERGtpFTDSEEMFLELLGKLVSR 153
                                       679************9999********877777789************998875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.76
                                       EEEE-TTS---EEEEES CS
                             GAF_2  95 avPlisegrvvGvlnly 111
                                       a P+i++g vvGv +++
  gi|313126511|ref|YP_004036781.1| 267 ATPVIEDGDVVGVQGVG 283
                                       67999999999998873 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.1
                                       T-S-B---TT.HHHHHHHHTS-EEES CS
                             GAF_2  48 aaldrplgeg.lvgealrtgrpviln 72 
                                       +++  +++++  +++a+  g+pv+++
  gi|313126511|ref|YP_004036781.1| 351 EQT--DPERSqRLETAIDAGEPVVVE 374
                                       344..555565789999999999986 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     4e-07   0.00048       4      52 ..     529     579 ..     526     639 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4e-07
                       HATPase_c_3   4 ekAlaelvdNsldAdaen...vkievnknrgktgeivieDdGkGmseeelkn 52 
                                       ++ ++el++N++  +  n   v ievn+n g+  +iv+ D+G G++e e k 
  gi|313126511|ref|YP_004036781.1| 529 KQMVTELIENAIKHNLSNdphVVIEVNNN-GEWIDIVVSDNGPGIDEMEAKV 579
                                       6779*********77777777*******8.689*************998765 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-05     0.075      88     157 ..     374     441 ..     363     446 .. 0.74
   2 ?   -3.4   0.1       5.1   6.1e+03     140     155 ..     536     551 ..     532     555 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                         HisKA_4TM  88 rllegrtiaePvfvvlvaaevGavaGllaGylaararadasrakrisdalafvndlirhdlrndlvvirg 157
                                        l++ r    P +  +  a v   +G ++ y  +  ++d +  kr+ + +  +n ++rh+lrnd++ + g
  gi|313126511|ref|YP_004036781.1| 374 ELINYRRDGTPFWNQIYLAPVDDKTGAITHY--VGFQQDVTERKRTEQLIQVLNRVLRHNLRNDMNALLG 441
                                       5555555555555555555566666666555..55689***************************97765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.1
                         HisKA_4TM 140 vndlirhdlrndlvvi 155
                                       +++ i+h+l nd  v+
  gi|313126511|ref|YP_004036781.1| 536 IENAIKHNLSNDPHVV 551
                                       66789******97765 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.012        14     134     176 ..     225     269 ..     212     273 .. 0.82
   2 ?    5.7   0.1     0.008       9.6      59      95 ..     534     570 ..     528     584 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHH.HHTT--SEEEEEE.EEETTTEEEEEEEESS- CS
                   Dala_Dala_lig_C 134 veekiqelalkay.kaldlrGlaRvDf.flteegeivlnEvNtlP 176
                                       ++e+  e+a +ay ++ld + +  + + fl+++g++v+ EvN  P
  gi|313126511|ref|YP_004036781.1| 225 TTEAAAEVAAEAYaRVLDNQNVQNLELdFLDDTGSVVVLEVNATP 269
                                       56677889999994578999998887767899***********99 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.008
                                       GGHHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSS CS
                   Dala_Dala_lig_C  59 eelkeaieeafkydekvlvEeaiegreievavlgnek 95 
                                       e +++ai++ ++ d +v++E + +g+ i++ v +n+ 
  gi|313126511|ref|YP_004036781.1| 534 ELIENAIKHNLSNDPHVVIEVNNNGEWIDIVVSDNGP 570
                                       55789***************************99875 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.8   8.8e-05      0.11     189     286 ..     428     523 ..     401     554 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.8e-05
                              FUSC 189 ararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpe.laallaela 264
                                        r++l  d++al ++ +++   ++r +++ r++ r+ +++l+++ ++++l++  +r r  e+  +   l a++ e +
  gi|313126511|ref|YP_004036781.1| 428 LRHNLRNDMNALLGWHNHLYGSDSRNADAERRVERIAQDLLSMSERARELEQYARRERIPERLDPTVlLTAVVNEQR 504
                                       5899999*********************************************9888776665553335666666666 PP

                              FUSC 265 aleaaaaaealeaalaalrarl 286
                                       +   ++  ++++ a+++ r+ +
  gi|313126511|ref|YP_004036781.1| 505 E---QWPNATIQLAIQTDRDIC 523
                                       6...444555555555555544 PP

>> DUF5132  Protein of unknown function (DUF5132)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.8   0.00034      0.41      27      46 ..     217     236 ..     212     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                           DUF5132  27 vGEeLeDlvAEvkAEllAae 46 
                                        GE+  D + E++AE++A++
  gi|313126511|ref|YP_004036781.1| 217 TGEQFTDFTTEAAAEVAAEA 236
                                       7**************88875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (648 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 4112.12
//
Query:       gi|313126512|ref|YP_004036782.1|  [L=316]
Description: 1,4-dihydroxy-2-naphtoate prenyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-38  130.3  19.5    8.9e-38  130.0  19.5    1.1  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0  19.5   4.9e-42   8.9e-38       3     236 ..      26     281 ..      24     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 4.9e-42
                              UbiA   3 ipalvg.lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme.rt.pnRPlvsGrispkealifaivl 76 
                                        p++vg  ++ + g++ +l +l++++g++l+++++n+ Ndy+D+  +ad++ r    R  + G+i pk ++++++++
  gi|313126512|ref|YP_004036782.1|  26 APIFVGvGLAVHDGVFAALPALAAFVGAALIQIGTNFANDYYDAVQGADTAdREgFTRVTAGGLIAPKSVKRAMYLT 102
                                       5777886555568888999******************************9975568999****************** PP

                              UbiA  77 lilgllll...alllnpltallgllalllyvvYt.g.lrlKrrtllgtvvggiafglppllgwaavtgsl....... 141
                                       +++++ll+   ++  + +++++gll+++ +++Yt g ++l++++l g+++++i+fg++++ g ++v+          
  gi|313126512|ref|YP_004036782.1| 103 FAAAILLGtylVYVGGVPILVIGLLSVASGIAYTgGpFPLGYHGL-GDLFVFIFFGVVAVTGTYYVQAAAviadpls 178
                                       **********999999*******************88********.*******************8888889***** PP

                              UbiA 142 ........sllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllal 210
                                               ++ a++++lav++l++ i+++n++rd+e+D+  g++tl+v++G   +r  ++++la+++l+++++ + +
  gi|313126512|ref|YP_004036782.1| 179 vgippntlPFDAFVASLAVAALSTNILVVNNVRDKEEDETTGKRTLAVRFGYTFSRGEYLAMLALAYLVPVWFATRQ 255
                                       *********************************************************99989999998855555555 PP

                              UbiA 211 llllylllalllaalallraarlvrr 236
                                       + +  ++l l+ +++a+ +a  ++++
  gi|313126512|ref|YP_004036782.1| 256 TFGGVVFLPLVTLPYAISVARTVLTK 281
                                       55555555555555555554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2100.03
//
Query:       gi|313126513|ref|YP_004036783.1|  [L=343]
Description: enolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-42  145.5   8.2    1.7e-42  145.5   8.2    1.5  2  MR_MLE_C     Enolase C-terminal domain-like
    0.00012   22.5   0.1     0.0078   16.6   0.1    2.2  1  Radical_SAM  Radical SAM superfamily
     0.0082   15.3   0.1      0.015   14.5   0.1    1.4  1  MAAL_C       Methylaspartate ammonia-lyase C-terminus
     0.0095   15.6   0.1      0.019   14.6   0.1    1.5  1  DeoC         DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.79   3.5e+03     136     151 ..      91     106 ..      78     115 .. 0.76
   2 !  145.5   8.2   3.8e-46   1.7e-42       3     212 ..     127     329 ..     125     333 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHHTT-E CS
                          MR_MLE_C 136 tearkvaalaeafgvp 151
                                       t +r +a+la+++gv 
  gi|313126513|ref|YP_004036783.1|  91 TDVRLCARLAAEHGVG 106
                                       4566778888888876 PP

  == domain 2  score: 145.5 bits;  conditional E-value: 3.8e-46
                                       HHHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEES CS
                          MR_MLE_C   3 aeearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEE 79 
                                       a+++re+v+  gf+ vK+kvg+ +++ d +r+ra+r+a+ p+  ++l+ Dan+aw ++tA +++ + +eld++++E+
  gi|313126513|ref|YP_004036783.1| 127 ADAVREMVE-SGFDVVKIKVGAREPEADRARLRAARDAA-PD--AELRADANGAWGRETAAEMLDAAAELDYAYVEQ 199
                                       677877555.5****************************.75..5******************************** PP

                                       SSSTTTHHHHHHHHHHHHSSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS CS
                          MR_MLE_C  80 PvppeddleglaelrarasipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs 156
                                       P+p+ ddl glaelr   ++ +a++E l+s+  ++++l+a+a+d++ ++++  gG++++++ a+ a+ +gv+ ++ +
  gi|313126513|ref|YP_004036783.1| 200 PLPA-DDLTGLAELR-GCGVGVAVDETLASH-AVAAVLDADAADVLVLKPMALGGPDRTLDAAQTARDAGVEAIVTT 273
                                       ****.78********.4489********996.578899**********************************99999 PP

                                       C.SSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBT CS
                          MR_MLE_C 157 g.sgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGl 212
                                         +g ++++ +lh+aaaip +      +++  l ++l+++p ++++G + vpdgpGl
  gi|313126513|ref|YP_004036783.1| 274 TiDGVVARLGALHVAAAIPDVPACGLATGSL-LADDLAPDPAPIREGAMSVPDGPGL 329
                                       6369***************999999999886.************************9 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.7e-06    0.0078      31     149 ..     123     275 ..     112     280 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHHHHTT..SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT..-S CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                       Radical_SAM  31 veeileevkelkaekg..vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg..vd 103
                                       + e ++ v+e+ +e g  v  + +g  ep +++   ++++ +a    p+ +++  +ng +  +e ++++l++   +d
  gi|313126513|ref|YP_004036783.1| 123 PTETADAVREM-VESGfdVVKIKVGAREPEADRARLRAARDAA----PDAELRADANGAWG-RETAAEMLDAAaeLD 193
                                       44444455555.3333348888888888888643322222222....56666666666666.555555555554444 PP

                                       EEEEEEBSSSHH....................................HHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxx....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 104 rvslgleaadde....................................kvlklmnrghtfeevlealeklreagikr 144
                                       + ++    + d+                                     vlk+m   ++++++l+a +++r+ag++ 
  gi|313126513|ref|YP_004036783.1| 194 YAYVEQPLPADDltglaelrgcgvgvavdetlashavaavldadaadvLVLKPM-ALGGPDRTLDAAQTARDAGVEA 269
                                       4444444444445555555555555555555555555555555555555*****.779*****************97 PP

                                       .EEEEE CS
                                       .xxxxx RF
                       Radical_SAM 145 .vvdri 149
                                        v+++i
  gi|313126513|ref|YP_004036783.1| 270 iVTTTI 275
                                       655444 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.3e-06     0.015     136     200 ..     213     276 ..     200     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-06
                            MAAL_C 136 kgikvelvaDeWcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscn 200
                                       +g  v +  De   + + + +  da+aad++ +k   lGg ++t++a + +++ gv+a +  + +
  gi|313126513|ref|YP_004036783.1| 213 RGCGVGVAVDETL-ASHAVAAVLDADAADVLVLKPMALGGPDRTLDAAQTARDAGVEAIVTTTID 276
                                       5666777777754.45679999************************************9987765 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   4.2e-06     0.019     118     218 ..      93     190 ..      78     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.2e-06
                                       HHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCH CS
                              DeoC 118 ikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvikaa 194
                                       ++ ++  ++e+g    + +++ ++++ d+   p  +a+A r  +e G D++K +v++   +a     ++ +d++ +a
  gi|313126513|ref|YP_004036783.1|  93 VRLCARLAAEHGVGPSADAVPVNATVGDDT--PTETADAVREMVESGFDVVKIKVGAREPEADRARLRAARDAAPDA 167
                                       556666666666666667777788888887..************************776777777777777777777 PP

                                       SSTEEEEETTS.SHHHHHHHHHHHH CS
                              DeoC 195 pvpgvvlsGGv.seedfletvedAv 218
                                       ++     + G+ + e+ +e+++ A+
  gi|313126513|ref|YP_004036783.1| 168 ELR--ADANGAwGRETAAEMLDAAA 190
                                       666..66667777777788877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2288.91
//
Query:       gi|313126514|ref|YP_004036784.1|  [L=265]
Description: enoyl-CoA hydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-51  173.7   0.0    4.7e-51  173.5   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    4.1e-32  112.0   0.2    1.1e-27   97.4   0.1    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.5   0.0   5.3e-55   4.7e-51       3     250 ..      14     264 ..      12     265 .] 0.93

  Alignments for each domain:
  == domain 1  score: 173.5 bits;  conditional E-value: 5.3e-55
                                       ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC...HHHHHHH.. CS
                             ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek...akqallk.. 74 
                                       e g+a ++lnrP++ Nal+  +++ + +al  l+dd   r v+L+G ++aF+aG+d+++m++        ++ ++  
  gi|313126514|ref|YP_004036784.1|  14 EGGIATLTLNRPDVRNALTTDVTAGVRDALDSLDDD--TRCVILEGAGGAFCAGGDVNAMLQLRAdewTTDEAVRhv 88 
                                       789*********************************..***********************9865444333333311 PP

                                       .CCHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHH CS
                             ECH_1  75 .eevlelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAe 150
                                        +   +  +++y++++p++a + G a+g+G  lalacD+++ + + ++g n+ +lGl  ++g++  l+r+vG   A+
  gi|313126514|ref|YP_004036784.1|  89 iNDTADVVKRVYDCEYPTVAKIDGPAVGAGGALALACDVRVFSAEGQIGFNFEQLGLAIDSGVSYLLPREVGAGVAK 165
                                       145567899******************************************************************** PP

                                       HHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             ECH_1 151 eilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfest 227
                                       e++++g+ + a+ a++vGl ++v+ ee+++ e  + +e +a+ + aalr+ k  l++ +e  l +++e ea  + ++
  gi|313126514|ref|YP_004036784.1| 166 ELVYTGEILDAERAADVGLANRVF-EEDFEAEFDAFVETIASGPTAALRTSKRLLRRGFEVSLDTAIEHEAAAQGAM 241
                                       **********************99.678************************************************* PP

                                       CTSHHHHHHHHHHHTCSH----- CS
                             ECH_1 228 fskddikeGlqaflEkrkpefed 250
                                       f++dd +eG++aflE r+pef++
  gi|313126514|ref|YP_004036784.1| 242 FETDDHEEGIDAFLEHRDPEFGG 264
                                       *********************86 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.1   1.2e-31   1.1e-27       2     175 ..      18     192 ..      17     199 .. 0.93
   2 !   13.3   0.0   4.9e-06     0.044     250     312 ..     198     259 ..     190     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 1.2e-31
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS..-THH.HHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakeg..kkee.eeffre 75 
                                       +++tLnrp+  NaL++++   +++al++   dd++++v+l+gag  afCAGgDv+a+ + + ++  ++e+ ++++++
  gi|313126514|ref|YP_004036784.1|  18 ATLTLNRPDVRNALTTDVTAGVRDALDSL--DDDTRCVILEGAG-GAFCAGGDVNAMLQLRADEwtTDEAvRHVIND 91 
                                       689*************************8..77789******99.8*************99999753334799**** PP

                                       HHHHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHH CS
                             ECH_2  76 eYklnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlyla 151
                                       + ++ +++ +++ p+va +dG ++G G +l++ + +rv + + ++     ++Gl  D G+sy+L+r  g  +++ l 
  gi|313126514|ref|YP_004036784.1|  92 TADVVKRVYDCEYPTVAKIDGPAVGAGGALALACDVRVFSAEGQIGFNFEQLGLAIDSGVSYLLPREVGaGVAKELV 168
                                       ******************************************************************75559****** PP

                                       HH---B-HHHHHHTTS--EE--GG CS
                             ECH_2 152 lTGarlkgadalaaglathyvpse 175
                                        TG+ l+++ a  +gla+ +++++
  gi|313126514|ref|YP_004036784.1| 169 YTGEILDAERAADVGLANRVFEED 192
                                       ******************998876 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.9e-06
                                       HHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-- CS
                             ECH_2 250 kktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkd 312
                                       ++ +et+++    +l+ + ++lrrg + s l++++++E ++  ++++++D  eG+ a l  +d
  gi|313126514|ref|YP_004036784.1| 198 DAFVETIASGPTAALRTSKRLLRRGFEVS-LDTAIEHEAAAQGAMFETDDHEEGIDAFLEHRD 259
                                       56788999999999**************5.***************************997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1746.09
//
Query:       gi|313126515|ref|YP_004036785.1|  [L=357]
Description: NADH dehydrogenase subunit h [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-96  320.6  16.2    1.2e-95  320.3  16.2    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.3  16.2  6.6e-100   1.2e-95       5     299 .]      36     349 ..      32     349 .. 0.96

  Alignments for each domain:
  == domain 1  score: 320.3 bits;  conditional E-value: 6.6e-100
                                       HHHHHHHHHHH.HHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHH CS
                            NADHdh   5 lllvvlllvva.lltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilal 80 
                                       ++++++ l +a ++++++Rkv+A++ dR+ Pnr+Gp+Gll  ++D+++ll Ke i+p+++d+  + ++p+l+ ++al
  gi|313126515|ref|YP_004036785.1|  36 VIVALVPLNCAaVVIWAKRKVTAAFTDRIAPNRTGPFGLLVIVTDVFRLLSKELIVPDGVDRPAYDIGPILVPFSAL 112
                                       344445555555***************************************************************** PP

                                       CTTTTS-SSS......SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            NADHdh  81 lafaviPfge......vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavv 151
                                       l faviP+g+      +lad ++gl +++a++s++++g+ + G+asn+k++l+G+lR++a  ++yE++l++++ +vv
  gi|313126515|ref|YP_004036785.1| 113 LGFAVIPMGSifgielQLADPETGLAYAFAVASIATLGLTMCGYASNNKFSLIGGLRAIAANLAYEIPLVVTAASVV 189
                                       *********66678899************************************************************ PP

                                       HHH-SS-HHHHHHCCCTT...........-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHH CS
                            NADHdh 152 llagslslseiveaqeei...........wfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkf 217
                                       l++gsl++seiv++q++            w+++++++af++flia lae++r PFD pea +ELvaG++tEYs++ +
  gi|313126515|ref|YP_004036785.1| 190 LFTGSLQMSEIVATQTNPlltvmgvtipsWYAFVNPFAFVLFLIANLAEVGRNPFDAPEAPTELVAGYQTEYSSVYW 266
                                       ***************9879*********999********************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHCT.SS-HCCS.HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHH CS
                            NADHdh 218 alfflaeyanmvlvsalavllFlgGwllpfs.gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplala 293
                                       +l++++e+++++l  a+++++FlgG ++p+  g++wfl+K++++++++ w r+++pRlR+dql+++gwk ll l+++
  gi|313126515|ref|YP_004036785.1| 267 VLIYMGEFIHLFLGGAILATVFLGGPAGPVLpGFVWFLVKIWAVFLFTQWARSAVPRLRIDQLIEVGWKGLLVLSFV 343
                                       ***************************99988********************************************* PP

                                       HHHHHH CS
                            NADHdh 294 nlllta 299
                                       nlllta
  gi|313126515|ref|YP_004036785.1| 344 NLLLTA 349
                                       ***985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2332.91
//
Query:       gi|313126516|ref|YP_004036786.1|  [L=216]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-16   60.4   0.3    1.8e-16   59.6   0.3    1.4  1  HTH_10    HTH DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.3     1e-20   1.8e-16       1      53 []     161     213 ..     161     213 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT +q+e++ +A+ +GY+++PR++t+ ++A el+ ++st+ ehL+kae ++i+
  gi|313126516|ref|YP_004036786.1| 161 LTSRQREAVLAAMSLGYYETPRKATIVDVAAELDCARSTAAEHLQKAEARIIR 213
                                       9*************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1198.92
//
Query:       gi|313126517|ref|YP_004036787.1|  [L=68]
Description: hypothetical protein Hbor_17740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-17   64.1   2.8    1.4e-17   64.0   2.8    1.0  1  DUF2061   Predicted membrane protein (DUF2061)


Domain annotation for each model (and alignments):
>> DUF2061  Predicted membrane protein (DUF2061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   2.8   7.5e-22   1.4e-17       1      52 []       8      59 ..       8      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 7.5e-22
                           DUF2061  1 ilKtlswrvihtvvtflvaylltgslalAgaialvEpvvktvlYyfHERlWn 52
                                      ilK++s+r+++t+ +f++a++ tg++  A++i++  +v+kt+lYyf+ERlW+
  gi|313126517|ref|YP_004036787.1|  8 ILKAASYRLFATSLVFGIAFVYTGQFGSAAKIGISAAVAKTALYYFWERLWD 59
                                      79*************************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 388.98
//
Query:       gi|313126518|ref|YP_004036788.1|  [L=242]
Description: trehalose utilization protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-33  114.1   0.0    1.2e-32  113.9   0.0    1.1  1  ThuA      Trehalose utilisation


Domain annotation for each model (and alignments):
>> ThuA  Trehalose utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.0   6.4e-37   1.2e-32       2     210 .]       7     221 ..       6     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 6.4e-37
                                       EEEEE-..-.SHHHH-...HHHHHH-............HHHT-EE.EEETTS.G..--HHHHHT-SEEEEE-..G.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxx.xxxxxxxx..xxxxxxxxxxxxxxxx..xxx RF
                              ThuA   2 VLvfsgtagerhdsieaaieaieklg............kengfev.datedaav..fteenLaqydvvvfls..teg 61 
                                       ++v+++   +rh++ ++ ++a+   +            +e+gf+  +at+d+ +  +te +L+++dv+ +++  +++
  gi|313126518|ref|YP_004036788.1|   7 ITVWNE---YRHERDSDDVAAV---YpdgiheaiaegfEERGFDTrTATLDDPEhgLTEGVLDDTDVLTWWGhrAHD 77 
                                       567777...4666666333333...33336666667769****9988888554459****************55467 PP

                                       GS-HHHHHH.HHHHHHTT-EEEEEGGGGS.....HHHH.HH-S....EEEEET............TSGGGTT--.SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThuA  62 evldaaqeaalqryveaGgGfvglhsAadaeerskwfsgLiGa....rfvghppvqeatvkvedrshpateglpeew 134
                                       +v d+ +e+ + ++v++G+G+++lhsA       +++s L+G+    +++++   ++ ++ v ++ hp++eglpe++
  gi|313126518|ref|YP_004036788.1|  78 AVSDHIVER-VVERVHDGMGLLVLHSAHY---SKPFKS-LMGTscslKWREA--DERERIWVIEPGHPIAEGLPEQI 147
                                       999999999.99***************55...246888.****775544444..4568888999************* PP

                                       EEE.EEEEE..-.S---SE..EEEEE...............ETE...TTEEEEEE----TTS.GGG-HHHHHHHHHH CS
                                       xxx.xxxxx..x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                              ThuA 135 ert.dewYn..f.kpnprgvhvlatvdestydpngadhPiaWcreydgkGrvFytalGhtee.syeepefrkhllgg 206
                                       e++  e+Y+  f  p+p++  +++t+ ++     g+ +    c +  g+GrvFy+++Gh+++ +y+ +++r++l+++
  gi|313126518|ref|YP_004036788.1| 148 EIPeAEMYGerFdVPAPDE--LVFTSWFEG----GEVFRSGCCYTR-GSGRVFYFRPGHETYpIYYRDDIRDVLANA 217
                                       ***99****7555555555..****94443....333433344433.99**************************** PP

                                       HHHC CS
                                       xxxx RF
                              ThuA 207 lkWa 210
                                        +Wa
  gi|313126518|ref|YP_004036788.1| 218 AEWA 221
                                       ***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1371.69
//
Query:       gi|313126519|ref|YP_004036789.1|  [L=107]
Description: swim zinc finger-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-06   25.9   0.0    8.7e-06   25.3   0.0    1.3  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   4.9e-10   8.7e-06       1      37 [.      51      83 ..      51      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.9e-10
                              SWIM  1 yrVtlddervrlnkatCsCpefqkngipCkHalAvll 37
                                      yrV + d+     +++CsCp+ + +  pC H++Av++
  gi|313126519|ref|YP_004036789.1| 51 YRVRIRDG----IPHSCSCPADESGDGPCNHRVAVAI 83
                                      88889976....99*********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 611.91
//
Query:       gi|313126520|ref|YP_004036790.1|  [L=415]
Description: hypothetical protein Hbor_17770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.14   12.4   0.6        0.6   10.3   0.2    2.2  2  UPF0489     UPF0489 domain
       0.17   11.7   0.1        0.3   11.0   0.1    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> UPF0489  UPF0489 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.26   2.3e+03      49     101 ..      67     123 ..      51     141 .. 0.67
   2 ?   10.3   0.2   6.7e-05       0.6      69     112 ..     250     294 ..     225     389 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.26
                           UPF0489  49 vfnallkil.ekl..aeelleelsidnwIlpavyaghi.srvvwikpawaqqitegr 101
                                        +n+l+k+  ++   ae++++  si  + l+ + +g + ++ v++++++++qi++++
  gi|313126520|ref|YP_004036790.1|  67 FLNKLTKNRsRAFldAEQAFNSESIIGYNLIRLKKGTVhEQFVVVNRENKNQIETNK 123
                                       555655555444366677777777766666666666662467778888888888766 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.7e-05
                           UPF0489  69 sidnwIlpavyaghisrvvwikpawaqqi.tegrkellvgkdres 112
                                       + d++  p v++g+++r  +i++ w q     ++  l vg+ +e 
  gi|313126520|ref|YP_004036790.1| 250 DRDEYCSPSVQTGWLNRRCVINHDWDQYKnDVSTEDLIVGTTPEG 294
                                       3499**********************4331357889999998886 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.3e-05       0.3       3      19 ..      11      27 ..       9      30 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaa 19
                                      SRR+ LK  +A+a  ++
  gi|313126520|ref|YP_004036790.1| 11 SRRSVLKCLGATALVMG 27
                                      9************8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2352.11
//
Query:       gi|313126521|ref|YP_004036791.1|  [L=334]
Description: hypothetical protein Hbor_17780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.05   13.5   1.5       0.18   11.7   1.5    2.0  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.5   9.8e-06      0.18       1      24 [.       5      28 ..       5      30 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-06
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalggca 24
                                      +lSRR  L  ++ ++ A+a++g++
  gi|313126521|ref|YP_004036791.1|  5 ELSRRAVLALGGTVGSAGAVAGLL 28
                                      58*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 1887.25
//
Query:       gi|313126522|ref|YP_004036792.1|  [L=37]
Description: hypothetical protein Hbor_17790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   11.4   1.4       0.31   11.1   1.4    1.2  1  GPHR_N    The Golgi pH Regulator (GPHR) Family N-terminal


Domain annotation for each model (and alignments):
>> GPHR_N  The Golgi pH Regulator (GPHR) Family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4   1.7e-05      0.31      11      25 ..      22      36 ..      18      37 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.7e-05
                            GPHR_N 11 vsviGvtlmAiLSGf 25
                                      v v+G++++A LSG+
  gi|313126522|ref|YP_004036792.1| 22 VFVTGIVVIAYLSGV 36
                                      569***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 227.80
//
Query:       gi|313126523|ref|YP_004036793.1|  [L=292]
Description: hypothetical protein Hbor_17800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0031   16.9   0.0     0.0044   16.4   0.0    1.2  1  DUF4838         Domain of unknown function (DUF4838)
  ------ inclusion threshold ------
      0.021   14.2   0.0      0.035   13.5   0.0    1.3  1  Glyco_hydro_42  Beta-galactosidase


Domain annotation for each model (and alignments):
>> DUF4838  Domain of unknown function (DUF4838)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.9e-07    0.0044      34     104 ..      77     160 ..      51     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.9e-07
                           DUF4838  34 sqlCltneevvkivleeikkkldknpeakvfsvsqnDnsayCeceackaldkkyg.............s.psgallr 96 
                                       + +C tne+  +  le + + +d+np++++ +v+    ++yC+c++c++l ++               + +++++ +
  gi|313126523|ref|YP_004036793.1|  77 AYICPTNEDYREGLLEIVTDCADENPDVRLDDVGFP-RDGYCRCDRCERLFDEWVeengvdgdeddwyEwRAEIITE 152
                                       569******************************976.679*********9887553333444444443333666666 PP

                           DUF4838  97 fvnkvaea 104
                                       fv + a++
  gi|313126523|ref|YP_004036793.1| 153 FVAEAADR 160
                                       66666665 PP

>> Glyco_hydro_42  Beta-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.9e-06     0.035      78     159 ..      52     133 ..      49     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-06
                                       HH-GGGS-B-TTS-B--SSSS....----TT-HHHHHHHHHHHHHHHHHHTT-TTEEEEE-SSSTTTTS--SHHHHH CS
                    Glyco_hydro_42  78 kkyPeilavdadgskrkfgsr....qhiclsspvyrekvakivealaerYkdhpavilwhidnEygchecycetcee 150
                                       +++Pe ++vd +g+  +  +r     +ic++++ yre   +iv+  a+   ++p v l  +    ++ +c c++ce+
  gi|313126523|ref|YP_004036793.1|  52 NSNPELVPVDGEGTLATRDQRyfdwAYICPTNEDYREGLLEIVTDCAD---ENPDVRLDDVGFPRDG-YCRCDRCER 124
                                       678**********99888777444468*****************9997...7999999888877666.********* PP

                                       HHHHHHHHH CS
                    Glyco_hydro_42 151 aFrkwlkek 159
                                        F +w++e+
  gi|313126523|ref|YP_004036793.1| 125 LFDEWVEEN 133
                                       ******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1659.80
//
Query:       gi|313126524|ref|YP_004036794.1|  [L=34]
Description: hypothetical protein Hbor_17810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 208.52
//
Query:       gi|313126525|ref|YP_004036795.1|  [L=154]
Description: aspartate carbamoyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-33  113.9   0.5      4e-33  113.5   0.5    1.1  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    1.5e-14   53.6   0.2    2.8e-14   52.8   0.2    1.5  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   0.5   4.5e-37     4e-33       1      94 []       6      98 ..       6      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 4.5e-37
                                      X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EE CS
                              PyrI  1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnati 79
                                      l+v+ki++G+ViDH++ag+al+vl +L++d+ + +e+v+i++nv+s++l +Kdi+k+e++els++e+d+l++i+p+ati
  gi|313126525|ref|YP_004036795.1|  6 LRVSKIRDGTVIDHLTAGQALNVLAILGIDG-SGGESVSIGMNVPSDRLARKDIVKVEDRELSQSEVDVLSVISPEATI 83
                                      689***************************8.7777******************************************* PP

                                      EEEETTEEEEEE--. CS
                              PyrI 80 niIkdgevveKkkve 94
                                      ni++d+evv+Kk+ve
  gi|313126525|ref|YP_004036795.1| 84 NIVRDYEVVDKKRVE 98
                                      ************985 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.2   3.1e-18   2.8e-14       1      48 []     102     147 ..     102     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 3.1e-18
                                       EEESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--EEEHHHH CS
                            PyrI_C   1 eiegvlkCpNpnCItnn.epveskFkvedkekvklkCkYCekeiseeei 48 
                                       e++gv++CpN nCItn  epv+s+F+v ++    l+C YC+++++e+e+
  gi|313126525|ref|YP_004036795.1| 102 EVTGVVSCPNRNCITNAdEPVASRFEVLSDG---LRCGYCGTIVREDEV 147
                                       699**************99*******87665...*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 864.76
//
Query:       gi|313126526|ref|YP_004036796.1|  [L=303]
Description: aspartate carbamoyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-46  156.8   0.0    6.8e-46  156.0   0.0    1.4  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    3.3e-27   95.5   0.0    4.4e-27   95.1   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.0   0.0   7.6e-50   6.8e-46       2     148 .]       5     144 ..       4     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 156.0 bits;  conditional E-value: 7.6e-50
                                       -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSC CS
                          OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediq 78 
                                       hl+s ++ls++++e++ld+aa++ ++++    ++  +g +l+l+F+epStRTr+Sf++A+krlGg+++ ++ +  ++
  gi|313126526|ref|YP_004036796.1|   5 HLISATQLSRDDVEAVLDRAADIDADPA--AWRQRHAGTVLGLCFFEPSTRTRMSFDTAMKRLGGRTVDMG-P--VE 76 
                                       9***********************9997..78888899*********************************.5..57 PP

                                       TTTGGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  79 lssvskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       +ssv+kg  Esl+Dt+rv+++y+daiv+Rhp  ga  ++   ++ +vpviNagdg+g+HPtQ+L+Dl+tire
  gi|313126526|ref|YP_004036796.1|  77 SSSVKKG--ESLADTVRVVEGYGDAIVLRHPleGA--AKMASEFVDVPVINAGDGAGQHPTQTLLDLYTIRE 144
                                       8999***..**********************8666..66556666*************************98 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.0   4.9e-31   4.4e-27       2     156 ..     150     298 ..     149     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 4.9e-31
                                       C.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   2 glkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       +l+i ++Gd k++++++sl+++l+ +++  ++++P++l+   +    ++ + + sg+++  +++l+e++ + Dv+y 
  gi|313126526|ref|YP_004036796.1| 150 DLTIGIMGDlKYGRTVHSLAEALTNFDARQHFISPESLRLPRN----VRYDLHGSGAQVREHTELSEVLPELDVLYV 222
                                       789**********************************988444....45677789********************** PP

                                       --SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHH CS
                            OTCace  78 dvwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhti 150
                                       ++++     +er+   ++++k+++ yq++++ l++ak+ + v+H+LP  r +E++ eV++  ++ +feqa N + ++
  gi|313126526|ref|YP_004036796.1| 223 TRIQ-----RERFpdeNEYRKVAGqYQIDADDLSDAKDSLTVMHPLP--RVDEIAPEVDETAHAKYFEQAHNAVPVR 292
                                       ****.....5555555788888888**********************..**************************** PP

                                       HHHHHH CS
                            OTCace 151 kAllvl 156
                                       +All +
  gi|313126526|ref|YP_004036796.1| 293 MALLDM 298
                                       ***976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1714.26
//
Query:       gi|313126527|ref|YP_004036797.1|  [L=246]
Description: hypothetical protein Hbor_17840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.0   0.0    2.9e-07   30.3   0.0    1.3  1  DICT      Sensory domain in DIguanylate Cyclases and Two-comp


Domain annotation for each model (and alignments):
>> DICT  Sensory domain in DIguanylate Cyclases and Two-component system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.6e-11   2.9e-07      16     127 ..      99     205 ..      88     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.6e-11
                              DICT  16 splvvskatLlalvraleDllieqkipatlwvklqrekiwqselerYrrl.agsssqvyilaarepeeefkeeptks 91 
                                          ++  + ++a +r++eD++++  +++ l   +qr + +++++  Y++l  +s  +v +la   p+++  +     
  gi|313126527|ref|YP_004036797.1|  99 MFTSYDTKRMVAASREIEDRAWR--SSGRLYSGFQRYSDFEKQIPVYEQLgSKSYLDVTVLAH--PDTDLPD----- 166
                                       4567999****************..6************************5566689999999..7776666..... PP

                              DICT  92 sepvesvqlepnsqLrrewfLivlsp...qfsslilAqe 127
                                       ++ + +v     +++r+ wf+ +++    + ++++lA+e
  gi|313126527|ref|YP_004036797.1| 167 HDGTFEVYPSRAKEIRDVWFVAFDGGgndEAKCALLAEE 205
                                       5666677666667************999999******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1364.40
//
Query:       gi|313126528|ref|YP_004036798.1|  [L=418]
Description: glutamate dehydrogenase (NADp) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-74  248.6   0.3    9.4e-74  248.2   0.3    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    6.2e-54  181.4   0.0    1.1e-53  180.5   0.0    1.4  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0009   18.6   0.1     0.0018   17.7   0.1    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.011   14.5   0.0      0.016   13.9   0.0    1.2  1  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
      0.018   14.6   0.2      0.028   14.0   0.2    1.3  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.2   0.3   2.6e-77   9.4e-74       1     243 []     181     415 ..     181     415 .. 0.97

  Alignments for each domain:
  == domain 1  score: 248.2 bits;  conditional E-value: 2.6e-77
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HH CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldie 77 
                                       GGs++r eaTg++++ +++e++++l+ d +eg++va++G+Gn gs+aa+ll++ ga++vavsDssG+iy + G+d++
  gi|313126528|ref|YP_004036798.1| 181 GGSEGRVEATGRSTMLTAREAFDYLDKD-IEGATVAVQGYGNAGSVAANLLEDIGANIVAVSDSSGAIYREGGFDTA 256
                                       9***********************9999.************************************************ PP

                                       HHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHH CS
                     ELFV_dehydrog  78 ellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeA 154
                                       + +++k+e++sv+ y++  ++  e ++ne ell+l+vd+l+P+A++n+id+e a+  ++  +++vvE+AN+p+t+eA
  gi|313126528|ref|YP_004036798.1| 257 AAKQFKRETGSVSGYDQ--AD--EEMTNE-ELLTLDVDLLIPAALENAIDGELAQ-DVQ--ADVVVEAANGPLTPEA 325
                                       ****************4..33..678886.9************************.999..**************** PP

                                       HHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-T.HHHHHHHH CS
                     ELFV_dehydrog 155 keileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqe.lvkgania 230
                                       ++ l+ ++v+v+pd++aNaGGVtvS++E++qn +r++wtee+v+++l++  +e+f+++ve++++++ +  +++a+++
  gi|313126528|ref|YP_004036798.1| 326 DDELTGRDVYVFPDILANAGGVTVSYFEWVQNRQRFYWTEERVNDELERVITEAFDNLVEAYDSHDLPnFRTAAYVV 402
                                       ****************************************************************99999******** PP

                                       HHHHHHHHHHHCT CS
                     ELFV_dehydrog 231 gfekvaeamkaqG 243
                                       ++++v++a +++G
  gi|313126528|ref|YP_004036798.1| 403 AIQRVVDAYSDNG 415
                                       ********99987 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.5   0.0   3.1e-57   1.1e-53       1     129 [.      35     162 ..      35     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.5 bits;  conditional E-value: 3.1e-57
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       pervl+ +++v +d+G+ + +k++r+q++  +gP+kGGiR+hp+v+ devkaL+ +m+yK+a+vd+p+GG+kgg+ i
  gi|313126528|ref|YP_004036798.1|  35 PERVLELNLSVDMDDGTRKRFKAFRSQFNGDRGPYKGGIRYHPNVSRDEVKALSGWMVYKCAVVDIPYGGGKGGIVI 111
                                       89*************************************************************************** PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                                       dp+++s +eleritr+f++el+ ++iG+++D+pApDv+tg+rem+w+ d+y+
  gi|313126528|ref|YP_004036798.1| 112 DPREHSAAELERITRSFAKELR-PLIGEDQDIPAPDVNTGQREMNWIKDTYE 162
                                       **********************.****************************8 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     5e-07    0.0018      27      69 ..     202     244 ..     186     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5e-07
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69 
                                        ++l k+++g tv++ G+G+ G+ +a++l+ +g++++a++ s 
  gi|313126528|ref|YP_004036798.1| 202 FDYLDKDIEGATVAVQGYGNAGSVAANLLEDIGANIVAVSDSS 244
                                       577889********************************99875 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.6e-06     0.016     258     348 ..     197     293 ..     179     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHH....HHHHHHS.TT...SEEEES CS
                    Oxidored_nitro 258 rlldaladyheylagkrvaiygdpdrvvalarllkelGmevvaagtetahrdde....erlkaeleeg..epevidd 328
                                       ++ +a+  + + ++g++va+ g++      a ll+++G+++va++ +++    e    + + ++++ +  +   +d+
  gi|313126528|ref|YP_004036798.1| 197 TAREAFDYLDKDIEGATVAVQGYGNAGSVAANLLEDIGANIVAVSDSSGAIYREggfdTAAAKQFKREtgSVSGYDQ 273
                                       556677778899******************************99877775555544544445555555676678999 PP

                                       .CHHHHHHHHHHHT-SEEEE CS
                    Oxidored_nitro 329 adleeleelikelkpdlllg 348
                                       ad+e ++e + +l +dll+ 
  gi|313126528|ref|YP_004036798.1| 274 ADEEMTNEELLTLDVDLLIP 293
                                       99999999999999999985 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   7.9e-06     0.028       2      38 ..     209     245 ..     208     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-06
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT- CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregs 38 
                                       ++g ++av GyG+ G + a+ l d g ++v    +++
  gi|313126528|ref|YP_004036798.1| 209 IEGATVAVQGYGNAGSVAANLLEDIGANIVAVSDSSG 245
                                       6889************************976544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2309.67
//
Query:       gi|313126529|ref|YP_004036799.1|  [L=431]
Description: glutamate dehydrogenase (NADp) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-74  249.8   0.0    9.6e-74  248.2   0.0    1.7  2  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    1.1e-55  187.0   0.0      2e-55  186.2   0.0    1.5  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
    0.00047   19.6   0.0    0.00082   18.8   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
       0.05   13.2   0.1      0.077   12.6   0.1    1.5  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.056   13.9   0.0       0.13   12.7   0.0    1.7  1  NAD_binding_7    Putative NAD(P)-binding
       0.15    9.5   0.0       0.27    8.7   0.0    1.3  1  Bac_GDH          Bacterial NAD-glutamate dehydrogenase


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.42   1.3e+03      66      90 ..     123     148 ..     120     159 .. 0.80
   2 !  248.2   0.0   3.2e-77   9.6e-74       1     243 []     196     428 ..     196     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.42
                                       EEEEETTEE-HHHHHHHHHCSSS.ST CS
                     ELFV_dehydrog  66 GviydpeGldieellelkeerks.vk 90 
                                       Gv++dp+ l+ ee+ +l ++ ++ ++
  gi|313126529|ref|YP_004036799.1| 123 GVVVDPKDLSEEEVERLTRRFAQeLR 148
                                       999******99999999877765555 PP

  == domain 2  score: 248.2 bits;  conditional E-value: 3.2e-77
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HH CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldie 77 
                                       GGs++r++a g++v+++++e++k+++ d l++++va++G+G vg +aa+ll ++ga+vvavsD +G+iydp+Gld++
  gi|313126529|ref|YP_004036799.1| 196 GGSEGRDGAPGRSVAIITREAVKYYDWD-LSETTVAVQGFGSVGANAARLLDDWGANVVAVSDVNGAIYDPDGLDTR 271
                                       9***********************9999.************************************************ PP

                                       HHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHH CS
                     ELFV_dehydrog  78 ellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeA 154
                                       ++  +kee ++v +y+     + ++++ne e+lel+vd+l+P+A+ n+i+++na+  i+  ++++vEgAN+ptt +A
  gi|313126529|ref|YP_004036799.1| 272 DVPTHKEEPEAVMTYD-----APQKLSNE-EILELDVDVLIPAAIGNVITADNAD-DIQ--ADVIVEGANGPTTFAA 339
                                       ****************.....24799**7.*************************.999..**************** PP

                                       HHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHH CS
                     ELFV_dehydrog 155 keileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkganiag 231
                                       +e+l+e+g+ v+pd++aNaGGVtvS++E+lq+++r  w+ e+v+e+l+++m+++++av +e+e ++++++++a+i++
  gi|313126529|ref|YP_004036799.1| 340 DEMLTERGIPVIPDILANAGGVTVSYFEWLQDINRRAWSLERVHEELESEMNDAWNAVRDEVEARDVSWRDAAYIVA 416
                                       ***************************************************************************** PP

                                       HHHHHHHHHHCT CS
                     ELFV_dehydrog 232 fekvaeamkaqG 243
                                       +e++aea++++G
  gi|313126529|ref|YP_004036799.1| 417 LERIAEAHERRG 428
                                       *********998 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.2   0.0   6.8e-59     2e-55       1     130 []      50     178 ..      50     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.2 bits;  conditional E-value: 6.8e-59
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p +v +vtvp++rd+G+le ++g+raqh+s++gP+kGG+Rfhp v+ +e+  L+++mt+K+a++dlpfGGakggv +
  gi|313126529|ref|YP_004036799.1|  50 PAQVHEVTVPIRRDDGTLEAYTGFRAQHDSVRGPYKGGLRFHPGVTREECIGLSMWMTWKCAVMDLPFGGAKGGVVV 126
                                       6799************************************************************************* PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       dpk+lseee+er+trrf++el+ +++Gp++D+pApD+gt+a++m+w++d y++
  gi|313126529|ref|YP_004036799.1| 127 DPKDLSEEEVERLTRRFAQELR-DVVGPHTDIPAPDMGTDAQTMSWFMDAYSM 178
                                       **********************.****************************97 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.7e-07   0.00082      29      68 ..     219     258 ..     207     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.7e-07
                                       GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrs 68 
                                       +   +ls+ tv++ G+G++G ++a++l  +g++v+a++  
  gi|313126529|ref|YP_004036799.1| 219 YYDWDLSETTVAVQGFGSVGANAARLLDDWGANVVAVSDV 258
                                       556799*****************************99865 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.6e-05     0.077       2      35 ..     224     257 ..     223     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE- CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglr 35 
                                       l++ ++av G+Gs G + a+ l d g +vv    
  gi|313126529|ref|YP_004036799.1| 224 LSETTVAVQGFGSVGANAARLLDDWGANVVAVSD 257
                                       67899***********************986554 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.5e-05      0.13       3      40 ..     222     259 ..     221     329 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                       +dl++ +v v G G+v+a+ +r l + ga+v+ v+   
  gi|313126529|ref|YP_004036799.1| 222 WDLSETTVAVQGFGSVGANAARLLDDWGANVVAVSDVN 259
                                       899******************************99874 PP

>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   8.9e-05      0.27    1050    1099 ..     318     367 ..     314     372 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 8.9e-05
                           Bac_GDH 1050 ngkelrakvvgEGgNLGltQlgRiEyalkggrintDaiDNsaGVdcSDhE 1099
                                        n+ +++a v+ EG+N   t  +    +++g+ +  D + N++GV +S  E
  gi|313126529|ref|YP_004036799.1|  318 NADDIQADVIVEGANGPTTFAADEMLTERGIPVIPDILANAGGVTVSYFE 367 
                                        899************9999999888999*****************99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.51
# Mc/sec: 2555.39
//
Query:       gi|313126530|ref|YP_004036800.1|  [L=285]
Description: citrate lyase subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-49  167.4   0.6    3.4e-49  167.0   0.6    1.2  1  HpcH_HpaI       HpcH/HpaI aldolase/citrate lyase family
    7.9e-10   38.4   0.0    1.4e-06   27.7   0.0    2.1  2  C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   0.6   3.8e-53   3.4e-49       1     221 []       4     219 ..       4     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 3.8e-53
                                       EEEEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHH CS
                         HpcH_HpaI   1 riglflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqd 77 
                                       r++lf+pg++++l++ka+ agaD++ +DlEdav   +Kd+AR  v+++l ++ +  +a  e+ VRv s    ++++d
  gi|313126530|ref|YP_004036800.1|   4 RSLLFSPGDRPELMRKAPSAGADVLCFDLEDAVVPSKKDDARAAVRDVLSDPSFDPDA--EILVRVASE---TVADD 75 
                                       799***************************************************8888..******864...45666 PP

                                       GG.......HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEE CS
                         HpcH_HpaI  78 le.......vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgv 147
                                       l         +d  +++++v k   a++++ev++ l+ +         ++++ a iE+a+gv+na++Iaa     ++
  gi|313126530|ref|YP_004036800.1|  76 LDgvlgpdgDVDVRLDGIMVSKAGYAADIREVDNELAARG-------WTLPVFALIETARGVLNAPDIAAEGPTTAL 145
                                       66644555568999**********************9999.......99**************************** PP

                                       EE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEHHHHHHHH CS
                         HpcH_HpaI 148 flGaeDlsadlgtkrspegtevldareriltaaraagiaaldtvasdiddaegflaegalfvalGfdgkllinp 221
                                       ++GaeDl+ad+g++r++egtevl+arer++  a a++i+a+dtv++d +d++g++++ +++ +lG+dgk++i+p
  gi|313126530|ref|YP_004036800.1| 146 IFGAEDLAADIGATRTEEGTEVLYARERVVVVAAAEEIDAIDTVHTDFEDESGLREQTEFARSLGYDGKMAIHP 219
                                       *************************************************************************8 PP

>> C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   9.2e-05      0.82      11      94 ..       7      80 ..       5     132 .. 0.72
   2 !   27.7   0.0   1.6e-10   1.4e-06     248     330 ..     194     279 ..     165     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 9.2e-05
                    C-C_Bond_Lyase 11 LYmPatrediaekilkqklegltslvlclEDavseeeveaAeenlkellkelaeaekekekeelpllFvRvRspeqlke 89
                                      L+ P++r+++++k      +g+  l+++lEDav  ++ ++A + ++++l++ +             + vRv s  ++++
  gi|313126530|ref|YP_004036800.1|  7 LFSPGDRPELMRKA---PSAGADVLCFDLEDAVVPSKKDDARAAVRDVLSDPSFD-------PDAEILVRVASETVADD 75
                                      88999998887665...557888999*********************99876653.......23345556655555555 PP

                    C-C_Bond_Lyase 90 llerl 94
                                      l   l
  gi|313126530|ref|YP_004036800.1| 76 LDGVL 80
                                      55555 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 1.6e-10
                    C-C_Bond_Lyase 248 kdldglirEvalDkanGlvGKtvIhPsqialvqallvVskeeyedAldilesakg......gvfkseyankmnEvkp 318
                                       +d  gl + ++  ++ G  GK +IhP+q+++++ +++ s ++ e A+++l+++++      gvf+++  ++m+  +p
  gi|313126530|ref|YP_004036800.1| 194 EDESGLREQTEFARSLGYDGKMAIHPAQVPVINDAFTPSPDQVEWAEKVLDARDEaetsgaGVFRVD--DEMI-DAP 267
                                       445688889999999***********************************97442234557899888..****.689 PP

                    C-C_Bond_Lyase 319 hraWAekilkra 330
                                         a Ae+il+ra
  gi|313126530|ref|YP_004036800.1| 268 LIAQAERILERA 279
                                       ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.55
# Mc/sec: 1567.17
//
Query:       gi|313126531|ref|YP_004036801.1|  [L=150]
Description: acyl dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-24   85.7   0.2    2.1e-24   85.4   0.2    1.1  1  MaoC_dehydratas  MaoC like domain
    5.9e-06   26.5   0.2    1.7e-05   24.9   0.2    1.6  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
  ------ inclusion threshold ------
       0.08   13.3   0.2       0.38   11.2   0.2    2.1  1  4HBT             Thioesterase superfamily


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.2   3.5e-28   2.1e-24       6     117 ..      11     123 ..       8     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 3.5e-28
                                       TTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTT.EGGGEEEE CS
                   MaoC_dehydratas   6 igekvetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdn.vvarvgei 81 
                                       +ge++ +ek++tv+e+d+ ++  ++++ +p+H+d efA+ ++fg + ++G++t++++ +l + + +d+ +va++  +
  gi|313126531|ref|YP_004036801.1|  11 VGETIVHEKRRTVSESDNQRFCDMTMNQQPLHLDSEFAADTQFGDRLVNGLYTMSLAVGLSIPDTTDGtIVANLSYD 87 
                                       899************************************************************************** PP

                                       EEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  82 kvrFtkpVlpgdtlkvelevvgkrdvrktkkvevtk 117
                                       +v  + pV++gdt++++ +v++kr+  +   + vt 
  gi|313126531|ref|YP_004036801.1|  88 NVEHPHPVFHGDTIRAQSTVTDKRETSDGERGVVTM 123
                                       **********************99988665666555 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   2.9e-09   1.7e-05       3     131 ..      11     137 ..      10     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.9e-09
                   MaoC_dehydrat_N   3 iGaef.epvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhg 78 
                                       +G  + ++++ +v++++ ++f+  + + +p++ld e a+++ +++  +   +++ la      +++   d+  + ++
  gi|313126531|ref|YP_004036801.1|  11 VGETIvHEKRRTVSESDNQRFCDMTMNQQPLHLDSEFAADTQFGDRLVNGLYTMSLAVGL--SIPDT-TDGTIVANL 84 
                                       67777789999**********************************************988..44433.455555556 PP

                   MaoC_dehydrat_N  79 e.qefeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                       +  ++e  +p+  GD+++ +s+++d ++  + G+  ++++  +  nq++e v++
  gi|313126531|ref|YP_004036801.1|  85 SyDNVEHPHPVFHGDTIRAQSTVTDKRET-SDGERGVVTMHVEAFNQDDELVCE 137
                                       656788889******************95.48*******************987 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   6.3e-05      0.38      36      79 .]      87     136 ..      61     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                                       EEEEESS-BBTTCEEEEEEEEEEEESSE......EEEEEEEEETTSCEEE CS
                              4HBT  36 lsidflrpvrlgdeltvearvlrlgrts......avvevevrdedgrlva 79 
                                       +++++ +pv  gd+++++ +v+    ts      ++++ve +++d++lv+
  gi|313126531|ref|YP_004036801.1|  87 DNVEHPHPVFHGDTIRAQSTVTDKRETSdgergvVTMHVEAFNQDDELVC 136
                                       799999***************99887755555559999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 985.71
//
Query:       gi|313126532|ref|YP_004036802.1|  [L=259]
Description: hypothetical protein Hbor_17890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-14   54.4   0.0    1.9e-14   53.6   0.0    1.4  1  bPH_2     Bacterial PH domain
  ------ inclusion threshold ------
      0.081   13.3   0.4       0.13   12.6   0.4    1.3  1  DUF3811   YjbD family (DUF3811)


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   2.1e-18   1.9e-14       2      79 ..      55     130 ..      54     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.1e-18
                             bPH_2   2 rattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeelae 78 
                                       r+t+y++t   ++ +sGil+r+   + ++++q+ s++q++l+   g+g++ i+taggs+  ve ++ sv++++++ae
  gi|313126532|ref|YP_004036802.1|  55 RNTHYVVTTAGLYRKSGILSRDVQKVGFDKVQNTSYSQGILGSSVGFGNVDISTAGGSG--VEMRFQSVENPRDVAE 129
                                       89********************************************************9..**************98 PP

                             bPH_2  79 l 79 
                                       l
  gi|313126532|ref|YP_004036802.1| 130 L 130
                                       5 PP

>> DUF3811  YjbD family (DUF3811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   1.5e-05      0.13      13      56 ..     158     202 ..     152     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                           DUF3811  13 eqrevktlLdrar.kklgreLtNaEqNrikdeaidkimaereaaa 56 
                                       e re++tlL+r   ++l+ + t +E+ ++  ++id+++ er +  
  gi|313126532|ref|YP_004036802.1| 158 ELREIRTLLERDEsAALDTTRTAGESEQVEMNTIDELVSERPDDE 202
                                       679*******9652789***********************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1404.89
//
Query:       gi|313126533|ref|YP_004036803.1|  [L=183]
Description: hypothetical protein Hbor_17900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-12   45.9   0.2    7.6e-12   45.2   0.2    1.3  1  bPH_2     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.2   4.3e-16   7.6e-12       3      77 ..      74     144 ..      72     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.3e-16
                             bPH_2   3 attytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeela 77 
                                       +t + +tdr v+ ++G  +r+ +++ l+r+q+vs++qs ++  lg+gt+ +e agg+     + l  v d++++a
  gi|313126533|ref|YP_004036803.1|  74 TTAFLVTDRAVYTKRGRRSRRVTTLELDRVQDVSYSQSAVGGVLGYGTVTVEIAGGGN----VSLSAVGDPKAVA 144
                                       67799****************************************************5....5555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1031.44
//
Query:       gi|313126534|ref|YP_004036804.1|  [L=119]
Description: hypothetical protein Hbor_17910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.9   0.4      0.014   15.6   0.4    1.1  1  DUF63     Membrane protein of unknown function DUF63


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.4   7.9e-07     0.014     175     232 ..      26      82 ..       3      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.9e-07
                             DUF63 175 klnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvlipvl 232
                                        l ++++++ llD++ t +g++ lg+ E  +v ++ + l+G    m++lk+ v+  ++
  gi|313126534|ref|YP_004036804.1|  26 VLWVAVVVTYLLDVALTAYGLS-LGFEEANPVARATMVLFGPLPAMVALKTFVIGVAV 82 
                                       4667899*************97.7*****************999*******9986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 675.18
//
Query:       gi|313126535|ref|YP_004036805.1|  [L=594]
Description: acetyl-CoA carboxylase, carboxyl transferase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.5e-128  427.7   0.0   7.6e-128  427.2   0.0    1.1  1  Carboxyl_trans  Carboxyl transferase domain


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.2   0.0  4.2e-132  7.6e-128      35     493 ..     138     592 ..     115     593 .. 0.92

  Alignments for each domain:
  == domain 1  score: 427.2 bits;  conditional E-value: 4.2e-132
                                       HHHHHHHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEEECHHHHHHHHHTEEEEEEEEE-ES.SSGHH CS
                    Carboxyl_trans  35 telgrkkklprdgvvtgsGaviGravevvaqdktvlggslgpakgekllkaqeeaikagepligindsgGa.egriq 110
                                       +e    ++lp+dg++tg  + +Gr  +++a+d+tv++gs+  + +ek l+ q++a+k+g p++++ ds+G   +++ 
  gi|313126535|ref|YP_004036805.1| 138 EEDDEGNRLPADGLITGAATFEGRDLHFMANDFTVKAGSMARHGVEKFLRMQQRALKNGKPVLYLMDSSGGrIDQQT 214
                                       44444578************************************************************999666555 PP

                                       SSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEETTEEEEESSTHHHHHHHHSSCC-SSCH CS
                    Carboxyl_trans 111 egveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvimveetskifltGpdvikkvlgreevtsee 187
                                         + +++g+Gk  ++ s +sg++pqi++++g+c++g+aY p ++d++imve+ s++ +++p+++++v+g ee+++++
  gi|313126535|ref|YP_004036805.1| 215 GFFANREGIGKYYYNHSMLSGRVPQICVLYGPCIAGAAYTPVFADFTIMVEGMSAMAIASPRMVEMVTG-EEIDMQD 290
                                       55799****************************************************************.******* PP

                                       HHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSSGSSSH....HCS-CTTTS---HHH CS
                    Carboxyl_trans 188 lgGatqhmtksGvahltaeddeealelirkllsylPkkasnnresaPivetadepdrd..lieivPdnakkpyDvre 262
                                       lgGa++h+++sG a+l+a d+ +a +l+ +l+sylP+ka +   ++P  et+++      ++e++P+ +++pyDv++
  gi|313126535|ref|YP_004036805.1| 291 LGGARMHAEESGSADLVARDEAHARQLVAQLMSYLPDKAGE---KPPQSETVPPKYSPdgIDELIPEAPNRPYDVHD 364
                                       ************************************88888...666666654444336689*************** PP

                                       HHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-B CS
                    Carboxyl_trans 263 viarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaGqvlfidsavKaarfirlcdaenlPlviladv 339
                                       ++ r+vd g+ +E+k++y+k++V++fAr++G+pvGvvAn++++ +G  +f+d+a+Kaa+fi++cda ++Pl+ l d+
  gi|313126535|ref|YP_004036805.1| 365 LLDRVVDAGSVFELKPDYGKEIVTAFARIDGRPVGVVANQPTQRSG-AIFPDAAEKAAEFIWTCDAYEIPLLYLCDT 440
                                       **********************************************.****************************** PP

                                       SEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHH CS
                    Carboxyl_trans 340 rGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmdskingadlvaawptariaVlgpegavei 416
                                       +Gf+ G++ e++ il  G k ++a ++a+vPk tv++rkayG++ ++m++++++++ v+a p+ +i+++gpe a+++
  gi|313126535|ref|YP_004036805.1| 441 PGFMAGSQVEKDAILEKGKKFIYATSSATVPKQTVVVRKAYGAGIYAMGGPAYDPESVIALPSGEIGIMGPEAAINA 517
                                       ***************************************************************************** PP

                                       HSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTTSSSEEEHGGGHHHHHHHHHHH CS
                    Carboxyl_trans 417 lfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetraklvialelewkkarklparkrrn 493
                                       ++ +++a+ +    +++++r+++l+e  +e +   + a+  ++D++++ps++ra+l+ + +++++  ++lp +k++ 
  gi|313126535|ref|YP_004036805.1| 518 VYANKLAEIDDP--EERKQREDELREEYREDIDAHRMASEVVIDEIVPPSDLRAELAGRFAFYADVDKSLPDKKHGT 592
                                       *****9877633..23334455555444444999*******************************99999*999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.56
# Mc/sec: 3215.42
//
Query:       gi|313126536|ref|YP_004036806.1|  [L=299]
Description: d-fructose 1,6-bisphosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.7e-24   84.9   0.1    6.9e-24   84.4   0.1    1.3  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain
     0.0001   22.0   0.1    0.00032   20.3   0.0    1.7  2  Inositol_P  Inositol monophosphatase family
  ------ inclusion threshold ------
       0.04   13.4   0.0      0.075   12.5   0.0    1.4  1  SEO_C       Sieve element occlusion C-terminus


Domain annotation for each model (and alignments):
>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.1   1.2e-27   6.9e-24      51     187 ..      44     166 ..      16     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 1.2e-27
                            FBPase  51 agaeNvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSnidtnvsvGtif 127
                                       a + N  G+ q++ Dv+ad++l e +   + v   +SEE++ +i+      ++ +v++DPlDGSSn+  n ++Gti+
  gi|313126536|ref|YP_004036806.1|  44 AEEDNPSGETQMEADVYADDLLCERIGDIDGVGEYASEERPAVIDT----GSGLSVCVDPLDGSSNLKPNNTMGTIV 116
                                       7889*************************************99998....7899*********************** PP

                            FBPase 128 siyrkksedeettidvlqpGkeqvAAgyvvYGsstmlVltlgaGvngFtlDpslgefilt 187
                                       ++y       +    +  +G +++AA+yv+YG+ t+++++ ++ v ++++ +++ge+  +
  gi|313126536|ref|YP_004036806.1| 117 AVYD-----AP----IPATGADMLAAAYVLYGATTTMIVARDDTVTEYVI-QEDGEYEAV 166
                                       ***9.....34....3569******************************9.889999766 PP

>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   5.4e-08   0.00032       5     121 ..      18     127 ..      14     136 .. 0.85
   2 ?   -1.2   0.0      0.19   1.2e+03     228     267 ..     252     292 ..     250     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.4e-08
                                       HHHHHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.S CS
                        Inositol_P   5 vtkaavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgeksel 81 
                                        ++  ++++a+a+  +r+ ++++++ +ee+    + +++ +ad  +++l++e++ +     +  +ee  a ++    
  gi|313126536|ref|YP_004036806.1|  18 TITQIFDVVARAAPEIRSGLPGRRIYAEEDN--PSGETQMEADVYADDLLCERIGDIDGVGEYASEERPAVID---- 88 
                                       44457899999**********8888888777..9999*********************99*************.... PP

                                       SSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEEEEE CS
                        Inositol_P  82 tedgltwivDPiDGTknFvrgipqvaVsigllvegkpvlG 121
                                       t +gl ++vDP+DG +n  +  + +++ +++++   p  G
  gi|313126536|ref|YP_004036806.1|  89 TGSGLSVCVDPLDGSSNL-KPNNTMGTIVAVYDAPIPATG 127
                                       8888***********995.444788888888877666655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.19
                                       HHHHTTEEEEESSSCSSSTTSSEEEEES.CHHHHHHHHHHH CS
                        Inositol_P 228 ileeaGGvvtdakgegrlllargiiaan.qkelaellaaav 267
                                       i+e aGG+  d +++ +++++ +++a +   + +e l++++
  gi|313126536|ref|YP_004036806.1| 252 IIETAGGRSSDGEQSLLAVEKDELHARTpVYVGNEELIEKL 292
                                       8999******9999988888888888776555555555555 PP

>> SEO_C  Sieve element occlusion C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.3e-05     0.075      32      64 ..     175     207 ..     169     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                             SEO_C  32 gkyiclyGgedleWireftstakkvakaagiql 64 
                                       + +++ +Gg   +W+++ft+ a++++++a+++l
  gi|313126536|ref|YP_004036806.1| 175 DPTVYGFGGRVPDWVESFTEYARDIESDASMKL 207
                                       5567889********************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1634.12
//
Query:       gi|313126537|ref|YP_004036807.1|  [L=347]
Description: hypothetical protein Hbor_17940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-07   31.5   0.0    0.00037   21.0   0.0    2.3  2  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.035   14.3   0.0        2.8    8.2   0.0    2.3  2  Cdd1      Pathogenicity locus
      0.077   13.2   0.0       0.19   12.0   0.0    1.6  1  DUF4332   Domain of unknown function (DUF4332)
       0.17   11.2   0.0       0.29   10.4   0.0    1.3  1  TMP-TENI  Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00086       3.8       6      29 ..      73      95 ..      65     117 .. 0.79
   2 !   21.0   0.0   8.3e-08   0.00037       9      56 ..     296     343 ..     291     344 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00086
                                      TSTT--HHHHHHHHTTT--SHHHH CS
                             HHH_5  6 svsGiGpktAlallsaGiesvedl 29
                                      ++  iGpktA al +  i+ ved+
  gi|313126537|ref|YP_004036807.1| 73 ELRFIGPKTAEALRDSAIG-VEDI 95
                                      6778999999999998443.6666 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 8.3e-08
                                       T--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   9 GiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       G+    A +l++aGi+sv  la ad+e +a++  + ++++er++++++
  gi|313126537|ref|YP_004036807.1| 296 GVDDTHADRLADAGIRSVRRLATADPESVADALELDQRRVERWCEAAR 343
                                       88888999**************************************98 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.016        70       5      29 ..      68      94 ..      64     101 .. 0.79
   2 ?    8.2   0.0   0.00063       2.8      11      50 ..     294     333 ..     285     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                              Cdd1  5 lkelqdiPniGkalaedlv..elGirs 29
                                       ++++++  iG+++ae l+  ++G+++
  gi|313126537|ref|YP_004036807.1| 68 PETFEELRFIGPKTAEALRdsAIGVED 94
                                      578999************954566665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00063
                              Cdd1  11 iPniGkalaedlvelGirsveelkgedpeelyeklekltg 50 
                                       + ++    a+ l + Girsv+ l+  dpe++ ++le  ++
  gi|313126537|ref|YP_004036807.1| 294 LGGVDDTHADRLADAGIRSVRRLATADPESVADALELDQR 333
                                       5667778899**********************99987665 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.2e-05      0.19       5      52 ..     299     341 ..     293     345 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.2e-05
                           DUF4332   5 keeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanl 52 
                                       +++a++L+ aGi+++++L+++ +++     +a++l++++r+v ++ ++
  gi|313126537|ref|YP_004036807.1| 299 DTHADRLADAGIRSVRRLATADPES-----VADALELDQRRVERWCEA 341
                                       4455666666666666666663333.....244666666666666555 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.4e-05      0.29     142     175 ..     279     313 ..     268     316 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.4e-05
                          TMP-TENI 142 lkelaeale.iPvvaiGGitlenvaevleagadgv 175
                                        +e++e++   Pv ++GG++  +++++++ag+++v
  gi|313126537|ref|YP_004036807.1| 279 EAEWREQSApTPVTVLGGVDDTHADRLADAGIRSV 313
                                       45677776669********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2162.84
//
Query:       gi|313126538|ref|YP_004036808.1|  [L=288]
Description: 3-hydroxyacyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-62  210.7   1.8    1.9e-62  210.3   1.8    1.1  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    2.6e-33  114.5   0.3    1.9e-32  111.7   0.0    2.3  3  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
      0.006   16.0   0.1      0.011   15.1   0.1    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.011   15.9   3.0      0.014   15.5   2.2    1.8  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.017   14.4   0.7      0.028   13.7   0.7    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.026   14.1   0.5      0.044   13.4   0.5    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.046   13.3   2.1      0.076   12.6   2.1    1.3  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
      0.048   14.2   1.9       0.18   12.4   0.4    2.4  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
        0.2   12.6   0.2       0.44   11.5   0.0    1.6  2  DAZAP2          DAZ associated protein 2 (DAZAP2)


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.3   1.8   9.6e-66   1.9e-62       1     174 [.      11     184 ..      11     189 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 9.6e-66
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77 
                                       +v+v+GaGtmG+gia+v+a ag++Vv+ di+ e++e++l++ie+sl+++vek +l++ e+++al+ri+ tt+l++++
  gi|313126538|ref|YP_004036808.1|  11 TVGVVGAGTMGNGIAQVAAMAGYDVVMRDIKMEFVERGLDSIEDSLSRFVEKDQLSQTEADDALDRIRGTTELADLA 87 
                                       69*************************************************************************** PP

                                       C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT CS
                           3HCDH_N  78 dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgek 154
                                        adlv+Ea+vE++++Kr++fa+l++++++d++la+nTS+lsi+ +a+a++rpe+v+g+HF+nP+plmk vEvv gek
  gi|313126538|ref|YP_004036808.1|  88 VADLVVEAAVEDMDVKRDIFADLDEVTDEDVVLATNTSTLSITTIAAATDRPENVVGVHFMNPVPLMKGVEVVVGEK 164
                                       ***************************************************************************** PP

                                       --HHHHHHHHHHHHHTT-EE CS
                           3HCDH_N 155 Tseetvatvvelakkigktp 174
                                       T++++v+ ++e++++++k++
  gi|313126538|ref|YP_004036808.1| 165 TDSKVVELAHEFSEELDKET 184
                                       ****************9986 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.98     2e+03      41      89 ..      22      68 ..       5      76 .. 0.58
   2 ?   -1.1   0.0       1.5   2.9e+03      41      58 ..      78      95 ..      44     116 .. 0.64
   3 !  111.7   0.0   9.6e-36   1.9e-32       1      97 []     192     287 ..     192     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.98
                                      SCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--BGG CS
                             3HCDH 41 mGpfelldlvgldvakkilevlaeelgerayapsplleklveagrlgrk 89
                                       G+ +++ ++g dv+ + ++  + e g +  +  + l+++ve+++l++ 
  gi|313126538|ref|YP_004036808.1| 22 NGIAQVAAMAGYDVVMRDIKMEFVERGLDSIE--DSLSRFVEKDQLSQT 68
                                      57777777777777655544222222222333..566777777666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                                      SCHHHHHHHHHHHHHHHH CS
                             3HCDH 41 mGpfelldlvgldvakki 58
                                       G+ el+dl+  d++  +
  gi|313126538|ref|YP_004036808.1| 78 RGTTELADLAVADLVVEA 95
                                      466777777766665544 PP

  == domain 3  score: 111.7 bits;  conditional E-value: 9.6e-36
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GFv+nR+l+p++ne +r+++egva+ ediD+ m+lg+++pmGp++l+d +gld++++++++l+eelg+r y+p+ ll
  gi|313126538|ref|YP_004036808.1| 192 GFVTNRILMPWINEGIRAYDEGVATKEDIDRGMTLGTNVPMGPLTLADHIGLDICLDASQTLHEELGDR-YKPAYLL 267
                                       9*******************************************************************9.7889*** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       ++ v+ag+lg+ktg+gfy+y
  gi|313126538|ref|YP_004036808.1| 268 KRKVDAGDLGKKTGQGFYDY 287
                                       ******************99 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   5.5e-06     0.011      37      70 ..      10      43 ..       3      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.5e-06
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                      +tvG++G+G +G+ +a++++  g +v++ d + +
  gi|313126538|ref|YP_004036808.1| 10 ETVGVVGAGTMGNGIAQVAAMAGYDVVMRDIKME 43
                                      69*************************9998855 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   2.2   7.2e-06     0.014       1      41 [.      11      51 ..      11     145 .. 0.71
   2 ?   -2.7   0.0       2.9   5.8e+03      20      41 ..     154     175 ..     141     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.2e-06
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvae 41
                                      ++g++G G+MG+ +a+  + agy+v++ + + e ve+ +++
  gi|313126538|ref|YP_004036808.1| 11 TVGVVGAGTMGNGIAQVAAMAGYDVVMRDIKMEFVERGLDS 51
                                      58***************************998777766554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.9
                                       HTT-EEEEE-SSHHHHHHHHHT CS
                     NAD_binding_2  20 kagykvavynrtkekveelvae 41 
                                        +g +v+v + t +kv el++e
  gi|313126538|ref|YP_004036808.1| 154 MKGVEVVVGEKTDSKVVELAHE 175
                                       5788888888888888887765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   1.4e-05     0.028      30     119 ..      11     101 ..       5     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH.HHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleq.leslgakfvevlksqeellaeavkeadvvigtvlipGkk 105
                                       +v v+G+G+ G   +++a+  g +V++ D++++  e+ l+s++ +  + +++++ + +ea    d + gt  +   +
  gi|313126538|ref|YP_004036808.1|  11 TVGVVGAGTMGNGIAQVAAMAGYDVVMRDIKMEFVERgLDSIEDSLSRFVEKDQLSQTEADDALDRIRGTTELADLA 87 
                                       588****************************9976542788888877777778878888888889999999999999 PP

                                       ---SC-HHHHHTS- CS
                       AlaDh_PNT_C 106 aPkLvteemvksMk 119
                                        + Lv e+ v+ M 
  gi|313126538|ref|YP_004036808.1|  88 VADLVVEAAVEDMD 101
                                       99999999999995 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   2.2e-05     0.044       2      79 ..      11      91 ..      10     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHH....HHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekv....dklnsgkipiyepgLeelvkkavesgrlsfttdvekavee 76
                                      ++ v+G+G +G   a v a +g +v++ Di  e v    d+++ + + ++e+++ +  ++  + +r+++tt++   ++ 
  gi|313126538|ref|YP_004036808.1| 11 TVGVVGAGTMGNGIAQVAAMAGYDVVMRDIKMEFVerglDSIEDSLSRFVEKDQLSQTEADDALDRIRGTTELAD-LAV 88
                                      689***************************987762222679999999999998888888888899999999877.555 PP

                                      -SE CS
                    UDPG_MGDP_dh_N 77 adv 79
                                      ad+
  gi|313126538|ref|YP_004036808.1| 89 ADL 91
                                      554 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.1   3.8e-05     0.076       4     111 ..      18     134 ..      13     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE.... CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvn.... 75 
                                         +G +iA+ +a +G++vv+ d++ e  ++ +++++++  ++++e D  ++++ +++ ++++ +++  D +v     
  gi|313126538|ref|YP_004036808.1|  18 GTMGNGIAQVAAMAGYDVVMRDIKMEFvERGLDSIEDS-LSRFVEKDQLSQTEADDALDRIRGTTELADLAVAdlvv 93 
                                       569************************55555555554.56799*****************9999888876551111 PP

                                       -----EG.....CSS-GGGH-HHHHHHHHHHHTHHHHHHHH CS
                      adh_short_C2  76 nagiapk.....lkgpfletsreefdraldvnlyslfllak 111
                                        a++ +      + +++ e+++e++  a ++++ s++ +a 
  gi|313126538|ref|YP_004036808.1|  94 EAAVEDMdvkrdIFADLDEVTDEDVVLATNTSTLSITTIAA 134
                                       56666667655666666777888888888888888777665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   9.3e-05      0.18       1      31 [.      11      37 ..      11      76 .. 0.78
   2 ?   -1.7   0.0       2.3   4.5e+03      59      66 ..     113     120 ..      72     150 .. 0.63
   3 ?   -0.2   0.0      0.77   1.5e+03      26      48 ..     157     178 ..     153     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.3e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivva 31
                                      ++g++GaG mg ++a+ ++ ag   +++v  
  gi|313126538|ref|YP_004036808.1| 11 TVGVVGAGTMGNGIAQVAAMAG---YDVV-M 37
                                      58********************...7777.2 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                                       HHH-SEEE CS
                     F420_oxidored  59 aeeadvvv 66 
                                       +++ dvv+
  gi|313126538|ref|YP_004036808.1| 113 VTDEDVVL 120
                                       33333333 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.77
                                       GCEEEEEESSCCCHHHHHHHHC- CS
                     F420_oxidored  26 heivvansrnpekaeelaeelgv 48 
                                        e+vv+ +++ +k+ ela e++ 
  gi|313126538|ref|YP_004036808.1| 157 VEVVVG-EKTDSKVVELAHEFSE 178
                                       588977.9999******999874 PP

>> DAZAP2  DAZ associated protein 2 (DAZAP2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.44      97     121 ..      24      48 ..      17      52 .. 0.83
   2 ?   -3.3   0.0       8.3   1.7e+04     102     115 ..     153     166 ..     151     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                            DAZAP2  97 aAQlAamqGqnvvltqkkenflsGg 121
                                        AQ+Aam+G +vv++  k +f++ g
  gi|313126538|ref|YP_004036808.1|  24 IAQVAAMAGYDVVMRDIKMEFVERG 48 
                                       6********************9866 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.3
                            DAZAP2 102 amqGqnvvltqkke 115
                                        m+G +vv+++k +
  gi|313126538|ref|YP_004036808.1| 153 LMKGVEVVVGEKTD 166
                                       599******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1666.24
//
Query:       gi|313126539|ref|YP_004036809.1|  [L=50]
Description: hypothetical protein Hbor_17960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.5   0.0       0.37   10.7   0.0    1.3  1  DUF5633   Family of unknown function (DUF5633)


Domain annotation for each model (and alignments):
>> DUF5633  Family of unknown function (DUF5633)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.1e-05      0.37      27      37 ..       4      14 ..       4      16 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.1e-05
                           DUF5633 27 evaqgadGryy 37
                                      +v+q+adGr++
  gi|313126539|ref|YP_004036809.1|  4 TVVQDADGRWH 14
                                      699*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 300.54
//
Query:       gi|313126540|ref|YP_004036810.1|  [L=75]
Description: hypothetical protein Hbor_17970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        8.9    6.1   6.4       0.91    9.3   0.2    2.2  2  DUF4538          Domain of unknown function (DUF4538)


Domain annotation for each model (and alignments):
>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   5.1e-05      0.91       5      17 ..      18      30 ..      16      40 .. 0.91
   2 ?   -0.8   1.5     0.072   1.3e+03       7      15 ..      62      70 ..      53      74 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 5.1e-05
                           DUF4538  5 kyvllvggvvgli 17
                                      +++l+vgg+v+l+
  gi|313126540|ref|YP_004036810.1| 18 RTALFVGGFVALV 30
                                      89*********98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.072
                           DUF4538  7 vllvggvvg 15
                                      v l++gvv 
  gi|313126540|ref|YP_004036810.1| 62 VFLFAGVVV 70
                                      455555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 467.05
//
Query:       gi|313126541|ref|YP_004036811.1|  [L=328]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-29  101.0   0.0    1.4e-28  100.2   0.0    1.3  1  ABC_tran  ABC transporter
    5.1e-12   46.2   0.0    1.2e-05   25.3   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.8e-07   31.2   0.1      1e-06   29.4   0.1    1.9  1  DUF4162   Domain of unknown function (DUF4162)
     0.0021   18.3   0.0     0.0043   17.3   0.0    1.5  1  AAA_22    AAA domain
     0.0059   17.1   0.0     0.0098   16.4   0.0    1.3  1  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.027   14.2   0.3      0.056   13.2   0.3    1.7  1  AAA_30    AAA domain
      0.028   14.2   0.0        0.4   10.4   0.0    2.4  2  AAA_24    AAA domain
      0.045   13.5   0.0       0.19   11.4   0.0    1.8  2  AAA_15    AAA ATPase domain
      0.051   13.2   0.0      0.089   12.4   0.0    1.3  1  AAA_27    AAA domain
      0.095   12.9   0.2       0.42   10.8   0.2    2.1  1  AAA_33    AAA domain
       0.13   11.8   0.1       0.24   11.0   0.1    1.4  1  SRP54     SRP54-type protein, GTPase domain
       0.19   11.5   0.1       0.35   10.6   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
       0.25   11.3   0.0       0.39   10.6   0.0    1.2  1  Rad17     Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   9.8e-32   1.4e-28       5     136 ..      21     157 ..      18     158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 9.8e-32
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                       +++++ege+ ++vG+nGaGK+t lk+l+gl +pteG+ ++ + d  +   +++r+++g+lp+e+ l +++t+r+   
  gi|313126541|ref|YP_004036811.1|  21 DFEVEEGEIFGVVGPNGAGKTTTLKMLSGLIEPTEGTARIGEYDAGD---PEMRRHLGFLPEESPLYEDMTARSYlh 94 
                                       799*************************************9999998...9********************9999** PP

                                       ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                  +++++ e+ l++l+l++ +d+++      +S+G+k++va+ar+l+++p+ll+ DEp 
  gi|313126541|ref|YP_004036811.1|  95 ffadlydvpreAATRRTEDTLDRLELEH-RDRRL----GDMSKGMKRKVAIARSLVNDPDLLIYDEPA 157
                                       **********999999************.99999....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.5e-07    0.0009       2      56 ..      30      68 ..      29     126 .. 0.67
   2 !   25.3   0.0   8.9e-09   1.2e-05     232     300 ..     125     190 ..     102     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.5e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpei 56
                                       +++GpNg+GK++ L+ l++l                  ++ + ++    ++ ++
  gi|313126541|ref|YP_004036811.1| 30 FGVVGPNGAGKTTTLKMLSGLIE----------------PTEGTARIGEYDAGDP 68
                                      689*****************954................4444444444444444 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 8.9e-09
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       + + ++S G+kr  a++ +l  ++   +ll+ DEp +gL+P  +  +le+ ++l+++g  v+++ H+ +
  gi|313126541|ref|YP_004036811.1| 125 RRLGDMSKGMKRKVAIARSLVNDP---DLLIYDEPASGLDPLTTNYVLEFTRDLAERGKTVVFSAHNLY 190
                                       5689*****************999...9**************************************975 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   7.3e-10     1e-06       1      80 [.     211     285 ..     211     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 7.3e-10
                                       E-HHHHHTTS-SSEEEEE-------..---EEEE-TT.S-EEEEE-------------.----EEEEEEEE---HHH CS
                           DUF4162   1 GtleeiKrsygknrieveadaeelleepgveeveeeg.gelelkledeeaanellkal.tsgveirsFeeeePsLnd 75 
                                       Gt+ ei++++g++ ++v +       + +ve  e+++ g+++  ++d +a +++ +++ ++++e++ ++ +ePsL+d
  gi|313126541|ref|YP_004036811.1| 211 GTVPEIREQHGETSYHVFT-------TTAVENAETTDdGRYRRVVPDMDAVESVREEAeAADGEVVDIRTHEPSLED 280
                                       99**************873.......44455665555499*******99*********77***************** PP

                                       HHHHH CS
                           DUF4162  76 IFiek 80 
                                       IF+ +
  gi|313126541|ref|YP_004036811.1| 281 IFLDL 285
                                       **975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.1e-06    0.0043       8     117 ..      30     177 ..      24     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.1e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee............erpevv..fvtlpsstsskdllrellralglelka 70 
                                         v+G+ G+GKTt+l++l    +  +  ++            ++ +++  +  l ++++ ++ l+ ++  ++++++a
  gi|313126541|ref|YP_004036811.1|  30 FGVVGPNGAGKTTTLKMLSGLIEPTEGTARigeydagdpemrRHLGFLpeESPLYEDMTARSYLHFFADLYDVPREA 106
                                       5599****************99777777769*****99986555555566666666679999999999999999999 PP

                            AAA_22  71 erlsseellealeqalrarav....................ielliiDEaqh.lr...seealeeLrslln 117
                                       ++ ++e+ l++le   r+r+                     + lli DE    l+   ++ +le+ r+l++
  gi|313126541|ref|YP_004036811.1| 107 ATRRTEDTLDRLELEHRDRRLgdmskgmkrkvaiarslvndPDLLIYDEPASgLDpltTNYVLEFTRDLAE 177
                                       55555555544444444443333333333344444457778888888887777765544777777777766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.1e-06    0.0098      16      38 ..      21      46 ..       2      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.1e-06
                            AAA_23 16 dF...skgltlItGpNGaGKTTildA 38
                                      dF   +  ++ ++GpNGaGKTT l  
  gi|313126541|ref|YP_004036811.1| 21 DFeveEGEIFGVVGPNGAGKTTTLKM 46
                                      445556679*************9875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   4.1e-05     0.056      20      45 ..      29      54 ..      22     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa 45
                                      +  ++Gp G+GKtt+lk l  ++e  
  gi|313126541|ref|YP_004036811.1| 29 IFGVVGPNGAGKTTTLKMLSGLIEPT 54
                                      6789**************99998866 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00029       0.4       6      32 ..      31      55 ..      27     111 .. 0.80
   2 ?    0.8   0.0      0.24   3.4e+02     109     130 ..     166     187 ..     163     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                            AAA_24  6 liyGpsgiGKTtlakelgpkplfidte 32
                                       ++Gp+g+GKTt++k+l  + l+  te
  gi|313126541|ref|YP_004036811.1| 31 GVVGPNGAGKTTTLKML--SGLIEPTE 55
                                      689************99..44554554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.24
                            AAA_24 109 eefrrllkklqelrknvifiah 130
                                       + + ++ ++l e +k+v+f ah
  gi|313126541|ref|YP_004036811.1| 166 NYVLEFTRDLAERGKTVVFSAH 187
                                       6788999**************9 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.19      23      48 ..      28      52 ..      20     106 .. 0.86
   2 ?   -0.2   0.0      0.48   6.6e+02     322     367 ..     146     190 ..     129     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                            AAA_15 23 eeltvliGkNnsGKSsilealdlFln 48
                                      e +  ++G+N++GK++ l++l  +++
  gi|313126541|ref|YP_004036811.1| 28 E-IFGVVGPNGAGKTTTLKMLSGLIE 52
                                      4.6679**************987765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.48
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       +++++l+++EP   L p   + + +  ++la+ +k  v+++ H+ +
  gi|313126541|ref|YP_004036811.1| 146 NDPDLLIYDEPASGLDPLTTNYVLEFTRDLAERGK-TVVFSAHNLY 190
                                       7899******************************9.8999999876 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.4e-05     0.089      19      49 ..      20      50 ..       3      52 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.4e-05
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                       df+ ee ++  ++GpN AGK+t+l+ +s l
  gi|313126541|ref|YP_004036811.1| 20 SDFEVEEGEIFGVVGPNGAGKTTTLKMLSGL 50
                                      578888888889*************988766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00031      0.42       4      33 ..      32     121 ..      29     263 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                            AAA_33   4 lvGlpGsGKstlaerl...lkklg.avllssdt............................................ 32 
                                       +vG++G+GK+t ++ l   ++++  + ++ + +                                            
  gi|313126541|ref|YP_004036811.1|  32 VVGPNGAGKTTTLKMLsglIEPTEgTARIGEYDagdpemrrhlgflpeesplyedmtarsylhffadlydvpreaat 108
                                       79*********999875544444467788877777776666666666666666666666555555555555555544 PP

                            AAA_33  33 ............l 33 
                                                   +
  gi|313126541|ref|YP_004036811.1| 109 rrtedtldrlelE 121
                                       4444444444440 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00018      0.24       6      24 ..      32      50 ..      28      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                      EEESTTSSHHHHHHHHHHH CS
                             SRP54  6 lvGlqGaGKTttlaKLaal 24
                                      +vG++GaGKTttl  L+ l
  gi|313126541|ref|YP_004036811.1| 32 VVGPNGAGKTTTLKMLSGL 50
                                      89**********9888765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00025      0.35      16      43 ..      21      48 ..      16      59 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiq 43
                                      ++e+++ +++ ++Gp+G+GK+T l  ++
  gi|313126541|ref|YP_004036811.1| 21 DFEVEEGEIFGVVGPNGAGKTTTLKMLS 48
                                      567775558999**********885555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00028      0.39      46      67 ..      28      49 ..      18      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                             Rad17 46 riLLisGPsGCgkstvvkvLsk 67
                                      +i  + GP G gk+t++k+Ls 
  gi|313126541|ref|YP_004036811.1| 28 EIFGVVGPNGAGKTTTLKMLSG 49
                                      577899**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2090.49
//
Query:       gi|313126542|ref|YP_004036812.1|  [L=629]
Description: ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-08   32.2   0.5    4.9e-07   29.3   0.5    2.4  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00073   18.7  15.3    0.00073   18.7  15.3    2.6  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.16   11.0   0.0       0.32   10.0   0.0    1.4  1  DUF2625          Protein of unknown function DUF2625


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.5   8.2e-11   4.9e-07      19     278 ..      33     486 ..      13     501 .. 0.56

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 8.2e-11
                   ABC2_membrane_2  19 lltvllpli.................................................................... 27 
                                       ++ ++ +++                                                                    
  gi|313126542|ref|YP_004036812.1|  33 VFLLVAVVLaggiasagmlsggvaldrdiyrvgvasdspyyepvaaapaltpkdpdpdalkngdldilidrervfgp 109
                                       44444444455566666666666666666666666666666666666666666666666666666666666666666 PP

                   ABC2_membrane_2  28 .......dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkv..................... 76 
                                               +ala+l+d+ ++  + + ++ e+++a  +  a s             +                     
  gi|313126542|ref|YP_004036812.1| 110 pvvtqknRAALAALNDAVRRYNTAMMQQEENQTAA-FPVAVSL------------Qyvsrstslpdgavadggsdgg 173
                                       66666665666666665555555444444444442.2222222............0112222333344477777888 PP

                   ABC2_membrane_2  77 ............................................................................. 76 
                                                                                                                    
  gi|313126542|ref|YP_004036812.1| 174 aatgdgsgtgadssgtsaggssssssnaasgssatdgtstsqsgdtaadgsdgplsipnlgginpfsggssgspaei 250
                                       88888888888888888888888888888888888888888888889999999999999999999999999999999 PP

                   ABC2_membrane_2  77 ........vstimavlipvi..aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatv 142
                                               +++++a+l+p+     + g+++++ E+ ++  +llL  Pvs ++i+lgK + +l++ l  +av++la+ 
  gi|313126542|ref|YP_004036812.1| 251 qppfpfgsLMLAFAFLVPMNfvVQAYGSTMLN-ERINRRGELLLVAPVSPGDIVLGKTLPYLTVVLGvTAVIALAV- 325
                                       9*****99999*******98334555666665.6666677************************555555555544. PP

                   ABC2_membrane_2 143 ll.......................alaiilalgivlaledllllvvasvlllllv...vflalglllSsvarssre 193
                                                                a++     +  + + ++ +++ a +++ +++   + +al   l  v+r+ + 
  gi|313126542|ref|YP_004036812.1| 326 -GgglvsvaavvpiglvflgatfvgAMFARSFKELTFVTVAVSVFLTAYTFVPAIFtqvTPIALISPLTLVVRDLQP 401
                                       .2234444444444444444444443333333222222222222222222222222223333333344444444444 PP

                   ABC2_membrane_2 194 aaalalglfvvlailvpivlygvaellagpavp....qeindflsllsptsayntllneilagsdlnalgstatnll 266
                                        a+++lg f++    + + +  + +l ag +      ++ +  l++l+  +a     + +   s     +s ++ ++
  gi|313126542|ref|YP_004036812.1| 402 TATVSLGAFLFSTGPFVLCGGVLFALGAGVYREedmfTQRSVPLKFLDALDARVSRPRDVALVS----GLSIPFVFI 474
                                       4444444444443333333322222222222213333333333333333333333333333333....366666666 PP

                   ABC2_membrane_2 267 illlllavllvl 278
                                       + ll +avl+vl
  gi|313126542|ref|YP_004036812.1| 475 AELLAIAVLFVL 486
                                       666666666665 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  15.3   1.2e-07   0.00073     163     285 ..     256     382 ..      31     432 .. 0.75
   2 ?    1.6   0.2      0.02   1.2e+02     186     229 ..     453     498 ..     437     545 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-07
                   ABC2_membrane_3 163 lvgliliilifitasfiav....siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafglgipf 235
                                       + +l+l+++++++++f+++     +++E+ +r  el+lv++vsp  ++l+k l +++v l ++++i l + g  +++
  gi|313126542|ref|YP_004036812.1| 256 FGSLMLAFAFLVPMNFVVQaygsTMLNERINRRGELLLVAPVSPGDIVLGKTLPYLTVVLGVTAVIALAVGGGLVSV 332
                                       5568999999999999999555457********************************99977777766555533333 PP

                   ABC2_membrane_3 236 gnlglllllfllfglayialgyllsslfkns....etaqilifivilllsgffg 285
                                         ++ + l+f    l ++++g+++   fk      +++++++++ ++++ +f  
  gi|313126542|ref|YP_004036812.1| 333 AAVVPIGLVF----LGATFVGAMFARSFKELtfvtVAVSVFLTAYTFVPAIFTQ 382
                                       3333333333....3444444444444444411003333333333332222222 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.02
                   ABC2_membrane_3 186 Ekesrikelqlvsgvsplqywlskilgdflvyllqlllil..llaf 229
                                        + sr + + lvsg+s    +++ +l+++++++l++ l++  ll+f
  gi|313126542|ref|YP_004036812.1| 453 ARVSRPRDVALVSGLSIPFVFIAELLAIAVLFVLPVELTVpvLLVF 498
                                       5778888899999***9999************99996654212333 PP

>> DUF2625  Protein of unknown function DUF2625
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   5.4e-05      0.32      41      77 ..     397     433 ..     391     449 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.4e-05
                           DUF2625  41 lklqvttrSvlGavvyetGGlliddGwlrvlGsgsek 77 
                                        +lq t+   lGa+++ tG  ++ +G l  lG+g  +
  gi|313126542|ref|YP_004036812.1| 397 RDLQPTATVSLGAFLFSTGPFVLCGGVLFALGAGVYR 433
                                       68999*****************************766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3846.40
//
Query:       gi|313126543|ref|YP_004036813.1|  [L=352]
Description: sodium ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-17   61.9   0.0    7.2e-17   61.5   0.0    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
      4e-14   52.6   4.3    5.5e-14   52.1   4.3    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein
    2.8e-08   33.5   2.1    2.8e-08   33.5   2.1    1.9  2  ABC2_membrane    ABC-2 type transporter
    1.3e-06   28.5   2.7    5.7e-06   26.4   1.4    2.3  2  ABC2_membrane_4  ABC-2 family transporter protein
    0.00097   18.7   1.3     0.0017   18.0   0.2    1.8  2  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
        7.1    6.4   5.6        1.2    8.9   1.8    1.7  2  FA_desaturase    Fatty acid desaturase


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   2.4e-20   7.2e-17       4     296 ..      22     306 ..      20     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 2.4e-20
                   ABC2_membrane_3   4 liitlllPiilvlllglifsnsve..ddentpiavvdedn.sslsqqlvealeaspsvelvyevdseeeakkalkng 77 
                                       +++ l+l ++++++  +++   v+  d+ +t  + vd     + s++lv+a    + v+    +++e+ a++a+++ 
  gi|313126543|ref|YP_004036813.1|  22 IVLALVLQVFIAAFSSFLVVGLVSlyDPGQTGEYGVDVAIaGDASEELVQAATDVSGVN-PTVYSDESAAMRAFESP 97 
                                       55555555666665555555555443322222211222224557999999999988888.99************775 PP

                   ABC2_membrane_3  78 ...didgilvipkgfskdllkgesatvtvlinssnlnss...kailnalnsllqqlnasalvlqseatstsaninve 148
                                          +id++lv ++ + + +       v++++ +sn++++    +++  l sl + +        +e +++  +++v+
  gi|313126543|ref|YP_004036813.1|  98 sktGIDAVLVGESRDGRVF-------VSATVPDSNVQTTvvvVQLRDVLRSLERSE-------RIERAESLETLPVQ 160
                                       2336777777777776654.......466666666655546677777777754443.......47889999999999 PP

                   ABC2_membrane_3 149 stqleeelsnvasf...lvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllql 221
                                       + + +++++ +  +   l + l+l++++fi++s ++ s+ eE+e++++el+ v++vs  +++ +k+l+  +++  q+
  gi|313126543|ref|YP_004036813.1| 161 LPPETQSSPYYGFTytvL-VpLLLFLPVFISGSLTVDSLTEERERGTLELLRVAPVSLREIVDGKLLAATALAPAQA 236
                                       999977776555542234.36******************************************************** PP

                   ABC2_membrane_3 222 llilll.afglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsa 296
                                       +l+l+l  f+ g  + + + ll+l+   + ++ +l+++   l+ + ++aq    + ++  +++fgg+ ++++  ++
  gi|313126543|ref|YP_004036813.1| 237 ALWLVLlGFN-GTRVASPVMLLVLVAALSTLVCSLAAATALLSPDRRSAQF---LYSIGVLFVFGGTTLFPN--NP 306
                                       ****973666.45555556666777777888888999999999999**996...444444566666665543..33 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   4.3   1.8e-17   5.5e-14       2     205 ..       7     296 ..       6     315 .. 0.76

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.8e-17
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllpli.......................dvalaylkdlgsslqseakaikeatlal 55 
                                       +iak+E++ l++ ++++l  vl ++i                        v +a+  d++++l + a +++   +++
  gi|313126543|ref|YP_004036813.1|   7 TIAKRELSTLRKEKTIVLALVLQVFIaafssflvvglvslydpgqtgeyGVDVAIAGDASEELVQAATDVSGVNPTV 83 
                                       89*****99988888888888888889*******************9995556666788888888888888888888 PP

                   ABC2_membrane_2  56 eyveaasa..sdeaedtdqdlkv...................................................... 76 
                                        ++e a++  ++ +++t +d+                                                        
  gi|313126543|ref|YP_004036813.1|  84 YSDESAAMraFESPSKTGIDAVLvgesrdgrvfvsatvpdsnvqttvvvvqlrdvlrslerserieraesletlpvq 160
                                       77776655113334444444433888888888********************************************* PP

                   ABC2_membrane_2  77 ................vstimavlipvi.aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiav 136
                                                       v  ++ +++pv+    +++d++++E+ergTl+ll   Pvs +ei+ gK+++  a+      
  gi|313126543|ref|YP_004036813.1| 161 lppetqsspyygftytVLVPLLLFLPVFiSGSLTVDSLTEERERGTLELLRVAPVSLREIVDGKLLAATAL-----A 232
                                       **********999999555555555555489************************************9999.....4 PP

                   ABC2_membrane_2 137 allatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsvarss.reaaalalglfvvl 205
                                        + a++   l++   +g+ +a   +ll++va++ +l+    ++l+++ + ++ ++ + + ++++g+++v+
  gi|313126543|ref|YP_004036813.1| 233 PAQAALW--LVLLGFNGTRVASPVMLLVLVAALSTLV----CSLAAATALLSPDRrSAQFLYSIGVLFVF 296
                                       4444433..3333444444433333333333332233....44444444444433066788999999998 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.25   7.3e+02      21      37 ..      23      38 ..       6      52 .. 0.46
   2 !   33.5   2.1   9.3e-12   2.8e-08      53     173 ..     179     296 ..     155     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.25
                     ABC2_membrane 21 gllwrliqplllalvfg 37
                                        l+ ++q ++ a+   
  gi|313126543|ref|YP_004036813.1| 23 V-LALVLQVFIAAFSSF 38
                                      2.333333333332222 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 9.3e-12
                     ABC2_membrane  53 pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsr 129
                                       + ll f+ +f++  +lt  +++ ererg+le ++v+p+ sl ++v +k+l+  +++ +qa+++l++  f  g ++ +
  gi|313126543|ref|YP_004036813.1| 179 VPLLLFLPVFIS-GSLTVDSLTEERERGTLELLRVAPV-SLREIVDGKLLAATALAPAQAALWLVLLGFN-GTRVAS 252
                                       446677777777.5777777******************.**************************99997.888876 PP

                     ABC2_membrane 130 fflflllllltalaasslgllisalapsfedasqlaslvllpll 173
                                        +++l+l+ +++ ++ sl+ + + l+p+ + a++l s+ +l+ +
  gi|313126543|ref|YP_004036813.1| 253 PVMLLVLVAALSTLVCSLAAATALLSPDRRSAQFLYSIGVLFVF 296
                                       7999999999999999*******************998776643 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.16   4.8e+02      13      32 ..      21      40 ..      10      58 .. 0.52
   2 !   26.4   1.4   1.9e-09   5.7e-06      42     175 ..     166     296 ..     159     302 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.16
                   ABC2_membrane_4 13 kivwllvlaallvpllally 32
                                       iv++lvl ++++++  +l+
  gi|313126543|ref|YP_004036813.1| 21 TIVLALVLQVFIAAFSSFLV 40
                                      23333333333333333332 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 1.9e-09
                   ABC2_membrane_4  42 dpaefysls.vfgftlllllp.lilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtfli 116
                                       + + +y ++ ++ + lll+lp +i g +++ ++++E++ +tl  L++ Pvs ++++ +Kl++   l+ +        
  gi|313126543|ref|YP_004036813.1| 166 QSSPYYGFTyTVLVPLLLFLPvFISGSLTVDSLTEERERGTLELLRVAPVSLREIVDGKLLAATALAPAQA------ 236
                                       5555666542333445566661567889*********************************9866543333...... PP

                   ABC2_membrane_4 117 tvlfallsgfvgfsvkl..vlellkkclelgllvffavlpiialvllkksyvlpliltlvy 175
                                        +l  +l+gf g+ v++  +l +l+  l + +++++a ++++       ++++++++ +v+
  gi|313126543|ref|YP_004036813.1| 237 -ALWLVLLGFNGTRVASpvMLLVLVAALSTLVCSLAAATALLSPDRRSAQFLYSIGVLFVF 296
                                       .233345555555555411444445555555555555554444445666788888888776 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.39   1.2e+03      23      49 ..      27      37 ..      10      49 .. 0.42
   2 !   18.0   0.2   5.6e-07    0.0017      38     195 ..     180     338 ..     168     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.39
                   ABC2_membrane_5 23 llaiiiliflndsvllifsilslvisi 49
                                      +l ++i++f                s+
  gi|313126543|ref|YP_004036813.1| 27 VLQVFIAAF----------------SS 37
                                      222222222................11 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5.6e-07
                   ABC2_membrane_5  38 lifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgnvtis 114
                                        ++++l+++is +l + +l  ++  ++  +l   Pv+ +eiV  K l ++ l  +   + l+ll     ++g+  + 
  gi|313126543|ref|YP_004036813.1| 180 PLLLFLPVFISGSLTVDSLTEERERGTLELLRVAPVSLREIVDGKLLAATALAPAQAALWLVLL----GFNGTR-VA 251
                                       456789999999999*******************************999999988887777776....356663.34 PP

                   ABC2_membrane_5 115 evllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifsl......sklelslidlsnyillii 185
                                       + ++ ++++ +++++++++     ++   +++  +l  i ++++f+++ +f +       +l +   d s ++++  
  gi|313126543|ref|YP_004036813.1| 252 SPVMLLVLVAALSTLVCSLAAATALLSPDRRSAQFLYSIGVLFVFGGTTLFPNnpvntaARLAIGSADASAPFVVAA 328
                                       66677777778888888888888888888888777777777777778878777355444444666777777777777 PP

                   ABC2_membrane_5 186 llviilllii 195
                                       ++v ++ +++
  gi|313126543|ref|YP_004036813.1| 329 YAVGGIGIYV 338
                                       7777777765 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.7   5.1e+03     138     155 ..      24      39 ..       6      47 .. 0.41
   2 ?    8.9   1.8   0.00042       1.2     128     180 ..     214     270 ..     149     305 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
                     FA_desaturase 138 lawlllllawlglwlall 155
                                       la++l ++  ++++  +l
  gi|313126543|ref|YP_004036813.1|  24 LALVLQVF--IAAFSSFL 39 
                                       22222222..22222222 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00042
                     FA_desaturase 128 sksrrrk..wrllawlllllawlglwlalllllglall..lwlvplllllfllalvl 180
                                       + s r      lla+ +l++a ++lwl+ll+++g  ++  ++l++l+++l++l++ l
  gi|313126543|ref|YP_004036813.1| 214 PVSLREIvdGKLLAATALAPAQAALWLVLLGFNGTRVAspVMLLVLVAALSTLVCSL 270
                                       2233322667788888888888***************9***********99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2117.53
//
Query:       gi|313126544|ref|YP_004036814.1|  [L=114]
Description: hypothetical protein Hbor_18010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00011   22.3   3.8    0.00013   22.0   3.8    1.2  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
     0.0015   18.5   3.9     0.0028   17.7   3.9    1.4  1  Med9            RNA polymerase II transcription mediator comp
     0.0029   16.8   0.9     0.0029   16.8   0.9    1.1  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
     0.0046   15.9   7.1     0.0053   15.7   7.1    1.1  1  Spc7            Spc7 kinetochore protein
     0.0049   17.5   2.4     0.0064   17.1   2.4    1.2  1  YabA            Initiation control protein YabA
  ------ inclusion threshold ------
      0.012   16.1   2.4      0.016   15.7   2.4    1.2  1  eIF3_N          eIF3 subunit 6 N terminal domain
      0.016   15.0   1.9      0.019   14.8   1.9    1.0  1  SKA1            Spindle and kinetochore-associated protein 1
      0.021   13.9   2.7      0.024   13.8   2.3    1.3  1  RmuC            RmuC family
      0.021   14.6   2.1      0.041   13.7   0.3    2.2  2  Rop-like        Rop-like
      0.026   14.6   6.6      0.027   14.5   6.0    1.3  1  T2SSM           Type II secretion system (T2SS), protein M
      0.032   14.1   4.7       0.04   13.8   4.7    1.1  1  FTA4            Kinetochore complex Fta4 of Sim4 subunit, or 
      0.034   13.9   0.4      0.053   13.3   0.4    1.2  1  Synaptonemal_3  Synaptonemal complex central element protein 
      0.035   14.2   5.6      0.044   13.9   5.6    1.1  1  RP-C_C          Replication protein C C-terminal region
      0.041   13.8   3.7      0.049   13.5   3.7    1.1  1  SPX             SPX domain
      0.064   13.3   1.0      0.099   12.7   0.7    1.4  1  DUF1664         Protein of unknown function (DUF1664)
       0.11   12.0   6.3       0.12   11.9   6.3    1.1  1  DUF2381         Protein of unknown function (DUF2381)
       0.13   12.3   5.4      0.088   12.8   1.6    1.9  2  Laminin_II      Laminin Domain II
       0.13   12.4   1.1       0.16   12.1   1.1    1.3  1  Fib_alpha       Fibrinogen alpha/beta chain family
       0.15   12.5   2.6        0.3   11.6   2.6    1.5  1  Fungal_TACC     Fungal Transforming acidic coiled-coil (TACC)
        0.2   11.8   3.3       0.39   10.9   3.3    1.6  1  DUF3782         Protein of unknown function (DUF3782)
       0.25    9.2   0.3       0.27    9.2   0.3    1.0  1  Prominin        Prominin
       0.26   11.5  10.7       0.31   11.3   6.7    2.4  2  LPD22           Large polyvalent protein associated domain 22
       0.29   10.4   1.0       0.33   10.2   1.0    1.1  1  TMPIT           TMPIT-like protein
       0.49   10.0   7.4       0.98    9.0   7.3    1.6  1  Trimer_CC       Trimerisation motif
       0.59   10.3   5.7        1.2    9.2   4.8    2.0  2  Swi5            Swi5
       0.77    9.7   4.5       0.42   10.5   2.6    1.6  1  EMP24_GP25L     emp24/gp25L/p24 family/GOLD
       0.81    8.1   9.0       0.94    7.9   9.0    1.0  1  FUSC            Fusaric acid resistance protein family
       0.97    9.7   7.1       0.16   12.2   2.3    2.0  2  XhlA            Haemolysin XhlA
        1.1    7.1   4.0        1.2    7.0   4.0    1.0  1  V_ATPase_I      V-type ATPase 116kDa subunit family
        1.6    9.4   6.4        2.3    8.9   6.4    1.3  1  AATF-Che1       Apoptosis antagonizing transcription factor
        1.9    7.8  13.8        2.4    7.4  13.8    1.1  1  DUF4407         Domain of unknown function (DUF4407)
        3.7    7.7   6.8        6.2    7.0   3.6    2.3  2  PspB            Phage shock protein B
        3.8    7.8   8.7        8.8    6.6   8.7    1.7  1  Spc24           Spc24 subunit of Ndc80
        4.3    7.4  13.4        6.8    6.8  13.4    1.3  1  DivIVA          DivIVA protein
        6.5    7.5  10.9          3    8.5   2.9    2.6  2  SlyX            SlyX


Domain annotation for each model (and alignments):
>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   3.8   2.6e-07   0.00013      59     123 ..       8      73 ..       3      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-07
                    CENP-F_leu_zip  59 eeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenllee.kEqekvqmkee 123
                                       +++++ ae  ++  + L++lr++  e+ +  q+ +er++ Le+ n + + lle  +Eqe + ++  
  gi|313126544|ref|YP_004036814.1|   8 KKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQRALLEAlAEQEGIDVEAV 73 
                                       6889999999******************************************98458887766654 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   3.9   5.5e-06    0.0028      20      78 ..       9      64 ..       4      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.5e-06
                              Med9 20 sskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkkykn 78
                                        +++   + ++  +L++ re+++e   +  + +e  ++i+ le ++a +r+lL+ + +
  gi|313126544|ref|YP_004036814.1|  9 KLQKVAEMAEDVYARLNELREQLAE---MRQTAQETRERIDRLETENAEQRALLEALAE 64
                                      56788888899999********999...**************************98876 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.9   5.6e-06    0.0029      64     124 ..       5      65 ..       1     105 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.6e-06
                             Atg14  64 nkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqne 124
                                        +++kl++     +d  +rl+el+++l + ++  +e+++++ +l  ++++ r+ le+l ++
  gi|313126544|ref|YP_004036814.1|   5 GTAKKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQRALLEALAEQ 65 
                                       5678888999999999999999999999999999999999999999999888888777655 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   7.1     1e-05    0.0053     183     259 ..       7      82 ..       3     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                              Spc7 183 leklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                       ++klq+ ++e+++   ++L+elre+lae  ++ +e ++++++l+++ +e+++ +e+l+eq     e++ +  ++ e+
  gi|313126544|ref|YP_004036814.1|   7 AKKLQK-VAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQRALLEALAEQEGIDVEAVTANAHIHEA 82 
                                       677887.5567777799**************************************9999876555555555544444 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.4   1.3e-05    0.0064      11      53 ..      18      76 ..       8     102 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH................X CS
                              YabA 11 eeleeqleelleeleelkeelaelleenaeLeleneklrerl................e 53
                                      e++  +l+el e+l+e++++ +e+ e+ ++Le+en + r +l                +
  gi|313126544|ref|YP_004036814.1| 18 EDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQRALLealaeqegidveavtaN 76
                                      34445556666666666666666666666666666666666633333335554444430 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   2.4   3.1e-05     0.016      55     125 ..       8      75 ..       3      81 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-05
                            eIF3_N  55 kelegeeevpeelekkreevleeleeleeeaekvlelledeevvsnlrsdkkqnlefLkeehgitpemida 125
                                       k+l++ +e++e++ ++ +e+ e+l e++++a++  e +++ e++++   +++++le L e+ gi++e ++a
  gi|313126544|ref|YP_004036814.1|   8 KKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENA---EQRALLEALAEQEGIDVEAVTA 75 
                                       5666666677777777777777777777777777777766664444...8999************999976 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.9   3.8e-05     0.019      16     101 ..      16      99 ..       6     113 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-05
                                       ........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  16 qdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaee 92 
                                       + +++    l+++++++ +++++ ++ ++++++ e+ + ++++++ea ++q+  +   +   ++h+++ +++     
  gi|313126544|ref|YP_004036814.1|  16 MAEDV-YARLNELREQLAEMRQTAQETRERIDRLETENAEQRALLEALAEQEG-IDVEAVTANAHIHEAESDADDAA 90 
                                       33333.56788888889999999999999999988888888888888885555.55555566666655555555544 PP

                                       XXXXXXXXX CS
                              SKA1  93 skssspeee 101
                                       s+ss+++ +
  gi|313126544|ref|YP_004036814.1|  91 SDSSEETAD 99 
                                       444433332 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.3   4.8e-05     0.024     225     282 ..       7      66 ..       5      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-05
                              RmuC 225 eknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle..gnilrkaeklk 282
                                       +k+ +++ae ++++y +++++ e+l ++++  +++++ +d++ ++ +  + +l+ + + +
  gi|313126544|ref|YP_004036814.1|   7 AKKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAeqRALLEALAEQE 66 
                                       688999999999999999999999999999999999999997776667677776666655 PP

>> Rop-like  Rop-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   7.9e-05     0.041      37      63 ..       9      35 ..       7      36 .. 0.93
   2 ?    0.3   0.1       1.3   6.5e+02      40      58 ..      36      54 ..      33      64 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.9e-05
                                      GHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Rop-like 37 eipevAqktyeafaelaeakaeLkale 63
                                      ++ +vA+ + +++a+l+e++++L+++ 
  gi|313126544|ref|YP_004036814.1|  9 KLQKVAEMAEDVYARLNELREQLAEMR 35
                                      799*********************985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHHHHHHHHHH CS
                          Rop-like 40 evAqktyeafaelaeakae 58
                                      ++Aq+t e   +l++ +ae
  gi|313126544|ref|YP_004036814.1| 36 QTAQETRERIDRLETENAE 54
                                      5677777776666665554 PP

>> T2SSM  Type II secretion system (T2SS), protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   6.0   5.3e-05     0.027      40     103 ..      14      75 ..      10      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHCT--EEEEEE CS
                             T2SSM  40 serieraqaelqklraqlawveeqaaevralraapasalsgaaleqvvtrsarqagLalarlqp 103
                                        e++e+  a+l++lr+qla+++++a+e r+     + ++++a+ ++++++ a+q g++++ +++
  gi|313126544|ref|YP_004036814.1|  14 AEMAEDVYARLNELREQLAEMRQTAQETRERI--DRLETENAEQRALLEALAEQEGIDVEAVTA 75 
                                       678899999******************99777..444455667789999999999999887766 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   4.7   7.9e-05      0.04     116     184 ..      11      79 ..       6      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.9e-05
                              FTA4 116 eaeeepleallerYaelrarLielserrqqlqarlarlrklkallepflgsedpqesvqenlvtrdgel 184
                                       ++ +e+ e+  +r +elr++L+e++++ q++++r++rl++ +a+   +l+   +qe ++ + vt +  +
  gi|313126544|ref|YP_004036814.1|  11 QKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQRALLEALAEQEGIDVEAVTANAHI 79 
                                       455667789999***************************988877777777788888888888887665 PP

>> Synaptonemal_3  Synaptonemal complex central element protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4    0.0001     0.053      23      90 ..       8      76 ..       5      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                    Synaptonemal_3 23 kdleklteqmedvsvkltwmaydmvvlr.tnPdlaeslrrledeflkCkavlcsladeqekkvhellad 90
                                      k+l+k+ e  edv  +l  +   +  +r t  +  e + rle e  + +a+l +la+++  +v+ ++a+
  gi|313126544|ref|YP_004036814.1|  8 KKLQKVAEMAEDVYARLNELREQLAEMRqTAQETRERIDRLETENAEQRALLEALAEQEGIDVEAVTAN 76
                                      89*************************9456677899************************99999886 PP

>> RP-C_C  Replication protein C C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   5.6   8.7e-05     0.044       4      89 ..      19     105 ..      16     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.7e-05
                            RP-C_C   4 qleqrfralverlp.rkatlaeleelleelealreevenalesalkaenssanesqnerhiqnsnpdsssesepase 79 
                                       ++ +r+++l+e+l   ++t++e +e +++le+  +e +++le+ +++e  + ++ + ++hi++ ++d++   + +se
  gi|313126544|ref|YP_004036814.1|  19 DVYARLNELREQLAeMRQTAQETRERIDRLETENAEQRALLEALAEQEGIDVEAVTANAHIHEAESDADDAASDSSE 95 
                                       678899*******988999***********************************************85555443333 PP

                            RP-C_C  80 kereekeaaa 89 
                                       ++++ + +aa
  gi|313126544|ref|YP_004036814.1|  96 ETADGAADAA 105
                                       3333333333 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.7   9.6e-05     0.049     205     261 ..      17      98 ..       8     113 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.6e-05
                               SPX 205 eeefterlesLrkqlealrprrikeaeerksdlyrwre.........................ifglk.sveaqvfe 255
                                        e++++rl++Lr+ql+++r+ +++  +er + l++++                          i++++   ++++++
  gi|313126544|ref|YP_004036814.1|  17 AEDVYARLNELREQLAEMRQTAQE-TRERIDRLETENAeqrallealaeqegidveavtanahIHEAEsDADDAASD 92 
                                       5789**************885555.3333222222222344465555555554444443333322222112222222 PP

                               SPX 256 ssreld 261
                                       ss e+ 
  gi|313126544|ref|YP_004036814.1|  93 SSEETA 98 
                                       222222 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   0.00019     0.099      71     115 ..       6      50 ..       2      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                           DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                         kkl++++e+++++ + ++e+re+l+e+++  ++ +e +  le+
  gi|313126544|ref|YP_004036814.1|   6 TAKKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLET 50 
                                       568999999999999999999999999999999999999999987 PP

>> DUF2381  Protein of unknown function (DUF2381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   6.3   0.00024      0.12     124     187 ..      12      80 ..       9     100 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                           DUF2381 124 Rrarsaealqaelaelrarnealeeelerlr..aarsaarglaglvlsgll.geegvsir..lekdvea 187
                                       + a+ ae++ a+l+elr++ +++++  +++r   +r +++++++ +l+++l ++eg+ ++    +++ +
  gi|313126544|ref|YP_004036814.1|  12 KVAEMAEDVYARLNELREQLAEMRQTAQETRerIDRLETENAEQRALLEALaEQEGIDVEavTANAHIH 80 
                                       557778888888888888888888888888876778888888888888888788888888532222222 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.6   0.00017     0.088      10      52 ..       8      50 ..       4      65 .. 0.80
   2 ?    1.5   0.5      0.53   2.7e+02      29      61 ..      61      93 ..      48     107 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 10 etakevleqlaplsqnlentkeklseinrsveetnekvkdank 52
                                      +++++v e  +++ ++l++++e+l e++++++et e ++ + +
  gi|313126544|ref|YP_004036814.1|  8 KKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLET 50
                                      6789999999999999999999999999999999998875544 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.53
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 29 tkeklseinrsveetnekvkdankairdArrsv 61
                                        ++ ++i+ ++   n+++++a    +dA + +
  gi|313126544|ref|YP_004036814.1| 61 ALAEQEGIDVEAVTANAHIHEAESDADDAASDS 93
                                      444444555555555555555555555544433 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.1   0.00032      0.16      28      69 ..      15      56 ..       7      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                                      CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekq 69
                                      ++ +dv  +l++l+++l+e++++ +e++e + ++++  +e+ 
  gi|313126544|ref|YP_004036814.1| 15 EMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQR 56
                                      567899999******************999999988766654 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.6   0.00058       0.3       4      59 ..      11      64 ..       6      72 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00058
                       Fungal_TACC  4 krlqelaedLYvqYSsKHEqKVkllkkgyeakyqkkldklelenkslkqeieqLkk 59
                                      +++ e+aed Y +  +  Eq  ++ ++  e   ++++d+le+en +++  +e L +
  gi|313126544|ref|YP_004036814.1| 11 QKVAEMAEDVYARLNELREQLAEMRQTAQE--TRERIDRLETENAEQRALLEALAE 64
                                      344455667777777777776666555553..356777777777777766666655 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.3   0.00076      0.39       1      45 [.      29      73 ..       8      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00076
                           DUF3782  1 eelekleeeeeetkedleelekeieklertigaLGaRWGlvsEea 45
                                      e+l ++++  +et+e++++le+e ++ +  ++aL+   G++ E++
  gi|313126544|ref|YP_004036814.1| 29 EQLAEMRQTAQETRERIDRLETENAEQRALLEALAEQEGIDVEAV 73
                                      678888888***************************999999986 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3   0.00052      0.27     236     310 ..      12      84 ..       4     106 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00052
                          Prominin 236 paLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldt 310
                                       ++ +  e +   l+e +eqL +++++ +e r+  ++L++   +++  l+ +++++    + + +  +++i++ ++
  gi|313126544|ref|YP_004036814.1|  12 KVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQRALLEALAEQEGI--DVEAVTANAHIHEAES 84 
                                       222333445556899999999999999999999999999988888888777777333..4555555555544444 PP

>> LPD22  Large polyvalent protein associated domain 22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.58     3e+02      68      96 ..      11      39 ..       5      41 .. 0.65
   2 ?   11.3   6.7   0.00061      0.31       6      52 ..      44      90 ..      39     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.58
                             LPD22 68 pdnaavAhDDvenLsrlekalrslkeale 96
                                      ++ a++A D ++ L +l  +l +++++++
  gi|313126544|ref|YP_004036814.1| 11 QKVAEMAEDVYARLNELREQLAEMRQTAQ 39
                                      56677777777777777766666666555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00061
                             LPD22  6 alelaqnenPDeaAralrlaeelGlppdvvernleaferaaeaedwd 52
                                       ++  ++en ++ A +++lae+ G++ ++v++n +  e++++a d++
  gi|313126544|ref|YP_004036814.1| 44 RIDRLETENAEQRALLEALAEQEGIDVEAVTANAHIHEAESDADDAA 90
                                      5666799**************************76555555444433 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.0   0.00064      0.33      11      83 ..      10      60 ..       4      93 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00064
                             TMPIT 11 fkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83
                                      ++++ e a       e++ +  +++++++++ ++ ++e ++++++l+++                +e+++ l+
  gi|313126544|ref|YP_004036814.1| 10 LQKVAEMA-------EDVYARLNELREQLAEMRQTAQETRERIDRLETE---------------NAEQRALLE 60
                                      23333333.......3333333333333333333333333333333333...............333332222 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   7.3    0.0019      0.98      19      47 ..      19      50 ..      11      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                                      XX--HHH...HHHHHHHHHHHHHHHHHHHHHH CS
                         Trimer_CC 19 davSRLE...EelrkLqatVQelQkRLDrLEe 47
                                      d+  RL    E l +++ t Qe  +R+DrLE 
  gi|313126544|ref|YP_004036814.1| 19 DVYARLNelrEQLAEMRQTAQETRERIDRLET 50
                                      5666654122688899**************95 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.8    0.0024       1.2       3      71 ..       8      73 ..       6      82 .. 0.80
   2 ?    3.6   0.4      0.14        70       4      40 ..      44      79 ..      43     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0024
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHCGGG CS
                              Swi5  3 aeikeleeqleelekelaelkeelkekkdpeetvkrhIklLheYNEiKDvgqgLigliAeargvrikev 71
                                      ++++++ e+ e + + l+el+e+l e  + +++ ++ I++L + N        L++ +Ae++g+ +  v
  gi|313126544|ref|YP_004036814.1|  8 KKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQ---RALLEALAEQEGIDVEAV 73
                                      68899999*********************************9888433...356666666666666665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHH CS
                              Swi5  4 eikeleeqleelekelaelkeelkekkdpeetvkrhI 40
                                      +i +le + +e ++ l++l e+ + +   + t + hI
  gi|313126544|ref|YP_004036814.1| 44 RIDRLETENAEQRALLEALAEQEGIDV-EAVTANAHI 79
                                      566777777777777777777766543.555666666 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.6   0.00082      0.42     117     155 ..       7      45 ..       3      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00082
                       EMP24_GP25L 117 eselkkleekldsikreqkylrereerlrdtnestnsrv 155
                                        ++l+k+ e  ++++  ++ lre+ +++r+t+++t +r+
  gi|313126544|ref|YP_004036814.1|   7 AKKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERI 45 
                                       568999999999999999999999999999999999887 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   9.0    0.0018      0.94     218     301 ..      21      94 ..      11     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                              FUSC 218 aralrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrrale 294
                                        ++l++l+ +++++ +++++++++  rl +e+a++    +all++la+      +e+++ ++ +  a++ +++++++
  gi|313126544|ref|YP_004036814.1|  21 YARLNELREQLAEMRQTAQETRERIDRLETENAEQ----RALLEALAE------QEGIDVEAVTANAHIHEAESDAD 87 
                                       5799**************************99999....789999999......78888888888888888887777 PP

                              FUSC 295 adadtaa 301
                                       ++a+ + 
  gi|313126544|ref|YP_004036814.1|  88 DAASDSS 94 
                                       3333322 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.3   0.00032      0.16       4      47 ..       8      51 ..       6      53 .. 0.86
   2 ?   10.0   1.6    0.0015      0.78       1      39 [.      26      64 ..      26      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00032
                              XhlA  4 erlerietkldnleervdkleekaaeaeekiknleedlkklesn 47
                                      ++l+++ ++ ++   r+++l e  ae+++ ++++ e++++le  
  gi|313126544|ref|YP_004036814.1|  8 KKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETE 51
                                      567777777777778**************************975 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0015
                              XhlA  1 eikerlerietkldnleervdkleekaaeaeekiknlee 39
                                      e++e l+++ +   +  er+d+le  +ae+++ ++ l e
  gi|313126544|ref|YP_004036814.1| 26 ELREQLAEMRQTAQETRERIDRLETENAEQRALLEALAE 64
                                      568899999999999999999999999999999998877 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.0    0.0024       1.2      69     141 ..      15      92 ..       4     111 .. 0.39

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0024
                        V_ATPase_I  69 keldeleeelekleeelkelnenleklkkelnelvelkavlekakefleee.....eeeeeeeeseeeeeekeeeee 140
                                       +  +++ ++l++l e+l e+++++++ +++  +l+ ++a  +   e l+e+     e+ +++++ +e+e++++++ +
  gi|313126544|ref|YP_004036814.1|  15 EMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQRALLEALAEQegidvEAVTANAHIHEAESDADDAAS 91 
                                       33445555555555555555555555555544444333333333333332210001112222222222222222222 PP

                        V_ATPase_I 141 e 141
                                       +
  gi|313126544|ref|YP_004036814.1|  92 D 92 
                                       2 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.4    0.0044       2.3      52      87 ..       7      80 ..       4     111 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0044
                         AATF-Che1 52 eealeeaekalkklleslleLreelleqneikkla......................................e 87
                                      +++l+++++ +++++  l eLre+l e  ++++ +                                      +
  gi|313126544|ref|YP_004036814.1|  7 AKKLQKVAEMAEDVYARLNELREQLAEMRQTAQETreridrletenaeqrallealaeqegidveavtanahiH 80
                                      57888888999999999999999996666655444566666666666666666666666655554444333331 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  13.8    0.0047       2.4     122     223 ..      11     108 ..       5     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0047
                           DUF4407 122 elkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqae 198
                                       +  +++a++  a+l+el++q+a+++++ ++ ++r+d+l++e +++      +     +G   +a +++a++ +a+ +
  gi|313126544|ref|YP_004036814.1|  11 QKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLETENAEQRAL--LEALAEQEGIDVEAVTANAHIHEAESD 85 
                                       455667777889999999999999999999999999999998877665..555566789999999999999999999 PP

                           DUF4407 199 laelkakldatarlaalraelaele 223
                                        +++ ++  +++++a+  a +a+++
  gi|313126544|ref|YP_004036814.1|  86 ADDAASD--SSEETADGAADAADAD 108
                                       9999999..7777777777766654 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.45   2.3e+02      41      60 ..       8      27 ..       5      29 .. 0.86
   2 ?    7.0   3.6     0.012       6.2      40      62 ..      28      50 ..      24      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.45
                              PspB 41 krLeellekAekleeRietL 60
                                      k+L++++e Ae   +R++ L
  gi|313126544|ref|YP_004036814.1|  8 KKLQKVAEMAEDVYARLNEL 27
                                      78999******999999876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                              PspB 40 ekrLeellekAekleeRietLEr 62
                                      +++L+e++++A++ +eRi+ LE+
  gi|313126544|ref|YP_004036814.1| 28 REQLAEMRQTAQETRERIDRLET 50
                                      689******************95 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   8.7     0.017       8.8      11      69 ..       8      72 ..       5     105 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
                             Spc24 11 kelsdleselesleselaelkeeleeleeeseekeser.....ve.detllklklYrsLGielek 69
                                      k+l+++ + +e++ ++l+el+e+l+e+ +  +e ++++     ++ ++ +l   l ++ Gi++e 
  gi|313126544|ref|YP_004036814.1|  8 KKLQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIdrletENaEQRALLEALAEQEGIDVEA 72
                                      55555555555555555555555555555555522222232222212222333344444555544 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  13.4     0.013       6.8      27     109 ..      10      97 ..       7     110 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  27 LdqvakdyeallkeneelkekvkeleeklkeykeleetL......kktlvvaqetaeevkanakkeaeliikeAekk 97 
                                       L++va+  e+++ + +el+e+++e++++ +e +e+ + L      +++l+ a    e +  +a   a+  i+eAe +
  gi|313126544|ref|YP_004036814.1|  10 LQKVAEMAEDVYARLNELREQLAEMRQTAQETRERIDRLetenaeQRALLEALAEQEGIDVEAV-TANAHIHEAESD 85 
                                       8899999999999999999999999999999998887742222224455555555554444443.345555555555 PP

                                       XXXXXXXXXXXX CS
                            DivIVA  98 aekiveeaeeea 109
                                       a++  ++++ee+
  gi|313126544|ref|YP_004036814.1|  86 ADDAASDSSEET 97 
                                       555555555544 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.5      0.17        86      38      55 ..      22      39 ..       6      43 .. 0.55
   2 ?    8.5   2.9    0.0059         3       2      24 ..      42      64 ..      41      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.17
                                      HHHHHHHHT-XXXXXXXX CS
                              SlyX 38 rqlrllaerlkeleessg 55
                                      ++l++l+e+l+e++++++
  gi|313126544|ref|YP_004036814.1| 22 ARLNELREQLAEMRQTAQ 39
                                      445555555555554433 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0059
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  2 eerleeLEiklafqedtieeLnd 24
                                       er+++LE++ a q  ++e+L +
  gi|313126544|ref|YP_004036814.1| 42 RERIDRLETENAEQRALLEALAE 64
                                      59*****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2609  (0.145518); expected 358.6 (0.02)
Passed bias filter:                     1204  (0.0671538); expected 358.6 (0.02)
Passed Vit filter:                       248  (0.0138323); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 655.72
//
Query:       gi|313126545|ref|YP_004036815.1|  [L=326]
Description: cystathionine beta-synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-57  195.3   1.5    1.6e-57  195.2   1.5    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.2   1.5   8.8e-62   1.6e-57       3     292 ..      13     305 ..      11     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 195.2 bits;  conditional E-value: 8.8e-62
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH.HHTT..TTTSEEEEEBSSHHHHHHHHHHHH CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllar.lkeg..tgaktvveassGNhgralAaaaal 76 
                                         +g+TPlvr+++  +e   p+++KlEs+np+ S+KdR   y+l+r l+ g   ++ tv+e ++GN+g+++A aa  
  gi|313126545|ref|YP_004036815.1|  13 ETVGETPLVRVHASPDEA--PVYAKLESFNPGASIKDRIGKYMLERmLEDGtlPEGGTVIEPTAGNTGIGIAVAAGQ 87 
                                       5789*********77554..5*************************8777799999********************* PP

                                       HT-EEEEEEETTS-HHHHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHH CS
                              PALP  77 lGlkvtivvpadaspekvallrllGaevvev..ggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEi 150
                                       l ++++ vvp+  s ek++l+r+lGa+vv +  +++   a ++a+ela+e ++a++ +qf+np+++e+ y+t+g+Ei
  gi|313126545|ref|YP_004036815.1|  88 LDVEAVFVVPERFSLEKQQLMRALGATVVNTptEDGMGGAIDRAHELAEEVDDAVVPQQFSNPLNTEAhYETTGPEI 164
                                       *******************************777779999999********************************** PP

                                       HHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTT CS
                              PALP 151 leqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspse 227
                                       ++ l+g++ a+v+++G++g+++Gia++  e+++++ v +vep+gs  l++++     ++ ++ +   +g++++ p++
  gi|313126545|ref|YP_004036815.1| 165 YDALDGEVGAIVAGCGTAGTLMGIARYALEQDSETYVAAVEPAGS--LYSTV---LGEDAEEDPYKTEGIGTHDPTT 236
                                       ******************************************933..33333...2234455589999**9995555 PP

                                       CCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-H.HHHHHHHHH...HHHHHHCCTTC.EEEEEEE CS
                              PALP 228 lafelldrlvdeivtvsdeealeamrllarregivvep.ssaaalaal...klreagelkeg.drvvvil 292
                                         +    +lvde+++++de a++ +++la +eg++v   ++aa+laa    +  ++ge+++  d+v +i+
  gi|313126545|ref|YP_004036815.1| 237 NEL-FDPELVDEVIQIPDENAHAEVQRLAGEEGHLVASsAAAASLAARdvaERIRDGEIDAPhDSVATIF 305
                                       555.447999****************************56666666667777777777766656666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1812.64
//
Query:       gi|313126546|ref|YP_004036816.1|  [L=140]
Description: CoA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-36  125.8   0.0    1.3e-36  125.6   0.0    1.0  1  CoA_binding_2  CoA binding domain
    0.00011   22.9   0.0    0.00016   22.3   0.0    1.2  1  CoA_binding    CoA binding domain
  ------ inclusion threshold ------
      0.021   14.6   0.0      0.041   13.7   0.0    1.6  1  TusA           Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.0   2.1e-40   1.3e-36       2     115 ..      15     135 ..      14     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 2.1e-40
                                       -EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T......T--EEEE-S-HHHHGGGHHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslae.d.pepvdlvdvftppeatpeivkeal 76 
                                       t+aVvG+s++pgk+++ +++yl++hg++v+p+np ++ ilge++y sla+ + + ++d+vdvf+p+e++ +i+ +a+
  gi|313126546|ref|YP_004036816.1|  15 TVAVVGCSTTPGKAAHDIPAYLQNHGYRVIPINPFADDILGETAYDSLADvPgDADIDIVDVFRPSEEAGDIAAAAV 91 
                                       89***********************************************98899**********************9 PP

                                       HH.....--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHHH CS
                     CoA_binding_2  77 al.....gakavwlqpgsedeeaaelaeeagirvvgdrCilveg 115
                                       ++     ++++vwlq+g+ +++a ++++e g+++v+drC++ve+
  gi|313126546|ref|YP_004036816.1|  92 ERhesvgDVRSVWLQLGITNDDAKQRVQESGLEYVQDRCMKVEH 135
                                       99655544**********************************98 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.7e-08   0.00016       5      84 ..      15      92 ..      12      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.7e-08
                                      EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHH CS
                       CoA_binding  5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelv 83
                                       v+v+G + + ++ + ++   l+ +   v+++np   ++++lg ++y+s+++++ + ++d+  ++ P+e+a +++ ++v
  gi|313126546|ref|YP_004036816.1| 15 TVAVVGCSTTPGKAAHDIPAYLQNHGYRVIPINPF--ADDILGETAYDSLADVPGDADIDIVDVFRPSEEAGDIAAAAV 91
                                      69********************************9..*******************5566655666**********999 PP

                                      H CS
                       CoA_binding 84 e 84
                                      e
  gi|313126546|ref|YP_004036816.1| 92 E 92
                                      8 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.8e-06     0.041      21      57 ..      10      46 ..       1      67 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.8e-06
                                      HCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEE CS
                              TusA 21 lekleegevlevladdpaatediprfakklghelvev 57
                                      +  ++  +v+   ++   a +dip++++++g++++ +
  gi|313126546|ref|YP_004036816.1| 10 ILDADTVAVVGCSTTPGKAAHDIPAYLQNHGYRVIPI 46
                                      444444455667899999***************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 804.82
//
Query:       gi|313126547|ref|YP_004036817.1|  [L=203]
Description: hypothetical protein Hbor_18040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-05   25.1   0.1    1.5e-05   24.8   0.1    1.3  1  DUF835         Protein of unknown function (DUF835)
    4.1e-05   23.0   0.0    0.00014   21.3   0.0    1.7  1  ATPase         KaiC
     0.0064   16.2   0.0      0.013   15.2   0.0    1.6  2  Peptidase_C28  Foot-and-mouth virus L-proteinase
  ------ inclusion threshold ------
      0.049   12.5   0.0       0.21   10.4   0.0    1.8  2  AAA_35         AAA-like domain


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   3.3e-09   1.5e-05      57     136 .]      99     184 ..      48     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.3e-09
                            DUF835  57 sPtnlekltetivkflkeaekg......vvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeek 127
                                       sP +++ +  ++++fl+  ++        +++ +l  L+++ + ++v++fl+    ++ + +g+ ++vid +a ++k
  gi|313126547|ref|YP_004036817.1|  99 SPVDMTGIGIKLSEFLQAFYQDrnieqnRIMLHSLSTLLMYADLQTVFRFLHVFTGRIQSVEGLGLFVIDSSAHDDK 175
                                       56666655555555555544444444669************************************************ PP

                            DUF835 128 elalLkref 136
                                        ++ Lk+ f
  gi|313126547|ref|YP_004036817.1| 176 TMNTLKQLF 184
                                       *****9977 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.1e-08   0.00014      17     187 ..      13     190 ..       7     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.1e-08
                            ATPase  17 pegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesae 93 
                                       p g+  li+G p tGK  +al  l +ga + g+  ++vt+   a+ +  ++++         +   +a++d ++ ++
  gi|313126547|ref|YP_004036817.1|  13 PPGTNLLISGPPLTGKRSLALDILSEGATN-GDGAIIVTTKDGAKRVLSDFEKR-----TTYDGKPVAVVDCVTRQQ 83 
                                       778999************************.*************9999988853.....333344677777777666 PP

                            ATPase  94 esaee.............kdkedleelieelaeaikeika..krvviDsitgl.ayeekeavaReilrqlvrvlkkl 154
                                       +  e              + +    +l+e l+   ++ ++  +r+++ s+++l +y + + v+R  l+ ++ +++  
  gi|313126547|ref|YP_004036817.1|  84 GVGEIrdddrikytsspvDMTGIGIKLSEFLQAFYQDRNIeqNRIMLHSLSTLlMYADLQTVFR-FLHVFTGRIQSV 159
                                       5333255677777744433333334666666666654444449**********66666666665.799********* PP

                            ATPase 155 gvTailvsekssseeaaggygveefivdgvivL 187
                                       +   ++v + ss ++ ++ + +++ + dg+i  
  gi|313126547|ref|YP_004036817.1| 160 EGLGLFVID-SSAHDDKTMNTLKQ-LFDGIITT 190
                                       *********.55667778888888.99999975 PP

>> Peptidase_C28  Foot-and-mouth virus L-proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     3e-06     0.013     121     178 ..      46     104 ..      11     127 .. 0.83
   2 ?   -2.4   0.0      0.73   3.3e+03      43      61 ..     167     185 ..     155     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-06
                     Peptidase_C28 121 psevcmvdgtdmcladfhagiflkgqdhavfacvts.dgwyaiddedfypwtpnpadvl 178
                                          v   dg+  +l+df       g+  av+ cvt  +g   i d+d   +t  p d+ 
  gi|313126547|ref|YP_004036817.1|  46 AIIVTTKDGAKRVLSDFEKRTTYDGKPVAVVDCVTRqQGVGEIRDDDRIKYTSSPVDMT 104
                                       4567788***************************96269999*************9975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.73
                     Peptidase_C28  43 srpnnhdncwlnailqlfr 61 
                                            hd+  +n++ qlf 
  gi|313126547|ref|YP_004036817.1| 167 IDSSAHDDKTMNTLKQLFD 185
                                       5567899999999999985 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   4.6e-05      0.21      30      80 ..      14      64 ..       7      69 .. 0.94
   2 ?   -0.7   0.0      0.11   5.1e+02     185     204 ..      96     116 ..      92     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.6e-05
                            AAA_35 30 pGalirikapkkmGKtSLlarilakakqqgyktvsldlqladkeilsdldk 80
                                      pG+ + i +p  +GK SL   il++ +++g  ++ +  +   k++lsd++k
  gi|313126547|ref|YP_004036817.1| 14 PGTNLLISGPPLTGKRSLALDILSEGATNGDGAIIVTTKDGAKRVLSDFEK 64
                                      899999*****************************************9998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.11
                            AAA_35 185 inqSpf.nvGlpieLpeFtke 204
                                        ++Sp   +G+ i+L+eF ++
  gi|313126547|ref|YP_004036817.1|  96 YTSSPVdMTGIGIKLSEFLQA 116
                                       567888557888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1206.59
//
Query:       gi|313126548|ref|YP_004036818.1|  [L=302]
Description: geranylgeranylglycerol-phosphate geranylgeranyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-47  161.0  18.0    3.8e-47  160.7  18.0    1.1  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.7  18.0   2.1e-51   3.8e-47       4     243 ..      41     277 ..      38     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 2.1e-51
                              UbiA   4 palvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilg 80 
                                        ++ g ++aag  +++ ++l+++l+t++a++a+na+NdyfDreiD +  ++p+RP+++G++s + al+f++vl++ +
  gi|313126548|ref|YP_004036818.1|  41 LTFTGSFVAAGVFTTPYHVLAAVLATVFATGAGNAVNDYFDREIDMI--NRPDRPIPRGAVSARGALAFSLVLFLGA 115
                                       689999*****************************************..**************************** PP

                              UbiA  81 llllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltw 157
                                       ++++ ++l   ++++++++ll++v+Yt+ ++K  + +g+vv+g   g  +l+g+aav++ l + +l+l+ + +l t+
  gi|313126548|ref|YP_004036818.1| 116 VVCA-VFLPVEALVIAVVNLLALVAYTE-YFKGLPGVGNVVVGYLTGSTFLFGAAAVNNALAPSVLILFGLAALATV 190
                                       ****.**********************8.************************************************ PP

                              UbiA 158 aialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraarl 233
                                       +  +++d++d+ gDr+ g+ktlp+v G++ a+++ + +++a++ ++++ ++  +++l yl+l++++ +l+l+  ++ 
  gi|313126548|ref|YP_004036818.1| 191 TREIVKDVEDIAGDREEGLKTLPIVVGERPALFIgVSAMVAAVGASVYPYFNSGFGLAYLVLVIPADILMLAACVQS 267
                                       *********************************96554555555557889999999999999999999999887777 PP

                              UbiA 234 vrrrdakkaa 243
                                       + + +a++++
  gi|313126548|ref|YP_004036818.1| 268 FEDPSAAQKR 277
                                       7766665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1815.79
//
Query:       gi|313126549|ref|YP_004036819.1|  [L=222]
Description: hypothetical protein Hbor_18070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-51  173.4  12.0    4.3e-51  173.0  12.0    1.1  1  DUF1405   Protein of unknown function (DUF1405)


Domain annotation for each model (and alignments):
>> DUF1405  Protein of unknown function (DUF1405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.0  12.0   2.4e-55   4.3e-51       1     157 []      39     210 ..      39     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 173.0 bits;  conditional E-value: 2.4e-55
                           DUF1405   1 gtvyGyiyYgkqlaetplllwpfvpDSPtAtlffalallllllgrelellealAfvtlikyGlWtvvvlllvllkgg 77 
                                       gtv+G++yY++ql +++l++wp vpDSP+Atl++a++l+ ++lg+++++++alAfv+++kyG+W v+v+++++    
  gi|313126549|ref|YP_004036819.1|  39 GTVFGFWYYRFQLLNSHLVIWPAVPDSPLATLLMAVSLVSWKLGQDRNWIHALAFVGNLKYGFWVVIVQIVINDVLV 115
                                       8*******************************************************************999873222 PP

                           DUF1405  78 ...leelmLilsHlamavealllarilrfsvkalavalawlllndvvDYvlgvlpelhetl............eeel 139
                                          + +++L++sH++m ++al+++r+++f+v ++ava++w+ +nd+vDY+l++++++h+t+            ++++
  gi|313126549|ref|YP_004036819.1| 116 sgdPYHWFLLVSHFGMGLQALVIYRYAEFTVPSVAVATLWFSFNDMVDYFLPLVGDYHHTYfgprlvsagdhgTRAH 192
                                       44599*******************************************************************7777* PP

                           DUF1405 140 eliaafavvltvlsllla 157
                                       +++aa a+ lt+l+++la
  gi|313126549|ref|YP_004036819.1| 193 DVAAASAIGLTILATFLA 210
                                       ***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1385.96
//
Query:       gi|313126550|ref|YP_004036820.1|  [L=255]
Description: hypothetical protein Hbor_18080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-29  102.2  35.1    2.5e-16   59.7   9.2    3.0  3  UPF0016    Uncharacterized protein family UPF0016


Domain annotation for each model (and alignments):
>> UPF0016  Uncharacterized protein family UPF0016
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   9.3   8.6e-19   1.5e-14       1      75 []      24      98 ..      24      98 .. 0.98
   2 !   59.7   9.2   1.4e-20   2.5e-16       2      75 .]     142     217 ..     141     217 .. 0.97
   3 ?    0.1   1.3     0.057     1e+03      33      56 ..     229     252 ..     222     255 .] 0.64

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 8.6e-19
                           UPF0016  1 laaflliflaElGDkTqlaaalLaarykplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75
                                      +++f++ fla +GDk qla+++La+ y++ +Vf+Gav+A+a+ +++ v++Gs++ + lp  ++ +++++lF+l+G
  gi|313126550|ref|YP_004036820.1| 24 VTSFVTNFLATFGDKGQLAVITLATIYDAKRVFAGAVAAFAIWNIIEVTVGSAVLGALPAGVTPIFTGALFVLVG 98
                                      589************************9999*****************************************998 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 1.4e-20
                           UPF0016   2 aaflliflaElGDkTqlaaalLaary..kplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75 
                                        af++i++aE+GDkTq++++ L+a +  +p++V++Ga+l+la+ t++ +++G+++ ++lp+ +i+ ++a++F+++G
  gi|313126550|ref|YP_004036820.1| 142 IAFVAIAIAEFGDKTQILTINLGATFpnAPIAVIVGAWLGLAVRTGIDAFVGTAMEHLLPMAFIQAAGAAVFVAVG 217
                                       69************************988999*****************************************988 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.057
                           UPF0016  33 flGavlAlalmtvlsvllGsslak 56 
                                       ++G+++A ++  v +++  +++a+
  gi|313126550|ref|YP_004036820.1| 229 VVGVAVAAVAFAVSGAFYRHWVAS 252
                                       456666666666666665577765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1489.92
//
Query:       gi|313126551|ref|YP_004036821.1|  [L=80]
Description: iron dependent repressor-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00019   21.6   0.0    0.00025   21.2   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
       0.03   14.6   0.0      0.034   14.4   0.0    1.1  1  FeoA            FeoA domain


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.8e-08   0.00025       1      31 [.       1      32 [.       1      44 [. 0.91

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.8e-08
                                      X--HHHHHHHHHHHHHHH.HHSSB-HHHHHHH CS
                    Fe_dep_repress  1 dLvestEdYLetIYtlse.ekkvvktkdlaer 31
                                      +L++++E YL+ IY l+  e+ +v+t+dl er
  gi|313126551|ref|YP_004036821.1|  1 MLSDVIEYYLKSIYGLQQrEEPPVRTSDLEER 32
                                      89**************************9776 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.8e-06     0.034      26      73 ..      27      73 ..      10      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                                      HHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA 26 rrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                        L+e G+ pGar+ +v+  p  ++++  v+ +rv+ + e A++I Ve
  gi|313126551|ref|YP_004036821.1| 27 SDLEERGVEPGARLDMVELTPI-DTVTGCVDSKRVSFPTETAASIRVE 73
                                      579**************98887.899999*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.35s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 442.75
//
Query:       gi|313126552|ref|YP_004036822.1|  [L=35]
Description: hypothetical protein Hbor_18100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      134  (0.00747392); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.51
# Mc/sec: 208.28
//
Query:       gi|313126553|ref|YP_004036823.1|  [L=167]
Description: hypothetical protein Hbor_18110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1308  (0.0729544); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 969.06
//
Query:       gi|313126554|ref|YP_004036824.1|  [L=258]
Description: hypothetical protein Hbor_18120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-75  252.0   2.7    5.5e-75  251.8   2.7    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.8   2.7   3.1e-79   5.5e-75       1     234 [.      12     254 ..      12     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 251.8 bits;  conditional E-value: 3.1e-79
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       itL +DFG  +py++amkgv+ls+ +dar+vD++Hd+p++dvr+ af+L+++lpyfp+ ++hl+vVDpgvgt+r a+
  gi|313126554|ref|YP_004036824.1|  12 ITLSSDFG--TPYPAAMKGVLLSR-TDARLVDVAHDFPRQDVRATAFWLREVLPYFPA-ATHLVVVDPGVGTDRAAI 84 
                                       9*******..**************.********************************6.79**************** PP

                                       EEEETTSEEEEESSSTTHHHH.....SEEEEEEGSSCC.--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGGGS-S CS
                   SAM_adeno_trans  78 vveakggyfvgPDNGlltlal.....lleeaveieeee.ssatFhgrDvFapvaarlaagvsleelgeeldpeelvr 148
                                       vvea++++fv+PDNG++ +a+        ++++++ ++ +s+tFhgrDvFap+aa+++++ +++++++ ++ ee+v+
  gi|313126554|ref|YP_004036824.1|  85 VVEAGEHTFVAPDNGVVLPAVreiagDDFDVYDVAYDDvPSNTFHGRDVFAPAAANVHDASAVTDIERITPVEEFVD 161
                                       ******************99975544227788888777999*************************99777799998 PP

                                       SS.....E.CSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEE.EEEEE.SSGGGSTTTSEEEEE-TTSEEEEEE CS
                   SAM_adeno_trans 149 le.....e.derlegevlyvDrFGNvitniskelleelekerkva.klkkv.etyaevaegellalvnssglleiav 217
                                       l        d++++gevl+vD+FGNv+tn+++++l+ le+ +  + +   v ++ya+v++g++l++v+s+g++e+av
  gi|313126554|ref|YP_004036824.1| 162 LTfpapvVgDGQATGEVLVVDDFGNVVTNVPGRVLDGLEQVSV-NgEPAPVgDSYAAVEPGDRLVTVGSHGNVEFAV 237
                                       8888765268999**********************98866544.35556777************************* PP

                                       TTC-HHHHHT--TT-EE CS
                   SAM_adeno_trans 218 nkgsaaellglkvgdev 234
                                       n+g+ ++++gl+vgd+v
  gi|313126554|ref|YP_004036824.1| 238 NRGRGDDAFGLAVGDTV 254
                                       ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1527.15
//
Query:       gi|313126555|ref|YP_004036825.1|  [L=359]
Description: spermidine/putrescine ABC transporter ATPase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-35  121.3   0.0    6.8e-35  120.6   0.0    1.4  1  ABC_tran         ABC transporter
    4.7e-10   39.5   0.3    4.7e-10   39.5   0.3    3.2  3  TOBE_2           TOBE domain
    3.3e-08   33.7   0.0     0.0003   20.7   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    7.1e-05   23.2   0.5     0.0015   19.0   0.5    2.2  1  AAA              ATPase family associated with various cellul
    0.00023   20.7   0.0     0.0096   15.4   0.0    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
     0.0015   18.9   0.1      0.015   15.7   0.0    2.0  2  AAA_16           AAA ATPase domain
     0.0038   17.5   0.5      0.015   15.6   0.5    2.0  1  AAA_22           AAA domain
     0.0092   15.9   0.0      0.016   15.1   0.0    1.3  1  Rad17            Rad17 P-loop domain
  ------ inclusion threshold ------
      0.025   15.2   0.1       0.21   12.2   0.0    2.5  2  CysA_C_terminal  CysA C-terminal regulatory domain
      0.031   14.0   0.3       0.15   11.7   0.2    2.1  1  AAA_30           AAA domain
      0.035   13.4   0.3        0.1   11.9   0.0    1.8  3  Zeta_toxin       Zeta toxin
      0.063   12.9   1.9       0.16   11.6   0.5    2.4  2  AAA_25           AAA domain
      0.066   12.9   0.0       0.13   11.9   0.0    1.5  1  Fimbrial_PilY2   Type 4 fimbrial biogenesis protein PilY2
      0.074   13.4   1.1       0.16   12.3   0.1    2.1  1  TOBE             TOBE domain
      0.096   12.8   0.3       0.28   11.4   0.3    1.8  1  AAA_33           AAA domain
        0.1   12.4   0.1        0.2   11.4   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
       0.11   12.5   0.0       0.41   10.7   0.0    1.9  2  AAA_14           AAA domain
       0.13   12.4   0.1          1    9.5   0.0    2.3  2  Ribosomal_S17    Ribosomal protein S17


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.0   6.8e-38   6.8e-35       1     136 [.      19     162 ..      19     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 6.8e-38
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++vsl++ ege   +vG++G+GK+t l+l+agl++pt G +++dg+d+++  ++  ++++gv++q+  lfp++tvr
  gi|313126555|ref|YP_004036825.1|  19 LHEVSLSVDEGEFFTLVGPSGCGKTTTLRLVAGLETPTDGVVRFDGEDVSS--TPTEDRNVGVVFQNYALFPHMTVR 93 
                                       689************************************************..99999******************* PP

                                       HH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en              + de+++++l+ ++l e+ d+       +LSgGq+qrvalaral+ +p++lllDEp+
  gi|313126555|ref|YP_004036825.1|  94 ENvayglkfddpptgmTVDERVSELLAMMNLGEMGDRDP----DNLSGGQQQRVALARALAPEPDVLLLDEPM 162
                                       ***************9999**************999998....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0         2   1.9e+03      34      69 ..      47      82 ..      44      87 .. 0.72
   2 ?    6.4   0.0      0.01        10      45      73 ..     253     284 ..     232     285 .. 0.67
   3 !   39.5   0.3   4.7e-13   4.7e-10       2      73 ..     278     356 ..     277     359 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2
                            TOBE_2 34 ryvvelaggqlvvvrqpnadrdsalapGdtVelswd 69
                                      r+v  l+  ++ vvr + +d +s+++++  V++ ++
  gi|313126555|ref|YP_004036825.1| 47 RLVAGLETPTDGVVRFDGEDVSSTPTEDRNVGVVFQ 82
                                      666667777777777777764589999999999887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                            TOBE_2  45 vvvrqpnadr.d..salapGdtVelswdpdda 73 
                                        vvr+++++     ++ ++G+tV+ +++p+++
  gi|313126555|ref|YP_004036825.1| 253 TVVRVADTSFeLppTDADVGETVQFCVRPEHL 284
                                       344555554433345677***********996 PP

  == domain 3  score: 39.5 bits;  conditional E-value: 4.7e-13
                            TOBE_2   2 aiRPEklrla..........aagga.......nglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapG 61 
                                       ++RPE+l+ a          +   +       n+l++tVe +e+lG+ tr++++ ag +  vvr+++ +      + 
  gi|313126555|ref|YP_004036825.1| 278 CVRPEHLSAAtmteaptetaG---EtatvpktNRLTATVETTEFLGDVTRLHCRWAGRSV-VVRVAAVP------ER 344
                                       8***********999865441...245677767************************988.55555554......56 PP

                            TOBE_2  62 dtVelswdpdda 73 
                                       d++el++dp  a
  gi|313126555|ref|YP_004036825.1| 345 DRLELGFDPGVA 356
                                       888888888766 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00027      0.27       1      23 [.      31      53 ..      31      89 .. 0.77
   2 !   20.7   0.0     3e-07    0.0003     231     298 ..     129     194 ..     100     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      +  l+Gp g+GK++ L++  +l 
  gi|313126555|ref|YP_004036825.1| 31 FFTLVGPSGCGKTTTLRLVAGLE 53
                                      5689**************99883 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3e-07
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       ++++++lS G+++  al+ al+  +   ++ll+DEp + L+ +l + l + +k+ ++  ++  + +TH+
  gi|313126555|ref|YP_004036825.1| 129 DRDPDNLSGGQQQRVALARALAPEP---DVLLLDEPMSALDARLREQLRRSVKRVQKeLNVTTLYVTHD 194
                                       56788999**999989999999888...************************88888899********8 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   1.5e-06    0.0015       3     111 ..      34     194 ..      32     209 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       l+Gp G+GKT++ + va        +++++g ++ s                                         
  gi|313126555|ref|YP_004036825.1|  34 LVGPSGCGKTTTLRLVAGLETptDGVVRFDGEDVSSTptedrnvgvvfqnyalfphmtvrenvayglkfddpptgmt 110
                                       89***************984222336666666666555666666666666666666666666666666666666666 PP

                                       ....................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  38 ....................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                                              + +   ++ ++ a++ a +p +l++DE  +   +r          + +qL + +
  gi|313126555|ref|YP_004036825.1| 111 vdervsellammnlgemgdrDPDNLSGGQQQRVALARALApEPDVLLLDEPMSALDAR----------LREQLRRSV 177
                                       6666666666666666444444444555555555566666779999999999988888..........566666666 PP

                                       HHTTTSSSTEEEEEEESS CS
                               AAA  94 dgvkkkeskvivigatnr 111
                                       ++v+k+ + v+ + +t++
  gi|313126555|ref|YP_004036825.1| 178 KRVQKELN-VTTLYVTHD 194
                                       66666544.555555554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.05        49      25      39 ..      30      44 ..      11      50 .. 0.81
   2 !   15.4   0.0   9.6e-06    0.0096     114     201 ..     112     197 ..      68     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.05
                                      SEEEEEESTTSSHHH CS
                                      xxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsn 39
                                      +f  +vGp G+GK+ 
  gi|313126555|ref|YP_004036825.1| 30 EFFTLVGPSGCGKTT 44
                                      58899********96 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 9.6e-06
                                       TTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--S.EEEECTTTTTS-HHHHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 114 ngkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpap.lyllDeidaaLDeknvkkvaellkekskn 189
                                       +++  +   +++l e+ + ++++LSgG+++ vala  +A     p+p + llDe  +aLD++ ++++ + +k+ +k+
  gi|313126555|ref|YP_004036825.1| 112 DERVSELLAMMNLGEMGDRDPDNLSGGQQQRVALARALA-----PEPdVLLLDEPMSALDARLREQLRRSVKRVQKE 183
                                       4444555555555555666778***********998776.....44436799********************88877 PP

                                       ..SEEEEE-SSHHH CS
                                       ..xxxxxxxxxxxx RF
                             SMC_N 190 ..aQfivislreem 201
                                         +  + +++++e 
  gi|313126555|ref|YP_004036825.1| 184 lnVTTLYVTHDQEE 197
                                       22444556665554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-05     0.015      23      55 ..      28      60 ..      10      98 .. 0.73
   2 ?    1.1   0.0      0.47   4.7e+02      70     106 ..     143     178 ..     112     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd.ggif 55
                                      ++e   l+G+sG+GK++ +r ++  le+  +g++
  gi|313126555|ref|YP_004036825.1| 28 EGEFFTLVGPSGCGKTTTLRLVAG-LETPtDGVV 60
                                      348899**************9994.444423444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.47
                            AAA_16  70 salaqalareellrqlldeaesaeleawrekleeala 106
                                       +ala+ala  e    llde+ sa+ ++ re+l+++++
  gi|313126555|ref|YP_004036825.1| 143 VALARALAP-EPDVLLLDEPMSALDARLREQLRRSVK 178
                                       557777766.444556666677788888888887777 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   1.5e-05     0.015       5      29 ..      29      53 ..      26     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                        + +++G+sG+GKTt+lr ++   
  gi|313126555|ref|YP_004036825.1| 29 GEFFTLVGPSGCGKTTTLRLVAGLE 53
                                      56889**************987654 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.016      34      66 ..      18      50 ..      10      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                             Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      +l+  +L   + +   + GPsGCgk+t+++ ++
  gi|313126555|ref|YP_004036825.1| 18 ALHEVSLSVDEGEFFTLVGPSGCGKTTTLRLVA 50
                                      66666777777778899************9876 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.9   1.9e+03       9      22 ..      57      71 ..      56      80 .. 0.75
   2 ?   12.2   0.0   0.00021      0.21       1      41 [.     239     284 ..     239     286 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.9
                   CysA_C_terminal  9 dGklriGglalp.vP 22
                                      dG +r++g ++   P
  gi|313126555|ref|YP_004036825.1| 57 DGVVRFDGEDVSsTP 71
                                      89****999988555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00021
                   CysA_C_terminal   1 NlFhGrvedGk.....lriGglalpvPelagadgqevvayVRPhDl 41 
                                       N+F G v d +     +r++++++++P +++  g+ v+  VRP++l
  gi|313126555|ref|YP_004036825.1| 239 NVFSGAVLDATdektvVRVADTSFELPPTDADVGETVQFCVRPEHL 284
                                       66666665543334559**********5555569**********98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00015      0.15      18      45 ..      29      56 ..      20     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaa 45
                                        + +l+Gp G GKtt+l+ ++ + +  
  gi|313126555|ref|YP_004036825.1| 29 GEFFTLVGPSGCGKTTTLRLVAGLETPT 56
                                      458899*************998776655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001       0.1      20      54 ..      33      67 ..      23      70 .. 0.91
   2 ?   -3.1   0.1       3.9   3.9e+03     164     189 ..     171     196 ..     163     209 .. 0.65
   3 ?   -3.6   0.0       5.6   5.6e+03     118     133 ..     328     343 ..     312     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                        Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpDdl 54
                                       l+G +G+GK+++++l++   +++++vvr+d+ d+
  gi|313126555|ref|YP_004036825.1| 33 TLVGPSGCGKTTTLRLVAGLETPTDGVVRFDGEDV 67
                                      58999*************9999*********9875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                        Zeta_toxin 164 eglresvealeeekqldrvkikdrdg 189
                                       e+lr+sv+++++e  +  + ++  ++
  gi|313126555|ref|YP_004036825.1| 171 EQLRRSVKRVQKELNVTTLYVTHDQE 196
                                       56677777777766666555554444 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.6
                        Zeta_toxin 118 kkaGYevevvvvavkk 133
                                       + aG++v v+v av++
  gi|313126555|ref|YP_004036825.1| 328 RWAGRSVVVRVAAVPE 343
                                       5679999999999886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00016      0.16      31     157 ..      27     167 ..      22     198 .. 0.49
   2 ?   -2.1   0.0       2.4   2.4e+03      85     140 ..     263     316 ..     243     319 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                            AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.......... 97 
                                        +ge+  l+G++g+GKtt +  +a   +   p  g v+     V    +Ed++ ++    +a++ ++          
  gi|313126555|ref|YP_004036825.1|  27 DEGEFFTLVGPSGCGKTTTLRLVAGLET---PTDGVVRFDGEDVSSTPTEDRNVGVVFQNYALFPHMtvrenvaygl 100
                                       689**************96543333222...2223222244455555555555555555555555554544444444 PP

                            AAA_25  98 .........rddarllvld.lagv..eslpLfakdrggtl.ltadvdaleaaieev.egvrlvviDplsralgg 157
                                                +      v   + ++    ++L +++++++  l +  ++  a +++  ++++++ +D   +al++
  gi|313126555|ref|YP_004036825.1| 101 kfddpptgmT------VDErV-SEllAMMNLGEMGDRDPDnLSGGQQQRVALARALaPEPDVLLLDEPMSALDA 167
                                       3342222221......22221.1112234555555555555433333333333333134777777766666554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                            AAA_25  85 elrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieev 140
                                       el++  + vge++++  r   l++a++  +   ++++g+t++ +++++l a++e +
  gi|313126555|ref|YP_004036825.1| 263 ELPPTDADVGETVQFCVRPEHLSAATM--TEAPTETAGETATVPKTNRLTATVETT 316
                                       566666667777777777777777777..223355666666667788888888765 PP

>> Fimbrial_PilY2  Type 4 fimbrial biogenesis protein PilY2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.13      20      77 ..     237     292 ..     228     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                    Fimbrial_PilY2  20 daetfeasGavsevqleknLitidkklyrLPnstvrnGtPailqlkPGsviafsGtva 77 
                                       d + f  sGav +   ek ++ + ++ ++LP   +  G  + + ++P  + a++ t+a
  gi|313126555|ref|YP_004036825.1| 237 DNNVF--SGAVLDATDEKTVVRVADTSFELPPTDADVGETVQFCVRPEHLSAATMTEA 292
                                       55555..8****************************************9999888876 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00016      0.16       5      54 ..     307     358 ..     305     359 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                              TOBE   5 NqlpgtVvvveplgseveVrvdlggga..tLtArvtrrsaeeLgLapGeeVf 54 
                                       N+l++tV+  e+lg  ++++ + +g      +A v++r + eLg+ pG   f
  gi|313126555|ref|YP_004036825.1| 307 NRLTATVETTEFLGDVTRLHCRWAGRSvvVRVAAVPERDRLELGFDPGVATF 358
                                       99*************************4333577899*******99997655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00028      0.28       4      33 ..      34      92 ..      32     207 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                            AAA_33  4 lvGlpGsGKstlaerllkklg....avllssdt.........................l 33
                                      lvG++G+GK+t ++ ++  ++    +v+ +  +                         +
  gi|313126555|ref|YP_004036825.1| 34 LVGPSGCGKTTTLRLVAGLETptdgVVRFDGEDvsstptedrnvgvvfqnyalfphmtV 92
                                      79**********99886544445444444433345555555555555555555555550 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0002       0.2      13      39 ..      20      46 ..      14      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      ++ ++++d+ +++ l+GpsG GK+T l
  gi|313126555|ref|YP_004036825.1| 20 HEVSLSVDEGEFFTLVGPSGCGKTTTL 46
                                      44566777555999**********976 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00042      0.41       4      48 ..      31      74 ..      28     103 .. 0.79
   2 ?   -1.1   0.0       1.8   1.8e+03      61      86 ..     150     180 ..     116     204 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkklad 48
                                        +++G+  +GKTt l+ ++  +  + + ++ ++ +d + +  +d
  gi|313126555|ref|YP_004036825.1| 31 FFTLVGPSGCGKTTTLRLVAGLET-PTDGVVRFDGEDVSSTPTED 74
                                      6789************99986666.99999999999877755444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                            AAA_14  61 keekktylflDEiqev......pewekalksl 86 
                                        + +  +l+lDE   +      +++++ +k++
  gi|313126555|ref|YP_004036825.1| 150 AP-EPDVLLLDEPMSAldarlrEQLRRSVKRV 180
                                       33.67788888866664433333333333333 PP

>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0     0.001         1      20      55 ..     175     210 ..     169     214 .. 0.88
   2 ?   -0.5   0.0       1.4   1.4e+03      27      51 ..     252     276 ..     243     282 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.001
                                       EEETTTTEEEEEEEEEEEE-TTTS--TT-EEEEEEE CS
                     Ribosomal_S17  20 vkhpkykkyvkrrkkylahdennsvkvGDiVrieec 55 
                                          ++++k  + ++ y  hd+++ + v D+V+++  
  gi|313126555|ref|YP_004036825.1| 175 RSVKRVQKELNVTTLYVTHDQEEALAVSDRVAVMNG 210
                                       567899**************************9976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                                       EEEEEEEEEEEE-TTTS--TT-EEE CS
                     Ribosomal_S17  27 kyvkrrkkylahdennsvkvGDiVr 51 
                                       k+v r    +   ++  + vG +V+
  gi|313126555|ref|YP_004036825.1| 252 KTVVRVADTSFELPPTDADVGETVQ 276
                                       4444444444555556666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 1946.23
//
Query:       gi|313126556|ref|YP_004036826.1|  [L=463]
Description: efflux protein, mate family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-46  157.7  25.5      1e-23   83.8   9.9    2.3  2  MatE             MatE
    7.4e-07   29.3   4.8    7.4e-07   29.3   4.8    4.4  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   7.6   1.9e-26   1.7e-22       1     160 [.      24     183 ..      24     184 .. 0.99
   2 !   83.8   9.9   1.1e-27     1e-23       1     160 [.     249     412 ..     249     413 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.9e-26
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P++ +n++ +  + idt++vgrlg++a+Aa++++++i  ll+++++++ ++ ++  +q +Ga     a+++ +++++
  gi|313126556|ref|YP_004036826.1|  24 PLVAQNFALVAQQVIDTFWVGRLGTDAVAAIGLVIPIGALLTIPITAIFVGSQVTSSQHVGADEEALARRTPVHAVV 100
                                       89999************************************************************************ PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l+ll+s +++ +v++f+e+ l+ +  ++ v+el+++y+    l+++  +l+  l + + g g+t+ ++ ++l ++ l
  gi|313126556|ref|YP_004036826.1| 101 LMLLISTVLVGVVYFFAEPVLKQLYPTASVIELGATYMFGWSLSLVMSSLSDGLESGFVGFGDTRSAFLVNLTAIGL 177
                                       ***************************************************************************** PP

                              MatE 155 niplny 160
                                       n++l++
  gi|313126556|ref|YP_004036826.1| 178 NVVLDP 183
                                       ***987 PP

  == domain 2  score: 83.8 bits;  conditional E-value: 1.1e-27
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       Pia  n+  ++  ++++++v    g+  +Aa++++ +++ + fv++ gls+a+t++vgq++Ga  ++ra+ a+r g+
  gi|313126556|ref|YP_004036826.1| 249 PIAAKNAGRQIARAVMISIVTLAgGAAGIAAYTVGARLSTVAFVPIQGLSSATTSVVGQNIGADEPERAAAATRFGV 325
                                       88999999999999*************************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdee..vlelakrylrililgipalalqlvlsgilrgagktkvplyislis 151
                                       +l+++   +i l+ +  +  +++ f  +     l ++ +ylril++g+ a+a+  v+ + + gag+t +++y +l+ 
  gi|313126556|ref|YP_004036826.1| 326 LLGAVALGVIGLFQWTSPTLLAQTFIPEISgqTLTWTIDYLRILAYGYWAFAFIYVIEAGFSGAGRTDLSMYSTLVQ 402
                                       **************************998888********************************************* PP

                              MatE 152 l.llniplny 160
                                       + ++++p+++
  gi|313126556|ref|YP_004036826.1| 403 YwVVRLPIAV 412
                                       *******987 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   4.8      0.38   3.4e+03     119     136 ..      84     116 ..      17     123 .. 0.61
   2 !   29.3   4.8   8.3e-11   7.4e-07       6     138 ..     142     284 ..     137     289 .. 0.73
   3 ?   -2.4   2.6      0.49   4.4e+03      81      81 ..     305     305 ..     265     356 .. 0.53
   4 !    8.2   6.6   0.00027       2.4       1      79 [.     365     446 ..     365     456 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.38
                   Polysacc_synt_C 119 a...............alalllavlvgalvYll 136
                                                        l ll++ ++ ++vY++
  gi|313126556|ref|YP_004036826.1|  84 GadeealarrtpvhavVLMLLISTVLVGVVYFF 116
                                       155555555555554333666777777777776 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 8.3e-11
                   Polysacc_synt_C   6 alsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavln.ly 75 
                                       +ls++++sls  l s + g g ++ a+++++ ++ ++++l  ++i      p++g+ Gaaiat ++++ + +l   +
  gi|313126556|ref|YP_004036826.1| 142 SLSLVMSSLSDGLESGFVGFGDTRSAFLVNLTAIGLNVVLDPFFIfgwgpfPEWGVFGAAIATGVGYAGGGLLAvAI 218
                                       789999***************************************999999999**************999998677 PP

                   Polysacc_synt_C  76 alrrllgikl.....ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYllll 138
                                       al+ ++ ++l      + r+++  ++ +    + +    +++  + +  ++++l+++++g+++Y + +
  gi|313126556|ref|YP_004036826.1| 219 ALSGRTSFSLrrdafWFGRDMFGQIIRTGSPIA-AKNAGRQIARAVMI-SIVTLAGGAAGIAAYTVGA 284
                                       888899999965443222222222222221111.22233333333332.4688888889999998766 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.49
                   Polysacc_synt_C  81 l 81 
                                       +
  gi|313126556|ref|YP_004036826.1| 305 V 305
                                       0 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.00027
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvig.alvklilnllli..plfgivGaaiatvlallvvavlnl 74 
                                       +L+ila++   ++++ v  + + g gr+++ ++++++   +v l + ++ +   ++g+  + +a +l+ +++a+ ++
  gi|313126556|ref|YP_004036826.1| 365 YLRILAYGYWAFAFIYVIEAGFSGAGRTDLSMYSTLVQyWVVRLPIAVVGVyvLSMGVHAVFWAVTLSNVAAAIGLF 441
                                       69*********************************99835789999998884457799****************999 PP

                   Polysacc_synt_C  75 yalrr 79 
                                       ++ r 
  gi|313126556|ref|YP_004036826.1| 442 VFYRF 446
                                       88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2631.98
//
Query:       gi|313126557|ref|YP_004036827.1|  [L=150]
Description: hypothetical protein Hbor_18150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.8    8.4   4.7        2.4    8.6   0.3    2.5  3  DUF2583   Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.18   3.3e+03      27      53 ..      18      44 ..      10      46 .. 0.73
   2 ?    8.6   0.3   0.00013       2.4       9      58 ..      46      93 ..      39     104 .. 0.87
   3 ?    1.2   0.2     0.028   4.9e+02       8      28 ..     103     123 ..      99     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.18
                           DUF2583 27 ysvlnqlpelelpellaeaallgifiG 53
                                       +vl  l+e+e    +   ++++ f+G
  gi|313126557|ref|YP_004036827.1| 18 LTVLLLLFEVETRSQIGMFEVVARFVG 44
                                      566777778877777777777777777 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00013
                           DUF2583  9 lGnvlmglGlllmvaslaysvlnqlpelelpellaeaallgifiGallWl 58
                                       Gn+ +g+ l+++ +++a+ +l    e ++p   ++ a+ g+ +GallW+
  gi|313126557|ref|YP_004036827.1| 46 PGNTTVGFALFVLAGTVAWPLLFVAAEESIPG--TDPAIKGLGVGALLWI 93
                                      599999***************99999988887..588999*********8 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.028
                           DUF2583   8 llGnvlmglGlllmvaslays 28 
                                       l G +++++G +++va lay 
  gi|313126557|ref|YP_004036827.1| 103 LAGAIVLAFGGMTLVAHLAYG 123
                                       679999999999****99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 865.14
//
Query:       gi|313126558|ref|YP_004036828.1|  [L=670]
Description: heme/copper-type cytochrome/quinol oxidase subunit 1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-141  472.5  54.2   1.6e-141  472.1  54.2    1.1  1  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.1  54.2  8.9e-146  1.6e-141       1     432 []      99     559 ..      99     559 .. 0.97

  Alignments for each domain:
  == domain 1  score: 472.1 bits;  conditional E-value: 8.9e-146
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCTCT.....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS CS
                              COX1   1 kigllylilalvlllvggllgllirlqlafp.....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgard 72 
                                       +ig+lyl+++l+++l+g + +++ir++l++p     d++tyn+l+t Hg +m+f+f+tp+++g++ny++pll+ a+d
  gi|313126558|ref|YP_004036828.1|  99 DIGILYLLFGLAAGLWGATDAVMIRTELFTPttdvwDAHTYNALFTTHGLTMLFFFVTPVFTGLANYFLPLLIDADD 175
                                       599**************************998888888*************************************** PP

                                       -S-HHHHHHHHHHHHHHHHHHHHHHH....CS.................S-STTTTTTTC.......SHHHHHHHHH CS
                              COX1  73 lafprlnalsfwlvvlgvvllllsll....ga.................attgwteYapls......evdlwllgll 122
                                       +afpr+na++fwl++ ++vl+ ++ll     +                 +t gwt Y+p +      +vdl+llgl+
  gi|313126558|ref|YP_004036828.1| 176 MAFPRINAIAFWLLPPSFVLVRAGLLtevlAKmidavgprieflyalepPTPGWTLYVPQAiqltnpQVDLLLLGLH 252
                                       ************9999999999999865551166777889999999999**********99**************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SSSC..E-HH CS
                              COX1 123 lvvvssllgainfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslg.kffsp..gdpl 196
                                       l+++++++ga+n+ivti++ r + + ++++ ++ w++l+t+ +il+a+p+l  all+llldr++g  ff    g p+
  gi|313126558|ref|YP_004036828.1| 253 LSGLATVMGAVNIIVTIFTERGERVGWSNMDILSWSLLTTSGIILFAFPILGSALLMLLLDRNFGtAFFALeaGGPI 329
                                       *********************************************************************5555**** PP

                                       HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHH CS
                              COX1 197 ldqhlfWffgHpeVyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsv 273
                                       l+qhlfWffgHpeVyil+lpa+g+ + ilpkfagr+lf+ k++v+++++i++lsf vwaHH+f tg+++ l+a ++v
  gi|313126558|ref|YP_004036828.1| 330 LWQHLFWFFGHPEVYILVLPAFGLTSQILPKFAGRRLFGFKFIVYSTLAIGVLSFGVWAHHMFATGMDPRLRASFMV 406
                                       ***************************************************************************** PP

                                       HHHHTHHHHHHCCCHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTH CS
                              COX1 274 fslliavPsglkvfnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllga 350
                                       ++l+iavPs++k+fnw+atlw+g++r+++pm f+lg + lfi+gG+tG++la+ +v++v+h+ty+vvaHfH++++g+
  gi|313126558|ref|YP_004036828.1| 407 ITLAIAVPSAVKTFNWMATLWNGNVRLEAPMQFLLGGIALFIVGGVTGIFLASIPVDLVLHGTYYVVAHFHFIVVGI 483
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHH CS
                              COX1 351 vvfllfaaiyyllpkltgrmlserlaklhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrt 427
                                       ++f +faa yy++p +tgrm+++rla +h +l + G++++f+p++ilGl+g+prr+a+y        +++ l++++t
  gi|313126558|ref|YP_004036828.1| 484 IAFSMFAASYYWYPLFTGRMYNKRLATIHAVLSIGGVIVTFFPLFILGLMGLPRRSAQY------PVQFTSLQQIAT 554
                                       *********************************************************99......359********* PP

                                       HHHHH CS
                              COX1 428 iggvl 432
                                       +g+++
  gi|313126558|ref|YP_004036828.1| 555 VGAFI 559
                                       **996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (670 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.74u 0.35s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 3685.64
//
Query:       gi|313126559|ref|YP_004036829.1|  [L=272]
Description: hypothetical protein Hbor_18170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-85  286.4   4.9    2.2e-85  286.2   4.9    1.0  1  BtpA            BtpA family
     0.0031   16.4   0.8     0.0073   15.2   0.6    1.8  1  Trp_syntA       Tryptophan synthase alpha chain
  ------ inclusion threshold ------
      0.028   13.9   5.8       0.08   12.4   0.6    2.8  3  PcrB            PcrB family
       0.17   12.1   3.1        0.7   10.1   3.0    2.3  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain


Domain annotation for each model (and alignments):
>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.2   4.9   4.8e-89   2.2e-85       3     253 ..      11     268 ..       9     269 .. 0.97

  Alignments for each domain:
  == domain 1  score: 286.2 bits;  conditional E-value: 4.8e-89
                              BtpA   3 kpvigvvHLkpLPgsaeyka..nleevidkAvkeakaleegGvDavilenygdaPf.lkevdpetvaamtvivkevk 76 
                                        +v+g+vHL++LPg ++y+a  +l++v + A+++a +l++gGvDav++en+gdaPf + +v + tva+mt ++++v 
  gi|313126559|ref|YP_004036829.1|  11 DAVVGMVHLHTLPGAPNYDAeaGLDAVRESALEDAAKLDAGGVDAVMIENFGDAPFyPDDVPKHTVASMTAVIDAVA 87 
                                       68*****************9889********************************72566***************** PP

                              BtpA  77 sdvsiplGvnvLrndavaalaiAkavgakFiRvnvltgvalsdeGilegkaaellrykkllesrvkiladvavkhav 153
                                       ++v +p+GvnvLrnda aal+iA a+ga+F+Rvnv +g +++d+G++eg a+e++r++ +l+++v+++adv vkh+ 
  gi|313126559|ref|YP_004036829.1|  88 REVDVPVGVNVLRNDAEAALSIAAATGASFVRVNVHAGSRVTDQGVVEGRAHETMRLRDQLDADVAVFADVGVKHSE 164
                                       ***************************************************************************** PP

                              BtpA 154 plv.erdlesavkdtvergladavilsGkatGgevdleelklaketvk...vkvlvgsGvseenlekllsiadGviv 226
                                       pl+ e+ l  av++ v rglad+v++sG  tG ++d  +l++++++++    + lvgsGv++e +++ l++adGviv
  gi|313126559|ref|YP_004036829.1| 165 PLGpETPLDVAVEEVVGRGLADGVVVSGSGTGAPTDDSDLETVAHAADeagAPALVGSGVTAETVAETLEYADGVIV 241
                                       **95678999*******************************99999999999************************* PP

                              BtpA 227 gtsikkdGkianaiDkervrkivelae 253
                                       gt +k +G+++ ++D++rvr++v++a+
  gi|313126559|ref|YP_004036829.1| 242 GTALKEGGETTAPVDESRVRAVVSAAH 268
                                       ************************997 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6   1.6e-06    0.0073     189     231 ..     206     247 ..     185     271 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHH CS
                         Trp_syntA 189 lverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvk 231
                                       +v++  +   +P++vG G+  +e+v++  + adGvivG al +
  gi|313126559|ref|YP_004036829.1| 206 TVAHAADEAGAPALVGSGVT-AETVAETLEYADGVIVGTALKE 247
                                       45555666789*******96.678888899*********9855 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.5   2.2e+03      17      36 ..      39      58 ..      33      61 .. 0.67
   2 ?    3.2   0.1     0.011        50      19      41 ..     172     196 ..     159     211 .. 0.69
   3 ?   12.4   0.6   1.8e-05      0.08     183     217 ..     218     251 ..     202     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.5
                                      S-CHHHHHHHHCTT-SEEEE CS
                              PcrB 17 enpdEiveiviesgtDavmi 36
                                      e   E +  +  +g Davmi
  gi|313126559|ref|YP_004036829.1| 39 ESALEDAAKLDAGGVDAVMI 58
                                      44445555566899999998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.011
                                       CHHHHHHH.HCTT-SEEEEECST.C CS
                              PcrB  19 pdEiveiv.iesgtDavmigGsq.s 41 
                                        d +ve v  ++ +D+v+++Gs  +
  gi|313126559|ref|YP_004036829.1| 172 LDVAVEEVvGRGLADGVVVSGSGtG 196
                                       4555655527888********9743 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 1.8e-05
                                       EEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHHC CS
                              PcrB 183 livGGGirsaEkAkevveaADvivvGnvveekder 217
                                        +vG G+  aE+ +e++e+AD ++vG++++e +e+
  gi|313126559|ref|YP_004036829.1| 218 ALVGSGVT-AETVAETLEYADGVIVGTALKEGGET 251
                                       57899985.79999****************98854 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.0   0.00016       0.7      19      69 ..     179     232 ..      41     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                       HHHT.T--EEEEEEBTTTB--H..HHHHHHHHHHTTT-EEEEEESSSBS----- CS
                    Asparaginase_C  19 llkk.gakGvvlegtGvGnlps..allealkeakargivvvatsqcpsgsvsns 69 
                                       ++ + +a+Gvv+ g G+G+ ++  +l  ++  a ++g +  + s +  ++v+++
  gi|313126559|ref|YP_004036829.1| 179 VVGRgLADGVVVSGSGTGAPTDdsDLETVAHAADEAGAPALVGSGVTAETVAET 232
                                       4444379*************9776888888888899999999999888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1640.77
//
Query:       gi|313126560|ref|YP_004036830.1|  [L=378]
Description: NADH dehydrogenase, fad-containing subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-30  105.7   2.1    3.7e-30  105.2   2.1    1.2  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    9.2e-13   48.6   2.0    9.7e-10   38.9   0.1    2.9  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    5.8e-06   26.4   1.1       0.91    9.5   0.0    3.4  3  NAD_binding_9    FAD-NAD(P)-binding
      1e-05   25.3   5.7       0.63    9.6   0.2    4.1  4  DAO              FAD dependent oxidoreductase
     0.0011   19.2   0.5       0.27   11.5   0.0    2.6  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0043   17.3   3.2        2.2    8.6   0.0    3.6  3  NAD_binding_8    NAD(P)-binding Rossmann-like domain
     0.0098   16.9   2.0       0.19   12.7   0.1    2.8  2  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.053   13.8   0.2        3.1    8.1   0.0    2.6  2  TrkA_N           TrkA-N domain
       0.12   11.9   0.2       0.42   10.1   0.0    2.0  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   2.1   1.9e-33   3.7e-30       2     294 .]       2     290 ..       1     290 [. 0.89

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 1.9e-33
                                       SEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...HHHHCHHHHCCCCHC CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeias...evvkklnqgielllg 72 
                                       +v+v+G+G AG+++a++l     + a+ ++v +e   ++++  ++ ++++ + ++ i+    e +++       ++ 
  gi|313126560|ref|YP_004036830.1|   2 RVLVLGAGYAGVTVARRLESclpSDAELIVV-DESDSHLVQHEVHRVIRRPGLAETIRVpltELFDRAAVR---VA- 73 
                                       89******************9999*******.999999999999999999999998888655444433333...33. PP

                                       CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp....... 142
                                         v ++d+++++v+l     + +e+++yd+  ++ G+ +   g+pGv+ +   l + +++a a+++  l        
  gi|313126560|ref|YP_004036830.1|  74 -RVEGLDREARTVHL-----DGGETLDYDYAAVCLGAGTAYYGLPGVEAHSLPL-KRVADATAIRESFLSatdegdt 143
                                       .3777**********.....7899***********************9999888.99*************9999987 PP

                                       SEEEEES-SHHHHHHHHHHHHHT-......EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgk......evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgng 213
                                         +vv G+G+ Gv +A++la l++      ++t++e++d + ++++ +++aa++++le++G+++++ t v+++++++
  gi|313126560|ref|YP_004036830.1| 144 VTAVVGGAGLSGVQTAGELAALADeedvdaNITVIEQLDDVAPNFPANFRAAVRDELEARGIDIRTSTAVERATSET 220
                                       77788899***********999888999989***************************************9999555 PP

                                       EEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.....TECCSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxx RF
                       Pyr_redox_2 214 eklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.....ggkggpe 285
                                            v+++ e++  d+ v+a G+  +t+           ++++ vv + lr  ++  +++GD a     +g+ +p+
  gi|313126560|ref|YP_004036830.1| 221 -----VETETETFTSDTFVWAGGIAGQTAM----------NGDRPVVRSDLRL-DDYTFVVGDAArivdaDGEPVPA 281
                                       .....6788888************999844..........6788889999987.8888************999**** PP

                                       -HHHHHHHH CS
                                       xxxxxxxxx RF
                       Pyr_redox_2 286 laqaAvqqG 294
                                       +a aA +++
  gi|313126560|ref|YP_004036830.1| 282 SASAALREA 290
                                       *****9987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0016       3.3       1      33 [.       2      37 ..       2      73 .. 0.77
   2 !   38.9   0.1   4.8e-13   9.7e-10       2      71 ..     146     221 ..     145     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                                      EEEEECSSHHHHHHHHHHHH.TT..SEEEEEESSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalae.lg..kkVtvversdk 33
                                      +v+v+G+Gy g+ +A  l   l   ++  vv+ sd 
  gi|313126560|ref|YP_004036830.1|  2 RVLVLGAGYAGVTVARRLEScLPsdAELIVVDESDS 37
                                      79*************999653442244555555555 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 4.8e-13
                                       EEEECSSHHHHHHHHHHHHTT......SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelg......kkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsed 71 
                                       +vv G+G++g+  Ag+la+l+      +++tv+e  d + +++++ ++++++++le++gi+++++t ve+ + ++ 
  gi|313126560|ref|YP_004036830.1| 146 AVVGGAGLSGVQTAGELAALAdeedvdANITVIEQLDDVAPNFPANFRAAVRDELEARGIDIRTSTAVERATSETV 221
                                       588899***********999988887789****************************************9996654 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0011       2.2       2      36 ..       5      37 ..       4      54 .. 0.84
   2 !    5.5   0.1     0.008        16     121     155 ..      72     104 ..      61     105 .. 0.74
   3 !    9.5   0.0   0.00046      0.91       4      33 ..     150     180 ..     146     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                      + GaG +G++v++rL +    +s+ e+ ++d+s +
  gi|313126560|ref|YP_004036830.1|  5 VLGAGYAGVTVARRLESCL--PSDAELIVVDESDS 37
                                      67****************8..9*********9543 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.008
                     NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvLAlGh 155
                                        a+v+ l+++a  ++v+l++g++l++d+  ++lG 
  gi|313126560|ref|YP_004036830.1|  72 VARVEGLDREA--RTVHLDGGETLDYDYAAVCLGA 104
                                       34455555443..479*****************95 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00046
                     NAD_binding_9   4 GaGprGlavlerLlara.kkkspleitlfdp 33 
                                       GaG +G+ ++ +L+a a +++ + +it++++
  gi|313126560|ref|YP_004036830.1| 150 GAGLSGVQTAGELAALAdEEDVDANITVIEQ 180
                                       79***************989999******98 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00044      0.87       2      26 ..       3      32 ..       2      46 .. 0.72
   2 ?    0.3   0.0      0.21   4.2e+02     167     206 ..      73     110 ..      59     141 .. 0.66
   3 !    5.8   0.2    0.0043       8.5       3      32 ..     147     184 ..     145     187 .. 0.76
   4 !    9.6   0.2   0.00031      0.63     145     205 ..     189     242 ..     188     278 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                                      EEEECTSHHHHHHHHHHHHT..T....EEEE CS
                               DAO  2 vviiGGGiiGlstAyeLarr..g....Vtll 26
                                      v++ G+G++G+++A+ L +   +     +++
  gi|313126560|ref|YP_004036830.1|  3 VLVLGAGYAGVTVARRL-ESclPsdaeLIVV 32
                                      99***************.4323234554444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.21
                                       ECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGHH..H CS
                               DAO 167 tevtgleeedgkvwgverttp.gen.daadavVnaaGawsd..l 206
                                       ++v+gl++e   + +v  + + ge+ d  d+  ++ Ga++    
  gi|313126560|ref|YP_004036830.1|  73 ARVEGLDRE---ARTV--HLDgGETlDY-DYAAVCLGAGTAyyG 110
                                       468888765...6777..3344777554.99******9986432 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0043
                                       EEECTSHHHHHHHHHHHHT.T.......EEEEESSSST CS
                               DAO   3 viiGGGiiGlstAyeLarr.g.......Vtllekgdia 32 
                                       v+ G+G  G+ tA eLa+          +t++e+ d++
  gi|313126560|ref|YP_004036830.1| 147 VVGGAGLSGVQTAGELAALaDeedvdanITVIEQLDDV 184
                                       44479***********864324568899*****97665 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH CS
                               DAO 145 pakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd 205
                                       pa + aa+++++ea+G++i++ t v++         +v  +t+ ++ ++ d+ V a G+  +
  gi|313126560|ref|YP_004036830.1| 189 PANFRAAVRDELEARGIDIRTSTAVERAT-----SETV--ETEtETFTS-DTFVWAGGIAGQ 242
                                       67788999**************9999872.....5678..554344345.99******8754 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00013      0.27       1      37 [.       3      39 ..       3     109 .. 0.88
   2 !    5.6   0.1    0.0092        18       5      61 ..     150     212 ..     146     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHH CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskekl 37
                                      vl++GaG+ G  va+ l+   + dae++v+d s+++l
  gi|313126560|ref|YP_004036830.1|  3 VLVLGAGYAGVTVARRLESCLPSDAELIVVDESDSHL 39
                                      89*********************99*******99985 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0092
                                       --SHHHHHHHHHHHCTCCT-G...EEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHH CS
                   Sacchrp_dh_NADP   5 GaGsvGqavaellarhfdvda...eitvadrskeklealaaka...lgvrfeaialdaenyea 61 
                                       GaG  G  +a +la+  d ++   +itv+++ ++ + +  a+     + ++ea+ +d+   +a
  gi|313126560|ref|YP_004036830.1| 150 GAGLSGVQTAGELAALADEEDvdaNITVIEQLDDVAPNFPANFraaVRDELEARGIDIRTSTA 212
                                       557777777777666555544555*******99999988887766666666666666666555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0029       5.8       1      26 [.       5      33 ..       5      38 .. 0.73
   2 !    8.6   0.0    0.0011       2.2       3      31 ..     150     184 ..     147     191 .. 0.78
   3 ?   -1.7   0.6       1.7   3.5e+03       2      12 ..     354     364 ..     353     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0029
                                      EE--SHHHHHHHHHHHC...CTEEEEEE- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLak...agfdvllle 26
                                      ++GaG +G + A++L      +++  +++
  gi|313126560|ref|YP_004036830.1|  5 VLGAGYAGVTVARRLESclpSDAELIVVD 33
                                      89*************86433355555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                                       --SHHHHHHHHHHHC...C...TEEEEEE-SSSSS CS
                     NAD_binding_8   3 GaGlsGlvaAylLak...a...gfdvlllekrdrl 31 
                                       GaGlsG  +A +La    +   +++++++e+ d++
  gi|313126560|ref|YP_004036830.1| 150 GAGLSGVQTAGELAAladEedvDANITVIEQLDDV 184
                                       78********999864332556778*****99876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.7
                                       E--SHHHHHHH CS
                     NAD_binding_8   2 vGaGlsGlvaA 12 
                                       vGaG  G+v A
  gi|313126560|ref|YP_004036830.1| 354 VGAGHLGSVGA 364
                                       9******9876 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   9.7e-05      0.19       4      82 ..       7      94 ..       4     103 .. 0.74
   2 ?    2.8   0.3      0.12   2.5e+02      35      73 ..     159     195 ..     127     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.7e-05
                   Methyltransf_24  4 GvysGvstlwllralrrnga..grlvavdhdpg...aeeaaalareaglddrvrlikadseeala.sla.....agsiD 71
                                      G  +G+  + ++r l++      +l++vd       ++e+ +++r+ gl++++r+   ++++ +a ++a     +++  
  gi|313126560|ref|YP_004036830.1|  7 G--AGYAGVTVARRLESCLPsdAELIVVDESDShlvQHEVHRVIRRPGLAETIRVPLTELFDRAAvRVArveglDREAR 83
                                      5..555555555555554444469******887799999*****************999987655444456688899** PP

                   Methyltransf_24 72 llfiDgghaae 82
                                       +++Dgg + +
  gi|313126560|ref|YP_004036830.1| 84 TVHLDGGETLD 94
                                      ******97654 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                   Methyltransf_24  35 aeeaaalareaglddrvrlikadseealaslaagsiDll 73 
                                       a e aala+e+ +d+++++i++ ++++++++    +  +
  gi|313126560|ref|YP_004036830.1| 159 AGELAALADEEDVDANITVIEQ-LDDVAPNFP-ANFRAA 195
                                       3356666777777777777765.455555554.333333 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0016       3.1       1      37 [.       3      42 ..       3      51 .. 0.81
   2 ?    3.1   0.0     0.055   1.1e+02       2      38 ..     147     189 ..     146     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                                      EEEES-SHHHHHHHHHHHHTT...EEEEEEESSHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLsegg...kdvvvidkdeerveel 37
                                      ++++G+G  G ++a++L++      + +v+d +++++ ++
  gi|313126560|ref|YP_004036830.1|  3 VLVLGAGYAGVTVARRLESCLpsdAELIVVDESDSHLVQH 42
                                      68***************99335895599999999887665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.055
                                       EEES-SHHHHHHHHHHHH.TT.....EEEEEEESSHHHHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.gg.....kdvvvidkdeerveelr 38 
                                       ++ G+G  G + a eL + +       +++vi++ ++++ ++ 
  gi|313126560|ref|YP_004036830.1| 147 VVGGAGLSGVQTAGELAAlADeedvdANITVIEQLDDVAPNFP 189
                                       6788999999999999996658899966999999888776655 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00021      0.42       1      55 [.       1      57 [.       1      70 [. 0.80
   2 ?   -2.9   0.1       2.1   4.2e+03       5      17 ..     353     365 ..     351     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                                      SEEEEE--STTHHHHHHHHHHCT...SEEEEE-S-HHHHHHHCTTS-SS--TTHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeig...hevigvDideekvdklnsgkipiyepgLeelv 55
                                      m++ v+G+GY G++ a  l +      e+i+vD ++++  + +  +  i  pgL+e +
  gi|313126560|ref|YP_004036830.1|  1 MRVLVLGAGYAGVTVARRLESCLpsdAELIVVDESDSHLVQHEVHR-VIRRPGLAETI 57
                                      89****************9987677799*****9998876654433.46677777665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                                       EE--STTHHHHHH CS
                    UDPG_MGDP_dh_N   5 viGlGYvGlvtaa 17 
                                        +G+G++G v a+
  gi|313126560|ref|YP_004036830.1| 353 TVGAGHLGSVGAV 365
                                       69****9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2131.63
//
Query:       gi|313126561|ref|YP_004036831.1|  [L=324]
Description: diphosphomevalonate decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-07   31.3   0.1    2.5e-07   30.6   0.1    1.2  1  MDD_C           Mevalonate 5-diphosphate decarboxylase C-term
    1.9e-06   28.0   1.9    0.00022   21.4   0.4    2.5  2  GHMP_kinases_N  GHMP kinases N terminal domain
     0.0052   16.7   0.9     0.0091   15.9   0.9    1.4  1  TarH            Tar ligand binding domain homologue


Domain annotation for each model (and alignments):
>> MDD_C  Mevalonate 5-diphosphate decarboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1   4.2e-11   2.5e-07      22     133 ..     192     301 ..     179     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.2e-11
                             MDD_C  22 svetSeLlkhrakevvperieelekAikekdFetfaeitmkdSnqlhavcldtyPpifYlndtSraiielvhelNea 98 
                                        ++ S++++ r+++ v+++++e+++A+++ dF++  e++ +dS +l a+ ++     +Y +    a+ + v+el   
  gi|313126561|ref|YP_004036831.1| 192 EAADSHMFQARMAH-VHHQLDEMRDALHAADFDRAFELAEHDSLSLTATTMTGPAGWVYWQPKTIAVFNAVRELR-D 266
                                       556799********.9**********************************************************8.7 PP

                             MDD_C  99 agkikvAYtFDAGpNavlyleekdveellsllkkl 133
                                       +++i v ++ D G+   + ++e +v+++ ++++++
  gi|313126561|ref|YP_004036831.1| 267 EEEIPVYFSTDTGASVYVNTTEAHVDRVEEAISAC 301
                                       899***********************999998765 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.4   3.6e-08   0.00022       2      42 ..      90     130 ..      89     135 .. 0.82
   2 !    5.5   0.0    0.0033        19      16      42 ..     136     166 ..     136     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.6e-08
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHH CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeakla 42 
                                       +++++ +P   G+GSS++  +a+++Al+++ +l ++ ++++
  gi|313126561|ref|YP_004036831.1|  90 LESENSFPSNIGFGSSSSGFAAAAMALAEAAELGMSRPEIS 130
                                       78999************************997655445555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHHHHHHHT.TEHHHH...HHHH CS
                    GHMP_kinases_N  16 SSAAlavalvaAllall.glslee...akla 42 
                                       +S+++a a++ A+ +l+ g++ e+    ++ 
  gi|313126561|ref|YP_004036831.1| 136 GSSSAARAVTGAFSHLYsGMNDEDcrsERIE 166
                                       58899999999999*9943332333443333 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.9   1.5e-06    0.0091      89     153 ..     168     231 ..     146     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHHHHHHTS---GGGHH.HHHHHHHHHHH.HHHHHHHHHHHHHTT-HHHHHHS-HH CS
                              TarH  89 raeeslaqseeawkaYlalprtaeeeealaaelkakyka.lqdglapliaaleagnleaffdlptq 153
                                       + e+ l+   ++  aY+++++   +e a+++ + +++ a ++++l+++ +al+a +++++f+l+ +
  gi|313126561|ref|YP_004036831.1| 168 ELEDELRTVAAHVPAYKETEQAH-KE-AADSHMFQARMAhVHHQLDEMRDALHAADFDRAFELAEH 231
                                       55666777777777899998888.54.5777777788888*********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 1834.02
//
Query:       gi|313126562|ref|YP_004036832.1|  [L=36]
Description: hypothetical protein Hbor_18200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      128  (0.00713927); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 210.77
//
Query:       gi|313126563|ref|YP_004036833.1|  [L=139]
Description: polyketide cyclase/dehydrase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-12   47.3   4.4    3.1e-12   47.0   4.4    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
     0.0013   19.0   0.2     0.0018   18.5   0.2    1.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
       0.03   14.6   0.4      0.054   13.7   0.0    1.6  2  YqjK             YqjK-like protein


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   4.4   5.2e-16   3.1e-12       3     110 ..      16     116 ..      15     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 5.2e-16
                                       EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS.SEEEEEEEEEETTTTEEEEE CS
                   Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr.gtvreelvevdpegrllsyr 78 
                                       ++ v+++ +ap++++w+++   ++wp+W p+v+ v+++++ ++  gv g+v+ +g+  +v  e++++d++ r+++++
  gi|313126563|ref|YP_004036833.1|  16 RLVVTRELDAPADDAWDVLVETRTWPEWGPSVTAVRGPDRISA--GVTGEVQIAGLgLWVPFEVTTFDADARRWTWT 90 
                                       578999***************************9999987777..899********988*********88******* PP

                                       EE.SSS-TSEEEEEEEEECCETEEEEEEEEEE CS
                   Polyketide_cyc2  79 ivkpvpvanyvatwtvtpdgggtrvtwtgefd 110
                                       +   vp     +  +v++ g+ +r +  +e+ 
  gi|313126563|ref|YP_004036833.1|  91 VA-RVP----ATGHRVEALGD-CRCRVGFEIP 116
                                       *3.333....4469*****99.7777666443 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   3.1e-07    0.0018       1     101 [.      23     115 ..      23     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.1e-07
                                       ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...E..EEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCC CS
                    Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaesglsa..dlevgfggltesftarvtldppeeitfklvegdfk 75 
                                       ++apad++++++     +pe+ p ++ v+  ++      a  ++ev+ +gl+     +vt    +            
  gi|313126563|ref|YP_004036833.1|  23 LDAPADDAWDVLVETRTWPEWGPSVTAVRGPDRIS----AgvTGEVQIAGLGLWVPFEVTTFDADA----------- 84 
                                       58*********************777655555544....444899999999999999998888877........... PP

                                       EEEEEEEECTECCEEE......CEEEEEEEEE CS
                    Polyketide_cyc  76 slegkWtieslppnsg......gtrtkvalev 101
                                         + +Wt++ +p + +      ++r++v +e+
  gi|313126563|ref|YP_004036833.1|  85 -RRWTWTVARVPATGHrvealgDCRCRVGFEI 115
                                       .7999999999986557888889999998875 PP

>> YqjK  YqjK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     9e-06     0.054      21      50 ..      22      51 ..       8      66 .. 0.86
   2 ?   -3.5   0.1       2.2   1.3e+04      16      25 ..      84      93 ..      81     103 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9e-06
                              YqjK 21 kalapvDrgwqtlrslrkhlilvsgllall 50
                                      +  ap+D +w++l  +r+++ ++ ++ a+ 
  gi|313126563|ref|YP_004036833.1| 22 ELDAPADDAWDVLVETRTWPEWGPSVTAVR 51
                                      5559**********************9984 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.2
                              YqjK 16 aepwekalap 25
                                      a++w  ++a+
  gi|313126563|ref|YP_004036833.1| 84 ARRWTWTVAR 93
                                      4555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.35s 00:00:00.84 Elapsed: 00:00:00.54
# Mc/sec: 781.52
//
Query:       gi|313126564|ref|YP_004036834.1|  [L=194]
Description: hypothetical protein Hbor_18220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-23   82.3   0.4      5e-23   81.8   0.4    1.1  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.4   2.8e-27     5e-23       4     139 ..      20     159 ..      17     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 2.8e-27
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEE....TTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslr....lpsstadalkeagefvinllsesqealadafsq 76 
                                       v++p+a+v+t  p++  + a++s+    + dPp+++fs +     ++++a++  e+g fv n++ e+ +++++++s+
  gi|313126564|ref|YP_004036834.1|  20 VPRPIAWVSTRAPDGTHNLAPYSFSNVATTDPPTLLFSSGgtgdDRKDSARNAIETGAFVYNVVTEDVAEAMNETSA 96 
                                       89********999999999*********************999989******************************* PP

                                       ...SCCCCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTE CS
                     Flavin_Reduct  77 ksgprtddksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgdda 139
                                            + d+++ ag+t+ +s  + ap++++a +s+eC++ +++e+g +++++geVv+++v+++ 
  gi|313126564|ref|YP_004036834.1|  97 TLE-PDGDEFEHAGVTPADSvVVDAPRVAEATVSFECRLADTLEVGASTVVLGEVVHAHVDESV 159
                                       888.9***************999*************************************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1127.72
//
Query:       gi|313126565|ref|YP_004036835.1|  [L=223]
Description: hypothetical protein Hbor_18230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00025   20.9   0.1    0.00065   19.6   0.1    1.7  1  HTH_1         Bacterial regulatory helix-turn-helix protein, 
     0.0013   18.6   0.1     0.0045   16.9   0.0    2.0  2  HTH_Crp_2     Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.028   14.5   0.0    1.6  1  HTH_20        Helix-turn-helix domain
      0.014   15.3   0.1      0.067   13.1   0.0    2.1  2  MarR_2        MarR family
      0.043   13.7   0.0       0.11   12.4   0.0    1.6  2  HTH_5         Bacterial regulatory protein, arsR family
      0.047   13.8   0.0      0.072   13.2   0.0    1.2  1  Replic_Relax  Replication-relaxation
      0.096   12.6   0.0       0.16   11.9   0.0    1.4  1  TrmB          Sugar-specific transcriptional regulator TrmB
       0.19   11.9   0.0          5    7.3   0.0    2.2  2  DUF2250       Uncharacterized protein conserved in archaea (D


Domain annotation for each model (and alignments):
>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.9e-07   0.00065      20      59 ..      36      79 ..      33      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.9e-07
                                      HHHHTS-HHHHHHHHHHHHHHHTS-SEE...ESSSE.EEE-HHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEeelgvpLfe...Rtgrg.lrLTeaG 59
                                      A +Lg +qp+vsr++++L+++  v+L++    ++++   LT +G
  gi|313126565|ref|YP_004036835.1| 36 ASKLGFAQPHVSRALSELRDRNVVELLVpesQQKGRlYGLTREG 79
                                      89**************************5432333479999999 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06    0.0045      27      52 ..      35      60 ..      32      78 .. 0.91
   2 ?   -4.3   0.0         8   1.8e+04      38      45 ..     149     156 ..     147     160 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                                      HHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 27 lAsmlGltretvsrilseLkreglis 52
                                      +As lG  + +vsr+lseL+++++++
  gi|313126565|ref|YP_004036835.1| 35 IASKLGFAQPHVSRALSELRDRNVVE 60
                                      9***********************98 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 8
                                       HHHHHHHH CS
                         HTH_Crp_2  38 vsrilseL 45 
                                       + r++++L
  gi|313126565|ref|YP_004036835.1| 149 IARLIAAL 156
                                       44444444 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-05     0.028       8      56 ..      13      61 ..       6      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                      S-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  8 ahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +++ R  ++++L r+++  +s +a  l+ ++  +s+ L +L++   ve+
  gi|313126565|ref|YP_004036835.1| 13 SSRYRVSVCKYLDREGPELPSRIASKLGFAQPHVSRALSELRDRNVVEL 61
                                      5699**************************************9999985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05     0.067      16      53 ..      26      61 ..      22      71 .. 0.82
   2 ?   -1.8   0.0       1.3     3e+03       6      18 ..     148     160 ..     145     165 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                                      CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      r+++ +  ++ +a +lg  ++ vsr+l +L ++  ve 
  gi|313126565|ref|YP_004036835.1| 26 REGP-E-LPSRIASKLGFAQPHVSRALSELRDRNVVEL 61
                                      4444.4.89*************************9986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHCTT CS
                            MarR_2   6 aqarvLaaLgrrp 18 
                                       ++ar++aaL++++
  gi|313126565|ref|YP_004036835.1| 148 SIARLIAALRAGE 160
                                       4567777776655 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     5e-05      0.11      13      46 ..      26      60 ..      17      60 .. 0.86
   2 ?   -3.6   0.0       4.8   1.1e+04       7      18 ..     152     163 ..     150     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-05
                                      T.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 13 e.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      + g+   + +a +lg  q+ vS+ L+ Lr+ ++Ve
  gi|313126565|ref|YP_004036835.1| 26 ReGPELPSRIASKLGFAQPHVSRALSELRDRNVVE 60
                                      558999999*********************99996 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
                                       HHHHHTTSSEEH CS
                             HTH_5   7 ILklLaegelcv 18 
                                       ++ +L+ ge+++
  gi|313126565|ref|YP_004036835.1| 152 LIAALRAGETTI 163
                                       567888888887 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.2e-05     0.072      24      74 ..      44      88 ..      33     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                      Replic_Relax 24 ratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqra 74
                                         ++r+L +Lr++ +++ l ++ +++++      Y Lt  G+++l+  r+
  gi|313126565|ref|YP_004036835.1| 44 P-HVSRALSELRDRNVVELLVPESQQKGR-----LYGLTREGKQALTRLRG 88
                                      3.489**************8888455555.....************43333 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     7e-05      0.16      19      53 ..      26      60 ..      14      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7e-05
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      ++gp   + ia++lg  ++ v ++L++L d+ +Ve
  gi|313126565|ref|YP_004036835.1| 26 REGPELPSRIASKLGFAQPHVSRALSELRDRNVVE 60
                                      67888899*************************98 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0022         5       8      52 ..      15      59 ..       9      65 .. 0.89
   2 ?    2.4   0.0     0.074   1.7e+02      75      92 ..      68      85 ..      61      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0022
                           DUF2250  8 elalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLl 52
                                      +  + v+k+l++ +++ +  ia +l   + +v+++l +L++   +
  gi|313126565|ref|YP_004036835.1| 15 RYRVSVCKYLDREGPELPSRIASKLGFAQPHVSRALSELRDRNVV 59
                                      55689**********************************987655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.074
                           DUF2250 75 khHtYYrltreGelllre 92
                                      ++   Y+ltreG+++l +
  gi|313126565|ref|YP_004036835.1| 68 QKGRLYGLTREGKQALTR 85
                                      56677********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1264.73
//
Query:       gi|313126566|ref|YP_004036836.1|  [L=143]
Description: hypothetical protein Hbor_18240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 818.76
//
Query:       gi|313126567|ref|YP_004036837.1|  [L=233]
Description: sensor protein/domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-14   51.9   0.0      9e-14   51.3   0.0    1.2  1  DICT      Sensory domain in DIguanylate Cyclases and Two-comp


Domain annotation for each model (and alignments):
>> DICT  Sensory domain in DIguanylate Cyclases and Two-component system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0     5e-18     9e-14      10     127 ..      90     201 ..      83     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 5e-18
                              DICT  10 salappsplvvskatLlalvraleDllieqkipatlwvklqrekiwqselerYrrlagsssqvyilaarepeeefke 86 
                                       s + + +  ++  +++ a +r++eD++++  +++ l++ +q+ +++ ++ + Yr+la++s +++++a+  p++    
  gi|313126567|ref|YP_004036837.1|  90 SRIDRTTFTSYDGSQMAATSREIEDRAWR-FGRGSLHAGFQHASTLSTQEQVYRDLARKSLDIHAYAV--PDK---- 159
                                       5666677889999****************.6*************************************..333.... PP

                              DICT  87 eptkssepvesvqlepnsqLrrewfLivlsp...qfsslilAqe 127
                                         +  + + ++v+l + +++++ wf++++++   + +++++A+e
  gi|313126567|ref|YP_004036837.1| 160 --DAPPLEGVNVHLVEADEIAKTWFVVYDGNgddESKCALIAEE 201
                                       ..3344556667777777************999999******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1344.41
//
Query:       gi|313126568|ref|YP_004036838.1|  [L=623]
Description: s-layer domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-17   61.3  13.7    0.00063   20.0   0.0    6.9  6  NPCBM_assoc     NPCBM-associated, NEW3 domain of alpha-galact
    1.1e-12   48.0  17.6    0.00055   20.2   0.3    5.2  5  CARDB           CARDB
    1.8e-07   31.3   0.7       0.99    9.2   0.0    4.1  4  DUF4832         Domain of unknown function (DUF4832)
    3.9e-07   30.3  27.5       0.14   12.5   0.1    6.9  5  DUF11           Domain of unknown function DUF11
    1.6e-05   25.0   0.3        2.3    8.4   0.0    4.4  5  Transglut_C     Transglutaminase family, C-terminal ig like d
      9e-05   21.7   0.8      0.012   14.7   0.0    2.6  3  PHTB1_C         PTHB1 C-terminus
     0.0012   18.2   0.8        3.7    6.7   0.0    3.9  4  TRAP_alpha      Translocon-associated protein (TRAP), alpha s
     0.0029   17.3   0.1      0.046   13.5   0.0    2.5  2  PEP-utilizers   PEP-utilising enzyme, mobile domain
     0.0033   17.9   2.7          7    7.2   0.1    4.5  4  MG2             MG2 domain
     0.0057   16.9   0.3         10    6.4   0.0    3.7  3  DUF4625         Domain of unknown function (DUF4625)
     0.0073   16.4   0.1        9.5    6.4   0.0    4.4  4  Fn3-like        Fibronectin type III-like domain
  ------ inclusion threshold ------
      0.061   13.7   0.3         16    5.9   0.1    3.7  3  DUF1081         Domain of Unknown Function (DUF1081)
      0.071   14.0   4.4       0.91   10.5   0.5    4.2  2  DUF756          Domain of unknown function (DUF756)
      0.092   12.9   0.1        0.5   10.6   0.1    2.4  1  DUF4469         Domain of unknown function (DUF4469) with IG-
       0.19   11.5   0.0          1    9.1   0.0    2.2  2  FAS_meander     Fatty acid synthase meander beta sheet domain
       0.51    9.7   9.3        4.5    6.6   0.0    4.2  4  DUF5305         Family of unknown function (DUF5305)
        1.1    9.2   6.0        1.3    9.0   0.6    3.3  3  Neocarzinostat  Neocarzinostatin family
        1.4    9.9  12.2        1.7    9.6   3.6    3.9  3  Pilin           Pilin (bacterial filament)


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00072      0.72       2      78 ..      40     121 ..      39     122 .. 0.66
   2 ?    1.4   0.7      0.38   3.8e+02       6      27 ..     163     184 ..     150     187 .. 0.85
   3 ?    3.9   0.0     0.065        65      48      78 ..     208     238 ..     197     239 .. 0.87
   4 !   10.9   0.3   0.00041      0.41       9      76 ..     280     347 ..     276     350 .. 0.70
   5 !   20.0   0.0   6.3e-07   0.00063       4      78 ..     387     461 ..     384     462 .. 0.92
   6 !   17.8   0.0   3.1e-06     0.003       3      77 ..     498     571 ..     496     573 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00072
                       NPCBM_assoc   2 epGetvtltltvtnd....gtaaatnvslslslPeGWtv.vevspasaaslapGetveatvkVtppagaaaGdyevt 73 
                                       +pG ++t+++ ++nd    ++ a+t+ ++++++ ++  + v ++   +++la G+ v  t+++++p+++  G+y++ 
  gi|313126568|ref|YP_004036838.1|  40 SPGVENTVNFQLVNDpngpENNAITATNVRVRVSDNAPInVLTERLYVSKLADGKPVMKTLRMQVPSDINSGTYRIP 116
                                       56777777777777622222344444444444444444203344445569**************************9 PP

                       NPCBM_assoc  74 akarl 78 
                                       +++++
  gi|313126568|ref|YP_004036838.1| 117 LTVTY 121
                                       99987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.38
                       NPCBM_assoc   6 tvtltltvtndgtaaatnvsls 27 
                                       + tlt+t+ n+g++aa++  ++
  gi|313126568|ref|YP_004036838.1| 163 RGTLTVTMRNTGQEAASDATFT 184
                                       6799**********99987766 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.065
                       NPCBM_assoc  48 apGetveatvkVtppagaaaGdyevtakarl 78 
                                       + G+t +++ + + +++a++G y +++++ +
  gi|313126568|ref|YP_004036838.1| 208 EKGATKTFEYDARLGESAQPGNYSLEGTVAY 238
                                       67999*********************99986 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00041
                       NPCBM_assoc   9 ltltvtndg..taaatnvslslslPeGWtvvevspasaa.slapGetveatvkVtppagaaaGdyevtaka 76 
                                       ++ t+tn+g  ta    v ++   P   t+++v+++ a  sl+p+e++++ ++V++ ++a +G ++  +++
  gi|313126568|ref|YP_004036838.1| 280 IKGTITNTGplTAHSAVVAFQSNSP---TAQAVETEYAIgSLEPNESTSFSFTVSVDSKANPGPRQYGVQV 347
                                       5667777775555555566666667...456677776667***********************95444443 PP

  == domain 5  score: 20.0 bits;  conditional E-value: 6.3e-07
                       NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa.slapGetveatvkVtppagaaaGdyevtakarl 78 
                                       Ge+ tl  t++n+ ++++tn  l+   P+G t++ v+++ a  +l+pGe+ e+ ++V ++++   G ++  +++++
  gi|313126568|ref|YP_004036838.1| 387 GEEGTLSGTLVNTDDDPVTNAVLRFN-PAGQTITPVETEYAIgRLDPGEAREFSFDVEVSSSSSGGPRQFNFQVNY 461
                                       999******************99975.**********999888***********************9998888876 PP

  == domain 6  score: 17.8 bits;  conditional E-value: 3.1e-06
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                       +Ge+ ++++ vtn+ ++++t++s ++  Pe    ++ s a +++l+pGe+ +  +k++++ +a a +y+v++  +
  gi|313126568|ref|YP_004036838.1| 498 AGESGEFRVNVTNTREETLTDISAKIF-PESPLSSSNSEAFIEELEPGESETIVFKLSASGDALAKTYPVKMDFQ 571
                                       89********************99885.555555889999999***************************98765 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.5   0.00017      0.16       7      84 ..      31     119 ..      27     125 .. 0.83
   2 !   14.6   0.4   2.9e-05     0.029       2      83 ..     147     235 ..     146     241 .. 0.86
   3 !   20.2   0.3   5.5e-07   0.00055       5      88 ..     262     351 ..     249     352 .. 0.87
   4 ?    1.2   0.1      0.45   4.5e+02      14      86 ..     383     461 ..     375     475 .. 0.70
   5 !    8.9   0.1    0.0018       1.8      14      82 ..     495     566 ..     486     579 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                                       .EEEC-SEEETTSEEEEEEEEEE..-SSS-..EEEEEEEEEETTEEE.....EEEEESEE-CTEEEEEEEEEE-S.. CS
                             CARDB   7 tntlnpseafvgeentitvtvkN..qGtaa..sgatkvalyldgelv.....gtvtvpsLaagesttvsftwtte.. 72 
                                       +++++  ++++g ent+++++ N  +G ++   +at+v++ ++++       +  +v++La g+ +  ++ ++++  
  gi|313126568|ref|YP_004036838.1|  31 QTIVPQPTVSPGVENTVNFQLVNdpNGPENnaITATNVRVRVSDNAPinvltERLYVSKLADGKPVMKTLRMQVPsd 107
                                       5578889999*************6778877557899999***999888889899999*******9988888888877 PP

                                       -S-CEEEEEEEE CS
                             CARDB  73 ategevtltvvv 84 
                                       +++g++ + ++v
  gi|313126568|ref|YP_004036838.1| 108 INSGTYRIPLTV 119
                                       999999976655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.9e-05
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.......EEEEESEE-CTEEEEEEEEEE- CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.......gtvtvpsLaagesttvsftwtt 71 
                                       p +tv  t + s+a+v    t+tvt +N+G++a+ + + +l  + +         +t  v++ + g+++t ++    
  gi|313126568|ref|YP_004036838.1| 147 PRFTV--TDTNSTATVDGRGTLTVTMRNTGQEAASDATFTLASNNNDIalgggakATRFVSNWEKGATKTFEYDARL 221
                                       56667..6777788888889******************9999999998899999899999**********9999999 PP

                                       S..-S-CEEEEEEE CS
                             CARDB  72 e..ategevtltvv 83 
                                          a++g++ l+ +
  gi|313126568|ref|YP_004036838.1| 222 GesAQPGNYSLEGT 235
                                       88899999988755 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 5.5e-07
                                       EE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S..-S- CS
                             CARDB   5 tvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtte..ate 75 
                                       t +++   s++ v ++ +i+ t++N+G  ++ +  va+  +  ++    ++  + sL+++est+ sft+ ++  a++
  gi|313126568|ref|YP_004036838.1| 262 TFDVSDVQSSVRVADSGKIKGTITNTGPLTAHSAVVAFQSNSPTAqaveTEYAIGSLEPNESTSFSFTVSVDskANP 338
                                       55666778889999999************************9998888888999****************9988888 PP

                                       CEEEEEEEESTT- CS
                             CARDB  76 gevtltvvvDpdn 88 
                                       g  ++ v+v   n
  gi|313126568|ref|YP_004036838.1| 339 GPRQYGVQVNYRN 351
                                       8888888887665 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.45
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEE CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtte..ategevtltvvv 84 
                                       ++ vgee t++ t+ N+ ++  ++  +++   g++     ++  +  L++ge ++ sf + ++   + g  +++++v
  gi|313126568|ref|YP_004036838.1| 383 TLRVGEEGTLSGTLVNTDDDPVTNAVLRFNPAGQTItpveTEYAIGRLDPGEAREFSFDVEVSssSSGGPRQFNFQV 459
                                       5666777777777777766667777777776777666777788889********99999888754444555566666 PP

                                       ST CS
                             CARDB  85 Dp 86 
                                         
  gi|313126568|ref|YP_004036838.1| 460 NY 461
                                       55 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0018
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEE CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtteategevtltv 82 
                                       +  +ge+ +++v+v+N+ +++ ++++++++ +  l    +++ +++L++ges+t+ f+  ++  +   t+ v
  gi|313126568|ref|YP_004036838.1| 495 AYAAGESGEFRVNVTNTREETLTDISAKIFPESPLSssnSEAFIEELEPGESETIVFKLSASGDALAKTYPV 566
                                       45678999*********************998877766688999*************999884444444444 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0     0.003         3     157     203 ..      79     125 ..      37     136 .. 0.76
   2 !    9.2   0.1     0.001         1      99     193 ..     141     232 ..     129     248 .. 0.79
   3 !    9.2   0.0   0.00099      0.99     113     198 ..     267     348 ..     262     360 .. 0.83
   4 ?   -0.3   0.0      0.82   8.2e+02     152     212 ..     414     474 ..     404     478 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.003
                           DUF4832 157 yklkldadprkwlpgttttitiklklpselakGkykvyLnlpdpseg 203
                                         l++   ++k++ g+ + +t+ +++ps++++G+y++ L ++ + e+
  gi|313126568|ref|YP_004036838.1|  79 NVLTERLYVSKLADGKPVMKTLRMQVPSDINSGTYRIPLTVTYEYES 125
                                       35667777888899999999999****************99877665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.001
                           DUF4832  99 irkhLGYRfvlessslskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegee..kyklkldadprkwlpgtt 173
                                       +r + G Rf++++++ +++v   g+ +l++t++N+G  a+    ++ ++l ++++        k++  +++w +g t
  gi|313126568|ref|YP_004036838.1| 141 VRVQSGPRFTVTDTNSTATVD--GRGTLTVTMRNTGQEAA---SDATFTLASNNNDIalGGGAKATRFVSNWEKGAT 212
                                       56666889*****99998886..9************8654...567777777777764422346888899******* PP

                           DUF4832 174 ttitiklklpselakGkykv 193
                                       +t++ ++ l ++ + G+y++
  gi|313126568|ref|YP_004036838.1| 213 KTFEYDARLGESAQPGNYSL 232
                                       **9999***********987 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00099
                           DUF4832 113 slskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklkldadprkwlpgttttitiklklpselakG 189
                                       +++++v+ +++ +++ t++N+G   ++  +++ + +++++ ++ + +++++ + ++ p+++t+++ +++++s+ + G
  gi|313126568|ref|YP_004036838.1| 267 DVQSSVRVADSGKIKGTITNTG---PLTAHSAVVAFQSNSPTA-QAVETEYAIGSLEPNESTSFSFTVSVDSKANPG 339
                                       5667788889999********9...899999999998888877.5899***************************** PP

                           DUF4832 190 kykvyLnlp 198
                                         + ++++ 
  gi|313126568|ref|YP_004036838.1| 340 PRQYGVQVN 348
                                       555555544 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.82
                           DUF4832 152 egeekyklkldadprkwlpgttttitiklklpselakGkykvyLnlpdpseglkdrpeysI 212
                                        g++ + +++++ + ++ pg+  +++ ++++ s+ + G  +  +++  ++e+ ++r+ + I
  gi|313126568|ref|YP_004036838.1| 414 AGQTITPVETEYAIGRLDPGEAREFSFDVEVSSSSSGGPRQFNFQVNYRDEDNQQRTTNPI 474
                                       4556677889999********9999999999999999966666666666666556666666 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.28   2.8e+02      46      84 ..      19      59 ..      13      69 .. 0.67
   2 ?    0.2   0.5      0.97   9.7e+02      24      78 ..      61     104 ..      37     148 .. 0.55
   3 !    7.5  11.0     0.005         5       5      84 ..     153     338 ..     148     344 .. 0.86
   4 !   12.5   0.1   0.00014      0.14       8      84 ..     382     450 ..     367     457 .. 0.89
   5 !    8.8   0.1     0.002         2       9      81 ..     495     558 ..     483     564 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.28
                             DUF11 46 vsvsasqgtasaltsv..gsLeagesatlsftvrvtrtaas 84
                                      v+v a++++ + +t v  +++ +g + t++f++   + + +
  gi|313126568|ref|YP_004036838.1| 19 VPVAAATSNPDIQTIVpqPTVSPGVENTVNFQLVNDPNGPE 59
                                      44444444555666668999999999999999877666543 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.97
                             DUF11  24 NtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrv 78 
                                       N  +a+  +v+v+D  P ++ + +   s           +L+ g+    +++++v
  gi|313126568|ref|YP_004036838.1|  61 NAITATNVRVRVSDNAPINVLTERLYVS-----------KLADGKPVMKTLRMQV 104
                                       4445555556666665533332222222...........3333333333333333 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.005
                             DUF11   5 vdksevrpGdtvtytltvtNtgpasangvvvtDtl.......................................... 39 
                                        ++s+++  +  t t+t++Ntg+ +a++++ t                                             
  gi|313126568|ref|YP_004036838.1| 153 DTNSTATVDGRGTLTVTMRNTGQEAASDATFTLASnnndialgggakatrfvsnwekgatktfeydarlgesaqpgn 229
                                       45567777778899999999999999888876555999999999999999999999999999999999999999999 PP

                             DUF11  40 ................................................................Paglayvsvsasq 52 
                                                                                                        a +a++s+s + 
  gi|313126568|ref|YP_004036838.1| 230 yslegtvaykdasgnsktspsltvgmralpemtfdvsdvqssvrvadsgkikgtitntgpltahSAVVAFQSNSPTA 306
                                       99999999999999999999999999999999999999999999999999999999999776666888888888886 PP

                             DUF11  53 gtasaltsvgsLeagesatlsftvrvtrtaas 84 
                                        + ++++ +gsLe+ es+ +sftv+v  +a+ 
  gi|313126568|ref|YP_004036838.1| 307 QAVETEYAIGSLEPNESTSFSFTVSVDSKANP 338
                                       666666666*****************998876 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00014
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaas 84 
                                       s++r G++ t   t+ Nt  ++ +++v++   Pag ++ +v +        + +g+L +ge + +sf v+v+ +++ 
  gi|313126568|ref|YP_004036838.1| 382 STLRVGEEGTLSGTLVNTDDDPVTNAVLRF-NPAGQTITPVETE-------YAIGRLDPGEAREFSFDVEVSSSSSG 450
                                       4789999999999***************95.8************.......5558****************998775 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.002
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrt 81 
                                       + ++G+  ++ + vtNt   +++++  + + P++    s+s s      +  +++Le+ges t+ f+++++  
  gi|313126568|ref|YP_004036838.1| 495 AYAAGESGEFRVNVTNTREETLTDISAK-IFPESPL--SSSNS------EAFIEELEPGESETIVFKLSASGD 558
                                       5688999999999999999999555554.3455433..22222......33449*************999865 PP

>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.9   5.9e+03      59      82 ..      36      59 ..      30      71 .. 0.78
   2 ?   -1.1   0.0       2.1   2.1e+03       9      35 ..     156     182 ..     150     188 .. 0.74
   3 ?    4.8   0.0     0.029        29      41      75 ..     297     331 ..     259     350 .. 0.71
   4 !    8.4   0.0    0.0023       2.3       7      74 ..     380     442 ..     375     460 .. 0.85
   5 ?    5.7   0.0     0.016        16       9      75 ..     494     554 ..     491     571 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.9
                                      EEEE-TTEEEEEEEEE-HHSHEEE CS
                       Transglut_C 59 eltLePkeeksvrlkilpskyGer 82
                                      + t++P+ e++v ++++    G++
  gi|313126568|ref|YP_004036838.1| 36 QPTVSPGVENTVNFQLVNDPNGPE 59
                                      568999999999999886666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                                       SCEBTTSEEEEEEEEEE-SSS-BEEEE CS
                       Transglut_C   9 esavlgqdltvsvllkNplseelkdvk 35 
                                       ++a +    t++v+++N+ +e+  d++
  gi|313126568|ref|YP_004036838.1| 156 STATVDGRGTLTVTMRNTGQEAASDAT 182
                                       567777888889999998888766655 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.029
                                       EEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE- CS
                       Transglut_C  41 qtveynGvlaaefkkksleltLePkeeksvrlkil 75 
                                        +  +n  +a+ ++++++ ++LeP+e+ s++++++
  gi|313126568|ref|YP_004036838.1| 297 VAFQSNSPTAQAVETEYAIGSLEPNESTSFSFTVS 331
                                       44455555678999****************99986 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0023
                                       ESSCEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE CS
                       Transglut_C   7 vlesavlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlki 74 
                                       + +++++g + t+s +l N+ ++++++      +     +G + + ++++++ ++L+P+e  ++++++
  gi|313126568|ref|YP_004036838.1| 380 LESTLRVGEEGTLSGTLVNTDDDPVTN-----AVLRFNPAGQTITPVETEYAIGRLDPGEAREFSFDV 442
                                       567899*******************99.....88899999**99****************99887665 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.016
                                       SCEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE- CS
                       Transglut_C   9 esavlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlkil 75 
                                       ++ + g + ++ v ++N+ +e+l+d    ++a +   + +  ++++++ +  +LeP+e++++ +k++
  gi|313126568|ref|YP_004036838.1| 494 NAYAAGESGEFRVNVTNTREETLTD----ISAKIFPESPL--SSSNSEAFIEELEPGESETIVFKLS 554
                                       566678888899999*******999....67777777777..5899***************999984 PP

>> PHTB1_C  PTHB1 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.7   2.7e+03      11      74 ..      64     127 ..      61     137 .. 0.59
   2 ?    4.7   0.0     0.014        14      10      86 ..     290     366 ..     281     368 .. 0.81
   3 !   14.7   0.0   1.2e-05     0.012       2      79 ..     506     583 ..     505     591 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
                           PHTB1_C  11 tlenvqlsvqvdkplaaskstfviesldesasteliisvflkgslipaslevevvasYtsktgi 74 
                                       t  nv++ v+ + p+ +  +++  ++l ++++   ++ + +  ++     ++  +++Y+ ++g+
  gi|313126568|ref|YP_004036838.1|  64 TATNVRVRVSDNAPINVLTERLYVSKLADGKPVMKTLRMQVPSDINSGTYRIPLTVTYEYESGT 127
                                       5578889999999999999999999995554444444444433333333444445555544443 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.014
                           PHTB1_C  10 ttlenvqlsvqvdkpl.aaskstfviesldesasteliisvflkgslipaslevevvasYtsktgiprvvqksvkLP 85 
                                        t ++  + +q ++p  +a + ++ i sl++++st+++++v +  ++ p   +  v + Y++ +g p v + +v+LP
  gi|313126568|ref|YP_004036838.1| 290 LTAHSAVVAFQSNSPTaQAVETEYAIGSLEPNESTSFSFTVSVDSKANPGPRQYGVQVNYRNGDGDP-VQSDTVDLP 365
                                       5556666666666665157778899*************************************99998.677788888 PP

                           PHTB1_C  86 l 86 
                                       +
  gi|313126568|ref|YP_004036838.1| 366 V 366
                                       7 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.2e-05
                           PHTB1_C   2 vkvtlkssttlenvqlsvqvdkplaaskstfviesldesasteliisvflkgslipaslevevvasYtsktgiprvv 78 
                                       v+vt + + tl +++  +  ++pl  s+s+ +ie+l++++s++++++   +g+++     v+    Y+ ++g++ ++
  gi|313126568|ref|YP_004036838.1| 506 VNVTNTREETLTDISAKIFPESPLSSSNSEAFIEELEPGESETIVFKLSASGDALAKTYPVKMDFQYEDSQGETTIS 582
                                       78999999****************************************************************99876 PP

                           PHTB1_C  79 q 79 
                                        
  gi|313126568|ref|YP_004036838.1| 583 D 583
                                       5 PP

>> TRAP_alpha  Translocon-associated protein (TRAP), alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.29   2.8e+02     149     181 ..     213     245 ..     203     249 .. 0.89
   2 !    6.7   0.0    0.0038       3.7     143     202 ..     318     377 ..     310     380 .. 0.89
   3 ?    0.6   0.0      0.26   2.6e+02     144     181 ..     431     468 ..     422     473 .. 0.86
   4 ?    4.8   0.0     0.014        14     141     199 ..     539     597 ..     534     614 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.29
                        TRAP_alpha 149 atleYsFipaeafagRPfGlvinlaYkdaeGnq 181
                                        t+eY+    e+ +   + l  ++aYkda+Gn+
  gi|313126568|ref|YP_004036838.1| 213 KTFEYDARLGESAQPGNYSLEGTVAYKDASGNS 245
                                       68999999999999999**************96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0038
                        TRAP_alpha 143 vkPkkqatleYsFipaeafagRPfGlvinlaYkdaeGnqfqeavfnetvnivEveeglDg 202
                                       ++P++ ++++++  +  +    P    ++++Y++ +G   q+   +  v++ E + g+D 
  gi|313126568|ref|YP_004036838.1| 318 LEPNESTSFSFTVSVDSKANPGPRQYGVQVNYRNGDGDPVQSDTVDLPVTVGESDAGFDI 377
                                       679999999999988888888888888999***************************995 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.26
                        TRAP_alpha 144 kPkkqatleYsFipaeafagRPfGlvinlaYkdaeGnq 181
                                        P++   ++++  ++ + +g P  ++ +++Y+d++ +q
  gi|313126568|ref|YP_004036838.1| 431 DPGEAREFSFDVEVSSSSSGGPRQFNFQVNYRDEDNQQ 468
                                       677888899999999999***************98765 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.014
                        TRAP_alpha 141 kvvkPkkqatleYsFipaeafagRPfGlvinlaYkdaeGnqfqeavfnetvnivEveeg 199
                                       ++++P++  t+ ++   +    ++ + ++++++Y d++G++  +  +   v ++E + g
  gi|313126568|ref|YP_004036838.1| 539 EELEPGESETIVFKLSASGDALAKTYPVKMDFQYEDSQGETTISDAYQVPVDVTESDGG 597
                                       567899999999999999999999*******************************9965 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.46   4.6e+02      41      71 ..     133     163 ..     120     164 .. 0.79
   2 !   13.5   0.0   4.6e-05     0.046      22      50 ..     276     306 ..     266     324 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.46
                                       HHHHTT--EEE--SSHH.HH--TEEEEEETT CS
                     PEP-utilizers  41 vArelgiPaVvgvgeatielkegdlitvDgs 71 
                                       + r++g+ + v+ g   ++  ++ ++tvDg+
  gi|313126568|ref|YP_004036838.1| 133 ITRSMGVSVRVQSGPRFTVTDTNSTATVDGR 163
                                       67999999999999988555555******95 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.6e-05
                                       -..GEEEEEES--TTHHHHHHHHHHTT--EE CS
                     PEP-utilizers  22 d..kaaGivterGGmtSHaAivArelgiPaV 50 
                                       d  k++G +t++G  t H+A+vA + + P+ 
  gi|313126568|ref|YP_004036838.1| 276 DsgKIKGTITNTGPLTAHSAVVAFQSNSPTA 306
                                       34499******************99988875 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.031        31      26      81 ..      58     122 ..      32     143 .. 0.70
   2 !    7.2   0.1     0.007         7      52      85 ..     206     242 ..     192     253 .. 0.74
   3 ?   -0.6   0.0       1.9   1.9e+03      13      50 ..     320     359 ..     306     371 .. 0.56
   4 ?    1.2   0.0      0.51   5.1e+02      26      80 ..     447     508 ..     430     523 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.031
                                       TTCSB---EEEEEEEE-TTSSEEEEEEE.....EE-CTTEEEEEEE--TT--SEEEEEEE....E CS
                               MG2  26 etlqglaklplkltirdpdgkevkelpl.....atdetggaesefalpeaaklGeysvel....s 81 
                                       ++ ++++ ++++++++d    +v +++l     a+ +  +   ++++p++   G+y++ l    +
  gi|313126568|ref|YP_004036838.1|  58 PENNAITATNVRVRVSDNAPINVLTERLyvsklADGKPVMKTLRMQVPSDINSGTYRIPLtvtyE 122
                                       55666677888888888888888777777644344444458999**************9944331 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.007
                                       EEEE-CTTEEEEEEE--TT--SEEEEEEE...EECST CS
                               MG2  52 platdetggaesefalpeaaklGeysvel...sadsa 85 
                                        +++ +t ++e++ +l e+a+ G+ys+e     +d  
  gi|313126568|ref|YP_004036838.1| 206 NWEKGATKTFEYDARLGESAQPGNYSLEGtvaYKDAS 242
                                       567889999******************9755433333 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.9
                                       TT-EEEEEEEEES..TTCSB---EEEEEEEE-TTSSEEEE CS
                               MG2  13 PgetVslkallrd..etlqglaklplkltirdpdgkevke 50 
                                       P+e  s+++ + +  ++  g++++ ++++ r+ dg  v++
  gi|313126568|ref|YP_004036838.1| 320 PNESTSFSFTVSVdsKANPGPRQYGVQVNYRNGDGDPVQS 359
                                       4444444444422222223333355555555555555555 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.51
                                       TTCSB---EEEEEEEE-TTSSEEEEEEE.EE-CTTEEEEEEE--......TT--SEEEEEEE CS
                               MG2  26 etlqglaklplkltirdpdgkevkelpl.atdetggaesefalp......eaaklGeysvel 80 
                                       +++ g+++ +++++ rd+d+++  + p+ + ++ g  + ef++       +a + Ge++v++
  gi|313126568|ref|YP_004036838.1| 447 SSSGGPRQFNFQVNYRDEDNQQRTTNPIeVRTDIGAKSDEFEVTpvsnayAAGESGEFRVNV 508
                                       55566666778888888888888888886555556666677665222222344567777776 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.04        40      96     116 ..     100     120 ..      86     137 .. 0.82
   2 ?    6.4   0.0      0.01        10      90     124 ..     211     247 ..     180     252 .. 0.77
   3 ?    1.1   0.1      0.43   4.3e+02      73     106 ..     548     593 ..     459     595 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.04
                           DUF4625  96 eeieiPadaeaGdYhlvirvt 116
                                         +++P+d++ G Y + ++vt
  gi|313126568|ref|YP_004036838.1| 100 LRMQVPSDINSGTYRIPLTVT 120
                                       6799**********9999887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                           DUF4625  90 keyelheeieiPadaeaGdYhl..virvtDasGnete 124
                                        +++++ + +  ++a++G+Y l  ++   DasGn++ 
  gi|313126568|ref|YP_004036838.1| 211 ATKTFEYDARLGESAQPGNYSLegTVAYKDASGNSKT 247
                                       3578888999999*******993346668*****975 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.43
                           DUF4625  73 g............ekewsfeksydlsgskkeyelheeieiPadaea 106
                                       +             k + ++++++ + s+ e+++   +++P d+++
  gi|313126568|ref|YP_004036838.1| 548 TivfklsasgdalAKTYPVKMDFQYEDSQGETTISDAYQVPVDVTE 593
                                       0445555555555788888889999999899999999999988875 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.6   6.6e+03      42      63 ..     259     280 ..     252     285 .. 0.77
   2 ?    0.8   0.0      0.55   5.5e+02      28      44 ..     317     333 ..     313     337 .. 0.87
   3 ?    2.8   0.0      0.13   1.3e+02      29      59 ..     430     472 ..     425     484 .. 0.66
   4 !    6.4   0.0    0.0095       9.5      28      44 ..     540     556 ..     538     582 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.6
                                       ECGGG-EEETTTTEEE--SCEE CS
                          Fn3-like  42 drkdlsvwdeekqkwvvepGey 63 
                                       ++  + v d++++ +v+++G++
  gi|313126568|ref|YP_004036838.1| 259 PEMTFDVSDVQSSVRVADSGKI 280
                                       5667778888888889888876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.55
                                       EE-TT-EEEEEEEEECG CS
                          Fn3-like  28 eLapGesktvtftldrk 44 
                                       +L+p es+  +ft++++
  gi|313126568|ref|YP_004036838.1| 317 SLEPNESTSFSFTVSVD 333
                                       59***********9875 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.13
                                       E-TT-EEEEEEEEECGG............G-EEETTTTEEE-- CS
                          Fn3-like  29 LapGesktvtftldrkd............lsvwdeekqkwvve 59 
                                       L pGe ++ +f++++++            + + de+ q++ + 
  gi|313126568|ref|YP_004036838.1| 430 LDPGEAREFSFDVEVSSsssggprqfnfqVNYRDEDNQQRTTN 472
                                       99***********998745555555555555555555555555 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0095
                                       EE-TT-EEEEEEEEECG CS
                          Fn3-like  28 eLapGesktvtftldrk 44 
                                       eL+pGes+t+ f+l+++
  gi|313126568|ref|YP_004036838.1| 540 ELEPGESETIVFKLSAS 556
                                       49***********9974 PP

>> DUF1081  Domain of Unknown Function (DUF1081)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.86   8.5e+02      47      77 ..     317     347 ..     301     369 .. 0.65
   2 ?    5.9   0.1     0.016        16      40      91 ..     436     490 ..     435     510 .. 0.77
   3 ?    2.0   0.0      0.27   2.7e+02      62     102 ..     538     578 ..     500     589 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.86
                           DUF1081  47 elektdvreytakityelqkeanskvdklkf 77 
                                       +le+++ ++++++++ + + + + ++  ++ 
  gi|313126568|ref|YP_004036838.1| 317 SLEPNESTSFSFTVSVDSKANPGPRQYGVQV 347
                                       5666666666666666665555544444443 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                           DUF1081  40 gptkfavelekt...dvreytakityelqkeanskvdklkfstpaskgsrdteat 91 
                                       ++++f+ve+  +    +r+++++++y+ + +++ +++ ++  t   + s+++e+t
  gi|313126568|ref|YP_004036838.1| 436 REFSFDVEVSSSssgGPRQFNFQVNYRDEDNQQRTTNPIEVRTDIGAKSDEFEVT 490
                                       78999999987643679***********877777777777776666566666665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.27
                           DUF1081  62 yelqkeanskvdklkfstpaskgsrdteatlelkynrdkkt 102
                                        e+ + ++s++  +k+s+ +++ +++  +++ ++y++++  
  gi|313126568|ref|YP_004036838.1| 538 IEELEPGESETIVFKLSASGDALAKTYPVKMDFQYEDSQGE 578
                                       44445777777888888888888888888888888876644 PP

>> DUF756  Domain of unknown function (DUF756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.5   0.00092      0.91      11      42 ..     158     204 ..     117     235 .. 0.71
   2 ?    1.7   0.1       0.5     5e+02      19      34 ..     319     334 ..     264     378 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00092
                            DUF756  11 a.....gnlrltlrNtgk...aaarftVydnaka.......pwtytv 42 
                                       a     g+l++t+rNtg+   + a+ft+ +n++         +t +v
  gi|313126568|ref|YP_004036838.1| 158 AtvdgrGTLTVTMRNTGQeaaSDATFTLASNNNDialgggaKATRFV 204
                                       05566699*********8666777******98777666666444444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.5
                            DUF756  19 rNtgkaaarftVydna 34 
                                        + ++++  ftV    
  gi|313126568|ref|YP_004036838.1| 319 EPNESTSFSFTVSVDS 334
                                       3333344444444443 PP

>> DUF4469  Domain of unknown function (DUF4469) with IG-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0005       0.5      64      97 ..      98     133 ..      63     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                                       TEEEEE--TT--SEEEEEEEEE--..SSSSS--SS- CS
                           DUF4469  64 seLifllPasleaGeYtlevtTqy..ssskkllkep 97 
                                       ++L +++P+++++G+Y++ +t  y  +s++ + k++
  gi|313126568|ref|YP_004036838.1|  98 KTLRMQVPSDINSGTYRIPLTVTYeyESGTGDSKQI 133
                                       6899*************8766555337777777776 PP

>> FAS_meander  Fatty acid synthase meander beta sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.2   2.2e+03      94     119 ..     102     127 ..      52     134 .. 0.71
   2 ?    9.1   0.0     0.001         1      53     127 ..     505     584 ..     491     587 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.2
                       FAS_meander  94 vtlieertaegesvpLeleFeYkpet 119
                                       +++ ++ ++++  +pL+ ++eY+  t
  gi|313126568|ref|YP_004036838.1| 102 MQVPSDINSGTYRIPLTVTYEYESGT 127
                                       44445555566678888888887665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                       FAS_meander  53 lveieeadspektvvtvk....eakesgelkkav.eiklsedkeIsvtlieertaegesvpLeleFeYkpetglapI 124
                                       +v+++++ +++ t +++k    ++ +s++ ++ + e++  e+++I  +l  + +a +++ p++++F+Y+ ++g + I
  gi|313126568|ref|YP_004036838.1| 505 RVNVTNTREETLTDISAKifpeSPLSSSNSEAFIeELEPGESETIVFKLSASGDALAKTYPVKMDFQYEDSQGETTI 581
                                       5777777776666666654442233344444443379999999******************************9999 PP

                       FAS_meander 125 hEv 127
                                       ++ 
  gi|313126568|ref|YP_004036838.1| 582 SDA 584
                                       875 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.9      0.11   1.1e+02      48     108 ..     110     173 ..      96     187 .. 0.67
   2 ?    0.3   0.0      0.37   3.7e+02      44     115 ..     221     294 ..     213     301 .. 0.71
   3 ?    2.1   0.2      0.11   1.1e+02      55     115 ..     455     518 ..     435     524 .. 0.86
   4 ?    6.6   0.0    0.0045       4.5      85     137 ..     562     620 ..     545     623 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                           DUF5305  48 vgtseltvvlevnvegeidg.esieesktsrlpipl.teqtyeikkdetd...eengeitetvtvk 108
                                       +gt ++ ++++ ++  e+   +s ++++++ +++ + ++  ++++++++    +  g++t+t +++
  gi|313126568|ref|YP_004036838.1| 110 SGTYRIPLTVTYEY--ESGTgDSKQITRSMGVSVRVqSGPRFTVTDTNSTatvDGRGTLTVTMRNT 173
                                       55555555555555..44444999********9999888899999877655444445555554444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
                           DUF5305  44 lglsvgtseltvvlevnvegeidgesieesktsrlpiplteqtyeikkdetd...eengeitetvtvkespslae 115
                                       lg s++  + +++ +v +++ + + +++ s t  +   l e t+++++ +++    ++g+i++t+t++ + +  +
  gi|313126568|ref|YP_004036838.1| 221 LGESAQPGNYSLEGTVAYKDASGNSKTSPSLTVGMR-ALPEMTFDVSDVQSSvrvADSGKIKGTITNTGPLTAHS 294
                                       555666666777888888885555555555555554.46888999998888888899*******99999988766 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.11
                           DUF5305  55 vvlevnvegeidgesieesktsrlpiplteqtyeikkdetd...eengeitetvtvkespslae 115
                                        +++vn+ +e +++++++    r++i   ++ +e++  +++    e+ge +++vt++++++l+ 
  gi|313126568|ref|YP_004036838.1| 455 FNFQVNYRDEDNQQRTTNPIEVRTDIGAKSDEFEVTPVSNAyaaGESGEFRVNVTNTREETLTD 518
                                       5789999999999999************999999998888777799999999999999988876 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0045
                           DUF5305  85 qtyeikkdetd.eengeitetvtvkespslae.....gilliilgllaliglvvlirri 137
                                       +ty +k+d +  + +ge+t +   +++ +++e     ++l++i++++ ++g++ ++++ 
  gi|313126568|ref|YP_004036838.1| 562 KTYPVKMDFQYeDSQGETTISDAYQVPVDVTEsdgggLPLGLIALVIVALGAIGFVYYR 620
                                       78999999999888999999999999999999999997888888888888888777764 PP

>> Neocarzinostat  Neocarzinostatin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.6    0.0013       1.3      18      64 ..     125     171 ..     119     196 .. 0.90
   2 ?   -0.3   0.3         1     1e+03      56      85 ..     281     312 ..     231     331 .. 0.65
   3 ?    0.1   0.0      0.77   7.6e+02      48      79 ..     548     580 ..     542     594 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                    Neocarzinostat  18 sgtGftagstlalgeCvavapggvaCnkaagavvtadasGkisaslt 64 
                                       sgtG  ++ t  +g  v+v+ g++    ++++  t+d+ G++++++ 
  gi|313126568|ref|YP_004036838.1| 125 SGTGDSKQITRSMGVSVRVQSGPRFTVTDTNSTATVDGRGTLTVTMR 171
                                       89***************************************998864 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1
                    Neocarzinostat  56 sGkisas..ltvaksFegvlsdGssigavdca 85 
                                       +G+i+ +  lt +++  ++ s+  +  av+++
  gi|313126568|ref|YP_004036838.1| 281 KGTITNTgpLTAHSAVVAFQSNSPTAQAVETE 312
                                       46664433377777777777777777777765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.77
                    Neocarzinostat  48 gavvtadasGki.sasltvaksFegvlsdGssi 79 
                                         v+  +asG + +++  v+  F+   s+G+++
  gi|313126568|ref|YP_004036838.1| 548 TIVFKLSASGDAlAKTYPVKMDFQYEDSQGETT 580
                                       5667799***99899*********999999875 PP

>> Pilin  Pilin (bacterial filament)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.6    0.0017       1.7      47      86 ..     154     197 ..     114     221 .. 0.68
   2 ?    1.6   0.5      0.53   5.3e+02      59      79 ..     278     298 ..     223     364 .. 0.58
   3 ?    1.2   0.0      0.71   7.1e+02      22      84 ..     348     415 ..     339     421 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                                       CEEEEECCCEEC.....CEEEEEECCCSSTCCTTEEEEEEEECT......T CS
                             Pilin  47 gvisvtveaatg.....gtitatfggnaaakikgktltltrtad......s 86 
                                       ++++       +     gt+t+t++++++++++ +t+tl+ +++       
  gi|313126568|ref|YP_004036838.1| 154 TNST-------AtvdgrGTLTVTMRNTGQEAASDATFTLASNNNdialggG 197
                                       1223.......144445************99*********99885655550 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.53
                                       CEEEEEECCCSSTCCTTEEEE CS
                             Pilin  59 gtitatfggnaaakikgktlt 79 
                                       g+i+ t+++++  +++ +++ 
  gi|313126568|ref|YP_004036838.1| 278 GKIKGTITNTGPLTAHSAVVA 298
                                       666666666654333333333 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.71
                                       HHCCCSSSCTCCCCC.....TTBSTCSCCTC....EEEEECCCEECCEEEEEECCCSSTCCTTEEEEEEEEC CS
                             Pilin  22 aalnegktpttaaad.....iGlasstaicg....visvtveaatggtitatfggnaaakikgktltltrta 84 
                                       ++ n+   p+++++      +G ++    +g    + ++t   +++gt++ t+ ++   ++ +++l++++  
  gi|313126568|ref|YP_004036838.1| 348 NYRNGDGDPVQSDTVdlpvtVGESD----AGfdirNLESTLRVGEEGTLSGTLVNTDDDPVTNAVLRFNPAG 415
                                       5555545555444433442222222....22334466777777777**********9999*****9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.84u 0.36s 00:00:01.20 Elapsed: 00:00:00.56
# Mc/sec: 3350.97
//
Query:       gi|313126569|ref|YP_004036839.1|  [L=884]
Description: rnd superfamily exporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-38  131.9  22.8    3.5e-19   68.9   7.6    2.4  2  MMPL            MMPL family
    2.7e-17   62.2  21.7    1.2e-09   36.9   7.3    2.3  2  Patched         Patched family
    6.3e-12   45.6   8.4    7.8e-08   32.3   0.3    2.5  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
     0.0006   19.3  25.9      0.019   14.4  12.6    2.6  2  SecD_SecF       Protein export membrane protein
  ------ inclusion threshold ------
       0.13    9.9  26.5      0.031   11.9  15.8    2.2  2  ACR_tran        AcrB/AcrD/AcrF family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   7.6   9.7e-23   3.5e-19      26     305 ..     125     395 ..      90     407 .. 0.74
   2 !   68.4   7.2   1.4e-22     5e-19      54     305 ..     567     814 ..     530     823 .. 0.78

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 9.7e-23
                              MMPL  26 sdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdflsdpd.vaaafvSkDgkaaralvtlegdpgst 101
                                        d+ +++++  +  +l++ a++a v++ v++  ++++  g +s+ ++++   a+ ++   +++++  v+     + +
  gi|313126569|ref|YP_004036839.1| 125 IDPQATTLD-RQITTLEQ-ATQADVRAAVRQNADNPAFTGTLSNDFNKKSaSASSTIGVVKHSLTSEVSSS---AGQ 196
                                       233333333.33333333.5666666666666555555555555544444455555555555555555555...566 PP

                              MMPL 102 eadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvv 178
                                        + + ++ i++ +++ +++++ ++ v G++++++++  + + +l +++ +++++i++ L+i+yr l+   l+l+t +
  gi|313126569|ref|YP_004036839.1| 197 SGSSPLTPIQQQIQRIVATTDGDITVFGTGIIADEFGAVISDSLLIVTPAAVILIILFLVIAYRDLLD--LLLGTFA 271
                                       67777899999999999*************************************************97..5667777 PP

                              MMPL 179 vsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaa 254
                                       + +++ +++  l la + + ++  +v++    ll+avG+D+ +  + Ryre ++ g   e a+  a  +   + ++ 
  gi|313126569|ref|YP_004036839.1| 272 LAMAVIWTFgFLGLAGIPFNQIMIAVPP----LLLAVGIDFGIHAINRYREDRETGLGIEGAMRVATDQLLVAFFIV 344
                                       7777777762355555555555544444....689**************************************9998 PP

                              MMPL 255 GltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGra 305
                                       + t +i +l+ ++++lp ++ +Gv++++G+ +++li   +lPA  v + r+
  gi|313126569|ref|YP_004036839.1| 345 TGTTVIGFLSNLASDLPPIRDFGVVAGVGITFTFLIFGVFLPAAKVWMDRR 395
                                       8888888888889************************9999*987776666 PP

  == domain 2  score: 68.4 bits;  conditional E-value: 1.4e-22
                              MMPL  54 vdelkkdtkhvgevsdflsdpd...vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvev 127
                                       vd+    ++++ge+ d+l++      a+  +++D++++r++ t+ gd++++ea e ++ +++   + r  +  ++  
  gi|313126569|ref|YP_004036839.1| 567 VDDNGVPDDNLGEIYDYLETSPvssQADRYLAEDHRSTRVVYTVSGDASDKEATEDARIVAD---RFR--SRYDATA 638
                                       555545567789999999998878888999***************99888888665555544...444..5569999 PP

                              MMPL 128 tGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvl 204
                                       tG ++++++++d+  +++ +  +++l   +v L+ +y  l     + l  +v +++a++ v+ +  llg+  + f++
  gi|313126569|ref|YP_004036839.1| 639 TGNTVVFQEVSDLIFSSAVTSLILALGGTVVFLVFIYWLLDGLPSIALANLVPIVVAVAGVAGTMRLLGISFNAFTA 715
                                       ************98777666666665555555555554333333333334556666777777778889********* PP

                              MMPL 205 gllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaia 281
                                       ++l+ l+i+ G+DY + +v R+ +e+++   + +a+ r+v +tg++ +++ +t a+ +  Lv++ l+vl+q+Gv  a
  gi|313126569|ref|YP_004036839.1| 716 TILS-LTIGLGIDYSVHVVHRFLDERKEADLQ-TALERTVVGTGGALMGSMFTTAFGIGVLVLSVLSVLGQFGVLTA 790
                                       9986.89******************9886555.7******************************************* PP

                              MMPL 282 lGvlvdvlivlTllPAllvllGra 305
                                       l+++ ++ ++l +lP+ lv+  r+
  gi|313126569|ref|YP_004036839.1| 791 LSIVYSFVASLVVLPSALVVWDRF 814
                                       **************9999887776 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   6.4   2.4e-11   8.5e-08     258     379 ..     266     388 ..     239     401 .. 0.85
   2 !   36.9   7.3   3.2e-13   1.2e-09     618     807 ..     614     809 ..     589     814 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.4e-11
                           Patched 258 ilgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdmflmvaawkrteakls....vkkrigealseagv 330
                                       +lg ++  +A++  +G+l + G++fn+i+  +P L La+G+D     ++a++r +  ++    ++  +  a  +  v
  gi|313126569|ref|YP_004036839.1| 266 LLGTFALAMAVIWTFGFLGLAGIPFNQIMIAVPPLLLAVGIDF---GIHAINRYREDREtglgIEGAMRVATDQLLV 339
                                       57888999**********************************5...456666666655544568888888888899* PP

                           Patched 331 aitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaav 379
                                       a +i + T v+ F     ++lp i  F ++++v i f+f+   +f+ a+
  gi|313126569|ref|YP_004036839.1| 340 AFFIVTGTTVIGFLSNLASDLPPIRDFGVVAGVGITFTFLIFGVFLPAA 388
                                       ***************************************8666666554 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 3.2e-13
                           Patched 618 tdrtkllkelRsiadkese.lnvtvfdedaafadqlltilpstiqnivlal....lcmfvvallfipelitvlvitl 689
                                       +  +++++  R +ad+++  +++t   +   f +    i +s++++++lal    + ++ + +l+   + ++l+  +
  gi|313126569|ref|YP_004036839.1| 614 ASDKEATEDARIVADRFRSrYDATATGNTVVFQEVSDLIFSSAVTSLILALggtvVFLVFIYWLLDGLPSIALANLV 690
                                       566889999*******9877**************************9998633225566666777677788888999 PP

                           Patched 690 sivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHiayafvrsekd.dakeRvvealealgwPvvqgalST 765
                                        iv    gv+G + l g+   + +   + + iG  +d+s H+ ++f  ++k+ d +  + +++   g  ++ +   T
  gi|313126569|ref|YP_004036839.1| 691 PIVVAVAGVAGTMRLLGISFNAFTATILSLTIGLGIDYSVHVVHRFLDERKEaDLQTALERTVVGTGGALMGSMFTT 767
                                       999999******************99999**********************9999999999999999999999999* PP

                           Patched 766 ilgvlvLlfvdsymvqvFfktvvLvvvigllHgLlilPills 807
                                         g+ vL++   ++   F     L++v +++  L++lP  l 
  gi|313126569|ref|YP_004036839.1| 768 AFGIGVLVLSVLSVLGQFGVLTALSIVYSFVASLVVLPSALV 809
                                       *******999999999999999****************7765 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.3   2.2e-11   7.8e-08      10     141 ..     266     397 ..     262     405 .. 0.83
   2 !   15.7   2.9   2.9e-06      0.01       8     135 ..     684     810 ..     679     822 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2.2e-11
                                       HHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTT.TCHHHHHHHHHHHHCCCC CS
                    Sterol-sensing  10 lagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrs.ldeseriaealgevgpsi 85 
                                       l g++ ++++v+ ++g+l + g++++ i++  +P l+lavg+d     ++ +++  ++ l  +  +  a  +  ++ 
  gi|313126569|ref|YP_004036839.1| 266 LLGTFALAMAVIWTFGFLGLAGIPFNQIMI-AVPPLLLAVGIDFGIHAINRYREDRETgLGIEGAMRVATDQLLVAF 341
                                       5688999***********************.677799******6655555555544441344888888888889999 PP

                                       HHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHH CS
                    Sterol-sensing  86 lltsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirree 141
                                       ++ + t ++ +l  +++d+p ++ F + a v+++++Fl+  +f  a   +  rr+e
  gi|313126569|ref|YP_004036839.1| 342 FIVTGTTVIGFLSNLASDLPPIRDFGVVAGVGITFTFLIFGVFLPAAKVWMDRRKE 397
                                       9999999999999999**********************999888887776666665 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCC CS
                    Sterol-sensing   8 LglagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrsldeseriaealgevgps 84 
                                       ++la ++ ++++va   g + +lg++++  ++  +  l +  g+d +  +v+ + +  ++ d +  + +++  +g +
  gi|313126569|ref|YP_004036839.1| 684 IALANLVPIVVAVAGVAGTMRLLGISFNAFTA-TILSLTIGLGIDYSVHVVHRFLDERKEADLQTALERTVVGTGGA 759
                                       78999999************************.666799************************************** PP

                                       CHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHH CS
                    Sterol-sensing  85 illtsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsl 135
                                       ++ +++t ++ + + +l++++++ +F + +a++++ +F+  +++  + L +
  gi|313126569|ref|YP_004036839.1| 760 LMGSMFTTAFGIGVLVLSVLSVLGQFGVLTALSIVYSFVASLVVLPSALVV 810
                                       ******9988888778999********************999887777655 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   5.3   0.00011      0.39       4     110 ..     211     318 ..     208     387 .. 0.74
   2 !   14.4  12.6   5.2e-06     0.019      13     164 ..     636     795 ..     626     810 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                                       TTT--SSS-EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHH.HHHHHHHHHHHHHHHHHHTT CS
                         SecD_SecF   4 kllkevdkdaekisvetvgpsvskelaekavlallialvliliyvalrFewrvala.aiialvhDviitvgvlsllg 79 
                                        +++++d d+++     +  +++  +  + ++   +a++li++++++++++ + l     al+  vi t g+l l g
  gi|313126569|ref|YP_004036839.1| 211 RIVATTDGDITVFGTGIIADEFGAVISDSLLIVTPAAVILIILFLVIAYRDLLDLLlGTFALAMAVIWTFGFLGLAG 287
                                       5677788888899999999********************************9987515778**************** PP

                                       ----HHHHHH..HHHHTTSSSHHHHHHHHHHHH CS
                         SecD_SecF  80 ievdlatvaa..lLtiiGYSvndtvvvfdrvre 110
                                       i+++  ++a   lL  +G  ++  +   +r re
  gi|313126569|ref|YP_004036839.1| 288 IPFNQIMIAVppLLLAVG--IDFGIHAINRYRE 318
                                       ****99988422555444..4555555555555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.2e-06
                                       EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-H.....HHHHHHHHHHHHHHHHHHHHHHHTT----H CS
                         SecD_SecF  13 aekisvetvgpsvskelaekavlallialvliliyvalrFew.....rvalaaiialvhDviitvgvlsllgievdl 84 
                                       a+++   +v ++vs+ ++ +av +l++al + ++++++++       ++ala ++ +v  v  ++g + llgi ++ 
  gi|313126569|ref|YP_004036839.1| 636 ATATGNTVVFQEVSDLIFSSAVTSLILALGGTVVFLVFIYWLldglpSIALANLVPIVVAVAGVAGTMRLLGISFNA 712
                                       555666788899*****************9999988888865222225666666667777777888999******97 PP

                                       HHHHHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHHHT.TTTH CS
                         SecD_SecF  85 atvaalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslt..tllvvvallllgg.dslk 158
                                        t   l   iG  ++ +v v  r  +++++   +t+ e +  +    L+ ++ t++    +lv+  l +lg+ ++l+
  gi|313126569|ref|YP_004036839.1| 713 FTATILSLTIGLGIDYSVHVVHRFLDERKEADLQTALERTVVGTGGALMGSMFTTAFgiGVLVLSVLSVLGQfGVLT 789
                                       6655555569*****************99999999999999999999*****9999765677777888999888888 PP

                                       HHHHHH CS
                         SecD_SecF 159 dfalal 164
                                        ++++ 
  gi|313126569|ref|YP_004036839.1| 790 ALSIVY 795
                                       888775 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.9     0.003        11     851     978 ..     225     353 ..     134     357 .. 0.69
   2 ?   11.9  15.8   8.7e-06     0.031     337     485 ..     662     807 ..     636     813 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.003
                                       EHHHHHHHHH..HCHHHHHHHHHHHHHHHHHHHHHTSSSTCHHHHTTHHHHHHHHHHHHHHTT--BS.HHHHHH.HH CS
                          ACR_tran 851 tgqaeqeqea..snsllilvalalllvflvLaalyeslsepllilltvPlalvGallalllrglels.viaqvG.li 923
                                       tg  + e  a  s slli+ ++a++l+ l L + y  l++ ll  + + +a++  +  l l+g++++ ++++v  l+
  gi|313126569|ref|YP_004036839.1| 225 TGIIADEFGAviSDSLLIVTPAAVILIILFLVIAYRDLLDLLLGTFALAMAVIWTFGFLGLAGIPFNqIMIAVPpLL 301
                                       44444443332267899999999999999999999999999999999999999999999999998652555564255 PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                          ACR_tran 924 lliGlavkNaillvefakelrekegksleeaileaakeRLrPiLMTalaailGvl 978
                                       l +G+    +i  ++ ++e re  g+ +e a+  a  + L +    + ++++G+l
  gi|313126569|ref|YP_004036839.1| 302 LAVGI--DFGIHAINRYREDRE-TGLGIEGAMRVATDQLLVAFFIVTGTTVIGFL 353
                                       55666..458888888888888.88888888888888888777777777777765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.7e-06
                                       HHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHH..HHHHHHTT--BCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 337 LleaivLvvlvvflFLqnlratlipaiavPlsllgt..favlkalgfslNlltLfgLvlAiGlvvDdAiVvvEnier 411
                                       L ++  +v+lv +  L +   ++  a  vP+++ ++     + +lg+s N++t   L l iGl +D ++ vv   +r
  gi|313126569|ref|YP_004036839.1| 662 LALGGTVVFLVFIYWLLDGLPSIALANLVPIVVAVAgvAGTMRLLGISFNAFTATILSLTIGLGIDYSVHVV---HR 735
                                       44455789999999999999999999999987765421568***************************9885...89 PP

                                       HHHHHTS-HHHHHHH.HHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          ACR_tran 412 kleeegekpleaalk.smkeiqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvaltltPal 485
                                        l e++e  l++al+ ++   +gal  +++  +a+ + +l+l+ +   +  qf++  +l+i+ s + +l++ P++
  gi|313126569|ref|YP_004036839.1| 736 FLDERKEADLQTALErTVVGTGGAL-MGSMFTTAFGIGVLVLSVL--SVLGQFGVLTALSIVYSFVASLVVLPSA 807
                                       9*99777776666550555555555.5667788999999999765..5788999999999999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (884 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.52
# Mc/sec: 5109.21
//
Query:       gi|313126570|ref|YP_004036840.1|  [L=263]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-16   59.2   0.1    4.7e-16   58.4   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    3.8e-05   23.4   0.3    0.00015   21.5   0.1    2.1  2  HTH_IclR        IclR helix-turn-helix domain
     0.0045   16.8   0.1      0.011   15.6   0.1    1.7  1  MarR_2          MarR family
     0.0065   16.5   0.0      0.012   15.7   0.0    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.015   15.2   0.0    1.3  1  PLDc_2          PLD-like domain
      0.017   14.4   0.1      0.023   13.9   0.1    1.2  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
      0.017   15.1   0.0      0.033   14.2   0.0    1.5  1  Cdc6_C          CDC6, C terminal winged helix domain
      0.024   14.7   0.7      0.047   13.8   0.1    1.8  2  HTH_20          Helix-turn-helix domain
      0.042   14.1   0.0       0.11   12.7   0.0    1.6  1  DUF424          Protein of unknown function (DUF424)
      0.085   12.9   0.0       0.22   11.6   0.0    1.7  1  HTH_29          Winged helix-turn helix


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   2.6e-19   4.7e-16       1      67 [.      22      88 ..      22      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 2.6e-19
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      L++lGLs y a+v++aL +lg  ta+ei+  +gvprs+vY + ++Le+ GlVe ++++pk+Yr v++
  gi|313126570|ref|YP_004036840.1| 22 LEHLGLSNYAARVFVALQRLGVGTAKEIHDVAGVPRSQVYGAAEELESLGLVELQQSTPKRYRSVSL 88
                                      789************************************************************9975 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.7     3e+03      36      47 ..      16      27 ..      11      27 .. 0.79
   2 !   21.5   0.1   8.5e-08   0.00015       6      50 ..      32      75 ..      31      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.7
                                      HHHHHHHHHTTS CS
                          HTH_IclR 36 hRlLqtLvelGy 47
                                      h  +  L++lG+
  gi|313126570|ref|YP_004036840.1| 16 HEAIEALEHLGL 27
                                      778889999997 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 8.5e-08
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +++  al + + + t +e+++ +g+p+S v++    L+ lG+ve 
  gi|313126570|ref|YP_004036840.1| 32 ARVFVALQRLGVG-TAKEIHDVAGVPRSQVYGAAEELESLGLVEL 75
                                      6677777777776.99***************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   6.3e-06     0.011       2      56 ..      26      78 ..      18      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.3e-06
                                      T--HHHHHHHHHHHCTTTSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdl.tvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      gl+   arv  aL r +   + t++e+ +  g+++s v  + ++L++ GLve + +
  gi|313126570|ref|YP_004036840.1| 26 GLSNYAARVFVALQRLG---VgTAKEIHDVAGVPRSQVYGAAEELESLGLVELQQS 78
                                      56666788888998888...67******************************9864 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.6e-06     0.012       4      57 ..      25      78 ..      18      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.6e-06
                           DUF2250  4 leedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerveg 57
                                      l  ++ a +v   l++++v  ak i +   +p+++v  + ++Le+lGL+e +++
  gi|313126570|ref|YP_004036840.1| 25 LGLSNYAARVFVALQRLGVGTAKEIHDVAGVPRSQVYGAAEELESLGLVELQQS 78
                                      556677889999*************************************97765 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   8.2e-06     0.015       2      47 ..     140     185 ..     139     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.2e-06
                            PLDc_2   2 iqliksAkksidiatyyf.vsdreildallkaakrgvkvrilldskk 47 
                                       i+l +++++++ +a +++   ++++++al++ a+++v+vr++  s +
  gi|313126570|ref|YP_004036840.1| 140 IELVEQSQERVLFAAPSLlFITDDLVKALRERAANNVDVRVVSES-A 185
                                       789999**********997788999*****************987.3 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.3e-05     0.023       2      95 ..     126     225 ..     125     252 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGH..HHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE- CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselL..eelreeliaaaergvtVllliypdedleeldleevatevrv 76 
                                       vw++++ e v++r+ el+e+ ++ ++ ++ps l+   +l + l+++a + v V ++  +++ ++ +++   +++   
  gi|313126570|ref|YP_004036840.1| 126 VWTIRGHEPVNNRVIELVEQSQERVLFAAPSLLFitDDLVKALRERAANNVDVRVVSESADVRDRFETVPDVSASGP 202
                                       9*******************************996668******************999888888887777665544 PP

                                       S---S..EE...EEETTTEEEEE CS
                    Regulator_TrmB  77 rrsga.pll...vivDrkrgvva 95 
                                        ++++  +    ++vDr+ ++ +
  gi|313126570|ref|YP_004036840.1| 203 DEEPPvDFTgrvLLVDRRVVLLS 225
                                       44444222244466666655555 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.9e-05     0.033      33      75 ..      51      89 ..      45      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                                      T-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEES CS
                            Cdc6_C 33 gvdpltqrevsdllseLemlgileleksskGrregrtrkisLn 75
                                      +v  + +++v+    eLe+lg++el++s      +r+r +sL+
  gi|313126570|ref|YP_004036840.1| 51 DVAGVPRSQVYGAAEELESLGLVELQQS----TPKRYRSVSLD 89
                                      56677799********************....89*******97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.6e-05     0.047      13      57 ..      32      76 ..      20      79 .. 0.89
   2 ?   -3.1   0.1       4.8   8.6e+03      41      52 ..     103     114 ..      86     123 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +r++ aL r +  ta+e+++  ++++++++   ++Le+ gLve++
  gi|313126570|ref|YP_004036840.1| 32 ARVFVALQRLGVGTAKEIHDVAGVPRSQVYGAAEELESLGLVELQ 76
                                      6777777777889*****************************975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHCT CS
                            HTH_20  41 lsyHLrvLeeag 52 
                                       +++ ++ Le a 
  gi|313126570|ref|YP_004036840.1| 103 ANRAFNYLEAAR 114
                                       444444444443 PP

>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.4e-05      0.11      42      90 ..      14      61 ..       8      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.4e-05
                                      -HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEETTEEEEEEE CS
                            DUF424 42 seeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvidgvphaqig 90
                                      se+eai++Le +  +N   + +v+l+ + G+   ++++ ++gvp+ q++
  gi|313126570|ref|YP_004036840.1| 14 SEHEAIEALEHLGLSNYAARVFVALQ-RLGVGTAKEIHDVAGVPRSQVY 61
                                      789***********************.********************98 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.22       9      62 ..      40      93 ..      35      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                            HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn.rlseeqe 62
                                      + Gv+t ++i  + g+ r++vy + +  e  Gl  l+    ++r+r   l+++ +
  gi|313126570|ref|YP_004036840.1| 40 RLGVGTAKEIHDVAGVPRSQVYGAAEELESLGLVELQQ-STPKRYRSvSLDAAHR 93
                                      569999*******************************7.679*****99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1720.16
//
Query:       gi|313126571|ref|YP_004036841.1|  [L=270]
Description: inositol monophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.3e-47  160.9   2.2    5.4e-47  160.6   2.2    1.0  1  Inositol_P  Inositol monophosphatase family


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.6   2.2     3e-51   5.4e-47       8     264 ..      19     265 ..      12     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 3e-51
                                       HHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSS CS
                        Inositol_P   8 aavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekselted 84 
                                       +a ++aa+ + v +  f+ +++  eeks  +++d+v++ad a+++ il+++a+++p+++++gee+  + e   ++e 
  gi|313126571|ref|YP_004036841.1|  19 VAEAAAAAGADVAMAMFE-RDIETEEKS--SKTDVVSEADGAAQDEILTTIADHYPDDVVVGEEGNTPKE---IPET 89 
                                       455555555556666665.777777776..**********************************999999...7777 PP

                                       SEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEE CS
                        Inositol_P  85 gltwivDPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflngeklplsrappiseallv 161
                                       g  w+vDPiDGT+n+++g+  ++ +++ + +  pv++++  P++g +y a + + +  ng +  +s++++ ++++++
  gi|313126571|ref|YP_004036841.1|  90 GDSWVVDPIDGTSNYLHGFTVWCQAVAAVRDASPVAAAVTRPAVGDTYVADDTEFR-KNGDPTTVSDESDPERFVVA 165
                                       778*********************************************98866654.89999999999977777776 PP

                                       EEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEEEEEC.EBHHHHHHHHHHHHHTTEEEEE CS
                        Inositol_P 162 tlfavssrkdtseasllekvesavsaegvrsvgssalklaavaeGkadaylefgrekkWDhAAGeaileeaGGvvtd 238
                                        +++v ++++ +  s++e   + + +   r++gs++l la+va+G++d+ l +gr ++WD+ AG+  ++ aGG+vtd
  gi|313126571|ref|YP_004036841.1| 166 PTLRVGDDNRDQYLSVIETCFADLGDL--RRIGSAQLTLAMVAAGSIDVALGIGRSHPWDTVAGVHMIRTAGGTVTD 240
                                       655555544444446666666666555..************************************************ PP

                                       SSSCSSSTTSSEEEEESCHHHHHHHH CS
                        Inositol_P 239 akgegrlllargiiaanqkelaella 264
                                       ++g+++ + + g++a+n ++ +++++
  gi|313126571|ref|YP_004036841.1| 241 LDGNPWRHDSDGLVASN-GQAHDAVL 265
                                       ****************9.66666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1720.82
//
Query:       gi|313126572|ref|YP_004036842.1|  [L=81]
Description: hypothetical protein Hbor_18300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.01   16.2   1.8      0.016   15.6   1.7    1.4  1  MrpF_PhaF  Multiple resistance and pH regulation protein F (M


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.7   8.8e-07     0.016       9      48 ..      27      66 ..      21      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.8e-07
                         MrpF_PhaF  9 llgtllvallallailtgrpayldvalvlAllgFvgtvaf 48
                                      l++tl++++l++ + ++g +++ +v l+lAl gFv  +++
  gi|313126572|ref|YP_004036842.1| 27 LIVTLGTGFLLVRGPFLGGTLLKPVPLMLALAGFVVGIVV 66
                                      89*********************************88775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 531.15
//
Query:       gi|313126573|ref|YP_004036843.1|  [L=93]
Description: acylphosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-25   89.5   0.1    1.6e-25   89.3   0.1    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.1   8.7e-30   1.6e-25       2      85 .]       9      91 ..       8      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 8.7e-30
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++v+GrVQgv++R+ +r++A+++ ++G+v+Nl+dg+Ve+v+eg+e++ve+++e++++g+++a v++veve ++ ++e 
  gi|313126573|ref|YP_004036843.1|  9 HVFVSGRVQGVYYRASTRDAARNRDIEGWVKNLDDGRVEAVFEGSENAVEEMIEWCHTGSEAADVESVEVEYEAPKGE- 86
                                      789*******************************************************************98888887. PP

                   Acylphosphatase 81 kdFei 85
                                      ++F+i
  gi|313126573|ref|YP_004036843.1| 87 SGFRI 91
                                      99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 586.49
//
Query:       gi|313126574|ref|YP_004036844.1|  [L=460]
Description: phosphomannomutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-34  117.5   0.0      7e-34  116.5   0.0    1.5  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    4.7e-18   65.7   0.2    4.7e-18   65.7   0.2    2.7  3  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    4.2e-12   46.1   0.1    1.7e-11   44.1   0.1    2.1  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
    0.00078   19.6   0.0     0.0021   18.3   0.0    1.7  2  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   0.0   1.6e-37     7e-34       2     133 ..       2     128 ..       1     132 [. 0.95

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 1.6e-37
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fgt+G+Rg v  + +tpel++++g+a++    a++++++vvvGrD+R+s++ la+a+ agl ++G++v+++g++p
  gi|313126574|ref|YP_004036844.1|   2 ELFGTAGIRGDVV-TRVTPELALSVGRAVGMDAVASDGRAEVVVGRDGRTSGPALASAVEAGLESAGADVHRVGVVP 77 
                                       58**********9.669************98888889**************************************** PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCC CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiek 133
                                       tPa++fa r      gim+taSHnpp++ngiKv+   G ++++  e+ +e+++++
  gi|313126574|ref|YP_004036844.1|  78 TPALAFASRG---RRGIMLTASHNPPTDNGIKVFVD-GEEYDRTLERGVEERVAS 128
                                       *********9...68********************9.9*********99999876 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.2   1.1e-21   4.7e-18       2     103 .]     149     255 ..     148     256 .. 0.92
   2 ?   -3.4   0.2       3.5   1.6e+04      88     100 ..     272     284 ..     271     287 .. 0.79
   3 ?   -0.8   0.0      0.53   2.4e+03      69      89 ..     309     329 ..     298     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 1.1e-21
                                       HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHG CS
                        PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielv 78 
                                       +Y +a+ + +  +    +gl +v+d+++G ++  ++++l+elg++vv+ln + d++fp++ + p++ e+l +l +  
  gi|313126574|ref|YP_004036844.1| 149 DYRNAVIDYARDHGADADGLNIVVDCGNGMSALGTPQVLRELGARVVTLNGQVDGHFPGRESKPTP-ETLTDLRAFL 224
                                       588888888888899999*****************************************9999999.9999998888 PP

                                       GGG......G-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  79 kke......gadlglafDgDaDRlgvvderG 103
                                        ++      ++d+g+a+DgD DR+++v ++G
  gi|313126574|ref|YP_004036844.1| 225 ADDetepggDFDFGIAHDGDSDRIVIVGPDG 255
                                       888899*9899****************7766 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.5
                                       EE-TTS-BEEEEE CS
                        PGM_PMM_II  88 afDgDaDRlgvvd 100
                                       + D DaD  +vv+
  gi|313126574|ref|YP_004036844.1| 272 VRDSDADDPVVVT 284
                                       5699***999996 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.53
                                       -TTTTHHHHGGGGG-SEEEEE CS
                        PGM_PMM_II  69 ealkllielvkkegadlglaf 89 
                                        al++ i++++++g d+++a 
  gi|313126574|ref|YP_004036844.1| 309 GALHEGIAAAREDGGDVVFAA 329
                                       5789999***********996 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.1   3.8e-15   1.7e-11       7      70 ..     390     452 ..     376     457 .. 0.72

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 3.8e-15
                                       CC-TT...EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHH CS
                        PGM_PMM_IV   7 eekak.vvaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeeva 70 
                                       +++++  ++a++++    ++  g++  l d++++ vRpSGTep++rvy+Ea++ ++l   a +v+
  gi|313126574|ref|YP_004036844.1| 390 ASLETtLPDAFPDADV--DTEHGVRLELPDASWVLVRPSGTEPYVRVYAEADDVDALVGEASDVV 452
                                       3333344566666633..699*******************************7776655555444 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       3.6   1.6e+04      29      46 ..     178     195 ..     174     197 .. 0.80
   2 !   18.3   0.0   4.6e-07    0.0021       2     100 ..     260     360 ..     259     373 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.6
                                       TS-THHHHHHHHTT-EEE CS
                       PGM_PMM_III  29 mtslalervakklgiklv 46 
                                       m+ l++ +v+++lg+++v
  gi|313126574|ref|YP_004036844.1| 178 MSALGTPQVLRELGARVV 195
                                       788888999999999886 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.6e-07
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTT...ECEEEETTCEEE CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeeg...avlGgEeSghii 75 
                                        d ++a++a+++ ++  +++ +vv+t   s  +++ ++++g+++ +++ G  + + +  +e+   +v++ E   hi 
  gi|313126574|ref|YP_004036844.1| 260 EDTVVAIVAEHFVRDSDADDPVVVTTPNASGRIDERVREAGGRVERVRLGALHEGIAAAREDggdVVFAAEPWKHIH 336
                                       589999****998874555558****************************7765544444323579*****999998 PP

                                       ETTTBSS--HHHHHHHHHHHHHHHT CS
                       PGM_PMM_III  76 fldeattkDGilaallvleilaetg 100
                                        +    + DG+ +a+ +  ++ae+g
  gi|313126574|ref|YP_004036844.1| 337 PGLG-GWIDGVASAAVLTRLVAESG 360
                                       8744.58999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2932.79
//
Query:       gi|313126575|ref|YP_004036845.1|  [L=376]
Description: nucleoside-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-63  214.6   4.9    4.4e-63  213.1   4.9    1.6  1  Bmp           ABC transporter substrate-binding protein PnrA-
    2.6e-08   33.8   1.7    4.4e-08   33.0   1.7    1.3  1  Peripla_BP_4  Periplasmic binding protein domain
    0.00068   19.4   1.2    0.00068   19.4   1.2    1.9  2  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.1   4.9   7.4e-67   4.4e-63       5     299 ..      63     372 ..      59     375 .. 0.84

  Alignments for each domain:
  == domain 1  score: 213.1 bits;  conditional E-value: 7.4e-67
                                       EEECSS-TTTSCHHHHHHHHHHHHHHHCTTEEEEEEEEC..GGGHHHHHHHHHHCTT-SEEEEESCCHHHHHHHHHH CS
                               Bmp   5 avlvegtidDksfnessyeGirrlkkeqnieliskessll.tdedyiadlknlkeegsdlivatgfalqdalqevss 80 
                                       +v + g + Dksfn  +  Gi+r+k+e +ie  +++ s++       + + + ++  +dli  +gfa++ al+++s+
  gi|313126575|ref|YP_004036845.1|  63 MVYALGGLGDKSFNDAAKRGIERAKSELGIEYNEAQPSAAeEFPTFQRRFAQSANPDYDLICCIGFAQKSALKQTSK 139
                                       677789*************************999998886344566788999999********************** PP

                                       H-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEEC.............SS-SCCCHHCHH CS
                               Bmp  81 dfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmsktnkigfvg.............Gveipvvksfin 144
                                       +fp++kF+ +D +++ +  nv+s++F++ eg+FL+G++a+l++ ++     g             G e p++k+f +
  gi|313126575|ref|YP_004036845.1| 140 NFPDQKFMLVDDQIDRD--NVASYTFKEHEGSFLVGHLAGLLTTQQFEAGAGstsgnskkvgfvgGREAPLIKKFQA 214
                                       *****************..*********************9986554444444555555555555************ PP

                                       HHHHHHHHH-TT-EEEEEE-SSSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES--CG CS
                               Bmp 145 gFeaGikyvnpdievvvkvagtfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsnyvIgvdkdqsy 221
                                       gFeaG+k +++++ v++ +ag+fsD++kgk++A+s+y++g+d++++aag++g gv++aa+e+g+   +Igvd+dqs+
  gi|313126575|ref|YP_004036845.1| 215 GFEAGAKHADEELTVSTAYAGSFSDSAKGKEIATSMYEDGADIVYHAAGGTGLGVFQAAQEQGKF--AIGVDSDQSK 289
                                       ***************************************************************99..********99 PP

                                       CSTT..CCEEEEEEEHHHHHHHHHHHHHCCT---TTEEEEE-CCCTSEEE-...S--TCCHHHHCHHHHHH.HHHHH CS
                               Bmp 222 lape..nvitsiiknvedlvvsiiekvakgevlaggevitlglkegvvgld...eesdvledekvkeqlkk.enkki 292
                                         p+  nvi+ +++++ +++v+   + + + + +gge  tlgl++ +++ +   e       e+vk ++++ ++ +i
  gi|313126575|ref|YP_004036845.1| 290 TDPNyaNVILASMVKRVETAVHTSVENITEDEYNGGEKTTLGLEKNGIECVygqE-IGGGIPEDVKTAVSEsRQAII 365
                                       98874479998888888877777766666666*****************987742.333333444444333033444 PP

                                       CCCCHHS CS
                               Bmp 293 ikeisvp 299
                                        + isvp
  gi|313126575|ref|YP_004036845.1| 366 DGDISVP 372
                                       4455655 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   1.7   7.4e-12   4.4e-08       9     220 ..      71     287 ..      63     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 7.4e-12
                                       STC.HHHHHHHHHHHHHHHTTCEEEEEECSTT-H.HHHHHHHHHHHHTT-SEEE.E--SSHHHHHHHHHHHHHTT-E CS
                      Peripla_BP_4   9 snp.ffsaaregleeaakelgaevtvvgdaenda.aeQvaqiedaiakgvdgii.vapvdstalapalkkakaaGIp 82 
                                       ++  f +aa+ g+e a  elg+e++  +++ ++   + +  + +  +  +d+i+ +  ++ +al+++ k   ++  +
  gi|313126575|ref|YP_004036845.1|  71 GDKsFNDAAKRGIERAKSELGIEYNEAQPSAAEEfPTFQRRFAQSANPDYDLICcIGFAQKSALKQTSKNFPDQ--K 145
                                       555599*******************999999999999998888888999****99999****************..9 PP

                                       EEEESTTGCTTT-CEEEEEC-HHHH...HHHHHHHHHHHCTTH........EEEEEETSCCCHHHHHHHHHHHHHHH CS
                      Peripla_BP_4  83 Vvafdsddapsgerlayvgfdneaa...Gelqaeylaeklggk.......kgkvvilaGspgdpnaeeriegfrkvl 149
                                       ++ +d + ++ +++++y     e +   G+l++ +  ++  ++       ++kv  + G   +p  +++ +gf++  
  gi|313126575|ref|YP_004036845.1| 146 FMLVDDQ-IDRDNVASYTFKEHEGSflvGHLAGLLTTQQFEAGagstsgnSKKVG-FVGGREAPLIKKFQAGFEAGA 220
                                       9******.99999999988776654444*****8888888888888888556666.669999**************9 PP

                                       HH-T.TCEECCEEESTTTCHHHHHHHHHHHHHTTTECEEEESSCCHHHCHHHHHHHTTTTSTEEEEEES-HH CS
                      Peripla_BP_4 150 keyp.gikivaevaganwdaekaqqalealltanpldgilaandgmaegalealeaaglagkvvvtgqDatp 220
                                       k +  ++++ + +ag   d +k+++ ++++      d ++ a +g+++g+ +a ++   +gk+  +g+D+++
  gi|313126575|ref|YP_004036845.1| 221 KHADeELTVSTAYAGSFSDSAKGKEIATSMYEDG-ADIVYHAAGGTGLGVFQAAQE---QGKF-AIGVDSDQ 287
                                       996669**999888988***************88.89*******************...5566.99999886 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.2   1.1e-07   0.00068       2      24 ..       1      23 [.       1      25 [. 0.81
   2 ?   -4.4   1.3         3   1.8e+04      17      21 ..     262     266 ..     261     269 .. 0.32

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      ++RR FLK++++a+ A+++g  +
  gi|313126575|ref|YP_004036845.1|  1 MDRRKFLKATGVAGIAGLAGCSG 23
                                      79************888666544 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 3
                        TAT_signal  17 Aaalg 21 
                                       A+++g
  gi|313126575|ref|YP_004036845.1| 262 AGGTG 266
                                       22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2333.35
//
Query:       gi|313126576|ref|YP_004036846.1|  [L=528]
Description: nucleoside ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-45  153.8   0.0      1e-28  100.6   0.0    2.2  2  ABC_tran     ABC transporter
    8.7e-10   38.9   0.0    0.00015   21.7   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00011   21.9   0.5      0.028   14.1   0.0    3.0  4  AAA_29       P-loop containing region of AAA domain
    0.00044   20.1   0.0       0.86    9.2   0.0    2.1  2  AAA_15       AAA ATPase domain
    0.00079   19.3   1.8     0.0021   18.0   0.1    2.4  3  Bac_DnaA     Bacterial dnaA  protein
     0.0019   17.9   0.2       0.04   13.6   0.0    2.4  2  AAA_30       AAA domain
     0.0032   16.9   0.1          4    6.8   0.0    2.9  3  SMC_N        RecF/RecN/SMC N terminal domain
     0.0054   16.7   0.1        0.1   12.5   0.0    2.5  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.014   15.9   0.0      0.027   14.9   0.0    1.4  1  AAA_23       AAA domain
      0.066   12.0   0.2       0.44    9.3   0.0    1.9  2  DLIC         Dynein light intermediate chain (DLIC)
      0.071   12.7   0.0       0.16   11.5   0.0    1.5  1  AAA_27       AAA domain
      0.076   13.4   0.0       0.25   11.7   0.0    1.9  1  AAA_16       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   6.7e-32     1e-28       2     137 .]      21     171 ..      20     171 .. 0.94
   2 !   51.2   0.0   1.2e-16   1.8e-13       2     136 ..     276     431 ..     275     432 .. 0.85

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 6.7e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++v+l++++g+++a++GenGaGK+tL+++l+gl++pteG++ ++g++ k   ++   ++ +g+++q+  l + +tv 
  gi|313126576|ref|YP_004036846.1|  21 DDVDLTVERGTVHALLGENGAGKTTLMNVLYGLYRPTEGRVVIEGTERKFsSPKDAIKAGVGMIHQHFMLVDPMTVT 97 
                                       689*****************************************99999988999************99999999** PP

                                       HH..................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en                   ++++++++ +++g + +++ ++    + +S G +qrv++ ++l + +++l+lDEpt
  gi|313126576|ref|YP_004036846.1|  98 ENivlgneprkwfglavdreGARRDVQALSDRYGFDVDPEATI----EDVSVGVQQRVEILKTLYRGADILILDEPT 170
                                       *******999999998877666666999999999999999999....*****************************9 PP

                                       T CS
                                       x RF
                          ABC_tran 137 a 137
                                       a
  gi|313126576|ref|YP_004036846.1| 171 A 171
                                       7 PP

  == domain 2  score: 51.2 bits;  conditional E-value: 1.2e-16
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS...--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe...pqlfpel 74 
                                       ++vs++++ege+ +i G  G G S L++ ++gl +pt G++++ g d+++  +  + ++ ++++p++     l  + 
  gi|313126576|ref|YP_004036846.1| 276 SDVSFTVREGEVFGIAGVDGNGQSELIESITGLRTPTDGSVTYLGSDITDaPRSDRIDAGMAYIPEDrheRGLVMDF 352
                                       69************************************************777889999******995554455555 PP

                                       BHHHH....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEE CS
                                       xxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpklll 131
                                        + +n                    + ++++e+++++++       + + +++sLSgG +q+    r + ++p+l++
  gi|313126576|ref|YP_004036846.1| 353 DLVQNgilgsqhskpfaergnidwgTTRRHAEAIIDEYDVRP---PNPDANAESLSGGNQQKFIAGREFERNPELVV 426
                                       544559999999999999999988777788999999999777...3334478***********99999999999998 PP

                                       EESTT CS
                                       xxxxx RF
                          ABC_tran 132 lDEpt 136
                                       +  pt
  gi|313126576|ref|YP_004036846.1| 427 ATHPT 431
                                       76666 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.016       2      24 ..      33      55 ..      32      82 .. 0.79
   2 !   21.7   0.0     1e-07   0.00015     227     297 ..     133     200 ..      99     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       +l G Ng+GK++L+  l++l r
  gi|313126576|ref|YP_004036846.1| 33 HALLGENGAGKTTLMNVLYGLYR 55
                                      689*****************976 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1e-07
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       + + e ++ ++S G+++   +l  l+r +   ++l++DEp + L P+ ++ l+++l+el++ g  +i+ TH
  gi|313126576|ref|YP_004036846.1| 133 DVDPEATIEDVSVGVQQRVEILKTLYRGA---DILILDEPTAVLTPQEVEDLFDVLEELTDQGKTIIFITH 200
                                       5667889999******999********99...*************************************** PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.9e-05     0.028      15      40 ..      23      48 ..      18      60 .. 0.77
   2 ?   -3.7   0.0         7     1e+04      38      50 ..     165     177 ..     165     178 .. 0.84
   3 ?    4.6   0.0     0.018        27      16      50 ..     279     313 ..     272     318 .. 0.79
   4 ?   -4.2   0.0       9.8   1.5e+04       7      15 ..     374     382 ..     374     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                            AAA_29 15 htieidlkg.atlltGpsGsGKSTllD 40
                                       ++++++ g ++ l G++G+GK+Tl+ 
  gi|313126576|ref|YP_004036846.1| 23 VDLTVER-GtVHALLGENGAGKTTLMN 48
                                      5566764.4599*************94 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7
                            AAA_29  38 llDAiqalLvpak 50 
                                       +lD  +a+L+p++
  gi|313126576|ref|YP_004036846.1| 165 ILDEPTAVLTPQE 177
                                       6888899***986 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.018
                            AAA_29  16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                       ++++++ +++ ++G  G+G S l+ +i+ l +p+ 
  gi|313126576|ref|YP_004036846.1| 279 SFTVREGEVFGIAGVDGNGQSELIESITGLRTPTD 313
                                       55666444999****************99988876 PP

  == domain 4  score: -4.2 bits;  conditional E-value: 9.8
                            AAA_29   7 vNWgtfdgh 15 
                                       ++Wgt ++h
  gi|313126576|ref|YP_004036846.1| 374 IDWGTTRRH 382
                                       68**99876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00057      0.86      25      48 ..      32      55 ..      20      79 .. 0.78
   2 !    8.8   0.0   0.00081       1.2     291     364 ..     137     200 ..      95     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00057
                            AAA_15 25 ltvliGkNnsGKSsilealdlFln 48
                                      +  l G+N++GK++++++l+ +  
  gi|313126576|ref|YP_004036846.1| 32 VHALLGENGAGKTTLMNVLYGLYR 55
                                      66899**************97765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00081
                            AAA_15 291 elplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       e ++++++ Gvq+ + ++  +++           +il+++EP a L pq  + l++ l el +++k  +i+ TH
  gi|313126576|ref|YP_004036846.1| 137 EATIEDVSVGVQQRVEILKTLYRGA---------DILILDEPTAVLTPQEVEDLFDVLEELTDQGK-TIIFITH 200
                                       5667777777777777766665544.........56*****************************9.7888888 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.3   1.9e+03      40      53 ..      36      49 ..      33      60 .. 0.87
   2 !   18.0   0.1   1.4e-06    0.0021      86     172 ..     149     232 ..     137     269 .. 0.81
   3 ?   -1.3   0.0       1.1   1.6e+03     118     167 ..     440     488 ..     437     500 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                                      E-SSSSSHHHHHHH CS
                          Bac_DnaA 40 ygevGlGktHLlka 53
                                       ge G Gkt L++ 
  gi|313126576|ref|YP_004036846.1| 36 LGENGAGKTTLMNV 49
                                      699********986 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.4e-06
                                       T-HHHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE CS
                          Bac_DnaA  86 kkaeefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvd 162
                                       +++e +k  +r +D+L++D+   + + ++  e+lf ++++l+++gk +++ + +  ++++  +d   + ++ G +v 
  gi|313126576|ref|YP_004036846.1| 149 QRVEILKTLYRGADILILDEPTAVLTPQE-VEDLFDVLEELTDQGKTIIFITHKLGEAMHAADDV--TVLRDGKNVG 222
                                       667889**************988887775.589**********************9999999884..3444555555 PP

                                       -----HHHHH CS
                          Bac_DnaA 163 ieppdletrl 172
                                         +++  tr 
  gi|313126576|ref|YP_004036846.1| 223 TVKTEDTTRE 232
                                       5555555555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.1
                                       HHHH.HHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE----- CS
                          Bac_DnaA 118 elfh.tfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppd 167
                                       e++h  + +l ++gk v+l s +   e++ l drl   ++ G  +d+ +pd
  gi|313126576|ref|YP_004036846.1| 440 EFIHdRLLELRDSGKAVLLVSSKL-DEVQGLSDRLAV-MHDGEFMDVVDPD 488
                                       555535778999999999999886.689999999965.4555556665555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.7e-05      0.04      15      51 ..      27      63 ..      22      73 .. 0.84
   2 ?    1.5   0.1      0.14     2e+02      81     122 ..     148     198 ..      98     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                       ++  v++l G  G+GKtt++++l  +++  +grv++
  gi|313126576|ref|YP_004036846.1| 27 VERGTVHALLGENGAGKTTLMNVLYGLYRPTEGRVVI 63
                                      4555799*********************999777765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                            AAA_30  81 k......grarlepg.tllivDEagmv....dtkqlaallkaaekagakvilv 122
                                       +      +  +l +g ++li DE   v      ++l ++l++++++g ++i++
  gi|313126576|ref|YP_004036846.1| 148 QqrveilK--TLYRGaDILILDEPTAVltpqEVEDLFDVLEELTDQGKTIIFI 198
                                       34555432..3444559******998876666777788888888888888876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0026         4      25      44 ..      31      50 ..      18      58 .. 0.78
   2 !    6.0   0.0    0.0047       7.1     156     207 ..     158     210 ..     154     223 .. 0.76
   3 ?   -0.4   0.0      0.42   6.3e+02      27      44 ..     288     305 ..     276     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0026
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                       + a++G+NG+GK+ l++ +
  gi|313126576|ref|YP_004036846.1| 31 TVHALLGENGAGKTTLMNVL 50
                                      46899**********99865 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0047
                                       CS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                             SMC_N 156 vkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadk 207
                                       ++ a + +lDe  a L  ++v+ + ++l+e +++   +i i+++ +   +a  
  gi|313126576|ref|YP_004036846.1| 158 YRGADILILDEPTAVLTPQEVEDLFDVLEELTDQgKTIIFITHKLGEAMHAAD 210
                                       5667789*************************994556668888654444433 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.42
                                       EEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAi 44 
                                         i G  G G s l+++i
  gi|313126576|ref|YP_004036846.1| 288 FGIAGVDGNGQSELIESI 305
                                       5699*************9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   6.9e-05       0.1      99     121 ..      30      52 ..      20      65 .. 0.86
   2 ?    1.0   0.0      0.23   3.5e+02      88     121 ..     273     307 ..     255     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.9e-05
                                       TSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                       + + +l+G+ G+GK+tL+n+l +
  gi|313126576|ref|YP_004036846.1|  30 GTVHALLGENGAGKTTLMNVLYG 52 
                                       57899***************976 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.23
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       e++++++  +++ ++  ++G  G G S Li+++++
  gi|313126576|ref|YP_004036846.1| 273 EAVSDVSFTVREgEVFGIAGVDGNGQSELIESITG 307
                                       455566667776699999************99986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.8e-05     0.027      21      43 ..      32      53 ..      16      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                            AAA_23 21 ltlItGpNGaGKTTildAiklaL 43
                                      + ++ G+NGaGKTT+++ + ++L
  gi|313126576|ref|YP_004036846.1| 32 VHALLGENGAGKTTLMNVL-YGL 53
                                      56789***********965.555 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0003      0.44      30      55 ..      35      60 ..      27      71 .. 0.90
   2 ?    0.1   0.0      0.18   2.7e+02      30      89 ..     290     348 ..     282     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0003
                              DLIC 30 vlGedgsGkttliaklqGveeekkGr 55
                                      +lGe+g+Gkttl+  l G+  +  Gr
  gi|313126576|ref|YP_004036846.1| 35 LLGENGAGKTTLMNVLYGLYRPTEGR 60
                                      89****************99999887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                              DLIC  30 vlGedgsGkttliaklqGveeekkGrGleylyldvkdedrddltrlnvwildGdlyhkgl 89 
                                       + G dg G++ li  + G+  +  G+ + yl  d+ d  r d    ++  +  d   +gl
  gi|313126576|ref|YP_004036846.1| 290 IAGVDGNGQSELIESITGLRTPTDGS-VTYLGSDITDAPRSDRIDAGMAYIPEDRHERGL 348
                                       56889*******************98.78*********9999988887777777766666 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.16      12      47 ..      16      51 ..      12      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                            AAA_27 12 GkftdrsldfsaeeadlhliyGpNEAGKstalrAis 47
                                      G +++  +d+  e+  +h ++G N AGK+t+++ + 
  gi|313126576|ref|YP_004036846.1| 16 GVIANDDVDLTVERGTVHALLGENGAGKTTLMNVLY 51
                                      677889999**9******************998655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.25      28      63 ..      34      70 ..      24     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_16 28 llsGesGvGKsslvrellralekdg.giflrgkcdql 63
                                       l Ge G GK++l++ l+  ++ ++  ++++g+ +++
  gi|313126576|ref|YP_004036846.1| 34 ALLGENGAGKTTLMNVLYGLYRPTEgRVVIEGTERKF 70
                                      689***************9888886356699999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 3085.50
//
Query:       gi|313126577|ref|YP_004036847.1|  [L=453]
Description: nucleoside ABC transporter membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-40  139.2  37.3    1.6e-40  139.0  29.9    2.0  2  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.8    0.0006        11      52     100 ..      28      75 ..      13     125 .. 0.77
   2 !  139.0  29.9   8.8e-45   1.6e-40       5     267 ..     133     414 ..     129     415 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0006
                      BPD_transp_2  52 lsllllallvallvgaavglllgllvlrlkvdeliitllllsvlvgltl 100
                                       l   l+al++a+ vga + l+ g+++++ +   +++++++ +  + +++
  gi|313126577|ref|YP_004036847.1|  28 LI-SLAALVLAIFVGAGLILVSGRITTCSQAAAVYFGTGFCYDPTEVFF 75 
                                       33.689999********************99999999997665555554 PP

  == domain 2  score: 139.0 bits;  conditional E-value: 8.8e-45
                      BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl...........lllallvallvgaavg 70 
                                       +l  +++l++++l++a+ f +aG++n+g +g++++G+ v+al++  l +            ++++ l++ ++g++ +
  gi|313126577|ref|YP_004036847.1| 133 TLKETTLLVFTGLSVAVAF-RAGLFNIGTQGQLVIGGLVTALVVGILVPVvpggfagsillIPVGTLAGAAAGGLYA 208
                                       5677899************.*************************99999*************************** PP

                      BPD_transp_2  71 lllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv...........l 136
                                       ++ g+l+++   +e+i+t++l+++++ l+++ + + ++ + +q     + + +     +l++v++           l
  gi|313126577|ref|YP_004036847.1| 209 AIPGALKAYADANEVITTIMLNFIAAKLAYVAVSEFFKNPDSQV----IETAPLPDYATLGSVVFpqgsdfsilslL 281
                                       ******************************76666666665444....4444444444444444446668899**** PP

                      BPD_transp_2 137 lalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvg.l 212
                                       +alllv+ +++l+ rt++G+ lr  g ++eaa++ G++ kr+ ++++++sgal+g+ Ga+ +l+  +++ ++gv+ l
  gi|313126577|ref|YP_004036847.1| 282 FALLLVIGIWYLIERTSYGFDLRTSGIQPEAAEYGGVDAKRTVVTSMMLSGALGGIGGAMWVLMVMGKW-QTGVPsL 357
                                       ****************************************************************99999.777655* PP

                      BPD_transp_2 213 gfnaiaavvlGgagsllgtviGaliigvvksllltllgi....ptelarvllgallilv 267
                                       gf++i++ +l+g+ ++lg++ +al++g++ks ++ ++++    p +l  vl g+++++v
  gi|313126577|ref|YP_004036847.1| 358 GFDGITVSILAGN-NPLGAIPAALLFGTLKS-GSLAVQFntgvPKQLVGVLRGLIILFV 414
                                       *************.*****************.666666668889*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2841.20
//
Query:       gi|313126578|ref|YP_004036848.1|  [L=366]
Description: nucleoside ABC transporter membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-34  119.1  31.1    2.8e-34  118.5  31.1    1.2  1  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5  31.1   1.6e-38   2.8e-34       3     268 .]      58     345 ..      56     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 1.6e-38
                      BPD_transp_2   3 lnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl........lllallvallvgaavgl 71 
                                       ++ l+l+ ++++aAlG  +   ++Gvin+g +g+++++a+va l+ a l+++        l++++l+++l+++++++
  gi|313126578|ref|YP_004036848.1|  58 SSALRLSVPIVFAALGGIFAE-KSGVINIGLEGLLIISAFVAILVPAVLGPEgttlflpnLWVGFLAGILASVLFAA 133
                                       67899****************.******************************************************* PP

                      BPD_transp_2  72 llgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagall...sflsaviv.....llall 140
                                       l+++ ++r+k d++i++l++ ++++gl+ +  t + +gv++   +++l +++   l   +f +av++     + +l+
  gi|313126578|ref|YP_004036848.1| 134 LFAVVCIRYKADQIIAGLAVWLIALGLAPFSATVYYGGVNTDYIGTTLPTWEIPVLsdlPFFGAVFSatpavYAMLI 210
                                       ***************************98888877777777764444444433333000333334447888899*** PP

                      BPD_transp_2 141 lvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp...nigvglgf 214
                                       +v a++++l+rt+fG ++ra gen++a + +G++v rv+ ++ ++sg+l g+ Ga+l+l lg        +  g gf
  gi|313126578|ref|YP_004036848.1| 211 AVPAAWFVLNRTSFGGHVRASGENPRALDTVGVDVSRVRYASALLSGFLTGIGGAALSLGLGQFLGnnqTMVNGKGF 287
                                       **********************************************************9988765545588889*** PP

                      BPD_transp_2 215 naiaavvlGgagsllgtviGaliigvvksllltllgi.....ptelarvllgallilvl 268
                                        ai+a + G   +++g++ ++++++ ++++ + l +i     p el + + ++ +++vl
  gi|313126578|ref|YP_004036848.1| 288 IAIVAYLFGNY-NPFGAFGASFLFAGLEAVQIRLQQIqgyavPDELIQTIPYVTVLVVL 345
                                       ***********.*****************999999888888878888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2326.10
//
Query:       gi|313126579|ref|YP_004036849.1|  [L=310]
Description: hypothetical protein Hbor_18370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.93    7.7   3.1        1.2    7.3   3.1    1.1  1  TcdA_TcdB_pore  TcdA/TcdB pore forming domain


Domain annotation for each model (and alignments):
>> TcdA_TcdB_pore  TcdA/TcdB pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.1   6.7e-05       1.2     227     279 ..      30      85 ..      21     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 6.7e-05
                    TcdA_TcdB_pore 227 vGigaglvGasiva.avlsil..lvplaGlsvGftaLaeafgavaddAkavgnYFd 279
                                       +G+  gl G ++ a a ++ l  +v+laG++ G+ta+     ++  +A av +  d
  gi|313126579|ref|YP_004036849.1|  30 AGVWYGLNGGTTLAtATATRLvpAVVLAGVGLGVTAVGRTAVRLDANAAAVSDRLD 85 
                                       55666666666555134444333689*************************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2027.92
//
Query:       gi|313126580|ref|YP_004036850.1|  [L=52]
Description: hypothetical protein Hbor_18380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.065   14.0   0.3      0.073   13.9   0.3    1.1  1  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma


Domain annotation for each model (and alignments):
>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   4.1e-06     0.073      62      85 ..       3      26 ..       1      27 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-06
                                      SHHHHHHHHHHHHHHHHHHCHHTT CS
                   Ribosomal_S30AE 62 dlyaaidlavdklerqlrkykekl 85
                                      +l a id+++ ++erq+r++  +l
  gi|313126580|ref|YP_004036850.1|  3 TLDAEIDALARRIERQIRRNEARL 26
                                      68899**************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 341.40
//
Query:       gi|313126581|ref|YP_004036851.1|  [L=457]
Description: 2,3-di-O-geranylgeranylglyceryl phosphate reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-15   57.2   1.8    2.5e-11   43.1   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    6.1e-12   45.3   6.1    3.7e-06   26.3   3.9    2.4  2  FAD_binding_2   FAD binding domain
    4.6e-10   39.9   1.4    0.00093   19.7   0.6    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    5.2e-10   39.1   2.9    3.2e-09   36.5   2.9    2.1  1  FAD_binding_3   FAD binding domain
    9.4e-10   38.4   7.2    2.1e-05   24.1   3.2    2.4  2  FAD_oxidored    FAD dependent oxidoreductase
    7.7e-09   35.6   8.6    0.00041   20.0   1.3    2.6  2  DAO             FAD dependent oxidoreductase
    6.8e-08   32.0   0.3    1.4e-07   31.0   0.3    1.5  1  GIDA            Glucose inhibited division protein A
    1.9e-07   30.6   1.2    7.7e-07   28.6   0.3    2.1  2  Thi4            Thi4 family
      3e-07   30.0   7.5    7.3e-05   22.1   0.2    2.6  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.1e-06   25.0   1.1    0.00019   20.2   0.3    2.1  2  HI0933_like     HI0933-like protein
    2.6e-05   24.4   0.9    2.6e-05   24.4   0.9    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.3e-05   23.1   1.6     0.0071   15.4   0.4    2.2  2  Lycopene_cycl   Lycopene cyclase protein
     0.0066   15.7   0.5      0.027   13.7   0.3    1.9  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0094   15.9   0.2      0.016   15.1   0.2    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.021   14.5   0.3       0.04   13.6   0.3    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
       0.04   13.2   0.6       0.04   13.2   0.6    1.7  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.04   13.4   0.1      0.088   12.3   0.1    1.6  1  FBPase          Fructose-1-6-bisphosphatase, N-terminal domai
      0.067   13.2   1.2       0.62   10.0   0.2    2.4  2  NAD_binding_9   FAD-NAD(P)-binding
      0.081   13.0   0.0       0.14   12.2   0.0    1.4  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
        0.1   11.1   0.5        1.3    7.5   0.0    2.1  2  GDI             GDP dissociation inhibitor
       0.11   12.7   0.5        1.1    9.4   0.2    2.4  2  Ferredoxin_N    N-terminal region of 4Fe-4S ferredoxin iron-s
       0.12   11.7   0.0       0.24   10.7   0.0    1.4  1  ThiF            ThiF family


Domain annotation for each model (and alignments):
>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.6   3.8e-05     0.031       1      35 [.       8      39 ..       8      52 .. 0.82
   2 !   43.1   0.0   3.1e-14   2.5e-11     151     370 ..     101     341 ..      76     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      ++v+vG+Gt+G  aAa++a+ +   l+v +ve ++
  gi|313126581|ref|YP_004036851.1|  8 DVVVVGAGTSGCYAAATIAREG---LDVVIVERKT 39
                                      69*******************9...9999999765 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 3.1e-14
                                       E-HHHHHHHHHHHHHHCT-EEEE--E.EEEEE-TTS-EEEEEETT.S-EE..E-SEEEE-SGGG-IIIIII.T---E CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkv.vevqldedgrveslrled.grev..eadlfiDcsGfrgllieqa.Lktgf 222
                                       +d+ +y + L + a+++Gv+   ++v ++v++++dgrv+++r ++ g +v  ead+ +D  G  ++l +++ +++++
  gi|313126581|ref|YP_004036851.1| 101 IDRWEYGRRLIDGAKNAGVEFHYDTVvQDVTQNDDGRVTGVRAKQnGDVVeyEADMTVDGAGSLSILQDKTdFSGTT 177
                                       689999**************87666516788888********998765542279**************998334444 PP

                                       EE-TTT----EEEEEEEE--H---SSEEEEE-.....SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT CS
                    Trp_halogenase 223 edwsdvLltdrAlavqveseelvepytratae.....kaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeld 293
                                        d   +     +   ++ ++e +  +++a  +     +aG +W+ P ++++ n G+ +        + +++l+++l 
  gi|313126581|ref|YP_004036851.1| 178 FDTNVSYSQFCSAYREIVEVEEPVEWSDALVFkpaevAAGYIWYFPRTETTINaGLGFQMTEE-PMKLVDDLKRDLR 253
                                       343333322223333444444555556544431111279********9999888888865443.4567777788888 PP

                                       --TTTS-EEEE---EE.......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHH CS
                    Trp_halogenase 294 gkleaeprkirfttGr.......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaa 359
                                       +++e ++  ++ + G          +a  +++va+G+a+g v+P  + +i+ + +    a ++ ++ + d+ +++ a
  gi|313126581|ref|YP_004036851.1| 254 ARPEFKNATVSDKLGAalptrrpYDSAVAPGFVAVGDAAGHVNPTTGGGIAGAAYagkyAGEQAVRAISDGDVSEEA 330
                                       888888777777777777777777899***********************999887777889999999999999999 PP

                                       HHHHHHHHHHH CS
                    Trp_halogenase 360 iaefnrevare 370
                                       + ++n++v  +
  gi|313126581|ref|YP_004036851.1| 331 LWHYNERVMDH 341
                                       99999998765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   3.9   4.6e-09   3.7e-06       1      33 [.       8      40 ..       8      55 .. 0.87
   2 !   18.8   0.0   8.7e-07   0.00071     146     203 ..     109     165 ..     102     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.6e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      Dv+V+G+G +G+ AA+++a++Gl+v++ve + +
  gi|313126581|ref|YP_004036851.1|  8 DVVVVGAGTSGCYAAATIAREGLDVVIVERKTA 40
                                      9***************************98766 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 8.7e-07
                                       HHHHHHHTCTEEEEESEEEEEEEEC.TTEEEEEEEEETTTTCEEEEEESEEEE-----G CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLive.dgrvtGavvenpesgrevrirakavvlatgGfg 203
                                       rl+++a++agv+f+  t +++++++ dgrvtG+ ++  ++g  v+++a+ +v+ +g  +
  gi|313126581|ref|YP_004036851.1| 109 RLIDGAKNAGVEFHYDTVVQDVTQNdDGRVTGVRAK--QNGDVVEYEADMTVDGAGSLS 165
                                       8999********************6266********..***********9999888766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.6   1.1e-06   0.00093       2      31 ..       9      38 ..       8      42 .. 0.95
   2 !   18.2   0.0   3.4e-06    0.0028      44      79 ..     108     144 ..     104     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      vvvvG+G++g+ +A+++a+ g +V +ver+
  gi|313126581|ref|YP_004036851.1|  9 VVVVGAGTSGCYAAATIAREGLDVVIVERK 38
                                      8***************************98 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.4e-06
                                       HHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEEEE CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsedg.vesvklk 79 
                                       ++l +  ++ g+e++++t+v+ +++++dg v++v+ k
  gi|313126581|ref|YP_004036851.1| 108 RRLIDGAKNAGVEFHYDTVVQDVTQNDDGrVTGVRAK 144
                                       5666778899************************987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   2.9   3.9e-12   3.2e-09       1     307 [.       6     306 ..       6     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3.9e-12
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealy 77 
                                       e+dV++VGaG +G  +a   ++ G +vv+ve+ + +     a+g   +  + + ++  + +i+   +   + +  ++
  gi|313126581|ref|YP_004036851.1|   6 EYDVVVVGAGTSGCYAAATIAREGLDVVIVERKTADEAGHIACGDALKGADAFPDAIPKSQIEPAFTNTGVDHGRFE 82 
                                       589**********************************9999999999999999888777777777766666666777 PP

                                       EECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvr 154
                                        +     +  + l+    p + +v+  +e  r L++ a+++g++++ +t v+ ++q+++g  + vr k++g   + +
  gi|313126581|ref|YP_004036851.1|  83 IP-----QEDTVLD-IPIPGELAVIDRWEYGRRLIDGAKNAGVEFHYDTVVQDVTQNDDGRVTGVRAKQNGDVVEYE 153
                                       77.....7777777.45678899****************************************************** PP

                                       EEEEEE--GTT-HHHHHHTGGEEEEEEEEE.EEEEEEEEEC.-SCCCTTC.CEEEEECCTTEE...EEEECCETEEE CS
                     FAD_binding_3 155 akYlvGaDGgrStvrktlgiefegeetvye.agvldvlfda.dlsdivep.lvlilsaesrgv...mviPlentler 225
                                       a+ +v   G  S+  ++ +++ ++++t +  +++ ++  +  +++++ve    l+ ++ +         P    +++
  gi|313126581|ref|YP_004036851.1| 154 ADMTVDGAGSLSILQDKTDFSGTTFDTNVSySQFCSAYREIvEVEEPVEWsDALVFKPAEVAAgyiWYFP----RTE 226
                                       ****977777777777777775555544321344444444444444444454444444444332223344....555 PP

                                       EEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSH CS
                     FAD_binding_3 226 fyvqvearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGq 302
                                        ++ + ++ + +e++ k   +++k++lr+  + k ++v+ +   a++ ++ + +    g v  +GDAa  + Pt+G 
  gi|313126581|ref|YP_004036851.1| 227 TTINAGLGFQMTEEPMKLV-DDLKRDLRARPEFKNATVSDKLGAALPTRRPYDSAVAPGFV-AVGDAAGHVNPTTGG 301
                                       7889999998888888776.57899999999999999998889999999999988888866.58****999999999 PP

                                       HHHHH CS
                     FAD_binding_3 303 GlNta 307
                                       G+  a
  gi|313126581|ref|YP_004036851.1| 302 GIAGA 306
                                       98665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   3.2   2.5e-08   2.1e-05       1      31 [.       8      38 ..       8      40 .. 0.96
   2 !   15.8   0.1   8.6e-06     0.007      98     144 ..     115     162 ..     100     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.5e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      DvvVvG+g++G+ AA + ar+G  v++ve++
  gi|313126581|ref|YP_004036851.1|  8 DVVVVGAGTSGCYAAATIAREGLDVVIVERK 38
                                      9****************************96 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8.6e-06
                      FAD_oxidored  98 aeagvtvllntrlveveke.gkriesvtveskegrktirAkvfiDATg 144
                                       ++agv+  ++t++++v+++ ++r+++v+++++    +++A++++D+ g
  gi|313126581|ref|YP_004036851.1| 115 KNAGVEFHYDTVVQDVTQNdDGRVTGVRAKQNGDVVEYEADMTVDGAG 162
                                       6799**************74689******76556***********876 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.3     5e-07   0.00041       1      32 [.       8      40 ..       8      60 .. 0.89
   2 !   19.4   0.9     8e-07   0.00065     141     204 ..      99     165 ..      94     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdia 32
                                      dvv++G+G  G+ +A   ar+g  V+++e++  a
  gi|313126581|ref|YP_004036851.1|  8 DVVVVGAGTSGCYAAATIAREGldVVIVERK-TA 40
                                      9*****************************9.44 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 8e-07
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEE.EEEETCEEEEEEECT.EEEEEEEE..EEE--GGGH CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgl.eeedgkvwgverttp.gendaada..vVnaaGaws 204
                                       +++d +++ + l + a+++Gve+++ t v+++ +++dg+v+gv r+++ g +++++a   V  aG  s
  gi|313126581|ref|YP_004036851.1|  99 AVIDRWEYGRRLIDGAKNAGVEFHYDTVVQDVtQNDDGRVTGV-RAKQnGDVVEYEAdmTVDGAGSLS 165
                                       678999999**********************955577******.777778874444444888888655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.3   1.7e-10   1.4e-07       1      47 [.       8      55 ..       8      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGGTT--SSSSEEE-T CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.thkldtiaelsCnpsiggi 47
                                      dv+V+G+G +Gc AA+++ar G++v+++  +  d+ ++++C ++++g 
  gi|313126581|ref|YP_004036851.1|  8 DVVVVGAGTSGCYAAATIAREGLDVVIVeRKTADEAGHIACGDALKGA 55
                                      79**************************6677799*********9986 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.3   9.4e-10   7.7e-07      15      61 ..       4      49 ..       1      58 [. 0.88
   2 ?    0.2   0.0      0.45   3.7e+02     111     137 ..     117     143 ..      98     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.4e-10
                                      HTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTS CS
                              Thi4 15 yaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGG 61
                                        e Dvv+vGaG+sG  aa ++a++ +l v+i+er+ +   G    G
  gi|313126581|ref|YP_004036851.1|  4 THEYDVVVVGAGTSGCYAAATIARE-GLDVVIVERKTADEAGHIACG 49
                                      5689*********************.**********99887766555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.45
                                       TTEEEEESEEEEEEEEETBTEEEEEEE CS
                              Thi4 111 anvkllnavaveDlivregegvaGvvi 137
                                       a+v     ++v D+   ++ +v+Gv  
  gi|313126581|ref|YP_004036851.1| 117 AGVEFHYDTVVQDVTQNDDGRVTGVRA 143
                                       778888889999999999999999865 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   8.9e-08   7.3e-05       1      33 [.       7      39 ..       7      83 .. 0.84
   2 !   12.2   0.1   9.6e-05     0.079     188     236 ..     109     162 ..     103     175 .. 0.80
   3 ?   -3.0   0.4         4   3.3e+03       7      21 ..     300     314 ..     299     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.9e-08
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      +dvvv+G+G  G+ aa t+a+ g++v++ve+++
  gi|313126581|ref|YP_004036851.1|  7 YDVVVVGAGTSGCYAAATIAREGLDVVIVERKT 39
                                      69***************************6332 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 9.6e-05
                                       HHHHHHHHTTEEEEESCEEEEEEETTE.EEE....EEETTSCEEEESEEEE-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx....xxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 188 aleealekeGvevklgtsvkeidgnge.kle....vvledgeeidadlvvvavG 236
                                       +l +  ++ Gve++  t+v+++++n++ +++     +++d  e++ad+ v ++G
  gi|313126581|ref|YP_004036851.1| 109 RLIDGAKNAGVEFHYDTVVQDVTQNDDgRVTgvraKQNGDVVEYEADMTVDGAG 162
                                       566677899******************955553245555666699999998887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4
                                       --SHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Pyr_redox_2   7 GgGpAGlaaaltlaq 21 
                                       GgG+AG a a + a 
  gi|313126581|ref|YP_004036851.1| 300 GGGIAGAAYAGKYAG 314
                                       899999887765554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.3   2.4e-07   0.00019       1      33 [.       7      39 ..       7      43 .. 0.94
   2 ?    3.3   0.0     0.034        28     115     166 ..     110     165 ..     108     171 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.4e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +dv+v+G+G +G +aA+++a++g +V+++e+++
  gi|313126581|ref|YP_004036851.1|  7 YDVVVVGAGTSGCYAAATIAREGLDVVIVERKT 39
                                      59****************************875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.034
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EE.EEE.TTE...EEEESEEEE----SS CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfr.vktksee...eleadklvlAtGGlS 166
                                       l+  +k+agv+++++t v++v++++dg+++ v++k+++   e+ead +v   G+lS
  gi|313126581|ref|YP_004036851.1| 110 LIDGAKNAGVEFHYDTVVQDVTQNDDGRVTgVRAKQNGdvvEYEADMTVDGAGSLS 165
                                       5667899**************99998865426664433223456666666666665 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.9   3.1e-08   2.6e-05       1      28 [.      11      38 ..      11      58 .. 0.88
   2 ?    0.1   2.2       1.2     1e+03       3      14 ..     300     311 ..     299     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.1e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vGaG sG++aA+++a++g+dv+++e+ 
  gi|313126581|ref|YP_004036851.1| 11 VVGAGTSGCYAAATIAREGLDVVIVERK 38
                                      8*************************86 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                                       --SHHHHHHHHH CS
                     NAD_binding_8   3 GaGlsGlvaAyl 14 
                                       G+G++G+++A  
  gi|313126581|ref|YP_004036851.1| 300 GGGIAGAAYAGK 311
                                       9*******9955 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   8.7e-06    0.0071       1      31 [.       8      36 ..       8      43 .. 0.94
   2 !    6.7   0.0    0.0039       3.2     255     295 ..     282     322 ..     246     394 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.7e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      Dvvv+GaG  g+  Aa +  a+ gl vv++e
  gi|313126581|ref|YP_004036851.1|  8 DVVVVGAGTSGCYAAATI--AREGLDVVIVE 36
                                      9*****************..**********8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0039
                     Lycopene_cycl 255 eqkvlaiGaaaglvhPaTGYsvarslaeaplla.saiaaalr 295
                                       ++  +a+G aag v P+TG  +a +  + + +a +  ++a  
  gi|313126581|ref|YP_004036851.1| 282 APGFVAVGDAAGHVNPTTGGGIAGAAYAGK-YAgEQAVRAIS 322
                                       455789*************99998765554.54133333333 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.3   3.3e-05     0.027     164     198 ..       6      40 ..       1      52 [. 0.84
   2 ?   -0.6   0.0      0.74     6e+02      91     113 ..     114     136 ..      76     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                       + +vvV+G++ S++ aA  ++r+g +V +v r++ 
  gi|313126581|ref|YP_004036851.1|   6 EYDVVVVGAGTSGCYAAATIAREGLDVVIVERKTA 40 
                                       56899999999999999999999999999999875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.74
                       Pyr_redox_3  91 aksfelpiklfeeVesvkkedeg 113
                                       ak+  ++ ++++ V++v+++d+g
  gi|313126581|ref|YP_004036851.1| 114 AKNAGVEFHYDTVVQDVTQNDDG 136
                                       44455566666666666665554 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.9e-05     0.016       2      33 ..       9      40 ..       8      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                      v v+GaGt G   aa +a++gl+Vv+v+++++
  gi|313126581|ref|YP_004036851.1|  9 VVVVGAGTSGCYAAATIAREGLDVVIVERKTA 40
                                      89**************************9765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   4.9e-05      0.04       1      31 [.       9      39 ..       9      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      ++++GaG  G++ aa++a+ g dv+++ r+ 
  gi|313126581|ref|YP_004036851.1|  9 VVVVGAGTSGCYAAATIAREGLDVVIVERKT 39
                                      689************************9976 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   4.9e-05      0.04      29      64 ..       7      42 ..       1      61 [. 0.87
   2 ?   -2.8   0.5         4   3.3e+03      34      52 ..     299     317 ..     282     338 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparl 64
                                        v+v+G+G+ G  A+at ++ g +V++++ ++a  
  gi|313126581|ref|YP_004036851.1|  7 YDVVVVGAGTSGCYAAATIAREGLDVVIVERKTADE 42
                                      579**************************9988765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4
                                       ESTSHHHHHHHHHHHHTT- CS
                       AlaDh_PNT_C  34 iGgGvaGlqAiatakglga 52 
                                        GgG+aG + +   +g +a
  gi|313126581|ref|YP_004036851.1| 299 TGGGIAGAAYAGKYAGEQA 317
                                       4999999876665555555 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00011     0.088      99     171 ..     159     234 ..     123     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                            FBPase  99 ekegkyvvafDPlDGSS.nidtnvsvGtifsiyrkks.edeetti.dvlqpGkeqvAAgyvvYGsstmlVltlgaG 171
                                          g+ +++ D  D S    dtnvs     s yr+    +e+++  d+l      vAAgy+ Y ++t   +  g G
  gi|313126581|ref|YP_004036851.1| 159 DGAGSLSILQDKTDFSGtTFDTNVSYSQFCSAYREIVeVEEPVEWsDALVFKPAEVAAGYIWYFPRTETTINAGLG 234
                                       55788999999999885268**************8775677788799999999**************987776666 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00076      0.62       1      41 [.      10      46 ..      10      53 .. 0.84
   2 ?    1.3   0.1      0.38   3.1e+02     106     137 ..     109     142 ..     104     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00076
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrv 41
                                      ++vGaG +G ++++ ++++      l++ +++++++  ag++
  gi|313126581|ref|YP_004036851.1| 10 VVVGAGTSGCYAAATIARE-----GLDVVIVERKTAdEAGHI 46
                                      69***************99.....5*******9776465665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.38
                     NAD_binding_9 106 ellarlpegvtvevhraevv.dleeradgq..avl 137
                                       +l++ ++ +  ve+h ++vv d+++++dg+   v+
  gi|313126581|ref|YP_004036851.1| 109 RLIDGAK-NAGVEFHYDTVVqDVTQNDDGRvtGVR 142
                                       5666664.578999999887469998888632233 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.14      11      52 ..       5      46 ..       1      56 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHH CS
                      Shikimate_DH 11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakel 52
                                      +e  v+++GaG  +  +a  ++++g++ v+v   t + a ++
  gi|313126581|ref|YP_004036851.1|  5 HEYDVVVVGAGTSGCYAAATIAREGLDVVIVERKTADEAGHI 46
                                      6788***********************555554566666665 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0016       1.3       3      36 ..       5      38 ..       3      47 .. 0.92
   2 ?    1.5   0.1       0.1        84     247     273 ..     120     146 ..     114     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                                      XEECEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                               GDI  3 eeydvivlGtGlkecilsGllsvdgkkvlhldrn 36
                                      +eydv+v+G+G   c  +  ++ +g  v+ ++r+
  gi|313126581|ref|YP_004036851.1|  5 HEYDVVVVGAGTSGCYAAATIAREGLDVVIVERK 38
                                      69***************************99997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                                       EEETS--ECEEEE-TTS-EEEEEETTE CS
                               GDI 247 tymlnkpvdevvldedgkvvGvkseee 273
                                        +  ++ v++v  ++dg+v+Gv+++++
  gi|313126581|ref|YP_004036851.1| 120 EFHYDTVVQDVTQNDDGRVTGVRAKQN 146
                                       57789999**************98653 PP

>> Ferredoxin_N  N-terminal region of 4Fe-4S ferredoxin iron-sulfur binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0         1   8.2e+02      18      36 ..     227     245 ..     225     247 .. 0.83
   2 ?    9.4   0.2    0.0013       1.1      25      58 ..     310     343 ..     306     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                      Ferredoxin_N  18 teYDaeLGlemarDAvrvt 36 
                                       t   a LG +m++  ++++
  gi|313126581|ref|YP_004036851.1| 227 TTINAGLGFQMTEEPMKLV 245
                                       666799*******999986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                      Ferredoxin_N  25 GlemarDAvr.vtkGeLseaeFhekYheaVlaEFg 58 
                                       G+  ++ Avr ++ G++se++   +Y+e+V++ Fg
  gi|313126581|ref|YP_004036851.1| 310 GKYAGEQAVRaISDGDVSEEALW-HYNERVMDHFG 343
                                       67778889886789******998.6*********9 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00029      0.24      20      42 ..       8      30 ..       3      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                      EEEEE--SHHHHHHHHHHHHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 20 kvllvGaGglGsellknLalsGv 42
                                       v++vGaG+ G++++ ++a+ G+
  gi|313126581|ref|YP_004036851.1|  8 DVVVVGAGTSGCYAAATIAREGL 30
                                      69******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2813.87
//
Query:       gi|313126582|ref|YP_004036852.1|  [L=423]
Description: amidohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-23   83.6   5.1    2.3e-23   83.0   5.1    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.1e-13   51.1   0.7    2.5e-13   49.9   0.7    1.6  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
      0.054   14.0   0.1         47    4.6   0.0    3.2  3  Biotin_carb_N  Biotin carboxylase, N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   5.1   3.9e-27   2.3e-23       2     206 ..     104     416 ..     103     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 3.9e-27
                                       EEEES-BSS.TTCGGGSSS.TTSEE...ETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTS. CS
                                       xxxxxxxxx.xxxxxxxxx.xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Peptidase_M20   2 lgsHlDvVp.eeetdgwtt.pfslt...eedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEE. 72 
                                       l+ ++D +p +e + + ++ p ++    e++G+++++G+d + ++ l++l a+++   ++   +gt+++ fqp EE 
  gi|313126582|ref|YP_004036852.1| 104 LRVDIDGLPiTESE-DADHaPAAGGfrsENEGYMHACGHDSHATIGLGVLDAIAES--DF---EGTLKVFFQPGEEq 174
                                       799******86666.4577787777777677**********************883..33...78***********4 PP

                                       STTTHHHHHHH.HHHTTTCESEEEEEEEESSSBTCHSTETEEEE................................. CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................. RF
                     Peptidase_M20  73 ggrgGakalle.gleerekvdavfelhieepgileagklaigvv................................. 115
                                       +  +G k++++ g    ++vd+++++hi+  ++++ g++++g+                                  
  gi|313126582|ref|YP_004036852.1| 175 I--AGGKSMAKsGH--LDDVDYLLAAHIG-LDHPS-GEIVAGIDgflavshfeaeftgapahagarpeqgdnaiqam 245
                                       4..9*******544..469**********.99999.89888888********************************* PP

                                       ......................................................................EEEEEEE CS
                                       ......................................................................xxxxxxx RF
                     Peptidase_M20 116 ......................................................................kvevell 122
                                                                                                             ++ev   
  gi|313126582|ref|YP_004036852.1| 246 ataiqnlysiprhadgatrvnagvveggtatniipeeasiggevrgettelmeymeeksrrvirsaaemhACEVAIN 322
                                       *********************************************************************74666655 PP

                                       .EEESHEEECCHHHHHHHHHHHHHHH.TSCEEEE.EESSSBHTHHHH.TTT.E.....EEEEEESSG.GCTTSTTTE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxx.xxx.x.....xxxxxxxxx.xxxxxxxxx RF
                     Peptidase_M20 123 .eggapvtlndsplvkalaeaaeelf.gekveli.vsgpggtdarff.agi.p.....tvmifgpgs.glaHspnEy 188
                                        eg ap +++d++lv++++++a++    e+v +  v g g++da ++ +++       +++++g++  g+ H+   +
  gi|313126582|ref|YP_004036852.1| 323 tEGKAPSATSDDELVAIVSDVAKSNAsVESVIDRdVLG-GSEDATYLmQEVqDngglaAYIGVGTDHpGGHHTRTFD 398
                                       46777777779*************87434455555999.********98885245553445566554799999**** PP

                                       EEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 189 vdledlekgikvlarlle 206
                                       vd++++  g++vla +++
  gi|313126582|ref|YP_004036852.1| 399 VDEDSIGIGVEVLAGAIL 416
                                       **************9986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.7   4.1e-17   2.5e-13       9     105 ..     220     312 ..     216     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 4.1e-17
                                       EEEEEE-B-EEGG.-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEH CS
                         M20_dimer   9 gkitvkgkagHsg.apgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRl 84 
                                       ++ +++g  +H+g  p+ g+NAi ++a +++ l + +++       + t +n +++egG+a+n+ip+ea+   ++R 
  gi|313126582|ref|YP_004036852.1| 220 FEAEFTGAPAHAGaRPEQGDNAIQAMATAIQNLYSIPRH-----ADGATRVNAGVVEGGTATNIIPEEASIGGEVRG 291
                                       78899*******************************877.....56******************************9 PP

                                       HHHHHHHHHHHHHHHHHTSCC CS
                         M20_dimer  85 lpgedpeevleeieeilekea 105
                                       + +e  e  +e+ + +++++a
  gi|313126582|ref|YP_004036852.1| 292 ETTELMEYMEEKSRRVIRSAA 312
                                       999999988888888887765 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0078        47      59      92 ..      23      56 ..       5      63 .. 0.87
   2 ?    0.8   0.0      0.12   6.9e+02      75     104 ..     119     148 ..     111     150 .. 0.76
   3 ?    4.1   0.1     0.011        64      14      63 ..     304     350 ..     299     371 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0078
                                      GGG-HHHHHHHHHHTT-SEEE--SSTTTT-HHHH CS
                     Biotin_carb_N 59 sYlniekivkaakesgadavhpGyGflsEnaefa 92
                                      ++   +++v+ +++++ da+++G   lsE++++a
  gi|313126582|ref|YP_004036852.1| 23 EFYTTARLVDELETRDLDALYVGPEVLSEDDRMA 56
                                      56778899999*******************9987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                                       -SEEE--SSTTTT-HHHHHHHHHTT-EESS CS
                     Biotin_carb_N  75 adavhpGyGflsEnaefaeaveeagivfiG 104
                                       ad      Gf sEn+ + +a+ +   + iG
  gi|313126582|ref|YP_004036852.1| 119 ADHAPAAGGFRSENEGYMHACGHDSHATIG 148
                                       555555569************988777776 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-H CS
                     Biotin_carb_N  14 AvriiravrelgietvavyseedanslhvreadeavelgpasasesYlni 63 
                                         r+ir++ e++   va+ +e +a s  ++  de v +  ++ ++s +++
  gi|313126582|ref|YP_004036852.1| 304 SRRVIRSAAEMHACEVAINTEGKAPS--ATSDDELVAIV-SDVAKSNASV 350
                                       68*********999999999876554..45566777664.3334444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2634.38
//
Query:       gi|313126583|ref|YP_004036853.1|  [L=505]
Description: transporter, nhac family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-38  130.8  45.4    3.2e-22   79.1  18.3    2.3  2  Na_H_antiporter  Na+/H+ antiporter family


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6  23.4   7.7e-21   1.4e-16     108     302 ..      27     221 ..      16     222 .. 0.87
   2 !   79.1  18.3   1.8e-26   3.2e-22      29     303 .]     198     475 ..     191     475 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 7.7e-21
                   Na_H_antiporter 108 ivkafivalafqntdvatalvvgalaglivatllelaslseidkllnrGiksmlgailil..llAwgiggvlealgv 182
                                       iv+a++  + + +   +t+lvvg lagli+ +l    +++++ +++ +G+   + a +i+  l A  +++ ++a g 
  gi|313126583|ref|YP_004036853.1|  27 IVWAIVQSG-LLGVGDTTGLVVGMLAGLIIGMLFVKGPWKDYADVIFDGMTERVAATAIVawLWAGMFAETIQAGGF 102
                                       444444444.556778899999***********9988************8877777666612555559999999999 PP

                   Na_H_antiporter 183 teslvsslakgvvskgllplilflvallvafatGtswgtigIilpiavplaaklgisllalvraveaggtlgdhlsP 259
                                       ++ lv    + +v +gl p+++fl+a+l a ++Gt +gt +  + +  p ++ lg ++  l +a+++g+++gd l P
  gi|313126583|ref|YP_004036853.1| 103 VDGLVWAADAVNVGAGLFPALTFLLAALLATGIGTGYGTAIAFTALVFPAGVVLGSNPVLLFGAILSGAVFGDNLAP 179
                                       99999988888899*************************************************************** PP

                   Na_H_antiporter 260 isdttilsstglnadhidhvsytqlpyallvapitailllvfG 302
                                       +sdtti+s+ +  ad   +v  + + ya ++a++++  +l++G
  gi|313126583|ref|YP_004036853.1| 180 VSDTTIVSAVTQDADIGGVVA-SRIKYAVVAAIFAFAAYLIAG 221
                                       ************999778888.89***************9998 PP

  == domain 2  score: 79.1 bits;  conditional E-value: 1.8e-26
                   Na_H_antiporter  29 eiaalgmlvqsipanvysifallvvglvvl.llrdigamlraeaear..........eleekeltklpiavliiltl 94 
                                        +a  + + ++++a +++++a+l++g ++    +d+g + +   +a           ++ ++++ +  i  +++ ++
  gi|313126583|ref|YP_004036853.1| 198 VVA--SRIKYAVVAAIFAFAAYLIAGRSMAsAPLDVGGVSTG-GSALglvhllsigiVIVTAVAGRHIIEAVSWGLI 271
                                       555..4778899*****************9999999999998.3333566655443333333333345555566666 PP

                   Na_H_antiporter  95 skmpytgalalvaivkafivalafqntdvatalvvgalaglivatllelaslseidkllnrGiksmlgaililllAw 171
                                       ++m + ++l+l+ ++ a++   a qn+ +++ +  + ++g +v  + +    + + ++l++G+ +++++i+++ll +
  gi|313126583|ref|YP_004036853.1| 272 TSMVLNIGLDLA-DASAMLAFKAPQNSGLVQQIDALPVIGAVVVPVEAG--NTAVAGSLYAGASGFFPLIVLVLLIV 345
                                       777777777743.444666666688888888888777777777777776..6789********************** PP

                   Na_H_antiporter 172 giggvlealgvteslvsslakgv.vskgllplilflvallvafatGtswgtigIilpiavplaaklgisllalvrav 247
                                       + ++v+++ g++e++++ l+++v ++++++ +++++ +++v+++++ ++++ + i+p+++ l+ +++i+ ++ ++++
  gi|313126583|ref|YP_004036853.1| 346 AGAQVMQRGGGFEAIQDFLLNSVaTTVRRAEMTMVIGTAMVNAMITINTAAEIAIAPYIRTLGRRFNINGYRRANIL 422
                                       ***************************************************************************** PP

                   Na_H_antiporter 248 eaggtlgdhlsPisdttilsstglnadhidhvsytqlpyallvapitailllvfGi 303
                                        a++    +++P++ + +   t+    ++ + +y +++ a++v+p+++ +++++G+
  gi|313126583|ref|YP_004036853.1| 423 DANTSALGYIFPWGGGLLAGFTAM---QQLPNEYEWFTQAMVVNPASVWPYVFHGW 475
                                       ************************...****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3085.61
//
Query:       gi|313126584|ref|YP_004036854.1|  [L=87]
Description: hypothetical protein Hbor_18420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 552.10
//
Query:       gi|313126585|ref|YP_004036855.1|  [L=110]
Description: 30S ribosomal protein s10 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-08   35.2   0.0    1.4e-08   34.9   0.0    1.1  1  Ribosomal_S10  Ribosomal protein S10p/S20e


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   7.6e-13   1.4e-08       2      97 ..       7      97 ..       6      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7.6e-13
                                      EEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--S--EEEEEEEEEEEEEEEE.E-HHHHHH CS
                     Ribosomal_S10  2 irlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvdkksreqfeirthkRlidisdatketidt 80
                                      ++++S ++  Le+ v++++++++++g+++kgp++ P++++ v+ +++     +  + ++++++ R ++i+  +++ +++
  gi|313126585|ref|YP_004036855.1|  7 LTFQSGNRYELEEQVSDLQEMLERKGAECKGPHASPPEQHTVPQYRNLEP-GDEFSSWNYTVYSRKLEIH-GNDHIARE 83
                                      899********************************************999.9*****************5.77777777 PP

                                      HS-...S---SS-EEEE CS
                     Ribosomal_S10 81 llkllqlnlpegVsvev 97
                                      + +   +++pe  +ve+
  gi|313126585|ref|YP_004036855.1| 84 VGH---MEFPESLHVEI 97
                                      777...89999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 708.32
//
Query:       gi|313126586|ref|YP_004036856.1|  [L=153]
Description: ntp pyrophosphohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-18   65.2   0.3    6.8e-18   65.0   0.3    1.1  1  NUDIX     NUDIX domain
     0.0029   18.0   0.0     0.0037   17.7   0.0    1.3  1  AAA_17    AAA domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.3   7.5e-22   6.8e-18       4     126 ..       6     127 ..       3     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 7.5e-22
                                       EEEEEEEEETT.SE..EEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEE CS
                             NUDIX   4 ravgvvllnek.ge..vLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapyd 75 
                                       +++g++l+++  g+   Ll++++    pg We+P+G+ve  E+++++A+RE++EE+G+++ +l++ +   +y + ++
  gi|313126586|ref|YP_004036856.1|   6 VSAGAILFRDTrGRreYLLLKSR----PGdWEFPKGGVEGKEELQQTAIREVKEEAGIQEfRLVDGFR-EDYDYVFE 77 
                                       78899955555255898888766....466*********999****************8888885443.45555555 PP

                                       EEEEEEEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHH CS
                             NUDIX  76 gpygdeheilyvfl.eevegelepndenevsevrwvpleellkeklaaesrk 126
                                       +  ++ h  +++f  +++e   e+  + e+++++w ++e++l +  +++ r+
  gi|313126586|ref|YP_004036856.1|  78 ANGKTIHKTVHLFIaRSFEASAEL--STEHRDLQWRDYEQALNTITQDGPRD 127
                                       555556777777774555555444..699************55555555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.1e-07    0.0037      21     113 ..       3     100 ..       1     121 [. 0.66

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.1e-07
                                       EEEEEHHHHHHHHHHTT.T...SHSSH..HHHCTSHHHHHHHHHHHHHHHHHHHHHSSEE.EEEE-SEEEETTEEEE CS
                            AAA_17  21 fthlsaGdllreeakrg.g...lakar..demrklpleekkelqkeaaekiaeeakkkgv.lvdghprikeqagfld 90 
                                       ++ +saG +l+   + + +   l++     e+ k+  e k+elq++a+++++eea+ +++ lvdg+    e+ +++ 
  gi|313126586|ref|YP_004036856.1|   3 VQAVSAGAILFRDTRGRrEyllLKSRPgdWEFPKGGVEGKEELQQTAIREVKEEAGIQEFrLVDGFR---EDYDYVF 76 
                                       577999999885554442444323333114555**********************888877****97...4566654 PP

                                       SSHHHHHHHH..SEEEE..EE--HH CS
                            AAA_17  91 glpkevleelkpdaiil..leadpe 113
                                       +   +++++  ++++i   +ea++e
  gi|313126586|ref|YP_004036856.1|  77 EANGKTIHKT-VHLFIArsFEASAE 100
                                       4444444443.34444444666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 937.82
//
Query:       gi|313126587|ref|YP_004036857.1|  [L=41]
Description: hypothetical protein Hbor_18450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 278.55
//
Query:       gi|313126588|ref|YP_004036858.1|  [L=371]
Description: hypothetical protein Hbor_18460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.075   13.3   0.4       0.24   11.7   0.3    1.9  2  PaaX      PaaX-like protein


Domain annotation for each model (and alignments):
>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   1.3e-05      0.24      38      61 ..     127     150 ..     123     153 .. 0.92
   2 ?   -3.6   0.0      0.77   1.4e+04      22      42 ..     162     182 ..     160     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                              PaaX  38 slvRaalsRlakaGwlvrekegrr 61 
                                       + vRaa++R a +G + + ++g+r
  gi|313126588|ref|YP_004036858.1| 127 RYVRAAVHRAAGRGVVEKRRKGNR 150
                                       68********************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.77
                              PaaX  22 wlgsLirllaelGiseslvRa 42 
                                       w++  +++ ++ ++++s+ Ra
  gi|313126588|ref|YP_004036858.1| 162 WVRRIVAIENKPDLDASAARA 182
                                       888899999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2407.13
//
Query:       gi|313126589|ref|YP_004036859.1|  [L=167]
Description: hypothetical protein Hbor_18470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.049   13.5   0.2       0.23   11.4   0.0    2.1  2  TrmB           Sugar-specific transcriptional regulator TrmB
      0.072   12.9   0.1       0.21   11.4   0.0    1.9  2  DUF4817        Helix-turn-helix domain (DUF4817)
      0.093   12.5   0.0        2.3    8.1   0.0    2.3  2  LexA_DNA_bind  LexA DNA binding domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.33     2e+03      14      35 ..      11      32 ..       3      43 .. 0.73
   2 ?   11.4   0.0   3.8e-05      0.23      39      61 ..     129     152 ..     125     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.33
                                      CHHHHHHCCCHHCHHCCCTTSS CS
                              TrmB 14 YlaLlklgpatadeiaeelgvp 35
                                       + +++l+p + +e+ e+ g++
  gi|313126589|ref|YP_004036859.1| 11 LADVVRLQPTKNKELQEQWGLE 32
                                      5667888888999999988876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHHCTSEEEESST.TTE CS
                              TrmB  39 vYevLrsLedkGlVerekgr.pkl 61 
                                       v ++L+sL +kG+Ve++ ++ p++
  gi|313126589|ref|YP_004036859.1| 129 VRRALQSLRRKGVVEVVYRTvPTF 152
                                       789*************99886555 PP

>> DUF4817  Helix-turn-helix domain (DUF4817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.94   5.6e+03      12      20 ..      49      57 ..      46      60 .. 0.70
   2 ?   11.4   0.0   3.5e-05      0.21      16      54 ..     106     142 ..      91     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.94
                           DUF4817 12 Yykngesvt 20
                                      Yy+ + s++
  gi|313126589|ref|YP_004036859.1| 49 YYRDDNSLI 57
                                      888887765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.5e-05
                           DUF4817  16 gesvtatqrafrrrFpnrsvPsrstirrlvkkfeetGsv 54 
                                        esv+ ++++ r++F   + P+  ++rr  + ++ +G v
  gi|313126589|ref|YP_004036859.1| 106 SESVVSVLNKIREEFD--EDPDVDAVRRALQSLRRKGVV 142
                                       57*************9..99*****************98 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.034     2e+02      29      48 ..      23      42 ..      16      52 .. 0.86
   2 ?    8.1   0.0   0.00038       2.3      42      58 ..     128     144 ..     125     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.034
                                      HHHHHHHTS-.HHHHHHHHH CS
                     LexA_DNA_bind 29 reiaralglkSpsaveehLk 48
                                      +e+ ++ gl+S s v++ L+
  gi|313126589|ref|YP_004036859.1| 23 KELQEQWGLESGSEVHQYLE 42
                                      699999*********99987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind  42 aveehLkaLerKGyier 58 
                                       av   L+ L+rKG++e+
  gi|313126589|ref|YP_004036859.1| 128 AVRRALQSLRRKGVVEV 144
                                       78999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1156.17
//
Query:       gi|313126590|ref|YP_004036860.1|  [L=257]
Description: short chain enoyl-CoA hydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-65  219.2   0.1    6.1e-65  219.0   0.1    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    3.4e-34  118.8   0.1    5.6e-34  118.1   0.1    1.3  1  ECH_2     Enoyl-CoA hydratase/isomerase
     0.0013   17.8   0.0     0.0021   17.1   0.0    1.3  1  SDH_sah   Serine dehydrogenase proteinase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   0.1     1e-68   6.1e-65       5     249 ..      13     257 .]       9     257 .] 0.98

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 1e-68
                                       TEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHH CS
                             ECH_1   5 gvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeekakqallkeevlel 80 
                                        va + ++rP+++Nal+ ++l+ + +al+++ +  ++r  v+tG gd+aF aGad+  m+  ++a ++ + e+    
  gi|313126590|ref|YP_004036860.1|  13 DVATLVIDRPDQMNALNVQTLDAIEEALAEAGEK-EARCLVVTGeGDEAFVAGADISYMTDLGPAAAQAYAEQGHRI 88 
                                       689999************************9776.9***************************************** PP

                                       HHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT- CS
                             ECH_1  81 wtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgk 157
                                        + + + p p+iaavnG+a+gGG+elalacD+++a++ a  g++e+ lG+ipg ggtq+l+  vG ++A++++ +g+
  gi|313126590|ref|YP_004036860.1|  89 ASTIESFPAPTIAAVNGYAFGGGCELALACDLRVASERALLGQTEIDLGIIPGWGGTQRLPALVGDELARRMIFFGE 165
                                       ***************************************************************************** PP

                                       EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHH CS
                             ECH_1 158 kisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddik 234
                                       ++ a +a ++Glv +vv++++l ++  e+ae+la k++ alr++kealna  ++   ++le ea+  + +f ++d +
  gi|313126590|ref|YP_004036860.1| 166 RVDATDAFERGLVGEVVAHDELRDHVAEMAEELAAKPKFALRAAKEALNAFHNSPRSTALEHEARAWSGLFGTHDQR 242
                                       ***************************************************************************** PP

                                       HHHHHHHTCSH---- CS
                             ECH_1 235 eGlqaflEkrkpefe 249
                                       eG++af+Ekr+++fe
  gi|313126590|ref|YP_004036860.1| 243 EGMNAFVEKRDADFE 257
                                       ************996 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.1   9.4e-38   5.6e-34       2     233 ..      15     243 ..      14     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 9.4e-38
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk 78 
                                       +++ ++rp+++NaL+ + ++a++eal e + ++e++++v++g+g++af AG D+  +++   + +++   + ++ ++
  gi|313126590|ref|YP_004036860.1|  15 ATLVIDRPDQMNALNVQTLDAIEEALAE-AGEKEARCLVVTGEGDEAFVAGADISYMTDLGPAAAQA---YAEQGHR 87 
                                       57889***********************.578899*************************9997644...9****** PP

                                       HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH- CS
                             ECH_2  79 lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTG 154
                                       + ++i+++p p++a ++G++ GgG+ l++ + +rv++er+++   E+ +G++P  Gg+  L+ l g el++ +   G
  gi|313126590|ref|YP_004036860.1|  88 IASTIESFPAPTIAAVNGYAFGGGCELALACDLRVASERALLGQTEIDLGIIPGWGGTQRLPALVGdELARRMIFFG 164
                                       ***************************************************************9776********** PP

                                       --B-HHHHHHTTS--EE--GGGHHHHHHHHHTT............--------......----SHHHHHHHHHHHT. CS
                             ECH_2 155 arlkgadalaaglathyvpseklealeeaLaelessd....eeaveevleelaeeaeeeeeeselaekreaidrlfs 227
                                       +r++++da++ gl   +v +++l +  +++ae   ++     +a +e+l+++++++++    ++l+++++a + lf+
  gi|313126590|ref|YP_004036860.1| 165 ERVDATDAFERGLVGEVVAHDELRDHVAEMAEELAAKpkfaLRAAKEALNAFHNSPRS----TALEHEARAWSGLFG 237
                                       ********************99976666655544444445578888888888876665....566666667777776 PP

                                       -S-TTT CS
                             ECH_2 228 adsvee 233
                                       +++ +e
  gi|313126590|ref|YP_004036860.1| 238 THDQRE 243
                                       555444 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.6e-07    0.0021     109     163 ..      86     140 ..      74     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.6e-07
                           SDH_sah 109 tqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqyp 163
                                        +ia ++++ +a+t   v  ya+ GG+ +ala d  +  e+a+lG  + +lg +p
  gi|313126590|ref|YP_004036860.1|  86 HRIASTIESFPAPTIAAVNGYAFGGGCELALACDLRVASERALLGQTEIDLGIIP 140
                                       679******************************************9998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1545.57
//
Query:       gi|313126591|ref|YP_004036861.1|  [L=483]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-39  135.1  55.1    6.4e-37  127.0  28.2    3.3  3  MCPsignal     Methyl-accepting chemotaxis protein (MCP) signa
    2.8e-11   43.6   0.2    1.8e-10   41.0   0.0    2.4  3  PAS_9         PAS domain
      3e-10   40.1   1.1    2.3e-09   37.3   0.0    2.8  2  PAS           PAS fold
    3.2e-08   33.8   0.1    3.2e-08   33.8   0.1    2.6  2  PAS_4         PAS fold
    4.6e-05   23.9   5.8    0.00023   21.7   0.0    3.5  3  PAS_10        PAS domain
    0.00054   20.2  28.6       0.51   10.7   0.9    4.7  4  BLOC1_2       Biogenesis of lysosome-related organelles compl
      0.007   16.4   0.0      0.021   14.8   0.0    1.9  1  PAS_8         PAS domain
     0.0093   16.2  37.8       0.16   12.3   4.1    5.6  4  DUF948        Bacterial protein of unknown function (DUF948)
  ------ inclusion threshold ------
      0.017   15.2  31.4       0.38   10.8   4.4    4.3  4  DUF1664       Protein of unknown function (DUF1664)
      0.047   13.4  36.5       0.11   12.2   4.2    3.6  4  YkyA          Putative cell-wall binding lipoprotein
      0.055   13.7  26.5       0.19   12.0   5.4    4.3  4  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
      0.075   13.3   0.0       0.24   11.7   0.0    2.0  1  PAS_3         PAS fold
       0.12   12.5  33.8      0.026   14.6   9.1    3.3  2  ApoLp-III     Apolipophorin-III precursor (apoLp-III)
       0.15   11.8  32.1          1    9.1  12.2    3.1  3  DUF745        Protein of unknown function (DUF745)
       0.21   11.9   8.1        1.2    9.5   0.4    4.2  5  KxDL          Uncharacterized conserved protein
       0.62   10.2  10.2         13    6.0   0.3    3.9  3  COG5          Golgi transport complex subunit 5
       0.86    8.8   5.9        2.3    7.4   0.9    2.7  2  GLE1          GLE1-like protein
        1.1    9.7  14.4         24    5.4   1.4    4.4  3  Syntaxin_2    Syntaxin-like protein
        1.2    7.6  17.6      0.089   11.3  10.7    1.9  2  FUSC          Fusaric acid resistance protein family
        1.3    8.0  13.5        1.5    7.8   5.0    2.2  2  Atg14         Vacuolar sorting 38 and autophagy-related subun
        2.2    8.3  41.2        0.3   11.1   4.5    4.8  5  Laminin_II    Laminin Domain II
        3.4    7.7  11.2        1.4    8.9   0.7    4.1  5  Noelin-1      Neurogenesis glycoprotein
        3.9    7.1   8.6        1.9    8.1   0.4    2.8  3  BAR_3         BAR domain of APPL family
          6    7.3  14.3         15    6.1   0.9    4.3  3  Goodbye       fungal STAND N-terminal Goodbye domain
        6.3    7.1  19.2         21    5.5   6.6    4.2  2  Rx_N          Rx N-terminal domain
        7.8    5.0  29.6        1.4    7.5   5.3    3.0  3  AAA_13        AAA domain
        8.9    5.5  10.8        5.4    6.2   1.4    2.5  2  Vps54_N       Vacuolar-sorting protein 54, of GARP complex
        9.3    6.9  26.5        4.5    7.9   3.6    4.5  4  Syntaxin-6_N  Syntaxin 6, N-terminal


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4  13.3   3.8e-05     0.024      77     162 ..     160     245 ..     147     255 .. 0.74
   2 !  127.0  28.2     1e-39   6.4e-37      15     167 ..     252     418 ..     238     423 .. 0.86
   3 ?    5.0   3.8     0.029        19     103     154 ..     410     461 ..     407     472 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  77 VrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaasee 153
                                       V  + ++  q  k  e+l +e++  +++++++ e +   v+e+s++++e +e+++e++ +v++++++v++iaa+++e
  gi|313126591|ref|YP_004036861.1| 160 VTPVVKQQNQIKKAQETLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENMEEVSGEVGSLSATVEQIAASADE 236
                                       44455555555566667778888888888888888888888888888888888888888888888888888888888 PP

                                       HHHHHHHHH CS
                         MCPsignal 154 qsasieevn 162
                                       + + +ee  
  gi|313126591|ref|YP_004036861.1| 237 INERSEEAE 245
                                       887777765 PP

  == domain 2  score: 127.0 bits;  conditional E-value: 1e-39
                                       HHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHH CS
                         MCPsignal  15 gkevanvvkqmeeieks..............skeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEV 77 
                                        +  + +v++me++++s              ++ei di+eVi++iadQTN+LALNA iEAARAGe+G+GFaVVA+EV
  gi|313126591|ref|YP_004036861.1| 252 TEAGERAVGRMEDVAESgeeaaeqtrelaeqVAEIDDIVEVINDIADQTNILALNANIEAARAGEAGEGFAVVANEV 328
                                       4444455555555555555555555555555********************************************** PP

                                       HHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  78 rkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeq 154
                                       ++LA++ ++ ++ ie++i e  ++  ++v+s+e ++ +v ++++ v+e  ++ ++i +av+  ++ +++ia a+++q
  gi|313126591|ref|YP_004036861.1| 329 KSLANEVQNESERIEEIIHETREDASETVNSIETVTDEVRSSADAVREMVDNQESILDAVNATSTGMEDIAGATDDQ 405
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHH CS
                         MCPsignal 155 sasieevnqavee 167
                                       +   eev++ ++ 
  gi|313126591|ref|YP_004036861.1| 406 AVRTEEVASMIDT 418
                                       *******998876 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.029
                                       .......HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 103 ndsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeq 154
                                       ++++++++ +++r ++ +e+ve++++a +e v+ va++a+ ++ + +a+ e+
  gi|313126591|ref|YP_004036861.1| 410 EEVASMIDTATERSKKVAEEVETAADANAEQVTLVADIASAMERLESAVGEL 461
                                       4555555555555555556666666666666666666666666555555554 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   2.8e-13   1.8e-10       3     103 ..      63     161 ..      61     162 .. 0.90
   2 ?   -1.9   0.0       6.4   4.1e+03      47      91 ..     273     319 ..     259     330 .. 0.62
   3 ?   -2.0   0.0       6.7   4.3e+03      36      55 ..     342     365 ..     322     403 .. 0.55

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.8e-13
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                       g+++ n+d++++y+N+++ +l+G +++ v+g++  ++f + +  +++l++  eq  +  re+++ ++    +t wv+
  gi|313126591|ref|YP_004036861.1|  63 GFAV-NDDHELTYFNDTVSELYGRGADNVIGRDAYEVF-QTEGKDKTLAQTAEQTGDVIREDDYREVPTAKGTRWVR 137
                                       5665.69999****************************.788888888887777777889999999999999***** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDit 103
                                         a+p++  dge vg++ i++D+t
  gi|313126591|ref|YP_004036861.1| 138 GMAIPFFAPDGESVGAVEIVEDVT 161
                                       ***********************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.4
                             PAS_9  47 nerlraaleqgrkkerevevvlirkngetfwvl.ltaspvkdd.dge 91 
                                       +e  r++ eq  ++   vev++   +++ +++l +++ + + +  ge
  gi|313126591|ref|YP_004036861.1| 273 AEQTRELAEQVAEIDDIVEVINDIADQTNILALnANIEAARAGeAGE 319
                                       44444444444445577888888888888887777777776654444 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.7
                             PAS_9  36 itdlf....vtdpeanerlraale 55 
                                       i++++    ++++e+ + ++ + +
  gi|313126591|ref|YP_004036861.1| 342 IEEIIhetrEDASETVNSIETVTD 365
                                       444443333333333333333333 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   3.5e-12   2.3e-09       3     112 ..      52     159 ..      50     160 .. 0.83
   2 ?   -0.1   0.1       1.4   8.7e+02      27      81 ..     392     445 ..     387     455 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3.5e-12
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       ++++++++p p f+v+ d++ +y+N++  el G  ++ v+g+  ++++ +e      + l q +eq+ +   ++  +
  gi|313126591|ref|YP_004036861.1|  52 FEQVVNNIPQPGFAVNDDHELTYFNDTVSELYGRGADNVIGRDAYEVFQTEG---KDKTLAQTAEQTGDVIREDDYR 125
                                       899*********************************************9885...4455555555555555555555 PP

                                       EC.TTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  80 kl.rdgrpihlevraspvrdaggeilgflgvlrd 112
                                       ++ + +++++++  a p++ ++ge  g++ ++ d
  gi|313126591|ref|YP_004036861.1| 126 EVpTAKGTRWVRGMAIPFFAPDGESVGAVEIVED 159
                                       5559*******************98888777666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                                       CHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS  27 NaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfkl 81 
                                       ++ +e++ G + +++++   + +++ +  a e+ +++ +  e++ +++a+++++  
  gi|313126591|ref|YP_004036861.1| 392 STGMEDIAGATDDQAVRTEEVASMIDT--AtERSKKVAEEVETAADANAEQVTLVA 445
                                       556889999999999999999888744..447888888888888888888887765 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1     5e-11   3.2e-08       1     107 [.      56     162 ..      56     165 .. 0.83
   2 ?   -2.1   0.0       7.2   4.6e+03      56      68 ..     403     415 ..     372     437 .. 0.64

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..p 75 
                                       ++++p++ +++++d   +y N +  el+g+ ++ ++G+  +e++ +e ++   +  + + +++++i++ +++     
  gi|313126591|ref|YP_004036861.1|  56 VNNIPQPGFAVNDDHELTYFNDTVSELYGRGADNVIGRDAYEVFQTEGKDK--TLAQTAEQTGDVIREDDYREVptA 130
                                       5899****************************************9863333..333344455555555554444679 PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTe 107
                                       +++r++   ++P+++++Ge +g+++i+ D+T 
  gi|313126591|ref|YP_004036861.1| 131 KGTRWVRGMAIPFFAPDGESVGAVEIVEDVTP 162
                                       ******************************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.2
                             PAS_4  56 lrrvlegeepief 68 
                                       +++++++ee++++
  gi|313126591|ref|YP_004036861.1| 403 DDQAVRTEEVASM 415
                                       4455555555554 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.6e-07   0.00023       6     106 .]      57     161 ..      53     161 .. 0.78
   2 ?   -2.2   0.1       9.6   6.1e+03      38      44 ..     194     200 ..     166     238 .. 0.55
   3 ?    3.3   0.2      0.19   1.2e+02      50      98 ..     355     401 ..     321     403 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.6e-07
                            PAS_10   6 nstpieltflDdnlqirrFtpaakklfklipa.dvGrpladihpk.kavknveeviealrt..gekdevevvvpkng 78 
                                       n++p     ++d+ ++++F+++ ++l+ + ++  +Gr+  ++ ++  + k + +  e+  +  +e+d+ ev+ +k  
  gi|313126591|ref|YP_004036861.1|  57 NNIPQPGFAVNDDHELTYFNDTVSELYGRGADnVIGRDAYEVFQTeGKDKTLAQTAEQTGDviREDDYREVPTAKGT 133
                                       56666666799************999999765157******965535555555555555441135578888999*** PP

                            PAS_10  79 kwvlvrylpyrdedgeiaGvvetfvDit 106
                                       +wv     p+   dge  G+ve++ D+t
  gi|313126591|ref|YP_004036861.1| 134 RWVRGMAIPFFAPDGESVGAVEIVEDVT 161
                                       **************************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.6
                            PAS_10  38 dvGrpla 44 
                                        vG+ + 
  gi|313126591|ref|YP_004036861.1| 194 RVGDAVH 200
                                       2222222 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.19
                            PAS_10  50 kavknveeviealrtgekdevevvvpkngkwvlvrylpyrdedgeiaGv 98 
                                       + v+++e v++++r++ + + e+v   n++ +l  + +  +  ++iaG+
  gi|313126591|ref|YP_004036861.1| 355 ETVNSIETVTDEVRSSADAVREMV--DNQESILDAVNATSTGMEDIAGA 401
                                       566777888888888888877765..56777777777777777777775 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   4.2    0.0016         1       7      92 ..     160     245 ..     155     249 .. 0.67
   2 !    8.7   0.6    0.0032       2.1      35      75 ..     261     301 ..     250     308 .. 0.50
   3 ?    5.1   2.6     0.042        27      23      85 ..     344     403 ..     323     411 .. 0.68
   4 !   10.7   0.9    0.0008      0.51      39      86 ..     416     463 ..     405     467 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                           BLOC1_2   7 vskyleaeleatvedyklLeklNeaasekykklkdvaas.lekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                       v+ +++++ ++ +++  l e++   +  + +++++++ + +++ ++  +e+ e++++   ++  + ++v+++ + ++
  gi|313126591|ref|YP_004036861.1| 160 VTPVVKQQNQIKKAQETLSEEVTD-TVDQATDVTERVGDaVHEASSMAQEQAENMEEVSGEVGSLSATVEQIAASAD 235
                                       555666666666555555555544.44455555555555055555555666669999999***************** PP

                           BLOC1_2  83 eLDeyskeLE 92 
                                       e++e s e E
  gi|313126591|ref|YP_004036861.1| 236 EINERSEEAE 245
                                       **99998866 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0032
                           BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqqidqiekqvt 75 
                                       + ++++++ ++++++  +l e+ +e++  ++ i++i +q++
  gi|313126591|ref|YP_004036861.1| 261 RMEDVAESGEEAAEQTRELAEQVAEIDDIVEVINDIADQTN 301
                                       33344444444444444444444445555555555555544 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.042
                           BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLD 85 
                                       +++++  e ase ++++++v++++++++++++e    ++++ + +d+++++ t +e+++ + D
  gi|313126591|ref|YP_004036861.1| 344 EIIHETREDASETVNSIETVTDEVRSSADAVRE---MVDNQESILDAVNATSTGMEDIAGATD 403
                                       356666777888888888888888888888888...677777777777777777777776655 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.0008
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                       ++++++  +k +e+++   ++ +++++ + +i    ++Le+av eLD+
  gi|313126591|ref|YP_004036861.1| 416 IDTATERSKKVAEEVETAADANAEQVTLVADIASAMERLESAVGELDS 463
                                       34556666777899999999***************************8 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.3e-05     0.021       3      43 ..      52      93 ..      50     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-05
                             PAS_8  3 lralfesspd.giavvdlgdrivdvNqaalellGys.adlkge 43
                                      ++++++++p+ g av d +  +++ N++  el+G   + ++g 
  gi|313126591|ref|YP_004036861.1| 52 FEQVVNNIPQpGFAVND-DHELTYFNDTVSELYGRGaDNVIGR 93
                                      89********9999655.446*************444444443 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   3.7    0.0084       5.4      38      86 ..     156     204 ..     152     207 .. 0.78
   2 ?    4.2   5.2     0.078        50      30      81 ..     229     297 ..     199     307 .. 0.46
   3 !   12.3   4.1   0.00025      0.16      18      85 ..     322     389 ..     320     399 .. 0.79
   4 ?    3.4   3.7      0.15        94      29      72 ..     410     456 ..     383     467 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0084
                            DUF948  38 lekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       + ++v+p++k+ +++ +  ++l e+v++ +++   +te v+d+    s+
  gi|313126591|ref|YP_004036861.1| 156 IVEDVTPVVKQQNQIKKAQETLSEEVTDTVDQATDVTERVGDAVHEASS 204
                                       5678888888888888888889999999888888888888887666665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.078
                            DUF948  30 eaaatieele.................kqvdpilkevedllakvnelledvneklekvdplteavadlg 81 
                                       ++aa+ +e++                 +++ + +++v++  +++ e + ++ e+++++d ++e ++d++
  gi|313126591|ref|YP_004036861.1| 229 QIAASADEINerseeaerlaaesteagERAVGRMEDVAESGEEAAEQTRELAEQVAEIDDIVEVINDIA 297
                                       222222222222222223333333333444444444444444444445555555555555555555555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00025
                            DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       +vv +++k++++e+++  e +e+ ++++ +++ ++++ +++++++v++  ++v +++++ + + ++v+
  gi|313126591|ref|YP_004036861.1| 322 AVVANEVKSLANEVQNESERIEEIIHETREDASETVNSIETVTDEVRSSADAVREMVDNQESILDAVN 389
                                       56778888888899999999998888888888888888888888888888888888888777666655 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.15
                            DUF948  29 deaaatieelekqvdpilkevedllakvne...lledvneklekvdp 72 
                                       +e+a++i++ +++ +++ +eve++ +   e   l++d+ + +e++++
  gi|313126591|ref|YP_004036861.1| 410 EEVASMIDTATERSKKVAEEVETAADANAEqvtLVADIASAMERLES 456
                                       34555555555555555555554433222223344455555544444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.4    0.0006      0.38      55     121 ..     168     231 ..     154     246 .. 0.51
   2 ?    5.4   1.2     0.028        18      55     105 ..     249     299 ..     233     311 .. 0.70
   3 ?    6.9   3.6    0.0092       5.9      60     119 ..     327     387 ..     318     391 .. 0.59
   4 ?    7.5   2.7    0.0064       4.1      41     122 ..     386     463 ..     377     465 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0006
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       ++++++++ Ls++   v +++d+ +++++ + + v+e+++  +e  e++e+v+  v +l +++e+i 
  gi|313126591|ref|YP_004036861.1| 168 NQIKKAQETLSEE---VTDTVDQATDVTERVGDAVHEASSMAQEQAENMEEVSGEVGSLSATVEQIA 231
                                       3444444444443...344455555555555555555554444444444444444444444444443 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.028
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                       ++ +++ ++   r++ v ++ +e +e ++e++e+v+e+ + ++ i++  ++
  gi|313126591|ref|YP_004036861.1| 249 AESTEAGERAVGRMEDVAESGEEAAEQTRELAEQVAEIDDIVEVINDIADQ 299
                                       555555566667888888888888888888888888888877777766554 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0092
                           DUF1664  60 tkrhLssridrvdkkldeqk.eiskeikeevtevredlseigedvesvkeavegleskler 119
                                         + L++++++  ++++e + e+ ++ +e v++++  ++e+++  ++v+e+v + es l+ 
  gi|313126591|ref|YP_004036861.1| 327 EVKSLANEVQNESERIEEIIhETREDASETVNSIETVTDEVRSSADAVREMVDNQESILDA 387
                                       4455666666666666664314555556666666666666666666777777666666555 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0064
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       dav+  s+ +e    ++a + ++ + r ++v + +d  +e sk+++eev+++ +  +e  + v  + +a+e les +
  gi|313126591|ref|YP_004036861.1| 386 DAVNATSTGME----DIAGATDDQAVRTEEVASMIDTATERSKKVAEEVETAADANAEQVTLVADIASAMERLESAV 458
                                       55555555554....566777777889999********************999999888899999999999999999 PP

                           DUF1664 118 eriee 122
                                        ++++
  gi|313126591|ref|YP_004036861.1| 459 GELDS 463
                                       98865 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  16.3     0.002       1.3      12     138 ..     155     283 ..     154     303 .. 0.78
   2 ?    1.0  11.0      0.46     3e+02      52     120 ..     321     388 ..     253     392 .. 0.62
   3 ?    8.0   9.4    0.0032       2.1      22     118 ..     326     427 ..     314     436 .. 0.78
   4 ?   12.2   4.2   0.00017      0.11       2      94 ..     359     450 ..     358     467 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.002
                              YkyA  12 eavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekik 88 
                                       e+ve+  ++++qq++++++++   e  ++++++ +d  +++ + + ea ++++e+ e +e+    + +    +e+i 
  gi|313126591|ref|YP_004036861.1| 155 EIVEDVTPVVKQQNQIKKAQETLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENMEEVSGEVGSLSATVEQIA 231
                                       577888999****************************************************9999999999999999 PP

                              YkyA  89 eeieei..edeelkkeaeelieameeryeaydklykaYkealeldkeLYemL 138
                                       ++ +ei    ee++  a e  ea e     ++++ ++ +ea e+ +eL e+ 
  gi|313126591|ref|YP_004036861.1| 232 ASADEIneRSEEAERLAAESTEAGERAVGRMEDVAESGEEAAEQTRELAEQV 283
                                       9999994334455555555566666666666666666666666666665544 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.46
                              YkyA  52 ikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeaeelieameeryeaydkl 120
                                       +   ++e+ ++++e +++ e  +e+i+e++e  ++  ++ie + de +++ a+++ e ++++++  d++
  gi|313126591|ref|YP_004036861.1| 321 FAVVANEVKSLANEVQNESERIEEIIHETREDASETVNSIETVTDE-VRSSADAVREMVDNQESILDAV 388
                                       4445667777777777777777788999999999999999999777.9999999999988888877765 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0032
                              YkyA  22 eqqekLtelekkeqelyeeiielgmdefdk....ikklsdealenveeReellekekesieeakeefekikeeieei 94 
                                       ++ ++L +  ++e e  eeii  + ++ ++    i++  de+ +++++ +e++++++ ++++ +   + ++++   +
  gi|313126591|ref|YP_004036861.1| 326 NEVKSLANEVQNESERIEEIIHETREDASEtvnsIETVTDEVRSSADAVREMVDNQESILDAVNATSTGMEDIAGAT 402
                                       56677888888999999999998888765545558888899999999999999997777777788888888888888 PP

                              YkyA  95 edeelk.keaeelieameeryeayd 118
                                       +d++++ +e+ ++i++  er ++  
  gi|313126591|ref|YP_004036861.1| 403 DDQAVRtEEVASMIDTATERSKKVA 427
                                       8886642789999999999998765 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00017
                              YkyA   2 peekiyealeeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesie 78 
                                       ++e++++ + +++++ +e++++qe++ ++ +      e+i  + +d++   +++++ +++++ eR +++++e e   
  gi|313126591|ref|YP_004036861.1| 359 SIETVTDEVRSSADAVREMVDNQESILDAVNATSTGMEDIAGA-TDDQAVRTEEVASMIDTATERSKKVAEEVETAA 434
                                       57899999999*****************************985.56669999***********************99 PP

                              YkyA  79 eakeefekikeeieei 94 
                                       +a+ e  ++ ++i + 
  gi|313126591|ref|YP_004036861.1| 435 DANAEQVTLVADIASA 450
                                       9999988887777666 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.2      0.47     3e+02      68     105 ..     159     196 ..     149     214 .. 0.68
   2 ?   12.0   5.4   0.00029      0.19      22     107 ..     211     296 ..     200     297 .. 0.91
   3 ?   10.1   1.1    0.0012      0.75      43     102 ..     326     386 ..     317     390 .. 0.89
   4 ?    2.5   0.7      0.26   1.7e+02      43      93 ..     414     461 ..     397     468 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.47
                                       -TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS- CS
                      Seryl_tRNA_N  68 daeeliaevkelkeelkaleaelkeleaeleklllaiP 105
                                       d + ++++ +++k+  ++l++e+++  ++ ++++ +++
  gi|313126591|ref|YP_004036861.1| 159 DVTPVVKQQNQIKKAQETLSEEVTDTVDQATDVTERVG 196
                                       55556666666666666666666666666666555554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00029
                                       TCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  22 gedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaele 98 
                                       ++ ++   e+ +l +  +++ + ++e+++++ e+ +  ++  +++e a   +++v+e +ee ++ + el+e  ae++
  gi|313126591|ref|YP_004036861.1| 211 ENMEEVSGEVGSLSATVEQIAASADEINERSEEAERLAAESTEAGERAVGRMEDVAESGEEAAEQTRELAEQVAEID 287
                                       467777889999***************************************************************** PP

                                       HHHCTS--- CS
                      Seryl_tRNA_N  99 klllaiPNi 107
                                       +++ +i +i
  gi|313126591|ref|YP_004036861.1| 288 DIVEVINDI 296
                                       ***999776 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       +e+ +l +e  + s+ I++++ +  eda+e +++++++ +e+    ++++e+ +++e++l 
  gi|313126591|ref|YP_004036861.1| 326 NEVKSLANEVQNESERIEEIIHETrEDASETVNSIETVTDEVRSSADAVREMVDNQESILD 386
                                       5777788888888999*****9999***************************999999886 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkel 93 
                                       + ++ + ++++++++e++ a +++++       v+++   +++le ++ el
  gi|313126591|ref|YP_004036861.1| 414 SMIDTATERSKKVAEEVETAADANAEQV---TLVADIASAMERLESAVGEL 461
                                       4456666667777777777776664433...34444445555555555444 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00038      0.24       2      86 ..      73     154 ..      72     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy.egeyRirrkdGeyrwveararvird 77 
                                       +y +++v+e++G  ++ ++g+  + +++   e  +++ ++ +e   +g ++ e +yR +    ++rwv+  a +++ 
  gi|313126591|ref|YP_004036861.1|  73 TYFNDTVSELYGRGADNVIGR--DAYEVFQTEGKDKTLAQTAEQ--TGDVIrEDDYREVPTAKGTRWVRGMAIPFFA 145
                                       699******************..9***99999988877777654..577775888********************** PP

                             PAS_3  78 engkpvrvi 86 
                                        +g+ v  +
  gi|313126591|ref|YP_004036861.1| 146 PDGESVGAV 154
                                       ***988765 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4  16.6      0.47     3e+02       6     108 ..     159     256 ..     153     305 .. 0.43
   2 ?   14.6   9.1   4.1e-05     0.026      42     146 .]     328     433 ..     318     458 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.47
                         ApoLp-III   6 elqksvkkqlnlpsqeevvetiKensenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevk 82 
                                       ++ + vk+q n  + +   et+ e+++  vdq+ +v + + +++ ++s+ ++e  +++  +++  + +ls+   +++
  gi|313126591|ref|YP_004036861.1| 159 DVTPVVKQQ-N--QIKKAQETLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENME-EVSGEVGSLSATVEQIA 231
                                       444444444.2..2222233344455555555555555555555555544444444443.23333333333333333 PP

                         ApoLp-III  83 kkaqelqekvQsgvqslvkesqklae 108
                                        +a+e +e   +  + l+ es +++e
  gi|313126591|ref|YP_004036861.1| 232 ASADEINERS-EEAERLAAESTEAGE 256
                                       3333333332.223444444444433 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.1e-05
                         ApoLp-III  42 ikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekv..Qsgvqslvkesqklaeslkensqe 116
                                        ksl +e++++s+ +ee++ e++++ +et+++++    ev  +a++ +e v  Q   +s++  ++++   +++ + +
  gi|313126591|ref|YP_004036861.1| 328 VKSLANEVQNESERIEEIIHETREDASETVNSIETVTDEVRSSADAVREMVdnQ---ESILDAVNATSTGMEDIAGA 401
                                       689999*****************************7778888888777777333...44444444444444444333 PP

                         ApoLp-III 117 akekl..akaikqayddaveaaqklakqLkea 146
                                       + ++   ++ + +++d a+e ++k+a+++++a
  gi|313126591|ref|YP_004036861.1| 402 TDDQAvrTEEVASMIDTATERSKKVAEEVETA 433
                                       33332113346678999**********99975 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  12.2    0.0016         1      61     166 ..     175     277 ..     170     286 .. 0.90
   2 ?    1.4   2.3      0.35   2.2e+02      71     132 ..     286     351 ..     274     357 .. 0.42
   3 ?    8.0  10.7    0.0034       2.2      65     159 ..     340     434 ..     310     451 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                            DUF745  61 qqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaek 137
                                       ++l e++++ +  a +v +++ ++++++++ a+  a+ ++++  ++ +l+a+++++ ++++++++ +++a++ +ae 
  gi|313126591|ref|YP_004036861.1| 175 ETLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENMEEVSGEVGSLSATVEQIAASADEINERSEEAERLAAES 251
                                       56789999999****************************************************************** PP

                            DUF745 138 tqlleaAkkRveeLkkqlkearkdlektk 166
                                       t+  e A  R+e + +  +ea +    t+
  gi|313126591|ref|YP_004036861.1| 252 TEAGERAVGRMEDVAESGEEAAEQ---TR 277
                                       **************9998888754...33 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.35
                            DUF745  71 lreaeavvqeekkslqsseanakaaakaakqaqqqleal....kallkaakenlenaeqvaagaqq 132
                                       + +  +v++++ ++++    na++ a+ a +a + ++++    k+l ++++++ e++e++ ++  +
  gi|313126591|ref|YP_004036861.1| 286 IDDIVEVINDIADQTNILALNANIEAARAGEAGEGFAVVanevKSLANEVQNESERIEEIIHETRE 351
                                       333334444444444444444444444444444444443000033344444444444444444433 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0034
                            DUF745  65 eqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqll 141
                                       e++e+ ++e+ +  +e  +s+++    +++ a+a++++  + e++ ++++a+++ +e++  + +  +   +e ++++
  gi|313126591|ref|YP_004036861.1| 340 ERIEEIIHETREDASETVNSIETVTDEVRSSADAVREMVDNQESILDAVNATSTGMEDIAGATDDQAVRTEEVASMI 416
                                       66778889999999999999999999999999999999999************************************ PP

                            DUF745 142 eaAkkRveeLkkqlkear 159
                                       ++A +R +++ +++++a 
  gi|313126591|ref|YP_004036861.1| 417 DTATERSKKVAEEVETAA 434
                                       ************999875 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4    0.0018       1.2      10      80 ..     159     229 ..     156     234 .. 0.94
   2 ?   -1.3   0.0       4.2   2.7e+03      24      59 ..     236     271 ..     228     300 .. 0.60
   3 ?    2.3   0.1      0.33   2.1e+02      31      73 ..     327     369 ..     324     376 .. 0.87
   4 ?    1.4   0.1       0.6   3.9e+02       9      34 ..     372     397 ..     367     431 .. 0.79
   5 ?   -0.6   0.0       2.6   1.7e+03      33      54 ..     413     434 ..     403     464 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                              KxDL  10 dldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                                       d+  ++++Q+q+ +  +  ++e+++  +++    +++ + + +   +++e  +++e +   + sl a++++
  gi|313126591|ref|YP_004036861.1| 159 DVTPVVKQQNQIKKAQETLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENMEEVSGEVGSLSATVEQ 229
                                       6777899**********************************************************999875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.2
                              KxDL  24 rlnkknreLlelnalsqerlaklrarfkqgtkllke 59 
                                       ++n+ ++e ++l a+s e  +++  r+++ ++   e
  gi|313126591|ref|YP_004036861.1| 236 EINERSEEAERLAAESTEAGERAVGRMEDVAESGEE 271
                                       566666666666666666666666555555444433 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.33
                              KxDL  31 eLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirs 73 
                                       e++ l +++q++ +++++ + +  ++++e+ + +e+++  +rs
  gi|313126591|ref|YP_004036861.1| 327 EVKSLANEVQNESERIEEIIHETREDASETVNSIETVTDEVRS 369
                                       7889999999999999999999999999999999999998886 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.6
                              KxDL   9 edldeilalQaqtsgrlnkknreLle 34 
                                       +++ e+++ Q+ +++  n+++  +++
  gi|313126591|ref|YP_004036861.1| 372 DAVREMVDNQESILDAVNATSTGMED 397
                                       567899999******99999976665 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 2.6
                              KxDL  33 lelnalsqerlaklrarfkqgt 54 
                                         +++ + er +k+ ++++  +
  gi|313126591|ref|YP_004036861.1| 413 ASMIDTATERSKKVAEEVETAA 434
                                       4455555555555555554443 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3      0.02        13      53     112 ..     156     216 ..     153     228 .. 0.88
   2 ?    4.8   0.3     0.047        30      74     115 ..     325     366 ..     317     378 .. 0.84
   3 ?    3.2   0.2      0.14        91      22      92 ..     438     462 ..     376     469 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHH CS
                              COG5  53 itsnhleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeaeklqsalkrl 112
                                       i++  +++ ++ +++k++++ + +e++  +++ +   er+   v+e    a++  + ++ +
  gi|313126591|ref|YP_004036861.1| 156 IVEDVTPVVKQQNQIKKAQEtLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENMEEV 216
                                       667778899999********99999*********************999999888777665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.047
                                       XXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHH CS
                              COG5  74 lselksslesLsasyerlkskvlepyeeaeklqsalkrlhqt 115
                                        +e+ks  +++++  er+++ ++e  e+a++ +++++++ + 
  gi|313126591|ref|YP_004036861.1| 325 ANEVKSLANEVQNESERIEEIIHETREDASETVNSIETVTDE 366
                                       5678888899999*******************9999998765 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.14
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              COG5  22 nnnddteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlk 92 
                                        ++ +                                              ++ ++ s +e+L++++  l 
  gi|313126591|ref|YP_004036861.1| 438 AEQVT----------------------------------------------LVADIASAMERLESAVGELD 462
                                       22222..............................................44445555555544444433 PP

>> GLE1  GLE1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.9    0.0036       2.3       5      60 ..     155     210 ..     153     258 .. 0.85
   2 ?    3.2   0.4     0.068        44       8      67 ..     329     387 ..     324     461 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0036
                              GLE1   5 qikknlleqvkedkelkkllgdlkrkInpkvgQltnsseqlkkitkelkellesgk 60 
                                       +i +++ ++vk++ ++kk   +l  +++ +v Q t  +e + + ++e  ++ +++ 
  gi|313126591|ref|YP_004036861.1| 155 EIVEDVTPVVKQQNQIKKAQETLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQA 210
                                       68899**********************************99999999888884333 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.068
                              GLE1   8 knlleqvke.dkelkkllgdlkrkInpkvgQltnsseqlkkitkelkellesgkpvkvadk 67 
                                       k+l ++v++ ++ + +++++ +   + +v+ + + ++++++ +++++e++++++++   d+
  gi|313126591|ref|YP_004036861.1| 329 KSLANEVQNeSERIEEIIHETREDASETVNSIETVTDEVRSSADAVREMVDNQESI--LDA 387
                                       55666666668999999999***************************999555443..333 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.4     0.037        24      17      66 ..     165     212 ..     155     258 .. 0.57
   2 ?    1.9   0.2      0.45   2.9e+02      45      45 ..     272     272 ..     210     311 .. 0.43
   3 ?    3.5   5.7      0.14        89      32      66 ..     313     373 ..     272     464 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.037
                        Syntaxin_2  17 klvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssds 66 
                                       k+++q++++  +e l e++ +++++++++ +++ + +++ s++++ +  +
  gi|313126591|ref|YP_004036861.1| 165 KQQNQIKKA--QETLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQAEN 212
                                       445555544..445666666666666666666666666666666555433 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.45
                        Syntaxin_2  45 l 45 
                                        
  gi|313126591|ref|YP_004036861.1| 272 A 272
                                       1 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.14
                        Syntaxin_2  32 r..........................eklhelieeinelikktnellkklsqldnsssds 66 
                                       r                          e+++e+i+e++e +++t ++++ ++   +ss d 
  gi|313126591|ref|YP_004036861.1| 313 RageagegfavvanevkslanevqnesERIEEIIHETREDASETVNSIETVTDEVRSSADA 373
                                       0555555555555555555555555559999999999999999999998888777777665 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  10.7   0.00014     0.089     155     331 ..     178     368 ..     163     396 .. 0.67
   2 ?    0.3   2.4      0.29   1.9e+02     216     286 ..     369     447 ..     333     470 .. 0.42

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                              FUSC 155 apalrarlrallrdalalaaaalageegaeareaararlaadilalealrsqaayesprirararalrrllsrmlal 231
                                       ++++ ++++++ + + +   a+ ++++ a+++ ++++++ +++  l+a ++q a+   +i +r++ + rl ++ +++
  gi|313126591|ref|YP_004036861.1| 178 SEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENMEEVSGEVGSLSATVEQIAASADEINERSEEAERLAAESTEA 254
                                       4444445555554444555555556666666678899**************************************** PP

                              FUSC 232 lallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrrale.....adadtaall 303
                                         ++ +  +  a+  +e a++++ela+ +ae++++ +     a+++++ al a ++a+r+ ++       a+    l
  gi|313126591|ref|YP_004036861.1| 255 GERAVGRMEDVAESGEEAAEQTRELAEQVAEIDDIVEVINDIADQTNILALNANIEAARAGEAgegfaVVANEVKSL 331
                                       ****9999999999999999999999999999999555556677888888888888888877766666444444444 PP

                              FUSC 304 larlaellaelaqllaslraleaaiaa.........a 331
                                       + +++++ ++  ++ ++ r++++++++         +
  gi|313126591|ref|YP_004036861.1| 332 ANEVQNESERIEEIIHETREDASETVNsietvtdevR 368
                                       4444444444444444444444444444433333332 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.29
                              FUSC 216 araralrrllsrmlallallsslarllarlraeeaaavpe...laallaelaal.....eaaaaaealeaalaalra 284
                                         a+a+r++   + ++l  ++++ + +++   + ++++     +a +++++ +      e+ + a++  a+  +l a
  gi|313126591|ref|YP_004036861.1| 369 SSADAVREMVDNQESILDAVNATSTGMEDIAGATDDQAVRteeVASMIDTATERskkvaEEVETAADANAEQVTLVA 445
                                       33333444444444444333333333333333333332222223333333333333322111112222222222222 PP

                              FUSC 285 rl 286
                                       ++
  gi|313126591|ref|YP_004036861.1| 446 DI 447
                                       22 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.0    0.0023       1.5      28     139 ..     164     285 ..     156     317 .. 0.75
   2 ?    5.1   1.5     0.016        10      35     140 ..     329     434 ..     305     458 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0023
                             Atg14  28 rerlaklksekeslkkkiekalegke........eaeqledkiknkkakleelksliadlrerlqelkdklsqlkke 96 
                                        ++  ++k+++e+l +++++ + + +        +++++++ ++ +++++ee   ++ +l++ ++++ ++ ++ +++
  gi|313126591|ref|YP_004036861.1| 164 VKQQNQIKKAQETLSEEVTDTVDQATdvtervgdAVHEASSMAQEQAENMEEVSGEVGSLSATVEQIAASADEINER 240
                                       5678899*******************888888887778888888888888888888888888888888888887777 PP

                             Atg14  97 ieekkkklaklsdklk....kRrsdleslqneleerrkkqiaklqda 139
                                        ee+ ++la+ s +       R++d +   +e +e  +++ +++  +
  gi|313126591|ref|YP_004036861.1| 241 SEEA-ERLAAESTEAGeravGRMEDVAESGEEAAEQTRELAEQVA-E 285
                                       7766.4555555555578888888888888887777777666665.3 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                             Atg14  35 ksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekk...kklakls 108
                                       ks  ++++++ e+++e  +   ++++++  + +++e+   +++++ + ++e+ d +++  +++++++   + +a+  
  gi|313126591|ref|YP_004036861.1| 329 KSLANEVQNESERIEEIIH---ETREDASETVNSIETVTDEVRSSADAVREMVDNQESILDAVNATStgmEDIAGAT 402
                                       3333333333333333333...3335555555555555555555555555555555555555555552223455555 PP

                             Atg14 109 dklkkRrsdleslqneleerrkkqiaklqdai 140
                                       d+ + R+++ +s+ +   er kk  +++ +a 
  gi|313126591|ref|YP_004036861.1| 403 DDQAVRTEEVASMIDTATERSKKVAEEVETAA 434
                                       55568888888888888888888777776554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   3.5     0.079        51      12      64 ..     153     205 ..     150     208 .. 0.83
   2 ?    9.7   8.0    0.0013       0.8       5     101 ..     199     292 ..     195     302 .. 0.62
   3 ?    3.7   0.9     0.087        56       7      55 ..     264     312 ..     257     319 .. 0.68
   4 ?   11.1   4.5   0.00047       0.3      12      73 ..     325     386 ..     311     398 .. 0.59
   5 ?    1.5   2.9      0.44   2.8e+02       8      66 ..     402     456 ..     384     467 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.079
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkL 64 
                                       a+e+ e+++p+ ++ +++k+  +++ ++v  t +++ d ++ + dA ++ + +
  gi|313126591|ref|YP_004036861.1| 153 AVEIVEDVTPVVKQQNQIKKAQETLSEEVTDTVDQATDVTERVGDAVHEASSM 205
                                       56788999999999999999999999999999999999999888887777766 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       ++ea++ a+e  e ++++s ++  +++ +++i++s++e+ne      +a r+A +s    e+ + +++d  ++ ++ 
  gi|313126591|ref|YP_004036861.1| 199 VHEASSMAQEQAENMEEVSGEVGSLSATVEQIAASADEINERS---EEAERLAAESTEAGERAVGRMEDVAESGEEA 272
                                       6788888899899999999999999999999999988888754...4445555555555555555555544444444 PP

                                       HHH...HHHHHHHHHHHHHH CS
                        Laminin_II  82 eeassslsdniseikelIaq 101
                                        e+   l +++ ei  ++++
  gi|313126591|ref|YP_004036861.1| 273 AEQTRELAEQVAEIDDIVEV 292
                                       44444455555444444443 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.087
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankair 55 
                                       ++ e+ +e  eq+ +l++++ ++ + ++ in+ +++tn ++ +an   +
  gi|313126591|ref|YP_004036861.1| 264 DVAESGEEAAEQTRELAEQVAEIDDIVEVINDIADQTNILALNANIEAA 312
                                       5556666677777777777777777777777777777777666665555 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00047
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld 73 
                                       a+ev++  ++++++ e+++e ++e ++++ et + ++  +  +r+  ++v+++  + + +ld
  gi|313126591|ref|YP_004036861.1| 325 ANEVKSLANEVQNESERIEEIIHETREDASETVNSIETVTDEVRSSADAVREMVDNQESILD 386
                                       44555555555555555555555555555555555555555555555666666555555555 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.44
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-- CS
                        Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLek 66 
                                        +++a+ ++e+   +++ +e+ k+ ++e+++ ++       +  + ++d  +++  Le 
  gi|313126591|ref|YP_004036861.1| 402 TDDQAVRTEEVASMIDTATERSKKVAEEVETAADANA----EQVTLVADIASAMERLES 456
                                       4555555666666666666666655555555533222....333444444444444444 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.3       1.4   8.9e+02      38      84 ..     167     214 ..     145     244 .. 0.57
   2 ?    2.1   0.0      0.29   1.9e+02      37      60 ..     272     295 ..     261     304 .. 0.85
   3 ?    8.9   0.7    0.0022       1.4      39      88 ..     326     376 ..     323     387 .. 0.78
   4 ?   -1.1   0.1         3   1.9e+03      44      92 ..     384     432 ..     379     440 .. 0.71
   5 ?   -0.2   0.1       1.6   9.9e+02      44      91 ..     419     466 ..     399     470 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.4
                          Noelin-1  38 srqlrqllekv.qnlsqsievldlRtsrdlqyvrktetllktlesklk 84 
                                       ++q+++ +e   + +++++++ +  t+r  + v+++ ++ ++  ++++
  gi|313126591|ref|YP_004036861.1| 167 QNQIKKAQETLsEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENME 214
                                       444444444431245555555555555555555555554444444444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.29
                          Noelin-1  37 rsrqlrqllekvqnlsqsievldl 60 
                                         +q r+l e+v+ + + +ev++ 
  gi|313126591|ref|YP_004036861.1| 272 AAEQTRELAEQVAEIDDIVEVIND 295
                                       56799***************9975 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0022
                          Noelin-1  39 rqlrqllekvqnlsqsievldlRtsrdl.qyvrktetllktlesklkvvee 88 
                                       +++++l ++vqn s+ ie + + t++d  + v++ et+ ++++s  + v+e
  gi|313126591|ref|YP_004036861.1| 326 NEVKSLANEVQNESERIEEIIHETREDAsETVNSIETVTDEVRSSADAVRE 376
                                       5799**************999999888725678888888888877665554 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3
                          Noelin-1  44 llekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveedrke 92 
                                       +l+ v+  s+ +e ++  t  +    +++ ++++t +++ k+v e+ ++
  gi|313126591|ref|YP_004036861.1| 384 ILDAVNATSTGMEDIAGATDDQAVRTEEVASMIDTATERSKKVAEEVET 432
                                       5667777788888888777776666777778888888888777776655 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.6
                          Noelin-1  44 llekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveedrk 91 
                                        +e+ + +++++e  +   ++++  v +  + ++ les + ++++d +
  gi|313126591|ref|YP_004036861.1| 419 ATERSKKVAEEVETAADANAEQVTLVADIASAMERLESAVGELDSDSE 466
                                       456777788888888888888888888888888888888877777665 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.9      0.27   1.8e+02      34      99 ..     156     222 ..     153     286 .. 0.62
   2 ?    0.4   0.1       0.7   4.5e+02      16      97 ..     226     307 ..     222     310 .. 0.81
   3 ?    8.1   0.4     0.003       1.9      16      67 ..     345     402 ..     337     448 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.27
                             BAR_3  34 llKlckrlieagkaysaaqkqfaqsLrelkkes.kgdeetdesLkkfsellqelenehtilldqaqr 99 
                                       ++ ++  +++ ++++ +aq+++++++ +   +     e + ++ ++ s++ qe +++ ++ + ++ +
  gi|313126591|ref|YP_004036861.1| 156 IVEDVTPVVKQQNQIKKAQETLSEEVTDTVDQAtDVTERVGDAVHEASSMAQEQAENMEEVSGEVGS 222
                                       6777788888999999999999999998666653444555566666666666666666666555443 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.7
                             BAR_3  16 sleevEaeleelekklkkllKlckrlieagkaysaaqkqfaqsLrelkkeskgdeetdesLkkfsellqelenehti 92 
                                       ++e+  a ++e++++ ++  +l  + +eag+  +  ++ +a+s +e + + ++ +e  +    + e+++ ++++ +i
  gi|313126591|ref|YP_004036861.1| 226 TVEQIAASADEINERSEEAERLAAESTEAGERAVGRMEDVAESGEEAAEQTRELAEQVAEIDDIVEVINDIADQTNI 302
                                       67888888888888888888888888899988888888888888888888888888888888888888888888888 PP

                             BAR_3  93 lldqa 97 
                                       l+ +a
  gi|313126591|ref|YP_004036861.1| 303 LALNA 307
                                       87766 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.003
                             BAR_3  16 sleevEaeleelekklkkllKlckrlieagkaysaaqkqfaqsLrelkkes......k 67 
                                        ++e+ ++++e+ + ++ ++ ++++  +a ++++++q+++ + ++  +         +
  gi|313126591|ref|YP_004036861.1| 345 IIHETREDASETVNSIETVTDEVRSSADAVREMVDNQESILDAVNATSTGMediagaT 402
                                       589999*********************************9999998776554444433 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.9     0.023        15      22      76 ..     152     206 ..     145     239 .. 0.85
   2 ?    0.8   0.6         1   6.5e+02      26      51 ..     222     247 ..     206     305 .. 0.56
   3 ?    5.7   2.1     0.031        20      17     103 ..     350     436 ..     339     456 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.023
                           Goodbye  22 kelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqgasma 76 
                                        +++ ved++  ++++++ ++ +++ +e++++++ ++  + + +g+ + ++ sma
  gi|313126591|ref|YP_004036861.1| 152 GAVEIVEDVTPVVKQQNQIKKAQETLSEEVTDTVDQATDVTERVGDAVHEASSMA 206
                                       566779999999*****98888889999**********************99998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1
                           Goodbye  26 svedllkqieaekdkfeefrekkekl 51 
                                       s+ + ++qi a++d+ +e +e+ e+l
  gi|313126591|ref|YP_004036861.1| 222 SLSATVEQIAASADEINERSEEAERL 247
                                       55555555555555554444333333 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.031
                           Goodbye  17 kdealkelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqgasmaFgPaslcfnAvsyLika 93 
                                       +++a ++++s+e +++++++++d+ +e   ++e++ +a++ + + ++ ++g   + a  +   as++ +A     k+
  gi|313126591|ref|YP_004036861.1| 350 REDASETVNSIETVTDEVRSSADAVREMVDNQESILDAVNATSTGMEDIAGATDDQAVRTEEVASMIDTATERSKKV 426
                                       456688999*****************999***********9999999999999888888877788887777777777 PP

                           Goodbye  94 akkvseiyda 103
                                       a++v+++ da
  gi|313126591|ref|YP_004036861.1| 427 AEEVETAADA 436
                                       7777766665 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   6.6     0.033        21       3      54 ..     196     247 ..     194     316 .. 0.85
   2 ?    4.3   2.0     0.076        48      22      76 ..     327     389 ..     321     409 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.033
                              Rx_N   3 sallqkLadllaeeakllkgvkeeleklkdeLesiqavLedaeerqikdeav 54 
                                       + ++   +++++e+a+  ++v +e+ +l  + e+i a  ++  er ++ e +
  gi|313126591|ref|YP_004036861.1| 196 GDAVHEASSMAQEQAENMEEVSGEVGSLSATVEQIAASADEINERSEEAERL 247
                                       56777889999*********************************99877654 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.076
                              Rx_N  22 gvkeeleklkdeLesiqavLedaee........rqikdeavkeWlkelrdlaydaeDvlDefe 76 
                                       +vk+  ++ ++e e+i+ ++++  e         ++  ++v+   + +r+++ + e +lD ++
  gi|313126591|ref|YP_004036861.1| 327 EVKSLANEVQNESERIEEIIHETREdasetvnsIETVTDEVRSSADAVREMVDNQESILDAVN 389
                                       566666777777777777777666633335544444568899999999999999999998776 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.3    0.0021       1.4     390     465 ..     165     239 ..     157     243 .. 0.89
   2 ?    1.6   1.4      0.13        82     422     466 ..     252     296 ..     240     312 .. 0.78
   3 ?    7.1   8.1    0.0028       1.8     279     403 ..     333     458 ..     321     469 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0021
                            AAA_13 390 eekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeink 465
                                       ++++++kk+ e  l ee+++ +d+ ++  +++ +a+ ++   ++e++++++++ +e+  L ++++++  +a+ein+
  gi|313126591|ref|YP_004036861.1| 165 KQQNQIKKAQE-TLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENMEEVSGEVGSLSATVEQIAASADEINE 239
                                       55666665555.59999**********************************************************7 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                            AAA_13 422 ekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinke 466
                                       ++a e +  ++++ ++  ++++e+ +eL +q+ ++  ++e+in++
  gi|313126591|ref|YP_004036861.1| 252 TEAGERAVGRMEDVAESGEEAAEQTRELAEQVAEIDDIVEVINDI 296
                                       445566666777888888999999999999999999999999986 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0028
                            AAA_13 279 defeekqerLekliekveskkselleklkavsde.asensafeedkeelkaeaealeeqLkglqraleaKrkepfks 354
                                       +e++++ er+e++i +  ++ se ++++++v+de  s   a +e +++ ++ ++a++++ +g+++   a  ++ +++
  gi|313126591|ref|YP_004036861.1| 333 NEVQNESERIEEIIHETREDASETVNSIETVTDEvRSSADAVREMVDNQESILDAVNATSTGMEDIAGATDDQAVRT 409
                                       67999999999999999999999999999999974555566777788888899999999999999999999999999 PP

                            AAA_13 355 velesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl 403
                                        e+ s+ + +++ +k+vae  e+ a+ N+    l ++ ++a + le  +
  gi|313126591|ref|YP_004036861.1| 410 EEVASMIDTATERSKKVAEEVETAADANAEQVTLVADIASAMERLESAV 458
                                       9999999999999999999999999999998888888888888887644 PP

>> Vps54_N  Vacuolar-sorting protein 54, of GARP complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.4    0.0084       5.4      29      86 ..     173     230 ..     162     252 .. 0.83
   2 ?    4.1   1.4     0.037        24      36      86 ..     327     377 ..     318     399 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0084
                           Vps54_N  29 syesiekevkklksqhdvvskklsqlilekreefvkelseveeiekelkesvvickng 86 
                                       + e++ +ev+    q + v++++ + + e ++  +++ +++ee+  e+ +  ++++++
  gi|313126591|ref|YP_004036861.1| 173 AQETLSEEVTDTVDQATDVTERVGDAVHEASSMAQEQAENMEEVSGEVGSLSATVEQI 230
                                       457799999999********************************99998776666555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.037
                           Vps54_N  36 evkklksqhdvvskklsqlilekreefvkelseveeiekelkesvvickng 86 
                                       evk l ++ +  s+++ + i e re  ++ ++ +e + +e+++s++ +++ 
  gi|313126591|ref|YP_004036861.1| 327 EVKSLANEVQNESERIEEIIHETREDASETVNSIETVTDEVRSSADAVREM 377
                                       66677777777899****************************999887765 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.2     0.073        47       7      64 ..     178     234 ..     163     248 .. 0.66
   2 ?    6.6   2.1     0.018        12       9      72 ..     229     298 ..     215     311 .. 0.72
   3 ?    7.9   3.6     0.007       4.5       3      68 ..     321     389 ..     320     409 .. 0.74
   4 ?    2.3   0.6      0.39   2.5e+02       8      61 ..     410     462 ..     405     469 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.073
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetv 64 
                                        eeV +++++a+ + +r  +  +++ss   +e  e ++e+  +++s++ ++e++  + 
  gi|313126591|ref|YP_004036861.1| 178 SEEVTDTVDQATDVTERVGDAVHEASS-MAQEQAENMEEVSGEVGSLSATVEQIAASA 234
                                       578888888888888888665555554.356666666666666666666666655544 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.018
                      Syntaxin-6_N   9 eVqkslnkaeslyrrwerlledtsss......tseeldetrteLrkalrsiewdledLeetvriveknps 72 
                                       ++  s++++++  ++ erl  +++++      + e++ e  +e  ++ r++ +++ ++++ v++++   +
  gi|313126591|ref|YP_004036861.1| 229 QIAASADEINERSEEAERLAAESTEAgeravgRMEDVAESGEEAAEQTRELAEQVAEIDDIVEVINDIAD 298
                                       4455555555555555555555444356778889999999999999999999999999999999876554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.007
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrwerlledtss..s.tseeldetrteLrkalrsiewdledLeetvrive 68 
                                       F +v++eV++ +n++++  +r e++ ++t++  s t ++++  ++e+r++ + +++ +++ e   ++v+
  gi|313126591|ref|YP_004036861.1| 321 FAVVANEVKSLANEVQNESERIEEIIHETREdaSeTVNSIETVTDEVRSSADAVREMVDNQESILDAVN 389
                                       889*******************99888877643135666666777777777777666666555555554 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.39
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLe 61 
                                       eeV + +++a++  ++  +  e++  + + e   +  ++ +a++ +e  + +L+
  gi|313126591|ref|YP_004036861.1| 410 EEVASMIDTATERSKKVAEEVETAA-DANAEQVTLVADIASAMERLESAVGELD 462
                                       7888888888888888854233322.3477777788888888888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2297  (0.128116); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        87  (0.00485247); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 1.59u 0.37s 00:00:01.96 Elapsed: 00:00:00.61
# Mc/sec: 2390.32
//
Query:       gi|313126592|ref|YP_004036862.1|  [L=85]
Description: hypothetical protein Hbor_18500 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 547.21
//
Query:       gi|313126593|ref|YP_004036863.1|  [L=107]
Description: DNA-directed RNA polymerase subunit m [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-18   64.7   4.1      5e-18   64.7   4.1    2.9  3  TFIIS_C          Transcription factor S-II (TFIIS)
    3.6e-07   30.0   8.8    0.00075   19.4   1.3    2.3  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    1.6e-06   27.9   0.6    1.6e-06   27.9   0.6    3.1  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    6.9e-05   22.1   7.9       0.02   14.3   1.0    3.0  3  zf-ribbon_3      zinc-ribbon domain
    9.1e-05   22.4   6.8     0.0014   18.6   1.8    2.3  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0023   17.9   9.4        2.7    8.0   0.0    4.1  4  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.006   16.6  10.3         10    6.2  10.3    2.8  1  DZR              Double zinc ribbon
     0.0066   16.6   6.5        2.9    8.2   0.0    4.0  4  zf-RING_7        C4-type zinc ribbon domain
     0.0075   16.2   6.0      0.082   12.8   0.3    2.9  3  Prok-RING_1      Prokaryotic RING finger family 1
  ------ inclusion threshold ------
      0.019   14.5   8.9          2    8.1   0.1    4.0  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.033   14.4   4.2        2.4    8.4   0.2    2.1  2  PHF5             PHF5-like protein
      0.044   14.1   5.2       0.18   12.1   0.4    2.3  2  zf-UBP           Zn-finger in ubiquitin-hydrolases and other 
      0.045   13.3   1.5      0.045   13.3   1.5    3.6  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.046   13.4  11.4      0.076   12.7   0.1    3.9  4  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.054   13.6   8.5       0.32   11.1   1.4    2.8  2  Ribosomal_L37ae  Ribosomal L37ae protein family
      0.077   12.9   9.8       0.15   12.0   0.1    3.5  3  zinc_ribbon_4    zinc-ribbon domain
      0.081   13.2   1.4         16    5.9   0.0    2.8  2  Ribosomal_L32p   Ribosomal L32p protein family
       0.12   12.5   0.2       0.12   12.5   0.2    4.0  4  UPF0547          Uncharacterised protein family UPF0547
       0.14   11.9  13.8        2.1    8.1   0.3    4.1  4  Rubredoxin_2     Rubredoxin metal binding domain
       0.27   10.9   7.0        3.6    7.2   1.6    2.2  2  TackOD1          Thaumarchaeal output domain 1
       0.32   10.9  10.9          8    6.5   0.1    3.6  3  Nudix_N_2        Nudix N-terminal
       0.33   11.1  12.6       0.51   10.5   0.8    4.0  4  Zn-ribbon_8      Zinc ribbon domain
       0.36   11.0   8.8        1.2    9.4   3.6    2.5  2  DUF2387          Probable metal-binding protein (DUF2387)
       0.77    9.8   8.9    1.6e+02    2.3   9.0    2.7  1  HypA             Hydrogenase/urease nickel incorporation, met
          1    9.4   9.4        2.4    8.2   0.5    2.5  2  zinc-ribbons_6   zinc-ribbons
        1.5    9.2   6.2       0.31   11.4   0.5    2.2  2  DUF3268          zinc-finger-containing domain
        1.5    8.6  13.5       0.92    9.3   0.2    3.7  4  zinc_ribbon_2    zinc-ribbon domain
        2.2    8.3  14.6        1.3    9.0   0.8    3.8  4  HalOD2           Halobacterial output domain 2
        3.8    8.3  10.5        8.2    7.2   0.6    3.5  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        3.8    7.8  13.1    3.3e+03   -1.6  13.1    3.0  1  IBR              IBR domain, a half RING-finger domain
        9.5    6.0  14.2         64    3.4   0.1    4.1  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
         10    6.6  13.2        4.5    7.8   0.1    3.7  3  zf-IS66          zinc-finger binding domain of transposase IS


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.84   4.7e+02       3       8 ..       4       9 ..       3      12 .. 0.69
   2 ?    1.9   0.1      0.36     2e+02       3      11 ..      20      28 ..      18      30 .. 0.79
   3 !   64.7   4.1   8.8e-21     5e-18       2      39 .]      66     103 ..      65     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.84
                           TFIIS_C 3 CpkCgs 8
                                     C +Cgs
  gi|313126593|ref|YP_004036863.1| 4 CDECGS 9
                                     777776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.36
                           TFIIS_C  3 CpkCgsrea 11
                                      C +Cg ++a
  gi|313126593|ref|YP_004036863.1| 20 CGSCGFEKA 28
                                      999998876 PP

  == domain 3  score: 64.7 bits;  conditional E-value: 8.8e-21
                           TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                       kCp+Cg+++a + ++Q+RsaDE++t+f++C++C h+Wr
  gi|313126593|ref|YP_004036863.1|  66 KCPECGHDRARYEMKQIRSADESETRFFTCVECSHKWR 103
                                       9************************************8 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.3   1.3e-06   0.00075      31      59 ..       4      30 ..       2      32 .. 0.95
   2 !   14.7   1.2   3.8e-05     0.021      27      58 ..      63     104 ..      56     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-06
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfeadrD 59
                                      C eCgs +k+  +g +++C +Cgfe  rD
  gi|313126593|ref|YP_004036863.1|  4 CDECGSMMKT--DGGVWVCGSCGFEKARD 30
                                      **********..****************9 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.8e-05
                    OrfB_Zn_ribbon  27 TSktCseCgsknke..........alsgrtfkCpnCgfeadr 58 
                                       T  +C+eCg+   +          + ++r f+C +C +++  
  gi|313126593|ref|YP_004036863.1|  63 TTVKCPECGHDRARyemkqirsadESETRFFTCVECSHKWRE 104
                                       7789******999999999***999999*********99865 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.6   2.8e-09   1.6e-06       1      31 [.       1      27 [.       1      31 [. 0.94
   2 ?    1.3   0.8      0.57   3.2e+02       4       8 ..      67      71 ..      66      72 .. 0.93
   3 ?    2.3   0.1      0.28   1.6e+02      16      28 ..      86      99 ..      82     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.8e-09
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYee 31
                                      ++FC +Cg+++  ++++++    C +Cg e+
  gi|313126593|ref|YP_004036863.1|  1 MEFCDECGSMMKTDGGVWV----CGSCGFEK 27
                                      99*****************....****9886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.57
                                      ESTTT CS
                    RNA_POL_M_15KD  4 CpkCg 8 
                                      Cp+Cg
  gi|313126593|ref|YP_004036863.1| 67 CPECG 71
                                      ****8 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.28
                                      CSCCCE.EEESSSS CS
                    RNA_POL_M_15KD 16 dkegkn.feCrqCg 28
                                      d++ ++ f C  C+
  gi|313126593|ref|YP_004036863.1| 86 DESETRfFTCVECS 99
                                      55666679999997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.0   3.6e-05      0.02       2      24 ..       1      25 [.       1      26 [. 0.92
   2 !   10.7   0.2   0.00047      0.26       2      10 ..      64      72 ..      63      76 .. 0.85
   3 ?   -0.3   0.0       1.4   7.6e+02       4      10 ..      94     100 ..      92     106 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-05
                       zf-ribbon_3  2 tvrCPnCGa.p.lssddnvCpyCGt 24
                                      + +C +CG+    + ++ vC +CG 
  gi|313126593|ref|YP_004036863.1|  1 MEFCDECGSmMkTDGGVWVCGSCGF 25
                                      679******988************6 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00047
                       zf-ribbon_3  2 tvrCPnCGa 10
                                      tv+CP+CG+
  gi|313126593|ref|YP_004036863.1| 64 TVKCPECGH 72
                                      789999997 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                       zf-ribbon_3   4 rCPnCGa 10 
                                       +C +C +
  gi|313126593|ref|YP_004036863.1|  94 TCVECSH 100
                                       6999965 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.016       9.2      21      45 ..       4      25 ..       2      26 .. 0.84
   2 !   18.6   1.8   2.4e-06    0.0014      19      45 ..      65     100 ..      60     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                     Zn_Tnp_IS1595 21 CPhCgsrkayriktrglfqCkeCrk 45
                                      C  Cg  +  ++ + g++ C +C+ 
  gi|313126593|ref|YP_004036863.1|  4 CDECG--SMMKTDG-GVWVCGSCGF 25
                                      77888..8888999.********86 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.4e-06
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayrikt........rglfqCkeCrk 45 
                                       + CP Cg++   y++k+         + f C eC++
  gi|313126593|ref|YP_004036863.1|  65 VKCPECGHDrARYEMKQirsadeseTRFFTCVECSH 100
                                       67*******99999999999**************98 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4      0.26   1.4e+02      22      27 ..       4       9 ..       3       9 .. 0.84
   2 !    8.0   0.0    0.0048       2.7      16      28 ..      14      26 ..      13      26 .. 0.91
   3 ?    6.3   0.2     0.016       9.1      22      27 ..      67      72 ..      63      75 .. 0.83
   4 ?    4.7   0.1     0.052        29      19      29 ..      92     102 ..      76     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.26
                    PhnA_Zn_Ribbon 22 CpeCah 27
                                      C+eC++
  gi|313126593|ref|YP_004036863.1|  4 CDECGS 9 
                                      999986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0048
                    PhnA_Zn_Ribbon 16 dgallvCpeCahE 28
                                      dg ++vC  C+ E
  gi|313126593|ref|YP_004036863.1| 14 DGGVWVCGSCGFE 26
                                      999*******977 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.016
                    PhnA_Zn_Ribbon 22 CpeCah 27
                                      CpeC+h
  gi|313126593|ref|YP_004036863.1| 67 CPECGH 72
                                      888887 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.052
                    PhnA_Zn_Ribbon  19 llvCpeCahEw 29 
                                        + C eC+h w
  gi|313126593|ref|YP_004036863.1|  92 FFTCVECSHKW 102
                                       5789*****99 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  10.3     0.019        10      13      35 ..       2      71 ..       1     107 [] 0.67

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.019
                               DZR 13 rfCseCgtklkavaa...............................................edrCpsCg 35
                                      +fC+eCg+ +k                                                     +Cp+Cg
  gi|313126593|ref|YP_004036863.1|  2 EFCDECGSMMKTDGGvwvcgscgfekardaaqeshmtstasredseivdmsdvddaeigpttTVKCPECG 71
                                      5888888888866664444444444444444555555555555555555555555555555555555555 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.012       6.5      25      32 ..       3      10 ..       1      11 [. 0.83
   2 ?    0.6   0.1       1.2   6.5e+02       1       7 [.      19      25 ..      19      38 .. 0.86
   3 !    8.2   0.0    0.0051       2.9      23      30 ..      64      71 ..      41      71 .. 0.74
   4 ?    1.9   0.1      0.46   2.6e+02      15      29 ..      80      98 ..      78      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                                      E-TTT--E CS
                         zf-RING_7 25 tCpeCGRI 32
                                      +C+eCG +
  gi|313126593|ref|YP_004036863.1|  3 FCDECGSM 10
                                      9*****87 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.2
                                      EETTT-- CS
                         zf-RING_7  1 tCgGChm 7 
                                      +Cg C+ 
  gi|313126593|ref|YP_004036863.1| 19 VCGSCGF 25
                                      6999986 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0051
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                       v+CpeCG
  gi|313126593|ref|YP_004036863.1| 64 TVKCPECG 71
                                      59*****9 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.46
                                      HHHCCSTB....-EE-TTT CS
                         zf-RING_7 15 selragde....vvtCpeC 29
                                      +++r +de     +tC eC
  gi|313126593|ref|YP_004036863.1| 80 KQIRSADEsetrFFTCVEC 98
                                      6788887766668999999 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.3   0.00015     0.082       6      32 ..       3      29 ..       1      47 [. 0.86
   2 ?    5.5   0.1     0.028        16      21      27 ..      65      71 ..      56      81 .. 0.82
   3 ?   -0.4   0.1         2   1.1e+03       6      18 ..      94     106 ..      91     107 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCgtpyHr 32
                                       C  Cg  +k +  + vC  Cg    r
  gi|313126593|ref|YP_004036863.1|  3 FCDECGSMMKTDGGVWVCGSCGFEKAR 29
                                      5*********************76655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.028
                       Prok-RING_1 21 VvCpeCg 27
                                      V CpeCg
  gi|313126593|ref|YP_004036863.1| 65 VKCPECG 71
                                      8899999 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2
                       Prok-RING_1   6 kCpvCgkelkeed 18 
                                        C  C+++ +e+d
  gi|313126593|ref|YP_004036863.1|  94 TCVECSHKWREDD 106
                                       5888888877765 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0036         2       4      14 ..       3      13 ..       1      15 [. 0.85
   2 ?    1.6   0.0      0.37   2.1e+02       3      18 ..      18      34 ..      16      37 .. 0.72
   3 ?    6.4   0.2     0.012       6.6       2      10 ..      64      72 ..      63      78 .. 0.90
   4 ?    1.9   0.2      0.31   1.7e+02       3      11 ..      93     101 ..      91     107 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0036
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C++Cg+++ +
  gi|313126593|ref|YP_004036863.1|  3 FCDECGSMMKT 13
                                      8******9976 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.37
                            zf_UBZ  3 ylCerCgkeipes.elq 18
                                      ++C  Cg e   + +++
  gi|313126593|ref|YP_004036863.1| 18 WVCGSCGFEKARDaAQE 34
                                      79****98877664444 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.012
                            zf_UBZ  2 tylCerCgk 10
                                      t+ C++Cg+
  gi|313126593|ref|YP_004036863.1| 64 TVKCPECGH 72
                                      899****96 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.31
                            zf_UBZ   3 ylCerCgke 11 
                                       ++C +C ++
  gi|313126593|ref|YP_004036863.1|  93 FTCVECSHK 101
                                       89****986 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0042       2.4      30      56 ..       4      30 ..       2      47 .. 0.84
   2 ?    7.9   0.6    0.0061       3.4      33      81 ..      55     104 ..      36     107 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0042
                              PHF5 30 cpicdslvkpatkvricdecsfgklee 56
                                      c  c s++k+   v +c +c f k ++
  gi|313126593|ref|YP_004036863.1|  4 CDECGSMMKTDGGVWVCGSCGFEKARD 30
                                      888999999999999999999988765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0061
                              PHF5  33 cdslvkpatkvricdecsfgkl..eekciicgskgvsdayyclecvrlekd 81 
                                        d+ + p+t+v+ c ec   +   e k i  + +++++ + c+ec++  ++
  gi|313126593|ref|YP_004036863.1|  55 DDAEIGPTTTVK-CPECGHDRAryEMKQIRSADESETRFFTCVECSHKWRE 104
                                       577888889888.999*987663377888888899999999****987655 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   0.00033      0.18       1      31 [.       4      38 ..       4      49 .. 0.76
   2 ?    4.2   0.5     0.097        55       1      19 [.      67     100 ..      67     104 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00033
                                      -TTTH...--.SSEEEETTT--EEE-TTTT.-HHH CS
                            zf-UBP  1 CseCn...senknlWlCLkCghvgCgrksn.ghal 31
                                      C eC+   ++++ +W+C +Cg+    ++ + +h++
  gi|313126593|ref|YP_004036863.1|  4 CDECGsmmKTDGGVWVCGSCGFEKARDAAQeSHMT 38
                                      9999955323566********98877766657775 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.097
                                       -TTTH................--.SSEEEETTT-- CS
                            zf-UBP   1 CseCn................senknlWlCLkCgh 19 
                                       C eC+                s +++ + C++C h
  gi|313126593|ref|YP_004036863.1|  67 CPECGhdraryemkqirsadeS-ETRFFTCVECSH 100
                                       6667766666666666666433.5889******98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   7.4       2.3   1.3e+03       3      26 ..       4      24 ..       4      25 .. 0.52
   2 ?   13.3   1.5   8.1e-05     0.045       2      32 ..      66     105 ..      65     107 .] 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.3
                                      ETTTTCEECHEETSTTCEEESSSS CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCG 26
                                      C +Cgs +    ++ g  vC++CG
  gi|313126593|ref|YP_004036863.1|  4 CDECGSMM---KTDGGVWVCGSCG 24
                                      55566532...2334445777777 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.1e-05
                                       EETTTTCEE.C........HEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon   2 kCPnCgstn.l........veDpergelvCtdCGlVledn 32 
                                       kCP+Cg+++            + e+  ++C +C   + ++
  gi|313126593|ref|YP_004036863.1|  66 KCPECGHDRaRyemkqirsADESETRFFTCVECSHKWRED 105
                                       9******985599999995555777777*****7777665 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.32   1.8e+02      20      25 ..       4       9 ..       3      13 .. 0.75
   2 ?    1.6   0.5       0.4   2.2e+02       3       7 ..      20      24 ..      18      33 .. 0.78
   3 ?   12.7   0.1   0.00014     0.076       8      25 ..      55      72 ..      54      75 .. 0.90
   4 ?    2.2   0.1      0.27   1.5e+02       2       9 ..      94     101 ..      93     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.32
                                      -SSS-- CS
                    DNA_RNApol_7kD 20 CkeCGh 25
                                      C eCG+
  gi|313126593|ref|YP_004036863.1|  4 CDECGS 9 
                                      888885 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.4
                                      -SSS- CS
                    DNA_RNApol_7kD  3 CgeCg 7 
                                      Cg Cg
  gi|313126593|ref|YP_004036863.1| 20 CGSCG 24
                                      88887 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00014
                                      -B----SSS----SSS-- CS
                    DNA_RNApol_7kD  8 aevslkkgdpiRCkeCGh 25
                                      ++ ++ ++  ++C eCGh
  gi|313126593|ref|YP_004036863.1| 55 DDAEIGPTTTVKCPECGH 72
                                      57889999*********9 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.27
                                       B-SSS--B CS
                    DNA_RNApol_7kD   2 iCgeCgae 9  
                                       +C eC+++
  gi|313126593|ref|YP_004036863.1|  94 TCVECSHK 101
                                       58888776 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4   0.00057      0.32      38      66 ..       3      32 ..       1      49 [. 0.74
   2 ?    5.4   0.9     0.035        20      24      56 ..      55      87 ..      49     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00057
                                      SSSSS.EEEEEETTEEEETTTTEEEE-BSS CS
                   Ribosomal_L37ae 38 fcgkt.kvkRkavgiwkCkkcgktvaGgAy 66
                                      fc++  ++ ++  g+w C++cg + a  A 
  gi|313126593|ref|YP_004036863.1|  3 FCDECgSMMKTDGGVWVCGSCGFEKARDAA 32
                                      566655899999**********99886664 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.035
                                      HHHHHHHHS-BEESSSSSSEEEEEETTEEEETT CS
                   Ribosomal_L37ae 24 kkieisqhakytCpfcgktkvkRkavgiwkCkk 56
                                       + ei   ++ +Cp+cg+++ + +   i + ++
  gi|313126593|ref|YP_004036863.1| 55 DDAEIGPTTTVKCPECGHDRARYEMKQIRSADE 87
                                      556666677778888888887777766665544 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       1.5   8.6e+02      28      32 ..      20      24 ..       8      26 .. 0.66
   2 ?   12.0   0.1   0.00027      0.15      14      33 ..      54      72 ..      52      73 .. 0.89
   3 ?    5.0   0.5     0.042        24      26      36 .]      93     103 ..      87     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.5
                     zinc_ribbon_4 28 CskCg 32
                                      C  Cg
  gi|313126593|ref|YP_004036863.1| 20 CGSCG 24
                                      66665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00027
                     zinc_ribbon_4 14 iddeklpakgvkvrCskCgh 33
                                      +dd+ + ++ + v+C+ Cgh
  gi|313126593|ref|YP_004036863.1| 54 VDDAEIGPT-TTVKCPECGH 72
                                      889999998.89*******9 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.042
                     zinc_ribbon_4  26 vrCskCghvFr 36 
                                        +C  C+h++r
  gi|313126593|ref|YP_004036863.1|  93 FTCVECSHKWR 103
                                       689******97 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4     0.036        20      41      53 ..      19      31 ..       1      34 [. 0.77
   2 ?    5.9   0.0     0.028        16      24      34 ..      62      72 ..      56      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.036
                                      -BTTTTBSSSBXS CS
                    Ribosomal_L32p 41 vcpscGyYkgrev 53
                                      vc scG+ k r+ 
  gi|313126593|ref|YP_004036863.1| 19 VCGSCGFEKARDA 31
                                      9********9975 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.028
                                      --EEEETTTCC CS
                    Ribosomal_L32p 24 pnlvecpncge 34
                                       + v+cp+cg+
  gi|313126593|ref|YP_004036863.1| 62 TTTVKCPECGH 72
                                      478999*9997 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4      0.13        72      14      21 ..       1       8 [.       1       8 [. 0.92
   2 ?    1.5   0.3      0.57   3.2e+02      16      23 ..      19      26 ..      17      26 .. 0.79
   3 ?   12.5   0.2   0.00021      0.12      11      22 ..      61      72 ..      57      73 .. 0.84
   4 ?    1.2   0.4       0.7   3.9e+02      17      24 ..      95     102 ..      94     104 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.13
                           UPF0547 14 aqfCphCG 21
                                      ++fC +CG
  gi|313126593|ref|YP_004036863.1|  1 MEFCDECG 8 
                                      78*****9 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.57
                           UPF0547 16 fCphCGyv 23
                                      +C  CG++
  gi|313126593|ref|YP_004036863.1| 19 VCGSCGFE 26
                                      5977**96 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00021
                           UPF0547 11 PvaaqfCphCGy 22
                                      P+ +++Cp+CG+
  gi|313126593|ref|YP_004036863.1| 61 PTTTVKCPECGH 72
                                      667899*****9 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.7
                           UPF0547  17 CphCGyvF 24 
                                       C +C + +
  gi|313126593|ref|YP_004036863.1|  95 CVECSHKW 102
                                       44555555 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.092        52       3       8 ..       4       9 ..       3      13 .. 0.77
   2 ?    8.1   0.3    0.0038       2.1       1      11 [.      18      28 ..      18      29 .. 0.85
   3 ?    5.6   0.4     0.023        13      16      22 ..      66      72 ..      66      77 .. 0.72
   4 ?    2.1   0.3      0.29   1.6e+02       1       8 [.      93     100 ..      93     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.092
                      Rubredoxin_2 3 CsqCGf 8
                                     C++CG+
  gi|313126593|ref|YP_004036863.1| 4 CDECGS 9
                                     888886 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0038
                      Rubredoxin_2  1 YvCsqCGfesa 11
                                      +vC +CGfe a
  gi|313126593|ref|YP_004036863.1| 18 WVCGSCGFEKA 28
                                      89******976 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.023
                      Rubredoxin_2 16 rCpsCgs 22
                                      +Cp+Cg+
  gi|313126593|ref|YP_004036863.1| 66 KCPECGH 72
                                      5777775 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.29
                      Rubredoxin_2   1 YvCsqCGf 8  
                                       + C +C++
  gi|313126593|ref|YP_004036863.1|  93 FTCVECSH 100
                                       78999987 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.4      0.01       5.6     148     180 ..       3      35 ..       1      42 [. 0.58
   2 ?    7.2   1.6    0.0064       3.6      73     114 ..      64     103 ..      61     107 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.01
                           TackOD1 148 kCnsCkslfsepevkarClsCekesesddlkvr 180
                                        C++C+s+++      +C sC+ e + d+++  
  gi|313126593|ref|YP_004036863.1|   3 FCDECGSMMKTDGGVWVCGSCGFEKARDAAQES 35 
                                       466666666666666666666666555555544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0064
                           TackOD1  73 irlCpsCksghlnvrevCpkCkSidieeqelihhftCgnvgp 114
                                       ++ Cp+C + +  +  + ++ +S+d +e+ ++ +++C +   
  gi|313126593|ref|YP_004036863.1|  64 TVKCPECGHDRARY--EMKQIRSADESETRFFTCVECSHKWR 103
                                       678****9988665..56899****************98655 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.014         8       2      11 ..       3      12 ..       2      14 .. 0.84
   2 ?    2.9   0.5      0.19   1.1e+02      24      30 ..      19      25 ..      18      25 .. 0.88
   3 ?    6.1   1.4     0.018        10       3      29 ..      67      99 ..      67     101 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.014
                                      B-TTT--B-E CS
                         Nudix_N_2  2 FCsqCGtpve 11
                                      FC +CG+ ++
  gi|313126593|ref|YP_004036863.1|  3 FCDECGSMMK 12
                                      9*****9776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                                      EETTTTE CS
                         Nudix_N_2 24 vCpaCgt 30
                                      vC +Cg+
  gi|313126593|ref|YP_004036863.1| 19 VCGSCGF 25
                                      9****96 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.018
                                      -TTT--B.-E...EE--.TT-SS-EE.EETTTT CS
                         Nudix_N_2  3 CsqCGtp.ve...lrip.dgDnreRl.vCpaCg 29
                                      C++CG+   +    +i  ++++++R+ +C  C+
  gi|313126593|ref|YP_004036863.1| 67 CPECGHDrARyemKQIRsADESETRFfTCVECS 99
                                      9****9844444434443677777753677776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1       0.3   1.7e+02      29      34 ..       4       9 ..       1      14 [. 0.69
   2 ?    3.8   0.1      0.11        61       7      22 ..      19      32 ..      17      39 .. 0.73
   3 ?   10.5   0.8   0.00092      0.51      26      37 ..      63      76 ..      40      79 .. 0.71
   4 ?    0.3   0.3       1.4     8e+02       6      14 ..      93     101 ..      91     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.3
                       Zn-ribbon_8 29 CPeCgs 34
                                      C eCgs
  gi|313126593|ref|YP_004036863.1|  4 CDECGS 9 
                                      777776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.11
                       Zn-ribbon_8  7 rCeeCghefevlqsis 22
                                       C +Cg  fe+ + ++
  gi|313126593|ref|YP_004036863.1| 19 VCGSCG--FEKARDAA 32
                                      599999..88776555 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00092
                       Zn-ribbon_8 26 lta.CPeCgs.evr 37
                                       t+ CPeCg+ ++r
  gi|313126593|ref|YP_004036863.1| 63 TTVkCPECGHdRAR 76
                                      6777*****96665 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1.4
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       + C eC h+
  gi|313126593|ref|YP_004036863.1|  93 FTCVECSHK 101
                                       678888875 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.062        35      32      53 ..      19      40 ..       3      59 .. 0.74
   2 ?    9.4   3.6    0.0021       1.2      10      39 ..      66     101 ..      62     107 .] 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.062
                           DUF2387 32 ECvsCgftdelsekgqsvakel 53
                                       C sCgf  +++++++s  +  
  gi|313126593|ref|YP_004036863.1| 19 VCGSCGFEKARDAAQESHMTST 40
                                      499****999999866655544 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0021
                           DUF2387  10 vCPrCs......emDkirmweedeveyrECvsCgft 39 
                                        CP C       em +ir  +e e+++  Cv+C++ 
  gi|313126593|ref|YP_004036863.1|  66 KCPECGhdraryEMKQIRSADESETRFFTCVECSHK 101
                                       699997333333577*******************96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   9.0      0.29   1.6e+02      69      97 ..      16      75 ..       2     104 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.29
                                      -EEEETTTS-EEECHHHHH................................S-TTTSSS-E CS
                              HypA 69 vkvrCreCgkefeleekal................................rCpkCgsadv 97
                                       +  C +Cg e   +++                                  +Cp+Cg+ + 
  gi|313126593|ref|YP_004036863.1| 16 GVWVCGSCGFEKARDAA-QeshmtstasredseivdmsdvddaeigptttvKCPECGHDRA 75
                                      45567777755543332.1235577777777777777777777777777777777777654 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.5    0.0043       2.4       3      26 ..       4      27 ..       2      38 .. 0.85
   2 ?    4.7   2.8     0.053        30       2      25 ..      66     101 ..      65     106 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0043
                                      -SSS-S--EE-SSEEE-TTT--EE CS
                    zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedl 26
                                      C eC + ++++g    C +C  + 
  gi|313126593|ref|YP_004036863.1|  4 CDECGSMMKTDGGVWVCGSCGFEK 27
                                      99*******99999*****98655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.053
                                       --SSS-S--EE-S............SEEE-TTT--E CS
                    zinc-ribbons_6   2 kCpeCqqelekrg............eqyhCeaCqed 25 
                                       kCpeC +   + +            + ++C +C+++
  gi|313126593|ref|YP_004036863.1|  66 KCPECGHDRARYEmkqirsadesetRFFTCVECSHK 101
                                       79***9998866655666666666555666666665 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.7   9.7e+02      29      37 ..      16      24 ..      10      44 .. 0.75
   2 ?   11.4   0.5   0.00056      0.31       2      37 ..      64      99 ..      63     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.7
                           DUF3268 29 llylCpkCd 37
                                       +++C +C+
  gi|313126593|ref|YP_004036863.1| 16 GVWVCGSCG 24
                                      578898887 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00056
                           DUF3268  2 ttrCpyCGekvilvsaseiYkerskgkllylCpkCd 37
                                      t++Cp CG+  +  + ++i ++ + ++ ++ C +C 
  gi|313126593|ref|YP_004036863.1| 64 TVKCPECGHDRARYEMKQIRSADESETRFFTCVECS 99
                                      689********************************7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1      0.04        22      15      21 ..       3       9 ..       1      11 [. 0.81
   2 ?    2.1   0.7       0.3   1.7e+02      16      21 ..      20      25 ..      19      27 .. 0.57
   3 ?    9.3   0.2    0.0016      0.92      14      21 ..      65      72 ..      57      73 .. 0.62
   4 ?   -1.7   0.3       4.9   2.8e+03       2       5 ..      95      98 ..      91     101 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.04
                     zinc_ribbon_2 15 FCpyCGt 21
                                      FC +CG+
  gi|313126593|ref|YP_004036863.1|  3 FCDECGS 9 
                                      8999986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.3
                     zinc_ribbon_2 16 CpyCGt 21
                                      C  CG+
  gi|313126593|ref|YP_004036863.1| 20 CGSCGF 25
                                      555555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0016
                     zinc_ribbon_2 14 kFCpyCGt 21
                                      + Cp+CG+
  gi|313126593|ref|YP_004036863.1| 65 VKCPECGH 72
                                      45777777 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.9
                     zinc_ribbon_2  2 CpnC 5 
                                      C +C
  gi|313126593|ref|YP_004036863.1| 95 CVEC 98
                                      5555 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.4   1.4e+03      34      40 ..       4      10 ..       3      15 .. 0.72
   2 ?    9.0   0.8    0.0023       1.3      31      48 ..      17      36 ..      12      39 .. 0.79
   3 ?    3.9   0.1     0.091        51       4      11 ..      66      73 ..      60      79 .. 0.67
   4 ?    3.0   0.7      0.17        97       5      12 ..      95     102 ..      93     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.4
                            HalOD2 34 CtrCGev 40
                                      C +CG +
  gi|313126593|ref|YP_004036863.1|  4 CDECGSM 10
                                      7788875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0023
                            HalOD2 31 vWkCtrCG..evqaaAdpSh 48
                                      vW C+ CG  +   aA+ Sh
  gi|313126593|ref|YP_004036863.1| 17 VWVCGSCGfeKARDAAQESH 36
                                      9*******544667888888 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.091
                            HalOD2  4 kCseCsld 11
                                      kC+eC+ d
  gi|313126593|ref|YP_004036863.1| 66 KCPECGHD 73
                                      45555544 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.17
                            HalOD2   5 CseCsldW 12 
                                       C eCs +W
  gi|313126593|ref|YP_004036863.1|  95 CVECSHKW 102
                                       ******** PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.16        88       4      17 ..       3      16 ..       2      18 .. 0.84
   2 ?    3.3   0.1      0.24   1.4e+02       2      16 ..      17      31 ..      16      37 .. 0.82
   3 ?    7.2   0.6     0.015       8.2       3      17 ..      65      79 ..      63      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.16
                           zf-ISL3  4 rCPnCgsktvvkhg 17
                                       C +Cgs ++++ g
  gi|313126593|ref|YP_004036863.1|  3 FCDECGSMMKTDGG 16
                                      69******998865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.24
                           zf-ISL3  2 phrCPnCgsktvvkh 16
                                      +++C  Cg  ++++ 
  gi|313126593|ref|YP_004036863.1| 17 VWVCGSCGFEKARDA 31
                                      589*****9998886 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.015
                           zf-ISL3  3 hrCPnCgsktvvkhg 17
                                       +CP+Cg   ++   
  gi|313126593|ref|YP_004036863.1| 65 VKCPECGHDRARYEM 79
                                      68*****99766554 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6  13.1       5.9   3.3e+03      25      46 ..       6      72 ..       1     107 [] 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.9
                               IBR 25 dCeaiiekseg...cks..........................................vtCskCgf 46
                                      +C+++++ + g   c+s                                          v+C++Cg+
  gi|313126593|ref|YP_004036863.1|  6 ECGSMMKTDGGvwvCGScgfekardaaqeshmtstasredseivdmsdvddaeigptttVKCPECGH 72
                                      5666665555555544444455555555555555566666666666666666666666666666665 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   4.6      0.14        76       6      28 ..       3      24 ..       1      27 [. 0.74
   2 ?    2.4   0.2      0.22   1.3e+02       7      11 ..      67      71 ..      65      78 .. 0.76
   3 ?    3.4   0.1      0.11        64      21      30 ..      92     101 ..      92     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.14
                           zf-RRN7  6 pCgvCgcrsftl.ddGfyyCrrCh 28
                                       C++Cg+      d G ++C +C+
  gi|313126593|ref|YP_004036863.1|  3 FCDECGS--MMKtDGGVWVCGSCG 24
                                      5888888..556688888888888 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                           zf-RRN7  7 CgvCg 11
                                      C++Cg
  gi|313126593|ref|YP_004036863.1| 67 CPECG 71
                                      88888 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.11
                           zf-RRN7  21 fyyCrrChtq 30 
                                       f+ C++C ++
  gi|313126593|ref|YP_004036863.1|  92 FFTCVECSHK 101
                                       899***9776 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.073        41       3      13 ..       3      13 ..       2      19 .. 0.76
   2 ?    2.2   0.5      0.45   2.5e+02       3      13 ..      19      30 ..      19      52 .. 0.68
   3 ?    7.8   0.1     0.008       4.5       3      12 ..      66      80 ..      65      90 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.073
                           zf-IS66  3 tCpcCGgllkp 13
                                       C++CG+ +k 
  gi|313126593|ref|YP_004036863.1|  3 FCDECGSMMKT 13
                                      6*****98775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.45
                           zf-IS66  3 tCpcCGg.llkp 13
                                      +C  CG  + + 
  gi|313126593|ref|YP_004036863.1| 19 VCGSCGFeKARD 30
                                      599999944333 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.008
                           zf-IS66  3 tCpcCGgl.....lk 12
                                      +Cp+CG++     +k
  gi|313126593|ref|YP_004036863.1| 66 KCPECGHDraryeMK 80
                                      5*****952544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        46  (0.00256568); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 606.15
//
Query:       gi|313126594|ref|YP_004036864.1|  [L=200]
Description: hypothetical protein Hbor_18520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1276.07
//
Query:       gi|313126595|ref|YP_004036865.1|  [L=242]
Description: tRNA(1-methyladenosine) methyltransferase-like methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-17   64.0   0.0    2.7e-14   53.4   0.0    2.0  2  GCD14            tRNA methyltransferase complex GCD14 subunit
    1.4e-09   37.9   0.0      2e-09   37.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    8.8e-08   31.9   0.0    1.6e-07   31.0   0.0    1.4  1  MTS              Methyltransferase small domain
    9.8e-08   32.6   0.3    2.5e-07   31.3   0.1    1.7  2  Methyltransf_25  Methyltransferase domain
    4.3e-07   30.9   0.1    9.6e-07   29.8   0.1    1.5  1  Methyltransf_24  Methyltransferase domain
    6.8e-06   25.7   0.0    1.1e-05   25.1   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.5e-05   25.5   0.1    3.7e-05   24.3   0.1    1.7  1  Methyltransf_11  Methyltransferase domain
    1.6e-05   24.8   0.0      2e-05   24.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.8e-05   24.0   0.0    2.2e-05   23.7   0.0    1.1  1  Methyltransf_3   O-methyltransferase
    1.9e-05   23.8   0.0    2.5e-05   23.5   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00072   19.3   0.0     0.0012   18.6   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0013   18.6   0.0     0.0028   17.5   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   16.2   0.0      0.026   15.2   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
      0.014   15.3   0.0      0.022   14.7   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.029   14.3   0.1      0.047   13.7   0.1    1.4  1  ADH_zinc_N       Zinc-binding dehydrogenase
       0.04   13.7   0.0      0.052   13.3   0.0    1.2  1  Met_10           Met-10+ like-protein
       0.12   11.9   0.0       0.16   11.5   0.0    1.1  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   2.6e-17   2.7e-14      26     179 ..      69     218 ..      54     222 .. 0.93
   2 !    9.1   0.0   0.00092      0.97     229     247 .]     223     241 ..     217     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.6e-17
                             GCD14  26 taDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvc 102
                                         Di li+ +     G +v+++GtG+g ls ++ r  a    + t+e   + a+ are++r  +++++v v+  Dv 
  gi|313126595|ref|YP_004036865.1|  69 PRDIGLIVGHTGAAAGDRVLDAGTGTGVLSAYLGRMHA---EVTTYERDPDFADVARENMRLAGVEEYVDVRAGDVT 142
                                       579********************************865...789********************************* PP

                             GCD14 103 keGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllrtyev 179
                                       +e  +   +g  D + LD     + + ha + l ++gg +  +sP +e  + ++ea re g +e+et+e  +r+ + 
  gi|313126595|ref|YP_004036865.1| 143 EELDSVAEEGPFDLLTLDTGDAADVVAHAPELL-RSGGYVAVYSPFVENSRAAVEAAREAGLNEVETFETIQRRMDF 218
                                       98776677799**********************.99**********************************9998765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00092
                             GCD14 229 lkPvselkghtgyLtfatk 247
                                       ++P +  +ghtgyL+fa++
  gi|313126595|ref|YP_004036865.1| 223 SRPSTAGVGHTGYLVFARY 241
                                       7999999**********85 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.9e-12     2e-09       4     124 ..      84     197 ..      82     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.9e-12
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDli 78 
                                       g rvlD+G+GtG l+  l    +++aev+  +++++   +Aren +  g++  v +++gd++e l++  e+ +fDl+
  gi|313126595|ref|YP_004036865.1|  84 GDRVLDAGTGTGVLSAYLG---RMHAEVTTYERDPDFADVARENMRLAGVEeYVDVRAGDVTEeLDSVAEEGPFDLL 157
                                       679***********99888...569**************************899*********88865777*****8 PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllaelpakvee 124
                                       +      ++ d +++   ++++l++gg++++ +p   ++ +a ve+
  gi|313126595|ref|YP_004036865.1| 158 TL-----DTGDAADVVAHAPELLRSGGYVAVYSPF-VENSRAAVEA 197
                                       88.....6**********************99987.4444444444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.5e-10   1.6e-07      30     137 ..      82     183 ..      73     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.5e-10
                                       CTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE- CS
                               MTS  30 elsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivsN 104
                                       ++ ++vlD G+G+Gvl+a l +++ e  vt ++ d    ++a+en++  ++e  v+v+a dv+ee++      +   
  gi|313126595|ref|YP_004036865.1|  82 AAGDRVLDAGTGTGVLSAYLGRMHAE--VTTYERDPDFADVARENMRLAGVEeyVDVRAGDVTEELD-----SVAEE 151
                                       56789*****************8877..9999999999*************9889999998877655.....99999 PP

                                       --STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                               MTS 105 PPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                        Pf   +  ++  a +++a+A+e L++gG   +
  gi|313126595|ref|YP_004036865.1| 152 GPFDLLTL-DTGDAADVVAHAPELLRSGGYVAV 183
                                       ***87766.666677899*********998764 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   2.4e-10   2.5e-07       1      97 []      87     179 ..      87     179 .. 0.86
   2 ?   -1.8   0.0       4.9   5.2e+03      27      50 ..     188     208 ..     185     222 .. 0.57

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.4e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC.CGBS..SSTTTEEEEEEES CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgda.edlp..fedgsfDlvvssg 72 
                                       vLd+G+GtG l+++l +    a+vt  + ++++ + are+++ +g+   v+++ gd+ e+l+   e+g fDl ++  
  gi|313126595|ref|YP_004036865.1|  87 VLDAGTGTGVLSAYLGRMH--AEVTTYERDPDFADVARENMRLAGVeeYVDVRAGDVtEELDsvAEEGPFDLLTLD- 160
                                       9***************995..*********************9*99*9*********66687556999****9993. PP

                                       TGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  73 alhhlsdedlekalkeiarvLkpgG 97 
                                               d++++++++ ++L+ gG
  gi|313126595|ref|YP_004036865.1| 161 ------TGDAADVVAHAPELLRSGG 179
                                       ......2356677777777777777 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                                       EESSHHHHHHHHHHHHHTTTTEEE CS
                   Methyltransf_25  27 vDiseemleaareraeeeglnvef 50 
                                       v+ s +++eaare   +   +ve 
  gi|313126595|ref|YP_004036865.1| 188 VENSRAAVEAAREAGLN---EVET 208
                                       55677777777776633...3333 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   9.1e-10   9.6e-07       8     101 ..      91     181 ..      88     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 9.1e-10
                   Methyltransf_24   8 Gvstlwllralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealasla.agsiDllfiDggh 79 
                                       G  t +l + l r +a ++++ + dp   ++a +are    ag++++v+++ +d  e+l s+a +g++Dll +D g 
  gi|313126595|ref|YP_004036865.1|  91 GTGTGVLSAYLGRMHA-EVTTYERDP---DFADVAREnmrlAGVEEYVDVRAGDVTEELDSVAeEGPFDLLTLDTG- 162
                                       4555555555666776.799999999...777777777777**********************999********99. PP

                   Methyltransf_24  80 aaeavledleallprlapggvv 101
                                       +a++v     ++ ++l++gg+v
  gi|313126595|ref|YP_004036865.1| 163 DAADVV---AHAPELLRSGGYV 181
                                       344443...3566677777766 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     1e-08   1.1e-05     161     278 ..      83     204 ..      76     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1e-08
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.......eekadvi 230
                                       +g++vlD GtG+G+L+    ++ +++v+ +  D+   +va+eN++l +ve+ ++v + +++++       e+++d++
  gi|313126595|ref|YP_004036865.1|  83 AGDRVLDAGTGTGVLSAYLGRM-HAEVTTYERDPDFADVARENMRLAGVEEYVDVRA-GDVTEeldsvaeEGPFDLL 157
                                       6789***********9666666.5689************************999942.3333211122336777776 PP

                              PrmA 231 vaNILaevlielaedikklvkeggll.ilSGilkekaeevaealeqgfe 278
                                                 + + ++ +l+++gg++ + S  +++ + +v++a e+g++
  gi|313126595|ref|YP_004036865.1| 158 TLD--TGDAADVVAHAPELLRSGGYVaVYSPFVENSRAAVEAAREAGLN 204
                                       544..33445556666666777776524566666666666666666555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   3.5e-08   3.7e-05       1      94 [.      88     181 ..      88     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.5e-08
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC.T.S.S-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaek.l.p.fednsfDlvvssevlh 72 
                                       Ld+G+GtG l+++l +  a+v++ + ++ + ++a+e+ + +g+   v+++ +d+++ l    e++ fDl ++     
  gi|313126595|ref|YP_004036865.1|  88 LDAGTGTGVLSAYLGRMHAEVTTYERDPDFADVARENMRLAGVeeYVDVRAGDVTEeLdSvAEEGPFDLLTLDT--- 161
                                       8**************999*****************99999999988999****996564335557888887653... PP

                                       C-CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  73 hvedpekalkeiaRvLkpgGll 94 
                                          d +++++ +  +L+ gG++
  gi|313126595|ref|YP_004036865.1| 162 --GDAADVVAHAPELLRSGGYV 181
                                       ..46666666666666666665 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.9e-08     2e-05      72     170 ..      82     182 ..      65     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.9e-08
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGG...TTGGG-SEE CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrk...GyeekaPYd 144
                                        +g+rvL+ G+G+G l+a l r+  e++   + er +++++ a++n++  ++e  v v+ gD ++    ++e+ P+d
  gi|313126595|ref|YP_004036865.1|  82 AAGDRVLDAGTGTGVLSAYLGRMHAEVT---TYERDPDFADVARENMRLAGVEeYVDVRAGDVTEeldSVAEEGPFD 155
                                       5799******************988877...9*******************99789******886222678899*** PP

                                       EEEE..SSBBSS--HHHHHTEEEEEEEE CS
                              PCMT 145 aihv..gaaapeiPealidQLkeGGrlv 170
                                        + +  g aa+ +     + L +GG + 
  gi|313126595|ref|YP_004036865.1| 156 LLTLdtGDAADVV-AHAPELLRSGGYVA 182
                                       9876214444444.45567777777765 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.1e-08   2.2e-05      73     155 ..     106     183 ..      74     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.1e-08
                                       -EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---EEEEEE-S-GGGHHHHHHHHHHTEEE CS
                    Methyltransf_3  73 GkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpefDfifvDaDkssyvnyyeklleLvkv 149
                                        ++++ + d++ +++a++ ++ agv+e ++++ gd ++ L+ + ++ +   fD++ +D    + v  +  + eL++ 
  gi|313126595|ref|YP_004036865.1| 106 AEVTTYERDPDFADVARENMRLAGVEEYVDVRAGDVTEELDSVAEEGP---FDLLTLDTGDAADVVAH--APELLRS 177
                                       579*****************************************9996...****9998766655544..5588888 PP

                                       EEEEEE CS
                    Methyltransf_3 150 Ggliai 155
                                       Gg +a+
  gi|313126595|ref|YP_004036865.1| 178 GGYVAV 183
                                       888876 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.4e-08   2.5e-05      29      74 ..      82     130 ..      71     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.4e-08
                                       GTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT...T CS
                            RrnaAD  29 eekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls...k 74 
                                          + vl+ g+G+G+l++ L  +  +v+ +E d+++a + +++++    
  gi|313126595|ref|YP_004036865.1|  82 AAGDRVLDAGTGTGVLSAYLGRMHAEVTTYERDPDFADVARENMRlagV 130
                                       56799************************************98875444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0012      41     143 ..      83     182 ..      74     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                        g rvLD   G+G+l+   l R  ++++  e+d+  + + +en++  ++ee +++   d +e+l++  +++++fd+ 
  gi|313126595|ref|YP_004036865.1|  83 AGDRVLDAGTGTGVLSA-YLGRMHAEVTTYERDPDFADVARENMRLAGVEEYVDVRAGDVTEELDSV-AEEGPFDLL 157
                                       57799**9999999987.59******************************99999999999999998.56789***9 PP

                                       EE--SSSTTCH.HHHHHHHHHTT-EE CS
                     Cons_hypoth95 118 flDPPyakellieevlelleekkllk 143
                                        lD   a++ +  ++ ell++ + ++
  gi|313126595|ref|YP_004036865.1| 158 TLDTGDAADVV-AHAPELLRSGGYVA 182
                                       99966555543.55555555555555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.7e-06    0.0028      22     115 ..      83     181 ..      55     221 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-06
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                                       ag rvLd G+GtG l+ +l +  ++vt ++ +p   + a+        +                    +  + + +
  gi|313126595|ref|YP_004036865.1|  83 AGDRVLDAGTGTGVLSAYLGRMHAEVTTYERDPDFADVARenmrlagvE-------------------EYVDVRAGD 140
                                       567****************999888888777765444333333333330...................444444444 PP

                   Methyltransf_23  91 vlehvpdpp................ellrqiatllkpgGyl 115
                                       v+e +++++                 +++++ +ll+ gGy+
  gi|313126595|ref|YP_004036865.1| 141 VTEELDSVAeegpfdlltldtgdaaDVVAHAPELLRSGGYV 181
                                       44444444444444444444444445555555555555555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.5e-05     0.026       1      89 [.      88     171 ..      88     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg....ssfDlvvas 73 
                                       L+ G+GtG l+++l +   ++e+t ++ +p++ + a+e ++  + +  + v+++a d+ ++ ++    + fDl +  
  gi|313126595|ref|YP_004036865.1|  88 LDAGTGTGVLSAYLGRM--HAEVTTYERDPDFADVARENMRLAGVE--EYVDVRAGDVTEELDSvaeeGPFDLLT-- 158
                                       89***************..**************7676666555543..355555555544332234446666655.. PP

                   Methyltransf_12  74 nvlhhl..kdirevldni 89 
                                            l   d ++v++++
  gi|313126595|ref|YP_004036865.1| 159 -----LdtGDAADVVAHA 171
                                       .....0224444444444 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.1e-05     0.022      14      79 ..      83     146 ..      78     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk 79 
                                        g+rv+D Gt  g+l++yl +  +  +v+  +  +   + a+en++ ag+e+ ++vr +d  e+l+
  gi|313126595|ref|YP_004036865.1|  83 AGDRVLDAGTGTGVLSAYLGR--MHAEVTTYERDPDFADVARENMRLAGVEEYVDVRAGDVTEELD 146
                                       5789***************96..55679999999**************************999886 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.4e-05     0.047      12      89 ..     103     185 ..      91     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                                       HTT-EEEEEESSHHHHHHHHHT....TESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSC.SHHHHHHHHHCEEEE CS
                        ADH_zinc_N  12 alGaeviavdsseeklelakkl....Gadevinykea.dlverikeltggegvdvvfecvG.sgatleaalkllkpg 82 
                                        + aev++  ++++ ++ a+++    G++e+++  +a d+ e++ +  +++++d+    +G + +++  a +ll+ g
  gi|313126595|ref|YP_004036865.1| 103 RMHAEVTTYERDPDFADVARENmrlaGVEEYVDV-RAgDVTEELDSVAEEGPFDLLTLDTGdAADVVAHAPELLRSG 178
                                       577899999*****999999977899********.888***********99***965555548999*********** PP

                                       EEEEECS CS
                        ADH_zinc_N  83 GrlvvvG 89 
                                       G ++v+ 
  gi|313126595|ref|YP_004036865.1| 179 GYVAVYS 185
                                       ***9986 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.9e-05     0.052     100     163 ..      83     144 ..      78     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                                       TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG- CS
                            Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrev 163
                                        g++V+d   G G ++  +++     +v + + +P+     +en++l  ve++v +  +D+ e 
  gi|313126595|ref|YP_004036865.1|  83 AGDRVLDAGTGTGVLSAYLGR--MHAEVTTYERDPDFADVARENMRLAGVEEYVDVRAGDVTEE 144
                                       799*****************9..77889****************************99999875 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.16       3      68 ..      86     151 ..      84     171 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkle 68 
                                        +lD+ +G+G  +  + +++ +v + e +++   +a +N ++ gv++ +++  gdv+e l ++ +e
  gi|313126595|ref|YP_004036865.1|  86 RVLDAGTGTGVLSAYLGRMHAEVTTYERDPDFADVARENMRLAGVEEYVDVRAGDVTEELDSVAEE 151
                                       6899999999999999******************************************99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1628.10
//
Query:       gi|313126596|ref|YP_004036866.1|  [L=131]
Description: nascent polypeptide associated complex nac [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-17   63.5   0.8    1.9e-17   63.0   0.8    1.2  1  NAC       NAC domain
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.049   13.4   0.0    1.5  1  CUE       CUE domain
       0.28   11.1   0.2       0.28   11.1   0.2    1.9  2  UBA       UBA/TS-N domain


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.8   3.2e-21   1.9e-17       1      55 [.       9      65 ..       9      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 3.2e-21
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeae 55
                                      ++K+++++k++g+  +e+ ++eeV+i+++d ++lvf++++V+  +++g++ty+++G++e
  gi|313126596|ref|YP_004036866.1|  9 PRKMKQMMKQMGIdvTEL-DAEEVVIKTAD-EELVFTDAQVTrmDAQGQETYQIVGQPE 65
                                      79************8888.9**********.**************************98 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.2e-06     0.049      15      38 ..     107     130 ..     106     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-06
                                       S-HHHHHHHHHHCTTTHHHHHHHH CS
                               CUE  15 ldeevIravLrasngnvEatinaL 38 
                                       +++++ r +L+a+ng++ a+i++L
  gi|313126596|ref|YP_004036866.1| 107 VGKSDAREALEAENGDLAAAISRL 130
                                       678999****************98 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8   1.3         3   1.8e+04       7      13 ..      14      20 ..      14      20 .. 0.83
   2 ?   11.1   0.2   4.6e-05      0.28      16      37 .]     109     130 ..     108     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 3
                                      HHHHHTT CS
                               UBA  7 qrLveMG 13
                                      q +++MG
  gi|313126596|ref|YP_004036866.1| 14 QMMKQMG 20
                                      6789999 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHHHTTTSHHHHHHHH CS
                               UBA  16 reevveALratgnNeErAveyL 37 
                                       +++++eAL+a ++++ +A+  L
  gi|313126596|ref|YP_004036866.1| 109 KSDAREALEAENGDLAAAISRL 130
                                       689***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 822.56
//
Query:       gi|313126597|ref|YP_004036867.1|  [L=216]
Description: o-methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-11   44.3   0.0    1.4e-11   44.0   0.0    1.2  1  Methyltransf_3   O-methyltransferase
      5e-10   40.3   0.1    9.1e-10   39.5   0.1    1.4  1  Methyltransf_24  Methyltransferase domain
    1.8e-06   28.6   0.0    3.2e-06   27.7   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.033   13.7   0.0      0.047   13.2   0.0    1.2  1  MTS              Methyltransferase small domain
        0.1   12.3   0.0       0.14   11.9   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   3.9e-15   1.4e-11      31     159 ..      34     156 ..      14     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3.9e-15
                                       --HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES- CS
                    Methyltransf_3  31 vsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegd 107
                                       v+++ g  L++L +l++a  v+e G   Gys+   a ++   G+++  + d+++ ++a++++    +    +++ gd
  gi|313126597|ref|YP_004036867.1|  34 VGPAAGGTLRVLARLTDAESVFEFGSGFGYSATWWARGMA-GGRVVLTEHDPDELDMAREWLSAGEYPVSFDYRDGD 109
                                       67888999******************************96.7*********************************** PP

                                       HHHHHHHHHTSSS---EEEEEE-S-GGGHHHHHHHHHHTEEEEEEEEEE-TT CS
                    Methyltransf_3 108 alkvLeelvkdkklpefDfifvDaDkssyvnyyeklleLvkvGgliaiDntL 159
                                       al+++ e   d   + fD ++vD  k+ yv  ++++ e v  Gg+++ Dn++
  gi|313126597|ref|YP_004036867.1| 110 ALSIVTEY--D---GPFDCVLVDHQKERYVDGFDEVREKVAPGGVVVADNVI 156
                                       **998764..3...56**********************************97 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.1   2.5e-13   9.1e-10       2     106 .]      56     155 ..      55     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.5e-13
                   Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDg 77 
                                       E G+  G+s+ w++r +     gr+v  +hdp+    a++++   ++   ++ + +d+ + +++ + g++D++++D 
  gi|313126597|ref|YP_004036867.1|  56 EFGSGFGYSATWWARGMAG---GRVVLTEHDPDeLDMAREWLSAGEYPVSFDYRDGDALSIVTEYD-GPFDCVLVD- 127
                                       99************88764...4677778888424446777777999999***************9.*********. PP

                   Methyltransf_24  78 ghaaeavledleallprlapggvvlfdDi 106
                                        h++e++ + ++ +++++apggvv+ d++
  gi|313126597|ref|YP_004036867.1| 128 -HQKERYVDGFDEVREKVAPGGVVVADNV 155
                                       .9************************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     9e-10   3.2e-06       1      97 []      54     148 ..      54     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 9e-10
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG.BSSSTTTEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgdaed.lpfedgsfDlvvssga 73 
                                       v ++G G G  + ++a+ + g ++v+ ++ +++ l+ are +++ ++  +++++ gda + + + dg fD+v++   
  gi|313126597|ref|YP_004036867.1|  54 VFEFGSGFGYSATWWARGMaG-GRVVLTEHDPDELDMAREWLSAGEYpvSFDYRDGDALSiVTEYDGPFDCVLVD-- 127
                                       7899*************9966.********************9976724555566666652357999*******4.. PP

                                       GGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  74 lhhlsdedlekalkeiarvLkpgG 97 
                                         h ++e++ + ++e+++ + pgG
  gi|313126597|ref|YP_004036867.1| 128 --H-QKERYVDGFDEVREKVAPGG 148
                                       ..4.45778899999999999999 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.047      26      94 ..      47     115 ..      38     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve 94 
                                        l++  +++v  +G+G+G+ +++ a+     +v+l++ d   l++a+e l+a +     +++  d+l+ v+
  gi|313126597|ref|YP_004036867.1|  47 RLTD--AESVFEFGSGFGYSATWWARGMAGGRVVLTEHDPDELDMAREWLSAGEYPvsFDYRDGDALSIVT 115
                                       4444..5679*****************************************99998334444555555444 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.9e-05      0.14      69     148 ..      45     126 ..      35     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                                       TT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGG.G-S CS
                              PCMT  69 le.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyee.kaP 142
                                       l  l++ ++v e GsG Gy +   ar + + grvv  e+ ++  + a++ l + ++  +   + gD    + e   P
  gi|313126597|ref|YP_004036867.1|  45 LArLTDAESVFEFGSGFGYSATWWARGM-AGGRVVLTEHDPDELDMAREWLSAGEYPvSFDYRDGDALSIVTEyDGP 120
                                       444999******************9987.46899*****99999999999887665433344444444444331456 PP

                                       EEEEEE CS
                              PCMT 143 Ydaihv 148
                                       +d ++v
  gi|313126597|ref|YP_004036867.1| 121 FDCVLV 126
                                       666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1285.76
//
Query:       gi|313126598|ref|YP_004036868.1|  [L=558]
Description: methylmalonyl-CoA mutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.2e-225  750.0   1.6   1.4e-225  749.7   1.6    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
  ------ inclusion threshold ------
      0.048   13.3   0.1        0.2   11.3   0.1    2.1  2  GIT_SHD        Spa2 homology domain (SHD) of GIT


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  749.7   1.6  1.6e-229  1.4e-225       5     513 .]      42     552 ..      38     552 .. 0.98

  Alignments for each domain:
  == domain 1  score: 749.7 bits;  conditional E-value: 1.6e-229
                     MM_CoA_mutase   5 gievkplYtaedl.eek.klgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsvaf 79 
                                       g ev++lYt++d+ +++      +PGe P+tRGv++tm+rgr Wt+rqyag++ta+etner+++l+e+G +gls+af
  gi|313126598|ref|YP_004036868.1|  42 GQEVDRLYTPDDIaDQNyCEDVGFPGEEPYTRGVYPTMHRGRLWTMRQYAGMGTAAETNERFNYLIENGSSGLSMAF 118
                                       789**********7444455668****************************************************** PP

                     MM_CoA_mutase  80 dlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdleklsg 156
                                       dlpt+ gyDsd ++a+gevGkaGvaid+l+dme+++dgi+ld+vs+smtina+a  llamy+a+ ++qgv++e+l+g
  gi|313126598|ref|YP_004036868.1| 119 DLPTQKGYDSDAAMAAGEVGKAGVAIDTLRDMEVVFDGIPLDEVSTSMTINAPAGVLLAMYIAIGDKQGVPREQLRG 195
                                       ***************************************************************************** PP

                     MM_CoA_mutase 157 tiqnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvrall 233
                                       tiqnDiLke++ar+ yiyppe s+rli+di+e++a+e+p+fntis+sgyhireaG+ta+qE+Aftl dG+eYv+a+l
  gi|313126598|ref|YP_004036868.1| 196 TIQNDILKEYIARNLYIYPPESSMRLITDIFEFCAEETPNFNTISISGYHIREAGSTAAQEIAFTLGDGIEYVQAAL 272
                                       ***************************************************************************** PP

                     MM_CoA_mutase 234 eaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvNilR 310
                                       +aGldvd+fap+lsFff++++++fee+Ak+RAaRr+Wa+i++++fga+++ks +l++h+qT+g++ltaq++++N++R
  gi|313126598|ref|YP_004036868.1| 273 DAGLDVDDFAPQLSFFFNAHNNIFEEVAKFRAARRMWAKIMEDRFGAENPKSKQLKFHTQTGGSTLTAQQVENNVVR 349
                                       ***************************************************************************** PP

                     MM_CoA_mutase 311 ttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawklf 387
                                       + ++alaAvlggtqslhtn  Deal+lPte+s+r+A++tq+ila+Esg a+++DPl+GSyyvE+LTdel+++a +++
  gi|313126598|ref|YP_004036868.1| 350 VGYQALAAVLGGTQSLHTNGKDEALSLPTEQSVRTALRTQQILAHESGAADTIDPLAGSYYVESLTDELEAEAFDIL 426
                                       ***************************************************************************** PP

                     MM_CoA_mutase 388 qeieeaGGmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlealra 464
                                       +e++++GGml a+es +vq++i++ a++rq++ie+++++ivGvN+++  +ee + +++++dee e+rq+erl+a+++
  gi|313126598|ref|YP_004036868.1| 427 DEVDRRGGMLDAVESQWVQRQIQDVAYERQQEIEDGERIIVGVNEYQ-VDEEPDADIEDVDEEDEKRQKERLQAVKD 502
                                       **********************************************5.555899*********************** PP

                     MM_CoA_mutase 465 erdeaavkaaLaalgeaarse.nllaraveaaralatlGeisdaleevfg 513
                                       erd+++v+aaLaa++++ars+ nl++ +vea++++at+Geis+al++vfg
  gi|313126598|ref|YP_004036868.1| 503 ERDDEEVEAALAAIKDTARSDaNLMPPIVEAVKVYATVGEISNALRDVFG 552
                                       *******************889**************************98 PP

>> GIT_SHD  Spa2 homology domain (SHD) of GIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.32   2.8e+03      16      21 ..     221     226 ..     220     227 .. 0.86
   2 ?   11.3   0.1   2.3e-05       0.2      18      28 ..     423     433 ..     422     434 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.32
                           GIT_SHD  16 LvtDVy 21 
                                       L+tD++
  gi|313126598|ref|YP_004036868.1| 221 LITDIF 226
                                       9****8 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.3e-05
                           GIT_SHD  18 tDVydEldRRe 28 
                                        D++dE+dRR+
  gi|313126598|ref|YP_004036868.1| 423 FDILDEVDRRG 433
                                       7*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3453.51
//
Query:       gi|313126599|ref|YP_004036869.1|  [L=105]
Description: hypothetical protein Hbor_18570 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.4   3.0      0.023   14.9   3.0    1.2  1  DUF2530   Protein of unknown function (DUF2530)


Domain annotation for each model (and alignments):
>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   3.0   1.3e-06     0.023       8      67 ..      27      84 ..      21      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-06
                           DUF2530  8 rrLtdprpvivvgtll.WlvalvvllvvgdaleswlpvclaGlvvGllGlaiflwQRrAaR 67
                                      rr +dp  ++ +g+++ +++alvv+      ++s+  v+++G+v+ ++G ai    R+AaR
  gi|313126599|ref|YP_004036869.1| 27 RRCADPSTAVQLGIVVgFVAALVVASYPAAVTASVAIVTAVGMVTTAVGRAI---DRAAAR 84
                                      6788999999888765277777777777788888999999999999999987...566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 689.70
//
Query:       gi|313126600|ref|YP_004036870.1|  [L=418]
Description: transposase, is605 orfb family, central region [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-24   84.2   2.3    8.8e-24   83.2   2.3    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    2.7e-21   76.0   0.2    6.9e-21   74.7   0.0    1.8  2  OrfB_IS605       Probable transposase
     0.0059   16.9   1.9      0.016   15.5   1.9    1.7  1  C1_2             C1 domain
  ------ inclusion threshold ------
        0.1   12.6   3.8       0.23   11.5   3.8    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.13   12.4   2.9      0.096   12.8   0.7    1.9  2  Ribosomal_L37ae  Ribosomal L37ae protein family


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   2.3   2.4e-27   8.8e-24       1      69 []     309     378 ..     309     378 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.4e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++++ leyka+eyGi v  v++++TSktCs+Cg++ +  ++++ +++C++C +++++Dvn+a+Ni ++
  gi|313126600|ref|YP_004036870.1| 309 FNRFTNLLEYKAEEYGILVDRVDEENTSKTCSCCGKIRDSnRVERGLYVCSSCETTMNADVNGAVNIRRK 378
                                       89*************************************9999************************985 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.7   6.2e+03      58      73 ..      54      69 ..      53      85 .. 0.58
   2 !   74.7   0.0   1.9e-24   6.9e-21       3     119 ..     176     285 ..     156     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                        OrfB_IS605 58 aelqsklkksknykka 73
                                      ael s lk++k+y   
  gi|313126600|ref|YP_004036870.1| 54 AELKSELKDHKRYSDL 69
                                      5667777777765443 PP

  == domain 2  score: 74.7 bits;  conditional E-value: 1.9e-24
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       +++ e + + ++gn++agiDlGi+n ++   edg+++ly g+ lk+d+ y+++e  + +            s++ ++
  gi|313126600|ref|YP_004036870.1| 176 VCKKEIPVEDAPGNNTAGIDLGISNYLAIDYEDGESELYPGNVLKEDKHYFTREEYQTEGENGP-------SKRARK 245
                                       56666678899******************************************99888777544.......567888 PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                         +k+srr +h+lh l++h+++++ e+gve++ vg+++di
  gi|313126600|ref|YP_004036870.1| 246 ARQKLSRRKDHFLHTLSKHIVERCVEEGVEKIAVGDLSDI 285
                                       88999********************************987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.9   4.4e-06     0.016      14      42 ..     332     365 ..     319     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-06
                              C1_2  14 dssesfnCsaCgrk..idgff.....YsCseCdfsl 42 
                                       +++ s++Cs+Cg+   +  ++     Y Cs C+ ++
  gi|313126600|ref|YP_004036870.1| 332 EENTSKTCSCCGKIrdS--NRverglYVCSSCETTM 365
                                       56778*********554..4455999******9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.8   6.4e-05      0.23      19      45 ..     337     363 ..     333     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                        +C  Cg+   + r+++ gl+ C++C +
  gi|313126600|ref|YP_004036870.1| 337 KTCSCCGKIrDSNRVER-GLYVCSSCET 363
                                       57*****9999999997.********86 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.1   7.7e+03      31      50 ..     261     280 ..     245     280 .. 0.75
   2 ?   12.8   0.7   2.7e-05     0.096      31      62 ..     334     366 ..     326     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.1
                                       HS-BEESSSSSSEEEEEETT CS
                   Ribosomal_L37ae  31 hakytCpfcgktkvkRkavg 50 
                                        +k+  ++c ++ v++ avg
  gi|313126600|ref|YP_004036870.1| 261 LSKHIVERCVEEGVEKIAVG 280
                                       56788888888888888886 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.7e-05
                                       HS-BEESSSSSS.EEEEEETTEEEETTTTEEEE CS
                   Ribosomal_L37ae  31 hakytCpfcgkt.kvkRkavgiwkCkkcgktva 62 
                                       +++ tC+ cgk  + +R+  g++ C++c+ t+ 
  gi|313126600|ref|YP_004036870.1| 334 NTSKTCSCCGKIrDSNRVERGLYVCSSCETTMN 366
                                       44569******9899**************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2690.25
//
Query:       gi|313126601|ref|YP_004036871.1|  [L=107]
Description: hypothetical protein Hbor_18590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 618.36
//
Query:       gi|313126602|ref|YP_004036872.1|  [L=129]
Description: hypothetical protein Hbor_18600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-38  129.4   2.9    8.9e-38  129.1   2.9    1.1  1  YbjQ_1           Putative heavy-metal-binding
      0.001   19.5   0.2        0.1   13.0   0.1    2.2  2  SeleniumBinding  Selenium binding protein
  ------ inclusion threshold ------
      0.032   14.6   0.3      0.058   13.7   0.3    1.6  1  DUF4156          Domain of unknown function (DUF4156)


Domain annotation for each model (and alignments):
>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   2.9   1.5e-41   8.9e-38       1     103 [.       1     102 [.       1     103 [. 0.99

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 1.5e-41
                            YbjQ_1   1 mivtttesiegkeivevlgivtgetvrsrnvlkdilaglrslvGGelkayeeeleeareeAlerlkeeAeelGAnAv 77 
                                       m+ tttes++g+e+vevlg+v+g+tvr+rnv++d++++lr+lvGGel++y+ ++++ar+eA +r++eeAe++GA+Av
  gi|313126602|ref|YP_004036872.1|   1 MLSTTTESVPGREVVEVLGVVRGNTVRARNVGRDVTQSLRNLVGGELNSYTGLMTDARDEAEKRMQEEAEAVGADAV 77 
                                       899************************************************************************** PP

                            YbjQ_1  78 vgvrldtseigekgmlevlayGTAVk 103
                                       v+vr++ts++++ +++e+layGTAV+
  gi|313126602|ref|YP_004036872.1|  78 VNVRFTTSDVAQ-SAAEILAYGTAVR 102
                                       **********99.************7 PP

>> SeleniumBinding  Selenium binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0068        40       8      36 ..       2      32 ..       1      55 [. 0.74
   2 !   13.0   0.1   1.7e-05       0.1      36      74 ..      59     102 ..      50     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0068
                   SeleniumBinding  8 iittaneiPGvely.ylgivs.avvesdnvd 36
                                      + tt++ +PG e+   lg+v  ++v++ nv 
  gi|313126602|ref|YP_004036872.1|  2 LSTTTESVPGREVVeVLGVVRgNTVRARNVG 32
                                      569*******998626788852677877775 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.7e-05
                   SeleniumBinding  36 dkilkaleekvkekkglaligfkltaidg.....kllGyGtavk 74 
                                       d+  k ++e + + ++ a++  + t+ d      ++l yGtav+
  gi|313126602|ref|YP_004036872.1|  59 DEAEKRMQEEAEAVGADAVVNVRFTTSDVaqsaaEILAYGTAVR 102
                                       77778999***********999999998777889*********8 PP

>> DUF4156  Domain of unknown function (DUF4156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   9.6e-06     0.058      27      73 ..      35      85 ..      10     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.6e-06
                           DUF4156 27 vtgsqgnwlsgiftsnkelvrgaa....ndLrneAaalGgntivlvtstat 73
                                      vt s +n + g ++s + l+++a+      +++eA+a+G++ +v v  t++
  gi|313126602|ref|YP_004036872.1| 35 VTQSLRNLVGGELNSYTGLMTDARdeaeKRMQEEAEAVGADAVVNVRFTTS 85
                                      55555566666666666666665511115799************9987743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 723.51
//
Query:       gi|313126603|ref|YP_004036873.1|  [L=127]
Description: methylmalonyl-CoA epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-15   55.4   0.1    7.8e-15   55.1   0.1    1.1  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    4.6e-07   30.1   1.3    5.1e-07   30.0   1.3    1.1  1  Glyoxalase_3  Glyoxalase-like domain
    5.6e-05   23.3   0.4    6.8e-05   23.1   0.4    1.1  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
     0.0035   18.1   0.2     0.0044   17.8   0.2    1.1  1  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.1   1.7e-18   7.8e-15       1     109 []       4     111 ..       4     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.7e-18
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT...-THHHTS-EEEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp...eflaehgeglhhlay 74 
                                       d++g+++ D    +a f++l++  +  +  +e  ++++ f++l +g  + eL ep+e+      l+++g+g+hh+a+
  gi|313126603|ref|YP_004036873.1|   4 DHLGVATADATGLAALFTELFDAPVAHE--EEFDGMTVLFLELEDG--YFELLEPHEDGaigRYLENNGPGIHHVAL 76 
                                       6999999999999999999999644444..3446899********9..88*******99999*************** PP

                                       EES-HHHHHHHHCTTTEEEEEEEE-GGGTT-EEEE CS
                      Glyoxalase_4  75 wvddldaavarleeqGfevvqkgvragaagrrfay 109
                                       ++dd++ a+++++ +G+e++++++r+ga g+++a+
  gi|313126603|ref|YP_004036873.1|  77 HTDDIEGALETARGAGVELIDHEPRPGAWGHDVAF 111
                                       ****************************9***998 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   1.3   1.1e-10   5.1e-07       1     112 [.       3     103 ..       3     127 .] 0.73

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.1e-10
                      Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdgYlEllavdpeapaperprlfgldrlakgeg 77 
                                       +DH+++a+ d +  aa f++   f +    e +  g     + + dgY+Ell+++++ +    +r ++    ++g+g
  gi|313126603|ref|YP_004036873.1|   3 FDHLGVATADATGLAALFTEL--FDAPVAHEEEFDGMTVLFLELEDGYFELLEPHEDGAI---GRYLE----NNGPG 70 
                                       8*****************877..554444444444677888999*********8666664...56542....479** PP

                      Glyoxalase_3  78 lhtlalrtddidataarlraaGvd.eagrrvrpdgg 112
                                       +h++al+tddi+ + +++r aGv+     + +p  g
  gi|313126603|ref|YP_004036873.1|  71 IHHVALHTDDIEGALETARGAGVElI---DHEPRPG 103
                                       **********************8652...3333333 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.4   1.5e-08   6.8e-05       2     128 .]       3     124 ..       2     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhva 78 
                                       +dh+ ++++d+   ++ +t+ +++ +  +++     +g++  f+  ++g  el+  + ++         e+++ +++
  gi|313126603|ref|YP_004036873.1|   3 FDHLGVATADATGLAALFTELFDAPVAHEEE----FDGMTVLFLELEDGYFELLEPHEDGAIGRYL---ENNGPGIH 72 
                                       5899999999999999999999999999999....8899999999999999998877766555554...668***** PP

                                       EEEEEHCHHHHHHHHHHHTTGE.EEEEEECHHCTEEEEE.EEEETTSEEEEE CS
                        Glyoxalase  79 fialdvedvgkaldrlkeagvk.vvaepgrhyfgalysf.yfrDpdGillei 128
                                       ++al ++d++ al+ ++ agv+ ++ ep    +g+ + f + +  +G+l+e+
  gi|313126603|ref|YP_004036873.1|  73 HVALHTDDIEGALETARGAGVElIDHEPRPGAWGHDVAFlHPKSTGGVLVEF 124
                                       *********************9456788889999888776888889999987 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   9.9e-07    0.0044       4      94 ..       8     106 ..       5     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.9e-07
                      Glyoxalase_6   4 ldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe....................paknrv 60 
                                       +++ad+  laa + ++++ +v++ee            + d++t+lf + ++                     +    
  gi|313126603|ref|YP_004036873.1|   8 VATADATGLAALFTELFDAPVAHEE------------EFDGMTVLFLELEDgyfellephedgaigrylenNGPGIH 72 
                                       7899*********************............2345567777777777777777777888888765333458 PP

                      Glyoxalase_6  61 HldlavedldaevarlvalGArvlreprdgthgr 94 
                                       H+ l+++d++ + + +  +G + ++++  +++++
  gi|313126603|ref|YP_004036873.1|  73 HVALHTDDIEGALETARGAGVELIDHEPRPGAWG 106
                                       **********************999988887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 741.87
//
Query:       gi|313126604|ref|YP_004036874.1|  [L=73]
Description: hypothetical protein Hbor_18620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.015   14.1   1.9      0.017   14.0   1.9    1.0  1  Spore_permease  Spore germination protein
       0.31   10.9   2.2       0.38   10.6   2.2    1.1  1  Pga1            GPI-Mannosyltransferase II co-activator


Domain annotation for each model (and alignments):
>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.9   1.9e-06     0.017      86     137 ..      10      61 ..       6      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-06
                    Spore_permease  86 ilyFlllaafelRefseliqvflledtplwiiilllllvilYlvvkGiesla 137
                                       ++ Fl+ ++++  ++++++ ++l+ ++   + +l+++lv +Yl   Gi ++ 
  gi|313126604|ref|YP_004036874.1|  10 LTLFLVSVVVVNTDLGDVFPMSLFSTLAYLVALLVMILVPAYLFADGIVDIQ 61 
                                       6789999999**************************************9886 PP

>> Pga1  GPI-Mannosyltransferase II co-activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.2   4.2e-05      0.38     137     170 ..      13      48 ..       5      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.2e-05
                              Pga1 137 vpinvsviklklg..ipvdLYsiivylillvillvv 170
                                       + ++v v+++ lg   p+ L+s+++yl++l+++++v
  gi|313126604|ref|YP_004036874.1|  13 FLVSVVVVNTDLGdvFPMSLFSTLAYLVALLVMILV 48 
                                       568999******9878**************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 412.16
//
Query:       gi|313126605|ref|YP_004036875.1|  [L=568]
Description: o-succinylbenzoate-CoA ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-94  317.1   0.3    1.8e-94  316.8   0.3    1.1  1  AMP-binding    AMP-binding enzyme
    5.1e-16   59.4   0.1    1.7e-15   57.8   0.1    2.0  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.8   0.3     2e-98   1.8e-94       2     422 ..       6     397 ..       5     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 316.8 bits;  conditional E-value: 2e-98
                                       HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                        ++a++ pd++alv+  +g+ + + eld  v+++A  L +lGv +gd+V+++l++++e+v +++a++++G+++vpl 
  gi|313126605|ref|YP_004036875.1|   6 SHRARTSPDATALVRAVTGEAWDFTELDGMVDEMAGRLVALGVAPGDHVGVVLQPRVEYVTLIHAAMRLGVTLVPLG 82 
                                       57899**********8899********************************************************** PP

                                       TTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS CS
                       AMP-binding  79 ptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeee 155
                                       ++lta+ela ++e ++++vl+  + +e  +++ ea++++       +l+ ++  ++e +  ++  +    +p ++++
  gi|313126605|ref|YP_004036875.1|  83 DRLTARELAEQIETADVTVLV--CGAETEARAVEATDDV------PLLSVESTTTTEVVSLTSVLP----DPIPPAS 147
                                       *********************..7766644444444433......333333333333333333333....2446778 PP

                                       -BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEE CS
                       AMP-binding 156 lkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvv 232
                                       ++  d+ ++++TSGTTG+PK+V l+ +nl+a++++  +  r ++++dd++l++l+l+h+ g+ + +l + l G+tvv
  gi|313126605|ref|YP_004036875.1| 148 WSLADVQLLLFTSGTTGEPKAVKLTMGNLLASATASMF--RLGFDPDDRWLVTLSLHHMGGI-APVLRMPLYGMTVV 221
                                       999*****************************988434..356779***************7.999999999***** PP

                                       E-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC CS
                       AMP-binding 233 llpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge 309
                                       l ++++a   ++ +++i+++ vt + +vP++l+++l+s+  +        sslr+vllgg+p ++el++++r+  ++
  gi|313126605|ref|YP_004036875.1| 222 LRDEFDA---GAAADDIDRYDVTAVSLVPTMLRRMLDSRG-T------LASSLRTVLLGGAPAPRELVERCRDYSIP 288
                                       *998877...4558***********************742.2......4567**********************987 PP

                                       EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHH CS
                       AMP-binding 310 evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeata 386
                                        v+ +YG+TEt+  v++++++e    +g+vG+pl  ++v +v+e+ g ++p+ge+Ge +v+gp+v +gY+++peata
  gi|313126605|ref|YP_004036875.1| 289 -VYPTYGMTETSSQVATARPDEAFDHVGTVGRPLFWTDVTVVNED-GDRLPPGETGEFVVSGPTVSPGYYNNPEATA 363
                                       .**************88888999999******************9.99***************************** PP

                                       HHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 387 eafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                        afd e r l+TGD+g++de G+l+++ R +d i++
  gi|313126605|ref|YP_004036875.1| 364 AAFD-E-RGLHTGDVGYVDEGGRLYVLNRVDDRIVT 397
                                       ***9.6.78**********99***********9986 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.1   1.9e-19   1.7e-15       1      75 [.     406     479 ..     406     480 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.9e-19
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsG 75 
                                       ev  +l shp+V ++aVvG+pd+ +Ge++ a+Vv +++ e+ +  L++++r++l+ ++ p+ + f delp+t sG
  gi|313126605|ref|YP_004036875.1| 406 EVADVLRSHPDVHDVAVVGIPDAEWGECVSALVVSDTD-ELDRSGLRDFAREQLAGFKIPRVIAFADELPRTVSG 479
                                       78899*****************************9433.4468*****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.58
# Mc/sec: 2950.37
//
Query:       gi|313126606|ref|YP_004036876.1|  [L=571]
Description: acyl-CoA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-95  320.2   0.0    2.1e-95  319.8   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    3.3e-23   82.5   0.4    7.8e-23   81.2   0.4    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.8   0.0   2.3e-99   2.1e-95       2     422 ..      17     455 ..      16     456 .. 0.87

  Alignments for each domain:
  == domain 1  score: 319.8 bits;  conditional E-value: 2.3e-99
                                       HHHHHHSTTSEEEEE.CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEE CS
                       AMP-binding   2 eeqaaktpdkvalvd.sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpl 77 
                                       +++ + +pd+ ++ + +++ +++TY+e+ +rv +lA++L  +G+++gdrV+ +++n ++++ a++a+ ++Ga + ++
  gi|313126606|ref|YP_004036876.1|  17 WRAQKMFPDREVVSRtHEGRERYTYSEYGARVAQLANALAGAGIEDGDRVGTFCWNHHRHFEAYFAVPSMGAQLHTI 93 
                                       56778899***997798899********************88*********************************** PP

                                       ETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT.S...-T CS
                       AMP-binding  78 nptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseeka.e...kp 150
                                       np l+ ++++yi+e++  ++l+  vd  l+ekl+ a +++   +++  +  ++    ++l++ ++ e +  +   ++
  gi|313126606|ref|YP_004036876.1|  94 NPLLPDHHIQYIVENAADRLLF--VDPSLVEKLAGAYDEDAFESVEQFVVMGSEVPDTPLENVTDYE-SFvGgeeTD 167
                                       **********************..9999988887766655444333333333333344555555333.223145656 PP

                                       SCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHH CS
                       AMP-binding 151 eeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllall 226
                                        + ++l ++++a ++YTSGTTGkPKGV ++++ l + + + +l++   +l+++dvv+ ++p++h+ ++  + + + +
  gi|313126606|ref|YP_004036876.1| 168 YDWPNLPEEQPAGMCYTSGTTGKPKGVEYTQQMLWSHTMA-SLPEAgLDLRSSDVVMPVVPMFHVNAW-GFPFSTTA 242
                                       67778999***********************999766555.46777677889****************.******** PP

                                       TT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHH CS
                       AMP-binding 227 sGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrff 303
                                       +Ga+ v++ ++++  p+ l+ lie+++vt++agvP+v+  lle  a++    + d+ssl+ +++gg++ +++++r+f
  gi|313126606|ref|YP_004036876.1| 243 AGAKHVYPGPSPT--PEDLATLIEEEGVTITAGVPTVWLGLLEYLAEN----DADMSSLERIVIGGSAAPKSVIRRF 313
                                       *******999988..77799***********************54444....45*********************** PP

                                       HHHHTCEEEEEEEEGGGSSECEE.........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE.TTSE.EEEEE CS
                       AMP-binding 304 ralfgeevlegYGlTEttgvvtv.........lpleedkkklgsvGkplpgvevkivDeetgepvp.dgee.Gellv 369
                                        + +  +v +++G+TE+++  tv         lp+ee+ +k+ ++G  +pg e+++vD++ ge+vp +ge  Gel+v
  gi|313126606|ref|YP_004036876.1| 314 DEEYDVTVTHAWGMTEMAPLGTVanlkpgmesLPKEEQYEKQAKQGLLVPGLEMRVVDDD-GEEVPwNGEDfGELWV 389
                                       ****99***************88899******8889999999*****************9.88998566669***** PP

                                       EETTS-SEBTT-HHHHHHHEEE...........T.CC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 370 rgpgvmkgYlkkpeataeafds...........e.gr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                       rgp+v+  Y+ +pea++e f             e  + wl+TGD++++d++Gy++iv+R+kd+ik+
  gi|313126606|ref|YP_004036876.1| 390 RGPWVTTEYFERPEANEEDFEVpaggasgqsadEvSGvWLKTGDVVTVDPEGYVKIVDRAKDVIKS 455
                                       ********************85789999***9956577**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.4   8.7e-27   7.8e-23       1      76 []     464     541 ..     464     541 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 8.7e-27
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE----.--.HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgs.ea.leeeLkahvrkelgpyavpkkvvfvdelpktrsG 75 
                                       e+E+al++ ++Vaea VvGvp+e++ e++vafVv+ +g+ e+ l++eL++ v++e++++++p++vvf++e+pkt++G
  gi|313126606|ref|YP_004036876.1| 464 ELENALMANDNVAEATVVGVPHERWQERPVAFVVPTRGTdEDsLKAELIEMVEDEFPKWWAPDEVVFIEEVPKTATG 540
                                       89*********************************77864447********************************** PP

                                       - CS
                     AMP-binding_C  76 K 76 
                                       K
  gi|313126606|ref|YP_004036876.1| 541 K 541
                                       9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 3098.65
//
Query:       gi|313126607|ref|YP_004036877.1|  [L=382]
Description: acyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-43  146.2   1.6      1e-42  145.9   0.8    1.5  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    5.5e-28   97.0   0.2    1.5e-27   95.6   0.2    1.8  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    4.6e-26   91.7   0.3    1.1e-25   90.4   0.3    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    9.3e-19   68.0   0.3    1.5e-18   67.4   0.3    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    2.5e-05   24.1   0.7    0.00012   21.9   0.7    2.0  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.5   1.2e+04     102     117 ..      55      70 ..      54      83 .. 0.66
   2 !  145.9   0.8   2.9e-46     1e-42       1     148 [.     233     380 ..     233     381 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.5
                                       HHHHHHHHHGGGTTSG CS
                     Acyl-CoA_dh_1 102 vadlamqllGgaGyle 117
                                       va++  + +Gg+Gy  
  gi|313126607|ref|YP_004036877.1|  55 VAQDISEEYGGKGYDL 70 
                                       5677778899999953 PP

  == domain 2  score: 145.9 bits;  conditional E-value: 2.9e-46
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       g Gf+     +nh+R++v+   +gla+ a+ee++e++++r+ fg+ + d+q+ ++ la+m+ e eaar+l++raae+
  gi|313126607|ref|YP_004036877.1| 233 GGGFYMLADFFNHGRVVVGGHGIGLAAHAIEETWEFVHEREGFGRNISDFQSTQHILADMRMEFEAARSLNWRAAEK 309
                                       57*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                       + +g++++  a+ aK + +e+a+ +a++ mql+Gg+++l+eyp++r yrd+r+  i+eG++eiqrn+i r+
  gi|313126607|ref|YP_004036877.1| 310 VANGENAGFWAASAKTKSTETAMMCAERGMQLHGGRSVLNEYPISRVYRDVRIPVIYEGANEIQRNLIYRQ 380
                                       ********************************************************************986 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.2   4.2e-31   1.5e-27       1      97 []     125     221 ..     125     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 4.2e-31
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvr 76 
                                       ++a++Epq+Gsd+a+++t +ae+ ++++vlnGeK w++na +a++++v+a+t+++d r+ + ++f+v++d++g + +
  gi|313126607|ref|YP_004036877.1| 125 GLAVSEPQTGSDMAGMTT-TAEKTDDGWVLNGEKYWVGNAVEADWLTVYAKTGDTDdRYSNYTMFIVETDTEGYEAE 200
                                       589***************.55555567************************8888889******************* PP

                                       ----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  77 rieeklGlrglptgelvfedv 97 
                                       +i+ek+G+r  ++g++vf+d+
  gi|313126607|ref|YP_004036877.1| 201 HIPEKMGMRASKQGHIVFDDC 221
                                       *******************97 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.3   3.1e-29   1.1e-25       2     113 .]      11     121 ..      10     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 3.1e-29
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                       e  +++++t+refaee+++p+a+e++e+ge+p++++++  ++Gl++  + eeygG g d l+ + + eel r+dag+
  gi|313126607|ref|YP_004036877.1|  11 EHARDVKQTAREFAEEHIRPQAEEYYESGEYPWDILEAGMDAGLVAQDISEEYGGKGYDLLQILAINEELYRVDAGI 87 
                                       677899*********************************************************************** PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                       al+l++  s +++++  +G++eqk++yL+++a+ e
  gi|313126607|ref|YP_004036877.1|  88 ALTLMLA-SFGCEIVEDYGSQEQKEKYLRPVAENE 121
                                       **88885.58889******************9875 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.3   4.2e-22   1.5e-18       4     133 ..     251     370 ..     248     371 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 4.2e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                     Acyl-CoA_dh_2   4 aavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedr 80 
                                       +   +G+A  a++e+ e+++er +  +g++++d++ tq+ la+++++ +AAr l  raa++    +a+g++      
  gi|313126607|ref|YP_004036877.1| 251 GGHGIGLAAHAIEETWEFVHEREG--FGRNISDFQSTQHILADMRMEFEAARSLNWRAAEK----VANGENA----G 317
                                       56689*******************..***********************************....9999996....8 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  81 aearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                         a+ a++  +e+a  ++++ ++++Gg+++++e+p+ R++RD+++  +++++n
  gi|313126607|ref|YP_004036877.1| 318 FWAASAKTKSTETAMMCAERGMQLHGGRSVLNEYPISRVYRDVRIPVIYEGAN 370
                                       889999**************************************999998876 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.7   3.2e-08   0.00012     127     271 ..     107     229 ..      80     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.2e-08
                                       HHHHHHHHHHHHHHT--EEEEES--SS-TTS-GGGSSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEEEE---S CS
                            HpaB_N 127 aenfrkyleyvqendlvlthaitdpkgdRskrpseqedpdvyvrvveetddGivVrGakvlaTgaaladeilvlptr 203
                                       +e+ +kyl+ v+en+ +   a+ +p++              +    e+tddG v +G k    +a+ ad++ v+   
  gi|313126607|ref|YP_004036877.1| 107 QEQKEKYLRPVAENEQISGLAVSEPQTGSD--------MAGMTTTAEKTDDGWVLNGEKYWVGNAVEADWLTVYAKT 175
                                       577778888888888888888888876544........223456789***************************994 PP

                                       S-..TTSGGG-EEEEEETT-TTEEEEE-------S..-TTT-TTTTT----EEEEEEEEEEEEGGGEE CS
                            HpaB_N 204 amlkeedkdyavafavpvdapGlklicresfedkleesefdyplssrfdendalvvfDdVfVPwerVf 271
                                          +++      +f+v++d++G +    ++            ++      ++  +vfDd+ VP e+V+
  gi|313126607|ref|YP_004036877.1| 176 GD-TDDRYSNYTMFIVETDTEGYEAEHIPEKM----------GMR---ASKQGHIVFDDCVVPEENVI 229
                                       33.4444444579*********7653333322..........222...3467899***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2161.56
//
Query:       gi|313126608|ref|YP_004036878.1|  [L=567]
Description: hypothetical protein Hbor_18660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0015   18.1   0.0     0.0031   17.1   0.0    1.5  1  Peptidase_M1   Peptidase family M1 domain
  ------ inclusion threshold ------
      0.013   15.8   1.6       0.29   11.5   0.1    2.5  2  Peptidase_M61  M61 glycyl aminopeptidase
      0.024   13.6   0.0      0.036   13.0   0.0    1.1  1  GRAS           GRAS domain family


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.2e-07    0.0031       2     190 ..     189     357 ..     188     376 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.2e-07
                                       HHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHH CS
                      Peptidase_M1   2 alevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHq 78 
                                       a++ t+  l+ l+ +f++ ++++++   + p+ ++g     g  + +++ ll   ++     + +v +v+ HE++H 
  gi|313126608|ref|YP_004036878.1| 189 AMNETADHLQTLATEFDTGFQYDEVVTFIPPKSAFGPSDLAGRAV-KHTILLRP-RSVG---TDTVGNVVSHEYVHT 260
                                       688888889999999999999999888888888888877777654.44444444.4433...4789*********** PP

                                       HBTTTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSS CS
                      Peptidase_M1  79 WfGnlVtmkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevFd 155
                                         G     +     wL EG a+y+ +l++ ++        ++  ee ++ + +d  ++s  +   +++ ++ ++ F 
  gi|313126608|ref|YP_004036878.1| 261 RLGAFFGSAE----WLREGSAQYYGALLSVNAGV-----GSF--EEFHSYVTTDKYADSGVV---LRDTETWNSKF- 322
                                       ****999887....5********99988766333.....333..555888999999988888...45555556666. PP

                                       HHHHHHHHHHHHHHHHHCT.HHHHHHHHHHHHHHCT CS
                      Peptidase_M1 156 siaYeKGasllrmlekllg.eevFqkglksYlkefk 190
                                        ++Y+KGa +l  l + +    + q+ l+ ++++ +
  gi|313126608|ref|YP_004036878.1| 323 -VPYQKGAHVLAALDAEIRvRTDGQQTLRDVFEKRS 357
                                       .89999999999998877656667777777777655 PP

>> Peptidase_M61  M61 glycyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.023   1.4e+02       4      13 ..     251     260 ..     248     265 .. 0.86
   2 ?   11.5   0.1   4.9e-05      0.29      37      67 ..     269     299 ..     264     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.023
                                       HHHHHHHHHT CS
                     Peptidase_M61   4 gllaHEyfHs 13 
                                       ++++HEy+H+
  gi|313126608|ref|YP_004036878.1| 251 NVVSHEYVHT 260
                                       689******7 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.9e-05
                                       THHHHTHHHHHHHHHHHHHTTSS-HHHHHHH CS
                     Peptidase_M61  37 llwvaEGlTsYygdlllarsgliseeeylee 67 
                                         w+ EG  +Yyg ll++ +g+ s ee+ + 
  gi|313126608|ref|YP_004036878.1| 269 AEWLREGSAQYYGALLSVNAGVGSFEEFHSY 299
                                       56********************999888765 PP

>> GRAS  GRAS domain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.1e-06     0.036     131     182 ..     165     214 ..     164     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-06
                                       HHHCHTTS--EEEEEEEECE.TTHHHHHHHHHHHHHHHHHHHT--EEEEEEE CS
                              GRAS 131 aLasRpggppslRiTgvgspekgskeeleetgerLakfAeklgvpfefnvlv 182
                                        +asR+ + p+  +T+v++p+++s e+++et++ L+ +A++++  f+++ +v
  gi|313126608|ref|YP_004036878.1| 165 RFASRTTDGPT--VTVVAAPNTTSPEAMNETADHLQTLATEFDTGFQYDEVV 214
                                       68889888887..5999999999*************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 2997.46
//
Query:       gi|313126609|ref|YP_004036879.1|  [L=391]
Description: zn-dependent hydrolase, glyoxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.9e-16   58.3   6.7      2e-15   57.3   6.7    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily
    7.5e-09   36.1   0.0    1.3e-08   35.3   0.0    1.4  1  Rhodanese      Rhodanese-like domain
    0.00057   19.5   0.5     0.0011   18.6   0.5    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   6.7   3.4e-19     2e-15       5     163 ..     141     280 ..     137     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 3.4e-19
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       ++ +yli+ d+++ ++D++         +    +   +  +++vi TH H+DHi+gl++l+ +t+++++  a +a  
  gi|313126609|ref|YP_004036879.1| 141 GCLAYLIVSDDEAAVVDPLRAFTDRYVTD----AAEYGASIEYVIDTHVHADHISGLRELAAETGAKTVLSATAADR 213
                                       6889**********************985....9999**************************************** PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                       +    +                   dv  e++d++++g+ + +v+++pgh++g  +  +  g+vl+tGD l++ + +
  gi|313126609|ref|YP_004036879.1| 214 GVAYVV-------------------DVLVEDGDTITLGDADIKVIHTPGHTSGMTS--LLVGDVLLTGDGLFTDSVA 269
                                       999999...................5777777777777777777776666666655..56789************** PP

                                       CCCC....... CS
                       Lactamase_B 159 ridl......t 163
                                       r dl       
  gi|313126609|ref|YP_004036879.1| 270 RPDLeagsegA 280
                                       **995433331 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   2.1e-12   1.3e-08       1     106 [.      17     117 ..      17     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.1e-12
                         Rhodanese   1 sakelkellekgkva.llDvRppeeYekghI.pgAvnvskdtlsrakkseapllelpeellel...gidnkktvvvy 72 
                                       +a+ lk +l++g+   llD+Rpp+++e+++I   +v        +   ++  + el +    +   g+ +++++vv+
  gi|313126609|ref|YP_004036879.1|  17 TAETLKSRLDDGEELmLLDTRPPAKHEEWRIdADSVTY-----VNRPYDNYLDGELTD----ElvaGLPDDEEFVVF 84 
                                       6899*****8888778***************7777777.....233333333333333....3444889******** PP

                         Rhodanese  73 cdgggraaaaaallkklGyknvsvldGGfkawke 106
                                       c++g+ ++++a  l+ +G ++   l+ G+++w++
  gi|313126609|ref|YP_004036879.1|  85 CAKGHTSEFVAGKLRLAG-YDAVALEDGMEGWAR 117
                                       ******************.8************85 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.5   1.8e-07    0.0011      28      99 ..     174     232 ..     154     261 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-07
                                       ..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEEC CS
                     Lactamase_B_2  28 lppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelg 99 
                                        ++i+ V+ th H+DH+ gl  l++ ++ k        ++a+ ++++v+ + ++        ++ g++++lg
  gi|313126609|ref|YP_004036879.1| 174 GASIEYVIDTHVHADHISGLRELAAETGAK------TVLSATAADRGVAYVVDVL-------VEDGDTITLG 232
                                       4689*******************9943322......2223333333333333333.......4455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2275.47
//
Query:       gi|313126610|ref|YP_004036880.1|  [L=172]
Description: transporter component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-12   47.6  13.9    2.1e-12   47.3  13.9    1.1  1  Sulf_transp  Sulphur transport
  ------ inclusion threshold ------
       0.48   10.1   4.8       0.48   10.1   0.6    2.3  2  UNC-93       Ion channel regulatory protein UNC-93


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3  13.9   2.3e-16   2.1e-12     178     306 ..      28     156 ..       8     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.3e-16
                       Sulf_transp 178 slvlgavllgllavlawllsak.tgrsfglgftvp.gakilqylvlgtskflnwgvvlvlGiilGaflaallsgefk 252
                                       +++lg+vl+gl + +++l ++  +g s+ l  t++ ++++ ++   +  +  +w vv+  Gi+lGa+l  +  g   
  gi|313126610|ref|YP_004036880.1|  28 DYALGGVLIGLGVSVIYLSTGIiAGASTFLESTLSyVSDLPRFNRGKYVRSRDWRVVFTGGIVLGAALYTVTLGPGG 104
                                       67899*****7766666544322233333333332133333333444455679************************ PP

                       Sulf_transp 253 leapkarellaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvflll 306
                                       ++   + + ++ +lGG+l+G+G+rl+ GC++G+g+ gi s s ++++ +++++l
  gi|313126610|ref|YP_004036880.1| 105 WT--TQVQPWRLFLGGTLVGVGTRLGKGCTSGHGVCGIGSGSNTSFVNVATFML 156
                                       *6..78999**************************************7776664 PP

>> UNC-93  Ion channel regulatory protein UNC-93
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6   5.3e-05      0.48      70     111 ..       6      48 ..       3      60 .. 0.87
   2 ?    1.6   0.2     0.023     2e+02      86     105 ..     108     127 ..      85     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.3e-05
                            UNC-93  70 lvigallyaifqlgFlllnkyyly.issallGvgaallwtgqG 111
                                       l +++++  ++ +g l++n +  y ++ +l+G+g+++++ + G
  gi|313126610|ref|YP_004036880.1|   6 LSAAGATVPLVVVGDLFPNGWIDYaLGGVLIGLGVSVIYLSTG 48 
                                       667888899999*********9883689***********9998 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.023
                            UNC-93  86 llnkyylyissallGvgaal 105
                                       ++  + l+++ +l+Gvg+ l
  gi|313126610|ref|YP_004036880.1| 108 QVQPWRLFLGGTLVGVGTRL 127
                                       56789999999999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 962.92
//
Query:       gi|313126611|ref|YP_004036881.1|  [L=155]
Description: transporter component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-08   34.2   5.2      2e-08   34.2   5.2    2.0  2  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.5   4.2    0.0049        89      56      71 ..      13      28 ..       2      30 .. 0.79
   2 !   34.2   5.2   1.1e-12     2e-08       5     108 ..      31     139 ..      27     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.0049
                       Sulf_transp 56 glivGGllFGvGMala 71
                                       +++GG+lFG+G+ l+
  gi|313126611|ref|YP_004036881.1| 13 VILLGGVLFGFGLGLS 28
                                      4699********9876 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 1.1e-12
                       Sulf_transp   5 cfagairdivvekdgrllralllaiavaavgfqllaaag.lidl.....pksafpv.vglivGGllFGvGMalaGgC 74 
                                         ++ + d++ ++d+ ll ++  a av+av+f++   ++  ++l     ++ + ++   ++vGG +FGvG  l+G C
  gi|313126611|ref|YP_004036881.1|  31 ARPEVVLDFLQFEDFGLLFVMGGAAAVTAVVFTVGVRLHrGAPLtgrpyERREKSFdRNVLVGGTVFGVGWGLSGIC 107
                                       566778899999999999999999999999888887665244553322233333334999***************** PP

                       Sulf_transp  75 asgtlyrvGeGslralitllffilgavalltgil 108
                                       ++ +++ +G G++  l+++ ++ +ga++  +g+l
  gi|313126611|ref|YP_004036881.1| 108 PGAAYASLGVGNVPILWAIGGMFVGAYV--QGYL 139
                                       **************************98..3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.36s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 882.32
//
Query:       gi|313126612|ref|YP_004036882.1|  [L=135]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-18   64.5   0.0      8e-18   64.1   0.0    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
    2.7e-06   27.1   0.1    4.5e-06   26.4   0.1    1.4  1  HTH_IclR         IclR helix-turn-helix domain
    4.6e-06   27.0   0.0    5.9e-06   26.6   0.0    1.1  1  Penicillinase_R  Penicillinase repressor
    6.4e-05   22.8   0.0    0.00014   21.7   0.0    1.5  1  MarR             MarR family
    0.00041   20.2   0.0    0.00061   19.7   0.0    1.3  1  HTH_11           HTH domain
     0.0006   20.0   0.1     0.0049   17.1   0.1    2.3  1  DUF4777          Domain of unknown function (DUF4777)
    0.00076   19.3   0.1     0.0011   18.8   0.1    1.3  1  MarR_2           MarR family
     0.0038   17.3   0.1     0.0067   16.5   0.1    1.4  1  HTH_20           Helix-turn-helix domain
     0.0071   16.8   0.0      0.011   16.2   0.0    1.4  1  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.015   14.8   0.0    1.2  1  UMPH-1           Pyrimidine 5'-nucleotidase (UMPH-1)
      0.015   14.8   0.0      0.021   14.3   0.0    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.025   14.5   0.3      0.065   13.2   0.3    1.7  1  PadR             Transcriptional regulator PadR-like family
      0.032   14.0   0.2      0.039   13.8   0.2    1.2  1  2OG-Fe_Oxy_2     2OG-Fe dioxygenase
       0.04   13.6   0.2      0.076   12.7   0.2    1.4  1  GntR             Bacterial regulatory proteins, gntR family
      0.047   13.7   0.0        0.1   12.6   0.0    1.6  1  Dimerisation     Dimerisation domain
      0.056   13.3   0.0       0.11   12.4   0.0    1.5  1  HTH_23           Homeodomain-like domain
      0.065   13.3   0.0       0.13   12.3   0.0    1.5  1  HTH_29           Winged helix-turn helix
      0.074   13.3   0.0       0.15   12.3   0.0    1.5  1  Ribosomal_S25    S25 ribosomal protein
       0.09   13.1   1.2        3.3    8.1   0.1    2.6  2  PqqD             Coenzyme PQQ synthesis protein D (PqqD)


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   8.5e-21     8e-18       1      68 []      19      94 ..      19      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 8.5e-21
                                      HH.HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE--HH CS
                              TrmB  1 Lq.klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYravdpe 68
                                      L+  +GL++ +  v+ +L+ + +p+t+de+a +++++rs++Y+++++L++ G+V++e+ +      +++Yr++dp+
  gi|313126612|ref|YP_004036882.1| 19 LEcIHGLKQLDKLVFRTLVeSAEPLTVDEVADRVERERSTAYRAIQRLLQTGFVQKEQVNydqggyYHVYRPTDPD 94
                                      67789**************999*******************************************999******95 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   4.8e-09   4.5e-06       9      50 ..      33      74 ..      31      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.8e-09
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       + l e +++lt+ e+A+r    +St++R +q L + G+v++
  gi|313126612|ref|YP_004036882.1| 33 FRTLVESAEPLTVDEVADRVERERSTAYRAIQRLLQTGFVQK 74
                                      56788999********************************97 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   6.2e-09   5.9e-06       8      98 ..      32     121 ..      26     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 6.2e-09
                                       HHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHH.HHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXX CS
                   Penicillinase_R   8 vmeilwekge.atvkevveeleeekelaysTVktllr.rLvkKgllsrekegrafiYsplvseeeavasavkqlldk 82 
                                       v ++l e+ e +tv+ev +++e+e+++ay  ++ ll+   v+K+ ++ ++ g  ++Y+p+      va  ++ +l+ 
  gi|313126612|ref|YP_004036882.1|  32 VFRTLVESAEpLTVDEVADRVERERSTAYRAIQRLLQtGFVQKEQVNYDQGGYYHVYRPTDPD--EVADDMQRMLND 106
                                       55555555555*************************726********************8654..477889999999 PP

                                       XXXXXXXXXXXXXXXX CS
                   Penicillinase_R  83 lfegsvkelvaafvee 98 
                                        ++ ++ +l+++f ++
  gi|313126612|ref|YP_004036882.1| 107 WYA-KMGTLIQEFRDK 121
                                       996.999999988776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.5e-07   0.00014      12      51 ..      37      76 ..      34      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-07
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      +++ +pl+v e a++++ ++st+ r++ rL + G++++++
  gi|313126612|ref|YP_004036882.1| 37 VESAEPLTVDEVADRVERERSTAYRAIQRLLQTGFVQKEQ 76
                                      67889********************************998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.4e-07   0.00061       8      54 ..      35      84 ..      27      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.4e-07
                            HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgrGY 54
                                       L e+ +p++ +e A++ ++ r+t +r I++L  +g     ++  ++g GY
  gi|313126612|ref|YP_004036882.1| 35 TLVESAEPLTVDEVADRVERERSTAYRAIQRLLQTGfvqkEQVNYDQG-GY 84
                                      4889999**************************999666656665555.55 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   5.2e-06    0.0049       3      34 ..      26      57 ..      25      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.2e-06
                           DUF4777  3 kqngalvlealkvlnrPaTldEivervaeryd 34
                                      kq ++lv ++l +  +P+T+dE+++rv + + 
  gi|313126612|ref|YP_004036882.1| 26 KQLDKLVFRTLVESAEPLTVDEVADRVERERS 57
                                      7999*********************9955444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.1e-06    0.0011      10      55 ..      32      76 ..      23      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      v   L  + ++ ltv e+a+r   ++s++ r+++rL + G+v+++ 
  gi|313126612|ref|YP_004036882.1| 32 VFRTLVESAEP-LTVDEVADRVERERSTAYRAIQRLLQTGFVQKEQ 76
                                      55566666666.******************************9875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.1e-06    0.0067      15      55 ..      32      73 ..      25      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.1e-06
                                      HHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 15 ilraL.araegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++r L  +ae+lt+ e+a+r++  ++t+++ ++ L + g+v 
  gi|313126612|ref|YP_004036882.1| 32 VFRTLvESAEPLTVDEVADRVERERSTAYRAIQRLLQTGFVQ 73
                                      45666789*******************************996 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05     0.011       2      60 ..      26      86 ..      25      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                            HTH_27  2 trqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre..k 60
                                      ++++ lv +++ +  ++ +  ++++r+ +e s++  ++ +L   G+v++++   d++    
  gi|313126612|ref|YP_004036882.1| 26 KQLDKLVFRTLVESAEPLTVDEVADRVERERSTAYRAIQRLLQTGFVQKEQVNYDQGGyyH 86
                                      677778888999999999*****************************99998888887434 PP

>> UMPH-1  Pyrimidine 5'-nucleotidase (UMPH-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.6e-05     0.015      18      78 ..      65     123 ..      49     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                            UMPH-1  18 gildesklineevkkklkeLyhkYrpieidpsltieekvkymveWwskshaLlieqklkke 78 
                                        +l+ + + +e+v+ ++   yh Yrp   dp+   ++  +++ +W++k ++L+ e++ k++
  gi|313126612|ref|YP_004036882.1|  65 RLLQTGFVQKEQVNYDQGGYYHVYRPT--DPDEVADDMQRMLNDWYAKMGTLIQEFRDKYD 123
                                       5788888899999*************6..788889999999*************9986665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.3e-05     0.021       7      47 ..      31      72 ..      25      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                            HTH_24  7 kILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                       + ++L + +  ++  e+A+r+   +st  r ++rL + G++
  gi|313126612|ref|YP_004036882.1| 31 LVFRTLVESAEpLTVDEVADRVERERSTAYRAIQRLLQTGFV 72
                                      5556666655559***************************98 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   6.9e-05     0.065      28      67 ..      53      92 ..      43      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.9e-05
                                      CTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESH CS
                              PadR 28 elseGslYpaLkrLekeglveseweesgegpprkyYrlTd 67
                                      e + ++ Y+a +rL + g+v++e+++ ++g+   +Yr Td
  gi|313126612|ref|YP_004036882.1| 53 ERERSTAYRAIQRLLQTGFVQKEQVNYDQGGYYHVYRPTD 92
                                      5567899******************99*****99999887 PP

>> 2OG-Fe_Oxy_2  2OG-Fe dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.1e-05     0.039       7      79 ..      43     109 ..      37     126 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                                       -EE--S-TTSEEEE-BEEEEEETTTEEEE-----EEEESSTT-SS-CEEE---B--HHHHTSHHHHHHHHHHH CS
                      2OG-Fe_Oxy_2   7 LplDpylkdgyRkrrysrfeldedtslerlphqpfaqskeynpldggieReFeeledellqnpllqallaaka 79 
                                       L  D+ +++  R+r+ +        +++rl ++ f+q++++n+ +gg    +++ +++ +++++ + l  + a
  gi|313126612|ref|YP_004036882.1|  43 LTVDEVADRVERERSTAYR------AIQRLLQTGFVQKEQVNYDQGGYYHVYRPTDPDEVADDMQRMLNDWYA 109
                                       5566666544444443333......799***************************998888765554444444 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2     8e-05     0.076      11      57 ..      30      75 ..      26      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8e-05
                                      HHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 11 edIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                       ++ ++ ++  ++L ++ e+a++ +  r+t  +A++rL + g v+ +
  gi|313126612|ref|YP_004036882.1| 30 KLVFRTLVESAEPL-TVDEVADRVERERSTAYRAIQRLLQTGFVQKE 75
                                      5555666777899*.***************************99976 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011       0.1      11      47 ..      32      67 ..      27      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                      Dimerisation 11 lldiiakaggkplspsEiaskLptknpeapvlldRlL 47
                                      ++ ++++++ +pl++ E+a +++  +++a   ++RlL
  gi|313126612|ref|YP_004036882.1| 32 VFRTLVESA-EPLTVDEVADRVERERSTAYRAIQRLL 67
                                      678999999.9*************************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.11      18      46 ..      43      71 ..      32      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            HTH_23 18 lsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      l+v e+A++  + r+T yr ++r  + G+
  gi|313126612|ref|YP_004036882.1| 43 LTVDEVADRVERERSTAYRAIQRLLQTGF 71
                                      5899*******************987775 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.13      11      40 ..      40      70 ..      33      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            HTH_29 11 Gvs.tvsqiAkllglsrrtvyrwlkrfeegG 40
                                      +++ tv ++A ++   r+t yr++ r  ++G
  gi|313126612|ref|YP_004036882.1| 40 AEPlTVDEVADRVERERSTAYRAIQRLLQTG 70
                                      44459*********************98888 PP

>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.15      51      89 ..      37      75 ..      26      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                     Ribosomal_S25 51 vpkyklitpsvvserlkingslArraLreleekgliklv 89
                                      v++++ +t+  v++r++ + s A ra++ l++ g++++ 
  gi|313126612|ref|YP_004036882.1| 37 VESAEPLTVDEVADRVERERSTAYRAIQRLLQTGFVQKE 75
                                      5667778999************************99875 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.12   1.1e+02      36      59 ..      45      68 ..      34      69 .. 0.86
   2 ?    8.1   0.1    0.0035       3.3       6      52 ..      78     131 ..      77     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                                      HHHHHHHCT--HHHHHHHHHHHHH CS
                              PqqD 36 vaalaeeydvdeeeaeadvlafld 59
                                      v+++a++ + ++ +a+++++++l+
  gi|313126612|ref|YP_004036882.1| 45 VDEVADRVERERSTAYRAIQRLLQ 68
                                      677888888899999999999997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0035
                                       -SS-..EE......E--CHHHHHHHH-SSSS-...HHHHHHHHHHHCT--HHHHHH CS
                              PqqD   6 dpetgkyi......sLnetgafiWklldgers...veeivaalaeeydvdeeeaea 52 
                                       ++++g+y+        +e++ ++ ++l++      + +++++++++yd++  +aea
  gi|313126612|ref|YP_004036882.1|  78 NYDQGGYYhvyrptDPDEVADDMQRMLND--WyakMGTLIQEFRDKYDEEVPRAEA 131
                                       55666665555555778999999999955..23469***********998555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 855.45
//
Query:       gi|313126613|ref|YP_004036883.1|  [L=66]
Description: hypothetical protein Hbor_18710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0074   16.4   0.9        1.8    8.8   0.1    2.1  2  NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.037   14.0   0.6      0.058   13.4   0.6    1.3  1  DZR           Double zinc ribbon


Domain annotation for each model (and alignments):
>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0002       1.8      23      48 ..      12      37 ..       5      51 .. 0.78
   2 !    6.9   0.1   0.00078         7      26      37 ..      52      63 ..      47      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0002
                      NOB1_Zn_bind 23 kkFCpkCGnktLkrvavsvdengelk 48
                                       ++C+ CG +t + v++ ++ + + +
  gi|313126613|ref|YP_004036883.1| 12 TEYCDICGVRTPHNVSIELKTESTKQ 37
                                      579**************999885433 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00078
                      NOB1_Zn_bind 26 CpkCGnktLkrv 37
                                      C kCG ++L+r+
  gi|313126613|ref|YP_004036883.1| 52 CVKCGDENLQRM 63
                                      99*********8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   6.5e-06     0.058      12      38 ..      12      59 ..       5      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-06
                               DZR 12 arfCseCgtklkavaa.....................edrCpsCgekv 38
                                       ++C+ Cg + +   +                      + C++Cg ++
  gi|313126613|ref|YP_004036883.1| 12 TEYCDICGVRTPHNVSielktestkqtnqefsrepyrVTECVKCGDEN 59
                                      679*******76544478888999********************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.56
# Mc/sec: 355.58
//
Query:       gi|313126614|ref|YP_004036884.1|  [L=135]
Description: response regulator with chey-like receiver domain and winged-helix DNA-binding domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-17   63.0   0.0    2.9e-17   62.8   0.0    1.1  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   1.6e-21   2.9e-17       1     109 [.      15     120 ..      15     123 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.6e-21
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vl++dD+ ++ + ++ +l  + y +v++a dg+eal+ +  + vd++llD  mpg++G +++ +++e + +++  +l
  gi|313126614|ref|YP_004036884.1|  15 VLVADDEVALTDSIAVWLS-DSY-RVRTAYDGHEALREFGPS-VDIVLLDRHMPGLSGEHVMARLNEMSANPQAALL 88 
                                       89****************9.889.9**************998.********************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlk 109
                                       ta+s+++ + e+ ++g d +l+Kp++++eLl 
  gi|313126614|ref|YP_004036884.1|  89 TATSTDDFRSEVDELGFDAYLTKPISKTELLG 120
                                       *****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 748.80
//
Query:       gi|313126615|ref|YP_004036885.1|  [L=602]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-36  125.3   9.9    1.9e-36  125.3   9.9    2.3  2  BAT           GAF and HTH_10 associated domain
    1.6e-19   69.5   0.0    3.1e-19   68.5   0.0    1.5  1  HTH_10        HTH DNA binding domain
    6.7e-17   61.7   0.9    1.9e-16   60.2   0.9    1.8  1  Response_reg  Response regulator receiver domain
    3.1e-09   37.0   7.8    3.1e-09   37.0   7.8    3.5  4  HalX          HalX domain
    4.7e-08   33.4   2.2    1.8e-07   31.6   0.1    2.8  3  GAF_2         GAF domain
    0.00015   22.1   0.0    0.00063   20.1   0.0    2.1  2  GAF_3         GAF domain
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.065   12.8   0.0    2.1  2  Sigma70_r4    Sigma-70, region 4
      0.088   13.4   0.0       0.24   12.0   0.0    1.8  1  GAF           GAF domain
      0.096   12.7   3.2        0.6   10.1   1.5    2.5  2  Noelin-1      Neurogenesis glycoprotein


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       3.2   6.3e+03      24      46 ..     118     142 ..     108     155 .. 0.55
   2 !  125.3   9.9   9.8e-40   1.9e-36       1     155 [.     365     519 ..     365     520 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.2
                               BAT  24 ldcrveleglvprsd..gevlvfft 46 
                                       +d r ++++lv rs+  +ev+ ff 
  gi|313126615|ref|YP_004036885.1| 118 TDVREAVKELVVRSEfdEEVREFFA 142
                                       3444444444444433345555555 PP

  == domain 2  score: 125.3 bits;  conditional E-value: 9.8e-40
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+ veLe++ +d+ d++v+l+a +++rv+l+g  p +dg+  ++ +v++a++e+v + ++++++v+ +r ++++ ++
  gi|313126615|ref|YP_004036885.1| 365 DTAVELEFTHEDRGDLFVDLSAVVNGRVSLQGFSPATDGGISCYTSVEEAAAEDVLEYLTAHEDVQHARTITDTPEK 441
                                       99*************************************************************************** PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                       +l+e++v+ ++++  l e G++v +++a +g+++lvv v+pgad+R + +++++++p+v +va+re+er+v+++++f
  gi|313126615|ref|YP_004036885.1| 442 SLFEVRVDASTVLVPLIEFGASVDTLTAMGGEGSLVVTVSPGADLRVLNDTVQSAFPAVGVVAKREVERSVQSTEAF 518
                                       **************************************************************************999 PP

                               BAT 155 r 155
                                       +
  gi|313126615|ref|YP_004036885.1| 519 K 519
                                       6 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0   1.6e-22   3.1e-19       1      52 [.     526     577 ..     526     578 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.6e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT +q  vl +A+ +GYFd+PR  t++e+A+ lGI+++t++ehLr+ e+kl+
  gi|313126615|ref|YP_004036885.1| 526 LTSRQHDVLETAFVSGYFDWPRGSTAEEVAESLGITAPTFHEHLRAGEKKLM 577
                                       9**************************************************9 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.9   9.4e-20   1.9e-16       1     111 [.      20     124 ..      20     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 9.4e-20
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vl+vdDd+++++ +  +l+ ++y +v++a +g++al+ ++e+ vd++llD +mp+++G ++l+ +re+  ++ v ++
  gi|313126615|ref|YP_004036885.1|  20 VLVVDDDEDLADTCVYWLQ-DDY-DVRAAYSGEDALAEADES-VDVVLLDRRMPKISGDDVLDALRERGLDCHVAMM 93 
                                       8*****************9.999.***************988.********************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       ta +     +e +++  dd+l+Kp++++++++a+
  gi|313126615|ref|YP_004036885.1|  94 TAVEP---DTEIVDMPFDDYLVKPVTKTDVREAV 124
                                       *8886...4678899***************9998 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   7.8   1.6e-12   3.1e-09       1      57 [.     129     184 ..     129     199 .. 0.90
   2 ?   -2.0   0.0       2.3   4.6e+03      43      51 ..     211     219 ..     193     231 .. 0.54
   3 ?   -0.5   0.0      0.79   1.6e+03      46      68 .]     271     292 ..     263     292 .. 0.88
   4 ?   -2.4   0.2       3.1   6.2e+03      38      51 ..     520     533 ..     506     538 .. 0.56

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.6e-12
                              HalX   1 trseYdeelqelfaLasKravLeaekseaeLadseeYqeLearleelraqldetlde 57 
                                       +rse+dee++e+faL+s++++L++  + ++L+d e   +L++++ee+r+ ++ ++++
  gi|313126615|ref|YP_004036885.1| 129 VRSEFDEEVREFFALESTEQALKS-RDNEDLRDPEVLKQLREQVEEVRRGHENEIAR 184
                                       59********************99.9*************************999887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                              HalX  43 rleelraql 51 
                                       + ee+++ +
  gi|313126615|ref|YP_004036885.1| 211 TREEIERAV 219
                                       334444444 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.79
                              HalX  46 elraqldetldelddaddfealf 68 
                                       +l+++  e++d +d  d+fea+f
  gi|313126615|ref|YP_004036885.1| 271 ALQDRTVELIDGIDP-DHFEAVF 292
                                       7999999*****999.99*9987 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 3.1
                              HalX  38 qeLearleelraql 51 
                                       +eLe+ l + ++++
  gi|313126615|ref|YP_004036885.1| 520 RELEDKLTSRQHDV 533
                                       34444444444444 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       6.1   1.2e+04      20      41 ..      30      49 ..      21      62 .. 0.52
   2 ?    0.1   0.0      0.46   9.2e+02       9      37 ..      75     103 ..      74     173 .. 0.72
   3 !   31.6   0.1   8.9e-11   1.8e-07       2     137 ..     210     353 ..     209     354 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.1
                                      ..EEEEEEE-TTS-EEEEEEEE CS
                             GAF_2 20 aalgyillvdddgglrlaawge 41
                                      a+ ++++l dd +    aa+++
  gi|313126615|ref|YP_004036885.1| 30 ADTCVYWLQDDYDV--RAAYSG 49
                                      44556666554333..333333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.46
                                       HHHHHHHHH..SS..EEEEEEE-TTS-EEEE CS
                             GAF_2   9 dlvldelve..lgaalgyillvdddgglrla 37 
                                       d vld+l+e  l+++++++  v++d++  ++
  gi|313126615|ref|YP_004036885.1|  75 DDVLDALRErgLDCHVAMMTAVEPDTE--IV 103
                                       579999966577999999999998877..33 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 8.9e-11
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEE....EEEES-TTSTT-S-B---TT.H.HHHHHHHTS-EEE CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgglrla....awgeaeeefgaaldrplgeg.l.vgealrtgrpvil 71 
                                       ++ ee+ ++v++ l+ ++  ++++++ +   + +++     a+g a++ f++++    g+  + +  al+++   ++
  gi|313126615|ref|YP_004036885.1| 210 TTREEIERAVCESLASFDtYTAAWVARYS--DTVETIscrtAAGVAPPVFDGQI----GSLtPrIRSALQDRTVELI 280
                                       7899*************76********99..44223345565666666665555....3333547777777655556 PP

                                       S-GGG...-S-HHHHHHHHHTT--E....EEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  72 ndlee...dpdkkglpaghaglrsf....lavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       + ++    ++   + + + +++ ++    ++vP+ +++ v+G+l++y+++  +f e+d+++++el+++i+  i
  gi|313126615|ref|YP_004036885.1| 281 DGIDPdhfEAVFTSDRTETPDVTPEglstVVVPIAYRETVYGALVVYTDDNVTFGEDDRAVFDELGATIGHGI 353
                                       66555456333333333444444445566*****88668********999999****************9876 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         5     1e+04      21      56 ..      32      60 ..      30      92 .. 0.59
   2 !   20.1   0.0   3.2e-07   0.00063      82     127 ..     308     353 ..     285     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5
                             GAF_3 21 vgalllldedgnklqvaagwdgkpalsesldedsal 56
                                       ++ +l d++     v+a++ g++al e   +d+++
  gi|313126615|ref|YP_004036885.1| 32 TCVYWLQDDY----DVRAAYSGEDALAE---ADESV 60
                                      5666666633....55666656666633...34444 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.2e-07
                             GAF_3  82 aalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       + ++vP++ +++v+G l+++++++  f+++d++ +++l++ i+ +i
  gi|313126615|ref|YP_004036885.1| 308 STVVVPIAYRETVYGALVVYTDDNVTFGEDDRAVFDELGATIGHGI 353
                                       5699*****99******************************99877 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.98     2e+03       3      16 ..     262     275 ..     261     279 .. 0.83
   2 ?   12.8   0.0   3.3e-05     0.065       3      34 ..     524     562 ..     524     576 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.98
                                       HHS-HHHHHHHHHH CS
                        Sigma70_r4   3 asLpererevlelr 16 
                                        sL++r r  l+ r
  gi|313126615|ref|YP_004036885.1| 262 GSLTPRIRSALQDR 275
                                       68******999988 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       HHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-H CS
                        Sigma70_r4   3 asLpererevlelrf.......geglTleEIgerlgiSr 34 
                                       ++L+ r+ +vle  f        +g T eE++e lgi+ 
  gi|313126615|ref|YP_004036885.1| 524 DKLTSRQHDVLETAFvsgyfdwPRGSTAEEVAESLGITA 562
                                       68*****************99999*************95 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.24      54     130 ..     270     350 ..     213     353 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                       HHHHHSSSEEESTGGTSTTHHTT...HHHHHHHHTTES....EEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHH CS
                               GAF  54 qvlatgqplvipdstpdprfaqy...nrrdllenmgir....sslvvPlvndgelwGllvlhnpsp.pftreelell 122
                                        +l+ + + +i++   dp++ ++      d  e + +     s +vvP+  ++ ++G+lv++  ++  f +++++++
  gi|313126615|ref|YP_004036885.1| 270 SALQDRTVELIDG--IDPDHFEAvftS--DRTETPDVTpeglSTVVVPIAYRETVYGALVVYTDDNvTFGEDDRAVF 342
                                       4455444444444..444444444431..333333333455599*******************77789*******99 PP

                                       HHHHHHHH CS
                               GAF 123 qvladqva 130
                                        +l++ ++
  gi|313126615|ref|YP_004036885.1| 343 DELGATIG 350
                                       99988776 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.5    0.0003       0.6      39      88 ..     162     211 ..     144     220 .. 0.84
   2 ?    0.9   0.0      0.22   4.5e+02      41      89 ..     486     532 ..     482     537 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                          Noelin-1  39 rqlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvvee 88 
                                       + l+ql e+v+ + +  e    R +r+l+ +++ + ll+++++ l +++ 
  gi|313126615|ref|YP_004036885.1| 162 EVLKQLREQVEEVRRGHENEIARRQRQLDRLHHINDLLREVDKALVDATT 211
                                       469***************9999*********************9988765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                          Noelin-1  41 lrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveed 89 
                                       lr l + vq     + v+++R  +    v++te   ++le+kl++ ++d
  gi|313126615|ref|YP_004036885.1| 486 LRVLNDTVQSAFPAVGVVAKREVE--RSVQSTEAFKRELEDKLTSRQHD 532
                                       788889999999999999988654..35779999999999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.56
# Mc/sec: 3251.35
//
Query:       gi|313126616|ref|YP_004036886.1|  [L=779]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-41  139.0   9.8    2.6e-17   63.1   0.1    4.0  4  PAS_4        PAS fold
    8.8e-35  119.1   0.1    2.6e-14   53.3   0.0    3.6  3  PAS_9        PAS domain
    1.3e-25   89.6   0.2    2.1e-09   37.4   0.0    3.5  3  PAS          PAS fold
    2.6e-17   63.3   0.1      8e-17   61.8   0.0    1.9  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.2e-16   61.2   0.0    3.5e-16   59.8   0.0    1.9  1  GAF_2        GAF domain
    1.4e-09   38.0   0.1    3.5e-09   36.7   0.1    1.7  1  HATPase_c_2  Histidine kinase-like ATPase domain
    3.4e-09   36.5   0.1      0.029   14.4   0.0    3.8  3  PAS_8        PAS domain
    4.8e-06   27.2   0.0    1.2e-05   26.0   0.0    1.7  1  GAF          GAF domain
    1.5e-05   25.2   1.6    0.00044   20.5   0.1    3.1  3  PAS_3        PAS fold
    0.00022   21.4   0.2        1.5    9.0   0.0    4.7  4  PAS_7        PAS fold
     0.0019   18.8   0.0       0.39   11.3   0.0    3.1  2  PAS_10       PAS domain
     0.0098   16.2   0.0       0.03   14.6   0.0    1.9  1  GAF_3        GAF domain
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.021   14.7   0.0    1.5  1  HATPase_c_5  GHKL domain
       0.02   14.4   0.0      0.033   13.8   0.0    1.3  1  HisKA_4TM    Archaeal 4TM region of histidine kinase


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.1     2e-20   2.6e-17       1     109 [.      20     120 ..      20     121 .. 0.97
   2 ?   -3.2   0.3       7.6   9.8e+03      48      74 ..     283     309 ..     280     314 .. 0.73
   3 !   37.8   0.0   1.5e-12   1.9e-09       7     110 .]     325     430 ..     323     430 .. 0.89
   4 !   42.9   0.1   3.8e-14   4.9e-11      13     110 .]     451     553 ..     440     553 .. 0.82

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 2e-20
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l++++da++++dp+++++y+N  a el+ ++++el+G+t ++ +p+  +  ++++++r+ e+++p++f+e++++   
  gi|313126616|ref|YP_004036886.1|  20 LERISDAVFAVDPEFHFTYLNSKATELLDRDADELIGETIWDEFPDAIGSTFQEQYERAFEEKDPVTFTEYYTP--L 94 
                                       6899*************************************99*******************************..* PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++++e++++P +       g+ v++rD+T+rr
  gi|313126616|ref|YP_004036886.1|  95 DKWFEVSAYPSET------GLTVYFRDVTDRR 120
                                       **********966......************8 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.6
                             PAS_4  48 daarleralrrvlegeepiefleelll 74 
                                       + ++l +a+++++++ e+ +++ el++
  gi|313126616|ref|YP_004036886.1| 283 SLQQLGDAVTHAIDTVERRQEERELKR 309
                                       556778888999999888888888877 PP

  == domain 3  score: 37.8 bits;  conditional E-value: 1.5e-12
                             PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelll.pgeerhy 81 
                                       a++ ld+dg++  +N+ a+++ g+   e+lG+++  +++e+   +++ + + + ++ +  ++++  +++ +g++ + 
  gi|313126616|ref|YP_004036886.1| 325 AIFRLDADGHIASWNRGAEDIEGYKESEVLGEHFSLFYTESeIEDGHPSEVLETARRDGQCKDEGWRVRkDGSQFWA 401
                                       68899******************************888877666667777777777777888888888899****** PP

                             PAS_4  82 elrllPlrdesGevigvlvisrDiTerrr 110
                                       +++l+ l+de+G ++g++ ++rD+Ter+r
  gi|313126616|ref|YP_004036886.1| 402 SVTLTALKDEDGSCRGFVKVIRDMTERKR 430
                                       ***************************97 PP

  == domain 4  score: 42.9 bits;  conditional E-value: 3.8e-14
                             PAS_4  13 pdgrvlyaNaaaaelfgappeellGktlae..llpee..daarleralrrvlegeepiefleelll..pgeerhyel 83 
                                       pdg+vl +N aa e  g+++e l+Gk+l+e  ++ +     ++  +a+ r+++++e+++ + +  +   gee ++++
  gi|313126616|ref|YP_004036886.1| 451 PDGTVLKVNDAAIEFSGVEREKLVGKHLWEetWWDANqeNVDEMKDAI-RLASTGEFVRYEVTGEDpdTGEEFVMDF 526
                                       8****************************5456666574555555555.5555556666555555569********* PP

                             PAS_4  84 rllPlrdesGevigvlvisrDiTerrr 110
                                       +++P+ de+Gev+ ++  +rDiTer++
  gi|313126616|ref|YP_004036886.1| 527 SITPVTDERGEVVLLVPEGRDITERKQ 553
                                       *************************85 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06    0.0014       2     103 ..      25     117 ..      24     118 .. 0.72
   2 !   53.3   0.0     2e-17   2.6e-14       4     104 .]     326     427 ..     323     427 .. 0.88
   3 !   42.9   0.0   3.7e-14   4.7e-11       8     104 .]     450     550 ..     445     550 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkng.etfw 77 
                                       d+++ ++p+++ +y N +a +ll  +++e++g  i+d f  ++   +++++++e+    e+ ++v+++        w
  gi|313126616|ref|YP_004036886.1|  25 DAVFAVDPEFHFTYLNSKATELLDRDADELIGETIWDEF--PDAIGSTFQEQYERAF--EEKDPVTFTEYYTpLDKW 97 
                                       6778788********************************..6666666666666666..555555444332223348 PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDit 103
                                       ++++a+p        +g+ v +rD+t
  gi|313126616|ref|YP_004036886.1|  98 FEVSAYPS------ETGLTVYFRDVT 117
                                       88888887......233446777777 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 2e-17
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvl 79 
                                       i+  + dg+i ++N++a+++ Gy++ evlg +++ ++ +++ ++   +++le+ r+  ++ +e   +rk+g++fw+ 
  gi|313126616|ref|YP_004036886.1| 326 IFRLDADGHIASWNRGAEDIEGYKESEVLGEHFSLFYTESEIEDGHPSEVLETARRdGQCKDEGWRVRKDGSQFWAS 402
                                       554679*******************************6666666666666666666668****************** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       +t++++kd+dg  +g++ ++rD+te
  gi|313126616|ref|YP_004036886.1| 403 VTLTALKDEDGSCRGFVKVIRDMTE 427
                                       ************************8 PP

  == domain 3  score: 42.9 bits;  conditional E-value: 3.7e-14
                             PAS_9   8 npdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk.kerevevvlirkngetfwvl.l 80 
                                        pdg++l++N+aa+++ G  +e ++gk++++    + ++e+ +++++a++  ++ ++ ++ev+  +++ ++ +v+ +
  gi|313126616|ref|YP_004036886.1| 450 KPDGTVLKVNDAAIEFSGVEREKLVGKHLWEETwwDANQENVDEMKDAIRLASTgEFVRYEVTGEDPDTGEEFVMdF 526
                                       49**************************99988899999999999999999999************9986666666* PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       +++pv d+ ge+v+++   rDite
  gi|313126616|ref|YP_004036886.1| 527 SITPVTDERGEVVLLVPEGRDITE 550
                                       ***********************8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.3e-08     3e-05       7      72 ..      20      85 ..      14     105 .. 0.88
   2 !   37.4   0.0   1.6e-12   2.1e-09      13     113 .]     325     425 ..     312     425 .. 0.88
   3 !   24.2   0.0     2e-08   2.5e-05      20     107 ..     452     542 ..     448     548 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.3e-08
                                      HHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-E CS
                               PAS  7 leslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgees 72
                                      le + d++f+vD    ++y N++a+ell  +++e++g+++ d+++    ++++e++e++ e++ + 
  gi|313126616|ref|YP_004036886.1| 20 LERISDAVFAVDPEFHFTYLNSKATELLDRDADELIGETIWDEFPDAIGSTFQEQYERAFEEKDPV 85
                                      67799****************************************988889999999988877665 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 1.6e-12
                                       EEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEE CS
                               PAS  13 pifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpih 88 
                                       +if +D+dg i  +N+ ae++ G++++evlg++++ ++ e + +  +++++++ ++   +++++  ++++ dg+ ++
  gi|313126616|ref|YP_004036886.1| 325 AIFRLDADGHIASWNRGAEDIEGYKESEVLGEHFSLFYTESEIEdGHPSEVLETARRDGQCKDEGWRVRK-DGSQFW 400
                                       7999*******************************99988765587788887777777777787777888.****** PP

                                       EEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  89 levraspvrdaggeilgflgvlrdi 113
                                       + v+ + + d++g  +gf+ v+rd+
  gi|313126616|ref|YP_004036886.1| 401 ASVTLTALKDEDGSCRGFVKVIRDM 425
                                       ***********************96 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 2e-08
                                       TSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC...TTSSEEEEEEEE CS
                               PAS  20 dgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl...rdgrpihlevra 93 
                                       dg +l vN+aa e+ G +re ++gk+l ++ + + ++e +++++ +++ ++ ++ ++  ++      g+++ ++   
  gi|313126616|ref|YP_004036886.1| 452 DGTVLKVNDAAIEFSGVEREKLVGKHLWEETWWDANQENVDEMKDAIRLASTGEFVRYEVTGedpDTGEEFVMDFSI 528
                                       89**********************************************9999999999999999************* PP

                                       EEEEETTEEEEEEE CS
                               PAS  94 spvrdaggeilgfl 107
                                       +pv+d+ ge+  ++
  gi|313126616|ref|YP_004036886.1| 529 TPVTDERGEVVLLV 542
                                       ********975554 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0   6.2e-20     8e-17       6     109 ..     676     777 ..     672     779 .] 0.85

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 6.2e-20
                                       HHHHHHHHHHHHHHHHSTTTEEEEEEEEEE...TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfatkageieveikase...ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGls 79 
                                       L q++ n+++Nav++ +++   +v++++++   + + ++v DnG+Gip e+ +++ ek ++       + g+G+Gl+
  gi|313126616|ref|YP_004036886.1| 676 LPQVFENVLSNAVQH-NDKAVPRVSVSVEQrgdGAVAVRVADNGPGIPDEEKQRIVEKDVE----GLATPGSGFGLY 747
                                       779************.545544555555344568**********************97777....34589******* PP

                                       HHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlp 109
                                       +vk+lv+ +gG+i v++++ +G  ft+tl+
  gi|313126616|ref|YP_004036886.1| 748 LVKELVDSYGGTIDVSDNDPEGAVFTITLQ 777
                                       ***************9999********997 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   2.7e-19   3.5e-16       4     138 .]     156     296 ..     153     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.7e-19
                                       HHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B..---TTHHHHHHHHTS-EEES-GGG- CS
                             GAF_2   4 leelldlvldelvelg.aalgyillvdddgglrlaawgeaeeefgaaldr..plgeglvgealrtgrpvilndleed 77 
                                        + + +lv+++l+e++  ++++++ vd+d+ ++ +aw++ae +  ++l++  ++g+g++  a+++++  i +++e++
  gi|313126616|ref|YP_004036886.1| 156 RDHIEQLVCNRLIETTpLRFVWVGRVDGDD-IEPSAWAGAEQGSVEELPDdkMIGRGPAKCAAAENEVQITSSIEDS 231
                                       677889********866**********655.7888*******999999996555****999999999999999***9 PP

                                       S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......-.-.HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  78 pdkkglp..aghaglrsflavPlisegrvvGvlnlyankppaf.d.eedlelLeelaeqiaiaie 138
                                         + +++  a ++g++++++vPl ++g  +Gvl+ly+++++af + +   e L++l++ +  ai+
  gi|313126616|ref|YP_004036886.1| 232 SGWEQWRaeALEHGFNACACVPLEYRGANYGVLCLYSDRKGAFgTqDGPTESLQQLGDAVTHAID 296
                                       999999999**************66689***************4335557889999999999886 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   2.7e-12   3.5e-09      39     124 ..     683     775 ..     679     776 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.7e-12
                       HATPase_c_2  39 actNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvDev.. 112
                                       +++Nav+h+ +  p  +v+v+ +++++a+ v+vaD+Gpg  d e+++  +++      + +G+Gl+l+k+lvD++  
  gi|313126616|ref|YP_004036886.1| 683 VLSNAVQHNDKAVPRVSVSVE-QRGDGAVAVRVADNGPGiPDEEKQRIVEKDVEGLATPGSGFGLYLVKELVDSYgg 758
                                       589***********9999999.999**************8888766655555557889999*************987 PP

                       HATPase_c_2 113 ey.....dgegnvvtms 124
                                        +     d+eg v t++
  gi|313126616|ref|YP_004036886.1| 759 TIdvsdnDPEGAVFTIT 775
                                       33447778888888775 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.2e-05     0.029       8      52 ..      21      66 ..      20      83 .. 0.70
   2 !    7.3   0.0    0.0037       4.7       3      45 ..     314     358 ..     312     380 .. 0.82
   3 !   10.0   0.0   0.00055      0.71      19      47 ..     452     482 ..     437     502 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                             PAS_8  8 esspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvl 52
                                      e ++d+++ vd +  ++++ N +a ell  + ++l+ge++++ +p+ 
  gi|313126616|ref|YP_004036886.1| 21 ERISDAVFAVDpEF-HFTYLNSKATELLDRDaDELIGETIWDEFPDA 66
                                      6689*******555.5************9667777777776444443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0037
                             PAS_8   3 lralfesspd.giavvdlgdrivdvNqaalellGys.adlkgell 45 
                                       + +++e + + +i+ +d++++i  +N+ a+++ Gy+  +++ge +
  gi|313126616|ref|YP_004036886.1| 314 FSTFVEDVEEyAIFRLDADGHIASWNRGAEDIEGYKeSEVLGEHF 358
                                       78899999999******7777*************99888887765 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00055
                             PAS_8  19 lgdrivdvNqaalellGys.adlkgellg..q 47 
                                       +g+ ++ vN+aa+e+ G++ + l g+ l+  +
  gi|313126616|ref|YP_004036886.1| 452 DGT-VLKVNDAAIEFSGVErEKLVGKHLWeeT 482
                                       445.*************996666665554433 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   9.1e-09   1.2e-05       4     133 .]     134     295 ..     131     295 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 9.1e-09
                                       HHHHHHHHHHHHHHTESEEEEEE............EEETTEEE.............CEEEEECC........EEEET CS
                               GAF   4 elldtvveelrellgadrvalyl............pdydGlhy.............dipqasrw........lfmkn 47 
                                       ++l+t ++ ++e+  a + a+ +            +      +             d  + s+w         + ++
  gi|313126616|ref|YP_004036886.1| 134 DILETFTQVISEVSSASENAVSRdhieqlvcnrliE------TtplrfvwvgrvdgDDIEPSAWagaeqgsvEELPD 204
                                       566666666666666666666554433333333330......03333333333444333333334555566434444 PP

                                       TSHHHH....HHHHHSSSEEEST.GGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CS..HH CS
                               GAF  48 grgicg....qvlatgqplvipd.stpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pf..tr 116
                                       +++ +g    +++a    ++i+  + +++ + q  +r  + ++g++++++vPl  +g  +G+l+l++ ++  f  ++
  gi|313126616|ref|YP_004036886.1| 205 DKM-IGrgpaKCAAAENEVQITSsIEDSSGWEQ--WRAEALEHGFNACACVPLEYRGANYGVLCLYSDRKgAFgtQD 278
                                       555.66677777777788888863445555888..9999****************************8888895455 PP

                                       HHHHHHHHHHHHHHHHH CS
                               GAF 117 eelellqvladqvaval 133
                                          e lq+l+d v  a+
  gi|313126616|ref|YP_004036886.1| 279 GPTESLQQLGDAVTHAI 295
                                       55999999999987765 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.1     4e+03       2      23 ..      37      60 ..      36      90 .. 0.71
   2 !   20.5   0.1   3.4e-07   0.00044       2      88 ..     336     421 ..     335     422 .. 0.84
   3 ?    2.5   0.0      0.14   1.8e+02       2      83 ..     456     539 ..     455     542 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.1
                             PAS_3  2 iyvserveeilGyspeellgk..v 23
                                      +y++ +  e+l+ +++el+g   +
  gi|313126616|ref|YP_004036886.1| 37 TYLNSKATELLDRDADELIGEtiW 60
                                      688999999999999999998333 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.4e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                        ++++  e+i Gy ++e+lg  ++ l +   e  +   +++ e ++++++ + e  ++rkdG+ +w + + ++++de
  gi|313126616|ref|YP_004036886.1| 336 ASWNRGAEDIEGYKESEVLGE-HFSLFYTESEIEDGHPSEVLETARRDGQCKDEGWRVRKDGSQFWASVTLTALKDE 411
                                       58*******************.444444444447788888888888888899999999******************* PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g +  +++v
  gi|313126616|ref|YP_004036886.1| 412 DGSCRGFVKV 421
                                       *****99988 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.14
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealq..ealkkgepyegeyRirrk.dGeyrwveararvi 75 
                                       + v+++  e  G+++e l gk + w +      +e+v e  +  +++++ge +  e+    +  Ge + ++ +++++
  gi|313126616|ref|YP_004036886.1| 456 LKVNDAAIEFSGVEREKLVGK-HLWEETWWDANQENVDEMKDaiRLASTGEFVRYEVTGEDPdTGEEFVMDFSITPV 531
                                       6789999999***********.7777766666655554333322345777777777777777668888888888888 PP

                             PAS_3  76 rdengkpv 83 
                                        de g++v
  gi|313126616|ref|YP_004036886.1| 532 TDERGEVV 539
                                       88888776 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.015        19      64     115 .]      76     124 ..      20     124 .. 0.63
   2 !    9.0   0.0    0.0011       1.5       8     114 ..     326     432 ..     322     433 .. 0.84
   3 ?    0.3   0.0      0.59   7.6e+02      64      98 ..     432     466 ..     430     468 .. 0.83
   4 ?   -2.8   0.0       5.3   6.8e+03     105     114 ..     546     555 ..     542     556 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
                             PAS_7  64 errlaaaragkphsfererpdgrvievrgnplpdgGfVttytDiTerrraee 115
                                       er ++  +++  +++e  +p  ++ ev + p +  G+ + + D+T+rr+ ee
  gi|313126616|ref|YP_004036886.1|  76 ERAFE--EKDPVTFTEYYTPLDKWFEVSAYPSE-TGLTVYFRDVTDRRKREE 124
                                       44443..34556677788888888888888864.6778889*****999885 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpd 84 
                                       i  +Dad+ +  wNr   ++ ++ e+ v  g ++        ++ e+++g +++ +e+  +  + +++ +  r+  +
  gi|313126616|ref|YP_004036886.1| 326 IFRLDADGHIASWNRGAEDIEGYKESEV-LGEHF----SLFYTESEIEDGHPSEVLETARRDGQCKDEGWRVRKDGS 397
                                       6679*********************999.55555....555667788888889999999989999999999999999 PP

                             PAS_7  85 grvievrgnplpd.....gGfVttytDiTerrrae 114
                                         + +v+ ++l d     +GfV +  D Ter+r e
  gi|313126616|ref|YP_004036886.1| 398 QFWASVTLTALKDedgscRGFVKVIRDMTERKRRE 432
                                       9999999999965444447*************998 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.59
                             PAS_7  64 errlaaaragkphsfererpdgrvievrgnplpdg 98 
                                       errl+a+ +++ + +  ++pdg+v++v+  +++  
  gi|313126616|ref|YP_004036886.1| 432 ERRLDAVFNRTFQLMGLMKPDGTVLKVNDAAIEFS 466
                                       678888888888899999*********99988755 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.3
                             PAS_7 105 tDiTerrrae 114
                                        DiTer++ e
  gi|313126616|ref|YP_004036886.1| 546 RDITERKQRE 555
                                       59*****988 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.061        78      12      89 ..      27     106 ..      19     117 .. 0.73
   2 !   11.3   0.0   0.00031      0.39      14     106 .]     328     426 ..     316     426 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.061
                            PAS_10  12 ltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknveeviealrtgek.devevvvpkngkwvlvryl 86 
                                       +  +D + ++++ + +a++l+++ +++ +G+++ d  p+ + + ++e  e+  ++++ ++ + + +  +kw+ v   
  gi|313126616|ref|YP_004036886.1|  27 VFAVDPEFHFTYLNSKATELLDRDADElIGETIWDEFPDAIGSTFQEQYERAFEEKDpVTFTEYYTPLDKWFEVSAY 103
                                       556999*****************987747999999888887777766665544444415555555677888877776 PP

                            PAS_10  87 pyr 89 
                                       p +
  gi|313126616|ref|YP_004036886.1| 104 PSE 106
                                       655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00031
                            PAS_10  14 flDdnlqirrFtpaakklfklipadv.Grpladihpkkavknv..eeviealrtgekdevevvvp...kngkwvlvr 84 
                                        lD + +i  +++ a+ +  +++++v G++ + + +++++++    ev+e+ r+  + ++e ++     ++ w  v+
  gi|313126616|ref|YP_004036886.1| 328 RLDADGHIASWNRGAEDIEGYKESEVlGEHFSLFYTESEIEDGhpSEVLETARRDGQCKDEGWRVrkdGSQFWASVT 404
                                       58999999999999999988887764499999999997777765689******9999888888743334567899** PP

                            PAS_10  85 ylpyrdedgeiaGvvetfvDit 106
                                         +++dedg+ +G v ++ D+t
  gi|313126616|ref|YP_004036886.1| 405 LTALKDEDGSCRGFVKVIRDMT 426
                                       ********************96 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.4e-05      0.03      15     127 ..     169     295 ..     157     297 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                             GAF_3  15 kllgaevgalllldedgnklqvaagwdgkpalsesld....edsalarralssgevvsepsfaeedglpd....... 80 
                                       +++ + ++ ++ +d+d  ++ + a  ++++  +e+l+    ++   a+ a+++ ev+++ s ++ +g+++       
  gi|313126616|ref|YP_004036886.1| 169 ETTPLRFVWVGRVDGD--DIEPSAWAGAEQGSVEELPddkmIGRGPAKCAAAENEVQITSSIEDSSGWEQwraeale 243
                                       5556655555445544..66555533566666776663334334445577788889888777665554444444444 PP

                             GAF_3  81 ...raalavPLvagr.qviGvlalastkprafdaed..lelleslArqiatai 127
                                          +a  +vPL   r   +Gvl+l+s++++af+ +d  +e l+ l++ +  ai
  gi|313126616|ref|YP_004036886.1| 244 hgfNACACVPLEY-RgANYGVLCLYSDRKGAFGTQDgpTESLQQLGDAVTHAI 295
                                       44477799*****.55***************8554412666666666666655 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.6e-05     0.021       8      91 ..     678     766 ..     672     777 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                       HATPase_c_5   8 vilgnlLdNAieacskieeekrfIrltvrekk.ksliisieNsyeg....ekkkless...kskkeehGiGlksire 76 
                                        ++ n+L NA++  +k     + ++++v+++  +++ +++  +  g    ek+++ ++      +   G+Gl  ++e
  gi|313126616|ref|YP_004036886.1| 678 QVFENVLSNAVQHNDKAV---PRVSVSVEQRGdGAVAVRVADNGPGipdeEKQRIVEKdveGLATPGSGFGLYLVKE 751
                                       699********9999977...67777777666355777766654443443445544331224567899********* PP

                       HATPase_c_5  77 ivkkykgnlsieaed 91 
                                       +v++y+g+++++ +d
  gi|313126616|ref|YP_004036886.1| 752 LVDSYGGTIDVSDND 766
                                       *********998776 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-05     0.033     130     163 ..     558     591 ..     529     592 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                         HisKA_4TM 130 akrisdalafvndlirhdlrndlvvirgyaeaie 163
                                        +r  + l f+n ++rh+l n+l+v+ +++e+++
  gi|313126616|ref|YP_004036886.1| 558 LRRERKRLEFMNRILRHNLLNGLNVVSARSEILQ 591
                                       45667789*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.76u 0.36s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 4274.14
//
Query:       gi|313126617|ref|YP_004036887.1|  [L=94]
Description: metal-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-10   41.0   0.0      2e-10   40.8   0.0    1.0  1  UPF0058   Uncharacterised protein family UPF0058


Domain annotation for each model (and alignments):
>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   1.1e-14     2e-10       1      71 [.       1      72 [.       1      89 [. 0.89

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.1e-14
                                      --HHHHHHHHHHHHHHHHHH.TSTT--TTTTHHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHC CS
                           UPF0058  1 MhKdeLieLHqllvevkkel.eeeevekeefkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekees 71
                                      M+K+e++++H llv + +++  +  +e+eef eY+ L  sP  +   +a+h+aA+ +L+ ++++a+++ e  
  gi|313126617|ref|YP_004036887.1|  1 MRKNEIVHIHALLVLIAEKFvGQGLIEAEEFAEYRLLGTSPMSLRAPRADHEAAVRLLADTLSTAVERYEAA 72
                                      9*******************6566789999***********************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.53
# Mc/sec: 530.77
//
Query:       gi|313126618|ref|YP_004036888.1|  [L=573]
Description: DNA mismatch repair protein, muts family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-07   31.5   0.0    2.9e-07   30.7   0.0    1.4  1  MutS_V          MutS domain V
     0.0037   17.5   0.4      0.013   15.7   0.0    2.2  2  AAA_28          AAA domain
     0.0046   16.8   0.0      0.015   15.1   0.0    1.9  1  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0051   17.4   1.3      0.036   14.7   0.0    2.9  3  HHH_5           Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.022   14.8   0.0    1.6  1  AAA_14          AAA domain
      0.016   15.5   0.0      0.035   14.4   0.0    1.7  1  IMS_HHH         IMS family HHH motif
      0.058   13.9   0.0       0.14   12.6   0.0    1.6  1  AAA_23          AAA domain
       0.11   12.2   0.1       0.29   10.9   0.1    1.7  1  AAA_29          P-loop containing region of AAA domain
       0.66    9.8  10.6      0.087   12.7   5.6    2.0  2  Apolipoprotein  Apolipoprotein A1/A4/E domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.4e-10   2.9e-07       2      47 ..     381     427 ..     380     449 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.4e-10
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEE.EEE CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdki.ftR 47 
                                       ++tG+n +Gk t+l   + +vlla +G  vpae+ae++ +d+i f R
  gi|313126618|ref|YP_004036888.1| 381 VLTGANSGGKTTLLETLCQVVLLASMGLPVPAESAEVGDFDTIvFHR 427
                                       89***************************************983555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       3.8   7.5e+03     132     142 ..     100     110 ..      62     130 .. 0.50
   2 !   15.7   0.0   6.6e-06     0.013       3      30 ..     381     414 ..     379     429 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.8
                            AAA_28 132 eereaiderlr 142
                                       e  ea +erl 
  gi|313126618|ref|YP_004036888.1| 100 EHVEAREERLD 110
                                       22222222222 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.6e-06
                            AAA_28   3 vitGgestGKTtlleaLaar......gypvvpEa 30 
                                       v+tG+ s+GKTtlle L +       g pv +E+
  gi|313126618|ref|YP_004036888.1| 381 VLTGANSGGKTTLLETLCQVvllasmGLPVPAES 414
                                       9**************9974333334477766665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.7e-06     0.015       1      19 [.     379     397 ..     379     434 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.7e-06
                            AAA_21   1 lnvliGpNgsGKSnLLdal 19 
                                       ++vl+G+N+ GK++LL++l
  gi|313126618|ref|YP_004036888.1| 379 VAVLTGANSGGKTTLLETL 397
                                       68***************99 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-05     0.036       9      52 ..       8      52 ..       3      56 .. 0.86
   2 ?   -1.3   0.2       1.8   3.6e+03      14      42 ..     150     180 ..     149     181 .. 0.80
   3 ?   -1.5   0.0         2   3.9e+03      18      35 ..     223     240 ..     219     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                                      T--HHHHHHHHTT.T--.SHHHHHHS-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  9 GiGpktAlallsa.Gie.svedlaaadveeLakipGiGkktAerii 52
                                      G+Gpkt  +l ++ G+e  ve++  ad+ +La++ G+   +A ri+
  gi|313126618|ref|YP_004036888.1|  8 GVGPKTSERLRETlGVErAVEAIEGADIRTLADA-GLPRGRAVRIL 52
                                      9************9999569************98.77777776665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                                       HHHHHHTTT--..SHHHHHHS-HHHHHTSTT CS
                             HHH_5  14 tAlallsaGie..svedlaaadveeLakipG 42 
                                        Al+l +aG +  ++++l   d ++L ++ G
  gi|313126618|ref|YP_004036888.1| 150 AALSLREAGLRgtTFDALDGVDDDALRDAAG 180
                                       5899999997776899998888888888776 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2
                                       HHTTT--SHHHHHHS-HH CS
                             HHH_5  18 llsaGiesvedlaaadve 35 
                                       + s G++s++++ +a ve
  gi|313126618|ref|YP_004036888.1| 223 VRSRGVRSLDEFQSAFVE 240
                                       67889******9998555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.1e-05     0.022       3      78 ..     378     466 ..     376     493 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell.......vkkesilyinldderdkkla.dpe.kllelileklke.......e 63 
                                       ++ v+tGa   GKTtll++l +  l       v++es    ++d+  + ++   ++  +le  l+   +        
  gi|313126618|ref|YP_004036888.1| 378 RVAVLTGANSGGKTTLLETLCQVVLlasmglpVPAESAEVGDFDTIVFHRRHaSFNaGVLESTLK---SivpplasG 451
                                       789******************9999999****999999999****99965441343333333333...233357778 PP

                            AAA_14  64 kktylflDEiqevpe 78 
                                       ++t+++ DE   ++e
  gi|313126618|ref|YP_004036888.1| 452 GRTLMLVDEFEAITE 466
                                       999******998865 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-05     0.035      13      32 .]       3      23 ..       1      23 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                           IMS_HHH 13 itkipGiGgklgek.LeklGi 32
                                      + + +G+G+k+ e+  e+lG+
  gi|313126618|ref|YP_004036888.1|  3 LQDYWGVGPKTSERlRETLGV 23
                                      789***********6666886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.1e-05      0.14      19      42 ..     377     400 ..     361     414 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                            AAA_23  19 kgltlItGpNGaGKTTildAikla 42 
                                       + + ++tG N  GKTT+l+ ++ +
  gi|313126618|ref|YP_004036888.1| 377 DRVAVLTGANSGGKTTLLETLCQV 400
                                       56889***************9975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00015      0.29      22      45 ..     376     400 ..     364     408 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                            AAA_29  22 kg.atlltGpsGsGKSTllDAiqal 45 
                                        + + +ltG++  GK+Tll  +  +
  gi|313126618|ref|YP_004036888.1| 376 GDrVAVLTGANSGGKTTLLETLCQV 400
                                       336899*************987544 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       1.6   3.1e+03      15      35 ..     104     126 ..      99     153 .. 0.56
   2 ?   12.7   5.6   4.4e-05     0.087      78     170 ..     198     312 ..     190     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                                       CHHHCHHCH..HHHHHHHHHHHH CS
                    Apolipoprotein  15 eleeqlapl..aqelrdrlskel 35 
                                         ee+l ++  a+e++  l +++
  gi|313126618|ref|YP_004036888.1| 104 AREERLDDVldAREAWSSLDEDA 126
                                       33344444433334444444443 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHH.......................HHHH CS
                    Apolipoprotein  78 yteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelr.......................qkla 131
                                        +++lr++l+ +++el++    + e +r+r  r++++ ++ + +yv e                         + l+
  gi|313126618|ref|YP_004036888.1| 198 ELDRLRDKLD-AVRELENGALDVLESVRSRGVRSLDEFQSAFVEYVAEESglrrgrieaattgdaydeadfasTTLR 273
                                       4667777777.788888888888888999999999999999999998877899****************999989** PP

                                       HHHHHHHH-----..-----SSSHHHHHHHTS-TTSHHH CS
                    Apolipoprotein 132 erleelkeslaphaeeveerlssrveelrekleeqaeel 170
                                         +eel+  ++++ e+v + l+  ve++r+ +++++ ++
  gi|313126618|ref|YP_004036888.1| 274 TLVEELEADVDAREESVAADLRADVEAARADVDAAVTAV 312
                                       *******************************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 3325.67
//
Query:       gi|313126619|ref|YP_004036889.1|  [L=418]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-23   82.0   1.6    4.4e-23   81.0   1.6    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      7e-21   74.7   0.0    1.6e-20   73.5   0.0    1.6  1  OrfB_IS605       Probable transposase
     0.0029   17.9   1.7     0.0077   16.5   1.7    1.7  1  C1_2             C1 domain
  ------ inclusion threshold ------
      0.077   13.1   1.8       0.16   12.1   0.8    2.0  2  Ribosomal_L37ae  Ribosomal L37ae protein family
      0.078   13.0   3.6       0.21   11.6   3.6    1.7  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   1.6   1.2e-26   4.4e-23       1      69 []     309     378 ..     309     378 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++++ leyka+e+Gi v  v++++TSktCs+Cg++ +  + ++ +++C++C +++++Dvn+a+Ni +r
  gi|313126619|ref|YP_004036889.1| 309 FDRFTRLLEYKAEEHGILVDRVDEENTSKTCSCCGKIRDSnRMERGLYVCSSCETTMNADVNGAVNIRRR 378
                                       889************************************9999************************987 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   4.4e-24   1.6e-20       2     119 ..     175     285 ..     174     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 4.4e-24
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                       ++++ve + ++++g ++agiDlGi+n ++   edg+ +ly g+ lk+d+ y+++e  + +   + s       ++ +
  gi|313126619|ref|YP_004036889.1| 175 LVCKVEIPVETAPGDNTAGIDLGISNYLAIDYEDGANELYPGNVLKEDKHYFTREEYQTEGENSPS-------KRAR 244
                                       6788888899********************************************998887775555.......5777 PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       +  +++srr +h+lh l++h+++++ e+gve++ vg+++di
  gi|313126619|ref|YP_004036889.1| 245 KARQRLSRRKDHFLHTLSKHIVERCVEEGVEKIAVGDLSDI 285
                                       77788999******************************987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.7   2.1e-06    0.0077      13      42 ..     331     365 ..     319     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                              C1_2  13 edssesfnCsaCgrk..idgff...YsCseCdfsl 42 
                                       ++++ s++Cs+Cg+   ++ ++   Y Cs C+ ++
  gi|313126619|ref|YP_004036889.1| 331 DEENTSKTCSCCGKIrdSNRMErglYVCSSCETTM 365
                                       467788*********6554444999******9876 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.4   8.7e+03      32      50 ..     262     280 ..     250     280 .. 0.76
   2 ?   12.1   0.8   4.4e-05      0.16      31      62 ..     334     366 ..     326     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.4
                                       S-BEESSSSSSEEEEEETT CS
                   Ribosomal_L37ae  32 akytCpfcgktkvkRkavg 50 
                                       +k+  ++c ++ v++ avg
  gi|313126619|ref|YP_004036889.1| 262 SKHIVERCVEEGVEKIAVG 280
                                       6788888888888888887 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.4e-05
                                       HS-BEESSSSSS.EEEEEETTEEEETTTTEEEE CS
                   Ribosomal_L37ae  31 hakytCpfcgkt.kvkRkavgiwkCkkcgktva 62 
                                       +++ tC+ cgk  + +R   g++ C++c+ t+ 
  gi|313126619|ref|YP_004036889.1| 334 NTSKTCSCCGKIrDSNRMERGLYVCSSCETTMN 366
                                       44569******9899**************9985 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.6   5.8e-05      0.21      19      45 ..     337     363 ..     333     364 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.8e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                        +C  Cg+   + r+++ gl+ C++C +
  gi|313126619|ref|YP_004036889.1| 337 KTCSCCGKIrDSNRMER-GLYVCSSCET 363
                                       57*****9999999997.********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.59
# Mc/sec: 2123.25
//
Query:       gi|313126620|ref|YP_004036890.1|  [L=80]
Description: hypothetical protein Hbor_18780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 498.35
//
Query:       gi|313126621|ref|YP_004036891.1|  [L=457]
Description: hypothetical protein Hbor_18790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.7e-23   80.7  14.0    9.7e-09   35.7   0.3    5.3  5  VCBS        Repeat domain in Vibrio, Colwellia, Bradyrhizobiu
    1.5e-15   56.9   0.0    4.1e-15   55.5   0.0    1.8  2  UnbV_ASPIC  ASPIC and UnbV
    5.1e-06   26.5  17.9      0.028   14.6   0.1    5.5  6  FG-GAP      FG-GAP repeat
  ------ inclusion threshold ------
       0.12   11.4   1.0         16    4.4   0.0    3.5  4  Itfg2       Integrin-alpha FG-GAP repeat-containing protein 2
        1.9    8.2   4.7         37    4.2   0.1    3.5  4  EF-hand_1   EF hand


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.9   1.9e-07   0.00069      10      61 .]      31      84 ..      27      84 .. 0.84
   2 ?    0.8   0.2      0.21   7.6e+02       5      20 ..     106     123 ..     102     168 .. 0.80
   3 !   31.3   0.2   6.5e-11   2.3e-07       7      61 .]     189     245 ..     187     245 .. 0.86
   4 !   35.7   0.3   2.7e-12   9.7e-09       1      59 [.     234     292 ..     234     294 .. 0.92
   5 !   14.9   0.0   8.2e-06      0.03      36      61 .]     319     344 ..     290     344 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.9e-07
                              VCBS 10 lvvandgg.lrvyrnngdGtftdvtktslgg.sgggtgvavgDlDgDGdlDllv 61
                                      ++v+++g+ +rv+  +  G  +dvt+ +l++ +g + gv+++D+D DG ++++v
  gi|313126621|ref|YP_004036891.1| 31 IFVSGYGTeNRVFAPKDGGGVSDVTPDALADrTGHALGVVAADIDADGVEEVYV 84
                                      56777544499999998999******99999566666**************998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.21
                              VCBS   5 DGrlDlvva..ndgglrv 20 
                                       +G+ D++++  ndg+ +v
  gi|313126621|ref|YP_004036891.1| 106 NGWRDIFALpvNDGRDNV 123
                                       699999998877777665 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 6.5e-11
                              VCBS   7 rlDlvvan.dgglrvyrnngdGtftdvtkt.slggsgggt.gvavgDlDgDGdlDllv 61 
                                       r D++v+n +g+++++rn+  G+f+dv+++  l ++g ++ gva++D DgDG+ Dl++
  gi|313126621|ref|YP_004036891.1| 189 RTDVFVGNeRGPNYLLRNE-RGHFSDVAPNfGLEAPGEHArGVALVDPDGDGQFDLVI 245
                                       78******88********9.69*****986577776666559*************985 PP

  == domain 4  score: 35.7 bits;  conditional E-value: 2.7e-12
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDl 59 
                                       D dgDG  Dlv++n +g++++++ +g+  f dv++ +  ++ + ++v ++D+D+DG  ++
  gi|313126621|ref|YP_004036891.1| 234 DPDGDGQFDLVIGNwEGPNHILERRGS-EFVDVAPDEWMAPSRTRTVLAADFDNDGSCEV 292
                                       99************7799******987.8******9999999**************7665 PP

  == domain 5  score: 14.9 bits;  conditional E-value: 8.2e-06
                              VCBS  36 slggsgggtgvavgDlDgDGdlDllv 61 
                                       +  + g gtg++v D+DgDG l+llv
  gi|313126621|ref|YP_004036891.1| 319 ATEPRGLGTGATVCDMDGDGTLELLV 344
                                       3444677899**************98 PP

>> UnbV_ASPIC  ASPIC and UnbV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.3   1.2e+04      22      31 ..     207     216 ..     204     223 .. 0.68
   2 !   55.5   0.0   1.1e-18   4.1e-15       2      68 .]     379     449 ..     378     449 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.3
                        UnbV_ASPIC  22 grGylsssdp 31 
                                        rG++s + p
  gi|313126621|ref|YP_004036891.1| 207 ERGHFSDVAP 216
                                       6888887766 PP

  == domain 2  score: 55.5 bits;  conditional E-value: 1.1e-18
                        UnbV_ASPIC   2 iGArVtvtyagatqlrevdpgrGylsssdprlhFGLGkatkid....svevrWpdGkvqtlenvkanqtlt 68 
                                         A+Vt++++++tq+r + +g+Gyl++ +p++hFGLG +t+      +v+vrWpdG+  t+e +++ ++lt
  gi|313126621|ref|YP_004036891.1| 379 RNAVVTLRTDRDTQTRLICGGSGYLCQTEPVAHFGLGGDTAPFstprTVTVRWPDGRARTVEAPEPESELT 449
                                       579*****9877**************************653323444*****************9998875 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.9    0.0037        13       5      20 ..      69      84 ..      67      92 .. 0.86
   2 ?   -2.9   0.1       2.3   8.3e+03       2       9 ..     126     133 ..     125     133 .. 0.88
   3 ?   -2.7   0.0         2   7.1e+03      16      29 ..     190     199 ..     189     202 .. 0.72
   4 !   14.6   0.1   7.7e-06     0.028       4      21 ..     229     246 ..     227     259 .. 0.87
   5 ?    4.5   0.2     0.011        39       4      14 ..     278     288 ..     276     289 .. 0.89
   6 !   10.5   0.1   0.00015      0.52       2      21 ..     326     345 ..     325     353 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0037
                                      EEEESTSSSSS-EEEE CS
                            FG-GAP  5 lavgDvNGDGyaDLav 20
                                      + ++D++ DG+ ++ v
  gi|313126621|ref|YP_004036891.1| 69 VVAADIDADGVEEVYV 84
                                      7899******988765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                                       TSSEEEES CS
                            FG-GAP   2 GyslavgD 9  
                                       G s+a++D
  gi|313126621|ref|YP_004036891.1| 126 GRSVAAVD 133
                                       89****99 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2
                                       -EEEEEETT-ETCS CS
                            FG-GAP  16 aDLavGApeskgga 29 
                                       +D+ vG    ++++
  gi|313126621|ref|YP_004036891.1| 190 TDVFVG----NERG 199
                                       8*****....5554 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 7.7e-06
                                       SEEEESTSSSSS-EEEEE CS
                            FG-GAP   4 slavgDvNGDGyaDLavG 21 
                                       ++a++D +GDG +DL++G
  gi|313126621|ref|YP_004036891.1| 229 GVALVDPDGDGQFDLVIG 246
                                       7899999*********** PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.011
                                       SEEEESTSSSS CS
                            FG-GAP   4 slavgDvNGDG 14 
                                       ++ ++D+++DG
  gi|313126621|ref|YP_004036891.1| 278 TVLAADFDNDG 288
                                       6889******9 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00015
                                       TSSEEEESTSSSSS-EEEEE CS
                            FG-GAP   2 GyslavgDvNGDGyaDLavG 21 
                                       G++++v D++GDG  +L+v 
  gi|313126621|ref|YP_004036891.1| 326 GTGATVCDMDGDGTLELLVV 345
                                       7778888***********97 PP

>> Itfg2  Integrin-alpha FG-GAP repeat-containing protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.055     2e+02      82     101 ..      69      88 ..      63      91 .. 0.88
   2 ?   -0.8   0.0      0.17   6.2e+02      82      98 ..     230     246 ..     223     256 .. 0.82
   3 ?    4.4   0.0    0.0044        16      76      95 ..     273     292 ..     268     316 .. 0.86
   4 ?    0.9   0.1     0.051   1.8e+02      84      99 ..     331     346 ..     327     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.055
                             Itfg2  82 vliaDidgDgkvElvvgytD 101
                                       v+ aDid Dg  E+ v  tD
  gi|313126621|ref|YP_004036891.1|  69 VVAADIDADGVEEVYVHNTD 88 
                                       6789**********999999 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.17
                             Itfg2  82 vliaDidgDgkvElvvg 98 
                                       v + D dgDg+ +lv+g
  gi|313126621|ref|YP_004036891.1| 230 VALVDPDGDGQFDLVIG 246
                                       55668899999999998 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0044
                             Itfg2  76 pantkvvliaDidgDgkvEl 95 
                                       p+ t++vl aD d+Dg +E+
  gi|313126621|ref|YP_004036891.1| 273 PSRTRTVLAADFDNDGSCEV 292
                                       7889***************8 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.051
                             Itfg2  84 iaDidgDgkvElvvgy 99 
                                       + D+dgDg++El+v +
  gi|313126621|ref|YP_004036891.1| 331 VCDMDGDGTLELLVVH 346
                                       78**********9987 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       3.3   1.2e+04      10      15 ..      73      78 ..      72      79 .. 0.70
   2 ?    4.2   0.1      0.01        37       8      18 ..     232     242 ..     230     243 .. 0.84
   3 ?    0.5   0.0      0.15   5.5e+02       9      16 ..     282     289 ..     280     292 .. 0.76
   4 ?    2.9   0.0     0.026        92       9      18 ..     332     341 ..     330     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.3
                                      TTTSSS CS
                         EF-hand_1 10 DkDgdG 15
                                      D D dG
  gi|313126621|ref|YP_004036891.1| 73 DIDADG 78
                                      778777 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.01
                                       HHTTTSSSEEE CS
                         EF-hand_1   8 efDkDgdGkId 18 
                                       ++D DgdG+ d
  gi|313126621|ref|YP_004036891.1| 232 LVDPDGDGQFD 242
                                       79******976 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.15
                                       HTTTSSSE CS
                         EF-hand_1   9 fDkDgdGk 16 
                                       +D D+dG 
  gi|313126621|ref|YP_004036891.1| 282 ADFDNDGS 289
                                       68888885 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.026
                                       HTTTSSSEEE CS
                         EF-hand_1   9 fDkDgdGkId 18 
                                        D DgdG+++
  gi|313126621|ref|YP_004036891.1| 332 CDMDGDGTLE 341
                                       69*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2890.45
//
Query:       gi|313126622|ref|YP_004036892.1|  [L=60]
Description: hypothetical protein Hbor_18800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.5   5.3        0.4   10.7   5.3    1.9  1  zf-FCS    MYM-type Zinc finger with FCS sequence motif


Domain annotation for each model (and alignments):
>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.3   2.2e-05       0.4      29      41 .]      46      58 ..      15      58 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.2e-05
                            zf-FCS 29 vgqFCStsCldsY 41
                                        +FCS +C+d+Y
  gi|313126622|ref|YP_004036892.1| 46 YRHFCSDDCRDEY 58
                                      468********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 353.93
//
Query:       gi|313126623|ref|YP_004036893.1|  [L=801]
Description: DNA helicase, rad3 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-28   97.6   0.0    1.7e-27   96.7   0.0    1.5  1  Helicase_C_2  Helicase C-terminal domain
    1.4e-07   31.3   0.0    3.1e-07   30.2   0.0    1.6  1  DEAD_2        DEAD_2
    0.00026   21.1   0.0     0.0054   16.7   0.0    2.1  2  ResIII        Type III restriction enzyme, res subunit
    0.00064   19.2   0.0     0.0015   18.1   0.0    1.6  1  PhoH          PhoH-like protein
     0.0033   17.2   0.0       0.64    9.8   0.0    2.5  2  DEAD          DEAD/DEAH box helicase
     0.0087   15.3   0.0      0.087   12.0   0.0    2.0  2  DUF2075       Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.051   13.9   0.0       0.93    9.8   0.0    2.6  3  AAA_22        AAA domain
       0.21   11.2   0.0       0.42   10.3   0.0    1.4  1  HBB           Helical and beta-bridge domain


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.0   7.4e-31   1.7e-27       6     166 ..     598     775 ..     594     780 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 7.4e-31
                      Helicase_C_2   6 evvpggvlvffpSyklleevverlkeeleskkieifvee.keesrekvleeykekkkkgaillavcrGklsEGidfs 81 
                                       +  pg+vlv +pSy+  e ++ +l+++l+  k  +++e+ ++  +e++ +++    +++++l+ ++rG+l EG+d++
  gi|313126623|ref|YP_004036893.1| 598 SRSPGNVLVGMPSYAEAEWMAGELDTRLS--KTVLLDESsDDGATERLKADFFG--GEEKVLVTSLRGTLTEGVDYR 670
                                       5689***********************95..44555555488899999999999..********************* PP

                      Helicase_C_2  82 ddllraviivglPfpnpkdpeveakreyldekgk.................knsgkewylpealravnQaiGRliRh 141
                                       +d+l+a +++g+P  n+++p+++a +  +d++++                 +++++ + + +a+r+ +Q iGR+iR 
  gi|313126623|ref|YP_004036893.1| 671 GDRLSAAVVCGVPIINTSSPRTRAVKTAYDREFGnvpasdssgsprgasasRDGFEAALTVPAVRKARQTIGRVIRG 747
                                       *************************************************99999*********************** PP

                      Helicase_C_2 142 kdDygaivllDeRfak...eeireklpk 166
                                       +++ g+  l+D R+a+   +++re+lp+
  gi|313126623|ref|YP_004036893.1| 748 SEEVGIRALVDARYARdswNSVREYLPE 775
                                       ***************9333445555554 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.4e-10   3.1e-07       6     168 ..      81     308 ..      77     316 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.4e-10
                                       HHHHHHHHHHHHHHHHHCHH.HS---EEEE--CCCC-SC..HHCCCHHCCCCHHHHHHHHHCCHHCCH......... CS
                            DEAD_2   6 hsqleqvvkelkklesykkk.kekvkvviLgSRknlCin..eevkkekkekavneaCkelkkkkaeek......... 70 
                                       ++ql+q+ k+l+ +++   +  + v  ++L +++++C    e+v    + ++v ++C+ l++ + +           
  gi|313126623|ref|YP_004036893.1|  81 KQQLRQFEKDLRTINENLPEdWNPVSGLTLVGKSDVCPYsrENVAG-IDDTTVYDRCEGLRERTRNLVgdggltstg 156
                                       5799999999999987766656789999999999999641134444.446777789999998886555999999999 PP

                                       ............................................TTTTTT-SCC........CCHHHH....HHHHH CS
                            DEAD_2  71 ............................................eekCsffenl........eelkkl....kklll 91 
                                                                                   +e C+f+ ++                   + + 
  gi|313126623|ref|YP_004036893.1| 157 klvkearaaqtglldtgssgggptyletageptpylpetteyedTEYCPFYATFlddlpedgDP---IeavpFDVTE 230
                                       99999999999999999999999999999999999999999999999****9988776644422...2333567788 PP

                                       HC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH.T..GCGCEEEECTCCCHHHHHHHCC CS
                            DEAD_2  92 eevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslk.gislknsivilDEAhNiedvceeaa 167
                                        ++vd e+lv+l    ++CP+ ++ ++l+++++++  Y   +d+ +  s++  +    + v+ DEAh +e  ++e++
  gi|313126623|ref|YP_004036893.1| 231 LGLVDTEELVRLSAGYGTCPHSVMGAVLPHVEVVVGNYYHAFDPTTVGSFTgALADDSTFVVCDEAHMLEPRVRELV 307
                                       899**********************************************99777788889**********9999998 PP

                                       - CS
                            DEAD_2 168 s 168
                                       s
  gi|313126623|ref|YP_004036893.1| 308 S 308
                                       8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.4e-06    0.0054       4      80 ..      21      97 ..      18     121 .. 0.80
   2 ?    1.9   0.0     0.086   1.9e+02     128     144 ..     283     299 ..     260     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.4e-06
                                      E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII  4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkg.keekflflvprkslleqtleefkkflse 80
                                      +++ Q++ ie+ +++   ++d  ++++ a+GtGKT++a ++ i+r++    ++e++++l   k+ l q +++++ + ++
  gi|313126623|ref|YP_004036893.1| 21 PYPEQADGIEAAIDAA--EDDGFLVVEGACGTGKTMLAlTAGIDRVRDPDsDYERVFVLTSVKQQLRQFEKDLRTINEN 97
                                      6788899999999887..5788888*************88889999875404459999999999999998888766655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.086
                                       HHTTT-SEEEEETGGGT CS
                            ResIII 128 llrdrfdviiiDEaHrl 144
                                       +l d + ++++DEaH l
  gi|313126623|ref|YP_004036893.1| 283 ALADDSTFVVCDEAHML 299
                                       56677789*******76 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.5e-07    0.0015      11      54 ..      31      76 ..      23     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.5e-07
                                      HHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT..TS-SEEEE CS
                              PhoH 11 eylealkkndivfaiGpaGtGKtylavalavealkk..kkvkriil 54
                                      ++++a ++  ++++ G  GtGKt+la++++++ +++  ++++r+ +
  gi|313126623|ref|YP_004036893.1| 31 AAIDAAEDDGFLVVEGACGTGKTMLALTAGIDRVRDpdSDYERVFV 76
                                      456666778899**********************986567777654 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00028      0.64       6      72 ..      31      96 ..      22     116 .. 0.82
   2 ?    4.7   0.0      0.01        23      91     134 ..     255     300 ..     232     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00028
                                      HHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  6 eaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk 72
                                      +ai+++ ++g ++v+++ G+GKT+ +l + +++v +  +++  ++++++  ++  +q  ++l+++ +
  gi|313126623|ref|YP_004036893.1| 31 AAIDAAEDDGFLVVEGACGTGKTMLALTAGIDRVRD-PDSDYERVFVLTSVKQQLRQFEKDLRTINE 96
                                      4566666778899*********************65.888888999999999999998888887766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                                       HHHHHTTCSEEEEEHHHHHHHHHCTSSH...CTTEEEEEEETHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                              DEAD  91 lskldngvdivvgtpgrlddllstgkln...lsqvrflVlDEadrll 134
                                        ++l  +v++vvg+    +d ++ g+++    ++ +f+V DEa++l 
  gi|313126623|ref|YP_004036893.1| 255 GAVL-PHVEVVVGNYYHAFDPTTVGSFTgalADDSTFVVCDEAHMLE 300
                                       5556.6789999999999997755665555588999********986 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   3.9e-05     0.087       4      44 ..      42      83 ..      40      99 .. 0.80
   2 ?    0.7   0.0      0.11   2.4e+02      87     101 ..     286     300 ..     266     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.9e-05
                           DUF2075  4 vlVtGvaGtGKtvvllnllael.eddeeertavylsvNhplv 44
                                      ++V+G+ GtGKt+++l++  +  +d ++++++v+++ + +++
  gi|313126623|ref|YP_004036893.1| 42 LVVEGACGTGKTMLALTAGIDRvRDPDSDYERVFVLTSVKQQ 83
                                      79**************99887778888888888887765554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.11
                           DUF2075  87 pkedvvivDEAhrll 101
                                       ++ ++v++DEAh l 
  gi|313126623|ref|YP_004036893.1| 286 DDSTFVVCDEAHMLE 300
                                       56789*******875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00042      0.93       4      26 ..      38      60 ..      34     104 .. 0.72
   2 ?    0.7   0.0      0.27     6e+02      93     107 ..     289     302 ..     278     334 .. 0.75
   3 ?   -3.5   0.0       5.1   1.1e+04      48      68 ..     357     377 ..     341     389 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00042
                            AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                      ++g+lvv G  GtGKT+l+ +  
  gi|313126623|ref|YP_004036893.1| 38 DDGFLVVEGACGTGKTMLALTAG 60
                                      789***************97665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
                            AAA_22  93 elliiDEaqhlrsee 107
                                        +++ DEa+ l +++
  gi|313126623|ref|YP_004036893.1| 289 TFVVCDEAHML-EPR 302
                                       599********.432 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.1
                            AAA_22  48 psstsskdllrellralglel 68 
                                        ++++ +d+ r++ ++l+++ 
  gi|313126623|ref|YP_004036893.1| 357 RELKETRDFVRDVREELDRRV 377
                                       444455666666666666544 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00019      0.42     132     183 ..     510     568 ..     495     573 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                                       HHHHHHCHCCCCCCTS-SSHHHHHHHHT............EEE.S..S.GGHCCCCCCCC CS
                               HBB 132 lrflkerlssllmsgtltpleeysdiiGle........aklkkfpspfpkEnlivlfatd 183
                                       ++ l e    +lms tl+pl+ ++++ Gl+         + +++   fp+En+ ++fa d
  gi|313126623|ref|YP_004036893.1| 510 AEQLGEFGGGVLMSATLEPLDVFREVSGLNaleadgrpVVERTYGLGFPEENR-ASFAVD 568
                                       56666777789******************876655554467899999999997.455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.52
# Mc/sec: 4609.44
//
Query:       gi|313126624|ref|YP_004036894.1|  [L=481]
Description: subtilase protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-15   56.2   7.3    1.2e-09   37.9   1.6    2.3  2  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.4   9.5e-09   0.00017      86     191 ..     136     237 ..      83     314 .. 0.73
   2 !   37.9   1.6   6.6e-14   1.2e-09     177     283 ..     327     415 ..     314     431 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 9.5e-09
                                       STTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH..HHHHHH.CCT-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                      Peptidase_S8  86 apgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsieal..ainravnkkgvlvvi 160
                                       ap+ +++ + +++++       +   +a+++ +e++vdvi  s       pkt + +++l   +++a+ +++v++v+
  gi|313126624|ref|YP_004036894.1| 136 APKSELYLAAIGSEPT-----PERYHEAVRWLIEHDVDVIVDSGS---YFPKTMSASANLsqTAQYAI-DHDVIYVT 203
                                       6666666555553322.....278899*************88855...7777777777678899****.9******* PP

                                       E--SS-T-HH....EEE-TTCEECTTTSTTCEEEE CS
                                       xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 161 SaGNngktgs....slqagspvgtpstsknvitvg 191
                                       SaGN    ++    ++ +g+   ++ +  n+++ g
  gi|313126624|ref|YP_004036894.1| 204 SAGNYA-GHHwsgtGTESGWVNFSDDGQANALGTG 237
                                       ****98.3334565334444333333334455555 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 6.6e-14
                                       CEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 177 pvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPn 253
                                       +v +p t k++itvga  ++g++ ++Ss G        +d++ap g      +++s          +++GTS+A+P+
  gi|313126624|ref|YP_004036894.1| 327 SVVAPTTGKGIITVGALGPNGSVRSYSSLGADGT----VDLSAPDGV-----ETDS--------SGAFYGTSAATPF 386
                                       566799999**********************996....******996.....7777........578********** PP

                                       HHHHHHHHHHHHTT--HHHHHHHHHCCS-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 254 aagaaAlllsalpkltpetvraallntAqd 283
                                       + gaaAl+ s  + ltp++ + +l++t + 
  gi|313126624|ref|YP_004036894.1| 387 VGGAAALVASQGN-LTPAQTEYILEQTSRE 415
                                       *********8766.9************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2940.18
//
Query:       gi|313126625|ref|YP_004036895.1|  [L=208]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-11   44.1   0.3    2.7e-11   43.3   0.3    1.3  1  HTH_20           Helix-turn-helix domain
    1.2e-06   28.3   0.0    2.1e-06   27.5   0.0    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0002   21.2   0.1    0.00038   20.3   0.1    1.4  1  MarR_2           MarR family
    0.00064   19.6   0.0     0.0011   18.7   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00081   18.9   0.0     0.0013   18.2   0.0    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0011   19.3   0.0     0.0019   18.5   0.0    1.3  1  Rrf2             Transcriptional regulator
  ------ inclusion threshold ------
      0.065   13.6   0.4       0.17   12.3   0.0    1.8  2  FaeA             FaeA-like protein
       0.08   13.1   0.0       0.12   12.5   0.0    1.2  1  DUF2250          Uncharacterized protein conserved in archaea
      0.098   12.6   0.0       0.13   12.2   0.0    1.3  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
        0.1   12.6   0.0       0.16   11.9   0.0    1.3  1  HTH_11           HTH domain
       0.16   11.8   0.0       0.33   10.8   0.0    1.5  1  LexA_DNA_bind    LexA DNA binding domain
       0.44   10.6   5.0        2.1    8.4   1.0    2.8  3  DUF3185          Protein of unknown function (DUF3185)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.3   1.8e-14   2.7e-11       2      60 ..      36      93 ..      35      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.8e-14
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      q++  L++ + r+ ++aL ++e+ tasela+++d+s +++++HL+ L+ agLv+v +++
  gi|313126625|ref|YP_004036895.1| 36 QLIGCLSSDTARDTFAAL-QREPSTASELADTVDTSLQNIRHHLDNLRNAGLVRVADTR 93
                                      667789************.***********************************98876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.4e-09   2.1e-06      10      46 ..      52      88 ..      51      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.4e-09
                                      HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +L++++ +++ela+ ++ s  +++hHL  Lr+aGLV+
  gi|313126625|ref|YP_004036895.1| 52 ALQREPSTASELADTVDTSLQNIRHHLDNLRNAGLVR 88
                                      7999********************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.6e-07   0.00038       6      54 ..      45      90 ..      41      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.6e-07
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + ++  aaL r+p    t++ela++ + s +++  +l+ L  aGLv+  
  gi|313126625|ref|YP_004036895.1| 45 TARDTFAALQREPS---TASELADTVDTSLQNIRHHLDNLRNAGLVRVA 90
                                      6678899******6...*****************************865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.7e-07    0.0011      18      63 ..      53     105 ..      41     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.7e-07
                                       HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEE CS
                              TrmB  18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYr 63 
                                       l+++p+ta+e+a  ++ + +++   L +L ++GlV++ + r        k+Y 
  gi|313126625|ref|YP_004036895.1|  53 LQREPSTASELADTVDTSLQNIRHHLDNLRNAGLVRVADTRysvkgreMKVYA 105
                                       789*********************************99888666665555555 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.9e-07    0.0013      19      48 .]      59      88 ..      44      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.9e-07
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + +eLA+ ++ S+++++ +l++L ++Gl++
  gi|313126625|ref|YP_004036895.1| 59 TASELADTVDTSLQNIRHHLDNLRNAGLVR 88
                                      789*************************96 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.3e-06    0.0019      22      57 ..      54      89 ..      49      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      ++ep +++e+a+ +++s + +++ l +Lr+aglv++
  gi|313126625|ref|YP_004036895.1| 54 QREPSTASELADTVDTSLQNIRHHLDNLRNAGLVRV 89
                                      34579*****************************86 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012      0.17      13      51 ..      55      93 ..      45      99 .. 0.87
   2 ?   -1.8   0.1       2.8   4.2e+03      25      33 ..     198     206 ..     197     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                      S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--S CS
                              FaeA 13 kapckTreiAdalglsaYQaRyYLeqLekegkikrspvr 51
                                      + p + +e+Ad +  s   +R+ L +L+ +g ++ +  r
  gi|313126625|ref|YP_004036895.1| 55 REPSTASELADTVDTSLQNIRHHLDNLRNAGLVRVADTR 93
                                      579999*************************99977766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.8
                                       HTS-HHHHH CS
                              FaeA  25 lglsaYQaR 33 
                                       l++ aYQ R
  gi|313126625|ref|YP_004036895.1| 198 LAVRAYQSR 206
                                       6899***99 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     8e-05      0.12      25      66 ..      60     102 ..      51     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
                           DUF2250  25 aksiakeleipleevrellkkLeelGLlerve.gktikrteak 66 
                                       a  +a+ ++ +l+++r+ l++L+++GL+   + + ++k +e k
  gi|313126625|ref|YP_004036895.1|  60 ASELADTVDTSLQNIRHHLDNLRNAGLVRVADtRYSVKGREMK 102
                                       66789999********************865426677777665 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.9e-05      0.13      52      94 ..      56      97 ..      15     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-05
                   Phage_rep_org_N 52 ipytaemlalifnreletvrlaLkvlkdlelieisedkvikik 94
                                       p+ta +la  ++  l+++r  L+ l++ +l+ ++ d+ + +k
  gi|313126625|ref|YP_004036895.1| 56 EPSTASELADTVDTSLQNIRHHLDNLRNAGLVRVA-DTRYSVK 97
                                      689*******************************9.6666665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.16      12      46 ..      54      89 ..      49      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                            HTH_11 12 argpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpI 46
                                      +r+p +++eLA+  + S + +r +++ L+ +g v++
  gi|313126625|ref|YP_004036895.1| 54 QREPSTASELADTVDTSLQNIRHHLDNLRNAGlVRV 89
                                      67889*************************997665 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00022      0.33      26      62 ..      58      93 ..      47      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                                      --HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG- CS
                     LexA_DNA_bind 26 PsireiaralglkSpsaveehLkaLerKGyierdpgk 62
                                       +  e+a+ +  +S + + +hL  L++ G++++ +++
  gi|313126625|ref|YP_004036895.1| 58 STASELADTVD-TSLQNIRHHLDNLRNAGLVRVADTR 93
                                      45568888888.67999***************99875 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.2   1.8e+03      13      27 ..     112     126 ..     111     133 .. 0.80
   2 ?    2.4   0.1      0.11   1.6e+02      10      42 ..     134     166 ..     131     173 .. 0.89
   3 ?    8.4   1.0    0.0014       2.1       3      21 ..     187     205 ..     186     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                           DUF3185  13 vLlvfGynasdSlgs 27 
                                       v +v G + +dS+ +
  gi|313126625|ref|YP_004036895.1| 112 VVCVSGTQDKDSVLD 126
                                       67899******9865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                           DUF3185  10 aGivLlvfGynasdSlgsqvseaftGsttdktl 42 
                                       aG++Llv  +     +g  v+ ++  +tt++ +
  gi|313126625|ref|YP_004036895.1| 134 AGAALLVSALAVQTLFGAGVTDLGGPETTPRVI 166
                                       79********************99999998865 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0014
                           DUF3185   3 iGiiLlvaGivLlvfGyna 21 
                                       +G  Llv+G++L+v  y++
  gi|313126625|ref|YP_004036895.1| 187 LGGGLLVLGVFLAVRAYQS 205
                                       7999**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 1406.70
//
Query:       gi|313126626|ref|YP_004036896.1|  [L=393]
Description: arabinose efflux permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.4e-37  126.9  71.4    5.1e-32  111.2  41.2    2.0  2  MFS_1       Major Facilitator Superfamily
    1.6e-08   33.8  12.5    1.6e-08   33.8  12.5    2.2  2  MFS_1_like  MFS_1 like family
    0.00017   20.3  22.0    0.00017   20.3  22.0    2.4  2  MFS_2       MFS/sugar transport protein
  ------ inclusion threshold ------
       0.06   13.2   0.1       0.21   11.4   0.1    1.9  1  DUF5596     Domain of unknown function (DUF5596)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2  41.2   1.1e-35   5.1e-32       3     344 ..      11     334 ..       9     337 .. 0.87
   2 !   29.5  22.1   7.7e-11   3.5e-07      31     172 ..     236     378 ..     233     391 .. 0.83

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 1.1e-35
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglll 78 
                                        ++fl+ ++r++++p++  + +++lg+sp ++gl++tl+ +g+a+  +p+G+l + + r r vl +g+ll++ +++ 
  gi|313126626|ref|YP_004036896.1|  11 GLVFLVNFGRTAFAPLVE-TFQNQLGASPEAVGLMTTLVWVGTALPRIPVGYLLTHIPRHRvVLGTGALLTVTAAFT 86 
                                       57899************9.******************************************9999999999999555 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                       ++ ass+ ++ v+ +  Gl++ga+f a++ l+ +++p+   graig+ +++++l+a++++++   ++++  Wr +f+
  gi|313126626|ref|YP_004036896.1|  87 AT-ASSIRTVQVGAFGIGLASGAYFVAAVPLVGELYPD-AVGRAIGVHGTAAQLAAVVAAPVVVTFVALEDWRTTFW 161
                                       55.47777******************************.*****************999888888887999****** PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllpl 232
                                       +la++++ + v+  l ++++ ++   ++++++   ++  +l+  w++++        ++++ +++f+++gl+ +  +
  gi|313126626|ref|YP_004036896.1| 162 LLAALAAAVTVV--LAYTARGVDAVVETDTDR---DFLGALRH-WRLIFV------GMLMISTAGFVWQGLFNFYVS 226
                                       *********996..777777777777766666...33333333.777766......5555555566*********** PP

                             MFS_1 233 ylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl 309
                                       yl++   ++   +a+++l +++++g++++ l+grl+dr++r +++l++l++ ++a+++l  ++ +   + +l+v ++
  gi|313126626|ref|YP_004036896.1| 227 YLVDAKPFT-TAQASTMLTVVFAAGVPAFWLSGRLADRFPRVPYILVTLAVYVAALFALTEVSGY---APVLVVTAV 299
                                       *********.8******************************999999999998888888888888...555556677 PP

                             MFS_1 310 iGfglgfvfpsllalasdlappeeagtasglfnta 344
                                       +G +    fp+l +++ d +p+  + +a+++f+ +
  gi|313126626|ref|YP_004036896.1| 300 LGYTIHSLFPALDSWVLDTLPAAVRSSAYAVFSGV 334
                                       77766666************************976 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 7.7e-11
                             MFS_1  31 pseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpag 106
                                        ++++++lt+++++ + a  + Grl+drf r +++l++l++++++l++l+ + s++ ++lv+ ++ G +  +lfpa 
  gi|313126626|ref|YP_004036896.1| 236 TAQASTMLTVVFAAGVPAFWLSGRLADRFPRVPYILVTLAVYVAALFALTeV-SGYAPVLVVTAVLGYTIHSLFPAL 311
                                       5789*************************8888************4444455.999999****************** PP

                             MFS_1 107 aaliadwfpkeergraigllsagfslGailgpllggllasslg.Wravfyilaivsllafvlfllll 172
                                        +++ d  p   r++a++++s+ + l  + g ++ g+l+ ++  +  vf  +a+ ++ ++ +  ll+
  gi|313126626|ref|YP_004036896.1| 312 DSWVLDTLPAAVRSSAYAVFSGVSLLLEASGSGVVGFLTGYGYaFDTVFRTFAFCLAGVVAVLTLLY 378
                                       ***************************************4433677776666665555533323333 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.7    0.0033        15     233     344 ..      12     123 ..       4     136 .. 0.70
   2 !   33.8  12.5   3.6e-12   1.6e-08     180     383 ..     157     363 ..     124     365 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0033
                        MFS_1_like 233 valilgmswgiienFlflYLkelgasntllGslvalgvvae.iplfffaeklleklGhvklliia.llayilrflly 307
                                        ++++ +   ++   ++ + ++lgas + +G +++l  v++ +p   ++  l+++  h+++l ++ ll++++ f   
  gi|313126626|ref|YP_004036896.1|  12 LVFLVNFGRTAFAPLVETFQNQLGASPEAVGLMTTLVWVGTaLPRIPVGYLLTHIPRHRVVLGTGaLLTVTAAFTAT 88 
                                       555666666666666889999**********9999887764388888888899999999999876144555556555 PP

                        MFS_1_like 308 aiienawlvlpievLhgisfgllwaaaveyvskiapk 344
                                       a+ + ++ v    +  g++ g++++aav  v ++ p+
  gi|313126626|ref|YP_004036896.1|  89 ASSIRTVQV--GAFGIGLASGAYFVAAVPLVGELYPD 123
                                       554444433..34445888888888888888777776 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 3.6e-12
                        MFS_1_like 180 sallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviif.llvalilgmswgiienFlflYL.ke 254
                                       ++ + +laal  ++++v++     +  +++  t +++++l  l++ ++i++ +l++   g++w  + nF+  YL + 
  gi|313126626|ref|YP_004036896.1| 157 RTTFWLLAALAAAVTVVLAYTA--RGVDAVVETDTDRDFLGALRHWRLIFVgMLMISTAGFVWQGLFNFYVSYLvDA 231
                                       4556666666666665522222..22333444445699******999998845666689***************999 PP

                        MFS_1_like 255 lgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllw 331
                                       + +++  +++++++  +a +p f+++ +l +++  v  ++++l +y++ ++ +  ++    vl++ +  g++++ l+
  gi|313126626|ref|YP_004036896.1| 232 KPFTTAQASTMLTVVFAAGVPAFWLSGRLADRFPRVPYILVTLAVYVAALFALTEVSGYAPVLVVTAVLGYTIHSLF 308
                                       ***************************************************999999999999999999******** PP

                        MFS_1_like 332 aaaveyvskiapksleatgqgllsglyfgl...GralGsliGGllwdlksaiflF 383
                                        a+ ++v +  p  +++   +++sg++  l   G+++  ++ G+ +  ++ + +F
  gi|313126626|ref|YP_004036896.1| 309 PALDSWVLDTLPAAVRSSAYAVFSGVSLLLeasGSGVVGFLTGYGYAFDTVFRTF 363
                                       *************************976442114444445555555555555555 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   2.3     0.012        55     252     341 ..      31     119 ..       8     127 .. 0.80
   2 !   20.3  22.0   3.7e-08   0.00017     147     380 ..     136     353 ..     123     380 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.012
                             MFS_2 252 tyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfg 327
                                       +  lg + +a+ +++++v ++++l  + + +l +++ +++++l   +l+ v  +++  +  s++ ++ v ++ +g++
  gi|313126626|ref|YP_004036896.1|  31 QNQLGaSPEAVGLMTTLVWVGTALPRIPVGYLLTHIPRHRVVLGTGALLTVTAAFTATA--SSIRTVQVGAFGIGLA 105
                                       55677788899999999999999999999**********99998887777766655555..8888888888888888 PP

                             MFS_2 328 vgvaallpwsmlad 341
                                        g+ ++++  ++++
  gi|313126626|ref|YP_004036896.1| 106 SGAYFVAAVPLVGE 119
                                       88877777666655 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3.7e-08
                             MFS_2 147 gvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrn 223
                                        +laa++a ++v+ + +     + ++++ ++ a+L+++++++++++ +  +++           + + +++   +r+
  gi|313126626|ref|YP_004036896.1| 136 AQLAAVVAAPVVVTFVA----LEDWRTTFWLLAALAAAVTVVLAYTARGVDAV---------VETDTDRDFLGALRH 199
                                       45666666666666665....699************99999998888866555.........334445555555555 PP

                             MFS_2 224 raflillllfllaalalgvlnglllYyltyvlg.ngs...aasvfllvvtisallgiplwqplakrlgkkntyllga 296
                                         +++++++ l+ ++a++v+ gl+ +y+ y ++ + +   +as++l+vv+++++ ++ l  +la r+ +  ++l+ +
  gi|313126626|ref|YP_004036896.1| 200 --WRLIFVGMLMISTAGFVWQGLFNFYVSYLVDaKPFttaQASTMLTVVFAAGVPAFWLSGRLADRFPRVPYILVTL 274
                                       ..9999***************************77652225667777777777777777778888887776666655 PP

                             MFS_2 297 lltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgig 373
                                       +++++ l+ +   + s ++++lv++++ g ++ +++   +++ + v D        +++ vf +v ++++  ++g+ 
  gi|313126626|ref|YP_004036896.1| 275 AVYVAALFALT--EVSGYAPVLVVTAVLGYTIHSLF---PALDSWVLDTLPAAVRSSAYAVFSGVSLLLEASGSGVV 346
                                       55555444444..45999999999999999955555...55555566666666678888888888888888888888 PP

                             MFS_2 374 lgvsgll 380
                                       ++++g+ 
  gi|313126626|ref|YP_004036896.1| 347 GFLTGYG 353
                                       8887775 PP

>> DUF5596  Domain of unknown function (DUF5596)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.7e-05      0.21      18      50 ..     157     189 ..     150     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                           DUF5596  18 eelfllyallaaapdvleayrkrGIseeifwaT 50 
                                         +f+l+a laaa +v+ ay +rG++  +  +T
  gi|313126626|ref|YP_004036896.1| 157 RTTFWLLAALAAAVTVVLAYTARGVDAVVETDT 189
                                       4568*********************99998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 2105.25
//
Query:       gi|313126627|ref|YP_004036897.1|  [L=476]
Description: yjef-like protein, hydroxyethylthiazole kinase-related [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-51  172.6   1.3    1.6e-50  171.9   1.3    1.3  1  Carb_kinase  Carbohydrate kinase
    5.8e-40  137.0   1.6    5.8e-40  137.0   1.6    2.0  2  YjeF_N       YjeF-related protein N-terminus
    4.3e-07   29.6   0.1    8.1e-07   28.7   0.1    1.4  1  HK           Hydroxyethylthiazole kinase family


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.9   1.3   2.6e-54   1.6e-50       1     243 [.     228     469 ..     228     470 .. 0.93

  Alignments for each domain:
  == domain 1  score: 171.9 bits;  conditional E-value: 2.6e-54
                                       EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SEEE CS
                       Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerldavv 72 
                                       vlv+gG   ytGA+ l+a+aalr+ga+lv+va+ +  + +++ y++++iv p++    + +++    +++   d+vv
  gi|313126627|ref|YP_004036897.1| 228 VLVVGG-GPYTGAPALSAQAALRAGADLVRVACPKSVAREIQGYSENLIVRPFDgdhlQPSHVdGLTALAADHDVVV 303
                                       578888.9**********************************************9998667775566777889**** PP

                                       E-TT-SSSHCHHHHCHHHCCCCS-.EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHH CS
                       Carb_kinase  73 iGpGLgrdekikklleevlekdep.lviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelar 148
                                        GpGLg ++++  ++  +le +e+  v+DAd+L+++ +     +  a ++ TPh++E  ++ +       +r +l++
  gi|313126627|ref|YP_004036897.1| 304 FGPGLGDEDATLDAVADFLESYEGtAVVDADALQVVPE----VDTDATLVCTPHQGELLKMGGKTADDWRERTDLVE 376
                                       ************************9************9....589*******************999999******* PP

                                       HHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHH CS
                       Carb_kinase 149 elaqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdea 225
                                        +a++l+ v l+kg++d+i + ++ +  n tg++++++GG+GDvLaG  gal ++ + + +aa+++a+++g+a+d+a
  gi|313126627|ref|YP_004036897.1| 377 SFAAELGHVLLVKGAYDIISD-GEVTRVNRTGNPGMTVGGTGDVLAGTTGALACVRN-ARHAAAVGAYANGRAGDAA 451
                                       *****************9987.7777799*********************9877766.899999************* PP

                                       CCCT-TS-HCHHHHHHHC CS
                       Carb_kinase 226 aekkgvgmlatelskiip 243
                                        e++g+g+lat+l + +p
  gi|313126627|ref|YP_004036897.1| 452 VEENGYGLLATDLVDRLP 469
                                       *************99876 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0   1.6   9.7e-44   5.8e-40       2     171 .]      22     184 ..      21     184 .. 0.93
   2 ?   -1.0   0.1      0.23   1.4e+03      29      59 ..     228     258 ..     213     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 9.7e-44
                            YjeF_N   2 eeLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtv.llleeeekldedaeralel 77 
                                       ++Lme++g ava+++r+++   +++++v v++G+gnnGgd+++a r+L   +++Vtv ll ++e   ++ a++++++
  gi|313126627|ref|YP_004036897.1|  22 KQLMESSGNAVARAVRDIA---DPGAQVAVVAGRGNNGGDAFVAVRFL--DDYDVTVhLLGRPETISTDIARENWDA 93 
                                       69*****************...9*************************..7777777446667778889999***** PP

                            YjeF_N  78 lkkaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsg 154
                                       l++ + ++ + +++++l      ++d+v+DA+lG+g+ g+lre+ a+++e +n+ +a+v+avD+PSG+dadtG  +g
  gi|313126627|ref|YP_004036897.1|  94 LEASEYDTRTVTDSKALGL---GDPDVVVDAMLGTGVTGALREPEATAAEAVNDLDATVVAVDVPSGVDADTGTAAG 167
                                       *******999999998864...57***************************************************** PP

                            YjeF_N 155 tavkadvtvtfgapkrg 171
                                       +av ad +vtf+  k+g
  gi|313126627|ref|YP_004036897.1| 168 VAVDADRVVTFHDEKPG 184
                                       ***********988876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.23
                            YjeF_N  29 vlvlvGsgnnGgdglaaArhLaqegak.Vtvl 59 
                                       vlv+ G+  +G+ +l a + L ++ga+ V+v 
  gi|313126627|ref|YP_004036897.1| 228 VLVVGGGPYTGAPALSAQAAL-RAGADlVRVA 258
                                       555555559999999999999.7777767773 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   1.4e-10   8.1e-07     140     240 ..     371     468 ..     354     473 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.4e-10
                                       HHHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHH CS
                                HK 140 avaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllyk 216
                                           v++ A +l+ v +v G+ D++sdg+ + + + G++ ++ + ++G +l+ + +a + v +++  aav a +   
  gi|313126627|ref|YP_004036897.1| 371 RTDLVESFAAELGHVLLVKGAYDIISDGEVTRVNRTGNPGMT-VGGTGDVLAGTTGALACVRNARHAAAVGAYA-NG 445
                                       3568999**********************************7.9*************99999988888888765.57 PP

                                       HHH.HHHHHHHTTHHHHHHHHHHH CS
                                HK 217 vAgkeaaarsegsgsFqvelldal 240
                                        Ag  aa +++g g   + l+d+l
  gi|313126627|ref|YP_004036897.1| 446 RAG-DAAVEENGYGLLATDLVDRL 468
                                       899.777888999*9999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2819.35
//
Query:       gi|313126628|ref|YP_004036898.1|  [L=177]
Description: GTP cyclohydrolase subunit moac [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-49  165.5   2.4    7.6e-49  165.3   2.4    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   2.4   4.3e-53   7.6e-49       1     135 [.      35     174 ..      35     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 4.3e-53
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       mvdv++k++t+r+AvA+g+++l+e+t+++i+++++ kGdvla+ari++i+a+K+t+e+ip+cH++p+t+ve+++++ 
  gi|313126628|ref|YP_004036898.1|  35 MVDVGSKPDTRRRAVARGTIHLTESTVDAIRDDQIGKGDVLATARIGAIQAVKHTWETIPMCHQIPITNVETTFDVA 111
                                       9*************************************************************************876 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEES CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsg 135
                                         +e+v++++tv+t+gktG+emEAL++v++++ +v+DmvKa++k+       ++i++v++v+K++
  gi|313126628|ref|YP_004036898.1| 112 --DERVTLTVTVETTGKTGCEMEALEGVTTGLNVVWDMVKAAEKDddgqypdTQISDVQVVSKEK 174
                                       ..79****************************************99*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1040.61
//
Query:       gi|313126629|ref|YP_004036899.1|  [L=993]
Description: hypothetical protein Hbor_18870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.4e-05   22.8   8.9    6.4e-05   22.8   8.9    1.8  2  PGF-CTERM  PGF-CTERM motif
  ------ inclusion threshold ------
        2.8    6.0  20.0        4.7    5.3  20.0    1.4  1  Nop14      Nop14-like family
          9    4.5  16.5         20    3.3  16.5    1.6  1  CDC45      CDC45-like protein


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.8       2.7   1.6e+04       1       4 [.     916     919 ..     916     919 .. 0.95
   2 !   22.8   8.9   1.1e-08   6.4e-05       1      23 []     970     992 ..     970     992 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.7
                         PGF-CTERM   1 tPGF 4  
                                       tPGF
  gi|313126629|ref|YP_004036899.1| 916 TPGF 919
                                       9*** PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.1e-08
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       +PGFGa+++ a+LLa+a LaRRr
  gi|313126629|ref|YP_004036899.1| 970 APGFGALVTFAALLAVAVLARRR 992
                                       6*********************9 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  20.0   0.00079       4.7     315     415 ..     629     734 ..     603     873 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.00079
                             Nop14 315 saDdldddfvleeeeeeeefglgkglkataeeeeeededdfeedddlveseseeeeeeeeedeeeeedeeeeeeeee 391
                                       s Dd   d +++ + ++ e+ l+ + +   ++ ++  +dd ++dd+  +++s+++++++++d++ ++ +++ +++++
  gi|313126629|ref|YP_004036899.1| 629 SNDDGSIDISMNIHYSSGEVSLSPDAS--GDDTSSSGDDDTSSDDSSTDDTSSSSDSDDDDDSSTDSTDDSTTDDST 703
                                       555555555555555555555555553..222222222222333322222222222222222222222222221111 PP

                             Nop14 392 deddlsdlese...eeeeedeleeel.....l 415
                                       d+ +  ++ +    e +e+d+ ++e+     l
  gi|313126629|ref|YP_004036899.1| 704 DD-TTTETTTTddaETNESDDASNETdllpeL 734
                                       11.11111111122222222222222344441 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  16.5    0.0033        20      90     189 ..     613     720 ..     608     802 .. 0.45

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0033
                             CDC45  90 nleNlfgsseekerivvfDDgdieeeleeereayealeeeeesdeede....eeeeeddddeeeeeeeeedeedeee 162
                                       nl+  +++++++   +  DDg i+ +++ + ++ e ++  ++++ +d+    + ++ ++dd+++++ ++++++d+++
  gi|313126629|ref|YP_004036899.1| 613 NLTGTYQGQSRSITTTSNDDGSIDISMNIHYSSGE-VSLSPDASGDDTsssgD-DDTSSDDSSTDDTSSSSDSDDDD 687
                                       44444444443333344499988666665444333.33333333233312221.22222222222222222222222 PP

                             CDC45 163 deeeskkkrksksdeeee......sddddersr 189
                                       d+++++ ++++++d++++      ++dd+e ++
  gi|313126629|ref|YP_004036899.1| 688 DSSTDSTDDSTTDDSTDDtttettTTDDAETNE 720
                                       222222222222222222222222111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (993 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1466  (0.081767); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.27u 0.38s 00:00:01.65 Elapsed: 00:00:00.59
# Mc/sec: 5105.33
//
Query:       gi|313126630|ref|YP_004036900.1|  [L=450]
Description: GTP-binding protein HflX [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-21   75.5   0.0    9.1e-21   74.3   0.0    1.6  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    6.2e-18   64.9   0.0    1.8e-17   63.5   0.0    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
    3.6e-16   59.5   5.9    8.1e-16   58.4   5.9    1.6  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    6.2e-10   38.9   0.1    1.9e-09   37.3   0.0    1.9  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    2.1e-06   27.7   0.0      0.038   13.9   0.0    2.6  3  RsgA_GTPase   RsgA GTPase
    8.9e-06   25.4   0.1    0.00076   19.1   0.0    2.4  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
    0.00038   20.0   0.0       0.73    9.3   0.0    2.8  2  FeoB_N        Ferrous iron transport protein B
     0.0015   19.1   0.2     0.0096   16.5   0.0    2.5  3  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.013   15.9   1.1       0.03   14.7   0.2    2.1  2  AAA_16        AAA ATPase domain
      0.016   15.2   0.0      0.031   14.3   0.0    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.031   14.5   0.0         11    6.3   0.0    2.4  2  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.036   13.5   0.3         12    5.4   0.0    2.6  3  Arf           ADP-ribosylation factor family
      0.095   12.7   0.0       0.21   11.6   0.0    1.6  1  AAA_14        AAA domain
       0.11   12.8   0.1       0.38   11.0   0.0    2.0  2  AAA_22        AAA domain
       0.15   11.8   0.0         14    5.4   0.0    2.3  2  ATP_bind_1    Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   7.6e-24   9.1e-21       3      88 ..      20     106 ..      18     107 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 7.6e-24
                         GTP-bdg_N   3 sleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekel..evkV 77 
                                       +l+E+ +La++ag+evvg++ q+r k d+a+ +G+Gkv+e+++lv+e++a +vi+d++L p q  n+  +l  +v+V
  gi|313126630|ref|YP_004036900.1|  20 DLSEITDLARAAGYEVVGTLSQSR-KEDAAFHFGEGKVDELTALVAETDAAAVIVDNRLGPYQTYNIGGKLpeGVEV 95 
                                       799********************8.78******************************************99778*** PP

                         GTP-bdg_N  78 iDRtqLILdIF 88 
                                       iDR +LIL+IF
  gi|313126630|ref|YP_004036900.1|  96 IDRFTLILEIF 106
                                       *********** PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.8   8.2e+03      70      84 ..      59      74 ..      13      86 .. 0.62
   2 !   63.5   0.0   1.5e-20   1.8e-17       2     114 .]     193     325 ..     192     325 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.8
                                      HHH.HHCTSEEEEEEE CS
                          MMR_HSR1 70 fla.leeadlillvvd 84
                                      + a + e+d+++++vd
  gi|313126630|ref|YP_004036900.1| 59 LTAlVAETDAAAVIVD 74
                                      2222334666666666 PP

  == domain 2  score: 63.5 bits;  conditional E-value: 1.5e-20
                                       EEEEESTTSSHHHHHHHHHT..............S.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg..............e.kaivsdkpgtTrdinegrvklkgkeielvDtpGliegasee 63 
                                       va++G++N+GKStL+++l +              + +a+ +d+ +tT+ ++++r +++ +++ l+Dt+G+++  +  
  gi|313126630|ref|YP_004036900.1| 193 VALAGYTNAGKSTLMRRLAEdlevgenedlhpdlDpTAESEDRLFTTLGTTTRRADTGTRDVLLTDTVGFVS--DLP 267
                                       89*****************777777777787765469*******************888**********765..445 PP

                                       HHHHHHHHH....HHCTSEEEEEEETT..TTCSHHHHHHHHHHHHH.TTSEEEEEEES CS
                          MMR_HSR1  64 kglgkafla....leeadlillvvdas..eeklkpldeeleellee.akkplilvlnk 114
                                       ++l ++f++    + +adl+llvvdas   e+++++  +++++l e ++ p++ vlnk
  gi|313126630|ref|YP_004036900.1| 268 HWLVESFKStldsVYRADLVLLVVDASepVEEMRDKLVTCHDTLYErNEAPIVTVLNK 325
                                       56777777633336679********99442235555566666665579999999**98 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   5.9   6.8e-19   8.1e-16       1      79 []     109     185 ..     109     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 6.8e-19
                                       H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                         GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrk 77 
                                       rA+t++a+lQVelA+l+y+lpr e +++  +r +   g++G Ge+  e++++ i+++i+++k+eL+++++k+e++r+
  gi|313126630|ref|YP_004036900.1| 109 RANTRKAQLQVELAELRYELPRAEAKASLAKRDE-RPGFMGLGEYD-ESREQDIKNQISRIKNELDSIAEKEETRRE 183
                                       9**********************64444444443.346********.****************************** PP

                                       .T CS
                         GTP-bdg_M  78 kR 79 
                                       +R
  gi|313126630|ref|YP_004036900.1| 184 QR 185
                                       99 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       4.8   5.8e+03      86     107 ..      58      79 ..      56      82 .. 0.79
   2 !   37.3   0.0   1.6e-12   1.9e-09       6     188 ..     193     366 ..     190     411 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.8
                                       HHHHHHHT-SEEEEEEETTTBS CS
                          GTP_EFTU  86 evirglrvlDgavlvvdaveGv 107
                                       e ++ ++ +D a ++vd + G+
  gi|313126630|ref|YP_004036900.1|  58 ELTALVAETDAAAVIVDNRLGP 79 
                                       6677788999*****9988775 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 1.6e-12
                                       EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvd 82 
                                       ++++g +++GK+TL+ rL ++++  +++  + +    lD ++e + r +T   +++    +t ++ + l Dt G v+
  gi|313126630|ref|YP_004036900.1| 193 VALAGYTNAGKSTLMRRLAEDLEVGENEDLHPD----LDPTAESEDRLFTTLGTTTRRA-DTGTRDVLLTDTVGFVS 264
                                       5678899************99999777444445....***********99988888888.8*************985 PP

                                       ....GHHHHHHH....HHT-SEEEEEEETTTBSTHHHHHHH....HHHHHTTTEEEEEEESCGST.HHHHHHHHHHH CS
                          GTP_EFTU  83 ....Fskevirg....lrvlDgavlvvdaveGvepqteevl....rlalkegvpiivfiNKmDrl.kaelkeiveev 146
                                           +  e  ++    +  +D+++lvvda+e ve+   +++     l  +++ pi++++NK+D++  +el +  +++
  gi|313126630|ref|YP_004036900.1| 265 dlphWLVESFKStldsVYRADLVLLVVDASEPVEEMRDKLVtchdTLYERNEAPIVTVLNKIDKVdADELGRKMDAL 341
                                       4554554443333333999***********998887776651111566677888***********545555555555 PP

                                       HHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHH CS
                          GTP_EFTU 147 kqklsrkeeklekygekgekevpvvfgSalkgegvktlleal 188
                                       +  l                  + v +S+l+ge+v +l + +
  gi|313126630|ref|YP_004036900.1| 342 Q-ALA------------P----NPVSVSGLTGENVGALADRI 366
                                       5.551............1....23445555555555555554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.3   6.3e+03      61      85 ..      18      41 ..       7      48 .. 0.67
   2 !   11.1   0.0   0.00023      0.28      66     124 ..     158     215 ..     137     265 .. 0.69
   3 !   13.9   0.0   3.2e-05     0.038      16      99 ..     284     368 ..     271     371 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.3
                                      HHHHHHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase 61 eeeeleelkeelealgyevllvsak 85
                                      ++ +l+e+ +  +a+gyev+ + ++
  gi|313126630|ref|YP_004036900.1| 18 SA-DLSEITDLARAAGYEVVGTLSQ 41
                                      33.4888999999999999865444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  66 eelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpele 124
                                       +++k++++++  e+  + +k +e+ +e +++   ++++l+G + +GKStL+ +l+++le
  gi|313126630|ref|YP_004036900.1| 158 QDIKNQISRIKNELDSIAEK-EETRREQRRESGFDLVALAGYTNAGKSTLMRRLAEDLE 215
                                       45566666665555555333.3333333444444899*****************99843 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 3.2e-05
                                       --EEEEEEESTTT..T--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTH CS
                       RsgA_GTPase  16 vdqllivvslkep..elslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegl 90 
                                        d +l+vv ++ep  e++ +l++   +l+e++++++v vlnKiD ++ +e l + +++l+al  +++ vs  t+e++
  gi|313126630|ref|YP_004036900.1| 284 ADLVLLVVDASEPveEMRDKLVTCHDTLYERNEAPIVTVLNKIDKVDADE-LGRKMDALQALAPNPVSVSGLTGENV 359
                                       566777776666533677778888888999********************.************************** PP

                                       HHHHHHCTT CS
                       RsgA_GTPase  91 eelkellkd 99 
                                        +l+++++ 
  gi|313126630|ref|YP_004036900.1| 360 GALADRIER 368
                                       **9998875 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.027        32       3      22 ..     193     212 ..     191     226 .. 0.84
   2 !   19.1   0.0   6.3e-07   0.00076      79     164 ..     246     340 ..     218     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.027
                                       EEEEESTTCCHHHHHHHHHC CS
                              cobW   3 tvltGflGsGKTtLlnhlle 22 
                                       + l+G+  +GK+tL+++l e
  gi|313126630|ref|YP_004036900.1| 193 VALAGYTNAGKSTLMRRLAE 212
                                       5789************9984 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 6.3e-07
                                       HH..TT-SEEEEEECTTTTHHHH.HTT..SHHHHHCCCECEEEEEEETTTH.....CCHCCHHHHHHHHHHTSSEEE CS
                              cobW  79 re..erldviliEttGlaePapv.aft..eeelksdltldavvavvDaknl....eaeeekieekaedqlaaadllv 146
                                       r   +  dv+l  t+G ++  p  +++  +++l s +++d v+ vvDa++      ++  + ++++ +  +a  + v
  gi|313126630|ref|YP_004036900.1| 246 RAdtGTRDVLLTDTVGFVSDLPHwLVEsfKSTLDSVYRADLVLLVVDASEPveemRDKLVTCHDTLYERNEAPIVTV 322
                                       3366678*********777776633446899*****************9984443344444455666666777789* PP

                                       EE-HHHHCHC..HHHHHH CS
                              cobW 147 lnKtDlldeealleklee 164
                                       lnK+D +d+++l +k+++
  gi|313126630|ref|YP_004036900.1| 323 LNKIDKVDADELGRKMDA 340
                                       *********988666654 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0019       2.3       3      22 ..     193     212 ..     191     219 .. 0.87
   2 !    9.3   0.0   0.00061      0.73      78     155 ..     283     365 ..     239     366 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
                                       EEEEESTTSSHHHHHHHHHT CS
                            FeoB_N   3 valvGnpnvGkttlfnaltg 22 
                                       val+G  n+Gk+tl+ +l++
  gi|313126630|ref|YP_004036900.1| 193 VALAGYTNAGKSTLMRRLAE 212
                                       89*************99975 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00061
                                       SSSEEEEEEEGGG....HHHHHHHHH.HHHHTT.SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT CS
                            FeoB_N  78 epdvvvnvvdatn....lernLyLtl.qllelg.vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkeg 148
                                       ++d+v+ vvda++    ++ +L+     l e + +p+v +ln+id+++++++   +++L++ L  + v++s+ ++e+
  gi|313126630|ref|YP_004036900.1| 283 RADLVLLVVDASEpveeMRDKLVTCHdTLYERNeAPIVTVLNKIDKVDADELGRKMDALQA-LAPNPVSVSGLTGEN 358
                                       6899999999987211133344433324677654899************999999999976.555556888888888 PP

                                       HHHHHHH CS
                            FeoB_N 149 ieellka 155
                                       + +l ++
  gi|313126630|ref|YP_004036900.1| 359 VGALADR 365
                                       8888765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       5.1   6.1e+03      45      64 ..     151     170 ..     114     184 .. 0.64
   2 !   16.5   0.0   8.1e-06    0.0096       1     103 [.     193     295 ..     193     320 .. 0.78
   3 ?   -0.6   0.0       1.6   1.9e+03      38      69 ..     311     346 ..     292     380 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.1
                            AAA_18  45 aldeskrldedkldklldal 64 
                                       ++des++ d++++ + +++ 
  gi|313126630|ref|YP_004036900.1| 151 EYDESREQDIKNQISRIKNE 170
                                       57788888877776555443 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 8.1e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe....aldeskrldedkldklldaleenssalee 73 
                                       ++l+G+  +GK+tl ++L++ l++g +  d++++ ++  e ++         ++r+d++ +d+ll+   +  s   +
  gi|313126630|ref|YP_004036900.1| 193 VALAGYTNAGKSTLMRRLAEDLEVG-ENEDLHPDLDPTAESEDRlfttLGTTTRRADTGTRDVLLTDTVGFVS---D 265
                                       689***************9997654.45788888888888888888877788899999999999998888865...5 PP

                            AAA_18  74 gknlvidghlaeleseaakdikkvvLtasp 103
                                         +++++++ + l s ++ d++  v++as+
  gi|313126630|ref|YP_004036900.1| 266 LPHWLVESFKSTLDSVYRADLVLLVVDASE 295
                                       566689999988888888888776666665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.6
                            AAA_18  38 llevdpe....aldeskrldedkldklldaleenss 69 
                                       l+e++++     l++ +++d d l + +dal++ + 
  gi|313126630|ref|YP_004036900.1| 311 LYERNEApivtVLNKIDKVDADELGRKMDALQALAP 346
                                       333333345666677788888888888888777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       2.1   2.5e+03      74     107 ..      94     129 ..      35     184 .. 0.60
   2 ?   14.7   0.2   2.5e-05      0.03      20     158 ..     186     344 ..     161     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.1
                            AAA_16  74 qalareellrqlldeaesaeleawrekleeala......a 107
                                       ++++r +l+ ++  +     ++  +++l+ +la      +
  gi|313126630|ref|YP_004036900.1|  94 EVIDRFTLILEIFGQ----RANTRKAQLQVELAelryelP 129
                                       445555555555555....333444444444443333331 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.5e-05
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                       r+++  lv l G+   GKs+l+r+l++ le      + ++ d +     +++ a+    ++l++ l++ ++ a+ + 
  gi|313126630|ref|YP_004036900.1| 186 RESGFDLVALAGYTNAGKSTLMRRLAEDLE------VGENEDLH---PDLDPTAESE--DRLFTTLGTTTRRADTGT 251
                                       3334499********************998......55666666...4456677777..479999999988888888 PP

                            AAA_16  97 wrekleeala............................avpelagaea......srllellkrll.allsrderplv 138
                                        +  l+++++                                            + ++++l  +   l++r+e p+v
  gi|313126630|ref|YP_004036900.1| 252 RDVLLTDTVGfvsdlphwlvesfkstldsvyradlvllV--------VdasepvEEMRDKLVTCHdTLYERNEAPIV 320
                                       888888888888888888888888877766666554332........033345699999999999999999999*** PP

                            AAA_16 139 lvlDdlqwade....aslqllaaL 158
                                        vl  ++++d+      +++l+aL
  gi|313126630|ref|YP_004036900.1| 321 TVLNKIDKVDAdelgRKMDALQAL 344
                                       *******99983344344444444 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.6e-05     0.031      56     103 ..     317     369 ..     291     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                      MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare.....pnsvviSaekelnldeLkekiwee 103
                                        p ++vlNKiD+++ +el +         pn v +S  ++ n+ +L ++i +e
  gi|313126630|ref|YP_004036900.1| 317 APIVTVLNKIDKVDADELGRKMDAlqalaPNPVSVSGLTGENVGALADRIERE 369
                                       6899**********9998665443355679*****************999666 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.014        17       2      22 ..     193     213 ..     192     223 .. 0.86
   2 ?    6.3   0.0    0.0091        11      67     120 .]     272     328 ..     271     328 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
                                       EEEESSTTSSHHHHHHCHCT- CS
                               Roc   2 vvlvGdsgvGKtsllkrfved 22 
                                       v l G +++GK++l++r+ ed
  gi|313126630|ref|YP_004036900.1| 193 VALAGYTNAGKSTLMRRLAED 213
                                       568899***********9976 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0091
                                       GCTTTT-HHHHCTSCEEEEEEE.GHHHHCHHHHHHHHHHH...CSSS-EEEEEE-TTT CS
                               Roc  67 erfrslhplylreaalailvyd.srssenlkeWlkelkkv...agkspvilvgnkiDl 120
                                       e f+s+ ++ +r++ l++lv+d s+  e++++ l  +++    ++++p++ v nkiD+
  gi|313126630|ref|YP_004036900.1| 272 ESFKSTLDSVYRAD-LVLLVVDaSEPVEEMRDKLVTCHDTlyeRNEAPIVTVLNKIDK 328
                                       67888877777766.555666636666766665555555322256789********95 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.2   2.7e+03      95     114 ..     162     181 ..     159     185 .. 0.84
   2 ?    5.3   0.0      0.01        12      19      39 ..     195     215 ..     182     234 .. 0.76
   3 ?    5.4   0.0    0.0097        12      83     132 ..     285     333 ..     277     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.2
                                       TTHHHHHHHHHHHCTSGCCT CS
                               Arf  95 eRleeakeeLkalleeeelk 114
                                       + ++  k+eL+++ e+ee +
  gi|313126630|ref|YP_004036900.1| 162 NQISRIKNELDSIAEKEETR 181
                                       5788999******9999987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                                       EEESTTSSHHHHHHHHHHSSC CS
                               Arf  19 llGLDnaGKtTilkklkleel 39 
                                       l G  naGK+T++ +l ++  
  gi|313126630|ref|YP_004036900.1| 195 LAGYTNAGKSTLMRRLAEDLE 215
                                       45899**********987744 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0097
                                       SEEEEEEETT-CTTHHHHHHHHHHHCTS.GCCTTSEEEEEEE-TTSTTSS- CS
                               Arf  83 davifvvDsadreRleeakeeLkallee.eelkevallvlaNKqDlpeals 132
                                       d v+ vvD+++   +ee++++L +  ++  e +e++++ + NK+D  +a +
  gi|313126630|ref|YP_004036900.1| 285 DLVLLVVDASE--PVEEMRDKLVTCHDTlYERNEAPIVTVLNKIDKVDADE 333
                                       67888999875..4677777777766542456799**********998854 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.21       5      85 ..     193     272 ..     190     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewek 81 
                                       +++ G   +GK+tl+++l+++l v +++ l  +ld   +++ + +++l +  ++  ++  + +l+ D +  v+++ +
  gi|313126630|ref|YP_004036900.1| 193 VALAGYTNAGKSTLMRRLAEDLEVGENEDLHPDLDPTAESEDRLFTTLGTTTRRADTG-TRDVLLTDTVGFVSDLPH 268
                                       78999999***********999999999999****99999999997777777666555.778888888888877766 PP

                            AAA_14  82 alks 85 
                                       +l +
  gi|313126630|ref|YP_004036900.1| 269 WLVE 272
                                       6655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.7   5.6e+03      37      72 ..     136     179 ..     118     193 .. 0.64
   2 ?   11.0   0.0   0.00032      0.38       8      38 ..     193     232 ..     185     324 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.7
                            AAA_22  37 e.....erpevv...fvtlpsstsskdllrellralglelkaer 72 
                                             erp+++   +++ + + + k+  +++ ++l++ +++e+
  gi|313126630|ref|YP_004036900.1| 136 SlakrdERPGFMglgEYDESREQDIKNQISRIKNELDSIAEKEE 179
                                       34555667777777777777777777778888888887777722 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00032
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.........e 38 
                                       +++ G + +GK+tl+rrl+e l+  ++ +           
  gi|313126630|ref|YP_004036900.1| 193 VALAGYTNAGKSTLMRRLAEDLEVGENEDLhpdldptaeS 232
                                       67889999*************9877665557777766641 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.027        32       2      37 ..     196     231 ..     195     235 .. 0.86
   2 ?    5.4   0.0     0.011        14     144     179 ..     302     340 ..     236     391 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.027
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAae 37 
                                       +G   +GK+t++++l+e le  + +     LDP ae
  gi|313126630|ref|YP_004036900.1| 196 AGYTNAGKSTLMRRLAEDLEVGENEDLHPDLDPTAE 231
                                       68889************9998888888888888887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                        ATP_bind_1 144 gllsals.aml.rlelPhvvvlnkfDllkek.lekelef 179
                                         l+++  +++ r e P v+vlnk+D ++ + l ++++ 
  gi|313126630|ref|YP_004036900.1| 302 DKLVTCHdTLYeRNEAPIVTVLNKIDKVDADeLGRKMDA 340
                                       434444313333789***********9996665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 2435.29
//
Query:       gi|313126631|ref|YP_004036901.1|  [L=110]
Description: hypothetical protein Hbor_18890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-21   74.6   4.8    7.7e-21   74.3   4.8    1.1  1  FUN14     FUN14 family
  ------ inclusion threshold ------
       0.42   10.0   1.7       0.59    9.5   1.7    1.2  1  DUF3482   Domain of unknown function (DUF3482)


Domain annotation for each model (and alignments):
>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   4.8   8.6e-25   7.7e-21       2      91 .]      19     107 ..      18     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 8.6e-25
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                             FUN14   2 giGaviGlvtGfalkkvgKlaaiavGggllllqilasqgyikvnwdkiekdveelldrnkdgklgtede....kllt 74 
                                       g GaviG+++Gfa+kk++K++a+++G++l+l+++l+s+g++ v+w+k+++ + +   +++ + ++ +      +++ 
  gi|313126631|ref|YP_004036901.1|  19 GSGAVIGGIIGFAAKKIAKIIAVIIGLELALFKFLESRGILAVDWEKLTNGFMK---STE-AATSGA-PpswiSTIL 90 
                                       78***********************************************77664...222.223333.146778899 PP

                                       xxxxxxxxxxxxxxxxx RF
                             FUN14  75 enlpfsagFlaGfllGl 91 
                                       ++l++sagF +Gfl+G+
  gi|313126631|ref|YP_004036901.1|  91 STLSISAGFSGGFLVGF 107
                                       99**************8 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.7   6.6e-05      0.59     163     190 ..       8      35 ..       7      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 6.6e-05
                           DUF3482 163 giDlavgGltLGaaaaiGalaGglaatl 190
                                       ++D   +Gl +G +a+iG+++G +a+ +
  gi|313126631|ref|YP_004036901.1|   8 SLDPTSLGLEFGSGAVIGGIIGFAAKKI 35 
                                       5788899***************887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 656.21
//
Query:       gi|313126632|ref|YP_004036902.1|  [L=241]
Description: hypothetical protein Hbor_18900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-21   73.8   0.0    1.4e-20   73.2   0.0    1.3  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    3.7e-19   68.9   0.0    6.9e-19   68.0   0.0    1.4  1  SBDS_C    SBDS protein C-terminal domain


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.0   1.5e-24   1.4e-20       3      88 .]       8      94 ..       6      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.5e-24
                                      EEEEEEETTEEEEEEE-HHHHHHHHCTT.---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEE CS
                              SBDS  3 sivrykkgkkrFeiavyknklleyregk.eidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGei 80
                                      +++r++++++rFe++++++++l  ++g+ e dL+ev+++e++F++as+G++  +++le++f+t++  eii e++k+Gei
  gi|313126632|ref|YP_004036902.1|  8 VTARLESHGERFEVLIDPDAALAIKRGEfEGDLEEVIAAEDVFEDASRGDRPAENDLETVFETTDPMEIIPEVVKRGEI 86
                                      789***********************888************************************************** PP

                                      E--HHHHH CS
                              SBDS 81 qvsaeerk 88
                                      q +ae+r+
  gi|313126632|ref|YP_004036902.1| 87 QITAEQRR 94
                                      *****996 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   7.7e-23   6.9e-19       2     115 ..     101     219 ..     100     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 7.7e-23
                                       HHHHHHHHHHHEEBTTT.TB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...C CS
                            SBDS_C   2 ekeiieivaeklvnpqt.krpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsik 77 
                                       +k+ i+ +a+++vnpq  ++p+++++Ie+al+e+g++v++ ++++sQ+ e+++aL+  ipi++ ++ +++++p   +
  gi|313126632|ref|YP_004036902.1| 101 RKQLINTIARNAVNPQMdNAPHPPERIERALEEAGFKVDPMEKVESQVDEALDALRPVIPIRFDEVTVAVQIP---A 174
                                       799*************9678*****************************************************...9 PP

                                       CCHHHHHHHH.HH.....S.EE......EEEEEEGGGHHHHHHHH CS
                            SBDS_C  78 dkilklieqv.esqkvaekewe......vvvliePgaykeleefv 115
                                       d++ k  +qv e  +++ +ew+       vv  ++g+++++ ++v
  gi|313126632|ref|YP_004036902.1| 175 DYAGKTQAQVrEYGDLEREEWQndgswvGVVTFPAGLQNDFYDMV 219
                                       999999999987777666776666665366669999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1456.83
//
Query:       gi|313126633|ref|YP_004036903.1|  [L=112]
Description: thioredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-28   96.7   0.0    7.4e-28   96.6   0.0    1.0  1  Thioredoxin    Thioredoxin
    5.4e-08   33.2   0.1    6.3e-06   26.6   0.1    2.1  1  Thioredoxin_2  Thioredoxin-like domain
    6.8e-05   23.0   0.0    0.00013   22.1   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like
     0.0018   18.2   0.1     0.0033   17.4   0.1    1.5  1  Thioredoxin_3  Thioredoxin domain
     0.0021   18.4   0.0      0.013   15.8   0.0    2.0  2  Thioredoxin_8  Thioredoxin-like
      0.006   16.4   0.0     0.0077   16.0   0.0    1.2  1  Thioredoxin_9  Thioredoxin
     0.0076   16.1   0.0     0.0095   15.8   0.0    1.1  1  TraF           F plasmid transfer operon protein
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.074   13.0   0.0    1.4  1  AhpC-TSA       AhpC/TSA family
      0.079   13.2   0.0       0.13   12.5   0.0    1.4  1  Glutaredoxin   Glutaredoxin
       0.12   12.1   0.1       0.29   10.8   0.0    1.6  1  Redoxin        Redoxin
        0.2   11.0   0.0       0.24   10.7   0.0    1.2  1  OST3_OST6      OST3 / OST6 family, transporter family


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   4.5e-31   7.4e-28       4     102 ..      12     108 ..       9     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 4.5e-31
                                       ESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEE CS
                       Thioredoxin   4 vltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfk 80 
                                       +++++++ ee+ + ++ vlv+FyA+wCg+Ck+l+P+++++a e+     ++kvd+de ++la++ +++++Ptl+++ 
  gi|313126633|ref|YP_004036903.1|  12 HVESQDHLEELVAGENVVLVDFYADWCGPCKMLEPTVDEIAAETD--ALVLKVDIDELQELARDQGIRSVPTLQFYA 86 
                                       45555666666666****************************998..999*************************** PP

                                       TTEEEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  81 ngkevkkyegarekeklaaflk 102
                                       +g+++k++ g ++k++l++ ++
  gi|313126633|ref|YP_004036903.1|  87 DGEQAKQVIGVQDKDDLVEVVE 108
                                       ******************9886 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   3.9e-09   6.3e-06       7     107 ..      28     105 ..      23     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.9e-09
                     Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt 83 
                                        vlv+f++++C+ Ck l+ +++e+              ++e+ a  ++ + ++          +elar  g+r++Pt
  gi|313126633|ref|YP_004036903.1|  28 VVLVDFYADWCGPCKMLEPTVDEI--------------AAETDALVLKVDIDE---------LQELARDQGIRSVPT 81 
                                       699********************9..............334444444444444.........3689*********** PP

                     Thioredoxin_2  84 iv.fldgkeivarlpGyvpaeelea 107
                                       +  + dg+  + ++ G  ++++l +
  gi|313126633|ref|YP_004036903.1|  82 LQfYADGE-QAKQVIGVQDKDDLVE 105
                                       77478888.7789999999988866 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   7.7e-08   0.00013      18      81 ..      27      85 ..      15      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.7e-08
                                      --EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT-..--SSEEEEE CS
                     Thioredoxin_7 18 kpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanilelde..qgvPvvafl 81
                                        vlv+f a+wc++C+ le ++ +      a+  +  +l+vd++e ++   + d+  + vP++ f+
  gi|313126633|ref|YP_004036903.1| 27 NVVLVDFYADWCGPCKMLEPTVDEI-----AAETDALVLKVDIDELQEL--ARDQgiRSVPTLQFY 85
                                      569***************9888776.....4569999******999983..334434459998886 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.1e-06    0.0033      10      75 ..      38     107 ..      28     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                                       STTCHHHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEE..ECTTCE..EEESS---CCHHHHHH CS
                     Thioredoxin_3  10 CakCpklekavkeaaaekgikaevekvtdfeei.ekygVmsvPal..vidgkv..vvsGkvpseeeirkll 75 
                                       C  C+ le  v e+aae +  +  +++ +++e+  + g++svP+l  + dg+    v G v +++++ +++
  gi|313126633|ref|YP_004036903.1|  38 CGPCKMLEPTVDEIAAETDALVLKVDIDELQELaRDQGIRSVPTLqfYADGEQakQVIG-VQDKDDLVEVV 107
                                       999***************9888888999*****9***********95567765224667.77777777766 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.8e-06     0.013       2      29 ..      27      54 ..      25      64 .. 0.85
   2 ?    0.8   0.0      0.38   6.3e+02      62      86 ..      58      82 ..      52      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.8e-06
                                      SEEEEEE--SSSHHHHHHHHHHHHHHHH CS
                     Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyek 29
                                       vvl+ f+a+wc pck   p+++e+  +
  gi|313126633|ref|YP_004036903.1| 27 NVVLVDFYADWCGPCKMLEPTVDEIAAE 54
                                      69********************998655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.38
                                      EE.EE-TT-HHHHTT-S--TT-SEE CS
                     Thioredoxin_8 62 lsvpfddkkrnklkkkynvkaiPtl 86
                                      l + +d ++ ++l++  ++ ++Ptl
  gi|313126633|ref|YP_004036903.1| 58 LVLKVDIDELQELARDQGIRSVPTL 82
                                      55666667789999999******98 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.7e-06    0.0077      41     109 ..      26      90 ..       9      98 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.7e-06
                                       S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT-- CS
                     Thioredoxin_9  41 kklkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildeege 109
                                       +++ ++ + +dwCg + +  P +++ia +++ + +k+ + de +el ++   +g r++Ptl ++ ++ +
  gi|313126633|ref|YP_004036903.1|  26 ENVVLVDFYADWCGPCKMLEPTVDEIAAETDALVLKVDI-DELQELARD---QGIRSVPTLQFYADGEQ 90 
                                       4445555889********************776666544.555555554...58999999988876544 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.8e-06    0.0095     129     210 ..      26      96 ..      13     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-06
                              TraF 129 keygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqk 205
                                       +++ L+ Fy+  c+ c+++ p+++++a ++   v+ V++d+ +   l+            g++++P+l +    +q 
  gi|313126633|ref|YP_004036903.1|  26 ENVVLVDFYADWCGPCKMLEPTVDEIAAETDALVLKVDIDELQE--LAR---------DQGIRSVPTLQFYADGEQA 91 
                                       5688999*********************************9866..777.........8899999999887777776 PP

                              TraF 206 vvpva 210
                                         +++
  gi|313126633|ref|YP_004036903.1|  92 KQVIG 96 
                                       66665 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.5e-05     0.074      19      56 ..      18      56 ..       6      74 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.5e-05
                                      ECHHH.TT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCC CS
                          AhpC-TSA 19 slsdy.kg.kpvvlffypkdwcpvCttelpalaklyeefk 56
                                      +l+++ +g ++v++ fy+  wc +C+   p   + + e +
  gi|313126633|ref|YP_004036903.1| 18 HLEELvAGeNVVLVDFYAD-WCGPCKMLEPTVDEIAAETD 56
                                      5677777756777778887.*****988777777666655 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.3e-05      0.13       7      53 ..      36      82 ..      28      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.3e-05
                                      TSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEE CS
                      Glutaredoxin  7 ptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqv 53
                                       +C+ Ck+   + +e  ++ +   +  d ++ +el +  g+r+vP++
  gi|313126633|ref|YP_004036903.1| 36 DWCGPCKMLEPTVDEIAAETDALVLKVDIDELQELARDQGIRSVPTL 82
                                      79***************9977666666666677777777******97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.29      23      56 ..      19      53 ..      10      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                      HHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHH CS
                           Redoxin 23 lse.fkgkkvvvnfvpgafcPtCsaehpyleklae 56
                                      l+e ++g +vv++ + + +c++C+   p ++++a+
  gi|313126633|ref|YP_004036903.1| 19 LEElVAGENVVLVDFYADWCGPCKMLEPTVDEIAA 53
                                      667788888877766666*****875556666655 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.24      46     109 ..      38      92 ..      28     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                         OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppkkgpk 109
                                       C +C+ +ep ++ +a            + +  kvd+de +++ ++ g++s+P l ++   ++ k
  gi|313126633|ref|YP_004036903.1|  38 CGPCKMLEPTVDEIAAET---------DALVLKVDIDELQELARDQGIRSVPTLQFYADGEQAK 92 
                                       666666666666666544.........45579*************************9855544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 689.86
//
Query:       gi|313126634|ref|YP_004036904.1|  [L=220]
Description: 2,5-diamino-6-(5-phosphoribosylamino)pyrimidin-4(3h)-one reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-51  172.7   0.2    9.1e-51  172.5   0.2    1.0  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.5   0.2   5.1e-55   9.1e-51       2     200 .]       2     215 ..       1     215 [. 0.97

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 5.1e-55
                                       EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH.HTT.GSS- CS
                            RibD_C   2 yvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae.adaearqp 77 
                                       +v++++a+S+DGkl+++++e+ +i+g ++ a+v+++ra++da+lvG+gtvlad+p+ltv  ++ r ++  d+ + +p
  gi|313126634|ref|YP_004036904.1|   2 HVVVNAATSADGKLSTRRREQIKISGADDFARVDRVRADSDAVLVGVGTVLADDPHLTVDDADYRDERqSDGREPHP 78 
                                       799**************************************************************999888888*** PP

                                       EEEEEETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCC.....E......SE-HHHHHHHHHHTT--EEEEEET CS
                            RibD_C  78 vrvVvdstlrvpldakvltddaptlvatteeadkekveklk.....v......rvdlkelleeLkergirsllveGG 143
                                        rvV+ds+ r+p da++l+d a+t v+++e+a+ ++v+ l+     v      rv ++e+++eL +rgi++l+veGG
  gi|313126634|ref|YP_004036904.1|  79 ARVVADSRARTPTDARILDDAATTYVLVSESAPADRVSALEktggtVvtagdtRVSFPEAFAELEARGIDRLMVEGG 155
                                       *******************99********************988872578889************************ PP

                                       HHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS..EEEEEEEEEEETTEEEE CS
                            RibD_C 144 atLagsllraglvDelrlyiaPkllGg.agktlfdgegfka..lklklvksealgegvvl 200
                                       + ++ sl+++ lvDel +y+ +++lGg +++tl dg gf +  ++l+l  +e++++gv+l
  gi|313126634|ref|YP_004036904.1| 156 GEVIFSLFEDELVDELSVYVGSVVLGGrDAPTLADGDGFVEsfPTLDLRDVERIDDGVLL 215
                                       ********************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1449.45
//
Query:       gi|313126635|ref|YP_004036905.1|  [L=343]
Description: (1-_4)-alpha-d-glucan synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-28   97.6   0.0    1.3e-27   96.4   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    3.3e-23   82.6   0.0    5.2e-23   82.0   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.6e-21   77.0   0.0    3.2e-21   76.1   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    3.3e-18   66.7   0.0    5.3e-18   66.0   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    4.3e-06   26.6   0.0     0.0045   16.7   0.0    2.7  2  Glyco_transf_5   Starch synthase catalytic domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.0   3.7e-31   1.3e-27      14     155 ..     177     312 ..     169     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 3.7e-31
                                       T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                   Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                       + +++++vgr + +Kg+++l+ a+++l+   +++v lv+ G+g+  ++lkk a+ l ++d+++++g+v++e+l  ++
  gi|313126635|ref|YP_004036905.1| 177 DGNMLFFVGRHTDQKGISHLVYAMEKLC---RDDVTLVVGGSGHLTEQLKKFADLLDVEDQIEWVGYVPEEALGDYY 250
                                       67899**********************9...79******************************************** PP

                                       HCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHH CS
                   Glycos_transf_1  91 knadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkl 155
                                        +ad+f+ ps sE+fGi+++EA++ag+ v+a+ +g    + +d +   +   ++ +++a++i+  
  gi|313126635|ref|YP_004036905.1| 251 ASADLFISPSLSEPFGITITEALSAGTRVVATESGVSEVLPEDCV---IEVDPSSDSIADGIDYG 312
                                       ********************************9776554444444...44444688888887765 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   1.5e-26   5.2e-23       3     128 ..     180     309 ..     178     314 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.5e-26
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaad 74 
                                        + fvGr +  +kg+  l+ a+++l ++dv+lv+ G+g    e+l++ a+  ++e+++e++G+v  e l +++a+ad
  gi|313126635|ref|YP_004036905.1| 180 MLFFVGRHT-DQKGISHLVYAMEKLCRDDVTLVVGGSGHlT-EQLKKFADllDVEDQIEWVGYVpeEALGDYYASAD 254
                                       689*****5.56**********9999778*******99954.6999877678999*********8555********* PP

                                       EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHH CS
                   Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeai 128
                                       +f+ Ps  e fg+++ Ea++ag+ vVat+  g++ev+ ++  + v+p +++++a+ i
  gi|313126635|ref|YP_004036905.1| 255 LFISPSlsEPFGITITEALSAGTRVVATES-GVSEVLpEDCVIEVDP-SSDSIADGI 309
                                       *******99*********************.99**996654444543.478888877 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   8.9e-25   3.2e-21       2     165 ..      12     159 ..      11     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 8.9e-25
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                       GG  +hv e+  +L++rG+++++v p+   p e+e      + +vp+       r+ + +++++++++  + D+vH+
  gi|313126635|ref|YP_004036905.1|  12 GGLDTHVGEMFDGLRARGVDIDLVLPAEYAPDERE-----GIYGVPTGEGDIITRIGRLSSAFAERAE--DADIVHT 81 
                                       9**************************99999999.....4555555555556666666677777665..******* PP

                    Glyco_transf_4  79 hspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvp 155
                                       h+++  g + +a     ++  V+t+H+l        r+    +++ + err++ r+d+++avSe ta++++e yg +
  gi|313126635|ref|YP_004036905.1|  82 HDWFGYGPGSRAKSN-ADVEWVTTFHSLSS-----DRNLDPPKREVETERRIVERCDHLLAVSELTARRVKEQYGGS 152
                                       *********888887.*************3.....33333344555679**************************77 PP

                    Glyco_transf_4 156 pekitVipnG 165
                                       p   +Vi+nG
  gi|313126635|ref|YP_004036905.1| 153 P---EVIYNG 159
                                       6...*****9 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   1.5e-21   5.3e-18       1     157 [.      12     156 ..      12     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.5e-21
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       gG  ++v e+  +L+arG++++++ pa++++++     +  ++++p++ +        ++ +l ++++ r+e  d+v
  gi|313126635|ref|YP_004036905.1|  12 GGLDTHVGEMFDGLRARGVDIDLVLPAEYAPDE-----REGIYGVPTGEGD----IITRIGRLSSAFAERAEDADIV 79 
                                       899***********************9999998.....5568999999885....7999********99******** PP

                   Glyco_trans_4_4  78 hahsptaglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrllrradavlvvseaeaeelra.lgvpad 152
                                       h+h++ + +++ +a+  +++ +v t+h+l  +r   +++ r + + err++ r+d++l+vse  a+++ + +g+ ++
  gi|313126635|ref|YP_004036905.1|  80 HTHDWFGYGPGSRAKSNADVEWVTTFHSLSSDRNlDPPK-REV-ETERRIVERCDHLLAVSELTARRVKEqYGGSPE 154
                                       *****9999999999899**********99888845555.444.69************************8888764 PP

                   Glyco_trans_4_4 153 rvvvv 157
                                          v+
  gi|313126635|ref|YP_004036905.1| 155 ---VI 156
                                       ...44 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00074       2.7       5      43 ..       2      39 ..       1      46 [. 0.84
   2 !   16.7   0.0   1.3e-06    0.0045      96     232 ..      44     148 ..      39     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00074
                    Glyco_transf_5  5 vasEvaplaktGGLadvvgaLpkaLaklghdvrvilPry 43
                                      +++ ++p    GGL  +vg++   L+++g+d++++lP+ 
  gi|313126635|ref|YP_004036905.1|  2 LGWGFPP-NVSGGLDTHVGEMFDGLRARGVDIDLVLPAE 39
                                      5666777.789**************************86 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.3e-06
                    Glyco_transf_5  96 dreglYgdkgedyednaerfalfsraalelleklgwkpdvihahDWhtalvpallkelykerglfkkiktvftiHNl 172
                                       +reg+Yg    +  d   r+  +s a +e +e      d++h+hDW     +  +k+         ++  v t H+l
  gi|313126635|ref|YP_004036905.1|  44 EREGIYGVP-TGEGDIITRIGRLSSAFAERAED----ADIVHTHDWFGYGPGSRAKSNA-------DVEWVTTFHSL 108
                                       588899775.44479999999999999999999....8********9877766666643.......599******99 PP

                    Glyco_transf_5 173 ayqgrfpkdelaalglpaedfekldglefygkvnflkagivyadavttVSptyakEiltp 232
                                       + ++++++ +                    ++v   +  +  +d++++VS+ +a+ + ++
  gi|313126635|ref|YP_004036905.1| 109 SSDRNLDPPK--------------------REVETERRIVERCDHLLAVSELTARRVKEQ 148
                                       9999887422....................245555566666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2436.16
//
Query:       gi|313126636|ref|YP_004036906.1|  [L=42]
Description: hypothetical protein Hbor_18940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       116  (0.00646996); expected 358.6 (0.02)
Passed bias filter:                      109  (0.00607954); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.49
# Mc/sec: 258.02
//
Query:       gi|313126637|ref|YP_004036907.1|  [L=138]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-20   72.9   0.8    4.4e-20   72.6   0.8    1.1  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.8   2.4e-24   4.4e-20       4     139 ..       3     128 ..       1     130 [. 0.95

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 2.4e-24
                                       EEEEEE-SSHHHHHHHHHHHH.HHHH.CTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   4 rIlVavDgseeskkAlewAle.laka.rgaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       ++l+++Dg+ee  +A   A++ l  a    e++ll+v d+++ ++v ++++  +  ++  +++ +            
  gi|313126637|ref|YP_004036907.1|   3 TVLLPIDGNEEHGAAQADAVAvLPNAvETVEVTLLYVFDDEDRAEVTAPKQINGGRAAHNRLMDA------------ 67 
                                       69***********99999999977777789********************************965............ PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                       gv+ve   ++gdpa eil +a e dad iV+G r+rs l  ll+GSvs++v+  a+ pV++
  gi|313126637|ref|YP_004036907.1|  68 GVSVEEMSRVGDPAAEILAAAAEVDADYIVLGGRKRSPLGSLLFGSVSQAVILDADRPVTI 128
                                       9**********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 902.18
//
Query:       gi|313126638|ref|YP_004036908.1|  [L=126]
Description: hypothetical protein Hbor_18960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.25   11.2   0.0    1.4  2  DUF2835   Protein of unknown function (DUF2835)


Domain annotation for each model (and alignments):
>> DUF2835  Protein of unknown function (DUF2835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.4e-05      0.25       2      44 ..      12      55 ..      11      60 .. 0.80
   2 ?   -3.8   0.0      0.68   1.2e+04      27      36 ..     105     114 ..     104     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.4e-05
                           DUF2835  2 rlvfdLnisaeeflayYqGa.akkvvvraedGrrvqlpashlrp 44
                                      +++f+L+i+  e     +G   ++vvv +e+G r+ lp + + +
  gi|313126638|ref|YP_004036908.1| 12 QVTFSLSIEDGETVITMRGDrDTAVVVESESGERIYLPPEDFER 55
                                      67899999987777766765156899************999876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.68
                           DUF2835  27 vraedGrrvq 36 
                                       v ++dG r++
  gi|313126638|ref|YP_004036908.1| 105 VPTTDGYRIR 114
                                       5688999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 701.24
//
Query:       gi|313126639|ref|YP_004036909.1|  [L=423]
Description: single-stranded DNA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.022   14.7   3.5        6.9    6.7   0.0    3.8  4  tRNA_anti-codon  OB-fold nucleic acid binding domain
       0.05   13.8   0.2       0.11   12.7   0.2    1.6  1  zf-RING_7        C4-type zinc ribbon domain
      0.083   13.3   0.3         23    5.4   0.1    2.5  2  4HBT             Thioesterase superfamily


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0033        20       4      69 ..      74     139 ..      71     143 .. 0.77
   2 ?    0.9   0.0     0.076   4.6e+02      22      73 ..     202     248 ..     187     251 .. 0.77
   3 ?   -2.6   0.0      0.97   5.8e+03      21      30 ..     288     297 ..     276     298 .. 0.71
   4 ?    6.7   0.0    0.0012       6.9      19      37 ..     326     365 ..     303     404 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0033
                                       EEEEEEEE......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
                   tRNA_anti-codon   4 aGrvtsis......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69 
                                         +v ++       +++++ +   +  D tg+i  + +          +++Gd v +    v++++g+ +el+
  gi|313126639|ref|YP_004036909.1|  74 TVKVLTVGrrsiryQGEEQTIREGEFADATGKISYTSWE------DFGFEPGDSVTIGnANVREWEGE-PELN 139
                                       444444444466677888888888999************......88888999999988888888877.7775 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.076
                                       EEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEEE CS
                   tRNA_anti-codon  22 dlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkveei 73 
                                       ++ D+tgr+  + +         +l+eG   r +  +v++++g  ++++ +e+
  gi|313126639|ref|YP_004036909.1| 202 VVADETGRLPFTDWG-----ARPELREGETFRFEdVYVREFRGV-PQVNLSEF 248
                                       688999999999999.....788888888888888888888888.88777766 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.97
                                       EEEEETTEEE CS
                   tRNA_anti-codon  21 idlrDgtgri 30 
                                       +++rDg+g i
  gi|313126639|ref|YP_004036909.1| 288 LEVRDGSGLI 297
                                       4577777765 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0012
                                       EEEEEEETTEEEEEEEET.....................H CS
                   tRNA_anti-codon  19 ifidlrDgtgriqvvlfr.....................e 37 
                                       + ++l+Dg+g++++vl r                      
  gi|313126639|ref|YP_004036909.1| 326 VKAILDDGSGTVTAVLGRelteqlyggtmaeameaareaM 365
                                       5678************996666666666665555444443 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.9e-05      0.11      15      33 .]     288     307 ..     285     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                       HHHCCS.TB-EE-TTT--EE CS
                         zf-RING_7  15 selrag.devvtCpeCGRIL 33 
                                        e+r g + + +Cp CGR L
  gi|313126639|ref|YP_004036909.1| 288 LEVRDGsGLIERCPDCGRVL 307
                                       588999899*********87 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0039        23      48      68 ..      69      89 ..      64      90 .. 0.85
   2 ?    5.3   0.0    0.0043        26       4      38 ..     349     385 ..     348     386 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0039
                                      CEEEEEEEEEEEESSEEEEEE CS
                              4HBT 48 deltvearvlrlgrtsavvev 68
                                        +tv+++vl +gr+s+ ++ 
  gi|313126639|ref|YP_004036909.1| 69 GNVTVTVKVLTVGRRSIRYQG 89
                                      389*************99876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0043
                                       B-HHHHHHHHHHHHHHHHHHTTST..TEEEEEEEEEE CS
                              4HBT   4 vhgGvylallDeaagaalrslggr..gilvvvvelsi 38 
                                       ++gG+++++++ a+ a+ ++   +  ++ vv++e+++
  gi|313126639|ref|YP_004036909.1| 349 LYGGTMAEAMEAAREAMDKEVVADeiRRQVVGREFRV 385
                                       79************99877777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2369.94
//
Query:       gi|313126640|ref|YP_004036910.1|  [L=664]
Description: hypothetical protein Hbor_18980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1247  (0.0695521); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.36u 0.43s 00:00:01.79 Elapsed: 00:00:00.57
# Mc/sec: 3504.09
//
Query:       gi|313126641|ref|YP_004036911.1|  [L=264]
Description: phosphoesterase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-08   35.5   0.0    1.7e-08   35.2   0.0    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    2.4e-07   31.1   0.2    3.4e-07   30.6   0.2    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   1.9e-12   1.7e-08       4     123 ..      33     149 ..      31     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.9e-12
                                       EEEESBTB...............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.....HHHHHHHHHHHHH CS
                       Metallophos   4 lvigDlHl...............algggqlddllkllddllreekpdlvllaGDlvdrg.....dlekellellaal 60 
                                       lv++D H                ++++ +l++ll+lld++    +pd ++++GDl +r      d   el+ ++++ 
  gi|313126641|ref|YP_004036911.1|  33 LVVADYHAgieaglryergveldSDADVRLARLLRLLDET----NPDRLVVLGDLGHRIgapkgDEADELETFVERT 105
                                       8999999999999999999977766667777777777666....99999999******8888886666688888888 PP

                                       HHHTSEEEEEC-TTS.......CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE CS
                       Metallophos  61 vkypipvylllGNHe.......gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg 123
                                       v++ +p+ l++GNH+       g                       +  +    +++  g  +v ++hG+
  gi|313126641|ref|YP_004036911.1| 106 VAR-VPITLVRGNHDggiaeafG-----------------------DRIDVTDGSGIRLG--RVGFVHGH 149
                                       885.9**********44433331.......................33333333334444..44444444 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.2   3.8e-11   3.4e-07       4     103 ..      33     156 ..      31     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.8e-11
                     Metallophos_2   4 aiiSDlH.................snldaleavlealkevgvdaiihaGDl..eeeep.....evleellela.... 52 
                                       ++++D H                 ++  +l+++l+ l+e+++d+++++GDl    ++p     + le++ e++    
  gi|313126641|ref|YP_004036911.1|  33 LVVADYHagieaglryergveldsDADVRLARLLRLLDETNPDRLVVLGDLghRIGAPkgdeaDELETFVERTvarv 109
                                       688888888888888877777776666678888*****************654222334444467777777777788 PP

                     Metallophos_2  53 pvlaVrGNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdpl....g 103
                                       p++ VrGN+D        +  a+ +g+++  ++   ++  +v+++Hg+++     
  gi|313126641|ref|YP_004036911.1| 110 PITLVRGNHD--------GGIAEAFGDRIDVTDGSGIRLGRVGFVHGHTWpsceV 156
                                       **********........77788888888766667788889******95444431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1516.82
//
Query:       gi|313126642|ref|YP_004036912.1|  [L=87]
Description: hypothetical protein Hbor_19000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   14.1   0.3       0.04   13.7   0.3    1.1  1  DUF2976   Protein of unknown function (DUF2976)
        2.3    8.5   0.1        2.3    8.5   0.1    2.5  3  LHC       Antenna complex alpha/beta subunit


Domain annotation for each model (and alignments):
>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   4.5e-06      0.04      15      77 ..      18      80 ..      12      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-06
                           DUF2976 15 dllelikgylkdgvillgLvlaavaflaVakaalkkfneisegkaewgkfgltlvvGvvllvv 77
                                      +ll+ +  y+++g +++ L + + +f+   +   ++  e  ++ ++wg +  + v+G +l ++
  gi|313126642|ref|YP_004036912.1| 18 GLLHGVTEYVYEGQTVGLLTIFGGGFVIALTGYNTVRPESYDSPEKWGTLVYLTVIGSLLFAM 80
                                      7888999*******************998888888889999****************998765 PP

>> LHC  Antenna complex alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00026       2.3       8      27 ..       1      20 [.       1      20 [. 0.94
   2 ?    3.1   1.2     0.013   1.1e+02      12      26 ..      33      47 ..      32      48 .. 0.91
   3 ?   -2.8   0.1       0.9   8.1e+03      15      15 ..      73      73 ..      67      83 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00026
                                      ...HHHHHHHHHHHHHHHHH CS
                               LHC  8 vdPhrglvallgffavlAll 27
                                      ++P++g+ +++++f++++ll
  gi|313126642|ref|YP_004036912.1|  1 MNPRVGYQLSFFVFGTVGLL 20
                                      59****************97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.013
                                      HHHHHHHHHHHHHHH CS
                               LHC 12 rglvallgffavlAl 26
                                      +gl +++g+ +v+Al
  gi|313126642|ref|YP_004036912.1| 33 VGLLTIFGGGFVIAL 47
                                      799***********8 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.9
                                      H CS
                               LHC 15 v 15
                                      +
  gi|313126642|ref|YP_004036912.1| 73 I 73
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.35s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 506.65
//
Query:       gi|313126643|ref|YP_004036913.1|  [L=948]
Description: ATP dependent helicase, lhr family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-35  121.6   0.3    8.9e-35  120.2   0.0    1.9  2  DEAD_assoc     DEAD/H associated
    9.3e-32  110.2   0.0    5.6e-31  107.7   0.0    2.1  2  DEAD           DEAD/DEAH box helicase
    6.8e-22   77.9   0.0    2.1e-20   73.1   0.1    2.4  2  Helicase_C     Helicase conserved C-terminal domain
    7.5e-10   39.1   0.0    1.9e-09   37.8   0.0    1.6  2  ResIII         Type III restriction enzyme, res subunit
    3.4e-05   24.2   0.0    0.00071   19.9   0.0    2.5  2  AAA_19         AAA domain
     0.0012   18.5   0.8     0.0046   16.6   0.8    2.0  1  AAA_25         AAA domain
     0.0016   17.2   0.0     0.0033   16.2   0.0    1.4  1  SNF2_N         SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.028   14.7   0.2       0.29   11.4   0.1    2.7  2  AAA_22         AAA domain
      0.043   13.3   0.0      0.075   12.5   0.0    1.3  1  UvrD-helicase  UvrD/REP helicase N-terminal domain
      0.073   13.1   0.1        0.2   11.7   0.1    1.7  1  HypA           Hydrogenase/urease nickel incorporation, metal


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       3.4   6.1e+03     144     174 ..     130     160 ..     122     168 .. 0.74
   2 !  120.2   0.0   4.9e-38   8.9e-35       1     190 [.     619     790 ..     619     791 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.4
                        DEAD_assoc 144 dfpllleavrevledqlDlerlaellrriaa 174
                                       d p +l +  e l+ +l  e+l+ +l+++++
  gi|313126643|ref|YP_004036913.1| 130 DPPDVLVTTPETLQAMLTGEKLRTALSDVRH 160
                                       6666778888899999999999999998886 PP

  == domain 2  score: 120.2 bits;  conditional E-value: 4.9e-38
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       +Pt+++l++E   +     ++ ++sp+G+rvne+l+++laa + +r+g+++++  + +++  ++p+++++ + ++e+
  gi|313126643|ref|YP_004036913.1| 619 VPTADRLVIEGQGR-----KVTLNSPYGHRVNETLGRMLAALVGQRTGSSIGIETDAYRVTFEVPPNASV-HDFTEV 689
                                       8**********976.....79*******************************************888888.6899** PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavre 154
                                       le+++pd++e +le al+ se +k ++ +vAa++++l+r + +       +r+  ++Ll++++   d+p+++eavre
  gi|313126643|ref|YP_004036913.1| 690 LETTDPDHVEGVLELALKHSESLKFTLAQVAAKFGALKRYQGN-------KRFGGDRLLAALE---DTPIYDEAVRE 756
                                       ***************************************9999.......9************...*********** PP

                        DEAD_assoc 155 vledqlDlerlaellrriaageirvvevetprpSpf 190
                                       v++ +l +++++ellr+i++ge+ +++   ++ +p+
  gi|313126643|ref|YP_004036913.1| 757 VFHVDLAVPETTELLRKIQDGEVALET--ARERTPI 790
                                       **************************9..7777775 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.0   3.1e-34   5.6e-31       1     170 [.      33     202 ..      33     207 .. 0.89
   2 ?   -1.0   0.0       0.7   1.3e+03      46     105 ..     267     326 ..     253     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 3.1e-34
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                                       t+ Q++aip +  g++ lv a+TG+GKT+ +++pvl++++e+  +++ g  al+v+P+r+L +++ ++l  +++++d
  gi|313126643|ref|YP_004036913.1|  33 TEPQRRAIPPLAAGKNALVIAPTGTGKTETAMLPVLDSIVESpdEDRAGLSALYVTPLRALNRDMRERLDWWGEELD 109
                                       577**************************************99999******************************* PP

                                       SEEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 lrvlliiggvaardqlskldng.vdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnql 149
                                       ++v +  g ++++ q++k  n+ +d++v+tp+ l+ +l+ +kl+  ls+vr +V+DE+++l + +++ ++   l++l
  gi|313126643|ref|YP_004036913.1| 110 IEVDVRHG-DTTQYQRQKQANDpPDVLVTTPETLQAMLTGEKLRtaLSDVRHVVVDEVHELASAKRGAQLTVGLERL 185
                                       99986655.55556666665667***************66666666******************************* PP

                                       HHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 150 pqitcdgklqrqvivlSATlp 170
                                       +     g+   q i lSAT+ 
  gi|313126643|ref|YP_004036913.1| 186 RA--LAGP--FQRIGLSATVG 202
                                       64..4556..45*******86 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.7
                                       TS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEEEEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                              DEAD  46 tgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivvgtp 105
                                       ++  +l+ + tr+ ae   +++k++ ++i +   ++ ++v+  d  ++++ g +d ++ t 
  gi|313126643|ref|YP_004036913.1| 267 DHESTLVFVNTRQTAEALGSRFKRLNEPIAVHHGSLSKDVRI-DVEDRFKTGeLDGLICTS 326
                                       5567999999*************9999987555544444333.444444333466666665 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.15   2.7e+02      33      62 ..     102     131 ..      77     143 .. 0.77
   2 !   73.1   0.1   1.2e-23   2.1e-20       8     108 ..     263     360 ..     255     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.15
                                       HHHHHHTTSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  33 klllekkgikvavlhgelpqnereeileqf 62 
                                       ++  e+ +i+v v hg+++q +r++  ++ 
  gi|313126643|ref|YP_004036913.1| 102 DWWGEELDIEVDVRHGDTTQYQRQKQANDP 131
                                       4445556899**************998876 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 1.2e-23
                                       HHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTST CS
                        Helicase_C   8 ellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidip 83 
                                       +++   ++++ +l+fvnt++++e   + + ++ +  +av+hg+l+++ r+++ ++f+ ge d Li+t+ +e Gid+ 
  gi|313126643|ref|YP_004036913.1| 263 DIV---RDHESTLVFVNTRQTAEAlGSRF-KRLNEPIAVHHGSLSKDVRIDVEDRFKTGELDGLICTSSMELGIDVG 335
                                       444...78999*********996553333.33389****************************************** PP

                                       TESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  84 kvnlVinfdlprnvtsyiqriGRtg 108
                                       +v++V++++ pr+v+++ qr+GR+g
  gi|313126643|ref|YP_004036913.1| 336 RVDHVVQYGSPREVSRLLQRVGRAG 360
                                       ************************9 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0     1e-12   1.9e-09      24     169 ..      46     201 ..      18     203 .. 0.79
   2 ?   -3.7   0.0       5.6     1e+04      54      79 ..     268     293 ..     259     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1e-12
                                       TSEEEEEESTTSTHHHHH.HHHHHHH-S.........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B- CS
                            ResIII  24 dkrglikmaTGtGKTlva.aklierllkkgkee....kflflvprkslleqtleefkkflseaykeigkkvsgdkkk 95 
                                        k++l+ ++TGtGKT +a + + +++ ++ +e+     +l + p ++l   ++e++  + +e +  +  + +gd+ +
  gi|313126643|ref|YP_004036913.1|  46 GKNALVIAPTGTGKTETAmLPVLDSIVESPDEDraglSALYVTPLRALNRDMRERLDWWGEELDI-EVDVRHGDTTQ 121
                                       57899************978888899998888899*********************999988753.33333444433 PP

                                       -.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEEE CS
                            ResIII  96 a..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavll 163
                                          ++++++  ++lvtt ++l+a +   + e+ +   +    +++DE+H l+++k         +++     ++ ++
  gi|313126643|ref|YP_004036913.1| 122 YqrQKQANDPPDVLVTTPETLQAML---TGEKLRTALSDVRHVVVDEVHELASAKrgaqltvGLERLRALAGPFQRI 195
                                       344556788899*************...88899999999999***********9744444444444444445699** PP

                                       EEESS- CS
                            ResIII 164 glTATp 169
                                       gl+AT 
  gi|313126643|ref|YP_004036913.1| 196 GLSATV 201
                                       *****6 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.6
                                       ..-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII  54 eekflflvprkslleqtleefkkfls 79 
                                        e +l++v++++  e + ++fk++ +
  gi|313126643|ref|YP_004036913.1| 268 HESTLVFVNTRQTAEALGSRFKRLNE 293
                                       35789999999998888888887765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.9e-07   0.00071       1     115 [.      36     170 ..      36     179 .. 0.69
   2 ?    1.4   0.0      0.21   3.7e+02      42      78 ..     268     416 ..     253     472 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.9e-07
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkh.ivallvelggvkp..eeillvaftgrAakelrerlaalgae..... 68 
                                       qr+a+   ++ k+ lv+a+ GtGKT++ +  ++  +ve  +++    + l v++ +   + +rerl+  g+e     
  gi|313126643|ref|YP_004036913.1|  36 QRRAIPpLAAGKNALVIAPTGTGKTETAMLpVLDSIVESPDEDRagLSALYVTPLRALNRDMRERLDWWGEEldiev 112
                                       8999988999***************986651455555555554433678899999999999*****99888899997 PP

                            AAA_19  69 ......atTiHrlal...............ldfddlltealelleeaeeekklqeeellivDEfqdvd 115
                                             +       +               + +++++    ++l  ++ ++ l +  +++vDE+ ++ 
  gi|313126643|ref|YP_004036913.1| 113 dvrhgdT-------TqyqrqkqandppdvlV-TTPET--LQAMLTGEKLRTALSDVRHVVVDEVHELA 170
                                       7766431.......12333345656665422.22222..223344556777887777******98875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.21
                            AAA_19  42 peeillvaftgrAakelrerlaalgaeatTiHrlal......................................... 77 
                                        e+ l+   t++ a+ l  r + l++++   H+  l                                         
  gi|313126643|ref|YP_004036913.1| 268 HESTLVFVNTRQTAEALGSRFKRLNEPIAVHHGS-Lskdvridvedrfktgeldglictssmelgidvgrvdhvvqy 343
                                       4778888889999999999999999998888854.223666666666666555555555555555555555555555 PP

                            AAA_19  78 ........................................................................l 78 
                                                                                                               +
  gi|313126643|ref|YP_004036913.1| 344 gsprevsrllqrvgraghrrdqtsrgtivtssaddthealaiarkaeageveparihhasldtvanqivgvvM 416
                                       5555555555555555555555555555555555555555555555555555555555555555555555541 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.8   2.6e-06    0.0046       9     155 ..      23     170 ..      18     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                            AAA_25   9 avsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds.ed 84 
                                       a+s +++ +p +p+r  ++ l +ag+ al+++++gtGKt  a+  +l+    +p  +         lyv    + + 
  gi|313126643|ref|YP_004036913.1|  23 ALSERGFTTPTEPQRRAIPPL-AAGKNALVIAPTGTGKTETAMLPVLDSIVESPDED---RAGLSALYVTPLRAlNR 95 
                                       467788999************.69***************888887777776565323...38999999998888778 PP

                            AAA_25  85 elrrRlravgeal............rddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvvi 148
                                       ++r+Rl ++ge+l            +       ++++++  + p +  ++ +tl  +++   e+  ++  +vr+vv+
  gi|313126643|ref|YP_004036913.1|  96 DMRERLDWWGEELdievdvrhgdttQ-------YQRQKQaNDPPDVLVTTPETL--QAMLTGEKLRTALSDVRHVVV 163
                                       9***********97776654433331.......112222222222222222222..222223344444556999999 PP

                            AAA_25 149 Dplsral 155
                                       D + ++ 
  gi|313126643|ref|YP_004036913.1| 164 DEVHELA 170
                                       9887765 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.8e-06    0.0033      91     200 ..      76     180 ..      33     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-06
                                       ......S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT.. CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  91 rkdtlagptLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreael 166
                                       ++d++   +L v P  +l +   + ++ + ++  ++v v +g++++ ++    +++     dv++tt ++l+     
  gi|313126643|ref|YP_004036913.1|  76 DEDRAGLSALYVTPLrALNRDMRERLDWWGEELDIEVDVRHGDTTQYQR----QKQANDPPDVLVTTPETLQAMLTG 148
                                       3455556678888884444444445666778889999999998755555....66666778***********99999 PP

                                       ....TTS-S-S-SEEEES-GGGT--TTSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 167 qkkrsvlkqvewkrvvlDEghtlknstskaaeav 200
                                       +k r++l++v+   vv+DE h l + ++ a+ +v
  gi|313126643|ref|YP_004036913.1| 149 EKLRTALSDVR--HVVVDEVHELASAKRGAQLTV 180
                                       9999*999875..7************98888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00016      0.29       7     117 ..      48     190 ..      44     207 .. 0.66
   2 ?   -2.0   0.0       2.2   3.9e+03      39      90 ..     698     748 ..     683     777 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsst..sskdllrellralglelka......... 70 
                                         +v++++GtGKT ++   +    ++++++e  ++ + ++vt+      + ++ l +  ++l+ e +          
  gi|313126643|ref|YP_004036913.1|  48 NALVIAPTGTGKTETAMLPVLD-SIVESPDEdrAGLSALYVTPLRALnrDMRERLDWWGEELDIEVDVrhgdttqyq 123
                                       5799*********987665554.467777773355555555544333466666666667777666666999999999 PP

                            AAA_22  71 ..............erlsseell.ealeqalraravielliiDEaqhlr..s.....eealeeLrslln 117
                                                      + +++++l     + + +   ++ +++DE++ l   +        le Lr l+ 
  gi|313126643|ref|YP_004036913.1| 124 rqkqandppdvlvtTPETLQAMLtGEKLRTALSD--VRHVVVDEVHELAsaKrgaqlTVGLERLRALAG 190
                                       9999999888877755555555544444444444..447********9865155667777777777765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                            AAA_22  39 rpevvfvtlpsstsskdllrellralglelkaerlsseell.ealeqalrara 90 
                                         +v++  l++s+s+k  l +++ ++g  + +  + ++++  ++l  al+++ 
  gi|313126643|ref|YP_004036913.1| 698 VEGVLELALKHSESLKFTLAQVAAKFGALKRY--QGNKRFGgDRLLAALEDTP 748
                                       55566777777777777788888888876666..4444444466666655554 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.2e-05     0.075       5     101 ..      36     170 ..      33     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                                       HHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGG....EEEEESSHHHHHHHHHHHHH........ CS
                     UvrD-helicase   5 qreaias..lggpilveAsAGsGKTfvlaerilrlikeeeiepdr....ilvvTFTnkAaeElkeRiee........ 67 
                                       qr+ai +   g++ lv+A  G+GKT + +  +l  i e   + dr     l vT  ++  + ++eR+          
  gi|313126643|ref|YP_004036913.1|  36 QRRAIPPlaAGKNALVIAPTGTGKTETAMLPVLDSIVES-PDEDRaglsALYVTPLRALNRDMRERLDWwgeeldie 111
                                       67777666689*****************99999999999.66666888889999999999******99999999999 PP

                                       .........................HHHHCCHHCTT-HHHHHHHHHCTTSEEEEHHHHH CS
                     UvrD-helicase  68 .........................alkkaeqessdderlrlalqnlseanisTlHsfc 101
                                                                ++ + +q  +  e+lr al+ ++++ +  +H+++
  gi|313126643|ref|YP_004036913.1| 112 vdvrhgdttqyqrqkqandppdvlvTTPETLQAMLTGEKLRTALSDVRHVVVDEVHELA 170
                                       99998887777666666666666665555555555666888888888888888888776 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011       0.2      57      99 ..     812     859 ..     741     864 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       TTT-EEEEEEE--EEEETTTS-EEECHH...HHH....S-TTTSSS-EEE CS
                              HypA  57 legaeLeieevpvkvrCreCgkefelee...kal....rCpkCgsadvei 99 
                                       ++  + +i++ +v ++C +C  ++++++   + +    +Cp+Cg+++v +
  gi|313126643|ref|YP_004036913.1| 812 IQAIKERIQNDRVILQCLHCT-DWKTTRkvrR-VrdqpECPECGATRVAC 859
                                       4445556999999*******9.5554432431.14445*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (948 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.88u 0.32s 00:00:01.20 Elapsed: 00:00:00.54
# Mc/sec: 5303.29
//
Query:       gi|313126644|ref|YP_004036914.1|  [L=236]
Description: methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-09   37.6   0.2    3.8e-09   37.1   0.2    1.2  1  Methyltransf_11  Methyltransferase domain
      6e-09   36.5   0.3      9e-09   35.9   0.3    1.3  1  Methyltransf_25  Methyltransferase domain
    7.3e-06   25.8   0.0    9.4e-06   25.5   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
     0.0031   17.4   0.0     0.0038   17.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.021   15.6   0.0      0.029   15.1   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
      0.026   14.1   0.1      0.035   13.6   0.1    1.2  1  MTS              Methyltransferase small domain
      0.043   13.9   0.0      0.053   13.6   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
       0.21   11.6   0.0       0.32   11.0   0.0    1.2  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.2   1.7e-12   3.8e-09       1      93 [.      64     153 ..      64     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.7e-12
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-... CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv... 74 
                                       +dvGcG+G +a+ +++rg +vv++D s+ ++++a+++++++       vad+   p++d+ f   +++ +  ++   
  gi|313126644|ref|YP_004036914.1|  64 VDVGCGAGNHARVVQNRG-DVVAFDASPMAVRTARARGVDA------FVADMFAPPVADDGFETALVNGTQATLaqs 133
                                       59*************888.***************9999887......79********************88888777 PP

                                       .CCHHHHHHHHHHHEEEEEE CS
                   Methyltransf_11  75 .edpekalkeiaRvLkpgGl 93 
                                        ++++++l e+aRv    G 
  gi|313126644|ref|YP_004036914.1| 134 eAERRDFLCELARVTTATGE 153
                                       78************998886 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.3     4e-12     9e-09       2      97 .]      64     152 ..      63     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 4e-12
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG. CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh. 76 
                                       +d+GcG G++++ +++r   ++v+++D s+ ++++ar+r       v+  ++d+ + p +d+ f   +++g+   + 
  gi|313126644|ref|YP_004036914.1|  64 VDVGCGAGNHARVVQNR---GDVVAFDASPMAVRTARARG------VDAFVADMFAPPVADDGFETALVNGTqATLa 131
                                       6**************99...6******************9......9**********************98876665 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                        s+++++++l e+arv++  G
  gi|313126644|ref|YP_004036914.1| 132 QSEAERRDFLCELARVTTATG 152
                                       6788999*********98766 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   4.2e-09   9.4e-06       6     113 ..      62     160 ..      58     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.2e-09
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       +++D+GCG+G+ + +       +++vv +D s+ a++ Ar++        v   ++d+++ +  ++d+ f   l n+
  gi|313126644|ref|YP_004036914.1|  62 PLVDVGCGAGNHARVVQ----NRGDVVAFDASPMAVRTARAR-------GVDAFVADMFAPP--VADDGFETALVNG 125
                                       689**********9999....4689****************8.......77899********..99**********7 PP

                   Methyltransf_31  83 vl....naladpdkileeiervlkpggilliedpr 113
                                       +     +  a+  ++l e+ rv +  g+  i++++
  gi|313126644|ref|YP_004036914.1| 126 TQatlaQSEAERRDFLCELARVTTATGEAWIDSYD 160
                                       76555777788888999999999999999998887 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.7e-06    0.0038      22      62 ..      59     120 ..      29     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......................k 62 
                                        +  ++d+GcG G+ ++v  +n+ +v+++D+sp+av  a+                      +
  gi|313126644|ref|YP_004036914.1|  59 LRTPLVDVGCGAGNHARVV-QNRGDVVAFDASPMAVRTARargvdafvadmfappvaddgfeT 120
                                       455689***********98.5667*************99888766666666665555555541 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.3e-05     0.029       1      39 [.      64      99 ..      64     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakek 39
                                      +++GcG G+ +r++ ++    ++++ D sp a+  a+++
  gi|313126644|ref|YP_004036914.1| 64 VDVGCGAGNHARVVQNR---GDVVAFDASPMAVRTARAR 99
                                      69************999...*************555544 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.6e-05     0.035      31      73 ..      59      98 ..      50     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                      TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHH CS
                               MTS 31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesake 73
                                      l+  ++D+GcGaG  + +++++    +v+++d++ +A++ a++
  gi|313126644|ref|YP_004036914.1| 59 LRTPLVDVGCGAGNHARVVQNRG---DVVAFDASPMAVRTARA 98
                                      445689*******9888777644...489**********9986 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.4e-05     0.053      23      77 ..      61     115 ..      37     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                                       -EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS....HHH.TTEEEECS-CCCSSHHH CS
                              FtsJ  23 ktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm....apl.pgvttiqgditdpetie 77 
                                       +  vD+g++ G+ + v+ +r    g vva+D  pm    a +  gv  + +d + p +++
  gi|313126644|ref|YP_004036914.1|  61 TPLVDVGCGAGNHARVVQNR----GDVVAFDASPMavrtA-RaRGVDAFVADMFAPPVAD 115
                                       458**************999....46*********65533.2589999999999887776 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.32      27      70 ..      61      99 ..      50     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                   Methyltransf_32 27 ltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekr 70
                                      + +vDvG+G g  ++v++      +  vv++da+   v++a++r
  gi|313126644|ref|YP_004036914.1| 61 TPLVDVGCGAGNHARVVQN-----RGDVVAFDASPMAVRTARAR 99
                                      679**************99.....79*********999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1341.34
//
Query:       gi|313126645|ref|YP_004036915.1|  [L=718]
Description: ATPase AAA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-93  309.0   0.0      4e-46  156.7   0.0    2.4  2  AAA              ATPase family associated with various cellul
      2e-26   91.5   8.0    2.2e-13   49.8   0.2    2.6  2  AAA_lid_3        AAA+ lid domain
    3.1e-23   81.7   0.6    1.2e-22   79.9   0.7    2.1  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.6e-14   54.0   0.1    1.5e-05   24.8   0.0    3.6  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.6e-13   51.2   0.0    6.7e-06   26.3   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.1e-13   51.0   3.8    3.9e-05   24.1   0.0    4.1  2  AAA_16           AAA ATPase domain
    2.9e-12   47.0   0.0    3.5e-05   24.0   0.0    2.8  2  AAA_33           AAA domain
    1.3e-10   41.4   0.7     0.0019   18.2   0.2    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
    3.2e-10   40.1   0.0    0.00049   20.1   0.0    2.6  2  AAA_14           AAA domain
    1.5e-09   37.5   0.0    0.00047   19.5   0.0    2.4  2  TIP49            TIP49 P-loop domain
      6e-09   36.3   0.9      0.017   15.4   0.0    3.8  3  AAA_22           AAA domain
    8.8e-07   28.8   0.0      0.042   13.6   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    1.6e-06   28.0   0.0       0.11   12.2   0.0    3.7  3  Sigma54_activat  Sigma-54 interaction domain
    1.8e-06   27.5   0.4      0.064   12.6   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      2e-06   28.1   0.0      0.032   14.5   0.0    3.0  2  AAA_28           AAA domain
    2.5e-06   28.0   0.0      0.099   13.2   0.0    2.9  2  AAA_18           AAA domain
    5.3e-06   27.0   0.0      0.055   14.0   0.0    2.5  2  ABC_tran         ABC transporter
    6.1e-06   26.6   0.0      0.089   13.2   0.0    2.8  2  RNA_helicase     RNA helicase
      7e-06   25.7   1.8    1.8e-05   24.4   0.1    2.6  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.1e-05   25.3   0.0      0.099   12.5   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    1.4e-05   25.0   0.0       0.14   11.9   0.0    2.3  2  AAA_11           AAA domain
    1.6e-05   24.9   0.0       0.15   12.1   0.0    2.3  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      2e-05   24.5   0.2       0.66    9.8   0.0    3.3  3  CPT              Chloramphenicol phosphotransferase-like prot
    2.3e-05   24.2   0.1       0.32   10.7   0.0    2.7  2  AAA_30           AAA domain
    3.2e-05   23.3   0.0       0.31   10.3   0.0    2.6  2  Zeta_toxin       Zeta toxin
    3.5e-05   23.8   0.8       0.43   10.5   0.0    3.5  3  NACHT            NACHT domain
    4.5e-05   23.0   0.0      0.039   13.5   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
    8.2e-05   23.0   0.0       0.72   10.2   0.0    2.7  2  AAA_19           AAA domain
    0.00011   21.6   0.0        0.2   10.9   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00012   22.2   0.0       0.79    9.8   0.0    3.4  3  Sigma54_activ_2  Sigma-54 interaction domain
    0.00019   20.7   0.0       0.53    9.3   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00019   21.0   0.2       0.58    9.6   0.1    2.4  2  PhoH             PhoH-like protein
    0.00034   20.4   0.0        1.3    8.7   0.0    2.9  3  AAA_24           AAA domain
    0.00046   20.6   0.0       0.73   10.3   0.0    2.9  2  AAA_17           AAA domain
     0.0007   18.9   0.0        1.2    8.2   0.0    2.3  2  NB-ARC           NB-ARC domain
    0.00092   18.6   0.0        1.3    8.4   0.0    2.9  3  ATPase           KaiC
     0.0022   17.9   0.0        4.5    7.2   0.0    3.7  3  NTPase_1         NTPase
     0.0022   17.2   0.0        2.2    7.4   0.0    2.8  2  DUF815           Protein of unknown function (DUF815)
     0.0063   16.3   0.0        3.2    7.4   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0085   16.2   0.0        5.9    7.0   0.0    2.4  2  Torsin           Torsin
     0.0093   15.7   0.1        2.4    7.9   0.0    2.8  2  Cytidylate_kin   Cytidylate kinase
  ------ inclusion threshold ------
      0.014   15.7   0.8       0.98    9.7   0.1    2.5  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.017   15.1   0.0        6.4    6.6   0.0    2.2  2  Rad17            Rad17 P-loop domain
      0.017   14.7   8.8        1.3    8.6   0.1    4.1  4  AAA_25           AAA domain
      0.023   14.8   0.0       0.89    9.7   0.0    2.5  2  Cytidylate_kin2  Cytidylate kinase-like family
       0.03   14.5   0.1          7    6.8   0.1    2.5  2  SKI              Shikimate kinase
      0.042   13.9   0.0        7.6    6.5   0.0    2.7  3  ResIII           Type III restriction enzyme, res subunit
      0.048   12.8   0.0        3.9    6.5   0.0    2.2  2  DAP3             Mitochondrial ribosomal death-associated pro
      0.053   12.4   0.0        8.9    5.1   0.0    2.3  2  AFG1_ATPase      AFG1-like ATPase
       0.12   11.7   0.0         20    4.5   0.0    2.9  2  TniB             Bacterial TniB protein
       0.13   11.9   0.0        9.2    5.9   0.0    3.1  3  Zot              Zonular occludens toxin (Zot)
       0.15   11.9   0.0         15    5.4   0.0    3.0  2  ATPase_2         ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.7   0.0   1.2e-48     4e-46       1     131 [.     230     358 ..     230     359 .. 0.98
   2 !  150.0   0.0   1.4e-46   4.7e-44       1     131 [.     496     627 ..     496     628 .. 0.97

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 1.2e-48
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKTl+akava+e++++f++isg+e++sk+ gese+k+re f+ea+++a p i+f+DEid++a++r ++
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDATFITISGPEIMSKFKGESEEKLREKFEEARTNA-PAIIFFDEIDSIATKR-DD 304
                                       79******************************************************9.****************.89 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                         ++e+rvv qLl+ +dg++ + ++vivigatnr+d+ldpal+r gRfdr+iei+
  gi|313126645|ref|YP_004036915.1| 305 GGDVENRVVGQLLSLMDGLDAR-GDVIVIGATNRVDSLDPALRRgGRFDREIEIG 358
                                       99*******************7.66***************************996 PP

  == domain 2  score: 150.0 bits;  conditional E-value: 1.4e-46
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       vll+GppGtGKTlla+a+a e++v+f+ + g+ell+ yvgesek++re+f++a++ a p i+f+DEida+a++r   
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGESEVNFIHVAGPELLDRYVGESEKSVREVFERARQAA-PAIVFFDEIDAIATNRdaM 571
                                       79******************************************************9.****************999 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       gs+s+++ervv+qLlteld++ ++  +v+v++atnr ++ldpallr gR+++++ ++
  gi|313126645|ref|YP_004036915.1| 572 GSDSGVGERVVSQLLTELDRLVDN-PNVVVLAATNRKETLDPALLRpGRLESHVLVP 627
                                       99*******************996.66*************************99876 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.2   6.2e-16   2.2e-13       1      43 [.     381     434 ..     381     436 .. 0.76
   2 !   44.3   2.7   3.3e-14   1.1e-11       1      45 []     650     708 ..     650     708 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 6.2e-16
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr...........gikeitmedf 43 
                                       dvd ++LA+rT+G++GADl++l +eAa+ Alrr           ++ e++ e+f
  gi|313126645|ref|YP_004036915.1| 381 DVDMDRLAARTHGFVGADLESLAKEAAMTALRRarrgggesvsfTELEVSRENF 434
                                       9********************************444444444322334555555 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 3.3e-14
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr..............gikeitmedfee 45 
                                       +vdl+eLA+ ++G SGAD++a+cr A ++A++               ++  +t+e+fe+
  gi|313126645|ref|YP_004036915.1| 650 NVDLDELAAHMDGLSGADIQAVCRDATMRAIEAiadayegaaanehaDEILVTQEHFEA 708
                                       7******************************55444555555544334446******95 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.7   3.5e-25   1.2e-22       2      84 ..       9      90 ..       8      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 3.5e-25
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      L+V+ a+++d+grgi+r+ +++ ++lg+ +gd+v +eg+r+Tva+vwpa+  ++ +g++ +d+ tR+na+++iG++V+V
  gi|313126645|ref|YP_004036915.1|  9 LTVRGAEKRDAGRGIARLPESARQRLGVLSGDTVVVEGSRETVAKVWPADGGTP-DGVVLIDADTRANADAKIGETVHV 86
                                      99************************************************9977.************************ PP

                                      EEE- CS
                           CDC48_N 81 rkae 84
                                      rk++
  gi|313126645|ref|YP_004036915.1| 87 RKVD 90
                                      **97 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   4.3e-08   1.5e-05      35      72 ..     229     266 ..     220     304 .. 0.73
   2 !   22.9   0.0   1.7e-07   5.8e-05      34      69 ..     494     529 ..     484     571 .. 0.73
   3 ?    1.3   0.0      0.73   2.5e+02      14      38 ..     591     615 ..     584     620 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.3e-08
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvleka 72 
                                        vll+GpPG Gkt +ak +a+e+++++ + sgP +  +
  gi|313126645|ref|YP_004036915.1| 229 GVLLHGPPGTGKTLIAKAVATEVDATFITISGPEIMSK 266
                                       69*******************************98643 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.7e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                         vll+GpPG Gkt la+ ia e +v++ + +gP l
  gi|313126645|ref|YP_004036915.1| 494 SGVLLHGPPGTGKTLLARAIAGESEVNFIHVAGPEL 529
                                       569*******************************76 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.73
                            RuvB_N  14 kvkeklkifieaakkreealdhvll 38 
                                       ++ ++ ++++ aa +r+e+ld  ll
  gi|313126645|ref|YP_004036915.1| 591 RLVDNPNVVVLAATNRKETLDPALL 615
                                       56678899*************9988 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.9e-08   6.7e-06       6     105 ..     230     322 ..     225     328 .. 0.79
   2 !   22.3   0.0   3.4e-07   0.00012       5     101 ..     495     587 ..     491     599 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                       +ll gp g+Gkt++aka+a   ++    ++i++   e++   + +   ++ + ++    + +   i+++DEid i+ 
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDA----TFITISGPEIMS--KFKGESEEKLREKFEEARTNAPAIIFFDEIDSIAT 300
                                       6899******************96....************..44444334444444444455556************ PP

                                       ----------HHHHHHHHHHHH- CS
                             AAA_2  83 kessgadvSregVqrdLLqileg 105
                                       k+  g dv +  V+  LL +++g
  gi|313126645|ref|YP_004036915.1| 301 KRDDGGDVENR-VVGQLLSLMDG 322
                                       99999999775.77788999997 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3.4e-07
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                        +ll gp g+Gkt+la+a+a   +v    ++i +   ell     + + ++++  ++   +a +    iv++DEid 
  gi|313126645|ref|YP_004036915.1| 495 GVLLHGPPGTGKTLLARAIAGESEV----NFIHVAGPELLD----RYVGESEKSVREVFERARQAApaIVFFDEIDA 563
                                       57899*****************998....***********9....66666666667777777777688********* PP

                                       ----.--------.-HHHHHHHHH CS
                             AAA_2  80 ihpk.essgadvS.regVqrdLLq 101
                                       i+ + + +g+d   +e V+  LL 
  gi|313126645|ref|YP_004036915.1| 564 IATNrDAMGSDSGvGERVVSQLLT 587
                                       ***886666554325666666664 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.1e-07   3.9e-05      24     141 ..     226     332 ..     197     345 .. 0.71
   2 !   23.1   1.4   2.3e-07   7.9e-05      15      55 ..     484     521 ..     480     714 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.1e-07
                            AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawre 99 
                                       p   vll+G++G+GK+ +++++++++ ++   f++    +      +s   +  ++e+l ++ +++ ++a +  + +
  gi|313126645|ref|YP_004036915.1| 226 PpKGVLLHGPPGTGKTLIAKAVATEVDAT---FITISGPEI-----MS-KFKGESEEKLREKFEEARTNAPAIIFFD 293
                                       2589*******************999988...666666666.....22.4455557688888877777767777777 PP

                            AAA_16 100 kleealaavpelagaeasrllellkrllallsrderplvlvl 141
                                       ++++ ++  +++ g+ ++r+  +l +l++ l  +++  v+v+
  gi|313126645|ref|YP_004036915.1| 294 EIDSIAT-KRDDGGDVENRVVGQLLSLMDGLDARGD--VIVI 332
                                       7766666.6777777779999999999988877666..4444 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 2.3e-07
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggif 55 
                                       ++e+++++ p+ vll+G++G+GK+ l+r+++ + e +   f
  gi|313126645|ref|YP_004036915.1| 484 LFEAANTSPPSGVLLHGPPGTGKTLLARAIAGESEVN---F 521
                                       7888999999******************999544433...3 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.4e-06   0.00049       2      47 ..     230     290 ..     230     394 .. 0.76
   2 !   24.0   0.0     1e-07   3.5e-05       2      50 ..     496     546 ..     496     650 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.4e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.............d 47 
                                       vll+G+pG+GK+  a+ ++ + +  ++++s ++++++ +g+ +++++              
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDatFITISGPEIMSKFKGESEEKLRekfeeartnapaiI 290
                                       799****************99999999*********9999766665533434444444440 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdytr 50 
                                       vll+G+pG+GK+ la+ ++ +    +++++ ++l++r++g+ ++s ++  +
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGESEvnFIHVAGPELLDRYVGESEKSVREVFE 546
                                       799******************99*****************87777664333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.7e-06    0.0023       1      77 [.     229     298 ..     229     348 .. 0.74
   2 !   18.2   0.2   5.4e-06    0.0019       1     133 [.     495     613 ..     495     616 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.7e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ +a+ +a  + +++ ++ +++ ++  ++kg+ e ++ ++++++       r   ++i+++DE++
  gi|313126645|ref|YP_004036915.1| 229 GVLLHGPPGTGKTLIAKAVATEVDATFITISGPEIMS--KFKGESE-EKLREKFEEA------RtnAPAIIFFDEID 296
                                       59****************************9999886..4777777.2223333222......12377888888887 PP

                                       G- CS
                             AAA_5  76 ra 77 
                                        +
  gi|313126645|ref|YP_004036915.1| 297 SI 298
                                       55 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 5.4e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +vlL GppGtgK+ la+ +a   + ++  v++++      l+ r+   ++ ++ v  ++ ra +  ++i+++DE++ 
  gi|313126645|ref|YP_004036915.1| 495 GVLLHGPPGTGKTLLARAIAGESEVNFIHVAGPE------LLDRYV--GESEKSVREVFERARQaAPAIVFFDEIDA 563
                                       59******************99999999999987......888888..45555555666655558899999999998 PP

                                       --..HHHHHHHHHHHHSSEEE...-SSSEEE---......-EEEEEESS--.-TT-TTHH CS
                             AAA_5  77 ae..sevlnsLlslleerrllle.eggelvkaknddllerfrviatanpldrslnelspa 133
                                       +   +++++s   + e+   +l  e+++lv+ +n      + v+a++n+ +     l+pa
  gi|313126645|ref|YP_004036915.1| 564 IAtnRDAMGSDSGVGERVVSQLLtELDRLVDNPN------VVVLAATNRKE----TLDPA 613
                                       7644666666655555554444313333333333......66666666666....55555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.4e-06   0.00049       5     106 ..     230     340 ..     227     357 .. 0.77
   2 !   17.1   0.0   1.2e-05    0.0042       5      92 ..     496     597 ..     494     625 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla.dpekllelileklkeekktylflDEiqev.... 76 
                                       +++ G+  +GKT ++k ++ e       ++ i+  +   k +   +ekl e + e  ++    ++f+DEi  +    
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVD---ATFITISGPEIMSKFKGeSEEKLREKFEEARTN-APAIIFFDEIDSIatkr 302
                                       7899*************998777...888888877765533331344777888886544.899**********9999 PP

                            AAA_14  77 .......pewekalkslvd..egknldvivtGSnsklls 106
                                              +++   l sl+d  +  ++dviv G  + + s
  gi|313126645|ref|YP_004036915.1| 303 ddggdveNRVVGQLLSLMDglD-ARGDVIVIGATNRVDS 340
                                       9999999889999999999533.5889999998877765 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.2e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT l++ ++ e+     +++ ++  +  d+   ++ek  ++++e++++    ++f+DEi  +     
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGESE---VNFIHVAGPELLDRYVGESEKSVREVFERARQAAPAIVFFDEIDAIatnrd 569
                                       6899***************9988...778888777777776666666677777775556899**********88888 PP

                            AAA_14  77 .............pewekalkslvdegkn 92 
                                                    +++ + l +lvd+  n
  gi|313126645|ref|YP_004036915.1| 570 amgsdsgvgervvSQLLTELDRLVDNP-N 597
                                       888888888888878888888888877.5 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.4e-06   0.00047      51      92 ..     228     267 ..     226     283 .. 0.83
   2 !   15.4   0.0   2.4e-05    0.0084      52      97 ..     495     538 ..     488     551 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysle 92 
                                       ++vLl Gp+gtGkt +a a++ e+     f+++sg e+ s  
  gi|313126645|ref|YP_004036915.1| 228 KGVLLHGPPGTGKTLIAKAVATEVD--ATFITISGPEIMSKF 267
                                       89*********************97..78*********9964 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       +vLl Gp+gtGkt la ai+ e  ++v f++++g e+    v  +e
  gi|313126645|ref|YP_004036915.1| 495 GVLLHGPPGTGKTLLARAIAGE--SEVNFIHVAGPELLDRYVGESE 538
                                       79******************98..57*********99776665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   6.5e-05     0.023       8      43 ..     230     256 ..     225     340 .. 0.81
   2 !   15.4   0.0   4.9e-05     0.017       8      43 ..     496     530 ..     490     553 .. 0.69
   3 ?   -0.3   0.0       3.6   1.2e+03      84     117 ..     547     594 ..     529     606 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.5e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                                       ++++G++GtGKT+ ++ ++ + d         ++++
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVD---------ATFI 256
                                       689***************99984.........3333 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.9e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                                       ++++G++GtGKT+l+r ++ +  e++++  ++pe++
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGES-EVNFIHVAGPELL 530
                                       689**************99886.3444444555555 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.6
                            AAA_22  84 qalraravielliiDEaqhlr.......s.........eealeeLrslln 117
                                       +a  ++a ++++  DE++ +        s          ++l+eL +l++
  gi|313126645|ref|YP_004036915.1| 547 RAR-QAA-PAIVFFDEIDAIAtnrdamgSdsgvgervvSQLLTELDRLVD 594
                                       333.333.479999****99766544431556666677777777766666 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00023     0.078      48      70 ..     228     250 ..     221     305 .. 0.79
   2 !   13.6   0.0   0.00012     0.042      48      70 ..     494     516 ..     462     562 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                       ++++l Gp+G+GK+ +a a+++e
  gi|313126645|ref|YP_004036915.1| 228 KGVLLHGPPGTGKTLIAKAVATE 250
                                       6799**************99876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00012
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                        +++l Gp+G+GK+ la a++ e
  gi|313126645|ref|YP_004036915.1| 494 SGVLLHGPPGTGKTLLARAIAGE 516
                                       5799***************9865 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1    0.0012       0.4      23      46 ..     228     251 ..     219     302 .. 0.87
   2 !   12.2   0.0   0.00033      0.11      22      47 ..     493     518 ..     481     528 .. 0.82
   3 ?   -0.3   0.0       2.2   7.7e+02      30      59 ..     574     603 ..     537     615 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                                       S-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheas 46 
                                         vl++G  GtGK+l+a+a+ ++ 
  gi|313126645|ref|YP_004036915.1| 228 KGVLLHGPPGTGKTLIAKAVATEV 251
                                       579***************997654 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00033
                                       SS-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheask 47 
                                       ++ vl++G  GtGK+llarai  +s+
  gi|313126645|ref|YP_004036915.1| 493 PSGVLLHGPPGTGKTLLARAIAGESE 518
                                       378*****************987765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.2
                                       STTSSHHHHHHHHHHHSTTTTS-EEEEETT CS
                   Sigma54_activat  30 esGtGKellaraiheaskrkekpfvavnca 59 
                                       +sG+G  ++++++ e  +  ++p v v  a
  gi|313126645|ref|YP_004036915.1| 574 DSGVGERVVSQLLTELDRLVDNPNVVVLAA 603
                                       466666666666666666666655555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00018     0.064      25      43 ..     230     248 ..     225     273 .. 0.92
   2 !   12.4   0.1   0.00022     0.076      25      43 ..     496     514 ..     490     516 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt++ak+++
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVA 248
                                       79**************986 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00022
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt+la++++
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIA 514
                                       79*************9986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0018      0.63       2      39 ..     230     272 ..     229     302 .. 0.69
   2 !   14.5   0.0   9.2e-05     0.032       2      49 ..     496     544 ..     495     576 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0018
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekl 39 
                                       + + G+++tGKT +++a a +     +++  pE++ ++  e  
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEvdatFITISgPEIMSKFKGESE 272
                                       6799***************665332333336666665544444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 9.2e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaareileeklakgedalpwv 49 
                                       + + G+++tGKT l++a+a + +++ +    pE   +++ e      +  ++v
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGEsEVNFIhvagPELLDRYVGESE----KSVREV 544
                                       6799***************554444440036666666654444....333333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00077      0.27       1      66 [.     230     322 ..     230     362 .. 0.62
   2 !   13.2   0.0   0.00029     0.099       1      44 [.     496     537 ..     496     607 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00077
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe.........aldesk 50 
                                       +ll G+pG+GKt +ak+++ +  +                   ++lr+ + e ++  +   +         + d+  
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVdATfitisgpeimskfkgesEEKLREKFEEARTNAPAIIFfdeidsiatKRDDGG 306
                                       7899**************88742224555555555555555533333333333333333333333444455555555 PP

                            AAA_18  51 rldedkldklldalee 66 
                                        ++  ++ +ll+++++
  gi|313126645|ref|YP_004036915.1| 307 DVENRVVGQLLSLMDG 322
                                       5555555555555555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00029
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                       +ll G+pG+GKt la++++ +    vn ++va  + l  +v + 
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGES--EVNFIHVAGPELLDRYVGES 537
                                       7899**************7765..67777766655554444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0     0.002      0.69       7      50 ..     223     264 ..     220     322 .. 0.77
   2 !   14.0   0.0   0.00016     0.055      14      73 ..     496     554 ..     489     667 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.002
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlk 50 
                                        + + + v + G+ G+GK+ ++k++a +++ t  +i   g ++ 
  gi|313126645|ref|YP_004036915.1| 223 GVDPPKGVLLHGPPGTGKTLIAKAVATEVDATFITI--SGPEIM 264
                                       566777899*******************98754444..444444 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00016
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpe 73 
                                       v + G+ G+GK+ L++++ag+++     i++ g +l ++   +++k+++ +++   q  p 
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGESE--VNFIHVAGPELLDRYVGESEKSVREVFERaRQAAPA 554
                                       7899*****************97..578888999999977777788877777774444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00026     0.089       1      36 [.     230     265 ..     230     304 .. 0.78
   2 !   10.5   0.0    0.0018      0.61       1      21 [.     496     516 ..     496     568 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00026
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++l+Gp+g+GK+++ak +a+++  ++ +++ ++++s
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDATFITISGPEIMS 265
                                       689*****************9998885555555544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0018
                      RNA_helicase   1 iwlyGpsgeGKStlakeLaka 21 
                                       ++l+Gp+g+GK++la+ +a +
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGE 516
                                       689*************95543 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       5.1   1.8e+03      41      53 ..      54      72 ..      36      74 .. 0.54
   2 !   24.4   0.1   5.2e-08   1.8e-05       8      59 ..     115     165 ..     109     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.1
                                      ECCCC......SCEEECTS CS
                           CDC48_2 41 tePkg......pvgitetT 53
                                      + P++      +v i+ +T
  gi|313126645|ref|YP_004036915.1| 54 VWPADggtpdgVVLIDADT 72
                                      4444444444488888777 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 5.2e-08
                                       HHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEES CS
                           CDC48_2   8 aylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgt 59 
                                       + +kr++++rp+  G +++fe +  + ++v+ +t+P g v++t +T  +l +
  gi|313126645|ref|YP_004036915.1| 115 ELIKRAIQDRPIQSGGQIRFESL-SADPFVISETSPDGMVRVTSSTRLKLAK 165
                                       489*******************8.689*******************988765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00029     0.099       2      30 ..     230     258 ..     229     298 .. 0.91
   2 !   10.4   0.0    0.0013      0.44       2      37 ..     496     530 ..     495     608 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00029
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++ktl++ka+a+ +d++f  i
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDATFITI 258
                                       89*********************999766 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0013
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdll 37 
                                       vll+g PG++ktll++a+a   +++f  +   p+ll
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGESEVNFIHVA-GPELL 530
                                       89*****************99999997774.45555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00094      0.33      20      38 ..     230     248 ..     207     286 .. 0.78
   2 !   11.9   0.0   0.00041      0.14      19      72 ..     495     546 ..     483     556 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00094
                            AAA_11  20 tliqGPPGtgKTktivell 38 
                                       +l++GPPGtgKT    ++ 
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVA 248
                                       79**********6554444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00041
                            AAA_11  19 itliqGPPGtgKTktivellsqllsrrkseeeksakpriL..vCapSNaAvDelle 72 
                                        +l++GPPGtgKT    ++  +     + +  + a+p++L  + ++S+++v e+ e
  gi|313126645|ref|YP_004036915.1| 495 GVLLHGPPGTGKTLLARAIAGES----EVNFIHVAGPELLdrYVGESEKSVREVFE 546
                                       479**********8877777666....33344555555554455555555555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0016      0.54      20      51 ..     228     261 ..     204     275 .. 0.79
   2 !   12.1   0.0   0.00042      0.15      21      51 ..     495     527 ..     466     541 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0016
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       + +lL+G+ G+GKT +++++a +++ +  +++ P
  gi|313126645|ref|YP_004036915.1| 228 KGVLLHGPPGTGKTLIAKAVATEVDATfiTISGP 261
                                       449*******************998876556555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00042
                                       EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        +lL+G+ G+GKT l+r++a + +v+  +v  P
  gi|313126645|ref|YP_004036915.1| 495 GVLLHGPPGTGKTLLARAIAGESEVNfiHVAGP 527
                                       49******************9999986677666 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0021      0.72       4      37 ..     230     263 ..     228     318 .. 0.86
   2 !    9.8   0.0    0.0019      0.66       4      42 ..     496     534 ..     494     585 .. 0.83
   3 ?    0.4   0.3       1.5   5.1e+02      64     104 ..     672     711 ..     643     717 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0021
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDaf 37 
                                       +lL+G + +GK+ +a+a+ + +d++++ +   + 
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDATFITISGPEI 263
                                       89************************99876555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0019
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS- CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafvealp 42 
                                       +lL+G + +GK+ lara+   ++  ++h++  +++++  
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGESEVNFIHVAGPELLDRYV 534
                                       89**************************99777776654 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHHTT-EEEEEE--TTTHHHHHHHHH CS
                               CPT  64 eldlllaalyeavaamaraGnnvivDdvilekewlvdllrr 104
                                        +d++++a+     a+  a +n  +D++++++e+   +l +
  gi|313126645|ref|YP_004036915.1| 672 CRDATMRAIEAIADAYEGAAANEHADEILVTQEHFEAAL-D 711
                                       234444444444446666778889999999999855444.4 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0011      0.38      20      42 ..     229     251 ..     217     264 .. 0.80
   2 !   10.7   0.0   0.00093      0.32      10      39 ..     485     514 ..     482     526 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                            AAA_30  20 vavltGpAGtGKttalkalreaw 42 
                                        ++l+Gp+GtGKt + ka++  +
  gi|313126645|ref|YP_004036915.1| 229 GVLLHGPPGTGKTLIAKAVATEV 251
                                       5789*************997654 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00093
                            AAA_30  10 vealltsgdrvavltGpAGtGKttalkalr 39 
                                       +ea+ ts+   ++l+Gp+GtGKt + +a++
  gi|313126645|ref|YP_004036915.1| 485 FEAANTSPPSGVLLHGPPGTGKTLLARAIA 514
                                       6777788888899***********999986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0     0.001      0.35      15      50 ..     226     259 ..     219     278 .. 0.87
   2 !   10.3   0.0   0.00089      0.31      14      51 ..     491     526 ..     483     548 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.001
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                        Pk +ll G pG GK+ +a+++++e+  +  +++++
  gi|313126645|ref|YP_004036915.1| 226 PPKGVLLHGPPGTGKTLIAKAVATEV--DATFITIS 259
                                       5999*********************9..66666665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00089
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       + P  +ll G pG GK+ la++++ e   + n++++ +
  gi|313126645|ref|YP_004036915.1| 491 SPPSGVLLHGPPGTGKTLLARAIAGES--EVNFIHVAG 526
                                       568899********************8..899999865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1     0.008       2.8       3      24 ..     230     251 ..     228     254 .. 0.89
   2 !   10.5   0.0    0.0013      0.43       3      21 ..     496     514 ..     494     520 .. 0.91
   3 ?    1.6   0.0      0.65   2.2e+02      61     114 ..     533     591 ..     527     633 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.008
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l+G++G GKT  ++ +a++ 
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEV 251
                                       79**************999875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                                       EEEEC-TTTCHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                       v+l+G++G GKT L++ +a
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIA 514
                                       79**************998 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.65
                                       CCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH...............HHHHHC CS
                             NACHT  61 qlpepaapvsevwavllelperlLlilDglDelvtdlgq......kekqpvrtlLselir 114
                                          e+++ v+e + ++++++  +   +D +D ++t  ++       +++ v +lL+el r
  gi|313126645|ref|YP_004036915.1| 533 YVGESEKSVRE-VFERARQAAPAIVFFDEIDAIATNRDAmgsdsgVGERVVSQLLTELDR 591
                                       55678888888.55678888888899*********8888996666555555555555544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00011     0.039      29      63 ..     223     256 ..     215     286 .. 0.83
   2 !    7.2   0.0    0.0096       3.3      35      54 ..     495     514 ..     487     525 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                             AAA_7  29 llknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                                        ++  k vll Gp GtGKt+i+k + +++d  +++
  gi|313126645|ref|YP_004036915.1| 223 GVDPPKGVLLHGPPGTGKTLIAKAVATEVD-ATFI 256
                                       5666789*****************999999.4444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0096
                             AAA_7  35 pvllvGptGtGKtviikdll 54 
                                        vll Gp GtGKt++++ + 
  gi|313126645|ref|YP_004036915.1| 495 GVLLHGPPGTGKTLLARAIA 514
                                       59************998765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0021      0.72      11      62 ..     228     279 ..     224     343 .. 0.79
   2 !    9.9   0.0    0.0025      0.85       3      30 ..     486     513 ..     485     568 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0021
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62 
                                       k +l+ ++pGtGKT + k++ +++ ++      + ++  f g + ++lre+ 
  gi|313126645|ref|YP_004036915.1| 228 KGVLLHGPPGTGKTLIAKAVATEVDATFITISGPEIMSKFKGESEEKLREKF 279
                                       56899*********99988877776655444455555666666666666666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0025
                            AAA_19   3 eavealkekvllvtaGpGtGKTrvlkhi 30 
                                       ea+++++ + +l+ ++pGtGKT + ++i
  gi|313126645|ref|YP_004036915.1| 486 EAANTSPPSGVLLHGPPGTGKTLLARAI 513
                                       57778899999***********887766 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00058       0.2       4      25 ..     230     251 ..     227     303 .. 0.75
   2 !    8.5   0.0     0.003         1       4      25 ..     496     517 ..     494     567 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00058
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl +G +GtGKt+++ ++++e+
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEV 251
                                       6889***************999 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl +G +GtGKt+++ +++ e 
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGES 517
                                       6789***********9999887 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.021       7.3      24      44 ..     230     250 ..     225     302 .. 0.69
   2 !    9.8   0.0    0.0023      0.79      22      80 ..     494     563 ..     484     571 .. 0.59
   3 ?    1.1   0.0       1.1   3.8e+02      29      68 ..     574     613 ..     570     621 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.021
                                       EEEEEETT--HHHHHHCC--T CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhkn 44 
                                       v+l G++G+gk+l+A++ + +
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATE 250
                                       9***************98754 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0023
                                       S-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..........HHHHHH...TTTSEEEEEE-TT CS
                   Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhknsgpwleifvverlaklp..........ldlleq...akggtLylkdiad 80 
                                       + v+l G++G+gk+l Ar+++ +s+ +   +   +l               +++e+   a +++ ++ +i+ 
  gi|313126645|ref|YP_004036915.1| 494 SGVLLHGPPGTGKTLLARAIAGESEVNFIHVAGPELL--DryvgeseksvREVFERarqAAPAIVFFDEIDA 563
                                       569*****************98877543221111111..111222222335555553334677777777765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.1
                                       ETT--HHHHHHCC--TTS-EE--SSTTHHHH-HHHHHHHT CS
                   Sigma54_activ_2  29 ekGsgkelvArlLhknsgpwleifvverlaklpldlleqa 68 
                                       + G g  +v++lL + +  ++++ vv   a+  +++l+ a
  gi|313126645|ref|YP_004036915.1| 574 DSGVGERVVSQLLTELDRLVDNPNVVVLAATNRKETLDPA 613
                                       6799****************99999977777888888765 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0     0.002      0.69     117     139 ..     230     252 ..     225     256 .. 0.90
   2 !    9.3   0.0    0.0015      0.53     117     136 ..     496     515 ..     480     525 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavp 139
                                       v+++Gp+ tGkt +a+a a+ v+
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVD 252
                                       789***************99876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v+++Gp+ tGkt la+aIa 
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAG 515
                                       899***************95 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0017      0.58      22      42 ..     230     250 ..     225     257 .. 0.87
   2 !    8.8   0.0     0.003         1      22      40 ..     496     514 ..     489     520 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt++a a+a e
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATE 250
                                       5678***********999976 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.003
                                       EEEE--TTSSTTHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavala 40 
                                       v   Gp GtGKt+la a+a
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIA 514
                                       5678***********9988 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0039       1.3       5      28 ..     230     255 ..     227     304 .. 0.65
   2 !    8.2   0.0    0.0055       1.9       5      23 ..     496     516 ..     493     571 .. 0.77
   3 ?   -1.3   0.0       4.5   1.6e+03     111     135 ..     582     608 ..     576     613 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0039
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplf 28 
                                       +l+ Gp+g+GKT +ak    + ++ f
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVatEVDATF 255
                                       799************98855444444 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0055
                            AAA_24   5 iliyGpsgiGKTtlakel..g 23 
                                       +l+ Gp+g+GKT la+ +  +
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIagE 516
                                       789************988653 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.5
                            AAA_24 111 frrllkklqelrk..nvifiahektrk 135
                                       +++ll+ l+ l +  nv++ a +  ++
  gi|313126645|ref|YP_004036915.1| 582 VSQLLTELDRLVDnpNVVVLAATNRKE 608
                                       6899999******99999999887665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0021      0.73       2      51 ..     234     284 ..     233     309 .. 0.76
   2 ?    7.2   0.0     0.018       6.3       2      30 ..     500     530 ..     499     571 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0021
                                       E-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHH CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklpl 51 
                                       G+PG GK+ +++ ++ +++ t+++  G  +++  k ++ +k r++++++  
  gi|313126645|ref|YP_004036915.1| 234 GPPGTGKTLIAKAVATEVDATFITIsGPEIMSKFKGESEEKLREKFEEART 284
                                       9*****************999987657788888877776777777766554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.018
                                       E-TTSSHHHHHHHHH..HHHTEEEEEHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklv..ekygfthlsaGdll 30 
                                       G+PG GK+ +++ ++   +++f h+   +ll
  gi|313126645|ref|YP_004036915.1| 500 GPPGTGKTLLARAIAgeSEVNFIHVAGPELL 530
                                       9*************94445689998765555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0036       1.2      23      44 ..     230     251 ..     217     257 .. 0.83
   2 !    8.1   0.0     0.004       1.4      23      46 ..     496     518 ..     485     523 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0036
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l+G +G GKt +ak +  + 
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEV 251
                                       789*************998875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.004
                                       EEEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksde 46 
                                       v l+G +G GKt la+ i  + +e
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGE-SE 518
                                       779*************99887.44 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0037       1.3      19      38 ..     227     246 ..     195     320 .. 0.85
   2 ?   -2.7   0.0         9   3.1e+03      70     139 ..     395     471 ..     384     479 .. 0.59
   3 !    7.0   0.0    0.0097       3.3      22      37 ..     496     511 ..     492     524 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0037
                            ATPase  19 grvvlitGepGtGKtifalq 38 
                                        + vl+ G pGtGKt++a+ 
  gi|313126645|ref|YP_004036915.1| 227 PKGVLLHGPPGTGKTLIAKA 246
                                       56799***********9975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9
                            ATPase  70 lGwdlekleeegklaiidasesaeesaee.....kdkedleelieela.eaikeika..krvviDsitglayeekea 138
                                       +G dle l +e  ++ +  ++ + +++ +      ++e+ e  +++++ +a++e+ a    +  D ++gl +e+k  
  gi|313126645|ref|YP_004036915.1| 395 VGADLESLAKEAAMTALRRARRGGGESVSfteleVSRENFETAMASVEpSAMREYVAeaPTTTFDDVGGL-EEAKRT 470
                                       5777777777766666665555555444456555445555544444432566776653345677777777.666555 PP

                            ATPase 139 v 139
                                       +
  gi|313126645|ref|YP_004036915.1| 471 L 471
                                       5 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0097
                            ATPase  22 vlitGepGtGKtifal 37 
                                       vl+ G pGtGKt++a 
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLAR 511
                                       899***********96 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.013       4.5       2      32 ..     230     260 ..     229     295 .. 0.89
   2 ?    1.5   0.0      0.73   2.5e+02      63     119 ..     416     476 ..     389     483 .. 0.71
   3 ?    4.5   0.0     0.084        29       2      30 ..     496     524 ..     495     529 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + k v+ +++   ++++G
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDATFITISG 260
                                       6789**************9999887777776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.73
                                       TT---SSEETTEEE-HHHHHHHHHH....HHHHHHHHH-EEEE---STTGGG-HHHHHHHH CS
                          NTPase_1  63 veakreprvgkyvvdvesfeelale....alrkalseadviviDEiGkmElkskkfkeave 119
                                       +++ +++++ +  v  e+fe+ +++    a+r+ + ea     D +G +E   ++++++v+
  gi|313126645|ref|YP_004036915.1| 416 RGGGESVSFTELEVSRENFETAMASvepsAMREYVAEAPTTTFDDVGGLEEAKRTLERSVT 476
                                       33677777788888888888776651111456666888899**********9999999886 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.084
                                       EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                       v++ GppG+GKt l + ++ + + + ++v
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGESEVNFIHV 524
                                       6789*********9999987766555555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.011       3.7      52      82 ..     226     256 ..     213     335 .. 0.87
   2 !    7.4   0.0    0.0063       2.2      18      80 ..     449     520 ..     434     565 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegL 82 
                                       p + vLL G  GtGK  + ka+ +e+ ++ +
  gi|313126645|ref|YP_004036915.1| 226 PPKGVLLHGPPGTGKTLIAKAVATEVDATFI 256
                                       6678*******************99987665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0063
                            DUF815  18 pveevdevklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaee 80 
                                        v+e+ ++++dd+ g+++ k++l + ++         + ++  p + vLL G  GtGK  l +a+  e + +
  gi|313126645|ref|YP_004036915.1| 449 YVAEAPTTTFDDVGGLEEAKRTLERSVTwpltyaplfEAANTSPPSGVLLHGPPGTGKTLLARAIAGESEVN 520
                                       56777777888888888888888877652221111112244556678*****************98876554 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.018       6.2       2      71 ..     231     295 ..     230     299 .. 0.72
   2 !    7.4   0.0    0.0094       3.2       2      71 ..     497     561 ..     496     566 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk...pklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       + hG pG GK+ + + ++ +      +  t++ ++      ++++ ++ +  ++f++a+++     i+++DE+
  gi|313126645|ref|YP_004036915.1| 231 LLHGPPGTGKTLIAKAVATE------VDATFITISGPEimsKFKGESEEKLREKFEEARTNA--PAIIFFDEI 295
                                       68********9977777766......444444444433666677777777778899998876..789999997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0094
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       + hG pG GK+ l r ++ +s +++ +++   ell + + +++++  + ++ + +a+       i+++DE+
  gi|313126645|ref|YP_004036915.1| 497 LLHGPPGTGKTLLARAIAGESeVNF-IHVAGPELLDRYVGESEKSVREVFERARQAA-----PAIVFFDEI 561
                                       68******************97444.3444478888888666666555555544444.....359999997 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.017       5.9      56      76 ..     230     250 ..     216     266 .. 0.84
   2 ?    6.5   0.0     0.024       8.4      53      75 ..     493     515 ..     483     522 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.017
                                       EEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaen 76 
                                       + +hG +GtGk  +a+ +a +
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATE 250
                                       458*************99875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.024
                                       -EEEEEEE-TTSSHHHHHHHHHH CS
                            Torsin  53 pLvlsfhGwtGtGknfvaeiiae 75 
                                       p  + +hG +GtGk  +a+ ia 
  gi|313126645|ref|YP_004036915.1| 493 PSGVLLHGPPGTGKTLLARAIAG 515
                                       555679*************9985 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0068       2.4       3      27 ..     232     256 ..     230     260 .. 0.90
   2 ?    4.9   0.0     0.056        19       3      28 ..     498     523 ..     496     526 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0068
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+a+a++++++++
  gi|313126645|ref|YP_004036915.1| 232 LHGPPGTGKTLIAKAVATEVDATFI 256
                                       68******************99997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.056
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g+GK  +ara+a + +++++ 
  gi|313126645|ref|YP_004036915.1| 498 LHGPPGTGKTLLARAIAGESEVNFIH 523
                                       68***************999988875 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0028      0.98       2      30 ..     230     258 ..     229     265 .. 0.93
   2 ?    4.0   0.1      0.15        53       2      22 ..     496     516 ..     495     525 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0028
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++hG+P +GKt +a ++a + +a ++ti
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDATFITI 258
                                       689***********************999 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.15
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakk 22 
                                       +++hG+P +GKt  a ++a +
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGE 516
                                       689**********99999865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.019       6.4      48     114 ..     230     297 ..     221     310 .. 0.76
   2 ?    6.0   0.0      0.03        10      48     122 ..     496     571 ..     483     587 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.019
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkeleL 114
                                       +L+ GP+G gk+ + k ++ e    ++  + p  + + +   ++ ++ ++e   +  + i  f e+  
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDATFITISGPEIMSKFKGeSEEKLREKFEEARTNAPAIIFFDEIDS 297
                                       6899*****************99999999998775544432556667777776666777777777755 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.03
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslke.pdnqksdfkgltekesrflsqiesfkeleLkdakylkl 122
                                       +L+ GP+G gk+   + ++ e  +++++   p +l       ++ ++ ++e   +  + i  f e+   +++   +
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAIAGESEVNFIHVAGPELLDRyVGESEKSVREVFERARQAAPAIVFFDEIDAIATNRDAM 571
                                       6899************************999998854145578888999999888899999999998888877555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0037       1.3      36      97 ..     230     286 ..     224     344 .. 0.59
   2 ?    6.9   0.1     0.012       4.1      36      53 ..     496     513 ..     493     516 .. 0.86
   3 ?    1.5   0.2      0.57     2e+02     129     185 ..     540     602 ..     518     608 .. 0.77
   4 ?   -0.6   0.2       2.4   8.4e+02      74     173 ..     598     681 ..     587     709 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0037
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds.edelrrRlravgeal 97 
                                       +ll G+pgtGKt +a  +a +v     +     +  g+ ++  + +  e+ lr++++++++++
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEVDA--TFI----TISGPEIMSKFKGEsEEKLREKFEEARTNA 286
                                       689***********9888877742..122....245555555554443345666666666655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll G+pgtGKt la  +
  gi|313126645|ref|YP_004036915.1| 496 VLLHGPPGTGKTLLARAI 513
                                       689***********9665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.57
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralgg.densnsd......vgalvealeriarrtgaavll 185
                                        v+++ +++++ + ++ v +D ++++  + d   ++       v++l++ l+r+ ++ ++ vl+
  gi|313126645|ref|YP_004036915.1| 540 SVREVFERARQ-AAPAIVFFDEIDAIATNrDAMGSDSgvgervVSQLLTELDRLVDNPNVVVLA 602
                                       57788889999.569*********9777744444444677775588888889988888888775 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.4
                            AAA_25  74 VlyvsaEdsedelrrRlravg...eal.....rddarllvldlagveslpLfakdrggtlltadvdaleaaieeveg 142
                                       V++++a ++ ++l + l + g    ++     + dar ++l ++++ + pL +        + d+d+l+a+++   g
  gi|313126645|ref|YP_004036915.1| 598 VVVLAATNRKETLDPALLRPGrleSHVlvpqpDVDARRAILEVHTK-EKPLGD--------NVDLDELAAHMDGLSG 665
                                       5555555555555555554332223335555555566666665554.334432........2333333333333322 PP

                            AAA_25 143 ..vrlvviDplsralggdensnsdvgalveale 173
                                         ++ v+ D                     a+e
  gi|313126645|ref|YP_004036915.1| 666 adIQAVCRDATM-----------------RAIE 681
                                       223333333333.................3333 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0026      0.89       8      55 ..     236     284 ..     232     332 .. 0.87
   2 ?    2.2   0.0       0.5   1.7e+02       8      80 ..     502     580 ..     498     603 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0026
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersr 55 
                                        G+g++ i++a+A++    f+    +e ++k +g see++ e+++e+++
  gi|313126645|ref|YP_004036915.1| 236 PGTGKTLIAKAVATEVDATFITISGPEIMSKFKGESEEKLrEKFEEART 284
                                       69**************************************999999444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.5
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydr...eiieevakelglseeev.eevdersrlssflskllaarvagdtl..dekld 78 
                                        G+g++ +++a+A + +++f+     e++++ + e++ s  ev e++ +++++  f++++ a     d +  d+   
  gi|313126645|ref|YP_004036915.1| 502 PGTGKTLLARAIAGESEVNFIHVagpELLDRYVGESEKSVREVfERARQAAPAIVFFDEIDAIATNRDAMgsDSGVG 578
                                       699*************9999998333555555555544444444555544444444444444433333334444444 PP

                   Cytidylate_kin2  79 de 80 
                                       ++
  gi|313126645|ref|YP_004036915.1| 579 ER 580
                                       44 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1      0.02         7       1      40 [.     236     276 ..     236     285 .. 0.73
   2 ?    5.2   0.0     0.059        20       1      42 [.     502     548 ..     502     552 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.02
                                       TTSSHHHHHHHHHHHHTSEEEEHHH.HHHHHHTS-HHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDe.liekrtgksiaeife 40 
                                       +G+GK+ ++k++A +++ +fi +   +i  +++ + +e ++
  gi|313126645|ref|YP_004036915.1| 236 PGTGKTLIAKAVATEVDATFITISGpEIMSKFKGESEEKLR 276
                                       69******************987433555555555555555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.059
                                       TTSSHHHHHHHHHHHHTSEEEEH......HHHHHHHHTS-HHHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl......Deliekrtgksiaeifeee 42 
                                       +G+GK+ +++++A + +++fi +      D+++ + ++ s++e+fe+ 
  gi|313126645|ref|YP_004036915.1| 502 PGTGKTLLARAIAGESEVNFIHVagpellDRYVGESEK-SVREVFERA 548
                                       69******************986442222555544444.788888765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.022       7.6      24      48 ..     227     251 ..     202     285 .. 0.85
   2 ?   -1.6   0.0         7   2.4e+03     122     140 ..     268     294 ..     250     301 .. 0.61
   3 ?    4.0   0.0      0.13        46      26      45 ..     495     514 ..     455     543 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.022
                                       TSEEEEEESTTSTHHHHHHHHHHHH CS
                            ResIII  24 dkrglikmaTGtGKTlvaaklierl 48 
                                        k +l++ + GtGKTl+a +++ ++
  gi|313126645|ref|YP_004036915.1| 227 PKGVLLHGPPGTGKTLIAKAVATEV 251
                                       577899***********98777665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7
                                       .....HHHTTT-S........EEEEET CS
                            ResIII 122 eeeseellrdrfd........viiiDE 140
                                       + esee+lr++f+        +i++DE
  gi|313126645|ref|YP_004036915.1| 268 KGESEEKLREKFEeartnapaIIFFDE 294
                                       344444444444444455556999999 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.13
                                       EEEEEESTTSTHHHHHHHHH CS
                            ResIII  26 rglikmaTGtGKTlvaakli 45 
                                        +l++ + GtGKTl+a +++
  gi|313126645|ref|YP_004036915.1| 495 GVLLHGPPGTGKTLLARAIA 514
                                       678999********997665 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.067        23      24      59 ..     228     262 ..     221     279 .. 0.71
   2 ?    6.5   0.0     0.011       3.9      15      57 ..     485     524 ..     470     532 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.067
                                       -EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES- CS
                              DAP3  24 krlvltGekgsGKSvlLlqalayAlekgwvvlhvpe 59 
                                       k ++l+G +g+GK++ +++a+a  +++ ++ ++ pe
  gi|313126645|ref|YP_004036915.1| 228 KGVLLHGPPGTGKTL-IAKAVATEVDATFITISGPE 262
                                       5589*********96.46666655555555554444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                                       TTS-SSS---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEE CS
                              DAP3  15 kkadkkkkvkrlvltGekgsGKSvlLlqalayAlekgwvvlhv 57 
                                        +a ++++   ++l+G +g+GK++l + a+  A e+++  +hv
  gi|313126645|ref|YP_004036915.1| 485 FEAANTSPPSGVLLHGPPGTGKTLL-ARAI--AGESEVNFIHV 524
                                       56678999999***********975.4444..44555555555 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.033        11      59      78 ..     224     243 ..     217     254 .. 0.87
   2 ?    5.1   0.0     0.026       8.9      57      78 ..     488     509 ..     445     514 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.033
                       AFG1_ATPase  59 vepvrglYlwGgvGrGKtyl 78 
                                       v p++g+ l+G+ G GKt +
  gi|313126645|ref|YP_004036915.1| 224 VDPPKGVLLHGPPGTGKTLI 243
                                       579***************87 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.026
                       AFG1_ATPase  57 ksvepvrglYlwGgvGrGKtyl 78 
                                        ++ p+ g+ l+G+ G GKt l
  gi|313126645|ref|YP_004036915.1| 488 ANTSPPSGVLLHGPPGTGKTLL 509
                                       3678****************88 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.059        20      33      56 ..     225     248 ..     216     256 .. 0.80
   2 ?    3.6   0.0      0.11        38      26      54 ..     484     512 ..     479     521 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.059
                              TniB  33 krmpnlllvGdsnnGKtmivekFa 56 
                                       + ++ +ll+G++ +GKt i++  a
  gi|313126645|ref|YP_004036915.1| 225 DPPKGVLLHGPPGTGKTLIAKAVA 248
                                       556889*************98765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivek 54 
                                       L+e+++ + ++ +ll+G++ +GKt +++ 
  gi|313126645|ref|YP_004036915.1| 484 LFEAANTSPPSGVLLHGPPGTGKTLLARA 512
                                       566677777889************99876 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.027       9.2       4      62 ..     231     294 ..     230     311 .. 0.76
   2 ?    0.7   0.0         1   3.4e+02       4      17 ..     497     510 ..     495     514 .. 0.87
   3 ?    0.2   0.0       1.4   4.9e+02      64      98 ..     536     570 ..     520     617 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.027
                               Zot   4 lvtGapGsgKts..gavkkdllp.alk..egRkiitnidGlrlerieqvlgekvs.tarliridn 62 
                                       l +G+pG+gKt+  +av  ++   +    +g +i+ + +G   e+++  ++e+ + ++ +i+ d+
  gi|313126645|ref|YP_004036915.1| 231 LLHGPPGTGKTLiaKAVATEVDAtF-ItiSGPEIMSKFKGESEEKLREKFEEARTnAPAIIFFDE 294
                                       679********72256877776643.335799999999999999999999988888888988773 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
                               Zot   4 lvtGapGsgKtsga 17 
                                       l +G+pG+gKt+ a
  gi|313126645|ref|YP_004036915.1| 497 LLHGPPGTGKTLLA 510
                                       789********976 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.4
                               Zot  64 egaetlkefakwatidkgallviDEcqeifpvrak 98 
                                       e+++ + e++ +a+ +  a++++DE   i  +r +
  gi|313126645|ref|YP_004036915.1| 536 ESEKSVREVFERARQAAPAIVFFDEIDAIATNRDA 570
                                       667778888899998899*******9988777665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.28        95      23      74 ..     230     280 ..     220     332 .. 0.56
   2 ?    5.4   0.0     0.045        15      13      45 ..     486     518 ..     483     600 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.28
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeee 74 
                                       +++ Gp g GKt + k ++++  d  +  i   ++ +++  + +e+++e+ e
  gi|313126645|ref|YP_004036915.1| 230 VLLHGPPGTGKTLIAKAVATEV-DATFITISGPEIMSKFKGESEEKLREKFE 280
                                       6778999999987777777766.33443333222222222222222222222 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.045
                          ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienle 45 
                                       e ++++p + +++ Gp g GKt L + i+ ++e
  gi|313126645|ref|YP_004036915.1| 486 EAANTSPPSGVLLHGPPGTGKTLLARAIAGESE 518
                                       5677888888999**********9999988773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              52  [number of targets reported over threshold]
# CPU time: 0.85u 0.36s 00:00:01.21 Elapsed: 00:00:00.56
# Mc/sec: 3857.41
//
Query:       gi|313126646|ref|YP_004036916.1|  [L=45]
Description: hypothetical protein Hbor_19040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.038   14.4   0.0       0.04   14.3   0.0    1.1  1  DUF4379    Probable Zinc-ribbon domain
      0.039   13.8   0.3      0.066   13.0   0.3    1.5  1  zf-C2H2_3  zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.5e-06      0.04      21      53 ..       3      35 ..       1      37 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-06
                           DUF4379 21 tpgskkkvwW.kCakCgheWeasvsnrtkgsskC 53
                                      + ++k  + W +C++Cg  + ++++  t++++ C
  gi|313126646|ref|YP_004036916.1|  3 STTQKDDAEWfRCEECGLLFDSEIDATTHERN-C 35
                                      556666665559****************8877.9 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   7.4e-06     0.066       8      39 ..       6      36 ..       2      37 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.4e-06
                         zf-C2H2_3  8 qksfga.sqCkeCgMvYnpgspeDeklHkkfHa 39
                                      qk+  +  +C eCg+++  +s+ D+ +H++ ++
  gi|313126646|ref|YP_004036916.1|  6 QKDDAEwFRCEECGLLF--DSEIDATTHERNCD 36
                                      555444456******98..78999****99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 288.07
//
Query:       gi|313126647|ref|YP_004036917.1|  [L=76]
Description: hypothetical protein Hbor_19050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.30s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 503.45
//
Query:       gi|313126648|ref|YP_004036918.1|  [L=142]
Description: hypothetical protein Hbor_19060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0055   16.5   0.0     0.0096   15.7   0.0    1.4  1  KTSC      KTSC domain


Domain annotation for each model (and alignments):
>> KTSC  KTSC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.4e-07    0.0096      18      49 ..      22      53 ..      16      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.4e-07
                                      EEEETTTEEEEEES--HHHHHHHHH-S-HHHH CS
                              KTSC 18 eieFkngsvyqYsgVpeevyeallsAeSkgsy 49
                                      ++e+ +g++  Y+gVpe v   l +A+ k ++
  gi|313126648|ref|YP_004036918.1| 22 QVEYTDGRTTLYHGVPETVTGTLTTAPGKETH 53
                                      8*************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 860.01
//
Query:       gi|313126649|ref|YP_004036919.1|  [L=146]
Description: acyl dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-19   67.9   0.0    6.8e-19   67.6   0.0    1.1  1  MaoC_dehydratas  MaoC like domain
    2.4e-08   34.2   0.1    3.9e-08   33.5   0.1    1.3  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
  ------ inclusion threshold ------
      0.039   13.6   0.0      0.045   13.4   0.0    1.2  1  FabA             FabA-like domain
      0.098   13.0   0.0       0.18   12.2   0.0    1.4  1  DUF296           Plants and Prokaryotes Conserved (PCC) domai


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.0   1.5e-22   6.8e-19       7     119 ..      10     123 ..       6     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1.5e-22
                                       TSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTT..EGGGEEEE CS
                   MaoC_dehydratas   7 gekvetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdn..vvarvgei 81 
                                       g+++e+  e t+te++i  +a+   D +p H+d e+ +++ fgg +a+G++t+ +  +l +e ++++   +   g +
  gi|313126649|ref|YP_004036919.1|  10 GDTFEA-GETTLTEDEITSFAG-EYDPQPFHLDHEAGEESMFGGLVASGLHTYCTCNRLATEAFFSRvaFMGGRGVD 84 
                                       666677.7899***********.*******************************************9776788899* PP

                                       EEEE-S--BTTCEEEEEEEEEEEEEEE.EEEEEEEEEEE CS
                   MaoC_dehydratas  82 kvrFtkpVlpgdtlkvelevvgkrdvr.ktkkvevtkev 119
                                       ++r+++pV+pgdtl + +ev++kr  + +   + v++ v
  gi|313126649|ref|YP_004036919.1|  85 ELRWQRPVRPGDTLSAAVEVTEKRVSEsNPERGYVNVDV 123
                                       **********************99988666666555555 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   8.8e-12   3.9e-08       2     131 ..       8     135 ..       7     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 8.8e-12
                   MaoC_dehydrat_N   2 liGaefepvkaevereavrefakavgetnpayldeeaaraagyrsliaP..ptflivlatkapellealgidlsrll 76 
                                       ++G  fe  +++++++++ +fa    +++p +ld ea +++ +++l+a    t+ ++   + + +++ +   + r +
  gi|313126649|ref|YP_004036919.1|   8 AVGDTFEAGETTLTEDEITSFAGE-YDPQPFHLDHEAGEESMFGGLVASglHTYCTCNRLATEAFFSRVAFMGGRGV 83 
                                       58999****************976.4799*******************72256666555444359999998888754 PP

                   MaoC_dehydrat_N  77 hgeqefeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                           e+++++p+r+GD+l+   ++++ ++ +++ +  ++ v+ t +n++Ge v t
  gi|313126649|ref|YP_004036919.1|  84 ---DELRWQRPVRPGDTLSAAVEVTEKRVSESNPERGYVNVDVTGMNAEGETVIT 135
                                       ...79***************************99999***************987 PP

>> FabA  FabA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     1e-05     0.045      81     134 ..      76     133 ..      40     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                                       -EEEEEEECEEEE-S---TT-.EEEEEEEEEEE....EECCTCEEEEEEEEE.ETTEEE CS
                              FabA  81 klvlfagvdevkfrgqvtPgdkklvleveikkv....seekrviiiadaell.vdgklv 134
                                       + +   gvde +++++v+Pgd +l+  ve+++     s+ +r+++ +d++ + ++g++v
  gi|313126649|ref|YP_004036919.1|  76 AFMGGRGVDELRWQRPVRPGD-TLSAAVEVTEKrvseSNPERGYVNVDVTGMnAEGETV 133
                                       3444569**************.9998888876433555556677777766441455555 PP

>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.1e-05      0.18      52     101 ..      20      66 ..       4      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.1e-05
                                       -S-EEEEEEEEEEEETTEEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEE CS
                            DUF296  52 lgrfeilslsGtilpdglHlhvslagedgqvvgGhlaegplvaattvevv 101
                                       l + ei+s+ G + p+   +h     ++++++gG +a+g l ++ t+   
  gi|313126649|ref|YP_004036919.1|  20 LTEDEITSFAGEYDPQP--FHLDHEAGEESMFGGLVASG-LHTYCTCNRL 66 
                                       45679**********98..6666666668********99.8888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 936.02
//
Query:       gi|313126650|ref|YP_004036920.1|  [L=299]
Description: shikimate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-12   47.1   1.4      2e-12   47.1   1.4    2.1  2  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.042   14.2   0.1       0.12   12.7   0.1    1.8  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   1.4   2.3e-16     2e-12       2      66 .]      78     146 ..      77     146 .. 0.92
   2 ?   -3.6   0.2       1.5   1.4e+04       8      19 ..     231     242 ..     228     251 .. 0.64

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.3e-16
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEH.H.HH.HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallgls.l.ee.aklaleaerlaqggngsggDv.aasvyGg 66 
                                       ++++s++P++aGL SS+A+a a+v+A +++lg++   ee  +l+++a r ++++ ++ +D+ +as++Gg
  gi|313126650|ref|YP_004036920.1|  78 VRTESDVPMAAGLKSSSAAANATVLATADALGVEpDrEEaCRLGVQAARDVGVTITGAFDDaSASMLGG 146
                                       6789****************************99645558********************999999998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.5
                                       SHTTSSSCHHHH CS
                    GHMP_kinases_N   8 iPvgaGLGSSAA 19 
                                       +P++aG + S++
  gi|313126650|ref|YP_004036920.1| 231 MPHAAGVSLSGT 242
                                       577777666654 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.4e-05      0.12      38      73 ..     226     257 ..     217     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                    GHMP_kinases_C  38 elleal.selGalgaklsGaGgGptvfalfkdkdeae 73 
                                        ++ea+  ++G   ++lsG+  Gp+v+a+++  ++a 
  gi|313126650|ref|YP_004036920.1| 226 PAVEAMpHAAG---VSLSGT--GPSVVAVAERGSAAH 257
                                       56777755666...999999..*******96666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1873.31
//
Query:       gi|313126651|ref|YP_004036921.1|  [L=106]
Description: chorismate mutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-14   53.0   3.7    3.9e-14   52.7   3.7    1.1  1  CM_2            Chorismate mutase type II
  ------ inclusion threshold ------
      0.045   13.6   1.7       0.11   12.4   1.7    1.6  1  Pox_A_type_inc  Viral A-type inclusion protein repeat


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   3.7   4.4e-18   3.9e-14       1      72 [.      25     100 ..      25     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4.4e-18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHHH CS
                              CM_2   1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasra 72 
                                       R+eI +iD+e++eL+a+R  +a+ v+++K e++lp  d+++e+ v+er  e+a    +d++ +++ifr +i+  + 
  gi|313126651|ref|YP_004036921.1|  25 RDEIADIDRELVELIARRTYVADTVARVKDERDLPTTDESQEEVVMERAGENAerfdVDSNLVKAIFRLLIELNKV 100
                                       99*************************************************77788899************98765 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.7   1.2e-05      0.11       2      17 ..      20      35 ..      19      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                    Pox_A_type_inc  2 EmsrlRsRIsDLErqL 17
                                      ++++lR++I D++r+L
  gi|313126651|ref|YP_004036921.1| 20 SLDELRDEIADIDREL 35
                                      589************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 664.71
//
Query:       gi|313126652|ref|YP_004036922.1|  [L=59]
Description: hypothetical protein Hbor_19100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0071   16.5   0.2     0.0071   16.5   0.2    1.0  1  DUF3792   Protein of unknown function (DUF3792)
  ------ inclusion threshold ------
      0.055   14.2   0.5       0.06   14.1   0.5    1.1  1  PrgI      PrgI family protein
       0.11   11.5   6.8       0.13   11.2   6.8    1.0  1  MtrC      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   1.2e-06    0.0071       9      59 ..       5      55 ..       1      59 [] 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-06
                           DUF3792  9 llialvitlilllilalllyftslsekvlsililiililsvfigGflagkk 59
                                      l++++ i+++l  + + + + ++lse+++ ++  ++ ++ v++gG+ +g++
  gi|313126652|ref|YP_004036922.1|  5 LAVGVGIVVALAGVASTMTTGGELSEAIMWVVFAMVPAAIVALGGIPSGYS 55
                                      789999***************************************988876 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5     1e-05      0.06      24      69 ..       9      54 ..       2      58 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                              PrgI 24 flvlallvaiglylllrafleelasvlvillavPvaalgfyk.kdgl 69
                                      + ++++l++++  + + + l+e+ +++v +++vP+a++++   ++g+
  gi|313126652|ref|YP_004036922.1|  9 VGIVVALAGVASTMTTGGELSEAIMWVV-FAMVPAAIVALGGiPSGY 54
                                      4455556688888888888855555555.7799*8888765335555 PP

>> MtrC  Tetrahydromethanopterin S-methyltransferase, subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   6.8   2.3e-05      0.13      79     120 ..       5      47 ..       3      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.3e-05
                              MtrC  79 lalgmGivaalaglavgsalkl.lagpiialvvaliiglvvgv 120
                                       la+g+Giv alag+a + ++   l  +i+ +v+a++ +++v++
  gi|313126652|ref|YP_004036922.1|   5 LAVGVGIVVALAGVASTMTTGGeLSEAIMWVVFAMVPAAIVAL 47 
                                       799************99988879*************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 398.09
//
Query:       gi|313126653|ref|YP_004036923.1|  [L=266]
Description: 5'-nucleotidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-44  150.3   0.2    6.4e-44  150.1   0.2    1.1  1  SurE      Survival protein SurE


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.1   0.2   3.6e-48   6.4e-44       1     190 [.       7     193 ..       7     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 150.1 bits;  conditional E-value: 3.6e-48
                                       EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHH CS
                              SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvkla 77 
                                       iLltNDDGie+ g ral+ea+ +  ++v+ vaP++++S++g+++  ++ + v+     e+e  ya++GtPadc+ ++
  gi|313126653|ref|YP_004036923.1|   7 ILLTNDDGIESTGFRALYEAFDQ-FADVTAVAPAADQSAVGRKM--SNDVDVT-----EHELGYAIDGTPADCTVVG 75 
                                       8*********************6.56******************..4444432.....56899************** PP

                                       HHTTTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSS......SS-SSS---HHHHHH CS
                              SurE  78 leellkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskk......eeekkeedtfeaaak 147
                                       le+l+++   d+Vv+G+N+GaN+g+ v   SGTv+Aa+eaa+ ++pa+AvSl +        +e++++  ++++aa+
  gi|313126653|ref|YP_004036923.1|  76 LEALCPD--VDMVVAGCNKGANIGAYVlGRSGTVSAAVEAAFFDVPAMAVSLYVPPggdvpwTEKADDIADYRHAAD 150
                                       *****86..6*****************999**********************9988999998555556666999999 PP

                                       HHHHHHTTETTS-...SS-EEEEEEESS.GCG-SEEEE-B--C CS
                              SurE 148 vaaklveklieklllekvellnvNvPeleeeeikgvkvtrlgr 190
                                        a+ l+++  e+ ++e++e+lnvN P  + ++ + +++t+ ++
  gi|313126653|ref|YP_004036923.1| 151 AATYLAKNAPEAGVFEEAEYLNVNAPMPNGQDPAPIEITTPSK 193
                                       9999*****999**************77777777788887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1827.23
//
Query:       gi|313126654|ref|YP_004036924.1|  [L=479]
Description: methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-07   32.5   0.0    2.6e-07   31.3   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    4.2e-07   30.0   0.0    8.3e-07   29.0   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    1.7e-05   24.3   0.0    2.7e-05   23.6   0.0    1.2  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
    4.4e-05   23.3   0.0    7.8e-05   22.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00027   21.6   0.0    0.00067   20.3   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    0.00066   20.3   0.0     0.0019   18.8   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
        0.2   11.4   0.2        4.8    6.9   0.0    2.7  3  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0     1e-10   2.6e-07       1      98 [.     165     268 ..     165     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1e-10
                   Methyltransf_12   1 LeiGcGtGsllrallekl...pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg....ssfDlv 70 
                                       L++G+GtG  +  l ++l   + +ey++v++s+sa    ++ l++ + n+ + v+ e+ +++d ++     + fDlv
  gi|313126654|ref|YP_004036924.1| 165 LDVGAGTGGPALGLHDYLpenSLVEYHAVEPSASAD-VLEAMLSETRSNFKTTVHRETAEAFDPASVlpdgEGFDLV 240
                                       8*******987766666666699*************.7888888888888778877777777766668899****** PP

                   Methyltransf_12  71 vasnvlhhlkdirevldnirklLkpgGr 98 
                                         +nvl+ l+d+ +v ++  + ++++G 
  gi|313126654|ref|YP_004036924.1| 241 CFANVLSELDDPTSVAERYLDYVADDGS 268
                                       ******************9999999986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   3.2e-10   8.3e-07      20     120 ..     158     274 ..     134     324 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.2e-10
                   Methyltransf_23  20 lraggrvLdiGcGtGillevl....rengf.svtgvDlspeaveiae...kakkaqkdqfdeqeaae........pq 80 
                                       l++  rvLd+G+GtG  +  l     en   ++ +v++s  a  + +   +++ ++k+ ++++ a+         + 
  gi|313126654|ref|YP_004036924.1| 158 LPRVLRVLDVGAGTGGPALGLhdylPENSLvEYHAVEPSASADVLEAmlsETRSNFKTTVHRETAEAfdpasvlpDG 234
                                       56777**********65544511113343359999999976555544999444444444444433333444555355 PP

                   Methyltransf_23  81 gkfdlIvlrevlehvpdppellrqiatllkpgGylllsep 120
                                       + fdl++  +vl  ++dp+++  +  ++++++G ++   p
  gi|313126654|ref|YP_004036924.1| 235 EGFDLVCFANVLSELDDPTSVAERYLDYVADDGSFVGIAP 274
                                       5********************************9987665 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.1e-08   2.7e-05       2     118 ..     128     251 ..     127     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.1e-08
                             Rsm22   2 eesiaYalarlpatyavlrrvLdelaervpdflPkslldvgegpgtalwaaselwe..eleevlvidaseelleisk 76 
                                       e+++ Y ++ lp  ya++  vLd laer    +   +ldvg+g+g   +  ++  +  +l e+  ++ s+++  +  
  gi|313126654|ref|YP_004036924.1| 128 EAALGYGIYHLPDYYAAVGYVLDGLAERGLLPRVLRVLDVGAGTGGPALGLHDYLPenSLVEYHAVEPSASADVLEA 204
                                       56789**********************9877777899********99999999988677899*************** PP

                             Rsm22  77 elaadapelkeaalrrs.virealeleea....dLviisyvLleled 118
                                        l +   + k++ +r++    + + + ++    dLv  + vL el d
  gi|313126654|ref|YP_004036924.1| 205 MLSETRSNFKTTVHRETaEAFDPASVLPDgegfDLVCFANVLSELDD 251
                                       ****99999998665541445667777779***************88 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     3e-08   7.8e-05       5     111 ..     162     273 ..     160     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3e-08
                   Methyltransf_31   5 lrvlDlGCGtGeltfelae..elgpkaevvGiD..iseeaielArenaqklgldnveFeqgdieelekl.led.ekf 75 
                                       lrvlD+G+GtG  ++ l++    ++  e++ ++   s++++e + +++++++ + v+ e +++++ + + l d e f
  gi|313126654|ref|YP_004036924.1| 162 LRVLDVGAGTGGPALGLHDylPENSLVEYHAVEpsASADVLEAMLSETRSNFKTTVHRETAEAFD-PASvLPDgEGF 237
                                       68*****************5533445679999933456779999999999998888888888888.44557778*** PP

                   Methyltransf_31  76 Dlilsnevlnaladpdkileeiervlkpggillied 111
                                       Dl++  +vl  l dp ++ e+  +++ ++g ++   
  gi|313126654|ref|YP_004036924.1| 238 DLVCFANVLSELDDPTSVAERYLDYVADDGSFVGIA 273
                                       ******************************998555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.6e-07   0.00067       1      87 [.     164     257 ..     164     267 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.6e-07
                                       EEEET-TTSHHHHHHHCTS..T.SSEEEEEESSHHH..HHHHHHHHHHTTTTEEEEESBCCGBS.....SSTTTEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl..g.kakvtgvDiseem..leaareraeeeglnvefvqgdaedlp.....fedgsfDl 67 
                                       vLd+G+GtG  +l l++ l  +   ++++v++s+++  lea+ ++ + ++++ ++++  ae+++      + + fDl
  gi|313126654|ref|YP_004036924.1| 164 VLDVGAGTGGPALGLHDYLpeNsLVEYHAVEPSASAdvLEAMLSETR-SNFKTTVHRETAEAFDpasvlPDGEGFDL 239
                                       9****************996525677888887643321444444442.4457777877777765344424667**** PP

                                       EEEESTGGGSSHHHHHHHHH CS
                   Methyltransf_25  68 vvssgalhhlsdedlekalk 87 
                                       v+ +++l+ l+d+    + +
  gi|313126654|ref|YP_004036924.1| 240 VCFANVLSELDDPT--SVAE 257
                                       ***98898888654..4444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.3e-07    0.0019       1      95 [.     165     270 ..     165     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.3e-07
                                       EEET-TTSHHHHHHHHTT.....SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT.S...S-T.T-EEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.....arvvgvDlskemlklakekaseegl.kvefvvadaekl.p...fed.nsfDlvv 66 
                                       LdvG+GtG  a  l+++       ++ +v++s+ +  l  + ++++ + k ++++++ae + p   ++d + fDlv+
  gi|313126654|ref|YP_004036924.1| 165 LDVGAGTGGPALGLHDYLpenslVEYHAVEPSASADVLEAMLSETRSNfKTTVHRETAEAFdPasvLPDgEGFDLVC 241
                                       8**************666666689999999999988666666666666777889999998755777999679***** PP

                                       EES-CCC-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  67 ssevlhhvedpekalkeiaRvLkpgGllv 95 
                                         +vl  ++dp ++ +     +  +G +v
  gi|313126654|ref|YP_004036924.1| 242 FANVLSELDDPTSVAERYLDYVADDGSFV 270
                                       ************99998888888888765 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0019       4.8      31      89 ..     116     176 ..      91     194 .. 0.65
   2 ?    0.0   0.0      0.24   6.1e+02      16      41 ..     196     221 ..     182     231 .. 0.78
   3 ?    0.1   0.0      0.22   5.7e+02      84     141 ..     376     428 ..     360     430 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0019
                                       GGGSSCGGGGGTTSSS-EEEETTEEE--HH..HHHHHHHHTT....--TT-EEEEES-TTSHHHH CS
                              PCMT  31 eefvpesfkekaYedaplsigynatiSaph..mvalalelle....lkkgarvLevGsGsGylta 89 
                                       + + ++   e aY++ +  +gy+ +    +   v+++l+ l     l ++ rvL+vG+G+G  + 
  gi|313126654|ref|YP_004036924.1| 116 DYYYQN---EVAYDEEAA-LGYGIYHLPDYyaAVGYVLDGLAerglLPRVLRVLDVGAGTGGPAL 176
                                       333333...567776665.77775544333014556677666788789999**********7665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.24
                                       ---HHHHHHHHHS-GGGGSSCGGGGG CS
                              PCMT  16 iksdkvaealeevdReefvpesfkek 41 
                                        +s  v+ea+++  R++f ++ ++e+
  gi|313126654|ref|YP_004036924.1| 196 SASADVLEAMLSETRSNFKTTVHRET 221
                                       46889*************99977765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.22
                                       TSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG- CS
                              PCMT  84 sGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeeka 141
                                       sG + a +a++ ++++     +ri  l+ + ++ l ++d +n  ++v+DG + +e++a
  gi|313126654|ref|YP_004036924.1| 376 SGERYAKMAEMERHVT-----NRIDLLAVKLSHDLTEHDGANPLFKVSDGSESVEHYA 428
                                       6666666777766666.....88999999999999999999*********99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2920.49
//
Query:       gi|313126655|ref|YP_004036925.1|  [L=268]
Description: prephenate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-12   46.4   0.5    1.1e-10   41.0   0.5    2.0  1  PDH              Prephenate dehydrogenase
    0.00023   21.7   0.2    0.00087   19.8   0.0    2.0  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0016   18.3   0.8      0.012   15.5   0.0    2.4  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.046   13.4   0.0    1.6  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.027   14.5   0.0      0.048   13.7   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.03   14.5   0.3      0.099   12.8   0.0    2.0  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.046   14.0   0.0       0.44   10.8   0.0    2.4  2  TrkA_N           TrkA-N domain
      0.052   13.8   1.5      0.064   13.5   0.0    2.0  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.053   14.4   1.5       0.27   12.1   0.0    2.7  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.5   5.3e-14   1.1e-10      17     219 ..      28     210 ..      20     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 5.3e-14
                                       E-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHHHHHHC CS
                               PDH  17 ydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKekvvreleell 93 
                                        d+d+ +a aa      d +t +++  +++d v lavP+ ++ e + ++ap  + ++ + Dv++v  ++v +++e  
  gi|313126655|ref|YP_004036925.1|  28 ADRDPDAARAA--ATSTDGRTVSLATEETFDAVCLAVPISAVDEAVFDHAP--RAERAVFDVTGVMDAPVTAMREAA 100
                                       57777777666..4567888888899999**********************..9*********************** PP

                                       C..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHHHTH CS
                               PDH  94 kegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvilmspeeHDrvvavvsh 170
                                       ++  +  + hP++                na+       + +    e v + l   g  v +++p+eHD+++  v+ 
  gi|313126655|ref|YP_004036925.1| 101 AD-RERLSLHPLFAA-------------ANAPGTVAAVRDAPGPVTERVCDTLSAAGNEVFETTPAEHDEAMETVQA 163
                                       *5.5667******99.............44555555555666678889***************************** PP

                                       HHHHH..HHHHHHHHHCHHCCCCHHHHCGTCCHHHHHCGGGS-HHHHHHHH CS
                               PDH 171 lphvv..aialaatlkekkndekeirklasggfrdvtRiaksnPelwadil 219
                                         h++  a+alaa  ++++  ++ + +l+s    +v  + ++ P+++++i+
  gi|313126655|ref|YP_004036925.1| 164 SAHAAvlAYALAAEDVREEFATPVSESLSS----LVETVTGGTPRVYREIQ 210
                                       999641166777755555555555555544....56677777777777776 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.4e-07   0.00087       3      81 ..       4      74 ..       2      86 .. 0.83
   2 ?   -1.5   0.0         2   3.9e+03      18      45 ..     139     163 ..     129     184 .. 0.49

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.4e-07
                                      EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                     F420_oxidored  3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81
                                       +iGaG+mg+ + s l+a+     ++ +a +r+p+ a+++a +   ++ + ++ee+    d v lav+ ++v+e++ + 
  gi|313126655|ref|YP_004036925.1|  4 LVIGAGEMGRWVGSTLTAE----FDVAFA-DRDPDAARAAATSTDGRTVSLATEETF---DAVCLAVPISAVDEAVFDH 74
                                      58************99998....7***99.***********9998777776777777...7***********9987665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                                       HHHTTS-GGCEEEEEESSCCCHHHHHHH CS
                     F420_oxidored  18 llaagaqpheivvansrnpekaeelaee 45 
                                       l+aag   +e+  ++  + ++a e+ ++
  gi|313126655|ref|YP_004036925.1| 139 LSAAG---NEVFETTPAEHDEAMETVQA 163
                                       55555...55554433333333333332 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.1e-06     0.012       2      54 ..       3      54 ..       2      82 .. 0.84
   2 ?    0.7   0.2      0.21   4.2e+02      69     100 ..     205     237 ..     137     247 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.1e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTS CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgk 54
                                      v viGaG mG+ +   ++ a+++V   d++++a+++a+ +   ++ +l+ ++ 
  gi|313126655|ref|YP_004036925.1|  3 VLVIGAGEMGR-WVGSTLTAEFDVAFADRDPDAARAAATSTDGRTVSLATEET 54
                                      78********8.66678899****************99998887776666555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.21
                                       EES-HHHHH.C-SEEEE-S-SSHHHHHHHHHHH CS
                           3HCDH_N  69 fttdleeav.dadlviEavvEnlelKrkvfael 100
                                       +  +++e   +ad v  a++E  +  +k+f++l
  gi|313126655|ref|YP_004036925.1| 205 VYREIQESFpGADRVADAATELASADAKTFEQL 237
                                       334555555566666667766666666666666 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.3e-05     0.046       1      47 [.       3      51 ..       3      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH..HHHHCEEEEETT CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea..lkknGlrltseg 47
                                      ++++GaG +G+ ++ +L  a  dv + +r++  + a   +++G +++  +
  gi|313126655|ref|YP_004036925.1|  3 VLVIGAGEMGRWVGSTL-TAEFDVAFADRDPdAARAaaTSTDGRTVSLAT 51
                                      68***************.6799*******985433322445555554444 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.4e-05     0.048      14      60 ..       2      46 ..       1      62 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgee 60
                                      +vl+iGaGem++ v + L a+ + +v+ a R+ + a++ a++ +g  
  gi|313126655|ref|YP_004036925.1|  2 EVLVIGAGEMGRWVGSTLTAE-F-DVAFADRDPDAARAAATSTDGRT 46
                                      69****************954.4.59999999999999998887764 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     5e-05     0.099       3      79 ..       4      77 ..       2     108 .. 0.67
   2 ?   -0.9   0.1      0.81   1.6e+03      67      67 ..     177     177 ..     132     237 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                                      EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC CS
                     NAD_binding_2  3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllea 79
                                       +iG G+MG+   +  l a+++va+ +r+++++++++++  ++ +   +  ++ d+v + v+  +avde +++ +++
  gi|313126655|ref|YP_004036925.1|  4 LVIGAGEMGRWVGST-LTAEFDVAFADRDPDAARAAATST-DGRTVSLATEETFDAVCLAVPI-SAVDEAVFDHAPR 77
                                      58*******987665.5789*********99999888664.2222222233445888888887.5566666664444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.81
                                       H CS
                     NAD_binding_2  67 k 67 
                                       +
  gi|313126655|ref|YP_004036925.1| 177 E 177
                                       1 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00022      0.44       1      38 [.       3      39 ..       3      71 .. 0.87
   2 ?    0.2   0.0      0.43   8.6e+02       7      38 ..     129     158 ..     128     181 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelr 38
                                      +++iG+G++Gr +  +L+++  dv   d+d+++++ ++
  gi|313126655|ref|YP_004036925.1|  3 VLVIGAGEMGRWVGSTLTAEF-DVAFADRDPDAARAAA 39
                                      68*****************99.6*********999876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.43
                                       SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHH CS
                            TrkA_N   7 GrvGrslaeeLse.ggkdvvvidkdeerveelr 38 
                                       G v+++++++Ls+ g++   v ++ ++  +e+ 
  gi|313126655|ref|YP_004036925.1| 129 GPVTERVCDTLSAaGNE---VFETTPAEHDEAM 158
                                       67888888999885554...6666665544443 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.2e-05     0.064       1      47 [.       3      45 ..       3      87 .. 0.86
   2 ?   -2.5   0.0       2.9   5.8e+03      42      54 ..     162     174 ..     132     194 .. 0.59
   3 ?   -3.7   0.1       6.7   1.3e+04      34      58 ..     220     243 ..     216     249 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTT CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgv 47
                                      vl+iGaG +G+ v   l ++fdv    + adr+ + ++a+a ++ g 
  gi|313126655|ref|YP_004036925.1|  3 VLVIGAGEMGRWVGSTLTAEFDV----AFADRDPDAARAAATSTDGR 45
                                      89******************987....9*******998888766333 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                                       CHHTTTCEEEEE- CS
                   Sacchrp_dh_NADP  42 akalgvrfeaial 54 
                                       ++ ++  + a+al
  gi|313126655|ref|YP_004036925.1| 162 QASAHAAVLAYAL 174
                                       2223333333333 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 6.7
                                       HHHHHHHHCHHTTTCEEEEE--TTT CS
                   Sacchrp_dh_NADP  34 keklealaakalgvrfeaialdaen 58 
                                        + + +l a+a  ++fe+   da+ 
  gi|313126655|ref|YP_004036925.1| 220 ADAATEL-ASADAKTFEQLYRDAST 243
                                       4443333.34466666666666665 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.27       2      72 ..       2      64 ..       1     106 [. 0.76
   2 ?    0.7   0.3      0.45   8.9e+02      35      59 ..     172     196 ..     141     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                      EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpn 72
                                       v++iGaG +g++ +  l ++++    va+ d+d+ +a+a+a s++   +     l++++  dav+ a+p 
  gi|313126655|ref|YP_004036925.1|  2 EVLVIGAGEMGRWVGSTLTAEFD----VAFADRDPDAARAAATSTDGRTV----SLATEETFDAVCLAVPI 64
                                      799************77777643....6799********99999988855....46666778899998886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.45
                                       SHHHHHHHHHHTTHEEESSHHHHHT CS
                      GFO_IDH_MocA  35 daeraeavaesfgveaysdleella 59 
                                        a +ae+v+e+f  ++ ++l+ l++
  gi|313126655|ref|YP_004036925.1| 172 YALAAEDVREEFATPVSESLSSLVE 196
                                       4456777778887777777666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1638.96
//
Query:       gi|313126656|ref|YP_004036926.1|  [L=282]
Description: hypothetical protein Hbor_19140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-34  119.1   0.0    2.1e-34  118.7   0.0    1.1  1  adh_short     short chain dehydrogenase
    2.3e-29  102.6   0.0    3.2e-29  102.1   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    4.2e-09   36.6   0.0    5.7e-09   36.1   0.0    1.1  1  KR            KR domain
     0.0054   16.2   0.1     0.0085   15.6   0.1    1.4  1  Epimerase     NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   0.0   4.7e-38   2.1e-34       2     179 ..      10     194 ..       9     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 4.7e-38
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHH.......HHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHH CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseek.......leevakelkeegakalaiqvDvtdreevealveka 71 
                                       v+++tG s+GIG+a+a ela +G+kvv ++++ e+       + e+ +e+++ g + +  q+Dv+d+e+v a++e+ 
  gi|313126656|ref|YP_004036926.1|  10 VAFITGTSRGIGKALALELADAGVKVVSTGKTVEEkdelpgtIVETTEEIRSRGGESIWRQIDVRDEESVAAAIEDT 86 
                                       89**************************9988776111111134455666666999********************* PP

                                       HHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHH CS
                         adh_short  72 vkklgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaa 148
                                       v+++g++d ++nNAG  + +pf+e+  ++++ + evN+ g++ +t+a+lp++ ++  +++   s  +++ + +g+aa
  gi|313126656|ref|YP_004036926.1|  87 VEEFGGIDFVINNAGAIHIAPFEETPPRRYDLLTEVNVRGTYVTTQAALPHLRESDHAHVLAFSPPVTNPARPGMAA 163
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE CS
                         adh_short 149 YsAsKaavagltrslakelaptgirvnavaP 179
                                       Y+ sK +++  ++sla+el+ + i  n++ P
  gi|313126656|ref|YP_004036926.1| 164 YAVSKYGMTIVMQSLADELSGDDIALNSLWP 194
                                       ***************************9988 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.0   7.2e-33   3.2e-29       1     179 [.      15     203 ..      15     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 7.2e-33
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.H.......HHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHS CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.k.......krveelaeelgaev.lecDVtdeeqvealveevvekfg 68 
                                       G  +gIG+a+A +la++G +vv t    e+ +       +++ee+ +++g+++  ++DV+dee+v+a++e++ve+fg
  gi|313126656|ref|YP_004036926.1|  15 GTSRGIGKALALELADAGVKVVSTGKTVEEkDelpgtivETTEEIRSRGGESIwRQIDVRDEESVAAAIEDTVEEFG 91 
                                       7789*******************9887776322333333567888888888877*********************** PP

                                       SEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHH CS
                      adh_short_C2  69 klDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynayga 143
                                       ++D+++nnag  +   +pf+et+   +d   +vn+++++ +++aalp+++e+  + +++ s    + + p+ +ay++
  gi|313126656|ref|YP_004036926.1|  92 GIDFVINNAGAIHI--APFEETPPRRYDLLTEVNVRGTYVTTQAALPHLRESdhAHVLAFSPPVTNPARPGMAAYAV 166
                                       *************9..*******************************888887899********************* PP

                                       HHHHHHHHHHHHHHHHGGGTEEEEEEEE.--BHCTGG CS
                      adh_short_C2 144 aKaalealtrylAvelgpkgiRvNavsp.gpikTlaa 179
                                       +K ++  ++++lA el  + i  N+  p  +i+ +a+
  gi|313126656|ref|YP_004036926.1| 167 SKYGMTIVMQSLADELSGDDIALNSLWPvAAIESEAT 203
                                       ************************9998345665555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   1.3e-12   5.7e-09       4     135 ..      12     150 ..      10     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.3e-12
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHH......HHHHHHHHTT-EEEE----TT-HHHHHHHHHH CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedsk......aliaelealgaevevvaaDvsdkdaveallee 74 
                                       +itG   g+G++la  la+ g + +v ++++ ++++  +      ++++e++++g e  ++++Dv d+++v+a++e+
  gi|313126656|ref|YP_004036926.1|  12 FITGTSRGIGKALALELADAGVK-VVSTGKTVEEKD--ElpgtivETTEEIRSRGGESIWRQIDVRDEESVAAAIED 85 
                                       79******************975.789999953333..2234444799***************************** PP

                                       HHHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEE CS
                                KR  75 ikaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfS 135
                                         +e++ i  vi+ Ag+++ +++ee+   +++ +++  v+G+ +  ++  +    ++  +++ fS
  gi|313126656|ref|YP_004036926.1|  86 TVEEFGGIDFVINNAGAIHIAPFEETPPRRYDLLTEVNVRGTYVTTQAALPhlreSDHAHVLAFS 150
                                       *****************************************998877755445323444455555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.9e-06    0.0085       2      84 ..      12     112 ..      11     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...............EEEE--TT-HH....HHHHH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl...............elveldltdrs....alerl 59 
                                       ++tG +  iG+al+ +l+++g++v+   +  +++  ++   +                + ++d++d++    a+e+ 
  gi|313126656|ref|YP_004036926.1|  12 FITGTSRGIGKALALELADAGVKVVSTGKTVEEK-DELPG-TivetteeirsrggesIWRQIDVRDEEsvaaAIEDT 86 
                                       79*******************9999888883333.23333.25799***********99********9666666677 PP

                                       HHHH.T-SEEEE--S---HHHHHHSH CS
                         Epimerase  60 fkee.qpdavihlAavggvaassedp 84 
                                       ++e+ ++d vi+ A+  ++a   e+p
  gi|313126656|ref|YP_004036926.1|  87 VEEFgGIDFVINNAGAIHIAPFEETP 112
                                       777889*******9988887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1742.45
//
Query:       gi|313126657|ref|YP_004036927.1|  [L=170]
Description: hypothetical protein Hbor_19150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.02   15.3   0.0      0.075   13.5   0.0    1.8  2  FAA_hydro_N_2  Fumarylacetoacetase N-terminal domain 2


Domain annotation for each model (and alignments):
>> FAA_hydro_N_2  Fumarylacetoacetase N-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.2e-06     0.075       1      55 [.       1      57 [.       1      62 [. 0.90
   2 ?   -1.2   0.0      0.15   2.7e+03      30      48 ..     137     155 ..     122     166 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.2e-06
                     FAA_hydro_N_2  1 mkLAtlkngtrDGeLvv..VsrdlkkavdaseiaptlqaaLdnWdevepaLeelyea 55
                                      mk+ ++   t DG+ v   V+ + ++ + + ++ +  q+++d+W+ ++++L+e+y++
  gi|313126657|ref|YP_004036927.1|  1 MKFPSVPGRTTDGRRVHlpVDFEGEQTLVVLSFHQRQQSLVDSWRGFANRLREEYDH 57
                                      9************865425888899999999***********************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.15
                     FAA_hydro_N_2  30 eiaptlqaaLdnWdevepa 48 
                                       + a+ l ++L + ++++++
  gi|313126657|ref|YP_004036927.1| 137 STAEALESLLSEYESAQNR 155
                                       4456666666665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1212.21
//
Query:       gi|313126658|ref|YP_004036928.1|  [L=390]
Description: xaa-pro aminopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-50  169.3   1.8    1.2e-49  168.9   1.8    1.2  1  Peptidase_M24  Metallopeptidase family M24
    6.1e-09   36.6   0.1    1.6e-08   35.3   0.1    1.6  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.9   1.8   1.3e-53   1.2e-49       1     209 []     152     375 ..     152     375 .. 0.91

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 1.3e-53
                                       HHHHHHHHHHHHHHHHHHHHHHT.....T........CBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTT CS
                     Peptidase_M24   1 elirkaariasaaleavleaikp.....g........vterelaaeieattlkrhgarglafppivasgenaavlhy 64 
                                       e++r+a+++ ++a++a+ + i       g         t++ + +eie t l rhg++ +  ++iva+g+naa +h 
  gi|313126658|ref|YP_004036928.1| 152 EHVRAAQNANEEAMRAAENLIAAadvedGtlvyegapLTSERVKEEIEVT-LLRHGCGLD--DTIVACGANAADPHD 225
                                       579**************776664233334444333445**********77.999**9988..79************* PP

                                       BCSSSB--TTEEEEEEEEEEET..TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHH CS
                     Peptidase_M24  65 tpndrvlkegdlvlidagaeyd..gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarev 139
                                       +  + +l++++ ++id+ ++ +  gy++D+trT++ G++++e re ++++ ea++aa++av+pGvt++++++++++ 
  gi|313126658|ref|YP_004036928.1| 226 QG-SGPLHADEAIIIDIFPRSKetGYHADMTRTFVKGDPSEEIRERFDLTHEALNAALDAVEPGVTGADVHDVVCDR 301
                                       88.69********************************9999************************************ PP

                                       HHHTTB.........CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEE CS
                     Peptidase_M24 140 lesagl.........akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlv 207
                                        e+ag+         ++ f h++GHgvGl+vh+  p+++  sn g++l++G+v+tiEpg+y  p++ggvried  +v
  gi|313126658|ref|YP_004036928.1| 302 YEEAGYdtlrsnataETGFIHSTGHGVGLDVHEL-PRIA--SN-GEELKPGHVITIEPGLY-DPSVGGVRIEDIAVV 373
                                       ***************9999*************98.***9..45.9****************.89************* PP

                                       ES CS
                     Peptidase_M24 208 te 209
                                       te
  gi|313126658|ref|YP_004036928.1| 374 TE 375
                                       *7 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   1.7e-12   1.6e-08       5      92 ..       8      92 ..       6     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.7e-12
                                      HHHHHHHTT-SEEEEECC...HHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEESTHSSH CS
                      Creatinase_N  5 lralmeekgldallvtsp...enlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveyddpvea 80
                                      l +l+e++++d++lv +    + + Yl+Gf   + + +++ + t+++++llv al+y++a+++s + +ev+ +++   +
  gi|313126658|ref|YP_004036928.1|  8 LDDLLEAEDADGYLVDDTshnSTQKYLSGF---EAHDPFVTLYTPEKTILLVSALEYGRAKKQS-RADEVRRVAE--YD 80
                                      67899**********99988899*******...7777777779*********************.9999988884..78 PP

                                      HHHHHHHHHHHT CS
                      Creatinase_N 81 ladllkellese 92
                                      + +l++e++++e
  gi|313126658|ref|YP_004036928.1| 81 YRELVSEHGPAE 92
                                      999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2578.75
//
Query:       gi|313126659|ref|YP_004036929.1|  [L=432]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     5e-108  361.5   0.1   6.1e-108  361.2   0.1    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.2   0.1  3.4e-112  6.1e-108       4     416 ..       7     421 ..       5     422 .. 0.94

  Alignments for each domain:
  == domain 1  score: 361.2 bits;  conditional E-value: 3.4e-112
                                       SS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE CS
                     EPSP_synthase   4 gkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfea 80 
                                       ++r++g+ ++p+sks+++ra+l+A    g+ t+ n+L s+D+++++ a+ ++g+++  l+++++ + v+g+ g+ e+
  gi|313126659|ref|YP_004036929.1|   7 PSRIDGRTRAPPSKSYTHRAILAAG-YGGQATVLNPLVSADTKATMRAVDAFGGDT-DLSADESSLSVSGFDGRPEV 81 
                                       689*****************98776.56999**********************877.66699*************** PP

                                       -HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BE CS
                     EPSP_synthase  81 peelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkg 156
                                       p ++v+++ nsgt++rl+ta +al +g +vLtGd+s+r+RP  +llda + lG + e+ + ++ apl v     +++
  gi|313126659|ref|YP_004036929.1|  82 P-ADVVNCENSGTTMRLVTACAALGDGLTVLTGDDSLRSRPQGPLLDAVTDLGGRGESTRRNGQAPLVVGDaMDGGT 157
                                       *.7****************************************************************99889***** PP

                                       EEEETSSTTHHHHHHHHHHHTTSBS.EEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SS..B--EE CS
                     EPSP_synthase 157 veikaevsSqqvtsllllaallaeg.ttelee.lasepsiddtlkmlkkfgikietsgteesitvkGkek..lpgte 229
                                       v+i ++vsSq++++ll++ a++ eg ++ele+ l+s+p++d+tl++l +fg++ e+  t + + v G+++   +g e
  gi|313126659|ref|YP_004036929.1| 158 VSIPGDVSSQYISALLMAGAVTDEGiDIELETeLKSAPYVDITLELLDEFGVEAEQ--TADGFSVAGGQSydPTGGE 232
                                       ********************99999****************************999..7788*********98888* PP

                                       EE--B-HHHHHHHHHHHHHT..T-.EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTS.EEEEEETTS--BEEE CS
                     EPSP_synthase 230 yvvegDassAayflvaAait..gg.evtvenvginslqGdiealdeilekmgaeitqeeda.sivvgpsglklkdvd 302
                                       y+v+gD ss +y+l+a+ai+  +g  v+ve++++ s qGd++++d i+++mga++t+  da  ++v++  l++  vd
  gi|313126659|ref|YP_004036929.1| 233 YEVPGDFSSISYLLAAGAIAaaEGeSVVVEGARP-SAQGDAAIVD-IVRDMGADVTWDRDAgELTVSRATLTGTTVD 307
                                       ****************9986333459***99987.6799*98888.**********88765245666669******* PP

                                       EEBGSTTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TT CS
                     EPSP_synthase 303 ietlpdeaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesyd 379
                                       + + pd++pt+a+l a+a+g tvie+ +++r+ketdr+ ama+eL k+Ga v+ee+d l+i+++e  l ga+ve  +
  gi|313126659|ref|YP_004036929.1| 308 VGDTPDLLPTIATLGAVADGDTVIENCEHVRYKETDRVSAMADELGKMGASVTEEQDRLTIHGGETDLVGATVEGRH 384
                                       ***************************************************************************** PP

                                       STTTTHHHHHHHHHSBSEEEEETTHHHHHHSSSHHHH CS
                     EPSP_synthase 380 DhRiamalalaglvaegeveiddiectdksfpefeek 416
                                       DhRi m+la+aglvaege++++ +e++d+sfp+f++ 
  gi|313126659|ref|YP_004036929.1| 385 DHRIVMSLAIAGLVAEGETTVTGAEHVDVSFPNFFDA 421
                                       ***********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2712.22
//
Query:       gi|313126660|ref|YP_004036930.1|  [L=159]
Description: hypothetical protein Hbor_19180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1025.68
//
Query:       gi|313126661|ref|YP_004036931.1|  [L=383]
Description: chorismate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.2e-121  402.7   0.0   9.4e-121  402.5   0.0    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.5   0.0  5.2e-125  9.4e-121       1     327 []      10     354 ..      10     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 402.5 bits;  conditional E-value: 5.2e-125
                                       SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE CS
                   Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallie 77 
                                       ++vtt+GeShg+a+g+++ g+paglelde+d+qkeLdrR+pgqs +tt+r E D+v i sG+++g+t+Gtpi ++ie
  gi|313126661|ref|YP_004036931.1|  10 FQVTTYGESHGDAMGVTVSGCPAGLELDEDDVQKELDRRKPGQSMITTSRGEPDAVVINSGTQDGYTTGTPIGMVIE 86 
                                       89*************************************************************************** PP

                                       -TTS-..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE. CS
                   Chorismate_synt  78 NkdqrskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei. 153
                                       Nkd+rs +ye + ++pRp+H+D+ty++k+g+r++ gggrsSaReT+  vaaGa+ak++L++++++++a+v++ig+i 
  gi|313126661|ref|YP_004036931.1|  87 NKDARSGKYEPYVTAPRPSHGDFTYSAKFGTRNWGGGGRSSARETVNWVAAGAIAKQILEAHDVQVKAHVNQIGDIe 163
                                       **************************************************************************888 PP

                                       ..........CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTS CS
                   Chorismate_synt 154 ..........ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsi 220
                                                 e+++en+vrc+++e+ae+m+e+i+e+++egds+Gg v + ++gvp GlG+p fd++ a+L++a+m+i
  gi|313126661|ref|YP_004036931.1| 164 appvtfeemlEHTEENEVRCAHPETAEQMREKIDEYQEEGDSIGGSVYFETRGVPRGLGSPRFDSFSARLGQAMMAI 240
                                       8999998776555889************************************************************* PP

                                       TTEEEEEETTGGGGGGSBHHHHS--EE.......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS CS
                   Chorismate_synt 221 pAvkgveiGsGfeaaelkGseanDeiv.......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdlet 290
                                       pA+ ++e+G G ea e +G++ n+ ++       +   n++GGi+GGi++G+p++ +v+ ++  si keq+tvd et
  gi|313126661|ref|YP_004036931.1| 241 PAATAFEFGLGREAREWTGKDRNEDWTfdededpVPVGNKHGGIQGGITTGQPVFGEVTWHAPTSIPKEQTTVDWET 317
                                       *************************996666655459**************************************** PP

                                       -E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
                   Chorismate_synt 291 keevelevkgrhDpcvvpravvvveamvalvladall 327
                                        ee e++v grhDp++ prav+vveam++l+++d++l
  gi|313126661|ref|YP_004036931.1| 318 GEEKEIQVVGRHDPVLPPRAVPVVEAMLNLTIVDFML 354
                                       **********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2675.49
//
Query:       gi|313126662|ref|YP_004036932.1|  [L=632]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-49  166.3   0.0    1.3e-48  165.4   0.0    1.3  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    1.5e-48  165.6   0.2    3.4e-48  164.4   0.2    1.6  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    5.1e-12   46.0   0.0      1e-11   45.0   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    4.2e-05   23.2   0.1    0.00011   21.8   0.1    1.7  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.35   10.8   0.0    1.7  1  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.0   3.5e-52   1.3e-48       1     177 []      14     198 ..      13     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 3.5e-52
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEES............. CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllval............. 64 
                                       +G+G+ ++++++aka++r+G++v+++r+y+s+irGgh+y+++r+s++ +v+s++ +++++l+al             
  gi|313126662|ref|YP_004036932.1|  14 SGDGIASTSQNFAKALMRSGLHVFTHRHYPSRIRGGHTYTEIRASAD-PVKSRG-DGYNFLLALgdsfarnpqenay 88 
                                       5**********************************************.9*****.********************** PP

                                       ...SH.HHHHHHGGGEEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHH CS
                               POR  65 ...da.etlsehldglkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlG 137
                                          ++ + lse+ld+l++gg+iiy+s+ l+ +e+++++e+  e++    ++vy++d++ +a+++g+ e+++Nt+++G
  gi|313126662|ref|YP_004036932.1|  89 ygnEEiKPLSENLDELREGGVIIYDSGLLDASEIEDFDERVEENN----WHVYDLDLRTMARDHGR-EVMRNTAGVG 160
                                       **9555999*****************************9887776....6****************.********** PP

                                       HHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 138 alaallglplealeeaikkrfpkkkeviekNlkafragye 177
                                       a++al+g++ e +ee +++++p+k  ++e Nl+ ++++ye
  gi|313126662|ref|YP_004036932.1| 161 ATCALAGIDTEWIEELMRDAMPEK--ILEPNLEILQEAYE 198
                                       **********************95..*************7 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.4   0.2   9.5e-52   3.4e-48       2     229 ..     234     479 ..     233     481 .. 0.89

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 9.5e-52
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a+  g+++ia+YP+TP +e++  +++ l++ +       q+e+Ei+a++ +iGA+ aG++a+  +Sg G++Lm+e 
  gi|313126662|ref|YP_004036932.1| 234 GALDEGCRFIAGYPMTPWTEVFTIMSQNLPELGG---ISEQVEDEIAAAALAIGASHAGVKAMSGSSGGGFALMSEP 307
                                       678889**************************95...889************************************* PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       lgla ++e+Pvv+v ++Ra+pstg++++++q+Dl  ++     d+  +v+a++ ++ea+  + +Af++A ++++P i
  gi|313126662|ref|YP_004036932.1| 308 LGLAEMTETPVVLVEAMRAGPSTGMPTKPEQGDLEHVLytsqgDSHRVVFAPSGAEEAYHQTRRAFQIAYEYQIPSI 384
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC..-SGG....GS-----SBXXXXXXXX.............SXXXBXXTXXTSSXXEEESB CS
                             POR_N 151 vlfDgfllshevekvel..pdee...delklikekleeyerkey.............aldpekpiargtaanpdtgl 209
                                       vl D+  +  e ++v+    dee   d+ ++++e++ +  + +              +++p++ + +++ ++ + g 
  gi|313126662|ref|YP_004036932.1| 385 VLYDQKNG-GELQNVPAsvFDEEpngDLGSVMTEEELADAPHDDsgkynrfqhegenGVSPRSIPGQKGGRYLAAGN 460
                                       ********.88888875222333212444555555444444333788899999************************ PP

                                       XBXTTSXBXXXXHHHHHHHH CS
                             POR_N 210 ehrekgneaedaaekvveev 229
                                       eh+ +g+++ed  e++v +v
  gi|313126662|ref|YP_004036932.1| 461 EHMPAGHISED-PENRVLQV 479
                                       **********9.99998877 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   2.8e-15     1e-11       1      79 [.     509     587 ..     509     605 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.8e-15
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Ae+ i+++Gs  gt+++a+d+l ++g++v  l +  + P+P e+++e+l++v+  +v+++n+s  ++G   +ev + 
  gi|313126662|ref|YP_004036932.1| 509 AEYGIMTFGSQQGTVEEAIDRLNDRGYSVKALGVSEMAPYPVEQVSEFLESVEDCLVVEMNASAQFRGLTQKEVGRF 585
                                       89***********************************************************************9887 PP

                                       TG CS
                           PFOR_II  78 lk 79 
                                        +
  gi|313126662|ref|YP_004036932.1| 586 GE 587
                                       44 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   3.1e-08   0.00011       2     154 ..     226     382 ..     225     387 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.1e-08
                                       EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       ++++a++    ++g + + g+p +  ++++  +s++  ++  +    E   a+aA ++  ++  + +   +sg G++
  gi|313126662|ref|YP_004036932.1| 226 SGSDAIAYGALDEGCRFIAGYPMTPWTEVFTIMSQNLpELGGISEQVEDEIAAAALAIGASHAGVKAMSGSSGGGFA 302
                                       5789999999999***************9999999977888888889999*************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHH......S..TC--T-CCHH....HCCCSSEEEE-SSGGGHHHHHHHHH CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrg......qgvlqqeldqlal....frpvtkyaervtspeelpealrrAi 144
                                        +   l  A  + +P++++ + r+  ++g      q       d +++      +  + ++ ++ +ee+ ++ rrA+
  gi|313126662|ref|YP_004036932.1| 303 LMSEPLGLAEMTETPVVLVEAMRAGPSTGmptkpeQ------GDLEHVlytsQGDSHRVVFAPSGAEEAYHQTRRAF 373
                                       *****************************5443333......3444442222224455578899999999999**** PP

                                       HHHHSSS--E CS
                      TPP_enzyme_N 145 rtalsgrpgP 154
                                       ++a ++ + P
  gi|313126662|ref|YP_004036932.1| 374 QIA-YEYQIP 382
                                       **9.777776 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.7e-05      0.35      33      92 ..     499     560 ..     476     579 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.7e-05
                   Glyco_tran_WecB  33 ieelleraeeeglrvfllGgkpevlekaaerlrekypglriagthdg..ykeeeeeaiieai 92 
                                        +++l   e++++ ++ +G++++++e+a++rl+++   ++  g+++   y+ e+  +++e +
  gi|313126662|ref|YP_004036932.1| 499 SNNTLYGPEDAEYGIMTFGSQQGTVEEAIDRLNDRGYSVKALGVSEMapYPVEQVSEFLESV 560
                                       5566666777899**********************999999998877323334444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.23s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 4687.58
//
Query:       gi|313126663|ref|YP_004036933.1|  [L=312]
Description: 2-oxoacid:acceptor oxidoreductase subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-29  102.3   0.1    2.9e-29  101.8   0.1    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
       0.14   12.3   2.4       0.37   11.0   2.4    1.8  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.1   3.2e-33   2.9e-29       2     152 ..      61     207 ..      60     208 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 3.2e-33
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+             +sy+   g+++ +G++lp+A +akla+ + +vva  GDG+ + i ++++++ +r+n++it
  gi|313126663|ref|YP_004036933.1|  61 IGCSGK----------LNSYFEsYGFHTIHGRSLPIARAAKLANSGLTVVAAGGDGDGYGIgGNHFMHTARENHDIT 127
                                       666666..........7899996679*****************9999****************************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       ++v+nNe++g+t+gq   ++p+g+k+k++p+g+ ++p+++  +   +Ga+ +ar    ++++ ++++ ea++++g++
  gi|313126663|ref|YP_004036933.1| 128 YIVFNNEIFGLTKGQtspTSPKGHKSKTQPHGSAKEPLRPLSMSLNAGASyVARTAAVNPNQAKDIIVEAIQHDGFS 204
                                       *****************999*************9****************999999999****************** PP

                                       EEE CS
                      TPP_enzyme_C 150 lie 152
                                        ++
  gi|313126663|ref|YP_004036933.1| 205 HVD 207
                                       998 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.4   4.1e-05      0.37       1      61 [.     212     278 ..     212     283 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.1e-05
                                       XTTTXSSSXSXXXXX-EEEGGG..S.T---EEHHHHHHHHT----.....-EEEEEEEE.TTS--HHHHH CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervyklee..d.gyDpsdlekAlekalewgd.....kiplGifYk.eekptyeerl 61 
                                       C+t+Nk    ++     +++++  d + D sd+++A + + e +d      + +G  Y+ e++p+y+++ 
  gi|313126663|ref|YP_004036933.1| 212 CPTWNKDAK-QY-VP-YIDINDseDyDIDISDRKSAADMMYETEDalhegTVLTGRYYHdEDRPSYQQEK 278
                                       888887542.22.22.223333213468899***********8889998889**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2241.81
//
Query:       gi|313126664|ref|YP_004036934.1|  [L=142]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-13   48.5   0.0    7.8e-13   47.8   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    5.9e-10   39.0   0.0    9.3e-10   38.3   0.0    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    4.4e-09   36.0   0.0    7.8e-09   35.2   0.0    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.5e-07   31.2   0.0    4.7e-07   29.6   0.0    1.8  1  HTH_11          HTH domain
      4e-06   26.6   0.1    1.8e-05   24.5   0.0    2.0  3  MarR_2          MarR family
    8.6e-06   25.4   0.0    1.4e-05   24.7   0.0    1.3  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    1.2e-05   25.0   0.0    2.1e-05   24.2   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
    1.6e-05   24.9   0.0    2.6e-05   24.2   0.0    1.3  1  HTH_20          Helix-turn-helix domain
    2.4e-05   24.2   0.0    5.7e-05   23.0   0.0    1.6  2  MarR            MarR family
    4.2e-05   23.2   0.0    8.3e-05   22.3   0.0    1.4  1  HTH_23          Homeodomain-like domain
    5.1e-05   23.4   0.0    0.00011   22.3   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00015   22.0   0.0    0.00033   20.9   0.0    1.5  1  Rrf2            Transcriptional regulator
    0.00016   21.6   0.0     0.0003   20.7   0.0    1.5  1  HTH_36          Helix-turn-helix domain
    0.00057   19.7   0.0      0.001   18.9   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0019   18.1   0.0      0.005   16.8   0.0    1.7  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0021   18.1   0.0     0.0033   17.4   0.0    1.4  1  HTH_29          Winged helix-turn helix
     0.0034   17.0   0.0     0.0075   15.9   0.0    1.6  1  GntR            Bacterial regulatory proteins, gntR family
     0.0035   17.0   0.0      0.009   15.7   0.0    1.6  1  Sigma70_r4_2    Sigma-70, region 4
     0.0036   17.1   0.0      0.006   16.4   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0061   16.3   0.1      0.015   15.1   0.1    1.7  1  HTH_10          HTH DNA binding domain
     0.0064   16.8   0.0      0.011   16.1   0.0    1.3  1  FaeA            FaeA-like protein
     0.0079   16.1   0.0      0.013   15.4   0.0    1.3  1  HTH_6           Helix-turn-helix domain, rpiR family
     0.0087   16.2   0.0      0.016   15.3   0.0    1.4  1  HTH_28          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.086   12.6   0.0       0.36   10.7   0.0    1.9  2  LacI            Bacterial regulatory proteins, lacI family
        0.1   12.4   0.1       0.22   11.4   0.1    1.5  1  TetR_N          Bacterial regulatory proteins, tetR family
       0.12   11.9   0.0       0.24   11.0   0.0    1.5  1  Sigma70_r4      Sigma-70, region 4
       0.12   12.2   0.0       0.21   11.4   0.0    1.3  1  TFIIE_alpha     TFIIE alpha subunit


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.2e-15   7.8e-13       4      47 ..       6      49 ..       4      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.2e-15
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      t+ +IL +L++++  s++e+A+r ++S++tv++++++Le++G+I
  gi|313126664|ref|YP_004036934.1|  6 TEGRILAVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDGVI 49
                                      7889***************************************9 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   1.4e-12   9.3e-10       1      74 [.      69     139 ..      69     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.4e-12
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       v++ + +++   + e+ +al++l+ V+++y+ +Gd+ ++++v++ d +al +++ e++  ++gv+  + s+  e
  gi|313126664|ref|YP_004036934.1|  69 VGIDVASER---YVEATRALKDLEPVESLYSSSGDHMLMAEVRATDGDALGDVIAEEILGIEGVTAAHPSFLQE 139
                                       678888777...99***************************************************999999766 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   1.2e-11   7.8e-09       7      42 .]       9      44 ..       5      44 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.2e-11
                     HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +IL+ L++da +syae+A+r  +S +tv++ +++Le
  gi|313126664|ref|YP_004036934.1|  9 RILAVLEQDAQASYAEIADRADVSKPTVRKYIQKLE 44
                                      8*********************************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   7.1e-10   4.7e-07       5      46 ..      10      50 ..       7      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 7.1e-10
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      il  L e++ + s +e+A++ +vS+ tvr++I++Le+ gv +
  gi|313126664|ref|YP_004036934.1| 10 ILAVL-EQDAQASYAEIADRADVSKPTVRKYIQKLESDGVIV 50
                                      88999.89999****************************865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.7e-08   1.8e-05       4      52 ..       4      50 ..       2      59 .. 0.93
   2 ?   -2.9   0.0       9.6   6.4e+03      38      45 ..      81      88 ..      76      89 .. 0.72
   3 ?   -1.5   0.0       3.7   2.4e+03       7      26 ..     100     117 ..      97     125 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.7e-08
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      t ++ r+La+L        + +e+a+r ++sk++v + +++L++ G ++
  gi|313126664|ref|YP_004036934.1|  4 TSTEGRILAVLEQDAQ--ASYAEIADRADVSKPTVRKYIQKLESDGVIV 50
                                      67999**********9..9***************************996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.6
                                      HHHHHHHH CS
                            MarR_2 38 vsrilkrL 45
                                      ++r+lk+L
  gi|313126664|ref|YP_004036934.1| 81 ATRALKDL 88
                                      57777777 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.7
                                       HHHHHHHHHCTTTSEEEHHH CS
                            MarR_2   7 qarvLaaLgrrpgrdltvge 26 
                                       +++++a++++ +g   + g+
  gi|313126664|ref|YP_004036934.1| 100 DHMLMAEVRATDGD--ALGD 117
                                       57888999999883..3333 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.1e-08   1.4e-05       4      44 ..       9      49 ..       7      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.1e-08
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                       il  l+q+   s  e++++ +vS+ T+R+ +++Le +g++
  gi|313126664|ref|YP_004036934.1|  9 RILAVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDGVI 49
                                      6999***********************************98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.1e-08   2.1e-05       7      47 ..       9      48 ..       8      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.1e-08
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGy 47
                                      +iL  l++ +q+ + +e+A+r++++k+tv+ ++q L+  G 
  gi|313126664|ref|YP_004036934.1|  9 RILAVLEQDAQA-SYAEIADRADVSKPTVRKYIQKLESDGV 48
                                      699999999998.9**********************99886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     4e-08   2.6e-05      14      54 ..       9      49 ..       3      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4e-08
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      ril+ L +++ ++ +e+a+r d+sk t+++ +++Le+ g +
  gi|313126664|ref|YP_004036934.1|  9 RILAVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDGVI 49
                                      8************************************9987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   8.5e-08   5.7e-05       2      47 ..       4      49 ..       3      57 .. 0.96
   2 ?   -2.5   0.0       7.5     5e+03      34      42 ..      81      89 ..      81      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.5e-08
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      t t+ +iL+ l++  ++s +e+a++  vsk+tv + + +Le +G i
  gi|313126664|ref|YP_004036934.1|  4 TSTEGRILAVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDGVI 49
                                      889****************************************987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.5
                                      HHHHHHHHH CS
                              MarR 34 vtrvldrLe 42
                                      +tr+l+ Le
  gi|313126664|ref|YP_004036934.1| 81 ATRALKDLE 89
                                      599999998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.3e-07   8.3e-05      12      45 ..      11      47 ..       9      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.3e-07
                            HTH_23 12 lllae...GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      l+++e    +s++eIA++ +vs+ Tv++++++ + +G
  gi|313126664|ref|YP_004036934.1| 11 LAVLEqdaQASYAEIADRADVSKPTVRKYIQKLESDG 47
                                      444544679***********************86577 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.7e-07   0.00011      13      51 ..      10      48 ..       9      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.7e-07
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGy 51
                                      I+ + e+ + ++ +++a r +vs+++V + ++kLe+dG 
  gi|313126664|ref|YP_004036934.1| 10 ILAVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDGV 48
                                      66778889999**************************95 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     5e-07   0.00033      17      55 ..      11      49 ..       8      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5e-07
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglv 55
                                      La  e++ ++s +eia+r ++s++ ++k ++kL+  g++
  gi|313126664|ref|YP_004036934.1| 11 LAVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDGVI 49
                                      66677777799**************************98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.5e-07    0.0003      26      53 ..      20      47 ..      10      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.5e-07
                            HTH_36 26 psqetlakrlglsknTvsraikeLeqlG 53
                                      +s++ +a r  +sk Tv+++i++Le  G
  gi|313126664|ref|YP_004036934.1| 20 ASYAEIADRADVSKPTVRKYIQKLESDG 47
                                      8************************877 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.5e-06     0.001       9      52 ..       6      49 ..       3      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-06
                                      HCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                              TrmB  9 yEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlV 52
                                      +E ++ ++L +  +a+  eia +++v++++v +++++Le+ G++
  gi|313126664|ref|YP_004036934.1|  6 TEGRILAVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDGVI 49
                                      56666777778899999************************987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.5e-06     0.005      21      52 ..      19      50 ..       4      62 .. 0.85
   2 ?   -2.5   0.0       7.8   5.2e+03      38      46 ..      81      89 ..      78      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.5e-06
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                      + + +e+A++  ++  tv + +++L+ +g+i 
  gi|313126664|ref|YP_004036934.1| 19 QASYAEIADRADVSKPTVRKYIQKLESDGVIV 50
                                      56899**************************8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.8
                                      HHHHHHHHH CS
                         HTH_Crp_2 38 vsrilseLk 46
                                       +r+l++L+
  gi|313126664|ref|YP_004036934.1| 81 ATRALKDLE 89
                                      589999997 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.9e-06    0.0033       1      41 [.       9      48 ..       9      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.9e-06
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      R++a+l  +   s  ++iA + ++s++tv++++   e +G+
  gi|313126664|ref|YP_004036934.1|  9 RILAVLEQDAQAS-YAEIADRADVSKPTVRKYIQKLESDGV 48
                                      7888887777776.*************************95 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05    0.0075      28      54 ..      23      49 ..      12      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglv 54
                                       e+a++ +Vs++tvR+ +++Le++g++
  gi|313126664|ref|YP_004036934.1| 23 AEIADRADVSKPTVRKYIQKLESDGVI 49
                                      69***********************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05     0.009      28      49 ..      21      42 ..      18      43 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                                      -HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrlsR 49
                                      sy+EIA + ++s  tV++++++
  gi|313126664|ref|YP_004036934.1| 21 SYAEIADRADVSKPTVRKYIQK 42
                                      9*******************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.1e-06     0.006       6      45 ..       9      49 ..       5      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.1e-06
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +IL  L++  +++  e+a+  ++s++tv+ +  kL+  G++
  gi|313126664|ref|YP_004036934.1|  9 RILAVLEQdAQASYAEIADRADVSKPTVRKYIQKLESDGVI 49
                                      68888888888999**********************99986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.3e-05     0.015      19      49 ..      15      45 ..      14      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                            HTH_10 19 dyPRrvtlkeLAkelGIskstlsehLrkaes 49
                                      +++ +++ +e+A++ ++sk+t+ ++++k es
  gi|313126664|ref|YP_004036934.1| 15 EQDAQASYAEIADRADVSKPTVRKYIQKLES 45
                                      56778999*******************9886 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.6e-05     0.011       5      45 ..      10      49 ..       7      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                                      HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSE CS
                              FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegki 45
                                      Il  l +  a +  +eiAd + +s   +R Y+++Le  g i
  gi|313126664|ref|YP_004036934.1| 10 ILAVLEQ-DAQASYAEIADRADVSKPTVRKYIQKLESDGVI 49
                                      6666777.7888899*********************99987 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     2e-05     0.013      25      62 ..      10      47 ..       2      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                                      HHH-S---TT--HHHHHHHTT--HHHHHHHH---S-SS CS
                             HTH_6 25 ilaspdkaielsikalAkaaavSeativrfakkLGfkG 62
                                      ila  ++  + s +++A  a vS++t+ +  +kL   G
  gi|313126664|ref|YP_004036934.1| 10 ILAVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDG 47
                                      5555666678899*********************8776 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.4e-05     0.016       5      41 ..      12      48 ..       9      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-05
                            HTH_28  5 iikllaaGhsvreaArelgisrrtvyrWikryeegGi 41
                                      ++++  a+ s++e+A +  +s  tv++ i+++e+ G+
  gi|313126664|ref|YP_004036934.1| 12 AVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDGV 48
                                      333334566************************9985 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.7   2.4e+03      29      40 ..       5      16 ..       3      17 .. 0.82
   2 ?   10.7   0.0   0.00054      0.36       4      22 ..      24      42 ..      22      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.7
                                      HHHHHHHHHHHH CS
                              LacI 29 etrerVeaamee 40
                                      +t  r++a++e+
  gi|313126664|ref|YP_004036934.1|  5 STEGRILAVLEQ 16
                                      689999999985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00054
                                      HHHHHCTS-HHHHHHHCTT CS
                              LacI  4 DVArlAGVSkaTVSrvLnn 22
                                      ++A++A VSk TV +++++
  gi|313126664|ref|YP_004036934.1| 24 EIADRADVSKPTVRKYIQK 42
                                      8************888875 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00033      0.22      17      33 ..      20      36 ..      18      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                                      --HHHHHHHHTSSHHHH CS
                            TetR_N 17 ttvreIAkrAGvskgal 33
                                      ++ +eIA+rA vsk+++
  gi|313126664|ref|YP_004036934.1| 20 ASYAEIADRADVSKPTV 36
                                      6779***********98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00036      0.24      20      39 ..      19      38 ..       9      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                                      T--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 20 glTleEIgerlgiSrerVrq 39
                                        +++EI++r ++S+ +Vr 
  gi|313126664|ref|YP_004036934.1| 19 QASYAEIADRADVSKPTVRK 38
                                      679***************97 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.21      16      64 ..       8      57 ..       2      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                      HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSE.EEEEEEE CS
                       TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlv.kykrrrd 64
                                        +l vL ++++ +  ++a    + ++ +rk + +L +++++  y   +d
  gi|313126664|ref|YP_004036934.1|  8 GRILAVLEQDAQASYAEIADRADVSKPTVRKYIQKLESDGVIvGYSADVD 57
                                      57999**********************************98624555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1041.49
//
Query:       gi|313126665|ref|YP_004036935.1|  [L=445]
Description: nucleotidyltransferase/DNA polymerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-40  137.1   0.1    1.1e-39  135.8   0.0    1.6  2  IMS              impB/mucB/samB family
    2.1e-13   51.0   0.0    1.9e-12   47.9   0.0    2.1  2  IMS_C            impB/mucB/samB family C-terminal domain
    8.2e-08   32.1   0.0    1.9e-07   31.0   0.0    1.7  1  IMS_HHH          IMS family HHH motif
    1.2e-06   29.0   0.0    4.1e-06   27.3   0.0    1.9  1  HHH_5            Helix-hairpin-helix domain
    1.9e-05   24.4   0.0    4.1e-05   23.3   0.0    1.5  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0094   16.2   0.0      0.022   15.0   0.0    1.6  1  Cdd1             Pathogenicity locus
  ------ inclusion threshold ------
      0.042   14.2   0.8        3.6    8.0   0.0    3.8  4  DUF1805          Domain of unknown function (DUF1805)
        1.3    9.5   7.3         25    5.5   3.3    2.6  2  Alpha_GJ         Alphavirus glycoprotein J


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.0   4.9e-43   1.1e-39       1     150 []      23     190 ..      23     190 .. 0.90
   2 ?   -2.2   0.0       1.7   3.8e+03      99     132 ..     283     316 ..     273     322 .. 0.58

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 4.9e-43
                                       EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEE........ CS
                               IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcpdlivv........ 66 
                                       +Dmd+Fyas+er+r+peL+g+Pvvv+ g e+    g v+++syeAr+yG+ ++++i++a++  p++  +        
  gi|313126665|ref|YP_004036935.1|  23 VDMDCFYASCERLREPELRGEPVVVGMGYEAgesFGAVATASYEAREYGIDSAQPISQALERLPQIENAaddepggh 99 
                                       7***************************99888889*****************************955555555555 PP

                                       ..EEE-HHHHHHHHHHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-S......HHHHHHHHHHHHHHHH---EE CS
                               IMS  67 ..kvdlekyrraskkileilkrfispkvekasiDEayldltgleelaese......gaalakelrkaikeelgltvs 135
                                         +vd+e y+++ +++ eil++  ++ v+++siDEayld+t++   + +e      ++ + + ++++i  e+g+++s
  gi|313126665|ref|YP_004036935.1| 100 yrPVDMEFYKSVASEVKEILHDC-ADVVREVSIDEAYLDVTDRTAWQTVEgddrtlAEGVGRHVKQRISREVGVPAS 175
                                       55*********************.77****************444444445568899******************** PP

                                       EEEESSHHHHHHHHH CS
                               IMS 136 iGiasnkllAKlase 150
                                       +G+a+n+ +AK+as+
  gi|313126665|ref|YP_004036935.1| 176 VGVAPNMSAAKVASD 190
                                       *************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                                       EEEEE-HH.HHHHHH-SHHHHHHHHHHHHHHHH-- CS
                               IMS  99 Eayldltg.leelaesegaalakelrkaikeelgl 132
                                        a+++ t+ +ee+a++  +ala+ + ++  ++  +
  gi|313126665|ref|YP_004036935.1| 283 SAFAEATEdTEEKANVV-TALAADVAERARSRGAM 316
                                       56666666555555553.66666666555555555 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.37   8.2e+02      38      85 ..      32      85 ..       1     111 [. 0.65
   2 !   47.9   0.0   8.5e-16   1.9e-12       2     115 ..     270     382 ..     269     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.37
                             IMS_C 38 arrLrdkglvartitlklrys...dfh..asrsatLprpt.sdtreileaalkL 85
                                      ++rLr+ +l + ++++  +y    +f   a+ s    ++  ++++ i +a+ +L
  gi|313126665|ref|YP_004036935.1| 32 CERLREPELRGEPVVVGMGYEageSFGavATASYEAREYGiDSAQPISQALERL 85
                                      7999999999*****999998766333566666655554425555554444443 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 8.5e-16
                             IMS_C   2 vearpepksissektfpe.pydesklkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtr 76 
                                       v+++  pks+s e  f+e + d ++  +++  La+++a+r r++g + rti +k+ + +++ ++r  +L+ p +d++
  gi|313126665|ref|YP_004036935.1| 270 VTPTGRPKSLSRESAFAEaTEDTEEKANVVTALAADVAERARSRGAMYRTIGIKVVTPPYDvNTRAQSLSGPVDDPE 346
                                       567889************6555333445666************************9998889*************** PP

                             IMS_C  77 eileaalkLlrrlidepglpirligvsasnlvekaesqa 115
                                       ++ e al Ll + +d      r++gv++snl+  +++q+
  gi|313126665|ref|YP_004036935.1| 347 LVREVALDLLSEFED---AATRKVGVRVSNLSFTDADQS 382
                                       **********88877...**************7777765 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   8.5e-11   1.9e-07       1      32 []     202     233 ..     202     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 8.5e-11
                           IMS_HHH   1 pddvkefLwplpitkipGiGgklgekLeklGi 32 
                                       p++v+efL+pl++t+++G+G++++ k++ +Gi
  gi|313126665|ref|YP_004036935.1| 202 PGSVSEFLAPLSVTEVHGVGPVTARKMAEMGI 233
                                       689***********************999998 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.8e-09   4.1e-06       3      38 ..     213     248 ..     211     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.8e-09
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLa 38 
                                       ++++v G+Gp+tA+++++ Gi +  dlaaad+ +L 
  gi|313126665|ref|YP_004036935.1| 213 SVTEVHGVGPVTARKMAEMGIQTAGDLAAADPSTLE 248
                                       5789*****************************997 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.8e-08   4.1e-05       4      35 ..     215     247 ..     214     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.8e-08
                   DNA_pol_lambd_f   4 tkvyGVGpktAkkwyakGirtledlra.krakL 35 
                                       t+v+GVGp+tA+k  ++Gi t  dl a ++++L
  gi|313126665|ref|YP_004036935.1| 215 TEVHGVGPVTARKMAEMGIQTAGDLAAaDPSTL 247
                                       68***********************99544555 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   9.7e-06     0.022       8      46 ..     214     252 ..     210     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                              Cdd1   8 lqdiPniGkalaedlvelGirsveelkgedpeelyekle 46 
                                        +++ ++G+ +a+++ e+Gi++  +l+  dp  l e++ 
  gi|313126665|ref|YP_004036935.1| 214 VTEVHGVGPVTARKMAEMGIQTAGDLAAADPSTLEERFG 252
                                       578999**************************9998875 PP

>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0016       3.6      37      63 .]      59      85 ..      57      85 .. 0.93
   2 ?    1.1   0.0      0.23   5.1e+02      14      36 ..     221     242 ..     212     247 .. 0.81
   3 ?   -0.4   0.0      0.66   1.5e+03       8      28 ..     354     370 ..     352     373 .. 0.86
   4 ?   -3.4   0.1       5.6   1.3e+04      40      57 ..     393     410 ..     392     411 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                                      B-SEE-HHHHHTT--TT-BHHHHGGGG CS
                           DUF1805 37 pvesvteaAeelGikeGmtgkeaLekl 63
                                       v+ ++ +A+e+Gi   +   +aLe+l
  gi|313126665|ref|YP_004036935.1| 59 AVATASYEAREYGIDSAQPISQALERL 85
                                      58999*******************987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.23
                                       T--EEE-....-S--SHHHHHHS CS
                           DUF1805  14 gdlaarvivagsGVrtledllaa 36 
                                       g + ar+ +a++G++t  dl aa
  gi|313126665|ref|YP_004036935.1| 221 GPVTARK-MAEMGIQTAGDLAAA 242
                                       5566777.788******999987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.66
                                       HHHHHTT--EEE-....-S-- CS
                           DUF1805   8 ealeklgdlaarvivagsGVr 28 
                                       ++l +++d+a r+    +GVr
  gi|313126665|ref|YP_004036935.1| 354 DLLSEFEDAATRK----VGVR 370
                                       678999******9....9997 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 5.6
                                       EE-HHHHHTT--TT-BHH CS
                           DUF1805  40 svteaAeelGikeGmtgk 57 
                                       s+te A   G  e+  ++
  gi|313126665|ref|YP_004036935.1| 393 SATEDATTAGAMEDAPVA 410
                                       789999999988877665 PP

>> Alpha_GJ  Alphavirus glycoprotein J
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.013        29      19      78 ..     279     341 ..     275     357 .. 0.67
   2 ?    5.5   3.3     0.011        25      37      83 ..     380     425 ..     359     429 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                          Alpha_GJ  19 ltpkaalatgttatvgaana.aavanatganatsaaaa.stiaatvgapp.tdstvaaetPgp 78 
                                       l+ ++a+a  t+ t   an+ +a a   ++ a s +a   ti   v +pp +  t+a+   gp
  gi|313126665|ref|YP_004036935.1| 279 LSRESAFAEATEDTEEKANVvTALAADVAERARSRGAMyRTIGIKVVTPPyDVNTRAQSLSGP 341
                                       788999999999999999995444444455566655432577665555551556666666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                          Alpha_GJ  37 naaavanatganatsaaaastiaatvgapptdstvaaetPgpflptd 83 
                                       + ++    +ga a +++ a+t+ a+ +ap +ds +a + P +  pt+
  gi|313126665|ref|YP_004036935.1| 380 DQSSLDGWEGASASATEDATTAGAMEDAPVADS-PAEDIPAAEQPTE 425
                                       445556667888888888999999999999999.8888998887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2662.54
//
Query:       gi|313126666|ref|YP_004036936.1|  [L=588]
Description: ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-13   50.7   0.5    6.4e-13   49.3   0.0    1.9  2  DUF87           Helicase HerA, central domain
     0.0011   18.9   4.2     0.0027   17.7   4.2    1.6  1  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
     0.0024   17.9   0.0     0.0043   17.1   0.0    1.6  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0027   17.7   3.8       0.01   15.9   3.6    2.1  2  Med9            RNA polymerase II transcription mediator comp
     0.0029   16.3   0.9      0.034   12.8   0.0    2.4  3  DUF853          Bacterial protein of unknown function (DUF853
     0.0031   17.4   2.8      0.005   16.7   2.8    1.3  1  ERM             Ezrin/radixin/moesin family
     0.0045   16.9   0.1      0.011   15.6   0.0    1.7  1  APS_kinase      Adenylylsulphate kinase
  ------ inclusion threshold ------
       0.01   16.2   1.2       0.26   11.6   0.0    3.0  3  AAA_16          AAA ATPase domain
      0.013   15.5   0.0      0.025   14.6   0.0    1.3  1  ResIII          Type III restriction enzyme, res subunit
       0.02   13.8   0.0      0.042   12.8   0.0    1.5  1  TrwB_AAD_bind   Type IV secretion-system coupling protein DNA
      0.024   13.6   0.1       0.13   11.1   0.0    2.0  2  AAA_10          AAA-like domain
      0.038   14.5   3.3      0.099   13.2   3.3    1.7  1  APG6_N          Apg6 coiled-coil region
      0.078   12.9   5.8       0.12   12.3   4.4    2.1  2  Pox_A_type_inc  Viral A-type inclusion protein repeat
      0.081   11.1   1.5       0.13   10.4   1.5    1.2  1  EzrA            Septation ring formation regulator, EzrA
      0.084   12.7   0.8       0.14   12.0   0.8    1.3  1  SKA1            Spindle and kinetochore-associated protein 1
      0.088   13.1   0.1        2.3    8.5   0.0    2.6  2  DUF4754         Domain of unknown function (DUF4754)
      0.091   10.3   4.8       0.12    9.8   4.8    1.1  1  DUF3584         Protein of unknown function (DUF3584)
      0.097   12.8   0.0       0.32   11.1   0.0    1.8  1  AAA_33          AAA domain
      0.099   12.6   0.0       0.21   11.5   0.0    1.5  1  NTPase_1        NTPase
       0.14   10.5   0.1        0.2   10.0   0.1    1.1  1  WDCP            WD repeat and coiled-coil-containing protein 
       0.16   10.8   3.3       0.29    9.9   3.3    1.4  1  Spc7            Spc7 kinetochore protein
       0.18   11.6   6.8       0.18   11.6   2.7    2.1  2  DUF4515         Domain of unknown function (DUF4515)
       0.19   11.5   0.3       0.43   10.3   0.3    1.5  1  AAA_29          P-loop containing region of AAA domain
       0.23   11.2   3.8       0.54   10.1   3.8    1.6  1  DivIC           Septum formation initiator
       0.31   11.3   3.1       0.59   10.4   3.1    1.4  1  DUF5082         Domain of unknown function (DUF5082)
       0.32   11.3   6.7        0.6   10.4   4.9    2.0  2  OmpH            Outer membrane protein (OmpH-like)
       0.85    8.6   2.0        1.2    8.1   2.0    1.2  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
        1.4    9.2   3.6        3.2    8.1   3.6    1.6  1  Spc24           Spc24 subunit of Ndc80
        1.5    9.2   6.0        7.1    7.0   4.2    2.6  2  DUF641          Plant protein of unknown function (DUF641)
        1.6    8.0   7.1        2.7    7.3   7.1    1.2  1  DUF4407         Domain of unknown function (DUF4407)
        2.2    7.9   7.3        1.1    8.9   4.6    1.8  2  Med4            Vitamin-D-receptor interacting Mediator subun


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   1.1e-15   6.4e-13       9     108 ..      24     114 ..      17     172 .. 0.82
   2 ?   -1.8   0.2       4.6   2.7e+03     141     177 ..     307     328 ..     280     357 .. 0.51

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.1e-15
                             DUF87   9 gsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitpspsa 85 
                                       + ++pv+l +  ++t +  i g++GsGKSnt++v +e+ll +++ ++li+D +GEY+ ++     e+++++ +    
  gi|313126666|ref|YP_004036936.1|  24 DPGTPVKLPVVDILTGRGFITGKSGSGKSNTASVVIEKLL-SNNFPVLIVDTDGEYYGLK-----EQFELLHAG--- 91 
                                       5679************************************.*******************.....777777776... PP

                             DUF87  86 kdkelkinpwsldpeelldllee 108
                                        d e  i+++    e l++l+ e
  gi|313126666|ref|YP_004036936.1|  92 ADDECDIQVSPEHAEKLAHLALE 114
                                       56666666666666666655544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.6
                             DUF87 141 epveklleelkkekeelrklknqaiarlldkledllr 177
                                       + ++ l               +q  +++++k++dl+r
  gi|313126666|ref|YP_004036936.1| 307 SEIADL---------------RQELEKKEAKIRDLKR 328
                                       222222...............2222222222222222 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   4.2   4.7e-06    0.0027      17      59 ..     291     333 ..     289     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.7e-06
                        TMF_DNA_bd  17 LmeEGekLskkelklnntikkLrkknkelekeikelkkklekl 59 
                                       L +E+++ s++  + +  i  Lr+++++ e +i++lk++le+ 
  gi|313126666|ref|YP_004036936.1| 291 LVSELQDISDEKARRESEIADLRQELEKKEAKIRDLKRELEEA 333
                                       899*************************************986 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.4e-06    0.0043       4      55 ..      43     158 ..      41     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.4e-06
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                       + +k+G+GK+ +a   +  l  +++ Vl vD+D +      ++gl+++ e                           
  gi|313126666|ref|YP_004036936.1|  43 ITGKSGSGKSNTASVVIEKLLSNNFPVLIVDTDGE------YYGLKEQFELlhagaddecdiqvspehaeklahlal 113
                                       679*******9999999999999***********9......777777777777778888866666665555555555 PP

                                       ............................................C CS
                                       ............................................x RF
                              CbiA  55 ............................................d 55 
                                                                                    
  gi|313126666|ref|YP_004036936.1| 114 eqnvpiildvsgyldeddaqklltevaknlfakekklkkpflmlV 158
                                       555555555555555554444444444444444444444444440 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.6   1.8e-05      0.01      41      78 ..     291     328 ..     290     330 .. 0.95
   2 ?   -1.7   0.0       5.6   3.3e+03      37      50 ..     462     475 ..     460     484 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                              Med9  41 lirelpgidrsveeqeaeieeleeqlakKrelLkkykn 78 
                                       l++el++i+  ++ +e ei++l+++l+kK++ ++++k+
  gi|313126666|ref|YP_004036936.1| 291 LVSELQDISDEKARRESEIADLRQELEKKEAKIRDLKR 328
                                       799********************************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.6
                              Med9  37 karelirelpgidr 50 
                                       + r+++++lp+++r
  gi|313126666|ref|YP_004036936.1| 462 RLRNVVASLPDVSR 475
                                       6899*******997 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   5.8e-05     0.034      21      66 ..      38      83 ..      22     105 .. 0.88
   2 ?    1.4   0.0      0.16        91     289     313 ..     186     210 ..     146     227 .. 0.87
   3 ?   -4.3   0.8       8.9   5.1e+03     402     454 ..     295     345 ..     291     372 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                            DUF853 21 nrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiak 66
                                         G+i+G  G Gk  t  v+ e+l +   pv+++d  G+  g+ +
  gi|313126666|ref|YP_004036936.1| 38 TGRGFITGKSGSGKSNTASVVIEKLLSNNFPVLIVDTDGEYYGLKE 83
                                      5679***********************************9999876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                            DUF853 289 rskGvGvyfvtqnPldlPdtvLaqL 313
                                       r  G G+  ++q P+d+ ++ ++q 
  gi|313126666|ref|YP_004036936.1| 186 RKHGLGIVGISQRPADVKKDFITQC 210
                                       889***************9999986 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 8.9
                            DUF853 402 vagkydeeidresayevLakkvaeaaeaaeqaaaeeekeeesgllgalkdtal 454
                                       ++   de+  res    L +++++++++ ++ + e e  e  +l  + +++a 
  gi|313126666|ref|YP_004036936.1| 295 LQDISDEKARRESEIADLRQELEKKEAKIRDLKRELE--EARDLSHMADQFAQ 345
                                       5555566666666666666666665555544433333..22332222222222 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.8   8.6e-06     0.005      76     137 ..     294     375 ..     284     462 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.6e-06
                               ERM  76 ekeklerklreaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstpsks................ 136
                                       e +++ ++ ++ e+e+a+l++e e+ke++ + Lk+eleear+    a +  +++ ++++                  
  gi|313126666|ref|YP_004036936.1| 294 ELQDISDEKARRESEIADLRQELEKKEAKIRDLKRELEEARDLSHMADQFAQAMFQKAE-Apyrggqgrnlkrpeek 369
                                       556778889999****************************9988766654444444443.34777777555444333 PP

                               ERM 137 .....e 137
                                            e
  gi|313126666|ref|YP_004036936.1| 370 qsalgE 375
                                       222210 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     2e-05     0.011       6      74 ..      42     112 ..      40     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT..--SSHHHHHHHHHHHHHHHHHHHHTT CS
                        APS_kinase   6 wltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkd..LgfseedRkenirrvaevaklladag 74 
                                       ++tG sgsGKs  a  + +kL +++  v ++d d    gL+++  L    +d + +i+   e a++la+ +
  gi|313126666|ref|YP_004036936.1|  42 FITGKSGSGKSNTASVVIEKLLSNNFPVLIVDTDGEYYGLKEQfeLLHAGADDECDIQVSPEHAEKLAHLA 112
                                       79********************************9999998861155566777778888878777776643 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00045      0.26      28     145 ..      42     162 ..      35     179 .. 0.70
   2 ?    0.3   0.4       1.4   7.9e+02      82     129 ..     298     350 ..     277     357 .. 0.68
   3 ?    0.2   0.0       1.5   8.6e+02       2      20 ..     453     471 ..     378     494 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                            AAA_16  28 llsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                       +++G sG+GKs  +  + + l  +++ +l  ++d       y+ l +++   ell + +d++ + ++++ +++ ++ 
  gi|313126666|ref|YP_004036936.1|  42 FITGKSGSGKSNTASVVIEKLLSNNFPVLIVDTDGE-----YYGLKEQF---ELLHAGADDECDIQVSPEHAEKLAH 110
                                       79*******************999866655555555.....56888888...7777777773333333333333333 PP

                            AAA_16 105 la..........avpelagaeasrllellkrll.allsrderplvlvlDdlq 145
                                       la           ++ l+ ++a+ ll ++++ l a+ ++ ++p+++++++ +
  gi|313126666|ref|YP_004036936.1| 111 LAleqnvpiildVSGYLDEDDAQKLLTEVAKNLfAKEKKLKKPFLMLVEECH 162
                                       335566666666445555555566666665555599999999**99999988 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                            AAA_16  82 lrqlldeaesaeleawrekleealaavpelagaea.....srllellkrll.al 129
                                       + +++++ +++e ++ r++le+  a +++l+++++     s++++++++++ ++
  gi|313126666|ref|YP_004036936.1| 298 ISDEKAR-RESEIADLRQELEKKEAKIRDLKRELEeardlSHMADQFAQAMfQK 350
                                       4444444.4447777777777777777777777777777777777777766555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.5
                            AAA_16   2 lvGReeeleqLlsalervr 20 
                                       l GRe+ +e+L++++ ++ 
  gi|313126666|ref|YP_004036936.1| 453 LTGREDVVERLRNVVASLP 471
                                       4456666666665555443 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.3e-05     0.025      26     145 ..      40     165 ..      36     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-05
                                       EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--...... CS
                            ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka..kekd 100
                                       rg+i    G+GK+ +a  +ie+ll+++     +++v++   +  ++e+f+ +   a++e    vs ++ ++  +   
  gi|313126666|ref|YP_004036936.1|  40 RGFITGKSGSGKSNTASVVIEKLLSNNF---PVLIVDTDGEYYGLKEQFELLHAGADDECDIQVSPEHAEKlaHLAL 113
                                       67889999***************99833...4899********************9998555566666666555667 PP

                                       ...-SEEEEEHHHHHHTH...........HHHTTT-S....EEEEETGGGTT CS
                            ResIII 101 stnkkilvttiqsldadseee...eeeseellrdrfd....viiiDEaHrlg 145
                                       ++n  i++     ld+d  ++   e +++ + +++++    ++++ E+H + 
  gi|313126666|ref|YP_004036936.1| 114 EQNVPIILDVSGYLDEDDAQKlltEVAKNLFAKEKKLkkpfLMLVEECHEYI 165
                                       77999999999999999977799844444444444446666********875 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.3e-05     0.042      19      56 ..      42      79 ..      33     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-05
                     TrwB_AAD_bind 19 livGttGsGKtqalekllrairargdraivlDltGafv 56
                                      +i+G  GsGK+++++  ++++ + +  ++++D+ G+++
  gi|313126666|ref|YP_004036936.1| 42 FITGKSGSGKSNTASVVIEKLLSNNFPVLIVDTDGEYY 79
                                      79**********************************98 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.13      25      70 ..      42      87 ..      37     160 .. 0.81
   2 ?   -0.3   0.0      0.67   3.9e+02     258     289 ..     175     205 ..     135     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                            AAA_10 25 liiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe 70
                                      +i+G+ G GKS +a +++  ++  +  +li+D   e +  ke++  
  gi|313126666|ref|YP_004036936.1| 42 FITGKSGSGKSNTASVVIEKLLSNNFPVLIVDTDGEYYGLKEQFEL 87
                                      89**********************************9999998844 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.67
                            AAA_10 258 GkkllkelvRiGRsynaavylvtqsadDvlke 289
                                       Gk +l ++ + GR++   ++ ++q + Dv+k+
  gi|313126666|ref|YP_004036936.1| 175 GK-MLIKIGKRGRKHGLGIVGISQRPADVKKD 205
                                       44.44456677******************886 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.3   0.00017     0.099      65     107 ..     290     332 ..     261     352 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                            APG6_N  65 elleeLkelekereeleaelaaleeelealeeeeerfwreyne 107
                                       +l++eL+++ +e+++ e+e+a+l++ele++e++ +   re  e
  gi|313126666|ref|YP_004036936.1| 290 NLVSELQDISDEKARRESEIADLRQELEKKEAKIRDLKRELEE 332
                                       4555555555555555555555555555555555444444443 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.3   1.4e+03       8      18 ..     307     317 ..     305     319 .. 0.87
   2 ?   12.3   4.4    0.0002      0.12       1      22 [.     314     335 ..     314     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.3
                    Pox_A_type_inc   8 sRIsDLErqLs 18 
                                       s+I DL ++L+
  gi|313126666|ref|YP_004036936.1| 307 SEIADLRQELE 317
                                       6899**99997 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0002
                    Pox_A_type_inc   1 rEmsrlRsRIsDLErqLseCrr 22 
                                       +E++ +  +I+DL+r+L+e+r+
  gi|313126666|ref|YP_004036936.1| 314 QELEKKEAKIRDLKRELEEARD 335
                                       57888888************96 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.5   0.00023      0.13     441     496 ..     297     352 ..     291     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                                       THHHHSTTTSTTTHHHHHHHT-TT--HHHHHHHHHTTTTTSGGGTHHHHHHHHHHH CS
                              EzrA 441 syleelkeasdeieelakeLekkpinikevnkrldeardlveklyektneliktAt 496
                                       ++ +e    + ei +l++eLekk  +i +++++l+eardl +  ++ ++ + ++A+
  gi|313126666|ref|YP_004036936.1| 297 DISDEKARRESEIADLRQELEKKEAKIRDLKRELEEARDLSHMADQFAQAMFQKAE 352
                                       56677778899*******************************99999999999985 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   0.00024      0.14      23     106 ..     293     372 ..     283     420 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                              SKA1  23 edlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaas.saeesksssp 98 
                                       + l++i++e    e+ +++l++el+++e  i +lk e+e+ +     l+h++++  + + +k +a  + ++ ++ ++
  gi|313126666|ref|YP_004036936.1| 293 SELQDISDEKARRESEIADLRQELEKKEAKIRDLKRELEEAR----DLSHMADQFAQAMFQKAEAPyRGGQGRNLKR 365
                                       667888888888899999999999999999999998888777....7899999988887766655404455555555 PP

                                       XXXXXXXX CS
                              SKA1  99 eeeeetes 106
                                       +ee++ ++
  gi|313126666|ref|YP_004036936.1| 366 PEEKQ-SA 372
                                       54443.22 PP

>> DUF4754  Domain of unknown function (DUF4754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0     0.004       2.3      22      60 ..     100     138 ..      95     148 .. 0.87
   2 ?    1.4   0.0       0.7   4.1e+02      45      71 ..     478     503 ..     441     509 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.004
                           DUF4754  22 asgahaelaaresltraikslydvafyiddldaldelsi 60 
                                        s  hae+ a  +l + +  + dv+ y+d+ da + l++
  gi|313126666|ref|YP_004036936.1| 100 VSPEHAEKLAHLALEQNVPIILDVSGYLDEDDAQKLLTE 138
                                       6789****************************9776665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.7
                           DUF4754  45 vafyiddldaldelsilvcaaengehi 71 
                                        afy  ++da d +   v a e g++ 
  gi|313126666|ref|YP_004036936.1| 478 LAFYR-EIDACDPVDAHVAAGEVGDKQ 503
                                       37775.69****************975 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.8   0.00021      0.12     816     910 ..     280     373 ..     276     421 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
                           DUF3584 816 erpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqldqldenlrklrdllsklaelkldadaeqa 892
                                       erp lk+   +l s+++++ +e +r +++    r++lek+   +++++ +l+e+   l  +  + a+  +++  +  
  gi|313126666|ref|YP_004036936.1| 280 ERPDLKSIDGNLVSELQDISDEKARRESEIADLRQELEKKEAKIRDLKRELEEARD-LSHMADQFAQAMFQKAEAPY 355
                                       799999999***************************************99988755.99999999**9999999999 PP

                           DUF3584 893 egelaerlaaleelkrkr 910
                                        g ++  l++ ee ++++
  gi|313126666|ref|YP_004036936.1| 356 RGGQGRNLKRPEEKQSAL 373
                                       999998888888766655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00056      0.32       4      93 ..      43     141 ..      42     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00056
                            AAA_33   4 lvGlpGsGKstlaerllkklg.....avllssdtlrrrlfg..tdqqsktdytrvldrlyqilnelarkalsagrnv 73 
                                       + G +GsGKs  a  +++kl      + ++++d ++  l++  +  +   d     +   ++ ++la+ al+++ ++
  gi|313126666|ref|YP_004036936.1|  43 ITGKSGSGKSNTASVVIEKLLsnnfpVLIVDTDGEYYGLKEqfELLHAGADDECDIQVSPEHAEKLAHLALEQNVPI 119
                                       679*******999999888877887777899999888888776333344444445566778889999999******* PP

                            AAA_33  74 il.datnlsr.rerarflklar 93 
                                       il  +++l++ ++++ + ++a+
  gi|313126666|ref|YP_004036936.1| 120 ILdVSGYLDEdDAQKLLTEVAK 141
                                       **44678888555566666666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00036      0.21       3      30 ..      42      69 ..      40      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                                      EEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkv 30
                                      fiTG++G+GK+   + v+e+l s++++v
  gi|313126666|ref|YP_004036936.1| 42 FITGKSGSGKSNTASVVIEKLLSNNFPV 69
                                      8**********************99987 PP

>> WDCP  WD repeat and coiled-coil-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00034       0.2     558     611 ..     294     351 ..     248     356 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00034
                              WDCP 558 e....kkknlekekeaeqlskelerlsekltevqqsLseltdllqngkk.sspvYplsq 611
                                       e    + +++++e e+  l +ele+  +k+ +++++L e +dl++   + +++++ +  
  gi|313126666|ref|YP_004036936.1| 294 ElqdiSDEKARRESEIADLRQELEKKEAKIRDLKRELEEARDLSHMADQfAQAMFQK-A 351
                                       033335788899*********************************999834455444.3 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.3   0.00051      0.29     205     249 ..     292     336 ..     278     353 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00051
                              Spc7 205 reelaelkaeieekkkelaelqeqleeleekieelkeqkseleee 249
                                        +el++++ e ++++ e+a+l+++le++e+ki +lk + +e+++ 
  gi|313126666|ref|YP_004036936.1| 292 VSELQDISDEKARRESEIADLRQELEKKEAKIRDLKRELEEARDL 336
                                       456777777777777777777777777777777777776666544 PP

>> DUF4515  Domain of unknown function (DUF4515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.39   2.2e+02     149     180 ..     131     162 ..     126     165 .. 0.91
   2 ?   11.6   2.7   0.00031      0.18      22      79 ..     286     339 ..     281     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.39
                           DUF4515 149 aAkkalseftrsvkreNqeLrkeLlqliketk 180
                                        A+k l e  ++++++ ++L+k  l l +e++
  gi|313126666|ref|YP_004036936.1| 131 DAQKLLTEVAKNLFAKEKKLKKPFLMLVEECH 162
                                       6999*************************997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00031
                           DUF4515  22 slwkqyvqeleeierekqelaskyekqtaeLqkqLlqkekeqaklkkeLqalediakl 79 
                                       s+  ++v el++i +ek++ +    +++a L+++L +ke ++ +lk+eL + +d++++
  gi|313126666|ref|YP_004036936.1| 286 SIDGNLVSELQDISDEKARRE----SEIADLRQELEKKEAKIRDLKRELEEARDLSHM 339
                                       566677778888888887664....468888888888888888888888888888766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00075      0.43      23      36 ..      39      52 ..      31      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00075
                            AAA_29 23 gatlltGpsGsGKS 36
                                      g  ++tG+sGsGKS
  gi|313126666|ref|YP_004036936.1| 39 GRGFITGKSGSGKS 52
                                      4579*********9 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.8   0.00093      0.54      21      51 ..     304     334 ..     290     349 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00093
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                       + ++eia+l +el+k+ a++++L++e+++ +
  gi|313126666|ref|YP_004036936.1| 304 RRESEIADLRQELEKKEAKIRDLKRELEEAR 334
                                       4566777777777777777777777777665 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.1     0.001      0.59       3      36 ..     300     333 ..     298     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktkl 36 
                                        ++++++++ia+lr+e+++ e kI+ Lk+  ++ 
  gi|313126666|ref|YP_004036936.1| 300 DEKARRESEIADLRQELEKKEAKIRDLKRELEEA 333
                                       699************************9543333 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.2   1.3e+03      70      99 ..     130     159 ..     108     167 .. 0.76
   2 ?   10.4   4.9     0.001       0.6      11      73 ..     292     356 ..     283     379 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  70 qelqqkqqqkaqelqkkqqellkpildkin 99 
                                       ++ q+++ + a++l +k+++l kp+l  ++
  gi|313126666|ref|YP_004036936.1| 130 DDAQKLLTEVAKNLFAKEKKLKKPFLMLVE 159
                                       566777777777888888887777776665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                                       HHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS...-HHHHHH..HHHHHHHHH CS
                              OmpH  11 leespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e.keekeqe..lqkkeqelq 73 
                                       ++e ++  + +++ e+++++l++ele+ke+++++l++el+ +a++l     + + +  +qk e+ ++
  gi|313126666|ref|YP_004036936.1| 292 VSELQDISDEKARRESEIADLRQELEKKEAKIRDLKRELE-EARDLsHmADQFA-QamFQKAEAPYR 356
                                       5566666666667777777777777777777777777775.3333322322222.224555555444 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.0    0.0021       1.2      67     110 ..     293     336 ..     280     378 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0021
                             Atg14  67 akleelksliadlrerlqelkdklsqlkkeieekkkklaklsdk 110
                                         l+++  ++a+ +++++ l++ l++  ++i++ k++l++ +d 
  gi|313126666|ref|YP_004036936.1| 293 SELQDISDEKARRESEIADLRQELEKKEAKIRDLKRELEEARDL 336
                                       45666666666666667777777777777777777776666654 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.6    0.0055       3.2       6      44 ..     295     335 ..     290     353 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0055
                             Spc24   6 kfriakelsdleselesleselaelkeeleeleeesee..k 44 
                                       +++i+ e    ese+ +l++el+++++++++l++e ee  +
  gi|313126666|ref|YP_004036936.1| 295 LQDISDEKARRESEIADLRQELEKKEAKIRDLKRELEEarD 335
                                       56666666666777777777777777777777766666332 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.63   3.7e+02      38      58 ..     283     303 ..     278     305 .. 0.84
   2 ?    7.0   4.2     0.012       7.1      87     120 ..     302     335 ..     285     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.63
                            DUF641  38 kiqaADkavvseLkklselkr 58 
                                        +++ D  +vseL+ +s+ k 
  gi|313126666|ref|YP_004036936.1| 283 DLKSIDGNLVSELQDISDEKA 303
                                       678999***********9885 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                            DUF641  87 lktyeitvkkleaelkakdseieeLkekLeeaek 120
                                        +  e  + +l++el++k+++i  Lk++Leea+ 
  gi|313126666|ref|YP_004036936.1| 302 KARRESEIADLRQELEKKEAKIRDLKRELEEARD 335
                                       4556788899999999999999999999999876 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.1    0.0046       2.7     130     237 ..     297     421 ..     276     428 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0046
                           DUF4407 130 altaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...........gtgttgvaGkgpaake...kkaql 192
                                       + ++e a+ e++ia+l++e++++ea++++l++e+++  d              +++ + + G+g + k+   k+++l
  gi|313126666|ref|YP_004036936.1| 297 DISDEKARRESEIADLRQELEKKEAKIRDLKRELEEARDLSHmadqfaqamfqKAEAPYRGGQGRNLKRpeeKQSAL 373
                                       34555555555555555555555555555555555444444355555555555555566777777777755566666 PP

                           DUF4407 193 daaqaelaelkakld....atarlaalraelaeleaerakeraasqaaa 237
                                        +++a  +  +++ d    ++a +aa+++  a+++++ ++e++a ++a+
  gi|313126666|ref|YP_004036936.1| 374 GEYNAPKNGSDGT-DaatsSDAGTAAADDATASVREDESHEEEAVTSAT 421
                                       6666655555555.33444555555555555555555444444444443 PP

>> Med4  Vitamin-D-receptor interacting Mediator subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.6    0.0019       1.1       9      57 ..     286     335 ..     282     356 .. 0.79
   2 ?   -2.6   0.0       6.6   3.8e+03     165     179 ..     394     410 ..     345     422 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0019
                              Med4   9 aaddelskslkele.ehqknearilqLraeveslDekikeivksLkeyek 57 
                                       + d +l + l+ ++ e   +e +i  Lr+e e+++ ki+++ ++L e++ 
  gi|313126666|ref|YP_004036936.1| 286 SIDGNLVSELQDISdEKARRESEIADLRQELEKKEAKIRDLKRELEEARD 335
                                       56666777777665145567899**********************99985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                              Med4 165 rkseeaegr..reeeer 179
                                       + ++ a+    +++e +
  gi|313126666|ref|YP_004036936.1| 394 AGTAAADDAtaSVREDE 410
                                       22222211122222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1351  (0.0753528); expected 358.6 (0.02)
Passed bias filter:                      943  (0.0525964); expected 358.6 (0.02)
Passed Vit filter:                       232  (0.0129399); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.87u 0.36s 00:00:01.23 Elapsed: 00:00:00.53
# Mc/sec: 3311.31
//
Query:       gi|313126667|ref|YP_004036937.1|  [L=214]
Description: triosephosphate isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-08   32.0   0.0    9.6e-08   31.7   0.0    1.1  1  TIM             Triosephosphate isomerase
     0.0031   16.8   1.4     0.0031   16.8   1.4    2.2  2  ThiG            Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
       0.07   12.3   0.0       0.12   11.6   0.0    1.6  1  IGPS            Indole-3-glycerol phosphate synthase
        0.1   12.7   2.2       0.42   10.7   0.3    2.5  2  Hydrolase_like  HAD-hyrolase-like
       0.56    9.2   7.8       0.07   12.2   3.0    1.9  2  FMN_dh          FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.7e-11   9.6e-08      22     122 ..      20     112 ..       1     118 [. 0.78

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.7e-11
                                       HHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHHHHTT-SEEEES-HHHHHHS CS
                               TIM  22 klkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaemlkdlgvkyviiGHsErrqlf 98 
                                       ++++  +e+ v++++ap++  +++v    +++ +++ aq v+ +  G++TG++ ae ++++g++ ++i HsE+r  +
  gi|313126667|ref|YP_004036937.1|  20 AAHEVAEESGVRIAVAPQAADVRRV----ADTGVETWAQHVDPNGYGSHTGSTLAEAVAEAGADGTLINHSEKRLKL 92 
                                       333444456899******9999975....56889****************************************988 PP

                                       T--HHHHHHHHHHHHHTT-EEEEE CS
                               TIM  99 kEtdelvakKvkaalksglkpilC 122
                                        + d      v+aa  +gl++ +C
  gi|313126667|ref|YP_004036937.1|  93 ADID----GSVQAAARAGLETCVC 112
                                       7655....5556666667777666 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.6      0.15   5.2e+02     190     206 ..      70      86 ..      27     125 .. 0.69
   2 !   16.8   1.4   8.7e-07    0.0031     175     215 ..     165     205 ..     150     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                                       HHHHHHTT-SEEEESHH CS
                              ThiG 190 aaqamelGadavllnta 206
                                       a ++ e Gad+ l+n +
  gi|313126667|ref|YP_004036937.1|  70 AEAVAEAGADGTLINHS 86 
                                       33456888888888865 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 8.7e-07
                                       SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 175 kvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                       +v v   AGi s  d+ +a +lGa+++ll++ va+a+dp a
  gi|313126667|ref|YP_004036937.1| 165 SVEVFCGAGISSGDDVDAAGDLGATGILLASGVAKADDPRA 205
                                       6888999*******************************965 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.3e-05      0.12     201     254 .]     157     210 ..      70     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
                                       HHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 201 eLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekairel 254
                                       e a+ v+++v + +  Gi++ +dv +  + g+ ++L  + + +++d ++a+++l
  gi|313126667|ref|YP_004036937.1| 157 EAAANVDESVEVFCGAGISSGDDVDAAGDLGATGILLASGVAKADDPRAALEDL 210
                                       55677889999*************************************999876 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.19   6.7e+02      35      49 ..      99     113 ..      92     132 .. 0.80
   2 ?   10.7   0.3   0.00012      0.42      33      59 ..     178     203 ..     175     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.19
                                       HHHHHHCT-EEEEES CS
                    Hydrolase_like  35 iagAnnaGwksvLVl 49 
                                       +++A +aG++++  +
  gi|313126667|ref|YP_004036937.1|  99 VQAAARAGLETCVCA 113
                                       6899*****999765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                                       THHHHHHHCT-EEEEESSSSS-TTTHH CS
                    Hydrolase_like  33 tDiagAnnaGwksvLVltGvtrpedle 59 
                                       +D+ +A + G++++L ++Gv +++d +
  gi|313126667|ref|YP_004036937.1| 178 DDVDAAGDLGATGILLASGVAKADD-P 203
                                       79******************99988.3 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.38   1.4e+03      81     106 ..      99     124 ..      73     132 .. 0.78
   2 ?   12.2   3.0   1.9e-05      0.07     263     301 ..     157     195 ..     141     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.38
                                       HHHHHHHTS-EEEETT-SS-HHHHHH CS
                            FMN_dh  81 araaakagipfvlstvastsleevaa 106
                                       ++aaa+ag+  ++  ++ +++ +vaa
  gi|313126667|ref|YP_004036937.1|  99 VQAAARAGLETCVCANNPAQIGAVAA 124
                                       67888888888888888888887776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.9e-05
                                       HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESH CS
                            FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGR 301
                                       e +++v++++ev++  Gi++G Dv  A  lGA+++ll+ 
  gi|313126667|ref|YP_004036937.1| 157 EAAANVDESVEVFCGAGISSGDDVDAAGDLGATGILLAS 195
                                       456777789*************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1262.99
//
Query:       gi|313126668|ref|YP_004036938.1|  [L=142]
Description: hypothetical protein Hbor_19260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1035.58
//
Query:       gi|313126669|ref|YP_004036939.1|  [L=175]
Description: XRE family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-10   39.4   0.2    9.2e-10   38.4   0.2    1.4  1  HTH_3           Helix-turn-helix
    6.5e-09   35.7   0.3      1e-08   35.1   0.3    1.3  1  HTH_19          Helix-turn-helix domain
    1.5e-07   31.7   0.0    2.6e-07   30.9   0.0    1.4  1  HTH_31          Helix-turn-helix domain
    2.7e-05   23.9   0.1    4.4e-05   23.2   0.1    1.3  1  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.062   11.6   7.1      0.056   11.7   7.1    1.1  1  RAP1            Rhoptry-associated protein 1 (RAP-1)
        0.1   12.5   0.0       0.17   11.9   0.0    1.3  1  HTH_37          Helix-turn-helix domain
       0.14   10.7   6.2       0.14   10.7   6.2    1.0  1  Macoilin        Macoilin family
       0.17   12.3   1.5       0.28   11.6   1.5    1.4  1  IATP            Mitochondrial ATPase inhibitor, IATP
       0.42   10.3   6.1        0.6    9.8   6.1    1.4  1  CCDC106         Coiled-coil domain-containing protein 106
          1    7.0   7.7       0.98    7.1   7.7    1.2  1  PI3K_1B_p101    Phosphoinositide 3-kinase gamma adapter prote
        1.1    8.0   7.7        1.4    7.7   7.7    1.1  1  Apt1            Golgi-body localisation protein domain
        1.2    9.2  13.0        4.8    7.2  13.0    1.8  2  Pox_A12         Poxvirus A12 protein
        1.9    9.1  18.4        1.5    9.4  15.9    2.0  2  Secretin_N_2    Secretin N-terminal domain
        2.9    7.9  10.5        4.1    7.4  10.5    1.3  1  DUF4614         Domain of unknown function (DUF4614)
        3.2    5.7  11.7        4.2    5.3  11.7    1.1  1  Sporozoite_P67  Sporozoite P67 surface antigen
        3.2    6.1  11.7        3.6    5.9  11.7    1.2  1  DUF515          Protein of unknown function (DUF515)
        8.5    5.9  21.4         11    5.5  21.4    1.2  1  RSRP            Arginine/Serine-Rich protein 1


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.2   8.7e-13   9.2e-10       1      54 [.      95     148 ..      95     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 8.7e-13
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54 
                                       ++++R+ +g+sqe+LA+ l+ + s i+++E+G+  P   + kkl++ L++sl e
  gi|313126669|ref|YP_004036939.1|  95 IRQARENNGMSQEDLADSLNEKASLIRKLERGDILPPDNVRKKLERKLDISLVE 148
                                       8**************************************************975 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.3   9.7e-12     1e-08       3      56 ..      94     146 ..      93     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 9.7e-12
                            HTH_19   3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidl 56 
                                       r+++aRe++g++qe+la+ l    s i+++E g +  p+ ++ +k+ ++l+i+l
  gi|313126669|ref|YP_004036939.1|  94 RIRQARENNGMSQEDLADSLNEKASLIRKLERGDI-LPPDNVRKKLERKLDISL 146
                                       9********************************88.777666688888888874 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.4e-10   2.6e-07       5      57 ..      94     145 ..      93     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.4e-10
                            HTH_31   5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57 
                                       + r++Re  G+sqe++A+ l+  +s +++lE+G + +p+  v  +l r l+ +
  gi|313126669|ref|YP_004036939.1|  94 RIRQARENNGMSQEDLADSLNEKASLIRKLERGDI-LPPDNVRKKLERKLDIS 145
                                       88*********************************.9**99999999988876 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   4.2e-08   4.4e-05       1      35 [.      94     128 ..      94     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.2e-08
                                       HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                            HTH_25   1 rLraaRearglsleevaketkIrkdylealEeddf 35 
                                       r r+aRe  g+s e++a+ ++ +++++++lE++d+
  gi|313126669|ref|YP_004036939.1|  94 RIRQARENNGMSQEDLADSLNEKASLIRKLERGDI 128
                                       579*****************************974 PP

>> RAP1  Rhoptry-associated protein 1 (RAP-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   7.1   5.4e-05     0.056     121     176 ..      27      82 ..       3     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                              RAP1 121 efkasqsvvktskpkststeslksssdskskasaksnvksaskyGesssseesatd 176
                                       ef ++     +s   st+ ++  ss  s+s++sa s++ s+s  G+s+      +d
  gi|313126669|ref|YP_004036939.1|  27 EFGTEVRTESSSASGSTKYSTSSSSGSSSSSSSASSGSSSSSSSGGSTRRRRDMFD 82 
                                       44444433334444444444444555556666777788888888888766555554 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016      0.17      22      56 ..      94     128 ..      80     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                                       HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                            HTH_37  22 aiaeliekrelsqseaaqllgiaqPkvsrllrgkl 56 
                                       +i++ +e ++ sq+++a  l+ + + + +l+rg++
  gi|313126669|ref|YP_004036939.1|  94 RIRQARENNGMSQEDLADSLNEKASLIRKLERGDI 128
                                       599*****************************975 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   6.2   0.00014      0.14     320     401 ..      32     113 ..       4     148 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                          Macoilin 320 ssssssssnknskkasagsagssnssskkhsessksvtsssssknskkqklpaGkssaalkdaaenslpnnqlskkd 396
                                         ++sss++ ++k ++++s+gss+sss   s ss+s +s+ s++  +     + + +a   d++ +   nn +s++d
  gi|313126669|ref|YP_004036939.1|  32 VRTESSSASGSTKYSTSSSSGSSSSSSSASSGSSSSSSSGGSTRRRRDMFDDMDEIAADYDDRIRQARENNGMSQED 108
                                       23333333333333333333333333332222222222222222222222223344446666666666666666666 PP

                          Macoilin 397 alvrL 401
                                           L
  gi|313126669|ref|YP_004036939.1| 109 LADSL 113
                                       54333 PP

>> IATP  Mitochondrial ATPase inhibitor, IATP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.5   0.00026      0.28      16      70 ..      45     101 ..      32     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                              IATP  16 vsaasfsvaarrmgEgdsGapkgtGggGsireagdafgkrE..aAsEeeyirqreke 70 
                                        s++s+s  ++  +   sG+  ++ +gGs r++ d f  ++  aA+ +  irq +++
  gi|313126669|ref|YP_004036939.1|  45 YSTSSSSGSSSSSSSASSGSSSSSSSGGSTRRRRDMFDDMDeiAADYDDRIRQAREN 101
                                       356667777777778899999999999***********9974567888899987654 PP

>> CCDC106  Coiled-coil domain-containing protein 106
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.1   0.00057       0.6      58     105 ..      34      80 ..      19     122 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00057
                           CCDC106  58 skksekkaeksesessssseesddsssdssessessegsstekkkkkk 105
                                       +++s ++  ++ s+ssss+++s +sss+ss ss+ss++  ++++++  
  gi|313126669|ref|YP_004036939.1|  34 TESSSASGSTKYSTSSSSGSSS-SSSSASSGSSSSSSSGGSTRRRRDM 80 
                                       3333333333344444444444.3444455555555554555555544 PP

>> PI3K_1B_p101  Phosphoinositide 3-kinase gamma adapter protein p101 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.7   0.00093      0.98     325     411 ..      23     106 ..       4     173 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00093
                      PI3K_1B_p101 325 deeedleeeeeeeeedslarsstlstvsssskdsmlsllslsssslassvsslssgvdsdyvedsdessssspvaek 401
                                       d+ +++ +e  ++e++s++ s+++st sss   s++s++s ss s++ss+s+ s     d+++d+de   +   + +
  gi|313126669|ref|YP_004036939.1|  23 DDCSEFGTE-VRTESSSASGSTKYSTSSSS--GSSSSSSSASSGSSSSSSSGGSTRRRRDMFDDMDEIAADYDDRIR 96 
                                       333333333.33333444455555554444..333455555555555555666666666999999998887773333 PP

                      PI3K_1B_p101 402 kekkskkksk 411
                                       + ++++  s+
  gi|313126669|ref|YP_004036939.1|  97 QARENNGMSQ 106
                                       3333333333 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   7.7    0.0013       1.4     315     359 ..      37      93 ..       7     148 .. 0.38

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                              Apt1 315 eeddesdeesessssssssssssassssssssrssslelrlkpt.............s 359
                                       ++ + s++ s+ssss sssssssass sssss+s+ +++r++ +             +
  gi|313126669|ref|YP_004036939.1|  37 SSASGSTKYSTSSSSGSSSSSSSASSGSSSSSSSGGSTRRRR-DmfddmdeiaadydD 93 
                                       111111111111111111111111111111222221111111.112223222222220 PP

>> Pox_A12  Poxvirus A12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   3.8      0.18   1.9e+02      69      94 ..      28      53 ..      10      55 .. 0.79
   2 ?    7.2  13.0    0.0046       4.8      64     119 ..      42     103 ..      23     105 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.18
                           Pox_A12 69 lislskkkssssskstrksskkssGa 94
                                        +  ++ sss+s st+ s++ ssG+
  gi|313126669|ref|YP_004036939.1| 28 FGTEVRTESSSASGSTKYSTSSSSGS 53
                                      555668899999***********997 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0046
                           Pox_A12  64 kkskklislskkkssssskst.rksskkssGapvrkktvfssvne.....dtqivqavtnaG 119
                                       + +  ++s s + sssss s  + ss+ s G+ +r++++f +++e     d +i qa  n G
  gi|313126669|ref|YP_004036939.1|  42 STKYSTSSSSGSSSSSSSASSgSSSSSSSGGSTRRRRDMFDDMDEiaadyDDRIRQARENNG 103
                                       22222333444444444544414445555577889999**9988643334566777777666 PP

>> Secretin_N_2  Secretin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  15.9    0.0014       1.5      19      72 ..      30      83 ..      23      89 .. 0.57
   2 ?   -1.4   0.0       3.3   3.5e+03      31      38 ..     156     163 ..     138     171 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                      Secretin_N_2 19 tsvtsGsvsssgsssssssssssssgsssssssssnsssgtkietesesdfwge 72
                                      t+v + s s+sgs++ s+ssss+ss+ssss ss+s+sss++  +t+   d++++
  gi|313126669|ref|YP_004036939.1| 30 TEVRTESSSASGSTKYSTSSSSGSSSSSSSASSGSSSSSSSGGSTRRRRDMFDD 83
                                      667777777777766666666655444444444444445555555555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.3
                      Secretin_N_2  31 ssssssss 38 
                                       + s++ss+
  gi|313126669|ref|YP_004036939.1| 156 EWSGGSST 163
                                       22222222 PP

>> DUF4614  Domain of unknown function (DUF4614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  10.5    0.0039       4.1      13      61 ..      37      76 ..      23     120 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0039
                           DUF4614 13 ssesessssssessssrslssssesslssksssstdsksssqssestkk 61
                                      ss+s s++ s +sss +s+         s+ss+s+ s+sss+s  st++
  gi|313126669|ref|YP_004036939.1| 37 SSASGSTKYSTSSSSGSSS---------SSSSASSGSSSSSSSGGSTRR 76
                                      1111111111111111111.........112222222122222222221 PP

>> Sporozoite_P67  Sporozoite P67 surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  11.7    0.0039       4.2     271     313 ..      34      76 ..      10      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0039
                    Sporozoite_P67 271 gaatssssttspssstttttpassgpsaqgshgsssrnavtrs 313
                                        +++s+s +t+ s+s+++  ++ss+ +++gs  sss  ++tr+
  gi|313126669|ref|YP_004036939.1|  34 TESSSASGSTKYSTSSSSGSSSSSSSASSGSSSSSSSGGSTRR 76 
                                       4677788889999999999999888888999999999999986 PP

>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  11.7    0.0034       3.6     325     368 ..      29      69 ..      11     115 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0034
                            DUF515 325 sstsssessstsespGdvsisdsssasdsssvsqstseslsssi 368
                                       + +  +esss+s   G + +s sss+ +sss s ++s s+sss 
  gi|313126669|ref|YP_004036939.1|  29 GTEVRTESSSAS---GSTKYSTSSSSGSSSSSSSASSGSSSSSS 69 
                                       444444443333...33333333333333333333333333322 PP

>> RSRP  Arginine/Serine-Rich protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  21.4     0.011        11      17      63 ..      33      78 ..      21     102 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                              RSRP 17 ksPstsssGsssrl.ssrsrsrsssrssrshsrsssrsssrsrsrprr 63
                                       + s+s+sGs+  + ss s s+sss s++s+s+sss  ss   +r rr
  gi|313126669|ref|YP_004036939.1| 33 RTESSSASGSTKYStSSSSGSSSSSSSASSGSSSSS--SSGGSTRRRR 78
                                      455777777764330333344444444444444444..4444455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1287  (0.0717831); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1143.12
//
Query:       gi|313126670|ref|YP_004036940.1|  [L=200]
Description: phosphatidylglycerophosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-07   30.2   1.5    5.8e-07   30.2   1.5    2.2  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   1.5   3.2e-11   5.8e-07       3      66 .]      28      93 ..      26      93 .. 0.81
   2 ?    0.3   0.4     0.071   1.3e+03       6      18 ..     150     162 ..     101     190 .. 0.61

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.2e-11
                                      HHHHHHHHHHHHHHHHHGGGS-H......HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyp....lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      P+ ++++ + ++++a + ++   +    + l+ l++++ + +D++DG lAR  +  s+ G+llD+++D
  gi|313126670|ref|YP_004036940.1| 28 PDGVSVVAFGFALAAGVAFYL--GgtmwYALGGLFVFLNGWLDLVDGALARAQGIASEGGDLLDHVLD 93
                                      888888888888888875533..235656677777789***************99999********99 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.071
                                       HHHHHHHHHHHHH CS
                   CDP-OH_P_transf   6 iTllrlllsvlai 18 
                                       + l++l++ v+a+
  gi|313126670|ref|YP_004036940.1| 150 LALIGLFAFVAAA 162
                                       3344444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1276.45
//
Query:       gi|313126671|ref|YP_004036941.1|  [L=171]
Description: nucleoside kinase, cmp and amp kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-25   88.8   0.2    5.3e-25   88.4   0.2    1.2  1  AAA_18           AAA domain
    1.5e-07   31.9   0.2     0.0042   17.5   0.0    2.4  3  AAA_17           AAA domain
    2.4e-07   31.0   0.5     0.0085   16.3   0.0    2.1  2  AAA_33           AAA domain
    4.5e-06   26.9   0.3      0.057   13.5   0.1    2.1  2  SKI              Shikimate kinase
    0.00022   21.2   0.0    0.00041   20.4   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00046   20.5   0.7    0.00046   20.5   0.7    2.2  2  AAA_28           AAA domain
    0.00049   20.5   0.1     0.0013   19.1   0.1    1.9  1  AAA              ATPase family associated with various cellul
    0.00062   19.7   0.3       0.19   11.6   0.0    2.1  2  dNK              Deoxynucleoside kinase
     0.0064   16.2   0.2        1.9    8.1   0.0    2.1  2  Thymidylate_kin  Thymidylate kinase
     0.0066   16.7   0.1      0.012   15.9   0.2    1.6  1  AAA_22           AAA domain
     0.0075   16.7   1.8      0.017   15.5   1.8    1.7  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.012   14.9   0.1      0.041   13.2   0.0    1.8  2  Zeta_toxin       Zeta toxin
      0.019   14.9   0.4      0.046   13.6   0.1    1.8  2  NTPase_1         NTPase
      0.044   14.1   0.1      0.089   13.1   0.1    1.5  1  AAA_19           AAA domain
       0.08   12.7   0.5      0.097   12.4   0.5    1.5  1  AAA_24           AAA domain
        0.1   12.3   0.0       0.22   11.3   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.11   11.7   0.0       0.18   11.0   0.0    1.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.18   11.5   4.7        0.6    9.8   3.9    2.3  2  AAA_30           AAA domain
       0.51   10.0   2.3        2.3    7.8   0.3    2.5  2  CoaE             Dephospho-CoA kinase
       0.82    9.0   3.0          1    8.6   0.7    2.0  2  ATPase           KaiC


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.2     6e-28   5.3e-25       2     130 .]       6     118 ..       5     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 6e-28
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknl 77 
                                       ++tGtpG+GKtt+++ ++ r+ + +++l+d ++e++l +e+d++  ++s+++d d ++++l ++++           
  gi|313126671|ref|YP_004036941.1|   6 VITGTPGTGKTTVSDLVAARTDLdVIHLNDAIREEELFTERDAD--RDSLVADVDAVAEWLGEWDG----------- 69 
                                       69******************999*********************..**********9999988888........... PP

                            AAA_18  78 vidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                       ++d+hla+l++++      vvL+++peel+eRl++R+++eak +en e+e+ld
  gi|313126671|ref|YP_004036941.1|  70 ILDSHLAHLFDADEA----VVLRCHPEELKERLRERDESEAKVAENAESEALD 118
                                       9***********999....*******************************985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.7e-06    0.0042       1      33 [.       8      40 ..       8      61 .. 0.86
   2 !   12.9   0.1   0.00012      0.11      71     133 ..      50     113 ..      41     116 .. 0.70
   3 ?   -2.9   0.0       9.6   8.6e+03      29      65 ..     119     154 ..     118     159 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.7e-06
                                      EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllree 33
                                      +G PG GK+t+++ ++ + ++ ++   d +ree
  gi|313126671|ref|YP_004036941.1|  8 TGTPGTGKTTVSDLVAARTDLDVIHLNDAIREE 40
                                      69*****************99999999****87 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                                       SSEEEEEE-SEEEETTEEEESSHHHHHHHH...SEEEEEE--HHHHHHHHHHHTTST-.TS-SHH CS
                            AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkp.daiilleadpeeilerrlkdrtrgr.dddnee 133
                                       ++ ++ d  ++ ++  g++dg+ +  l+ l+  d  ++l + pee+ er+ ++++++    +n+e
  gi|313126671|ref|YP_004036941.1|  50 RDSLVADVDAVAEW-LGEWDGILDSHLAHLFDaDEAVVLRCHPEELKERLRERDESEAkVAENAE 113
                                       44455555555544.6778888887777775549***************9999666552666766 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.6
                                       HHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHH CS
                            AAA_17  29 llreeakrgglakardemrklpleekkelqkeaaeki 65 
                                       ++ +e  ++  +++  e+++   ++ + + + ++++i
  gi|313126671|ref|YP_004036941.1| 119 VILAETVERFGEESVYEIDTT-DRPPESVADDVIAAI 154
                                       555555555444444444333.355555555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.5e-06    0.0085       3      43 ..       6      47 ..       5      74 .. 0.67
   2 !   13.4   0.3   7.4e-05     0.067      93     138 ..      77     122 ..      57     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.5e-06
                            AAA_33  3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqq 43
                                      ++ G pG+GK+t+++ ++++++  +++l+  +  + lf  +++
  gi|313126671|ref|YP_004036941.1|  6 VITGTPGTGKTTVSDLVAARTDldVIHLNDAIREEELFT-ERD 47
                                      578***************999965555554433337775.333 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.4e-05
                            AAA_33  93 rrlgvpvrivvvetdeetlkeRlakRaang.ddrsevpeealdrqka 138
                                       + ++ ++++vv+++ +e+lkeRl++R +++ +++ +++ eald  +a
  gi|313126671|ref|YP_004036941.1|  77 HLFD-ADEAVVLRCHPEELKERLRERDESEaKVAENAESEALDVILA 122
                                       4444.589********************9866777899999887766 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00024      0.21       1      30 [.      11      40 ..      11      47 .. 0.89
   2 !   13.5   0.1   6.3e-05     0.057      87     157 ..      83     154 ..      70     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                      TTSSHHHHHHHHHHHHTSEEEEHHHHHHHH CS
                               SKI  1 mGaGKstvGkllAkklglefiDlDeliekr 30
                                      +G+GK+tv  l+A + +l++i l + i ++
  gi|313126671|ref|YP_004036941.1| 11 PGTGKTTVSDLVAARTDLDVIHLNDAIREE 40
                                      69********************99888654 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.3e-05
                                       EEEEEE--HHHHHHHHHHTTS.SGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHHHHHH CS
                               SKI  87 iviyLdvsleellerlkadke.RPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeeileal 157
                                         + L++++eel erl++++e  + + e+ ++e+l+  lae  + + e + + +d++++++e va+ +++a+
  gi|313126671|ref|YP_004036941.1|  83 EAVVLRCHPEELKERLRERDEsEAKVAENAESEALDVILAETVERFGEESVYEIDTTDRPPESVADDVIAAI 154
                                       567899**********9999988888888888888888888888888889*****************99987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.5e-07   0.00041       2      56 ..       5      56 ..       4     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.5e-07
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--......... CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvd 56
                                      +++ G pGtgK+++++ +aa++   + ++ l++ ++ee+l+ +r+  +++    d
  gi|313126671|ref|YP_004036941.1|  5 LVITGTPGTGKTTVSDLVAART--DLDVIHLNDAIREEELFTERDA-DRDSLVAD 56
                                      6899***************987..57789***************95.55544444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.7   5.1e-07   0.00046       1      33 [.       4      39 ..       4      65 .. 0.74
   2 ?    2.3   0.4       0.2   1.8e+02      53      87 ..      31      64 ..      26     141 .. 0.49

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.1e-07
                            AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaare 33
                                      + vitG+++tGKTt++   aar +  v+   +a re
  gi|313126671|ref|YP_004036941.1|  4 RLVITGTPGTGKTTVSDLVAARtDLDVIhlNDAIRE 39
                                      579*****************9875555434777664 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                            AAA_28 53 lafaervleeqleeeaaaaankvlfcDrglldtla 87
                                      +++++++ ee+l +e++a +++ l+ D ++++++ 
  gi|313126671|ref|YP_004036941.1| 31 IHLNDAIREEELFTERDA-DRDSLVADVDAVAEWL 64
                                      555555555555555554.5555555555555443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.5e-06    0.0013       2      33 ..       6      37 ..       5     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-06
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTT CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgse 33
                                      +++G+pGtGKT++   va  ++ +++ ++ + 
  gi|313126671|ref|YP_004036941.1|  6 VITGTPGTGKTTVSDLVAARTDLDVIHLNDAI 37
                                      689*****************999988887554 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0067         6       1      27 [.       5      31 ..       5      40 .. 0.87
   2 !   11.6   0.0   0.00021      0.19     114     160 ..      72     118 ..      37     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0067
                                      EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                      +v+ G+ g GK+t+ +l + +++  v+
  gi|313126671|ref|YP_004036941.1|  5 LVITGTPGTGKTTVSDLVAARTDLDVI 31
                                      6899**************999987665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00021
                                       HHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHH CS
                               dNK 114 dnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLh 160
                                       d  l +l   d  + L++++e+++er+++R+++e k  e +  e+L 
  gi|313126671|ref|YP_004036941.1|  72 DSHLAHLFDADEAVVLRCHPEELKERLRERDESEAKVAENAESEALD 118
                                       4444455559999******************9998866665555555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0065       5.8       3      21 ..       9      27 ..       7      45 .. 0.83
   2 !    8.1   0.0    0.0021       1.9     122     179 ..      85     144 ..      67     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0065
                                      ESTTSSHHHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlk 21
                                      G  G+GKtt+++l+++r +
  gi|313126671|ref|YP_004036941.1|  9 GTPGTGKTTVSDLVAARTD 27
                                      888***********99865 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                                       EEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHH..TTSTEEEEETTS-.HH CS
                   Thymidylate_kin 122 flldvdpevalkRlakrdeldeeeeeqldflrkvrerylelak..ederiliidasks.ie 179
                                       + l + pe+  +Rl++rde++ +++e+ ++ + +   + e ++   +e+++ id+++   e
  gi|313126671|ref|YP_004036941.1|  85 VVLRCHPEELKERLRERDESEAKVAENAES-EALDVILAETVErfGEESVYEIDTTDRpPE 144
                                       456779*************88888888773.444444444444345777778887765345 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   1.3e-05     0.012       8      36 ..       5      33 ..       2     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakae 36
                                      lv+tG +GtGKTt+   ++ + d +  + 
  gi|313126671|ref|YP_004036941.1|  5 LVITGTPGTGKTTVSDLVAARTDLDVIHL 33
                                      79*************99999886544443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.8   1.9e-05     0.017      26     127 ..       4     125 ..       1     160 [. 0.50

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                            AAA_16  26 lvllsGesGvGKsslvrellralekd..........ggiflrgkcdqlesa........ipysalaqalareellrq 84 
                                        ++++G +G+GK+++ + ++ +   d          + +f++ ++d+   +        ++ +  ++ +   + l+ 
  gi|313126671|ref|YP_004036941.1|   4 RLVITGTPGTGKTTVSDLVAARTDLDvihlndaireEELFTERDADRD--SlvadvdavAEWLGEWDGILD-SHLAH 77 
                                       689*****************7555554444433443233333333333..022222222222332222212.22333 PP

                            AAA_16  85 lldeaesaeleawrekleeala.....avpelagaea.....srllellkrll 127
                                       l d++e+  l+ ++e+l+e+l+     +++      a     ++l   l++ +
  gi|313126671|ref|YP_004036941.1|  78 LFDADEAVVLRCHPEELKERLRerdesEAKV-----AenaesEALDVILAETV 125
                                       3333444455555555555555333321112.....12222355555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.5e-05     0.041      20      56 ..       6      39 ..       4      66 .. 0.85
   2 ?   -0.8   0.1      0.87   7.8e+02     128     155 ..      86     110 ..      76     142 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                        Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                                      ++ G pG GK+++++l+++++  + +v++l+ D +Re
  gi|313126671|ref|YP_004036941.1|  6 VITGTPGTGKTTVSDLVAART--DLDVIHLN-DAIRE 39
                                      689*****************9..89****97.66665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.87
                        Zeta_toxin 128 vvavkkelSrlgvldRyeeevaegRlvp 155
                                       v+ +++e+  +++++R e e   + +++
  gi|313126671|ref|YP_004036941.1|  86 VLRCHPEELKERLRERDESE---AKVAE 110
                                       45555555555555555444...22222 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.1e-05     0.046       2      21 ..       5      24 ..       4      33 .. 0.86
   2 ?   -1.5   0.0       2.3   2.1e+03     133     156 ..      90     109 ..      72     136 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-05
                                      EEEE--TTSSHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvle 21
                                      ++iTG pG+GKtT+ + v+ 
  gi|313126671|ref|YP_004036941.1|  5 LVITGTPGTGKTTVSDLVAA 24
                                      79***********9988876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                                       -SS--SHHHHHHHT-TT-EEEE-- CS
                          NTPase_1 133 hrrkdlalveeirerkdvkvfevt 156
                                       h   +++l e++rer + +  +v 
  gi|313126671|ref|YP_004036941.1|  90 H---PEELKERLRERDE-SEAKVA 109
                                       3...4467777777643.333343 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.9e-05     0.089      12      28 ..       4      20 ..       1      37 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                            AAA_19 12 vllvtaGpGtGKTrvlk 28
                                       l++t+ pGtGKT+v  
  gi|313126671|ref|YP_004036941.1|  4 RLVITGTPGTGKTTVSD 20
                                      689**********9854 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   0.00011     0.097       3      22 ..       3      22 ..       1     149 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      ++++i+G +g+GKTt+    
  gi|313126671|ref|YP_004036941.1|  3 RRLVITGTPGTGKTTVSDLV 22
                                      799************97655 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024      0.22      36      59 ..       5      28 ..       2      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgv 59
                                      ++++G PG Gktt++ ++a+  + 
  gi|313126671|ref|YP_004036941.1|  5 LVITGTPGTGKTTVSDLVAARTDL 28
                                      6799**************987665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.18       4      24 ..       5      25 ..       2      55 .. 0.80
   2 ?   -3.2   0.0       4.3   3.9e+03     208     224 ..      91     107 ..      75     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                           DUF2075  4 vlVtGvaGtGKtvvllnllae 24
                                      +++tG +GtGKt v   ++a+
  gi|313126671|ref|YP_004036941.1|  5 LVITGTPGTGKTTVSDLVAAR 25
                                      79**********997665555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.3
                           DUF2075 208 leelkkalkeknkesgr 224
                                       +eelk+ l+e+++ + +
  gi|313126671|ref|YP_004036941.1|  91 PEELKERLRERDESEAK 107
                                       56666666666655544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.9   0.00066       0.6      21      59 ..       5      40 ..       1     109 [. 0.59
   2 ?   -0.1   0.1      0.72   6.4e+02     149     173 ..      92     116 ..      84     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00066
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrviglAptgkaA 59
                                       v+tG +GtGKtt+   +++       +vi l    +  
  gi|313126671|ref|YP_004036941.1|  5 LVITGTPGTGKTTVSDLVAART---DLDVIHLNDAIREE 40
                                      689**********977665433...34555555555554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.72
                            AAA_30 149 aeLtevvRqkeseeraaalalregd 173
                                        eL+e  R ++++e+++a++ ++  
  gi|313126671|ref|YP_004036941.1|  92 EELKERLRERDESEAKVAENAESEA 116
                                       6899999999999999998877665 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0026       2.3       5      30 ..       7      33 ..       4      56 .. 0.84
   2 ?    0.5   0.1      0.46   4.1e+02     123     152 ..      82     111 ..      70     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0026
                                      EEESTTSSHHHHHHHHHH.TT-EEEEH CS
                              CoaE  5 ltGgiasGKstvanlfad.lgvpivDa 30
                                      +tG  ++GK+tv++l a+ + ++++  
  gi|313126671|ref|YP_004036941.1|  7 ITGTPGTGKTTVSDLVAArTDLDVIHL 33
                                      8**************998777887765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.46
                                       SEEEEEE--HHHHHHHHHHCCTSTHHHHHH CS
                              CoaE 123 ervlvvdvelelqveRlvardgvseeevka 152
                                       ++ +v+ +++e+  eRl +rd+ +++ +++
  gi|313126671|ref|YP_004036941.1|  82 DEAVVLRCHPEELKERLRERDESEAKVAEN 111
                                       567899999999999999999876655544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.7    0.0011         1      21      36 ..       4      19 ..       1      26 [. 0.86
   2 ?    0.6   0.1      0.33   2.9e+02     146     157 ..      93     104 ..      22     141 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                            ATPase 21 vvlitGepGtGKtifa 36
                                         itG+pGtGKt+++
  gi|313126671|ref|YP_004036941.1|  4 RLVITGTPGTGKTTVS 19
                                      568**********986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.33
                            ATPase 146 qlvrvlkklgvT 157
                                       +l+++l++++  
  gi|313126671|ref|YP_004036941.1|  93 ELKERLRERDES 104
                                       444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1180.60
//
Query:       gi|313126672|ref|YP_004036942.1|  [L=363]
Description: histidinol phosphate aminotransferase apoenzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-63  215.2   0.0    1.6e-63  215.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0012   17.8   0.1     0.0029   16.5   0.0    1.5  2  Alliinase_C      Allinase
     0.0021   18.0   0.1      0.004   17.1   0.1    1.4  1  FTR              Formylmethanofuran-tetrahydromethanopterin f
  ------ inclusion threshold ------
      0.087   12.6   0.0       0.16   11.7   0.0    1.4  1  DdrB             DdrB-like protein
       0.11   12.5   0.1         20    5.3   0.0    3.1  3  DUF4911          Domain of unknown function (DUF4911)
       0.11   12.8   0.0       0.32   11.4   0.0    1.7  1  HTH_Tnp_1        Transposase
       0.16   10.5   0.0       0.24    9.9   0.0    1.1  1  Met_gamma_lyase  Methionine gamma-lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.1   0.0   6.3e-67   1.6e-63       2     363 .]      31     351 ..      30     351 .. 0.95

  Alignments for each domain:
  == domain 1  score: 215.1 bits;  conditional E-value: 6.3e-67
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       ++++L+sne++++    ++p++++a     +a ++++ y+++  +++l  ala+ +       l+ e +v+v+ G +
  gi|313126672|ref|YP_004036942.1|  31 ELTKLSSNENPHG----PSPDAVEAVE---AAASEIHVYPKTS-HADLTDALAERWD------LTSE-QVWVSAGGD 92 
                                       6789*********....********94...7************.*************......9999.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        +++ l +++ l+p+d++l p+p ++ y   +r+++gev +y+l++++df  + e +++a++         ++++++
  gi|313126672|ref|YP_004036942.1|  93 GALDNLSRAF-LEPDDRVLTPKPGFSYYAMSARYHHGEVAEYSLSKADDFAQTPETILDAYDG-------ERIVYLT 161
                                       **********.***************************************************5.......569**** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       +phNPtG+ + +e++++ll+ ++  + l++vDeaY++   ++    +++ +++e++nl++ +++sKafGlaG+R+Gy
  gi|313126672|ref|YP_004036942.1| 162 TPHNPTGSEMAREDIVTLLESVED-HTLVVVDEAYGEYSEEP----SAIGLLDEYDNLAVIRTFSKAFGLAGLRIGY 233
                                       ***********************7.99***********9994....34***************************** PP

                                       EEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmfll 309
                                       +++ +a++++ +++ +pf  s ++ +a++aal +++    ++e+++++    r++ rdeL   + + ++s ++++l+
  gi|313126672|ref|YP_004036942.1| 234 AAVPEAWADAYARVNTPFAASKVACRAALAALGNEE----HIEKSVETARWAREYYRDEL---NANTWPSGGNFVLV 303
                                       **********************************99....99******************...779999999***** PP

                                       EEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 310 tdlsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleelveal 363
                                        +++a    ++  + +++ g++v+  +sf++p+++R+++  +t+ee +++ve l
  gi|313126672|ref|YP_004036942.1| 304 EVGDAT---AV-AEATKRRGIIVRDTSSFGLPACIRVSC--GTREETKRAVEVL 351
                                       ****99...44.4466666********************..**********975 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-06    0.0029      95     210 ..     105     238 ..      92     252 .. 0.76
   2 ?   -2.5   0.0      0.68   1.7e+03     226     249 ..     338     360 ..     333     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-06
                                       SSEEEEE-SS--THHHHHTTTT-BTTEEEE.EESTT-.......--S..S-EEEEEESS-TTT-..-------.... CS
                       Alliinase_C  95 kpvkvvaavPyysvykeqtslldsklykwe.Gdaaayv......kkknpeefielvtsPnnPdg..llreavv.... 158
                                       +  +v++  P +s y   +++ + +  +++  +a +++       +   +e i   t P nP g  + re +v    
  gi|313126672|ref|YP_004036942.1| 105 PDDRVLTPKPGFSYYAMSARYHHGEVAEYSlSKADDFAqtpetiLDAYDGERIVYLTTPHNPTGseMAREDIVtlle 181
                                       55689999999999999999999999998746799998443333223357889999******984347999997776 PP

                                       .-TT-EEEEEE-TT..-STTTS---..S-B--SEEEEEHHHHHS-GGG-EEEEEES- CS
                       Alliinase_C 159 .kgseakviyDlay..YWPhytpit..skadedimLftlskltGhaGsrlGWalvkd 210
                                         ++++ v++D ay  Y  + ++i    + d+  ++ t+sk  G aG r+G+a v +
  gi|313126672|ref|YP_004036942.1| 182 sVEDHTLVVVDEAYgeYSEEPSAIGllDEYDNLAVIRTFSKAFGLAGLRIGYAAVPE 238
                                       556677899***9977776666665114556667789****************9865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.68
                                       SS--HHHHHHHHHHHHHHHHHTT- CS
                       Alliinase_C 226 iGvskesqlrvlkilkvvlaeikt 249
                                        G+  e   r++++l++v+a++++
  gi|313126672|ref|YP_004036942.1| 338 CGTREE-TKRAVEVLNEVIADVEA 360
                                       565544.56999******999876 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.5e-06     0.004       5      53 ..     213     261 ..     210     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                                       TEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-E CS
                               FTR   5 gveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaE 53 
                                       +  +  tf+ aF  +  r+   a  ++wa++ a+  t fa+s ++c+a 
  gi|313126672|ref|YP_004036942.1| 213 NLAVIRTFSKAFGLAGLRIGYAAVPEAWADAYARVNTPFAASKVACRAA 261
                                       667889****************************************974 PP

>> DdrB  DdrB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.4e-05      0.16      78     111 ..     313     345 ..     283     359 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                                       EEEEEEEE--EECSSCEE--EEEEEEE--TTS-G CS
                              DdrB  78 kvykRRelsvvDvkklklpaaikysrgaketdpe 111
                                       ++ kRR   v D+    lpa i+ s+g++e+  +
  gi|313126672|ref|YP_004036942.1| 313 EATKRRGIIVRDTSSFGLPACIRVSCGTREET-K 345
                                       5789*************************987.3 PP

>> DUF4911  Domain of unknown function (DUF4911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.67   1.7e+03      14      20 ..     148     154 ..     146     168 .. 0.66
   2 ?    5.3   0.0    0.0078        20      18      36 ..     211     229 ..     207     232 .. 0.82
   3 ?    3.1   0.0     0.037        96      35      54 ..     333     352 ..     332     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.67
                           DUF4911  14 IlEaydg 20 
                                       Il aydg
  gi|313126672|ref|YP_004036942.1| 148 ILDAYDG 154
                                       8999998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0078
                           DUF4911  18 ydgLavvttvdkkkGlvri 36 
                                       yd+Lav++t  k+ Gl  +
  gi|313126672|ref|YP_004036942.1| 211 YDNLAVIRTFSKAFGLAGL 229
                                       9********9988887655 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.037
                           DUF4911  35 rirttpdtkeellelLesLk 54 
                                       +ir++ +t+ee+++++e L 
  gi|313126672|ref|YP_004036942.1| 333 CIRVSCGTREETKRAVEVLN 352
                                       69************999886 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.32      17      44 ..       9      36 ..       7      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                         HTH_Tnp_1 17 reslepgksvsevArrhgvspnqLykWr 44
                                      +e++ pg+   evAr++g +p+ L k  
  gi|313126672|ref|YP_004036942.1|  9 HEAYVPGRGAEEVARELGMDPEELTKLS 36
                                      68899******************99865 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   9.4e-05      0.24     179     213 ..     174     206 ..     169     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.4e-05
                   Met_gamma_lyase 179 eeiiklvkeinedvivfvdncyGefveekePtevG 213
                                       e+i++l+ +++++++v vd+ yGe+ e  eP ++G
  gi|313126672|ref|YP_004036942.1| 174 EDIVTLLESVEDHTLVVVDEAYGEYSE--EPSAIG 206
                                       6799*********************87..677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2611.60
//
Query:       gi|313126673|ref|YP_004036943.1|  [L=318]
Description: ABC tungstate transporter, permease component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-20   72.6   0.1    5.1e-20   72.3   0.1    1.1  1  PBP_like_2      PBP superfamily domain
    1.8e-07   31.2   0.4    6.3e-07   29.4   0.4    1.8  1  SBP_bac_11      Bacterial extracellular solute-binding protei
    3.4e-07   29.8   0.1    4.9e-07   29.3   0.1    1.2  1  LysR_substrate  LysR substrate binding domain


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.1   8.5e-24   5.1e-20      11     279 ..      49     274 ..      26     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 8.5e-24
                        PBP_like_2  11 e....ifgaGsttpapalrklada.fekaapgakvnyastGSgagikalrngdvdfagsdrplteseia.agwaang 81 
                                              ++++t+++++l++ + + f +   g++v++ s+G+ga+++  r+gd+d+++++++ +e++++ +g++ n+
  gi|313126673|ref|YP_004036943.1|  49 LdatlTLATATTAYDTGLLDTLHTaFTERF-GIQVKTLSQGTGAALRTARDGDADVVIAHARPAEDQFIrDGHGVNR 124
                                       0334367888899999***97766799996.********************************************** PP

                        PBP_like_2  82 aggliqvpvaigaialvvnkdnpln.....lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfsta 153
                                             +  +++++ +v+++d+p+      +  +a+++I               a+    + +r+d+sg      t+
  gi|313126673|ref|YP_004036943.1| 125 ------RALMHNDFLIVGPPDDPAAvadidDPVAAFEAI---------------ATSEALFLSRGDDSG------TH 174
                                       ......******************998888888889999...............8**************......** PP

                        PBP_like_2 154 laeqgpwtasgigasgsegvasavsnngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnp 230
                                         eq++w+ ++ +   +eg  ++++++g+++++  a+++   +y+l+d     ++++  +aa++             
  gi|313126673|ref|YP_004036943.1| 175 RREQKLWSRADAS---PEGRWYQAAGDGMGDTLRQASRR--GAYTLVD-----RGTFRVFAADI----DL------- 230
                                       ********99998...88877888************999..89****9.....88888883333....32....... PP

                        PBP_like_2 231 lawslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyll 279
                                             +ve + + g   l + +++i  +p a h++ ++la+ ++ +l+
  gi|313126673|ref|YP_004036943.1| 231 ----NALVEGPLGGGPNSLLNEYGVIPTNP-ARHDVAYELAMLYVGFLT 274
                                       ....44566666688888888888888886.566788999999998887 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.4     1e-10   6.3e-07      10     226 ..      64     284 ..      53     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1e-10
                                       HHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEEEEES CS
                        SBP_bac_11  10 aaalrelaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplviavp 86 
                                       +  l+ l  aF+++ g++v+  ++g g+++r+ +dg ++Dv+i+    + ++ +++g+++  ++++l ++   i+ p
  gi|313126673|ref|YP_004036943.1|  64 TGLLDTLHTAFTERFGIQVKTLSQGTGAALRTARDG-DADVVIAHARPAEDQFIRDGHGV--NRRALMHNDFLIVGP 137
                                       45789999****************************.*******999999**********..*************** PP

                                       TT-TT---SHHHHHHS....S-..-EEEE--T-TTTTHH.HHHHGGG--.......HHHHHHHHHTEEEEESSHHHH CS
                        SBP_bac_11  87 kgnpkkikgwadLlkp....gl..klavadPttspsGlaalalleaaga.......qellkalekkvvklgessrql 150
                                       ++ p+ + +++d  ++     +   l ++    s++ ++ ++l+ +a a       q+  + + +  +    s r +
  gi|313126673|ref|YP_004036943.1| 138 PDDPAAVADIDDPVAAfeaiATseALFLSRGDDSGTHRREQKLWSRADAspegrwyQAAGDGMGDTLR--QASRRGA 212
                                       ****9999999966665444223346666666788888999****99777775576666666666666..3455899 PP

                                       HHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--...HHHHHHHHHTTSHHHHHHH CS
                        SBP_bac_11 151 ltaveageadagivyeseakaaengdkleavylpeglnldpldypaavlkkaakr...eaAraFlafLrspeaqail 224
                                       +t v++g   ++ +   + +      ++++   p +l+    +y+++ ++ a++    e A  ++ fL+++++qa++
  gi|313126673|ref|YP_004036943.1| 213 YTLVDRGTFRVFAADIDLNA----LVEGPLGGGPNSLLN---EYGVIPTNPARHDvayELAMLYVGFLTGRDGQAVI 282
                                       999*******9999877544....234444555777774...78888888777767779****************99 PP

                                       HH CS
                        SBP_bac_11 225 rk 226
                                       r+
  gi|313126673|ref|YP_004036943.1| 283 RE 284
                                       87 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   8.1e-11   4.9e-07       3     134 ..      48     192 ..      46     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 8.1e-11
                                       TSCEEEEEEEECCCHHHHHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSS.......CCTTEEE CS
                    LysR_substrate   3 glrgrLrigapptlaryllppllarfraryPevelelvegdseelldllaegelDlairagpp.......edsglea 72 
                                       gl  +L++++ +t+  + l + l     +  ++++   +  + + l+  ++g++D++i++ +p       + +g+  
  gi|313126673|ref|YP_004036943.1|  48 GLDATLTLATATTAYDTGLLDTLHTAFTERFGIQVKTLSQGTGAALRTARDGDADVVIAHARPaedqfirDGHGVNR 124
                                       667899*******999999999999999999********************************************** PP

                                       EEEEEEEEEEEEETTSGGGG...SSSE.CGGGGCTSEEEEESTTST..HHHHHHHHHHCTTEECEEEE CS
                    LysR_substrate  73 rpLaeeplvlvaspdhpLar...gepv.sledLadeplilleegsg..lrdlledalreaglkprval 134
                                       r L+++ +++v +pd p a     +pv ++e++a  + ++l++g    ++++ +++  +a  +p++++
  gi|313126673|ref|YP_004036943.1| 125 RALMHNDFLIVGPPDDPAAVadiDDPVaAFEAIATSEALFLSRGDDsgTHRREQKLWSRADASPEGRW 192
                                       ****************988899*99999******9888888766665688888888888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1890.01
//
Query:       gi|313126674|ref|YP_004036944.1|  [L=538]
Description: choline dehydrogenase-like flavoprotein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-25   88.3   0.8    2.8e-24   86.3   0.8    2.0  1  GMC_oxred_C    GMC oxidoreductase
    2.6e-13   50.0   0.0    6.4e-13   48.7   0.0    1.7  1  GMC_oxred_N    GMC oxidoreductase
      2e-10   40.8   0.4    0.00073   19.2   0.1    2.8  3  DAO            FAD dependent oxidoreductase
    1.3e-07   31.0   1.6     0.0025   17.0   0.5    2.3  2  FAD_binding_2  FAD binding domain
    1.5e-05   24.4   0.1     0.0012   18.1   0.1    3.1  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    5.1e-05   23.4   1.0    0.00014   22.0   0.2    2.2  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    7.9e-05   21.9   0.2    0.00012   21.2   0.2    1.2  1  Lycopene_cycl  Lycopene cyclase protein
    0.00012   21.4   2.2      0.005   16.1   0.2    2.4  2  FAD_binding_3  FAD binding domain
     0.0012   17.6   0.6     0.0071   15.1   0.4    1.9  2  HI0933_like    HI0933-like protein
     0.0045   16.4   2.1        1.1    8.6   2.2    2.4  2  FAD_oxidored   FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.036   13.7   0.2       0.11   12.1   0.0    1.9  2  ApbA           Ketopantoate reductase PanE/ApbA
        0.1   12.9   0.0       0.35   11.1   0.0    1.8  2  BtrH_N         Butirosin biosynthesis protein H, N-terminal
       0.12   11.6   0.0       0.47    9.7   0.0    1.8  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.16   12.6   0.8       0.35   11.5   0.8    1.6  1  Fer4_7         4Fe-4S dicluster domain
        0.2   10.9   0.1       0.37   10.0   0.1    1.3  1  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> GMC_oxred_C  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.8   2.3e-27   2.8e-24       1     144 []     408     530 ..     408     530 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 2.3e-27
                                       ----EEEEEST..T-TCCEEEEE--TT-SHHHHHHHHHHHHHHHHHCTSGGGTTEECCEECCCTTTTS.HCHHCHHC CS
                       GMC_oxred_C   1 PesrGrvtlss..sdptgaplidpnylsdprdlaalvealkaarkilaaaaldvleeeltpgaaeetsdaavesdea 75 
                                       P++++r+tl++  +d +g+p++++++  d + +aal++a +  r+++++ +   +++ +t+g+           ++ 
  gi|313126674|ref|YP_004036944.1| 408 PRAENRITLDQsrTDDHGNPVPHVEWSLDAQTKAALRRANEIQRRVFEELG---ATVDWTVGP-----------EH- 469
                                       899*******999************************99999999999993...445555555...........33. PP

                                       HHCHHHHH-EE-S--B-TT-B-STCGCBSB-TTSBBTT-CSEEE-SGGGSSS--SS-THHHHHHHHHHH CS
                       GMC_oxred_C  76 lekfvkeavltsaHplGtcrMGadpkdsVVDsdlrvhgvdnLrVvDaSvfPsapganptltilalAeka 144
                                               +   +H++Gt+rMG+dp++sVVD+++r+h+++nL++v++SvfP+ +  nptlti al  +a
  gi|313126674|ref|YP_004036944.1| 470 --------TGPAFHQMGTTRMGTDPDSSVVDAEMRTHDLSNLWIVGSSVFPTGGAMNPTLTIGALSLRA 530
                                       ........45679*************************************************9998876 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   5.4e-16   6.4e-13       3     266 ..      24     299 ..      22     323 .. 0.70

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 5.4e-16
                       GMC_oxred_N   3 elveggGsagsvvAaRLsedpstsvlvleaggreknrl...imvlalalklidkklntayetepekalngrrlilpa 76 
                                         v+g+G ag+ vA RL++  ++ v+vleag+r        +m+  ++  + +           + +     l  ++
  gi|313126674|ref|YP_004036944.1|  24 VCVVGSGPAGALVAHRLAAA-NAAVVVLEAGPRFDFSRrleQMEEHIRPGMGNPWEMGGPRDDYTTSGRHYPLNAAR 99 
                                       5689*************986.67899******955444345444433333222222222222222222333344456 PP

                       GMC_oxred_N  77 GktlGGgsvvNwsayiRtpaadldeWeeeagleg...wssdevlpafkkvetaqalesdlhgvdgrlgvtekgkees 150
                                        k++GG+++   ++ +R ++ d++  +++ g+     +s+d+++p ++++e       d  gv+g l    + ++e+
  gi|313126674|ref|YP_004036944.1| 100 VKGVGGTTLHWQGMVMRLHERDFEMQSRH-GVGTdwpLSYDDLKPHYREAE-------DAFGVAGALDNPYAPPREE 168
                                       689********************986666.775443469************.......5666666665532222222 PP

                       GMC_oxred_N 151 p....ln......kallkaaeelGlp.....vprdlngk....hqcGvcllgvtcrtgarqstarawLrpalerpnl 208
                                       p    ++      +++ +a+e+lG++       r+++        +G++  + +c++ga++ ta++ +r a ++ ++
  gi|313126674|ref|YP_004036944.1| 169 PfplpAFppshsdSIFAEACERLGIDmhsvpNARNSEPYdgraACQGFGTCKPVCPSGAKY-TAESHVRAAEKA-GA 243
                                       211111111123489***********9996544555544444545677777888******9.566777877777.** PP

                       GMC_oxred_N 209 eiltgakaekiilegrkkravGVeasdkkgtvkrlvvaakevvvaaGalnsPqlLqrS 266
                                       +++ +a ++++  ++ ++r+    + + +gt  +   +a+  vva+G +++  lL++S
  gi|313126674|ref|YP_004036944.1| 244 RVIDHAPVQRLEHDDSGDRIERAVYATPDGT--EHEQEARRFVVACGGVENARLLLLS 299
                                       ***********88888999987777778888..789999****************999 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   6.1e-07   0.00073       1      31 [.      23      55 ..      23      62 .. 0.93
   2 !   18.7   0.0   8.6e-07     0.001     153     203 ..     235     291 ..     101     308 .. 0.80
   3 ?   -1.2   0.0         1   1.2e+03     110     152 ..     485     526 ..     381     533 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.1e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                      dv+++G+G +G+ +A+ La+++  V++le+g++
  gi|313126674|ref|YP_004036944.1| 23 DVCVVGSGPAGALVAHRLAAANaaVVVLEAGPR 55
                                      9******************9988*******976 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 8.6e-07
                                       HHHHHHTT-EEEESECEEEEEEEE..TCEEEEE...EECT.EEEE..EEEE.EEE--GGG CS
                               DAO 153 araaealGveilegtevtgleeed..gkvwgve...rttp.gend..aada.vVnaaGaw 203
                                        raae++G++++ +++v++le++d  +   ++e    +tp g+++  +a+  vV + G+ 
  gi|313126674|ref|YP_004036944.1| 235 VRAAEKAGARVIDHAPVQRLEHDDsgD---RIEravYATPdGTEHeqEARRfVVACGGVE 291
                                       5789****************8866443...555556566668873345577466666654 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1
                                       TTTEEEEEHH.HHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHH CS
                               DAO 110 gldaelldae.evrelepalpgllgalfypdtgqvdpakltaal 152
                                       ++d++++dae ++ +l+  l  ++g+ ++p++g ++p   + al
  gi|313126674|ref|YP_004036944.1| 485 DPDSSVVDAEmRTHDLSN-L-WIVGSSVFPTGGAMNPTLTIGAL 526
                                       233345555422333332.1.24566666666666666555555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   2.1e-06    0.0025       1      34 [.      23      56 ..      23      60 .. 0.95
   2 !   12.9   0.0   3.5e-05     0.042     147     205 ..     234     294 ..     201     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqef 34
                                      Dv V+GsG AG   A+++a a++ v+v+e +++f
  gi|313126674|ref|YP_004036944.1| 23 DVCVVGSGPAGALVAHRLAAANAAVVVLEAGPRF 56
                                      99****************************9986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.5e-05
                                       HHHHHHTCTEEEEESEEEEEEEECTT..EEEEEEEEETTTTCEEEEEESEEEE-----GG.. CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedg..rvtGavvenpesgrevrirakavvlatgGfgr.a 205
                                        v++a+kag ++ +++++++L ++d   r+  av +   +g+e++ +a++ v+a+gG+++  
  gi|313126674|ref|YP_004036944.1| 234 HVRAAEKAGARVIDHAPVQRLEHDDSgdRIERAVYA-TPDGTEHEQEARRFVVACGGVENaR 294
                                       567888999**************8777899988888.567888888*************841 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     1e-06    0.0012       2      33 ..      23      54 ..      22      69 .. 0.88
   2 ?    0.3   0.0      0.27   3.3e+02     192     243 ..     237     295 ..     222     307 .. 0.68
   3 ?    1.5   0.0      0.12   1.4e+02     228     279 ..     458     514 ..     370     527 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      dv+v+G+GpAG  +a++la+a+a v+++e++ 
  gi|313126674|ref|YP_004036944.1| 23 DVCVVGSGPAGALVAHRLAAANAAVVVLEAGP 54
                                      89*************************97654 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                                       HHHHTTEEEEESCEEEEEEETTE..EEE...EEETTSCE..EEESEEEE-S-EEES-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxx...xxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 192 alekeGvevklgtsvkeidgnge..kle...vvledgee..idadlvvvavGvrpstel 243
                                       a ek G +v  ++ v++++ +++  ++e   + + dg+e   +a+  vva G   + +l
  gi|313126674|ref|YP_004036944.1| 237 AAEKAGARVIDHAPVQRLEHDDSgdRIEravYATPDGTEheQEARRFVVACGGVENARL 295
                                       56677777777777777777777773334456666666655777777777765555544 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.12
                                       ESEEEE-S-EEES-HHCSHCCT-EE..EETTEEE--TTSBES.STTEEE-GGGC...T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx.xxxxxxxxxxx...x RF
                       Pyr_redox_2 228 adlvvvavGvrpstelleeklglel..derggivvdeflrtn.vpgiyaiGDva...g 279
                                         +v + vG +   + +  ++g +   ++ +  vvd  +rt    +++ +G  +   g
  gi|313126674|ref|YP_004036944.1| 458 GATVDWTVGPEHTGPAF-HQMGTTRmgTDPDSSVVDAEMRTHdLSNLWIVGSSVfptG 514
                                       55677888888888887.77777765666677799*****988999999997665554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.2e-07   0.00014       1      30 [.      26      55 ..      26      57 .. 0.96
   2 ?   -2.8   0.0       6.3   7.6e+03      31      44 ..     327     341 ..     325     356 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                      +vG+G +G++ A++La a++ v++le+++r
  gi|313126674|ref|YP_004036944.1| 26 VVGSGPAGALVAHRLAAANAAVVVLEAGPR 55
                                      8**************************998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.3
                                       SSGGG-EECETT.CE CS
                     NAD_binding_8  31 lGGraasyevpg.vr 44 
                                       +GGr+ ++++++ v 
  gi|313126674|ref|YP_004036944.1| 327 VGGRVERETRQNhVG 341
                                       688888877755333 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2     1e-07   0.00012       1      37 [.      23      57 ..      23      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1e-07
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsll 37
                                      Dv v+G+GpAg ++A+rl  a+++ +vv++ea+p   
  gi|313126674|ref|YP_004036944.1| 23 DVCVVGSGPAGALVAHRL--AAANAAVVVLEAGPRFD 57
                                      9*****************..999999*******9875 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   4.2e-06     0.005       2      32 ..      22      52 ..      21      57 .. 0.92
   2 ?    4.6   0.1     0.013        16     106     165 ..     229     291 ..     195     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.2e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                      +dV++VG+GpaG++ a+ L+ a   vv++e 
  gi|313126674|ref|YP_004036944.1| 22 ADVCVVGSGPAGALVAHRLAAANAAVVVLEA 52
                                      79********************999999985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHTEEETCSEEEECCEECCCC...CCCEEEECCTTEEEEEEE.EEEEE--GTT CS
                     FAD_binding_3 106 eleriLvehaeerglqvrfktevesleqdeeg...vtaevrdketgeeetvra.kYlvGaDGgr 165
                                       ++    v +ae++g++v  ++ v+ le+d++g   ++a++    +g+e + +a +++v++ G+ 
  gi|313126674|ref|YP_004036944.1| 229 YTAESHVRAAEKAGARVIDHAPVQRLEHDDSGdriERAVYATP-DGTEHEQEArRFVVACGGVE 291
                                       5555567889*******************98833344555555.55555555527*****9985 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   5.9e-06    0.0071       2      34 ..      23      55 ..      22      58 .. 0.94
   2 ?    0.1   0.0      0.21   2.5e+02     117     165 ..     236     290 ..     224     295 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.9e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      dv v+G G+AG + A ++a++++ V++le++++
  gi|313126674|ref|YP_004036944.1| 23 DVCVVGSGPAGALVAHRLAAANAAVVVLEAGPR 55
                                      89***************************9876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.21
                                       HHHHHHT-EEE-S--EEEEECETTE.EEEEE........TTEEEEESEEEE----S CS
                       HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktk.......seeeleadklvlAtGGl 165
                                       +++++ag ++  +  v+++e++++g  r++         +e+e ea++ v+A+GG 
  gi|313126674|ref|YP_004036944.1| 236 RAAEKAGARVIDHAPVQRLEHDDSG-DRIERAvyatpdgTEHEQEARRFVVACGGV 290
                                       6677888888888888888777665.333322223344477789999999999996 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   2.2   0.00089       1.1       1      32 [.      23      54 ..      23      56 .. 0.94
   2 !    5.2   0.0    0.0093        11      82     140 ..     214     284 ..     178     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00089
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveerg 32
                                      Dv+VvG+gpaG   A   a a a v+++e  +
  gi|313126674|ref|YP_004036944.1| 23 DVCVVGSGPAGALVAHRLAAANAAVVVLEAGP 54
                                      9***************************9876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0093
                      FAD_oxidored  82 n......tfepevakavleeml...aeagvtvllntrlveveke..gkriesvtveskeg.rktirAkvfi 140
                                       +      ++ p+ ak ++e  +   ++ag +v+ ++ +++ e +  g+rie  + ++ +g +++ +A++f+
  gi|313126674|ref|YP_004036944.1| 214 QgfgtckPVCPSGAKYTAESHVraaEKAGARVIDHAPVQRLEHDdsGDRIERAVYATPDGtEHEQEARRFV 284
                                       1444455899************998889**************9734589******9999779*****9998 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.2e-05      0.11       1      29 [.      24      52 ..      24      64 .. 0.87
   2 ?   -2.0   0.0         2   2.4e+03       6      21 ..     312     328 ..     312     341 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.2e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilr 29
                                      ++++G+G  G l+a++La+a+a v+++  
  gi|313126674|ref|YP_004036944.1| 24 VCVVGSGPAGALVAHRLAAANAAVVVLEA 52
                                      69*****************9999988755 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                                       -SHHHHHHHHHHHH.HT CS
                              ApbA   6 aGaiGsllaakLak.ag 21 
                                       +Ga+G+++  +L +  g
  gi|313126674|ref|YP_004036944.1| 312 SGAVGRYFMDHLFAgVG 328
                                       69******999976555 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0003      0.35      21      70 ..     149     198 ..     135     208 .. 0.78
   2 ?   -2.8   0.0         6   7.2e+03      53      69 ..     447     463 ..     439     469 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                            BtrH_N  21 plvFglGgglgfvYlp.akklnplpllagrtkpgdlekrlakrlglkvevk 70 
                                       + +Fg++g+l+  Y p +++ +plp++  +++ +++++++++rlg++++  
  gi|313126674|ref|YP_004036944.1| 149 EDAFGVAGALDNPYAPpREEPFPLPAFPPSHS-DSIFAEACERLGIDMHSV 198
                                       679*************5566666666666655.7*************9875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6
                            BtrH_N  53 gdlekrlakrlglkvev 69 
                                        ++ +r+++ lg++v++
  gi|313126674|ref|YP_004036944.1| 447 NEIQRRVFEELGATVDW 463
                                       489999*******9998 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00039      0.47       2      32 ..      26      55 ..      25      81 .. 0.82
   2 ?   -1.0   0.0      0.68   8.2e+02     228     274 ..     244     296 ..     228     307 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00039
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgni 32
                                      ++G GPaG  +a+ l  a+   +++lE g  
  gi|313126674|ref|YP_004036944.1| 26 VVGSGPAGALVAHRLAAANA-AVVVLEAGPR 55
                                      8******************9.8*****9965 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.68
                       Pyr_redox_3 228 kvlfnaevkeikekeeeykvk.....tedgkkvev.kddvvlatGykpdlsfl 274
                                       +v+++a v++++++++  +++     t+dg+++e+   ++v+a G   ++++l
  gi|313126674|ref|YP_004036944.1| 244 RVIDHAPVQRLEHDDSGDRIEravyaTPDGTEHEQeARRFVVACGGVENARLL 296
                                       56666666666666554444333334888888877467788888888777765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8    0.0003      0.35      10      52 .]     186     227 ..     185     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                            Fer4_7  10 aaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +aC    i+++ + n++   +++     C+g g C  vCP+ga
  gi|313126674|ref|YP_004036944.1| 186 EACERLGIDMHSVPNARN-SEPYDGRAACQGFGTCKPVCPSGA 227
                                       577777778877755544.666667889*************98 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00031      0.37      18      49 ..      22      52 ..      19      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                      +Dv +vG+G++G   a+ la + +  v++le+
  gi|313126674|ref|YP_004036944.1| 22 ADVCVVGSGPAGALVAHRLAAA-NAAVVVLEA 52
                                      7*******************99.999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3460.77
//
Query:       gi|313126675|ref|YP_004036945.1|  [L=203]
Description: hypothetical protein Hbor_19330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-08   33.3   0.0    7.4e-08   32.7   0.0    1.2  1  Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
  ------ inclusion threshold ------
      0.013   15.5   0.0       0.18   11.9   0.0    2.6  3  DUF2059          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   8.2e-12   7.4e-08       6     136 .]      60     181 ..      56     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 8.2e-12
                   Gluconate_2-dh3   6 llaaladrIiPstdtgpgakeagvaafidrqladaplppeqeayrkg....laaldayaraeygksFveldgaqqda 78 
                                       +++a+a++I+Ps  +   a ++    f++r++ +   ++ +eayr+g     a+lda ar+  + +F+ l+ +++d+
  gi|313126675|ref|YP_004036945.1|  60 VMDAAAAVIFPS--E-VEAHRT----FVERYVLG--RTAGREAYRRGltetAAELDAIARDWRDSPFAALPRDERDE 127
                                       789999999999..3.556665....55555555..444478888883333577888999999************** PP

                   Gluconate_2-dh3  79 lLealekeaeakgtgealeasaeahfFsllreltlegyftspigggna.lgwrligfpG 136
                                       +L+ l  e+ +  ++++ + s++ +f+  + ++ l ++++sp gg  + +++ +ig+pG
  gi|313126675|ref|YP_004036945.1| 128 ILRGLGVETAD--PEPDGTISERLRFY--VVNDLLFAFYSSPTGGRLVgIEN-PIGHPG 181
                                       ******99664..43433433333444..88999**********98887776.888887 PP

>> DUF2059  Uncharacterized protein conserved in bacteria (DUF2059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.34   3.1e+03      42      57 ..      53      68 ..      48      70 .. 0.60
   2 ?   -0.9   0.1       0.2   1.7e+03       9      24 ..      92     109 ..      91     110 .. 0.71
   3 ?   11.9   0.0     2e-05      0.18      23      40 ..     158     175 ..     156     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.34
                                      HHHHHHHHHHHHHCTT CS
                           DUF2059 42 ataesmqaaqeaaqel 57
                                      +++++++++ +aa+ +
  gi|313126675|ref|YP_004036945.1| 53 VSDDLLDVMDAAAAVI 68
                                      5556666666666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.2
                                       HHHHHHS-HH..HHHHHH CS
                           DUF2059   9 aiyaktftea..elkail 24 
                                       ++y++ +te   el+ai+
  gi|313126675|ref|YP_004036945.1|  92 EAYRRGLTETaaELDAIA 109
                                       577788877655899886 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 2e-05
                                       HHHHHHSHHHHHHHHHHH CS
                           DUF2059  23 ilaFYkSPlGkkllekep 40 
                                       ++aFY+SP+G +l+  e+
  gi|313126675|ref|YP_004036945.1| 158 LFAFYSSPTGGRLVGIEN 175
                                       68***********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1262.86
//
Query:       gi|313126676|ref|YP_004036946.1|  [L=128]
Description: hypothetical protein Hbor_19340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-12   44.4   2.0    9.4e-12   44.4   2.0    2.0  3  DUF1648   Protein of unknown function (DUF1648)


Domain annotation for each model (and alignments):
>> DUF1648  Protein of unknown function (DUF1648)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   2.0   5.3e-16   9.4e-12       2      48 ..      13      58 ..      12      59 .. 0.95
   2 ?   -2.8   0.1       0.3   5.4e+03       5       6 ..      89      90 ..      82     100 .. 0.50
   3 ?   -2.6   0.1      0.25   4.5e+03      41      46 ..     109     114 ..     107     121 .. 0.67

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 5.3e-16
                           DUF1648  2 llllplvvglllypkLPdqiPtHfnasGepDgygsKlfalfllPllm 48
                                      +l ++++vgl++ p+LPdq ++Hf+++G +D++ s +++lfllP+++
  gi|313126676|ref|YP_004036946.1| 13 VLGATALVGLVFLPSLPDQFAIHFGMDG-ADSFVSTPVGLFLLPAIG 58
                                      67899***********************.****************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.3
                           DUF1648  5 lp 6 
                                      l+
  gi|313126676|ref|YP_004036946.1| 89 LA 90
                                      22 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.25
                           DUF1648  41 lfllPl 46 
                                       lf+lP+
  gi|313126676|ref|YP_004036946.1| 109 LFVLPA 114
                                       666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 844.13
//
Query:       gi|313126677|ref|YP_004036947.1|  [L=244]
Description: 2-keto-4-pentenoate hydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-66  224.4   0.0    1.5e-66  224.2   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
      0.025   15.5   0.3        0.7   10.8   0.3    2.9  1  DUF2437        Domain of unknown function (DUF2437)


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.2   0.0   1.7e-70   1.5e-66       1     218 []      45     241 ..      45     241 .. 0.97

  Alignments for each domain:
  == domain 1  score: 224.2 bits;  conditional E-value: 1.7e-70
                                       .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T-- CS
                     FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevls 77 
                                       kivc+g+nya+h++e+    +++pd     +p +flk++++l ++gd++++Pag e++d+E+ELavvig+++r+v +
  gi|313126677|ref|YP_004036947.1|  45 KIVCIGRNYADHAAELD---NDVPD-----RPLLFLKPPNTLAAHGDTVTLPAGKERVDWEAELAVVIGTQARNV-A 112
                                       69*************96...89999.....777******************************************.9 PP

                                       HHHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGG CS
                     FAA_hydrolase  78 veeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntk 154
                                       +e+A+d++aG+t +nDvs Rd q +e+   +w++gk+fd+++p+Gp++ tpde++d  d +++lrvnge++q+s+ +
  gi|313126677|ref|YP_004036947.1| 113 AEDAMDYVAGFTCMNDVSNRDDQNKEQ---NWVRGKAFDNSAPLGPVLATPDEVPD--DASVELRVNGETKQSSSRD 184
                                       ***************************...9***********************76..9****************** PP

                                       GTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 155 dmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                        m+fs+++li++++  ltLepGd+++tGTp+gvg        l dgD+v ve+eg+G l+++V+
  gi|313126677|ref|YP_004036947.1| 185 YMMFSVPDLIEEITTYLTLEPGDVVSTGTPEGVG-------PLSDGDHVAVEVEGVGVLEHDVR 241
                                       ********************************98.......5*******************995 PP

>> DUF2437  Domain of unknown function (DUF2437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   7.8e-05       0.7      17      50 .]      18      40 ..       1      40 [. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.8e-05
                                      EE.EEEEEESS-TTSS-EEEEEEEEGGGSEEE-S CS
                           DUF2437 17 legdtvvvlagdpfgavqpTGervpLadVrLLAP 50
                                        +d            v + Ge++ La+V++L+P
  gi|313126677|ref|YP_004036947.1| 18 WHDD-----------HVSFGGETYSLAEVEILPP 40
                                      4444...........3456699***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1616.68
//
Query:       gi|313126678|ref|YP_004036948.1|  [L=240]
Description: zn-dependent hydrolase of beta-lactamase fold family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-19   70.5   0.6    2.1e-19   70.0   0.3    1.4  2  Lactamase_B_3  Beta-lactamase superfamily domain
    1.7e-15   57.1   2.2    2.5e-15   56.5   2.2    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.1e-10   41.8   5.4    1.6e-10   41.3   5.0    1.6  2  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.3   3.4e-23   2.1e-19       1     163 []       4     201 ..       4     201 .. 0.83
   2 ?   -3.4   0.0       1.3     8e+03      60      73 ..     226     239 ..     218     240 .] 0.78

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 3.4e-23
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfka...nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvlee....... 67 
                                       eltw+gh+++ ++++g++ l+DPf+    +     + e++D +l++++++dH   +       +++v+         
  gi|313126678|ref|YP_004036948.1|   4 ELTWHGHSTWHVDVDGTTFLIDPFFDnpfTDLSPSDVEDPDYLLLTHGHADHISDAGAFT---DATVVGVpemtgym 77 
                                       69**********************8744344444444****************9997776...99999987888888 PP

                     Lactamase_B_3  68 ..............geslevggleiravatshdav....ggsergenngflleqd.........gltiyhlGhlahe 117
                                                     g+++e+g++ ++ ++++h+++     ++  g   gf+++++           t+yh G++a  
  gi|313126678|ref|YP_004036948.1|  78 eaevgftdsigmnlGGTVECGNAFVTMHRADHTNGlntgYEHDIGMPAGFIISDKkptqeadedATTFYHAGDTALM 154
                                       88888888888888899***************77632113445577999***99444556666699********997 PP

                     Lactamase_B_3 118 lsseel.kelgrvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                        ++++  ++  ++D   +P g+++t+g+ +a+ ++ +L+ +   Pmh
  gi|313126678|ref|YP_004036948.1| 155 SEMKDViAQYLEPDAAAVPCGDHFTMGPVQAAIAVDWLNVDHAFPMH 201
                                       76666547888***********************************9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                     Lactamase_B_3  60 envkvleegeslev 73 
                                        +v+vl+++es+++
  gi|313126678|ref|YP_004036948.1| 226 AEVHVLDGDESFTL 239
                                       47999999999986 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   2.2   4.2e-19   2.5e-15       1     201 []      20     202 ..      20     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 4.2e-19
                                       SEEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHH CS
                     Lactamase_B_2   1 rriLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyl 77 
                                       + +LiD+++d   +++ +  P    +++++ d +llth+H+DH+ ++  +       +++++ +++  ++ea+    
  gi|313126678|ref|YP_004036948.1|  20 TTFLIDPFFD--NPFTDLS-P----SDVEDPDYLLLTHGHADHISDAGAFTD-----ATVVGVPEMTGYMEAEVG-- 82 
                                       579*******..5544443.4....5799***************99888888.....689988888888888853.. PP

                                       HCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C..TCCE-TTTSEEEEEE..CTTEE.........EEEES CS
                     Lactamase_B_2  78 aleeepavnvheldwgesfelgdggleitatparhksgr..rldrnagdtlGlrie..gggkr.........vyyig 141
                                             +++   +++g+++e+g+    +t++ a h+ g   + + + g  +G++i   +   +         +y++g
  gi|313126678|ref|YP_004036948.1|  83 ------FTDSIGMNLGGTVECGN--AFVTMHRADHTNGLntGYEHDIGMPAGFIISdkK--PTqeadedattFYHAG 149
                                       ......5566789********95..45************7666666779*******551..44456666777***** PP

                                       S-S---..HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 142 Dtgyip..eeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       Dt+ ++  +++ +++  +d + ++++         +++++ p +a+ a++ l++  ++++H+
  gi|313126678|ref|YP_004036948.1| 150 DTALMSemKDVIAQYLEPDAAAVPCG---------DHFTMGPVQAAIAVDWLNVDHAFPMHY 202
                                       *****977557778888*********.........799***********************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   5.0   2.7e-14   1.6e-10       4      77 ..       8      75 ..       5     143 .. 0.90
   2 ?   -2.2   0.0      0.58   3.5e+03     147     176 ..     147     186 ..     136     199 .. 0.62

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2.7e-14
                                      CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEH CS
                       Lactamase_B  4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavae 77
                                       +++++ ++ dg+++LiD+ ++++++++         + +d+d+++lTH+H+DHi+++g +++at v v +   
  gi|313126678|ref|YP_004036948.1|  8 HGHSTWHVDVDGTTFLIDPFFDNPFTDLS------PSDVEDPDYLLLTHGHADHISDAGAFTDATVVGVPEMTG 75
                                      5678888999*****************95......9*****************************998766555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.58
                                       EECTTTSSHHCCCCCC...........TTCEEE-SHCHHH CS
                       Lactamase_B 147 ftGDallagetgridl..........tlrgaevrdpsdae 176
                                        +GD+ l  e  ++            + ++++++ p++a+
  gi|313126678|ref|YP_004036948.1| 147 HAGDTALMSEMKDVIAqylepdaaavPCGDHFTMGPVQAA 186
                                       5677777766666666666666666645555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1631.74
//
Query:       gi|313126679|ref|YP_004036949.1|  [L=132]
Description: redox protein, regulator of disulfide bond formation [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-13   51.6   0.0    1.4e-13   51.2   0.0    1.2  1  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   7.8e-18   1.4e-13       2      98 ..      31     124 ..      29     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 7.8e-18
                                       TXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT-.--SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHH CS
                              OsmC   2 dgsgpsPeelllaalasCfaitlravakkkgi.kledleveveaerdpegakgiteirlkvevkipgadseeklkkl 77 
                                       d++gp+P   l+a +asCf  ++r   +++g  +l +++++++a+ d +  + ++++r++++v+++  d  ++++++
  gi|313126679|ref|YP_004036949.1|  31 DEQGPNPNAVLVADYASCFLPAFRVGGQQRGHdDLGKIQIDADADLDGDD-D-LSGVRFSIHVEADLGD--DEFDEI 103
                                       467***************************99667999****99999774.4.9*********988888..****** PP

                                       HHHHHHHSHHHHHHCT-SSSE CS
                              OsmC  78 lekaekrCpvsntlkngvkve 98 
                                       +++ae+ C v+ +l+++ + e
  gi|313126679|ref|YP_004036949.1| 104 VARAEDICHVHAALREELHAE 124
                                       **************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.75
# Mc/sec: 534.42
//
Query:       gi|313126680|ref|YP_004036950.1|  [L=56]
Description: hypothetical protein Hbor_19380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 356.19
//
Query:       gi|313126681|ref|YP_004036951.1|  [L=196]
Description: intracellular protease, pfpi family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.6e-55  186.7   0.0    3.2e-55  186.4   0.0    1.1  1  DJ-1_PfpI   DJ-1/PfpI family
      2e-05   24.2   0.0      3e-05   23.7   0.0    1.3  1  Catalase_C  C-terminal domain found in long catalases
      4e-05   23.5   0.0      5e-05   23.2   0.0    1.3  1  GATase      Glutamine amidotransferase class-I
     0.0017   18.0   0.0     0.0024   17.5   0.0    1.2  1  GATase_3    CobB/CobQ-like glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.076   12.7   0.0    1.9  2  ThiJ_like   ThiJ/PfpI family-like
      0.048   12.8   0.0      0.068   12.3   0.0    1.3  1  GATase_5    CobB/CobQ-like glutamine amidotransferase domain
      0.057   13.7   0.0       0.09   13.0   0.0    1.4  1  SnoaL_3     SnoaL-like domain


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.4   0.0   1.2e-58   3.2e-55       1     164 [.       3     180 ..       3     181 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.4 bits;  conditional E-value: 1.2e-58
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESS................TSEEEETTSEEEE-SEEGGGCTCCG CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvd................keevkgsrGlkvtvdaslddvkaae 61 
                                       kk+l++++d  ed+E++vp+++l+  g++vd+v++d                ++++ + rG+++ v+a++d++++ae
  gi|313126681|ref|YP_004036951.1|   3 KKILMIVGDFGEDYETMVPFQALQMVGHEVDAVCPDksagetvktaihdfrgDQTYLEERGHDFEVNATFDEIDPAE 79 
                                       79*************************************************************************** PP

                                       -SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SS CS
                         DJ-1_PfpI  62 yDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdk 138
                                       yDalv+pGGra pe+lr+ e+v+++v++f+++gk+vaa+C+gpq+Laaagvl+g  +T+ypav+ ++e+ag ++vd+
  gi|313126681|ref|YP_004036951.1|  80 YDALVVPGGRA-PEYLRTYEEVLDTVRHFFDEGKPVAAVCHGPQILAAAGVLDGYEMTAYPAVRAEVEAAGCSWVDE 155
                                       ***********.****************************************************************9 PP

                                       SEEEETTEEEESSGGGHHHHHHHHHH CS
                         DJ-1_PfpI 139 rvvvdgnlvTsrgpgaaiefalelle 164
                                        v vd+nlvT++++++++e++ ++le
  gi|313126681|ref|YP_004036951.1| 156 -VTVDKNLVTAQAWPDHPEWLAKFLE 180
                                       .**********************998 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.2e-08     3e-05      40     117 ..      62     129 ..      36     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.2e-08
                        Catalase_C  40 klgsaegvnrTYstadaveFDaivvadgaeslfsakataasslfpagrplqllldayrhgKpigalGsgaealkaag 116
                                       +  ++  vn+T+   d +e+Da+vv +g          a++ l  ++++l  ++  +  gKp++a+ +g ++l+aag
  gi|313126681|ref|YP_004036951.1|  62 RG-HDFEVNATFDEIDPAEYDALVVPGGR---------APEYLRTYEEVLDTVRHFFDEGKPVAAVCHGPQILAAAG 128
                                       44.5567*********************2.........4566889****************************9998 PP

                        Catalase_C 117 i 117
                                       +
  gi|313126681|ref|YP_004036951.1| 129 V 129
                                       7 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.9e-08     5e-05      28      90 ..      67     130 ..      26     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.9e-08
                                       ETTSHHHHHHHTHHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT CS
                            GATase  28 pidasaeeilellknpdgilvsgGpgspg...vegkieaikearenkiPiLGICLGmQllaiefgr 90 
                                       +++a+++ei+    ++d+++v+gG    +   +e+ ++++++++++++P+  +C G Q+la +   
  gi|313126681|ref|YP_004036951.1|  67 EVNATFDEID--PAEYDALVVPGGRAPEYlrtYEEVLDTVRHFFDEGKPVAAVCHGPQILAAAGVL 130
                                       3444555663..679*********77777779****************************988665 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   9.2e-07    0.0024      13      90 ..      52     126 ..      44     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.2e-07
                          GATase_3  13 yt.dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmL 88 
                                       +  d   Le+++      +++ + +  +++d++++pGg+  +    +++   + + ++++  +g+pv ++C G q+L
  gi|313126681|ref|YP_004036951.1|  52 FRgDQTYLEERGHDFEVNATFDEIDP-AEYDALVVPGGRAPEYLRTYEE---VLDTVRHFFDEGKPVAAVCHGPQIL 124
                                       55566777777755555555555555.56*********98776665554...699*********************9 PP

                          GATase_3  89 Ge 90 
                                         
  gi|313126681|ref|YP_004036951.1| 125 AA 126
                                       76 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.29   7.5e+02      10      33 ..      17      40 ..      10      75 .. 0.77
   2 ?   12.7   0.0     3e-05     0.076      83     154 ..      78     140 ..      59     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.29
                         ThiJ_like 10 evaipwkvlkdagfsveFvtekgk 33
                                      e+ +p++ l+  g +v+ v +   
  gi|313126681|ref|YP_004036951.1| 17 ETMVPFQALQMVGHEVDAVCPDKS 40
                                      677899999999999999988754 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3e-05
                         ThiJ_like  83 eeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPl 154
                                        eyd++ +pGG+ +    l + e + +++++++       ++ k ++a+c+g   la+a      + t+ P+
  gi|313126681|ref|YP_004036951.1|  78 AEYDALVVPGGRAPEY--LRTYEEVLDTVRHFF-------DEGKPVAAVCHGPQILAAAGVLDGYEMTAYPA 140
                                       68***********987..6678899999*****.......5789************9998766677777775 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.6e-05     0.068      72     114 ..      94     135 ..      80     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                          GATase_5  72 lllneklrealekflnredtlaLGiCnGfqlLvklglvpggei 114
                                       l++ e++ + +++f+++ ++ + ++C G q+L+  g+++g e 
  gi|313126681|ref|YP_004036951.1|  94 LRTYEEVLDTVRHFFDE-GKPVAAVCHGPQILAAAGVLDGYEM 135
                                       677799***********.******************9988554 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.5e-05      0.09      26      72 ..      81     127 ..      68     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.5e-05
                           SnoaL_3  26 ddivfigtgadelltgreevrrslkqifakgegisfeltdvrvtesg 72 
                                       d +v  g  a+e+l+++eev++ ++  f++g+++  +++  ++ ++ 
  gi|313126681|ref|YP_004036951.1|  81 DALVVPGGRAPEYLRTYEEVLDTVRHFFDEGKPVAAVCHGPQILAAA 127
                                       55666688999***************************999997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1417.74
//
Query:       gi|313126682|ref|YP_004036952.1|  [L=264]
Description: sugar phosphatase of had superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-24   85.6   0.0    4.8e-24   84.4   0.0    1.7  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
    1.7e-23   82.4   0.7      1e-22   80.0   0.3    2.3  2  Hydrolase_like   HAD-hyrolase-like
    4.6e-08   33.6   0.3    6.6e-08   33.1   0.3    1.3  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.2e-05   24.6   0.1    8.4e-05   22.7   0.0    2.0  3  HAD_2            Haloacid dehalogenase-like hydrolase
    0.00079   19.1   0.1     0.0022   17.6   0.1    1.8  2  PGP_phosphatase  Mitochondrial PGP phosphatase
  ------ inclusion threshold ------
       0.05   13.9   1.6       0.23   11.8   0.1    2.2  2  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   1.6e-27   4.8e-24       1     100 [.       6     105 ..       6     106 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 1.6e-27
                                       EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkr 77 
                                       +++D+dG+++rgd++ipg+ + l+a+ aag + v+++Nn +k + +y++++ + g+++++++v+t++t++a+yl+++
  gi|313126682|ref|YP_004036952.1|   6 VILDVDGTVVRGDEPIPGSGDGLDAIDAAGLERVFVSNNPTKRPAAYVERFARAGFEMAASEVITAGTVTARYLREE 82 
                                       689************************************************************************** PP

                                       SXXXEEEEESXHHHHHHHHHTTX CS
                       Hydrolase_6  78 kadkkvlvigeeglreelkeagf 100
                                       ++d+ ++v+ge gl ++l +ag+
  gi|313126682|ref|YP_004036952.1|  83 RPDDDLFVVGESGLVDILTDAGL 105
                                       ********************997 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.36   1.1e+03      17      36 ..      69     100 ..      46     106 .. 0.64
   2 !   80.0   0.3   3.3e-26     1e-22       1      74 [.     181     254 ..     181     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                                       H............---GGGEEEEES-TTTHHH CS
                    Hydrolase_like  17 l............gsdpeevlmiGDrlatDia 36 
                                       +            + + ++ +++G +   Di+
  gi|313126682|ref|YP_004036952.1|  69 ItagtvtarylreERPDDDLFVVGESGLVDIL 100
                                       14444444444545667889999988777775 PP

  == domain 2  score: 80.0 bits;  conditional E-value: 3.3e-26
                                       E.STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   1 vlgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                       vlgKP+ ++ d+ale+lg++ e vl++GDrl+tDia + +aG++++LV+tGvt++e l++  ++p+yv+d+l +
  gi|313126682|ref|YP_004036952.1| 181 VLGKPSDTARDMALEHLGVPAESVLVVGDRLDTDIALGERAGMTTALVKTGVTDEETLAASSITPDYVLDSLGD 254
                                       68*********************************************************999*********987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.3   2.2e-11   6.6e-08       2     210 .]       4     222 ..       3     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.2e-11
                                       SEEEEESBTTTBCHH...HHHHHHHHHHCHHHHHHHHHH....HHCHHHHHHHHHHHHH..HHHHHHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.. RF
                         Hydrolase   2 ktvvfDkdGTLttge...psvedvivsaalalaaaletg....sehpigkalvaaakar..sgaltgfatfigrg.. 67 
                                       + v++D+dGT+++g    p   d ++ +    aa le +    +++   +a+v+ +     + a +++ t    g  
  gi|313126682|ref|YP_004036952.1|   4 RGVILDVDGTVVRGDepiPGSGDGLDAI---DAAGLERVfvsnNPTKRPAAYVERFARAgfEMAASEVIT---AGtv 74 
                                       6799***********7776666655555...555555555544555566666666666633333333333...2223 PP

                                       .............HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHH CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 .............ayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLk 131
                                                                  +       ++ + ++g +v+  ++  + +++  d+ + ++ + ea+ +L 
  gi|313126682|ref|YP_004036952.1|  75 tarylreerpdddL-------------FVVGESGLVDILTDAGLSVVEADDSPDTLVASVDEEFDYDSLCEALWTLS 138
                                       44223333333333.............44445566666699************************************ PP

                                       HTTEEEEEEESSEH..HHHHHHHHHTT..GGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.H CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                         Hydrolase 132 aagievvlltgdnp..etaeraanqlG..ddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvn.D 202
                                       + g+  ++ t  +     aer     G   +++++v ++d ++  +kps  +   a++ L+++ e v++VGD++  D
  gi|313126682|ref|YP_004036952.1| 139 DDGV-AFIGTDPDTviPAAERDVPGSGaiINAIAGVAERDPDVvLGKPSDTARDMALEHLGVPAESVLVVGDRLDtD 214
                                       ****.888885544322222444445587777788888888889********************************* PP

                                       HHHHHHTT CS
                                       xxxxxxxx RF
                         Hydrolase 203 aaalaaAg 210
                                       +a +++Ag
  gi|313126682|ref|YP_004036952.1| 215 IALGERAG 222
                                       ****9998 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.86   2.6e+03       1      10 [.       6      15 ..       6      24 .. 0.86
   2 ?   -2.6   0.0       1.6   4.9e+03      80     115 ..      20      55 ..      14      75 .. 0.59
   3 !   22.7   0.0   2.8e-08   8.4e-05     131     178 .]     180     228 ..     168     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.86
                             HAD_2  1 iiFDlDgTll 10
                                      +i D+DgT +
  gi|313126682|ref|YP_004036952.1|  6 VILDVDGTVV 15
                                      799*****87 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                             HAD_2  80 pydgvkelLeeLkeagyklgivTsksreaveekleq 115
                                       p++g  + L+ + +ag++   v+++ ++     +e+
  gi|313126682|ref|YP_004036952.1|  20 PIPGSGDGLDAIDAAGLERVFVSNNPTKRPAAYVER 55 
                                       666666666666666666666666655444333333 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 2.8e-08
                             HAD_2 131 vekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                       v   KP+ +    ale+l++ +e+v++vGD   tDi  + +ag++++ v
  gi|313126682|ref|YP_004036952.1| 180 VVLGKPSDTARDMALEHLGVPAESVLVVGDRLdTDIALGERAGMTTALV 228
                                       55679****************************************9876 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.7   5.2e+03      41      53 ..       3      15 ..       2      19 .. 0.80
   2 !   17.6   0.1   7.4e-07    0.0022     136     167 ..     201     232 ..     184     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                   PGP_phosphatase 41 ikavvlDKDncla 53
                                       ++v+lD D ++ 
  gi|313126682|ref|YP_004036952.1|  3 YRGVILDVDGTVV 15
                                      589****999875 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7.4e-07
                   PGP_phosphatase 136 adeiavvgDRllTdvllanmmGslgvwlrdgv 167
                                       a+ ++vvgDRl Td+ l+++ G ++ +++ gv
  gi|313126682|ref|YP_004036952.1| 201 AESVLVVGDRLDTDIALGERAGMTTALVKTGV 232
                                       789********************999999998 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.7e-05      0.23      45      93 ..      54     104 ..      53     127 .. 0.85
   2 ?    1.2   0.1      0.14   4.2e+02      61      87 ..     188     214 ..     169     251 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.7e-05
                           acVLRF1  45 qRfaRrrenqadalleavaeaaarllaeesae..vvlgGdrslvaevleda 93 
                                       +RfaR   + a + + ++    ar l+ee+++  ++++G+  lv+ + +  
  gi|313126682|ref|YP_004036952.1|  54 ERFARAGFEMAASEVITAGTVTARYLREERPDddLFVVGESGLVDILTDAG 104
                                       59***************************9999***********9988874 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                           acVLRF1  61 avaeaaarllaeesaevvlgGdrslva 87 
                                       ++++ a ++l+  +++v+++Gdr  ++
  gi|313126682|ref|YP_004036952.1| 188 TARDMALEHLGVPAESVLVVGDRLDTD 214
                                       455555566655555599999986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1687.38
//
Query:       gi|313126683|ref|YP_004036953.1|  [L=96]
Description: hypothetical protein Hbor_19410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00054   19.2   1.3    0.00062   19.0   1.3    1.0  1  MASE1      MASE1
     0.0088   16.2   1.8     0.0097   16.1   1.8    1.1  1  C166       Family of unknown function
  ------ inclusion threshold ------
      0.037   14.3   2.3      0.049   13.9   2.3    1.3  1  Adeno_E3B  Adenovirus E3B protein
       0.18   11.1   1.1       0.21   10.9   1.1    1.1  1  TMEM43     Transmembrane protein 43
        4.5    7.1   4.7          6    6.7   1.3    2.2  2  B12D       NADH-ubiquinone reductase complex 1 MLRQ subunit


Domain annotation for each model (and alignments):
>> MASE1  MASE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.3   1.7e-07   0.00062      50     106 ..      26      89 ..      20      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-07
                             MASE1  50 wpgil.laavlas......islfllfagnlllalaiaavntleallgalllrrllpsrnrletl 106
                                       ++gi+ l++ ++s      +  ++++  +ll ++aia+v ++ +++++lll  ++ ++ r++++
  gi|313126683|ref|YP_004036953.1|  26 VFGIIgLGITILSvfltysLLVGIVSLVPLLSTTAIAFVGVVTWVVVWLLLDLAYEHYVRQRST 89 
                                       5555554444444444447999***********************************9999876 PP

>> C166  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.8   2.7e-06    0.0097      90     155 ..      14      78 ..       2      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-06
                              C166  90 dglaPiiviadlvidvfrtvvrvlsdllniliGkvGllskvPvlGPflaavllivefvlvielikl 155
                                       dg  P +   ++v+ +    +++ls +l  +   vG++s vP+l     a++ +v  v+v+ l++l
  gi|313126683|ref|YP_004036953.1|  14 DGFHPKTARNHYVFGIIGLGITILSVFLT-YSLLVGIVSLVPLLSTTAIAFVGVVTWVVVWLLLDL 78 
                                       56666666666777777766777776665.34469****************************988 PP

>> Adeno_E3B  Adenovirus E3B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.3   1.4e-05     0.049      13      47 ..      42      74 ..      23      91 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                         Adeno_E3B 13 tvyllygfvtlilicslvtvviafiqfidwvcvri 47
                                      t  ll g+v+l  +  l t  iaf+  + wv v +
  gi|313126683|ref|YP_004036953.1| 42 TYSLLVGIVSL--VPLLSTTAIAFVGVVTWVVVWL 74
                                      22344555554..45567999**********9975 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.1     6e-05      0.21     186     234 ..      24      72 ..       7      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6e-05
                            TMEM43 186 twllRllGfllmflglllllsplsvlvslipllgelvglglalvallls 234
                                         ++ ++G+ +++l+++l++s+l  +vsl+pll++ + + +++v++++ 
  gi|313126683|ref|YP_004036953.1|  24 HYVFGIIGLGITILSVFLTYSLLVGIVSLVPLLSTTAIAFVGVVTWVVV 72 
                                       55677899999*********************98877777777777765 PP

>> B12D  NADH-ubiquinone reductase complex 1 MLRQ subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.3    0.0017         6       9      28 ..      27      46 ..      26      48 .. 0.92
   2 ?    1.6   0.1     0.066   2.4e+02       5      22 ..      52      69 ..      50      87 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0017
                              B12D  9 fvfigagvggavfylvRlll 28
                                      f++ig+g+++++ +l+++ll
  gi|313126683|ref|YP_004036953.1| 27 FGIIGLGITILSVFLTYSLL 46
                                      89***************997 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.066
                              B12D  5 liPLfvfigagvggavfy 22
                                      l+PL+  ++++ +g+v  
  gi|313126683|ref|YP_004036953.1| 52 LVPLLSTTAIAFVGVVTW 69
                                      667766666666665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 694.74
//
Query:       gi|313126684|ref|YP_004036954.1|  [L=261]
Description: GTP cyclohydrolase II [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-88  294.6   0.0    6.4e-88  294.2   0.0    1.0  1  GCH_III   GTP cyclohydrolase III
    8.5e-07   29.2   0.0      0.027   14.7   0.0    2.2  2  GGDEF_2   GGDEF-like domain
    0.00014   22.2   0.0       0.01   16.2   0.0    2.2  2  mCpol     minimal CRISPR polymerase domain


Domain annotation for each model (and alignments):
>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.2   0.0   1.1e-91   6.4e-88       2     235 ..       7     245 ..       6     255 .. 0.97

  Alignments for each domain:
  == domain 1  score: 294.2 bits;  conditional E-value: 1.1e-91
                                       EEEEETTHHHHCCSSS---HHHHHHHHHHHHHHHHHHHHTTT-EEE-TTSSEEEEE-TT--HHHHHHHHHHHHHHSS CS
                           GCH_III   2 tviqidnYgpWtvepaprreadlqalqarlyadlqkelaardGlvfatRfDnllaitngidleehkRiqesirnryp 78 
                                       ++iqidnYgpWtv+p prre+dlq+lq+rl+adl++++++rdG+vf+tRfDn++a+tng+d ++h+ +qesi+nryp
  gi|313126684|ref|YP_004036954.1|   7 SLIQIDNYGPWTVTPEPRREMDLQTLQSRLFADLAQFVGSRDGYVFFTRFDNMVAVTNGLDEADHELLQESIANRYP 83 
                                       68*************************************************************************** PP

                                       S-EEEEEEEESSHHHHHHHHHHHHHHH--TT-TT----EEES--....-SS--EEEEEEEETTHHHHTTTTS-HHHH CS
                           GCH_III  79 vtvsmgigaaetPldaleaaseaLreagsaqdeeRkevlsvdel....vtegyvqiahiDinnitgtltdivsavrt 151
                                       vt+s+gig    P++alea +  L++agsaqd +R+evl+ d l     t++  qiah+D+n++tg +td    +++
  gi|313126684|ref|YP_004036954.1|  84 VTISLGIGVDSSPIEALEAGTAGLQHAGSAQDGDRREVLAGDALpvsdRTDEDLQIAHFDVNDATGKYTDRLNEFDS 160
                                       *****************************************98877777899************************* PP

                                       HHHHHHHHHHHHHHH.HTTT---EEEETTEEEEE-TT--HHHHHHHHHHHHHHHS--EEEEEEEESSHHHHHHHHHH CS
                           GCH_III 152 ylevnkvkaklakkl.ekegallqfiGGDnilavcneleeedvldiinevkekvdvdlkaGiGiadtaedaaalade 227
                                        +++++  a+l+++l e++g l +f+GGDni++vc+++ e +  d+i +v+++++v+lk+G+G ++ta++a+  a++
  gi|313126684|ref|YP_004036954.1| 161 FIHIEQGYATLMRYLrEEYGGLSFFVGGDNIISVCPNMGEAGYRDAIRHVEQEAGVELKVGVGTGRTAHEAGFAAKH 237
                                       ***************999*********************************************************** PP

                                       HHHHHHTT CS
                           GCH_III 228 aLeeiRgk 235
                                       aLe +R +
  gi|313126684|ref|YP_004036954.1| 238 ALEVCREH 245
                                       ******54 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0     2e-05      0.12      34      94 ..      33      91 ..       8     103 .. 0.81
   2 !   14.7   0.0   4.5e-06     0.027      38      96 ..     168     225 ..     133     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                           GGDEF_2 34 aerllraleealralgpdalvavrgdrlvlllpaedeedaeallerlarrlgglsvriGiG 94
                                      ++rl + l++++ ++  ++++++r d+ v++  + de+d e l+e +a+r++  ++++GiG
  gi|313126684|ref|YP_004036954.1| 33 QSRLFADLAQFVGSR-DGYVFFTRFDNMVAVTNGLDEADHELLQESIANRYPV-TISLGIG 91
                                      334555566666654.789999******************************9.*****99 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.5e-06
                           GGDEF_2  38 lraleealralgpdalvavrgdrlvlllpaedeedaeallerlarrlgglsvriGiGsp 96 
                                       +++l ++lr+   +  ++v gd+++ ++p  +e+  ++++++++++ g  ++++G+G+ 
  gi|313126684|ref|YP_004036954.1| 168 YATLMRYLREEYGGLSFFVGGDNIISVCPNMGEAGYRDAIRHVEQEAGV-ELKVGVGTG 225
                                       6789999*99999*********************9*************9.888888864 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.011        68      39      92 ..      40      93 ..      30     102 .. 0.71
   2 !   16.2   0.0   1.7e-06      0.01      33     104 ..     165     239 ..     152     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                             mCpol 39 lkkllkdelgasvifaaGDsilaksslee.dllvelsrvyqkitgltvSiGvGkt 92
                                      l++++ +     v f   D+++a ++     +   l++   +   +t+S+G+G +
  gi|313126684|ref|YP_004036954.1| 40 LAQFVGSR-DGYVFFTRFDNMVAVTNGLDeADHELLQESIANRYPVTISLGIGVD 93
                                      56666666.778999999999999964332444445555555559*******976 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.7e-06
                             mCpol  33 keaikklkkllkdelgasvifaaGDsilaksslee.dllve.lsrvyqkit.gltvSiGvGktlrealiaLkkAk 104
                                       ++    l ++l +e g    f++GD+i+  ++      + + +++v q+ + +l+v +G+G+t++ea  a k A 
  gi|313126684|ref|YP_004036954.1| 165 EQGYATLMRYLREEYGGLSFFVGGDNIISVCPNMGeAGYRDaIRHVEQEAGvELKVGVGTGRTAHEAGFAAKHAL 239
                                       55667788899999988899***********865465555515555555559***************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1610.54
//
Query:       gi|313126685|ref|YP_004036955.1|  [L=94]
Description: hypothetical protein Hbor_19430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-15   57.4   0.0    1.6e-15   57.1   0.0    1.1  1  HalOD1      Halobacterial output domain 1
  ------ inclusion threshold ------
      0.076   13.7   0.1       0.11   13.2   0.1    1.5  1  Cadherin_4  Bacterial cadherin-like domain


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   1.8e-19   1.6e-15       3      72 ..      20      85 ..      18      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.8e-19
                            HalOD1  3 espstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeie 72
                                      e++++++v+ v +v+g++p++lepL ++ DpdAL++L+++    +a ++ ++ F+yeg +  + sdg+ie
  gi|313126685|ref|YP_004036955.1| 20 ERMTVEIVSLVTDVKGCQPMDLEPLSNVTDPDALENLIRE----TAAGEFEIGFDYEGGRLSISSDGTIE 85
                                      7899************************************....77888********************8 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.2e-05      0.11      36      72 .]      43      86 ..       4      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                        Cadherin_4 36 vlandtDvdgddltvtavtvag........tyGtltlnadGsftY 72
                                       l+n tD+d  +  + +++ ag        ++G l++++dG++++
  gi|313126685|ref|YP_004036955.1| 43 PLSNVTDPDALENLIRETA-AGefeigfdyEGGRLSISSDGTIEF 86
                                      579******9886666665.333444444489**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 609.37
//
Query:       gi|313126686|ref|YP_004036956.1|  [L=133]
Description: hypothetical protein Hbor_19440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-15   57.2   0.0    1.7e-15   56.9   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
      4e-07   30.1   0.0    4.8e-07   29.8   0.0    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
     0.0013   18.3   0.0     0.0015   18.1   0.0    1.1  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   2.9e-19   1.7e-15       3      84 ..       6      88 ..       4      92 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.9e-19
                                      HHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEEEE CS
                    Putative_PNPOx  3 eelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.lgrgvrieGt 80
                                      + ++++++++ +++l+T  +dG+P+v+pv+  ++ + d++++ t + +rk +n++++prva++  d++  +r ++++G+
  gi|313126686|ref|YP_004036956.1|  6 ADFQDLFEKQTFAHLSTLLPDGSPHVTPVWIDYDVDADRLLVNTERGRRKEKNIRNDPRVAISMTDPDnPYRMLSVQGE 84
                                      57899*****************************999*******************************9*********9 PP

                                      EEEE CS
                    Putative_PNPOx 81 aelv 84
                                      +   
  gi|313126686|ref|YP_004036956.1| 85 VDEM 88
                                      9765 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   8.1e-11   4.8e-07       6     138 ..       9     129 ..       5     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 8.1e-11
                                       HHHHHC-SEEEEEEEE.TTEEEEEEEEEEEE..TTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEEE CS
                      Pyridox_ox_2   6 lalLdegevgrlafvd.dgepvilPvnyvvd..gdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnsln 78 
                                        +l +++ +++l++   dg p+++Pv   +d  +d+l++ +++g r+ + +r+ p v+++ t+ d+           
  gi|313126686|ref|YP_004036956.1|   9 QDLFEKQTFAHLSTLLpDGSPHVTPVWIDYDvdADRLLVNTERGRRKEKNIRNDPrVAISMTDPDN-----P----- 75 
                                       57889999*****9997888*****96555444999****************7778*******999.....4..... PP

                                       EEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTT.GGCSB---CCCCCTEEEEEEEEEEEE CS
                      Pyridox_ox_2  79 yrSVvvrGraeevtdeeekaealellvekivpgr.wenlrpptrkelkatsvlrlkieevs 138
                                       yr   v+G++ e+t+e  +++++e + ++++ +  + n       + ++  ++++k+e+vs
  gi|313126686|ref|YP_004036956.1|  76 YRMLSVQGEVDEMTTEGAREQIDE-MSKRYMGKDeYPNPI-----Q-TERVMISIKPEHVS 129
                                       *************77777777665.667886655454333.....2.22466777777776 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.6e-07    0.0015       6     103 ..       8     105 ..       5     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-07
                     Pyrid_ox_like   6 lkelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskk.kyvsvsGt 81 
                                       +++l ++  +a L t   dg+ ++ P  +  + + ++l   t++  +k k+ir+d++v + + d+++    +sv+G+
  gi|313126686|ref|YP_004036956.1|   8 FQDLFEKQTFAHLSTLLPDGSPHVTPVWIDYDVDADRLLVNTERGRRKEKNIRNDPRVAISMTDPDNPyRMLSVQGE 84 
                                       78999999********************************************************8774145899999 PP

                     Pyrid_ox_like  82 aevvedrakieelWspvvkawf 103
                                       ++ ++ +  ++e  +++ k ++
  gi|313126686|ref|YP_004036956.1|  85 VDEMTTE-GAREQIDEMSKRYM 105
                                       8765543.34455555665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 957.98
//
Query:       gi|313126687|ref|YP_004036957.1|  [L=99]
Description: hypothetical protein Hbor_19450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.023   15.5   2.0      0.042   14.7   2.0    1.5  1  zf-C2H2_4    C2H2-type zinc finger
      0.026   14.1   0.3      0.048   13.3   0.3    1.4  1  zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
      0.062   13.2   0.2       0.11   12.5   0.1    1.5  2  HalOD2       Halobacterial output domain 2


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.0   7.1e-06     0.042       1      23 [.      20      42 ..      20      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.1e-06
                         zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkth 23
                                      f+C+ Cg++  s  +L  H+++h
  gi|313126687|ref|YP_004036957.1| 20 FRCTECGQTAMSLGSLHAHCEQH 42
                                      89*******************99 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3     8e-06     0.048       5      37 ..      20      51 ..      18      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-06
                       zf_C2H2_ZHX  5 FvCveCsfsakkfegLalHNarsHpgetnftlq 37
                                      F C+eC+ +a +  +L +H  + H g t+f +q
  gi|313126687|ref|YP_004036957.1| 20 FRCTECGQTAMSLGSLHAH-CEQHRGYTRFGFQ 51
                                      99*****************.5789999999887 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.8e-05      0.11      28      49 ..      15      37 ..       6      40 .. 0.75
   2 ?   -3.8   0.0       2.2   1.3e+04      22      28 ..      43      49 ..      41      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                            HalOD2 28 Gayv.WkCtrCGevqaaAdpShq 49
                                      G+ v ++Ct+CG++ ++  + h 
  gi|313126687|ref|YP_004036957.1| 15 GSLVlFRCTECGQTAMSLGSLHA 37
                                      665548*********99776665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.2
                            HalOD2 22 eGyrqLG 28
                                      +Gy++ G
  gi|313126687|ref|YP_004036957.1| 43 RGYTRFG 49
                                      4898887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 614.79
//
Query:       gi|313126688|ref|YP_004036958.1|  [L=139]
Description: hypothetical protein Hbor_19460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 938.34
//
Query:       gi|313126689|ref|YP_004036959.1|  [L=160]
Description: hypothetical protein Hbor_19470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1037.92
//
Query:       gi|313126690|ref|YP_004036960.1|  [L=72]
Description: hypothetical protein Hbor_19480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        3.1    7.4   6.1       0.96    9.1   2.5    1.7  2  DUF4131    Domain of unknown function (DUF4131)
        6.1    7.1  10.5        2.4    8.4   0.2    3.0  3  PEP-CTERM  PEP-CTERM motif


Domain annotation for each model (and alignments):
>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.5   0.00011      0.96       5      49 ..       3      45 ..       1      50 [. 0.85
   2 ?    0.8   0.2     0.038   3.5e+02       5      22 ..      49      66 ..      43      71 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00011
                           DUF4131  5 lalvllalllllllllllllrrrprrrvllllllllllallgfal 49
                                      + lv+l+l++++ ll l +   r +    l+l+++++++++++++
  gi|313126690|ref|YP_004036960.1|  3 STLVFLGLVGFASLLDLPFP--RHHLLAPLSLGAVAFAIVSYLQV 45
                                      56778888888888888887..9*******************987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.038
                           DUF4131  5 lalvllalllllllllll 22
                                      +   ++a+l++++++ + 
  gi|313126690|ref|YP_004036960.1| 49 VGGTAIAILGIAIAFMYG 66
                                      333444444444444433 PP

>> PEP-CTERM  PEP-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.8      0.01        94       6      19 ..       3      14 ..       3      17 .. 0.51
   2 ?   -0.1   0.1      0.13   1.2e+03      12      19 ..      31      38 ..      29      41 .. 0.64
   3 ?    8.4   0.2   0.00026       2.4       6      22 ..      51      68 ..      51      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.01
                         PEP-CTERM  6 sTllLlGlGllGla 19
                                      sTl  l  Gl+G+a
  gi|313126690|ref|YP_004036960.1|  3 STLVFL--GLVGFA 14
                                      565555..555543 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.13
                         PEP-CTERM 12 GlGllGla 19
                                       lG++++a
  gi|313126690|ref|YP_004036960.1| 31 SLGAVAFA 38
                                      46766654 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00026
                         PEP-CTERM  6 sT.llLlGlGllGlalrR 22
                                      +T +++lG++++ +++rR
  gi|313126690|ref|YP_004036960.1| 51 GTaIAILGIAIAFMYGRR 68
                                      6889******99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 457.39
//
Query:       gi|313126691|ref|YP_004036961.1|  [L=136]
Description: hypothetical protein Hbor_19490 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 885.41
//
Query:       gi|313126692|ref|YP_004036962.1|  [L=31]
Description: hypothetical protein Hbor_19510 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        66  (0.00368119); expected 358.6 (0.02)
Passed bias filter:                       57  (0.00317921); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 202.18
//
Query:       gi|313126693|ref|YP_004036963.1|  [L=74]
Description: hypothetical protein Hbor_19520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.046   13.8   3.7       0.65   10.2   0.2    2.2  2  Zn-ribbon_8  Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   3.6e-05      0.65      22      36 ..      30      45 ..      21      47 .. 0.77
   2 ?    4.6   0.5    0.0019        34       6      12 ..      61      67 ..      60      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.6e-05
                       Zn-ribbon_8 22 s.dapltaCPeCgsev 36
                                      s ++++ +CPeC ++v
  gi|313126693|ref|YP_004036963.1| 30 SiEDADRDCPECDGNV 45
                                      33788899****9876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0019
                       Zn-ribbon_8  6 YrCeeCg 12
                                      Y+C++C 
  gi|313126693|ref|YP_004036963.1| 61 YKCQDCE 67
                                      ******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 514.09
//
Query:       gi|313126694|ref|YP_004036964.1|  [L=337]
Description: hypothetical protein Hbor_19530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2000.55
//
Query:       gi|313126695|ref|YP_004036965.1|  [L=72]
Description: hypothetical protein Hbor_19540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       115  (0.00641419); expected 358.6 (0.02)
Passed bias filter:                      111  (0.00619109); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 473.39
//
Query:       gi|313126696|ref|YP_004036966.1|  [L=107]
Description: ferredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-15   57.2   0.3    1.8e-15   56.6   0.3    1.2  1  Fer2      2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.3     1e-19   1.8e-15       5      77 ..      14      85 ..      11      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1e-19
                                      TEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTT.SSSSTHHHHHTTEEEEGGGSEE CS
                              Fer2  5 gkevevevadgettlldaaeenggidipysCggggCgtClvevlegev.qsd.etelegeeldegklrlaCqtiv 77
                                      g+e ++ + ++et +l+aae++ +i +p++C+ g+C+tC+ ++ +g++  +  +++l  ++ ++g++ l+C +++
  gi|313126696|ref|YP_004036966.1| 14 GREETTRASEDET-ILEAAESA-DISLPFGCRTGACATCVGRLIDGNIsYDRpPRALKTRHIESGYV-LCCIARP 85
                                      88999999999*9.*******9.*************************7444689999999888877.****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 680.71
//
Query:       gi|313126697|ref|YP_004036967.1|  [L=464]
Description: 56kda selenium binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     6e-193  641.8   0.2     7e-193  641.5   0.2    1.0  1  SBP56        56kDa selenium binding protein (SBP56)
  ------ inclusion threshold ------
       0.16   10.8   0.0       0.27   10.0   0.0    1.4  1  Beta_propel  Beta propeller domain


Domain annotation for each model (and alignments):
>> SBP56  56kDa selenium binding protein (SBP56)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.5   0.2  7.8e-197    7e-193       3     453 ..      21     463 ..      19     464 .] 0.98

  Alignments for each domain:
  == domain 1  score: 641.5 bits;  conditional E-value: 7.8e-197
                             SBP56   3 adPgyasPkeai.kapreklayvaaleanteiekpDalavvdvdpesetyskvvhrvelpnlgdelhhfGWnaCss. 77 
                                       ++Pgya+P++ai ++++e++ayv+ l+++t+i++pD++avvdvdp+sety ++++rve+pn+gdelhhfGWnaCss 
  gi|313126697|ref|YP_004036967.1|  21 EGPGYATPQAAIeESEPESVAYVMGLYVGTDIDAPDFMAVVDVDPDSETYQEIINRVEMPNRGDELHHFGWNACSSs 97 
                                       69**********999***********************************************************996 PP

                             SBP56  78 chaedaskerrylivPglrssriyvvdtktdprkpklvkviepeevaektglsrphtvhClpegeilisalgdaeGe 154
                                       ch   +  errylivPg rssr++v+dtk ++r+p++ +viep+ v+e  +ls+pht+hC+p+g+i+is+lg+a+Ge
  gi|313126697|ref|YP_004036967.1|  98 CH--IGGLERRYLIVPGNRSSRLHVIDTK-NRRNPQIERVIEPDAVHE-YDLSAPHTTHCIPDGDIVISMLGNADGE 170
                                       77..77889*******************9.9************88887.7*************************** PP

                             SBP56 155 gkggillldketfevkgrWekdrekqelaYDfwyqlrkdvmvsseWgaPkafekGldledleegkyGkrlhvwdlee 231
                                        +gg+l l ++  e+kgrW+ ++e  +++YDfwyq+r++vmvsseW+aP++++ G+d+ed+eegkyG+rl++w++ee
  gi|313126697|ref|YP_004036967.1| 171 LPGGFLELGDD-LEIKGRWDPPNE-IDFNYDFWYQPRHNVMVSSEWAAPATYQPGFDMEDVEEGKYGHRLNFWNWEE 245
                                       *********99.********9987.89************************************************** PP

                             SBP56 232 rkllqtidlgeegqlvlevrflhdPkkaegfvgvvLsssvfrfykeedekweaekvieipakkvegeelpelpglvt 308
                                       ++l+qtidlgeeg ++le rflh+P++++g+v+++Lss++f+f++ e+++++aekvi++++++ + +++p  p+l t
  gi|313126697|ref|YP_004036967.1| 246 HELEQTIDLGEEGLIPLETRFLHTPESTHGYVNAALSSNIFHFWE-ENDRYHAEKVIDFESRELDDWDMPV-PALPT 320
                                       *********************************************.9999******************997.***** PP

                             SBP56 309 DillslDDrflyvsnWltGdlrqydisdpkkPkltgqvrlGGiirkaehpavkgrkleggPqmvelslDGkrlYvtn 385
                                       Dil+s+DDr+l+  +Wl+G++++ydisdpk+P++++++++GG++ +   ++v++r+l +gPqm++lslDG+rlY+t+
  gi|313126697|ref|YP_004036967.1| 321 DILISMDDRYLFGGSWLHGEVWMYDISDPKSPRRADSISIGGYFGDI--RTVQDRELVAGPQMLQLSLDGERLYWTT 395
                                       *******************************************9877..789************************* PP

                             SBP56 386 sLysawddqfypelvkkgsvllkidvdtekGglsldknflvdfgkepegparahevryegGDassDiy 453
                                       sLys+wd+qf+pe+ +kgsv+lk+dv+++kG+l+ld++flvdfg+  +gparahe+r+++GD++sD++
  gi|313126697|ref|YP_004036967.1| 396 SLYSSWDNQFFPEMAEKGSVMLKADVNPRKGTLTLDEDFLVDFGEVATGPARAHEIRWPDGDCTSDVW 463
                                       ******************************************************************** PP

>> Beta_propel  Beta propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0     3e-05      0.27      94     126 ..     340     372 ..     303     413 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3e-05
                       Beta_propel  94 kvliyDisdkenpkllreleldGsyvssRkigd 126
                                       +v +yDisd+++p+ + ++++ G++ + R + d
  gi|313126697|ref|YP_004036967.1| 340 EVWMYDISDPKSPRRADSISIGGYFGDIRTVQD 372
                                       57799*******************999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3014.10
//
Query:       gi|313126698|ref|YP_004036968.1|  [L=499]
Description: inosine-5'-monophosphate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.4e-140  468.2   7.9   1.6e-140  468.0   7.9    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      2e-23   82.6   6.2    3.3e-12   46.7   0.6    2.8  2  CBS           CBS domain
    2.2e-09   36.8   2.9    3.3e-09   36.2   2.9    1.3  1  FMN_dh        FMN-dependent dehydrogenase
      8e-09   35.3   5.7      8e-06   25.5   2.2    2.3  2  NMO           Nitronate monooxygenase
    0.00012   21.4   3.2    0.00023   20.4   3.2    1.4  1  Glu_synthase  Conserved region in glutamate synthase
     0.0013   18.0   1.2      0.003   16.8   1.0    1.6  2  DHO_dh        Dihydroorotate dehydrogenase
     0.0019   17.5   1.9     0.0019   17.5   1.9    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
     0.0042   16.6   1.3      0.025   14.0   0.1    1.9  1  His_biosynth  Histidine biosynthesis protein
     0.0099   15.0   0.5      0.025   13.7   0.2    1.7  2  Dus           Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.0   7.9  8.1e-144  1.6e-140       1     345 []      20     483 ..      20     483 .. 0.99

  Alignments for each domain:
  == domain 1  score: 468.0 bits;  conditional E-value: 8.1e-144
                                       E--GGGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH   1 gltfddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevk 77 
                                       +ltfddvll p +s+v+p+++d++t+++k+++ln+P++saamdtvtes mAi +areGg+gv+h+n++ie+ ++e++
  gi|313126698|ref|YP_004036968.1|  20 ALTFDDVLLRPMESRVEPDDADVSTRVSKNVELNVPILSAAMDTVTESGMAIGMAREGGLGVLHRNMDIEAMVAEIE 96 
                                       69*************************************************************************** PP

                                       HHHTS........................................................................ CS
                                       xxxxx........................................................................ RF
                             IMPDH  78 kvkrs........................................................................ 82 
                                       +vkr+                                                                        
  gi|313126698|ref|YP_004036968.1|  97 RVKRAdelvirrenvvtarpgqtvrdvdemmeregvsgapvvdeedvvlgiisgtdirpylevgesdevreamtdev 173
                                       ***************************************************************************** PP

                                       ................................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHH CS
                                       ................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  83 ................................................pnaakdekgrllvgaavgvkedalervka 111
                                                                                       ++aa+d++grl++g avg  e  ++r++a
  gi|313126698|ref|YP_004036968.1| 174 itaerdvtardalelmydhkiervpvvdeeghlvglvtmqgilqrrehEHAARDDDGRLVCGVAVGPFE--TDRAEA 248
                                       ************************************************99******************6..89**** PP

                                       HHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 112 lveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagv 188
                                         eag+dvl++d+ah+h+ +vl+  +eik++v e +v++Gn+ t+e+a++ ++  ad++kvGiGpGsiCttrvv+g+
  gi|313126698|ref|YP_004036968.1| 249 ADEAGADVLFIDCAHAHNLNVLDSAREIKQSV-EADVVVGNIGTREAAEEAVDF-ADGLKVGIGPGSICTTRVVSGA 323
                                       ********************************.7******************99.********************** PP

                                       ---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 189 GvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgs 265
                                       G+pq+tAvaeva++a+  gvpviaDGGi+ysgd +kA+aaGadavmlGs++agt+E+pg+vi+++g+kyK+yrGmgs
  gi|313126698|ref|YP_004036968.1| 324 GMPQITAVAEVADVAAPEGVPVIADGGIRYSGDAIKAVAAGADAVMLGSYFAGTDEAPGRVITMNGKKYKQYRGMGS 400
                                       ***************************************************************************** PP

                                       HHHHHH-SS-TTS-.....--SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHH CS
                                       xxxxxxxxxxxxxx..x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 266 lgamkkgskdryfq..k.keklvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaagl 339
                                       +gamk+g  dry +  + +e++vpeGve+++pykg++++ ++qlvgg+rsgmgy+Ga+ti ++ke+a+fvr+++ag+
  gi|313126698|ref|YP_004036968.1| 401 VGAMKSGGGDRYLKdaDdDEEFVPEGVEAATPYKGTLASELHQLVGGMRSGMGYVGAETIPDFKERAEFVRVSSAGQ 477
                                       ************98542466********************************************************* PP

                                       HHHS-- CS
                                       xxxxxx RF
                             IMPDH 340 keshvH 345
                                       +e+h+H
  gi|313126698|ref|YP_004036968.1| 478 TEGHPH 483
                                       *****9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.7   1.1e-12   2.2e-09       6      54 ..     108     156 ..     101     158 .. 0.90
   2 !   46.7   0.6   1.6e-15   3.3e-12       1      54 [.     165     218 ..     165     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.1e-12
                                       BSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   6 trdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +++vvt++p +t++++ e+m+++gvs+ PVVde++ ++Gi++ +D+  +
  gi|313126698|ref|YP_004036968.1| 108 RENVVTARPGQTVRDVDEMMEREGVSGAPVVDEEDVVLGIISGTDIRPY 156
                                       5699****************9999***********888*******9755 PP

  == domain 2  score: 46.7 bits;  conditional E-value: 1.6e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V++ mt++v+t+  d t ++alelm ++++ r+PVVde+g+lvG+vt+  +l+ 
  gi|313126698|ref|YP_004036968.1| 165 VREAMTDEVITAERDVTARDALELMYDHKIERVPVVDEEGHLVGLVTMQGILQR 218
                                       7899********************************************999986 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   2.9   1.7e-12   3.3e-09     193     303 ..     257     374 ..     166     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.7e-12
                                       HHCCCHB-TC--HHH.HHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHH CS
                            FMN_dh 193 efvgkqldpsltwdd.ikwlreqtklplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLp 262
                                        f++    ++l+  d  +++++ ++  +vv  + t e a++av+  +dg+ v    G     R + ga ++ i +  
  gi|313126698|ref|YP_004036968.1| 257 LFIDCAHAHNLNVLDsAREIKQSVEADVVVGNIGTREAAEEAVDF-ADGLKVGIGPGsicttRVVSGAgMPQITAVA 332
                                       566666677777664489999999999999999999999999999.6999998877767777877776356688888 PP

                                       HHHHHH..S.S-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 263 eiveavggr.ievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       e+++ ++ + ++v++DgGir   D++kA+a GAdav+lG  f
  gi|313126698|ref|YP_004036968.1| 333 EVADVAAPEgVPVIADGGIRYSGDAIKAVAAGADAVMLGSYF 374
                                       8888777545*****************************766 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1    0.0001       0.2       4      59 ..      46     100 ..      43     105 .. 0.86
   2 !   25.5   2.2     4e-09     8e-06     182     238 ..     328     387 ..     278     414 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                               NMO   4 ltellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvka 59 
                                       +++ ++ + p+  + m  +++  +a   + +GgLGvl    +    + +ei++vk+
  gi|313126698|ref|YP_004036968.1|  46 VSKNVELNVPILSAAMDTVTESGMAIGMAREGGLGVLH-RNMDIEAMVAEIERVKR 100
                                       566677889****************************9.66666789999999987 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 4e-09
                               NMO 182 faLvpqvldavd...iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahk 238
                                       ++ v++v+d+ +   +PviA GGi    +   a a+GA +v +g+ f +t+e++ ++++ 
  gi|313126698|ref|YP_004036968.1| 328 ITAVAEVADVAApegVPVIADGGIRYSGDAIKAVAAGADAVMLGSYFAGTDEAPGRVITM 387
                                       55677888888899**********9999988889*******************9888764 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   3.2   1.1e-07   0.00023     224     304 ..     292     372 ..     264     375 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.1e-07
                                       HHTT-SEEE.EE-TT---SSE...EHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT CS
                      Glu_synthase 224 akanadiil.idGleGGTGAs...pkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalG 296
                                        +a  +++   dGl+ G G      + ++  aG+P ++a+aev  +   eg    v +iadGg++ + d +ka+a G
  gi|313126698|ref|YP_004036968.1| 292 REAAEEAVDfADGLKVGIGPGsicTTRVVSGAGMPQITAVAEVADVAAPEG----VPVIADGGIRYSGDAIKAVAAG 364
                                       3344444431478888887651114678899***********998877665....89******************** PP

                                       -SEEE-SH CS
                      Glu_synthase 297 Adavgigt 304
                                       Adav +g+
  gi|313126698|ref|YP_004036968.1| 365 ADAVMLGS 372
                                       *****997 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.7   5.3e+03     195     226 ..     108     137 ..      89     139 .. 0.64
   2 !   16.8   1.0   1.5e-06     0.003     229     276 ..     329     374 ..     316     384 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.7
                                       E...BSEE--CTTCCGCCCCTTSSEEEEEGGG CS
                            DHO_dh 195 vtNttvqrlaidlkseknvkanktGGlsGkal 226
                                         N ++ r+  +++  +++ +    G+sG+++
  gi|313126698|ref|YP_004036968.1| 108 RENVVTARPGQTVRDVDEMME--REGVSGAPV 137
                                       467777777777777666665..556999987 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                       +a++ + ++++     +p+I+ GGi  + Da+  + aGA +v +++ +
  gi|313126698|ref|YP_004036968.1| 329 TAVAEVADVAAPEG--VPVIADGGIRYSGDAIKAVAAGADAVMLGSYF 374
                                       35555666665555..***************************99965 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.06   1.2e+02     188     232 ..     244     288 ..     232     301 .. 0.82
   2 !   17.5   1.9   9.8e-07    0.0019     157     212 ..     321     379 ..     313     388 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.06
                                       HHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHH CS
                              ThiG 188 sdaaqamelGadavllntavaeakdpvamArafklaveaGrlayl 232
                                         a +a e Gad ++++ a a+  +    Ar +k++vea  +  +
  gi|313126698|ref|YP_004036968.1| 244 DRAEAADEAGADVLFIDCAHAHNLNVLDSAREIKQSVEADVVVGN 288
                                       56778889******************************9766555 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 9.8e-07
                                       S----S-HHHHHHHHHH-...SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                              ThiG 157 sglGllnkealkiiieea...kvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                       sg G+ + +a+  + + a    vPvi D Gi+ + da++a+  Gadav+l +  a +++
  gi|313126698|ref|YP_004036968.1| 321 SGAGMPQITAVAEVADVAapeGVPVIADGGIRYSGDAIKAVAAGADAVMLGSYFAGTDE 379
                                       6667666666666655543447****************************998887665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.3e-05     0.025      65     104 ..     334     373 ..     319     387 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                       HHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHH CS
                      His_biosynth  65 veeiaeevfipvqvGGGIrsledveelleagadkviigta 104
                                       v+ +a    +pv  +GGIr   d+ +++ agad v++g+ 
  gi|313126698|ref|YP_004036968.1| 334 VADVAAPEGVPVIADGGIRYSGDAIKAVAAGADAVMLGSY 373
                                       3444444458888888888888888888888888888885 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         1   2.1e+03     173     210 ..     271     305 ..     246     313 .. 0.74
   2 !   13.7   0.2   1.3e-05     0.025     172     213 ..     328     371 ..     289     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEE CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgv 210
                                       ++ +e+kq+v+  v++ G+I ++e+a+++++   adg+
  gi|313126698|ref|YP_004036968.1| 271 DSAREIKQSVEADVVV-GNIGTREAAEEAVDF--ADGL 305
                                       5567888888866665.888888888887776..6665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.3e-05
                                       CHHHHHHHHH-S...S-EEEESS--SHHHHHHHHHHH--SEEEES CS
                               Dus 172 weaIkevkqavs...ipviaNGdIkdaedaqaileetGadgvmig 213
                                       + a++ev +      +pvia G+I++  da ++++  Gad+vm g
  gi|313126698|ref|YP_004036968.1| 328 ITAVAEVADVAApegVPVIADGGIRYSGDAIKAVAA-GADAVMLG 371
                                       556666666555577********************9.******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3211.68
//
Query:       gi|313126699|ref|YP_004036969.1|  [L=362]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-61  207.4   0.1    2.1e-61  207.1   0.1    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    2.9e-15   55.9   0.0    5.4e-15   55.0   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00088   19.2   0.0     0.0026   17.7   0.0    1.8  1  PadR            Transcriptional regulator PadR-like family
     0.0021   17.9   0.1     0.0051   16.7   0.1    1.6  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.046   13.5   0.0       0.12   12.2   0.0    1.7  1  HTH_IclR        IclR helix-turn-helix domain
      0.062   13.2   0.0       0.17   11.8   0.0    1.7  1  MarR            MarR family
        0.1   12.2   0.0       0.24   11.0   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.1   0.1   8.3e-65   2.1e-61       2     231 ..     111     358 ..     110     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 207.1 bits;  conditional E-value: 8.3e-65
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS.....----GGGSSSSEEEE CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp.....dedleeldleevate 73 
                                       +++vk++etv +r++++I++Aene+++s+++ + eel++ l++a e+g  V +++++      +  e  d+e+v+te
  gi|313126699|ref|YP_004036969.1| 111 LSIVKRFETVFQRAASIIREAENEVQLSVTADQYEELKPALREAFENGAIVKVSLHTdperdGPSFESMDFEGVVTE 187
                                       89**********************************************999999999666433334566899***** PP

                                       EE-S---S.EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-H CS
                    Regulator_TrmB  74 vrvrrsgapllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssi 150
                                       +r+r +++p++++vDr+++++ap+     + +ey++++++++l++v+++yF t+lW+  + +++++ +e p+ +++ 
  gi|313126699|ref|YP_004036969.1| 188 ARHRTLPTPFVLLVDRTQTCFAPH---AHSLNEYGVLVDDYTLTYVFHWYFQTCLWEVLDQVYSARDDEPPVVYADV 261
                                       ************************...799*********************************************** PP

                                       HHHHHHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEE................EETTTTEEEEEEEETTEEE CS
                    Regulator_TrmB 151 rlavedikkllraglkveaeveGrdtetgeevtieGrvveat................lnstpgvaslvvetedgev 211
                                       r++v+di++ l+++++v+a+v+G dt tg++v+++G+++e+                 l++ +g+  ++++ +++++
  gi|313126699|ref|YP_004036969.1| 262 RRCVRDIEPTLSEDATVRATVTGLDTGTGDHVELTGEITEVYysgmtdttagadstpaLSQLAGQVCFTLRAGEETY 338
                                       ****************************************889********************************** PP

                                       EEE-TT--SSSEEEEEEEEE CS
                    Regulator_TrmB 212 tVGGlgAvlEDieaeeitle 231
                                       tVGG+gAvlED+ea+++t++
  gi|313126699|ref|YP_004036969.1| 339 TVGGWGAVLEDVEATRVTVT 358
                                       ******************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   2.1e-18   5.4e-15       1      68 []      10      77 ..      10      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2.1e-18
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                      L++ GLs+y a++Y aLl+lg a+a+e+a +  vp +++Y+vLr Le kG++e+ ++   + ra dpe
  gi|313126699|ref|YP_004036969.1| 10 LEDAGLSQYQAEAYNALLQLGAASATELADACAVPTARIYDVLRDLETKGYIETYEQDSLRARACDPE 77
                                      6788**************************************************99998888888886 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     1e-06    0.0026      26      54 ..      40      68 ..      28      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1e-06
                                      -CCTTHHHHHHHHHHHHHTTSEEEEEE-S CS
                              PadR 26 llelseGslYpaLkrLekeglvesewees 54
                                      + ++  +++Y++L++Le +g++e+++++s
  gi|313126699|ref|YP_004036969.1| 40 ACAVPTARIYDVLRDLETKGYIETYEQDS 68
                                      4678899********************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     2e-06    0.0051      18      55 ..      30      65 ..      13      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2e-06
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +    +++ela+++ ++ +++  +l++L+ +G++e+ +
  gi|313126699|ref|YP_004036969.1| 30 GA--ASATELADACAVPTARIYDVLRDLETKGYIETYE 65
                                      33..59****************************9973 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.8e-05      0.12      19      49 ..      32      62 ..      24      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.8e-05
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyve 49
                                       + +elA+++++p +  +  L+ L+  Gy+e
  gi|313126699|ref|YP_004036969.1| 32 ASATELADACAVPTARIYDVLRDLETKGYIE 62
                                      488**************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.7e-05      0.17      13      49 ..      27      63 ..      24      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.7e-05
                                      HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                       + g++s +eLa++  v ++ +  vl+ Le kG+ie 
  gi|313126699|ref|YP_004036969.1| 27 LQLGAASATELADACAVPTARIYDVLRDLETKGYIET 63
                                      5899*******************************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.5e-05      0.24      18      48 .]      32      62 ..      22      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.5e-05
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       s +eLA+++ ++ + +   l+ Le +G+I+
  gi|313126699|ref|YP_004036969.1| 32 ASATELADACAVPTARIYDVLRDLETKGYIE 62
                                      6889**************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2424.55
//
Query:       gi|313126700|ref|YP_004036970.1|  [L=200]
Description: response regulator with chey-like receiver domain and winged-helix DNA-binding domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-24   86.5   9.6    1.1e-24   86.5   9.6    2.5  3  HalX             HalX domain
    3.5e-19   69.0   0.1    5.8e-19   68.3   0.1    1.4  1  Response_reg     Response regulator receiver domain
  ------ inclusion threshold ------
          1   10.4   3.7        2.2    9.4   0.7    2.2  2  Methyltransf_24  Methyltransferase domain
        1.1    9.6  10.1       0.15   12.4   4.4    2.4  3  ABC_tran_CTD     ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4      0.49   2.2e+03      44      54 ..      41      51 ..      38      70 .. 0.60
   2 ?   -2.4   0.1       1.4   6.2e+03      49      57 ..     106     114 ..     104     116 .. 0.51
   3 !   86.5   9.6   2.5e-28   1.1e-24       1      67 [.     117     183 ..     117     184 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.49
                              HalX 44 leelraqldet 54
                                      l+el +++d +
  gi|313126700|ref|YP_004036970.1| 41 LDELDDDVDVV 51
                                      45555555544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                              HalX  49 aqldetlde 57 
                                       + l+et+++
  gi|313126700|ref|YP_004036970.1| 106 EALEETVEN 114
                                       345555554 PP

  == domain 3  score: 86.5 bits;  conditional E-value: 2.5e-28
                              HalX   1 trseYdeelqelfaLasKravLeaekseaeLadseeYqeLearleelraqldetldelddaddfeal 67 
                                       +r +Y++ +qelf+LasK+a+Le+ek++a+L+d+eeYqeL arl  lr++ldetl+++d+++d++a+
  gi|313126700|ref|YP_004036970.1| 117 RRNTYNDGVQELFSLASKKALLESEKDPATLEDNEEYQELDARLSKLREDLDETLQQFDEERDIAAV 183
                                       699************************************************************9986 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.1   1.3e-22   5.8e-19       1     111 [.       8     112 ..       8     113 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.3e-22
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vliv+D+p++++l +++l+ e++ +v++a  g+eal+ l+ + vd++llD +mp+++G e+l+eir++  e++v ++
  gi|313126700|ref|YP_004036970.1|   8 VLIVEDEPDLADLYATWLR-EKC-RVRVAYGGREALDELDDD-VDVVLLDRRMPDLSGDEALTEIRNRGFECRVAMV 81 
                                       8******************.999.9**************976.********************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       ta + + d+v    +g dd+l+Kp+++e+L + +
  gi|313126700|ref|YP_004036970.1|  82 TAVEPDFDIV---AMGFDDYLVKPVSKEALEETV 112
                                       *999877765...68***************9987 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.093   4.2e+02      46      76 ..      24      54 ..       3      72 .. 0.75
   2 ?    9.4   0.7   0.00049       2.2      30      79 ..     141     189 ..      81     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.093
                   Methyltransf_24 46 glddrvrlikads.eealaslaagsiDllfiD 76
                                       l++  r+++a   +eal +l+ +++D++++D
  gi|313126700|ref|YP_004036970.1| 24 WLREKCRVRVAYGgREALDELD-DDVDVVLLD 54
                                      5667777777776688999999.99****999 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00049
                   Methyltransf_24  30 dhdpgaeeaaalare....aglddrvrlikadseealasla.agsiDllfiDggh 79 
                                       ++dp  ++ +    +    ++ld+r+  +++d++e+l++++ +++i  ++ D g 
  gi|313126700|ref|YP_004036970.1| 141 EKDP--ATLE----DneeyQELDARLSKLREDLDETLQQFDeERDIAAVYRDLGD 189
                                       3333..2222....2344599********************88889999999874 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   5.2e+03      56      65 ..      16      25 ..      14      26 .. 0.84
   2 ?   -0.7   0.3      0.39   1.7e+03      53      61 ..     108     116 ..     104     142 .. 0.46
   3 ?   12.4   4.4   3.2e-05      0.15      25      65 ..     135     175 ..     126     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                      ABC_tran_CTD 56 eLeelyerWe 65
                                      +L+ ly+ W+
  gi|313126700|ref|YP_004036970.1| 16 DLADLYATWL 25
                                      68999****7 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.39
                      ABC_tran_CTD  53 leaeLeely 61 
                                       le+  e+l+
  gi|313126700|ref|YP_004036970.1| 108 LEETVENLL 116
                                       222222222 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 3.2e-05
                      ABC_tran_CTD  25 aeleaeladpelysdpeklaelsaeleeleaeLeelyerWe 65 
                                       ++l +   dp+  +d e+ +el a+l +l+++L+e ++++ 
  gi|313126700|ref|YP_004036970.1| 135 KALLESEKDPATLEDNEEYQELDARLSKLREDLDETLQQFD 175
                                       4455555789999**********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1227  (0.0684366); expected 358.6 (0.02)
Passed bias filter:                      770  (0.0429472); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1292.48
//
Query:       gi|313126701|ref|YP_004036971.1|  [L=47]
Description: hypothetical protein Hbor_19600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 320.10
//
Query:       gi|313126702|ref|YP_004036972.1|  [L=716]
Description: hypothetical protein Hbor_19610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.088   12.2   0.0       0.16   11.4   0.0    1.5  1  CHAT      CHAT domain


Domain annotation for each model (and alignments):
>> CHAT  CHAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.8e-06      0.16     104     203 ..     469     555 ..     377     599 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.8e-06
                                       xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CHAT 104 pgteaEaeaiakllaegel...kvllgeaatesalksalsrryrvvHfatHgvfnanpplqsglvlsaenseedglL 177
                                       p+ ++E e ++   +++e+    v ++ ++t+++l++al+++ +++H ++H   +       g+        +dg L
  gi|313126702|ref|YP_004036972.1| 469 PRMADEREDVEAVYGSREKlpfDVQVQYELTKDELREALATQTDFFHYIGHIDND-------GFQC------SDGTL 532
                                       7778888888888888888889999999************************999.......6666......47777 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CHAT 178 taeeilelnldgaelVvLsACqtglg 203
                                       +a+ + ++    ++   L+AC++  +
  gi|313126702|ref|YP_004036972.1| 533 DASTLSDVG---MDAFLLNACRSYEQ 555
                                       777777743...34666777777644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 4497.51
//
Query:       gi|313126703|ref|YP_004036973.1|  [L=247]
Description: hypothetical protein Hbor_19620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1504.31
//
Query:       gi|313126704|ref|YP_004036974.1|  [L=188]
Description: hypothetical protein Hbor_19630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-22   78.7   0.0    4.6e-22   78.4   0.0    1.1  1  DUF218    DUF218 domain


Domain annotation for each model (and alignments):
>> DUF218  DUF218 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0   2.6e-26   4.6e-22       2     128 ..       2     156 ..       1     159 [. 0.78

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 2.6e-26
                            DUF218   2 aivVLGaal......pllaeRldeaaelyrag...kiivsGg..gadedvseaeamaeylrelgvpeeailledrsr 67 
                                       ++vVLG++l      + l++R++++++ ++a+    + +sGg  +++ d++e  +m ey++++gv++++i+l++ + 
  gi|313126704|ref|YP_004036974.1|   2 IVVVLGHRLessqihERLRARVNAGIRAFNATdasSLFFSGGqtNQHIDRTECGVMGEYAVRQGVDPDRIVLDPFAH 78 
                                       5899**77777778999***************8755******9877799*****************99********* PP

                            DUF218  68 nTeenarfskell.....kersillVTsafHmpRalllfrka.g.....apt.......psaealsasees..alra 124
                                       +T  na f++ l+     +++++ lVT++fH pRa+++f ++ g       t          ++ + + ++  ++++
  gi|313126704|ref|YP_004036974.1|  79 DTIGNAYFTRVLCdnlglDIDELSLVTDDFHAPRAKYAFDQCfGadvavE-TthaveteT--DCDDSTCQQklQRTR 152
                                       *****************86669*****************99963555430.233332221..111111111245556 PP

                            DUF218 125 alrE 128
                                       a+ E
  gi|313126704|ref|YP_004036974.1| 153 AFFE 156
                                       6555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1233.37
//
Query:       gi|313126705|ref|YP_004036975.1|  [L=418]
Description: ferrichrome ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-13   50.7   0.1    2.5e-13   50.2   0.1    1.3  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.1   1.4e-17   2.5e-13      50     233 ..     142     356 ..      94     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.4e-17
                                       B-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS.....................HHHHHHHHHHH CS
                      Peripla_BP_2  50 idvEklaalkPDlvilskglgltdedeellksgiptvivessntg.....................eslkeqiralg 105
                                       ++ Ekl +l+ D+ ++++    ++ +e  ++s+i+ +  +  +++                     + l e++  ++
  gi|313126705|ref|YP_004036975.1| 142 PTKEKLYELDSDVHLADPAR--VATAEGWDESDIEEIKENVAPWFgntfsdahqqppaawqdgyeyYTLWETFGRVA 216
                                       45588888888888888877..444444444444444444444444444555599999*****999999999999** PP

                                       HHTT-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEEETTE..EEEE-TTSTTTHHHHT.S--EESTTT--. CS
                      Peripla_BP_2 106 ellgledeaeklvaeidsklaaaksaidse...kpkpvlvfggadeggyvvagsnsyigdllda.lgieniaaesk. 177
                                       +++++e+++++l+  ++s l  +++ ++ e      ++++f+++d++++ + ++ ++  + +   lg+ +++ e   
  gi|313126705|ref|YP_004036975.1| 217 QVFQEEERYKALADVHNSLLTTIEANLPPEserPSAAMVLFSSSDDSMWGYKTNAPGYYASHTRpLGATDALTEAVg 293
                                       ******************************97555566777788889999988888888888888******777656 PP

                                       .....STT-EEE-HHHHHHH--SEEEEEEH..HHHT-S--HHHHT-SHHHHTSHHHHTT-EEE CS
                      Peripla_BP_2 178 .....kseyeeisaEqilasdpdvifvsgr..aeadnktgleflkenpllaelpAvkngrVya 233
                                             ++ ++++ E++l++dpdv++v g   +  + + + ++l+ ++++++++Av++g+Vy 
  gi|313126705|ref|YP_004036975.1| 294 dsyenVGDDITLDYETLLEADPDVLLVLGPmtEYHNIDDIRAKLEDHDVAKKITAVEEGQVYV 356
                                       999999999999******************999999**************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2823.90
//
Query:       gi|313126706|ref|YP_004036976.1|  [L=383]
Description: aspartate/tyrosine/aromatic aminotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-71  239.1   0.0    9.2e-71  238.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0012   17.9   0.0     0.0019   17.2   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
     0.0067   15.7   0.0      0.012   14.9   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.9   0.0   1.5e-74   9.2e-71       2     363 .]      29     377 ..      28     377 .. 0.95

  Alignments for each domain:
  == domain 1  score: 238.9 bits;  conditional E-value: 1.5e-74
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi Lg++e+++      + +++ a+++  +  +++++y+ ++g  el+ea+a  +  ++  +++++++++v+ Ga+
  gi|313126706|ref|YP_004036976.1|  29 DVISLGVGEPDFS----APWAARTAAID--SLERGRTSYTSNRGMRELREAIAGRVE-RYDQQYDPDDEILVTAGAS 98 
                                       79***********....***********..999************************.99***************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++ ++++++l +++gd + vp+p+y sy++ +  +gge  ++p++ e+df +  ++le+a +       +  v++++
  gi|313126706|ref|YP_004036976.1|  99 EAVDLAMRAL-VDTGDIVAVPEPSYISYEPTVSFAGGEALSVPTRAEADFAVGYDDLERAGAA------EADVLVLC 168
                                       **********.9***********************************************8887......7789**** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                        p+NPtG+v+t++el +++++a+++ l++++De+Ya++ +++ d+v+ +a++    + +++ +++sKa++++G+R+G
  gi|313126706|ref|YP_004036976.1| 169 YPNNPTGAVMTRDELADVAEFAREHDLFVLSDEIYAALRYED-DHVS-IATLPGMRErTVVFNGFSKAYAMTGLRLG 243
                                       ****************************************96.7777.555544444589***************** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       y+lg aa++++++++++      ++ +q+a+++a++  ++    ++emr+ + +rr+++ ++++++g ++++ ++++
  gi|313126706|ref|YP_004036976.1| 244 YALGPAAIIDAMNRIHQYTMLsaPTTAQYAALEAIESCDD---AVDEMRRAYDRRRRFVISRFNDIGMDCFEAKGAF 317
                                       ***************99766669999*********99996...9********************************* PP

                                       EEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       +++  +++   ++++++++Ll+e++v+++pg+ f+   +g+lR+++ +++ +el+ +++++
  gi|313126706|ref|YP_004036976.1| 318 YVFPKCPPGweDDEAFAEALLQEEKVALVPGRVFGEsgEGHLRVSY-ATSMSELKTALNRI 377
                                       ********999***********************************.***********997 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.1e-07    0.0019      59     177 ..      86     202 ..      54     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.1e-07
                                       STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH CS
                       Aminotran_5  59 eseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekl 135
                                       + ++ei++t G++ea+ l++++l   +++gd + v e  + +   p +  a  + + v   +++++  +  d+le +
  gi|313126706|ref|YP_004036976.1|  86 DPDDEILVTAGASEAVDLAMRAL---VDTGDIVAVPEPSYISYE-PTVSFAGGEALSV-PTRAEADFAVGYDDLERA 157
                                       5679*******************...9***************99.8888885555555.66788889999******* PP

                                       --TTEEEEEEESBETTTTE...B--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 136 lnektklvaithvsnvtGt...iqpveeigklakkkgalvlvDaa 177
                                        + +++++ ++  +n tG     ++++++++ a++++ +vl D  
  gi|313126706|ref|YP_004036976.1| 158 GAAEADVLVLCYPNNPTGAvmtRDELADVAEFAREHDLFVLSDEI 202
                                       ******************832246899999999******999965 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.1e-06     0.012      12     167 ..      45     200 ..      39     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-06
                                       HHHHHHHHCS----CCCT--HHHHHHHHHHHHHTT-SEEEE.......ES-H.HHHHHHHHHHH--TTEEEEEETT- CS
                   Beta_elim_lyase  12 eamsdaqaaamlGdesYgedktvnrLedavaelfgkeaalf.......vpqG.taAnsillkillqrgeevivtepa 80 
                                       +a ++a+  ++ G  sY  ++++++L +a+a  ++   + +       v+ G   A  +++++l+  g+ v v ep+
  gi|313126706|ref|YP_004036976.1|  45 AARTAAIDSLERGRTSYTSNRGMRELREAIAGRVERYDQQYdpddeilVTAGaSEAVDLAMRALVDTGDIVAVPEPS 121
                                       555666688999*******************966665555555666655555267888999********99999999 PP

                                       HHHHSSTTHHHHCC--EEEEE-EBTTTBE-H..HHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHH CS
                   Beta_elim_lyase  81 hihfdetgaiaelagvklrdlknkeaGkmdl..ekleaaikevgaheekiklisltvTnntagGqvvsleelrevaa 155
                                        i    t   + +ag ++  ++++++ ++ +  ++le+a ++      +  +++l   nn   G v++ +el+ va+
  gi|313126706|ref|YP_004036976.1| 122 YISYEPT---VSFAGGEALSVPTRAEADFAVgyDDLERAGAA------EADVLVLCYPNNP-TGAVMTRDELADVAE 188
                                       9987766...44567777888877755554422566665555......6678888888884.8************** PP

                                       HHHHCT-EEEEE CS
                   Beta_elim_lyase 156 iakkygiplhlD 167
                                       +a+++++ ++ D
  gi|313126706|ref|YP_004036976.1| 189 FAREHDLFVLSD 200
                                       *******99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2327.19
//
Query:       gi|313126707|ref|YP_004036977.1|  [L=162]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-18   64.6   0.1    1.2e-17   63.6   0.1    1.5  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    3.9e-09   35.9   0.2    8.2e-09   34.9   0.2    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    6.9e-06   25.8   3.0    1.2e-05   25.0   1.3    2.2  3  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    4.5e-05   23.3   0.1    9.7e-05   22.2   0.1    1.6  1  MarR_2          MarR family
    0.00014   21.6   0.1    0.00029   20.6   0.1    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    0.00027   21.0   0.8    0.00048   20.2   0.8    1.4  1  DprA_WH         DprA winged helix domain
     0.0033   17.3   0.3     0.0051   16.7   0.3    1.3  1  TFIIE_alpha     TFIIE alpha subunit
  ------ inclusion threshold ------
      0.012   15.5   0.0       0.02   14.8   0.0    1.4  1  MarR            MarR family
      0.047   14.1   0.0      0.083   13.3   0.0    1.4  1  Streptin-Immun  Lantibiotic streptin immunity protein
      0.072   13.3   0.1       0.15   12.3   0.1    1.6  1  SelB-wing_2     Elongation factor SelB, winged helix
      0.087   12.8   0.0       0.19   11.7   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
        0.1   12.1   0.1       0.17   11.5   0.1    1.4  1  HTH_47          winged helix-turn-helix
       0.11   12.4   0.0        0.2   11.5   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.11   12.4   0.0       0.17   11.8   0.0    1.3  1  Utp13           Utp13 specific WD40 associated domain
       0.13   12.2   0.1       0.45   10.5   0.1    1.9  2  DUF2621         Protein of unknown function (DUF2621)
       0.14   11.7   0.0       0.25   10.9   0.0    1.5  1  Gp_dh_C         Glyceraldehyde 3-phosphate dehydrogenase, C-t
       0.19   12.4   0.0       0.41   11.3   0.0    1.5  1  RPA_C           Replication protein A C terminal


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.1   1.1e-20   1.2e-17       2      75 .]      70     141 ..      67     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.1e-20
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       +v+l+++    +ee+ +++a++peV+++  v+Gdyd+ l v   ++++ +rf++e++a +p+v++t t++v+et
  gi|313126707|ref|YP_004036977.1|  70 NVELDRET--GYEEISRRIAKFPEVTSLCLVSGDYDFALTVEGDSMHDVSRFISERIAPIPEVTQTVTHFVMET 141
                                       46666555..9*************************************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.2   7.8e-12   8.2e-09       6      48 .]       5      47 ..       4      47 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7.8e-12
                            HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      r++L lL +n+r s  ++A+++gl  ++v + +++Lee+G+I+
  gi|313126707|ref|YP_004036977.1|  5 RELLDLLLRNARESPEDIARQTGLDAAAVEALIDELEEDGVIR 47
                                      899***************************************7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   1.3   1.2e-08   1.2e-05       6      41 ..       5      40 ..       3      41 .. 0.90
   2 ?   -0.9   0.0       1.4   1.5e+03       7      16 ..      35      44 ..      34      46 .. 0.86
   3 ?   -1.5   0.0       2.2   2.4e+03      20      27 ..      79      86 ..      74      88 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.2e-08
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      r +L++L ++aR s +++A+++Gl++++v + ++ L
  gi|313126707|ref|YP_004036977.1|  5 RELLDLLLRNARESPEDIARQTGLDAAAVEALIDEL 40
                                      789**************************8766666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                     HTH_AsnC-type  7 kILeaLqeda 16
                                      +++++L+ed+
  gi|313126707|ref|YP_004036977.1| 35 ALIDELEEDG 44
                                      6999****98 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.2
                     HTH_AsnC-type 20 yaeLAerv 27
                                      y+e+++r+
  gi|313126707|ref|YP_004036977.1| 79 YEEISRRI 86
                                      66666664 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   9.2e-08   9.7e-05       9      52 ..       6      47 ..       3      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.2e-08
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                       +L  L r+ + + ++ ++ar +gl+ +av  ++++L++ G ++
  gi|313126707|ref|YP_004036977.1|  6 ELLDLLLRNAR-E-SPEDIARQTGLDAAAVEALIDELEEDGVIR 47
                                      67888999986.3.***************************997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.7e-07   0.00029       8      49 ..       7      47 ..       6      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.7e-07
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +Ld+l + ++e +  ++Ar+tgl  ++v  l+  L+e G ++
  gi|313126707|ref|YP_004036977.1|  7 LLDLLLRNARE-SPEDIARQTGLDAAAVEALIDELEEDGVIR 47
                                      8*********9.9************************99876 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.8   4.6e-07   0.00048      12      56 ..       2      47 ..       1      49 [. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.6e-07
                           DprA_WH 12 dlerrvLaaLgpePv.hvDqLvrrtglpaaevsaaLleLELaGlve 56
                                      d++r +L++L   ++ + ++++r+tgl+aa+v a+  eLE +G ++
  gi|313126707|ref|YP_004036977.1|  2 DDKRELLDLLLRNAReSPEDIARQTGLDAAAVEALIDELEEDGVIR 47
                                      678899999865555499**********************999886 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   4.8e-06    0.0051      16      61 ..       5      51 ..       2      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.8e-06
                                      HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE.EEE CS
                       TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk.ykr 61
                                       + ld Ll+++  + ed+a+++++d   +  l+ +L e++++  y+ 
  gi|313126707|ref|YP_004036977.1|  5 RELLDLLLRNARESPEDIARQTGLDAAAVEALIDELEEDGVIRgYQA 51
                                      5789*************************************963444 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.9e-05      0.02      15      51 ..      14      50 ..       4      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      +   s  ++a++ g++ ++v  ++d+Le++G i+ ++
  gi|313126707|ref|YP_004036977.1| 14 NARESPEDIARQTGLDAAAVEALIDELEEDGVIRGYQ 50
                                      4455677*************************98665 PP

>> Streptin-Immun  Lantibiotic streptin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.9e-05     0.083      52      89 ..      53      93 ..      48      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.9e-05
                    Streptin-Immun 52 vtleqiekeieklqnelskkide...yeelvrkldkfvkvl 89
                                      v  +++++e  + q el+ ++d+   yee+ r++ kf +v 
  gi|313126707|ref|YP_004036977.1| 53 VDWDRVDEEHVQAQVELNVELDRetgYEEISRRIAKFPEVT 93
                                      6789*****************96666***********9986 PP

>> SelB-wing_2  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014      0.15      29      49 ..      27      47 ..       7      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                      SS-HCCHHHHHHHHHHTTSEE CS
                       SelB-wing_2 29 rlpaklfqallealvargila 49
                                      +l+a++++al+++l+++g + 
  gi|313126707|ref|YP_004036977.1| 27 GLDAAAVEALIDELEEDGVIR 47
                                      89****************997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.19      23      54 ..      18      49 ..       5      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrg 54
                                      + e++A+  Gl    v  ++ eL+++g+i+  
  gi|313126707|ref|YP_004036977.1| 18 SPEDIARQTGLDAAAVEALIDELEEDGVIRGY 49
                                      669**************************943 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00016      0.17      51      77 ..      21      47 ..       2      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                      HHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 51 diAeriglpfdrvaaiaraLaeaglla 77
                                      diA ++gl++++v+a++++L+e g+++
  gi|313126707|ref|YP_004036977.1| 21 DIARQTGLDAAAVEALIDELEEDGVIR 47
                                      9************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019       0.2      17      53 ..      11      47 ..       3      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      Ll++ + + ++ia+++g++ + v   + +Le+ G+++
  gi|313126707|ref|YP_004036977.1| 11 LLRNARESPEDIARQTGLDAAAVEALIDELEEDGVIR 47
                                      6699******************************986 PP

>> Utp13  Utp13 specific WD40 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.17      23      92 ..       1      72 [.       1      97 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                      SSSTHHHHHHHHHHHS-SS--STSSSSS..HHHHHHHHC--HHHHHHHHHHHHHHHTSTTTHHHHHHHHHHH CS
                             Utp13 23 ldqpkrllkllkevleseeeeeesitgs..kevdevlkslskeqleklLkyirdWntnartsevAqrvLnai 92
                                      +d  ++ll+ll + +++++e+  ++tg+  ++v++++++l+++ + +  + + dW      +  Aq+ Ln+ 
  gi|313126707|ref|YP_004036977.1|  1 MDDKRELLDLLLRNARESPEDIARQTGLdaAAVEALIDELEEDGVIRGYQAVVDWDRVDEEHVQAQVELNVE 72
                                      57778899998888888888666666654479**********************************999875 PP

>> DUF2621  Protein of unknown function (DUF2621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00042      0.45      59     112 ..       2      52 ..       1      87 [. 0.81
   2 ?   -0.9   0.0       1.4   1.4e+03      61      80 ..     116     135 ..     111     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                           DUF2621  59 deekelleelvspvpelfrdvakekiagkigelaleekakeitedliikGyila 112
                                       d+++ell+ l++   e   d+a+++    +   a+e   +e++ed +i+Gy + 
  gi|313126707|ref|YP_004036977.1|   2 DDKRELLDLLLRNARESPEDIARQT---GLDAAAVEALIDELEEDGVIRGYQAV 52 
                                       799********************96...578899999**************654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                           DUF2621  61 ekelleelvspvpelfrdva 80 
                                         +++ e ++p+pe+ + v+
  gi|313126707|ref|YP_004036977.1| 116 VSRFISERIAPIPEVTQTVT 135
                                       5678999999***9988775 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.25      40     111 ..      12      91 ..       2     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                       TTTTSBTTCSSEEEE-THHHHHHHHSGGGT..TTEEEEEEEESSSSE......EEEEEEEEESSTS-HHHHHHHHHH CS
                           Gp_dh_C  40 lrraraaaeniiptstgaakavglVlpelk..gkldglAvrVPtpnv......svvdlvvelekevtveevnaalke 108
                                       lr+ar   e+i   +   a av+  ++el+  g + g+   V    v       +v+l vel++e+ +ee+ + + +
  gi|313126707|ref|YP_004036977.1|  12 LRNARESPEDIARQTGLDAAAVEALIDELEedGVIRGYQAVVDWDRVdeehvqAQVELNVELDRETGYEEISRRIAK 88 
                                       68888888888887777899999999999733679999887776555222222479****************99998 PP

                                       HHH CS
                           Gp_dh_C 109 aae 111
                                        +e
  gi|313126707|ref|YP_004036977.1|  89 FPE 91 
                                       876 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00039      0.41      71      97 ..      20      46 ..      17      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                                      HHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 71 deiaqklrlsvndvkqavdeLsneGii 97
                                      + ia++++l+ + v+  +deL+++G+i
  gi|313126707|ref|YP_004036977.1| 20 EDIARQTGLDAAAVEALIDELEEDGVI 46
                                      579***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 964.64
//
Query:       gi|313126708|ref|YP_004036978.1|  [L=337]
Description: molybdate ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-27   96.3   0.2    2.7e-27   96.0   0.2    1.1  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    5.7e-05   23.2   1.3     0.0016   18.5   0.4    2.2  2  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.13   11.7   0.2       0.29   10.5   0.0    1.7  2  SBP_bac_6   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.2   4.6e-31   2.7e-27       1     228 [.      40     301 ..      40     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 4.6e-31
                                       .EEEE-SSTHHHHHHHHHHHHHHH---EEEEESSHHHHHHHH.HHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEE CS
                        SBP_bac_11   1 ltvaaagslaaalrelaaaFeahtgvkvevsaggsgklarqi.adgarpDvwipassawlellaaaglvqaesavpl 76 
                                       lt++ agsl+++++++ aaFe++++v+v+ +a+gs +  ++i ++g+r+Dv+   +   +++ +  ++++  +++ +
  gi|313126708|ref|YP_004036978.1|  40 LTIFHAGSLEPPFSAAEAAFEEQYDVEVNREAKGSVASTKKItQQGRRADVLGVSDFRLIRNRVLPEYGK--WYSIF 114
                                       89****************************************55556*********99999999999999..***** PP

                                       EEEEEEEEESTT-.....TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--..........HHHHHHHHH CS
                        SBP_bac_11  77 assplviavpkgn.....pkkikgwadLlkpglklavadPttspsGlaalalleaaga..........qellkalek 138
                                       +++ + i +++++       ++ +w+ L ++g++++ +dP+ +p+G++a+++ +  ga          q ++++l+ 
  gi|313126708|ref|YP_004036978.1| 115 TTNSMSIQYREDSngaedISTDNWWEVLSRDGVTIGHSDPAVDPGGYRAVMTQQL-GAksfdgaklydQSTYEKLRA 190
                                       ************9774322255577778889****************99987775.445667778999********* PP

                                       TEEEEESSHHHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--.......................... CS
                        SBP_bac_11 139 kvvklgessrqlltaveageadagivyeseakaaengdkleavylpeglnl.d........................ 190
                                       + v+ ++++++l  ++++g+ d++i+y+s         +l+++ l +++ l +                        
  gi|313126708|ref|YP_004036978.1| 191 NSVVPTGTETNLEGQLKSGKLDYAIYYQSISS----TSELPYIDLQPQVDLsKatseyaehyakatvetdsgtftga 263
                                       *99999999999999**************998....78899999999998855899999999999999999999999 PP

                                       ..EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT CS
                        SBP_bac_11 191 pldypaavlkkaakreaAraFlafLrspeaqailrkyG 228
                                       p++y+++v++ a+ ++  +++++f++  e+q++l++ G
  gi|313126708|ref|YP_004036978.1| 264 PIAYGITVPDVADAPNLGAKWVEFMLNGEGQNALEAKG 301
                                       ************************************99 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.01        61       5      44 ..      49      84 ..      45      98 .. 0.66
   2 !   18.5   0.4   2.6e-07    0.0016     179     314 ..     172     294 ..     144     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.01
                                      HH.HHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHH CS
                         SBP_bac_1  5 te.gaalqalvakafekehpgikVeiesvgsgslaqkltla 44
                                      ++ ++a +a+    fe+  ++++V+ e  gs +   k+t +
  gi|313126708|ref|YP_004036978.1| 49 EPpFSAAEAA----FEE-QYDVEVNREAKGSVASTKKITQQ 84
                                      4433444444....666.58*****9999888888866655 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.6e-07
                                       GGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEE CS
                         SBP_bac_1 179 kvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkv 255
                                       k fd+                  kly++   +k  ++ ++++ +++++ +++++G+ + ai + +   ++ + ++  
  gi|313126708|ref|YP_004036978.1| 172 KSFDG-----------------AKLYDQSTYEKLRANSVVPTGTETNLEGQLKSGKLDYAIYYQSISSTSELPYIDL 231
                                       44443.................233333333566689999999********************99966666555443 PP

                                       ....CHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 256 ....afaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                           ++ ++++++ e++++a + +  g  +g ++ayg+++p  ++ p    k+++f+l+ e+q
  gi|313126708|ref|YP_004036978.1| 232 qpqvDLSKATSEYAEHYAKATVETDSGTFTGAPIAYGITVPDVADAPNLGAKWVEFMLNGEGQ 294
                                       55559999999999999999866555555555**************************98877 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.62   3.7e+03      48      73 ..     107     133 ..      99     144 .. 0.75
   2 ?   10.5   0.0   4.9e-05      0.29     187     222 ..     274     316 ..     218     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.62
                         SBP_bac_6  48 dgkyy.pygvgplvlavnkdrlkgrpv 73 
                                        gk+y +++++ +++ + +d  +++++
  gi|313126708|ref|YP_004036978.1| 107 YGKWYsIFTTNSMSIQYREDSNGAEDI 133
                                       566666999999999888888777765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 4.9e-05
                         SBP_bac_6 187 g.kkkelakafidfllspevqailakaggvfPvv.......tnp 222
                                           ++l +++++f+l  e+q++l++ g+ +Pv         ++
  gi|313126708|ref|YP_004036978.1| 274 VaDAPNLGAKWVEFMLNGEGQNALEAKGL-VPVEpavvpksGAD 316
                                       24588999********************9.99744433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2059.78
//
Query:       gi|313126709|ref|YP_004036979.1|  [L=278]
Description: sulfate ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-16   60.9  10.8    1.3e-16   60.9  10.8    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.39   11.1   5.8      0.094   13.0   0.4    2.8  2  DUF4149       Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.16   1.4e+03       1       7 [.      31      37 ..       7      72 .. 0.63
   2 !   60.9  10.8   1.5e-20   1.3e-16       2     175 ..      74     267 ..      73     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.16
                      BPD_transp_1  1 gillGil 7 
                                      g++l+++
  gi|313126709|ref|YP_004036979.1| 31 GLPLAMF 37
                                      2233333 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 1.5e-20
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrl 70 
                                       +++G+ +a  l+r+++++ l+  l++++l +P+ + +i++++ f        l++lg +++++++++++ +apy++ 
  gi|313126709|ref|YP_004036979.1|  74 VIFGVPLAlaLSRGFPGRTLVASLVDLPLVVPHSAAGIIVLFGFgrggafPQLTVLG-TVTGMVLAMVFVSAPYAVN 149
                                       678888888899*****************************999****966666666.9999*************** PP

                      BPD_transp_1  71 irraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailg 147
                                         r+a++++++ l+ a+r+ Gasr+++fr+v+ P+a++ i+tg +la+++++ ++ ++ +++     + +++ +  g
  gi|313126709|ref|YP_004036979.1| 150 SAREAFEAVDDRLEYASRIHGASRFETFRRVTGPLAVRGIVTGGVLAWARSVSEFGAVAIVA----YSVRFFYPPAG 222
                                       **************************************************************....44444444444 PP

                      BPD_transp_1 148 ydyseis.................nggvlalviavlllnlvadil 175
                                       + +++                    ++++ l+++  ++ l++++l
  gi|313126709|ref|YP_004036979.1| 223 REVTSQHapvfirkayltggldqsGAVTFLLLLVSTAVFLIIRWL 267
                                       444433347889999999887665444444444444444444444 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.7      0.29   2.6e+03      56      56 ..      32      32 ..       4      85 .. 0.61
   2 ?   13.0   0.4     1e-05     0.094       2      60 ..     128     196 ..     127     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.29
                           DUF4149 56 e 56
                                       
  gi|313126709|ref|YP_004036979.1| 32 L 32
                                      1 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1e-05
                           DUF4149   2 slglllGsqlwvtfvvapvlfrsLprhqfgelqskl...........Fplyfglglalsvlllltevavg 60 
                                       +lg+ +G++l+++fv+ap++  s  r++f+++  +l           F+ + ++ + l+v  ++t ++  
  gi|313126709|ref|YP_004036979.1| 128 VLGTVTGMVLAMVFVSAPYAVNS-AREAFEAVDDRLeyasrihgasrFETFRRVTGPLAVRGIVTGGVLA 196
                                       589********************.7788999999999888889999988888888888877777777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1781.36
//
Query:       gi|313126710|ref|YP_004036980.1|  [L=319]
Description: spermidine/putrescine ABC transporter ATPase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-30  105.6   0.0    4.4e-30  105.0   0.0    1.2  1  ABC_tran     ABC transporter
    6.6e-07   29.4   0.1     0.0092   15.8   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.6e-05   24.3   0.4    7.4e-05   22.8   0.4    1.8  1  TOBE_2       TOBE domain
      0.002   17.6   0.0          2    7.8   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0029   18.0   0.1     0.0059   17.0   0.1    1.6  1  AAA_16       AAA ATPase domain
      0.008   15.5   0.1       0.58    9.4   0.0    2.8  3  Zeta_toxin   Zeta toxin
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.026   14.3   0.0    1.7  1  AAA_29       P-loop containing region of AAA domain
      0.015   15.6   0.0      0.034   14.4   0.0    1.8  1  AAA_22       AAA domain
      0.049   13.5   0.1        0.1   12.5   0.0    1.5  2  RsgA_GTPase  RsgA GTPase
      0.058   13.1   0.0      0.086   12.6   0.0    1.4  1  AAA_30       AAA domain
       0.17   11.9   0.3        5.8    6.9   0.0    2.3  2  AAA_5        AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   2.7e-33   4.4e-30       5     136 ..      24     156 ..      21     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 2.7e-33
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                        +++k+ge+ +++G++G+GKS Ll+++ag ++   G++ ldg+dl+   +   ++++g+++q+  lfp++tv+en  
  gi|313126710|ref|YP_004036980.1|  24 AFEVKRGETAVVLGPSGSGKSLLLETVAGFHS-HDGSVALDGTDLTP--KAPENRRFGFVFQNYMLFPNMTVAENvr 97 
                                       699***************************87.79***********9..888999*********************9 PP

                                       ......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             e + +++++l++lg+++l+d+      s+LSgG+kqrvalar+l  +p++lllDEp 
  gi|313126710|ref|YP_004036980.1|  98 ygdryhETTGDAAELLAELGISDLADRYP----STLSGGEKQRVALARSLYVRPDVLLLDEPL 156
                                       99998888888************999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00011      0.18       2      24 ..      33      55 ..      32      76 .. 0.76
   2 !   15.8   0.0   5.7e-06    0.0092     228     298 ..     120     186 ..      70     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                      +v+ Gp gsGKS LL++  ++++
  gi|313126710|ref|YP_004036980.1| 33 AVVLGPSGSGKSLLLETVAGFHS 55
                                      699**************988854 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 5.7e-06
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHS 298
                                       d  ++ ++ lS G k+  al+ +l+ ++   ++ll+DEp + L+   ++rl  ++l+ l    +  + +TH+
  gi|313126710|ref|YP_004036980.1| 120 DLADRYPSTLSGGEKQRVALARSLYVRP---DVLLLDEPLSALDVPTQTRLRqDMLDVLDG--VTAVYVTHD 186
                                       5566778899******99********99...9********************999999966..999999998 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.4   4.5e-08   7.4e-05       1      73 [.     252     316 ..     252     319 .] 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.5e-08
                            TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpdda 73 
                                       la+RPE++rl  + g + ++++Ve+v+   +  r+++++ + ++       +d   ++apG+ V++s++  + 
  gi|313126710|ref|YP_004036980.1| 252 LAVRPENVRL--DNGSGDVTARVERVVREDAVFRVTLAVSDHRI---DAYTTD---PPAPGSSVGVSFEESAS 316
                                       79********..44457***********9888888888888866...666676...99**********98765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0012         2      25      44 ..      31      50 ..      18      59 .. 0.77
   2 !    7.7   0.0    0.0013       2.2     122     183 ..     108     171 ..      87     205 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      +  +++Gp GSGKs ll+ +
  gi|313126710|ref|YP_004036980.1| 31 ETAVVLGPSGSGKSLLLETV 50
                                      345678********999876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0013
                                       HHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 122 evsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                       + +ell++ gis        +LSgGek+ vala       v+p  + llDe  +aLD    +++ + +
  gi|313126710|ref|YP_004036980.1| 108 DAAELLAELGISDLadrypsTLSGGEKQRVALARS---LYVRPD-VLLLDEPLSALDVPTQTRLRQDM 171
                                       566666666665433333339*******9999865...455665.55899999999988887776543 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.6e-06    0.0059      19      53 ..      27      59 ..      20     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.6e-06
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekdgg 53
                                      v++g  e  ++ G+sG+GKs l+++++   + dg 
  gi|313126710|ref|YP_004036980.1| 27 VKRG--ETAVVLGPSGSGKSLLLETVAGFHSHDGS 59
                                      5555..6799***************9965555543 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00035      0.58      20      60 ..      34      73 ..      20      77 .. 0.84
   2 ?   -0.8   0.0      0.48   7.7e+02     132     165 ..     185     217 ..     178     224 .. 0.62
   3 ?    2.3   0.0     0.052        85      40      57 ..     226     242 ..     217     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00035
                        Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                      ++ G +G+GKs l+e ++  + ++++ v ld++dl +  Pe
  gi|313126710|ref|YP_004036980.1| 34 VVLGPSGSGKSLLLETVAGFH-SHDGSVALDGTDLTPKAPE 73
                                      556889*************99.6**********99887776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.48
                        Zeta_toxin 132 kkelSrlgvldRyeeevaegRlvpkeehdeafeg 165
                                       + ++++  ++dR +   +egR+v+  + d++f++
  gi|313126710|ref|YP_004036980.1| 185 HDRTTARTLADRILVM-NEGRIVQRGTPDAVFDR 217
                                       3333334455666665.67899998888888765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.052
                        Zeta_toxin  40 lerqgnvvrldpDdlRel 57 
                                       + +++n+v ld+DdlR+ 
  gi|313126710|ref|YP_004036980.1| 226 F-TGSNCVPLDTDDLRSA 242
                                       3.589***********85 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.6e-05     0.026      16      40 ..      24      48 ..      18      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllD 40
                                       +e+++ ++ ++ GpsGsGKS ll 
  gi|313126710|ref|YP_004036980.1| 24 AFEVKRGETAVVLGPSGSGKSLLLE 48
                                      57788666999**********9985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.1e-05     0.034       8      31 ..      33      56 ..      27     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqlde 31
                                       vv G+sG+GK++ll++++  +  
  gi|313126710|ref|YP_004036980.1| 33 AVVLGPSGSGKSLLLETVAGFHSH 56
                                      799**************9988853 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.4e-05       0.1      96     121 ..      27      52 ..       4      61 .. 0.79
   2 ?   -3.5   0.0       5.3   8.7e+03      19      43 ..     178     202 ..     167     206 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                                       HCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                                       + +++t+v++G+SG GKS L++++++
  gi|313126710|ref|YP_004036980.1|  27 VKRGETAVVLGPSGSGKSLLLETVAG 52 
                                       44569****************98876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.3
                                       EEEEEESTTTT--HHHHHHHHHHHH CS
                       RsgA_GTPase  19 llivvslkepelslnlldrfLvlae 43 
                                       +  v  +++ ++   l dr+Lv+ e
  gi|313126710|ref|YP_004036980.1| 178 VTAVYVTHDRTTARTLADRILVMNE 202
                                       5555566667777778888888765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05     0.086      17      47 ..      29      65 ..      20     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag......g 47
                                      +  +av+ Gp G+GK+ +l++++  + ++g       
  gi|313126710|ref|YP_004036980.1| 29 RGETAVVLGPSGSGKSLLLETVAGFHSHDGsvaldgT 65
                                      44589********************999985555552 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0036       5.8       3      20 ..      34      51 ..      32      64 .. 0.88
   2 ?    2.7   0.0      0.07   1.1e+02      13      52 ..     165     204 ..     163     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0036
                                      EEE--SSSSHHHHHHHGG CS
                             AAA_5  3 lLvGppGtgKselaerla 20
                                      +++Gp+G+gKs l e +a
  gi|313126710|ref|YP_004036980.1| 34 VVLGPSGSGKSLLLETVA 51
                                      579***********9987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.07
                                       HHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..... CS
                             AAA_5  13 selaerlaaalnreveyvqltrdtteedlkgrreikngtt 52 
                                       ++l + ++ +l   + ++  +++tt+++l  r+ ++n+++
  gi|313126710|ref|YP_004036980.1| 165 TRLRQDMLDVLDGVTAVYVTHDRTTARTLADRILVMNEGR 204
                                       7788899999999999999*************99986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1960.91
//
Query:       gi|313126711|ref|YP_004036981.1|  [L=71]
Description: hypothetical protein Hbor_19700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 473.73
//
Query:       gi|313126712|ref|YP_004036982.1|  [L=598]
Description: n-terminal double-transmembrane domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-18   67.5   4.5    1.9e-18   66.6   4.5    1.5  1  BatA      Aerotolerance regulator N-terminal
    2.1e-05   25.1   0.1    5.8e-05   23.7   0.1    1.7  1  VWA_2     von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.068   13.1   0.3       0.14   12.1   0.3    1.4  1  DUF4714   Domain of unknown function (DUF4714)
       0.11   12.7   0.3        0.4   11.0   0.3    2.0  1  DUF58     Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   4.5   4.1e-22   1.9e-18       3      77 .]       6      82 ..       1      82 [. 0.96

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 4.1e-22
                              BatA  3 pFlnPllLlallllplpiillyllkrrpqevvfsslrlleevekdeea...lqrlkknllllLrllalallvlalArP 77
                                       Fl+Pl ++al+++++ i++lyl++++p++++f++ ++l e ++++e+   ++rlk++ lllL+ll+++ll+ al++P
  gi|313126712|ref|YP_004036982.1|  6 VFLTPLGFAALAAAIP-ILILYLVRPDPRRIQFPTYQFLTEDQRENESnpvFERLKRSTLLLLQLLVILLLATALSTP 82
                                      7**********99999.***********************************************************99 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.3e-08   5.8e-05       1     106 [.      95     190 ..      95     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsd..gpevlipltkdkakilnalrnleakggg 75 
                                       +v+v+D S+Sm+ +  g tr+++a + +++ +      + ++v+ +   ++e+ +++ +d +++l+ l  ++     
  gi|313126712|ref|YP_004036982.1|  95 TVLVVDASASMNVQSDGGTRFSRAVSEAQDAVTG----TTSIVVAGAepRVELRSGPADDAKSVLTGLSPTD---AP 164
                                       79************99**************9998....4555555550255666677788777777666655...56 PP

                             VWA_2  76 tnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                        +l +a+++a ++  ++     ++iv+++D 
  gi|313126712|ref|YP_004036982.1| 165 GDLRSAISTAASIAGEG-----SRIVVVSDF 190
                                       99***********9977.....599999995 PP

>> DUF4714  Domain of unknown function (DUF4714)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   3.2e-05      0.14      77     115 ..      53      93 ..      49     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
                           DUF4714  77 spvhgr..gafllllallvltclalailavylsvlqseslr 115
                                       +pv +r   + llll llv+  la a+ + y+s  qse++ 
  gi|313126712|ref|YP_004036982.1|  53 NPVFERlkRSTLLLLQLLVILLLATALSTPYVSTSQSETVE 93 
                                       566665325789**************************875 PP

>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3     9e-05       0.4      28      70 ..      80     122 ..      76     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                             DUF58  28 gelyvrefeaerartvllvldlspemslgstgdekletavsaa 70 
                                        ++yv   ++e+  +++lv+d+s++m+ +s+g + + +avs a
  gi|313126712|ref|YP_004036982.1|  80 STPYVSTSQSETVEETVLVVDASASMNVQSDGGTRFSRAVSEA 122
                                       578999************************9966666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3652.94
//
Query:       gi|313126713|ref|YP_004036983.1|  [L=785]
Description: mg-chelatase subunit chld [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-14   54.6   0.0    6.8e-11   42.7   0.0    2.7  3  VWA           von Willebrand factor type A domain
    8.4e-13   48.9   0.0    1.2e-11   45.1   0.0    2.5  2  VWA_2         von Willebrand factor type A domain
    8.1e-12   45.3   0.0    2.1e-11   44.0   0.0    1.7  2  VWA_3         von Willebrand factor type A domain
    3.4e-07   29.9   0.0    6.8e-05   22.4   0.0    2.4  2  VWA_CoxE      VWA domain containing CoxE-like protein
     0.0064   16.0   0.0       0.17   11.3   0.0    2.2  2  GATase1_like  Putative glutamine amidotransferase
  ------ inclusion threshold ------
      0.014   15.6   3.0      0.014   15.6   3.0    3.1  3  Big_3_5       Bacterial Ig-like domain (group 3)
      0.047   14.1   2.0       0.19   12.2   0.3    2.8  3  CBM60         Ca-dependent carbohydrate-binding module xylan-
       0.24   11.8   0.1       0.24   11.8   0.1    2.8  3  BatA          Aerotolerance regulator N-terminal
       0.28   11.0   3.4        2.7    7.9   0.5    3.5  2  PKD           PKD domain
        2.3    9.1   7.1        5.4    7.9   5.4    2.6  2  Big_7         Bacterial Ig domain


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.5   6.3e+03       2      22 ..      82     104 ..      82     109 .. 0.64
   2 !    8.7   0.0    0.0011         2     100     145 ..     135     179 ..     113     198 .. 0.85
   3 !   42.7   0.0   3.8e-14   6.8e-11       1     170 [.     374     529 ..     374     533 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.5
                                       EEEEEE-STTS..CHHHHHHHHH CS
                               VWA   2 ivfvlDgSgsm..geenfekvke 22 
                                       +++++D S+s    +++ +kv +
  gi|313126713|ref|YP_004036983.1|  82 VTLLVDRSDSTtvAPQRADKVAS 104
                                       67999***998444444445555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
                                       STTSEEEEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEESSSHHH CS
                               VWA 100 RenakkviilltdGksndg.dpkeaaneakeqgikvfavGvgnadek 145
                                       Re  +  ++ll+dG+ ++g +++e+ + a++ + +v +v    ++++
  gi|313126713|ref|YP_004036983.1| 135 RE--NGSVLLLSDGRVTEGrSLSEVTELARSLNTTVSTVSPEPNTKE 179
                                       44..6689**********88******************998777665 PP

  == domain 3  score: 42.7 bits;  conditional E-value: 3.8e-14
                                       EEEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHC.HHHHHHHHHHTGSGGGG CS
                               VWA   1 DivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndys.skeellsalnnlkysgg 76 
                                       +iv+ +D+Sgs  ++ +   k    + +++l    +   vg+v f++ ++ ++  +    ++e+l++ +++l  + g
  gi|313126713|ref|YP_004036983.1| 374 NIVLSIDVSGSS-KGGMRVQKAVSLSALKQLG---DENEVGIVGFNHRTYSVAERQPLGpNREALADRIRRL--QAG 444
                                       79*********7.9******************...*************88888888877799*********8..777 PP

                                       SSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSSHTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHSS CS
                               VWA  77 gttntgkalkyaleklfkssagaRenakkviilltdGksndgdpkeaaneakeqgikvfavGvgnadekelLnkias 153
                                       g t+++ +l  a + ++    g        +il++dG++  ++    a++++++g +++a+G g++ ++++L++ia 
  gi|313126713|ref|YP_004036983.1| 445 GATDIAGGLRGAGK-MLGDDPG-------TVILISDGHDRVEESISYAKQLRSEGKRIIAIGAGKNPNEKNLRTIAR 513
                                       7777******7766.5555555.......7*********8889999*****************88888888****** PP

                                       SSCHHCEEEESSHHHHH CS
                               VWA 154 epgeghvftvtdfeele 170
                                        +g g +f++t+ + l+
  gi|313126713|ref|YP_004036983.1| 514 ASG-GSYFRATETNRLN 529
                                       ***.******9998765 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.45     8e+02       1      29 [.      82     107 ..      82     110 .. 0.86
   2 !   45.1   0.0   6.9e-15   1.2e-11       1     107 []     375     474 ..     375     474 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.45
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdave 29 
                                       + +++D S S +     p+r +++++a+e
  gi|313126713|ref|YP_004036983.1|  82 VTLLVDRSDSTTVA---PQRADKVASAIE 107
                                       579********998...899999999987 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 6.9e-15
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslp.gdrvglvtfsd...gpevlipltkdkakilnalrnleakg 73 
                                       +v+ +D+SgS  +g      +  +k+   + lk+l  ++ vg+v f++   ++    pl  +++++ +++r+l+a g
  gi|313126713|ref|YP_004036983.1| 375 IVLSIDVSGSSKGG------MRVQKAVSLSALKQLGdENEVGIVGFNHrtySVAERQPLGPNREALADRIRRLQA-G 444
                                       5888*********9......9999*999*******6699*********533356777999**************9.6 PP

                             VWA_2  74 ggtnlaaaLqlarkalkkrrkgekrvivlitDge 107
                                       g+t++a +L+ a k+l ++    + +++li+Dg+
  gi|313126713|ref|YP_004036983.1| 445 GATDIAGGLRGAGKMLGDD----PGTVILISDGH 474
                                       *****************88....5********96 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         5     9e+03      99     119 ..     139     157 ..     134     171 .. 0.62
   2 !   44.0   0.0   1.2e-14   2.1e-11       2     153 ..     374     519 ..     373     520 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5
                             VWA_3  99 svilltDgssaqgeervsdli 119
                                       sv+ll+Dg  ++g     +++
  gi|313126713|ref|YP_004036983.1| 139 SVLLLSDGRVTEGR--SLSEV 157
                                       79999999854433..33333 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 1.2e-14
                             VWA_3   2 evvivvDvsssmsaenklvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkikelelslgas 78 
                                       ++v+ +Dvs s++++   +k+    al+qL ++ ++ +++f  ++     + + +    ++++++ i  l++  ga+
  gi|313126713|ref|YP_004036983.1| 374 NIVLSIDVSGSSKGGMRVQKAVSLSALKQLGDENEVGIVGFNHRTY-SVAERQPLG-PNREALADRIRRLQA-GGAT 447
                                       79************98888888888******************966.445566666.789************.**** PP

                             VWA_3  79 nlegaLkealrqpakpgevrsvilltDgssaqgeervsdlisrar....ekirfhalglgsslsaamlqaLAeasgG 151
                                       + +g L+ a +       + +vil++Dg+     +rv+++is a+    e  r++a+g g+  ++++l+++A+asgG
  gi|313126713|ref|YP_004036983.1| 448 DIAGGLRGAGKM--LGDDPGTVILISDGH-----DRVEESISYAKqlrsEGKRIIAIGAGKNPNEKNLRTIARASGG 517
                                       *******99996..68899**********.....455555554433434669************************* PP

                             VWA_3 152 ty 153
                                       +y
  gi|313126713|ref|YP_004036983.1| 518 SY 519
                                       98 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0083        15     148     196 ..     134     181 ..      98     192 .. 0.77
   2 !   22.4   0.0   3.8e-08   6.8e-05      56     188 ..     371     499 ..     358     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0083
                          VWA_CoxE 148 LsrravvvlvsDglergdreellaelarlvrr.arrlvwlnplsdagtpg 196
                                       L +  +v+l+sDg  r    ++l+e+++l r+    + ++ p+++++ + 
  gi|313126713|ref|YP_004036983.1| 134 LRENGSVLLLSDG--RVTEGRSLSEVTELARSlNTTVSTVSPEPNTKERY 181
                                       456678*******..77788889999999998345677888887776655 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 3.8e-08
                          VWA_CoxE  56 kprelvllvDvSgSmaaysaiflallhAllqqlp...rtevfaFdtrlvdlTralrerDpaeaLarvsaavedlgGg 129
                                       +++++vl +DvSgS +   ++  a+  ++l+ql    ++ ++ F+ r+ ++ +        eaLa+   ++ + gG 
  gi|313126713|ref|YP_004036983.1| 371 QSTNIVLSIDVSGSSKGGMRVQKAVSLSALKQLGdenEVGIVGFNHRTYSVAERQPLGPNREALADRI-RRLQAGGA 446
                                       4559*************9***9999988888887789999************9988667778887766.45569*** PP

                          VWA_CoxE 130 TrigaalaeflelvtrpaLsrravvvlvsDglergdreellaelarlvrrarrlvwlnp 188
                                       T+i+ +l+ + ++          +v+l+sDg  ++ +ee+ +  ++l++ + r++ + +
  gi|313126713|ref|YP_004036983.1| 447 TDIAGGLRGAGKMLGDDP----GTVILISDG--HDRVEESISYAKQLRSEGKRIIAIGA 499
                                       **********99999444....678999***..88899999999999999999987755 PP

>> GATase1_like  Putative glutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   9.6e-05      0.17      98     141 ..     326     365 ..     309     370 .. 0.88
   2 ?    2.1   0.0      0.06   1.1e+02     179     216 ..     565     601 ..     538     607 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.6e-05
                      GATase1_like  98 kllkdyvaeGggllmvGGylsfqGidgkarykktpvedvlPvtc 141
                                         l++yv +G gll+vGG  sf+    + +y+ ++++ +lPvt 
  gi|313126713|ref|YP_004036983.1| 326 DALQEYVIDGNGLLVVGGPNSFE----NGNYESSSLASMLPVTT 365
                                       5689******************7....56899999******996 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.06
                      GATase1_like 179 yneveakdnaevlatvsedshPllvvGeygkGrtaaft 216
                                        n+v  + +a+ l   sed+ P +++ +yg Gr+a+ t
  gi|313126713|ref|YP_004036983.1| 565 TNDVSIRRGADFLVA-SEDGTPAVATWRYGLGRVATIT 601
                                       699999999999865.7889*************99866 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       2.8     5e+03      22      32 ..     110     120 ..      70     142 .. 0.57
   2 ?   15.6   3.0   7.7e-06     0.014       3      76 ..     189     261 ..     187     272 .. 0.82
   3 ?   -0.8   0.2         1   1.8e+03      45      62 ..     672     689 ..     630     701 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                                       TTS--EEEEEE CS
                           Big_3_5  22 gtptGtVtftd 32 
                                       g+p  t t+ +
  gi|313126713|ref|YP_004036983.1| 110 GVPVATTTIAS 120
                                       22223333333 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.7e-06
                                       -EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEEEE-TTS---S CS
                           Big_3_5   3 svtagqtvtltatVtaasggtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitAtYsGdanyaas 76 
                                       + ++g + t+ ++V ++ + ++  +Vt+ ++g ++ +++  +a+    +t+++ ++Gth itA+   +++++++
  gi|313126713|ref|YP_004036983.1| 189 KTSVGVESTFLVSVGGV-EINTPAKVTVAVDGEQVLETTIQNATDAREFTHTFSETGTHRITAEMESTDKFEQN 261
                                       56777888888888888.5556679****999888777777889*******************98888888765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1
                                       TTSEEEEEEE-SS-EEEE CS
                           Big_3_5  45 anGtAtltvsalaaGths 62 
                                       ++G   ++v+  +aG h+
  gi|313126713|ref|YP_004036983.1| 672 GDGAYRASVTPDEAGFHE 689
                                       256666666666666665 PP

>> CBM60  Ca-dependent carbohydrate-binding module xylan-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.9e+03       6      31 ..      71      95 ..      69     118 .. 0.75
   2 ?   12.2   0.3   0.00011      0.19       2      54 ..     198     249 ..     197     253 .. 0.72
   3 ?   -2.9   0.0       5.3   9.4e+03       8      56 ..     516     571 ..     513     582 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                             CBM60  6 Aagdqa.gdeppefrllvdGqkvgead 31
                                      A++++  g+  p+++llvd +  +++ 
  gi|313126713|ref|YP_004036983.1| 71 AQSTETlGE--PKVTLLVDRSDSTTVA 95
                                      677777788..********98888766 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00011
                             CBM60   2 ivVrAagdqagdeppefrllvdGqkvgead.vasteaktytftadltag.ahklq 54 
                                       + V++ g + ++ p+++++ vdG++v e++  ++t+a+++t  +++ ++ +h+++
  gi|313126713|ref|YP_004036983.1| 198 FLVSVGGVEINT-PAKVTVAVDGEQVLETTiQNATDAREFT--HTFSETgTHRIT 249
                                       667888888877.9*************98834555555555..555544488775 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.3
                             CBM60   8 gdqa..gdeppefrllvdGqkvg....eadvasteaktytftadltag.ahklqir 56 
                                       g ++   +e+ ++++l +G +       + v+  ++ t  + +++++g ++ ++ir
  gi|313126713|ref|YP_004036983.1| 516 GGSYfrATETNRLNILFGGAQSYegegLTMVDPNTFITSGVRLTANPGsTNDVSIR 571
                                       55555444556677777777776333211234444444455555556667777776 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   2.9      0.84   1.5e+03       7      24 ..      17      31 ..       1      42 [. 0.57
   2 ?   11.8   0.1   0.00013      0.24      52      77 .]      43      68 ..      33      68 .. 0.86
   3 ?   -1.6   0.1         2   3.5e+03      54      67 ..     747     760 ..     734     774 .. 0.52

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.84
                              BatA  7 PllLlallllplpiilly 24
                                      P   l+ll+lp+ +ill 
  gi|313126713|ref|YP_004036983.1| 17 P---LFLLALPIGVILLW 31
                                      4...56666666433332 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                              BatA 52 qrlkknllllLrllalallvlalArP 77
                                      +++++++ +++r+l ++llv+  A+P
  gi|313126713|ref|YP_004036983.1| 43 SNRSRQWFFVVRILTVVLLVVSAAGP 68
                                      5699********************99 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                              BatA  54 lkknllllLrllal 67 
                                       ++ +  l+L l+++
  gi|313126713|ref|YP_004036983.1| 747 KTDWTWLALVLALV 760
                                       33333333333332 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5    0.0015       2.7      38      62 ..     228     252 ..     200     259 .. 0.74
   2 ?    1.1   0.1       0.2   3.6e+02      14      42 ..     574     602 ..     564     605 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                                       EEEEETTEEEEEE-SSEEEEEEEEE CS
                               PKD  38 vqvlseptvthtYlspGeYeVtvta 62 
                                          +  +++tht++++G++ +t   
  gi|313126713|ref|YP_004036983.1| 228 QNATDAREFTHTFSETGTHRITAEM 252
                                       45667899************99765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
                                       EEEEEES.-SS-SEEEEE--SS--EEEEE CS
                               PKD  14 vaftaavpdganvtysWdfgdgsvvqvls 42 
                                       + f  a++dg+++  +W  g g v+++++
  gi|313126713|ref|YP_004036983.1| 574 ADFLVASEDGTPAVATWRYGLGRVATITT 602
                                       56677789*************99999875 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.4     0.003       5.4       2      70 .]     167     250 ..     167     250 .. 0.63
   2 ?   -1.6   0.0       2.7   4.8e+03      38      67 ..     663     689 ..     642     691 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.003
                                       EEEEEE--TT-...-EB.TS....EEEEEEEEE-S.S-E.....EEEEEEETTEE.....EEEE-SSSEEEEEE--. CS
                             Big_7   2 tvtitsPanga...tvs.gg....tvtisasAsdd.ggv.....skVefyvdgtl.g...lgtdtsapysltwttta 60 
                                       tv+ +sP++++   +vs +g    +v ++ +   + ggv     +kV++ vdg++     ++ ++++  ++t t + 
  gi|313126713|ref|YP_004036983.1| 167 TVSTVSPEPNTkerYVSvNGpsktSVGVESTFLVSvGGVeintpAKVTVAVDGEQvLettIQ-NATDAREFTHTFS- 241
                                       56777777777666666666444444444455555555566777**********86577543.3344445555554. PP

                                       ..SEEEEEEE CS
                             Big_7  61 ltagthtltV 70 
                                        ++gth +t+
  gi|313126713|ref|YP_004036983.1| 242 -ETGTHRITA 250
                                       .57*****97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                                       ETTEE.EEEE-SSSEEEEEE--...SEEEE CS
                             Big_7  38 vdgtlglgtdtsapysltwtttaltagtht 67 
                                       v g++ + +  ++ y++++t++  +ag h 
  gi|313126713|ref|YP_004036983.1| 663 VEGVS-FRQVGDGAYRASVTPD--EAGFHE 689
                                       55666.7777788999999998..677775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (785 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 4827.07
//
Query:       gi|313126714|ref|YP_004036984.1|  [L=193]
Description: hypothetical protein Hbor_19730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-08   32.9  26.3    0.00053   19.7   0.6    3.8  5  DivIC            Septum formation initiator
    5.5e-08   33.1  33.7    9.2e-07   29.1  23.5    2.1  2  Rootletin        Ciliary rootlet component, centrosome cohesi
    1.3e-07   31.7  33.2     0.0011   19.1  27.1    3.1  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    1.6e-06   27.2  30.4    0.00012   21.1  19.1    2.0  1  Spc7             Spc7 kinetochore protein
    2.3e-06   27.1  30.5    7.2e-05   22.2  18.8    2.2  2  GAS              Growth-arrest specific micro-tubule binding
    3.5e-06   27.1  32.0     0.0075   16.3  16.0    2.5  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    1.1e-05   24.7  19.4    2.3e-05   23.5  19.2    1.6  1  IFT57            Intra-flagellar transport protein 57
    2.2e-05   24.3  26.0    0.00032   20.5  26.1    2.3  1  DUF4201          Domain of unknown function (DUF4201)
    2.7e-05   24.5  24.3     0.0057   17.0   5.8    3.9  3  FlaC_arch        Flagella accessory protein C (FlaC)
    3.4e-05   23.9  19.9    0.00017   21.7  12.6    2.3  2  Laminin_II       Laminin Domain II
    3.7e-05   22.3  23.9    5.1e-05   21.8  23.9    1.2  1  MAD              Mitotic checkpoint protein
    3.9e-05   23.1  19.8    0.00064   19.1   9.0    2.0  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
    4.1e-05   23.6  16.0      0.029   14.4   6.2    2.8  3  DUF1664          Protein of unknown function (DUF1664)
    4.7e-05   23.7  37.3    0.00017   22.0  11.6    3.2  2  ZapB             Cell division protein ZapB
    5.1e-05   23.4  27.3      0.016   15.3  15.1    2.5  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
    5.8e-05   22.0  14.2    7.5e-05   21.6  14.2    1.1  1  AAA_13           AAA domain
    6.9e-05   22.6  10.3    9.2e-05   22.1  10.3    1.3  1  Exonuc_VII_L     Exonuclease VII, large subunit
    7.3e-05   21.6  19.5    9.9e-05   21.2  19.5    1.2  1  GOLGA2L5         Putative golgin subfamily A member 2-like pr
    7.3e-05   21.1  21.4      0.012   13.9   8.5    2.1  2  EzrA             Septation ring formation regulator, EzrA
    9.7e-05   22.3  37.4       0.02   14.9   6.3    3.0  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
     0.0001   22.0  11.0    0.00098   18.9   0.9    2.6  2  DASH_Duo1        DASH complex subunit Duo1
    0.00011   22.4  19.8    0.00011   22.4  17.5    2.0  2  FliJ             Flagellar FliJ protein
    0.00013   22.1  20.2     0.0086   16.3   5.3    3.1  3  KxDL             Uncharacterized conserved protein
    0.00015   21.0  26.5     0.0028   16.8  13.4    2.0  2  Atg14            Vacuolar sorting 38 and autophagy-related su
    0.00019   21.5  26.4      0.001   19.1   4.6    3.8  3  bZIP_1           bZIP transcription factor
    0.00021   20.7  26.8     0.0083   15.5  18.9    2.1  2  DUF2353          Uncharacterized coiled-coil protein (DUF2353
    0.00027   21.5  37.2     0.0019   18.7  24.9    2.1  2  APG6_N           Apg6 coiled-coil region
    0.00036   20.4  22.6      0.063   13.1  13.5    2.3  2  Phage_GP20       Phage minor structural protein GP20
    0.00039   20.7  35.8    0.00073   19.8  31.0    2.1  2  ATG16            Autophagy protein 16 (ATG16)
    0.00063   19.2  21.7      0.068   12.5  14.8    2.1  2  DUF4407          Domain of unknown function (DUF4407)
    0.00074   20.0  25.4     0.0011   19.5  25.4    1.3  1  Fez1             Fez1
     0.0008   18.8  25.6     0.0047   16.3  11.6    2.2  2  DUF3450          Protein of unknown function (DUF3450)
    0.00081   19.0  30.4     0.0066   16.0  30.8    2.0  2  MscS_porin       Mechanosensitive ion channel porin domain
    0.00084   17.3  26.5     0.0011   16.9  26.5    1.0  1  Myosin_tail_1    Myosin tail
    0.00097   19.3  28.8     0.0022   18.1  25.3    2.0  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
     0.0011   18.6  26.9      0.004   16.7  11.1    1.9  2  HMMR_N           Hyaluronan mediated motility receptor N-term
     0.0011   18.6  26.7      0.005   16.5  26.7    1.8  1  Filament         Intermediate filament protein
     0.0011   19.2  20.7       0.12   12.7  10.6    2.9  3  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0012   18.8  32.8     0.0033   17.3  32.8    1.7  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
     0.0013   18.9  12.1        3.1    8.1   0.1    4.2  3  WXG100           Proteins of 100 residues with WXG
     0.0015   18.7  31.3       0.14   12.2  15.8    2.2  2  ADIP             Afadin- and alpha -actinin-Binding
     0.0016   16.0  22.8     0.0022   15.6  22.8    1.2  1  DUF3584          Protein of unknown function (DUF3584)
     0.0017   18.0  25.6      0.097   12.2   7.2    3.1  3  PspA_IM30        PspA/IM30 family
     0.0021   18.2  35.8      0.015   15.5  34.5    2.3  2  Tropomyosin_1    Tropomyosin like
     0.0022   16.3  19.6     0.0022   16.3  19.6    2.0  2  HOOK             HOOK protein
     0.0024   16.1  31.1      0.064   11.4  18.6    2.0  2  FPP              Filament-like plant protein, long coiled-coi
     0.0026   17.4  21.9        1.2    8.8  21.9    3.1  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
     0.0026   17.4  12.6     0.0032   17.1  12.0    1.4  1  PEARLI-4         Arabidopsis phospholipase-like protein (PEAR
      0.003   17.9  31.1      0.078   13.3  19.5    2.3  2  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
     0.0034   17.3  24.5      0.015   15.2  24.5    1.7  1  CEP63            Centrosomal protein of 63 kDa
     0.0034   17.7  21.2       0.25   11.8   1.3    3.1  3  Snapin_Pallidin  Snapin/Pallidin
     0.0038   17.4  17.2     0.0038   17.4  12.1    2.1  2  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0051   16.0  28.1      0.074   12.2  27.4    2.1  2  CCDC144C         CCDC144C protein coiled-coil region
     0.0061   16.2  25.0      0.014   15.1  11.5    2.5  2  DUF2968          Protein of unknown function (DUF2968)
     0.0072   16.3  32.4      0.071   13.1   4.1    3.5  3  Prefoldin_2      Prefoldin subunit
     0.0079   16.4  32.5      0.036   14.3  23.3    2.2  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.008   16.0  16.7       0.26   11.1   6.5    2.6  2  She9_MDM33       She9 / Mdm33 family
     0.0082   16.0  21.1       0.03   14.1  12.3    2.0  2  DUF724           Protein of unknown function (DUF724)
     0.0089   15.9   6.9     0.0089   15.9   6.9    2.4  2  Sec34            Sec34-like family
     0.0098   16.1  23.3        0.2   11.9  11.9    2.4  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
      0.011   15.4  31.9       0.02   14.6  31.9    1.4  1  Lebercilin       Ciliary protein causing Leber congenital ama
      0.011   15.8  18.1       0.97    9.5   9.3    3.2  2  COG2             COG (conserved oligomeric Golgi) complex com
      0.012   16.3  23.3       0.29   11.8   9.3    3.0  2  YabA             Initiation control protein YabA
      0.012   15.0  24.8      0.014   14.8  11.1    2.1  2  Cluap1           Clusterin-associated protein-1
      0.012   16.2  17.3       0.03   14.9   0.6    3.3  3  GTP-bdg_M        GTP-binding GTPase Middle Region
      0.012   15.7  30.2       0.11   12.6   8.2    3.3  2  Cnn_1N           Centrosomin N-terminal motif 1
      0.013   14.3   7.7       0.19   10.4   2.9    2.0  2  Vps52            Vps52 / Sac2 family
      0.014   15.1  19.5       0.29   10.8   9.9    2.2  2  BCAS2            Breast carcinoma amplified sequence 2 (BCAS2
      0.014   15.3  27.8       0.19   11.7   8.6    2.4  2  YscO             Type III secretion protein YscO
      0.014   15.1   1.8      0.014   15.1   1.8    3.3  3  MctB             Copper transport outer membrane protein, Mct
      0.015   14.9  24.8      0.024   14.2  13.3    2.0  2  Leu_zip          Leucine zipper
      0.017   15.5  14.5       0.55   10.7   2.2    4.2  4  LPP              Lipoprotein leucine-zipper
      0.018   15.5  23.6       0.37   11.3   1.9    3.4  3  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
      0.018   14.3  32.3       0.56    9.4  32.3    2.0  1  HAP1_N           HAP1 N-terminal conserved region
      0.019   15.4  15.0       0.31   11.5   3.1    3.2  3  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.02   14.7   2.8       0.02   14.7   2.8    2.0  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      0.022   14.1  13.4      0.038   13.4  13.4    1.3  1  FAM76            FAM76 protein
      0.023   15.3   3.7      0.023   15.3   3.7    3.8  3  SlyX             SlyX
      0.023   13.9  17.9       0.35   10.1   7.2    2.1  2  TMPIT            TMPIT-like protein
      0.025   13.1   9.4      0.033   12.7   9.4    1.2  1  FUSC             Fusaric acid resistance protein family
      0.026   13.7  17.8      0.019   14.1   8.2    2.0  2  APG17            Autophagy protein Apg17
      0.027   13.1  19.7       0.36    9.4  11.2    2.0  2  FapA             Flagellar Assembly Protein A
      0.028   14.8  24.9        0.4   11.0  12.9    2.6  2  OmpH             Outer membrane protein (OmpH-like)
       0.03   14.2   3.6       0.03   14.2   3.6    3.2  2  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
       0.03   14.4  20.9      0.051   13.7   5.0    3.4  2  Med9             RNA polymerase II transcription mediator com
      0.034   14.1   2.6      0.043   13.7   2.6    1.2  1  GP41             Retroviral envelope protein
      0.036   14.5  22.9       0.17   12.4  15.5    2.2  2  Spectrin         Spectrin repeat
      0.038   14.2   3.6      0.038   14.2   3.6    3.7  2  JIP_LZII         JNK-interacting protein  leucine zipper II
      0.039   14.0  28.9       0.28   11.3   7.3    3.3  3  TolA_bind_tri    TolA binding protein trimerisation
      0.039   14.3  22.7        2.8    8.3  16.5    3.0  2  HrpB7            Bacterial type III secretion protein (HrpB7)
       0.04   12.8  25.6       0.53    9.1  25.7    2.0  1  DUF812           Protein of unknown function (DUF812)
       0.04   13.7  31.3       0.17   11.7  17.5    2.1  1  ERM              Ezrin/radixin/moesin family
      0.041   14.4  18.9       0.26   11.8  10.4    2.3  2  DUF16            Protein of unknown function DUF16
      0.041   14.5  29.5       0.11   13.2  17.7    2.7  3  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
      0.043   14.1  28.5        3.7    7.8  15.6    3.0  3  THOC7            Tho complex subunit 7
      0.045   13.8   0.7      0.045   13.8   0.7    4.7  4  bZIP_2           Basic region leucine zipper
      0.046   14.1  23.6      0.087   13.2   8.9    3.1  3  DUF641           Plant protein of unknown function (DUF641)
      0.052   13.8  20.6          1    9.6  11.3    3.1  2  DUF5082          Domain of unknown function (DUF5082)
      0.055   13.2  15.6       0.24   11.1  14.2    2.0  2  DUF745           Protein of unknown function (DUF745)
      0.056   11.7  18.8       0.23    9.6   6.2    2.1  2  COG6             Conserved oligomeric complex COG6
      0.063   12.1  20.8        0.8    8.5  20.8    2.1  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
      0.068   12.6  28.8        0.1   12.1  26.8    1.8  2  Golgin_A5        Golgin subfamily A member 5
      0.069   12.5  32.0      0.038   13.4  27.4    2.1  2  Tropomyosin      Tropomyosin
      0.073   13.2  16.7        3.1    7.9   6.5    2.7  2  RasGAP_C         RasGAP C-terminus
      0.073   12.8  19.8       0.23   11.2  10.9    2.1  2  zf-CpG_bind_C    CpG binding protein zinc finger C terminal d
      0.076   13.4  28.0       0.22   11.9   1.5    4.0  4  CLZ              C-terminal leucine zipper domain of cyclic n
      0.092   13.0  15.0        5.9    7.2   6.0    2.9  2  DUF948           Bacterial protein of unknown function (DUF94
      0.098   12.6  31.5       0.32   11.0   4.9    3.6  3  Sec2p            GDP/GTP exchange factor Sec2p
        0.1   12.8  28.3       0.79   10.0   7.3    3.5  3  XhlA             Haemolysin XhlA
       0.11   12.5  16.5        1.6    8.7   0.4    3.0  3  DUF4446          Protein of unknown function (DUF4446)
       0.12   11.5  33.8       0.53    9.4  21.9    2.0  2  DUF4686          Domain of unknown function (DUF4686)
       0.12   13.0  24.3        8.5    7.0  15.1    2.8  2  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.12   12.1   0.7        3.9    7.3   0.0    2.5  2  Oleosin          Oleosin
       0.13   12.3  20.1       0.27   11.4   4.4    2.7  3  Nup54            Nucleoporin complex subunit 54
       0.13   11.6  23.8         18    4.6  23.8    2.4  1  DUF4618          Domain of unknown function (DUF4618)
       0.14   12.2  18.9        1.4    8.9   9.1    2.8  3  DUF1043          Protein of unknown function (DUF1043)
       0.14   12.2  23.3       0.46   10.6   3.7    3.6  3  Swi5             Swi5
       0.15   12.4  29.9        0.2   12.0   6.1    4.9  4  TSC22            TSC-22/dip/bun family
       0.15   12.8  11.3        5.6    7.8   3.7    2.6  2  Occludin_ELL     Occludin homology domain
       0.15   13.2  23.9       0.14   13.3  14.4    3.0  2  SOGA             Protein SOGA
       0.15   11.7  22.4        2.5    7.8  13.1    2.1  2  SHE3             SWI5-dependent HO expression protein 3
       0.16    9.9  15.1        0.1   10.5   6.4    1.9  2  Prominin         Prominin
       0.16   11.6  22.7       0.51   10.0  15.7    2.3  2  YkyA             Putative cell-wall binding lipoprotein
       0.17   11.8   0.9       0.25   11.2   0.3    1.6  1  Ploopntkinase3   P-loop Nucleotide Kinase3
       0.17   11.7  16.9       0.67    9.7   6.7    2.4  2  Spc29            Spindle Pole Component 29
       0.17   12.1  33.6        1.1    9.5  23.9    2.4  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.17   12.5   9.4        0.1   13.2   1.3    2.5  3  DUF4665          Domain of unknown function (DUF4665)
       0.18   11.1  27.4      0.075   12.4  15.4    2.0  2  Rab5-bind        Rabaptin-like protein
       0.19   10.8  20.7       0.61    9.1  20.7    1.6  1  AIP3             Actin interacting protein 3
        0.2   11.8  26.3       0.12   12.4  15.5    2.1  2  BRE1             BRE1 E3 ubiquitin ligase
        0.2   10.1  25.8       0.69    8.4   6.7    2.0  2  Macoilin         Macoilin family
       0.22   11.6  35.5      0.054   13.5  10.6    3.6  3  DHR10            Designed helical repeat protein 10 domain
       0.23   11.7   4.0        1.4    9.1   0.8    2.3  2  PI_PP_I          Phosphoinositide phosphatase insertion domai
       0.24   11.5  14.8         14    5.7  14.8    2.4  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.24   11.0  26.7        2.4    7.7  13.3    2.1  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.25   11.0  26.7    1.1e+02    2.4  17.5    3.0  2  GrpE             GrpE
       0.26   11.7  10.5       0.19   12.1   0.9    3.4  4  Flagellin_C      Bacterial flagellin C-terminal helical regio
       0.29   10.7  16.9       0.36   10.3   8.6    2.4  2  Vps5             Vps5 C terminal like
        0.3   11.5  27.1       0.84   10.1  10.2    2.6  2  CENP-H           Centromere protein H (CENP-H)
        0.3   11.5  30.1       0.76   10.2  19.7    2.5  2  DUF4200          Domain of unknown function (DUF4200)
       0.32   10.3  24.9       0.93    8.7  12.2    2.1  2  DUF4763          Domain of unknown function (DUF4763)
       0.32   10.1  19.0        1.7    7.7   8.0    2.3  2  RmuC             RmuC family
       0.34   11.0  22.3       0.47   10.5   6.0    2.7  2  DivIVA           DivIVA protein
       0.35   10.5  23.1       0.74    9.4   2.0    2.8  2  DUF4795          Domain of unknown function (DUF4795)
       0.35   10.4  12.1        0.9    9.0   4.6    2.1  2  Allexi_40kDa     Allexivirus 40kDa protein
       0.37   11.5  25.1        1.4    9.7   3.2    2.5  2  DUF4472          Domain of unknown function (DUF4472)
       0.38   11.4  27.1          1   10.0  14.4    3.0  2  BST2             Bone marrow stromal antigen 2
       0.39   10.6  26.5         31    4.4   5.0    3.0  2  Wtap             WTAP/Mum2p family
        0.4   10.6  15.5       0.43   10.5   8.1    2.1  2  Cauli_AT         Aphid transmission protein
       0.45    9.9  34.2        2.5    7.4  29.8    2.5  2  DUF3552          Domain of unknown function (DUF3552)
       0.48   10.9  26.1        1.8    9.1   2.6    3.6  3  UPF0449          Uncharacterised protein family UPF0449
       0.51    9.4  17.6        1.6    7.8  13.5    2.7  2  FH2              Formin Homology 2 Domain
       0.55   11.0  13.0          2    9.2   5.1    2.9  2  FliD_N           Flagellar hook-associated protein 2 N-termin
       0.57   10.1  23.5        6.5    6.7   4.1    3.8  1  Prefoldin        Prefoldin subunit
       0.64    8.8  29.8        4.1    6.1  19.2    2.0  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
       0.65   10.3  31.7        2.1    8.6   5.9    3.3  3  Spc24            Spc24 subunit of Ndc80
       0.65   10.1  38.1         39    4.4  18.3    3.7  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
       0.69    9.0  27.3       0.49    9.5   9.9    2.1  2  Taxilin          Myosin-like coiled-coil protein
        0.7   10.6  27.0        2.9    8.6   2.7    3.3  3  KfrA_N           Plasmid replication region DNA-binding N-ter
       0.71    9.6   9.6          1    9.1   3.9    2.1  2  Hormone_1        Somatotropin hormone family
       0.76    9.9  16.8        1.4    9.1   6.2    2.8  3  DUF2730          Protein of unknown function (DUF2730)
        0.8   10.4  20.2       0.81   10.4  11.1    2.1  2  AATF-Che1        Apoptosis antagonizing transcription factor
       0.83    9.2  21.1        2.2    7.8   8.5    2.9  3  Fzo_mitofusin    fzo-like conserved region
       0.83    8.8  18.8        1.5    8.0   4.9    2.1  2  Tho2             Transcription factor/nuclear export subunit 
       0.83    9.8  11.9        4.8    7.4   2.3    3.0  2  MbeD_MobD        MbeD/MobD like
       0.86    9.7  24.9          6    7.0  22.7    2.6  2  End3             Actin cytoskeleton-regulatory complex protei
       0.86    9.8  16.8       0.25   11.5   8.4    2.2  2  GCN5L1           GCN5-like protein 1 (GCN5L1)
       0.87    9.6  14.2        3.1    7.8   0.1    2.7  2  Halogen_Hydrol   5-bromo-4-chloroindolyl phosphate hydrolysis
       0.89    9.8  23.7        2.2    8.6   4.5    4.2  4  HALZ             Homeobox associated leucine zipper
       0.94    9.9  30.3       0.13   12.6   9.1    3.3  2  Csm1_N           Csm1 N-terminal domain
        1.1    9.2  27.4         16    5.4  27.4    2.1  1  JAKMIP_CC3       JAKMIP CC3 domain
        1.3    9.8  16.5    2.1e+02    2.6  16.5    2.4  1  DUF2203          Uncharacterized conserved protein (DUF2203)
        1.3    8.7  17.1         10    5.7   1.8    3.0  2  LXG              LXG domain of WXG superfamily
        1.3    8.3  17.4      0.064   12.6   0.9    2.3  2  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
        1.4    7.5  19.9       0.52    9.0  11.7    2.0  2  DUF773           CDK5 regulatory subunit-associated protein 3
        1.4    9.4  26.4       0.26   11.8   4.0    3.5  3  bZIP_Maf         bZIP Maf transcription factor
        1.4    8.1  22.4       0.78    9.0   4.1    2.8  2  FmiP_Thoc5       Fms-interacting protein/Thoc5
        1.6    9.2  13.6       0.86   10.1   8.4    2.1  2  T3SSipB          Type III cell invasion protein SipB
        1.6    6.5  19.0       0.41    8.4  13.7    1.5  2  Nup88            Nuclear pore component
        1.6    9.7   7.4        1.5    9.7   2.7    2.9  1  DUF5339          Family of unknown function (DUF5339)
        1.6    8.9  22.9       0.32   11.2   5.3    3.4  3  DUF3847          Protein of unknown function (DUF3847)
        1.8    9.5  28.5         85    4.1   0.4    2.8  1  PRKG1_interact   cGMP-dependent protein kinase interacting do
        1.8    8.7  27.1        2.1    8.5   7.0    3.2  3  HR1              Hr1 repeat
        1.9    7.0   8.5       0.85    8.2   3.7    2.0  2  Tweety           Tweety
        2.1    8.0  12.4        2.3    7.9   0.5    3.1  3  RPW8             Arabidopsis broad-spectrum mildew resistance
        2.3    8.4  29.5       0.91    9.7  12.7    4.0  3  DMPK_coil        DMPK coiled coil domain like
        2.4    8.6  23.8        2.2    8.7   1.5    3.3  3  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
        2.5    8.5  15.5        6.6    7.1   4.7    3.6  3  kleA_kleC        Uncharacterized KorC regulated protein A
        2.6    7.9  11.6          4    7.2   4.3    2.3  2  USP8_interact    USP8 interacting
        2.7    8.5  27.6    1.8e+04  -12.1  27.6    3.7  0  DUF4140          N-terminal domain of unknown function (DUF41
        2.8    8.1  10.9         55    3.9  11.0    2.3  1  Cob_adeno_trans  Cobalamin adenosyltransferase
        2.9    8.4  21.9       0.34   11.4   1.5    3.6  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
        2.9    7.8  13.6         12    5.7   0.3    4.3  5  DASH_Dam1        DASH complex subunit Dam1
          3    7.6  15.5         19    5.0  15.1    2.1  2  SKA1             Spindle and kinetochore-associated protein 1
        3.3    7.6  29.5       0.35   10.8   7.3    3.1  1  Ax_dynein_light  Axonemal dynein light chain
        3.6    6.7  21.2        2.5    7.2   5.7    3.0  4  DLP_helical      Dynamin-like helical domain
        3.6    5.9  10.5       0.83    8.0   5.8    2.0  2  Hemagglutinin    Haemagglutinin
        3.8    7.9  21.3        1.9    8.9   2.1    3.0  3  Tup_N            Tup N-terminal
          4    7.7  30.2        2.9    8.1   3.9    3.2  3  Med21            Subunit 21 of Mediator complex
        4.1    7.8  11.4        2.2    8.7   2.6    2.9  2  HCMV_UL139       Human Cytomegalovirus UL139 protein
        4.1    5.2  17.7        8.8    4.1  17.7    1.5  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        4.2    6.9  14.0        7.5    6.1   4.0    2.6  2  DUF3053          Protein of unknown function (DUF3053)
        4.2    7.9  32.3        1.7    9.2   4.5    3.0  3  KELK             KELK-motif containing domain of MRCK Ser/Thr
        4.6    6.8  20.4        7.2    6.1  12.6    2.2  2  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
        5.1    6.6  26.5         24    4.4  16.7    2.7  2  DegS             Sensor protein DegS
        5.7    6.4  23.0        9.6    5.7  12.9    2.0  2  CENP-K           Centromere-associated protein K
        6.3    6.6  12.9    2.7e+02    1.3  12.9    2.3  1  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
        6.3    7.4  21.9       0.75   10.3   5.0    4.2  3  BMFP             Membrane fusogenic activity
        6.3    6.7  17.9       0.31   10.9   0.2    3.8  3  LapA_dom         Lipopolysaccharide assembly protein A domain
        7.3    6.1  11.7         10    5.7   2.4    2.6  3  AAA_27           AAA domain
        7.4    6.7  20.9         29    4.8  12.9    2.7  2  CREPT            Cell-cycle alteration and expression-elevate
        7.7    4.9  16.1          3    6.3   4.5    2.1  2  Herpes_UL6       Herpesvirus UL6 like
        7.9    5.2   8.9         11    4.8   8.9    1.2  1  ALMT             Aluminium activated malate transporter
        8.7    6.4  19.1        3.7    7.6   9.6    2.4  2  DUF4337          Domain of unknown function (DUF4337)


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.6   6.3e-06   0.00053       2      53 ..      10      61 ..      10      75 .. 0.89
   2 ?    5.0   0.3      0.25        21      22      49 ..      51      78 ..      50      89 .. 0.66
   3 ?    0.5   0.2         6     5e+02      23      37 ..      66      80 ..      60      98 .. 0.52
   4 ?    3.5   4.5       0.7        58      22      59 ..      97     134 ..      88     135 .. 0.80
   5 !   19.3   8.0   8.4e-06    0.0007      18      56 ..     131     169 ..     127     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.3e-06
                                      XXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                             DivIC  2 lllfllllifgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksd 53
                                      l+l+++++ ++++++ a +  ++   +l+ ++++l+++n++L ae++  + +
  gi|313126714|ref|YP_004036984.1| 10 LALVAVVALLLTGTVGATMMYQSSASDLETQNDQLRERNKNLRAELESARTE 61
                                      578999999*************************************998755 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.25
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                             DivIC 22 lkqeiaalqaelaklkaeneeLeaevkd 49
                                      l++e++    el+ l+++ ++L++ +++
  gi|313126714|ref|YP_004036984.1| 51 LRAELESARTELKVLRERVNDLNQSLQQ 78
                                      5666666666777777777666666555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 6
                                      HHHHHHHHHHHHHHH CS
                             DivIC 23 kqeiaalqaelaklk 37
                                      ++ +++l++ l++ +
  gi|313126714|ref|YP_004036984.1| 66 RERVNDLNQSLQQTQ 80
                                      333333443333333 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                             DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                       l+   a+l+++  +l +++e+Le+  ++L   ++ iee
  gi|313126714|ref|YP_004036984.1|  97 LNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEE 134
                                       56667899999999999999999999999666666666 PP

  == domain 5  score: 19.3 bits;  conditional E-value: 8.4e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksdedy 56 
                                       ++ +l+++ ++l++++a+lk en+eL +ev+dL++d+d 
  gi|313126714|ref|YP_004036984.1| 131 KIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDD 169
                                       67899*****************************99885 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.1     0.011      0.89      92     141 ..      29      78 ..      23      83 .. 0.69
   2 !   29.1  23.5   1.1e-08   9.2e-07      29     137 ..      66     186 ..      63     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.011
                         Rootletin  92 lLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeeeafne 141
                                       +++      +++n++L+e +++l++++e++r+el+   ++ ++ ++++++
  gi|313126714|ref|YP_004036984.1|  29 MYQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQ 78 
                                       66777777777788888888888888888888877666666655555544 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 1.1e-08
                         Rootletin  29 kkrcseleqrlle.......ktselektkltlll............ssareleeeesadleealakLeeErqrsekl 86 
                                       ++r+++l+q l++         +ele       +            +++++  ee+ ++le+++ +L+e r + e+l
  gi|313126714|ref|YP_004036984.1|  66 RERVNDLNQSLQQtqgdvghVAAELE-------StekllnhtqaelERTETSLEEKREQLESVRDNLDEARSKIEEL 135
                                       56666666666663333333223333.......122222333455556677777888899***************** PP

                         Rootletin  87 aqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeee 137
                                       ++ n++L eq+ e +++n++L+e+++ l++d + l+ +l++  ++w ee +
  gi|313126714|ref|YP_004036984.1| 136 EKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDDWSEEAN 186
                                       ***********************************************9975 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  27.1   1.3e-05    0.0011      15     126 ..      32     146 ..      30     149 .. 0.80
   2 !   13.3   1.1   0.00078     0.065      58      97 ..     145     184 ..     144     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-05
                        TPR_MLP1_2  15 eekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleese 91 
                                       ++++++e++  +l+e  ++ +++++ a    +      ++  ++lq++  ++ ++ ae+++ ++ ++ ++aele+ e
  gi|313126714|ref|YP_004036984.1|  32 SSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTE 108
                                       55666777777777777777777777777666666677888889999999999999999999999999999999999 PP

                        TPR_MLP1_2  92 esweeqkeele...kelselekriedlneqNklLhdQl 126
                                        s+ee++e+le   ++l+e++++ie+l+++Nk+L +Q 
  gi|313126714|ref|YP_004036984.1| 109 TSLEEKREQLEsvrDNLDEARSKIEELEKKNKTLEEQV 146
                                       999999999983335899*****************997 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00078
                        TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaeleeseesweeq 97 
                                       ++++l++e +el +e+ +l++++++++ +l e    w+e+
  gi|313126714|ref|YP_004036984.1| 145 QVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDDWSEE 184
                                       6788999999999999999999999999999999888887 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1  19.1   1.4e-06   0.00012     163     252 ..      88     176 ..      85     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.4e-06
                              Spc7 163 eeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieel 239
                                       +el++  + l++ +aele++ ++l+e++e+les+ +++L e+r++++el+++ + +++++ael+++ +el+e++++l
  gi|313126714|ref|YP_004036984.1|  88 AELESTEKLLNHTQAELERTETSLEEKREQLESV-RDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDL 163
                                       6778888889999999999999999999998886.7899*************************************9 PP

                              Spc7 240 keqkseleeeiae 252
                                       ++ +++l+ +++e
  gi|313126714|ref|YP_004036984.1| 164 RDDRDDLQRDLRE 176
                                       9999999998875 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2  16.8    0.0043      0.36      36     126 ..      35     129 ..      27     131 .. 0.77
   2 !   22.2  18.8   8.6e-07   7.2e-05      37     138 ..      85     183 ..      77     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0043
                               GAS  36 eelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdk....qslknlkarlkelekelkdlkweh 108
                                        +l++++++ + + +++ +e ++ + +Lk ++e v+ L++ l++ + d     ++l+++++ l++++ el++++ + 
  gi|313126714|ref|YP_004036984.1|  35 SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVghvaAELESTEKLLNHTQAELERTETSL 111
                                       56778888888888888888888888888888888888888888887753322678888888888888888888888 PP

                               GAS 109 evleqrfekvekerdely 126
                                       e +++++e+v +  de +
  gi|313126714|ref|YP_004036984.1| 112 EEKREQLESVRDNLDEAR 129
                                       888888888888877766 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 8.6e-07
                               GAS  37 elkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleq 113
                                       +  ++ e++ek+l+++++e +r +  L++ +e++e  r +l + ++   ++++l++++k+le+++ +lk e++ l++
  gi|313126714|ref|YP_004036984.1|  85 HVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARS---KIEELEKKNKTLEEQVAELKTENKELSE 158
                                       556778999******************9999999999988877655...8889999********************* PP

                               GAS 114 rfekvekerdelykkfeaaiqevqq 138
                                       +++ + ++rd+l++  +++ ++ ++
  gi|313126714|ref|YP_004036984.1| 159 EVDDLRDDRDDLQRDLREVCDDWSE 183
                                       ***************9999888766 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  16.0     9e-05    0.0075      55     138 ..      42     125 ..      28     127 .. 0.72
   2 !   12.4  17.9    0.0015      0.12      16      91 ..     105     176 ..     101     183 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9e-05
                    CENP-F_leu_zip  55 etlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeL 131
                                        +l+e  ++l++el+  +++L+ lr+  ++L+++lq+ q  v    +  +s+e+ll++  +e  + + + +++ e+L
  gi|313126714|ref|YP_004036984.1|  42 DQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQL 118
                                       34666666777777777777777778888888888888888888888888888888888888888888888888888 PP

                    CENP-F_leu_zip 132 qtqlkel 138
                                       ++   +l
  gi|313126714|ref|YP_004036984.1| 119 ESVRDNL 125
                                       7766555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0015
                    CENP-F_leu_zip  16 erkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqk 91 
                                       er + sL++k e+Le     +  n++++    E+  ++ +tl+e++ el++e +el+ ++++lr ++++L+++l++
  gi|313126714|ref|YP_004036984.1| 105 ERTETSLEEKREQLE----SVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       444444554444443....455566666666666666667777777777777777777777777777777777765 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5  19.2   2.7e-07   2.3e-05     214     330 ..      43     162 ..      34     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.7e-07
                             IFT57 214 tikadakdWrahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylns...qleellqeyreaqeels 287
                                       ++++++k  ra+le+ ++  k ++e +++++++l++ + d+  +  ++es Ek ln    +le + + ++e++e+l+
  gi|313126714|ref|YP_004036984.1|  43 QLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHtqaELERTETSLEEKREQLE 119
                                       66899999***********************************************8522256666777999999999 PP

                             IFT57 288 evkekykqlsegvseltrelaeiseelekvkqemeergssmtD 330
                                       +v+++++++ ++++el+++ ++++e++ ++k+e +e ++++ D
  gi|313126714|ref|YP_004036984.1| 120 SVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDD 162
                                       9999999999999999999999999999999999988887766 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5  26.1   3.8e-06   0.00032      20     166 ..      32     172 ..      27     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.8e-06
                           DUF4201  20 hqlakiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselsel 96 
                                       ++ ++++++ ++++e + +L++ + e++++e + l++++++ n+ L++ +  ++    +l+ + + l+  ++el++ 
  gi|313126714|ref|YP_004036984.1|  32 SSASDLETQNDQLRERNKNLRA-ELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERT 107
                                       5667788999999999999986.79**************************************************** PP

                           DUF4201  97 kkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrr 166
                                       +++l+ek e+l+++r++l +++ + + l+k+n+ l++q ++l+ +      ++  e+v+++r+  + L+r
  gi|313126714|ref|YP_004036984.1| 108 ETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTE-----NKELSEEVDDLRDDRDDLQR 172
                                       ***************************************997654.....33334444444444444444 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   1.6    0.0084       0.7       7      38 ..      46      77 ..      29      83 .. 0.88
   2 ?    7.5   2.1     0.065       5.5       6      31 ..     101     126 ..      83     129 .. 0.71
   3 !   17.0   5.8   6.8e-05    0.0057       1      36 [.     131     166 ..     131     172 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0084
                         FlaC_arch  7 nklsklsteletvkkeneelsksveelkenVk 38
                                      ++ ++l  ele++++e++ l++ v++l+++ +
  gi|313126714|ref|YP_004036984.1| 46 ERNKNLRAELESARTELKVLRERVNDLNQSLQ 77
                                      55578899********************9986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.065
                         FlaC_arch   6 Enklsklsteletvkkeneelsksve 31 
                                       + +l++++t+le  ++++e+++++++
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLD 126
                                       45677777777777777777777666 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 6.8e-05
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelken 36 
                                       +i+elE+k + l+ +++ +k+en+els++v++l ++
  gi|313126714|ref|YP_004036984.1| 131 KIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDD 166
                                       8*******************************9876 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.2     0.052       4.4      11      62 ..      33      84 ..      26      91 .. 0.71
   2 !   21.7  12.6     2e-06   0.00017       7      96 ..      78     164 ..      73     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.052
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvk 62
                                      +a+  + q  +l ++ +n++++l++++++++   e v+d+n+ +++ +  v 
  gi|313126714|ref|YP_004036984.1| 33 SASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVG 84
                                      5666667777777777788888888888888888888888877777766665 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       + +  + +v + l+  ++ l++t+++l++ ++s+ee  e++++    +++Ar+++ +Lek+   L++++ elk+ ++
  gi|313126714|ref|YP_004036984.1|  78 QTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENK 154
                                       555667789999999999999999**********************************************9999999 PP

                                       H...HHHHHHHHH CS
                        Laminin_II  84 assslsdniseik 96 
                                       +   ls++++ ++
  gi|313126714|ref|YP_004036984.1| 155 E---LSEEVDDLR 164
                                       9...*****9988 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8  23.9   6.1e-07   5.1e-05      55     178 ..      35     159 ..      28     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.1e-07
                               MAD  55 krikllekreeekeealreqiElarlkkknl.ealnkkekekesklaearevisalk...nelaelkrqiekqelel 127
                                        +++  +++  e++++lr+++E ar+ +k l e +n +++  ++++ ++  v  +l+   + l+  + ++e++e  l
  gi|313126714|ref|YP_004036984.1|  35 SDLETQNDQLRERNKNLRAELESARTELKVLrERVNDLNQSLQQTQGDVGHVAAELEsteKLLNHTQAELERTETSL 111
                                       56777788889999999999999999888753678888888888888888888776511155888999999999999 PP

                               MAD 128 sekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefe 178
                                       +ek+++le+++ +ld+ + k++ele+++++le++  el+++++ + e   e
  gi|313126714|ref|YP_004036984.1| 112 EEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSE---E 159
                                       99999999999999999999999999999999999999999965544...3 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   9.0   7.6e-06   0.00064       7     102 ..      13     110 ..       8     117 .. 0.72
   2 ?    8.6   5.9     0.012         1      36      94 ..     114     172 ..     106     185 .. 0.43

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.6e-06
                              HemX   7 lallallvalavgaglyylgqqqvqeltaev....aelqqqlaaleqqlaqveaekeqkqeleerlqqlaekleale 79 
                                       +a++all+   vga+++y +     +l++++    ++ ++  a+le++ ++++ ++e+ ++l ++lqq+++++ + +
  gi|313126714|ref|YP_004036984.1|  13 VAVVALLLTGTVGATMMYQSSAS--DLETQNdqlrERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVA 87 
                                       67888888888888855544443..344444112344444445666777779999999999999*****99999999 PP

                              HemX  80 keleqlqkqleelqqqlskvsga 102
                                       +ele+++k l+++q++l++ + +
  gi|313126714|ref|YP_004036984.1|  88 AELESTEKLLNHTQAELERTETS 110
                                       99999999999999999998765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.012
                              HemX  36 evaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqq 94 
                                       + ++l++   +l+++ +++e++++++++lee++++l+++ ++l++e+++l  + + lq+
  gi|313126714|ref|YP_004036984.1| 114 KREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       22333333333333333344444444444444444444444444444444444444444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   2.6   0.00042     0.035      53     119 ..      33      99 ..      21     103 .. 0.86
   2 !   14.4   6.2   0.00034     0.029      61     121 ..      97     157 ..      85     159 .. 0.80
   3 !   12.0   5.4    0.0019      0.16      48     106 ..     116     177 ..     107     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00042
                           DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                         ++l+++ ++L +r +++ ++l++     k ++e v+++++ l++++ dv +v +  e+ e+ l++
  gi|313126714|ref|YP_004036984.1|  33 SASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNH 99 
                                       447899999********************************************99999888877665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00034
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                        +h +++++r +++l+e  e  ++++++++e+r++++e++++ ++++e v +l+++ ++++
  gi|313126714|ref|YP_004036984.1|  97 LNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELS 157
                                       2455678899999**************************************9998877765 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.0019
                           DUF1664  48 kqleqvseslaatk...rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                       +qle+v ++l +++   ++L+++ +++++++ e k   ke++eev+++r+d +++++d+++v
  gi|313126714|ref|YP_004036984.1| 116 EQLESVRDNLDEARskiEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       67777877777776222456777777777777778888888888888888888888888776 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   7.7    0.0068      0.57      28      65 ..      35      72 ..      31      78 .. 0.86
   2 !   22.0  11.6     2e-06   0.00017      11      65 ..     123     177 ..     116     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0068
                              ZapB 28 eeLkeeneelkeenreleeeneqlkeereawqerlkkL 65
                                      ++L+ +n +l e+n++l++e+e  ++e + ++er++ L
  gi|313126714|ref|YP_004036984.1| 35 SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDL 72
                                      679999************************99999987 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2e-06
                              ZapB  11 skiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                          ++a  +i++L ++++ L+e+++elk en+el+ee++ l+++r  +q+ l+ +
  gi|313126714|ref|YP_004036984.1| 123 DNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       556667779*****************************************99976 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  11.6     0.044       3.7      31     106 ..      30     106 ..      19     113 .. 0.77
   2 ?    5.6   8.5      0.19        16      37      82 ..      92     137 ..      74     138 .. 0.48
   3 !   15.3  15.1   0.00019     0.016       6      95 ..      94     185 ..      89     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.044
                             Mod_r  31 lkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell.qkfspdallarLqtavae 106
                                       ++++ ++l+++n +l e+n +l+ ele  r el+  +e ++ l++++++ + +  ++  +  s + ll+  q+++++
  gi|313126714|ref|YP_004036984.1|  30 YQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAaELESTEKLLNHTQAELER 106
                                       67788999999999999999999999999999999999999999999999988866662333444555555555555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.19
                             Mod_r  37 ellaeneslaeknlsl.epeleelrselqekleelkelekefeekeq 82 
                                       + ++   ++ ++ l++ e++lee+r++l++ +++l+e++++ ee+e+
  gi|313126714|ref|YP_004036984.1|  92 STEKLLNHT-QAELERtETSLEEKREQLESVRDNLDEARSKIEELEK 137
                                       222222222.2223333456666666666666666666666665555 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 0.00019
                             Mod_r   6 eeLqellede.eklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeek 80 
                                       e+L    + e e  e  +++  +++++++++++e++ ++e+l +kn  le+++ el+ e +e  ee++ l++  +++
  gi|313126714|ref|YP_004036984.1|  94 EKLLNHTQAElERTETSLEEKrEQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDL 170
                                       5555555555455555566565889**************************************************** PP

                             Mod_r  81 eqeldellqkfspda 95 
                                       +++l e+++++s++a
  gi|313126714|ref|YP_004036984.1| 171 QRDLREVCDDWSEEA 185
                                       **********99987 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6  14.2     9e-07   7.5e-05     313     455 ..      31     176 ..      19     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9e-07
                            AAA_13 313 asensafeedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkakiesikklvaeineliakhNekvanl 388
                                       +s  s  e ++++l+++ ++l+++L++++ +l+  r+++   + +l+++++++ ++  ++++ ++l +   +  ++ 
  gi|313126714|ref|YP_004036984.1|  31 QSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDlNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERT 107
                                       55566677888888888889999988887766655555555444789999999999999999999999999999999 PP

                            AAA_13 389 eeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                       e++ ee +++le  +  + e++s+++e++kk k le+++ +l++e ke ++e+  l+++  +L++ lr+
  gi|313126714|ref|YP_004036984.1| 108 ETSLEEKREQLESVRdnLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       999999999998654337999999999999999999999999999999999999999999999999886 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1  10.3   1.1e-06   9.2e-05     142     260 ..      34     153 ..       4     178 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-06
                      Exonuc_VII_L 142 kaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelk 218
                                        ++le q ++l++r +k+++  le+++++l+ l++r+++ ++ l++ +  + +++++le+ ++k l++ +++le+++
  gi|313126714|ref|YP_004036984.1|  34 ASDLETQNDQLRER-NKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELES-TEKLLNHTQAELERTE 108
                                       33444443433333.445555666667777777777776667777777777776666666.6666666666666666 PP

                      Exonuc_VII_L 219 erl.k..ekleekkerlkklkerlelleekkerleeleekleals 260
                                       ++l +  e+le+ +++l++ ++++e+le+k+++lee+ ++l++ +
  gi|313126714|ref|YP_004036984.1| 109 TSLeEkrEQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTEN 153
                                       666335555555555555555555566666666666655555433 PP

>> GOLGA2L5  Putative golgin subfamily A member 2-like protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2  19.5   1.2e-06   9.9e-05     207     329 ..      41     163 ..      29     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXX CS
                          GOLGA2L5 207 lGqlqeelgelketlelksqeaqslqeqrdqylahlqqYvaayqqlasekeelhkqlllqtql.mdrlqheevqgkv 282
                                         ql+e+ ++l+ +le   +e + l e+ +++   lqq      ++a+e e+ +k ll +tq  ++r +    + + 
  gi|313126714|ref|YP_004036984.1|  41 NDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEK-LLNHTQAeLERTETSLEEKRE 116
                                       569************************************************9887.566666439999999999*** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXX CS
                          GOLGA2L5 283 alelarkeLqeaqerLealakenqqLkaqlsllaapse..Gdgveseek 329
                                       +le  r +L+ea+ ++e+l k+n+ L+ q+ +l+++++   ++v+  + 
  gi|313126714|ref|YP_004036984.1| 117 QLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKelSEEVD--DL 163
                                       *********************************988874433333..33 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   7.1   0.00037     0.031      98     174 ..      43     119 ..      34     120 .. 0.90
   2 !   13.9   8.5   0.00014     0.012      95     154 ..     117     176 ..     114     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00037
                                       HTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH- CS
                              EzrA  98 kakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqlenie 174
                                       +++++ ++l++el+++++++k ++e +++l +s ++ +  + ++  + ++++k l++++++++ ++++le++ e++e
  gi|313126714|ref|YP_004036984.1|  43 QLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLE 119
                                       56778889999999999999999999999999999999999999999999999999999999999999999988887 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00014
                                       HHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--T CS
                              EzrA  95 kfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkklla 154
                                       ++ +++ +l+e++++++e+e+k k++ e+++el++ +++ +ee+++l+++ ++l+++l++
  gi|313126714|ref|YP_004036984.1| 117 QLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       5678999**********************************************9999987 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   6.3   0.00023      0.02      23      67 ..      36      80 ..      32      85 .. 0.93
   2 ?    3.3   5.6      0.96        81      24      60 ..      90     119 ..      82     128 .. 0.47
   3 !   13.6  19.5    0.0006      0.05       4      69 ..     101     166 ..      98     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 0.00023
                        TMF_DNA_bd 23 kLskkelklnntikkLrkknkelekeikelkkkleklekeleele 67
                                      +L+ ++++l++  k+Lr++++ + +e+k l +++++l+++l++ +
  gi|313126714|ref|YP_004036984.1| 36 DLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQ 80
                                      6999************************************99865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.96
                        TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkklekle 60 
                                       L+++e  ln t+ +L  ++  le++ ++l       e
  gi|313126714|ref|YP_004036984.1|  90 LESTEKLLNHTQAELERTETSLEEKREQL-------E 119
                                       33334444444444444444444333333.......3 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.0006
                        TMF_DNA_bd   4 ekklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                       ++ l+  +  +++++e +e  +++ ++ + +i +L kknk le++++elk ++++l++e++ l++ 
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDD 166
                                       56666667778999*************************************************986 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.9   1.2e-05   0.00098       2      46 ..      55      99 ..      50     109 .. 0.90
   2 ?    7.8   2.9     0.034       2.8       1      39 [.     110     148 ..     110     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-05
                         DASH_Duo1  2 LekEleqLrkinevienviesLkkaksniervketvestntLLdk 46
                                      Le   ++L+ ++e ++++++sL+++++++ +v+  +est++LL+ 
  gi|313126714|ref|YP_004036984.1| 55 LESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNH 99
                                      6666778999*********************************95 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.034
                         DASH_Duo1   1 aLekEleqLrkinevienviesLkkaksniervketves 39 
                                       +Le+  eqL+++++ ++  ++++++ ++++++++e+v +
  gi|313126714|ref|YP_004036984.1| 110 SLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAE 148
                                       69999******************************9986 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4  17.5   1.4e-06   0.00011       2     115 ..      43     156 ..      42     163 .. 0.92
   2 ?    4.6   0.5      0.42        35       3      36 ..     142     175 ..     140     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-06
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqve 76 
                                       + +++ ++ ++el++a+ +l  l++  +++ ++l++++   g  aael  +++ +++ + ++++++ +l+ +++q+e
  gi|313126714|ref|YP_004036984.1|  43 QLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQgDvGHVAAELESTEKLLNHTQAELERTETSLEEKREQLE 119
                                       666777889999******************99999999989************************************ PP

                              FliJ  77 kareewqearqerkklekLkerekkeeqkeenrrEqkql 115
                                         r+++ ear + + lek  +++  eeq +e + E+k+l
  gi|313126714|ref|YP_004036984.1| 120 SVRDNLDEARSKIEELEK--KNKTLEEQVAELKTENKEL 156
                                       ************999996..8889999999999999986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.42
                              FliJ   3 aareLaeaqrelqqaeekleeleqyrqeyqkqls 36 
                                        ++++ae ++e ++  e+++ l++ r+++q  l+
  gi|313126714|ref|YP_004036984.1| 142 LEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       5788999999999999999999999999987766 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   3.2    0.0052      0.44      23      80 ..      35      92 ..      22      94 .. 0.86
   2 !   16.3   5.3    0.0001    0.0086      10      78 ..      71     139 ..      70     141 .. 0.84
   3 ?    9.5   1.9     0.014       1.1      24      66 ..     134     176 ..     133     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0052
                              KxDL 23 grlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80
                                        l+ +n +L e n+ + ++l+++r+++k   + ++++++ L++++  + +  a+l++
  gi|313126714|ref|YP_004036984.1| 35 SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELES 92
                                      4699999************************************999999988888876 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 0.0001
                              KxDL  10 dldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                       dl+++l++ +  +g+  ++ +  ++l + +q++l+++++ ++++ + l +v+++L+  ++ki+ l++k 
  gi|313126714|ref|YP_004036984.1|  71 DLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKN 139
                                       566666666666677777777778889999************************************996 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.014
                              KxDL  24 rlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLes 66 
                                       +l+kkn++L+e+ a+++++ ++l++++ +   +  ++++dL+ 
  gi|313126714|ref|YP_004036984.1| 134 ELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       699**************************99999999999986 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   6.2     0.004      0.33      84     129 ..      35      80 ..      26      96 .. 0.53
   2 !   16.8  13.4   3.3e-05    0.0028      37     121 ..      92     177 ..      82     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.004
                             Atg14  84 qelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerr 129
                                       + l+++ +ql++++++ +++l++ + +lk  r++ + l+++l++ +
  gi|313126714|ref|YP_004036984.1|  35 SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQ 80 
                                       4445555555555555555555555555555555555555555543 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.3e-05
                             Atg14  37 ekeslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk 112
                                         e l ++ +++le++e + e++++++++ +++l+e +s+i++l++++++l++++ +lk e++e ++++  l+d+  
  gi|313126714|ref|YP_004036984.1|  92 STEKLLNHTQAELERTEtSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRD 168
                                       4566667777777777768889999************************************************9988 PP

                             Atg14 113 kRrsdlesl 121
                                       + ++dl+ +
  gi|313126714|ref|YP_004036984.1| 169 DLQRDLREV 177
                                       777777655 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   2.3    0.0039      0.33      28      60 ..      34      66 ..      30      70 .. 0.62
   2 ?    0.4   6.7       8.3     7e+02      28      62 ..     101     138 ..      87     141 .. 0.66
   3 !   19.1   4.6   1.2e-05     0.001      27      61 ..     138     172 ..     134     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0039
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 28 ieeLerrvkaLekeNksLkseleelkkevekLk 60
                                       + Le++ ++L + Nk+L+ ele+ + e + L+
  gi|313126714|ref|YP_004036984.1| 34 ASDLETQNDQLRERNKNLRAELESARTELKVLR 66
                                      556666667777777777777766666666555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 8.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHH CS
                            bZIP_1  28 ieeLerrvkaLekeNksLkseleelkk...evekLksk 62 
                                       ++eLer    Le++ ++L s  ++l +   ++e+L++k
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLDEarsKIEELEKK 138
                                       67788888888887777766555554400045555555 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                       + + Le++v++L++eNk+L++e++ l+++++ L+ 
  gi|313126714|ref|YP_004036984.1| 138 KNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       5689*************************999876 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  18.9   9.9e-05    0.0083      48     162 ..      36     152 ..      24     152 .. 0.72
   2 !   10.5  16.1    0.0033      0.28      27      99 ..     106     175 ..      89     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.9e-05
                           DUF2353  48 eekakaadlkeekekekklsqlleesreenkalkleveeLrqklkeaqgDiklLReqlarq.rlglkdedlletrhs 123
                                       + +++++   + +e++k+l + le +r e k l++ v++L q l+  qgD+  + ++l+++ +l  +++  le +++
  gi|313126714|ref|YP_004036984.1|  36 DLETQND---QLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTeKLLNHTQAELERTET 109
                                       2233332...33899*************************************9995554430333334444555555 PP

                           DUF2353 124 s.aeereel..v.kqlEklkekiqqlerdlkavldekeelvte 162
                                       s +e+re+l  v  +l ++++ki++le++ k++ ++  el+te
  gi|313126714|ref|YP_004036984.1| 110 SlEEKREQLesVrDNLDEARSKIEELEKKNKTLEEQVAELKTE 152
                                       5355565553332589****************99999999987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0033
                           DUF2353  27 qyklmaeqLqerlsalkkqleeekakaadlkeekekekklsqlleesreenkalkleveeLrqklkeaqgDik 99 
                                       +  +    L+e+ ++l++   + ++ +++++e ++k+k+l + ++e + enk+l++ev++Lr+  +++q D +
  gi|313126714|ref|YP_004036984.1| 106 RTETS---LEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       33333...333444443333344444444444499***********************************975 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  11.7      0.16        13      63     132 ..      34     103 ..      26     106 .. 0.53
   2 !   18.7  24.9   2.3e-05    0.0019      17     118 ..      82     180 ..      76     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.16
                            APG6_N  63 eeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyehaqnq 132
                                        ++l+++ ++l + +++l+ael++++ el+ l e  +   ++ ++ q ++     el+s e  ++h+q++
  gi|313126714|ref|YP_004036984.1|  34 ASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAE 103
                                       4445555555555555555555555555555555555555555555555555555555555555555544 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.3e-05
                            APG6_N  17 qleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelea 93 
                                        +  + +e ++ e+ l++ ++e + +   +++lee +e+le +++  +e+ ++++elek+++ le+++a+l+ e ++
  gi|313126714|ref|YP_004036984.1|  82 DVGHVAAELESTEKLLNHTQAELERT---ETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKE 155
                                       55566777778888888888885554...58********************************************** PP

                            APG6_N  94 leeeeerfwreynelqlelleleee 118
                                       l ee +    ++ +lq++l e  ++
  gi|313126714|ref|YP_004036984.1| 156 LSEEVDDLRDDRDDLQRDLREVCDD 180
                                       *******************998775 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   3.6    0.0033      0.28      17      76 ..      38      94 ..      23     105 .. 0.82
   2 !   13.1  13.5   0.00075     0.063      16      73 ..     107     161 ..      91     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0033
                        Phage_GP20 17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeaki 76
                                      +++ d++ e +++l  +l+ + ++L+ L +    +++L++ +++ q ++    ae e+  
  gi|313126714|ref|YP_004036984.1| 38 ETQNDQLRERNKNLRAELESARTELKVLRER---VNDLNQSLQQTQGDVGHVAAELESTE 94
                                      678899**********************999...78888888888888888877777654 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00075
                        Phage_GP20  16 tkakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeye 73 
                                       t+++l+e  e+ +++ ++l+++ +++e+L+kk   n++L++q++el+++nk+ ++e +
  gi|313126714|ref|YP_004036984.1| 107 TETSLEEKREQLESVRDNLDEARSKIEELEKK---NKTLEEQVAELKTENKELSEEVD 161
                                       4788889999999999*************999...99**************9888765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  31.0   8.7e-06   0.00073      69     184 ..      34     156 ..      21     158 .. 0.92
   2 !   10.2   9.5    0.0078      0.65     120     165 ..     127     172 ..     124     186 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.7e-06
                             ATG16  69 nskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreee 145
                                       +s+ +++  +l ++ + lr+el+ +  +   l +r+++ln++lq+ +      +++l++ e+  ++ + +l++ e  
  gi|313126714|ref|YP_004036984.1|  34 ASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETS 110
                                       4456778889999999************************************************************* PP

                             ATG16 146 lrekeklvqdlqDElsaLqlqlnqaEeklr.......klekENkeL 184
                                       l+ek++ ++ ++D l+  + + + +E+k++       +l++ENkeL
  gi|313126714|ref|YP_004036984.1| 111 LEEKREQLESVRDNLDEARSKIEELEKKNKtleeqvaELKTENKEL 156
                                       ******************************8999999999999998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0078
                             ATG16 120 edeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLql 165
                                       e +++++ele+++++le+++++++ e +e+ + v+dl+D+ + Lq 
  gi|313126714|ref|YP_004036984.1| 127 EARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       3445556666666666666666666666666666666665555554 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5  14.8   0.00082     0.068     118     232 ..      32     138 ..      22     144 .. 0.49
   2 !   11.1   3.9    0.0022      0.19     121     168 ..     133     179 ..     126     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00082
                           DUF4407 118 eeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaG.kgpaakekkaqld 193
                                       ++        a++l+++ ++l++++++l+ae+++a+++l+ lr+ +++  +    ++t+g+ G   ++ ++ ++ l+
  gi|313126714|ref|YP_004036984.1|  32 SS--------ASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQS-L-QQTQGDVGhVAAELESTEKLLN 98 
                                       33........344555555566666666666666666666555555543332.2.2222333302344445556666 PP

                           DUF4407 194 aaqaelaelkakld.atarlaalraelaeleaerakeraa 232
                                         qael+  +++l+ ++++l++ r++l+e+++++++ +++
  gi|313126714|ref|YP_004036984.1|  99 HTQAELERTETSLEeKREQLESVRDNLDEARSKIEELEKK 138
                                       6666666666664444444444455555444444444443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0022
                           DUF4407 121 kelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeld 168
                                       +el++  +++l++++ael++++++l++e+d +++++d+l++++++ +d
  gi|313126714|ref|YP_004036984.1| 133 EELEK-KNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCD 179
                                       33322.244599*****************************9998776 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5  25.4   1.3e-05    0.0011      18     148 ..      47     178 ..      31     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-05
                              Fez1  18 QLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekveklee 94 
                                         k+ +ae+ +   e+  l+ ++ +l+++l++++  + ++ ++le+ ++ l++ ++el+r++++ e +re++e++ +
  gi|313126714|ref|YP_004036984.1|  47 RNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRD 123
                                       44667899999999*************************************************************** PP

                              Fez1  95 elkelreelselsleeeeaalesdeakaqrqe.aeeleelkreverlraeLkeer 148
                                       +l e r++++el++++++ +++  e k++++e +ee+++l+ + + l++ L+e  
  gi|313126714|ref|YP_004036984.1| 124 NLDEARSKIEELEKKNKTLEEQVAELKTENKElSEEVDDLRDDRDDLQRDLREVC 178
                                       ***********99999999999999998877657899999999999999999865 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   9.7     0.018       1.5      34     109 ..      29     104 ..      20     105 .. 0.83
   2 !   16.3  11.6   5.7e-05    0.0047      14     109 ..      86     181 ..      83     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.018
                           DUF3450  34 qsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrL 109
                                       + q+  ++l+ + ++l ++ ++l++eles++ + + l++ v++++q++++ + +   + +  ++ + ll  + ++L
  gi|313126714|ref|YP_004036984.1|  29 MYQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAEL 104
                                       6788889999999999999999999999999999999999999999999999888888888888888887777766 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.7e-05
                           DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       +aa+l++++k  + ++a+ +++++  ++  ++ +++ +++ ++++++e+le++n+ le++va++++e ++l e+ ++
  gi|313126714|ref|YP_004036984.1|  86 VAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDD 162
                                       588999999999999999999999999999999999999***********************************999 PP

                           DUF3450  91 ieeierelvpllekmidrL 109
                                       ++  +++l+  l+++ d+ 
  gi|313126714|ref|YP_004036984.1| 163 LRDDRDDLQRDLREVCDDW 181
                                       9999999988888887765 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.4      0.31        26     147     181 ..      30      64 ..      14      71 .. 0.55
   2 !   16.0  30.8   7.9e-05    0.0066      36     190 ..      31     176 ..      26     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.31
                        MscS_porin 147 sqaqrtalqaelaaleaqieeleqellsnnnrqeL 181
                                        q+    l+++   l+ +++ l+ el+s+ +  + 
  gi|313126714|ref|YP_004036984.1|  30 YQSSASDLETQNDQLRERNKNLRAELESARTELKV 64 
                                       45555555555566666666666665555443333 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.9e-05
                        MscS_porin  36 kkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelq 112
                                       ++ a +l+++ d+  ++ ++l++ele+        ++ +  +   ++L+q l+qt+ ++  + ++l + +++l+ +q
  gi|313126714|ref|YP_004036984.1|  31 QSSASDLETQNDQLRERNKNLRAELESA------RTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQ 101
                                       4444444445555555555555555544......3333333445789999999999999999999999999999999 PP

                        MscS_porin 113 trperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdll 189
                                         +er  + l e r++l+ +r++L++     +++++ ++     e++  e+++e  e++ +  + r +   lqrdl 
  gi|313126714|ref|YP_004036984.1| 102 AELERTETSLEEKREQLESVRDNLDEA---RSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       999999999999999999999999777...33666666666667888888888888888888888888888888886 PP

                        MscS_porin 190 k 190
                                       +
  gi|313126714|ref|YP_004036984.1| 176 E 176
                                       5 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  26.5   1.3e-05    0.0011     931    1075 ..      32     175 ..      23     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-05
                     Myosin_tail_1  931 sasqksesarqqlerqnkelkakLqelegavkskykssiaaleakiaqleeqleqeskerqaaaklvrrtekklk 1005
                                        s++   e+   ql  +nk+l+a L+   +++k  ++  +  l+  ++q+   + + + e + ++kl+ +t+  l 
  gi|313126714|ref|YP_004036984.1|   32 SSASDLETQNDQLRERNKNLRAELESARTELKV-LRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELE 105 
                                        566677888888888888888888887777775.67888888888888888888888888888888888888888 PP

                     Myosin_tail_1 1006 evllqvedeRrnadqykdqvekansrlkqlkrqLeeaeeeasRanaarRklqReLddatesaealnRevs 1075
                                         +   +e+ R + + ++d+++ a+s++ +l ++    ee+++  +++++ l  e+dd  +  + l+R++ 
  gi|313126714|ref|YP_004036984.1|  106 RTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175 
                                        8888888888888888888888888888888888888888888888888888888888888888888875 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1  25.3   2.6e-05    0.0022      61     189 ..      28     156 ..       8     156 .. 0.85
   2 !   13.4  17.6   0.00073     0.061      67     143 ..     101     177 ..      93     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-05
                           UPF0242  61 lkeklekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae...dfe 134
                                       +  +  +s le+++ +l e +   k+ + +le ++ e + L+e+++  ++ l++ + +  ++  +le + +     +
  gi|313126714|ref|YP_004036984.1|  28 MMYQSSASDLETQNDQLRERN---KNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKllnHTQ 101
                                       333337788999999999999...99****************************************99999776677 PP

                           UPF0242 135 elkleleeqLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEiktL 189
                                       + +   e  L+ek+e+l+  + ++ e rs +e+ +++++ Le +V  l+ E k L
  gi|313126714|ref|YP_004036984.1| 102 AELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKEL 156
                                       777778999***************************************9998866 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00073
                           UPF0242  67 kskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeq 143
                                       + +le  e  l e++e+l+  +++l e++++ eeL+++ +  ee++++lk en++L+e+  +   d ++l+++l e 
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       45677888888888888888888888888888888888888888888888888888888888888888888777664 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  11.6       0.2        16     260     331 ..      40     107 ..      27     117 .. 0.28
   2 !   16.7  11.1   4.8e-05     0.004     188     252 ..     115     176 ..     107     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.2
                            HMMR_N 260 kndeiesLkssLeekeqelskqvkdlnekckllekekeelvreeeekeqtlsaEleelkeklklkeqeaqkl 331
                                       +nd++ +  ++L+++ +   ++ k l e+++ l++++    ++ +    ++ aEle++++ l+  + e ++ 
  gi|313126714|ref|YP_004036984.1|  40 QNDQLRERNKNLRAELESARTELKVLRERVNDLNQSL----QQTQGDVGHVAAELESTEKLLNHTQAELERT 107
                                       2222222222222222222222222222222222111....1233333333333333333333333332222 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.8e-05
                            HMMR_N 188 eaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaq 252
                                         +l+++  nL+e+++k+ +L+ k+++le++ +e k+e+++l e+++ l+  ++ l   + d+++
  gi|313126714|ref|YP_004036984.1| 115 REQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDL---QRDLRE 176
                                       5699*********************************************9999998...555554 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  26.7     6e-05     0.005      22     150 ..      36     166 ..      27     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  22 aLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkr 98 
                                        LE++n++L+ + ++l+ + ++++++l ++  + +++l + l++++ +  ++ +el+++++ l++ ++ +e+  ++ 
  gi|313126714|ref|YP_004036984.1|  36 DLETQNDQLRERNKNLRAELESARTEL-KVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSL 111
                                       69****************987777755.567889*************************************999999 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXX CS
                          Filament  99 eevEaelkalrkdldeatlarvdLekkvesLkeelaflkkvh...eeEvkelqkq 150
                                       ee  ++l+++r +ldea  +  +Lekk ++L+e++a lk+     +eEv++l+  
  gi|313126714|ref|YP_004036984.1| 112 EEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENkelSEEVDDLRDD 166
                                       99999****************************9999997651115788888765 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.5     0.033       2.8      17      92 ..      29     105 ..      21     108 .. 0.81
   2 !   12.7  10.6    0.0015      0.12      36      93 ..     101     158 ..      87     161 .. 0.80
   3 ?    2.9   0.1       1.6   1.3e+02      25      52 ..     149     176 ..     147     181 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.033
                           BLOC1_2  17 atvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLDeyskeLE 92 
                                       + ++  + Le+ N +  e+ k+l+ +++s++++l+ l+e+ + l++ lqq + ++    +eLe++ + L++   eLE
  gi|313126714|ref|YP_004036984.1|  29 MYQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQgDVGHVAAELESTEKLLNHTQAELE 105
                                       55667777999999999999999999999999999999999999999999863566666778888877777777777 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0015
                           BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                        ++l++   sle+k e+l++  ++l++  ++i+++ek+ ++Lee v+eL +  keL +
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSE 158
                                       4677778888999999999999999999999999999999999999999888888765 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 1.6
                           BLOC1_2  25 LeklNeaasekykklkdvaaslekklek 52 
                                       L++ N++ se++++l+d  ++l+++l +
  gi|313126714|ref|YP_004036984.1| 149 LKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       5566777777777777777777766655 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3  32.8     4e-05    0.0033       8     140 ..      32     175 ..      26     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4e-05
                          KASH_CCD   8 stvadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklkstQ........qalqkaklleeEleelkalv 76 
                                       s+  dL++ N +L e n+ L++ +e+a  + + L e +++L + l+ tQ         +   +kll+   +el ++ 
  gi|313126714|ref|YP_004036984.1|  32 SSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQgdvghvaaELESTEKLLNHTQAELERTE 108
                                       4678***************************************9999994444222112245777888888888888 PP

                          KASH_CCD  77 keleEkrarlkaqnkqleken...qsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlh 140
                                       ++leEkr++l+  + +l+  +   + L++k ++L+e+   l++e+ el + + +L + +++L+++l 
  gi|313126714|ref|YP_004036984.1| 109 TSLEEKREQLESVRDNLDEARskiEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       8888888888877777764431125566666777777777777777777777777777777776665 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.8      0.17        14      51      85 ..      60      94 ..      27      95 .. 0.72
   2 ?    5.9   0.3      0.18        15      50      85 ..     101     136 ..      97     137 .. 0.84
   3 ?    8.1   0.1     0.038       3.1       6      45 ..     146     185 ..     141     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.17
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 51 aefeewkqaaqklvdaLeeisealkqaanafedaD 85
                                       e++ +++ +++l++ L++++  + ++a+++e+++
  gi|313126714|ref|YP_004036984.1| 60 TELKVLRERVNDLNQSLQQTQGDVGHVAAELESTE 94
                                      45566777888888888888888888888888887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  50 qaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                       qae+e+   ++++  ++Le+++++l++a ++ e+ +
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLDEARSKIEELE 136
                                       678888889999999999999999999999988877 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHH CS
                            WXG100   6 peelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaa 45 
                                        +el +  ++++++ ++l+d  ++l++++ ++ ++Ws +a
  gi|313126714|ref|YP_004036984.1| 146 VAELKTENKELSEEVDDLRDDRDDLQRDLREVCDDWSEEA 185
                                       6788899999999***********************9877 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2  15.8    0.0017      0.14      46     131 ..      31     117 ..      27     118 .. 0.91
   2 !   12.0  11.1     0.002      0.17      48     115 ..     111     178 ..     109     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0017
                              ADIP  46 qardrdleqr.eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrl 121
                                       q++ +dle++  +l e++++l+ae+e+ +++ + l +++ +l + l++ q +  +  ++l+++e+ l+ ++ el+r+
  gi|313126714|ref|YP_004036984.1|  31 QSSASDLETQnDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERT 107
                                       5566777765158999************************************************************* PP

                              ADIP 122 knalqqiktq 131
                                       ++ l++ + q
  gi|313126714|ref|YP_004036984.1| 108 ETSLEEKREQ 117
                                       **99998877 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.002
                              ADIP  48 rdrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknek 115
                                       +++ +eq es+ + + + ++ ie l++k + l++q+++l++e++ + ++  +l+ +  +l++ l++  
  gi|313126714|ref|YP_004036984.1| 111 LEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVC 178
                                       67889999999999999999999999999999999999999999999999999999999998887755 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6  22.8   2.7e-05    0.0022     598     734 ..      38     172 ..      24     187 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-05
                           DUF3584 598 aaseeeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdkleka 674
                                         ++++Lrer + l  +l+sa+ + k + e++++ln+ l++ +  v + a++l+ +++ l    n+ ++e ++ e +
  gi|313126714|ref|YP_004036984.1|  38 ETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLL----NHTQAELERTETS 110
                                       344556666666666666666666666666666666666666666666666666555433....3444444444444 PP

                           DUF3584 675 iaerkqqaeeqlqkldaqlkqle...eqqkaaleelkedlseerlekkakwqevvgeldeqla 734
                                       ++e+++q e  +++ld++   +e   +++k ++e+++e + e++ e ++++ ++  ++d+  +
  gi|313126714|ref|YP_004036984.1| 111 LEEKREQLESVRDNLDEARSKIEeleKKNKTLEEQVAELKTENK-ELSEEVDDLRDDRDDLQR 172
                                       45555555544444444433332000222222222222222222.444444444444443333 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.7     0.018       1.5      96     144 ..      30      78 ..      24      95 .. 0.82
   2 !   12.2   7.2    0.0012     0.097      96     138 ..     100     142 ..      84     143 .. 0.77
   3 ?    8.6   1.6     0.015       1.2      92     130 ..     138     176 ..     137     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.018
                         PspA_IM30  96 lekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkareka 144
                                       ++++a +letq +q+r+  ++lr++le + t ++ l++ ++ l   +++
  gi|313126714|ref|YP_004036984.1|  30 YQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQ 78 
                                       789999**************************99999999988655554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0012
                         PspA_IM30  96 lekqaealetqlaqqrsaveqlrkqlealetkieelkakkell 138
                                        + ++e+ et+l++ r++ e +r +l+++  kieel++k ++l
  gi|313126714|ref|YP_004036984.1| 100 TQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTL 142
                                       3556788888888888888888888888888888888888877 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.015
                         PspA_IM30  92 eikslekqaealetqlaqqrsaveqlrkqlealetkiee 130
                                       + k+le+q+++l+t+ +++ + v++lr   ++l + ++e
  gi|313126714|ref|YP_004036984.1| 138 KNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       6799**********************9988888777766 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  34.5   0.00018     0.015      12     138 ..      37     167 ..      26     172 .. 0.89
   2 !   14.1  12.9   0.00046     0.039       2      69 ..     118     185 ..     117     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 0.00018
                     Tropomyosin_1  12 aqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnne.altrkiqlLEe 87 
                                         ++ ++l+e++K+l  e ++   e+k L ++++ l++ + +++ ++  + +++e++ek+  +   +l+r    LEe
  gi|313126714|ref|YP_004036984.1|  37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQaELERTETSLEE 113
                                       5567899****************************************************98888768********97 PP

                     Tropomyosin_1  88 ...eleesdkkLkettekLretdvkaeelERkvkaLeqerdewekkyeeleeky 138
                                          +le+   +L e+  k++e ++k  +lE +v++L +e++e  + +++l +  
  gi|313126714|ref|YP_004036984.1| 114 kreQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDR 167
                                       3336888889********************************999999988765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00046
                     Tropomyosin_1   2 lnsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeese 69 
                                       l+s++ + +ea  k eele+k+K+le++  e   e k+L++ ++ l ++ + l+ +l+e+ +  +e++
  gi|313126714|ref|YP_004036984.1| 118 LESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDDWSEEA 185
                                       67778888888888999999999998888888888888888888888888899999888877777665 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  19.6   2.6e-05    0.0022     477     579 ..      31     137 ..      23     138 .. 0.83
   2 !   11.2  13.4   0.00085     0.071     475     544 ..     113     179 ..     110     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-05
                              HOOK 477 eekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaed....ssllkkkleehleklkev 549
                                       +   ++l+++ ++ ++r+++L+ e  +a+  ++ L+++v++l+++lq+ ++          +++k l++ + +l++ 
  gi|313126714|ref|YP_004036984.1|  31 QSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHvaaeLESTEKLLNHTQAELERT 107
                                       5677899999********************************9998876554443322134455667777889**** PP

                              HOOK 550 qeelqkkkeqleelepklssnkqkieelee 579
                                       +  l++k+eqle++  +l+++ +kieele+
  gi|313126714|ref|YP_004036984.1| 108 ETSLEEKREQLESVRDNLDEARSKIEELEK 137
                                       ****************************97 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00085
                              HOOK 475 seeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehle 544
                                       +++e+l+++ + l++a+ +++eLe++n++ ++++ eL+++  el ++ ++     +d   l+++l e  +
  gi|313126714|ref|YP_004036984.1| 113 EKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDD---LQRDLREVCD 179
                                       568899999999999999999999999999999999999988888777776666665...7777777655 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   4.5    0.0012     0.099     742     791 ..      30      79 ..      26      83 .. 0.94
   2 !   11.4  18.6   0.00077     0.064     707     791 ..      86     170 ..      80     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0012
                               FPP 742 lkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLeee 791
                                       ++ s s +etq ++  e +++l   ++ +++el+ l+++++ L++ L++ 
  gi|313126714|ref|YP_004036984.1|  30 YQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQT 79 
                                       68999******************************************986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00077
                               FPP 707 levelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkiea 783
                                       +++el+s ++ l++++a l+ +E +l+e +++Les+++    a +++++ +  +++le + +el++e +el ++++ 
  gi|313126714|ref|YP_004036984.1|  86 VAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDD 162
                                       67889999999999999999999999999999999999999999999999999999999999999999999999998 PP

                               FPP 784 LeveLeee 791
                                       L  + ++ 
  gi|313126714|ref|YP_004036984.1| 163 LRDDRDDL 170
                                       87654443 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  21.9     0.014       1.2      25     137 ..      33     172 ..      28     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.014
                     PI3K_P85_iSH2  25 qlqekskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqi.klqekfskea.............q........ 79 
                                          + +++ dql e  ++++ e++  r+ l++ +e ++ +++ + ++q  +   a             q        
  gi|313126714|ref|YP_004036984.1|  33 SASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLqQTQGDVGHVAaelestekllnhtQaelertet 109
                                       55666777788888888888888888888888888766554443145555555444555555444444044444444 PP

                     PI3K_P85_iSH2  80 .....ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqk 137
                                            ++  e++ +nl++++s+++el+++ + Lee++ + k+e++el  e+  l+ +   Lq+
  gi|313126714|ref|YP_004036984.1| 110 sleekREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       44443666789***************************************9999999888887 PP

>> PEARLI-4  Arabidopsis phospholipase-like protein (PEARLI 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1  12.0   3.8e-05    0.0032     160     255 ..      54     150 ..      49     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-05
                          PEARLI-4 160 DlEsvkikvgWlrsvleEiveavkyy.deqetavvEKevkerdvllkkqEmekqekelaekEKeikevrekvtemaa 235
                                       +lEs++ +   lr+ ++++ ++ +   ++  ++  E e +e+ +   + E+e++e+ l ek  +++ vr ++ e ++
  gi|313126714|ref|YP_004036984.1|  54 ELESARTELKVLRERVNDLNQSLQQTqGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARS 130
                                       689******************98765167789999****************************************** PP

                          PEARLI-4 236 klgelemkrarlekrlafls 255
                                       k+ ele k   le+++a l+
  gi|313126714|ref|YP_004036984.1| 131 KIEELEKKNKTLEEQVAELK 150
                                       *************9887665 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.8     0.015       1.2      34      78 ..      37      79 ..      25      92 .. 0.45
   2 !   13.3  19.5   0.00094     0.078       9      85 ..      89     163 ..      84     176 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.015
                       Uso1_p115_C 34 leqkeakkaaesqakeleaenkklekeleklraelkeekekekek 78
                                      le +  + + ++++k+l+ae ++ + el+ lr+++++ +++ +++
  gi|313126714|ref|YP_004036984.1| 37 LETQ--NDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQT 79
                                      1111..222333344444444444444444444444444444444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00094
                       Uso1_p115_C   9 eaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqkEldDL 85 
                                       e +s +++ + ++ael+ ++++le+++++  +++ + + +e+++++++lek+ ++l+++++e k ++ke  +E+dDL
  gi|313126714|ref|YP_004036984.1|  89 ELESTEKLLNHTQAELERTETSLEEKREQ--LESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDL 163
                                       44555555555556666666555555555..5556666777777777777777777777777777776666666666 PP

>> CEP63  Centrosomal protein of 63 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2  24.5   0.00018     0.015      30     181 ..      34     176 ..      28     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 0.00018
                             CEP63  30 traletrlkireeeLasarnaldekhkEvgllrqqleelekekqelvakyeqqlqklreelsklkrsyekLqrkqlk 106
                                          let+ ++  e  +++r+ l++  +E ++lr+++++l+++ q    + + ++ ++ +el+    s ekL ++   
  gi|313126714|ref|YP_004036984.1|  34 ASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQ----QTQGDVGHVAAELE----STEKLLNHTQA 102
                                       45566666666666677788888888888888877777766544....34567777777774....78899998887 PP

                             CEP63 107 earekeakskeedrvelsrlnskleefrqkslewekqrlqyqkqvasleaqrkaLaekleliqsaaykvqlekrk 181
                                       e +  ++ s ee+r +l+ + ++l+e r+k  e ek++    +qva l  ++k L+e+++ ++      q+  r+
  gi|313126714|ref|YP_004036984.1| 103 ELE-RTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       777.46799999999999999999999999999999999999999999999999999999888755555555555 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.3     0.003      0.25      34      83 ..      35      80 ..      29      86 .. 0.89
   2 ?    8.9   4.3     0.023       1.9       4      51 ..      93     140 ..      92     143 .. 0.94
   3 ?    8.0   2.9     0.045       3.8      16      50 ..     140     174 ..     135     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.003
                   Snapin_Pallidin 34 eqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklk 83
                                      ++l+++n++L+e +++      ++l++ +  L+ ++ r++ ln++lq+++
  gi|313126714|ref|YP_004036984.1| 35 SDLETQNDQLRERNKNLR----AELESARTELKVLRERVNDLNQSLQQTQ 80
                                      578999999998888888....99***********************998 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.023
                   Snapin_Pallidin   4 aegllellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                       +e ll++ + +l++++++l+e r++ e ++++ld+ ++k++ele+ ++
  gi|313126714|ref|YP_004036984.1|  93 TEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNK 140
                                       689****************************************99887 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.045
                   Snapin_Pallidin  16 deldeklkelrqsQeeLleqldrlnekLkeleeaq 50 
                                       ++l+e+++el+++ +eL+e++d l+++ ++l+++ 
  gi|313126714|ref|YP_004036984.1| 140 KTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDL 174
                                       7899********************99988888765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.3     0.026       2.2      79     122 ..      37      80 ..      25      84 .. 0.80
   2 !   17.4  12.1   4.5e-05    0.0038      26     138 ..      65     180 ..      63     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  79 ikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLe 122
                                       ++  +++l+e+  +l++++ +  ++++vL++ +++++q++q+ +
  gi|313126714|ref|YP_004036984.1|  37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQ 80 
                                       45667889999999999999999999999999999999998755 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.5e-05
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...CCCHHHHHHHC CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee...eilrlketida 99 
                                       l +  +d++++l++ + ++ +++ + +++e+l ++++  l+++++s +++ + +++++++l+e   +i++l+++ ++
  gi|313126714|ref|YP_004036984.1|  65 LRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEarsKIEELEKKNKT 141
                                       667778999****************************************9999999999998722256666777777 PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-EE CS
                         Fib_alpha 100 qesnirvLqnvlesneqkiqkLeqdidqkerkCkepCkd 138
                                        e+++ +L++  +++++++ +L+ d d ++r+ +e C d
  gi|313126714|ref|YP_004036984.1| 142 LEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDD 180
                                       88*********************************9987 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.4      0.11       9.3     138     220 ..      40      94 ..      25      97 .. 0.49
   2 !   12.2  27.4   0.00088     0.074     108     241 ..      42     178 ..      40     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.11
                          CCDC144C 138 dvsnlkdknevLsqqLskaeskansLenelhetrdaLrektlllesvqrdlsqaqcqikeleqmyqneeekvnkyia 214
                                       +  +l+++n+ L  +                            les+  +l+  + ++++l+q +q+ ++ v ++ a
  gi|313126714|ref|YP_004036984.1|  40 QNDQLRERNKNLRAE----------------------------LESARTELKVLRERVNDLNQSLQQTQGDVGHVAA 88 
                                       223344444444444............................4555555555555555555555555555555555 PP

                          CCDC144C 215 kqesle 220
                                       + es+e
  gi|313126714|ref|YP_004036984.1|  89 ELESTE 94 
                                       544444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00088
                          CCDC144C 108 eqsqtskrdlelalqrerdewlrlqdkln...fdvsnlkdknevLsqqLskaeskansLenelhetrdaLrektlll 181
                                       +q  + +++l  +l+ +r e   l++++n     + +++  +  +  +L+ +e+ +n  + el++t+++L ek   l
  gi|313126714|ref|YP_004036984.1|  42 DQLRERNKNLRAELESARTELKVLRERVNdlnQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQL 118
                                       56666777888888899999988888866211444555666778999999999999999999999999999999999 PP

                          CCDC144C 182 esvqrdlsqaqcqikeleqmyqneeekvnkyiakqesleerlaqlqsenmlLrqqLedaq 241
                                       esv  +l++a+++i ele+++++ ee+v +   +++ l e +  l+ +   L++ L +++
  gi|313126714|ref|YP_004036984.1| 119 ESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVC 178
                                       999999999999999999999999999999999999999999998888888887777765 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.5     0.067       5.6     137     178 ..      35      76 ..      26      83 .. 0.80
   2 !   15.1  11.5   0.00016     0.014     106     178 ..      88     160 ..      82     179 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.067
                           DUF2968 137 qavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqq 178
                                       + ++++ +q+r+  + L+a+ e+a+++l+ l++++++L++  
  gi|313126714|ref|YP_004036984.1|  35 SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSL 76 
                                       556777889999999999999999999999999999998764 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 0.00016
                           DUF2968 106 aqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqq 178
                                       a+ +++e+++++++a++er ++ l+ +r+Q ++v ++ ++ar++ + Le++++ +++q+ +l+ + ++L ++ 
  gi|313126714|ref|YP_004036984.1|  88 AELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEV 160
                                       5555666666666666666666666666666666666666666666666666666666666665555554443 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   4.1   0.00085     0.071      59     104 ..      36      81 ..      25      83 .. 0.93
   2 ?    5.0   7.1      0.28        23      59      99 ..      92     132 ..      82     134 .. 0.64
   3 ?    9.2   8.8     0.013       1.1      68     102 ..     122     156 ..     119     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00085
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklq 104
                                       d+e+ +++L er ++l +e+++   +l+ l++++++l ++lq+ ++
  gi|313126714|ref|YP_004036984.1|  36 DLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQG 81 
                                       789999************************************9887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.28
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                       + e+++++ ++++e+ e+ +++  +qle+++ +l+e ++++
  gi|313126714|ref|YP_004036984.1|  92 STEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKI 132
                                       45666666666666666666666666666666666666665 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                       Prefoldin_2  68 eerketlekeiktlekqleklekeleelkeelqkk 102
                                        ++++++  +i++lek+ ++le++++elk+e++++
  gi|313126714|ref|YP_004036984.1| 122 RDNLDEARSKIEELEKKNKTLEEQVAELKTENKEL 156
                                       55666666666666666666666666666666654 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.2     0.051       4.3      78     121 ..      35      78 ..      26      82 .. 0.55
   2 !   14.3  23.3   0.00043     0.036      46     152 ..      70     179 ..      66     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.051
                     Jnk-SapK_ap_N  78 eeleeiedqweeerkelqekveqleeenrelelkaknaadqlsr 121
                                        +le   dq++e++k+l++++e+ ++e + l  +++++++ l++
  gi|313126714|ref|YP_004036984.1|  35 SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQ 78 
                                       45555666666666666666666666666666444444444433 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00043
                     Jnk-SapK_ap_N  46 eeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqle...eenrelelkaknaadql 119
                                       +  ++ l++ + ++ +   e+e   +l ++++ ele++e+++ee+r++l++   +l+   ++++ele+k k +++q+
  gi|313126714|ref|YP_004036984.1|  70 NDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDearSKIEELEKKNKTLEEQV 146
                                       5678999999**************************************99865555511167888999********* PP

                     Jnk-SapK_ap_N 120 srleekeaelkkeysklheretellkklkelve 152
                                       ++l+ +++el++e + l +   +l + l+e+ +
  gi|313126714|ref|YP_004036984.1| 147 AELKTENKELSEEVDDLRDDRDDLQRDLREVCD 179
                                       *******************99999999999987 PP

>> She9_MDM33  She9 / Mdm33 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.4     0.071       5.9      33     110 ..      42     119 ..      35     129 .. 0.75
   2 !   11.1   6.5    0.0031      0.26       4      77 ..     106     177 ..     104     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.071
                        She9_MDM33  33 eklkksieeleeeleeakeevreakeayeeaiekrsksqrevneLLqRkssWspedlerft..elyrkdhanekeee 107
                                       ++l++++++l +ele+a++e++ ++e+ ++ +++ +++q +v ++ +  +  s+e l ++t  el r+++++e++ e
  gi|313126714|ref|YP_004036984.1|  42 DQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELE--STEKLLNHTqaELERTETSLEEKRE 116
                                       79****************************************98876544..3444444441246666666666555 PP

                        She9_MDM33 108 eak 110
                                       +++
  gi|313126714|ref|YP_004036984.1| 117 QLE 119
                                       554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0031
                        She9_MDM33   4 kleelldslqetlltaskalndvtGYseieklkksieeleeeleeakeevreakeayeeaiekrsksqrevneL 77 
                                       ++e+ l++ +e+l ++  +l++    s+ie+l k++++lee+++e k+e +e+ e+ ++  ++r + qr++ e+
  gi|313126714|ref|YP_004036984.1| 106 RTETSLEEKREQLESVRDNLDEA--RSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       56667777777777777777776..489******************************************9886 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.3     0.028       2.4     131     181 ..      33      83 ..      25      89 .. 0.59
   2 !   14.1  12.3   0.00036      0.03     106     178 ..      99     178 ..      82     188 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.028
                            DUF724 131 eidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeF 181
                                       + ++le +  +l+++++ l+++ e+a  e++ l+  +++l+++l++++ ++
  gi|313126714|ref|YP_004036984.1|  33 SASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDV 83 
                                       444555555555555555666666666666666666666666666666555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00036
                            DUF724 106 klleerkklekkieeeesekrkleeeid.......elekkilelerqlallkekkeaadkeiarlkseaekleeele 175
                                       +++ e+++ e ++ee++++ +++ +++d       elekk ++le+q a lk+++++ ++e+ +l+ + ++l+++l+
  gi|313126714|ref|YP_004036984.1|  99 HTQAELERTETSLEEKREQLESVRDNLDearskieELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       33444444555555555555555555550000000555555555555555555555555555555555555555555 PP

                            DUF724 176 dve 178
                                       +v 
  gi|313126714|ref|YP_004036984.1| 176 EVC 178
                                       554 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.0       0.4        34       3      48 ..      53      98 ..      36     110 .. 0.64
   2 !   15.9   6.9   0.00011    0.0089       4      69 ..     110     175 ..     107     179 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.4
                             Sec34  3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheace 48
                                       +Les + e++ l e++++++++L++ + ++ +v+++ +s ++  +
  gi|313126714|ref|YP_004036984.1| 53 AELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLN 98
                                      4677777777777777777777777777777777666554433333 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 0.00011
                             Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                        Le+k+e+++++ +++dea +++eele+k k+ +e+  +l+++ ++l ee ++l++  ++++ +L+
  gi|313126714|ref|YP_004036984.1| 110 SLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       7999**************************************************999999999885 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.1     0.071       5.9      11      97 ..      37     125 ..      30     130 .. 0.67
   2 !   11.9  11.9    0.0024       0.2      26      93 ..     113     177 ..     102     187 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.071
                                       HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCC....CCCHHHHHHH CS
                      Seryl_tRNA_N  11 peavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeli....aevkelkeel 83 
                                       +e+  ++l++R+  k++ +el ++ ++ + l+ ++++l++   + +  +g   ++ e +e+l+    ae +   + l
  gi|313126714|ref|YP_004036984.1|  37 LETQNDQLRERN--KNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLnhtqAELERTETSL 111
                                       555566676664..778888888888888888888888888888888888888887666555411114555555555 PP

                                       HHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  84 kaleaelkeleael 97 
                                       +++ ++l+ ++++l
  gi|313126714|ref|YP_004036984.1| 112 EEKREQLESVRDNL 125
                                       55666666555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkel 93 
                                       ++ ++l ++ ++  e+++++eel ++ ++l ++++++k ++   +el +ev++l ++ ++l+ +l+e+
  gi|313126714|ref|YP_004036984.1| 113 EKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTEN---KELSEEVDDLRDDRDDLQRDLREV 177
                                       33345555555555666666666666666666666666543...456666666666666666666655 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6  31.9   0.00024      0.02      52     188 ..      45     176 ..      29     177 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 0.00024
                        Lebercilin  52 edteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkk.LsedknLaereeLqkkLe 127
                                        +++++L   l++ + E++vlrer+ ++ ++ ++++ ++ +  ael+++++ l++ ++ L +  +    ee  ++Le
  gi|313126714|ref|YP_004036984.1|  45 RERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAeLERTET--SLEEKREQLE 119
                                       34455555555555555555555555555555555555555555555555555555553332221..22455677** PP

                        Lebercilin 128 eleakleekeekikeLerkleleeksfrrqlaaekkktkeaqeevkalqeeierlkqklke 188
                                       +++++l+e++ ki+eLe+k    +k+ + q+a  k   ke+ eev++l++  ++l+++l+e
  gi|313126714|ref|YP_004036984.1| 120 SVRDNLDEARSKIEELEKK----NKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       ****************997....7888899999999999*****************99986 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.9     0.014       1.1      67     114 ..      51      98 ..      43     111 .. 0.77
   2 ?    9.5   9.3     0.012      0.97      65     118 ..      98     151 ..      95     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.014
                              COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeakeleekre 114
                                       l++ele  +++l+ +r++v++++++l++++ +v    +e ++ e+  +
  gi|313126714|ref|YP_004036984.1|  51 LRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLN 98 
                                       677888888999999999999999999999988888888887776554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.012
                              COG2  65 vglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellkl 118
                                          q+ele+ e++l++ r+++esvr++l+e+++++e+  ++ k lee+ + lk 
  gi|313126714|ref|YP_004036984.1|  98 NHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKT 151
                                       556788888888888888888888888888888888877777777766544443 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1  12.4       3.5   2.9e+02       4      74 ..      49     119 ..      22     131 .. 0.56
   2 ?   11.8   9.3    0.0034      0.29       8      62 ..     116     170 ..     102     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLa 74 
                                       k+l ++le+  ++l+ l e++++l+++l+++  +  ++ +e e+  ++l++++++ ++++++l+e +e+L+
  gi|313126714|ref|YP_004036984.1|  49 KNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLE 119
                                       34444444444444455555555555555555555555555444444445555555555555555555554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekek 62 
                                       ++le++ ++l+e  +++eel+++ ++l e+ aeL++en++l e++++ ++++++ 
  gi|313126714|ref|YP_004036984.1| 116 EQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDL 170
                                       4566666666666666666666666666666666666666666664444333333 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8  11.1   0.00016     0.014     142     218 ..      36     113 ..      23     122 .. 0.87
   2 ?    4.6   8.3      0.22        19     148     200 ..     120     172 ..     112     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 0.00016
                            Cluap1 142 lLekevelreartkalsrqleleeie.kalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLq 217
                                        Le++++  ++r+k l+++le ++ e k l+e++++++++l++t+ ++ +++++ ++ e+ +++ ++eler+++ L+
  gi|313126714|ref|YP_004036984.1|  36 DLETQNDQLRERNKNLRAELESARTElKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLE 112
                                       57888888899***************55679*****************************************99886 PP

                            Cluap1 218 s 218
                                       +
  gi|313126714|ref|YP_004036984.1| 113 E 113
                                       4 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.22
                            Cluap1 148 elreartkalsrqleleeiekalkeaikkvkeelektkkalenlesdeanLea 200
                                       ++r++ ++a s+  ele+ +k+l+e++ ++k+e +++++++++l++d + L++
  gi|313126714|ref|YP_004036984.1| 120 SVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       35555566666666677777788888888888888888888888888888776 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.6   0.00036      0.03      39      77 ..      29      67 ..      16      68 .. 0.84
   2 ?    4.9   7.5      0.49        41      15      77 ..      61     127 ..      58     145 .. 0.71
   3 ?    3.5   2.2       1.3   1.1e+02      46      79 .]     134     167 ..     132     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 0.00036
                                      XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                         GTP-bdg_M 39 trGpGetkleldrrlireriaklkkeLekvkkkrelqrk 77
                                      +  +  + le++  ++rer ++l+ eLe+ +++ +++r+
  gi|313126714|ref|YP_004036984.1| 29 MYQSSASDLETQNDQLRERNKNLRAELESARTELKVLRE 67
                                      55688899***********************99999987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.49
                                       HHHHHHHHHCXXXXXXXXX..X......XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                         GTP-bdg_M  15 qlkyllprLeglgkelsrqgGgig....trGpGetkleldrrlireriaklkkeLekvkkkrelqrk 77 
                                       +lk l+ r+++l+++l++++G +g       + e+ l   + ++++ +++l+++ e++++ r+ + +
  gi|313126714|ref|YP_004036984.1|  61 ELKVLRERVNDLNQSLQQTQGDVGhvaaELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDE 127
                                       799999*************998665554445666666666666666666666666666655555544 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 1.3
                                       XXHHHHHHHHHHHHHHHHHHHHHHHHHH.....T CS
                         GTP-bdg_M  46 kleldrrlireriaklkkeLekvkkkrelqrkkR 79 
                                       +le + ++++e++a+lk+e ++++++ + +r  R
  gi|313126714|ref|YP_004036984.1| 134 ELEKKNKTLEEQVAELKTENKELSEEVDDLRDDR 167
                                       6777888888888888888888777777666655 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.5    0.0014      0.12      35      71 ..      38      74 ..      26      76 .. 0.84
   2 ?   12.6   8.2    0.0014      0.11      22      68 ..     131     176 ..     122     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0014
                            Cnn_1N 35 eeqkeellkenielkveveslqkelkekkkllreaek 71
                                      e+q+++l + n +l+ e+es + elk ++++++++++
  gi|313126714|ref|YP_004036984.1| 38 ETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQ 74
                                      37999*************************9999876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0014
                            Cnn_1N  22 riyfLeerleklseeqkeellkenielkveveslqkelkekkkllre 68 
                                       +i +Le++ + l+e q+ el  en el +ev +l+++ + +++ lre
  gi|313126714|ref|YP_004036984.1| 131 KIEELEKKNKTLEE-QVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       66677776666655.88888999999999999999888888888887 PP

>> Vps52  Vps52 / Sac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.028       2.3      36      80 ..      47      91 ..      30      94 .. 0.85
   2 ?   10.4   2.9    0.0023      0.19      22      82 ..     103     163 ..      88     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.028
                             Vps52 36 lLeeFqsdlssissdikklqekSnelqlrLenrkaveaklsklvd 80
                                        ++   +l+s+ +++k l+e+ n+l+  L+  +   ++++++++
  gi|313126714|ref|YP_004036984.1| 47 RNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELE 91
                                      55667889**************************99999998876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0023
                             Vps52  22 qiaaidsvleqledlLeeFqsdlssissdikklqekSnelqlrLenrkaveaklsklvddl 82 
                                       +++  ++ le+  + Le+  ++l+ + s i+ l++k + l+ +    k+ + +ls++vddl
  gi|313126714|ref|YP_004036984.1| 103 ELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDL 163
                                       45556677888889999*******************************************7 PP

>> BCAS2  Breast carcinoma amplified sequence 2 (BCAS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   9.1    0.0038      0.32     125     201 ..      44     120 ..      37     125 .. 0.94
   2 ?   10.8   9.9    0.0034      0.29     130     203 ..      98     167 ..      94     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0038
                             BCAS2 125 WrvhneqleaelkklekeleetkeeieevnrqRkseQeeageeLksleekWrelvsknleieaaceeleaeieelkr 201
                                        r +n++l ael++++ el+ ++e+++++n++ +++Q ++g+  ++le++ + l  +  e+e+  ++le++ e+l++
  gi|313126714|ref|YP_004036984.1|  44 LRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLES 120
                                       5778******************************************************************9999875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0034
                             BCAS2 130 eqleaelkklekeleetkeeieevnrqRkseQeeageeLksleekWrelvsknleieaaceeleaeieelkrqa 203
                                       ++++ael+++e  lee++e+ e+v    +++ +ea++++++le+k ++l +++ e++ +++el +e+++l+ ++
  gi|313126714|ref|YP_004036984.1|  98 NHTQAELERTETSLEEKREQLESV----RDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDR 167
                                       567889999999999999999999....467899***********************************99875 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   9.0    0.0052      0.44      65     128 ..      52     115 ..      49     122 .. 0.87
   2 ?   11.7   8.6    0.0023      0.19      66     131 ..     123     185 ..     120     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0052
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  65 lkelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvr 128
                                       + ele ++ ++  Lre++++l + +++ +  + + + +l++ +k l +++ ++e+ +   +  r
  gi|313126714|ref|YP_004036984.1|  52 RAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKR 115
                                       579**************************************************99655444443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  66 kelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraea 131
                                       + l+++++++  L++k + le+qv+e+k + ++  e+++++r+     +r + +   + +++++ea
  gi|313126714|ref|YP_004036984.1| 123 DNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE---VCDDWSEEA 185
                                       689**************************9999999999999999999998776...777777776 PP

>> MctB  Copper transport outer membrane protein, MctB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.8   0.00017     0.014      23      67 ..      23      67 ..      10      80 .. 0.80
   2 ?    0.1   4.8       6.3   5.3e+02      36      63 ..     110     137 ..      87     148 .. 0.48
   3 ?    6.6   2.5     0.064       5.4      35      67 ..     140     172 ..     133     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 0.00017
                              MctB 23 vlGsgvlsdnlldtlegqveelreekeelraeadaleaqleaadd 67
                                       +G++++ ++ +++le q+++lre++++lrae ++++++l+   +
  gi|313126714|ref|YP_004036984.1| 23 TVGATMMYQSSASDLETQNDQLRERNKNLRAELESARTELKVLRE 67
                                      479**********************************99886555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 6.3
                              MctB  36 tlegqveelreekeelraeadaleaqle 63 
                                       +le+++e+l++ +++l + ++++e+  +
  gi|313126714|ref|YP_004036984.1| 110 SLEEKREQLESVRDNLDEARSKIEELEK 137
                                       3333333333333333333333333333 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.064
                              MctB  35 dtlegqveelreekeelraeadaleaqleaadd 67 
                                       +tle+qv+el++e++el++e+d l+ + ++ ++
  gi|313126714|ref|YP_004036984.1| 140 KTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       688999999999999999999998877665554 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2  13.3   0.00029     0.024     126     229 ..      25     132 ..      19     135 .. 0.81
   2 ?    6.4   4.9     0.068       5.7     135     178 ..     132     175 ..     129     187 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00029
                           Leu_zip 126 GgaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgek.kdekenskeiskleeklaelk 201
                                       G++ + +   + L+ +n++L+er k+l ++++sa  e + l++ +++l+++l+++  d+ + ++e+++ e+ l++ +
  gi|313126714|ref|YP_004036984.1|  25 GATMMYQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTqGDVGHVAAELESTEKLLNHTQ 101
                                       777788899999***********************************988877762566668899999999999999 PP

                           Leu_zip 202 ldlek...tleektasaksleedlastkhel 229
                                       ++le+   +leek ++ +s++++l +++ ++
  gi|313126714|ref|YP_004036984.1| 102 AELERtetSLEEKREQLESVRDNLDEARSKI 132
                                       9998833344555666667778888888765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.068
                           Leu_zip 135 ierLkeenekLkerlkelEkqatsaleeksklekalkelqkelg 178
                                       ie+L+++n++L+e++ el ++ +++ ee   l+ + ++lq++l 
  gi|313126714|ref|YP_004036984.1| 132 IEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       55555555555555555555555555555555555555544443 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3      0.65        54      10      36 ..      35      61 ..      30      63 .. 0.89
   2 ?    6.7   0.3      0.12       9.7       5      32 ..      65      92 ..      61     107 .. 0.71
   3 ?    2.7   0.5       1.9   1.6e+02       8      26 ..     131     149 ..      95     152 .. 0.69
   4 ?   10.7   2.2    0.0066      0.55       4      35 ..     141     172 ..     124     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.65
                               LPP 10 sqLkskvdqlssdvnsakaaaqaakeE 36
                                      s+L+++ dql +  ++++a++++a+ E
  gi|313126714|ref|YP_004036984.1| 35 SDLETQNDQLRERNKNLRAELESARTE 61
                                      8999**************999999877 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.12
                               LPP  5 LssqVsqLkskvdqlssdvnsakaaaqa 32
                                      L + V++L++  +q + dv +++a++++
  gi|313126714|ref|YP_004036984.1| 65 LRERVNDLNQSLQQTQGDVGHVAAELES 92
                                      5566778888888888887777776655 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 1.9
                               LPP   8 qVsqLkskvdqlssdvnsa 26 
                                        +++L++k + l+++v+++
  gi|313126714|ref|YP_004036984.1| 131 KIEELEKKNKTLEEQVAEL 149
                                       4444444444444444443 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.0066
                               LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                        L +qV +Lk++ ++ls++v++++++ ++ + 
  gi|313126714|ref|YP_004036984.1| 141 TLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       67788888888888888888888888777664 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.9    0.0044      0.37       8      50 ..      39      81 ..      32      93 .. 0.88
   2 ?    3.8   4.8      0.97        81      27      74 ..      86     121 ..      76     137 .. 0.42
   3 ?    9.2   6.1     0.019       1.6       8      62 ..     130     179 ..     124     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0044
                       Cep57_MT_bd  8 spkeaLaevlkeLedEfehlklelqelaaqynaldpslgkrkR 50
                                      + +++L e  k+L  E+e  + el+ l+++ n+l++sl++ + 
  gi|313126714|ref|YP_004036984.1| 39 TQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQG 81
                                      5678999999****************************98765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.97
                       Cep57_MT_bd  27 lklelqelaaqynaldpslgkrkRkdLaeeleelvkrlEaKadqIykL 74 
                                         +el+  ++ +n +++ l            e+   +lE+K +q  ++
  gi|313126714|ref|YP_004036984.1|  86 VAAELESTEKLLNHTQAEL------------ERTETSLEEKREQLESV 121
                                       5555555555555555333............22222222222222222 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.019
                       Cep57_MT_bd   8 spkeaLaevlkeLedEfehlklelqelaaqynaldpslgkrkRkdLaeeleelvk 62 
                                       s  e+L++  k+Le+++++lk e +el+++  +l        R+dL+++l+e+ +
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTENKELSEEVDDLR-----DDRDDLQRDLREVCD 179
                                       55567777779***********************9.....99*********9977 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  32.3    0.0066      0.56     142     287 ..      39     180 ..      31     186 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0066
                            HAP1_N 142 eeseeseelreeesleslqklvqldlLqeklreLeeeNekLreeasqLktetdtlEekEqqLvldcveqlseanqqi 218
                                       +++ +  e +++   e+++   +l +L+e++++L++    L++   ++ + + +lE  E +L++   ++l+ +++++
  gi|313126714|ref|YP_004036984.1|  39 TQNDQLRERNKNLRAELESARTELKVLRERVNDLNQS---LQQTQGDVGHVAAELESTE-KLLNHTQAELERTETSL 111
                                       2222222223344445555666666666666666433...3333333333355555555.45666666666666666 PP

                            HAP1_N 219 aelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqek 287
                                       +e  e+l++ +++l++ + +i++L  +  +l++++ el++en+el+++    ++ + +L+ +L+++ + 
  gi|313126714|ref|YP_004036984.1| 112 EEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDD 180
                                       666666666666666666666666666666666666666666666666666666666666666666554 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.7      0.24        20      22      66 ..      36      77 ..      30      83 .. 0.80
   2 ?    9.7   1.9     0.014       1.1       6      60 ..      62     113 ..      57     128 .. 0.68
   3 ?   11.5   3.1    0.0037      0.31       9      64 ..     128     180 ..     120     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.24
                           NPV_P10 22 alqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                       l++q d+++e  ++   l ++L++  ++L+ l + v++ ++ L 
  gi|313126714|ref|YP_004036984.1| 36 DLETQNDQLRERNKN---LRAELESARTELKVLRERVNDLNQSLQ 77
                                      577888888888888...889999999999999999999888776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.014
                           NPV_P10   6 LlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       L v r+ ++++++ ++  q  v +v+++l+ +++l   L+  +a+L+  et++e+
  gi|313126714|ref|YP_004036984.1|  62 LKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKL---LNHTQAELERTETSLEE 113
                                       67889999999999999999999999999997655...44555555555554433 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0037
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                        r+ i+++++k + l++qv++++++ ++   l+e++d++ +  ++l+  + ++ d 
  gi|313126714|ref|YP_004036984.1| 128 ARSKIEELEKKNKTLEEQVAELKTENKE---LSEEVDDLRDDRDDLQRDLREVCDD 180
                                       5899********************8877...8899999999999999888877665 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2       1.5   1.3e+02     103     142 ..      49      88 ..      14      93 .. 0.50
   2 ?   14.7   2.8   0.00024      0.02      90     162 ..      92     164 ..      83     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 1.5
                                       .......HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH CS
                         MCPsignal 103 ndsvesleetrqrveegselveetgealkeiveavaevad 142
                                       ++  + le++r++ ++  e v++ +++l++    v++va+
  gi|313126714|ref|YP_004036984.1|  49 KNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAA 88 
                                       2233334444444444444444444444444444444444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 0.00024
                                       HHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  90 eiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevn 162
                                        +e+l+ + q+e +++ +slee r++ e+  +  +e++++++e+ ++ + ++++v e+++  +e+s+ +++  
  gi|313126714|ref|YP_004036984.1|  92 STEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLR 164
                                       578999999*********************************************************9998865 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4  13.4   0.00045     0.038     202     300 .]      47     154 ..      23     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00045
                             FAM76 202 snetskksldsnssdhlv...avtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelek... 272
                                       +n++ +++l+s+ ++  v    v++L++ +++ +  + +   el + +k + + +ael+++e++l+ek ++le+   
  gi|313126714|ref|YP_004036984.1|  47 RNKNLRAELESARTELKVlreRVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESvrd 123
                                       22222223333333332212235666666666666666667889999999*********999999998777664333 PP

                             FAM76 273 ...eakekieklekkirellkevaelskkkk 300
                                          ea++kie+lekk+++l  +vael+ ++k
  gi|313126714|ref|YP_004036984.1| 124 nldEARSKIEELEKKNKTLEEQVAELKTENK 154
                                       3337889*******************99876 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.8      0.66        55      31      57 ..      32      58 ..      27      61 .. 0.71
   2 ?    4.2   2.4       0.8        67      19      58 ..      90     129 ..      81     134 .. 0.71
   3 ?   15.3   3.7   0.00027     0.023       3      65 ..     130     191 ..     128     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.66
                                      HHHHHHHHHHHHHHHT-XXXXXXXXXX CS
                              SlyX 31 qqidrlqrqlrllaerlkeleessgas 57
                                         + l++q ++l+er k+l+++ +++
  gi|313126714|ref|YP_004036984.1| 32 SSASDLETQNDQLRERNKNLRAELESA 58
                                      556778888888888888888776654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                              SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58 
                                       +e+  + + + q +++r ++ l++ +e+l++++++  +++
  gi|313126714|ref|YP_004036984.1|  90 LESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEAR 129
                                       5555666777788888888888888888888887766544 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeeepPP 65 
                                       +++eeLE k   +e+++ eL  +  e  +++d l+   + l++ l+e+ ++ + +ea+ +pPP
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDDWS-EEANSPPPP 191
                                       689******************************************99999965.443555555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   7.2    0.0041      0.35       8      92 ..      31     114 ..      26     121 .. 0.72
   2 ?    9.3   8.2     0.007      0.59       7      85 ..     100     177 ..      97     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0041
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlke 84 
                                       ++++ +le+++++++++ ++l +  ++ ++e+k  ++r+++l++sl++++ +v+ + + e+e+ ++ l+++++ l++
  gi|313126714|ref|YP_004036984.1|  31 QSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVG-HVAAELESTEKLLNHTQAELER 106
                                       567778888889999999999999999999999999999999999999998875.5555555555555555555555 PP

                             TMPIT  85 vesllpkk 92 
                                       +e +l +k
  gi|313126714|ref|YP_004036984.1| 107 TETSLEEK 114
                                       55555554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.007
                             TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                        + e+++ e++ +e +++le++    ++ +++i++ +k+ k l++++ +lk++ ++e +eev++l+++ ++ ++ l+
  gi|313126714|ref|YP_004036984.1| 100 TQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTE-NKELSEEVDDLRDDRDDLQRDLR 175
                                       56666777777777788889999999999999999999999999999999998.57888999999999888888887 PP

                             TMPIT  84 ev 85 
                                       ev
  gi|313126714|ref|YP_004036984.1| 176 EV 177
                                       76 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   9.4    0.0004     0.033     179     325 ..      30     178 ..      11     191 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0004
                              FUSC 179 geegaeareaararlaadilalealrsqaayesprirararal....rrllsrmlallallsslarllarlraeeaa 251
                                        +++a++ e+++ +l ++   l a ++ a++e   +r+r++ l    ++ ++++  + a l s+++ll+  +ae ++
  gi|313126714|ref|YP_004036984.1|  30 YQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLnqslQQTQGDVGHVAAELESTEKLLNHTQAELER 106
                                       44444444555555555555555555555555555555554440000445555556677777777777777777776 PP

                              FUSC 252 avpelaallaelaal.....eaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslra 323
                                       ++ +l++  ++l+++     ea+   e+le++ ++l++++++l+++++       +l +++++l ++  +l+++lr+
  gi|313126714|ref|YP_004036984.1| 107 TETSLEEKREQLESVrdnldEARSKIEELEKKNKTLEEQVAELKTENK-------ELSEEVDDLRDDRDDLQRDLRE 176
                                       666677777777776655654444455555555555555555555555.......4444444444444444444443 PP

                              FUSC 324 le 325
                                         
  gi|313126714|ref|YP_004036984.1| 177 VC 178
                                       33 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.6      0.23        19      41      85 ..      37      81 ..      19      94 .. 0.43
   2 ?   14.1   8.2   0.00022     0.019       8      90 ..      95     177 ..      90     185 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.23
                                      HHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHH CS
                             APG17 41 teflrdglkqQlkllekirkslerklekgkeefkdlikeldaane 85
                                      +e   d+l++  k l++  +s +++l+ ++e+++dl ++l++ ++
  gi|313126714|ref|YP_004036984.1| 37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQG 81
                                      222223333333333333333333333333333333333333333 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHH CS
                             APG17   8 ksLseaqtlcqrAnelltsarqeleeavkllakteflrdglkqQlkllekirkslerklekgkeefkdlikeldaan 84 
                                       k L+++q   +r++++l++ r++le+  + l++++  ++ l++  k+le+   +l+++ ++++ee++dl +++d+ +
  gi|313126714|ref|YP_004036984.1|  95 KLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQ 171
                                       55666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                                       HHHHHH CS
                             APG17  85 erLekt 90 
                                       + L++ 
  gi|313126714|ref|YP_004036984.1| 172 RDLREV 177
                                       666554 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.2    0.0076      0.64     329     403 ..      38     117 ..      15     119 .. 0.51
   2 ?    9.4  11.2    0.0043      0.36     336     411 ..     108     177 ..      95     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0076
                              FapA 329 gldepelkeklkeleeeleeleeeleklkkkikklpklka.....ekqlesekkeqlkklletkeklkeeleeleee 400
                                       + ++ +l+e+ k+l+ ele+ + el+ l+++++ l+++ +      + + +e +++ k l +t+ +l++  ++lee+
  gi|313126714|ref|YP_004036984.1|  38 ETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQqtqgdVGHVAAELESTEKLLNHTQAELERTETSLEEK 114
                                       44456666666777777777766666666665444442220000133444444444444444444444444444444 PP

                              FapA 401 lke 403
                                       +++
  gi|313126714|ref|YP_004036984.1| 115 REQ 117
                                       444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0043
                              FapA 336 keklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                         +l+e +e+le+++++l++ ++ki++l+k       +++ +eq+++l+++ ++l+ee+ +l++++++l+  l++ 
  gi|313126714|ref|YP_004036984.1| 108 ETSLEEKREQLESVRDNLDEARSKIEELEK------KNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       334455566666666666666666777777......3456789999999999**********99999999998765 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.8     0.016       1.4      32      82 ..      34      82 ..      26      92 .. 0.49
   2 ?   11.0  12.9    0.0048       0.4      14      92 ..      90     165 ..      82     186 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.016
                                      HHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH 32 qaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqe 82
                                      + +le+++++l++  ++l ++ ++   +++ + l++++++l+q++qq++++
  gi|313126714|ref|YP_004036984.1| 34 ASDLETQNDQLRERNKNLRAELES--ARTELKVLRERVNDLNQSLQQTQGD 82
                                      344444444444444444322211..2333333666666666666666644 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0048
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHH...HHHHHH CS
                              OmpH  14 spegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqka...qelqkk 86 
                                        + +++         +  qaele+ e++l++++e+l+    +l e + k +el+kk++ l+++ ++ +   +el ++
  gi|313126714|ref|YP_004036984.1|  90 LESTEKL-------LNHTQAELERTETSLEEKREQLESVRDNLdEARSKIEELEKKNKTLEEQVAELKtenKELSEE 159
                                       3333333.......455666666666666666666654444443344444444444444444222222222333333 PP

                                       HHHHHH CS
                              OmpH  87 qqellk 92 
                                         +l++
  gi|313126714|ref|YP_004036984.1| 160 VDDLRD 165
                                       333333 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   4.5       7.4   6.2e+02      27      56 ..      36      65 ..      27      81 .. 0.65
   2 ?   14.2   3.6   0.00036      0.03      21      66 .]     121     166 ..     116     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 7.4
                            GIT_CC 27 aseakiqqLlkvNtslsdelrlLQskvqkL 56
                                        e +  qL + N++l  el+    +++ L
  gi|313126714|ref|YP_004036984.1| 36 DLETQNDQLRERNKNLRAELESARTELKVL 65
                                      345555567777777777776655555555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00036
                            GIT_CC  21 lKkalaaseakiqqLlkvNtslsdelrlLQskvqkLqaeNaqlrdq 66 
                                       +  +l  + +ki++L k N+ l++++++L  + ++L +e ++lrd+
  gi|313126714|ref|YP_004036984.1| 121 VRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDD 166
                                       567788999**********************************985 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   9.7       8.6   7.2e+02      25      56 ..      38      80 ..      18     120 .. 0.46
   2 ?   13.7   5.0   0.00061     0.051      28      67 ..     118     157 ..     116     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 8.6
                              Med9 25 etktgelrhkLkkarelirelpg...........idrsveeqe 56
                                      et+ + lr + k+ r+ +++              ++ s ++ +
  gi|313126714|ref|YP_004036984.1| 38 ETQNDQLRERNKNLRAELESARTelkvlrervndLNQSLQQTQ 80
                                      5555555555444444444422222222222222222222222 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00061
                              Med9  28 tgelrhkLkkarelirelpgidrsveeqeaeieeleeqla 67 
                                       + ++r+ L++ar+ i+el+  +++ eeq ae+++ +++l 
  gi|313126714|ref|YP_004036984.1| 118 LESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELS 157
                                       5789****************************99988875 PP

>> GP41  Retroviral envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.6   0.00052     0.043      27     142 ..      37     161 ..      13     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00052
                                       HHHHHHH....HHHHHHHHHCHHHH..........HHHHHHHH....S..TTSCCHHHHHCHHH...HH..HHHHHH CS
                              GP41  27 leeqqel....dkkleaRlsAleevvrvlgedvaslktrmklq....ChanykliCvtkvPynasd.sWdkvkksLe 94 
                                       le+q++     +k+l a l+     ++vl e v++l++  +       h + +l  + ++  n ++   ++++ sLe
  gi|313126714|ref|YP_004036984.1|  37 LETQNDQlrerNKNLRAELESARTELKVLRERVNDLNQSLQQTqgdvGHVAAELEST-EKLLNHTQaELERTETSLE 112
                                       444544445559*******9999999**********987554448888888877655.5555555559********* PP

                                       HHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHH CS
                              GP41  95 giWnnt.evsydlaelhnliediqnqqektldeldkldklaqslanwfk 142
                                       +  ++   v+ +l e  ++ie+ +++++  ++++ +l+  ++ l + ++
  gi|313126714|ref|YP_004036984.1| 113 EKREQLeSVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVD 161
                                       *9999857******************99999999999988888877776 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.5     0.043       3.6      31      80 ..      35      85 ..      25      92 .. 0.73
   2 ?   12.4  15.5     0.002      0.17       2      96 ..      75     174 ..      74     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.043
                                      SSHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHH CS
                          Spectrin 31 kdleevqallk.khkaleaelaaqqervkalnelaeklldeghsaseeiee 80
                                      +dle+  ++l+ + k l+ael+++++++k l e  ++l ++ ++++ ++ +
  gi|313126714|ref|YP_004036984.1| 35 SDLETQNDQLReRNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGH 85
                                      566655555555999999999999999999999999997777777666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHHHHHHHHHHH..CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT...HT CS
                          Spectrin   2 llqqfaqdadeleeWieekeell..ssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeg...hs 73 
                                        lqq + d+ ++ + +e +e+ll  ++ +l+++ ++++++ ++++ ++++l++++ ++++l++  + l++     + 
  gi|313126714|ref|YP_004036984.1|  75 SLQQTQGDVGHVAAELESTEKLLnhTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVaelKT 151
                                       589999999999999********9888899********************************777777444445689 PP

                                       THHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  74 aseeieerleelnerWeeLkela 96 
                                       +++e++e +++l++  ++L++ +
  gi|313126714|ref|YP_004036984.1| 152 ENKELSEEVDDLRDDRDDLQRDL 174
                                       99*****************9876 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   3.6   0.00045     0.038      30      71 .]      36      77 ..      33      77 .. 0.92
   2 ?   10.0   3.9    0.0088      0.74      33      66 ..     144     177 ..     138     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00045
                          JIP_LZII 30 dLIarvdeLtsereiLreEleslqkakerlesrikelEeelk 71
                                      dL ++ d+L ++++ Lr Eles +++++ l++r+++l + l+
  gi|313126714|ref|YP_004036984.1| 36 DLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQ 77
                                      666788********************************9985 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0088
                          JIP_LZII  33 arvdeLtsereiLreEleslqkakerlesrikel 66 
                                       ++v eL++e++ L+eE++ l++ ++ l+  ++e+
  gi|313126714|ref|YP_004036984.1| 144 EQVAELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       799*************************999997 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   7.3    0.0033      0.28      18      65 ..      32      79 ..      26      89 .. 0.90
   2 ?    5.8   7.1      0.17        14       6      55 ..      90     146 ..      83     152 .. 0.52
   3 ?   10.4   4.3    0.0063      0.53       4      51 ..     130     177 ..     127     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0033
                     TolA_bind_tri 18 qlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDer 65
                                      ++  +l +q ++l++  + LR ++E  + +l+ l+er +dl + l + 
  gi|313126714|ref|YP_004036984.1| 32 SSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQT 79
                                      67789************************************9998875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.17
                     TolA_bind_tri   6 varLErilears.......qlllelqqqlealqqelreLRGqiEelqyqleqleerQ 55 
                                       +++ E++l++ +        +l e  +qle+ +  l+e R +iEel+ ++++lee+ 
  gi|313126714|ref|YP_004036984.1|  90 LESTEKLLNHTQaelerteTSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQV 146
                                       666666666655222222233334445555556666666666666666666665554 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0063
                     TolA_bind_tri   4 drvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleql 51 
                                       +++++LE++ +  ++   el ++ ++l++e+++LR + ++lq +l+++
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       679999999999999999999999***********9999999999876 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  16.5     0.033       2.8      22     122 ..      39     138 ..      33     148 .. 0.64
   2 ?    4.3   2.7      0.58        49      22      55 ..     140     173 ..     133     182 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.033
                             HrpB7  22 aeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegrvraaeaelaaa 98 
                                        +  + r++ +++ a+l++a ++++  r++v++ +++l+++ +     ++a++ + + ++ + +++++  e  l+  
  gi|313126714|ref|YP_004036984.1|  39 TQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDV-GHVAAELESTEKLLNHTQAELERTETSLEEK 114
                                       455566777777777777777777777777777777777765444.4677777777777777777777777777777 PP

                             HrpB7  99 rqaldaaedavaatarkiaRndaq 122
                                       r++l+  +d++ + + ki  ++ +
  gi|313126714|ref|YP_004036984.1| 115 REQLESVRDNLDEARSKIEELEKK 138
                                       777777777777777666655544 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.58
                             HrpB7  22 aeleaaraalaaaeaalaaaqaqveaardavrah 55 
                                         le++ a+l++++++l +  + ++ +rd++++ 
  gi|313126714|ref|YP_004036984.1| 140 KTLEEQVAELKTENKELSEEVDDLRDDRDDLQRD 173
                                       4567777777777777777777777777777665 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  25.7    0.0064      0.53     234     376 ..      32     162 ..      26     184 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0064
                            DUF812 234 srlteeeykkrkkeklqkrlaeqlrkaalkseeaessasksksdlaellsefseksetdslktkgsrfthaekl.qf 309
                                       s+ ++ e ++++ ++ +k+l ++l++a ++ +       ++ +dl+++l++ + +     + + +++++++ekl + 
  gi|313126714|ref|YP_004036984.1|  32 SSASDLETQNDQLRERNKNLRAELESARTELKV----LRERVNDLNQSLQQTQGD-----VGHVAAELESTEKLlNH 99 
                                       445555555555666666666666655433332....234455666666665222.....23344666666666333 PP

                            DUF812 310 tkeelakkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeenee 376
                                       t++e    ++te  l++kre +le+++++++e++skieele++ k+le+++ +++ e +e+ ee   
  gi|313126714|ref|YP_004036984.1| 100 TQAE---LERTETSLEEKRE-QLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDD 162
                                       3332...2234444444443.4455555555555555555555555555555555555554444443 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  17.5     0.002      0.17       8      75 ..     105     172 ..     101     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.002
                               ERM   8 releerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeee 75 
                                       ++ e  L++ +e+ e  +++L e+  ++e+L++k++ +ee+  +L+ +++e+ ee + l+ ++ + ++
  gi|313126714|ref|YP_004036984.1| 105 ERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       5567899999************************************************9998877555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.9      0.15        12      24     100 ..      43     119 ..      29     121 .. 0.82
   2 ?   11.8  10.4    0.0031      0.26      31      96 ..      99     164 ..      93     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.15
                                       HHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHH CS
                             DUF16  24 qlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlD 100
                                       ql e  ++  ++L+   +++++l e++n l+q  ++ +  + +  +e +  ++ ln+ +  le    +L++  + l 
  gi|313126714|ref|YP_004036984.1|  43 QLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLE 119
                                       455555556789999999999*************9999999999999999999999888888888888877766665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0031
                                       .BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHH CS
                             DUF16  31 snkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkin 96 
                                        ++++L++ e+ ++ + eq++ + ++ ++   ki+el+++ k+ +e++ +++   + + e ++++ 
  gi|313126714|ref|YP_004036984.1|  99 HTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLR 164
                                       577888888888888888888888888888888888888888888888866666666666555554 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.8    0.0071      0.59      44      95 ..      38      89 ..      26      92 .. 0.74
   2 ?   13.2  17.7    0.0013      0.11      16      99 .]      74     156 ..      70     156 .. 0.94
   3 ?    3.5   0.4       1.3   1.1e+02      24      50 ..     148     174 ..     145     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0071
                    HIP1_clath_bdg 44 erkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqaE 95
                                      e + ++ +e  ++L++ele+ r+el+ l++ +++ +qs +q +  +    aE
  gi|313126714|ref|YP_004036984.1| 38 ETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAE 89
                                      3344445566678999999999999999999999999999988887777666 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.0013
                    HIP1_clath_bdg  16 svarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaL 92 
                                       ++ +q+q +v  +  ele   e+l ++++ +le  ++ le+ +++le+ r++l++++s +e+ e+++++l++q+a+L
  gi|313126714|ref|YP_004036984.1|  74 QSLQQTQGDVGHVAAELES-TEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAEL 149
                                       5679*************86.58999999************************************************* PP

                    HIP1_clath_bdg  93 qaEkesL 99 
                                       ++E+++L
  gi|313126714|ref|YP_004036984.1| 150 KTENKEL 156
                                       ***9887 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 1.3
                    HIP1_clath_bdg  24 everekkeleeelerlkeeaerkleeq 50 
                                       e+++e kel+ee+++l+++++   ++ 
  gi|313126714|ref|YP_004036984.1| 148 ELKTENKELSEEVDDLRDDRDDLQRDL 174
                                       677788888888888887776655554 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.2     0.051       4.2      73     118 ..      30      76 ..      26      80 .. 0.78
   2 ?    7.1   9.7     0.077       6.4      39     103 ..      73     137 ..      64     141 .. 0.75
   3 ?    7.8  15.6     0.044       3.7      28     100 ..     101     176 ..      92     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.051
                             THOC7  73 yeaekeeieseieavreeieelkaqLeearatra.nrkeydelaekI 118
                                       y+   +++e++  ++re +++l+a+Le ar++++  r+ ++ l + +
  gi|313126714|ref|YP_004036984.1|  30 YQSSASDLETQNDQLRERNKNLRAELESARTELKvLRERVNDLNQSL 76 
                                       78888899999999999999999999999998873466666666555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.077
                             THOC7  39 eqlkedllldfaafelsierlqllakanerereryeaekeeieseieavreeieelkaqLeeara 103
                                        q  ++ + d+     ++e ++ l++ ++ e er e+  ee  +++e+vr++ +e ++++ee  +
  gi|313126714|ref|YP_004036984.1|  73 NQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEK 137
                                       45555666666677777888888888888888888888888888888888888888888888765 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.044
                             THOC7  28 tsla...esteeeleqlkedllldfaafelsierlqllakanerereryeaekeeieseieavreeieelkaqLee 100
                                       +++    e++ ee ++  e++  ++ + ++ ie l+  +k+ e++++++++e++e+ +e  ++r++ ++l+ +L e
  gi|313126714|ref|YP_004036984.1| 101 QAELertETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       22224446668999999999999***********************************************999976 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   0.00053     0.045      31      54 .]      31      54 ..      28      54 .. 0.91
   2 ?    0.8   0.4       6.4   5.4e+02      35      49 ..      63      77 ..      55      82 .. 0.48
   3 ?   11.6   4.7    0.0027      0.23      30      54 .]     128     152 ..     119     152 .. 0.84
   4 ?    3.7   0.2       0.8        67      25      46 ..     151     172 ..     150     177 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00053
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 31 eervkeLeeeNaqLrqkveqLeke 54
                                      ++ + +Le++N+qLr+++++L++e
  gi|313126714|ref|YP_004036984.1| 31 QSSASDLETQNDQLRERNKNLRAE 54
                                      56789****************987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 6.4
                                      HHHHHHHHHHHHHHH CS
                            bZIP_2 35 keLeeeNaqLrqkve 49
                                      k L+e+ + L q ++
  gi|313126714|ref|YP_004036984.1| 63 KVLRERVNDLNQSLQ 77
                                      333444444433333 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  30 leervkeLeeeNaqLrqkveqLeke 54 
                                         ++++eLe++N +L+++v++L++e
  gi|313126714|ref|YP_004036984.1| 128 ARSKIEELEKKNKTLEEQVAELKTE 152
                                       5678999999999999999999987 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.8
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  25 akeeeleervkeLeeeNaqLrq 46 
                                        +++el e+v +L+ + + L++
  gi|313126714|ref|YP_004036984.1| 151 TENKELSEEVDDLRDDRDDLQR 172
                                       4566777777777766666654 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.3     0.019       1.6      65     119 ..      41      94 ..      21      96 .. 0.84
   2 ?   13.2   8.9     0.001     0.087      67     128 .]      77     138 ..      62     138 .. 0.86
   3 ?    7.7   4.2     0.051       4.3      78     120 ..     130     172 ..     129     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.019
                            DUF641  65 kkkaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeae 119
                                       +++  ++++++l+ae++  r  lk++  +v++l++ l++ + ++ ++ ++Le++e
  gi|313126714|ref|YP_004036984.1|  41 NDQL-RERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTE 94 
                                       2222.389999************************************99999876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.001
                            DUF641  67 kaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkklekr 128
                                       ++++ +  +++ae++   +ll+  ++ +++ e+ l++k++++e+++++L+ea+++ ++lek+
  gi|313126714|ref|YP_004036984.1|  77 QQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKK 138
                                       222478899***************************************************98 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.051
                            DUF641  78 aeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaek 120
                                       ++i+e+ ++ kt+e  v +l++e k+  +e++ L++  +++++
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       689999****************************998777665 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.3     0.079       6.6      79     122 ..      30      73 ..      26      74 .. 0.93
   2 ?    9.6  11.3     0.012         1       8      96 ..      97     184 ..      90     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.079
                           DUF5082  79 yqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                       yq + ++l++  d++ e  ++L+ ++++a + l+ l + +n+l+
  gi|313126714|ref|YP_004036984.1|  30 YQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLN 73 
                                       8999999**********************************997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.012
                           DUF5082   8 lqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvd 84 
                                       l++ +ael+ +  +leek e L+++++ l+++ +++++ +kk ++ + + +++k ++ ++ ++++ +l ++ +  ++
  gi|313126714|ref|YP_004036984.1|  97 LNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTEN-KELSEEVDDLRDDRDDLQR 172
                                       688899999999999999999999999999999999999999999999998887655.4456666788888888888 PP

                           DUF5082  85 kldelidaieeE 96 
                                       +l+e+ d  +eE
  gi|313126714|ref|YP_004036984.1| 173 DLREVCDDWSEE 184
                                       888888776666 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  14.2    0.0029      0.24      72     168 ..      42     138 ..      30     150 .. 0.66
   2 ?   10.5   8.0    0.0045      0.38      59     121 ..      92     154 ..      86     179 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0029
                            DUF745  72 reaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRv 148
                                           +  ++  ++l+s+ + +k+ ++ +++ +q+l++ +  + ++ ++le++e++ ++ q+el+  ++ le+ ++++
  gi|313126714|ref|YP_004036984.1|  42 DQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQL 118
                                       44444444555666677777777777777777777777777777777777777777777777777777777777777 PP

                            DUF745 149 eeLkkqlkearkdlektkka 168
                                       e+++ +l+ear+  e+ +k+
  gi|313126714|ref|YP_004036984.1| 119 ESVRDNLDEARSKIEELEKK 138
                                       77777777777766666554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0045
                            DUF745  59 GKqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenle 121
                                         + l++++++el+ +e+ ++e  ++l+s   n++ a++  ++ +++ ++l++ +++ k++ +
  gi|313126714|ref|YP_004036984.1|  92 STEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENK 154
                                       444455555555555555555555555555555555555555555555555554444443332 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   7.8    0.0044      0.37      30     103 ..      46     123 ..      35     124 .. 0.82
   2 ?    9.6   6.2    0.0027      0.23      37      92 ..     116     171 ..     112     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0044
                              COG6  30 kineefleefqpvaeqLkriesdveklnelcdemkk...klssakeetsdlleeae.eLkeekkklelkqkllkafl 102
                                       + n++  +e++ ++++Lk ++++v++ln++ ++++    ++ +  e+t++ll++++ eL++++++le+k++ l++ +
  gi|313126714|ref|YP_004036984.1|  46 ERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGdvgHVAAELESTEKLLNHTQaELERTETSLEEKREQLESVR 122
                                       4577777899************************963336778889999999998637*************999877 PP

                              COG6 103 k 103
                                       +
  gi|313126714|ref|YP_004036984.1| 123 D 123
                                       6 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0027
                              COG6  37 eefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkle 92 
                                       e+++ v+++L++ +s++e+l++ ++++++++ + k+e+++l ee+++L+ ++++l+
  gi|313126714|ref|YP_004036984.1| 116 EQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQ 171
                                       68899*********************************************999876 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  20.8    0.0096       0.8     164     263 ..      53     152 ..      27     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0096
                        Fmp27_WPPW 164 kendpervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkese 240
                                       +e +++r+  ++l+eR+++l++++++++ +++++  + e++++ l++   ele++  +l+ek+e le++ ++l+e +
  gi|313126714|ref|YP_004036984.1|  53 AELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEAR 129
                                       55678899********************************999999999999999999********99999999998 PP

                        Fmp27_WPPW 241 esseeeeskskelsaastsesfs 263
                                       ++ ee e+k+k+l+++  + +++
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTE 152
                                       86664444333333332222222 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  26.8    0.0012       0.1      41     164 ..      33     158 ..      21     165 .. 0.79
   2 ?    9.1  16.6    0.0093      0.78      45     133 ..      86     173 ..      79     187 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0012
                         Golgin_A5  41 sstalsaeldelkqerdllreelqklnqqieqlrtelqdlea...qqqaeaeslreqlqeleeqleeerkakeevea 114
                                       s+  l+++ d+l+++++ lr+el++++++++ lr  ++dl++   q+q ++ ++  +l++ e+ l++ +++ e++e+
  gi|313126714|ref|YP_004036984.1|  33 SASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQslqQTQGDVGHVAAELESTEKLLNHTQAELERTET 109
                                       44557788899999999****************99999998722144557778888888889999999999999999 PP

                         Golgin_A5 115 elerlkeelryleeelvrskatlqsrikdrekeieklrnqlttkslssss 164
                                        le+++e+l++++++l +++++++ ++++++k +e++ ++l+t++++ s+
  gi|313126714|ref|YP_004036984.1| 110 SLEEKREQLESVRDNLDEARSKIE-ELEKKNKTLEEQVAELKTENKELSE 158
                                       99**********999998887765.5778888888888888877665444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0093
                         Golgin_A5  45 lsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlke 121
                                       ++ael+++++  +++++el+++++++e+ r +l+ + ++   ea+s  e+l++ +++lee+ ++ ++ ++el++  +
  gi|313126714|ref|YP_004036984.1|  86 VAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNL-DEARSKIEELEKKNKTLEEQVAELKTENKELSEEVD 161
                                       4566777777777777777777777777777776666554.455554555555555555555555555555555555 PP

                         Golgin_A5 122 elryleeelvrs 133
                                       +lr  +++l+r 
  gi|313126714|ref|YP_004036984.1| 162 DLRDDRDDLQRD 173
                                       555555555543 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.3    0.0043      0.36       6      66 ..      37      96 ..      28     102 .. 0.54
   2 ?   13.4  27.4   0.00045     0.038       4     126 ..      56     178 ..      53     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0043
                       Tropomyosin  6 veeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekL 66
                                      +e++ d+ +er +++ ++le+a+ + +   + v  ln+++q++  ++ ++  +le+ +ekL
  gi|313126714|ref|YP_004036984.1| 37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELES-TEKL 96
                                      45555555555555555555555555555555555555555555555555555555.3444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00045
                       Tropomyosin   4 kqveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaadeserar 80 
                                       +++++el   +er ++++++l++++    +  aE ++ ++ ++ + +elerte+ lee+ e+Le +  + de    +
  gi|313126714|ref|YP_004036984.1|  56 ESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKI 132
                                       6778999999******************************************************************* PP

                       Tropomyosin  81 KvlEnrelkdeekleeleaqlkeakeiaeeadrkyeEvarklvvve 126
                                         lE+++   ee+++el ++ ke  e  ++  +  +  +r l  v 
  gi|313126714|ref|YP_004036984.1| 133 EELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVC 178
                                       *******************999988877777777777777666655 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.8     0.039       3.2      18      91 ..      21      94 ..       9     110 .. 0.76
   2 ?    7.9   6.5     0.037       3.1      35      78 ..     108     151 ..      98     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.039
                          RasGAP_C 18 lgvisrennyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkk 91
                                      +g +     yq+  +++++   +++++ ++ ++Eles+++ lk L+e+ n l++ l++ +  + +v ++l++++
  gi|313126714|ref|YP_004036984.1| 21 TGTVGATMMYQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTE 94
                                      56666666788888888888888889999999999999999999999999999999999988888888887774 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.037
                          RasGAP_C  35 akdirnkgrlrekrkeElesleetlktLseknnylesqlesYka 78 
                                       ++ + +k+++ e+++  l+ +++ +++L++kn+ le+q++++k+
  gi|313126714|ref|YP_004036984.1| 108 ETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKT 151
                                       5668899999*****************************99886 PP

>> zf-CpG_bind_C  CpG binding protein zinc finger C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.4      0.11       8.8      16      64 ..      30      81 ..      25     105 .. 0.72
   2 ?   11.2  10.9    0.0028      0.23       9      80 ..      97     169 ..      88     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.11
                     zf-CpG_bind_C 16 wqssps...vaeeenkkklekirkeqeeakkklkelekklkkLeeliekakk 64
                                      +qss s   + +++ +++ +++r e e+a+++lk l ++ ++L++ +++++ 
  gi|313126714|ref|YP_004036984.1| 30 YQSSASdleTQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQG 81
                                      45555522244556677889999*********************99987654 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0028
                     zf-CpG_bind_C   9 LpqriqewqsspsvaeeenkkklekirkeqeeakkklkelekklkkLeeliekakklslkeeeeee..edeeds 80 
                                       L +  +e +++++++e e++++le++r +  ea++k++elekk k+Lee +++ k+ + + +ee +  +d++d+
  gi|313126714|ref|YP_004036984.1|  97 LNHTQAELERTETSLE-EKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDdlRDDRDD 169
                                       4444455555666665.56899******************************9988755444443312443332 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.3      0.12        10      32      62 ..      33      63 ..      26      64 .. 0.90
   2 ?   11.9   1.5    0.0026      0.22      24      70 ..      60     106 ..      58     107 .. 0.91
   3 ?    2.4   5.4       2.5   2.1e+02      13      47 ..      95     129 ..      94     142 .. 0.75
   4 ?    8.4   5.9     0.032       2.7      10      56 ..     137     183 ..     133     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.12
                               CLZ 32 kverLessLeaLqtrlarLlaeyessqrkLk 62
                                       ++ Le++ ++L  r + L ae+es+ ++Lk
  gi|313126714|ref|YP_004036984.1| 33 SASDLETQNDQLRERNKNLRAELESARTELK 63
                                      67889**********************9998 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0026
                               CLZ  24 aeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqRitkLEk 70 
                                       +e k l e+v+ L++sL++ q  +  + ae+es+++ L++  ++LE+
  gi|313126714|ref|YP_004036984.1|  60 TELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELER 106
                                       5667899*******************************999999986 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 2.5
                               CLZ  13 glLDeeaakagaeqkeleekverLessLeaLqtrl 47 
                                        lL  + a+ + ++ +leek e+Les  ++L+   
  gi|313126714|ref|YP_004036984.1|  95 KLLNHTQAELERTETSLEEKREQLESVRDNLDEAR 129
                                       68888889999999999999999999888876544 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.032
                               CLZ  10 lKdglLDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyes 56 
                                        K   L+e++a+ ++e+kel e v+ L    + Lq  l+ + ++ ++
  gi|313126714|ref|YP_004036984.1| 137 KKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDDWSE 183
                                       57889******************************999988877665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.1     0.072         6      21      86 ..      62     134 ..       8     136 .. 0.75
   2 ?    7.2   6.0      0.07       5.9      23      69 ..     120     166 ..      94     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.072
                            DUF948  21 llklkktldeaaatieelekqvdpilkeve...dllakvne....lledvneklekvdplteavadlgesvse 86 
                                       l+ l++ ++ +++++++++ +v+ +  e+e   +ll+++++    +   ++ek e+++++ +++ ++  +++e
  gi|313126714|ref|YP_004036984.1|  62 LKVLRERVNDLNQSLQQTQGDVGHVAAELEsteKLLNHTQAelerTETSLEEKREQLESVRDNLDEARSKIEE 134
                                       5667889999999999999888888777551114555555533333334444777777777776666666665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.07
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklek 69 
                                       ++++ ldea++ ieelek+ + + ++v++l ++ +el e+v +  ++
  gi|313126714|ref|YP_004036984.1| 120 SVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDD 166
                                       56778888888888888888877777777777777777777654444 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.9    0.0038      0.32      43      84 ..      39      80 ..      27      86 .. 0.72
   2 ?    8.5   4.3     0.024         2      43      82 ..      88     127 ..      82     131 .. 0.84
   3 ?    5.5   7.0      0.19        16      40      78 ..     127     165 ..     124     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0038
                                      HHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXX CS
                             Sec2p 43 kekealekkneklkeqLkeketlleslqeqLkeLkevlekme 84
                                       ++++l+++n++l+++L+ ++t l+ l e  ++L + l++ +
  gi|313126714|ref|YP_004036984.1| 39 TQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQ 80
                                      566777777777777777777777777777777777777765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTT CS
                             Sec2p  43 kekealekkneklkeqLkeketlleslqeqLkeLkevlek 82 
                                        e e+ ek  ++ +++L+ +et le++ eqL++ ++ l +
  gi|313126714|ref|YP_004036984.1|  88 AELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDE 127
                                       56778899999********************999988766 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHH CS
                             Sec2p  40 aarkekealekkneklkeqLkeketlleslqeqLkeLke 78 
                                       +ar + e+lekkn+ l+eq++e +t  ++l+e+  +L++
  gi|313126714|ref|YP_004036984.1| 127 EARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRD 165
                                       578888999999999999999999999999999999986 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.6      0.07       5.9       9      47 ..      37      75 ..      31      79 .. 0.90
   2 ?   10.0   7.3    0.0094      0.79       3      47 ..     101     145 ..      99     146 .. 0.92
   3 ?    8.2   4.1     0.034       2.8       2      40 ..     142     180 ..     141     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.07
                              XhlA  9 ietkldnleervdkleekaaeaeekiknleedlkklesn 47
                                      +et+ d l er + l    + a++++k l e++++l ++
  gi|313126714|ref|YP_004036984.1| 37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQS 75
                                      7999999999999999******************99876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0094
                              XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkklesn 47 
                                       + +ler+et l++  e+++ + ++ +ea++ki++le++ k le++
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQ 145
                                       678**********************************98888875 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.034
                              XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleed 40 
                                       ++e +++++t+ ++l+e+vd+l ++ +  +  + ++++d
  gi|313126714|ref|YP_004036984.1| 142 LEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDD 180
                                       5899******************************99987 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4     0.019       1.6      11      73 ..      21      81 ..       8      89 .. 0.47
   2 ?    5.5   1.9      0.19        16      40      82 ..      90     132 ..      85     134 .. 0.89
   3 ?    7.1   2.7     0.059         5      37      78 ..     136     177 ..     127     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.019
                           DUF4446 11 villillivllvklkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieelee 73
                                        ++ ++++   + + l+++ ++l   +++k+l   l++  +e++ l+e++++l++++++ + 
  gi|313126714|ref|YP_004036984.1| 21 TGTVGATMMYQSSASDLETQNDQLR--ERNKNLRAELESARTELKVLRERVNDLNQSLQQTQG 81
                                      2222233333334444444444443..355666666666666666666666666666665554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.19
                           DUF4446  40 gksleellkekleeveelkeeseelekeieeleeklkkslqkv 82 
                                        +s e+ll+++ +e+e+ +++ ee ++++e+++++l+++ +k+
  gi|313126714|ref|YP_004036984.1|  90 LESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKI 132
                                       578999****************************999988886 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.059
                           DUF4446  37 gkdgksleellkekleeveelkeeseelekeieeleeklkks 78 
                                       +k++k+lee+++e  +e +el+ee+++l+++ ++l+++l++ 
  gi|313126714|ref|YP_004036984.1| 136 EKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       357888888888888888888888888888888888888776 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.2     0.053       4.5     152     198 ..      33      79 ..      24      85 .. 0.85
   2 ?    9.4  21.9    0.0063      0.53     175     264 ..      88     177 ..      77     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.053
                           DUF4686 152 ekkqLeekikeaseneaklkqqlqeeqqkrklLdqnveeLqqqvrsl 198
                                       + + Le +  +++e +++l+++l+  + + k+L ++v++L q ++  
  gi|313126714|ref|YP_004036984.1|  33 SASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQT 79 
                                       56789999999999999999999999999999999999999988765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0063
                           DUF4686 175 qeeqqkrklLdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlkklenekrksdehl....ksnqeLsekL 247
                                        e  ++ klL+++  eL +   sl++k +qle +  ++    +++  ++++le+++++ +e++      n+eLse++
  gi|313126714|ref|YP_004036984.1|  88 AELESTEKLLNHTQAELERTETSLEEKREQLESVRDNL----DEARSKIEELEKKNKTLEEQVaelkTENKELSEEV 160
                                       57788899999999999999999999999999887766....57777777777777777777667767889999999 PP

                           DUF4686 248 sslqqekealqeelqqv 264
                                         l+ + + lq++l++v
  gi|313126714|ref|YP_004036984.1| 161 DDLRDDRDDLQRDLREV 177
                                       99999999999988876 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  10.7      0.24        20      32      96 ..      38     105 ..      20     119 .. 0.62
   2 ?    7.0  15.1       0.1       8.5      10      84 ..      86     159 ..      69     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.24
                      Syntaxin-6_N  32 ssstseeldetrteLrkalrsiewdledLeetvrivek....npskfkidekelsrrrafveevreevk 96 
                                       + +++++l+e +++Lr++l+s++++l+ L+e v+ +++     + +++  ++el++ ++++++++ e++
  gi|313126714|ref|YP_004036984.1|  38 E-TQNDQLRERNKNLRAELESARTELKVLRERVNDLNQslqqTQGDVGHVAAELESTEKLLNHTQAELE 105
                                       2.3589999999999999999999999999999644433332444455555555555555555555544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.1
                      Syntaxin-6_N  10 VqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrr 84 
                                       V  +l+++e+l++  +  le t++s  ee +e+ + +r +l++++ ++e+Le+  +++e++ ++ k ++kels+ 
  gi|313126714|ref|YP_004036984.1|  86 VAAELESTEKLLNHTQAELERTETS-LEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEE 159
                                       7788999999999987545554444.8888999999999********************************9975 PP

>> Oleosin  Oleosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.047       3.9      43     106 ..       7      70 ..       3      89 .. 0.76
   2 ?    3.1   0.2      0.94        79      81     105 ..     115     139 ..      84     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.047
                           Oleosin  43 PvlvPaaiviaLavagflasgafgvaalsslswlykyvrgkhpagadkldqakrrladkasevk 106
                                       P+ + ++ v+aL+++g + ++++  +  s l     ++r+++++   +l++a+ +l+   + v+
  gi|313126714|ref|YP_004036984.1|   7 PINLALVAVVALLLTGTVGATMMYQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVN 70 
                                       6666677778888888888888888888888888888888889999999999888765555444 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.94
                           Oleosin  81 rgkhpagadkldqakrrladkasev 105
                                       r++ + + d+ld+a++++++  ++ 
  gi|313126714|ref|YP_004036984.1| 115 REQLESVRDNLDEARSKIEELEKKN 139
                                       4556677888899998887765554 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.6     0.063       5.3      96     135 ..      28      71 ..      20      72 .. 0.70
   2 ?    4.0   6.9      0.59        50      34      99 ..      44      80 ..      42     114 .. 0.49
   3 ?   11.4   4.4    0.0032      0.27      40      86 ..     113     158 ..     108     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.063
                                       HHHTT-SS---SSHHHHHHHHHHHHHHHS-H....HH.HHHHHH CS
                             Nup54  96 eilrsrgyaldaeEeelrarletleaqlndp....aqlkgrvne 135
                                        +++s+++ l+++ ++lr+r ++l a+l++     ++l+ rvn+
  gi|313126714|ref|YP_004036984.1|  28 MMYQSSASDLETQNDQLRERNKNLRAELESArtelKVLRERVND 71 
                                       46688888888888888888888888888633334566666665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.59
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                             Nup54 34 LakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilr 99
                                      L++R k  ++e++ +r  lk +++r+++l+                             + l+  +
  gi|313126714|ref|YP_004036984.1| 44 LRERNKNLRAELESARTELKVLRERVNDLN-----------------------------QSLQQTQ 80
                                      444444444444444444444444444444.............................4444333 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  40 aQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelsh 86 
                                         +++++  r  l+e ++++eele k++ ++ ++++++k++++els+
  gi|313126714|ref|YP_004036984.1| 113 EKREQLESVRDNLDEARSKIEELE-KKNKTLEEQVAELKTENKELSE 158
                                       568999******************.********************97 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  23.8      0.22        18      77     224 ..      35     175 ..      23     179 .. 0.44

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.22
                           DUF4618  77 ekeekklekLeqqleqlnakvqklqeelnvLstYkDkeYpvkavqIanlvrqlqqlkds...qqdeldeleeli... 147
                                       + +e +  +L++  ++l a+++++++el+vL+            ++  l ++lqq++ +      el+ +e+l+   
  gi|313126714|ref|YP_004036984.1|  35 SDLETQNDQLRERNKNLRAELESARTELKVLRE-----------RVNDLNQSLQQTQGDvghVAAELESTEKLLnht 100
                                       333333344444444444444444444444443...........233333333333222110123333333333000 PP

                           DUF4618 148 kevleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqae 224
                                       +++le  ++++++k+e+l  s +++ l++ ++ +++   +n++l++++++ + + +el ee+++L+ + ++Lq++ +
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLE-S-VRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       3333333333333333332.2.3555566666666666666666666666666666666666666666666665555 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   9.1     0.017       1.4      21     102 ..      26     112 ..       8     117 .. 0.68
   2 ?    5.0   7.2      0.27        22      24      75 ..      95     149 ..      82     152 .. 0.75
   3 ?    6.0   1.8      0.14        12      28      74 ..     130     176 ..     120     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.017
                           DUF1043  21 sklkkqkklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeL......lpeleeqelfqq 91 
                                       + +   ++ + +le+++++l e +++l   ++++++ L+ l e+ ++L+q l++++         l + e+  +  q
  gi|313126714|ref|YP_004036984.1|  26 A-TMMYQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVghvaaeLESTEKLLNHTQ 101
                                       2.2334455679999999999999999999************************99999777665444555555555 PP

                           DUF1043  92 kkleekkaeae 102
                                       ++le ++ + e
  gi|313126714|ref|YP_004036984.1| 102 AELERTETSLE 112
                                       55555554443 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.27
                           DUF1043  24 kkqkklekelekakaeleeqkqele...dHfaqsaelLetlaedyqkLyqhlaks 75 
                                       k  + +++ele++++ lee +++le   d ++++++ +e+l+++ ++L +++a+ 
  gi|313126714|ref|YP_004036984.1|  95 KLLNHTQAELERTETSLEEKREQLEsvrDNLDEARSKIEELEKKNKTLEEQVAEL 149
                                       5556778888888888888888876333679999999***********9999985 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.14
                           DUF1043  28 klekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlak 74 
                                       +  +elek++++leeq +el++  ++ +e +++l +d ++L++ l +
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       55579999999999999999999999999999999999999988865 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.2       0.1       8.5       4      43 ..      33      72 ..      30      79 .. 0.65
   2 ?    2.0   8.4       2.7   2.2e+02       6      47 ..      98     139 ..      65     141 .. 0.70
   3 ?   10.6   3.7    0.0054      0.46       1      41 [.     135     175 ..     129     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.1
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                              Swi5  4 eikeleeqleelekelaelkeelkekkdpeetvkrhIklL 43
                                      + ++le q ++l++  ++l++el++  +  +++++ ++ L
  gi|313126714|ref|YP_004036984.1| 33 SASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDL 72
                                      5566777777777777777777776666666666665555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHH CS
                              Swi5   6 keleeqleelekelaelkeelkekkdpeetvkrhIklLheYN 47 
                                       +  +++le++e++l+e +e+l++  d  ++ +++I+ L + N
  gi|313126714|ref|YP_004036984.1|  98 NHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKN 139
                                       344566666666666666666666677777777777776655 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0054
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHH CS
                              Swi5   1 leaeikeleeqleelekelaelkeelkekkdpeetvkrhIk 41 
                                       le+++k+leeq++el++e +el+ee ++  d  + ++r ++
  gi|313126714|ref|YP_004036984.1| 135 LEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       57889999999999999999999999988888888887776 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.0     0.064       5.4      24      44 ..      35      55 ..      31      59 .. 0.87
   2 ?    4.7   0.5      0.46        39      13      34 ..      59      80 ..      57      96 .. 0.89
   3 ?   12.0   6.1    0.0024       0.2      12      42 ..     121     151 ..     114     157 .. 0.91
   4 ?    3.9   0.3       0.8        67      14      32 ..     158     176 ..     155     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.064
                             TSC22 24 keLeernseleeENslLkala 44
                                       +Le +n +l+e N+ L+a +
  gi|313126714|ref|YP_004036984.1| 35 SDLETQNDQLRERNKNLRAEL 55
                                      69****************876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.46
                             TSC22 13 rEeVevLkekIkeLeernsele 34
                                      r e  vL+e++ +L +  ++ +
  gi|313126714|ref|YP_004036984.1| 59 RTELKVLRERVNDLNQSLQQTQ 80
                                      77899*********99999877 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.0024
                             TSC22  12 VrEeVevLkekIkeLeernseleeENslLka 42 
                                       Vr+  ++ ++kI eLe++n++lee+ + Lk+
  gi|313126714|ref|YP_004036984.1| 121 VRDNLDEARSKIEELEKKNKTLEEQVAELKT 151
                                       9************************999996 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.8
                             TSC22  14 EeVevLkekIkeLeernse 32 
                                       EeV+ L++   +L+ + +e
  gi|313126714|ref|YP_004036984.1| 158 EEVDDLRDDRDDLQRDLRE 176
                                       9*******99999988776 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.6     0.068       5.7      16      98 ..      54     134 ..      29     137 .. 0.61
   2 ?    7.8   3.7     0.067       5.6      25      74 ..     119     168 ..     110     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.068
                      Occludin_ELL  16 eFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshi 92 
                                       e ++  +e k l ++++++++ +++ + ++ + + + + ++k+ ++ + e+++   +++  ek++++e  ++ L+  
  gi|313126714|ref|YP_004036984.1|  54 ELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERT--ETSLEEKREQLESVRDNLDEA 128
                                       333333445555555555555555555555555555555555555555555555..566667777777777777777 PP

                      Occludin_ELL  93 Kklike 98 
                                       +++i+e
  gi|313126714|ref|YP_004036984.1| 129 RSKIEE 134
                                       766665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.067
                      Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpe 74 
                                        ++ ++l+e+++k++eLe++ k+l+e+  e k+ ++e+ +e  +l+ d++
  gi|313126714|ref|YP_004036984.1| 119 ESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRD 168
                                       45667788888888888888888888888888888888888888776543 PP

>> SOGA  Protein SOGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  14.4    0.0017      0.14       2      95 .]      48     142 ..      47     142 .. 0.90
   2 ?    4.8   0.6      0.77        65      19      53 ..     142     176 ..     140     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0017
                              SOGA   2 aaeLrrhLqfveeEaeLlrrslseleeenkqlteeLnkyksklgeeessleeeeea.ssdsskeaelkeeLklarlq 77 
                                       +++Lr  L+ +  E ++lr ++ +l++  +q + ++ +   +l+++e+ l++++++ ++ +++ +e +e+L+++r +
  gi|313126714|ref|YP_004036984.1|  48 NKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAElERTETSLEEKREQLESVRDN 124
                                       578*********************************************999987551445566788999******** PP

                              SOGA  78 ineLsgkvvkLqvenrvL 95 
                                        +e   k+ +L+ +n+ L
  gi|313126714|ref|YP_004036984.1| 125 LDEARSKIEELEKKNKTL 142
                                       ***************987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.77
                              SOGA  19 lrrslseleeenkqlteeLnkyksklgeeesslee 53 
                                       l  +++el+ enk+l ee+  ++ + ++ ++ l+e
  gi|313126714|ref|YP_004036984.1| 142 LEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       56688999999999999999888887777666654 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   9.3     0.041       3.5      69     150 ..      35     119 ..      30     126 .. 0.81
   2 ?    7.8  13.1      0.03       2.5      51     120 ..     101     170 ..      94     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  69 kdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqY...dalvdsqkeYkehYqqeieeLkesl 142
                                        dle+++ +l+e++ +l++e +  +++l+ + ++ ++l++ l++ + +     a ++s ++  +h q e+e+ ++sl
  gi|313126714|ref|YP_004036984.1|  35 SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVghvAAELESTEKLLNHTQAELERTETSL 111
                                       58999999999999999999999999999999999999999999987641115678999999999999999999999 PP

                                       HHHHHHHH CS
                              SHE3 143 eklklene 150
                                       e+ +++ e
  gi|313126714|ref|YP_004036984.1| 112 EEKREQLE 119
                                       98655544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH CS
                              SHE3  51 khENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqYdal 120
                                       + E +   + L+ K  +l  + ++l e ++++eel++++k+l++++ +++ +++el+ee++ l+ + d l
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDL 170
                                       55666677789999999******************************************99998776655 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   7.5     0.055       4.6     242     324 ..      42     125 ..      20     131 .. 0.64
   2 ?   10.5   6.4    0.0012       0.1     634     709 ..      91     175 ..      79     186 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.055
                          Prominin 242 erllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcldql 317
                                       ++l e  k+ +++Le+ +  +k Lr+  ++L+++l++ + d+ +++++ + +++  ++++ +le ++  ++++ +ql
  gi|313126714|ref|YP_004036984.1|  42 DQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAElESTEKLLNHTQAELERTETSLEEKREQL 118
                                       46777778888888888888888888888888888888888888888844443444444444444333333333555 PP

                          Prominin 318 pnvdevl 324
                                       ++v + l
  gi|313126714|ref|YP_004036984.1| 119 ESVRDNL 125
                                       5555444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                          Prominin 634 eelanelsngk...knlkqslkneaqdlraiqqe......lvlplessvkklkksvkkldeensdlqesikkllaav 701
                                       e+  + l++ +   +  ++sl+++ ++l+++ ++      ++++le++ k+l+++v +l++en++l+e++++l +  
  gi|313126714|ref|YP_004036984.1|  91 ESTEKLLNHTQaelERTETSLEEKREQLESVRDNldearsKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDR 167
                                       33333332222333344444444444444444430000003455888888888888888888888888888888877 PP

                          Prominin 702 eraenflk 709
                                       ++++  l+
  gi|313126714|ref|YP_004036984.1| 168 DDLQRDLR 175
                                       77776555 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.4      0.11       8.9     126     174 ..      43      91 ..      29     100 .. 0.76
   2 ?   10.0  15.7    0.0061      0.51      51     122 ..      92     165 ..      85     183 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.11
                              YkyA 126 ealeldkeLYemLkkeeltleeleeqiekiNesyeevkeaneqFneatk 174
                                       ++ e +k+L  +L++  ++l+ l+e+++++N+s ++++  +     +++
  gi|313126714|ref|YP_004036984.1|  43 QLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELE 91 
                                       4557788888999999999999999999999999998877766665555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0061
                              YkyA  51 kikklsdealenveeReellekekesieeakeefekikeeieei..edeelkkeaeelieameeryeaydklyk 122
                                         +kl +  ++ +e  e+ le+ +e +e+ ++++++++++iee+  ++++l++++ el++  +e  e  d+l +
  gi|313126714|ref|YP_004036984.1|  92 STEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELekKNKTLEEQVAELKTENKELSEEVDDLRD 165
                                       44555555555555555555555555555555555555555555444555566666666666666666555544 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3     0.003      0.25     108     178 ..      87     158 ..      83     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.003
                    Ploopntkinase3 108 eaGyevtlalldhdqadawrkarskklgrvqneswvkgrlsasrkladalik..aaekgkvkvlaGhPdelrs 178
                                       +a  e t  ll+h qa+  r++ s + +r+q es v+  l  +r+  ++l k  ++ + +v  l+ +  el +
  gi|313126714|ref|YP_004036984.1|  87 AAELESTEKLLNHTQAELERTETSLEEKREQLES-VRDNLDEARSKIEELEKknKTLEEQVAELKTENKELSE 158
                                       666777889************************9.56666666666665555332333344444444444444 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.0     0.051       4.2     112     163 ..      29      78 ..      20     102 .. 0.83
   2 ?    9.7   6.7    0.0081      0.67     117     165 ..     102     150 ..      87     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.051
                             Spc29 112 iyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkr 163
                                       +y+s  +  +le + d+ +++ k+L+ ele  rt  + L e+v+ l++++++
  gi|313126714|ref|YP_004036984.1|  29 MYQSSAS--DLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQ 78 
                                       5555444..7888889999999*************************99854 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0081
                             Spc29 117 kkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrla 165
                                        + +++e  l+++++++++ + +l++ r  ++eL +k + lee+v +l+
  gi|313126714|ref|YP_004036984.1| 102 AELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELK 150
                                       45678888*************************************7665 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2  15.3       1.2     1e+02      17      94 ..      30     118 ..      22     121 .. 0.56
   2 ?    9.5  23.9     0.013       1.1      14     106 ..      69     165 ..      67     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 1.2
                       TMF_TATA_bd  17 lsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelek..............eleelqer 79 
                                        +s+   lE++  +l+e++++l ae ++ar e+  l +++++l+++   l++++                l+  q +
  gi|313126714|ref|YP_004036984.1|  30 YQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQS---LQQTQGdvghvaaelestekLLNHTQAE 103
                                       5777778888888999999999999888888888777555444433...2222221111111222222244445555 PP

                       TMF_TATA_bd  80 yetlLellGeksEev 94 
                                       +e + + l ek E+ 
  gi|313126714|ref|YP_004036984.1| 104 LERTETSLEEKREQL 118
                                       555555555555554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.013
                       TMF_TATA_bd  14 verlsseirrlEgElaslkeelerleaerdeareei....vklmkeneelkelkkeleelekeleelqeryetlLel 86 
                                       v+ l++++++ +g++ ++  ele+ e+  + +++e+     +l ++ e+l++  ++l+e ++++eel+++ +tl e 
  gi|313126714|ref|YP_004036984.1|  69 VNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELerteTSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQ 145
                                       7889999999999999999999998887777777772222456677788888888899999999******9999999 PP

                       TMF_TATA_bd  87 lGeksEeveELraDvaDlKe 106
                                         e + e++EL ++v+Dl++
  gi|313126714|ref|YP_004036984.1| 146 VAELKTENKELSEEVDDLRD 165
                                       99999999999999999986 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.3    0.0012       0.1      31      96 ..      57     118 ..      41     121 .. 0.80
   2 ?    2.0   4.3       3.9   3.3e+02      43      91 ..     114     162 ..     100     170 .. 0.69
   3 ?    3.0   1.4       1.8   1.5e+02      25      58 ..     137     171 ..     120     187 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0012
                           DUF4665  31 pVttnLKkinavkkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdeaaell 96 
                                          t+LK +    +e+v++l+++l++ q d+ +++ +l++++k  ++ + + e ++++++e  e+l
  gi|313126714|ref|YP_004036984.1|  57 SARTELKVL----RERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQL 118
                                       556888888....9**********************999888877777777777777777777665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 3.9
                           DUF4665  43 kkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvde 91 
                                       k+e+ e++   l + + ++++l kk k+ +++  ++k ++++ +++vd+
  gi|313126714|ref|YP_004036984.1| 114 KREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDD 162
                                       5666777777777777777777777777777777666666666666665 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 1.8
                           DUF4665  25 aKaKA.kpVttnLKkinavkkekvenldkalvdiq 58 
                                       +K+K+    + +LK  n   +e v +l     d+q
  gi|313126714|ref|YP_004036984.1| 137 KKNKTlEEQVAELKTENKELSEEVDDLRDDRDDLQ 171
                                       22222111123344444444444444444444444 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   6.0      0.22        18       8      67 ..      31      90 ..      27      95 .. 0.75
   2 ?   12.4  15.4    0.0009     0.075     198     282 ..      82     163 ..      78     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.22
                         Rab5-bind  8 EkqLqaiqeqEaelrdqvkklqellrraneqLekerkdkkeLedslkelseetskqvsel 67
                                            + +q+ +lr++ k+l+  l+ a+ +L+  r+  ++L++sl++++ ++ +  +el
  gi|313126714|ref|YP_004036984.1| 31 QSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAEL 90
                                      555566778888888888888888888888888888888888888888888877665555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0009
                         Rab5-bind 198 eierlkeelasisslkveleeikvekeslekslaektrqldklqtikselEeqlkelekekaaveqlvleeknkaqr 274
                                       ++ ++  el+s       l+++++e e  e+sl+ek +ql++ +   +e  ++++elek+  ++e++v e k   + 
  gi|313126714|ref|YP_004036984.1|  82 DVGHVAAELES---TEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKE 155
                                       55566666666...455689999****************************************************** PP

                         Rab5-bind 275 LqtELDvs 282
                                       L +E+D  
  gi|313126714|ref|YP_004036984.1| 156 LSEEVDDL 163
                                       ****9864 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  20.7    0.0072      0.61      92     220 ..      37     173 ..      20     178 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0072
                                       XXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........................XXXXXXXXXXXXXXXXX CS
                              AIP3  92 lkelkssiesqkaslqevserqeeaakekasesla................kkelkaqlkevqslrrdLavlrqlys 152
                                       l+  ++++++ +++l+                  +                +++l++   +v ++  +L+++ +l +
  gi|313126714|ref|YP_004036984.1|  37 LETQNDQLRERNKNLRAEL---------------EsartelkvlrervndlNQSLQQTQGDVGHVAAELESTEKLLN 98 
                                       2222222222222222211...............0222223344444445556677777789999999999988888 PP

                                       XXXXXXXXXXXXXXXXXXXXX.......XXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 153 efkseikeslselrekakkvk.......easlastkkssnrayiekgkkkLseesdklvtkvddLqDlvedlrkD 220
                                       + + e++ + ++l+ek ++++       ea+ +  + +++++ +e+  ++L++e ++l ++vddL D  +dl+ D
  gi|313126714|ref|YP_004036984.1|  99 HTQAELERTETSLEEKREQLEsvrdnldEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRD 173
                                       887776655555555555554332666544454455577777777778888888888888888888877777777 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.0      0.26        22      50      91 ..      37      78 ..      30      82 .. 0.77
   2 ?   12.4  15.5    0.0015      0.12       3      91 ..      88     176 ..      86     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.26
                              BRE1 50 amrskdalenelkkLnkllsKsselieqLkelekefvrklke 91
                                      ++ + d+l+  +k+L++ l+  +   + L e+ ++++++l++
  gi|313126714|ref|YP_004036984.1| 37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQ 78
                                      566778888888888888888888888888888888888765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0015
                              BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLk 79 
                                       +EL++ ek  + ++++l+   ++l+   e++  +  + ++a+ k+ +++++ ++le ++  L++ ++  se +++L 
  gi|313126714|ref|YP_004036984.1|  88 AELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLR 164
                                       7**************************************************************************** PP

                              BRE1  80 elekefvrklke 91 
                                       +   +++r l e
  gi|313126714|ref|YP_004036984.1| 165 DDRDDLQRDLRE 176
                                       *88888888765 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   6.7    0.0082      0.69     419     480 ..      34      95 ..      27     105 .. 0.88
   2 ?    6.4  13.2     0.033       2.7     395     471 ..     101     177 ..      94     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0082
                          Macoilin 419 eqelrskissltseerslkselqqlkkendllqtklhelvsakqkdkqtlqqlekrLkeeke 480
                                        ++l+ + + l +++++l++el++ + e  +l++++++l ++ q+ +  + ++   L++ ++
  gi|313126714|ref|YP_004036984.1|  34 ASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEK 95 
                                       57999******************************************999999988887655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.033
                          Macoilin 395 kdalvrLeadikkLkaeLqasrqteqelrskissltseerslkselqqlkkendllqtklhelvsakqkdkqtlqql 471
                                       + +l+r e+ ++  + +L++ r + +e rski+ l +++++l +++ +lk en +l + +++l + +   ++ l ++
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       45688********************************************************9999987766666665 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   3.8      0.75        63      72     102 ..      33      63 ..      26      70 .. 0.76
   2 ?   13.5  10.6   0.00065     0.054      44     109 ..      54     119 ..      53     121 .. 0.94
   3 ?    2.8   9.0       1.4   1.2e+02      50      83 ..     130     163 ..     125     180 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.75
                             DHR10  72 elrelerkeerlqrqlenaeeklerlreqae 102
                                        +++le++ ++l+ + +n + +le +r + +
  gi|313126714|ref|YP_004036984.1|  33 SASDLETQNDQLRERNKNLRAELESARTELK 63 
                                       5678888888888888888888888887655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00065
                             DHR10  44 eieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaak 109
                                       e+e+   +l+  ++++++l++ l++ + ++  + ++ e  ++ l++ + +ler + + eekre+ +
  gi|313126714|ref|YP_004036984.1|  54 ELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLE 119
                                       67788888999999*************************************************986 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 1.4
                             DHR10  50 akleeakkklkelrdaleekeielrelerkeerl 83 
                                        k ee +kk k l+++++e+++e +el+ + + l
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTENKELSEEVDDL 163
                                       3455555555555555555555555554443333 PP

>> PI_PP_I  Phosphoinositide phosphatase insertion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.87        73      36      77 ..      37      78 ..      26      98 .. 0.74
   2 ?    9.1   0.8     0.017       1.4      18      82 ..     110     174 ..      87     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.87
                                      HHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS-HHHHH CS
                           PI_PP_I 36 fllkWeeikktslsLeedLnkiannktplPsWfnelskaqqe 77
                                      + ++ +++++++ +L ++L++ +++ + l +  n+l+++ q+
  gi|313126714|ref|YP_004036984.1| 37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQ 78
                                      556667778888888888888888877777777777776665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.017
                                       C--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS-HHHHHHHHHH CS
                           PI_PP_I  18 nleskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannktplPsWfnelskaqqellrvl 82 
                                       +le k+++l++++ +l +   k ee++k++ +Lee+  +++++++ l +  ++l   + +l r l
  gi|313126714|ref|YP_004036984.1| 110 SLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDL 174
                                       58999999*********************************999999888888877776666555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  14.8      0.16        14      11     111 ..      48     156 ..      18     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.16
                      Baculo_PEP_C  11 ggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlks...llaeldtrldtlltnLtdalnalq.... 80 
                                       + n   +L  + + ++ +   + ++l++ l++ ++ +++++++l+s   ll++ +++l+ + t L+++  +l+    
  gi|313126714|ref|YP_004036984.1|  48 NKNLRAELESARTELKVLRERV-NDLNQSLQQTQGDVGHVAAELEStekLLNHTQAELERTETSLEEKREQLEsvrd 123
                                       4455566666667777777777.788888888888888887777542226666666788888888777777776666 PP

                      Baculo_PEP_C  81 ..dtlrneLtnlnsiltnLlssvtNinstLnnl 111
                                         d+ r++++ l+++  +L  +v+ +++  + l
  gi|313126714|ref|YP_004036984.1| 124 nlDEARSKIEELEKKNKTLEEQVAELKTENKEL 156
                                       666677777777777777777777666555555 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  13.3     0.029       2.4      64     147 ..      32     115 ..      23     121 .. 0.87
   2 ?    5.1  15.7      0.18        15      56     135 ..     100     173 ..      88     186 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.029
                      HAUS-augmin3  64 edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraen 140
                                       ++ + le + ++++e  ++L++el+ ++ e + + +r n L+    + q     +++e ++++k l+ +q+el+++ 
  gi|313126714|ref|YP_004036984.1|  32 SSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTE 108
                                       45667788999999**********************************************************99988 PP

                      HAUS-augmin3 141 aetnavL 147
                                         +++  
  gi|313126714|ref|YP_004036984.1| 109 TSLEEKR 115
                                       7776655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.18
                      HAUS-augmin3  56 iepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkea 132
                                        +       + e +e +lee++e+le  ++ l+e+++  + ++k+ + L+ q+a+l+ e+++l+ee +  + +  ++
  gi|313126714|ref|YP_004036984.1| 100 TQ------AELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDL 170
                                       22......333444444444444444444444444444444444444444444444444444444444444444444 PP

                      HAUS-augmin3 133 qee 135
                                       q++
  gi|313126714|ref|YP_004036984.1| 171 QRD 173
                                       444 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7  12.1       2.1   1.8e+02       4      76 ..      45     126 ..      37     128 .. 0.59
   2 ?    2.4  17.5       1.3   1.1e+02       4      54 ..     129     179 ..      86     188 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 2.1
                                       ...CTTTHHHHCCCCCCTTCHHHCTTSCCCCCC.......TTTTTTTTHHH...HHHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE   4 eeeeeeeedeeeeleeeleelekevkelkekll.......rllaefenlrk...rtekekeeakkfaiekfakdLLp 70 
                                       +e+++++++e+e+ ++el+ l+++v++l+++l+       + +ae+e  +k   +t+ e+e  + +++e+  ++L +
  gi|313126714|ref|YP_004036984.1|  45 RERNKNLRAELESARTELKVLRERVNDLNQSLQqtqgdvgHVAAELESTEKllnHTQAELERTE-TSLEEKREQLES 120
                                       5678888889999999999999999999999995555555333444433330003333333333.333344566666 PP

                                       HHHHHH CS
                              GrpE  71 vlDnle 76 
                                       v+Dnl+
  gi|313126714|ref|YP_004036984.1| 121 VRDNLD 126
                                       666665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 1.3
                                       ...CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHH CS
                              GrpE   4 eeeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekeke 54 
                                       +++ ee+e+++++lee+++el++e kel+e+++ l+ + + l++ +++  +
  gi|313126714|ref|YP_004036984.1| 129 RSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCD 179
                                       344555666666666666666666666666666666666666665555444 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       8.7   7.3e+02      14      37 ..      33      56 ..      23      67 .. 0.62
   2 ?   12.1   0.9    0.0022      0.19       4      48 ..      69     113 ..      66     122 .. 0.91
   3 ?    5.4   0.4      0.28        24      12      48 ..      98     134 ..      97     141 .. 0.87
   4 ?    3.3   0.6       1.2     1e+02      22      47 ..     139     164 ..     116     168 .. 0.54

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 8.7
                                      HHHHHHHHHHHHHHHHHHHHHHHC CS
                       Flagellin_C 14 vrselGavqnRlesaitnlkaqse 37
                                       +s+l +   +l + ++nl a  e
  gi|313126714|ref|YP_004036984.1| 33 SASDLETQNDQLRERNKNLRAELE 56
                                      455555556666666666655544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCC CS
                       Flagellin_C   4 vdeaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrled 48 
                                       v++  ++l++++ ++G v + les+ + l+ ++  l++ e++le+
  gi|313126714|ref|YP_004036984.1|  69 VNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEE 113
                                       6778899*******************************9999986 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCC CS
                       Flagellin_C  12 dkvrselGavqnRlesaitnlkaqsenlkaaesrled 48 
                                       + +++el   ++ le+  ++l+   +nl++a+s++e+
  gi|313126714|ref|YP_004036984.1|  98 NHTQAELERTETSLEEKREQLESVRDNLDEARSKIEE 134
                                       5678889999999999999999999999999999997 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHCHHHHHHCHHC CS
                       Flagellin_C  22 qnRlesaitnlkaqsenlkaaesrle 47 
                                        + le+++++lk+  + l++++ +l+
  gi|313126714|ref|YP_004036984.1| 139 NKTLEEQVAELKTENKELSEEVDDLR 164
                                       23356666666666666666666666 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.2      0.17        14     136     187 ..      29      77 ..      10      83 .. 0.76
   2 ?   10.3   8.6    0.0043      0.36     137     193 ..      90     146 ..      85     184 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.17
                              Vps5 136 kwqsaeqelskkkeqleKlekaaksqqdklqqlkkeveelerkvqeaekeFe 187
                                        +qs+ ++l+    q ++l+  +k+ +  l++++ e++ l+++v++++++ +
  gi|313126714|ref|YP_004036984.1|  29 MYQSSASDLET---QNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQ 77 
                                       55666666654...555566666777889***************99988765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0043
                              Vps5 137 wqsaeqelskkkeqleKlekaaksqqdklqqlkkeveelerkvqeaekeFeeiseti 193
                                       ++s e+ l+ ++++le++e++ ++++++l++++++++e+++k++e+ek+ +++ e++
  gi|313126714|ref|YP_004036984.1|  90 LESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQV 146
                                       566777788888888888888888888888888888888888888887766665543 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  15.0      0.93        78       7      86 ..      40     122 ..      26     133 .. 0.59
   2 ?   10.1  10.2      0.01      0.84      20      76 ..     116     175 ..     111     187 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.93
                            CENP-H   7 qrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksrq 80 
                                       q+d+l ++ ++l +el++++ el  +++   +l++  ++   ++   a e es++   +++++ele+ e+ l+++r+
  gi|313126714|ref|YP_004036984.1|  40 QNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEkllNHTQAELERTETSLEEKRE 116
                                       55555556666666666666666666666655555555555555333333333334665566666666666666666 PP

                            CENP-H  81 rwrvvk 86 
                                       + + v+
  gi|313126714|ref|YP_004036984.1| 117 QLESVR 122
                                       666554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.01
                            CENP-H  20 qelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelk 76 
                                       ++l++++++l+e++ ++ +l++kn++l ++++el+ e+++ +   ++l++  + l+++l+
  gi|313126714|ref|YP_004036984.1| 116 EQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSeevDDLRDDRDDLQRDLR 175
                                       455555555555555555555555555555555555555444444334444444444443 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  15.2      0.18        15      14     104 ..      36     126 ..      30     127 .. 0.95
   2 ?   10.2  19.7    0.0091      0.76      19     102 ..      87     166 ..      76     178 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.18
                           DUF4200  14 aleakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeie 90 
                                        le++++++++++++l+ + e  + + + l+e+++ +++ l++ +        + e+ +kl  + +ae+++ ++++e
  gi|313126714|ref|YP_004036984.1|  36 DLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLE 112
                                       699************************************************************************** PP

                           DUF4200  91 tlkseiekleekle 104
                                       + ++++e   ++l+
  gi|313126714|ref|YP_004036984.1| 113 EKREQLESVRDNLD 126
                                       *****999998886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0091
                           DUF4200  19 keeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkse 95 
                                        +e++ +e++l++ ++ele++e  lee+ ++++       ++  +a+ k+ee +k++k  e+++++lk+e ++l +e
  gi|313126714|ref|YP_004036984.1|  87 AAELESTEKLLNHTQAELERTETSLEEKREQLES----VRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEE 159
                                       5677777777777777777777777766644333....333333344444444444444444444444444444444 PP

                           DUF4200  96 iekleek 102
                                        + l + 
  gi|313126714|ref|YP_004036984.1| 160 VDDLRDD 166
                                       4433332 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   7.6     0.021       1.8     103     159 ..      42      98 ..      26     105 .. 0.53
   2 ?    8.7  12.2     0.011      0.93      56     146 ..      88     176 ..      82     186 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.021
                           DUF4763 103 leLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlneldsfkr 159
                                        +L+ +n  Lr +l+++   lk  r+ +++l++sl+q +  + + +++l+  ++  +
  gi|313126714|ref|YP_004036984.1|  42 DQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLN 98 
                                       355555555555555555555555555555555555555555555555555544433 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.011
                           DUF4763  56 delekiKqrvlelrskLalnvpecPeidecvdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslke 132
                                       +ele  ++ +++ + +L  +  e    ++ ++ +   ++l++   +i eL ++n  L  q+ael+   k+  +++ +
  gi|313126714|ref|YP_004036984.1|  88 AELESTEKLLNHTQAELERT--ETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDD 162
                                       45666666666666666644..4444455555566666666666666666666666666666666666666666666 PP

                           DUF4763 133 lreslcqekkrlrk 146
                                       lr+++  +++ lr+
  gi|313126714|ref|YP_004036984.1| 163 LRDDRDDLQRDLRE 176
                                       66666665555554 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.6     0.073       6.1     219     272 ..      39      94 ..      26     117 .. 0.67
   2 ?    7.7   8.0      0.02       1.7       6      61 ..     117     175 ..     105     179 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.073
                              RmuC 219 wrqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle..g 272
                                        ++++++++ +++  +l++  ++++ + e++++l+++l+++q ++  ++ +le  +
  gi|313126714|ref|YP_004036984.1|  39 TQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELEstE 94 
                                       46677777777777777777777777777777777777777777777777776653 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.02
                              RmuC   6 llkplkeklekfeekveees...keeaeeleslkeqlkelqelneqlgdeaenLtkaLk 61 
                                        l+ ++++l++ + k+ee +   k+ +e+ ++lk++ kel+e   +l+d+ ++L++ L+
  gi|313126714|ref|YP_004036984.1| 117 QLESVRDNLDEARSKIEELEkknKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLR 175
                                       33444444444444444444322566666666777777777777777777777666665 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.8     0.071       5.9      35     120 ..      42     129 ..      35     131 .. 0.82
   2 ?   10.5   6.0    0.0057      0.47      21      66 ..     119     164 ..     117     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.071
                                       HHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX.XXXXXXXXXXXX CS
                            DivIVA  35 eallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliik.eAekk.aekiveeaeeea 109
                                        +l ++n++l+++++ ++++lk  +e+ ++L+++l  +q    +v a+ +   +l+ + +Ae +  e+ +ee +e++
  gi|313126714|ref|YP_004036984.1|  42 DQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHtQAELErTETSLEEKREQL 118
                                       678899*********************************99999999988777776541455441456678999999 PP

                                       XXXXXXXXXXX CS
                            DivIVA 110 kkiaeeieelk 120
                                       + ++++++e +
  gi|313126714|ref|YP_004036984.1| 119 ESVRDNLDEAR 129
                                       99999998876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXX CS
                            DivIVA  21 deVdeFLdqvakdyeallkeneelkekvkeleeklkeykeleetLk 66 
                                       + V++ Ld+  +++e+l k+n++l+e+v+el+++ ke +e  ++L+
  gi|313126714|ref|YP_004036984.1| 119 ESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLR 164
                                       679999****************************999999888887 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.0    0.0089      0.74      13      57 ..      31      75 ..      20      90 .. 0.79
   2 ?    2.9  15.1      0.85        71       5      73 ..      93     161 ..      74     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0089
                           DUF4795 13 qeaieklqeelekleekvkelekrledkekklealkkqieelekv 57
                                      q+  ++l+++ ++l e+ k+l  +le  + +l++l++ +++l+++
  gi|313126714|ref|YP_004036984.1| 31 QSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQS 75
                                      566678888888888888888888888888888888888888875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.85
                           DUF4795   5 saellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekad 73 
                                       +++ll++ q+++e  +++le+  e+ +++ ++l + ++k+e l+k+ + le++ a+ ++ ++el+e +d
  gi|313126714|ref|YP_004036984.1|  93 TEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVD 161
                                       466788888888888888888888888888888888888888888888888777665555555555444 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.3      0.13        11     106     153 ..      41      89 ..      20     106 .. 0.62
   2 ?    9.0   4.6     0.011       0.9      71     148 ..     109     188 ..      82     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.13
                      Allexi_40kDa 106 lsaetasdskllkklesietsleelhakldelsssetseseg.Pssspt 153
                                       +++ ++ +++l  +les  t+l+ l +++++l +s ++++    +++ +
  gi|313126714|ref|YP_004036984.1|  41 NDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDvGHVAAE 89 
                                       2223344556677888888888888888888888888776652344443 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.011
                      Allexi_40kDa  71 vsllsqttlLselrdalrtltklldklksvekklelsaet..asdskllkklesietsleelhakldelsssetses 145
                                       +sl  +  +L  +rd+l + ++++++l++++k+le++  +  +++++l ++++ +  + ++l++ l+e+    ++e 
  gi|313126714|ref|YP_004036984.1| 109 TSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAElkTENKELSEEVDDLRDDRDDLQRDLREVCDDWSEEA 185
                                       22333566777777777777777777777777666665431144566677778888878888888888877766666 PP

                      Allexi_40kDa 146 egP 148
                                       ++P
  gi|313126714|ref|YP_004036984.1| 186 NSP 188
                                       655 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.2     0.016       1.4      41      92 ..      31      82 ..      26      90 .. 0.77
   2 ?    7.1  14.2      0.11       8.8      34     104 ..      93     171 ..      84     174 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.016
                           DUF4472 41 enrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqaleke 92
                                      +++  +le ++++++e +++lr++l+ +++e k l+e++  l++++q+ + +
  gi|313126714|ref|YP_004036984.1| 31 QSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGD 82
                                      5667788888888888888888888888888888888888888888876655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.11
                           DUF4472  34 knkvlalenr...vlelelerek.....aaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqe 102
                                       + k+l++ +     +e++le+++      + + +++r++ +ele+++k lee+++ lk++ ++l++e ++ ++  + 
  gi|313126714|ref|YP_004036984.1|  93 TEKLLNHTQAeleRTETSLEEKReqlesVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDD 169
                                       44444433321112223333333334445555666666777777777777777777777777777777776666666 PP

                           DUF4472 103 ls 104
                                       l+
  gi|313126714|ref|YP_004036984.1| 170 LQ 171
                                       65 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.5      0.23        19      49      88 ..      43      82 ..      25      85 .. 0.71
   2 ?   10.0  14.4     0.012         1      17      86 ..      92     164 ..      84     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.23
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2 49 tLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeae 88
                                      +L++  ++ +a+ + ++++++ l++ +++Lnq+Lq+++ +
  gi|313126714|ref|YP_004036984.1| 43 QLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGD 82
                                      4555555666666666777899999999999999988765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.012
                                       HHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  17 nvtrlL...erqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdae 86 
                                        +++lL   +++L +++ sl+e+  q  +    + + ++ +e+ + +++  +++v el+ e+k+L ++++d +
  gi|313126714|ref|YP_004036984.1|  92 STEKLLnhtQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLR 164
                                       4555542227799999999999999999999999999999999999999999999999999999999998876 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   5.0      0.37        31      98     152 ..      37      93 ..      25      97 .. 0.76
   2 ?    1.4  24.8       3.3   2.8e+02       7     142 ..      49     160 ..      43     174 .. 0.43

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.37
                              Wtap  98 LeqENeELgkvlee..grvakLeselalqkkfveelkkaleeleelleeleeevevl 152
                                       Le +N+ L + +++  +++++  +el+++++ v++l+++l++ +  +  + +e+e  
  gi|313126714|ref|YP_004036984.1|  37 LETQNDQLRERNKNlrAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELEST 93 
                                       777777776655542266778888999999999999999999998888888888865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 3.3
                              Wtap   7 alllarlsakeqelqelksslqelkqslqppsssqlrqvllD.PAvnlvfsrlrkeleeaenkleeaqeeLqalkft 82 
                                       + l a l++   el+ l++ +++l+qslq+++  +   v+ +  +++ ++++ ++ele +e++lee++e+L++++ +
  gi|313126714|ref|YP_004036984.1|  49 KNLRAELESARTELKVLRERVNDLNQSLQQTQ-GDVGHVAAElESTEKLLNHTQAELERTETSLEEKREQLESVRDN 124
                                       44444455555555555555555555554433.12222222213344444445555555555555555555555444 PP

                              Wtap  83 pdsqtGkrLmakcrvLeqENeELgkvleegrvakLeselalqkkfveelkkaleeleell 142
                                        d                       ++   ++++Le++ + ++++v+elk++++el e +
  gi|313126714|ref|YP_004036984.1| 125 LDE----------------------AR--SKIEELEKKNKTLEEQVAELKTENKELSEEV 160
                                       443......................22..2344444444444444444444444444444 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.7      0.26        22     117     159 ..      38      84 ..      23      88 .. 0.69
   2 ?   10.5   8.1    0.0051      0.43      97     155 ..     109     171 ..      86     178 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.26
                          Cauli_AT 117 qnrikkleeetkklaekivte....kllkeevkdlderlseirdslk 159
                                       + + ++l e++k+l  ++++     k l+e v dl+++l++ + ++ 
  gi|313126714|ref|YP_004036984.1|  38 ETQNDQLRERNKNLRAELESArtelKVLRERVNDLNQSLQQTQGDVG 84 
                                       44667788888888777664322235788999999999999888775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0051
                          Cauli_AT  97 keggedkekktklletLkeaqnrikkleeetkklaekivt....ekllkeevkdlderlseir 155
                                        + +e++e+     + L ea+++i++le+++k l+e++      +k l eev dl +    ++
  gi|313126714|ref|YP_004036984.1| 109 TSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAElkteNKELSEEVDDLRDDRDDLQ 171
                                       3344555555556678999999**************975311113445555555555555555 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  29.8      0.03       2.5      53     150 ..      53     153 ..      11     156 .. 0.79
   2 ?    6.1   9.3     0.077       6.5      89     131 ..     130     172 ..     126     187 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.03
                           DUF3552  53 ealleakeeihklr...eelekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleeke 126
                                         l  a+ e++ lr   ++l++ l++ + ++ ++   l++ e+ L++ +++le+ e+sleek+++l++ +++l+e +
  gi|313126714|ref|YP_004036984.1|  53 AELESARTELKVLRervNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEAR 129
                                       4444566666666611256788999999************************************************* PP

                           DUF3552 127 eeleelveeqrqeLerisgLtkee 150
                                       +++eel +++++  e++++L++e+
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTEN 153
                                       *****98888888889****9885 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.077
                           DUF3552  89 qkeetLdrkeeslekkeesleekekelkqkeqsleekeeelee 131
                                       +k e+L++k+++le++ ++l++++kel+++ ++l+  +++l++
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       4566666666666666666666666666666666666655554 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.3      0.58        49      50      97 ..      34      78 ..      23      82 .. 0.64
   2 ?    9.1   2.6     0.022       1.8      70      98 ..     100     128 ..      86     132 .. 0.86
   3 ?    8.4   4.4     0.035       2.9      72     100 ..     133     161 ..     126     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.58
                           UPF0449 50 eedleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLee 97
                                      ++dle++ ++l e+   + +l  +Le+a++eLk  +e+ + ++++L++
  gi|313126714|ref|YP_004036984.1| 34 ASDLETQNDQLRER---NKNLRAELESARTELKVLRERVNDLNQSLQQ 78
                                      33334444433333...3456778888888888888888888888876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.022
                           UPF0449  70 lnerLeeakeeLkqkceeLktageeLeee 98 
                                       ++ +Le+++++L++k+e+L++++++L+e+
  gi|313126714|ref|YP_004036984.1| 100 TQAELERTETSLEEKREQLESVRDNLDEA 128
                                       6679********************99875 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.035
                           UPF0449  72 erLeeakeeLkqkceeLktageeLeeeie 100
                                       e+Le+++++L++++ eLkt ++eL+ee++
  gi|313126714|ref|YP_004036984.1| 133 EELEKKNKTLEEQVAELKTENKELSEEVD 161
                                       67889999999999999999999998886 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  13.5     0.019       1.6     261     344 ..      66     149 ..      28     151 .. 0.81
   2 ?    2.7   0.5      0.68        57     282     322 ..     143     184 ..     140     188 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.019
                                       GGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 261 ldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkea 337
                                        +  ++L++  + ++ ++ ++++e++  ek l +++ ele+ e++ e++ + le++++ l+ea++k+++le++ k++
  gi|313126714|ref|YP_004036984.1|  66 RERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTL 142
                                       34444555445556668999999999999999999999999999999999999999999999999999999999999 PP

                                       HHHHHHH CS
                               FH2 338 kelvkel 344
                                       +e+v el
  gi|313126714|ref|YP_004036984.1| 143 EEQVAEL 149
                                       9988775 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.68
                                       HHHHHHHHHHHHHHHHHHHHCCT.TSSTT-THHHHHHHHHHH CS
                               FH2 282 ekevkklekglkklekelessek.keepsdkflevlkeflke 322
                                       e++v +l+++ k+l++e+++ +   ++ +  ++ev  ++ +e
  gi|313126714|ref|YP_004036984.1| 143 EEQVAELKTENKELSEEVDDLRDdRDDLQRDLREVCDDWSEE 184
                                       555555555555555555555553334444455555544444 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.3      0.41        35       4      55 ..      36      91 ..      23     105 .. 0.65
   2 ?    9.2   5.1     0.024         2      21      65 ..     102     147 ..      89     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.41
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHH....HHHX CS
                            FliD_N  4 Dtdslvkqlmkaerakldkleqkktklewkqsayrelnsklsnlksal....sals 55
                                      D+++  +ql +  ++   +le++ t+l+  ++ +++ln++l++ + ++    ++l+
  gi|313126714|ref|YP_004036984.1| 36 DLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVghvaAELE 91
                                      45555566666666666677788888888888888888888777776533321333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.024
                                       XXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXX.GGGGGXEEE CS
                            FliD_N  21 dkleqkktklewkqsayrelnsklsnlksalsalsk.sstfsakka 65 
                                        +le+ +t+le+k++ +++++ +l++ +s++++l+k ++t++++ a
  gi|313126714|ref|YP_004036984.1| 102 AELERTETSLEEKREQLESVRDNLDEARSKIEELEKkNKTLEEQVA 147
                                       3477777777777777777777777777777677554555544322 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.1     0.077       6.5      79     111 ..     139     171 ..     132     180 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.077
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittle 111
                                        ++l+++++el+   ++l ee+++l+d  + l+
  gi|313126714|ref|YP_004036984.1| 139 NKTLEEQVAELKTENKELSEEVDDLRDDRDDLQ 171
                                       344555555555555555555555555555554 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  19.2      0.05       4.1      47     137 ..      87     180 ..      76     186 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.05
                          CALCOCO1  47 lqaqeaanrqrekekeeykrdreeldrerkeles...rveelkeelkesrekveeleekqkelerlseelaeeksal 120
                                         + e++++  ++ + e +r  ++l+++r++les   +++e++++++e+++k ++lee+  el++ ++el+ee + l
  gi|313126714|ref|YP_004036984.1|  87 AAELESTEKLLNHTQAELERTETSLEEKREQLESvrdNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDL 163
                                       55566667777777777777777777777776642225556666666666677777777777777777777777777 PP

                          CALCOCO1 121 leakeesearirELEeD 137
                                        + +++ +  +rE+ +D
  gi|313126714|ref|YP_004036984.1| 164 RDDRDDLQRDLREVCDD 180
                                       77777777777777776 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.9     0.025       2.1       2      43 ..      37      78 ..      33      93 .. 0.87
   2 ?    3.9   8.4      0.76        64       9      47 ..      93     131 ..      84     139 .. 0.56
   3 ?    7.4   7.5     0.062       5.2      12      48 ..     124     160 ..     120     186 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.025
                             Spc24  2 ldnekfriakelsdleselesleselaelkeeleeleeesee 43
                                      l++++ ++ + +++l +eles ++el+ l+e++++l+++ ++
  gi|313126714|ref|YP_004036984.1| 37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQ 78
                                      7899999999****************************9998 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.76
                             Spc24   9 iakelsdleselesleselaelkeeleeleeeseekese 47 
                                       + k l+++++ele+ e++l+e++e+le + ++  e +s+
  gi|313126714|ref|YP_004036984.1|  93 TEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSK 131
                                       455566666666666666666666666665555553332 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.062
                             Spc24  12 elsdleselesleselaelkeeleeleeeseekeser 48 
                                       +l+++ s++e+le++ + l+e+++el++e++e ++e+
  gi|313126714|ref|YP_004036984.1| 124 NLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEV 160
                                       5556666666666666666666666666666522222 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  18.3      0.47        39       1      65 [.      37     101 ..      35     117 .. 0.87
   2 ?    1.5  18.0       3.9   3.3e+02      10      61 ..     116     170 ..     104     183 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.47
                       Cep57_CLD_2   1 LeaevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELkeqr 65 
                                       Le+++ +L++r++ l+ +l+++ +elk L+   +   ++L++   ++    ae+e+ +k L ++ 
  gi|313126714|ref|YP_004036984.1|  37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQ 101
                                       79999999999999999999999999999888888888999999999999999999999876655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 3.9
                       Cep57_CLD_2  10 nrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkE...L 61 
                                       ++L+s++  l ++ + +++L k + + + q  +   e+ eL++ev+ lr +   L
  gi|313126714|ref|YP_004036984.1| 116 EQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDrddL 170
                                       4444444444444455555555555555555555555555555555555543332 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  25.4      0.23        19      14     158 ..      35     150 ..      26     161 .. 0.42
   2 ?    9.5   9.9    0.0058      0.49       4      64 ..     116     176 ..     113     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.23
                           Taxilin  14 espeekleaLvkkyaelleerkrlqkqlkklkkkleqlqkekeqlqaelskaalaksKLekLcRelqkqnkklkees 90 
                                       ++ e + ++L ++ ++l +e ++   +lk+l+++++ l++  +q q +   +a+  +  ekL    q          
  gi|313126714|ref|YP_004036984.1|  35 SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQA--------- 102
                                       22233444444444445555555555555555555555555555555555554444444444444444......... PP

                           Taxilin  91 kqrareeeekrkelaekfqakLkdiqaqieekserneklreenaelteKlkslieqyelreehfekll 158
                                                           +L+  ++++eek+e+ e++r+   e ++K+++l ++ ++ ee++ +l 
  gi|313126714|ref|YP_004036984.1| 103 --------------------ELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELK 150
                                       ....................444444444444444444444444444444444444444444443321 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0058
                           Taxilin   4 eqlkeslsklespeekleaLvkkyaelleerkrlqkqlkklkkkleqlqkekeqlqaelsk 64 
                                       eql++  ++l++  +k+e+L kk + l e++ +l+ ++k+l+++++ l  +++ lq++l++
  gi|313126714|ref|YP_004036984.1| 116 EQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       788899999999999********99999999999999999999999999999999999886 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.7     0.034       2.9      74     112 ..      35      73 ..      14      76 .. 0.63
   2 ?    3.3  11.1       1.6   1.3e+02      69     107 ..      97     138 ..      67     146 .. 0.51
   3 ?    6.7   4.3      0.14        11      82     113 ..     134     165 ..     126     174 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.034
                            KfrA_N  74 aaleeaeeelaaaraelqaaraaleaeraeaearveele 112
                                       + le+++++l+++++ l+a+ + +++e++ +++rv  l 
  gi|313126714|ref|YP_004036984.1|  35 SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLN 73 
                                       344556666666666666666666666666666666665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 1.6
                            KfrA_N  69 aalwqaaleeaeeelaaaraelqaaraaleaer...aeaear 107
                                           qa le  e++l++ r++l++ r+ l+++r   +e+e++
  gi|313126714|ref|YP_004036984.1|  97 LNHTQAELERTETSLEEKREQLESVRDNLDEARskiEELEKK 138
                                       233344444455566666666666666555555444555555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.14
                            KfrA_N  82 elaaaraelqaaraaleaeraeaearveelea 113
                                       el++ ++ l+++ a+l++e +e++++v+ l++
  gi|313126714|ref|YP_004036984.1| 134 ELEKKNKTLEEQVAELKTENKELSEEVDDLRD 165
                                       55555666666666666666666666666554 PP

>> Hormone_1  Somatotropin hormone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2      0.32        27     120     158 ..      24      61 ..      12      88 .. 0.68
   2 ?    9.1   3.9     0.012         1      86     149 ..      88     151 ..      84     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.32
                                       GSSS------TTTGGGHHHHHHHHHHHHHHHH------- CS
                         Hormone_1 120 kevsetilskakeieeklkeLlegierilskvevpverk 158
                                        +++  + s+a+++e ++ +L+e  +++   +e  ++ +
  gi|313126714|ref|YP_004036984.1|  24 VGATMMYQSSASDLETQNDQLRERNKNLRAELES-ARTE 61 
                                       567788999************9998888888873.3333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.012
                                       ------HHHHHHHHHHHHTTTTGGGGGG....GGGSSS------TTTGGGHHHHHHHHHHHHHH CS
                         Hormone_1  86 aqqtsneeLlklslllleswkePLkhlvtelssmkevsetilskakeieeklkeLlegierils 149
                                       a+  s+e+Ll  +   le  + +L++ +++l+s+ ++ ++ +sk +e+e+k+k L+e + ++ +
  gi|313126714|ref|YP_004036984.1|  88 AELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKT 151
                                       56678899999999999999*************************************9988754 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.8      0.18        15      37      91 ..      43      95 ..       9      99 .. 0.60
   2 ?    5.7   2.3      0.18        15      32      88 ..      59     113 ..      50     119 .. 0.77
   3 ?    9.1   6.2     0.016       1.4      31      89 ..     114     170 ..     109     178 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.18
                           DUF2730 37 klaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlsh 91
                                      +l e  ++ +  l+++ t+++ L  ++ +++L+  l++++g++ +++ae+++ ++
  gi|313126714|ref|YP_004036984.1| 43 QLRERNKNLRAELESARTELKVL--RERVNDLNQSLQQTQGDVGHVAAELESTEK 95
                                      33333344444444444444444..556788888888888888888888887766 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.18
                           DUF2730  32 redleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrq 88 
                                       r +l+ l e v++ ++ l++++  v ++  a +le+ ++ll+++++el+ +e ++++
  gi|313126714|ref|YP_004036984.1|  59 RTELKVLRERVNDLNQSLQQTQGDVGHV--AAELESTEKLLNHTQAELERTETSLEE 113
                                       7788888888888888888888888876..677888888888888888888887766 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.016
                           DUF2730  31 kredleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrql 89 
                                       kre+le++ ++++e +++++ele k ++L  ++++++Lk++ ++l  e+++l+ + + l
  gi|313126714|ref|YP_004036984.1| 114 KREQLESVRDNLDEARSKIEELEKKNKTL--EEQVAELKTENKELSEEVDDLRDDRDDL 170
                                       77788888777777777777777777666..4556666666666666666665555544 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.7      0.43        36      42      79 ..      42      78 ..      21      95 .. 0.60
   2 ?   10.4  11.1    0.0097      0.81      48     138 ..      97     183 ..      85     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.43
                         AATF-Che1 42 keflesseefeealeeaekalkklleslleLreelleq 79
                                       ++ e++++++++le+a+++lk l e + +L ++l +q
  gi|313126714|ref|YP_004036984.1| 42 DQLRERNKNLRAELESARTELKVLRERVNDLNQSL-QQ 78
                                      23333466777777777777777777777777777.22 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0097
                         AATF-Che1  48 seefeealeeaekalkklleslleLreelleqne.ikklaeskeeeekkkskrkrkkkkkeetsleelwkeleklek 123
                                        ++++++le +e++l++  e+l ++r++l e  + i++l++     ++k+ +++  + k+e+++l+e  ++l++  +
  gi|313126714|ref|YP_004036984.1|  97 LNHTQAELERTETSLEEKREQLESVRDNLDEARSkIEELEK-----KNKTLEEQVAELKTENKELSEEVDDLRDDRD 168
                                       3567999999999999999*********9444444443322.....2223333333335666778888999****** PP

                         AATF-Che1 124 alkpfrnatldkWse 138
                                       +l++  +++ d Wse
  gi|313126714|ref|YP_004036984.1| 169 DLQRDLREVCDDWSE 183
                                       *************96 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.6      0.03       2.5     112     156 ..      39      80 ..      23      85 .. 0.70
   2 ?    7.8   8.5     0.026       2.2      95     156 ..      86     150 ..      83     155 .. 0.81
   3 ?    2.3   0.4       1.3   1.1e+02     115     133 ..     147     165 ..     140     187 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.03
                     Fzo_mitofusin 112 etekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                       +++++l+e+ k+l+   ++le++ +++k+lr++ + l+++L++ +
  gi|313126714|ref|YP_004036984.1|  39 TQNDQLRERNKNLR---AELESARTELKVLRERVNDLNQSLQQTQ 80 
                                       23333333333333...36899*******************9865 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.026
                     Fzo_mitofusin  95 vqqelsstfarl...cqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                       v  el+st + l   +++ ++te++lee+ ++le+  ++l+e+ +k + l +k ++le+++++ +
  gi|313126714|ref|YP_004036984.1|  86 VAAELESTEKLLnhtQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELK 150
                                       5667777766551114567899999*********************************9998776 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 1.3
                     Fzo_mitofusin 115 keleeeikelekeieklee 133
                                       +el++e kel++e++ l +
  gi|313126714|ref|YP_004036984.1| 147 AELKTENKELSEEVDDLRD 165
                                       3444444444444444432 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.9     0.018       1.5      26      93 ..      29      96 ..      24     113 .. 0.85
   2 ?    4.8   8.5      0.16        13      35      96 ..     115     183 ..      99     190 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.018
                              Tho2 26 qYekeieklkseieelakdrsde.raaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekks 93
                                       Y++  + l+++ ++l ++r+++ ra+ ++ + e k l+e+++ L++ +++ +  v +v ++L++  k 
  gi|313126714|ref|YP_004036984.1| 29 MYQSSASDLETQNDQL-RERNKNlRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKL 96
                                      69999**********9.7777777***************************999999999999887654 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.16
                              Tho2  35 kseieelakdrsde.raaakkkkkekkrlkeliekLeeEkkeqiehve.......kvkkrLkeekkswfk 96 
                                       ++++e++ +d+ de r+++++ +k++k l+e++++L++E+ke +e+v          ++ L+e++++w +
  gi|313126714|ref|YP_004036984.1| 115 REQLESV-RDNLDEaRSKIEELEKKNKTLEEQVAELKTENKELSEEVDdlrddrdDLQRDLREVCDDWSE 183
                                       3333333.33333336666666666666666666666666666665540000000455666677777766 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.3     0.059       4.9      20      64 ..      38      82 ..      30      87 .. 0.82
   2 ?    7.4   2.3     0.057       4.8      29      68 ..     124     163 ..      90     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.059
                         MbeD_MobD 20 eqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseq 64
                                      e + ++  +  ++l++  e  + e+  L+e+v++L q  ++  + 
  gi|313126714|ref|YP_004036984.1| 38 ETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGD 82
                                      5666666777789999999******************99987665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.057
                         MbeD_MobD  29 afaelqrmfeltqrenaaLseqvtgLsqQVesLseqvrRl 68 
                                          e +  +e  +++n  L+eqv +L    ++Lse+v+ l
  gi|313126714|ref|YP_004036984.1| 124 NLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDL 163
                                       4444555555555566688888888888888888888754 PP

>> End3  Actin cytoskeleton-regulatory complex protein END3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  22.7     0.072         6      85     198 ..      33     149 ..      25     164 .. 0.68
   2 ?    0.9   2.6       5.4   4.5e+02     109     129 ..     142     162 ..     135     187 .. 0.42

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.072
                              End3  85 kgtdfsatkgtdwe.evrLkreLaeLeeklekveeeaekrkekereessksalvkrel...eqLLkYKeeqlrelee 157
                                       +++d+++++++  e + +L+ eL+   ++l+ ++e++++ +++ ++++ +   v +el   e+LL++ + +l+++e+
  gi|313126714|ref|YP_004036984.1|  33 SASDLETQNDQLRErNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELestEKLLNHTQAELERTET 109
                                       444555444555554455666666666666666666655544444444444555555422279*********88877 PP

                              End3 158 gegkskeknlksvkedietveeqVegLesylssrkeeLeqL 198
                                       +  ++k+++l+sv++++++ ++ +e+Le+  ++ +e+ ++L
  gi|313126714|ref|YP_004036984.1| 110 SL-EEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAEL 149
                                       65.556799*******************8766666666555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 5.4
                              End3 109 Leeklekveeeaekrkekere 129
                                       Lee++++++ e+++ +e+ ++
  gi|313126714|ref|YP_004036984.1| 142 LEEQVAELKTENKELSEEVDD 162
                                       222222222222222111111 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   2.2       1.6   1.3e+02      11      86 ..      43      78 ..      33     102 .. 0.47
   2 ?   11.5   8.4     0.003      0.25       6      89 ..     100     179 ..      94     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 1.6
                            GCN5L1 11 erreeqekakkeaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlalvesfnsalke 86
                                      ++r                                        +  k+l+a+++  + + +   + v+++n++l++
  gi|313126714|ref|YP_004036984.1| 43 QLR----------------------------------------ERNKNLRAELESARTELKVLRERVNDLNQSLQQ 78
                                      333........................................333444444444444444444444444444433 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.003
                            GCN5L1   6 qakqaerreeqekakkeaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlalvesfns 82 
                                        +++    e++e++ +e  e+++++ ++l d+ +s+++e+ +++k le+++ +l+++ +++++++d      +++++
  gi|313126714|ref|YP_004036984.1| 100 TQAE---LERTETSLEEKREQLESVRDNL-DEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       3333...3445555556666677787776.7889******************************************* PP

                            GCN5L1  83 alkeiGD 89 
                                       +l+e+ D
  gi|313126714|ref|YP_004036984.1| 173 DLREVCD 179
                                       ****977 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1     0.037       3.1      30      80 ..      19      79 ..       2      89 .. 0.65
   2 ?    5.3   7.8      0.21        17     139     187 ..     102     152 ..      85     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.037
                    Halogen_Hydrol 30 lliailggilvyvasr..........knkkkkhlkksglsrkelkyiretlkeakekikrl 80
                                      ll++ +g+ ++y  s           ++++k + ++ + +r+elk++re +++  + +++ 
  gi|313126714|ref|YP_004036984.1| 19 LLTGTVGATMMYQSSAsdletqndqlRERNKNLRAELESARTELKVLRERVNDLNQSLQQT 79
                                      4455777777777666788776666555555555556677778888888888877777765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.21
                    Halogen_Hydrol 139 aeLskqpvksketrealeetrqlLdelaealek..dlqklledDlddLdvE 187
                                       aeL++++ + +e re+le++r  Lde  +++e+  + +k le+++ +L++E
  gi|313126714|ref|YP_004036984.1| 102 AELERTETSLEEKREQLESVRDNLDEARSKIEEleKKNKTLEEQVAELKTE 152
                                       788888888888888888888888888888885335677888888888887 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.0     0.052       4.4      17      37 ..      37      57 ..      32      70 .. 0.85
   2 ?    8.6   4.5     0.027       2.2      15      40 ..     126     151 ..     116     154 .. 0.86
   3 ?    7.4   0.7     0.062       5.2      24      40 ..     149     165 ..     148     168 .. 0.91
   4 ?    3.3   0.6       1.1        96      17      37 ..     156     176 ..     154     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.052
                              HALZ 17 LksdydsLkkenekLkaelqe 37
                                      L +++d+L++ n++L+ael++
  gi|313126714|ref|YP_004036984.1| 37 LETQNDQLRERNKNLRAELES 57
                                      888999999999999999986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.027
                              HALZ  15 daLksdydsLkkenekLkaelqeLke 40 
                                       d  +s+ + L+k n++L+ +++eLk 
  gi|313126714|ref|YP_004036984.1| 126 DEARSKIEELEKKNKTLEEQVAELKT 151
                                       5567899*****************96 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.062
                              HALZ  24 LkkenekLkaelqeLke 40 
                                       Lk en++L  e+  L++
  gi|313126714|ref|YP_004036984.1| 149 LKTENKELSEEVDDLRD 165
                                       99*************96 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 1.1
                              HALZ  17 LksdydsLkkenekLkaelqe 37 
                                       L  ++d L+++++ L+  l+e
  gi|313126714|ref|YP_004036984.1| 156 LSEEVDDLRDDRDDLQRDLRE 176
                                       677889999999999987765 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  11.0      0.13        11      15      70 .]      90     145 ..      85     145 .. 0.86
   2 ?   12.6   9.1    0.0015      0.13       9      63 ..     119     173 ..     118     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.13
                            Csm1_N  15 ldsAdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkkqeEe 70 
                                       l+s + l +    E    ++ le k +++es++ +l+e+++k++ele+++k+ eE+
  gi|313126714|ref|YP_004036984.1|  90 LESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQ 145
                                       677777777777777778899*******************************9996 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0015
                            Csm1_N   9 esVqerldsAdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleer 63 
                                       esV++ ld+A   ++ l + N +L++++   ++e ++L e+++ l+ ++++l+ +
  gi|313126714|ref|YP_004036984.1| 119 ESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRD 173
                                       79**********************************************9999876 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  27.4      0.19        16      78     180 ..      43     168 ..      27     177 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.19
                        JAKMIP_CC3  78 qLlaeyqalqrayalLreklggeldaerelk.areqleselrktkskikdLeeaLaqk................... 134
                                       qL + ++ l+ ++   r++l + ++ ++ l    +q + ++ ++ ++++                            
  gi|313126714|ref|YP_004036984.1|  43 QLRERNKNLRAELESARTELKVLRERVNDLNqSLQQTQGDVGHVAAELES-------Tekllnhtqaelertetsle 112
                                       33333333333333333333333333322220122233333333333333.......14444444777777777777 PP

                        JAKMIP_CC3 135 .............GqdskwveekQalikrnqeLvekikkleeeeskLkqeiqdlrdqne 180
                                                     +    +ee   l k+n+ L e++ +l++e++ L +e++dlrd ++
  gi|313126714|ref|YP_004036984.1| 113 ekreqlesvrdnlDEARSKIEE---LEKKNKTLEEQVAELKTENKELSEEVDDLRDDRD 168
                                       7777777777764333344555...889****************************987 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6  16.5       2.5   2.1e+02       5      86 ..      55     149 ..      17     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 2.5
                           DUF2203   5 leeAnalLpllkelleelr...........alrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelvee 68 
                                       le A++ L +l+e++++l+           ++++ele++e+ l++++ae e++e   +e++++le+++++++e+ ++
  gi|313126714|ref|YP_004036984.1|  55 LESARTELKVLRERVNDLNqslqqtqgdvgHVAAELESTEKLLNHTQAELERTEtsLEEKREQLESVRDNLDEARSK 131
                                       67888888888888888887777666666666666666666666666665555577778888888888888888888 PP

                           DUF2203  69 ieelGvevkdleaglvDF 86 
                                       ieel  + k le+ + + 
  gi|313126714|ref|YP_004036984.1| 132 IEELEKKNKTLEEQVAEL 149
                                       888888888887766655 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.8      0.12        10     147     197 ..      30      80 ..      25      85 .. 0.85
   2 ?    5.0   7.8      0.21        17     108     184 ..     104     172 ..      91     189 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.12
                               LXG 147 lqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemtskgk 197
                                       +q++ + +++++++l + + ++ ++l+++  +lk l   v++L++  ++ +
  gi|313126714|ref|YP_004036984.1|  30 YQSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQ 80 
                                       678888899999999999999999999999999999999999999887765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.21
                               LXG 108 lkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalkt 184
                                       l++ + ++ee  ++++++ ++ ++         ++ +++l+k +k+++e++  l++ + e+++++++l +d + l++
  gi|313126714|ref|YP_004036984.1| 104 LERTETSLEEKREQLESVRDNLDEA--------RSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       2222222222222222222222222........33334444444444444444555555555555555555555555 PP

>> Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.9   0.00076     0.064     204     243 ..      34      73 ..      28      90 .. 0.89
   2 ?   -0.0   9.9       5.6   4.7e+02     176     230 ..     110     165 ..      86     179 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00076
                   Phlebovirus_NSM 204 veesmArvkdlkeelkiltdelsqikseiqilrkkikdfe 243
                                        ++++ ++ +l+e++k l  el+ +++e+++lr+++ d +
  gi|313126714|ref|YP_004036984.1|  34 ASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLN 73 
                                       6899999****************************99865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 5.6
                   Phlebovirus_NSM 176 eieqlknelqkkRndikrgqek.rdakklveesmArvkdlkeelkiltdelsqiks 230
                                        +e ++++l+  R ++  ++ k ++ +k  + ++ +v++lk e+k l++e++++++
  gi|313126714|ref|YP_004036984.1| 110 SLEEKREQLESVRDNLDEARSKiEELEKKNKTLEEQVAELKTENKELSEEVDDLRD 165
                                       33444455555555544444332455566666666666666677766666555544 PP

>> DUF773  CDK5 regulatory subunit-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.4      0.31        26     447     492 ..      32      77 ..      15      83 .. 0.68
   2 ?    9.0  11.7    0.0063      0.52     404     492 ..      77     161 ..      70     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.31
                            DUF773 447 kqeeklkeklkdleekreelqeelselepkleklvkktrelkklie 492
                                       ++++ l+++  +l+e++++l+ el++ +++l+ l ++  +l + ++
  gi|313126714|ref|YP_004036984.1|  32 SSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQ 77 
                                       4455566666667777777777777777777777776666666655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0063
                            DUF773 404 ekmlsaveealslltnkklqqLiliktspryvdrlvasLeqklkqeeklkeklkdleekreelqeelselepklekl 480
                                       ++ + +v ++ ++l+++   +  l+ + +  ++r ++sLe+k++q e ++++l ++++k eel+++ ++le ++++l
  gi|313126714|ref|YP_004036984.1|  77 QQTQGDVGHVAAELESTE--K--LLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAEL 149
                                       555555555555555433..3..456777779999****************************************** PP

                            DUF773 481 vkktrelkklie 492
                                        ++ +el ++++
  gi|313126714|ref|YP_004036984.1| 150 KTENKELSEEVD 161
                                       *****9999875 PP

>> bZIP_Maf  bZIP Maf transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   4.4      0.19        16      55      90 ..      36      71 ..      29      80 .. 0.58
   2 ?    2.7   4.2       2.1   1.8e+02      54      88 ..      98     132 ..      84     136 .. 0.59
   3 ?   11.8   4.0    0.0031      0.26      52      91 ..     131     170 ..     126     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.19
                          bZIP_Maf 55 elekekeeleeelerlqqelsrlrqekdalkrkneq 90
                                      +le+++ +l+e++++l++el+ +r e+  l+++ + 
  gi|313126714|ref|YP_004036984.1| 36 DLETQNDQLRERNKNLRAELESARTELKVLRERVND 71
                                      456666666666666666666666666555555443 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 2.1
                          bZIP_Maf  54 eelekekeeleeelerlqqelsrlrqekdalkrkn 88 
                                       + +++e e++e++le+ +++l+ +r ++d+ ++k 
  gi|313126714|ref|YP_004036984.1|  98 NHTQAELERTETSLEEKREQLESVRDNLDEARSKI 132
                                       34555566666666666666666666666666555 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.0031
                          bZIP_Maf  52 qkeelekekeeleeelerlqqelsrlrqekdalkrkneql 91 
                                       + eelek+++ lee++ +l+ e+++l++e d+l++  + l
  gi|313126714|ref|YP_004036984.1| 131 KIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDL 170
                                       67999*************************9999876655 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.1    0.0094      0.78     106     155 ..      36      85 ..      31      97 .. 0.75
   2 ?    0.8  12.5       2.7   2.3e+02      71     142 ..      98     163 ..      89     187 .. 0.42

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0094
                        FmiP_Thoc5 106 elaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealgl 155
                                       +l++q ++l e++k+l +e e+ + +L+ L +++++l +++++ q ++g 
  gi|313126714|ref|YP_004036984.1|  36 DLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGH 85 
                                       57778888888888888888888888888888888888888888887763 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.7
                        FmiP_Thoc5  71 eeapeeiskpedtkkeadehelmlaRLewEleqRkelaeqlkeleekkkkleqeieekkkfLssLppkLksl 142
                                       +++++e+   e t+++ +e +++l+     l+   e+ ++++ele+k+k+le++++e k + ++L++++++l
  gi|313126714|ref|YP_004036984.1|  98 NHTQAEL---ERTETSLEEKREQLESVRDNLD---EARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDL 163
                                       3333333...2222222333333333333332...2333344444444444444444444444444444444 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   2.4      0.91        76      67     123 ..      39      90 ..      16     106 .. 0.54
   2 ?   10.1   8.4      0.01      0.86      17     120 ..      73     173 ..      72     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.91
                                       HHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHHHHHHHHH CS
                           T3SSipB  67 ekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaadalqadeal 123
                                        + dq+    +++ + ++ a + lk L        +l++  qQ +   d +++ + l
  gi|313126714|ref|YP_004036984.1|  39 TQNDQLRERNKNLRAELESARTELKVL---RERVNDLNQSLQQTQ--GDVGHVAAEL 90 
                                       344555555566666666666666666...344445555555555..4444444333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.01
                                       HHCHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  17 nkSLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                       n+SL+q +  +    a  +++++ + +   el++     ++  ++le   +++d+a s++++++kk +   +++ eL
  gi|313126714|ref|YP_004036984.1|  73 NQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAEL 149
                                       789999999999999999999999999999*********************************************** PP

                                       --------CHHHHHHHHH..HHHHHHH CS
                           T3SSipB  94 aPdePekakleaaeqQagaaadalqad 120
                                          + e ++l +++  + +  d lq d
  gi|313126714|ref|YP_004036984.1| 150 ---KTENKELSEEVDDLRDDRDDLQRD 173
                                       ...889999999999999888877765 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  13.7    0.0049      0.41     601     709 ..      40     146 ..      29     147 .. 0.78
   2 ?    2.0   0.8      0.43        36     556     597 ..     142     183 ..     139     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0049
                             Nup88 601 kQeklvrrvkkv...lkrlnsklpvlseaeremkkelekikeklkslknalkqvkkkldkqrkqiakskeeekkssl 674
                                       + ++l +r k++   l++++++l vl e   ++++ l++++ ++ +++++l+  +k l+  + ++++     +++sl
  gi|313126714|ref|YP_004036984.1|  40 QNDQLRERNKNLraeLESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELER-----TETSL 111
                                       4455555555553337777888888888888999999999999999999999999888888888873.....45668 PP

                             Nup88 675 elsekqkktikeiLkeegeeieelikqvkdikkiv 709
                                       e + +q + ++++L e  ++ieel k+ k ++++v
  gi|313126714|ref|YP_004036984.1| 112 EEKREQLESVRDNLDEARSKIEELEKKNKTLEEQV 146
                                       889999999******************99999887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.43
                             Nup88 556 iekrvkllkkqkeqqleelqsleeerkslseraeklAekyee 597
                                       +e +v  lk++ ++  ee+ +l+++r+ l+ +  ++ ++++e
  gi|313126714|ref|YP_004036984.1| 142 LEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDDWSE 183
                                       566777888888888888888888888888777777776655 PP

>> DUF5339  Family of unknown function (DUF5339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.7     0.018       1.5      20      50 ..     108     139 ..      91     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.018
                           DUF5339  20 ekq.pgtktqadaikkqleqsKkqilalpkeq 50 
                                       e+  +++ +q+++ +++l++++++i +l+k++
  gi|313126714|ref|YP_004036984.1| 108 ETSlEEKREQLESVRDNLDEARSKIEELEKKN 139
                                       33378999*********************997 PP

>> DUF3847  Protein of unknown function (DUF3847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.7      0.27        23       4      32 ..      50      78 ..      40      82 .. 0.84
   2 ?    3.4   1.3         1        84       7      27 ..      88     108 ..      82     117 .. 0.58
   3 ?   11.2   5.3    0.0038      0.32       2      35 ..     118     153 ..     117     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.27
                           DUF3847  4 eLkaelekaekklrqaehkekiLenrlky 32
                                      +L+aele a+++l+  + + + L++ l++
  gi|313126714|ref|YP_004036984.1| 50 NLRAELESARTELKVLRERVNDLNQSLQQ 78
                                      69999999999999999999999887766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 1
                           DUF3847   7 aelekaekklrqaehkekiLe 27 
                                       aele +ek l+  + + ++ e
  gi|313126714|ref|YP_004036984.1|  88 AELESTEKLLNHTQAELERTE 108
                                       555555555555555544444 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0038
                           DUF3847   2 leeLkaelekaekklrqaehkekiLenrlkyle..R 35 
                                       le+ + +l++a++k+++ e+k+k Le ++++l+   
  gi|313126714|ref|YP_004036984.1| 118 LESVRDNLDEARSKIEELEKKNKTLEEQVAELKteN 153
                                       899***************************998543 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4         1        85       8      37 ..     148     177 ..     146     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 1
                    PRKG1_interact   8 eekeenerLkreLeelekelselkselekl 37 
                                       e k+en++L +e+++l+ + ++l+  l ++
  gi|313126714|ref|YP_004036984.1| 148 ELKTENKELSEEVDDLRDDRDDLQRDLREV 177
                                       567889999999999988888888877765 PP

>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.0     0.025       2.1      18      69 .]      25      80 ..      24      80 .. 0.85
   2 ?    7.8   8.0     0.041       3.4      27      65 ..     101     146 ..      90     149 .. 0.71
   3 ?    0.9   1.0         6     5e+02      35      57 ..     144     166 ..     137     176 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.025
                               HR1 18 GAenllralesk.ktqnkkvrqe...aeselsesnskielLreqLeelqasvqnsq 69
                                      GA  +++  +s+  tqn ++r++     +el++++++++ Lre+ ++l++s q++q
  gi|313126714|ref|YP_004036984.1| 25 GATMMYQSSASDlETQNDQLRERnknLRAELESARTELKVLRERVNDLNQSLQQTQ 80
                                      888899999999999999988873336789999*****************999876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.041
                               HR1  27 e......sk.ktqnkkvrqeaeselsesnskielLreqLeelqasv 65 
                                       +          +  +++++ +  +l+e++skie+L+++ ++l+ +v
  gi|313126714|ref|YP_004036984.1| 101 QaelertETsLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQV 146
                                       4555554222556777********************9977777655 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 6
                               HR1  35 kvrqeaeselsesnskielLreq 57 
                                       ++ +e ++e +e + +++ Lr+ 
  gi|313126714|ref|YP_004036984.1| 144 EQVAELKTENKELSEEVDDLRDD 166
                                       47777777778888788877775 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.7      0.01      0.85     100     184 ..      32     121 ..      19     123 .. 0.73
   2 ?    2.9   1.7      0.42        35     122     162 ..     110     150 ..      93     183 .. 0.40

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.01
                            Tweety 100 kanhtlagikklvseteesleekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselp.flkkk....dvsl 171
                                       +    l + +++  e +++l+ +le+  t+l+ + ++ +dl ++l+++q+ v +v+++l++ + +l+++    + + 
  gi|313126714|ref|YP_004036984.1|  32 SSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEkLLNHTqaelERTE 108
                                       55566778889999999999999999999999999999999999999999999999999988753444422222333 PP

                            Tweety 172 telaeqvelvely 184
                                       t+l e+ e++e++
  gi|313126714|ref|YP_004036984.1| 109 TSLEEKREQLESV 121
                                       4556666666665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.42
                            Tweety 122 kleeeLtkleeifakrtdlletlrlvqeqveevvqqlselp 162
                                       +lee+ ++le++ ++  +  + ++ ++++ +++ +q++el+
  gi|313126714|ref|YP_004036984.1| 110 SLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELK 150
                                       22222222222222222222222222222222222222222 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5     0.028       2.3      35      81 ..      53      99 ..      37     102 .. 0.87
   2 ?    5.2   2.9      0.19        16      36      71 ..     103     138 ..      98     153 .. 0.78
   3 ?   -0.0   0.2       7.7   6.5e+02      50      73 ..     152     175 ..     139     177 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.028
                              RPW8 35 krLestleritPvvkeieklnkeldrpreeieeLkklLekaekLVek 81
                                       +Les  ++++ ++++++ ln+ l++ + ++ +   +Le+ ekL++ 
  gi|313126714|ref|YP_004036984.1| 53 AELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNH 99
                                      4688888899999******************************9875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.19
                              RPW8  36 rLestleritPvvkeieklnkeldrpreeieeLkkl 71 
                                       +Le+t ++++  ++++e+++++ld+ r++ieeL+k+
  gi|313126714|ref|YP_004036984.1| 103 ELERTETSLEEKREQLESVRDNLDEARSKIEELEKK 138
                                       688888888889999999999999999999998764 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 7.7
                              RPW8  50 eieklnkeldrpreeieeLkklLe 73 
                                       e ++l++e+d  r++ ++L++ L+
  gi|313126714|ref|YP_004036984.1| 152 ENKELSEEVDDLRDDRDDLQRDLR 175
                                       445677777777777777777776 PP

>> DMPK_coil  DMPK coiled coil domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   4.1      0.99        83      35      60 ..      35      60 ..      25      83 .. 0.80
   2 ?    9.7  12.7     0.011      0.91      18      56 ..     116     154 ..     100     156 .. 0.90
   3 ?    4.8   0.7      0.36        30      40      59 ..     152     171 ..     148     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.99
                         DMPK_coil 35 keaEkknreLeeeleqLkkemEelra 60
                                       + E +n +L e  ++L+ e+E  r 
  gi|313126714|ref|YP_004036984.1| 35 SDLETQNDQLRERNKNLRAELESART 60
                                      56678888888888888888877665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.011
                         DMPK_coil  18 eeLekvkaanlafeskLkeaEkknreLeeeleqLkkemE 56 
                                       e+Le v++   ++ sk+ e Ekkn+ Lee++++Lk e  
  gi|313126714|ref|YP_004036984.1| 116 EQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENK 154
                                       78*********************************9865 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.36
                         DMPK_coil  40 knreLeeeleqLkkemEelr 59 
                                        n+eL ee++ L+++ + l+
  gi|313126714|ref|YP_004036984.1| 152 ENKELSEEVDDLRDDRDDLQ 171
                                       69***********9987776 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.5     0.027       2.2       7      52 ..      38      84 ..      32      88 .. 0.85
   2 ?    2.4  14.8       2.4     2e+02      10      99 ..      77     156 ..      71     157 .. 0.77
   3 ?    3.0   8.7       1.5   1.3e+02      13      51 ..     115     156 ..     113     178 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.027
                            CC2-LZ  7 eaekvk.keeieeLkaqlqaaeealaakqeeidelkeeikkkeeele 52
                                      e+++ + +e  ++L a+l++a   l+  +e++++l++++++ + ++ 
  gi|313126714|ref|YP_004036984.1| 38 ETQNDQlRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVG 84
                                      556666689999****************************9988775 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 2.4
                            CC2-LZ  10 kvkkeeieeLkaqlqaaeealaakqeeidelkeeikkkeeeletisvlkaQaevYrsDFeaEReaReklheekerla 86 
                                       ++ + ++ ++ a+l++ e+ l++ q e+++ ++++++k+e+le +          r   +  R+  e+l +++++l+
  gi|313126714|ref|YP_004036984.1|  77 QQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESV----------RDNLDEARSKIEELEKKNKTLE 143
                                       455778888999999999999999999999999988888866665..........5566666888888888888888 PP

                            CC2-LZ  87 aqleelqkqneqL 99 
                                       +q++el+++n++L
  gi|313126714|ref|YP_004036984.1| 144 EQVAELKTENKEL 156
                                       8888888888887 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 1.5
                            CC2-LZ  13 keeieeLkaqlqaaeealaakqeeidelkeeikkkee...el 51 
                                       +e++e++  +l++a  ++++ +++ + l+e++++ ++   el
  gi|313126714|ref|YP_004036984.1| 115 REQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTenkEL 156
                                       455555556666555555555555555555554444311133 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4      0.16        14      30      56 ..      31      57 ..      25      62 .. 0.86
   2 ?    0.6   0.5       8.9   7.5e+02      25      36 ..      85      96 ..      54     115 .. 0.50
   3 ?    7.1   4.7     0.079       6.6      11      49 ..     117     155 ..     103     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.16
                         kleA_kleC 30 laeAeeLvrqaeeLRakvyeesaaLed 56
                                      + +A +L+ q ++LR + ++ +a Le 
  gi|313126714|ref|YP_004036984.1| 31 QSSASDLETQNDQLRERNKNLRAELES 57
                                      5789************99999999985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 8.9
                         kleA_kleC 25 kiAaklaeAeeL 36
                                      ++Aa l++ e L
  gi|313126714|ref|YP_004036984.1| 85 HVAAELESTEKL 96
                                      344444444444 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.079
                         kleA_kleC  11 eLpevatdlvarRdkiAaklaeAeeLvrqaeeLRakvye 49 
                                       +L+ v ++l   R ki ++ ++ + L+ q++eL+++ +e
  gi|313126714|ref|YP_004036984.1| 117 QLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKE 155
                                       688999999999999999999999999999999987655 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.1      0.42        35      14      58 ..      42      90 ..      30     110 .. 0.56
   2 ?    7.2   4.3     0.048         4       7      58 ..     112     163 ..      90     186 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.42
                     USP8_interact 14 aelkkevaeqkqqlseqkrelellkeyiralrstn....pvlraladql 58
                                       +l+++ ++ + +l++ + el++l+e ++ l ++     + + ++a +l
  gi|313126714|ref|YP_004036984.1| 42 DQLRERNKNLRAELESARTELKVLRERVNDLNQSLqqtqGDVGHVAAEL 90
                                      5566666666777777777777777666544433211114444444444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.048
                     USP8_interact   7 qkqqqkiaelkkevaeqkqqlseqkrelellkeyiralrstnpvlraladql 58 
                                       +++++++++++++++e +++++e +++ ++l+e ++ l++ n++l +  d+l
  gi|313126714|ref|YP_004036984.1| 112 EEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDL 163
                                       4444455555555555555555555555555555555555554444333333 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  11.0      0.65        55      50     106 ..      69     122 ..      17     184 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.65
                                       THHHHHHHHHHHHHHHHHHHHHHT..........-BTCCG-S--HHHHHHHHHHHHHHHHHS--EE CS
                   Cob_adeno_trans  50 eeelkeaLeeiqneLfdlgaelatp.........ekkkekkkiteeeveelekeideleaelpplk 106
                                        ++l++ L++ q ++ ++ ael ++         e            +e+ e+ ++e +++l+ ++
  gi|313126714|ref|YP_004036984.1|  69 VNDLNQSLQQTQGDVGHVAAELESTekllnhtqaE------------LERTETSLEEKREQLESVR 122
                                       44555666666666666666664332333322220............2222222222222222111 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.5    0.0041      0.34      35      70 ..      29      64 ..      25      71 .. 0.89
   2 ?    6.7   3.9      0.12        10      24      59 ..     131     165 ..     127     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0041
                       Fungal_TACC 35 kyqkkldklelenkslkqeieqLkkqleaerkEKqe 70
                                       yq++ + le++n++l++  ++L+ +le++r+E + 
  gi|313126714|ref|YP_004036984.1| 29 MYQSSASDLETQNDQLRERNKNLRAELESARTELKV 64
                                      69*****************************99665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.12
                       Fungal_TACC  24 KVkllkkgyeakyqkkldklelenkslkqeieqLkk 59 
                                       K++ l k+  ++ ++++ +l++enk+l++e++ L++
  gi|313126714|ref|YP_004036984.1| 131 KIEELEKKN-KTLEEQVAELKTENKELSEEVDDLRD 165
                                       555555554.66778888888888888888888865 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3      0.15        12      13      36 ..      53      76 ..      41      78 .. 0.86
   2 ?    1.9   0.2       2.3     2e+02       7      31 ..     103     127 ..      97     130 .. 0.80
   3 ?    4.0   0.4      0.52        44       3      31 ..     116     144 ..     114     149 .. 0.83
   4 ?    4.8   0.3      0.28        24       3      30 ..     130     157 ..     128     161 .. 0.88
   5 ?    4.7   0.7      0.31        26       2      30 ..     143     171 ..     142     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.15
                         DASH_Dam1 13 etLdknledLqqihesLsdfNeSF 36
                                      ++L++  ++L+ ++e+++d+N+S+
  gi|313126714|ref|YP_004036984.1| 53 AELESARTELKVLRERVNDLNQSL 76
                                      47999999*************996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 2.3
                         DASH_Dam1   7 eLaDsletLdknledLqqihesLsd 31 
                                       eL+   + L+++ e+L++++++L++
  gi|313126714|ref|YP_004036984.1| 103 ELERTETSLEEKREQLESVRDNLDE 127
                                       6666667899999999999999975 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.52
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLsd 31 
                                       +++++  D+l++ ++++e+L++ +++L++
  gi|313126714|ref|YP_004036984.1| 116 EQLESVRDNLDEARSKIEELEKKNKTLEE 144
                                       68899999999999999999999988876 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.28
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLs 30 
                                        +++eL+++ +tL++++ +L+  +++Ls
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTENKELS 157
                                       58999**************999888887 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.31
                         DASH_Dam1   2 epafaeLaDsletLdknledLqqihesLs 30 
                                       e++ aeL+ + ++L++ ++dL + +++L+
  gi|313126714|ref|YP_004036984.1| 143 EEQVAELKTENKELSEEVDDLRDDRDDLQ 171
                                       66777777777777777777776666554 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  15.1      0.22        19      16     118 ..      47     150 ..      27     162 .. 0.55
   2 ?    3.9   4.7       0.5        42      13      57 ..     120     164 ..     109     185 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.22
                                       ........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  16 qdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaee 92 
                                       ++++l +  l+  ++e++ l+e +n+l + lq+ +    ++ +e+e + k  +++q  +e + + l++k+++ ++++
  gi|313126714|ref|YP_004036984.1|  47 RNKNL-RAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVR 122
                                       33333.66777777777777777777777777777777777777777765555566666666666665555555433 PP

                                       XXXXXXXXXXXXXXXXX..XXXXXXXXX CS
                              SKA1  93 skssspeeeeeteskke..keeeaekak 118
                                        + ++  ++ e+ +kk+   ee+ ++ k
  gi|313126714|ref|YP_004036984.1| 123 DNLDEARSKIEELEKKNktLEEQVAELK 150
                                       3333333222222222223222222222 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.5
                                       ...........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  13 ainqdpallkedlskieaevsaleellnklkkelqeeeeaikklk 57 
                                       ++  + + ++++++++e++ ++lee++++lk+e +e +e  ++l+
  gi|313126714|ref|YP_004036984.1| 120 SVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLR 164
                                       333333334566777777777777777777665444444443333 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   7.3    0.0042      0.35     125     164 ..     129     168 ..     121     186 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0042
                   Ax_dynein_light 125 ekkikeLeeekeelekqvaelkaklealekrekerrqeee 164
                                       ++ki+eLe+++++le+qvaelk++ ++l ++  + r+ ++
  gi|313126714|ref|YP_004036984.1| 129 RSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRD 168
                                       4455555555555555555555555555444444333333 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.3      0.25        21      83     124 ..      34      75 ..      25      82 .. 0.60
   2 ?    2.1   7.2       1.1        91      75     122 ..      61     108 ..      37     114 .. 0.70
   3 ?    4.4   5.9      0.21        18      77     116 ..      91     130 ..      64     138 .. 0.52
   4 ?    7.2   5.7      0.03       2.5      75     129 ..     117     174 ..     115     186 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.25
                       DLP_helical  83 leelekevekleesakriekelaelkkeieearielreelka 124
                                       +++le++ ++l+e++k++++el++++ e++  r+ +++  ++
  gi|313126714|ref|YP_004036984.1|  34 ASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQS 75 
                                       455666666666666666666666666666655555444333 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 1.1
                       DLP_helical  75 qlpeaeerleelekevekleesakriekelaelkkeieearielreel 122
                                       +l++ +er+++l++ +++ + ++ +  +el++++k ++++++el++  
  gi|313126714|ref|YP_004036984.1|  61 ELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTE 108
                                       566677777777777777777777777777777777777777776655 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.21
                       DLP_helical  77 peaeerleelekevekleesakriekelaelkkeieeari 116
                                       +  e+ l+++++e+e+ e+s+++ +++l++++ ++ ear 
  gi|313126714|ref|YP_004036984.1|  91 ESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARS 130
                                       3333344444444444444444444444444444444444 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.03
                       DLP_helical  75 qlpeaeerleelekevekleesakriek...elaelkkeieearielreelkayfsdL 129
                                       ql+ ++++l+e+ +++e+le+++k++e+   el++ +ke++e   +lr+  +++  dL
  gi|313126714|ref|YP_004036984.1| 117 QLESVRDNLDEARSKIEELEKKNKTLEEqvaELKTENKELSEEVDDLRDDRDDLQRDL 174
                                       7788888888888877777776666665111455556777777777777777777776 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       3.3   2.8e+02     400     434 ..      36      70 ..      26      80 .. 0.62
   2 ?    8.0   5.8      0.01      0.83     361     426 ..      85     156 ..      74     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.3
                                       TTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Hemagglutinin 400 elekrieeldkkvddgfldvityniellvllener 434
                                       +le + ++l ++ +++++++ + + el vl e  +
  gi|313126714|ref|YP_004036984.1|  36 DLETQNDQLRERNKNLRAELESARTELKVLRERVN 70 
                                       56666666666666666666666777666654433 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.01
                                       EEEEXHHHHHHHHHHHHHHHH...HHHHHTTTEEEBXSSXXTTTTHHHHHHHHH...HHHHHHHHHHHHHHH CS
                     Hemagglutinin 361 avaadkkstqeainkitkkvn...sliekenkqleavgkelnelekrieeldkk...vddgfldvityniel 426
                                        vaa+++st + +n    +++   +  e +  qle+v  +l+e + +ieel+kk   +++  +++ t n el
  gi|313126714|ref|YP_004036984.1|  85 HVAAELESTEKLLNHTQAELErteTSLEEKREQLESVRDNLDEARSKIEELEKKnktLEEQVAELKTENKEL 156
                                       58************998877522156788899*******************887333566677777777776 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.1     0.022       1.9      16      57 ..      37      78 ..      31      92 .. 0.83
   2 ?    2.6   6.6         2   1.7e+02      12      71 ..      89     151 ..      83     152 .. 0.55
   3 ?    6.4   7.8      0.13        11       2      66 ..     121     185 ..     115     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.022
                             Tup_N 16 lsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrk 57
                                      l++++ +l+++++++ + ++s   El+ +r+ + +L+++ ++
  gi|313126714|ref|YP_004036984.1| 37 LETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQ 78
                                      677888899999999999999999999999999999887655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 2
                             Tup_N  12 EfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahr...kikqqYEeeiarLka 71 
                                       E ++ ++ +++++a+ +  e++++++ + l+++r +l e  ++ +   k  ++ Ee++a+Lk+
  gi|313126714|ref|YP_004036984.1|  89 ELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEeleKKNKTLEEQVAELKT 151
                                       555555556666666666666666666666666666666554433111334456667776665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.13
                             Tup_N   2 lnelLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYEeei 66 
                                       + + Ld  ++ +++l++++++l++q  e+ +  ++  +E++ +r    +L++  r++ + + ee 
  gi|313126714|ref|YP_004036984.1| 121 VRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDDWSEEA 185
                                       45667777777777777777777777777777777777778888888888877777777777775 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.9     0.035       2.9      97     143 ..      31      77 ..      29      78 .. 0.90
   2 ?    3.5   6.3      0.92        77     101     143 ..      91     133 ..      85     134 .. 0.87
   3 ?    7.8   6.9     0.044       3.7     105     138 ..     130     163 ..     126     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.035
                             Med21  97 gsseeeqeerikeLeeelreveeereekvkekeellkkveellrava 143
                                       +ss  + e++ ++L e +++ ++e+e +++e + l+++v++l ++++
  gi|313126714|ref|YP_004036984.1|  31 QSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQ 77 
                                       578888999999****************************9987765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.92
                             Med21 101 eeqeerikeLeeelreveeereekvkekeellkkveellrava 143
                                       e+ e+ ++  ++el++ e+ +eek+++ e ++++++e+ ++++
  gi|313126714|ref|YP_004036984.1|  91 ESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIE 133
                                       56788888999*************************9988775 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.044
                             Med21 105 erikeLeeelreveeereekvkekeellkkveel 138
                                        +i+eLe++++  ee+ +e  +e++el ++v++l
  gi|313126714|ref|YP_004036984.1| 130 SKIEELEKKNKTLEEQVAELKTENKELSEEVDDL 163
                                       6788888888888888888888888888888876 PP

>> HCMV_UL139  Human Cytomegalovirus UL139 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   4.5       6.8   5.7e+02      50      83 ..     101     134 ..      34     142 .. 0.59
   2 ?    8.7   2.6     0.026       2.2      25      77 ..     132     184 ..     125     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 6.8
                        HCMV_UL139  50 rseidaldakyvaisrdlrslkgeveeaerkeee 83 
                                       ++e++  ++  +   ++l s++ + +ea +k ee
  gi|313126714|ref|YP_004036984.1| 101 QAELERTETSLEEKREQLESVRDNLDEARSKIEE 134
                                       3444444444444444445555555555555444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.026
                        HCMV_UL139  25 irslerrcllLerkiadlnsrilslrseidaldakyvaisrdlrslkgeveea 77 
                                       i  le+    Le ++a+l      l  e+d+l+  ++   rdlr+++ + +e+
  gi|313126714|ref|YP_004036984.1| 132 IEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLREVCDDWSEE 184
                                       566777777899999999999999999********************998886 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  17.7      0.11       8.8      31     126 ..      54     159 ..      28     187 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                        V_ATPase_I  31 rcdemerklrfleeeieklekavikeeea..........eesleapeekeldeleeelekleeelkelnenleklkk 97 
                                        ++    +l++l+e +++l++  ++++ +          +e+l +++++el++ e++le++ e+l+++++nl++ ++
  gi|313126714|ref|YP_004036984.1|  54 ELESARTELKVLRERVNDLNQSLQQTQGDvghvaaelesTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARS 130
                                       45666667777777777766666665555666544444444444555555555555555555555555555555555 PP

                        V_ATPase_I  98 elnelvelkavlekakefleeeeeeeeee 126
                                       + +el+++++ le+  + l++e++e +ee
  gi|313126714|ref|YP_004036984.1| 131 KIEELEKKNKTLEEQVAELKTENKELSEE 159
                                       55555555555544444443332222211 PP

>> DUF3053  Protein of unknown function (DUF3053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   3.7      0.21        18      88     133 ..      51      96 ..      22     108 .. 0.66
   2 ?    6.1   4.0     0.089       7.5      73     121 ..     108     154 ..      98     179 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.21
                           DUF3053  88 spqdyltrrdelrqaagalneleqqlqnakaqadkaraaLkqpddl 133
                                         +++ + r el+  ++++n l+q+lq+++  + +  a L+  + l
  gi|313126714|ref|YP_004036984.1|  51 LRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKL 96 
                                       3345556788888888888888888888888888888877766655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.089
                           DUF3053  73 etslepvvdalqsirspqdyl.trrdelrqaagalneleqqlqnakaqad 121
                                       etsle++    ++++s++d+l + r+++++ +++++ le+q+++ k++++
  gi|313126714|ref|YP_004036984.1| 108 ETSLEEK---REQLESVRDNLdEARSKIEELEKKNKTLEEQVAELKTENK 154
                                       3333333...3344455444423455555555555555555555555554 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.5      0.02       1.7      16      63 ..      34      81 ..      26      91 .. 0.84
   2 ?    3.6  15.9       1.1        94       4      72 ..      92     160 ..      88     162 .. 0.89
   3 ?    7.0   1.0     0.092       7.7       3      26 ..     154     177 ..     152     184 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.02
                              KELK 16 keelqkelaeaqErlksqkkeLkdaisqrklamqefsevneklselrs 63
                                        +l+ +  +++Er k+   eL  a +  k+ ++  +++n+ l++++ 
  gi|313126714|ref|YP_004036984.1| 34 ASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQG 81
                                      568999999999999999999999999999999999999999988875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 1.1
                              KELK   4 eLekqlrllkqEkeelqkelaeaqErlksqkkeLkdaisqrklamqefsevneklselrsqkqklsRql 72 
                                       + ek l +++ E e ++  l+e +E+l s   +L +a s+ +   +  + ++e+++el+++ ++ls ++
  gi|313126714|ref|YP_004036984.1|  92 STEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEV 160
                                       4577778888888888999*********************************************99776 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.092
                              KELK   3 keLekqlrllkqEkeelqkelaea 26 
                                       keL +++  l+ ++++lq++l e+
  gi|313126714|ref|YP_004036984.1| 154 KELSEEVDDLRDDRDDLQRDLREV 177
                                       677777777777777777777776 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   9.7      0.89        74     140     226 ..      39     123 ..      13     124 .. 0.64
   2 ?    6.1  12.6     0.085       7.2     142     218 ..      90     164 ..      64     182 .. 0.51

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.89
                           HAUS6_N 140 kkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkae.keaakkekkeased 215
                                       +++ +l++ ++  r++l+   +e++     r++++++ q+l++ + ++ +  +el++  k+    +a+ e+ e s +
  gi|313126714|ref|YP_004036984.1|  39 TQNDQLRERNKNLRAELESARTELKVL---RERVNDLNQSLQQTQGDVGHVAAELESTEKLLnHTQAELERTETSLE 112
                                       344466777777777777777777777...77777777777777777666666665544433355556666666777 PP

                           HAUS6_N 216 aeeekikkvrn 226
                                       +++e+ ++vr 
  gi|313126714|ref|YP_004036984.1| 113 EKREQLESVRD 123
                                       77777777775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.085
                           HAUS6_N 142 aqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekkeasedaee 218
                                        ++++kl  +++++l+r+ + ++++ +  + +++n+++ + k++el+++++ l++++  e  + +++++ ++ d ++
  gi|313126714|ref|YP_004036984.1|  90 LESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTLEEQVA-EL-KTENKELSEEVDDLR 164
                                       3344444444444444444444444444777888888888888888888887777775.22.222222222222222 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   9.1       0.9        75      84     145 ..      46     107 ..      37     114 .. 0.72
   2 ?    4.4  16.7      0.29        24      31     117 ..      85     177 ..      77     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.9
                              DegS  84 eeakelqvelallrekEkqlrerRdelerrLkklketierAeklvsqvgvvlnyLsgdlkqv 145
                                       e+ k+l++el  +r + k lrer ++l+++L++++  +      +++ +  ln  + +l++ 
  gi|313126714|ref|YP_004036984.1|  46 ERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERT 107
                                       67789999999999999999999999999999998877665555555555555555555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.29
                              DegS  31 rlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkys......eeeikeaYeeakelqvelallrekEk 101
                                       ++  ele +++ ++++ +e +++e+   ++r++L  V  + ++ +      e++ k+  e++ el++e + l e+  
  gi|313126714|ref|YP_004036984.1|  85 HVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARskieelEKKNKTLEEQVAELKTENKELSEEVD 161
                                       5555555555555555555555555555555555555555544321111225667888999999999999999999* PP

                              DegS 102 qlrerRdelerrLkkl 117
                                       +lr+ Rd+l+r+L+++
  gi|313126714|ref|YP_004036984.1| 162 DLRDDRDDLQRDLREV 177
                                       *************987 PP

>> CENP-K  Centromere-associated protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.6      0.22        18      89     148 ..      31      90 ..      22     101 .. 0.79
   2 ?    5.7  12.9      0.11       9.6     108     179 ..      99     167 ..      90     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.22
                            CENP-K  89 qklksqLelvlsiiqsknkklkedLkrEqewleeqqeilesLkektkelkkqvvafsekt 148
                                       q  +s+Le     ++ +nk+l+++L+  ++ l+  +e ++ L+++ ++ + +v ++  + 
  gi|313126714|ref|YP_004036984.1|  31 QSSASDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAEL 90 
                                       566789********************9998888888888888888888887777766554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.11
                            CENP-K 108 klkedLkrEqewleeqqeilesLkektkelkkqvvafsektrksaelkekirkikeykeeLltaLgefLdeh 179
                                       + +++L+r  + lee++e les+    +e +++ +++ +k    + l+e+  ++k+ ++eL + ++++ d+ 
  gi|313126714|ref|YP_004036984.1|  99 HTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKK---NKTLEEQVAELKTENKELSEEVDDLRDDR 167
                                       4567888888889999998888888888888666666555...67788888888888888888888776665 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  12.9       3.2   2.7e+02     103     174 ..      65     146 ..      27     184 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 3.2
                      Bacillus_HBL 103 llellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdv.......deltsi...lagdsgvisqlqneied 169
                                       l e++++L++++qq q  v ++++eL++ ++ l++ +++++ +        ++l+s+   l     +i++l++++++
  gi|313126714|ref|YP_004036984.1|  65 LRERVNDLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTEtsleekrEQLESVrdnLDEARSKIEELEKKNKT 141
                                       44556666666666666666666555544443333333333222222222255555422244444666666666666 PP

                      Bacillus_HBL 170 lqgki 174
                                       l++++
  gi|313126714|ref|YP_004036984.1| 142 LEEQV 146
                                       66665 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.4      0.58        48      55      76 ..      52      73 ..      45      74 .. 0.87
   2 ?    1.8   0.6       4.2   3.5e+02      50      73 ..      89     112 ..      87     114 .. 0.85
   3 ?   10.3   5.0     0.009      0.75      47      76 ..     114     143 ..     113     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.58
                              BMFP 55 revlartrekleaLearvaaLE 76
                                      r+ l+ +r++l+ L++rv+ L 
  gi|313126714|ref|YP_004036984.1| 52 RAELESARTELKVLRERVNDLN 73
                                      677999************9996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 4.2
                              BMFP  50 EFdvqrevlartrekleaLearva 73 
                                       E++   ++l  t+++le+ e  ++
  gi|313126714|ref|YP_004036984.1|  89 ELESTEKLLNHTQAELERTETSLE 112
                                       889999***********8887665 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.009
                              BMFP  47 tREEFdvqrevlartrekleaLearvaaLE 76 
                                       +RE ++ +r+ l ++r k+e+Le++ + LE
  gi|313126714|ref|YP_004036984.1| 114 KREQLESVRDNLDEARSKIEELEKKNKTLE 143
                                       69******************9999999988 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2    0.0038      0.31      16      64 .]       7      56 ..       2      77 .. 0.69
   2 ?    6.1   1.8      0.12       9.7      45      63 ..     128     146 ..     122     147 .. 0.92
   3 ?    0.7   0.1       5.4   4.5e+02      50      63 ..     147     160 ..     145     167 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0038
                          LapA_dom 16 elpLsllllvafgiGallgwllslwsyl.rlrrelrrlkkkikklekele 64
                                       ++L+l+ +va+++   +g  +++ s    l  ++ +l++++k l++ele
  gi|313126714|ref|YP_004036984.1|  7 PINLALVAVVALLLTGTVGATMMYQSSAsDLETQNDQLRERNKNLRAELE 56
                                      67889999999999888888888844443455555555555555555543 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.12
                          LapA_dom  45 lrrelrrlkkkikklekel 63 
                                        r+++ +l+kk+k+le+++
  gi|313126714|ref|YP_004036984.1| 128 ARSKIEELEKKNKTLEEQV 146
                                       5999*************98 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 5.4
                          LapA_dom  50 rrlkkkikklekel 63 
                                        +lk ++k+l +e+
  gi|313126714|ref|YP_004036984.1| 147 AELKTENKELSEEV 160
                                       56677777777776 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.9      0.15        13     142     200 ..      22      79 ..      15      84 .. 0.72
   2 ?    5.7   2.4      0.12        10     135     201 ..      74     136 ..      73     146 .. 0.71
   3 ?    5.0   2.8      0.19        16     146     199 ..     123     176 ..     101     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.15
                            AAA_27 142 gelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelrea 200
                                       g +g +++  s++ ++l++  ++L+++ ++l ++ +s++++++  +e++++++++l++ 
  gi|313126714|ref|YP_004036984.1|  22 GTVGATMMYQSSA-SDLETQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQT 79 
                                       5566555544443.678888888888888888888888888888888888888877765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.12
                            AAA_27 135 ealleaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelreaq 201
                                       ++l +++g++g++  e ++  + l++++++Le+  ++l ++r++ +      +++l+ea+++++e +
  gi|313126714|ref|YP_004036984.1|  74 QSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQLE----SVRDNLDEARSKIEELE 136
                                       5788999******999999999999999999999999988887776....33444444444444333 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.19
                            AAA_27 146 qlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                         L ea++ +++l++  ++Le++  el +++k+ ++++ + +++ +++++ lre
  gi|313126714|ref|YP_004036984.1| 123 DNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQRDLRE 176
                                       345567777777777777777777777777777777777777777777777665 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   6.5      0.54        45      55     114 ..      39      98 ..      26     111 .. 0.67
   2 ?    4.8  12.9      0.34        29      64     123 ..      83     142 ..      70     179 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.54
                             CREPT  55 ealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrk 114
                                       +   +l e nk L aele  ++  k l++ ++ ++++l++++  + ++   le +++  +
  gi|313126714|ref|YP_004036984.1|  39 TQNDQLRERNKNLRAELESARTELKVLRERVNDLNQSLQQTQGDVGHVAAELESTEKLLN 98 
                                       455678999999999999888877888888888888888888776666555555444332 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.34
                             CREPT  64 nkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                       ++  +aele  +kl +  ++ le   ++l++++e+le++++ l++ +s+ +el+++ + L
  gi|313126714|ref|YP_004036984.1|  83 VGHVAAELESTEKLLNHTQAELERTETSLEEKREQLESVRDNLDEARSKIEELEKKNKTL 142
                                       555666666666666666666666666666666666666666666666666666655554 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.5     0.036         3     381     443 ..      34      95 ..      11     112 .. 0.77
   2 ?    4.4   3.9      0.13        11     370     411 ..     121     162 ..     112     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.036
                        Herpes_UL6 381 iekLkkenelllkklkelekeLerlreeakk.eakarevdlltsstdaslenlpessalsklkk 443
                                        ++L+++n++l +++k+l+ eLe +r+e k    + ++ + + ++t+ +++++   ++l+  +k
  gi|313126714|ref|YP_004036984.1|  34 ASDLETQNDQLRERNKNLRAELESARTELKVlRERVNDLNQSLQQTQGDVGHV--AAELESTEK 95 
                                       579**********************9998876777788888888888888888..444444444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.13
                        Herpes_UL6 370 leeqineqfdtiekLkkenelllkklkelekeLerlreeakk 411
                                       + + ++e   +ie+L+k+n++l+++++el++e ++l ee   
  gi|313126714|ref|YP_004036984.1| 121 VRDNLDEARSKIEELEKKNKTLEEQVAELKTENKELSEEVDD 162
                                       55666777789999*********9999999999888666554 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   8.9      0.13        11     296     407 ..      41     153 ..      11     186 .. 0.42

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.13
                              ALMT 296 keelqrvslesakvlrelaesvkkmkklsk.veellkevkvaaeeLqskldskskLlvnsekweaakkkekaeevee 371
                                       +++l++ +++    l++   ++k  ++  +  +++l++ +  + ++ ++l+s  kLl +++ + + ++++ +e+ e+
  gi|313126714|ref|YP_004036984.1|  41 NDQLRERNKNLRAELESARTELKVLRERVNdLNQSLQQTQGDVGHVAAELESTEKLLNHTQAELERTETSLEEKREQ 117
                                       34444444444444444444444333322224455555555555555555555555544444222222222222222 PP

                              ALMT 372 kkeeekeseskkeeaeaveeaeseseksllkeskrs 407
                                        ++ +++ ++ +++ e+ e+++++ e+++ + ++++
  gi|313126714|ref|YP_004036984.1| 118 LESVRDNLDEARSKIEELEKKNKTLEEQVAELKTEN 153
                                       222222222222222222222222111111111111 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   8.0       2.8   2.4e+02      14     116 ..      12     117 ..      10     129 .. 0.51
   2 ?    7.6   9.6     0.044       3.7      51     112 ..     109     172 ..      97     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 2.8
                           DUF4337  14 llAisslkggnaqteailaqaeasdqWafYQAksikehlaeleleqlelllkak...aeelaaavdkkiakykkkia 87 
                                       l+A+++l  + ++ +++++q+ asd        + +++ ++ ele+++++lk      ++l++  ++++ ++ + +a
  gi|313126714|ref|YP_004036984.1|  12 LVAVVALLLTGTVGATMMYQSSASDLETQNDQLRERNKNLRAELESARTELKVLrerVNDLNQSLQQTQGDVGHVAA 88 
                                       56777777777888888888888887554433333334444444444444333333444444445555555555555 PP

                           DUF4337  88 rykkekkeikkkAkeleaerdeaneasdk 116
                                       + ++ +k +++   ele++ + ++e+ ++
  gi|313126714|ref|YP_004036984.1|  89 ELESTEKLLNHTQAELERTETSLEEKREQ 117
                                       55555444555555555555555554444 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.044
                           DUF4337  51 hlaeleleqlelllkak..aeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdeane 112
                                       + +e ++eqle  +++   a+ + ++ +kk++++++++a+ k+e ke++++ ++l ++rd++++
  gi|313126714|ref|YP_004036984.1| 109 TSLEEKREQLESVRDNLdeARSKIEELEKKNKTLEEQVAELKTENKELSEEVDDLRDDRDDLQR 172
                                       3456667777777777677777777888888888888888888888888888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3293  (0.183669); expected 358.6 (0.02)
Passed bias filter:                     1328  (0.0740699); expected 358.6 (0.02)
Passed Vit filter:                       389  (0.0216967); expected 17.9 (0.001)
Passed Fwd filter:                       283  (0.0157845); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             214  [number of targets reported over threshold]
# CPU time: 2.08u 0.37s 00:00:02.45 Elapsed: 00:00:00.60
# Mc/sec: 971.49
//
Query:       gi|313126715|ref|YP_004036985.1|  [L=367]
Description: hypothetical protein Hbor_19740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.31    9.1   7.7       0.45    8.5   0.1    2.0  2  Sporozoite_P67  Sporozoite P67 surface antigen


Domain annotation for each model (and alignments):
>> Sporozoite_P67  Sporozoite P67 surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   2.5e-05      0.45     101     236 ..      19     164 ..       2     209 .. 0.65
   2 ?    3.8   2.1   0.00067        12     641     686 ..     288     333 ..     278     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 2.5e-05
                    Sporozoite_P67 101 sdteined.dkGskedseedddeeeeednkstsskdgkgskkaqpgvssssgsttsqtdlstklsqtglg...asGs 173
                                         +e +++ ++ +   s+ d de +  d+    + d+ ++  ++   ++++ +t++++d+st++ ++ ++     G 
  gi|313126715|ref|YP_004036985.1|  19 WTVESKDGaGDAATAVSNGDSDETDGSDDSNEVTPDEAETAAGEAN-EATANETAADRDTSTAQMRAAISevrREGR 94 
                                       4454444313334445666666666677777777777777766665.88999999*******999998885545677 PP

                    Sporozoite_P67 174 haqqdpavsvsgvvgvp.GlgvpGvGvpGvggvgvlpgvgvprvgvapgvGvgglggvpgvgv......l 236
                                       +     a+  +g+v  +  +g         gg+  lpg   +  gv+p +  g +    g+g+       
  gi|313126715|ref|YP_004036985.1|  95 KIAFLYALLDAGLVALAvNIGLRLFRPDALGGALSLPGAVAGAGGVVPATIYGSTIAGLGIGIltfvaeF 164
                                       7666677777777664314555555555678999999999999999999988844444455555555550 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.00067
                    Sporozoite_P67 641 dpskvtptqpsnlpqvptsgqgngteGkeqqpsagngsgnGegGkd 686
                                       d   ++  + s+   v  +g+g+gt G++ +ps+ + sg  ++  +
  gi|313126715|ref|YP_004036985.1| 288 DAENISAGDESINASVQGTGSGEGTSGSTAPPSSYDDSGFADAAVE 333
                                       556777888899999*******************999887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2253.67
//
Query:       gi|313126716|ref|YP_004036986.1|  [L=314]
Description: moxr-like ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-61  204.4   0.2    8.2e-61  203.6   0.2    1.4  1  AAA_3            ATPase family associated with various cellul
    3.8e-19   68.3   0.6    7.8e-19   67.3   0.6    1.6  1  AAA_lid_2        AAA lid domain
    1.7e-11   44.3   0.0      3e-11   43.5   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    3.4e-07   29.6   0.0      6e-07   28.8   0.0    1.4  1  MCM              MCM P-loop domain
    1.7e-05   25.3   0.0    3.2e-05   24.3   0.0    1.5  1  AAA              ATPase family associated with various cellul
    0.00095   18.9   0.0     0.0082   15.9   0.0    2.0  2  Sigma54_activat  Sigma-54 interaction domain
     0.0038   17.0   0.0      0.033   14.0   0.0    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.024   14.0   0.0       0.35   10.2   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.087   13.2   0.0        8.6    6.7   0.0    2.3  2  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.6   0.2   4.1e-64   8.2e-61       2     131 .]      44     175 ..      43     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.6 bits;  conditional E-value: 4.1e-64
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvfanllladeinrapp 76 
                                        lle+ PGl+kt+lv+++a++ dl+f+riq tpdl+Psdi+Gte+++e +  +ef f+kGpvfanl+ladeinra+p
  gi|313126716|ref|YP_004036986.1|  44 ALLESNPGLGKTTLVRTVAEVTDLSFSRIQNTPDLMPSDITGTEIIREIDdgREFVFEKGPVFANLVLADEINRATP 120
                                       599*******************************************9866669************************ PP

                             AAA_3  77 ktqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       ktq+alleam+e+qvt++get++lp+pf++latqnPi+q Gtyplpeaq drfl+
  gi|313126716|ref|YP_004036986.1| 121 KTQAALLEAMQEQQVTAAGETYELPRPFFILATQNPIDQGGTYPLPEAQTDRFLM 175
                                       *****************************************************98 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.6   3.9e-22   7.8e-19       2      72 ..     238     309 ..     237     310 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 3.9e-22
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeivee 72 
                                        tr+++ +e+g+s+r a++ l+ aA+A+A+l+gr +V+ eDv+e+a ++L+HR+    ++e+eg t e+ v++
  gi|313126716|ref|YP_004036986.1| 238 STREAENVEFGASPR-ASMGLVLAAKARAFLAGRSHVSWEDVEEMALPILRHRILldFRAEREGITPEDAVRQ 309
                                       699************.****************************************99999999999999987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   1.5e-14     3e-11       3     138 .]      45     173 ..      43     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.5e-14
                                       EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGG CS
                             AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEve 75 
                                       lL  +pG gK++l++ +a+++  ++  +q+t d+ ++d++g   i+    +++ +++++p+      + +++ DE++
  gi|313126716|ref|YP_004036986.1|  45 LLESNPGLGKTTLVRTVAEVTDLSFSRIQNTPDLMPSDITGTEIIReiddGREFVFEKGPVF-----ANLVLADEIN 116
                                       56668***********************************9877777878888999******.....99******** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra ++++++Ll  + e+++  + g +++  ++      f ++at np d ++  +l +a  +Rf
  gi|313126716|ref|YP_004036986.1| 117 RATPKTQAALLEAMQEQQVT-AAGETYELPRP------FFILATQNPIDqGGTYPLPEAQTDRF 173
                                       *******************9.55555555555......9**********888888888888888 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0     3e-10     6e-07      53     175 ..      37     160 ..       6     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3e-10
                                       BBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSS..SSSSHS..SSEEEEESSSSSEEEEETHHHHTTTSEE CS
                               MCM  53 klrgdinvllvgdpgtaKsqlLkyveklapravytsgkg..ssaagL..taavvrdeetgefvleaGalvladkGvc 125
                                        +  d n ll ++pg++K++l+++v+++++ +     ++     +++  t  ++  ++ +efv+e G +      ++
  gi|313126716|ref|YP_004036986.1|  37 CILCDGNALLESNPGLGKTTLVRTVAEVTDLSFSRIQNTpdLMPSDItgTEIIREIDDGREFVFEKGPVFAN---LV 110
                                       56678899******************99877654433331144555522566677788899******98754...89 PP

                                       EEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S..S CS
                               MCM 126 ciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk..a 175
                                       + De+++ + +++ al+Eam +q+++   aG ++ L+    +la  np+  +
  gi|313126716|ref|YP_004036986.1| 111 LADEINRATPKTQAALLEAMQEQQVT--AAGETYELPRPFFILATQNPIdqG 160
                                       9*******************999875..68999***************8434 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.6e-08   3.2e-05       2     113 ..      45     158 ..      44     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.6e-08
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEE.ETTTCS.SS.....STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
                               AAA   2 llyGppGtGKTllakavakelgveflei.sgsell.sk.....yvgesekkirelfkeakekakpsilfiDEidala 71 
                                       ll  +pG GKT+l++ va+ ++ +f +i + ++l+ s+     ++ e  +  + +f++    a    ++ DEi + +
  gi|313126716|ref|YP_004036986.1|  45 LLESNPGLGKTTLVRTVAEVTDLSFSRIqNTPDLMpSDitgteIIREIDDGREFVFEKGPVFA--NLVLADEINRAT 119
                                       78889*****************99987735678884447666666666777777777666655..99********** PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTS.......SSTEEEEEEESS.GG CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkk.......eskvivigatnr.pd 113
                                       ++            +++Ll+++++++           + ++i+at++ +d
  gi|313126716|ref|YP_004036986.1| 120 PKT-----------QAALLEAMQEQQVTaagetyeLPRPFFILATQNpID 158
                                       ***...........9********999999999999444566666665333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.25     5e+02      11      44 ..      30      63 ..      23      77 .. 0.80
   2 !   15.9   0.0   4.1e-06    0.0082      98     142 ..     111     154 ..     103     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.25
                                      HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellaraihe 44
                                      ++e++  ++  d + l++ + G GK++l r++ e
  gi|313126716|ref|YP_004036986.1| 30 VIERLLVCILCDGNALLESNPGLGKTTLVRTVAE 63
                                      5666666777888999***********9998866 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.1e-06
                                       EEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  98 fLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                       + Dei++ ++++Q+ Ll+++qe++v+  G++ e +  + i  at+
  gi|313126716|ref|YP_004036986.1| 111 LADEINRATPKTQAALLEAMQEQQVTAAGETYELPRPFFI-LATQ 154
                                       56****************************9998876644.4444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.6e-05     0.033       9     111 ..      24     133 ..      16     141 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                            RuvB_N   9 yigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaa..lltnl 82 
                                        +gq++v e+l ++i +           ll   PGlGkttl + +a+  + ++ +i  +P l  ++d+++  ++ ++
  gi|313126716|ref|YP_004036986.1|  24 IVGQSDVIERLLVCILCD-------GNALLESNPGLGKTTLVRTVAEVTDLSFsRIQNTPDLM-PSDITGteIIREI 92 
                                       566666666666666543.......246999***************99888763566667664.4555432255555 PP

                            RuvB_N  83 eek............dvlfideihrlsraveevlysamedf 111
                                       +++            ++++ dei r +++++  l  am++ 
  gi|313126716|ref|YP_004036986.1|  93 DDGrefvfekgpvfaNLVLADEINRATPKTQAALLEAMQEQ 133
                                       54211111111111134455666666666666666666655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00018      0.35       3      44 ..      22      63 ..      21      76 .. 0.91
   2 ?    1.1   0.0      0.11   2.2e+02     111     162 ..     111     160 ..     106     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                      Mg_chelatase  3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                      k ++Gq++  + l +++    n ll  +pG GKt l + +++
  gi|313126716|ref|YP_004036986.1| 22 KRIVGQSDVIERLLVCILCDGNALLESNPGLGKTTLVRTVAE 63
                                      5799********************************998876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                      Mg_chelatase 111 fLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcg 162
                                       + DE+   + k+  +L e +++++vt   a ++ e p  f ++a+ Np   g
  gi|313126716|ref|YP_004036986.1| 111 LADEINRATPKTQAALLEAMQEQQVTA--AGETYELPRPFFILATQNPIDQG 160
                                       569999999999999999999999876..56677889999999999998665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0043       8.6      11      33 ..      42      64 ..      35      75 .. 0.84
   2 ?    4.1   0.0     0.028        55     103     137 ..     107     140 ..      84     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0043
                            AAA_19 11 kvllvtaGpGtGKTrvlkhival 33
                                      ++ l+   pG GKT++++++ ++
  gi|313126716|ref|YP_004036986.1| 42 GNALLESNPGLGKTTLVRTVAEV 64
                                      56788899********9998776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.028
                            AAA_19 103 eellivDEfqdvd.elqyrLlkallgekkklllvGD 137
                                       ++l++ DE+   + ++q +Ll+a+  e++ +++ G 
  gi|313126716|ref|YP_004036986.1| 107 ANLVLADEINRATpKTQAALLEAMQ-EQQ-VTAAGE 140
                                       55899********99*********9.444.777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1935.48
//
Query:       gi|313126717|ref|YP_004036987.1|  [L=286]
Description: hypothetical protein Hbor_19760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-20   71.2   0.2      2e-19   69.6   0.0    1.9  2  DUF58     Protein of unknown function DUF58
    2.4e-05   24.9   0.1     0.0001   22.9   0.0    2.1  2  VWA_2     von Willebrand factor type A domain
    0.00026   20.5   0.1      0.009   15.4   0.1    2.4  2  VWA_CoxE  VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
        0.1   12.8   0.0       0.22   11.8   0.0    1.7  1  BtrH_N    Butirosin biosynthesis protein H, N-terminal


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   4.5e-23     2e-19       1      85 [.      38     122 ..      38     123 .. 0.95
   2 ?   -2.1   0.0       1.1     5e+03      61      67 ..     163     169 ..     136     198 .. 0.53

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 4.5e-23
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarql 77 
                                       gl f++ R Y+pgD+ r IdW+++ARt e+yv++fe+er+ tv +++d+s++m+ g+ +  k+e  +++ +  a+  
  gi|313126717|ref|YP_004036987.1|  38 GLTFSDYRRYAPGDDTRLIDWRVYARTEEYYVKQFEEERNLTVHVLVDTSASMDYGDGDAHKFEFGAKIGLGFAYLT 114
                                       57899***************************************************************999999999 PP

                             DUF58  78 ldegdrvg 85 
                                       ++e++ ++
  gi|313126717|ref|YP_004036987.1| 115 AEENNDFR 122
                                       99998776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                             DUF58  61 ekletav 67 
                                       ++le+ +
  gi|313126717|ref|YP_004036987.1| 163 SALEEYA 169
                                       2333322 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.3e-08    0.0001       3     105 ..      82     183 ..      80     201 .. 0.86
   2 ?   -1.3   0.0      0.76   3.4e+03       9      35 ..     239     260 ..     238     274 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.3e-08
                             VWA_2   3 fvlDtSgSmrngdygptrleaakdaveallk..slpgdrvglvtfsdgpevlipltkdkakilnalrnleak..ggg 75 
                                       +++DtS+Sm  gd    ++e  +++   +    +  ++ +   tf+++p++l +  ++++++l+ ++ l+++  +++
  gi|313126717|ref|YP_004036987.1|  82 VLVDTSASMDYGDGDAHKFEFGAKIGLGFAYltAEENNDFRFSTFRNRPKRLDTGRSNRGDLLRVVDLLNETelSDK 158
                                       79*******99988666666665555555551155688********************************99***** PP

                             VWA_2  76 tnlaaaLqlarkalkkrrkgekrvivlitD 105
                                        +l +aL+   +++++r+      +v+++D
  gi|313126717|ref|YP_004036987.1| 159 ADLVSALEEYASTIHSRS-----LVVVVSD 183
                                       **********99999875.....9999998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.76
                             VWA_2   9 gSmrngdygptrleaakdaveallksl 35 
                                       gSm+n+     +++++++ vea++++ 
  gi|313126717|ref|YP_004036987.1| 239 GSMANK-----YHDRLQSHVEAISERA 260
                                       688888.....7788888887777744 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.017        77      44      71 ..      64      91 ..      51      93 .. 0.76
   2 !   15.4   0.1     2e-06     0.009     138     189 ..     163     211 ..     116     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.017
                          VWA_CoxE 44 lvelvrrkprerkprelvllvDvSgSma 71
                                      ++e+  ++  e+++  + +lvD S+Sm+
  gi|313126717|ref|YP_004036987.1| 64 TEEYYVKQFEEERNLTVHVLVDTSASMD 91
                                      5555566656667778889********7 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2e-06
                          VWA_CoxE 138 eflelvtrpaLsrravvvlvsDglergdreellaelarlvrrarrlvwlnpl 189
                                       ++le  + +++++r++vv+vsD+    d +e+++++a+l +  + lv   + 
  gi|313126717|ref|YP_004036987.1| 163 SALEEYA-STIHSRSLVVVVSDF--LTDPDEVESAVAALEENDVILVQTLAP 211
                                       4444444.5667899********..678999999****99987777765555 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.9e-05      0.22      19      57 ..      97     135 ..      78     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
                            BtrH_N  19 sEplvFglGgglgfvYlpakklnplpllagrtkpgdlek 57 
                                       ++++ Fg   glgf+Yl+a++ n++ + ++r++p++l+ 
  gi|313126717|ref|YP_004036987.1|  97 AHKFEFGAKIGLGFAYLTAEENNDFRFSTFRNRPKRLDT 135
                                       5778999999***********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1950.43
//
Query:       gi|313126718|ref|YP_004036988.1|  [L=42]
Description: hypothetical protein Hbor_19770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       142  (0.00792013); expected 358.6 (0.02)
Passed bias filter:                      131  (0.0073066); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 254.60
//
Query:       gi|313126719|ref|YP_004036989.1|  [L=141]
Description: hypothetical protein Hbor_19780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-11   43.2  14.9    4.6e-11   43.0  14.9    1.1  1  EamA           EamA-like transporter family
    0.00013   21.2   5.8    0.00013   21.2   5.8    1.5  2  Mg_trans_NIPA  Magnesium transporter NIPA
     0.0099   15.9   4.2      0.017   15.1   4.2    1.5  1  TMEM234        Putative transmembrane family 234


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0  14.9   7.7e-15   4.6e-11       4     136 ..       4     139 ..       1     140 [. 0.85

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 7.7e-15
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllgtvl 77 
                                       + +a+la   +a+  +l+k++ +  +++  ++  +++ ++l++ +a +   ++     +   +   +++ + l+ ++
  gi|313126719|ref|YP_004036989.1|   4 LPWAVLALAAYAFVSPLMKVATQGEPSIPSNVAALMANSLLVFGTASIVVYNDsdvIGYLTHSKSKYVFAAGLCLTV 80 
                                       5699**********************99888877777777776665555555554555555556666777779**** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       + l+++ al+ +++s++s+i+ +  v++ ++++++l+e+lt ++ lgi+l++++v+l+ 
  gi|313126719|ref|YP_004036989.1|  81 GILAYYRALSIGQVSIVSPIFGMFLVLSSVIGIVFLNESLTARKALGIGLAIIAVYLVA 139
                                       *********************************************************96 PP

>> Mg_trans_NIPA  Magnesium transporter NIPA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.22   1.3e+03      67      97 ..      11      44 ..       8      53 .. 0.67
   2 !   21.2   5.8   2.1e-08   0.00013      48     119 ..      67     138 ..      49     141 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.22
                     Mg_trans_NIPA 67 faayaf.aPatLvtPLGalsv..ivsavlasllL 97
                                      +aayaf +P + v+  G  s+   v+a++a+ lL
  gi|313126719|ref|YP_004036989.1| 11 LAAYAFvSPLMKVATQGEPSIpsNVAALMANSLL 44
                                      5788863578888887777763335666665554 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.1e-08
                     Mg_trans_NIPA  48 kevlWwaGlltmavGeaanfaayafaPatLvtPLGalsvivsavlasllLkekLkllgllGcllailGstvl 119
                                       k+ + +a  l ++vG  a + a ++  +++v+P+  + +++s+v+  ++L+e L +   lG+ lai+  +++
  gi|313126719|ref|YP_004036989.1|  67 KSKYVFAAGLCLTVGILAYYRALSIGQVSIVSPIFGMFLVLSSVIGIVFLNESLTARKALGIGLAIIAVYLV 138
                                       5555566667789*****************************************************998876 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   4.2   2.9e-06     0.017      12     115 ..      18     138 ..       8     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-06
                           TMEM234  12 nPllkrgskgleevkeksklsqlllelkf..................lllrlkyliplllNqs.gSvlfflllgkad 69 
                                        Pl+k +++g  ++ ++ +   +  +l +                  + ++ ky+++  l ++ g + ++ +l+  +
  gi|313126719|ref|YP_004036989.1|  18 SPLMKVATQGEPSIPSNVAA-LMANSLLVfgtasivvyndsdvigylTHSKSKYVFAAGLCLTvGILAYYRALSIGQ 93 
                                       68888888888888765332.1222222245577888888888888888999****999998626667999****** PP

                           TMEM234  70 lslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       +s+++pi     ++  v+   +l+e + ++++ lg++l +++++l+
  gi|313126719|ref|YP_004036989.1|  94 VSIVSPIFGMFLVLSSVIGIVFLNESL-TARKALGIGLAIIAVYLV 138
                                       ********9888777777777777665.566679*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 865.98
//
Query:       gi|313126720|ref|YP_004036990.1|  [L=186]
Description: peroxiredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-15   56.4   0.0    3.7e-15   55.9   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    1.9e-11   43.9   0.0    2.4e-11   43.6   0.0    1.1  1  Redoxin        Redoxin
     0.0073   16.8   0.4      0.017   15.6   0.3    1.7  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.17   11.2   0.0    1.1  1  TatD_DNase     TatD related DNase


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   8.4e-19   3.7e-15       2     119 ..      13     131 ..      12     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 8.4e-19
                                       TSB----EEESTTCEEEECHHHTT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH...... CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdykg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe...... 71 
                                       gd apdf+l+ +dget++l+ +++ + ++++f+++ +cp+++++  +l+ l+  ++   + v+g+++++ e      
  gi|313126720|ref|YP_004036990.1|  13 GDVAPDFSLPGTDGETYTLDSFADyDALLVVFTCN-HCPYAQAKFDELNYLARTYD--ELAVVGINPNDAEeypdds 86 
                                       899*******************9967777777777.********************..6789*****99999***** PP

                                       ..HHHHHHHH-H.SSE.EEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTS CS
                          AhpC-TSA  72 ..shkkfiekeslnfp.llsDeegkvakaygvlkeekglalratfvidkeg 119
                                         ++++ +e+  ++++ +l De+++va++yg++      +++  f++ keg
  gi|313126720|ref|YP_004036990.1|  87 fdRMQELVEDGTIQYTaYLRDESQDVAREYGAV------CTPDPFLFEKEG 131
                                       ************99974799*************......888888888887 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   5.3e-15   2.4e-11       3     125 ..      13     131 ..      11     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 5.3e-15
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.... CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.... 75 
                                       gd aPdf+lp+  tdg++++l++f++  ++++++++++cP+ +a+  +l+ la+ + e    vv+++ ++ +     
  gi|313126720|ref|YP_004036990.1|  13 GDVAPDFSLPG--TDGETYTLDSFADYDALLVVFTCNHCPYAQAKFDELNYLARTYDEL--AVVGINPNDAEEypdd 85 
                                       8999*****99..*******************************998777777776666..6788988887778788 PP

                                       ....HHHHHHHTT-TSEE.EE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETT CS
                           Redoxin  76 ....vkefwgkeglkfpv.lsDgsaaftkalGlrleedaseglrtpryavidedg 125
                                           ++e +++  ++++  l D+s+++++++G+          +tp  +++ ++g
  gi|313126720|ref|YP_004036990.1|  86 sfdrMQELVEDGTIQYTAyLRDESQDVAREYGAV---------CTPDPFLFEKEG 131
                                       77888888888777787769************88.........777777776666 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   3.8e-06     0.017       8      96 ..      40     138 ..      35     150 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.8e-06
                     Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkelddvtvrvllfp.lkpsfepkavaiwcakekkkafkd.............ieenv 70 
                                       +lvvft ++Cpy ++  +el  l +  + + ++  ++p+    a++   +      +++              +e++
  gi|313126720|ref|YP_004036990.1|  40 LLVVFTCNHCPYAQAKFDELNYLARTYDEL-AVVgINPN---DAEEYPDDSFD--RMQElvedgtiqytaylRDESQ 110
                                       79***********99777777773333332.22245555...22222222111..233366678889999999**** PP

                     Thioredoxin_2  71 elarkygvrgtPtivfldgk..eivarl 96 
                                       ++ar+yg   tP+ ++++++  e v+r 
  gi|313126720|ref|YP_004036990.1| 111 DVAREYGAVCTPDPFLFEKEgdEFVLRF 138
                                       *************888888766666655 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.8e-05      0.17      39      86 ..      54      97 ..      23     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                                      GGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHHHHCCCT CS
                        TatD_DNase 39 kdskavlelakkypnkvyavlGiHPnevdeasedlleelkelanvkhs 86
                                      ++++++  la++y++   av+Gi Pn+++e  +d ++ ++el  v++ 
  gi|313126720|ref|YP_004036990.1| 54 AKFDELNYLARTYDE--LAVVGINPNDAEEYPDDSFDRMQEL--VEDG 97
                                      467789999999999..8**********************99..8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1171.24
//
Query:       gi|313126721|ref|YP_004036991.1|  [L=149]
Description: exosome subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-33  113.8   0.5    6.8e-33  113.5   0.5    1.1  1  RNA_binding  RNA binding
  ------ inclusion threshold ------
       0.12   10.5   0.1       0.13   10.3   0.1    1.1  1  FragX_IP     Cytoplasmic Fragile-X interacting family


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   0.5   7.6e-37   6.8e-33       1     119 []       8     120 ..       8     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 7.6e-37
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCHHHH CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeeikeL 76 
                                       +i++r+f+++TEde++V+ a+++llpee +eie+ e +Gh+g++i++++a++e++++ ++vl+kl +  + e    L
  gi|313126721|ref|YP_004036991.1|   8 YIDLRTFCYETEDEKRVEAAIRSLLPEE-FEIERIENTGHHGDRIIVFSARVERANEvRHVLSKLSDIQDFE---GL 80 
                                       69************************88.89********************************999766555...6* PP

                                       HHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEEE CS
                       RNA_binding  77 lkeleervdekgklylrldKQaaylgklslvegddvIkvkikv 119
                                       l+el+erv+e+++l++rldKQaa++++ +l   +d I++++kv
  gi|313126721|ref|YP_004036991.1|  81 LDELDERVTENCELFMRLDKQAAFRDETRL---GDGITFRAKV 120
                                       ******************************...99***99985 PP

>> FragX_IP  Cytoplasmic Fragile-X interacting family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   1.5e-05      0.13     382     444 ..      23      89 ..       8     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.5e-05
                          FragX_IP 382 rlnealrksl..elaisrfessdlts..iveLeklleilrlthkLLsefleldpFdellreanenvs 444
                                       r+++a+r+ l  e+ i+r+e+++  +  i+ + + +e  ++ ++ Ls+   +++F+ ll e +e v+
  gi|313126721|ref|YP_004036991.1|  23 RVEAAIRSLLpeEFEIERIENTGHHGdrIIVFSARVERANEVRHVLSKLSDIQDFEGLLDELDERVT 89 
                                       7777777777667889999999997555***********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 998.17
//
Query:       gi|313126722|ref|YP_004036992.1|  [L=69]
Description: hypothetical protein Hbor_19810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00041   19.9   0.1     0.0005   19.6   0.1    1.2  1  DUF1918   Domain of unknown function (DUF1918)


Domain annotation for each model (and alignments):
>> DUF1918  Domain of unknown function (DUF1918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.8e-08    0.0005       1      52 [.       1      52 [.       1      62 [. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.8e-08
                                      ----TTEEEEES-TTTS--EEEEEEEE-S-SS.S-S-EEEEETTTTEEEEE-- CS
                           DUF1918  1 MkAkvGDrlvvegrtvgepereGeiveVrged.GaPPYlVRweddgheslvfP 52
                                      M+ + GD +v + ++ +   + G+i+ V  +  G++ Y+V ++ +g+e  ++P
  gi|313126722|ref|YP_004036992.1|  1 MEFDEGDAVVLNDKHSEFDGQVGKITQVVETMfGDETYVVSFD-EGQEVGISP 52
                                      66678**********************987767**********.999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 458.69
//
Query:       gi|313126723|ref|YP_004036993.1|  [L=187]
Description: ADP-ribose pyrophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-18   64.6   0.1    1.4e-17   63.9   0.1    1.3  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
       0.12   11.3   0.1       0.15   11.0   0.1    1.1  1  ANTH      ANTH domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.1   1.6e-21   1.4e-17       7     129 ..      62     180 ..      57     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.6e-21
                                       EEEEEETTSEEEEEEESSSSTTT...EESSEEECBTTSHHHHHHHHHHHHHHSEEE..EEEEEEEEEEEEEEEEEEE CS
                             NUDIX   7 gvvllnekgevLlvrrskkpfpg...WelPgGkvepgEtpeeAArREleEEtGlea..ellellgrlhylapydgpy 78 
                                         +++++ +e+Llvr+      g   W lPgG+v+++Et++eAA+REl EE+G++a  + l + +r++    +    
  gi|313126723|ref|YP_004036993.1|  62 HTIVYRDTDELLLVRHD-----GvdlWVLPGGEVREDETYREAAIRELGEEAGVSAdyRGLAIANRIDICCDDY--- 130
                                       5678999999****977.....5558***************************987334446666555544444... PP

                                       EEEEEEE..EEEEEEECSGCSST.STTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
                             NUDIX  79 gdeheil..yvfleevegelepn.denevsevrwvpleellkeklaaesrkllp 129
                                         e++ +  ++f+++++ +l+++  ++e+s++ w+++ +l  ++++ ++ +ll+
  gi|313126723|ref|YP_004036993.1| 131 --ETWGVmpVFFAAAEDVDLHVDdPDDEISDAGWFSFSDL--PADTRDRGDLLA 180
                                       ..55555546666999999999989999************..555555555555 PP

>> ANTH  ANTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.7e-05      0.15      94     131 ..      12      49 ..       3      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.7e-05
                                       HHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHSS-...C CS
                              ANTH  94 ddssskswdysafiraYakyLderlefhrklkvdkgel 131
                                        +s++++++y++++++Y++yLde  + +   ++++  +
  gi|313126723|ref|YP_004036993.1|  12 EASQRAEQAYHRLCEQYSNYLDEHRTRRVSRRRFRTLA 49 
                                       578899****************9877777777774333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1281.66
//
Query:       gi|313126724|ref|YP_004036994.1|  [L=63]
Description: hypothetical protein Hbor_19830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-05   23.6   0.7      0.067   13.1   0.0    2.3  2  Nudix_N_2        Nudix N-terminal
    0.00097   18.7   0.2       0.39   10.3   0.1    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
     0.0014   18.2   1.1       0.81    9.5   0.1    2.7  3  zinc_ribbon_2    zinc-ribbon domain
     0.0017   18.4   1.3       0.74   10.0   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
     0.0059   16.7   1.2       0.48   10.6   0.3    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
     0.0069   15.8   1.3       0.32   10.5   0.3    2.3  2  zf-ribbon_3      zinc-ribbon domain
     0.0084   16.0   0.1       0.05   13.6   0.1    1.9  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
  ------ inclusion threshold ------
      0.014   15.1   1.3       0.61    9.9   0.3    2.1  2  zinc_ribbon_5    zinc-ribbon domain
      0.021   14.9   0.2        3.6    7.6   0.0    2.1  2  CpXC             CpXC protein
      0.022   14.7   0.7        1.1    9.2   0.7    2.0  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.026   14.6   1.3       0.27   11.3   1.3    2.0  1  DZR              Double zinc ribbon
      0.029   14.3   1.6       0.07   13.0   0.3    1.9  2  zf-trcl          Probable zinc-ribbon domain
      0.033   14.6   0.3      0.071   13.5   0.3    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.034   14.4   2.4       0.48   10.7   0.1    2.2  2  zinc_ribbon_9    zinc-ribbon
      0.038   12.6   0.0      0.042   12.4   0.0    1.0  1  Terminase_GpA    Phage terminase large subunit (GpA)
      0.042   13.8   0.7        5.8    7.0   0.0    2.3  2  ADK_lid          Adenylate kinase, active site lid
      0.047   13.6   1.2        4.2    7.4   0.1    2.2  2  zinc_ribbon_4    zinc-ribbon domain
      0.057   13.5   1.8        1.5    9.0   0.1    2.1  2  UPF0547          Uncharacterised protein family UPF0547
      0.062   13.0   2.4        1.7    8.4   0.0    2.1  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.064   12.9   1.4          2    8.2   0.1    2.2  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.065   13.1   1.2        8.3    6.4   0.1    2.3  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.076   13.3   0.0        0.1   12.8   0.0    1.2  1  IBR              IBR domain, a half RING-finger domain
      0.083   13.0   2.7       0.61   10.2   0.2    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.091   12.8   1.1       0.25   11.4   1.1    1.7  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        0.1   12.5   0.9       0.55   10.1   0.1    2.0  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.11   12.5   1.2          2    8.4   0.0    2.1  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
       0.12   12.1   1.6        2.7    7.8   0.2    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.13   12.6   0.3        6.6    7.1   0.0    2.0  2  GFA              Glutathione-dependent formaldehyde-activatin
       0.13   12.0   1.0        3.3    7.5   0.1    2.1  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.22   12.0   0.5        1.7    9.3   0.0    2.1  2  zf-C2H2          Zinc finger, C2H2 type
       0.92    9.8   5.8          1    9.7   2.5    2.4  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00012     0.067       3      18 ..       8      23 ..       8      26 .. 0.93
   2 !    9.1   0.2    0.0021       1.2      19      30 ..      41      52 ..      32      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                                      -TTT--B-EEE--TT- CS
                         Nudix_N_2  3 CsqCGtpvelripdgD 18
                                      C++CG+ v l +pdg 
  gi|313126724|ref|YP_004036994.1|  8 CPACGASVYLSLPDGN 23
                                      *************995 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                                      SS-EEEETTTTE CS
                         Nudix_N_2 19 nreRlvCpaCgt 30
                                      ++ Rl+C++Cgt
  gi|313126724|ref|YP_004036994.1| 41 TEKRLTCEDCGT 52
                                      578*******97 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0086         5       2      12 ..       5      15 ..       4      19 .. 0.84
   2 !   10.3   0.1   0.00068      0.39       3      14 ..      45      56 ..      43      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0086
                            zf_UBZ  2 tylCerCgkei 12
                                      +++C+ Cg+++
  gi|313126724|ref|YP_004036994.1|  5 SVPCPACGASV 15
                                      579*****998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00068
                            zf_UBZ  3 ylCerCgkeipe 14
                                       +Ce+Cg+e+p 
  gi|313126724|ref|YP_004036994.1| 45 LTCEDCGTEFPA 56
                                      59********96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0014      0.81      13      22 ..       5      14 ..       2      15 .. 0.79
   2 ?   -1.0   0.0       2.7   1.6e+03       9      15 ..      19      25 ..      18      25 .. 0.87
   3 ?    6.7   0.1     0.011       6.3      16      22 ..      47      53 ..      40      54 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                     zinc_ribbon_2 13 akFCpyCGtp 22
                                      ++ Cp CG+ 
  gi|313126724|ref|YP_004036994.1|  5 SVPCPACGAS 14
                                      5789999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.7
                     zinc_ribbon_2  9 lqdnakF 15
                                      l+d+++F
  gi|313126724|ref|YP_004036994.1| 19 LPDGNRF 25
                                      89**999 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.011
                     zinc_ribbon_2 16 CpyCGtp 22
                                      C+ CGt+
  gi|313126724|ref|YP_004036994.1| 47 CEDCGTE 53
                                      8888876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2    0.0064       3.7      28      35 ..       7      14 ..       1      16 [. 0.76
   2 !   10.0   0.1    0.0013      0.74       7      19 ..      46      58 ..      44      63 .] 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0064
                       Zn-ribbon_8 28 aCPeCgse 35
                                      +CP+Cg+ 
  gi|313126724|ref|YP_004036994.1|  7 PCPACGAS 14
                                      4****986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                       Zn-ribbon_8  7 rCeeCghefevlq 19
                                       Ce+Cg+ef +l+
  gi|313126724|ref|YP_004036994.1| 46 TCEDCGTEFPALH 58
                                      5********8887 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.3   0.00082      0.48      15      29 ..       4      18 ..       2      20 .. 0.90
   2 ?    5.2   0.0     0.038        22      14      24 ..      42      52 ..      32      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00082
                          zf-Mss51 15 vdfeCpdCGiptycs 29
                                      v++ Cp CG ++y s
  gi|313126724|ref|YP_004036994.1|  4 VSVPCPACGASVYLS 18
                                      6789*********88 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.038
                          zf-Mss51 14 hvdfeCpdCGi 24
                                      + +++C dCG 
  gi|313126724|ref|YP_004036994.1| 42 EKRLTCEDCGT 52
                                      56899*****5 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.3   0.00055      0.32       3      11 ..       6      15 ..       5      18 .. 0.80
   2 ?    4.4   0.0     0.046        27      18      25 ..      46      53 ..      40      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00055
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      v CP+CGa +
  gi|313126724|ref|YP_004036994.1|  6 VPCPACGAsV 15
                                      67*****944 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.046
                       zf-ribbon_3 18 vCpyCGtk 25
                                      +C  CGt+
  gi|313126724|ref|YP_004036994.1| 46 TCEDCGTE 53
                                      799***97 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   8.6e-05      0.05       4      29 ..       7      54 ..       1      55 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.6e-05
                    PhnA_Zn_Ribbon  4 kCplCaSeytY......................edgallvCpeCahEw 29
                                      +Cp C++++ +                           l C++C+ E+
  gi|313126724|ref|YP_004036994.1|  7 PCPACGASVYLslpdgnrfvtaepgegdddrddLTEKRLTCEDCGTEF 54
                                      7********99*****************99988778889******998 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.059        34       4      10 ..       7      13 ..       4      17 .. 0.82
   2 ?    9.9   0.3    0.0011      0.61       3      12 ..      45      54 ..      44      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.059
                     zinc_ribbon_5  4 rCpdCdt 10
                                       Cp+C+ 
  gi|313126724|ref|YP_004036994.1|  7 PCPACGA 13
                                      6****96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                     zinc_ribbon_5  3 irCpdCdtkF 12
                                        C+dC+t F
  gi|313126724|ref|YP_004036994.1| 45 LTCEDCGTEF 54
                                      68******99 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0063       3.6      36      51 ..       4      19 ..       2      23 .. 0.79
   2 ?    5.7   0.0     0.025        15      38      48 ..      45      55 ..      35      59 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0063
                              CpXC 36 featCpkCgataklea 51
                                       ++ Cp+Cga+++l+ 
  gi|313126724|ref|YP_004036994.1|  4 VSVPCPACGASVYLSL 19
                                      5678999999988875 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                              CpXC 38 atCpkCgatak 48
                                       tC++Cg+++ 
  gi|313126724|ref|YP_004036994.1| 45 LTCEDCGTEFP 55
                                      56777776654 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.7    0.0019       1.1      40      56 ..      33      54 ..       4      56 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                    OrfB_Zn_ribbon 40 e.....alsgrtfkCpnCgfea 56
                                            +l++++++C++Cg+e+
  gi|313126724|ref|YP_004036994.1| 33 GdddrdDLTEKRLTCEDCGTEF 54
                                      0333447888889999998875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.3   0.00047      0.27      15      38 ..       8      54 ..       2      62 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
                               DZR 15 CseCgtklkavaa.........................edrCpsCgekv 38
                                      C++Cg+++    +                           +C  Cg++ 
  gi|313126724|ref|YP_004036994.1|  8 CPACGASVY--LSlpdgnrfvtaepgegdddrddltekRLTCEDCGTEF 54
                                      666666642..11223455555555566666666665555666666554 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.4   7.8e+02       7      12 ..       8      13 ..       5      16 .. 0.65
   2 ?   13.0   0.3   0.00012      0.07       2      14 ..      42      54 ..      41      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.4
                           zf-trcl  7 CkdCga 12
                                      C  Cga
  gi|313126724|ref|YP_004036994.1|  8 CPACGA 13
                                      666665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                           zf-trcl  2 DktltCkdCgaef 14
                                       k ltC+dCg+ef
  gi|313126724|ref|YP_004036994.1| 42 EKRLTCEDCGTEF 54
                                      589*********9 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   0.00012     0.071       5      36 ..       7      52 ..       4      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigq..............cvyCadCga 36
                                      pCP Cg    l    +++   ++                +C+dCg 
  gi|313126724|ref|YP_004036994.1|  7 PCPACGASVYLSLPDGNRFVTAEpgegdddrddltekRLTCEDCGT 52
                                      9********99998888875555899******************98 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.15        85      22      28 ..       7      12 ..       2      14 .. 0.80
   2 ?   10.7   0.1   0.00083      0.48       9      31 ..      23      54 ..      23      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                     zinc_ribbon_9 22 vlCPhCg 28
                                      + CP Cg
  gi|313126724|ref|YP_004036994.1|  7 P-CPACG 12
                                      5.****8 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00083
                     zinc_ribbon_9  9 drfVsvspdedsd.........vlCPhCgggF 31
                                      +rfV+++p e +d          +C +Cg  F
  gi|313126724|ref|YP_004036994.1| 23 NRFVTAEPGEGDDdrddltekrLTCEDCGTEF 54
                                      79*****995555699**998659*****998 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.3e-05     0.042     199     236 ..       6      53 ..       4      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.3e-05
                     Terminase_GpA 199 vpCphCgelqels.ferlkw........pege...aeekaryvCphcgsl 236
                                       vpCp Cg+   ls  +  ++        +  +   + ++ r++C++cg++
  gi|313126724|ref|YP_004036994.1|   6 VPCPACGASVYLSlPDGNRFvtaepgegD--DdrdDLTEKRLTCEDCGTE 53 
                                       9**********996666555556555541..045588899********97 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.026        15       4      10 ..       8      14 ..       6      43 .. 0.78
   2 ?    7.0   0.0      0.01       5.8       1       9 [.      44      52 ..      44      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                                      -TTT--E CS
                           ADK_lid  4 CpkCGrs 10
                                      Cp+CG+s
  gi|313126724|ref|YP_004036994.1|  8 CPACGAS 14
                                      *****95 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.01
                                      EEE-TTT-- CS
                           ADK_lid  1 RrvCpkCGr 9 
                                      R++C++CG+
  gi|313126724|ref|YP_004036994.1| 44 RLTCEDCGT 52
                                      999999997 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.033        19      26      33 ..       6      13 ..       4      15 .. 0.60
   2 ?    7.4   0.1    0.0073       4.2       3      12 ..      45      54 ..      41      55 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.033
                     zinc_ribbon_4 26 vrCskCgh 33
                                      v C++Cg+
  gi|313126724|ref|YP_004036994.1|  6 VPCPACGA 13
                                      55666664 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0073
                     zinc_ribbon_4  3 itCpsCkaky 12
                                       tC+ C++++
  gi|313126724|ref|YP_004036994.1| 45 LTCEDCGTEF 54
                                      5777777766 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.086        50       3       8 ..       8      13 ..       5      17 .. 0.70
   2 ?    9.0   0.1    0.0025       1.5      17      26 .]      47      56 ..      45      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.086
                           UPF0547  3 CPeCea 8 
                                      CP C a
  gi|313126724|ref|YP_004036994.1|  8 CPACGA 13
                                      666655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0025
                           UPF0547 17 CphCGyvFqa 26
                                      C +CG++F a
  gi|313126724|ref|YP_004036994.1| 47 CEDCGTEFPA 56
                                      99******86 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.1     0.071        41      17      22 ..       8      13 ..       7      14 .. 0.86
   2 ?    8.4   0.0    0.0029       1.7       3      15 ..      47      59 ..      46      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.071
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+Cg+
  gi|313126724|ref|YP_004036994.1|  8 CPACGA 13
                                      999997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0029
                      Rubredoxin_2  3 CsqCGfesakwfG 15
                                      C++CG e++++ G
  gi|313126724|ref|YP_004036994.1| 47 CEDCGTEFPALHG 59
                                      *********9987 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0034         2       6      12 ..       7      13 ..       5      22 .. 0.79
   2 ?    4.0   0.1     0.069        40       2      11 ..      42      51 ..      41      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0034
                           zf-RRN7  6 pCgvCgc 12
                                      pC++Cg+
  gi|313126724|ref|YP_004036994.1|  7 PCPACGA 13
                                      9*****9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.069
                           zf-RRN7  2 ekgppCgvCg 11
                                      ek+  C+ Cg
  gi|313126724|ref|YP_004036994.1| 42 EKRLTCEDCG 51
                                      68999**998 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.021        12      14      22 ..       8      16 ..       7      18 .. 0.82
   2 ?    6.4   0.1     0.014       8.3      14      24 ..      47      56 ..      37      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.021
                           DUF35_N 14 CpdCGtvqf 22
                                      Cp+CG+ ++
  gi|313126724|ref|YP_004036994.1|  8 CPACGASVY 16
                                      999998776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                           DUF35_N 14 CpdCGtvqfPP 24
                                      C dCGt  fP+
  gi|313126724|ref|YP_004036994.1| 47 CEDCGTE-FPA 56
                                      9999998.675 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00018       0.1      19      48 ..       6      54 ..       4      61 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                               IBR 19 kwCprpdCeaii.............eksegcks..............vtCskCgfef 48
                                      + Cp   C+a +             e                     +tC++Cg+ef
  gi|313126724|ref|YP_004036994.1|  6 VPCP--ACGASVylslpdgnrfvtaE------PgegdddrddltekrLTCEDCGTEF 54
                                      5699..77776655555555555441......044445556666667*********9 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2    0.0011      0.61       4      12 ..       8      16 ..       6      17 .. 0.94
   2 ?    3.2   0.3      0.17        97       4       9 ..      47      52 ..      45      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                            zf-ACC  4 CpsCgemly 12
                                      Cp+Cg+++y
  gi|313126724|ref|YP_004036994.1|  8 CPACGASVY 16
                                      ********9 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
                            zf-ACC  4 CpsCge 9 
                                      C+ Cg+
  gi|313126724|ref|YP_004036994.1| 47 CEDCGT 52
                                      ****96 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   0.00043      0.25      21      45 ..       8      52 ..       4      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                     Zn_Tnp_IS1595 21 CPhCgsrkayrikt....................rglfqCkeCrk 45
                                      CP+Cg + + ++ +                     +++ C++C++
  gi|313126724|ref|YP_004036994.1|  8 CPACGASVYLSLPDgnrfvtaepgegdddrddltEKRLTCEDCGT 52
                                      *****9999999999999999**********************86 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.77   4.5e+02       4       8 ..       8      12 ..       6      15 .. 0.87
   2 ?   10.1   0.1   0.00095      0.55      15      33 ..      37      56 ..      35      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.77
                                      ESTTT CS
                    RNA_POL_M_15KD  4 CpkCg 8 
                                      Cp Cg
  gi|313126724|ref|YP_004036994.1|  8 CPACG 12
                                      89997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00095
                                      ECSCCCE.EEESSSS-EEES CS
                    RNA_POL_M_15KD 15 edkegkn.feCrqCgYeepa 33
                                      +d+++   + C  Cg e+pa
  gi|313126724|ref|YP_004036994.1| 37 RDDLTEKrLTCEDCGTEFPA 56
                                      5667766788*********7 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0035         2      30      49 ..       5      24 ..       2      27 .. 0.79
   2 ?    3.2   0.3      0.15        89       7      25 ..      38      56 ..      34      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0035
                                      ..E-TTTTTSSEEE-HHHHH CS
                         Anti-TRAP 30 sleCPkCsGkglipTaqGqk 49
                                      s++CP+C+    +   +G++
  gi|313126724|ref|YP_004036994.1|  5 SVPCPACGASVYLSLPDGNR 24
                                      89*****9888887777776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                                      HHCEEE-TTTTTTSEETTE CS
                         Anti-TRAP  7 peLEtkCdaCngsGkiepe 25
                                      ++L +k  +C+  G + p+
  gi|313126724|ref|YP_004036994.1| 38 DDLTEKRLTCEDCGTEFPA 56
                                      8999999999999998887 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0046       2.7      24      32 .]       8      16 ..       6      16 .. 0.89
   2 ?    3.7   0.1     0.086        50      24      31 ..      47      54 ..      45      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0046
                     zf-NADH-PPase 24 CpaCglehY 32
                                      CpaCg+ +Y
  gi|313126724|ref|YP_004036994.1|  8 CPACGASVY 16
                                      999999988 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.086
                     zf-NADH-PPase 24 CpaCgleh 31
                                      C++Cg+e+
  gi|313126724|ref|YP_004036994.1| 47 CEDCGTEF 54
                                      *****985 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.011       6.6      52      79 ..       8      35 ..       2      44 .. 0.76
   2 ?    4.7   0.1     0.064        37      48      60 ..      43      55 ..      34      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                               GFA 52 CpeCgsplyseesaapevvivrvGtldd 79
                                      Cp+Cg+ +y +    + +v+ + G  dd
  gi|313126724|ref|YP_004036994.1|  8 CPACGASVYLSLPDGNRFVTAEPGEGDD 35
                                      *********9877777777777666665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.064
                               GFA 48 trsfCpeCgsply 60
                                      +r  C++Cg+++ 
  gi|313126724|ref|YP_004036994.1| 43 KRLTCEDCGTEFP 55
                                      5789*****9875 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.12        71      24      30 ..       8      14 ..       7      15 .. 0.93
   2 ?    7.5   0.1    0.0057       3.3      22      32 ..      45      55 ..      41      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                     A2L_zn_ribbon 24 CieCgas 30
                                      C+ Cgas
  gi|313126724|ref|YP_004036994.1|  8 CPACGAS 14
                                      *****98 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0057
                     A2L_zn_ribbon 22 lvCieCgasfp 32
                                      l C +Cg++fp
  gi|313126724|ref|YP_004036994.1| 45 LTCEDCGTEFP 55
                                      67******998 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       1.2   6.7e+02       2       9 ..       7      14 ..       6      16 .. 0.81
   2 ?    9.3   0.0    0.0029       1.7       2      12 ..      46      56 ..      45      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.2
                                      EETTTTEE CS
                           zf-C2H2  2 kCpdCgks 9 
                                      +Cp Cg s
  gi|313126724|ref|YP_004036994.1|  7 PCPACGAS 14
                                      6****965 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0029
                                      EETTTTEEESS CS
                           zf-C2H2  2 kCpdCgksFkr 12
                                      +C+dCg  F+ 
  gi|313126724|ref|YP_004036994.1| 46 TCEDCGTEFPA 56
                                      8********86 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.5    0.0018         1       4      16 ..       6      24 ..       5      35 .. 0.65
   2 ?    0.4   0.1       1.5   8.5e+02       5      10 ..      46      51 ..      42      54 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                                      E--TTTT-T......TTEE CS
                    Prim_Zn_Ribbon  4 spCPvCGGr......DrFr 16
                                      +pCP CG++      D++r
  gi|313126724|ref|YP_004036994.1|  6 VPCPACGASvylslpDGNR 24
                                      7******974444446666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.5
                                      --TTTT CS
                    Prim_Zn_Ribbon  5 pCPvCG 10
                                       C  CG
  gi|313126724|ref|YP_004036994.1| 46 TCEDCG 51
                                      566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 450.38
//
Query:       gi|313126725|ref|YP_004036995.1|  [L=120]
Description: hypothetical protein Hbor_19840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-08   33.8   0.5    3.7e-08   33.2   0.5    1.4  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
       0.13   12.3   1.5       0.18   11.8   1.5    1.5  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.5   4.1e-12   3.7e-08      19      77 ..      23      87 ..       4      88 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4.1e-12
                                      HHHHHH..HTTTTTSTTSSSSSS.SSTTEEEEEESCE..CTT....SSSSTHHHHHTTEE...........EEGGGSEE CS
                              Fer2 19 lldaae..enggidipysCgggg.CgtClvevlegev..qsd....etelegeeldegkl...........rlaCqtiv 77
                                      ll a e  +n g +  ++C+g g CgtC+v v+ g v  + +                 l           rl+Cqt+v
  gi|313126725|ref|YP_004036995.1| 23 LLAAGEspHN-GSADMLNCRGRGtCGTCAVAVE-GAVtdRTKreetR------------LsfpphhpdsglRLSCQTRV 87
                                      5555554445.666669****777******866.7775422222220............233444666666******98 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.5     2e-05      0.18      51      70 ..      39      59 ..       4      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                            Fer2_3 51 sCr.egiCGscavainGkptl 70
                                      +Cr  g CG+cava++G +t 
  gi|313126725|ref|YP_004036995.1| 39 NCRgRGTCGTCAVAVEGAVTD 59
                                      675369***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 821.21
//
Query:       gi|313126726|ref|YP_004036996.1|  [L=222]
Description: protein-disulfide isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-32  111.8   0.0    4.6e-32  111.5   0.0    1.1  1  Thioredoxin_4  Thioredoxin
    3.4e-11   43.3   1.9      2e-08   34.2   1.9    2.1  1  DSBA           DSBA-like thioredoxin domain
  ------ inclusion threshold ------
       0.06   13.2   6.8       0.12   12.3   6.8    1.5  1  TAT_signal     TAT (twin-arginine translocation) pathway sign


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.0   7.6e-36   4.6e-32       4     161 ..      46     209 ..      43     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 7.6e-36
                                       SSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---S.TTTHHHHHHHTT--TT. CS
                     Thioredoxin_4   4 tdiviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkek.eslkaamaarcagees. 77 
                                        ++++G +dA+vtv++yed++CphCa+++ +v+ k+++ yidtGk+++++ dfp++  k +s+ +a aar++++ + 
  gi|313126726|ref|YP_004036996.1|  46 PTPTLGPEDADVTVDVYEDFACPHCATYNVDVFpKVKQNYIDTGKIRYRFFDFPIPVSKqWSWGGAIAARAVQDRTd 122
                                       6899*****************************9**********************9999*************9944 PP

                                       .HHHHHHHHHHHHTHHHHTTS-...HHHHH.......HHHH.HTS-------HHHHHHHHHHHHHHT--SS-EEEET CS
                     Thioredoxin_4  78 .peaflaikallysqqeewaes...lkela..aealdkdek.feacleeekldalveaeskeakkagiestPtfiin 147
                                        +++f+++k+l+++q e  ++           a+++d d + ++a +e++ ++  v+ + ++  + +i +tP +i+n
  gi|313126726|ref|YP_004036996.1| 123 dETYFKYAKRLFEKQNELTSNGytvI---HdvANEFDVDGCeVMASVEQDIYRSVVKSDRQRGIEVDIGGTPAIIVN 196
                                       699*******9999999888884443...4444555554443788899999999999999999************** PP

                                       TEEE-TT--HHHHH CS
                     Thioredoxin_4 148 gekveepqtyeelk 161
                                       ge ++    +e++k
  gi|313126726|ref|YP_004036996.1| 197 GEHLS-GAGWETVK 209
                                       **998.55666655 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   1.9   3.4e-12     2e-08       1     182 [.      58     203 ..      58     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.4e-12
                                       EEEEEEBTTBHHHHHHH.HHHHHHHHHC.CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT.. CS
                              DSBA   1 tvdeffDvlCPyCylgk.erleklaars.pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegip 75 
                                       tvd++ D+ CP+C + + ++++k+ +++ +  k+++r f++   +                      k+        
  gi|313126726|ref|YP_004036996.1|  58 TVDVYEDFACPHCATYNvDVFPKVKQNYiDTGKIRYRFFDFPIPVS---------------------KQ-------- 105
                                       79************99935678999999655999999999988822.....................11........ PP

                                       ..GGSSHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHTSSS-TSSHHH..HHHHHHHTTS.HHHHHHHHTSHHHH CS
                              DSBA  76 lrfpkdklknstraarlllaagaeglaekvvrelfealwsegqaitddqe..llevaekaGldaeeldealeseavk 150
                                                 s   a ++ a++ +   ++ + +++++l++++ ++t++    + +va++  +d  e+ + +e++ + 
  gi|313126726|ref|YP_004036996.1| 106 ---------WSWGGAIAARAVQDR-TDDETYFKYAKRLFEKQNELTSNGYtvIHDVANEFDVDGCEVMASVEQDIYR 172
                                       .........355555555555555.4678888999*******99999964449************************ PP

                                       HHHHHHHHHHHHTT-SSSSEEEETTCEEEESS CS
                              DSBA 151 eavrentaaaqslgvtGvPtvvvdgkrmvfGa 182
                                       + v+ ++++++++++ G+P+++v+g+  ++Ga
  gi|313126726|ref|YP_004036996.1| 173 SVVKSDRQRGIEVDIGGTPAIIVNGE-HLSGA 203
                                       *************************9.78876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   6.8     2e-05      0.12       3      25 ..       4      24 ..       2      25 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      +RR+ L   AA++A+aa++gc++
  gi|313126726|ref|YP_004036996.1|  4 TRRSYLA--AAGGALAATAGCLG 24
                                      89*****..************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1392.52
//
Query:       gi|313126727|ref|YP_004036997.1|  [L=172]
Description: thiol-disulfide isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-14   52.8   0.0    3.8e-14   52.6   0.0    1.1  1  Redoxin        Redoxin
    1.5e-09   37.8   0.0      2e-09   37.4   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    1.4e-06   28.5   0.0    2.1e-06   28.0   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
    0.00017   21.5   0.0    0.00056   19.9   0.0    1.7  2  Thioredoxin    Thioredoxin
    0.00027   21.4   0.0     0.0004   20.8   0.0    1.3  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   1.1e-17   3.8e-14      27     145 ..      56     166 ..      37     172 .] 0.92

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.1e-17
                                       TTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH........HHHHHHHTT-TSEEEE-TTS CS
                           Redoxin  27 kgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf........vkefwgkeglkfpvlsDgsa 95 
                                       +gk++v+  +++ +c +Csa++   e l++l++e g+dv +v++ n+ f        v+++w++++  ++v +D+++
  gi|313126727|ref|YP_004036997.1|  56 PGKPTVLDLFAT-WCVPCSAQM---ESLTALHEEFGDDVAFVSVTNEGFgdnltaddVRKWWADHDGAWTVGHDPES 128
                                       89**********.*********...8888888889****************************************** PP

                                       HHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                           Redoxin  96 aftkalGlrleedaseglrtpryavidedgkvvylevepepeteesnaea 145
                                        ++k lG+          ++p +av+d+dg  ++++++  +   esn+ a
  gi|313126727|ref|YP_004036997.1| 129 RLMKVLGAG---------GLPYLAVFDADGTATWTHRGLAS---ESNLRA 166
                                       *******88.........******************99888...566554 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   5.6e-13     2e-09      25     120 ..      57     150 ..      49     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 5.6e-13
                                       TSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH........HHHHHHHH-H.SSEEEE-TTSH CS
                          AhpC-TSA  25 gkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe........shkkfiekeslnfpllsDeegk 93 
                                       gkp+vl  +++ wc +C +++++l +l+eef + +v  + v+ +           +++k+ ++++  +++ +D+e+ 
  gi|313126727|ref|YP_004036997.1|  57 GKPTVLDLFAT-WCVPCSAQMESLTALHEEFGD-DVAFVSVTNE--GfgdnltadDVRKWWADHDGAWTVGHDPESR 129
                                       9**********.********************5.5656666554..344788888********************** PP

                                       HHHHTT-EETTTTECSCEEEEE-TTSB CS
                          AhpC-TSA  94 vakaygvlkeekglalratfvidkegk 120
                                       ++k +g+        l+   v+d++g+
  gi|313126727|ref|YP_004036997.1| 130 LMKVLGAG------GLPYLAVFDADGT 150
                                       ********......8888888888886 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   5.8e-10   2.1e-06       1      93 [.      57     149 ..      57     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 5.8e-10
                                       .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-....SS.-HHHHHHHGGGS-TTSEE.EE-TT-HH CS
                     Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl....dk.keeefekylkknkkpwlsvpfddkkrn 72 
                                       gk ++L  +a+wc pc a +++l++l+e++   ++v +v+v +    d+ + ++++k  +++  +w+    + +  +
  gi|313126727|ref|YP_004036997.1|  57 GKPTVLDLFATWCVPCSAQMESLTALHEEFG--DDVAFVSVTNegfgDNlTADDVRKWWADHDGAWTV---GHDPES 128
                                       699***************************9..**********5554333455555555555444544...667788 PP

                                       HHTT-S--TT-SEEEEE-TT- CS
                     Thioredoxin_8  73 klkkkynvkaiPtlvvldkng 93 
                                        l k ++  ++P l v d +g
  gi|313126727|ref|YP_004036997.1| 129 RLMKVLGAGGLPYLAVFDADG 149
                                       999999999999999999888 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.6e-07   0.00056      17      58 ..      56      97 ..      47     111 .. 0.87
   2 ?   -0.9   0.0      0.44   1.6e+03      58     101 ..     124     168 ..     119     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.6e-07
                                      TSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEET CS
                       Thioredoxin 17 ekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdv 58
                                      + k+ +++ +A+wC +C a    l++l ee+ d+v ++ v +
  gi|313126727|ref|YP_004036997.1| 56 PGKPTVLDLFATWCVPCSAQMESLTALHEEFGDDVAFVSVTN 97
                                      56899********************************99865 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.44
                                       TTTSHHHHHHTT-SSSSEEEEEETTE.EEEEEESS-HHHHHHHHH CS
                       Thioredoxin  58 vdenedlakkyevegiPtlklfkngk.evkkyegarekeklaafl 101
                                       +d ++ l k ++  g+P l +f ++  +  +  g +++++l+a +
  gi|313126727|ref|YP_004036997.1| 124 HDPESRLMKVLGAGGLPYLAVFDADGtATWTHRGLASESNLRAQI 168
                                       566777778888889999999976553666777777777777766 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.1e-07    0.0004       5     107 ..      57     166 ..      53     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.1e-07
                     Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfp.....lkpsfepkavaiwcakekkkafkd........ie 67 
                                       gkp++++  +++C  C + ++ l  l +++ + v+++      ++++  +  v+ w a        d         +
  gi|313126727|ref|YP_004036997.1|  57 GKPTVLDLFATWCVPCSAQMESLTALhEEFGDDVAFVSvtnegFGDNLTADDVRKWWA--------DhdgawtvgHD 125
                                       8****************98887777775555554444433345555544444444444........45555555999 PP

                     Thioredoxin_2  68 envelarkygvrgtPtivfldgk.eivarlpGyvpaeelea 107
                                        ++ l++ +g  g+P++ ++d++ +   + +G+ ++ +l+a
  gi|313126727|ref|YP_004036997.1| 126 PESRLMKVLGAGGLPYLAVFDADgTATWTHRGLASESNLRA 166
                                       9**********************988889999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1202.30
//
Query:       gi|313126728|ref|YP_004036998.1|  [L=223]
Description: cytochrome c biogenesis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-17   61.5  15.2    1.3e-16   61.2  15.2    1.1  1  DsbD      Cytochrome C biogenesis protein transmembrane regio
  ------ inclusion threshold ------
      0.053   13.8   0.1       0.12   12.6   0.1    1.5  1  Tgi2PP    Effector immunity protein Tgi2PP


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2  15.2   1.4e-20   1.3e-16       3     210 ..      18     211 ..      16     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.4e-20
                              DsbD   3 laGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevir 79 
                                        aG ++fl+PC  pl+P y+sy  g   +d         ++++    ++G  +v+v+++ +  ++g+ ++   + ++
  gi|313126728|ref|YP_004036998.1|  18 SAGAATFLAPCAYPLLPGYISYYVGRDDSDTGG------AIVRGTAAAIGALVVLVTVAGVLFTAGTAVVSHLTLLE 88 
                                       69********************98665555444......466777888999999998877766666666688999** PP

                              DsbD  80 rvaglivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskeslak 156
                                        ++g+  i+lG  f+       l +   l+    +   sv g  ++G ++al ++ C+ Pv+  v++ + +   + k
  gi|313126728|ref|YP_004036998.1|  89 PIIGVALIVLGALFA-------LGHAPTLHMQLPERRSSVGGFAVFGGVYALAAAGCVVPVFVGVVTQSLTLS-TGK 157
                                       ***********8877.......444444444444444445677789********************9887776.89* PP

                              DsbD 157 gallllvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGvl 210
                                       +a++ll+y+l  a+p+  v++l  l    ++ l+ky   v+ ++gv++vl+G+ 
  gi|313126728|ref|YP_004036998.1| 158 AAIVLLAYALSVAAPLAAVTVLGALGSYAFRDLSKYIGSVQRIAGVVMVLAGLW 211
                                       ************************999*************************86 PP

>> Tgi2PP  Effector immunity protein Tgi2PP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.3e-05      0.12      21      39 ..      31      49 ..      29      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                                      -SSTTEEEEEEEE--TTSS CS
                            Tgi2PP 21 pylpGYadFlvlyestkag 39
                                      p lpGY ++ v+++++  g
  gi|313126728|ref|YP_004036998.1| 31 PLLPGYISYYVGRDDSDTG 49
                                      889*************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1351.56
//
Query:       gi|313126729|ref|YP_004036999.1|  [L=139]
Description: signal-transduction protein containing camp-binding and cbs domains [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-23   82.7   6.4    2.1e-11   44.1   0.6    2.2  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.7   5.9e-15   1.1e-10       1      52 [.       3      52 ..       3      53 .. 0.93
   2 !   44.1   0.6   1.2e-15   2.1e-11       1      53 [.      67     118 ..      67     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 5.9e-15
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52
                                      V+++m+++vvtv+ d+tl+ea++ m e++v+++ VV + g ++ ivt++D l
  gi|313126729|ref|YP_004036999.1|  3 VAQVMSSPVVTVTLDATLREAVRSMLERRVGSV-VVLDTG-PISIVTRSDAL 52
                                      789******************************.653699.*********76 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 1.2e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V+d+m+rd+v+ +++t++  al++m++++v  lPV  +  +lvGi+t++D+++
  gi|313126729|ref|YP_004036999.1|  67 VTDVMSRDLVMTTEQTSITTALDTMKQHEVKKLPVR-DGMELVGIITMTDIAE 118
                                       89***********************9999******7.4559**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1029.29
//
Query:       gi|313126730|ref|YP_004037000.1|  [L=84]
Description: hypothetical protein Hbor_19890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      119  (0.00663729); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 516.39
//
Query:       gi|313126731|ref|YP_004037001.1|  [L=429]
Description: hypothetical protein Hbor_19900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00016   21.4   5.9    0.00036   20.2   5.9    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   5.9     2e-08   0.00036       3      24 ..       7      28 ..       6      30 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2e-08
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggca 24
                                      SRR+FLK + A++ A+al +c 
  gi|313126731|ref|YP_004037001.1|  7 SRRTFLKSAVALGGATALSACM 28
                                      9********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2731.43
//
Query:       gi|313126732|ref|YP_004037002.1|  [L=229]
Description: hypothetical protein Hbor_19910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-17   64.1   0.0    1.5e-17   63.8   0.0    1.1  1  SCO1-SenC   SCO1/SenC
    4.2e-05   23.2   6.4    6.2e-05   22.7   6.4    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
      0.097   11.9   0.1        0.2   10.9   0.1    1.4  1  DUF3666     Ribose-5-phosphate isomerase


Domain annotation for each model (and alignments):
>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   2.5e-21   1.5e-17      13     133 ..      74     202 ..      70     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 2.5e-21
                         SCO1-SenC  13 avteedlegkpslvffgFthCpdvCpttlanmaevldalgeea..ekvqplfiTvDPerDtpevlkeyleafdprii 87 
                                        v+ +d+eg p + +f+Ft+C +vCp  ++ +++v+ +  +e+  ++v+++ ++ DP+rD+ e+ ++ +++++ ++ 
  gi|313126732|ref|YP_004037002.1|  74 DVSVRDIEG-PHFHTFFFTNCMTVCPLLISSLRKVQVHSINEGydDEVSFYPVSFDPARDDAEAFRKEAKQMNIDMD 149
                                       566666666.5567899*******************99988876799*****************************9 PP

                         SCO1-SenC  88 g.....ltG.skeeiakaake.frvyvekvedeesdytvdHsssvyLvdpdgr 133
                                       +     l+   k+e +++++e f+v++ek+e+ ++ y++ H+s v+Lv+ dg 
  gi|313126732|ref|YP_004037002.1| 150 AgnwhfLRPdGKSEARRIVDEtFGVFFEKQENGDKPYMFAHTSVVLLVNGDGY 202
                                       99***96543677778888877***************************9985 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   6.4     1e-08   6.2e-05       2      25 ..       1      24 [.       1      25 [. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1e-08
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR+FL+++++++AA+++g +++
  gi|313126732|ref|YP_004037002.1|  1 MNRRSFLRAAGVTGAAGLAGCLGG 24
                                      89************9997776654 PP

>> DUF3666  Ribose-5-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   3.3e-05       0.2      22      36 ..      80      94 ..      77      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.3e-05
                                      T-STTHHHHHTTT-- CS
                           DUF3666 22 isGerFqeyFFancq 36
                                      i G++F   FF nc 
  gi|313126732|ref|YP_004037002.1| 80 IEGPHFHTFFFTNCM 94
                                      89************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1522.35
//
Query:       gi|313126733|ref|YP_004037003.1|  [L=399]
Description: sugar phosphate permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-32  113.1  61.9    5.5e-20   71.6  30.2    2.0  2  MFS_1     Major Facilitator Superfamily
      0.002   17.1   8.3      0.002   17.1   8.3    2.8  3  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
        3.3    5.9   9.3       0.37    9.0   3.4    2.0  2  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3  24.1   2.2e-16   1.3e-12       2     179 ..      11     190 ..      10     214 .. 0.82
   2 !   71.6  30.2   9.1e-24   5.5e-20       6     169 ..     216     378 ..     212     386 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.2e-16
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispse..igllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg 75 
                                       +la++ +  +  +l+p +   l ++lg ++++    + l++ +++++ ++ ++G+ sd +Grrr ++++g+l+ alg
  gi|313126733|ref|YP_004037003.1|  11 ALAVWAVLVSQVLLYPGVA-DLVHELGGTGDVqsGMWFLVAEFAAFVTFAGVWGAASDALGRRRsLIVTGALGGALG 86 
                                       6677777778888888888.899999955555327789999999********************************* PP

                             MFS_1  76 lllll.fa...sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllassl 148
                                        l+l+ ++    s++++l  r+l G ++ ++f+++++++ad++++   g+ +g ++++++lGa+lg ++gg la  +
  gi|313126733|ref|YP_004037003.1|  87 YLVLAaVPalgVSFTAVLGIRALGGTMTIGAFSLSMTALADLSSE--NGKNMGAAGIAIGLGAALGSVVGGRLA-DA 160
                                       444442325756677****************************95..***************************.55 PP

                             MFS_1 149 gWravfyilaivsllafvlfllllpeepper 179
                                          ++ y +a ++++a+v+ ++ +p++ p+ 
  gi|313126733|ref|YP_004037003.1| 161 DPLYPLYGAATLLVVAAVI-VATVPDRTPDG 190
                                       7788888888888888884.34445555544 PP

  == domain 2  score: 71.6 bits;  conditional E-value: 9.1e-24
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                       f+  +++++++++   ++ +++g+++  +gl+l ++++ +av+++plG+lsdr+Gr   +++g ++f+l++++  +a
  gi|313126733|ref|YP_004037003.1| 216 FIDRMTAGFFSLVGV-FYFRSFGLDAFGAGLALFAFFFPFAVLQYPLGVLSDRVGRFVPVIVGSIGFGLTIIVVGVA 291
                                       555566666666666.8889**************************************************3333356 PP

                             MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                       ++l+l +v+ +l G++++++ p+ +al++d++ ++erg a+g ++++ slG++ g ++gg+ +s + +  +f+++++
  gi|313126733|ref|YP_004037003.1| 292 PTLPLAIVSMILVGVFGALVSPSTMALVTDIADPDERGAALGGFNVFGSLGFLTGFVVGGFTTSTADFLTAFLVVGL 368
                                       9999***********************************************************************99 PP

                             MFS_1 160 vsllafvlfl 169
                                         +  +++++
  gi|313126733|ref|YP_004037003.1| 369 SEVAIALVAA 378
                                       8777777655 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   5.3    0.0013       7.6     299     366 ..      52     121 ..      30     131 .. 0.59
   2 ?   -0.1   0.8     0.055   3.3e+02      47      94 ..     135     181 ..     104     190 .. 0.63
   3 !   17.1   8.3   3.4e-07     0.002      66     166 ..     261     358 ..     239     385 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHH..HHHHHS-SHH.HHHHHHHHHHHHHHHHH...HHHHTTSS...CHHHHHHHHHHHHHHHTT CS
                          Sugar_tr 299 vnfvatfvai..flvdrfGRRt.llllGaagmaicfvilg.ivalllvakskaasivaivfialfialfalg 366
                                         +++tf+++    +d +GRR+ l ++Ga+g+a+  ++l+  + +l+v+ + + +i a+ +  + i +f+l+
  gi|313126733|ref|YP_004037003.1|  52 FAAFVTFAGVwgAASDALGRRRsLIVTGALGGALGYLVLAaVP-ALGVSFTAVLGIRALGG-TMTIGAFSLS 121
                                       3445566665346899999876255679999999999999444.44444433444433333.3334455554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.055
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqa 94 
                                        +g+   +  +Ga++Gs+++g l+d     + l  aa+l+v++av+ a
  gi|313126733|ref|YP_004037003.1| 135 NMGAAGIAIGLGAALGSVVGGRLADADPLYP-LYGAATLLVVAAVIVA 181
                                       455666677799*********9999755544.4555555555555544 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 3.4e-07
                                       HHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHH CS
                          Sugar_tr  66 agllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvsl 142
                                       +g l+dr+GR    +++++ f   +++ ++a+   ++ + iv+ +lvG++  l+s  +  ++  iA ++ Rga  + 
  gi|313126733|ref|YP_004037003.1| 261 LGVLSDRVGRFVPVIVGSIGFGLTIIVVGVAP---TLPLAIVSMILVGVFGALVSPSTMALVTDIADPDERGAALGG 334
                                       799*****************************...9***************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHTSS- CS
                          Sugar_tr 143 yqlaitfGilvaaifglglnktsn 166
                                       ++++ ++G+l ++++g ++  t +
  gi|313126733|ref|YP_004037003.1| 335 FNVFGSLGFLTGFVVGGFTTSTAD 358
                                       ***************999877777 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3     0.046   2.7e+02     336     377 ..     139     180 ..     131     184 .. 0.80
   2 ?    9.0   3.4   6.2e-05      0.37     134     193 ..     296     355 ..     283     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.046
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 336 tGvvvipgaalGillgGllvkklklsakklaklvlvvsllsl 377
                                       +G+++ +gaalG ++gG l     l +   a+  lvv+ + +
  gi|313126733|ref|YP_004037003.1| 139 AGIAIGLGAALGSVVGGRLADADPLYPLYGAATLLVVAAVIV 180
                                       6889999**********9999888888877777777766655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 6.2e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 134 lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                       l +++ +l+G+ ++++ +  ++ + D +++ +    lg + ++  lG   Gf++G+++++
  gi|313126733|ref|YP_004037003.1| 296 LAIVSMILVGVFGALVSPSTMALVTDIADPDERGAALGGFNVFGSLGFLTGFVVGGFTTS 355
                                       7899****************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2381.71
//
Query:       gi|313126734|ref|YP_004037004.1|  [L=324]
Description: oxidoreductase, aryl-alcohol dehydrogenase like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-70  237.5   0.0      2e-70  237.3   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.3   0.0   1.1e-74     2e-70       1     291 [.      15     313 ..      15     316 .. 0.94

  Alignments for each domain:
  == domain 1  score: 237.3 bits;  conditional E-value: 1.1e-74
                                       .EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE... CS
                      Aldo_ket_red   1 elglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv... 70 
                                       +++lG +++g+     +++++e   el++ra+e GinffDtA++Y +g+se++lGeal+    +r+e ++atK+   
  gi|313126734|ref|YP_004037004.1|  15 RICLGCMSFGTSdwreWVVDEEAGKELVDRAIELGINFFDTANMYSEGESERILGEALEG---RRDEAVVATKLyfq 88 
                                       59********999*9999******************************************...***********997 PP

                                       --SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHH CS
                      Aldo_ket_red  71 dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqle 147
                                        ++ ++++ gls++ i+++l++sl rLg d+vDll++Hr+d+++p ie +l+al++ v+  k+r++G S+  + q  
  gi|313126734|ref|YP_004037004.1|  89 MDDSDPNSGGLSRKAIEQELDNSLDRLGMDTVDLLQIHRWDYDTP-IETTLRALDDAVRREKVRYLGASSMWAHQFA 164
                                       7788899999***********************************.***********************98877777 PP

                                       HH....HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------. CS
                      Aldo_ket_red 148 ka....kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd. 219
                                       +a     + +  ++v+ q++ynll ++ee+++l+lc+k++v++i++spl++G+  +  q+ +++e++e+++    + 
  gi|313126734|ref|YP_004037004.1| 165 EAlhtsDRLGFDRFVTMQNHYNLLYREEEREMLPLCEKENVGVIPWSPLARGWVARPHQEARSTERGETDELAHGHp 241
                                       7777766666777******************************************9999999999988888776667 PP

                                       TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 220 ertsknldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                           + ++ +e++++la e+gv++aq+ l+++++++ v  +i+g+++ie+led ++al++ ls++++++l+e
  gi|313126734|ref|YP_004037004.1| 242 YLEGGGREINERVQQLADEKGVKMAQIGLAWLFHKDWVDAPIVGTTSIEHLEDAVEALDISLSDSDIDYLEE 313
                                       7778899*************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1937.40
//
Query:       gi|313126735|ref|YP_004037005.1|  [L=430]
Description: membrane protein/domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-20   72.1   4.0    5.3e-20   72.1   4.0    2.8  2  RDD       RDD family
  ------ inclusion threshold ------
      0.064   13.1   0.0        9.3    6.1   0.0    2.1  2  TraB      TraB family
        5.1    7.4   6.2        1.2    9.5   1.1    2.4  2  DUF1269   Protein of unknown function (DUF1269)


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   6.9       1.2   6.9e+03      43      64 ..     154     175 ..     116     205 .. 0.40
   2 !   72.1   4.0   8.9e-24   5.3e-20       3     141 .]     283     418 ..     281     418 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                               RDD  43 vagslllllllvlllvllvyql 64 
                                       v  + + ++++++++v +++++
  gi|313126735|ref|YP_004037005.1| 154 VHRLFWGVVSVAVTAVVGWFWF 175
                                       2222222222222222222221 PP

  == domain 2  score: 72.1 bits;  conditional E-value: 8.9e-24
                               RDD   3 slgrRllAfliDlvllliislllallivall.....nakasaneavagslllllllvlllvllvyqllllskkgqTl 74 
                                        +grR++A+++D+++l+ + ++ ++++  ++      a+a  ++   +++ +lll +++l+ ++y++ l+s++g+T+
  gi|313126735|ref|YP_004037005.1| 283 VFGRRIAALVVDWMVLIPVIAVGTTVGILVVgisieLAGADFSSLADWQVVALLLGSAFLADMAYWTALESRYGKTV 359
                                       689*************999999888888877889998888888999999999999999******************* PP

                               RDD  75 GklllglkvvdedgrklglaqaliRalllllllvlglslvlllllligflfvlfsrkrqalhDklag 141
                                       Gk+l+gl vvd+d r +g+ +al R++l         ++ +l + ++g l++l++++ q+l D++a+
  gi|313126735|ref|YP_004037005.1| 360 GKRLVGLVVVDADDRYPGVRTALRRNIL--------RPVDWLPFYVVGGLVALVTKRGQRLGDLVAN 418
                                       ***************************6........6888888999999999************996 PP

>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0016       9.3      12      84 ..       4      74 ..       2      83 .. 0.79
   2 ?    4.8   0.0    0.0037        22     206     246 ..     194     236 ..     190     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0016
                              TraB 12 syLfGTiHvskksvyplspeveealeksdtvvvEldlsddtdeatqkelaklkllpdgktlsdllseelyarl 84
                                      + LfG+iH+ + s  ++++e+    + +d+++vE     +++ + ++ + ++ l + g  l+ ++ + lya +
  gi|313126735|ref|YP_004037005.1|  4 VKLFGSIHADRRS--KVRRELASFASDADALFVEYPTEPYDAREYVELFIRAPLVTLGFLLTAVMQKPLYALF 74
                                      569******9866..58999999999*********99888888877777777777767667777666666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0037
                              TraB 206 fpelkevlldeRnrrwaekieall.kep.gsvfvaVGagHlaG 246
                                       f++ +++ + +Rn+ ++++i+a   +++ ++v    G +H++G
  gi|313126735|ref|YP_004037005.1| 194 FAWQMRATIGRRNEFMLDRIAAECdEHGyENVCLTTGYAHVFG 236
                                       67889999*************9995666899999999999987 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.1    0.0002       1.2       7      36 ..     120     146 ..     117     169 .. 0.80
   2 ?   -0.9   0.3      0.34     2e+03       8      32 ..     290     312 ..     286     327 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0002
                           DUF1269   7 wGllvGllflnPllGaavGAaaGAlvgals 36 
                                       wG+lvG l+l P    avG+++G+++ a+s
  gi|313126735|ref|YP_004037005.1| 120 WGILVGALVLAP---FAVGGTVGSIALAFS 146
                                       9***********...778888888776654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                           DUF1269   8 GllvGllflnPllGaavGAaaGAlv 32 
                                       +l+v  ++l P++  avG+++G lv
  gi|313126735|ref|YP_004037005.1| 290 ALVVDWMVLIPVI--AVGTTVGILV 312
                                       6677788888966..7888888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2365.22
//
Query:       gi|313126736|ref|YP_004037006.1|  [L=550]
Description: acyl-CoA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-77  261.5   0.0    1.4e-77  261.1   0.0    1.2  1  AMP-binding    AMP-binding enzyme
    6.2e-24   84.8   0.8    1.4e-23   83.6   0.8    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.1   0.0   1.6e-81   1.4e-77       4     422 ..      29     447 ..      26     448 .. 0.85

  Alignments for each domain:
  == domain 1  score: 261.1 bits;  conditional E-value: 1.6e-81
                                       HHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEE CS
                       AMP-binding   4 qaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpl 77 
                                       +a+ + d+va+ +   +g     TY++l++  nr+A++L ++Gv+kgdrV+ l+p+ p+ +++ l++lk Ga++vp+
  gi|313126736|ref|YP_004037006.1|  29 HADSFGDRVAVRFrgaDGVRDERTYADLRDDMNRFANALAEMGVGKGDRVMHLVPRHPDVFAIQLGALKRGAILVPC 105
                                       788999*****99999888999******************************************************* PP

                                       ETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCC CS
                       AMP-binding  78 nptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeee 154
                                       ++ l+++++ay  +d+ea++++   ++ l+e+++e++++ +  +    ++ +++++ +++ ++  + ++a   ++ +
  gi|313126736|ref|YP_004037006.1| 106 SSMLKPKDIAYRANDCEASTVV--AHESLVEMVDEVREETPL-ERF--ISLGGAPQGWQSFSSLVDGREA--THDGP 175
                                       **********************..777779999999986433.333..3445666676666666555554..44677 PP

                                       S-BTTSEEEEEEE--SSSS-EEEEEEHHHH.....HHHHHHHH.HHHCSCCTT...............T-EE.EESS CS
                       AMP-binding 155 elkpddlayiiYTSGTTGkPKGVmlshrnl.....vanvaslk.letrfklke...............ddvv.lsil 209
                                       el ++d++ i YTSGTTG+PK Vm++hr +     v++ ++ + ++      +               dd++ +++ 
  gi|313126736|ref|YP_004037006.1| 176 ELASSDPMSINYTSGTTGQPKPVMHRHRWMrcfelVNAPYW-WgVT------AegevppgetaepadlDDELlWATT 245
                                       99**************************9964443222222.2333......3333445788889999777736668 PP

                                       -TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT.- CS
                       AMP-binding 210 plahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlss.l 285
                                          ++  + + + + ++ Gat  l++++  +dp+++l  +++++vt +++vP+ ++++ +++ l+      +    l
  gi|313126736|ref|YP_004037006.1| 246 GTGWAKWFWSPVGVGITTGATQLLYDGE--FDPETFLSIMAEEGVTRLCAVPTQYRMFSQAD-LS------EYDIdL 313
                                       888888877899999*********9966..6799************************8853.44......34455* PP

                                       SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETT CS
                       AMP-binding 286 rlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdg 362
                                       r +l++gepl++e ++++++ fg +  +gYG+TEt + vt ++ ++ ++k+gs Gkp pg    i+De+ + ++p+g
  gi|313126736|ref|YP_004037006.1| 314 RAALSAGEPLNREPIEAIESAFGVTPRDGYGQTETVALVT-NY-PGIEVKPGSMGKPTPGLGTTIIDED-ETELPPG 387
                                       ************************889************9.55.555579******************9.78899** PP

                                       SEEEEE..EEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 363 eeGell..vrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       e Ge+   v  pg++ gY+ ++++ +e+f   g+++rTGDl+ +dedG +++ gR++d+i++
  gi|313126736|ref|YP_004037006.1| 388 EIGEIAvpVNCPGIFDGYYEREDLDEETFY--GDYYRTGDLASRDEDGFFFFEGRADDIIIS 447
                                       *****9556788*****************9..68**************************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.8   1.6e-27   1.4e-23       1      76 []     456     534 ..     456     534 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 1.6e-27
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evE alvsh+aVaeaa+vG p+e +G +++a+Vvl +g   se+l +e+++++++e +py+ p++v+fvdelpkt s
  gi|313126736|ref|YP_004037006.1| 456 EVEDALVSHEAVAEAAAVGSPHEERGDVVKAYVVLTEGydgSEELTNEIQEFMKEETAPYKYPRRVEFVDELPKTSS 532
                                       8**********************************777542355********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|313126736|ref|YP_004037006.1| 533 GK 534
                                       *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 3055.23
//
Query:       gi|313126737|ref|YP_004037007.1|  [L=265]
Description: hypothetical protein Hbor_19960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-70  236.3   1.2    3.7e-70  236.1   1.2    1.0  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.1   1.2   2.1e-74   3.7e-70       2     241 .]       5     240 ..       4     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 236.1 bits;  conditional E-value: 2.1e-74
                      Creatininase   2 eltwpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTis 78 
                                       + twpe+ ++++++++a++P+GstEqHGphlpl+tD+liaeala+++a++++  +l++Pt+++Gvs++h++f GT++
  gi|313126737|ref|YP_004037007.1|   5 DRTWPELGDYVAAESLAVVPLGSTEQHGPHLPLATDHLIAEALAREAADRTD--VLCTPTVNVGVSPHHRQFHGTMW 79 
                                       579***********************************************99..*********************** PP

                      Creatininase  79 lspetliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaae.aa 154
                                       +++  ++++++ + ++la hG++r+v vn+Hggn + l+e+ r+lr++ +  a++             ++ +++  +
  gi|313126737|ref|YP_004037007.1|  80 VDAPQFRDYVESMTRNLAYHGIDRVVYVNAHGGNAQHLREVGRRLRDDGTMYAIE-------------WMWDESiPD 143
                                       ************************************************9665543.............333444455 PP

                      Creatininase 155 eeseeee.gggHAgelEtSlmlalrpelVrmdraedpeeaklakeg.........vstaedaeelspsGvlGdpska 221
                                        ++e  e +g H+g+ Et+++++++pelVr+dr+ed+++  l + +         ++t  da e s++Gv+Gd+++a
  gi|313126737|ref|YP_004037007.1| 144 LVNEVFEhNGPHGGPKETAMIMHIAPELVREDRLEDARDGGLVDLDdsdrymkhgARTFYDAIENSENGVFGDQTDA 220
                                       55555555****************************9999888777999****9988888888889*********** PP

                      Creatininase 222 taekGealleaaveelaell 241
                                       t+e Ge+l+eaa+e+l+ l+
  gi|313126737|ref|YP_004037007.1| 221 TPETGERLFEAATEQLVHLI 240
                                       ****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1446.04
//
Query:       gi|313126738|ref|YP_004037008.1|  [L=139]
Description: protein-tyrosine-phosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-25   89.8   0.0    2.6e-25   89.4   0.0    1.2  1  LMWPc     Low molecular weight phosphotyrosine protein phosph
  ------ inclusion threshold ------
      0.078   12.3   0.0       0.11   11.8   0.0    1.1  1  MTD       methylene-5,6,7,8-tetrahydromethanopterin dehydroge


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.0   2.9e-29   2.6e-25       1     142 []       6     132 ..       6     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 2.9e-29
                                       EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHH CS
                             LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelae 77 
                                       v+fvC++N++RS+mA+a++++e  +++l+  v+v + Gt   +++++++++ve++ + g++ls++++r+++ ee++ 
  gi|313126738|ref|YP_004037008.1|   6 VAFVCVQNAGRSQMATAFAEQETADRDLD--VNVVTGGTR--PADHVHENVVETMYDVGFDLSDRTPREVTFEEISG 78 
                                       79********************9998665..59*******..*********************************** PP

                                       SSEEEESSHHHHHHHHHHCCTTGGGGEEEGGGGSSTSS---HTTSSHHHHHHHHHHHHHHHHHHH CS
                             LMWPc  78 lDlilamdeenkreleslapekekakvkllgeyteqldieDPyygeieafeevldeieeavkkll 142
                                        D++++m  +++ ++++   ++e          ++++ ++DP +++ e+  e++dei+++v +++
  gi|313126738|ref|YP_004037008.1|  79 SDYVITMGCSAE-DVCPAGWGGE----------NRDWGLDDPHGQDAETTAEIRDEIQRRVAAFF 132
                                       *******77777.8****99944..........479*************************9986 PP

>> MTD  methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.3e-05      0.11       3      60 ..       6      63 ..       5      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                                      EEEEEES--HHHHHTT.GGGSTTS--SSEEEEEEEEET--SHHHHHHHHHHHHHH--SE CS
                               MTD  3 igiiklGnigtslvid.lllDeradRedievrvvgsgaklkkeeveevveklkefdpdl 60
                                      ++++ + n g s++   ++  e adR d++v+vv+ g++   +  e+vve++ ++  dl
  gi|313126738|ref|YP_004037008.1|  6 VAFVCVQNAGRSQMATaFAEQETADR-DLDVNVVTGGTRPADHVHENVVETMYDVGFDL 63
                                      67888999999999762677899999.*************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 810.04
//
Query:       gi|313126739|ref|YP_004037009.1|  [L=64]
Description: cold-shock DNA-binding protein family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-20   73.1   0.2    1.3e-20   73.0   0.2    1.0  1  CSD           'Cold-shock' DNA-binding domain
     0.0089   15.9   0.8      0.013   15.4   0.8    1.4  1  S1-like       S1-like
  ------ inclusion threshold ------
      0.052   13.2   1.5       0.08   12.6   1.5    1.4  1  OB_RNB        Ribonuclease B OB domain
      0.063   13.2   0.0      0.067   13.1   0.0    1.1  1  Rho_RNA_bind  Rho termination factor, RNA-binding domain
       0.12   12.3   0.0       0.15   12.0   0.0    1.3  1  CusF_Ec       Copper binding periplasmic protein CusF


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.2   3.7e-24   1.3e-20       2      65 ..       3      63 ..       2      64 .] 0.96

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 3.7e-24
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      +GtV  fn+  g+GFI+ ed d+dvF+H+ ++ g +   L+egqeVeF++++ +kgp+A+n+++
  gi|313126739|ref|YP_004037009.1|  3 KGTVAFFNDTGGYGFIESEDSDEDVFFHMEDVGGPD---LEEGQEVEFDIEQADKGPRAKNLQR 63
                                      8*******************************9999...**********************986 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   3.7e-06     0.013      14      46 ..      14      51 ..       1      60 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.7e-06
                           S1-like 14 tfGfv.....DeevfFqrsvvkGrlpkvgdrVlveAvy 46
                                       +Gf+     De+vfF+++ v G+  + g  V+++  +
  gi|313126739|ref|YP_004037009.1| 14 GYGFIesedsDEDVFFHMEDVGGPDLEEGQEVEFDIEQ 51
                                      599997777789******************99987655 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.5   2.2e-05      0.08       8      28 ..      13      33 ..       4      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                                      SS-EEEEECT.TEEEEE-HHH CS
                            OB_RNB  8 kGFGFlipdegkeDifippeq 28
                                       G+GF++ ++ +eD+f + e+
  gi|313126739|ref|YP_004037009.1| 13 GGYGFIESEDSDEDVFFHMED 33
                                      59**************87766 PP

>> Rho_RNA_bind  Rho termination factor, RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.9e-05     0.067       3      63 ..       4      63 ..       2      64 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                                      EEEEE-TT..S-EEEE-GTT---TT-EEE-CCCCCCTT--TT-EEEEEEE---SSS-SEEECE CS
                      Rho_RNA_bind  3 GiLeilpd..gygFlRtsnylpgpedvYVsasqirkfgLrtGDaveGkvrppkerekynaLlr 63
                                      G++ +++d  gygF+ ++    ++edv+ +++ +   +L +G  ve  + ++ ++ + ++L r
  gi|313126739|ref|YP_004037009.1|  4 GTVAFFNDtgGYGFIESE---DSDEDVFFHMEDVGGPDLEEGQEVEFDIEQADKGPRAKNLQR 63
                                      66677776669****997...89************************9999988888888766 PP

>> CusF_Ec  Copper binding periplasmic protein CusF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.3e-05      0.15      42      66 ..      38      61 ..      25      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.3e-05
                                      S-STT-EEEEEEEEETTCEEEEEEE CS
                           CusF_Ec 42 glkaGdkVrFefekrdggeyvitki 66
                                      +l++G++V+F++e++d+g ++ + +
  gi|313126739|ref|YP_004037009.1| 38 DLEEGQEVEFDIEQADKG-PRAKNL 61
                                      799*************99.776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.36s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 356.40
//
Query:       gi|313126740|ref|YP_004037010.1|  [L=135]
Description: transcriptional regulator with copg/arc/metj DNA-binding domain and metal-binding domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-15   56.6   0.1    3.6e-15   55.9   0.1    1.3  1  NikR_C          NikR C terminal nickel binding domain
    1.3e-05   24.9   0.1    2.6e-05   24.0   0.1    1.5  1  RHH_1           Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.067   13.1   0.0    1.6  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.1     6e-19   3.6e-15       5      74 ..      55     123 ..      53     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 6e-19
                                       EEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEE CS
                            NikR_C   5 tivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkl 74 
                                       ++ +d++++ + ++l+++qh+++ +i ++ h h   d+c+ev +++G+ae++++l+ +lr  + V++v +
  gi|313126740|ref|YP_004037010.1|  55 VVAFDYEHEAVIQELHTVQHDFEGVIEATSHTH-HGDWCFEVAFCDGPAERVRRLVYRLRDFDAVRRVSV 123
                                       6889*****************************.99******************************9976 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   4.4e-09   2.6e-05       1      38 [.       2      40 ..       2      41 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.4e-09
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      r+s+ +++++l+++d+   ++g  SrS +IReA +ey+e
  gi|313126740|ref|YP_004037010.1|  2 RTSLNVPDDVLAEFDAVWQAEGlDSRSRAIREAMLEYVE 40
                                      899**********************************97 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.067       1      42 [.       1      45 [.       1      49 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                                      XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXX-------H CS
                    VapB_antitoxin  1 MrtnIeiDDeLlae...AirltglktKrEaVnlALreLiqrrkre 42
                                      Mrt +++ D+ lae   + +  gl  ++ a+++A+ e+++++ r 
  gi|313126740|ref|YP_004037010.1|  1 MRTSLNVPDDVLAEfdaVWQAEGLDSRSRAIREAMLEYVESHTRL 45
                                      9******9999987776999999*****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 772.82
//
Query:       gi|313126741|ref|YP_004037011.1|  [L=391]
Description: hypothetical protein Hbor_20000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.4    7.5  11.9       0.63    9.9   7.5    1.8  2  DsbD_2    Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.5   3.5e-05      0.63     120     199 .]      11      95 ..       5      95 .. 0.77
   2 ?   -0.9   0.1     0.076   1.4e+03      78     129 ..     342     389 ..     324     391 .] 0.41

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.5e-05
                            DsbD_2 120 salllGllnGllpCglvysalllalasgs.aleGalvmlaFgLGT...lpalllfglllgllskklrkkllr.lagv 191
                                       +a++lG+++G+ p      a+++a+ +g+ +l+Ga++  ++g+G     +a++++ ++++   + ++  +   +agv
  gi|313126741|ref|YP_004037011.1|  11 GAVALGFVHGVEPGHGWPIAATYAMEKGNkWLYGAAAGTILGIGHlvsSIAMVVVFFAAKSYFNLTQLPWISqIAGV 87 
                                       78999********98888889999988763789**********983224456666666666666666777666**** PP

                            DsbD_2 192 llillgll 199
                                       llillgl+
  gi|313126741|ref|YP_004037011.1|  88 LLILLGLY 95 
                                       *****986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.076
                            DsbD_2  78 gllllllglklllkkkllklerlgkllsrllkklakklkslasalllGllnG 129
                                       ++++++++  ll  ++  ++e   + +++++  +++       +++lG+l+G
  gi|313126741|ref|YP_004037011.1| 342 VIVGIVSLTLLL-VAGYYRYEDRVESVAEHFPTISA---AILISMGLGFLFG 389
                                       222222222222.22222222222223333333332...3445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.65
# Mc/sec: 1811.86
//
Query:       gi|313126742|ref|YP_004037012.1|  [L=302]
Description: hypothetical protein Hbor_20010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0035   17.8   0.1        8.6    6.9   0.0    3.5  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.037   13.7   0.3        0.1   12.3   0.0    1.8  2  DUF4559   Domain of unknown function (DUF4559)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.9   1.7e+04      22      35 ..      29      42 ..      24      47 .. 0.71
   2 !    6.9   0.0   0.00095       8.6      11      42 ..      64     102 ..      56     111 .. 0.78
   3 ?   -0.7   0.0      0.23   2.1e+03      45      51 ..     161     167 ..     155     173 .. 0.75
   4 !    6.1   0.0    0.0017        16      10      29 ..     223     242 ..     210     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.9
                                      HHHHHHHTSSEEEE CS
                               CBS 22 lelmrekgvsrlPV 35
                                      l ++r+ g++++P+
  gi|313126742|ref|YP_004037012.1| 29 LSRYRDLGYTHIPI 42
                                      55666777889997 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00095
                                       EEETTSBHHHHHHHH.......HHHTSSEEEEEETTTBE CS
                               CBS  11 tvppdttleealelm.......rekgvsrlPVVdedgkl 42 
                                        ++++t l ++l+l+       ++++++++++V + g++
  gi|313126742|ref|YP_004037012.1|  64 IIHEETHLMDVLRLIqnkpfllIDRRIGSYYIVTDAGEF 102
                                       5899999*****999444443334669999999889985 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.23
                                       EEEHHHH CS
                               CBS  45 ivtlrDl 51 
                                       i+tl+D+
  gi|313126742|ref|YP_004037012.1| 161 IITLSDI 167
                                       8999998 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0017
                                       EEEETTSBHHHHHHHHHHHT CS
                               CBS  10 vtvppdttleealelmrekg 29 
                                       v + + ttl++++e++r+++
  gi|313126742|ref|YP_004037012.1| 223 VHIAEYTTLRDIMEILRSSN 242
                                       58999***********8655 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.26   2.4e+03     201     251 ..     138     185 ..     118     207 .. 0.59
   2 ?   12.3   0.0   1.1e-05       0.1     128     157 ..     245     274 ..     243     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.26
                           DUF4559 201 kqefeislkeddevrvltdvllslqklkeleeellkedatkldelvlraee 251
                                       +qe+  +  e+++++v ++   +   l++++++++ke   +l +++ +  +
  gi|313126742|ref|YP_004037012.1| 138 EQELREEYPEIAKSEVPVGNPYQIITLSDINDRMMKE---MLYSVFAELTS 185
                                       4455555555555566665555666666777777777...44444433333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.1e-05
                           DUF4559 128 llksCkhfekldvekvknvievRNklMHSp 157
                                       +++ C    k d+++++++i++RN++MH  
  gi|313126742|ref|YP_004037012.1| 245 FVEACGFEAKDDIDSLRKIIDIRNHVMHPN 274
                                       6677877777799***************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1655.68
//
Query:       gi|313126743|ref|YP_004037013.1|  [L=206]
Description: hypothetical protein Hbor_20020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.2   0.0        5.2    6.9   0.0    2.4  2  HTH_DeoR  DeoR-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00029       5.2      19      51 ..      79     109 ..      76     115 .. 0.78
   2 ?    2.8   0.0    0.0054        97       4      29 ..     146     171 ..     144     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00029
                          HTH_DeoR  19 elvellgvSeaTiRRDLneLeeqglltRthGGa 51 
                                       +++++lgvSe+T+ R L +++++     thGG 
  gi|313126743|ref|YP_004037013.1|  79 DVAAELGVSEETAARVLGIHDAEQR--GTHGGT 109
                                       789**********998888877655..567775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0054
                          HTH_DeoR   4 qilellkqqgklsveelvellgvSea 29 
                                        ile+l  +  l v e+ e l+++e+
  gi|313126743|ref|YP_004037013.1| 146 RILEYLYIRCGLGVSEIEEVLDIAEN 171
                                       69*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1153.48
//
Query:       gi|313126744|ref|YP_004037014.1|  [L=73]
Description: hypothetical protein Hbor_20030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 430.09
//
Query:       gi|313126745|ref|YP_004037015.1|  [L=98]
Description: hypothetical protein Hbor_20040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 532.51
//
Query:       gi|313126746|ref|YP_004037016.1|  [L=59]
Description: hypothetical protein Hbor_20050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 346.13
//
Query:       gi|313126747|ref|YP_004037017.1|  [L=35]
Description: hypothetical protein Hbor_20060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.33s 00:00:00.76 Elapsed: 00:00:00.52
# Mc/sec: 203.40
//
Query:       gi|313126748|ref|YP_004037018.1|  [L=311]
Description: site-specific recombinase xerd [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-38  130.8   0.3    6.9e-38  130.1   0.3    1.3  1  Phage_integrase  Phage integrase family
    1.4e-06   28.6   0.0    3.2e-06   27.5   0.0    1.6  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    4.3e-06   26.9   0.1    3.1e-05   24.2   0.0    2.4  3  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   0.3   1.2e-41   6.9e-38       2     170 ..     113     294 ..     112     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 1.2e-41
                                       HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHH CS
                   Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseeale 78 
                                       +lt+dev++l+++++++ k+r+ l++++l++tG+R +El++ ++ d++ e++ i++  +  K+  +r+v  + ++  
  gi|313126748|ref|YP_004037018.1| 113 YLTPDEVQQLVDNVHSPPKLRNELIIKMLFQTGMRRGELCKVKLHDVNREERSIRI--HADKTHSNRTVYYQPSLST 187
                                       89******************************************************..8889999*******99999 PP

                                       HHHHHHHHH...CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S............SC--TTHHHHHHHHH CS
                   Phage_integrase  79 llkellska...leeaeksellfaskrgkplsrqtvrkafkraveeagie............kpltpHtlRhsfata 140
                                        l  +++ +   + +a++s  lf+ +++++++ ++v++++++a+eeagi+             ++t+HtlRhsfa a
  gi|313126748|ref|YP_004037018.1| 188 PLNIWIDAErngVLTADDSPHLFPTQKAEHIKPNSVSRIVREAAEEAGIQevmyhdkggrpkRKITGHTLRHSFAVA 264
                                       99999999989999***********************************************99************** PP

                                       HHHHCTSHHHHHHHHT-SSCCHHHHHHCCC CS
                   Phage_integrase 141 LleagvdlrvvqkllGHssisttqiYthva 170
                                        l++g+d+r++qkl+GH++i+ttq Y ++a
  gi|313126748|ref|YP_004037018.1| 265 ALKNGMDVRTLQKLMGHADIETTQMYLDLA 294
                                       **************************9876 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   5.4e-10   3.2e-06      14      78 ..      15      80 ..       4      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 5.4e-10
                   Phage_int_SAM_4 14 lserTiksYlsaikrflrflkkk..apeeltkedieaYlnyLanerklsastqknalnalsffykkv 78
                                      ++e T + Y sai+r+ ++l+++  ++ + +++d+e+ l +La ++ +++ + k a++ +  fy ++
  gi|313126748|ref|YP_004037018.1| 15 QTEGTANRYASAIRRYRDWLDERgvEFGDANQDDVESHLLDLA-DEDYAKGSLKIARAGIAKFYDEM 80
                                      6899****************97788******************.9999***************9876 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   5.2e-09   3.1e-05       1      78 [.       4      78 ..       4      82 .. 0.91
   2 ?   -1.8   0.0      0.66   3.9e+03      39      59 ..     213     233 ..     209     237 .. 0.81
   3 ?   -2.3   0.0      0.96   5.8e+03      24      38 ..     270     284 ..     250     289 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.2e-09
                                      HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHH CS
                   Phage_int_SAM_1  1 leqfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfq 78
                                      ++ f++++++ +  ++ T + Y  ++rr+ ++l+e ++  +  ++++dv + l  l++e+++  sl+++++ + +F++
  gi|313126748|ref|YP_004037018.1|  4 IDTFQQHVSVKQ--TEGTANRYASAIRRYRDWLDE-RGVEFGDANQDDVESHLLDLADEDYAKGSLKIARAGIAKFYD 78
                                      567888887544..59*******************.*****************************************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.66
                                       --TTT--HHHHHHHHHS---- CS
                   Phage_int_SAM_1  39 esleqlttedvraflaeleee 59 
                                       +++e++++++v+++++e +ee
  gi|313126748|ref|YP_004037018.1| 213 QKAEHIKPNSVSRIVREAAEE 233
                                       567899999999999988775 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.96
                                       HHHHHHHHHHHH.TS CS
                   Phage_int_SAM_1  24 rdLrrflkflaergk 38 
                                       +d+r ++k + ++ +
  gi|313126748|ref|YP_004037018.1| 270 MDVRTLQKLMGHADI 284
                                       577777777777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1658.96
//
Query:       gi|313126749|ref|YP_004037019.1|  [L=173]
Description: hypothetical protein Hbor_20080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1035.10
//
Query:       gi|313126750|ref|YP_004037020.1|  [L=199]
Description: alkylhydroperoxidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-10   38.8   0.1    1.7e-09   37.6   0.1    1.7  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.065   12.8   0.0       0.12   11.9   0.0    1.4  1  DUF2982   Protein of unknown function (DUF2982)


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1   1.9e-13   1.7e-09       1      72 [.      49     122 ..      49     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.9e-13
                                       HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--H...HHHHHHHHHHHHHHS CS
                               CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvte...eeiaevlaqaaayag 72 
                                       p  +ra++++++al+  + +Ld+ e e+i +avs +n+c yC  aH +  +   +++   +++ + ++qa++   
  gi|313126750|ref|YP_004037020.1|  49 PSHFRAFFDYHDALVD-DTALDREEVEMIVVAVSGVNHCYYCNVAHGALVRIYAKDPtlaDQLVANYRQADISEK 122
                                       6679***********8.9*************************99998877666666555888888888887655 PP

>> DUF2982  Protein of unknown function (DUF2982)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.3e-05      0.12     108     142 ..      41      76 ..      16      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                           DUF2982 108 vlAmfanrmeklrellGYd.lyiseseLDreaeefv 142
                                       v A+fa + ++ r +++Y+  ++ +++LDre+ e++
  gi|313126750|ref|YP_004037020.1|  41 VFAAFAYKPSHFRAFFDYHdALVDDTALDREEVEMI 76 
                                       78****************64899*********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1208.05
//
Query:       gi|313126751|ref|YP_004037021.1|  [L=287]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-62  208.5  13.0    3.5e-31  108.6   6.9    2.0  2  Usp       Universal stress protein family
     0.0045   16.6   0.1       0.78    9.3   0.0    2.5  2  SRP54     SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.027   14.4   0.0      0.062   13.2   0.0    1.6  1  DUF3013   Protein of unknown function (DUF3013)
      0.095   12.6   0.2        8.7    6.3   0.0    2.6  2  XPB_DRD   Xeroderma pigmentosum group B helicase damage recog
      0.099   12.6   0.0       0.26   11.3   0.0    1.6  1  FR47      FR47-like protein


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.4   2.5e-33   8.9e-30       1     139 [.       1     136 [.       1     138 [. 0.98
   2 !  108.6   6.9   9.7e-35   3.5e-31       2     141 .]     149     285 ..     148     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 2.5e-33
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+rIl++vDgs+ + ++l +A e a+ +g+ + ll v d+ +++ +  +++ +   e+e +e   ea    + ++ 
  gi|313126751|ref|YP_004037021.1|   1 MYERILLPVDGSTGANEVLYHAGEIAQWTGGSVQLLFVADTARDSVTVVENDVVDALEQEGSEIVDEAG---EVLDS 74 
                                       9***************************************************************99987...7**** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                        gv+  ++v++gdp ++i+e+a+++d+d +V+ +rgr glsr llGSv+e+v+r ++ pVl 
  gi|313126751|ref|YP_004037021.1|  75 LGVEYSTDVVQGDPVPTIVEYADRYDYDVVVMPTRGRQGLSRQLLGSVTEKVVRLCEQPVLT 136
                                       ************************************************************96 PP

  == domain 2  score: 108.6 bits;  conditional E-value: 9.7e-35
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       y+rI+V++Dgs+++++A+e+A++ a+a +a++++l ++d++  g    ++ +++e e++  ea +  +     ae +
  gi|313126751|ref|YP_004037021.1| 149 YERIVVPTDGSPAATHAAEHAIDVAAALDATIHVLSAVDDSLLGFDVRSAVSEAEGEKAANEAVENVA---SSAESR 222
                                       99*****************************************9999999999999999999888765...79**** PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +v+v+ +ve g+p e+il+ + e++ad +V+G++g+++++r+llGSv+e+ +r +p+pV+ Vr
  gi|313126751|ref|YP_004037021.1| 223 DVDVVRHVERGSPHEMILDCVAENEADAVVMGTTGKRAVDRILLGSVAEKTIRTSPVPVVSVR 285
                                       ***********************************************************9887 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0049        18      75     105 ..      92     122 ..      68     189 .. 0.84
   2 !    9.3   0.0   0.00022      0.78      44     106 ..     211     270 ..     206     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0049
                                       HHHHHHHTTSSEEEEEE--SSTTHHHHHHHH CS
                             SRP54  75 avekakeekidvvlvDTaGrlqndkelmeel 105
                                        ve a++ ++dvv++ T Gr+   ++l+  +
  gi|313126751|ref|YP_004037021.1|  92 IVEYADRYDYDVVVMPTRGRQGLSRQLLGSV 122
                                       578899999************9999887655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHH CS
                             SRP54  44 AveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndkelmeelk 106
                                       Ave ++  ae+ +v+v+++ e  +p +++ + v + ++   d+v++ T+G+ + d+ l+  ++
  gi|313126751|ref|YP_004037021.1| 211 AVENVASSAESRDVDVVRHVERGSPHEMILDCVAENEA---DAVVMGTTGKRAVDRILLGSVA 270
                                       89999999***********9999******999987766...************9998876655 PP

>> DUF3013  Protein of unknown function (DUF3013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05     0.062      40     106 ..      54     124 ..      39     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                       EEEE--S----S----------EEEEEEEEEEE-TTT...---BGGGS.SEEEE-BGGGBEEHHHHHHHHH CS
                           DUF3013  40 leaenkeeveleDaeGevseediiefedavllydpek...skfdeddy.LavipyegkkGlskevlkalve 106
                                       + a ++e+ e+ D+ Gev ++  +e++  v+  dp        d  dy ++v+p  g++Gls+++l ++ e
  gi|313126751|ref|YP_004037021.1|  54 VDALEQEGSEIVDEAGEVLDSLGVEYSTDVVQGDPVPtivEYADRYDYdVVVMPTRGRQGLSRQLLGSVTE 124
                                       556788999**************************986444556667766789***********9987765 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.018        63      41      57 .]      52      68 ..      51      68 .. 0.94
   2 ?    6.3   0.0    0.0024       8.7      27      43 ..     137     153 ..     131     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.018
                                      HHHHHHHCTT--EEEES CS
                           XPB_DRD 41 dlveaLraagiefeDrv 57
                                      d+v+aL+++g e+ D++
  gi|313126751|ref|YP_004037021.1| 52 DVVDALEQEGSEIVDEA 68
                                      89*************97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0024
                                       TTTTEEEEEGGGHHHHH CS
                           XPB_DRD  27 eRvekyRapAlrYrdlv 43 
                                       +R+++ Ra+A+ Y ++v
  gi|313126751|ref|YP_004037021.1| 137 ARTGTDRALAFPYERIV 153
                                       6*************998 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.2e-05      0.26      27      74 ..     103     151 ..      99     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.2e-05
                                       EEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHH.HHH CS
                              FR47  27 lqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirl.yek 74 
                                       + v p+  r+Gl ++l  ++++++++  ++++l ++++ +++ ++ ye+
  gi|313126751|ref|YP_004037021.1| 103 VVVMPTRGRQGLSRQLLGSVTEKVVRLCEQPVLTARTGTDRALAFpYER 151
                                       7899999******************************999998876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1648.48
//
Query:       gi|313126752|ref|YP_004037022.1|  [L=168]
Description: membrane-bound metal-dependent hydrolase (duf457) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-15   56.5  10.9      2e-14   53.3  10.9    2.0  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
        2.1    8.7  12.0       0.66   10.3   7.3    2.4  2  DUF4395   Domain of unknown function (DUF4395)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3  10.9   2.2e-18     2e-14       4     163 ..       4     164 ..       1     168 [] 0.68

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 2.2e-18
                              YdjM   4 ltHallGaalglalaallgaake.avllavavlg...AllPDiDhpsstlgrklgllskklaklvgHRgftHSllfl 76 
                                         H  +++++++ ++  l        +++v+v+    A+lPD+D       ++++ +         HRg tHSl f+
  gi|313126752|ref|YP_004037022.1|   4 QGHYGVSLIVFAPVGFALIHLGRpDLAFVVGVVMlwlAMLPDVD-------HRIPGI--------PHRGPTHSLAFA 65 
                                       5777777777776665555444444666666666789*******.......566553........49********** PP

                              YdjM  77 allalvlllllrlfgrsa..............lrlglllllg...vlsHlllDlltkyGvpllwPfskkkvrlsllf 136
                                        l++ v++l+ + +                  +   +++l+g   v+ Hll+D+lt++Gv +lwP+s++++++s+  
  gi|313126752|ref|YP_004037022.1|  66 GLVGGVFALVGQGLVLAGvddiglaaiadgsvV--VFGFLVGfltVFAHLLGDALTPAGVNFLWPLSGYEYTISAWR 140
                                       *9998888877666655568899**99998553..3344444334889*******************9999998888 PP

                              YdjM 137 iiidplltllsrrglvalelvllvlyl 163
                                         ++       +  +v + +v+++lyl
  gi|313126752|ref|YP_004037022.1| 141 ADNKL--AN-YGLFGVGIFAVAAALYL 164
                                       74443..11.22333333344444444 PP

>> DUF4395  Domain of unknown function (DUF4395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.3   7.4e-05      0.66      28     111 ..      11     102 ..       8     113 .. 0.79
   2 ?   -1.1   0.3      0.25   2.2e+03     103     109 ..     153     159 ..     107     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.4e-05
                           DUF4395  28 llallavvfalralagprlsplgllarrlvap......rlgpkpeledaapkrFAqliGlvfllvalvlfllgapvl 98 
                                       l+++  v+fal  l +p l+ +  ++ +++a       r+   p++ + +   FA l+G vf+lv+  l l+g+  +
  gi|313126752|ref|YP_004037022.1|  11 LIVFAPVGFALIHLGRPDLAFVVGVVMLWLAMlpdvdhRIPGIPHRGPTHSLAFAGLVGGVFALVGQGLVLAGVDDI 87 
                                       56777789999999999999998888888887677777777889999999999*********************996 PP

                           DUF4395  99 glvlt..alllvaaf 111
                                       gl+++  + ++v+ f
  gi|313126752|ref|YP_004037022.1|  88 GLAAIadGSVVVFGF 102
                                       655540045555544 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.25
                           DUF4395 103 talllva 109
                                       +++++va
  gi|313126752|ref|YP_004037022.1| 153 VGIFAVA 159
                                       2222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1056.53
//
Query:       gi|313126753|ref|YP_004037023.1|  [L=385]
Description: small-conductance mechanosensitive channel [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-41  142.0   0.0    3.3e-41  141.1   0.0    1.5  1  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.0   1.9e-45   3.3e-41       5     206 .]     141     338 ..     137     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 1.9e-45
                                       HHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS.SEEEEEEEE- CS
                        MS_channel   5 kiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig.dieGtVedig 80 
                                       ++++++ g  + l+l+ ++++ ll ++G++g+a+g+a+kd+++n+++Gi l+f++++k+GD + +  + +G+V+++g
  gi|313126753|ref|YP_004037023.1| 141 TLVVLLGGAATLLWLWEIEITPLLGAAGVAGIAVGFAAKDTVANFFGGIALYFDDTYKLGDCIVLDdGTSGSVVKVG 217
                                       5677777888888999999**********************************************9899******** PP

                                       SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EE CS
                        MS_channel  81 lrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkell 157
                                       +r+t++ t+d  +vt+Pns l  ++i+N s  + +rri+v  gv+y++d   +++      e+++ ++ vl+++++ 
  gi|313126753|ref|YP_004037023.1| 218 IRSTTLLTRDELMVTVPNSVLNAAKITNESAPQRRRRIRVPLGVAYGTD---VDDFEALAIEVAEAESLVLDSPKPR 291
                                       *************************************************...99*********************** PP

                                       EEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 158 vvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                        ++ +fg s+l++e+ ++v    p ++ + q+e+n+    +++ ++iei
  gi|313126753|ref|YP_004037023.1| 292 MRFRRFGSSALEYELLCWVAA--PTRRRRAQHELNRALYMAVTDAEIEI 338
                                       *********************..**************999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2538.85
//
Query:       gi|313126754|ref|YP_004037024.1|  [L=73]
Description: hypothetical protein Hbor_20130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 448.63
//
Query:       gi|313126755|ref|YP_004037025.1|  [L=823]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   6.9e-297  986.3  93.8   1.2e-296  985.5  93.8    1.4  1  DUF5059       Domain of unknown function (DUF5059)
    3.9e-15   56.1   0.1    1.3e-14   54.5   0.1    2.0  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    6.4e-05   22.6   2.7    6.4e-05   22.6   2.7    4.3  5  TAT_signal    TAT (twin-arginine translocation) pathway signa
     0.0056   16.8   0.1      0.045   13.8   0.1    2.4  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
       0.13   12.2   0.8         17    5.3   0.1    3.6  4  Flg_hook      Flagellar hook-length control protein FliK
       0.15   12.0  22.0       0.19   11.7   0.2    5.0  5  TarH          Tar ligand binding domain homologue


Domain annotation for each model (and alignments):
>> DUF5059  Domain of unknown function (DUF5059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  985.5  93.8  4.1e-300  1.2e-296       1     622 []      63     683 ..      63     683 .. 1.00

  Alignments for each domain:
  == domain 1  score: 985.5 bits;  conditional E-value: 4.1e-300
                           DUF5059   1 avaaewnvyrarLyDavalgeaGktgagaavaqeiferfeqasGeygaheqLeetsesaYegfeealgelrealeeg 77 
                                       avaaewn+yrarLyDa+alg aGkt+aga vaq++f+rfe+asGe+gaheqLe+t+es+Ye+fee+lg+lr+al+eg
  gi|313126755|ref|YP_004037025.1|  63 AVAAEWNAYRARLYDALALGVAGKTTAGAGVAQQTFKRFEGASGEWGAHEQLEATNESNYESFEEHLGGLRSALSEG 139
                                       8**************************************************************************** PP

                           DUF5059  78 dieeaaeeaekasdnLraaqqalvgeeavqaldllllgsraadaavlaaagafdaaatvaeealerfedaavhdale 154
                                       +i+ea+++a++a++nL aaq+++v+ ++++al+++l+g+r++d+a+laaa++++aaatv+e++le+fe+a+vhda+e
  gi|313126755|ref|YP_004037025.1| 140 SIDEARSMASQADQNLLAAQRGRVDGPVIDALSIALYGVRTRDVAMLAAADSTEAAATVGESVLEDFENASVHDAVE 216
                                       ***************************************************************************** PP

                           DUF5059 155 eadgelYeafesalesvasaaeeedaegvkssaaaaldaavdgaYalapesvagagelaalqargyDaaalaglgGp 231
                                       ea++elYeafe++l+s++saae++dae++k++a++a+ aa++++Y+lape+vag++elaalq++g+Daaa+a+l+Gp
  gi|313126755|ref|YP_004037025.1| 217 EASSELYEAFEGGLKSAVSAAEKDDAEAAKTQAEKAFGAALSAGYELAPEKVAGVAELAALQSVGFDAAAVANLSGP 293
                                       ***************************************************************************** PP

                           DUF5059 232 stefahaaaLtaYrarvkDaawlaeagesdaaakvvkdvfadfeGaraheaLeeadedaYegfegGleaLaeaieng 308
                                       +te+ahaa+Lt+Yrarv+D++wla++gesdaa+k++kdvfadfeGaraheaLeead+daYe+fegGl++L++ai+ng
  gi|313126755|ref|YP_004037025.1| 294 GTEYAHAASLTRYRARVYDVDWLAARGESDAAEKMAKDVFADFEGARAHEALEEADHDAYESFEGGLSDLRKAIKNG 370
                                       ***************************************************************************** PP

                           DUF5059 309 daegvadavetvDenlvaGieaLaggeaaavleagffrarlaDareryrrGeaevaaeiveelferfeanelgfhet 385
                                       dae++a+ave++D++l+aGieaL+ggea+avle++ffrar+aDa+ery+rGe++vaaei+++lferfe ne+gfhet
  gi|313126755|ref|YP_004037025.1| 371 DAEARASAVESIDAALLAGIEALVGGEASAVLESAFFRARFADANERYQRGENDVAAEIAQHLFERFEVNEAGFHET 447
                                       ***************************************************************************** PP

                           DUF5059 386 leetsedlYerfeeehlagLiealengdddavtthaeGvldaLlefeaaigataevsaaesaylaarafDaaalaal 462
                                       +eetsed+Y+rfeeehl++Li+a++ngdd+avt+h+eGvl++L+efe++ig+ a++++aesa++aarafDaaala+l
  gi|313126755|ref|YP_004037025.1| 448 VEETSEDIYHRFEEEHLSALITAYKNGDDEAVTKHHEGVLSTLVEFESMIGT-AYSAPAESAFMAARAFDAAALATL 523
                                       ***************************************************9.************************ PP

                           DUF5059 463 gasdraatvvqealeafesgagGfhealeeadhdlYesfeeaLgsvrsaaedggdvfaaakafeekavdavyavvaa 539
                                       g+sdraa+v+++a++afe+++gGfhe+le+adhdlYesfe++L++vrsaa+dggdvfaaa+a+e+kavda+yavva+
  gi|313126755|ref|YP_004037025.1| 524 GQSDRAASVIKSAFTAFEKDTGGFHESLEHADHDLYESFESELSAVRSAANDGGDVFAAATAYETKAVDAIYAVVAS 600
                                       ***************************************************************************** PP

                           DUF5059 540 aggdlgaaaasvvsdvfatfeearvhelLeeaDkeaYeafeaaledyvaaLesgsevdaaveafataalraqfavaG 616
                                       ++g+l+++aa +v+++f++fe+a+vhelLeeaDk+aYe+fea+++d+++aLesgsev++a++a+a+a+++aqfavaG
  gi|313126755|ref|YP_004037025.1| 601 GSGELSGVAAGIVQAAFQYFEGATVHELLEEADKGAYETFEAKIRDLKNALESGSEVTVALNAYADATTTAQFAVAG 677
                                       ***************************************************************************** PP

                           DUF5059 617 avdaaP 622
                                       a+++aP
  gi|313126755|ref|YP_004037025.1| 678 AIENAP 683
                                       *****9 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.1   4.2e-18   1.3e-14       7      99 .]     719     822 ..     713     822 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 4.2e-18
                                       ETTETSEEESSEEEEETTEEEEEEEESSSSBEEEEET............TSSTTTGGGTTSCTTC...EEEEBSTTE CS
                       Copper-bind   7 vesgdlqFetkeitvkkgekvtfvnlavmgHNvvldk............dgvpagvdkdkvkaed...etkliggGe 68 
                                       v+ ++ +F+++e+tv+ g++v f + a+ +HNvv  +            +    g+d++k ++e     +   ++G 
  gi|313126755|ref|YP_004037025.1| 719 VKAKAAAFKPSELTVSVGDTVAFEWAAGDAHNVVAREeklpdgatywasG----GFDSEKATQEGwdnGKGALTEGT 791
                                       5666689******************************5555544432221....344444444336655557889** PP

                                       EEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
                       Copper-bind  69 kdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                                       ++  tf++ag+  ++C PH aagM+g+++ve
  gi|313126755|ref|YP_004037025.1| 792 AYVHTFETAGEHPYYCIPHEAAGMEGTIVVE 822
                                       ****************************996 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   2.7   2.1e-08   6.4e-05       3      23 ..       4      24 ..       4      27 .. 0.95
   2 ?   -7.5   4.4         6   1.8e+04      12      17 ..      60      65 ..      60      66 .. 0.31
   3 ?   -6.0   4.4         6   1.8e+04       9      14 ..      86      91 ..      78      94 .. 0.52
   4 ?   -2.7   1.1       2.2   6.5e+03      14      24 ..     284     294 ..     284     295 .. 0.59
   5 ?   -3.2   1.2         3   9.1e+03      14      21 ..     517     524 ..     517     525 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.1e-08
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggc 23
                                      +RRd+LK+sA aaA a+++gc
  gi|313126755|ref|YP_004037025.1|  4 TRRDLLKASALAAATATFAGC 24
                                      7*******************9 PP

  == domain 2  score: -7.5 bits;  conditional E-value: 6
                        TAT_signal 12 AAaaAA 17
                                      AA+a A
  gi|313126755|ref|YP_004037025.1| 60 AAVAVA 65
                                      333333 PP

  == domain 3  score: -6.0 bits;  conditional E-value: 6
                        TAT_signal  9 KgsAAa 14
                                      K++A+a
  gi|313126755|ref|YP_004037025.1| 86 KTTAGA 91
                                      333333 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.2
                        TAT_signal  14 aaAAaalggca 24 
                                       aaA a l g++
  gi|313126755|ref|YP_004037025.1| 284 AAAVANLSGPG 294
                                       45555577766 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 3
                        TAT_signal  14 aaAAaalg 21 
                                       aaA+a+lg
  gi|313126755|ref|YP_004037025.1| 517 AAALATLG 524
                                       56666665 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.5e-05     0.045      17     104 .]     711     821 ..     704     821 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                      Cupredoxin_1  17 aaaektveitvkdggfePskievkagekvklkiknkdkt.................peefesed......lgeekvl 70 
                                       ++a++ +++++k  +f+Ps+++v  g  v +++ + d+                  +  f se+       + +  l
  gi|313126755|ref|YP_004037025.1| 711 DEADADHVVKAKAAAFKPSELTVSVGDTVAFEWAAGDAHnvvareeklpdgatywaSGGFDSEKatqegwDNGKGAL 787
                                       56788899*****************************9988888888888877776344444444444432233678 PP

                      Cupredoxin_1  71 apgktttitiaplkpGeYeftcdmhm.d.akGkliV 104
                                       + g +++ t+  +++Ge++++c  h+   ++G+++V
  gi|313126755|ref|YP_004037025.1| 788 TEGTAYVHTF--ETAGEHPYYCIPHEaAgMEGTIVV 821
                                       8888888888..889999999988885578888887 PP

>> Flg_hook  Flagellar hook-length control protein FliK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0058        17      39      76 ..     111     148 ..     104     155 .. 0.80
   2 ?   -0.6   0.0      0.43   1.3e+03      45      68 ..     207     229 ..     205     243 .. 0.83
   3 ?   -3.3   0.0       2.8   8.4e+03      47      64 ..     350     367 ..     346     371 .. 0.85
   4 ?    2.1   0.0     0.061   1.8e+02      46      66 ..     633     653 ..     618     670 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0058
                                       EEEEEE-SCHHHHHHHHTHHHHHHHHHCCTTCCEEEEE CS
                          Flg_hook  39 svqltaenpetrelLeqnlprLreaLaaaGlklddlsv 76 
                                       + ql a n+  +e +e++l+ Lr+aL++  +  ++   
  gi|313126755|ref|YP_004037025.1| 111 HEQLEATNESNYESFEEHLGGLRSALSEGSIDEARSMA 148
                                       5688999********************99888775444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.43
                                       -SCHHHHHHHHTHHHHHHHHHCCT CS
                          Flg_hook  45 enpetrelLeqnlprLreaLaaaG 68 
                                       en+ + +++e+++ +L ea++  G
  gi|313126755|ref|YP_004037025.1| 207 ENASVHDAVEEASSELYEAFEG-G 229
                                       899***************9986.5 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.8
                                       CHHHHHHHHTHHHHHHHH CS
                          Flg_hook  47 petrelLeqnlprLreaL 64 
                                        +++e +e  l +Lr+a 
  gi|313126755|ref|YP_004037025.1| 350 HDAYESFEGGLSDLRKAI 367
                                       57999**********986 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.061
                                       SCHHHHHHHHTHHHHHHHHHC CS
                          Flg_hook  46 npetrelLeqnlprLreaLaa 66 
                                        + ++e +e+++++L++aL++
  gi|313126755|ref|YP_004037025.1| 633 DKGAYETFEAKIRDLKNALES 653
                                       56799**************97 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   6.2e-05      0.19      95     163 ..      92     160 ..      83     165 .. 0.92
   2 ?    8.7   0.9   0.00051       1.5     104     159 ..     206     257 ..     175     264 .. 0.80
   3 ?    3.5   0.6      0.02        59     101     146 ..     333     374 ..     318     388 .. 0.77
   4 ?    0.7   0.1      0.14   4.2e+02     123     153 ..     454     485 ..     407     496 .. 0.75
   5 ?   -3.3   0.1       2.4   7.3e+03      86     105 ..     522     541 ..     506     573 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHHHHHTS---GGGHH.HHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHS-HHHHHHHHHHHH CS
                              TarH  95 aqseeawkaYlalprtaeeeealaaelkakykalqdglapliaaleagnleaffdlptqkiqplfealy 163
                                       + +++ +k+++ ++ + +  e+l a  +++y+ +++ l  l  al++g ++++   + q+ q+l  a +
  gi|313126755|ref|YP_004037025.1|  92 GVAQQTFKRFEGASGEWGAHEQLEATNESNYESFEEHLGGLRSALSEGSIDEARSMASQADQNLLAAQR 160
                                       6799*******************************************************9999987765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00051
                                       HHTS---GGGHH.HHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHS-HHHHHHHH CS
                              TarH 104 Ylalprtaeeeealaaelkakykalqdglapliaaleagnleaffdlptqkiqplf 159
                                       +++++ ++    a+ ++ ++ y+a++ gl+ ++ a e++++ea+ +++ +++ ++ 
  gi|313126755|ref|YP_004037025.1| 206 FENASVHD----AVEEASSELYEAFEGGLKSAVSAAEKDDAEAAKTQAEKAFGAAL 257
                                       55555555....444577889***************************99987765 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.02
                                       HHHHHTS---GGGHH.HHHHHHHHHHHHHHHHHHHHHHHHTT-HHH CS
                              TarH 101 wkaYlalprtaeeeealaaelkakykalqdglapliaaleagnlea 146
                                       +++++ + +++    al ++  ++y+ ++ gl  l +a+++g++ea
  gi|313126755|ref|YP_004037025.1| 333 FADFEGARAHE----ALEEADHDAYESFEGGLSDLRKAIKNGDAEA 374
                                       55555555555....677788899*******************987 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.14
                                       HHHHH.HHHHHHHHHHHHHTT-HHHHHHS-HH CS
                              TarH 123 akyka.lqdglapliaaleagnleaffdlptq 153
                                       + y++  ++ l +li+a ++g+ ea+ ++   
  gi|313126755|ref|YP_004037025.1| 454 DIYHRfEEEHLSALITAYKNGDDEAVTKHHEG 485
                                       45777777889999999999999999887655 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHHHHHHHHH CS
                              TarH  86 llaraeeslaqseeawkaYl 105
                                       +l + ++  + +++a+ a++
  gi|313126755|ref|YP_004037025.1| 522 TLGQSDRAASVIKSAFTAFE 541
                                       33333333333444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (823 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 5455.89
//
Query:       gi|313126756|ref|YP_004037026.1|  [L=526]
Description: xanthine/uracil permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-72  244.3  42.4    9.6e-72  241.8  42.4    2.0  1  Xan_ur_permease  Permease family


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.8  42.4   5.3e-76   9.6e-72       3     386 ..      22     433 ..      20     435 .. 0.90

  Alignments for each domain:
  == domain 1  score: 241.8 bits;  conditional E-value: 5.3e-76
                                       HHHHHHHHHHHHHHHHHHHHHTTTS-..........H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHH....H CS
                   Xan_ur_permease   3 llllglQhllamfaalvvvPllvgdalgl.aeelrqlisatllasGiatllqllifgirlpillgssfafvt....a 74 
                                        lllg+Qh l+m++a + vPl+++ alg  +  + + + + +++sGiatl+q++ fg r pi++g  f  ++    +
  gi|313126756|ref|YP_004037026.1|  22 SLLLGVQHYLTMVGANIAVPLILAGALGMpDSIVPRFVGTFFVVSGIATLAQTT-FGNRYPIVQGAPFSMLApalaV 97 
                                       689***********************999666666999****************.**************99954444 PP

                                       HHGGG-...........HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTT CS
                   Xan_ur_permease  75 lmialGsa.......edieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvg 144
                                            G+        +++++al  l+ga+++a+v+ + ++ +gl g+l+ ++ Pvv++p++ liGlsl  +    ++
  gi|313126756|ref|YP_004037026.1|  98 ----VGVVtasnpagPEWQAALLQLQGAIVAAAVIEVAVGYFGLLGKLRSFLSPVVIAPTIALIGLSLFNTPQVTAA 170
                                       ....44334556***99***************************************************998765555 PP

                                       SS-..BTT.B---HHHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHH..........HH CS
                   Xan_ur_permease 145 ggwaavegltvvslkllllavvvllvilllsvflkglfsqlpiLigiiagwllalfmgivnlspe..........vs 211
                                        g             ll+l +v++++    +  +  +f+++p+L+gi+a++l+a+++ i+ +             v 
  gi|313126756|ref|YP_004037026.1| 171 DGN----------ISLLALTLVLIVIFSQYIDTAHRVFQLFPVLLGIVAAYLVAAALSITGVYAPgapgyvdlesVL 237
                                       553..........34566666666666666666************************97776655689999999977 PP

                                       S-SS-----------HH.......................H.HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TIIII CS
                   Xan_ur_permease 212 eapwfqlpsplkfgtpl.....................fnlgliltvlavalvavvesvGdiravakvvgrslkpkp 267
                                       +ap f++ +pl++g                        f+ + i+ +la + ++++es+Gd++ava+++g   + ++
  gi|313126756|ref|YP_004037026.1| 238 AAPAFMPIYPLQWGFAGgpntftvglplvgdmafgipqFSSSFIIGMLAGVCASMIESLGDYHAVARLSGIGAPSEK 314
                                       88888888888888777777888888888888888888*************************************** PP

                                       IHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHHHHHTB--HHHHHHHHHHHHHHT--HHHHHHHTTS-HHHHHHHH CS
                   Xan_ur_permease 268 dlrralladGlatllsgllGalpvttyaeniGvvaltkvasrrvmvtagvilillglipklaallssIPepvlgGvl 344
                                       ++++++  +G++ ++sgl+G+++ t+y+eniG + lt+vasr+v+++++ +++++g+++ +++l+++IP+p++gG  
  gi|313126756|ref|YP_004037026.1| 315 RINHGIGMEGVMNIFSGLMGGSGSTSYSENIGAIGLTGVASRYVVQVGAAVMLVVGFVGYFGQLVATIPDPIVGGLY 391
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHTTS-SHHHHHHHHHHHHHHHH---- CS
                   Xan_ur_permease 345 lvvfgmiaasgvsnlqtvdldsarnllivavslvlGlgvatv 386
                                       +++fg i+a+g+snl+ vdlds+rn++iv+v+l++Gl v+t+
  gi|313126756|ref|YP_004037026.1| 392 IAMFGQIVAVGLSNLKYVDLDSSRNIFIVGVTLFVGLAVPTY 433
                                       ***************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3188.39
//
Query:       gi|313126757|ref|YP_004037027.1|  [L=160]
Description: chemotaxis protein CheW [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-27   93.7   0.1    9.1e-27   93.4   0.1    1.1  1  CheW      CheW-like domain


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.1   5.1e-31   9.1e-27       1     130 [.      25     153 ..      25     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 5.1e-31
                                       EEEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTTSTCEEEEEEEET CS
                              CheW   1 qlllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpeesrentrvivvelg 77 
                                       q+l f+lg+ety+++++ v ei++  ++t +p+ap++v gv++lrG++  +++ ++ll+++  +  e++r+++ +++
  gi|313126757|ref|YP_004037027.1|  25 QVLEFKLGDETYCVDIEYVSEIVDKGSLTAVPNAPDYVDGVMDLRGRTTSIVNPKALLNVDAADG-ESKRIVIFDSN 100
                                       799*************************************************************6.*********99 PP

                                       ....TEEEEEEESEEEEEEEEECCGEETTTSSTSSTCCCEEEEEECTTSEEEEEE-C CS
                              CheW  78 ....nqvvGllVdevkgiqeivikqiepplglssdlagyisGatklgdgrlvliLDv 130
                                           +  +G lVdev ++++++ ++ie+p+     + + i G++k  dg+lv+++ +
  gi|313126757|ref|YP_004037027.1| 101 kfedDAAIGWLVDEVYQVVRVSMDEIEEPPL---EKDDSIEGVIKR-DGELVIWISP 153
                                       9999*************************66...55666******9.*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 947.69
//
Query:       gi|313126758|ref|YP_004037028.1|  [L=387]
Description: chemotaxis response regulator containing a chey-like receiver domain and a methylesterase domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-53  179.2   1.4      8e-53  178.6   0.3    1.8  2  CheB_methylest  CheB methylesterase
    3.7e-27   94.7   0.9    8.8e-27   93.5   0.6    1.8  2  Response_reg    Response regulator receiver domain


Domain annotation for each model (and alignments):
>> CheB_methylest  CheB methylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.49   4.4e+03      10      35 ..      74      96 ..      68     117 .. 0.57
   2 !  178.6   0.3   8.9e-57     8e-53       2     170 .]     201     380 ..     200     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.49
                                      HHHHTTTGGGS-TT-SS-EEEE.E--- CS
                    CheB_methylest 10 lealkellaalpedfpaavvvv.qhmp 35
                                      +ea++ ++++ p+    +v+++  h +
  gi|313126758|ref|YP_004037028.1| 74 IEAVEAIMEDCPT----PVLMLsAHAE 96
                                      5555555555554....4433303433 PP

  == domain 2  score: 178.6 bits;  conditional E-value: 8.9e-57
                                       EEEE-TTHHHHHTTTGGGS-TT-SS-EEEEE---TT-HHHHHHHHHHH-SSEEEE--TT-B--TTEEEE--TTSEEE CS
                    CheB_methylest   2 vigaStGGlealkellaalpedfpaavvvvqhmppsftsslaelLnresslkVkeaedgeelepgrvyvapgdkhll 78 
                                       vigaStGG++ ++e+l +lp+d ++ ++vvqhmp++ft+++a++L+ +s+++V+ea+dge++ +g++ vapg+ hl+
  gi|313126758|ref|YP_004037028.1| 201 VIGASTGGPNVVEEVLGELPADANLRILVVQHMPEGFTRRFADRLDTRSAYNVQEATDGEKIGAGEARVAPGGSHLV 277
                                       9**************************************************************************** PP

                                       EE..............EE.-.-SS-HHHHHHHHHHHH.GGEEEEE-SBSS-TTHHHHHHHHHTT-EEEEE-GGG-SS CS
                    CheB_methylest  79 ie........lals..ak.kgerpsiDvlfesaaeaygeraigviLtGmgsDGaeGlkaikeaggltiaqdpesavv 144
                                       ++        l+l+  ++ +g +p+iD +++sa e++++ + g +LtGmg+DG++G+ +i+eagg t+aqd++++++
  gi|313126758|ref|YP_004037028.1| 278 VDrdrrgqltLKLTdtKPvHGVKPAIDLTMASAVETVDGPLAGALLTGMGRDGVDGMGRIHEAGGHTVAQDEATSAI 354
                                       **99998866444443355777***************99************************************** PP

                                       BSHHHHHHHTT--SEEE-GGGHHHHH CS
                    CheB_methylest 145 pgmPkaaieagavdevlpleeiaeel 170
                                       +gmP +aie+g+ + v+p+e++a+ +
  gi|313126758|ref|YP_004037028.1| 355 FGMPMRAIETGCIEVVAPAEKVASSI 380
                                       ***********999*******99875 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.6   9.8e-31   8.8e-27       2     102 ..      17     118 ..      16     122 .. 0.94
   2 ?   -3.2   0.0         1   9.4e+03      18      34 ..     245     261 ..     237     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 9.8e-31
                                       EEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEE CS
                      Response_reg   2 livdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviilt 78 
                                       +ivdD++ +r+l+r+lle+ g+ +vaea+dg++a+e + e+++d++++Di+mp+m+G+e+++ i e+   +pv++l+
  gi|313126758|ref|YP_004037028.1|  17 VIVDDSRFMRTLIRTLLEDGGIDVVAEASDGAAAVETVTEHAPDVVTMDIEMPEMNGIEAVEAIMEDC-PTPVLMLS 92 
                                       69**************************************************************9977.8******* PP

                                       SSTS..HHHHHHHHHCTESEEEESSG CS
                      Response_reg  79 ahse..eedavealkagaddflsKpf 102
                                       ah+e   +++ eal+ ga+df++Kp 
  gi|313126758|ref|YP_004037028.1|  93 AHAEddADVTFEALDKGAVDFVTKPG 118
                                       887744678899************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1
                                       HH.HTTEEEEEEESSHHH CS
                      Response_reg  18 le.eegyeevaeaedgke 34 
                                       l+ ++ y +v+ea+dg++
  gi|313126758|ref|YP_004037028.1| 245 LDtRSAY-NVQEATDGEK 261
                                       4436778.9999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.37s 00:00:01.05 Elapsed: 00:00:00.56
# Mc/sec: 2073.00
//
Query:       gi|313126759|ref|YP_004037029.1|  [L=831]
Description: chemotaxis protein histidine kinase-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-18   65.7   1.6    7.5e-18   64.6   0.3    2.4  2  Hpt           Hpt domain
      7e-18   65.2   0.5      5e-17   62.4   0.1    2.3  2  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    1.2e-17   63.8   1.6    2.3e-17   62.9   1.6    1.4  1  CheW          CheW-like domain
      1e-08   35.1   0.0    5.5e-08   32.8   0.0    2.3  2  P2            P2 response regulator binding domain
    9.8e-06   25.9   3.2    9.8e-06   25.9   3.2    2.0  2  H-kinase_dim  Signal transducing histidine kinase, homodimeri
     0.0013   18.7   0.1     0.0053   16.7   0.1    2.1  1  HATPase_c_2   Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
       0.23    9.9   6.6       0.34    9.4   6.6    1.1  1  Macoilin      Macoilin family


Domain annotation for each model (and alignments):
>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.3   2.9e-21   7.5e-18       1      82 [.       4      95 ..       4     105 .. 0.89
   2 ?   -2.1   0.0       1.9     5e+03      71      82 ..     436     447 ..     427     473 .. 0.64

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2.9e-21
                                      HHHHHHHHHHHHHHHHHHHHH........SCCHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHH..HCTSCHHHH CS
                               Hpt  1 ellelfleeaeelleqleqal........dqedlqelaraaHtLKGsagmlGltelaelahelEdlld..ragelelep 69
                                      el+++f+ e+ee ++ql+++l        d e++++++r aHtLKG  g +G++  a +ah++Edlld  r ++le++p
  gi|313126759|ref|YP_004037029.1|  4 ELYQAFITESEESITQLNNSLleleanpdDTEAIDDIFRQAHTLKGNFGAMGFDNAATVAHAVEDLLDeiRHERLEVTP 82
                                      789***********************988888*********************************************** PP

                                      HHHH....HHHHHHHHH CS
                               Hpt 70 elle....alkalleal 82
                                      + ++         ++++
  gi|313126759|ref|YP_004037029.1| 83 DRMDlifdG----MDEI 95
                                      ****55552....4433 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHH CS
                               Hpt  71 llealkalleal 82 
                                       +l++l++l+e+l
  gi|313126759|ref|YP_004037029.1| 436 QLDELHELVEQL 447
                                       444555555554 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.36   9.3e+02       4      64 ..     438     504 ..     435     519 .. 0.66
   2 !   62.4   0.1   1.9e-20     5e-17       3     110 ..     535     674 ..     533     676 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHSTTTEEEEEEEE.....EE.TEEEEEEEESSSSSTTHHHTGTCSTTCH.H CS
                         HATPase_c   4 krLrqiisnlvdNavkfatkageieveika.....se.ddlvisveDnGiGipkedlkklfekfsq.d 64 
                                       + L++++ +lv+  +k   +a e+e  +++     +e d+++   +++   +    lkk+f+kf +  
  gi|313126759|ref|YP_004037029.1| 438 DELHELVEQLVTSRIKL-RQAMEGEADMTSgldtlDElDKISTNLQNTVMDMRLIPLKKVFDKFPRmV 504
                                       67999999999999998.44555555555433333236677777777777777777779999888752 PP

  == domain 2  score: 62.4 bits;  conditional E-value: 1.9e-20
                                       HHHHHHHHHHHHHHHHHH......HSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHT................ CS
                         HATPase_c   3 ekrLrqiisnlvdNavkf......atkageieveikase..ddlvisveDnGiGipkedlk................ 55 
                                       ++ L+++++n+vd+ ++       ++k+ +++ve+ a+   d++vi+v+D+G Gi+ + l                 
  gi|313126759|ref|YP_004037029.1| 535 SDPLMHVLRNAVDHGIELpdereaNGKSRTGTVELAARRehDTVVITVSDDGSGINADALRdkvvseglatrdelne 611
                                       689***************888875457778899999833469*********************************** PP

                                       ........GTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  56 ........klfe.kfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                                +f   +s+ +++ ++ +g+G+G+ +vk  ve ++G++ v+s+pg+G+ ft++lp 
  gi|313126759|ref|YP_004037029.1| 612 lpdeevyeYVFHpGLST-NDEITDVSGRGVGMDVVKTTVEALDGSVGVSSTPGEGSVFTIRLPV 674
                                       ****9999999978888.9999999*************************************96 PP

>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   1.6   8.8e-21   2.3e-17       2     133 ..     681     802 ..     680     803 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 8.8e-21
                                       EEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTTSTCEEEEEEEETT CS
                              CheW   2 lllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpeesrentrvivvelgn 78 
                                       +l +r+ge+++++p+  + ei + ++   +++++ga  +v+ +++++ p+i+Lr  l ++ +e+ ++  ++ ++  +
  gi|313126759|ref|YP_004037029.1| 681 VLFVRVGEREFGVPIKYIDEISRRQA---VQTVNGA--EVVVHEDDIFPLIRLRDALDVDIDER-DSGMIVRIRPAD 751
                                       899*********************99...7777777..8************************6.9999999***** PP

                                       EEEEEEESEEEEEEEEECCGEETTTSSTSSTCCCEEEEEECTTSEEEEEE-CCCH CS
                              CheW  79 qvvGllVdevkgiqeivikqiepplglssdlagyisGatklgdgrlvliLDveal 133
                                       + v+l  d v++++e+v+ +++ pl+   + +g +sG++++gdg++++iLDv  l
  gi|313126759|ref|YP_004037029.1| 752 RQVALHCDHVTRQEEVVVTPLQGPLS---GTNG-LSGTAVIGDGNVIPILDVSTL 802
                                       ************************99...8899.******************876 PP

>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.6   1.2e+04      22      43 ..      98     116 ..      96     120 .. 0.71
   2 !   32.8   0.0   2.1e-11   5.5e-08       2      80 ..     170     246 ..     169     247 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.6
                                       HHHHHHHTTEEEEEES-HHHHH CS
                                P2  22 vfkaLeelgeiiksiPsvedie 43 
                                       +++++ee+ge  ks P   d+ 
  gi|313126759|ref|YP_004037029.1|  98 ILHDIEEHGE-SKSDP--SDLV 116
                                       6888999998.47777..5554 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 2.1e-11
                                       EEEEEE--TT-SSHHHHHHHHHHHHHHTTEEEEEES-HHHHHTT-SSSEEEEEEEESS-HHHHHHHHHTSSS-SEEE CS
                                P2   2 ykikvkldedclmksvRaflvfkaLeelgeiiksiPsvedieeekfdegfevvlltkeskeeikealasiseiesve 78 
                                       y++ ++ld + +mk+v a l +  L +  +++ s+P+ + ie+++f++gf++++   ++++e+   la+  ++e++e
  gi|313126759|ref|YP_004037029.1| 170 YHAAIELDAG-EMKGVDAGLFLGGLPDDLDVVGSSPDIDSIEDGEFEDGFTLFI-AGTPESELGPLLADQWKVEHAE 244
                                       9*******99.*******************************************.8999999999999899999888 PP

                                       EE CS
                                P2  79 ve 80 
                                       ++
  gi|313126759|ref|YP_004037029.1| 245 LT 246
                                       76 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.0         7   1.8e+04      46      55 ..      18      27 ..      10      34 .. 0.49
   2 !   25.9   3.2   3.8e-09   9.8e-06       2      69 .]     428     488 ..     427     488 .. 0.94

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 7
                      H-kinase_dim 46 telksslqnl 55
                                      t+l+ sl +l
  gi|313126759|ref|YP_004037029.1| 18 TQLNNSLLEL 27
                                      3333333332 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 3.8e-09
                      H-kinase_dim   2 stlRVdakrlDyLlnlvGElVitkarLnqsleefrfenglkasvtelksslqnlgrisgeLQegvmki 69 
                                       +++RVd+  lD+L +lv  lV ++ +L+q +e  +         t   ++l++l++is++LQ+ vm +
  gi|313126759|ref|YP_004037029.1| 428 KSVRVDVGQLDELHELVEQLVTSRIKLRQAMEGEA-------DMTSGLDTLDELDKISTNLQNTVMDM 488
                                       589***************************99888.......8889999*****************86 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.1e-06    0.0053      48     103 ..     559     641 ..     522     671 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.1e-06
                       HATPase_c_2  48 yleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep...........................keslke 97 
                                       + + ++g+ve+++++++++++++v+D+G g ++ +l+d+ + e                            +e  + 
  gi|313126759|ref|YP_004037029.1| 559 NGKSRTGTVELAARREHDTVVITVSDDGSGINADALRDKVVSEGlatrdelnelpdeevyeyvfhpglstnDEITDV 635
                                       33344699*******************************99998899998888888888888888888888555555 PP

                       HATPase_c_2  98 gGrGla 103
                                       +GrG+ 
  gi|313126759|ref|YP_004037029.1| 636 SGRGVG 641
                                       555544 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   6.6   0.00013      0.34     268     437 ..     288     478 ..     227     515 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00013
                          Macoilin 268 dskkkhehnesvdsklqekeymenkskskrlsksessgsesellveesvkskssssssssnknskkasagsagssns 344
                                        s  + +++++ d++ +e   +e    ++ +   es  s se    +++++    +ss+++ +  ++ + sag+ +s
  gi|313126759|ref|YP_004037029.1| 288 ASDPESTDEDAADTDESEDGAVEPSEAEAAVAAVESAYSDSESADGNETDADGVDDSSADETTAGTSDGASAGADSS 364
                                       22222233344444444444444444445555555555555555555555555555555555555555666666666 PP

                          Macoilin 345 sskkhsessksvtsssssknskkq....................klpaGkssaalkdaaenslpnnql..skkdalv 399
                                       ++++ +++++ ++++s +++s+                      k  + ks +++kd+    + + ++  ++ d+l 
  gi|313126759|ref|YP_004037029.1| 365 AAASEETANGDTAEASDTDDSDDTddgddasddggsddsgsdgdKKESKKSDKKEKDRSISAVKSVRVdvGQLDELH 441
                                       66666677777666664444443345566666666666554333333344444445544445554433559999999 PP

                          Macoilin 400 rLeadikkLkaeLqasrqteqelrskissltseerslk 437
                                        L +++   + +L+++ + e ++ s +++l + ++ + 
  gi|313126759|ref|YP_004037029.1| 442 ELVEQLVTSRIKLRQAMEGEADMTSGLDTLDELDK-IS 478
                                       99999999999*************99999887665.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (831 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 1.18u 0.40s 00:00:01.58 Elapsed: 00:00:00.60
# Mc/sec: 4163.74
//
Query:       gi|313126760|ref|YP_004037030.1|  [L=276]
Description: methylase of chemotaxis methyl-accepting protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-48  163.8   0.0    4.2e-48  163.4   0.0    1.1  1  CheR             CheR methyltransferase, SAM binding domain
    2.6e-12   46.3   0.8    4.7e-12   45.4   0.8    1.5  1  CheR_N           CheR methyltransferase, all-alpha domain
    1.8e-06   28.6   0.0    1.1e-05   26.1   0.0    2.1  1  Methyltransf_12  Methyltransferase domain
    7.2e-06   26.6   0.0     0.0023   18.6   0.0    2.7  2  Methyltransf_25  Methyltransferase domain
    6.9e-05   22.7   0.0       0.06   13.1   0.0    2.5  3  Methyltransf_31  Methyltransferase domain
    0.00093   19.4   0.3     0.0018   18.4   0.3    1.4  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
     0.0062   17.2   0.0       0.32   11.7   0.0    2.4  2  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.015   15.3   0.0        3.1    7.8   0.0    2.2  2  APAF1_C          APAF-1 helical domain
      0.017   14.7   0.0      0.027   14.1   0.0    1.3  1  NodS             Nodulation protein S (NodS)
       0.19   11.3   0.0       0.41   10.2   0.0    1.5  1  CobU             Cobinamide kinase / cobinamide phosphate gua


Domain annotation for each model (and alignments):
>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.0   2.4e-51   4.2e-48       1     191 [.      75     263 ..      75     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 2.4e-51
                                       SS--TTTTCHHHHHHHHCCH.HHHHHHHTSSSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHH CS
                              CheR   1 neTeffreakhfeelekevlepllakaknekrvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvl 77 
                                       n+T+ffr+++ +++l++ + +     + +  rv+iwsa+cs+G E+Ys+Aml+++  +   + kvkil+tDi  +++
  gi|313126760|ref|YP_004037030.1|  75 NVTSFFRNPEVWDALREVIAD-----IASDGRVNIWSAACSDGREAYSMAMLAHDDDRIDPN-KVKILGTDIKPEII 145
                                       79***************9994.....66779************************5555555.************** PP

                                       HHHHHTEEECCHHTTS-HHH.....HHHHEEEEETTCEEE-HHHHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC CS
                              CheR  78 ekAkagvykeeeleglseel.....leryfekseddsykvkkeikelvkFeklnllekksvlgklDvifcrnvliYf 149
                                        +A+ag y+++e ++++e+l      +ry+ + ++d y+v +e+k+lv F+k++l++ +++++ +D+++crn++iY+
  gi|313126760|ref|YP_004037030.1| 146 RAARAGEYHASETNDIEEQLeplsqNNRYV-ERDGDIYRVTDEVKSLVSFRKHDLVQ-ERPPDTFDLVVCRNLFIYI 220
                                       *************999887522222689*9.77777*********************.999**************** PP

                                       -CHHHHHHHHHHHCCEEEEEEEEE-TTB--S.SSCCCCCEEEE CS
                              CheR 150 deetqekvlerfaeklkpgglLllGhsEslk.klkdkfevvks 191
                                       ++e+++++ + + ++l p+g+L +G +E+++ + +d+f+ v+ 
  gi|313126760|ref|YP_004037030.1| 221 NSEAKQAIFDTLGSALTPDGYLTIGMTETIPpSCRDRFDPVEK 263
                                       *******************************999999998875 PP

>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.8   2.6e-15   4.7e-12       3      52 ..      12      61 ..      10      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.6e-15
                                      HHHHHHHHHHTT-EE--SSTHHHHHTHHHHHHHTTT-SSSHHHHHHTSHS CS
                            CheR_N  3 ferlleliyertGidlsdyKrallkrRlsrRmralglksfeeYldlLrsd 52
                                      f++ll++++ +  +  s+y+ a+l rR+s Rmr++g++s++eY+ lL  d
  gi|313126760|ref|YP_004037030.1| 12 FRELLDYVESSLSFATSSYNDAYLDRRISARMRRRGVESYDEYQSLLDGD 61
                                      99*********************************************987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   6.2e-09   1.1e-05      18      99 .]     124     242 ..     108     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.2e-09
                   Methyltransf_12  18 l......pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg........................ 64 
                                                ++++g+Di p+ i  ++++  ++++  +n +e + + l++   +                        
  gi|313126760|ref|YP_004037030.1| 124 DddridpNKVKILGTDIKPEII--RAARAGEYHASETNDIEEQLEPLSQNN-Ryverdgdiyrvtdevkslvsfrkh 197
                                       244555558899**********..666666666666666665555544433.35899999***************** PP

                   Methyltransf_12  65 ........ssfDlvvasnvlhhl..kdirevldnirklLkpgGrl 99 
                                               ++fDlvv+ n++ ++  + +++++d + ++L+p+G+l
  gi|313126760|ref|YP_004037030.1| 198 dlvqerppDTFDLVVCRNLFIYInsEAKQAIFDTLGSALTPDGYL 242
                                       ************************99999**************87 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0        10   1.8e+04      73      89 ..      76      92 ..      62      98 .. 0.63
   2 !   18.6   0.0   1.3e-06    0.0023      47      97 .]     191     240 ..     104     240 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 10
                                      TGGGSSHHHHHHHHHHH CS
                   Methyltransf_25 73 alhhlsdedlekalkei 89
                                      + +++ ++++ +al+e+
  gi|313126760|ref|YP_004037030.1| 76 VTSFFRNPEVWDALREV 92
                                      34455556666666655 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.3e-06
                                       TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  47 nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                        v+f+++d+ +   + ++fDlvv+++ + +++ e  +++++ + ++L+p+G
  gi|313126760|ref|YP_004037030.1| 191 LVSFRKHDLVQER-PPDTFDLVVCRNLFIYINSEAKQAIFDTLGSALTPDG 240
                                       4666666665544.455*******98899********************99 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.1   5.5e+03      34      53 ..      16      35 ..      15      44 .. 0.77
   2 !    7.0   0.0    0.0026       4.7       6      46 ..     103     150 ..      98     174 .. 0.78
   3 !   13.1   0.0   3.4e-05      0.06      60     109 ..     196     244 ..     183     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.1
                   Methyltransf_31 34 iDiseeaielArenaqklgl 53
                                      +D+ e ++++A++   +  l
  gi|313126760|ref|YP_004037030.1| 16 LDYVESSLSFATSSYNDAYL 35
                                      79999999999987666555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0026
                   Methyltransf_31   6 rvlDlGCGtGeltfelae......elgp.kaevvGiDiseeaielAre 46 
                                       ++  ++C  G+ ++ +a       ++ p k ++ G Di++e i+ Ar+
  gi|313126760|ref|YP_004037030.1| 103 NIWSAACSDGREAYSMAMlahdddRIDPnKVKILGTDIKPEIIRAARA 150
                                       55667899999999999877676644445777**************97 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 3.4e-05
                   Methyltransf_31  60 qgdieeleklledekfDlilsnevl..naladpdkileeiervlkpggilli 109
                                       + d  +      +++fDl+++++++      ++++i+  + ++l+p+g+l i
  gi|313126760|ref|YP_004037030.1| 196 KHDLVQER---PPDTFDLVVCRNLFiyINSEAKQAIFDTLGSALTPDGYLTI 244
                                       44444422...249**********98989999*****************987 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3     1e-06    0.0018       6      90 ..      40     123 ..      36     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
                    Acetyltransf_6   6 nlrrkrrkleelgevrfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrl.dgr 81 
                                       + r +rr  e+ +e++  ++ d+e+  all +++   + + + f++p++++ lr+++a+ a++g++ ++ + + dgr
  gi|313126760|ref|YP_004037030.1|  40 SARMRRRGVESYDEYQSLLDGDEEEQTALLNALS--VNVT-SFFRNPEVWDALREVIADIASDGRVNIWSAACsDGR 113
                                       4455555556667***99**************95..5699.**************************9999994444 PP

                    Acetyltransf_6  82 .pvAvalglr 90 
                                          ++a++ +
  gi|313126760|ref|YP_004037030.1| 114 eAYSMAMLAH 123
                                       2444444444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.11     2e+02       5      38 ..     109     152 ..     106     174 .. 0.62
   2 !   11.7   0.0   0.00018      0.32      45      95 ..     192     243 ..     182     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                                       -TTSHHHHHHH......HTT....SEEEEEES-HHHHHHHHHHC CS
                   Methyltransf_11   5 cGtGrlaeala......krg....arvvgvDlskemlklakeka 38 
                                       c  Gr a  +a      +r      +++g+D+ +e +++a++  
  gi|313126760|ref|YP_004037030.1| 109 CSDGREAYSMAmlahddDRIdpnkVKILGTDIKPEIIRAARAGE 152
                                       555555555554445442224556799**********9987544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00018
                                       EEETTEECCCTSS-TT-EEEEEEES-CCC-..CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  45 vefvvadaeklpfednsfDlvvssevlhhv..edpekalkeiaRvLkpgGllv 95 
                                       v+f++ d+ +   + ++fDlvv+++ + ++  e  +++++ +   L p+G+l 
  gi|313126760|ref|YP_004037030.1| 192 VSFRKHDLVQ-ERPPDTFDLVVCRNLFIYInsEAKQAIFDTLGSALTPDGYLT 243
                                       5667777776.44556**************9989999**************96 PP

>> APAF1_C  APAF-1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0017       3.1      57     107 ..      34      83 ..      24      88 .. 0.87
   2 ?    5.2   0.0     0.011        19      87     130 ..     183     226 ..     159     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                           APAF1_C  57 wieakvkltgpsslledyvkyrkileendeeeledfeeflsvnahlleekp 107
                                       ++++++   + +  +e y +y+ +l+  deee   +++ lsvn   ++++p
  gi|313126760|ref|YP_004037030.1|  34 YLDRRISARMRRRGVESYDEYQSLLD-GDEEEQTALLNALSVNVTSFFRNP 83 
                                       78899999999999***********9.566667789999********9998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                           APAF1_C  87 eeledfeeflsvnahlleekpfpdiiQlalsqpessevyqqAkk 130
                                       ++ +++++++s + h l++++ pd   l +++    ++  +Ak+
  gi|313126760|ref|YP_004037030.1| 183 RVTDEVKSLVSFRKHDLVQERPPDTFDLVVCRNLFIYINSEAKQ 226
                                       6778999*************************999999999987 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.5e-05     0.027      86     147 ..     189     247 ..     155     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                              NodS  86 kesshiswivsdvqqfstdekfdlivvaevlyyiedvaelraavrnlvsllapdgqlvfGsa 147
                                       k  s +s+ + d+ q    + fdl+v+ +++ yi+  a+ +a    l s l+pdg+l  G +
  gi|313126760|ref|YP_004037030.1| 189 K--SLVSFRKHDLVQERPPDTFDLVVCRNLFIYINSEAK-QAIFDTLGSALTPDGYLTIGMT 247
                                       3..5789999************************97655.788899***********99965 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00023      0.41      28      96 ..      24      87 ..      13     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                              CobU 28 YiATaealDeemaeRiarHrerRpaeWetveepldlaealkeeekkevvLvDcltlwltnllleeeaek 96
                                        AT+  +D+ +++Ri++  +rR+     ve++ + +++l+ +e+++++L+++l++ +t+++ + e ++
  gi|313126760|ref|YP_004037030.1| 24 SFATSSYNDAYLDRRISARMRRRG-----VESYDEYQSLLDGDEEEQTALLNALSVNVTSFFRNPEVWD 87
                                      57***************9988886.....677777888888888889*************999877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1666.30
//
Query:       gi|313126761|ref|YP_004037031.1|  [L=294]
Description: hypothetical protein Hbor_20200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-74  250.5   0.0    2.2e-74  249.9   0.0    1.3  1  CheF-arch  Chemotaxis signal transduction system protein F fr
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.047   13.8   0.0    1.5  1  bPH_4      Bacterial PH domain
       0.11   12.5   0.0        0.3   11.2   0.0    1.7  1  EFP        Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> CheF-arch  Chemotaxis signal transduction system protein F from archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.9   0.0   3.7e-78   2.2e-74       1     216 [.       7     212 ..       7     213 .. 0.99

  Alignments for each domain:
  == domain 1  score: 249.9 bits;  conditional E-value: 3.7e-78
                         CheF-arch   1 kiadfkGkfllvvkkgrkkkdvkWekgrilLsnkrlvlasedkkitiplssvedvggevPrklkdifddtvtdakvs 77 
                                       k+ad++G+fl+v+++gr+ +d++W +grilLsn+rlvla++++k+t plss+        ++l+++fd+++++a+vs
  gi|313126761|ref|YP_004037031.1|   7 KVADTNGRFLQVKRGGRNLNDANWANGRILLSNQRLVLAGTGGKRTFPLSSI--------EQLGGRFDVNQRIATVS 75 
                                       79**************************************************........***************** PP

                         CheF-arch  78 gyialktkdgenvllieaedesiekFetkLfkalLngkevlvkhpAvvGGvvqdtewekgklkvekkaielatkkgs 154
                                       +y al+ +dge+v+l++ +d  +e+Fe +L+ alLn +++lv+hpAv+GGvvq+tewe ++lkve++a+++at +gs
  gi|313126761|ref|YP_004037031.1|  76 DYLALHYNDGEDVVLVAPAD--FEEFELELYGALLNSTRFLVRHPAVEGGVVQNTEWEGARLKVEEDAVSIATVNGS 150
                                       ********************..******************************************************* PP

                         CheF-arch 155 fveielsdvgdvereektvdgeerpvleveht.edgesvttylagkdkrkvslLerylreeye 216
                                       fv+++l+d+gd+e++ +tv++e+r+v+eveh+ ++g+s++ty++g++ r v++L+++++ ++e
  gi|313126761|ref|YP_004037031.1| 151 FVNVQLDDIGDIEMGRRTVRDESREVIEVEHSdDEGTSLQTYVSGPE-RPVNILKSLFQIGEE 212
                                       *********************************9*************.***********9987 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.9e-06     0.047      18      69 ..      50     102 ..      36     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.9e-06
                             bPH_4  18 rkkIpiedIkkirktksplsspalsldrleIkygkydt.ilisPkkkeeFiee 69 
                                       ++++p+++I++     ++  + a+++d+l  +y++ +  +l+ P + eeF  e
  gi|313126761|ref|YP_004037031.1|  50 KRTFPLSSIEQLGGRFDVNQRIATVSDYLALHYNDGEDvVLVAPADFEEFELE 102
                                       67788888888888888888**************98888***********655 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     5e-05       0.3       7      27 ..      82     102 ..      78     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5e-05
                                       EEETTEEEEEETTT--EEEEE CS
                               EFP   7 YkdgdeyvFMdnetYeqielp 27 
                                       Y+dg+++v+  + ++e++el+
  gi|313126761|ref|YP_004037031.1|  82 YNDGEDVVLVAPADFEEFELE 102
                                       ******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1587.47
//
Query:       gi|313126762|ref|YP_004037032.1|  [L=286]
Description: hypothetical protein Hbor_20210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.9e-47  160.0   0.1    1.4e-46  159.0   0.1    1.5  1  CheF-arch    Chemotaxis signal transduction system protein F 
  ------ inclusion threshold ------
       0.64    9.9   2.8        1.2    9.0   0.6    2.1  2  TFIIE_alpha  TFIIE alpha subunit


Domain annotation for each model (and alignments):
>> CheF-arch  Chemotaxis signal transduction system protein F from archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.0   0.1   1.6e-50   1.4e-46      20     214 ..      13     203 ..       2     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 159.0 bits;  conditional E-value: 1.6e-50
                         CheF-arch  20 kdvkWekgrilLsnkrlvlasedkkitiplssvedvg.gevPrklkdifddtvtdakvsgyialktkdgenvlliea 95 
                                       ++v   kgr+l+s+ rl+l+++  k+ +p++s++d++ g+vP++++++fd tv        + + + +++++++i +
  gi|313126762|ref|YP_004037032.1|  13 DPV---KGRVLMSEHRLILVTSKAKTVVPVTSIFDIAvGQVPPEVEEFFDYTVM-------VGYIVGNRRRTTVIGG 79 
                                       567...9***********************************************.......8888888899999999 PP

                         CheF-arch  96 edesiekFetkLfkalLngkevlvkhpAvvGGvvqdtewekgklkvekkaielatkkgsfve......ielsdvgdv 166
                                       + e+iekF+  Lf+a Lng + lvkhpA vGG+v dt+ +++ l ++ +++ +  ++ ++ e      i+l++v  +
  gi|313126762|ref|YP_004037032.1|  80 DRETIEKFSLLLFRAALNGSTTLVKHPAKVGGRVMDTPKRETGLHLDYESVVFPGND-VLGEsdepfeIDLASVIFF 155
                                       999************************************************887655.3333455777********* PP

                         CheF-arch 167 ereektvdgeerpvlevehtedgesvttylagkdkrkvslLerylree 214
                                       e+ e+t+d+e+r vl+v+h+e+g++vtt +++ + rk+++L+rylr+ 
  gi|313126762|ref|YP_004037032.1| 156 EVIERTIDDEKRLVLSVQHVENGQTVTTEISMGSRRKMNILGRYLRLI 203
                                       *********************************************975 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.053   4.8e+02       5      48 ..     156     200 ..     153     207 .. 0.79
   2 ?    9.0   0.6   0.00014       1.2      11      57 ..     216     260 ..     205     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.053
                                       HHHHHCS-HHHHHHHHHH.HCTTSEBHHHHHHHHTS-HHHHHHHH CS
                       TFIIE_alpha   5 evvrkfygeeavlvldvL.lekgevteedlakelkidlnelrklL 48 
                                       ev+ +  ++e  lvl v  +e+g++   +++   + + n+l++ L
  gi|313126762|ref|YP_004037032.1| 156 EVIERTIDDEKRLVLSVQhVENGQTVTTEISMGSRRKMNILGRYL 200
                                       899999999999999985367888888888888888888887766 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00014
                                       S-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSE CS
                       TFIIE_alpha  11 ygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlv 57 
                                        +ee  +vl  L   +   e d+a +l ++  el + L++L+++ l+
  gi|313126762|ref|YP_004037032.1| 216 IEEETLEVLVGLY--STGPEIDIASLLDLEEDELEHRLAELFDDDLI 260
                                       5778899999998..556799************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1571.29
//
Query:       gi|313126763|ref|YP_004037033.1|  [L=583]
Description: flagella assembly protein j [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-14   52.4   2.5    1.1e-09   38.3   0.2    3.4  4  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.2   6.3e-14   1.1e-09       2     121 ..     104     228 ..     103     230 .. 0.96
   2 ?   -4.8   1.5         1   1.8e+04     108     121 ..     243     256 ..     242     258 .. 0.67
   3 ?   -2.5   0.0      0.25   4.5e+03      88     114 ..     280     306 ..     275     311 .. 0.44
   4 !   22.6   0.2   4.4e-09   7.9e-05       1     122 [.     364     489 ..     364     492 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 6.3e-14
                                       HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqliragee 73 
                                       ++++ +l+ + +  v +++ l++e e+g+la e++ri + ++ +  sl++a e    + ps+ +++++++l  + ++
  gi|313126763|ref|YP_004037033.1| 104 ITHMTVLSTTNIDRVSVFRQLGKEEEYGELAIEMRRITELVDTWNqSLDDACErrarQVPSKPLADFLDRLAYSLSA 180
                                       7899*****************************************999*****99999999**************** PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllilla 121
                                       g++++++L   ++ + +++ + +++++  le++  l++ +++++ + +
  gi|313126763|ref|YP_004037033.1| 181 GQDIDDFLLGEQSAMVQKYITVYESALGNLEVMKDLYLSMILSMTFAV 228
                                       *****************************************9988876 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXX CS
                             T2SSF 108 llvvallvllilla 121
                                       +l +a++++l++++
  gi|313126763|ref|YP_004037033.1| 243 TLTIAAVIVLFVFV 256
                                       56677777777775 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHHTTXXXXXXXXX CS
                             T2SSF  88 leeerelrrkllaallepllllvvall 114
                                       ++ ++++++++++  +  l +++v++l
  gi|313126763|ref|YP_004037033.1| 280 YRTKADRQIDIALYGAVALSFVLVGIL 306
                                       444444444444444433444444333 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 4.4e-09
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirage 72 
                                       f+r l+   sa  +  +a+    +++++g+l++e++r++ rl++ + + +++     +  ss +  ++  ++    +
  gi|313126763|ref|YP_004037033.1| 364 FIRALGASESAKQSTTTAVLKTLRTKDFGVLSREIDRLYVRLNMRIGPTRSWFfftaEA-SSYLiQKFSEMYNIGRQ 439
                                       788888888888899999998889999****************************9644.44555999999999999 PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillai 122
                                        gg+  +  e ++++++e  +lrr++  a+   + +l+ + + +++ ++i
  gi|313126763|ref|YP_004037033.1| 440 MGGTPKQLGELISSNMNEIVKLRRQREQATVTLIGVLYGITASASFAFFI 489
                                       9******************************9999999999988888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.53
# Mc/sec: 3325.57
//
Query:       gi|313126764|ref|YP_004037034.1|  [L=555]
Description: ATPase, type iv secretory pathway virb11 component like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-44  152.0   0.0    2.3e-44  151.5   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
    9.3e-05   22.9   0.0     0.0019   18.6   0.0    2.3  2  AAA_16        AAA ATPase domain
    0.00075   19.8   0.0     0.0024   18.1   0.0    1.8  2  AAA_22        AAA domain
     0.0062   16.3   0.0      0.076   12.7   0.0    2.2  2  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.9   0.0      0.067   13.7   0.0    2.1  2  ABC_tran      ABC transporter
      0.047   13.7   0.0        0.1   12.6   0.0    1.6  1  Dynamin_N     Dynamin family
      0.051   13.3   0.0       0.11   12.3   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.068   12.7   0.0       0.12   11.9   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
       0.09   12.1   0.0        0.2   10.9   0.0    1.6  1  AIG1          AIG1 family
       0.17   11.2   0.0       0.35   10.2   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
       0.48   10.9   1.9       0.59   10.6   0.1    2.0  2  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   0.0   1.4e-47   2.3e-44       3     244 ..     172     417 ..     170     434 .. 0.95

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 1.4e-47
                             T2SSE   3 illeallddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvr 79 
                                        +le++++d+   dihv  p++v v   v g+   +ve+ +k++    ++++    +  +s+ +p++d +lp +g r
  gi|313126764|ref|YP_004037034.1| 172 GPLEPIMRDPANEDIHVIGPQQVDVDHGVYGLLETTVEFGSKDQFDNWLRNMGERIGDPVSDAHPIVDSTLP-DGSR 247
                                       578999*******************9999999999*************************************.**** PP

                             T2SSE  80 lrvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                       ++++    v     +l+iR+ +   l++ ++ + ++l++++   l  a++++ +i v G T sGKtt+l+a+l++i+
  gi|313126764|ref|YP_004037034.1| 248 INIIYSDDVSLkgSSLTIRQGDDVPLSIFQITKWGTLSPELCGYLWMALENERTIFVVGETASGKTTTLNAILSFIP 324
                                       **9998644333599************************************************************** PP

                             T2SSE 155 ksderivtvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlg 226
                                       ++  +i t+ED++E+ + ++   ql ++     + +v++ dl+ aaLR rPD i+vGE+R++e   + +A++TGH++
  gi|313126764|ref|YP_004037034.1| 325 QD-SKIYTAEDTAEVLPPHDTWQQLLTRegrgaDSEVDMFDLVAAALRSRPDYIIVGEVRGEEGRMAFQAAQTGHPV 400
                                       *9.*************************9**9999****************************************** PP

                             T2SSE 227 slsTlHansaagalerLe 244
                                        + T Ha + ++ ++r  
  gi|313126764|ref|YP_004037034.1| 401 -MLTFHASDIVSMIQRFT 417
                                       .*************9975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.19     3e+02      72     126 ..      92     145 ..      57     152 .. 0.75
   2 !   18.6   0.0   1.2e-06    0.0019      22      81 ..     298     354 ..     287     407 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.19
                            AAA_16  72 laqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrl 126
                                       + ++  +++ll+   ++++     ++ +++ee l+++  l+g++  r++el++rl
  gi|313126764|ref|YP_004037034.1|  92 VFDQV-KDKLLERSVSKPAPEGDVEYEDRIEELLEEIVVLEGKQTGRVHELIQRL 145
                                       55566.5577777777777777888888888888899999999998888888875 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.2e-06
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareel 81 
                                       ++ + ++++Ge ++GK++ ++++l  + +d  +++++ +++ l    p +++ q+l+re+ 
  gi|313126764|ref|YP_004037034.1| 298 NE-RTIFVVGETASGKTTTLNAILSFIPQDSkIYTAEDTAEVL---PPHDTWQQLLTREGR 354
                                       44.89********************999995588899999998...777778888877544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.1   6.7e+03      73      91 ..      87     105 ..      64     144 .. 0.61
   2 !   18.1   0.0   1.5e-06    0.0024       4      99 ..     298     381 ..     295     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.1
                            AAA_22  73 lsseellealeqalrarav 91 
                                        +++e+++++ + l +r+v
  gi|313126764|ref|YP_004037034.1|  87 EEEQEVFDQVKDKLLERSV 105
                                       3455555555555555543 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.5e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseell 79 
                                       +++ ++v+Ge+ +GKTt+l+ +l+  ++       ++++++ + +++   + d +++ll   g+++++    + +++
  gi|313126764|ref|YP_004037034.1| 298 NERTIFVVGETASGKTTTLNAILSFIPQ-------DSKIYTAEDTAEVlPPHDTWQQLLTREGRGADS----EVDMF 363
                                       577899********************96.......566666666666677777788888888865554....99999 PP

                            AAA_22  80 ealeqalraravielliiDE 99 
                                       ++++ alr+r +   +i+ E
  gi|313126764|ref|YP_004037034.1| 364 DLVAAALRSRPD--YIIVGE 381
                                       999999999988..777766 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.22   3.6e+02     209     250 ..      84     128 ..      78     166 .. 0.74
   2 !   12.7   0.0   4.7e-05     0.076      22      51 ..     297     327 ..     292     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                            AAA_15 209 edsekkssllgklkekileealqekl...eeelteklkeiqeklk 250
                                       e++e+++++++++k+k+le ++++ +   + e ++ ++e++e++ 
  gi|313126764|ref|YP_004037034.1|  84 ELDEEEQEVFDQVKDKLLERSVSKPApegDVEYEDRIEELLEEIV 128
                                       67899999***********99988888885555555555555554 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.7e-05
                            AAA_15  22 see.ltvliGkNnsGKSsilealdlFlnnke 51 
                                       ++e + +++G+ +sGK++ l+a+  F+ +++
  gi|313126764|ref|YP_004037034.1| 297 ENErTIFVVGETASGKTTTLNAILSFIPQDS 327
                                       55547899******************98773 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.8   4.6e+03      79      88 ..      95     123 ..      11     152 .. 0.57
   2 ?   13.7   0.0   4.1e-05     0.067       7      42 ..     295     329 ..     292     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                                       H...................HHHTCHHHH CS
                                       x...................xxxxxxxxx RF
                          ABC_tran  79 n...................esdeeieka 88 
                                       +                   e++++ie++
  gi|313126764|ref|YP_004037034.1|  95 QvkdkllersvskpapegdvEYEDRIEEL 123
                                       23333333333334444444444444444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.1e-05
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGei 42 
                                        l++ +++ +vGe+ +GK+t l++++    p+  +i
  gi|313126764|ref|YP_004037034.1| 295 ALENERTIFVVGETASGKTTTLNAILSFI-PQDSKI 329
                                       6788999******************9986.556666 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.4e-05       0.1       1      33 [.     302     332 ..     302     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-05
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33 
                                       i vvG++ sGK++ lna+l     p ++ + T+
  gi|313126764|ref|YP_004037034.1| 302 IFVVGETASGKTTTLNAILSF--IPQDSKIYTA 332
                                       78*****************75..5888888887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-05      0.11       4      44 ..     276     321 ..     273     330 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                            AAA_29   4 lqlvNWgtfdght....ieidlkg.atlltGpsGsGKSTllDAiqa 44 
                                       +q+  Wgt++ +     ++  +++ +++++G++ sGK+T l Ai  
  gi|313126764|ref|YP_004037034.1| 276 FQITKWGTLSPELcgylWMALENErTIFVVGETASGKTTTLNAILS 321
                                       5777788777543122133333445999**************9975 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.4e-05      0.12      28      61 ..     294     327 ..     289     338 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.4e-05
                             AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkek 61 
                                       + l+n++ +++vG+t +GKt++++ +l+ +++++
  gi|313126764|ref|YP_004037034.1| 294 MALENERTIFVVGETASGKTTTLNAILSFIPQDS 327
                                       56899********************999998665 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012       0.2       2      23 ..     301     322 ..     300     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                       EEEEESSTTSSHHHHHHHHHTS CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgk 23 
                                       ti +vG t +Gk +T N+il  
  gi|313126764|ref|YP_004037034.1| 301 TIFVVGETASGKTTTLNAILSF 322
                                       89*****************975 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00022      0.35      41      60 ..     301     320 ..     275     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                       SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE  41 hllvaGatgsGKStalntLi 60 
                                        + v+G t sGK+t+ln+++
  gi|313126764|ref|YP_004037034.1| 301 TIFVVGETASGKTTTLNAIL 320
                                       588**************975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       3.1     5e+03     175     192 ..      99     127 ..      63     143 .. 0.56
   2 ?   10.6   0.1   0.00036      0.59      23      39 ..     303     319 ..     296     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                            AAA_23 175 l...........eqekekekeleeleeel 192
                                       +           e   e+e+++eel ee+
  gi|313126764|ref|YP_004037034.1|  99 KllersvskpapEGDVEYEDRIEELLEEI 127
                                       11222234444433333444444444444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00036
                            AAA_23  23 lItGpNGaGKTTildAi 39 
                                        ++G++ +GKTT l+Ai
  gi|313126764|ref|YP_004037034.1| 303 FVVGETASGKTTTLNAI 319
                                       679*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.78u 0.38s 00:00:01.16 Elapsed: 00:00:00.59
# Mc/sec: 2822.05
//
Query:       gi|313126765|ref|YP_004037035.1|  [L=249]
Description: flagella biogenesis ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-16   58.6   0.1    8.5e-16   58.0   0.1    1.3  1  ATPase    KaiC
    0.00012   22.1   0.2     0.0011   18.9   0.2    2.1  1  NACHT     NACHT domain
     0.0025   17.4   0.2      0.022   14.3   0.2    2.1  1  AAA_25    AAA domain
     0.0053   17.0   0.1      0.014   15.6   0.1    1.7  1  AAA_22    AAA domain
     0.0069   16.4   0.0      0.013   15.5   0.0    1.4  1  TsaE      Threonylcarbamoyl adenosine biosynthesis protein Ts
  ------ inclusion threshold ------
      0.011   16.2   0.2      0.028   14.8   0.2    1.7  1  AAA_16    AAA ATPase domain
       0.04   13.2   0.2       0.13   11.5   0.1    1.7  2  Rad51     Rad51
       0.04   14.1   0.2       0.15   12.3   0.1    2.0  2  FF        FF domain
      0.046   12.9   0.1       0.27   10.4   0.0    1.9  2  DAP3      Mitochondrial ribosomal death-associated protein 3


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.1   4.3e-19   8.5e-16      10     207 ..      18     222 ..       8     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 4.3e-19
                            ATPase  10 eilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaii 86 
                                       + l gGip+g++vli G++G+GK++++++F++   ++ +  + ++++e   + +  +++sl  d+ k   ++++ +i
  gi|313126765|ref|YP_004037035.1|  18 KELGGGIPRGAIVLIEGDYGAGKSVLSQRFTYGFSQE-DIVTSLISTELGVRGFLDQMHSLEYDMVKPLLNEEVLFI 93 
                                       4456****************************77666.**************************9887777788888 PP

                            ATPase  87 dasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl..ayeekeavaRe........ilrqlvrvlkk 153
                                        a  +a++  +  + ++ ++l+++l+ea    +a  ++iD+ +++  +  + ea++R+        ++  ++r+l  
  gi|313126765|ref|YP_004037035.1|  94 PAEIDASGALTGGNASERKQLLRRLMEAETLWEADVTIIDTFDAIlrNDPQFEALVRQneerqaalEIISFFRELTT 170
                                       888888887777899999***********************999853333445556653333333368889999999 PP

                            ATPase 154 lgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRg 207
                                       ++ T il+ + s+ +e a g+     i+d  ++L+  e+ ++++R + +    g
  gi|313126765|ref|YP_004037035.1| 171 KNKTIILTVDPSTVDEDAIGP-FRS-IADVYLQLEMVEVGNDVRRNIFVKRFAG 222
                                       **********77755555554.345.899******************9987655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   5.5e-07    0.0011       2     134 ..      29     186 ..      28     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.5e-07
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-......-HCHHHCCCCTS--SSS-C.... CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna...rsladllfsqlpepaapvse.... 71 
                                       +v+++G+ G GK++L q++     +++        +  l +r + ++  +     ++ ll ++ + + a+++     
  gi|313126765|ref|YP_004037035.1|  29 IVLIEGDYGAGKSVLSQRFTYGFSQEDIVT--SLISTELGVRGFLDQMHSleyDMVKPLLNEEVLFIPAEIDAsgal 103
                                       589************************999..578888888888888766666677777777777777777779997 PP

                                       ...CHHHHCCSCCCEE..........EEEE-STT-SS-TCH.................HHHHHCTTTTT--EEEEEE CS
                             NACHT  72 ...vwavllelperlL..........lilDglDelvtdlgq........kekqpvrtlLselirkkllpeasllltv 127
                                            +++ +l +rl+           i+D +D + + ++q        +e+q++ + + + +r+   ++ +++ltv
  gi|313126765|ref|YP_004037035.1| 104 tggNASERKQLLRRLMeaetlweadvTIIDTFDAILRNDPQfealvrqnEERQAALEII-SFFRELTTKNKTIILTV 179
                                       77733333333333336666679999***********99999******66666666666.99***9999999***** PP

                                       ECCCHHH CS
                             NACHT 128 rpralrd 134
                                        p+++ +
  gi|313126765|ref|YP_004037035.1| 180 DPSTVDE 186
                                       ***9976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   1.1e-05     0.022      22     163 ..      16     147 ..       3     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                            AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal. 97 
                                       +++ ++g +p+g+++l+ G+ g+GK++l     +  ++ +          + + ++s+E +  ++   ++ +  ++ 
  gi|313126765|ref|YP_004037035.1|  16 LQKELGGGIPRGAIVLIEGDYGAGKSVLSQRFTYGFSQED----------IVTSLISTELGVRGFLDQMHSLEYDMv 82 
                                       455566778********************99999999855..........456799*****99*******9999998 PP

                            AAA_25  98 rddarllvldlagv..eslpLfakdrggtlltadvdaleaaieeveg...vrlvviDplsralggdensns 163
                                       ++  ++ vl ++ +   s  L    +gg+  +++ ++l +++ e+e    +++ +iD+++++l++d++ ++
  gi|313126765|ref|YP_004037035.1|  83 KPLLNEEVLFIPAEidASGAL----TGGN--ASERKQLLRRLMEAETlweADVTIIDTFDAILRNDPQFEA 147
                                       444444455444431233333....2233..34455555555555555559***********999987655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   7.2e-06     0.014       6     116 ..      28     152 ..      25     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.2e-06
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdl.lrellralglelka........ 70 
                                        i+++ G  G+GK++l +r+++ + +e        ++++ +l + +      +l + ++   l++e           
  gi|313126765|ref|YP_004037035.1|  28 AIVLIEGDYGAGKSVLSQRFTYGFSQEDI----VTSLISTELGVRGfldQMHSLeYDMVKPLLNEEVLFipaeidas 100
                                       588999******************76433....44444555555554444444445555555554444488888888 PP

                            AAA_22  71 .......erlsseellealeqalrarav..ielliiDEaqh.lrseealeeLrsll 116
                                              +    +e  ++l++ ++a       + iiD ++  lr++ ++e L++  
  gi|313126765|ref|YP_004037035.1| 101 galtggnA----SERKQLLRRLMEAETLweADVTIIDTFDAiLRNDPQFEALVRQN 152
                                       88744433....443344444444444455569********664699999886554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.6e-06     0.013       8      50 ..      14      59 ..       9      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.6e-06
                                      HHHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT--.---- CS
                              TsaE  8 ealgkklakal..gdvilLeGdLGaGKTtlvrglakalgve.evkS 50
                                      ++l k+l+  +  g+++l+eGd GaGK++l++ +  ++  e  v+S
  gi|313126765|ref|YP_004037035.1| 14 DRLQKELGGGIprGAIVLIEGDYGAGKSVLSQRFTYGFSQEdIVTS 59
                                      4556666665577889******************999988766776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   1.4e-05     0.028      22     149 ..      25     140 ..      10     182 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawr 98 
                                       +r+ +vl+ G+ G GKs l +++   ++++++++    ++           ++ +   + +  l+ +  + +l++  
  gi|313126765|ref|YP_004037035.1|  25 PRGAIVLIEGDYGAGKSVLSQRFTYGFSQEDIVTSLISTELG---------VRGF-L-DQMHSLEYDMVKPLLNEEV 90 
                                       44589*******************999999766633333333.........2223.2.1222222222222455555 PP

                            AAA_16  99 ekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwade 149
                                        ++++++ a+++l+g  as   +ll+rl+ a +  +++  v ++D ++ +  
  gi|313126765|ref|YP_004037035.1|  91 LFIPAEIDASGALTGGNASERKQLLRRLMeAETLWEAD--VTIIDTFDAILR 140
                                       55555555555666666666666666666555555444..666666663222 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   6.6e-05      0.13      25      56 ..      15      46 ..       5      52 .. 0.87
   2 ?   -1.0   0.0      0.44   8.7e+02     118     162 ..     112     159 ..     104     190 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.6e-05
                                      HHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                             Rad51 25 klDelLgGGietgsiteifGefrsGktqlcht 56
                                      +l + LgGGi+ g+i  i G++++Gk+ l++ 
  gi|313126765|ref|YP_004037035.1| 15 RLQKELGGGIPRGAIVLIEGDYGAGKSVLSQR 46
                                      57788**********************99875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                                       HHHHHHTHHHHHHS-EEEEEEETTTGGGCH-..------TH.HHHHHH CS
                             Rad51 118 eellqqaaallaedkfallivDsvtalyRtd..fsgrgela.kRqqkl 162
                                       ++ll+++ +  +  +  + i+D+  a  R+d  f+ +   + +Rq  l
  gi|313126765|ref|YP_004037035.1| 112 KQLLRRLMEAETLWEADVTIIDTFDAILRNDpqFEALVRQNeERQAAL 159
                                       555555544444445566677777777777766554433320344333 PP

>> FF  FF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.4   2.8e+03      40      48 ..     107     115 ..     102     118 .. 0.81
   2 ?   12.3   0.1   7.3e-05      0.15      26      48 ..     136     159 ..     112     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                                       SHHHHHHHH CS
                                FF  40 dkseReelF 48 
                                       ++seR++l 
  gi|313126765|ref|YP_004037035.1| 107 NASERKQLL 115
                                       789***996 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.3e-05
                                       HHHCTTSCCCHHG.TSHHHHHHHH CS
                                FF  26 kkilenDpRYlal.ldkseReelF 48 
                                         il+nDp++ al +  +eR+++ 
  gi|313126765|ref|YP_004037035.1| 136 DAILRNDPQFEALvRQNEERQAAL 159
                                       5699***************99876 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013      0.27      26      62 ..      30      65 ..      14      80 .. 0.87
   2 ?    0.2   0.0      0.17   3.4e+02     123     164 ..     144     180 ..     112     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                      EEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-GGG CS
                              DAP3 26 lvltGekgsGKSvlLlqalayAlekgwvvlhvpeaed 62
                                      ++++G+ g GKSv L+q  +y+++++ +v ++ ++e 
  gi|313126765|ref|YP_004037035.1| 30 VLIEGDYGAGKSV-LSQRFTYGFSQEDIVTSLISTEL 65
                                      5799********8.8***********99988877665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.17
                                       EHHHHHHHHHH-SSSHHHHHHHHHHHHHHHTTSS--EEEEEE CS
                              DAP3 123 tLleLvklgikdaksawdvfqallkeLkaqskgrvpvlvtvD 164
                                         ++Lv+++ +++++    +  +++eL+ ++k    +++tvD
  gi|313126765|ref|YP_004037035.1| 144 QFEALVRQNEERQAALE--IISFFRELTTKNK---TIILTVD 180
                                       56777877766666665..6778899999888...7888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.39s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 1347.98
//
Query:       gi|313126766|ref|YP_004037036.1|  [L=150]
Description: flagellar protein g [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-20   73.5   4.2    2.5e-20   73.3   4.2    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.029   15.3   0.7      0.053   14.4   0.7    1.5  1  DUF756          Domain of unknown function (DUF756)
      0.066   13.5   1.6        0.1   12.9   1.4    1.4  1  CARDB           CARDB


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   4.2   4.1e-24   2.5e-20       3     154 ..       4     139 ..       2     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 4.1e-24
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS CS
                    Arch_flagellin   3 vgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGs 79 
                                       v++ tlI+fIA +++AA ++gvlint+++++++ ++ g   ++ +++++ei++d   s +++   ++t+yvk n+G 
  gi|313126766|ref|YP_004037036.1|   4 VSAPTLILFIASLVIAAGVSGVLINTVTDISSALDDRGADVSKNIRTDVEIISDSESSVYDSGSGNLTLYVK-NTGT 79 
                                       6778********************************************************************.**** PP

                                       --EEGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE- CS
                    Arch_flagellin  80 spidlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvp 154
                                        ++  +  t +v+++                ++ + ++ +gd  + +  +v++++      ++ ++++++v++v 
  gi|313126766|ref|YP_004037036.1|  80 RTLPATGQTFDVIVNA------------QYRTNVTVTVADGDSHWGPHGVVKVVIGD---LSLADNEDHRVKLVV 139
                                       ***************9............457889999999999************95...789********9986 PP

>> DUF756  Domain of unknown function (DUF756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   8.9e-06     0.053       6      47 ..      62     110 ..      58     150 .] 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.9e-06
                            DUF756   6 pYdlaagnlrltlrNtgkaaa.....rftVydnaka..pwtytveagdq 47 
                                        Yd  +gnl+l  +Ntg++++     +f V  na++  + t+tv+ gd+
  gi|313126766|ref|YP_004037036.1|  62 VYDSGSGNLTLYVKNTGTRTLpatgqTFDVIVNAQYrtNVTVTVADGDS 110
                                       599999***********8655555669999999999999*****99954 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   1.7e-05       0.1       6      88 ..      54     143 ..      49     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                                       E.EEEC-SEEETTSEEEEEEEEEE-SSS-..EEEEEEEEEETTEEEEEEEE......SEE-CTEEEEEEEEEE-S-S CS
                             CARDB   6 vtntlnpseafvgeentitvtvkNqGtaa..sgatkvalyldgelvgtvtv......psLaagesttvsftwtteat 74 
                                       +  + ++s++++  + ++t+ vkN+Gt +  ++  + +++++ +  ++vtv      +   + + ++v + +   a 
  gi|313126766|ref|YP_004037036.1|  54 I-ISDSESSVYDSGSGNLTLYVKNTGTRTlpATGQTFDVIVNAQYRTNVTVtvadgdSHWGPHGVVKVVIGDLSLAD 129
                                       5.566788899999999************555556788899999999999988999999999999999999998888 PP

                                       -CEEEEEEEESTT- CS
                             CARDB  75 egevtltvvvDpdn 88 
                                         ++ +++vvD d 
  gi|313126766|ref|YP_004037036.1| 130 NEDHRVKLVVDGDE 143
                                       88888999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 816.53
//
Query:       gi|313126767|ref|YP_004037037.1|  [L=150]
Description: flagellar protein f [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-12   45.6   4.5    9.2e-12   45.5   4.5    1.0  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   4.5   5.1e-16   9.2e-12       5     161 ..       7     143 ..       2     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 5.1e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS-- CS
                    Arch_flagellin   5 igtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGssp 81 
                                        +t+I+f  ++++  ++++++ +t+ +l ++ +s  e   e  ++g+++t++++  ++n+ +  + i vk n+G  +
  gi|313126767|ref|YP_004037037.1|   7 GSTAIIFLGVLIATGTLYTTVSDTTEMLNDAEDSNSEHLLERRNTGINVTSVTY--SNNSGTYPMDIRVK-NTG--T 78 
                                       58****************************************************..33333456******.***..5 PP

                                       EEGGG-EEEEEESS--EE--E....................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SS CS
                    Arch_flagellin  82 idlnkttisvtddgqetlltadefgivvisdtdgsltng..devlekgekvelevnvneddgitagdevsvevvpen 156
                                       + l+  ++sv++++          ++  +s+++ +++ +  ++++ ++e++ +e++v       +++  +v++v+en
  gi|313126767|ref|YP_004037037.1|  79 LTLSANDTSVLVNN----------EYQQPSGSTRTVDGTsgTDIWAPNETLLIELTV-------DNEPKRVKIVTEN 138
                                       68888888888888..........77777777777776666***************9.......588999999**** PP

                                       S--EE CS
                    Arch_flagellin 157 Gastt 161
                                       G++++
  gi|313126767|ref|YP_004037037.1| 139 GVTDS 143
                                       *9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 871.91
//
Query:       gi|313126768|ref|YP_004037038.1|  [L=456]
Description: flagella protein/flagella accessory protein c (flac) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-23   79.9   0.0    2.6e-22   78.5   0.0    1.8  1  Arch_fla_DE  Archaeal flagella protein
    2.3e-21   75.9   2.7    2.9e-21   75.6   1.1    2.1  2  FlaC_arch    Flagella accessory protein C (FlaC)
     0.0071   16.8   0.4     0.0071   16.8   0.4    3.7  4  ZapB         Cell division protein ZapB
     0.0093   16.4   0.5       0.02   15.3   0.5    1.5  1  NPV_P10      Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
      0.054   13.6   0.7        1.3    9.2   0.7    2.8  1  bZIP_1       bZIP transcription factor
      0.076   12.0   0.0       0.12   11.3   0.0    1.3  1  ASC          Amiloride-sensitive sodium channel
       0.12   12.4   0.4       0.26   11.3   0.4    1.5  1  DUF1664      Protein of unknown function (DUF1664)
       0.96    9.7   3.6       0.41   10.9   0.2    2.1  3  DUF948       Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   1.1e-25   2.6e-22       2      95 .]     343     433 ..     342     433 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.1e-25
                       Arch_fla_DE   2 ekpyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelkksel 78 
                                       +++yL++lp++y+ae v+leW +fLv+ +g  +aa+al+ Y+e +Wis++v++++++++++     +  ee   ++l
  gi|313126768|ref|YP_004037038.1| 343 SDVYLASLPASYVAESVALEWTRFLVSVGGAIGAARALRQYREQEWISRTVEKQMNAHVRNAAA-STTAEE--PQDL 416
                                       579***********************************************************86.433334..579* PP

                       Arch_fla_DE  79 tvedHvkSllyieklag 95 
                                       +ve+H++Sl+y+++lag
  gi|313126768|ref|YP_004037038.1| 417 RVEHHKESLTYVSRLAG 433
                                       ***************96 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   1.1   1.3e-24   2.9e-21       1      55 []      78     132 ..      78     132 .. 0.99
   2 ?   -3.2   0.0       5.3   1.2e+04      22      32 ..     385     395 ..     383     402 .. 0.66

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1.3e-24
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsnqvNPFv 55 
                                       r+ +lEn++s +s++++tv++en+++ ++veel+++V++ll++YE+V++++NPFv
  gi|313126768|ref|YP_004037038.1|  78 RVSDLENEVSATSSSVNTVREENKQIGETVEELDDTVRKLLDIYEMVTRGINPFV 132
                                       899***************************************************8 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.3
                         FlaC_arch  22 eneelsksvee 32 
                                       e+e +s +ve+
  gi|313126768|ref|YP_004037038.1| 385 EQEWISRTVEK 395
                                       66777777775 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   3.2e-06    0.0071      19      67 ..      71     119 ..      70     120 .. 0.97
   2 ?   -1.7   2.0       1.9   4.2e+03      29      50 ..     179     200 ..     175     220 .. 0.63
   3 ?   -7.7  10.2         8   1.8e+04      23      52 ..     231     293 ..     227     319 .. 0.56
   4 ?   -3.4   0.2       6.4   1.4e+04      42      54 ..     406     419 ..     380     422 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.2e-06
                              ZapB  19 titlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLg 67 
                                       ti++L  ++++L+ e+++ ++  + ++een+q  e+ e++ + ++kLL+
  gi|313126768|ref|YP_004037038.1|  71 TIAELEDRVSDLENEVSATSSSVNTVREENKQIGETVEELDDTVRKLLD 119
                                       9**********************************************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                              ZapB  29 eLkeeneelkeenreleeeneq 50 
                                       eL+ee+ee +  ++   +ene+
  gi|313126768|ref|YP_004037038.1| 179 ELEEESEEAELAAEDELAENER 200
                                       4444444444444444455554 PP

  == domain 3  score: -7.7 bits;  conditional E-value: 8
                              ZapB  23 LqmeieeLkeeneelkeenrele.................................eeneqlk 52 
                                       L+ e+ee +   ee +ee +e+                                  ee e l+
  gi|313126768|ref|YP_004037038.1| 231 LKSEYEEEEGWDEEDEEEDEEVDdspldtddlavedddiptteelvgeedaeseeeEEEETLE 293
                                       555666665555555555555555555555555555555555555544332222223333333 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 6.4
                              ZapB  42 rele...eeneqlkee 54 
                                       +  +   ee + l+ e
  gi|313126768|ref|YP_004037038.1| 406 A--SttaEEPQDLRVE 419
                                       1..1233555555555 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.5     9e-06      0.02      12      70 ..      71     129 ..      69     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9e-06
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpdev 70 
                                        i++++d+V+ l+++v   ++ +++v e n+++ +  ++L++   k+ +I ++ +  + 
  gi|313126768|ref|YP_004037038.1|  71 TIAELEDRVSDLENEVSATSSSVNTVREENKQIGETVEELDDTVRKLLDIYEMVTRGIN 129
                                       58888899999999998888888888888888888888888888888888888775555 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.7   0.00059       1.3      29      59 ..      73     103 ..      70     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00059
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  29 eeLerrvkaLekeNksLkseleelkkevekL 59 
                                       +eLe+rv+ Le+e ++ +s +++ ++e+++ 
  gi|313126768|ref|YP_004037038.1|  73 AELEDRVSDLENEVSATSSSVNTVREENKQI 103
                                       6677777777777666666666666666553 PP

>> ASC  Amiloride-sensitive sodium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.3e-05      0.12     390     427 ..     340     375 ..     280     376 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ASC 390 enlakvevyfeelnyerleeseaysltdllsdlGGllG 427
                                       +     +vy  +l+  ++ es+a ++t +l+++GG +G
  gi|313126768|ref|YP_004037038.1| 340 D--EASDVYLASLPASYVAESVALEWTRFLVSVGGAIG 375
                                       2..4679****************************998 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00011      0.26      68     113 ..      72     117 ..      69     124 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       i+++++++ + ++  +++++ v++vre+ ++ige ve+++++v++l
  gi|313126768|ref|YP_004037038.1|  72 IAELEDRVSDLENEVSATSSSVNTVREENKQIGETVEELDDTVRKL 117
                                       6666666666666677777777777777777777777777777665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00018      0.41      27      74 ..      71     118 ..      69     139 .. 0.60
   2 ?   -4.0   0.1         8   1.8e+04      34      43 ..     331     340 ..     326     344 .. 0.45
   3 ?   -2.7   0.0       3.4   7.6e+03      37      53 ..     392     408 ..     377     437 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplt 74 
                                       t+ e+++++ +le++v +++  v+++ ++ +++ e v+e  ++v +l 
  gi|313126768|ref|YP_004037038.1|  71 TIAELEDRVSDLENEVSATSSSVNTVREENKQIGETVEELDDTVRKLL 118
                                       566666666666666666666666666666665555554444444443 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 8
                            DUF948  34 tieelekqvd 43 
                                       t +++ +q+d
  gi|313126768|ref|YP_004037038.1| 331 TADQTSQQTD 340
                                       3344444443 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.4
                            DUF948  37 elekqvdpilkevedll 53 
                                       ++ekq+++ ++++++ +
  gi|313126768|ref|YP_004037038.1| 392 TVEKQMNAHVRNAAAST 408
                                       56666666666655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1377  (0.0768029); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.98u 0.34s 00:00:01.32 Elapsed: 00:00:00.52
# Mc/sec: 2633.68
//
Query:       gi|313126769|ref|YP_004037039.1|  [L=248]
Description: RecA-superfamily ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-50  171.0   0.0    2.8e-50  170.8   0.0    1.0  1  ATPase    KaiC
    7.2e-05   22.4   0.0    0.00011   21.8   0.0    1.3  1  AAA_25    AAA domain
     0.0015   17.9   0.0     0.0021   17.4   0.0    1.2  1  DUF2075   Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.019   14.2   0.4      0.032   13.5   0.1    1.4  2  Rad51     Rad51
      0.022   14.5   0.0      0.042   13.6   0.0    1.5  1  AAA_24    AAA domain
      0.061   12.6   0.0      0.081   12.3   0.0    1.3  1  DnaB_C    DnaB-like helicase C terminal domain
       0.07   12.6   0.0       0.11   12.0   0.0    1.2  1  AAA_7     P-loop containing dynein motor region
       0.12   12.7   0.1       0.26   11.7   0.1    1.7  2  AAA_16    AAA ATPase domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   0.0   1.2e-53   2.8e-50       1     229 [.       5     227 ..       5     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 1.2e-53
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwd.lek 76 
                                       vktg+eglD il+gGi ++++vli+G+pGtGK+i++lq+l++g+ ky+e g++ t+ee + d++e a+s+G d + +
  gi|313126769|ref|YP_004037039.1|   5 VKTGVEGLDSILNGGIVKNAAVLISGNPGTGKSILGLQYLYNGVDKYDEGGIYLTFEEAEDDIQEAAESIGFDrWSE 81 
                                       79**********************************************************************989** PP

                            ATPase  77 leeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlk 152
                                       + eegk+ + d  +  +         d ++ ++++   ++++   r+v+Ds+t +    e+e++ R++l +++ +lk
  gi|313126769|ref|YP_004037039.1|  82 YVEEGKIKVYDKRTLLR-------DGDFSSTLDRILGDLQDTSYDRLVLDSLTMFqLFFEDEKEQRQYLLKFIDILK 151
                                       ***********999875.......4788888888888889999************778899999************* PP

                            ATPase 153 klgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvlee 229
                                       + ++T++l++e+ s     ++ g+e+f+ dg+i L +  +  +  R++ + kmR  ++++ ++p+eI+e+gi+++e+
  gi|313126769|ref|YP_004037039.1| 152 DSDLTSLLTTEQ-SAIFPETEIGLENFLTDGNIYLIQSPAGATSNRYVWVAKMRKQSIKNSMFPLEINEGGIQIYEQ 227
                                       ***********5.555778899*****************************************************97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   5.1e-08   0.00011      21     161 ..      11     138 ..       3     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.1e-08
                            AAA_25  21 prrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                        ++ ++ g +++++ +l+ G pgtGK+ l l+  +  +                +y+ +E++ed++++ ++ +g ++
  gi|313126769|ref|YP_004037039.1|  11 GLDSILNGGIVKNAAVLISGNPGTGKSILGLQYLYNGVDKYD---------EGGIYLTFEEAEDDIQEAAESIGFDR 78 
                                       56778899999*************************997553.........3679*******************886 PP

                            AAA_25  98 ....rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg..dens 161
                                            + ++  v+     ++++L+ +++ +++    +d++  ++++   ++ +v+D+l+ +     de++
  gi|313126769|ref|YP_004037039.1|  79 wseyVEEGKIKVY-----DKRTLLRDGDFSST----LDRILGDLQD-TSYDRLVLDSLTMFQLFfeDEKE 138
                                       3332223333333.....34566555544444....5667777888.45889999999875333225544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   9.3e-07    0.0021       2      28 ..      24      49 ..      23      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.3e-07
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeledd 28
                                      a vl++G++GtGK++++l+ l++   d
  gi|313126769|ref|YP_004037039.1| 24 AAVLISGNPGTGKSILGLQYLYNG-VD 49
                                      579*****************9986.33 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.4e-05     0.032      19      56 ..       5      42 ..       4      56 .. 0.92
   2 ?   -3.3   0.0       1.9   4.3e+03     127     145 ..     112     129 ..      81     150 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                                      E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                             Rad51 19 lttGskklDelLgGGietgsiteifGefrsGktqlcht 56
                                      + tG + lD++L+GGi   +   i G+ ++Gk+ l  +
  gi|313126769|ref|YP_004037039.1|  5 VKTGVEGLDSILNGGIVKNAAVLISGNPGTGKSILGLQ 42
                                      67*******************************88765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
                                       HHHHS-EEEEEEETTTGGG CS
                             Rad51 127 llaedkfallivDsvtaly 145
                                        l+++ +  l++Ds+t ++
  gi|313126769|ref|YP_004037039.1| 112 DLQDTSYDRLVLDSLT-MF 129
                                       5566667777777765.34 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.042       2      84 ..      23     136 ..      22     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakel........gpkplfidtekGlksldadkfpdieswedfldevvel........... 59 
                                       ++ +li G +g+GK+ l +++         +  +++ +e+  ++++ +  ++i +++ + ++v+e            
  gi|313126769|ref|YP_004037039.1|  23 NAAVLISGNPGTGKSILGLQYlyngvdkyDEGGIYLTFEEAEDDIQEAA-ESI-GFDRWSEYVEEGkikvydkrtll 97 
                                       67899****************8888888877788888888776666666.334.77777777777788899999999 PP

                            AAA_24  60 ..............aaeladyktlviDtideleelclae 84 
                                                     + ++  y+ lv+D+++ +  +  +e
  gi|313126769|ref|YP_004037039.1|  98 rdgdfsstldrilgDLQDTSYDRLVLDSLTMFQLFFEDE 136
                                       **************9999************996555444 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.6e-05     0.081       2      62 ..       5      66 ..       5     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeq 62
                                      ++tg + LD++++ G+ k+  ++i + p++Gk+ l l+   n + k++ + ++  +e ++++
  gi|313126769|ref|YP_004037039.1|  5 VKTGVEGLDSILNgGIVKNAAVLISGNPGTGKSILGLQYLYNGVDKYDEGGIYLTFEEAEDD 66
                                      6899*****987526999999*****************999988777766666666655555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.9e-05      0.11      29      80 ..      19      69 ..      10      75 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                             AAA_7 29 llknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqd 80
                                       + ++  vl+ G+ GtGK+++  ++l +   +ky    i ++      ++q+
  gi|313126769|ref|YP_004037039.1| 19 GIVKNAAVLISGNPGTGKSILGLQYLYNGV-DKYDEGGIYLTFEEAEDDIQE 69
                                      5678899**************999665544.577666666666666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012      0.26      25      43 ..      24      42 ..      10     158 .. 0.75
   2 ?   -1.2   0.0         1   2.3e+03      64      91 ..     137     164 ..     103     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                            AAA_16 25 elvllsGesGvGKsslvre 43
                                       +vl+sG++G+GKs l  +
  gi|313126769|ref|YP_004037039.1| 24 AAVLISGNPGTGKSILGLQ 42
                                      589***********98644 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                            AAA_16  64 esaipysa.laqalareellrqlldeaes 91 
                                       ++++ y+  ++++l +++ l+ ll+ ++s
  gi|313126769|ref|YP_004037039.1| 137 KEQRQYLLkFIDIL-KDSDLTSLLTTEQS 164
                                       33345644477777.55666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1604.52
//
Query:       gi|313126770|ref|YP_004037040.1|  [L=212]
Description: flagellin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-34  119.6  15.3    1.9e-34  119.2  15.3    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.036   13.9   0.1      0.054   13.3   0.1    1.3  1  Phi-29_GP16_7   Bacteriophage phi-29 early protein GP16.7
       0.12   12.4   0.6        0.2   11.6   0.6    1.4  1  RF-1            RF-1 domain


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2  15.3   3.1e-38   1.9e-34       1     161 [.      11     192 ..      11     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 3.1e-38
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--T CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklna 77 
                                       G+vgigtlIvfIAmVlVAA+aagvl+ntagflq+ a++ ge+s+++v++++e+++  g    ++ti +i+++v+l+a
  gi|313126770|ref|YP_004037040.1|  11 GQVGIGTLIVFIAMVLVAAIAAGVLVNTAGFLQATAEDAGEQSVNKVTNRVEVLNTHGV-VGDDTIRSINMTVRLAA 86 
                                       89********************************************************5.555579*********** PP

                                       TS--EEGGG-EEEEEESS.--EE--E....................................T-EE-TT-EEEEEEE CS
                    Arch_flagellin  78 Gsspidlnkttisvtddg.qetlltad..............efgivvisdtdgsltng....devlekgekvelevn 135
                                       Gss++d+n+t++ ++ ++ ++tl++ +              efg+ +++d dgs+ +     d ++   ++ ++e  
  gi|313126770|ref|YP_004037040.1|  87 GSSSVDMNETSVKYLSSDtVQTLTNQTtsdgdgtvktadanEFGLDKVTDDDGSFGVLnsmnDRYVATINTSDIEAG 163
                                       ******************555555555**************999999999999998774455666666666666666 PP

                                       --...TTT---TT-EEEEEEE-SSS--EE CS
                    Arch_flagellin 136 vn...eddgitagdevsvevvpenGastt 161
                                       +n    ++g+++gd v++e+++ +G +t 
  gi|313126770|ref|YP_004037040.1| 164 TNdagHSNGLNTGDSVTLEITSRTGGTTQ 192
                                       55**99*******************9876 PP

>> Phi-29_GP16_7  Bacteriophage phi-29 early protein GP16.7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     9e-06     0.054      33      99 ..      47     114 ..      18     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXSSXSSS-HHHHHHHHHHHHTT----HHHHHHHHTT-- CS
                     Phi-29_GP16_7  33 edyledlnkrvvqrtqilselnevisn..rsidktvnlsacevavldlyeqsniripsdiiedlvnqrl 99 
                                       ed  e+  ++v +r ++l     v  +  rsi+ tv l+a   + +d+ e s   + sd ++ l nq  
  gi|313126770|ref|YP_004037040.1|  47 EDAGEQSVNKVTNRVEVLNTHGVVGDDtiRSINMTVRLAAGSSS-VDMNETSVKYLSSDTVQTLTNQTT 114
                                       677777777899999999877666433349********998765.6********************975 PP

>> RF-1  RF-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   3.4e-05       0.2      18      46 ..      45      70 ..      41     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                                      ---SSSSSSGCSSSCEEEEEETTTTEEEE CS
                              RF-1 18 rssGaGGQnVNktesaVrlthlptgvivv 46
                                       ++ aG Q+VNk+  +V++++ + g  vv
  gi|313126770|ref|YP_004037040.1| 45 TAEDAGEQSVNKVTNRVEVLN-THG--VV 70
                                      5789***************77.444..34 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1415.58
//
Query:       gi|313126771|ref|YP_004037041.1|  [L=226]
Description: flagellin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-32  112.0  11.5      4e-32  111.7  11.5    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.099   12.1   3.4      0.042   13.3   1.2    1.5  2  Peptidase_A4    Peptidase A4 family


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7  11.5   4.5e-36     4e-32       1     161 [.      10     206 ..      10     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 4.5e-36
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE...EEE-SSSSSEEEEEEE CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg...dsatngtineitiyvk 74 
                                       G+vgigtlIvfIAmVlVAA+aagvl+ntagflq+ aq+ g+es+++v++++++++  g   d+++  ++++++++v+
  gi|313126771|ref|YP_004037041.1|  10 GQVGIGTLIVFIAMVLVAAIAAGVLVNTAGFLQATAQDAGQESVNKVTNRVDVVSEHGivnDTGDGLAVDSLNLTVR 86 
                                       89*******************************************************95555555556666****** PP

                                       --TTS--EEGGG-EEEEEESS--EE--E................................................. CS
                    Arch_flagellin  75 lnaGsspidlnkttisvtddgqetlltad...............................efgivvisdtdgsltng 120
                                       l+aGs ++ l++tti ++  +++++l +d                               ef  ++++d d+++   
  gi|313126771|ref|YP_004037041.1|  87 LAAGSGSVSLEDTTIKYVSGTTARNLVYDnattdadgtklgnvskydgaaalgndglnntEFAAYALEDGDDTSFPV 163
                                       *********************777777777****************************9999999999999888877 PP

                                       T-EE-TT-EEEEEEE--....TTT---TT-EEEEEEE-SSS--EE CS
                    Arch_flagellin 121 devlekgekvelevnvn....eddgitagdevsvevvpenGastt 161
                                         +  + +++e  +n++    +  g+ +gd v++e+++ +G st 
  gi|313126771|ref|YP_004037041.1| 164 --LSGQADRYEMIINTSvvegNGAGVSTGDSVKLEITSRSGGSTQ 206
                                       ..88899********99***99999***************98875 PP

>> Peptidase_A4  Peptidase A4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0      0.71   6.4e+03     164     177 ..      40      53 ..      32      67 .. 0.52
   2 ?   13.3   1.2   4.7e-06     0.042      12     117 ..      97     210 ..      87     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.71
                      Peptidase_A4 164 Ftdasattsdgksv 177
                                       F +a+a+  +++sv
  gi|313126771|ref|YP_004037041.1|  40 FLQATAQDAGQESV 53 
                                       44444444444332 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.7e-06
                      Peptidase_A4  12 e.sgftsVtgtftvPklslpsggdes.........aeysasawVGiDGaa.dtcssallqaGvdftvd.snGe.qsy 75 
                                       e ++++ V+gt +   +  ++    +          +y  +a  G DG++ ++  +  l+ G d+++   +G+   y
  gi|313126771|ref|YP_004037041.1|  97 EdTTIKYVSGTTARNLVYDNATT--DadgtklgnvSKYDGAAALGNDGLNnTEFAAYALEDGDDTSFPvLSGQaDRY 171
                                       23888888888665555333333..2246688885555599*******99778888999***999988677773344 PP

                      Peptidase_A4  76 dawyewyPayavdfsglavsaGDsvtvtvtatsatsgtvtie 117
                                       +  +     + v+ +g  vs+GDsv++++t+ s  s  v+++
  gi|313126771|ref|YP_004037041.1| 172 EMIIN---TSVVEGNGAGVSTGDSVKLEITSRSGGSTQVILT 210
                                       44444...4666667799***************999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1543.01
//
Query:       gi|313126772|ref|YP_004037042.1|  [L=211]
Description: flagellin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-35  121.5  13.6    4.8e-35  121.2  13.6    1.0  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
        8.2    7.0   9.6        0.6   10.7   2.2    2.3  2  Cadherin-like   Cadherin-like beta sandwich domain


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2  13.6   5.4e-39   4.8e-35       1     161 [.      11     191 ..      11     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 5.4e-39
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--T CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklna 77 
                                       G+vgigtlIvfIAmVlVAA+aagvl+ntagflq+ a++ g+es+++v++++e+++  g+ +++ ti +i ++v+l+a
  gi|313126772|ref|YP_004037042.1|  11 GQVGIGTLIVFIAMVLVAAIAAGVLVNTAGFLQATAEDAGQESVNKVTNRVEVLNTHGEVGDD-TIRNIQMTVRLAA 86 
                                       89********************************************************66665.69*********** PP

                                       TS--EEGGG-EEEEEESS--EE--E.................................T-EE-TT-EEEEEEE--.. CS
                    Arch_flagellin  78 Gsspidlnkttisvtddgqetlltad...............efgivvisdtdgsltngdevlekgekvelevnvn.. 137
                                       Gss++d+n+t++ ++  +++++lt++               ef + +++d dgs+ +     + ++++ +++n++  
  gi|313126772|ref|YP_004037042.1|  87 GSSSVDMNETSVKYLSATTVQTLTNQtdddsegliqeadsdEFALTEVTDDDGSFGVL---NSMNDRYGVTINTTkv 160
                                       ******************555555555************9999999999999999776...5689999999999999 PP

                                       .......TTT---TT-EEEEEEE-SSS--EE CS
                    Arch_flagellin 138 .......eddgitagdevsvevvpenGastt 161
                                               d+g+++g++v++e+++ +G +t 
  gi|313126772|ref|YP_004037042.1| 161 eagdsanHDKGLKTGEQVTLEITSRTGGTTQ 191
                                       *******9999****************8876 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   1.6      0.14   1.3e+03      54      75 ..      77      98 ..      41     142 .. 0.57
   2 ?   10.7   2.2   6.7e-05       0.6      36      81 ..     147     191 ..     124     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.14
                     Cadherin-like 54 tetkdvsLneGrnkieikvtae 75
                                      +  ++v L  G + ++   t+ 
  gi|313126772|ref|YP_004037042.1| 77 NIQMTVRLAAGSSSVDMNETSV 98
                                      3444444444444444443333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.7e-05
                     Cadherin-like  36 edsvatvtvngvaveegstetkdvsLneGrnkieikvtaedgsttr 81 
                                       +++ + vt+n+++ve g++   d  L+ G +++++++t+  g tt+
  gi|313126772|ref|YP_004037042.1| 147 MNDRYGVTINTTKVEAGDSANHDKGLKTG-EQVTLEITSRTGGTTQ 191
                                       4899***********************9*.8899999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1321.46
//
Query:       gi|313126773|ref|YP_004037043.1|  [L=225]
Description: flagellin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-35  122.9  11.4    1.8e-35  122.6  11.4    1.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6  11.4   9.9e-40   1.8e-35       1     159 [.      10     203 ..      10     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 9.9e-40
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE...EEE-SSSSSEEEEEEE CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg...dsatngtineitiyvk 74 
                                       G+vgigtlIvfIAmVlVAA+aagvl+ntagflq+ aq+ g+es+++v++++++++  g   d+a++ t+++++++v+
  gi|313126773|ref|YP_004037043.1|  10 GQVGIGTLIVFIAMVLVAAIAAGVLVNTAGFLQATAQDAGQESVNKVTNRVDVVSTHGivnDEANELTVDSLNLTVR 86 
                                       89*****************************************************9999999999999********* PP

                                       --TTS--EEGGG-EEEEEESS--EE--E...............................................T- CS
                    Arch_flagellin  75 lnaGsspidlnkttisvtddgqetlltad.............................efgivvisdtdgsltngde 122
                                       l+aGs ++ l++tti ++ d ++++l +d                             ef+ ++++d d+++     
  gi|313126773|ref|YP_004037043.1|  87 LAAGSGSVSLEDTTIKYVSDSTARNLVYDnattdadgtslgnvsandknfgsdglnntEFTAYALEDGDDTSFPV-- 161
                                       *********************777777777*********************999999999999999999999888.. PP

                                       EE-TT-EEEEEEE--.....TTT---TT-EEEEEEE-SSS-- CS
                    Arch_flagellin 123 vlekgekvelevnvn.....eddgitagdevsvevvpenGas 159
                                       + ++g+++e+++n++      ++g+ +g+ v++e+++ +G s
  gi|313126773|ref|YP_004037043.1| 162 LSNQGDRYEIVINTSvvedtPTKGLSTGESVKLEITSRSGGS 203
                                       99***********99**9998899*************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1577.85
//
Query:       gi|313126774|ref|YP_004037044.1|  [L=112]
Description: hypothetical protein Hbor_20330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-09   35.5   0.2    1.1e-08   35.0   0.2    1.3  1  HTH_20     Helix-turn-helix domain
    0.00019   21.3   0.0    0.00036   20.4   0.0    1.5  1  HTH_11     HTH domain
    0.00069   19.1   0.0     0.0012   18.3   0.0    1.5  1  HTH_24     Winged helix-turn-helix DNA-binding
     0.0017   18.2   0.0      0.003   17.4   0.0    1.5  1  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0045   16.9   0.1     0.0068   16.3   0.1    1.3  1  MarR_2     MarR family
     0.0048   16.7   0.0     0.0078   16.0   0.0    1.4  1  HTH_IclR   IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.092   12.7   0.0       0.16   12.0   0.0    1.4  1  HTH_Crp_2  Crp-like helix-turn-helix domain
        0.1   12.2   0.0       0.25   10.9   0.0    1.6  2  HTH_47     winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.2   4.8e-12   1.1e-08       2      57 ..       5      58 ..       4      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 4.8e-12
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      + ++AL++    +ilra   +e+++a e+ e ld++ +t+++++++L +agL+e+ 
  gi|313126774|ref|YP_004037044.1|  5 RTLSALGNDYNPDILRAA--DEPHSAQEFSEMLDIPIATCYRRIEELTSAGLLELH 58
                                      678999999999****99..*********************************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.6e-07   0.00036       8      43 ..      18      53 ..      17      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.6e-07
                            HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      +L++a++p s++e +e L++  +t +r+I++L+++g
  gi|313126774|ref|YP_004037044.1| 18 ILRAADEPHSAQEFSEMLDIPIATCYRRIEELTSAG 53
                                      799*******************************99 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.4e-07    0.0012      15      47 ..      23      55 ..      17      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.4e-07
                            HTH_24 15 nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +   s +e +e+l+++++t+ rr+++L+++Gl+
  gi|313126774|ref|YP_004037044.1| 23 DEPHSAQEFSEMLDIPIATCYRRIEELTSAGLL 55
                                      5557778889*********************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-06     0.003      20      54 ..      23      57 ..      18      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                       +p +a+e +e+l++p +++Y+ +++L ++Gl e 
  gi|313126774|ref|YP_004037044.1| 23 DEPHSAQEFSEMLDIPIATCYRRIEELTSAGLLEL 57
                                      57899**************************9885 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     3e-06    0.0068      14      61 ..      19      68 ..      17      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3e-06
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE...EEEESSSSSS CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv...errpgpeDkR 61
                                      L++++++  +++e  + l+++ ++  r++++L +aGL+    r+ ++e++R
  gi|313126774|ref|YP_004037044.1| 19 LRAADEP-HSAQEFSEMLDIPIATCYRRIEELTSAGLLelhDRVLSDEHRR 68
                                      5566665.6*****************************4443445566666 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.5e-06    0.0078      10      51 ..      17      58 ..      17      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.5e-06
                                      CT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 10 dalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      d+l++a+++ + +e ++ +++p +t +R +  L+  G++e +
  gi|313126774|ref|YP_004037044.1| 17 DILRAADEPHSAQEFSEMLDIPIATCYRRIEELTSAGLLELH 58
                                      6899***********************************975 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     7e-05      0.16      20      55 ..      24      60 ..       5      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET.E CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrg.r 55
                                       p + +e ++ml +   t+ r + eL  +gl++ + r
  gi|313126774|ref|YP_004037044.1| 24 EPHSAQEFSEMLDIPIATCYRRIEELTSAGLLELHdR 60
                                      57899***************************95414 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.25      38      77 ..      17      56 ..      12      57 .. 0.94
   2 ?   -1.8   0.0       1.1   2.4e+03      43      57 ..      83      97 ..      64     109 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                      HHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 38 wvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      ++L  aD  +s  + +e +++p+++++  +++L+ agll+
  gi|313126774|ref|YP_004037044.1| 17 DILRAADEPHSAQEFSEMLDIPIATCYRRIEELTSAGLLE 56
                                      578899999*****************************96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                      -EEEEEHHHHHHHHT CS
                            HTH_47 43 aDGkrsLldiAerig 57
                                       DG++  ++i er +
  gi|313126774|ref|YP_004037044.1| 83 FDGQECNIQITERPE 97
                                      477777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 759.87
//
Query:       gi|313126775|ref|YP_004037045.1|  [L=189]
Description: hypothetical protein Hbor_20340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12    9.7   0.0       0.15    9.4   0.0    1.0  1  RdRP_5    Reovirus RNA-dependent RNA polymerase lambda 3


Domain annotation for each model (and alignments):
>> RdRP_5  Reovirus RNA-dependent RNA polymerase lambda 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   8.4e-06      0.15     114     179 ..      94     160 ..      84     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 8.4e-06
                            RdRP_5 114 seaiendakelraesariastfykiassqarqvkld..plrklellllvsarprvnsGlslddpvlrd 179
                                         + e+  ++ +  s  +a++f+ ia+  a qv +d  p + l++lll s+   v+   ++  pvlr+
  gi|313126775|ref|YP_004037045.1|  94 TASFEESIEQRELFSDDVATAFGDIAQWYASQVEADasPAEVLGILLLASD-TDVTFPTKVLAPVLRE 160
                                       445555555444455589***************9876699****9999998.5677777777787776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1199.83
//
Query:       gi|313126776|ref|YP_004037046.1|  [L=122]
Description: response regulator containing chey-like receiver domain and arac-type DNA-binding domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-31  106.9   0.2    6.6e-31  106.8   0.2    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.086   12.8   0.2        4.1    7.4   0.0    2.0  2  ADH_zinc_N    Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.2   7.4e-35   6.6e-31       1     111 [.       5     114 ..       5     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 7.4e-35
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vl+vdD+  +r+ll+qll+ e+  +v+eae+g ea+e+++e ++d++++D+ mp  +G+e+++ei+  dp+  vi++
  gi|313126776|ref|YP_004037046.1|   5 VLVVDDSAFMRNLLKQLLDGEHE-VVGEAENGVEAVEMYRELEPDVVTMDVVMPIRNGIEATTEIKSLDPNSSVIMC 80 
                                       8******************8777.9**************************************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       t+ ++ee + ea++agad++++Kpf++ ++l+a+
  gi|313126776|ref|YP_004037046.1|  81 TSVGQEEKMREAVEAGADGYITKPFQKPNVLQAI 114
                                       ***************************9999998 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1    0.0047        42      16      61 ..       4      49 ..       1      80 [. 0.75
   2 ?    7.4   0.0   0.00045       4.1      20      50 ..      82     114 ..      75     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0047
                                      EEEEEESSHHHHHHHHHT..TESEEEET.TTC.HHHHHHHHHTTTSSEEE CS
                        ADH_zinc_N 16 eviavdsseeklelakkl..Gadeviny.kea.dlverikeltggegvdv 61
                                      +v +vd s+  + l+k+l  G +ev+ + ++  + ve+ +el     +dv
  gi|313126776|ref|YP_004037046.1|  4 TVLVVDDSAFMRNLLKQLldGEHEVVGEaENGvEAVEMYRELE----PDV 49
                                      7999*************88999999999444445555555554....444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00045
                                       EESSHHHHHHHHHTTESEEEET...TTCHHHHHH CS
                        ADH_zinc_N  20 vdsseeklelakklGadeviny...keadlveri 50 
                                        +++eek + a + Gad +i+    k  ++ ++i
  gi|313126776|ref|YP_004037046.1|  82 SVGQEEKMREAVEAGADGYITKpfqKP-NVLQAI 114
                                       67899***************9865322.555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 752.99
//
Query:       gi|313126777|ref|YP_004037047.1|  [L=399]
Description: chemotaxis protein CheC [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-26   92.2   0.4    4.4e-14   52.1   0.1    3.1  3  CheC      CheC-like family
      7e-22   77.4   0.1    1.5e-09   37.9   0.0    2.5  2  CheX      Chemotaxis phosphatase CheX


Domain annotation for each model (and alignments):
>> CheC  CheC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.77   6.9e+03      18      33 ..      29      45 ..      25      45 .. 0.71
   2 !   37.1   0.0   2.3e-13   2.1e-09       1      35 [.     101     135 ..     101     137 .. 0.95
   3 !   52.1   0.1   4.9e-18   4.4e-14       1      35 [.     300     334 ..     300     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.77
                                      HHHHHTCCT.S-EEE-- CS
                              CheC 18 atalatlln.fkidisP 33
                                      +t+++t+ n  ki+ s+
  gi|313126777|ref|YP_004037047.1| 29 LTGIETFVNvTKIEVST 45
                                      47788888877777765 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 2.3e-13
                                       HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---E CS
                              CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPPt 35 
                                       m+ S l+E+gNI+ G++++++a+ l+  idi++Pt
  gi|313126777|ref|YP_004037047.1| 101 MATSGLKELGNIMLGGFLDGWADYLDTSIDITTPT 135
                                       78899*****************************8 PP

  == domain 3  score: 52.1 bits;  conditional E-value: 4.9e-18
                                       HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---E CS
                              CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPPt 35 
                                       m++SA++EigNI+++++++++a+ l+ +idisPPt
  gi|313126777|ref|YP_004037047.1| 300 MQQSAIQEIGNIVTSGFIDGWANALETTIDISPPT 334
                                       99********************************9 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   1.7e-13   1.5e-09       1      75 [.      59     139 ..      59     155 .. 0.89
   2 !   37.0   0.0   3.2e-13   2.8e-09       3      83 ..     262     346 ..     261     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.7e-13
                              CheX   1 vtgiiglaGdisGliilsadeelalkiasal...gedeeeieedvndavgEltNmiaGnak...skl.geevklspP 70 
                                       vt+ ig++G i+G  +l++d++ a++++ al     d+++  e++ + + El N+++G++    +++ + ++++++P
  gi|313126777|ref|YP_004037047.1|  59 VTVHIGFNGGIDGRTVLAFDRQEAVQLVDALvpgAADQPD-GEMATSGLKELGNIMLGGFLdgwADYlDTSIDITTP 134
                                       7999**************************7694455788.********************999777799******* PP

                              CheX  71 lvisg 75 
                                       + ++ 
  gi|313126777|ref|YP_004037047.1| 135 TYVDM 139
                                       *9975 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 3.2e-13
                              CheX   3 giiglaGdisGliilsadeelalkiasalged.eeeieedvndavgEltNmiaGnak....sklgeevklspPlvis 74 
                                       ++ ++ G+ sG+i++ +de++a ++a al+   e +  ++ ++a++E+ N+++ ++     + l+ ++++spP+ ++
  gi|313126777|ref|YP_004037047.1| 262 VVLEFMGTPSGYIAILFDETSADRVADALMPGmEAD-PAMQQSAIQEIGNIVTSGFIdgwaNALETTIDISPPTYVD 337
                                       67899***********************54431333.679*****************999888899*********** PP

                              CheX  75 gkeltisep 83 
                                       + + +i +p
  gi|313126777|ref|YP_004037047.1| 338 DLGSAIIDP 346
                                       998887555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2383.30
//
Query:       gi|313126778|ref|YP_004037048.1|  [L=169]
Description: chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-31  108.7   0.1    2.1e-31  108.2   0.1    1.2  1  CheD      CheD chemotactic sensory transduction


Domain annotation for each model (and alignments):
>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.1   1.2e-35   2.1e-31       1     108 [.      61     160 ..      61     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 1.2e-35
                                       -BS--....SS-TTSCCCBHHHHHHHHHHHHHTTT--GGG-EEEEEE----S.....---SS-HHHHHHHHHHHHHH CS
                              CheD   1 mLPdskeskeksasnpakyadtaielLinellklgakkerleaklaGGAqmfafessksdvlniGerNveavkelLk 77 
                                       mLP +     + ++++akyadtai++L+++++++gak++r++ak+aGG++mf+f+s   +  +iGerN+ a+ke+L+
  gi|313126778|ref|YP_004037048.1|  61 MLPYA-----DGDTDEAKYADTAIRALLEAMVEKGAKRRRIRAKIAGGSTMFEFSS---ADGSIGERNAVAAKETLA 129
                                       78888.....455689**************************************65...4568************** PP

                                       HTT--EEEEEE-SSS-EEEEEETTTTEEEEE CS
                              CheD  78 eegipivaedvggnygRtvlfdpatgkvlvk 108
                                       +e+i +vaedvgg++gR++++d+++g++ v+
  gi|313126778|ref|YP_004037048.1| 130 REDIDLVAEDVGGEHGRSLELDVSNGNLEVR 160
                                       ****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1104.56
//
Query:       gi|313126779|ref|YP_004037049.1|  [L=338]
Description: flagellar protein d/e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-27   93.7   0.1    7.4e-27   93.1   0.1    1.3  1  Arch_fla_DE  Archaeal flagella protein
  ------ inclusion threshold ------
       0.22   11.3   0.0       0.34   10.6   0.0    1.2  1  DUF835       Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.1   8.3e-31   7.4e-27       2      94 ..     234     321 ..     233     322 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 8.3e-31
                       Arch_fla_DE   2 ekpyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelkksel 78 
                                       ekpyL+++p++yaae vv++WlefLv ++g +++++al+yY++++Wi+e+v++eL++yl g++  + ++    ++e+
  gi|313126779|ref|YP_004037049.1| 234 EKPYLSSVPKEYAAERVVFDWLEFLVLKGGFKRTMDALRYYHSVDWITEDVETELHDYLIGFSG-NVSD----TTEF 305
                                       69************************************************************96.4432....4679 PP

                       Arch_fla_DE  79 tvedHvkSllyiekla 94 
                                       +v+dH+ Slly+++la
  gi|313126779|ref|YP_004037049.1| 306 DVDDHHLSLLYVAQLA 321
                                       **************98 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.8e-05      0.34      77     103 ..     247     273 ..     235     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.8e-05
                            DUF835  77 kgvvliDgleyLvlengFesvlkfllt 103
                                       ++ v+ D le+Lvl+ gF+++++ l +
  gi|313126779|ref|YP_004037049.1| 247 AERVVFDWLEFLVLKGGFKRTMDALRY 273
                                       4479******************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2124.99
//
Query:       gi|313126780|ref|YP_004037050.1|  [L=356]
Description: hypothetical protein Hbor_20390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.013   14.3   0.0      0.021   13.7   0.0    1.5  1  MreB_Mbl     MreB/Mbl protein
       0.02   14.4   0.0      0.031   13.8   0.0    1.2  1  DNA_gyraseB  DNA gyrase B
      0.047   13.9   0.0       0.13   12.5   0.0    1.7  1  CheX         Chemotaxis phosphatase CheX
      0.047   13.2   0.0       0.15   11.5   0.0    1.8  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.6e-06     0.021     175     322 ..     200     354 ..      94     356 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.6e-06
                                       -SHHHHHHHHHHHHHHHH..SEE--HHHHHHHHHHH-BSS--HHHHEEEEEEEETTTTCEEEEEEEHHHHHHHHHHH CS
                          MreB_Mbl 175 vaGdeldeaiikyirkky..nlliGertaekikieigsavkeeeeekmeikGrdlvtglpkevevsseevrealkep 249
                                       v+G+e+d  i + + ++   ++ i  +ta++ k e +     e    +++   +   g  +e++++  +v e l + 
  gi|313126780|ref|YP_004037050.1| 200 VTGNEVDRRIANAVEEETqgRVNIDLTTAREYKEEHADFDDFE--AFTDVI--QQPGGGSHEFTIER-SVMEPLDDY 271
                                       6666666666666665441135566666666666544332222..222332..23345566666653.455555555 PP

                                       HHHHHHHHH.HHHHTS-HHHHHH...HHHH-EEEESGGGGSBTH....HHHHHHHHS..S-EEE-SSTTTHHHHHHH CS
                          MreB_Mbl 250 vsaiveavk.evLektppeLaad...ivdrgivltGGgallkgl....dkllseetg..lpvkvaedpltcvakGtg 316
                                       +   v++v+ + L + + + ++     + + ivltGG a + g+    ++ lsee++  ++ + a++p  + a+G+ 
  gi|313126780|ref|YP_004037050.1| 272 LDDAVDEVAnNFLAQLANDHMKPyqlALSKPIVLTGGMACIPGIveefETRLSEELDrdVECIAADRPDLAPAEGAR 348
                                       554444433133444444433222225789*********9988722225567777752277788************9 PP

                                       HTTC-H CS
                          MreB_Mbl 317 kvlekl 322
                                       +++e+l
  gi|313126780|ref|YP_004037050.1| 349 RIAERL 354
                                       999876 PP

>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.9e-06     0.031      25      83 ..     214     275 ..     192     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.9e-06
                       DNA_gyraseB  25 gekaveev..ievevalqwtssyse..nilsFvNniatpeGGtHvdgfksaltktlneyakkk 83 
                                       +e+ ++ +  i +  a +++++ ++    + F+  i++p GG+H+  +++++++ l++y+++ 
  gi|313126780|ref|YP_004037050.1| 214 EEE-TQGRvnIDLTTAREYKEEHADfdDFEAFTDVIQQPGGGSHEFTIERSVMEPLDDYLDDA 275
                                       222.2333358999999999777766899*****************************99875 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05      0.13      38      76 ..     268     308 ..     256     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                              CheX  38 ieedvndavgEltNmiaGnakskl..geevklspPlvisgk 76 
                                        ++++ dav E++N+ + ++ ++    ++++ls P v++g 
  gi|313126780|ref|YP_004037050.1| 268 LDDYLDDAVDEVANNFLAQLANDHmkPYQLALSKPIVLTGG 308
                                       489******************99966779********9986 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.32   1.4e+03       1      21 [.      23      43 ..      23     139 .. 0.75
   2 ?   11.5   0.0   3.4e-05      0.15     207     266 ..     284     350 ..     261     351 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.32
                                      EEEEE-SSEEEEEEEETTTEE CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmdekgev 21
                                      vG+ +GsT t    +d +g++
  gi|313126780|ref|YP_004037050.1| 23 VGVKLGSTRTILQFYDGDGDL 43
                                      788899998887777777664 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.4e-05
                                       HHHHHTT---SS.......EEEESGGGG-HHHHHHH.....HHHH-S.-EE--GGGGGHHHHHHHHH CS
                       BcrAD_BadFG 207 ialisrsggvtde......vtltGGvakneaavkelrklvkenygev.kininpdsiytgalGAalf 266
                                        a+       + +      ++ltGG+a   ++v+e+++ ++e+  +  +      ++ ++a GA  +
  gi|313126780|ref|YP_004037050.1| 284 LAQLANDHMKPYQlalskpIVLTGGMACIPGIVEEFETRLSEELDRDvECIAADRPDLAPAEGARRI 350
                                       3333333222222333344************************9876688899999*******9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2107.84
//
Query:       gi|313126781|ref|YP_004037051.1|  [L=326]
Description: sugar kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-66  222.9   0.1    6.2e-66  222.7   0.1    1.0  1  PfkB            pfkB family carbohydrate kinase
    0.00055   19.4   0.0    0.00078   18.9   0.0    1.1  1  Phos_pyr_kin    Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.19   11.2   0.0       0.32   10.4   0.0    1.3  1  Methyltransf_5  MraW methylase family


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.7   0.1     1e-69   6.2e-66       3     301 ..      13     316 ..      11     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 222.7 bits;  conditional E-value: 1e-69
                                       EEEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEE CS
                              PfkB   3 kvvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdt 79 
                                       +vvv Ge+lid+ ++ ++    l  v++++k++GGa+aNvAval++l    af ++vGdD+fG+fl e+l+++g+dt
  gi|313126781|ref|YP_004037051.1|  13 RVVVAGEMLIDFLPDRQG---PLESVASFTKRPGGAPANVAVALSQLDETPAFATRVGDDPFGDFLVETLSEAGLDT 86 
                                       79*************999...888***************************************************** PP

                                       TTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES..EECTTSHHHHHHHHHHH CS
                              PfkB  80 dyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisg..llsselpeavleelaea 154
                                       + v++d++++t+la++ + e+++r + f+r  +ad + ++   + + l++ad+++++g  l ++++++a++ +++  
  gi|313126781|ref|YP_004037051.1|  87 ELVERDPEAKTSLAFVALGEEADRGFSFYRDRTADTRMQPGSVPDATLASADWVHVGGvtLADEPSRTATFDLMRRG 163
                                       ***************************************999*********************************** PP

                                       HHHTTE..EEEEECESSSHH..HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEE CS
                              PfkB 155 aknggt..fdpnlldplgaq..fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtl 227
                                         +g t  fdpn ++ l+++  f   + e+++lad++k++ e+leal  e   d+e  ++++      g+ tv+ tl
  gi|313126781|ref|YP_004037051.1| 164 QDAGATvsFDPNARPELWDEfdFEASVAEAFELADVVKATPEDLEALDYEG--DPETMARRIRS---DGPHTVFLTL 235
                                       ******************99*************************998888..99999999888...9********* PP

                                       GGGEEEEEE........TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSS CS
                              PfkB 228 GkeGalvve........kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgai 296
                                       G++G+lv+         +++++ ++  + v++vDttGAGD+f++g++aal+eg+sl+e l fanavAa++++ +ga+
  gi|313126781|ref|YP_004037051.1| 236 GSKGSLVSAseespwvtEETVVSHEG-YDVEPVDTTGAGDAFTAGVVAALVEGQSLAETLSFANAVAAVTTTATGAM 311
                                       ********99*****98888888888.99************************************************ PP

                                       TCSCC CS
                              PfkB 297 aslpt 301
                                       ++lp+
  gi|313126781|ref|YP_004037051.1| 312 TALPD 316
                                       *9986 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.3e-07   0.00078     109     226 ..     186     299 ..     176     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-07
                                       HHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-S.SSEEEEEEEETSSEEE CS
                      Phos_pyr_kin 109 vealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghleg.eeavvtdvlydgeeve 184
                                       +ea   e ++la+v+    +++eaL     + e d +++a+++++ g ++V ++ g   +  +a  +  ++++e+v+
  gi|313126781|ref|YP_004037051.1| 186 FEASVAEAFELADVVKATPEDLEAL-----DYEGDPETMARRIRSDGPHTVFLTLGSKGSlVSASEESPWVTEETVV 257
                                       5556666677777776655566655.....34779999**************9766532233333357899****** PP

                                       EEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHH CS
                      Phos_pyr_kin 185 eleaerietknthGtGCtlssaiaaelakgesleeAvkkAke 226
                                         e+  +e  +t G+G+++ + + a l +g+sl e+++ A++
  gi|313126781|ref|YP_004037051.1| 258 SHEGYDVEPVDTTGAGDAFTAGVVAALVEGQSLAETLSFANA 299
                                       ***********************************9887764 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.4e-05      0.32     109     130 ..     107     128 ..     100     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.4e-05
                                       -GGG---SSS--BS---S-TTS CS
                    Methyltransf_5 109 kaerGFsfaedapLDmRmdqsa 130
                                       +a+rGFsf +d + D Rm++ +
  gi|313126781|ref|YP_004037051.1| 107 EADRGFSFYRDRTADTRMQPGS 128
                                       789***************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1976.66
//
Query:       gi|313126782|ref|YP_004037052.1|  [L=83]
Description: hypothetical protein Hbor_20410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.15   12.2   0.0    1.1  1  RelE      RelE toxin of RelE / RelB toxin-antitoxin system


Domain annotation for each model (and alignments):
>> RelE  RelE toxin of RelE / RelB toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.5e-06      0.15       4      34 ..      14      44 ..      12      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-06
                              RelE  4 fktkwfarwarkekisdeeLleaveevekGl 34
                                      f   ++ar+ar+ +i++++L+ea+ e ++G 
  gi|313126782|ref|YP_004037052.1| 14 FDGDVIARVAREMSIEEATLWEAIAEHQHGV 44
                                      5566899*******************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 551.69
//
Query:       gi|313126783|ref|YP_004037053.1|  [L=776]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-42  145.8  17.0    2.6e-42  145.4  17.0    1.1  1  HisKA_7TM    N-terminal 7TM region of histidine kinase
    3.3e-23   82.1  11.0    1.2e-11   44.9   0.2    3.4  4  PAS_4        PAS fold
    3.2e-22   78.7   0.0    9.9e-10   38.4   0.0    2.9  2  PAS          PAS fold
      4e-15   56.0   0.0    7.7e-09   35.7   0.0    2.8  3  PAS_9        PAS domain
    4.4e-13   49.3   0.3    2.1e-11   43.9   0.0    3.3  4  PAS_3        PAS fold
    1.1e-11   45.2   0.1    4.9e-11   43.1   0.0    2.0  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.1e-10   39.8   0.0    0.00092   19.2   0.0    2.9  2  PAS_8        PAS domain
    8.5e-09   35.4   0.2    2.4e-06   27.5   0.1    2.5  2  HATPase_c_2  Histidine kinase-like ATPase domain
    2.9e-07   30.6   1.2     0.0019   18.3   0.0    4.0  3  PAS_7        PAS fold
    2.5e-05   24.2   0.7    5.6e-05   23.1   0.7    1.6  1  HisKA        His Kinase A (phospho-acceptor) domain
    0.00039   20.0   0.2     0.0012   18.5   0.2    1.9  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
     0.0056   16.5   0.3      0.037   13.9   0.1    2.2  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


Domain annotation for each model (and alignments):
>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4  17.0   1.7e-45   2.6e-42       3     220 .]      15     235 ..       9     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 1.7e-45
                         HisKA_7TM   3 lisallslvlaiyaw.rrrskpgaraflllllavalwslgyalellattleakllwaklqylgivfipvlwllfale 78 
                                       l+++++++vl  y +  rr    + +f++l la+a+w+++y+++l+++ l +kllw++l +++++f+p+lw++f+l 
  gi|313126783|ref|YP_004037053.1|  15 LCASVTIIVLLRYRFyARRV---RIPFAVLNLACAIWATAYGFQLMVPLLGEKLLWFSLWQVAAAFTPTLWFVFTLV 88 
                                       23334444444444235555...9***************************************************** PP

                         HisKA_7TM  79 ytgkrrwltrrrlallllvp..vltlilvltnplhhlfy.....vsagsfvvlefehGplfwvhlaysyllliagvv 148
                                       y+g++  l+rr +a+l+++p  v++l lv    +  lf      +s++s v+l+++hGpl+ vhl+y+ +ll++g+v
  gi|313126783|ref|YP_004037053.1|  89 YAGDETILSRRSVAALCIEPtvVAILGLVGVVGISDLFVgdfgrISTSSGVFLSMTHGPLYNVHLLYVSALLLVGSV 165
                                       ***9999***********9976566666655667789966778999***************88************** PP

                         HisKA_7TM 149 lliralirssglyrrqalllligllvPwlanllyllglsplpgidltplafaltglllaiaifryrlldivP 220
                                       ++ r l+r +g yrr +++ll ++ +P++a+++ ll  +p+p++d+tp+a+ l+++++++++ + +l+d++P
  gi|313126783|ref|YP_004037053.1| 166 VMGRLLVRGDGNYRRGTVVLLSAASIPVFAFAMQLL--GPFPRFDVTPIALGLSSIVVLFGLRSDDLFDVTP 235
                                       ***********************************6..79999****************************9 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.2   7.8e-15   1.2e-11       3     110 .]     244     344 ..     242     344 .. 0.90
   2 !   43.8   0.1   1.7e-14   2.5e-11       2     110 .]     354     461 ..     353     461 .. 0.90
   3 ?   -2.6   0.1       4.3   6.4e+03      51      83 ..     506     540 ..     485     541 .. 0.66
   4 ?   -2.8   0.2       5.1   7.6e+03      44      74 ..     681     711 ..     662     718 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 7.8e-15
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                        + d+ +vld+ grv+ +N+aa  lf +p+ee++G++ a++   ++    + al  + +++  i+ ++    +ge r
  gi|313126783|ref|YP_004037053.1| 244 EMRDGMVVLDDRGRVVELNPAALPLFTVPQEEIIGSHIADI---CHNSLGMYALLDADRSRLDITVED----DGEKR 313
                                       678999**********************************8...667777777777777777777777....9**** PP

                             PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +ye +++Pl   +G  +g+ +++rD+Terrr
  gi|313126783|ref|YP_004037053.1| 314 YYEATATPLGSGEGHDRGWALVLRDTTERRR 344
                                       *****************************97 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 1.7e-14
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +++ d++ vld+dg+ +ya++a+ +++g+p+ el G+  + +++p+ d+++++++ + v + + +i+ +  +++ +g
  gi|313126783|ref|YP_004037053.1| 354 ENSRDLISVLDADGNHTYASPASKHVLGIPRSELEGSNSFkQIHPD-DREDIRSQFDTVESRD-TIRAEFRHKHaDG 428
                                       7999*********************************999788888.***********97775.55555555555** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       ++r+++  ++ l+d +  v g+++ +rD+T r+r
  gi|313126783|ref|YP_004037053.1| 429 SWRVLDAVAVNLLD-DPAVGGIVINARDVTSRHR 461
                                       *********99997.8889*************97 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.3
                             PAS_4  51 rleralrrvlegeepiefleelll..pgeerhyel 83 
                                        +++  + +++ +e++++ + +l+  ++e+r++e+
  gi|313126783|ref|YP_004037053.1| 506 TIQQKAKSLVSLGERAREIDRTLHgeDRERRPVEV 540
                                       55555556666677777777777777888888886 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.1
                             PAS_4  44 lpeedaarleralrrvlegeepiefleelll 74 
                                        pe+d ++ ++ ++  +++ ++i ++ e+++
  gi|313126783|ref|YP_004037053.1| 681 PPERDEQDESAEDDTTAATADTIGTESERTH 711
                                       4555888999999999999999888888877 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   6.6e-13   9.9e-10       9     112 ..     244     338 ..     239     339 .. 0.92
   2 !   37.2   0.0   1.6e-12   2.4e-09       2     111 ..     348     454 ..     347     456 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 6.6e-13
                                       HSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSS CS
                               PAS   9 slpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgr 85 
                                        ++d+++v+D +gr+++ N+aa  l+  ++ee++g+++ d  h          l  +++   +++  +i+++  dg+
  gi|313126783|ref|YP_004037053.1| 244 EMRDGMVVLDDRGRVVELNPAALPLFTVPQEEIIGSHIADICH--------NSLGMYALLDADRSRLDITVED-DGE 311
                                       589************************************7664........5688888888888889******.*** PP

                                       EEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  86 pihlevraspvrdaggeilgflgvlrd 112
                                       +++ e +a+p+++++g  +g+ +vlrd
  gi|313126783|ref|YP_004037053.1| 312 KRYYEATATPLGSGEGHDRGWALVLRD 338
                                       **************************9 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 1.6e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+++e+++d i v+D+dg+ +y+++a    lG++r+e+ g++ + +ih++d+    e ++ +  + e++ + +  
  gi|313126783|ref|YP_004037053.1| 348 KFRTLIENSRDLISVLDADGNHTYASPASKHVLGIPRSELEGSNSFKQIHPDDR----EDIRSQFDTVESRDTIRAE 420
                                       689*************************************************65....5555555555555555555 PP

                                       EEC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                               PAS  79 fkl..rdgrpihlevraspvrdaggeilgflgvlr 111
                                       f+    dg+ + l+  a+ ++d      g++  +r
  gi|313126783|ref|YP_004037053.1| 421 FRHkhADGSWRVLDAVAVNLLDDPAVG-GIVINAR 454
                                       555555666666666666666665543.5555555 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   5.2e-12   7.7e-09       2     104 .]     247     341 ..     246     341 .. 0.93
   2 !   17.3   0.0   2.8e-06    0.0042       4     103 ..     360     457 ..     357     458 .. 0.85
   3 ?   -3.4   0.0       7.7   1.2e+04      59      81 ..     512     541 ..     489     544 .. 0.64

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 5.2e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       dg+++ ++ gr++  N+aal l+    ee++g +i d++    ++   + a+l++ r    ++  + + ++ge+ ++
  gi|313126783|ref|YP_004037053.1| 247 DGMVVLDDRGRVVELNPAALPLFTVPQEEIIGSHIADIC----HNSLGMYALLDADR----SRLDITVEDDGEKRYY 315
                                       7999999********************************....99999999999999....67777778889999** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       ++ta+p+ +++g  +g++++lrD te
  gi|313126783|ref|YP_004037053.1| 316 EATATPLGSGEGHDRGWALVLRDTTE 341
                                       ************************98 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.8e-06
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvl 79 
                                       i + + dg+ +ya++a + +lG  + e+ g + +  +  +p+++e++r ++++ ++    + e  + + +g+    +
  gi|313126783|ref|YP_004037053.1| 360 ISVLDADGNHTYASPASKHVLGIPRSELEGSNSFKQI--HPDDREDIRSQFDTVESrDTIRAEFRHKHADGSWRVLD 434
                                       556779**************************88888..8**************99988999999999999999977 PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDit 103
                                       + a+ + d d  + gi++  rD+t
  gi|313126783|ref|YP_004037053.1| 435 AVAVNLLD-DPAVGGIVINARDVT 457
                                       55555544.45677799******9 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7.7
                             PAS_9  59 k.......kerevevvlirkngetfwvllt 81 
                                       k        +re + +l  +++e+ +v++t
  gi|313126783|ref|YP_004037053.1| 512 KslvslgeRAREIDRTLHGEDRERRPVEVT 541
                                       233334336677777777777788888776 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.65   9.6e+02       2      32 ..     259     287 ..     258     297 .. 0.89
   2 ?   -2.8   0.0       5.6   8.4e+03      62      78 ..     309     325 ..     306     332 .. 0.79
   3 !   43.9   0.0   1.4e-14   2.1e-11       2      75 ..     370     440 ..     369     445 .. 0.90
   4 ?   -0.5   0.0         1   1.5e+03      24      48 ..     522     546 ..     514     553 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.65
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhp 32 
                                       + ++++   ++ + +ee++g+  +++d++h 
  gi|313126783|ref|YP_004037053.1| 259 VELNPAALPLFTVPQEEIIGS--HIADICHN 287
                                       6789999999999********..*******5 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.6
                             PAS_3  62 dGeyrwveararvirde 78 
                                       dGe r+ ea+a+++ + 
  gi|313126783|ref|YP_004037053.1| 309 DGEKRYYEATATPLGSG 325
                                       9999*******998444 PP

  == domain 3  score: 43.9 bits;  conditional E-value: 1.4e-14
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvi 75 
                                       +y+s++ +++lG+ ++el+g+  +  + +hp+Dre +r++++++  ++  +  e+R +++dG++r ++a a+ +
  gi|313126783|ref|YP_004037053.1| 370 TYASPASKHVLGIPRSELEGS--NSFKQIHPDDREDIRSQFDTVE-SRDTIRAEFRHKHADGSWRVLDAVAVNL 440
                                       79*******************..******************9775.5555******************998766 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1
                             PAS_3  24 eswldlvhpeDrervrealqealkk 48 
                                       +++   +h eDrer   ++ +++++
  gi|313126783|ref|YP_004037053.1| 522 REIDRTLHGEDRERRPVEVTDVIAE 546
                                       5677889*******99998888866 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.2   4.8e+03      36      47 ..     300     311 ..     280     316 .. 0.81
   2 !   43.1   0.0   3.3e-14   4.9e-11       8     109 ..     578     677 ..     573     680 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.2
                                       TEEEEEEEESSS CS
                         HATPase_c  36 ddlvisveDnGi 47 
                                        +l i+veD+G 
  gi|313126783|ref|YP_004037053.1| 300 SRLDITVEDDGE 311
                                       58999*****96 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 3.3e-14
                                       HHHHHHHHHHHHHHS.TTTEEEEEEEEEE....TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHH CS
                         HATPase_c   8 qiisnlvdNavkfat.kageieveikase....ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGls 79 
                                        +i n+vdNa++++    +++ ++++  +    d+++i+v DnG+Gip ++l     ++   +++++ +  +GlGl 
  gi|313126783|ref|YP_004037053.1| 578 TAITNVVDNALEHNDrAIPRVGISVS--KsihtDEVEIRVVDNGPGIPASELA----ALEA-GTETQLQHVSGLGLW 647
                                       6799********93323334455555..445669*******************....3333.334466899****** PP

                                       HHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlp 109
                                       +vk +    + +i++e+++grGt ++++++
  gi|313126783|ref|YP_004037053.1| 648 LVKWILAGSHATIEFEERSGRGTAVVMRFQ 677
                                       ***96663555*************998876 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.3e-06    0.0035       6      45 ..     241     281 ..     239     302 .. 0.81
   2 !   19.2   0.0   6.2e-07   0.00092       1      64 [.     347     409 ..     347     412 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                             PAS_8   6 lfesspdgiavvdlgdrivdvNqaalellGys.adlkgell 45 
                                       +f  ++dg++v+d+ +r+v+ N+aal l+ ++ ++++g+ +
  gi|313126783|ref|YP_004037053.1| 241 VFSEMRDGMVVLDDRGRVVELNPAALPLFTVPqEEIIGSHI 281
                                       67789******995557************988888888655 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 6.2e-07
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpvlrplle.daeqlld 64 
                                       +++r+l+e+s+d i v+d++++ +++ +a  + lG +   ++ +  + +++++p  + d++  +d
  gi|313126783|ref|YP_004037053.1| 347 AKFRTLIENSRDLISVLDADGNHTYASPASKHVLGIP--RSELEGSNSFKQIHPDDReDIRSQFD 409
                                       58****************6666*************66..44444448888888888866666655 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.013        19      60     105 ..     295     335 ..     268     342 .. 0.80
   2 !   27.5   0.1   1.6e-09   2.4e-06      30     124 ..     574     675 ..     559     676 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                       HATPase_c_2  60 lesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlali 105
                                       l+ d  +l ++v+D+G+   +e+ + p      +s++ ++rG al+
  gi|313126783|ref|YP_004037053.1| 295 LDADRSRLDITVEDDGEKRYYEATATPL-----GSGEGHDRGWALV 335
                                       55667789**********7777666553.....7889999999886 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1.6e-09
                       HATPase_c_2  30 deirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalik 106
                                       +++  a++ ++ Na eh+ +  p   ++v+ ++ +++++++v D+Gpg ++++l+  ++ + ++ +  +G+Gl l+k
  gi|313126783|ref|YP_004037053.1| 574 NHVGTAITNVVDNALEHNDRAIPRVGISVSKSIHTDEVEIRVVDNGPGIPASELAALEAGTETQLQHVSGLGLWLVK 650
                                       578889999999************************************999999988888889************98 PP

                       HATPase_c_2 107 glvDev....ey...dgegnvvtms 124
                                        +        e+   +g+g+ v+m+
  gi|313126783|ref|YP_004037053.1| 651 WILAGShatiEFeerSGRGTAVVMR 675
                                       7655442222447677778888776 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.3e-06    0.0019       2      55 ..     243     293 ..     242     347 .. 0.64
   2 !    7.2   0.0    0.0038       5.6       5     115 .]     357     464 ..     353     464 .. 0.63
   3 ?   -1.2   0.1       1.5   2.2e+03      33      88 ..     513     570 ..     504     576 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg 55 
                                       ++m++G++v+D ++r+v  N   l l+ +p+e + +g +++++++     g ++
  gi|313126783|ref|YP_004037053.1| 243 SEMRDGMVVLDDRGRVVELNPAALPLFTVPQEEI-IGSHIADICHNSL--GMYA 293
                                       68********************************.9******998664..3333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0038
                             PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg.agdveaeverrlaaaragkphsfer 80 
                                       ++ isv+Dad++ +       ++l++p++ ++   +++++     +r++++ + d+ +  +++ a+ r+++++   r
  gi|313126783|ref|YP_004037053.1| 357 RDLISVLDADGNHTYASPASKHVLGIPRSELEGSNSFKQIHP--DDREDIRsQFDTVESRDTIRAEFRHKHADGSWR 431
                                       556888888888888888888888888888888888888854..455555522333333344445555555555555 PP

                             PAS_7  81 erpdgrvievrgnpl....pdgGfVttytDiTerrraee 115
                                         ++       +  l    + gG+V+   D+T r+r e+
  gi|313126783|ref|YP_004037053.1| 432 VLDA------VAVNLlddpAVGGIVINARDVTSRHRYEQ 464
                                       4433......333332332459*************9986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.5
                             PAS_7  33 elvqvgvpleellrynaergefg.agdveaeverrlaaaragkph.sfererpdgrvi 88 
                                       +lv  g + +e+ r ++ +   + + +v + +++ l+a+++ +p+  ++ + pd++++
  gi|313126783|ref|YP_004037053.1| 513 SLVSLGERAREIDRTLHGEDRERrPVEVTDVIAEKLEAMQESNPSlVVNTHLPDEQWV 570
                                       6677777777777777444333337888888999999998877661455667777765 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.7   3.7e-08   5.6e-05       6      60 ..     470     523 ..     465     530 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.7e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA   6 lagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLd 60 
                                          + H+Lr+ +++ilg a++L +    +++ ++ ++ti++ a+ l +l e+ ++
  gi|313126783|ref|YP_004037053.1| 470 NRILRHDLRNDMNVILGHADLLGEM-TDDPKRRAHVKTIQQKAKSLVSLGERARE 523
                                       56789*****************663.67899999**********99888666655 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   7.9e-07    0.0012     123     161 ..     453     490 ..     426     493 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.9e-07
                         HisKA_4TM 123 aradasrakrisdalafvndlirhdlrndlvvirgyaea 161
                                       ar d +  +r  + l  +n ++rhdlrnd++vi g+a+ 
  gi|313126783|ref|YP_004037053.1| 453 AR-DVTSRHRYEQRLRVLNRILRHDLRNDMNVILGHADL 490
                                       44.55556788999*********************9975 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.67     1e+03      16      42 ..     296     310 ..     279     314 .. 0.53
   2 !   13.9   0.1   2.5e-05     0.037       5      52 ..     578     629 ..     574     643 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.67
                       HATPase_c_3  16 dAdaenvkievnknrgktgeivieDdG 42 
                                       dAd  +             +i++eDdG
  gi|313126783|ref|YP_004037053.1| 296 DADRSRL------------DITVEDDG 310
                                       3444444............55555555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.5e-05
                       HATPase_c_3   5 kAlaelvdNsldAdaen...vkievnknr.gktgeivieDdGkGmseeelkn 52 
                                       +A++ +vdN+l+ + +    v i+v+k   +++ ei++ D+G G++ +el  
  gi|313126783|ref|YP_004037053.1| 578 TAITNVVDNALEHNDRAiprVGISVSKSIhTDEVEIRVVDNGPGIPASELAA 629
                                       6999*******97776666689999987657889************999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (776 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 4973.94
//
Query:       gi|313126784|ref|YP_004037054.1|  [L=380]
Description: acyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-47  160.7   1.1    3.7e-47  160.3   1.1    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      2e-38  131.5   0.5    3.9e-38  130.6   0.1    1.7  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    8.5e-24   83.6   0.1    1.3e-23   83.0   0.1    1.3  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      2e-16   60.5   1.5    3.3e-16   59.8   1.5    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.3   1.1   8.3e-51   3.7e-47       1     149 [.     230     378 ..     230     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 8.3e-51
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       g G++++m+tl+ +R+++aa + gla+ a+e a  ya +r++fgkp+ +++++r+kl++m+ ++e arll+ +aa +
  gi|313126784|ref|YP_004037054.1| 230 GAGWKQTMKTLDGGRISIAALSTGLAQGAYEAAKTYAGDREQFGKPISKFDAIRDKLVDMHRKTERARLLTHKAATR 306
                                       68*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       +dag+  + e+++aKl ase+a+eva++a+q+lGg+Gy+e+ + +r+yrda++++igeGtseiq ++i+r l
  gi|313126784|ref|YP_004037054.1| 307 YDAGESVSRESALAKLDASEAAREVAEDAVQVLGGYGYTEDFAPQRFYRDAKLMEIGEGTSEIQHLVIGREL 378
                                       ********************************************************************9976 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.1   8.7e-42   3.9e-38       2     113 .]       7     118 ..       6     118 .. 0.99
   2 ?   -3.2   0.0       2.8   1.3e+04      28      45 ..     327     344 ..     303     355 .. 0.58

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 8.7e-42
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                        e++++rdtvref+eee+ p a+e+++e++fp+e++++la+l++lg+++ eeygG+g+d l +a+v+eel+r++ g+
  gi|313126784|ref|YP_004037054.1|   7 SEHRMIRDTVREFCEEEISPIAQEIEDEHRFPEEIFEELADLDMLGVPISEEYGGLGGDQLMYALVTEELGRVSGGI 83 
                                       69*************************9************************************************* PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                       +l++++h sl++++i  fGteeqk+r+L++la+ge
  gi|313126784|ref|YP_004037054.1|  84 GLSYAAHISLASKPIELFGTEEQKERWLRPLAEGE 118
                                       *********************************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.8
                                       HHTSGHHHHHHHHHHTTC CS
                     Acyl-CoA_dh_N  28 eegefprelwkklaelGl 45 
                                       +++e+ +++++ l+  G+
  gi|313126784|ref|YP_004037054.1| 327 AAREVAEDAVQVLGGYGY 344
                                       222455555555555555 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.1   2.9e-27   1.3e-23       2      97 .]     123     218 ..     122     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 2.9e-27
                                       EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE...GGGEEE-- CS
                     Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvp.rdapgvsvrr 77 
                                        alTEp++Gsd+ +++t +ae+dg+e+v++G+K++itna+ a  +lv a t+  ++++g+s+f+v+ + + g++v+ 
  gi|313126784|ref|YP_004037054.1| 123 WALTEPSSGSDASDMDT-TAEKDGDEWVIDGSKQFITNANVAGSVLVKAVTDPGEGYDGISTFIVDpEEDDGFEVTT 198
                                       599**************.99999999************************544448**********78888****** PP

                                       ---BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                       +++k+Gl+  pt+el f++v
  gi|313126784|ref|YP_004037054.1| 199 VWDKMGLNCSPTCELAFDEV 218
                                       *****************986 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   1.5   7.4e-20   3.3e-16       2     127 ..     246     361 ..     245     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 7.4e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       +iaa  +G+A++a++++  +a++r +  +g++++ + a+  +l ++  + + Ar+l+++aa+r     +ag++v   
  gi|313126784|ref|YP_004037054.1| 246 SIAALSTGLAQGAYEAAKTYAGDREQ--FGKPISKFDAIRDKLVDMHRKTERARLLTHKAATR----YDAGESV--- 313
                                       79************************..***********************************....9*****9... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                         +e+++a++ a+e a++++++++++ Gg++++++   qR++RDa+ ++
  gi|313126784|ref|YP_004037054.1| 314 -SRESALAKLDASEAAREVAEDAVQVLGGYGYTEDFAPQRFYRDAKLME 361
                                       .999*****************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2482.12
//
Query:       gi|313126785|ref|YP_004037055.1|  [L=144]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-39  134.1   3.2    5.4e-39  133.9   3.2    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.072   12.7   0.5        1.7    8.3   0.1    2.1  2  SpoVAE    Stage V sporulation protein AE1


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   3.2     6e-43   5.4e-39       1     141 []       1     141 [.       1     141 [. 0.98

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 6e-43
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+rIlV++Dgs+++ +A+++A++la +++ae+++l+v+d r sg+  +a ++++  e+ +e  +++ ++ ++++e 
  gi|313126785|ref|YP_004037055.1|   1 MYDRILVPTDGSDCANAAVDHAADLASKYDAEVHILYVVDVRVSGQGQWALDTEAVYEAGQEHGQAVVEQVAEQLES 77 
                                       9*************************************************999999999999999999999****** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       + v+v+ vv+ g p++ei e+++e  +dl+V+G++gr+gl+r+llGSv+e+++r +++pVl Vr
  gi|313126785|ref|YP_004037055.1|  78 KAVAVKPVVKTGVPGREIREYVDEGACDLVVMGTHGRTGLDRYLLGSVAERIVRTSDVPVLTVR 141
                                       *************************************************************998 PP

>> SpoVAE  Stage V sporulation protein AE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1    0.0087        78       2      21 ..       5      24 ..       4      33 .. 0.85
   2 ?    8.3   0.1   0.00019       1.7       8      59 ..      60     111 ..      56     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0087
                            SpoVAE  2 vilvtDGDevakravekaak 21
                                      +++ tDG ++a+ av++aa+
  gi|313126785|ref|YP_004037055.1|  5 ILVPTDGSDCANAAVDHAAD 24
                                      5566************9986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00019
                            SpoVAE   8 GDevakravekaakeiggrcisasagnPtklsgeelvelikeakkdpvlvmv 59 
                                       G e+ + +ve++a++++ + ++      t + g+e+ e++ e + d v++  
  gi|313126785|ref|YP_004037055.1|  60 GQEHGQAVVEQVAEQLESKAVAVKPVVKTGVPGREIREYVDEGACDLVVMGT 111
                                       889999***************************************9987644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1017.37
//
Query:       gi|313126786|ref|YP_004037056.1|  [L=265]
Description: serine/threonine protein kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-12   45.7   0.0    8.9e-12   45.0   0.0    1.2  1  RIO1            RIO1 family
    2.1e-06   27.2   0.0    3.6e-06   26.5   0.0    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    2.5e-06   27.0   0.0    3.4e-06   26.6   0.0    1.1  1  Pkinase         Protein kinase domain
    6.2e-05   23.0   2.0     0.0012   18.9   0.4    2.4  2  APH             Phosphotransferase enzyme family
    0.00023   20.9   0.0    0.00034   20.3   0.0    1.3  1  WaaY            Lipopolysaccharide core biosynthesis protein 
     0.0019   17.5   0.0     0.0021   17.4   0.0    1.2  1  Pkinase_Tyr     Protein tyrosine kinase
  ------ inclusion threshold ------
      0.038   13.9   0.1      0.056   13.4   0.1    1.3  1  Kinase-PolyVal  Serine/Threonine/Tyrosine Kinase found in pol


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   3.5e-15   8.9e-12      54     151 ..      95     190 ..      91     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 3.5e-15
                                       HHHHHHHHHHHHHHTT--S--EEEEET....TEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTST CS
                              RIO1  54 waekEfrnLkrleeagvpvPkpielkr....hvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeag 126
                                       +ae E ++ +r++e+g+++P+p+e  +     +lv+e+++       +l++++ +e  ++l+ +v +++r +  +++
  gi|313126786|ref|YP_004037056.1|  95 MAEHELEATRRMREIGLNAPEPVESFEvdglGILVLEYLQ----DFRTLDKLD-REVEKRLAPQVFSSLRTMH-DHN 165
                                       79*********************987644457********....677788888.5566778888888776666.*** PP

                                       EEESS-STTSEEEETTEEEE--GTT CS
                              RIO1 127 lvHaDLSeyNvlvdedkvviIDvsQ 151
                                       lvH+DL   Nvl+ +d+v++ID   
  gi|313126786|ref|YP_004037056.1| 166 LVHGDLRAENVLIVDDEVYFIDATN 190
                                       **********************765 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.4e-09   3.6e-06      58     165 ..      96     187 ..      82     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.4e-09
                               Kdo  58 avrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrliakl 134
                                       a  E+++ +r++e g+++p+pv + +v        +l+ e l++++ L++l +       e++++l  +v    + +
  gi|313126786|ref|YP_004037056.1|  96 AEHELEATRRMREIGLNAPEPVESFEVDG----LGILVLEYLQDFRTLDKLDR-------EVEKRLAPQVFSSLRTM 161
                                       5578999***************8776543....359************98766.......6999************* PP

                               Kdo 135 hragvnHadlyaknillqqeeeeeaeiwliD 165
                                       h+ ++ H+dl a n+l+  +e     +++iD
  gi|313126786|ref|YP_004037056.1| 162 HDHNLVHGDLRAENVLIVDDE-----VYFID 187
                                       ****************99886.....88887 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.3e-09   3.4e-06      72     137 ..     125     183 ..      94     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.3e-09
                                       EEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEE CS
                           Pkinase  72 elylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgel 137
                                         +lvley++ +  ++ l    +l+ e  k++a q++++l+ +H+++++H Dl  eN+Li + +e+
  gi|313126786|ref|YP_004037056.1| 125 LGILVLEYLQ-D--FRTLD---KLDREVEKRLAPQVFSSLRTMHDHNLVHGDLRAENVLIVD-DEV 183
                                       5578888888.2..44444...4899999*******************************94.444 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.2    0.0015       3.9      33     108 ..      92     164 ..      33     165 .. 0.87
   2 !   18.9   0.4   4.6e-07    0.0012     144     193 ..     138     188 ..     132     240 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0015
                                       -HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH CS
                               APH  33 aaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhqv 108
                                       + e ++ e++  r +++ g+ +Pe++    + e+ gl  +++ey+     l+kl+ ++ ++l+ ++ + l+ +h++
  gi|313126786|ref|YP_004037056.1|  92 PLEMAEHELEATRRMREIGLNAPEPVE---SFEVDGLGILVLEYLQDFRTLDKLDREVEKRLAPQVFSSLRTMHDH 164
                                       55667889999****************...9*************87777777899999999999999888888875 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 4.6e-07
                                       HHHHHHHHHHHHHHHH--S....SS-EEEE-SS-SGGGEEEC..TTEEEEE--- CS
                               APH 144 lleeleeqvlaalaallpg....elptvllHgDlhpgNllvdpddgrvtGviDf 193
                                        l +l+++v  +la+ + +      ++ l+HgDl+  N+l+   d++v ++iD 
  gi|313126786|ref|YP_004037056.1| 138 TLDKLDREVEKRLAPQVFSslrtMHDHNLVHGDLRAENVLIV--DDEV-YFIDA 188
                                       4678888888888888888888888999**************..8898.9***7 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.3e-07   0.00034     114     182 ..     122     192 ..      81     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                              WaaY 114 yvkvyimiieyiegielvdm..peiddevkakikqsieklhqlgmvsgdphrgnfivkkdevriidlsgkr 182
                                            i+++ey++     d    e+++ +  ++ +s++++h++++v gd    n ++ +dev  id +  +
  gi|313126786|ref|YP_004037056.1| 122 VDGLGILVLEYLQDFRTLDKldREVEKRLAPQVFSSLRTMHDHNLVHGDLRAENVLIVDDEVYFIDATNVS 192
                                       445568999***99988886224688899999**********************************87544 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   8.2e-07    0.0021      98     144 ..     140     186 ..      63     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.2e-07
                                       TTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE CS
                       Pkinase_Tyr  98 ekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvki 144
                                       +kl+ +   ++a qv + ++ +++++lvH dl+a NvL+ +++v  i
  gi|313126786|ref|YP_004037056.1| 140 DKLDREVEKRLAPQVFSSLRTMHDHNLVHGDLRAENVLIVDDEVYFI 186
                                       4555666667889999***********************99877655 PP

>> Kinase-PolyVal  Serine/Threonine/Tyrosine Kinase found in polyvalent proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.2e-05     0.056     128     155 ..     162     189 ..     134     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                    Kinase-PolyVal 128 kelgliledlhdeNVltkdgtlyfIDtv 155
                                       ++++l+  dl +eNVl  d+++yfID+ 
  gi|313126786|ref|YP_004037056.1| 162 HDHNLVHGDLRAENVLIVDDEVYFIDAT 189
                                       56778889******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1682.73
//
Query:       gi|313126787|ref|YP_004037057.1|  [L=119]
Description: hypothetical protein Hbor_20460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-34  118.9   0.3    1.2e-34  118.7   0.3    1.0  1  DUF4112   Domain of unknown function (DUF4112)


Domain annotation for each model (and alignments):
>> DUF4112  Domain of unknown function (DUF4112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   0.3   6.6e-39   1.2e-34       2     105 .]      14     116 ..      13     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 6.6e-39
                           DUF4112   2 lkkvrklayllDkalripgcglrfGldpiigliPvvGdvisallslylvleakkaeglpkslllrmlvnialDllig 78 
                                       l++vr la+++D+a++ipg+++ +Gld+++gl+Pv Gd+++a++sly v ea  + g+ ++++ +ml+n+a+D+ +g
  gi|313126787|ref|YP_004037057.1|  14 LRRVRFLAKIMDEAVTIPGTNVGIGLDSVVGLLPVSGDLVTAVVSLYAVGEA-VRLGADRHVIGQMLFNVAIDFGVG 89 
                                       789*************************************************.9999******************** PP

                           DUF4112  79 lvPvvGdlfdvlfkantrNaallekhl 105
                                        vPv+Gd+fd+++k+n rNa+llekhl
  gi|313126787|ref|YP_004037057.1|  90 SVPVLGDVFDAVWKSNVRNANLLEKHL 116
                                       *************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 769.67
//
Query:       gi|313126788|ref|YP_004037058.1|  [L=250]
Description: amino acid/amide ABC transporter ATP-binding protein 2, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-34  117.7   0.0    7.4e-34  117.2   0.0    1.2  1  ABC_tran      ABC transporter
    8.2e-14   52.1   0.4    1.3e-05   25.2   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0002   21.0   0.0    0.00034   20.3   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
    0.00033   20.5   0.0      0.002   17.9   0.0    1.9  2  AAA_15        AAA ATPase domain
    0.00039   19.9   0.0      0.029   13.8   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00054   20.2   0.1      0.016   15.5   0.0    2.1  2  AAA_22        AAA domain
     0.0013   19.3   0.0     0.0022   18.5   0.0    1.3  1  AAA_23        AAA domain
     0.0016   18.9   0.0     0.0022   18.4   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0016   18.4   0.0     0.0032   17.4   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.003   18.0   0.1      0.038   14.4   0.1    2.1  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.024   14.2   0.0    1.4  1  AAA_27        AAA domain
      0.033   13.9   0.0       0.14   11.9   0.0    1.8  2  AAA_30        AAA domain
      0.039   14.0   0.0      0.078   13.0   0.0    1.5  1  AAA_5         AAA domain (dynein-related subfamily)
      0.093   12.2   0.0       0.14   11.6   0.0    1.2  1  AAA_7         P-loop containing dynein motor region
       0.11   12.7   0.0       0.18   12.0   0.0    1.5  1  AAA_33        AAA domain
       0.15   11.5   0.0       0.28   10.5   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.15   11.8   0.1       0.22   11.2   0.1    1.2  1  AAA_24        AAA domain
       0.15   12.0   0.1       0.26   11.2   0.1    1.4  1  NACHT         NACHT domain
       0.16   10.7   0.1          5    5.8   0.0    2.0  2  ABC_ATPase    Predicted ATPase of the ABC class
       0.17   11.9   0.0       0.33   11.0   0.0    1.6  1  AAA_14        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.0   8.2e-37   7.4e-34       1     137 []      31     175 ..      31     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 8.2e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l++++l+l++ge+v ++G+nGaGKSt+lk++ gllkp eG+++ldgkd++  +++  +r  +g++pq +++f  lt+
  gi|313126788|ref|YP_004037058.1|  31 LHDLNLHLERGEIVCLIGPNGAGKSTVLKTIFGLLKPWEGSVTLDGKDITGtDPEDLVRMGVGYVPQVDNVFGSLTI 107
                                       789***********************************************9899999******************** PP

                                       HHH......HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx......xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren......esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        en      ++++ ie+++s+l     +  ++ + ++++LSgGq+q +a aral+ +p++ll+DEp+a
  gi|313126788|ref|YP_004037058.1| 108 DENlrmggvARSSGIEEVISELYERFpILRDKREAKARTLSGGQRQVLAFARALVMEPDVLLIDEPSA 175
                                       ********97777788887777666553444445688*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   1.5e-08   1.3e-05       1      50 [.      43      80 ..      43     120 .. 0.68
   2 !   25.2   0.0   1.4e-08   1.3e-05     228     280 ..     138     187 ..     115     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.5e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslld 50
                                      + +liGpNg+GKS++L+++ +l              +  g+ + + + ++
  gi|313126788|ref|YP_004037058.1| 43 IVCLIGPNGAGKSTVLKTIFGLLK------------PWEGSVTLDGKDIT 80
                                      578****************99943............22233333333333 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.4e-08
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrlle 280
                                       d +e  ar lS G++++la++ al   +   ++lliDEp +gL P++++ ++e
  gi|313126788|ref|YP_004037058.1| 138 DKREAKARTLSGGQRQVLAFARALVMEP---DVLLIDEPSAGLAPSIVEDVFE 187
                                       577888999*****************99...9**************9998874 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.8e-07   0.00034      15      48 ..      34      67 ..      26      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.8e-07
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                        +++++ +++ l+Gp+G+GKST+l  i  lL p
  gi|313126788|ref|YP_004037058.1| 34 LNLHLERGEIVCLIGPNGAGKSTVLKTIFGLLKP 67
                                      4566665559***************888888876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.2e-06     0.002      20      48 ..      37      66 ..      31      92 .. 0.75
   2 ?    0.1   0.0      0.57   5.1e+02     288     338 ..     138     179 ..     104     194 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                            AAA_15 20 dlsee.ltvliGkNnsGKSsilealdlFln 48
                                      +l+   + +liG+N++GKS++l+ +  +l+
  gi|313126788|ref|YP_004037058.1| 37 HLERGeIVCLIGPNGAGKSTVLKTIFGLLK 66
                                      44444599***************9966655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.57
                            AAA_15 288 ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHp 338
                                       d+ e ++   + G+++ l  ++ ++  ++        ++lli+EP a L p
  gi|313126788|ref|YP_004037058.1| 138 DKREAKARTLSGGQRQVL--AFARALVMEP-------DVLLIDEPSAGLAP 179
                                       555555555555555543..3445555555.......78888888877765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.3e-05     0.029      25      46 ..      42      62 ..      32      67 .. 0.85
   2 ?    4.2   0.0     0.028        25     135     149 ..     128     159 ..      69     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                                      SEEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAilF 46
                                      ++ +++GpNG+GKs +l  i F
  gi|313126788|ref|YP_004037058.1| 42 EIVCLIGPNGAGKSTVLKTI-F 62
                                      46799************999.5 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.028
                                       T.................CS-HHHHHHHHHHH CS
                                       x.................xxxxxxxxxxxxxx RF
                             SMC_N 135 e.................lLSgGektLvalaL 149
                                       e                 +LSgG+++++a a 
  gi|313126788|ref|YP_004037058.1| 128 ElyerfpilrdkreakarTLSGGQRQVLAFAR 159
                                       0555555555555555559********99874 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-05     0.016       4      32 ..      40      68 ..      37      95 .. 0.86
   2 ?    2.9   0.0      0.14   1.3e+02      78     111 ..     150     188 ..     115     221 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldee 32
                                      +  i++++G+ G+GK+t+l++++  l+ +
  gi|313126788|ref|YP_004037058.1| 40 RGEIVCLIGPNGAGKSTVLKTIFGLLKPW 68
                                      56799****************99877655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                            AAA_22  78 llealeqalrarav.ielliiDEaqh.lr.s..eealee 111
                                         +++   +ra  + + +l+iDE    l  s  e+++e+
  gi|313126788|ref|YP_004037058.1| 150 GQRQVLAFARALVMePDVLLIDEPSAgLApSivEDVFED 188
                                       334444444444446666666664444432233333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-06    0.0022      12      40 ..      33      62 ..      26      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                            AAA_23 12 dqeidFsk.gltlItGpNGaGKTTildAik 40
                                      d ++++++  +++++GpNGaGK+T+l  i 
  gi|313126788|ref|YP_004037058.1| 33 DLNLHLERgEIVCLIGPNGAGKSTVLKTIF 62
                                      566667553699*************98775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.5e-06    0.0022      22      59 ..      39      77 ..      27     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdggif.lrgk 59
                                       r+e+v l+G+ G GKs+++++++  l+  +g + l gk
  gi|313126788|ref|YP_004037058.1| 39 ERGEIVCLIGPNGAGKSTVLKTIFGLLKPWEGSVtLDGK 77
                                      3559********************877776544424444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.5e-06    0.0032      78     121 ..      19      63 ..       2      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
                                       EEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  78 evllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       + +     + + l++l+ +l+  ++++l+G+ G+GKSt+++++ +
  gi|313126788|ref|YP_004037058.1|  19 SGVDSGYGEAQVLHDLNLHLERgEIVCLIGPNGAGKSTVLKTIFG 63 
                                       44455556678899999999988*****************99876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.3e-05     0.038       1      69 [.      44     175 ..      44     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-05
                                       EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS...................................... CS
                               AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellsk...................................... 37 
                                       v+l+Gp G GK+++ k +   l+     ++++g++++                                        
  gi|313126788|ref|YP_004037058.1|  44 VCLIGPNGAGKSTVLKTIFGLLKpwEGSVTLDGKDITGTdpedlvrmgvgyvpqvdnvfgsltidenlrmggvarss 120
                                       79*******************98755568888888885557777777888777777777777777788888888888 PP

                                       ......................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGG CS
                               AAA  38 ......................yvgesekkirelfkeakeka.kpsilfiDEida 69 
                                                                  +   r++++ a++   +p +l+iDE  a
  gi|313126788|ref|YP_004037058.1| 121 gieeviselyerfpilrdkreaKARTLSGGQRQVLAFARALVmEPDVLLIDEPSA 175
                                       8888777788888877776666333333334444444444335588888888655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05     0.024      18      50 ..      33      65 ..      24      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                       l+++ e+ ++  ++GpN AGKst+l+ i  ll
  gi|313126788|ref|YP_004037058.1| 33 DLNLHLERGEIVCLIGPNGAGKSTVLKTIFGLL 65
                                      455555678888999************998776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016      0.14      17      40 ..      40      63 ..      29      77 .. 0.82
   2 ?   -0.6   0.0         1   9.2e+02      67      98 ..     141     174 ..     107     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                            AAA_30 17 gdrvavltGpAGtGKttalkalre 40
                                      +  +++l Gp G+GK+t+lk++  
  gi|313126788|ref|YP_004037058.1| 40 RGEIVCLIGPNGAGKSTVLKTIFG 63
                                      446999**************9855 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                            AAA_30  67 gieastiakllkrlk..grarlepgtllivDEag 98 
                                       +++a+t+    ++    +ra + + ++l++DE +
  gi|313126788|ref|YP_004037058.1| 141 EAKARTLSGGQRQVLafARALVMEPDVLLIDEPS 174
                                       4455555544433336655556666888888865 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.7e-05     0.078       2      35 ..      44      78 ..      43     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.7e-05
                                      EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrd 35
                                      v+L+Gp G gKs++ + +  +l  +e  + +  +d
  gi|313126788|ref|YP_004037058.1| 44 VCLIGPNGAGKSTVLKTIFGLLkPWEGSVTLDGKD 78
                                      8***************9999997666655555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.14      26      54 ..      34      62 ..      27      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdll 54
                                      l+l+l+++  v+l+Gp G GK++++k+++
  gi|313126788|ref|YP_004037058.1| 34 LNLHLERGEIVCLIGPNGAGKSTVLKTIF 62
                                      78999*******************99865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.18       2      21 ..      44      63 ..      43     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                            AAA_33  2 vllvGlpGsGKstlaerllk 21
                                      v l+G++G+GKst+++ +  
  gi|313126788|ref|YP_004037058.1| 44 VCLIGPNGAGKSTVLKTIFG 63
                                      789***********998754 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00031      0.28      25      58 ..      44      77 ..      25      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealeva 58
                                      + l+Gp G+GK+ + k + +ll p + + +l+ +
  gi|313126788|ref|YP_004037058.1| 44 VCLIGPNGAGKSTVLKTIFGLLKPWEGSVTLDGK 77
                                      789*******************998877766655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00024      0.22       5      22 ..      44      61 ..      40      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++++Gp+g+GK+t++k++
  gi|313126788|ref|YP_004037058.1| 44 VCLIGPNGAGKSTVLKTI 61
                                      89*************997 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00029      0.26       2      26 ..      43      67 ..      42      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      +v+l G++G GK+t l+ +  +++ 
  gi|313126788|ref|YP_004037058.1| 43 IVCLIGPNGAGKSTVLKTIFGLLKP 67
                                      699***************9888775 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.05        45     242     264 ..      38      61 ..      35      65 .. 0.88
   2 ?    5.8   0.0    0.0056         5     302     349 ..     126     173 ..     120     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.05
                                       E-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                       + +G ++ ++G++  GKsT L+ +
  gi|313126788|ref|YP_004037058.1|  38 LERGeIVCLIGPNGAGKSTVLKTI 61 
                                       56788999*************987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0056
                                       -TTTB---CCC--STTEEESS--HHHHHHHHHHHHHHTT-SEEEEEGG CS
                        ABC_ATPase 302 ispFinnLPegkdttkfstedASGStsqAanimealeagakllLiDED 349
                                       is   ++ P  +d +++  ++ SG   q  + ++al ++ ++lLiDE 
  gi|313126788|ref|YP_004037058.1| 126 ISELYERFPILRDKREAKARTLSGGQRQVLAFARALVMEPDVLLIDEP 173
                                       788889999999999********************************5 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00037      0.33       2      33 ..      41      71 ..      40     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesi 33
                                      ++i+++ G+  +GK+t+lk+++  l  + e  
  gi|313126788|ref|YP_004037058.1| 41 GEIVCLIGPNGAGKSTVLKTIFGLLK-PWEGS 71
                                      5799****************995544.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1568.06
//
Query:       gi|313126789|ref|YP_004037059.1|  [L=278]
Description: branched-chain amino acid ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-30  106.5   0.0    2.1e-30  106.0   0.0    1.2  1  ABC_tran      ABC transporter
    3.4e-12   46.8   1.9    1.5e-05   25.0   0.2    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.2e-09   37.9   0.0    2.4e-09   36.9   0.0    1.5  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    1.1e-05   25.0   0.1      0.096   12.1   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00075   19.2   0.2     0.0018   18.0   0.2    1.6  1  AAA_29        P-loop containing region of AAA domain
     0.0026   17.5   0.0       0.11   12.1   0.0    2.1  2  AAA_15        AAA ATPase domain
      0.003   18.1   1.2     0.0049   17.4   1.2    1.3  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.031   14.2   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.055   13.5   0.0       0.12   12.4   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
      0.073   12.0   0.0      0.098   11.6   0.0    1.4  1  AAA_10        AAA-like domain
       0.14   11.9   0.0       0.26   11.0   0.0    1.5  1  AAA_30        AAA domain
       0.16   12.0   0.1        3.3    7.8   0.0    2.6  3  DUF2559       Protein of unknown function (DUF2559)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.0   1.4e-33   2.1e-30       2     137 .]      44     204 ..      43     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 1.4e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       + vs+++++g++++++G+nGaGKStL++l++g ++ + G+++++++d+++ ++ e +r+ +   +q+p+  +++tvr
  gi|313126789|ref|YP_004037059.1|  44 DGVSVEIERGTITGMIGPNGAGKSTLFNLISGFYELDGGRVWVNDTDVTDlKPYETAREGLVRTFQTPRRLEGMTVR 120
                                       689************************************************************************** PP

                                       HH............................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHT CS
                                       xx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en............................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkk 126
                                       e                             +  e++e++l+++++ +l d++     + LSgGq + v+lara+ ++
  gi|313126789|ref|YP_004037059.1| 121 EAmlvgatnqsgesilplwlspskvlneerANVERAERLLERFEIGHLIDQPS----TDLSGGQLKLVELARAFTTD 193
                                       ***********************9998776666669***********999998....******************** PP

                                       SSEEEEESTTT CS
                                       xxxxxxxxxxx RF
                          ABC_tran 127 pkllllDEpta 137
                                       p++lllDEp a
  gi|313126789|ref|YP_004037059.1| 194 PDILLLDEPVA 204
                                       *********75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1     1e-07   0.00015       1      26 [.      55      85 ..      55     109 .. 0.76
   2 !   25.0   0.2   9.9e-09   1.5e-05     219     302 ..     155     239 ..     118     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl.....d 26
                                      ++++iGpNg+GKS+L+ +++++  l     +
  gi|313126789|ref|YP_004037059.1| 55 ITGMIGPNGAGKSTLFNLISGFYELdggrvW 85
                                      799****************998765444442 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 9.9e-09
                            AAA_21 219 r...gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv 292
                                       r    +  +e g+  + p+++lS G+++l  l+ a+  ++   ++ll+DEp +g +P l   + ++++el+++g  +
  gi|313126789|ref|YP_004037059.1| 155 RaerLLERFEIGHLIDQPSTDLSGGQLKLVELARAFTTDP---DILLLDEPVAGVNPTLANDIKRFIRELNDEGQTF 228
                                       144578899****************************999...9****************99999998888866666 PP

                            AAA_21 293 iltTHS.plll 302
                                       ++  H+ p+++
  gi|313126789|ref|YP_004037059.1| 229 LIIEHDmPFIM 239
                                       77766666666 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   1.6e-12   2.4e-09       1      23 []     252     274 ..     252     274 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.6e-12
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                       +v+ eGtP++vr+d rVi+AYLG
  gi|313126789|ref|YP_004037059.1| 252 KVLMEGTPEAVRSDQRVIDAYLG 274
                                       6999******************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00014      0.21      25      44 ..      54      73 ..      42      81 .. 0.82
   2 !   12.1   0.0   6.5e-05     0.096     112     203 ..     145     239 ..     104     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                       +t ++GpNG+GKs l++ i
  gi|313126789|ref|YP_004037059.1| 54 TITGMIGPNGAGKSTLFNLI 73
                                      47899*********999766 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.5e-05
                                       EETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 112 kingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvael 182
                                        +n+++++ +  ++lle+ +i          LSgG+ +Lv la  f +   +p  + llDe  a    +  + + ++
  gi|313126789|ref|YP_004037059.1| 145 VLNEERANVERAERLLERFEIGHLidqpstDLSGGQLKLVELARAFTT---DP-DILLLDEPVAGVNPTLANDIKRF 217
                                       5799999999999999999998655666669************99865...34.47899****************** PP

                                       HHHHCTTSE.EEEE-SSHHHCC CS
                                       xxxxxxxxx.xxxxxxxxxxxx RF
                             SMC_N 183 lkeksknaQ.fivislreemle 203
                                       ++e +++ Q f++i ++  ++ 
  gi|313126789|ref|YP_004037059.1| 218 IRELNDEGQtFLIIEHDMPFIM 239
                                       ***9999884667777766655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   1.2e-06    0.0018      13      39 ..      44      70 ..      41      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      dg ++ei++  +t ++Gp+G+GKSTl+
  gi|313126789|ref|YP_004037059.1| 44 DGVSVEIERGTITGMIGPNGAGKSTLF 70
                                      66889999655**************97 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   7.6e-05      0.11      19      48 ..      48      78 ..      43     108 .. 0.79
   2 ?    3.3   0.0     0.036        54     322     360 ..     192     228 ..     181     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                            AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlFln 48
                                      ++++   +t  iG+N++GKS++ +++  F +
  gi|313126789|ref|YP_004037059.1| 48 VEIERGtITGMIGPNGAGKSTLFNLISGFYE 78
                                      5555555999***************988866 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.036
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQvi 360
                                       ++++ill++EP a   p + + + + ++el +++  Q++
  gi|313126789|ref|YP_004037059.1| 192 TDPDILLLDEPVAGVNPTLANDIKRFIRELNDEG--QTF 228
                                       689**************************99998..554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.2   3.3e-06    0.0049      15      39 ..      48      73 ..      35      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.3e-06
                            AAA_23 15 idFsk.gltlItGpNGaGKTTildAi 39
                                      ++ ++  +t  +GpNGaGK+T+++ i
  gi|313126789|ref|YP_004037059.1| 48 VEIERgTITGMIGPNGAGKSTLFNLI 73
                                      55644259999************988 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.1e-05     0.031      99     124 ..      53      78 ..      42      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                                       TSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpele 124
                                       + ++ ++G+ G+GKStL n + +  e
  gi|313126789|ref|YP_004037059.1|  53 GTITGMIGPNGAGKSTLFNLISGFYE 78 
                                       47899**************9987555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.4e-05      0.12       3      29 ..      57      89 ..      55     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.4e-05
                                      EEEESTTSSHHHHHHHHHT......STEEESSS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltg......ekaivsdk 29
                                      + +G   +GKStL+n ++g       ++ v+d+
  gi|313126789|ref|YP_004037059.1| 57 GMIGPNGAGKSTLFNLISGfyeldgGRVWVNDT 89
                                      689*************99754443225555555 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.6e-05     0.098      22      70 ..      54     102 ..      39     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.6e-05
                            AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe 70 
                                         + +iG+ G+GKS l +l+  +  l gg++ + D      k +et++e
  gi|313126789|ref|YP_004037059.1|  54 TITGMIGPNGAGKSTLFNLISGFYELDGGRVWVNDTDVTDLKPYETARE 102
                                       555689************************9998876665555555544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.26      19      51 ..      54      86 ..      47     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvig 51
                                       ++ + Gp G+GK+t+ + +   +e +ggrv +
  gi|313126789|ref|YP_004037059.1| 54 TITGMIGPNGAGKSTLFNLISGFYELDGGRVWV 86
                                      477889*******************99988865 PP

>> DUF2559  Protein of unknown function (DUF2559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.3     5e+03      35      51 ..      20      36 ..      14      37 .. 0.78
   2 ?    7.8   0.0    0.0022       3.3      19      36 ..     107     124 ..     101     130 .. 0.86
   3 ?    0.5   0.0      0.45   6.8e+02      21      38 ..     171     188 ..     171     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.3
                                      -S-HHHHHHHHHHHHHH CS
                           DUF2559 35 tltaeealaRLeeLRrh 51
                                       l ++++  R e LR+ 
  gi|313126789|ref|YP_004037059.1| 20 NLGKDDVVLRTEDLRKT 36
                                      57788889999999975 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0022
                                       HHHHHHHHTT-------S CS
                           DUF2559  19 nFqaSrrLeGlevplvtl 36 
                                        Fq  rrLeG++v +  l
  gi|313126789|ref|YP_004037059.1| 107 TFQTPRRLEGMTVREAML 124
                                       7************98776 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.45
                                       HHHHHHTT-------S-H CS
                           DUF2559  21 qaSrrLeGlevplvtlta 38 
                                       q S+ L G +++lv+l +
  gi|313126789|ref|YP_004037059.1| 171 QPSTDLSGGQLKLVELAR 188
                                       66999*********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1732.52
//
Query:       gi|313126790|ref|YP_004037060.1|  [L=364]
Description: branched-chain amino acid ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-52  177.1  28.0    3.8e-52  177.1  28.0    1.8  2  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
        5.2    6.8   6.4          8    6.2   0.0    3.1  3  DUF5381       Family of unknown function (DUF5381)


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3     0.055     5e+02     189     203 ..      33      47 ..      28      54 .. 0.75
   2 !  177.1  28.0   4.3e-56   3.8e-52       2     268 .]      57     338 ..      56     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.055
                      BPD_transp_2 189 lAglaGallalllgs 203
                                       lAg+aG++l+lll++
  gi|313126790|ref|YP_004037060.1|  33 LAGVAGIALVLLLAT 47 
                                       788888888877655 PP

  == domain 2  score: 177.1 bits;  conditional E-value: 4.3e-56
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl.....lllallvallvgaavglll 73 
                                       +l+ll+la+ ++++ lGl++++g+aG+in+++++f ++Gay+aall+a   +l     +++++ +a++v+a++++l+
  gi|313126790|ref|YP_004037060.1|  57 LLSLLSLAGMYVLLTLGLNVQWGYAGLINFSVAAFWGIGAYSAALLSAPTSPLglglhPIFGFFAAIVVSAILAVLI 133
                                       6789************************************************************************* PP

                      BPD_transp_2  74 gllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllr 150
                                       g+++lrl++d+l+i+ l+l ++v+ + l+ +++t g+ g+s+++el+++ +   +    +i + ++ lv+++l +++
  gi|313126790|ref|YP_004037060.1| 134 GIPTLRLREDYLAIASLGLAEVVRRIILNEEQWTAGSSGISGIPELFESLPLTQNATNLAIIVGLIGLVYVFLRRVH 210
                                       ***************9999999999999************************************************* PP

                      BPD_transp_2 151 rtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgag 226
                                       r+++Gr lr ++++e++a+alG+n+  +k+++fv+++++ ++aGa+++ +   i+p +  + ++f++++av+lGg+g
  gi|313126790|ref|YP_004037060.1| 211 RSPWGRVLRTIRSDEDLAKALGKNTYAFKMQAFVLGSIIMAIAGAFYVHMNLYIDPsDLIPLTTFYIWVAVILGGTG 287
                                       ********************************************************99999**************** PP

                      BPD_transp_2 227 sllgtviGaliigvvksllltllgi....p.....telarvllgallilvl 268
                                       s++g+v+Ga ++ ++ + +++l  +    +       l+ +++g+l+ilv+
  gi|313126790|ref|YP_004037060.1| 288 SNRGAVLGAATVIAIREGTRFLNDVqaftAlgldlAPLRLLFVGVLIILVV 338
                                       *****************88888877665516666799***********996 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   1.9      0.46   4.1e+03      15      46 ..      43      73 ..      32      98 .. 0.65
   2 ?    6.2   0.0    0.0009         8      23      57 ..     172     206 ..     163     228 .. 0.78
   3 ?    2.5   0.3     0.012   1.1e+02      12      37 ..     240     265 ..     229     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.46
                           DUF5381 15 lflatvglglaglfllfeglkfeskysllyii 46
                                      l+l +++lg++ l  l + l + + y ll ++
  gi|313126790|ref|YP_004037060.1| 43 LLL-ATVLGVVRLPFLLSLLSLAGMYVLLTLG 73
                                      333.3445666666666777777777777665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0009
                           DUF5381  23 glaglfllfeglkfeskysllyiiigiigtifgli 57 
                                       g+ g+  lfe l+++ + + l+ii+g+ig+++++ 
  gi|313126790|ref|YP_004037060.1| 172 GISGIPELFESLPLTQNATNLAIIVGLIGLVYVFL 206
                                       68889999***********************9754 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.012
                           DUF5381  12 rvllflatvglglaglfllfeglkfe 37 
                                           +l+++++++ag f + + l ++
  gi|313126790|ref|YP_004037060.1| 240 MQAFVLGSIIMAIAGAFYVHMNLYID 265
                                       456789***********998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 2118.07
//
Query:       gi|313126791|ref|YP_004037061.1|  [L=315]
Description: amino acid/amide ABC transporter membrane protein 1, haat family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-40  137.6  42.3      5e-40  137.4  42.3    1.0  1  BPD_transp_2  Branched-chain amino acid transport system / pe
     0.0016   18.4   2.6     0.0016   18.4   2.6    3.8  4  DUF997        Protein of unknown function (DUF997)


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4  42.3   5.6e-44     5e-40       2     268 .]      16     303 ..      15     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 5.6e-44
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl............lllallvallvg 66 
                                       ++n+++ ++++++a++Gl+lv+ ia   n++hg  m++Ga+ a+  +  l +              ++allv+++++
  gi|313126791|ref|YP_004037061.1|  16 LVNGIVFSSVIVLASIGLSLVYSIADFANFAHGDTMTVGAFGALASAGVLAPAmegilifgfpvwMFVALLVGMAAA 92 
                                       689*************************************9666655555555899*****6666666666666666 PP

                      BPD_transp_2  67 aavglllgllvlrlkvdel.......iitllllsvlvgltlllltgitsgvkgqs..svkellgfagallsflsavi 134
                                       a+v +l+++ + r     l       +it +++ ++++ + +l +g  s  +g++  ++ ++l+   +++ +  +v+
  gi|313126791|ref|YP_004037061.1|  93 AVVVVLTEFVIYRP----LdtgsielLITSIGVALAYRAVIFLAFGTGSSRYGVPreGPIPVLRELFNIAVTPRQVV 165
                                       66666666666664....44443444555555555555555566665555555553355566666777777777777 PP

                      BPD_transp_2 135 v.llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigv 210
                                       + + al+lv  ++l+l++t +Gr++ra+++++++ar++Gi++k v+++ +vi+galA+  G++l l + + p  +g+
  gi|313126791|ref|YP_004037061.1| 166 AvVSALVLVGTLHLVLQYTTLGRKMRATADDPNLARVSGIRTKEVIIAMWVIGGALAAAGGVFLGLETLIHP-RMGF 241
                                       77888999999******************************************************9976666.**** PP

                      BPD_transp_2 211 glgfnaiaavvlGgagsllgtviGaliigvvksllltllgi...p..telarvllgallilvl 268
                                        + + ++aav+lGg+gs++g+++G+l+ig++++l + l++    p  te+a ++ +++++++l
  gi|313126791|ref|YP_004037061.1| 242 DILLIVFAAVILGGIGSVYGAMLGGLVIGLLYEL-TPLFSLvgiPigTEYAAAVAFVIMVVIL 303
                                       *********************************5.555444355466*************987 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.6   1.8e-07    0.0016      32      70 ..      69     107 ..      53     113 .. 0.84
   2 ?    0.4   0.1     0.073   6.5e+02       5      31 ..     113     139 ..     111     144 .. 0.75
   3 ?   -3.0   0.0      0.87   7.8e+03       4      13 ..     208     217 ..     206     227 .. 0.67
   4 ?   -1.1   1.3      0.21   1.9e+03      37      61 ..     281     303 ..     267     307 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-07
                            DUF997  32 veeyyilglPlWfflscillpilfivlvillvkfvFkdi 70 
                                        e + i+g+P W+f++ ++++  + v+v+l   ++++ +
  gi|313126791|ref|YP_004037061.1|  69 MEGILIFGFPVWMFVALLVGMAAAAVVVVLTEFVIYRPL 107
                                       46789***************9999999998877777755 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.073
                            DUF997   5 EalltllltllyflwwllfaYglgske 31 
                                       E l+t + ++l   + +++a+g+gs++
  gi|313126791|ref|YP_004037061.1| 113 ELLITSIGVALAYRAVIFLAFGTGSSR 139
                                       677777777777777789999999765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.87
                            DUF997   4 kEalltlllt 13 
                                       kE+ +++++ 
  gi|313126791|ref|YP_004037061.1| 208 KEVIIAMWVI 217
                                       6666666654 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.21
                            DUF997  37 ilglPlWfflscillpilfivlvil 61 
                                       ++g+P   +++  + +++++v+  l
  gi|313126791|ref|YP_004037061.1| 281 LVGIPIGTEYAAAVAFVIMVVI--L 303
                                       5677777777766665444443..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2044.04
//
Query:       gi|313126792|ref|YP_004037062.1|  [L=410]
Description: branched-chain amino acid ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-39  135.8   9.8    3.4e-39  135.5   9.8    1.1  1  Peripla_BP_6  Periplasmic binding protein
    1.7e-27   96.5   0.0    2.2e-27   96.1   0.0    1.1  1  ANF_receptor  Receptor family ligand binding region
    1.5e-07   30.8   1.9    6.7e-06   25.3   0.3    2.1  2  Peripla_BP_5  Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   9.8   5.7e-43   3.4e-39       2     310 ..      38     343 ..      37     366 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 5.7e-43
                                       EEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTT.EETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-B CS
                      Peripla_BP_6   2 ikiGlltplsGpyassgksllagaqaafeeiNaaG.GinGrkielverDdaydpdraaeaarrlvdqdgvdalvgpl 77 
                                       ++iG++ +l+G +a++g    +g ++a++ iN+ G G  G ++ + ++D +++ + +++aa++lv+q+gv +++g++
  gi|313126792|ref|YP_004037062.1|  38 YTIGMVDALTGSLAPYGNRNQRGKDLAVAAINETGiGSEGAQLSIAVEDSESSNQSGVTAAQKLVEQNGVPLFIGAV 114
                                       79*******************************753666************************************** PP

                                       SHHHHHHHHHHHHH.HT-EEEESS-HHCC.TTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHH CS
                      Peripla_BP_6  78 ssavaaavaevlak.dgvpvigpagltge.kcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregi 152
                                       +s+v  a+ + ++k  gv+ i+  ++++e ++ p   +++ps sa+++al++++a + +  kva+   ++ +g  + 
  gi|313126792|ref|YP_004037062.1| 115 GSGVSIAMYDSVTKgSGVVQISQNSTSPElTTRPGLLRTSPSGSAKGKALAQFVAGD-DHDKVAVTWINNDYGSGLS 190
                                       ********997766599999998888887699*********************9997.889**************** PP

                                       HHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEE..CCC- CS
                      Peripla_BP_6 153 aalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillv..swsg 227
                                       + +++ ++   gevv +ep+++g++++s  ++++++  a a l+ ++++ +++++++a ++G++  ++  +   +++
  gi|313126792|ref|YP_004037062.1| 191 EVFAENFE---GEVVFNEPHDQGQSSYSGTLTKMASTDASAWLFLTYANEMTVMANEAFDQGYNT-GVDYYgaESTI 263
                                       ********...9*****************************888888888999***********7.46666215569 PP

                                       CHHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHHH CS
                      Peripla_BP_6 228 seedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaagsltreav 304
                                       ++e l+ + +++++g+ ++t  +p+ d +  + fv ++++ y+    p+ +aa +y+a+ + + a++aa+++t+ a+
  gi|313126792|ref|YP_004037062.1| 264 ADEILENTPEGSLNGMKGITESAPA-DQENYQNFVSRFKSEYDTS--PTVWAAYAYDAVTIAAIAIEAADEFTGSAL 337
                                       999*******************998.89***************98..****************************99 PP

                                       HHHHHH CS
                      Peripla_BP_6 305 raales 310
                                       ++  + 
  gi|313126792|ref|YP_004037062.1| 338 KSVVRD 343
                                       877665 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.0   3.7e-31   2.2e-27       6     351 ..      61     398 ..      56     401 .. 0.85

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 3.7e-31
                                       HHHHHHHHHT-TTSSTTEEEEEEEEE-TT-HHHHHHHHHHHCCCC.EEEEEE-SSHHHHHHH.HHHHCCTT-EEEES CS
                      ANF_receptor   6 mklAveeinsdpnllpgiklgyeiidtccdfslaleaaldflkgk.vvaviGpssssvsdav.aslanlfkiPvisy 80 
                                        +lAv  in+ +  + g +l + ++d++++ + ++ aa+++++++ v  +iG+++s+vs+a+  s+++   + +is 
  gi|313126792|ref|YP_004037062.1|  61 KDLAVAAINETGIGSEGAQLSIAVEDSESSNQSGVTAAQKLVEQNgVPLFIGAVGSGVSIAMyDSVTKGSGVVQISQ 137
                                       579********9999999*************************966**********999988469999********* PP

                                       S---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEES CS
                      ANF_receptor  81 gstspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqaleeeleergicvalkekip 157
                                        stspel+     p +lrt+ps +  ++A+++ +     +kva+ + ++dyg ++ + + e++e    +v++ e  +
  gi|313126792|ref|YP_004037062.1| 138 NSTSPELTT---RPGLLRTSPSGSAKGKALAQFVAGDDHDKVAVTWINNDYGSGLSEVFAENFEG---EVVFNEPHD 208
                                       ******887...599**********************************************8887...899999988 PP

                                       TCHHHCHHHHHHHHHHTT.T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHHHTT CS
                      ANF_receptor 158 essnddevvrkllkeiks.karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgleaaeg 233
                                          + ++ ++ +l++++s +a + ++ +++ ++    ++a ++g++++   + + ++ +++ +l + +   +  + g
  gi|313126792|ref|YP_004037062.1| 209 ---QGQSSYSGTLTKMAStDASAWLFLTYANEMTVMANEAFDQGYNTG-VDYYGAESTIADEILENTP---EGSLNG 278
                                       ...777778877777888799**************************6.9999888888888888775...556788 PP

                                       -EEEEE.--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHH............ CS
                      ANF_receptor 234 vlgfrl.kdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkk............ 297
                                       + g++  ++++++++++f+         + ++++++ ++ + +a++ YdaV + a A++ + + +            
  gi|313126792|ref|YP_004037062.1| 279 MKGITEsAPADQENYQNFV---------SRFKSEYDTSPTVWAAYA-YDAVTIAAIAIEAADEFTgsalksvvrdvt 345
                                       888887678999*******.........566666666665555555.**************9666888877776666 PP

                                       .......SSSHCCB-HHHHCCHHHHHHHHHHHT-EEEETTSCEEB-TTSBBE-EEEEEEEE CS
                      ANF_receptor 298 .......kpgralscntlkpweggqkllrylrnvnfeGltGdvkfdengdrvptydilnlq 351
                                                      ++++ +++g + +    +vn++G++G v++dengd ++ y+++ + 
  gi|313126792|ref|YP_004037062.1| 346 rpegqevF----TFSEAAEILRDGGSPS----DVNYQGVSGPVDLDENGDPPGLYQVYSVA 398
                                       55433221....1223334555555555....9************************9875 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.3   1.1e-09   6.7e-06       2      78 ..      39     116 ..      38     131 .. 0.93
   2 !    4.9   0.1    0.0018        11     253     311 ..     289     345 ..     263     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.1e-09
                      Peripla_BP_5   2 kvGvLhSlsGtmaisekslkdaallaieeinaag.GvlgrkieavvvdpasdwelfaekaeklieedkvevvfGcwt 77 
                                        +G++  l+G++a   +  +++  la++ in++g G +g ++   v+d++s  +   + a+kl+e+++v   +G+  
  gi|313126792|ref|YP_004037062.1|  39 TIGMVDALTGSLAPYGNRNQRGKDLAVAAINETGiGSEGAQLSIAVEDSESSNQSGVTAAQKLVEQNGVPLFIGAVG 115
                                       5899999**************************9999*************************************987 PP

                      Peripla_BP_5  78 S 78 
                                       S
  gi|313126792|ref|YP_004037062.1| 116 S 116
                                       7 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0018
                      Peripla_BP_5 253 dtpenkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekvreallgqe 311
                                       d+++ ++fv++fk++++++   + ++  ay +v++ a A+e+a++ + +++++ +++++
  gi|313126792|ref|YP_004037062.1| 289 DQENYQNFVSRFKSEYDTSP--TVWAAYAYDAVTIAAIAIEAADEFTGSALKSVVRDVT 345
                                       44556788888888887755..456777999************9999999888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2532.70
//
Query:       gi|313126793|ref|YP_004037063.1|  [L=276]
Description: l-proline dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-25   90.2   0.0      3e-25   89.4   0.0    1.4  1  Pro_dh        Proline dehydrogenase
     0.0059   16.1   0.2     0.0068   15.9   0.2    1.2  1  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.076   13.3   1.7        2.4    8.5   0.1    2.8  3  PqqD          Coenzyme PQQ synthesis protein D (PqqD)


Domain annotation for each model (and alignments):
>> Pro_dh  Proline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.0   5.1e-29     3e-25       4     293 ..      21     269 ..      18     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 5.1e-29
                                       HHHHHHHTTEEEEEEES-SS--SHHHHHHHHHHHHHHHHHHHHHHCCS-TTCC-SEEE-GGGTT-SGGGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh   4 tieklkkrgvrlsldllgeavlteedadryleayleaiksiekaskalkvleapgvsvklsaprletaeeeevmeel 80 
                                       ++++ ++rg++ +++llge + +++da++  e yle+ ++i++         +  +svk+s+  l+    e     +
  gi|313126793|ref|YP_004037063.1|  21 HVAETNERGISGIVNLLGEHYDDRSDAAADTEVYLELAEQIDERDL------DCCLSVKPSQIGLDIG--ED---VF 86 
                                       56667768**9******************************66665......5569***997444443..33...35 PP

                                       HHHHHHHHHHHHHTT-EEEE----GGGHHHHHHHHHHHHHSCCTTT---EEEEEETTBTTHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh  81 verlrtlakeakelgvrlliDaEeaklqeltlelfrklnkepelkdwevvgntyQaYlkdalevlqkllelAeregf 157
                                        ++l++++++a e+g+ +++D+E+++  + tl++f++       +++ +vg+ +Qa lk+++e+l++l++l      
  gi|313126793|ref|YP_004037063.1|  87 RRNLSRIVEHADEHGIFVWVDMEDHDTTDATLDAFEENA-----REYGDVGVCVQANLKRTAEDLRRLADL------ 152
                                       678999*****************************9998.....56677*****************99875...... PP

                                       -EEEEEE--S-HHHHHHHHHHTT-S-SB-SSHHHHHHHHHHHHHHHHHTTTTEEEEEE-S-HHHHHHHHHHHHHT.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh 158 rlgvkLVrGAYldsErkraqelgyespifdtkeeTDanYdavaelllenrdeiypavAsHNaesvakalalaeelgq 234
                                       + +v+LV+GAY   E+k           + +k+  D++Y + + +++e+ d+ ++av+sH +  +++a+   +e   
  gi|313126793|ref|YP_004037063.1| 153 PGKVRLVKGAY--DEPK--------EIAYRDKATVDEKYREYLTFMFEEFDD-GIAVGSHDVAMINHAADCYREY-- 216
                                       789********..5666........45699*****************99987.689*******************.. PP

                                       T--GGGEEEEEETTSSHHHHHHHHHTTS-EEEEEEECEHHHHHHHHHHHHHHHH-TT-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh 235 ekeksevefqqLlGMadnlsfalakagynvrkYlPvGpveevlpYLvRRleENtanssf 293
                                           + +e+q+L+G  +nl+++l ++  +v+ Y+P+Gp  +  +Y  RR  E ++n+ f
  gi|313126793|ref|YP_004037063.1| 217 ---GTPFEVQMLMGVRENLQDELVDSM-PVYQYVPYGP--KWFSYFTRRVRERKENALF 269
                                       ...99******************9887.9********9..79**********9988765 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   1.1e-06    0.0068     264     332 ..      89     156 ..      21     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-06
                      Amidohydro_3 264 alaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegv.tesqiervaalqvaa 332
                                        l ++v+ ade+g+ v +   +++++d++ldafe+ a+++g+ ++  +  a    t+++++r+a+l +  
  gi|313126793|ref|YP_004037063.1|  89 NLSRIVEHADEHGIFVWVDMEDHDTTDATLDAFEENAREYGDVGV--CVQANLKrTAEDLRRLADLPGKV 156
                                       4999***************************************95..777777789********999876 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0004       2.4      31      59 ..      27      56 ..      18      61 .. 0.80
   2 ?    3.1   0.0      0.02   1.2e+02      16      41 ..      98     123 ..      83     149 .. 0.69
   3 ?   -2.0   0.0      0.76   4.6e+03      39      53 ..     159     173 ..     156     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0004
                                      -..HHHHHHHHHHHCT--HHHHHHHHHHHHH CS
                              PqqD 31 s..veeivaalaeeydvdeeeaeadvlafld 59
                                         ++ iv  l e+yd+    a+ad++ +l+
  gi|313126793|ref|YP_004037063.1| 27 ErgISGIVNLLGEHYDDR-SDAAADTEVYLE 56
                                      34499**********865.88*****99987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.02
                                       -CHHHHHHHH-SSSS-HHHHHHHHHH CS
                              PqqD  16 netgafiWklldgersveeivaalae 41 
                                       +e+g f+W  ++++ + ++  +a+ e
  gi|313126793|ref|YP_004037063.1|  98 DEHGIFVWVDMEDHDTTDATLDAFEE 123
                                       89******999887775555555543 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.76
                                       HHHHCT--HHHHHHH CS
                              PqqD  39 laeeydvdeeeaead 53 
                                       ++  yd+++e a++d
  gi|313126793|ref|YP_004037063.1| 159 VKGAYDEPKEIAYRD 173
                                       6668999*9999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 1841.71
//
Query:       gi|313126794|ref|YP_004037064.1|  [L=242]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-20   70.8   0.1    1.1e-19   70.0   0.1    1.5  1  HTH_10        HTH DNA binding domain
    0.00038   20.1   0.6       0.35   10.6   0.0    2.3  2  Sigma70_r4_2  Sigma-70, region 4
    0.00089   19.0   0.1      0.052   13.3   0.0    2.4  2  HTH_psq       helix-turn-helix, Psq domain
     0.0013   18.3   0.0     0.0031   17.0   0.0    1.7  1  HTH_24        Winged helix-turn-helix DNA-binding
     0.0027   17.7   0.1       0.01   15.9   0.1    2.0  1  HTH_20        Helix-turn-helix domain
     0.0069   16.3   0.7      0.027   14.4   0.1    2.3  3  MarR_2        MarR family
  ------ inclusion threshold ------
      0.012   15.1   0.1      0.034   13.7   0.1    1.8  1  Sigma70_r4    Sigma-70, region 4
      0.013   15.4   0.1       0.03   14.2   0.1    1.6  1  HTH_5         Bacterial regulatory protein, arsR family
      0.023   14.5   0.3       0.17   11.7   0.0    2.5  2  TetR_N        Bacterial regulatory proteins, tetR family
       0.03   13.9   0.0       0.15   11.7   0.0    2.1  1  GerE          Bacterial regulatory proteins, luxR family
      0.038   14.1   0.0      0.063   13.4   0.0    1.3  1  HTH_Tnp_1_2   Helix-turn-helix of insertion element transposa
      0.042   13.5   0.0       0.11   12.1   0.0    1.7  1  HTH_50        Helix-turn-helix domain
      0.052   13.5   0.0       0.11   12.5   0.0    1.5  1  TubC_N        TubC N-terminal docking domain
      0.093   13.1   0.1       0.93    9.8   0.0    2.2  2  Nif11         Nif11 domain
        0.1   12.8   0.0        0.2   11.9   0.0    1.5  1  Coat_F        Coat F domain
       0.23   11.4   1.2       0.56   10.2   0.2    2.1  2  HTH_15        Helix-turn-helix domain of alkylmercury lyase


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.1   9.5e-23   1.1e-19       1      52 [.     186     237 ..     186     238 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 9.5e-23
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+ q+ev  lA e GY+ +PR v++++LA el+Isk+tl+ehLrkae kl+
  gi|313126794|ref|YP_004037064.1| 186 LTPTQREVFELARERGYYQWPRGVSTRDLAAELDISKTTLLEHLRKAEAKLL 237
                                       9*************************************************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00031      0.35       7      26 ..     182     201 ..     180     204 .. 0.87
   2 !    7.6   0.1    0.0027         3      26      54 .]     208     236 ..     207     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                                       HHTTS-HHHHHHHHHHHTS- CS
                      Sigma70_r4_2   7 alaeLperqreifllryleg 26 
                                        l +L++ qre+f+l ++ g
  gi|313126794|ref|YP_004037064.1| 182 RLGTLTPTQREVFELARERG 201
                                       6899***********99877 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0027
                                       ---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  26 glsykEIAellgisegtVksrlsRArkkL 54 
                                       g s+++ A++l+is +t   +l++A +kL
  gi|313126794|ref|YP_004037064.1| 208 GVSTRDLAAELDISKTTLLEHLRKAEAKL 236
                                       7899*********************9997 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.061        68       3      23 ..     147     170 ..     145     172 .. 0.82
   2 !   13.3   0.0   4.7e-05     0.052      12      42 ..     203     234 ..     201     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.061
                           HTH_psq   3 ealaaAleavv..nGk.mSirkAA 23 
                                        +++ Al+av+   G+ +S+ + A
  gi|313126794|ref|YP_004037064.1| 147 GNIETALDAVReeAGAeISVERIA 170
                                       67899******8888889988766 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.7e-05
                           HTH_psq  12 vv..nGkmSirkAArkYgiPrsTLwrrkrgkys 42 
                                       ++  +G +S+r +A + +i+++TL +++r  + 
  gi|313126794|ref|YP_004037064.1| 203 YQwpRG-VSTRDLAAELDISKTTLLEHLRKAEA 234
                                       566678.*********************98776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.8e-06    0.0031      17      43 ..     208     234 ..     204     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.8e-06
                            HTH_24  17 risqreLAerlglSpstvnrrlkrLee 43 
                                       + s r+LA +l++S++t++++l++ e 
  gi|313126794|ref|YP_004037064.1| 208 GVSTRDLAAELDISKTTLLEHLRKAEA 234
                                       5899*******************9886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     9e-06      0.01      22      47 ..     206     231 ..     180     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9e-06
                                       CTTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  22 aegltaselaerldlskntlsyHLrv 47 
                                       ++g++  +la++ld+sk+tl  HLr+
  gi|313126794|ref|YP_004037064.1| 206 PRGVSTRDLAAELDISKTTLLEHLRK 231
                                       6899********************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         3   3.3e+03      24      38 ..      81      95 ..      68     107 .. 0.62
   2 ?   -2.4   0.0       4.2   4.7e+03      10      28 ..     152     170 ..     151     172 .. 0.82
   3 !   14.4   0.1   2.4e-05     0.027       3      48 ..     186     235 ..     184     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3
                                      HHHHHHHHTSSHHHH CS
                            MarR_2 24 vgelarrlglsksav 38
                                      v+el +r+g + + v
  gi|313126794|ref|YP_004037064.1| 81 VQELQERFGQTAAQV 95
                                      455555555554433 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                                       HHHHHHCTTTSEEEHHHHH CS
                            MarR_2  10 vLaaLgrrpgrdltvgela 28 
                                       +L a++ + g +++v  +a
  gi|313126794|ref|YP_004037064.1| 152 ALDAVREEAGAEISVERIA 170
                                       6888999999888998888 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 2.4e-05
                                       --HHHHHHHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2   3 ltpaqarvLaaLgrrpgr.....dltvgelarrlglsksavsrilkrLvaa 48 
                                       ltp+q+ v ++L+r+ g+      ++ ++la++l++sk ++  +l++++a+
  gi|313126794|ref|YP_004037064.1| 186 LTPTQREV-FELARERGYyqwprGVSTRDLAAELDISKTTLLEHLRKAEAK 235
                                       67777777.6777777788999889**********************9986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     3e-05     0.034       2      36 ..     183     224 ..     182     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                                       HHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHH CS
                        Sigma70_r4   2 LasLpererevlelrf.......geglTleEIgerlgiSrer 36 
                                       L +L++ +rev+el +        +g +  +++++l+iS+ +
  gi|313126794|ref|YP_004037064.1| 183 LGTLTPTQREVFELARergyyqwPRGVSTRDLAAELDISKTT 224
                                       789*************99998888999999*****9999876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.7e-05      0.03      18      38 ..     211     231 ..     209     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  18 vcelaeelglsqstvShHLkk 38 
                                         +la+el++s+ t+ +HL+k
  gi|313126794|ref|YP_004037064.1| 211 TRDLAAELDISKTTLLEHLRK 231
                                       579****************97 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       1.4   1.6e+03      11      28 ..     145     162 ..     143     171 .. 0.74
   2 ?   11.7   0.0   0.00015      0.17       7      36 ..     195     228 ..     194     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                                       HHHTTT--HHHHHHHHTS CS
                            TetR_N  11 erGydattvreIAkrAGv 28 
                                       erG  +t ++++ ++AG 
  gi|313126794|ref|YP_004037064.1| 145 ERGNIETALDAVREEAGA 162
                                       566667888888888885 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                                       HHHHHHHT....TT--HHHHHHHHTSSHHHHHHH CS
                            TetR_N   7 elfaerGy....dattvreIAkrAGvskgalYry 36 
                                       el  erGy    +++++r++A+++ +sk +l  +
  gi|313126794|ref|YP_004037064.1| 195 ELARERGYyqwpRGVSTRDLAAELDISKTTLLEH 228
                                       56677777333357****************9876 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.15      14      45 ..     205     236 ..     184     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       HCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  14 laeGksnkeIAeelniSekTVkvhksnimkKL 45 
                                       +  G s+ + A+el+iS++T   h++ +  KL
  gi|313126794|ref|YP_004037064.1| 205 WPRGVSTRDLAAELDISKTTLLEHLRKAEAKL 236
                                       3469*********************9999887 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.6e-05     0.063       3      50 ..     181     232 ..     179     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                                       HHHHHS-HHHHHHHHHHHHHHH....--S-HHHHHHHHTS-HHHHHHHHH-H CS
                       HTH_Tnp_1_2   3 kkldeLtakQkkaaellvendy....ekltldeiaeevgvsrsTlykWkkkk 50 
                                       ++l  Lt  Q+ + el  e+ y      ++++++a+e+ +s++Tl + ++k 
  gi|313126794|ref|YP_004037064.1| 181 RRLGTLTPTQREVFELARERGYyqwpRGVSTRDLAAELDISKTTLLEHLRKA 232
                                       677789****************9998889****************9988775 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.8e-05      0.11      25      46 ..     210     231 ..     202     232 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-05
                            HTH_50  25 StRklAkrLGvShtaianklrk 46 
                                       StR lA+ L +S+t+ +  lrk
  gi|313126794|ref|YP_004037064.1| 210 STRDLAAELDISKTTLLEHLRK 231
                                       9****************99997 PP

>> TubC_N  TubC N-terminal docking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.5e-05      0.11      24      51 ..     203     230 ..     202     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.5e-05
                            TubC_N  24 frApkgaltpelraklkerKaeIiafLq 51 
                                       ++ p+g+ t++l+a+l   K++++++L+
  gi|313126794|ref|YP_004037064.1| 203 YQWPRGVSTRDLAAELDISKTTLLEHLR 230
                                       5669***********************8 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.6   6.7e+02       3      24 ..      62      89 ..      61      96 .. 0.80
   2 ?    9.8   0.0   0.00083      0.93      15      41 ..     171     202 ..     148     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.6
                             Nif11  3 eeqlkaFlekvkq......Dpalreqlk 24
                                      +e+++ +l+++++       ++l+e++ 
  gi|313126794|ref|YP_004037064.1| 62 VEEVETLLDAIEAseyggeVQELQERFG 89
                                      5888999999999888888899999875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00083
                             Nif11  15 q....Dpalreqlkacs.dheevvalAkeaGy 41 
                                       +     p+++ +l + + +  ev +lA+e+Gy
  gi|313126794|ref|YP_004037064.1| 171 SsdtvEPERARRLGTLTpTQREVFELARERGY 202
                                       166667999999999966************** PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018       0.2      47      62 ..     190     205 ..     185     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                            Coat_F  47 qeelfnlmnqkGwYpv 62 
                                       q+e+f+l+ ++G+Y+ 
  gi|313126794|ref|YP_004037064.1| 190 QREVFELARERGYYQW 205
                                       9*************97 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2    0.0005      0.56      37      65 ..      50      78 ..      45      82 .. 0.91
   2 ?   -2.1   0.0       3.5   3.9e+03      33      43 ..     161     171 ..     150     183 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                            HTH_15 37 tveeLAaatgrsveevrqaLaalpstEyd 65
                                      tv++L +a g +veev+  L a+   Ey 
  gi|313126794|ref|YP_004037064.1| 50 TVNGLFTAYGDTVEEVETLLDAIEASEYG 78
                                      8999*******************999996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.5
                            HTH_15  33 GepVtveeLAa 43 
                                       G+ ++ve++A 
  gi|313126794|ref|YP_004037064.1| 161 GAEISVERIAS 171
                                       55666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.38s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1286.78
//
Query:       gi|313126795|ref|YP_004037065.1|  [L=508]
Description: NAD-dependent aldehyde dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.9e-143  477.0   0.0   6.1e-143  476.7   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
    0.00014   21.8   0.8    0.00027   20.9   0.8    1.4  1  OmdA      Bacteriocin-protection, YdeI or OmpD-Associated
  ------ inclusion threshold ------
      0.018   14.1   0.0      0.037   13.1   0.0    1.4  1  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.7   0.0    1e-146  6.1e-143       1     458 [.      15     481 ..      15     484 .. 0.97

  Alignments for each domain:
  == domain 1  score: 476.7 bits;  conditional E-value: 1e-146
                                       EET-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHH CS
                            Aldedh   1 wveses.etievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaelet 76 
                                       w+++++ +t+e+ nPatge++++++++t+edvdaa+aaAk+a ++w++l+  +Rae+L  + + l++r+eel e+ +
  gi|313126795|ref|YP_004037065.1|  15 WTDGTGdSTFESENPATGETLGEFRRGTPEDVDAALAAAKDAEEEWQALSHIDRAEYLWDIYHELKDRHEELGEIVS 91 
                                       888888677******************************************************************** PP

                                       HHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEEC.TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHH CS
                            Aldedh  77 letGkplaearaeveeaidvlryyaelaeklegevlpss.egklalvrrePlGvvgaItPWNfPlllaawklapala 152
                                       +e+Gk ++e +a+v+ea ++++++a+ a++ +g+v+ps+ ++k+a++rr+P Gv+g++tPWNfP++++ w++a  l+
  gi|313126795|ref|YP_004037065.1|  92 KECGKEISEGKADVTEAWHMVEWAAGDARHPKGDVVPSEiASKDAYMRRKPRGVIGCVTPWNFPVAIPFWHMAVSLV 168
                                       **************************************55************************************* PP

                                       TT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHH.HHCT CS
                            Aldedh 153 aGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiaka.aakn 228
                                        GNtvv+KPae+tp++  ++ae+fe+ag+P+gv+n+v+g g ++gea+v++ +vd v ftGs evg++ia++  ++ 
  gi|313126795|ref|YP_004037065.1| 169 EGNTVVWKPAEQTPWCGQIIAEMFEDAGIPDGVFNMVQGFG-DAGEAIVDDSRVDTVLFTGSAEVGHEIASKvGGEP 244
                                       ***************************************88.6*****************************55588 PP

                                       TSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT CS
                            Aldedh 229 lkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplded 305
                                        k  + E+GGkn ++v+e+aDld av+++v+++f ++GQ+C++ +rl+v+es+ydef e++veaak++ vgdpl+ed
  gi|313126795|ref|YP_004037065.1| 245 GKLAACEMGGKNGIVVTENADLDIAVHSAVMSSFKTTGQRCVSSERLIVHESVYDEFKERFVEAAKNVAVGDPLKED 321
                                       999************************************************************************** PP

                                       -SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.....E.SB-SSSTTEE--EEEE.S-TTTSHHHHS---SSEEE CS
                            Aldedh 306 tdvGPliseaqlekvekyveeakeegaklllGge.....reeaglekgyfvePtvla.nvtpdmriaqeEiFGPVls 376
                                       t +GPli+e + ekv+ky e ak+e +++l++ +     +  +g e+gy++ P v + + + d r+ +eE+FGP ++
  gi|313126795|ref|YP_004037065.1| 322 TFMGPLIEEGHHEKVTKYNELAKKEDVNVLVDRTeldadEIPDGHEEGYWIGPFVYEaDAHADLRCTHEEVFGPHVA 398
                                       *******************************99888776667899**********9637999*************** PP

                                       EEEES.SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHH CS
                            Aldedh 377 vikfk.deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkeg 452
                                       +++++ d+eea+ei Ndt+yGLa++++++d ++++++ ++ e+G  y N ++ ga+ +lpfgGvk+Sg+G  + +e+
  gi|313126795|ref|YP_004037065.1| 399 LLEYSgDIEEAVEIHNDTNYGLAGAIISEDYREINYYRDNAEVGLAYGNLPCIGAEVHLPFGGVKKSGNGYPSAREV 475
                                       ****99*********************************************************************** PP

                                       HHHTEE CS
                            Aldedh 453 leeyte 458
                                       +e++te
  gi|313126795|ref|YP_004037065.1| 476 IEAVTE 481
                                       *99998 PP

>> OmdA  Bacteriocin-protection, YdeI or OmpD-Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.8   4.6e-08   0.00027       5      38 ..      43      76 ..      42      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.6e-08
                              OmdA  5 PedlaaaLdadpaakaaFealtpsyrreylrwie 38
                                      Ped+ aaL+a ++a + ++al++  r eyl+ i 
  gi|313126795|ref|YP_004037065.1| 43 PEDVDAALAAAKDAEEEWQALSHIDRAEYLWDIY 76
                                      9******************************994 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.1e-06     0.037      80     263 ..     134     308 ..     128     317 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-06
                              LuxC  80 keksyekaqprglvlhvlsgNvpl.lpvmsilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvy 155
                                       k+  y+++ prg++  v++ N p+ +p++ ++ +l+ +n  + k+  + p     ++  + d  +   + + +    
  gi|313126795|ref|YP_004037065.1| 134 KD-AYMRRKPRGVIGCVTPWNFPVaIPFWHMAVSLVEGNTVVWKPAEQTPWCGQIIAEMFEDAGIPDGVFNMVQ--G 207
                                       44.8*******************7589*******************9999999988888888777655555433..3 PP

                              LuxC 156 f.ksgdtkleeeivqnaDvvvawGgeeaikaisekl...kpgkqlikfGakvSfavvdkealeeealdkaaeraAkD 228
                                       f ++g+  + ++    +D v   G+ e  + i++k+   +++    + G k ++ v ++++     ld a++ a   
  gi|313126795|ref|YP_004037065.1| 208 FgDAGEAIVDDS---RVDTVLFTGSAEVGHEIASKVggePGKLAACEMGGKNGIVVTENAD-----LDIAVHSAVMS 276
                                       423333333333...4788888888777777776551113445667778888877766665.....77777777777 PP

                              LuxC 229 iivfdQqAClspqvvfvekddkieidefaeaLaaa 263
                                       +     q C+s+  + v    +  +def+e+  +a
  gi|313126795|ref|YP_004037065.1| 277 SFKTTGQRCVSSERLIVH---ESVYDEFKERFVEA 308
                                       776677777777777777...44777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2759.96
//
Query:       gi|313126796|ref|YP_004037066.1|  [L=139]
Description: hypothetical protein Hbor_20550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-18   64.8   0.9    1.1e-17   64.6   0.9    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    0.00012   22.2   0.2    0.00015   22.0   0.2    1.1  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    0.00024   20.9   0.0     0.0003   20.5   0.0    1.2  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.9   1.8e-21   1.1e-17       2     142 ..       3     135 ..       2     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1.8e-21
                                       EEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS.....SEEEEEEEEEETTTT CS
                   Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr.....gtvreelvevdpegr 73 
                                       v+v+++ +++app+++w++++d++n ++ ++ v ++ +e  + +  +v ++v+           ++   ve++p +r
  gi|313126796|ref|YP_004037066.1|   3 VRVRRAFEFDAPPADIWEFIADPRNRAEAISVVEKYDVEP-NTN--EVTWHVSLPIPilnstVAIKTNDVERNP-PR 75 
                                       799*******************************998885.777..777999977778998877**********.** PP

                                       EEEEEEE.SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  74 llsyrivkpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkarl 142
                                       ++++ +  + +v++++++ tv+++++g+r+t+++ +d+       + p +++++k++l++ Le+L+a+l
  gi|313126796|ref|YP_004037066.1|  76 FVRFVG--KSKVMRVSGEHTVEETETGSRLTNEFVVDG-------RVPGVERFFKRNLDRELENLEAAL 135
                                       ******..699***********************9994.......6699*****************986 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   2.5e-08   0.00015       2     130 .]      12     136 ..      11     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-08
                                       SS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE....EEEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCCEE CS
                    Polyketide_cyc   2 papadqvyalvadvesypeflphcssvevleeaes.glsadlevgfggltesftarvtldppeeitfklvegdfksl 77 
                                       +ap++++++++ad  +  e ++ +++  v  ++++  ++++l +    +t   ++ +++  p +         f ++
  gi|313126796|ref|YP_004037066.1|  12 DAPPADIWEFIADPRNRAEAISVVEKYDVEPNTNEvTWHVSLPIPILNSTVAIKTNDVERNPPR---------FVRF 79 
                                       69********************999999999999898899999999999999999998888888.........7788 PP

                                       EEEEEECTECCEEE.....CEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHHHH CS
                    Polyketide_cyc  78 egkWtieslppnsg.....gtrtkvalevdfkfaspllgalvgqvaervldellaale 130
                                       +gk +++ ++  ++     +t+ +++ e+ +++++p ++ + +  ++r+l++l aal+
  gi|313126796|ref|YP_004037066.1|  80 VGKSKVMRVSG-EHtveetETGSRLTNEFVVDGRVPGVERFFKRNLDRELENLEAALR 136
                                       88888877775.3345555788888888889999**********99999999999886 PP

>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     5e-08    0.0003       3      94 ..       9     100 ..       8     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5e-08
                                       EEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEET..TEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE..EEEEE CS
                              COXG   3 frvaapkeavwefLndpeklarciPGvksvekeg..deykvkvklkvGplkgsfkarvelselekensttieikGkG 77 
                                       f+ +ap++++wef+ dp + a++i  v+++++e   +e++  v+l + +l +  ++ ++ +++e +    +++ Gk 
  gi|313126796|ref|YP_004037066.1|   9 FEFDAPPADIWEFIADPRNRAEAISVVEKYDVEPntNEVTWHVSLPIPILNS--TVAIKTNDVERNPPRFVRFVGKS 83 
                                       67799***********************987765348888899999999999..77788888877777779999999 PP

                                       E-SSEEEEEEEEEEEEE CS
                              COXG  78 rgagvaidfalvvlvee 94 
                                       + + v+ + +++   ++
  gi|313126796|ref|YP_004037066.1|  84 KVMRVSGEHTVEETETG 100
                                       99988877776665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 784.96
//
Query:       gi|313126797|ref|YP_004037067.1|  [L=74]
Description: hypothetical protein Hbor_20560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00065   20.0   0.2    0.00079   19.7   0.2    1.1  1  FaeA            FaeA-like protein
     0.0084   15.9   0.2      0.016   15.1   0.2    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.039   14.0   0.0      0.082   12.9   0.0    1.5  1  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
      0.048   13.4   0.0      0.071   12.9   0.0    1.3  1  LexA_DNA_bind   LexA DNA binding domain
        0.1   12.2   0.1       0.31   10.6   0.0    1.7  2  HTH_24          Winged helix-turn-helix DNA-binding
        0.1   12.6   0.1       0.15   12.1   0.1    1.3  1  z-alpha         Adenosine deaminase z-alpha domain


Domain annotation for each model (and alignments):
>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   2.7e-07   0.00079       4      60 ..      10      71 ..       7      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.7e-07
                                      HHHHHHHH.....S----HHHHHHHHTS-HHHHHHHHHHH.HHHSSEEEE--SSSSS-EEEE CS
                              FaeA  4 eIleylnsi....kapckTreiAdalglsaYQaRyYLeqL.ekegkikrspvrrGvstlWel 60
                                       I+ yl +     +   + ++iA+a+glsa Q+   L  L ek   ++    +r  st W++
  gi|313126797|ref|YP_004037067.1| 10 RIIAYLRESvgagERYFRAKNIAEAIGLSAKQVGARLPRLaEKSEEVEIEKWGRARSTTWRV 71
                                      6888887644444444689******************999678999**99**********98 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   5.2e-06     0.016      21      41 ..      29      49 ..       9      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.2e-06
                     HTH_AsnC-type 21 aeLAervGlSestvlrRvrrL 41
                                      + +Ae++GlS+ +v +R+ rL
  gi|313126797|ref|YP_004037067.1| 29 KNIAEAIGLSAKQVGARLPRL 49
                                      569**************9998 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.7e-05     0.082      15      44 ..      13      42 ..      10      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHHTT--EE-HHHHHHHCTS-HHHH CS
                    Put_DNA-bind_N 15 ryLeelkeegveriSSteLaealgvtaaqv 44
                                       yL+e   +g+ +  ++ +aea+g++a qv
  gi|313126797|ref|YP_004037067.1| 13 AYLRESVGAGERYFRAKNIAEAIGLSAKQV 42
                                      59999999*********************9 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.4e-05     0.071       1      53 [.       1      52 [.       1      65 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                                      XX---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind  1 mkkLTerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerK 53
                                      m++ T+  ++++ ++++s+         ++ia+a+gl+ ++ v  +L +L+ K
  gi|313126797|ref|YP_004037067.1|  1 MSDYTDEEQRIIAYLRESVGAGERYFRAKNIAEAIGLS-AKQVGARLPRLAEK 52
                                      78889999999999999999988888999********7.************99 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.84   2.5e+03       6      14 ..       9      17 ..       8      20 .. 0.80
   2 ?   10.6   0.0    0.0001      0.31      21      44 ..      29      52 ..      28      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.84
                            HTH_24  6 rkILelLqk 14
                                       +I+ +L++
  gi|313126797|ref|YP_004037067.1|  9 QRIIAYLRE 17
                                      589999886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0001
                            HTH_24 21 reLAerlglSpstvnrrlkrLeee 44
                                      + +Ae++glS   v +rl rL e+
  gi|313126797|ref|YP_004037067.1| 29 KNIAEAIGLSAKQVGARLPRLAEK 52
                                      579*****************9885 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     5e-05      0.15       1      49 [.       3      53 ..       3      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                                      HHHHHHHHHHHHHHHC.-TTCE...CCHHHHHHHHCC-HHHHHHHHHHHHHTT CS
                           z-alpha  1 iaqeqaekilelLeel.gekka...atalalergLstpkreiNrvLydlerkg 49
                                      ++ +++++i+ +L+e+ g ++    a+++a ++gLs  ++ + + L +l++k 
  gi|313126797|ref|YP_004037067.1|  3 DYTDEEQRIIAYLRESvGAGERyfrAKNIAEAIGLS--AKQVGARLPRLAEKS 53
                                      67899********9963444424449**********..89***9999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 453.79
//
Query:       gi|313126798|ref|YP_004037068.1|  [L=59]
Description: hypothetical protein Hbor_20570 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.21   11.8   1.5       0.21   11.8   1.5    2.9  2  YbgT_YccB  Membrane bound YbgT-like protein
        1.5    8.1   3.6        1.7    8.0   3.6    1.0  1  TMEM43     Transmembrane protein 43


Domain annotation for each model (and alignments):
>> YbgT_YccB  Membrane bound YbgT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.5   2.3e-05      0.21       9      22 ..      11      24 ..      11      26 .. 0.91
   2 ?   -1.0   4.3      0.23   2.1e+03      13      20 ..      47      54 ..      35      57 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                         YbgT_YccB  9 GvlLAvlfgilnal 22
                                      G+++Avlf+i+ ++
  gi|313126798|ref|YP_004037068.1| 11 GIGFAVLFSIITVI 24
                                      9**********876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.23
                         YbgT_YccB 13 Avlfgiln 20
                                      A+++++++
  gi|313126798|ref|YP_004037068.1| 47 AASLAVVA 54
                                      55556655 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.6   0.00019       1.7     199     245 ..      12      58 ..      10      59 .] 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00019
                            TMEM43 199 lglllllsplsvlvslipllgelvglglalvalllslslsllviala 245
                                       +g+++l+s+++v+    +++g+ ++++++++  ++++sl+++   + 
  gi|313126798|ref|YP_004037068.1|  12 IGFAVLFSIITVIGAAGMIVGDQLTAAVGFAVAIIAASLAVVAAQTF 58 
                                       8***********99999999988889999888888888887765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.35s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 342.96
//
Query:       gi|313126799|ref|YP_004037069.1|  [L=430]
Description: hypothetical protein Hbor_20580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-19   68.2   0.2    3.3e-09   37.2   0.0    2.5  2  LEA_2     Late embryogenesis abundant protein
  ------ inclusion threshold ------
      0.072   13.5   1.5         12    6.3   0.2    2.8  2  PapD_C    Pili assembly chaperone PapD, C-terminal domain


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.2   1.6e-10   1.5e-06       1      84 [.      62     145 ..      62     160 .. 0.78
   2 !   37.2   0.0   3.7e-13   3.3e-09       4      97 ..     212     301 ..     209     303 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.6e-10
                                       EEEEEESSSS-EEEEEEE..EEEEESSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEE CS
                             LEA_2   1 tlrvrNPNsfgvrydgle..ldlsyngqrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevglele 75 
                                       t++v NP +fg+ + g++  ++++ n++r+a  +  +g+ + +++ t ++++  +++++++ ++r+++ +  ++ ++
  gi|313126799|ref|YP_004037069.1|  62 TISVSNPSPFGISLGGVAvnYSVWMNDVRIA-DGEKSGVAIDSGNAT-VNTTTQMQNERIIPWWRSHVRNGEHTVVQ 136
                                       689**************96666667******.**************9.9999********99999999333444444 PP

                                       EEEEEEEE. CS
                             LEA_2  76 ytlrgrlkv 84 
                                       ++ ++r ++
  gi|313126799|ref|YP_004037069.1| 137 IDPTVRSET 145
                                       444555553 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 3.7e-13
                                       EEESSSS-EEEEEEEEEEEESSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEEEEEEE CS
                             LEA_2   4 vrNPNsfgvrydgleldlsyngqrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevgleleytlrg 80 
                                       v+NP + ++++++l +d+s n++ ++ g+s++g  +p+++t+t+e++  + +++l +++ ++l  e+++ ++++++ 
  gi|313126799|ref|YP_004037069.1| 212 VYNPKPYPITVTRLGYDISMNDVAMGDGASESGYVIPPKSTKTIETTTYIRNENLDEWWGSHL--ERNQVTDLRIDF 286
                                       9*****************************************************999999999..788888888888 PP

                                       EEE.EEETTTSCEEEEE CS
                             LEA_2  81 rlkvlgkpilgsvtvpv 97 
                                       ++++  ++   + ++p+
  gi|313126799|ref|YP_004037069.1| 287 HARL--DLAGETIRIPL 301
                                       8885..55557778877 PP

>> PapD_C  Pili assembly chaperone PapD, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0028        25       1      17 [.      65      81 ..      65      89 .. 0.92
   2 ?    6.3   0.2    0.0013        12       1      38 [.     212     255 ..     212     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0028
                                      EEE-SSS-EEEEEEEEE CS
                            PapD_C  1 VkNptPYyvtfsslevk 17
                                      V+Np+P+ +++ ++ v+
  gi|313126799|ref|YP_004037069.1| 65 VSNPSPFGISLGGVAVN 81
                                      89*********999886 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0013
                                       EEE-SSS-EEEEEEEEEETTEEEEEEE......EEE-TTEEEEE CS
                            PapD_C   1 VkNptPYyvtfsslevkgggkslalea......gmvaPfssatf 38 
                                       V Np PY +t+++l  + + +++a ++       +++P+s++t+
  gi|313126799|ref|YP_004037069.1| 212 VYNPKPYPITVTRLGYDISMNDVAMGDgasesgYVIPPKSTKTI 255
                                       569999999999988777777777766779998899******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 2376.10
//
Query:       gi|313126800|ref|YP_004037070.1|  [L=128]
Description: hypothetical protein Hbor_20590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 802.23
//
Query:       gi|313126801|ref|YP_004037071.1|  [L=343]
Description: phosphate uptake regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-14   52.4  10.0    5.5e-13   49.2   0.0    2.6  3  PhoU            PhoU domain
    2.2e-07   30.7   0.0    3.9e-07   29.8   0.0    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.92   8.2e+03      30      47 ..      60      77 ..      51     104 .. 0.65
   2 !   49.2   0.0   6.2e-17   5.5e-13       1      89 []     139     231 ..     139     231 .. 0.89
   3 !    5.6   5.0    0.0025        22       2      86 ..     250     332 ..     249     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.92
                                      HHHHHHHHHHHHHHHHHH CS
                              PhoU 30 vierddeidrlekeiers 47
                                      ++++   +d+le++i  +
  gi|313126801|ref|YP_004037071.1| 60 IRADALNADALERAIVAQ 77
                                      555555566676666444 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 6.2e-17
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH.HHHH...HHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae.dlre...llsllriar 73 
                                       l+r+ ++ ++m  +a++al++++ +la++ ++r++++++++ ++ r +++a+ + + +++  l+    l++++++a+
  gi|313126801|ref|YP_004037071.1| 139 LERLENTGSTMRGEAIKALAHGNPDLAQRALNRERQANKIFVLLLRLIFTAYQNPNLCRAvGLESgfpLIGYRSVAK 215
                                       679999**********************************************8877666664444334699****** PP

                                       HHHHHHHHHHHHHHHH CS
                              PhoU  74 dlERigDhavniaerv 89 
                                       +lE  +D a++ia++v
  gi|313126801|ref|YP_004037071.1| 216 NLELTADNAEDIANIV 231
                                       *************985 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHH.HHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrel.lsllriardlER 77 
                                       r+  + v ++   a+++++e+d +l  e +e+ ++i + e++i ++ l ++ +++ l  ++re+ +sl + a++  R
  gi|313126801|ref|YP_004037071.1| 250 REFTDQVDKITATAVQSVVERDYDLTVECRELFRDIRDKERDILDD-LDEMDNQKLL--QIREVlVSLQQTAQYAMR 323
                                       6677889999999******************************999.9999876655..588873556669999999 PP

                                       HHHHHHHHH CS
                              PhoU  78 igDhavnia 86 
                                        +  a+n+a
  gi|313126801|ref|YP_004037071.1| 324 NAEIAANLA 332
                                       888888877 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   4.4e-11   3.9e-07       5      34 ..      12      40 ..       8      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.4e-11
                                      TEEEEEE-CCCHHHCCEECTCEEEEEECTT CS
                    MazE_antitoxin  5 nsgavriPkevrfelgireGdevelevdgd 34
                                      +++a+++P+e+++e+++++Gdev l+ +g+
  gi|313126801|ref|YP_004037071.1| 12 STLAMTLPAEWAKEHNVNKGDEVSLR-MGG 40
                                      899*********************94.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1998.77
//
Query:       gi|313126802|ref|YP_004037072.1|  [L=360]
Description: hypothetical protein Hbor_20610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-45  154.3   0.3    4.5e-45  154.1   0.3    1.0  1  NAD_kinase    ATP-NAD kinase
    1.6e-05   24.5   2.8    2.6e-05   23.9   0.1    2.5  3  DAGK_cat      Diacylglycerol kinase catalytic domain
     0.0017   18.9   0.2     0.0076   16.9   0.1    2.1  2  ThiS          ThiS family
  ------ inclusion threshold ------
      0.012   15.1   1.8      0.067   12.8   1.1    2.3  3  Peripla_BP_4  Periplasmic binding protein domain
       0.03   13.6   0.0      0.045   13.1   0.0    1.2  1  PFK           Phosphofructokinase


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.3   1.2e-48   4.5e-45       1     290 [.       2     357 ..       2     359 .. 0.92

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 1.2e-48
                                       .EEEEESSC........................GGTCSHHHHHHHHHHHCT-..EEEEECCGGCCSSSTT--HHHHT CS
                        NAD_kinase   1 kvgivvnpi........................kkeaieraeevarwLldalsrvlevtveeklgeslaeaaefrse 53 
                                       ++g+vvnpi                        ++ a +ra+++++ L da   v  ++  +++ges+a+ ++  +e
  gi|313126802|ref|YP_004037072.1|   2 RIGVVVNPIagmggrvglkgtdgkveearargaDPRAPNRARRMFEALRDANEAVTVFVWGGEMGESEATDIGLSPE 78 
                                       69***************************77776677777777777777774378888899**************** PP

                                       TTT--........EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHH....CT-EEEEEESSS--SS-SE..EGGG CS
                        NAD_kinase  54 visvlkkvkttd.dtrkaleafadagvdliivvGGDGTaldvarllqk....aeiPvlgvnaGvkgfltef..epea 123
                                       v + +k+++tt+ dtr+a+eaf+da vdl+++vGGDGTa dva++l++    +++P lg +aGvk+++++f  +pe+
  gi|313126802|ref|YP_004037072.1|  79 VLGAPKSAETTAeDTRRAVEAFVDAAVDLVLFVGGDGTAADVAEALAAagadETVPMLGAPAGVKVYSSVFavSPED 155
                                       **********999*******************************9987777799*********************** PP

                                       HHHHHHHHHHT-SEEEEEEEEE........................EEEEETTE...............EEEEEEES CS
                        NAD_kinase 124 aaellekllegeirvekrevld........................avimrskgee.........diadiviensvl 167
                                       aa++++++ +    +e rev+d                        + ++ sk+            +ad +++    
  gi|313126802|ref|YP_004037072.1| 156 AATVATTFDR----TERREVMDideddyregevhpelravatvpvaDDMQSSKQLGggtvdalaaGVADDIRDA--- 225
                                       ******9988....********9999999999999999999999987777777755988987777677777555... PP

                                       SEEEEEESSSSS-EE..EEEEETTEEEEEEEESEE.......................EEE-TGGGGTHHHHTT--E CS
                        NAD_kinase 168 nevviirgpgstlie..lelyvdtelleadqldgl.......................ivstPtGstayslsaGgpl 219
                                       +e ++++gpgst+    +el+ +++++++d+ +++                       iv++P+G++++++++G+p+
  gi|313126802|ref|YP_004037072.1| 226 SEKTFVLGPGSTVGAvkAELGFEGSPIGVDVWRDGevvvrdateseildalgsegenvIVVSPIGGQGFVFGRGNPQ 302
                                       5************9999************************************************************ PP

                                       E-TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEE CS
                        NAD_kinase 220 isPgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfkli 290
                                       +sP+v +           + ++ +++s+ kl+     +   l +++ ++el+ ++ ++ rv++++++ ++ 
  gi|313126802|ref|YP_004037072.1| 303 LSPDVIR-----------QCDVEIIASRAKLD-----GVGELHVDTDDPELDEELTGWTRVRVGRFERRMM 357
                                       *******...........99************.....99***************************98876 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.19   6.9e+02       4      64 ..       5      63 ..       2      64 .. 0.52
   2 !   23.9   0.1   7.2e-09   2.6e-05      38      91 ..      88     141 ..      78     173 .. 0.79
   3 ?   -2.6   0.1       1.1   3.9e+03      65      77 ..     208     220 ..     206     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.19
                                      EEE-TTCTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHC.C-SEEEEEES CS
                          DAGK_cat  4 vivNpksGkgkgekllrkvrelleeagvelelieteepgdakelakeakee.gvdlivvaGG 64
                                      v+vNp +G g g+  l+    ++eea    +  +   p+ a+++++ ++++ ++ +++v GG
  gi|313126802|ref|YP_004037072.1|  5 VVVNPIAGMG-GRVGLKGTDGKVEEARA--RGADPRAPNRARRMFEALRDAnEAVTVFVWGG 63
                                      7888888733.33333444444444433..44455556666666666555313466777776 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 7.2e-09
                                       --STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT.HHCTTSEEEEEE-S CS
                          DAGK_cat  38 teepgdakelakeakeegvdlivvaGGDGtvsevlnglle.elatkpplgiiPlG 91 
                                       t  ++d ++ ++   ++ vdl++ +GGDGt+  v+++l+   +++++p+   P+G
  gi|313126802|ref|YP_004037072.1|  88 T-TAEDTRRAVEAFVDAAVDLVLFVGGDGTAADVAEALAAaGADETVPMLGAPAG 141
                                       4.4788899999999999*********************9855555555545666 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHCT CS
                          DAGK_cat  65 DGtvsevlnglle 77 
                                        Gtv +++ g+++
  gi|313126802|ref|YP_004037072.1| 208 GGTVDALAAGVAD 220
                                       4888888888877 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.4   4.8e+03      20      35 ..     113     128 ..     101     145 .. 0.65
   2 !   16.9   0.1   2.1e-06    0.0076      10      76 ..     225     291 ..     218     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                                       STSBHHHHHHHHHHHT CS
                              ThiS  20 egstvaelleaLgery 35 
                                        + t a++ eaL++ +
  gi|313126802|ref|YP_004037072.1| 113 GDGTAADVAEALAAAG 128
                                       4556666666666544 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.1e-06
                                       HHTCEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGC.CTTTSB-....-TTCEEEEEESTTC CS
                              ThiS  10 lageeelelaegstvaelleaLgerypelalerrvavavNgeivpr.lwldtel....kdgDevailppVaG 76 
                                       +  e++++l+ gstv+++ ++Lg+++    ++ +v v ++ge+v r   ++++l    ++g  v ++ p++G
  gi|313126802|ref|YP_004037072.1| 225 AS-EKTFVLGPGSTVGAVKAELGFEG----SPIGVDVWRDGEVVVRdATESEILdalgSEGENVIVVSPIGG 291
                                       44.6999*******************....789*************6699999999999***********99 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   1.9e-05     0.067     132     211 ..      35     133 ..      13     144 .. 0.67
   2 ?   -2.4   0.0      0.77   2.8e+03      58      79 ..     148     169 ..     140     179 .. 0.81
   3 ?   -0.6   0.0      0.22   7.9e+02      42      66 ..     267     291 ..     239     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                                       CCCHHHHHHH.HHHHHHHHHH.................-T.TCEECCEEESTTTCHHHHHHHHHHHHHTTTECEE.E CS
                      Peripla_BP_4 132 spgdpnaeer.iegfrkvlke.................yp.gikivaevaganwdaekaqqalealltanpldgi.l 188
                                       +p +pn + r +e+ r++ ++                  + + ++++    a+++ae++++a+ea+  a  +d + +
  gi|313126802|ref|YP_004037072.1|  35 DPRAPNRARRmFEALRDANEAvtvfvwggemgeseatdIGlSPEVLGAPKSAETTAEDTRRAVEAFVDAA-VDLVlF 110
                                       344455544445666666555777776666666664443334455555568899**************99.787744 PP

                                       ESSCCHHHCHHHHHHHTTTTSTE CS
                      Peripla_BP_4 189 aandgmaegalealeaaglagkv 211
                                         +dg+a  ++eal+aag++  v
  gi|313126802|ref|YP_004037072.1| 111 VGGDGTAADVAEALAAAGADETV 133
                                       566777777*********97765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.77
                                       EEEE--SSHHHHHHHHHHHHHT CS
                      Peripla_BP_4  58 giivapvdstalapalkkakaa 79 
                                       +++v+p d++++a+++++ + +
  gi|313126802|ref|YP_004037072.1| 148 VFAVSPEDAATVATTFDRTERR 169
                                       6899999999999998887665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHTT-SEEEE--SSH CS
                      Peripla_BP_4  42 aeQvaqiedaiakgvdgiivapvds 66 
                                       a++ ++++++ + g ++i+v+p+ +
  gi|313126802|ref|YP_004037072.1| 267 ATESEILDALGSEGENVIVVSPIGG 291
                                       7788888899999999999999876 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.045      64     129 ..      78     141 ..      49     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                       -TT-----GGGGSHHHHHHHHHHHHHHT--EEEEEESHHHH.HHHHHHHHT..T....--EEEEEEE CS
                               PFK  64 tiLgsaRskefkeregrkkaaenlkklgidaLvviGGdgsl.kganklseerkglleelkivgiPkT 129
                                        +Lg  +s e  + e++++a+e +++  +d ++ +GGdg+  ++a++l+ +  g  e++++ g P+ 
  gi|313126802|ref|YP_004037072.1|  78 EVLGAPKSAET-TAEDTRRAVEAFVDAAVDLVLFVGGDGTAaDVAEALAAA--GADETVPMLGAPAG 141
                                       68999999997.5677***********************972567777766..56699999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2264.60
//
Query:       gi|313126803|ref|YP_004037073.1|  [L=37]
Description: hypothetical protein Hbor_20620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 242.07
//
Query:       gi|313126804|ref|YP_004037074.1|  [L=232]
Description: competence/damage-inducible protein cina [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-37  126.5   0.2    8.8e-37  126.0   0.2    1.2  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.049   13.8   0.4       0.14   12.3   0.0    1.9  2  CinA_KH        Damage-inducible protein CinA KH domain
      0.052   13.5   0.0       0.15   12.1   0.0    1.7  2  PsbU           Photosystem II 12 kDa extrinsic protein (PsbU)


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.2   1.5e-40   8.8e-37       1     137 [.       4     156 ..       4     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 1.5e-40
                                       EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHH CS
                     MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpea 77 
                                       av+tvGdell+g++++tn+++lae+l+++gv+v+++t+vpD  +ei++ + +  +e+d++i+tGG+Gpt+dD+t + 
  gi|313126804|ref|YP_004037074.1|   4 AVVTVGDELLAGDTVNTNASWLAERLTARGVRVERVTTVPDRVAEIARVVNEYRAEYDAVIVTGGLGPTHDDLTMAG 80 
                                       79************************************************5555677******************** PP

                                       HHHHHSEE-HHHHHHHHHHHHHHCC.....................TTSHGGGGGGE.EETTEEEEE-SSHHHHHHH CS
                     MoCF_biosynth  78 laklfekelegfeeafrrvslkpgk.....................pvgvapgailsravgktiigLPGspkavkea 133
                                       +a++ ++el+++e+a++ ++ + g                      +vgvapga++++     i++LPG+p ++k++
  gi|313126804|ref|YP_004037074.1|  81 VAAAVGRELVEHEAALEWLTEHGGYaaaelsegttdlpararmlpnEVGVAPGAVVED-----IYVLPGVPEEMKAM 152
                                       **********************888*******************************84.....************** PP

                                       HHHH CS
                     MoCF_biosynth 134 leei 137
                                       +e i
  gi|313126804|ref|YP_004037074.1| 153 FERI 156
                                       **88 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.66   3.9e+03      41      60 ..      28      47 ..      24      59 .. 0.54
   2 ?   12.3   0.0   2.4e-05      0.14       4      49 ..     170     213 ..     167     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.66
                                      EEE...EEHHHHHHHHH... CS
                           CinA_KH 41 Rltakaaneeeaealiapve 60
                                      Rlta++   e +  + ++v 
  gi|313126804|ref|YP_004037074.1| 28 RLTARGVRVERVTTVPDRVA 47
                                      56666555555544444333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.4e-05
                                       EEE-S--HHHHHHHHGGGS-BSSSEEEEEEETTEEEEEEE...EEH CS
                           CinA_KH   4 LktfGigESavaekladlidrenptlAiyakegevtvRltakaane 49 
                                       ++t+   ES++  +l d+ +  + t++ y+ + +v+++lta+ ++e
  gi|313126804|ref|YP_004037074.1| 170 VRTVE-PESELVGRLHDVQEMFDVTVGSYPGD-DVRLKLTANDESE 213
                                       56666.7***********************86.69*****887766 PP

>> PsbU  Photosystem II 12 kDa extrinsic protein (PsbU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         1   6.2e+03      48      70 ..      36      58 ..      31      63 .. 0.71
   2 ?   12.1   0.0   2.5e-05      0.15      42      76 ..     130     164 ..     122     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                                      GGGGGG-TT--HHHHHHHHHHGG CS
                              PsbU 48 vedvlniPgLsekqkelleknle 70
                                      ve v  +P+  ++  ++++++  
  gi|313126804|ref|YP_004037074.1| 36 VERVTTVPDRVAEIARVVNEYRA 58
                                      77788888877777777766665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.5e-05
                                       S---SSGGGGGG-TT--HHHHHHHHHHGGGEE--- CS
                              PsbU  42 naPYdsvedvlniPgLsekqkelleknlekftvte 76 
                                        aP + ved++ +Pg+ e+ k+++e+ +++f    
  gi|313126804|ref|YP_004037074.1| 130 VAPGAVVEDIYVLPGVPEEMKAMFERIESEFNGET 164
                                       689999***********************997554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1508.59
//
Query:       gi|313126805|ref|YP_004037075.1|  [L=299]
Description: glycerophosphoryl diester phosphodiesterase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-28   99.2   0.0    4.6e-28   98.7   0.0    1.3  1  GDPD      Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0   2.5e-32   4.6e-28       1     258 [.      14     274 ..      14     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 2.5e-32
                                       TTTTTTTSSTTSHHHHHHHH.HTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH......BGGGS-HHHHHTST CS
                              GDPD   1 HRGasgnlpEnTlesfakAa.elGadyiEfDvqlTkDgvpVvlHDfnldrttdvagr.....ldvkdltleelkrld 71 
                                       HRG+ g +pEnT+ +  +A   + a ++E D++ T Dg++Vv+HD+ l    ++ +       +v+d ++eel++ +
  gi|313126805|ref|YP_004037075.1|  14 HRGFAGVYPENTVGAVGRATwGDDAEMVEIDIVPTADGKVVVFHDSELSGRDGGERGptdldGYVWDHSWEELQETE 90 
                                       ****************99953799*********************999765555555677777***********999 PP

                                       ECCTTCCCCSCCCSSGCCB...BHHHHHHH.HHHCCSEEEEEEECCCCCCCHHHH.....HHTCHHHCCCCCSCHH. CS
                              GDPD  72 kiakenkaqlsenrvrlefpfptleevlkk.pqnvglnieikipmlseakeeeel.....qivkeilksvdeilkk. 141
                                        +  +     s++++      p+le+v++  p + g+nie+k p + ++  +e+l     +    + ++++ + +  
  gi|313126805|ref|YP_004037075.1|  91 -V-LQ-----SGETI------PRLEQVFDAiPDDAGVNIEFKNPGTTNVRFAEKLsaaelE---SQMEVWRPMAETa 151
                                       .3.22.....46666......**********************999888766666563222...3333333333332 PP

                                       ..TT..STTCSCEEEESTHHHHHHHHHTCTCTEEEEEEHHHHHHC-E........EECHCCCCCCCTCCCCHHCCCH CS
                              GDPD 142 ..vlkkadkrkvifssfnpdilkllrekqpklpllflteggteaead.......ssleraakfakadallgevsava 209
                                         ++ +  + +v +ssf+ ++l  +r  +p++p+  l+ +  e   +             ++ ++   +      ++
  gi|313126805|ref|YP_004037075.1| 152 leIAAD-AENDVLVSSFHEAALAVVRDIDPDVPIGCLFWDSIETGLAitreydcEAIHPPYNMIQGTPFFEDEYYLS 227
                                       224444.4578888***********************9766665555444454544455566666666655555555 PP

                                       CCCEB.CHHHHHHHTT-EEEEBSB-THSHHHHHHHHCCC-SEEEES-HH CS
                              GDPD 210 eglgdpdlVkraksrglvvhvytvnnedeeemkrlleagvdgvitDfpd 258
                                         + d dlV+ a++ g  v ++t  ++   +  rl eagvdg+i D+p+
  gi|313126805|ref|YP_004037075.1| 228 GPFADVDLVEVAHEEGRTVNTWTIGTW--YQAERLAEAGVDGLIADYPN 274
                                       5556***********************..*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2104.33
//
Query:       gi|313126806|ref|YP_004037076.1|  [L=265]
Description: hypothetical protein Hbor_20650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1615.96
//
Query:       gi|313126807|ref|YP_004037077.1|  [L=226]
Description: hypothetical protein Hbor_20660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-93  312.2   0.0    2.1e-93  312.0   0.0    1.0  1  DUF2110   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2110  Uncharacterized protein conserved in archaea (DUF2110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.0   0.0   1.2e-97   2.1e-93       1     223 []       4     224 ..       4     224 .. 0.97

  Alignments for each domain:
  == domain 1  score: 312.0 bits;  conditional E-value: 1.2e-97
                           DUF2110   1 latkvY...dareralesleslvenelkdLdveleisvreddfvkvtleGedeevaanllreefgeitkeveegevy 74 
                                       latk+Y   dareral+sl+sl++n++++Ldv+++i+vr+ddf++vt++G+d+++a+nll +e+ge+t++++ege+y
  gi|313126807|ref|YP_004037077.1|   4 LATKCYvegDARERALDSLDSLIRNDIGELDVSWDIGVRDDDFISVTVSGDDATAARNLLGDEWGEVTPHLTEGETY 80 
                                       689************************************************************************** PP

                           DUF2110  75 vGtlesldedgfvldigve..vripkdelkpLgegspeqiaerFGlvqhlpleveveeveeeekeiearltdeqvdr 149
                                       vGtl+++dedgf+ld+g++  vrip+de++ Lg+gsp+qi++rFG+vqh+pl+++++e  +      +rl+de++d+
  gi|313126807|ref|YP_004037077.1|  81 VGTLDEWDEDGFILDVGFHnyVRIPADEIG-LGTGSPTQIRDRFGIVQHTPLSFVYDE--D-----GSRLSDETRDK 149
                                       *****************9999*********.*************************33..3.....589******** PP

                           DUF2110 150 lyewkk.gkedrlivnsatrsevkaalnraGhardivtverlglleqsvvcredtdapGlvaeiGpylpaelkvv 223
                                       ly+w++ ++++r++vnsatr+ev+a++nraGha+divtverlglleqs+vc e+td+pGl+a+iG+ylpaelk+v
  gi|313126807|ref|YP_004037077.1| 150 LYDWTReEGSGRVNVNSATRGEVRATVNRAGHAKDIVTVERLGLLEQSIVCPEGTDPPGLLASIGSYLPAELKCV 224
                                       *****96679****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1274.44
//
Query:       gi|313126808|ref|YP_004037078.1|  [L=174]
Description: transcription factor IIE subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-20   71.8   0.1    9.5e-20   70.4   0.0    1.7  2  TFIIE_alpha  TFIIE alpha subunit
      0.002   18.2   0.2      0.006   16.7   0.0    1.9  2  Sigma70_r3   Sigma-70 region 3
  ------ inclusion threshold ------
       0.37   10.5   1.4       0.99    9.1   0.0    2.2  3  GntR         Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   1.6e-23   9.5e-20      25     103 ..      33     111 ..      11     113 .. 0.96
   2 ?   -1.4   0.0      0.35   2.1e+03      79      96 ..     151     168 ..     143     172 .. 0.62

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.6e-23
                                       TTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHHHHHHHC CS
                       TFIIE_alpha  25 kgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkkLeekle 101
                                       +gevt+e+la+el+++ln +r++L+ Lye  l++y+r rde+ +w +y w ++ye++++ + +++ +++  Lee le
  gi|313126808|ref|YP_004037078.1|  33 DGEVTDEELAEELGLELNDVRRALFILYENDLASYRRVRDEDSGWLTYLWTFHYENIPENLEEEMYRLLDALEERLE 109
                                       69**************************************************************************9 PP

                                       CC CS
                       TFIIE_alpha 102 ke 103
                                        e
  gi|313126808|ref|YP_004037078.1| 110 YE 111
                                       88 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.35
                                       CCHCCCHHHHHHHHHHHH CS
                       TFIIE_alpha  79 eklvdvvkrkleevvkkL 96 
                                       + +vd++ r++ee++ +L
  gi|313126808|ref|YP_004037078.1| 151 DDMVDAMERRIEELRDEL 168
                                       455566666666655554 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     1e-06     0.006      20      41 ..      35      56 ..      33      75 .. 0.91
   2 ?   -1.5   0.0      0.47   2.8e+03       9      22 ..     160     173 ..     146     174 .] 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-06
                                      XXXHHHHHHHHTXXHHHHHHHH CS
                        Sigma70_r3 20 ePtpeEiAeeLglseekVrevl 41
                                      e t+eE+AeeLgl++++Vr++l
  gi|313126808|ref|YP_004037078.1| 35 EVTDEELAEELGLELNDVRRAL 56
                                      679****************997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.47
                                       HHHHHHHHHSSXXX CS
                        Sigma70_r3   9 aqreLeqelgrePt 22 
                                        ++eL+ el+ e+t
  gi|313126808|ref|YP_004037078.1| 160 RIEELRDELNVEAT 173
                                       46777777777776 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00017      0.99      27      55 ..      38      66 ..      31      71 .. 0.85
   2 ?   -2.8   0.1      0.86   5.1e+03       7      27 ..      87     106 ..      86     108 .. 0.61
   3 ?   -0.9   0.0      0.22   1.3e+03      27      38 ..     161     172 ..     160     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00017
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglve 55
                                       +eLa+e+g   + vR+AL  L + +l+ 
  gi|313126808|ref|YP_004037078.1| 38 DEELAEELGLELNDVRRALFILYENDLAS 66
                                      58*****************9998888766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.86
                                       HHHHHHHHTTSS-TTSB---H CS
                              GntR   7 erLredIlsgelrpGdkLPse 27 
                                       e + e + +  +r  d+L +e
  gi|313126808|ref|YP_004037078.1|  87 ENIPENLEEEMYRLLDAL-EE 106
                                       556666666667777777.55 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.22
                                       HHHHHHHHTS-H CS
                              GntR  27 ereLaaefgVsr 38 
                                        +eL++e++V +
  gi|313126808|ref|YP_004037078.1| 161 IEELRDELNVEA 172
                                       689*****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1144.86
//
Query:       gi|313126809|ref|YP_004037079.1|  [L=192]
Description: hypothetical protein Hbor_20680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-48  163.1   0.0      3e-48  162.6   0.0    1.2  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.0   1.7e-52     3e-48       1     119 []      58     175 ..      58     175 .. 0.97

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 1.7e-52
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE...EEEEE------TCHHHHSSEEEESS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkek..dllvvvGaekvprevyeladynvsvg 75 
                                       +Gg+f ve+++ l+++i++++   g+vvhltmyGe++++v e+++++++  ++l+vvG+ekvp+evye+adynv+v+
  gi|313126809|ref|YP_004037079.1|  58 FGGPFGVELTDALNAVIRNWE---GVVVHLTMYGERVQDVEEDVREVHEetPILIVVGGEKVPFEVYEHADYNVGVT 131
                                       8********************...*********************9766559************************* PP

                                       SS---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                             Trm56  76 nqPhsevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                       nqPhseva+la+fldrl++g+el++e+e+a+ kviP+++gkkvv
  gi|313126809|ref|YP_004037079.1| 132 NQPHSEVAGLAVFLDRLFDGRELDREWENADRKVIPKATGKKVV 175
                                       ******************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.94
# Mc/sec: 618.40
//
Query:       gi|313126810|ref|YP_004037080.1|  [L=316]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-52  175.8   0.0    1.2e-51  175.6   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.8e-41  141.2   0.1      2e-40  139.2   0.1    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.9e-19   69.9   0.1    2.5e-19   69.5   0.1    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.9e-13   50.1   0.0    2.5e-13   49.7   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.6e-13   49.8   0.2    3.1e-12   46.3   0.2    2.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.9e-12   46.8   0.0    4.7e-12   46.2   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    8.4e-09   35.0   0.1    3.6e-07   29.6   0.0    2.7  2  NAD_binding_4    Male sterility protein
    1.1e-05   25.1   0.4     0.0014   18.2   0.1    2.1  2  NmrA             NmrA-like family
    3.6e-05   24.0   0.2    8.4e-05   22.8   0.2    1.7  1  TrkA_N           TrkA-N domain
    0.00042   19.8   0.6     0.0066   15.9   0.4    2.8  2  adh_short        short chain dehydrogenase
     0.0074   16.6   0.1      0.013   15.7   0.1    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.024   14.7   0.1    1.5  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
      0.033   13.7   0.1        1.1    8.8   0.0    2.1  2  DUF1188          Protein of unknown function (DUF1188)
      0.069   13.3   0.1       0.15   12.2   0.1    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6   0.0   9.1e-55   1.2e-51       1     241 []       8     235 ..       8     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 9.1e-55
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       ++VtG++G++Gs+l+++l +++ +v++ d ls++ ++   + +e+v++dltd+s++++++ e ++d+v+h+Aa    
  gi|313126810|ref|YP_004037080.1|   8 VVVTGGAGLVGSHLAQYLRDEN-DVVVADDLSKGTRERVPDGVEFVKADLTDASDVAEVITE-DVDVVFHFAA--YT 80 
                                       68******************97.9*******999999999999******************7.9*******77..77 PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS.BSTCSTTS----SSHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp.keettltgplkpnspYaaaKlageklv 153
                                       +++  dp +++e+n+++t+n+le + + gv ++ f sSs+vYG+ ++ p  e+++   pl+p s Y+a+Kla e l+
  gi|313126810|ref|YP_004037080.1|  81 DTNYADPRKLFEENTEMTYNVLERMEEVGVSNIAFTSSSTVYGEAPR-PtPEDYA---PLEPISVYGASKLADEGLL 153
                                       8899***************************************9998.7467777...******************* PP

                                       HHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                         Epimerase 154 eayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                         ya++ ++ +  +r  n++Gp     ++ +vip +i+k+le  + +t+lg+g++   +l+veD+++ai +v+e+ +
  gi|313126810|ref|YP_004037080.1| 154 STYAHSKDVTVWLFRFANIVGPK----QRGNVIPDFIEKLLEDPETLTILGNGRQEKSYLHVEDCVRAISHVVENAE 226
                                       **********************9....***************999******************************55 PP

                                       T-STTEEEEES CS
                         Epimerase 231 agdkgeiyniG 241
                                         ++ ++yn+G
  gi|313126810|ref|YP_004037080.1| 227 --QSMNTYNLG 235
                                       ..4678***98 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.1   1.5e-43     2e-40       2     264 ..      10     251 ..       9     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 1.5e-43
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       +TG+aG +Gs+la++L +++  v++ +++s+ +     e++         + ++++k+DltD+s + +++ e  +d 
  gi|313126810|ref|YP_004037080.1|  10 VTGGAGLVGSHLAQYLRDEND-VVVADDLSKGT----RERVP--------DGVEFVKADLTDASDVAEVITED-VDV 72 
                                       9***************99965.54545554443....34433........3578****************995.9** PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaa 155
                                       v+++AA    d+ + +P + +e n   t+++Le + ++g++    + ++S+s+vYG++ +   ++  p++P s Y+a
  gi|313126810|ref|YP_004037080.1|  73 VFHFAAYT--DTNYADPRKLFEENTEMTYNVLERMEEVGVS---NIAFTSSSTVYGEAPRPTPEDYAPLEPISVYGA 144
                                       ******75..7888*************************96...5777***********9999999*********** PP

                                       HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHH CS
                     GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyvea 232
                                       +Kl+ + +   y ++ ++ +   ++ n  +p++      + i++++ + +++ ++ ++lGn+++ ++++hv+D v+a
  gi|313126810|ref|YP_004037080.1| 145 SKLADEGLLSTYAHSKDVTVWLFRFANIVGPKQR----GNVIPDFIEKLLEDPETLTILGNGRQEKSYLHVEDCVRA 217
                                       ********************************84....569************************************ PP

                                       HHHHHHCSS-..--EEE-TT-EEECHHCHHCCHH CS
                     GDP_Man_Dehyd 233 mwlmlqqdkp..edyviatgethsvrefvelafl 264
                                       +  ++++ ++  ++y+++t +t+sv +++++   
  gi|313126810|ref|YP_004037080.1| 218 ISHVVENAEQsmNTYNLGTRTTTSVTTIADIVSD 251
                                       *****98654237899999999999887776543 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.1   1.9e-22   2.5e-19       2     235 ..       7     257 ..       6     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.9e-22
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..............T--TTSHHHHHHHHHHH--SEEEE------H CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..............eldltdaeavaellkeakpdvvvnaAAytav 64 
                                       +++vtG+ G++Gs+La+ l+ e+  v+a + +              ++dltda+ vae++ e + dvv + AAyt+ 
  gi|313126810|ref|YP_004037080.1|   7 RVVVTGGAGLVGSHLAQYLRDENDVVVADDLSkgtrervpdgvefvKADLTDASDVAEVITE-DVDVVFHFAAYTDT 82 
                                       799******************998888876667899*************************9.99**********99 PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TT.S----SSHHHHHHHHHHHHHHH. CS
                     RmlD_sub_bind  65 DkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeed.detsPlnvYGrtKlaGEqavla. 138
                                         a  ++++ ++ n e + ++ e  ++vg+  + + S+  V+ Ge++rp  ed ++ +P++vYG++Kla E      
  gi|313126810|ref|YP_004037080.1|  83 NYA--DPRKLFEENTEMTYNVLERMEEVGVSnIAFTSSSTVY-GEAPRPTPEDyAPLEPISVYGASKLADEGLLSTy 156
                                       998..57888999****************9725567788887.77788855542788**************998875 PP

                                       ...H-SSEEEEEE-SEESS..SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-E CS
                     RmlD_sub_bind 139 ...agkkalivRtswvyge..kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekelag 208
                                          +  +++++R++ + g   +g+     + +l+++ e+l++     q  s  +++d  +++ +++e+a +      
  gi|313126810|ref|YP_004037080.1| 157 ahsKDVTVWLFRFANIVGPkqRGNVIPDFIEKLLEDPETLTILGNgrQEKSYLHVEDCVRAISHVVENAEQ---SMN 230
                                       4334457889*******874244445566677779*******97533777778899999999999999986...689 PP

                                       EEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 209 vyHlanegetswlefArailkeagads 235
                                       +y l+ + +ts   +A+ + + ++ d+
  gi|313126810|ref|YP_004037080.1| 231 TYNLGTRTTTSVTTIADIVSDVMDLDP 257
                                       *****************9999888776 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   1.9e-16   2.5e-13       1     154 [.       9     150 ..       9     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.9e-16
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleeal.egvdvvihlasl 76 
                                       vvtGgaG +G++l + L +++   +v v+D   +  ++e     +v+ ++++D+td++++ e++ e+vdvv+h a++
  gi|313126810|ref|YP_004037080.1|   9 VVTGGAGLVGSHLAQYLRDEN---DVVVADDLSKG-TRE-RVPDGVE-FVKADLTDASDVAEVItEDVDVVFHFAAY 79 
                                       8************99998777...58888743333.323.3344566.9***********9986379********** PP

                         3Beta_HSD  77 vdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                       +d    + ++ + + n + T nvle   + gv  + +tSs  v g+     +      e + +  + ++y  sK   
  gi|313126810|ref|YP_004037080.1|  80 TDTNYADPRK-LFEENTEMTYNVLERMEEVGVSNIAFTSSSTVYGE--APRPT----PEDYAPLEPISVYGASKLAD 149
                                       **99966666.9999***************************9998..22222....23445555666666666544 PP

                         3Beta_HSD 154 E 154
                                       E
  gi|313126810|ref|YP_004037080.1| 150 E 150
                                       4 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.2   2.4e-15   3.1e-12       1     242 [.       8     248 ..       8     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.4e-15
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       v+vtG++G +Gs+l + + ++  + +++ +       +++k ++e++ +  ++     v +d++d++ ++++++  +
  gi|313126810|ref|YP_004037080.1|   8 VVVTGGAGLVGSHLAQYLRDE--NDVVVAD-------DLSKGTRERVPD-GVE----FVKADLTDASDVAEVIT-ED 69 
                                       789999999999987665433..4555554.......344444444554.343....3479************9.8* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE.............GGG.SS--SHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt.............DKA.vnPtnvmGa 140
                                       vdvvfh AA+     +   p + ++ N   t nv+e   e gv+++ + S+             D A  +P++v+Ga
  gi|313126810|ref|YP_004037080.1|  70 VDVVFHFAAYTDTNYA--DPRKLFEENTEMTYNVLERMEEVGVSNIAFTSSstvygeaprptpeDYApLEPISVYGA 144
                                       **********987765..68999**********************99998733444444444445555689****** PP

                                       HHHHHHHHHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHHHHHHHTT.SSEEES.-TT-EEEEE-HHHHHHHH CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekktkfvvvRfGNVlg..SrGSviplFkkqikeg.gpvtvT.dpemtRyfmtieeavqLv 213
                                       +K++ e ll ++a+++   + ++ + Rf N++g   rG vip F +++ e+ + +t+  + +  + ++ +e+ v+ +
  gi|313126810|ref|YP_004037080.1| 145 SKLADEGLLSTYAHSK---DVTVWLFRFANIVGpkQRGNVIPDFIEKLLEDpETLTILgNGRQEKSYLHVEDCVRAI 218
                                       **********999998...89999********94458*******999888768899852557778888888888888 PP

                                       HHHHHH--SS.-EEEE--.-EEEHHHHHHH CS
                   Polysacc_synt_2 214 lqalalakgg.eifvldmGepvkivdlaka 242
                                        + +++a+++ + + l    +++++ +a  
  gi|313126810|ref|YP_004037080.1| 219 SHVVENAEQSmNTYNLGTRTTTSVTTIADI 248
                                       777777665413454444444455555544 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   3.6e-15   4.7e-12       1     129 [.      12     150 ..      12     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.6e-15
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHH.TT-SEEEES---TCC... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaeal.kgadaVvsalggggk... 73 
                                       G+ G vG++l++ l +++  +v +++ + +k ++ +  +g+e v++d+td++d+ae++ +++d+V+  ++ +++   
  gi|313126810|ref|YP_004037080.1|  12 GGAGLVGSHLAQYLRDEN--DV-VVADDLSKGTRERVPDGVEFVKADLTDASDVAEVItEDVDVVFHFAAYTDTnya 85 
                                       999************996..33.5678888887655569*******************5599999877755555566 PP

                                       ........HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH..HCCHHHHHHHHHHHH CS
                    NAD_binding_10  74 ........deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnk..ellkaylaakraaee 129
                                               ++e++ n+++ ++e gv+ + + s+  v+ e+p++++e +   e ++ ++ a + a+e
  gi|313126810|ref|YP_004037080.1|  86 dprklfeeNTEMTYNVLERMEEVGVSNIAFTSSSTVYGEAPRPTPEDYAplEPIS-VYGASKLADE 150
                                       555677666666*****************************99988665222333.3444444433 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.063        81       1      20 [.      10      29 ..      10      40 .. 0.79
   2 !   29.6   0.0   2.8e-10   3.6e-07      78     214 ..      60     180 ..      29     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.063
                                      EE-TTSHHHHHHHHHHHHHS CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrtt 20
                                      +TG+ G +G++L + L +++
  gi|313126810|ref|YP_004037080.1| 10 VTGGAGLVGSHLAQYLRDEN 29
                                      7**********977654443 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 2.8e-10
                                       HHHHHHHHHH--EEEE--SS-S.ST.TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfde.pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvye 153
                                       ++ ++ ++e vdv++h aA ++ ++ + ++l++ N+e t +vle  +++     + + S+++v+ge  +        
  gi|313126810|ref|YP_004037080.1|  60 SDVAEVITEDVDVVFHFAAYTDTNYaDPRKLFEENTEMTYNVLERMEEVGVS-NIAFTSSSTVYGEAPRP------- 128
                                       35566679**************99867889*****************99888.999****9999999954....... PP

                                       ......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST- CS
                     NAD_binding_4 154 egekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGw 214
                                                + e     +    Y  sK + E l+ ++++++++ v  +R  +i+g  + G 
  gi|313126810|ref|YP_004037080.1| 129 ---------TPEDYAPLEPISVYGASKLADEGLLSTYAHSKDVTVWLFRFANIVGPKQRGN 180
                                       .........4555566667779999999999999999999999999999999998555553 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.1e-06    0.0014       1      83 [.       8      88 ..       8     120 .. 0.80
   2 ?    5.2   0.0     0.011        14     155     226 ..     184     254 ..     175     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHH.TT-SEEEE---GGS-H CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslveal.kgvdvvfsvtgfyske 78
                                      ++v+G++G  G++++++l +++     +v d  s+  ++    Gve+vk+dl d + ++e++ ++vdvvf   ++++++
  gi|313126810|ref|YP_004037080.1|  8 VVVTGGAGLVGSHLAQYLRDENDV---VVADDLSKGTRERVPDGVEFVKADLTDASDVAEVItEDVDVVFHFAAYTDTN 83
                                      68***************9988754...5668888888888899************9999998468*****999877555 PP

                                      HHHHH CS
                              NmrA 79 iedgk 83
                                       +d  
  gi|313126810|ref|YP_004037080.1| 84 YADPR 88
                                      55444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                                       S-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHT CS
                              NmrA 155 lkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkig 226
                                        +++++ ++ +++t+lg+g  +  +l ++eD  +++ +++++ ++  + +   +  t s+++i+++ + +++
  gi|313126810|ref|YP_004037080.1| 184 DFIEKLLEDPETLTILGNGRQEKSYL-HVEDCVRAISHVVENAEQSMNTYNLGTRTTTSVTTIADIVSDVMD 254
                                       455555555569********999999.***************999999999999999999999999998776 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   6.5e-08   8.4e-05       5      68 ..      13      75 ..       8     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.5e-08
                                      S-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE CS
                            TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadavia 68
                                      G+G vG++la++L++++ dvvv d+  +  +e   +g+e+v++d td + ++e   e++d+v  
  gi|313126810|ref|YP_004037080.1| 13 GAGLVGSHLAQYLRDEN-DVVVADDLSKGTRERVPDGVEFVKADLTDASDVAEVITEDVDVVFH 75
                                      89*************99.6****************************************99875 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   5.2e-06    0.0066       1     165 [.       6     158 ..       6     165 .. 0.80
   2 ?   -2.6   0.0       2.5   3.2e+03     151     168 ..     292     309 ..     280     312 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.2e-06
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k v+vtG+++ +G  +a+ l  e+  vv+ d s+ + e+v +        + ++++D+td+++v +++ +       
  gi|313126810|ref|YP_004037080.1|   6 KRVVVTGGAGLVGSHLAQYLRDENDVVVADDLSKGTRERVPDG-------VEFVKADLTDASDVAEVITE------D 69 
                                       679***************9999987777777776666555554.......77********9999988865......6 PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEE..GGGTSB-TT....... CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsS..vagkvpvag....... 145
                                       +dv+ + A+        +++ ++ ++++e N     ++t  vl+ m +    +I ++sS  v g+ p +        
  gi|313126810|ref|YP_004037080.1|  70 VDVVFHFAAY------TDTNYADPRKLFEENT----EMTYNVLERMEEVGVSNIAFTSSstVYGEAPRPTpedyapl 136
                                       9********9......6899999999*99997....688999999**9*********99444577665543333333 PP

                                       ..BHHHHHHHHHHHHHHHHHHH CS
                         adh_short 146 ..vaaYsAsKaavagltrslak 165
                                          ++Y+AsK a +gl ++ a+
  gi|313126810|ref|YP_004037080.1| 137 epISVYGASKLADEGLLSTYAH 158
                                       3379999999999999998876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHHHG CS
                         adh_short 151 AsKaavagltrslakela 168
                                       +s  av+  tr+la el+
  gi|313126810|ref|YP_004037080.1| 292 SSDDAVRRATRELAAELR 309
                                       444566666666666665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     1e-05     0.013       5      81 ..      13      81 ..       8      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                                      --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS.SEEEE-SSGGG CS
                   Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg.dlvvnlsppis 81
                                      GaG vG+ +a++l +++dv    +vad   ++  ++        +e+++ d  + ++ +a++++e  d+v + + ++ 
  gi|313126810|ref|YP_004037080.1| 13 GAGLVGSHLAQYLRDENDV----VVADDLSKG-TRER---VPDGVEFVKADLTDASD-VAEVITEDvDVVFHFAAYTD 81
                                      66**************997....666654444.4554...57889999*********.666666666***99988874 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.9e-05     0.024       2     112 ..       7     112 ..       6     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                                       EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE.SSGGGGTTESEEEE-- CS
                           Ldh_1_N   2 kvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse.keeealkdadvvvita 77 
                                       +v+v+G aG +G++la  l  ++   ++++ D      +G    + ++  f++++    +   e +++d+dvv   a
  gi|313126810|ref|YP_004037080.1|   7 RVVVTGGAGLVGSHLAQYLRDEN---DVVVADDL---SKGTRERVPDGVEFVKADLTDASdVAEVITEDVDVVFHFA 77 
                                       89***************999874...34444443...578888888888888888777664788899********** PP

                                       S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTS CS
                           Ldh_1_N  78 gvprkpGetRddLlkvNakIvkeiveaiakvapna 112
                                       + +  +  + + L++ N +++ ++ e +++v+ + 
  gi|313126810|ref|YP_004037080.1|  78 AYTDTNYADPRKLFEENTEMTYNVLERMEEVGVSN 112
                                       *************************9999998443 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00083       1.1      41      88 ..       3      52 ..       1      72 [. 0.75
   2 ?    3.0   0.0      0.05        64     138     182 ..     209     253 ..     180     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00083
                                      E..EEEEEE.S-CCCHHHHHHHHCCCEEEEEEE.SSGGGGGGSSSTHHHH CS
                           DUF1188 41 leeknvlvi.GaYltGaaiakkLskkeevtlvD.iephlkellekdvefk 88
                                      l+ek+v+v  Ga l+G+ +a+ L+ +++v++ D   +  +e ++++vef 
  gi|313126810|ref|YP_004037080.1|  3 LSEKRVVVTgGAGLVGSHLAQYLRDENDVVVADdLSKGTRERVPDGVEFV 52
                                      5677888873589*************999999725667888888888884 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.05
                                       HHH--HHHHHGGTTTSEEEEEEETTS--SB--HHHHHHHHHHHHH CS
                           DUF1188 138 keanntekrlesveaekkgiLktkglesKTSGtmTLtvdvlrdal 182
                                        +++++ + ++ v  + + +++t+ l ++T  ++T   d++ d++
  gi|313126810|ref|YP_004037080.1| 209 LHVEDCVRAISHVVENAEQSMNTYNLGTRTTTSVTTIADIVSDVM 253
                                       566778888888888888999999999999999998888888887 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012      0.15       2      75 ..       7      77 ..       6      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH.-SEEEE-S CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek.advliDFT 75
                                      +v+v+G +G +G+++++ +++++d+ ++  +++ +     + + + +++ k +++  +d++ev+++ +dv+  F 
  gi|313126810|ref|YP_004037080.1|  7 RVVVTGGAGLVGSHLAQYLRDENDVVVADDLSKGT----RERVPDGVEFVKADLTDASDVAEVITEdVDVVFHFA 77
                                      89************************999999987....334444444555577767888888887799998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.74u 0.38s 00:00:01.12 Elapsed: 00:00:00.59
# Mc/sec: 1620.00
//
Query:       gi|313126811|ref|YP_004037081.1|  [L=248]
Description: hypothetical protein Hbor_20700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-30  105.8   9.3    1.4e-25   90.6   5.9    2.4  2  DUF2797   Protein of unknown function (DUF2797)


Domain annotation for each model (and alignments):
>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   5.9   7.7e-30   1.4e-25       1     155 [.      29     173 ..      29     191 .. 0.85
   2 !   16.3   0.0   3.8e-07    0.0068     200     231 .]     197     231 ..     181     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 7.7e-30
                           DUF2797   1 GkelaltltgerrCvn.......C.........grktkksfsqgvCakCfkklaeadecimkpekchahlgtclrdp 61 
                                       G+el++tl ger+C++       C         +r++++++                        c   +gtcl+d 
  gi|313126811|ref|YP_004037081.1|  29 GTELTYTL-GERHCAGvmtddehCacendaapyCRDHRSTW-----------------------VCAKCTGTCLKD- 80 
                                       88999999.*******4444444222444444444444444.......................455559******. PP

                           DUF2797  62 eweekaclqphvVYLa..nssevKVGiTrkeqvptRwidQGAvqaiplaevanRrlaglvevalketvaDktnwrkm 136
                                           ++c  +h +YLa  +++ +KVG+T++++++tR+ +QGA+ + ++ +van+r+a+++e+ l++ ++D+++  ++
  gi|313126811|ref|YP_004037081.1|  81 ---VMDCHDSHAIYLAafAPDVFKVGVTKEWRLETRLREQGADRGAHIRTVANGRIAREIEAGLADEIPDRIRVPTK 154
                                       ...9************999********************************************************** PP

                           DUF2797 137 lksevedvdlsaeaeelae 155
                                       + + + +vd++a+++ l e
  gi|313126811|ref|YP_004037081.1| 155 RDGLHRKVDEAAWESLLSE 173
                                       **********999876655 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.8e-07
                           DUF2797 200 eveGtllGikGqylildtgt...vlnirkleGyev 231
                                         +Gt++G++G++l+ld+++   ++++r+l G+ev
  gi|313126811|ref|YP_004037081.1| 197 IATGTVRGVQGRLLVLDHAGstyAVDLRDLVGHEV 231
                                       469***************99999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1412.17
//
Query:       gi|313126812|ref|YP_004037082.1|  [L=147]
Description: hypothetical protein Hbor_20710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.026   14.8   0.0       0.03   14.5   0.0    1.0  1  MutS_III     MutS domain III
      0.096   11.5   0.3      0.096   11.5   0.3    1.7  2  XRCC4        DNA double-strand break repair and V(D)J recombi
        2.7    8.5   6.0          3    8.4   0.6    2.1  2  DUF4140      N-terminal domain of unknown function (DUF4140)


Domain annotation for each model (and alignments):
>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.1e-06      0.03     127     185 ..      34     146 ..       6     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHB-SS--SSGGGS--B-T.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                          MutS_III 127 laelleeaideeplalekegedlra.................................................... 151
                                       ++e++ee               +r+                                                    
  gi|313126812|ref|YP_004037082.1|  34 FRERVEE---------------IRKrreeereegerpspeemmgggggpgggnpfaqmmsgmmggggpgmgggmggg 95 
                                       3333333...............2223333334445555688999999999999999999999999999999999999 PP

                                       ..................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHH CS
                                       ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 ..................iealeqelfqelleeveealerlrrlaealaeLD 185
                                                         +e+l +e +++l++ev++a+ +l+r+a+a+  LD
  gi|313126812|ref|YP_004037082.1|  96 pggppgaaggrgesesagNEELVRE-VRQLRDEVRDATRQLQRIAQAVEDLD 146
                                       9999999999999999865555555.99**********************99 PP

>> XRCC4  DNA double-strand break repair and V(D)J recombination protein XRCC4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.1      0.22   1.3e+03     201     201 ..      36      36 ..       3      60 .. 0.45
   2 ?   11.5   0.3   1.6e-05     0.096     142     178 ..     110     146 ..     106     147 .] 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.22
                             XRCC4 201 k 201
                                       +
  gi|313126812|ref|YP_004037082.1|  36 E 36 
                                       1 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.6e-05
                             XRCC4 142 lqakNehLqkENerLlrdwsdvterlekyvkakEele 178
                                       + a Ne L +E  +L+ + +d t +l+++++a+E+l+
  gi|313126812|ref|YP_004037082.1| 110 ESAGNEELVREVRQLRDEVRDATRQLQRIAQAVEDLD 146
                                       6789******************************996 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.6     0.022   1.3e+02      65      87 ..      23      51 ..       4      56 .. 0.62
   2 ?    8.4   0.6    0.0005         3      60      89 ..     115     143 ..     104     147 .] 0.66

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.022
                           DUF4140 65 e......elkalraeleeledelaalede 87
                                      +      e k+ r+++ee+++++++ ++e
  gi|313126812|ref|YP_004037082.1| 23 AgadgddEEKSFRERVEEIRKRREEEREE 51
                                      04455545677777777777777766665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0005
                           DUF4140  60 reaeeeelkalraeleeledelaaledela 89 
                                       +e ++ e+++lr+e++ ++++l+++ ++ +
  gi|313126812|ref|YP_004037082.1| 115 EELVR-EVRQLRDEVRDATRQLQRIAQAVE 143
                                       22222.588888888888888888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      829  (0.0462379); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 857.86
//
Query:       gi|313126813|ref|YP_004037083.1|  [L=371]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-31  107.0   0.0    2.1e-30  105.5   0.0    1.7  2  Glycos_transf_1  Glycosyl transferases group 1
    2.4e-27   96.0   0.2    7.4e-27   94.4   0.4    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.4e-22   80.5   0.0    7.3e-22   78.2   0.0    2.1  2  Glyco_trans_1_4  Glycosyl transferases group 1
    2.7e-13   50.6   4.0      1e-12   48.8   1.6    2.4  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0024   18.3   0.1     0.0072   16.7   0.0    1.8  2  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.038   14.0   0.0    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.65     2e+03      89     102 ..     142     155 ..     132     173 .. 0.77
   2 !  105.5   0.0     7e-34   2.1e-30      13     161 ..     197     337 ..     186     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.65
                                       HHHCESEEEEEESS CS
                   Glycos_transf_1  89 llknadifvlpsis 102
                                       ++ +ad++v+ps+ 
  gi|313126813|ref|YP_004037083.1| 142 FFGRADAVVCPSQA 155
                                       56789******997 PP

  == domain 2  score: 105.5 bits;  conditional E-value: 7e-34
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                        + +++ + gr  +eK++d ++ka++ l      ++ +v+ G+g+ ++el++la + +l  + +flg+++re+l+++
  gi|313126813|ref|YP_004037083.1| 197 PDGPLVGYTGRHGYEKNLDEFLKAADGL------DATVVFGGDGPAREELESLATKMGL--DAHFLGFLPREELPAF 265
                                       477899********************66......789**********************..999************* PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeel 161
                                       +++ d+fv+ps  E  G+v+lEA a+g+pv+ +n g ++++v+dg+tG+++  ++ +a  +ai+++l+++e+
  gi|313126813|ref|YP_004037083.1| 266 YSALDAFVFPSPVETQGLVALEANACGTPVVGVNEGALSDTVVDGVTGYHYSLGDTDACRAAIERVLDERET 337
                                       ********************************************************************9975 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.4   2.5e-30   7.4e-27       1     170 []      15     181 ..      15     181 .. 0.89
   2 ?   -2.1   0.0       1.1   3.4e+03     127     142 ..     262     277 ..     220     286 .. 0.61

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 2.5e-30
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvH 77 
                                       v+Gv   v +   ++++r  + +vv pg+d+  +++    + v++v +p+++++++    ++r+  +++  ++D+vH
  gi|313126813|ref|YP_004037083.1|  15 VNGVSYTVQTWRDHWRERDGRMDVVYPGTDDYVPDA--GEYPVRSVSFPFYEGYRL---GVPRVPSRVD--DVDLVH 84 
                                       68****************************999999..445666666666665555...4567778888..9***** PP

                    Glyco_transf_4  78 ahspaalgaallalrrrlgiplVltvHglye.....krllkarlkplsrllralerrllrradrviavSeatadelr 149
                                       ah+p+alg+++l+l+r++++p+++++H++        +   ++ ++ + l +++er+++ rad+v+++S+at+d+l+
  gi|313126813|ref|YP_004037083.1|  85 AHTPFALGLSGLRLARQKNLPFIASYHTPTGeyadyLTSRDSFEQRIESLSERYERWFFGRADAVVCPSQATRDHLH 161
                                       ******************************9999987777788889999**************************** PP

                    Glyco_transf_4 150 erygvppekitVipnGvDler 170
                                          gv+   + V+ nG+D++r
  gi|313126813|ref|YP_004037083.1| 162 NVVGVE-GEVIVLSNGIDTDR 181
                                       *****9.7999********98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                    Glyco_transf_4 127 errllrradrviavSe 142
                                       +  ++++ d+++ +S+
  gi|313126813|ref|YP_004037083.1| 262 LPAFYSALDAFVFPSP 277
                                       3345666666666665 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.89   2.7e+03      69      81 ..     142     157 ..     115     171 .. 0.72
   2 !   78.2   0.0   2.5e-25   7.3e-22       2     133 ..     200     333 ..     199     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.89
                                       HHHH-SEEEE--...- CS
                   Glyco_trans_1_4  69 llaaadvfvaPs...e 81 
                                       ++ +ad +v+Ps   +
  gi|313126813|ref|YP_004037083.1| 142 FFGRADAVVCPSqatR 157
                                       5778999999995442 PP

  == domain 2  score: 78.2 bits;  conditional E-value: 2.5e-25
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaa 73 
                                       p ++++Gr    +k++d +l+a+  l    +++v+ Gdgp r eele+la   gl  + +f+Gf+  e+l+++++a 
  gi|313126813|ref|YP_004037083.1| 200 PLVGYTGRH-GYEKNLDEFLKAADGLD---ATVVFGGDGPaR-EELESLATkmGL--DAHFLGFLprEELPAFYSAL 269
                                       67899***9.455*************9...57999*****65.6***98864666..6*******9889******** PP

                                       SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                       d fv+Ps  e+ gl++lEa a+g+pvV  + g+++++v  g++g+  + gd++a  +ai+r+l+
  gi|313126813|ref|YP_004037083.1| 270 DAFVFPSpvETQGLVALEANACGTPVVGVNEGALSDTVvdGVTGYHYSLGDTDACRAAIERVLD 333
                                       *******************************99999888**********************997 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   1.6   3.3e-16     1e-12       6     160 .]      21     176 ..      16     176 .. 0.62
   2 ?    1.7   0.0       0.1     3e+02      15      63 ..     220     272 ..     218     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.3e-16
                   Glyco_trans_4_4   6 yvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhahsp 82 
                                        v+ +  ++++r  +++v+ p+ +   p++ e  vr +++p++ +  +l+ ++ + ++          +d+vhah+p
  gi|313126813|ref|YP_004037083.1|  21 TVQTWRDHWRERDGRMDVVYPGTDDYVPDAGEYPVRSVSFPFYEG-YRLGVPRVPSRV--------DDVDLVHAHTP 88 
                                       555555566666666666666555555533333444444444433.233333333333........667*******7 PP

                   Glyco_trans_4_4  83 .taglaarlarrrrgiplvvtlh......glllrrgsgavrrly...ralerrllrradavlvvseaeaeelra.lg 148
                                         +gl +++++r++++p++ ++h      ++ l+++ ++++r+     + er+ + radav+++s+a +++l+   g
  gi|313126813|ref|YP_004037083.1|  89 fALGLSGLRLARQKNLPFIASYHtptgeyADYLTSRDSFEQRIEslsERYERWFFGRADAVVCPSQATRDHLHNvVG 165
                                       2566666555549**********443333222334455555543334888************************666 PP

                   Glyco_trans_4_4 149 vpadrvvvvpng 160
                                       v    v v+ ng
  gi|313126813|ref|YP_004037083.1| 166 VE-GEVIVLSNG 176
                                       76.677888887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.1
                   Glyco_trans_4_4  15 aarGheVtvltpapapgape....leedgvrvhrlpvprrpspladlaalral 63 
                                       aa+G + tv+  ++ p+++e    ++  g+  h l + +r++++a ++al a+
  gi|313126813|ref|YP_004037083.1| 220 AADGLDATVVFGGDGPAREEleslATKMGLDAHFLGFLPREELPAFYSALDAF 272
                                       67899999999888888777323333457777777777777666555555444 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.7   1.4e+04      45      59 ..     120     134 ..     111     141 .. 0.56
   2 !   16.7   0.0   2.4e-06    0.0072       5      67 ..     275     339 ..     269     358 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.7
                   Glyco_trans_1_2  45 lfedleelaekiryl 59 
                                       +  + ++++++i+ l
  gi|313126813|ref|YP_004037083.1| 120 YLTSRDSFEQRIESL 134
                                       344666666666655 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.4e-06
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerr 67 
                                       ps  e+  l+ +Ea acG++++     +l + + +g ++  ++  d++ + ++i+++l+++e  +
  gi|313126813|ref|YP_004037083.1| 275 PSPVETQGLVALEANACGTPVVGVNEGALSDTVVDGVTGYHYSlgDTDACRAAIERVLDERETLS 339
                                       56667778899*************99********************************8887655 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.038      75     135 ..      80     149 ..      76     153 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                   Glyco_trans_4_2  75 PDvvhahyakpygllgslaarlsgvipvvlsvwGldv..lkfpkksk.........lkklllklalkkatkv 135
                                        D+vhah++  +gl g  +ar ++  p+++s + + +  +++   s+         l + ++++ + +a++v
  gi|313126813|ref|YP_004037083.1|  80 VDLVHAHTPFALGLSGLRLARQKN-LPFIASYH-TPTgeYADYLTSRdsfeqriesLSERYERWFFGRADAV 149
                                       59********************99.******99.66666444444333323333333333666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 1956.81
//
Query:       gi|313126814|ref|YP_004037084.1|  [L=92]
Description: ribonuclease p protein subunit rpp21 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-12   46.9   0.1    2.9e-12   46.7   0.1    1.1  1  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
     0.0005   20.0   2.7     0.0096   15.9   0.1    2.4  2  PriA_CRR         PriA DNA helicase Cys-rich region (CRR) doma
     0.0027   17.9   2.1     0.0049   17.0   2.1    1.5  1  zf-RING_7        C4-type zinc ribbon domain
  ------ inclusion threshold ------
      0.031   14.3   0.1       0.74    9.9   0.0    2.2  2  zinc_ribbon_6    Zinc-ribbon
       0.15   11.5   0.0       0.17   11.3   0.0    1.1  1  DUF3878          Domain of unknown function, E. rectale Gene 
        0.3   11.1   2.2       0.57   10.2   2.2    1.4  1  zf-DNL           DNL zinc finger
        0.3   11.9   3.4       0.76   10.6   0.4    2.3  2  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.1   1.1e-15   2.9e-12       1      90 []       7      84 ..       7      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.1e-15
                                      HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E....... CS
                              Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka 79
                                      r++ L+ +a+ +  e   + sr +++ +r+++++++  lp+s++r++C +C+ +l pg++++vrv++   +        
  gi|313126814|ref|YP_004037084.1|  7 RIERLHGLAREAATEGEFDRSREYVRLARRIAERNRCGLPKSFQRSTCDACDVYLRPGQNARVRVHR---G-------- 74
                                      66777777877777888899*********************************************64...3........ PP

                                      ..EEEEETTTT CS
                              Rpr2 80 dvlvvtClaCg 90
                                       +++v+C+ Cg
  gi|313126814|ref|YP_004037084.1| 75 -RVIVRCHDCG 84
                                      .3679****97 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.4     0.016        42       1       8 [.      54      61 ..      54      62 .. 0.92
   2 !   15.9   0.1   3.8e-06    0.0096       8      27 .]      69      88 ..      66      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.016
                          PriA_CRR  1 CpnCdvsl 8 
                                      C  Cdv+l
  gi|313126814|ref|YP_004037084.1| 54 CDACDVYL 61
                                      9*****98 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.8e-06
                          PriA_CRR  8 ltyHksrnrLrCHyCgyteP 27
                                        +H++r  +rCH Cg+te+
  gi|313126814|ref|YP_004037084.1| 69 VRVHRGRVIVRCHDCGATER 88
                                      568***************97 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.1   1.9e-06    0.0049       1      31 [.      53      85 ..      53      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-06
                                      EETTT--B--CCHHHHHCCS..TB-EE-TTT-- CS
                         zf-RING_7  1 tCgGChmelppqvlselrag..devvtCpeCGR 31
                                      tC +C + l+p+  +++r +   ++v+C  CG+
  gi|313126814|ref|YP_004037084.1| 53 TCDACDVYLRPGQNARVRVHrgRVIVRCHDCGA 85
                                      8****************88876889******96 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.058   1.5e+02       2      29 ..      25      55 ..      24      60 .. 0.69
   2 ?    9.9   0.0   0.00029      0.74      24      43 ..      72      91 ..      64      92 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.058
                     zinc_ribbon_6  2 dmeayfraldaeiaeqp...mpeeyknkkvk 29
                                      d ++ + +l + iae +   +p+++++++++
  gi|313126814|ref|YP_004037084.1| 25 DRSREYVRLARRIAERNrcgLPKSFQRSTCD 55
                                      5567777888888887777788888776554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00029
                     zinc_ribbon_6 24 knkkvkilCnDCekksevkf 43
                                      ++ +v + C+DC+++ + +f
  gi|313126814|ref|YP_004037084.1| 72 HRGRVIVRCHDCGATERYPF 91
                                      566899*******9998877 PP

>> DUF3878  Domain of unknown function, E. rectale Gene description (DUF3878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.7e-05      0.17     206     270 ..      30      90 ..      13      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.7e-05
                           DUF3878 206 ekelsrkLkskkraklyeliykkvveasdeypqrdyGerinlkikekrkelekkllekGfvGkyP 270
                                        ++l+r++++++r+ l +  ++  ++a d+y +   G   n +++ +r ++  + +++G + +yP
  gi|313126814|ref|YP_004037084.1|  30 YVRLARRIAERNRCGLPKSFQRSTCDACDVYLRP--G--QNARVRVHRGRVIVRCHDCGATERYP 90 
                                       4689***************************874..4..577788888889999999*9999999 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.2   0.00022      0.57       5      36 ..      53      85 ..      51      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                            zf-DNL  5 tCkaCetrss.keiskkaYekGvVivqCpgCkn 36
                                      tC aC+   +  + ++   ++G Viv+C++C +
  gi|313126814|ref|YP_004037084.1| 53 TCDACDVYLRpGQNARVRVHRGRVIVRCHDCGA 85
                                      7888886544256678888************75 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4    0.0003      0.76      16      26 ..      51      61 ..      41      61 .. 0.85
   2 ?    1.7   0.2      0.19   4.9e+02       2       6 ..      79      83 ..      78      88 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                   Tnp_zf-ribbon_2 16 riiCqeCdvpl 26
                                      r +C++Cdv+l
  gi|313126814|ref|YP_004037084.1| 51 RSTCDACDVYL 61
                                      89********8 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.19
                   Tnp_zf-ribbon_2  2 RCkvC 6 
                                      RC +C
  gi|313126814|ref|YP_004037084.1| 79 RCHDC 83
                                      55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 528.33
//
Query:       gi|313126815|ref|YP_004037085.1|  [L=82]
Description: RNA-binding protein containing kh domain, possibly ribosomal protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-12   47.6   0.2    1.7e-12   47.3   0.2    1.0  1  CRS1_YhbY  CRS1 / YhbY (CRM) domain


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.2   9.4e-17   1.7e-12       6      84 .]       3      82 .]       2      82 .] 0.92

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 9.4e-17
                         CRS1_YhbY  6 lrrLrhlairlkpkvkiGkaGvtkevvdeiheklkteelvkvkc..egppalnmkrmaeiLeektgglviqrsgtsivL 82
                                      ++ Lr+ a++++ +v +Gk+G+  +v +e+ ++l ++ lvk+k+       ++++++ e+L+++++++vi+++g++ v+
  gi|313126815|ref|YP_004037085.1|  3 KQDLRKEAHDIDVTVWVGKSGI-SAVEEELSDQLADRDLVKIKFlrSARAGTTVEELTEELADRVNAEVIETRGNTGVV 80
                                      578*******************.68********************94456677***********************998 PP

                         CRS1_YhbY 83 YR 84
                                       R
  gi|313126815|ref|YP_004037085.1| 81 HR 82
                                      87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 539.36
//
Query:       gi|313126816|ref|YP_004037086.1|  [L=308]
Description: small-conductance mechanosensitive channel [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-51  175.3   0.1    1.4e-51  175.0   0.1    1.1  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.13   11.7   6.4        0.2   11.1   6.4    1.2  1  SfLAP       Sap, sulfolipid-1-addressing protein


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0   0.1   1.6e-55   1.4e-51       3     206 .]      82     283 ..      80     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 1.6e-55
                                       HHHHHHHHHHHHHHHHTTT--..SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvn..vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVe 77 
                                       ++++++++vgi +++   g++  +++l ++++a+ la+g+a++d+++n+vaGi++ ++kpf+iGD++e+ + +G Ve
  gi|313126816|ref|YP_004037086.1|  82 VTSVVVVFVGITVAFGAAGFEnfLQSLATIAAAATLAIGFAMQDVLQNFVAGIFIFTDKPFRIGDWIEWDGNSGVVE 158
                                       7899****************99******************************************************* PP

                                       EE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS CS
                        MS_channel  78 diglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdk 154
                                       di++r+ +irtfd++++t+Pns+l++  i+N    ++t r++v +g+ y+ d   ++ ++++++e+++ +pe+l+d+
  gi|313126816|ref|YP_004037086.1| 159 DISFRVSRIRTFDNELLTVPNSQLTDGVIKNPVA-KDTLRLQVPFGIGYGDD---IDTAADIILEEARAQPEILDDP 231
                                       **********************************.*****************...********************** PP

                                       -EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 155 ellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                        ++v+l+e+g ss+ ++ r+++ + + ++  ++++e ++r+k+ ++e+gi+i
  gi|313126816|ref|YP_004037086.1| 232 GPTVRLTELGGSSVVLTSRFWISNPSRADFVKTKAEYTQRVKERFDEQGIDI 283
                                       ************************999***********************86 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.4   2.2e-05       0.2      27     120 ..      36     122 ..      34     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.2e-05
                             SfLAP  27 pvlnllaFlvgwlvvlvalglivlfvlrsllsgasaapssaikalqivlGvlllllaaveavrrpkassrselprll 103
                                       p+ + +aF+++ ++v++ + ++v  vl++++ ++++ + +a k+l+ v+ v+++++++ +a  +      ++++  l
  gi|313126816|ref|YP_004037086.1|  36 PLGRVIAFVAAFVAVYLLGRIVVFPVLNRMM-DSRSLEDHAQKPLRRVTSVVVVFVGITVAFGA------AGFENFL 105
                                       667899**********999999999999999.888999***********************999......6777777 PP

                             SfLAP 104 srleslleggalwvAlv 120
                                       ++l+++  ++ l+ +++
  gi|313126816|ref|YP_004037086.1| 106 QSLATIAAAATLAIGFA 122
                                       77766666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1851.20
//
Query:       gi|313126817|ref|YP_004037087.1|  [L=268]
Description: hypothetical protein Hbor_20760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-10   39.1   2.6    7.5e-10   39.1   2.6    1.6  2  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   2.6   4.2e-14   7.5e-10      21     121 ..      90     180 ..      51     181 .. 0.78
   2 ?   -3.7   0.0      0.74   1.3e+04      71      88 ..     236     255 ..     227     260 .. 0.53

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 4.2e-14
                                       H....HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH..........HHHHHH CS
                                HD  21 e....eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld..........ledvak 83 
                                            e++  ++ laa lHDiG+++++d             +H+ ++  ++ +++ r+               +v++
  gi|313126817|ref|YP_004037087.1|  90 QglaeEDEAVIVALAATLHDIGHIVHRD-------------EHAYYSIPLAADLLDRFLPQfydtsevvrmKAEVLH 153
                                       0445477888999************999.............355555555555444442224459*****9999*** PP

                                       HHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  84 lirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       +i+ hh  ++           +l+ ea ++++aD+l++
  gi|313126817|ref|YP_004037087.1| 154 AILCHHTEED-----------PLTTEAGVIRVADALDM 180
                                       *********9...........***************97 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.74
                                       HHHHHHH...HHHHHHHHHTT CS
                                HD  71 ekrlgld...ledvaklireh 88 
                                       +k +  +   led++++++ +
  gi|313126817|ref|YP_004037087.1| 236 LKAKL-HnsrLEDLIRIVAVN 255
                                       33332.235566777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1805.86
//
Query:       gi|313126818|ref|YP_004037088.1|  [L=159]
Description: peroxiredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-32  112.1   0.0    1.7e-32  111.9   0.0    1.0  1  AhpC-TSA    AhpC/TSA family
    2.8e-23   82.2   0.1    3.3e-23   82.0   0.1    1.0  1  Redoxin     Redoxin
     0.0049   17.0   0.0       0.24   11.5   0.0    2.1  2  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.0   2.9e-36   1.7e-32       1     123 [.       4     134 ..       4     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 2.9e-36
                                       TTSB----EEE..STTCEEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHH CS
                          AhpC-TSA   1 vgdkapdfelk..nadgetvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshk 74 
                                       vgd apdf+++  ++d e+++ls+     p+vl f+p++++  Ctte++ +++++ +f++ g++v+g s+d+p++++
  gi|313126818|ref|YP_004037088.1|   4 VGDDAPDFTAPlaDGDVESFTLSEHlDEAPIVLAFFPAAFTSTCTTEMCTFRDRMANFEDIGATVYGASIDTPFTLN 80 
                                       79*********888889*******95559************************************************ PP

                                       HHHHH-H.SSEEEE-TTSHHHHHTT-EETT.....TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  75 kfiekeslnfpllsDeegkvakaygvlkee.....kglalratfvidkegkiry 123
                                       +f e+++lnf l+sD++++++++y+v  +      +++a ra+fv+d++g++ y
  gi|313126818|ref|YP_004037088.1|  81 EFREQNDLNFALISDTNRELIHEYDVAMDFdslgvHNVAKRAVFVVDTDGTVSY 134
                                       ***************************6669*********************98 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.1   5.5e-27   3.3e-23       2     146 ..       4     150 ..       3     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 5.5e-27
                                       TTSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvk 77 
                                       +gd aPdft pla+ d +s++lse + + ++v+ f+p+af+ tC++e++ +++  + +++ g +v + ++d+    +
  gi|313126818|ref|YP_004037088.1|   4 VGDDAPDFTAPLADGDVESFTLSEhLDEAPIVLAFFPAAFTSTCTTEMCTFRDRMANFEDIGATVYGASIDTPFTLN 80 
                                       79***********************************************666666666*********99999999** PP

                                       HHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG..EEE-EEEEEEETTEEEEEEESSSCHTSTTSHHHH CS
                           Redoxin  78 efwgkeglkfpvlsDgsaaftkalGlrleedaseg..lrtpryavidedgkvvylevepepeteesnaeav 146
                                       ef ++++l+f ++sD + ++  +++++++ d      ++ ++++v+d dg v+y  v ++p + e+++++v
  gi|313126818|ref|YP_004037088.1|  81 EFREQNDLNFALISDTNRELIHEYDVAMDFDSLGVhnVAKRAVFVVDTDGTVSYAWVSDDP-GAEPDYDEV 150
                                       *****************************99766699***********************9.569999886 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0     4e-05      0.24       5      51 ..      57     104 ..      53     113 .. 0.87
   2 ?    3.5   0.0     0.012        73      95     111 ..     122     138 ..     118     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                        AhpC-TSA_2   5 dkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqal 51 
                                       + + +++ g ++++ +i++p  + +F+++++ +f l+ D +++l ++ 
  gi|313126818|ref|YP_004037088.1|  57 RMANFEDIGATVYGASIDTPfTLNEFREQNDLNFALISDTNRELIHEY 104
                                       567788899***********99********************998775 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.012
                        AhpC-TSA_2  95 Gtflfdkqgelvyehrd 111
                                       ++f++d++g + y++  
  gi|313126818|ref|YP_004037088.1| 122 AVFVVDTDGTVSYAWVS 138
                                       68************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1030.56
//
Query:       gi|313126819|ref|YP_004037089.1|  [L=127]
Description: hypothetical protein Hbor_20780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-14   53.7   3.9    2.4e-14   53.7   3.9    1.4  2  DoxX       DoxX
     0.0079   16.3   2.5     0.0079   16.3   2.5    1.5  2  DoxX_2     DoxX-like family
  ------ inclusion threshold ------
      0.012   15.8   0.2      0.041   14.1   0.1    1.8  2  HR_lesion  HR-like lesion-inducing
       0.14   12.5   1.5       0.62   10.4   0.4    2.0  2  DUF2516    Protein of unknown function (DUF2516)


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   3.9   5.3e-18   2.4e-14       3      84 ..       8      87 ..       6      88 .. 0.96
   2 ?   -2.9   0.2       2.5   1.1e+04      72      77 ..     112     117 ..     102     121 .. 0.47

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 5.3e-18
                              DoxX  3 lllRlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllvatl 81
                                       l+R+l+g+ f   G++ l   +++++ ++ +++glp p++l+ +a l+ +vgg+ll+lGl++ l+A+a+a++ll++t 
  gi|313126819|ref|YP_004037089.1|  8 VLARVLFGAKFARDGYDNLS--NIDDMIGYAESVGLPFPNVLVPAASLLLFVGGVLLALGLAPLLGAAAIAAFLLGVTP 84
                                      589*****************..9*****************************************************998 PP

                              DoxX 82 tvh 84
                                       +h
  gi|313126819|ref|YP_004037089.1| 85 QMH 87
                                      888 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                              DoxX  72 lavtll 77 
                                        a++  
  gi|313126819|ref|YP_004037089.1| 112 GAAVAF 117
                                       222222 PP

>> DoxX_2  DoxX-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.5   1.8e-06    0.0079       3      71 ..      11      79 ..       9      87 .. 0.86
   2 ?   -2.5   0.1       1.3   5.7e+03      76      80 ..     113     117 ..     103     124 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                            DoxX_2  3 tvllalffllsGvakllraeevvakfaqlg..fpssfvrllGvvellgalgLllplvtaprltplAavgla 71
                                       vl+ + f+ +G+ +l + +++    +++g  fp  +v +  ++ ++g+++L l+l  ap l+ +A++ ++
  gi|313126819|ref|YP_004037089.1| 11 RVLFGAKFARDGYDNLSNIDDMIGYAESVGlpFPNVLVPAASLLLFVGGVLLALGL--APLLGAAAIAAFL 79
                                      6899999********************9998899*********************7..8966665555544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                            DoxX_2  76 gAiat 80 
                                       +A+a+
  gi|313126819|ref|YP_004037089.1| 113 AAVAF 117
                                       23332 PP

>> HR_lesion  HR-like lesion-inducing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       0.2   8.9e+02       6      36 ..       8      38 ..       4      55 .. 0.72
   2 ?   14.1   0.1   9.1e-06     0.041      75     135 ..      57     117 ..      36     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.2
                         HR_lesion  6 fiGrvlfasvfllsawqdyaefgadggpaek 36
                                      ++ rvlf + f    +++ ++     g ae 
  gi|313126819|ref|YP_004037089.1|  8 VLARVLFGAKFARDGYDNLSNIDDMIGYAES 38
                                      5679999999988888887777666666555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 9.1e-06
                         HR_lesion  75 lggLlfilg..sslgaylLllyqaiatvvlydfynydldtkeflrlllkfvqnlalvGaLLff 135
                                       +gg+l  lg    lga  +++++  +t+ ++df+n + d+++  + +  fv+n + +Ga + f
  gi|313126819|ref|YP_004037089.1|  57 VGGVLLALGlaPLLGAAAIAAFLLGVTPQMHDFWNMSGDERD--EEFDAFVRNASFFGAAVAF 117
                                       56666655522579999999999999*********9888765..8999**********97766 PP

>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00014      0.62      49      88 ..      48      88 ..      43      94 .. 0.84
   2 ?    0.9   0.0      0.12   5.6e+02      12      31 ..     106     125 ..      98     127 .] 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                           DUF2516 49 lgvallvlll.glfgalsllgliavvaalvYlvDVRPavre 88
                                      + +a+l+l++ g+  al+l  l++++a++ +l+ V P++++
  gi|313126819|ref|YP_004037089.1| 48 VPAASLLLFVgGVLLALGLAPLLGAAAIAAFLLGVTPQMHD 88
                                      4566666666799999*********************9876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                           DUF2516  12 alvvlvlslvAlvdalrrra 31 
                                         + +  ++vA++ a+r+r 
  gi|313126819|ref|YP_004037089.1| 106 RNASFFGAAVAFAAAIRERR 125
                                       55677788899999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 832.38
//
Query:       gi|313126820|ref|YP_004037090.1|  [L=88]
Description: twin-arginine translocation protein TatA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-15   54.5   0.0    7.6e-15   54.0   0.0    1.3  1  MttA_Hcf106  mttA/Hcf106 family
  ------ inclusion threshold ------
      0.036   14.4   1.7      0.036   14.4   1.7    1.4  2  PBP1_TM      Transmembrane domain of transglycosylase PBP1 at
       0.04   14.9   0.0      0.046   14.7   0.0    1.1  1  DUF4834      Domain of unknown function (DUF4834)
      0.042   14.2   0.1      0.045   14.1   0.1    1.1  1  DUF5497      Family of unknown function (DUF5497)
      0.056   13.3   1.1      0.085   12.7   1.1    1.3  1  CAP18_C      LPS binding domain of CAP18 (C terminal)


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   2.1e-18   7.6e-15       2      52 ..      13      63 ..      12      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.1e-18
                                      -HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH---XXXX CS
                       MttA_Hcf106  2 gapelliIlvValllFGpkkLPEvaraLGktLreFkkavkeleeenekeaa 52
                                      g pelli+l+V +llFG++k+P +ar+ G+++ eF+    e eee ++ ++
  gi|313126820|ref|YP_004037090.1| 13 GGPELLIVLLVLVLLFGANKIPKLARSTGQAMGEFQRGRNEIEEELKQMEN 63
                                      88******************************************9777654 PP

>> PBP1_TM  Transmembrane domain of transglycosylase PBP1 at N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.3   3.0         5   1.8e+04      80      84 ..      19      23 ..      17      27 .. 0.34
   2 ?   14.4   1.7     1e-05     0.036      30      58 ..      49      77 ..      31      87 .. 0.66

  Alignments for each domain:
  == domain 1  score: -6.3 bits;  conditional E-value: 5
                           PBP1_TM 80 lvlvv 84
                                      +vl+v
  gi|313126820|ref|YP_004037090.1| 19 IVLLV 23
                                      22222 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1e-05
                           PBP1_TM 30 rrdddyddeyddeedDdddddeeeevprk 58
                                      r  +++++e ++ e+Ddd+d++ee+ +  
  gi|313126820|ref|YP_004037090.1| 49 RGRNEIEEELKQMENDDDEDEDEETTTTT 77
                                      33567788888888888877777776554 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.3e-05     0.046       7      70 ..      18      82 ..      16      88 .] 0.53

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                           DUF4834  7 ilifiiailviglsilsvilrtvfg..lgsrkkssksaqkqfgnstnsnqqksqsrsetkeegeii 70
                                      ++++++++l++g+  + ++ r+  g  +g+ +++ ++ +++ ++  n++ + ++++++t++++++ 
  gi|313126820|ref|YP_004037090.1| 18 LIVLLVLVLLFGANKIPKLARST-GqaMGEFQRGRNEIEEELKQMENDDDEDEDEETTTTTSTSTS 82
                                      567888899999999*****999.544444444444444444444444433333333333332222 PP

>> DUF5497  Family of unknown function (DUF5497)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.3e-05     0.045      19      72 ..      32      84 ..      22      88 .] 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                           DUF5497 19 kigevaqrlnyylqeyanlemqieeeikyievddgeeintiktfllnsmstseq 72
                                      ki ++a+     + e+     +ieee+k +e dd e+ +   t    s sts  
  gi|313126820|ref|YP_004037090.1| 32 KIPKLARSTGQAMGEFQRGRNEIEEELKQMENDDDEDEDEE-TTTTTSTSTSTS 84
                                      6667777777778888888999**********998865543.333344444433 PP

>> CAP18_C  LPS binding domain of CAP18 (C terminal)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.1   2.4e-05     0.085       4      16 ..      47      59 ..      45      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHHHHHH CS
                           CAP18_C  4 LrkggeKIgEKLk 16
                                      +++g+++I+E+Lk
  gi|313126820|ref|YP_004037090.1| 47 FQRGRNEIEEELK 59
                                      8***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1700  (0.0948185); expected 358.6 (0.02)
Passed bias filter:                      814  (0.0454013); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 632.84
//
Query:       gi|313126821|ref|YP_004037091.1|  [L=1122]
Description: ATPase, type iv secretory pathway virb11 component like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-43  148.2   0.0    4.2e-43  147.4   0.0    1.3  1  T2SSE     Type II/IV secretion system protein
     0.0051   16.5   0.1     0.0099   15.6   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.0   4.7e-47   4.2e-43      12     245 ..     503     742 ..     496     765 .. 0.90

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 4.7e-47
                             T2SSE  12 ekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPv 87 
                                        +v di    +++ v+v    d  ++       + +l  ++ ++a+ +++ is++rp +da+lp +g r ++ l   
  gi|313126821|ref|YP_004037091.1| 503 INVEDISCDGYNSpVFV-YHSDYEQIISNVVHAETELDDFVVKLAQRSGKGISKRRPQVDATLP-DGSRAQLTLGRE 577
                                       57889999999999999.66666455555555566677788899********************.999999999888 PP

                             T2SSE  88 vag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivt 162
                                       v +  ++++iR+ +   +t  dl+  ++++ +  ++l   ++++++++++GgT sGKtt+l+a+  +i+++  +iv 
  gi|313126821|ref|YP_004037091.1| 578 VSDhgTNYTIRQFKDVPFTPIDLVNWNTFSLEEMAFLWLCIENHKSLIFAGGTASGKTTSLNAVSLFIPSN-SKIVS 653
                                       7776799***************************************************************9.***** PP

                             T2SSE 163 vEDpvEiqleganqvqlnak.......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlH 232
                                       +ED++E++l + n ++ +++       k++v+  dll+aaLR+rPD i++GEiR++e  ++ + ++TGH    +T H
  gi|313126821|ref|YP_004037091.1| 654 IEDTREVELPQRNWIASVTRpsfsdddKGDVDEFDLLEAALRQRPDYIVMGEIRGEEGRTLFQVMSTGHTT-YTTFH 729
                                       ******************999**************************************************.***** PP

                             T2SSE 233 ansaagalerLeq 245
                                       a+s+ ++l+r  +
  gi|313126821|ref|YP_004037091.1| 730 ADSVGEVLKRFTT 742
                                       ********99764 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.1e-06    0.0099       4      48 ..     598     646 ..     595     652 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-06
                            AAA_29   4 lqlvNWgtfdghtiei.....dlkgatlltGpsGsGKSTllDAiqalLvp 48 
                                       ++lvNW tf+ +++ +     + + + +++G + sGK+T l A++   +p
  gi|313126821|ref|YP_004037091.1| 598 IDLVNWNTFSLEEMAFlwlciENHKSLIFAGGTASGKTTSLNAVSLF-IP 646
                                       89********9777642222255558999************998754.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 7421.35
//
Query:       gi|313126822|ref|YP_004037092.1|  [L=682]
Description: flagella assembly protein j [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-29  100.2   7.1    3.1e-14   53.0   0.9    2.8  2  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.7   1.8e-17   3.2e-13       3     124 ..     160     287 ..     158     288 .. 0.93
   2 !   53.0   0.9   1.7e-18   3.1e-14       2     123 ..     469     593 ..     469     594 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.8e-17
                                       HHHHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTSSH.HHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   3 rqlatllsaGvplveaLellaeeae.ngplaeelkriarrlraGgsl.seale....rtpssefpelvvqliragee 73 
                                         ++ l+ +G++ +e+Le++++  + +g++a+e+++i+++ ++ g+  ++a++     tps+e++++++ +++++ +
  gi|313126822|ref|YP_004037092.1| 160 SFMYALSVGGLNQLEILEAMGRAEDtYGEVAREFQSIVQETEYFGTDyRNAIRdqamVTPSDELSQFLTDMLSIVNS 236
                                       568899999************99999*******************66346666777799****************** PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                       ggn++++L++  e + + ++++++  +++le   +++++l ++++ll+i+l
  gi|313126822|ref|YP_004037092.1| 237 GGNMEQFLDDKKEKHLRTAKQEQEMTLETLELFGEMYMTLSLFPLLLIIIL 287
                                       *************************************************97 PP

  == domain 2  score: 53.0 bits;  conditional E-value: 1.7e-18
                                       HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirageeg 74 
                                       lr l+++  +G +l+e+++++++++ +g+la+e++ + +++++G+sl+ al     ++  + ++++v  ++ a e++
  gi|313126822|ref|YP_004037092.1| 469 LRKLSSANDTGQTLLESVKTVSDTS-SGKLADEFEVMHAKVNYGMSLRSALVefnnKYHIPRLARTVKLISKAQEAS 544
                                       6899*********************.**************************7776444479*************** PP

                                       T-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  75 gnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       +++++vL+ +a+  e++ +++r++++++   +++++++ l ll+++ail
  gi|313126822|ref|YP_004037092.1| 545 SQITDVLSTAAQASENQDDIERERKSRTRMQVAIILMTYLTLLAVMAIL 593
                                       **********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 4440.97
//
Query:       gi|313126823|ref|YP_004037093.1|  [L=191]
Description: hypothetical protein Hbor_20830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0033   17.6   0.0     0.0055   16.8   0.0    1.3  1  DUF4519   Domain of unknown function (DUF4519)
  ------ inclusion threshold ------
      0.066   13.2   0.0       0.12   12.3   0.0    1.4  1  DUF3915   Protein of unknown function (DUF3915)
       0.11   12.6   0.1       0.17   11.9   0.1    1.3  1  DUF2116   Uncharacterized protein containing a Zn-ribbon (DUF


Domain annotation for each model (and alignments):
>> DUF4519  Domain of unknown function (DUF4519)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.2e-07    0.0055       7      49 ..       9      53 ..       6      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.2e-07
                           DUF4519  7 gktKEtrkd.KkeRrkenkeaqekv.ttvVlPvlavlillivvfv 49
                                      g  +Et+++   eR++e ++aq  + +tv + +++++++++v+fv
  gi|313126823|ref|YP_004037093.1|  9 GRGRETEREcRHERKQEHERAQTTMdFTVGISIFLLVVVFVVAFV 53
                                      567999988467************978****************98 PP

>> DUF3915  Protein of unknown function (DUF3915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.1e-05      0.12      22      80 ..      12      61 ..       5      69 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                           DUF3915 22 rdrerererederekerekkkerhavcnvlasiavgtelsllsikgnvtfrnvifegfa 80
                                      r+ ere+ +e         +k++h+  +   + +vg  + ll +   v+f   ife f 
  gi|313126823|ref|YP_004037093.1| 12 RETERECRHE---------RKQEHERAQTTMDFTVGISIFLLVVVFVVAFVPGIFEPFE 61
                                      1222222222.........2333334445567888999999999999999999998875 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.8e-05      0.17      23      58 ..      17      52 ..      14      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                           DUF2116 23 kCqeeyekkrkkvarsqqilfgililllavvlvlkf 58
                                      +C++e +++  ++++++   +gi i ll+vv v++f
  gi|313126823|ref|YP_004037093.1| 17 ECRHERKQEHERAQTTMDFTVGISIFLLVVVFVVAF 52
                                      8***********************999999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1176.72
//
Query:       gi|313126824|ref|YP_004037094.1|  [L=209]
Description: hypothetical protein Hbor_20840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1235.69
//
Query:       gi|313126825|ref|YP_004037095.1|  [L=310]
Description: hypothetical protein Hbor_20850 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1806.80
//
Query:       gi|313126826|ref|YP_004037096.1|  [L=195]
Description: hypothetical protein Hbor_20860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1222.41
//
Query:       gi|313126827|ref|YP_004037097.1|  [L=492]
Description: hypothetical protein Hbor_20870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2904.79
//
Query:       gi|313126828|ref|YP_004037098.1|  [L=256]
Description: hypothetical protein Hbor_20880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1355.57
//
Query:       gi|313126829|ref|YP_004037099.1|  [L=112]
Description: hypothetical protein Hbor_20890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.016   15.0   0.0    1.3  1  DUF5362   Family of unknown function (DUF5362)
      0.043   14.0   0.3        0.1   12.8   0.1    1.6  2  HemY_N    HemY protein N-terminus


Domain annotation for each model (and alignments):
>> DUF5362  Family of unknown function (DUF5362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.8e-06     0.016      14      64 ..      32      83 ..      19      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-06
                           DUF5362 14 lliilGaltcLsIigiiigvllIivglklfkaakaikealrsksee.klkea 64
                                       +i+lG+++c +++g   +  l+ + ++l+++ ++i++al+ ++++  l++a
  gi|313126829|ref|YP_004037099.1| 32 TAILLGVMFCGGVFGLYLAYQLVGAFVRLVDSVERIADALEGSDGAdRLRTA 83
                                      579************************************9988875146665 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.24   2.2e+03      13      31 ..       6      24 ..       2      36 .. 0.59
   2 ?   12.8   0.1   1.2e-05       0.1      17      67 ..      34      84 ..      29      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.24
                            HemY_N 13 etslvvavlllvllfvlly 31
                                      ++s + a ++lv+l + ++
  gi|313126829|ref|YP_004037099.1|  6 SVSSNEARIVLVALCFGIL 24
                                      5566666666666655544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.2e-05
                            HemY_N 17 vvavlllvllfvllylllrllrlllrlparvrrwrrrrrerkarealseGl 67
                                      +++ +++ ++++ lyl+++l+++++rl  +v r  ++     + ++l++++
  gi|313126829|ref|YP_004037099.1| 34 ILLGVMFCGGVFGLYLAYQLVGAFVRLVDSVERIADALEGSDGADRLRTAV 84
                                      677789999**********************99988888777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 644.49
//
Query:       gi|313126830|ref|YP_004037100.1|  [L=50]
Description: hypothetical protein Hbor_20900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.015   15.1   1.1      0.022   14.6   1.1    1.2  1  PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein k
      0.033   14.4   0.1      0.035   14.3   0.1    1.1  1  DUF2304    Uncharacterized conserved protein (DUF2304)
      0.066   12.7   0.0      0.069   12.7   0.0    1.1  1  BRI3BP     Negative regulator of p53/TP53


Domain annotation for each model (and alignments):
>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.1   3.6e-06     0.022       7      22 ..      32      47 ..      29      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-06
                         PKcGMP_CC  7 DERIRELEkrlaekde 22
                                      DERI ELE+r+ae ++
  gi|313126830|ref|YP_004037100.1| 32 DERITELEQRVAELED 47
                                      9**********99776 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   5.9e-06     0.035      67     104 ..       8      46 ..       2      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.9e-06
                           DUF2304  67 lfllgivfllvilfslslklskl.eekikeLaqeiAlle 104
                                       l+++++ +l++++++++l  ++  +e+i+eL q++A le
  gi|313126830|ref|YP_004037100.1|   8 LLYFAVPILIIVAVYNYLDGKRAyDERITELEQRVAELE 46 
                                       78999999999999999998875389*********9665 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05     0.069     139     180 .]       8      50 .]       1      50 [] 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                            BRI3BP 139 avyv...LlgslglyaksseesgasleakvrsLerqvrelnkrqk 180
                                       ++y+   +l ++++y   +   +   ++++ +Le++v el+ rq+
  gi|313126830|ref|YP_004037100.1|   8 LLYFavpILIIVAVYNYLD--GKRAYDERITELEQRVAELEDRQS 50 
                                       3444111333444444444..678899**************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1211  (0.0675442); expected 358.6 (0.02)
Passed bias filter:                      926  (0.0516482); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 310.55
//
Query:       gi|313126831|ref|YP_004037101.1|  [L=487]
Description: hypothetical protein Hbor_20910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-27   96.6  37.7    1.1e-12   48.1   6.9    3.4  3  Beta_helix  Right handed beta helix region
    2.1e-24   86.1  25.1    1.2e-09   37.8   3.4    4.5  4  NosD        Periplasmic copper-binding protein (NosD)
    0.00093   18.9   5.4      0.002   17.9   5.4    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   6.9   1.9e-16   1.1e-12      12     157 ..      75     230 ..      63     231 .. 0.88
   2 !   32.6  11.4     1e-11   6.3e-08      12     157 ..     254     411 ..     237     412 .. 0.92
   3 !   29.7   4.5   8.2e-11   4.9e-07       8      87 ..     403     486 ..     398     486 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.9e-16
                                       EEESEEEES-SS-SEEE-SSS-..EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EE CS
                        Beta_helix  12 tiknntisnsggyGiylrgssn.vvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnliennei 87 
                                         +++t+sn  g +i +  + + v+++n+++++   +G+ + g +++t+ nn +s+n+ +gi l++++++ ie + +
  gi|313126831|ref|YP_004037101.1|  75 DGQGHTVSNDAGECISIFVGADnVTVKNTRVSG-DRNGFLVAG-NDATLFNNLVSGNGRSGILLSAGKRTKIEACVV 149
                                       346799999999999998665548888999999.********9.********************************* PP

                                       ES-SS-SEE-TT......-S--EEES-EEESTT--SEE---TT---EEES-EEES-S......SEEEE-TT-SS--E CS
                        Beta_helix  88 tdnggsGiylny......ssnntienNiidnnagsGividdsssnvtvtnNtitnnk......gaGiavvgsssnvt 152
                                       ++n+  Gi+ ++      ++ +t+  +++ +n+  Gi ++ ++ +  v+ + +++n+      g+Gi ++++ +++ 
  gi|313126831|ref|YP_004037101.1| 150 RENSLIGISGSDtedrgsADETTVFTSVVADNGLEGILLRRTD-DAAVERCLVSGNGtddatrGHGIGLIDRTRDLR 225
                                       ********99986667666669999999999999*********.9999***************************** PP

                                       EES-E CS
                        Beta_helix 153 vrnNt 157
                                       ++nN+
  gi|313126831|ref|YP_004037101.1| 226 LANNQ 230
                                       ****8 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 1e-11
                                       EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---................SEEE CS
                        Beta_helix  12 tiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn................gggi 72 
                                       +  +n + n+g++G+ +r+  n+ +e+n++a  +g G++ +  +++ i++n++ dn                 g+g+
  gi|313126831|ref|YP_004037101.1| 254 NAVGNAVANNGSAGFGFRDLVNADVEQNVFAR-NGRGVEGRF-DRSHIRGNQFVDNDfsgacvhslvrengfvGDGV 328
                                       57899***************************.********9.**********9999999***************** PP

                                       -TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS CS
                        Beta_helix  73 alfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss 149
                                       al++  ++ +  n+i+  +++G+++   +  t++ N+i +  g+G+  d+   ++ v+ N++++n+g+G++   + +
  gi|313126831|ref|YP_004037101.1| 329 ALNAFAHSEFLENTIIGSSQHGFSTAFVEESTFSSNTIVGSMGDGVWTDEFF-GNDVRWNNLSGNSGNGFTTEQGVG 404
                                       ***********************99999************************.8889*************7777766 PP

                                       --EEES-E CS
                        Beta_helix 150 nvtvrnNt 157
                                         t++ N 
  gi|313126831|ref|YP_004037101.1| 405 -STFKFNA 411
                                       .8888886 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 8.2e-11
                                       S-E.EEESEEEES-SS-SEEE-SSS-......EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S- CS
                        Beta_helix   8 ssnvtiknntisnsggyGiylrgssn.....vvienneiannsgsGiyilgssnntisnntisdnngggialfgasn 79 
                                       +++ t+k n ++++gg+G+ l g +n      ++++n+++ n+g Gi +  + ++++++n++  n gg i ++g   
  gi|313126831|ref|YP_004037101.1| 403 VGS-TFKFNAVTGNGGDGLSLSGFDNddpgtYLVRKNTTSANGGAGILLIDTVDSQVTRNRVCANAGGSIETQGLAD 478
                                       455.9999**********************999999***************************************** PP

                                       -EEES-EE CS
                        Beta_helix  80 nliennei 87 
                                       n+ienn i
  gi|313126831|ref|YP_004037101.1| 479 NVIENNQI 486
                                       ******87 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   3.4     2e-13   1.2e-09      25     173 ..      70     235 ..      30     237 .. 0.58
   2 !   24.2   0.2     3e-09   1.8e-05      51     169 ..     174     309 ..     166     316 .. 0.71
   3 !   25.9   1.9   8.6e-10   5.1e-06      83     172 ..     326     415 ..     312     429 .. 0.53
   4 !   20.0   2.4   5.5e-08   0.00033      76     145 ..     410     486 ..     405     487 .] 0.51

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2e-13
                              NosD  25 egsei..snneisnsrdgi..lldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnntle 96 
                                       ++ +i  ++ ++sn        +  ++n+t+++++++  r+G  + +++  t+ +n +s+n+ sGi+l+  +++ +e
  gi|313126831|ref|YP_004037101.1|  70 SNVTIdgQGHTVSNDAGECisIFVGADNVTVKNTRVSGDRNGFLVAGNDA-TLFNNLVSGNGrSGILLSAGKRTKIE 145
                                       23333222222222222223444455555555555555555544444444.55555555555555555555555555 PP

                              NosD  97 nNtisnnenyGillsdssn......ntisnNtis.nnnkGiflensssntitgNriesn......qkiGilllssse 160
                                         ++++n+  Gi+ sd ++      +t+   ++  n  +Gi l+++++  ++++ +++n      +++Gi l++ + 
  gi|313126831|ref|YP_004037101.1| 146 ACVVRENSLIGISGSDTEDrgsadeTTVFTSVVAdNGLEGILLRRTDDAAVERCLVSGNgtddatRGHGIGLIDRTR 222
                                       55555555555555554444444444444444477999999999999999999999999999999999999****** PP

                              NosD 161 gntiynNyFinns 173
                                       + ++ nN+++ n 
  gi|313126831|ref|YP_004037101.1| 223 DLRLANNQLLSNV 235
                                       *********9986 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 3e-09
                              NosD  51 itgntienlryGihlenses.....ntiedntlssne..sGialmsssnn.tlenNtisnnenyGillsdssn.... 115
                                       +t  +  n+ +Gi l  +++     + +++n +++ +   Gi l + +++  l nN + +n   G++ ++ +     
  gi|313126831|ref|YP_004037101.1| 174 FTSVVADNGLEGILLRRTDDaaverCLVSGNGTDDATrgHGIGLIDRTRDlRLANNQLLSNVADGVSFRTRDAertl 250
                                       45556667789999999999666666666666666667888888888877799999999999999988887776666 PP

                              NosD 116 ...ntisnNtisnnnkGiflensssntitgNriesnqkiGil...llsssegntiynNyF 169
                                          n + n ++ n ++G+ +++  +  +++N +++n + G+      s+  gn++++N+F
  gi|313126831|ref|YP_004037101.1| 251 fglNAVGNAVANNGSAGFGFRDLVNADVEQNVFARN-GRGVEgrfDRSHIRGNQFVDNDF 309
                                       664444444445888899999999999999999999.88887444555556666666666 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 8.6e-10
                              NosD  83 sGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllss 158
                                       +G+al    ++ +  Nti++++++G+++ + +++t s Nti+ + ++G++ ++  +n ++ N++++n + G+  +++
  gi|313126831|ref|YP_004037101.1| 326 DGVALNAFAHSEFLENTIIGSSQHGFSTAFVEESTFSSNTIVgSMGDGVWTDEFFGNDVRWNNLSGNSGNGFT-TEQ 401
                                       4555555555544455555555555555555555555555555555555555555555555555555555555.555 PP

                              NosD 159 segntiynNyFinn 172
                                       + g t+  N   +n
  gi|313126831|ref|YP_004037101.1| 402 GVGSTFKFNAVTGN 415
                                       55544444443333 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 5.5e-08
                              NosD  76 ntlssne.sGialmsss....nn.tlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNri 145
                                       n +++n+ +G++l+       ++  +++Nt s n ++Gill d  ++++++N++  n +  i  ++  +n+i++N+i
  gi|313126831|ref|YP_004037101.1| 410 NAVTGNGgDGLSLSGFDnddpGTyLVRKNTTSANGGAGILLIDTVDSQVTRNRVCaNAGGSIETQGLADNVIENNQI 486
                                       33333333333333222222223356666666666666666666666666666665666666666666666666665 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   5.4   3.3e-07     0.002       2      19 ..       7      24 ..       6      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.3e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaa 19
                                       SRRd LK++AAaa +aa
  gi|313126831|ref|YP_004037101.1|  7 PSRRDVLKAGAAAAGLAA 24
                                      7*******9999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2730.61
//
Query:       gi|313126832|ref|YP_004037102.1|  [L=151]
Description: 30S ribosomal protein S15 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-21   75.6   0.0    3.6e-21   74.9   0.0    1.3  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    9.6e-15   54.6   0.2    1.4e-14   54.0   0.2    1.2  1  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
      0.047   13.7   0.8      0.082   12.9   0.8    1.5  1  DUF4298          Domain of unknown function (DUF4298)


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   6.1e-25   3.6e-21       4      57 ..       1      54 [.       1      56 [. 0.98

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 6.1e-25
                                      SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHC CS
                   Ribosomal_S13_N  4 mhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDq 57
                                      mh+r++G+SgS +P+  e+p+W+++++e++e+ +v+la++G++pSqIG++LRD+
  gi|313126832|ref|YP_004037102.1|  1 MHTRRRGQSGSDKPVADEPPEWSDVDAEDIESRVVELAEQGHEPSQIGLKLRDE 54
                                      9****************************************************7 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.2   2.4e-18   1.4e-14       4      73 ..      75     141 ..      71     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.4e-18
                                       HHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H.HHHHH CS
                     Ribosomal_S15   4 likefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv.erYkk 73 
                                       +++e+  ++    ++++++ +l+er+++l+eh++en++Dk+++r+L++++sk+r+l+ Y++  +  e++++
  gi|313126832|ref|YP_004037102.1|  75 ILEENDAAP----ELPEDLRNLMERAVRLREHMDENPQDKQNKRALQNTESKIRRLVSYYQGDELdEDFTY 141
                                       578888888....99**********************************************9998777766 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   1.4e-05     0.082      10      52 ..     101     143 ..      75     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTSHHHHHHHTS-- CS
                           DUF4298  10 eisallqqLeealeqwkklqkklakLdeYYqseqwredleasn 52 
                                       e  + ++q +++ + +++ ++k++ L  YYq ++  ed+ +s 
  gi|313126832|ref|YP_004037102.1| 101 EHMDENPQDKQNKRALQNTESKIRRLVSYYQGDELDEDFTYSY 143
                                       555667777888899***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 977.91
//
Query:       gi|313126833|ref|YP_004037103.1|  [L=398]
Description: hypothetical protein Hbor_20940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2660.95
//
Query:       gi|313126834|ref|YP_004037104.1|  [L=89]
Description: hypothetical protein Hbor_20950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.4   1.3      0.021   14.9   1.3    1.3  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.3   1.2e-06     0.021      10      73 ..      23      81 ..      17      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-06
                                      SHHHHHHHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1 10 terlAsialrtLqvDkelsplavkrslslegnvLqveykAttnrmLRvavngfleslglvletm 73
                                      t+++A ++  +L++D+  s      ++ +egn+L+++++ +t   L+ +v+    +l ++  ++
  gi|313126834|ref|YP_004037104.1| 23 THADADAVAAALRPDNTDSI-----EMVVEGNTLVTTITRETTGGLQSTVDDTVVNLTVADAVI 81
                                      899************87754.....5789**********************9999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 559.21
//
Query:       gi|313126835|ref|YP_004037105.1|  [L=215]
Description: 30S ribosomal protein S3ae [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-58  196.1   0.1    5.6e-58  195.8   0.1    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8   0.1   3.1e-62   5.6e-58       8     202 .]       8     192 ..       2     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 3.1e-62
                                       -TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEESSEEE CS
                    Ribosomal_S3Ae   8 DkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqgknal 84 
                                        + + K+Wy++ aP++f ++e+G+t++       +++ek+ gr++ev+l+DLt+d+  + ++kl +k+++v+ ++a+
  gi|313126835|ref|YP_004037105.1|   8 KQKRGKRWYTLIAPEQFDREELGETMA-------DEPEKVDGRTIEVTLGDLTGDQ-GANNTKLTFKVNDVSSDSAY 76 
                                       45567**********************.......*********************7.666***************** PP

                                       EEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS- CS
                    Ribosomal_S3Ae  85 tnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseld 161
                                       t+F ++el+rD+lrslvr++ s+I a ++v tkD+y +++ +vafT+k+   a +sq++aIr++m ++++e a+e +
  gi|313126835|ref|YP_004037105.1|  77 TEFIKHELARDYLRSLVRRGASKISASITVLTKDDYRVQIQPVAFTTKK---ADRSQEQAIRRVMIDFVEEAAQERT 150
                                       *************************************************...************************* PP

                                       HHHHHHHHTT.THHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                    Ribosomal_S3Ae 162 lkelvkklip.eslgkeiekeakkIyplrnveirKvkvlkkP 202
                                       ++elv+  +    l++ i+ eak+Iyplr+ve++K  +  +P
  gi|313126835|ref|YP_004037105.1| 151 FEELVDSAVVdGRLSSAIYGEAKTIYPLRRVEVQKLTLEARP 192
                                       ******9998877**********************9987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1344.14
//
Query:       gi|313126836|ref|YP_004037106.1|  [L=145]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-17   64.2   0.0    2.1e-17   63.4   0.0    1.4  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    8.7e-05   22.6   0.0     0.0035   17.4   0.0    2.1  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.035   13.9   5.8      0.067   13.1   5.8    1.5  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
      0.071   13.0   1.6       0.52   10.2   0.0    2.7  3  PKD           PKD domain
       0.17   11.3   1.0       0.42   10.0   1.0    1.7  1  UCR_Fe-S_N    Ubiquitinol-cytochrome C reductase Fe-S subunit


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   5.8e-21   2.1e-17       6      99 .]      39     144 ..      35     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 5.8e-21
                                       EETTETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTC............EEEEBSTTEEE CS
                       Copper-bind   6 gvesgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaed............etkliggGekd 70 
                                       +v  ++ +F+++++tv+ g++v++ n+ + gH v    d +p+ ++ +++   +               li +G+++
  gi|313126836|ref|YP_004037106.1|  39 DVGMTAVAFNPSSLTVSVGDEVVWQNTSSRGHTVTAYDDRIPDDAEFFASGDYEstkaardafnneIGGLIDSGQSF 115
                                       5677889*****************************996666544433332222444555676544567999***** PP

                                       EEEEESSEEEEEEETTTTTTTSEEEEEEE CS
                       Copper-bind  71 svtfdeagtYkffCsPHaaagMkgkvtve 99 
                                       s tf+ +g+Y++ C PH a+gM+g+++ve
  gi|313126836|ref|YP_004037106.1| 116 SHTFEIPGEYQYLCIPHEAQGMVGTIIVE 144
                                       **************************996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   9.8e-07    0.0035      20     104 .]      35     143 ..      21     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.8e-07
                      Cupredoxin_1  20 ektveitvkdggfePskievkagekvklkiknkdktpeefesed..........................lgeekvl 70 
                                       +  + + ++  +f+Ps+++v  g   ++ ++n++++ ++++++d                           ++   +
  gi|313126836|ref|YP_004037106.1|  35 QGDYDVGMTAVAFNPSSLTVSVGD--EVVWQNTSSRGHTVTAYDdripddaeffasgdyestkaardafnNEIGGLI 109
                                       555667778889***********9..88********99999988888888888889899999999999655566889 PP

                      Cupredoxin_1  71 apgktttitiaplkpGeYeftcdmhm.d.akGkliV 104
                                       ++g++++ t+  + pGeY++ c  h+ + + G++iV
  gi|313126836|ref|YP_004037106.1| 110 DSGQSFSHTF--EIPGEYQYLCIPHEaQgMVGTIIV 143
                                       *********9..99********99996689999998 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.8   1.9e-05     0.067       3      25 ..      11      32 ..       9      34 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      SRR FL g + +aAA+ l+gc++
  gi|313126836|ref|YP_004037106.1| 11 SRRRFLAGIGSVAAAG-LAGCST 32
                                      9******999998777.566654 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.4   1.4e+03      53      62 ..      35      44 ..      32      54 .. 0.74
   2 ?    0.3   0.4      0.17   6.2e+02      32      47 ..      56      73 ..      43      75 .. 0.68
   3 ?   10.2   0.0   0.00015      0.52      36      57 ..     105     126 ..      87     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.4
                                      SEEEEEEEEE CS
                               PKD 53 pGeYeVtvta 62
                                      +G+Y V +ta
  gi|313126836|ref|YP_004037106.1| 35 QGDYDVGMTA 44
                                      6899998887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                                      --SS..--EEEEETTEEE CS
                               PKD 32 fgdg..svvqvlseptvt 47
                                      +gd+   + ++++++tvt
  gi|313126836|ref|YP_004037106.1| 56 VGDEvvWQNTSSRGHTVT 73
                                      455444456777777776 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00015
                                       --EEEEETTEEEEEE-SSEEEE CS
                               PKD  36 svvqvlseptvthtYlspGeYe 57 
                                         +++ s+++++ht++ pGeY+
  gi|313126836|ref|YP_004037106.1| 105 IGGLIDSGQSFSHTFEIPGEYQ 126
                                       567899***************6 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.0   0.00012      0.42       5      27 ..       6      27 ..       2      30 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                        UCR_Fe-S_N  5 esdeptRRDFLyiATgavgaVGa 27
                                       +d+ +RR+FL ++ g+v+a G 
  gi|313126836|ref|YP_004037106.1|  6 RADGSSRRRFL-AGIGSVAAAGL 27
                                      56889******.55555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 906.78
//
Query:       gi|313126837|ref|YP_004037107.1|  [L=232]
Description: archaetidylserine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-11   43.5   5.1    4.2e-11   43.5   5.1    3.0  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   5.1   2.3e-15   4.2e-11       3      66 .]      12      72 ..      11      72 .. 0.91
   2 ?   -1.6   4.1      0.26   4.7e+03      35      35 ..     161     161 ..      96     227 .. 0.59

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.3e-15
                                      HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      ++a+T+++ +l+++a++  +++  ++la+ l+l+a+++DalDG++ARr++  +  G++lD laD
  gi|313126837|ref|YP_004037107.1| 12 ADAVTVANAALGFFAAV--AATVSITLAARLILLAAIADALDGVIARRRGG-TAVGEYLDALAD 72
                                      799************97..456668999999******************99.99*********9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.26
                                       H CS
                   CDP-OH_P_transf  35 l 35 
                                       l
  gi|313126837|ref|YP_004037107.1| 161 L 161
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1492.43
//
Query:       gi|313126838|ref|YP_004037108.1|  [L=91]
Description: hypothetical protein Hbor_20990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 550.76
//
Query:       gi|313126839|ref|YP_004037109.1|  [L=117]
Description: transcriptional regulator, padr family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0006   19.7   0.1     0.0006   19.7   0.1    1.5  2  PadR      Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.4e-08    0.0006       6      71 ..      26      84 ..      20      88 .. 0.86
   2 ?   -3.1   0.1      0.43   7.7e+03      46      60 ..      92     105 ..      91     106 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.4e-08
                                      CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR  6 eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                      + +++ G +++ +le++++   ++ + s Y +L+ L  +g+++++ e     +   +Y+lTd G r
  gi|313126839|ref|YP_004037109.1| 26 DAGELRGQKLKTRLEAYYDT--RIDPQSFYGTLDALVSKGYLVRRTE-----GIHDVYELTDPGVR 84
                                      458889***********975..999******************9976.....589*******9966 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.43
                                       SEEEEEE-STSSS-E CS
                              PadR  46 lveseweesgegppr 60 
                                       +++++ e++ e+ +r
  gi|313126839|ref|YP_004037109.1|  92 WLTKRVEPK-EQERR 105
                                       566666664.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 680.94
//
Query:       gi|313126840|ref|YP_004037110.1|  [L=387]
Description: butyryl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-48  163.0   1.1    7.7e-48  162.5   1.1    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    9.2e-36  122.9   0.6    2.5e-35  121.5   0.1    2.0  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    7.5e-26   91.0   1.0    1.2e-25   90.3   1.0    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    2.5e-24   85.3   0.0    5.3e-24   84.2   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
       0.16   12.0   0.3       0.28   11.2   0.3    1.3  1  DUF743         Protein of unknown function (DUF743)


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.5   1.1   2.1e-51   7.7e-48       1     149 [.     235     383 ..     235     384 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.5 bits;  conditional E-value: 2.1e-51
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       g+Gf +a++tln +R+++aa+++g+ar+al+ a++ya +r++f +p++++q++++kla+m ++++aa++l  +aa +
  gi|313126840|ref|YP_004037110.1| 235 GEGFVQALKTLNGGRITIAARSIGIARAALDDAVAYADDREQFDQPIAEFQAIKHKLADMDTKVQAAKMLMHKAADL 311
                                       68*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                         +g+   +ea+ aKl+ase+ +eva++ +q++Gg+Gy+++ p er+yrda++++i+eGtsei+rn+i++rl
  gi|313126840|ref|YP_004037110.1| 312 KIRGESYIKEAAQAKLYASEISREVANEGIQIHGGYGYTKDFPAERYYRDAKLNEIYEGTSEILRNTIGDRL 383
                                       ********************************************************************9986 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   0.1   7.1e-39   2.5e-35       2     113 .]      12     123 ..      11     123 .. 0.98
   2 ?   -1.1   0.1      0.84     3e+03      36      43 ..     304     311 ..     260     344 .. 0.54

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 7.1e-39
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                        eq+++rd+v ef++ee++p+aae+de++efp++l+ ++aelGl+g+++peey Gagldy ++ai +ee++r++ gl
  gi|313126840|ref|YP_004037110.1|  12 AEQRQIRDMVSEFVDEEIRPRAAEIDETDEFPDDLISEMAELGLMGMPFPEEYDGAGLDYHSYAIGLEEISRGSGGL 88 
                                       79*************************************************************************** PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                       ++++++h+sl+++++++fG e+qk++yL  l +ge
  gi|313126840|ref|YP_004037110.1|  89 GTVVAAHTSLAGNMLYEFGDEAQKQEYLTSLNTGE 123
                                       *****************************999987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.84
                                       HHHHHHHT CS
                     Acyl-CoA_dh_N  36 lwkklael 43 
                                       l++k+a+l
  gi|313126840|ref|YP_004037110.1| 304 LMHKAADL 311
                                       23333333 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   1.0   3.5e-29   1.2e-25       1     133 [.     250     372 ..     250     373 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 3.5e-29
                                       .HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----H CS
                     Acyl-CoA_dh_2   1 lgiaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtv 77 
                                       ++iaa  +G+Araal+++v++a +r +  + +++a+++a++++la++ ++++AA++l+++aa+       +g+++  
  gi|313126840|ref|YP_004037110.1| 250 ITIAARSIGIARAALDDAVAYADDREQ--FDQPIAEFQAIKHKLADMDTKVQAAKMLMHKAADL----KIRGESY-- 318
                                       579************************..***********************************....5566665.. PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  78 edraearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                          +ea+ a+++a+e++++++++ ++++Gg++++k+ p +R++RDa+  +++++++
  gi|313126840|ref|YP_004037110.1| 319 --IKEAAQAKLYASEISREVANEGIQIHGGYGYTKDFPAERYYRDAKLNEIYEGTS 372
                                       ..7*********************************************99999886 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   1.5e-27   5.3e-24       1      96 [.     127     222 ..     127     223 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 1.5e-27
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE...GGGEEE CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvp.rdapgvsv 75 
                                       afal+E +aGsdv +++t +a++d++eyv+nG K wi+n+  a++++v+a+ ++pd +++g+s f+v  + + g+ v
  gi|313126840|ref|YP_004037110.1| 127 AFALSEAGAGSDVPAMDT-TATKDDDEYVINGGKLWISNGSVADTVTVFAK-TDPDaGNKGISSFVVRpEEDDGFIV 201
                                       79****************.66777779************************.556669*********978888**** PP

                                       -----BSS-TTS-EEEEEEE. CS
                     Acyl-CoA_dh_M  76 rrieeklGlrglptgelvfed 96 
                                       + +e+klG +g+pt+el+f++
  gi|313126840|ref|YP_004037110.1| 202 EGTEDKLGDKGCPTAELRFDE 222
                                       *******************97 PP

>> DUF743  Protein of unknown function (DUF743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   7.9e-05      0.28      15      92 ..     245     321 ..     235     334 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.9e-05
                            DUF743  15 veGkkldlaarqleldkaaldterelalaklalerqalnnqvekfdkilelrvqGdlqrvrllraaGlrvdPysytr 91 
                                       ++G ++ +aar + + +aald    +a  + ++++   + q  k  k  ++  + ++ ++ + +aa l++   sy +
  gi|313126840|ref|YP_004037110.1| 245 LNGGRITIAARSIGIARAALDDAVAYADDREQFDQPIAEFQAIKH-KLADMDTKVQAAKMLMHKAADLKIRGESYIK 320
                                       46778*****************************99888787775.4555555556677778899999999888866 PP

                            DUF743  92 q 92 
                                        
  gi|313126840|ref|YP_004037110.1| 321 E 321
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2257.82
//
Query:       gi|313126841|ref|YP_004037111.1|  [L=356]
Description: farnesyl-diphosphate farnesyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-50  170.0   1.8    8.6e-50  169.7   1.8    1.1  1  SQS_PSY         Squalene/phytoene synthase
  ------ inclusion threshold ------
      0.056   13.4   0.1       0.23   11.4   0.0    2.1  2  Band_7          SPFH domain / Band 7 family
      0.056   14.0   0.0       0.69   10.5   0.0    2.7  3  Arg_decarbox_C  Arginine decarboxylase C-terminal helical ext


Domain annotation for each model (and alignments):
>> SQS_PSY  Squalene/phytoene synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.7   1.8   1.4e-53   8.6e-50       2     261 ..      23     317 ..      22     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: 169.7 bits;  conditional E-value: 1.4e-53
                                       XHH-HHHHHHHTTS-HHHHHHHHHHHHHHHHHT-.-----..........------------............... CS
                           SQS_PSY   2 raasksfylaslllppelRdalgalYafcreaddlvDdvs..eplqararldwwrdavdavya.............. 62 
                                       + +s++f+l++ +l++++   +++ Y++cr ad+++D +   +p+qa+  l+++ + +d   +              
  gi|313126841|ref|YP_004037111.1|  23 QGVSRTFALTVDVLDEPMSSYICVGYLVCRIADTVEDASRisPPEQADL-LRTYDAVLDPDNDttveefvtavephl 98 
                                       578************************************9888888888.777777777555488887878887788 PP

                                       .......---------THHHHHHHHHHHT.--HHHHHHHHHHTS--SS-........--SHHHHHHHHHHHHHHHHH CS
                           SQS_PSY  63 ......edklkpprepvlralaqlirtyk.lpkellleliegmeadlef......tryetlddLeeYcyrvagvVge 126
                                             +++  +++++v r +++l ++ + +   + +el++gm+ ++e+       r+++ ++LeeYcy+ ag+Vg 
  gi|313126841|ref|YP_004037111.1|  99 peemndDWRVVRDAPRVIRTFEHLPEDVRnAVTPPARELVQGMALFVERyddtggLRIQSREELEEYCYYAAGTVGN 175
                                       776654489999***************99999****************976666666******************** PP

                                       HHHHHH-S.....S-HHHHHHHHHHHHHHHHHHHHHT---SH.HHHTT..S-HHHHHHHT--HHHHHHT-.-SHHHH CS
                           SQS_PSY 127 lclrllgar....rsdralaeaarrlGkalQltnilRdvpeD.aergrvyLPadvlkefgvseedllrkgvrsaelr 198
                                       l+++l+       +++r+l++ a+++G+ lQl+ni +dv  D +++++vyLPa++l+++gv ++++++ + +++++ 
  gi|313126841|ref|YP_004037111.1| 176 LITNLVTRGdisaDRRRQLYDTAEQFGLLLQLVNISKDVYDDyTAENNVYLPAEWLAAEGVPQDEVVAPE-HEEAAS 251
                                       ******886777755579*************************99**********************988.6666** PP

                                       HHHHHHHHHHHHHHHHHHHTGGGS...-HHHHHHHHHHHHHHHHHHHHHHHTTT-.TTT------H CS
                           SQS_PSY 199 allrrlaerArelldearellkqlp..drrarpalllavalyrailerieaadyd.vlsrrvklsl 261
                                       +++rr ae A   ld+a+++l+ +p  d++  +a+++++ l   +l+++ a+++d +++  vk+s+
  gi|313126841|ref|YP_004037111.1| 252 SVVRRTAEHAASFLDDAQTYLETVPatDGNTLAAWAVPFLLSVGTLRELLARPEDaLSKTGVKVSR 317
                                       ***********************7755889999**********************66669999997 PP

>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.9e-05      0.23      69     129 ..     106     163 ..     105     320 .. 0.78
   2 ?   -1.1   0.0      0.27   1.6e+03      99     126 ..     318     345 ..     303     346 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.9e-05
                            Band_7  69 yrvpddapklvaaveresanldnlirrvlesalrevisemtl.eellsnreelaeelkneln 129
                                       +rv  dap++++++    ++l++ +r+++ + +re+++ m l  e +++ ++l+ + ++el 
  gi|313126841|ref|YP_004037111.1| 106 WRVVRDAPRVIRTF----EHLPEDVRNAVTPPARELVQGMALfVERYDDTGGLRIQSREELE 163
                                       67779*********....**********************9998888764444444444433 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.27
                            Band_7  99 salrevisemtleellsnreelaeelkn 126
                                       +++ +v++em++++  ++ +e++e++++
  gi|313126841|ref|YP_004037111.1| 318 KEVFAVVAEMSGDTNRDALAEIREQIAA 345
                                       4455667899997777776666666665 PP

>> Arg_decarbox_C  Arginine decarboxylase C-terminal helical extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.69      16      45 ..      50      79 ..      47      81 .. 0.86
   2 ?   -1.5   0.0      0.64   3.8e+03      13      37 ..     135     162 ..     134     167 .. 0.79
   3 ?   -1.9   0.0      0.87   5.2e+03      25      39 ..     183     196 ..     175     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                    Arg_decarbox_C 16 lerlrrqveaagrLtpeerqalleeleagL 45
                                      + r+ + ve a r++p e+++ll++++a L
  gi|313126841|ref|YP_004037111.1| 50 VCRIADTVEDASRISPPEQADLLRTYDAVL 79
                                      557778888889***************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.64
                    Arg_decarbox_C  13 eeLlerlrrqveaa...grLtpeerqal 37 
                                       +eL++ +   ve+    g+L+ + r++l
  gi|313126841|ref|YP_004037111.1| 135 RELVQGMALFVERYddtGGLRIQSREEL 162
                                       6888888888888888888888888876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.87
                    Arg_decarbox_C  25 aagrLtpeerqalle 39 
                                       + g+++++ r++l++
  gi|313126841|ref|YP_004037111.1| 183 R-GDISADRRRQLYD 196
                                       3.7999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2204.92
//
Query:       gi|313126842|ref|YP_004037112.1|  [L=289]
Description: heme/copper-type cytochrome/quinol oxidase subunit 3 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-36  124.9  19.0    8.9e-36  124.0  19.0    1.4  1  COX3          Cytochrome c oxidase subunit III


Domain annotation for each model (and alignments):
>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0  19.0     5e-40   8.9e-36       9     255 ..      28     280 ..      24     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 5e-40
                                       -SHHHHHHHHHHHHHHHHHHHHHSS-..-...HH.....HHHHHHHHHHHHHHHHHHHHHHHTTT----HHHHHHHH CS
                              COX3   9 spwplvlsvalllltsalvlflhgykess...tl.....lilallslllvmllwfrdivaeatllGehtlavqkGlk 77 
                                       s wp+v++v ++ + +++ l++ g  e+    ++     +  ++ + l+  + w+        ++ + +    + l+
  gi|313126842|ref|YP_004037112.1|  28 SWWPFVTAVGAAGIYAGAGLYILGRGENAivgQMvgpaaFAGSVAIFLAGLYGWVYHAFVSHFWSRDASEKGANKLR 104
                                       667777777777777777776654433320112211111222344456667778777777777777778888899** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHS--GGGTSSSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHTTBHH CS
                              COX3  78 lGlilfiisevllflalfwaffhsalsPtvelGatwpPvGikavnPlevPllntiillssGvtvtyahhsliegnrk 154
                                       +G+i f+ se+  f alf  +f        e+      vG+  +    + l+nt++l++s +t+ +ah ++ +++r 
  gi|313126842|ref|YP_004037112.1| 105 WGMIAFLGSELGTFGALFGYYFYIRAGDWNEI-----LVGVPELTG-SLVLINTALLVASSITLHWAHVAIRNNDRG 175
                                       ******************99998765554444.....367777765.678*************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH....-SS-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--BSS CS
                              COX3 155 kalkgllltillavlftllqaveyle....asftisdgvyGsvfylatGlhglhviigtillavallrllkyhltkn 227
                                       k l+gl +t+ll+++f++ q++ey+e    + fti+ g +Gs+f+  tGlhglhv +g++ll + ++r l+  ++++
  gi|313126842|ref|YP_004037112.1| 176 KFLSGLAVTLLLGIIFIGGQVYEYYEfivhSDFTITSGLFGSAFFGLTGLHGLHVSLGAVLLGIVFIRALAGQYSAE 252
                                       ************************86444489********************************************* PP

                                       B-HHHHHHHHHHHHHHHHHHHHHHHTTT CS
                              COX3 228 hhlGfeaailywhfvdvvwlflyvsvyw 255
                                        h+   +a +ywhfvdvvw+fl v++y 
  gi|313126842|ref|YP_004037112.1| 253 RHVSVSTASMYWHFVDVVWIFLVVVLYV 280
                                       **************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1827.37
//
Query:       gi|313126843|ref|YP_004037113.1|  [L=550]
Description: k+ transporter, NAD-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-41  138.7  10.5    6.1e-23   81.3   0.3    3.7  3  TrkA_N         TrkA-N domain
    6.3e-25   86.8   1.3    7.5e-13   48.1   0.1    2.6  2  TrkA_C         TrkA-C domain
    0.00017   21.5   7.2    0.00037   20.4   7.2    1.5  1  Ion_trans_2    Ion channel
  ------ inclusion threshold ------
      0.023   14.0   0.5      0.072   12.4   0.9    1.5  2  TMEM132        Transmembrane protein family 132
       0.22   12.0   6.9       0.57   10.7   0.1    3.4  3  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.3   1.7e-26   6.1e-23       1     116 []     121     235 ..     121     235 .. 0.97
   2 !   60.6   1.8   4.4e-20   1.6e-16       1     114 [.     349     454 ..     349     456 .. 0.91
   3 ?   -0.3   0.1      0.34   1.2e+03      20      41 ..     505     525 ..     490     544 .. 0.62

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.7e-26
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       +ii+ +   G +l+eeL+++g ++vv+d d+e++++l +e++evv+g++ + ++Le+a++e+a a++a  +dde+n+
  gi|313126843|ref|YP_004037113.1| 121 VIICSFTSRGDTLVEELESRGVPYVVVDEDRETAQRLYAEEYEVVHGNPESVDTLEAANAEDAMALVAD-DDDETNA 196
                                       79*****************7757****************************************998888.899**** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                        ++l+ak+  p++++i+ ++d    ++ k +gad+v+sp
  gi|313126843|ref|YP_004037113.1| 197 SIILSAKQAAPDLHVISLIEDGTLSDYHKYAGADEVVSP 235
                                       *************************************98 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 4.4e-20
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       +i++G+G+vG + a+ L +++ + +v d        + + g++ v+gdat++++  +a+i++ ++vi a+++d++ i
  gi|313126843|ref|YP_004037113.1| 349 VIVAGYGEVGATAADALVSANVPSLVLDE-------VDKPGVD-VIGDATNKQAFLSADIDEGQSVILALDNDTTAI 417
                                       79*****************7745777777.......4556665.56******************************* PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvi 114
                                       +a+l++k+l p+ ++iara+d+e + +l+++ga++v+
  gi|313126843|ref|YP_004037113.1| 418 FATLVIKQLSPETEVIARANDAESIAKLYRAGAEYVL 454
                                       *********************************9986 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.34
                                       TTEEEEEEESSHHHHHHHHHTT CS
                            TrkA_N  20 ggkdvvvidkdeerveelreeg 41 
                                       ++  v+++++++e + e+  ++
  gi|313126843|ref|YP_004037113.1| 505 NCT-VIAVERNDELLTEVGPDF 525
                                       335.999999999888876555 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.1   5.5e-13     2e-09       1      68 [.     267     336 ..     267     338 .. 0.97
   2 !   48.1   0.1   2.1e-16   7.5e-13       5      66 ..     483     546 ..     480     550 .] 0.90

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 5.5e-13
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       ++ev v  +s l G t++e+ + +r gv++++   Rg++++ p+++ v  e  +llv g  ++l++l+el
  gi|313126843|ref|YP_004037113.1| 267 VAEVLVQRDSALEGDTIAESAIGRRtGVNIIGAwFRGEFVTPPDPEAVVDEHTILLVTGREEQLERLKEL 336
                                       689******************************99********************************987 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 2.1e-16
                                       EEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C   5 tvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       + +   +++G+tl+e+++rar +++v+a+ R+ + l+  ++d+++++ D+l+v+g+++d++++ 
  gi|313126843|ref|YP_004037113.1| 483 VRTTAPQIAGQTLAEADVRARtNCTVIAVERNdELLTEVGPDFTIRSEDTLIVAGTDDDINQFN 546
                                       5555567*************************9999*************************996 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   7.2     1e-07   0.00037       7      71 ..      28      96 ..      17     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1e-07
                                      CHHHHHHHHT.........T---HHHHHHHHHHHHTTS----SSTT..-----HHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  7 lifgaviysl.....eegwekwsfldalYfsfvtltTiGYGdivpe..tdagrlftivyillGlalfalfla 71
                                      l ++a++ +      ++   + s++dal  ++ t+tT GYG+ +++  tda +l+ti  ++ G+++++l+l 
  gi|313126843|ref|YP_004037113.1| 28 LGYAALYQWGmatfeGT---SVSYIDALHVVVETFTTTGYGEDAARwtTDAMKLITIPMMVSGVTVIFLTLP 96
                                      44444444445433222...55********************9998878999***************99985 PP

>> TMEM132  Transmembrane protein family 132
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       1.9   6.7e+03       7      31 ..     199     223 ..     198     226 .. 0.89
   2 ?   12.4   0.9     2e-05     0.072     148     264 ..     394     515 ..     390     521 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.9
                           TMEM132   7 vLtGkqvavplkvvavsaagtvtdv 31 
                                       +L+ kq+a  l v++  ++gt++d 
  gi|313126843|ref|YP_004037113.1| 199 ILSAKQAAPDLHVISLIEDGTLSDY 223
                                       89999***************99986 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2e-05
                           TMEM132 148 rFvaedadsgrvsyl.lgrdwlvdvteLvasslrvedprvaklklegrvlqGrevGrtevqVlsplsdsvlg....e 219
                                        F+++d d+g+   l l +d+ +  + Lv ++l+ e + +a+ +  +++ +  ++G   v  ls +s+++l+    e
  gi|313126843|ref|YP_004037113.1| 394 AFLSADIDEGQSVILaLDNDTTAIFATLVIKQLSPETEVIARANDAESIAKLYRAGAEYVLALSTVSGRILAsnltE 470
                                       69999999888887746699**********************988999********************998732225 PP

                           TMEM132 220 kevrvlddkvsiteLsvqvvsglslslspssgseraivattsaqe 264
                                       +ev + +++v+i++  +  ++g +l  +  ++ +++ v+ + +++
  gi|313126843|ref|YP_004037113.1| 471 EEVIAPESQVEIVRTTAPQIAGQTLAEADVRARTNCTVIAVERND 515
                                       69***************9999977776666776666666555544 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.5     0.041   1.5e+02      23      84 ..     134     204 ..     108     213 .. 0.60
   2 ?   10.7   0.1   0.00016      0.57       5      72 ..     344     413 ..     341     419 .. 0.77
   3 ?   -0.8   0.1      0.59   2.1e+03      56      74 ..     497     517 ..     429     547 .. 0.54

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.041
                     NAD_binding_7  23 vrklleagakvtvvapevkeeleelvklaeee...........lekdlegadlviaatddrelneriaeaaka 84 
                                       v+ l + g   +vv+++  +e+ +++ ++e e           le+  ++ +++++a dd+e n+ i   ak+
  gi|313126843|ref|YP_004037113.1| 134 VEELESRGVPYVVVDED--RETAQRLYAEEYEvvhgnpesvdtLEAANAEDAMALVADDDDETNASIILSAKQ 204
                                       55555666666777777..333333333333311111111111233344445999999999999999888875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvkla..eeelekdlegadlviaatddr 72 
                                       +++ kv+v+G Gev+a+ +  l++a+    v+++  k+ ++ + +++  +  l++d+++ + vi a d++
  gi|313126843|ref|YP_004037113.1| 344 FRRGKVIVAGYGEVGATAADALVSANVPSLVLDEVDKPGVDVIGDATnkQAFLSADIDEGQSVILALDND 413
                                       67789********************888888888855555533334311444599999999999999986 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.59
                     NAD_binding_7  56 ekdlegad..lviaatddrel 74 
                                       e+d+      +via+  ++el
  gi|313126843|ref|YP_004037113.1| 497 EADVRARTncTVIAVERNDEL 517
                                       333322223344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3719.88
//
Query:       gi|313126844|ref|YP_004037114.1|  [L=109]
Description: hypothetical protein Hbor_21050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 743.83
//
Query:       gi|313126845|ref|YP_004037115.1|  [L=817]
Description: penicilin amidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.5e-194  646.3  14.0   1.1e-193  646.0  14.0    1.1  1  Penicil_amidase  Penicillin amidase


Domain annotation for each model (and alignments):
>> Penicil_amidase  Penicillin amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.0  14.0    6e-198  1.1e-193       2     668 ..      60     795 ..      59     798 .. 0.92

  Alignments for each domain:
  == domain 1  score: 646.0 bits;  conditional E-value: 6e-198
                                       EEEEEEGGGEEEEE-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH-TBHHHHHHHHHHHT-HHHHHHHHH CS
                   Penicil_amidase   2 VeirrDewgvphIyAkneedlffaqGyvhAqdrlwqmellrrtarGrlaelfGpealesDrllrtlglrraaeaela 78 
                                       +++r+De+gvph+ A+ne+ l++a+Gyv+A+drl+qm+l+rr++ G+l++ fG++a+esDr++r++++r aa+a+++
  gi|313126845|ref|YP_004037115.1|  60 ATVRYDEFGVPHVSAANEKALYYAVGYVQARDRLFQMDLQRRLIGGNLSAAFGERAVESDRFYRKMDFRSAADASWR 136
                                       79**************************************************************************9 PP

                                       TS.....HHHHHHHHHHHHHHHHH-..-ST-HH.HHHH---....S.........SS-.XXXXXX.....XXX.XXX CS
                   Penicil_amidase  79 alldpetralleaYaaGvNaylaelkakalPlefallgykpepWtpvdslavakvmaldlagnleeelararalaak 155
                                       +l+ +e+ a l+aY+aGvN+y+++++    P+efallgy+p++W+p+dsl++ k++a+ l+gn+  +l ra  l+++
  gi|313126845|ref|YP_004037115.1| 137 ELEGTEAGAGLKAYTAGVNRYIDTGA---RPPEFALLGYEPTRWEPADSLLIGKLIAWRLSGNFA-DLRRAT-LKSR 208
                                       9999999***************9988...59******************************9*98.899987.**** PP

                                       XXXXX................................................................X-EEEEE- CS
                   Penicil_amidase 156 lgdekvaelfpp.........................................................gSNnwvvs 175
                                       lg+e++ el+p+                                                         gSNnwvvs
  gi|313126845|ref|YP_004037115.1| 209 LGPEATSELYPDsmahdtpiirngsdaasfdpaavatdasaagadggetagdfaalydavepfesrsgvGSNNWVVS 285
                                       ***********6677889999******************************************************** PP

                                       TTTBTTSS-EEEEE-EEESSGGG--EEEEEEETT.EEEEEEE-TT-S.SSEEEESSEEEEEEE-SS-SEEEEEEEEE CS
                   Penicil_amidase 176 gerTasGkpllanDPHlglsapslwyqahlqapg.ldviGaslpGlPgvliGhnediAWglTnagadvqdlyaekln 251
                                       ge+TasG p+lanDPHl+ls+p++wy++h +a + +d++G+++pG+P+v+iG+++d+AWg+Tn+g d +d y ++++
  gi|313126845|ref|YP_004037115.1| 286 GENTASGTPILANDPHLSLSTPAVWYEMHTTAGEsMDARGVTFPGVPFVIIGRTADVAWGVTNVGGDFTDEYTYETR 362
                                       ********************************989***************************************988 PP

                                       TTEEEEEEETTEEEE-EEEEEEEEEE-TT.EEEEEEEEETTEEEE-......TB--EEEEG-TTHHHHHHHHHT--S CS
                   Penicil_amidase 252 pddptrylydgkwepmetrtetikvkggddsvtltvreTrhGPvvsd.gkavalrwtalepgdrsldallalnrarn 327
                                       +   +rylydg+++++et teti+v++++d  t++vr++ hGPv+++ g++v ++w++   + ++  ++++ln+a++
  gi|313126845|ref|YP_004037115.1| 363 N---GRYLYDGEYRKFETTTETIPVADAPD-ATVEVRKSVHGPVIERgGRTVGVAWPGFSAT-NESVGVYRLNHAET 434
                                       3...67*********************998.88**************7666*****999965.8888********** PP

                                       HHHHHHHHHHH---SEEEEEEETT--EEEE--S--B---.......TT--EEETT-GGGS--...........TB-- CS
                   Penicil_amidase 328 vaefraalkdlaapaqnvvyADreGnigyqaagrvPvrp.aad...dgllpvpGsdsayeWt...........gyip 389
                                       +a++r+al+ +++paqn+v+A r+G+++y+ ag++P+r  +     +g ++++Gs ++ eW            g++p
  gi|313126845|ref|YP_004037115.1| 435 MADVRDALRIWDVPAQNFVAATRAGETLYYPAGQYPIRVtD-GevvRGDRIFNGSAGEGEWPgytpygtsswsGFVP 510
                                       **************************************952.24688999***********5599*******9**** PP

                                       GGGS-EEEE..SSEEEESSS----S...........--T-HHHHHHHHHH..S.S...-B-HHHHHHHHHT-BBTHH CS
                   Penicil_amidase 390 feelPqvvnPargyivtaNnrvlpddypaalg..sdwappyRarrirelLeek.aagkkvtledmaalqtdtrslla 463
                                       fe +P+v +   ++++taN+r+++d  p ++g   ++++pyR+ ri+e+L+++ a  +  t+edm a+q+d+rs +a
  gi|313126845|ref|YP_004037115.1| 511 FESIPHVDD--PDVLATANQRTTDD-PPFYMGtsLTYSEPYRGARIYEMLDARtA--DGATPEDMLAVQRDVRSQAA 582
                                       *********..66********6665.6775552255**************88844..458***************** PP

                                       HHHHHHH......-..GGGHHHHHHHHH-.SB-STT-THHHHHHHHHHHHTT......................... CS
                   Penicil_amidase 464 erllpll...aleaaeaeaaaaldlLraWdgrmdadsaaaalfaawlaalvralfedelg.........rlaealek 528
                                          ++          +++a+++++ L++Wdg+m+ads++a++ + +++++v+a+f+de++         ++ ++++ 
  gi|313126845|ref|YP_004037115.1| 583 VSYATIArnaS-AGLSPDARELAAELEEWDGEMRADSRGALVTHLFREEFVNATFADEFSaagldaeyyPNPYVTAG 658
                                       *9999668541.5567777889*****************************************99998644445555 PP

                                       .....---TTSTTT-SE.SHH.HHHHHHHHHHHHHHHST-T-B.....HHHHEEEE.E............EE---B- CS
                   Penicil_amidase 529 lledasfwwddptttpk.trdelllaalaealaeleaaglgadpakwrwgklhrlelrhplg...fnrg.lpvgGge 600
                                       l +d s+w+dd +t+++ tr+++++ al+++++++ ++g+++      +g+++rl+l+hp++   +n    p++G++
  gi|313126845|ref|YP_004037115.1| 659 LAAD-SQWFDDGRTDATeTRADVARVALERTADRIDRHGYET------YGDVNRLDLNHPFDrefLNWPeRPMNGSQ 728
                                       5555.99*******999*********************7654......************99***99999******* PP

                                       GGG.........EEEEEEE-EEEEEE--T.S....EEEEETT-S-S-TTSTTSSHHHHHHHTT--EEE--S CS
                   Penicil_amidase 601 etvnatsysarafrvtrgpsyrmvvdladrdk...aravlpgGqsgnpgsphyaDqlelwaegeylplpft 668
                                       +tv++ ++       + g+s+rmvv ++++ +   a++v+pgGqsg   s hy+Dql+ wa+gey+pl ++
  gi|313126845|ref|YP_004037115.1| 729 YTVSNFRSGG----DNVGSSWRMVVAFGETPAedtAKGVIPGGQSGVFWSDHYHDQLDEWATGEYKPLTLD 795
                                       ***9776643....4579*********99944478********************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (817 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 4330.05
//
Query:       gi|313126846|ref|YP_004037116.1|  [L=106]
Description: hypothetical protein Hbor_21070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        2.4    7.7   5.1         12    5.4   0.2    2.5  2  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family


Domain annotation for each model (and alignments):
>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3    0.0014        25      12      25 ..      27      40 ..      25      44 .. 0.85
   2 ?    5.4   0.2   0.00067        12      16      26 ..      53      63 ..      45      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0014
                                      CHHHHHHHHHHHHH CS
                   ATP1G1_PLM_MAT8 12 sLrlgGLifAglLf 25
                                      s+  +G+++Ag+L 
  gi|313126846|ref|YP_004037116.1| 27 SVHWVGIVVAGVLV 40
                                      78889*******95 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.00067
                                      HHHHHHHHHHH CS
                   ATP1G1_PLM_MAT8 16 gGLifAglLfi 26
                                       GL+fAglL +
  gi|313126846|ref|YP_004037116.1| 53 LGLTFAGLLVA 63
                                      6*******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 643.45
//
Query:       gi|313126847|ref|YP_004037117.1|  [L=253]
Description: hypothetical protein Hbor_21080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-30  105.3   0.0    2.6e-30  105.0   0.0    1.1  1  DUF547    Protein of unknown function, DUF547


Domain annotation for each model (and alignments):
>> DUF547  Protein of unknown function, DUF547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   1.5e-34   2.6e-30       3     123 .]      51     176 ..      49     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1.5e-34
                            DUF547   3 els.reeklAfwiNlYNalvlhaileygpesnvkrlslfkkaayniggqslslddIehgiLrkn.....lsrlkkka 73 
                                       +ls ++ ++Afw+N+YNa+v   +    pe +++r+++f++a++ ++gq lsl+dIehgiLr++     l  l +++
  gi|313126847|ref|YP_004037117.1|  51 RLSdDARRIAFWLNVYNAFVQDCLS-DDPE-SFDRTRFFRRAKVPVAGQLLSLNDIEHGILRRSmlswgLGYLPRPF 125
                                       67768899**********9877666.3355.589******************************7666633344444 PP

                            DUF547  74 .rderrkyaleqpdprihfaLvcgsascpplriytaerleeqLeaaaeeFl 123
                                        +  +r+  ++++d+rihfaL+cg+ascpp+ +y++e+l+++L+  +e++l
  gi|313126847|ref|YP_004037117.1| 126 pNAFERAARVDERDFRIHFALNCGAASCPPVAVYDPETLDADLDWITEDYL 176
                                       7889999****************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 1389.32
//
Query:       gi|313126848|ref|YP_004037118.1|  [L=726]
Description: hypothetical protein Hbor_21090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0059   16.7  18.0      0.019   15.1  18.0    1.8  1  Cep57_CLD_2   Centrosome localisation domain of PPC89
  ------ inclusion threshold ------
       0.08   13.0   2.4       0.16   12.0   2.4    1.4  1  DUF1664       Protein of unknown function (DUF1664)
        1.2    9.3   8.4        3.6    7.9   8.4    1.8  1  XhlA          Haemolysin XhlA
        5.8    5.7  23.3         11    4.8  23.3    1.4  1  Spc7          Spc7 kinetochore protein
        6.1    7.6  13.7         21    5.8   7.7    3.6  4  YabA          Initiation control protein YabA


Domain annotation for each model (and alignments):
>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  18.0   5.2e-06     0.019       4      63 ..     421     480 ..     419     482 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.2e-06
                       Cep57_CLD_2   4 evktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELke 63 
                                       ++  L+++L+ ++++ ++  ee+++L  ERd++ ++  +   +++eL +eve+l+ EL+ 
  gi|313126848|ref|YP_004037118.1| 421 AIAKLKDKLEEAEERREKLAEERDELEVERDEYRQRAEELNARVEELESEVERLKTELEA 480
                                       6889*****************************************************986 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.4   4.4e-05      0.16      66     121 ..     420     475 ..     409     477 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                           DUF1664  66 sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       + i+++ +kl+e +e  ++++ee +e++ + +e ++  e++++ ve+les++er++
  gi|313126848|ref|YP_004037118.1| 420 EAIAKLKDKLEEAEERREKLAEERDELEVERDEYRQRAEELNARVEELESEVERLK 475
                                       6799*************************************************997 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.4     0.001       3.6       2      47 ..     425     470 ..     424     474 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.001
                              XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkklesn 47 
                                       +k++le+ e++ ++l e+ d+le   +e ++++++l+ ++++les 
  gi|313126848|ref|YP_004037118.1| 425 LKDKLEEAEERREKLAEERDELEVERDEYRQRAEELNARVEELESE 470
                                       699**************55************************985 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  23.3     0.003        11     160     259 ..     378     480 ..     363     488 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.003
                              Spc7 160 kqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkelaelqeqleele 233
                                       +++++ +e+ ++ ++e+++ +++ e   +aa+e ++      e +++l+++l+e+++  e++ +e +el+ +++e +
  gi|313126848|ref|YP_004037118.1| 378 QRKQQRQEARQRRRKEEQQAKRRREAAAAAAAESAEetgESAEAIAKLKDKLEEAEERREKLAEERDELEVERDEYR 454
                                       45667788888888888888888888877666655544466999********************************* PP

                              Spc7 234 ekieelkeqkseleeeiaeaervlee 259
                                       ++ eel+++ +ele+e+++ +  le+
  gi|313126848|ref|YP_004037118.1| 455 QRAEELNARVEELESEVERLKTELEA 480
                                       *****************999988776 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.8   6.4e+03      65      81 ..      16      32 ..       8      33 .. 0.86
   2 ?   -0.5   0.5      0.53   1.9e+03      33      75 ..     382     424 ..     367     425 .. 0.58
   3 ?    5.8   7.7    0.0058        21      14      73 ..     419     478 ..     406     486 .. 0.77
   4 ?    2.8   0.0     0.049   1.8e+02      66      86 ..     691     712 ..     630     718 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.8
                                      XXXXXXXXXXXXXXXXX CS
                              YabA 65 elsegkenLarlYeeGF 81
                                       +++g+e L+rl ++GF
  gi|313126848|ref|YP_004037118.1| 16 PVESGYEGLHRLADDGF 32
                                      67899***********9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  33 elleenaeLeleneklrerleeeekkekekkkelsegkenLar 75 
                                       +  e  ++ + e ++ ++r e + ++++e+ +e++e+ e +a+
  gi|313126848|ref|YP_004037118.1| 382 QRQEARQRRRKEEQQAKRRREAAAAAAAESAEETGESAEAIAK 424
                                       3334444555566666666666666666666666666666665 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  14 eeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenL 73 
                                        e +++l+++lee +e+ ++l ee +eLe+e ++ r+r ee +++ +e ++e+++ k++L
  gi|313126848|ref|YP_004037118.1| 419 AEAIAKLKDKLEEAEERREKLAEERDELEVERDEYRQRAEELNARVEELESEVERLKTEL 478
                                       577888999999999999999999999999999999999777777666666666665555 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.049
                                       XXXXXXXXXXXX.XXXXXXXXX CS
                              YabA  66 lsegkenLarlY.eeGFHiCnv 86 
                                       +++ k+++ +l  ++G+H+C v
  gi|313126848|ref|YP_004037118.1| 691 SRSKKKSFVKLSrKQGYHVCLV 712
                                       334445555554279*****76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2760  (0.153941); expected 358.6 (0.02)
Passed bias filter:                      935  (0.0521501); expected 358.6 (0.02)
Passed Vit filter:                       315  (0.0175693); expected 17.9 (0.001)
Passed Fwd filter:                       118  (0.00658152); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.99u 0.45s 00:00:02.44 Elapsed: 00:00:00.61
# Mc/sec: 3581.83
//
Query:       gi|313126849|ref|YP_004037119.1|  [L=101]
Description: hypothetical protein Hbor_21100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0029   17.5   0.1     0.0066   16.4   0.0    1.7  1  HTH_12           Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.025   14.4   0.1      0.059   13.2   0.1    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
      0.039   13.9   0.1      0.077   12.9   0.0    1.6  2  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
      0.051   13.5   0.1      0.084   12.8   0.1    1.5  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.069   13.8   0.4        6.8    7.4   0.0    2.3  2  SlyX             SlyX
        0.1   12.5   0.1       0.12   12.2   0.1    1.3  1  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
       0.35   11.3   6.1        2.5    8.5   1.1    2.2  2  CLZ              C-terminal leucine zipper domain of cyclic n


Domain annotation for each model (and alignments):
>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.6e-06    0.0066      24      61 ..      35      69 ..      16      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.6e-06
                            HTH_12 24 kkrgydigeravRyrLrkleergltrrvgyagreltEk 61
                                      +++gy      vRy Lr+lee++l++  + + +  tE+
  gi|313126849|ref|YP_004037119.1| 35 NETGYPH--HKVRYSLRVLEEENLIEPSSQG-AITTER 69
                                      4557766..88***************98876.777887 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.3e-05     0.059       5      46 ..      16      58 ..      13      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      l++Lk++ e ++  +   ++e+g +  +v++ L++L+e++L+e
  gi|313126849|ref|YP_004037119.1| 16 LQVLKMVIEsEPIGIVKMSNETGYPHHKVRYSLRVLEEENLIE 58
                                      789999999666999999***********************96 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.49   1.3e+03      66      93 ..       8      33 ..       3      39 .. 0.49
   2 ?   12.9   0.0     3e-05     0.077      59     107 ..      33      81 ..      20      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.49
                   Phage_rep_org_N 66 eletvrlaLkvlkdlelieisedkviki 93
                                      e++ ++  L+vlk   +ie    +++k+
  gi|313126849|ref|YP_004037119.1|  8 EVDMLERHLQVLKM--VIESEPIGIVKM 33
                                      44455555555542..244444444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3e-05
                   Phage_rep_org_N  59 lalifnreletvrlaLkvlkdlelieisedkvikiknwekhqnieskek 107
                                       ++ ++  + ++vr  L+vl++ +lie s++++i+ + +++++ +  ++ 
  gi|313126849|ref|YP_004037119.1|  33 MSNETGYPHHKVRYSLRVLEEENLIEPSSQGAITTERTAEFVDELDEKL 81 
                                       6788888999**************************9999987655544 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.3e-05     0.084       5      56 ..      10      61 ..       5      75 .. 0.87
   2 ?   -1.6   0.0         1   2.6e+03      38      47 ..      80      89 ..      60      99 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                      HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      ++ e   +v + +++++p  + + ++e+g p+ kv  +Lr Le+  l+e + 
  gi|313126849|ref|YP_004037119.1| 10 DMLERHLQVLKMVIESEPIGIVKMSNETGYPHHKVRYSLRVLEEENLIEPSS 61
                                      55667788999999**********************************9775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                                      CHHHHHHHHH CS
                              TrmB 38 kvYevLrsLe 47
                                      k  e++ +Le
  gi|313126849|ref|YP_004037119.1| 80 KLDEIVDKLE 89
                                      4444445554 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0027       6.8      33      51 ..       2      20 ..       1      41 [. 0.80
   2 ?    5.1   0.1     0.014        36      32      55 ..      73      96 ..      54     101 .] 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0027
                                      HHHHHHHHHHHHHT-XXXX CS
                              SlyX 33 idrlqrqlrllaerlkele 51
                                      idrl++++++l+++l+ l+
  gi|313126849|ref|YP_004037119.1|  2 IDRLEKEVDMLERHLQVLK 20
                                      8889999999988887554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                                      HHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX 32 qidrlqrqlrllaerlkeleessg 55
                                       +d+l ++l++++++l++++ +++
  gi|313126849|ref|YP_004037119.1| 73 FVDELDEKLDEIVDKLESMKIEEA 96
                                      579999999999999999887755 PP

>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.7e-05      0.12      59      97 ..      45      86 ..      20     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                                      EEEEEEEC..TTCEEETTGGG-.-TTHHHHHHHT-EEE..... CS
                      PhosphMutase 59 RcnlvtvdeedgiiidrragristeeakeLikalneel....e 97
                                      R  l  ++ e+++i+  + g i+te ++e++++l+e+l    +
  gi|313126849|ref|YP_004037119.1| 45 RYSLRVLE-EENLIEPSSQGAITTERTAEFVDELDEKLdeivD 86
                                      66677775.699*************************975441 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3    0.0082        21      34      50 ..       3      19 ..       1      26 [. 0.58
   2 ?    8.5   1.1   0.00097       2.5       8      50 ..      50      91 ..      48     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0082
                               CLZ 34 erLessLeaLqtrlarL 50
                                      +rLe+++++L+ +l+ L
  gi|313126849|ref|YP_004037119.1|  3 DRLEKEVDMLERHLQVL 19
                                      56666666666555544 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00097
                               CLZ  8 ILlKdglLDeeaakagaeqkeleekverLessLeaLqtrlarL 50
                                      +L  ++l++ +  +   + + + e v++L+++L+ + ++l+ +
  gi|313126849|ref|YP_004037119.1| 50 VLEEENLIEPS-SQGAITTERTAEFVDELDEKLDEIVDKLESM 91
                                      67889999999.5666788888899999999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1398  (0.0779742); expected 358.6 (0.02)
Passed bias filter:                      810  (0.0451782); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 629.60
//
Query:       gi|313126850|ref|YP_004037120.1|  [L=443]
Description: adenylosuccinate synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.5e-157  522.4   0.0   9.7e-157  522.2   0.0    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  522.2   0.0  5.4e-161  9.7e-157       2     419 .]       4     435 ..       3     435 .. 0.96

  Alignments for each domain:
  == domain 1  score: 522.2 bits;  conditional E-value: 5.4e-161
                                       EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHH CS
                   Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealle 78 
                                       ++vG+q GDEGKG +vDl   +advv+R+qGG+nAGHtvv dg +ykl+l+pSG+++ g++ ++Gng+v++p++l++
  gi|313126850|ref|YP_004037120.1|   4 TIVGSQLGDEGKGALVDLWGGDADVVARYQGGDNAGHTVVEDGDEYKLSLVPSGAVR-GKIGILGNGCVINPKTLFS 79 
                                       79******************************************************7.9999*************** PP

                                       HHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH..----------TTHHHHHHHHHTT---BGGGGGSHH CS
                   Adenylsucc_synt  79 EieeleakgvelskerllisdrahlvlpyhkalDkleeaa..kgkkkiGtTkkGiGpayadkvarrgirvgdlldee 153
                                       Ei+el+++g++    ++++++rah+++pyh+ lD++ee+a  +++ ++GtT++GiGp+y+dk+ rrgirvgdlld+e
  gi|313126850|ref|YP_004037120.1|  80 EIDELRERGLDP---DVRLAERAHVIMPYHRRLDNIEEEAkaDSELTVGTTGRGIGPTYEDKAGRRGIRVGDLLDPE 153
                                       **********87...8***********************95444459****************************** PP

                                       HHHHHHHHHHHHTHHHHHHT.......T-----HHHHHHHHHHHHGG..GEE-HHHHHHHHHHTT--EEEE--S-GG CS
                   Adenylsucc_synt 154 eleeklekllelknkllekldk....eeleveelleellkyaerlkp..yvvdtvallnealkegkkvLfEGaqgtl 224
                                       +l+++le ++ +k++l+e+++     ee++ve+l+e++ +y +rl++  + v++ ++l+e  ++g++v+fEGaqgtl
  gi|313126850|ref|YP_004037120.1| 154 VLRQRLEYVVPKKRALIENVYGleagEECDVEKLFEQYAEYGRRLESenMTVNCGNFLAERRSAGENVMFEGAQGTL 230
                                       ********************9999999******************9766899************************* PP

                                       G-TTTSSTTSS-SS--SHHHHHHHTT--GGGEE..EEEEEEESSEEESSSS--TTB--.....SHHHHHHHHHTT-B CS
                   Adenylsucc_synt 225 lDidhGtYPfvTsSnttaggaltglglapkkid..evlgvvKAyttrvGeGpfptelk.....devgeklrekGkEf 294
                                       +DidhG+YP+vTsSn+tagga+tg+g++p+ ++  ev+g+vKAy +rvGeGp+ptelk     +e ++++rekG+Ef
  gi|313126850|ref|YP_004037120.1| 231 IDIDHGSYPYVTSSNPTAGGAATGTGVGPTVVGqgEVVGIVKAYLSRVGEGPMPTELKndehqEELADYIREKGGEF 307
                                       *******************************9555*********************75333335889999******* PP

                                       -TTT--B-EEE-EEHHHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEE CS
                   Adenylsucc_synt 295 gtttgrpRrcGwlDlvllryavrvngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeel 371
                                       gt+tgrpRr+GwlD+++lr+++rv+g+t+la+++lDvl+glde+kv+ +Y+ldg+e+ ++pa++e+++++ep+++e+
  gi|313126850|ref|YP_004037120.1| 308 GTVTGRPRRIGWLDIPMLRHSARVSGLTGLAVNHLDVLAGLDEVKVGHSYTLDGEEYLTMPATTERWAQCEPNLREF 384
                                       ********************************************************99******************* PP

                                       E--..S--TT-..--GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
                   Adenylsucc_synt 372 pgWk.edisgv..rsfedlpenakkyvefieellgvpvkiisvGpereqti 419
                                       + W+  d+++v  + ++++p++a++y+e+i+e++g+p+  ++vGp+r++t+
  gi|313126850|ref|YP_004037120.1| 385 ETWDdVDWTEVaaEGYDAIPAAAQDYLEYISEEVGAPIYAVGVGPDRAETV 435
                                       ***856799888899********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2613.96
//
Query:       gi|313126851|ref|YP_004037121.1|  [L=125]
Description: hypothetical protein Hbor_21120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-23   83.1   0.1    1.9e-23   82.9   0.1    1.0  1  Bac_globin   Bacterial-like globin
     0.0038   17.1   0.4      0.011   15.6   0.4    1.8  1  Protoglobin  Protoglobin


Domain annotation for each model (and alignments):
>> Bac_globin  Bacterial-like globin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.1   2.1e-27   1.9e-23       1     119 [.       5     117 ..       5     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 2.1e-27
                                       -HHHHHTHHHHHHHHHHHHHHHHHT-CCCCCCGGGTTSSHHHHHHHHHHHHHHHTTSSSHHHHHHSS-.HHHHHTTS CS
                        Bac_globin   1 tlydaiGgeatveelvdrfYervdedeeealseifsgtdlegsreklveFlvqalgGPelYverrGhPrlrkrHapf 77 
                                       tly  +Gg +++ ++vd fY+r+ +d+e  l+++f+  d++++r+++ +Fl ++ gGP  Y    G   + + H  +
  gi|313126851|ref|YP_004037121.1|   5 TLYRRLGGRDALASVVDTFYDRILADDE--LRPFFEDVDMTKQRAHQTQFLSAVAGGPVEY---DGEN-MAAAHEHL 75 
                                       69**************************..*******************************...7*99.******** PP

                                       --BHHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHH CS
                        Bac_globin  78 eitaaerdawlkhlaeAleetgvssedreeklellealahaa 119
                                       +it++e da++ hl  Ale  +v++ dre+ l  +e +++++
  gi|313126851|ref|YP_004037121.1|  76 DITHEEYDAIAAHLDAALEIHDVPADDRETVLTAVESFRDDI 117
                                       **************************************9876 PP

>> Protoglobin  Protoglobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   1.3e-06     0.011      32      78 ..      15      60 ..      12     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-06
                                      CHHHHHHHHHHHHCTSHHHHHHHCHHCHHHHHHHHHHHHHHHCCCSS CS
                       Protoglobin 32 lipavvdafYekllsfpetarifetssqierlkdflksyllklfsgp 78
                                      ++  vvd+fY+++l  +e++ +fe+   + + ++++ ++l+ +  gp
  gi|313126851|ref|YP_004037121.1| 15 ALASVVDTFYDRILADDELRPFFED-VDMTKQRAHQTQFLSAVAGGP 60
                                      67789********************.444444555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 768.68
//
Query:       gi|313126852|ref|YP_004037122.1|  [L=62]
Description: hypothetical protein Hbor_21130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0026   18.3   0.1      0.006   17.1   0.1    1.6  1  Trm112p   Trm112p-like protein


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   3.4e-07     0.006       1      68 []       2      49 ..       2      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-07
                                      BTGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEETT CS
                           Trm112p  1 kllllniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkdG 68
                                      k+ l++iL+ p++k+ L++++  +                       +i++g Lv + +g  YpI+dG
  gi|313126852|ref|YP_004037122.1|  2 KESLMDILCDPLDKSDLELKVTERDG--------------------DEIITGRLVGTVTGEEYPIEDG 49
                                      6789***********99544444444....................48*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 406.79
//
Query:       gi|313126853|ref|YP_004037123.1|  [L=195]
Description: hypothetical protein Hbor_21140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00059   20.2   2.9     0.0009   19.6   2.9    1.3  1  DUF3995   Protein of unknown function (DUF3995)
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.27   11.2   0.0    1.6  1  DUF543    Domain of unknown function (DUF543)


Domain annotation for each model (and alignments):
>> DUF3995  Protein of unknown function (DUF3995)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   2.9     1e-07    0.0009      21      85 ..     130     194 ..     125     195 .] 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-07
                           DUF3995  21 slaeavvgekegsavPsavatlavallllaaAllvlalarll.gaplssrllrlaawvvaavlllR 85 
                                       sl+e+++++ +g   Ps++a+ +v+llll+ A++ ++l  ++ +a++ s  + l+a  v+av+llR
  gi|313126853|ref|YP_004037123.1| 130 SLTEELAETIDG-VLPSRGALPIVGLLLLVLAVAGVILSAVQsTAVVLSVGVVLGAATVGAVFLLR 194
                                       566777777776.79**********************99888678999999**************9 PP

>> DUF543  Domain of unknown function (DUF543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05      0.27      14      65 ..     129     185 ..     116     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                            DUF543  14 e...sdldekwDaclsn..llvkvglgllvGvvasvllfrrRaapvalGaGvGiGaA 65 
                                           ++l e++D +l +  +l  vgl llv +va+v+l   +   v+l++Gv +GaA
  gi|313126853|ref|YP_004037123.1| 129 PsltEELAETIDGVLPSrgALPIVGLLLLVLAVAGVILSAVQSTAVVLSVGVVLGAA 185
                                       2345777888888885423577789999999************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1290.42
//
Query:       gi|313126854|ref|YP_004037124.1|  [L=376]
Description: hypothetical protein Hbor_21150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-45  152.6   0.9      3e-45  152.6   0.9    2.0  2  DR2241    DR2241 stabilising domain
    4.2e-27   94.4   0.7    7.8e-27   93.5   0.7    1.5  1  Fer4_23   4Fe-4S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DR2241  DR2241 stabilising domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.6   0.9   3.3e-49     3e-45       1     111 []      95     205 ..      95     205 .. 0.99
   2 ?   -2.4   0.2      0.48   4.3e+03      48      70 ..     319     343 ..     290     356 .. 0.55

  Alignments for each domain:
  == domain 1  score: 152.6 bits;  conditional E-value: 3.3e-49
                                       HHHHHHHHHHHHHH-ETTEEEEEE...TT..EEEEEEGGGTT--GGGSEEE-SHHHHHHHTSB-TTS-B-SSTTBS- CS
                            DR2241   1 vaeryaalaegaerelgellvtaelddagervyelrhaddegadeeeletyddpedaRelvrldeegryRPlktapt 77 
                                       v+erya+la+g+++e+gel++ta+ld ager+ye+rh+dd++ad+++l++y+dp+daRel+++d++gryRPlktapt
  gi|313126854|ref|YP_004037124.1|  95 VPERYAELADGVHTEWGELRITATLDAAGERRYEIRHEDDADADRSKLDEYTDPLDARELATFDDRGRYRPLKTAPT 171
                                       689************************************************************************** PP

                                       --SSEE.EEE-TTTHHHHHHHHSTTHHHHHHHHH CS
                            DR2241  78 lprGWrfavldeadlveavellYPAtvenwyrer 111
                                       + +GW+f++ld++dl+eav+++YPAt++nw+ er
  gi|313126854|ref|YP_004037124.1| 172 IVSGWVFPELDGRDLIEAVDAFYPATIANWNLER 205
                                       ******************************9886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.48
                                       SEEE-SHH..HHHHHTSB-TTS-B- CS
                            DR2241  48 letyddpe..daRelvrldeegryR 70 
                                       ++++ d +  d+Re   ++ + ryR
  gi|313126854|ref|YP_004037124.1| 319 IDAVADGRidDIREADVYEGANRYR 343
                                       3444443222667666666666666 PP

>> Fer4_23  4Fe-4S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.7   8.7e-31   7.8e-27       1      82 []     206     291 ..     206     291 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 8.7e-31
                           Fer4_23   1 rgrlvvtslretaeRQtGiYavvkklt....deqaervvealCadsvClkrrlWavekgeklevegaagelPCaEaC 73 
                                       +g+l+v ++ et+eRQtGiY+v+++ +    +e +e+v+e++C ds+Clkrr+W++++  +le++g++g +PC+E+C
  gi|313126854|ref|YP_004037124.1| 206 EGELDVSHWEETVERQTGIYSVIETWNrgggHEHVEWVAETCCDDSQCLKRREWQYNEETELEADGGDGVFPCREPC 282
                                       599*********************997444479******************************************** PP

                           Fer4_23  74 slfvaaaRk 82 
                                       sl++aa+Rk
  gi|313126854|ref|YP_004037124.1| 283 SLVIAASRK 291
                                       *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2563.12
//
Query:       gi|313126855|ref|YP_004037125.1|  [L=291]
Description: hypothetical protein Hbor_21160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-42  143.6   0.1    3.3e-20   72.4   0.0    2.4  2  CbiX      CbiX
    3.6e-07   29.8   0.0     0.0017   17.7   0.1    2.1  2  CbiK      Cobalt chelatase (CbiK)
  ------ inclusion threshold ------
      0.095   12.6   0.0        4.3    7.3   0.0    2.3  2  DUF4860   Domain of unknown function (DUF4860)


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0   5.5e-24   3.3e-20       1     106 [.       9     129 ..       9     130 .. 0.90
   2 !   68.9   0.0   6.6e-23     4e-19       1     106 [.     152     262 ..     152     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 5.5e-24
                                       -STSS.CCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHC CS
                              CbiX   1 HGSrd.pesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeel 76 
                                       HGS++ p+s+ + + +a+++r+ ++f++v++gf + eepsl+e+lr++   + ++++vvPlf+++G++++++Ip+el
  gi|313126855|ref|YP_004037125.1|   9 HGSHLnPDSSTPTQRHADTIRATDAFDEVKTGF-WKEEPSLREVLRTV---ESDEVFVVPLFISEGYFTEQVIPREL 81 
                                       9**776***************************.99***********9...99************************ PP

                                       T....--SSSS-..................TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  77 e....eaeeahp..................kdveieytepLGthplvaevlk 106
                                       +    +                         + +++y+ p+Gth+++++vl+
  gi|313126855|ref|YP_004037125.1|  82 RldgwD----VSqwdsdglsadtatltaedTSQTVHYCGPVGTHESMTDVLV 129
                                       955542....334446888899999999777788***************997 PP

  == domain 2  score: 68.9 bits;  conditional E-value: 6.6e-23
                                       -ST.SSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHH.. CS
                              CbiX   1 HGS.rdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpe.. 74 
                                       HG+ r+++s +++e +a+++r++++f++v+  +++ eep+++++ + +   + ++ivvvPlf+++G+h++eDIpe  
  gi|313126855|ref|YP_004037125.1| 152 HGTeRNENSAKAIEYHADRVRQMDRFDEVQALYMD-EEPEVDDVTDYF---ESDDIVVVPLFIADGFHTQEDIPEdm 224
                                       9**899*****************************.***********9...99**********************66 PP

                                       .HCT--SSSS-.....TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  75 .eleeaeeahp.....kdveieytepLGthplvaevlk 106
                                        +++++++ ++     ++++i+y+ ++Gt+ l+a+v+ 
  gi|313126855|ref|YP_004037125.1| 225 gLTDDYRTGYDvpaavDGHRIWYAGAVGTEGLMADVVL 262
                                       56667777777999999******************986 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   5.3e-05      0.31     142     210 ..       2      70 ..       1     101 [. 0.80
   2 !   17.7   0.1   2.9e-07    0.0017     146     221 ..     149     224 ..     113     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.3e-05
                                       EEEEEEE---SCH...HHHHHHHHHHHHHHCT-S.EEEEETTSSS-HHHHHHHHHHHT--EEEEEE-SSS-- CS
                              CbiK 142 ealvfvgHGtehe...snavyaeldkvlkekdfkqvvvgtvegyPeveevieelkkkgikevkliPlmlvAG 210
                                       +alv v+HG++ +   s+ + ++ d++     f++v  g  +  P++ ev+++++ ++   v ++Pl++  G
  gi|313126855|ref|YP_004037125.1|   2 QALVIVAHGSHLNpdsSTPTQRHADTIRATDAFDEVKTGFWKEEPSLREVLRTVESDE---VFVVPLFISEG 70 
                                       589******98642214445566666767799********************998765...66677776665 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.9e-07
                                       EEE---SCHHHHHHH...HHHHHHHHCT-S.EEEEETTSSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCCCS CS
                              CbiK 146 fvgHGtehesnavya...eldkvlkekdfkqvvvgtvegyPeveevieelkkkgikevkliPlmlvAGdHaknDmas 219
                                        vgHGte + n++ a   + d+v +  +f++v    ++  Pev++v ++ + ++i    ++Pl++  G H ++D+ +
  gi|313126855|ref|YP_004037125.1| 149 VVGHGTERNENSAKAieyHADRVRQMDRFDEVQALYMDEEPEVDDVTDYFESDDI---VVVPLFIADGFHTQEDIPE 222
                                       69***9987665433112567888889***********************99875...678**************88 PP

                                       SS CS
                              CbiK 220 de 221
                                       d 
  gi|313126855|ref|YP_004037125.1| 223 DM 224
                                       74 PP

>> DUF4860  Domain of unknown function (DUF4860)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00072       4.3      12      65 ..      26      81 ..      17      87 .. 0.86
   2 ?    2.8   0.1     0.017     1e+02       5      31 ..     162     188 ..     158     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00072
                           DUF4860 12 ekirqnDeegavsveelegtqaL..vlkeeiddeeyetyiYyydgkLkElfvkeda 65
                                        ir+ D+ ++v+++  +++++L  vl++  +de++++ +++++g+  E+++ ++ 
  gi|313126855|ref|YP_004037125.1| 26 DTIRATDAFDEVKTGFWKEEPSLreVLRTVESDEVFVVPLFISEGYFTEQVIPREL 81
                                      579*************9999999545688889999**************9987665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.017
                           DUF4860   5 talsYitekirqnDeegavsveelegt 31 
                                        a+ Y + ++rq D+ ++v+   ++++
  gi|313126855|ref|YP_004037125.1| 162 KAIEYHADRVRQMDRFDEVQALYMDEE 188
                                       57889999*******999987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1955.00
//
Query:       gi|313126856|ref|YP_004037126.1|  [L=167]
Description: hypothetical protein Hbor_21170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   15.2   0.1      0.084   13.3   0.0    1.8  2  DUF5628   Family of unknown function (DUF5628)


Domain annotation for each model (and alignments):
>> DUF5628  Family of unknown function (DUF5628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.7e-06     0.084       5      54 ..      17      67 ..      14      72 .. 0.83
   2 ?   -0.9   0.0      0.13   2.3e+03      24      39 ..      76      91 ..      67     133 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-06
                           DUF5628  5 lkWdltsGva..tdtpeslansGldpeaeathgrafaedlptrdlnpseakv 54
                                      l + l  Gv   t ++esl   G d+++ at  r fa+dlp  ++++ e  v
  gi|313126856|ref|YP_004037126.1| 17 LLYALRAGVVnyTAAAESLDVEG-DTDSIATALRRFADDLPPVEIEHREVTV 67
                                      77888899873356689**9999.78889999*************9999766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.13
                           DUF5628 24 sGldpeaeathgrafa 39
                                      +G d +a+a ++r+++
  gi|313126856|ref|YP_004037126.1| 76 AGEDVDADADDDRVLT 91
                                      6777777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1140.70
//
Query:       gi|313126857|ref|YP_004037127.1|  [L=495]
Description: cysteinyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   9.5e-104  347.0   0.2   6.2e-103  344.3   0.2    2.0  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    3.7e-13   49.7   2.5    5.3e-13   49.2   1.0    2.0  2  DALR_2        DALR domain
    1.2e-10   40.8   0.3    0.00014   20.8   0.0    2.1  2  tRNA-synt_1g  tRNA synthetases class I (M)
    6.4e-07   28.6   0.0    0.00046   19.2   0.0    2.3  2  tRNA-synt_1f  tRNA synthetases class I (K)
     0.0017   16.7   0.0     0.0061   14.9   0.0    1.8  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
      0.029   14.1   0.2        0.1   12.4   0.2    2.0  1  UVR           UvrB/uvrC motif
      0.031   13.4   0.1        1.8    7.6   0.0    2.3  2  Dak1_2        Dihydroxyacetone kinase family
      0.065   13.0   0.0       0.12   12.1   0.0    1.4  1  FTO_CTD       FTO C-terminal domain
       0.11   11.3   0.0       0.21   10.4   0.0    1.4  1  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d
       0.14   11.6   4.4        2.2    7.7   0.6    3.1  3  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.3   0.2  3.4e-106  6.2e-103       2     300 ..      16     334 ..      15     335 .. 0.93

  Alignments for each domain:
  == domain 1  score: 344.3 bits;  conditional E-value: 3.4e-106
                                       ---SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTT..S-HHHHH CS
                      tRNA-synt_1e   2 vkpleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareee..ksvkela 76 
                                       ++p +++ v lYvCG tv d++hlGhaR  +  D+++r+l++ gY v++v+n+tD+++ki +r  ++e  +s  ++a
  gi|313126857|ref|YP_004037127.1|  16 FEPQDDDDVLLYVCGLTVSDDAHLGHARLWMHADVMHRWLEHEGYTVHHVENFTDVNEKIAARIGDDElgQSEPDVA 92 
                                       56778899*******************************************************977651167778** PP

                                       HHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT CS
                      tRNA-synt_1e  77 ekfieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelg 153
                                        +f ++  +d++ Ln++++++ prvse+v++ii+l+e+l e+gyaY+++ g vyfdv+++e+Ygkls+q++ee+e++
  gi|313126857|ref|YP_004037127.1|  93 RHFTDHVIRDMRGLNLKRAEVYPRVSEHVPQIIDLIETLTENGYAYESN-GSVYFDVTAFEDYGKLSNQKIEEMEAQ 168
                                       ***********************************************99.*************************** PP

                                       ----S--S-SSTT-EEEEEE.....--TTS.................--B--TTSSEEE-SSHHHHHHHHHHH-SSE CS
                      tRNA-synt_1e 154 aegevseekkdkkDfaLWka.....skege.................pswdsPwgkGRPGWhieCsvmaskllgsei 208
                                        e +  +ek+++ DfaLWka                            +w+sPwg+GRPGWhieCs+m+++ lg++i
  gi|313126857|ref|YP_004037127.1| 169 GEADERAEKRHPADFALWKAgavspD---AvaehrpeeldpiedacgETWESPWGEGRPGWHIECSAMSMTHLGDTI 242
                                       *99999*************8333220...12223444577777777779**************************** PP

                                       EEEEEEGGGTTTHHHHHHHHHHHHSSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-T CS
                      tRNA-synt_1e 209 dihsGGiDLafPhhenelaqseaafdkqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahy 285
                                       dih+GG DL+fPhhene+aqseaa+++++++y+lh g l++e++kms sL+nf+t+ d+l +f   ++R + ls+ y
  gi|313126857|ref|YP_004037127.1| 243 DIHVGGRDLVFPHHENEVAQSEAATGQTFARYWLHVGLLQMEDDKMSSSLGNFFTVSDALDEFGVDVIRTFYLSTGY 319
                                       ***************************************************************************** PP

                                       TS-EEE-HHHHHHHH CS
                      tRNA-synt_1e 286 rsqldfkeelleeak 300
                                         +  f++++++ea+
  gi|313126857|ref|YP_004037127.1| 320 GAEQTFSDSAMAEAE 334
                                       ***********9985 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   1.0   2.9e-16   5.3e-13       2      58 ..     376     436 ..     375     440 .. 0.90
   2 ?   -2.1   0.0       3.2   5.7e+03      35      56 ..     462     483 ..     453     488 .. 0.55

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.9e-16
                                       HHHHHTBT--HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH....HGGGT-S-S- CS
                            DALR_2   2 FeeaMdDDFNTaeAiavlFelakeiNralkeedkaaasalkallrel....aevLGllqee 58 
                                       F++aM+DDFN  eA+a+l ela+++N++ +++d+++ + l+++++++    ++v+Gl   +
  gi|313126857|ref|YP_004037127.1| 376 FQKAMNDDFNVREAMAALIELARAVNTHVNDADEYDYRGLREAIETFedlgGDVFGLSFGD 436
                                       9***************************************9888888888*******5544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHHHHHGGGT-S- CS
                            DALR_2  35 kaaasalkallrelaevLGllq 56 
                                       +a + + ++ lr+  + LG+  
  gi|313126857|ref|YP_004037127.1| 462 EAGNYERADELRDELDALGVEV 483
                                       3333333477788888888844 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   5.8e-07     0.001      10     125 ..      33     149 ..      26     166 .. 0.82
   2 !   20.8   0.0   7.6e-08   0.00014     287     358 ..     246     318 ..     238     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.8e-07
                                       -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHH..HHHHHTTS-HHHHHHHHHHHHHHHHHHTT-- CS
                      tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpie..lkAekegvtpeelvekvheeikelfkklnis 84 
                                       ++++ HlGh++  + aD+++R+   +g+ v++v        +i+  +  ++ g +  ++++++++++ ++++ ln++
  gi|313126857|ref|YP_004037127.1|  33 VSDDAHLGHARLWMHADVMHRWLEHEGYTVHHVENFTDVNEKIAarIGDDELGQSEPDVARHFTDHVIRDMRGLNLK 109
                                       56789****************************8755555555511556788899999******************8 PP

                                       -SE.EEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETT CS
                      tRNA-synt_1g  85 fdk.ygrttseehkelvqeifkklkekgliyekeieqlycpk 125
                                         + y r +  eh     +++++l+e+g+ ye++ +++++++
  gi|313126857|ref|YP_004037127.1| 110 RAEvYPRVS--EHVPQIIDLIETLTENGYAYESNGSVYFDVT 149
                                       755166655..4566667999************999999876 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 7.6e-08
                                       EEEGGGH.HHHHTHHHHHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS CS
                      tRNA-synt_1g 287 figkdii.kFHtifwPaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaea 358
                                       + g+d + ++H         +++ ++ +     + l++e++K+S+S g++ ++++al+++ +d++R ++++++
  gi|313126857|ref|YP_004037127.1| 246 VGGRDLVfPHHENEVAQSEAATGQTFARYWLHVGLLQMEDDKMSSSLGNFFTVSDALDEFGVDVIRTFYLSTG 318
                                       55666542566666666667788888888888999*******************************5555433 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0   0.00097       1.7      18      70 ..      18      70 ..       4      81 .. 0.81
   2 !   19.2   0.0   2.6e-07   0.00046     278     341 ..     284     346 ..     155     374 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00097
                      tRNA-synt_1f 18 kkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70
                                       +++ d  +   G+++S   H+G +r  + ad++ r l++ g +v+++    d
  gi|313126857|ref|YP_004037127.1| 18 PQDDDDVLLYVCGLTVSDDAHLGHARLWMHADVMHRWLEHEGYTVHHVENFTD 70
                                      333566777889******************************99999876655 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.6e-07
                      tRNA-synt_1f 278 ggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyfa 341
                                       +++kmssS Gn++t++d+l+    +v+r ++l++    + +++ +  + ++ + +d+ler+y +
  gi|313126857|ref|YP_004037127.1| 284 EDDKMSSSLGNFFTVSDALDEFGVDVIRTFYLSTGYGAEQTFSDS-AMAEAEERWDRLERAYET 346
                                       345******************************888888888877.****************72 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2      0.27   4.8e+02      37      66 ..      36      65 ..      26      79 .. 0.89
   2 !   14.9   0.0   3.4e-06    0.0061     519     601 ..     244     325 ..     198     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.27
                       tRNA-synt_1 37 slHiGhalaktlkdivirykrmkGkevlyv 66
                                        H+Gha   +  d++ r+ + +G++v++v
  gi|313126857|ref|YP_004037127.1| 36 DAHLGHARLWMHADVMHRWLEHEGYTVHHV 65
                                      57***********************99865 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.4e-06
                       tRNA-synt_1 519 mlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdv 595
                                       + + G D ++   ++ + +s a tg++  +  l  gl+   e  KmS slgN    +d +++ g+d++R + +++ +
  gi|313126857|ref|YP_004037127.1| 244 IHVGGRDLVFPHHENEVAQSEAATGQTFARYWLHVGLLQM-EDDKMSSSLGNFFTVSDALDEFGVDVIRTFYLSTGY 319
                                       5566667777777777777777777765555555666554.5579************************99999999 PP

                       tRNA-synt_1 596 grdinl 601
                                       g++  +
  gi|313126857|ref|YP_004037127.1| 320 GAEQTF 325
                                       988765 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   5.8e-05       0.1      17      33 ..     463     479 ..     462     481 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.8e-05
                               UVR  17 nedFEkAAklRDqinal 33 
                                       + ++E+A +lRD++ al
  gi|313126857|ref|YP_004037127.1| 463 AGNYERADELRDELDAL 479
                                       569**********9887 PP

>> Dak1_2  Dihydroxyacetone kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00099       1.8      58      81 ..     150     173 ..     148     204 .. 0.71
   2 ?    3.3   0.0      0.02        35     165     233 ..     301     384 ..     286     392 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00099
                            Dak1_2  58 aalkyGelskikienMreqheell 81 
                                       a+  yG+ls++kie+M+ q e+  
  gi|313126857|ref|YP_004037127.1| 150 AFEDYGKLSNQKIEEMEAQGEADE 173
                                       5678***************97554 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.02
                            Dak1_2 165 laedk.nvvviptktivqGlaallvfdper..sleenveamaeaaka.............vktgevtyAvrdtkidg 225
                                       ++ d+  v vi t  ++ G++a   f  ++  ++ee ++++++a ++             v+ ++++ A+++t++d 
  gi|313126857|ref|YP_004037127.1| 301 AL-DEfGVDVIRTFYLSTGYGAEQTFSDSAmaEAEERWDRLERAYETaieacdspdayasVEDADLREAIETTQTDF 376
                                       44.442599*************99998887679999**********9999999999999999999999999999998 PP

                            Dak1_2 226 geikkgdl 233
                                        + +++d+
  gi|313126857|ref|YP_004037127.1| 377 QKAMNDDF 384
                                       88888876 PP

>> FTO_CTD  FTO C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.9e-05      0.12      42     107 ..     298     370 ..     280     406 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.9e-05
                           FTO_CTD  42 leeihnEvEfeWlRqfwlqGsrhaklhdyWkrkieeLeeawkkmElltrlvLdalrkasetlete........e 107
                                       + +++ E  ++ +R f+l  + + + +++   +++e ee w+++E  ++++++a  + +  ++ e        e
  gi|313126857|ref|YP_004037127.1| 298 VSDALDEFGVDVIRTFYLS-TGYGAEQTFSDSAMAEAEERWDRLERAYETAIEACDSPDAYASVEdadlreaiE 370
                                       567788889999*****97.6799999************************99977665555444334444443 PP

>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00012      0.21      50      97 ..      93     140 ..      70     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE CS
                      tRNA-synt_1c  50 eeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvc 97 
                                         +++++++d+  l++k  e   + s++  ++ +++e L ++G+AY  
  gi|313126857|ref|YP_004037127.1|  93 RHFTDHVIRDMRGLNLKRAEVYPRVSEHVPQIIDLIETLTENGYAYES 140
                                       357899************887889**********************86 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.8     5e+03      31      55 ..      49      73 ..      40     103 .. 0.62
   2 ?    4.4   0.5     0.012        22      75     177 ..     298     391 ..     264     409 .. 0.62
   3 ?    7.7   0.6    0.0012       2.2      66     120 ..     409     463 ..     360     481 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                                      HHHHHHHHHTTSEEEEEEECCCHST CS
                      AP_endonuc_2 31 relrkaldelglriaslslftrfgy 55
                                      + ++++l+  g++++ ++ ft+ + 
  gi|313126857|ref|YP_004037127.1| 49 DVMHRWLEHEGYTVHHVENFTDVNE 73
                                      4555666666666665555555444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.012
                                       HHHHHHHHTBSEEEEEBCCGBCTTTSGHH.HHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHH CS
                      AP_endonuc_2  75 aielaaaLGapllvlhpGtagagpkgsee.eawerlaeslneladyaekegvklalEtlagsgvelgdeelarllda 150
                                         ++  ++G++++ ++  + g+g++++   +a + + e++++l +  e      a+E +++++++    e a+l +a
  gi|313126857|ref|YP_004037127.1| 298 VSDALDEFGVDVIRTFYLSTGYGAEQTFSdSAMAEAEERWDRLERAYE-----TAIEACDSPDAYAS-VEDADLREA 368
                                       567788999999999988655555555447888888888888888854.....78888887777666.333444444 PP

                                       HTTTTEEEEEEHHHHHHHTTTHHHHHH CS
                      AP_endonuc_2 151 vdspnvgvclDtgHlliaeedvddalr 177
                                       ++      + D+  ++   ++v++a++
  gi|313126857|ref|YP_004037127.1| 369 IET----TQTDFQKAMNDDFNVREAMA 391
                                       442....23444444444444444444 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  66 eesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladya 120
                                       e   + l++aie+ ++LG+++  l +G+a +g++ +++e++  l  +++e+ ++a
  gi|313126857|ref|YP_004037127.1| 409 EYDYRGLREAIETFEDLGGDVFGLSFGDAADGGDVEIAEDLVSLLLNVREAEREA 463
                                       555899*********************8777777777787777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2908.73
//
Query:       gi|313126858|ref|YP_004037128.1|  [L=95]
Description: hypothetical protein Hbor_21190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-32  109.7   0.1    6.5e-32  109.4   0.1    1.1  1  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.1   3.6e-36   6.5e-32       1      73 []      11      83 ..      11      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 3.6e-36
                                      HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                            DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                      rY r+le+al+ ++ia+++e+plg+aa ++ ema sYleD+ +f+e++d+vnAlasfsY++GwLDag+r+gl+
  gi|313126858|ref|YP_004037128.1| 11 RYGRMLEDALAAATIAVPPETPLGDAAVDIEEMAISYLEDGHHFRENDDPVNALASFSYGYGWLDAGVRMGLF 83
                                      8**********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 606.07
//
Query:       gi|313126859|ref|YP_004037129.1|  [L=150]
Description: hypothetical protein Hbor_21200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.044   12.9   7.6      0.061   12.4   7.6    1.2  1  Acyl_transf_3  Acyltransferase family
        4.2    7.7  14.1         38    4.5  14.1    2.1  1  TctB           Tripartite tricarboxylate transporter TctB fam


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   7.6   6.8e-06     0.061     162     244 ..      26     133 ..       9     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxxxxxx RF
                     Acyl_transf_3 162 lllllilllllslvfirhelfgpatsvgllplpsvla.........................llfflfGalladadd 213
                                       + +l i ++ll+lvf+ +e++ + t vg++++ps l+                         +++++f +l + +  
  gi|313126859|ref|YP_004037129.1|  26 ARSLAISVGLLPLVFLAYEYYSQQTLVGAAFFPSPLGalvvfaaaiaayrnrggvaiisfgvFPPLGFALLSHLHVL 102
                                       5678999*****************************87777777777777777777777777777777777777777 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 214 rdrnlsrglkislllsllllalillalfgqt 244
                                       ++    r +++++  +l++ +++  + ++++
  gi|313126859|ref|YP_004037129.1| 103 HRPLTERLTLAATSSALIVGFVFACFGWAFG 133
                                       7777777666666666666666555554444 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  14.1    0.0043        38       4     131 ..      34     133 ..      25     135 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0043
                              TctB   4 gllllllagvafavgaldtgarvgpgffPlllgvllallgllllvaadgekeekearedwrkllklvlallaallly 80 
                                       gll l++    +a++ ++ ++ vg++ffP  lg+l+++++++ +              ++r+ +        a++ +
  gi|313126859|ref|YP_004037129.1|  34 GLLPLVF----LAYEYYSQQTLVGAAFFPSPLGALVVFAAAIAAY-------------RNRGGV--------AIISF 85 
                                       2222333....3355555447899*****9999999988666555.............122222........23333 PP

                              TctB  81 allleplGfilatalflllllg...reerkwlkalilavvlallvyllFtklLg 131
                                       + +++plGf l + l +           +++ +a+  +++++ +v+  F +++g
  gi|313126859|ref|YP_004037129.1|  86 G-VFPPLGFALLSHLHV----LhrpL-TERLTLAATSSALIVGFVFACFGWAFG 133
                                       3.58999**99999888....32332.456788888888888889999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 991.18
//
Query:       gi|313126860|ref|YP_004037130.1|  [L=354]
Description: thioredoxin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-43  148.1   0.6    3.6e-43  147.9   0.6    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    9.3e-18   64.5   0.1    1.6e-16   60.4   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-17   64.1   0.5    6.8e-16   58.6   0.1    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    6.5e-05   22.7   2.0       0.35   10.4   0.0    3.1  3  DAO             FAD dependent oxidoreductase
    0.00011   21.0   0.2        1.3    7.7   0.0    3.8  4  HI0933_like     HI0933-like protein
    0.00032   20.9   0.0     0.0018   18.4   0.0    2.3  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0023   17.1   7.4       0.22   10.6   0.0    3.4  4  FAD_binding_2   FAD binding domain
     0.0054   17.2   0.0      0.019   15.4   0.0    1.9  3  NAD_binding_7   Putative NAD(P)-binding
     0.0077   14.7   0.0       0.13   10.6   0.0    2.0  2  FMO-like        Flavin-binding monooxygenase-like
  ------ inclusion threshold ------
      0.022   14.1   0.0        3.9    6.7   0.0    2.4  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.042   12.9   0.5         36    3.3   0.0    3.6  4  GIDA            Glucose inhibited division protein A
      0.092   11.6   0.8        4.2    6.1   0.0    3.0  3  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.9   0.6   2.4e-46   3.6e-43       2     294 .]      13     322 ..      12     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 2.4e-46
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgiel 69 
                                       ++++ G+G+ Gl+aa+++++++ + +++  eg  ++g+  l+++++++++++e +s         e+ ++++++i+ 
  gi|313126860|ref|YP_004037130.1|  13 KLIIAGSGISGLSAAIYAGRSNNEPLVF--EGDEPGGQLTLTTEVENYPGFPEGISgpeliqnmkEQAERFGAEIDH 87 
                                       68999***********************..8889***********************97776666555555555553 PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkriv 146
                                            v ++  +++ ++++    +++  +++d+++ A+G+s+r+lgipG+ e  g++++t++++++      +  i+
  gi|313126860|ref|YP_004037130.1|  88 GI---VESVSADERPFTVTM---KNGDVYTADAIIAASGASARTLGIPGEDELMGYGLSTCATCDGAFFRGEK--IL 156
                                       33...455666777788854...45669***************************************988876..** PP

                                       EES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE....EEE.E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx.x RF
                       Pyr_redox_2 147 vvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge....kle.v 218
                                       v+GgG  ++E A++l+k++++v++ ++r+++    ++ + ++++e++e++ +e++ +t+v+e+ g +e    +++ v
  gi|313126860|ref|YP_004037130.1| 157 VIGGGDAAMEEASFLTKFASKVYIAHRREEFR--AEDYWVDRVMEKVEDDEIELMRNTEVTELHGTPEdgvdHVTmV 231
                                       *******************************8..889999****************************988744444 PP

                                       EETTSCE.............EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.....BESSTTEEE-GGG CS
                                       xxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxx RF
                       Pyr_redox_2 219 vledgee.............idadlvvvavGvrpstelleeklglelderggivvdefl.....rtnvpgiyaiGDv 277
                                        + +g+              +d+  v++a+G +p+ + l e  g+e d++g+++ +        +t vpgi+a+GDv
  gi|313126860|ref|YP_004037130.1| 232 RHPEGHPtdklddpeteefdFDVGAVFYAIGHTPNADYL-EGTGVERDDDGYVKAKGGTgggqtATDVPGIFAAGDV 307
                                       44444436677777778999*******************.*************99987778855678********** PP

                                       CTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 278 aggkggpelaqaAvqqG 294
                                       +  ++ +++a +A   G
  gi|313126860|ref|YP_004037130.1| 308 V--DYHYQQAATAGGDG 322
                                       *..9********98876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.079   1.2e+02       1      33 [.      15      46 ..      15      59 .. 0.87
   2 !   60.4   0.0   1.1e-19   1.6e-16      78     305 .]      65     305 ..      52     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.079
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      iI G G  Gl+aai + +++  + l+ E ++ g
  gi|313126860|ref|YP_004037130.1| 15 IIAGSGISGLSAAIYAGRSNN-EPLVFEGDEPG 46
                                      899**************9998.57899987655 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 1.1e-19
                       Pyr_redox_3  78 lsrkealeYlrevaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeek...lv 150
                                       +s+ e+ + ++e a++f  +i     Vesv+ +++ f+v+ +++ +y+A+ +i A G     ++l+ipGe++   + 
  gi|313126860|ref|YP_004037130.1|  65 ISGPELIQNMKEQAERFGAEIDH-GIVESVSADERPFTVTMKNGdVYTADAIIAASGA--SARTLGIPGEDElmgYG 138
                                       56667777777777777777765.469**************99879***********9..99*********643334 PP

                       Pyr_redox_3 151 khyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeeki 227
                                         +    + + ++g+k++ViGg++ a++ A  l +  ++V +++r++e ++e++ ++  ++ +  +++e + ++e  
  gi|313126860|ref|YP_004037130.1| 139 LSTCATCDGAFFRGEKILVIGGGDAAMEEASFLTKFASKVYIAHRREEFRAEDYWVDRVMEKVEDDEIELMRNTEVT 215
                                       4444555667799************************************9998666666666666666555444444 PP

                       Pyr_redox_3 228 kvlfn.....aevkeikekeeey..kvktedgkkvev.kddvvlatGykpdlsflkkslfeldedgrpvlteet... 293
                                       +++ +      +v+ ++++e +   k+  +++++++     v++a+G +p+++ l+  ++e+d+dg+++ +  t   
  gi|313126860|ref|YP_004037130.1| 216 ELHGTpedgvDHVTMVRHPEGHPtdKLDDPETEEFDFdVGAVFYAIGHTPNADYLEGTGVERDDDGYVKAKGGTggg 292
                                       444331111145666666655541133344444444433457788**********************9998754222 PP

                       Pyr_redox_3 294 .eetnvpglflaG 305
                                          t vpg+f aG
  gi|313126860|ref|YP_004037130.1| 293 qTATDVPGIFAAG 305
                                       27899*****998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.094   1.4e+02       1      24 [.      13      36 ..      13      48 .. 0.81
   2 !   58.6   0.1   4.6e-19   6.8e-16       1      78 [.     154     230 ..     154     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.094
                                      EEEEECSSHHHHHHHHHHHHTTSE CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkk 24
                                      k+++ G+G +gl +A ++ + +++
  gi|313126860|ref|YP_004037130.1| 13 KLIIAGSGISGLSAAIYAGRSNNE 36
                                      689************998766665 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 4.6e-19
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesv 76 
                                       k++v+GgG+ ++E+A++l+++++kV++ +r+++++   ++   ++++ek+e+  ie++ nt+v+e++g+++  v +v
  gi|313126860|ref|YP_004037130.1| 154 KILVIGGGDAAMEEASFLTKFASKVYIAHRREEFR--AEDYWVDRVMEKVEDDEIELMRNTEVTELHGTPEDgVDHV 228
                                       79*********************************..999999999*********************9999889999 PP

                                       EE CS
                         Pyr_redox  77 kl 78 
                                       ++
  gi|313126860|ref|YP_004037130.1| 229 TM 230
                                       86 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00036      0.54       2      35 ..      14      47 ..      13      55 .. 0.85
   2 !   10.4   0.0   0.00024      0.35     146     206 ..      68     126 ..      60     144 .. 0.80
   3 ?   -0.5   0.0      0.48   7.2e+02     152     184 ..     197     231 ..     192     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00036
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                      ++i G+Gi Gls+A ++ r +   +++e + ++g g
  gi|313126860|ref|YP_004037130.1| 14 LIIAGSGISGLSAAIYAGRSNnePLVFEGD-EPG-G 47
                                      6899*************7665799999999.888.5 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.H CS
                               DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.l 206
                                        +l++ + ++ae+ G+ei  g  v+++++ d++  +v  t + g + +ada++ a Ga ++ l
  gi|313126860|ref|YP_004037130.1|  68 PELIQNMKEQAERFGAEIDHG-IVESVSA-DERPFTV--TMKnGDVYTADAIIAASGASARtL 126
                                       679999**************9.9999966.5689999..5555988667**********9843 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.48
                                       HHHHHHHTT-EEEESECEEEE.EEEETCEEEEE.E CS
                               DAO 152 laraaealGveilegtevtgl.eeedgkvwgve.r 184
                                       +++++e+  +e+ ++tevt+l   ++++v +v  +
  gi|313126860|ref|YP_004037130.1| 197 VMEKVEDDEIELMRNTEVTELhGTPEDGVDHVTmV 231
                                       66788889999999999999723355667777553 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0016       2.4       2      33 ..      13      44 ..      12      56 .. 0.87
   2 !    7.7   0.0   0.00085       1.3     102     171 ..      61     127 ..      51     133 .. 0.76
   3 ?    0.0   0.0      0.18   2.7e+02       2      30 ..     154     182 ..     153     188 .. 0.81
   4 ?    0.8   0.0      0.11   1.6e+02     373     388 ..     296     311 ..     293     326 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0016
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      ++i+ G G +Gl aAi a++ +++ l++e  +
  gi|313126860|ref|YP_004037130.1| 13 KLIIAGSGISGLSAAIYAGRSNNEPLVFEGDE 44
                                      689*************************9764 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00085
                                       EETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT CS
                       HI0933_like 102 FpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklG 171
                                       Fp+  +  ++++ +++++++ g ++     v+sv++ +++ f+v++k+++ ++ad+++ A  G+S+ +lG
  gi|313126860|ref|YP_004037130.1|  61 FPEGISGPELIQNMKEQAERFGAEIDHG-IVESVSA-DERPFTVTMKNGDVYTADAIIAA-SGASARTLG 127
                                       7777777888999999999999988754.5788866.5555*****77777777777666.667776666 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.18
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVllle 30 
                                       +++viGgG A +  A  + k  ++V +  
  gi|313126860|ref|YP_004037130.1| 154 KILVIGGGDAAMEEASFLTKFASKVYIAH 182
                                       789*******9999988888888887765 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.11
                                       TTSTTEEE-GGGBSEE CS
                       HI0933_like 373 kkvpgLffaGEvlDve 388
                                         vpg+f aG v+D +
  gi|313126860|ref|YP_004037130.1| 296 TDVPGIFAAGDVVDYH 311
                                       679***********76 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.2e-06    0.0018       1      36 [.      16      50 ..      16      81 .. 0.85
   2 ?   -1.3   0.0       1.8   2.7e+03       1      17 [.     157     173 ..     157     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      I G+G+sGl+aA ++ + + + l++e +d +GG+++
  gi|313126860|ref|YP_004037130.1| 16 IAGSGISGLSAAIYAGRSNNEPLVFE-GDEPGGQLT 50
                                      67***********************7.689***987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                                       EE--SHHHHHHHHHHHC CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLak 17 
                                       ++G+G +++  A++L+k
  gi|313126860|ref|YP_004037130.1| 157 VIGGGDAAMEEASFLTK 173
                                       89***999988888887 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00014      0.22       2      37 ..      14      48 ..      13      53 .. 0.84
   2 ?    0.9   0.0      0.12   1.9e+02       2      35 ..     155     188 ..     154     193 .. 0.86
   3 ?   -0.4   0.0       0.3   4.6e+02     142     170 ..     192     220 ..     177     262 .. 0.75
   4 !    5.8   2.4    0.0041       6.2     358     416 ..     256     322 ..     221     323 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                      +i+ GsG++GL+AA+ a + + + +v e  ++ gg+
  gi|313126860|ref|YP_004037130.1| 14 LIIAGSGISGLSAAIYAGRSNNEPLVFEGDEP-GGQ 48
                                      69*************99999888888888877.555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                       ++ViG+G A +  A  +++   kv +    +ef+
  gi|313126860|ref|YP_004037130.1| 155 ILVIGGGDAAMEEASFLTKFASKVYIAHRREEFR 188
                                       79**********9999999999999988888777 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHTCTEEEEESEEEEEEEEC CS
                     FAD_binding_2 142 allarlvesarkagvdfqerteadeLive 170
                                         + r++e++++ +++++ +te++eL  +
  gi|313126860|ref|YP_004037130.1| 192 YWVDRVMEKVEDDEIELMRNTEVTELHGT 220
                                       56789999999999***********9553 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0041
                                       .......EEEEEEEES-.EEEBETTSBE.......STTEEESSBTEEE-STCEESSSSTTS--TTHH CS
                     FAD_binding_2 358 gpfyavkvvpaqhytmg.Gvetdengrv.......ldadgqpipGLYAaGevaaggvhganrlgGns 416
                                       + fya+  +p + y  g Gve d++g v        +++ + +pG +AaG v   +++ a   gG +
  gi|313126860|ref|YP_004037130.1| 256 AVFYAIGHTPNADYLEGtGVERDDDGYVkakggtgGGQTATDVPGIFAAGDVVDYHYQQAATAGGDG 322
                                       55777777777766654489999999998888877788899************99999999998866 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.3   1.1e+04       8      79 ..      12      29 ..       6      45 .. 0.57
   2 ?   -3.1   0.0       7.2   1.1e+04      48      69 ..      93     119 ..      72     123 .. 0.61
   3 !   15.4   0.0   1.3e-05     0.019       5      45 ..     150     189 ..     149     269 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.3
                     NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelneria 79
                                      +k                                                      l+ia      l+++i+
  gi|313126860|ref|YP_004037130.1| 12 RK------------------------------------------------------LIIAGSGISGLSAAIY 29
                                      44......................................................4444444455555555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.2
                     NAD_binding_7  48 vklaeeel.....ekdlegadlviaat 69 
                                       v++ e+ +     ++d+  ad +iaa 
  gi|313126860|ref|YP_004037130.1|  93 VSADERPFtvtmkNGDVYTADAIIAAS 119
                                       444455554444446677777888775 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.3e-05
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele 45 
                                       ++g+k+lv+GgG+ A++ ++ l ++  kv +   + +e+  
  gi|313126860|ref|YP_004037130.1| 150 FRGEKILVIGGGDAAMEEASFLTKFASKVYIAHRR-EEFRA 189
                                       6899*********************9999986665.23322 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.036        54       2      40 ..      12      49 ..      11      58 .. 0.77
   2 !   10.6   0.0   8.8e-05      0.13     160     216 ..     129     185 ..     101     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.036
                          FMO-like  2 kkvaviGaGvsGlasikccleegleptcfersddiGGlw 40
                                      +k+ + G+G+sGl++       + ep  fe  +  GG  
  gi|313126860|ref|YP_004037130.1| 12 RKLIIAGSGISGLSAAIYAGRSNNEPLVFEGDE-PGGQL 49
                                      688999********9988899999*****9654.45544 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.8e-05
                          FMO-like 160 pGiekfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrsG 216
                                       pG +++ G  + +    + + f+g ++lviG G+++ + a+ l++ a +v+++ r+ 
  gi|313126860|ref|YP_004037130.1| 129 PGEDELMGYGLSTCATCDGAFFRGEKILVIGGGDAAMEEASFLTKFASKVYIAHRRE 185
                                       666666666666666667789*******************************99875 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0099        15      26      49 ..       9      32 ..       7      44 .. 0.85
   2 ?    6.7   0.0    0.0026       3.9      29      64 ..     153     188 ..     139     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0099
                                      B---EEEEESTSHHHHHHHHHHHH CS
                       AlaDh_PNT_C 26 vepakvlviGgGvaGlqAiatakg 49
                                      ve+ k ++ G G+ Gl+A+  a +
  gi|313126860|ref|YP_004037130.1|  9 VEHRKLIIAGSGISGLSAAIYAGR 32
                                      567899*************99866 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0026
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparl 64 
                                        k+lviGgG a ++ ++  +++  kV++   r++ +
  gi|313126860|ref|YP_004037130.1| 153 EKILVIGGGDAAMEEASFLTKFASKVYIAHRREEFR 188
                                       589*************************99988754 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.024        36       2      24 ..      14      36 ..      13      56 .. 0.86
   2 ?    2.3   0.0     0.047        70     113     150 ..      85     121 ..      70     139 .. 0.80
   3 ?    2.2   0.0     0.052        77       1      28 [.     154     181 ..     154     198 .. 0.86
   4 ?   -0.4   0.1      0.31   4.6e+02     354     390 ..     297     335 ..     294     337 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.024
                                      EEEE-SSHHHHHHHHHHHHTT-- CS
                              GIDA  2 viViGgGhAGceAAlaaarlGak 24
                                      +i+ G G +G+ AA+ a r++ +
  gi|313126860|ref|YP_004037130.1| 14 LIIAGSGISGLSAAIYAGRSNNE 36
                                      6899*************998865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.047
                                       EEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 113 iieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       i ++ ve+++  +++   v++++g +++a+a++ a+G+
  gi|313126860|ref|YP_004037130.1|  85 IDHGIVESVSA-DERPFTVTMKNGDVYTADAIIAASGA 121
                                       55667777754.778889*******************9 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.052
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi 28 
                                       ++ ViGgG A +e A  + +   kv + 
  gi|313126860|ref|YP_004037130.1| 154 KILVIGGGDAAMEEASFLTKFASKVYIA 181
                                       589**********999999999998765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.31
                                       SSBTEEE-CGGGTB-SHHHHHH...HHHHHHHHHHHHHCT CS
                              GIDA 354 kvkgLflAGqinGteGYeEaaa...qGllAGinaarkakg 390
                                       +v+g+f+AG++     Y  aa     G+ A++ a  ++++
  gi|313126860|ref|YP_004037130.1| 297 DVPGIFAAGDVVDYH-YQQAATaggDGVKAALDADDYLEN 335
                                       689********9999.555554255677777777766665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.12   1.8e+02       1      22 [.      13      34 ..      13      39 .. 0.85
   2 ?    6.1   0.0    0.0028       4.2     158     212 ..      72     124 ..      68     128 .. 0.88
   3 ?    1.0   0.0     0.097   1.4e+02       1      22 [.     154     175 ..     154     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                                      EEEEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                      k++i+G G++G  aA++ ++  
  gi|313126860|ref|YP_004037130.1| 13 KLIIAGSGISGLSAAIYAGRSN 34
                                      679************9988765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-I CS
                    Trp_halogenase 158 kfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgl 212
                                       + +++ ae+ G ++ +g v++v  de+ +   +++++g ++ ad +i +sG  ++
  gi|313126860|ref|YP_004037130.1|  72 QNMKEQAERFGAEIDHGIVESVSADERPF--TVTMKNGDVYTADAIIAASGASAR 124
                                       568999***************99998877..799999**************8765 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.097
                                       EEEEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakal 22 
                                       ki+++GGG a+   A+ l k  
  gi|313126860|ref|YP_004037130.1| 154 KILVIGGGDAAMEEASFLTKFA 175
                                       79*************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2359.37
//
Query:       gi|313126861|ref|YP_004037131.1|  [L=94]
Description: hypothetical protein Hbor_21220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 612.71
//
Query:       gi|313126862|ref|YP_004037132.1|  [L=280]
Description: divalent heavy-metal cations transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-16   58.6  17.7    6.3e-15   55.2   5.4    3.0  2  Zip       ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   4.6    0.0008        14     246     326 ..      10      94 ..       5     101 .. 0.59
   2 !   55.2   5.4   3.5e-19   6.3e-15     179     330 ..     114     275 ..     100     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0008
                               Zip 246 vllnllfaltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnek..........gsssl 312
                                       +++ +++al++ lG++  ++      +  ++  +  l ++++G++l  +++ l+  E l e           ++   
  gi|313126862|ref|YP_004037132.1|  10 FVAGFITALATGLGAIPFFF-----VQDISDRWNVALWGIASGIMLSASVFGLVL-EALGEYisvslagisvSPIPT 80 
                                       36667777777777776666.....667777777777777777777777777777.777776666655444333333 PP

                               Zip 313 kqsllqllglllGf 326
                                       +++ll  +gl++G+
  gi|313126862|ref|YP_004037132.1|  81 RTFLLLGAGLIAGI 94 
                                       33333333333333 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 3.5e-19
                               Zip 179 laslkvraiilllgl.ilHsfidGLAlG...vssssstg............islfiAvllHelpeelglgaiLlkag 239
                                       +++   r ++l+lg+  +Hsf++G+A+G   +  + + g            ++++iA+++H++pe++++ ++L ++g
  gi|313126862|ref|YP_004037132.1| 114 YEEADFRKLLLILGIlTIHSFPEGVAIGvafADLGLEGGlqlfgvvvpllaVFMTIAISIHNIPEGVAISIPLRSMG 190
                                       5666788999****7369**********9973334444411111111111145679********************* PP

                               Zip 240 lsrkkavllnllfaltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsl 316
                                        +++  v ++++++l  p+G++i++        + a    ++ ++++aG ++   l+e++p E l+  ++   +   
  gi|313126862|ref|YP_004037132.1| 191 VPNWRLVWWSVFSSLPQPIGAVIAFY-----FVRLAREFLPVGFGFAAGAMIFLVLTEFIP-EALERGAELPRGGRR 261
                                       **************************.....8999**************************.*99999888999999 PP

                               Zip 317 lqllglllGfalml 330
                                          +g+ +G++ m+
  gi|313126862|ref|YP_004037132.1| 262 ELCAGIACGVLAMV 275
                                       99999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1684.00
//
Query:       gi|313126863|ref|YP_004037133.1|  [L=105]
Description: nucleotide pyrophosphohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.5e-05   23.9   0.1      5e-05   23.4   0.1    1.2  1  MazG       MazG nucleotide pyrophosphohydrolase domain
    0.00051   20.2   0.1    0.00064   19.9   0.1    1.3  1  MazG-like  MazG-like family
     0.0061   17.0   0.8     0.0073   16.7   0.8    1.2  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   8.3e-09     5e-05       8      69 ..      27      92 ..      22      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.3e-09
                                      HHHHHHHHHHHHHHHT........T-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH CS
                              MazG  8 aylleEvgEvaeaIkk........edrdeleeELGDvLlqvlflaniaeeeggidledvaetileKlerR 69
                                      + l+ EvgE+a   +k        ++ d  ++ELGD L+ +  la     e+++d   ++++ ++K+e R
  gi|313126863|ref|YP_004037133.1| 27 LDLAAEVGELAADAAKsseygaspDKLDVKRDELGDALFCLYALAD----ELDVDAAAALDESVAKYEAR 92
                                      56899*****9888887888877666666689**************....6*****************99 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.1e-07   0.00064      31      68 ..      53      91 ..      27     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                         MazG-like 31 eeeildeLAdviiylylLAdrlGidfee.ideklkkklk 68
                                       +   deL d++  ly LAd+l++d    +de ++k + 
  gi|313126863|ref|YP_004037133.1| 53 LDVKRDELGDALFCLYALADELDVDAAAaLDESVAKYEA 91
                                      55567****************************999876 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.8   1.2e-06    0.0073      30      78 ..      28      84 ..       1      88 [. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHHHHHHT-SC........HHHHHHHHHHHHHHHHHHHHHHCT--CHHHHHH CS
                            PRA-PH 30 ligEEavElleaaseg........dlaeladelaDllYvtygllvllGidldavfee 78
                                       ++ E+ El + a+++        +l    del D l+ +y+l+++l++d+ a ++e
  gi|313126863|ref|YP_004037133.1| 28 DLAAEVGELAADAAKSseygaspdKLDVKRDELGDALFCLYALADELDVDAAAALDE 84
                                      455567777764443345666664888888********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 710.20
//
Query:       gi|313126864|ref|YP_004037134.1|  [L=163]
Description: hypothetical protein Hbor_21250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-34  117.3   0.0    5.2e-34  117.0   0.0    1.1  1  tRNA_edit  Aminoacyl-tRNA editing domain


Domain annotation for each model (and alignments):
>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.0   2.9e-38   5.2e-34       2     123 .]      32     153 ..      31     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 2.9e-38
                         tRNA_edit   2 pgtktieelaaalgvdpsaiaKtlvlkdkkgelvlvllpgdreldlkklakllga..kklrlaseeelrellgvepG 76 
                                       +gtkt++++a+a+g+d ++ia++lv+++ +g lv+v+++g++++d+ +la ++g+    +++a++e +r+++g+++G
  gi|313126864|ref|YP_004037134.1|  32 EGTKTAADAASAIGCDVGQIASSLVFEV-DGSLVVVITSGANRVDESRLADHFGVstGTVSMADPETIRDAVGWSIG 107
                                       789************************8.666**********************5458******************* PP

                         tRNA_edit  77 gvgPlglkaagvpvllDeslkeyptvvvgagengatlelspedlrkl 123
                                       gv+P+++ +  +pvl+D+sl +y+tv+++ag+++a++ ++p++lr+l
  gi|313126864|ref|YP_004037134.1| 108 GVPPFCH-ETTLPVLFDNSLSQYDTVWAAAGTPEAVFPIDPAELRRL 153
                                       ******9.8***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1089.09
//
Query:       gi|313126865|ref|YP_004037135.1|  [L=100]
Description: hypothetical protein Hbor_21260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 613.75
//
Query:       gi|313126866|ref|YP_004037136.1|  [L=697]
Description: acyl-CoA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-76  254.2   0.3    1.5e-75  253.5   0.3    1.3  1  ATP-grasp_5    ATP-grasp domain
    6.8e-54  181.4   1.1    1.4e-53  180.4   0.3    2.0  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.6e-23   83.4   2.2    1.6e-22   80.2   0.2    3.2  3  CoA_binding_2  CoA binding domain
    7.2e-09   36.2   1.2    7.2e-09   36.2   1.2    2.5  3  CoA_binding    CoA binding domain
     0.0016   18.0   0.0     0.0047   16.5   0.0    1.8  1  ATP-grasp_2    ATP-grasp domain
  ------ inclusion threshold ------
       0.52   10.0   1.9        6.9    6.5   0.5    2.4  2  Yae1_N         Essential protein Yae1, N terminal


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.5   0.3     5e-79   1.5e-75       9     222 .]     479     692 ..     472     692 .. 0.97

  Alignments for each domain:
  == domain 1  score: 253.5 bits;  conditional E-value: 5e-79
                       ATP-grasp_5   9 lLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeil 85 
                                       +    ea++ll+aygi++++  +++ ++ea+e+ae i+  vv+KivspdilhK+d+gGv++++ + eev +a+e+++
  gi|313126866|ref|YP_004037136.1| 479 TRLGVEAMDLLDAYGIQTPDGDIVDAPAEALEVAEDIEGDVVMKIVSPDILHKSDIGGVKVGVPN-EEVYDAYEDLV 554
                                       44478**********************************************************98.89********* PP

                       ATP-grasp_5  86 ervkekspeariegvlVqemakr.ggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliert 161
                                       +r+++++p+a+i gv+Vqem++  +g+E ivg+++Dp+FGp+++fGlGG+ vevl+d++++++p+++++a+e+ e++
  gi|313126866|ref|YP_004037136.1| 555 TRARNYQPDANIIGVQVQEMVDLdSGVETIVGMNRDPQFGPLLMFGLGGIFVEVLEDTTFRVAPVSESEAHEMTEEI 631
                                       ********************9999***************************************************** PP

                       ATP-grasp_5 162 kaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarirl 222
                                        +++ll+g rg++++d+a + e+++rlsqLv+d+p I eldinPl+++++gv a+D+r+++
  gi|313126866|ref|YP_004037136.1| 632 DSAPLLRGARGRDPVDVAGVTETIQRLSQLVTDFPAILELDINPLVATPDGVQAVDVRLTV 692
                                       **********************************************************987 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   3.8e+03      81     102 ..      87     110 ..      78     121 .. 0.67
   2 !  180.4   0.3   4.8e-57   1.4e-53       1     138 []     150     287 ..     150     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                      Succ_CoA_lig  81 k..kpvvvlksGrseagaraaash 102
                                       +    vvv+ +G  e+g++ a+ +
  gi|313126866|ref|YP_004037136.1|  87 AgiRNVVVVTAGFGETGSEGASRE 110
                                       444679999999888888877554 PP

  == domain 2  score: 180.4 bits;  conditional E-value: 4.8e-57
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       pG+++++sqSGa+++a+ldwa+++g+gf+ vvslGn+a +d+ad+++++++d++t+vi+ ylE+i++gr+f+++ar+
  gi|313126866|ref|YP_004037136.1| 150 PGNMSFMSQSGAFITAVLDWANDQGIGFKDVVSLGNKAVLDEADFVDAWGDDEDTEVIIGYLEGISEGREFIDTARE 226
                                       79*************************************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       ++++ p+v++ksGr++aga+aa+shtg +agsd++++a + qaGv+r++s++elfdaa++l
  gi|313126866|ref|YP_004037136.1| 227 VTQDTPIVLVKSGRTDAGAQAASSHTGTIAGSDQAYEAGLDQAGVIRAESVQELFDAARVL 287
                                       **********************************************************986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.2   5.4e-26   1.6e-22       1     114 [.      11     133 ..      11     135 .. 0.96
   2 ?    0.9   0.0       0.2   6.1e+02      53     104 ..     368     427 ..     349     433 .. 0.78
   3 ?   -2.5   0.0       2.4   7.1e+03      40      78 ..     515     556 ..     510     570 .. 0.69

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 5.4e-26
                                       --EEEET--S-TTSHHHHHHHHHHH..HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle..hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkea 75 
                                       r+iaVvGa +++g+ g+ ++++l++   g +vvpVnpk++e++g++++a++ e  ++ dl+++++pp+++++ v+e 
  gi|313126866|ref|YP_004037136.1|  11 RRIAVVGATEREGSVGRAIMENLVAdfDG-DVVPVNPKYDEVFGVPAVADVGE--SDADLAVIVVPPHIAVDAVRES 84 
                                       78***********************9999.**********************6..69******************** PP

                                       HHH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  76 lalgakavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                       +++g++ v++  +          s+++e+ e+aee+++++vg+++++++
  gi|313126866|ref|YP_004037136.1|  85 GKAGIRNVVVVTAgfgetgsegaSREQELTEVAEEYDLNLVGPNSLGLM 133
                                       ******99999999*******************************9986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                                       ..T--EEEE-S-HHHHGGGHHHHHHH........--SEEEE-TT---HHHHHHHHHTT-E CS
                     CoA_binding_2  53 pepvdlvdvftppeatpeivkealal........gakavwlqpgsedeeaaelaeeagir 104
                                       +e+v +++v+t p+a++++ + a++         ++ a+ ++ g++ + aae++ +agi+
  gi|313126866|ref|YP_004037136.1| 368 DENVGCAVVLTAPTAVLDYEQLAADTvelqekydKPVAACFMGGERVKPAAEALSDAGIP 427
                                       467788999999999998877665555666666669999999999999999999999885 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.4
                                       ETTEES----T.......T--EEEE-S-HHHHGGGHHHHHHH CS
                     CoA_binding_2  40 ilgekvyaslaed...pepvdlvdvftppeatpeivkealal 78 
                                       i+g  v + +++d   ++++  v v +p e++ + +++++++
  gi|313126866|ref|YP_004037136.1| 515 IEGDVVMKIVSPDilhKSDIGGVKVGVPNEEVYDAYEDLVTR 556
                                       555444444443345566777899999999999999988654 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   1.2   2.4e-12   7.2e-09       4      96 .]      11      98 ..       8      98 .. 0.92
   2 ?   -2.6   0.0         3     9e+03      56      88 ..     395     427 ..     391     428 .. 0.81
   3 ?   -3.8   0.0         6   1.8e+04      70      84 ..     541     555 ..     537     558 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.4e-12
                                      EEEEEETTTSHHHHHHHHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHH CS
                       CoA_binding  4 tkviviGagglgiaglyhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavde 81
                                       +++v+Ga+ +++ ++  + e+l   +   v++vnp+  ++ev g+p+    +++ e+ ++d avi+vP+  a +av e
  gi|313126866|ref|YP_004037136.1| 11 RRIAVVGATEREGSVGRAIMENLVADFDgDVVPVNPK--YDEVFGVPAV---ADVGES-DADLAVIVVPPHIAVDAVRE 83
                                      68*********9999988888899999999*******..********99...777777.799***************** PP

                                      HHHTT-SEEEEESST CS
                       CoA_binding 82 lveagikgiviiteg 96
                                        +agi+ +v++t+g
  gi|313126866|ref|YP_004037136.1| 84 SGKAGIRNVVVVTAG 98
                                      ************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                                       HHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-S CS
                       CoA_binding  56 eleektevdvavitvPaesaqeavdelveagik 88 
                                       el ek +  va  ++  e+++ a+++l +agi+
  gi|313126866|ref|YP_004037136.1| 395 ELQEKYDKPVAACFMGGERVKPAAEALSDAGIP 427
                                       566666777888889999999999999999996 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 6
                                       S-HHHHHHHHHHHHH CS
                       CoA_binding  70 vPaesaqeavdelve 84 
                                       vP+e++++a ++lv 
  gi|313126866|ref|YP_004037136.1| 541 VPNEEVYDAYEDLVT 555
                                       899999999998875 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-06    0.0047       6     201 ..     484     677 ..     482     678 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCT..TCEEEESSHHHHHHHHHCCTTSEE CS
                       ATP-grasp_2   6 qakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKa..gGvklvkskeeakeaakellgkel 80 
                                       +a+++l  yg+++p g +++ + ea e+a+++++++ v+K  v      K+  gGvk+   +ee+++a ++l+    
  gi|313126866|ref|YP_004037136.1| 484 EAMDLLDAYGIQTPDGDIVDAPAEALEVAEDIEGDV-VMKI-VSPDILHKSdiGGVKVGVPNEEVYDAYEDLVTRAR 558
                                       5899*****************************999.6664.44344444455**************9999987665 PP

                                       E-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HH CS
                       ATP-grasp_2  81 vtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkee 157
                                         +q ++   ++  v v+e++d++  +   + + r+ +   +++   GG+ +E v + +  +++ v+   a++++ee
  gi|313126866|ref|YP_004037136.1| 559 N-YQPDA---NIIGVQVQEMVDLDSGVETIVGMNRDPQFGPLLMFGLGGIFVE-VLEDTTFRVAPVSESEAHEMTEE 630
                                       5.66654...4566778888888877777777777777666666667888776.55566666666666666666555 PP

                                       HHHH..HHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEE.EEEEEEE CS
                       ATP-grasp_2 158 qare..iakklglekelvkkaakiikklyklfveldatl.vEiNPLv 201
                                             +  + g +   v  ++++i++l +l+++  a l ++iNPLv
  gi|313126866|ref|YP_004037136.1| 631 IDSAplLRGARGRDPVDVAGVTETIQRLSQLVTDFPAILeLDINPLV 677
                                       43321133334444455667777777777777777776546777776 PP

>> Yae1_N  Essential protein Yae1, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.5    0.0023       6.9       1      11 [.     209     219 ..     209     219 .. 0.96
   2 ?    2.4   0.0     0.044   1.3e+02       7      27 ..     247     267 ..     246     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0023
                            Yae1_N   1 GYreGiaeGke 11 
                                       GY+eGi+eG+e
  gi|313126866|ref|YP_004037136.1| 209 GYLEGISEGRE 219
                                       9********98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.044
                            Yae1_N   7 aeGkeqglqeGfdeGyqeGaq 27 
                                       a++ + g ++G d+ y+ G +
  gi|313126866|ref|YP_004037136.1| 247 AASSHTGTIAGSDQAYEAGLD 267
                                       67788999*********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 4465.95
//
Query:       gi|313126867|ref|YP_004037137.1|  [L=366]
Description: protein with phosphotransacetylase biod-like n-terminal domain, partial [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-35  122.3   0.0    2.9e-35  121.9   0.0    1.2  1  AAA_26         AAA domain
      1e-26   92.8   0.1    1.5e-25   89.0   0.0    2.4  2  DRTGG          DRTGG domain
    5.5e-06   26.4   0.0    9.9e-06   25.6   0.0    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.021   13.9   0.2        5.7    5.9   0.1    2.1  2  LpxK           Tetraacyldisaccharide-1-P 4'-kinase
      0.045   14.0   0.0       0.21   11.9   0.0    2.1  3  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi
       0.11   13.1   1.7       0.86   10.1   0.5    2.5  2  NBD_C          Nucleotide-binding C-terminal domain
       0.12   12.9   0.1          1    9.8   0.1    2.5  2  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.0   1.1e-38   2.9e-35       2     196 ..       3     210 ..       2     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 1.1e-38
                            AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie......ededselikellgldqtyelpeplalsap 72 
                                       t++vt+t ++ GKT+v+l+L +  +++g  vgy+KP +t ++       ded+ l++e+l+ld++++ +ep+++s  
  gi|313126867|ref|YP_004037137.1|   3 TLLVTSTHESTGKTAVTLALGKLAQERGLDVGYMKPKGTRLQsnvgktLDEDPMLAREILDLDAEMHQMEPVVYSPT 79 
                                       89****************************************888885588************************99 PP

                            AAA_26  73 lspelaarqegedidlekiv....kelekdadivvVEGagglgvpiteellnadiaknlgapvilVarggl.gtinq 144
                                       + + +   qe+ d  l +i+    ++l++++d++++EG g  +++ + +l+++d+a +lga+v+lV ++++ g i++
  gi|313126867|ref|YP_004037137.1|  80 FIDGAIRGQEDGDE-LGEIIgeyfEQLANQKDLMLIEGGGVWSTGGIVDLTDVDVADQLGADVLLVSTYEKpGDIDD 155
                                       99888888777555.777888888*********************************************9989**** PP

                            AAA_26 145 llltiealrqknvrvlGvilNkvrnp......envetlekksgipvlGvvPylpdlea 196
                                       +l+++e + +   r++Gv +N v+++      ++v  + +  g+pv+GvvP +++l  
  gi|313126867|ref|YP_004037137.1| 156 VLAAAEQFGD---RLAGVLFNSVTDAvfdeleQEVVPFLEGRGVPVVGVVPREQQLAG 210
                                       ******9988...8********99997776654999999999***********99975 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.12   3.2e+02      47      89 ..     150     199 ..     132     203 .. 0.67
   2 !   89.0   0.0   5.8e-29   1.5e-25       2     103 ..     216     319 ..     215     321 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                                       ETT-HHHHHHHTT-T..EEEEEEETT-.....---HHHHHHHHHHT--EE CS
                             DRTGG  47 pGDRediqlaaleag..iaalilTggl.....epseevlklaeeaglpvl 89 
                                       pGD +d++ aa + g  +a++++++       e+++ev+ ++e++g+pv+
  gi|313126867|ref|YP_004037137.1| 150 PGDIDDVLAAAEQFGdrLAGVLFNSVTdavfdELEQEVVPFLEGRGVPVV 199
                                       67777777777776677777777654322233567778888888888776 PP

  == domain 2  score: 89.0 bits;  conditional E-value: 5.8e-29
                                       HHHHTT-EEEE--..SS--E-EEEE-SS-HHHHHHHHHT..SEEEEEETT-HHHHHHHTT-T.EEEEEEETT----H CS
                             DRTGG   2 iaealgaevlnggeeelrrvekvvvgamsvenmlerlke..gdlvivpGDRediqlaaleag.iaalilTgglepse 75 
                                       +a++lga+v+++g+ e   ve+++vgams +++l+++++  +++vi++GDR++i++aalea  ++ +ilTgg++p++
  gi|313126867|ref|YP_004037137.1| 216 LADELGADVVTDGD-EDAYVERFLVGAMSGDAALRYFRRtkDAAVITGGDRSEIITAALEAPgVKTIILTGGHRPPA 291
                                       7899*********7.5557*******************999********************99************** PP

                                       HHHHHHHHHT--EEE-SS-HHHHHHHHH CS
                             DRTGG  76 evlklaeeaglpvlsveldtfttakrin 103
                                       +vl  aee+g+pv+ v+ dt++++ r +
  gi|313126867|ref|YP_004037137.1| 292 AVLGKAEEKGVPVMLVNGDTLSVVDRAE 319
                                       ***********************99876 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   3.9e-09   9.9e-06       2     119 ..       5     209 ..       4     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.9e-09
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +++st   +GKT ++++L+++ ++rgl+V   +  p ++ l +  g+  d++p                        
  gi|313126867|ref|YP_004037137.1|   5 LVTSTHESTGKTAVTLALGKLAQERGLDVGYMK--PKGTRLQSNVGKTLDEDPmlareildldaemhqmepvvyspt 79 
                                       799******************************..55555554466666666688999******************* PP

                                       ........................................................................CCHCC CS
                                       ........................................................................xxxxx RF
                              CbiA  55 ........................................................................dlkrl 59 
                                                                                                               d++ +
  gi|313126867|ref|YP_004037137.1|  80 fidgairgqedgdelgeiigeyfeqlanqkdlmliegggvwstggivdltdvdvadqlgadvllvstyekpgDIDDV 156
                                       ***************************************************************************** PP

                                       CHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  60 lellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeava 119
                                       l  +e++g +      +agv++n v     ++l++e +  l +  gvpv+gv+pr +++a
  gi|313126867|ref|YP_004037137.1| 157 LAAAEQFGDR------LAGVLFNSVTDAVFDELEQEVVPFL-EGRGVPVVGVVPREQQLA 209
                                       ********77......8********9885555444444444.344**********99886 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0022       5.7      47      69 ..      12      34 ..       8      37 .. 0.91
   2 ?    5.8   0.0    0.0024       6.1      94     134 ..     242     283 ..     229     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0022
                                      -HSHHHHHHHHHHHTTTS..-EE CS
                              LpxK 47 GtGKTPlvialvkllqarglkvg 69
                                       tGKT +++al kl q+rgl vg
  gi|313126867|ref|YP_004037137.1| 12 STGKTAVTLALGKLAQERGLDVG 34
                                      69******************998 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0024
                                       HH-HHHHHHHHHST.SEEEEESSHHHHHHHHHHHC--SEEEE CS
                              LpxK  94 evGDEplllarrtg.vpvvVgsdRvaaarallakaeldviil 134
                                         GD +l   rrt+ ++v+ g dR + ++a+l++ ++++iil
  gi|313126867|ref|YP_004037137.1| 242 MSGDAALRYFRRTKdAAVITGGDRSEIITAALEAPGVKTIIL 283
                                       68999****************************999****98 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.5   8.9e+03      33      49 ..      20      36 ..       2      39 .. 0.62
   2 ?   -2.8   0.0       3.2   8.3e+03      43      62 ..     169     188 ..     158     189 .. 0.77
   3 ?   11.9   0.0   8.1e-05      0.21       8      56 ..     269     314 ..     267     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.5
                     SpoU_sub_bind 33 eellklakkrgikvelv 49
                                        l kla++rg  v ++
  gi|313126867|ref|YP_004037137.1| 20 LALGKLAQERGLDVGYM 36
                                      45667788888877666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.2
                     SpoU_sub_bind  43 gikvelvdkekLdklsgtan 62 
                                       g+    v+++++d+l + ++
  gi|313126867|ref|YP_004037137.1| 169 GVLFNSVTDAVFDELEQEVV 188
                                       67777899999999877665 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 8.1e-05
                     SpoU_sub_bind   8 VleaLksgrriekllvtegradkrleellklakkrgikvelvdkekLdk 56 
                                       + +aL++ + ++++++t g + +    +l +a+++g++v lv+ + L  
  gi|313126867|ref|YP_004037137.1| 269 ITAALEA-PGVKTIILTGGHRPPA--AVLGKAEEKGVPVMLVNGDTLSV 314
                                       7899999.67*********88888..*****************999865 PP

>> NBD_C  Nucleotide-binding C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.14   3.7e+02      92     136 ..      91     144 ..      41     172 .. 0.63
   2 ?   10.1   0.5   0.00034      0.86      92     137 ..     236     281 ..     176     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHCT....ECE..EEEESHH...HHHHHHHHCT--EEEE CS
                             NBD_C  92 geriaaalaeiarrlverg....vrr..lviaGGd...tssavlkaLgvkglei 136
                                       g+++++ ++e  ++l++++    +++  +  +GG+   t  +v+++Lg++ l +
  gi|313126867|ref|YP_004037137.1|  91 GDELGEIIGEYFEQLANQKdlmlIEGggVWSTGGIvdlTDVDVADQLGADVLLV 144
                                       555555566666666533223344444255558885555678888888877666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHHHHHHHHCTECEEEEESHHHHHHHHHHCT--EEEEE CS
                             NBD_C  92 geriaaalaeiarrlvergvrrlviaGGdtssavlkaLgvkgleil 137
                                       + +++a  ++ a r ++r  +  vi+GGd s  ++ aL++ g++ +
  gi|313126867|ref|YP_004037137.1| 236 RFLVGAMSGDAALRYFRRTKDAAVITGGDRSEIITAALEAPGVKTI 281
                                       4466777777788888885556**********99999988877653 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0       0.1   2.7e+02      50     106 ..     134     199 ..     121     200 .. 0.76
   2 ?    9.8   0.1   0.00041         1      19     106 ..     187     305 ..     178     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.1
                                       T.....T--EEEE-S-HHHHGGGHHHHHHH-..-SEEEE-TT......---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  50 aed.pepvdlvdvftppeatpeivkealalg..akavwlqpg......sedeeaaelaeeagirvv 106
                                       a++   +v lv+ + +p ++ +++ +a++ g   ++v +++       + ++e++ ++e +g++vv
  gi|313126867|ref|YP_004037137.1| 134 ADQlGADVLLVSTYEKPGDIDDVLAAAEQFGdrLAGVLFNSVtdavfdELEQEVVPFLEGRGVPVV 199
                                       43235678899999*************999755777877777777777777777777777888777 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00041
                                       HHHHHHHHT--EEEESSS-SEETTEES----T......T--.............................EEEE-S- CS
                     CoA_binding_2  19 vlryllehglpvvpVnpkeeeilgekvyaslaed..pepvd.............................lvdvftp 64 
                                       v+ +l  +g+pvv V p+e+++ g++ ++ la++    +v                               + v+t 
  gi|313126867|ref|YP_004037137.1| 187 VVPFLEGRGVPVVGVVPREQQLAGVT-VEGLADElgADVVTdgdedayverflvgamsgdaalryfrrtkDAAVITG 262
                                       6778888*****************76.45555433322232688999999999999999999999999998888888 PP

                                       HHHHGGGHHHHHHH--SEEEE-TT---HH.HHHHHHHTT-EEE CS
                     CoA_binding_2  65 peatpeivkealalgakavwlqpgsedee.aaelaeeagirvv 106
                                        ++ + i  +++a g+k+++l  g + ++ ++ +aee+g++v+
  gi|313126867|ref|YP_004037137.1| 263 GDRSEIITAALEAPGVKTIILTGGHRPPAaVLGKAEEKGVPVM 305
                                       8888888888888899999999997766515678888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2439.38
//
Query:       gi|313126868|ref|YP_004037138.1|  [L=371]
Description: xaa-pro aminopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-66  223.6   0.5    2.6e-66  223.3   0.5    1.1  1  Peptidase_M24  Metallopeptidase family M24
    4.8e-29  101.7   0.0      1e-28  100.6   0.0    1.5  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.3   0.5   2.9e-70   2.6e-66       2     209 .]     151     356 ..     150     356 .. 0.95

  Alignments for each domain:
  == domain 1  score: 223.3 bits;  conditional E-value: 2.9e-70
                                       HHHHHHHHHHHHHHHHHHHHHT...TCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikp...gvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegd 75 
                                       ++r+a++ a++a++av + +     g+te elaa +e   l++ g++g +f+++v++g ++a++hy+++dr++++gd
  gi|313126868|ref|YP_004037138.1| 151 ALRRAGDTADEAMDAVRA-LGSdaiGMTESELAARVESL-LSEAGGNGTSFETVVGAGSHGAMPHYRHGDRTIQPGD 225
                                       68**************55.6644459***********87.99*********************************** PP

                                       EEEEEEEEEETTEEEEEEEEEECS.SGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSS CS
                     Peptidase_M24  76 lvlidagaeydgyasDitrTvlvG.kftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffph 151
                                       +v++d+g ++dgy sD trTv+++ +++++ re++++v+eaq+aa++a++pGvt++ id+aarev+e+ag+++ f h
  gi|313126868|ref|YP_004037138.1| 226 PVVLDFGTRVDGYPSDQTRTVVFDgEPSDRFREVHDVVREAQQAAVDAAEPGVTAESIDRAAREVIEAAGYGDRFVH 302
                                       *********************88669999************************************************ PP

                                       CSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                     Peptidase_M24 152 glGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                       ++GHgvGl+vh+e p++   ++++r+le+Gmvf++Epgiy  p+e+gvried+v+vte
  gi|313126868|ref|YP_004037138.1| 303 RTGHGVGLDVHEE-PYIV--EGNDRELEPGMVFSVEPGIY-LPDEFGVRIEDLVVVTE 356
                                       ************9.**98..577*****************.89999***********7 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   1.1e-32     1e-28       1     131 [.       9     142 ..       9     143 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 1.1e-32
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEEST CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveydd 76 
                                       R + ++a+++++ +dal++++++nl+Yl+Gf +e+g+r+l ++v+adg+ ++lv++l+++++++ + + ++v++++d
  gi|313126868|ref|YP_004037138.1|   9 RTRDAQAALDDAAADALVCFPSRNLSYLSGFSEEPGERHLFFFVPADGDpIFLVPELYEEQVRAAT-WIDDVRTWAD 84 
                                       667899************************************************************.********** PP

                                       ...HSSHHHHHHHHH.HHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHS CS
                      Creatinase_N  77 ...pvealadllkel.lesekrvgveldaltvafyealkealpdaelvdaselieelRv 131
                                          pv a a++++ l l++e  v ++++ +++af+++l+++l+da++  ase++  lR+
  gi|313126868|ref|YP_004037138.1|  85 dddPVTATAAAVEALdLPDEPHVLFDDT-MWAAFTQDLRAVLSDATFGLASEVVSPLRI 142
                                       9*999999999998845566*******9.9***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2216.94
//
Query:       gi|313126869|ref|YP_004037139.1|  [L=351]
Description: hypothetical protein Hbor_21300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 2045.62
//
Query:       gi|313126870|ref|YP_004037140.1|  [L=444]
Description: arabinose efflux permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.4e-59  199.7  59.4      8e-52  176.3  37.4    2.0  2  MFS_1       Major Facilitator Superfamily
    1.6e-10   40.4   5.4    1.6e-10   40.4   5.4    2.6  3  Sugar_tr    Sugar (and other) transporter
    6.5e-06   25.2   9.0    6.5e-06   25.2   9.0    2.7  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
      0.014   13.8   1.0      0.025   12.9   0.1    1.9  2  OATP        Organic Anion Transporter Polypeptide (OATP) fami
       0.15   10.4   5.3       0.12   10.8   2.0    2.0  2  TRI12       Fungal trichothecene efflux pump (TRI12)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.3  37.4   2.2e-55     8e-52       1     353 []      13     393 ..      13     393 .. 0.90
   2 !   37.3  14.0   4.2e-13   1.5e-09      51     173 ..     285     425 ..     285     443 .. 0.80

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 2.2e-55
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       +++++f+  l+++il+p++p ++a ++g+++ + +ll++ y++ +++a+++lGrlsd  Grr+vlll+l++++++ +
  gi|313126870|ref|YP_004037140.1|  13 VFVIVFVDLLGFGILIPVIP-LYALSFGATEFVGSLLIASYSAMQFLAAPFLGRLSDTRGRRPVLLLSLTGSVIA-W 87 
                                       68999***************.8999**************************************************.5 PP

                             MFS_1  78 lll.fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg... 149
                                        l+ + +++  +l+++r+l+G++ g+ +++++a+iad++p+e+r+r++gll+a+f+lG+i+gp+lgg++as +    
  gi|313126870|ref|YP_004037140.1|  88 TLFgL-AGSLaVLFAARMLAGVM-GGNIATAQAYIADVTPPEDRARGLGLLGAAFGLGFIFGPALGGFFASEFVvsa 162
                                       55546.66666***********9.8999999***************************************88889** PP

                             MFS_1 150 .............Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwill 213
                                                    ++++ +++a+++   +v +++llpe++p+++r++++e+   + ++ l++ +   l+   l  l+
  gi|313126870|ref|YP_004037140.1| 163 aqsvfpawlpateFSLPSFAAAAITGTNLVAAYVLLPESRPPEERVASRER---DRESRLTE-LADALRTHGLGTLV 235
                                       *************9999********************************99...68888888.555555555658** PP

                             MFS_1 214 ialllfffgfsglltllplylqevlglsglllaglllallalvgail.allagrlsdrlgrrrrlllallllllaal 289
                                       +a++l++f+fs+l + + +++++++g++ + ++++ll  +++++ai+ + l+g l dr+g  r  + + ++ +++++
  gi|313126870|ref|YP_004037140.1| 236 VAFFLVSFAFSALESQFIFLTNDQYGYG-ATENAILLTYFGVIIAIVqGGLIGPLTDRYGEYRVAIAGAAIQVFTLA 311
                                       ************666666669*******.799999999999999999899**********98888888888888888 PP

                             MFS_1 290 glallavt.................ssavllllvlvl.iGfglgfvfpsllalasdlappeeagtasglfntagslg 348
                                       ++ +++ +                  sav++l v+v+ + fg +++++sl++l+s++a ++e+g a+gl+++agsl+
  gi|313126870|ref|YP_004037140.1| 312 AVPFAPYFgsyipsvepllpvgptlPSAVIALGVIVTpLAFGNAITNVSLNTLVSRSATADEQGGAFGLTQSAGSLA 388
                                       88888888999999999999998655555555566669*************************************** PP

                             MFS_1 349 galgp 353
                                       + +gp
  gi|313126870|ref|YP_004037140.1| 389 RTFGP 393
                                       ***98 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 4.2e-13
                             MFS_1  51 plGrlsdrfGrrrvlllglllfalglllll.f.........a........sslw.lllvlrv...lqGlgagalfpa 105
                                       ++G+l+dr+G  rv ++g+++ +++ l+++ f         +        ++l+ ++++l v     ++g ++ + +
  gi|313126870|ref|YP_004037140.1| 285 LIGPLTDRYGEYRVAIAGAAIQVFT-LAAVpFapyfgsyipSvepllpvgPTLPsAVIALGVivtPLAFGNAITNVS 360
                                       58***********************.444455233354443044445556668888888888555689********* PP

                             MFS_1 106 gaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllp 173
                                        ++l+++ ++ +e+g a+gl +++ sl+  +gp+l+g+l++++ + a+f++ +++++  +vl   l +
  gi|313126870|ref|YP_004037140.1| 361 LNTLVSRSATADEQGGAFGLTQSAGSLARTFGPALAGFLYTAIDYWAPFVLGGALMIPIVVL---LAR 425
                                       ********************************************999**********99885...333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   5.4   4.5e-14   1.6e-10      49     194 ..      46     201 ..      11     220 .. 0.88
   2 ?   -0.6   0.5      0.13   4.5e+02      31      86 ..     251     306 ..     230     322 .. 0.64
   3 ?   -0.9   0.2      0.16   5.8e+02      44      87 ..     374     417 ..     343     425 .. 0.69

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.5e-14
                                       HHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  49 glivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPm 125
                                       +l+ +++++ +++ + f+g l+d+ GR+++ll + + +vi+  l ++a    s+ vl+++R+l+G+ +G+  +++  
  gi|313126870|ref|YP_004037140.1|  46 SLLIASYSAMQFLAAPFLGRLSDTRGRRPVLLLSLTGSVIAWTLFGLAG---SLAVLFAARMLAGV-MGGNIATAQA 118
                                       78899********************************************...9************7.79999***** PP

                                       HHHTTS-SCCH....HHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.........TTHHHHHHHCCHHHHHHHHHHG. CS
                          Sugar_tr 126 yisEiApkklR....galvslyqlaitfGilvaaifglglnktsn.........adgwrillglqlvpallllill. 188
                                       yi+ ++p++ R    g l+  + l+ +fG  ++ +f   +  + +         a+++ ++ + +++++ + l++  
  gi|313126870|ref|YP_004037140.1| 119 YIADVTPPEDRarglGLLGAAFGLGFIFGPALGGFFASEFVVSAAqsvfpawlpATEFSLPSFAAAAITGTNLVAAy 195
                                       *******9988667778888888888888888888877774444457999999999999998888887777665553 PP

                                       GGS--- CS
                          Sugar_tr 189 lflPES 194
                                       ++lPES
  gi|313126870|ref|YP_004037140.1| 196 VLLPES 201
                                       899999 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.13
                                       TSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                          Sugar_tr  31 nfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlf 86 
                                       +f + ++++  + ++    l++ + +++ai+ + ++g+l+dr+G   + +++a++ 
  gi|313126870|ref|YP_004037140.1| 251 QFIFLTNDQYGYGATENAILLTYFGVIIAIVQGGLIGPLTDRYGEYRVAIAGAAIQ 306
                                       44445555555555556666666666777776777777888888766666655554 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.16
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfv 87 
                                       +    gl+ s+ ++ +++G  +ag+l + +++   ++ +++l++
  gi|313126870|ref|YP_004037140.1| 374 QGGAFGLTQSAGSLARTFGPALAGFLYTAIDYWAPFVLGGALMI 417
                                       35567899999999999*******99999999988888877765 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   9.0   1.8e-09   6.5e-06     226     374 ..       9     155 ..       5     167 .. 0.92
   2 !    3.7   2.9    0.0062        22     217     307 ..     221     313 ..     181     410 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.8e-09
                        MFS_1_like 226 eviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayil 302
                                        ++++++++++    +gi+   + lY  + ga++++ + l+a   +++     f  +l ++ G + +l+++l+  ++
  gi|313126870|ref|YP_004037140.1|   9 ALAVVFVIVFVDLLGFGILIPVIPLYALSFGATEFVGSLLIASYSAMQFLAAPFLGRLSDTRGRRPVLLLSLTGSVI 85 
                                       456777777777788899999999***************************************************** PP

                        MFS_1_like 303 rfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllw 374
                                        + l ++  ++ +++ + +L g+  g + a+a  y+++++p++ +a+g gll ++ fglG  +G  +GG++ 
  gi|313126870|ref|YP_004037140.1|  86 AWTLFGLAGSLAVLFAARMLAGVMGGNI-ATAQAYIADVTPPEDRARGLGLLGAA-FGLGFIFGPALGGFFA 155
                                       ***********************99999.**********************9876.*************975 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0062
                        MFS_1_like 217 vllnilknpeviifllvalilgmswgiien.FlflYLkelgasntllGslva.lgvvaeiplfffaeklleklGhvk 291
                                       +l   l+ + + +++++ +++ ++++++e+ F+fl  +++g+  t   +l++ +gv+  i+   +   l++++G  +
  gi|313126870|ref|YP_004037140.1| 221 ELADALRTHGLGTLVVAFFLVSFAFSALESqFIFLTNDQYGYGATENAILLTyFGVIIAIVQGGLIGPLTDRYGEYR 297
                                       56666677777777777777777766666425555558888877766665433788888888888888888888888 PP

                        MFS_1_like 292 lliiallayilrflly 307
                                       + i++  + ++++  +
  gi|313126870|ref|YP_004037140.1| 298 VAIAGAAIQVFTLAAV 313
                                       8888877777766554 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.9e-06     0.025     133     248 ..      97     210 ..      82     230 .. 0.74
   2 ?   -3.1   0.1      0.47   1.7e+03     465     516 ..     345     395 ..     339     400 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 133 llfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdidseisltpkdp 209
                                        ++f+a +l+G+ +  i   +++Yi D + +++ +  lg+l a+  lG ++G +lG+++++ +v        ++  p
  gi|313126870|ref|YP_004037140.1|  97 AVLFAARMLAGVMGGNIA-TAQAYIADVTPPEDRARGLGLLGAAFGLGFIFGPALGGFFASEFVVS----AAQSVFP 168
                                       4899*******9998865.58***************************************998876....4444567 PP

                                       xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 210 rWvgaW...WlgflilgvllllaaiplffFPkelpkkkeera 248
                                        W+ a       f  +++    ++  ++++P++ p +++ ++
  gi|313126870|ref|YP_004037140.1| 169 AWLPATefsLPSFAAAAITGTNLVAAYVLLPESRPPEERVAS 210
                                       777664222223555555555555666666666555544444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.47
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 465 illflvsflgalgrvpallvilRcVkkedksfalGlqlllirllgliPgPii 516
                                       ++++ ++f  a+++v+  +++ R+   ++   a Gl++   +l +   gP +
  gi|313126870|ref|YP_004037140.1| 345 VIVTPLAFGNAITNVSLNTLVSRSATADEQGGAFGLTQSAGSL-ARTFGPAL 395
                                       3444444555555555555555666666666666666555555.55555555 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.0   3.3e-05      0.12      82     169 ..      47     136 ..      30     161 .. 0.78
   2 ?    0.4   0.1     0.045   1.6e+02      67     117 ..     255     305 ..     225     325 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.3e-05
                             TRI12  82 lfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpagasplfvgel 158
                                       l+ + ++  q ++   +grl+d  grrp+++l+    ++   +   a  +  l+aa  l gv  g   ++  ++ ++
  gi|313126870|ref|YP_004037140.1|  47 LLIASYSAMQFLAAPFLGRLSDTRGRRPVLLLSLTGSVIAWTLFGLAGSLAVLFAARMLAGVMGGNIATAQAYIADV 123
                                       55556666777788899***********8887655555555566679999********************99*9998 PP

                             TRI12 159 ms..nktkflgll 169
                                           ++++ lgll
  gi|313126870|ref|YP_004037140.1| 124 TPpeDRARGLGLL 136
                                       7511455556665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.045
                             TRI12  67 lpnilqdvgqsensslfstlwttgqavsilvmgrltdrfgrrpfvilthil 117
                                       l n     g +en  l++ +  +   v   ++g ltdr+g   + i+   +
  gi|313126870|ref|YP_004037140.1| 255 LTNDQYGYGATENAILLTYFGVIIAIVQGGLIGPLTDRYGEYRVAIAGAAI 305
                                       44555557888998888887777788888899********98888876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2673.33
//
Query:       gi|313126871|ref|YP_004037141.1|  [L=58]
Description: hypothetical protein Hbor_21320 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0059   16.7   1.0     0.0097   16.0   1.0    1.3  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
       0.05   12.9   0.4        7.6    6.0   0.0    2.3  2  zf-TFIIB        Transcription factor zinc-finger
      0.058   13.3   0.5         10    6.2   0.0    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.093   12.8   1.7        7.1    6.8   0.0    2.2  2  DUF2752         Protein of unknown function (DUF2752)
      0.094   12.7   3.5        1.2    9.2   0.4    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.28   10.6   4.7       0.53    9.8   0.8    2.1  2  zf-ribbon_3     zinc-ribbon domain
       0.32   10.9   4.3       0.48   10.3   1.4    2.1  2  HscB_4_cys      Co-chaperone HscB tetracysteine metal binding
       0.36   10.4   3.9        1.7    8.2   0.8    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.41   11.1   3.0         11    6.5   0.4    2.1  2  zf-IS66         zinc-finger binding domain of transposase IS6
       0.43   10.9   7.8        5.8    7.3   4.7    2.6  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
          2    8.4  11.0        3.7    7.6   2.6    2.9  3  DUF1610         Domain of unknown function (DUF1610)
        2.5    7.8   8.6       0.28   10.9   2.5    2.0  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        3.4    7.4   7.0       0.46   10.1   0.7    2.1  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.0   7.1e-06    0.0097       6      35 ..       9      39 ..       8      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.1e-06
                       Zn-ribbon_8  6 YrCeeCghefevlqsis.daplta.CPeCgse 35
                                      ++C++Cg   e+  ++  d+   + CP+Cg +
  gi|313126871|ref|YP_004037141.1|  9 FECTACG-GLERADAVGyDSLGYPeCPNCGTR 39
                                      89*****.***99999988877777*****84 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0055       7.6      19      28 ..       8      17 ..       2      17 .. 0.82
   2 ?    5.5   0.1    0.0078        11       2       8 ..      33      39 ..      32      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0055
                          zf-TFIIB 19 idyCpqCrGv 28
                                       + C++C+G+
  gi|313126871|ref|YP_004037141.1|  8 YFECTACGGL 17
                                      678******5 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0078
                          zf-TFIIB  2 CPkCqde 8 
                                      CP+C++ 
  gi|313126871|ref|YP_004037141.1| 33 CPNCGTR 39
                                      9999874 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0072        10      47      62 ..       9      24 ..       5      28 .. 0.88
   2 ?    6.0   0.1    0.0081        11      30      40 ..      32      42 ..      31      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0072
                    OrfB_Zn_ribbon 47 fkCpnCgfeadrDvnA 62
                                      f+C++Cg    +D ++
  gi|313126871|ref|YP_004037141.1|  9 FECTACGGLERADAVG 24
                                      99******99999987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0081
                    OrfB_Zn_ribbon 30 tCseCgsknke 40
                                      +C++Cg +  +
  gi|313126871|ref|YP_004037141.1| 32 ECPNCGTRTGP 42
                                      69999998766 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0051       7.1       3      17 ..       3      17 ..       2      22 .. 0.84
   2 ?    5.6   0.6     0.012        17      10      16 ..      32      38 ..      25      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0051
                           DUF2752  3 fkaltGipCPGCGlt 17
                                      f ++  ++C +CG++
  gi|313126871|ref|YP_004037141.1|  3 FEWVSYFECTACGGL 17
                                      6777789******96 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                           DUF2752 10 pCPGCGl 16
                                      +CP CG+
  gi|313126871|ref|YP_004037141.1| 32 ECPNCGT 38
                                      6*****7 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.013        18      15      26 ..       5      16 ..       1      25 [. 0.71
   2 ?    9.2   0.4   0.00087       1.2      19      28 ..      31      41 ..      18      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.013
                     Zn_Tnp_IS1595 15 WpngfvCPhCgs 26
                                      W + f C +Cg+
  gi|313126871|ref|YP_004037141.1|  5 WVSYFECTACGG 16
                                      666677777776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00087
                     Zn_Tnp_IS1595 19 fvCPhCgsr.k 28
                                      + CP+Cg r  
  gi|313126871|ref|YP_004037141.1| 31 PECPNCGTRtG 41
                                      78*****8754 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.068        94      19      23 ..      11      15 ..       7      18 .. 0.75
   2 ?    9.8   0.8   0.00038      0.53      19      24 ..      33      38 ..      31      41 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.068
                       zf-ribbon_3 19 CpyCG 23
                                      C+ CG
  gi|313126871|ref|YP_004037141.1| 11 CTACG 15
                                      77777 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00038
                       zf-ribbon_3 19 CpyCGt 24
                                      Cp+CGt
  gi|313126871|ref|YP_004037141.1| 33 CPNCGT 38
                                      555555 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.22     3e+02       3       8 ..      11      16 ..       9      26 .. 0.68
   2 ?   10.3   1.4   0.00034      0.48       1      18 [.      31      48 ..      31      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.22
                                      -SSS-- CS
                        HscB_4_cys  3 CWnCGg 8 
                                      C  CGg
  gi|313126871|ref|YP_004037141.1| 11 CTACGG 16
                                      667887 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00034
                                      -B-SSS--B--SS-S--- CS
                        HscB_4_cys  1 PrCWnCGgpgapgrgdef 18
                                      P C nCG   +p+ g ++
  gi|313126871|ref|YP_004037141.1| 31 PECPNCGTRTGPLAGSGH 48
                                      99**********999775 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.038        52      22      26 ..      11      16 ..       7      23 .. 0.73
   2 ?    8.2   0.8    0.0013       1.7       3       9 ..      33      39 ..      31      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.038
                                      ESSS.S CS
                      TF_Zn_Ribbon 22 CtdC.G 26
                                      Ct+C G
  gi|313126871|ref|YP_004037141.1| 11 CTACgG 16
                                      999944 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                                      ETTTTCE CS
                      TF_Zn_Ribbon  3 CPnCgst 9 
                                      CPnCg++
  gi|313126871|ref|YP_004037141.1| 33 CPNCGTR 39
                                      *****97 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.019        26       4      15 ..      11      24 ..      10      28 .. 0.68
   2 ?    6.5   0.4    0.0079        11       3      12 ..      32      41 ..      31      46 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.019
                           zf-IS66  4 CpcCGg.l.lkpig 15
                                      C  CGg +  + +g
  gi|313126871|ref|YP_004037141.1| 11 CTACGGlErADAVG 24
                                      ******44555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0079
                           zf-IS66  3 tCpcCGgllk 12
                                       Cp+CG+   
  gi|313126871|ref|YP_004037141.1| 32 ECPNCGTRTG 41
                                      6*****9544 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.048        66       5      13 ..      10      18 ..       8      20 .. 0.81
   2 ?    7.3   4.7    0.0042       5.8       5      14 ..      32      41 ..      30      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.048
                                      --TTTT-TT CS
                    Prim_Zn_Ribbon  5 pCPvCGGrD 13
                                      +C  CGG  
  gi|313126871|ref|YP_004037141.1| 10 ECTACGGLE 18
                                      7999**965 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0042
                                      --TTTT-TTT CS
                    Prim_Zn_Ribbon  5 pCPvCGGrDr 14
                                      +CP+CG r++
  gi|313126871|ref|YP_004037141.1| 32 ECPNCGTRTG 41
                                      8******997 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.2     0.027        37       1       6 [.      11      16 ..      11      17 .. 0.90
   2 ?    7.6   2.6    0.0027       3.7      19      23 ..      33      37 ..      32      38 .. 0.93
   3 ?   -0.4   0.0      0.83   1.1e+03       7      15 ..      42      50 ..      41      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.027
                           DUF1610  1 CtSCGa 6 
                                      Ct+CG+
  gi|313126871|ref|YP_004037141.1| 11 CTACGG 16
                                      *****7 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0027
                           DUF1610 19 CPNCG 23
                                      CPNCG
  gi|313126871|ref|YP_004037141.1| 33 CPNCG 37
                                      ****9 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.83
                           DUF1610  7 elaprErav 15
                                      +la+ ++++
  gi|313126871|ref|YP_004037141.1| 42 PLAGSGHGT 50
                                      799999998 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4      0.41   5.6e+02      24      28 ..      11      15 ..      10      17 .. 0.79
   2 ?   10.9   2.5    0.0002      0.28       6      20 ..      33      48 ..      33      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.41
                     zf-NADH-PPase 24 CpaCg 28
                                      C aCg
  gi|313126871|ref|YP_004037141.1| 11 CTACG 15
                                      88887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0002
                     zf-NADH-PPase  6 CgrCGaptepaeg.gw 20
                                      C+ CG++t p +g g+
  gi|313126871|ref|YP_004037141.1| 33 CPNCGTRTGPLAGsGH 48
                                      *********9998666 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.8      0.31   4.3e+02      13      17 ..      11      15 ..      10      17 .. 0.86
   2 ?   10.1   0.7   0.00033      0.46      12      21 ..      32      41 ..      27      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                           zf-tcix 13 CpkCG 17
                                      C+ CG
  gi|313126871|ref|YP_004037141.1| 11 CTACG 15
                                      ****9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00033
                           zf-tcix 12 kCpkCGtyNG 21
                                       Cp+CGt  G
  gi|313126871|ref|YP_004037141.1| 32 ECPNCGTRTG 41
                                      7******887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 380.08
//
Query:       gi|313126872|ref|YP_004037142.1|  [L=77]
Description: hypothetical protein Hbor_21330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 466.68
//
Query:       gi|313126873|ref|YP_004037143.1|  [L=262]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-24   85.2   2.2    1.3e-11   44.7   0.7    2.8  3  CBS       CBS domain
    7.8e-10   38.9   0.1    3.9e-09   36.7   0.1    2.1  1  ParBc     ParB-like nuclease domain
    0.00044   20.4   0.1     0.0035   17.4   0.1    2.0  1  ParBc_2   Putative ParB-like nuclease


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   1.6e-13   9.3e-10       1      52 [.       7      58 ..       7      61 .. 0.92
   2 !   44.7   0.7   2.2e-15   1.3e-11       4      54 ..      69     119 ..      66     122 .. 0.95
   3 ?   -3.0   0.0       1.8   1.1e+04      17      32 ..     128     141 ..     125     143 .. 0.62

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.6e-13
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHH CS
                               CBS  1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDll 52
                                      V+++mtr+v tv+p +++++++++++e++ ++++PV  e  k+ G vt rDll
  gi|313126873|ref|YP_004037143.1|  7 VKEYMTREVQTVSPADSVADVAKRIVESDgHNGFPVC-EGRKVEGFVTARDLL 58
                                      89**********************987777*******.5667**********9 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 2.2e-15
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +mt+d+++++pd+ + +a++ + ++g+  lPVVd+ g+lvGi++ +D++r 
  gi|313126873|ref|YP_004037143.1|  69 VMTEDIIVAHPDMAVNDAARVILRSGIQKLPVVDDAGNLVGIISNTDVIRS 119
                                       7********************88***99********************996 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.8
                                       BHHHHHHHHHHHTSSE CS
                               CBS  17 tleealelmrekgvsr 32 
                                        ++++++++++  +++
  gi|313126873|ref|YP_004037143.1| 128 KVGKLMRTLEQ--IHG 141
                                       56677777744..665 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   6.6e-13   3.9e-09       3      81 ..     151     224 ..     111     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 6.6e-13
                             ParBc   3 vplseirpnplqprkdspekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivleidde 79 
                                       v+l+ + p++ +++   ++++e  + +++ +Gl +P++v +++ g y + +G++R+ Aa+ lg  +++++++ +dd 
  gi|313126873|ref|YP_004037143.1| 151 VELDALIPTQGRVY---ADELEGRKYELE-RGLAEPLVVINNN-GTYILADGHHRVMAAHQLGTGQMDAYIIVVDDP 222
                                       56666666666666...778888888888.************9.************************999998876 PP

                             ParBc  80 ea 81 
                                       ++
  gi|313126873|ref|YP_004037143.1| 223 IE 224
                                       65 PP

>> ParBc_2  Putative ParB-like nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   5.9e-07    0.0035       3      87 ..     151     222 ..     149     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.9e-07
                                       EEGGGCB-SBSEE-HHHHHHHHHHHHT------.---TT-BEEEEEE-STT-EEE-S-HHHHHHHHHTT-....-EE CS
                           ParBc_2   3 veiadLrPTQlavGldeveyklgeleelkekkkldkflekklvpvVigpdgelYliDhHHllrallesgvggaekkv 79 
                                       ve+++L PTQ  v  de+e +  ele+  ++             vVi+++g + l D+HH + a ++ g+   + ++
  gi|313126873|ref|YP_004037143.1| 151 VELDALIPTQGRVYADELEGRKYELERGLAE-----------PLVVINNNGTYILADGHHRVMAAHQLGT--GQMDA 214
                                       7899999999999999998888887433322...........34788889999999***********776..66677 PP

                                       EEEEEEE- CS
                           ParBc_2  80 lvkvvadl 87 
                                       ++ vv+d 
  gi|313126873|ref|YP_004037143.1| 215 YIIVVDDP 222
                                       77777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1559.95
//
Query:       gi|313126874|ref|YP_004037144.1|  [L=489]
Description: exopolyphosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-13   50.1   0.0    5.1e-13   49.1   0.0    1.5  1  DHH            DHH family
    1.1e-12   48.6   0.1    1.7e-11   44.7   0.1    2.4  3  DHHA1          DHHA1 domain
    4.7e-06   26.9   0.0    1.1e-05   25.6   0.0    1.7  1  TrkA_N         TrkA-N domain
    0.00028   21.3   0.0    0.00061   20.2   0.0    1.5  1  NAD_binding_7  Putative NAD(P)-binding
  ------ inclusion threshold ------
       0.11   12.1   0.1        0.2   11.3   0.1    1.4  1  MotB_plug      Membrane MotB of proton-channel complex MotA/M


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   1.4e-16   5.1e-13       3     101 .]     152     294 ..     150     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.4e-16
                                       EEE-ECSSSHHHHHHHHHHHHC................................................ECS--TC CS
                                       xxxxxxxxxxxxxxxxxxxxxx................................................xxxxxxx RF
                               DHH   3 livghknpDtDsigSaialanl................................................lvDhnek 31 
                                       ++v+h npD D+i+Sa+al ++                                                lvDh+++
  gi|313126874|ref|YP_004037144.1| 152 AVVMHDNPDPDAIASALALVRIaesvgldadpcyfgdishqenralvnlldidlvnlergedtddyggiaLVDHSRP 228
                                       6899*****************6666666777777777777777777777777777777777777777777******* PP

                                       GGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  32 sqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                                +++e  i++DHH +  ++e    +l l+ ++g+t+++++++l++ ++e+++++a++ll gi
  gi|313126874|ref|YP_004037144.1| 229 GVNDGL--PKDTEVDIVVDHHPPRAPVEAR--YLDLRRELGATSTLMTNYLRRLGIEPDATVATALLFGI 294
                                       988855..9**************9666665..89999******************************998 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.23   8.4e+02      35      69 ..      83     116 ..      68     122 .. 0.60
   2 ?   -1.3   0.0      0.77   2.8e+03       3      60 ..     109     168 ..     107     172 .. 0.65
   3 !   44.7   0.1   4.8e-15   1.7e-11      38     126 ..     349     436 ..     335     452 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.23
                                       EEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBT CS
                             DHHA1  35 eevkgvkvlvaevgeewdagalgiaadklksklkk 69 
                                       +e   + +l+a+vg ++d +++++a d+l ++l +
  gi|313126874|ref|YP_004037144.1|  83 RERFPDAYLLAYVGSDAD-HDTREALDELADRLVD 116
                                       444466777778855544.4666666666665533 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.77
                                       HHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC...TCEEEEEECHCCHHHHHHHHHH CS
                             DHHA1   3 slneerkelekeleelkealaklkaeellekaeevk...gvkvlvaevgeewdagalgiaa 60 
                                       +l +++ + ++ l +  ++l++ +a++ l+++++v      +++v+   ++ d++a+++a 
  gi|313126874|ref|YP_004037144.1| 109 ELADRLVDGRRILTDRLTELTEGAAADRLHRLFRVLkslSGPLAVVMH-DNPDPDAIASAL 168
                                       555666666666655555555555555555555555778888888888.999999998875 PP

  == domain 3  score: 44.7 bits;  conditional E-value: 4.8e-15
                                       C.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHSS-HHHHHHHHHHHTTCCEE CS
                             DHHA1  38 k.gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkdgvdagelakeaaaklgggGG 112
                                       +    vl+++vge  +++al++a d l++  ++    ++v++ ++ +v+vs+r+++ +vd+ge +++a + +g  G 
  gi|313126874|ref|YP_004037144.1| 349 DvRGDVLATNVGEIRNRDALAQASDHLLN--MEgIRLTVVYGFKDGTVYVSGRARGTDVDLGETLRDALSPIGSAG- 422
                                       2478899999*9*****************..8867777777666669*******988**********888888887. PP

                                       EETCEEEEEEEHCH CS
                             DHHA1 113 GHdlAaGagipaek 126
                                       GH+ +aGa+ip + 
  gi|313126874|ref|YP_004037144.1| 423 GHADMAGAQIPLGI 436
                                       *********99654 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   3.2e-09   1.1e-05       2     103 ..       5     102 ..       4     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.2e-09
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       +++G+G  +++ +e+L e  g   +v  ++  +v+++r++g+ +    +td e    a  e++d+v +a +d +an+
  gi|313126874|ref|YP_004037144.1|   5 LVLGCGSAAQRAVERLAEwPGT-LTVLSQRSGVVDSFRDDGVSAERCAPTDHE----AFPEEVDVVFVASDDAAANL 76 
                                       69****************9995.***************************975....6689**************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehae 103
                                        ++l+a+e +p+++  a + ++++ +
  gi|313126874|ref|YP_004037144.1|  77 DVALTARERFPDAYLLAYVGSDADHD 102
                                       ************99999888877654 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.7e-07   0.00061       9      84 ..       3      84 ..       1      90 [. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.7e-07
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev...keeleelvk...laeeelekdlegadlviaatddrelneriaea 81
                                      + lv G G+ A+r v++l+e   ++tv+++++    ++ ++ v+   +a+++ e+  e++d+v++a dd++ n  +a +
  gi|313126874|ref|YP_004037144.1|  3 RRLVLGCGSAAQRAVERLAEWPGTLTVLSQRSgvvDSFRDDGVSaerCAPTDHEAFPEEVDVVFVASDDAAANLDVALT 81
                                      679****************************7666555555444222556777777999****************9999 PP

                     NAD_binding_7 82 aka 84
                                      a++
  gi|313126874|ref|YP_004037144.1| 82 ARE 84
                                      986 PP

>> MotB_plug  Membrane MotB of proton-channel complex MotA/MotB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   5.7e-05       0.2      16      28 ..     313     325 ..     302     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.7e-05
                         MotB_plug  16 erWlvtYaDlmtL 28 
                                        +Wlv+YaDl tL
  gi|313126874|ref|YP_004037144.1| 313 AAWLVSYADLSTL 325
                                       36********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3201.70
//
Query:       gi|313126875|ref|YP_004037145.1|  [L=132]
Description: hypothetical protein Hbor_21360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 750.57
//
Query:       gi|313126876|ref|YP_004037146.1|  [L=504]
Description: NADH dehydrogenase subunit n [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-67  225.5  23.6    7.9e-67  225.5  23.6    2.0  3  Proton_antipo_M  Proton-conducting membrane transporter
    3.2e-05   23.9   1.6    0.00014   21.8   1.6    2.2  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.5      0.17   1.5e+03     118     162 ..      16      58 ..       4      66 .. 0.57
   2 ?   -3.1   2.1      0.38   3.4e+03      35      52 ..      44      61 ..      17     112 .. 0.48
   3 !  225.5  23.6   8.8e-71   7.9e-67       1     292 [.     139     441 ..     139     442 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.17
                   Proton_antipo_M 118 allAatlvkagvlllirlllllavssneisqlllilaiismllgs 162
                                       a   a+++ + +lll+++ ++    ++e s ll+ ++++++l++ 
  gi|313126876|ref|YP_004037146.1|  16 AVAPAIILGLTGLLLLVIDSIN--TGEENSALLASISTVGALFAF 58 
                                       5554455555555555332222..467777777777777777764 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.38
                   Proton_antipo_M 35 slklflltllgsliLLlg 52
                                      +l + + t  + +++ ++
  gi|313126876|ref|YP_004037146.1| 44 ALLASISTVGALFAFAVA 61
                                      222233222222222222 PP

  == domain 3  score: 225.5 bits;  conditional E-value: 8.8e-71
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       +n+L++ +++lEl +lp+y L+g+ k+++ s+eA+lk+fl+++++s ++ +gi+l+y++tg+l + ++++al    +
  gi|313126876|ref|YP_004037146.1| 139 SNSLATAFVSLELASLPSYALVGFLKDNKGSVEAALKYFLIGAVSSAVFAFGISLVYAVTGSLLLADVASALGGSTE 215
                                       799********************************************************************966666 PP

                   Proton_antipo_M  78 slellll.lllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla......vssneis 147
                                         ++l +  l++l g+++K+a vp+h+W p+ay++aP+p+sa+l + ++ka++++++ ++++ a        + ++ 
  gi|313126876|ref|YP_004037146.1| 216 MVGVLGIgVLMILGGFAFKTASVPFHFWAPEAYEGAPAPISAFL-SSASKAAGFAIAFRVFFEAfplaklPTGVDWV 291
                                       666665515667789*****************************.559******999776654444545778999** PP

                   Proton_antipo_M 148 qlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqyg.....veaaiihllthalfkallFlla 219
                                         + +la+++m lg+++a +q ++Kr+lAySsi+h Gy li+la+ t+ g     + a+++hl+++++++ + Fl++
  gi|313126876|ref|YP_004037146.1| 292 LAFQVLAVVTMTLGNFAAATQENVKRMLAYSSIGHAGYALIGLAAITANGpnanvLGASMAHLMVYGFMNTGAFLFI 368
                                       *******************************************9966655222225689****************** PP

                   Proton_antipo_M 220 gsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvl 292
                                         +++     r++++y+gL  k P+ ++++ v+++slaGlPp+ gF+sk  ++++a++ + ++l+++  v s+l
  gi|313126876|ref|YP_004037146.1| 369 ALAEHWG-VGRTFEDYNGLGSKAPMACVAMSVFMFSLAGLPPFGGFFSKYVLFMSAIESGFWWLAAVgAVNSAL 441
                                       7765554.789*****************************************************9998887776 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.6   1.6e-08   0.00014      16      56 ..      85     125 ..      83     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-08
                   Proton_antipo_N  16 fllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfay 56 
                                       + +D++s+ ++l+ t+v+++v++ S+ Y a+ + ++ F+++
  gi|313126876|ref|YP_004037146.1|  85 LVVDGMSLFFTLIFTIVAAMVCIASLDYVAEQRYQAEFYSL 125
                                       789***************************9999999*987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3075.12
//
Query:       gi|313126877|ref|YP_004037147.1|  [L=509]
Description: NADH dehydrogenase subunit m [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-73  247.5  27.8    1.6e-73  247.5  27.8    1.6  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0035   17.4   2.3     0.0035   17.4   2.3    3.3  3  Oxidored_q5_N    NADH-ubiquinone oxidoreductase chain 4, amin


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1      0.64   5.8e+03       8      24 ..      78      94 ..      76     104 .. 0.73
   2 !  247.5  27.8   1.8e-77   1.6e-73       2     289 ..     132     430 ..     131     435 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.64
                   Proton_antipo_M  8 ylglElvllplylLigl 24
                                      ++g ++++lpl++L ++
  gi|313126877|ref|YP_004037147.1| 78 FVGVDGISLPLIVLTTI 94
                                      67888888888888765 PP

  == domain 2  score: 247.5 bits;  conditional E-value: 1.8e-77
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgil.llynltg...tlefeelskal.. 72 
                                        d +  ++++E+vl+p+y+Lig+w+   ++ +A++k+f++t ++sl++++g++ l+++l     ++ ++e+++al  
  gi|313126877|ref|YP_004037147.1| 132 LDFFVWFIFWEAVLVPMYFLIGIWGGP-RRKYAAIKFFVYTNIASLVMFIGFIaLVFGLGDsvsSMRLPEIAMALra 207
                                       678899******************765.99*********************996777777666678888888888** PP

                   Proton_antipo_M  73 ......elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vs 142
                                                 ++   l++++++++g++vK++++plh+Wlpda+veaPtp s++lA++l+k+g ++l+r+++ ++  +
  gi|313126877|ref|YP_004037147.1| 208 nelggfAGLNAETLKLVAFVAMFFGFAVKVPVAPLHTWLPDAHVEAPTPASVMLAGVLLKMGTYALLRFNFTMMpDV 284
                                       ***996666677888999********************************************************999 PP

                   Proton_antipo_M 143 sneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFlla 219
                                       ++++   ++++a+is+++g+++alaq d+Kr++AySs+s +Gy++++l++ t ygv +a +++++h+l++ l+F+++
  gi|313126877|ref|YP_004037147.1| 285 AKALVVPIAAIAVISVIYGAILALAQQDLKRIVAYSSVSSMGYVILGLVAYTTYGVGGATFQMIAHGLISGLMFMVV 361
                                       99999************************************************************************ PP

                   Proton_antipo_M 220 gsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavva 289
                                        +viy++++tr + +++g+a +mP+ + +++ ++++++GlP++agF ++f i+++a+a  +  ++ +++a
  gi|313126877|ref|YP_004037147.1| 362 -GVIYNTTHTRMVGDMSGMADRMPVASGIFVAGAFGYMGLPLMAGFAGEFFIFQGAFASTVHSAMPLFTA 430
                                       .888*****************************************************9998877766444 PP

>> Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.3   3.9e-07    0.0035      52     103 ..      74     121 ..       5     130 .. 0.81
   2 ?   -0.4   0.1      0.13   1.2e+03       5      42 ..     145     183 ..     142     197 .. 0.71
   3 ?   -3.6   0.2       1.3   1.2e+04      37      41 ..     356     361 ..     343     379 .. 0.45

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.9e-07
                     Oxidored_q5_N  52 nlsyllglDslSapLilLSlWllpLmilASqkhlkkepknrqrlFllllilL 103
                                        +  ++g+D +S+pLi+L++ l+ L i++ +  +      rq+ F  l++++
  gi|313126877|ref|YP_004037147.1|  74 DVHWFVGVDGISLPLIVLTTILTTLAIVSAWTPIDM----RQSQFYGLMLFM 121
                                       57789************************9999988....444444444443 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.13
                     Oxidored_q5_N   5 llptlmliplvllskkkllwststlvslllallsll.ll 42 
                                       l+p+ +li ++   ++k+  + +++++ + +l++++ ++
  gi|313126877|ref|YP_004037147.1| 145 LVPMYFLIGIWGGPRRKYAAIKFFVYTNIASLVMFIgFI 183
                                       677777777777777777777777888877777777443 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.3
                     Oxidored_q5_N  37 lsll.l 41 
                                       l+++ +
  gi|313126877|ref|YP_004037147.1| 356 LMFMvV 361
                                       222211 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3219.51
//
Query:       gi|313126878|ref|YP_004037148.1|  [L=671]
Description: NADH dehydrogenase subunit l [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-78  262.1  15.4    5.5e-78  262.1  15.4    2.8  3  Proton_antipo_M  Proton-conducting membrane transporter
      4e-21   74.8   0.9      2e-17   63.0   0.1    3.1  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
     0.0015   18.2   0.3      0.015   14.9   0.0    2.7  3  NADH5_C          NADH dehydrogenase subunit 5 C-terminus
     0.0036   17.0   0.0      0.009   15.7   0.0    1.7  1  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.2       0.4   1.8e+03     119     151 ..      34      66 ..      10     105 .. 0.63
   2 !  262.1  15.4   1.2e-81   5.5e-78       1     274 [.     138     422 ..     138     429 .. 0.92
   3 ?    0.2   0.3     0.077   3.5e+02     203     267 ..     440     506 ..     430     518 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.4
                   Proton_antipo_M 119 llAatlvkagvlllirlllllavssneisqlll 151
                                        +A+++ +ag +ll   +++    +++++q ++
  gi|313126878|ref|YP_004037148.1|  34 AFAGIVATAGSFLLSIATFFTVSQGQTYNQTIY 66 
                                       345666666666665554444444455555444 PP

  == domain 2  score: 262.1 bits;  conditional E-value: 1.2e-81
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg......tlefeelska 71 
                                       a++Ll+ ++++Elv+l++ylLig+w+++p   +A+ k+fl+t++g+ ++L+g++++++  g        +f+ l+++
  gi|313126878|ref|YP_004037148.1| 138 ADNLLMAFMFFELVGLCSYLLIGFWFREPGPPSAAKKAFLVTRFGDYFFLIGVVAVFATFGtaafagGESFPHLAEQ 214
                                       79*******************************************************99993333334456667666 PP

                   Proton_antipo_M  72 l........elgln.slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllll 138
                                       +        ++g++ +  ++++ ll+l g++ Ksaq+plh+Wlpda +e+Ptpvsal+ Aat+v+agv+l++r+  +
  gi|313126878|ref|YP_004037148.1| 215 AlhgehavnTFGFEpQTWFTIVGLLVLGGVVGKSAQFPLHTWLPDA-MEGPTPVSALIhAATMVAAGVYLVARMYGF 290
                                       69**9999844444144567778888999*****************.****************************** PP

                   Proton_antipo_M 139 lavssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkall 215
                                       +a  s+++  ++++++  ++l+++++++++++iK++lAyS+is+ Gym+++l+     g+ aa +hl+tha+fkall
  gi|313126878|ref|YP_004037148.1| 291 YA-LSPNALAIIALIGGFTALFAATMGVVKREIKQVLAYSTISQYGYMMLGLGG---GGYIAATFHLMTHAFFKALL 363
                                       **.***************************************************...7889**************** PP

                   Proton_antipo_M 216 FllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLea 274
                                       Fl agsvi ++++ +d+ ++ggL  +mP+++ ++l + l+laG+ p+agF+sk+++L+ 
  gi|313126878|ref|YP_004037148.1| 364 FLGAGSVIIAMHHNEDMWDMGGLKDRMPVTYYTFLSGSLALAGIVPFAGFWSKDEVLYE 422
                                       ********************************************************986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.077
                   Proton_antipo_M 203 ihllthalfkallFllagsviyerektrdirayggLak..kmPilalvllvlllslaGlPptagFls 267
                                       + ll+  ++ + +F ++  + + + +t++ r+  g ++  k P++ l +l ++ +l+ + p+a F +
  gi|313126878|ref|YP_004037148.1| 440 MGLLAVFFTGFYTFRMVFLTFHGKPRTQTARDPHGVRWnvKFPLVVLGILAATAGLVNMTPVAEFTG 506
                                       5566666777888999988889999999999999999977789999999999999999988888876 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   0.00029       1.3      27      45 ..      12      30 ..       8      55 .. 0.83
   2 !   63.0   0.1   4.5e-21     2e-17       2      57 ..      66     125 ..      65     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00029
                   Proton_antipo_N 27 lvvtfvsllvhlYSigYMa 45
                                      ++  fvs+lv l++ +YM 
  gi|313126878|ref|YP_004037148.1| 12 VLLPFVSFLVALFAGKYMP 30
                                      56679*************6 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 4.5e-21
                   Proton_antipo_N   2 ftWls.vgg.lsieigfllDklsalmllvvtfvsllvhlYSigYMad..degyqRFfayl 57 
                                       +tW +  +g +++e+g+l+D+lsa+ml++vt++++lvh++S+gYM d  ++g +R++a l
  gi|313126878|ref|YP_004037148.1|  66 YTWANgLDGaVTLEFGLLIDPLSAMMLVIVTLIAFLVHVFSLGYMNDegETGLPRYYAGL 125
                                       89999988779**********************************8633689*****965 PP

>> NADH5_C  NADH dehydrogenase subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2       1.3     6e+03      37      84 ..     299     314 ..     296     339 .. 0.53
   2 !   14.9   0.0   3.4e-06     0.015       1      46 [.     451     496 ..     451     505 .. 0.96
   3 ?   -0.7   0.0       0.2     9e+02     142     179 ..     624     661 ..     611     663 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.3
                           NADH5_C  37 algsiiaGsllswlifpktpvitlplllKllallvtilGlllglelsk 84 
                                       a++++i                                G +++l  ++
  gi|313126878|ref|YP_004037148.1| 299 AIIALI--------------------------------GGFTALFAAT 314
                                       444444................................4444444444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.4e-06
                           NADH5_C   1 YSlRliyyvllgsprfsslspineenptllnpilrLalgsiiaGsl 46 
                                       Y++R++++++ g+pr+++    +   +++  p+++L +++ +aG++
  gi|313126878|ref|YP_004037148.1| 451 YTFRMVFLTFHGKPRTQTARDPHGVRWNVKFPLVVLGILAATAGLV 496
                                       9*******************************************87 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.2
                           NADH5_C 142 kglaklllklskliqnlqkglikiyLlsflltllllll 179
                                       +g+++++l   + i  +q+g +  y +++ l l++lll
  gi|313126878|ref|YP_004037148.1| 624 NGISSVSLFSGSRIRRIQSGVVSNYAMLLTLGLTVLLL 661
                                       68888888999999999999999998888887777765 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     2e-06     0.009      78     178 ..     457     568 ..     450     601 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-06
                   Proton_antipo_C  78 fititefenkktlsyPhEsdntmlfpllvLvlftlfvGliGip....fnqegidldilskwLtpsin.....llhkn 145
                                       f+t +   +++t + Ph   +++ fpl+vL ++    Gl+ +     f   g++++ l++wL+  ++       h+ 
  gi|313126878|ref|YP_004037148.1| 457 FLTFHGKPRTQTARDPHGVRWNVKFPLVVLGILAATAGLVNMTpvaeF--TGLHIEFLHQWLNHGVEgltnhHYHEL 531
                                       45555555677899**************************98755334..48999********99985444422333 PP

                   Proton_antipo_C 146 snesv..dwyef..ltnaifSvsialfGifiAsllYk 178
                                        ++++     e+  l    +S+++al G  +A +lY+
  gi|313126878|ref|YP_004037148.1| 532 LENVAgyHAAELnpLAPGAVSLALALAGAGLAHMLYN 568
                                       3333211223331145567889999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:01.08
# Mc/sec: 1875.80
//
Query:       gi|313126879|ref|YP_004037149.1|  [L=100]
Description: NADH dehydrogenase subunit k [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-23   82.9   6.3    1.2e-23   82.8   6.3    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   6.3   6.4e-28   1.2e-23       2     103 ..       7      95 ..       6     100 .] 0.97

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 6.4e-28
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaiviga 78 
                                       +l+l+a++f+iGl+g+l+rrn+l  l+++el++na+n++lv++++f+             +++ +q++ L+ ++++a
  gi|313126879|ref|YP_004037149.1|   7 YLVLSAAVFCIGLFGILTRRNALLFLMSVELMLNAANINLVAFSYFW-------------GNVTGQTFGLFTMALAA 70 
                                       899********************************************.............***************** PP

                                       HHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  79 aetavgLallvrlyreygtddvqel 103
                                       ae+avg+++++ lyr+ g +dv e 
  gi|313126879|ref|YP_004037149.1|  71 AEVAVGIGIILVLYRDFGDVDVTEA 95 
                                       **********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 610.21
//
Query:       gi|313126880|ref|YP_004037150.1|  [L=125]
Description: hypothetical protein Hbor_21410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-05   23.4   1.9    4.9e-05   23.1   1.9    1.1  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
        1.7    8.2   5.2          1    8.9   0.3    2.0  2  SseC         Secretion system effector C (SseC) like family
        5.2    7.2  10.1       0.95    9.5   0.9    2.9  2  PGF-CTERM    PGF-CTERM motif


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   1.9   8.1e-09   4.9e-05      79     144 .]      15      89 ..       2      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.1e-09
                                       HHHHHHHHHHHHTT--......--------TT-HHHHHHHHTTT.........THHHHHHHHHHHHHHHHHHHHC CS
                       Oxidored_q3  79 alligllllalllllllessssavdaqvadvsnieaigsllftk.........yllpfelasllLLvaligaivl 144
                                         l++++l++++++++ ++s ++ +    dv+ +++ig ++f+          +l++fe++ ++L +al+ga++l
  gi|313126880|ref|YP_004037150.1|  15 PGLAAVALFVVMVAAFVTASFPEPQGFGGDVNITASIGYAMFNLgfgevasesFLVAFEIIDIVLVAALVGAVML 89 
                                       344445555555555555455666888999999****9999996699999999*******************986 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.8     0.026   1.6e+02     136     152 ..      17      33 ..      13      40 .. 0.82
   2 ?    8.9   0.3   0.00017         1     131     176 ..      70     115 ..      45     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.026
                              SseC 136 vgavvaavavvaavvav 152
                                       ++av ++v++vaa+v++
  gi|313126880|ref|YP_004037150.1|  17 LAAVALFVVMVAAFVTA 33 
                                       67888899999998764 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00017
                              SseC 131 lageivgavvaavavvaavvavgsaakgaaaavksgaaklaeavae 176
                                       +a+ei+  v++a  v+a+++a ++ + +a++++++g+++l +++++
  gi|313126880|ref|YP_004037150.1|  70 VAFEIIDIVLVAALVGAVMLARRETGDSAGQVLADGGQRLKQTLTG 115
                                       689*******999999999*****************9999998876 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   2.6     0.072   4.3e+02      12      20 ..      16      24 ..      16      30 .. 0.72
   2 ?    9.5   0.9   0.00016      0.95      10      22 ..      80      92 ..      80      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.072
                         PGF-CTERM 12 GLLaaalLa 20
                                      GL+a+al++
  gi|313126880|ref|YP_004037150.1| 16 GLAAVALFV 24
                                      677777654 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00016
                         PGF-CTERM 10 laGLLaaalLaRR 22
                                      +a+L +a+ LaRR
  gi|313126880|ref|YP_004037150.1| 80 VAALVGAVMLARR 92
                                      79**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 769.48
//
Query:       gi|313126881|ref|YP_004037151.1|  [L=86]
Description: NADH dehydrogenase subunit j [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-18   66.8   6.6    1.6e-18   66.8   6.6    1.3  2  Oxidored_q3      NADH-ubiquinone/plastoquinone oxidoreductase
  ------ inclusion threshold ------
       0.22   11.7  14.1       0.23   11.6  12.1    2.0  2  DUF4040          Domain of unknown function (DUF4040)


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1         1   9.3e+03      85      88 ..       9      12 ..       4      16 .. 0.37
   2 !   66.8   6.6   1.8e-22   1.6e-18       1      62 [.      18      79 ..      18      86 .] 0.92

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1
                                      HHHH CS
                       Oxidored_q3 85 llla 88
                                      +l+a
  gi|313126881|ref|YP_004037151.1|  9 ALFA 12
                                      2222 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 1.8e-22
                                      HHHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSST CS
                       Oxidored_q3  1 gallvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimlles 62
                                      ++l+v++ + + +sal L  ++++va+ +++l+aeFla++qilvYvG++l+l+ F++ml+++
  gi|313126881|ref|YP_004037151.1| 18 CSLGVVLVRDIWHSALLLGGALLSVAVHYVMLQAEFLAAMQILVYVGGVLILVTFAVMLTRT 79
                                      589********************************************************744 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.2   1.8e+03      50      60 ..       3      13 ..       1      16 [. 0.63
   2 ?   11.6  12.1   2.5e-05      0.23       2      63 ..      14      77 ..      13      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                           DUF4040 50 veglttvllll 60
                                       e++  +l++l
  gi|313126881|ref|YP_004037151.1|  3 YETIAFALFAL 13
                                      56777777766 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.5e-05
                           DUF4040  2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveg..lttvllllalr 63
                                      ++v ++l +vl+rd  ++++llg + l va+ +v+l+A  +A  q++v  g  l++v +++ l 
  gi|313126881|ref|YP_004037151.1| 14 ITVGCSLGVVLVRDIWHSALLLGGALLSVAVHYVMLQAEFLAAMQILVYVGgvLILVTFAVMLT 77
                                      7899*****************************************9654440044444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 473.51
//
Query:       gi|313126882|ref|YP_004037152.1|  [L=153]
Description: NADH-quinone oxidoreductase subunit i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-12   47.6  10.1      3e-12   47.0  10.1    1.3  1  Fer4_7         4Fe-4S dicluster domain
      2e-12   46.3   9.6    1.4e-06   27.9   2.9    2.2  2  Fer4           4Fe-4S binding domain
    1.1e-10   42.3   4.2    7.4e-06   26.8   0.2    2.2  2  Fer4_16        4Fe-4S double cluster binding domain
    1.5e-09   37.8   8.7    2.1e-09   37.3   8.7    1.2  1  Fer4_21        4Fe-4S dicluster domain
    3.3e-09   36.8  22.1    1.7e-07   31.3  11.3    1.5  2  Fer4_9         4Fe-4S dicluster domain
    2.1e-07   30.9  20.1    4.4e-06   26.7  11.7    1.7  2  Fer4_10        4Fe-4S dicluster domain
    1.2e-05   25.6   9.9    0.00083   19.7  12.1    2.1  2  Fer4_8         4Fe-4S dicluster domain
    1.6e-05   25.4  12.3     0.0063   17.0   1.5    2.3  2  Fer4_17        4Fe-4S dicluster domain
    1.7e-05   24.7  13.7     0.0059   16.6   1.7    2.3  2  Fer4_6         4Fe-4S binding domain
    4.6e-05   23.3  12.0     0.0022   18.0   1.8    2.4  2  Fer4_2         4Fe-4S binding domain
    0.00018   21.8  13.6     0.0034   17.8   3.9    2.2  2  Fer4_4         4Fe-4S binding domain
    0.00023   21.9  14.6     0.0038   18.0   3.0    2.3  2  Fer4_3         4Fe-4S binding domain
     0.0035   17.5  10.2       0.16   12.2   1.9    2.2  2  Fer4_18        4Fe-4S dicluster domain
     0.0041   17.9   3.9       0.35   11.7   0.3    2.3  2  Fer4_22        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.054   13.6   8.1       0.19   11.9   8.1    1.8  1  ETF_QO         Electron transfer flavoprotein-ubiquinone oxid
       0.16   12.5  12.8       0.55   10.8   1.5    2.7  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
       0.35   11.3   7.3        5.4    7.5   1.3    2.5  2  TNFR_c6        TNFR/NGFR cysteine-rich region
        6.3    6.7   7.2         23    4.9   1.3    2.5  2  zf_PR_Knuckle  PR zinc knuckle motif


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0  10.1     3e-15     3e-12       1      52 []      46      96 ..      46      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 3e-15
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      rCi C++C+++Cp+++i++ ++++ +g e+++++  +C++C+ C++vCP++a
  gi|313126882|ref|YP_004037152.1| 46 RCIWCRQCENVCPNDTIQIVQDDQRNG-EQYNLHIGQCIYCRLCEEVCPVDA 96
                                      8*******************9976666.99********************97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.5   6.4e-08   6.4e-05       3      23 ..      42      62 ..      40      63 .. 0.90
   2 !   27.9   2.9   1.4e-09   1.4e-06       7      23 ..      81      97 ..      78      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.4e-08
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                      + +e+Ci C +C++vCP++ I
  gi|313126882|ref|YP_004037152.1| 42 FSQERCIWCRQCENVCPNDTI 62
                                      679****************98 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.4e-09
                                      TSSS-THHHHHSTTTEE CS
                              Fer4  7 kCigCGaCvevCPvgAI 23
                                       Ci+C +C+evCPv+AI
  gi|313126882|ref|YP_004037152.1| 81 QCIYCRLCEEVCPVDAI 97
                                      5***************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   9.2e-06    0.0092       1      20 [.      46      65 ..      40      77 .. 0.80
   2 !   26.8   0.2   7.5e-09   7.4e-06       1      40 [.      81     122 ..      81     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.2e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      rC+ C++C +vCP + i+  
  gi|313126882|ref|YP_004037152.1| 46 RCIWCRQCENVCPNDTIQIV 65
                                      59999999999999988754 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 7.5e-09
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekei..earecisyntaekkd 40 
                                       +C+ C+ C evCP++ai  ++++e+  ++++++ yn+++ k+
  gi|313126882|ref|YP_004037152.1|  81 QCIYCRLCEEVCPVDAILLTQNFEFtaDTKDEFVYNKEQLKN 122
                                       6****************9996666511555555566666555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   8.7   2.1e-12   2.1e-09       4      57 ..      43      97 ..      40      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.1e-12
                           Fer4_21  4 dedkCigCgkCliaCedtshqaieidakt..vlkvvedeCvGCnlCssvCPvedci 57
                                       +++Ci C +C  +C++ ++q ++ d+++  ++++   +C+ C lC +vCPv d+i
  gi|313126882|ref|YP_004037152.1| 43 SQERCIWCRQCENVCPNDTIQIVQDDQRNgeQYNLHIGQCIYCRLCEEVCPV-DAI 97
                                      689********************877765115566689*************9.776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   3.0   3.1e-06    0.0031      23      51 .]      34      62 ..      28      62 .. 0.79
   2 !   31.3  11.3   1.7e-10   1.7e-07       1      51 []      46      97 ..      46      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.1e-06
                            Fer4_9 23 erkarlraaseeaCigCgaCveaCpkgai 51
                                      +r++ ++++s+e+Ci C++C+++Cp++ i
  gi|313126882|ref|YP_004037152.1| 34 PRFRGVHKFSQERCIWCRQCENVCPNDTI 62
                                      5566667777899************9865 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 1.7e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51
                                      +C+ C++C+++Cp+++++  +  + +   +++    +Ci C+ C+e+Cp +ai
  gi|313126882|ref|YP_004037152.1| 46 RCIWCRQCENVCPNDTIQIVQDDQRNGE-QYNLhiGQCIYCRLCEEVCPVDAI 97
                                      5****************98888888765.44446899*************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7  11.7   4.4e-09   4.4e-06       5      56 .]      43      93 ..      40      93 .. 0.80
   2 !   15.8   1.2   1.1e-05     0.011       8      29 ..      81     111 ..      75     126 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.4e-09
                           Fer4_10  5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       +++Ci C++C ++CP   t + +++ + ++e+ +  +++C+ c  C e+CP
  gi|313126882|ref|YP_004037152.1| 43 SQERCIWCRQCENVCPN-DTIQIVQDDQRNGEQYNLHIGQCIYCRLCEEVCP 93
                                      6799*************.4445555555556666668**************9 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.1e-05
                           Fer4_10   8 tCirCgkCvkaCPadl.........tsvgak 29 
                                       +Ci C+ C ++CP+d+         t++ + 
  gi|313126882|ref|YP_004037152.1|  81 QCIYCRLCEEVCPVDAilltqnfefTADTKD 111
                                       7************988777666665444444 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  12.1   8.4e-07   0.00083       3      64 ..      45      95 ..      43      96 .. 0.77
   2 !   16.3   0.8   9.9e-06    0.0099       4      27 ..      81     108 ..      78     127 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.4e-07
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      e+Ci C  C++ Cp  ++t      + +++++ +q + +      +++C  c+ C+evCpv+
  gi|313126882|ref|YP_004037152.1| 45 ERCIWCRQCENVCP--NDT--IQIVQDDQRNG-EQYNLH------IGQCIYCRLCEEVCPVD 95
                                      79***********9..333..44445555555.556666......8**************96 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.9e-06
                            Fer4_8   4 kCieCgaCqsaCp...vlrrtk.khlld 27 
                                       +Ci C +C++ Cp   +l +++ ++  d
  gi|313126882|ref|YP_004037152.1|  81 QCIYCRLCEEVCPvdaILLTQNfEFTAD 108
                                       6888888888888664333333333333 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   3.4     8e-05     0.079      44      59 ..      45      60 ..      35      62 .. 0.88
   2 !   17.0   1.5   6.4e-06    0.0063      38      58 ..      74      94 ..      61      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++Ci C++Ce +CP++
  gi|313126882|ref|YP_004037152.1| 45 ERCIWCRQCENVCPND 60
                                      79************97 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.4e-06
                           Fer4_17 38 ekeekaslCieCgeCerkCPq 58
                                      + +  +++Ci C++Ce++CP 
  gi|313126882|ref|YP_004037152.1| 74 QYNLHIGQCIYCRLCEEVCPV 94
                                      233589**************6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.7     6e-06    0.0059       4      20 ..      42      58 ..      41      64 .. 0.88
   2 !   13.2   4.5     7e-05     0.069       9      24 .]      82      97 ..      80      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6e-06
                            Fer4_6  4 idpdkCigCgdCvrvCP 20
                                      + +++Ci C+ C++vCP
  gi|313126882|ref|YP_004037152.1| 42 FSQERCIWCRQCENVCP 58
                                      789************** PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7e-05
                            Fer4_6  9 CigCgdCvrvCPegai 24
                                      Ci C+ C+ vCP +ai
  gi|313126882|ref|YP_004037152.1| 82 CIYCRLCEEVCPVDAI 97
                                      999**********998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.8   2.2e-06    0.0022       5      22 .]      42      59 ..      38      59 .. 0.88
   2 !   10.4   2.9   0.00059      0.59      10      21 ..      82      93 ..      79      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                      +  +rCi C+ C ++CP+
  gi|313126882|ref|YP_004037152.1| 42 FSQERCIWCRQCENVCPN 59
                                      6789*************5 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00059
                            Fer4_2 10 CigCgaCvsaCP 21
                                      Ci C+ C  +CP
  gi|313126882|ref|YP_004037152.1| 82 CIYCRLCEEVCP 93
                                      ************ PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   3.9   3.4e-06    0.0034       1      15 [.      44      58 ..      44      75 .. 0.89
   2 !    9.7   2.0    0.0013       1.3       4      16 ..      82      94 ..      69     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-06
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      qerCi C++C+++CP
  gi|313126882|ref|YP_004037152.1| 44 QERCIWCRQCENVCP 58
                                      79************* PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      Ci C+ C+ +CP+
  gi|313126882|ref|YP_004037152.1| 82 CIYCRLCEEVCPV 94
                                      999*********6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   3.9    0.0023       2.3       1      13 [.      47      59 ..      47      60 .. 0.85
   2 !   18.0   3.0   3.9e-06    0.0038       1      15 []      82      96 ..      82      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0023
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+ C++C++vCP+
  gi|313126882|ref|YP_004037152.1| 47 CIWCRQCENVCPN 59
                                      666*********7 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.9e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C++C+evCPv+A
  gi|313126882|ref|YP_004037152.1| 82 CIYCRLCEEVCPVDA 96
                                      9************98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.7   0.00042      0.42      56      77 ..      42      64 ..      31      77 .. 0.71
   2 !   12.2   1.9   0.00016      0.16      48      74 ..      69      95 ..      60      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                           Fer4_18 56 kgagdcidcescvkvcPtg.idi 77
                                       ++  ci c++c +vcP + i i
  gi|313126882|ref|YP_004037152.1| 42 FSQERCIWCRQCENVCPNDtIQI 64
                                      56778************742444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                           Fer4_18 48 kekeerkekgagdcidcescvkvcPtg 74
                                      +++ e+ +   g+ci c+ c +vcP++
  gi|313126882|ref|YP_004037152.1| 69 QRNGEQYNLHIGQCIYCRLCEEVCPVD 95
                                      444555677889*************85 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.3   0.00035      0.35       1      24 [.      46      69 ..      36      80 .. 0.76
   2 !    7.5   0.3    0.0073       7.3       1      16 [.      81      96 ..      81     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                           Fer4_22  1 rClsCgaCtlvCptCsCfdvedet 24
                                      rC+ C +C  vCp  +   v+d++
  gi|313126882|ref|YP_004037152.1| 46 RCIWCRQCENVCPNDTIQIVQDDQ 69
                                      688888888888887777777766 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0073
                           Fer4_22  1 rClsCgaCtlvCptCs 16
                                      +C+ C  C  vCp   
  gi|313126882|ref|YP_004037152.1| 81 QCIYCRLCEEVCPVDA 96
                                      6999999999999755 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.1   0.00019      0.19      42      90 ..      49      97 ..      38     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                      HS-THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--E CS
                            ETF_QO 42 yagpeqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqni 90
                                      +   ++ +CP    +iv+d++ +++++++   +C++C+ C+   p + i
  gi|313126882|ref|YP_004037152.1| 49 WCRQCENVCPNDTIQIVQDDQRNGEQYNLHIGQCIYCRLCEEVCPVDAI 97
                                      6677899*********************************988877766 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.5   0.00056      0.55       3      18 ..      44      59 ..      43      71 .. 0.93
   2 ?    6.3   4.1     0.014        14       5      17 ..      81      93 ..      80     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00056
                           Fer4_13  3 rdtCiacgaCvelaPd 18
                                      +++Ci c +C +++P+
  gi|313126882|ref|YP_004037152.1| 44 QERCIWCRQCENVCPN 59
                                      589************6 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                           Fer4_13  5 tCiacgaCvelaP 17
                                      +Ci c +C e++P
  gi|313126882|ref|YP_004037152.1| 81 QCIYCRLCEEVCP 93
                                      7***********9 PP

>> TNFR_c6  TNFR/NGFR cysteine-rich region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.3    0.0054       5.4      13      23 ..      44      55 ..      37      67 .. 0.55
   2 ?    6.8   0.5    0.0089       8.9      12      23 ..      78      90 ..      70     101 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0054
                                      C.SEEEEE-BGC CS
                           TNFR_c6 13 k.eClpCtrCpp 23
                                      + +C  C++C++
  gi|313126882|ref|YP_004037152.1| 44 QeRCIWCRQCEN 55
                                      224666666632 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0089
                                      TC.SEEEEE-BGC CS
                           TNFR_c6 12 sk.eClpCtrCpp 23
                                      +  +C  C+ C++
  gi|313126882|ref|YP_004037152.1| 78 HIgQCIYCRLCEE 90
                                      2235****99964 PP

>> zf_PR_Knuckle  PR zinc knuckle motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.3     0.023        23      11      23 ..      48      60 ..      42      62 .. 0.84
   2 ?    4.6   0.5     0.029        29      10      22 ..      82      94 ..      75      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.023
                     zf_PR_Knuckle 11 iWCtLCeksYpSd 23
                                      iWC  Ce   p d
  gi|313126882|ref|YP_004037152.1| 48 IWCRQCENVCPND 60
                                      9******987765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.029
                     zf_PR_Knuckle 10 siWCtLCeksYpS 22
                                       i+C LCe   p 
  gi|313126882|ref|YP_004037152.1| 82 CIYCRLCEEVCPV 94
                                      59******87665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 855.08
//
Query:       gi|313126883|ref|YP_004037153.1|  [L=353]
Description: NADH dehydrogenase subunit h [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-93  311.7  14.7    5.7e-93  311.5  14.7    1.0  1  NADHdh    NADH dehydrogenase
  ------ inclusion threshold ------
      0.018   15.5   0.2       0.04   14.4   0.2    1.6  1  PC_rep    Proteasome/cyclosome repeat


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.5  14.7   6.3e-97   5.7e-93       6     299 .]      38     346 ..      33     346 .. 0.96

  Alignments for each domain:
  == domain 1  score: 311.5 bits;  conditional E-value: 6.3e-97
                                       HHHHHHHHHH.HHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHC CS
                            NADHdh   6 llvvlllvva.lltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilall 81 
                                       +  +ll+ +a    +++Rk++A++ dR+  nrvGp+Gll  +aDa++ll Ke ++p+++d+  + ++p+++ ++all
  gi|313126883|ref|YP_004037153.1|  38 IANLLLIQTAvAGPWAKRKITAAFTDRIAVNRVGPFGLLVIVADAVRLLSKELVVPEGVDRPAWDIGPLVIPFSALL 114
                                       44445555565899*************************************************************** PP

                                       TTTTS-SSS..SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S CS
                            NADHdh  82 afaviPfge..vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllags 156
                                        faviP+g+   lad ++gl +++a ss++ +g++++G+ sn+kY+llG+lR++a  ++yE++l+++  +vv+++gs
  gi|313126883|ref|YP_004037153.1| 115 GFAVIPMGNgiHLADPETGLAFAFAASSIASIGLVMMGYGSNNKYSLLGGLRAIAANLAYEIPLVITGASVVIFTGS 191
                                       ********77899**************************************************************** PP

                                       S-HHHHHHCCCTT...........-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHH CS
                            NADHdh 157 lslseiveaqeei...........wfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalffl 222
                                       l++s+iv++q++            wf++++++af++f++a lae++r PFD+pea +E+vaG++tEYs++ f+l++l
  gi|313126883|ref|YP_004037153.1| 192 LQMSHIVAEQANPlltvagvtipqWFAFVNPFAFVLFVLANLAEVGRNPFDIPEAPTEIVAGYQTEYSSVYFVLIYL 268
                                       **********9879*************************************************************** PP

                                       HHHHHHHHHHHHHHHHCT.SS-HCCS.HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHHH CS
                            NADHdh 223 aeyanmvlvsalavllFlgGwllpfs.gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlllt 298
                                       +e+++++l  a+a++lFlgG ++pf  g++wf++K++++++++ w+r+++pRlR+dq++++gwk +l l++anl+lt
  gi|313126883|ref|YP_004037153.1| 269 GEFIHIFLGGAIAATLFLGGPAGPFLpGFVWFIIKIWAFYLFTQWMRSAIPRLRVDQFLDVGWKGMLVLSFANLVLT 345
                                       ************************999************************************************98 PP

                                       H CS
                            NADHdh 299 a 299
                                       a
  gi|313126883|ref|YP_004037153.1| 346 A 346
                                       5 PP

>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   4.4e-06      0.04       1      22 [.     141     162 ..     141     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-06
                                       HHHHHHHHHCTTSTCHHHHHHH CS
                            PC_rep   1 GAllALGlihaGsgneeaislL 22 
                                       ++++++Gl+++G+g++  +slL
  gi|313126883|ref|YP_004037153.1| 141 SSIASIGLVMMGYGSNNKYSLL 162
                                       589****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2344.19
//
Query:       gi|313126884|ref|YP_004037154.1|  [L=558]
Description: NADH dehydrogenase subunit d; NADH dehydrogenase subunit c [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-83  279.7   0.0      5e-82  275.0   0.0    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    3.8e-34  117.9   0.3    6.9e-34  117.1   0.3    1.4  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.021   14.3   0.0      0.047   13.2   0.0    1.6  1  Autoind_bind    Autoinducer binding domain


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.0   0.0   8.4e-86     5e-82       5     271 .]     308     558 .]     304     558 .] 0.93

  Alignments for each domain:
  == domain 1  score: 275.0 bits;  conditional E-value: 8.4e-86
                                       HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---T...THHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   5 ltvflyafreRekildlleevtGaRltasyiriGGvarDlpe...gllekikeflkelekkldeleklltknrifkk 78 
                                       +++f+ya+r+Re i ++le++tG+R++ +y+r+GGv +Dlpe   +++eki++fl+ l+++l+e+++l+++n+i++ 
  gi|313126884|ref|YP_004037154.1| 308 TAIFMYAMRDREIIQNILEDLTGQRMMFNYFRLGGVVWDLPEpreEFFEKIRDFLDDLPTALEEYHDLISSNEILQV 384
                                       4689*************************************98889******************************* PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                       Rt + gvl  e a ++g+tGpv+R+sG++yDlR+++pY  Ydeld+dv++++ +D y+R+lvr++E+++S+kIi+q+
  gi|313126884|ref|YP_004037154.1| 385 RTIDTGVLPPEVAKSYGATGPVARGSGIDYDLRRDDPYGYYDELDWDVVTEDGCDNYSRLLVRMREVEESAKIIQQC 461
                                       ***************************************************************************** PP

                                       HHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEE CS
                    Complex1_49kDa 156 leklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlki 232
                                       ++ l++ p   +++++    +++v ++++                + e+y+avEa+kGelg+y+  dg++kp r+ki
  gi|313126884|ref|YP_004037154.1| 462 VDLLEDWP--EDERTI----QSNVPRTLRP-------------EDDKEIYRAVEAAKGELGIYIRGDGTDKPGRFKI 519
                                       ****8654..333332....3344444432.............3468****************************** PP

                                       E-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 233 rapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       r+p+f nlq+l e+++ge++ D++a lgsldivlgevDR
  gi|313126884|ref|YP_004037154.1| 520 RSPCFSNLQTLGEMSNGEYIPDMIASLGSLDIVLGEVDR 558
                                       **************************************9 PP

>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.3   1.1e-37   6.9e-34       2     119 ..      46     161 ..      45     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.1e-37
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--.S-.-EEEEEE....-S-BEE--TTT-STH CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllsl.eknerirvkvevdeeepevpSvtdlfpga 77 
                                       v++p+d++e++  l+d  e gfd+ls++ta ++ e+r+e +yhl+s+ ++ ++++v v + +++p+ +S   +f++a
  gi|313126884|ref|YP_004037154.1|  46 VIRPDDVQETLFRLRD--EAGFDHLSCVTAEER-EDRYESIYHLTSYdDRTREVSVVVPAAKDNPHSQSGNAVFRTA 119
                                       789*************..599*********997.7************5445889999977889************** PP

                                       HHHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-TTSTTS--- CS
                    Complex1_30kDa  78 dwyEREayDmfGivfeghpdlrrillpedfeghPLRkdfpls 119
                                       dw+EREayD++Gi++++hpdlrrillpe+++ghPL  df+ +
  gi|313126884|ref|YP_004037154.1| 120 DWHEREAYDLVGIEYDDHPDLRRILLPETWQGHPLSMDFDQD 161
                                       ***************************************876 PP

>> Autoind_bind  Autoinducer binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.8e-06     0.047       2      45 ..      49      92 ..      48      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-06
                                      HHHHHHHHHHHHHHTTCSEEEEEEEETTSCESCEEEEEESS-HH CS
                      Autoind_bind  2 eeelfdlltrlaaalGfdrfaygarapskdsaedvlllsnyPae 45
                                      ++++ ++l rl+++ Gfd+++++  + ++d+ e+++ l++y + 
  gi|313126884|ref|YP_004037154.1| 49 PDDVQETLFRLRDEAGFDHLSCVTAEEREDRYESIYHLTSYDDR 92
                                      68999************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3834.95
//
Query:       gi|313126885|ref|YP_004037155.1|  [L=236]
Description: NADH dehydrogenase subunit b [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-21   77.2   0.2    1.5e-21   76.6   0.2    1.2  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.2   8.3e-26   1.5e-21      32     131 .]      98     183 ..      71     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 8.3e-26
                                       S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S CS
                       Oxidored_q6  32 adskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevv 108
                                       a         + ++adv++v G++++k ++++++++++++++k+v+ +G+C ++GG ++ +   +v   +++++ev+
  gi|313126885|ref|YP_004037155.1|  98 A---------SPRQADVIIVPGTIVSKFAPRMKRVYDQMPEPKFVVGMGSCTVSGGPFQEGY--NV---IKGAEEVI 160
                                       2.........2349********************************************5555..33...46899*** PP

                                       -E.EEE-SSS--HHHHHHHHHHH CS
                       Oxidored_q6 109 pvdinipGCPphpeailetllal 131
                                       pvdi++pGCPp+pea+++++++l
  gi|313126885|ref|YP_004037155.1| 161 PVDIHVPGCPPRPEALIYGVAKL 183
                                       *****************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1698.43
//
Query:       gi|313126886|ref|YP_004037156.1|  [L=138]
Description: NADH:ubiquinone oxidoreductase subunit 3 (chain a) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.3e-32  109.7   0.3    7.7e-32  109.4   0.3    1.1  1  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.3   4.3e-36   7.7e-32       3      99 .]      20     122 ..      18     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 4.3e-36
                                       HHHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST........HHHH CS
                       Oxidored_q4   3 lllllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkel......glfg 73 
                                        ++++sa+l+p+ p++ k+++YE+G  p+g+ar++f++++y+vallF++FD+e+v++fpw+v ++++       ++ 
  gi|313126886|ref|YP_004037156.1|  20 GMMAVSAILRPSVPEQGKSATYESGEIPTGTARVQFNIQYYMVALLFVVFDIETVLIFPWTVIYRSAlsqgadLATV 96 
                                       6899***********************************************************99886654333555 PP

                                       HHHHHHHHHHHHHHHHHHHHH-S-XX CS
                       Oxidored_q4  74 liemllFllillvglvYewkkgaLeW 99 
                                       l+ ml+F+++l+vgl+++w++ga+eW
  gi|313126886|ref|YP_004037156.1|  97 LLPMLIFIGVLVVGLAWAWRNGAVEW 122
                                       9************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 890.57
//
Query:       gi|313126887|ref|YP_004037157.1|  [L=211]
Description: phosphoribosylaminoimidazole carboxylase, pure protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-50  169.1   0.0    5.9e-50  168.7   0.0    1.1  1  AIRC      AIR carboxylase
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.18   11.7   0.0    1.3  1  PUB       PUB domain


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.7   0.0   6.5e-54   5.9e-50       1     145 [.      32     186 ..      32     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 6.5e-54
                                       EEEEEESSGGGHHHHHHHHHHHHHTT-..............EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEE CS
                              AIRC   1 kVgiimGSdsDlevmkkaaeilkelgv..............eyevrvvSahrtpeelleyaeeaeerglkviIagAG 63 
                                       +VgiimGSdsDl+vm +a+e+l+elg+              +ye++vvSahrtp+ +++y ++a +rgl+viIagAG
  gi|313126887|ref|YP_004037157.1|  32 DVGIIMGSDSDLDVMCGAHEALDELGFeeqtdftdapdarfTYETYVVSAHRTPDLMYAYGQTAMDRGLDVIIAGAG 108
                                       69*************************************************************************** PP

                                       S.S--HHHHHHHHS.SS-EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHH CS
                              AIRC  64 g.aahLpgvvaslt.tlPVigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekl 138
                                       g +a+Lp+++as++ +lPV+gvPv++      +s+ S++ mP+g+p+++v++gk+ nAal+A+q+la++++ l+++l
  gi|313126887|ref|YP_004037157.1| 109 GkSADLPNMTASIAyPLPVVGVPVQE------KSVDSVIGMPTGAPIVAVDAGKSFNAALSAVQMLAREHDVLEDRL 179
                                       99***********99***********......9******************************************** PP

                                       HHHHHHH CS
                              AIRC 139 eeyreel 145
                                        ey+e+l
  gi|313126887|ref|YP_004037157.1| 180 LEYHESL 186
                                       ***9975 PP

>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.1e-05      0.18      41      64 ..      43      69 ..      40      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                               PUB 41 vlplegavelLealGFeekne...eee 64
                                      +++ +ga+e L++lGFee+++   +++
  gi|313126887|ref|YP_004037157.1| 43 LDVMCGAHEALDELGFEEQTDftdAPD 69
                                      67899*************999776333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1608.78
//
Query:       gi|313126888|ref|YP_004037158.1|  [L=383]
Description: 5-(carboxyamino)imidazole ribonucleotide synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-50  169.7   0.0    5.7e-50  169.2   0.0    1.2  1  ATP-grasp        ATP-grasp domain
    1.6e-18   66.1   0.0    3.4e-18   65.1   0.0    1.6  1  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
    7.6e-08   32.6   0.0      1e-07   32.1   0.0    1.2  1  ATP-grasp_3      ATP-grasp domain
    5.6e-07   29.1   0.0    1.2e-06   28.0   0.0    1.6  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      5e-05   22.9   0.1    0.00021   20.9   0.1    2.0  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
     0.0015   19.0   0.0     0.0037   17.8   0.0    1.7  1  XdhC_C           XdhC Rossmann domain
     0.0097   15.8   0.1       0.02   14.8   0.0    1.6  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.053   14.1   0.1        0.2   12.2   0.0    2.1  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   0.0   2.5e-53   5.7e-50       2     171 .]     116     282 ..     115     282 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 2.5e-53
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEE CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekEl 78 
                                       +++g+pvp+f  v+++e+l++a++e+g  v++Kar++gydG+G+  vr+e+++e+al+a+ +++ ++E fv+f +El
  gi|313126888|ref|YP_004037158.1| 116 DDAGVPVPPFRRVDDAEDLRAALDEFGS-VMLKARTGGYDGRGNVPVRDESEVEDALDAV-GGPAMAEAFVDFAREL 190
                                       6789***********************7.679****************************.9*************** PP

                                       EEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEE CS
                         ATP-grasp  79 svlvvrsaeGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnE 155
                                       sv++v+  +  ++++pv e+++e +ilr+ v+pa+ +++ +++a e+a+++++ L+g Gvf++ElF+++dg++ vnE
  gi|313126888|ref|YP_004037158.1| 191 SVIAVQGDDE-VRTFPVGENIHEAEILRETVVPARTTDEVLARADEVARDVLSVLDGRGVFGIELFETQDGDISVNE 266
                                       *****98775.****************************************************************** PP

                                       EESS--GGGGGHHHHB CS
                         ATP-grasp 156 lapRpHnsGhvtldaa 171
                                       +apRpHnsGh+t+++a
  gi|313126888|ref|YP_004037158.1| 267 IAPRPHNSGHWTIEGA 282
                                       *************985 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   1.5e-21   3.4e-18       1      54 [.     308     367 ..     308     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.5e-21
                            PurK_C   1 avMvNlLGedae......ekleellaipgahlHlYgKeearpgRKmGHitvvgdsaeele 54 
                                       +vM N+LG+ +e       + e++la +ga+lH+YgK+earp RKmGH+tv+gd+ ++++
  gi|313126888|ref|YP_004037158.1| 308 TVMANVLGTVDEsrpatlGHVESVLAAEGASLHWYGKDEARPLRKMGHLTVIGDDGADID 367
                                       79*********955555544445*******************************988875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   4.7e-11     1e-07       1     159 [.     105     272 ..     105     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.7e-11
                                       HTSHHHHHHHHTTT.S---..........-EESS--SSSEEEEESS-.------B--SS--TTE..........EEE CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP......tkleaeeleeeekklvvKprdG.aggesvrvveekeeaeaaieeve...lvq 67 
                                       ++dKl   ++L++agv+vP      +      +  e  ++ +K r+G  +g +++ v+++ e e a++ v    ++ 
  gi|313126888|ref|YP_004037158.1| 105 IEDKLVQKRALDDAGVPVPpfrrvdDAEDLRAALDEFGSVMLKARTGgYDGRGNVPVRDESEVEDALDAVGgpaMAE 181
                                       58*****************9976643333344455588899999986269***********9999999887888*** PP

                                       E---.SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEE CS
                       ATP-grasp_3  68 efie.GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekleglaGyvGvD 141
                                       +f++  ++lSv ++    +v+++ v +++ e     ++ +  v+p++t++    ++ e+a++v++ l + +G++G++
  gi|313126888|ref|YP_004037158.1| 182 AFVDfARELSVIAVQGDDEVRTFPVGENIHEA----EILRETVVPARTTDevLARADEVARDVLSVL-DGRGVFGIE 253
                                       ***9789**********************988....889999*****99855678899*********.99******* PP

                                       EE.ESS.SEEEEEEESS-- CS
                       ATP-grasp_3 142 lv.lkdeepyviEvNPRlt 159
                                       l   +d+++ v E+ PR+ 
  gi|313126888|ref|YP_004037158.1| 254 LFeTQDGDISVNEIAPRPH 272
                                       *9566799*********96 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   5.6e-10   1.2e-06      33     103 ..       4      80 ..       1      83 [. 0.79
   2 ?   -3.7   0.0       2.9   6.5e+03      79      95 ..     220     236 ..     210     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 5.6e-10
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH....CHHHHTC..EECSHHHHHHH-SEEEE-S--ST CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee....eeeelgv..elvsleellaesDivslhlpltp 103
                                       ++ g+t+Gi+G G++G+ +a+ ++++g++v++ d++++  +    +++ +g   + + + el +++D+++  + l +
  gi|313126888|ref|YP_004037158.1|   4 TVPGSTLGIVGGGQLGRMLAEAAAPLGVEVVVLDPTPDCPAapvvRDQIVGDfdDPEAFRELASRADVLTFEIELAD 80 
                                       5779********************************9954445442222222235668999********99888765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.9
                                       TCEECSHHHHHHH-SEE CS
                      2-Hacid_dh_C  79 gvelvsleellaesDiv 95 
                                        v   + +e+la++D v
  gi|313126888|ref|YP_004037158.1| 220 VVPARTTDEVLARADEV 236
                                       45566788888888866 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   9.5e-08   0.00021      74     176 ..     177     271 ..     115     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9.5e-08
                                       CEEEEE--.ESEEEEE.EEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHH CS
                   Dala_Dala_lig_C  74 kvlvEeai.egreiev.avlgneklevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkayka 148
                                         + E+++  +re+ v av g++++++++vge + + ++            + +vpa+ ++ev ++  e+a ++ ++
  gi|313126888|ref|YP_004037158.1| 177 PAMAEAFVdFARELSViAVQGDDEVRTFPVGENIHEAEIL----------RETVVPARTTDEVLARADEVARDVLSV 243
                                       5677888866888875478888888888888888777765..........3679*********************** PP

                                       TT--SEEEEEEEEETTTEEEEEEEESS- CS
                   Dala_Dala_lig_C 149 ldlrGlaRvDfflteegeivlnEvNtlP 176
                                       ld+rG+  + +f t++g+i +nE+ + P
  gi|313126888|ref|YP_004037158.1| 244 LDGRGVFGIELFETQDGDISVNEIAPRP 271
                                       ************************8877 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.6e-06    0.0037       2      61 ..      11      84 ..      10     101 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG..............-GGG-TT-SE-EEEE--S-HHHHHHHH CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefa..............tkerfpeadetavvvlthdhklDaeal 61
                                       i+G+g+ ++ la+ aa lg++v+v+dp ++                ++e f e ++ a v+  +    D e+l
  gi|313126888|ref|YP_004037158.1| 11 GIVGGGQLGRMLAEAAAPLGVEVVVLDPTPDCPaapvvrdqivgdfdDPEAFRELASRADVLTFEIELADSELL 84
                                      69***************************975545666555555555455554444344444444445555555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   9.1e-06      0.02       2      34 ..      10      42 ..       9      65 .. 0.92
   2 ?   -3.6   0.1         4     9e+03     149     169 ..     219     239 ..     216     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.1e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      ++++G G++G+ +a+++a  g+eVv++d +++ 
  gi|313126888|ref|YP_004037158.1| 10 LGIVGGGQLGRMLAEAAAPLGVEVVVLDPTPDC 42
                                      79**************************98875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4
                                       EEE-TT--HHHHHHHHHHHHH CS
                           3HCDH_N 149 vvrgekTseetvatvvelakk 169
                                        v  ++T +e++a++ e+a++
  gi|313126888|ref|YP_004037158.1| 219 TVVPARTTDEVLARADEVARD 239
                                       556677888899998888775 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     9e-05       0.2       3      30 ..      11      38 ..       9      44 .. 0.90
   2 ?   -3.8   0.0         8   1.8e+04      14      29 ..     179     194 ..     178     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                                      EEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvver 30
                                       +vGgG +g +lA+a+a lg +V v++ 
  gi|313126888|ref|YP_004037158.1| 11 GIVGGGQLGRMLAEAAAPLGVEVVVLDP 38
                                      69*********************99875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8
                                       HHHHHHHTTSEEEEEE CS
                         Pyr_redox  14 lAgalaelgkkVtvve 29 
                                       +A+a+ +++ + +v+ 
  gi|313126888|ref|YP_004037158.1| 179 MAEAFVDFARELSVIA 194
                                       6888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2798.73
//
Query:       gi|313126889|ref|YP_004037159.1|  [L=616]
Description: membrane-bound mannosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-14   53.3   5.5    3.5e-14   53.3   5.5    2.6  2  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
  ------ inclusion threshold ------
      0.016   15.1   1.8        1.3    8.9   0.0    2.7  3  EptA_B_N  Phosphoethanolamine transferase EptA/EptB


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   5.5   3.9e-18   3.5e-14       2     138 ..      95     231 ..      94     235 .. 0.92
   2 ?   -0.1   0.3      0.11   9.9e+02     122     154 ..     410     445 ..     402     454 .. 0.55

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 3.9e-18
                             PMT_2   2 hPPliawllalftklfgfselairlvsalagvltilllyllarrlfg.kraallaalllavvplfvalsalftpdap 77 
                                       h P+ + +   +++++  s++ +r++ al+g l  l+ +l  +rl + +++al+++l l+  pl+v++s+ +++d++
  gi|313126889|ref|YP_004037159.1|  95 HGPFLPVVNDWLFAIAPVSDFLARFPVALIGGLFPLCAWLFRERLSNvEVVALAGVLALN--PLMVYYSRFMRNDVL 169
                                       8899999999**********************************9997777777776665..688************ PP

                             PMT_2  78 lvllwalalylllraleknklkywllagvlfGlgflsKytaallliaall..yllisarrilk 138
                                         ++ ++al +++r  +++kl+y + a++++Gl+f +K +a+++++ +l   +ll++  r+lk
  gi|313126889|ref|YP_004037159.1| 170 VAAFSLFALGFIVRGFDTGKLRYAFPAAASLGLAFTTKENALVYVLCFLGagALLAD-HRLLK 231
                                       **********************************************98889999999.77776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                             PMT_2 122 liaall...yllisarrilkekkpylalllalllfs 154
                                       +i+a++   +++ sar  l ++ +  ++l a+++ +
  gi|313126889|ref|YP_004037159.1| 410 AIPAAVgiaFIVESARDALSTDDAVSVGLAAIVVLA 445
                                       333333343344445557777777665555555444 PP

>> EptA_B_N  Phosphoethanolamine transferase EptA/EptB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2      0.65   5.8e+03     110     128 ..     149     167 ..     134     181 .. 0.58
   2 ?    4.7   0.1    0.0029        26      72     119 ..     242     289 ..     239     291 .. 0.91
   3 ?    8.9   0.0   0.00015       1.3      65     147 ..     399     484 ..     393     488 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.65
                                       HHHHHHTTHHHHHHHHHH- CS
                          EptA_B_N 110 ivlvallfykdyaslfRnn 128
                                        vl++      y+ ++Rn+
  gi|313126889|ref|YP_004037159.1| 149 GVLALNPLMVYYSRFMRND 167
                                       2233333455566666664 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0029
                                       HHHTHHHHHHHHH-EE----HHHHHHHHHHHHHHHHHHHHHHHHTTHH CS
                          EptA_B_N  72 lllgvlPallllrvkikrksllkellkrlalllvallvivlvallfyk 119
                                       +++g  Pa++  rv+ + +s+ + +++ +++l+ a++++ +v+++fy 
  gi|313126889|ref|YP_004037159.1| 242 VVFGQWPAAIRRRVRNHGTSTSQGWVRVFGTLVGAFALFWAVFIFFYA 289
                                       578999999999999999999999*9999***************9995 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHTHHHHHHHHH-EE.----HHHH..HHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH-TTGGGGSTTH CS
                          EptA_B_N  65 lklllyllllgvlPallllrvki.krksllke..llkrlalllvallvivlvallfykdyaslfRnnkelrylinPt 138
                                       ++ ++++++  ++Pa++ ++  + + ++ l++   ++  + ++v l+ +++va+++ + + s+  +++++ + + P+
  gi|313126889|ref|YP_004037159.1| 399 PWAAIHVVVPLAIPAAVGIAFIVeSARDALSTddAVSVGLAAIVVLASVGGVAVANAEYFNSASNEDRQVLQWAQPS 475
                                       6778899999999998877766665555554443555559999999******************************* PP

                                       HHHHHHHHH CS
                          EptA_B_N 139 nyiyslvky 147
                                       n +  +++ 
  gi|313126889|ref|YP_004037159.1| 476 NDLKPTMQK 484
                                       998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4470.44
//
Query:       gi|313126890|ref|YP_004037160.1|  [L=134]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-33  113.7   1.0    6.1e-33  113.6   1.0    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
       0.13   12.0   0.7        4.3    7.1   0.1    2.4  2  FMN_red        NADPH-dependent FMN reductase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.6   1.0   6.8e-37   6.1e-33       3     139 ..       3     132 ..       1     134 [] 0.94

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 6.8e-37
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHH CS
                     DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphf 79 
                                        +++Vva+fn+++t+++ ++a+d+++e+ +  +  dv +VPG+++ plaa++la++ + +dav ++G+++ G+t+h+
  gi|313126890|ref|YP_004037160.1|   3 TLGLVVAEFNSSVTEQMADAARDAAAERDA--DVSDVLHVPGVYDSPLAADRLARR-QDIDAVAVVGAIVTGDTSHD 76 
                                       5799*************************7..599********************5.447***************** PP

                                       HHHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHHH CS
                     DMRL_synthase  80 eyvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaalemanl 139
                                        ++ +a++++l+++sl++++Pv+fgv  +  + ++a+er+      kG+ea++aa++m+++
  gi|313126890|ref|YP_004037160.1|  77 RVIGDATAQALTDISLERDKPVTFGVSGPGqSGAEARERV-----SKGAEAVNAAVDMVEV 132
                                       *****************************98889999999.....9************987 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1   0.00048       4.3      13      45 ..      13      47 ..       3      70 .. 0.75
   2 ?    3.4   0.1    0.0066        59     108     130 ..      94     115 ..      48     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00048
                                      T-HHHHHHHHHHCCT-T.T-CE.EEEETTTS..-- CS
                           FMN_red 13 gsntrklaewaaealkeagaev.elidladl.ilp 45
                                       s t+++a++a +a++e++a+v +++++ +  + p
  gi|313126890|ref|YP_004037160.1| 13 SSVTEQMADAARDAAAERDADVsDVLHVPGVyDSP 47
                                      799**************999994444655554555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0066
                                       TT-EEEEEEE-SSTTTTHHHHHH CS
                           FMN_red 108 rgKpvalvavgggrrgglraeeq 130
                                       r+Kpv + + g+g++g+ +a+e 
  gi|313126890|ref|YP_004037160.1|  94 RDKPVTFGVSGPGQSGA-EARER 115
                                       58999999888775555.55444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 987.82
//
Query:       gi|313126891|ref|YP_004037161.1|  [L=382]
Description: aspartate/tyrosine/aromatic aminotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-63  215.0   0.0      2e-63  214.8   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.3e-05   23.9   0.0    2.4e-05   23.1   0.0    1.4  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00035   19.7   0.0    0.00061   18.8   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    0.00037   19.9   0.0    0.00069   19.0   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.034   13.5   0.1      0.057   12.7   0.1    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.8   0.0   5.4e-67     2e-63       2     363 .]      33     376 ..      32     376 .. 0.92

  Alignments for each domain:
  == domain 1  score: 214.8 bits;  conditional E-value: 5.4e-67
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dv++L+++e+++     t+++++ a ++  ++  + + y+ + g  el+ea+a+ l+   +++ +++ +v+v++G +
  gi|313126891|ref|YP_004037161.1|  33 DVVDLSVGEPDFP----TPQNIIDAGQD--AMDAGHTGYTSSNGIRELREAIAEKLR-ADGVDADAD-EVIVTPGGK 101
                                       89**********9....***********..8888999********************.99*******.9******** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-..HHHHHHHHTTHHCTTETEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhld..lealeealkeapegnkktkvil 153
                                       +++   ++ l ++ gde+++ dp + sy+ + +lsgg + r+ l  + df+l   l++l ea+++       t +++
  gi|313126891|ref|YP_004037161.1| 102 QALFETFQTL-IDDGDEVVLLDPAWVSYEAMTKLSGGSLNRVDLA-PYDFQLEpaLDDLAEAVSN------DTELLV 170
                                       ***9999999.9*******************************77.5555543225666666665......67**** PP

                                       EESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG- CS
                     Aminotran_1_2 154 vesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeR 229
                                       v+sp+NPtG+v++ + le + dla ++ + +++De+Y+   +g  ++++ +  ++   + +++v+++sKa++++G+R
  gi|313126891|ref|YP_004037161.1| 171 VNSPSNPTGAVYSDAALEGVRDLAVEHDITVISDEMYEQITYG-VEPTS-LGSLDGMADrTVTVNGFSKAYSMTGWR 245
                                       *******************************************.34444.555555555689*************** PP

                                       EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSC CS
                     Aminotran_1_2 230 vGyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqs 304
                                       +Gy+ + ++++sq++kl+++  s   + +q+a  +a+ ++++    ++emr+ + +rr+ l+d +ae g++v   ++
  gi|313126891|ref|YP_004037161.1| 246 LGYVHAPEELISQAAKLHSHSVScaVNFVQRAGIEAITNTDD---AVTEMRDAFRERRDMLVDLFAEHGVDVPVGDG 319
                                       ***********************88999***********997...9******************************* PP

                                       SSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 305 gmflltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleelveal 363
                                       +++++  +++  + + ++  +e  +v+ +pg+ f+ pg  Ri++ + +ee l+e+ve+l
  gi|313126891|ref|YP_004037161.1| 320 AFYMMLPVDED-DAAWCEGAIEDAHVATVPGSAFGSPGYARISY-AASEERLREAVERL 376
                                       *********98.66666679999*********************.99**********97 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.6e-09   2.4e-05      67     177 ..      91     208 ..      73     234 .. 0.81
   2 ?   -3.7   0.0      0.91   3.3e+03      91     138 ..     252     300 ..     245     304 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.6e-09
                                       -SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTS...SHHHHHHHHHTHHHTTCE.EEEESTTSHHHHHHHCCTTEE CS
                   Cys_Met_Meta_PP  67 geaalavssGmaAiaaailallkaGdeivvsddl...Yggtqrllkkvlkklgie.vkfvdtsdleelekaikentk 139
                                       ++++++++ G  A++ ++++l+  Gde+v+ d +   Y+   +l    l+++ +  ++f     l++l++a+++ t+
  gi|313126891|ref|YP_004037161.1|  91 ADEVIVTPGGKQALFETFQTLIDDGDEVVLLDPAwvsYEAMTKLSGGSLNRVDLApYDFQLEPALDDLAEAVSNDTE 167
                                       68899*************************998723366666666667777766513444456899*********** PP

                                       EEEEESS-TTTT---.-..HHHHHHHHHHTT-EEEEEGTTT CS
                   Cys_Met_Meta_PP 140 lvylEtptnpllkvv.D..iekiaklakkagvlvvvDntfa 177
                                       l+ + +p+np+  v  D  +e + +la +++++v+ D  + 
  gi|313126891|ref|YP_004037161.1| 168 LLVVNSPSNPTGAVYsDaaLEGVRDLAVEHDITVISDEMYE 208
                                       ***********88853344899999******9999998765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.91
                                       TEEEEEE.STSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTE CS
                   Cys_Met_Meta_PP  91 Gdeivvs.ddlYggtqrllkkvlkklgievkfvdtsdleelekaikent 138
                                        +e++++  +l++ + +   +++++ gie+     + + e++ a++e+ 
  gi|313126891|ref|YP_004037161.1| 252 PEELISQaAKLHSHSVSCAVNFVQRAGIEAITNTDDAVTEMRDAFRERR 300
                                       5555554135666666667777788888877777777777777777765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.7e-07   0.00061      35     175 ..      61     204 ..      45     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-07
                                       SHHHHHHHHHHHHHHHHHHHHHT-S....TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHH CS
                       Aminotran_5  35 hhlgkeatkaveearekvaelinae....seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqe 107
                                       +h g   ++ ++e re +ae + a+    +++e+i+t G+ +a+    ++l   +++gde+v+ +    +   ++ +
  gi|313126891|ref|YP_004037161.1|  61 GHTGYTSSNGIRELREAIAEKLRADgvdaDADEVIVTPGGKQALFETFQTL---IDDGDEVVLLDPAWVSYE-AMTK 133
                                       5666677788888888888888774333367********************...9********998777766.9999 PP

                                       HHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB...--HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 108 lakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGti...qpveeigklakkkgalvlvD 175
                                       l+     +v+ +p d + e  ld+l+++++++t+l+ ++  sn tG +     +e + +la ++++ v+ D
  gi|313126891|ref|YP_004037161.1| 134 LSGGSLNRVDLAPYDFQLEPALDDLAEAVSNDTELLVVNSPSNPTGAVysdAALEGVRDLAVEHDITVISD 204
                                       99899999**************************************9622234666677777777776665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.9e-07   0.00069      16     167 ..      52     204 ..      44     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-07
                                       HHH.HCS----CCCT--HHHHHHHHHHHH.......HTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHH CS
                   Beta_elim_lyase  16 daq.aaamlGdesYgedktvnrLedavae.......lfgkeaalfvpqGtaAnsillkillqrgeevivtepahihf 84 
                                       da   a+ +G+  Y  ++++++L +a+ae        ++++ ++ +p G +A    +++l+  g+ev++ +pa +  
  gi|313126891|ref|YP_004037161.1|  52 DAGqDAMDAGHTGYTSSNGIRELREAIAEklradgvDADADEVIVTPGGKQALFETFQTLIDDGDEVVLLDPAWVSY 128
                                       44447899*********************999998888999999****************************97764 PP

                                       SSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT CS
                   Beta_elim_lyase  85 detgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkyg 161
                                           a+  l+g  l+ ++ +   +++le   + ++e  +  ++++l+++    n   G v+s + l+ v+++a +++
  gi|313126891|ref|YP_004037161.1| 129 ---EAMTKLSGGSLNRVDLAP-YDFQLEPALDDLAEAVS--NDTELLVVNSPSNP-TGAVYSDAALEGVRDLAVEHD 198
                                       ...467777888888888888.67777755555555333..57888888888884.8******************** PP

                                       -EEEEE CS
                   Beta_elim_lyase 162 iplhlD 167
                                       i+++ D
  gi|313126891|ref|YP_004037161.1| 199 ITVISD 204
                                       ***988 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.6e-05     0.057      38     144 ..      91     204 ..      48     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                       -SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GG..GCGGG--TTE CS
                   DegT_DnrJ_EryC1  38 vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpa..aieaaitert 112
                                       ++ +i +  G +Al  + + l +++gdeV+     +v+  ++   +g     vD  p +++++pa  ++++a+ + t
  gi|313126891|ref|YP_004037161.1|  91 ADEVIVTPGGKQALFETFQTL-IDDGDEVVLLDPAWVSYEAMTKLSGGSLNRVDLAPYDFQLEPAldDLAEAVSNDT 166
                                       456777778888888888776.788*************************************9963379******** PP

                                       EEEE...EB-GGGB-...--HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 113 kaIl...pVhlyGqv...admdalkaiaakhglkvieD 144
                                          +   p +  G+v   a ++ ++++a +h++ vi+D
  gi|313126891|ref|YP_004037161.1| 167 ELLVvnsPSNPTGAVysdAALEGVRDLAVEHDITVISD 204
                                       876523345566766333589***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2907.17
//
Query:       gi|313126892|ref|YP_004037162.1|  [L=385]
Description: lipoprotein release ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-23   83.4   2.9    2.7e-23   83.4   2.9    2.4  3  MacB_PCD         MacB-like periplasmic core domain
    4.2e-11   43.2   2.6    4.2e-11   43.2   2.6    2.9  3  FtsX             FtsX-like permease family
  ------ inclusion threshold ------
       0.18   10.6   1.2        2.4    6.8   1.2    2.3  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   2.9   4.5e-27   2.7e-23       1     194 [.      28     227 ..      28     228 .. 0.75
   2 ?   -1.4   0.9      0.43   2.6e+03       9      38 ..     259     288 ..     255     317 .. 0.75
   3 ?   -3.4   2.1       1.8   1.1e+04       6      20 ..     352     366 ..     349     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 4.5e-27
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk..gsgeslsdpdvealrrevpve.avapvv. 73 
                                       s+l+ LGi+iGv a+ +++++g++l+a  ++q+ d gn ++++p++  g  e+l+++dv ++rr v  e  v+pv  
  gi|313126892|ref|YP_004037162.1|  28 SALAALGIIIGVLAIASLGMFGTTLRAGATDQLGDIGNGIRISPNAqeG-YERLTERDVVDIRR-VADEgTVVPVRt 102
                                       89************************************99999997533.33467777744544.222225788765 PP

                          MacB_PCD  74 ...tvrgggsgeeevtvvgvdpdyfkvfgl.klaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl..kpft 143
                                          + ++g+++ + +tv+g d +  +++   +   Gr   +      ++++++g+++a++l    G +i++  ++f+
  gi|313126892|ref|YP_004037162.1| 103 rhsELSYGDKK-TVSTVYGID-NPGEMYEAtD---GRA--PGR---LHRGALVGSRVADQLEiESGNRITVgnQSFR 169
                                       66533566543.235899999.7777776634...753..322...5688**********88*99************ PP

                          MacB_PCD 144 VvGvledppgsgsalg.ddavylplttl.......qrrsitvrlkdgadleaaaaelek 194
                                       V+Gvle+++g +s l+ + av++p++++        +++++v++ +++ ++++a ++++
  gi|313126892|ref|YP_004037162.1| 170 VIGVLEEQDG-FSLLNpNGAVMIPVKSFsgynygsGYSQVVVQTPSSEAANETAVAVRQ 227
                                       *****87644.445556999****555543354444777*******9999998877765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.43
                          MacB_PCD   9 aiGvaaviaivslgeglqasvlsqisdlgn 38 
                                        iGv++++++v+ ++ l+ ++ s+i+  + 
  gi|313126892|ref|YP_004037162.1| 259 LIGVGSISLVVAGVSILNVMLMSTIERRQE 288
                                       689999999988777777666666665544 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.8
                          MacB_PCD   6 LGiaiGvaaviaivs 20 
                                       +G+a+G++ v++++s
  gi|313126892|ref|YP_004037162.1| 352 IGLAVGFGIVTSVLS 366
                                       79*********9986 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.16   9.4e+02      29      42 ..      31      43 ..      22      74 .. 0.53
   2 ?    1.0   0.1     0.097   5.8e+02      64      83 ..     249     268 ..     186     282 .. 0.53
   3 !   43.2   2.6   7.1e-15   4.2e-11       1      93 [.     286     376 ..     286     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.16
                              FtsX 29 tlvalviGlglgll 42
                                      ++++++iG+ l+++
  gi|313126892|ref|YP_004037162.1| 31 AALGIIIGV-LAIA 43
                                      444444441.1111 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.097
                              FtsX  64 idlitvliiivlllllalla 83 
                                        +++ +l ++++++  ++l+
  gi|313126892|ref|YP_004037162.1| 249 NQFFGILNAFLIGVGSISLV 268
                                       33333333444444333333 PP

  == domain 3  score: 43.2 bits;  conditional E-value: 7.1e-15
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvl.iiivll 76 
                                       ++eig+lra+G+ k +v++++l e+ l++lv+ ++G +l+++a  +l++v+ s+   + l++  + + ++ ++++++
  gi|313126892|ref|YP_004037162.1| 286 RQEIGVLRAVGVQKLDVVRMILAEAGLLGLVGGFFGAILAVFAGLILNQVVISN---PWLTFAPQNLLYIgLAVGFG 359
                                       79*************************************************999...77777776655551567799 PP

                              FtsX  77 lllallagllsiskilk 93 
                                       +++ +l+gl++++k++ 
  gi|313126892|ref|YP_004037162.1| 360 IVTSVLSGLYPAWKAAT 376
                                       9999**********976 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.2    0.0004       2.4     383     439 ..     310     374 ..       4     381 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0004
                           DUF2207 383 lsalglgliilglilillallllvll...............lvfllilllillliaiivlllfsrllgrrte 439
                                        ++lgl+++++g il+++       +               + + ++l ++l++ + iv+ ++s+l +++++
  gi|313126892|ref|YP_004037162.1| 310 AGLLGLVGGFFGAILAVF-------AglilnqvvisnpwltFAPQNLLYIGLAVGFGIVTSVLSGLYPAWKA 374
                                       333333333333333333.......13333555888889888888888888888888888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2711.98
//
Query:       gi|313126893|ref|YP_004037163.1|  [L=231]
Description: antimicrobial peptide ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-35  122.3   0.0    2.7e-35  121.9   0.0    1.2  1  ABC_tran     ABC transporter
    7.5e-07   28.8   0.2    5.7e-05   22.7   0.2    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    2.3e-05   24.4   0.5      0.046   13.5   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00021   21.0   0.0    0.00036   20.2   0.0    1.3  1  AAA_29       P-loop containing region of AAA domain
    0.00051   20.0   0.0    0.00081   19.3   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
     0.0016   18.8   0.1      0.003   17.9   0.1    1.5  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.013   16.0   0.2      0.031   14.8   0.0    1.7  2  AAA_23       AAA domain
      0.017   14.9   0.1      0.061   13.0   0.0    1.8  2  AAA_30       AAA domain
       0.02   15.2   0.3      0.076   13.3   0.3    2.0  1  AAA_22       AAA domain
      0.022   14.9   0.6      0.084   13.0   0.6    2.1  1  MMR_HSR1     50S ribosome-binding GTPase
      0.023   14.8   0.2      0.066   13.4   0.2    1.8  1  AAA_33       AAA domain
      0.039   13.5   0.1       0.46   10.0   0.0    2.1  2  AAA_25       AAA domain
       0.09   12.5   0.0       0.21   11.3   0.0    1.6  2  IstB_IS21    IstB-like ATP binding protein
      0.098   13.2   0.0        0.3   11.6   0.0    1.8  2  AAA_18       AAA domain
       0.13   11.0   0.0       0.17   10.6   0.0    1.3  1  RNA12        RNA12 protein
       0.17   12.2   0.1          3    8.1   0.1    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
        0.2   11.6   0.0       0.34   10.8   0.0    1.3  1  Rad17        Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.0   2.6e-38   2.7e-35       1     136 [.      23     169 ..      23     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 2.6e-38
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       lk+v+++ ++ge vai+G++G+GKSt+l+++  l  p eG i+ldg+d+++    + +++ ++ ig+++q+ +l p+
  gi|313126893|ref|YP_004037163.1|  23 LKDVNFTAQPGEFVAIMGPSGSGKSTMLNVIGLLDAPSEGVIRLDGRDVTDltdeEMTTQRKRAIGFVFQNFFLIPT 99 
                                       79**************************************************998888999999************* PP

                                       SBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       l++ en           e++e+ +++l+++gl +  +++      +LSgGqkqrva+ar+l+++p++ll+DEpt
  gi|313126893|ref|YP_004037163.1| 100 LSALENvemptlfendpEARERGTELLERVGLGDRLTHRP----DQLSGGQKQRVAIARSLINEPRILLADEPT 169
                                       **************99999999999999999999666665....*****************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   5.4e-08   5.7e-05      25     211 ..      34     214 ..      20     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.4e-08
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE.E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi.s 100
                                       +f ai+Gp GSGKs +l+ i    G      l  +  + +i   + ++ ++  + e+t + + +   + ++ + i +
  gi|313126893|ref|YP_004037163.1|  34 EFVAIMGPSGSGKSTMLNVI----G------LLDAPSEGVIRL-DGRDVTDLTDEEMTTQRKRAIGFVFQNFFLIpT 99 
                                       699**************999....5......334456677776.677777777777776666666555555555524 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                        ++ ++ e    +++    ++  +elle++g+         +LSgG+k+ va+a       ++   + l De   +L
  gi|313126893|ref|YP_004037163.1| 100 LSALENVEMPTLFENDPEARERGTELLERVGLGDRlthrpdQLSGGQKQRVAIARS----LINEPRILLADEPTGNL 172
                                       55566666777778888888888999999999766666666********9998754....4555668899******* PP

                                       -HHHHHHHHHHHHHHCTTSE..EEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 172 DeknvkkvaellkeksknaQ..fivislreemlekadklvgv 211
                                       D +  + v el+ e +++a   +i +++++++ e ad++v +
  gi|313126893|ref|YP_004037163.1| 173 DRETGRDVLELFTELKTEADvaIIAVTHDDQLREYADRVVNL 214
                                       *************99888661156678888999999998865 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00061      0.64       1      24 [.      35      57 ..      35     115 .. 0.75
   2 !   13.5   0.1   4.4e-05     0.046     209     301 ..     132     204 ..      76     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00061
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      + ++ Gp gsGKS+ L  + ll +
  gi|313126893|ref|YP_004037163.1| 35 FVAIMGPSGSGKSTMLNVIGLL-D 57
                                      57899**************888.2 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.4e-05
                            AAA_21 209 iasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.ke 284
                                        ++  +r                  +++lS G+k+  a++ +l+  +   ++ll DEp  +L+ +  r +lel+ ++
  gi|313126893|ref|YP_004037163.1| 132 GDRLTHR------------------PDQLSGGQKQRVAIARSLINEP---RILLADEPTGNLDRETGRDVLELFtEL 187
                                       4444444..................6779*******99999999988...************************766 PP

                            AAA_21 285 lsrngaQviltTHSpll 301
                                       +++ ++ +i++TH+  l
  gi|313126893|ref|YP_004037163.1| 188 KTEADVAIIAVTHDDQL 204
                                       6669*********9765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.4e-07   0.00036      16      41 ..      27      52 ..      20      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.4e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDA 41
                                       ++ ++ +++ ++GpsGsGKST+l  
  gi|313126893|ref|YP_004037163.1| 27 NFTAQPGEFVAIMGPSGSGKSTMLNV 52
                                      5566666799*************954 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.7e-07   0.00081      84     119 ..      17      53 ..       5      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.7e-07
                                       TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                       ++t e+l++++   +  ++++++G+SG GKSt++n++
  gi|313126893|ref|YP_004037163.1|  17 TETVEALKDVNFTAQPgEFVAIMGPSGSGKSTMLNVI 53 
                                       456677888888888779*****************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   2.9e-06     0.003      21     112 ..      29     143 ..      16     196 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.9e-06
                            AAA_16  21 sgrp.elvllsGesGvGKsslvrellralekd..ggiflrgkcdql....esaipysa.laqalareellrqllde. 88 
                                       + +p e v + G+sG+GKs++++ +   l +   g+i l g+ +      e+ + +   +  ++ +  l+  l +  
  gi|313126893|ref|YP_004037163.1|  29 TAQPgEFVAIMGPSGSGKSTMLNVIG-LLDAPseGVIRLDGRDVTDltdeEMTTQRKRaIGFVFQNFFLIPTLSALe 104
                                       3444599***************9887.34444323444555555554443233333222333333333333333333 PP

                            AAA_16  89 ........aesaeleawrekleeala.......avpela 112
                                               +++ e+++  ++l+e+++         ++l+
  gi|313126893|ref|YP_004037163.1| 105 nvemptlfENDPEARERGTELLERVGlgdrlthRPDQLS 143
                                       333332221223333333444444446666666333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     3e-05     0.031      16      40 ..      27      54 ..      17      56 .. 0.76
   2 ?   -1.4   0.0       2.7   2.9e+03     110     110 ..     124     124 ..      65     211 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                            AAA_23 16 dF..sk.gltlItGpNGaGKTTildAik 40
                                      +F   +  +++I Gp G+GK+T l+ i 
  gi|313126893|ref|YP_004037163.1| 27 NFtaQPgEFVAIMGPSGSGKSTMLNVIG 54
                                      44334424789*************9885 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.7
                            AAA_23 110 e 110
                                       e
  gi|313126893|ref|YP_004037163.1| 124 E 124
                                       1 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.8e-05     0.061      13      38 ..      28      53 ..      21      82 .. 0.86
   2 ?   -0.8   0.0      0.98     1e+03     103     128 ..     178     204 ..     130     206 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                            AAA_30 13 lltsgdrvavltGpAGtGKttalkal 38
                                      +++++  ++++ Gp G+GK+t+l+++
  gi|313126893|ref|YP_004037163.1| 28 FTAQPGEFVAIMGPSGSGKSTMLNVI 53
                                      566777899**************998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.98
                            AAA_30 103 kqlaallkaaek.agakvilvGDerQl 128
                                       +++ +l++++++ a++ +i v  ++Ql
  gi|313126893|ref|YP_004037163.1| 178 RDVLELFTELKTeADVAIIAVTHDDQL 204
                                       334444444444357888888888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   7.2e-05     0.076       6      25 ..      34      53 ..      30     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrl 25
                                       +++++G+sG+GK+t l+ +
  gi|313126893|ref|YP_004037163.1| 34 EFVAIMGPSGSGKSTMLNVI 53
                                      6899***********99765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6     8e-05     0.084       2      20 ..      36      54 ..      35     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
                                      EEEEESTTSSHHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinalt 20
                                      vai+G + +GKSt++n + 
  gi|313126893|ref|YP_004037163.1| 36 VAIMGPSGSGKSTMLNVIG 54
                                      89**************984 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.2e-05     0.066       2     107 ..      36     201 ..      35     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                            AAA_33   2 vllvGlpGsGKstlaerl..lkklg..avllssdt....................................lrrrlf 38 
                                       v + G++GsGKst +  +  l +    +++l+  +                                    ++ +lf
  gi|313126893|ref|YP_004037163.1|  36 VAIMGPSGSGKSTMLNVIglLDAPSegVIRLDGRDvtdltdeemttqrkraigfvfqnffliptlsalenvEMPTLF 112
                                       5678**********987554444444588888777788888888888888888888888888877777776555555 PP

                            AAA_33  39 gtdqqskt.............dytrvldrlyqilnelarkalsagrn...vildat..nlsrrerarflklarrlgv 97 
                                       ++d++  +             ++t+  d+l + +++++++a+s  +    +++d +  nl+r++ +++l+l+ +l+ 
  gi|313126893|ref|YP_004037163.1| 113 ENDPEARErgtellervglgdRLTHRPDQLSGGQKQRVAIARSLINEpriLLADEPtgNLDRETGRDVLELFTELKT 189
                                       55444333566777777777766677777666666666666554333221555666669999999999988887766 PP

                            AAA_33  98 p..vrivvvetd 107
                                       +  v+i++v+ d
  gi|313126893|ref|YP_004037163.1| 190 EadVAIIAVTHD 201
                                       532333333333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00044      0.46      32      50 ..      32      50 ..      26      58 .. 0.89
   2 ?    0.9   0.0      0.27   2.9e+02     162     188 ..     173     200 ..     164     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00044
                            AAA_25 32 agelallaGapgtGKttla 50
                                       ge+++++G++g+GK+t++
  gi|313126893|ref|YP_004037163.1| 32 PGEFVAIMGPSGSGKSTML 50
                                      599**************97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                            AAA_25 162 nsdv.galvealeriarrtgaavllvhH 188
                                       ++++ + ++e + +++++ ++a+++v H
  gi|313126893|ref|YP_004037163.1| 173 DRETgRDVLELFTELKTEADVAIIAVTH 200
                                       555558899999**************99 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.21      32      68 ..      17      54 ..       6      84 .. 0.84
   2 ?   -2.4   0.0       3.2   3.3e+03     110     143 ..     161     193 ..     145     213 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                         IstB_IS21 32 krkvkeLatlsfiek.kenivllGpsGvGKshlaialg 68
                                       ++v++L   +f+++  e ++++GpsG GKs +   +g
  gi|313126893|ref|YP_004037163.1| 17 TETVEALKDVNFTAQpGEFVAIMGPSGSGKSTMLNVIG 54
                                      567899999999987368899**********8877666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.2
                         IstB_IS21 110 dllilDdlgllpldqaeaellfeviekryerrsi 143
                                       ++l+ D+  + +ld++  ++++e+  +    + +
  gi|313126893|ref|YP_004037163.1| 161 RILLADE-PTGNLDRETGRDVLELFTELKTEADV 193
                                       4554444.34567777777777766555444333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00029       0.3       1      35 [.      36      78 ..      36     106 .. 0.74
   2 ?   -1.5   0.0       3.2   3.4e+03      44      44 ..     196     196 ..     145     227 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                            AAA_18  1 IlltGtpGvGKttlakeL....skrlgf....gvnlrdvaken 35
                                      ++++G++G+GK+t+ + +    + ++g+    g+ ++d+  e+
  gi|313126893|ref|YP_004037163.1| 36 VAIMGPSGSGKSTMLNVIglldAPSEGVirldGRDVTDLTDEE 78
                                      689**********998885554333333556666666666555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                            AAA_18  44 e 44 
                                        
  gi|313126893|ref|YP_004037163.1| 196 I 196
                                       2 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.17      13      61 ..      29      79 ..      12     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                             RNA12 13 eEnvntFivvkGPrGSGkkeLvldrvlkdrkk..vlvidCdelvkarndae 61
                                      + ++  F+ + GP GSGk+ ++    l d  +  v+ +d +++++ + +++
  gi|313126893|ref|YP_004037163.1| 29 TAQPGEFVAIMGPSGSGKSTMLNVIGLLDAPSegVIRLDGRDVTDLTDEEM 79
                                      566788*************99843444444335688888888777654444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0029         3      62      89 ..     158     185 ..     123     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                       + +r+++ DE  ++lD e+ + +lel++
  gi|313126893|ref|YP_004037163.1| 158 NEPRILLADEPTGNLDRETGRDVLELFT 185
                                       34899999***********999999986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00032      0.34      33      65 ..      21      53 ..      11      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvL 65
                                      e+lk      ++ + + i GPsG gkst+++v+
  gi|313126893|ref|YP_004037163.1| 21 EALKDVNFTAQPGEFVAIMGPSGSGKSTMLNVI 53
                                      56677777788889999************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1550.39
//
Query:       gi|313126894|ref|YP_004037164.1|  [L=486]
Description: hypothetical protein Hbor_21550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-09   35.9  12.6     0.0079   16.4   0.0    4.1  4  CARDB         CARDB
    0.00026   21.1   0.2        2.4    8.3   0.1    3.4  3  Transglut_C   Transglutaminase family, C-terminal ig like dom
  ------ inclusion threshold ------
      0.048   13.9   9.7      0.063   13.5   0.5    5.0  5  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos
      0.092   12.1   0.2       0.17   11.2   0.2    1.4  1  GidB          rRNA small subunit methyltransferase G
       0.39   11.0   8.6       0.23   11.7   0.6    3.1  3  ASH           Abnormal spindle-like microcephaly-assoc'd, ASP


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.2e-06    0.0079       8      84 ..      33     113 ..      29     118 .. 0.87
   2 !   11.9   1.9   5.7e-05       0.2       8      83 ..     140     217 ..     131     229 .. 0.75
   3 !   12.2   0.1   4.7e-05      0.17      10      94 ..     243     326 ..     236     333 .. 0.89
   4 ?   -0.5   0.4      0.43   1.5e+03      62      90 ..     411     439 ..     354     447 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.2e-06
                                       EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEE.EEEEETTEEEEEEEE......SEE-CTEEEEEEEEEE-S-S-CE CS
                             CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatk.valyldgelvgtvtv......psLaagesttvsftwtteatege 77 
                                       +t++p+++++ge +ti+ t+kN+ +++sg ++ +++y+ +   +t ++       ++ +g+s++v +t   e ++g+
  gi|313126894|ref|YP_004037164.1|  33 VTVSPKNPVPGERFTIQTTIKNS-EQSSGGFQiTDVYIRRPG-STDEIgrvenpGNIPPGASIKVPLTASFE-NPGT 106
                                       6889*******************.777777762679998887.888888999999****************9.**** PP

                                       EEEEEEE CS
                             CARDB  78 vtltvvv 84 
                                        +l+v+v
  gi|313126894|ref|YP_004037164.1| 107 RELRVHV 113
                                       *999987 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.7e-05
                                       EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S-S-CEEEE CS
                             CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtteategevtl 80 
                                       ++l+ ++++vg ent++vt  N   ++s+a +v++ l+g+ v    +t  +++L+ + + + s+t + + +e + +l
  gi|313126894|ref|YP_004037164.1| 140 VSLSTGDVVVGAENTVKVTAVNG--ENSPARSVRVSLSGTDVqvedDTRLLAKLNESRTFNFSVTPQSADAELDAEL 214
                                       57788899***********9996..7888888888888888877977888899988777777776655544444445 PP

                                       EEE CS
                             CARDB  81 tvv 83 
                                       +++
  gi|313126894|ref|YP_004037164.1| 215 QYT 217
                                       555 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 4.7e-05
                                       EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEEST CS
                             CARDB  10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvvvDp 86 
                                       + +++a  g +  + v ++N G+a  ++  ++l  ++++    + +++a+++++tv++++t + ++g  +++v    
  gi|313126894|ref|YP_004037164.1| 243 VDATTAGSGAQPAVAVDISNLGNAPLENPVIELSRNDTVLLRRPAKEVASDQTRTVKLNVTDI-ESGPLDVRVGYHM 318
                                       56677778888999**********************************************998.9999999998877 PP

                                       T-SS--SS CS
                             CARDB  87 dnevaEsn 94 
                                       +++ +Es+
  gi|313126894|ref|YP_004037164.1| 319 GDQASEST 326
                                       77777765 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.43
                                       EEEEEEEEE-S-S-CEEEEEEEESTT-SS CS
                             CARDB  62 sttvsftwtteategevtltvvvDpdnev 90 
                                       ++tv +t+t+  +  e t++ +vD ++ +
  gi|313126894|ref|YP_004037164.1| 411 TETVPITVTYLSNGTERTVRKNVDVSDLI 439
                                       34555555555444444566666665555 PP

>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00086       3.1       9      85 ..      38     110 ..      33     115 .. 0.87
   2 !    8.3   0.1   0.00068       2.4       9      68 ..     145     207 ..     138     227 .. 0.85
   3 ?   -0.7   0.0      0.43   1.6e+03      67      87 ..     411     431 ..     395     441 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00086
                                       SCEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-HHSHEEECCE CS
                       Transglut_C   9 esavlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlkilpskyGerkll 85 
                                       +++v g  +t++ ++kN+ +++      +++   +   G +  e+ + ++ +++ P+++ +v+l+ ++++ G+r+l 
  gi|313126894|ref|YP_004037164.1|  38 KNPVPGERFTIQTTIKNSEQSS-GG--FQITDVYIRRPGST-DEIGRVENPGNIPPGASIKVPLTASFENPGTRELR 110
                                       6778899999999999996666.44..77888999999998.69****************************99875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00068
                                       SCEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEE...ECTTTEEEEEEEEEEEEEE-TTEEE CS
                       Transglut_C   9 esavlgqdltvsvllkNplseelkdvklnlcaqtv...eynGvlaaefkkksleltLePkeek 68 
                                       ++ v+g + tv v+  N   ++ + v+++l++  v     + +la+ ++++++++++ P++ +
  gi|313126894|ref|YP_004037164.1| 145 GDVVVGAENTVKVTAVNGENSPARSVRVSLSGTDVqveDDTRLLAKLNESRTFNFSVTPQSAD 207
                                       67899**************************8776222579999999999*********9865 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.43
                                       EEEEEEEE-HHSHEEECCEEE CS
                       Transglut_C  67 eksvrlkilpskyGerkllve 87 
                                       +++v++++++   G+++++ +
  gi|313126894|ref|YP_004037164.1| 411 TETVPITVTYLSNGTERTVRK 431
                                       568999999999999877655 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.32   1.2e+03       3      19 ..      42      58 ..      41      68 .. 0.82
   2 ?   13.5   0.5   1.7e-05     0.063       4      30 ..     150     176 ..     147     219 .. 0.85
   3 ?    0.7   0.0      0.18   6.3e+02       4      28 ..     251     275 ..     239     277 .. 0.74
   4 ?   -0.9   0.0      0.56     2e+03      47      60 ..     290     303 ..     281     311 .. 0.65
   5 ?   -1.0   0.1      0.58   2.1e+03      56      67 ..     404     415 ..     399     436 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.32
                       NPCBM_assoc  3 pGetvtltltvtndgta 19
                                      pGe+ t+++t++n++++
  gi|313126894|ref|YP_004037164.1| 42 PGERFTIQTTIKNSEQS 58
                                      78889999999988865 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.7e-05
                       NPCBM_assoc   4 Getvtltltvtndgtaaatnvslslsl 30 
                                       G+++t+++t++n+++++a++v++sls+
  gi|313126894|ref|YP_004037164.1| 150 GAENTVKVTAVNGENSPARSVRVSLSG 176
                                       99***********************86 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.18
                       NPCBM_assoc   4 Getvtltltvtndgtaaatnvslsl 28 
                                       G++ ++ + ++n g+a+++n  ++l
  gi|313126894|ref|YP_004037164.1| 251 GAQPAVAVDISNLGNAPLENPVIEL 275
                                       6777778888888888888866665 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.56
                       NPCBM_assoc  47 lapGetveatvkVt 60 
                                       +a ++t +++++Vt
  gi|313126894|ref|YP_004037164.1| 290 VASDQTRTVKLNVT 303
                                       55555555555554 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.58
                       NPCBM_assoc  56 tvkVtppagaaa 67 
                                       t++Vtp++++++
  gi|313126894|ref|YP_004037164.1| 404 TAQVTPGTETVP 415
                                       566666666554 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   4.8e-05      0.17      45      68 ..     443     466 ..     424     476 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.8e-05
                                       S-CCC-.EEEETSTTTTTHHHHHH CS
                              GidB  45 lkekrdkviDvGsGaGlPGipLai 68 
                                       +++k+d+  D GsG+GlP+ipL i
  gi|313126894|ref|YP_004037164.1| 443 VENKQDSGSDGGSGGGLPSIPLLI 466
                                       56667678899***********77 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.6   1.3e+04      39      45 ..      48      54 ..      28      65 .. 0.51
   2 ?   11.7   0.6   6.4e-05      0.23       2      79 ..     130     206 ..     129     222 .. 0.79
   3 ?    2.7   0.8     0.039   1.4e+02      17      74 ..     367     420 ..     357     437 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                                      -EEEEEE CS
                               ASH 39 aevkvsk 45
                                      ++++++ 
  gi|313126894|ref|YP_004037164.1| 48 IQTTIKN 54
                                      3333333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.4e-05
                                       EEEE-TTB--EEEEE-----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                               ASH   2 vlllapfsrkpfvsFgdvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete.levqpgesvtltvtwtPt 77 
                                       v+++++  +++++s gdv vG   + ++t +N+ + pa+     ++   + ++ve ++ l  + +es t++++ tP+
  gi|313126894|ref|YP_004037164.1| 130 VVTVRQSGPQVSLSTGDVVVGAENTVKVTAVNGENSPARSVRVSLS--GTDVQVEDDTrLLAKLNESRTFNFSVTPQ 204
                                       6788999999*************************99665544444..67778887775556677888888888887 PP

                                       XX CS
                               ASH  78 ee 79 
                                       ++
  gi|313126894|ref|YP_004037164.1| 205 SA 206
                                       75 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.039
                                       -----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXX.XXXXXXX CS
                               ASH  17 gdvkvGssaerlLtveNpseepaevkvskvpaaekgfsveetelevqpges.vtltvtw 74 
                                       ++v++ +++++++t + p+    e +v+ +p  +  f    ++ +v+pg++ v +tvt+
  gi|313126894|ref|YP_004037164.1| 367 DSVTIRTIKTETVTPVRPNS---EYFVGSIP--SSDFATFDLTAQVTPGTEtVPITVTY 420
                                       57888888888888888888...67999999..88888888888888876515588876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3256.74
//
Query:       gi|313126895|ref|YP_004037165.1|  [L=654]
Description: superfamily ii helicase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.9e-20   71.0   0.0    1.8e-19   70.2   0.0    1.4  1  DEAD        DEAD/DEAH box helicase
    9.1e-07   29.2   0.0    8.4e-06   26.1   0.0    2.3  1  Helicase_C  Helicase conserved C-terminal domain
    2.5e-05   24.4   0.0    3.9e-05   23.7   0.0    1.3  1  ResIII      Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.0     3e-23   1.8e-19       4     172 ..      28     178 ..      25     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 3e-23
                                       HHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 Qaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                       Q +a+++ + +g+ +++a++T+sGKT ++ +++l        + +  al+++P+r+La++ ++++ ++     ++v 
  gi|313126895|ref|YP_004037165.1|  28 QVAAVEAGVtEGERLVAAIPTASGKTFIAELAML--------TAEGPALYIVPLRALAREKYETFAELPG---VSV- 92 
                                       66667766658999********************........44558*********************99...344. PP

                                       EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  80 liiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdg 156
                                         i+  + ++  ++l ++ divv+t +++d+ ++tg   ++++ ++V+DE++ l ++g++++++  l++l++   + 
  gi|313126895|ref|YP_004037165.1|  93 -GISTGDFDSTDEDL-ADNDIVVATAEKVDSAIRTGAPWIESLACVVVDEVHLLGSDGRGPTLEVTLATLQR---RA 164
                                       .35656677888899.899******************99*******************************54...44 PP

                                       T.TTSEEEEEESSBSHH CS
                                       x.xxxxxxxxxxxxxxx RF
                              DEAD 157 k.lqrqvivlSATlpkd 172
                                       + lq  +++lSAT+  +
  gi|313126895|ref|YP_004037165.1| 165 PgLQ--IVALSATVD-N 178
                                       4455..*******97.4 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.4e-09   8.4e-06      39     109 ..     304     386 ..     231     388 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.4e-09
                                       T....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS........SS.HHHHHH CS
                        Helicase_C  39 k....gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp........rn.vtsyiq 102
                                            +  va +h+   + +r  + ++f++++ +v+ at  ++ G+++p  + V++ dl+        +  v +++q
  gi|313126895|ref|YP_004037165.1| 304 LadvvESGVAFHHAGVRSGHRALVESAFREKRLKVICATPTLAAGVNVPA-RRVVIRDLKrytgekmtWLpVLEVHQ 379
                                       044456778999999*********************************95.555556666344434333345***** PP

                                       HHTTSSS CS
                        Helicase_C 103 riGRtgR 109
                                       + GR+gR
  gi|313126895|ref|YP_004037165.1| 380 MCGRAGR 386
                                       ******* PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   6.6e-09   3.9e-05      10     169 ..      30     176 ..      13     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.6e-09
                                       HHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GE CS
                            ResIII  10 eaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeig 86 
                                        a+e+ +     ++ +r++ +++T +GKT++a  ++           +l +vp ++l    +e+f+++         
  gi|313126895|ref|YP_004037165.1|  30 AAVEAGV-----TEGERLVAAIPTASGKTFIAELAMLTAEG-----PALYIVPLRALAREKYETFAELPGVS----V 92 
                                       4444443.....5678999************9888887776.....79***********9999999998876....5 PP

                                       EEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....T....TTHHHHHT CS
                            ResIII  87 kkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...k....swreilek 156
                                       ++ +gd ++   +d  +++i+v+t +++d+++      +     ++  ++++DE+H lg++        +   + + 
  gi|313126895|ref|YP_004037165.1|  93 GISTGDFDST-DEDLADNDIVVATAEKVDSAI-----RTGAPWIESLACVVVDEVHLLGSDgrgPtlevTLATLQRR 163
                                       7888888888.88889****************.....67777888888**********9975441333333333334 PP

                                       ---SEEEEEESS- CS
                            ResIII 157 fkeavllglTATp 169
                                        +   +++l+AT 
  gi|313126895|ref|YP_004037165.1| 164 APGLQIVALSATV 176
                                       4447788888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3898.91
//
Query:       gi|313126896|ref|YP_004037166.1|  [L=420]
Description: ribulose 1,5-bisphosphate carboxylase large subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-94  316.9   0.3    2.6e-94  315.8   0.3    1.5  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    1.8e-40  137.9   0.0    3.5e-40  136.9   0.0    1.5  1  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai
  ------ inclusion threshold ------
      0.016   14.5   0.1      0.033   13.5   0.0    1.4  1  Glyco_hydro_97   Glycoside hydrolase 97


Domain annotation for each model (and alignments):
>> RuBisCO_large  Ribulose bisphosphate carboxylase large chain, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.8   0.3   4.4e-98   2.6e-94      12     299 .]     146     414 ..     136     414 .. 0.97

  Alignments for each domain:
  == domain 1  score: 315.8 bits;  conditional E-value: 4.4e-98
                                       .T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHHHHSS--EEEEE CS
                     RuBisCO_large  12 egrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqdetGekklyaln 88 
                                       e+rpil+t+ KPk+GLs++ +a+v ye++lgg+D++KdDEnl++q f++++dr+ + +   ++a+detGekk y +n
  gi|313126896|ref|YP_004037166.1| 146 EDRPILATVPKPKVGLSTDRHAEVGYEAWLGGVDLLKDDENLTDQSFNPYHDRLVESLALRDDAEDETGEKKSYLIN 222
                                       68*************************************************************************** PP

                                       ---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--SEE-HHHHHHHH CS
                     RuBisCO_large  89 itaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskhGisfrvlakll 165
                                       +tad+ + ml+r ++++e g e v+vdv+++G+aa++++r++++++++++H+Hra+h+a++r ++hG+s+rvla++ 
  gi|313126896|ref|YP_004037166.1| 223 VTADT-NTMLERVDLAAEEGCEYVMVDVITTGWAAVQTVRERCEDHGIAIHAHRAMHAAFDRLENHGVSMRVLAQIS 298
                                       **888.99********************************************************************* PP

                                       HHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS--TTTHHHHHHHH CS
                     RuBisCO_large 166 RLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGihagqlpellenl 242
                                       RL+Gvd+lhtgt+g+gkl ++++   g                + +++++l++l++vlpvasgG+h g +p+ll+++
  gi|313126896|ref|YP_004037166.1| 299 RLCGVDQLHTGTAGLGKLANEDT--VG---------------INDWMRSELYGLNDVLPVASGGLHPGLIPDLLDAT 358
                                       *********************99..33...............4579******************************* PP

                                       S---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                     RuBisCO_large 243 gesdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                       g+ +v++qaGGGi+gHpdg+ aGa+alr a++   +G++lee A++++eLa+A++ w
  gi|313126896|ref|YP_004037166.1| 359 GT-NVCVQAGGGIHGHPDGTRAGAAALRAAVDGYAAGKSLEESADDSPELATAIDEW 414
                                       **.****************************************************99 PP

>> RuBisCO_large_N  Ribulose bisphosphate carboxylase large chain, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   0.0   5.9e-44   3.5e-40       1     119 [.       8     123 ..       8     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 5.9e-44
                   RuBisCO_large_N   1 dyvdedyepketdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkdellkklkakvyeieeveeekelvki 77 
                                       d++d +yep+e+dl+++fr++Paeg++ve aa++vA+eSS+gtw+++ t +   ++++ a++++i+ + +++  v +
  gi|313126896|ref|YP_004037166.1|   8 DFLDLSYEPDESDLVCTFRIAPAEGMDVEAAASRVASESSNGTWAALPTGEG--FTDMGATTFDIRGS-DDSAEVDV 81 
                                       689**********************************************999..99*********995.79****** PP

                   RuBisCO_large_N  78 AYplelFeegsipqllssiaGnifgmkavkalrleDirlPka 119
                                       AYp  lFe gs+pq+ls+iaGni+gmkav+++rl D+++P+a
  gi|313126896|ref|YP_004037166.1|  82 AYPAGLFEPGSMPQILSCIAGNIMGMKAVDTIRLADCQWPEA 123
                                       ****************************************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.6e-06     0.033      30      63 ..     223     256 ..     209     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-06
                    Glyco_hydro_97  30 hgantetvkryiDfAaengleyvlvegwdegWee 63 
                                         a+t+t+ + +D+Aae g eyv+v+   +gW+ 
  gi|313126896|ref|YP_004037166.1| 223 VTADTNTMLERVDLAAEEGCEYVMVDVITTGWAA 256
                                       56899***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2754.56
//
Query:       gi|313126897|ref|YP_004037167.1|  [L=200]
Description: hypothetical protein Hbor_21580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1385.27
//
Query:       gi|313126898|ref|YP_004037168.1|  [L=320]
Description: ribose 1,5-bisphosphate isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-76  255.1   1.5    8.1e-76  254.9   1.5    1.0  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.9   1.5   4.5e-80   8.1e-76       1     282 []      23     298 ..      23     298 .. 0.98

  Alignments for each domain:
  == domain 1  score: 254.9 bits;  conditional E-value: 4.5e-80
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakk 77 
                                       ++rG+++ia aa+++l++ ++++++++++eL+ elr a+++L  +rPtavsl na+r++l     + + ++v+++++
  gi|313126898|ref|YP_004037168.1|  23 EIRGAATIADAAAKALRTQAEQSSAETADELRAELRAAARVLHDTRPTAVSLPNALRYVLF----DADGATVEDVRA 95 
                                       589*********************************************************9....689********* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHH CS
                             IF-2B  78 sliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeL 154
                                       s++  + e+ ++ e+a+   g+++a+++ dgdti+T+c+s  vl+ ++aa++++k+++ iv E+rPrlqG+ ta eL
  gi|313126898|ref|YP_004037168.1|  96 SVVTSVVEFCDRLENAQTDLGRVGANRLRDGDTIMTHCHSTDVLACVEAAVEQGKDLTAIVKETRPRLQGHITAREL 172
                                       ***************************************************************************** PP

                                       HHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGG CS
                             IF-2B 155 vqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlded 231
                                       v+ g++vtli+dsa++  m+  vd v+vGAd+i+++G+++nkiGTs lAv A+ + +p+  +a+++k+++ + +++ 
  gi|313126898|ref|YP_004037168.1| 173 VEMGVDVTLIVDSAARRYMND-VDHVLVGADSIAADGSVINKIGTSGLAVTARDRGTPIVCAAQTIKLHPDTLTGHT 248
                                       *********************.******************************************************* PP

                                       SSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 232 ifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       + ie+r++ e++  ++ +    ++ v npafDvtPp+++++i+Te G  pp
  gi|313126898|ref|YP_004037168.1| 249 VDIEMREESEVIDPDEADEIG-DITVKNPAFDVTPPRYVDAIVTERGQYPP 298
                                       *************99998866.9************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2398.81
//
Query:       gi|313126899|ref|YP_004037169.1|  [L=492]
Description: amp phosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-11   41.8   0.0    1.2e-10   40.8   0.0    1.5  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
      7e-09   35.6   2.3    4.3e-08   33.1   2.3    2.0  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    7.7e-09   35.3   0.0    2.2e-08   33.8   0.0    1.8  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    0.00022   21.2   0.1    0.00051   20.0   0.1    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0011   17.8   0.0      0.002   17.0   0.0    1.3  1  DUF2254          Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   3.5e-14   1.2e-10       1      71 [.     413     476 ..     413     480 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.5e-14
                                       EEEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHHHH CS
                            PYNP_C   1 yvseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklkka 71 
                                       +v+ i++r ++ +a+++GA       p  ++ G+elh  +Gd+V +G+pl+ti+a+ +e+l ea++ +++a
  gi|313126899|ref|YP_004037169.1| 413 VVTHINNRLVNDVARRAGA-------PRAPGSGLELHHSVGDAVAQGDPLYTIHAEASERLSEAATYAEDA 476
                                       699****************.......**************************************9988765 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   2.3   1.2e-11   4.3e-08       4      79 ..     156     228 ..     153     333 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.2e-11
                                       BEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   4 lvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                       ++D++  GG+  n    +     +vAaaGv+++k + r+v+s +G+aD++e + + ++l+++e++ +++e++ ++ 
  gi|313126899|ref|YP_004037169.1| 156 VADKHCVGGVSGNR--TTPIIVSIVAAAGVTIPKTSSRAVTSAAGTADTMEVF-CPVDLSAKEIRTVVAETNGCIA 228
                                       789999***97777..35566678999************************98.8999999999999998877764 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0     6e-12   2.2e-08       2      63 .]      85     146 ..      84     146 .. 0.97
   2 ?   -2.8   0.0       1.7   6.1e+03      12      22 ..     210     220 ..     209     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 6e-12
                                       HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                       ++i+k++d  eL ++e+  ++++i +++++d++++A   A++++G +  E+  l e m ++g
  gi|313126899|ref|YP_004037169.1|  85 EFIRKKLDDDELEYDELDRIVRDIRDDRLSDVELGAYVCAMYINGTSLSETMHLSESMADAG 146
                                       79********************************************************9875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                                       ---HHHHHHHH CS
                   Glycos_trans_3N  12 eLtaeeirfai 22 
                                       +L+a eir ++
  gi|313126899|ref|YP_004037169.1| 210 DLSAKEIRTVV 220
                                       799****9987 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.4e-07   0.00051      27      80 ..      13      66 ..       4      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-07
                                      SSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS.B-TTEEEEESSH CS
                   Molydop_binding 27 pepevveinpedAaalGikdGdlVevesrrGsvevrakvter.vrpGvvfmpfgw 80
                                      ++p +v+++ +dAa+lG+   d+V++e++  +v+  ++++++ v  G ++++   
  gi|313126899|ref|YP_004037169.1| 13 RAP-TVLMHGDDAATLGLHPLDRVQIETESETVVGIVELSNElVDTGELAVTRRL 66
                                      455.9********************************999997888888777655 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.7e-07     0.002     183     252 ..     394     468 ..     369     483 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.7e-07
                           DUF2254 183 deeeseeeeatpiraersGylqaidveaLvklaeehdl......vielevrpGdfvvkgeplakvwgeeddeelae 252
                                       + e  + + +++++a r+G++++i+ + + ++a+++++       +el++++Gd v++g+pl +++ e+ +e+l e
  gi|313126899|ref|YP_004037169.1| 394 PSELVPGRYEQTVTAGRDGVVTHINNRLVNDVARRAGAprapgsGLELHHSVGDAVAQGDPLYTIHAEA-SERLSE 468
                                       55566777899**********************998653333337********************9888.333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3446.86
//
Query:       gi|313126900|ref|YP_004037170.1|  [L=146]
Description: thioredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-30  104.5   0.0    3.6e-30  104.0   0.0    1.2  1  Thioredoxin    Thioredoxin
      2e-08   34.7   0.1    1.4e-06   28.7   0.1    2.2  1  Thioredoxin_2  Thioredoxin-like domain
    1.1e-06   28.9   0.0     0.0074   16.6   0.0    2.2  2  Thioredoxin_8  Thioredoxin-like
    2.6e-06   27.4   0.0    4.1e-06   26.8   0.0    1.2  1  TraF           F plasmid transfer operon protein
    0.00021   21.0   0.0    0.00027   20.7   0.0    1.3  1  Thioredoxin_9  Thioredoxin
    0.00031   20.6   0.2     0.0011   18.8   0.0    1.8  2  DSBA           DSBA-like thioredoxin domain
    0.00054   19.9   0.0    0.00086   19.3   0.0    1.3  1  HyaE           Hydrogenase-1 expression protein HyaE
    0.00092   19.3   0.1     0.0021   18.2   0.1    1.6  1  Thioredoxin_7  Thioredoxin-like
      0.002   18.0   0.0     0.0036   17.2   0.0    1.4  1  AhpC-TSA       AhpC/TSA family
      0.004   17.5   0.0     0.0075   16.7   0.0    1.5  1  DUF836         Glutaredoxin-like domain (DUF836)
     0.0044   17.0   0.0     0.0066   16.5   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
     0.0085   15.5   0.0       0.01   15.2   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
  ------ inclusion threshold ------
      0.019   13.9   0.0      0.029   13.3   0.0    1.3  1  Phosducin      Phosducin
      0.048   13.3   0.0      0.065   12.9   0.0    1.2  1  Thioredoxin_5  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   2.8e-33   3.6e-30       7     102 ..      51     143 ..      46     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 2.8e-33
                                       HHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                       Thioredoxin   7 kenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngk 83 
                                        ++Fe+ va+  + vlv+FyA+wCg+Ck++aP++++la e++   ++akvd+d+n++la++y+v+g+Ptl+lf +g+
  gi|313126900|ref|YP_004037170.1|  51 GDEFESLVAS-TSVVLVDFYADWCGPCKMIAPTVNSLAAETT--ATVAKVDIDQNQTLASQYNVRGVPTLLLFSDGD 124
                                       578*****99.*****************************99..99******************************* PP

                                       EEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  84 evkkyegarekeklaaflk 102
                                        v++++g r+k++l+  ++
  gi|313126900|ref|YP_004037170.1| 125 PVEQVVGVRDKSTLRGLIE 143
                                       ************9987775 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   1.1e-09   1.4e-06       7     106 ..      63     139 ..      59     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.1e-09
                     Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt 83 
                                        vlv+f++++C+ Ck +  ++ +l               + +  + + + +        i++n+ la +y+vrg+Pt
  gi|313126900|ref|YP_004037170.1|  63 VVLVDFYADWCGPCKMIAPTVNSL---------------AAETTATVAKVD--------IDQNQTLASQYNVRGVPT 116
                                       589****************99999...............112222222222........3345679*********** PP

                     Thioredoxin_2  84 .ivfldgkeivarlpGyvpaeele 106
                                        ++f dg+ +v++++G  ++  l+
  gi|313126900|ref|YP_004037170.1| 117 lLLFSDGD-PVEQVVGVRDKSTLR 139
                                       555*****.999999988777665 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.8e-06    0.0074       3      32 ..      63      92 ..      61      99 .. 0.82
   2 !   10.8   0.0   0.00036      0.46      67      90 ..      98     121 ..      90     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                                      EEEEEE--SSSHHHHHHHHHHHHHHHHHHH CS
                     Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkk 32
                                      vvl+ f+a+wc pck + p+++ l  +  +
  gi|313126900|ref|YP_004037170.1| 63 VVLVDFYADWCGPCKMIAPTVNSLAAETTA 92
                                      8********************998766654 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00036
                                       -TT-HHHHTT-S--TT-SEEEEE- CS
                     Thioredoxin_8  67 ddkkrnklkkkynvkaiPtlvvld 90 
                                       d +++++l+++ynv ++Ptl++ +
  gi|313126900|ref|YP_004037170.1|  98 DIDQNQTLASQYNVRGVPTLLLFS 121
                                       446799**************9976 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.2e-09   4.1e-06     129     202 ..      61     123 ..      58     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.2e-09
                              TraF 129 keygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpk 202
                                       +++ L+ Fy+  c+ c++ ap+++++a ++  +v  V++d+++   l++         +++v+ +P+l+l++  
  gi|313126900|ref|YP_004037170.1|  61 TSVVLVDFYADWCGPCKMIAPTVNSLAAETTATVAKVDIDQNQT--LAS---------QYNVRGVPTLLLFSDG 123
                                       5678999***********************************99..899.........************9876 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.1e-07   0.00027      48     106 ..      68     122 ..      32     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.1e-07
                                       E--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-T CS
                     Thioredoxin_9  48 ltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliilde 106
                                       + +dwCg + ++ P ++ +a ++ + +v  +  d+n+ l  qy     r +Ptl+++ +
  gi|313126900|ref|YP_004037170.1|  68 FYADWCGPCKMIAPTVNSLAAET-TATVAKVDIDQNQTLASQYNV---RGVPTLLLFSD 122
                                       679********************.*******************55...88999887754 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.27   3.4e+02       2      27 ..      66      90 ..      65      97 .. 0.81
   2 !   18.8   0.0   8.3e-07    0.0011     144     191 ..      90     141 ..      82     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.27
                                      EEEEEBTTBHHHHHHHHHHHHHHHHC CS
                              DSBA  2 vdeffDvlCPyCylgkerleklaars 27
                                      vd++ D  C+ C++ ++ +++laa  
  gi|313126900|ref|YP_004037170.1| 66 VDFYAD-WCGPCKMIAPTVNSLAAET 90
                                      788888.5999******999999876 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 8.3e-07
                                       HTSHHHHHHHHHHHHHHHHTT-SSSSEEEE..TTC..EEEESSSSHHHHHHH CS
                              DSBA 144 leseavkeavrentaaaqslgvtGvPtvvv..dgk..rmvfGadrldtlada 191
                                       +    +k ++++n+ +a +++v+GvPt ++  dg    +v+G+ +  tl+  
  gi|313126900|ref|YP_004037170.1|  90 TTATVAKVDIDQNQTLASQYNVRGVPTLLLfsDGDpvEQVVGVRDKSTLRGL 141
                                       555678899*******************999977667799999998888766 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.7e-07   0.00086      59     104 ..      88     134 ..      76     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.7e-07
                                       TS-EEEEEE.THHHHHHHHHCCT-TSSSEEEEEETTEEEEEEESSST CS
                              HyaE  59 nalraavva.dreqeealaerfgvlktPsllflrdgeylgvlakird 104
                                       + ++a+v++ d +q+++la++++v+ +P+ll++ dg+ +  + ++rd
  gi|313126900|ref|YP_004037170.1|  88 AETTATVAKvDIDQNQTLASQYNVRGVPTLLLFSDGDPVEQVVGVRD 134
                                       444555555699*************************9999999988 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.6e-06    0.0021      17      81 ..      61     120 ..      53     122 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                                       T--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE CS
                     Thioredoxin_7  17 gkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafl 81 
                                        + vlv+f a+wc++C+ ++ ++ s      a+     + +vd+++++    ++  +gvP+++++
  gi|313126900|ref|YP_004037170.1|  61 TSVVLVDFYADWCGPCKMIAPTVNSL-----AAETTATVAKVDIDQNQTLASQYNVRGVPTLLLF 120
                                       5679*************999888776.....2445555555555555543334444789998887 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0036      25      88 ..      61     120 ..      47     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                                       TSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE CS
                          AhpC-TSA  25 gkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfplls 88 
                                        ++v++ fy+  wc +C+  +p  + l+ e +   ++v  v +d+ ++++++ +  +++  ll 
  gi|313126900|ref|YP_004037170.1|  61 TSVVLVDFYAD-WCGPCKMIAPTVNSLAAETT---ATVAKVDIDQNQTLASQYNVRGVPTLLLF 120
                                       47899999999.****************9988...78999999999999988888887766654 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.9e-06    0.0075      10      49 ..      73     112 ..      68     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.9e-06
                                       -HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHCCCCTT CS
                            DUF836  10 ChlCeqakekLkelkleegleleviDIakdeeleakYgle 49 
                                       C+ C+ +   +  l+ e   ++ ++DI+++++l ++Y+++
  gi|313126900|ref|YP_004037170.1|  73 CGPCKMIAPTVNSLAAETTATVAKVDIDQNQTLASQYNVR 112
                                       999**********************************986 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.1e-06    0.0066      10      75 ..      73     142 ..      64     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                                       STTCHHHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEE..ECTT..CEEEESS---CCHHHHHH CS
                     Thioredoxin_3  10 CakCpklekavkeaaaekgikaevekvtdfeei.ekygVmsvPal..vidg..kvvvsGkvpseeeirkll 75 
                                       C  C+ ++  v+++aae   ++  +++ +++++ ++y+V+ vP+l  + dg  +  v+G v ++  +r l+
  gi|313126900|ref|YP_004037170.1|  73 CGPCKMIAPTVNSLAAETTATVAKVDIDQNQTLaSQYNVRGVPTLllFSDGdpVEQVVG-VRDKSTLRGLI 142
                                       999***************9999999999999999**********954445411334667.77666666665 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.8e-06      0.01      45     104 ..      72     122 ..      35     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.8e-06
                         OST3_OST6  45 kCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                                        C +C+ ++p ++ +a   +++          akvd+d+++ + ++++++ +P lllf+ 
  gi|313126900|ref|YP_004037170.1|  72 WCGPCKMIAPTVNSLAAETTAT---------VAKVDIDQNQTLASQYNVRGVPTLLLFSD 122
                                       4889999999999888888888.........79*************************87 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.3e-05     0.029     131     220 ..      49     135 ..       1     139 [. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                                       -SHHHHHHHHHSS-TT-EEEEEEE-TTSTTHHHHHHHHHHHHHH-.TTSEEEEEEHHHH--TTSS-TTT-SEEEEEE CS
                         Phosducin 131 esgeqfldtidkeqkitlivvhiyedgvkgtealnssliclaaey.ptvkfckvkasvigasdrfsrdvlpallvyk 206
                                       + g++f  ++     +++++v  y d    ++ +  ++  laae   tv    +   ++ a +++    +p+ll++ 
  gi|313126900|ref|YP_004037170.1|  49 NGGDEFESLVA---STSVVLVDFYADWCGPCKMIAPTVNSLAAETtATVAKVDIDQNQTLA-SQYNVRGVPTLLLFS 121
                                       33444433332...345789************************72467777777766666.56777889******* PP

                                       TTEEEEEETTGGGG CS
                         Phosducin 207 agellsnfvrvtdq 220
                                        g+ + + v v d+
  gi|313126900|ref|YP_004037170.1| 122 DGDPVEQVVGVRDK 135
                                       *****999999875 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     5e-05     0.065     129     166 ..      85     122 ..      78     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-05
                     Thioredoxin_5 129 efkeDlesklakkafqcDlklakemgvtevPtlvffne 166
                                        + +   +++ak   ++ + la++++v+ vPtl +f +
  gi|313126900|ref|YP_004037170.1|  85 SLAAETTATVAKVDIDQNQTLASQYNVRGVPTLLLFSD 122
                                       56666778899999*******************99983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1069.46
//
Query:       gi|313126901|ref|YP_004037171.1|  [L=97]
Description: hypothetical protein Hbor_21620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.17   11.5   3.9       0.25   11.0   0.1    2.4  2  DUF3149          Protein of unknown function (DUF3149)


Domain annotation for each model (and alignments):
>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.4e-05      0.25       9      34 ..       8      34 ..       4      37 .. 0.85
   2 ?    0.9   0.8     0.019   3.4e+02       4      15 ..      84      95 ..      80      96 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.4e-05
                           DUF3149  9 vGLl.SliVIvftigmgaffiryFirK 34
                                       +L+  liV    i++++  i+yF++K
  gi|313126901|ref|YP_004037171.1|  8 PILAtALIVVQTGILIIGGLITYFSYK 34
                                      5677788999999*************9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.019
                           DUF3149  4 LFssdvGLlSli 15
                                      L+++ ++ +Sl 
  gi|313126901|ref|YP_004037171.1| 84 LIGFAIIMYSLY 95
                                      455555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 636.59
//
Query:       gi|313126902|ref|YP_004037172.1|  [L=125]
Description: IclR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-10   41.4   0.7    2.1e-10   40.5   0.7    1.4  1  HTH_20      Helix-turn-helix domain
    5.5e-06   26.1   0.1    1.1e-05   25.2   0.1    1.4  1  HTH_IclR    IclR helix-turn-helix domain
     0.0015   18.4   0.1     0.0019   18.0   0.1    1.3  1  MarR_2      MarR family
     0.0041   16.7   0.0     0.0044   16.6   0.0    1.1  1  ArsR        ArsR transcriptional regulator
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.015   15.1   0.0    1.3  1  TrmB        Sugar-specific transcriptional regulator TrmB
      0.017   14.9   0.0       0.03   14.2   0.0    1.4  1  HTH_5       Bacterial regulatory protein, arsR family
       0.02   14.4   0.0      0.033   13.7   0.0    1.4  1  Sigma70_r4  Sigma-70, region 4
      0.035   14.3   0.0      0.051   13.7   0.0    1.3  1  DUF1492     Protein of unknown function (DUF1492)
      0.036   14.6   0.4      0.083   13.4   0.3    1.9  2  HTH_27      Winged helix DNA-binding domain
      0.058   13.5   0.0      0.062   13.5   0.0    1.3  1  FUR         Ferric uptake regulator family
       0.11   12.1   0.0       0.23   11.1   0.0    1.6  1  HTH_24      Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.7   1.3e-13   2.1e-10       3      57 ..      16      69 ..      14      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.3e-13
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTT.EEEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagL.vevv 57
                                      +++AL++   r+i raL   e++tasel +++d++ +t ++ L+ L ea+L ve++
  gi|313126902|ref|YP_004037172.1| 16 VLDALDDADARAIIRAL--VEPMTASELSDECDIPLSTTYRKLDLLTEADLlVEGT 69
                                      89***************..********************************66655 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   6.5e-09   1.1e-05       6      48 ..      14      65 ..      13      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.5e-09
                                      HHHHCT-CTTBSS.........-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  6 laiLdalaeapqe.........ltlselArrtglpkStvhRlLqtLvelGyv 48
                                      l++Ldal  a+ +         +t sel++++++p St++R L  L+e  ++
  gi|313126902|ref|YP_004037172.1| 14 LSVLDALDDADARaiiralvepMTASELSDECDIPLSTTYRKLDLLTEADLL 65
                                      7899999999999999999999**********************99998887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.2e-06    0.0019       9      54 ..      15      68 ..      13      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHCTTTS........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  9 rvLaaLgrrpgr........dltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       vL aL +++ r        ++t++el ++++++ s++ r l+ L +a L+++ 
  gi|313126902|ref|YP_004037172.1| 15 SVLDALDDADARaiiralvePMTASELSDECDIPLSTTYRKLDLLTEADLLVEG 68
                                      59999*****99***9999999****************************9664 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.7e-06    0.0044       3     110 ..       9     117 ..       7     125 .] 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                              ArsR   3 dpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsqWrmpepgekpekeYht 76 
                                       +p+eL+++l ++d+++ + + ++l +  +t++el+++++     + + l+lL +++l+ +  ++     + +  Y +
  gi|313126902|ref|YP_004037172.1|   9 EPSELLSVLDALDDADARAIIRALVEP-MTASELSDECDIPlstTYRKLDLLTEADLLVEGTEIRA-DGHHTTTYEV 83 
                                       79**********************875.**********9764447789********9887777776.4667789*** PP

                              ArsR  77 sYskvqanfqcsledlsdiievafmsdeeleelv 110
                                       ++++v++ ++   +   ++++    +d++l ++ 
  gi|313126902|ref|YP_004037172.1|  84 TFDEVRIELTDERRLDVNVVRPEQAPDQQLADIW 117
                                       ******9987655544455555555555555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   9.4e-06     0.015      18      51 ..      33      64 ..      19      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.4e-06
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTS CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGl 51
                                      +  +p+ta+e++ e ++p s+ Y+ L  L +++l
  gi|313126902|ref|YP_004037172.1| 33 V--EPMTASELSDECDIPLSTTYRKLDLLTEADL 64
                                      4..89*********************99999886 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.8e-05      0.03       7      45 ..      28      65 ..      22      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                                      HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      I+++L  ++++++el++e +++ st+ + L  L ea+L+
  gi|313126902|ref|YP_004037172.1| 28 IIRALV-EPMTASELSDECDIPLSTTYRKLDLLTEADLL 65
                                      555555.59***************************995 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05     0.033       1      36 [.      16      51 ..      16      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                      HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHH CS
                        Sigma70_r4  1 aLasLpererevlelrfgeglTleEIgerlgiSrer 36
                                      +L+ L++ + + +    +e++T +E++++ +i++++
  gi|313126902|ref|YP_004037172.1| 16 VLDALDDADARAIIRALVEPMTASELSDECDIPLST 51
                                      59*******************************997 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.1e-05     0.051      46      93 ..      11      57 ..       4      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                           DUF1492 46 lelqrlidklensdsrsvLrmvyidkltvwqvidklnisrstyyrllr 93
                                       el +++d l+++d+r+++r   ++ +t+ ++ d+ +i  st yr+l 
  gi|313126902|ref|YP_004037172.1| 11 SELLSVLDALDDADARAIIRA-LVEPMTASELSDECDIPLSTTYRKLD 57
                                      68999**************96.69********************9986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   5.1e-05     0.083      12      62 ..      29      81 ..      12      95 .. 0.83
   2 ?   -3.3   0.0       8.2   1.3e+04      11      27 ..     102     119 ..     100     123 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                            HTH_27 12 irhrrrrkkladlcgrlnvedshisyslkkLtekGLv.ertgdeadrre.krv 62
                                      ir  ++++++++l++  ++  s++   l+ Lte++L+ e t+ +ad+   +++
  gi|313126902|ref|YP_004037172.1| 29 IRALVEPMTASELSDECDIPLSTTYRKLDLLTEADLLvEGTEIRADGHHtTTY 81
                                      566789*******************************7777777777665334 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.2
                            HTH_27  11 lirhrrrrkkl.adlcgr 27 
                                       ++r +++++ + ad+  +
  gi|313126902|ref|YP_004037172.1| 102 VVRPEQAPDQQlADIWSA 119
                                       555444444444777555 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.8e-05     0.062      35      60 ..      42      67 ..      15     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                                      HTTTT--HHHHHHHHHHHHHTTSEEE CS
                               FUR 35 eedpeislaTVYrtLklleeaglvke 60
                                      +++ +i l+T Yr L+ll+ea+l+ e
  gi|313126902|ref|YP_004037172.1| 42 SDECDIPLSTTYRKLDLLTEADLLVE 67
                                      567899****************9854 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.23      17      46 ..      35      64 ..      25      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                            HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGl 46
                                       ++ +eL++++++++st+ r l+ L+e+ l
  gi|313126902|ref|YP_004037172.1| 35 PMTASELSDECDIPLSTTYRKLDLLTEADL 64
                                      6899******************99999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 832.92
//
Query:       gi|313126903|ref|YP_004037173.1|  [L=184]
Description: hypothetical protein Hbor_21640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-35  119.8   0.0    1.2e-34  119.5   0.0    1.1  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5   0.0   6.5e-39   1.2e-34       1     132 []      42     180 ..      42     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 6.5e-39
                                       B--GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC..........EE- CS
                               PBP   1 klpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega..........vqg 65 
                                       +lp+++  eg+ +sPpls+ +vp++t+s+alvv DpDap  +  f+Hw+++n+ ++++++pe+           +qg
  gi|313126903|ref|YP_004037173.1|  42 TLPNRFtcEGKGVSPPLSIAGVPDETESLALVVDDPDAPGSDP-FVHWLLWNLVPDTATIPEDVpdkttvldgaRQG 117
                                       589999999******************************5555.******************888888898888999 PP

                                       B-TTSSCCCCS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                               PBP  66 knslgeesesgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                       +n  g+    gY+++cPpkg+g+H+Y f+lya+d+  ld+ka ++r++l++a+++ +la+a++++++
  gi|313126903|ref|YP_004037173.1| 118 TNGGGN---VGYFPACPPKGHGTHTYRFTLYAVDQM-LDVKAAAERSQLQRALDESNLAQARITATF 180
                                       999999...***********************9988.58999999********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1365.81
//
Query:       gi|313126904|ref|YP_004037174.1|  [L=446]
Description: NADH:flavin oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-33  116.9   0.0    4.7e-30  105.0   0.0    2.1  2  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
     0.0089   15.2   0.0      0.015   14.4   0.0    1.3  1  Dus           Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.026   14.0   0.0    1.4  1  His_biosynth  Histidine biosynthesis protein
       0.17   11.8   4.2        0.1   12.6   1.6    2.0  2  Nudix_N_2     Nudix N-terminal


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   1.1e-33   4.7e-30       4     229 ..       6     234 ..       3     318 .. 0.84
   2 !   10.2   0.0   7.4e-05      0.33     284     337 ..     331     383 ..     304     387 .. 0.81

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1.1e-33
                                       S-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-.SCTTSEE-SSGGGH CS
                      Oxidored_FMN   4 kPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksg.gfdnapgiwdeeqi 79 
                                        P++ig +t+ nR++ +p+   +++  +  + d ++   ++ ae + +li  +a+ v  ++g + ++  +++d   +
  gi|313126904|ref|YP_004037174.1|   6 SPFQIGGVTVPNRLYRSPLLECAGNGSD--AVDCLISELEPAAEAGAGLICQGATLVRGEGGcAAPGMTRVHDRAFV 80 
                                       6******************888888888..44678888999*******************99999************ PP

                                       HHHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC............SS.ESSSSSTTT-.S...CS.-EE--HH CS
                      Oxidored_FMN  80 eewrklteavhengskvvvqlwhlGreakseyladqe..........vdspsdpvaldaqeeesaeevy.kkeltke 145
                                        e+  lt+a+h++g+k++vql h+G ++    +a  +          v sp     l  ++  ++   y ++ lt +
  gi|313126904|ref|YP_004037174.1|  81 SELSRLTDAIHDHGGKIAVQLEHGGLRSMETWHAGYRranpeleqlaVSSPP---RLLRAMAATGFLDYdAHVLTTD 154
                                       *************************999544443333455567765444443...3333334577777889****** PP

                                       HHHHHHHHHHHHHHHHHHTT-SEEEEEE-CTSHHHHHH-TTT----STTS.SSHHHHHHHHHHHHHHHHHHH-SSSE CS
                      Oxidored_FMN 146 eikqliqefveAAkraieAgfDgVeihganGYLlnqFlspksnkrtDeyg.GslenRarFllevvdaVkeavgeerv 221
                                       e+ +l  +f + A+ + +Ag+D++   gan  L++qFlsp +n+r De+g G     +rFl  ++d+++ ++g   v
  gi|313126904|ref|YP_004037174.1| 155 EVYELAADFGRSAAWCADAGYDVIHLAGANMGLIHQFLSPFYNRRNDEFGdG-----VRFLEVILDEIRSRAGDVPV 226
                                       *************************************************966.....8*************998888 PP

                                       EEEEECE- CS
                      Oxidored_FMN 222 gyRlSped 229
                                       ++++ +e+
  gi|313126904|ref|YP_004037174.1| 227 MTKVPAET 234
                                       88876665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 7.4e-05
                                       HHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHC CS
                      Oxidored_FMN 284 tefvkevwkkplitvgriadeekaaeivaegeadLvamgRefladpdlveklkk 337
                                          v+ v+++p++  g+i   +++ + +  +  d v++gR+f a+p l+ ++  
  gi|313126904|ref|YP_004037174.1| 331 CRRVRRVVEVPVLCEGGIRGRDEM-DRLLGDACDAVGLGRPFYAEPRLPARVLD 383
                                       46899**************99955.55667899*****************9865 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.3e-06     0.015     175     233 ..     331     385 ..     317     404 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-06
                                       HHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHHHHHSC CS
                               Dus 175 IkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaestavktge 233
                                        + v++ v++pv+  G+I+ ++++++ l    +d+v  gr  + +P l a   +v  g 
  gi|313126904|ref|YP_004037174.1| 331 CRRVRRVVEVPVLCEGGIRGRDEMDRLLGD-ACDAVGLGRPFYAEPRLPA---RVLDGD 385
                                       57899999********************99.9****************98...555544 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-06     0.026      61     114 ..     327     380 ..     323     393 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                                       HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHH CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelike 114
                                       n dl +++++ v++pv   GGIr  +++++ll   +d v +g     +p l  +
  gi|313126904|ref|YP_004037174.1| 327 NADLCRRVRRVVEVPVLCEGGIRGRDEMDRLLGDACDAVGLGRPFYAEPRLPAR 380
                                       566777777777788888888888888888887777777777777666666555 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   4.9e+03      17      31 ..     351     365 ..     347     365 .. 0.80
   2 ?   12.6   1.6   2.2e-05       0.1      11      29 ..     378     396 ..     373     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                                       T-SS-EEEETTTTEE CS
                         Nudix_N_2  17 gDnreRlvCpaCgti 31 
                                        D+  Rl  +aC+++
  gi|313126904|ref|YP_004037174.1| 351 RDEMDRLLGDACDAV 365
                                       588899999999876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.2e-05
                                       EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2  11 elripdgDnreRlvCpaCg 29 
                                         r+ dgD ++R vC++C+
  gi|313126904|ref|YP_004037174.1| 378 PARVLDGDRETRVVCESCN 396
                                       57999*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2802.65
//
Query:       gi|313126905|ref|YP_004037175.1|  [L=172]
Description: phosphatase, c-terminal domain of histone macro h2a1 like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-26   92.9   0.0    1.9e-26   92.4   0.0    1.2  1  Macro         Macro domain
  ------ inclusion threshold ------
      0.048   13.1   0.0      0.089   12.2   0.0    1.4  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.0   2.1e-30   1.9e-26       1     118 []      19     131 ..      19     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 2.1e-30
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEES.E-TTTSTSTTHHH CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvg.plftsskskeeee 76 
                                       VnAa ++l +g+gvaga+ r +g++l+e++ +     g+++lG ++vt+a++l+a +vih+++ p +  ++++ ++e
  gi|313126905|ref|YP_004037175.1|  19 VNAAGTSLRMGSGVAGALRRGGGSELNEAAMAE----GPVDLGAVAVTDAFELDADWVIHAAAmPHY--GDGQATAE 89 
                                       9****************************9999....9***********************664555..49****** PP

                                       HHHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                             Macro  77 llakayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                       ++++a +n+le a+e g++s+++Pa+++G+ g+ +e+ ar++
  gi|313126905|ref|YP_004037175.1|  90 SIRDAARNSLERADELGCESLVMPALGCGVAGFALEDGARII 131
                                       *************************************99985 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.9e-06     0.089      53      94 ..      79     148 ..      63     167 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-06
                                       HSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCC...............................G CS
                      AP_endonuc_2  53 fgypdederearreesvdalkraielaaaLGapllvlhpGt...............................a 94 
                                       ++y d    +a  e  +da+++ +e+a +LG++ lv+++ +                               +
  gi|313126905|ref|YP_004037175.1|  79 PHYGDG---QATAESIRDAARNSLERADELGCESLVMPALGcgvagfaledgariicevidghdpnslsdvrF 148
                                       333332...2224566*********************987777777777777777777765555555554442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 945.14
//
Query:       gi|313126906|ref|YP_004037176.1|  [L=727]
Description: dipeptidyl aminopeptidase/acylaminoacyl peptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-50  169.1   0.0    1.3e-49  168.5   0.0    1.2  1  Peptidase_S9   Prolyl oligopeptidase family
    3.5e-10   39.5  10.8    0.00061   19.7   0.1    5.7  5  PD40           WD40-like Beta Propeller Repeat
    8.8e-06   25.4   0.0    1.5e-05   24.6   0.0    1.3  1  DLH            Dienelactone hydrolase family
    1.3e-05   24.9   0.0      0.095   12.3   0.1    2.3  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    8.9e-05   21.9   0.0     0.0027   17.0   0.0    2.3  2  Hydrolase_4    Serine aminopeptidase, S33
    0.00047   19.0   0.0        1.8    7.2   0.0    3.6  3  DPPIV_N        Dipeptidyl peptidase IV (DPP IV) N-terminal re
  ------ inclusion threshold ------
       0.05   13.3   0.1       0.33   10.6   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
      0.071   12.8   0.0       0.13   11.9   0.0    1.4  1  FSH1           Serine hydrolase (FSH1)
       0.52   11.3   2.4         19    6.4   0.1    4.1  5  WD40           WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.5   0.0   6.7e-53   1.3e-49       3     208 ..     508     711 ..     506     712 .. 0.96

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 6.7e-53
                                       --HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHH CS
                      Peptidase_S9   3 fsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltg 79 
                                       f+++ +++++r+y v+ +n+rG++ yG++f++a+++++g++e++D+ a++++l+++g++ ++r++ +G SyGG   g
  gi|313126906|ref|YP_004037176.1| 508 FRFTHAVFTSRDYLVFRPNYRGGSSYGREFAEALRGQWGTVEVTDIAAGVRELVSRGWAAEDRIFGHGFSYGGIAQG 584
                                       778889999******************************************************************** PP

                                       HHHHH-GGG-SEEEEESE---CCCHHCSTTS..THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT- CS
                      Peptidase_S9  80 aalnqrpdlFkaavaevpvvdvlrydsdtdl..lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaD 154
                                        +++q+pdlF aa+ e +++d+++ + ++d   +t    e+g p+en+e +++ s++++  n  + +plL+i G +D
  gi|313126906|ref|YP_004037176.1| 585 FLVTQEPDLFTAAAPEHGIYDLRSAYGTDDShiWTD--NEFGVPWENPERFEASSSITDIGN--VRTPLLVIAGGED 657
                                       ************************999998866655..899*********************..99*********** PP

                                       SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHH CS
                      Peptidase_S9 155 drvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkea 208
                                        r+pp+++++l+   +k+g++++l+i+pde H vg+p++ +++l +++++++++
  gi|313126906|ref|YP_004037176.1| 658 WRCPPSQSEQLYVSAKKQGVEARLVIYPDEHHNVGDPDRAIHRLDEITSWYERH 711
                                       **************************************************9876 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.073   1.4e+02      15      29 ..      19      33 ..      16      41 .. 0.84
   2 !   19.7   0.1   3.1e-07   0.00061      13      30 ..      67      84 ..      63      90 .. 0.88
   3 !    6.0   0.1    0.0058        12      16      26 ..     176     186 ..     172     191 .. 0.84
   4 ?    1.9   0.2      0.11   2.2e+02      12      31 ..     257     275 ..     252     286 .. 0.80
   5 !   11.3   0.0   0.00013      0.26      16      25 ..     310     319 ..     307     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.073
                                      EE-TTSSEEEEEEEC CS
                              PD40 15 sfSPDGkrlaFsSdR 29
                                      ++SP G r aF+ + 
  gi|313126906|ref|YP_004037176.1| 19 ALSPTGDRAAFVASE 33
                                      89*********9875 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 3.1e-07
                                      EEEE-TTSSEEEEEEECT CS
                              PD40 13 aPsfSPDGkrlaFsSdRg 30
                                      +P++SPDG rlaF+  R+
  gi|313126906|ref|YP_004037176.1| 67 SPTWSPDGDRLAFVAART 84
                                      7************98776 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0058
                                       E-TTSSEEEEE CS
                              PD40  16 fSPDGkrlaFs 26 
                                       +SPDG r++ s
  gi|313126906|ref|YP_004037176.1| 176 WSPDGDRMVVS 186
                                       *******9865 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.11
                                       EEEEE-TTSSEEEEEEECT. CS
                              PD40  12 gaPsfSPDGkrlaFsSdRgs 31 
                                       ++P++ P+  r+a++ + g+
  gi|313126906|ref|YP_004037176.1| 257 MMPTWGPND-RIAYTAYEGE 275
                                       78*******.*****99883 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00013
                                       E-TTSSEEEE CS
                              PD40  16 fSPDGkrlaF 25 
                                       +SPDG+rlaF
  gi|313126906|ref|YP_004037176.1| 310 WSPDGSRLAF 319
                                       ********** PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   7.7e-09   1.5e-05      41     188 ..     520     690 ..     501     713 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 7.7e-09
                               DLH  41 YvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGala.llla 116
                                       Y+++ P+ Y+++    ++ +e a+al++ +  v   +v+d++ a v+ l s++ + ++++   Gf  GG    +l+ 
  gi|313126906|ref|YP_004037176.1| 520 YLVFRPN-YRGGS---SYGREFAEALRGQWGTV---EVTDIA-AGVRELVSRGWAAEDRIFGHGFSYGGIAQgFLVT 588
                                       5555555.33333...56677777777777777...787777.999***********************76526777 PP

                               DLH 117 aevpevdaavafYG..............................lspekeleeaakikapilalfgeeDefipadev 163
                                       +e + + aa++ +G                               ++++ ++++ ++ +p+l+++g+eD   p ++ 
  gi|313126906|ref|YP_004037176.1| 589 QEPDLFTAAAPEHGiydlrsaygtddshiwtdnefgvpwenperFEASSSITDIGNVRTPLLVIAGGEDWRCPPSQS 665
                                       7779**************************************9999999**************************** PP

                               DLH 164 ekleealkaanvdlelkvYpgagHa 188
                                       e+l    k+++v+++l++Yp+  H 
  gi|313126906|ref|YP_004037176.1| 666 EQLYVSAKKQGVEARLVIYPDEHHN 690
                                       *********************9995 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   4.8e-05     0.095      81     145 ..     548     612 ..     507     629 .. 0.81
   2 !   10.3   0.0    0.0002      0.39     221     268 ..     639     689 ..     627     690 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                                       THHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCCCCSEC CS
                     Peptidase_S15  81 deaedgadvidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyddyyre 145
                                        e++d a+ ++ l+   + +++++   G+SY+G+ q  + +++++   a++pe +i dl    y +
  gi|313126906|ref|YP_004037176.1| 548 VEVTDIAAGVRELVSRgWAAEDRIFGHGFSYGGIAQGFLVTQEPDLFTAAAPEHGIYDLRS-AYGT 612
                                       677787777777888878899999999*******************************998.5544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0002
                                       HHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EEEEECECTT CS
                     Peptidase_S15 221 sedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..klilgpwtHv 268
                                        +d+ +v++p+l++ G  Dw     ++ +ly  +k++gv  +l++ p +H 
  gi|313126906|ref|YP_004037176.1| 639 ITDIGNVRTPLLVIAGGEDWRCPpSQSEQLYVSAKKQGVeaRLVIYPDEHH 689
                                       347899*****************************************9996 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.046        92       3     102 ..     489     595 ..     487     600 .. 0.68
   2 !   17.0   0.0   1.3e-06    0.0027     187     233 ..     642     690 ..     634     693 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.046
                       Hydrolase_4   3 pkavvvlvHGlaehsgr..yaelaeaLaaqGfavyalDhrGhGrse......gkrghvpsfddyvdDlaafvekvke 71 
                                       p+ +vv +HG    ++   +  + + ++ +++ v+  ++rG G s         rg++  ++  v+D+aa v+++++
  gi|313126906|ref|YP_004037176.1| 489 PHPLVVAIHGGPVNYDEpvFRFTHAVFTSRDYLVFRPNYRG-GSSYgrefaeALRGQWGTVE--VTDIAAGVRELVS 562
                                       66678888876544432113334455789999999999999.44443666777788777776..8999999998886 PP

                       Hydrolase_4  72 ehpel..plfllGhSmGGliallyllrypdkva 102
                                       +   +  ++f  G S GG+    +++++pd ++
  gi|313126906|ref|YP_004037176.1| 563 RGWAAedRIFGHGFSYGGIAQGFLVTQEPDLFT 595
                                       65444479999999***9776666677776555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.3e-06
                       Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHe 233
                                         ++++Pll++ G++D+ ++p++s++ly +++++  + +l +yp   H 
  gi|313126906|ref|YP_004037176.1| 642 IGNVRTPLLVIAGGEDWRCPPSQSEQLYVSAKKQgvEARLVIYPDEHHN 690
                                       56789***************************99888899999998886 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0   0.00092       1.8      36      61 ..      57      81 ..      28      84 .. 0.80
   2 ?    3.0   0.0     0.017        34     104     175 ..     172     244 ..     166     276 .. 0.76
   3 !    3.9   0.0    0.0095        19      42      59 ..     302     319 ..     272     367 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00092
                                      EEEETTTT.BSEEEEESSTTEEEEEE CS
                           DPPIV_N 36 eelspgeeklqlakwSPagdklafvr 61
                                      ++l++  ++++ ++wSP+gd+lafv 
  gi|313126906|ref|YP_004037176.1| 57 HRLTRV-STAASPTWSPDGDRLAFVA 81
                                      444444.889999***********96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.017
                                       BEEEE-TTSSEEEEEEEECTTS-EEEEEESSSSC-SS-EEEEEE--BTTS--.-EEEEEEEECTTSCEEECS- CS
                           DPPIV_N 104 savwWspdgsrlaylrfdeseVpeitlpsytdeesqypevksikYPkaGskn.pkVelkvvdlasgktvevql 175
                                       +a+ Wspdg+r+++   d +e ++  l +  + +  + e  + k   aG  + ++  l+vvd++sg+t +++ 
  gi|313126906|ref|YP_004037176.1| 172 KAFDWSPDGDRMVVSARDPTEEEREYLDERREGGPIETERLQHKFDGAGYLDtVTTYLFVVDAESGDTGRLDD 244
                                       6889**************9998888887777777788888888899999887677778999998888766554 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0095
                                       TT.BSEEEEESSTTEEEE CS
                           DPPIV_N  42 eeklqlakwSPagdklaf 59 
                                       e+ + l++wSP+g +laf
  gi|313126906|ref|YP_004037176.1| 302 ERVTLLPQWSPDGSRLAF 319
                                       455666777777777776 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.35     7e+02       1      39 [.     491     529 ..     491     538 .. 0.88
   2 ?   10.6   0.0   0.00016      0.33     174     252 ..     617     691 ..     568     694 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.35
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETT CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrG 39 
                                       p++v +hG+p + d +  r+    +  +++ v+ ++ rG
  gi|313126906|ref|YP_004037176.1| 491 PLVVAIHGGPVNYDEPVFRFTHAVFTSRDYLVFRPNYRG 529
                                       6899**********9999888888888899999999998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                                       HHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCH.HHHHHHHHCHTS...EEEEEEE CS
                     Abhydrolase_1 174 gsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvpp.kaledlaqllpk...krlvvis 246
                                        ++++  ++ ++  + e++++  s   +++      v  p lvi+g +D+  pp ++   + ++ ++   +rlv+++
  gi|313126906|ref|YP_004037176.1| 617 IWTDNEFGVPWE--NPERFEASSSITDIGN------VRTPLLVIAGGEDWRCPPsQSEQLYVSAKKQgveARLVIYP 685
                                       444444444433..4455555555555555......555***************55544555556668888999999 PP

                                       TCSSSH CS
                     Abhydrolase_1 247 dagHla 252
                                       d+ H++
  gi|313126906|ref|YP_004037176.1| 686 DEHHNV 691
                                       988876 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.7e-05      0.13     157     201 ..     642     689 ..     559     691 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-05
                              FSH1 157 edkiqtptLhvlGelDtvvdeerseaLaeafkns...skvlkHpggHf 201
                                         +++tp L + G +D   ++++se+L+ + k++   ++++ +p  H+
  gi|313126906|ref|YP_004037176.1| 642 IGNVRTPLLVIAGGEDWRCPPSQSEQLYVSAKKQgveARLVIYPDEHH 689
                                       33459****************************999999999999996 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         9   1.8e+04      14      25 ..      16      27 ..      13      36 .. 0.64
   2 ?    0.7   0.0      0.55   1.1e+03      15      26 ..      61      78 ..      51      88 .. 0.71
   3 ?    6.4   0.1    0.0093        19      12      33 ..     170     191 ..     158     191 .. 0.79
   4 ?   -0.6   0.0       1.4   2.9e+03      17      29 ..     307     322 ..     277     325 .. 0.73
   5 ?   -3.4   0.0         9   1.8e+04      12      31 ..     638     657 ..     633     659 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9
                                      EEEEEETTSSEE CS
                              WD40 14 tslafspdgawl 25
                                      +++a sp g+  
  gi|313126906|ref|YP_004037176.1| 16 SAVALSPTGDRA 27
                                      567789999873 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.55
                                      EEE......EETTSSEEE CS
                              WD40 15 sla......fspdgawla 26
                                       ++      +spdg+ la
  gi|313126906|ref|YP_004037176.1| 61 RVStaasptWSPDGDRLA 78
                                      344444688******985 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0093
                                       SEEEEEEETTSSEEEEEETTSE CS
                              WD40  12 svtslafspdgawlasGsdDgt 33 
                                       +v ++++spdg+ ++ + +D+t
  gi|313126906|ref|YP_004037176.1| 170 GVKAFDWSPDGDRMVVSARDPT 191
                                       378888*******987777987 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.4
                                       E..EETTSSEEE.EEE CS
                              WD40  17 a..fspdgawla.sGs 29 
                                          +spdg+ la  G+
  gi|313126906|ref|YP_004037176.1| 307 LpqWSPDGSRLAfNGG 322
                                       1459****99875565 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 9
                                       SEEEEEEETTSSEEEEEETT CS
                              WD40  12 svtslafspdgawlasGsdD 31 
                                       s+t++ + +   ++++G++D
  gi|313126906|ref|YP_004037176.1| 638 SITDIGNVRTPLLVIAGGED 657
                                       46666222223335678877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (727 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4733.10
//
Query:       gi|313126907|ref|YP_004037177.1|  [L=267]
Description: inositol monophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-35  122.1   0.2    3.3e-35  121.9   0.2    1.0  1  Inositol_P   Inositol monophosphatase family
  ------ inclusion threshold ------
      0.048   12.5   0.0      0.072   11.9   0.0    1.3  1  FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-enco


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.2   3.7e-39   3.3e-35       1     249 [.      11     250 ..      11     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 3.7e-39
                                       CCHHHHHHHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCC CS
                        Inositol_P   1 dleevtkaavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakge 77 
                                       dl++++++a++++++ g  l+++f++ ++  + ++     d+ taad+a+ee +l++++e+fp+h++ gee+++ g+
  gi|313126907|ref|YP_004037177.1|  11 DLDSLAAVATRAVRAGGDYLEDAFRDGSVPGDYGT----DDVKTAADRAAEERVLDVIRESFPDHALHGEESGRNGD 83 
                                       688999******************98888888777....9************************************* PP

                                       CT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTS. CS
                        Inositol_P  78 kseltedgltwivDPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflngeklplsrap. 153
                                            ++ + w+vDP+DGT nF+ g p +a++ ++l +g pv+++i++Pl +++y a +g Ga+++ge+ +++++  
  gi|313126907|ref|YP_004037177.1|  84 -----HH-YEWVVDPLDGTNNFAAGLPAFATAACVLRDGDPVVSAIYEPLPDSTYVARRGAGATVDGEPVSAESDVs 154
                                       .....88.9**********************************************************9988888887 PP

                                       ..EGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEEEEEC.EBHHHHHHHHHH CS
                        Inositol_P 154 ..piseallvtlfavssrkdtseasllekvesavsaegvrsvgssalklaavaeGkadaylefgrekkWDhAAGeai 228
                                         + + +++v+l a ++++    a+ +e++ +  +++ v+s  s ++++ ++a+G ++  + f     +   AGe++
  gi|313126907|ref|YP_004037177.1| 155 leHGTVSFVVGLPAIRDEELAATADRIESAVEDRCKR-VVSTWSPCVDWGLLARGGLEGIVCFY-PDVYEQHAGELL 229
                                       7767777788888888888888888888888888888.99******************999999.9999999***99 PP

                                       HHHTTEEEEESSSC.SSSTTSS CS
                        Inositol_P 229 leeaGGvvtdakge.grlllar 249
                                         e G v+ + +g+ g+++ a+
  gi|313126907|ref|YP_004037177.1| 230 AAESG-VYSHGTGTdGLYVGAT 250
                                       99998.5555555545544443 PP

>> FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-encoded
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.1e-06     0.072      66      99 ..      74     107 ..      63     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-06
                       FBPase_glpX  66 iGekvGsgegpevdiavdpleGttlvAkglpnai 99 
                                       +Ge+ G++ +++++ +vdpl+Gt+  A glp   
  gi|313126907|ref|YP_004037177.1|  74 HGEESGRNGDHHYEWVVDPLDGTNNFAAGLPAFA 107
                                       79999*9877*******************98533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.58
# Mc/sec: 1398.36
//
Query:       gi|313126908|ref|YP_004037178.1|  [L=182]
Description: hypothetical protein Hbor_21690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1261.91
//
Query:       gi|313126909|ref|YP_004037179.1|  [L=152]
Description: hypothetical protein Hbor_21700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 1023.67
//
Query:       gi|313126910|ref|YP_004037180.1|  [L=286]
Description: hypothetical protein Hbor_21720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1914.15
//
Query:       gi|313126911|ref|YP_004037181.1|  [L=451]
Description: hypothetical protein Hbor_21730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-32  109.2   1.2    2.8e-31  107.6   1.2    2.0  1  DUF4157        Domain of unknown function (DUF4157)
     0.0038   17.7   0.1      0.045   14.3   0.0    2.7  3  TipAS          TipAS antibiotic-recognition domain
  ------ inclusion threshold ------
      0.018   15.3   0.5      0.045   14.0   0.0    1.9  2  Flagellin_IN   Flagellin hook IN motif
      0.039   13.9   0.1       0.11   12.4   0.1    1.9  1  ACT_6          ACT domain
       0.25   11.5   1.3         17    5.6   0.0    3.2  3  Ntox34         Bacterial toxin 34
       0.33   11.3   8.0       0.11   12.8   3.1    2.7  2  Peptidase_M91  Effector protein
        1.4    9.1   3.2          6    7.0   0.3    2.9  2  PKHD_C         PKHD-type hydroxylase C-terminal domain


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   1.2   1.1e-34   2.8e-31       2      78 ..      98     174 ..      97     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 1.1e-34
                           DUF4157   2 lpeavraemerafgadlsdVrvhtgsaaaraaralgAqAfTlgndivfaageyqpesaagrellaHELtHvvqqreg 78 
                                       l++++++ me ++g++lsdVr+ht+++aa+a+++++A+AfT+gn+i+f++gey+p+sa+g+++laHEL+Hv qq++g
  gi|313126911|ref|YP_004037181.1|  98 LDTSIQRAMEDRMGDNLSDVRIHTDPSAAKACEDINARAFTVGNHIAFNHGEYDPSSAEGQHILAHELAHVRQQTGG 174
                                       899***********************************************************************986 PP

>> TipAS  TipAS antibiotic-recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         1   2.7e+03      52      72 ..     150     170 ..      99     179 .. 0.75
   2 ?   -3.6   0.0         6   1.5e+04      32      44 ..     266     278 ..     256     288 .. 0.48
   3 !   14.3   0.0   1.8e-05     0.045      56     115 ..     326     387 ..     317     388 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXXXXXXXX CS
                             TipAS  52 kdpdseeaqelaeehraliee 72 
                                        dp+s+e q + +   a++++
  gi|313126911|ref|YP_004037181.1| 150 YDPSSAEGQHILAHELAHVRQ 170
                                       478888888887776666665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6
                                       XXXXXXXXXXXXX CS
                             TipAS  32 elkaelkelfakl 44 
                                        + a l+el  ++
  gi|313126911|ref|YP_004037181.1| 266 SAVADLEELATEI 278
                                       3333333333333 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 1.8e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX..XXXXXXXXXXXX CS
                             TipAS  56 seeaqelaeehralieefwgecskeilaglgqmYvadpr.ftenydkkg..eglaeflrdAik 115
                                       s++ q+l+e+h++l++e +++ s++il+ l+q  + ++  f+++++  g  +g a+ + +Ai+
  gi|313126911|ref|YP_004037181.1| 326 SQDQQKLVEKHKQLVSE-FETLSNDILSELQQGELPEEStFRDFLTDVGisTGVAAVVYKAIE 387
                                       7788************9.555**************66655********99999*******997 PP

>> Flagellin_IN  Flagellin hook IN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.8e-05     0.045      18      41 ..     266     289 ..     265     291 .. 0.93
   2 ?   -3.7   0.1       5.9   1.5e+04      36      43 ..     375     382 ..     373     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                       CTTTBCHHHHHHHHHHCCTTTEEE CS
                      Flagellin_IN  18 kagdtlddiadaINavssktGVsA 41 
                                       +a ++l+++a+ IN  s+ tGV+ 
  gi|313126911|ref|YP_004037181.1| 266 SAVADLEELATEINELSAATGVTV 289
                                       5789******************95 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.9
                                       TTTEEEEE CS
                      Flagellin_IN  36 ktGVsAsi 43 
                                       +tGV A++
  gi|313126911|ref|YP_004037181.1| 375 STGVAAVV 382
                                       59999986 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.5e-05      0.11      31      64 ..     237     270 ..     229     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                             ACT_6  31 lDieqavihgrlsLgllvsgpedalarlekaLlf 64 
                                        D eqa+i+++ + g+l++++ ++l++l++a+  
  gi|313126911|ref|YP_004037181.1| 237 GDTEQAIIEEEATQGVLLDIDPEKLEQLQSAVAD 270
                                       699*************************998754 PP

>> Ntox34  Bacterial toxin 34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.082   2.1e+02      57      77 ..      55      74 ..      34      77 .. 0.88
   2 ?    5.6   0.0    0.0068        17       9      33 ..      90     114 ..      85     137 .. 0.73
   3 ?    0.1   0.0      0.35     9e+02      17      51 ..     370     404 ..     366     411 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.082
                            Ntox34 57 GdiskkdrikktqkaknCrhs 77
                                       di +++ +k+ q++++  h 
  gi|313126911|ref|YP_004037181.1| 55 KDIERRN-AKSVQRSRGAHHE 74
                                      59999*9.*********9995 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0068
                            Ntox34   9 liarrGnvadtGiteevedlindrf 33 
                                       +i+++G + dt i   +ed + d +
  gi|313126911|ref|YP_004037181.1|  90 VISSPGQQLDTSIQRAMEDRMGDNL 114
                                       799***********99999997753 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.35
                            Ntox34  17 adtGiteevedlindrfwsdGkkadiCdvldelie 51 
                                        d Gi   v +++   + s+   a+   +l+  ++
  gi|313126911|ref|YP_004037181.1| 370 TDVGISTGVAAVVYKAIESQTDHATLASMLQSELD 404
                                       699**********9999999999999999998776 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.1   4.2e-05      0.11      38     135 ..     103     197 ..      68     308 .. 0.79
   2 ?   -2.6   0.2       2.3     6e+03      19      43 ..     318     342 ..     315     364 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                     Peptidase_M91  38 ksskse....gerkltikelvdedngtakyee..kekgegtdaeinynpafsseeegkegrPsavLyHElaHaydal 108
                                       ++++++    + +++ i+     d ++ak  e  + + ++ +++i +n         +  + +++L+HElaH+++++
  gi|313126911|ref|YP_004037181.1| 103 QRAMEDrmgdNLSDVRIHT----DPSAAKACEdiNARAFTVGNHIAFNHGEYDP---SSAEGQHILAHELAHVRQQT 172
                                       4444443332333344444....2222222223455566666777777663333...5556669************* PP

                     Peptidase_M91 109 ngtlddgeydgkdeedssgvpneErqA 135
                                        g +   +++g+ e d +   + Er+A
  gi|313126911|ref|YP_004037181.1| 173 GGAVSMLPQEGSLEIDPDP--RLEREA 197
                                       **99888887777666655..555554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                     Peptidase_M91  19 adLdmlsssptGqqlLeelksskse 43 
                                        dL  ++ s++ q+l+e+ k+ +se
  gi|313126911|ref|YP_004037181.1| 318 HDLSEMGLSQDQQKLVEKHKQLVSE 342
                                       6888999999999999888887776 PP

>> PKHD_C  PKHD-type hydroxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3    0.0024         6      10      24 ..       4      19 ..       3      24 .. 0.87
   2 ?    1.1   0.2      0.16   4.1e+02       9      22 ..      97     110 ..      96     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0024
                            PKHD_C 10 LDqaIqrlraelg.dd 24
                                      LD++Iqrl++++g d+
  gi|313126911|ref|YP_004037181.1|  4 LDTKIQRLAKKHGaDQ 19
                                      9************554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
                            PKHD_C   9 dLDqaIqrlraelg 22 
                                       +LD++Iqr  ++  
  gi|313126911|ref|YP_004037181.1|  97 QLDTSIQRAMEDRM 110
                                       69*****9877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3170.77
//
Query:       gi|313126912|ref|YP_004037182.1|  [L=266]
Description: hypothetical protein Hbor_21740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-69  234.2   0.9    2.6e-40  138.3   0.1    2.0  2  DUF2071   Uncharacterized conserved protein (COG2071)
     0.0029   17.2   0.0     0.0044   16.6   0.0    1.2  1  ADC       Acetoacetate decarboxylase (ADC)


Domain annotation for each model (and alignments):
>> DUF2071  Uncharacterized conserved protein (COG2071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.1   6.2e-31   5.6e-27       2      74 ..      16      85 ..      15      92 .. 0.93
   2 !  138.3   0.1   2.9e-44   2.6e-40      75     211 ..     116     256 ..     109     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 6.2e-31
                           DUF2071  2 qeWrdllflhwpvdpealapllPaglelDtfdGkayvslvpFrmedvrvrglpavpglstfpelNvRtYvrdk 74
                                      ++Wrd lf+hw+ dpe +a  lP+g+e+ tfdG+a++++v+F+med+r+ g+p  +gls fpelN+RtYv+++
  gi|313126912|ref|YP_004037182.1| 16 MRWRDALFAHWETDPETVAGRLPPGVEVATFDGHAWLGVVAFVMEDIRPCGVP--FGLS-FPELNLRTYVTRS 85
                                      89*************************************************98..7888.**********876 PP

  == domain 2  score: 138.3 bits;  conditional E-value: 2.9e-44
                           DUF2071  75 egrrGVvFlsldadrllivlvarllfglpYvtarmrveeee.geveyksrr.....sparfaatyrptaeveeaepg 145
                                       +  r+V+F++ldad++l v++arll+ lpY++a+mrv++   +++e++s+r     +pa+f+aty+p ++ +++epg
  gi|313126912|ref|YP_004037182.1| 116 DSARAVYFFNLDADDRLGVALARLLYSLPYYRADMRVRSGAdESIEFASQRthwnaPPAHFDATYEPVGDDFTPEPG 192
                                       6689**********************************555899***999889************************ PP

                           DUF2071 146 sleeflteryrlYtrrrgrlleyeveHepwplqeaellelentlleaaglplkpsseplvlyspgv 211
                                       +le+f +e+yr+Yt    rl++++++H+pwpl+ea++++++ntl++a+g+++ p++ep+v+yspg+
  gi|313126912|ref|YP_004037182.1| 193 TLEHFFVENYRFYTV-GRRLYYGDISHPPWPLYEANAEIRSNTLFAANGFET-PTDEPVVHYSPGI 256
                                       **************9.56*********************************8.988********97 PP

>> ADC  Acetoacetate decarboxylase (ADC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.9e-07    0.0044      11      57 ..      10      63 ..       4      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-07
                                      TTSSSEE.EEEEEEEEEEE-HHHHHTTSBTTEEECS......TSEEEEEEEEEE CS
                               ADC 11 ksalvpy.naealtvsyrtdpeaaaallPepLelae......rplvavyfaeyp 57
                                       +alv++  ++al ++++tdpe++a  lP++ e+a        ++va+++ +++
  gi|313126912|ref|YP_004037182.1| 10 DEALVQMrWRDALFAHWETDPETVAGRLPPGVEVATfdghawLGVVAFVMEDIR 63
                                      467777459**************************9956555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1865.34
//
Query:       gi|313126913|ref|YP_004037183.1|  [L=152]
Description: copper resistance protein d [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-07   32.2   4.7    1.1e-07   32.2   4.7    1.9  2  CopD      Copper resistance protein D


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4      0.08   1.4e+03      11      25 ..      16      30 ..       5      42 .. 0.68
   2 !   32.2   4.7     6e-12   1.1e-07      13     104 ..      56     144 ..      52     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.08
                              CopD 11 alaavavvlvtGvvn 25
                                      al++  vv+v Gvv+
  gi|313126913|ref|YP_004037183.1| 16 ALWVGSVVFVAGVVL 30
                                      445555555666554 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 6e-12
                              CopD  13 aavavvlvtGvvnallrvglagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqalrhrlrrsaa 89 
                                       aa ++++ tG  +a  r++++ l + ++G l+la+l+l+lvl+al  + r rlv  l+   +++ +++++  +  ++
  gi|313126913|ref|YP_004037183.1|  56 AASVIMFFTGGHLAGTRYTFDLLMNESRGHLVLAMLVLWLVLTALVEIGRSRLVDGLR---EKRVRTPAENAADIFR 129
                                       6789999**************************************************5...4666777777777777 PP

                              CopD  90 lelvlalvvlllaaa 104
                                       + +v++++ l+ a++
  gi|313126913|ref|YP_004037183.1| 130 AAAVVGILLLVDAGL 144
                                       777777777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 998.07
//
Query:       gi|313126914|ref|YP_004037184.1|  [L=42]
Description: hypothetical protein Hbor_21760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       158  (0.00881254); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 296.60
//
Query:       gi|313126915|ref|YP_004037185.1|  [L=344]
Description: phosphohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-16   61.6   1.7    1.8e-16   61.3   1.7    1.1  1  Metallophos    Calcineurin-like phosphoesterase
    2.5e-09   37.6   0.1    2.5e-08   34.3   0.1    2.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   1.7     2e-20   1.8e-16       2     204 .]      37     242 ..      36     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2e-20
                                       EEEEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.HHHHHHHHH.HHHHHHHTS CS
                       Metallophos   2 rilvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrg.dlekellel.laalvkypi 65 
                                       ri+v++D+Hl           ++++ +l++++++++dl    ++d+ l +GDl+ +g + e ++++  la l     
  gi|313126915|ref|YP_004037185.1|  37 RIAVVSDPHLtptatgtwkvyHRTETRLRAAIAAINDL----NVDATLSLGDLTRDGhPEEFDCVDElLADLDT--- 106
                                       8*************999988888888888888888888....**************964444444443666666... PP

                                       EEEEEC-TTS...CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE..EEEEEEESE.CEEETHHHHHHH CS
                       Metallophos  66 pvylllGNHe...gfee.ellnkygylgifsepwrsdaevfnnlplaslgsgs..lkvlllhGg.spellvsldklg 135
                                       p++ ++GNH+   ++++ e +   ++ ++++++   ++  ++++ l++l + s   +++  h g             
  gi|313126915|ref|YP_004037185.1| 107 PFVSVPGNHDvpkQWDDyEAPTVDEFGARYARGAFPFHVSVGGVDLIGLDTASgdGTLYDSHEGlV----------- 172
                                       *************99999************999999999999999999777777768888888831........... PP

                                       HHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESS...........CSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                       Metallophos 136 slnleleapepgdewlkdlekrekadwvivlgHsply...........rgsgylfgdealedllkkygvdlvisGHt 201
                                             ++++    wl +    ++++  iv +H+++            +  ++l + +++ ++l  +g  lv+sGH+
  gi|313126915|ref|YP_004037185.1| 173 ------PSEH--VAWLDE--TLSEVESPIVASHHNVFhprehtgqfadEDFYQLRNADEVVEVLSSGGDPLVLSGHI 239
                                       ......2222..455555..666677778888888887887788778777777777777779*************** PP

                                       SSE CS
                       Metallophos 202 Hvy 204
                                       H++
  gi|313126915|ref|YP_004037185.1| 240 HWP 242
                                       *96 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   2.8e-12   2.5e-08       2     139 ..      37     251 ..      37     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.8e-12
                     Metallophos_2   2 klaiiSDlH.............snldaleavlealkevgvdaiihaGDl....eeeepevleellela..pvlaVrG 59 
                                       ++a++SD H             +   +l+a+++a+++ +vda + +GDl      ee+++++ell+ +  p++ V+G
  gi|313126915|ref|YP_004037185.1|  37 RIAVVSDPHltptatgtwkvyhRTETRLRAAIAAINDLNVDATLSLGDLtrdgHPEEFDCVDELLADLdtPFVSVPG 113
                                       6899*****9999999999999888999999******************94444444458888877779******** PP

                     Metallophos_2  60 NnD..................................................eevveedvlreaaelgtdlpeeae 86 
                                       N+D                                                  +  +e  v  e   + ++  +e e
  gi|313126915|ref|YP_004037185.1| 114 NHDvpkqwddyeaptvdefgaryargafpfhvsvggvdligldtasgdgtlydS--HEGLVPSEHVAWLDETLSEVE 188
                                       ***988887777777777777777777777666666666666555554433220..233333333333333323333 PP

                     Metallophos_2  87 lelagekvlliHgdpl.................gvkdalaellkeaeegsdvvvcGHtHvpevekeggvl 139
                                              +   H+                    + +d++ e+l++   g+ +v++GH+H p   ++ggv+
  gi|313126915|ref|YP_004037185.1| 189 SP-----IVASHHNVFhprehtgqfadedfyqlRNADEVVEVLSS--GGDPLVLSGHIHWPATARRGGVR 251
                                       33.....33333322244444777777776655555777777777..6777**********999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2384.27
//
Query:       gi|313126916|ref|YP_004037186.1|  [L=253]
Description: hypothetical protein Hbor_21780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.034   14.0   0.5      0.083   12.7   0.5    1.7  1  DUF3670       SNF2 Helicase protein
      0.091   12.9   0.3       0.21   11.7   0.3    1.5  1  Ferredoxin_N  N-terminal region of 4Fe-4S ferredoxin iron-sul


Domain annotation for each model (and alignments):
>> DUF3670  SNF2 Helicase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   9.3e-06     0.083      76     116 ..     160     197 ..     110     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.3e-06
                           DUF3670  76 alGdeeLseeEldrLaeakrpLvrlrgqWvevdpeelrral 116
                                       al+de+Ls++ +++L +  +++v +r++   +d++++rr  
  gi|313126916|ref|YP_004037186.1| 160 ALDDEPLSKRSFENLTRLRESVVSVRDR---LDEAAVRRQT 197
                                       9**************************7...6666666554 PP

>> Ferredoxin_N  N-terminal region of 4Fe-4S ferredoxin iron-sulfur binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   2.3e-05      0.21      42      60 ..      82     100 ..      76     102 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                      Ferredoxin_N  42 eaeFhekYheaVlaEFgeD 60 
                                       e+e+ + Y e V+aEFgeD
  gi|313126916|ref|YP_004037186.1|  82 EDEYGDTYTESVTAEFGED 100
                                       78999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1645.74
//
Query:       gi|313126917|ref|YP_004037187.1|  [L=155]
Description: hypothetical protein Hbor_21790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-19   69.1   0.1    3.8e-19   68.6   0.1    1.2  1  bPH_2     Bacterial PH domain
  ------ inclusion threshold ------
      0.039   14.0   0.3      0.093   12.7   0.2    1.6  2  DUF1453   Protein of unknown function (DUF1453)


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.1   4.3e-23   3.8e-19       1      80 []      63     142 ..      63     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 4.3e-23
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeela 77 
                                       yr+++y+++++ +++ +G+++r+++++p+ rIq+v+ ++++++r +gl++ v++tag+ +a+v +p++  + a+el+
  gi|313126917|ref|YP_004037187.1|  63 YRSWGYEVREDSLYLERGVFTRVRTVVPFVRIQHVDSSRGPVERVIGLASTVVYTAGSRGADVSVPGLTADSADELR 139
                                       89*************************************************************************** PP

                             bPH_2  78 ell 80 
                                       e+l
  gi|313126917|ref|YP_004037187.1| 140 ERL 142
                                       976 PP

>> DUF1453  Protein of unknown function (DUF1453)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.033     3e+02      56      70 ..      16      31 ..       4      36 .. 0.59
   2 ?   12.7   0.2     1e-05     0.093      39      90 ..      27      81 ..      15      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.033
                           DUF1453 56 evleallvGa.lfsip 70
                                       +l al++Ga lf+++
  gi|313126917|ref|YP_004037187.1| 16 AALTALVIGAlLFAVV 31
                                      4567778887666654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1e-05
                           DUF1453 39 stGalmfvfpefrltll...evleallvGalfsipliktskfevrdgkiylkrsk 90
                                        ++++fv p+f +++      ++ +++Ga ++i   +   +evr++ +yl r  
  gi|313126917|ref|YP_004037187.1| 27 LFAVVQFVSPPFLPSWSpyaATAVVFVLGASLAIARYRSWGYEVREDSLYLERGV 81
                                      4567899999998777521145566889***********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1102.44
//
Query:       gi|313126918|ref|YP_004037188.1|  [L=563]
Description: hypothetical protein Hbor_21800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-47  159.1   3.2    1.3e-19   70.1   0.3    3.4  3  bPH_2     Bacterial PH domain
  ------ inclusion threshold ------
       0.19   11.9   0.0        1.1    9.4   0.0    2.2  2  bPH_4     Bacterial PH domain
       0.75    9.0  17.3        1.1    8.5   0.1    3.3  3  UbiA      UbiA prenyltransferase family
       0.83    8.3   3.2        8.6    5.0   0.1    2.8  3  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.3     3e-23   1.3e-19       1      79 [.      67     145 ..      67     146 .. 0.98
   2 !   36.8   0.0   7.4e-13   3.3e-09       1      76 [.     242     327 ..     242     331 .. 0.86
   3 !   51.1   0.2   2.6e-17   1.2e-13       1      79 [.     396     477 ..     396     478 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3e-23
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeela 77 
                                       yr++ty++t +++ + sG++ r++++ipl rIq+v+++++++qr +g++ +++etagg+  e++l+++s ++a++l+
  gi|313126918|ref|YP_004037188.1|  67 YRRFTYELTADTFDIESGVFARRNREIPLGRIQNVDISRNVIQRAMGIAAVSFETAGGTETEAKLRFVSFEEAKRLQ 143
                                       8***************************************************************************9 PP

                             bPH_2  78 el 79 
                                       + 
  gi|313126918|ref|YP_004037188.1| 144 RE 145
                                       86 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 7.4e-13
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsrae..........velpl 67 
                                       y++++ + + ++++  +G+l+r    ip++++q++++++++l r+ g++t+ +etag +  +          + +p+
  gi|313126918|ref|YP_004037188.1| 242 YYGFRLVQSADELQYERGLLQRYDGSIPFDKVQTLTIADNPLKRWAGYATLLVETAGYAPGQgdsgssrgseAAVPI 318
                                       67788888999**********************************************99877777777777777777 PP

                             bPH_2  68 rsvpdaeel 76 
                                        s+++ e+l
  gi|313126918|ref|YP_004037188.1| 319 ASRERIEDL 327
                                       777776666 PP

  == domain 3  score: 51.1 bits;  conditional E-value: 2.6e-17
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsrae...velplrsvpdae 74 
                                       +++ + ++ +++vv r G+l+r+t ++p+ rIq+v  +++++qrrl+l+t+ i+tag+ +     v   +++ + a+
  gi|313126918|ref|YP_004037188.1| 396 WKHRGLWLGENHVVTRNGVLKRETKIVPYYRIQTVIDSRTIFQRRLRLATVTIDTAGSLSLGgqdVAAVDIDTDYAD 472
                                       778889999************************************************97644667999999999999 PP

                             bPH_2  75 elael 79 
                                       el++ 
  gi|313126918|ref|YP_004037188.1| 473 ELRDE 477
                                       99876 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00024       1.1       2      38 ..      71     110 ..      70     123 .. 0.86
   2 ?   -1.2   0.0      0.51   2.3e+03      12      37 ..     410     438 ..     403     449 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00024
                             bPH_4   2 kYeitegvLliksG.firkk..IpiedIkkirktksplss 38 
                                       +Ye+t +++ i+sG f r+   Ip+ +I+++  +++++ +
  gi|313126918|ref|YP_004037188.1|  71 TYELTADTFDIESGvFARRNreIPLGRIQNVDISRNVIQR 110
                                       7*************88776567************998875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.51
                             bPH_4  12 iksGfirkk...IpiedIkkirktkspls 37 
                                        ++G ++++   +p+ +I+++  +++++ 
  gi|313126918|ref|YP_004037188.1| 410 TRNGVLKREtkiVPYYRIQTVIDSRTIFQ 438
                                       55564433324589999999999998886 PP

>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   4.5    0.0039        17      67     115 ..      23      71 ..      11      75 .. 0.73
   2 ?    2.6   1.8     0.015        68     196     237 ..     200     251 ..     187     260 .. 0.61
   3 ?    8.5   0.1   0.00025       1.1     191     236 ..     350     398 ..     323     403 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0039
                              UbiA  67 kealifaivllilgllllalllnpltallgllallly.vvYt.glrlKrrt 115
                                        +al fa++++  +l ++  +++pl+++ ++  ++++ v+Y    ++ r+t
  gi|313126918|ref|YP_004037188.1|  23 VAALGFALATGGFSLPFA-GITGPLVLVGLASLFAIAlVAYEfA-YYRRFT 71 
                                       478889999999999998.9999998887777777778888844.555554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.015
                              UbiA 196 lavllla..........llllllalllllylllalllaalallraarlvrrr 237
                                       ++v++l+          l++++l+ll  l+ +++ +++a+  ++ +rlv++ 
  gi|313126918|ref|YP_004037188.1| 200 TVVTSLFpsdlgpvvvvLGTFVLLLLVILASWITGAAIAIVNYYGFRLVQSA 251
                                       4455555555554444455566666666666666666666666666666655 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00025
                              UbiA 191 l...lalllavlllallllllalllllylllalllaalallraarlvrr 236
                                       +   + +++ ++ ++l +++  + l+l++++ l+l+++a + a++ ++ 
  gi|313126918|ref|YP_004037188.1| 350 YfgrYSIVIGAATAVLSVAGSVASLGLPWYAPLALIPVAAVAAHYKWKH 398
                                       2354344444444446777888888888888888888888888887765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.7     0.072   3.2e+02     388     438 ..      21      71 ..      13      81 .. 0.51
   2 ?    5.0   0.1    0.0019       8.6     349     419 ..     138     230 ..     103     258 .. 0.67
   3 ?    0.8   0.0     0.035   1.6e+02     376     425 ..     344     391 ..     313     402 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.072
                           DUF2207 388 lgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrt 438
                                        +++ lg++l+++++ l ++++++ l+l+ +  l+ai+++++  ++ +r+t
  gi|313126918|ref|YP_004037188.1|  21 SIVAALGFALATGGFSLPFAGITGPLVLVGLASLFAIALVAYEFAYYRRFT 71 
                                       455555555555555554443444444444444444444444444444444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0019
                           DUF2207 349 kakkfkkalkkwksavkk.......kergyfdkkgkkklkklsalglgliilglilillallllvll.......... 408
                                       +ak+++++l ++k++  +       +++++f+ +  ++l +l+al++ + + g+i+++++  l v++          
  gi|313126918|ref|YP_004037188.1| 138 EAKRLQRELGRLKRGESAdedadtpVAEELFKLE-GRELGILGALSFDFRVPGIIFLFFSGSLTVVTslfpsdlgpv 213
                                       7777777777777776667788888788888888.577789999999999999998888877777778888876555 PP

                           DUF2207 409 ......lvfllilllil 419
                                             +v+ll+++l+ 
  gi|313126918|ref|YP_004037188.1| 214 vvvlgtFVLLLLVILAS 230
                                       44332222222222222 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.035
                           DUF2207 376 gkkklkklsalglgliilglilillallllvlllvfllilllillliaii 425
                                       +++++ +++ ++++++ +  +l++++ ++      +++ +l +++++a++
  gi|313126918|ref|YP_004037188.1| 344 KRTRRRYFGRYSIVIGAATAVLSVAGSVASL--GLPWYAPLALIPVAAVA 391
                                       3555556666666666666666655555544..44555555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 3449.23
//
Query:       gi|313126919|ref|YP_004037189.1|  [L=119]
Description: hypothetical protein Hbor_21810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0031   17.7   1.7      0.056   13.6   1.7    2.0  1  Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygena


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   1.7   3.1e-06     0.056       9     128 .]      11     108 ..       5     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-06
                                       ESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHC CS
                        Glyoxalase   9 vgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdve 85 
                                       +++ e +++FYt+ +G+++  +                +   +++ +l+   +g+++           v f++++ +
  gi|313126919|ref|YP_004037189.1|  11 TTNRETTTAFYTDTVGAEVWLEQS-------------GCTILRHGNMLFGFCDGDETET------DGIVTFVYDTAD 68 
                                       556667777888888877766666.............4555666666666666666665......566899****** PP

                                       HHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  86 dvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       +v+++++r+ +a     + p  +   ++y f++ DpdG ++e+
  gi|313126919|ref|YP_004037189.1|  69 EVDEMHERVGDAA---REAPHENEQYDIYQFFAADPDGRTVEF 108
                                       *********9999...99999999*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 891.09
//
Query:       gi|313126920|ref|YP_004037190.1|  [L=229]
Description: carbonic anhydrase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-25   89.2   0.0    4.3e-25   88.8   0.0    1.1  1  Pro_CA    Carbonic anhydrase


Domain annotation for each model (and alignments):
>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.0   2.4e-29   4.3e-25       2     153 ..      35     190 ..      34     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 2.4e-29
                                       EEEEETTTTS-HHHHTTS-T.TSEEEEEETTG---TT...-HHHHHHHHHHHHTS--SEEEEEEETT-HHHHHHHS. CS
                            Pro_CA   2 lvigCsDSRvppelitdagp.GdlFvvrnvgnlvppa...dssvlaaleyAvevlkvkhivVlGHskCGavkaalk. 73 
                                       + ++CsDSRvp+e ++da+  GdlF+  nvg+   ++   +  v  a+ yAv++l+v+ i VlGH++CGav+aa++ 
  gi|313126920|ref|YP_004037190.1|  35 VSVSCSDSRVPAEGVWDANAdGDLFTSVNVGDQAWTDvdgELVVNDAVGYAVSALDVELIAVLGHTGCGAVTAAYEs 111
                                       679*************98654*************988887888899***************************9998 PP

                                       ..HHCCSTTSSHHHHHHHHHHHHHHHCHHHHHTTS...SHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHTTS-EEE CS
                            Pro_CA  74 ..aekseeeagaidkwlekirealekveeelesek...ekearerlleeenVaeqlenLlekpvvreavekgklkvh 145
                                          e++++  +a+++ + ++ +++e+ +e+   ++   + ea+++l +e++V+eq++ L+e+++v +      ++v 
  gi|313126920|ref|YP_004037190.1| 112 vtGESETSLLPAVEAAVARLTPIVESAREDGVFDDdtpRGEAVNKL-VERAVQEQVDFLVETDAVPDD-----VAVA 182
                                       8744556668899999999999999977665444456455555555.***************999855.....5788 PP

                                       EEEEETTT CS
                            Pro_CA 146 Glvydlet 153
                                       G vyd+++
  gi|313126920|ref|YP_004037190.1| 183 GFVYDFQH 190
                                       99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1653.97
//
Query:       gi|313126921|ref|YP_004037191.1|  [L=218]
Description: 2-keto-3-deoxy-phosphogluconate aldolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-44  150.5   2.3    4.6e-44  150.2   2.3    1.0  1  Aldolase    KDPG and KHG aldolase
     0.0012   18.1   6.5        1.4    8.1   1.5    3.0  3  DHO_dh      Dihydroorotate dehydrogenase
     0.0023   17.3   1.7       0.08   12.3   1.7    3.0  1  TMP-TENI    Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.029   14.4   0.0      0.097   12.8   0.0    1.8  2  YaiA        YaiA protein
      0.078   13.2   0.2       0.22   11.7   0.1    1.8  2  Ferritin_2  Ferritin-like domain


Domain annotation for each model (and alignments):
>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.2   2.3   1.3e-47   4.6e-44       5     195 ..      13     204 ..      10     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 1.3e-47
                                       HHCHSEEEEE--SSGGGHHHHHHHHHHTT--EEEEETTSTTHHHHHHHHHHH..-TTSEEEEES--SHHHHHHHHHC CS
                          Aldolase   5 lkeakvvpvivikdkedalplaeaLvagGlrvlevtlrteaaldairvlrke..rpdllvgaGtvlnaeqlaeakea 79 
                                       l  + vv+v++ +d++ +l++a+aL +gG+ + e+t   + a+d i  + +     +++vgaGtvl++e + +    
  gi|313126921|ref|YP_004037191.1|  13 LVDSGVVAVMRGADADTILEVAQALHDGGVTAYEITADNPDAMDLISEVSASfsETEAIVGAGTVLDSETARASIMN 89 
                                       566789****************************************877665115689******************* PP

                                       T-SEEEESS--HHHHHHHHHTTS-EEEEESSHHHHHHHHHTT--EEEETTTTTTTHHHHHHHHCTTTTT-EEEEBSS CS
                          Aldolase  80 GaqfvvsPGltadllkaavdlkipllPGvstpseimlaldlGlkrlklfPaeasGGvkalkalagpfaqvrfiPtGG 156
                                       Ga+fvv P + + ++++++   + + PG+ tp+e   a++ G + +k+fPa ++G  k l ++ gp +q+ ++PtGG
  gi|313126921|ref|YP_004037191.1|  90 GAEFVVGPSFDEGVVETCNRYGTIVAPGILTPTEAVDAYEAGADLVKVFPASVMG-PKHLASIKGPLPQIPLMPTGG 165
                                       ******************************************************9.89******************* PP

                                       --TTTHHHHHTSTTBS-EEESCCC-HHHHHTT-HHHHHH CS
                          Aldolase 157 ispanvrdylalpsvlvvgGswlveaslikkedldkitk 195
                                       i   nv dy+++++v+v +Gs +++a++i+++d+++it+
  gi|313126921|ref|YP_004037191.1| 166 IGIDNVADYIEAGAVVVGAGSAIMDADAIEAGDFEAITE 204
                                       ************************************985 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.1    0.0051        18     216     270 ..      37      94 ..      16     101 .. 0.82
   2 !    7.7   0.0   0.00052       1.9     248     289 ..     113     153 ..     103     157 .. 0.84
   3 !    8.1   1.5   0.00038       1.4     243     277 ..     156     189 ..     153     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0051
                                       TSSEEEEEGGG...HHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEE CS
                            DHO_dh 216 nktGGlsGkal...kdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslv 270
                                        + GG+   ++    + a+ +i e+++ ++++  i+g G +  +e a   i+ GA +v
  gi|313126921|ref|YP_004037191.1|  37 LHDGGVTAYEItadNPDAMDLISEVSASFSETEAIVGAGTVLDSETARASIMNGAEFV 94 
                                       466777777773334789*************************************887 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00052
                                       EEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHH CS
                            DHO_dh 248 IgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikk 289
                                       I   Gi +   a++ +eaGA lv+v+ a    gpk    ik 
  gi|313126921|ref|YP_004037191.1| 113 IVAPGILTPTEAVDAYEAGADLVKVFPAS-VMGPKHLASIKG 153
                                       55569*********************999.678888888876 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00038
                                       T.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                            DHO_dh 243 keipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                       ++ip++ +GGi   + + ++ieaGA +v  ++a++
  gi|313126921|ref|YP_004037191.1| 156 PQIPLMPTGGIG-IDNVADYIEAGAVVVGAGSAIM 189
                                       58*********6.57799**************986 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   1.7   2.2e-05      0.08     135     181 .]     141     188 ..      18     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                          TMP-TENI 135 eplgleglkelaeale.iPvvaiGGitlenvaevleagadgvavvsai 181
                                       +++g + l+ ++  l  iP++  GGi  +nva+ +eaga  v   sai
  gi|313126921|ref|YP_004037191.1| 141 SVMGPKHLASIKGPLPqIPLMPTGGIGIDNVADYIEAGAVVVGAGSAI 188
                                       89999999999999999**********************998887776 PP

>> YaiA  YaiA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.7e-05     0.097      13      46 ..      30      63 ..      25      73 .. 0.79
   2 ?   -2.0   0.0       1.1   3.9e+03      20      33 ..     120     133 ..     109     137 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                              YaiA 13 ivtvekGtagktvtwYeLRaDhPkPdtLisehet 46
                                      i +v +   +  vt Ye+ aD P    Lise  +
  gi|313126921|ref|YP_004037191.1| 30 ILEVAQALHDGGVTAYEITADNPDAMDLISEVSA 63
                                      566666677788*******************764 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                              YaiA  20 tagktvtwYeLRaD 33 
                                       t+ ++v  Ye  aD
  gi|313126921|ref|YP_004037191.1| 120 TPTEAVDAYEAGAD 133
                                       66667777776666 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.2e-05      0.22      80     110 ..      25      55 ..      12      75 .. 0.79
   2 ?   -1.9   0.0      0.96   3.4e+03      61     105 ..      87     133 ..      78     138 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                        Ferritin_2  80 adeksflalaavlEdvgvsAYlgaapllsnk 110
                                       ad +++l++a++l d+gv+AY  +a + +  
  gi|313126921|ref|YP_004037191.1|  25 ADADTILEVAQALHDGGVTAYEITADNPDAM 55 
                                       68899****************9888765544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.96
                        Ferritin_2  61 le.Gaaavakptfdf.afdpfadeksflalaavlEdvgvsAYlgaap 105
                                       +  Ga+ v  p fd   +++ +++ +++a     ++ +v+AY   a 
  gi|313126921|ref|YP_004037191.1|  87 IMnGAEFVVGPSFDEgVVETCNRYGTIVAPGILTPTEAVDAYEAGAD 133
                                       44577777777777643444455555555555556667777765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1384.61
//
Query:       gi|313126922|ref|YP_004037192.1|  [L=251]
Description: multidrug ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-24   86.9  11.5    1.2e-24   86.9  11.5    1.4  2  ABC2_membrane    ABC-2 type transporter
    4.4e-17   62.2   3.7    4.4e-17   62.2   3.7    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
    8.6e-09   35.1  17.5    2.6e-08   33.5  17.1    1.8  2  ABC2_membrane_2  ABC-2 family transporter protein
    0.00015   21.8   3.9    0.00015   21.8   3.9    1.5  2  ABC2_membrane_4  ABC-2 family transporter protein
     0.0037   16.4   2.8     0.0054   15.9   2.8    1.2  1  12TM_1           Membrane protein of 12 TMs
  ------ inclusion threshold ------
       0.83    9.8  11.5       0.19   11.9   3.7    2.9  3  DUF3792          Protein of unknown function (DUF3792)
        1.6    8.6   6.4       0.15   12.0   1.3    1.9  2  DUF2678          Protein of unknown function (DUF2678)
        4.9    8.0  15.7       0.98   10.2   0.1    3.3  3  DUF4282          Domain of unknown function (DUF4282)


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9  11.5   5.4e-28   1.2e-24       8     208 ..      12     218 ..       6     220 .. 0.93
   2 ?   -2.9   0.3       1.7   3.7e+03     112     123 ..     231     242 ..     225     247 .. 0.39

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 5.4e-28
                     ABC2_membrane   8 kreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr......pgllffsvlflafsaltsvapvfere 78 
                                         ++ +++r+++   ++ +++p+++ l+fg +   +++  + +++      pg l+  vlf+ +s + s+ + + re
  gi|313126922|ref|YP_004037192.1|  12 TASWHSFLRRRTAV-FFTFFFPVIIVLIFGALVQTQPTGGGLFAEppayyvPGYLAVVVLFTPLSRVGST-IARHRE 86 
                                       56788999999888.99*****************877777777668999**************7777777.****** PP

                     ABC2_membrane  79 rgvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rf..flflllllltalaasslgllis 152
                                          +e++ ++pl s+++ +l+++lv+++v+ l+al++l+++++++g+ +  r   + +++++ l + ++ +lg +++
  gi|313126922|ref|YP_004037192.1|  87 GNRFEKLATTPL-SRAEWLLSQTLVNVVVIGLAALALLVLTVVVTGVSIPlRPatLSIVAFVALGVTLFCGLGAILG 162
                                       ************.************************************995566999999999999********** PP

                     ABC2_membrane 153 alapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                        +a s++ ++  ++++ lpll+ls  f+++d +p w++  + l+Plty+ +++r++
  gi|313126922|ref|YP_004037192.1| 163 RVADSQDGVIAASNAIALPLLFLSETFVTPDLLPAWFRPAMNLSPLTYFARGVRAV 218
                                       ******************************************************86 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                     ABC2_membrane 112 alifllivyflv 123
                                       +l++l +v+f  
  gi|313126922|ref|YP_004037192.1| 231 ILAVLSVVFFAA 242
                                       333333333322 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   3.7    0.0096        22       4      25 ..      25      46 ..      22      58 .. 0.87
   2 !   62.2   3.7     2e-20   4.4e-17     161     345 .]      59     245 ..      53     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0096
                   ABC2_membrane_3  4 liitlllPiilvlllglifsns 25
                                      +++t+++P+i+vl++g +++++
  gi|313126922|ref|YP_004037192.1| 25 VFFTFFFPVIIVLIFGALVQTQ 46
                                      689*************998765 PP

  == domain 2  score: 62.2 bits;  conditional E-value: 2e-20
                   ABC2_membrane_3 161 sflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afglgip 234
                                       +++ g+++++++f ++s + + i++ +e +  e + ++++s+++ +ls  l  ++v  l +l +l+l   + g++ip
  gi|313126922|ref|YP_004037192.1|  59 YYVPGYLAVVVLFTPLSRVGSTIARHREGNRFEKLATTPLSRAEWLLSQTLVNVVVIGLAALALLVLtvvVTGVSIP 135
                                       66667*******************************************************99999866668887888 PP

                   ABC2_membrane_3 235 fg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapg 310
                                            ++++ ++ l+  ++  lg+ l+ + ++++ ++++  ++ l+l++++  +++ + lp +++ ++ + P+++++
  gi|313126922|ref|YP_004037192.1| 136 LRpATLSIVAFVALGVTLFCGLGAILGRVADSQDGVIAASNAIALPLLFLSETFVTPDLLPAWFRPAMNLSPLTYFA 212
                                       888889999************************************777777777778889***************** PP

                   ABC2_membrane_3 311 lgllrlitgdplweillsliilalfavvylllall 345
                                        g   + tg    + + +l+ila+++vv+++++++
  gi|313126922|ref|YP_004037192.1| 213 RGVRAVTTGS--GDPWSNLAILAVLSVVFFAAGAY 245
                                       ******9999..8999***************9875 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.6      0.24   5.4e+02      11      28 ..      18      39 ..      11      71 .. 0.67
   2 !   33.5  17.1   1.2e-11   2.6e-08      97     286 ..      81     250 ..      25     251 .] 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.24
                   ABC2_membrane_2 11 lvrsrrfllltvllpli....d 28
                                      ++r r+ + +t+++p+i    +
  gi|313126922|ref|YP_004037192.1| 18 FLRRRTAVFFTFFFPVIivliF 39
                                      5666666666666666622221 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 1.2e-11
                   ABC2_membrane_2  97 iagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvllll 173
                                       ia+ +e    + l ++P sR+e ll+  + ++++   i +a+la ++l+++   + g++++l   +l +va+v+l++
  gi|313126922|ref|YP_004037192.1|  81 IARHREGNRFEKLATTPLSRAEWLLSQTLVNVVV---IGLAALALLVLTVV---VTGVSIPLRPATLSIVAFVALGV 151
                                       677777777788889*******************...99999999777555...56888999999999999999999 PP

                   ABC2_membrane_2 174 lvvflalglllSsvarssreaaalalglfvvlailvpivlyg.vaellagpavpqeindflsllsptsayntllnei 249
                                       ++ f++lg+ l  va s+   +a++ ++ + l++l+  ++ + ++ +   pa+          lsp  ++  +++++
  gi|313126922|ref|YP_004037192.1| 152 TL-FCGLGAILGRVADSQDGVIAASNAIALPLLFLSETFVTPdLLPAWFRPAM---------NLSPLTYFARGVRAV 218
                                       99.8************************************7643333333444.........69************* PP

                   ABC2_membrane_2 250 lagsdlnalgstatnllilllllavllvlgyvlFkrk 286
                                       ++gs     g  ++nl+il +l +v+++ g+++  r 
  gi|313126922|ref|YP_004037192.1| 219 TTGS-----GDPWSNLAILAVLSVVFFAAGAYAIPRT 250
                                       ****.....9********************9987665 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.9   6.6e-08   0.00015       9     156 ..      19     161 ..      19     186 .. 0.68
   2 ?   -3.4   0.3       3.5     8e+03      20      28 ..     232     240 ..     227     247 .. 0.39

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.6e-08
                   ABC2_membrane_4   9 lkrskivwllvlaallvpllallyfnllgktgldpaefys....lsvfgftlllllplilgiiasylifrEeqndtl 81 
                                       l+r+  v+++++ ++++    +l+f +l +t+    +++     ++v g+ ++++l + l  ++s++  r ++++ +
  gi|313126922|ref|YP_004037192.1|  19 LRRRTAVFFTFFFPVII----VLIFGALVQTQPTGGGLFAeppaYYVPGYLAVVVLFTPLSRVGSTI-ARHREGNRF 90 
                                       56776666666655554....4455444444444444444233367889999999999998888875.5679999** PP

                   ABC2_membrane_4  82 knLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpii 156
                                        +L t P sr++ ll+  +v ++++ l  l+++    ++++++++v++   + + +++ ++ lg+++f  + +i+
  gi|313126922|ref|YP_004037192.1|  91 EKLATTPLSRAEWLLSQTLVNVVVIGLAALALL----VLTVVVTGVSIPLRPATLSIVAFVALGVTLFCGLGAIL 161
                                       ****************99997555444444433....34455666778888888888888888888887666655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.5
                   ABC2_membrane_4  20 laallvpll 28 
                                       la+l v+++
  gi|313126922|ref|YP_004037192.1| 232 LAVLSVVFF 240
                                       222222222 PP

>> 12TM_1  Membrane protein of 12 TMs
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.8   2.4e-06    0.0054     262     374 ..      20     148 ..      17     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                            12TM_1 262 lRksqalvlllvPivivlpnvfsivseaqpvl............ltifiialiivlSsvylilllaievsgfsllka 326
                                        R++ +++++  P++ivl+ + ++v+ ++++              +++++ l   lS v + ++   e++ f+ l  
  gi|313126922|ref|YP_004037192.1|  20 RRRTAVFFTFFFPVIIVLI-FGALVQTQPTGGglfaeppayyvpGYLAVVVLFTPLSRVGSTIARHREGNRFEKLAT 95 
                                       58999**************.7777777777668999****99998999999************************** PP

                            12TM_1 327 LPlerreillsKlltilliylvvsvvlvllvliykg.sn....alylliilps 374
                                        Pl+r e lls  l+ +++   + + l++l +++ g s     a +++++++ 
  gi|313126922|ref|YP_004037192.1|  96 TPLSRAEWLLSQTLVNVVVIGLAALALLVLTVVVTGvSIplrpATLSIVAFVA 148
                                       ***********988876665556655666555555422211113444444444 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.49   1.1e+03       9      27 ..      25      43 ..      20      54 .. 0.68
   2 ?   11.9   3.7   8.7e-05      0.19      11      64 ..     113     169 ..     104     206 .. 0.75
   3 ?    1.5   0.1      0.14   3.1e+02      35      58 ..     225     248 ..     208     251 .] 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.49
                           DUF3792  9 llialvitlilllilalll 27
                                      +++ +++ +i++li+ +l+
  gi|313126922|ref|YP_004037192.1| 25 VFFTFFFPVIIVLIFGALV 43
                                      5566666666666666665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.7e-05
                           DUF3792  11 ialvitlilllilalllyftsls..ekvlsililiililsvfig.Gflagkkakkkg 64 
                                       + + +++++ll+l+++++  s++   ++lsi++++ l++ +f+g G ++g+ a+++ 
  gi|313126922|ref|YP_004037192.1| 113 VVIGLAALALLVLTVVVTGVSIPlrPATLSIVAFVALGVTLFCGlGAILGRVADSQD 169
                                       45566777777777777776666669*************************999886 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.14
                           DUF3792  35 kvlsililiililsvfigGflagk 58 
                                          +++il++l + +f++G +a  
  gi|313126922|ref|YP_004037192.1| 225 PWSNLAILAVLSVVFFAAGAYAIP 248
                                       566788999999999999998865 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3       3.2   7.2e+03      62      72 ..      29      39 ..      22      44 .. 0.62
   2 ?   12.0   1.3   6.5e-05      0.15      26      78 ..     106     161 ..      91     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.2
                           DUF2678 62 iffavcillis 72
                                       ff v i+li 
  gi|313126922|ref|YP_004037192.1| 29 FFFPVIIVLIF 39
                                      46666666654 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.5e-05
                           DUF2678  26 rdriinlvvggltsl..lvlvtvvssfvfpslppkplni..ffavcillisssvivl 78 
                                        ++++n+vv gl++l  lvl  vv+ + +p l p +l i  f a+ + l ++   +l
  gi|313126922|ref|YP_004037192.1| 106 SQTLVNVVVIGLAALalLVLTVVVTGVSIP-LRPATLSIvaFVALGVTLFCGLGAIL 161
                                       6899****9999875215566666666666.55666655338889999999877665 PP

>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.6      0.17   3.9e+02       7      29 ..      21      43 ..      12      83 .. 0.58
   2 ?    3.0   4.0     0.079   1.8e+02      14      63 ..     111     159 ..      89     165 .. 0.50
   3 ?   10.2   0.1   0.00044      0.98       6      63 ..     188     244 ..     184     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.17
                           DUF4282  7 fitpkllkvlYilgivlialvll 29
                                        t  +  +++ ++ivli  +l+
  gi|313126922|ref|YP_004037192.1| 21 RRTAVFFTFFFPVIIVLIFGALV 43
                                      45555555666555555555444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.079
                           DUF4282  14 kvlYilgivlialvllslivgafaal.seslsagggllllllaviafllmi 63 
                                        v+ ++g+++ al++l+++v++++   + ++   +++++l +++++  l++
  gi|313126922|ref|YP_004037192.1| 111 NVV-VIGLAALALLVLTVVVTGVSIPlRPATLSIVAFVALGVTLFCG-LGA 159
                                       444.3444444444444444444444333333333333333333333.444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00044
                           DUF4282   6 rfitpkllkvlYilgivlialvllslivgafaalseslsagggllllllaviafllmi 63 
                                       +f+tp+ll+ ++  ++ l++l+ ++  v+a+++  +++++  + +l +l+v++f +++
  gi|313126922|ref|YP_004037192.1| 188 TFVTPDLLPAWFRPAMNLSPLTYFARGVRAVTTG-SGDPWSNLAILAVLSVVFFAAGA 244
                                       7****************************99999.99999999999999999997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1622.79
//
Query:       gi|313126923|ref|YP_004037193.1|  [L=333]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-28  100.3   0.0    1.9e-28   99.7   0.0    1.3  1  ABC_tran      ABC transporter
    1.2e-18   68.0   0.0    6.6e-12   45.8   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00027   20.8   0.0       0.54    9.9   0.1    2.1  2  AAA_15        AAA ATPase domain
     0.0006   20.4   0.4    0.00091   19.8   0.4    1.2  1  AAA_23        AAA domain
     0.0006   19.6   0.2     0.0013   18.4   0.2    1.7  2  AAA_30        AAA domain
      0.005   17.3   0.3      0.012   16.0   0.3    1.8  1  AAA_16        AAA ATPase domain
     0.0057   16.4   0.3      0.012   15.3   0.3    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0074   16.7   0.0      0.025   15.0   0.0    1.9  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.023   14.7   0.1    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.018   15.3   0.4      0.061   13.6   0.4    1.9  1  AAA_28        AAA domain
      0.021   15.0   0.2      0.034   14.3   0.2    1.6  1  AAA_33        AAA domain
      0.048   13.7   0.1       0.11   12.6   0.1    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
      0.052   13.8   0.1      0.087   13.1   0.1    1.5  1  AAA_22        AAA domain
      0.058   12.8   0.0       0.56    9.6   0.1    2.0  2  SMC_N         RecF/RecN/SMC N terminal domain
       0.06   13.1   0.0       0.99    9.1   0.1    2.1  2  IstB_IS21     IstB-like ATP binding protein
       0.09   12.7   0.2       0.15   12.0   0.2    1.3  1  RsgA_GTPase   RsgA GTPase
       0.11   12.2   0.1       0.71    9.6   0.2    2.0  2  AAA_24        AAA domain
       0.12   11.7   0.0       0.25   10.7   0.0    1.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.19   11.3   0.5       0.31   10.6   0.5    1.3  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.25   11.1   0.2       0.37   10.5   0.2    1.2  1  ATP_bind_1    Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0   2.1e-31   1.9e-28       1     136 [.      20     155 ..      20     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 2.1e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ vsl++++ge+ +++G+nGaGK+tL+++l+g + p eG++ + g++ +     + r++ig lpq  +   +lt+r
  gi|313126923|ref|YP_004037193.1|  20 LSGVSLSVSAGEVFGLIGPNGAGKTTLVRALTGTT-PVEGHVSVLGTSPTA----VERSRIGLLPQSFSPAARLTAR 91 
                                       6789*****************************96.79****999888877....9********************* PP

                                       HH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       e         ++ +++e +l+ +gl +++++++    + LSgGq++r ++a+al+++p++l+lDEpt
  gi|313126923|ref|YP_004037193.1|  92 ELvsyyaglyDEARDPESVLADVGLAGDDANTW---YEDLSGGQQRRACVAAALVNDPDVLFLDEPT 155
                                       *********878888************888887...79****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   5.1e-07   0.00046       2      21 ..      33      52 ..      32      85 .. 0.86
   2 !   45.8   0.0   7.4e-15   6.6e-12     226     300 ..     117     188 ..      78     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.1e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                       +liGpNg+GK++L +al +
  gi|313126923|ref|YP_004037193.1| 33 FGLIGPNGAGKTTLVRALTG 52
                                      68****************64 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 7.4e-15
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                        gd+ ++ + +lS G++r +++++al  ++   ++l++DEp +g++P+  r+l+ ll++l+++g+ v+lt+HS  
  gi|313126923|ref|YP_004037193.1| 117 AGDDANTWYEDLSGGQQRRACVAAALVNDP---DVLFLDEPTTGIDPAGRRSLWNLLDDLAAGGTTVFLTSHSMA 188
                                       467777778899*******99999999999...9***************************************65 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0006      0.54      27      43 ..      34      50 ..      22      51 .. 0.85
   2 !    8.7   0.0    0.0014       1.2     322     365 ..     144     186 ..     110     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0006
                            AAA_15 27 vliGkNnsGKSsileal 43
                                       liG+N++GK+++++al
  gi|313126923|ref|YP_004037193.1| 34 GLIGPNGAGKTTLVRAL 50
                                      59*************98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0014
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++++l+++EP + + p   ++l++ll +la  +   v++t+HS
  gi|313126923|ref|YP_004037193.1| 144 NDPDVLFLDEPTTGIDPAGRRSLWNLLDDLAAGGT-TVFLTSHS 186
                                       5899******************************7.9******9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.4     1e-06   0.00091      21      40 ..      32      51 ..      19      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-06
                            AAA_23 21 ltlItGpNGaGKTTildAik 40
                                      ++ ++GpNGaGKTT+++A++
  gi|313126923|ref|YP_004037193.1| 32 VFGLIGPNGAGKTTLVRALT 51
                                      7899**************98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.5e-06    0.0013      17      64 ..      29      80 ..      21     183 .. 0.70
   2 ?   -2.5   0.0         4   3.6e+03      45      68 ..     176     199 ..     170     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLa...e 64
                                         v  l Gp G+GKtt+++al+ +   +   +v+g +pt+    +++   +
  gi|313126923|ref|YP_004037193.1| 29 AGEVFGLIGPNGAGKTTLVRALTGTTPVEgHVSVLGTSPTAVERSRIGllpQ 80
                                      4458899********************99559999****9988777665552 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4
                            AAA_30  45 aggrviglAptgkaAkvLaeelgi 68 
                                        g +v++ +++ +  ++La+ +g+
  gi|313126923|ref|YP_004037193.1| 176 GGTTVFLTSHSMAEVERLADRVGL 199
                                       467777777777778888887774 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.3e-05     0.012      25     143 ..      31     153 ..      17     255 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdql.esa......ipysalaqalareellrqlldeaesae 93 
                                       e+  l+G+ G GK++lvr+l      + g++ + g+     e++       ++s+ a++ ar el+   +      +
  gi|313126923|ref|YP_004037193.1|  31 EVFGLIGPNGAGKTTLVRALTGTTPVE-GHVsVLGTSPTAvERSrigllpQSFSPAARLTAR-ELVSYYAGL---YD 102
                                       677799**************9533333.3333333333332333344444444554554433.444444443...12 PP

                            AAA_16  94 leawrekleealaavpelagaea....srllellkrll.allsrderplvlvlDd 143
                                        ++++e  +    a   lag++a    ++l    +r + + ++   +p vl+lD+
  gi|313126923|ref|YP_004037193.1| 103 EARDPESVL----ADVGLAGDDAntwyEDLSGGQQRRAcVAAALVNDPDVLFLDE 153
                                       222222222....333355555555554444444444444444444455555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   1.3e-05     0.012      14      42 ..      22      50 ..      18      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAi 42
                                      g +++++  +++ l+Gp+G+GK+Tl+ A+
  gi|313126923|ref|YP_004037193.1| 22 GVSLSVSAGEVFGLIGPNGAGKTTLVRAL 50
                                      5567777555999************9887 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.7e-05     0.025       3      23 ..      35      59 ..      33     194 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                                      EESSTTSSHHHHHHHHHHHH....T CS
                               AAA  3 lyGppGtGKTllakavakel....g 23
                                      l+Gp G GKT+l++a+  ++    +
  gi|313126923|ref|YP_004037193.1| 35 LIGPNGAGKTTLVRALTGTTpvegH 59
                                      89**************999633331 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.6e-05     0.023      17      48 ..      28      60 ..      16      70 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                                      CHTEEEEEEESTTSSHHHHHHHHHHHTT--.-- CS
                              TsaE 17 algdvilLeGdLGaGKTtlvrglakalgve.ev 48
                                      ++g+v+ L G+ GaGKTtlvr+l  +  ve +v
  gi|313126923|ref|YP_004037193.1| 28 SAGEVFGLIGPNGAGKTTLVRALTGTTPVEgHV 60
                                      3478999****************9988776643 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   6.8e-05     0.061       4      25 ..      35      60 ..      33     166 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                            AAA_28  4 itGgestGKTtlleaLaar....gyp 25
                                      ++G+ ++GKTtl++aL+ +    g++
  gi|313126923|ref|YP_004037193.1| 35 LIGPNGAGKTTLVRALTGTtpveGHV 60
                                      79**************9654554444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   3.8e-05     0.034       4      35 ..      35      71 ..      32     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                            AAA_33  4 lvGlpGsGKstlaerllkklg.....avllssdtlrr 35
                                      l+G++G+GK+tl++ l   ++      vl +s+t+ +
  gi|313126923|ref|YP_004037193.1| 35 LIGPNGAGKTTLVRALTGTTPveghvSVLGTSPTAVE 71
                                      79*************9887776666444445566544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00012      0.11       3      23 ..      34      54 ..      32      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                      EEEESTTSSHHHHHHHHHTST CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltgek 23
                                      +++G   +GK+tL++altg++
  gi|313126923|ref|YP_004037193.1| 34 GLIGPNGAGKTTLVRALTGTT 54
                                      89****************973 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.7e-05     0.087      10      32 ..      35      57 ..      29     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.7e-05
                            AAA_22 10 vtGesGtGKTtllrrlleqldee 32
                                      ++G+ G+GKTtl+r l+ + + e
  gi|313126923|ref|YP_004037193.1| 35 LIGPNGAGKTTLVRALTGTTPVE 57
                                      79**************9998643 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00062      0.56      27      44 ..      33      50 ..      12      53 .. 0.82
   2 ?    0.8   0.0      0.31   2.8e+02     136     206 ..     127     194 ..     103     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00062
                                      EEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlldAi 44
                                        ++GpNG+GK+ l+ A+
  gi|313126923|ref|YP_004037193.1| 33 FGLIGPNGAGKTTLVRAL 50
                                      4689***********998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.31
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekad 206
                                        LSgG++  + +a   A    +p  l+ lDe    +D + ++ + +ll+      + ++ +s++   +e+  
  gi|313126923|ref|YP_004037193.1| 127 DLSGGQQRRACVA---AALVNDPDVLF-LDEPTTGIDPAGRRSLWNLLDDLAAGgTTVFLTSHSMAEVERLA 194
                                       6999998755544...33446666655.79999999999999999999977665577788888776666654 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0011      0.99      45      75 ..      28      59 ..      16      70 .. 0.77
   2 ?    1.6   0.0      0.23   2.1e+02     103     151 ..     140     187 ..     128     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                         IstB_IS21 45 ekkenivllGpsGvGKshlaial.gveavrag 75
                                      ++ e + l+Gp G+GK+ l  al g+  v+  
  gi|313126923|ref|YP_004037193.1| 28 SAGEVFGLIGPNGAGKTTLVRALtGTTPVEGH 59
                                      5678889***************9334445544 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.23
                         IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                       ++ +  +d+l lD+   + +d a ++ l++++++     +++  +  ++
  gi|313126923|ref|YP_004037193.1| 140 AALVNDPDVLFLDEPT-TGIDPAGRRSLWNLLDDLAAGGTTVFLTSHSM 187
                                       44456689*****975.689************99876555554444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00017      0.15      98     123 ..      29      54 ..      11      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                       TTSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpel 123
                                       ++++  l+G+ G+GK+tL+ al++++
  gi|313126923|ref|YP_004037193.1|  29 AGEVFGLIGPNGAGKTTLVRALTGTT 54 
                                       4588889***************9874 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00079      0.71       5      23 ..      33      52 ..      29      65 .. 0.82
   2 ?   -0.2   0.0      0.77   6.9e+02     109     133 ..     164     188 ..     161     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00079
                            AAA_24  5 iliyGpsgiGKTtlakel.g 23
                                      + ++Gp+g+GKTtl++ l g
  gi|313126923|ref|YP_004037193.1| 33 FGLIGPNGAGKTTLVRALtG 52
                                      679************99853 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.77
                            AAA_24 109 eefrrllkklqelrknvifiahekt 133
                                       + +++ll++l + + +v +++h+  
  gi|313126923|ref|YP_004037193.1| 164 RSLWNLLDDLAAGGTTVFLTSHSMA 188
                                       678999****************975 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00028      0.25       5      48 ..      13      56 ..       9      73 .. 0.81
   2 ?   -3.5   0.0       6.4   5.7e+03     107     114 ..     146     153 ..     127     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                      Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpp 48
                                        G+++a   + ++++ g  + l+Gp G+GKt l ++l++  p 
  gi|313126923|ref|YP_004037193.1| 13 SYGDRDALSGVSLSVSAGEVFGLIGPNGAGKTTLVRALTGTTPV 56
                                      5677788888888988899999****************988775 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.4
                      Mg_chelatase 107 nGvLfLDE 114
                                         vLfLDE
  gi|313126923|ref|YP_004037193.1| 146 PDVLFLDE 153
                                       45899998 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00034      0.31       2      21 ..      32      51 ..      31      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      v++l G+ G+GKTtL+++l+
  gi|313126923|ref|YP_004037193.1| 32 VFGLIGPNGAGKTTLVRALT 51
                                      67899************997 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00042      0.37       2      24 ..      36      58 ..      35      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrg 24
                                      +Gp G+GKtt+v+al+ +++ +g
  gi|313126923|ref|YP_004037193.1| 36 IGPNGAGKTTLVRALTGTTPVEG 58
                                      8**************99988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2288.97
//
Query:       gi|313126924|ref|YP_004037194.1|  [L=476]
Description: glucose/sorbosone dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-28   99.2   0.4    1.8e-18   67.0   0.0    2.2  2  GSDH      Glucose / Sorbosone dehydrogenase
  ------ inclusion threshold ------
      0.063   13.8   4.8        3.3    8.3   0.1    3.8  3  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0     2e-22   1.8e-18      13     189 ..      83     291 ..      73     296 .. 0.76
   2 !   30.0   0.3   3.4e-11   3.1e-07     194     275 ..     317     405 ..     311     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 2e-22
                                       S-EEEEETTTEEEEEE.TTEE.EEEEE-..----...STT-SEEEEEE-TTTTTS-EEEEEEEE-.......TTSSE CS
                              GSDH  13 grlLvtersGrlrlvkadgklkepiagvp.evva...kgqgGlldvalhpdfaenrlvYltyaeaeee....kggag 81 
                                       +r +v  ++G++  v+++g+  ep  ++  +vv+    ++ Gll+va hpdfaen+ +++ y+  +++    +  ++
  gi|313126924|ref|YP_004037194.1|  83 DRQFVVDQPGTIYEVTENGRRDEPYLDIRdRVVDlggYSEQGLLGVAPHPDFAENGRLFVRYSAPRRDgtpqNYSHT 159
                                       4779999**************65555543377541114689**********************88333222122345 PP

                                       EEEEEEEE-SS...-EEEEEEEEEEE---TT-------EEE-TTS-EEEE---TT-...GG..............GG CS
                              GSDH  82 tavararlsed.eaaledlevifrqepkvesgahfGsrlafgpdgtLfvtvGdrsk...re..............ea 140
                                        ++++++++ + ++a  d+e+ + + p+  +++h+++ + fgpdg+L+v++Gd +    r               + 
  gi|313126924|ref|YP_004037194.1| 160 FVLSEFTVDPTaRTATPDEERTLLELPQ-PQSNHNAGAVGFGPDGYLYVGTGDGGAggdRGtghvedwydaiaggNG 235
                                       5777888876666777788888888898.6679********************999765115667778889999999 PP

                                       G-T.T-SSSEEEEE-..TTSS.....B-TT-TTTT-TTS-TTEEEE--SCE---EE- CS
                              GSDH 141 qdl.sselGkilrln..kdGs.....vpadnpfvgkagakpeiwsyGhRnpqGlald 189
                                       qd+ ++ lG+ilr+   ++G+     +p+dnp vg++g  +e ++ G Rnp  + +d
  gi|313126924|ref|YP_004037194.1| 236 QDVtENLLGSILRIDvdDEGEtrpygIPDDNPLVGSDG-LNEHYAWGLRNPWRFSFD 291
                                       99835679******9656675555558*******8665.5678*******9877666 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 3.4e-11
                                       -EEEEEE--SSSEEEEEE-TT-B--TTT-S......S-.......-S-TTS---SEEETT-......--EEEEEEE. CS
                              GSDH 194 eLwesEhGprggDelnlieaGknYGWplvsygeeYsgk.kiges.etreglekpvlvwtps......iapsglafyt 262
                                       +L+  + G+++  e+n++e+G+nYGW++ + g++  g+   +++  ++++l +pv+ +  s      ia+ g  +++
  gi|313126924|ref|YP_004037194.1| 317 DLYVADVGQNRYEEVNRVEKGGNYGWNVRE-GMHCFGAnDCPTTtPDDNSLVDPVIEYPHSgdgvsgIAVIGGYVVR 392
                                       6999**********************9888.6666665466666577888******999988556666666666777 PP

                                       .......TTEEEE CS
                              GSDH 263 gdafpewkgdllv 275
                                       g  +pe++g +++
  gi|313126924|ref|YP_004037194.1| 393 GGSLPELEGAYVF 405
                                       7888888887766 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.18   1.7e+03      15      32 ..      84     102 ..      72     102 .. 0.71
   2 ?    8.3   0.1   0.00037       3.3      21      32 ..     202     213 ..     180     214 .. 0.86
   3 ?    4.5   0.3     0.006        54       7      38 ..     373     419 ..     372     421 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.18
                             PQQ_3  15 sspavdg.glvyvgtgdGt 32 
                                       ++ +vd  g++y +t++G+
  gi|313126924|ref|YP_004037194.1|  84 RQFVVDQpGTIYEVTENGR 102
                                       4447775599999999986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00037
                             PQQ_3  21 gglvyvgtgdGt 32 
                                       +g++yvgtgdG+
  gi|313126924|ref|YP_004037194.1| 202 DGYLYVGTGDGG 213
                                       8*********96 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.006
                             PQQ_3   7 vqlpgpvnsspavdgglvyvgtg...............dGtlyAlDa 38 
                                       ++  g+++s+ av gg+v+ g++               +G+l+A D+
  gi|313126924|ref|YP_004037194.1| 373 YPHSGDGVSGIAVIGGYVVRGGSlpelegayvfadwraNGRLFAADP 419
                                       67778999*********999999999999999999999999999777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 3141.62
//
Query:       gi|313126925|ref|YP_004037195.1|  [L=340]
Description: oxidoreductase, aryl-alcohol dehydrogenase like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-66  224.1   0.0    2.5e-66  223.9   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.9   0.0   1.4e-70   2.5e-66       1     290 [.      17     327 ..      17     330 .. 0.93

  Alignments for each domain:
  == domain 1  score: 223.9 bits;  conditional E-value: 1.4e-70
                                       .EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-..TTTHHHHHHHHHHHH-TTTGGG-EEEEEE. CS
                      Aldo_ket_red   1 elglGtwqlgsk....eeiskeealellrraleaGinffDtAevY..gkgqseellGealkksrkkreeviiatKv. 70 
                                       el++Gtw++g +     e+skeea +ll+++ ++G nf+D+A+vY   +g+se ++G +l++   +re+++i++Kv 
  gi|313126925|ref|YP_004037195.1|  17 ELCFGTWRFGREtngvLETSKEEAHDLLDAFADRGGNFIDSANVYgtPNGRSESWIGDWLAE--RDRENYVITSKVy 91 
                                       69*********9*99999***************************8889*************..************8 PP

                                       ..--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHH CS
                      Aldo_ket_red  71 ..dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveq 145
                                          +   ++ sgls+ +ir ++e +l rLgt+y+Dl+++Hr+d ++p iee+l++l+ lv+eGk+ ++G S  +++q
  gi|313126925|ref|YP_004037195.1|  92 fpFDEENPNGSGLSRTHIRDQIEGTLDRLGTEYLDLYYIHRWDEETP-IEETLSTLNRLVEEGKVNYLGASTMAAWQ 167
                                       8777888999*************************************.***************************** PP

                                       HHHH....HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC------ CS
                      Aldo_ket_red 146 leka....kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkr 218
                                       l ka    + ++  ++ + q  ++    ++ + +l++c ++ +++ +yspl+gG+ltgky++ ++ +   p ++   
  gi|313126925|ref|YP_004037195.1| 168 LTKAlwksEVHEWERFEVTQPLFHAGYYEDVKDYLDVCGDQELAVCPYSPLAGGFLTGKYERADPDD---PTQVIAP 241
                                       *9999888788888899999999998999*******************************9766544...5555555 PP

                                       -.............TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTS.TT-SEEEE--SSHHHHHHHHGGGG--- CS
                      Aldo_ket_red 219 d.............ertsknldaaeelselakehgvslaqlalryalsq.pavgivipgasnieqlednldalelkl 281
                                       d                ++  + +++++ +a e + s+aq+alr+++   +a++i+i+ga++ eql++n++a ++ l
  gi|313126925|ref|YP_004037195.1| 242 DgsrasfddrfeqfYLSERGWNVLDTIRTVADEVDASPAQVALRWLMDYpEATVIPIVGARTEEQLDENVEAADVSL 318
                                       56667999999999888899999************************8877999*********************** PP

                                       -HHHHHHHH CS
                      Aldo_ket_red 282 seeevaeld 290
                                       se++++++ 
  gi|313126925|ref|YP_004037195.1| 319 SEDQWERIM 327
                                       ******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2255.87
//
Query:       gi|313126926|ref|YP_004037196.1|  [L=138]
Description: hypothetical protein Hbor_21880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00028   20.3   4.9    0.00039   19.8   4.9    1.2  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   4.9   2.2e-08   0.00039       1     114 [.       1     132 [.       1     136 [. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.2e-08
                              YdjM   1 MdgltHallGaalglalaallgaake....avllavavlgAllPDiD..hpsstlgrklgllskklak......... 62 
                                       M++  Ha++G ++++++a  l +        +l+ ++++ ++l D+D  + + +l++  ++l++ + +         
  gi|313126926|ref|YP_004037196.1|   1 MKSGEHAAVGGVVSVVAAFVLFPGSTgmahLALVGAGIVVSVLIDLDhfVIARWLTGDWRHLERAVKNprvglieqe 77 
                                       8999*****9888777766665554456744444445555*******444456777777788876666********* PP

                              YdjM  63 ..........lvgHRgftHSllflallalvlllllrlfgrsalrlglllllgvlsHlllDll 114
                                                 l+ +R ++H l++ ++  +v+l+   ++ +        +++ +  H+++D+l
  gi|313126926|ref|YP_004037196.1|  78 kvfadmdgegLTPRRLLSHHLIGGVVTFAVVLVGRPTLAAF-------VAIVLYAHIVCDYL 132
                                       *******************9988766666655554444443.......7777788***9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1052.71
//
Query:       gi|313126927|ref|YP_004037197.1|  [L=96]
Description: selt/selw/selh selenoprotein domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-16   58.6   0.0    6.2e-16   58.3   0.0    1.1  1  Rdx       Rdx family
     0.0012   18.9   0.0     0.0023   18.1   0.0    1.5  1  DUF2387   Probable metal-binding protein (DUF2387)


Domain annotation for each model (and alignments):
>> Rdx  Rdx family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   6.9e-20   6.2e-16       2      73 ..      24      93 ..      23      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 6.9e-20
                                      EEEEEETTTTTHHHHHHHHHHHHHHCCCCSSEEEEEEESTT-EEEEETTEEEEEHHHHTSS--HHHHHHHHH CS
                               Rdx  2 vtIeYCtqCkwmlraaelaqellstfpeslgevalqpstgGaFeVtldgelvwsrkeeggfpetkelkqrvr 73
                                      ++IeYC  C++  ra+ ++ ++l++f+e++ +v+l ++  G+ +V +d+e+vw++  ++   +++e+ +rvr
  gi|313126927|ref|YP_004037197.1| 24 IEIEYCVPCGFLDRAETIQHAVLQQFGERVNRVSLVTGDHGVLTVAVDDEIVWDKADDE--YDVDEITRRVR 93
                                      99*******************************************************99..99999999998 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.5e-07    0.0023      27      71 ..      23      67 ..      17      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-07
                           DUF2387 27 eveyrECvsCgftdelsekgqsvakelktrvnkdeekeasakvqt 71
                                      e+e+  Cv Cgf+d+ ++ +++v ++ ++rvn+ +    ++ v t
  gi|313126927|ref|YP_004037197.1| 23 EIEIEYCVPCGFLDRAETIQHAVLQQFGERVNRVSLVTGDHGVLT 67
                                      567788*************9************9987666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 762.74
//
Query:       gi|313126928|ref|YP_004037198.1|  [L=222]
Description: hypothetical protein Hbor_21900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.3    6.8  15.2        4.9    6.9   4.2    2.5  2  DUF2157   Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.2   0.00091        16      38     107 ..      15      90 ..       5     115 .. 0.71
   2 ?    6.9   4.2   0.00027       4.9      98     136 ..     174     212 ..     126     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.00091
                           DUF2157  38 llvlGalllglGlilfvAanWqglsrlvkfllllvllllslllgavlwrdr.........rvpprlgeallllaall 105
                                       +l+ + l+ +lG++ +v+ + ++++ ++      +ll+++++++a+ w++r         ++ ++++   +++ al+
  gi|313126928|ref|YP_004037198.1|  15 VLYAALLANTLGMLALVYVLVAEITVTQPRYAFYGLLWIAVGVIAI-WKTRpaptdektrQRARLIAV--GYVVALA 88 
                                       6888999999***************888777777777777766654.555558888765322222222..2333333 PP

                           DUF2157 106 lg 107
                                       + 
  gi|313126928|ref|YP_004037198.1|  89 FA 90 
                                       33 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00027
                           DUF2157  98 llllaalllgaaialvgqifqlsgdaysllllwalllll 136
                                       l+ l + ++g + alv+ +f ls d ++l+++  ++ll 
  gi|313126928|ref|YP_004037198.1| 174 LASLLTGVFGSSSALVAATFDLSYDISTLVFVVTVVLLY 212
                                       67788899*************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1518.68
//
Query:       gi|313126929|ref|YP_004037199.1|  [L=468]
Description: protoheme IX farnesyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-54  183.4  23.2    4.5e-54  183.4  23.2    3.0  2  UbiA            UbiA prenyltransferase family
    9.1e-08   31.5  20.8    3.9e-05   22.9  10.1    4.4  4  COX15-CtaA      Cytochrome oxidase assembly protein
  ------ inclusion threshold ------
       0.13   12.1   0.1       0.41   10.5   0.1    1.9  1  DUF5596         Domain of unknown function (DUF5596)
       0.36   10.9   6.0         13    5.9   0.0    3.3  3  Fumarate_red_C  Fumarate reductase subunit C


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -17.4  22.7         4   1.8e+04      85     160 ..      59     141 ..       8     150 .. 0.41
   2 !  183.4  23.2     1e-57   4.5e-54       5     250 ..     204     449 ..     199     456 .. 0.84

  Alignments for each domain:
  == domain 1  score: -17.4 bits;  conditional E-value: 4
                              UbiA  85 allln..pltallgllalllyvvYt.glrlKrrtllgtvvggia.fg.lppllgwaavtgsl....sllalllalav 152
                                       +l ++  + ++l+gll+++ +v+        rr l g +v++ + +   ++l++++av+g      +l +++ + ++
  gi|313126929|ref|YP_004037199.1|  59 WLAVGhrLAAVLVGLLGVVTLVMAVrS-GVERRVL-GSMVVAGVlYPvQAALGAFVAVGGADatlsTLHLVVGMGIF 133
                                       223321122222333333333222211.4455555.33333333122122222233333332333333333333333 PP

                              UbiA 153 flltwaia 160
                                       + l++a+a
  gi|313126929|ref|YP_004037199.1| 134 GSLVLALA 141
                                       44444444 PP

  == domain 2  score: 183.4 bits;  conditional E-value: 1e-57
                              UbiA   5 alvglalaaggspdl..llllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllil 79 
                                       a +g+alaa+ s+ l   ++l++l g++l ++a+ ++N++++r+iD++mert +RPl+  ++ +++a++f++vl+++
  gi|313126929|ref|YP_004037199.1| 204 ASAGMALAATTSTGLtpEIVLATLGGGVLSIGASGTFNHVLERDIDRRMERTSDRPLAVDLVPVRHAVAFGLVLAAA 280
                                       456666666666655559*********************************************************** PP

                              UbiA  80 gllllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfll 155
                                       +++l  +++n l+a+lg+ a+l+y vvYt l lK  t+++tv+gg+a++lp+l+gw+avtg++ +  llla+ +fl+
  gi|313126929|ref|YP_004037199.1| 281 SVALF-AWVNTLAAVLGVGAILFYsVVYT-LILKPNTVQNTVIGGAAGALPALIGWVAVTGEIGFGGLLLAAVIFLW 355
                                       *****.***********************.9********************************************** PP

                              UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaarillalllavllla..llllllalllllylllalllaalallra 230
                                       t a+++  +l  +++++++g++++pvv G+  +r   +l+++++ l+   +l+ + +l+ +y+l +++++a++l++ 
  gi|313126929|ref|YP_004037199.1| 356 TPAHFYNLALAYKDDYARGGFPMMPVVRGETETRKH-TLWYLGATLIaaGALAAMEALGVVYALTSVVFGAVFLYFV 431
                                       ******99***99999*******************6.4444444443334445555555556666667777777776 PP

                              UbiA 231 arlvrrrdakkaakfflfls 250
                                       ++l+  +++++a ++f  ++
  gi|313126929|ref|YP_004037199.1| 432 VQLHYEQTESAAFRAF--HA 449
                                       6666666666655555..54 PP

>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   2.9   1.2e-08   5.3e-05       3      49 ..      13      60 ..      11      63 .. 0.90
   2 !   22.9  10.1   8.7e-09   3.9e-05      76     172 ..      58     147 ..      54     161 .. 0.87
   3 !    5.8   3.9    0.0014       6.1     108     213 ..     190     295 ..     181     300 .. 0.81
   4 ?   -4.9   7.9       2.5   1.1e+04      90     136 ..     298     341 ..     295     466 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-08
                        COX15-CtaA  3 wlllvlllvllvvvlGgltRltdsGlsitdWppctGa.lppltdeewe 49
                                      +l ++++ v+l+ ++G+ t ltd+   +t+Wp c +  + p+t++ w 
  gi|313126929|ref|YP_004037199.1| 13 LLAATAMGVYLLLLVGATTALTDAAAACTAWPVCGDGfTAPTTAAGWL 60
                                      67889999**************************7666*****99996 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 8.7e-09
                        COX15-CtaA  76 awiEwiHRllgrllGllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLl 152
                                        w+   HRl + l+Gll +v l+++++   ++r++   ++++ +l  +Q++lG+++   g            ++HL+
  gi|313126929|ref|YP_004037199.1|  58 GWLAVGHRLAAVLVGLLGVVTLVMAVR-SGVERRVLGSMVVAGVLYPVQAALGAFVAVGGA------DATLSTLHLV 127
                                       688899******************997.799999*********************999997......9999****** PP

                        COX15-CtaA 153 laflllalllwlalrllake 172
                                       +++ +++ l++ ++ +l+ e
  gi|313126929|ref|YP_004037199.1| 128 VGMGIFGSLVLALAWVLETE 147
                                       *********99998887774 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0014
                        COX15-CtaA 108 relkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLllaflllalllwlalrllake....ae..saee 178
                                       r +k++l++ll+lv+  G+  +++ + gL       p ++ a L++++l +++   + + l ++     ++  +++ 
  gi|313126929|ref|YP_004037199.1| 190 RLMKPRLMWLLCLVASAGMALAATTSTGL------TPEIVLATLGGGVLSIGASGTFNHVLERDIdrrmERtsDRPL 260
                                       56899************************......89999999******9988766555544443445522346666 PP

                        COX15-CtaA 179 eaaakklrllallllallllqialGalvagldAgl 213
                                       +     +r +++++l+l ++ +al a+v +l A+l
  gi|313126929|ref|YP_004037199.1| 261 AVDLVPVRHAVAFGLVLAAASVALFAWVNTLAAVL 295
                                       677788999***********************998 PP

  == domain 4  score: -4.9 bits;  conditional E-value: 2.5
                        COX15-CtaA  90 GllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgL 136
                                       G+++++ ++y l+   +++++ +  ++  + ++l +l+Gw+ V+ ++
  gi|313126929|ref|YP_004037199.1| 298 GAILFYSVVYTLI---LKPNTVQNTVIGGAAGALPALIGWVAVTGEI 341
                                       4555555555554...5777778888888889999999999998765 PP

>> DUF5596  Domain of unknown function (DUF5596)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   9.1e-05      0.41      18      52 ..     194     228 ..     187     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.1e-05
                           DUF5596  18 eelfllyallaaapdvleayrkrGIseeifwaTla 52 
                                       ++l++l++l+a a  +l+a  + G+++ei +aTl+
  gi|313126929|ref|YP_004037199.1| 194 PRLMWLLCLVASAGMALAATTSTGLTPEIVLATLG 228
                                       79*******************************95 PP

>> Fumarate_red_C  Fumarate reductase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.3     6e+03      34      58 ..      19      43 ..      14      48 .. 0.75
   2 ?    5.9   0.0    0.0029        13      50      96 ..     180     226 ..     177     235 .. 0.87
   3 ?    5.8   1.0    0.0032        14      31      76 ..     417     462 ..     413     467 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                    Fumarate_red_C 34 valfalvlllgllaLaqgeaayeaf 58
                                      + ++ l+l+   +aL+++ aa++a+
  gi|313126929|ref|YP_004037199.1| 19 MGVYLLLLVGATTALTDAAAACTAW 43
                                      5567777777788898888888887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0029
                    Fumarate_red_C  50 qgeaayeafleflqnPlvlllniiaLaaallhavTwfelaPkavkiv 96 
                                       +++a+ +a+ ++++  l++ll ++a a + l a+T   l+P++v  +
  gi|313126929|ref|YP_004037199.1| 180 RAKATAAAYFRLMKPRLMWLLCLVASAGMALAATTSTGLTPEIVLAT 226
                                       56788899*********************************998554 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0032
                    Fumarate_red_C  31 avlvalfalvlllgllaLaqgeaayeafleflqnPlvlllniiaLa 76 
                                       a++ ++f +v l+ ++ L+  +++ +af++f+++  +l + ++a++
  gi|313126929|ref|YP_004037199.1| 417 ALTSVVFGAVFLYFVVQLHYEQTESAAFRAFHASNAYLGMLLLAVV 462
                                       68899***************************99988877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3016.08
//
Query:       gi|313126930|ref|YP_004037200.1|  [L=254]
Description: cytochrome C oxidase subunit II [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-21   74.1   2.4    1.6e-19   69.9   0.1    2.4  2  COX2          Cytochrome C oxidase subunit II, periplasmic do
    1.7e-14   53.7   0.5      3e-14   52.9   0.5    1.5  1  COX2_TM       Cytochrome C oxidase subunit II, transmembrane 
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.023   14.6   0.0    1.5  2  Claudin_3     Tight junction protein, Claudin-like
       0.12   12.5   0.0       0.26   11.4   0.0    1.5  1  Cupredoxin_1  Cupredoxin-like domain
       0.16   11.2   1.0        0.3   10.4   1.0    1.4  1  AgrB          Accessory gene regulator B
        0.2   11.9   1.9       0.47   10.7   0.7    1.9  2  TrbC          TrbC/VIRB2 family


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.012        37       2      21 ..     121     140 ..     120     144 .. 0.86
   2 !   69.9   0.1   5.5e-23   1.6e-19      44     120 .]     143     219 ..     139     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                              COX2   2 tikaiGhqwywsyeytdfed 21 
                                       +++a  +qw w+  y+++ +
  gi|313126930|ref|YP_004037200.1| 121 VVHAEAYQWGWEMSYPEDGN 140
                                       7999***********99875 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 5.5e-23
                              COX2  44 vdnrvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssmpivveav 120
                                       + +++v+p ++++ + vt+ dv+h f vp +g+k+da+pG++n v+++   e ++ G c+e cGv hs m   ve v
  gi|313126930|ref|YP_004037200.1| 143 TGTEIVVPKDRPVVFEVTSRDVIHGFHVPKMGMKTDAMPGQINTVKTVPYEEDTYQGYCTEYCGVAHSQMYFSVEVV 219
                                       56789*****************************************************************9999875 PP

>> COX2_TM  Cytochrome C oxidase subunit II, transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.5     1e-17     3e-14      12      87 ..      27      99 ..      11     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1e-17
                           COX2_TM 12 aasplmeeleelhdyilliltlililVlyilvlilvefrrrknkitakylvhgqeiEiiWTiiPalililialpSl 87
                                       as+++e +++l+  +l++++ i++lV++il++++v+fr++ n++++k   ++  +Ei WT+  a+il+++++ S+
  gi|313126930|ref|YP_004037200.1| 27 QASASAELINDLNSRLLYVAFPITLLVEFILLYAVVKFRNNDNPLPTK---ENRRLEITWTVATAIILLFVGVASY 99
                                      58999****************************************977...**********************997 PP

>> Claudin_3  Tight junction protein, Claudin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       3.1   9.1e+03      95     107 ..       7      19 ..       3      22 .. 0.53
   2 ?   14.6   0.0   7.8e-06     0.023      54     126 ..      37     110 ..      23     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.1
                         Claudin_3  95 fliallsllivil 107
                                        l++++s+li +l
  gi|313126930|ref|YP_004037200.1|   7 ALVSVFSVLILAL 19 
                                       4555555555444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.8e-06
                         Claudin_3  54 eaasimmyislalflvviliyivivrkvkkngysksvrklffl.iallslliviltviaviliavnvskfndsf 126
                                       ++ s ++y+++ ++l+v +i++++v k+++n+    ++ +  l i++++++++il+++ v  ++v ++++   +
  gi|313126930|ref|YP_004037200.1|  37 DLNSRLLYVAFPITLLVEFILLYAVVKFRNNDNPLPTKENRRLeITWTVATAIILLFVGVASYGVLADDNVTHQ 110
                                       67899**************************99887777655449*****************999888776655 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.6e-05      0.26      35      93 ..     145     202 ..     137     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.6e-05
                      Cupredoxin_1  35 skievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeftcd 93 
                                        +i v+++++v ++++ +d   + f ++++g +++ +pg+ +t++  p ++ +Y+ +c 
  gi|313126930|ref|YP_004037200.1| 145 TEIVVPKDRPVVFEVTSRD-VIHGFHVPKMGMKTDAMPGQINTVKTVPYEEDTYQGYCT 202
                                       5899*********999988.46***********************99*******99886 PP

>> AgrB  Accessory gene regulator B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.0   9.9e-05       0.3     101     155 ..      29      94 ..       7     107 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.9e-05
                              AgrB 101 s...........lllillliilliisliiilllaPvdtpnkpisskekkkklki.lsiivllillii 155
                                       s            ll++++ i+l++ +i+++ ++   +  +p+ +ke  ++l i +++ + +ill++
  gi|313126930|ref|YP_004037200.1|  29 SasaelindlnsRLLYVAFPITLLVEFILLYAVVKFRNNDNPLPTKE-NRRLEItWTVATAIILLFV 94 
                                       444555555555667788888889999999999999**********9.6677772444444444443 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.7   0.00016      0.47       6      60 ..       2      52 ..       1      65 [. 0.81
   2 ?   -0.2   0.0      0.39   1.2e+03      52      68 ..      84     100 ..      74     107 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                              TrbC  6 skarrlllalalalvllllaspalAqaaggdpvetvlqnivdfltgplakviati 60
                                      +k r +l++++++l+l+l+a+p+ Aqa+      ++++++ + l   +a++i ++
  gi|313126930|ref|YP_004037200.1|  2 RKTRLALVSVFSVLILALFADPVAAQAS---ASAELINDLNSRLLY-VAFPITLL 52
                                      47888999******************97...456677777777777.77777655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.39
                              TrbC  52 plakviatiaiivaGim 68 
                                        +a++i+++ + va+++
  gi|313126930|ref|YP_004037200.1|  84 TVATAIILLFVGVASYG 100
                                       34555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1746.79
//
Query:       gi|313126931|ref|YP_004037201.1|  [L=275]
Description: biotin--acetyl-CoA-carboxylase ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-07   31.5   0.4    2.4e-07   30.5   0.4    1.5  1  BPL_C          Biotin protein ligase C terminal domain
    3.4e-07   30.2   0.0    5.4e-07   29.6   0.0    1.2  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.4   2.7e-11   2.4e-07       1      44 [.     223     266 ..     223     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.7e-11
                                       STTSEEEEEE.TSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCC CS
                             BPL_C   1 hsGqeVtled.edgkveGiavGIdddGaLllktddglqpdinsGd 44 
                                       ++G +Vt+++ ++  v+Gia++++ +G Ll++td+  ++ ++ G+
  gi|313126931|ref|YP_004037201.1| 223 TLGSRVTVRRrGNADVTGIARDVSPRGGLLVETDER-TVEVTEGE 266
                                       69*********************************9.88888776 PP

>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0     6e-11   5.4e-07      20     115 ..      27     127 ..      14     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6e-11
                                       G--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TT CS
                     BPL_LplA_LipB  20 elesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegip 92 
                                         + g++vv+++ t+ r    n w  p g+++ s ll+p+    ++  + +++   ++av++a+       +  g+ 
  gi|313126931|ref|YP_004037201.1|  27 GAPHGTMVVANELTAARgrtgNEWAAPPGGIWSSTLLRPDL---STEHVGRLTFAGAMAVVDAV-------EPLGVD 93 
                                       5667778888888875555*******************998...98999999************.......9***** PP

                                       EEEETTTEEEE...........TTEEEEEEEEEE CS
                     BPL_LplA_LipB  93 vfikwpnDlyv...........ngrKlaGiavts 115
                                       ++ kwpnD++v             +KlaGi+++ 
  gi|313126931|ref|YP_004037201.1|  94 ARLKWPNDVVVaspsaedaadaVPKKLAGILTEP 127
                                       *******************99999******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2185.50
//
Query:       gi|313126932|ref|YP_004037202.1|  [L=145]
Description: fmn adenylyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-16   59.3   0.2    5.2e-16   59.1   0.2    1.0  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.028   14.8   0.0      0.039   14.3   0.0    1.2  1  Urm1             Urm1 (Ubiquitin related modifier)
       0.12   12.3   1.7       0.19   11.6   0.3    2.0  3  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.2   8.6e-20   5.2e-16       1     118 [.       6     116 ..       6     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 8.6e-20
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       +a GtFD++H GH ++l+ a++l++e l v+v+  e++ +k kp+ s  +R +m+ ++  v e+      ++    +
  gi|313126932|ref|YP_004037202.1|   6 IAQGTFDILHPGHVHYLRDAAELGDE-LHVIVARRENVTHKAKPILSDRQRRDMVAAIDVVTEAHLGHTEDIFV-PI 80 
                                       578***********************.999999988888888******************************98.9* PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEE CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrp 118
                                       ++++pd  ++v+g+d++ d+     ++  l+++++ +++ +
  gi|313126932|ref|YP_004037202.1|  81 ERIRPD--VIVLGHDQHHDA---DGIRAALDSRGIDCEVTR 116
                                       ******..***********7...899999999999998766 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.5e-06     0.039      25      70 ..      47      95 ..      25     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-06
                                      -...SSSSS-BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCE CS
                              Urm1 25 e...ieseevnleeliayikknlikerkevFlekdkvrPGilvLindaD 70
                                      +   +++++ ++   i+ +++ ++ + +++F+  +++rP ++vL  d+ 
  gi|313126932|ref|YP_004037202.1| 47 KpilSDRQRRDMVAAIDVVTEAHLGHTEDIFVPIERIRPDVIVLGHDQH 95
                                      23346889999999******************************88765 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   3.2e-05      0.19       7      39 ..       3      35 ..       1      56 [. 0.88
   2 ?   -2.2   0.0      0.55   3.3e+03      18      24 ..      68      74 ..      51      83 .. 0.72
   3 ?   -1.3   0.0      0.29   1.7e+03     113     143 ..      90     114 ..      76     123 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
                           FAD_syn  7 gavvtlGnFDGvHlGHqallkkaveaakekglp 39
                                      + v++ G FD +H GH + l++a e+ +e ++ 
  gi|313126932|ref|YP_004037202.1|  3 RRVIAQGTFDILHPGHVHYLRDAAELGDELHVI 35
                                      57999********************99887765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.55
                           FAD_syn 18 vHlGHqa 24
                                       HlGH +
  gi|313126932|ref|YP_004037202.1| 68 AHLGHTE 74
                                      6999975 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.29
                           FAD_syn 113 vGfdfrfGkkregdvellkelgaklgfevev 143
                                       +      G++++ d++ ++++ ++ g+++ev
  gi|313126932|ref|YP_004037202.1|  90 L------GHDQHHDADGIRAALDSRGIDCEV 114
                                       4......555555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1070.77
//
Query:       gi|313126933|ref|YP_004037203.1|  [L=164]
Description: proteasome rpn11 subunit jamm motif protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-10   40.3   0.0    2.9e-10   39.9   0.0    1.1  1  Prok-JAB  Prokaryotic homologs of the JAB domain
    0.00052   20.0   0.0    0.00081   19.3   0.0    1.3  1  RadC      RadC-like JAB domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.039   13.9   0.0    1.7  1  JAB       JAB1/Mov34/MPN/PAD-1 ubiquitin protease
      0.094   13.1   0.0       0.14   12.6   0.0    1.2  1  Myofilin  Myofilin


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   6.5e-14   2.9e-10       8     116 ..      20     123 ..      13     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 6.5e-14
                          Prok-JAB   8 lvaharrahpeEtcGlllgke.....seseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpg 79 
                                        +++ +++hp+E  G+l g+       ++  +++++++ +++     ++ + s++++   +  ++++ vg +HSHp+
  gi|313126933|ref|YP_004037203.1|  20 ALEASKETHPNEYMGFLRGEDarqlgLDRSGTVITDVLIIPG----TKSDPTSATVDS-NMIPNDMRAVGSIHSHPN 91 
                                       55677889*****************96666666666666554....335555666666.9***************** PP

                          Prok-JAB  80 gsarPSetDrrdaaalarvkalliivgdkaeelrawr 116
                                       g  rPS++D+ ++ +    + ++ii+g+ ++++  wr
  gi|313126933|ref|YP_004037203.1|  92 GVLRPSDADLDTFGQ----GQVHIILGH-PYRRSDWR 123
                                       *************99....788888887.56555665 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.8e-07   0.00081      15      87 ..      33     103 ..      14     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.8e-07
                                       SS-TTS-EEEEEEE-TTSBEEEEEEEEESTT-GGGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHH CS
                              RadC  15 ladleqEefvvllLdsknrliadeelseGtlnstlvdprevfkealklnAaavilaHnhPsgdlepSeeDiel 87 
                                       +  l+ E  + l Ld++  +i+d  +  Gt  ++      v ++++ ++  av  +H hP+g l+pS++D+++
  gi|313126933|ref|YP_004037203.1|  33 MGFLRGEDARQLGLDRSGTVITDVLIIPGT--KSDPTSATVDSNMIPNDMRAVGSIHSHPNGVLRPSDADLDT 103
                                       344456999999**************9999..446666778899999999********************986 PP

>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.6e-06     0.039      20     108 ..      24     103 ..      10     108 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.6e-06
                                       HHHHHHHTS--EEEEEEEESSSE......EEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHHHHCTTSEEEEE CS
                               JAB  20 alrtekeeeevmGlliGelnddt......tveitnvfalpfeetekdvdavsldqeylekksellkklrgrervvGW 90 
                                        ++t    +e mG l Ge  ++       tv it+v+++p  +++ +  +v+ ++            + +++r vG 
  gi|313126933|ref|YP_004037203.1|  24 SKETHP--NEYMGFLRGEDARQLgldrsgTV-ITDVLIIPGTKSDPTSATVDSNM------------IPNDMRAVGS 85 
                                       333333..58888888887777677777444.88888888777777733333332............3356****** PP

                                       EEESSSS-SS--HHHHHH CS
                               JAB  91 Yhshpditvwlsevdvrt 108
                                       +hshp+    +s  d++t
  gi|313126933|ref|YP_004037203.1|  86 IHSHPNGVLRPSDADLDT 103
                                       *******88888888876 PP

>> Myofilin  Myofilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.1e-05      0.14      32      74 ..      77     120 ..      61     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                          Myofilin  32 sddiratekihtrprgifrpl.sdypdlawpssksiyddpihas 74 
                                        +d+ra  +ih++p g++rp  +d+ +++  + + i  +p + s
  gi|313126933|ref|YP_004037203.1|  77 PNDMRAVGSIHSHPNGVLRPSdADLDTFGQGQVHIILGHPYRRS 120
                                       68******************999999999999888888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1290.74
//
Query:       gi|313126934|ref|YP_004037204.1|  [L=295]
Description: fructosamine-3-kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-38  131.6   0.0    4.1e-38  131.2   0.0    1.0  1  Fructosamin_kin  Fructosamine kinase
    1.7e-18   67.4   2.5    2.3e-18   67.0   2.5    1.1  1  APH              Phosphotransferase enzyme family
    0.00035   20.0   0.3    0.00083   18.8   0.3    1.5  1  APH_6_hur        Aminoglycoside/hydroxyurea antibiotic resist
      0.002   17.7   0.0      0.011   15.3   0.0    1.9  2  RIO1             RIO1 family


Domain annotation for each model (and alignments):
>> Fructosamin_kin  Fructosamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.0   9.2e-42   4.1e-38      11     275 ..      24     283 ..      13     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 9.2e-42
                   Fructosamin_kin  11 ealgkafeiteaekveggeineayllseeeqrfFv.klnekealemFeaEaesLealaetqtirvPkvlavGelkda 86 
                                       +++g+  ++t+a ++ gg++ +  +l+ ++++  v k+++    +  + Eae L+ l + +++ vP+v+++     +
  gi|313126934|ref|YP_004037204.1|  24 SQFGS--AVTNAAELDGGKVGSVSRLDFADRDAVVaKVSD----TPLTVEAEMLRYLDRESALPVPEVYHAT----T 90 
                                       44444..488999999999999999996666554415554....45679*******************9865....4 PP

                   Fructosamin_kin  87 sfLvleyLelk.lekkesaaelgqqLaklHraseqkefGfdvdntigktpqpNewqssWaeFfaeqRlgvqlelake 162
                                         L++ey+e + + ++    + +  La+lH+  ++++ Gf++d++ g  + pN w++sW++Ff+e Rl    ++a+e
  gi|313126934|ref|YP_004037204.1|  91 GCLLMEYVEGDgKFTEAVERDAADCLAELHE-VTAEQSGFPFDTLSGPYSLPNPWTESWIDFFREFRLRDVADAAAE 166
                                       67*******9965666677889999******.677888*************************************** PP

                   Fructosamin_kin 163 kgle.fakieelvervae..llskhqpkpsllHGdLWsgNaaltkdgepvifdPaayygdrEvdlamtelfggfpse 236
                                        g+   a+ e++ + +++   l ++   p+llHGd+Ws+N+ + +     ++dPa+yyg+ E++la +  f+ f+++
  gi|313126934|ref|YP_004037204.1| 167 AGTLpSADRERVAALTSDldSLLTEPAAPALLHGDVWSENVVVRDGHVRAFLDPAMYYGHPEIELAYILAFDTFGDA 243
                                       9996444444444333321134567889**************9999999**************************** PP

                   Fructosamin_kin 237 fyegYqsivpldegy.eeRkelYqLYhlLnhlnlFgggyl 275
                                       f+e Y++   +++g+ e+R ++Y ++  L  ++  g + l
  gi|313126934|ref|YP_004037204.1| 244 FFERYDDRRGIEDGFfETRAAVYTVFSSLELVRYSGCDKL 283
                                       ************995489********99987776665555 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   2.5     5e-22   2.3e-18      36     234 ..      63     258 ..      35     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 5e-22
                                       HHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH.-S CS
                               APH  36 eirrevallrlLakagv.pvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhqvdpa 111
                                        +  e+++lr+L +  + pvPev++     +  g   +l+eyv+g    +       +++ ++++++la+lh+v ++
  gi|313126934|ref|YP_004037204.1|  63 PLTVEAEMLRYLDRESAlPVPEVYH-----ATTG--CLLMEYVEGDGKFT-------EAVERDAADCLAELHEVTAE 125
                                       566799*******99889*******.....4444..78******998888.......999**************999 PP

                                       TTTB-.................SHHCHTCCHHHHHHCHHHCCCGCCTCC....HHHHHHHHHHHHHHHH--SSS-EE CS
                               APH 112 alpla.................dflaqdlellrqlesatarllaselld....lleeleeqvlaalaallpgelptv 167
                                       +++++                 +     ++++r +  +  ++ a+e +     ++e++++ +   l+ ll  + ++ 
  gi|313126934|ref|YP_004037204.1| 126 QSGFPfdtlsgpyslpnpwtesW-----IDFFREFRLRDVADAAAEAGTlpsaDRERVAA-LTSDLDSLLTEPAAPA 196
                                       99999777777777777444331.....33333333333333333333322355556666.77777777777***** PP

                                       EE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCHHHCSCHCCCHCHHHHHHHHCS-HHH CS
                               APH 168 llHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavllrswtseldpeflaallrayeqeagl 234
                                       llHgD  + N++v+  dg+v++++D  +  +g+p  +la+ l +  ++++++f +++ ++ ++e+g+
  gi|313126934|ref|YP_004037204.1| 197 LLHGDVWSENVVVR--DGHVRAFLDPAM-YYGHPEIELAYIL-A-FDTFGDAFFERYDDRRGIEDGF 258
                                       **************..9*********86.6************.5.4799999999999999988776 PP

>> APH_6_hur  Aminoglycoside/hydroxyurea antibiotic resistance kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   1.9e-07   0.00083      68     199 ..      90     235 ..      64     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-07
                         APH_6_hur  68 esalLLErlsgersltslvaegdDdeAtrilaellarL....hapspgplPpLlpleevfealfreaasdaga.... 136
                                        + lL+E+++g+   t+ v e+d ++ +++l e+ a      +    gp+   +p +e +   fre + +  a    
  gi|313126934|ref|YP_004037204.1|  90 TGCLLMEYVEGDGKFTEAV-ERDAADCLAELHEVTAEQsgfpFDTLSGPYSLPNPWTESWIDFFREFRLRDVAdaaa 165
                                       5789***********9999.446566665555544432222266666777446788888888888874433333377 PP

                         APH_6_hur 137 ........gasrlyveaaaiaaeLleepselrpLHgdlhhenvLagerrgWlaidPkglvGergfdlanll 199
                                               +++r+  +  +  + Ll ep    +LHgd+  env+  + +    +dP   +G +  +la +l
  gi|313126934|ref|YP_004037204.1| 166 eagtlpsaDRERV-AALTSDLDSLLTEPAAPALLHGDVWSENVVVRDGHVRAFLDPAMYYGHPEIELAYIL 235
                                       8888887444444.677777899*********************999888888999999999988777665 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.4e-06     0.011      56      98 ..      65     108 ..      44     126 .. 0.75
   2 ?   -0.2   0.0      0.14   6.4e+02     126     144 ..     196     214 ..     162     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHTT.--S--EEEEETTEEEEE--EETTEEGGBH CS
                              RIO1  56 ekEfrnLkrleeag.vpvPkpielkrhvlvmefigedgvaapkl 98 
                                       + E ++L+ l ++  +pvP++++    +l+me+++ dg     +
  gi|313126934|ref|YP_004037204.1|  65 TVEAEMLRYLDRESaLPVPEVYHATTGCLLMEYVEGDGKFTEAV 108
                                       5577778888655449*******************888765555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.14
                                       TEEESS-STTSEEEETTEE CS
                              RIO1 126 glvHaDLSeyNvlvdedkv 144
                                        l H+D+   Nv+v +++v
  gi|313126934|ref|YP_004037204.1| 196 ALLHGDVWSENVVVRDGHV 214
                                       689***9999*99999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1959.52
//
Query:       gi|313126935|ref|YP_004037205.1|  [L=640]
Description: recj-like exonuclease with dnaj-type zn-finger domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-07   31.2   0.0    3.1e-07   30.3   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    3.7e-06   27.2   0.7    3.7e-06   27.2   0.7    1.8  2  S1               S1 RNA binding domain
     0.0011   19.1   0.1     0.0022   18.2   0.1    1.5  1  DHH              DHH family
  ------ inclusion threshold ------
      0.071   13.3   0.0       0.15   12.3   0.0    1.5  1  tRNA_anti_2      OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0     7e-11   3.1e-07       2      74 ..     129     198 ..     128     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7e-11
                                       EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                        v+G v +i  +++g+   + + D+tg++ + +f ++  + + +++ +d vrv+G+ ++ +g  l+l v++++
  gi|313126935|ref|YP_004037205.1| 129 FVEGVVAQI--KQTGGPTVFRIADDTGIVSAAAFEDAGVRAHPEVELDDAVRVSGTAESHEGA-LQLEVNSMT 198
                                       599******..****************************************************.******987 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.7   8.2e-10   3.7e-06       3      66 ..      38      92 ..      36      97 .. 0.92
   2 ?   -3.6   0.2       3.4   1.5e+04       8      17 ..     130     139 ..     122     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 8.2e-10
                                      TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETT CS
                                S1  3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkd 66
                                      e+g+ + ++V  v+++G+fV++  +v+g+v+ s+l+r         ++ vGd++ v +++v+++
  gi|313126935|ref|YP_004037205.1| 38 EVGANYHAVVNGVVEYGVFVDISDEVSGLVHESNLDR---------TYEVGDRLIVSLDEVREN 92
                                      78999*******************************5.........699999999999999876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.4
                                       EEEEEEEEET CS
                                S1   8 veGeVtsvtk 17 
                                       veG+V ++ +
  gi|313126935|ref|YP_004037205.1| 130 VEGVVAQIKQ 139
                                       7888888876 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1     5e-07    0.0022       7      83 ..     261     401 ..     257     420 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5e-07
                                       ECSSSHHHHHHHHHHHH........................................................CECS CS
                                       xxxxxxxxxxxxxxxxx........................................................xxxx RF
                               DHH   7 hknpDtDsigSaialan........................................................llvD 27 
                                        ++ D+D++++++ ++                                                         l++D
  gi|313126935|ref|YP_004037205.1| 261 RHHADGDGMCASVPVQLalenfisevhddedaprhlfkrlpskapfyemedvtrdlnfalegrsrhgqrlpllLMLD 337
                                       5789*******999998777888888888888888888877777777777777777777777777777777777*** PP

                                       --TCGGCGCCH..HCCCSEEEEEEE-S---S.......S---SS--EEEE-SSS-HHHHHHHHHH CS
                                       xxxxxxxxxxx..xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  28 hneksqavege..akeeaedviiiDHHrlge.......efetlapilflnepvgstaeivaelle 83 
                                       +++++++v ++  ++  ++ + ++DHH +         +  + +p+l+ + +   t  + +el++
  gi|313126935|ref|YP_004037205.1| 338 NGSTEEDVPAYenLAHYDVPIAVVDHHHPDPeavepllD-AHVNPYLYDEDYRITTGMMCVELAR 401
                                       ******99887778999999********98788888844.4444788887777777777777755 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05      0.15      18      94 ..     126     197 ..     115     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                       tRNA_anti_2  18 lkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvYeprGsyqlivedi 94 
                                       +  +v v+G ++++k ++ g + f + D++  +sa+ f+ +  + + ++e ++ V v g+++ +e  G +ql v+++
  gi|313126935|ref|YP_004037205.1| 126 M--DVFVEGVVAQIK-QTGGPTVFRIADDTGIVSAAAFEDAGVRAHPEVELDDAVRVSGTAESHE--GALQLEVNSM 197
                                       3..599********5.46899******************87777777789999******999986..7789998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4492.62
//
Query:       gi|313126936|ref|YP_004037206.1|  [L=558]
Description: phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-42  142.7   0.0    2.8e-23   82.3   0.0    2.2  2  PLDc_2          PLD-like domain
    2.3e-07   30.7   1.4    0.00037   20.5   0.2    2.5  2  PLDc            Phospholipase D Active site motif
     0.0035   16.5   0.0        1.8    7.7   0.0    2.4  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB
     0.0085   15.7   0.0        1.1    8.7   0.0    2.3  2  PP_kinase_C_1   Polyphosphate kinase C-terminal domain 1
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.037   13.6   0.0    1.7  1  FAM83           FAM83 A-H
      0.036   13.8   0.2       0.11   12.3   0.2    1.7  2  Amidohydro_2    Amidohydrolase


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0     2e-19   5.9e-16       2     132 ..     201     331 ..     200     332 .. 0.89
   2 !   82.3   0.0   9.4e-27   2.8e-23       2     133 .]     387     520 ..     386     520 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2e-19
                            PLDc_2   2 iqliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfe.t 77 
                                       +++++sA +++ +a y++ s+  ++dal++a++rgv+vr+l+       g+v ++++ +l++l  +agv+v v   +
  gi|313126936|ref|YP_004037206.1| 201 VETLRSADERLFLAGYTL-SSARVADALVAAHHRGVRVRVLVEG--GPVGGVSRRQAETLDRL-VRAGVPVAVVAgP 273
                                       5799**************.************************9..46788999999999999.*********9862 PP

                            PLDc_2  78 ..llgslHaKlylidgktvivGSsNltkrgl..dlnlElnvviedkelakeleeeFerl 132
                                         ++++ HaK++++d++ + v + N+ ++g+  +  + ++v++e+ + a+el+  Fe++
  gi|313126936|ref|YP_004037206.1| 274 gaKFSFHHAKYAVVDDRAL-VLTENWKPAGTggRDSRGWGVRVESMRTAEELATVFEQD 331
                                       5445799*******97655.5579*******8777789******************986 PP

  == domain 2  score: 82.3 bits;  conditional E-value: 9.4e-27
                            PLDc_2   2 iqliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfet. 77 
                                       i+++++A+ +i ++++ + +d  +++al++aa+rgv vrill++ +  +++++e+   + ++l + +gv+++   + 
  gi|313126936|ref|YP_004037206.1| 387 IRRLDEAENQIAVVNPRLDPDGRFFAALVRAARRGVTVRILLSN-AWYDADENERVVTRTQAL-RDSGVPIEA--Ri 459
                                       7899***************************************8.5567888999********.******987..33 PP

                            PLDc_2  78 .....llgslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFerlw 133
                                            ++g +HaK++++dg+ v+vGS N+++ + + n+E+ ++++++e a+++++ F+++w
  gi|313126936|ref|YP_004037206.1| 460 aeprgQFGKVHAKGAVVDGESVLVGSLNWNDHAATENREVVLELDGPEPASYYQRAFDSDW 520
                                       34445559****************************************************9 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00067         2       4      19 ..     279     293 ..     277     298 .. 0.88
   2 !   20.5   0.2   1.2e-07   0.00037       5      26 ..     469     490 ..     465     492 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00067
                                       EE---EEEETTTEEEE CS
                              PLDc   4 thHqKivivDdrvafv 19 
                                       +hH+K  +vDdr a+v
  gi|313126936|ref|YP_004037206.1| 279 FHHAKYAVVDDR-ALV 293
                                       7**********9.554 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.2e-07
                                       E---EEEETTTEEEEE---SSH CS
                              PLDc   5 hHqKivivDdrvafvGgaNLcd 26 
                                       +H+K+ +vD++ ++vG++N++d
  gi|313126936|ref|YP_004037206.1| 469 VHAKGAVVDGESVLVGSLNWND 490
                                       7********************9 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00062       1.8      17      64 ..     202     251 ..     196     287 .. 0.82
   2 !    6.5   0.0    0.0014       4.2      19      64 ..     390     439 ..     373     490 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00062
                                       HHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS..----GG CS
                    Regulator_TrmB  17 elIesAenelivslpselLeelreeliaaaergvtVllliyp..dedlee 64 
                                       e ++sA++ l +++      ++ + l aa+ rgv+V +l+ +    + + 
  gi|313126936|ref|YP_004037206.1| 202 ETLRSADERLFLAGYTLSSARVADALVAAHHRGVRVRVLVEGgpVGGVSR 251
                                       7899999999999999999********************98755444444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0014
                                       HHH-SSEEEEEE-G.GGHHHHHHHHHHHHHTT-EEEEEESS...----GG CS
                    Regulator_TrmB  19 IesAenelivslps.elLeelreeliaaaergvtVllliyp...dedlee 64 
                                       +++Aen++ v  p      ++   l +aa+rgvtV +l+++   d+d++e
  gi|313126936|ref|YP_004037206.1| 390 LDEAENQIAVVNPRlDPDGRFFAALVRAARRGVTVRILLSNawyDADENE 439
                                       5667777666544312234677899****************765333333 PP

>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0077        23      48      71 ..     219     242 ..     212     307 .. 0.76
   2 !    8.7   0.0   0.00038       1.1      36     111 ..     394     476 ..     375     495 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0077
                                       S--HHHHHHHHHHHTT-EEEEEES CS
                     PP_kinase_C_1  48 kdskivkaLieAaengkqvtvlvE 71 
                                       +++++ +aL++A ++g +v vlvE
  gi|313126936|ref|YP_004037206.1| 219 SSARVADALVAAHHRGVRVRVLVE 242
                                       46799******************9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00038
                                       EEEEEEEES-S-S--HHHHHHHHHHHTT-EEEEEES--SSS--HHH...HHHHHHHHHHT-EEEE--TT.....--B CS
                     PP_kinase_C_1  36 vlaikitlYrvakdskivkaLieAaengkqvtvlvElkArfdeenN...iewakkleeagvkvvygvvg.....lkv 104
                                         +i +   r+  d +  +aL++Aa++g +v +l+  +A +d ++N   ++ +++l+++gv +   + +      kv
  gi|313126936|ref|YP_004037206.1| 394 ENQIAVVNPRLDPDGRFFAALVRAARRGVTVRILLS-NAWYDADENervVTRTQALRDSGVPIEARIAEprgqfGKV 469
                                       456777778999999*************99999886.799998877555677899*****99987776522232488 PP

                                       --EEEEE CS
                     PP_kinase_C_1 105 haklllv 111
                                       hak ++v
  gi|313126936|ref|YP_004037206.1| 470 HAKGAVV 476
                                       8887777 PP

>> FAM83  FAM83 A-H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.037     108     256 ..     369     506 ..     350     518 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                             FAM83 108 gvtrvtvytqppkekaphikevvrkliqkaqkviavvmdvf.tDvdilkdlleaaskrkvpvyilLdeknlklflem 183
                                       + t+v v+t p     +  k v+r+l  +a++ iavv   +  D   +  l+ aa+ r+v v ilL ++      + 
  gi|313126936|ref|YP_004037206.1| 369 HATNVRVLTTPG----NAGKAVIRRL-DEAENQIAVVNPRLdPDGRFFAALVRAAR-RGVTVRILLSNAWYD--ADE 437
                                       557777777776....4557788875.7788888888765527999******9987.78*******986443..334 PP

                             FAM83 184 ceklqvnkqhlknlrvRsvkGetyltrsgkkvkGqlkekfllvDgekvlsGsYsftWsssrlhrnlvtvltGq 256
                                        e++  ++q l+      v  e  ++       G+++ k  +vDge+vl+Gs  +   ++  +r++v  l G 
  gi|313126936|ref|YP_004037206.1| 438 NERVVTRTQALRD---SGVPIEARIAEPR-GQFGKVHAKGAVVDGESVLVGSLNWNDHAATENREVVLELDGP 506
                                       4444444444433...3333333233333.2359*****************9999999999999999999996 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   3.5e-05      0.11     100     162 ..     221     284 ..     180     296 .. 0.65
   2 ?   -2.4   0.0       1.1   3.2e+03     124     150 ..     405     429 ..     370     451 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHTTECEEEEESSTTTCCTTTCGGH.HHHHHHHHHHT-EEEEE....CHHHCHHHHH CS
                      Amidohydro_2 100 aeleraveelgfkGvrlnphvggddllgdrld.rpifealeelglpvdihtGpspewlfggpqe 162
                                       a+   a+  +  +Gvr+ + v+g++  g  +   +++ +l++ g+pv + +Gp +  +f+++ +
  gi|313126936|ref|YP_004037206.1| 221 ARVADALVAAHHRGVRVRVLVEGGPVGGVSRRqAETLDRLVRAGVPVAVVAGPGAKFSFHHAKY 284
                                       2223333455566699999999999888777778******************776666666554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                                       CTTTCGGHHHHHHHHHHHT-EEEEE.. CS
                      Amidohydro_2 124 dllgdrldrpifealeelglpvdihtG 150
                                       d++g++     + +++++g++v i  +
  gi|313126936|ref|YP_004037206.1| 405 DPDGRF--FAALVRAARRGVTVRILLS 429
                                       333333..3477788888888888744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3557.51
//
Query:       gi|313126937|ref|YP_004037207.1|  [L=439]
Description: pbs lyase heat-like hypothetical protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-19   67.8  13.5    6.2e-11   42.5   3.3    3.7  4  HEAT_2          HEAT repeats
    3.4e-12   45.8  19.1      0.001   19.5   1.3    6.4  7  HEAT_PBS        PBS lyase HEAT-like repeat
    3.7e-06   26.7   0.2     0.0079   16.4   0.1    4.0  4  HEAT            HEAT repeat
    5.9e-05   23.5   3.4    0.00049   20.5   2.3    3.1  3  HEAT_EZ         HEAT-like repeat
    0.00096   19.1   0.0      0.019   15.0   0.0    2.4  2  Arm             Armadillo/beta-catenin-like repeat
     0.0042   16.8   0.9     0.0087   15.8   0.2    2.0  2  DNA_alkylation  DNA alkylation repair enzyme
  ------ inclusion threshold ------
      0.021   14.8   0.1      0.081   12.9   0.0    2.0  2  G-gamma         GGL domain
       0.12   12.4   0.3       0.39   10.8   0.3    1.8  1  DUF2730         Protein of unknown function (DUF2730)


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3      0.68   1.5e+03      35      71 ..     151     195 ..     123     206 .. 0.62
   2 !    8.6   0.0    0.0011       2.4      26      69 ..     273     314 ..     266     316 .. 0.76
   3 !   32.5   0.2   3.8e-11   8.5e-08      18      78 ..     292     355 ..     287     356 .. 0.89
   4 !   42.5   3.3   2.8e-14   6.2e-11      13      86 ..     352     425 ..     348     426 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.68
                            HEAT_2  35 aLvellededpavRraaaeaLgaig........dpealpaLkell 71 
                                       a v++  d+++a  +a  +a++a+         d e++++L+e+ 
  gi|313126937|ref|YP_004037207.1| 151 ASVSVSGDDEAALTAALDDAISAVEsagldadeDAETIDSLLEAT 195
                                       555555555555555555566666322233322455677777754 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                            HEAT_2  26 rignpealpaLvellededpavRraaaeaLgaigd..pealpaLke 69 
                                       r+g+p +++ +++l++  d    ++a++aLg++g    ea++ L e
  gi|313126937|ref|YP_004037207.1| 273 RMGDPAVFDEMHQLAQRRD----KTAIKALGKMGAdaAEAVETLVE 314
                                       6788888888888887776....89********9634668888876 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 3.8e-11
                            HEAT_2  18 raairaLgrignp..ealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddv 78 
                                       ++ai+aLg++g +  ea+++Lve++ +d+dpa ++   +aLg+ig+ ea +a ++ l  d++ v
  gi|313126937|ref|YP_004037207.1| 292 KTAIKALGKMGADaaEAVETLVEYVdTDSDPALQKVTFKALGEIGSAEATQAIADKLVMDNENV 355
                                       579*****987654499********99****************************999888765 PP

  == domain 4  score: 42.5 bits;  conditional E-value: 2.8e-14
                            HEAT_2  13 dpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvvReaAaea 86 
                                       +++vr  a+raLg +g+++a++ L + l +ded  vR+aaa+aL +ig++eal+  ++ ++d+++++v+ +A+ a
  gi|313126937|ref|YP_004037207.1| 352 NENVRPFAARALGLLGDTRAIDPLADTLaDDEDNTVRAAAAWALRQIGTEEALETAAD-YTDEQSYLVQHEAELA 425
                                       789***********************77699***************************.5689999999998765 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       5.4   1.2e+04      20      27 .]     162     169 ..     161     169 .. 0.84
   2 ?   -1.9   0.1       3.7   8.2e+03      16      24 ..     186     194 ..     181     204 .. 0.62
   3 ?    1.3   0.0      0.36     8e+02       3      25 ..     265     287 ..     263     289 .. 0.82
   4 !   11.8   0.0   0.00014      0.32       5      25 ..     294     316 ..     292     318 .. 0.90
   5 ?    5.3   0.1     0.018        40       7      21 ..     330     344 ..     330     349 .. 0.84
   6 !   16.5   0.2   4.3e-06    0.0097       5      27 .]     359     381 ..     355     381 .. 0.88
   7 !   19.5   1.3   4.5e-07     0.001       1      19 [.     387     405 ..     387     406 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.4
                                       HHHHHCTC CS
                          HEAT_PBS  20 aLleaLqd 27 
                                       aL +aL+d
  gi|313126937|ref|YP_004037207.1| 162 ALTAALDD 169
                                       89999998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.7
                                       GGHHHHHHH CS
                          HEAT_PBS  16 eaipaLlea 24 
                                       e i+ Llea
  gi|313126937|ref|YP_004037207.1| 186 ETIDSLLEA 194
                                       566666665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.36
                                       HHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   3 raAakaLgqlgdeeaipaLleaL 25 
                                        ++++a  ++gd+++ +  +++ 
  gi|313126937|ref|YP_004037207.1| 265 EYCMEAFVRMGDPAVFDEMHQLA 287
                                       68999********9998877765 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00014
                                       HHHHHHHCTS..GGGHHHHHHHC CS
                          HEAT_PBS   5 AakaLgqlgd..eeaipaLleaL 25 
                                       A+kaLg++g+   ea+++L+e  
  gi|313126937|ref|YP_004037207.1| 294 AIKALGKMGAdaAEAVETLVEYV 316
                                       99*****************9865 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.018
                                       HHHHHCTSGGGHHHH CS
                          HEAT_PBS   7 kaLgqlgdeeaipaL 21 
                                       kaLg++g+ ea +a+
  gi|313126937|ref|YP_004037207.1| 330 KALGEIGSAEATQAI 344
                                       79******9998887 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 4.3e-06
                                       HHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   5 AakaLgqlgdeeaipaLleaLqd 27 
                                       Aa+aLg lgd++ai++L   L+d
  gi|313126937|ref|YP_004037207.1| 359 AARALGLLGDTRAIDPLADTLAD 381
                                       9****************887765 PP

  == domain 7  score: 19.5 bits;  conditional E-value: 4.5e-07
                                       HHHHHHHHHHHCTSGGGHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaip 19 
                                       vR+aAa+aL q+g+eea++
  gi|313126937|ref|YP_004037207.1| 387 VRAAAAWALRQIGTEEALE 405
                                       9****************98 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.9   4.3e+03      19      27 ..     293     301 ..     292     303 .. 0.84
   2 ?    4.9   0.0     0.017        38       4      29 ..     311     337 ..     308     338 .. 0.85
   3 ?   -0.9   0.0       1.3   2.9e+03      13      27 ..     352     366 ..     351     369 .. 0.78
   4 !   16.4   0.1   3.5e-06    0.0079       7      27 ..     378     398 ..     372     400 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.9
                                       HHHHHHHHH CS
                              HEAT  19 aAakaLgal 27 
                                       +A+kaLg++
  gi|313126937|ref|YP_004037207.1| 293 TAIKALGKM 301
                                       89*****87 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.017
                                       HHHHHH.T-SSHHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkll.sDpspeVReaAakaLgalae 29 
                                       +l++   +D++p   + ++kaLg++ +
  gi|313126937|ref|YP_004037207.1| 311 TLVEYVdTDSDPALQKVTFKALGEIGS 337
                                       67777779****************975 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                                       SHHHHHHHHHHHHHH CS
                              HEAT  13 speVReaAakaLgal 27 
                                       + +VR  Aa+aLg l
  gi|313126937|ref|YP_004037207.1| 352 NENVRPFAARALGLL 366
                                       56788889****977 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 3.5e-06
                                       HHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   7 kllsDpspeVReaAakaLgal 27 
                                       +l  D++  VR+aAa+aL ++
  gi|313126937|ref|YP_004037207.1| 378 TLADDEDNTVRAAAAWALRQI 398
                                       34499**************98 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.5   5.6e+03       7      14 ..     294     301 ..     292     334 .. 0.61
   2 ?    0.3   0.1      0.48   1.1e+03      42      53 ..     353     364 ..     341     366 .. 0.67
   3 !   20.5   2.3   2.2e-07   0.00049      27      55 .]     369     398 ..     353     398 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.5
                           HEAT_EZ   7 AawaLGrl 14 
                                       A+ aLG +
  gi|313126937|ref|YP_004037207.1| 294 AIKALGKM 301
                                       45555543 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                           HEAT_EZ  42 deVRaaAagaLg 53 
                                        +VR  Aa+aLg
  gi|313126937|ref|YP_004037207.1| 353 ENVRPFAARALG 364
                                       555555666665 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 2.2e-07
                           HEAT_EZ  27 peilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       ++++++L+ +L dd+d +VRaaAa+aL+++
  gi|313126937|ref|YP_004037207.1| 369 TRAIDPLADTLADDEDnTVRAAAAWALRQI 398
                                       4689999999999999899*********97 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.17   3.9e+02      12      39 ..     307     335 ..     305     337 .. 0.89
   2 !   15.0   0.0   8.3e-06     0.019      12      39 ..     370     398 ..     365     400 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
                                       THHHHHHHHTT.TSSHHHHHHHHHHHHHH CS
                               Arm  12 GavppLvrLLs.sedeevqeeAawALsNL 39 
                                        av+ Lv+  + + d+ +q++   AL+ +
  gi|313126937|ref|YP_004037207.1| 307 EAVETLVEYVDtDSDPALQKVTFKALGEI 335
                                       5899****************999999876 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 8.3e-06
                                       THHHHHHHHTT.TSSHHHHHHHHHHHHHH CS
                               Arm  12 GavppLvrLLs.sedeevqeeAawALsNL 39 
                                        a++pL + L  +ed +v+ +AawAL+ +
  gi|313126937|ref|YP_004037207.1| 370 RAIDPLADTLAdDEDNTVRAAAAWALRQI 398
                                       589***********************976 PP

>> DNA_alkylation  DNA alkylation repair enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   3.8e+03      94     127 ..     202     235 ..     170     275 .. 0.54
   2 !   15.8   0.2   3.9e-06    0.0087     151     187 ..     367     403 ..     291     432 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                    DNA_alkylation  94 vetinnWdlvDslaskivgalladk.perrdllke 127
                                       +e++++Wd   +  +k++++ ++d   + +d+  e
  gi|313126937|ref|YP_004037207.1| 202 LEDAEEWDDLETN-EKLQAQGFYDVlGHYKDYPPE 235
                                       4445555444443.444444444333333333333 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.9e-06
                    DNA_alkylation 151 tdlellleiaeelladkedfiqkAiGwaLrelsktdp 187
                                       +d+  +  +a++l++d+++ ++ A +waLr+++ + +
  gi|313126937|ref|YP_004037207.1| 367 GDTRAIDPLADTLADDEDNTVRAAAAWALRQIGTEEA 403
                                       5666677799***********************8743 PP

>> G-gamma  GGL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.6e-05     0.081      21      47 ..     301     327 ..     286     332 .. 0.86
   2 ?   -3.1   0.0       3.7   8.3e+03      12      23 ..     418     429 ..     409     429 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
                           G-gamma  21 erikvSkAceelidYvestkDpllpev 47 
                                        +  + +A+e+l++Yv++ +Dp+l+ v
  gi|313126937|ref|YP_004037207.1| 301 MGADAAEAVETLVEYVDTDSDPALQKV 327
                                       5567889*****************998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.7
                           G-gamma  12 eqLkkeLkreri 23 
                                        q + eL+rer+
  gi|313126937|ref|YP_004037207.1| 418 VQHEAELARERL 429
                                       577889999995 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00018      0.39      41      82 ..      28      69 ..      16      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                           DUF2730 41 kveendkrlteletkvenLPtakdlekLkllladlrgelkal 82
                                      ++e+ d+rl+++e  ++   t++dl++++ +l  ++ +l+a+
  gi|313126937|ref|YP_004037207.1| 28 TAESLDERLDSAEEDLDAAETESDLDEVESTLDAVESDLDAA 69
                                      68899*******************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2859.15
//
Query:       gi|313126938|ref|YP_004037208.1|  [L=254]
Description: amidohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-28   99.5   0.0    2.2e-28   99.3   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.0   1.2e-32   2.2e-28       2     249 ..       6     237 ..       5     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 1.2e-32
                                       EEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEE CS
                      CN_hydrolase   2 vAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiav 78 
                                       vAv Ql+      e n++ + e  a+  + ++++ ++PE+++tg++  ++  +aA    +e ++ l  +a +n+i +
  gi|313126938|ref|YP_004037208.1|   6 VAVPQLAVADLRPERNVASVRERTAA-LDDAVCVALFPEYALTGFVADERLGDAAL-TRAEAVEYLTPIADENDIDL 80 
                                       56666666556666666666666555.888***************88888888887.6889**************** PP

                                       EEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGG CS
                      CN_hydrolase  79 vigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCye 155
                                        +g+ er  ++  l  yn+a ++ +dg+   +yrK+hL+          e+ ++  g++  v+dtp gk G++ Cy+
  gi|313126938|ref|YP_004037208.1|  81 LAGYVER--DGAAL--YNAAAYVRPDGS-HRIYRKRHLW--------GGEEAMLDTGTECVVVDTPAGKTGLLTCYD 144
                                       *******..9****..************.7********9........5677889999999999************** PP

                                       GGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEE...HCETTEEEE--EEEE CS
                      CN_hydrolase 156 igfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvgg...yeqlilwpvghSaii 229
                                        +f   +  +  k+++ l+ +      + +   + w ll raral++  +v+ a ++g    +    +++ g S ++
  gi|313126938|ref|YP_004037208.1| 145 LNFVAESAEMTEKRVDALFVIG----AWPAAHSENWRLLCRARALDGVRWVVGAGRTGQrdvAGTRTTQYAGRSLVV 217
                                       ********************33....4566777999**************************99************* PP

                                       -TTS-EEEECCSSSTEEEEE CS
                      CN_hydrolase 230 dpdGrilaglgeeeegvlia 249
                                        pdG ++a+lg++e++++++
  gi|313126938|ref|YP_004037208.1| 218 RPDGAVAAALGRDERDLVYT 237
                                       **************998774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1750.73
//
Query:       gi|313126939|ref|YP_004037209.1|  [L=302]
Description: Fe3+-hydroxamate ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-21   75.6   0.0    5.5e-21   75.2   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.95   10.0   4.2       0.66   10.5   0.2    2.8  4  PQQ_3         PQQ-like domain


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   6.2e-25   5.5e-21       1     235 [.       3     258 ..       3     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 6.2e-25
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.................TS......-BSBESSSB-HHHHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee...............ai......vevgadgeidvEkla 56 
                                       ++sl ps te+l++lGa++   gv++++ +p +a++++                +i      ve g+  +idv+ la
  gi|313126939|ref|YP_004037209.1|   3 VVSLLPSATELLYGLGAEP--LGVSHSCDYPPAARAKPVltstvieygddrppaDIdrqtrnVE-GSTYDIDVDLLA 76 
                                       8999***************..***************9999997777666655551166655355.55558******* PP

                                       HH--SEEEE-GGG..........GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                      Peripla_BP_2  57 alkPDlvilskgl.......gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidskla 126
                                       +l+PDlv+ +++        +++ e+ e++  ++++++ ++ +  +++ + ++ +ge+ g  d a  l ae++ +++
  gi|313126939|ref|YP_004037209.1|  77 DLDPDLVVTQATCevcavdaSDVFEAVERRGIDADVLTLDPHSL-SDILDDLTRVGEAIGASDTAASLRAELEARIE 152
                                       ****************9988888888899999999*******96.******************************** PP

                                       HHHHTS-TT..-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH CS
                      Peripla_BP_2 127 aaksaidse.kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr 202
                                       ++ ++++ + +++ ++v+ + d+    v++ ++++ ++++ +g+ + + +   + + +  ++ + a dp+v++v+++
  gi|313126939|ref|YP_004037209.1| 153 RVTDRAAAAmDRPRTAVLDWTDP----VIAGGHWVPEMIERAGGTPGLVT--DGPSTPQHWDDVRAFDPEVLIVAPC 223
                                       *********99999999999999....9999****************999..7999999****************** PP

                                       ..HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 203 ..aeadnktgleflkenpllaelpAvkngrVyald 235
                                         + ++ +   ++l + +++a+l+Av+ g+Vy +d
  gi|313126939|ref|YP_004037209.1| 224 gfDVERGTDAISDLRSKDGWANLTAVQDGNVYVVD 258
                                       ********************************986 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.63   5.7e+03      31      39 ..      89      97 ..      78      98 .. 0.69
   2 ?   -2.8   0.0       1.2     1e+04      14      23 ..     172     181 ..     171     182 .. 0.80
   3 ?   -2.1   0.0      0.69   6.2e+03      31      38 ..     208     215 ..     190     216 .. 0.63
   4 ?   10.5   0.2   7.4e-05      0.66      17      33 ..     246     263 ..     226     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.63
                             PQQ_3 31 GtlyAlDae 39
                                        ++A+Da 
  gi|313126939|ref|YP_004037209.1| 89 CEVCAVDAS 97
                                      568999996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                             PQQ_3  14 nsspavdggl 23 
                                       ++ p+++gg+
  gi|313126939|ref|YP_004037209.1| 172 WTDPVIAGGH 181
                                       5679999996 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.69
                             PQQ_3  31 GtlyAlDa 38 
                                         ++A+D+
  gi|313126939|ref|YP_004037209.1| 208 DDVRAFDP 215
                                       45677776 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 7.4e-05
                             PQQ_3  17 p.avdgglvyvgtgdGtl 33 
                                       + av +g vyv++g+G +
  gi|313126939|ref|YP_004037209.1| 246 LtAVQDGNVYVVDGNGYV 263
                                       2599***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2111.09
//
Query:       gi|313126940|ref|YP_004037210.1|  [L=184]
Description: DNA-binding ferritin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-32  110.9   5.1    5.3e-32  110.7   5.1    1.1  1  Ferritin       Ferritin-like domain
     0.0095   16.3   0.2      0.041   14.2   0.0    2.1  2  DUF2383        Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
      0.045   13.8   3.8       0.11   12.5   0.4    2.8  3  Fe_dep_repr_C  Iron dependent repressor, metal binding and di
       0.91    9.6   3.6        4.9    7.3   0.3    2.9  3  HisKA          His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   5.1   1.2e-35   5.3e-32       2     139 ..      32     173 ..      31     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.2e-35
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH...C-SS CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee...ieap 75 
                                       +aLn  la+ +++++q ++++w+v+g ++++l+ ff+e +e   e ad+laer++alGg+p++  + lee   +e++
  gi|313126940|ref|YP_004037210.1|  32 NALNTDLAATYVLYHQLKKHHWNVEGAEFRDLHLFFEEAYENAEEFADELAERVQALGGVPIAGGKALEEhapVEPE 108
                                       89********************************************************************7775555 PP

                                       SS.CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  76 ke.fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                        e + +++  l++++e++ +++e+lre +ela++ gD+at  +l + le+ e+ ++++e++le+ 
  gi|313126940|ref|YP_004037210.1| 109 GEdVYDIRTSLRNDMEMYGDIIENLREHVELADSLGDHATSYMLRENLEDVEDDAHHIEHYLEDD 173
                                       55544*********************************************************986 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   9.2e-06     0.041      28      65 ..      59      96 ..      29     100 .. 0.71
   2 ?   -1.0   0.0       0.5   2.3e+03      78      99 ..     139     161 ..     119     171 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.2e-06
                                      -SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT------- CS
                           DUF2383 28 kdpqlktlleriaeereeaaeeLqseiralggepedgg 65
                                      +  +l  ++e+  e+ ee+a+eL+++++algg p  gg
  gi|313126940|ref|YP_004037210.1| 59 EFRDLHLFFEEAYENAEEFADELAERVQALGGVPIAGG 96
                                      33455568************************997776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.5
                                       ---------HHHHH.HHHHHHHH CS
                           DUF2383  78 lksaltsndeeail.eeleegEd 99 
                                       l ++l++++++ +l e+le +Ed
  gi|313126940|ref|YP_004037210.1| 139 LADSLGDHATSYMLrENLEDVED 161
                                       44444444444444234555555 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.71   3.2e+03      25      40 ..      19      34 ..      17      41 .. 0.65
   2 ?    0.9   0.1      0.11   4.9e+02      31      46 ..      68      83 ..      59      92 .. 0.59
   3 ?   12.5   0.4   2.6e-05      0.11      29      49 ..     155     175 ..     149     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.71
                                      HCT--CCCHHHHCCCC CS
                     Fe_dep_repr_C 25 vlgvdweeaheeAerl 40
                                       l +d+++a++ + +l
  gi|313126940|ref|YP_004037210.1| 19 ALRIDADRAEQIVNAL 34
                                      5667777777666554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                                      CCHHHHCCCCGGGS-H CS
                     Fe_dep_repr_C 31 eeaheeAerlEhalse 46
                                      eea+e+Ae++   l e
  gi|313126940|ref|YP_004037210.1| 68 EEAYENAEEFADELAE 83
                                      5566666665443333 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 2.6e-05
                                       -CCCHHHHCCCCGGGS-HHHH CS
                     Fe_dep_repr_C  29 dweeaheeAerlEhalseeli 49 
                                       + e+++++A+ +Eh+l ++++
  gi|313126940|ref|YP_004037210.1| 155 NLEDVEDDAHHIEHYLEDDTL 175
                                       5699**************986 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.12   5.5e+02      44      58 ..      20      34 ..      13      39 .. 0.80
   2 ?    1.0   0.1     0.096   4.3e+02      13      49 ..      34      75 ..      27      88 .. 0.66
   3 ?    7.3   0.3    0.0011       4.9      31      57 ..     146     172 ..     129     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                                      HHHHHHHHHHHHHHH CS
                             HisKA 44 iesearrldhlvedl 58
                                      ++  a+r +++v+ l
  gi|313126940|ref|YP_004037210.1| 20 LRIDADRAEQIVNAL 34
                                      556799******987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.096
                                      HHHHHHHHHHHHHHHHC.......T-HSSCHHHHHHHHHHHH CS
                             HisKA 13 LrtPLsailgnaeaLkre.....gklteelkeyletiesear 49
                                      L+t L+a +   + Lk++     g+   +l  ++e + ++a+
  gi|313126940|ref|YP_004037210.1| 34 LNTDLAATYVLYHQLKKHhwnveGAEFRDLHLFFEEAYENAE 75
                                      899999999999999887777663333444445555555554 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0011
                                       .T-HSSCHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  31 gklteelkeyletiesearrldhlved 57 
                                       ++++ +l+e+le++e+ a++++h +ed
  gi|313126940|ref|YP_004037210.1| 146 HATSYMLRENLEDVEDDAHHIEHYLED 172
                                       4667789*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1168.33
//
Query:       gi|313126941|ref|YP_004037211.1|  [L=53]
Description: hypothetical protein Hbor_22030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       135  (0.0075297); expected 358.6 (0.02)
Passed bias filter:                      118  (0.00658152); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.43
# Mc/sec: 366.62
//
Query:       gi|313126942|ref|YP_004037212.1|  [L=362]
Description: NADH:flavin oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-65  221.9   0.0    1.5e-65  221.7   0.0    1.0  1  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
  ------ inclusion threshold ------
      0.012   14.7   0.0      0.023   13.8   0.0    1.4  1  Dus           Dihydrouridine synthase (Dus)
      0.019   14.6   0.0        5.8    6.5   0.0    3.0  2  DUF4965       Domain of unknown function (DUF4965)


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.7   0.0   2.6e-69   1.5e-65       1     340 [.       4     347 ..       4     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 221.7 bits;  conditional E-value: 2.6e-69
                                       CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGG CS
                      Oxidored_FMN   1 kLFkPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksggfdnapgiwdee 77 
                                       +LF  +++  ++L nR++ +pm++++a+d g +++d+ + +   ra ++ ++++tea++v+p++++ + + giw++ 
  gi|313126942|ref|YP_004037212.1|   4 SLFSSLTLRGTELPNRVMLSPMCQYSAED-G-MATDWHLVHLGSRAVGGAGVVMTEATAVTPEGRISPRDLGIWSDT 78 
                                       59***********************9865.5.5999***************************************** PP

                                       GHHHHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC..............SS.ESSSSSTTT-.S...CS-EE- CS
                      Oxidored_FMN  78 qieewrklteavhengskvvvqlwhlGreakseyladqe............vdspsdpvaldaqeeesaeevykkel 142
                                       + ++++ ++  ++e+gs  ++ql+h+Gr+    + ++++            +++ps++ + +a+    +     +++
  gi|313126942|ref|YP_004037212.1|  79 HGHALEDVASFIREQGSVPAIQLAHAGRKGS-KTPPQEGsepipeseggweTVAPSADPYPYAD----GATAATRKM 150
                                       ****************************983.33333335678887777776777766666666....22222689* PP

                                       -HHHHHHHHHHHHHHHHHHHHTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SS CS
                      Oxidored_FMN 143 tkeeikqliqefveAAkraieAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgee 219
                                       t ++i++li++f  AAkr+ +Agf + e+h+a+GYLl++Flsp +n+r D ygGs enR r ++e+  aV+e+  e+
  gi|313126942|ref|YP_004037212.1| 151 TVDDIEDLIDAFRAAAKRSLDAGFEIAEVHAAHGYLLHEFLSPVTNHRDDDYGGSFENRTRLVREITAAVREVWPED 227
                                       ***************************************************************************** PP

                                       S.EEEEEECE--STTS--HHHH...HHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHHCCTTHHHHHHCCCHS CS
                      Oxidored_FMN 220 r.vgyRlSpedvvekgldfaet...aqkivllkelekrlkdgkklalvhaaeprkrgagsvrteqekntefvkevwk 292
                                         v++RlS+ d    + ++ +    a  + ll++ + +l+d++ + +   ++   +g+g ++ +    +e v e  +
  gi|313126942|ref|YP_004037212.1| 228 NpVFVRLSATDWLP-DRESWDLdqsARLAPLLADAGADLIDVSAGGIHPDQQVPDTGPGYQVPY----AEHVNEATE 299
                                       ********988664.444444444899999**********999988654334344566666665....999****** PP

                                       SEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTC CS
                      Oxidored_FMN 293 kplitvgriadeekaaeivaegeadLvamgRefladpdlveklkkglp 340
                                        ++ tvg+i+++e+a++i  +g ad+ a+gRe l++p +   ++++l 
  gi|313126942|ref|YP_004037212.1| 300 LAVGTVGKITEPEQADQIIRNGSADIAAVGREHLRNPYFSLEAAHELD 347
                                       *************************************99988888775 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.9e-06     0.023     105     232 ..     208     349 ..     193     358 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-06
                                       GSHHHHHHHHHHHHCCSS..S-EEEEEESESS......TTTC.HHHHHHHHHHCT-SEEEEESS..ECCCTT-C... CS
                               Dus 105 rkpdlvaqivkavvkave..iPvtvkirigid......deeenalelakiveaaGaqaltvHgR..traqnyeg... 168
                                       +  +lv +i +av++  +  +Pv v+ +           + +++ +la  + +aGa+ + v +    + q+      
  gi|313126942|ref|YP_004037212.1| 208 NRTRLVREITAAVREVWPedNPVFVRLSATDWlpdresWDLDQSARLAPLLADAGADLIDVSAGgiHPDQQVPDtgp 284
                                       55566666666666665555666665543322232222123445566666666666666666665522222222123 PP

                                       G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHS CS
                               Dus 169 tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stavktg 232
                                         +    ++v +a ++ v   G I+++e+a++i+++  ad   +gr+ l+nP+++ e  ++++++
  gi|313126942|ref|YP_004037212.1| 285 GYQVPYAEHVNEATELAVGTVGKITEPEQADQIIRNGSADIAAVGREHLRNPYFSLEaAHELDED 349
                                       344444568899999999999*********************************99877777765 PP

>> DUF4965  Domain of unknown function (DUF4965)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0055        33      67      93 ..      19      45 ..      14     110 .. 0.84
   2 ?    6.5   0.0   0.00097       5.8      95     174 .]     137     212 ..     127     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0055
                           DUF4965 67 kllLeplleyqesgkypkkfaahDlGt 93
                                      +++L+p+++y++ +   +++   +lG+
  gi|313126942|ref|YP_004037212.1| 19 RVMLSPMCQYSAEDGMATDWHLVHLGS 45
                                      579999999999999999999999998 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00097
                           DUF4965  95 YPnatgqndgedeqmpveesGnmlimalayaqasgdasllekyydllkqWadYLvengldpanqlstddfagalanq 171
                                       YP+a+g +   + +m v++  +++    a+a++s da +    ++       YL ++ l p ++   dd+ g+++n 
  gi|313126942|ref|YP_004037212.1| 137 YPYADGATA-ATRKMTVDDIEDLIDAFRAAAKRSLDAGFEIAEVHAA---HGYLLHEFLSPVTNHRDDDYGGSFENR 209
                                       ********9.589*********************9997755544444...4799*******************9999 PP

                           DUF4965 172 tnL 174
                                       t L
  gi|313126942|ref|YP_004037212.1| 210 TRL 212
                                       976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2429.71
//
Query:       gi|313126943|ref|YP_004037213.1|  [L=322]
Description: hypothetical protein Hbor_22050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2051.18
//
Query:       gi|313126944|ref|YP_004037214.1|  [L=123]
Description: nucleic-acid-binding protein containing a zn-ribbon [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-09   35.3   0.9    1.3e-08   34.7   0.9    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.9   7.4e-13   1.3e-08       2      64 ..      35      96 ..      34      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 7.4e-13
                                      EEE-G.G-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT......-EE-EEEEEEES..TT-B-EEE- CS
                     OB_aCoA_assoc  2 velsg.rGtvysftvvhrappgfaeeaPyvvgvVeLde...gvrimarlvgvdpdevriGmrVravf 64
                                      v+ls  +++v+++t+  + p   + ++P ++++Ve+d    +vr +++l+  d   v+iG++Vrav+
  gi|313126944|ref|YP_004037214.1| 35 VDLSEyTAEVVTWTTATATP--PGVRQPNHLAIVEFDVdgePVRAIGQLTSGD---VEIGDEVRAVY 96
                                      788888**************..679************9888*********999...66*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 902.66
//
Query:       gi|313126945|ref|YP_004037215.1|  [L=384]
Description: acetyl-CoA acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-56  190.1   0.0    6.3e-56  189.6   0.0    1.2  1  Thiolase_N       Thiolase, N-terminal domain
    4.3e-09   36.1   0.1    2.5e-08   33.6   0.1    2.0  2  Thiolase_C       Thiolase, C-terminal domain
    0.00016   21.7   0.3       0.24   11.4   0.0    3.3  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
  ------ inclusion threshold ------
      0.068   12.7   1.8       0.79    9.3   0.8    2.3  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.6   0.0   1.4e-59   6.3e-56       1     260 []       4     222 ..       4     222 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 1.4e-59
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TT CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipee 75 
                                       v++++a++t++g+     +d++++eLlaea++a+l++agv+p+++d+++v+n++++ +egq+ + +++a+++    +
  gi|313126945|ref|YP_004037215.1|   4 VAVIGASMTQFGQ-----RDAWIRELLAEAGQACLDDAGVSPDAIDHLYVSNMASGeFEGQTgVPNALAHDLSA-LP 74 
                                       79***********.....*************************************99****************9.9* PP

                                       SEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTT CS
                        Thiolase_N  76 vpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafne 152
                                       +++ ++++++sSg +++++a+qs+a+g++++++++G+E+m++++tae+tdv+++l++++e+++++++p+        
  gi|313126945|ref|YP_004037215.1|  75 AYTARIDQTSSSGGAGIYAAWQSVASGASEMTLLVGGEKMTHRTTAEATDVIASLTHPAEYKHGVTLPS-------- 143
                                       *********************************************************************........ PP

                                       SEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS CS
                        Thiolase_N 153 ehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLakl 229
                                        ++Glta+ ++++y+++Re++ ++Avk+h++++++++a+ F++e+              d d+ ++s+++a++L+ +
  gi|313126945|ref|YP_004037215.1| 144 -FAGLTARLYLDTYDAPRESLGKVAVKNHKNGVDNPHAQ-FRKEV--------------DLDTVLDSPIVADPLRLY 204
                                       .**************************************.*****..............99**************** PP

                                       -BSSSTTSS-BTTSB--BEEEEEEEEEEEHH CS
                        Thiolase_N 230 kpaFkkeGtvtAgnasqisDGaaavllmses 260
                                                    ++++i+DG+aa++l++es
  gi|313126945|ref|YP_004037215.1| 205 -------------DFCPITDGSAALMLCPES 222
                                       .............***************986 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.19   8.7e+02      25      45 ..      26      46 ..       4      55 .. 0.77
   2 !   33.6   0.1   5.6e-12   2.5e-08      16     119 ..     251     375 ..     240     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.19
                                      HHHHHHHHHHHT--GGGESEE CS
                        Thiolase_C 25 ayaikkvlkkagltvedidlf 45
                                      a a +++l++ag++ + id +
  gi|313126945|ref|YP_004037215.1| 26 AEAGQACLDDAGVSPDAIDHL 46
                                      6788999*******9999976 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 5.6e-12
                                       -GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT-- CS
                        Thiolase_C  16 dpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGG 74 
                                       dp+++g g ++ ++++ + a l+ +did+ E+++ F+   +   ++l++ +                    +N  GG
  gi|313126945|ref|YP_004037215.1| 251 DPTTMG-GVVNSSEQAYEMADLEPDDIDVAELHDMFTILEFLQSEDLGFFEkgegwkaveegvtdrdgdLPINTSGG 326
                                       666665.66889999*********************************9999**************99888****** PP

                                       HHHH-B-TTTHHHHHHHHHHHHHHHCTTSEEEEE....EEETTTEEEEE CS
                        Thiolase_C  75 aialGHPlGasGaRivvtllselkkeggklgvaa....lCigggqgval 119
                                         + GHPlGasG+ ++  +  +l  e g   v a    +C+ gg g+ +
  gi|313126945|ref|YP_004037215.1| 327 LKSKGHPLGASGVAQAYEIYAQLMGEAGDRQVEAqtglACNVGGFGNCV 375
                                       **************99999998877665554443223368888888765 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.025   1.1e+02      26      48 ..      25      47 ..       5      56 .. 0.81
   2 !   11.4   0.0   5.4e-05      0.24       2      52 ..     232     284 ..     231     289 .. 0.70
   3 ?    3.5   0.0     0.015        66      87     104 ..     330     347 ..     312     353 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.025
                                      HHHHHHHHHHHHT--GGGEEEEE CS
                   Ketoacyl-synt_C 26 qaraiekalaeagvdpedvdyve 48
                                      +a+a +++l++agv+p+ +d++ 
  gi|313126945|ref|YP_004037215.1| 25 LAEAGQACLDDAGVSPDAIDHLY 47
                                      4677899************9764 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.4e-05
                                       EEEEEEEEEE--..STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS- CS
                   Ketoacyl-synt_C   2 avikgsavnsdg..ahnsltapngeaqaraiekalaeagvdpedvdyveahgt 52 
                                        vi g++   d    h+ +      +  +  e+a+++a+++p+d+d+ e h+ 
  gi|313126945|ref|YP_004037215.1| 232 VVISGIGGATDThvVHERADPTTMGGVVNSSEQAYEMADLEPDDIDVAELHDM 284
                                       56777777774433344444444455566699*******************97 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.015
                                       H-B-GGGHHHHHHHHHHH CS
                   Ketoacyl-synt_C  87 iGHleaAaGvaelikvvl 104
                                        GH ++A+Gva++  +  
  gi|313126945|ref|YP_004037215.1| 330 KGHPLGASGVAQAYEIYA 347
                                       5**********9987655 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.033   1.5e+02      91     124 ..      24      57 ..       5      82 .. 0.75
   2 ?    9.3   0.8   0.00018      0.79     175     218 ..      84     127 ..      75     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESST CS
                     ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgag 124
                                       ll ea + +l dag++p+++d+  v +++  + +
  gi|313126945|ref|YP_004037215.1|  24 LLAEAGQACLDDAGVSPDAIDHLYVSNMASGEFE 57 
                                       677888999**********998777666655555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00018
                                       GGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT CS
                     ketoacyl-synt 175 CsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag 218
                                        sS+ + + aa+qs+ sg +++ l  G e +++  +  + + ++
  gi|313126945|ref|YP_004037215.1|  84 SSSGGAGIYAAWQSVASGASEMTLLVGGEKMTHRTTAEATDVIA 127
                                       578899999***********************999988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2481.58
//
Query:       gi|313126946|ref|YP_004037216.1|  [L=157]
Description: hypothetical protein Hbor_22080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.082   12.0  11.4        0.1   11.6  11.4    1.0  1  Acyl_transf_3  Acyltransferase family
       0.88    9.8   3.4         10    6.3   0.5    2.3  2  Pox_A14        Poxvirus virion envelope protein A14


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  11.4   1.1e-05       0.1     163     280 ..      34     154 ..      25     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 163 llllilllllslvfirhelfgpatsvgllplpsvlallfflfGalladaddrdrnlsr...glkislllsllllali 236
                                        lll+l+++ +++ i   +  +a ++ + p+      +f l+G++++ a  + r  +    gl ++l +++l++a+i
  gi|313126946|ref|YP_004037216.1|  34 SLLLALVVFAPALLISGSNASVADYYAAGPVGISVVGFFALLGIIIFLAGAQERTEPAiiaGLTLVLGVAMLAFAVI 110
                                       466666666666666666667776666666666555********************998889999999999999999 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 237 llalfgqtdggglvasvliqsaslllvslgimllllllfalpsr 280
                                       +++ + qt   ++   +++   ++++v++ ++++ +++ ++ +r
  gi|313126946|ref|YP_004037216.1| 111 WAFSLDQTLLFSFPSQYAWIANHRWAVIALTAVVPVAAGVYSRR 154
                                       9999999999*******************999999988877665 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1    0.0048        43      21      65 ..      35      80 ..      22      90 .. 0.66
   2 ?    6.3   0.5    0.0011        10      14      30 ..      97     113 ..      91     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0048
                           Pox_A14 21 LLilacifaf.vdfskstst.tdkawralsivsFilgivillglllf 65
                                      LL + ++fa  + +s s+ + +d  + a  +   ++g  +llg+++f
  gi|313126946|ref|YP_004037216.1| 35 LLLALVVFAPaLLISGSNASvAD-YYAAGPVGISVVGFFALLGIIIF 80
                                      55555666641344555554344.455555555699999*****998 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0011
                           Pox_A14  14 vliaGiiLLilacifaf 30 
                                        l+ G+++L+ a+i af
  gi|313126946|ref|YP_004037216.1|  97 TLVLGVAMLAFAVIWAF 113
                                       5899************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1064.87
//
Query:       gi|313126947|ref|YP_004037217.1|  [L=431]
Description: arabinose efflux permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.1e-36  123.8  37.1      4e-26   91.8  17.1    2.0  2  MFS_1       Major Facilitator Superfamily
    5.2e-05   21.8  17.4     0.0011   17.4   7.9    2.1  2  MFS_3       Transmembrane secretion effector
    5.8e-05   22.5  24.2     0.0006   19.2  23.2    2.5  1  MFS_4       Uncharacterised MFS-type transporter YbfB
    0.00017   20.6  17.0     0.0011   17.9   7.9    2.9  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
       0.16   10.2  10.6       0.28    9.4   2.7    2.6  3  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8  17.1   1.1e-29     4e-26       4     250 ..      23     258 ..      20     259 .. 0.87
   2 !   44.0  21.8   3.6e-15   1.3e-11       9     182 ..     229     427 ..     221     431 .] 0.86

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.1e-29
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       +af  + a+s++++al  ++a+++g ++ + gl  t++a+++++ +lplGr +d   ++ +ll+gl++ ++  ++++
  gi|313126947|ref|YP_004037217.1|  23 TAFARSQAYSTILIALA-LYADQFGTTGFVEGLFGTAFAVVQLLIVLPLGRKVDTGNAKHYLLAGLVVNVAV-FIGF 97 
                                       67888889999999999.99**********************************955555************.5555 PP

                             MFS_1  81 fa..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                        +  ++++ ++++r++qGlga++l+ +g +++ +++p++  gr +g ++  ++++++ g ++gg+l+ ++   +v++
  gi|313126947|ref|YP_004037217.1|  98 -TqvQNSTHVVLMRMVQGLGASLLWITGSTVVGEISPDDSSGRWLGAYNQVAAFSSLAGDVIGGYLLYAYQTYVVYM 173
                                       .33488889******************************************************************** PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg....llt 228
                                       +l +v++ af+l++ +l+e+p  rk +++++          ++ ++all +p +     +l++f ++fs     + +
  gi|313126947|ref|YP_004037217.1| 174 ALSAVTIAAFLLVWRYLRENPGGRKDPEEATG---------TETLRALLDRPMI----RSLVFFRLAFSVgkmaVII 237
                                       ************99999999999999988888.........556999*****55....4444443333334445*** PP

                             MFS_1 229 llplylqevlglsglllaglll 250
                                       +lp+++++++g++ ++ +g++l
  gi|313126947|ref|YP_004037217.1| 238 FLPIFAHKQFGIN-AFAIGWIL 258
                                       *************.78888665 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 3.6e-15
                             MFS_1   9 alarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.lllll... 80 
                                       + + ++++++lp++  +++gi++ +ig++l++  l+  va+  +G l+dr+G++  ++ +g++l+++g +l++l   
  gi|313126947|ref|YP_004037217.1| 229 SVGKMAVIIFLPIFAHKQFGINAFAIGWILAGGKLTKTVAQGYMGDLTDRLGSKHwFVAVGAALYGIGtALIPLaly 305
                                       556677889999999*************************************9999************888888753 PP

                             MFS_1  81 f....ass...............lwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailg 137
                                       f    + +               +++l+++  + G++ ++ +pa++al+++   + +  ++ ++l s+++ +G + g
  gi|313126947|ref|YP_004037217.1| 306 FegvvT-PiefsafgktqalggaFFALFAAYGVLGVADSIRLPASMALFVEEGERfDSVASSMSLRSISWKIGQVAG 381
                                       365440.1444455566666675779*************************************************** PP

                             MFS_1 138 pllggllasslgWravfyilaivslla.fvlfllllpeepperkrk 182
                                       p+l g + + ++ +a+f+ +a++ ++a +++ + +++++++e++r+
  gi|313126947|ref|YP_004037217.1| 382 PALVGTIKDVVSTTAAFLTAAAFIIVAtGIFLVTYYLTSRVESPRP 427
                                       ***************************7556678888888877776 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   7.9   3.2e-07    0.0011      75     288 ..      80     286 ..      54     327 .. 0.76
   2 !    9.8   2.2   6.4e-05      0.23     111     182 ..     336     407 ..     324     424 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.2e-07
                             MFS_3  75 RkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginia 151
                                       +++lla+ ++      +++ + ++++++   ++ + ++ g+Ga+l   + + +vge+ + +               +
  gi|313126947|ref|YP_004037217.1|  80 KHYLLAGLVV-----NVAVFIGFTQVQNSTHVVLMRMVQGLGASLLWITGSTVVGEISPDDSSGRWLGAYNQVAAFS 151
                                       4555544332.....33445567788888999999**********************99887665554333334556 PP

                             MFS_3 152 RsvGPAlgGvlvaavGaalafavnalsylalivallrwkrevrksslprEkllealraglRftaasreikavlvRaa 228
                                         +G  +gG l+ a  + +++ + +   +a  + ++r  re +  +   E+ ++  +++lR     + i++ +    
  gi|313126947|ref|YP_004037217.1| 152 SLAGDVIGGYLLYAYQTYVVYMALSAVTIAAFLLVWRYLRENPGGRKDPEEATG--TETLRALLDRPMIRSLVFFRL 226
                                       678**************9999887777777777888888888776666666554..58899999999999999999* PP

                             MFS_3 229 lFglsasavlaLLPlvardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvl 288
                                       +F +   av+  LP+ a++q + +a + G +l++  +   ++   +  L +rl+s++   
  gi|313126947|ref|YP_004037217.1| 227 AFSVGKMAVIIFLPIFAHKQFGINAFAIGWILAGGKLTKTVAQGYMGDLTDRLGSKHWFV 286
                                       ********************************9988888888888889999998876432 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 6.4e-05
                             MFS_3 111 lligiGaalndPaWqAs.vgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylal 182
                                        ++g+  ++  Pa  A  v+e  + + v + + L s+ + i   +GPAl G +  +v +++af  +a  ++++
  gi|313126947|ref|YP_004037217.1| 336 GVLGVADSIRLPASMALfVEEGERFDSVASSMSLRSISWKIGQVAGPALVGTIKDVVSTTAAFLTAAA-FIIV 407
                                       566777888889888862455555688*******************************9999987654.4433 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2  23.2   1.7e-07    0.0006      56     362 ..      78     412 ..      68     413 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.7e-07
                             MFS_4  56 aeRlrllagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGiav 132
                                       +++  llagl++ v++++    +++ + ++l+R++ G+++ +  + gs++v + + +  ++r +++ +  v +   +
  gi|313126947|ref|YP_004037217.1|  78 NAKHYLLAGLVVNVAVFIGFTQVQNSTHVVLMRMVQGLGASLLWITGSTVVGEISPDDSSGRWLGA-YNQVAAFSSL 153
                                       455669*****************************************9999888778888887775.7788888888 PP

                             MFS_4 133 sgllvllllqlglsasslWlalavlsavllllvalllp.....raalreasaaaeaakaeqkslpllalllaYgl.a 203
                                       +g ++   l ++ +  ++++al+++ ++++llv+  l+     r+ ++ea         +  ++p+++ l+ + l +
  gi|313126947|ref|YP_004037217.1| 154 AGDVIGGYLLYAYQTYVVYMALSAVTIAAFLLVWRYLRenpggRKDPEEATGTETL--RALLDRPMIRSLVFFRLaF 228
                                       889999999999999999*****************999666655555566555555..5566788888888887747 PP

                             MFS_4 204 GfGYiitatFlvaiardgaggalleallWllvG..laaivgvlvwlrvakrsglrralaaa....llieavgvllsl 274
                                        +G +++  Fl+ +a++++g + + a  W+l+G  l+  v+      + +r g + +++a+    + i  + + l+l
  gi|313126947|ref|YP_004037217.1| 229 SVGKMAVIIFLPIFAHKQFGIN-AFAIGWILAGgkLTKTVAQGYMGDLTDRLGSKHWFVAVgaalYGIGTALIPLAL 304
                                       9****************77655.55789*****66666666667788889999999986542111445555556778 PP

                             MFS_4 275 lspsplgli.vssv....llGltflaital..vlqlarelappat..............rrllglmTasfgigQilG 330
                                         ++++ +i  s+      lG++f+a  a   vl +a  +  pa                  ++l  +s+ igQ++G
  gi|313126947|ref|YP_004037217.1| 305 YFEGVVTPIeFSAFgktqALGGAFFALFAAygVLGVADSIRLPASmalfveegerfdsvASSMSLRSISWKIGQVAG 381
                                       88999988733433222347888887654323444444333332222344444556555667888899********* PP

                             MFS_4 331 pllasllaeatgslalallvaaaalvlaaliv 362
                                       p+l++ ++++ ++ ++a l aaa +++a  i+
  gi|313126947|ref|YP_004037217.1| 382 PALVGTIKDVVST-TAAFLTAAAFIIVATGIF 412
                                       ********99876.567888888999998886 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   7.9     3e-07    0.0011     221     384 ..      11     173 ..       4     174 .. 0.87
   2 !    6.4   1.7   0.00098       3.5      27      86 ..     245     301 ..     220     422 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-07
                        MFS_1_like 221 ilknpeviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliial 297
                                       +lk++e +++  +a+    +++ i   l lY ++ g ++++ G + +  +v ++ + +   + +++  +   l+++l
  gi|313126947|ref|YP_004037217.1|  11 LLKDREFAALAGTAFARSQAYSTILIALALYADQFGTTGFVEGLFGTAFAVVQLLIVLPLGRKVDTGNAKHYLLAGL 87 
                                       566666666666666666666666666******************8877777777777777779999999******* PP

                        MFS_1_like 298 layilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllw 374
                                       ++ ++ f++   ++n   v+++ + +g+   llw ++ ++v +i p+   ++  g ++ +   + +  G++iGG+l 
  gi|313126947|ref|YP_004037217.1|  88 VVNVAVFIGFTQVQNSTHVVLMRMVQGLGASLLWITGSTVVGEISPDDSSGRWLGAYNQV-AAFSSLAGDVIGGYLL 163
                                       **********************************************************99.7899**********99 PP

                        MFS_1_like 375 dlksaiflFr 384
                                         +++ ++++
  gi|313126947|ref|YP_004037217.1| 164 YAYQTYVVYM 173
                                       8888887775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00098
                        MFS_1_like  27 kskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfip 86 
                                       k+ g++a  ig i++  +lt+ +++  +g l Dr+g +   v++++ l  + ++   +ip
  gi|313126947|ref|YP_004037217.1| 245 KQFGINAFAIGWILAGGKLTKTVAQGYMGDLTDRLGSKHWFVAVGAALYGIGTA---LIP 301
                                       37799999******************************9999998888777666...344 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.7   7.9e-05      0.28     134     198 ..     105     169 ..      88     187 .. 0.90
   2 ?    6.1   0.0    0.0008       2.9     285     330 ..     207     252 ..     196     314 .. 0.79
   3 ?   -4.2   0.2         1   3.7e+03     364     380 ..     394     410 ..     374     419 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 7.9e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 134 lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdi 198
                                        ++l  +++G+Ga++++  G + + + +   +s   lg++  ++++    G ++G++ll  y + 
  gi|313126947|ref|YP_004037217.1| 105 HVVLMRMVQGLGASLLWITGSTVVGEISPDDSSGRWLGAYNQVAAFSSLAGDVIGGYLLYAYQTY 169
                                       4677789****************************************************999655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0008
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 285 kalkrllknpifllvilssvfeillvaGfitFlpkylEtqFslsas 330
                                       ++l+ ll  p+   +++     +++ +++i+Flp +  +qF+++a 
  gi|313126947|ref|YP_004037217.1| 207 ETLRALLDRPMIRSLVFFRLAFSVGKMAVIIFLPIFAHKQFGINAF 252
                                       5788888888888888888888999999999999999999998874 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 1
                                       xxxxxxxxxxxxxxxxx RF
                              OATP 364 klaklvlvvsllsllll 380
                                       ++a++ + ++++ +++ 
  gi|313126947|ref|YP_004037217.1| 394 TTAAFLTAAAFIIVATG 410
                                       33333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3004.67
//
Query:       gi|313126948|ref|YP_004037218.1|  [L=355]
Description: thioredoxin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-33  114.6   0.0    6.6e-33  114.2   0.0    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    8.6e-15   54.8   0.0    2.3e-09   36.9   0.0    2.3  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.6e-08   34.3   0.2     0.0044   17.5   0.5    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      3e-07   30.4   3.3    0.00012   21.8   1.5    2.6  2  DAO            FAD dependent oxidoreductase
    4.6e-07   29.3   4.8    4.9e-05   22.6   1.5    2.9  3  FAD_binding_2  FAD binding domain
    5.1e-05   22.8   0.6    5.1e-05   22.8   0.6    1.6  2  FAD_oxidored   FAD dependent oxidoreductase
    6.1e-05   22.3   0.3    0.00011   21.4   0.3    1.4  1  GIDA           Glucose inhibited division protein A
    6.4e-05   21.8   0.4    0.00056   18.7   0.5    2.0  2  HI0933_like    HI0933-like protein
     0.0001   21.6   0.0     0.0023   17.1   0.0    2.1  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    0.00042   19.7   0.7     0.0008   18.7   0.7    1.4  1  FAD_binding_3  FAD binding domain
      0.002   17.5   0.8     0.0073   15.6   1.0    1.9  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0021   17.4   0.2      0.012   14.9   0.1    2.1  2  Thi4           Thi4 family
     0.0021   18.2   0.2     0.0064   16.7   0.2    1.9  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.018   15.0   1.2        1.1    9.2   0.0    2.6  2  NAD_binding_9  FAD-NAD(P)-binding
      0.033   13.3   0.1      0.045   12.8   0.1    1.2  1  Lycopene_cycl  Lycopene cyclase protein
       0.12   12.3   0.0       0.31   11.0   0.0    1.6  1  HCBP_related   Haemolysin-type calcium binding protein relate
       0.16   12.4   0.0        7.3    7.1   0.0    2.3  2  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   0.0   6.2e-36   6.6e-33       1     294 []      10     289 ..      10     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 6.2e-36
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielll 71 
                                       +dvvviGgGpAGl++al+ a+ g+++++v+++g      +l ++ + gv e+ +  +      e+v+++++++++ l
  gi|313126948|ref|YP_004037218.1|  10 YDVVVIGGGPAGLQTALYTARLGHDTAVVDRGGGRAAM-MLDTHNVIGVTEEVSGNEllqtarEQVESYGADFHRDL 85 
                                       69***************************655533333.2223333333333333336889***********99999 PP

                                       CCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC..TCTTC.TTBEECCSECHHHHHHCCSS-TSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  72 geevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl..gipGvaenvgklvrtldsaealklkllpkriv 146
                                        +e++++d g+  ++l   + g++ ++ +d++vl +G++  ++  ++p     +gk+++++ +++a+    +p  + 
  gi|313126948|ref|YP_004037218.1|  86 VTEATRLDDGR--FHL---V-GNNSEFVADRIVLGMGFNDERPepPVP----RTGKGLHYCLHCDAYMFIDRP--VF 150
                                       989****8777..888...4.67789************9999954555....45778899*************..** PP

                                       EES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.EEE.EEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxx RF
                       Pyr_redox_2 147 vvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.kle.vvle 221
                                       v G G  +  +A+ + ++ +ev ++ +++++       +s++  e+l+++ +++  +t++  +++ ++  le  + e
  gi|313126948|ref|YP_004037218.1| 151 VMGTGESAAHVAMIMLNFTDEVDILLRGEEPA------WSEETDERLRAHPIDII-ETEISGMRKSDNgWLEaFEFE 220
                                       **********************9888877776......*****************.********9999866689*** PP

                                       TSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 222 dgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       dg++ +++  +   G   st+l+ e+lg+ l+e+g + v e ++t+v+g+ya+GD++    g +++++A+ +G
  gi|313126948|ref|YP_004037218.1| 221 DGTVRNYRGGFPMYGSNYSTDLA-EQLGCDLNEDGTVAVSEDGETSVEGVYAVGDIT---PGHNQIPVAMGKG 289
                                       ***********************.*********************************...7777777777665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   6.6e-06    0.0069       1      30 [.      13      41 ..      13      52 .. 0.90
   2 !   36.9   0.0   2.2e-12   2.3e-09      75     305 .]      58     273 ..      44     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.6e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      ++iG+GPaGl++a+   ++g  d  ++++g
  gi|313126948|ref|YP_004037218.1| 13 VVIGGGPAGLQTALYTARLGH-DTAVVDRG 41
                                      79******************9.68899998 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 2.2e-12
                       Pyr_redox_3  75 eeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvk 151
                                       +e++s++e+l+  re ++s+  + + +   e+   +d+ f++  +++++ A+++++ +G+ d    + +p    +  
  gi|313126948|ref|YP_004037218.1|  58 TEEVSGNELLQTAREQVESYGADFHRDLVTEATRLDDGRFHLVGNNSEFVADRIVLGMGFNDERPEPPVPRTG-KGL 133
                                       5678999***************99998766666668999***********************99999***999.899 PP

                       Pyr_redox_3 152 hyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekik 228
                                       hy    ++  + ++ v V G ++Sa+ +A+ + + + eV ++ rg+e            +  + +rl++    + i+
  gi|313126948|ref|YP_004037218.1| 134 HYCLHCDAYMFIDRPVFVMGTGESAAHVAMIMLNFTDEVDILLRGEEPA---------WSEETDERLRA----HPID 197
                                       **9999999999*********************************8411.........23345555554....4588 PP

                       Pyr_redox_3 229 vlfnaevkeikekeeey..kvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglfl 303
                                       ++++ e+  ++++++ +    ++edg +v+++   + + G + ++++ ++ + +l+edg++++ e + et v+g++ 
  gi|313126948|ref|YP_004037218.1| 198 IIET-EISGMRKSDNGWleAFEFEDG-TVRNYRGGFPMYGSNYSTDLAEQLGCDLNEDGTVAVSE-DGETSVEGVYA 271
                                       8776.899999999988545668887.6799999999**********************999975.67899*****9 PP

                       Pyr_redox_3 304 aG 305
                                       +G
  gi|313126948|ref|YP_004037218.1| 272 VG 273
                                       98 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   4.2e-06    0.0044       2      32 ..      12      42 ..      11      66 .. 0.90
   2 !   13.8   0.0   6.1e-05     0.064       2      80 ..     149     221 ..     148     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.2e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                      vvv+GgG  gl  A + a+lg+++ vv+r+ 
  gi|313126948|ref|YP_004037218.1| 12 VVVIGGGPAGLQTALYTARLGHDTAVVDRGG 42
                                      8***************************975 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.1e-05
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesvk 77 
                                       v v+G G ++  +A ++ ++ ++V ++ r++++        s+++ e+l+++ i+++ +t++  +++s++g +e+ +
  gi|313126948|ref|YP_004037218.1| 149 VFVMGTGESAAHVAMIMLNFTDEVDILLRGEEPA------WSEETDERLRAHPIDII-ETEISGMRKSDNGwLEAFE 218
                                       78********************************......***************98.6888888888888888777 PP

                                       EET CS
                         Pyr_redox  78 lkd 80 
                                       ++d
  gi|313126948|ref|YP_004037218.1| 219 FED 221
                                       765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.5   1.1e-07   0.00012       1      29 [.      11      41 ..      11      48 .. 0.92
   2 !    7.2   0.0    0.0032       3.4     146     227 ..      64     137 ..      56     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.1e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      dvv+iGGG +Gl tA++ ar g  ++++++g
  gi|313126948|ref|YP_004037218.1| 11 DVVVIGGGPAGLQTALYTARLGhdTAVVDRG 41
                                      9*****************99999******98 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEE.EETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTTTSEE.EE CS
                               DAO 146 akltaalaraaealGveilegtevtglee.edgkvwgverttp.gendaadavVnaaGawsdllgllkeldlpi.sp 219
                                        +l++  ++++e+ G+++++   vt+  + +dg+ + v   ++ +    ad +V+ +G   d+    +  ++p+ + 
  gi|313126948|ref|YP_004037218.1|  64 NELLQTAREQVESYGADFHRD-LVTEATRlDDGRFHLV--GNNsEF--VADRIVLGMGFN-DER---P--EPPVpRT 129
                                       5788889999***********.5555433266886666..232243..4799******55.221...2..3453355 PP

                                       EEEEEEEE CS
                               DAO 220 vrgqvlvl 227
                                        +g ++ l
  gi|313126948|ref|YP_004037218.1| 130 GKGLHYCL 137
                                       55555555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.5   4.6e-08   4.9e-05       1      32 [.      11      42 ..      11      49 .. 0.94
   2 ?    0.5   0.1      0.24   2.6e+02     136     166 ..      59      89 ..      40     116 .. 0.76
   3 !    6.1   0.0    0.0048         5     368     402 ..     240     276 ..     138     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.6e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      Dv+ViG+G AGL  Al  a+ G+++avv+ ++
  gi|313126948|ref|YP_004037218.1| 11 DVVVIGGGPAGLQTALYTARLGHDTAVVDRGG 42
                                      9***************************9986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.24
                                       ...HHHHHHHHHHHHHHTCTEEEEESEEEEE CS
                     FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteade 166
                                       + v+g++ll +  e+++++g df+  +  ++
  gi|313126948|ref|YP_004037218.1|  59 EEVSGNELLQTAREQVESYGADFHRDLVTEA 89 
                                       56899***************99998765444 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0048
                                       EEEEES-EEEBETTSBE..STTEEESSBTEEE-STCE CS
                     FAD_binding_2 368 aqhytmgGvetdengrv..ldadgqpipGLYAaGeva 402
                                       +++  + G+  +e+g v   +++++ ++G YA+G  +
  gi|313126948|ref|YP_004037218.1| 240 TDLAEQLGCDLNEDGTVavSEDGETSVEGVYAVGDIT 276
                                       56667789999999999867777889********987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.6   4.8e-08   5.1e-05       1      31 [.      11      41 ..      11      83 .. 0.92
   2 ?   -3.3   0.2         4   4.3e+03     400     414 ..     151     165 ..     149     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.8e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      DvvV+GGgpaG+  A+  ar G  +++v++ 
  gi|313126948|ref|YP_004037218.1| 11 DVVVIGGGPAGLQTALYTARLGHDTAVVDRG 41
                                      9***************************997 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4
                      FAD_oxidored 400 cmalGqAaGvaAala 414
                                       +m +G++a+++A + 
  gi|313126948|ref|YP_004037218.1| 151 VMGTGESAAHVAMIM 165
                                       799*******99875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.3   1.1e-07   0.00011       1      29 [.      11      48 ..      11      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE.........E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.........t 29
                                      dv+ViGgG AG+  Al +arlG++++ +          
  gi|313126948|ref|YP_004037218.1| 11 DVVVIGGGPAGLQTALYTARLGHDTAVVdrgggraamM 48
                                      79************************995554444330 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.5   5.3e-07   0.00056       1      32 [.      10      41 ..      10      49 .. 0.93
   2 ?    0.6   0.0      0.17   1.8e+02     109     163 ..      64     116 ..      58     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.3e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dv+viGgG+AGl +A+  a+ g+++++++++
  gi|313126948|ref|YP_004037218.1| 10 YDVVVIGGGPAGLQTALYTARLGHDTAVVDRG 41
                                      59***************************987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       ++++++  +++++ g +++ +  v+++++ +dg+f++   +++e+ ad++vl +G
  gi|313126948|ref|YP_004037218.1|  64 NELLQTAREQVESYGADFHRD-LVTEATRLDDGRFHLVG-NNSEFVADRIVLGMG 116
                                       677888888888889888866.56777788899899988.99**********998 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.071        75       2      25 ..       9      32 ..       8      50 .. 0.80
   2 !   17.1   0.0   2.2e-06    0.0023     141     234 ..     100     187 ..      67     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.071
                       K_oxygenase  2 ilDligiGiGpsnLsLailleevk 25
                                       +D++ iG Gp+ L  a+ ++   
  gi|313126948|ref|YP_004037218.1|  9 SYDVVVIGGGPAGLQTALYTARLG 32
                                      69999******9999888777665 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.2e-06
                       K_oxygenase 141 egeeeelearnlvlgvGtepkiPevlekle..gkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqk 215
                                        g+++e+ a ++vlg+G + + Pe   + +  g + ++H + y+         + + V+G G Saa++++ +l+  +
  gi|313126948|ref|YP_004037218.1| 100 VGNNSEFVADRIVLGMGFNDERPEPPVPRTgkGLHYCLHCDAYMFID------RPVFVMGTGESAAHVAMIMLNFTD 170
                                       478999***********766655543333311557899999999987......89***************9999888 PP

                       K_oxygenase 216 kvelklvtrsealepldds 234
                                         e+++++r+e+   ++++
  gi|313126948|ref|YP_004037218.1| 171 --EVDILLRGEEPAWSEET 187
                                       ..67777777776666665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.7   7.6e-07    0.0008       2      33 ..      10      41 ..       9      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.6e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +dV+++G+GpaGl +al  ++ G ++ +v++ 
  gi|313126948|ref|YP_004037218.1| 10 YDVVVIGGGPAGLQTALYTARLGHDTAVVDRG 41
                                      69****************************95 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.0   6.9e-06    0.0073      28      64 ..       9      45 ..       1      94 [. 0.82
   2 ?   -3.2   0.0       3.9   4.2e+03      31      56 ..     149     174 ..     148     203 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.9e-06
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparl 64
                                         v+viGgG aGlq +   ++lg ++ v+D    r+
  gi|313126948|ref|YP_004037218.1|  9 SYDVVVIGGGPAGLQTALYTARLGHDTAVVDRGGGRA 45
                                      668***************************9866555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.9
                                       EEEESTSHHHHHHHHHHHHTT-EEEE CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtv 56 
                                       v+v+G G    + + +  ++  +V +
  gi|313126948|ref|YP_004037218.1| 149 VFVMGTGESAAHVAMIMLNFTDEVDI 174
                                       78888876555555555555555544 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.1e-05     0.012      11      49 ..       3      40 ..       1      74 [. 0.86
   2 ?   -0.3   0.0      0.48   5.1e+02     155     205 ..     143     192 ..     132     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                      HHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 11 dllkyaesDvvivGaGssGLtaayylakkpdlkvailer 49
                                      ++ +    Dvv++G+G++GL +a y a+  +  +a+++r
  gi|313126948|ref|YP_004037218.1|  3 EMGDAESYDVVVIGGGPAGLQTALYTARL-GHDTAVVDR 40
                                      56666778******************998.777777665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.48
                                       EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHH CS
                              Thi4 155 lvirakvvvdatGhdgeivavvvkkikleakiekvkgeksldaekaedaiv 205
                                        +i+  v v  tG  +  va+++   ++e  +  ++ge ++++e++++ + 
  gi|313126948|ref|YP_004037218.1| 143 MFIDRPVFVMGTGESAAHVAMIMLNFTDEV-DILLRGEEPAWSEETDERLR 192
                                       567788888899999999988888888877.66788999999888877765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2     6e-06    0.0064       1      35 [.      14      45 ..      14      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      ++G+G +Gl +A + a+ g+d  +++++   GGra
  gi|313126948|ref|YP_004037218.1| 14 VIGGGPAGLQTALYTARLGHDTAVVDRG---GGRA 45
                                      8*************************98...5555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5     0.053        56       1      18 [.      13      30 ..      13      46 .. 0.82
   2 ?    9.2   0.0    0.0011       1.1     103     154 ..      66     116 ..      63     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.053
                     NAD_binding_9  1 aivGaGprGlavlerLla 18
                                      +++G+Gp+Gl ++   ++
  gi|313126948|ref|YP_004037218.1| 13 VVIGGGPAGLQTALYTAR 30
                                      69********99876655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                     NAD_binding_9 103 lfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       l++++ ++++ +   ++hr+ v++ ++ +dg+  l  +++++ ad++vL +G
  gi|313126948|ref|YP_004037218.1|  66 LLQTAREQVE-SYGADFHRDLVTEATRLDDGRFHLVGNNSEFVADRIVLGMG 116
                                       5666676764.46889***************99999999**********999 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.2e-05     0.045       1      31 [.      11      39 ..      11      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      DvvviG+GpAgl+ A     a+ g    +++
  gi|313126948|ref|YP_004037218.1| 11 DVVVIGGGPAGLQTALYT--ARLGHDTAVVD 39
                                      9**************988..66655555555 PP

>> HCBP_related  Haemolysin-type calcium binding protein related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.31      22      37 ..     209     224 ..     202     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                      HCBP_related  22 sgsyrieqieFaDGtv 37 
                                       s++ ++e +eF DGtv
  gi|313126948|ref|YP_004037218.1| 209 SDNGWLEAFEFEDGTV 224
                                       68999**********8 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0069       7.3       6      40 ..       8      42 ..       4      99 .. 0.66
   2 ?    3.1   0.0      0.12   1.3e+02       7      52 ..     146     195 ..     141     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0069
                     NAD_binding_7  6 kgkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                      +   v+v+GgG+ +++ +   ++ g +  vv+   
  gi|313126948|ref|YP_004037218.1|  8 ESYDVVVIGGGPAGLQTALYTARLGHDTAVVDRGG 42
                                      56689*****************9999999998774 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapev....keeleelvklae 52 
                                       ++ v v G Ge Aa+ +  +l++  +v ++        +ee++e++++++
  gi|313126948|ref|YP_004037218.1| 146 DRPVFVMGTGESAAHVAMIMLNFTDEVDILLRGEepawSEETDERLRAHP 195
                                       7899************9999999999988644432344445555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2321.11
//
Query:       gi|313126949|ref|YP_004037219.1|  [L=250]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-21   76.6   0.1      4e-21   75.5   0.1    1.6  1  Methyltransf_25  Methyltransferase domain
    6.5e-21   74.8   0.1    1.1e-20   74.1   0.1    1.3  1  Methyltransf_11  Methyltransferase domain
    8.1e-12   45.2   0.0    1.1e-11   44.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    8.5e-11   42.5   0.0    1.6e-10   41.6   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    3.6e-10   39.9   0.0    4.8e-10   39.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    6.8e-09   35.4   0.0    9.8e-09   34.9   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00024   20.6   0.0    0.00031   20.2   0.0    1.1  1  TehB             Tellurite resistance protein TehB
    0.00092   18.8   0.0     0.0013   18.4   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0022   17.9   0.0      0.013   15.4   0.0    1.9  1  Methyltransf_8   Hypothetical methyltransferase
     0.0033   16.5   0.0     0.0044   16.1   0.0    1.3  1  DREV             DREV methyltransferase
     0.0077   16.2   0.0      0.014   15.4   0.0    1.4  1  Methyltransf_17  S-adenosyl-L-methionine methyltransferase
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.027   14.2   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.027   14.4   0.0      0.041   13.9   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
       0.13   11.9   0.0       0.19   11.3   0.0    1.2  1  NodS             Nodulation protein S (NodS)
       0.13   12.4   0.0       0.32   11.2   0.0    1.6  1  DUF2087          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.1   3.4e-24     4e-21       2      97 .]      73     167 ..      73     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 3.4e-24
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG.S CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh.l 77 
                                       LdlGcG+Gr+++ +a+++  ++v+++D s ++l++arer +e+g+++++vqgda +lp+ d+s+ l v + +lhh  
  gi|313126949|ref|YP_004037219.1|  73 LDLGCGNGRHAEVMAEHV--ESVVALDASRGLLDQARERSAERGFSANLVQGDAASLPLRDDSVSLAVYVATLHHlR 147
                                       8****************9..9************************************************98899956 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +++ + + l+e+arvL pgG
  gi|313126949|ref|YP_004037219.1| 148 PRSARVASLSELARVLAPGG 167
                                       67788999***********9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.1   8.9e-24   1.1e-20       1      95 [.      73     170 ..      73     171 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 8.9e-24
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-... CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv... 74 
                                       Ld+GcG+Gr+ae +a+++++vv++D s  +l++a+e++ e+g++ ++v++da +lp++d+s+ l v   +lhh+   
  gi|313126949|ref|YP_004037219.1|  73 LDLGCGNGRHAEVMAEHVESVVALDASRGLLDQARERSAERGFSANLVQGDAASLPLRDDSVSLAVYVATLHHLrpr 149
                                       8******************************************999****************************988 PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                         + + l+e+aRvL pgG+ +
  gi|313126949|ref|YP_004037219.1| 150 SARVASLSELARVLAPGGRAL 170
                                       899999************976 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   9.1e-15   1.1e-11       8     113 ..      73     175 ..      67     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 9.1e-15
                   Methyltransf_31   8 lDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl 84 
                                       lDlGCG+G+ + ++ae + +   vv +D s   + +Are++++ g++ +++ qgd+ +l+  l d+++ l +  ++l
  gi|313126949|ref|YP_004037219.1|  73 LDLGCGNGRHAEVMAEHVES---VVALDASRGLLDQARERSAERGFS-ANLVQGDAASLP--LRDDSVSLAVYVATL 143
                                       9**************87655...***********************8.************..99************* PP

                   Methyltransf_31  85 nal...adpdkileeiervlkpggilliedpr 113
                                       ++l   ++  + l e+ rvl pgg+ l++  +
  gi|313126949|ref|YP_004037219.1| 144 HHLrprSARVASLSELARVLAPGGRALVSAWS 175
                                       66622256677788***********9998766 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   1.3e-13   1.6e-10       1      98 [.      73     168 ..      73     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.3e-13
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcG+G+ +++++e+    +++++D s+  +++a+e+ a+r+  ++n v+ +a +l  +d+  s+ l v   +lh
  gi|313126949|ref|YP_004037219.1|  73 LDLGCGNGRHAEVMAEH--VESVVALDASRGLLDQARERSAERGF-SANLVQGDAASLPLRDD--SVSLAVYVATLH 144
                                       8****************..88888*********888888888776.77888888888777776..************ PP

                   Methyltransf_12  78 hl...kdirevldnirklLkpgGr 98 
                                       hl     + ++l++++++L+pgGr
  gi|313126949|ref|YP_004037219.1| 145 HLrprSARVASLSELARVLAPGGR 168
                                       **9966666**************7 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0     4e-13   4.8e-10      20     164 ..      66     226 ..      42     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 4e-13
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaae.....pqgkfdlIvlrev 91 
                                       + +++r Ld+GcG G+ +ev++e++ sv++ D+s+ + + a++++  +  +++  + +       +++  l+v   +
  gi|313126949|ref|YP_004037219.1|  66 ETPPARGLDLGCGNGRHAEVMAEHVESVVALDASRGLLDQARERSAERGFSANLVQGDAaslplRDDSVSLAVYVAT 142
                                       57899*****************************988888774444444333222111133444677********** PP

                   Methyltransf_23  92 lehvpd...ppellrqiatllkpgGylllseplasl...kedrllld...wlylvpag..rhisffsarslkellee 157
                                       l+h+++     + l+ +a+ l+pgG++l+s + +++    ++  ++    w+++  +   r  + ++ ++++ +le+
  gi|313126949|ref|YP_004037219.1| 143 LHHLRPrsaRVASLSELARVLAPGGRALVSAWSVEHdrfDATDGFDTtvdWTLPGGEPvpRYYHIYDTDEFAADLED 219
                                       *****643344779*****************9888755434444554655666533334467799999999999999 PP

                   Methyltransf_23 158 aGlevve 164
                                       + l+vve
  gi|313126949|ref|YP_004037219.1| 220 STLSVVE 226
                                       9999987 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   8.2e-12   9.8e-09      45     152 ..      66     172 ..      58     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 8.2e-12
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EE... CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfD... 118
                                       + ++a+ lD+ +G g  a  ++++v++   vv lD +  +L++++++  e+g++  +++q++a  Lp  dds     
  gi|313126949|ref|YP_004037219.1|  66 ETPPARGLDLGCGNGRHAEVMAEHVES---VVALDASRGLLDQARERSAERGFS-ANLVQGDAASLPLRDDSVSlav 138
                                       5667889*****************996...899*******************97.699************9986322 PP

                                       EEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 119 vvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                       +v+  + lr  + +  +L e+ rvl pGGr +v 
  gi|313126949|ref|YP_004037219.1| 139 YVATLHHLRPRSARVASLSELARVLAPGGRALVS 172
                                       3455688**********************98875 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.6e-07   0.00031      29     148 ..      67     188 ..      41     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.6e-07
                                       S-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESS. CS
                              TehB  29 vkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfilstvv. 104
                                         p++ ldlgcg+gr +  ++     v a+d    s + l++ +e+ + ++ s++l++ ++a+l  r d +  +v  
  gi|313126949|ref|YP_004037219.1|  67 TPPARGLDLGCGNGRHAEVMAEHVESVVALD---ASRGLLDQARERSAERGFSANLVQGDAASLPLRDDSVSLAVYv 140
                                       3599***********9988877666666665...68899************************99888876555441 PP

                                       ..GGGS-GG..GHHHHHHHHHHTEEEEEEEEEEE.EB--SSS--SS--S CS
                              TehB 105 ..lmfleae..ripsiienmqectkvggynliva.amstddvpctvpfs 148
                                         l  l+++  r++s ++++ +   +gg  l+ a +++ d +  t +f 
  gi|313126949|ref|YP_004037219.1| 141 atLHHLRPRsaRVAS-LSELARVLAPGGRALVSAwSVEHDRFDATDGFD 188
                                       114455554113443.577888889999988755334555566666665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     1e-06    0.0013      33      91 ..      70     126 ..      44     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
                                       SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT CS
                               MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle 91 
                                        + lDlGcG+G  + ++a++ ++  v+++d++   l+ a+e  ++ ++++++v+ d+ +
  gi|313126949|ref|YP_004037219.1|  70 ARGLDLGCGNGRHAEVMAEHVES--VVALDASRGLLDQARERSAERGFSANLVQGDAAS 126
                                       468***************98888..9****************************99876 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05     0.013      78     157 ..      74     172 ..      70     191 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                       EES-TT-HHHHH--S.-..EEEEE.....SS.....-....SSTTEEES-TTS-S--TT-EEEEEEES---SS-... CS
                    Methyltransf_8  78 dlGcGeakiaeavre.kekvrsfd.....lv.....a....vnervvacdlakvPledesvdvavfclslmgtn... 136
                                       dlGcG+ + ae + e  e v ++d     l      +       ++v  d a +Pl d+sv +av+  +l       
  gi|313126949|ref|YP_004037219.1|  74 DLGCGNGRHAEVMAEhVESVVALDasrglLDqarerSaergFSANLVQGDAASLPLRDDSVSLAVYVATLHHLRprs 150
                                       9999999999666541577888883333221111111111123467889*****************99887543111 PP

                                       .HHHHHHHHHHHEEEEEEEEEE CS
                    Methyltransf_8 137 .ladflkeanrvlkvGGllkva 157
                                            l e  rvl +GG   v+
  gi|313126949|ref|YP_004037219.1| 151 aRVASLSELARVLAPGGRALVS 172
                                       1345799**********87765 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.7e-06    0.0044      94     134 ..      68     108 ..      54     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.7e-06
                              DREV  94 edkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkk 134
                                        + + ldlG G+G  ++ +a+++e v a ++s  + d+ + 
  gi|313126949|ref|YP_004037219.1|  68 PPARGLDLGCGNGRHAEVMAEHVESVVALDASRGLLDQARE 108
                                       46788***************************998887654 PP

>> Methyltransf_17  S-adenosyl-L-methionine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.014      22     145 ..      62     185 ..      51     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                       HHHTTT--S-EEEE--TTSHHHHHHHHH--SS-EEEEE..SS-..-S-GGG---..GGGEEES-HHHHHHHHHHH-S CS
                   Methyltransf_17  22 aaevadieGpvlelGLGnGRtydhlrellperriivfd..ral..aahpssvPe..eedlllGeieetlealakiga 92 
                                        +ev+++    l+lG GnGR  + + e+++   ++++d  r l  +a + s     +++l++G+++         + 
  gi|313126949|ref|YP_004037219.1|  62 DSEVETPPARGLDLGCGNGRHAEVMAEHVES--VVALDasRGLldQARERSAERgfSANLVQGDAASLPL----RDD 132
                                       56777888888*****************986..5566522544334444444332268999999876554....488 PP

                                       -EEEEEE----S-HHHHHHHHHHHHHHHGGGEEEEEE.EEESS----SS-EEE- CS
                   Methyltransf_17  93 kaalvhaDlGtgykekdavtatrlsdliagllapgGl.avsgqpldheeleelp 145
                                       +++l+ +    ++     +  + ls+l a++lapgG  +vs+ +++h+ +++ +
  gi|313126949|ref|YP_004037219.1| 133 SVSLAVYVATLHHLRPRSARVASLSEL-ARVLAPGGRaLVSAWSVEHDRFDATD 185
                                       999999999999999999999*****8.7899**99626899999999998765 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.3e-05     0.027      73     123 ..      68     115 ..      24     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTT CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldl 123
                                       + ar L++G+G G ++ v+a+ v++   vv+++ ++ l ++a+++  + + 
  gi|313126949|ref|YP_004037219.1|  68 PPARGLDLGCGNGRHAEVMAEHVES---VVALDASRGLLDQARERSAERGF 115
                                       56899***************99975...67************998766655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.4e-05     0.041      23      83 ..      66     120 ..      51     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                   Methyltransf_32  23 esgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrls 83 
                                       e+++ + +D+G+G+g  + v+a     +  +vv++da++ l ++a++r ++ g  f+++l 
  gi|313126949|ref|YP_004037219.1|  66 ETPPARGLDLGCGNGRHAEVMAE----HVESVVALDASRGLLDQARERSAERG--FSANLV 120
                                       56667779**************9....5669*******************999..866665 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.19      45     143 ..      70     170 ..      61     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                              NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararervkess.hiswivsdvqqfst.dekfdlivvaevlyyi 119
                                       a  l++Gc  G  +e +a + +++  +d     +++arer  e     + ++ d   + + d+   l v    l+++
  gi|313126949|ref|YP_004037219.1|  70 ARGLDLGCGNGRHAEVMAEHVESVVALDASRGLLDQARERSAERGfSANLVQGDAASLPLrDDSVSLAVYVATLHHL 146
                                       56799***********************************9886525677788999997626778999999999*** PP

                              NodS 120 edvaelraavrnlvsllapdgqlv 143
                                       +   +  a++ +l ++lap+g+ +
  gi|313126949|ref|YP_004037219.1| 147 RPRSARVASLSELARVLAPGGRAL 170
                                       999999999*********999754 PP

>> DUF2087  Uncharacterized protein conserved in bacteria (DUF2087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.32       4      45 ..       7      48 ..       6      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                           DUF2087  4 rlPskrkkrlvvLkhlaerfepgreysEkevneiLkevhdDh 45
                                      +lP + +  +   + +ae+f ++rey+  ev++ L +++ D 
  gi|313126949|ref|YP_004037219.1|  7 SLPDDAETPHETYDRIAEHFSSTREYPWPEVESFLDDYAADA 48
                                      578888888999999**********************99974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1493.02
//
Query:       gi|313126950|ref|YP_004037220.1|  [L=719]
Description: flagella assembly protein j [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-39  132.4   6.8    1.1e-20   73.9   2.1    2.8  2  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
       0.81    8.4   3.7        8.1    5.1   0.0    2.9  3  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.2   2.1e-20   1.9e-16       5     124 ..     180     305 ..     176     306 .. 0.96
   2 !   73.9   2.1   1.2e-24   1.1e-20       1     123 [.     505     630 ..     505     632 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 2.1e-20
                                       HHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT CS
                             T2SSF   5 latllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageegg 75 
                                       ++ l+++G+p++++L +l e+++ +g+ a+e+  ++++++  g +l++al+    rtps  ++++  +l+++  +g+
  gi|313126950|ref|YP_004037220.1| 180 IYALSRSGMPFQKVLATLTENQHvYGEAAREFGVAVNDVQTFGtDLPTALRrmaeRTPSQRLDDFTENLTSVLTSGQ 256
                                       6789***********************************9977699*****9999********************** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  76 nLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                       +L+++L+   + +++e e +++  ++ll + ++++v++lv+++l++i++
  gi|313126950|ref|YP_004037220.1| 257 SLSAFLHEQYDRFQAESEAQQQQYLELLATFAEVYVTVLVAGPLFLITI 305
                                       *********************************************9986 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 1.2e-24
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqliragee 73 
                                       fl+ +a+  +aGv++v++L++la+++  gp++eel+r+ r++++G sl++al+    r + +  ++ v+ + +a+ +
  gi|313126950|ref|YP_004037220.1| 505 FLDRMASVNEAGVTVVKSLHRLAQSD-LGPISEELRRTWRDIQWGASLRNALRgfdrRAQVPMVSRAVTLIMNAVAA 580
                                       89************************.*****************************65555566************* PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       +g +a vL+ +a + ++ r+l r+++ +++ +l+++++ ++v+l +++ l
  gi|313126950|ref|YP_004037220.1| 581 SGEVAPVLRIAANEAQDSRRLLRERRQEMMTYLVVIYISFFVFLGIVVAL 630
                                       ********************************************999876 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.4     0.053   4.8e+02     384     409 ..      74     127 ..       4     166 .. 0.61
   2 ?    5.1   0.0   0.00091       8.1     345     431 ..     254     340 ..     226     352 .. 0.51
   3 ?    2.8   0.1    0.0044        39     366     409 ..     592     669 ..     551     718 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.053
                           DUF2207 384 salglgliilglilillallllvll............................l 409
                                        + + +++i+g ++++++++l+v +                            +
  gi|313126950|ref|YP_004037220.1|  74 LLMSAVFGIAGSVFGVYFAALIVQTfavpasalrealppalgflaavasmpnlS 127
                                       222223333333333333333222244556665555555555555544444432 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.00091
                           DUF2207 345 kskkkakkfkkalkkwksavkkkergyfdkkg...kkklkklsalglgliilglilillallllvlllvfllillli 418
                                       + +++   +++++++++ + ++++++y++      + + + l a  l+li ++++++l+   +   l  + +i+ l+
  gi|313126950|ref|YP_004037220.1| 254 SGQSLSAFLHEQYDRFQAESEAQQQQYLELLAtfaEVYVTVLVAGPLFLITILVVVGLVMQDT---LPLLRVIIYLG 327
                                       444444455666677777777644444444321002222222222222222222222222222...25666677777 PP

                           DUF2207 419 llliaiivlllfs 431
                                       l+l++++++++  
  gi|313126950|ref|YP_004037220.1| 328 LPLASVAFVVYVD 340
                                       7777777666654 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.0044
                           DUF2207 366 k....kergyfdkkgkkklkklsalglgliilglilillallllvll.............................. 408
                                       +    ++r++++++ ++ +++l ++++ +++++ i++ l+l+++ ++                              
  gi|313126950|ref|YP_004037220.1| 592 AneaqDSRRLLRERRQEMMTYLVVIYISFFVFLGIVVALTLAFIPSVeaasqssaissgevqgvstgvfsglsdvdt 668
                                       04556678888888777777777777776666666665555554444666666666666666666666555555555 PP

                           DUF2207 409 l 409
                                        
  gi|313126950|ref|YP_004037220.1| 669 T 669
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4510.10
//
Query:       gi|313126951|ref|YP_004037221.1|  [L=639]
Description: ATPase, type iv secretory pathway virb11 component like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-45  154.8   0.0    3.8e-45  154.1   0.0    1.3  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
       0.17   11.4   0.0       0.31   10.5   0.0    1.3  1  AAA_7     P-loop containing dynein motor region
       0.32   11.3   2.3    1.1e+02    3.1   0.1    4.0  5  GGDEF_2   GGDEF-like domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.0   6.4e-49   3.8e-45       6     269 ..     204     468 ..     200     472 .. 0.91

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 6.4e-49
                             T2SSE   6 eallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlr 81 
                                       ++l++d+++ di    ++  ++     d +++++  +  +++l +++ r+a+ ++++is   p++  +lp +g r +
  gi|313126951|ref|YP_004037221.1| 204 DPLMQDPHIEDISCDGYDLpIFA-YHDDYTDIETNVSFGEEQLDQFVVRLAQRSGRHISVGDPVVGTTLP-DGSRAE 278
                                       67899**************6666.888889****************************************.888888 PP

                             T2SSE  82 vvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                       ++l   v     a++iR  +   +t  dl+  ++++ ++ + l   ++++++++++GgT sGKtt+++a+  +i+ +
  gi|313126951|ref|YP_004037221.1| 279 LALGEEVTPhgSAFTIRMYADDPFTPVDLVEFGTFSVEQMAYLWLCIEHNKSLIFAGGTASGKTTSMNAVSMFIPPR 355
                                       8876544333599**************************************************************** PP

                             T2SSE 157 derivtvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgsl 228
                                         +++ +ED++E+ l+++n ++ +++       ++++ dllr+aLR+rP  i+vGE+R++e++++ +A+nTGH   +
  gi|313126951|ref|YP_004037221.1| 356 -SKVLSIEDTRELSLHHDNWLSSVTRnrmheGSDIDMYDLLRSALRHRPEFIIVGEVRGEEAVTLFQAMNTGHTT-F 430
                                       .******************999999989998889*****************************************.* PP

                             T2SSE 229 sTlHansaagalerLeqlgaeveaaelkssilavvdivvrl 269
                                       sT+Ha+s   +++rLe+   +v++a+++s  l+    v+ l
  gi|313126951|ref|YP_004037221.1| 431 STMHADSIETVINRLENEPINVPRAMVQSLDLLC---VQTL 468
                                       ****************988788888887765555...4444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.3e-05      0.31      21      56 ..     316     351 ..     311     362 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.3e-05
                             AAA_7  21 rysyllelllknkkpvllvGptGtGKtviikdllkk 56 
                                        +   l l+++++k++++ G t +GKt+ ++ +   
  gi|313126951|ref|YP_004037221.1| 316 EQMAYLWLCIEHNKSLIFAGGTASGKTTSMNAVSMF 351
                                       555667799********************9986655 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       2.8   1.7e+04      75      86 ..      56      67 ..      43      73 .. 0.56
   2 ?    2.3   0.0     0.032   1.9e+02      20      84 ..     107     177 ..     103     188 .. 0.75
   3 ?   -1.3   0.0      0.43   2.6e+03      70      98 ..     242     267 ..     235     270 .. 0.79
   4 ?    2.0   0.0     0.039   2.3e+02      36      70 ..     390     425 ..     359     452 .. 0.71
   5 ?    3.1   0.1     0.019   1.1e+02      13      47 ..     547     581 ..     533     588 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.8
                           GGDEF_2 75 allerlarrlgg 86
                                      a+l++l+rrl++
  gi|313126951|ref|YP_004037221.1| 56 AALADLRRRLRR 67
                                      445555555444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.032
                           GGDEF_2  20 dgpyvvvvielee.daerllraleealralgpdalvavrgd.rlvlllpaedeedae....allerlarrl 84 
                                       ++py+ vvi+ +e ++ +++ a+e  l ++ +d+l  vr+d r  ll  +e+ ++ae    + l+++++++
  gi|313126951|ref|YP_004037221.1| 107 NAPYAYVVITYDEaASKHCYYAVEPDLDDFERDILERVREDiRDPLLYNTETGSSAEttlrRTLRTVLEQY 177
                                       789999****9996666699999999999999999999888888888888887776653335555555554 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.43
                           GGDEF_2  70 eedaeallerlarrlgglsvriGiGspve 98 
                                       ee++++++ rla+r g+   +i +G+pv 
  gi|313126951|ref|YP_004037221.1| 242 EEQLDQFVVRLAQRSGR---HISVGDPVV 267
                                       46788999999999999...777777775 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.039
                           GGDEF_2  36 rllraleealralgpdalva.vrgdrlvlllpaede 70 
                                       ++++ l++alr++   ++v+ vrg++ v l++a + 
  gi|313126951|ref|YP_004037221.1| 390 DMYDLLRSALRHRPEFIIVGeVRGEEAVTLFQAMNT 425
                                       4999*******9988888873588899999986664 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.019
                           GGDEF_2  13 rrlgldldgpyvvvvieleedaerllraleealra 47 
                                        +lg+d  ++++++v e   da+r+ ++le+++ a
  gi|313126951|ref|YP_004037221.1| 547 VELGIDDYRQFTALVNEYYADADRVMDRLESEVDA 581
                                       579***************99*********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4618.67
//
Query:       gi|313126952|ref|YP_004037222.1|  [L=167]
Description: hypothetical protein Hbor_22160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1202.53
//
Query:       gi|313126953|ref|YP_004037223.1|  [L=159]
Description: hypothetical protein Hbor_22170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1175.19
//
Query:       gi|313126954|ref|YP_004037224.1|  [L=195]
Description: uracil-DNA glycosylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   47.7   0.0    1.8e-12   47.5   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.034   13.7   0.0    1.2  1  DUF4918   Domain of unknown function (DUF4918)


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0     2e-16   1.8e-12       1     152 [.      10     169 ..      10     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2e-16
                                       HHC-CTT-SEEEEESSTCHH.HHHHSSSS.-STT--HHHHHHHCCCCCCCHHG...CTEEEEESSS....S.ECGCT CS
                               UDG   1 pgegppdakvvivGeaPgae.edatglpFsgragnllrkllneaglkrdlese...qgvyitnvvkcrppg.nrdtp 72 
                                       pg+g+++a   ++G  Pg + +  tg pF+ ++g +l+++l++agl + + ++    + ++  +      g + +tp
  gi|313126954|ref|YP_004037224.1|  10 PGYGDANAYFHVIGDHPGVHgGKITGVPFTNEPGIRLQAALADAGLLETTGDQptvAKTFLSYLHM----GvPDGTP 82 
                                       79******************9*************************99887778988888888888....533369* PP

                                       TCCCCTCCHHHHHHHHHHHHSSEEEEESHHHHHH............HHHHSCESCCCSCT..SEEEEES-SSTTTTT CS
                               UDG  73 tsaeikacaplleeeiellkprlivllGktaakall..........geklgklrgklleak.irvlplphPsplnrn 138
                                       ++ae +   +++++e++++  +++  +G+ a k++l            ++++l+g+ ++     vlp   P   n +
  gi|313126954|ref|YP_004037224.1|  83 SQAEYDDLERFFDAELRAIAAHVLFPVGARATKYVLenytaqarkiSVEMEELHGQEVRGSgFLVLPIADPRDWNET 159
                                       *******999*************************988888644433344466666666658999999999998888 PP

                                       TTTSHHHHHHHHHH CS
                               UDG 139 ffksnpelkaeawe 152
                                            +e++ ea++
  gi|313126954|ref|YP_004037224.1| 160 ----HHERLVEAID 169
                                       ....7888877775 PP

>> DUF4918  Domain of unknown function (DUF4918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.8e-06     0.034      47      77 ..      12      42 ..       6      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-06
                                      --S---EEEEE-S---SSGGGGTSSTT--HH CS
                           DUF4918 47 yndkkkRklilginPgRfgagvtgvpFtdak 77
                                      y d +    ++g  Pg +g+ +tgvpFt+  
  gi|313126954|ref|YP_004037224.1| 12 YGDANAYFHVIGDHPGVHGGKITGVPFTNEP 42
                                      889999999*******************864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1402.37
//
Query:       gi|313126955|ref|YP_004037225.1|  [L=243]
Description: hypothetical protein Hbor_22190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-06   27.3   2.7     0.0014   18.1   1.2    2.2  2  DUF4097   Putative adhesin
  ------ inclusion threshold ------
       0.28   11.2   4.0       0.27   11.2   1.4    2.2  2  BACON     Putative binding domain, N-terminal


Domain annotation for each model (and alignments):
>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   2.4e-05      0.21      11     108 ..      26     116 ..      17     129 .. 0.77
   2 !   18.1   1.2   1.5e-07    0.0014     113     251 ..     103     239 ..      98     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.4e-05
                           DUF4097  11 advtikesddekitveystakklkkqkveetggtLsitqkekngvstgfik..elssgekskitiylPkktkledlq 85 
                                        +vti+++++++++v++++ +   +++v      +s++ +  +gv t  ++  + +s   + +t++lP++    dlq
  gi|313126955|ref|YP_004037225.1|  26 GNVTIRPGSGDTVSVTVVKRGFGIDESV---LDRISVDRSVSDGVLTIAVVypSDVSRVSTDLTVSLPDSL---DLQ 96 
                                       68*****************999999976...67899*******999998889999999***********99...444 PP

                           DUF4097  86 .vkassGdlsvekatklkaetlel 108
                                        +++++G ++ve      + +++l
  gi|313126955|ref|YP_004037225.1|  97 lAETANGGVDVE----RVSGDATL 116
                                       134466666666....33334444 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.5e-07
                           DUF4097 113 GdltlsnvsaktltvksesGdvtiegseakklklqltsGdieleslsletldltsssGdltlsntklegsltitass 189
                                       G +++++vs+ ++t+ +++G v ++g+    l l++ +G+ie++++ +   ++ +  G ++++   + g ++++as 
  gi|313126955|ref|YP_004037225.1| 103 GGVDVERVSG-DATLRAGNGGVHAAGTP-GFLTLEAGNGGIEARDVGGI-DKVSAGNGGINIEIPAIRGDTEVSASN 176
                                       4445555543.34556666666655543.23677777888888888777.799999999****************** PP

                           DUF4097 190 GdvdlslpeekkaavdassesGdvslpk.kreeeekesnsisaseknakkkvsvstssGDitv 251
                                       G +d+s++   +a+++a++++G v+++  + ++ + + +++ ++ +++   ++++  +G i+v
  gi|313126955|ref|YP_004037225.1| 177 GGIDASISAGIDAMFEARVTNGGVDVSGlELTDATISPSRVIGTLGDGGPSLTLRAGNGGIDV 239
                                       *******988*****************977777777788888888888888887777777766 PP

>> BACON  Putative binding domain, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.4     3e-05      0.27      30      50 ..      19      42 ..       2      43 .. 0.71
   2 ?   -1.1   0.0      0.22     2e+03      17      43 ..      91     120 ..      76     123 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                             BACON 30 gee..Rtatitvtagsgegt.vtV 50
                                       +   Rt+++t+ +gsg+++ vtV
  gi|313126955|ref|YP_004037225.1| 19 VQVlnRTGNVTIRPGSGDTVsVTV 42
                                      33377***********97767777 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.22
                             BACON  17 as.tltvtvaaNtsgee.Rt.atitvtags 43 
                                       +s  l +  +aN + +  R  +  t+ ag+
  gi|313126955|ref|YP_004037225.1|  91 DSlDLQLAETANGGVDVeRVsGDATLRAGN 120
                                       445677777888866666765666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1511.55
//
Query:       gi|313126956|ref|YP_004037226.1|  [L=224]
Description: zn-dependent hydrolase, glyoxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-26   91.4   2.8    8.5e-26   91.2   2.8    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0001   21.9   0.7    0.00015   21.4   0.7    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0023   17.4   0.0     0.0035   16.8   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   2.8   1.4e-29   8.5e-26       3     182 ..      13     191 ..      11     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 1.4e-29
                                       CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                       +++vn+yl+++dg+  L+D+Gt+++a+r++  l ++ + p ++d+v++TH++lDH+G lg l    dvp++a + +a
  gi|313126956|ref|YP_004037226.1|  13 CRGVNAYLVDDDGTITLVDAGTPWDADRMRAMLSRANVFPAEIDRVLVTHYDLDHVGTLGLLDFDPDVPIYAAEPDA 89 
                                       789************************************************************************** PP

                                       HCCHCHHHHHHHHHCCHH.TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSH CS
                       Lactamase_B  80 palfmeeaddaasrkgll.lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallag 155
                                         l++++  +   +kg l +a+ ++      e  +  +++++++++v+  pgh++gh+v+   + + +f GD++ + 
  gi|313126956|ref|YP_004037226.1|  90 SFLLGDATPPFGNHKGMLqRATRPFLTAPKNEVRRVNDGDSVGGFGVYRAPGHTPGHVVYQHTDHGAAFLGDLVRES 166
                                       ********999999999975555555555555555556677888999****************************99 PP

                                       HCCCCCC.TTCEEE-SHCHHHHHHHHH CS
                       Lactamase_B 156 etgridltlrgaevrdpsdaekyldsl 182
                                         ++ +    ++ ++d+  ++++l+++
  gi|313126956|ref|YP_004037226.1| 167 AGALSPS--PWFVCYDAERNRESLRDI 191
                                       9999998..667777777766666555 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.7   2.5e-08   0.00015       4      64 ..      29      86 ..      26     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-08
                                      EES--TTHHHHHTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEH CS
                     Lactamase_B_2  4 LiDagpdlrqqalral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapk 64
                                      L+Dag+ + +  +ra+ ++  +   +++id Vl+th + DH+ g l l  + p ++p+ya +
  gi|313126956|ref|YP_004037226.1| 29 LVDAGTPWDADRMRAMlSR--ANVFPAEIDRVLVTHYDLDHV-GTLGLLDFDP-DVPIYAAE 86
                                      7888888666644444233..3344569**************.9999999988.59***654 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.9e-07    0.0035       2      74 ..      21      87 ..      20      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.9e-07
                     Lactamase_B_6  2 LeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlp 74
                                      +  d++  L+D G+    ++++ +l+  +    ++d +L++h +l+h+G + ll       +  ++p+ya  p
  gi|313126956|ref|YP_004037226.1| 21 VDDDGTITLVDAGTPWDADRMRAMLSRANVFPAEIDRVLVTHYDLDHVGTLGLLD------FDPDVPIYAAEP 87
                                      56678888*****77665666778888888889****************976544......345788888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1551.08
//
Query:       gi|313126957|ref|YP_004037227.1|  [L=361]
Description: dnaj-class molecular chaperone with c-terminal zn finger domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-22   78.0   1.1    6.3e-22   77.5   1.1    1.2  1  DnaJ        DnaJ domain
  ------ inclusion threshold ------
      0.051   13.5  14.2      0.065   13.2  14.2    1.2  1  SPX         SPX domain
       0.84    8.3   7.1      0.029   13.1   1.4    1.5  2  Presenilin  Presenilin
        2.2    7.4  20.1        2.7    7.1  20.1    1.1  1  SOG2        RAM signalling pathway protein
          3    5.9   5.1        4.1    5.4   5.1    1.2  1  Hid1        High-temperature-induced dauer-formation protein
        5.1    6.6   9.3        6.7    6.2   9.3    1.1  1  DUF572      Family of unknown function (DUF572)


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   1.1   2.1e-25   6.3e-22       1      63 []       3      64 ..       3      64 .. 0.99

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 2.1e-25
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      d+Y++L+vs+da++++Ik+a+r +a++yHPD n +d +a+ +Fk +++AyevLsd+++R++YD
  gi|313126957|ref|YP_004037227.1|  3 DFYDLLEVSEDATQSDIKRAWRGKAREYHPDVN-DDARANAQFKTLQKAYEVLSDETERAAYD 64
                                      79*******************************.9999************************9 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2  14.2   2.2e-05     0.065      62     171 ..      70     195 ..      27     243 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                               SPX  62 e..................rtepstsaaadesgnsaadasssepkdeaeslprrsplsrssrssssygglvssppsa 120
                                       +                  +t+++ ++++++s+ s++ ++ s+++ + +s++++s+   s+r+ss  ++  ss +s+
  gi|313126957|ref|YP_004037227.1|  70 SyvnqrldglptagmtrpdDTSTGGTRWSSNSSGSSSRSNTSSTANRTQSSDDTSSRTASGRTSSGSSQRGSSGSSR 146
                                       34444455555555544432222222222222222222222222222111111111111111111111111111111 PP

                               SPX 121 nsssssddssesnpa.dssssssssesesssssspsllrrlfsesesreeks 171
                                         ss+s ++s+s  + +s ss++ss++++sss+++s+ +r  s s+++++ks
  gi|313126957|ref|YP_004037227.1| 147 TGSSGSRTRSQS--GgRSRSSDRSSSNGGSSSRTRSSSHRQ-SGSSTNADKS 195
                                       111111111111..122222222222222222222222222.2122222222 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.4   9.7e-06     0.029     228     307 ..     112     192 ..      84     271 .. 0.53
   2 ?   -3.9   0.4       1.5   4.4e+03     357     366 ..     331     340 ..     321     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.7e-06
                        Presenilin 228 k.kaevaeseeeeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessesse 303
                                       + ++++++s+++++++++ +++s ss++ +s ++ + +s+++++s++  +++ss+ +ss+  ss++++s+++++s +
  gi|313126957|ref|YP_004037227.1| 112 StANRTQSSDDTSSRTASGRTSSGSSQRGSSGSSRTGSSGSRTRSQSGGRSRSSDRSSSNGGSSSRTRSSSHRQSGS 188
                                       11222222222222222222222222222222222222222222222222222222222222222222222222222 PP

                        Presenilin 304 eeee 307
                                       +++ 
  gi|313126957|ref|YP_004037227.1| 189 STNA 192
                                       2211 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.5
                        Presenilin 357 iGLclTLllL 366
                                       +GL+lTL++L
  gi|313126957|ref|YP_004037227.1| 331 AGLTLTLVVL 340
                                       6999999987 PP

>> SOG2  RAM signalling pathway protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  20.1    0.0009       2.7     241     346 ..      94     200 ..      33     222 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0009
                              SOG2 241 l...srsrrssssgnsaspaangaqsetsersasssgvqssasstPlgegstspp.galsrqslsttgststltsss 313
                                       +   s++++ sss+ ++s+ an  qs+ + +s ++sg +ss ss+ +++gs+++  + + + s s+ +s s+ +sss
  gi|313126957|ref|YP_004037227.1|  94 GtrwSSNSSGSSSRSNTSSTANRTQSSDDTSSRTASGRTSSGSSQRGSSGSSRTGsSGSRTRSQSGGRSRSSDRSSS 170
                                       02333333333333333333333344434444444444444444444444444422222222223333333333333 PP

                              SOG2 314 ksrsssrsntnasastprslattpappasaesf 346
                                       +  sssr+    s+s ++s ++t a  +++++ 
  gi|313126957|ref|YP_004037227.1| 171 NGGSSSRTR---SSSHRQSGSSTNADKSAGTNE 200
                                       333333333...444555555555544444442 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   5.1    0.0014       4.1     604     688 ..     103     195 ..      45     232 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0014
                              Hid1 604 sessrieesrsesrspslsevpelksslaitddeskaereksatessssqavs........qlremsekarakesae 672
                                        +ssr+++s++ +r++s+ + ++ ++s  ++++ s+  +++s+++ ss + +          + + s+++ + + + 
  gi|313126957|ref|YP_004037227.1| 103 GSSSRSNTSSTANRTQSSDDTSSRTASGRTSSGSSQRGSSGSSRTGSSGSRTRsqsggrsrSSDRSSSNGGSSSRTR 179
                                       22222222222222222222222222222222222222222222222211111111111111111111111222222 PP

                              Hid1 673 steesrqesatskksp 688
                                       s+++ ++ s+t++ + 
  gi|313126957|ref|YP_004037227.1| 180 SSSHRQSGSSTNADKS 195
                                       2222222222222222 PP

>> DUF572  Family of unknown function (DUF572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   9.3    0.0022       6.7     174     304 ..      44     194 ..       8     213 .. 0.31

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0022
                            DUF572 174 freekkereeeeedeealkekisle.kikllpedeedekkaklle.gkte........................... 221
                                       f++                    l+ + + l++++   ++a+  + g+t+                           
  gi|313126957|ref|YP_004037227.1|  44 FKT--------------------LQkAYEVLSDET---ERAAYDRlGHTSyvnqrldglptagmtrpddtstggtrw 97 
                                       211....................221222222222...223333333333444555555555555555555666644 PP

                            DUF572 222 ..slfasseesaksakkkpt.kk................esskekkkeslekklskltkkkad.............. 265
                                         +    s+ s++++++++t ++                +s ++++ +              +              
  gi|313126957|ref|YP_004037227.1|  98 ssN----SSGSSSRSNTSSTaNRtqssddtssrtasgrtSSGSSQRGS--------------Sgssrtgssgsrtrs 156
                                       331....22222222221111111111222222222221111111111..............112222211111111 PP

                            DUF572 266 sslvvrKkkkeeekskeskekteeeskeseeeskkeeet 304
                                       +s+   +++++ ++s+  +++++++s+++++ s++++++
  gi|313126957|ref|YP_004037227.1| 157 QSGGRSRSSDR-SSSNGGSSSRTRSSSHRQSGSSTNADK 194
                                       22222222222.122222222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1206  (0.0672653); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.80u 0.38s 00:00:01.18 Elapsed: 00:00:00.49
# Mc/sec: 2227.83
//
Query:       gi|313126958|ref|YP_004037228.1|  [L=131]
Description: hypothetical protein Hbor_22220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.5   2.3        1.5    9.1   0.4    2.2  2  DUF3040   Protein of unknown function (DUF3040)
        1.7    8.7   9.7        0.2   11.7   3.5    2.3  2  DUF2892   Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4   0.00017       1.5      40      75 ..      16      52 ..       5      59 .. 0.75
   2 ?    3.1   0.1     0.013   1.2e+02      33      61 ..      94     123 ..      83     130 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00017
                           DUF3040 40 slrrlavlavllfva.GllllvlGvaaaavvlgvvGf 75
                                      ++rr+a+ +v+++++ Gl+  v+G+    ++l+++G+
  gi|313126958|ref|YP_004037228.1| 16 QRRRYALGSVAAVATlGLVTWVFGFDGPVWALALAGV 52
                                      3466666667666668********9888888888886 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.013
                           DUF3040  33 aar.arrrslrrlavlavllfvaGllllvl 61 
                                       aar a  r++ +    a+++++aG+l+l++
  gi|313126958|ref|YP_004037228.1|  94 AARrADMRRAWQIHGYATATAIAGVLILFV 123
                                       444222222222234556666777777665 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.5   2.3e-05       0.2       3      47 ..       9      58 ..       4      77 .. 0.86
   2 ?    0.1   0.4     0.097   8.7e+02      13      23 ..     113     123 ..     103     130 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                           DUF2892  3 kNvgtldRilrivvGlvllllallglsggw.......gwllglvGavllltg 47
                                      +N+g ++   r ++G+v++++ l  ++  w        w l+l+G+ l+ t+
  gi|313126958|ref|YP_004037228.1|  9 CNIGEAEQRRRYALGSVAAVATLGLVT--WvfgfdgpVWALALAGVPLFGTA 58
                                      5***************99998888873..44799**8888888888787776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.097
                           DUF2892  13 rivvGlvllll 23 
                                        +++G+++l++
  gi|313126958|ref|YP_004037228.1| 113 TAIAGVLILFV 123
                                       34555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 999.39
//
Query:       gi|313126959|ref|YP_004037229.1|  [L=331]
Description: zn-dependent hydrolase, glyoxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-17   63.1  10.9    1.1e-16   61.4  10.9    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.017   14.7   5.6      0.027   14.0   2.5    2.6  2  Lactamase_B_2  Beta-lactamase superfamily domain
       0.18   11.2   0.1       0.29   10.6   0.1    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4  10.9   1.9e-20   1.1e-16       6     197 .]      17     233 ..      13     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.9e-20
                                       SEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                        n+yl+  ++ + L+D G s ++ r  l   l  +gl+  d+d ++lTH+H+DH+G +g+l  + +++v+a++++ap
  gi|313126959|ref|YP_004037229.1|  17 NNAYLL-SGEVTTLVDVGASLDEIRDDLdaGLDEVGLGVSDIDQILLTHWHADHTGLAGELQAESGAVVRAHEADAP 92 
                                       699999.9999***************99************************************************* PP

                                       CCHCHHHHHHHHHCCHH.......................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCC CS
                       Lactamase_B  81 alfmeeaddaasrkgll.......................lagvsadkpdvdeeeldgnaggrralyvtggpghghg 134
                                          +e     a+r+  l                       +  + + ++++++ +++ +++g+++l+v++ pgh +g
  gi|313126959|ref|YP_004037229.1|  93 LIAGETDAVHAERDIRLqrfdewgipegkreelvsflemhDDLEGESADVTPLTDGERIDAGDGELEVHHLPGHAAG 169
                                       *******9999998888***********************9999999999*************************99 PP

                                       EEEEEETTCCE.....EEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 135 hgvveygggkv.....lftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                          + ++gg+      +f+GDa+l+  t+ ++     a  r   + + y +sl  l++ ++++  pgH
  gi|313126959|ref|YP_004037229.1| 170 LTAFAFDGGSDgngeeAFVGDAILPKYTPNVGG----ADLRVERPLQTYVESLVSLIDWDVDRAWPGH 233
                                       9999755544333333********999999999....9999999999999999999888888888887 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.5   4.6e-06     0.027      28     108 ..      54     163 ..      33     191 .. 0.58
   2 ?   -1.4   0.1      0.24   1.4e+03      39      44 ..     295     300 ..     255     324 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-06
                                       ..SEEEEE-SS--HHHHGGGG.CCCC.......C--EEEEEEEE..HHHHH.......HCCTTCGHHHCHTT..... CS
                     Lactamase_B_2  28 lppidaVllthaHyDHlagll.tlre.......lrpkklplyap..kgvla.......vleanfvylaleee..... 82 
                                       +++id +llth H+DH+ gl   l++        ++ ++pl+a   + v+a         +++++++ + ee     
  gi|313126959|ref|YP_004037229.1|  54 VSDIDQILLTHWHADHT-GLAgELQAesgavvrAHEADAPLIAGetDAVHAerdirlqRFDEWGIPEGKREElvsfl 129
                                       679**************.55413444344443222222444432122222244444444444444444444444444 PP

                                       ........TTEEEEEE-TTSEEEECSTTEEEEEE CS
                     Lactamase_B_2  83 ........pavnvheldwgesfelgdggleitat 108
                                                  +v++l+ ge+++ gdg+le++  
  gi|313126959|ref|YP_004037229.1| 130 emhddlegESADVTPLTDGERIDAGDGELEVHHL 163
                                       4444454445555555555555555555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.24
                                       --HHHH CS
                     Lactamase_B_2  39 aHyDHl 44 
                                       aH DHl
  gi|313126959|ref|YP_004037229.1| 295 AHLDHL 300
                                       344444 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   4.8e-05      0.29       5      50 ..      24      71 ..      20      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.8e-05
                     Lactamase_B_6  5 dnvkiLlDvGwd..eskvslesalkelekviptvdliLLshatlehlG 50
                                       +v+ L+DvG +  e +++l+  l+e+   ++++d iLL+h  ++h G
  gi|313126959|ref|YP_004037229.1| 24 GEVTTLVDVGASldEIRDDLDAGLDEVGLGVSDIDQILLTHWHADHTG 71
                                      57899****986336677788888888889**************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2131.85
//
Query:       gi|313126960|ref|YP_004037230.1|  [L=94]
Description: DNA-directed RNA polymerase subunit l [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-16   58.5   0.0    4.9e-16   58.3   0.0    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    1.3e-06   27.8   0.0    2.4e-06   26.9   0.0    1.4  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   5.5e-20   4.9e-16       1      73 [.      12      87 ..      12      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 5.5e-20
                                      EEEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTT...SEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  1 eltfeingEDhTLgnlLrhlllknpsVefagYkipHPle...pkmnlriqtkssnnpleaLkkalkdlldicdele 73
                                      el++ei+gEDhT++n+++ +ll+ p+V +a+Y+++  ++       l ++t+s+++pl+aL +a ++++d+ +++ 
  gi|313126960|ref|YP_004037230.1| 12 ELRLEIAGEDHTFMNVIKGALLETPGVAAATYDVNPEQSggqTDPILSVKTESGTDPLDALADASQRVQDLSSDFT 87
                                      5899*********************************66666999999999999***************9988775 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.6e-10   2.4e-06       3      66 ..      16      80 ..      14      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.6e-10
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  3 llrgvdhtlgNaLRrillsevpgvaiea.......pvvkvntdkdklilevetdgslkPeealkeAlkiLk 66
                                      ++ g+dht++N ++  ll e pgva ++               ++  il+v+t   ++P +al+ A +  +
  gi|313126960|ref|YP_004037230.1| 16 EIAGEDHTFMNVIKGALL-ETPGVAAATydvnpeqS-----GGQTDPILSVKTESGTDPLDALADASQRVQ 80
                                      789***************.******99976664440.....4445568******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 724.62
//
Query:       gi|313126961|ref|YP_004037231.1|  [L=201]
Description: hypothetical protein Hbor_22250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-52  177.4   0.1    2.3e-52  177.0   0.1    1.2  1  DUF1684   Protein of unknown function (DUF1684)


Domain annotation for each model (and alignments):
>> DUF1684  Protein of unknown function (DUF1684)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.0   0.1   1.3e-56   2.3e-52       2     140 .]      58     198 ..      57     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 177.0 bits;  conditional E-value: 1.3e-56
                                       C--S-EE----GGGEEEEEEEE-CCEEEEEEEBSSSSCEEEEEEEEEEEEETTEE.EEEEEECTT-CSSEEEEEEEC CS
                           DUF1684   2 eFegleyfepdpawrveaelepadepeevevetstgeeveyervgevefelegkg.eLtvyreeeekealfvpfrDa 77 
                                       +F+gl+yfepd+++r+  el ++d++e+++v+t+t++e++y ++g++ fe +g++ +L++yr+e+e+++l+vpfrD+
  gi|313126961|ref|YP_004037231.1|  58 SFDGLSYFEPDQSYRIVTELDEYDTKETITVSTTTDGERDYLVWGSFAFERNGESvRLDAYRSEPESNRLWVPFRDE 134
                                       7**************************************************9999********************** PP

                                       CCCTTC-TT-EEEEE--TTTTT.EEEEEEGGGEB--HHHHTTTS--BB--GGGEESS---SSEE CS
                           DUF1684  78 tsgketYgggRyleleakkada.gtvvlDfNrAynppcAysdafsCPlppeeNrLdvaveAGek 140
                                       tsg+etYg+gRyl+le +++++ + +vlDfN+Aynp+cAy+++++CPl+p eN+L+v+++AGek
  gi|313126961|ref|YP_004037231.1| 135 TSGDETYGAGRYLDLEDPDDREgDAWVLDFNYAYNPFCAYNEQYECPLVPMENWLNVPIRAGEK 198
                                       ******************9998999**************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1440.63
//
Query:       gi|313126962|ref|YP_004037232.1|  [L=270]
Description: imidazole glycerol phosphate synthase subunit HisF [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-82  274.6   0.1    6.8e-82  274.4   0.1    1.0  1  His_biosynth  Histidine biosynthesis protein
    2.5e-09   36.7   0.0    3.2e-06   26.5   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    4.7e-08   32.6   0.1    5.7e-05   22.5   0.0    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
      3e-07   30.2   0.3    5.1e-05   22.8   0.1    2.1  2  NMO           Nitronate monooxygenase
    0.00028   20.3   0.0    0.00096   18.6   0.0    1.7  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
    0.00054   19.3   0.0     0.0051   16.1   0.0    2.0  2  DHO_dh        Dihydroorotate dehydrogenase
     0.0038   16.7   0.1     0.0063   16.0   0.1    1.3  1  PcrB          PcrB family
  ------ inclusion threshold ------
      0.021   13.8   0.1      0.043   12.8   0.0    1.5  2  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.026   13.8   0.1       0.28   10.5   0.0    2.1  2  TMP-TENI      Thiamine monophosphate synthase
      0.053   12.7   0.0      0.085   12.0   0.0    1.2  1  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.4   0.1   3.8e-85   6.8e-82       1     228 [.       5     252 ..       5     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 274.4 bits;  conditional E-value: 3.8e-85
                                       EEEEEEEE...ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SS CS
                      His_biosynth   1 riipalDl...kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfi 74 
                                       riip++D+   +dG+   ++ G++f++l+y gdpve+ak y+e+gade++++D++a++egre++ld v+++a+evfi
  gi|313126962|ref|YP_004037232.1|   5 RIIPCIDVdlnEDGEPA-VYTGVNFEDLQYTGDPVEMAKLYNEAGADEFVFLDITASAEGRETMLDTVSRVADEVFI 80 
                                       8*******998888755.5********************************************************** PP

                                       EEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.....C............E CS
                      His_biosynth  75 pvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.....g............y 134
                                       p++vGGGIr+ ed++e l+agadkv+i+taa++np+l++e a++fgsq+iv+++Darr     g            +
  gi|313126962|ref|YP_004037232.1|  81 PLTVGGGIRTREDIKETLRAGADKVSINTAALQNPDLVNEGARAFGSQCIVISVDARRrydeaGeyyaevdgescwF 157
                                       **********************************************************8877626666777899*9* PP

                                       EEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHH. CS
                      His_biosynth 135 kvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelk. 210
                                       ++++kg+re t++d+ve+a+++e++gage+ +++id+dGt++G+d++ltk+++++v+ pvias G+g +ed++e++ 
  gi|313126962|ref|YP_004037232.1| 158 ECTVKGGREGTDIDVVEWASEAESRGAGELFVNSIDADGTKDGYDVPLTKAVCDEVSTPVIASSGCGGPEDMYEVFt 234
                                       ****************************************************************************7 PP

                                       HTTCSEEEESHHHHTTSS CS
                      His_biosynth 211 segvdavivgsalyegel 228
                                       ++g+da +++s++++ e+
  gi|313126962|ref|YP_004037232.1| 235 EAGADAGLAASIFHFDEY 252
                                       7788**********9987 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.8e-09   3.2e-06     168     229 ..      63     125 ..      32     150 .. 0.80
   2 !    8.3   0.0   0.00059       1.1     169     212 ..     200     243 ..     160     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.8e-09
                                       C.G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHH CS
                               Dus 168 g.tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stav 229
                                       g +  +++++ v ++v ip+ + G+I+++ed+++ l+  Gad v i  +al+nP l++e   a+
  gi|313126962|ref|YP_004037232.1|  63 GrETMLDTVSRVADEVFIPLTVGGGIRTREDIKETLRA-GADKVSINTAALQNPDLVNEgARAF 125
                                       3356689******************************9.******************9865554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00059
                                       G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEE CS
                               Dus 169 tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmi 212
                                         d    k+v+++vs+pvia  ++  +ed+ ++  e Gad+ ++
  gi|313126962|ref|YP_004037232.1| 200 GYDVPLTKAVCDEVSTPVIASSGCGGPEDMYEVFTEAGADAGLA 243
                                       556666799*******************************9876 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   3.2e-08   5.7e-05     124     221 ..      28     126 ..      17     146 .. 0.86
   2 !    8.1   0.0   0.00083       1.5     168     204 ..     207     244 ..     194     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.2e-08
                                       -EEEEEE-S-HHHHHHHHHTT-SEBEEBSSSTTS----S-H.HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-S CS
                              ThiG 124 FevlpYvsdDlvlarrleevGcaavmPlaapiGsglGllnk.ealkiiieeakvPvivDAGigspsdaaqamelGad 199
                                       Fe l Y+ d + +a+  +e+G+   + l     s++G +++  +++ + +e+ +P+ v  Gi++ +d+ +++  Gad
  gi|313126962|ref|YP_004037232.1|  28 FEDLQYTGDPVEMAKLYNEAGADEFVFLD-ITASAEGRETMlDTVSRVADEVFIPLTVGGGIRTREDIKETLRAGAD 103
                                       88899*99999999999*****9988765.446788887762679999***************************** PP

                                       EEEESHHHHTSSSHHH.HHHHHH CS
                              ThiG 200 avllntavaeakdpva.mArafk 221
                                        v +nta  +  d v+  Araf 
  gi|313126962|ref|YP_004037232.1| 104 KVSINTAALQNPDLVNeGARAFG 126
                                       *******9999998862577775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00083
                                       HHHHHH-SS-BEEES---SHHHHHHHH.HTT-SEEEES CS
                              ThiG 168 kiiieeakvPvivDAGigspsdaaqam.elGadavlln 204
                                       k +++e++ Pvi   G g p+d  +++ e Gada l +
  gi|313126962|ref|YP_004037232.1| 207 KAVCDEVSTPVIASSGCGGPEDMYEVFtEAGADAGLAA 244
                                       7899*******************9986599***98876 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   2.8e-08   5.1e-05     179     226 ..      65     112 ..      38     119 .. 0.79
   2 !    5.5   0.0    0.0053       9.4     146     218 ..     173     240 ..     168     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.8e-08
                               NMO 179 kglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                       +  +  v +v+d v iP+   GGi +r++++  L++GA  v i t+ L
  gi|313126962|ref|YP_004037232.1|  65 ETMLDTVSRVADEVFIPLTVGGGIRTREDIKETLRAGADKVSINTAAL 112
                                       334455666666666******************************977 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0053
                               NMO 146 vkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLa.lGAsg 218
                                       v+ a ++e+rGa  l v+  +a G +    +     + L + v d v+ PviA  G    +++  +++ +GA +
  gi|313126962|ref|YP_004037232.1| 173 VEWASEAESRGAGELFVNSIDADGTKD--GY----DVPLTKAVCDEVSTPVIASSGCGGPEDMYEVFTeAGADA 240
                                       566778888888888888888877766..34....478999***************999999998887356665 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.3e-07   0.00096     127     170 ..      67     110 ..      65     112 .. 0.90
   2 ?   -1.6   0.0      0.87   1.6e+03     131     156 ..     206     231 ..     203     240 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.3e-07
                                       GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--H CS
                      G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnk 170
                                       + ++++++ +e+ ip+  GG i+t+ed++e l+aGa+ vs  + 
  gi|313126962|ref|YP_004037232.1|  67 MLDTVSRVADEVFIPLTVGGGIRTREDIKETLRAGADKVSINTA 110
                                       6678899999******************************8765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.87
                                       HCTSTTS...EEEEESS--SHHHHHH CS
                      G3P_antiterm 131 ikeikkelkipiiaGGLietkedvee 156
                                       +k++++e+++p+ia+      ed+ e
  gi|313126962|ref|YP_004037232.1| 206 TKAVCDEVSTPVIASSGCGGPEDMYE 231
                                       67899999*****9755555555544 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.8e-06    0.0051     229     281 ..      66     115 ..      61     123 .. 0.84
   2 ?    0.9   0.0      0.12   2.1e+02     245     285 ..     215     255 ..     205     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGT CS
                            DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegp 281
                                       + l ++ ++++++   ip+   GGi + eD  e ++aGA  v + ta   ++p
  gi|313126962|ref|YP_004037232.1|  66 TMLDTVSRVADEVF--IPLTVGGGIRTREDIKETLRAGADKVSINTAA-LQNP 115
                                       55677888888888..99999*************************98.4555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                                       S-EEEESS--SHHHHHHHH.HHTECEEEESHHHHHHGTCHHH CS
                            DHO_dh 245 ipiIgvGGiesgeDaleki.eaGAslvqvytalvfegpkiak 285
                                        p+I++ G    eD +e + eaGA +    + ++f+++ i +
  gi|313126962|ref|YP_004037232.1| 215 TPVIASSGCGGPEDMYEVFtEAGADAGLAASIFHFDEYSI-Q 255
                                       6999999999999999975379999888888887776654.4 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.5e-06    0.0063     158     214 ..      54     114 ..      38     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.5e-06
                                       EEE-TTSSS-HHHHHHHHHHHSSSE...EEEESS--SHHHHHHHHCC.SSEEEE-CHHHHH CS
                              PcrB 158 YlEasGaledveevialkkklekar...livGGGirsaEkAkevvea.ADvivvGnvveek 214
                                       +l+     e  e + +++ ++ ++    l vGGGir +E+ ke+++a AD + + ++  ++
  gi|313126962|ref|YP_004037232.1|  54 FLDITASAEGRETMLDTVSRVADEVfipLTVGGGIRTREDIKETLRAgADKVSINTAALQN 114
                                       555555555557777766666665412267********************99777665555 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.4e-05     0.043     129     171 ..      64     106 ..      25     110 .. 0.55
   2 ?   -3.0   0.0       1.6   2.8e+03     201     232 ..     208     240 ..     201     248 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                                       SHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 129 sekvleavkeikkkveeveviaGnvataegakaLieagadavk 171
                                        e++l++v+++ ++v     ++G + t+e +k+ ++agad v 
  gi|313126962|ref|YP_004037232.1|  64 RETMLDTVSRVADEVFIPLTVGGGIRTREDIKETLRAGADKVS 106
                                       3445555555555553322455555555555555555555554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                                       HHHCTCT-EEEEES---SHHHHHHHHH.TT-SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                             IMPDH 201 eaakkagvpviaDGGikysgdivkAla.aGada 232
                                       +++++   pvia  G    +d+   ++ aGada
  gi|313126962|ref|YP_004037232.1| 208 AVCDEVSTPVIASSGCGGPEDMYEVFTeAGADA 240
                                       567778888888888888888877665366665 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.28     137     178 ..      66     108 ..      37     111 .. 0.81
   2 ?    1.2   0.0      0.11     2e+02     130     173 ..     197     239 ..     167     245 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                          TMP-TENI 137 lgleglkelaealeiPvvaiGGit.lenvaevleagadgvavv 178
                                         l++++++a+++ iP+ + GGi+  e+++e l+agad v++ 
  gi|313126962|ref|YP_004037232.1|  66 TMLDTVSRVADEVFIPLTVGGGIRtREDIKETLRAGADKVSIN 108
                                       45788999999999*********62689***********9975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                          TMP-TENI 130 tKkdaeplgleglkelaealeiPvvaiGGi.tlenvaevl.eagad 173
                                       tK++    ++ + k+++++++ Pv+a  G   +e++ ev+ eagad
  gi|313126962|ref|YP_004037232.1| 197 TKDG---YDVPLTKAVCDEVSTPVIASSGCgGPEDMYEVFtEAGAD 239
                                       4433...466788999**********98873578888887566665 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.8e-05     0.085     275     307 ..      80     112 ..      63     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.8e-05
                                       -EEEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                      Glu_synthase 275 vsliadGglktgadvvkalalGAdavgigtaal 307
                                       + l++ Gg++t +d+  +l  GAd+v+i taal
  gi|313126962|ref|YP_004037232.1|  80 IPLTVGGGIRTREDIKETLRAGADKVSINTAAL 112
                                       56899**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2255.71
//
Query:       gi|313126963|ref|YP_004037233.1|  [L=64]
Description: hypothetical protein Hbor_22270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.2   0.0       0.03   14.1   0.0    1.0  1  CbtA      Probable cobalt transporter subunit (CbtA)


Domain annotation for each model (and alignments):
>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.7e-06      0.03      35      91 ..       4      60 ..       2      64 .] 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-06
                              CbtA 35 eayEeaaaaaeaaeaaaeHehaeaeepelvsrgvqrtlg..tvlanvltgvalglllaa 91
                                      e++E+  ++ e+++++ +H h e+++   v++ +q++     +++ v+++v+l++++++
  gi|313126963|ref|YP_004037233.1|  4 EKIENPSDQFESDHDQGDHHH-ESDDG-RVTSPMQEFSSgkAMTGLVVLAVGLAVIFGL 60
                                      556666666666666655555.44444.588888877532378999**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 462.54
//
Query:       gi|313126964|ref|YP_004037234.1|  [L=322]
Description: zn-dependent oxidoreductase, NADph:quinone reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-29  102.2   0.1      1e-28   99.9   0.0    2.0  2  ADH_zinc_N    Zinc-binding dehydrogenase
      4e-22   79.7   0.1    7.9e-22   78.7   0.1    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
      2e-10   40.5   0.1    5.8e-10   39.0   0.1    1.9  1  ADH_N         Alcohol dehydrogenase GroES-like domain


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.17     1e+03      64      85 ..     114     135 ..      63     137 .. 0.76
   2 !   99.9   0.0   1.7e-32     1e-28       1     116 [.     149     264 ..     149     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.17
                                       ESSCSHHHHHHHHHCEEEEEEE CS
                        ADH_zinc_N  64 ecvGsgatleaalkllkpgGrl 85 
                                       e++G +  + +a+++l+  G l
  gi|313126964|ref|YP_004037234.1| 114 EAAGFPVQFLTAYNCLHNWGDL 135
                                       6777888888888888888876 PP

  == domain 2  score: 99.9 bits;  conditional E-value: 1.7e-32
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG+aavqlA ++ ae ++++s++ekl+la +lG d+ iny+e+d+ e i e t+gegvd+v++ v+ g+t++++l+
  gi|313126964|ref|YP_004037234.1| 149 GVGTAAVQLADHADAESFGTASTQEKLDLASDLGLDHGINYEETDFREVIDEETDGEGVDLVLDGVN-GETFDRSLD 224
                                       9****************************************887***********************.********* PP

                                       CEEEEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSC CS
                        ADH_zinc_N  78 llkpgGrlvvvGg.gkgeeefdlrnlllkeksilGsllgs 116
                                       +l + Gr+vv+G+ +++  + d+ +ll+++ks+lG++lg+
  gi|313126964|ref|YP_004037234.1| 225 ALSHFGRVVVYGAaSGDIAKPDTTRLLFENKSVLGFHLGN 264
                                       *************77777779999***************9 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.1   1.3e-25   7.9e-22       1     133 []     181     320 ..     181     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.3e-25
                                       TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.....S-EEE-CHHHCTT CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpp....lsaallkpakkrk 69 
                                       lG d+ i+y+++df+    ++t+gegvD+vld v+ge++ ++sl++l++ Gr+v++g+ +     +++++ + ++++
  gi|313126964|ref|YP_004037234.1| 181 LGLDHGINYEETDFRevidEETDGEGVDLVLDGVNGETF-DRSLDALSHFGRVVVYGAASgdiaKPDTTRLLFENKS 256
                                       89*****************999*****************.*******999******964446553333344444445 PP

                                       T-EEEE--GGG...-..-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  70 grsvkyeflfsmkas.aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                         ++++   ++  +s +      el +l+++ +l++ v+++f+le+a++A +yle ++ +GK+Vl
  gi|313126964|ref|YP_004037234.1| 257 VLGFHLGNAIEKDPSrVLGS-VSELQRLLAQDELEVIVGETFDLEDAKDAQEYLEGRQSVGKVVL 320
                                       55555555554444444444.7******************************************8 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.1   9.7e-14   5.8e-10       1      63 [.      27      88 ..      27     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 9.7e-14
                                      TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-S CS
                             ADH_N  1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvep 63
                                      pgev+i+v+a+g++  D++  +g+ +   ++p+++G E++G++++vg++v+  +vGdrVv+  
  gi|313126964|ref|YP_004037234.1| 27 PGEVRIDVAATGLNFADVMQRRGHYRGGPEPPFVPGMEAAGTIDAVGEGVD-REVGDRVVALT 88
                                      689***********************************************6.6******9844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2364.29
//
Query:       gi|313126965|ref|YP_004037235.1|  [L=719]
Description: phosphoribosylformylglycinamidine synthase subunit ii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-43  147.8   5.2      2e-23   82.8   0.1    3.4  3  AIRS            AIR synthase related protein, N-terminal doma
    2.3e-35  122.0  14.1    2.7e-31  108.8   2.8    2.7  3  AIRS_C          AIR synthase related protein, C-terminal doma
    4.9e-08   33.4   0.0    1.6e-07   31.7   0.0    2.0  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.1   3.3e-27     2e-23       5      93 ..      71     190 ..      60     191 .. 0.85
   2 ?   -0.9   0.0      0.44   2.6e+03      24      41 ..     272     289 ..     246     353 .. 0.74
   3 !   65.0   0.8   1.2e-21   7.4e-18       1      93 [.     434     551 ..     434     552 .. 0.91

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 3.3e-27
                                       E...................EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......... CS
                              AIRS   5 v...................vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp......... 53 
                                                           ++ ++shn+p++v+p+++ +a++v+++++D ++mGA P+al +sl ++         
  gi|313126965|ref|YP_004037235.1|  71 DaaeasdetdsddaetetyiTMGIESHNHPSYVDPYDG-AATGVGGIVRDTLSMGAYPIALADSLYFGdfdrehsry 146
                                       03344444444444445555999***************.************************************** PP

                                       HHHHHHHHHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEE CS
                              AIRS  54 wleevvrglaeaaeelgvplvgGdtsfsne....ptisvtavGl 93 
                                        le+vv+g+a++++++gvp+v G ++f+++    p+++v++vGl
  gi|313126965|ref|YP_004037235.1| 147 LLEGVVEGIADYGNAIGVPTVAGSVEFHENyegnPLVNVACVGL 190
                                       ****************************8889***********8 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHTTTE CS
                              AIRS  24 iGakavavnlsDlaamGA 41 
                                       +Ga +++++ s l+a G+
  gi|313126965|ref|YP_004037235.1| 272 LGAAGLGGASSELVAKGG 289
                                       466666666666666665 PP

  == domain 3  score: 65.0 bits;  conditional E-value: 1.2e-21
                                       SSSEE..........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHH CS
                              AIRS   1 dDaav..........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleev 58 
                                       dDaav          +++   +++ + ++p+++ ++ ++ +n+ +laa GA+Pla++++l+ +          ++++
  gi|313126965|ref|YP_004037235.1| 434 DDAAVmaireanaglAISSGANPNWTTCAPYDG-ARAVALENATNLAAKGATPLAAVDCLNGGnpekpdvygGFKGI 509
                                       67774444444444499****************.******************************************* PP

                                       HHHHHHHHHHTT-EEEEEEEEEESS.......EEEEEEEEEE CS
                              AIRS  59 vrglaeaaeelgvplvgGdtsfsne.......ptisvtavGl 93 
                                       v+gla++++ l vp+vgG++s +n+       pt+++++vG+
  gi|313126965|ref|YP_004037235.1| 510 VDGLADMCRDLSVPVVGGNVSLYNDsvsgpipPTPTLAVVGT 551
                                       ***********************999*************995 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.1   1.3e+04     107     130 ..      44      67 ..      31      72 .. 0.78
   2 !  108.8   2.8   4.6e-35   2.7e-31       2     149 ..     204     353 ..     203     356 .. 0.94
   3 !   17.5   4.3   5.8e-07    0.0035       2     155 ..     565     695 ..     564     696 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.1
                                       HHCSTTTEEEEEEEHGGHHHHHHH CS
                            AIRS_C 107 llsensGrllvavppeeadavlai 130
                                       l +++s++  v+v p +++av+++
  gi|313126965|ref|YP_004037235.1|  44 LSAFSSEGDQVVVGPGDDAAVVRL 67 
                                       456899999999999999888765 PP

  == domain 2  score: 108.8 bits;  conditional E-value: 4.6e-35
                                       TTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHH CS
                            AIRS_C   2 pGdvliltgs....lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGLl 73 
                                       +G++l+l+g+    +Glgga+ ++++ + e+++++d+ avq+gd++ e+ li+++++l ++ +lv aa+D+++ GL 
  gi|313126965|ref|YP_004037235.1| 204 AGNKLVLVGNatgrDGLGGAS-FASEDLAEDAETEDRpAVQVGDPYSEKLLIEANEELVEA-NLVEAARDLGAAGLG 278
                                       7********************.5556666666666667**********************9.*************** PP

                                       HHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                            AIRS_C  74 galaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                       ga +e+++++g+gaei+ld+v  +++ +s+le+ll+e+++r++  v++e+ ++v +i+e+++l  ++vIGev +++
  gi|313126965|ref|YP_004037235.1| 279 GASSELVAKGGFGAEIELDRVHQREPNMSALEILLAESQERMCYEVREENVEQVADIAEKYDL-GCSVIGEVAEGN 353
                                       ***************************************************************.7*******9986 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 5.8e-07
                                       TTEEEEEEET.SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   2 pGdvliltgs.lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       +G +l++ +s   lgg+ ++++  ++  ++ ++  ++ +dvl++  l +v++a+        a+h v +GGL+++la
  gi|313126965|ref|YP_004037235.1| 565 EGELLVVGASgGALGGSEYLAQM-GGS-DAFPELPENASDVLAT--LADVADAET-----TLAVHEVNHGGLAVSLA 632
                                       67778888886778888855544.433.3344222223333333..555555555.....56*************** PP

                                       HHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEEE CS
                            AIRS_C  78 emapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeelsvi 154
                                       em+ +   ga ++++             +l+ e+ Gr   +v+  +adav+++++    p ++ +G++t+++ ls+ 
  gi|313126965|ref|YP_004037235.1| 633 EMVTDD-AGADVTVE--S--------VSALFDETPGRA--VVETTDADAVREAFDGVA-P-VTTLGKATEDGTLSLS 694
                                       *****5.*******9..2........3468999***99..677777788******765.5.9*******99988876 PP

                                       E CS
                            AIRS_C 155 v 155
                                       v
  gi|313126965|ref|YP_004037235.1| 695 V 695
                                       5 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.7e-11   1.6e-07      11      49 ..       2      37 ..       1      38 [. 0.90

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.7e-11
                    FGAR-AT_linker 11 aLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrH 49
                                      +Lsd++ + ++     lgr+Pt +E+ +f   wSEHC +
  gi|313126965|ref|YP_004037235.1|  2 SLSDADRELVVAE---LGRDPTSAETVLFENLWSEHCAY 37
                                      6888888888888...9********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 5236.27
//
Query:       gi|313126966|ref|YP_004037236.1|  [L=142]
Description: signal-transduction protein containing camp-binding and cbs domains [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-26   92.2   3.1    5.1e-13   49.2   0.2    2.2  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.3   1.5e-15   2.6e-11       1      56 [.       3      59 ..       3      60 .. 0.90
   2 !   49.2   0.2   2.9e-17   5.1e-13       1      55 [.      69     122 ..      69     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.5e-15
                                      HHHHSBS..SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  1 Vgdimtr..dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      V+di ++  +vv+++pdt++ e++++m++k+v+++ V++ dg++ Givt+rDl+ ++l
  gi|313126966|ref|YP_004037236.1|  3 VRDIARSkgEVVSARPDTPVNELAKTMASKKVGSV-VIETDGHIEGIVTDRDLALKIL 59
                                      67775556789****************9999****.*****************99886 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 2.9e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       ++d+m+++++t++ d+ + e+ + mre+gv+r+PV  e+gkl Givt+ Dll +l
  gi|313126966|ref|YP_004037236.1|  69 ARDVMSPKPFTADGDMGVMELCRAMREHGVRRVPVA-EEGKLSGIVTMDDLLVLL 122
                                       58*********************************9.9*************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 969.29
//
Query:       gi|313126967|ref|YP_004037237.1|  [L=227]
Description: metal-dependent phosphoesterase, php family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-21   74.0   0.3    5.3e-20   70.9   0.3    2.2  2  PHP_C     PHP-associated
    3.4e-08   34.0   0.0    3.8e-08   33.8   0.0    1.2  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.054   4.9e+02       6      19 ..      48      61 ..      45      63 .. 0.87
   2 !   70.9   0.3   5.9e-24   5.3e-20       1      56 []     140     195 ..     140     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.054
                             PHP_C  6 rArrfAeklglpgt 19
                                      +A+ +Ae +gl g+
  gi|313126967|ref|YP_004037237.1| 48 QAADIAEDYGLVGI 61
                                      89*********987 PP

  == domain 2  score: 70.9 bits;  conditional E-value: 5.9e-24
                             PHP_C   1 geaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegrt 56 
                                       g++Nr+A+rfA +++lp t+GSDAH+ e+VG+a+Te++++ +++  +l+ai  g+t
  gi|313126967|ref|YP_004037237.1| 140 GRSNRKADRFATARELPKTAGSDAHISEMVGQAVTEVATDDRSESGILDAITDGQT 195
                                       689**************************************************997 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   4.3e-12   3.8e-08       1      72 [.       5      72 ..       5     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.3e-12
                                      EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE....... CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvadds 72
                                      +lH+H++ s    +++  e l+++a++ gl+a+a+TDh+++++ ++++  a   ++ g+  i G+e++ a ++
  gi|313126967|ref|YP_004037237.1|  5 ELHAHSSLSyDARDPI--ELLLEQAEAVGLDALAVTDHDEIDASLQAADIA---EDYGLVGIPGMEVTSAAGH 72
                                      79*******7333566..*******************************99...5568999999996665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1565.73
//
Query:       gi|313126968|ref|YP_004037238.1|  [L=360]
Description: asparagine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-31  108.2   3.2    8.1e-20   71.8   0.5    2.1  2  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
      0.017   14.3   0.2      0.029   13.5   0.2    1.3  1  NAD_synthase   NAD synthase
       0.22   10.3   0.2       0.33    9.7   0.2    1.3  1  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.5   1.3e-23   8.1e-20      15     142 ..     111     233 ..      98     247 .. 0.89
   2 !   37.3   0.1   4.2e-13   2.5e-09     211     309 ..     246     341 ..     234     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1.3e-23
                      Asn_synthase  15 radvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdv 91 
                                       +    +++ +SGG+DS+++aa        ++ ++ +gf  +gs ++++a+ +a+++  e + ++lt ++l +a+p++
  gi|313126968|ref|YP_004037238.1| 111 VESEGLAVAFSGGVDSAVVAAGVP-----DAPCYVAGF--EGSHDVAAARDAADAMDRELHVVELTHDALREAVPEL 180
                                       555668899*********998664.....578******..************************************* PP

                      Asn_synthase  92 iyhlee..pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaa 142
                                       +++l +  p+ ++  +plyl+++++ ++g+  +  G+GaDElfgGY    ka+
  gi|313126968|ref|YP_004037238.1| 181 VSVLGRtnPMDIQIVLPLYLVAKQVAADGFDRLAVGQGADELFGGYAKVEKAP 233
                                       ****999***************************************9877777 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 4.2e-13
                      Asn_synthase 211 lyldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPeeileRpKeg 287
                                         +++ ++lp++l r   +  a+g+E   P+l++++v +al lp el + + + K  LRe++  ++P++++   K++
  gi|313126968|ref|YP_004037238.1| 246 AATEMVRTLPEQLERDVLTLRAAGVEPVAPLLHDDVVSAALPLPGELLVADSRRKVALREVAGELVPDSVASADKKA 322
                                       567788999999999999*********************************************************** PP

                      Asn_synthase 288 fsapvgewklkgelrelaeell 309
                                       +++++++    +el +la++  
  gi|313126968|ref|YP_004037238.1| 323 VQYGTYAA---RELDRLARQAG 341
                                       ***99888...67877777765 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   4.9e-06     0.029       4      36 ..      99     131 ..      96     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.9e-06
                                       HHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHH CS
                      NAD_synthase   4 elvdflkeyvkkagakgvvlGlSGGvDSslvaa 36 
                                       +++  ++  v++ +++g+ +  SGGvDS++vaa
  gi|313126968|ref|YP_004037238.1|  99 NVESAVHGAVQNVESEGLAVAFSGGVDSAVVAA 131
                                       567789999**********************96 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   5.5e-05      0.33       4      20 ..     117     133 ..     114     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 5.5e-05
                     tRNA_Me_trans   4 vvalSgGVDSsvaaall 20 
                                       +va+SgGVDS+v+aa +
  gi|313126968|ref|YP_004037238.1| 117 AVAFSGGVDSAVVAAGV 133
                                       89***********9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2258.91
//
Query:       gi|313126969|ref|YP_004037239.1|  [L=158]
Description: ADP-ribose pyrophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-13   50.9   0.1    2.2e-13   50.4   0.1    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.1   1.2e-17   2.2e-13       2     121 ..       5     140 ..       4     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.2e-17
                                       EEEEEEEEEEETTSEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   2 lrravgvvllnekgevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpy 78 
                                       ++ ++ v++ n+  +v l ++  +   +   PgG+v+ +E p eA +RE++EEtGl+aell+ ++ +++ +      
  gi|313126969|ref|YP_004037239.1|   5 RHFTATVYIVNDG-AVALHHHE-RLGIE-IPPGGHVDRDEIPHEAGLREVREETGLDAELLDDTDPVDSPDGRVL-- 76 
                                       6778888888888.35555555.33333.599************************9966655554444333333.. PP

                                       EE...................EEEEEEEEE.EEECSGCSST..STTTEEEEEEEEHHHHHHHHTH CS
                             NUDIX  79 gd...................eheilyvfl.eevegelepn..denevsevrwvpleellkekla 121
                                        +                     +i++++    +  ++ p+  de+  +++ w++ +el + +++
  gi|313126969|ref|YP_004037239.1|  77 -PdprhqmlydinihddgtvgHQHIDHIYYaTVESRDIDPDgdDEAGAEAWTWYDADELRENDID 140
                                       .355588888888888899987777788885333444444444777799999*******444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1087.84
//
Query:       gi|313126970|ref|YP_004037240.1|  [L=327]
Description: transcription initiation factor iib (tfiib) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-40  135.1   0.1    2.9e-19   68.9   0.1    2.2  2  TFIIB           Transcription factor TFIIB repeat
    1.5e-18   66.0   3.7    3.1e-18   65.0   3.7    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0003   20.2   1.3     0.0062   16.0   0.1    3.2  3  Sigma70_r4      Sigma-70, region 4
     0.0052   16.9   0.0        2.6    8.1   0.0    2.3  2  Cyclin_C        Cyclin, C-terminal domain
     0.0054   16.1   2.5      0.037   13.4   2.5    2.1  1  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.098   12.4   0.0    1.9  2  Cyclin_N        Cyclin, N-terminal domain
      0.048   13.6   0.6       0.11   12.5   0.6    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.054   13.5   0.6        0.1   12.6   0.6    1.4  1  DZR             Double zinc ribbon
       0.13   11.9   1.2          7    6.3   0.1    2.4  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.14   12.3   4.2       0.39   10.9   0.5    2.4  3  Zn-ribbon_8     Zinc ribbon domain
       0.46   10.3   2.6         11    5.9   2.7    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   4.7e-21   7.7e-18       1      71 []     147     217 ..     147     217 .. 0.98
   2 !   68.9   0.1   1.8e-22   2.9e-19       1      71 []     241     311 ..     241     311 .. 0.99

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 4.7e-21
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+a+al+Lpe V++ A  ++++al++++l Grs +g+a ++ly A+r++++ r++ e   v++V + +i
  gi|313126970|ref|YP_004037240.1| 147 IDRMASALGLPENVRETASVIYRRALDDDLLPGRSIEGVATSALYAAARQAGTPRSLDELETVSRVDKDEI 217
                                       789***************************************************************99987 PP

  == domain 2  score: 68.9 bits;  conditional E-value: 1.8e-22
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rfa++l+L ++ ++ A +l+++a+e+++++G+sp g+aAA++y A++++++k tq+e+s+v+++se+ti
  gi|313126970|ref|YP_004037240.1| 241 VPRFASELGLNDESERHARQLLRTAKEQGIHSGKSPVGLAAAAIYAASLLANEKVTQSEVSEVANISEVTI 311
                                       689******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   3.7   1.9e-21   3.1e-18       3      43 .]      32      72 ..      31      72 .. 0.99

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.9e-21
                                      ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      CP+Cgs+nl++D+e+ge+vC dCGlV+e++ id gpewr+f
  gi|313126970|ref|YP_004037240.1| 32 CPECGSSNLTTDAEHGETVCDDCGLVVEEDEIDRGPEWRAF 72
                                      ***************************************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.25   4.1e+02      34      46 ..     161     173 ..     151     174 .. 0.89
   2 ?   -0.5   0.1      0.54   8.8e+02      33      45 ..     254     266 ..     252     268 .. 0.83
   3 !   16.0   0.1   3.8e-06    0.0062      18      46 ..     292     320 ..     283     321 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAlr 46 
                                       re+++ i +rAl+
  gi|313126970|ref|YP_004037240.1| 161 RETASVIYRRALD 173
                                       89*********96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.54
                                       -HHHHHHHHHHHH CS
                        Sigma70_r4  33 SrerVrqiekrAl 45 
                                       S+ ++rq+++ A 
  gi|313126970|ref|YP_004037240.1| 254 SERHARQLLRTAK 266
                                       8999****99985 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 3.8e-06
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlr 46 
                                        e+ T++E++e+ +iS+ ++r + ++ l+
  gi|313126970|ref|YP_004037240.1| 292 NEKVTQSEVSEVANISEVTIRNRYHELLE 320
                                       5899********************99876 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0054       8.8      47      84 ..     185     222 ..     181     232 .. 0.91
   2 !    8.1   0.0    0.0016       2.6      43      89 ..     275     321 ..     237     325 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0054
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcve 84 
                                       +A++al++a ++ ++p   ++le +++++k++++  ++
  gi|313126970|ref|YP_004037240.1| 185 VATSALYAAARQAGTPRSLDELETVSRVDKDEISRTYR 222
                                       79*******************************98776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                                       -HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                          Cyclin_C  43 ppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                                       +p  +Aaaa+++a+   n++  ++++ ++  +s+  +++ ++ +le+
  gi|313126970|ref|YP_004037240.1| 275 SPVGLAAAAIYAASLLANEKVTQSEVSEVANISEVTIRNRYHELLEA 321
                                       56669******************************999999998875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   2.5   2.3e-05     0.037       5      25 ..      32      57 ..      28      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                       zf-ribbon_3  5 CPnCGa.plssdd....nvCpyCGtk 25
                                      CP+CG+ +l++d+    +vC  CG +
  gi|313126970|ref|YP_004037240.1| 32 CPECGSsNLTTDAehgeTVCDDCGLV 57
                                      ******99*9987444478****975 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     6e-05     0.098      39     126 ..     148     232 ..     111     233 .. 0.86
   2 ?   -0.9   0.0      0.76   1.2e+03      79     118 ..     282     325 ..     263     327 .] 0.59

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6e-05
                                       HHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHH CS
                          Cyclin_N  39 vevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemE 115
                                        ++a+ + l +++  +a +++ R l    +p + ++ v++++L+ Aa+   + p +l++l  +  + ++++ei +  
  gi|313126970|ref|YP_004037240.1| 148 DRMASALGLPENVRETASVIYRRALDDDLLPGRSIEGVATSALYAAARQAGT-PRSLDELETV--SRVDKDEISRTY 221
                                       5667777888888899*********************************888.9*******99..569********* PP

                                       HHHHHHTTT-- CS
                          Cyclin_N 116 rliLetLnfdl 126
                                       r+++++Ln ++
  gi|313126970|ref|YP_004037240.1| 222 RYVVRELNLEI 232
                                       *******9887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.76
                                       HHHHHHHHH..HSSS---HHHHHHHTTT..SS-HHHHHHHHHHH CS
                          Cyclin_N  79 tcLllAaKv..eeisppkledlvyitde..afteeeilemErli 118
                                       ++++ A+ +  e++   ++++++ i++     +  e+le+E+++
  gi|313126970|ref|YP_004037240.1| 282 AAIYAASLLanEKVTQSEVSEVANISEVtiRNRYHELLEAEEQL 325
                                       44444444422333344566666666553334446777777776 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   6.6e-05      0.11      30      58 ..      31      60 ..      22      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCgfeadr 58
                                       C+eCgs n + + ++ + +C++Cg++   
  gi|313126970|ref|YP_004037240.1| 31 LCPECGSSNLTtDAEHGETVCDDCGLVVEE 60
                                      6********99999***********98765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   6.3e-05       0.1      10      39 ..      27      59 ..      19      62 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                               DZR 10 pdarfCseCgtk.lkavaa...edrCpsCgekvd 39
                                      ++   C+eCg++ l    a   e++C+ Cg  v+
  gi|313126970|ref|YP_004037240.1| 27 DEETLCPECGSSnLTTD-AehgETVCDDCGLVVE 59
                                      56678999998864332.2367999999987665 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.02        32       4      13 ..      31      40 ..      28      46 .. 0.75
   2 ?    6.3   0.1    0.0043         7       4      17 ..      50      63 ..      47      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.02
                            zf_UBZ  4 lCerCgkeip 13
                                      lC++Cg++ +
  gi|313126970|ref|YP_004037240.1| 31 LCPECGSSNL 40
                                      8*****9755 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0043
                            zf_UBZ  4 lCerCgkeipesel 17
                                      +C++Cg  ++e+e 
  gi|313126970|ref|YP_004037240.1| 50 VCDDCGLVVEEDEI 63
                                      8*********9986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   0.00024      0.39      24      36 ..      27      40 ..      14      44 .. 0.71
   2 ?    2.4   0.2       0.1   1.7e+02      26      34 ..      48      56 ..      40      61 .. 0.65
   3 ?    1.8   0.2      0.17   2.7e+02       7      16 ..      50      59 ..      46      68 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                       Zn-ribbon_8 24 apltaCPeCgs.ev 36
                                      +++t CPeCgs ++
  gi|313126970|ref|YP_004037240.1| 27 DEETLCPECGSsNL 40
                                      33555******887 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                       Zn-ribbon_8 26 ltaCPeCgs 34
                                      +t+C +Cg 
  gi|313126970|ref|YP_004037240.1| 48 ETVCDDCGL 56
                                      666777774 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.17
                       Zn-ribbon_8  7 rCeeCghefe 16
                                       C++Cg + e
  gi|313126970|ref|YP_004037240.1| 50 VCDDCGLVVE 59
                                      3666665555 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3      0.02        33      23      30 ..      31      38 ..      26      41 .. 0.85
   2 ?    5.9   2.7    0.0066        11       6      30 ..      32      57 ..      31      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.02
                     A2L_zn_ribbon 23 vCieCgas 30
                                       C+eCg+s
  gi|313126970|ref|YP_004037240.1| 31 LCPECGSS 38
                                      5*****98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0066
                     A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                                      C  Cg+ ++   +e+g+ vC +Cg++
  gi|313126970|ref|YP_004037240.1| 32 CPECGSSNLTTdAEHGETVCDDCGLV 57
                                      66788888888889999******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2412.26
//
Query:       gi|313126971|ref|YP_004037241.1|  [L=92]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit C [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-16   60.9   4.5    1.6e-16   60.3   4.5    1.3  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   4.5   9.1e-21   1.6e-16       1      61 [.      22      87 ..      22      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 9.1e-21
                                      --HHHHHHHHHHHHHHHHHHTTCGCS--TT----S.....-EB-S--.....HHHHHTT-SSEETTEEE CS
                       Glu-tRNAGln  1 lseeEleklakelnsildyveqLqevdttgveplthp...vlReDev.....reelLknApetedgyfv 61
                                      l+e+E+e++a+++ +ildy+++L+ev   + ep       v+R Dev     ++e+L+nApe edg+f+
  gi|313126971|ref|YP_004037241.1| 22 LDEDEVEEFAGQFADILDYFDALDEVPEVEAEP---DlvnVMRTDEVrdgldQDEALQNAPEAEDGFFK 87
                                      79*************************436666...24678****9999**9999*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 669.53
//
Query:       gi|313126972|ref|YP_004037242.1|  [L=430]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit A [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     6e-143  477.1   1.5   7.2e-143  476.8   1.5    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.8   1.5    4e-147  7.2e-143      41     450 ..      13     421 ..       6     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: 476.8 bits;  conditional E-value: 4e-147
                                       ......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT-- CS
                           Amidase  41 rgkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkTnmdefamgsstensvfgp 117
                                        g ++gpL+G  ++vKDn+++ g++tt+Gs +l +y++++Datvve+Lk+aGa+i+gkTnmdef+mg +te+s+fgp
  gi|313126972|ref|YP_004037242.1|  13 DGADDGPLAGKTVAVKDNLSTDGLRTTCGSAMLDEYVPPYDATVVEHLKDAGATIVGKTNMDEFGMGGTTETSAFGP 89 
                                       67899************************************************************************ PP

                                       -BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEE CS
                           Amidase 118 trNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvGpla 194
                                       t+NP+d++r+pGGSSGGsAAavAag ++la+GtDtGGS+R PA+fcg+vG+KPtyg+vSr+g++a+++sl++vGp++
  gi|313126972|ref|YP_004037242.1|  90 TKNPVDEERVPGGSSGGSAAAVAAGKADLALGTDTGGSVRNPAAFCGVVGIKPTYGLVSRYGLIAYANSLEQVGPIG 166
                                       ***************************************************************************** PP

                                       SSHHHHHHHHHHHBS--TT-TTS----......HHHHHHHHCTT---TT-EEEEEGGGCSS---CCHHHHHHHHHHH CS
                           Amidase 195 rsvedlalllrvilgedpkdstssvip......eesedlaeelkkslkglriGvvkedgvasldpevqravekalka 265
                                        +ve++a+ll+vi+g d++d t+           e+ d+a+++  + +g+ +Gv++++  + +d+ v + +e+a+  
  gi|313126972|ref|YP_004037242.1| 167 STVEETAALLDVIAGADEHDATTRFDQtmdahpAENSDYAAAADGDVDGMTVGVITDLL-DGADDRVVETFEAAVSD 242
                                       ******************9998764335577779999********************99.8**************** PP

                                       HHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS.---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHH CS
                           Amidase 266 LeeaGhevvevelpsleealslyylilvaeassnlarylgvry.erlsetkvlsellpksraellgeevkrrielgn 341
                                       Le++G+ vvev+l sle+a+++yy i+++eassnlary+gvry   + +  +++++++ +r+e++g evkrri lg+
  gi|313126972|ref|YP_004037242.1| 243 LESQGAAVVEVSLDSLEHAVQAYYVIAMSEASSNLARYDGVRYgLSTGKEGNWNDVYADTREEGFGAEVKRRILLGT 319
                                       *******************************************9888888999************************ PP

                                       HHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGCCTTT...HHHHHT CS
                           Amidase 342 yalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynlldftavvvpvnla 418
                                       yalsa++ +kyy+kaq +r+ ++++f++a+ e Dvl++Pt+p  +p+lge      +++ ly++++ t   vpvnla
  gi|313126972|ref|YP_004037242.1| 320 YALSAGYHDKYYKKAQDARAWIKQDFDEALAEADVLATPTMPVLPPKLGESL---SDPLQLYLMDANT---VPVNLA 390
                                       **************************************************98...69***********...****** PP

                                       T--EEEEECCCCT.TECEEEEEEESTT-HHHH CS
                           Amidase 419 glpalsvpagksedglPvGvqvigkafqeetl 450
                                        lpa+svpag+  dglPvG+q+ig++f eet 
  gi|313126972|ref|YP_004037242.1| 391 NLPAISVPAGEA-DGLPVGLQLIGPKFGEETM 421
                                       **********96.6***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3386.73
//
Query:       gi|313126973|ref|YP_004037243.1|  [L=145]
Description: hypothetical protein Hbor_22370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00069   19.8   0.4     0.0011   19.3   0.4    1.4  1  AglB_L1    Archaeal glycosylation protein B long peripheral d
  ------ inclusion threshold ------
      0.046   13.7   4.6      0.046   13.7   4.6    2.3  3  PGF-CTERM  PGF-CTERM motif
        0.1   12.4   0.0       0.14   12.0   0.0    1.2  1  zf-ZPR1    ZPR1 zinc-finger domain


Domain annotation for each model (and alignments):
>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.4   1.8e-07    0.0011       3      63 ..      33      94 ..      32     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.8e-07
                                      EEEEEBSSS..SEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSE CS
                           AglB_L1  3 titGsaeag..atvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssve 63
                                      ti G+++ +  ++vt++v  + ++++ f  +++a+++edG fe t  +s ++ + ++ +++v 
  gi|313126973|ref|YP_004037243.1| 33 TIAGTTDLEagTNVTVRVASSGDTQPPFLKTDTATVGEDGGFEATFDFSEQNAS-DTFEVTVD 94
                                      5777775444499999999999***************************99643.33333333 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3       1.5   8.7e+03      10      17 ..       2       9 ..       2      10 .. 0.59
   2 ?   -0.7   0.2      0.27   1.6e+03       3       8 ..      73      78 ..      73      78 .. 0.88
   3 ?   13.7   4.6   7.8e-06     0.046       1      23 []     120     142 ..     120     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                         PGF-CTERM 10 laGLLaaa 17
                                      ++G  ++a
  gi|313126973|ref|YP_004037243.1|  2 VVGTTGVA 9 
                                      46666766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.27
                         PGF-CTERM  3 GFGavl 8 
                                      GF+a +
  gi|313126973|ref|YP_004037243.1| 73 GFEATF 78
                                      9**986 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 7.8e-06
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       +PGF +v+A++++ a+++ a Rr
  gi|313126973|ref|YP_004037243.1| 120 MPGFSVVVAVFAIVAVGAVAVRR 142
                                       7****************999998 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.14      43     110 ..      33     116 ..      27     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                           zf-ZPR1  43 vksageieekGkritlkveseedlnrqvlkSetatve................ipeleleippgtlegrlttvEGlL 103
                                       +  +++  e G+++t++v s+ d +   lk +tatv                    +e+++++ +++g +   EG++
  gi|313126973|ref|YP_004037243.1|  33 TIAGTTDLEAGTNVTVRVASSGDTQPPFLKTDTATVGedggfeatfdfseqnaSDTFEVTVDSDSSSGMVAEAEGVV 109
                                       3344444577**************************999********9999988889999999999*********99 PP

                           zf-ZPR1 104 eqikeel 110
                                       +  +e+ 
  gi|313126973|ref|YP_004037243.1| 110 RAPEEDT 116
                                       8877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1183.33
//
Query:       gi|313126974|ref|YP_004037244.1|  [L=226]
Description: k+ transporter, NAD-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-27   96.5   1.1    2.1e-27   95.7   1.1    1.4  1  TrkA_N           TrkA-N domain
    1.3e-17   63.3   0.2    9.2e-16   57.4   0.0    2.4  2  TrkA_C           TrkA-C domain
    3.8e-06   27.4   0.2    8.1e-06   26.3   0.2    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    3.5e-05   24.2   0.1    9.1e-05   22.9   0.1    1.7  1  NAD_binding_7    Putative NAD(P)-binding
    4.8e-05   23.6   0.2    7.4e-05   23.0   0.2    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0002   21.3   0.1    0.00032   20.6   0.1    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00039   20.5   0.1    0.00073   19.6   0.1    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00097   19.6   0.0     0.0015   19.0   0.0    1.3  1  XdhC_C           XdhC Rossmann domain
     0.0012   19.4   0.4      0.017   15.7   0.2    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0023   17.8   0.4     0.0038   17.1   0.4    1.5  1  NAD_binding_10   NAD(P)H-binding
     0.0027   17.3   0.3      0.033   13.8   0.1    2.2  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0032   17.6   0.0     0.0053   16.9   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0037   18.1   0.0     0.0059   17.4   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0045   17.0   0.0       0.35   10.8   0.1    2.2  2  ADH_zinc_N       Zinc-binding dehydrogenase
      0.005   16.2   0.4     0.0078   15.5   0.4    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0057   16.2   0.1      0.011   15.3   0.1    1.4  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.026   14.1   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.015   14.5   0.1      0.023   13.9   0.1    1.2  1  Thi4             Thi4 family
      0.024   14.0   0.0      0.039   13.3   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.032   14.5   0.0      0.047   14.0   0.0    1.3  1  Peripla_BP_3     Periplasmic binding protein-like domain
      0.059   12.8   0.1      0.089   12.2   0.1    1.2  1  TPALS            TIR- and PNP-associating SLOG family


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   1.1   2.4e-30   2.1e-27       1     115 [.       3     117 ..       3     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 2.4e-30
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddean 76 
                                       iii+G+G++G+ l+e  ++gg++vvvi++d e++ee++  + + v++ dat++++L +ag+++ada+i +t++d++n
  gi|313126974|ref|YP_004037244.1|   3 IIIVGAGNIGTPLIEIATRGGNEVVVIERDTEKAEEAASTFdCLVLNDDATEKQTLSDAGADRADALISTTDKDATN 79 
                                       8******************7668***************999999********************************* PP

                                       HHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                            TrkA_N  77 ilavllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                       i+++llakel   ++i++ +++peh  +++++g++++ +
  gi|313126974|ref|YP_004037244.1|  80 IMVCLLAKELQI-PNIVSVVHNPEHMGIYRRIGVNTMEN 117
                                       ********9666.9********************98765 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.069        59       5      36 ..       5      34 ..       1      43 [. 0.75
   2 !   57.4   0.0   1.1e-18   9.2e-16       1      70 []     147     221 ..     147     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.069
                                      EEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.- CS
                            TrkA_C  5 tvpagsplvGktlkelnlrar.gvlvvairRg.g 36
                                       v+ag   +G++l e  + +r g  vv i R+ +
  gi|313126974|ref|YP_004037244.1|  5 IVGAGN--IGTPLIE--IATRgGNEVVVIERDtE 34
                                      555555..9******..77777*******99964 PP

  == domain 2  score: 57.4 bits;  conditional E-value: 1.1e-18
                                       CEEEEEE--GGGTTSBHHHHT....HHHHS-EEEEEE-T..-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkeln....lrargvlvvairRg..geliipsgdtvLeeGDvllvvgspsdlaelrellg 70 
                                       ++e++v++++pl+G+t++e+     l a g l+vai R+  g++i p+g+tv+e+GD+l+v++   ++ e+++++g
  gi|313126974|ref|YP_004037244.1| 147 VFEIAVDENAPLAGQTIQEAAsegyLGA-GMLIVAIERDgtGDPITPRGNTVIEAGDLLTVYSAEGATPEVTDVFG 221
                                       79*****************554555555.*******9999******************************999986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.2   9.5e-09   8.1e-06       2      48 ..       3      51 ..       2     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 9.5e-09
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......- CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......v 48
                                      i i+GaGn+g  l++ +++ g   +e+vv+ +r+ ekaee+a+++        
  gi|313126974|ref|YP_004037244.1|  3 IIIVGAGNIGTPLIEIATRGG---NEVVVI-ERDTEKAEEAASTFDclvlndD 51
                                      5577***********999999...****99.*************994443331 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   1.1e-07   9.1e-05      10      98 ..       3     104 ..       1     108 [. 0.77

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-07
                     NAD_binding_7  10 vlvvGgGevAarkvrklleagakvtvvapevkeele.....elvklaeeelekd......legadlviaatddreln 75 
                                       +++vG+G++++  ++   + g +v+v+  +++++ e     + + l+++  ek+       ++ad +i +td+++ n
  gi|313126974|ref|YP_004037244.1|   3 IIIVGAGNIGTPLIEIATRGGNEVVVIERDTEKAEEaastfDCLVLNDDATEKQtlsdagADRADALISTTDKDATN 79 
                                       68****************************644434554443333444444444455556999************** PP

                     NAD_binding_7  76 eriaeaakarri..lvnvadkpelc 98 
                                         ++ +ak+ +i   v v+ +pe+ 
  gi|313126974|ref|YP_004037244.1|  80 IMVCLLAKELQIpnIVSVVHNPEHM 104
                                       ***********95558888888765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   8.7e-08   7.4e-05       1      57 [.       3      51 ..       3      89 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.7e-08
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TT CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdae 57
                                      ++i+GaG++G +++e   r ++   e++v++r+ ek+e++a++     f++  l+ +
  gi|313126974|ref|YP_004037244.1|  3 IIIVGAGNIGTPLIEIATRGGN---EVVVIERDTEKAEEAAST-----FDCLVLNDD 51
                                      89*****************998...6**********8888754.....344333322 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   3.7e-07   0.00032       2      72 ..       3      75 ..       2      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.7e-07
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH..HHHCCTTTTSS-HHHHCCCHHCEEEES- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek..sleklvekgklkeeeveaalarisfttd 72
                                      + ++GaG +G+ + +++ + g eVv++++++e++e+a+++       + + ek+ l+++ +++a a is+t++
  gi|313126974|ref|YP_004037244.1|  3 IIIVGAGNIGTPLIEIATRGGNEVVVIERDTEKAEEAASTFDClvLNDDATEKQTLSDAGADRADALISTTDK 75
                                      569************************************9998644456777888888888888888887654 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   8.5e-07   0.00073      15      85 ..       3      75 ..       1      91 [. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.5e-07
                                      EEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.....T.ET-EEEEGCGHHHHHHT-SEEEE-SSS CS
                      Shikimate_DH 15 vlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.....kgeeiealkleelkellaeadvvisatas 85
                                      ++++GaG++++ +++  +++g ++vvv+ R+ e+a+e a+ +     +++ +e ++l++     ++ad +is t  
  gi|313126974|ref|YP_004037244.1|  3 IIIVGAGNIGTPLIEI-ATRGGNEVVVIERDTEKAEEAASTFdclvlNDDATEKQTLSDAG--ADRADALISTTDK 75
                                      79***********986.5677777****************982211123333344444433..6788888888765 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.7e-06    0.0015       2      65 ..       4      62 ..       3     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE-EEEE--S-HHHHHHHHHHHS CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeadetavvvlthdhklDaealeaal 65
                                      +i+Gag+++ +l+++a + g +v+v++ ++e a  e   ea++t+ +++ +d +++++ l+ a 
  gi|313126974|ref|YP_004037244.1|  4 IIVGAGNIGTPLIEIATRGGNEVVVIERDTEKA--E---EAASTFDCLVLNDDATEKQTLSDAG 62
                                      8**************************999743..2...2224666666666666666666654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2     2e-05     0.017       2      32 ..       3      33 ..       2      44 .. 0.91
   2 ?    1.2   0.0      0.67   5.7e+02      30      53 ..      65      88 ..      63     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                      +++vG+G+ig  l +++++ g++V v+er  
  gi|313126974|ref|YP_004037244.1|  3 IIIVGAGNIGTPLIEIATRGGNEVVVIERDT 33
                                      79**************************976 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.67
                                      SSSSSSTTSSHHHHHHHHHHHHHT CS
                         Pyr_redox 30 rsdkllrllDeeaskilqeklekn 53
                                      r+d l +  D++a +i+   l k+
  gi|313126974|ref|YP_004037244.1| 65 RADALISTTDKDATNIMVCLLAKE 88
                                      78889999*********9999776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   4.4e-06    0.0038       3      74 ..       8      87 ..       7     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.4e-06
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT.T-SEEEES---TCC....... CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealk.gadaVvsalggggk....... 73
                                       G++G  l++ + +  g ev+++ R++ek++e +++  + v+  d+t++++l +a +  ada +s++ ++++       
  gi|313126974|ref|YP_004037244.1|  8 AGNIGTPLIEIATRG-GNEVVVIERDTEKAEEAASTFDCLVLNDDATEKQTLSDAGAdRADALISTTDKDATnimvcll 85
                                      79*******988877.69*************999889999999************872569******877764555544 PP

                                      .H CS
                    NAD_binding_10 74 .d 74
                                       +
  gi|313126974|ref|YP_004037244.1| 86 aK 87
                                      32 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   3.8e-05     0.033       1      39 [.       1      39 [.       1      52 [. 0.91
   2 ?    1.4   0.0      0.24     2e+02     121     156 ..      71     104 ..      65     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdkl 39
                                      m i ++G+G +G +   +  + g+ev+++  d+ek ++ 
  gi|313126974|ref|YP_004037244.1|  1 MYIIIVGAGNIGTPLIEIATRGGNEVVVIERDTEKAEEA 39
                                      6799************9999999**********998765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.24
                                       S---TTHHHHCHHHHHHHHCSS-TTCEEEEE----- CS
                    UDPG_MGDP_dh_N 121 STvpvgtaeelvkkileeaskkkgvdfdvvsnPEfl 156
                                       ST+   +++ ++ ++l+++ +     ++vv+nPE +
  gi|313126974|ref|YP_004037244.1|  71 STTDKDATN-IMVCLLAKELQIP-NIVSVVHNPEHM 104
                                       566656665.5555555555444.6899******75 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.2e-06    0.0053       3      43 ..       4      52 ..       2      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.2e-06
                                      EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........E CS
                     NAD_binding_2  3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........a 43
                                       ++G G++G+++++  ++ g +v+v++r++ek+ee++++         a
  gi|313126974|ref|YP_004037244.1|  4 IIVGAGNIGTPLIEIATRGGNEVVVIERDTEKAEEAASTFdclvlnddA 52
                                      589********************************99885555544443 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     7e-06    0.0059       3      65 ..       3      68 ..       1     106 [. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7e-06
                                      EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS....HHHHHTCT..TESE CS
                      GFO_IDH_MocA  3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd....leelladp..eida 65
                                      + i+GaG+ig++ +  +  +  + evv ++++d+e+ae++a +f++ + +d     + l++    ++da
  gi|313126974|ref|YP_004037244.1|  3 IIIVGAGNIGTPLI-EIATR-GGNEVV-VIERDTEKAEEAASTFDCLVLNDdateKQTLSDAGadRADA 68
                                      78************.56555.445555.8****************997766555544444433333444 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00041      0.35       2      51 ..      11      59 ..      10      80 .. 0.70
   2 ?    4.2   0.0     0.047        40       4      42 ..      80     119 ..      77     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                                      HHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTESEEEETTTCHHHHHHH CS
                        ADH_zinc_N  2 vGlaavqlAkalGaeviavdsseeklelakk.lGadevinykeadlverik 51
                                      +G+ ++++A   G ev+++ ++ ek+e a++ + + ++ +    + ++ + 
  gi|313126974|ref|YP_004037244.1| 11 IGTPLIEIATRGGNEVVVIERDTEKAEEAAStFDCLVLNDD-A-TEKQTLS 59
                                      78899**********************99995665544444.2.2333333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.047
                                       HHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETT CS
                        ADH_zinc_N   4 laavqlAkalGa.eviavdsseeklelakklGadevinyk 42 
                                       ++++ lAk l + +++ v++++e   + +++G++   n++
  gi|313126974|ref|YP_004037244.1|  80 IMVCLLAKELQIpNIVSVVHNPEHMGIYRRIGVNTMENPQ 119
                                       68999**********************9999998877774 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   9.1e-06    0.0078      31      98 ..       3      72 ..       2      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.1e-06
                                      EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHHH.HHH-SEEEE- CS
                       AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeellaea.vkeadvvigt 98
                                      ++++G+G  G+  i++a++ g +V+v++ +++++e+  s +   +++  + ++++l++a + +ad +i+t
  gi|313126974|ref|YP_004037244.1|  3 IIIVGAGNIGTPLIEIATRGGNEVVVIERDTEKAEEAAStFDCLVLNDDATEKQTLSDAgADRADALIST 72
                                      689**********************************997776666666666666655427789999988 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.3e-05     0.011       3      74 ..       4      75 ..       3      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                      ESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE---G CS
                              NmrA  3 viGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtgf 74
                                      +i ++G++G  +++++++ g++v ++ Rdt++ + ++ ++    ++++d+ +k+ l+ a  + +d+ +s+t  
  gi|313126974|ref|YP_004037244.1|  4 IIVGAGNIGTPLIEIATRGGNEVVVIERDTEKAE-EAASTFDCLVLNDDATEKQTLSDAgADRADALISTTDK 75
                                      55667************************95533.333455566779******99999856779999998873 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.1e-05     0.026       1      76 [.       3      84 ..       3     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEEETT.CEEEEEECEEECCH...SCCCCS-ESEEE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrltseg.geeilrppealsae...ekselepidlvi 73
                                      i i+GaG iG+ l    ++ g++v++i r+  ++e+  ++ ++ +  ++ +e++ + ++ ++ +    +  ++++ +++
  gi|313126974|ref|YP_004037244.1|  3 IIIVGAGNIGTPLIEIATRGGNEVVVIERDTeKAEEaASTFDCLVLNDDaTEKQTLSDAGADRAdalISTTDKDATNIM 81
                                      89**********9988888************999995555555555555644444444433333477444556666666 PP

                                      E-S CS
                              ApbA 74 vtv 76
                                      v++
  gi|313126974|ref|YP_004037244.1| 82 VCL 84
                                      664 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.7e-05     0.023      20     113 ..       3      94 ..       1     100 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                       EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTT..HHHHHHTT---EEESSEEEES CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpa..kelLdelgikyedegdyvvvk 94 
                                       ++ivGaG  G t    +a++ + +v+++er              f+ +v++++a  k+ L++ g    d     + k
  gi|313126974|ref|YP_004037244.1|   3 IIIVGAGNIG-TPLIEIATRGGNEVVVIERDTEKA---EEAASTFDCLVLNDDAteKQTLSDAGADRADALISTTDK 75 
                                       8*********.5667889999*********99875...556789********9943468************99**** PP

                                       EHHHHHHHHHHHHHTSTTE CS
                              Thi4  95 daalftstllskvlqlanv 113
                                       da+ ++  ll+k lq++n+
  gi|313126974|ref|YP_004037244.1|  76 DATNIMVCLLAKELQIPNI 94 
                                       *****************97 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.039      39      79 ..       3      42 ..       1      59 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                      EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHT CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelg 79
                                      + i+G+G+IG+ ++++++  g +v++++r  +k e e++  
  gi|313126974|ref|YP_004037244.1|  3 IIIVGAGNIGTPLIEIATRGGNEVVVIERDTEKAE-EAAST 42
                                      569**************************988666.43333 PP

>> Peripla_BP_3  Periplasmic binding protein-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.6e-05     0.047      55     107 ..      34      98 ..      17     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                                       SSHHHHH...............HHH.HHCC.-SEEEEESSCCHHHHHHHHHCCTT--TTTTEEEE CS
                      Peripla_BP_3  55 aaaaaaraal...ll.......qal.klaa.lPtAviaasDelAlgvlqalreaglrvPedlsvi 107
                                       + a++a++      l       q l +++a +++A+i ++D  A  ++ +l +++l++P+ +sv+
  gi|313126974|ref|YP_004037244.1|  34 EKAEEAASTFdclVLnddatekQTLsDAGAdRADALISTTDKDATNIMVCLLAKELQIPNIVSVV 98 
                                       222222222233322444444455574444699******************************98 PP

>> TPALS  TIR- and PNP-associating SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1    0.0001     0.089      34      91 ..      17      75 ..      15      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                             TPALS 34 ellkaggnlVvpvdaeptredglpltfdwliw.eaikenlasrpadasgplavvvshhk 91
                                      e+  +ggn Vv+++ +  + ++ + tfd l+  +   e+ + ++a a++  a +    k
  gi|313126974|ref|YP_004037244.1| 17 EIATRGGNEVVVIERDTEKAEEAASTFDCLVLnDDATEKQTLSDAGADRADALISTTDK 75
                                      67899************************665144444444555555555444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1527.95
//
Query:       gi|313126975|ref|YP_004037245.1|  [L=553]
Description: trk-type k+ transporter, membrane component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.6e-109  364.6  13.7   8.5e-109  364.3  13.7    1.1  1  TrkH      Cation transport protein


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.3  13.7  4.7e-113  8.5e-109      63     492 ..     130     546 ..      50     549 .. 0.90

  Alignments for each domain:
  == domain 1  score: 364.3 bits;  conditional E-value: 4.7e-113
                              TrkH  63 f....ldalfeavsgltttglsvivveeslprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeel 135
                                       +    l+alfe++sg+t +gl+++v+e+slpr+++++r+ +q++Gg+gv+vl++++l+++g+gs++ly+sea    +
  gi|313126975|ref|YP_004037245.1| 130 YfrnpLHALFESMSGWTGSGLTMAVNEPSLPRAIQWWRSLIQWVGGVGVIVLTVSILARPGSGSYALYRSEA----R 202
                                       255569******************************************************************....* PP

                              TrkH 136 ggkelrslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplw....waffhsmSafnnlGfsltpn 208
                                       ++k ++s+ ++++++++++vg++++++ +l+v+i++++ y++ +      plw    +a++h+m++++++Gfs+t n
  gi|313126975|ref|YP_004037245.1| 203 EEKIHPSVVSTVRTVWKIFVGYTLVSVTVLFVAIRLSD-YGSSL------PLWeagwQALNHAMTGLSTGGFSVTNN 272
                                       **************************************.****9......7776666******************** PP

                              TrkH 209 SlasfnknivillvaiifiilGnigFpillrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwlllle 285
                                       S+ ++++ ++i++v+++++ lG+i+Fp+++ v+ +++++             +l dl+++++++ + +g+v+l +++
  gi|313126975|ref|YP_004037245.1| 273 SITTYDS-PLIEFVLLPVMSLGAIAFPVHYVVLRDRDFSE------------LLGDLQTQWLLIAFIVGVVVLGIQN 336
                                       *******.******************************99............789********************** PP

                              TrkH 286 lavlnvtdnil...filldegslvvksipkgsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpg 358
                                       ++ +++t+ ++   + +l  gsl+  ++ +++++++++Fq++s++++ GF++++++++++  k++l  +m+igg++g
  gi|313126975|ref|YP_004037245.1| 337 VVSIPFTTKAFeggANWLGIGSLI--NPVVADAFRDSTFQWISALSCtGFQSAPIGKWSAGGKLILSGAMVIGGAAG 411
                                       **********95555677667665..55557********************************************** PP

                              TrkH 359 StaggIrrtnvyeefslgkyeieqekepk.avskksidgkhlerqllvdlws....lflvlliilileglklsdvqe 430
                                       St+ggI+++++y++ + + +++++ + p  +v+++++dg++l+r  ++  +s    + l+++i+l++++l l + ++
  gi|313126975|ref|YP_004037245.1| 412 STVGGIKIIRAYTISRGIAWQFRRVFLPAnTVVSIQMDGRRLDRTEMEREFSeaaiVSLLWVILLVVSSLLLVNLAG 488
                                       *******************************************************99999***************** PP

                              TrkH 431 pdfsffdiLfevvSaygtvGLSlGaknaslsaqlttisklvlialmirGrlrglpvlldrai 492
                                       p+f+++d+Lfev+Sa+g+vGLS+G    ++ ++++++++ +++++m++Grl+++p+l++++ 
  gi|313126975|ref|YP_004037245.1| 489 PNFTYADALFEVASAQGNVGLSTG----ITGPTMNPLAEGMFLLNMWVGRLEIIPILVFARA 546
                                       ************************....******************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 4118.00
//
Query:       gi|313126976|ref|YP_004037246.1|  [L=245]
Description: 3-oxoacyl-ACP reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-68  229.4   1.3      5e-68  229.2   1.3    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    3.9e-58  196.1   1.4    4.6e-58  195.9   1.4    1.1  1  adh_short      short chain dehydrogenase
    1.8e-21   76.8   0.4    2.2e-21   76.6   0.4    1.1  1  KR             KR domain
     0.0045   16.5   0.1     0.0079   15.7   0.2    1.5  2  Epimerase      NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.032   14.1   0.6      0.099   12.5   0.3    1.9  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.098   12.0   0.3       0.78    9.0   0.0    2.2  2  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
       0.14   12.0   2.2       0.35   10.7   2.2    1.7  1  DFP            DNA / pantothenate metabolism flavoprotein
       0.15   11.5   0.5       0.56    9.7   0.0    2.0  3  DUF3372        Domain of unknown function (DUF3372)


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.2   1.3   2.2e-71     5e-68       1     232 [.      10     242 ..      10     244 .. 0.96

  Alignments for each domain:
  == domain 1  score: 229.2 bits;  conditional E-value: 2.2e-71
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea..kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilv 74 
                                       G  +gIGr+iA+++ eeG++vv+ +++ ++  +++ve++++++g+++ +++DVtd eqve++ e++ e fg++D+lv
  gi|313126976|ref|YP_004037246.1|  10 GSSNGIGRGIAERFGEEGCNVVVNYRSSKEaaEEAVETVEASGGSAIaVQADVTDIEQVEQMREAAHEAFGQVDVLV 86 
                                       5669**********************9999878999999999999956***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH..HCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp..lmkeggsivnlssvgaervvpnynaygaaKaale 149
                                       nnagi ++    f e+s ee+d +ldv l ++f++++ +    + +e+g+++n+ss+ ++ +  +++ y++aKa++ 
  gi|313126976|ref|YP_004037246.1|  87 NNAGINQD--VLFKEMSHEEWDVVLDVHLDGAFHCTQVFYDdlVDAEQGRLINISSIVGKGGNFGQANYATAKAGIF 161
                                       ********..*******************************9555677***************************** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqt 226
                                       ++tr+lA el+++g + N+v+pg+i T+++++++  ++++e++++ +plgrlgt++evae+++fLasd++s+itG++
  gi|313126976|ref|YP_004037246.1| 162 GFTRTLALELAREGTTANCVAPGFISTRMVEELP--EKVKERIRNDTPLGRLGTVKEVAEVVAFLASDRSSFITGEI 236
                                       *********************************9..9**************************************** PP

                                       EEESTT CS
                      adh_short_C2 227 lvvDgG 232
                                       + ++gG
  gi|313126976|ref|YP_004037246.1| 237 IDINGG 242
                                       *****9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.9   1.4   2.1e-61   4.6e-58       1     193 [.       4     197 ..       4     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.9 bits;  conditional E-value: 2.1e-61
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                       k+ +vtG s+GIGr ia+++ +eG++vvv + +s+e++ee+++ +++ g +a+a+q+Dvtd e+ve++ e+a + +g
  gi|313126976|ref|YP_004037246.1|   4 KTCVVTGSSNGIGRGIAERFGEEGCNVVVnYRSSKEAAEEAVETVEASGGSAIAVQADVTDIEQVEQMREAAHEAFG 80 
                                       6889*************************99999******************************************* PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       ++dvLvnNAGi++++ f+e+s eew+ v++v l g+f++t+ +++ ++++++Gr +n+sS++gk +++g+a Y+++K
  gi|313126976|ref|YP_004037246.1|  81 QVDVLVNNAGINQDVLFKEMSHEEWDVVLDVHLDGAFHCTQVFYDDLVDAEQGRLINISSIVGKGGNFGQANYATAK 157
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                       a++ g+tr+la ela++g + n+vaPG+++T m++el ek
  gi|313126976|ref|YP_004037246.1| 158 AGIFGFTRTLALELAREGTTANCVAPGFISTRMVEELPEK 197
                                       **********************************998776 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.4   9.9e-25   2.2e-21       2     172 ..       5     180 ..       4     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 9.9e-25
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78 
                                       t ++tG   g+G+ +a+   e+g + +v+  Rs  ++e++++ ++++ea+g +  +v+aDv+d ++ve++ e++++ 
  gi|313126976|ref|YP_004037246.1|   5 TCVVTGSSNGIGRGIAERFGEEGCN-VVVNYRS--SKEAAEEAVETVEASGGSAIAVQADVTDIEQVEQMREAAHEA 78 
                                       568********************85.6666688..6788899*********************************** PP

                                       SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SE....EEEEEEHHHHH--TT-HHHHH CS
                                KR  79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldf....fvlfSSiagllgsagqanYaa 151
                                       ++++   ++ Ag+ +d l++em+ e+++ vl   ++Ga +  +++ d+ +d     ++ +SSi g  g++gqanYa+
  gi|313126976|ref|YP_004037246.1|  79 FGQVDVLVNNAGINQDVLFKEMSHEEWDVVLDVHLDGAFHCTQVFYDDLVDAeqgrLINISSIVGKGGNFGQANYAT 155
                                       **********************************************96666444449******************** PP

                                       HHH....HHHHHHHHHHHHHHTEEE CS
                                KR 152 aNa....flDalaeyrrsqglpavs 172
                                       a a    f  +la + +++g+ a +
  gi|313126976|ref|YP_004037246.1| 156 AKAgifgFTRTLALELAREGTTANC 180
                                       *873333555555555555555555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   3.5e-06    0.0079       2      73 ..       7      90 ..       6     147 .. 0.83
   2 ?   -2.9   0.0       1.7   3.8e+03     212     237 ..     211     236 ..     184     239 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.5e-06
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HH...HHHHHHHHH..T-SEE CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrs...alerlfkee..qpdav 68
                                      +VtG +  iG+ +++++ e+g +v++  r s++ ++++ e++         v++d+td +   +++++ +e   q+d+ 
  gi|313126976|ref|YP_004037246.1|  7 VVTGSSNGIGRGIAERFGEEGCNVVVNYRSSKEAAEEAVETVeasggsaIAVQADVTDIEqveQMREAAHEAfgQVDVL 85
                                      7**********************99999997777777777779******999999999994444444444444577777 PP

                                      EE--S CS
                         Epimerase 69 ihlAa 73
                                      ++ A+
  gi|313126976|ref|YP_004037246.1| 86 VNNAG 90
                                      77776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                                       EEEHHHHHHHHHHHHHHHTT-STTEE CS
                         Epimerase 212 flyveDvaeaillvlehvdagdkgei 237
                                       ++ v++vae++ +++   ++  +gei
  gi|313126976|ref|YP_004037246.1| 211 LGTVKEVAEVVAFLASDRSSFITGEI 236
                                       55677888888777776555555555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   4.4e-05     0.099      10      49 ..      15      55 ..       6     103 .. 0.71
   2 ?   -1.2   0.0      0.72   1.6e+03      58      86 ..     193     221 ..     165     236 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                                      CHHHHHHHHHHTT-EEEEE-S.-HHHHHHHHHHHHHHHHCC CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdi.seealekalekiekslekl 49
                                      +G+gia+ f ++g++Vv+  + s+ea+e+a e++e+s  ++
  gi|313126976|ref|YP_004037246.1| 15 IGRGIAERFGEEGCNVVVNYRsSKEAAEEAVETVEASGGSA 55
                                      8***************9977747889999999999843332 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.72
                                       HHHCCCHHCEEEES-HHHHHC-SEEEE-S CS
                           3HCDH_N  58 eeveaalarisfttdleeavdadlviEav 86 
                                       e  e++ +ri+ +t l ++  ++ v E v
  gi|313126976|ref|YP_004037246.1| 193 ELPEKVKERIRNDTPLGRLGTVKEVAEVV 221
                                       44444444444444444444444444433 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00035      0.78      37      76 ..       4      43 ..       1      64 [. 0.85
   2 ?    0.7   0.1      0.13   2.9e+02      71     109 ..      73     113 ..      54     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00035
                                      -EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHH CS
                     THF_DHG_CYH_C 37 kkvvvvGrsnivgkplallLleknatVtvchsktkdlaei 76
                                      k++vv G sn +g+ +a  + e+++ V v  +++k+ ae 
  gi|313126976|ref|YP_004037246.1|  4 KTCVVTGSSNGIGRGIAERFGEEGCNVVVNYRSSKEAAEE 43
                                      899************************9999999887765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.13
                                       CCHHHHHCCSSEEEE-SS-TT-B.-GGGS-TT.-EEEE--- CS
                     THF_DHG_CYH_C  71 kdlaeitreadivvvavGkpeli.kaemvkeg.avviDvGi 109
                                       +  +e   + d++v  +G  + +  +em +e+  vv+Dv +
  gi|313126976|ref|YP_004037246.1|  73 EAAHEAFGQVDVLVNNAGINQDVlFKEMSHEEwDVVLDVHL 113
                                       55667778899999999987654144554433268888865 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.2   0.00016      0.35      46      92 ..      45      91 ..       7     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                      EEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT-SEEEE---S CS
                               DFP 46 VtlvsgpvsletpegvevvkvesaeemleaveealkeadivimaAAv 92
                                      V+ v ++   +   +++v+++e++e+m+ea++ea+ + d+++  A +
  gi|313126976|ref|YP_004037246.1| 45 VETVEASGGSAIAVQADVTDIEQVEQMREAAHEAFGQVDVLVNNAGI 91
                                      3444433222223467899************************9976 PP

>> DUF3372  Domain of unknown function (DUF3372)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.67   1.5e+03     107     146 ..      30      72 ..      23      84 .. 0.60
   2 ?   -1.6   0.2      0.73   1.6e+03     107     120 ..      84      97 ..      38     123 .. 0.62
   3 ?    9.7   0.0   0.00025      0.56      51      79 ..     201     229 ..     189     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.67
                           DUF3372 107 vvfNa..speeqsitvpelagkkleLhpvqaesad.evvkqas 146
                                       vv+N   s+e+ +  v+++++++ +   vqa+ +d e v+q++
  gi|313126976|ref|YP_004037246.1|  30 VVVNYrsSKEAAEEAVETVEASGGSAIAVQADVTDiEQVEQMR 72 
                                       5555410444455555667777777777777777766666555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.73
                           DUF3372 107 vvfNaspeeqsitv 120
                                       v++N +  +q +  
  gi|313126976|ref|YP_004037246.1|  84 VLVNNAGINQDVLF 97 
                                       44444333333333 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00025
                           DUF3372  51 riRksspLfrLrtaeevqkrvsFhntGpd 79 
                                       riR+++pL rL+t +ev + v+F  ++++
  gi|313126976|ref|YP_004037246.1| 201 RIRNDTPLGRLGTVKEVAEVVAFLASDRS 229
                                       8**********************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1589.34
//
Query:       gi|313126977|ref|YP_004037247.1|  [L=534]
Description: trk-type k+ transporter, membrane component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-70  237.4   7.7    3.2e-70  237.0   7.7    1.1  1  TrkH      Cation transport protein
  ------ inclusion threshold ------
      0.012   15.3   0.2      0.096   12.4   0.2    2.6  1  DUF5353   Family of unknown function (DUF5353)


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.0   7.7   3.6e-74   3.2e-70       7     490 ..      44     527 ..      37     533 .. 0.82

  Alignments for each domain:
  == domain 1  score: 237.0 bits;  conditional E-value: 3.6e-74
                              TrkH   7 kggiitialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslaf..............ldalfe 69 
                                        ++++t++lg++l  l  e++  ++++++f  v a++ a++v g+++ l+e   l+               ++alfe
  gi|313126977|ref|YP_004037247.1|  44 VTIAVTVVLGTALERL--EPDPDIRAREGFLMVAATWFAVTVVGAIPYLVEALGLPPvvpaihpdstlanpANALFE 118
                                       4455555566655555..677889***********************998444443345666666677888****** PP

                              TrkH  70 avsgltttglsvivveesl..prsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrsls 144
                                       ++sg+tttg++v  + +     r + ++r+ +q++Gg+g+vvla+++lp l  g+a+l  +ea+++  + k +++++
  gi|313126977|ref|YP_004037247.1| 119 SMSGFTTTGATVLGDISFQthTRGIMMWRQLTQWLGGMGIVVLAVAILPELSVGGAQLMDAEAPGPGIE-KLTPRIA 194
                                       ************97755444499******************************************9987.679**** PP

                              TrkH 145 elikilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivill 221
                                       +++++l+  y+g+++l + ll+ l +++      +       l++a+ h+++++ ++Gfs  + S++ f +    ++
  gi|313126977|ref|YP_004037247.1| 195 QTARALWGAYLGFTVLEATLLFGLGVLQI--DPNM------TLYNAVAHALTTMPTGGFSPEAKSIEAFSA--AAQW 261
                                       *****************999943322222..2334......788**************************9..78** PP

                              TrkH 222 vaiifiilGnigFpillrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdnilfi 298
                                       ++i+f+++ +++F ++  ++      i  d ++++  ++ +      ++ +l  + f++  +++     v ++  f 
  gi|313126977|ref|YP_004037247.1| 262 IIIPFMVAAGTNFALFWHALTGDPRHIFED-SEFRFYIGVI----ATITAVLSVLLFTGAGFVQA----VPTQSTFS 329
                                       ******************999888888665.4444333333....33333444444444444441....22333455 PP

                              TrkH 299 lldegslvvksipkg..srvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyee 372
                                         d+g+ +v++i+     +v++a+Fq+vs  t+ G++++d+ +++p  + +l+++m+igg++gSt g +++++ y++
  gi|313126977|ref|YP_004037247.1| 330 AMDLGQ-YVGDIAGQiePSVRQAVFQVVSIVTTtGYASMDFNAWSPVAQYILLFAMFIGGSAGSTGGAVKIVRWYVI 405
                                       566654.566665331169************999******************************************* PP

                              TrkH 373 fslgkyeieqekepkavskksidgkhlerqllvdlwslflvlliilileglkl...sdvqepdfsffdiLfevvSay 446
                                        +++++e+ +  +p+av++++++g+ l++++++ ++++ l++l+i+++ +  l    +  + ++s+++ + +v++++
  gi|313126977|ref|YP_004037247.1| 406 LKSIRRELFTTAHPDAVRPVRLGGRALDERAIRGIYAFTLLYLVIFFVASGLLfidASRYGQSLSVLETMSAVAATL 482
                                       ******************************************999998877663332334569************** PP

                              TrkH 447 gtvGLSlGa.knaslsaqlttisklvlialmirGrlrglpvlldr 490
                                       g+vG+++G    + +   +++++kl +++lm++Grl++lpvl++ 
  gi|313126977|ref|YP_004037247.1| 483 GNVGPGFGTvGPMGSYLAFSDAGKLFMVVLMWIGRLEILPVLVLL 527
                                       ********7799******************************975 PP

>> DUF5353  Family of unknown function (DUF5353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.1e-05     0.096      14      51 ..     124     161 ..     111     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                           DUF5353  14 vavlsagLGfgAYrkyarGeLtwkvvglwagavGafav 51 
                                        +  +++LG   ++ ++rG + w+ +  w g +G++ +
  gi|313126977|ref|YP_004037247.1| 124 TTTGATVLGDISFQTHTRGIMMWRQLTQWLGGMGIVVL 161
                                       4667889***************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3506.90
//
Query:       gi|313126978|ref|YP_004037248.1|  [L=445]
Description: k+ transporter, NAD-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-51  173.6  11.1    4.9e-28   97.7   1.3    3.1  3  TrkA_N           TrkA-N domain
    6.8e-27   93.1  10.2    6.8e-15   54.7   0.1    3.5  4  TrkA_C           TrkA-C domain
    2.4e-12   47.2   2.5    7.7e-06   26.3   0.6    2.7  2  NAD_binding_7    Putative NAD(P)-binding
    2.6e-12   47.0   2.0    1.1e-05   25.5   0.2    3.0  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    3.1e-10   40.2   6.5    0.00015   21.7   0.2    2.7  2  NAD_binding_10   NAD(P)H-binding
    1.8e-09   37.9   1.1    0.00035   20.8   0.2    2.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      1e-07   32.5   3.2    8.8e-05   23.0   0.2    3.9  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.4e-07   31.1   0.1     0.0032   16.8   0.0    2.4  2  FAD_binding_3    FAD binding domain
    1.1e-06   29.2   0.8     0.0021   18.6   0.1    2.6  2  XdhC_C           XdhC Rossmann domain
    1.3e-05   24.8   0.1    0.00017   21.2   0.0    2.3  2  ApbA             Ketopantoate reductase PanE/ApbA
    2.4e-05   24.1   0.5     0.0012   18.5   0.1    2.7  2  DAO              FAD dependent oxidoreductase
    2.8e-05   24.6   0.4       0.47   11.0   0.0    3.1  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00011   21.6   2.8       0.16   11.2   0.2    2.4  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00016   21.4   0.1    0.00062   19.4   0.2    2.0  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00016   21.6   0.5      0.022   14.7   0.2    2.4  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00025   20.4   1.2       0.35   10.1   1.0    2.4  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0005   20.3   0.3      0.087   13.0   0.1    2.7  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00095   19.2   0.0      0.078   13.0   0.0    2.6  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0015   18.1   0.1        0.1   12.0   0.0    2.3  2  adh_short        short chain dehydrogenase
     0.0015   19.3   0.2      0.081   13.8   0.1    2.7  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0026   18.2   2.6       0.28   11.6   0.1    2.8  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0032   17.7   0.1       0.48   10.7   0.0    2.8  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
     0.0063   15.9   0.0        1.5    8.1   0.0    2.5  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0071   16.4   0.0        0.4   10.8   0.0    3.2  3  DUF2325          Uncharacterized protein conserved in bacteri
  ------ inclusion threshold ------
      0.013   15.0   0.6       0.22   10.9   0.1    2.2  2  Epimerase        NAD dependent epimerase/dehydratase family
      0.022   14.0   0.1        2.5    7.3   0.0    2.4  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
      0.023   14.6   2.2        1.2    9.0   0.1    2.9  2  Rossmann-like    Rossmann-like domain
      0.034   13.5   0.2       0.11   11.8   0.0    1.9  2  HEM4             Uroporphyrinogen-III synthase HemD
      0.039   13.9   0.0         11    6.0   0.0    2.6  2  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion
      0.044   14.3   0.8       0.34   11.4   0.0    2.7  3  YflT             Heat induced stress protein YflT
      0.064   12.8   0.1       0.17   11.4   0.0    1.8  1  DUF1188          Protein of unknown function (DUF1188)
      0.079   11.7   0.3       0.38    9.4   0.1    2.0  2  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
       0.13   12.9   0.6        1.9    9.2   0.3    2.7  2  PglD_N           PglD N-terminal domain
       0.17   11.2   5.1        4.2    6.7   0.4    3.4  4  ThiF             ThiF family


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   1.3   9.2e-31   4.9e-28       1     107 [.       3     108 ..       3     121 .. 0.90
   2 !   81.1   0.2   1.4e-25   7.2e-23       1     116 []     230     346 ..     230     346 .. 0.93
   3 ?    0.1   0.2       1.7   9.2e+02      11      38 ..     352     380 ..     348     396 .. 0.68

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 9.2e-31
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddean 76 
                                       ++i+G+G+vG+s+a  L ++++ vvvid+d+ervee+     +  + gd+t  ++Leeagi++ad+via t++de+n
  gi|313126978|ref|YP_004037248.1|   3 VVIVGAGQVGSSIAADLDDAHE-VVVIDRDPERVEEMNYSLdVLGISGDGTAVSTLEEAGIADADMVIASTDNDETN 78 
                                       79*****************995.**************9999899********************************* PP

                                       HHHHHHHHHHTSSSEEEEEESSGGGHHHHHH CS
                            TrkA_N  77 ilavllakelnpkkkiiaraqdpehaellkk 107
                                       i+++ +ak + + + +iar+++ e+ +  ++
  gi|313126978|ref|YP_004037248.1|  79 IVVCSTAKAISD-AFTIARVKNTEYLRTWQR 108
                                       ********8766.89**********877766 PP

  == domain 2  score: 81.1 bits;  conditional E-value: 1.4e-25
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSE..EEES-TTSHHHHHHTTGGGESEEEE-SSSHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreegle..vvvgdatdeevLeeagiekadaviaatgddea 75 
                                       ++i+G ++vG+++a+ L+e+g +  +i++d er+++l+e+  +  v+  datd e+Le+ +i +ad+v+aa+++de+
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERGFRPRLIERDGERARKLAEQLPDtvVMESDATDMEFLEREHIGDADLVVAALESDEK 306
                                       79*****************774589****************5544778***************************** PP

                                       HHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  76 nilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       n+l++lla  l    +++a +++ e+++l++ +g+dv +sp
  gi|313126978|ref|YP_004037248.1| 307 NLLVSLLAARLGV-ERTVAVIDTTEYVDLFEAVGVDVGVSP 346
                                       ********98887.69********************99987 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.7
                                       HHHHHHHHHTT.EEEEEEESSHHHHHHHH CS
                            TrkA_N  11 rslaeeLsegg.kdvvvidkdeerveelr 38 
                                       +++++  +egg +++ +i++d++ v e++
  gi|313126978|ref|YP_004037248.1| 352 EEITRFTREGGaENIALIESDKAEVLEIE 380
                                       45555556633578999999998887766 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       9.2   4.8e+03      29      56 ..      44      71 ..      34      77 .. 0.64
   2 !   54.7   0.1   1.3e-17   6.8e-15       1      67 [.     151     216 ..     151     219 .. 0.94
   3 ?   -1.1   0.1       3.3   1.7e+03      22      51 ..     246     279 ..     230     280 .. 0.75
   4 !   42.7   1.4   6.7e-14   3.6e-11       1      60 [.     376     436 ..     376     444 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.2
                                      EEEEE-T-EEES--TT-B--TT-EEEEE CS
                            TrkA_C 29 vvairRggeliipsgdtvLeeGDvllvv 56
                                      v++i  +g  ++  ++  +   D ++  
  gi|313126978|ref|YP_004037248.1| 44 VLGISGDGTAVSTLEEAGIADADMVIAS 71
                                      6677666666666666666666666655 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 1.3e-17
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       ++e+ v+++sp+ + t++e    +    + +a+ R+g ++ip+g tv+++GD+++v+g+p +++e+++
  gi|313126978|ref|YP_004037248.1| 151 MAEFQVAENSPVSNVTIRE--ADRFeALTFAAVLRNGAVEIPRGQTVIQPGDRVVVIGTPRSVQEFAR 216
                                       689****************..666679**************************************987 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.3
                                       HHHHS-EEEEEE-T....-EEES--TT-B--TT- CS
                            TrkA_C  22 lrargvlvvairRg....geliipsgdtvLeeGD 51 
                                       l++rg++   i R+     +l    +dtv +e D
  gi|313126978|ref|YP_004037248.1| 246 LEERGFRPRLIERDgeraRKLAEQLPDTVVMESD 279
                                       4445999999987767667777777888877766 PP

  == domain 4  score: 42.7 bits;  conditional E-value: 6.7e-14
                                       CEEEEEE--GGGTTSBHHHHT..HHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkeln..lrargvlvvairRggeliipsgdtvLeeGDvllvvgsps 60 
                                       + e++v+ +s l+G+ ++e+   l++ g+ v ai R+ e+i p+g+tv e GD+++++++ s
  gi|313126978|ref|YP_004037248.1| 376 VLEIEVDDDSILAGREIRESVpeLPD-GIVVGAITRNREFITPRGNTVVEVGDHVVLFVDAS 436
                                       579****************5446777.******************************99877 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.6   1.5e-08   7.7e-06       9      84 ..       2      87 ..       1     101 [. 0.75
   2 !   19.9   0.1   1.4e-06   0.00075       8      97 ..     228     331 ..     225     335 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.5e-08
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekd...........legadlviaatddrelne 76
                                      +v++vG+G+v+ + +  l +a  +v+v++ + ++  e +++l    +++d           +++ad+via td++e n 
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLDDA-HEVVVIDRDPERVEEMNYSLDVLGISGDgtavstleeagIADADMVIASTDNDETNI 79
                                      79*****************99.9******99644444444443333333333333444445****************** PP

                     NAD_binding_7 77 riaeaaka 84
                                       ++ +aka
  gi|313126978|ref|YP_004037248.1| 80 VVCSTAKA 87
                                      **999986 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.4e-06
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele......elvk....laeeel..ekdlegadlviaatddr 72 
                                       ++v++vGg ev+++ +r l e g +  ++  + +++ +      ++v     +++ e+  ++++ +adlv+aa + +
  gi|313126978|ref|YP_004037248.1| 228 EEVVIVGGSEVGYHVARLLEERGFRPRLIERDGERARKlaeqlpDTVVmesdATDMEFleREHIGDADLVVAALESD 304
                                       78****************************996222223333333333121133333465578************** PP

                     NAD_binding_7  73 elneriaeaakarri..lvnvadkpel 97 
                                       e n  +  +a + ++   v v d+ e 
  gi|313126978|ref|YP_004037248.1| 305 EKNLLVSLLAARLGVerTVAVIDTTEY 331
                                       *99998888876665446777776665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2   2.2e-08   1.1e-05      14      93 ..       2      83 ..       1      97 [. 0.77
   2 !   19.9   0.0   1.2e-06   0.00061      12      88 ..     227     306 ..     213     329 .. 0.81
   3 ?   -2.0   0.0       6.5   3.4e+03     101     120 ..     425     444 ..     372     445 .] 0.66

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.2e-08
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCGHHHH.HHT-SEEEE-SSSS.S- CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealkleelkel.laeadvvisatase.ep 88
                                      +v+++GaG++++ +a  L    +++vvv+ R+ er++e+  +l   g +   ++++ l+e+ +a+ad+vi++t    ++
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLD--DAHEVVVIDRDPERVEEMNYSLdvLGISGDGTAVSTLEEAgIADADMVIASTDNDeTN 78
                                      79****************8..7889**************99882223334456677776544***********865145 PP

                                      SB-HH CS
                      Shikimate_DH 89 ileke 93
                                      i+  +
  gi|313126978|ref|YP_004037248.1| 79 IVVCS 83
                                      55554 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.2e-06
                                       T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-E...EEEGCGHH.HHHHT-SEEEE-SS CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeie...alkleelk.ellaeadvvisata 84 
                                        ++v+++G  e++  va+ L ++g++    + R+ era++lae+l ++ +    a+++e l+ e++ +ad+v++a  
  gi|313126978|ref|YP_004037248.1| 227 AEEVVIVGGSEVGYHVARLLEERGFR-PRLIERDGERARKLAEQLPDTVVMesdATDMEFLErEHIGDADLVVAALE 302
                                       578**********************9.67789*************77655400155555554489**********99 PP

                                       SSS- CS
                      Shikimate_DH  85 seep 88 
                                       s e 
  gi|313126978|ref|YP_004037248.1| 303 SDEK 306
                                       9875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.5
                                       H.S..EEEEE--SS-SB-TT CS
                      Shikimate_DH 101 krkkplllvDiavPRdvepe 120
                                         ++ +l+vD +v  dv+p+
  gi|313126978|ref|YP_004037248.1| 425 VGDHVVLFVDASVAGDVTPQ 444
                                       33456789999998888875 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.5   3.5e-07   0.00018       3      91 ..       8      98 ..       7     109 .. 0.86
   2 !   21.7   0.2   2.8e-07   0.00015       5      80 ..     237     324 ..     234     341 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.5e-07
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---TCC..HHHH. CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggggk..deeg. 77
                                       G+vG+ +++ l ++  hev+++ R+pe+++e+  +  +  ++gd t v++l+ea +++ad V++++ ++++     + 
  gi|313126978|ref|YP_004037248.1|  8 AGQVGSSIAADLDDA--HEVVVIDRDPERVEEMNYSLDVLGISGDGTAVSTLEEAgIADADMVIASTDNDETniV--Vc 82
                                      7*********99877..9**************99888888899**********9978**********88777340..25 PP

                                      ..HHHHHHHHHHCT-- CS
                    NAD_binding_10 78 ..aknivdaakeagvk 91
                                        ak+i da   a vk
  gi|313126978|ref|YP_004037248.1| 83 stAKAISDAFTIARVK 98
                                      5589999998888887 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.8e-07
                                       HHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT.TTCEEEE--TT-CCHHH.HHHTT-SEEEES---TCC...... CS
                    NAD_binding_10   5 kvGrllvkellargghevtalvRnpeklaeleae.eglevvegdvtdvedla.ealkgadaVvsalggggk...... 73 
                                        vG ++++ l +r g++ +++ R+ e++ +l+++ + + v+e d+td e l+ e++ +ad Vv+al +++k      
  gi|313126978|ref|YP_004037248.1| 237 EVGYHVARLLEER-GFRPRLIERDGERARKLAEQlPDTVVMESDATDMEFLErEHIGDADLVVAALESDEKnllvsl 312
                                       5899999988888.6***************997779999**********99626899*********98777343333 PP

                                       .HHHH......HHH CS
                    NAD_binding_10  74 .deeg......akn 80 
                                           +      +++
  gi|313126978|ref|YP_004037248.1| 313 lA--ArlgverTVA 324
                                       21..0223333333 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   6.7e-07   0.00035       1      74 [.       3      69 ..       3      80 .. 0.79
   2 !   14.5   0.0     6e-05     0.032       1      98 [.     230     327 ..     230     338 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.7e-07
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEE CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvv 74
                                      v+i+GaG vG+++a +l + ++    ++v+dr+ e++e++     + ++  i+ d   ++  L+++ ++++d+v+
  gi|313126978|ref|YP_004037248.1|  3 VVIVGAGQVGSSIAADLDDAHE----VVVIDRDPERVEEMN---YSLDVLGISGDGTAVST-LEEAgIADADMVI 69
                                      89*****************995....6*********99887...56666666666666666.5555577777776 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6e-05
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       v+i+G+  vG  va+ll++++ +  +  +++r+ e++++la++   ++   ++ da + e +  +++ ++dlvv ++
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERG-F--RPRLIERDGERARKLAEQ--LPDTVVMESDATDMEFLEREHIGDADLVVAAL 301
                                       79*****************98.6..89*************996..588888999999999844566********988 PP

                                       SGG.....GHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  78 ppi.....ssldvlkaCietgvhyvd 98 
                                        +       sl  +++ +e+ v+++d
  gi|313126978|ref|YP_004037248.1| 302 ESDeknllVSLLAARLGVERTVAVID 327
                                       66544444455555555566666666 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   1.7e-07   8.8e-05       1      70 [.       2      73 ..       2      94 .. 0.76
   2 ?   -0.1   0.0       2.8   1.5e+03      54      87 ..     191     224 ..     151     227 .. 0.66
   3 ?    7.0   0.0     0.016       8.4       2      49 ..     230     279 ..     229     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.7e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........-EEECECHHHH.HHH-SEEEE-S- CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........vkvtavdneea.aeeadvvvlavk 70
                                      ++ i+GaG++g+++a  l  a    he+vv+ +r+pe++ee+  +l           v++   eea +++ad+v+ +  
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLDDA----HEVVVI-DRDPERVEEMNYSLDvlgisgdgTAVST--LEEAgIADADMVIASTD 73
                                      57899***********99888....9***99.**********999988888876433444..33331346888887765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.8
                                       CHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHT CS
                     F420_oxidored  54 dneeaaeeadvvvlavkpedveevlselakdalk 87 
                                         +++++  d vv+   p+ v+e+++++a+d++ 
  gi|313126978|ref|YP_004037248.1| 191 RGQTVIQPGDRVVVIGTPRSVQEFARSVAPDESP 224
                                       4566777888888888888888888888776665 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.016
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-E CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vk 49 
                                       + i+G+ ++g  +a+ l ++g++p   +++ +r+ e+a++lae+l        +
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERGFRP---RLI-ERDGERARKLAEQLPdtvvmeSD 279
                                       6788999**************544...445.8************9955544422 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00015     0.081       3      40 ..       2      38 ..       1     113 [. 0.75
   2 !   16.8   0.0     6e-06    0.0032       3      37 ..     229     263 ..     227     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp 40
                                       V+IVGaG +G + a  L  a  +vv++++  ++v++ 
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLDDA-HEVVVIDRDPERVEEM 38
                                      69*******************.9*******99988765 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37 
                                       +V+IVG++ +G   a+lL e+G r +l+e+  +++
  gi|313126978|ref|YP_004037248.1| 229 EVVIVGGSEVGYHVARLLEERGFRPRLIERDGERA 263
                                       79****************************98776 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0041       2.2       1      66 [.       3      87 ..       3     135 .. 0.72
   2 !   18.6   0.1   3.9e-06    0.0021       1     110 [.     230     343 ..     230     355 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0041
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG....................-GGG-TT-SE........-EEEE-- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefa....................tkerfpeade........tavvvlt 51
                                      +vi+Gag+v+ ++a+ +  +  +v+v+d ++e                      t                 ++v++ t
  gi|313126978|ref|YP_004037248.1|  3 VVIVGAGQVGSSIAADLDDA-HEVVVIDRDPERVeemnysldvlgisgdgtavsT--------LeeagiadaDMVIAST 72
                                      69**********99998887.5999****99744355555555555554443332........0444455557777777 PP

                                      S-HHHHHHHHHHHSS CS
                            XdhC_C 52 hdhklDaealeaalr 66
                                       + ++   ++++a +
  gi|313126978|ref|YP_004037248.1| 73 DNDETNIVVCSTAKA 87
                                      777777777776654 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.9e-06
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG..-GGG-TT-SE.......-EEEE--S-HHHHHHHHHHHSSS- CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa..tkerfpeade.......tavvvlthdhklDaealeaalrkk 68 
                                       +vi+G+++v+ ++arl+++ gfr  +++ + e a   +e++p+  +       t +  l ++h  Da+++ aal+++
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERGFRPRLIERDGERArkLAEQLPD--TvvmesdaTDMEFLEREHIGDADLVVAALESD 304
                                       69**************************999766444556663..1558888899999****************966 PP

                                       -S..EEEESS-HHHHHHHCTTS.--.......TTEESS-S--S- CS
                            XdhC_C  69 aa..yigllGSrkkaarrlerlraaglseeelarlhaPiGldig 110
                                        +   + ll++r   +r+++ +     + +e   l   +G+d+g
  gi|313126978|ref|YP_004037248.1| 305 EKnlLVSLLAARLGVERTVAVI-----DTTEYVDLFEAVGVDVG 343
                                       4345999999999888887777.....33444445555555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.3e-07   0.00017       1      38 [.       3      40 ..       3     104 .. 0.68
   2 ?    1.1   0.0      0.53   2.8e+02       1      38 [.     230     268 ..     230     326 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.3e-07
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkk 38
                                      ++i+GaG +Gs +aa L   +++v++i+r++ r+e+++ 
  gi|313126978|ref|YP_004037248.1|  3 VVIVGAGQVGSSIAADL-DDAHEVVVIDRDPeRVEEMNY 40
                                      68***************.5599*********88877543 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.53
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHH CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkk 38 
                                       ++i+G   +G  +a  L + g  + li r+  r+ +l +
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERGFRPRLIERDGeRARKLAE 268
                                       578888889999999998899999999999855554433 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.2e-06    0.0012       1      30 [.       2      32 ..       2      37 .. 0.89
   2 ?    2.8   0.0      0.14        72       2      29 ..     230     259 ..     229     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                                      EEEEECTSHHHHHHHHHHHHTT.EEEEESSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg.Vtllekgd 30
                                      +vvi+G+G +G+s+A +L  ++ V+++++++
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLDDAHeVVVIDRDP 32
                                      59****************86567******95 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekg 29 
                                       vvi+GG  +G  +A+ L +rg    l+e++
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERGfrPRLIERD 259
                                       9*******************9999999998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0016      0.84       1      33 [.       2      33 ..       2      41 .. 0.88
   2 !   11.0   0.0    0.0009      0.47       2      56 ..     230     284 ..     229     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdk 33
                                      +vv+vG+G +g   A+ l +   +V v++r ++
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLDDAH-EVVVIDRDPE 33
                                      79****************9966.9999999876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0009
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngie 56 
                                       vv+vGg+ +g  +A  l e g +  ++er  +  r+l e++ + +  +  +  +e
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERGFRPRLIERDGERARKLAEQLPDTVVMESDATDME 284
                                       9****************************99888777777777666665555555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2   0.00043      0.23     144     181 ..       2      38 ..       1      89 [. 0.82
   2 !   11.2   0.2    0.0003      0.16     132     238 ..     210     320 ..     175     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllral 181
                                       r+v+vG+G +G+ +Aa l ++ +ev+++++ ++ ++++
  gi|313126978|ref|YP_004037248.1|   2 RVVIVGAGQVGSSIAADLDDA-HEVVVIDRDPERVEEM 38 
                                       688999999999999888888.7788888877766554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0003
                                       HHHHHCCSS-T.......SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEE CS
                                       xxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 132 saealklkllp.......krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevk 201
                                       s++++ +   p       + +v+vGg+ +G  +A  l + g +  l+e+  +  r+l ++l +++  +  + + e+ 
  gi|313126978|ref|YP_004037248.1| 210 SVQEFARSVAPdespgtaEEVVIVGGSEVGYHVARLLEERGFRPRLIERDGERARKLAEQLPDTVVMESDATDMEFL 286
                                       55555555555666677799999999999999999999999999999998888899999999998888888888888 PP

                                       ESCEEEEEEETTE.EEEEEETTSCEEEESEEEE-S-EE CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 202 lgtsvkeidgnge.klevvledgeeidadlvvvavGvr 238
                                        ++ +    g+ +  +   ++d++ + ++l+    Gv+
  gi|313126978|ref|YP_004037248.1| 287 EREHI----GDADlVVAALESDEKNLLVSLLAARLGVE 320
                                       66666....44442344777777777777777666666 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   1.2e-06   0.00062       1      41 [.       1      40 [.       1      51 [. 0.93

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-06
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCT CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklns 41
                                      m+++++G+G vG   aa l    hev+++D d e+v+++n 
  gi|313126978|ref|YP_004037248.1|  1 MRVVIVGAGQVGSSIAADLDD-AHEVVVIDRDPERVEEMNY 40
                                      89***************9975.7****************95 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   4.1e-05     0.022       2      40 ..       3      40 ..       2      72 .. 0.89
   2 ?    4.9   0.0     0.042        22       2      49 ..     230     277 ..     229     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                                      v ++GaG++G++iaa +    +eVv++d+++e++e+ + 
  gi|313126978|ref|YP_004037248.1|  3 VVIVGAGQVGSSIAADLD-DAHEVVVIDRDPERVEEMNY 40
                                      89************9875.569***********998765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.042
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCC CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiekslekl 49 
                                       v ++G   +G  +a ++ ++g++ +l++++ e+++k +e++ +++   
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERGFRPRLIERDGERARKLAEQLPDTVVME 277
                                       899*********************************999998866554 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   1.0   0.00067      0.35      30      97 ..       2      70 ..       1      83 [. 0.70
   2 !    8.0   0.0    0.0029       1.5      29      99 ..     228     301 ..     213     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00067
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHH.HHHHHH-SEEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeell.aeavkeadvvig 97
                                      +v+++G+G +G + +a       +V+v+D +p+r e+++  l    ++      ++l +  +++ad+vi 
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAAD-LDDAHEVVVIDRDPERVEEMNYsLDVLGISGDGTAVSTLeEAGIADADMVIA 70
                                      79*********865554.445678999**********998543333333333333330345777777776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0029
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE.HCHHHHHH.HHHHHH-SEEEE-- CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev.lksqeell.aeavkeadvvigtv 99 
                                        +v+++Gg  +G + ++   + g + ++++ + +r+++l + l  ++v    + ++e l +e++ +ad+v+ + 
  gi|313126978|ref|YP_004037248.1| 228 EEVVIVGGSEVGYHVARLLEERGFRPRLIERDGERARKLAEqLPDTVVMEsDATDMEFLeREHIGDADLVVAAL 301
                                       489************************************997777755442333334333689********986 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   0.00016     0.087       2     102 ..       3     110 ..       2     118 .. 0.72
   2 ?    4.7   0.0     0.057        30       3      66 ..     231     304 ..     229     353 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........EEE-SSHHHH.HHHCSEEEE-SSSHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........akaaesieel.vasldvvitmvkagkav 69 
                                       + ++G G+ Gs++a  l +  ++v+v++r++e+vee+  +          +a++++ee+ +a++d+vi    + +++
  gi|313126978|ref|YP_004037248.1|   3 VVIVGAGQVGSSIAADLDD-AHEVVVIDRDPERVEEMNYSLdvlgisgdGTAVSTLEEAgIADADMVIASTDN-DET 77 
                                       5689************976.599*************9877567777777666667665436677888887554.556 PP

                                       HHHHHSHCCC--TT-EEEE-S---HHHHHHHHH CS
                     NAD_binding_2  70 deviegllealkkgdilidgstsspedtrelak 102
                                       + v+ + ++a++   ++  + ++++  t +++k
  gi|313126978|ref|YP_004037248.1|  78 NIVVCSTAKAISDAFTIARVKNTEYLRTWQRSK 110
                                       666666666666666666666666666666655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.057
                                       EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....EEE-SSHHHHHHHC.....SEEEE-SSSH CS
                     NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....akaaesieelvasl.....dvvitmvkag 66 
                                        ++G  + G + a+ l+++g++  +++r+ e++++l+++      ++  ++  e++++      d+v+  ++++
  gi|313126978|ref|YP_004037248.1| 231 VIVGGSEVGYHVARLLEERGFRPRLIERDGERARKLAEQLpdtvvMESDATDMEFLEREhigdaDLVVAALESD 304
                                       57899999*****************************9966655433333333444333444446666666654 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00015     0.078       2      40 ..       3      40 ..       2      46 .. 0.91
   2 ?    3.4   0.0      0.13        70       2      41 ..     230     269 ..     229     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHH CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeine 40
                                      + ++GaG+ G+++A+ l ++ hev+++ r++e +ee+n 
  gi|313126978|ref|YP_004037248.1|  3 VVIVGAGQVGSSIAADLDDA-HEVVVIDRDPERVEEMNY 40
                                      889**************875.6***************95 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeinee 41 
                                       + ++G+   G  +A++l+e+g + rl+ r+ e ++++ e+
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERGFRPRLIERDGERARKLAEQ 269
                                       8899999**********************99888888766 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.072        38       3      45 ..       3      43 ..       1      63 [. 0.81
   2 !   12.0   0.0    0.0002       0.1       3      65 ..     230     287 ..     228     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.072
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelk 45
                                      v+++Ga++ +G  ia  l  +  +vvv+dr +e++ee+  +l 
  gi|313126978|ref|YP_004037248.1|  3 VVIVGAGQ-VGSSIAADLDDA-HEVVVIDRDPERVEEMNYSLD 43
                                      78899886.9*******9888.89999********99877766 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0002
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHH CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreeve 65 
                                       v+++G+s  +G+ +a+ l ++G++  +++r  e+++++a++l +     ++++ D td+e +e
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGS-EVGYHVARLLEERGFRPRLIERDGERARKLAEQLPD----TVVMESDATDMEFLE 287
                                       7888888.59*********************************8....689999999988765 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   0.00015     0.081       1      72 [.       1      74 [.       1      93 [. 0.68
   2 ?    2.7   0.0      0.41   2.2e+02       3      76 ..     230     307 ..     229     325 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00015
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE....EESSHHHHHTCT..TESEEEE-S-G CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve....aysdleelladp..eidavivatpn 72
                                      +rv+i+GaG++gs  ++ l ++   +evv ++d+d+er e++  s++v       + ++ l +    ++d+vi  t n
  gi|313126978|ref|YP_004037248.1|  1 MRVVIVGAGQVGSSIAADLDDA---HEVV-VIDRDPERVEEMNYSLDVLgisgDGTAVSTLEEAGiaDADMVIASTDN 74
                                      69************99555555...5666.9**********9666665532252222444444444467777777666 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.41
                                       EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.....EESSHHHHHTCT..TESEEEE-S-G CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.....aysdleelladp..eidavivatpn 72 
                                       v+i+G+  +g++ +  l e+ r+ +   l+++d era+++ae++          +d+e l ++   ++d+v+ a  +
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVA-RLLEE-RGFRPR-LIERDGERARKLAEQLPDTvvmesDATDMEFLEREHigDADLVVAALES 303
                                       78999999998888.55555.566555.8899999999996665433211144444555555556677777777766 PP

                                       GGHH CS
                      GFO_IDH_MocA  73 gthe 76 
                                       ++ +
  gi|313126978|ref|YP_004037248.1| 304 DEKN 307
                                       6554 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.5     0.042        22       1      83 [.       2      81 ..       2      94 .. 0.64
   2 !   11.6   0.1   0.00052      0.28       2      98 ..     230     330 ..     229     355 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.042
                                      EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSG...GGTTTECEBEEE.GGGGGCTT-SEEEE-S CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavk...aleegkdlkved.vdeeelkevdivflal 74
                                      +v ivG  G vG+ ++  L++ h     vv++ ++    ++++e++     l    d +  +  +e+ ++++d+v+ ++
  gi|313126978|ref|YP_004037248.1|  2 RVVIVG-AGQVGSSIAADLDDaHE----VVVIDRDP---ERVEEMNYsldVLGISGDGTAVStLEEAGIADADMVIAST 72
                                      689999.79999999999998333....33344444...3333333333333333444333337788899999999999 PP

                                      CHHHHHHHH CS
                    Semialdhyde_dh 75 pagvskela 83
                                      +++ ++ ++
  gi|313126978|ref|YP_004037248.1| 73 DNDETNIVV 81
                                      999887666 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00052
                                       EEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSG....GGTTTECEBEEEGGGGGCTT-SEEEE- CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavk....aleegkdlkvedvdeeelkevdivfla 73 
                                       v ivG+   vG  ++rlLee  +   l   + ++ +  +klae  +    + ++ +d+++ +   e + ++d+v+ a
  gi|313126978|ref|YP_004037248.1| 230 VVIVGG-SEVGYHVARLLEErGFRPRL---IERDGERARKLAEQLPdtvvMESDATDMEFLE--REHIGDADLVVAA 300
                                       889994.57999999999996443333...33333445555555556555889999999988..999********** PP

                                       SCHHHHHHHHHHH.....HHTTSEEEESSS CS
                    Semialdhyde_dh  74 lpagvskelapkl.....aeagvkviDlss 98 
                                       l+++  + l+  l     +e+ v viD + 
  gi|313126978|ref|YP_004037248.1| 301 LESDEKNLLVSLLaarlgVERTVAVIDTTE 330
                                       ****99999988865555666668998875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00091      0.48       1      29 [.       5      32 ..       5      33 .. 0.93
   2 ?    3.8   0.0      0.13        68       1      27 [.     232     258 ..     232     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00091
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      IvGaG  G+++A+ L +a ++v+++++ +
  gi|313126978|ref|YP_004037248.1|  5 IVGAGQVGSSIAADLDDA-HEVVVIDRDP 32
                                      9***************98.9******875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                                       EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllek 27 
                                       IvG+   G   A+lL ++gf+  l+e+
  gi|313126978|ref|YP_004037248.1| 232 IVGGSEVGYHVARLLEERGFRPRLIER 258
                                       899*9*******************998 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0029       1.5      38      73 ..       2      36 ..       1      80 [. 0.76
   2 ?    5.4   0.0      0.02        11      37      74 ..     228     265 ..     209     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
                                      EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydrskkkee 73
                                      +v i+G+G++G+++a  l  a   +v+++dr +++ e
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLDdAH--EVVVIDRDPERVE 36
                                      799*************999444..4555555544333 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.02
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHC CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeee 74 
                                       ++v i+G  ++G +va++l++ g++   ++r  ++ ++
  gi|313126978|ref|YP_004037248.1| 228 EEVVIVGGSEVGYHVARLLEERGFRPRLIERDGERARK 265
                                       6899****************999888777777665543 PP

>> DUF2325  Uncharacterized protein conserved in bacteria (DUF2325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.6   3.2e+02      41      69 ..      59      87 ..      32     104 .. 0.68
   2 !   10.8   0.0   0.00076       0.4       2      53 ..     230     277 ..     229     282 .. 0.89
   3 ?   -1.7   0.0       6.3   3.3e+03      42      51 ..     289     298 ..     286     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.6
                           DUF2325 41 eskigkaDlvvlftdtvsHkavkkvkkea 69
                                      e+ i++aD+v+  td  + ++v +  ++a
  gi|313126978|ref|YP_004037248.1| 59 EAGIADADMVIASTDNDETNIVVCSTAKA 87
                                      67899******999976666665555555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00076
                           DUF2325   2 vlivGGddrmeeqyrklleklggklkvfdgrkekkkkkleskigkaDlvvlf 53 
                                       v+ivGG + +  ++ +lle++g++ + ++ + e + +kl++++  +D vv+ 
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSE-VGYHVARLLEERGFRPRLIERDGE-RARKLAEQL--PDTVVME 277
                                       99****99.999*************99999888.556******..9***985 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 6.3
                           DUF2325  42 skigkaDlvv 51 
                                       ++ig+aDlvv
  gi|313126978|ref|YP_004037248.1| 289 EHIGDADLVV 298
                                       78*******9 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00042      0.22       2      71 ..       4      83 ..       3     102 .. 0.76
   2 ?    2.3   0.0      0.19        98       4      68 ..     233     297 ..     230     329 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.............EEEE--TT-HHHHHHHHHHHT-SE CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.............elveldltdrsalerlfkeeqpda 67
                                      +++Ga G++Gs ++  l ++ +ev+++dr++++ ++ +   l             +l e+ + d++ + +  ++ + ++
  gi|313126978|ref|YP_004037248.1|  4 VIVGA-GQVGSSIAADLDDA-HEVVVIDRDPERVEEMNYS-LdvlgisgdgtavsTLEEAGIADADMVIASTDNDETNI 79
                                      55665.***********986.8********7666654433.25778999999999899999999888888888777776 PP

                                      EEE- CS
                         Epimerase 68 vihl 71
                                      v+  
  gi|313126978|ref|YP_004037248.1| 80 VVCS 83
                                      6655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                                       ETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEE CS
                         Epimerase   4 tGatGfiGsalvkallekg..yevigldrlssasntarledlelveldltdrsalerlfkeeqpdav 68 
                                       +G+   +G ++++ l+e+g   ++i +d ++ ++  ++l+d+ ++e d td + ler     ++d v
  gi|313126978|ref|YP_004037248.1| 233 VGG-SEVGYHVARLLEERGfrPRLIERDGERARKLAEQLPDTVVMESDATDMEFLEREHIG-DADLV 297
                                       555.359************544577777776666666666668888888887766664322.44444 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.034        18       1      30 [.       4      31 ..       2      78 .. 0.80
   2 ?    7.3   0.0    0.0048       2.5     158     201 ..     221     264 ..     147     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.034
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      +I+GaG  G ++a  l +a    +++++++
  gi|313126978|ref|YP_004037248.1|  4 VIVGAGQVGSSIAADLDDAHE--VVVIDRD 31
                                      688888888888888888875..7888876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0048
                       Pyr_redox_3 158 efhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiek 201
                                       + ++ + ++vv++Gg++ +  +A  l ++g + +++ r+ e+ +
  gi|313126978|ref|YP_004037248.1| 221 DESPGTAEEVVIVGGSEVGYHVARLLEERGFRPRLIERDGERAR 264
                                       55567899**********************99999999987655 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0023       1.2      12      37 ..       2      27 ..       1      37 [. 0.89
   2 ?    4.3   0.1     0.063        33      12      96 ..     229     321 ..     218     342 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
                     Rossmann-like 12 svGiisaGrvGtalgaaleraghvvv 37
                                       v i++aG+vG++++a l+ a+ vvv
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLDDAHEVVV 27
                                      688****************9987775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.063
                     Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvleve.........dvaaraellllavPda 79 
                                       +v i++  +vG  ++  le  g     i    + +r++ae+ lPd+ v+e +         + +  a+l++ a+   
  gi|313126978|ref|YP_004037248.1| 229 EVVIVGGSEVGYHVARLLEERGFRPRLIERDGERARKLAEQ-LPDTVVMESDatdmeflerEHIGDADLVVAALESD 304
                                       68899999999999999999999999999999999999985.89999987631111111113455677888877777 PP

                     Rossmann-like  80 elpglvkglaatgavra 96 
                                       e   lv+ laa   v  
  gi|313126978|ref|YP_004037248.1| 305 EKNLLVSLLAARLGVER 321
                                       77777777777655554 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.3   1.2e+03      19      75 ..      56     111 ..      48     115 .. 0.63
   2 ?   11.8   0.0   0.00022      0.11      79     133 ..     238     297 ..     198     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.3
                                       -EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHH..HTT---HHHHHCS CS
                              HEM4  19 lieiepaedraelraalddleagkydwliftSanavealfealk..reeedvkalaslk 75 
                                       ++e + + d + ++a  d    ++ +++++ +a+a+   f+ ++    e++ ++ +s+k
  gi|313126978|ref|YP_004037248.1|  56 TLEEAGIADADMVIASTD---NDETNIVVCSTAKAISDAFTIARvkNTEYLRTWQRSKK 111
                                       555555555555555555...45788899999999988888888655555555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00022
                                       SSHHHHHHHHHTT---SEE-..SSSHHHHGGGS-.....---EEE.EEE-SS.S--HHHH CS
                              HEM4  79 vGpaTaraLeelglrvdlvpseegtaegLaeelae....slagkr.vlllrgeiarddla 133
                                       vG   ar Lee+g+r++l+  + + a++Lae l+     +  ++   +l r++i+++dl+
  gi|313126978|ref|YP_004037248.1| 238 VGYHVARLLEERGFRPRLIERDGERARKLAEQLPDtvvmESDATDmEFLEREHIGDADLV 297
                                       78889***************************9985553222222244466666666665 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.039        21      63      91 ..     182     209 ..     149     221 .. 0.78
   2 ?    6.0   0.0     0.021        11      32      89 ..     379     434 ..     367     444 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.039
                   Castor_Poll_mid  63 assgkiylnPeddevlqegdkllviaedd 91 
                                        ++g + + P+ ++v+q gd+++vi+  +
  gi|313126978|ref|YP_004037248.1| 182 LRNGAVEI-PRGQTVIQPGDRVVVIGTPR 209
                                       56666666.9999************9755 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.021
                   Castor_Poll_mid  32 fylkelpelegkkyedvllafqeavviGikvassgkiylnPeddevlqegdkllviae 89 
                                       + + + + l+g + ++   ++++ +v+G   + + +  + P+ ++v++ gd++++  +
  gi|313126978|ref|YP_004037248.1| 379 IEVDDDSILAGREIRESVPELPDGIVVGA--ITRNREFITPRGNTVVEVGDHVVLFVD 434
                                       55666678999999999999********9..455678899************998754 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00065      0.34      13      41 ..      53      81 ..      51     114 .. 0.80
   2 ?   -1.5   0.0         7   3.7e+03      13      39 ..     282     308 ..     277     317 .. 0.81
   3 ?   -1.1   0.0       5.1   2.7e+03      10      88 ..     350     377 ..     342     388 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00065
                              YflT 13 aieelkaeGyneddiyvvakdkdrlerla 41
                                      a+++l+++G+++ d++++++d+d+++ + 
  gi|313126978|ref|YP_004037248.1| 53 AVSTLEEAGIADADMVIASTDNDETNIVV 81
                                      899********************997665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7
                              YflT  13 aieelkaeGyneddiyvvakdkdrler 39 
                                       ++e l++e + + d++v+a + d+ + 
  gi|313126978|ref|YP_004037248.1| 282 DMEFLEREHIGDADLVVAALESDEKNL 308
                                       567788999999999999999997655 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 5.1
                              YflT  10 llsaieelkaeGyneddiyvvakdkdrlerlaentdaetettseeglwdsiknlfrskgdelrekleslGltedeae 86 
                                       + ++i ++++eG + ++i  +  dk+++                                                 
  gi|313126978|ref|YP_004037248.1| 350 VAEEITRFTREGGA-ENIALIESDKAEV------------------------------------------------- 376
                                       55666666666643.3455555555444................................................. PP

                              YflT  87 ey 88 
                                        +
  gi|313126978|ref|YP_004037248.1| 377 -L 377
                                       .3 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.17      45      76 ..       2      33 ..       1      73 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                      EEEEES-CCCHHHHHHHHCCCEEEEEEESSGG CS
                           DUF1188 45 nvlviGaYltGaaiakkLskkeevtlvDieph 76
                                      +v+++Ga  +G+ ia  L+  +ev+++D +p+
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLDDAHEVVVIDRDPE 33
                                      69*****************99*******9997 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.1   1.1e+03     174     201 ..      43      70 ..       9      91 .. 0.64
   2 ?    9.4   0.1   0.00073      0.38     274     349 ..     229     300 ..     222     309 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.1
                                       EEEEEECTSB-HHHHGGGGG-SEEEEES CS
                    Oxidored_nitro 174 evnavftggtsleelraagraklnlvlc 201
                                       +v  +   gt ++ l++ag a++ +v+ 
  gi|313126978|ref|YP_004037248.1|  43 DVLGISGDGTAVSTLEEAGIADADMVIA 70 
                                       4445555555555555555555555554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00073
                                       EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEEES.CHHHHH..HHHHHHT-SEEEE CS
                    Oxidored_nitro 274 rvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleegepeviddadleele..elikelkpdlllg 348
                                        v+i+g+ +  +++arll+e G+++ ++    +++      ++ +e+  + v++++d +++e  e+ +   +dl+++
  gi|313126978|ref|YP_004037248.1| 229 EVVIVGGSEVGYHVARLLEERGFRPRLIERDGERA------RKLAEQLPDTVVMESDATDMEflEREHIGDADLVVA 299
                                       699***********************996544433......333333333556655666655115556667888876 PP

                                       - CS
                    Oxidored_nitro 349 g 349
                                        
  gi|313126978|ref|YP_004037248.1| 300 A 300
                                       5 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0036       1.9       1      45 [.       2      46 ..       2      81 .. 0.61
   2 ?    0.6   0.0       1.7   9.1e+02       2      22 ..     230     250 ..     229     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0036
                            PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk.teveg..ypvlg 45
                                      ++vI+GaG  g  +a  +++ +   +++++D +++  e+++  + vlg
  gi|313126978|ref|YP_004037248.1|  2 RVVIVGAGQVGSSIAADLDDAH---EVVVIDRDPErVEEMNysLDVLG 46
                                      589********99887666655...89999988762333333433333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.7
                            PglD_N   2 ivIiGaGGhgkvvadiieang 22 
                                       +vI+G +  g  va+++e +g
  gi|313126978|ref|YP_004037248.1| 230 VVIVGGSEVGYHVARLLEERG 250
                                       89***************9887 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4     0.008       4.2      19      37 ..       1      19 [.       1      32 [. 0.85
   2 ?    3.9   0.0     0.056        30      79     126 ..      33      81 ..      32      95 .. 0.88
   3 ?   -3.2   0.0         8   4.2e+03      20      42 ..     229     251 ..     226     253 .. 0.86
   4 ?    0.5   0.0       0.6   3.2e+02      94     134 ..     277     318 ..     261     347 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.008
                                      SEEEEE--SHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                              ThiF 19 skvllvGaGglGsellknL 37
                                      ++v++vGaG +Gs ++ +L
  gi|313126978|ref|YP_004037248.1|  1 MRVVIVGAGQVGSSIAADL 19
                                      59*************9887 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.056
                                       HHHHHT-TTSEEEEEES-CCG.CCS-HHHHTT-SEEEEESSSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  79 ealqeinpdveveavteritd.etvleellesvDlVvdalDniearrlv 126
                                       e+++e+n +++v  + ++ t+ +t++e  + ++D+V+  +Dn e+   v
  gi|313126978|ref|YP_004037248.1|  33 ERVEEMNYSLDVLGISGDGTAvSTLEEAGIADADMVIASTDNDETNIVV 81 
                                       6899*****************99899999*************8887776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8
                                       EEEEE--SHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  20 kvllvGaGglGsellknLalsGv 42 
                                       +v++vG   +G  ++++L   G+
  gi|313126978|ref|YP_004037248.1| 229 EVVIVGGSEVGYHVARLLEERGF 251
                                       699************99987777 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.6
                                       ES-CCG.CCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  94 teritd.etvleellesvDlVvdalDniearrlvnracvkkg 134
                                       + + td e +++e + ++DlVv al + e  +lv  ++++ g
  gi|313126978|ref|YP_004037248.1| 277 ESDATDmEFLEREHIGDADLVVAALESDEKNLLVSLLAARLG 318
                                       445555333577899999******999888888887777544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3046.50
//
Query:       gi|313126979|ref|YP_004037249.1|  [L=253]
Description: geranylgeranylglyceryl diphosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-41  140.2   0.7    1.2e-40  139.4   0.7    1.4  1  PcrB          PcrB family
    0.00016   21.2   0.0    0.00033   20.2   0.0    1.5  1  His_biosynth  Histidine biosynthesis protein
     0.0043   16.0   0.0       0.18   10.6   0.0    2.4  3  Trp_syntA     Tryptophan synthase alpha chain
      0.007   15.4   2.1       0.33    9.9   0.0    2.6  3  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
       0.15   11.1   0.0       0.34   10.0   0.0    1.5  2  Dus           Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.4   0.7   3.3e-44   1.2e-40       3     220 ..       5     250 ..       2     253 .] 0.92

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 3.3e-44
                                       GGGTSEEEEE-TTSS-CHHHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTS..SS-EEEEESSGGG--T.... CS
                              PcrB   3 ileerhltklDPeeenpdEiveiviesgtDavmigGsqsvtldntvrllkkvsri..klPivlepsnvegvvr.... 73 
                                       + +  h+tk+DP e+ p++ +e +  +gtD v++gGs++vt +nt+ +++kv+    +lP++ ep   + v+     
  gi|313126979|ref|YP_004037249.1|   5 WDRLSHVTKIDPAEHVPND-LELL--DGTDLVIVGGSDGVTAENTLDAVQKVKSQfpDLPVLQEPYRSSHVSSktvd 78 
                                       55667*********99986.7988..*************************9643358*******888887642222 PP

                                       TSSEEEEEEETTBSSTTTTTH..........................HHHHHHHHHHHHHHCTEEEEEEEEEBTTTS CS
                              PcrB  74 yaDalFvmsllnsanadWivg..........................ahalglkkvkklieseeilaegYlvvePds 124
                                        +D+l v++++n  +a+++                            +  ++ + v +l    +i+ egY++ + ds
  gi|313126979|ref|YP_004037249.1|  79 TVDYLSVPAVFNGDDAHFVRKhvelfteaaskpdevtgsglpvvgdaISSKAREAVSELA--TKIIGEGYVIQNCDS 153
                                       689****************99999*********************998999999999999..99************* PP

                                       HHHHHTTB-B-TTHHHHHHHHHHHHHHTT-SEEEEE-TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC CS
                              PcrB 125 kvaavteakvdlnkediaayallaakllglrliYlEasGaledveevialkkklekarlivGGGirsaEkAkevvea 201
                                       k+aav+ ++ +   e++a +al a+ ++g++++Y+E+sG+++ +  v+a ++ l+++ l++GGGi+ +E+ +e++ a
  gi|313126979|ref|YP_004037249.1| 154 KAAAVSGVETPYTTEEVAGAALAAESFYGFPIFYIEYSGTYGGPTDVAAASQYLDETVLLYGGGIETHEQTAEILDA 230
                                       ***************************************************************************** PP

                                       .SSEEEE-CHHHHHHHCHHH CS
                              PcrB 202 .ADvivvGnvveekderkid 220
                                        AD++vvG+  ++++e+  +
  gi|313126979|ref|YP_004037249.1| 231 gADAVVVGDCFHDDPEQYRQ 250
                                       *************9987655 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   9.3e-08   0.00033      75     114 ..     211     250 ..     193     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.3e-08
                                       EEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHH CS
                      His_biosynth  75 pvqvGGGIrsledveelleagadkviigtaavknpelike 114
                                        +  GGGI + e+ +e+l+agad v++g +  ++pe  ++
  gi|313126979|ref|YP_004037249.1| 211 VLLYGGGIETHEQTAEILDAGADAVVVGDCFHDDPEQYRQ 250
                                       5678*****************************9997665 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.013        48      67      91 ..      39      63 ..      33      77 .. 0.91
   2 ?   -3.1   0.0      0.75   2.7e+03      52      76 ..     143     168 ..     140     190 .. 0.63
   3 !   10.6   0.0   5.1e-05      0.18     199     227 ..     210     239 ..     198     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.013
                                      TT--HHHHHHHHHHHHHHCSSS-EE CS
                         Trp_syntA 67 kgvtlekvlelveevrkkevevPiv 91
                                       gvt e++l+ v++v+++ +++P++
  gi|313126979|ref|YP_004037249.1| 39 DGVTAENTLDAVQKVKSQFPDLPVL 63
                                      799***************9999986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.75
                                       TS-HHHHHHHHCCCC.TT--HHHHHH CS
                         Trp_syntA  52 adGPvIqaanlraLa.kgvtlekvle 76 
                                        +G vIq+ + +a a +gv++  + e
  gi|313126979|ref|YP_004037249.1| 143 GEGYVIQNCDSKAAAvSGVETPYTTE 168
                                       57888888776654325555555444 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 5.1e-05
                                       S-EEEESSS-SHHHHHHHH.TT-SEEEE-H CS
                         Trp_syntA 199 vPvavGFGistkeqvkqva.kvadGvivGS 227
                                       + ++ G Gi+t+eq +++  ++ad+v+vG 
  gi|313126979|ref|YP_004037249.1| 210 TVLLYGGGIETHEQTAEILdAGADAVVVGD 239
                                       4567899************9*********6 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0042        15     115     148 ..      28      62 ..       9      65 .. 0.85
   2 ?   -2.0   0.3      0.39   1.4e+03     185     229 ..     114     160 ..     112     176 .. 0.70
   3 !    9.9   0.0   9.2e-05      0.33     146     173 ..     211     238 ..     197     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0042
                                       TT-SEEEEE-STSSS.HHHHHHHHHHHHHTTTSEE CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                             IMPDH 115 agvdvlvvdsahghs.ekvleavkeikkkveevev 148
                                        g d+++v  ++g + e++l+av+++k++++++ v
  gi|313126979|ref|YP_004037249.1|  28 DGTDLVIVGGSDGVTaENTLDAVQKVKSQFPDLPV 62 
                                       589*********9752789***********99877 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.39
                                       HCSB---HH.HHHHHHHH.HHCTCT-EEEEES---SHHHHHHHHHTT CS
                                       xxxxxxxxx.xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 185 vagvGvpql.tAvaevae.aakkagvpviaDGGikysgdivkAlaaG 229
                                       v+g G p +  A+++ a+ a+++   ++i  G + ++ d   A + G
  gi|313126979|ref|YP_004037249.1| 114 VTGSGLPVVgDAISSKAReAVSELATKIIGEGYVIQNCDSKAAAVSG 160
                                       78888887635787655536777789999998887777765555555 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 9.2e-05
                                       SEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 146 veviaGnvataegakaLieagadavkvG 173
                                       v + +G + t+e+++++++agadav vG
  gi|313126979|ref|YP_004037249.1| 211 VLLYGGGIETHEQTAEILDAGADAVVVG 238
                                       4556788888888888888888888887 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.2   4.2e+03     170     186 ..      45      62 ..      40      63 .. 0.76
   2 ?   10.0   0.0   9.4e-05      0.34     183     223 ..     208     248 ..     198     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.2
                                       --CHHHHHHHHH-S.S-E CS
                               Dus 170 adweaIkevkqavs.ipv 186
                                         ++a+++vk +++ +pv
  gi|313126979|ref|YP_004037249.1|  45 NTLDAVQKVKSQFPdLPV 62 
                                       567889999999988887 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 9.4e-05
                                       S.S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHH CS
                               Dus 183 s.ipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlf 223
                                         ++++  G+I++ e+  +il+  Gad+v++g +   +P   
  gi|313126979|ref|YP_004037249.1| 208 DeTVLLYGGGIETHEQTAEILDA-GADAVVVGDCFHDDPEQY 248
                                       55677788**************9.***********9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1773.39
//
Query:       gi|313126980|ref|YP_004037250.1|  [L=177]
Description: polyketide cyclase/dehydrase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-12   47.4   0.2    2.9e-12   47.1   0.2    1.2  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    1.7e-09   38.0   0.2    4.2e-09   36.7   0.2    1.6  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.024   14.9   0.1      0.032   14.4   0.1    1.3  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.2   4.8e-16   2.9e-12       2     141 ..       2     156 ..       1     162 [. 0.74

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.8e-16
                                       EEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS.SEEEEEEEEEETTTTEEEE CS
                   Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr.gtvreelvevdpegrllsy 77 
                                        ++ vs+v+  p e+V++++ df+ ++ ++  +++v+ +g gg++++ + ++++  +  t++ e++e++p + ++++
  gi|313126980|ref|YP_004037250.1|   2 DEIVVSTVVYLPTEDVYDFLVDFPRYANYSKHLQDVTQRGDGGSGTRYALHFSWWKLtYTAHSEVTELEP-PNRIEW 77 
                                       57889999****************************9998677755555666633333679*********.****** PP

                                       EEE.SSS-TSEEEEEEEEECCE........T...EEEEEEEEEEE.......E--TT--HHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  78 rivkpvpvanyvatwtvtpdgg........g...trvtwtgefda.......gplggpfekpaaakavkgdleagLe 136
                                       +i   v+  +  ++w+v++ ++            +rv +++ +da         l+++++ +++   +k +l++  e
  gi|313126980|ref|YP_004037250.1|  78 QI---VKDIHAHGRWRVEALDTlpdaapndAetaCRVFFEVSYDAdsadkdsINLPRFVSFGWVIDKLKPALQTEAE 151
                                       **...6778899*******5543444444414469977777667544566665566777666777777777777777 PP

                                       HHHHH CS
                   Polyketide_cyc2 137 rLkar 141
                                       r+ +r
  gi|313126980|ref|YP_004037250.1| 152 RIVER 156
                                       66554 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2     7e-13   4.2e-09       4     107 ..      13     121 ..      10     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 7e-13
                                       -HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...EEEECSTTSSCEEEEEEEEEEETTT.EEECTTCCCCCEEEE CS
                    Polyketide_cyc   4 padqvyalvadvesypeflphcssvevleeaesglsadlevgfggltesftarvtldppee.itfklvegdfksleg 79 
                                       p ++vy+++ d+ +y  +++h+++v++  + +sg++  l+ +++ lt +  ++vt+ +p   i+ ++v+ d  + +g
  gi|313126980|ref|YP_004037250.1|  13 PTEDVYDFLVDFPRYANYSKHLQDVTQRGDGGSGTRYALHFSWWKLTYTAHSEVTELEPPNrIEWQIVK-D-IHAHG 87 
                                       889****************************************************98888834444444.4.44589 PP

                                       EEEECTECC......EEECEEEEEEEEEEEE-SS CS
                    Polyketide_cyc  80 kWtieslpp......nsggtrtkvalevdfkfas 107
                                       +W++e l++      n+ +t+++v +ev ++ +s
  gi|313126980|ref|YP_004037250.1|  88 RWRVEALDTlpdaapNDAETACRVFFEVSYDADS 121
                                       999999999998888888**********998665 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.4e-06     0.032       3      69 ..      13      82 ..      11     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-06
                                      -HHHHHHHHH-HHHHHHH...EEEEEEEE--STTEEEEEEETTTSEEEEEEEEEEEEETTTEEEEEEEEE CS
                             AHSA1  3 pperVfraltdpellkrW...ftlteaemdlrpGgkfrlrdspdgkefgnegeylevvpperlvytwrle 69
                                      p e+V++ l d  + +++   ++    + d   G ++ l+ s+    ++ + e++e++pp+r+++++  +
  gi|313126980|ref|YP_004037250.1| 13 PTEDVYDFLVDFPRYANYskhLQDVTQRGDGGSGTRYALHFSWWKLTYTAHSEVTELEPPNRIEWQIVKD 82
                                      8899*******99999997444444444444556677778889**********************96433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1331.86
//
Query:       gi|313126981|ref|YP_004037251.1|  [L=307]
Description: hypothetical protein Hbor_22450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.078   13.8   0.1         19    6.2   0.0    2.4  2  FliT      Flagellar protein FliT


Domain annotation for each model (and alignments):
>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2    0.0023        41      29      62 ..      44      81 ..      38      88 .. 0.86
   2 ?    6.2   0.0     0.001        19      35      84 ..     131     180 ..     112     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0023
                                      CS--ST--HHHHHHHHHHHH....HHHHHHHHHHHHHH CS
                              FliT 29 eldaaplspaereekrellr....rilandaeirallq 62
                                      ++d a+ +++++++ r +lr    ++l+ + eir+ ++
  gi|313126981|ref|YP_004037251.1| 44 SRDDAEHAADAAKDYRSALRrydpQVLQHESEIRNVAD 81
                                      455688999999999999999*************9876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.001
                                       --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHHHHHHHHH CS
                              FliT  35 lspaereekrellrrilandaeirallqprldelqkllgalrrqrkanna 84 
                                        ++a+ e    l + + ++d+   +ll   ++el   l+a+r++r ++ a
  gi|313126981|ref|YP_004037251.1| 131 VESAAMETYLTLAEVVTEQDDFCLTLLWSVMSELDVRLDASRQRRVVSAA 180
                                       5555556666666778899999999*******************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2008.19
//
Query:       gi|313126982|ref|YP_004037252.1|  [L=270]
Description: thioredoxin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-12   47.9   4.2    5.8e-07   29.0   0.3    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    9.8e-10   38.1   3.7    1.4e-07   31.0   1.0    2.2  2  FAD_binding_2   FAD binding domain
      5e-07   29.3   3.5      5e-05   22.7   0.3    2.2  2  FAD_binding_3   FAD binding domain
    3.3e-05   23.4   2.5    3.3e-05   23.4   2.5    1.6  2  FAD_oxidored    FAD dependent oxidoreductase
    6.1e-05   22.3   0.2    0.00011   21.4   0.2    1.4  1  GIDA            Glucose inhibited division protein A
    0.00019   21.6   0.1    0.00048   20.3   0.1    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00052   19.7  11.6     0.0013   18.4   0.6    3.0  3  DAO             FAD dependent oxidoreductase
     0.0014   18.0   0.3     0.0054   16.0   0.1    2.0  2  Thi4            Thi4 family
      0.002   17.4   0.3     0.0044   16.3   0.1    1.6  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0028   16.4   0.1     0.0044   15.8   0.1    1.2  1  HI0933_like     HI0933-like protein
     0.0058   15.7   0.9     0.0093   15.0   0.2    1.6  2  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
       0.01   16.3   0.2       0.01   16.3   0.2    2.2  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.012   14.9   0.1       0.11   11.8   0.0    2.0  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.02   13.8   5.2        1.1    8.0   1.8    2.2  2  Trp_halogenase  Tryptophan halogenase
      0.078   12.9   0.2       0.34   10.8   0.1    2.0  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.3   4.8e-10   5.8e-07       2      80 ..       8      88 ..       7     105 .. 0.68
   2 !   20.8   0.9   1.5e-07   0.00018     214     294 .]     106     186 ..      65     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.8e-10
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCHCCT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielllgee 74
                                      dv+v+GgG+AGl+aa++ a+ag+++++v++++ +ln+   l + + g+++  + ++      e+    +++++ + g  
  gi|313126982|ref|YP_004037252.1|  8 DVLVVGGGVAGLTAATFTARAGLDTLVVNDGESILNRNAHL-ENIPGFPAGVNARLfgdlldEQ--ASRNDVTQREG-R 82
                                      8***************************8888887776665.5555555555544466555322..23334555555.5 PP

                                      CEEEEE CS
                                      xxxxxx RF
                       Pyr_redox_2 75 vvkidp 80
                                      vv+i++
  gi|313126982|ref|YP_004037252.1| 83 VVSIER 88
                                      666654 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.5e-07
                                       E.EEEEEETTSCE..EEESEEEE-S-EEES-HHCSHCCT-EE...EETTEEE--TTSBESSTTEEE-GGGCTECCSS CS
                                       x.xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 214 e.klevvledgee..idadlvvvavGvrpstelleeklglel...derggivvdeflrtnvpgiyaiGDvaggkggp 284
                                          +  v++dg++  + ++ +v a +  ++   l ++l +++    +++++ vde +rt+v+g+ya+G  +   +++
  gi|313126982|ref|YP_004037252.1| 106 AwFVASVETDGTVetVRTRFIVAASWSDADY--L-DELDVTIrdaGSKRYVDVDECGRTSVEGVYAAGRLT---EKY 176
                                       3433355666666568888888888888884..5.8888888555566789********************...9** PP

                                       --HHHHHHHH CS
                                       xxxxxxxxxx RF
                       Pyr_redox_2 285 elaqaAvqqG 294
                                        +a++A  +G
  gi|313126982|ref|YP_004037252.1| 177 HQAVVAAGHG 186
                                       *****99987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   1.0   1.2e-10   1.4e-07       1      33 [.       8      40 ..       8      46 .. 0.95
   2 !    7.6   0.1    0.0014       1.7     363     410 ..     140     180 ..      61     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.2e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      Dv+V+G+G+AGL+AA+  a+aGl+++vv+ +++
  gi|313126982|ref|YP_004037252.1|  8 DVLVVGGGVAGLTAATFTARAGLDTLVVNDGES 40
                                      9***************************99875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0014
                                       ..EEEEEEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS CS
                     FAD_binding_2 363 vkvvpaqhytmgGvetdengrvldadgqpipGLYAaGevaaggvhgan 410
                                        +v++ + ++   v +de gr+       ++G YAaG  +   +h a 
  gi|313126982|ref|YP_004037252.1| 140 LDVTIRDAGSKRYVDVDECGRT------SVEGVYAAGRLT-EKYHQAV 180
                                       5677777777777999999**9......***********9.9999875 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3   4.2e-08     5e-05       2      32 ..       7      37 ..       6      47 .. 0.92
   2 !    7.5   0.2    0.0018       2.1     117     161 ..      81     129 ..      71     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.2e-08
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                      tdVl+VG+G aGl++a++ ++aG ++++v+ 
  gi|313126982|ref|YP_004037252.1|  7 TDVLVVGGGVAGLTAATFTARAGLDTLVVND 37
                                      8***************************985 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0018
                                       HHTEEETCSEEEEC..CEECCCCCCCEEE..ECCTTEEEEEEEEEEEE- CS
                     FAD_binding_3 117 erglqvrfkteves..leqdeegvtaevr..dketgeeetvrakYlvGa 161
                                        r +++++  e ++   e+d +g++a +    +++g+ etvr +++v+a
  gi|313126982|ref|YP_004037252.1|  81 GRVVSIERTDEANGaeTEHDADGEDAWFVasVETDGTVETVRTRFIVAA 129
                                       4456777777744311689999****887668899999**********9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   2.5   2.8e-08   3.3e-05       1      31 [.       8      38 ..       8      42 .. 0.94
   2 ?   -2.7   0.0       2.3   2.7e+03     109     134 ..      82     108 ..      43     139 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.8e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      Dv+VvGGg+aG++AA   araG  +l+v++ 
  gi|313126982|ref|YP_004037252.1|  8 DVLVVGGGVAGLTAATFTARAGLDTLVVNDG 38
                                      9***************************876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                      FAD_oxidored 109 rlvevekegkriesvtveske.g.rkti 134
                                       r+v++e+++ + ++ ++e+++ g +  +
  gi|313126982|ref|YP_004037252.1|  82 RVVSIERTD-EANGAETEHDAdGeDAWF 108
                                       233333332.334444443333333333 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   9.3e-08   0.00011       1      28 [.       8      35 ..       8      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.3e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dv V+GgG AG+ AA  +ar+G+++l +
  gi|313126982|ref|YP_004037252.1|  8 DVLVVGGGVAGLTAATFTARAGLDTLVV 35
                                      79***********************988 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1     4e-07   0.00048       1      30 [.      11      40 ..      11      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                      +vG+G++Gl+aA + a+ag+d l++  +++
  gi|313126982|ref|YP_004037252.1| 11 VVGGGVAGLTAATFTARAGLDTLVVNDGES 40
                                      8********************999877666 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.6   1.1e-06    0.0013       1      28 [.       8      37 ..       8      47 .. 0.87
   2 !    5.7   1.5    0.0076       9.1     144     214 ..      59     141 ..      53     155 .. 0.71
   3 ?    1.4   0.1      0.16   1.9e+02     179     206 ..     163     190 ..     145     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEES CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllek 28
                                      dv+++GGG++Gl++A + ar+g  ++++  
  gi|313126982|ref|YP_004037252.1|  8 DVLVVGGGVAGLTAATFTARAGldTLVVND 37
                                      8********************999777755 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0076
                                       EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEE.............TCEEEEE.EECTEEEEEEEE.EEE--GGGHH CS
                               DAO 144 dpakltaalaraaealGveilegtevtgleeed.............gkvwgve.rttpgendaada.vVnaaGawsd 205
                                       +++ +   l ++a ++ v+ +eg +v+++e++d             +++w v  ++t+g+++++++  ++aa  wsd
  gi|313126982|ref|YP_004037252.1|  59 NARLFGDLLDEQASRNDVTQREG-RVVSIERTDeangaetehdadgEDAWFVAsVETDGTVETVRTrFIVAA-SWSD 133
                                       666777777788***********.999**9966665555555566655666668777787756677899999.6998 PP

                                       ..HHHTTCTTT CS
                               DAO 206 ..llgllkeld 214
                                          l    eld
  gi|313126982|ref|YP_004037252.1| 134 adYL---DELD 141
                                       6555...4444 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.16
                                       EEEEE.EECTEEE.EEEEEEEE--GGGHH.H CS
                               DAO 179 vwgve.rttpgen.daadavVnaaGawsd.l 206
                                       v gv+     g+  +++++ V+aaG+++   
  gi|313126982|ref|YP_004037252.1| 163 VEGVYaA---GRLtEKYHQAVVAAGHGAEvA 190
                                       4444331...333345789******998742 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   4.5e-06    0.0054      18      48 ..       7      36 ..       2      41 .. 0.90
   2 ?   -1.1   0.0      0.78   9.4e+02       2      27 ..     124     149 ..     123     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.5e-06
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvaile 48
                                      +Dv++vG+G +GLtaa   a++ +l +++++
  gi|313126982|ref|YP_004037252.1|  7 TDVLVVGGGVAGLTAATFTARA-GLDTLVVN 36
                                      8********************9.99999876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.78
                                       HHHHHHHHHHHHHHTEEEEEEE--SH CS
                              Thi4   2 raiveryfedllkyaesDvvivGaGs 27 
                                       r iv ++ +d + + e Dv i  aGs
  gi|313126982|ref|YP_004037252.1| 124 RFIVAASWSDADYLDELDVTIRDAGS 149
                                       66777777777777788888888876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.7e-06    0.0044      29      58 ..       7      36 ..       3      59 .. 0.84
   2 ?   -2.6   0.0       2.4   2.8e+03      53      84 ..     141     172 ..     139     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.7e-06
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlD 58
                                        vlv+GgGvaGl A+   ++ g ++ v++
  gi|313126982|ref|YP_004037252.1|  7 TDVLVVGGGVAGLTAATFTARAGLDTLVVN 36
                                      679**************9999998877765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                                       EEEEEESSHHHHHHHHHTTTCECEEHCHHHHH CS
                       AlaDh_PNT_C  53 kVtvlDvrparleqleslgakfvevlksqeel 84 
                                       +Vt+ D  ++r   ++++g++ ve +++  +l
  gi|313126982|ref|YP_004037252.1| 141 DVTIRDAGSKRYVDVDECGRTSVEGVYAAGRL 172
                                       57777777777777777777777665544433 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.7e-06    0.0044       2      36 ..       8      42 ..       7      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.7e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      dv+v+GgG AGl aA   a++g ++l+++ +++++
  gi|313126982|ref|YP_004037252.1|  8 DVLVVGGGVAGLTAATFTARAGLDTLVVNDGESIL 42
                                      89**************************9998876 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   7.8e-06    0.0093       1      42 [.       8      47 ..       8      51 .. 0.92
   2 ?   -3.5   0.0       3.3   3.9e+03      86     117 ..      60      91 ..      56     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.8e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny 42
                                      Dv+v+G+G Agl  A     a++gl  ++++ ++s+l  n +
  gi|313126982|ref|YP_004037252.1|  8 DVLVVGGGVAGLTAATFT--ARAGLDTLVVNDGESILNRNAH 47
                                      9************99988..***************9877765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
                     Lycopene_cycl  86 skrlkeellerlvengvklleakvesveeeea 117
                                        + +   l e+   n v+ +e++v s+e  ++
  gi|313126982|ref|YP_004037252.1|  60 ARLFGDLLDEQASRNDVTQREGRVVSIERTDE 91 
                                       55566667777778889999999999887665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.2   8.7e-06      0.01       2      36 ..       9      44 ..       8      50 .. 0.91
   2 ?   -2.9   0.0       8.7     1e+04      17      32 ..     181     198 ..     178     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.7e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.T CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.r 36
                                      v+vvGgG+ gl +A++ a+ g ++ vv  ++ +l r
  gi|313126982|ref|YP_004037252.1|  9 VLVVGGGVAGLTAATFTARAGLDTLVVNDGESILnR 44
                                      89****************************999943 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.7
                                       HHHHTTSEE..EEEESSS CS
                         Pyr_redox  17 alaelgkkV..tvversd 32 
                                       ++a +g++V  t+++ sd
  gi|313126982|ref|YP_004037252.1| 181 VAAGHGAEValTLIHDSD 198
                                       566677777667888766 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.8e-05      0.11       1      30 [.      10      38 ..       7      50 .. 0.83
   2 ?    0.7   0.0       0.2   2.4e+02     249     305 .]     113     170 ..      80     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.8e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      +++G+G aGl+aa+   +agl d l++  g
  gi|313126982|ref|YP_004037252.1| 10 LVVGGGVAGLTAATFTARAGL-DTLVVNDG 38
                                      699******************.56777666 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.2
                       Pyr_redox_3 249 tedgkkvevkddvvlatGykpdlsflkk..slfeldedgrpvlteeteetnvpglflaG 305
                                       ++dg+  +v++++++a  + +d++ l++    + ++ ++r v  +e   t v+g++ aG
  gi|313126982|ref|YP_004037252.1| 113 ETDGTVETVRTRFIVAASW-SDADYLDEldVTIRDAGSKRYVDVDECGRTSVEGVYAAG 170
                                       4566777778888888765.5778888842333333333444445667899*****998 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.8   0.00094       1.1       1      23 [.       8      30 ..       8      42 .. 0.83
   2 ?    7.1   0.1    0.0018       2.1     151     183 ..      58      90 ..      43     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00094
                                      EEEEE--SHHHHHHHHHHHHHTT CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalk 23
                                      ++++vGGG aG +aA+  a+a+ 
  gi|313126982|ref|YP_004037252.1|  8 DVLVVGGGVAGLTAATFTARAGL 30
                                      699**************999983 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0018
                                       E-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-T CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkvvevqlde 183
                                       ++a+l+ ++L + a ++ vt++eg+vv+++  +
  gi|313126982|ref|YP_004037252.1|  58 VNARLFGDLLDEQASRNDVTQREGRVVSIERTD 90 
                                       799***********************9887655 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00028      0.34       2      38 ..       9      45 ..       8      88 .. 0.91
   2 ?   -0.2   0.0      0.69   8.2e+02      23      69 ..     140     186 ..     127     203 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                                      v v+G G+ G   a+ +a+agl++ +v+  e++l++ 
  gi|313126982|ref|YP_004037252.1|  9 VLVVGGGVAGLTAATFTARAGLDTLVVNDGESILNRN 45
                                      78************************99988888775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.69
                                       -EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEE CS
                           3HCDH_N  23 leVvlvdiseealekalekieksleklvekgklkeeeveaalarisf 69 
                                       l+V++ d  +++  ++ e  ++s+e + ++g+l+e+  +a++a  + 
  gi|313126982|ref|YP_004037252.1| 140 LDVTIRDAGSKRYVDVDECGRTSVEGVYAAGRLTEKYHQAVVAAGHG 186
                                       56666666666666666666666666666666666666665555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1610.92
//
Query:       gi|313126983|ref|YP_004037253.1|  [L=383]
Description: phosphopantothenoylcysteine decarboxylase; phosphopantothenate-cysteine ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-48  164.7   5.3    2.6e-48  164.3   0.8    2.5  3  DFP           DNA / pantothenate metabolism flavoprotein
    9.5e-35  119.7   0.2    1.5e-34  119.0   0.2    1.3  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.021   1.8e+02      33      54 ..      21      42 ..      16      87 .. 0.76
   2 ?   -2.0   0.0       0.3   2.7e+03      39      57 ..     109     126 ..     106     172 .. 0.74
   3 !  164.3   0.8   2.9e-52   2.6e-48       1     179 [.     179     348 ..     179     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.021
                                      HHHHHHHHHTT-EEEEEE-S-S CS
                               DFP 33 yalAeaaaarGaeVtlvsgpvs 54
                                      ++lA++++++Ga+V+ v  +++
  gi|313126983|ref|YP_004037253.1| 21 VELAHELRRQGANVRGVMTESA 42
                                      689***********99988853 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.3
                                       HHHTT-EEEEEE-S-SS-- CS
                               DFP  39 aaarGaeVtlvsgpvslet 57 
                                         a Ga+V +v +p   ++
  gi|313126983|ref|YP_004037253.1| 109 TTALGADVPVVVAPAM-HE 126
                                       5678999999999943.22 PP

  == domain 3  score: 164.3 bits;  conditional E-value: 2.9e-52
                                       TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHH CS
                               DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleave 77 
                                       l+g++v+vtaG+T E+iDp+R+++NrSSG++G ++A+a++ rGa+Vtlv+   +    + ++vv ve+++eml+av 
  gi|313126983|ref|YP_004037253.1| 179 LAGRHVVVTAGATSESIDPIRVLTNRSSGRTGREVARACYVRGADVTLVHDGDD---VPYADVVPVETSAEMLDAVL 252
                                       689***********************************************8844...4488**************** PP

                                       HHHTT-SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS...-HHHH CS
                               DFP  78 ealkeadivimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete...ellen 151
                                       + +++ad++++aAA++Dy++++ a+eK++    +e  tlele++p+++ ++ +++ ++  +vGF+aet+    +++ 
  gi|313126983|ref|YP_004037253.1| 253 SVAANADALVSAAAISDYTVET-AAEKLRS---GEPRTLELEPTPKLIDSV-REEYPDLAIVGFKAETSgdeAMVAA 324
                                       ********************96.6679985...56789*************.56667778*******9556799999 PP

                                       HHHHHHHTT-SEEEEEEGGGTTGGG-SS CS
                               DFP 152 areklerkgldlivaNdvskeeagfgsd 179
                                       ar+ l r +l ++vaNd+s      g++
  gi|313126983|ref|YP_004037253.1| 325 ARKILDRANLSFVVANDASVM----GQA 348
                                       *****************9964....444 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.0   0.2   1.7e-38   1.5e-34       2     156 ..       6     172 ..       5     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 1.7e-38
                                       EEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESEE CS
                      Flavoprotein   2 killgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadll 68 
                                       +++lg++Gs+aa+k++el ++L+++g++v+ v+t++A+ +i++  +++a+       ++++++h+el   + wad+l
  gi|313126983|ref|YP_004037253.1|   6 NVALGVSGSIAAVKVVELAHELRRQGANVRGVMTESAQGIIHPWAVEFATendvvteITGRVEHVELcgrDGWADVL 82 
                                       789***************************************99888877999999999********87666***** PP

                                       EEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHHH.T............... CS
                      Flavoprotein  69 viaPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekle.egvtvikPsegdigkg 142
                                       + aPa+ant++kia ++ d+++t+++    +a++p+++aPam+  my++p +l+ ++++e  gv++++P   ++gk+
  gi|313126983|ref|YP_004037253.1|  83 LLAPATANTVGKIAGAVDDTPVTTCATTalGADVPVVVAPAMHEPMYDHPGVLDAIDRVEsWGVQFVDPR-IEEGKA 158
                                       **********************999944489****************************65*********.9999** PP

                                       .GHHHHHHHHHHCH CS
                      Flavoprotein 143 kmaeieeivgkild 156
                                       k+a+ e+iv  + +
  gi|313126983|ref|YP_004037253.1| 159 KIATEEAIVTDVAR 172
                                       ********998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2933.66
//
Query:       gi|313126984|ref|YP_004037254.1|  [L=142]
Description: monovalent cation/proton antiporter, mnhg/phag subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-24   85.2   8.7    3.7e-24   84.7   8.7    1.2  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit
  ------ inclusion threshold ------
      0.061   13.2   0.2       0.11   12.4   0.2    1.4  1  TarH            Tar ligand binding domain homologue


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   8.7   4.2e-28   3.7e-24       1      78 [.      33     111 ..      33     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 4.2e-28
                    PhaG_MnhG_YufB   1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaaslkllliilfllltaPvaahliar 76 
                                       l+++G++f ++g++gllrlp+vy+R+ha++ka+tlG+ +i l+ ++++      l+ l++++fl+ltaP++ah+i+r
  gi|313126984|ref|YP_004037254.1|  33 LVVVGTFFLIVGTVGLLRLPNVYNRMHATSKATTLGAASIALAGFVFYgPGGDGLMSLVTVVFLFLTAPTGAHMISR 109
                                       79****************************************99997766666************************ PP

                    PhaG_MnhG_YufB  77 aa 78 
                                       aa
  gi|313126984|ref|YP_004037254.1| 110 AA 111
                                       *8 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.2e-05      0.11       7      55 ..      25      73 ..      23      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                      XXXXXXXXXXXXXXXXXXXXSSSSSSHHHHHHHCHHHHHHH.HHHHHHH CS
                              TarH  7 IrtrLllvlallgvLllvsgglglsglsrsndalrevytnrlqqqaaLa 55
                                      I t L+ vl+++g ++l++g +gl+ l +  ++++++++  +  +a +a
  gi|313126984|ref|YP_004037254.1| 25 IETALVSVLVVVGTFFLIVGTVGLLRLPNVYNRMHATSKATTLGAASIA 73
                                      8899**************************9999999887766665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1058.80
//
Query:       gi|313126985|ref|YP_004037255.1|  [L=97]
Description: multisubunit na+/h+ antiporter, mnhf subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-20   73.1   7.4    1.7e-20   73.1   7.4    2.0  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M
  ------ inclusion threshold ------
      0.038   14.1   1.2      0.046   13.9   1.2    1.0  1  SYS1       Integral membrane protein S linking to the trans G


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6     0.089     8e+02      11      24 ..      11      24 ..       5      32 .. 0.52
   2 !   73.1   7.4   1.9e-24   1.7e-20       1      52 [.      39      90 ..      39      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.089
                         MrpF_PhaF 11 gtllvallallail 24
                                      g l+ a+l++ a+l
  gi|313126985|ref|YP_004037255.1| 11 GLLVNAALVVSAAL 24
                                      33333444444433 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 1.9e-24
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                                      +DRvvAlD++gt++va+ +l+a++t++ +++dv lvlA++gF++t+ +ar++
  gi|313126985|ref|YP_004037255.1| 39 PDRVVALDTIGTNVVAIAVLYAMFTRQGFFIDVSLVLAIIGFISTITVARYV 90
                                      8**************************************************6 PP

>> SYS1  Integral membrane protein S linking to the trans Golgi network
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.2   5.1e-06     0.046      29     108 ..      10      89 ..       4      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-06
                              SYS1  29 lilltallagkelsldllfswesldvddtsgrllilvwvlnslvvvlallllveRsKlalDFalTihvihlvvvsly 105
                                       l ll+++ +  +  l ll s++++++ +   r+++l  + + +v++ +l ++  R+ + +D +l + +i ++ ++++
  gi|313126985|ref|YP_004037255.1|  10 LGLLVNAALVVSAALTLLVSYRVIKGPTVPDRVVALDTIGTNVVAIAVLYAMFTRQGFFIDVSLVLAIIGFISTITV 86 
                                       556677777788899*********************************************************99998 PP

                              SYS1 106 tra 108
                                        r 
  gi|313126985|ref|YP_004037255.1|  87 ARY 89 
                                       765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 761.64
//
Query:       gi|313126986|ref|YP_004037256.1|  [L=189]
Description: multisubunit na+/h+ antiporter, mnhe subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-42  145.1   2.4    1.4e-42  144.9   2.4    1.0  1  MNHE      Na+/H+ ion antiporter subunit
  ------ inclusion threshold ------
      0.079   12.8   1.2       0.11   12.3   0.1    1.7  2  DUF2955   Protein of unknown function (DUF2955)


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.9   2.4   1.5e-46   1.4e-42       2     143 ..      10     162 ..       9     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 144.9 bits;  conditional E-value: 1.5e-46
                              MNHE   2 lllflvWllltgs.......lgelllGlllallvalllrrll......lplrrvllrllayllvflweivkanldVa 65 
                                       lll+++W+++ g        ++e+++Gl++++++a+llr ++       ++ +v  ++  yllvfl+e+v+an+dVa
  gi|313126986|ref|YP_004037256.1|  10 LLLAILWIFVRGVeltprtlAEEFIVGLIVGMIIAYLLRGFYtptlgpGRALKVAPYATLYLLVFLKELVTANWDVA 86 
                                       689*********99************************99999887664444555559******************* PP

                              MNHE  66 krvlrpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldvedeeeeareeikgrlErr 142
                                       krvl p++pi+p++++vplr+++dla+t++ansitltPGTlt+d+d+++++lyvH +d +d ++++ e i +++E++
  gi|313126986|ref|YP_004037256.1|  87 KRVLAPSMPINPRVIEVPLRVRTDLAVTTIANSITLTPGTLTMDYDAETNTLYVHSIDGSD-RDALLEPI-RTWEDY 161
                                       ***********************************************************99.89998888.557777 PP

                              MNHE 143 l 143
                                       +
  gi|313126986|ref|YP_004037256.1| 162 A 162
                                       6 PP

>> DUF2955  Protein of unknown function (DUF2955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.3e-05      0.11      92     134 ..       3      45 ..       1      48 [. 0.92
   2 ?   -1.6   0.1      0.24   2.1e+03      23      51 ..      63      91 ..      60      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                           DUF2955  92 gskflfgamlvislsillvfasydttdvedlilsllaalllav 134
                                         + l g++l i+++++  +  ++ t++e++i++l++++++a 
  gi|313126986|ref|YP_004037256.1|   3 RRWPLTGLLLAILWIFVRGVELTPRTLAEEFIVGLIVGMIIAY 45 
                                       57899**********************************9985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.24
                           DUF2955 23 lgvfapvlpvllLtlvpklslkallqlll 51
                                      ++ +a+++ +++L    + +  ++  +l+
  gi|313126986|ref|YP_004037256.1| 63 VAPYATLYLLVFLKELVTANWDVAKRVLA 91
                                      56688999999997777777777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1476.91
//
Query:       gi|313126987|ref|YP_004037257.1|  [L=577]
Description: formate hydrogenlyase subunit 3/multisubunit Na+/H+ antiporter subunit MnhD [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-50  170.5  21.9    4.5e-50  170.5  21.9    2.7  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0055   16.7   0.3     0.0055   16.7   0.3    4.0  5  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
       0.15   12.4   0.1        2.2    8.6   0.0    2.3  2  MlaD             MlaD protein


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.5  21.9   7.5e-54   4.5e-50       3     278 ..     133     433 ..     131     455 .. 0.85
   2 ?   -3.5   2.3      0.77   4.6e+03     118     167 ..     525     573 ..     519     575 .. 0.83

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 7.5e-54
                   Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal....elg 75 
                                       d++ l++ +E++l+++y+L+ ++ + p+ ++A+l +++l+llgs ++Ll+i  ly+ tgtl++ +l++ l    +  
  gi|313126987|ref|YP_004037257.1| 133 DIFNLFVWFEVMLMSSYILVLFY-SGPEHTRAALNYVVLNLLGSAVMLLAIGGLYATTGTLNMADLARRLadpaTYD 208
                                       88999***************999.566*****************************************999976666 PP

                   Proton_antipo_M  76 lnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla............ 140
                                       ++   +  l+ +l+  +++K++ vp+++W+p ay +aP+pv+a+lA+++ k+gv++++rl + ++            
  gi|313126987|ref|YP_004037257.1| 209 VAVAPVIGLAAVLFSVFALKAGIVPFQFWVPAAYRAAPAPVTAMLAGVVKKVGVYAIVRLYFTVFaaaslpvslpfi 285
                                       6667777888899999*******************************************977655444444222211 PP

                   Proton_antipo_M 141 ...vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialav......at..qygveaaiihll 206
                                           +  +   +++++a++s+++g+++a+   di  llAySsis++G++++ +av      +t  + gv+a i++ +
  gi|313126987|ref|YP_004037257.1| 286 sgdSMLAFFGPVFFVMATASIVVGGVGAIGREDIDGLLAYSSISQVGFIILPFAVaamansRTvqMLGVTAGIVYAF 362
                                       12222334457899***********************************97655533323422114589999***** PP

                   Proton_antipo_M 207 thalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavav 278
                                        h+l k+llFl++g + +e + t  ++++ggLa + P+l++ +l+++l+l G+Pp++gF++k+l+++ a ++
  gi|313126987|ref|YP_004037257.1| 363 NHGLAKSLLFLASGTI-QEAVGTARFDQLGGLARRAPVLSAGFLLGALTLIGVPPLSGFFGKLLVFQTAADA 433
                                       *************555.8999*********************************************998765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.77
                   Proton_antipo_M 118 allAatlvkagvlllirlllllavssneisqlllilaiismllgslvala 167
                                       + +Aa++v++ ++++  +  ++++++ +++  l + + + ++lgs++al+
  gi|313126987|ref|YP_004037257.1| 525 VVVAALAVTVIAFGIG-FDAVYQTATTAAKAALNTEGYMKAVLGSVGALV 573
                                       4458888999888887.888888899999999999999999999999996 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   9.3e-07    0.0055      12      41 ..      73     102 ..      64     109 .. 0.85
   2 ?   -4.1   0.1         3   1.8e+04      22      29 ..     175     182 ..     168     184 .. 0.67
   3 ?   -2.6   0.0      0.99   5.9e+03      29      45 ..     328     344 ..     322     350 .. 0.77
   4 ?    1.7   0.1     0.046   2.8e+02      15      35 ..     433     453 ..     429     462 .. 0.85
   5 ?   -4.1   0.7       2.9   1.7e+04      23      34 ..     526     537 ..     523     540 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.3e-07
                   Proton_antipo_N  12 ieigfllDklsalmllvvtfvsllvhlYSi 41 
                                       + i +  D+lsa ml++  +vsl+ + YS+
  gi|313126987|ref|YP_004037257.1|  73 FGIVLVADPLSAFMLALTAIVSLCALTYSV 102
                                       5566788**********************8 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3
                   Proton_antipo_N  22 salmllvv 29 
                                       sa+mll +
  gi|313126987|ref|YP_004037257.1| 175 SAVMLLAI 182
                                       66777665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.99
                   Proton_antipo_N  29 vtfvsllvhlYSigYMa 45 
                                       ++ v+++++ +++  Ma
  gi|313126987|ref|YP_004037257.1| 328 ISQVGFIILPFAVAAMA 344
                                       77899999999988776 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.046
                   Proton_antipo_N  15 gfllDklsalmllvvtfvsll 35 
                                       +f lD + a  +l+v +v+++
  gi|313126987|ref|YP_004037257.1| 433 AFALDAIGAGAALIVALVGAV 453
                                       6899**************976 PP

  == domain 5  score: -4.1 bits;  conditional E-value: 2.9
                   Proton_antipo_N  23 almllvvtfvsl 34 
                                       ++ +l vt++++
  gi|313126987|ref|YP_004037257.1| 526 VVAALAVTVIAF 537
                                       566677777766 PP

>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.1   6.2e+02      18      33 ..     346     361 ..     339     366 .. 0.82
   2 ?    8.6   0.0   0.00037       2.2       6      34 ..     384     412 ..     382     419 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.1
                              MlaD  18 gapVryrGvtvGrVts 33 
                                          V++ Gvt G V +
  gi|313126987|ref|YP_004037257.1| 346 SRTVQMLGVTAGIVYA 361
                                       568*********9965 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00037
                              MlaD   6 taqfdnangLkvgapVryrGvtvGrVtsi 34 
                                       ta+fd+ +gL+ +apV  +G   G  t i
  gi|313126987|ref|YP_004037257.1| 384 TARFDQLGGLARRAPVLSAGFLLGALTLI 412
                                       79****************99988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3863.40
//
Query:       gi|313126988|ref|YP_004037258.1|  [L=113]
Description: multisubunit sodium/proton antiporter subunit MrpC [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-31  106.8   2.8    4.4e-31  106.6   2.8    1.0  1  Oxidored_q2      NADH-ubiquinone/plastoquinone oxidoreductase
  ------ inclusion threshold ------
       0.64    9.8   0.2       0.64    9.8   0.2    2.5  2  Phage_holin_2_3  Bacteriophage holin family HP1
        1.1    9.5   6.3       0.52   10.6   1.4    2.1  2  TrbC             TrbC/VIRB2 family


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   2.8   7.3e-35   4.4e-31       2     103 ..       6     108 ..       5     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 7.3e-35
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC...............TTSCGGHHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi..tnpatefadplpqalvLtaivi 76 
                                       l++++++lf++G+y+vl rr++++v+ g+++is a+n++lv++g +++ +++     +a++++dpl+qalvLtaivi
  gi|313126988|ref|YP_004037258.1|   6 LAAVLGILFALGTYLVL-RRDVVRVVWGISIISQAANVYLVTMGGLSGFAPITghGGSAESVTDPLVQALVLTAIVI 81 
                                       67899************.***************************996555559999999***************** PP

                                       HHHHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  77 gaaetavgLallvrlyreygtddvqel 103
                                       g+++ta++L+l++r+y+e+gt+d+ el
  gi|313126988|ref|YP_004037258.1|  82 GFGTTALALVLTYRVYEEHGTIDMYEL 108
                                       ***********************9887 PP

>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00011      0.64      27      41 ..       7      21 ..       5      24 .. 0.92
   2 ?    1.3   2.6     0.049   2.9e+02      28      43 ..      75      90 ..      34     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                   Phage_holin_2_3 27 AiviGIicgvvTfli 41
                                      A+v GI+++++T+l+
  gi|313126988|ref|YP_004037258.1|  7 AAVLGILFALGTYLV 21
                                      99**********986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.049
                   Phage_holin_2_3 28 iviGIicgvvTfliNw 43
                                      +++ I++g++T +++ 
  gi|313126988|ref|YP_004037258.1| 75 VLTAIVIGFGTTALAL 90
                                      5666777777766654 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.4   8.7e-05      0.52      63      95 ..       8      42 ..       2      46 .. 0.83
   2 ?    1.7   0.3     0.052   3.1e+02      48      64 ..      65      81 ..      52      94 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.7e-05
                              TrbC 63 ivaGimlafgrls..wrtlvmvviGiviifgAssi 95
                                      +v+Gi +a g      r++v+vv Gi+ii  A+++
  gi|313126988|ref|YP_004037258.1|  8 AVLGILFALGTYLvlRRDVVRVVWGISIISQAANV 42
                                      67788888887777779***************986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.052
                              TrbC 48 fltgplakviatiaiiv 64
                                      ++t pl++++++ ai++
  gi|313126988|ref|YP_004037258.1| 65 SVTDPLVQALVLTAIVI 81
                                      45555555554444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 747.65
//
Query:       gi|313126989|ref|YP_004037259.1|  [L=167]
Description: multisubunit na+/h+ antiporter, mnhb subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-36  123.2  10.7    8.6e-36  123.0  10.7    1.0  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0  10.7   4.8e-40   8.6e-36       1     124 []      22     159 ..      22     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 4.8e-40
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafglee.lekllrvkla.........pril 67 
                                       i rt++r++vp+il++++ lll+Ghn PGGGF+g++++ aa++l+y++fgl+  ++++lr +           +r+l
  gi|313126989|ref|YP_004037259.1|  22 ISRTITRIVVPFILVTAIGLLLQGHNLPGGGFIGAVLTVAAFVLIYVIFGLDYvQSEVLRLRSDndghspvelYRWL 98 
                                       789**************************************************8777776665567999******** PP

                              MnhB  68 eglglllavltgllglllg..fltslflel.el.llgevelgtallfdlgVylvVvgglll 124
                                       +g gl+lavl+gl+++++g  flt+ ++++ ++ l++e+el++a++fd+gVy++Vvg+ll+
  gi|313126989|ref|YP_004037259.1|  99 FGGGLALAVLSGLVPIFFGfdFLTQGVWFFkHVpLYEEFELASAVFFDFGVYFAVVGALLT 159
                                       ******************************7779999********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1247.30
//
Query:       gi|313126990|ref|YP_004037260.1|  [L=813]
Description: NADH:ubiquinone oxidoreductase subunit 5 (chain l)/multisubunit na+/h+ antiporter, mnha subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-70  236.1  20.5    4.7e-70  236.1  20.5    2.9  3  Proton_antipo_M  Proton-conducting membrane transporter
    4.3e-16   58.8  10.8    4.3e-16   58.8  10.8    5.7  7  DUF4040          Domain of unknown function (DUF4040)
      2e-12   47.0   1.5    6.2e-12   45.4   0.0    2.8  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.4     0.076   4.6e+02     118     163 ..      80     126 ..      64     129 .. 0.83
   2 !  236.1  20.5   7.9e-74   4.7e-70       1     281 [.     128     421 ..     128     440 .. 0.91
   3 ?   -2.9   6.1       0.5     3e+03     122     268 ..     600     752 ..     591     755 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.076
                   Proton_antipo_M 118 all.Aatlvkagvlllirlllllavssneisqlllilaiismllgsl 163
                                       all A +++ +gvl+l+     ++   ++++++  +la+++ +lg  
  gi|313126990|ref|YP_004037260.1|  80 ALLiAFLASGVGVLILTYSGGYMHGEPGQAKYYATLLAFMGSMLGVA 126
                                       45558889999999999888888899999999999999999888865 PP

  == domain 2  score: 236.1 bits;  conditional E-value: 7.9e-74
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg......tlefeelska 71 
                                       a+dL++l++++El++l+++lLig + ++++s +A+ k++l+t  g l++L+g+lll +++g      t +++ l+ +
  gi|313126990|ref|YP_004037260.1| 128 ASDLISLFVFWELTSLSSFLLIGHYTSEQSSQYAARKSMLITVSGGLFMLVGFLLLVWVSGqalpetTYSLTVLLDN 204
                                       78***********************************************************9888876677777776 PP

                   Proton_antipo_M  72 l....elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla... 140
                                       +    ++ +++  l+ +l+ll +g+++Ksaqvp+h Wlp+a +eaPtpvsa+l +at+vkagv+l+ r+ +l+    
  gi|313126990|ref|YP_004037260.1| 205 AdlirQALAENGLLVPVLVLLGLGAATKSAQVPFHIWLPNA-MEAPTPVSAFLhSATMVKAGVYLVGRFRPLFLske 280
                                       67885566666666667788889******************.*******************************9766 PP

                   Proton_antipo_M 141 .vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallF 216
                                           +e++ l++il++++m +++++a+a tdiK+llAyS+ shlG+++ a++ a++yg ea  +h+l ha fka+lF
  gi|313126990|ref|YP_004037260.1| 281 aPLFGEWTMLFAILGLLTMTVAAILAVAATDIKELLAYSTASHLGLIIAAFGFANKYGAEAGAFHILNHASFKAALF 357
                                       666789*********************************************************************** PP

                   Proton_antipo_M 217 llagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavsli 281
                                       l+ag +i ++  tr+i ++ggL+k+ P++a++ +v+ ls+aGlPp+ gF+sk l++eaa+ ++  
  gi|313126990|ref|YP_004037260.1| 358 LVAG-IIAHEAGTRKISKLGGLRKHLPVTAVIATVASLSMAGLPPFNGFYSKELLFEAAWYAGKD 421
                                       ***5.556667*************************************************88765 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.5
                   Proton_antipo_M 122 atlvkagvlllirllllla...vssneisqlllilaiismllgslvalaqtdiK..rllAySsishlGymlialava 193
                                        t++++g++l + +++ ++   v+ + is l ++ ai  +ll ++v+ + +di    + +  ++s lG+m+  + + 
  gi|313126990|ref|YP_004037260.1| 600 VTVLTLGGYLAAGVFSGYIpanVAFPGISDLAVTPAIFLVLLVAVVGAFAVDIApsHVAGVLTLSILGFMVAIFYI- 675
                                       478899999999888877767777888999999999999999999999999996324555679999***9999999. PP

                   Proton_antipo_M 194 tqygveaaiihllthalfkallFllags....viyerektrdirayggLakkmPilalvllvlllslaGlPptagFl 266
                                        +++ ++a+++l++  l+ + +Fll+++    +  e +++++ir+ g La ++  +  v ++++ + +   pt+gFl
  gi|313126990|ref|YP_004037260.1| 676 LADAPDLALTQLVVETLV-LVIFLLVLNrlpaFYGEVNRSQSIRD-GILALAVGATVFVTVLVTTAASPAEPTSGFL 750
                                       778889999999987665.44555554411112333445666655.5555555444444444444444445678888 PP

                   Proton_antipo_M 267 sk 268
                                       ++
  gi|313126990|ref|YP_004037260.1| 751 AE 752
                                       76 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.4      0.94   5.6e+03      15      30 ..      34      49 ..      19      54 .. 0.68
   2 ?   -3.3   0.7       1.8   1.1e+04      13      29 ..      75      91 ..      66      95 .. 0.53
   3 ?   -1.8   2.0      0.62   3.7e+03       2      31 ..     298     329 ..     297     331 .. 0.57
   4 ?   -1.5   0.4      0.47   2.8e+03      18      61 ..     598     640 ..     593     643 .. 0.65
   5 !   58.8  10.8   7.3e-20   4.3e-16       2      66 ..     642     705 ..     641     706 .. 0.97
   6 ?   -3.7   2.8       2.3   1.4e+04      47      61 ..     724     738 ..     722     741 .. 0.74
   7 ?   -3.9   0.3       2.6   1.6e+04      51      57 ..     794     800 ..     787     807 .. 0.46

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.94
                           DUF4040 15 drlaavillgvvGllv 30
                                        +aa+ +l  +Gl++
  gi|313126990|ref|YP_004037260.1| 34 AYFAAATALVCFGLVS 49
                                      5677777788888775 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.8
                           DUF4040 13 ardrlaavillgvvGll 29
                                        d la +i++ + G++
  gi|313126990|ref|YP_004037260.1| 75 YVDGLALLIAFLASGVG 91
                                      34445555555555555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.62
                           DUF4040   2 llvlaalaavlar..drlaavillgvvGllva 31 
                                       ++ +aa++av+a+  + l a    + +Gl++a
  gi|313126990|ref|YP_004037260.1| 298 TMTVAAILAVAATdiKELLAYSTASHLGLIIA 329
                                       57788888888882333444444455666665 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.47
                           DUF4040  18 aavillgvvGllvallfvllgAPDvAlTqaavveglttvlllla 61 
                                       a v +l + G+l+a +f  +    vA+  +    ++t++++l+ 
  gi|313126990|ref|YP_004037260.1| 598 AGVTVLTLGGYLAAGVFSGYIPANVAFPGI-SDLAVTPAIFLVL 640
                                       566677777777777777666666666666.5556666666665 PP

  == domain 5  score: 58.8 bits;  conditional E-value: 7.3e-20
                           DUF4040   2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlp 66 
                                       ++v++a+a+ +a++++a v+ l+++G++va++++l +APD+AlTq+ vve+l++v++ll+l+rlp
  gi|313126990|ref|YP_004037260.1| 642 VAVVGAFAVDIAPSHVAGVLTLSILGFMVAIFYILADAPDLALTQL-VVETLVLVIFLLVLNRLP 705
                                       7899******************************************.*****************9 PP

  == domain 6  score: -3.7 bits;  conditional E-value: 2.3
                           DUF4040  47 aavveglttvlllla 61 
                                       +av++++ + +l+ +
  gi|313126990|ref|YP_004037260.1| 724 LAVGATVFVTVLVTT 738
                                       459999999988866 PP

  == domain 7  score: -3.9 bits;  conditional E-value: 2.6
                           DUF4040  51 eglttvl 57 
                                       ++  +++
  gi|313126990|ref|YP_004037260.1| 794 AMAALAI 800
                                       2222222 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0     1e-15   6.2e-12       3      57 ..      63     115 ..      62     116 .. 0.93
   2 ?   -3.7   0.4       2.2   1.3e+04      27      39 ..     661     673 ..     658     674 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1e-15
                   Proton_antipo_N   3 tWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                       +W++  +l ++++f++D+l +l +++ ++v++l++ YS gYM++++g+++++a l
  gi|313126990|ref|YP_004037260.1|  63 EWIP--SLGVSLAFYVDGLALLIAFLASGVGVLILTYSGGYMHGEPGQAKYYATL 115
                                       7888..456********************************************87 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.2
                   Proton_antipo_N  27 lvvtfvsllvhlY 39 
                                       l+ ++++++v ++
  gi|313126990|ref|YP_004037260.1| 661 LTLSILGFMVAIF 673
                                       5667899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (813 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 5483.82
//
Query:       gi|313126991|ref|YP_004037261.1|  [L=114]
Description: IclR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-08   34.2   0.5    2.9e-08   33.7   0.5    1.2  1  HTH_20         Helix-turn-helix domain
    4.9e-07   29.5   0.2    6.8e-07   29.1   0.2    1.2  1  MarR_2         MarR family
    8.2e-07   28.7   0.1    1.2e-06   28.2   0.1    1.3  1  HTH_IclR       IclR helix-turn-helix domain
      5e-06   26.0   0.0    7.2e-06   25.5   0.0    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
    6.8e-05   22.7   0.1    8.6e-05   22.3   0.1    1.1  1  HTH_5          Bacterial regulatory protein, arsR family
    0.00015   21.6   0.0     0.0002   21.1   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00022   21.1   0.0    0.00033   20.5   0.0    1.3  1  MarR           MarR family
    0.00039   20.3   0.1    0.00079   19.3   0.1    1.5  1  PadR           Transcriptional regulator PadR-like family
    0.00042   20.3   0.0    0.00063   19.7   0.0    1.4  1  HTH_29         Winged helix-turn helix
    0.00042   20.4   0.0    0.00077   19.5   0.0    1.4  1  HTH_28         Helix-turn-helix domain
    0.00052   19.7   0.0     0.0011   18.8   0.0    1.5  1  HTH_23         Homeodomain-like domain
    0.00066   19.5   0.0     0.0011   18.7   0.0    1.5  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    0.00072   19.2   0.0      0.001   18.8   0.0    1.2  1  RP-C           Replication protein C N-terminal domain
    0.00078   19.6   0.0    0.00091   19.4   0.0    1.2  1  FUR            Ferric uptake regulator family
     0.0011   19.2   0.0     0.0018   18.6   0.0    1.2  1  Rrf2           Transcriptional regulator
      0.002   18.1   0.0      0.003   17.5   0.0    1.3  1  HTH_Crp_2      Crp-like helix-turn-helix domain
     0.0043   16.4   0.0      0.011   15.2   0.0    1.7  2  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
     0.0051   16.7   0.0     0.0074   16.2   0.0    1.3  1  HTH_11         HTH domain
     0.0052   16.6   0.0      0.011   15.6   0.0    1.5  1  HTH_30         PucR C-terminal helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.027   14.1   0.0    1.3  1  GntR           Bacterial regulatory proteins, gntR family
      0.026   14.3   0.0      0.046   13.5   0.0    1.4  1  HTH_10         HTH DNA binding domain
      0.038   13.8   0.0      0.048   13.5   0.0    1.1  1  TFIIE_alpha    TFIIE alpha subunit
      0.068   13.8   0.0       0.16   12.6   0.0    1.6  1  Mga            Mga helix-turn-helix domain
      0.076   12.7   0.1       0.16   11.7   0.0    1.6  1  Sigma70_r4_2   Sigma-70, region 4
      0.076   13.0   0.0       0.11   12.5   0.0    1.3  1  HTH_36         Helix-turn-helix domain
       0.15   12.2   0.0       0.34   11.1   0.0    1.5  2  DUF1492        Protein of unknown function (DUF1492)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.5   4.1e-11   2.9e-08       3      56 ..      10      62 ..       8      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 4.1e-11
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ++++L+++  r il+   +++  +a+ela++ +ls  t++++L+ L+e+gLv +
  gi|313126991|ref|YP_004037261.1| 10 LLDVLGDEDARSILASV-GERSCSAKELADEHGLSLPTVYRRLDRLAEHGLVAS 62
                                      7899*************.**********************************86 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.2   9.8e-10   6.8e-07      10      54 ..      10      63 ..       5      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.8e-10
                                      HHHHHHCTTTS.........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgr.........dltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +L +Lg+++ r          ++++ela++ gls ++v r+l+rL ++GLv   
  gi|313126991|ref|YP_004037261.1| 10 LLDVLGDEDARsilasvgerSCSAKELADEHGLSLPTVYRRLDRLAEHGLVASN 63
                                      5667777777777777777668*****************************655 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   1.8e-09   1.2e-06       9      51 ..      11      63 ..       9      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.8e-09
                                      HCT-CTTBSS..........-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  9 Ldalaeapqe..........ltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      Ld l+ ++ +           + +elA++ gl+ +tv+R L  L e+G+v  +
  gi|313126991|ref|YP_004037261.1| 11 LDVLGDEDARsilasvgersCSAKELADEHGLSLPTVYRRLDRLAEHGLVASN 63
                                      6666666666666666666689****************************876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0     1e-08   7.2e-06      16      47 ..      29      60 ..      20      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1e-08
                            HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                       ++s +eLA++ glS++tv rrl+rL e Gl+
  gi|313126991|ref|YP_004037261.1| 29 RSCSAKELADEHGLSLPTVYRRLDRLAEHGLV 60
                                      5699************************9997 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   1.2e-07   8.6e-05       2      46 ..      17      61 ..      16      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-07
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +  + IL ++ e+++++ ela+e gls +tv + L +L e GLV 
  gi|313126991|ref|YP_004037261.1| 17 EDARSILASVGERSCSAKELADEHGLSLPTVYRRLDRLAEHGLVA 61
                                      56678999999*********************************6 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     3e-07    0.0002      19      64 ..      27      78 ..      14      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3e-07
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYra 64
                                       + + +a+e+a e g++ ++vY+ L +L + GlV  ++        +k+Y+a
  gi|313126991|ref|YP_004037261.1| 27 GERSCSAKELADEHGLSLPTVYRRLDRLAEHGLVASNDTVeedgthYKRYEA 78
                                      5667789***************************988644467788888887 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.8e-07   0.00033      17      49 ..      30      62 ..      21      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.8e-07
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieR 49
                                      ++s +eLa+  g+s +tv r ldrL ++Gl+ +
  gi|313126991|ref|YP_004037261.1| 30 SCSAKELADEHGLSLPTVYRRLDRLAEHGLVAS 62
                                      799***************************975 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.2e-06   0.00079      29      66 ..      42      79 ..      32      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                                      TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEES CS
                              PadR 29 lseGslYpaLkrLekeglveseweesgegpprkyYrlT 66
                                      ls  ++Y+ L+rL ++glv+s+ + +++g   k Y+ T
  gi|313126991|ref|YP_004037261.1| 42 LSLPTVYRRLDRLAEHGLVASNDTVEEDGTHYKRYEAT 79
                                      56679******************************988 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   9.1e-07   0.00063      14      46 ..      32      64 ..      22      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.1e-07
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGlaalld 46
                                      + +++A  +gls +tvyr l+r  e+Gl a  d
  gi|313126991|ref|YP_004037261.1| 32 SAKELADEHGLSLPTVYRRLDRLAEHGLVASND 64
                                      4899***********************988665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.1e-06   0.00077      14      41 ..      32      59 ..      20      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                            HTH_28 14 svreaArelgisrrtvyrWikryeegGi 41
                                      s++e+A e+g+s  tvyr + r+ e+G+
  gi|313126991|ref|YP_004037261.1| 32 SAKELADEHGLSLPTVYRRLDRLAEHGL 59
                                      8899**********************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.5e-06    0.0011      20      47 ..      33      60 ..      32      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                            HTH_23 20 vreIAreLgvsrrTvyrwlkryreeGle 47
                                       +e A+e+g s  Tvyr l r +e+Gl 
  gi|313126991|ref|YP_004037261.1| 33 AKELADEHGLSLPTVYRRLDRLAEHGLV 60
                                      6899**********************85 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06    0.0011      19      41 ..      32      54 ..      17      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                     HTH_AsnC-type 19 syaeLAervGlSestvlrRvrrL 41
                                      s +eLA++ GlS +tv rR++rL
  gi|313126991|ref|YP_004037261.1| 32 SAKELADEHGLSLPTVYRRLDRL 54
                                      889*******************9 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.5e-06     0.001      73     112 ..      32      76 ..      30      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                              RP-C  73 sNaqLsralglsestlrrhlaaLveaGliirrDs.....pngkRy 112
                                       s+++L+ ++gls  t+ r l +L+e Gl++  D        +kRy
  gi|313126991|ref|YP_004037261.1|  32 SAKELADEHGLSLPTVYRRLDRLAEHGLVASNDTveedgTHYKRY 76 
                                       899**************************9877511111556666 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.3e-06   0.00091      35      74 ..      37      77 ..       4     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-06
                                      HTTTT--HHHHHHHHHHHHHTTSEEEEEET.TSEEEEEESS CS
                               FUR 35 eedpeislaTVYrtLklleeaglvkelefe.dgesryelak 74
                                       +++ +sl TVYr L+ l+e glv + ++  ++ ++y+  +
  gi|313126991|ref|YP_004037261.1| 37 ADEHGLSLPTVYRRLDRLAEHGLVASNDTVeEDGTHYKRYE 77
                                      456789******************99987547778887654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.7e-06    0.0018      17      58 ..      23      63 ..      19      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.7e-06
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      La+  e++ +s++e+a+++++s + + + l +L+++glv s 
  gi|313126991|ref|YP_004037261.1| 23 LASVGERS-CSAKELADEHGLSLPTVYRRLDRLAEHGLVASN 63
                                      66777766.******************************995 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.4e-06     0.003      19      54 ..      28      63 ..       7      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.4e-06
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisrg 54
                                      e + + +elA+  Gl+  tv r l +L ++gl+  +
  gi|313126991|ref|YP_004037261.1| 28 ERSCSAKELADEHGLSLPTVYRRLDRLAEHGLVASN 63
                                      4578999*************************9854 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.5e-05     0.011      20      51 ..      22      54 ..      19      55 .. 0.82
   2 ?   -2.1   0.0       3.9   2.7e+03      16      25 ..      80      89 ..      79      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                      HTH_Tnp_ISL3 20 ilellles.rsvkavArqlgvSwtTVwrildry 51
                                      il+++ e+  s k+ A+++g+S  TV r+ldr+
  gi|313126991|ref|YP_004037261.1| 22 ILASVGERsCSAKELADEHGLSLPTVYRRLDRL 54
                                      555555555599*******************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
                      HTH_Tnp_ISL3 16 leayilelll 25
                                      +e+++++l+ 
  gi|313126991|ref|YP_004037261.1| 80 FERAVVTLHG 89
                                      8999999975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05    0.0074      16      43 ..      31      58 ..      19      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                       s++eLA+e ++S  tv+r++++L e g
  gi|313126991|ref|YP_004037261.1| 31 CSAKELADEHGLSLPTVYRRLDRLAEHG 58
                                      69**********************8877 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05     0.011       9      38 ..      27      56 ..      20      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                      HHTTT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30  9 lenggnisatAkaLhvHrnTlryRLrriee 38
                                       e ++++++ A++ +++  T++ RL+r+ e
  gi|313126991|ref|YP_004037261.1| 27 GERSCSAKELADEHGLSLPTVYRRLDRLAE 56
                                      5779***********************998 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     4e-05     0.027      27      57 ..      33      63 ..      26      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverr 57
                                       +eLa+e g s +tv + L+rL++ glv ++
  gi|313126991|ref|YP_004037261.1| 33 AKELADEHGLSLPTVYRRLDRLAEHGLVASN 63
                                      58**************************876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.6e-05     0.046      22      46 ..      29      53 ..      27      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-05
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrk 46
                                      R +++keLA+e G+s +t++ +L +
  gi|313126991|ref|YP_004037261.1| 29 RSCSAKELADEHGLSLPTVYRRLDR 53
                                      99*******************9977 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.9e-05     0.048      13      73 ..      17      76 ..       7      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-05
                                      HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEE CS
                       TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyy 73
                                      e+a  +l ++ e+++ +  +la e ++ l+ + + L rL e +lv     ++e+ + yk y
  gi|313126991|ref|YP_004037261.1| 17 EDARSILASVGERSCSA-KELADEHGLSLPTVYRRLDRLAEHGLVASNDTVEEDGTHYKRY 76
                                      67788999999888766.67*******************************9877777665 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00023      0.16      28      55 ..      28      55 ..      18      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                                      HSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                               Mga 28 eeevsieelaqelyiSestlkrkikeln 55
                                      e+++s +ela+e+ +S  t++r +++l 
  gi|313126991|ref|YP_004037261.1| 28 ERSCSAKELADEHGLSLPTVYRRLDRLA 55
                                      7889*******************99986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00023      0.16      26      49 ..      30      53 ..      16      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                                      ---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksrlsR 49
                                       +s kE A + g+s  tV++rl R
  gi|313126991|ref|YP_004037261.1| 30 SCSAKELADEHGLSLPTVYRRLDR 53
                                      6899*****************966 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016      0.11      27      55 .]      32      60 ..      24      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s + la   gls  Tv+r ++ L+++G++
  gi|313126991|ref|YP_004037261.1| 32 SAKELADEHGLSLPTVYRRLDRLAEHGLV 60
                                      66889999*******************85 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0005      0.34      46      95 ..       5      55 ..       2      60 .. 0.86
   2 ?   -1.5   0.0       4.1   2.8e+03      27      56 ..      59      88 ..      55      95 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                           DUF1492 46 lelqrlidklensdsrsvLrmvyidkltvwqvidklnisrstyyrll.rva 95
                                      +e + l+d l + d+rs+L  v     ++ ++ d+ ++s  t yr l r a
  gi|313126991|ref|YP_004037261.1|  5 RERETLLDVLGDEDARSILASVGERSCSAKELADEHGLSLPTVYRRLdRLA 55
                                      7788999*********************************99997651555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.1
                           DUF1492 27 Lvvakediekktaeaikkklelqrlidkle 56
                                      Lv+ ++ +e++ +   + +  ++r + +l+
  gi|313126991|ref|YP_004037261.1| 59 LVASNDTVEEDGTHYKRYEATFERAVVTLH 88
                                      778888888887776666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 873.13
//
Query:       gi|313126992|ref|YP_004037262.1|  [L=132]
Description: hypothetical protein Hbor_22560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 964.61
//
Query:       gi|313126993|ref|YP_004037263.1|  [L=188]
Description: prpp-binding protein, adenine/guanine phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-18   65.5   2.3    5.4e-18   65.0   2.3    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00035   20.1   0.1    0.00049   19.6   0.1    1.3  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.017   14.6   0.8      0.025   14.1   0.8    1.3  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   2.3   9.1e-22   5.4e-18      13     142 ..      40     168 ..      32     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 9.1e-22
                                       EEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...........EE----T CS
                      Pribosyltran  13 davarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...rlledpa 86 
                                       ++v ++++++  e     d +v++a  G+ + ++++   ++pl+++rk+ y  dg  + +++   +          +
  gi|313126993|ref|YP_004037263.1|  40 EIVIKIIRKADLE---DVDKIVTPAAMGIHISTAVSLMTDIPLVVIRKREYGLDGEISLSQQTGYSEndmFINDVSE 113
                                       4556666666666...999*************************************999987765557776666789 PP

                                       TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.. CS
                      Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfs 142
                                       + +Vl++DD+l+tGgT++a+l++Lk+ g+e+v ++++++k    e +d  + +v++
  gi|313126993|ref|YP_004037263.1| 114 DDRVLVIDDVLSTGGTMCAVLDALKSTGAEVVDTVAVIKKAGPNELDD-TDHHVKT 168
                                       99************************************5544444333.2333333 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   8.2e-08   0.00049     119     160 ..     111     151 ..      92     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.2e-08
                           UPRTase 119 i.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvl 160
                                       + ++++vl++D v++TGg+++a+++ Lk+ g++   +  ++v+
  gi|313126993|ref|YP_004037263.1| 111 VsEDDRVLVIDDVLSTGGTMCAVLDALKSTGAE--VVDTVAVI 151
                                       447899***********************7765..45555555 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.8   4.2e-06     0.025     118     181 ..     111     174 ..      97     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-06
                          PRTase_2 118 laaakelvLvDDEistGktalnliralqeklprkryvvvslvdwrseedeaafaaleeelgiri 181
                                       ++++++++++DD +stG t++++++al+++  +   +v+ +     +e +++ +++++ +++++
  gi|313126993|ref|YP_004037263.1| 111 VSEDDRVLVIDDVLSTGGTMCAVLDALKSTGAEVVDTVAVIKKAGPNELDDTDHHVKTLINVTV 174
                                       467788999******************9988775555666655555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1236.87
//
Query:       gi|313126994|ref|YP_004037264.1|  [L=630]
Description: peptide ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-55  189.2   6.9    1.4e-55  188.8   6.9    1.1  1  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
  ------ inclusion threshold ------
       0.12   12.3   0.9        0.2   11.6   0.9    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.8   6.9   1.6e-59   1.4e-55       1     353 [.     110     522 ..     110     548 .. 0.88

  Alignments for each domain:
  == domain 1  score: 188.8 bits;  conditional E-value: 1.6e-59
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTS.SB-SHHHHHHHHHHHHTGGGHCTTHHHHHC.......TCTEEE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDG.tpltAeDvvfsferlldpdtasgyasllee.......dqdikk 69 
                                       e+vp   es  ++++D+k++tf+LR+++++sD   +ltAeD+v++ ++l + + ++ ++ + ++       d +  +
  gi|313126994|ref|YP_004037264.1| 110 EIVPMWVES--YTEKDKKEWTFTLRDNLRWSDPyGDLTAEDWVYTAQNLYGAKAPGESKTKENWagvvqysDWKNLT 184
                                       689******..77********************9************************999999*******999*** PP

                                       EEEEETTEEEEEESSETTTTTTHCHHHHHHHGC..........CHTCTCTTTTTGTTTSE-B.SSSEEEEEEETTTE CS
                         SBP_bac_5  70 veavddytvrftlkkpnalfltllaavpasiak..........kaaekeddkdkdtnekpvg.tGPYklkefkpgqk 135
                                       +e+  ++++++tl+ p++ f++ +a +                k  e  +++++ +   + g  GPY  +e++++++
  gi|313126994|ref|YP_004037264.1| 185 IEKAGKRKLKVTLPGPQPAFIASTAFWGGRCLPkdlvkgyvedKDIEGLKQDEELNSLSYTGnLGPYDYEEWQRESR 261
                                       *****************************99999******997444455555555555666689************* PP

                                       EEEEE-TTST.............TTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEE CS
                         SBP_bac_5 136 ivlernpdYw.............gggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvly 199
                                        v +r +dY+              +++p++++ e+k+i ++++r+a+l+ G++ +++++p + +eq+++ ++lk  +
  gi|313126994|ref|YP_004037264.1| 262 FVATRADDYYlrevagseeiperFAEAPYFEKYELKIIGEESTRLASLKEGDLTYFEDVPSQKVEQFQQMDHLKF-R 337
                                       *********99**********98779*************************************************.* PP

                                       EEEEEEEEEEEETTT...STGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH...S CS
                         SBP_bac_5 200 espgggvtylafNtk...kppfddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka...y 270
                                       + p++   + + N++   +++++ k+vR+Als Ai +++i++++++g  t+a+++ p++sp++  ++ +++     y
  gi|313126994|ref|YP_004037264.1| 338 FPPNPFCSMAYYNQRsngWEMLQRKEVRRALSTAISKKAIAENIYRGFPTVAHTFQPEWSPWYLTDKVEQFGVgdsY 414
                                       ***************************************************************99999887668888 PP

                                       HHHHHHHHHHHTT-BCSSTSCEETC.......EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEE.CHH... CS
                         SBP_bac_5 271 dpekAkklLkeaGykdgdggglrek.......klkltlllasgspaekaiaeliqqqlkkiGikvevktv.dwa... 336
                                         ekA+k++kea  +++ +g+  +k       + +l + + +gs+ ++ +ae+++q+l+kiGikv   +  +++   
  gi|313126994|ref|YP_004037264.1| 415 GSEKARKMMKEALSDTN-YGYDGDKlvdgngeQVELSFVYRAGSQNNQTVAEFFKQELAKIGIKVAPTNGgPFNtlq 490
                                       8***********88776.555555578889**9**********************************9998887788 PP

                                       ...............HHHHHHHHCTTESEEEE CS
                         SBP_bac_5 337 ...............atylervkdgdfdmill 353
                                                      ++  +++++  +d++ +
  gi|313126994|ref|YP_004037264.1| 491 nkymltstsdgtpsfNAGPDATSQEPWDLMYG 522
                                       77777777777777766666777777776665 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   2.2e-05       0.2       2      25 ..      10      32 ..       9      33 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR+ LK+ ++++AA+ l+gc++
  gi|313126994|ref|YP_004037264.1| 10 IDRRSWLKALGVGGAAG-LAGCSG 32
                                      689999**888888776.667765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (630 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 4038.23
//
Query:       gi|313126995|ref|YP_004037265.1|  [L=322]
Description: peptide ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-31  107.9  10.3    5.1e-31  107.9  10.3    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.021   15.3   3.4      0.021   15.3   3.4    3.3  3  FtsX          FtsX-like permease family
       0.05   13.5   0.1       0.05   13.5   0.1    3.2  4  Bac_export_3  Bacterial export proteins, family 3
       0.14   12.1   0.5       0.98    9.5   0.0    2.4  2  DUF1471       Protein of unknown function (DUF1471)
        0.2   11.8   0.4        0.5   10.6   0.4    1.6  1  TPR_2         Tetratricopeptide repeat
       0.32   11.4   5.2         25    5.3   5.1    2.8  1  CPBP          CPBP intramembrane metalloprotease
        1.5    9.1   0.0        1.5    9.1   0.0    3.3  3  CD225         Interferon-induced transmembrane protein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.9     0.056   1.4e+02      99     125 ..       3      29 ..       1     117 [. 0.84
   2 !  107.9  10.3     2e-34   5.1e-31       1     184 [.     118     318 ..     118     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.056
                      BPD_transp_1  99 rkvvlPnalppiitglilafggllgga 125
                                       ++++ ++a ++++t++il++++ l +a
  gi|313126995|ref|YP_004037265.1|   3 WYITRRLAWTVVATLIILSLTFGLMAA 29 
                                       788899999999999999999887766 PP

  == domain 2  score: 107.9 bits;  conditional E-value: 2e-34
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................vilsilghlilpviill 60 
                                       g+ +G+++a++rn+  d++ + + +++ s+P f++ail++l+f                   l+ +++l+ p ++++
  gi|313126995|ref|YP_004037265.1| 118 GVAIGLYSATHRNSLEDYAASAFAFFGISIPDFWFAILMILIFgvwlgwipiyyhsdvpwLSLQNAQQLVAPTLVVT 194
                                       799********************************************************99999************* PP

                      BPD_transp_1  61 llsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggl.lggavlleflgswpG 136
                                       l s+a  +r+ r+ al+ ++ ++v++a+a+Ga+ w+++ +++++ al p+ t l+  + ++ l  + l+e +++ pG
  gi|313126995|ref|YP_004037265.1| 195 LSSIASEMRFSRATALEYVNAEFVKTAKAKGANSWRRVTRHIFRPALVPLSTILVGDILNIvLVSSYLVEVVFGIPG 271
                                       ***********************************************************99788999********** PP

                      BPD_transp_1 137 lgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       lg+l   ail++d+s+ + g+vl+ +++ ++ nl+ d+ +++ldpr+ 
  gi|313126995|ref|YP_004037265.1| 272 LGQLSYKAILQQDVSLVL-GTVLIPTFIAIIGNLFQDLAYTVLDPRID 318
                                       ******************.***************************96 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.15   3.8e+02      19      39 ..       8      28 ..       1      56 [. 0.64
   2 ?   15.3   3.4   8.1e-06     0.021      22      90 ..     100     171 ..      87     175 .. 0.65
   3 ?   -1.3   2.6       1.2   3.1e+03      51      77 ..     280     300 ..     218     315 .. 0.53

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.15
                              FtsX 19 llllteillitlvalviGlgl 39
                                      +l +t ++ +++++l +Gl +
  gi|313126995|ref|YP_004037265.1|  8 RLAWTVVATLIILSLTFGLMA 28
                                      555666666666666666555 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 8.1e-06
                              FtsX  22 lteillitlvalviGlglgllaaqllsdvllssvfs.......selkisidlitvliiivlllllallagllsisk 90 
                                       +  +++++ +al+i++++g+++  +      +  +s         + + i++ +++++i+++l++ +  g+++i+ 
  gi|313126995|ref|YP_004037265.1| 100 WPYSVMYGTPALIISTVVGVAIGLY----SATHRNSledyaasAFAFFGISIPDFWFAILMILIFGVWLGWIPIYY 171
                                       3344455555555555555555444....33332222233444888999*************************96 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                              FtsX  51 llssvfsselkisidlitvliiivlll 77 
                                       +l+       ++s+ l tvli  ++++
  gi|313126995|ref|YP_004037265.1| 280 ILQ------QDVSLVLGTVLIPTFIAI 300
                                       222......223333333333333333 PP

>> Bac_export_3  Bacterial export proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.4      0.58   1.5e+03      14      30 ..      11      27 ..       6      29 .. 0.69
   2 ?   13.5   0.1     2e-05      0.05       2      37 ..      92     127 ..      91     129 .. 0.91
   3 ?   -2.7   0.9       2.3   5.9e+03      54      65 ..     153     164 ..     147     167 .. 0.71
   4 ?   -3.3   0.1       3.4   8.7e+03      16      25 ..     186     195 ..     180     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.58
                      Bac_export_3 14 lllsaplllvalvvGlv 30
                                       +++a l++ +l  Gl+
  gi|313126995|ref|YP_004037265.1| 11 WTVVATLIILSLTFGLM 27
                                      56677777777777775 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2e-05
                      Bac_export_3   2 vidlarealllvlllsaplllvalvvGlvvsifQaa 37 
                                       vi+ ++ea    ++  +p+l++++vvG+++++  a+
  gi|313126995|ref|YP_004037265.1|  92 VIQAISEAWPYSVMYGTPALIISTVVGVAIGLYSAT 127
                                       688899999999*******************98775 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.3
                      Bac_export_3  54 vllvllllgpwm 65 
                                        +l++l++g w+
  gi|313126995|ref|YP_004037265.1| 153 AILMILIFGVWL 164
                                       567778888776 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 3.4
                      Bac_export_3  16 lsaplllval 25 
                                       l+ap l+v+l
  gi|313126995|ref|YP_004037265.1| 186 LVAPTLVVTL 195
                                       5667776665 PP

>> DUF1471  Protein of unknown function (DUF1471)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.47   1.2e+03      32      48 ..      35      50 ..      33      53 .. 0.82
   2 ?    9.5   0.0   0.00038      0.98       9      36 ..     204     230 ..     200     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.47
                                      -SEEEECCECC..CTT.E CS
                           DUF1471 32 AkyYrItsarennggn.l 48
                                      A++Y+ ++++e  ggn +
  gi|313126995|ref|YP_004037265.1| 35 AASYVAQQVQE--GGNyQ 50
                                      899*9999999..99944 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00038
                                       ECSS-SSHHHHHHHHHHHHHHCT-SEEE CS
                           DUF1471   9 vsgvfgspsdledalskkAdekGAkyYr 36 
                                       +s ++++++ ++++  k A++kGA ++r
  gi|313126995|ref|YP_004037265.1| 204 FS-RATALEYVNAEFVKTAKAKGANSWR 230
                                       67.89999*****************997 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4    0.0002       0.5      14      28 ..      46      60 ..      34      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                             TPR_2 14 lgdyeeAleafekAl 28
                                       g+y+eA e +ekA 
  gi|313126995|ref|YP_004037265.1| 46 GGNYQEAQESYEKAR 60
                                      59***********96 PP

>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.1    0.0097        25      35      77 ..      10     172 ..       1     195 [. 0.71

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0097
                                       .S-.HHHHHHHHHHHHHCSGGGHHHH................................................... CS
                              CPBP  35 gss.tlailissilFglaHlpngpsv................................................... 59 
                                        +  +++++i s+ Fgl+ + + p+                                                    
  gi|313126995|ref|YP_004037265.1|  10 AWTvVATLIILSLTFGLMAASPDPQAasyvaqqvqeggnyqeaqesyekargldkplweryknymvgmvtldwgwse 86 
                                       44446777777788888887776664466677777777777777777777777777777777777777777777777 PP

                                       ....................................................................HHHHHHHHH CS
                              CPBP  60 ....................................................................llaalaGlv 68 
                                                                                                           l+++++G+ 
  gi|313126995|ref|YP_004037265.1|  87 trsqpviqaiseawpysvmygtpaliistvvgvaiglysathrnsledyaasafaffgisipdfwfaiLMILIFGVW 163
                                       77777777777777777777777777777777777777777777777777777777777777777777999999999 PP

                                       HHHHHHHTT CS
                              CPBP  69 lgylylktg 77 
                                       lg++ +++ 
  gi|313126995|ref|YP_004037265.1| 164 LGWIPIYYH 172
                                       999877665 PP

>> CD225  Interferon-induced transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00057       1.5       6      53 ..       9      62 ..       7      64 .. 0.86
   2 ?   -1.6   0.5       1.2   3.1e+03      55      66 ..     112     123 ..     110     125 .. 0.83
   3 ?   -0.6   0.3      0.58   1.5e+03       7      27 ..     151     171 ..     148     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00057
                             CD225  6 lvwsifntlf.cclplGivAl.....vySvkvrdrkmvGdvegAqsasstAkll 53
                                      l w++++tl+   l +G++A      + S+ +++ ++ G++++Aq++ ++A+ l
  gi|313126995|ref|YP_004037265.1|  9 LAWTVVATLIiLSLTFGLMAAspdpqAASYVAQQVQEGGNYQEAQESYEKARGL 62
                                      6899999999888899999975555578999****************9999977 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                             CD225  55 iialvlgiilii 66 
                                       ii++v+g+++ +
  gi|313126995|ref|YP_004037265.1| 112 IISTVVGVAIGL 123
                                       8999**999865 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.58
                             CD225   7 vwsifntlf.cclplGivAlvy 27 
                                       +++i+ +l+  ++ lG++ ++y
  gi|313126995|ref|YP_004037265.1| 151 WFAILMILIfGVW-LGWIPIYY 171
                                       5677777774344.79998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2220.71
//
Query:       gi|313126996|ref|YP_004037266.1|  [L=389]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-29  101.8   5.0    3.5e-29  101.8   5.0    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne
    1.4e-07   31.4   0.0    1.4e-07   31.4   0.0    4.2  5  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.6     0.076   6.8e+02     122     168 ..      72     117 ..      30     125 .. 0.64
   2 !  101.8   5.0   3.9e-33   3.5e-29       1     182 [.     206     386 ..     206     389 .] 0.95

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.076
                      BPD_transp_1 122 lggavlleflgswpGlgtllleailgydyseisnggvlalviavlll 168
                                       +   v + f++ +p   +++++   ++ +s +  ++v+ +v+++l++
  gi|313126996|ref|YP_004037266.1|  72 IATLVTVAFYAVYPLYDNPRMTRRYWREFSKNR-AAVISGVFLTLIF 117
                                       334444555555554555555566666666555.5555555555555 PP

  == domain 2  score: 101.8 bits;  conditional E-value: 3.9e-33
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       g+ +G +aa ++++  d+ll++++++ l++P+f l +ll++      + g+l+l ++i +l+s++ ++rl+r++al+
  gi|313126996|ref|YP_004037266.1| 206 GTAVGTIAA-YSGGLMDELLMRYVDIQLTFPTFFLYLLLLY-----LYGGTLFLLIVIFGLTSWGSTARLVRSEALQ 276
                                       6789*****.******************************7.....788899999********************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                        +++++++aa   Gas++ ++rk+++Pn+  ++it + l +++l+   ++ +flg    lg++++ +++g+ ++++ 
  gi|313126996|ref|YP_004037266.1| 277 RREEEYIQAAQSAGASEFWVIRKHLVPNVSNTVITNASLLIPSLILFEAAFSFLG----LGDPTI-PSWGQVIAAGR 348
                                       *******************************************************....997765.78888888888 PP

                      BPD_transp_1 155 ..........nggvlalviavlllnlvadilqrlldpr 182
                                                  ++ ++l   vl+ln+v d+l ++ldpr
  gi|313126996|ref|YP_004037266.1| 349 sdidtawwisTIPGVFLFTTVLALNFVGDALRDALDPR 386
                                       899999999*9999***********************9 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.08   7.2e+02      17      28 ..      34      45 ..      33      68 .. 0.64
   2 ?    0.6   0.3     0.065   5.8e+02      22      34 ..      71      85 ..      69      93 .. 0.75
   3 !   31.4   0.0   1.6e-11   1.4e-07       4      51 .]      94     141 ..      91     141 .. 0.79
   4 ?   -2.0   0.5      0.42   3.8e+03      18      30 ..     194     206 ..     194     223 .. 0.65
   5 ?   -2.3   0.8       0.5   4.5e+03      25      32 ..     251     258 ..     238     264 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.08
                            OppC_N 17 vvglvillllll 28
                                      +v++ il++ll+
  gi|313126996|ref|YP_004037266.1| 34 LVSMGILAVLLA 45
                                      578888887775 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.065
                            OppC_N 22 illlllliaifa..P 34
                                      ++++l+ +a++a  P
  gi|313126996|ref|YP_004037266.1| 71 LIATLVTVAFYAvyP 85
                                      6899999***98434 PP

  == domain 3  score: 31.4 bits;  conditional E-value: 1.6e-11
                            OppC_N   4 qdawrrFkrNklAvvglvilllllliaifaPliaPydp.qdliqnllpP 51 
                                       ++ wr F +N++Av++ v+l l++ + +++P+++   p  ++ ++++pP
  gi|313126996|ref|YP_004037266.1|  94 RRYWREFSKNRAAVISGVFLTLIFGLGLVGPMFVSK-PeLNVLAQYQPP 141
                                       678******************************733.232222237887 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.42
                            OppC_N  18 vglvillllllia 30 
                                       vgl+  l+++li 
  gi|313126996|ref|YP_004037266.1| 194 VGLITPLIIILIG 206
                                       6777777777774 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 0.5
                            OppC_N  25 lllliaif 32 
                                       l+lli+if
  gi|313126996|ref|YP_004037266.1| 251 LFLLIVIF 258
                                       33444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2709.69
//
Query:       gi|313126997|ref|YP_004037267.1|  [L=354]
Description: oligopeptide/dipeptide ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-26   91.8   0.0    7.4e-26   91.3   0.0    1.2  1  ABC_tran         ABC transporter
    1.4e-17   63.9   0.3    3.2e-17   62.8   0.3    1.6  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
      1e-05   25.6   0.1    0.00027   20.9   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0012   18.4   0.0     0.0028   17.1   0.0    1.5  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0022   18.3   0.2       0.04   14.2   0.0    2.1  2  AAA_22           AAA domain
     0.0046   17.4   0.0     0.0091   16.4   0.0    1.4  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.039   13.7   0.2       0.18   11.5   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
      0.041   13.9   0.0      0.091   12.8   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
      0.046   13.5   0.0       0.09   12.5   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.053   13.4   0.0      0.085   12.8   0.0    1.3  1  NACHT            NACHT domain
      0.065   12.7   0.0        0.1   12.1   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.065   12.9   0.0      0.093   12.4   0.0    1.4  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.13   11.9   0.3       0.55    9.9   0.0    1.9  2  IstB_IS21        IstB-like ATP binding protein
       0.15   12.2   0.0       0.27   11.3   0.0    1.4  1  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0   5.8e-29   7.4e-26       2     136 ..      26     184 ..      25     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 5.8e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.....EETTCEGGG...B-HHHCC.HCEEEE-SS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxx...xxxxxxx.xxxxxxxxx.. RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGei.....lldgkdlke...qeleslr.keigvlpqe.. 67 
                                       + vsl++ +ge+v +vGe+G+GK+  ++ +++l     Gei     ++dg+d+ +    ele lr  +ig ++q+  
  gi|313126997|ref|YP_004037267.1|  26 DGVSLDVDRGETVCVVGESGSGKTVTAESITRLIPEPPGEIvggevRFDGDDVLSmseSELEDLRgGRIGHIFQNpq 102
                                       78*******************************99955555555559999999888885555554279*******65 PP

                                       --S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEE CS
                                       xxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkll 130
                                         l+p +t++ +              e+ e+  ++l+++g+++ +++++++ p+++SgG+kqrv++a+al+++p+ll
  gi|313126997|ref|YP_004037267.1| 103 GALNPVYTIGWQireaiqlhddvsdeEAHERTIDLLDRVGIPD-ATSRIDDYPHEFSGGMKQRVVIAMALASNPDLL 178
                                       5699999988888999******999888888************.888889*************************** PP

                                       EEESTT CS
                                       xxxxxx RF
                          ABC_tran 131 llDEpt 136
                                       ++DEpt
  gi|313126997|ref|YP_004037267.1| 179 IADEPT 184
                                       *****9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.3   2.5e-20   3.2e-17       1      65 []     236     297 ..     236     297 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.5e-20
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E+g++ ++f++p HPYT+aLl+++p   ++ +    i g+ ps++  ++GC+F+pRCp+a++ C
  gi|313126997|ref|YP_004037267.1| 236 MEQGDVYEIFENPSHPYTRALLECLPGRGERME---AIGGSLPSTTSPPSGCRFNPRCPYAVADC 297
                                       7*************************8755555...***************************99 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.064        82       3      63 ..      39      87 ..      38     105 .. 0.78
   2 !   20.9   0.0   2.1e-07   0.00027     229     302 ..     149     220 ..      96     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.064
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                      +++G  gsGK+   + +  l            ++ + g+i + + ++d++d  + +e e+e
  gi|313126997|ref|YP_004037267.1| 39 CVVGESGSGKTVTAESITRL------------IPEPPGEIVGGEVRFDGDDVLSMSESELE 87
                                      689********999999998............77777777777777777777777777766 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.1e-07
                            AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       + +  ++e+S G+k+   ++ al++ +   +ll+ DEp + L+  ++  +l+ll++ ++  ++ +++ TH+  ++
  gi|313126997|ref|YP_004037267.1| 149 RIDDYPHEFSGGMKQRVVIAMALASNP---DLLIADEPTTALDVTIQMQILRLLNQVQDeFNTGIVMITHDLGVV 220
                                       344468999******944444444444...9***********************99999999*********8876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.2e-06    0.0028      26     213 ..      37     232 ..      24     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH...CCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrse...klsdlihk.skekasvkkaeveitfdnedkklkiekeevs 98 
                                         ++vG+ GSGK+   ++i  ++ e   + +  e   + +d+++  ++e + +  +++  +f+n++ +    ++ ++
  gi|313126997|ref|YP_004037267.1|  37 TVCVVGESGSGKTVTAESITRLIPEPPGEIVGGEvrfDGDDVLSMsESELEDLRGGRIGHIFQNPQGA---LNPVYT 110
                                       4579***************999977766544443111235677764777899999***********99...566677 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                       i  ++ +  + +  + ++e++++ + +ll ++gi            ++SgG k+ v +a+ +A +      l + De
  gi|313126997|ref|YP_004037267.1| 111 IGWQIREAIQLHDDVSDEEAHERTI-DLLDRVGIPDAtsriddyphEFSGGMKQRVVIAMALASN----PDLLIADE 182
                                       7777777666666688888887665.78999999877888888888********99999998854....358899** PP

                                       TTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-.SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 167 idaaLDeknvkkvaellkekskn..aQfivislreemleka.dklvgvtk 213
                                          aLD +   ++ +ll++ +++  + +++i+++ ++++++ d++v ++ 
  gi|313126997|ref|YP_004037267.1| 183 PTTALDVTIQMQILRLLNQVQDEfnTGIVMITHDLGVVAEVaDRVVVMYA 232
                                       ******************88876337788899998887665366666654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.1e-05      0.04       8      30 ..      38      60 ..      32     109 .. 0.84
   2 ?    2.1   0.1      0.17   2.2e+02      91     128 ..     170     213 ..     113     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                      ++v+GesG+GKT++++ +++  +
  gi|313126997|ref|YP_004037267.1| 38 VCVVGESGSGKTVTAESITRLIP 60
                                      789*************9988765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.17
                            AAA_22  91 v....ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       +    + lli DE    l+   ++++l+ L + ++  ++++ ++++
  gi|313126997|ref|YP_004037267.1| 170 AlasnPDLLIADEPTTaLDvtiQMQILRLLNQVQD--EFNTGIVMI 213
                                       23445789*****9998988666999999999999..999999887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.1e-06    0.0091      23      52 ..      34      64 ..      23     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.1e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd.g 52
                                      r+e v ++GesG+GK+  ++++ r + +  g
  gi|313126997|ref|YP_004037267.1| 34 RGETVCVVGESGSGKTVTAESITRLIPEPpG 64
                                      458899*****************98877752 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.18      20      45 ..      33      58 ..      16      70 .. 0.80
   2 ?   -0.4   0.0      0.65   8.3e+02     100     119 ..     181     201 ..     157     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                      TSSS-EEEECSTTSSHHHHHHHHHHH CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKellaraihea 45
                                      +   +v ++GesG+GK++ a++i + 
  gi|313126997|ref|YP_004037267.1| 33 DRGETVCVVGESGSGKTVTAESITRL 58
                                      556799***************99876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.65
                                       ET.GGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat 100 De.igelplelQekLlrvlqe 119
                                       De  + l++++Q ++lr+l++
  gi|313126997|ref|YP_004037267.1| 181 DEpTTALDVTIQMQILRLLNQ 201
                                       553457899999999999986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.1e-05     0.091       2      26 ..      38      62 ..      37      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                                      EEEE--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnre 26
                                      v++vG++G+gK+  ae++ +++  +
  gi|313126997|ref|YP_004037267.1| 38 VCVVGESGSGKTVTAESITRLIPEP 62
                                      89*******************9554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05      0.09      11      38 ..      24      51 ..      19      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTl 38
                                        dg ++++d+ +++ ++G+sGsGK+  
  gi|313126997|ref|YP_004037267.1| 24 AVDGVSLDVDRGETVCVVGESGSGKTVT 51
                                      5788999999777************975 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.6e-05     0.085       2      24 ..      37      59 ..      36      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-05
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      +v++ Ge+GsGKT+ ++++ +++
  gi|313126997|ref|YP_004037267.1| 37 TVCVVGESGSGKTVTAESITRLI 59
                                      89**************9998765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05       0.1      30      58 ..      32      60 ..      21      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                             AAA_7 30 lknkkpvllvGptGtGKtviikdllkkld 58
                                      ++++  v++vG++G+GKtv+++++++ ++
  gi|313126997|ref|YP_004037267.1| 32 VDRGETVCVVGESGSGKTVTAESITRLIP 60
                                      678899***************99887655 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.2e-05     0.093      11      37 ..      32      58 ..      22     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.2e-05
                                      EBTT-EEEEEESTTSSHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqslskq 37
                                      + +G++++++g++g Gktv ++s+++ 
  gi|313126997|ref|YP_004037267.1| 32 VDRGETVCVVGESGSGKTVTAESITRL 58
                                      569********************9986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00043      0.55      44      68 ..      32      56 ..      11      59 .. 0.82
   2 ?   -0.7   0.1       0.8     1e+03     105     149 ..     171     217 ..     160     222 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00043
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      +++ e ++++G sG GK+  a ++ 
  gi|313126997|ref|YP_004037267.1| 32 VDRGETVCVVGESGSGKTVTAESIT 56
                                      8999**************9999875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.8
                         IstB_IS21 105 rllkvdllilDdlgl..lpldqaeaellfeviekryerrsiiitsnl 149
                                          ++dlli D+  +      q +   l++ +++ +++  ++it +l
  gi|313126997|ref|YP_004037267.1| 171 LASNPDLLIADEPTTalDVTIQMQILRLLNQVQDEFNTGIVMITHDL 217
                                       45677999999954310333445555666667778888888888765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.27      14      48 ..      28      60 ..      19      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                             DUF87 14 vyldlnklvtrHlAilgsTGsGKSntvavLleell 48
                                      v+ld+++   + ++++g++GsGK+ t+ ++ + + 
  gi|313126997|ref|YP_004037267.1| 28 VSLDVDRG--ETVCVVGESGSGKTVTAESITRLIP 60
                                      67777665..7899****************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2184.33
//
Query:       gi|313126998|ref|YP_004037268.1|  [L=436]
Description: oligopeptide ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-33  116.6   0.0    1.8e-33  115.9   0.0    1.3  1  ABC_tran     ABC transporter
    2.7e-19   69.4   0.1    6.5e-19   68.2   0.1    1.7  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    5.5e-05   23.1   0.5    0.00047   20.1   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00013   22.2   0.1      0.002   18.4   0.1    2.2  1  AAA_22       AAA domain
     0.0048   17.3   0.2      0.021   15.2   0.0    2.0  2  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.067   12.8   0.0      0.067   12.8   0.0    1.2  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.088   12.4   0.1       0.35   10.4   0.1    1.9  2  AAA_25       AAA domain
       0.14   11.0   0.0       0.22   10.3   0.0    1.2  1  UxaC         Glucuronate isomerase
       0.17   11.8   0.0       0.28   11.1   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.21   11.1   0.0       0.33   10.4   0.0    1.2  1  AAA_7        P-loop containing dynein motor region
       0.22   11.5   0.4       0.46   10.4   0.4    1.5  1  DUF2909      Protein of unknown function (DUF2909)
       0.28    9.8   0.0       0.47    9.0   0.0    1.3  1  AAA_13       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.0   1.2e-36   1.8e-33       2     136 ..      35     185 ..      34     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 1.2e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + +s+ +++ge+v++vGe+G+GKSt +  l++l++pt Ge+l++g+d++e   +el+++r+e ++++q+  ++++p+
  gi|313126998|ref|YP_004037268.1|  35 DGISFAVERGETVGLVGESGCGKSTAATSLLRLEDPTDGEVLFEGRDITEyndKELKRFRREAQMIFQDptSSFDPR 111
                                       789***********************************************999****************888999** PP

                                       SBHHHH.............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxx.............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       ++++e+             e  ++   ++++l+++gl+    + +++ p+++SgGqkqr+ laral+ +pkl+++DE
  gi|313126998|ref|YP_004037268.1| 112 MSIGESvaepltvhgmrdrE--RRrriVKDLLERVGLSA---DDIDRYPHEFSGGQKQRIGLARALVLNPKLIVADE 183
                                       **************998542..33345888888888777...666788***************************** PP

                                       TT CS
                                       xx RF
                          ABC_tran 135 pt 136
                                       p 
  gi|313126998|ref|YP_004037268.1| 184 PV 185
                                       *7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.1   4.3e-22   6.5e-19       1      61 [.     237     298 ..     237     301 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 4.3e-22
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfa 61 
                                       vE g++++l ++p+HPYT+aLl+s+p++d+ k+ +++++ g++ps+++ ++GC+F++RCp +
  gi|313126998|ref|YP_004037268.1| 237 VEFGRTEDLYEDPQHPYTRALLSSIPQPDPTKRgNAVELTGDVPSPSNPPSGCRFHTRCPEV 298
                                       8**********************************************************986 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.19   2.9e+02       3      19 ..      48      64 ..      47      85 .. 0.80
   2 !   20.1   0.1   3.1e-07   0.00047     165     301 ..     103     220 ..      79     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                            AAA_21  3 vliGpNgsGKSnLLdal 19
                                      +l+G  g+GKS+    l
  gi|313126998|ref|YP_004037268.1| 48 GLVGESGCGKSTAATSL 64
                                      69*********976655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.1e-07
                            AAA_21 165 rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGt 241
                                       +    +++++ +g++   +l+ + +r + +++  + dl+e++ l+a+ ++r                  ++e+S G+
  gi|313126998|ref|YP_004037268.1| 103 DPTSSFDPRMSIGESVAEPLTVHGMRDRERRRRIVKDLLERVGLSADDIDR-----------------YPHEFSGGQ 162
                                       77778888999999999999999***************9999999988887.................688****** PP

                            AAA_21 242 krllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                       k+ ++l+ al   +   +l++ DEp + L+ ++++++l l+ke ++  g   +l +H+ ++
  gi|313126998|ref|YP_004037268.1| 163 KQRIGLARALVLNP---KLIVADEPVSALDVSIQAEILSLMKEIQDeFGLGMLLISHDLSV 220
                                       ***********999...99**********************98888788888888888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.3e-06     0.002      10     128 ..      49     214 ..      42     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsstsskdllrellralglelka............ 70 
                                       ++GesG+GK+t +  ll+  d        + ev+     +t  +++++k ++re   ++++++++            
  gi|313126998|ref|YP_004037268.1|  49 LVGESGCGKSTAATSLLRLEDPT------DGEVLfegrDITEYNDKELKRFRREAQMIFQDPTSSfdprmsigesva 119
                                       79****************98654......666666766677777778888888888888888888888888888888 PP

                            AAA_22  71 ................................erlsseellealeqalrarav...ielliiDEaqh.lr...seea 108
                                                                        r   e    + ++   ara    ++l++ DE    l+   ++e+
  gi|313126998|ref|YP_004037268.1| 120 epltvhgmrdrerrrrivkdllervglsaddiDRYPHEFSGGQKQRIGLARALvlnPKLIVADEPVSaLDvsiQAEI 196
                                       77777777765554444444444444444443333333333444444444444888899999997766878555889 PP

                            AAA_22 109 leeLrsllnlsrkgvqliLv 128
                                       l+  +++++  ++g+ ++L+
  gi|313126998|ref|YP_004037268.1| 197 LSLMKEIQD--EFGLGMLLI 214
                                       999899999..888888887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.021      23      52 ..      43      73 ..      32     154 .. 0.80
   2 ?   -1.0   0.1       1.4     2e+03      94     128 ..     348     382 ..     324     412 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd..g 52
                                      r+e v l+GesG+GKs+ +++llr le+   g
  gi|313126998|ref|YP_004037268.1| 43 RGETVGLVGESGCGKSTAATSLLR-LEDPtdG 73
                                      3378999****************5.6555442 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                            AAA_16  94 leawrekleealaavpelagaeasrllellkrlla 128
                                        ++ ++++++++ +  +la+a+a+++l    +lla
  gi|313126998|ref|YP_004037268.1| 348 EDRIKAEIRREFDIPEQLADASAESVLSDALELLA 382
                                       44444444444445555555555444433333332 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.5e-05     0.067       2      38 ..      31      68 ..      30     341 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-05
                                      SHHHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHS CS
                                      xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  2 irvlDal.fpivqGqrtlipgafgvGktvisqslskqs 38
                                      +r++D + f + +G++++++g++g+Gk++ + sl++  
  gi|313126998|ref|YP_004037268.1| 31 VRAVDGIsFAVERGETVGLVGESGCGKSTAATSLLRLE 68
                                      577887548999*******************9999875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00023      0.35      31      54 ..      42      65 ..      36      67 .. 0.91
   2 ?   -3.5   0.0       4.3   6.5e+03     167     188 ..     195     216 ..     186     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                            AAA_25 31 pagelallaGapgtGKttlaldla 54
                                       +ge++ l+G +g+GK+t+a++l 
  gi|313126998|ref|YP_004037268.1| 42 ERGETVGLVGESGCGKSTAATSLL 65
                                      6899999**************985 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.3
                            AAA_25 167 alvealeriarrtgaavllvhH 188
                                       ++++ +++i++++g   ll+ H
  gi|313126998|ref|YP_004037268.1| 195 EILSLMKEIQDEFGLGMLLISH 216
                                       5677788999999999999988 PP

>> UxaC  Glucuronate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00015      0.22     106     159 ..     353     406 ..     344     410 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                              UxaC 106 leLkrvFgidellseksaeeiwekanelLae.eefkarelleksnvevvcttDdP 159
                                        e++r F+i e l + sae++ + a elLa+ ++ +ar+ll + + e+vc t  P
  gi|313126998|ref|YP_004037268.1| 353 AEIRREFDIPEQLADASAESVLSDALELLANgDQSEARDLLGD-EFETVCETATP 406
                                       699**************************87256678888865.68999998777 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.28      86     120 ..      30      65 ..       8      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       + ++++ ++ +++  +t+ lvG+SG GKSt   +ll
  gi|313126998|ref|YP_004037268.1|  30 SVRAVDGISFAVERgETVGLVGESGCGKSTAATSLL 65 
                                       5566777777777769999***********887776 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00022      0.33      26      58 ..      37      69 ..      21      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkld 58
                                      ++  ++++  v lvG++G+GK++ +++ll+  d
  gi|313126998|ref|YP_004037268.1| 37 ISFAVERGETVGLVGESGCGKSTAATSLLRLED 69
                                      5677899999***************99988655 PP

>> DUF2909  Protein of unknown function (DUF2909)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00031      0.46      24      45 ..     127     148 ..     124     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                           DUF2909  24 vkdkgkskrmvraLalRVgLSi 45 
                                       ++d+++ +r+v+ L  RVgLS+
  gi|313126998|ref|YP_004037268.1| 127 MRDRERRRRIVKDLLERVGLSA 148
                                       8********************7 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00031      0.47     525     576 ..     174     223 ..     166     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00031
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffke 576
                                        + k +v D PvS LD  ++  + sl+k+   ++     l+i  H l+  +e
  gi|313126998|ref|YP_004037268.1| 174 LNPKLIVADEPVSALDVSIQAEILSLMKEIQ-DEFGLGMLLI-SHDLSVVRE 223
                                       57899***********************985.3333333333.466666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2575.36
//
Query:       gi|313126999|ref|YP_004037269.1|  [L=230]
Description: intracellular protease/amidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-12   46.1   1.6    2.5e-10   40.4   1.6    2.3  1  DJ-1_PfpI  DJ-1/PfpI family
    1.1e-07   31.8   0.0      4e-06   26.6   0.0    2.3  1  ThiJ_like  ThiJ/PfpI family-like
  ------ inclusion threshold ------
       0.17   11.4   0.0       0.25   10.9   0.0    1.2  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   1.6   4.1e-14   2.5e-10       4     163 ..       7     223 ..       4     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.1e-14
                                       EEEEE.TTBEHHHHHHHHHHHHHTTEEEEEEESS....................TSEEEETTSEEEE-SEEGG.... CS
                         DJ-1_PfpI   4 lvlla.dgvedvElivpvdvlkragikvdvvsvd....................keevkgsrGlkvtvdasld.... 55 
                                       l+++   g+   E ++p+  l++ag++v+v++++                    ++                +    
  gi|313126999|ref|YP_004037269.1|   7 LFIVSeAGYWGEECVEPLTTLSEAGVDVTVATPTgaqpvvdersvapdevgeemSQ----------------Kvlev 67 
                                       5555546777789*********************9777777666666666555533................03333 PP

                                       ..............GCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHH.HTT-EEEEETTTHHHHHHTT...... CS
                         DJ-1_PfpI  56 ..............dvkaaeyDalvlpGGragperlrenekvvelvkefa.ekgklvaaICagpqlLaaag...... 111
                                                      v+a +yDa+v pGG+    ++ ++  +++ + +++  +++    +C++  +La +       
  gi|313126999|ref|YP_004037269.1|  68 henddrladpvpiaTVDATDYDAVVFPGGHGTQWDINQDRHARQALLSAVaGEKGKALVVCHAVGILAFTReadgry 144
                                       334444444555559****************99999999988877666653566667789****9999776222333 PP

                                       TTTTSEE--SGGGHHHHHHTTSEE-SS.................................SEEEETTEEEESSGGGH CS
                         DJ-1_PfpI 112 vlkgrrvTsypavkdklekagakyvdk.................................rvvvdgnlvTsrgpgaa 155
                                       +++ r vT++p+  ++       +vd+                                 +v vdg+l+T+rgp+++
  gi|313126999|ref|YP_004037269.1| 145 LVEDREVTGFPNEWEE------GIVDEndllpdgrklpywiedevtavggawdaeldqetSVTVDGDLITARGPESS 215
                                       5666778888874433......233333333334555555555677777777777********************99 PP

                                       HHHHHHHH CS
                         DJ-1_PfpI 156 iefalell 163
                                        + a++l+
  gi|313126999|ref|YP_004037269.1| 216 AAAAETLI 223
                                       98887776 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   6.8e-10     4e-06       2     106 ..      11     108 ..      10     191 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 6.8e-10
                         ThiJ_like   2 adeGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllga..skeakdiYkelstleeFkeplsls 76 
                                       +++Gy+++e + p+ +l +ag+ v+ +t++g+ p  de+ + +     +g   s++  +++++    +   +p    
  gi|313126999|ref|YP_004037269.1|  11 SEAGYWGEECVEPLTTLSEAGVDVTVATPTGAQPVVDERSVAPDE---VGEemSQKVLEVHEN---DDRLADPVPI- 80 
                                       899***********************************9875533...332002233333322...2223344433. PP

                         ThiJ_like  77 sesFsleeydlvllpGGsdkavrelleser 106
                                           + ++yd+v  pGG++    ++ ++  
  gi|313126999|ref|YP_004037269.1|  81 -ATVDATDYDAVVFPGGHGTQW-DINQDRH 108
                                       .455778999999999999876.4444444 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.1e-05      0.25      29      85 ..      77     131 ..      59     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
                          GATase_3  29 fvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGl 85 
                                        vp+ + +  +d+d+v++pGg  t  d++ +r    +  + + a ++g+ l +C   
  gi|313126999|ref|YP_004037269.1|  77 PVPIATVDA-TDYDAVVFPGGHGTQWDINQDRH-ARQALLSAVAGEKGKALVVCHAV 131
                                       344445555.67***************999888.66777788888999999999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1610.32
//
Query:       gi|313127000|ref|YP_004037270.1|  [L=100]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-05   23.4   0.0      6e-05   22.8   0.0    1.2  1  HTH_5         Bacterial regulatory protein, arsR family
    5.4e-05   23.2   0.1    0.00012   22.1   0.1    1.6  2  HTH_20        Helix-turn-helix domain
     0.0015   18.4   0.0      0.002   17.9   0.0    1.2  1  TrmB          Sugar-specific transcriptional regulator TrmB
     0.0056   16.5   0.0      0.011   15.5   0.0    1.5  1  HTH_10        HTH DNA binding domain
  ------ inclusion threshold ------
      0.026   14.3   0.1      0.036   13.9   0.1    1.2  1  HTH_IclR      IclR helix-turn-helix domain
      0.034   14.0   1.0      0.034   14.0   1.0    2.0  2  zf-trcl       Probable zinc-ribbon domain
        2.1    8.1   7.0        2.2    8.1   0.4    2.2  2  Rubredoxin_2  Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.3e-08     6e-05       3      37 ..      10      44 ..       9      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.3e-08
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLk 37
                                      tR +I  +L++g++++++l+e +g+ +s    HLk
  gi|313127000|ref|YP_004037270.1| 10 TRERIADALRDGPKTATDLSETVGIARSSAYNHLK 44
                                      7888999***************************8 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   4.6e-08   0.00012      11      47 ..      10      45 ..       6      58 .. 0.88
   2 ?   -2.3   0.0       1.8   4.7e+03       4      11 ..      71      78 ..      71      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.6e-08
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrv 47
                                      +R ri +aL r+++ ta++l e+++++++++++HL+ 
  gi|313127000|ref|YP_004037270.1| 10 TRERIADAL-RDGPKTATDLSETVGIARSSAYNHLKH 45
                                      78899****.*************************96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                                      HHHHS-HH CS
                            HTH_20  4 aeALahPv 11
                                      ++A+++Pv
  gi|313127000|ref|YP_004037270.1| 71 FSAFDDPV 78
                                      7899**98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     8e-07     0.002      18      45 ..      18      45 ..      15      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8e-07
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHH CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrs 45
                                      l+ gp+ta++++e +g+ rs++Y+ L+ 
  gi|313127000|ref|YP_004037270.1| 18 LRDGPKTATDLSETVGIARSSAYNHLKH 45
                                      6789********************9986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.3e-06     0.011      25      50 ..      24      49 ..      20      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.3e-06
                            HTH_10 25 tlkeLAkelGIskstlsehLrkaesk 50
                                      t+ +L+++ GI++s++++hL+ + + 
  gi|313127000|ref|YP_004037270.1| 24 TATDLSETVGIARSSAYNHLKHVARS 49
                                      789*****************998775 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.4e-05     0.036      12      40 ..      18      44 ..      13      48 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHH CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLq 40
                                      l+ +p   t ++l++  g+++S+++++L+
  gi|313127000|ref|YP_004037270.1| 18 LRDGPK--TATDLSETVGIARSSAYNHLK 44
                                      444444..79***************9996 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4      0.27   6.8e+02       7      11 ..      66      70 ..      56      75 .. 0.73
   2 ?   14.0   1.0   1.3e-05     0.034      31      44 ..      79      92 ..      70      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.27
                           zf-trcl  7 CkdCg 11
                                      C++Cg
  gi|313127000|ref|YP_004037270.1| 66 CRNCG 70
                                      66665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.3e-05
                           zf-trcl 31 nepkRCkaCRkark 44
                                      n p+RC++CR++r 
  gi|313127000|ref|YP_004037270.1| 79 NYPSRCPDCRSERI 92
                                      89*********985 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4   0.00085       2.2       2      10 ..      65      73 ..      65      75 .. 0.87
   2 ?    3.3   1.4     0.027        69      16      22 ..      83      89 ..      83      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00085
                      Rubredoxin_2  2 vCsqCGfes 10
                                      +C++CGf++
  gi|313127000|ref|YP_004037270.1| 65 ECRNCGFSA 73
                                      6******97 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.027
                      Rubredoxin_2 16 rCpsCgs 22
                                      rCp+C+s
  gi|313127000|ref|YP_004037270.1| 83 RCPDCRS 89
                                      8****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 608.42
//
Query:       gi|313127001|ref|YP_004037271.1|  [L=319]
Description: nucleoside-diphosphate-sugar pyrophosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-39  135.2   0.0    3.6e-39  134.8   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    9.5e-09   35.8   0.0    1.2e-08   35.5   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.034   14.3   0.5       0.25   11.5   0.0    2.6  2  Pentapeptide_3   Pentapeptide repeats (9 copies)
       0.13   11.9   0.0       0.19   11.5   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.0   8.1e-43   3.6e-39       1     242 [.       2     237 ..       2     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 8.1e-43
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHTTSGGGT...S CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflveeqlkegskfg...v 73 
                                       kav+LaGG+ tRLwP+t+ ++k  +pv+++ ++i+  ++ l +  +i e+ v ++++ ++++ee+l++   f+   v
  gi|313127001|ref|YP_004037271.1|   2 KAVVLAGGYATRLWPITKHRPKMFLPVGDE-TVIDVIFEDLEEdDRISEVFVSTNERFEESFEEYLSDSP-FEkptV 76 
                                       79******************9999999999.***********9889999777788888899999999987.886778 PP

                                       EEEEEEESS--.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSE CS
                   NTP_transferase  74 evlialepegk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyG 149
                                       +v+ ++e+ +k g  +A+ +    +++e+ +e ++v++gD l + +++e+v+++++k+  +++++ +  +e+a++yG
  gi|313127001|ref|YP_004037271.1|  77 SVEETVEEDEKfGVVGALEQL---IDRENVEEDLIVIAGDNLLSFDVSEFVDFFEAKRTPCIAAYDVGSKERAKSYG 150
                                       888888887778998888665...555556667******************************************** PP

                                       EEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTE CS
                   NTP_transferase 150 vieadeegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkda 226
                                       ++e d+ +rv +f+EKP+ +k s+l+s   Y f  e l +  ++l++  +  de + +++ + ++g+v+ af f++ 
  gi|313127001|ref|YP_004037271.1| 151 LVELDG-DRVVDFQEKPDDPK-STLVSIACYAFPAETLPKFDEYLQDG-NNPDEPGWFIQWLQQRGDVH-AFTFDG- 222
                                       *****8.6*************.****************9994566665.78899999*****9**9999.78****. PP

                                       E-EEEXSSHHHHHHHH CS
                   NTP_transferase 227 eyWsDvGtldsllean 242
                                         W D+Gt++s+l+a 
  gi|313127001|ref|YP_004037271.1| 223 -AWFDIGTPESYLDAV 237
                                       .5***********985 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   2.7e-12   1.2e-08       1     122 [.       3     138 ..       3     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2.7e-12
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH...CHHHHHHTTC.....TS-E. CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraa.gvdevvvvggd...eevlaalarl.....gvrv. 62 
                                       av+LAGG ++R+      ++K +lp+g++++++ +++ l++   ++ev+v++++   e+ +++l ++      v+v 
  gi|313127001|ref|YP_004037271.1|   3 AVVLAGGYATRLwpitkHRPKMFLPVGDETVIDVIFEDLEEDdRISEVFVSTNErfeESFEEYLSDSpfekpTVSVe 79 
                                       79**********8777557********************999559********956445666665544443334434 PP

                                       .EE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                      NTP_transf_3  63 .vededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpt 122
                                        +++ed+  g +++l   +++ + ++ ++v+a+D  l  +  v ++++ ++a++  ++++ 
  gi|313127001|ref|YP_004037271.1|  80 eTVEEDEKFGVVGALEQLIDRENVEEDLIVIAGDNLL--SFDVSEFVDFFEAKRTPCIAAY 138
                                       477788899************999**********966..5667777777766665555444 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.46   2.1e+03      22      29 ..     219     226 ..     213     229 .. 0.66
   2 ?   11.5   0.0   5.7e-05      0.25      14      39 ..     272     297 ..     264     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.46
                    Pentapeptide_3  22 sFsnadFg 29 
                                       +F++a+F+
  gi|313127001|ref|YP_004037271.1| 219 TFDGAWFD 226
                                       46666663 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.7e-05
                    Pentapeptide_3  14 gatFsgaasFsnadFgsadFsgarFt 39 
                                       g+t ++++ Fsn+++++ad ++++ +
  gi|313127001|ref|YP_004037271.1| 272 GSTLEKTVVFSNTTIRNADIRNTIVD 297
                                       77888888888888888888888766 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.2e-05      0.19       2      65 ..       2      68 ..       1     113 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.2e-05
                                      EEEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG CS
                              IspD  2 vvvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld 65
                                       +v+ A G  +R+    + +pK+fl + ++t++    + l +  +++++ v  +e   e fe+ l+d
  gi|313127001|ref|YP_004037271.1|  2 KAVVLAGGYATRLwpiTKHRPKMFLPVGDETVIDVIFEDLEEDDRISEVFVSTNERFEESFEEYLSD 68
                                      68999******96444799***********************************9999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2139.86
//
Query:       gi|313127002|ref|YP_004037272.1|  [L=239]
Description: pp-loop superfamily ATP-utilizing enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-57  194.9   0.0    2.2e-57  194.1   0.0    1.3  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
       0.18   11.2   0.0        1.2    8.6   0.0    2.0  2  ComA             (2R)-phospho-3-sulfolactate synthase (ComA)
       0.22   11.1   0.0       0.32   10.6   0.0    1.3  1  ThiI             Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.1   0.0   3.6e-61   2.2e-57       5     218 ..       9     236 ..       6     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 194.1 bits;  conditional E-value: 3.6e-61
                   Diphthami_syn_2   5 vlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikl........etaGeeek 72 
                                        l+sGGkDs  a+y+al+   +v+ L +v + +++sym+hv+  hl +l aes+Gi+li+         e++   e+
  gi|313127002|ref|YP_004037272.1|   9 GLFSGGKDSSWAVYRALEAgLDVTRLLTVHP-GDDSYMYHVPATHLAALAAESLGIELIEVtpddlgaaEATDSSEQ 84 
                                       69****************99********987.6789**********************9862222221123333332 PP

                   Diphthami_syn_2  73 ...evedLkgtlkkld....veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvav 142
                                          e e L+  l+ l       +v+ Ga+eseyq +ri+ +C +l + ++aPLW++dp+el e +++++fe+ ++ v
  gi|313127002|ref|YP_004037272.1|  85 gdaELEPLEAALEALAaeidLAGVTAGAVESEYQTNRIQGMCDRLEIDLFAPLWQEDPRELGEAMIDAGFEIQIIQV 161
                                       2225667788888776333356899**************************************************** PP

                   Diphthami_syn_2 143 kaegldeslLGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldierak 218
                                       +a+gldes+LGr +d++ ++el +l+e+yg+++ gegGe+et+v D+P     +e+ e+e+ w+++rg+l+i  a+
  gi|313127002|ref|YP_004037272.1| 162 AAHGLDESWLGRTLDHDALEELVELNEQYGVHPLGEGGEFETFVTDGPHMSNPIEL-EYETVWEGTRGHLEITDAR 236
                                       *******************************************************7.79************98765 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.076   4.6e+02       7      44 ..      70     111 ..      57     132 .. 0.73
   2 ?    8.6   0.0    0.0002       1.2       5      82 ..     140     208 ..     137     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.076
                                       S-SSS-EEEEESS....--HHHHHHHHHHHGGG-SEEEE-TT CS
                              ComA   7 PrktGlTeviDkG....lglreledlletageyiDglKlggg 44 
                                       P   G  e  D +      l+ le  le +++ iD++ +  g
  gi|313127002|ref|YP_004037272.1|  70 PDDLGAAEATDSSeqgdAELEPLEAALEALAAEIDLAGVTAG 111
                                       666677777777676677778888888888888888766555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0002
                                       -SS-SSS-EEEEESS--HHHHHHHHHHHGGG-SEEEE-TTGGGGSTCHHHHHHHHHHHCTT-EEEE-HHHHHHHHHT CS
                              ComA   5 ekPrktGlTeviDkGlglreledlletageyiDglKlgggtsallpeeilrekielahehgvyvstGgtlfEaalaq 81 
                                       e Pr+ G  ++ D G+ ++    ++++a++ +D   lg      l++++l+e++el +++gv++   g  fE++++ 
  gi|313127002|ref|YP_004037272.1| 140 EDPRELGEAMI-DAGFEIQ----IIQVAAHGLDESWLG----RTLDHDALEELVELNEQYGVHPLGEGGEFETFVTD 207
                                       67999999999.9999887....889999999988887....4567789***************998889***9998 PP

                                       T CS
                              ComA  82 g 82 
                                       g
  gi|313127002|ref|YP_004037272.1| 208 G 208
                                       7 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.3e-05      0.32       3      33 ..       4      34 ..       2      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.3e-05
                              ThiI  3 qgkvlaLlSgGiDSpVaaylllkRGcrvvlv 33
                                      +g+ + L SgG DS  a y++l+ G+ v  +
  gi|313127002|ref|YP_004037272.1|  4 SGDWVGLFSGGKDSSWAVYRALEAGLDVTRL 34
                                      78999*********************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1600.63
//
Query:       gi|313127003|ref|YP_004037273.1|  [L=317]
Description: sulfate adenylyltransferase subunit 2 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-21   76.6   0.0    8.4e-19   68.3   0.0    2.8  2  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
  ------ inclusion threshold ------
      0.062   12.8   0.0       0.11   12.0   0.0    1.4  1  Diphthami_syn_2  Diphthamide synthase
      0.079   12.7   0.0       0.13   12.0   0.0    1.3  1  ATP_bind_3       PP-loop family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   1.4e-22   8.4e-19       2     146 ..      48     224 ..      47     232 .. 0.90
   2 !    4.8   0.0    0.0045        27     148     169 ..     254     275 ..     247     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.4e-22
                                       EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHH.HH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekina.ek 72 
                                       + v + gGkds+V+l  ++++  ++     pvvf+d  ++fpet++fv++ +++ +l+l v+++e+ v+    +  +
  gi|313127003|ref|YP_004037273.1|  48 PTVMWTGGKDSTVVLYVVREVAAEMgvevpPVVFIDHFEHFPETVAFVEQWADEWDLDLVVARNEDFVRLDASPgDE 124
                                       678899******************7789999*********************************9988766555134 PP

                                       -S-THHHC.......................HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTT CS
                       PAPS_reduct  73 hgsslyee.......................aaeriaKveplkkaLekldedalltGaRrdesksraklpiveided 126
                                       ++ ++  e                       + +++ K+++ +  +e  ++d +++G+R de++sra + +++ + d
  gi|313127003|ref|YP_004037273.1| 125 IPLADLSEttrrelerldyegdtltldadtfEGNHLLKTVAFNDVIEADGFDGIFSGVRWDEQESRADETFFSARHD 201
                                       5555555567779****************99999*****************************************99 PP

                                       T-S...CEEE-CCCT--HHHHHH CS
                       PAPS_reduct 127 fek...slrvfPllnWteedvwq 146
                                        ek   + rv+P+l+++e d+w+
  gi|313127003|ref|YP_004037273.1| 202 SEKyppHDRVHPILQFEEADIWD 224
                                       98888899**************7 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0045
                                       HHHCT--B-CCCCTT-SS--BC CS
                       PAPS_reduct 148 ilrenipynpLydqgfrsiGcv 169
                                       i ++++p+ p y++gfrs+G  
  gi|313127003|ref|YP_004037273.1| 254 IAATDLPISPKYFEGFRSLGTE 275
                                       77899***************75 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.8e-05      0.11       3      29 ..      48      73 ..      46     113 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                   Diphthami_syn_2  3 vavlysGGkDsilaLykalkesevesL 29
                                        v++ GGkDs++ Ly +  e+  e+ 
  gi|313127003|ref|YP_004037273.1| 48 PTVMWTGGKDSTVVLYVVR-EVAAEMG 73
                                      579*************653.3333333 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.1e-05      0.13       7      65 ..      53     110 ..      48     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                                       -SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE CS
                        ATP_bind_3   7 SgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiek 65 
                                        gG DS++ l+++ + + ++g+    ++ +dh    +  e  ++v++++++++++l++++
  gi|313127003|ref|YP_004037273.1|  53 TGGKDSTVVLYVVREVAAEMGVeVPPVVFIDHFE--HFPETVAFVEQWADEWDLDLVVAR 110
                                       7*******************99555799999985..556778999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2373.25
//
Query:       gi|313127004|ref|YP_004037274.1|  [L=323]
Description: sulfate adenylyltransferase subunit 2 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-20   71.6   0.0    3.7e-16   59.7   0.0    3.0  2  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
  ------ inclusion threshold ------
      0.041   13.4   0.0       0.17   11.3   0.0    2.0  2  Diphthami_syn_2  Diphthamide synthase
      0.076   12.8   0.0       0.14   11.9   0.0    1.4  1  ATP_bind_3       PP-loop family
       0.21   11.1   0.0       0.29   10.6   0.0    1.2  1  F_bP_aldolase    Fructose-bisphosphate aldolase class-II


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   8.2e-20   3.7e-16       1     146 [.      47     229 ..      47     237 .. 0.88
   2 !    6.5   0.0    0.0018       8.1     148     172 ..     260     284 ..     252     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 8.2e-20
                                       CEEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH CS
                       PAPS_reduct   1 elvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaek 72 
                                       ++vv + gGkds+  l  + ++ ++      p vf+d  ++f+e+ +fvd+ +++ +l+++++++e+ +a   +   
  gi|313127004|ref|YP_004037274.1|  47 NPVVMWTGGKDSTLCLYFIKEVAEKHgydvpPAVFIDHYQHFDEIHDFVDKWADEWDLDVIYARNEDVGAYVDEHSL 123
                                       6899************9999999996688989**********************************99998888887 PP

                                       -S-THHHC.............................HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSS CS
                       PAPS_reduct  73 hgsslyee.............................aaeriaKveplkkaLekldedalltGaRrdesksraklpi 120
                                        + ++                                  +++ K+++l+ aLe++d d +++G+R de+++ra + +
  gi|313127004|ref|YP_004037274.1| 124 SPGDDIDIselsehnqhhvrnlleyedetfpflldtyVGNHLLKTVALNDALEEYDVDGVISGVRWDEQEARADETF 200
                                       77766555566667889999999999999999999877789999999999*************************** PP

                                       EEECTTT-S....CEEE-CCCT--HHHHHH CS
                       PAPS_reduct 121 veidedfek....slrvfPllnWteedvwq 146
                                       ++ + d ++    + rv+P+l+++e  vwq
  gi|313127004|ref|YP_004037274.1| 201 FSPRHD-PDiyppHDRVQPILQFDEASVWQ 229
                                       **9998.33455699**************9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0018
                                       HHHCT--B-CCCCTT-SS--BCTTB CS
                       PAPS_reduct 148 ilrenipynpLydqgfrsiGcvpct 172
                                       +++ +ip+ p y++gfrs+G   +t
  gi|313127004|ref|YP_004037274.1| 260 LTQDDIPVSPKYFAGFRSLGSEVST 284
                                       67899***************88776 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.9e-05      0.17       4      22 ..      49      67 ..      46     100 .. 0.86
   2 ?   -1.2   0.0      0.27   1.2e+03      16      92 ..     170     186 ..     155     198 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
                   Diphthami_syn_2  4 avlysGGkDsilaLykalk 22
                                      +v++ GGkDs+l Ly + +
  gi|313127004|ref|YP_004037274.1| 49 VVMWTGGKDSTLCLYFIKE 67
                                      79*************7544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.27
                   Diphthami_syn_2  16 aLykalkesevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkgtlkkldveavviG 92 
                                       a                                                            L++ l++ dv++v++G
  gi|313127004|ref|YP_004037274.1| 170 A------------------------------------------------------------LNDALEEYDVDGVISG 186
                                       4............................................................4555555555555554 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05      0.14       6      65 ..      52     110 ..      48     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                                       --SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE CS
                        ATP_bind_3   6 vSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiek 65 
                                         gG DS++ l+++++ ++k g     a+ +dh   ++ +e +++v ++++++++++++++
  gi|313127004|ref|YP_004037274.1|  52 WTGGKDSTLCLYFIKEVAEKHGYdVPPAVFIDHY--QHFDEIHDFVDKWADEWDLDVIYAR 110
                                       67*****************99995568999***7..5678889999999999999887766 PP

>> F_bP_aldolase  Fructose-bisphosphate aldolase class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   6.4e-05      0.29      35      98 ..      42      97 ..      30     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.4e-05
                                      HHHHTS-EEEEE-HHHHHHHH-....HHHHHHHHHHHHHHHHT...-EEEEEE----GHHHHHHHHHH CS
                     F_bP_aldolase 35 aeeaksPvIlqlsegaaakyag....gaealaelvraaaeaykkasvpvalhlDHgakleglkkaiea 98
                                       e+ + Pv++                + +++  +++++ae+ +  +vp a+ +DH ++++++ + +++
  gi|313127004|ref|YP_004037274.1| 42 LEQYENPVVM-----------WtggkDSTLCLYFIKEVAEKHG-YDVPPAVFIDHYQHFDEIHDFVDK 97
                                      4444444444...........033335667889*******887.8*****************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2353.91
//
Query:       gi|313127005|ref|YP_004037275.1|  [L=187]
Description: hypothetical protein Hbor_22690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1245.68
//
Query:       gi|313127006|ref|YP_004037276.1|  [L=113]
Description: glutaredoxin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-15   55.8   0.0    6.4e-15   55.1   0.0    1.4  1  Glutaredoxin  Glutaredoxin


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   3.5e-19   6.4e-15       1      60 []      27      92 ..      27      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 3.5e-19
                                      EEEEES.....TSSHHHHHHHHHHHHTTGGEEEEEGCCSH.HHHHHHHHHHTSSSSSEEEETTEEE CS
                      Glutaredoxin  1 vvlftk.....ptCpyCkkakrlLkelgvkfeeidvdkde.eireelkelsgvrtvPqvfidgkhv 60
                                      vvlf+k     p+C+y+++a +l  +++ +fe++dv+    ++r++l+e sg++t+Pq f+dg++v
  gi|313127006|ref|YP_004037276.1| 27 VVLFMKgnqlmPQCGYSARALELIGKHRESFETVDVLPALdAYRAALEEHSGWETIPQTFVDGEFV 92
                                      89***********************************9845***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 794.30
//
Query:       gi|313127007|ref|YP_004037277.1|  [L=213]
Description: orotate phosphoribosyltransferase-like enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-17   61.5   0.1    1.2e-16   60.6   0.1    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00017   21.3   0.0    0.00045   19.9   0.0    1.7  1  HTH_23        Homeodomain-like domain
     0.0062   16.6   0.0      0.013   15.6   0.0    1.5  1  HTH_7         Helix-turn-helix domain of resolvase
  ------ inclusion threshold ------
      0.013   15.0   0.1      0.033   13.7   0.1    1.6  2  PRTase_2      Phosphoribosyl transferase
      0.024   14.2   0.0       0.05   13.2   0.0    1.5  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.025   14.5   0.1       0.11   12.5   0.1    2.1  2  HTH_11        HTH domain
      0.029   13.8   0.0      0.044   13.2   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
       0.03   13.9   0.0      0.052   13.1   0.0    1.4  1  Sigma70_r4    Sigma-70, region 4
      0.056   13.4   0.0       0.45   10.5   0.0    2.4  3  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.082   12.8   0.0       0.19   11.6   0.0    1.6  1  MarR_2        MarR family


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.1   6.7e-20   1.2e-16       2     137 ..      66     200 ..      65     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 6.7e-20
                                       HHHTTT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE.-EEEEEE-TTT--EE...... CS
                      Pribosyltran   2 gsellenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevpla.yvrkvkyrpdgseeaargssd 77 
                                       +s++ +  + +  +a+++a++l++ ++  d+ +gi++ G p+a+ +a+eL+  l  y  ++   ++g  +   gs  
  gi|313127007|ref|YP_004037277.1|  66 WSAIGRDSKRMGYIAHAMADLLQKQGEDVDLTIGIEKAGAPLATVVARELDTDLGtYAPAKHQWEEGDIDELGGSFS 142
                                       66667777778889************************************766654444444445555555544433 PP

                                       ..EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH- CS
                      Pribosyltran  78 esrlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdkna 137
                                         r+ + ++++ + +VDD +++G+T+++++++++e+g e   ++v+vdk   ee +   +
  gi|313127007|ref|YP_004037277.1| 143 --RNFSQIRDRQCYVVDDTITSGTTMTETIDAIREEGGEPAACVVIVDKQGLEEIDGVPV 200
                                       ..69*******************************************9998877665555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.5e-07   0.00045       8      35 ..       9      36 ..       6      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.5e-07
                            HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvy 35
                                      ++++ l+++Gls+ eIA+eL+vsr T +
  gi|313127007|ref|YP_004037277.1|  9 ASAAELADRGLSKGEIADELNVSRETAS 36
                                      567889999*****************86 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.1e-06     0.013      11      37 ..       8      34 ..       2      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.1e-06
                                      HGGGGSSTTTT--STTTSSSS---SSS CS
                             HTH_7 11 inrvvkLleeGisiskIAkevnisRsT 37
                                      i+++ +L + G s+ +IA+e+n+sR+T
  gi|313127007|ref|YP_004037277.1|  8 IASAAELADRGLSKGEIADELNVSRET 34
                                      788999*******************99 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1     2e+03      35      76 ..      79     116 ..      69     130 .. 0.62
   2 ?   13.7   0.1   1.9e-05     0.033     121     152 ..     150     181 ..     141     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                          PRTase_2  35 agaaLaellaeakkeelpepvlvigfAEtAtaLghgvadale 76 
                                       +++a+a+ll+    ++ ++  l+ig+  +   L+  va++l+
  gi|313127007|ref|YP_004037277.1|  79 IAHAMADLLQ----KQGEDVDLTIGIEKAGAPLATVVARELD 116
                                       4455555555....3445555667776666667777776664 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.9e-05
                          PRTase_2 121 akelvLvDDEistGktalnliralqeklprkr 152
                                       +++  +vDD i++G+t++++i+a++e+  +  
  gi|313127007|ref|YP_004037277.1| 150 DRQCYVVDDTITSGTTMTETIDAIREEGGEPA 181
                                       566778*******************9965522 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-05      0.05      14      40 ..      15      41 ..      13      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkr 40
                                      ++ ++s  e+A++l++S+ t ++ ++r
  gi|313127007|ref|YP_004037277.1| 15 ADRGLSKGEIADELNVSRETASWLVDR 41
                                      5889******************99876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.9e-05      0.11      13      32 ..      17      35 ..       9      36 .. 0.84
   2 ?   -2.5   0.0       2.8     5e+03      33      44 ..     167     184 ..     162     191 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                            HTH_11 13 rgpisgeeLAeeLnvSrrtv 32
                                      rg +s  e+A+eLnvSr t 
  gi|313127007|ref|YP_004037277.1| 17 RG-LSKGEIADELNVSRETA 35
                                      44.8999**********995 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                            HTH_11  33 rrdIkaLeelg......v 44 
                                          I+a++e g      v
  gi|313127007|ref|YP_004037277.1| 167 TETIDAIREEGgepaacV 184
                                       557888888886666654 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.044     118     166 ..     147     192 ..     140     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                           UPRTase 118 kiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegv 166
                                       +i++r+ +++D +i +G ++ + i+ ++e+g +      + v++ ++g+
  gi|313127007|ref|YP_004037277.1| 147 QIRDRQCYVVDDTITSGTTMTETIDAIREEGGEPAA---CVVIVDKQGL 192
                                       67999************************9976654...3445555555 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.9e-05     0.052      19      38 ..      17      36 ..      10      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                                      TT--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4 19 eglTleEIgerlgiSrerVr 38
                                      +gl+  EI+++l++Sre+++
  gi|313127007|ref|YP_004037277.1| 17 RGLSKGEIADELNVSRETAS 36
                                      678889************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025      0.45      21      39 ..      18      36 ..       6      40 .. 0.87
   2 ?   -2.5   0.0       2.9   5.3e+03      37      52 ..     140     155 ..     140     161 .. 0.74
   3 ?   -0.9   0.0      0.93   1.7e+03      57      68 .]     184     195 ..     168     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                                      EHHHHHHHHHTTSSHHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvs 39
                                       l++ e+A+ l+++ret s
  gi|313127007|ref|YP_004037277.1| 18 GLSKGEIADELNVSRETAS 36
                                      589**************87 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  37 tvsrilseLkreglis 52 
                                       ++sr +s+ +++++  
  gi|313127007|ref|YP_004037277.1| 140 SFSRNFSQIRDRQCYV 155
                                       5789999999988765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.93
                                       EEES-HHHHHHH CS
                         HTH_Crp_2  57 irildleaLral 68 
                                       ++i d ++L+++
  gi|313127007|ref|YP_004037277.1| 184 VVIVDKQGLEEI 195
                                       89*******986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.19      12      44 ..      12      41 ..      11      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                      HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkr 44
                                      a+L++r+   l+ ge+a++l++s+ ++s +++r
  gi|313127007|ref|YP_004037277.1| 12 AELADRG---LSKGEIADELNVSRETASWLVDR 41
                                      5788888...9****************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1518.41
//
Query:       gi|313127008|ref|YP_004037278.1|  [L=359]
Description: glucose 1-dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   3.9e-102  340.2   0.0     5e-102  339.8   0.0    1.1  1  Glu_dehyd_C  Glucose dehydrogenase C-terminus
    9.8e-11   41.5   0.0    1.5e-10   40.9   0.0    1.3  1  ADH_N        Alcohol dehydrogenase GroES-like domain
    7.8e-06   25.9   0.0    1.2e-05   25.2   0.0    1.3  1  ADH_zinc_N   Zinc-binding dehydrogenase
    0.00054   19.8   0.1     0.0011   18.8   0.1    1.4  1  ADH_N_2      N-terminal domain of oxidoreductase


Domain annotation for each model (and alignments):
>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.8   0.0  1.1e-105    5e-102       2     212 .]     143     352 ..     142     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 339.8 bits;  conditional E-value: 1.1e-105
                       Glu_dehyd_C   2 dvgvLvEPisiveKaielaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlvee 78 
                                       d+g+L+EPisi+eKa+ela+asrs+f+wepesa+vlG+GslGLL+lall+  + g++r+y+lgrrdrpdptid++e+
  gi|313127008|ref|YP_004037278.1| 143 DLGFLIEPISITEKAVELAYASRSSFTWEPESAIVLGNGSLGLLTLALLRD-KLGYDRLYCLGRRDRPDPTIDIIEK 218
                                       79***********************************************95.8************************ PP

                       Glu_dehyd_C  79 lGatYvdsretpvdeipeaseemdlvvEaTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNka 155
                                       lGatYvdsretpv+ +p++ e+mdlv+EaTG+akhaf++++alapnGva+LlGvp ++e+e+dgge+h+e+vl+Nka
  gi|313127008|ref|YP_004037278.1| 219 LGATYVDSRETPVSAVPDEFESMDLVYEATGYAKHAFDSVRALAPNGVATLLGVPGSWEFEIDGGEIHKEIVLHNKA 295
                                       ***************************************************************************** PP

                       Glu_dehyd_C 156 lvGsvNanrrhfeaavdtLaalpeslldelvtkvvdldeleeAfedddetiKtvvel 212
                                       l+GsvN++++hfe+avdtLaa+pe+++d+lvt+v+dld++++Afeddd+tiKt+v++
  gi|313127008|ref|YP_004037278.1| 296 LLGSVNSHVKHFESAVDTLAAYPEWFTDDLVTSVCDLDNFAAAFEDDDTTIKTAVQF 352
                                       *******************************************************98 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   3.4e-14   1.5e-10       2     109 .]      26     137 ..      25     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.4e-14
                                       TEEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE.-SSSHHHHT CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvveplis.cgeCaaCke 75 
                                       ge+l+++  +g+ g+D ++++gg    +  +  l+lGHE+vG+ve+  p+ ++++ Gd Vv  +  +  g  ++ ++
  gi|313127008|ref|YP_004037278.1|  26 GEALVRTLRVGVDGTDHEVISGGhgGFPDGEDHLVLGHEAVGVVED--PNGTRFEAGDVVVPTVRRPpNGGNEYFER 100
                                       799******************986556667777************9..66789*********9999978999***** PP

                                       T-GGG-TTBEETTTS...S-SSSBSEEEECGGGEEEE CS
                             ADH_N  76 geenlCeeakllgvs...ldGgfaeyvvvpekklvkl 109
                                       ge+++ +e+ ++  +    +G +aey+v +e++lv++
  gi|313127008|ref|YP_004037278.1| 101 GEPDMAPEGMYHERGivgEHGFMAEYFVSHEQYLVQI 137
                                       ******66555544444567*************9975 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.8e-09   1.2e-05      26     128 ..     212     314 ..     183     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.8e-09
                                       HHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC.TSSEEEEEHHH CS
                        ADH_zinc_N  26 klelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGg.gkgeeefdlrn 101
                                        +++ +klGa++v  + e ++v+++ + +  e  d+v+e++G+ +   +++++l+p+G  ++ G+ g+ e e+d + 
  gi|313127008|ref|YP_004037278.1| 212 TIDIIEKLGATYVDSR-E-TPVSAVPDEF--ESMDLVYEATGYAKHAFDSVRALAPNGVATLLGVpGSWEFEIDGGE 284
                                       568999****998888.6.7*********..69********************************544444466666 PP

                                       ....HHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N 102 ....lllkeksilGsllgslreefkealdll 128
                                           ++l++k +lGs+ ++  + f+ a+d l
  gi|313127008|ref|YP_004037278.1| 285 ihkeIVLHNKALLGSVNSH-VKHFESAVDTL 314
                                       666699*********9999.67777777765 PP

>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   2.5e-07    0.0011      20      89 ..      15      84 ..       9      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.5e-07
                           ADH_N_2 20 leeeelpelkdGevlvralylSvDPymRgrmndaksyvepvelgdvmrggavgeVveSknpdfkvGdlVv 89
                                      l++++ pe++ Ge+lvr+l ++vD +    ++  +   ++ e   v+  +avg V + +  +f++Gd+Vv
  gi|313127008|ref|YP_004037278.1| 15 LVDKPRPEPETGEALVRTLRVGVDGTDHEVISGGHGGFPDGEDHLVLGHEAVGVVEDPNGTRFEAGDVVV 84
                                      678899*********************************999999************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2428.73
//
Query:       gi|313127009|ref|YP_004037279.1|  [L=461]
Description: adenylosuccinate lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-49  168.3   0.0    3.3e-49  168.0   0.0    1.1  1  Lyase_1   Lyase
    2.1e-41  140.6   0.0    3.8e-41  139.8   0.0    1.4  1  ASL_C     Adenylosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.027   14.3   0.2      0.067   13.0   0.2    1.7  1  ScsC_N    Copper resistance protein ScsC N-terminal domain
      0.067   13.7   0.4       0.23   12.0   0.1    2.0  2  MRFAP1    MORF4 family-associated protein1


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.0   0.0   7.4e-53   3.3e-49      13     307 ..      30     320 ..      18     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: 168.0 bits;  conditional E-value: 7.4e-53
                                       HHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSS.......HHHH CS
                           Lyase_1  13 iftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqeg.......sgta 82 
                                         +e +++++r+      ++a +  a+a +++ + +  ++  + ++ + ++++ dd+  +k  +++       ++++
  gi|313127009|ref|YP_004037279.1|  30 YASEAALMRARVR-----VEAEYLLALADLDATPLSLSDEERETVRGLYDSFDGDDARLVKRLETEgaegysaTNHD 101
                                       5555555555555.....55666667777777776666777777777777777776666666665511111113444 PP

                                       HHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEET CS
                           Lyase_1  83 vnmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrTh 159
                                       v++ +++++   ++ +  +  ++h+g +s+D++++a+rl++k a++e+L+pa+e+ +d l++ a+e++ ++++ rTh
  gi|313127009|ref|YP_004037279.1| 102 VKA-VEYFVR--TETPERVHPWIHFGLTSEDVNNLAHRLLAKPAVEEVLVPAIEDVRDELTALAREHRATPMLARTH 175
                                       554.555555..447778899******************************************************** PP

                                       TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHH..HHHCSTEESSS CS
                           Lyase_1 160 lqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakela..kvtglpvkapn 234
                                       +q+AtP+t+g+e++ ya+ + +++ r+ke++  +l ++l g++++++++ a+++   + ++ ++  +vt l+     
  gi|313127009|ref|YP_004037279.1| 176 GQPATPTTFGKEMAVYAARIGQQLGRVKEAA-ATLSGKLAGASGTYAAHVAAYP--DVDWRSFSrtFVTDLGLEHTA 249
                                       *******************************.9******************999..9******9999*****88888 PP

                                       HHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHH CS
                           Lyase_1 235 sfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgva 307
                                        +++v+++D+++ l++al+ ++  L ++++D++++ s   ++  ++  ++e GSS+MP+KvNP+++E+  g +
  gi|313127009|ref|YP_004037279.1| 250 LTTQVNPCDDLAALFDALRGVNNVLLDLDRDVWMYVS--QRYLGQEATAGETGSSTMPHKVNPIDFENSEGNL 320
                                       999**********************************..7888888888888***************987755 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.0   8.5e-45   3.8e-41       1     115 []     337     451 ..     337     451 .. 1.00

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 8.5e-45
                                       -STT--TCHHHHHTTCHHHHHHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-TTHHHHHHH CS
                             ASL_C   1 SrlQRDLtdStvlRnlgvalahslialksllkglsklevneealaedLdenwevlaEaiqtvlrregiekpYeklke 77 
                                       SrlQRDL+dStv+Rn+g+++ah+li++ +++ gl+k+  ne++++e+L++++e+++Ea+qt+lrreg +++Ye++ke
  gi|313127009|ref|YP_004037279.1| 337 SRLQRDLSDSTVKRNIGSSFAHCLIGYGKTAAGLDKVVPNEQVMREELEAHPELIGEAVQTILRREGDAEAYERVKE 413
                                       9**************************************************************************** PP

                                       HHTTS---HHHHHHHHHCS-S-HHHHHHHHC--CCC-- CS
                             ASL_C  78 ltrgkkitkeslkefieslevseeakeeLkaltpatYi 115
                                       ltrg+++t e++++++++l+v+e++++eL+al+patY+
  gi|313127009|ref|YP_004037279.1| 414 LTRGRDVTIEDFRDLFDELDVDESVRAELRALSPATYV 451
                                       *************************************7 PP

>> ScsC_N  Copper resistance protein ScsC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   1.5e-05     0.067       6      26 ..     377     397 ..     377     404 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                            ScsC_N   6 ekivrdYLleNPEiLvEAlqa 26 
                                       e+++r+ L ++PE++ EA+q 
  gi|313127009|ref|YP_004037279.1| 377 EQVMREELEAHPELIGEAVQT 397
                                       799****************96 PP

>> MRFAP1  MORF4 family-associated protein1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.9   1.7e+04      99     105 ..      34      40 ..      17      54 .. 0.59
   2 ?   12.0   0.1     5e-05      0.23      16      46 ..     143     173 ..     137     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.9
                            MRFAP1  99 aarmgkr 105
                                       aa m  r
  gi|313127009|ref|YP_004037279.1|  34 AALMRAR 40 
                                       3333322 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5e-05
                            MRFAP1  16 pesllsPvlrevrediaalereharaylrar 46 
                                        e++l+P+++ vr++++al reh  + + ar
  gi|313127009|ref|YP_004037279.1| 143 VEEVLVPAIEDVRDELTALAREHRATPMLAR 173
                                       6899*******************88888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3274.97
//
Query:       gi|313127010|ref|YP_004037280.1|  [L=525]
Description: phosphoribosylformylglycinamidine synthase, clade II [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-85  286.3   0.0    3.7e-85  286.0   0.0    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
    2.1e-41  141.6   0.0    4.6e-41  140.5   0.0    1.5  2  Formyl_trans_N   Formyl transferase


Domain annotation for each model (and alignments):
>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.0   0.0   4.1e-89   3.7e-85      60     296 .]     204     453 ..     171     453 .. 0.91

  Alignments for each domain:
  == domain 1  score: 286.0 bits;  conditional E-value: 4.1e-89
                                       CSE...EEEEEEEEESSSSSTTS-EEEEE-TT..STTHHH-EEEE..SS---HHHHHHHHHHHHHHCTS..EEEEEE CS
                   AICARFT_IMPCHas  60 lpetlklslekkqkLrYGeNphQkaalyeeee..eeglakaeqlq..GkelsynNllDadaalelvkef..aavaiv 130
                                       +pe+  ++ +k+++LrYGeNphQ+aa+y++++  e+++++a ql+   k lsynN++Dad al+l+kef   a+a++
  gi|313127010|ref|YP_004037280.1| 204 FPERRLVTDDKVAELRYGENPHQDAAVYADDAceEASVVRAPQLNegAKGLSYNNYNDADGALNLIKEFdePAAAVI 280
                                       555555666899****************9888888999999999554599*******************764788** PP

                                       ETTEEEEEEEESSHHHHHHHHHCCSHHHHTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCCTTSSS-EE CS
                   AICARFT_IMPCHas 131 KHanpcGvAvgetlaeAyekAlaaDpvSaFGgiialnrevdaetaeeikkefleviiApsfeeealeilkkkknlrv 207
                                       KH+np+G+A++++l++AyekAl++Dp+SaFGgi+alnre+daetae+i + f ev++Ap+++++al++l++kknlrv
  gi|313127010|ref|YP_004037280.1| 281 KHTNPAGCATADSLSDAYEKALSTDPMSAFGGIVALNRECDAETAEQIIDSFKEVVVAPGYTDAALDVLTEKKNLRV 357
                                       ***************************************************************************** PP

                                       EE-SS..-.....EEEEETTEEEEEE--G..TTCCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTEEE CS
                   AICARFT_IMPCHas 208 lelke..e.....elrsvsgglLvqerdeakieeeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgqtv 277
                                       l++ e  +     + + + gg Lvqerd    +ee+l++vt++kpt+e+le +lfawkv+khvkSN i++a+ ++tv
  gi|313127010|ref|YP_004037280.1| 358 LDIGElgDrtdtlTEKPLVGGRLVQERDLWAPTEEDLDIVTETKPTDEQLETMLFAWKVLKHVKSNGILFADGTETV 434
                                       ***9965156666778899********************************************************** PP

                                       EEE-SSSSHHHHHHHHHHH CS
                   AICARFT_IMPCHas 278 giGaGqmsRvdsarlAvek 296
                                       g+G+Gq+sRvd++rlA+ k
  gi|313127010|ref|YP_004037280.1| 435 GVGMGQVSRVDAVRLAAMK 453
                                       ****************976 PP

>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.5   0.0   5.1e-45   4.6e-41       2     181 .]       3     179 ..       2     179 .. 0.90
   2 ?   -3.0   0.0      0.57   5.1e+03      61      88 ..     314     341 ..     273     346 .. 0.65

  Alignments for each domain:
  == domain 1  score: 140.5 bits;  conditional E-value: 5.1e-45
                                       EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCT CS
                    Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkel 78 
                                       ki+ l+s+ g nl ++ d+      +a+ ++v+sn+++a  l  a++ +ipt+v+e+ + e+r+ +e+ + + l ++
  gi|313127010|ref|YP_004037280.1|   3 KIAGLASNRGRNLLHI-DERTP--GGAELAVVLSNEEGAPVLDAAAERGIPTEVVERDDDESRESHERRVLDRLSSY 76 
                                       5666666666666433.33222..23689************************************************ PP

                                       T-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE CS
                    Formyl_trans_N  79 kadlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkve 155
                                         d+++l gym++l++++++a +   ln+HpS+LP+f+G++a++++l aG++ tG+t+h+v+ee+D G+i+ q++v+
  gi|313127010|ref|YP_004037280.1|  77 DFDVVCLDGYMRILTETFIDAAPT-TLNVHPSILPSFPGMDAHEQVLDAGVRMTGCTVHVVTEEVDAGPIVTQEAVP 152
                                       ***********************9.9*************************************************** PP

                                       --TT--HHHHHHHHHHHHH.HHHHHHH CS
                    Formyl_trans_N 156 iiaedtkeeleqrvadaeh.kalveal 181
                                       + + d++ +l++rv  +++  a+++a+
  gi|313127010|ref|YP_004037280.1| 153 VYESDDEASLKERVLYEGEfTAYPRAV 179
                                       *************99776668888875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.57
                                       SCCCCCCCHHHHHHHHCTT-SEEEEES- CS
                    Formyl_trans_N  61 leprsqfeeelaeelkelkadlivlagy 88 
                                       +  +++ + e ae++     +++v++gy
  gi|313127010|ref|YP_004037280.1| 314 VALNRECDAETAEQIIDSFKEVVVAPGY 341
                                       4445677777777777777778888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 3126.20
//
Query:       gi|313127011|ref|YP_004037281.1|  [L=145]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-33  115.8   3.0    2.3e-33  115.7   3.0    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.034   13.5   0.0      0.039   13.3   0.0    1.2  1  IPT       Isopentenyl transferase


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   3.0   2.6e-37   2.3e-33       1     140 [.       1     140 [.       1     141 [. 0.97

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 2.6e-37
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my  IlV++Dgs+ +kkAle+A+e a  ++a++++l v+d r + a++++ +++ +++l + + +++++  ++  ++
  gi|313127011|ref|YP_004037281.1|   1 MYNSILVPTDGSDGTKKALEHAIEIATLSDATIHVLSVVDRRLYLAAGEEQKDELQDSLHEDAVTAVNEV-ATTVRE 76 
                                       9***********************************************************9999999986.999999 PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTT.CSSBHHHHHHHHHTSSEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsr.lllGSvseyvlrhapcpVlvV 140
                                       ++v+ ++ v++g p + il++a+e+d+d +V+G++gr+g ++ + lGSv+e+v+++++ pVlvV
  gi|313127011|ref|YP_004037281.1|  77 ADVECTTAVRDGVPYRCILDYADEHDVDAVVMGTHGRTGRDKlASLGSVTERVVQNTSRPVLVV 140
                                       9*****************************************555******************9 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.4e-06     0.039     117     190 ..      30     106 ..      15     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-06
                               IPT 117 ewevkrlrlpdedvflak...akkRvrqmlrpeeegaslldElaelwkepkarailedidG..yryildyarkkkvt 188
                                        +++++l++ d+  +la+   +k   ++ l+   +    ++E+a   +e + + + +  dG  yr+ildya +++v 
  gi|313127011|ref|YP_004037281.1|  30 DATIHVLSVVDRRLYLAAgeeQKDELQDSLHE--DAVTAVNEVATTVREADVECTTAVRDGvpYRCILDYADEHDVD 104
                                       6789999*********8622245555565655..666789*****999988766555444444***********997 PP

                               IPT 189 id 190
                                         
  gi|313127011|ref|YP_004037281.1| 105 AV 106
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1095.02
//
Query:       gi|313127012|ref|YP_004037282.1|  [L=834]
Description: dihydropteroate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-78  261.2   0.2    1.6e-77  260.5   0.2    1.3  1  Pterin_bind   Pterin binding enzyme
    1.7e-17   64.0   0.0    3.1e-17   63.2   0.0    1.4  1  Mur_ligase_M  Mur ligase middle domain
      5e-10   39.5   0.0    1.8e-09   37.8   0.0    2.0  1  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.5   0.2   2.7e-81   1.6e-77       1     244 []     574     811 ..     574     811 .. 0.96

  Alignments for each domain:
  == domain 1  score: 260.5 bits;  conditional E-value: 2.7e-81
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpis 77 
                                       mgilNvtpdsf dgg+f d d+al+qa++m+e+GAdi+D+ggestrPgae+v++eee++r+vpvleal d  d ++s
  gi|313127012|ref|YP_004037282.1| 574 MGILNVTPDSFHDGGEFYDTDDALEQAEAMIEAGADIIDVGGESTRPGAEEVPVEEEIRRIVPVLEALDDV-DALLS 649
                                       9*****************************************************************99996.9**** PP

                                       EE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHH CS
                       Pterin_bind  78 iDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearv 154
                                       +Dt ka vaeaAl+agadi+Ndv+g+e dp+m  l+ae +++v+vmh+   p  +  + ++y+dvv +v  +l++r+
  gi|313127012|ref|YP_004037282.1| 650 VDTRKAAVAEAALDAGADILNDVTGLE-DPEMRFLAAERDVPVIVMHSIDAP-VVPGKDVDYDDVVGDVIDELRERI 724
                                       ***************************.********************9555.5556667***************** PP

                                       HHHHHTT--GGGEEEETTTTSSTTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHH CS
                       Pterin_bind 155 eaaeeaGvaperillDpgigfgkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaafla 231
                                         ae+aG+++e++++Dpgigfgk++ +n+ell+rl e+  al++p+l G+S ks+   +    ka +   +t+a++a
  gi|313127012|ref|YP_004037282.1| 725 LLAEKAGIPRENVIVDPGIGFGKSNAENFELLDRLGEF-DALGCPLLFGHSHKSMFELVG--SKAGDNLPATVAATA 798
                                       **************************************.***************998764..2367*********** PP

                                       HHHHTT-SEEEES CS
                       Pterin_bind 232 laaaaGadivrVh 244
                                       laa++GadivrVh
  gi|313127012|ref|YP_004037282.1| 799 LAADRGADIVRVH 811
                                       ************9 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   5.2e-21   3.1e-17       1     191 [.      44     268 ..      44     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 5.2e-21
                                       EESSS-HHHHHHHHHHHHHCTEEEEETTC............................................SS-T CS
                      Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvg............................................ttnn 33 
                                       v+G+nGK +t++++++il++ag ++g+                                              t+ +
  gi|313127012|ref|YP_004037282.1|  44 VAGSNGKGSTARMTESILREAGLTVGLYTsphfetvrerarvdgrkipesaicefverakpwlveraadgeplTFFE 120
                                       89*******************88888888889****************************************87777 PP

                                       HHHHHHHHHHHHHTT-SEEEEE--HCHHHCTTTCCHCBESEEEE---TSTTHHHH.SSHHHHHHHHHHHHHTSETTC CS
                      Mur_ligase_M  34 eiglpktlaemekkeaeyavlEvsshglgekrlegllkpdvavitnispdHldfh.gtlenyaeaKaelferlkeeg 109
                                        ++  +  + +e  e+++avlEv++   g+    ++++p++a++tn+s +H   + +t+e++ae Ka       ++ 
  gi|313127012|ref|YP_004037282.1| 121 VVTALSIWYFAEA-EVDVAVLEVGMG--GKLDATSVVDPAAAAVTNVSLEHTAVLgDTIEAIAEKKAAVEP---ADR 191
                                       7776666666665.************..664444449****************997899999999987543...445 PP

                                       EEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEEEEEEETTEEEEEEESSCSCHHHHHHH CS
                      Mur_ligase_M 110 iavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegteiellevkggeleieipllGkhnvyNal 186
                                        +v+ a  +      + +++++ +vvt+g+e++a+   +++ +++++++ ++++  ++ +++ +ipllG ++++Na 
  gi|313127012|ref|YP_004037282.1| 192 PLVTGATGD----ALATIRDHTTTVVTVGTEDDADVTVRSEGRVNHQESAVAVV-ADDWSVDSRIPLLGAYQAENAG 263
                                       788888888....45566677788**********65555588888898888777.799999***************9 PP

                                       HHHHH CS
                      Mur_ligase_M 187 aaiaa 191
                                       +a+++
  gi|313127012|ref|YP_004037282.1| 264 IACVL 268
                                       99987 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   2.9e-13   1.8e-09       1      88 [.     294     372 ..     294     375 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.9e-13
                                       CTTSSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEE CS
                      Mur_ligase_C   1 vkgRlevvgeadgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasaladslvv 77 
                                       ++gR+ev+ +  ++ v+ D ahnp++ + + ++l ++ +   l+lvfg++ +   +++     + +++ + ads+++
  gi|313127012|ref|YP_004037282.1| 294 WPGRFEVMET--DPFVVLDGAHNPGACESVASVLDDF-DVDALHLVFGAMHD---KDQR---KMVEALPD-ADSVIT 360
                                       79********..99********************998.779********999...6666...67777777.778666 PP

                                       EESS.-TTSTHH CS
                      Mur_ligase_C  78 lgdy.praedsi 88 
                                       +  + pr+ed++
  gi|313127012|ref|YP_004037282.1| 361 CRPNnPRSEDPE 372
                                       655449999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 5062.66
//
Query:       gi|313127013|ref|YP_004037283.1|  [L=248]
Description: hypothetical protein Hbor_22770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-24   86.4   0.0    1.8e-23   83.9   0.0    1.8  1  TANGO2    Transport and Golgi organisation 2


Domain annotation for each model (and alignments):
>> TANGO2  Transport and Golgi organisation 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0     1e-27   1.8e-23       1     159 [.       1     152 [.       1     230 [. 0.67

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 1e-27
                            TANGO2   1 MCIllftveahpkykLiLasNRDEflaRptkeaawweenseilsgrDlerkegGTWlGitkegrlAvLtNlrepsek 77 
                                       MC l ++++  ++ + ++a+NRDE ++Rp+++ +  e ++  +++rD e+  gGTW+G +++g +  +tN r  +  
  gi|313127013|ref|YP_004037283.1|   1 MCTLTIAWQVFEEAPVVVAANRDEAMNRPSEPPSAVEGDPAFVAPRDTEA--GGTWVGYNERGVFVGVTN-RWIDV- 73 
                                       *************************************************6..******************.55552. PP

                            TANGO2  78 ekkakkarsRGelvldfLtsseksseeyleelakeakkyggFnLlvgdlkskelayisnrskee.eelspgvhglSN 153
                                         +  ++rsRG+lv d L s++  ++  + e a e++ y +FnL+v+d    e+++++  ++ e ++l+pgvh++ N
  gi|313127013|ref|YP_004037283.1|  74 --EGGGERSRGQLVRDALRSESAADARETVESALETDTYDAFNLVVADAA--EAYLFEWDGSLEtTRLTPGVHVVVN 146
                                       ..23588***********653333333333334478**************..56666666644558899*******9 PP

                            TANGO2 154 slldsp 159
                                          d  
  gi|313127013|ref|YP_004037283.1| 147 VGADGA 152
                                       887653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1647.35
//
Query:       gi|313127014|ref|YP_004037284.1|  [L=117]
Description: hypothetical protein Hbor_22780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0068   16.3   0.0     0.0093   15.9   0.0    1.2  1  MarR            MarR family
  ------ inclusion threshold ------
       0.09   12.9   0.0       0.15   12.3   0.0    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-06    0.0093       1      50 [.      10      59 ..      10      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-06
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      l++ ++  L++++e g++ +s+ +k l +++   +r++ rL   +li+R+
  gi|313127014|ref|YP_004037284.1| 10 LSEDELAGLELIRETGGIHQSDFWKELDITSRKGSRIAERLDSLDLINRE 59
                                      68889999****************************************97 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05      0.15      17      66 ..      25      70 ..      15      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                    B-block_TFIIIC 17 sGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatkksistsl 66
                                       Gi qsd +ke+++ +r+   +   L +  LI + ++     +k+++t+ 
  gi|313127014|ref|YP_004037284.1| 25 GGIHQSDFWKELDITSRKGSRIAERLDSLDLINREET----VYKGHNTYH 70
                                      59***********************************....999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 789.38
//
Query:       gi|313127015|ref|YP_004037285.1|  [L=46]
Description: hypothetical protein Hbor_22790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 336.26
//
Query:       gi|313127016|ref|YP_004037286.1|  [L=255]
Description: proteasome subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-60  201.4   0.0    1.2e-59  201.1   0.0    1.1  1  Proteasome      Proteasome subunit
    9.1e-14   50.8   0.1    1.5e-13   50.1   0.1    1.4  1  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.1   0.0   1.3e-63   1.2e-59       1     190 []      33     217 ..      33     217 .. 0.99

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 1.3e-63
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vk+Gt+++G+++ +gvvlaadkr+   s l+++++veKi+k ddhig+a aG +aDar+l+++ar++ q  rlryg+
  gi|313127016|ref|YP_004037286.1|  33 VKRGTASIGVRTPEGVVLAADKRSR--SPLMEPTSVEKIHKSDDHIGIASAGHVADARQLIDFARRQSQVNRLRYGE 107
                                       79***********************..************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       pi +e+l+++v++++q+ytq +g rpfgv+lli+g+  +g+p+Ly++dpsG+ +e+k av+iG  +   +++le++y
  gi|313127016|ref|YP_004037286.1| 108 PIGIETLTKEVTDHIQQYTQVGGARPFGVALLIGGIE-NGTPRLYETDPSGTPYEWK-AVSIGADRGDLQGFLEENY 182
                                       ************************************9.999***************8.*****99************ PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                       ++dltl+e++ la++a+ ++ + d++ +++++va+i
  gi|313127016|ref|YP_004037286.1| 183 RDDLTLDEGIGLALRAIASTND-DEIEEGGVDVATI 217
                                       **********************.99********987 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.1   1.7e-17   1.5e-13       1      23 []      10      32 ..      10      32 .. 0.99

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.7e-17
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr +t+FSPdGRL+QVEYA +A
  gi|313127016|ref|YP_004037286.1| 10 YDRGITIFSPDGRLYQVEYAREA 32
                                      *********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1751.45
//
Query:       gi|313127017|ref|YP_004037287.1|  [L=159]
Description: ribonuclease p protein subunit rpp14 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-21   75.3   0.0    4.7e-21   75.0   0.0    1.1  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.0   2.6e-25   4.7e-21       1     102 [.      13     113 ..      13     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 2.6e-25
                                       EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTT..TEEEEEEEGGGHHHHHHHHHT CS
                     RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspat..staiiRcsresyrlvwaaLtl 75 
                                       RYl+ve+ +++ ++++++ +++++++ ++q+l+Gd g+++++   +v +fs a   + +i+R  r++ + ++aaLt+
  gi|313127017|ref|YP_004037287.1|  13 RYLAVELESWP-DAQFDRGDFQRELWYAAQNLYGDSGSAAADL--TVLSFSFADgdGETIVRAYRGEEDRARAALTC 86 
                                       9**********.556999***********************99..6777777665599******************* PP

                                       --EETTEEEEEEEEEEESSHHHHHHHT CS
                     RNase_P_Rpp14  76 itkiegrpvvfrvvrvsGTikkaeeea 102
                                       i++++g pv +rv ++sGT++++ee++
  gi|313127017|ref|YP_004037287.1|  87 ISTVNGSPVGVRVAGISGTVRACEERY 113
                                       ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1103.54
//
Query:       gi|313127018|ref|YP_004037288.1|  [L=212]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-19   70.5   0.1    3.1e-19   69.5   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
      4e-17   62.4   0.0    5.7e-17   61.9   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    9.2e-16   58.3   0.1    2.6e-15   56.9   0.0    1.7  2  Methyltransf_11  Methyltransferase domain
    1.2e-11   45.2   0.0    2.8e-11   44.0   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    1.3e-09   37.7   0.0    2.4e-09   36.9   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.1e-07   31.9   0.0    3.2e-07   30.3   0.0    1.7  2  Methyltransf_23  Methyltransferase domain
    1.3e-07   31.3   0.1      2e-07   30.7   0.1    1.2  1  MTS              Methyltransferase small domain
    0.00011   21.8   0.1    0.00015   21.2   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00067   19.6   0.0     0.0011   18.9   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
    0.00079   19.2   0.1     0.0099   15.6   0.1    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    0.00082   18.5   0.0     0.0012   17.9   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0015   18.5   0.0     0.0023   18.0   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0028   16.7   0.0     0.0045   16.0   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0075   15.4   0.0      0.011   14.8   0.0    1.3  1  DREV             DREV methyltransferase
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.015   14.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
      0.015   14.8   0.0      0.053   13.0   0.0    1.9  2  Methyltransf_4   Putative methyltransferase
      0.022   14.5   0.0      0.036   13.8   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.19   11.5   0.0       0.44   10.3   0.0    1.7  2  Methyltransf_16  Lysine methyltransferase
       0.21   11.3   0.0       0.28   10.8   0.0    1.2  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.1   3.3e-22   3.1e-19       1      90 [.      47     134 ..      47     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 3.3e-22
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vLdlG+GtG ++lala     ++v+g Dise+mle+are+a+++g+ nvef +g ++d ++ed ++D+v+s++a+hh
  gi|313127018|ref|YP_004037288.1|  47 VLDLGTGTGAIALALAPDA--KRVVGRDISEGMLEQAREKAQDAGIdNVEFGEGRFRDPNYED-EVDIVTSNFAMHH 120
                                       9***************996..9************************************99998.9************ PP

                                       SSHHHHHHHHHHHH CS
                   Methyltransf_25  77 lsdedlekalkeia 90 
                                       lsde+ ++a++ ia
  gi|313127018|ref|YP_004037288.1| 121 LSDEEKREAIAVIA 134
                                       *******9998776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0     6e-20   5.7e-17       3      92 ..      43     126 ..      41     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 6e-20
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       ++ +vlDlG+GtG+++++la    p+a+ vvG Dise ++e+Are+aq+ g+dnveF +g + + +  +e + +D++
  gi|313127018|ref|YP_004037288.1|  43 DEDVVLDLGTGTGAIALALA----PDAKrVVGRDISEGMLEQAREKAQDAGIDNVEFGEGRFRDPN--YE-DEVDIV 112
                                       6779****************....66666***********************************66..89.7***** PP

                   Methyltransf_31  79 lsnevlnaladpdk 92 
                                       +sn ++++l+d +k
  gi|313127018|ref|YP_004037288.1| 113 TSNFAMHHLSDEEK 126
                                       ***99988888654 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   2.7e-18   2.6e-15       1      81 [.      48     130 ..      48     136 .. 0.92
   2 ?   -2.2   0.0       7.2   6.8e+03       8      31 ..     170     193 ..     167     203 .. 0.64

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.7e-18
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-.. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv.. 74 
                                       Ld+G+GtG++a ala  ++rvvg D+s+ ml++a+eka+++g+ +vef ++++++ ++ed  +D+v+s++++hh+  
  gi|313127018|ref|YP_004037288.1|  48 LDLGTGTGAIALALAPDAKRVVGRDISEGMLEQAREKAQDAGIdNVEFGEGRFRDPNYED-EVDIVTSNFAMHHLsd 123
                                       8******************************************************99999.9*************76 PP

                                       CCHHHHH CS
                   Methyltransf_11  75 edpekal 81 
                                       e+ ++a+
  gi|313127018|ref|YP_004037288.1| 124 EEKREAI 130
                                       5555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.2
                                       SHHHHHHHHTTSEEEEEES-HHHH CS
                   Methyltransf_11   8 GrlaealakrgarvvgvDlskeml 31 
                                       G la al++ g  +++v+  +e++
  gi|313127018|ref|YP_004037288.1| 170 GTLADALTDEGFVLTAVERVHEQV 193
                                       556666666666666666665554 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0     3e-14   2.8e-11       1      91 [.      48     135 ..      48     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3e-14
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++G+GtG+++ al+++   ++++g Dis+ ++e+a+ek ++ + +n+++ e + +d   +d    +D+v++++++h
  gi|313127018|ref|YP_004037288.1|  48 LDLGTGTGAIALALAPD--AKRVVGRDISEGMLEQAREKAQDAGIDNVEFGEGRFRDPNYED---EVDIVTSNFAMH 119
                                       8****************..***********************99877777777777765554...8*********** PP

                   Methyltransf_12  78 hl..kdirevldnirk 91 
                                       hl  +++re+++ i++
  gi|313127018|ref|YP_004037288.1| 120 HLsdEEKREAIAVIAD 135
                                       **99999999988765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   2.5e-12   2.4e-09      47     134 ..      43     126 ..      27     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.5e-12
                                       -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEE CS
                   Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvs 123
                                           vlD+ +Gtg +a++l+  ++   +vv+ Di+e mL+++++k+++ g  n+ef  +   + +  +d  D+vt  
  gi|313127018|ref|YP_004037288.1|  43 DEDVVLDLGTGTGAIALALAPDAK---RVVGRDISEGMLEQAREKAQDAGIDNVEFGEGRFRDPN-YEDEVDIVTSN 115
                                       55679*************998765...79***************************999987755.55679****** PP

                                       S-GGG-S-HHH CS
                   Ubie_methyltran 124 fGlrnvtDklk 134
                                       f +  ++D +k
  gi|313127018|ref|YP_004037288.1| 116 FAMHHLSDEEK 126
                                       ********987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   3.4e-10   3.2e-07      20     112 ..      41     139 ..       4     155 .. 0.74
   2 ?   -1.1   0.0       1.6   1.5e+03      33      58 ..     169     194 ..     163     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.4e-10
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                                             vLd+G+GtG  +  l++  + v+g D+s+ + e a+      ++++ ++    +  +++ ++  d++++++
  gi|313127018|ref|YP_004037288.1|  41 PTDEDVVLDLGTGTGAIALALAPDAKRVVGRDISEGMLEQARekaqdaGIDNVEFGEG-RFRDPNYEDEVDIVTSNF 116
                                       455569******************************9999876654442222222222.123333566********* PP

                   Methyltransf_23  91 vlehvpd..ppellrqiatllkpg 112
                                        ++h+ d    e+++ ia+ l+p+
  gi|313127018|ref|YP_004037288.1| 117 AMHHLSDeeKREAIAVIAD-LNPD 139
                                       ******8667788888888.6666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                   Methyltransf_23  33 tGillevlrengfsvtgvDlspeave 58 
                                       +G+l++ l ++gf +t+v+   e+v+
  gi|313127018|ref|YP_004037288.1| 169 VGTLADALTDEGFVLTAVERVHEQVG 194
                                       47777888888888888887777665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   2.1e-10     2e-07      20     119 ..      32     130 ..      25     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.1e-10
                                       HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTT CS
                               MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleevee 95 
                                       ++l +e+ + + ++ vlDlG+G+G++++ala   ++  v+  d++   le a+e +++ +++ ve+ +    +   e
  gi|313127018|ref|YP_004037288.1|  32 ANLVVEHADPTDEDVVLDLGTGTGAIALALAPDAKR--VVGRDISEGMLEQAREKAQDAGIDnVEFGEGRFRDPNYE 106
                                       678899999999999***************997777..9***********************9**********999* PP

                                       S-EEEEEE---STTTCHCHHHHHH CS
                               MTS  96 kkfdlivsNPPfhagkatelavae 119
                                       +++d++ sN  +h+ +++e++ a 
  gi|313127018|ref|YP_004037288.1| 107 DEVDIVTSNFAMHHLSDEEKREAI 130
                                       *********999987776665555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.6e-07   0.00015     162     234 ..      44     116 ..      31     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                              PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadvivaNI 234
                                       ++ vlD+GtG+G +a+a a  +ak+vv+ Di e  ++ a+e a+  ++++ ++     ++   e ++d++ +N 
  gi|313127018|ref|YP_004037288.1|  44 EDVVLDLGTGTGAIALALA-PDAKRVVGRDISEGMLEQAREKAQDAGIDNvEFGEGRFRDPNYEDEVDIVTSNF 116
                                       45799*******9999866.59**********************999998666433333333468899999885 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-06    0.0011      14      68 ..      43      94 ..      32     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                   Methyltransf_18 14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkie 68
                                      ++++v+D Gt  g ++++l+    ak+v+  Di+eg le+a+e++++ag++ ++e
  gi|313127018|ref|YP_004037288.1| 43 DEDVVLDLGTGTGAIALALA--PDAKRVVGRDISEGMLEQAREKAQDAGID-NVE 94
                                      3569*********9999998..67899********************9995.455 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     1e-05    0.0099      76     128 ..      64     115 ..      26     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                                       H--.EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE- CS
                           UPF0020  76 elk.lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtn 128
                                       ++k ++g D+ + ++++are+a+ ag++  +ef +  +++ +  e+evd++ +n
  gi|313127018|ref|YP_004037288.1|  64 DAKrVVGRDISEGMLEQAREKAQDAGID-NVEFGEGRFRDPN-YEDEVDIVTSN 115
                                       444599********************95.699*******999.8889****999 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0012      19      73 ..      32      86 ..      27     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT CS
                            RrnaAD 19 ineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls 73
                                      +n +++++++++++ vl++g+G+G+    La  ak vv   + e +++  ++k +
  gi|313127018|ref|YP_004037288.1| 32 ANLVVEHADPTDEDVVLDLGTGTGAIALALAPDAKRVVGRDISEGMLEQAREKAQ 86
                                      57799*********************************99999999999999766 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.4e-06    0.0023      13      96 ..      31     107 ..      24     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-06
                   Methyltransf_32  13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsi 89 
                                       +a+l+ e a+ +++  v+D+G G g  + +la    +   +vvg d++e + e+a++ a+  g  + ++++f e+  
  gi|313127018|ref|YP_004037288.1|  31 CANLVVEHADPTDEDVVLDLGTGTGAIALALAP---D-AKRVVGRDISEGMLEQAREKAQDAG--I-DNVEFGEGRF 100
                                       445555557899999*****************9...4.889**********************..7.8899998887 PP

                   Methyltransf_32  90 eeatssk 96 
                                       ++ + ++
  gi|313127018|ref|YP_004037288.1| 101 RDPNYED 107
                                       7665433 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.7e-06    0.0045     196     253 ..      37      95 ..      29      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.7e-06
                   tRNA_U5-meth_tr 196 evtqeskgd.llelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqi 253
                                       e ++ +++d +l+l  G G  +lala   ++v+  +i+   +e a+   ++  idnv++
  gi|313127018|ref|YP_004037288.1|  37 EHADPTDEDvVLDLGTGTGAIALALAPDAKRVVGRDISEGMLEQAREKAQDAGIDNVEF 95 
                                       555555555269********************************************986 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.2e-05     0.011      93     136 ..      42      85 ..      25     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                              DREV  93 qedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkk 136
                                        ++  +ldlG+G G i+  +ap  ++v   ++se m ++ + k 
  gi|313127018|ref|YP_004037288.1|  42 TDEDVVLDLGTGTGAIALALAPDAKRVVGRDISEGMLEQAREKA 85 
                                       446679******************************99987764 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.6e-05     0.015      49     144 ..      30     125 ..       4     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-- CS
                              CMAS  49 aKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedld 125
                                       a  +l++e ++  + + +Ld+G+G G+++   +     +vvg  +S+   ++a+++ ++++  ++ve     ++d +
  gi|313127018|ref|YP_004037288.1|  30 ACANLVVEHADPTDEDVVLDLGTGTGAIALALAPD-AKRVVGRDISEGMLEQAREKAQDAG-IDNVEFGEGRFRDPN 104
                                       45556666666777789***********9999888.889**********************.577888889999855 PP

                                       -..--SEEEEES-GGGTSGGG CS
                              CMAS 126 e..kvdrvvsvgafehvgken 144
                                          +vd v s  a+ h+  e+
  gi|313127018|ref|YP_004037288.1| 105 YedEVDIVTSNFAMHHLSDEE 125
                                       334999999999999987665 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.7e-05     0.053       2      55 ..      44      95 ..      43     101 .. 0.90
   2 ?   -1.1   0.0       1.2   1.1e+03      96     115 ..     165     184 ..     127     200 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                                      -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEE CS
                    Methyltransf_4  2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlri 55
                                      + vvl++G+G G + +alA++   k ++G +i++ +++++ +k+++ ++ N++ 
  gi|313127018|ref|YP_004037288.1| 44 EDVVLDLGTGTGAIALALAPD--AKRVVGRDISEGMLEQAREKAQDAGIDNVEF 95
                                      5689*********99999987..5899************************975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                       SHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_4  96 qpellkelarvLkkgGvlel 115
                                        p+++  la++L  +G++ +
  gi|313127018|ref|YP_004037288.1| 165 DPATVGTLADALTDEGFVLT 184
                                       45566666777777776665 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.8e-05     0.036      72     131 ..      42      98 ..      14     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvg 131
                                       ++ + vL++G+G+G  +  la    +  rvv+ + ++ + e+a+++ +  +++nv + +g
  gi|313127018|ref|YP_004037288.1|  42 TDEDVVLDLGTGTGAIALALA---PDAKRVVGRDISEGMLEQAREKAQDAGIDNVEFGEG 98 
                                       56678*********6665555...5667899***********************998655 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00046      0.44      31      74 ..      28      69 ..       4      94 .. 0.74
   2 ?   -2.8   0.0       4.8   4.5e+03      79     101 ..     106     126 ..     104     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00046
                   Methyltransf_16 31 ylekklakelganelsklsvlELGsGtGlvGlavaellpeakvi 74
                                      yl+ +     +a+ + +  vl+LG GtG + la+a      +v+
  gi|313127018|ref|YP_004037288.1| 28 YLACANLVVEHADPTDEDVVLDLGTGTGAIALALAPD--AKRVV 69
                                      4444444446777888899***********9999976..44444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                   Methyltransf_16  79 eellellkknielnknalkskvk 101
                                       e+ ++++++n ++  ++l+++ k
  gi|313127018|ref|YP_004037288.1| 106 EDEVDIVTSNFAM--HHLSDEEK 126
                                       6677888888888..55665544 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.28      13      67 ..      36      94 ..      30     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                                      HCCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH....SHH CS
                   MethyltransfD12 13 kelipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlinlykalikn....nve 67
                                      +e+ + ++++++ ++ +G+ga+++++  + k+v+  Di e     ++ + ++    nve
  gi|313127018|ref|YP_004037288.1| 36 VEHADPTDEDVVLDLGTGTGAIALALAPDAKRVVGRDISEGMLEQAREKAQDagidNVE 94
                                      5666666999****************99**********999888888665555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1391.90
//
Query:       gi|313127019|ref|YP_004037289.1|  [L=231]
Description: ribonuclease p protein subunit rpp30 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-37  127.9   0.0      6e-37  127.2   0.0    1.3  1  RNase_P_p30  RNase P subunit p30


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   0.0   3.3e-41     6e-37       5     214 ..       5     201 ..       3     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 3.3e-41
                                       E-SH.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H.. CS
                       RNase_P_p30   5 ipwpsddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl. 80 
                                       ++  +d++++ +r+++t+a++gy+gv++  +       +p+  +          +e  + +++   ++++++p++  
  gi|313127019|ref|YP_004037289.1|   5 VHAHPDGDSTAARLAETAAQYGYDGVVVRGEDA-----RPDYET---------LCEAATCDVVDAAEIIAESPEQAs 67 
                                       678899999999****************99998.....333333.........46667799*************977 PP

                                       HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-HHHH CS
                       RNase_P_p30  81 qrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsglaR 157
                                       +++ ++r + +l+ vr++t +++r+a+e+ +vD+++ ++++  +  ++h++++aA ++gv++E+ ++p+lr+ g+ R
  gi|313127019|ref|YP_004037289.1|  68 GAVGNFRTSRTLVLVRGGTNRLNRFAVEQERVDVLTRPFAG--DGDVNHVLAKAAKRNGVRIEFALGPALRATGGHR 142
                                       ***************************************99..8889****************************** PP

                                       HHHHHHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTTH CS
                       RNase_P_p30 158 rnfisnarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedrakeavse 214
                                       ++++ n+rkl r+ ++  +++v+S++A s+lelR+p++++++++ +GL  +++ + ++e
  gi|313127019|ref|YP_004037289.1| 143 VQHLDNLRKLKRILDHydTPYVVSANAASHLELRAPRELAAVGEEIGLGAEWVCDGLTE 201
                                       **************************************************999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1749.57
//
Query:       gi|313127020|ref|YP_004037290.1|  [L=179]
Description: hypothetical protein Hbor_22840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1186.78
//
Query:       gi|313127021|ref|YP_004037291.1|  [L=372]
Description: acetylornithine deacetylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-21   75.6   0.6    7.7e-21   74.7   0.6    1.5  1  Peptidase_M20  Peptidase family M20/M25/M40
    6.7e-18   64.6   0.0    1.9e-17   63.2   0.0    1.8  2  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.6   8.6e-25   7.7e-21       2     205 ..      63     365 ..      62     367 .. 0.86

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 8.6e-25
                                       EEEES-BSSTTCGGGSSSTTSEE.......ETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwttpfslt.......eedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdE 71 
                                       ++ H+D+V      +   pf+ +       + d+++ GrG++d kg ++a+l+a+ a++ +       ++++++pdE
  gi|313127021|ref|YP_004037291.1|  63 FNTHIDTVS----PHV--PFERRdgrgdgdDSDDVIRGRGSCDAKGPLAAILAAFFAVEPAD---GARVTVAVTPDE 130
                                       899******....233..9999976555555566***********************99996...459********* PP

                                       SSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................. RF
                     Peptidase_M20  72 EggrgGakallegleerekvdavfelhieepgileagklaigvv................................. 115
                                       E+ + Ga a         ++da +  +++ep++l+       v+                                 
  gi|313127021|ref|YP_004037291.1| 131 EVLSTGADA--------LDLDADL-YIVGEPTGLD-------VCtaakgrfqgtlrlsgvashaaepasgvnavfal 191
                                       *85566633........3455555.669*******.......445567889************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|313127021|ref|YP_004037291.1| 192 eqaltairsfddgrdehpqlgaatltpttveggestnqvpaecrlvldrrsvppetaeefrsslesavrdavpddvg 268
                                       **************************************************************************986 PP

                                       .EEEEEEE..EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHHTTTEEEEEEESS...G...GCT CS
                                       .xxxxxxx..xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x...xxx RF
                     Peptidase_M20 116 .kvevell..eggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarffagiptvmifgpg...s...gla 182
                                        +++++++     ++++++ d++lv+++a+a +++ g + ++ +   ++t+a++f   p v +fgpg   +   + a
  gi|313127021|ref|YP_004037291.1| 269 vEFSLTDRptPFLEAFATDdDHELVQTVAAASRRA-GGSGDVRPFT-AATEASYFSPAPVV-VFGPGvlaDdhgAVA 342
                                       6566665577777788888***************8.7665665666.********777655.799997653799*** PP

                                       TSTTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 183 HspnEyvdledlekgikvlarll 205
                                       H++ Eyv+ +++++++ +l++++
  gi|313127021|ref|YP_004037291.1| 343 HAEREYVRTDAVRRAATALTDAA 365
                                       ****************9998876 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.52   4.7e+03      84     105 ..      16      37 ..       9      39 .. 0.79
   2 !   63.2   0.0   2.1e-21   1.9e-17       2     108 ..     160     266 ..     159     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHHHHHHTSCC CS
                         M20_dimer  84 llpgedpeevleeieeilekea 105
                                       +  +ed++e +e ++e l++++
  gi|313127021|ref|YP_004037291.1|  16 VASNEDVAEMRELLVETLASHG 37 
                                       5678999999999999998876 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 2.1e-21
                                       EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEE CS
                         M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaea 78 
                                       + kG  +g+++  g+a H++ p  g+NA+ +l ++l+++++ ++   e  +l+  tl++t++egG ++n +p+e+++
  gi|313127021|ref|YP_004037291.1| 160 AAKGRFQGTLRLSGVASHAAEPASGVNAVFALEQALTAIRSFDDGRDEHPQLGAATLTPTTVEGGESTNQVPAECRL 236
                                       77999*************************************999999***************************** PP

                                       EEEEEHHHHHHHHHHHHHHHHHHTSCCSTT CS
                         M20_dimer  79 kidiRllpgedpeevleeieeilekeaped 108
                                        +d+R +p e++ee +  +e++++++ p+d
  gi|313127021|ref|YP_004037291.1| 237 VLDRRSVPPETAEEFRSSLESAVRDAVPDD 266
                                       ************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2973.35
//
Query:       gi|313127022|ref|YP_004037292.1|  [L=289]
Description: diaminopimelate epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-48  161.8   2.4    1.3e-23   83.5   0.4    2.7  2  DAP_epimerase  Diaminopimelate epimerase
     0.0038   16.3   0.2       0.65    9.0   0.1    2.2  2  Pro_racemase   Proline racemase


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.1   1.5e-25   1.3e-21       1     120 [.      10     135 ..      10     136 .. 0.86
   2 !   83.5   0.4   1.4e-27   1.3e-23       2     119 ..     160     275 ..     159     277 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 1.5e-25
                                       EEEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEE...........EEETTEEEEEEEETTTEEE CS
                     DAP_epimerase   1 fakshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvk...........psgeediklryfnrdgsea 66 
                                       +ak+hG++nd++vvd  e +++++++++ a+c+re g+++dg ++               ++ ++ +     dgs+a
  gi|313127022|ref|YP_004037292.1|  10 VAKYHGTGNDFIVVDADE-SVPDRPAFASAHCNRESGIDGDGSERRGadgvlflalegRYSPPRVVMTLVQPDGSVA 85 
                                       58************8766.677778*************988877777555555557775566677777********* PP

                                       STTHCCHHHHHHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE--EE CS
                     DAP_epimerase  67 emCGnGvrvfaaylreggletkkevtvetlgGeleievkddgekvkvdmGkasl 120
                                        mCGnG+r++aa ++e+     +e+ ++t++G++ + v+dd   v+ +mG +s+
  gi|313127022|ref|YP_004037292.1|  86 AMCGNGARCAAAWAAERT--GSDELMIDTPAGTRHAVVEDDR--VTIEMGAPSF 135
                                       *****************8..57*************9999997..8*****9975 PP

  == domain 2  score: 83.5 bits;  conditional E-value: 1.4e-27
                                       EEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETT.TEEESTTHCC.HHHH CS
                     DAP_epimerase   2 akshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvkpsgeediklryfnrd.gseaemCGnG.vrvf 76 
                                       a ++G+p+++ +vddv+a  ++    ++a+ +   +p++ +v +  ++++  ++ r+f+r+ ++e+++CG+G v+v+
  gi|313127022|ref|YP_004037292.1| 160 ALNTGVPHAIAFVDDVDAVALES--VAPAVRHADVFPDGANVTVASQNDDGSFRQRTFERGvEGETQSCGTGaVAVV 234
                                       689**************999999..*******************************7666439************** PP

                                       HHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE--E CS
                     DAP_epimerase  77 aaylreggletkkevtvetlgGeleievkddgekvkvdmGkas 119
                                       aa+ r g ++ +++vtv+ +gGelei+v ddg      +G+a+
  gi|313127022|ref|YP_004037292.1| 235 AAAKRVGLVDGDDPVTVSPPGGELEITVPDDGP--ATLTGPAE 275
                                       ********************************9..78999986 PP

>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0   0.00081       7.3      74     125 ..      78     124 ..      58     143 .. 0.76
   2 !    9.0   0.1   7.2e-05      0.65      77     126 ..     220     266 ..     196     289 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.00081
                                       EESSS.B-SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECT CS
                      Pro_racemase  74 letsg.ylpmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecr 125
                                       ++++g + +mcG+++ ++++ ++e       + + +l+++tpaG+ ++ +e++
  gi|313127022|ref|YP_004037292.1|  78 VQPDGsVAAMCGNGARCAAAWAAER------TGSDELMIDTPAGTRHAVVEDD 124
                                       455542578************9995......3344699******987777654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 7.2e-05
                                       SSB-SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTS CS
                      Pro_racemase  77 sgylpmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrd 126
                                       +g +++cG ++++vv+++   Glv    p    ++  p+G +e+t+ +++
  gi|313127022|ref|YP_004037292.1| 220 EGETQSCGTGAVAVVAAAKRVGLVDGDDPV---TVSPPGGELEITVPDDG 266
                                       677899********************9999...7899****999997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2260.67
//
Query:       gi|313127023|ref|YP_004037293.1|  [L=441]
Description: diaminopimelate decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-40  138.8   0.0    2.4e-40  138.4   0.0    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    2.9e-24   85.1   0.0    3.1e-24   85.0   0.0    1.3  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
    7.8e-08   32.2   0.1    1.4e-07   31.4   0.1    1.4  1  Ala_racemase_N   Alanine racemase, N-terminal domain
  ------ inclusion threshold ------
       0.04   14.3   2.9       0.22   11.9   1.1    2.8  3  EccE             Putative type VII ESX secretion system trans


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4   0.0   5.5e-44   2.4e-40       2     247 .]      65     308 ..      64     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 5.5e-44
                                       HHHHHHHHHHHHHCTCCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHH CS
                     Orn_Arg_deC_N   2 asierklkrwkkalprikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelry 78 
                                       ++++++++r ++a+   +v YavKa++ +avle+++e Gl+ +caS +E+e++l+ag++ ++i +++ +  + +l +
  gi|313127023|ref|YP_004037293.1|  65 DRVQENCARLQEAFSAEEVRYAVKAHTGRAVLETVREAGLAAECASAGEVERALNAGYEGSEIQYTAVNPPARDLDH 141
                                       57999************************************************************************ PP

                                       HHHCTHT....EEEESSHHHHHHHHHHHCCEEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTT CS
                     Orn_Arg_deC_N  79 alekgvk....vvtvdnveeleklaklapeakvllRiktdvsaatcelistggessKFGaaleeavealleaakeen 151
                                       ++++  +     vtv+ ++  ++l++   + ++++R++++v a+++e + tg  + KFG+ + ++v+ l e + +++
  gi|313127023|ref|YP_004037293.1| 142 VVDRWRDhpelTVTVGAADTADRLRERGFDGRLCIRANPGVGAGHHEKVRTGA-NAKFGVPY-DDVPELAESI-ADD 215
                                       *99877767789************************************88886.89******.9999999987.578 PP

                                       EEEEEEE---BSSC-..SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHH CS
                     Orn_Arg_deC_N 152 lqlvGvsfHvGSgvs..dleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplkleeiaekireale 226
                                        +lvG++ H GSg+s  dl++  + v+++ +l  ++++   +l+++dvGGGfgv y+++e+pl+l+ +a + real+
  gi|313127023|ref|YP_004037293.1| 216 FDLVGLHAHAGSGISgdDLSNHRELVRRMGELTRNVESRVGSLEFVDVGGGFGVPYRADEPPLDLDSVADATREALG 292
                                       9************954499******************87779**********************************8 PP

                                       HHHHTSSS-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 227 eafpgdkevtiiaEpGRalva 247
                                       ++       t+ +EpGR++va
  gi|313127023|ref|YP_004037293.1| 293 DVS-----GTLAVEPGRYVVA 308
                                       884.....589********98 PP

>> Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-terminal sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   0.0   6.9e-28   3.1e-24       2      98 .]     305     398 ..      59     398 .. 0.75

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 6.9e-28
                                       EEEEGGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHCTT-S-E.ESBTT-SCEEC.EEEEEEEE-SSSSTT-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC   2 yvydeagvLvtrViavkesekkkfvivdaGmndllrpalygsfhei.pvkeeeaekeeeeeeevdvvGptCesgDvl 77 
                                       yv+ +agvL+trV++vke  + ++v vdaGm++llrpa+y+++hei +v++    +++ e  +++v+Gp+Ces+Dv+
  gi|313127023|ref|YP_004037293.1| 305 YVVADAGVLLTRVNTVKEAPDATVVGVDAGMTTLLRPAMYDAYHEIrNVSA----ADDVEAISATVAGPICESADVM 377
                                       5555****************99************************88863....34456789************** PP

                                       EEEEEEEE--TT-EEEESS-S CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC  78 akdrelpelevGdllafedaG 98 
                                       +++r l  +++G+lla+ +aG
  gi|313127023|ref|YP_004037293.1| 378 CENRLLAYPRRGNLLAVGNAG 398
                                       ******99***********98 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   3.1e-11   1.4e-07       1     176 [.      62     247 ..      62     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3.1e-11
                                       EEHHHHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESC. CS
                    Ala_racemase_N   1 idldalrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvleg. 76 
                                       id d++++N++rl++++ ++++++  vKa + g  ++e +r +  + a++     +e al     g   +i +    
  gi|313127023|ref|YP_004037293.1|  62 IDTDRVQENCARLQEAF-SAEEVRYAVKA-HTGRAVLETVREAGLA-AECASAGEVERALNAGYEG--SEIQYTAVn 133
                                       89***************.7788*******.7777777777756545.7766666666666666555..555555555 PP

                                       STGGGHHHHHH....T.TEEEEESSHHHHHHHHHHHHH........TTS-EEEEEEBESSSS.SSSBSCHHHHHHHH CS
                    Ala_racemase_N  77 fspeelaalae....y.dltvtvdsleqlealaaaare........agkplrvhlkidtgmg.RlGftpeeleelle 139
                                        ++++l+ +++    + +ltvtv   + +++l +   +         g  +  h k+ tg + + G++ ++++el+e
  gi|313127023|ref|YP_004037293.1| 134 PPARDLDHVVDrwrdHpELTVTVGAADTADRLRERGFDgrlciranPGVGAGHHEKVRTGANaKFGVPYDDVPELAE 210
                                       688999998888999669****************9988999999999999*************************** PP

                                       HHHHTTTEEEEEEE-S-SSTTSTS..HHHHHHHHHHHHH CS
                    Ala_racemase_N 140 alaalpglrleglmtHfasadepd..eeteaqlarfeea 176
                                        +a+   ++l+gl  H +s  + d  +  ++ ++r+ e+
  gi|313127023|ref|YP_004037293.1| 211 SIAD--DFDLVGLHAHAGSGISGDdlSNHRELVRRMGEL 247
                                       **97..69*********9984333222333344454444 PP

>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.36   1.6e+03      29      77 ..      34      82 ..      22      91 .. 0.80
   2 ?   11.9   1.1   4.9e-05      0.22      37      85 ..      89     147 ..      66     155 .. 0.77
   3 ?    0.1   0.0      0.22     1e+03      43      57 ..     161     175 ..     145     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.36
                              EccE 29 tegaaraaaaaarRlakaLreqGirarvleaeeldaalaalavglaaap 77
                                       ++++r+    a+Rla+  +e G    v + + +++  a+l ++ +a++
  gi|313127023|ref|YP_004037293.1| 34 NPQIRRLSEWDADRLARLADEYGTPLYVIDTDRVQENCARLQEAFSAEE 82
                                      5677788888899999999999999999999999998888877766655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.9e-05
                              EccE  37 aaaarRlakaLreqGirarvleaeeldaalaalavglaaapa..........dvreewr 85 
                                       a + r +++  re+G++a +++a e+++al a  +g++ + +          +v ++wr
  gi|313127023|ref|YP_004037293.1|  89 AHTGRAVLETVREAGLAAECASAGEVERALNAGYEGSEIQYTavnppardldHVVDRWR 147
                                       33456699****************************99888766666665555555555 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.22
                              EccE  43 lakaLreqGirarvl 57 
                                        a++Lre+G++ r++
  gi|313127023|ref|YP_004037293.1| 161 TADRLRERGFDGRLC 175
                                       478999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3370.49
//
Query:       gi|313127024|ref|YP_004037294.1|  [L=281]
Description: 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-21   76.9   0.1    1.6e-21   76.3   0.1    1.3  1  THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-ter
    3.9e-10   39.1   3.2    0.00034   20.2   0.3    3.5  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
    4.2e-05   23.2   7.6     0.0016   18.1   0.5    3.5  2  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.1   2.6e-25   1.6e-21       2      67 .]       3      74 ..       2      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.6e-25
                                      HHHHHHHHHHTGGG--.S.SS--HHHHHHHHHHHHHHHTTSS-SEEE....ETTEEEE-HHHHHHHHHHHHH CS
                         THDPS_N_2  2 LesdIeaawerrdele.p.etagaearaaveevleaLdaGelRvAek....kdgeWevneWvKkAiLLsFrl 67
                                      ++s+I+++w+r+++ + + +tag+e+ a+++++l +L++Ge+R+Ae+    + + W+vneWvK++iLL+F+l
  gi|313127024|ref|YP_004037294.1|  3 IQSEIDDLWQRYQDDDiDaATAGSETLATLDAFLVSLEQGEVRAAEQvgdsGPDGWVVNEWVKRGILLNFGL 74
                                      79**********99888669**************************654333347***************97 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.038   2.2e+02       6      21 ..     109     124 ..     107     127 .. 0.65
   2 !   15.5   0.1   1.8e-06     0.011       2      36 .]     135     169 ..     134     169 .. 0.79
   3 !   20.2   0.3   5.6e-08   0.00034       2      34 ..     179     211 ..     178     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.038
                                       TTEEE-TTEEEETTEE CS
                           Hexapep   6 snvlIgpfaviggnVk 21 
                                       ++++I+ +a +g++++
  gi|313127024|ref|YP_004037294.1| 109 DGTTIRRGAFLGSDCI 124
                                       4566666666666664 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.8e-06
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + +G+++l+++  ++g+ +++G nvk+ga++ igg
  gi|313127024|ref|YP_004037294.1| 135 AYVGDGTLVDSCDTVGSCAQLGQNVKLGANTLIGG 169
                                       67999999999777778888888888888888775 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 5.6e-08
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       ++I+++v +g+++ + ++ ++G+n+++g+++ +
  gi|313127024|ref|YP_004037294.1| 179 VIIEDGVSLGAGCRVTSGFHVGENTIVGENTLL 211
                                       79***************************9876 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   1.3    0.0036        22      19      32 ..     154     167 ..     110     168 .. 0.84
   2 !   18.1   0.5   2.7e-07    0.0016       1      30 [.     178     209 ..     178     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0036
                                       EE-TT-EE-TT-EE CS
                         Hexapep_2  19 slGdncvvgaGvvi 32 
                                       +lG n+++ga+  i
  gi|313127024|ref|YP_004037294.1| 154 QLGQNVKLGANTLI 167
                                       68888888888655 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.7e-07
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT- CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGv 30 
                                       pviI+d + +Ga + +  G ++G+n +vg + 
  gi|313127024|ref|YP_004037294.1| 178 PVIIEDGVSLGAGCRVtsGFHVGENTIVGENT 209
                                       8**************88***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2037.78
//
Query:       gi|313127025|ref|YP_004037295.1|  [L=256]
Description: dihydrodipicolinate reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-35  119.8   0.0    8.3e-35  119.4   0.0    1.2  1  DapB_C           Dihydrodipicolinate reductase, C-terminus
    3.1e-29  101.6   0.1    5.4e-29  100.8   0.1    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    1.4e-05   25.7   0.3    2.6e-05   24.9   0.3    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    0.00029   21.7   0.0    0.00056   20.7   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00044   20.5   0.1     0.0029   17.8   0.1    2.1  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.002   18.7   0.2     0.0044   17.7   0.2    1.5  1  CoA_binding      CoA binding domain
     0.0033   17.8   0.1      0.011   16.2   0.1    1.8  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0047   16.1   0.0     0.0079   15.3   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
     0.0068   15.9   0.0      0.013   15.0   0.0    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.022   14.7   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.021   15.3   0.3      0.031   14.8   0.3    1.3  1  CoA_binding_2    CoA binding domain
      0.077   13.3   0.9       0.21   11.9   0.1    2.2  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA


Domain annotation for each model (and alignments):
>> DapB_C  Dihydrodipicolinate reductase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.0   5.6e-38   8.3e-35       1     121 []     123     254 ..     123     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 5.6e-38
                                       HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH................-S-ETTCCCEEEE CS
                            DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaia............egkearkkkeigihsvR 65 
                                       Gv+ l ++v+ea ++l++ ydve++E+Hhn K DaPSGTA +l+ +i             eg+++r  +eig+h+ R
  gi|313127025|ref|YP_004037295.1| 123 GVAALRRAVREAVAALPN-YDVEVTETHHNGKRDAPSGTANTLLTEIDdvrgeservygrEGDQPRMGGEIGVHARR 198
                                       8999*************9.*****************************98887766666655559999********* PP

                                       TTT--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSSEESHHHHH CS
                            DapB_C  66 gggvvgehevlfagegevieikhealsreiFaeGallaaewlakkkkglysmedvL 121
                                       +ggv+gehevl+a +++ ++++h+a sr +Fa Gal+aa wla++++g y++++vL
  gi|313127025|ref|YP_004037295.1| 199 AGGVTGEHEVLLADDHQLLSLTHRAGSRGVFAAGALDAAVWLADRDAGRYDFDEVL 254
                                       ******************************************9**********998 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.1   3.6e-32   5.4e-29       1     124 []       5     120 ..       5     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 3.6e-32
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEB..SSHHHHHHH..-SEEE CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg.klgvavt..ddleevlek..advli 72 
                                       ++va++Ga+GrmG+e+++++++++d+e+v av+r++             ++  +gv+v   ddl e+l++   dv++
  gi|313127025|ref|YP_004037295.1|   5 VRVAITGAAGRMGRELIDVADSRDDVEVVLAVNRSP-------------IEaVSGVPVRdaDDLPELLAEtdPDVMV 68 
                                       69********************************99.............2225688887779*******98888*** PP

                                       E-S-HHHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTTSEEEE-S-- CS
                            DapB_N  73 DFTtpeavlenlklalekgvklViGTTGlseeelaeleelakkigvviapNf 124
                                       DFT pe+++e++++++e+gv +V+GTTG++e+ +a l+e+a++++++ a+Nf
  gi|313127025|ref|YP_004037295.1|  69 DFTGPESSVEYVAACAEAGVGVVVGTTGFDEDGHAALDEAAESVPLLHATNF 120
                                       ***************************************************8 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.3   1.7e-08   2.6e-05       5      90 ..      16      94 ..      12     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-08
                                      HHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTT CS
                     NAD_binding_3  5 iGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvlkaLkag 83
                                       G+++++  +++++  ++e+v+ ++r+       +    + +  +dl++l+a+ dpdv V+ +++e+  e+v+++ +ag
  gi|313127025|ref|YP_004037295.1| 16 MGRELIDV-ADSRD--DVEVVLAVNRS----PIEAVSGVPVRDADDLPELLAETDPDVMVDFTGPESSVEYVAACAEAG 87
                                      55555543.34444..68888888888....66667777888899*******99************************* PP

                                      EEEE-S- CS
                     NAD_binding_3 84 kdvvtan 90
                                      + vv+  
  gi|313127025|ref|YP_004037295.1| 88 VGVVVGT 94
                                      ****965 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.7e-07   0.00056       1      91 [.       5      92 ..       5      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.7e-07
                                      EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA  1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78
                                      +rvai Ga G++g++ +  + +s+++ evv ++++++   eav     v   +dl ella++++d+ +  t +++  e+
  gi|313127025|ref|YP_004037295.1|  5 VRVAITGAaGRMGRELI-DVADSRDDVEVVLAVNRSP--IEAV-SGVPVRDADDLPELLAETDPDVMVDFTGPESSVEY 79
                                      59***************.9999999999999999998..5555.33556699*************************** PP

                                      HHHHHHTT-EEEE CS
                      GFO_IDH_MocA 79 akaaleagkhvll 91
                                      + a++eag+ v++
  gi|313127025|ref|YP_004037295.1| 80 VAACAEAGVGVVV 92
                                      ********98875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1     2e-06    0.0029       4      99 ..      10      95 ..       7     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-06
                                      E--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS..SEEEE-SSG CS
                   Sacchrp_dh_NADP  4 iGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg..dlvvnlspp 79
                                       Ga G++G+ ++++   ++dv  e+++a  +++  ea+             + + + ++ L +ll+e+  d+ v+ ++p
  gi|313127025|ref|YP_004037295.1| 10 TGAaGRMGRELIDVADSRDDV--EVVLA-VNRSPIEAV-----------SGVPVRDADD-LPELLAETdpDVMVDFTGP 73
                                      566666666666666666666..33332.222332233...........2456677777.8888888889********* PP

                                      GGHHHHHHHHHHHT-EEEE..S CS
                   Sacchrp_dh_NADP 80 issldvlkaCietgvhyvd..t 99
                                       ss + ++aC+e+gv +v   t
  gi|313127025|ref|YP_004037295.1| 74 ESSVEYVAACAEAGVGVVVgtT 95
                                      ***************9886444 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   2.9e-06    0.0044       5      91 ..       6      92 ..       3      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-06
                                      EEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC...TTTEEEEES-HHHHHHHH CS
                       CoA_binding  5 kviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt...evdvavitvPaesaqeav 79
                                      +v++ Ga g+ + +l  + +++ +++++ ++  +p    + v+g+pv  + d+l+e +   ++dv+v ++ +es  e v
  gi|313127025|ref|YP_004037295.1|  6 RVAITGAAGRMGRELiDVADSRDDVEVVLAVNRSPI---EAVSGVPVR-DADDLPELLaetDPDVMVDFTGPESSVEYV 80
                                      899***988887777577777777555555555554...99*******.8888888887435********99******* PP

                                      HHHHHTT-SEEE CS
                       CoA_binding 80 delveagikgiv 91
                                       +++eag+ ++v
  gi|313127025|ref|YP_004037295.1| 81 AACAEAGVGVVV 92
                                      ********9998 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.1e-06     0.011       1      94 [.       6      91 ..       6     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.1e-06
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT...TTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssr...saGkklaeavkaleegkdlkvedvdeeelkevdivflalpa 76
                                      +vai Ga G +G+el+ + ++  +ve+v ++ +s      G ++++a     +  +l        +  + d+++  ++ 
  gi|313127025|ref|YP_004037295.1|  6 RVAITGAAGRMGRELIDVADSRDDVEVVLAVNRSPieaVSGVPVRDAD----DLPELL-------AETDPDVMVDFTGP 73
                                      79**************************99998883222233333331....122222.......33588999999999 PP

                                      HHHHHHHHHHHHTTSEEE CS
                    Semialdhyde_dh 77 gvskelapklaeagvkvi 94
                                      + s e+++++aeagv v+
  gi|313127025|ref|YP_004037295.1| 74 ESSVEYVAACAEAGVGVV 91
                                      999999999999999555 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.3e-06    0.0079       2      57 ..       6      69 ..       5      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.3e-06
                                      EEEEESTTSHHHHHHHHHCTTTS.EE.EEEE-TT......T--TTSHHHHHHHHHHH--SEEEE CS
                     RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeg.le.vlaltre......eldltdaeavaellkeakpdvvvn 57
                                      ++ +tGa G +G+eL++ +++++ +e vla++r+       + ++da+ + ell+e++pdv v+
  gi|313127025|ref|YP_004037295.1|  6 RVAITGAAGRMGRELIDVADSRDdVEvVLAVNRSpieavsGVPVRDADDLPELLAETDPDVMVD 69
                                      789***************99865244257889989999988999*****************996 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.4e-06     0.013       2      82 ..       8      78 ..       7      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.4e-06
                                      EEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.---HH CS
                         Epimerase  2 lVtGatGfiGsalvkallekg.yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vggva 78
                                       +tGa+G +G+ l++   +++ +ev+   ++s     +      +  + ++d+++l +l++e++pd+ + + + ++   
  gi|313127025|ref|YP_004037295.1|  8 AITGAAGRMGRELIDVADSRDdVEVVLAVNRSP---IE-----AVSGVPVRDADDLPELLAETDPDVMVDFTGpES--- 75
                                      69******************9988555555522...22.....456899********************9955444... PP

                                      HHHH CS
                         Epimerase 79 asse 82
                                       s+e
  gi|313127025|ref|YP_004037295.1| 76 -SVE 78
                                      .444 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.5e-05     0.022      53      95 ..      58     100 ..      23     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       HTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC.TSSEE CS
                        ADH_zinc_N  53 ltggegvdvvfecvGsgatleaalkllkpgGrlvvvGg.gkgee 95 
                                       l  + ++dv ++++G +++  ++++++++ G  vvvG+ g++e+
  gi|313127025|ref|YP_004037295.1|  58 LLAETDPDVMVDFTG-PESSVEYVAACAEAGVGVVVGTtGFDED 100
                                       334459*********.*********************9765554 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   2.1e-05     0.031       3      89 ..       7     104 ..       5     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                                       EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-.SEETTEE.....S----T.......T--EEEE-S-HHHHGG CS
                     CoA_binding_2   3 iaVvGasdnpgkfgykvlryllehglpvvpVnpke.eeilgek.....vyaslaed...pepvdlvdvftppeatpe 70 
                                       +a+ Ga  + g+    v++   + +  v++Vn    e++ g++       +    +   ++++d+ + ft pe  +e
  gi|313127025|ref|YP_004037295.1|   7 VAITGAAGRMGRELIDVADSRDDVE-VVLAVNRSPiEAVSGVPvrdadDLP----EllaETDPDVMVDFTGPESSVE 78 
                                       7888888777777777888877788.8889998888999998844333333....134589**************** PP

                                       GHHHHHHH--SEEEE-TT.......- CS
                     CoA_binding_2  71 ivkealalgakavwlqpg.......s 89 
                                       +v +++++g+ +v+   g       +
  gi|313127025|ref|YP_004037295.1|  79 YVAACAEAGVGVVVGTTGfdedghaA 104
                                       **************999966544432 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00014      0.21       1      32 [.       5      38 ..       5      52 .. 0.82
   2 ?   -1.7   0.1       2.5   3.8e+03      85      97 ..      85      97 ..      79     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                      CEEEEES.TSHHHHHHHHHHHHHTTCEEE.EEE- CS
                           Gp_dh_N  1 vkvainG.fGRIGrlvlralleekelevv.aind 32
                                      v+vai G  GR+Gr ++ ++ +++++evv a+n+
  gi|313127025|ref|YP_004037295.1|  5 VRVAITGaAGRMGRELIDVADSRDDVEVVlAVNR 38
                                      689***955*****************99834554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                                      HHTSSEEEE-SSS CS
                           Gp_dh_N 85 elgvdlVvestGv 97
                                      e+gv +Vv +tG+
  gi|313127025|ref|YP_004037295.1| 85 EAGVGVVVGTTGF 97
                                      7899*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1827.00
//
Query:       gi|313127026|ref|YP_004037296.1|  [L=308]
Description: dihydrodipicolinate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-94  315.0   0.0    3.3e-94  314.9   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.022   14.0   0.0      0.042   13.2   0.0    1.4  1  ThiG      Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.9   0.0   3.7e-98   3.3e-94       2     288 ..       6     291 ..       5     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 314.9 bits;  conditional E-value: 3.7e-98
                                       -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE-- CS
                             DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvG 78 
                                       ++g+ +a+ tpf  dg +d+e l+   + l  +gvdglv +G+tGEsatl ++e++++ve++veaa++ +pviag G
  gi|313127026|ref|YP_004037296.1|   6 LTGVYPAMTTPFAPDGSIDHETLADDTRRLERAGVDGLVPVGSTGESATLTHDEHIEVVETVVEAAED-VPVIAGSG 81 
                                       689************************************************************99875.******** PP

                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTST CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaele 155
                                       snst+ea++l+++++++Gadg+l++ PYYnkp+q+gl++h+++i+ + d p+i+Ynvpsrtg++++p+tv++La  e
  gi|313127026|ref|YP_004037296.1|  82 SNSTREALELSRRSADVGADGLLLISPYYNKPEQAGLIEHYQTIADEVDVPQIVYNVPSRTGSNIEPATVATLADHE 158
                                       *********************************************9999**************************** PP

                                       TEEEEEE-SS-CTHHHHHHCCCS.TTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHH CS
                             DHDPS 156 nivgvKeavgdleevikikkevg.kdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaae 231
                                       ni+g K+a+gd+ ++ +++++++ ++++i+sGdd+l+l+++s+G++Gvisvt ni +er +++++a+ +Gd++ a+e
  gi|313127026|ref|YP_004037296.1| 159 NIAGYKAASGDIGQISEVVERTReQEFAILSGDDALTLPVISVGGHGVISVTGNIEPERTAAMVHAALDGDFDSARE 235
                                       *****************999986257*************************************************** PP

                                       HHHHHHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHHH CS
                             DHDPS 232 lnekllplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleallka 288
                                       l+++l pl  +lf e+n+i+vk+a+e+ G   ++ lr+Plt+l +e++e lea+l++
  gi|313127026|ref|YP_004037296.1| 236 LHHELGPLSRQLFIETNPIPVKAAMEIRGYAPGT-LRPPLTELRDEHYEMLEATLEQ 291
                                       *******************************999.*******************997 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.7e-06     0.042     137     203 ..      32     105 ..      25     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-06
                                       HHHHHHTT-SEBEEBSSSTTS----S-HH...HHHHHHHH-.SS-BEEES---SHHHHHH....HHHTT-SEEEE CS
                              ThiG 137 arrleevGcaavmPlaapiGsglGllnke...alkiiieea.kvPvivDAGigspsdaaq....amelGadavll 203
                                       +rrle +G+  ++P+++   s+  l++ e   ++++++e a +vPvi   G  s+ +a +    + ++Gad++ll
  gi|313127026|ref|YP_004037296.1|  32 TRRLERAGVDGLVPVGSTGESA-TLTHDEhieVVETVVEAAeDVPVIAGSGSNSTREALElsrrSADVGADGLLL 105
                                       69**************985555.55555401156778899899****9999888888865222256778888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2143.70
//
Query:       gi|313127027|ref|YP_004037297.1|  [L=165]
Description: hypothetical protein Hbor_22910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-38  130.8   0.2    6.3e-38  130.5   0.2    1.0  1  NYN       NYN domain
     0.0051   15.3   0.1     0.0064   15.0   0.1    1.2  1  FMO-like  Flavin-binding monooxygenase-like
  ------ inclusion threshold ------
      0.069   12.8   0.1       0.22   11.2   0.1    1.7  2  DUF2529   Domain of unknown function (DUF2529)


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.5   0.2   1.1e-41   6.3e-38       1     146 [.       9     156 ..       9     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 1.1e-41
                               NYN   1 rvavfiDgenlpvpak...gkevdyrklleeirskgelvraraygn.wedeeqnkfqdalsstgikvkhkplkkrg. 72 
                                       rva++ D++nl+++a+   ++++dy++lle+ +s + l+ra ay+   +++e ++f dal ++g++ k k+ k++g 
  gi|313127027|ref|YP_004037297.1|   9 RVAILADAQNLYHSAQslySRNIDYSSLLEKGVSDRTLTRAIAYVVrADSPEEESFFDALVEIGFETKIKDIKTFGd 85 
                                       89*************9998888************************65566689999*****************999 PP

                               NYN  73 gsgkkavDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                       gs+k ++Dv++ +da++la  n++dt+vL++gDgDF++l+++lr++g+rVev++++ +st++eLi+aad+f+++
  gi|313127027|ref|YP_004037297.1|  86 GSKKADWDVGMSLDAVTLA--NHVDTVVLCTGDGDFSRLCSHLRHEGVRVEVIAFK-ESTADELIEAADTFLDM 156
                                       9999***************..99*******************************88.7*************987 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.1e-06    0.0064      97     148 ..      65     116 ..      60     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-06
                          FMO-like  97 fdllkyiqfkttvcsvkkrpdfstsGqwevvtekegkkesavfdavmvctGh 148
                                       fd l  i f+t++  +k   d s+   w+v    +  + ++  d+v++ctG 
  gi|313127027|ref|YP_004037297.1|  65 FDALVEIGFETKIKDIKTFGDGSKKADWDVGMSLDAVTLANHVDTVVLCTGD 116
                                       789999********************************************96 PP

>> DUF2529  Domain of unknown function (DUF2529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.23   1.4e+03      80     122 ..       9      48 ..       2      59 .. 0.66
   2 ?   11.2   0.1   3.6e-05      0.22      75     131 ..     104     157 ..      89     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.23
                                       EEEEEES-S--HHHHHHHHHHHHHT--EEEEESS---T..TGG CS
                           DUF2529  80 rvllfsresndkealklakkleekgievvavsskvkeedalte 122
                                       rv ++++ +   ++ + a++l+ ++i++  + +k  ++++lt 
  gi|313127027|ref|YP_004037297.1|   9 RVAILADAQ---NLYHSAQSLYSRNIDYSSLLEKGVSDRTLTR 48 
                                       555555444...4578888888888888888777777665444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.6e-05
                                       --TT-EEEEEES-S--HHHHHHHHHHHHHT--EEEEESS---T..TGGGSSS-EE-- CS
                           DUF2529  75 ltetDrvllfsresndkealklakkleekgievvavsskvkeedalteladvfidlk 131
                                        +++D+v+l++    d + ++l ++l+++g+ v +++ k++++d+l e ad+f+d++
  gi|313127027|ref|YP_004037297.1| 104 ANHVDTVVLCT---GDGDFSRLCSHLRHEGVRVEVIAFKESTADELIEAADTFLDMS 157
                                       56789999997...56788***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1223.53
//
Query:       gi|313127028|ref|YP_004037298.1|  [L=330]
Description: hypothetical protein Hbor_22920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        8.9    5.6   6.7        4.1    6.7   0.4    2.2  2  DUF3810   Protein of unknown function (DUF3810)


Domain annotation for each model (and alignments):
>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.2    0.0075   1.4e+02      25      85 ..     136     205 ..     108     222 .. 0.57
   2 ?    6.7   0.4   0.00023       4.1      12      44 ..     225     257 ..     220     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.0075
                           DUF3810  25 gellivllillvilylvlai..............klkkrkkkkkrllkvllrvllvllvvyflftllwglnYyre 85 
                                       + l iv++++++ +                    ++++ +  +k+ll++++  ++ +++v+++ + + g  Yyr+
  gi|313127028|ref|YP_004037298.1| 136 VGLGIVVVLVFIQF-----YpvavslgdtdaidsFRQSIRLVRKNLLSTIGYSVINAIAVLIMTLPVSGPMYYRQ 205
                                       23333444444444.....35555599999888744445555556666666666666666666666677777765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00023
                           DUF3810  12 ilsrlsglfpFSvgellivllillvilylvlai 44 
                                       + s++s+l+ FS  e++++ +i l++++l++++
  gi|313127028|ref|YP_004037298.1| 225 VSSQMSQLVQFSTQEVMLLSAISLAAMMLLFTF 257
                                       67899*****************99999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 2252.83
//
Query:       gi|313127029|ref|YP_004037299.1|  [L=59]
Description: hypothetical protein Hbor_22930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 483.50
//
Query:       gi|313127030|ref|YP_004037300.1|  [L=188]
Description: prefoldin subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-26   91.9   0.0    3.5e-26   91.1   0.0    1.4  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    2.6e-15   56.1   0.2    4.2e-15   55.5   0.2    1.3  1  PUA       PUA domain
  ------ inclusion threshold ------
      0.068   13.5   0.0       0.11   12.8   0.0    1.4  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   5.8e-30   3.5e-26       2      71 .]      41     110 ..      40     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 5.8e-30
                            TGT_C2   2 rlraiadYqFGagagdaLfped.vtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71 
                                        lr++a+YqFG gag+aLfp+d +t++rs++gr+rqvl+d+ r++++ ++dgr+tL++eG+ rl+es +pP
  gi|313127030|ref|YP_004037300.1|  41 DLRTVANYQFGSGAGAALFPDDnLTVRRSTSGRPRQVLADEGRIVSY-GTDGRFTLGVEGGIRLVESSSPP 110
                                       59*****************9999***********************9.*******************9998 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.2   7.1e-19   4.2e-15       2      71 ..     113     182 ..     112     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 7.1e-19
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveie 71 
                                       rv+v  ++  +++ g++ +a++v++v+ ++++gd+Va+v++d+ +++vG+a++s+e + +++ g++v ++
  gi|313127030|ref|YP_004037300.1| 113 RVTVGSESEPFVRDGKNAFAKFVTSVDPEVRPGDEVAVVTPDDVVIGVGRAELSAEAMIDFETGMAVFVR 182
                                       899999**********************************************************998766 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05      0.11      15      55 ..     127     167 ..     114     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                           UPF0113  15 GrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt 55 
                                       G++ + + + +++++v+ ++ v+V+  ++ ++G+G++  + 
  gi|313127030|ref|YP_004037300.1| 127 GKNAFAKFVTSVDPEVRPGDEVAVVTPDDVVIGVGRAELSA 167
                                       9999********************************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1417.35
//
Query:       gi|313127031|ref|YP_004037301.1|  [L=328]
Description: hypothetical protein Hbor_22950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-89  299.4  12.0    3.9e-89  298.9  12.0    1.2  1  SPP             Signal-peptide peptidase, presenilin aspartyl
    2.4e-06   27.3   6.5    0.00018   21.1   2.3    2.6  2  Peptidase_A22B  Signal peptide peptidase
  ------ inclusion threshold ------
      0.067   11.9   9.7         54    2.4  12.3    3.0  2  Presenilin      Presenilin


Domain annotation for each model (and alignments):
>> SPP  Signal-peptide peptidase, presenilin aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.9  12.0   6.4e-93   3.9e-89       3     283 .]      15     320 ..      13     320 .. 0.93

  Alignments for each domain:
  == domain 1  score: 298.9 bits;  conditional E-value: 6.4e-93
                               SPP   3 lfvvvqvlalllavplesaelqatedPtqvlnsvvyivlllvftlfvlivikkdkkliiskviyvivvavifyvflv 79 
                                       +f++vq++al+l++p++  + q+ edP ++ ns+vyi ++lv+t+ +l + k+d  + ++ ++ +++++  +yvf +
  gi|313127031|ref|YP_004037301.1|  15 IFLLVQLGALALVTPFYDGGFQTVEDPSDPTNSLVYIGAILVATAVMLAAFKYDFDWAVRALVVLTSGMLSWYVFSI 91 
                                       89*************************************************************************** PP

                               SPP  80 llsivlvvaglvnlaslvvaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvyk 156
                                       +l+ +++va          a+ + ++l  ypeWyvid+ G+i++ G++alfGis+g+lpavvll+alavydaisvy+
  gi|313127031|ref|YP_004037301.1|  92 ILPFLPAVAA---------AVLVAGALVVYPEWYVIDATGIIMGAGAAALFGISFGLLPAVVLLTALAVYDAISVYG 159
                                       *****99988.........4444578889************************************************ PP

                               SPP 157 tkhmialaegvvdlklPillvvPetlaysfveeafeeaeeaea..........................rnvlfiGl 207
                                       t+hm+ laegv+dl++P++lv+P+tl+ys++++ f  a++                             r+++fiGl
  gi|313127031|ref|YP_004037301.1| 160 TEHMLDLAEGVMDLHIPVVLVIPTTLSYSLLDDDFSSANDVHDdpdaeappspesdggdptddsdeegvRDAFFIGL 236
                                       **********************************999988665677788**************************** PP

                               SPP 208 GdavlPsilvvsaavfleshi...l..ag...lelavllalaGtlvGllvlsilvlrgrpaaGlPllnsGaiaGfli 276
                                       Gdav+P+++++saa+fl       l   g   l l+vl+a++Gt+ Gl  l  lvl+gr++aGlPlln+G+i G+li
  gi|313127031|ref|YP_004037301.1| 237 GDAVMPTVMIASAAFFLPDAAapsLgvPGlpiLTLPVLTAMVGTFAGLFALLWLVLKGRAHAGLPLLNGGTIGGYLI 313
                                       ****************965431113223433357999**************************************** PP

                               SPP 277 gvlaagv 283
                                       g++ +g+
  gi|313127031|ref|YP_004037301.1| 314 GAVLSGI 320
                                       ***9986 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.3   3.1e-08   0.00018      99     178 ..     104     187 ..      48     196 .. 0.76
   2 !    7.4   0.1   0.00048       2.8     187     204 ..     233     250 ..     220     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.1e-08
                                       ----S--XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXX CS
                    Peptidase_A22B  99 viavlwllkrhwilndilglalailviellrlp.slkvgalLLvglflYDifwVFgtdvmvevAk...eldiPillk 171
                                        +a   ++ ++w + d+ g+ +     +l  +   l  +++LL++l +YD   V+gt+ m+ +A+   +l+iP++l+
  gi|313127031|ref|YP_004037301.1| 104 LVAGALVVYPEWYVIDATGIIMGAGAAALFGISfGLLPAVVLLTALAVYDAISVYGTEHMLDLAEgvmDLHIPVVLV 180
                                       44445566777888888888887777776666534667899************************98899******* PP

                                       XXXXXXX CS
                    Peptidase_A22B 172 lPqlsne 178
                                       +P++ + 
  gi|313127031|ref|YP_004037301.1| 181 IPTTLSY 187
                                       **95444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00048
                                       XXXXXXXXXXXXXXXXXX CS
                    Peptidase_A22B 187 iLGlGDivlPGllialll 204
                                        +GlGD v+P ++ia + 
  gi|313127031|ref|YP_004037301.1| 233 FIGLGDAVMPTVMIASAA 250
                                       69************9765 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  12.3     0.009        54      62     119 ..      45     101 ..      42     161 .. 0.75
   2 ?    1.9   0.0     0.013        77     310     341 ..     222     251 ..     190     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.009
                        Presenilin  62 lnalililvivvvtfllvlLykyrcykvikgwlilsslllLflvsglllaevlkayni 119
                                       +n+l+ i++i+v+t ++++ +ky++   +++ ++l+s +l +++ + ++  +l a+  
  gi|313127031|ref|YP_004037301.1|  45 TNSLVYIGAILVATAVMLAAFKYDFDWAVRALVVLTSGML-SWYVFSIILPFLPAVAA 101
                                       59*****************************999999876.55555555555555544 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.013
                        Presenilin 310 eeeeeseseergvkLGLGDFiFYSvLvgkAal 341
                                       +  +++e+ +++  +GLGD +   v+++ Aa 
  gi|313127031|ref|YP_004037301.1| 222 D--SDEEGVRDAFFIGLGDAVMPTVMIASAAF 251
                                       1..112223347779**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2181.73
//
Query:       gi|313127032|ref|YP_004037302.1|  [L=77]
Description: snornp protein gar1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-10   39.7   0.0      4e-10   39.7   0.0    1.0  1  Gar1      Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
        0.1   12.7   0.1       0.19   11.8   0.0    1.5  2  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   4.4e-14     4e-10      20      98 ..       3      75 ..       1      77 [] 0.89

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 4.4e-14
                                      EEEEEEEEEEETTEEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTTTTSEEE CS
                              Gar1 20 vleiGtvssivenevviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfkvgdkvy 98
                                      ++ +Gtvs + +n  + ++   ge + +d++  + +e  +++G+V ++fGpv+ py++V  +   +++ +s+ vg+k+y
  gi|313127032|ref|YP_004037302.1|  3 MQRVGTVSRTAQNLAIARCE--GE-EHPDIGREVVDESLSSVGRVVDVFGPVSRPYVAVSTS--GRATPASL-VGTKLY 75
                                      6789***************9..65.89*********************************99..66666555.888888 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.77   6.9e+03      21      26 ..       5      10 ..       4      12 .. 0.81
   2 ?   11.8   0.0   2.1e-05      0.19      10      32 ..      29      50 ..      29      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.77
                                      EEEEEE CS
                               PRC 21 klGkVk 26
                                      ++G+V+
  gi|313127032|ref|YP_004037302.1|  5 RVGTVS 10
                                      899997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.1e-05
                                      TT-EEEETTSSEEEEEEEEEEET CS
                               PRC 10 iGkeVytedGeklGkVkDvvide 32
                                      iG+eV++e+   +G+V Dv + +
  gi|313127032|ref|YP_004037302.1| 29 IGREVVDESLSSVGRVVDV-FGP 50
                                      89*****************.865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 508.80
//
Query:       gi|313127033|ref|YP_004037303.1|  [L=93]
Description: signal recognition particle subunit srp19 (srp19) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-25   87.3   0.0    1.2e-24   87.1   0.0    1.1  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   6.6e-29   1.2e-24       1      91 [.       6      88 ..       6      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 6.6e-29
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCCEEEEEC-..........SS- CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanpGrVrvklkedgkevnekikn 79
                                      vi+P Yld++k+r+ GRrvp e av++Pt++eiaea++++g+++v+e++ ++Pr+w  +GrV vk          + ++
  gi|313127033|ref|YP_004037303.1|  6 VIWPRYLDAEKSRSAGRRVPLEDAVDDPTVDEIAEAVQQIGYDAVIERDVTHPREWEANGRVIVKGA--------DDST 76
                                      7****************************************************************85........4567 PP

                                      CHHHHHHHHHHH CS
                             SRP19 80 kkellkkiaell 91
                                      k++l++++a+++
  gi|313127033|ref|YP_004037303.1| 77 KNDLVQAVAAYV 88
                                      888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 658.45
//
Query:       gi|313127034|ref|YP_004037304.1|  [L=376]
Description: Fe3+-hydroxamate ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-32  110.4   1.3    9.9e-32  110.4   1.3    1.5  2  Peripla_BP_2  Periplasmic binding protein
    1.1e-07   31.6   3.0    2.1e-07   30.7   3.0    1.5  1  PGF-CTERM     PGF-CTERM motif
     0.0015   18.2   0.2     0.0015   18.2   0.2    2.1  2  Peripla_BP_4  Periplasmic binding protein domain
  ------ inclusion threshold ------
       0.81    9.5   4.2        1.2    8.9   4.2    1.3  1  RIFIN         Rifin


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   1.3   2.2e-35   9.9e-32       1     237 [.      59     279 ..      59     280 .. 0.95
   2 ?   -2.8   0.1      0.86   3.9e+03     117     139 ..     303     325 ..     300     342 .. 0.69

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 2.2e-35
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG.....GGG CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskgl..gltded 75 
                                       +++l+ps +++  +lGa+d+vvgv++++ +   ad    ++ +v++ + ++vE+++++ PD+v+++++      d+ 
  gi|313127034|ref|YP_004037304.1|  59 VVTLNPSAAQTMWELGASDEVVGVSKYATYLDGAD----EKQNVSGANGPSVERVLDANPDVVLVPNSTyaFAKDRV 131
                                       89********************************9....99**************************9988888899 PP

                                       HHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE..E CS
                      Peripla_BP_2  76 eellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvfggadeggy 151
                                       ++++++g  ++++e+++ ++ + +  +++g l+g+ +++++ ++ei +  +  ++ ++ e kp ++++f+      +
  gi|313127034|ref|YP_004037304.1| 132 DQIRAQGTTVFVFETGSSLSFVANKTEQIGRLTGNCEAGRQSAQEIRNSADLMREVLADEdKPVALNYFY------T 202
                                       9*****************9*****************************************6777777777......6 PP

                                       EEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHT CS
                      Peripla_BP_2 152 vvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkn 228
                                       + +gsn++igd++ ++g+ n aae +  ++++i+ E++++++p++i+v +          + +  ++++++++Av++
  gi|313127034|ref|YP_004037304.1| 203 YTSGSNTFIGDVMTTAGLTNGAAEANITGFAPINTETVVEMNPEYIIVPTG---------ATVPDTEAWNSTTAVQE 270
                                       999************************************************.........778889*********** PP

                                       T-EEEE-HH CS
                      Peripla_BP_2 229 grVyaldss 237
                                       g++++++s+
  gi|313127034|ref|YP_004037304.1| 271 GNIIEVNSN 279
                                       ****99876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHHHHHTS-TT.-EE CS
                      Peripla_BP_2 117 lvaeidsklaaaksaidsekpkp 139
                                       +++e++s  a+a++ + + ++++
  gi|313127034|ref|YP_004037304.1| 303 AFEEYQSMKAEAEATTTESTETT 325
                                       56777777777777777664443 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   3.0   4.7e-11   2.1e-07       1      23 []     354     376 .]     354     376 .] 0.99

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.7e-11
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       tPGFG++l+l+ +LaaalLa+Rr
  gi|313127034|ref|YP_004037304.1| 354 TPGFGVALTLVSMLAAALLATRR 376
                                       9*********************9 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   3.3e-07    0.0015      46     174 ..     104     270 ..      66     274 .. 0.79
   2 ?   -0.5   1.2      0.17   7.6e+02      13      45 ..     308     340 ..     294     371 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHHTT-SEEEE--SSHHHHHHHHHHHHHTT-EEEEESTTGCTTT-CEEEEEC-HHHHHHHHH.......... CS
                      Peripla_BP_4  46 aqiedaiakgvdgiivapvdstalapalkkakaaGIpVvafdsddapsgerlayvgfdneaaGelqa.......... 112
                                         +e ++++++d+++v     + +++ +++++a+G  V++f +      + l++v+   e++G+l +          
  gi|313127034|ref|YP_004037304.1| 104 PSVERVLDANPDVVLVPNSTYAFAKDRVDQIRAQGTTVFVFETG-----SSLSFVANKTEQIGRLTGnceagrqsaq 175
                                       578999******9999999999999******************9.....99************************** PP

                                       ......................HHHHHHCTTH...EEEEEETSCCCHHHHHHHHHHHHHHHHH.....-TTCEECC. CS
                      Peripla_BP_4 113 ......................eylaeklggk..kgkvvilaGspgdpnaeeriegfrkvlke.....ypgikiva. 159
                                                             +y   +  g+   +  v+ ++ +++ +ae+ i gf  + +e      p++ iv+ 
  gi|313127034|ref|YP_004037304.1| 176 eirnsadlmrevladedkpvalNYFYTYTSGSntFIGDVMTTAGLTNGAAEANITGFAPINTEtvvemNPEYIIVPt 252
                                       ******66665555555555554444444333564444555777888888888888888888899998999999998 PP

                                       ...EEESTTTCHHHHHHH CS
                      Peripla_BP_4 160 ...evaganwdaekaqqa 174
                                          + ++  w+ ++a q+
  gi|313127034|ref|YP_004037304.1| 253 gatVPDTEAWNSTTAVQE 270
                                       886555767999999986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHTTCEEEEEECSTT-H.HHHH CS
                      Peripla_BP_4  13 fsaaregleeaakelgaevtvvgdaenda.aeQv 45 
                                       +s ++  +e+   e   ++t +  a++++ ++ +
  gi|313127034|ref|YP_004037304.1| 308 QS-MKAEAEATTTESTETTTQTTTAQSTTtQAVN 340
                                       33.5555555555544444444333333322222 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.2   0.00027       1.2     226     282 ..     295     352 ..     202     356 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00027
                             RIFIN 226 sskekikkkvekive.kaekkaaaaaaeaaaeataeaekaetaaveattaslqtaiia 282
                                         + +  ++ e++++ kae +a+++++++++++t++a++++t+av+ tt+s qta  a
  gi|313127034|ref|YP_004037304.1| 295 IMQAVHPEAFEEYQSmKAEAEATTTESTETTTQTTTAQSTTTQAVNDTTTSAQTATGA 352
                                       2222222222222224666677777778888888899999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1746  (0.0973841); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 2552.78
//
Query:       gi|313127035|ref|YP_004037305.1|  [L=339]
Description: Fe3+-siderophore ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-90  302.0  34.4    5.1e-90  301.6  34.4    1.0  1  FecCD     FecCD transport family
    4.9e-06   26.2  18.4    4.9e-06   26.2  18.4    1.9  2  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.6  34.4   5.7e-94   5.1e-90       1     311 [.      17     332 ..      17     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 301.6 bits;  conditional E-value: 5.7e-94
                             FecCD   1 llllllllslllgavkispsevfeallgka........dsleaeivlelrlprvlaallvGaaLavaGallQtvtrN 69 
                                       ll++++l s  +g+v+i+p  v +a++g+          ++++ iv+++rlpr+l+a+lvG+aL++aG+++Q+ +rN
  gi|313127035|ref|YP_004037305.1|  17 LLVAVILGSAGVGPVSIPPMAVTSAVVGDLfpslgisvPRTQRVIVVNVRLPRILLAALVGFALSTAGVVMQGFFRN 93 
                                       68899999*******************999******99999999********************************* PP

                             FecCD  70 pLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsa 146
                                       p+adPsi+G+ssgaa+gav++++l +  +    l  aaf++al++++ v+lla++++++ +++l+LaG+av+++l++
  gi|313127035|ref|YP_004037305.1|  94 PMADPSIIGVSSGAAVGAVATIVLPFAFPLGLELQSAAFVSALITAFTVYLLATRGGHTPTATLLLAGVAVQTFLGS 170
                                       ***********************9988888899********************999999****************** PP

                             FecCD 147 ltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrll 223
                                       ++s++ll  + ++l+++++wl+G lsga+w++v++++v l  l+++ll++++++++l lg++ A+slG++ver++ +
  gi|313127035|ref|YP_004037305.1| 171 VISFMLLH-SGQSLRRVVYWLMGHLSGATWHEVAIVAVSLPPLFVVLLVYTNDMNVLLLGESDAHSLGIEVERTKRI 246
                                       ******99.889***************************************************************** PP

                             FecCD 224 llllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtal 300
                                       ll++++++tavava++G+igFvGLivPh +rl+vg+dhr llp+sal+Ga +l+++d+lar     +e+pvgivta+
  gi|313127035|ref|YP_004037305.1| 247 LLAVSSAVTAVAVAVSGVIGFVGLIVPHAMRLVVGPDHRVLLPASALAGASFLVATDTLARSG--AAEVPVGIVTAA 321
                                       *************************************************************99..58********** PP

                             FecCD 301 iGapffiylll 311
                                       +Gapff+yll+
  gi|313127035|ref|YP_004037305.1| 322 LGAPFFLYLLR 332
                                       *********97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.8     0.084   7.5e+02     215     252 ..      71     109 ..      57     115 .. 0.62
   2 !   26.2  18.4   5.5e-10   4.9e-06      47     252 ..     118     328 ..      99     333 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.084
                             ABC-3 215 ivAillglvsvvaGlllSyyld.latGavivlvatllfl 252
                                       ++A+l+g+  ++aG+++  ++    + ++i+ v++ + +
  gi|313127035|ref|YP_004037305.1|  71 LLAALVGFALSTAGVVMQGFFRnPMADPSIIGVSSGAAV 109
                                       456666777777777666555523355666666665555 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 5.5e-10
                             ABC-3  47 alayllgvnlllgailvgliaavalellkrk...tklkedtaigivlsvflalglvlvslikk.skvdldsyLfGni 119
                                        +a+ lg++l  +a++++li a+++ ll+++   t +++  + g+ +++fl+  + ++ l ++ s   +  +L+G +
  gi|313127035|ref|YP_004037305.1| 118 PFAFPLGLELQSAAFVSALITAFTVYLLATRgghTPTATLLLAGVAVQTFLGSVISFMLLHSGqSLRRVVYWLMGHL 194
                                       368889999******************9986322556666678********965555544444488999******** PP

                             ABC-3 120 ltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLviall 196
                                        + + +++ ++a+    ++++ll+   ++ ++ + e+ A++ g++v++ k +lla+ ++  +va+ + Gvi  + l 
  gi|313127035|ref|YP_004037305.1| 195 SGATWHEVAIVAVSLPPLFVVLLVYTNDMNVLLLGESDAHSLGIEVERTKRILLAVSSAVTAVAVAVSGVIGFVGL- 270
                                       **********************************************************************998885. PP

                             ABC-3 197 iiPaatArrltrslesllivAillglvsvvaG..lllSyyldlatGavivlvatllfl 252
                                       i+P a+ + ++ + + ll  ++l g+ ++va   l+ S  ++++ G v +++ + +fl
  gi|313127035|ref|YP_004037305.1| 271 IVPHAMRLVVGPDHRVLLPASALAGASFLVATdtLARSGAAEVPVGIVTAALGAPFFL 328
                                       7899998888888888887777777776666411444666667777666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2198.99
//
Query:       gi|313127036|ref|YP_004037306.1|  [L=446]
Description: cobalamin/Fe3+-siderophore ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-31  108.0   0.0    8.1e-31  107.4   0.0    1.3  1  ABC_tran       ABC transporter
    9.4e-09   35.5   3.1    1.6e-05   24.9   0.5    2.2  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.2e-05   24.8   0.0      4e-05   23.1   0.0    1.7  1  SMC_N          RecF/RecN/SMC N terminal domain
    1.9e-05   25.1   0.2    4.3e-05   24.0   0.2    1.6  1  AAA_16         AAA ATPase domain
    0.00015   22.3   0.0    0.00022   21.8   0.0    1.3  1  AAA_23         AAA domain
    0.00089   19.0   1.7     0.0031   17.2   0.0    2.3  2  AAA_30         AAA domain
     0.0018   18.5   0.0     0.0071   16.6   0.0    2.0  1  AAA_28         AAA domain
     0.0022   17.7   0.1     0.0053   16.5   0.1    1.6  1  AAA_29         P-loop containing region of AAA domain
     0.0057   15.5   0.3        2.5    6.8   0.0    2.1  2  ABC_ATPase     Predicted ATPase of the ABC class
     0.0069   15.8   0.1      0.015   14.7   0.1    1.6  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.053   13.2   0.0    1.7  2  AAA_15         AAA ATPase domain
      0.017   15.4   0.9       0.14   12.4   0.9    2.2  1  AAA_22         AAA domain
      0.018   15.5   0.1       0.15   12.5   0.0    2.3  3  AAA            ATPase family associated with various cellular
      0.022   14.3   0.9       0.16   11.6   0.1    2.2  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.031   14.7   1.2       0.13   12.7   0.5    2.4  3  NAD_binding_7  Putative NAD(P)-binding
      0.041   13.0   0.0      0.075   12.1   0.0    1.4  1  T2SSE          Type II/IV secretion system protein
      0.043   13.4   0.0        0.1   12.2   0.0    1.6  1  AAA_27         AAA domain
      0.066   13.1   0.3        1.1    9.2   0.1    2.4  2  NACHT          NACHT domain
      0.066   12.5   0.0       0.16   11.3   0.0    1.6  1  Zeta_toxin     Zeta toxin
      0.084   13.2   0.6        7.7    6.9   0.2    2.6  2  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
      0.085   12.8   0.2        0.2   11.6   0.2    1.6  1  RsgA_GTPase    RsgA GTPase
        0.1   12.8   1.3       0.34   11.1   0.4    2.4  1  AAA_33         AAA domain
       0.12   12.5   0.2       0.33   11.1   0.2    1.8  1  MMR_HSR1       50S ribosome-binding GTPase
       0.14   12.7   0.0       0.31   11.6   0.0    1.6  1  AAA_18         AAA domain
       0.16   12.0   0.0        0.4   10.7   0.0    1.6  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
       0.23   10.1   0.0        3.3    6.2   0.0    2.0  2  AAA_13         AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.0   1.2e-33   8.1e-31       1     137 []      35     184 ..      35     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 1.2e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ v+l + eg+ v+++G+nGaGK+tLl++l g  +p+ G++ + g+ +++ + + +++ ++++pq+++l  +  vr
  gi|313127036|ref|YP_004037306.1|  35 LESVDLAVDEGTFVGLIGPNGAGKTTLLRALNGAISPARGSVIISGEMVHSLSSKATSRLVATVPQDTSLTFNFDVR 111
                                       67899*********************************************************************9** PP

                                       HH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++                 ++++ +e+al++ +  el +++v    s LSgG++qrv +aral+++ ++lllDEpta
  gi|313127036|ref|YP_004037306.1| 112 QTirmgrtphrsrfggwreDDESAVERALDRTQTAELSERTV----SDLSGGERQRVLIARALAQETPVLLLDEPTA 184
                                       ****************97656666******************....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.5   2.3e-08   1.6e-05       1      22 [.      47      68 ..      47      93 .. 0.83
   2 !   11.1   0.1   0.00038      0.26     231     285 ..     150     201 ..     116     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.3e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + +liGpNg+GK++LL+al ++
  gi|313127036|ref|YP_004037306.1| 47 FVGLIGPNGAGKTTLLRALNGA 68
                                      678****************987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00038
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                       e+++++lS G ++   l++  l++    ++ll+DEp ++L+   + r lel+++l
  gi|313127036|ref|YP_004037306.1| 150 ERTVSDLSGGERQR-VLIARALAQET--PVLLLDEPTASLDINHQVRTLELVRDL 201
                                       56788889999999.55555555554..************996555555555554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   5.9e-08     4e-05      25     185 ..      46     200 ..      33     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.9e-08
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESS.SSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklk.iekeevsi 99 
                                        f  ++GpNG+GK+ ll A+   ++ +  + + s    +++h+ s++  s   a+v     +++ +++   ++ + +
  gi|313127036|ref|YP_004037306.1|  46 TFVGLIGPNGAGKTTLLRALNGAISPARGSVIIS---GEMVHSlSSKATSRLVATVPQ---DTSLTFNfDVRQTIRM 116
                                       57889***************77777555533333...344554222333333344433...3333333034455788 PP

                                       EEEEETTSEEEEEETTEEE-HHHHH..HHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevs..ellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                        r+  r+    ++ +++++ ++ +   +  e ++ + + LSgGe++ v +    A   ++ +p+ llDe  a LD +
  gi|313127036|ref|YP_004037306.1| 117 GRTPHRSRFGGWREDDESAVERALDrtQTAELSERTVSDLSGGERQRVLI----ARALAQETPVLLLDEPTASLDIN 189
                                       888888888888888888777655411455556667789*****996554....5555689**************** PP

                                       HHHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                             SMC_N 175 nvkkvaellke 185
                                       +  +  el++ 
  gi|313127036|ref|YP_004037306.1| 190 HQVRTLELVRD 200
                                       99998888875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   6.2e-08   4.3e-05      25     142 ..      46     180 ..      33     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.2e-08
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqllde............ 88 
                                         v l+G+ G GK++l+r+l  a++ ++g + ++g+ +++        l + + +++l++ + ++            
  gi|313127036|ref|YP_004037306.1|  46 TFVGLIGPNGAGKTTLLRALNGAISPARGSViISGEMVHS--------LSSKA-TSRLVATVPQDtsltfnfdvrqt 113
                                       67889**********************8666699999999........55555.33666666666555555555555 PP

                            AAA_16  89 .......aesaeleawrekleeala..............avpelagaeasrllellkrllallsrderplvlvlD 142
                                              ++s  ++ wre  e+a++               v++l+g e++r+  l++r+l   ++ e   vl+lD
  gi|313127036|ref|YP_004037306.1| 114 irmgrtpHRS-RFGGWREDDESAVEraldrtqtaelserTVSDLSGGERQRV--LIARAL---AQ-ET-PVLLLD 180
                                       5556663444.77777776666666666666444444444444444433333..333333...22.33.566666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   3.2e-07   0.00022      21      44 ..      47      70 ..      34     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.2e-07
                            AAA_23 21 ltlItGpNGaGKTTildAiklaLy 44
                                      ++ ++GpNGaGKTT+l+A+  a  
  gi|313127036|ref|YP_004037306.1| 47 FVGLIGPNGAGKTTLLRALNGAIS 70
                                      56789**************98876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.5e-06    0.0031      15      51 ..      42      78 ..      36     181 .. 0.85
   2 ?    0.3   0.6      0.73     5e+02      45     114 ..     305     379 ..     270     388 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.5e-06
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                       ++  ++ l Gp G+GKtt+l+al+ a+  a g+vi+
  gi|313127036|ref|YP_004037306.1| 42 VDEGTFVGLIGPNGAGKTTLLRALNGAISPARGSVII 78
                                      445569999******************9999767764 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.73
                            AAA_30  45 aggrviglAptgkaAkv.Laeelgieastiakllkrlk.....grarlepgtllivDEagmvdtkqlaallkaaek 114
                                       ag++v + A ++   ++  a++lg++  t++ +    +      ++r++++++++v  +  v+t +la+l +aae+
  gi|313127036|ref|YP_004037306.1| 305 AGYEVSVGALNEGDTDTeTARSLGLDVVTVNPFSAVGDaaqaeVATRVAEADCVVVADV-EVGTGNLANLRAAAEA 379
                                       44555444443333332245555555555555553333555553445555555555443.3455555555555554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     1e-05    0.0071       4      53 ..      50     104 ..      47     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-05
                            AAA_28   4 itGgestGKTtlleaLa.....argypvv.pEaareileeklakgedalpwvedll 53 
                                       ++G+ ++GKTtll+aL+     arg +++  E++  + ++ + +   + p+ ++ l
  gi|313127036|ref|YP_004037306.1|  50 LIGPNGAGKTTLLRALNgaispARGSVIIsGEMVHSLSSKATSRLVATVPQ-DTSL 104
                                       89***************8888878999888999999998888877776666.3555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.7e-06    0.0053      19      50 ..      42      73 ..      33      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.7e-06
                            AAA_29 19 idlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                      +d +g ++ l+Gp+G+GK+Tll A++  + pa+
  gi|313127036|ref|YP_004037306.1| 42 VD-EGtFVGLIGPNGAGKTTLLRALNGAISPAR 73
                                      55.3347779*************9998888775 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0037       2.6     241     268 ..      41      69 ..       5      72 .. 0.82
   2 !    6.8   0.0    0.0037       2.5     317     353 ..     150     186 ..     142     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0037
                                       EE-SS.EEEEEE-TTSSHHHHHHHHHHCC CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAlekGv 268
                                       ++ +G  + ++G++  GK+TLL+Al+  +
  gi|313127036|ref|YP_004037306.1|  41 AVDEGtFVGLIGPNGAGKTTLLRALNGAI 69 
                                       56667334478**************8765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0037
                                       TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                        ABC_ATPase 317 kfstedASGStsqAanimealeagakllLiDEDtsAt 353
                                       + + +d SG   q + i++al  ++++lL+DE t+  
  gi|313127036|ref|YP_004037306.1| 150 ERTVSDLSGGERQRVLIARALAQETPVLLLDEPTASL 186
                                       5577899*************************99865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.2e-05     0.015      16      71 ..      39      93 ..      24     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                      Mg_chelatase 16 eiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeek 71
                                      ++a+  g  + l+Gp G+GKt l ++l++ ++p   + ++  ++++s+++k + ++
  gi|313127036|ref|YP_004037306.1| 39 DLAVDEGTFVGLIGPNGAGKTTLLRALNGAISPARGSVIISGEMVHSLSSKAT-SR 93
                                      566666666779************************************99544.33 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.7e-05     0.053      19      44 ..      40      66 ..      34      92 .. 0.84
   2 ?   -0.8   0.0       1.4   9.4e+02     322     356 ..     172     206 ..     161     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.7e-05
                            AAA_15 19 idlsee.ltvliGkNnsGKSsileald 44
                                      + ++e  +  liG+N++GK+++l+al+
  gi|313127036|ref|YP_004037306.1| 40 LAVDEGtFVGLIGPNGAGKTTLLRALN 66
                                      55555557779**************96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       +++ +ll++EP a+L +++q    +l ++l+ ++k
  gi|313127036|ref|YP_004037306.1| 172 QETPVLLLDEPTASLDINHQVRTLELVRDLVGEGK 206
                                       4567899***********************99987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9    0.0002      0.14       5      38 ..      45      89 ..      42     213 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee...............e 38
                                       +++ ++G+ G+GKTtllr l         +++               +
  gi|313127036|ref|YP_004037306.1| 45 GTFVGLIGPNGAGKTTLLRALNGAIS----PARgsviisgemvhslssK 89
                                      567779*************9987753....2223445555555555432 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00022      0.15       3      48 ..      50      97 ..      48     114 .. 0.70
   2 ?   -0.8   0.0       2.8   1.9e+03      46      66 ..     162     181 ..     138     197 .. 0.68
   3 ?   -0.7   0.0       2.6   1.8e+03      14      46 ..     166     209 ..     163     216 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                                      EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelg..vefleisgsellskyvgesekkire 48
                                      l+Gp G GKT+l +a+   ++  +  + isg  + s   +++++ ++ 
  gi|313127036|ref|YP_004037306.1| 50 LIGPNGAGKTTLLRALNGAISpaRGSVIISGEMVHSLSSKATSRLVAT 97
                                      89**************99986433345555555554445555555544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHTSTSEEEEEET CS
                               AAA  46 irelfkeakekakpsilfiDE 66 
                                        r l+++a ++ ++ +l++DE
  gi|313127036|ref|YP_004037306.1| 162 QRVLIARALAQ-ETPVLLLDE 181
                                       44444444333.368888888 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.6
                                       HHHHHHHHH..........THEE.EEEETTTCSSSSTTHHHHHH CS
                               AAA  14 lakavakel..........gvef.leisgsellskyvgesekki 46 
                                       +a+a+a+e+          + ++  ++   el+ ++vge++  i
  gi|313127036|ref|YP_004037306.1| 166 IARALAQETpvllldeptaSLDInHQVRTLELVRDLVGEGKTAI 209
                                       56666666322222222112222234444444444555555544 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00023      0.16       3      36 ..      48      82 ..      46      97 .. 0.76
   2 ?    0.9   0.1      0.45   3.1e+02     115     152 ..     328     365 ..     308     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                      EEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS- CS
                              cobW  3 tvltGflGsGKTtLlnhll.enraglklavivNef 36
                                      ++l G+ G+GKTtLl++l  + +  +   +i +e+
  gi|313127036|ref|YP_004037306.1| 48 VGLIGPNGAGKTTLLRALNgAISPARGSVIISGEM 82
                                      5789************9985444455555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.45
                                       EEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                              cobW 115 vvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                        + vv ++ ++a ++  + ++   +a ad++v+  +++
  gi|313127036|ref|YP_004037306.1| 328 GLDVVTVNPFSAVGDAAQAEVATRVAEADCVVVADVEV 365
                                       5568888888999999999999*********9987765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.9   6.2e+03      58      76 ..     201     219 ..     143     225 .. 0.61
   2 ?   12.7   0.5    0.0002      0.13       9      68 ..     285     361 ..     280     385 .. 0.75
   3 ?    0.3   0.2       1.4   9.4e+02       2      38 ..     349     387 ..     348     417 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.9
                     NAD_binding_7  58 dlegadlviaatddrelne 76 
                                        + + +++iaa+ d +l +
  gi|313127036|ref|YP_004037306.1| 201 LVGEGKTAIAAIHDLNLAA 219
                                       3444455666666655555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0002
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeele..................elvklaeeelekdlegadlvia 67 
                                       ++ vvGgG  Aar ++ l +ag +v v a +    ++                     ++a+ e+   +++ad+v++
  gi|313127036|ref|YP_004037306.1| 285 HIHVVGGGGTAARYLYLLSAAGYEVSVGALNE-GDTDtetarslgldvvtvnpfsAVGDAAQAEVATRVAEADCVVV 360
                                       789************************99884.22224456677775555544443334677777888889998888 PP

                     NAD_binding_7  68 a 68 
                                       a
  gi|313127036|ref|YP_004037306.1| 361 A 361
                                       7 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                     NAD_binding_7   2 fldlkgkkvlvvGgGevAarkvrklleag..akvtvvap 38 
                                       ++++ +  ++vv   ev++  + +l +a    ++++v +
  gi|313127036|ref|YP_004037306.1| 349 ATRVAEADCVVVADVEVGTGNLANLRAAAeaERIVLVEE 387
                                       567888899999888888888888776543234555544 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011     0.075     119     198 ..      35     116 ..      17     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                             T2SSE 119 aevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak...kakvtfadll 192
                                        e +  av e   + + G+ g GKttll al   i       v++   +   l+ +  ++l+a    ++++tf+  +
  gi|313127036|ref|YP_004037306.1|  35 LESVDLAVDEGTFVGLIGPNGAGKTTLLRALNGAISPARGS-VIISGEMVHSLSSKATSRLVATvpqDTSLTFNFDV 110
                                       55566677777777788******************999444.4444444445555555555555555999******* PP

                             T2SSE 193 raaLRl 198
                                       r+++R+
  gi|313127036|ref|YP_004037306.1| 111 RQTIRM 116
                                       ***998 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015       0.1      18      47 ..      37      66 ..      23      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAis 47
                                      s+d+  +e  +  ++GpN AGK+t+lrA++
  gi|313127036|ref|YP_004037306.1| 37 SVDLAVDEGTFVGLIGPNGAGKTTLLRALN 66
                                      67888888899999**************86 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0015       1.1       4      20 ..      49      65 ..      46      75 .. 0.86
   2 ?    1.3   0.0      0.42   2.9e+02     112     148 ..     165     199 ..     150     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                                      EEEC-TTTCHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqkl 20
                                       l G++G GKTtLl+ l
  gi|313127036|ref|YP_004037306.1| 49 GLIGPNGAGKTTLLRAL 65
                                      589***********988 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.42
                                       HHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE CS
                             NACHT 112 lirkkllpeasllltvrpralrdleeqleeaivleve 148
                                       li ++l +e+++ll   p+a+ d+ +q+++     v+
  gi|313127036|ref|YP_004037306.1| 165 LIARALAQETPVLLLDEPTASLDINHQVRTL--ELVR 199
                                       89999999***************99999988..3444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.16      21      78 ..      50     108 ..      43     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                        Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilka.dpkkaseltqk 78 
                                       l G  GAGK++l+++l+ ++ ++++ v +++  + +l  ++ + l a  p+++s  ++ 
  gi|313127036|ref|YP_004037306.1|  50 LIGPNGAGKTTLLRALNGAISPARGSVIISGEMVHSLSSKATSRLVAtVPQDTSLTFNF 108
                                       55889************************998888777666553333255555555555 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.011       7.7      31      74 ..     330     376 ..     318     386 .. 0.83
   2 ?    3.8   0.0       0.1        71      59      82 ..     395     419 ..     394     430 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                                       E...E.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTT CS
                     Nitro_FeMo-Co  31 r...veeaadaegggggklaqllaeegvdvvivgkiGpralakleaa 74 
                                       +   v+++++ +  ++  +a ++ae+++ vv  +++G + la l+aa
  gi|313127036|ref|YP_004037306.1| 330 DvvtVNPFSAVGDAAQAEVATRVAEADCVVVADVEVGTGNLANLRAA 376
                                       444667899999999**************************999987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.1
                                       EESSSCHHHHHHHCTTTSEEEES.- CS
                     Nitro_FeMo-Co  59 ivgkiGpralakleaagievykg.a 82 
                                       ++g+ G++a+++l+++g+ v ++  
  gi|313127036|ref|YP_004037306.1| 395 YAGEAGRSAYNRLRERGVVVSSAdV 419
                                       57899*************9877544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00029       0.2      97     124 ..      42      70 ..      19      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                                       CTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  97 lkd.ktsvlvGqSGvGKStLinallpele 124
                                       +++  ++ l+G+ G+GK+tL+ al++  +
  gi|313127036|ref|YP_004037306.1|  42 VDEgTFVGLIGPNGAGKTTLLRALNGAIS 70 
                                       455366779***************99765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00049      0.34       4      20 ..      50      66 ..      47     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      l+G++G+GK+tl++ l 
  gi|313127036|ref|YP_004037306.1| 50 LIGPNGAGKTTLLRALN 66
                                      79************983 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00047      0.33       2      22 ..      48      68 ..      47      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00047
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      v+++G   +GK+tL++al g+
  gi|313127036|ref|YP_004037306.1| 48 VGLIGPNGAGKTTLLRALNGA 68
                                      89****************886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00044      0.31       1      20 [.      48      67 ..      48     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00044
                            AAA_18  1 IlltGtpGvGKttlakeLsk 20
                                      ++l G+ G+GKttl ++L+ 
  gi|313127036|ref|YP_004037306.1| 48 VGLIGPNGAGKTTLLRALNG 67
                                      6899**************43 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00059       0.4      18      41 ..      42      67 ..      23      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                                      H..TEEEEEEESTTSSHHHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglak 41
                                      +  g+++ L G+ GaGKTtl r+l  
  gi|313127036|ref|YP_004037306.1| 42 VdeGTFVGLIGPNGAGKTTLLRALNG 67
                                      14467799**************9865 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0048       3.3      23      39 ..      52      68 ..      50      98 .. 0.85
   2 ?    1.5   0.0      0.13        90     526     555 ..     173     202 ..     164     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0048
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G NGaGKTtL r+l+  
  gi|313127036|ref|YP_004037306.1| 52 GPNGAGKTTLLRALNGA 68
                                      99********9999765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrl 555
                                       +  +  +D P  SLD n++     l+++ +
  gi|313127036|ref|YP_004037306.1| 173 ETPVLLLDEPTASLDINHQVRTLELVRDLV 202
                                       678999*************99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3032.51
//
Query:       gi|313127037|ref|YP_004037307.1|  [L=343]
Description: transcription initiation factor iib (tfiib) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-38  128.3   0.1    2.3e-18   66.0   0.0    2.2  2  TFIIB          Transcription factor TFIIB repeat
      1e-17   63.3   3.5    2.2e-17   62.3   3.5    1.6  1  TF_Zn_Ribbon   TFIIB zinc-binding
    3.1e-05   24.0   0.0      0.043   13.9   0.0    2.3  2  Cyclin_C       Cyclin, C-terminal domain
    0.00034   20.4   0.0     0.0035   17.1   0.0    2.1  2  Cyclin_N       Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.026   14.0   0.1        0.5    9.9   0.0    2.8  2  Sigma70_r4     Sigma-70, region 4
       0.18   11.5   0.1       0.39   10.4   0.1    1.6  1  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
       0.24   11.0   0.9         11    5.7   0.1    2.4  2  zf_UBZ         Ubiquitin-Binding Zinc Finger
          3    8.0   4.9        4.8    7.4   0.6    2.4  3  Zn-ribbon_8    Zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0     1e-21   2.3e-18       1      70 [.     153     222 ..     153     223 .. 0.98
   2 !   60.4   0.0   5.6e-20   1.3e-16       2      71 .]     248     317 ..     247     317 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1e-21
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70 
                                       i r+a+al+Lpe V++ A  ++++ale+++l Grs +gia A+l  A+r+++v r++ e++ v++V e++
  gi|313127037|ref|YP_004037307.1| 153 IDRMASALGLPESVRETASVIYRRALEDDLLPGRSIEGIATASLHAAARMAQVPRSLDEVAHVSRVDEEE 222
                                       789*****************************************************************98 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 5.6e-20
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       +rfa+ ++ p++ ++ A el+++a++ ++++G+sp g+aAA+ly A+++ ++k tq+++s+v+ +se+ti
  gi|313127037|ref|YP_004037307.1| 248 PRFASDIDVPKETERTARELLENAKTVGIHSGKSPVGLAAAALYAAAQLTNEKVTQSDVSDVTDISEVTI 317
                                       79******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   3.5   9.9e-21   2.2e-17       3      43 .]      38      78 ..      36      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 9.9e-21
                                      ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      CP+C+s++lv+D  rge+vC+dCGlV++++ id gpewr+f
  gi|313127037|ref|YP_004037307.1| 38 CPECSSPTLVTDDGRGETVCEDCGLVVDEDEIDRGPEWRAF 78
                                      ***************************************98 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0014       3.2      47      88 ..     191     232 ..     187     240 .. 0.92
   2 !   13.9   0.0   1.9e-05     0.043       5      89 ..     245     327 ..     241     335 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                                       iA+a+l +a ++ + p   +++ h++++++e+++  ++ i+ 
  gi|313127037|ref|YP_004037307.1| 191 IATASLHAAARMAQVPRSLDEVAHVSRVDEEEFERAYRYIVR 232
                                       8*********************************99998875 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.9e-05
                                       HHHHHH.HCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHH CS
                          Cyclin_C   5 sFlrrf.lkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedlk 80 
                                        +l rf +++ d    +e++  a+ lle + +     + +p  +Aaaal++a +  n++  ++ +  +t +s+  ++
  gi|313127037|ref|YP_004037307.1| 245 EYLPRFaSDI-DV--PKETERTARELLENAKTVGIHSGKSPVGLAAAALYAAAQLTNEKVTQSDVSDVTDISEVTIR 318
                                       5666775556.22..34777778888887777777777788889********************************* PP

                                       HHHHHHHHH CS
                          Cyclin_C  81 pcvelilel 89 
                                       + ++ +le+
  gi|313127037|ref|YP_004037307.1| 319 NRYQELLEA 327
                                       ***999986 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.6e-06    0.0035      38     126 ..     153     238 ..     117     239 .. 0.85
   2 ?    1.0   0.0      0.15   3.4e+02      43      98 ..     252     306 ..     244     327 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHH CS
                          Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilem 114
                                       + ++a+ + l +++  +a +++ R l+   +p + ++ +++++L  Aa++ ++ p +l+++++++   ++eee+ ++
  gi|313127037|ref|YP_004037307.1| 153 IDRMASALGLPESVRETASVIYRRALEDDLLPGRSIEGIATASLHAAARMAQV-PRSLDEVAHVS--RVDEEEFERA 226
                                       55677778888888899*********************************999.9*********5..59******** PP

                                       HHHHHHHTTT-- CS
                          Cyclin_N 115 ErliLetLnfdl 126
                                        r+i+++L  ++
  gi|313127037|ref|YP_004037307.1| 227 YRYIVRELSLEI 238
                                       ******998766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                                       HHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHH CS
                          Cyclin_N  43 ekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledl 98 
                                       +  ++ +et  +a ++l+   +  +++ +    ++a++L+ Aa++ + + ++ +d+
  gi|313127037|ref|YP_004037307.1| 252 SDIDVPKETERTARELLENAKTVGIHSGKSPVGLAAAALYAAAQLTNEK-VTQSDV 306
                                       5555666666666666666666666666666778999999999996664.333333 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.18     4e+02      34      46 ..     167     179 ..     157     180 .. 0.89
   2 ?    9.9   0.0   0.00022       0.5      18      45 ..     298     325 ..     289     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAlr 46 
                                       re+++ i +rAl+
  gi|313127037|ref|YP_004037307.1| 167 RETASVIYRRALE 179
                                       89*********96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAl 45 
                                        e+ T+++++++ +iS+ ++r +  + l
  gi|313127037|ref|YP_004037307.1| 298 NEKVTQSDVSDVTDISEVTIRNRYQELL 325
                                       5899******************998776 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00018      0.39       5      30 ..      37      63 ..      33      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                     zf-NADH-PPase  5 FCgrCGaptepaeggwa.rvCpaCgle 30
                                       C+ C +pt + ++g++  vC++Cgl 
  gi|313127037|ref|YP_004037307.1| 37 LCPECSSPTLVTDDGRGeTVCEDCGLV 63
                                      6***************868******86 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.021        46       1      13 [.      34      46 ..      34      50 .. 0.77
   2 ?    5.7   0.1     0.005        11       4      17 ..      56      69 ..      53      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.021
                            zf_UBZ  1 dtylCerCgkeip 13
                                      +t lC++C ++ +
  gi|313127037|ref|YP_004037307.1| 34 ETLLCPECSSPTL 46
                                      5889****98755 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.005
                            zf_UBZ  4 lCerCgkeipesel 17
                                      +Ce+Cg  + e+e 
  gi|313127037|ref|YP_004037307.1| 56 VCEDCGLVVDEDEI 69
                                      8********99986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.6    0.0022       4.8      19      35 ..      28      45 ..      19      49 .. 0.68
   2 ?    1.9   0.2      0.11   2.5e+02      26      33 ..      54      61 ..      46      65 .. 0.69
   3 ?    1.4   0.3      0.16   3.6e+02       7      13 ..      56      62 ..      54      73 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0022
                       Zn-ribbon_8 19 qsisdaplta.CPeCgs.e 35
                                      q+   +++t  CPeC s +
  gi|313127037|ref|YP_004037307.1| 28 QT-ETDEETLlCPECSSpT 45
                                      43.34557777****9944 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                       Zn-ribbon_8 26 ltaCPeCg 33
                                      +t+C +Cg
  gi|313127037|ref|YP_004037307.1| 54 ETVCEDCG 61
                                      45577776 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.16
                       Zn-ribbon_8  7 rCeeCgh 13
                                       Ce+Cg 
  gi|313127037|ref|YP_004037307.1| 56 VCEDCGL 62
                                      3666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2378.80
//
Query:       gi|313127038|ref|YP_004037308.1|  [L=208]
Description: molybdenum cofactor guanylyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-37  129.2   0.4    2.2e-37  128.9   0.4    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
    0.00049   20.1   0.0     0.0012   18.8   0.0    1.6  2  CTP_transf_3  Cytidylyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.4   2.5e-41   2.2e-37       1     158 [.       8     169 ..       8     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 2.5e-41
                                       EEEEEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC...HHHHHHTTCTS-..EEE-TTSS-S CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.dKallplggkpllervldalraagvdevvvvggde...evlaalarlgvr..vvededpgkg 71 
                                       +viL GG S+R+g  dKal++l+gkpl+++v+++l+ + +d++vv+++d+   + +aa+++ gv+  v++d+ p++g
  gi|313127038|ref|YP_004037308.1|   8 GVILGGGYSTRFGDeDKALAELAGKPLVRHVAERLATV-CDRLVVNCRDDqttDFRAAVEGCGVPigVATDPIPDRG 83 
                                       79***********77***********************.**********7344677899999988446999****** PP

                                       HHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECC..EEEGGGHHHHHHH.. CS
                      NTP_transf_3  72 plaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpl..lfrarllsalaal.. 144
                                       p+a+++++l+a+ ++++++v+acDmP+++p+++ +l+ +a  +g+d++vp++++e+ +    ++  r+ s ++a+  
  gi|313127038|ref|YP_004037308.1|  84 PMAGIRTGLSAV-ESEYAAVVACDMPFVDPDFLSYLFTRA--DGYDAAVPQRDDEWYQTTqaVY--RVESMVRACer 155
                                       ***********9.9************************97..5*************99995555..44444443322 PP

                                       CTHTTHHHCHHHHH CS
                      NTP_transf_3 145 lgdqgarrllrrld 158
                                       + d+g  ++l++l+
  gi|313127038|ref|YP_004037308.1| 156 ALDRGDAKILAALE 169
                                       55999999999875 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-07    0.0012      10      56 ..      16      62 ..       9      78 .. 0.86
   2 ?   -1.3   0.0      0.19   1.7e+03      99     115 ..     106     122 ..      87     200 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-07
                                      SSSS..TTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHH CS
                      CTP_transf_3 10 SkRl..pgKnlldlggkpliayvleaalkskafekvivaTDseeiknva 56
                                      S+R+  ++K+l++l+gkpl+++v e++    + ++++v + ++++ ++ 
  gi|313127038|ref|YP_004037308.1| 16 STRFgdEDKALAELAGKPLVRHVAERLAT--VCDRLVVNCRDDQTTDFR 62
                                      67774468*******************99..99*******999998874 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.19
                                       T-TT--HHHHHHHHHHH CS
                      CTP_transf_3  99 dnPllqeevikkaietl 115
                                       d P++++  ++ ++ + 
  gi|313127038|ref|YP_004037308.1| 106 DMPFVDPDFLSYLFTRA 122
                                       44444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1401.59
//
Query:       gi|313127039|ref|YP_004037309.1|  [L=246]
Description: selenium-dependent hydroxylase accessory protein yqec [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1703.90
//
Query:       gi|313127040|ref|YP_004037310.1|  [L=342]
Description: methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-52  176.7   0.1    3.4e-51  173.9   0.1    2.0  1  Met_10           Met-10+ like-protein
    1.3e-11   44.2   0.0    2.7e-11   43.2   0.0    1.5  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    1.9e-08   34.9   0.0    6.1e-08   33.3   0.0    1.9  1  Methyltransf_25  Methyltransferase domain
    2.9e-07   30.2   0.0    5.3e-07   29.3   0.0    1.3  1  MTS              Methyltransferase small domain
    5.2e-07   29.6   0.0    1.4e-06   28.2   0.0    1.7  2  Methyltransf_31  Methyltransferase domain
    1.8e-06   27.7   0.0    2.6e-06   27.1   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.1e-05   25.0   0.0    2.1e-05   24.1   0.0    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    3.3e-05   23.6   0.0    7.5e-05   22.4   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
    7.7e-05   23.3   0.0     0.0002   22.0   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
    8.8e-05   22.3   0.1    0.00018   21.3   0.1    1.5  1  UPF0020          Putative RNA methylase family UPF0020
    0.00092   18.5   0.0     0.0016   17.7   0.0    1.4  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
     0.0012   18.5   0.2     0.0048   16.6   0.0    2.0  3  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0021   17.4   0.0     0.0034   16.7   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0071   16.2   0.0      0.011   15.5   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0083   16.1   0.0      0.014   15.3   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
       0.04   14.9   4.9       0.26   12.3   0.1    2.9  3  Methyltransf_24  Methyltransferase domain
       0.13   11.9   0.0       0.23   11.1   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.14   11.5   0.0       0.29   10.6   0.0    1.5  1  adh_short        short chain dehydrogenase
       0.15   12.9   0.0       0.31   11.8   0.0    1.7  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.9   0.1   3.6e-54   3.4e-51       3     199 .]      79     288 ..      77     288 .. 0.90

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 3.6e-54
                                       EEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEE.S-..............SE CS
                            Met_10   3 feiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaG.sd.............ste 64 
                                       +e+ Gdvvil+ ++     ++ i+++i++   + +tv+++ s+v+g +R+++  +l    d             ste
  gi|313127040|ref|YP_004037310.1|  79 YERLGDVVILDEDDAE--RASRIADAIAESDlRAETVVNRASKVKGALRVRDWDILVDdTDeelsaddqrssapSTE 153
                                       999******9866654..5699*********9*********************999753212222223333333589 PP

                                       EEEEETTEEEEEETTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHH CS
                            Met_10  65 tihkEngcrfklDvskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylk 141
                                       t+h+E+gc+f lD+++vyfs++l++Er+r++++v ege+V d+fAG+Gpf ip+ak  ++ +v++ dln ++v+yl+
  gi|313127040|ref|YP_004037310.1| 154 TVHREYGCEFLLDIAEVYFSPRLATERHRVVQQVTEGERVFDMFAGVGPFVIPMAK--RGAEVVGCDLNAAAVEYLR 228
                                       ********************************************************..999**************** PP

                                       HHHHHTT-TTCEEEEES-GGG---..TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 142 eniklNkvekvvkpileDgrevir..eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       en ++N ve++v++ ++D+r+v+   e  a+r+vmnlp+sa +Fld++++ + ++ v hy
  gi|313127040|ref|YP_004037310.1| 229 ENARRNGVEERVTARQGDVRDVADdyEGWANRIVMNLPHSADDFLDTAVRLAGEECVLHY 288
                                       ***********************99999*******************************9 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   2.9e-14   2.7e-11       1      43 [.       5      47 ..       5      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.9e-14
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S-- CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeep 43
                                      c++V+  egE +R++L++ +l d++y I+  ++ lyIPv++  
  gi|313127040|ref|YP_004037310.1|  5 CVRVSTDEGEATRRALADRDLVDQSYEITVHEGTLYIPVTDAS 47
                                      ****************************************975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   6.4e-11   6.1e-08       1      76 [.     193     267 ..     193     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 6.4e-11
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTT.TEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedg.sfDlvvssgal 74 
                                       v d+ +G G +++ +akr+  a+v+g+D++++++e+ re+a+++g+  +v+ +qgd++d+  + +   + +v++  l
  gi|313127040|ref|YP_004037310.1| 193 VFDMFAGVGPFVIPMAKRG--AEVVGCDLNAAAVEYLRENARRNGVeeRVTARQGDVRDVADDYEgWANRIVMN--L 265
                                       78999*************5..**************************************876544155555553..4 PP

                                       GG CS
                   Methyltransf_25  75 hh 76 
                                        h
  gi|313127040|ref|YP_004037310.1| 266 PH 267
                                       44 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   5.6e-10   5.3e-07      31     110 ..     189     270 ..     177     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.6e-10
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST..TS-EEEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve..ekkfdlivs 103
                                       + ++v D+ +G+G+  + +ak+  e  v+ +d +a+A+e  +en+++n++e  v++++ dv + ++  e+  + iv+
  gi|313127040|ref|YP_004037310.1| 189 EGERVFDMFAGVGPFVIPMAKRGAE--VVGCDLNAAAVEYLRENARRNGVEerVTARQGDVRDVADdyEGWANRIVM 263
                                       5678*****************9888..9***********************88777777776655533488999*** PP

                                       ---STTT CS
                               MTS 104 NPPfhag 110
                                       N P  a+
  gi|313127040|ref|YP_004037310.1| 264 NLPHSAD 270
                                       *986655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.1   2.9e+03      96     114 ..     113     132 ..      49     157 .. 0.62
   2 !   28.2   0.0   1.5e-09   1.4e-06       3      67 ..     189     251 ..     188     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.1
                   Methyltransf_31  96 eiervlkpggilliedpr.l 114
                                        + r+ k +g+l ++d + l
  gi|313127040|ref|YP_004037310.1| 113 VVNRASKVKGALRVRDWDiL 132
                                       34566666667766666643 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.5e-09
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieele 67 
                                       +g rv D  +G G +++ +a++   +aevvG D ++ a+e+ rena+++g++ +v+ +qgd+ +  
  gi|313127040|ref|YP_004037310.1| 189 EGERVFDMFAGVGPFVIPMAKR---GAEVVGCDLNAAAVEYLRENARRNGVEeRVTARQGDVRDVA 251
                                       57899***************66...79***********************************9944 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   2.7e-09   2.6e-06       3      63 ..     192     252 ..     190     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.7e-09
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfella 63 
                                        + D+f+G G  vi +a+ + +v++ + n   ++   +Na+  gv++++t  +gdv ++  
  gi|313127040|ref|YP_004037310.1| 192 RVFDMFAGVGPFVIPMAKRGAEVVGCDLNAAAVEYLRENARRNGVEERVTARQGDVRDVAD 252
                                       689*****************************************************98554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.2e-08   2.1e-05     157     222 ..     185     248 ..     180     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.2e-08
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell 222
                                       ++v ege+v+D+ +G G   i  ak ga +vv+ D++  Av+  +eNa++N+ve++++   ++++ 
  gi|313127040|ref|YP_004037310.1| 185 QQVTEGERVFDMFAGVGPFVIPMAKRGA-EVVGCDLNAAAVEYLRENARRNGVEERVTA-RQGDVR 248
                                       568899*********************8.699***********************9965.344443 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.9e-08   7.5e-05      36     136 ..     184     280 ..     179     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.9e-08
                                       HCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS- CS
                     Cons_hypoth95  36 laaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkke 112
                                       +++  eg+rv D+faG G   +  + Rga ++v  + +++av+ l+en ++ ++ee++++ + d  + ++     ++
  gi|313127040|ref|YP_004037310.1| 184 VQQVTEGERVFDMFAGVGPFVIPMAKRGA-EVVGCDLNAAAVEYLRENARRNGVEERVTARQGDVRDVADDY---EG 256
                                       678899**********************6.68889******************9986666666555555444...44 PP

                                       EEEEEEE--SSSTTCH.HHHHHHH CS
                     Cons_hypoth95 113 efdivflDPPyakellieevlell 136
                                         + + ++ P  +++++ ++++l 
  gi|313127040|ref|YP_004037310.1| 257 WANRIVMNLPHSADDFLDTAVRLA 280
                                       556777777777777666666655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.1e-07    0.0002       5      55 ..     198     250 ..     194     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.1e-07
                                       -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaekl 55 
                                       +G G ++ ++akrga+vvg+Dl+++++++ +e+a+++g+  +v+ +++d++++
  gi|313127040|ref|YP_004037310.1| 198 AGVGPFVIPMAKRGAEVVGCDLNAAAVEYLRENARRNGVeeRVTARQGDVRDV 250
                                       69999*********************************999999*****9984 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   1.9e-07   0.00018      75     131 ..     210     267 ..     177     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.9e-07
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE---- CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivtnpPY 131
                                       + ++++g Dl++++v+  reNa++ gv+++++++q d++++    eg  + iv n+P 
  gi|313127040|ref|YP_004037310.1| 210 RGAEVVGCDLNAAAVEYLRENARRNGVEERVTARQGDVRDVAdDYEGWANRIVMNLPH 267
                                       556799************************************777778999****996 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06    0.0016      52     149 ..     192     286 ..     144     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                                       EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE-- CS
                               TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDP 128
                                       +v+d +++ G   i  a+      ev+  D++  Ave ++eN++ n vee+v+++++d + +    +   + i +  
  gi|313127040|ref|YP_004037310.1| 192 RVFDMFAGVGPFVIPMAKR---GAEVVGCDLNAAAVEYLRENARRNGVEERVTARQGDVRDVADDYEGWANRIVMNL 265
                                       5777777777777777766...5688899*********************************999988889999987 PP

                                       SS--GGGHHHHHHHEEEEEEE CS
                               TRM 129 fGspapfldsavqsvkekglL 149
                                         s+ +fld+av+ + e+ +L
  gi|313127040|ref|YP_004037310.1| 266 PHSADDFLDTAVRLAGEECVL 286
                                       789999***999988777665 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         2   1.9e+03     101     151 ..       6      57 ..       3      74 .. 0.70
   2 ?   -3.3   0.0         6   5.7e+03      37      63 ..      87     113 ..      80     122 .. 0.65
   3 !   16.6   0.0   5.1e-06    0.0048       6      94 ..     187     272 ..     183     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                                       HHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEE.EEEES--STTTTHHHHH CS
                   Methyltr_RsmB-F 101 vklrrkekdiaqlaklqkellsaaidllkkgGvl.vYsTCsvlveEneevie 151
                                       v+++ +e + ++ a   ++l++   + + ++G+l +  T + +ve++ ev+ 
  gi|313127040|ref|YP_004037310.1|   6 VRVSTDEGEATRRALADRDLVDQSYEITVHEGTLyIPVTDASAVEDEYEVVS 57 
                                       7778888888888888899999999988888887233566666666666665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6
                                       EEEESSCCCHHHHHHHHHHTT--SEEE CS
                   Methyltr_RsmB-F  37 vAvdankeRlkrvaenlkrLgvtntiv 63 
                                       +  + ++eR++r+a+ +    ++  +v
  gi|313127040|ref|YP_004037310.1|  87 ILDEDDAERASRIADAIAESDLRAETV 113
                                       334556788888888877666664444 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 5.1e-06
                                       --TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC..EE CS
                   Methyltr_RsmB-F   6 pqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlggelfD 81 
                                         e+e+++D+ a+ G    ++  + k  ++vv  d n+  ++ + en +r gv+  ++  ++D+r + ++  g    
  gi|313127040|ref|YP_004037310.1| 187 VTEGERVFDMFAGVG---PFVIPMAKRGAEVVGCDLNAAAVEYLRENARRNGVEeRVTARQGDVRDVADDYEG-WAN 259
                                       57899*******988...58999999***************************95678889******999998.899 PP

                                       EEEEEE--CCGGG CS
                   Methyltr_RsmB-F  82 riLlDaPCsgtgv 94 
                                       ri +  P s+   
  gi|313127040|ref|YP_004037310.1| 260 RIVMNLPHSADDF 272
                                       *******998765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.6e-06    0.0034      59     129 ..     186     255 ..     176     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.6e-06
                                       T--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----S CS
                              CMAS  59 elkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvd 129
                                       ++ +G+++ d+ +G G  v+ +++r +++vvg  l +   ++ +++  + ++e++v+ +  d +d+++ ++
  gi|313127040|ref|YP_004037310.1| 186 QVTEGERVFDMFAGVGPFVIPMAKR-GAEVVGCDLNAAAVEYLRENARRNGVEERVTARQGDVRDVADDYE 255
                                       7899*********************.****************************************99764 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-05     0.011       8      62 ..     175     238 ..     167     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                   Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........k 62 
                                       +l+ +++r+++   +g rv d+ +G+G +   ++++g++v+g Dl+ +ave ++         +
  gi|313127040|ref|YP_004037310.1| 175 RLATERHRVVQQVTEGERVFDMFAGVGPFVIPMAKRGAEVVGCDLNAAAVEYLRenarrngveE 238
                                       56778899999889999*********************************99876555555541 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-05     0.014       7      80 ..     182     253 ..     173     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                   Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklke 80 
                                       ++++ v++g+rv D  +  g   i ++k+g   +v+ +D+n+ ++e  +en++++g+e+++++r +d  ++ ++
  gi|313127040|ref|YP_004037310.1| 182 RVVQQVTEGERVFDMFAGVGPFVIPMAKRGA--EVVGCDLNAAAVEYLRENARRNGVEERVTARQGDVRDVADD 253
                                       68899999******99999999999887765..6********************************98777664 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.5   1.4e+03      28      84 ..       7      67 ..       3      89 .. 0.60
   2 ?    3.0   0.9      0.22   2.1e+02      24      80 ..      83     139 ..      31     158 .. 0.80
   3 ?   12.3   0.1   0.00028      0.26      19      85 ..     209     273 ..     196     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.5
                   Methyltransf_24 28 avdhdpgaeeaaalare..aglddrvrlikads...eealasla..agsiDllfiDgghaaeav 84
                                       v +d+g+++ +ala++     +  ++++++++       ++ +  ++++ ++ +D +   +++
  gi|313127040|ref|YP_004037310.1|  7 RVSTDEGEATRRALADRdlVDQSYEITVHEGTLyipV---TDASavEDEYEVVSFDVESRETQT 67
                                      5666776667777777633333334888888884432...322223477888888877665544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.22
                   Methyltransf_24  24 grlvavdhdpgaeeaaalare.aglddrvrlikadseealaslaagsiDllfiDggha 80 
                                       g +v +d d  ae+a+++a+  a+ d r++ ++ +++++ + l+ ++ D+l+ D + +
  gi|313127040|ref|YP_004037310.1|  83 GDVVILDEDD-AERASRIADAiAESDLRAETVVNRASKVKGALRVRDWDILVDDTDEE 139
                                       5677777777.66777777778888999999999999999999999999999998755 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00028
                   Methyltransf_24  19 rrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDgghaaeavl 85 
                                       +r +  ++v +d +++  e  +++ar++g+++rv+ +++d ++++ + + g+   +++  +h+a++ l
  gi|313127040|ref|YP_004037310.1| 209 KRGA--EVVGCDLNAAaVEYLRENARRNGVEERVTARQGDVRDVADDYE-GWANRIVMNLPHSADDFL 273
                                       3443..699999999533336666777*******************999.99999****999987654 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.23      33      84 ..     185     235 ..     175     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                       .T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGG CS
                              TPMT  33 lkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepk 84 
                                        ++++g+rv+    G +  ++ +A++g evvG +l  +Ave   +e+  +  
  gi|313127040|ref|YP_004037310.1| 185 QQVTEGERVFDMFAGVGPFVIPMAKRGAEVVGCDLNAAAVEYL-RENARRNG 235
                                       4667777777777888888999******************985.44444233 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00031      0.29      19      62 ..     206     251 ..     198     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                                       HHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHH CS
                         adh_short  19 elakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdre 62 
                                        +ak+Ga+vv +d +++++e + ++ +++  +++++a q+Dv+d +
  gi|313127040|ref|YP_004037310.1| 206 PMAKRGAEVVGCDLNAAAVEYLRENARRNgvEERVTARQGDVRDVA 251
                                       589**************************99999*********754 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00033      0.31       5      60 ..     198     249 ..     194     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                   Methyltransf_12   5 cGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlld 60 
                                       +G+G ++ +++++  ++e++g+D++++a+e    + ++r+n   ++v+ ++ d+ d
  gi|313127040|ref|YP_004037310.1| 198 AGVGPFVIPMAKR--GAEVVGCDLNAAAVE--YLRENARRNGVEERVTARQGDVRD 249
                                       7999999999999..**************3..344444444566677777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 1794.64
//
Query:       gi|313127041|ref|YP_004037311.1|  [L=39]
Description: hypothetical protein Hbor_23060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 266.92
//
Query:       gi|313127042|ref|YP_004037312.1|  [L=288]
Description: hypothetical protein Hbor_23070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-21   77.2   7.2    1.6e-14   54.1   1.0    2.1  2  PQQ_2       PQQ-like domain
    2.2e-13   50.3  11.0     0.0085   16.6   0.0    6.2  6  PQQ_3       PQQ-like domain
    1.5e-07   31.0   0.5     0.0036   17.2   0.0    4.7  5  PQQ         PQQ enzyme repeat
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.28   11.0   0.0    1.5  1  PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransf


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   1.5   9.7e-12   4.4e-08      11     152 ..      11     145 ..       6     152 .. 0.81
   2 !   54.1   1.0   3.6e-18   1.6e-14       2     148 ..     124     266 ..     123     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 9.7e-12
                             PQQ_2  11 atGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettl.egpvvga..plvaegrvvvvas 84 
                                       a+G+  W+ d    +g g+  ++l+ggtl++      l al + +G+++W+ +  e+p   a  p+v ++ +v+++ 
  gi|313127042|ref|YP_004037312.1|  11 ADGKHSWQIDK---SGDGL-SPTLHGGTLYTQ-IVEGLLALAPRDGTERWRLDSvESPGPQApgPTVVDETLVAAT- 81 
                                       489999***84...55565.4777*******6.******************99765554444789****9996665. PP

                             PQQ_2  85 dgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvges.sgklvaldpkdGkvlWerel.aa 152
                                          ++++d  + ++ W+t  +      +r ++  a +++ v +g + +g +v   + dG ++We+++  +
  gi|313127042|ref|YP_004037312.1|  82 RTDIVGID-LTTRETWRTSHNA-----MRITGLAAGERGIVSAGIAdDGAVVSGYALDGTKRWEKQIpPS 145
                                       66899***.777889**55555.....7888888877889999988899999999**********99554 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 3.6e-18
                             PQQ_2   2 egvvsaldaatGaelWrvdlar.plgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaeg 77 
                                       ++vvs ++  +G++ W++ + + ++g+ +    lsg  + v t++grl alda++G+  W++ l++ +vg+p +a+g
  gi|313127042|ref|YP_004037312.1| 124 GAVVSGYAL-DGTKRWEKQIPPsDIGSDL-FVCLSGHDICVLTDKGRLDALDAEDGTRQWQANLSSGIVGRPALADG 198
                                       567788887.8*******77332366666.4566******************************************* PP

                             PQQ_2  78 rvvvvasdg..qlialdaedGkrlWstqqrseepaelrssaspavagdtvvvges..sgklvaldpkdGkvlWer 148
                                         +v as++  ++ a+d + G+ +W+ q+         +s s +v+gd+vvv+     ++  +l+++dG v  e+
  gi|313127042|ref|YP_004037312.1| 199 LFLVPASENrtAVHAYDVQQGDAAWT-QSVP------HRSFSLTVVGDVVVVPLDglENRTMVLSLADGTVEAEY 266
                                       ******99999***************.7777......3577788899******9966777899999999986665 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.015        68       5      26 ..      17      37 ..       6      50 .. 0.81
   2 !   11.0   0.2   0.00011      0.49       1      40 []      51      92 ..      51      92 .. 0.86
   3 ?   -0.1   0.1      0.33   1.5e+03       4      22 ..      95     113 ..      93     133 .. 0.50
   4 !   13.4   0.0   1.8e-05     0.082       1      40 []     134     176 ..     134     176 .. 0.94
   5 !   16.6   0.0   1.9e-06    0.0085       1      38 [.     177     216 ..     177     217 .. 0.92
   6 !    7.1   0.1    0.0018         8       1      29 [.     219     246 ..     219     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                             PQQ_3  5 Wsvqlpgpvnsspavdgglvyv 26
                                      W+ +  g++  sp++ gg++y+
  gi|313127042|ref|YP_004037312.1| 17 WQIDKSGDGL-SPTLHGGTLYT 37
                                      7777777775.7*********7 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                             PQQ_3  1 GevlWsv...qlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40
                                      G+++W+    + pgp   +p+v++ +++++t    ++ +D +t
  gi|313127042|ref|YP_004037312.1| 51 GTERWRLdsvESPGPQAPGPTVVDETLVAATR-TDIVGIDLTT 92
                                      99*****8776689888999***********8.8888888776 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.33
                             PQQ_3   4 lWsvqlpg.pvnsspavdgg 22 
                                        W+++  + ++ +++a++++
  gi|313127042|ref|YP_004037312.1|  95 TWRTSHNAmRI-TGLAAGER 113
                                       68886666555.34444332 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 1.8e-05
                             PQQ_3   1 GevlWsvqlpg.pvnssp..avdgglvyvgtgdGtlyAlDaet 40 
                                       G+ +W++q+p  +++s +   ++g  + v t+ G+l AlDae+
  gi|313127042|ref|YP_004037312.1| 134 GTKRWEKQIPPsDIGSDLfvCLSGHDICVLTDKGRLDALDAED 176
                                       999******766*******999**99***************97 PP

  == domain 5  score: 16.6 bits;  conditional E-value: 1.9e-06
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg..dGtlyAlDa 38 
                                       G+++W+ +l + +++ pa+++gl  v ++     ++A+D 
  gi|313127042|ref|YP_004037312.1| 177 GTRQWQANLSSGIVGRPALADGLFLVPASenRTAVHAYDV 216
                                       999************************9988888888885 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.0018
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg 29 
                                       G+  W++++p +  +s++v+g++v+v  +
  gi|313127042|ref|YP_004037312.1| 219 GDAAWTQSVPHRS-FSLTVVGDVVVVPLD 246
                                       6778******988.89*********9765 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.39   1.8e+03      18      25 ..      49      56 ..      49      60 .. 0.87
   2 ?    3.6   0.0     0.015        68      14      33 ..     131     147 ..     130     149 .. 0.78
   3 !   17.2   0.0   7.9e-07    0.0036       6      37 ..     162     194 ..     159     195 .. 0.90
   4 ?    3.9   0.0     0.012        55      11      37 ..     210     236 ..     202     237 .. 0.87
   5 ?   -2.7   0.0       1.6   7.1e+03      12      30 ..     252     270 ..     239     274 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.39
                                      TTCCEEEE CS
                               PQQ 18 dTGkvlWr 25
                                      ++G+++Wr
  gi|313127042|ref|YP_004037312.1| 49 RDGTERWR 56
                                      59*****8 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.015
                                       EEETTTCCEEEEEESSSCGS CS
                               PQQ  14 AlDadTGkvlWrfktggpvl 33 
                                       AlD   G+++W++++++ + 
  gi|313127042|ref|YP_004037312.1| 131 ALD---GTKRWEKQIPPSDI 147
                                       555...********998765 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 7.9e-07
                                       E.ETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ   6 g.sadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                         ++ G+l AlDa++G+  W+ ++++ ++++p+
  gi|313127042|ref|YP_004037312.1| 162 VlTDKGRLDALDAEDGTRQWQANLSSGIVGRPA 194
                                       34999*************************996 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.012
                                       EEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ  11 ylyAlDadTGkvlWrfktggpvlslpi 37 
                                        + A+D+  G+  W+  +++   sl++
  gi|313127042|ref|YP_004037312.1| 210 AVHAYDVQQGDAAWTQSVPHRSFSLTV 236
                                       589***************999988775 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 1.6
                                       EEEEETTTCCEEEEEESSS CS
                               PQQ  12 lyAlDadTGkvlWrfktgg 30 
                                          l +++G+v  +++ ++
  gi|313127042|ref|YP_004037312.1| 252 TMVLSLADGTVEAEYQYEH 270
                                       4456667777766666655 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.2e-05      0.28       7      59 ..     217     273 ..     211     285 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.2e-05
                                       -SEEEEEGGGSSSHHHHT-TTSEEEEEEE-SS.....EEEES--EEEEE--SSSSEEE CS
                        PTS_EIIA_1   7 vsGevvpleevpDevfaekmlGdGvaiepseg.....kvvapvdGkvekvfptkHaig 59 
                                        +G++   ++vp   f+  ++Gd v++  + g      v++ +dG+ve+ ++ +H ++
  gi|313127042|ref|YP_004037312.1| 217 QQGDAAWTQSVPHRSFSLTVVGDVVVVPLD-GlenrtMVLSLADGTVEAEYQYEHELF 273
                                       578899999**************9999775.2233336***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1905.21
//
Query:       gi|313127043|ref|YP_004037313.1|  [L=259]
Description: diphthine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-20   73.1   1.3    3.8e-20   72.7   1.3    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   1.3   2.1e-24   3.8e-20       1     212 [.       1     217 [.       1     218 [. 0.82

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 2.1e-24
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       +l+++G+G+ d   +Tv++++al++ad  +++  ++++++ + + e+le  +++   + + +++ e+  e + +a++
  gi|313127043|ref|YP_004037313.1|   1 MLTFIGLGLYDERSITVEGREALADADRAFAEF-YTSHLVGATV-EDLE-SYHDIDVAVRDRAGVEQHPEDILDAAE 74 
                                       799**************************8766.5555554433.3332.222222333455567777777777777 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl...lpglakeee 151
                                       +   Vv+l++GD ++++t+  l   lra e+gi+++vi Gv++ +aa   +g+  + +g+++++     +g +  ++
  gi|313127043|ref|YP_004037313.1|  75 DE-HVVFLTAGDTMISTTHVDLR--LRAVERGIDTRVIHGVTAQSAASGLTGLQNYRFGKAVTLPfpyAHGADGVPK 148
                                       75.5******************6..99999**************************************888899999 PP

                      TP_methylase 152 releallan....gdtlvllkapr.k.....laelaelLkealyddttpvavveragtedervvrgtleel 212
                                       + ++ + an     +tlv l+    +      +++ae L++ + d     +vv+rag ed  v   +l+el
  gi|313127043|ref|YP_004037313.1| 149 SVIDSIEANrergLHTLVYLDIKAdRdeymsGDYAAEMLADGWED--VLGIVVARAGSEDPLVAADRLSEL 217
                                       999999999999999999996666437888889999999999555..679*********999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1848.13
//
Query:       gi|313127044|ref|YP_004037314.1|  [L=312]
Description: hypothetical protein Hbor_23090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-23   82.6  17.3    4.3e-23   82.2  17.3    1.2  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2  17.3   2.4e-27   4.3e-23      24     250 ..       8     272 ..       1     278 [. 0.75

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 2.4e-27
                   Exosortase_EpsH  24 dyshgllvpllalyllwdrwrr.alaasasllg.llllllglfllallgels.rvlllsalslvlillglvllllGl 97 
                                        ++ + ++ ++ ++ll +r +r a+++ a+++  +++++l l+  +++  +s  +++ls  +++++l++ +ll +G+
  gi|313127044|ref|YP_004037314.1|   8 ALAWAAIITFILGSLLVRRNERtARYVTAAAWTlFAAFWLQLVPYYAFEHKSyIEGFLSLAAVPACLYAGYLLYSGR 84 
                                       445567999*******99999954477777773133334444337*******9************************ PP

                   Exosortase_EpsH  98 ralrlllfpllll.llalP...lpavlvaqlslp.....Lqllvaavagfllsllgip....vereG...nviql.p 157
                                        +l+ l+ +++ + +++lP   +pa+ +  +s+p     L++ va+++ fl++++g++    +  +G   +++ + +
  gi|313127044|ref|YP_004037314.1|  85 DTLFVLSKAVAAMgVIYLPfetIPAFALFGVSIPapkgvLMETVATQTHFLVNAFGYHpefiAGDQGylnTFLFMdG 161
                                       ********************************************************995554333336645555555 PP

                   Exosortase_EpsH 158 tg..qveVaeaCsGlrsllallalglllallfrrrlw.krklllllaavpiaflaNlvRilllvllayhygpeaaeg 231
                                       ++  +++V+ aC+Gl s+      +++ +l+ ++ ++ +rk++ l++a+pi++++Nl+R++++++++++   ++++ 
  gi|313127044|ref|YP_004037314.1| 162 DHrlTISVVLACTGLGSM------AIFGGLIAAVEAPlRRKFRALAIAIPIIYALNLLRTTFITITFGK---QYFQF 229
                                       55667*********5554......444444444444446779************************665...88876 PP

                   Exosortase_EpsH 232 llH........................eiaGwllfgvalllll 250
                                       +++                        +++++l ++ +++l++
  gi|313127044|ref|YP_004037314.1| 230 FVDeillmfgssdpymvsffisdriisQFLAVLALVGITYLVV 272
                                       7775555555555555555555555555555544444445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2316.70
//
Query:       gi|313127045|ref|YP_004037315.1|  [L=893]
Description: hypothetical protein Hbor_23100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-07   31.7   7.7    2.1e-07   30.6   7.7    1.6  1  PGF-CTERM    PGF-CTERM motif
  ------ inclusion threshold ------
      0.066   14.3   0.7      0.066   14.3   0.7    6.6  8  CopC         CopC domain
        2.7    8.1  13.9        3.3    7.9   0.2    6.2  7  DUF3244      Domain of unknown function (DUF3244)


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   7.7   3.6e-11   2.1e-07       1      23 []     870     892 ..     870     892 .. 0.98

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.6e-11
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       tPGFGav+A+++LLaaalLa Rr
  gi|313127045|ref|YP_004037315.1| 870 TPGFGAVVAVTALLAAALLAVRR 892
                                       9********************98 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.17     1e+03      36      73 ..      62     120 ..      37     121 .. 0.70
   2 ?   14.3   0.7   1.1e-05     0.066       4      83 ..     154     233 ..     152     244 .. 0.83
   3 ?   -0.1   0.0      0.33     2e+03      32      74 ..     268     314 ..     236     316 .. 0.58
   4 ?   -0.3   0.0      0.37   2.2e+03      34      72 ..     362     402 ..     332     404 .. 0.56
   5 ?   -1.0   0.0      0.62   3.7e+03      34      76 ..     417     469 ..     408     487 .. 0.60
   6 ?    0.1   0.0      0.29   1.7e+03      20      73 ..     480     532 ..     469     541 .. 0.70
   7 ?   -0.7   0.1      0.51   3.1e+03      63      87 ..     782     809 ..     739     820 .. 0.60
   8 ?   -2.4   1.7       1.8   1.1e+04      13      29 ..     831     847 ..     799     874 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.17
                              CopC  36 kvtdpdgke................evetvdaktveaelkvplp.....elaaGtYtVe 73 
                                       +v+d+dg++                + e++ +kt +   +v+l+      l+ GtY+V+
  gi|313127045|ref|YP_004037315.1|  62 TVYDSDGSQgdfivwvdedgdgawdANEPHANKTPGSDASVELTgidlsGLSTGTYNVS 120
                                       56666665566666666666677873334555555555666666666669999***995 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.1e-05
                              CopC   4 lvsstPaagatvaaapeevtLtFsepvel.skvkvtdpdgkeevetvdaktveaelkvplpelaaGtYtVewrvvsa 79 
                                       l+s++  ++ t ++   ev+L F+e++   +k++v+++dg++++ t + + ++ ++ ++l++    + +V+++v+ +
  gi|313127045|ref|YP_004037315.1| 154 LQSANHYDNDTSSNTDGEVELAFDEDIASvQKLNVSKEDGNTNL-TSSVSIDNGRVVATLNDVYTEDLEVTYKVTDT 229
                                       6777778899999999***********999**********8865.55555567778889999999999999999987 PP

                              CopC  80 DGHp 83 
                                        G +
  gi|313127045|ref|YP_004037315.1| 230 SGNA 233
                                       7765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.33
                              CopC  32 l...skvkvtdpdgke.evetvdaktveaelkvplpelaaGtYtVew 74 
                                       +   + v++t++d+++   ++++  t+++ +  + ++ ++G+Y + +
  gi|313127045|ref|YP_004037315.1| 268 NntaTDVEITGADDDNdFFRSGSTGTNSQVYVLDTEDREDGDYDIVF 314
                                       03335555566555445333444445556666677788889988765 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.37
                              CopC  34 kvkvtdpdgkeevetvdaktveaelkvplp....elaaGtYtV 72 
                                       +++++++d+  +ve++ +++ + + + +++    +l+ G+YtV
  gi|313127045|ref|YP_004037315.1| 362 TIELLNSDE--DVEKTIGADLTGQAEYEFEfnasDLDTGNYTV 402
                                       444555544..33333333333333333334466888888888 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.62
                              CopC  34 kvkvtdpdgke......evetvdaktveaelkvplp.....elaaGtYtVewrv 76 
                                       ++ v+++++ +      ++  ++++ + a+++v+l+     +la G+  V +r+
  gi|313127045|ref|YP_004037315.1| 417 SIVVSKAGEGKadiggdSI-ITEERGDVANVTVTLQntdtaTLAVGSADVGYRA 469
                                       4555544432246666522.2333334555666666555667777777777775 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 0.29
                              CopC  20 eevtLtFsepvel.....skvkvtdpdgkeevetvdaktveaelkvplpelaaGtYtVe 73 
                                        +v++ F+    +       ++v+++d+  ++ + ++ +++++++  l+   +G+Y ++
  gi|313127045|ref|YP_004037315.1| 480 GQVSVLFNTYTATtgvsgDVFEVANSDD--TI-DSTDFDSQNTVSSLLD---SGEYDIQ 532
                                       5677777777766677777788888887..33.4455555667777777...9999987 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 0.51
                              CopC  63 p...elaaGtYtVewrvvsaDGHpvsGs 87 
                                       +   + a +tY+++ r   aD  +v+G+
  gi|313127045|ref|YP_004037315.1| 782 DfseQEAGDTYEITVRNGPADDQTVEGT 809
                                       2332333446666666666666666665 PP

  == domain 8  score: -2.4 bits;  conditional E-value: 1.8
                              CopC  13 atvaaapeevtLtFsep 29 
                                       at +++p++ t t +e+
  gi|313127045|ref|YP_004037315.1| 831 ATTTEEPTTETATTTEE 847
                                       22222222222222222 PP

>> DUF3244  Domain of unknown function (DUF3244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.027   1.6e+02      68      88 ..     102     122 ..      92     133 .. 0.79
   2 ?   -1.7   0.2      0.52   3.1e+03      28      58 ..     202     234 ..     177     256 .. 0.53
   3 ?    7.9   0.2   0.00055       3.3      28      88 ..     257     315 ..     246     323 .. 0.82
   4 ?    1.1   0.0      0.07   4.2e+02      25      61 ..     352     388 ..     339     410 .. 0.79
   5 ?   -0.2   0.1      0.18   1.1e+03      28      58 ..     429     459 ..     425     477 .. 0.75
   6 ?   -3.3   0.0       1.7     1e+04      77      90 ..     523     536 ..     508     538 .. 0.76
   7 ?   -2.0   0.1      0.63   3.8e+03      68      82 ..     627     641 ..     612     674 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.027
                                       TTEEEEE-TTS-SEEEEEEEE CS
                           DUF3244  68 gstisidlsgeesgeYklelt 88 
                                        + + idlsg+++g+Y++   
  gi|313127045|ref|YP_004037315.1| 102 VELTGIDLSGLSTGTYNVSAA 122
                                       46788************9755 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.52
                                       EE.ETTEEEEEESS--SEEEEE..EEETTT--EE CS
                           DUF3244  28 si.egnilsiefesplsdvtit..ikdeetgevv 58 
                                       si +g ++   +++  +d+++t  ++d   g++ 
  gi|313127045|ref|YP_004037315.1| 202 SIdNGRVVATLNDVYTEDLEVTykVTDT-SGNAH 234
                                       3333333333334444444333114444.34444 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00055
                                       EEETTEEEEEESS--SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEE CS
                           DUF3244  28 siegnilsiefesplsdvtitikdeetgevvyestivnasgstisidlsgeesgeYklelt 88 
                                       +++g+++ +  +++ +dv+it  d++++     st +n+  +++++d +  e g+Y++ + 
  gi|313127045|ref|YP_004037315.1| 257 VYKGSTVAVVANNTATDVEITGADDDNDFFRSGSTGTNS--QVYVLDTEDREDGDYDIVFA 315
                                       568999999999999***999999976666666666666..*****************997 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.07
                                       EEEEEETTEEEEEESS--SEEEEEEEETTT--EEEEE CS
                           DUF3244  25 itasiegnilsiefesplsdvtitikdeetgevvyes 61 
                                       +ta + +  ++ie+ ++++dv+ ti  + tg++ ye 
  gi|313127045|ref|YP_004037315.1| 352 VTANAGDRPVTIELLNSDEDVEKTIGADLTGQAEYEF 388
                                       4677788889999999999999999888888877764 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.18
                                       EEETTEEEEEESS--SEEEEEEEETTT--EE CS
                           DUF3244  28 siegnilsiefesplsdvtitikdeetgevv 58 
                                        i g+ +  e + ++ +vt+t+++ +t + +
  gi|313127045|ref|YP_004037315.1| 429 DIGGDSIITEERGDVANVTVTLQNTDTATLA 459
                                       5667777778888999999999999886655 PP

  == domain 6  score: -3.3 bits;  conditional E-value: 1.7
                                       TS-SEEEEEEEEES CS
                           DUF3244  77 geesgeYkleltsk 90 
                                        ++sgeY+++ +s+
  gi|313127045|ref|YP_004037315.1| 523 LLDSGEYDIQVQSG 536
                                       56899999998865 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 0.63
                                       TTEEEEE-TTS-SEE CS
                           DUF3244  68 gstisidlsgeesge 82 
                                       +++is++++++e+g 
  gi|313127045|ref|YP_004037315.1| 627 NDVISLSIEQTEAGA 641
                                       556666665555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (893 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 5536.22
//
Query:       gi|313127046|ref|YP_004037316.1|  [L=256]
Description: lactoylglutathione lyase-like lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-19   70.2   3.2      3e-12   46.9   0.2    2.4  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    5.7e-09   36.2   2.1     0.0016   18.7   0.1    3.4  4  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    4.5e-08   33.8   2.9     0.0058   17.4   0.3    2.2  2  Glyoxalase_6  Glyoxalase-like domain
    0.00047   20.3   2.2        1.3    9.1   0.1    3.8  2  Glyoxalase_3  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.016   15.2   0.1       0.38   10.7   0.0    2.7  2  Glyoxalase_2  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.2   8.3e-16     3e-12       2     128 .]       5     123 ..       4     123 .. 0.88
   2 !   23.8   0.3   1.2e-08   4.2e-05       2     128 .]     134     250 ..     133     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 8.3e-16
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE.EEST.EEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdn.teet.eglriaffhaggghielvlneapsgaakhvkkieetvhh 76 
                                       +dhv+l+v dl++sld+Y+ +L+ +   +++  t  t   l+   +h++g ++el++n+ + +++ +         h
  gi|313127046|ref|YP_004037316.1|   5 LDHVMLRVEDLDESLDWYKTHLDYEEKGRWEAdT-FTnVYLGPEEMHEEGAMLELTYNHDDRSYEMGD-----AWGH 75 
                                       79***************************99532.2246667779**********************9.....699* PP

                                       EEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  77 vafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       +a+++ ++e ++  +++l ++gv+  + p  +  g++y f ++DpdG+++ei
  gi|313127046|ref|YP_004037316.1|  76 IAVRVPEDE-LESSYQQLMDEGVEDYRDP--ESCGGRYAF-VKDPDGHEVEI 123
                                       *****9755.6***********7766665..889999988.*********97 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.2e-08
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE.EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdn.teeteglriaffhaggghielvlneapsgaakhvkkieetvhhv 77 
                                       +dh++++v d++++l F+t+ +  + + +++  t +  +++     ++   +el++n    +++ +           
  gi|313127046|ref|YP_004037316.1| 134 LDHTMIRVEDADEALGFWTRKFEYEHTGRWESdTFANYFMKPEGAAEEAMAVELTYNYDGRTYDMGD--------AW 202
                                       89**********************9999998333333666666666777778888888888888888........89 PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       ++++   +d+g++++ l e++ +  + p  +  +++y f  +D dG+++ei
  gi|313127046|ref|YP_004037316.1| 203 GHLCVRADDLGEYWETLLERDAEEYRDP--ESCDNRYAF-TKDQDGHEIEI 250
                                       *********************7766666..889999987.*********97 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   1.1e-05     0.039       1      92 [.       6      98 ..       6     112 .. 0.78
   2 ?    1.9   0.0     0.073   2.6e+02      11      57 ..      83     128 ..      74     133 .. 0.70
   3 !   18.7   0.1   4.6e-07    0.0016       1      92 [.     135     225 ..     135     239 .. 0.83
   4 !    5.6   0.0    0.0053        19      15      57 ..     214     255 ..     210     256 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                      EEEEEE-S-HHHHHHHHHH.TT-EESS--E..EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEEE.. CS
                      Glyoxalase_4  1 dQigivVeDleaavarfsallGvgpwqryr.depqevdlafallgsgsvqieLieplegpeflaehgeglhhlaywv.. 76
                                      d++ + VeDl++ ++ ++++l++++  r++ d+ ++v l   ++ ++  ++eL  ++++++   e g    h+a++v  
  gi|313127046|ref|YP_004037316.1|  6 DHVMLRVEDLDESLDWYKTHLDYEEKGRWEaDTFTNVYLGPEEMHEEGAMLELTYNHDDRSY--EMGDAWGHIAVRVpe 82
                                      6999*******************9998886234467777666665555899*9999999766..899999999999955 PP

                                      S-HHHHHHHHCTTTEE CS
                      Glyoxalase_4 77 ddldaavarleeqGfe 92
                                      d+l+ + ++l ++G+e
  gi|313127046|ref|YP_004037316.1| 83 DELESSYQQLMDEGVE 98
                                      5899999999999987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.073
                                       HHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESS CS
                      Glyoxalase_4  11 eaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieple 57 
                                       ++   ++++l++ g+++   +e+ + ++af++  +g  ++e ++  +
  gi|313127046|ref|YP_004037316.1|  83 DELESSYQQLMDEGVEDYRDPESCGGRYAFVKDPDG-HEVEIVKRNH 128
                                       556667888888888887788888899999999998.5777766555 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 4.6e-07
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETT...EEEEEEEESSTT-THHHTS-EEEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgs...vqieLieplegpeflaehgeglhhlay 74 
                                       d++ i VeD ++a+ ++++ + ++ + r+  e+  + ++f++  ++    + +eL  + +g++  ++ g    hl++
  gi|313127046|ref|YP_004037316.1| 135 DHTMIRVEDADEALGFWTRKFEYEHTGRW--ESDTFANYFMKPEGAAeeaMAVELTYNYDGRT--YDMGDAWGHLCV 207
                                       69999**************8888766666..6778999999988876788*****99999954..58999999**** PP

                                       EES-HHHHHHHHCTTTEE CS
                      Glyoxalase_4  75 wvddldaavarleeqGfe 92 
                                       + ddl + +++l e+++e
  gi|313127046|ref|YP_004037316.1| 208 RADDLGEYWETLLERDAE 225
                                       ************999987 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0053
                                       HHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESS CS
                      Glyoxalase_4  15 arfsallGvgpwqryrdepqevdlafallgsgsvqieLieple 57 
                                       +++++ll  + ++   +e+ + ++af++ ++g  +ie  ep +
  gi|313127046|ref|YP_004037316.1| 214 EYWETLLERDAEEYRDPESCDNRYAFTKDQDG-HEIEILEPTD 255
                                       78999888877777778889999********9.7******987 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.2e-06    0.0081       2     106 ..       8     123 ..       7     124 .. 0.76
   2 !   17.4   0.3   1.6e-06    0.0058       3     106 ..     138     250 ..     136     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                      Glyoxalase_6   2 vvldaadpaalaaFwaaalgweveree.......aaledpegvgpaaedaatllfqrvpe.......paknrvHldl 64 
                                       v+l ++d ++  +++++ l++e + +        +    pe     +e++a l +    +        a+   H+ +
  gi|313127046|ref|YP_004037316.1|   8 VMLRVEDLDESLDWYKTHLDYEEKGRWeadtftnV-YLGPEE---MHEEGAMLELTYNHDdrsyemgDAW--GHIAV 78 
                                       789999****************9999877776642.222222...2335555555555556688755444..69999 PP

                      Glyoxalase_6  65 av..edldaevarlvalGArvlreprdgthgr..vlaDPeGneFcv 106
                                       +v  ++l+   ++l + G +  r+p++ ++ r   ++DP+G+e  +
  gi|313127046|ref|YP_004037316.1|  79 RVpeDELESSYQQLMDEGVEDYRDPESCGG-RyaFVKDPDGHEVEI 123
                                       9988999******************99875.56**********877 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.6e-06
                      Glyoxalase_6   3 vldaadpaalaaFwaaalgweveree......aaledpegvgpaaedaatllfqrvpe.......paknrvHldlav 66 
                                       ++ ++d++++ +Fw + +++e + +           +peg   aae+a+ + +    +        a+   Hl +++
  gi|313127046|ref|YP_004037316.1| 138 MIRVEDADEALGFWTRKFEYEHTGRWesdtfaNYFMKPEG---AAEEAMAVELTYNYDgrtydmgDAW--GHLCVRA 209
                                       67899****************9999888877633334444...3345555555555556677755444..7****** PP

                      Glyoxalase_6  67 edldaevarlvalGArvlreprdgthgr.vlaDPeGneFcv 106
                                       +dl +  + l++  A++ r+p++ +++    +D +G+e  +
  gi|313127046|ref|YP_004037316.1| 210 DDLGEYWETLLERDAEEYRDPESCDNRYaFTKDQDGHEIEI 250
                                       ***********************997669********9876 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1   0.00035       1.3       1      22 [.       5      26 ..       5     124 .. 0.80
   2 !    5.8   0.2    0.0037        13      70      99 ..     188     223 ..     134     249 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00035
                      Glyoxalase_3  1 lDHvvlavpdleeaaarfarrl 22
                                      lDHv+l v+dl+e  +++ + l
  gi|313127046|ref|YP_004037316.1|  5 LDHVMLRVEDLDESLDWYKTHL 26
                                      8****************96554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0037
                      Glyoxalase_3  70 d......rlakgeglhtlalrtddidataarlraaG 99 
                                              +++ g+ + +l++r dd+ +  ++l ++ 
  gi|313127046|ref|YP_004037316.1| 188 TynydgrTYDMGDAWGHLCVRADDLGEYWETLLERD 223
                                       233333255568888888888888888888777665 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.38       3     114 ..       7     124 ..       5     126 .. 0.71
   2 ?    1.3   0.0     0.084     3e+02      99     116 ..     236     253 ..     202     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                       ----EES-HHHHHHHHHHTT---EE....EE-SSEEEETTS-EEEEH..HHHHH.-------S...--SS-EEEEEE CS
                      Glyoxalase_2   3 lillvvkdieeskkFYedvlelkik....ldfGenvsfetgfalked..lkeli.nldesiae...qsnnfeLyFev 69 
                                        ++l v+d++es ++Y+  l+ + k    +d  +nv + +  +++e+  + el+ n d+  +e      ++ +   +
  gi|313127046|ref|YP_004037316.1|   7 HVMLRVEDLDESLDWYKTHLDYEEKgrweADTFTNV-YLGPEEMHEEgaMLELTyNHDDRSYEmgdAWGHIAVRVPE 82 
                                       578999************998654311114555555.444456666646556665666644442225678999999* PP

                                       S-HHHHHHHH..GGGS-EEEEEEE-TTS-EEEEEE-TT--EEEEE CS
                      Glyoxalase_2  70 edvdaflqklkeaeniellhelkekpWgqrvirfyDpDkhiiEig 114
                                       +++++  q+l +++ +e   ++  +  g r + + DpD+h +Ei 
  gi|313127046|ref|YP_004037316.1|  83 DELESSYQQLMDEG-VEDYRDP--ESCGGRYAFVKDPDGHEVEIV 124
                                       **********8877.7766665..56899**************96 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.084
                                       EEEEEE-TT--EEEEEE- CS
                      Glyoxalase_2  99 rvirfyDpDkhiiEiges 116
                                       r +   D D+h iEi e+
  gi|313127046|ref|YP_004037316.1| 236 RYAFTKDQDGHEIEILEP 253
                                       6667789********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1572.54
//
Query:       gi|313127047|ref|YP_004037317.1|  [L=490]
Description: efflux protein, mate family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-46  155.5  20.4    3.7e-26   91.7   6.7    2.4  3  MatE             MatE
      3e-07   30.6   4.0      3e-07   30.6   4.0    4.0  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    1.3e-06   27.3  10.4    0.00045   18.9   5.8    2.4  2  MurJ             Lipid II flippase MurJ


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   6.7   6.2e-30   3.7e-26       1     159 [.      50     209 ..      50     211 .. 0.97
   2 ?   -3.5   0.1       1.2   7.3e+03      29      49 ..     223     243 ..     220     247 .. 0.80
   3 !   73.4   1.8   2.6e-24   1.5e-20       1     161 []     278     441 ..     278     441 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 6.2e-30
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P +++ l+ ++ +++d+ lvg+  g  a+++v++a + + l f+++ g+++++ +lv+q++Ga + +++++a+r ++
  gi|313127047|ref|YP_004037317.1|  50 PRIVTGLARMSKNAVDVALVGSAsGVAAITGVGFAGPYWGLAFALGGGVAAGTLALVSQRYGADQSDGIGVAIRSST 126
                                       5577778888889**************************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisll 153
                                       +l++l  l+++++ +lf+ q++s++t++++v+ l++rylr+++lg+p+ +l+lv s++l ga ++ +++ +   +++
  gi|313127047|ref|YP_004037317.1| 127 LLVVLSTLPVTVIFWLFPVQLISVLTDNPNVIDLGARYLRLVGLGVPFAGLNLVGSRALVGADDAYTAMLLRSGGAV 203
                                       ***************************************************************************** PP

                              MatE 154 lnipln 159
                                        ni+l+
  gi|313127047|ref|YP_004037317.1| 204 TNIILS 209
                                       ***997 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                              MatE  29 Aavsialsilsllfvfllgls 49 
                                       Aav+ +ls + ++++f+lgl 
  gi|313127047|ref|YP_004037317.1| 223 AAVGTVLSNVVVTGAFALGLT 243
                                       788888888888888888875 PP

  == domain 3  score: 73.4 bits;  conditional E-value: 2.6e-24
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P++  +l+ ++  + +  +v+ +g++  Aa  i+ +i+ l+ ++++g++ a ++lvgqalG+ + + a+ + r ++ 
  gi|313127047|ref|YP_004037317.1| 278 PVFGRSLVWTVAEFPMLAIVNLFGKNVAAAFVITRRIWGLMNTPGWGFGLASSSLVGQALGKDDEDTAEAYGREIVR 354
                                       56666777777788888888888****************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee..vlelakrylrililgipalalqlvlsgilrgagktkvplyislisl 152
                                       ++++ +++ a+lv +f+e+i++ f +++   v++ a  ++ +++l ++ ++++ +++g l++ g+t +p+y  l+++
  gi|313127047|ref|YP_004037317.1| 355 FSVATYIVSAVLVAIFAEPIVRQFVKNPGpdVVPTAVGLVYAACLAVIMQGVSGASAGPLDASGDTSIPFYSQLLGM 431
                                       **************************99888********************************************** PP

                              MatE 153 .llniplnyl 161
                                         + ip++yl
  gi|313127047|ref|YP_004037317.1| 432 fGCSIPITYL 441
                                       *******997 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   2.1      0.22   1.3e+03      51      72 ..      86     107 ..      51     154 .. 0.49
   2 !   30.6   4.0     5e-11     3e-07       1      71 [.     164     236 ..     164     244 .. 0.92
   3 !    7.9   0.5   0.00051         3       5      76 ..     397     469 ..     393     472 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.22
                   Polysacc_synt_C  51 plfgivGaaiatvlallvvavl 72 
                                       p++g+  a+ + v+a ++++v 
  gi|313127047|ref|YP_004037317.1|  86 PYWGLAFALGGGVAAGTLALVS 107
                                       3333333333333333333333 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 5e-11
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvav 71 
                                       +L+++ l+++f++l+ v+s  L g + + +a++    ga+ ++il+  li    +++ Gaa++tvl+ +vv+ 
  gi|313127047|ref|YP_004037317.1| 164 YLRLVGLGVPFAGLNLVGSRALVGADDAYTAMLLRSGGAVTNIILSATLIfgLDMSVEGAAVGTVLSNVVVTG 236
                                       589999********************************************5556678*************986 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00051
                   Polysacc_synt_C   5 lalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllliplfgivGaaiatvlallvvavlnlya 76 
                                        +l++i++++s  +++ L + g + i++++ ++g++ + + +++l      i    +a ++  +v a++n+y+
  gi|313127047|ref|YP_004037317.1| 397 ACLAVIMQGVSGASAGPLDASGDTSIPFYSQLLGMFgCSIPITYLGAQTGHIEALYLALLAETTVPAAINYYR 469
                                       6899*******************************96777777777755556667777777777777777775 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   5.8   7.5e-08   0.00045     228     402 ..      73     244 ..      37     252 .. 0.85
   2 !   10.1   0.1   3.6e-05      0.22      46     141 ..     339     434 ..     296     461 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.5e-08
                              MurJ 228 laegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpiv 304
                                           +++ + +a  ++ l+++l g  +++  L+ +S+ + +++ d +   ++ ++ l++l ++pv++++ ++  +++
  gi|313127047|ref|YP_004037317.1|  73 SGVAAITGVGFAGPYWGLAFAL-GGGVAAGTLALVSQRYGADQSDGIGVAIRSSTLLVVLSTLPVTVIFWLFPVQLI 148
                                       4445666777888888888886.66788888999******************************************* PP

                              MurJ 305 sllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnills..llllpplgvv 379
                                       s+l      +++ +   a+ L++ +lg+++  l+ + +r++    d+ t++ +    +v+ni+ls  l++   ++v 
  gi|313127047|ref|YP_004037317.1| 149 SVLT----DNPNVIDLGARYLRLVGLGVPFAGLNLVGSRALVGADDAYTAMLLRSGGAVTNIILSatLIFGLDMSVE 221
                                       ***9....5688899999***********************************************99999999**** PP

                              MurJ 380 glalatslsaliglvllyvllrk 402
                                       g a++t+ls+++ ++ + + l++
  gi|313127047|ref|YP_004037317.1| 222 GAAVGTVLSNVVVTGAFALGLTR 244
                                       ***********999988777765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 3.6e-05
                              MurJ  46 kkdeekaaefvrkvltllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLn 122
                                       k+de+ a++  r+++++ +++ ++ +++  ++a+ ++r + +   ++    av l++   + +++ ++s+ + + L 
  gi|313127047|ref|YP_004037317.1| 339 KDDEDTAEAYGREIVRFSVATYIVSAVLVAIFAEPIVRQFVKNPGPDVVPTAVGLVYAACLAVIMQGVSGASAGPLD 415
                                       45899999********999999999999999999999999999999**********************999999999 PP

                              MurJ 123 arkkFfapafsPvllNvsv 141
                                       a++   +p +s++l  ++ 
  gi|313127047|ref|YP_004037317.1| 416 ASGDTSIPFYSQLLGMFGC 434
                                       9999999998888766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3274.95
//
Query:       gi|313127048|ref|YP_004037318.1|  [L=151]
Description: hypothetical protein Hbor_23130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1200.14
//
Query:       gi|313127049|ref|YP_004037319.1|  [L=455]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-31  108.7   0.2    3.5e-31  107.9   0.2    1.4  1  OrfB_IS605      Probable transposase
    2.2e-17   62.7   0.1      4e-17   61.9   0.1    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.012   16.0   1.3      0.019   15.3   1.3    1.4  1  zf-RING_2       Ring finger domain


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.2   5.8e-35   3.5e-31       9     119 ..     200     314 ..     180     315 .. 0.89

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 5.8e-35
                        OrfB_IS605   9 e.......lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                       e        + p  ++ a++D+G+nnL+++ t++g+++ly+gr l++++++++ eia+lqskl +    ++ sr+++
  gi|313127049|ref|YP_004037319.1| 200 EvenasrfRNSPLASEEAALDVGANNLVACTTTTGQQYLYEGRDLFARFRETTDEIARLQSKLREG---RYSSRRIR 273
                                       055556677889999*************************************************99...7******* PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       rl+rkr+rrr+h++++l+++l+++l+++gv t++vg+++d+
  gi|313127049|ref|YP_004037319.1| 274 RLYRKRTRRRDHAQDALVRDLLERLYAEGVATVYVGDLTDV 314
                                       **************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.1   6.6e-21     4e-17       1      69 []     333     400 ..     333     400 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 6.6e-21
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+ ++ +l++ a+eyGi+ve+ ++a T  tC++Cg++++++++g++f+Cp Cg+ea++D+ A++  l+r
  gi|313127049|ref|YP_004037319.1| 333 FQAFIDRLSDTAEEYGITVEVRSEADTTRTCPVCGEQDDTDRDGDVFRCP-CGHEAHADLCASRTFLER 400
                                       7899**********************************************.************998875 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.3   3.3e-06     0.019       2      34 ..     362     397 ..     361     402 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-06
                         zf-RING_2   2 eCpIC..leelssadsvlllpCgHvfhre.Clerwl 34 
                                       +Cp+C  +++ +++ +v ++pCgH  h + C++r +
  gi|313127049|ref|YP_004037319.1| 362 TCPVCgeQDDTDRDGDVFRCPCGHEAHADlCASRTF 397
                                       7****65577777778***********999998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2758.97
//
Query:       gi|313127050|ref|YP_004037320.1|  [L=245]
Description: hypothetical protein Hbor_23150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.061   13.0   0.0        0.1   12.3   0.0    1.4  1  AraC_binding_2  AraC-binding-like domain


Domain annotation for each model (and alignments):
>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.6e-06       0.1      59     101 ..      55      98 ..      15     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-06
                    AraC_binding_2  59 qlplsGraeveqggr.evvlgpgdavvldpgrpyrlrwsadceq 101
                                       ++++sG+a+  qgg+ ++ +  g+a++  + r+yr+++s d e 
  gi|313127050|ref|YP_004037320.1|  55 SFTISGSAVAKQGGErRTATYDGHAAFNRSERTYRMSISLDGES 98 
                                       6899*********654999*****************98876664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1558.84
//
Query:       gi|313127051|ref|YP_004037321.1|  [L=370]
Description: small GTP-binding protein domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-32  112.2   0.5    2.6e-32  111.0   0.2    1.8  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    7.5e-23   80.8   0.0    1.6e-22   79.8   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    1.5e-13   50.6   0.4    1.5e-12   47.3   0.1    2.2  2  FeoB_N        Ferrous iron transport protein B
    1.8e-10   40.7   0.0    3.2e-10   39.9   0.0    1.5  1  TGS           TGS domain
    5.6e-07   29.6   0.5      0.015   15.2   0.1    3.0  3  RsgA_GTPase   RsgA GTPase
    0.00012   22.2   0.0       0.11   12.6   0.1    2.6  2  Dynamin_N     Dynamin family
    0.00038   19.9   0.0    0.00083   18.7   0.0    1.5  1  AIG1          AIG1 family
     0.0054   16.2   0.1       0.36   10.3   0.0    2.5  2  Arf           ADP-ribosylation factor family
     0.0054   17.2   0.0       0.45   11.0   0.0    2.4  2  ABC_tran      ABC transporter
     0.0068   15.4   0.1      0.028   13.4   0.0    2.0  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
  ------ inclusion threshold ------
       0.01   15.4   0.6        3.5    7.2   0.0    2.7  3  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.014   15.2   0.1        1.9    8.2   0.0    2.3  2  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.03   14.6   0.1      0.083   13.1   0.0    1.8  1  AAA_28        AAA domain
      0.034   14.7   0.3       0.16   12.6   0.2    2.3  2  POTRA         Surface antigen variable number repeat
      0.056   13.5   0.0       0.15   12.1   0.0    1.7  1  RBD           Raf-like Ras-binding domain
      0.082   12.7   0.1       0.24   11.2   0.1    1.8  1  AAA_29        P-loop containing region of AAA domain
       0.12   12.7   0.0       0.26   11.7   0.0    1.5  1  AAA_16        AAA ATPase domain
       0.68   10.2   6.3       0.15   12.3   1.7    2.3  2  ABC_tran_CTD  ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.9   6.9e+03      82     102 ..     142     162 ..     130     163 .. 0.73
   2 !  111.0   0.2   2.6e-35   2.6e-32       1     106 []     181     293 ..     181     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.9
                      MMR_HSR1_Xtn  82 svviSaekelnldeLkekiwe 102
                                       ++++S+ +    ++L+e++++
  gi|313127051|ref|YP_004037321.1| 142 VFMLSVFELERYERLQEELYQ 162
                                       456888888888999999987 PP

  == domain 2  score: 111.0 bits;  conditional E-value: 2.6e-35
                      MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldela 77 
                                       kgGi++t t +++ ldeet+k++l+ey+++na+v+ir+d+t+D+lid i++nrvY+p+++++NK+Dli++++l +++
  gi|313127051|ref|YP_004037321.1| 181 KGGIQVTMTDDVS-LDEETIKDVLREYGYVNADVTIRGDLTIDELIDGIMDNRVYLPSMVTVNKADLIDQDYLPTVN 256
                                       69*****997755.************************************************************999 PP

                      MMR_HSR1_Xtn  78 re........pnsvviSaekelnldeLkekiweeLnL 106
                                       ++        +++v+iSaeke++l+ Lke++we+L+L
  gi|313127051|ref|YP_004037321.1| 257 EQlremdidpDEAVFISAEKEKGLEGLKETMWERLGL 293
                                       977889999669***********************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.0   1.6e-25   1.6e-22       2     101 ..      63     164 ..      62     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.6e-25
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.ad 77 
                                       va+vG p vGKStLinalt++ ++v+++ +tT+++n g ++++g +i+++D+pGliega  ++g gk++l++ + ad
  gi|313127051|ref|YP_004037321.1|  63 VALVGFPSVGKSTLINALTNADSEVGAYEFTTLNVNPGMLHYNGANIQILDVPGLIEGAAGGRGGGKEVLSVVRtAD 139
                                       9**********************************************************************99978* PP

                                       EEEEEEETT.TTCSHHHHHHHHHHH CS
                          MMR_HSR1  78 lillvvdas.eeklkpldeeleell 101
                                       l+++++++   e +++l+eel + +
  gi|313127051|ref|YP_004037321.1| 140 LVVFMLSVFeLERYERLQEELYQNK 164
                                       ******9777556888888877664 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1   1.5e-15   1.5e-12       2      57 ..      62     117 ..      61     167 .. 0.87
   2 ?    1.1   0.0      0.25   2.5e+02     106     155 ..     235     286 ..     224     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.5e-15
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE---- CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGi 57 
                                       tvalvG p vGk+tl+nalt+a+++vg +  +t + + g l+++g +++i+D+PG 
  gi|313127051|ref|YP_004037321.1|  62 TVALVGFPSVGKSTLINALTNADSEVGAYEFTTLNVNPGMLHYNGANIQILDVPGL 117
                                       89*****************************************************7 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.25
                                       SSEEEEEETHHHHHHTTEEE-HHHHHHH.HTS.-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 106 vpvvlalnmideaekkgieidlkkLsek.Lgv.pvvktsakkkegieellka 155
                                       +p ++ +n+ d ++++ +   +++L+e+ ++  + v +sa+k++g+e l+++
  gi|313127051|ref|YP_004037321.1| 235 LPSMVTVNKADLIDQDYLPTVNEQLREMdIDPdEAVFISAEKEKGLEGLKET 286
                                       57789999999999998877777776531543368999********999986 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   3.2e-13   3.2e-10       1      59 [.     294     367 ..     294     368 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.2e-13
                                       EEEEE.TTSSEEE......EETTB-.HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd......lprgat.veDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       irv++ ++G+ +d      l++g+    D+  k++ +l ++f+ A+V G       q+ g dh+L+d+d+++Iv
  gi|313127051|ref|YP_004037321.1| 294 IRVFMdKPGRGVDyeeplvLQEGENtLDDALDKLGGTLDERFRFARVTGpsakhdeQQIGRDHELQDEDILRIV 367
                                       89*********************98799999******************************************9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.5e-05     0.015      95     127 ..      56      87 ..      18     118 .. 0.83
   2 ?   -2.0   0.0         3     3e+03      68      99 ..     131     162 ..     128     167 .. 0.80
   3 !   11.6   0.0    0.0002       0.2      48     100 ..     236     290 ..     219     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                                       HHCTTSEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallpelelkt 127
                                       e+  d t++lvG   vGKStLinal++  + ++
  gi|313127051|ref|YP_004037321.1|  56 EKTGDVTVALVGFPSVGKSTLINALTNA-DSEV 87 
                                       556678999****************987.4444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                                       HHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  68 lkeelealgyevllvsaktkegleelkellkd 99 
                                       + + ++++++ v+++s+ + e +e+l+e+l +
  gi|313127051|ref|YP_004037321.1| 131 VLSVVRTADLVVFMLSVFELERYERLQEELYQ 162
                                       56778889999999999999999999999876 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0002
                                       EEEEEEE-GGG--HHHHHHHHHHHHHHTTS...EEEE--TTTHTTHHHHHHHCTTS CS
                       RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealgy...evllvsaktkegleelkellkdk 100
                                       + ++ +nK+Dl++++  l +++e+l+++++   e +++sa++++gle lke + ++
  gi|313127051|ref|YP_004037321.1| 236 PSMVTVNKADLIDQDY-LPTVNEQLREMDIdpdEAVFISAEKEKGLEGLKETMWER 290
                                       67999**********9.9999999999998222479*************9988665 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00011      0.11       1      22 [.      63      84 ..      63      99 .. 0.83
   2 !    7.0   0.0    0.0054       5.4     100     137 ..     106     146 ..      96     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      EEEEEBTTTTHHHHHHHHHTS- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                      +a+vG  S GKS+++naL+ +d
  gi|313127051|ref|YP_004037321.1| 63 VALVGFPSVGKSTLINALTNAD 84
                                      799***************9887 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0054
                                       S-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEE CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdq...elvkeyikkadiilavts 137
                                         ++ ++D+PGl++ +++     + v + ++ ad++++++s
  gi|313127051|ref|YP_004037321.1| 106 GANIQILDVPGLIEGAAGGRgggKEVLSVVRTADLVVFMLS 146
                                       5799************9999999999999999999999876 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.3e-07   0.00083       2     104 ..      62     161 ..      61     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.3e-07
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS-.--SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqs.vtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcl 77 
                                       t+ lvG   +GkS+ +N++ +    +s++ a +  t +++      +g +i++ D Pgl++  +      ke+   +
  gi|313127051|ref|YP_004037321.1|  62 TVALVGFPSVGKSTLINALTNA---DSEVGAYEfTTLNVNPGMLHYNGANIQILDVPGLIEGAAGGRGGGKEVLSVV 135
                                       788***************9765...4555554405567777777******************************755 PP

                                       HHCTT-ESEEEEEEETTB-SHHHHHHH CS
                              AIG1  78 llseegihalllvlslgrfteedekal 104
                                         +++ + ++l v++l+r+++  e++ 
  gi|313127051|ref|YP_004037321.1| 136 R-TADLVVFMLSVFELERYERLQEELY 161
                                       5.5555999999*******98777655 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00036      0.36      14      67 ..      60     116 ..      53     166 .. 0.71
   2 ?    3.2   0.0     0.054        54     117     168 ..     236     287 ..     220     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00036
                                       EEEEEEEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEEE-S CS
                               Arf  14 elrilllGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwDvGG 67 
                                       ++ + l+G  + GK+T+++ l++ + +       T+  n   l++++ ++++ Dv G
  gi|313127051|ref|YP_004037321.1|  60 DVTVALVGFPSVGKSTLINALTNADSEVgayEFTTLNVNPGMLHYNGANIQILDVPG 116
                                       5678899**************99887665557899*******************966 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.054
                                       EEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHH CS
                               Arf 117 allvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglkegl 168
                                       + +v  NK Dl ++     ++e+l   ++ +++ + i +      eglke++
  gi|313127051|ref|YP_004037321.1| 236 PSMVTVNKADLIDQDYLPTVNEQLREMDIDPDEAVFISAEKEKGLEGLKETM 287
                                       56899*************************9999999888777778887765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00045      0.45      13      36 ..      62      85 ..      56     114 .. 0.81
   2 ?    3.7   0.0     0.083        83      38     127 ..     180     301 ..     157     302 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00045
                                      EEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllk 36
                                      +va+vG    GKStL+++l++  +
  gi|313127051|ref|YP_004037321.1| 62 TVALVGFPSVGKSTLINALTNADS 85
                                      79*****************98765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.083
                                       SEEEEEET...TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.........................HHHTC.. CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxx.. RF
                          ABC_tran  38 teGeilld...gkdlkeqeleslrkeigvlpqepqlfpeltvren.........................esdee.. 84 
                                        +G i++    + +l+e++++ + +e g++  + ++  +lt+ e                          +      
  gi|313127051|ref|YP_004037321.1| 180 HKGGIQVTmtdDVSLDEETIKDVLREYGYVNADVTIRGDLTIDELidgimdnrvylpsmvtvnkadlidqD---Ylp 253
                                       45555554201333444888888888999999999998888888899988888877777776665553331...133 PP

                                       .HHHHHHHSTTGGTTCBGESTTS....GGS-HHHHHHHHHHHHHHHTS CS
                                       .xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  85 .iekalsklglkelkdtvvkssp....ssLSgGqkqrvalarallkkp 127
                                        +++ l++++++ +++  ++ ++    + L + +++r+ l r+++ kp
  gi|313127051|ref|YP_004037321.1| 254 tVNEQLREMDIDPDEAVFISAEKekglEGLKETMWERLGLIRVFMDKP 301
                                       355555555555444444433334445667777777777777777665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.8e-05     0.028      24      68 ..      56     100 ..      52     110 .. 0.75
   2 ?   -1.5   0.0      0.98   9.7e+02     171     181 ..     238     248 ..     214     296 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                                       GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT.--EEEEEE--- CS
                              MeaB  24 akaGraqvvGltGvPGaGkstlvealglelrrrG.krvavlavDPs 68 
                                       +k+G    v l G+P +Gkstl++al+    + G +  + l v+P+
  gi|313127051|ref|YP_004037321.1|  56 EKTGDV-TVALVGFPSVGKSTLINALTNADSEVGaYEFTTLNVNPG 100
                                       566654.57899**************99887777335666777766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.98
                                       EEEEE---HHH CS
                              MeaB 171 iivvnkaDkke 181
                                       ++ vnkaD+ +
  gi|313127051|ref|YP_004037321.1| 238 MVTVNKADLID 248
                                       56666666332 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0035       3.5       3      24 ..      63      84 ..      61     103 .. 0.87
   2 ?   -1.9   0.0       2.1   2.1e+03     109     139 ..     135     165 ..     127     168 .. 0.78
   3 ?    5.6   0.1     0.011        11     129     169 ..     223     262 ..     181     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0035
                                      EEEEESTTCCHHHHHHHHHCT- CS
                              cobW  3 tvltGflGsGKTtLlnhllenr 24
                                      + l+Gf+  GK+tL+n+l++  
  gi|313127051|ref|YP_004037321.1| 63 VALVGFPSVGKSTLINALTNAD 84
                                      679**************99654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                                       CCCECEEEEEEETTTH.CCHCCHHHHHHHHH CS
                              cobW 109 dltldavvavvDaknleaeeekieekaedql 139
                                         t+d vv+++++ +le+ e+ +ee++++++
  gi|313127051|ref|YP_004037321.1| 135 VRTADLVVFMLSVFELERYERLQEELYQNKI 165
                                       5578999999999999888888888888776 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.011
                                       CCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHH CS
                              cobW 129 ekieekaedqlaaadllvlnKtDlldeeallekleerlrql 169
                                       e i   +++ +   +++ +nK+Dl+d++ l  +++e+lr++
  gi|313127051|ref|YP_004037321.1| 223 ELIDGIMDNRVYLPSMVTVNKADLIDQDYL-PTVNEQLREM 262
                                       556667778888899************965.8888888876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0019       1.9       2      38 ..      66     103 ..      65     114 .. 0.84
   2 ?    4.6   0.0     0.024        24     153     206 ..     231     289 ..     221     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrg.rsvavvNLDPAaee 38 
                                       vG +++GK+t+++al++  ++ g +++ ++N  P+  +
  gi|313127051|ref|YP_004037321.1|  66 VGFPSVGKSTLINALTNADSEVGaYEFTTLNVNPGMLH 103
                                       899**************999887468999999998764 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                        ATP_bind_1 153 lrlelPhvvvlnkfDllkek.....lekeleffedvealslllekeeekykklaeaiae 206
                                        r+ lP  v +nk+Dl++++     +e+  e+  d+++   +  ++e+  + l+e++ e
  gi|313127051|ref|YP_004037321.1| 231 NRVYLPSMVTVNKADLIDQDylptvNEQLREMDIDPDEAVFISAEKEKGLEGLKETMWE 289
                                       57889*************98977765555666667777766666666666666666655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.3e-05     0.083       2      24 ..      63      85 ..      62      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-05
                            AAA_28  2 ivitGgestGKTtlleaLaargy 24
                                      ++++G +s GK+tl++aL++ + 
  gi|313127051|ref|YP_004037321.1| 63 VALVGFPSVGKSTLINALTNADS 85
                                      899***************98744 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00016      0.16      33      67 ..     189     220 ..     154     235 .. 0.83
   2 ?   -1.9   0.0       5.2   5.2e+03      24      65 ..     227     266 ..     220     271 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHHHHCTT-EE.EEEEEEHSSTTS CS
                             POTRA  33 pekleadkealksryanlGyfdasVqvelpedded 67 
                                       +++++ d+e++k+ +++ Gy++a+V+++    d +
  gi|313127051|ref|YP_004037321.1| 189 TDDVSLDEETIKDVLREYGYVNADVTIRG---DLT 220
                                       678899*******************9877...443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.2
                                       SSSTTSBHCHHHHHHHHHHHHHHHHCTT-EE.EE..EEEE.HSST CS
                             POTRA  24 elkegdvynpekleadkealksryanlGyfdasV..qvel.pedd 65 
                                       ++  ++vy p++++  k     ++ +++y+  +V  q ++ ++d+
  gi|313127051|ref|YP_004037321.1| 227 GIMDNRVYLPSMVTVNKA----DLIDQDYLP-TVneQLREmDIDP 266
                                       466778888888877777....777777776.6744444455555 PP

>> RBD  Raf-like Ras-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.15      14      56 ..     213     257 ..     210     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                               RBD  14 vevkpgetvrdaLekalkkRglnpsacaVylkgs..ekepldwdt 56 
                                       v+++ ++t+ +++++++  R   ps+++V +     +++ + +++
  gi|313127051|ref|YP_004037321.1| 213 VTIRGDLTIDELIDGIMDNRVYLPSMVTVNKADLidQDYLPTVNE 257
                                       899***************************998887666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00024      0.24      16      43 ..      52      81 ..      41      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                            AAA_29 16 tieidlkg..atlltGpsGsGKSTllDAiq 43
                                       + ++  g  ++ l+G   +GKSTl+ A++
  gi|313127051|ref|YP_004037321.1| 52 GYAVEKTGdvTVALVGFPSVGKSTLINALT 81
                                      5556666667889**************997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.26      25      47 ..      61      83 ..      53     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                            AAA_16 25 elvllsGesGvGKsslvrellra 47
                                        v l+G + vGKs+l+++l +a
  gi|313127051|ref|YP_004037321.1| 61 VTVALVGFPSVGKSTLINALTNA 83
                                      6899***************9964 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.7   0.00015      0.15      20      59 ..       3      43 ..       1      46 [. 0.86
   2 ?   -1.8   0.2       3.8   3.7e+03      49      57 ..     152     160 ..     149     169 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                      ABC_tran_CTD 20 LEeeiaeleaeladpelysdp.eklaelsaeleeleaeLee 59
                                      LEeei++l +e+a+  + +     + +l a+l+e +++Le+
  gi|313127051|ref|YP_004037321.1|  3 LEEEIEDLREEIANTPYNKSTeSHIGRLKAKLAEKKEKLEN 43
                                      9************99865444477***************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.8
                      ABC_tran_CTD  49 eleeleaeL 57 
                                       ++e+l++eL
  gi|313127051|ref|YP_004037321.1| 152 RYERLQEEL 160
                                       444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2277.42
//
Query:       gi|313127052|ref|YP_004037322.1|  [L=66]
Description: hypothetical protein Hbor_23170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        0.1   13.0   0.0        2.3    8.7   0.0    2.0  2  Propep_M14  Carboxypeptidase activation peptide


Domain annotation for each model (and alignments):
>> Propep_M14  Carboxypeptidase activation peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00013       2.3      28      55 ..       3      30 ..       1      33 [. 0.92
   2 ?    2.6   0.0    0.0099   1.8e+02      36      58 ..      42      64 ..      37      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00013
                        Propep_M14 28 ppsklgepvdilVppekledfeelLesl 55
                                      +ps+l ++++i+Vp  +l+d++e Le++
  gi|313127052|ref|YP_004037322.1|  3 DPSNLRDSTQIVVPCASLDDVREQLEQR 30
                                      5899999******************985 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0099
                        Propep_M14 36 vdilVppekledfeelLeslgis 58
                                       +i  +p + +++ ++L+++g++
  gi|313127052|ref|YP_004037322.1| 42 CKIIGSPVEIKAVNQFLTRHGVT 64
                                      56666899999*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 437.87
//
Query:       gi|313127053|ref|YP_004037323.1|  [L=121]
Description: hypothetical protein Hbor_23180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
          3    8.0   6.2       0.37   10.9   0.8    2.0  2  Cyt_c_ox_IV      Cytochrome c oxidase subunit IV
        6.3    7.0   6.9         27    5.0   6.9    1.8  1  VKOR             Vitamin K epoxide reductase family


Domain annotation for each model (and alignments):
>> Cyt_c_ox_IV  Cytochrome c oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   4.1e-05      0.37      79     121 ..      10      53 ..       1      60 [. 0.74
   2 ?    0.1   0.8     0.092   8.2e+02      92     103 ..      71      82 ..      48     113 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
                       Cyt_c_ox_IV  79 ffsPhSwwPlvlalaaalaalglalgwWllligvvlvli.alvG 121
                                        +   S wP+++al++ +  +g+ + ++ +++g +l++  +++G
  gi|313127053|ref|YP_004037323.1|  10 QYRMASPWPMFVALGIPISEIGILFDLFPIAVGGLLLFSgSVAG 53 
                                       6777899******************7777776665554314555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.092
                       Cyt_c_ox_IV  92 laaalaalglal 103
                                       +++ l+++g a+
  gi|313127053|ref|YP_004037323.1|  71 IGVLLLVVGGAF 82 
                                       333333333333 PP

>> VKOR  Vitamin K epoxide reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   6.9     0.003        27      45      90 ..      14      78 ..      10     114 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.003
                                      CSTTSEE..TTEEHHHHHHHHHHHHHHHHHS-..................HHHHHHHHHHHHHHH CS
                              VKOR 45 nSpyasi..lgvplsllGllayalvlllalapl.................lwlllllgslagvvf 90
                                      +Sp+  +  lg+p+s +G+l+ ++ ++++ + l                 +w+ l+++ ++ +v+
  gi|313127053|ref|YP_004037323.1| 14 ASPWPMFvaLGIPISEIGILFDLFPIAVGGLLLfsgsvagiaresgyaetPWTPLAAIGVLLLVV 78
                                      56666542279*********999999988777777888888888888887555554444432222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 881.11
//
Query:       gi|313127054|ref|YP_004037324.1|  [L=115]
Description: hypothetical protein Hbor_23190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.014   15.3   0.1    1.0  1  DUF2062   Uncharacterized protein conserved in bacteria (DUF2
      0.032   13.1   0.3      0.037   12.9   0.3    1.1  1  DUF2079   Predicted membrane protein (DUF2079)
      0.094   13.0   0.2       0.14   12.4   0.2    1.2  1  DUF3007   Protein of unknown function (DUF3007)


Domain annotation for each model (and alignments):
>> DUF2062  Uncharacterized protein conserved in bacteria (DUF2062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   2.3e-06     0.014      30      93 ..      15      88 ..      11     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-06
                           DUF2062 30 figflPifglqmllaallalllrvnlpaavagtwisnPltlppiyylayklGalllgeeaeal..........s 93
                                       ++++P++ + +++ a+++++  +  p+a a+ +    + ++++ +l+y  G+ + g+e++++          +
  gi|313127054|ref|YP_004037324.1| 15 TVNVIPLVIIAFFIGAFAVFPAFGVDPLASALQYGLLVVPFVFLAILTYLSGKAIAGDEKRSTvylpgqatvdD 88
                                      6889*****************9999999999999999999999999*********9999988877777665551 PP

>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   6.1e-06     0.037     247     307 ..      12      65 ..       3      87 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-06
                           DUF2079 247 lllflplgflpllsspawLlvalPllllnllsgyspqlslgyqYsllvipflvlaaifgla 307
                                       l l ++++ l+++         +  ++++ + g++ +l+  +qY llv+pf++la+++ l+
  gi|313127054|ref|YP_004037324.1|  12 LDLTVNVIPLVII------AFFIGAFAVFPAFGVD-PLASALQYGLLVVPFVFLAILTYLS 65 
                                       4455555555554......3334444444444444.677889**************99876 PP

>> DUF3007  Protein of unknown function (DUF3007)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   2.4e-05      0.14       6      55 ..      16      65 ..      12      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                           DUF3007  6 vlaiglgvlllgglaylvlqalGldslsagiwsqavlvlglvgWvltYll 55
                                      v +i+l+++++ + a++v+ a+G+d l +     +++v  ++  +ltYl 
  gi|313127054|ref|YP_004037324.1| 16 VNVIPLVIIAFFIGAFAVFPAFGVDPLASALQYGLLVVPFVFLAILTYLS 65
                                      45699999999999**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 839.20
//
Query:       gi|313127055|ref|YP_004037325.1|  [L=581]
Description: cytochrome c oxidase subunit i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     4e-149  497.1  58.9     4e-149  497.1  58.9    1.5  2  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3      0.15   2.7e+03      84     111 ..      14      36 ..       6      44 .. 0.47
   2 !  497.1  58.9  2.2e-153    4e-149       1     432 []      69     517 ..      69     517 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHCSS-STTTTTTTC CS
                              COX1  84 wlvvlgvvllllsllgaattgwteYapl 111
                                        +++++v+ +l+ +     + w  Y pl
  gi|313127055|ref|YP_004037325.1|  14 GVFLVAVAAWLARI-----ENWRTYSPL 36 
                                       13333333333333.....445555555 PP

  == domain 2  score: 497.1 bits;  conditional E-value: 2.2e-153
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCTCT.....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS CS
                              COX1   1 kigllylilalvlllvggllgllirlqlafp.....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgard 72 
                                       +ig+ly + al++++vggl+ +++r++la p     ++++yn l+t Hg++m+flf tp++++f+ny++pll+ a+d
  gi|313127055|ref|YP_004037325.1|  69 DIGILYGAYALIAFAVGGLMVVVMRVELADPgmtliSNTFYNSLLTSHGITMLFLFGTPILAAFSNYFIPLLIDADD 145
                                       599**************************887767677*************************************** PP

                                       -S-HHHHHHHHHHHHHHHHHHHHHHH.....CSS-STTTTTTTC............SHHHHHHHHHHHHHHHHHHHH CS
                              COX1  73 lafprlnalsfwlvvlgvvllllsll.....gaattgwteYapls...........evdlwllglllvvvssllgai 133
                                       +afpr+na++fwl++ +++l++++++       a+t wt+Y+pls           +vdl+llgl+l++vs+++gai
  gi|313127055|ref|YP_004037325.1| 146 MAFPRINAIAFWLLPPAALLIWAGFFpipdvIPAQTAWTMYTPLSagvgngnqvnaGVDLMLLGLHLSGVSATMGAI 222
                                       *************************98776555******************************************** PP

                                       HHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SSSC.E-HHHHHHHHHHHHTH CS
                              COX1 134 nfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslg.kffsp.gdplldqhlfWffgHp 208
                                       nfi+ti+  ra+++t+a+l +f w+vl+ + lil+a+p l  all+llldr++g  ff   gdp+l+qhlfWffgHp
  gi|313127055|ref|YP_004037325.1| 223 NFIATIFSERAEEVTWANLDIFSWTVLTQSGLILFAFPLLGSALLMLLLDRNFGtAFFVNgGDPILWQHLFWFFGHP 299
                                       **********************************************************556**************** PP

                                       HHHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHC CS
                              COX1 209 eVyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglk 285
                                       eVyil+lp +giv+y+lp+f+gr+lf+ k++v+++++i++lsf vwaHH+f tg+++ l+a ++++sl+ia+Ps++k
  gi|313127055|ref|YP_004037325.1| 300 EVYILVLPPMGIVSYVLPRFSGRRLFGFKFVVYSTLAIGVLSFGVWAHHMFATGIDPRLRASFMAVSLAIAIPSAVK 376
                                       ***************************************************************************** PP

                                       CCHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHH CS
                              COX1 286 vfnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyl 362
                                       +fnw++t+w+g+ir++tpml+++gf+  fiigG+tGv+la+ +v++++h+ty+vv+HfH++++ga++f+ fa+iyy+
  gi|313127055|ref|YP_004037325.1| 377 TFNWITTMWNGNIRLTTPMLYCIGFVSNFIIGGVTGVFLASIPVDIILHDTYYVVGHFHYIVMGAITFAGFAGIYYW 453
                                       ***************************************************************************** PP

                                       HHHHHSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
                              COX1 363 lpkltgrmlserlaklhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                                       +p  tgrm++++l+k+hfwl +iG++++f++m++lG+ gmprr+a+y      +p++ ++++++t+g+++
  gi|313127055|ref|YP_004037325.1| 454 FPIYTGRMYQRTLGKAHFWLSMIGTNVTFFAMILLGYGGMPRRYATY------LPQFITMHQIATLGALI 517
                                       ***********************************************......68************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 4392.21
//
Query:       gi|313127056|ref|YP_004037326.1|  [L=97]
Description: hypothetical protein Hbor_23210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.7    8.7   9.1        2.4    8.2   4.4    2.2  2  TPPK_C    Thiamine pyrophosphokinase C terminal


Domain annotation for each model (and alignments):
>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.4   0.00014       2.4      15      35 ..      27      47 ..      21      57 .. 0.81
   2 ?    3.0   0.1    0.0058     1e+02      18      33 ..      75      88 ..      68      95 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00014
                            TPPK_C 15 allllvlAaLvAvavallvsp 35
                                      +++l+++A+L++v+va+ v +
  gi|313127056|ref|YP_004037326.1| 27 YVALVAVAGLAGVLVAVFVDG 47
                                      99***************9976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0058
                            TPPK_C 18 llvlAaLvAvavallv 33
                                       lvl++ +A+++  +v
  gi|313127056|ref|YP_004037326.1| 75 ALVLGIPLALVI--YV 88
                                      577776666654..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 639.35
//
Query:       gi|313127057|ref|YP_004037327.1|  [L=131]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-17   64.5   0.5    4.3e-17   63.0   0.5    1.6  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.045   13.4   0.0    1.3  1  DAGK_cat  Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.5   4.8e-21   4.3e-17       1     140 [.       1     127 [.       1     128 [. 0.90

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 4.8e-21
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHH.CTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelaka.rgaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaae 76 
                                       my+ ++  +D+ +++++ +e  ++l  + ++ +++l+h   + +sga+++   +++e+ ++lee             
  gi|313127057|ref|YP_004037327.1|   1 MYHVVIGIDDEETHAHRCVEAVVNLPGDfDEKKVTLIHSFIDNPSGASATQVHSVREAGEMLEEH------------ 65 
                                       55555545556777779999999999999999999999999999999999999999999999985............ PP

                                       CTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  77 aggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                         g++ +v+  +gdpa +i+ v +e dadliVvG r+rs   ++l+GSv+++v+  a+ pV+v+
  gi|313127057|ref|YP_004037327.1|  66 --GIEYTVEESSGDPANAIVSVGDETDADLIVVGGRKRSPAGKALFGSVTQSVILGATRPVMVT 127
                                       ..99**********************************************************95 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     5e-06     0.045       5      63 ..      41      98 ..      37      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5e-06
                                      EE-TTCTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEE CS
                          DAGK_cat  5 ivNpksGkgkgekllrkvrelleeagvelelieteepgdakelakeakeegvdlivvaG 63
                                      i Np + + +  + +r++ e+lee+g+e+++ e +  + a+++++  +e+++dlivv G
  gi|313127057|ref|YP_004037327.1| 41 IDNPSGASATQVHSVREAGEMLEEHGIEYTVEESS-GDPANAIVSVGDETDADLIVVGG 98
                                      556766666666777*****************997.7889999*999999999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 981.96
//
Query:       gi|313127058|ref|YP_004037328.1|  [L=251]
Description: acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-18   65.5   0.0    9.5e-18   64.5   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.4e-14   53.3   0.0      4e-14   52.6   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.7e-12   47.6   0.1    4.1e-12   46.3   0.0    1.6  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.3e-07   30.4   0.4    9.7e-07   29.5   0.1    1.6  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
    8.7e-06   25.9   0.0    1.2e-05   25.5   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.4e-05   25.2   0.9      8e-05   22.7   0.2    2.3  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
    1.7e-05   24.7   0.0    3.5e-05   23.7   0.0    1.5  1  FR47             FR47-like protein
      0.002   18.2   0.0     0.0051   16.9   0.0    1.7  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.056   13.1   0.1    2.0  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   4.7e-21   9.5e-18      21     117 .]      45     140 ..      15     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 4.7e-21
                                       HHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE CS
                    Acetyltransf_1  21 eeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikki 97 
                                        +   e++ ++a +++va +dg ++Gf++ +     ++ v++i+ l+V p++rg G+Gs+Ll+ +e+++  +g+++i
  gi|313127058|ref|YP_004037328.1|  45 DDTLSEWLTDDAVEFIVAVDDGDVVGFVQSYVSEG-RETVGEIDWLHVIPDHRGEGIGSQLLKRAEQELTTRGVDRI 120
                                       2236677888999********************99.99*************************************** PP

                                       EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  98 vlaveedndaairlYeklGF 117
                                       +  v +dn+a   +Y + GF
  gi|313127058|ref|YP_004037328.1| 121 EGSVLADNEAGADFYAEQGF 140
                                       99*************88*99 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0     2e-17     4e-14       8     115 ..      33     149 ..      26     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2e-17
                   Acetyltransf_10   8 egietf.kefispealrerieegealllvaeeggkivGvi.el.rdgs....hisllfVdpeyrgqGigkaLleave 77 
                                       e ie+  +    +++l+e++++ ++ ++va ++g +vG++ ++ ++g+    +i  l V p++rg Gig++Ll+++e
  gi|313127058|ref|YP_004037328.1|  33 ETIEEAvEGWYGDDTLSEWLTDDAVEFIVAVDDGDVVGFVqSYvSEGRetvgEIDWLHVIPDHRGEGIGSQLLKRAE 109
                                       44433334444569**************************533344448899************************* PP

                   Acetyltransf_10  78 eeaekdgikl.eltvnasp.yavpfYeklGFkavgeeqee 115
                                       +e+ ++g    e +v a++ +  +fY  +GF+++++ + e
  gi|313127058|ref|YP_004037328.1| 110 QELTTRGVDRiEGSVLADNeAGADFYAEQGFERTDDRRIE 149
                                       *******************8889***********887765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   2.1e-15   4.1e-12       4      76 .]      58     142 ..      55     142 .. 0.78
   2 ?   -2.6   0.0       3.9   7.8e+03       4      12 ..     183     194 ..     180     214 .. 0.62

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.1e-15
                                       EEEEEEETTEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHH.HTT....SEEE.EEEEEE.THHHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld.....aeitrlaVdpeyrgkGiGraLle.aae....kgii.leqlel.naekaikf 68 
                                       e++Va ddg +vGf+  ++++     +ei +l V p++rg GiG++Ll+ a++    +g+  +e + l ++e+ ++f
  gi|313127058|ref|YP_004037328.1|  58 EFIVAVDDGDVVGFVQSYVSEgretvGEIDWLHVIPDHRGEGIGSQLLKrAEQelttRGVDrIEGSVLaDNEAGADF 134
                                       799************9999889999999999*****************9552245665644333334424446678* PP

                                       HHHTTEEE CS
                    Acetyltransf_7  69 YeklGFee 76 
                                       Y+  GFe+
  gi|313127058|ref|YP_004037328.1| 135 YAEQGFER 142
                                       ******95 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.9
                                       EEEEEEET...T CS
                    Acetyltransf_7   4 evfVaedd...g 12 
                                       +v++a+dd   g
  gi|313127058|ref|YP_004037328.1| 183 TVYIAYDDavrG 194
                                       678787763331 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   4.9e-10   9.7e-07       4     138 .]       3     141 ..       1     141 [. 0.77
   2 ?   -1.9   0.0       2.5     5e+03      44      57 ..     197     215 ..     157     229 .. 0.53

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.9e-10
                    Acetyltransf_3   4 LrplteeDlealfelrsdpevmry.lpepltleeaeewlera........waeeseeegygwaivlkdtgviGsvgl 71 
                                       Lr +t +D+ ++   +++ e m++ +++  ++e  ee +e +        w    +++++ +++ + d++v+G+v  
  gi|313127058|ref|YP_004037328.1|   3 LRDATTSDIRQIRT-VAN-ESMKAsYRHAIDEETIEEAVEGWygddtlseW---LTDDAVEFIVAVDDGDVVGFVQS 74 
                                       78889999999864.443.45665567755555555555544444464444...44577889998888889****99 PP

                    Acetyltransf_3  72 rdleeedeeaelgymla.psfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       +  e++++ +e++++   p+++g G+++  ++ + + + ++ g++r++  + ++Nea +  +   Gfe
  gi|313127058|ref|YP_004037328.1|  75 YVSEGRETVGEIDWLHViPDHRGEGIGSQLLKRAEQEL-TTRGVDRIEGSVLADNEAGADFYAEQGFE 141
                                       999999999*****977799******************.7778*************988888888875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                    Acetyltransf_3  44 a.....waeeseeegygwa 57 
                                       a     + +++e+e ygw+
  gi|313127058|ref|YP_004037328.1| 197 ApfyavYMNPEENERYGWM 215
                                       0333334444555555554 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   6.2e-09   1.2e-05       1     139 [.       3     145 ..       3     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 6.2e-09
                    Acetyltransf_4   1 iraateeDakeilaiyaey...vvntaitfeyevssveefe..kflealdsekeyvflvae.sdrivGyaylgqfkk 71 
                                       +r+at +D+ +i+ + +e      + ai++e  +++ve       l++  ++    f va  ++++vG  +    + 
  gi|313127058|ref|YP_004037328.1|   3 LRDATTSDIRQIRTVANESmkaSYRHAIDEETIEEAVEGWYgdDTLSEWLTDDAVEFIVAVdDGDVVGFVQSYVSEG 79 
                                       699************97754234556999998888888443247888887889999999888******999987777 PP

                    Acetyltransf_4  72 rakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgi 139
                                         ++  +e+  + +  d + eg+g++l++  eq l   ++ +++ ++ ++ne+ ++f+++ GFe + +
  gi|313127058|ref|YP_004037328.1|  80 --RETVGEIDWLHVIPDHRGEGIGSQLLKRAEQELTTRGVDRIEGSVLADNEAGADFYAEQGFERTDD 145
                                       ..7777777665554589*********************************************97765 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2     4e-08     8e-05       2     107 ..       3     117 ..       2     143 .. 0.85
   2 ?    0.4   0.0      0.32   6.5e+02      18      55 ..     152     194 ..     145     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4e-08
                                       EEEE-GGGHHHHHHHHHHHTT----H.....HHHHHHHHHHTTS...........EEEEEEETTEEEEEEEEEEEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespl..e.eireyfrkllees...........rvlgaedngelvgqlallplel 64 
                                       +r +t++d+ ++  + +++ + + +++  e +i+e+++  ++++           ++++a d+g++vg ++ +    
  gi|313127058|ref|YP_004037328.1|   3 LRDATTSDIRQIRTVANESMKASYRHAidEeTIEEAVEGWYGDDtlsewltddavEFIVAVDDGDVVGFVQSY---- 75 
                                       799**********************999955777888888884444444455567*************99876.... PP

                                       EETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT- CS
                    Acetyltransf_9  65 nvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegq 107
                                        v + + +++ + +  v p+hrg+g+ s+Ll+ra +e+  +g+
  gi|313127058|ref|YP_004037328.1|  76 -VSEGRETVGEIDWLHVIPDHRGEGIGSQLLKRAEQELTTRGV 117
                                       .7778889******************************99987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.32
                                       HHHTT----H.......HHHHHHHHHHTTSEEEEEEETTEEEE CS
                    Acetyltransf_9  18 kyaFqdeespl....e.eireyfrklleesrvlgaedngelvg 55 
                                       +++F++++  +    e e+    +++l+++r++ + +++ + g
  gi|313127058|ref|YP_004037328.1| 152 EESFEEQTYTQrlddEgERIITEERTLDDGRTVYIAYDDAVRG 194
                                       5566666655556655556666788888888887777777665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.8e-08   3.5e-05      18      82 ..      80     145 ..      70     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.8e-08
                                       E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEEEE CS
                              FR47  18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfekiee 82 
                                       r+ +ge+  l v p+hr++G gs+l k   +e+ +rg + +   v a+N++   +y   Gfe  + 
  gi|313127058|ref|YP_004037328.1|  80 RETVGEIDWLHVIPDHRGEGIGSQLLKRAEQELTTRGVDRIeGSVLADNEAGADFYAEQGFERTDD 145
                                       5678********************************9765516788999999*********98754 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.6e-06    0.0051       2      57 ..      59     116 ..      58     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                   Acetyltransf_CG   2 feltldegeevafl.eYe.vrkegvldfthTeVpeelrGkGiAkkLvkaalddareeg 57 
                                       f + +d+g+ v+f+ +Y  + +e v +++   V + +rG+Gi+++L k+a ++   +g
  gi|313127058|ref|YP_004037328.1|  59 FIVAVDDGDVVGFVqSYVsEGRETVGEIDWLHVIPDHRGEGIGSQLLKRAEQELTTRG 116
                                       66778889999**9779613444477999999*****************988877666 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.8e-05     0.056      40     141 ..      53     144 ..      36     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                                       .STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--E CS
                    Acetyltransf_8  40 adphsepliglldgepvgyfeiYwakedelaeyydaepgdrGiHlligeaeargkglttallralvhylfadprtrr 116
                                       +d+ +e +++  dg  vg++++Y  +           +    i+ l   +++rg+g++++ll++  + l ++ +++r
  gi|313127058|ref|YP_004037328.1|  53 TDDAVEFIVAVDDGDVVGFVQSYVSEGR---------ETVGEIDWLHVIPDHRGEGIGSQLLKRAEQELTTR-GVDR 119
                                       4777777788888899999999966655.........44444556666699************998888887.**** PP

                                       EEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8 117 vvvEPdvrNerairllekaGfekek 141
                                       + +   ++Ne+   +++++Gfe+ +
  gi|313127058|ref|YP_004037328.1| 120 IEGSVLADNEAGADFYAEQGFERTD 144
                                       *********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1733.73
//
Query:       gi|313127059|ref|YP_004037329.1|  [L=537]
Description: acyl-CoA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-94  316.2   2.5    3.1e-94  316.0   2.5    1.0  1  AMP-binding    AMP-binding enzyme
    5.2e-21   75.4   0.1    1.6e-20   73.8   0.1    1.9  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.0   2.5   3.5e-98   3.1e-94       4     422 ..      13     428 ..      10     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: 316.0 bits;  conditional E-value: 3.5e-98
                                       HHHHST.TSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                       AMP-binding   4 qaaktp.dkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                       +a+++  dk a+v   +g ++TY+el er++ ++a+L ++G++kgdrVa+l pn++ ++ a+++++++Gav+ pln 
  gi|313127059|ref|YP_004037329.1|  13 RARQYYgDKEAVVA-TTGDRYTYEELGERADGFSAALAAHGIEKGDRVAVLDPNTHYHLEAAYGTMQLGAVHTPLNY 88 
                                       5555555*****99.789********************99************************************* PP

                                       TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS- CS
                       AMP-binding  80 tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeel 156
                                       +l +++ +yil+d+++k++    d e +ek+++++++  +++++ v+ + +  + ++l ++e  +e++  + + +e 
  gi|313127059|ref|YP_004037329.1|  89 RLVPADYEYILTDADVKAVY--ADYEYAEKIEAIRDD--VPTETFVTNDTAQVDGDWLSFDELIAEST--DYDRPEM 159
                                       ********************..676778999999884..56667777878888899999999999887..4566689 PP

                                       BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE CS
                       AMP-binding 157 kpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvl 233
                                       ++d+l++i YTSGTTG PKGV  +hr  +  ++ +  + ++ +++ddv+l++lp++h+ g+   ++++  +Ga+ v+
  gi|313127059|ref|YP_004037329.1| 160 TEDELITINYTSGTTGDPKGVCRTHRTETLHAYLI--TSHQHISDDDVYLWTLPMFHVNGW-GHIYAVTGNGAKHVC 233
                                       *************************6544443553..44566789****************.*************** PP

                                       -TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC CS
                       AMP-binding 234 lpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfge 309
                                        ++ +a   + +++++++++v++++++P+vl++l++  ++    ++  d + +r   ++g++++++++r +++ fg 
  gi|313127059|ref|YP_004037329.1| 234 TRGVDA---EWIFDTVREEHVSYMCAAPTVLNMLMDyYDKQGGVETTGDVP-VRA-ATAGAAPPEATIRTVEDEFGW 305
                                       998877...5679***********************654444333333443.776.48******************* PP

                                       EEEEEEEEGGGSSECEE........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSE.EEEEEEETTS-SE CS
                       AMP-binding 310 evlegYGlTEttgvvtv........lpleedkkklgsvGkplpgvevkivDeetgepvpdgee.Gellvrgpgvmkg 377
                                        ++++YG TEt++ +t+        ++ +++ ++++ +G    g++v++vDe+++   +dg++ Ge++vrg++vm  
  gi|313127059|ref|YP_004037329.1| 306 YLMHVYGATETGPLITTsdarrffdDDSDDRFAVKKQQGIGYLGTDVRVVDEDGEDVARDGQTvGEIVVRGNQVMDR 382
                                       ***************9999****98665777778888999999**********55555788889************* PP

                                       BTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 378 Ylkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                       Y++kpeat eaf++  +++++ GDl+++de+G + i +Rkkd+i++
  gi|313127059|ref|YP_004037329.1| 383 YWNKPEATDEAFTDRlEGYYHMGDLAVVDENGFITIQDRKKDIIIS 428
                                       ************985668**************************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.1   1.8e-24   1.6e-20       1      76 []     437     516 ..     437     516 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.8e-24
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE----.--...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-T CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgs.ea...leeeLkahvrkelgpyavpkkvvfvdelpktr 73 
                                       e+E +l  h+aV ++aV+ +p e +Ge ++afVv++ g  ++   ++++L+a+ r+++++y+vpk+++fv elpkt+
  gi|313127059|ref|YP_004037329.1| 437 ELEDTLFDHDAVGDVAVIPMPSEEWGESPKAFVVPAHGDaDDpgvTADDLIAYTRERIATYKVPKEIEFVTELPKTA 513
                                       89*********************************7674233589******************************** PP

                                       TS- CS
                     AMP-binding_C  74 sGK 76 
                                       +GK
  gi|313127059|ref|YP_004037329.1| 514 TGK 516
                                       **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3631.52
//
Query:       gi|313127060|ref|YP_004037330.1|  [L=83]
Description: hypothetical protein Hbor_23250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 564.81
//
Query:       gi|313127061|ref|YP_004037331.1|  [L=659]
Description: acetyl-coenzyme a synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-91  306.1   0.0    3.8e-91  305.8   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    2.8e-24   85.9   1.2    5.3e-24   85.0   1.2    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    6.9e-15   54.7   2.9    2.3e-14   53.1   2.9    1.9  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.8   0.0   6.3e-95   3.8e-91       6     422 ..      93     535 ..      87     536 .. 0.86

  Alignments for each domain:
  == domain 1  score: 305.8 bits;  conditional E-value: 6.3e-95
                                       HHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                       AMP-binding   6 aktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                       +  +++va+ +   +ge +t+TY++l+++vn++Aa+L+ lGv+++d+V +++p+ pe+ +a+la++++Ga ++++ +
  gi|313127061|ref|YP_004037331.1|  93 NGDKNRVAIKWegeHGETRTYTYQDLYREVNEFAAALLDLGVEEDDVVTMYMPMVPELPIAMLACARIGAPHSVVFA 169
                                       4456999999899999************************************************************* PP

                                       TS-HHHHHHHHHHHTESEEE.........ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT CS
                       AMP-binding  80 tltaeelayiledseakvli.........atvdselleklleaaakleavklvivldadellkeeelkeeeeseeka 147
                                       +++a++la  ++++e+++l+         ++  ++l ++++   + ++ v++++v+d+ + +     ++ +++++++
  gi|313127061|ref|YP_004037331.1| 170 GFSADALATRMNSAESRFLVtcdgyyrrgDA-LDHLEKANDGLGGVDHGVDATVVVDRLGDDGF--GHDLKGNQHDW 243
                                       ********************99988764312.22223334444444555677777776654433..33444444444 PP

                                       S........-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCH CS
                       AMP-binding 148 e........kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahif 215
                                       +        + +e+++ +++d+++++YTSGTTG+PKGV ++++ ++a +++   ++   ++k++d++++ +++ +i+
  gi|313127061|ref|YP_004037331.1| 244 DdlldthdgERVEPVARDAEDMLFLMYTSGTTGEPKGVKHTTGGYLAYTSWT--SHAvLDIKPEDTYWCSADIGWIT 318
                                       24567888856688899*************************9998886664..333566899************** PP

                                       HHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEE CS
                       AMP-binding 216 glilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvll 290
                                       g+++ ++++l+ G t v+++++++ ++ ++l+el+ek+ v v++++P++++a+++   ++    +++dlsslrl+ +
  gi|313127061|ref|YP_004037331.1| 319 GHSYIVYGPLSLGTTTVMYEGTPDfPERDRLWELVEKYAVDVFYTAPTAIRAFMKwGTEFP---ERRDLSSLRLLGT 392
                                       ************************5559999************************776665...678********** PP

                                       ESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTS CS
                       AMP-binding 291 ggeplspellrffralfge...evlegYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdge 363
                                       +gep++p ++++++++ g+   +v++++++TEt+g++++ lp    + k+gs+G+plpg+++++vD+  ge+v+ g 
  gi|313127061|ref|YP_004037331.1| 393 VGEPINPRAWKWYYKHIGNeecPVVDTWWQTETGGMMVTtLP-GIGTMKPGSAGPPLPGIDARVVDPG-GEEVEAGR 467
                                       ******************9******************66466.4455789*****************7.******** PP

                                       EEEEEEEET..TS-SEBTT-HHHHHHHEEE......TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 364 eGellvrgp..gvmkgYlkkpeataeafds......egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                        G l v +p  g+ +  ++++e+  + +++       ++  +   D +++dedGy+ i+gR +d++++
  gi|313127061|ref|YP_004037331.1| 468 AGYLTVNKPwpGMLRTLYNNDERFISEYWEeysdpdADEwVYFPEDGAKIDEDGYITILGRVDDVLNV 535
                                       ********9778***********9999997788875255589999********************987 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   1.2   8.8e-28   5.3e-24       1      76 []     544     622 ..     544     622 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 8.8e-28
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       e+Esa+v +++VaeaaVvG ++evkGea+ a+V+l+dg   +++++++++a v++++gp+a+p++vvf++elpktrs
  gi|313127061|ref|YP_004037331.1| 544 EIESAIVGVEGVAEAAVVGGDHEVKGEAVYAYVILEDGyegTDEMRDKIVAGVEDAIGPIARPEQVVFTPELPKTRS 620
                                       8**********************************999642345********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|313127061|ref|YP_004037331.1| 621 GK 622
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   2.9   3.8e-18   2.3e-14       4      55 .]      35      86 ..      33      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 3.8e-18
                                      HHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  4 lykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      +y+e  ed    W+++a+ ldW++++d+vld+s++pf++WF++G+lN++yNc
  gi|313127061|ref|YP_004037331.1| 35 IYDEFEEDWPHSWERAAEMLDWFEDYDEVLDDSEEPFYEWFVNGTLNASYNC 86
                                      678888888888**************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 4422.40
//
Query:       gi|313127062|ref|YP_004037332.1|  [L=567]
Description: methylmalonyl-CoA mutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.8e-214  713.1   0.3     2e-214  712.9   0.3    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
  ------ inclusion threshold ------
      0.021   13.3   0.1      0.046   12.2   0.1    1.5  1  Met_asp_mut_E  Methylaspartate mutase E chain (MutE)


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  712.9   0.3  2.2e-218    2e-214       2     513 .]      38     557 ..      37     557 .. 0.98

  Alignments for each domain:
  == domain 1  score: 712.9 bits;  conditional E-value: 2.2e-218
                     MM_CoA_mutase   2 TaegievkplYtaedl.eek.klgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtgls 76 
                                       T +++ev+ lYt++d+ + + +    +PGe+PftRG+++tmyrgr+Wt+rq+agf+taeetner+++l+++Gqtgls
  gi|313127062|ref|YP_004037332.1|  38 TISNLEVDDLYTPNDVaDLDfEEDLGFPGEYPFTRGPYPTMYRGRTWTMRQFAGFGTAEETNERFHYLIDEGQTGLS 114
                                       8899************8333444456*************************************************** PP

                     MM_CoA_mutase  77 vafdlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdlek 153
                                       +afd+p+l+g Dsd+p a gevGk+Gva+d+l+dme+l+dgid+ +vs+s+tin +a+ ++amy+a+a++qgv++e+
  gi|313127062|ref|YP_004037332.1| 115 TAFDMPSLMGKDSDDPLADGEVGKEGVAVDTLRDMEILFDGIDVGEVSTSFTINPSAPVIYAMYIALADQQGVPREE 191
                                       ***************************************************************************** PP

                     MM_CoA_mutase 154 lsgtiqnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvr 230
                                       ++gt+qnD+Lke++a++++++ppepsl+l++d++++aa+++pkf++isvsgyhireaG+tavqElAftladG++Yv+
  gi|313127062|ref|YP_004037332.1| 192 IRGTLQNDMLKEFIAQKEWVIPPEPSLELVTDTVAFAAEQTPKFHPISVSGYHIREAGSTAVQELAFTLADGFAYVE 268
                                       ***************************************************************************** PP

                     MM_CoA_mutase 231 alleaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvN 307
                                        +l++G+dvd +ap lsFff+ ++ +fee+Ak+RAaRr++ar+++e ++a++ +s +l++h+qT+g sltaq+p +N
  gi|313127062|ref|YP_004037332.1| 269 DALDRGMDVDVVAPLLSFFFNSHNSIFEEVAKFRAARRIYARVMEEWYDAEKSESKRLKFHTQTAGQSLTAQQPLNN 345
                                       ***************************************************************************** PP

                     MM_CoA_mutase 308 ilRttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekaw 384
                                       i+R+t++ala+vlggtqslhtns+DealalP+e+++r+A++tq+i+aeEsg a+v+DPlgGS++vE+LTde++e+a+
  gi|313127062|ref|YP_004037332.1| 346 IVRVTIQALAGVLGGTQSLHTNSYDEALALPSEEAVRVALRTQQIIAEESGAADVIDPLGGSFFVESLTDEVEEEAM 422
                                       ***************************************************************************** PP

                     MM_CoA_mutase 385 klfqeieeaG......GmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerq 455
                                       ++++ei+e+G      G+l  i +G++++ei+e+++++q+++e+++e++vGvNk++  +e+++ ++l +dee++erq
  gi|313127062|ref|YP_004037332.1| 423 AYIEEIREMGdgsvrdGILTGIGEGYFHREIQEASYEYQERVEDEEEIVVGVNKYT-MDEDTRPDLLMVDEETQERQ 498
                                       *******************************************************5.666789************** PP

                     MM_CoA_mutase 456 aerlealraerdeaavkaaLaalgeaarse.nllaraveaaralatlGeisdaleevfg 513
                                        erle+++aerd+++v+aaL++++ea++ + n+++++++a++a+at+Gei+d++ e+ g
  gi|313127062|ref|YP_004037332.1| 499 LERLENVKAERDDEEVEAALDEIQEAVEAGdNVMPALIAAVKAYATMGEIMDVFAEEHG 557
                                       ****************************889**********************998765 PP

>> Met_asp_mut_E  Methylaspartate mutase E chain (MutE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.1e-06     0.046     267     362 ..     349     448 ..     289     461 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-06
                     Met_asp_mut_E 267 islgaavaalakatkvivKtphEalgvptkeanaaglratkqvlnlledqklee....teeleeekelikketrail 339
                                       +++ a + +l++++ + + + +Eal  p++ea   +lr+ + + +     ++ +    +  +e+ ++ +++e+ a +
  gi|313127062|ref|YP_004037332.1| 349 VTIQALAGVLGGTQSLHTNSYDEALALPSEEAVRVALRTQQIIAEESGAADVIDplggSFFVESLTDEVEEEAMAYI 425
                                       5667888999****************************98888776666665531211445788889999******* PP

                     Met_asp_mut_E 340 dkvlelgdGDvavgavrafeaGv 362
                                       +++ e+gdG v+ g++ ++ +G 
  gi|313127062|ref|YP_004037332.1| 426 EEIREMGDGSVRDGILTGIGEGY 448
                                       ****************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3823.34
//
Query:       gi|313127063|ref|YP_004037333.1|  [L=204]
Description: nitrous oxide reduction lipoprotein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-40  138.2   0.2    2.4e-40  137.9   0.2    1.1  1  NosL        NosL
      0.002   17.9   3.9     0.0035   17.1   3.9    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.24   11.1   0.0    1.5  1  PRY         SPRY-associated domain


Domain annotation for each model (and alignments):
>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9   0.2     4e-44   2.4e-40       2     131 .]      52     199 ..      51     199 .. 0.94

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 4e-44
                              NosL   2 veltaeaecdvCgMliaehpgpkgqifyede.....depakFcstrdlfafllepeerk.eikaiyvtDmsavdw.. 70 
                                       v++ ++++c+vCgM+i + pgp  +ify+d+     d+pa+F+s+ +++++ +e+++++ +  a+yvtD+s+v++  
  gi|313127063|ref|YP_004037333.1|  52 VTIPEGSTCEVCGMNIRQNPGPITEIFYQDKqpnghDNPARFDSVWEAYQYEFEKDDAGwTDVAFYVTDYSSVEYrt 128
                                       789999************************446677***************************************** PP

                              NosL  71 ..........esp.daeafidakkalyVvgsdveGaMGpelvpFsdeadAeaFaaehgGkvlrfedvteelv 131
                                                   + +++af+ a++++yVv+s+v+GaMG++lvpFs+++dAe+F++e gG+++++++vt+e++
  gi|313127063|ref|YP_004037333.1| 129 feeggdtfisS-NyESSAFVPATEVTYVVDSSVKGAMGRDLVPFSKASDAESFQSEFGGSLATHDEVTPEVI 199
                                       ********743.369*****************************************************9975 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.9   5.8e-07    0.0035       4      24 ..      15      35 ..      12      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.8e-07
                        TAT_signal  4 RRdFLKgsAAaaAAaalggca 24
                                      RR+FL +sA+++AA ++g ++
  gi|313127063|ref|YP_004037333.1| 15 RRHFLLASAGVGAASLAGCLG 35
                                      ************988666655 PP

>> PRY  SPRY-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.9e-05      0.24      22      41 ..      78      97 ..      75      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.9e-05
                               PRY 22 rysedrqslpdnpeRFdscp 41
                                       y++++ + +dnp RFds +
  gi|313127063|ref|YP_004037333.1| 78 FYQDKQPNGHDNPARFDSVW 97
                                      6889999**********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1333.23
//
Query:       gi|313127064|ref|YP_004037334.1|  [L=661]
Description: nitrous oxidase accessory protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-30  103.8  21.2    1.4e-14   54.3   4.5    2.3  3  Beta_helix       Right handed beta helix region
      1e-29  103.5   0.2    6.9e-28   97.5   0.1    2.1  2  NosD             Periplasmic copper-binding protein (NosD)
    3.1e-12   47.0   0.0      7e-12   45.8   0.0    1.6  1  NosL             NosL
    1.2e-10   41.6   5.5    4.7e-10   39.7   1.3    3.0  2  Pectate_lyase_3  Pectate lyase superfamily protein


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.4   2.3e-17     1e-13      22     157 ..     330     464 ..     312     465 .. 0.94
   2 !   54.3   4.5   3.1e-18   1.4e-14       1     157 [.     354     506 ..     354     512 .. 0.92
   3 !   24.7   2.8   3.9e-09   1.8e-05      71     157 ..     426     506 ..     425     541 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.3e-17
                                       SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---....SEEE-TT--S--EEES-EEES-SS-S CS
                        Beta_helix  22 ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn....gggialfgasnnlienneitdnggsG 94 
                                       g+++i l+++++ v+ + +i     sG+ ++ s++++++n t+++      g+  a+  + ++++e ++++d ++ G
  gi|313127064|ref|YP_004037334.1| 330 GDAAIVLDDADRGVVADVTIDT-PASGVIVRHSNESVLRNLTVNGADtaseGFMGAILIGARSVVEESTFYDGRD-G 404
                                       899*******************.********************99889999999*******************99.* PP

                                       EE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E CS
                        Beta_helix  95 iylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNt 157
                                       +y++ ++  ++++N++   + +G++ +++s ++ vt+N++ ++   Gi v+++ +n+ +++N 
  gi|313127064|ref|YP_004037334.1| 405 VYTHRADGSVVRENQFAPGR-YGVHEMYTS-ETLVTDNVVRDAQ-MGIIVMTRPTNNLIVGNE 464
                                       ****************9999.*********.999*********7.***************996 PP

  == domain 2  score: 54.3 bits;  conditional E-value: 3.1e-18
                                       -SEEE-SS-E.EEESEEEES-.....SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE CS
                        Beta_helix   1 sgisingssnvtiknntisns.....ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggi 72 
                                       sg++++ s++  ++n t++++     g  G  l g+++ v+e++++++ + +G+y+++++++++++n++  +  +g+
  gi|313127064|ref|YP_004037334.1| 354 SGVIVRHSNESVLRNLTVNGAdtaseGFMGAILIGARS-VVEESTFYD-GRDGVYTHRADGSVVRENQFAPGR-YGV 427
                                       699999999999***********999999999999999.*********.*********************999.*** PP

                                       -TT--S--EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-S CS
                        Beta_helix  73 alfgasnnlienneitdnggsGiyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgss 148
                                       + +++s +l+ +n ++d    Gi ++   +nn i +N +++ +  Giv   ++   +   N++++n  +G++v+g+ 
  gi|313127064|ref|YP_004037334.1| 428 HEMYTSETLVTDNVVRDAQM-GIIVMtRPTNNLIVGNEVRDSE-FGIVPAGGD--SYYAENVVVGNE-YGLQVAGDR 499
                                       ******************87.99999679*************9.*********..888********8.***888888 PP

                                       S--EEES-E CS
                        Beta_helix 149 snvtvrnNt 157
                                       +  t++ N+
  gi|313127064|ref|YP_004037334.1| 500 N--TFAANV 506
                                       7..555554 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 3.9e-09
                                       EE-TT--S--EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT CS
                        Beta_helix  71 gialfgasnnlienneitdnggsGiyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvg 146
                                       g++ +++s +l+ +n ++d    Gi ++   +nn i +N +++ +  Giv   ++   +   N++++n  +G++v+g
  gi|313127064|ref|YP_004037334.1| 426 GVHEMYTSETLVTDNVVRDAQM-GIIVMtRPTNNLIVGNEVRDSE-FGIVPAGGD--SYYAENVVVGNE-YGLQVAG 497
                                       6777788888888888888866.7777756888888888888888.888888888..667888888887.8886666 PP

                                       -SS--EEES-E CS
                        Beta_helix 147 sssnvtvrnNt 157
                                       + +  t++ N+
  gi|313127064|ref|YP_004037334.1| 498 DRN--TFAANV 506
                                       666..444443 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.0    0.0066        30      60     103 ..     331     374 ..     291     389 .. 0.71
   2 !   97.5   0.1   1.5e-31   6.9e-28      27     234 ..     391     582 ..     382     588 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0066
                              NosD  60 ryGihlensesntiedntlssnesGialmsssnntlenNtisnn 103
                                       +++i+l+++++ ++ d t++   sG+++  s++++l+n t+++ 
  gi|313127064|ref|YP_004037334.1| 331 DAAIVLDDADRGVVADVTIDTPASGVIVRHSNESVLRNLTVNGA 374
                                       55666666666666666666666777776666666666555554 PP

  == domain 2  score: 97.5 bits;  conditional E-value: 1.5e-31
                              NosD  27 seisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnn.tlenNtisn 102
                                       s++++ +  ++rdg++   +++  +++n++  +ryG+h ++++++ ++dn++++ ++Gi++m    n  + +N++++
  gi|313127064|ref|YP_004037334.1| 391 SVVEESTFYDGRDGVYTHRADGSVVRENQFAPGRYGVHEMYTSETLVTDNVVRDAQMGIIVMTRPTNnLIVGNEVRD 467
                                       67899999*****************************************************9998665********* PP

                              NosD 103 nenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkyd 179
                                       +e  Gi   + + +  ++N+++ n++G+++ + ++nt+  N + +n ++G+  ++   +n++++N+ + n   v+ +
  gi|313127064|ref|YP_004037334.1| 468 SEF-GIVPAGGD-SYYAENVVVGNEYGLQVAG-DRNTFAANVVVGN-DVGLRATDILPSNWVVRNDVVANARRVASN 540
                                       *88.*9998888.6799***************.8************.*****************************9 PP

                              NosD 180 gsnnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYeindgviDy 234
                                        +   +W++ +             GNyW      DadgDG+ D +Y+++++v D 
  gi|313127064|ref|YP_004037334.1| 541 LGPLRTWTHHG------------VGNYWGALPLPDADGDGVYDRAYQPSGSV-DA 582
                                       999****9999............9************************9998.75 PP

>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   1.6e-15     7e-12      54     127 ..     100     183 ..      63     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.6e-15
                              NosL  54 rkeikaiyvtDmsavdw..........espdaeafidakkalyVvgsdveGaMGpelvpFsdeadAeaFaaehgGkv 120
                                        +++ a+yv+D+s+ +           e+ +a  +++a++a++Vvgs+++ + Gp ++pFs+++dA++Faa++gG+v
  gi|313127064|ref|YP_004037334.1| 100 FGRPLAVYVSDFSTISPtlsedgfvvpEQGRAVGWTAAESAHFVVGSEARVPSGPAVLPFSKRQDATQFAAANGGDV 176
                                       347899*******88889999999997666899******************************************** PP

                              NosL 121 lrfedvt 127
                                       ++++ ++
  gi|313127064|ref|YP_004037334.1| 177 VDWKTLQ 183
                                       *998765 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   1.3     1e-13   4.7e-10      24     207 ..     237     420 ..     228     450 .. 0.76
   2 ?    2.1   0.2     0.032   1.4e+02     153     207 ..     476     531 ..     453     556 .. 0.58

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1e-13
                                       HH......HTSS-EEE-SEEEEESS-EEE-SSEEEEES-TTTEEEEE-TT-SS--SEEES-TTT-......-EEEEE CS
                   Pectate_lyase_3  24 aiscasatttgavVYfPaGtYlvsspiilksgvqLvGdgngrpvlkaaaafvgaglidgdpyvsg....gsealiat 96 
                                       a+   +a + + +V++PaGtY+v+s +  +  v++ G+g  ++v+++ ++ +  +l  +   v++    g  + + +
  gi|313127064|ref|YP_004037334.1| 237 AV---EAAPANTTVFLPAGTYRVDSVV-VNRSVTIAGAG-PQTVIRGDGNGTVFHLRADGAAVTDlritG-VGDVGS 307
                                       44...889999***************9.8999*******.789999988885555554444444433222.566788 PP

                                       EEEEEEGGGG-SS---S.SEEE..ES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-S CS
                   Pectate_lyase_3  97 nnfyrqirnlkiditav.apga..tgihwqtaqatslenvefemseasgtkhqgifiengsggflndlvfsglgdig 170
                                         f+r   +l  d+t   a g+  ++i    a++  + +v+++ + as     g++++++++++l++l+++g  d++
  gi|313127064|ref|YP_004037334.1| 308 RGFDRRNETLNWDTTVQlAYGYgdAAIVLDDADRGVVADVTIDTP-AS-----GVIVRHSNESVLRNLTVNG-ADTA 377
                                       8************99766555555778888888888999988777.44.....7999999999999999999.4444 PP

                                       EEE.S.....-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEE CS
                   Pectate_lyase_3 171 iav.g.....nqqftvrnitfnnattgievlwgwgwtlknvki 207
                                        +           ++v++ tf +   g+++++  g +++ +++
  gi|313127064|ref|YP_004037334.1| 378 SEGfMgailiGARSVVEESTFYDGRDGVYTHRADGSVVRENQF 420
                                       4442245677889999999999999999999977755555554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.032
                                       --EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-..S--SEEE-TT-EEEEEEEEE CS
                   Pectate_lyase_3 153 gsggflndlvfsglgdigiav.gnqqftvrnitfnn..attgievlwgwgwtlknvki 207
                                       g  +++ + v+ g  ++g++v g  +  + n+++ n    +++++l  ++w+++n  +
  gi|313127064|ref|YP_004037334.1| 476 GGDSYYAENVVVG-NEYGLQVaGDRNTFAANVVVGNdvGLRATDIL-PSNWVVRNDVV 531
                                       4445665555555.57777775555555555555553333344443.44555554333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 4292.62
//
Query:       gi|313127065|ref|YP_004037335.1|  [L=288]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-25   90.5   0.0    2.3e-25   89.7   0.0    1.4  1  ABC_tran         ABC transporter
    6.4e-19   68.9   0.0      6e-11   42.7   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00013   21.5   0.0      0.035   13.5   0.1    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00017   21.3   0.0    0.00037   20.2   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
    0.00018   22.1   0.0    0.00026   21.5   0.0    1.2  1  AAA_23           AAA domain
     0.0029   18.0   0.1     0.0055   17.1   0.1    1.7  1  AAA_16           AAA ATPase domain
     0.0032   17.4   0.1     0.0052   16.7   0.1    1.3  1  RsgA_GTPase      RsgA GTPase
     0.0074   16.0   0.0      0.027   14.2   0.1    1.7  2  AAA_15           AAA ATPase domain
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.023   14.8   0.0    1.5  1  AAA_33           AAA domain
      0.018   14.8   0.0        2.3    7.9   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
      0.022   14.8   0.8       0.04   14.0   0.8    1.3  1  Dynamin_N        Dynamin family
      0.057   13.1   0.1       0.17   11.6   0.1    2.0  1  AAA_30           AAA domain
       0.17   10.7   0.0       0.25   10.2   0.0    1.1  1  Rota_Capsid_VP6  Rotavirus major capsid protein VP6
       0.18   11.2   0.2        1.7    8.0   0.0    2.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.18   10.6   0.0       0.26   10.0   0.0    1.1  1  ABC_ATPase       Predicted ATPase of the ABC class
       0.18   11.3   0.1       0.69    9.5   0.1    1.9  2  cobW             CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0     2e-28   2.3e-25       2     135 ..      59     191 ..      58     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 2e-28
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n+s+ +++ge+  +vG+nG+GKStLl++lag      G++++        ++e   +e+g+lpq p++ ++ t+r+
  gi|313127065|ref|YP_004037335.1|  59 SNLSFGVERGEVFSLVGPNGSGKSTLLEVLAGVRPTSTGSVTVS-------QREDGVREVGYLPQRPSFRDGFTARD 128
                                       79***************************************665.......589999******************** PP

                                       H..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       +            d+e+++ l+++gl++++d+ v     sLSgG+ + + l +a+l +p +l+lDEp
  gi|313127065|ref|YP_004037335.1| 129 TldfyarfldgVGDDEVTETLERVGLSGVADRSV----GSLSGGMTRLLGLGQAVLGDPAVLVLDEP 191
                                       **********999999******************....****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.4e-08   1.6e-05       3      38 ..      72     104 ..      70     139 .. 0.70
   2 !   42.7   0.0   5.3e-14     6e-11     172     298 ..     120     223 ..     103     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.4e-08
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsg 38 
                                        l+GpNgsGKS+LL+ l +++ +   ++g+ +++++
  gi|313127065|ref|YP_004037335.1|  72 SLVGPNGSGKSTLLEVLAGVRPT---STGSVTVSQR 104
                                       59***************999543...3333333333 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 5.3e-14
                            AAA_21 172 fadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllall 248
                                       f+d f+  + +++  r+++++ ++e   +++++g                     ++  ++++ +lS G+ rll+l 
  gi|313127065|ref|YP_004037335.1| 120 FRDGFTARDTLDFYARFLDGVGDDEVTETLERVGL--------------------SGVADRSVGSLSGGMTRLLGLG 176
                                       56666666666666677777777766666665554....................4445667899************ PP

                            AAA_21 249 tallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        a+l ++   ++l++DEp +gL+P++++rl++++ el++ g+ v++++H 
  gi|313127065|ref|YP_004037335.1| 177 QAVLGDP---AVLVLDEPGSGLDPAMVERLFGIVGELAQSGSAVVVASHE 223
                                       *****99...************************999999*********6 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   3.1e-05     0.035      26      44 ..      70      88 ..      54     103 .. 0.88
   2 !    5.8   0.0    0.0073       8.2     137     210 ..     165     235 ..     138     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                      + ++vGpNGSGKs ll+ +
  gi|313127065|ref|YP_004037335.1| 70 VFSLVGPNGSGKSTLLEVL 88
                                      5679**********99865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0073
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvg 210
                                       LSgG   L+ l            ++ +lDe  + LD + v+++  ++ e  ++ + ++v s++   +e    +v 
  gi|313127065|ref|YP_004037335.1| 165 LSGGMTRLLGLGQA----VLGDPAVLVLDEPGSGLDPAMVERLFGIVGELAQSgSAVVVASHELPAIETYADTVA 235
                                       66666666554322....233345679*********************998876888888998888877666555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.3e-07   0.00037      12      40 ..      58      86 ..      56      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.3e-07
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllD 40
                                      f++ ++ +++ +++ l+Gp+GsGKSTll 
  gi|313127065|ref|YP_004037335.1| 58 FSNLSFGVERGEVFSLVGPNGSGKSTLLE 86
                                      56666777766699*************95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.3e-07   0.00026       8      39 ..      50      88 ..      43     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.3e-07
                            AAA_23  8 rsfrdqe....idF...skgltlItGpNGaGKTTildAi 39
                                      rsf+d++    + F      ++ ++GpNG+GK+T+l+ +
  gi|313127065|ref|YP_004037335.1| 50 RSFGDVSvfsnLSFgveRGEVFSLVGPNGSGKSTLLEVL 88
                                      677665421123446654569***************977 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     5e-06    0.0055      24     143 ..      68     190 ..      57     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipy...sa.laqalareellrqlldeaesael 94 
                                       +e+  l+G+ G+GKs+l++ l+  ++ +  g ++++++ d   +++ y    + + + +++++ l   ++ ++    
  gi|313127065|ref|YP_004037335.1|  68 GEVFSLVGPNGSGKSTLLEVLAG-VRPTstGSVTVSQREDGV-REVGYlpqRPsFRDGFTARDTLDFYARFLDGVGD 142
                                       37889*************99995.444433566688888888.4433333355577777665555555555444333 PP

                            AAA_16  95 eawrekleealaavpelagaeasrllellkrll..allsrderplvlvlDd 143
                                       ++  e+le++    + +a+ +  +l   ++rll   ++   ++p vlvlD+
  gi|313127065|ref|YP_004037335.1| 143 DEVTETLERVG--LSGVADRSVGSLSGGMTRLLglGQAV-LGDPAVLVLDE 190
                                       44444333332..23333333477777777777533333.36678888885 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.6e-06    0.0052      92     132 ..      60     101 ..      31     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.6e-06
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallpelelktgevse 132
                                       +l+  ++  ++  lvG+ G GKStL+++l++   ++tg+v  
  gi|313127065|ref|YP_004037335.1|  60 NLSFGVERgEVFSLVGPNGSGKSTLLEVLAGVRPTSTGSVTV 101
                                       5555555559999******************99999998865 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   2.4e-05     0.027      25      43 ..      70      88 ..      58      91 .. 0.87
   2 ?   -1.3   0.0       1.3   1.4e+03     323     364 ..     182     222 ..     180     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                            AAA_15 25 ltvliGkNnsGKSsileal 43
                                      +  l+G+N+sGKS++le+l
  gi|313127065|ref|YP_004037335.1| 70 VFSLVGPNGSGKSTLLEVL 88
                                      6679*************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++++l+++EP   L p + + l+    ela++++  v++ +H
  gi|313127065|ref|YP_004037335.1| 182 DPAVLVLDEPGSGLDPAMVERLFGIVGELAQSGS-AVVVASH 222
                                       6889***************************998.7777777 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.1e-05     0.023       2      30 ..      71     103 ..      70     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg....avllss 30 
                                       + lvG++GsGKstl+e l+  ++     v++s+
  gi|313127065|ref|YP_004037335.1|  71 FSLVGPNGSGKSTLLEVLAGVRPtstgSVTVSQ 103
                                       568*************99877665565555555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.002       2.3      41      68 ..      61      89 ..      39     111 .. 0.83
   2 ?    4.8   0.0     0.019        21     105     150 ..     179     223 ..     171     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                         IstB_IS21 41 lsf.iekkenivllGpsGvGKshlaialg 68
                                      lsf +e+ e + l+Gp G GKs l   l+
  gi|313127065|ref|YP_004037335.1| 61 LSFgVERGEVFSLVGPNGSGKSTLLEVLA 89
                                      556589999*************9977665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                         IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlp 150
                                        l  +++l+lD+ g   ld a  e lf ++ +  +  s ++ +  +
  gi|313127065|ref|YP_004037335.1| 179 VLGDPAVLVLDEPGS-GLDPAMVERLFGIVGELAQSGSAVVVASHE 223
                                       567789*******95.79**************99998887766554 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8   3.6e-05      0.04       3      32 ..      73     100 ..      72     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                                       EEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                         Dynamin_N   3 vvGsqSsGKSSvlnaLlgedilprgpnptT 32 
                                       +vG   sGKS++l+ L g +  p++++ +T
  gi|313127065|ref|YP_004037335.1|  73 LVGPNGSGKSTLLEVLAGVR--PTSTGSVT 100
                                       799****************9..99999888 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00015      0.17      19      49 ..      69      99 ..      63     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrv 49
                                       v  l+Gp G+GK+t+l++l+ +  ++ g+v
  gi|313127065|ref|YP_004037335.1| 69 EVFSLVGPNGSGKSTLLEVLAGVRPTSTGSV 99
                                      47889**************998877775454 PP

>> Rota_Capsid_VP6  Rotavirus major capsid protein VP6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00023      0.25      80     113 ..     125     158 ..     122     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                   Rota_Capsid_VP6  80 sarniidylvdfveavcddeivreasrnGiapqs 113
                                       +ar+++d+++ f++ v dde+    +r G++  +
  gi|313127065|ref|YP_004037335.1| 125 TARDTLDFYARFLDGVGDDEVTETLERVGLSGVA 158
                                       79********************999999987655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0015       1.7      26      50 ..      72      96 ..      61     109 .. 0.87
   2 ?    0.9   0.1      0.22   2.5e+02      18      58 ..     178     219 ..     164     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
                      Mg_chelatase 26 llvGppGsGKtmlakrlpsllppls 50
                                       lvGp GsGK+ l + l+++ p  +
  gi|313127065|ref|YP_004037335.1| 72 SLVGPNGSGKSTLLEVLAGVRPTST 96
                                      589**************99998766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                      Mg_chelatase  18 aaaGgHnlllvGppGsG.Ktmlakrlpsllpplseeealeva 58 
                                       a+ G   +l++  pGsG    + +rl +++ +l ++ +  v 
  gi|313127065|ref|YP_004037335.1| 178 AVLGDPAVLVLDEPGSGlDPAMVERLFGIVGELAQSGSAVVV 219
                                       778888999999999994457899999999999887665555 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00023      0.26     241     265 ..      64      89 ..      61      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                                       EE-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAle 265
                                       g+ +G v+ +vG++  GKsTLLe l+
  gi|313127065|ref|YP_004037335.1|  64 GVERGeVFSLVGPNGSGKSTLLEVLA 89 
                                       899999****************9885 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00062      0.69       2      21 ..      70      89 ..      69     107 .. 0.83
   2 ?   -0.8   0.0      0.91     1e+03     100     130 ..     218     248 ..     164     262 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00062
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      v+ l+G+ GsGK+tLl+ l 
  gi|313127065|ref|YP_004037335.1| 70 VFSLVGPNGSGKSTLLEVLA 89
                                      56799***********9876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.91
                                       HTTSHHHHHCCCECEEEEEEETTTH.CCHCC CS
                              cobW 100 afteeelksdltldavvavvDaknleaeeek 130
                                       ++ ++el +  t+  +vav+D+ ++ a++++
  gi|313127065|ref|YP_004037335.1| 218 VVASHELPAIETYADTVAVLDGGEFVARGTP 248
                                       3336666666777778888888777555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1971.72
//
Query:       gi|313127066|ref|YP_004037336.1|  [L=279]
Description: hypothetical protein Hbor_23310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-08   32.2  26.2    1.6e-07   30.9  25.9    1.6  2  ABC2_membrane_2  ABC-2 family transporter protein
      0.007   15.5  12.8     0.0086   15.2  12.8    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.044   13.2  12.9        0.1   12.0  12.9    1.6  1  ABC2_membrane    ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.11   6.9e+02       3      27 ..      12      36 ..      10      57 .. 0.76
   2 !   30.9  25.9   2.7e-11   1.6e-07      79     282 ..      60     269 ..      25     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.11
                   ABC2_membrane_2  3 iakkEfrdlvrsrrfllltvllpli 27
                                      +a +E+r   r + +l+l++ + + 
  gi|313127066|ref|YP_004037336.1| 12 VATRELRTVARTPALLALAAAFTVS 36
                                      6778888888888888888888776 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 2.7e-11
                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvll....alaiil 150
                                       t++ vl+p++a +fg+  +++++  g l +l ++ vsR +++ g  +g+ ++ +a +++al+ +  l    +  +  
  gi|313127066|ref|YP_004037336.1|  60 TFVEVLVPLLAFAFGYRTVVEDRLTGELDVLRTYDVSRIAYVGGVYVGRGVALVAtVVLALVLGGALvpllTADVPT 136
                                       66789***********************************************6665555554443336777777788 PP

                   ABC2_membrane_2 151 algivlaledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp 226
                                        l i++a+++ l++v ++vl ++++ v+la++l++S+ ar+ r+a ala +l +++++ ++  l++   l ag ++ 
  gi|313127066|ref|YP_004037336.1| 137 FLAINTAADSALRFVRFVVLAAAFTlVALAATLAVSAAARTVRTAFALAAVLAALFVLGIDTTLLA--GLAAGVVP- 210
                                       8999999999999999999888877899**********************************9955..56665555. PP

                   ABC2_membrane_2 227 qeindflsllsptsayntllneilagsdlna....lgstatnllilllllavllvlgyvl 282
                                       +e    l+ lsp sa++ l+ +   g          gs   n++ ll++ + +l+++ ++
  gi|313127066|ref|YP_004037336.1| 211 AEGIAGLLALSPNSAFRGLVLSSAVGVVG-GaevtAGSPLWNVIGLLVWWVGSLGIAVWR 269
                                       5567778899******9888776554422.124557777778888888888888887765 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2  12.8   1.4e-06    0.0086     174     317 ..      69     234 ..      27     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-06
                   ABC2_membrane_3 174 itasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl.................gi 233
                                       + ++f  + +ve++ ++ + ++ +  vs+++y+ + ++g +++ + +++l+l+l  +l                 + 
  gi|313127066|ref|YP_004037336.1|  69 LAFAFGYRTVVEDRLTGELDVLRTYDVSRIAYVGGVYVGRGVALVATVVLALVLGGALvplltadvptflaintaAD 145
                                       4577788899***********************************99999999844445667778999997765544 PP

                   ABC2_membrane_3 234 pfgnlglllllfllfglayialgyllsslfknsetaqilifivil.........llsgffgglfpledlpsalkwif 301
                                       +   ++ +++l   f l+++a ++++s++ ++ +ta++l+ ++           ll g+ +g++p e    +++ ++
  gi|313127066|ref|YP_004037336.1| 146 SALRFVRFVVLAAAFTLVALAATLAVSAAARTVRTAFALAAVLAAlfvlgidttLLAGLAAGVVPAE----GIAGLL 218
                                       444889999********************99998887764444442344556555555555555555....444455 PP

                   ABC2_membrane_3 302 siiPffapglgllrli 317
                                        + P++a+  + l+ +
  gi|313127066|ref|YP_004037336.1| 219 ALSPNSAFRGLVLSSA 234
                                       5666655555444444 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  12.9   1.7e-05       0.1       4     173 ..      10     193 ..       8     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                     ABC2_membrane   4 kallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr....pgllffsvlflafsaltsvapvfe 76 
                                       +++  re+++  r+p+l+ ++  ++++ +  v +   g      +++      + ++  +v  la +a+    +v +
  gi|313127066|ref|YP_004037336.1|  10 FVVATRELRTVARTPALL-ALAAAFTVSIVGVAWAGSG---GGGGFVPLtldlLTFVEVLVPLLA-FAFGYRTVVED 81 
                                       68899**********998.6555555555555555555...334444224666888888888888.55555559999 PP

                     ABC2_membrane  77 rergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.........gldls.......rfflfllll 137
                                       r  g l+ ++++ + s+ ayv + +++  +  ++ +++ l++   lv          l ++       rf+ f++l+
  gi|313127066|ref|YP_004037336.1|  82 RLTGELDVLRTYDV-SRIAYVGGVYVGRGVALVATVVLALVLGGALVplltadvptFLAINtaadsalRFVRFVVLA 157
                                       99************.**********999666666666666655555433444444433333778899999******* PP

                     ABC2_membrane 138 lltalaasslgllisalapsfedasqlaslvllpll 173
                                        +++l+a++  l++sa a+++++a  la ++  +++
  gi|313127066|ref|YP_004037336.1| 158 AAFTLVALAATLAVSAAARTVRTAFALAAVLAALFV 193
                                       ****************************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1982.22
//
Query:       gi|313127067|ref|YP_004037337.1|  [L=212]
Description: flavodoxin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-11   43.4   0.0    4.5e-11   43.0   0.0    1.2  1  FAD_binding_6  Oxidoreductase FAD-binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   2.5e-15   4.5e-11       3      98 ..       6      99 ..       4     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 2.5e-15
                                      EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--..TT-HHHHHH CS
                     FAD_binding_6  3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvy..pgGkmsqaL 79
                                      +++++++v ++t  ++f+ p+    ++  +Gq+v l++ ++ge++ R Yt +ss++ +G++e+ v +   + G +sq L
  gi|313127067|ref|YP_004037337.1|  6 TVAAVRDVGPETVAIEFESPDG---FEADPGQFVKLSAAVEGEEYSRFYT-LSSPDVEGTFEVTVGIDpeEAGPFSQFL 80
                                      7888899999999999999955...55899********************.99*************998889******* PP

                                      HCS-TT-EEEEEEEE-SEE CS
                     FAD_binding_6 80 delkigdtleikGPlGkfe 98
                                        l  gdtl+++GP+G+  
  gi|313127067|ref|YP_004037337.1| 81 VDLDTGDTLDVSGPFGQSY 99
                                      ****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1499.19
//
Query:       gi|313127068|ref|YP_004037338.1|  [L=581]
Description: 2-oxoacid:ferredoxin oxidoreductase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-59  200.6   0.4    4.6e-59  200.0   0.4    1.3  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.8e-39  134.3   0.1      1e-38  133.1   0.1    1.6  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    1.7e-05   24.5   0.2    3.2e-05   23.6   0.2    1.4  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
      2e-05   24.8   0.0    5.7e-05   23.4   0.0    1.8  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0093   15.8   0.0      0.023   14.6   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.0   0.4   1.3e-62   4.6e-59       2     230 ..     210     455 ..     209     456 .. 0.93

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 1.3e-62
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +aiaag++++a+YPITP+++++e l   +++++    +vvq+e+E++ai+ ++GAa aGar++TaTSg+G+ Lm e+
  gi|313127068|ref|YP_004037338.1| 210 GAIAAGCKFYAGYPITPATDVMEYLTGRIENFGG---HVVQAEDELAAINLALGAARAGARSMTATSGPGIDLMTET 283
                                       89*******************************5...**************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       +gl+a++e+P+viv+v+R++pstg++++++q+Dl++++     + +  vla+ +++e+f+ +++AfnlAek+++Pv 
  gi|313127068|ref|YP_004037338.1| 284 FGLVATSETPLVIVDVMRSGPSTGMPTKQEQGDLNMLLygghgEIPRFVLAPTTIAECFWKTVEAFNLAEKYQTPVY 360
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC-SGG..GS-----SBXXXXXXXX................SXXXBXXTXXTSSXXEEESBX CS
                             POR_N 151 vlfDgfllshevekvelpdee.delklikekleeyerkey................aldpekpiargtaanpdtgle 210
                                       ++ D  ++  + ++   +  + d++++ + k +++++ +                 +++p+ ++ ++  a   tgle
  gi|313127068|ref|YP_004037338.1| 361 LTADLAMA-VTEQTFSPEMFDmDKVEIDRGKVVDEDTISEwqnekgqfqphaitedGISPRAFPGTDEGAHMSTGLE 436
                                       ****9988.77777766666666777777777777777767777799****************************** PP

                                       BXTTSXBXXXXHHHHHHHHH CS
                             POR_N 211 hrekgneaedaaekvveeve 230
                                       h+e g+++ed  + ++e+v+
  gi|313127068|ref|YP_004037338.1| 437 HDELGRRTED-TDMRIEQVD 455
                                       *********9.888888875 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.1   2.9e-42     1e-38       1     175 [.      13     175 ..      11     177 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 2.9e-42
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       +G+G+ ++gki+a+a++raG +v++++++ s+irGg + ++vr + + +v+s+  ++ d+l+al + t++e+ld+l 
  gi|313127068|ref|YP_004037338.1|  13 AGDGIDSTGKIFAQALSRAGRHVFTSKDFASRIRGGYTAYKVRTAVD-PVQSVV-DRLDVLIALTPRTIEENLDELH 87 
                                       5**********************************************.999999.********************** PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeai 154
                                       +g++iiy+ e++  ++++    +            ++v+++++a+e+gg ++++N+v+lGa++ ++ +p+e l+ a+
  gi|313127068|ref|YP_004037338.1|  88 EGSVIIYDGERTTMENVEIPEGMI----------GLDVPLKRLAEEAGG-AIMRNVVALGAACEVAEFPIENLDSAL 153
                                       *********887777777766665..........489************.*************************** PP

                                       HCCS-CH..HHHHHHHHHHHHH CS
                               POR 155 kkrfpkkk.eviekNlkafrag 175
                                       +krf+ k+ ++++ N++a+r+g
  gi|313127068|ref|YP_004037338.1| 154 EKRFGSKGqQLVDNNKEAARKG 175
                                       *****999************99 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   8.8e-09   3.2e-05      13     159 ..     213     363 ..     202     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.8e-09
                                       HCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHH CS
                      TPP_enzyme_N  13 algvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeA 86 
                                       a+g + + g+p +  ++++++l  +    g +vv+a +E +a++ A g ara  +  +  +tsgpG+  ++      
  gi|313127068|ref|YP_004037338.1| 213 AAGCKFYAGYPITPATDVMEYLTGRIenfGGHVVQAEDELAAINLALGAARAGAR-SM-TATSGPGIDLMTETFGLV 287
                                       5688889999999999999999999888999*********************754.44.4569************** PP

                                       HHHT--EEEEEEE--CCCHHS..TC--T-CCHH.HCCCSSEEEE-SSGGGHHHHHH...HHHHHHHSSS--EEEEEE CS
                      TPP_enzyme_N  87 kvdriPllvlsgdrptslrgqgvlqqeldqlal.frpvtkyaervtspeelpealr...rAirtalsgrpgPvylel 159
                                       +++ +Pl+++   r+  ++g ++ q++ d + l +  + +  ++v  p++++e +    +A+  a ++ ++Pvyl+ 
  gi|313127068|ref|YP_004037338.1| 288 ATSETPLVIVDVMRSGPSTGMPTKQEQGDLNMLlYGGHGEIPRFVLAPTTIAECFWktvEAFNLA-EKYQTPVYLTA 363
                                       ********************999997777666555555555555555555555554222888888.999*****975 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.6e-08   5.7e-05       1      98 [.     480     567 ..     480     571 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A++++v  Gs  g + +a+d l e+gi+v +l + ++  FP+ +l e+ +++++v+v++ n++    Gq ++ ++  
  gi|313127068|ref|YP_004037338.1| 480 ADTLVVSWGSNEGAMIEAIDFLEEDGIDVRFLSIPYM--FPRYDLTEAFEEADEVIVVECNAT----GQFADIIEHD 550
                                       89*******************************9988..78*********************5....8877666666 PP

                                       TGGGTSEEEEEE--GGG---- CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrdit 98 
                                       +  +    v+ v++ +G  ++
  gi|313127068|ref|YP_004037338.1| 551 TLTR----VKRVNKYNGVRFK 567
                                       5444....5555555555555 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.5e-06     0.023       9      70 ..     479     538 ..     474     562 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.5e-06
                                       TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEE CS
                   Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveea 70 
                                         d ++v++Gs    ++eA++ Le++gi+++ ++++ + p    ++ e+ ++ ++++vve +
  gi|313127068|ref|YP_004037338.1| 479 DADTLVVSWGSNEGAMIEAIDFLEEDGIDVRFLSIPYMFPRY--DLTEAFEEADEVIVVECN 538
                                       6799*******************************9998876..555679999999999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 3606.79
//
Query:       gi|313127069|ref|YP_004037339.1|  [L=287]
Description: 2-oxoacid:acceptor oxidoreductase subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-32  111.4   0.7      5e-32  110.8   0.7    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    2.6e-17   62.7   0.9    4.9e-17   61.8   0.3    1.8  2  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.7   5.5e-36     5e-32       2     153 .]      51     198 ..      43     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 5.5e-36
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+             ++y++  +++g +G++lp++ G+kla+pd ev++  GDG+ + i   ++++avrrn+++t
  gi|313127069|ref|YP_004037339.1|  51 IGCSGK----------IGTYMHsYALHGVHGRALPVGAGVKLANPDLEVMVAGGDGDGYSIgAGHFVHAVRRNVDMT 117
                                       566665..........678888456************************************99************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       +vv++N++yg+t+gq   ++++  +++++p+g +++pv++ +la a+Ga+  a+  ++d    +e++++a+e++g+ 
  gi|313127069|ref|YP_004037339.1| 118 YVVMDNRIYGLTKGQaspTSREDFETSTTPEGPQQPPVNPMALALAAGATfIAQSFSTDARRHAEIVQKAIEHDGFG 194
                                       ***************998777888899999999*****************7776567778***************** PP

                                       EEEE CS
                      TPP_enzyme_C 150 liev 153
                                       +++v
  gi|313127069|ref|YP_004037339.1| 195 FVNV 198
                                       *987 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.6   1.5e+04      26      42 ..     176     191 ..     170     193 .. 0.69
   2 !   61.8   0.3   5.5e-21   4.9e-17       1      64 [.     202     265 ..     202     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.6
                                       --EEHHHHHHHHT---- CS
                        PFO_beta_C  26 DpsdlekAlekalewgd 42 
                                       D    ++ ++ka e +d
  gi|313127069|ref|YP_004037339.1| 176 DARRHAEIVQKAIE-HD 191
                                       66667777888887.55 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 5.5e-21
                                       XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT-----EEEEEEEE.TTS--HHHHHHT. CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgdkiplGifYk.eekptyeerleel 64 
                                       CvtFN+v+T+d++++ +++l e+++Dp+d+++A e++l+  dk   G++++ e + +y+e++ ++
  gi|313127069|ref|YP_004037339.1| 202 CVTFNDVDTYDYFRDSLVDLAEEDHDPTDYDAAKEVILD-ADKEFQGVVWQdEASVPYDEKHGVT 265
                                       **********************99**************9.********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1862.50
//
Query:       gi|313127070|ref|YP_004037340.1|  [L=62]
Description: hypothetical protein Hbor_23350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.033   14.2   0.0      0.038   14.0   0.0    1.2  1  Elf1            Transcription elongation factor Elf1 like
       0.04   14.0   2.0       0.18   11.9   2.0    1.9  3  Zn-ribbon_8     Zinc ribbon domain
      0.047   13.5   0.5        6.8    6.6   0.2    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.08   12.7   0.4        1.4    8.7   0.1    2.1  2  zinc_ribbon_5   zinc-ribbon domain
       0.15   12.0   1.6        1.8    8.6   0.1    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.1e-05     0.038      21      63 ..      22      61 ..       9      62 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                              Elf1 21 kFdCpfCnheksvevkldkkekiaevsCkvCgesfetkvnals 63
                                      ++dCp C+     ev +++  +   ++C  Cg++++++v++++
  gi|313127070|ref|YP_004037340.1| 22 VYDCPECEYG---EVLVTELIESPDARCLDCGTRYRLFVERVE 61
                                      689*******...666667777799*************99986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0022       7.8      24      33 ..      19      29 ..       9      39 .. 0.73
   2 ?   11.9   2.0   5.2e-05      0.18       6      36 ..      23      53 ..      20      57 .. 0.85
   3 ?    6.5   0.1    0.0025       8.9       7      19 ..      45      57 ..      43      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0022
                       Zn-ribbon_8 24 aplta.CPeCg 33
                                      ++l+  CPeC 
  gi|313127070|ref|YP_004037340.1| 19 DSLVYdCPECE 29
                                      45667799996 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.2e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsis.dapltaCPeCgsev 36
                                      Y C eC    evl++   ++p+  C +Cg + 
  gi|313127070|ref|YP_004037340.1| 23 YDCPECE-YGEVLVTELiESPDARCLDCGTRY 53
                                      99*****.8888887667999999****9865 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0025
                       Zn-ribbon_8  7 rCeeCghefevlq 19
                                      rC +Cg+++  ++
  gi|313127070|ref|YP_004037340.1| 45 RCLDCGTRYRLFV 57
                                      8*****9998765 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0045        16       2      11 ..      24      33 ..      18      38 .. 0.65
   2 ?    6.6   0.2    0.0019       6.8      30      39 .]      45      54 ..      44      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0045
                           TFIIS_C  2 kCpkCgsrea 11
                                       Cp+C   e+
  gi|313127070|ref|YP_004037340.1| 24 DCPECEYGEV 33
                                      4666666665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0019
                           TFIIS_C 30 kCtkCghrWr 39
                                      +C++Cg r+r
  gi|313127070|ref|YP_004037340.1| 45 RCLDCGTRYR 54
                                      7*******98 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.035   1.3e+02       3       9 ..      23      29 ..      21      37 .. 0.84
   2 ?    8.7   0.1   0.00039       1.4       4      15 ..      45      56 ..      44      62 .] 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.035
                     zinc_ribbon_5  3 irCpdCd 9 
                                        Cp+C+
  gi|313127070|ref|YP_004037340.1| 23 YDCPECE 29
                                      57****6 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00039
                     zinc_ribbon_5  4 rCpdCdtkFklv 15
                                      rC dC+t ++l 
  gi|313127070|ref|YP_004037340.1| 45 RCLDCGTRYRLF 56
                                      8*********95 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.031   1.1e+02       4      11 ..      22      29 ..      20      34 .. 0.86
   2 ?    8.6   0.1    0.0005       1.8       5      14 ..      44      53 ..      43      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.031
                    Zn_ribbon_SprT  4 vYrCtgCg 11
                                      vY C+ C 
  gi|313127070|ref|YP_004037340.1| 22 VYDCPECE 29
                                      699****6 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0005
                    Zn_ribbon_SprT  5 YrCtgCgrey 14
                                      +rC +Cg++y
  gi|313127070|ref|YP_004037340.1| 44 ARCLDCGTRY 53
                                      79*****875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 447.93
//
Query:       gi|313127071|ref|YP_004037341.1|  [L=455]
Description: 2,3-di-O-geranylgeranylglyceryl phosphate reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-12   47.4   1.1    3.3e-08   32.8   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    2.3e-10   40.4   5.7    5.1e-10   39.3   5.7    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    1.7e-09   37.3   7.0    1.4e-05   24.4   3.1    2.6  3  FAD_binding_2   FAD binding domain
    6.5e-09   35.8   1.2     0.0036   16.9   0.0    2.2  2  DAO             FAD dependent oxidoreductase
      4e-08   32.9   2.9    1.6e-07   30.9   2.9    1.9  1  FAD_binding_3   FAD binding domain
    4.4e-07   29.3   0.0    5.7e-07   29.0   0.0    1.2  1  GIDA            Glucose inhibited division protein A
    3.5e-06   26.0   1.0      3e-05   22.9   0.6    2.0  2  HI0933_like     HI0933-like protein
    1.1e-05   25.9   2.0       0.18   12.4   0.5    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.1e-05   23.4   4.2    0.00021   20.6   0.2    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.6e-05   23.6   1.1     0.0003   20.9   0.3    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00031   20.1   2.1     0.0031   16.9   0.1    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00095   18.3   2.0       0.16   11.0   0.5    2.5  3  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
       0.02   14.1   0.3       0.02   14.1   0.3    1.8  2  Thi4            Thi4 family
      0.026   14.4   0.7      0.061   13.2   0.6    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
        0.1   11.9   0.0        6.3    6.1   0.0    2.3  2  GMC_oxred_N     GMC oxidoreductase


Domain annotation for each model (and alignments):
>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.8   3.1e-05     0.037       2      44 ..       8      50 ..       7      75 .. 0.74
   2 !   32.8   0.0   2.8e-11   3.3e-08     151     372 ..     100     341 ..      65     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-...SSS---SS-EE CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlves...eeigtvgvGea 44
                                      +v+vGGGtaG  aAa+ a  +   l+v l+e    ee g +  G+a
  gi|313127071|ref|YP_004037341.1|  8 MVVVGGGTAGAFAAATAASEG---LDVVLLERkseEEAGHIACGDA 50
                                      79*************999888...99***99522267777777776 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 2.8e-11
                                       E-HHHHHHHHHHHHHHCT-EEEE--.EEEEEE-TTS-EEEEEETT.S-EE..E-SEEEE-SGGG-IIIIII.T---E CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegk.vvevqldedgrveslrled.grev..eadlfiDcsGfrgllieqa.Lktgf 222
                                       +d+++y +++ + a + G ++  ++ v++v +d+dgrv+++r +  g +v  ead  iD  G  ++l +++ +++++
  gi|313127071|ref|YP_004037341.1| 100 VDRKRYGEVILEEADRLGTDMHYDTvVQDVSQDDDGRVTGVRAKRnGDVVeyEADVTIDGAGALSILQDKTdFSGTT 176
                                       79*****************977655167899999********997665542279**************998222222 PP

                                       EE-TTT----EEEEEEEE--H....---S..SEEEE....E-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHH CS
                    Trp_halogenase 223 edwsdvLltdrAlavqvesee....lvep..ytrat....aekaGWtWkiPLqhrlgn.GyvyssahadddeAlael 288
                                        d   +          +        ++ep  y +a+    +e+ G  W+ P + +  n G+ +        + +++l
  gi|313127071|ref|YP_004037341.1| 177 FDTNVSY------SQFCSAYRevidVPEPvdYDDAIvfkpTEELGYLWYFPRSPTEINaGLGFQMTEE-PMKLVDDL 246
                                       2222222......2222222123345555115555522227789******988765555777754433.44666677 PP

                                       HHHCT--TTTS-EEEE---EE.......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT CS
                    Trp_halogenase 289 laeldgkleaeprkirfttGr.......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdks 354
                                       +++l  ++e e   +  + G          +a  ++++a G+++g v+P  + +i  + +    a+++ ++ + d+ 
  gi|313127071|ref|YP_004037341.1| 247 KRDLRNRPEFEGGTVTDKLGAalptrrpYDSAVAPGFIAAGDSAGHVNPTTGGGIPGAAKsahwAAKHAVKAISDGD 323
                                       777777777776666666666677666778999**********************88777677799*********** PP

                                       --HHHHHHHHHHHHHHHH CS
                    Trp_halogenase 355 depaaiaefnrevarele 372
                                       +++a++ e+nr v + ++
  gi|313127071|ref|YP_004037341.1| 324 VSEASLWEYNRDVMTDFG 341
                                       ***********9988776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   5.7   4.2e-13   5.1e-10       1     144 [.       7     161 ..       7     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 4.2e-13
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveerg..vlG....Glltsglvatdig.....nkaee..qvvtgiarefl 64 
                                       D vVvGGg+aG  AA +Aa +G  v+L+e++     G    G + +g  + ++       k  e  + ++ i r ++
  gi|313127071|ref|YP_004037341.1|   7 DMVVVGGGTAGAFAAATAASEGLDVVLLERKSeeEAGhiacGDAIKGTSTFPDVidldyLK--EesFTNQNITRAVF 81 
                                       89***************************65311334222366666665444333453233..34599999999999 PP

                      FAD_oxidored  65 erlrqrgga.rlkkrskwntfepevakavleemlaeagvtvllntrlveveke.gkriesvtveskegrktirAkvf 139
                                       e+ r   +  +   r + ++++ + + +v+ e  ++ g ++ ++t++++v ++ ++r+++v+++++    +++A+v+
  gi|313127071|ref|YP_004037341.1|  82 ENPRG--DDlDVPFRGAGAVVDRKRYGEVILEEADRLGTDMHYDTVVQDVSQDdDGRVTGVRAKRNGDVVEYEADVT 156
                                       99955..3323342233358**************999***************74689******76556********* PP

                      FAD_oxidored 140 iDATg 144
                                       iD+ g
  gi|313127071|ref|YP_004037341.1| 157 IDGAG 161
                                       **876 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   3.1   1.2e-08   1.4e-05       1      39 [.       7      46 ..       7      51 .. 0.84
   2 !   13.8   0.0     2e-05     0.023     145     204 ..     107     165 ..      92     184 .. 0.85
   3 ?   -2.2   0.0       1.4   1.7e+03     106     167 ..     288     349 ..     260     355 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.2e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.GGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg.ata 39
                                      D +V+G+G AG  AA++aa +Gl+v+++e ++e +  ++a
  gi|313127071|ref|YP_004037341.1|  7 DMVVVGGGTAGAFAAATAASEGLDVVLLERKSEEEAgHIA 46
                                      89**************************987764332555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2e-05
                                       HHHHHHHHTCTEEEEESEEEEEEEEC.TTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 145 arlvesarkagvdfqerteadeLive.dgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                       ++ +e+a+++g+d++  t ++++ ++ dgrvtG+ ++  ++g  v+++a+ +++ +g+ + 
  gi|313127071|ref|YP_004037341.1| 107 EVILEEADRLGTDMHYDTVVQDVSQDdDGRVTGVRAK--RNGDVVEYEADVTIDGAGALSI 165
                                       577899999****************7366********..**************99998874 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.4
                                       CCTSSB-EEE-TT-SSTEEEE-.STT-.......HHHHHHHHHHHHHHTCTEEEEESEEEEEE CS
                     FAD_binding_2 106 tedgpvdvrelGglsatartlhdaadarr.etlvtghallarlvesarkagvdfqerteadeL 167
                                       +  g+v+ +  Gg    a+++h aa++   +++ +g    a l e+ r+ ++df  r +a++L
  gi|313127071|ref|YP_004037341.1| 288 DSAGHVNPTTGGGIPGAAKSAHWAAKH-AvKAISDGDVSEASLWEYNRDVMTDFGKRFAAVDL 349
                                       445577777777777776777744444.44777777777777777777777777777777776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.2   3.3e-06    0.0039       1      31 [.       7      39 ..       7      56 .. 0.89
   2 !   16.9   0.0     3e-06    0.0036     140     204 ..      97     164 ..      78     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.3e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                      d v++GGG +G+++A  +a +g  V+lle++++
  gi|313127071|ref|YP_004037341.1|  7 DMVVVGGGTAGAFAAATAASEGldVVLLERKSE 39
                                      78*****************99*********954 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3e-06
                                       EEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEE.TCEEEEEEECT.EEE.E.EEEEEEE--GGGH CS
                               DAO 140 tgqvdpakltaalaraaealGveilegtevtgleeed.gkvwgverttp.gen.d.aadavVnaaGaws 204
                                       +++vd  ++   ++++a +lG ++++ t v++++++d g+v+gv r+++ g + + +ad  +  aGa s
  gi|313127071|ref|YP_004037341.1|  97 GAVVDRKRYGEVILEEADRLGTDMHYDTVVQDVSQDDdGRVTGV-RAKRnGDVvEyEADVTIDGAGALS 164
                                       5778999*************************966555******.666668774246677999999876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   2.9   1.3e-10   1.6e-07       3     317 ..       7     314 ..       5     338 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.3e-10
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyne 79 
                                       d ++VG+G aG+ +a   ++ G +vvl+e+ s++     a+g   +   ++ ++   d +++e  +n++++ a+ ++
  gi|313127071|ref|YP_004037341.1|   7 DMVVVGGGTAGAFAAATAASEGLDVVLLERKSEEEAGHIACGDAIKGTSTFPDVIDLDYLKEESFTNQNITRAVFEN 83 
                                       789***************************************99999999*99999999999999888888777777 PP

                                       CCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEE CS
                     FAD_binding_3  80 lsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrak 156
                                             +  dl++ +++   +v+  ++   +++e+a + g++++ +t v+ + qd++g  + vr k++g   + +a+
  gi|313127071|ref|YP_004037341.1|  84 -----PRGDDLDVPFRGAG-AVVDRKRYGEVILEEADRLGTDMHYDTVVQDVSQDDDGRVTGVRAKRNGDVVEYEAD 154
                                       .....69999**8887765.5677778888888888***************************************** PP

                                       EEEE--GTT-HHHHHHTGGEEEEEE.EEEEEEEEEEEEC.-SCCCTTC...CEEEEECCTTEEEEEECCETEEEEEE CS
                     FAD_binding_3 157 YlvGaDGgrStvrktlgiefegeet.vyeagvldvlfda.dlsdivep...lvlilsaesrgvmviPlentlerfyv 228
                                        ++   G+ S+  ++ +++ ++++t v  +++ ++  ++ d++++v+    +v+ + +e + +   P++       +
  gi|313127071|ref|YP_004037341.1| 155 VTIDGAGALSILQDKTDFSGTTFDTnVSYSQFCSAYREViDVPEPVDYddaIVFKPTEELGYLWYFPRSP----TEI 227
                                       *******************666665155678899999999999998887655555555666668888888....336 PP

                                       EEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHH CS
                     FAD_binding_3 229 qvearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlN 305
                                        + ++ + +e++ k   +++k++lr+  + +  +v  +   a++ ++ + +    g    aGD+a  + Pt+G G+ 
  gi|313127071|ref|YP_004037341.1| 228 NAGLGFQMTEEPMKLV-DDLKRDLRNRPEFEGGTVTDKLGAALPTRRPYDSAVAPG-FIAAGDSAGHVNPTTGGGIP 302
                                       6777776666666665.578999999999999988888888888888887777777.45689999999999999999 PP

                                       HHHHHHHHHHHH CS
                     FAD_binding_3 306 taiqDavnLawk 317
                                        a++ a+  a+ 
  gi|313127071|ref|YP_004037341.1| 303 GAAKSAHWAAKH 314
                                       999888877664 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   4.8e-10   5.7e-07       1      49 [.       7      56 ..       7     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.8e-10
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGGTT--SSSSEEE-TTH CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.thkldtiaelsCnpsiggiak 49
                                      d++V+GgG AG  AA++aa  G++v+L+  ++ ++ ++++C ++i+g++ 
  gi|313127071|ref|YP_004037341.1|  7 DMVVVGGGTAGAFAAATAASEGLDVVLLeRKSEEEAGHIACGDAIKGTST 56
                                      689*************************667778999*********9865 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.6   2.5e-08     3e-05       2      33 ..       7      38 ..       6      43 .. 0.93
   2 ?    1.1   0.0       0.1   1.2e+02     114     148 ..     108     143 ..     104     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.5e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      d++v+GgG AG +aA++aa++g +V+lle+++
  gi|313127071|ref|YP_004037341.1|  7 DMVVVGGGTAGAFAAATAASEGLDVVLLERKS 38
                                      89***************************975 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.1
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EE.EEE. CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfr.vktk 148
                                       ++l+e+++ g +++++t v++v++++dg+++ v++k
  gi|313127071|ref|YP_004037341.1| 108 VILEEADRLGTDMHYDTVVQDVSQDDDGRVTgVRAK 143
                                       67899*****************99999865425553 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.5   0.00015      0.18       2      33 ..       8      39 ..       7      42 .. 0.95
   2 !   12.3   0.0   0.00016      0.19      43      79 ..     106     143 ..     102     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                      +vvvGgG+ g  +A+++a  g +V ++er+++
  gi|313127071|ref|YP_004037341.1|  8 MVVVGGGTAGAFAAATAASEGLDVVLLERKSE 39
                                      79***************************975 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEEEE CS
                         Pyr_redox  43 skilqeklekngievllntkveeiegsedg.vesvklk 79 
                                       ++++ e+  ++g +++++t+v+ + +++dg v++v+ k
  gi|313127071|ref|YP_004037341.1| 106 GEVILEEADRLGTDMHYDTVVQDVSQDDDGrVTGVRAK 143
                                       56788999999************************987 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   1.8e-07   0.00021       1      57 [.       6      62 ..       6      91 .. 0.74
   2 ?    3.8   0.5     0.024        29     183     236 ..     103     161 ..      98     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.8e-07
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias 57
                                      +d+vv+GgG AG  aa t+a  g++v+l+e++ +   g++    a+ g++ +++++ 
  gi|313127071|ref|YP_004037341.1|  6 YDMVVVGGGTAGAFAAATAASEGLDVVLLERKSEEEAGHIACGDAIKGTSTFPDVID 62
                                      689**************************9665555555555566666666666555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.EEE..EEETTSCE..EEESEEEE-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx..xxxxxxxx..xxxxxxxxxxx RF
                       Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgnge.kle..vvledgee..idadlvvvavG 236
                                       k+ ++ + e+  + G +++  t+v+++ ++++ +++      +g++  ++ad  + ++G
  gi|313127071|ref|YP_004037341.1| 103 KRYGEVILEEADRLGTDMHYDTVVQDVSQDDDgRVTgvRAKRNGDVveYEADVTIDGAG 161
                                       56678889999999******************966654344444442266666655555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.3   2.5e-07    0.0003       1      29 [.      10      38 ..      10      64 .. 0.86
   2 ?   -0.1   0.0      0.92   1.1e+03      23      40 ..     108     125 ..      97     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.5e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      +vG+G +G+ aA+++a +g+dv+lle+ +
  gi|313127071|ref|YP_004037341.1| 10 VVGGGTAGAFAAATAASEGLDVVLLERKS 38
                                      8*************************975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.92
                                       EEE-SSSSSSGGG-EECE CS
                     NAD_binding_8  23 lllekrdrlGGraasyev 40 
                                       ++le +drlG +++  +v
  gi|313127071|ref|YP_004037341.1| 108 VILEEADRLGTDMHYDTV 125
                                       689999999998886655 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.6e-06    0.0031      30      66 ..       7      43 ..       2      80 .. 0.85
   2 ?    2.6   0.2      0.06        71     117     157 ..     119     159 ..     110     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleq 66
                                       ++v+GgG+aG  A+ata++ g +V++l+ +++    
  gi|313127071|ref|YP_004037341.1|  7 DMVVVGGGTAGAFAAATAASEGLDVVLLERKSEEEAG 43
                                      689*************************999887665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.06
                                       TS-TTEEEEETTGGGT-SBTT--TBBTTSEEEEETTEEEEE CS
                       AlaDh_PNT_C 117 sMkpgsVivDvAidqGGnvetsrltthgepvveekgvvhyg 157
                                        M+  +V+ Dv+ d  G v  +r  ++g+ v  e +v++ g
  gi|313127071|ref|YP_004037341.1| 119 DMHYDTVVQDVSQDDDGRVTGVRAKRNGDVVEYEADVTIDG 159
                                       6999***************************999*999866 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.5   0.00013      0.16       1      32 [.       7      36 ..       7      47 .. 0.90
   2 ?   -1.8   0.0         1   1.2e+03      86     132 ..     113     159 ..      88     226 .. 0.77
   3 !    6.0   0.0    0.0044       5.2     256     296 ..     281     321 ..     240     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      D+vv+G+G Ag   Aa    a  gl vvl+e 
  gi|313127071|ref|YP_004037341.1|  7 DMVVVGGGTAGAFAAATA--ASEGLDVVLLER 36
                                      99*********9999988..9********985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                     Lycopene_cycl  86 skrlkeellerlv.engvklleakvesveeeeageslvvleggrkira 132
                                        +rl   ++ + v ++  +  +++v+ v+++ +   +v  e++++i++
  gi|313127071|ref|YP_004037341.1| 113 ADRLGTDMHYDTVvQDVSQDDDGRVTGVRAKRN-GDVVEYEADVTIDG 159
                                       566777777776646666667788888888888.55666777777765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0044
                     Lycopene_cycl 256 qkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalre 296
                                       +  +a+G  ag v P+TG  ++ + + a   a+  ++a   
  gi|313127071|ref|YP_004037341.1| 281 PGFIAAGDSAGHVNPTTGGGIPGAAKSAHWAAKHAVKAISD 321
                                       446899**********************9888776666553 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   1.7e-05      0.02      18      56 ..       6      43 ..       3      60 .. 0.86
   2 ?   -2.1   0.1       1.5   1.8e+03      12      26 ..     148     161 ..     117     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                       D+v+vG+G++G  aa + a + +l v++ler+     G
  gi|313127071|ref|YP_004037341.1|  6 YDMVVVGGGTAGAFAAATAASE-GLDVVLLERKSEEEAG 43
                                      59******************99.********99765555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                       HHHHTEEEEEEE--S CS
                              Thi4  12 llkyaesDvvivGaG 26 
                                       +++y e+Dv i GaG
  gi|313127071|ref|YP_004037341.1| 148 VVEY-EADVTIDGAG 161
                                       4444.6777777777 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   5.1e-05     0.061       3      34 ..       9      40 ..       7      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                                      EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseea 34
                                       v+G Gt Ga  aa +as+gl+Vvl+++++e 
  gi|313127071|ref|YP_004037341.1|  9 VVVGGGTAGAFAAATAASEGLDVVLLERKSEE 40
                                      69*************************97664 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0053       6.3       1      44 [.       6      49 ..       6      84 .. 0.78
   2 ?    3.4   0.0     0.034        41     211     257 ..     121     163 ..     105     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                       GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvleaggreknrl.imvl 44
                                      +d +v+ggG+ag+  Aa  ++ +   v++le  ++e+       +
  gi|313127071|ref|YP_004037341.1|  6 YDMVVVGGGTAGAF-AAATAASEGLDVVLLERKSEEEAGHiACGD 49
                                      6899**********.999999999**********99987754444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.034
                       GMC_oxred_N 211 ltgakaekiilegrkkravGVeasdkkgtvkrlvvaakevvvaaGal 257
                                        +++ ++ +  ++ ++r++GV+a++++     + ++a++++  aGal
  gi|313127071|ref|YP_004037341.1| 121 HYDTVVQDV-SQDDDGRVTGVRAKRNGDV---VEYEADVTIDGAGAL 163
                                       444444444.46789**********9999...99*****99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2887.35
//
Query:       gi|313127072|ref|YP_004037342.1|  [L=276]
Description: aldo/keto reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-63  214.5   0.0    2.3e-61  207.6   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.6   0.0   1.3e-65   2.3e-61       2     293 ..      20     263 ..      19     264 .. 0.98

  Alignments for each domain:
  == domain 1  score: 207.6 bits;  conditional E-value: 1.3e-65
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                       lglGtwq        +e+ ++++++al  G++++DtA++Y    +ee++Ge ++++ ++re++++atKv      + 
  gi|313127072|ref|YP_004037342.1|  20 LGLGTWQNDE-----PEDCARAVETALNMGYRHIDTAQIY---GNEEFVGEGIENATVPREDIFLATKV------WI 82 
                                       7999998775.....79***********************...9*************************......** PP

                                       SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT- CS
                      Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkv 155
                                       ++ls +++ +  eesl++Lg++ vDll++H+p ++++  ee+++a++el++eGki  iG+Snf+ eq+e a k + v
  gi|313127072|ref|YP_004037342.1|  83 DNLSYDEVLATTEESLEKLGVESVDLLYVHWPAREYD-PEETFRAFNELYDEGKIDRIGISNFEPEQIETAVKSADV 158
                                       *************************************.*************************************** PP

                                       -EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHH CS
                      Aldo_ket_red 156 kivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeel 232
                                       +i a+qve ++l  l++e l+ +c+++++ ++ayspl++G                                 ++el
  gi|313127072|ref|YP_004037342.1| 159 PIFANQVELHPL--LQQEDLRAACEEHDIEVVAYSPLARGTVF-----------------------------EVPEL 204
                                       ************..**************************999.............................6899* PP

                                       HHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHHH CS
                      Aldo_ket_red 233 selakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldell 293
                                       +++a++hgvs aq++l+++   ++++++ip+a+  ++++dn ++l ++l++e+++++d+++
  gi|313127072|ref|YP_004037342.1| 205 EAIAEKHGVSEAQVSLAWLR--EKGVTAIPKATGEDHIRDNWQSLRVELDAEDIDRIDNIE 263
                                       ********************..************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1920.87
//
Query:       gi|313127073|ref|YP_004037343.1|  [L=65]
Description: hypothetical protein Hbor_23380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   18.3   1.5     0.0026   18.1   1.5    1.2  1  DUF308    Short repeat of unknown function (DUF308)


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.5   1.4e-07    0.0026       4      52 ..      13      62 ..       9      65 .] 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-07
                            DUF308  4 illivlGil.alllPvaallalvllfGilllvsGivqiiaafaarkknrg 52
                                      + l++lG + ++++P++ + ++ ++++  +lv+G++ ++ ++++ +++ +
  gi|313127073|ref|YP_004037343.1| 13 VGLVALGTVgLIMMPAMQTRTVLMMVAPSMLVFGAICLVLGIKHGEYRAS 62
                                      567888877255678999************************77776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 445.17
//
Query:       gi|313127074|ref|YP_004037344.1|  [L=372]
Description: hypothetical protein Hbor_23390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.7e-115  386.1   4.2   1.9e-115  385.9   4.2    1.0  1  DUF373    Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.9   4.2  1.1e-119  1.9e-115       2     335 .]       3     351 ..       2     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 385.9 bits;  conditional E-value: 1.1e-119
                            DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvg 78 
                                       tLvlcvDr +D+grkag+ tPvvG+eav++++++++ladPeDS+vN+l++a++v ++L++e+ed  vavv+G +++ 
  gi|313127074|ref|YP_004037344.1|   3 TLVLCVDRSNDIGRKAGLPTPVVGWEAVRSLVTDVGLADPEDSNVNCLLEALRVSRDLRDEKEDSIVAVVSGVNDTL 79 
                                       8**************************************************************************** PP

                            DUF373  79 veadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelrk 155
                                       v adr++a+q+d ++++++++saivV+D+a+De+v+p+i+sr+++dsv+rVvV+q+++iEstyyllk++l+d+elr+
  gi|313127074|ref|YP_004037344.1|  80 VGADRSLAAQVDALVDEYDPESAIVVVDSASDERVVPVIESRLRIDSVDRVVVRQAHDIESTYYLLKQFLADEELRS 156
                                       ***************************************************************************** PP

                            DUF373 156 tiLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvalllll 232
                                       tiLvplG++ll+++lll+   p+la+a+i  +lG++ll++G+ +d+ll+e++e+++++l++g++++vtyvva+ l+l
  gi|313127074|ref|YP_004037344.1| 157 TILVPLGATLLLMPLLLTRFEPQLAFAVIGSVLGAALLYKGLAIDQLLAESPERIRDALYSGQVSIVTYVVAAGLTL 233
                                       ******************7779******************************************************* PP

                            DUF373 233 igiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglv 309
                                       +g++ g  s++ ++  s +s +l+++++fiy+av+wlala+ltas+g+++de++ + +    ++l+lpf ++a+glv
  gi|313127074|ref|YP_004037344.1| 234 VGAFLGALSVTPLTG-SGTSATLISTMQFIYHAVPWLALAALTASAGRLLDELI-GTDGVSRQYLNLPFGIVALGLV 308
                                       *********999988.777899999*****************************.6679999*************** PP

                            DUF373 310 lygasaylls.................lsilalslvvgivval 335
                                       ++g+++++l+                  ++lal++v+givv++
  gi|313127074|ref|YP_004037344.1| 309 VRGFAGWFLQregilsdavlfswalsaRQRLALFIVGGIVVSV 351
                                       ********99******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2782.44
//
Query:       gi|313127075|ref|YP_004037345.1|  [L=330]
Description: signal peptide peptidase a [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-43  148.2   0.0    2.7e-43  147.6   0.0    1.2  1  Peptidase_S49  Peptidase family S49
    9.2e-05   21.6   0.0    0.00014   21.0   0.0    1.1  1  SDH_sah        Serine dehydrogenase proteinase


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.6   0.0     3e-47   2.7e-43       8     153 ..     138     282 ..     134     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 3e-47
                                       -EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS--HHH CS
                     Peptidase_S49   8 PvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrrelteee 84 
                                       P +a+a ++ aSggY++as++d+i+a   +ivgsiGvi + +n+++l+d+lgv+ + ++aG+yk+a++  +e + +e
  gi|313127075|ref|YP_004037345.1| 138 PTIAYATDTCASGGYWIASGCDEIWAHDVSIVGSIGVIGSSVNVHELADRLGVSYERFAAGKYKDAGTALKEPSADE 214
                                       899************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCHC CS
                     Peptidase_S49  85 reilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleelakv 153
                                       re+lq l+d+ y++Fv+ Va++R+++ +++ + +e+rv++g+ A +lgLvdelgt dd++++l+   +v
  gi|313127075|ref|YP_004037345.1| 215 REYLQGLVDDYYDDFVERVAEGREMDPDAIRD-TEARVYLGSRAHELGLVDELGTRDDVLDRLAARLDV 282
                                       *****************************975.8*****************************987776 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.6e-08   0.00014      78     155 ..      92     172 ..      90     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-08
                           SDH_sah  78 seevlrairltpkdkpid.li..ihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenav 151
                                       s++v+  i+++ +d  +d l+  + tpGG vl +++i +a+ e   +t         sGG  ia   dei   + ++
  gi|313127075|ref|YP_004037345.1|  92 SDDVVEQIQTAADDGAVDgLLvrLNTPGGAVLPSDDIRRAVAEFDGPTIAYATDTCASGGYWIASGCDEIWAHDVSI 168
                                       789999***********95332358*********************************************9999998 PP

                           SDH_sah 152 lGpv 155
                                       +G +
  gi|313127075|ref|YP_004037345.1| 169 VGSI 172
                                       8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2420.20
//
Query:       gi|313127076|ref|YP_004037346.1|  [L=307]
Description: hypothetical protein Hbor_23410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        1.3    9.0  32.9      0.047   13.7   9.7    3.5  5  Laminin_II    Laminin Domain II
        1.5    9.1  20.9       0.21   11.9   1.1    3.9  3  DUF948        Bacterial protein of unknown function (DUF948)
        4.4    7.8  36.6        1.5    9.2   5.0    5.6  5  DUF1771       Domain of unknown function (DUF1771)
        9.2    6.8   9.2        8.3    6.9   2.2    3.0  2  ocr           DNA mimic ocr


Domain annotation for each model (and alignments):
>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.45     2e+03      63      86 ..      36      59 ..      14      71 .. 0.60
   2 ?   13.7   9.7     1e-05     0.047      30     101 ..      70     135 ..      48     143 .. 0.78
   3 ?    3.8   7.3     0.012        55      17     106 ..     152     240 ..     142     243 .. 0.69
   4 ?    5.4   6.0    0.0038        17       4      84 ..     183     263 ..     178     270 .. 0.90
   5 ?    3.2   1.9     0.019        83       5      80 ..     219     292 ..     215     298 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.45
                                      XX--TTTTTGGGHHHHHHHHHH.. CS
                        Laminin_II 63 kLeklapqLldklkelkqleeass 86
                                      +L kla qL d+ + l+q  ++++
  gi|313127076|ref|YP_004037346.1| 36 QLIKLAGQLRDRRNDLNQMASERA 59
                                      455555555555555555555444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHHHH CS
                        Laminin_II  30 keklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseikelIaq 101
                                       +ek+    ++++e  e+ +++n+++++ +++  +L+ +a++L+dk++++k+  e     +++i+e+ke I+q
  gi|313127076|ref|YP_004037346.1|  70 REKV----DEAQEHREQRDSLNEQVQEHKNKRNELNAEANELFDKVEQMKEDLELDD--GKDIEELKEEIEQ 135
                                       2222....333445677779******************************9988877..99*******9998 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHH.HHHHHHH...HHHHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklke.lkqleeassslsdni 92 
                                       e +++++++ e++++k  ++++s  e +e++++a ++  +A++  +k+++la++  +  ++ ++  +ea   + d+ 
  gi|313127076|ref|YP_004037346.1| 152 ELIEKIENKREELRQKKDKVEDS-GELEELIEEAEEVRSEASQHHQKVTELADKAQEHHNQmIEAYREA-DDIRDKA 226
                                       55667777777777777777777.788888888888888888888888888887766554414444444.3377777 PP

                                       HHHHHHHHHHHHHH CS
                        Laminin_II  93 seikelIaqARkaA 106
                                       + + el   A +aA
  gi|313127076|ref|YP_004037346.1| 227 DAMHELFVEAQEAA 240
                                       77777777777766 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0038
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                        a+e+ + a++  +++++l+ + ++  +++ e+ r+++ + +k++++ +  ++A+++     +   ++ ++l+el++
  gi|313127076|ref|YP_004037346.1| 183 EAEEVRSEASQHHQKVTELADKAQEHHNQMIEAYREADDIRDKADAMHELFVEAQEAADRHHEDFVRVQKRLRELDK 259
                                       4677778888889999999999999999999********************************************99 PP

                                       HHHH CS
                        Laminin_II  81 leea 84 
                                       +ee+
  gi|313127076|ref|YP_004037346.1| 260 QEEE 263
                                       9987 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.019
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XX--TTTTTGGGHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvk..kLeklapqLldklkelk 79 
                                       a+++ ++a +  e   + ++  ++  e+  ++++ ++e +    +  +  rdA+r+ k    +++a+++ +k+ke +
  gi|313127076|ref|YP_004037346.1| 219 ADDIRDKADAMHELFVEAQEAADRHHEDFVRVQKRLRELD----KQEEEERDAERAEKreAAKEEAEEIYQKFKEGE 291
                                       6777888888888888888888888888888888866655....455556666654441146788889988888766 PP

                                       H CS
                        Laminin_II  80 q 80 
                                       +
  gi|313127076|ref|YP_004037346.1| 292 T 292
                                       5 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   3.5    0.0028        12      29      70 ..      77     118 ..      33     122 .. 0.81
   2 ?    0.6   2.0      0.15   6.7e+02      26      71 ..     124     172 ..     118     177 .. 0.78
   3 ?   11.9   1.1   4.6e-05      0.21      24      82 ..     184     241 ..     177     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0028
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekv 70 
                                       +e +++ ++l++qv++  ++ ++l a++nel + v++  e++
  gi|313127076|ref|YP_004037346.1|  77 QEHREQRDSLNEQVQEHKNKRNELNAEANELFDKVEQMKEDL 118
                                       455666777888888888888888888888888888766655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                            DUF948  26 ktldeaaatieele..kqvdpilkeve.dllakvnelledvneklekvd 71 
                                       k ++e+++ ie+le  +q++ +++e e +l++k+++  e++++k +kv+
  gi|313127076|ref|YP_004037346.1| 124 KDIEELKEEIEQLEfrQQTEVLSTEDErELIEKIENKREELRQKKDKVE 172
                                       5678888999999888888888776542788888888888888888886 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 4.6e-05
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                       ++++ +ea+++ +++++ +d+  +  +++++  +e ++d+++k +++ +l+ +++++++
  gi|313127076|ref|YP_004037346.1| 184 AEEVRSEASQHHQKVTELADKAQEHHNQMIEAYRE-ADDIRDKADAMHELFVEAQEAAD 241
                                       566778999**************************.*******************9876 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.5    0.0011         5       6      54 ..      39      89 ..      36      92 .. 0.92
   2 ?    4.5   0.3    0.0099        44       7      26 ..      89     108 ..      86     115 .. 0.65
   3 ?    9.2   5.0   0.00035       1.5      18      55 ..     180     219 ..     148     222 .. 0.74
   4 ?    4.8   0.1    0.0083        37       9      28 ..     223     242 ..     220     247 .. 0.83
   5 ?    0.2   1.1      0.22   9.9e+02      11      28 ..     269     286 ..     252     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                           DUF1771  6 aeAdeharkrnelfekAaeAyrrGd..gaaAkelseqGkehgekmeeanre 54
                                      + A ++ ++rn l + A+e  ++ d   a+ +e +++++eh+e+ + +n++
  gi|313127076|ref|YP_004037346.1| 39 KLAGQLRDRRNDLNQMASERASKRDdlNAKTREKVDEAQEHREQRDSLNEQ 89
                                      6799*********************888888899************99997 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0099
                           DUF1771   7 eAdeharkrnelfekAaeAy 26 
                                       +++eh +krnel ++A e +
  gi|313127076|ref|YP_004037346.1|  89 QVQEHKNKRNELNAEANELF 108
                                       55666666666666666655 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00035
                           DUF1771  18 lfekAaeAyrrGd..gaaAkelseqGkehgekmeeanreA 55 
                                       l e+A e +++    +++  el+++++eh ++m ea reA
  gi|313127076|ref|YP_004037346.1| 180 LIEEAEEVRSEASqhHQKVTELADKAQEHHNQMIEAYREA 219
                                       5555555555444557888888888888888888888887 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.0083
                           DUF1771   9 deharkrnelfekAaeAyrr 28 
                                       ++ a++++elf +A+eA  r
  gi|313127076|ref|YP_004037346.1| 223 RDKADAMHELFVEAQEAADR 242
                                       567899**********9765 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.22
                           DUF1771  11 harkrnelfekAaeAyrr 28 
                                        a+kr  + e+A e y++
  gi|313127076|ref|YP_004037346.1| 269 RAEKREAAKEEAEEIYQK 286
                                       567777777777777776 PP

>> ocr  DNA mimic ocr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.043   1.9e+02       6      37 ..     104     134 ..      99     143 .. 0.82
   2 ?    6.9   2.2    0.0018       8.3      10      53 ..     206     249 ..     198     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHHHHHHHTT---GGG-HHHHH CS
                               ocr   6 ysdvydhayellkeyiryddvrdeddlsdkih 37 
                                        ++++d+  e +ke +  dd +d ++l+++i 
  gi|313127076|ref|YP_004037346.1| 104 ANELFDKV-EQMKEDLELDDGKDIEELKEEIE 134
                                       56777775.56799***********9999986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHTT---GGG-HHHHHHHHHHHS--SHHHHHH CS
                               ocr  10 ydhayellkeyiryddvrdeddlsdkiheaadnavphyyadifs 53 
                                        +h  +++  y   dd+rd+ d   ++   a++a   ++ d + 
  gi|313127076|ref|YP_004037346.1| 206 QEHHNQMIEAYREADDIRDKADAMHELFVEAQEAADRHHEDFVR 249
                                       579999**************999989988888888877777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4006  (0.223437); expected 358.6 (0.02)
Passed bias filter:                      770  (0.0429472); expected 358.6 (0.02)
Passed Vit filter:                       226  (0.0126053); expected 17.9 (0.001)
Passed Fwd filter:                       109  (0.00607954); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 1.73u 0.41s 00:00:02.14 Elapsed: 00:00:00.62
# Mc/sec: 1499.65
//
Query:       gi|313127077|ref|YP_004037347.1|  [L=143]
Description: hypothetical protein Hbor_23420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-52  176.8   0.1    2.1e-52  176.6   0.1    1.0  1  DUF371    Domain of unknown function (DUF371)


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.6   0.1   1.2e-56   2.1e-52       1     133 []       6     143 .]       6     143 .] 0.97

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 1.2e-56
                                       EEEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS.....-EEEE CS
                            DUF371   1 ikarGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevge.....ledei 72 
                                       ++arGHenv+aeh+sT+e+t+dd+ltp+gdCI++vead++++d+++++++a+++e+atit+++ev++     +++++
  gi|313127077|ref|YP_004037347.1|   6 VRARGHENVSAEHASTFEVTSDDWLTPAGDCILAVEADRTPEDFDDDFVAACQDESATITAIVEVEDddgetYQQTV 82 
                                       78***************************************************************7666777999** PP

                                       EEE--TT-----SSEEEEESSS---TTEEEBS-S--GGGS-HHHHHHHHTT-EEEEEEEEE CS
                            DUF371  73 tgrGspkltlenerdlvvRkSdyvddrTllvkadkaaadldrelveaLkkgaeltveleve 133
                                       +g+G+p+lt+e +r++v R+SdyvddrT+lv ad+aa d+dr+lv+aL++g ++t++l+ve
  gi|313127077|ref|YP_004037347.1|  83 EGSGHPDLTFEGDRSHVGRTSDYVDDRTILVGADAAAGDFDRDLVAALANGGDVTFTLRVE 143
                                       **********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.53
# Mc/sec: 813.28
//
Query:       gi|313127078|ref|YP_004037348.1|  [L=277]
Description: endoiii-related endonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-16   58.6   0.0    1.1e-15   58.0   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
      7e-07   29.4   6.6    1.4e-06   28.4   6.6    1.6  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
    0.00036   20.3   0.0    0.00099   18.9   0.0    1.8  1  HHH            Helix-hairpin-helix motif
     0.0083   16.7   0.1      0.065   13.8   0.0    2.5  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.035   13.8   0.3        4.6    6.9   0.1    2.4  2  PRiA4_ORF3     Plasmid pRiA4b ORF-3-like protein
      0.082   12.9   0.1       0.19   11.7   0.0    1.5  2  DUF2400        Protein of unknown function (DUF2400)
       0.15   12.5   2.8       0.78   10.2   0.1    2.7  3  DUF732         Protein of unknown function (DUF732)


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   4.2e-19   1.1e-15       1     103 [.      57     215 ..      57     219 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 4.2e-19
                                       HHHHHHTTS-HHHHHHHHHHHHHHHS.............HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfg.............fptpedladadeekLrelirelGfyrrKakyikelAri 64 
                                       v++ilsq+tsd++  ++  +l++r+              +  + +lada++++L+e i ++G+y++K + i+ +A+ 
  gi|313127078|ref|YP_004037348.1|  57 VRTILSQNTSDVASQPAHDSLMDRYAggdgdsadgdsadGDLAAALADAEQSELAETIASAGLYNQKSEMIIGAAER 133
                                       799************************************999*********************************** PP

                                       HH............................................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHH CS
                                       xx............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  65 lv............................................gkpdvlivvDvhvrrilkrlrsikekktkkk 97 
                                       +                                             g+ + +++vD+hv+ri +r+++++++ +++ 
  gi|313127078|ref|YP_004037348.1| 134 ICesfggadgfdefvkdedpdtvrkrlldihgvgpktadcvllfsgGRGG-VFPVDTHVHRIGRRMGLASADADHED 209
                                       *********************************************97655.8899********************** PP

                                       HHHHHH CS
                                       xxxxxx RF
                           HhH-GPD  98 vekkle 103
                                       v+++le
  gi|313127078|ref|YP_004037348.1| 210 VREHLE 215
                                       **9995 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   6.6   5.6e-10   1.4e-06       1      17 []     238     258 ..     238     258 .. 1.00

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.6e-10
                     EndIII_4Fe-2S   1 CTARkPkC....eaCPLaDlC 17 
                                       C+ARkP+C    eaCPL+DlC
  gi|313127078|ref|YP_004037348.1| 238 CKARKPACldgpEACPLYDLC 258
                                       ********************* PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.9e-07   0.00099      13      30 .]     160     177 ..     157     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.9e-07
                                       HHTSTT-SHHHHHHHHHH CS
                               HHH  13 LlalPGVGpktAeaIlsy 30 
                                       Ll++ GVGpktA+++l +
  gi|313127078|ref|YP_004037348.1| 160 LLDIHGVGPKTADCVLLF 177
                                       899************976 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       0.7   1.8e+03      28      39 ..     101     112 ..      94     139 .. 0.69
   2 !   13.8   0.0   2.5e-05     0.065      25      49 ..     143     172 ..     109     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.7
                                       HHHHS-HHHHHT CS
                             HHH_5  28 dlaaadveeLak 39 
                                       +la+a++ eLa+
  gi|313127078|ref|YP_004037348.1| 101 ALADAEQSELAE 112
                                       667777766665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.5e-05
                                       SHHHHHHS.-....HHHHHTSTTS-HHHHH CS
                             HHH_5  25 svedlaaa.d....veeLakipGiGkktAe 49 
                                        ++++++  d    +++L +i+G+G+ktA+
  gi|313127078|ref|YP_004037348.1| 143 GFDEFVKDeDpdtvRKRLLDIHGVGPKTAD 172
                                       45665433242222477***********98 PP

>> PRiA4_ORF3  Plasmid pRiA4b ORF-3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0093        24     114     143 ..     119     149 ..     108     163 .. 0.77
   2 ?    6.9   0.1    0.0018       4.6     115     150 ..     240     275 ..     227     277 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0093
                        PRiA4_ORF3 114 ear.yprclagegacppEDvgGvgGyeelle 143
                                        ++    ++ g+ + + E  gG +G++e+++
  gi|313127078|ref|YP_004037348.1| 119 LYNqKSEMIIGAAERICESFGGADGFDEFVK 149
                                       444356688999*****************95 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0018
                        PRiA4_ORF3 115 aryprclagegacppEDvgGvgGyeelleiladpeh 150
                                       ar p cl+g +acp  D     G +e+ e++ dp +
  gi|313127078|ref|YP_004037348.1| 240 ARKPACLDGPEACPLYDLCDRVGVDEVEETVVDPAE 275
                                       458***************999999999999999875 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.5   6.4e+03      30      45 ..     124     139 ..     101     162 .. 0.44
   2 ?   11.7   0.0   7.2e-05      0.19     172     193 ..     184     205 ..     183     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                           DUF2400  30 rkqiikkleellelmd 45 
                                        ++ii  +e+++e ++
  gi|313127078|ref|YP_004037348.1| 124 SEMIIGAAERICESFG 139
                                       2334444444444333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.2e-05
                           DUF2400 172 iiPlDvHvarvarklgllkrkq 193
                                       ++P+D+Hv+r++r++gl +   
  gi|313127078|ref|YP_004037348.1| 184 VFPVDTHVHRIGRRMGLASADA 205
                                       57***************86433 PP

>> DUF732  Protein of unknown function (DUF732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.1   2.9e+03      14      31 ..      23      40 ..      14      73 .. 0.71
   2 ?   10.2   0.1   0.00031      0.78      14      60 ..      99     145 ..      96     163 .. 0.76
   3 ?    1.3   0.1      0.17   4.5e+02      14      52 ..     201     240 ..     195     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                            DUF732 14 apAaAdsaddaFlaalnq 31
                                       pA+Ad+  +a +++l q
  gi|313127078|ref|YP_004037348.1| 23 VPAEADTRAEAVVDELGQ 40
                                      577777666666666655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00031
                            DUF732  14 apAaAdsaddaFlaalnqagiaygspdaa.ialGkavCkkldsGksae 60 
                                       a A Ad+  +++ +++++ag  y+++ ++ i++++++C+++     ++
  gi|313127078|ref|YP_004037348.1|  99 AAALADAEQSELAETIASAGL-YNQKSEMiIGAAERICESFGGADGFD 145
                                       55677767888**********.66555555*********995444444 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.17
                            DUF732  14 apAaAdsadda..FlaalnqagiaygspdaaialGkavCkk 52 
                                       a+A Ad+ d +  + a++ ++   +g+++ +i++G++ Ck+
  gi|313127078|ref|YP_004037348.1| 201 ASADADHEDVRehLEADVPAEKCGFGHTA-MIQFGREYCKA 240
                                       67788766665668888888888888766.79999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1922.77
//
Query:       gi|313127079|ref|YP_004037349.1|  [L=709]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-45  153.6   0.0    3.5e-18   65.7   0.1    4.7  4  PAS_3          PAS fold
    2.4e-35  120.9   1.0    2.9e-15   56.2   0.0    4.9  4  PAS            PAS fold
    2.7e-30  104.8   6.9      3e-10   40.3   0.1    4.7  4  PAS_4          PAS fold
    2.1e-25   89.0   0.3      5e-12   46.0   0.0    4.5  5  PAS_9          PAS domain
      1e-15   57.3   0.1    6.4e-07   29.3   0.0    3.1  3  PAS_8          PAS domain
    5.5e-13   49.4   0.1    2.1e-12   47.5   0.1    2.1  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    2.8e-11   43.4   0.4    8.6e-11   41.9   0.4    1.9  1  HATPase_c_2    Histidine kinase-like ATPase domain
    0.00013   21.8   0.0    0.00033   20.5   0.0    1.7  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
  ------ inclusion threshold ------
        0.2   12.5   3.0        1.3    9.8   0.0    3.6  3  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   3.6e-11   7.1e-08      22      89 .]      48     114 ..      42     114 .. 0.90
   2 !   44.4   0.0   7.5e-15   1.5e-11       2      75 ..     148     221 ..     147     231 .. 0.89
   3 !   65.7   0.1   1.8e-21   3.5e-18       2      89 .]     274     361 ..     273     361 .. 0.97
   4 ?    4.9   0.0     0.016        32       4      46 ..     400     440 ..     397     450 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.6e-11
                             PAS_3  22 kveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrvigva 89 
                                       +++++ +++hpeDre+v e+l+ +l++g+++++e+Ri+  d e+  +e+r+++ r  +    rv+g+a
  gi|313127079|ref|YP_004037349.1|  48 SFDELSEIIHPEDREQVVETLESSLETGASFNIEFRILV-DDEVQVIETRGSIRREPEMGSPRVVGIA 114
                                       468899*****************************9985.77899*********98888888899985 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 7.5e-15
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqeal..kkgepyegeyRirrkdGeyrwveararvi 75 
                                        yvs++v++++Gy+ +e+lg   ++ dl++p Dr+ +   l  +   +k++p  +eyR+r+ dG++rwve+r+++ 
  gi|313127079|ref|YP_004037349.1| 148 EYVSPAVRRVFGYETDEILGA--NISDLIYPPDRDDALPVLLGSGmtDKNSPERVEYRLRHGDGSVRWVESRVSPR 221
                                       59*******************..***************999955433777799********************997 PP

  == domain 3  score: 65.7 bits;  conditional E-value: 1.8e-21
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + +  ++e+++ + +  ++g++e ++ +vh +D++ v++a+++ +++gepy+++yRi+r dG  rw+ ar++v+ d+
  gi|313127079|ref|YP_004037349.1| 274 VNWHSSCERVFRVPEGGFEGTYEAFARRVHDDDLPAVEAAINRTVNEGEPYHVDYRIIRDDGVERWITARGKVLSDS 350
                                       679999999999***************************************************************** PP

                             PAS_3  79 ngkpvrvigva 89 
                                       +g+p+r++gv+
  gi|313127079|ref|YP_004037349.1| 351 SGNPTRLLGVV 361
                                       *********96 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.016
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqeal 46 
                                       v+e+    +G s+eel+g+  s+ d +   D e+  + ++++ 
  gi|313127079|ref|YP_004037349.1| 400 VNEALAAAVGCSKEELIGT--SIGDQLESADAEESLQRIMALS 440
                                       899999*************..**99999999999888887665 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0047       9.4      46     100 ..      52     104 ..       9     117 .. 0.66
   2 !   56.2   0.0   1.5e-18   2.9e-15       2     101 ..     126     226 ..     125     236 .. 0.95
   3 !   10.6   0.0   0.00021      0.42      48     113 .]     299     364 ..     251     364 .. 0.69
   4 !   42.7   0.0   2.4e-14   4.8e-11       2      64 ..     376     438 ..     375     472 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0047
                                       GGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC.TTSSEEEEEEEEEEEEETT CS
                               PAS  46 lldliheeddaelaelleqlleqgeesrageisfkl.rdgrpihlevraspvrdag 100
                                       l++ ih+ed   + + +e+l+++ e + +++i f+  +d ++  +e+r s +r+++
  gi|313127079|ref|YP_004037349.1|  52 LSEIIHPED---REQVVETLESSLETGASFNIEFRIlVDDEVQVIETRGSIRREPE 104
                                       444467776...67777777777777777777777777*********999999986 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 1.5e-18
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesragei 77 
                                       ++++i+e++ d i vvD  g+i yv++a ++ +G++ +e+lg +++dli ++d++  l+ ll   + ++++++ +e 
  gi|313127079|ref|YP_004037349.1| 126 EFQTIVEQSSDVIAVVDDTGVIEYVSPAVRRVFGYETDEILGANISDLIYPPDRDdALPVLLGSGMTDKNSPERVEY 202
                                       799************************************************************************** PP

                                       EEECTTSSEEEEEEEEEEEEETTE CS
                               PAS  78 sfklrdgrpihlevraspvrdagg 101
                                       +++  dg+++++e r+sp++da +
  gi|313127079|ref|YP_004037349.1| 203 RLRHGDGSVRWVESRVSPRGDAMS 226
                                       ********************9855 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00021
                                       GGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  48 dliheedda.elaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         ++++dd   + +++ +  ++ge+ +  + ++ + dg ++++  r + + d +g+++ +lgv+ di
  gi|313127079|ref|YP_004037349.1| 299 ARRVHDDDLpAVEAAINRTVNEGEPYHV-DYRIIRDDGVERWITARGKVLSDSSGNPTRLLGVVIDI 364
                                       4556677775777777777777777766.5555555*****************************98 PP

  == domain 4  score: 42.7 bits;  conditional E-value: 2.4e-14
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHH CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleq 64 
                                       ++++i+e++pdpi v+De g++++vN+a +   G s ee++g s+ d++   d +e  +++  
  gi|313127079|ref|YP_004037349.1| 376 QYERIVETAPDPIYVLDETGDFTLVNEALAAAVGCSKEELIGTSIGDQLESADAEESLQRIMA 438
                                       89***********************************************99865444444433 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.8e-05     0.035      41     110 .]      53     122 ..      41     122 .. 0.92
   2 !   40.3   0.1   1.5e-13     3e-10       1     109 [.     131     240 ..     131     241 .. 0.90
   3 !   18.1   0.1   1.2e-06    0.0025      47     110 .]     305     369 ..     278     369 .. 0.88
   4 !   32.9   0.1     3e-11     6e-08       2     107 ..     382     489 ..     381     492 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                             PAS_4  41 aellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        e+  +ed++++ + l+  le++++   +   l ++e +++e+r +  r+++ +   v++i++DiTer+r
  gi|313127079|ref|YP_004037349.1|  53 SEIIHPEDREQVVETLESSLETGASFNIEFRILVDDEVQVIETRGSIRREPEMGSPRVVGIATDITERKR 122
                                       4777788****************99999999999***********9999***999*************97 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 1.5e-13
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlae.llpeedaarleralrrvlegeepiefleelll.. 74 
                                       +++++d++av+d+ g+++y+++a +++fg++ +e+lG    + ++p++  ++l   l   ++ + + e++e++l+  
  gi|313127079|ref|YP_004037349.1| 131 VEQSSDVIAVVDDTGVIEYVSPAVRRVFGYETDEILGANISDlIYPPDRDDALPVLLGSGMTDKNSPERVEYRLRhg 207
                                       699**************************************96778877888888888888888888888888888* PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +g+ r++e r++P  d+      +++ +rDiTer+
  gi|313127079|ref|YP_004037349.1| 208 DGSVRWVESRVSPRGDAMSS--NLVINTRDITERV 240
                                       *************9987777..99999******97 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.2e-06
                             PAS_4  47 edaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +d +++e+a++r + ++ep++      + +g er++  r   l d+sG +  +l++++DiTe+++
  gi|313127079|ref|YP_004037349.1| 305 DDLPAVEAAINRTVNEGEPYHVDYRIIRdDGVERWITARGKVLSDSSGNPTRLLGVVIDITEQKE 369
                                       477899*****************999999*********************************985 PP

  == domain 4  score: 32.9 bits;  conditional E-value: 3e-11
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelll..p 75 
                                       +  pd+++vld+ g ++ +N+a a+ +g++ eel+G +  + l    + + l+r+++     ee+ + +  l+l  p
  gi|313127079|ref|YP_004037349.1| 382 ETAPDPIYVLDETGDFTLVNEALAAAVGCSKEELIGTSIGDQLESAdAEESLQRIMALS--DEESDSPPLDLTLstP 456
                                       778*************************************8665541444444444333..333333333333357* PP

                             PAS_4  76 geerhyelrl.lPlrdesGevigvlvisrDiTe 107
                                       +++r ye+++ l  +d +G++  +++++rD+T+
  gi|313127079|ref|YP_004037349.1| 457 DGTRDYEVNIaLSGDDQRGDAPRTVGVARDVTD 489
                                       **********8888899999************7 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.36   7.1e+02      40     104 .]      56     119 ..      34     119 .. 0.58
   2 !   46.0   0.0   2.5e-15     5e-12       2     104 .]     136     238 ..     135     238 .. 0.91
   3 !   16.5   0.0   3.8e-06    0.0077      44     104 .]     308     366 ..     280     366 .. 0.89
   4 !   20.0   0.0   3.1e-07   0.00061       1     104 []     385     489 ..     385     489 .. 0.89
   5 ?   -2.7   0.0       3.5   6.9e+03      40      59 ..     522     543 ..     508     591 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.36
                             PAS_9  40 f..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                       +  ++ ++  e+l+  le+g    ++ e  +  +++ ++  + + s  ++ + +  ++++i +Dite
  gi|313127079|ref|YP_004037349.1|  56 IhpEDREQVVETLESSLETGA--SFNIEFRILVDDEVQVI-ETRGSIRREPEMGSPRVVGIATDITE 119
                                       333444444444444455555..67777777666664444.34444444447777778999999997 PP

  == domain 2  score: 46.0 bits;  conditional E-value: 2.5e-15
                             PAS_9   2 dgilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirknge 74 
                                       d i+++++ g ++ y+++a++r++Gy  +e+lg +i+dl+  +p++++ l  +l +g +   ++++ve+ l++ +g+
  gi|313127079|ref|YP_004037349.1| 136 DVIAVVDDTG-VIeYVSPAVRRVFGYETDEILGANISDLI-YPPDRDDALPVLLGSGMTdknSPERVEYRLRHGDGS 210
                                       6688888999.555**************************.************************************ PP

                             PAS_9  75 tfwvlltaspvkdd.dgelvgiivilrDite 104
                                         wv+ ++sp  d+ + +   +++  rDite
  gi|313127079|ref|YP_004037349.1| 211 VRWVESRVSPRGDAmSSN---LVINTRDITE 238
                                       ***********6664444...558*****98 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 3.8e-06
                             PAS_9  44 peanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                       p  +  +++ +++g+  +++v++ +ir++g + w+ ++   + d++g+ ++++++++Dite
  gi|313127079|ref|YP_004037349.1| 308 PAVEAAINRTVNEGE--PYHVDYRIIRDDGVERWITARGKVLSDSSGNPTRLLGVVIDITE 366
                                       556778889999999..*****************99999999999***************8 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 3.1e-07
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirknget 75 
                                       pd+i + ++ g  + +Nea++   G s+ee++g+si d + ++++a+e l++++   ++       +++l +++g t
  gi|313127079|ref|YP_004037349.1| 385 PDPIYVLDETGDFTLVNEALAAAVGCSKEELIGTSIGDQL-ESADAEESLQRIMALSDEesDSPPLDLTLSTPDG-T 459
                                       68899988********************************.9999999999999999998888999999999999.7 PP

                             PAS_9  76 fwvlltaspvkdd.dgelvgiivilrDite 104
                                         ++++++   dd  g   + +++ rD+t+
  gi|313127079|ref|YP_004037349.1| 460 RDYEVNIALSGDDqRGDAPRTVGVARDVTD 489
                                       777899988866657777778999999996 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 3.5
                             PAS_9  40 f..vtdpeanerlraaleqgrk 59 
                                       +  ++d++ ++r + +le+g++
  gi|313127079|ref|YP_004037349.1| 522 LteYPDQDIQNRAETILEAGES 543
                                       3455677777777777777774 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   3.2e-10   6.4e-07       3      49 ..     127     174 ..     125     189 .. 0.81
   2 ?   -2.5   0.0       2.8   5.6e+03       6      15 ..     256     265 ..     253     275 .. 0.82
   3 !   24.5   0.0   9.9e-09     2e-05       2      55 ..     376     430 ..     375     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.2e-10
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqll 49 
                                       +++++e+s+d iavvd+ + i +v +a  + +Gy+ ++++g+ + +l+
  gi|313127079|ref|YP_004037349.1| 127 FQTIVEQSSDVIAVVDDTGVIEYVSPAVRRVFGYEtDEILGANISDLI 174
                                       89*************94445***************9999998886332 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                             PAS_8   6 lfesspdgia 15 
                                       ++e+s+ gi+
  gi|313127079|ref|YP_004037349.1| 256 ALEASQAGIW 265
                                       499******9 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 9.9e-09
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       +++ ++e++pd+i v+d +gd ++ vN+a +   G s ++l+g  +g+ l+  + +
  gi|313127079|ref|YP_004037349.1| 376 QYERIVETAPDPIYVLDeTGD-FTLVNEALAAAVGCSkEELIGTSIGDQLESADAE 430
                                       799******************.*************987777777777555555554 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.7   7.4e+03      13      38 ..     573     598 ..     570     605 .. 0.63
   2 !   47.5   0.1     1e-15   2.1e-12       6     110 ..     606     706 ..     601     708 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.7
                                       HHHHHHHHHS.TTTEEEEEEEEEETEE CS
                         HATPase_c  13 lvdNavkfat.kageieveikaseddl 38 
                                        v++ v++a+ + ++ ++++++ e ++
  gi|313127079|ref|YP_004037349.1| 573 CVTHVVDEAQrQFPHATIRVHQ-EAEV 598
                                       6777888855567788888883.2233 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 1e-15
                                       HHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                       ++ ++ +lv+Na++++  +a+++e++++++e +++++v+D+G+G++  +++ + e   +         g+GlGl +v
  gi|313127079|ref|YP_004037349.1| 606 FELALTELVENAIRHSDrSAPTVEITVEKHESTVSVQVSDDGPGLTDMEQNVVLEGEET-----ALEHGSGLGLWLV 677
                                       566799*********55688889999997779*******************88885444.....4568********* PP

                                       HH.HHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  82 kk.lvelmgGeiwvesepgrGttftftlpl 110
                                       +  +++  gG+i v++++  Gt +  ++p 
  gi|313127079|ref|YP_004037349.1| 678 RWtIAN-SGGTIDVRNNDPTGTVVEARVPR 706
                                       **6666.9****************999986 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.4   4.3e-14   8.6e-11      18     106 ..     592     678 ..     571     703 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 4.3e-14
                       HATPase_c_2  18 vlrraglseelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepke 93 
                                       v ++a++ +e+ +  +la++E++ Na++h  ++ap  +ve+++e  e ++ v+v+D+Gpg  d e+ +   e e ++
  gi|313127079|ref|YP_004037349.1| 592 VHQEAEVWAEVHEAFELALTELVENAIRHSDRSAP--TVEITVEKHESTVSVQVSDDGPGlTDMEQ-NVVLEGEETA 665
                                       45667788888889*******************99..8888888****************777765.5555666679 PP

                       HATPase_c_2  94 slkegGrGlalik 106
                                        +  +G+Gl l++
  gi|313127079|ref|YP_004037349.1| 666 LEHGSGLGLWLVR 678
                                       9999999999987 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.7e-07   0.00033       3      49 ..     606     654 ..     603     668 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                       HATPase_c_3   3 lekAlaelvdNsld...AdaenvkievnknrgktgeivieDdGkGmseee 49 
                                       +e Al+elv+N++     +a +v+i+v+k + +t ++++ DdG G++  e
  gi|313127079|ref|YP_004037349.1| 606 FELALTELVENAIRhsdRSAPTVEITVEKHE-STVSVQVSDDGPGLTDME 654
                                       489*********9643366777*******87.79***********98754 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00066       1.3      15      62 ..     402     446 ..     399     472 .. 0.84
   2 ?   -0.6   0.1       1.1   2.3e+03      43      69 ..     535     564 ..     528     572 .. 0.68
   3 ?   -1.0   0.2       1.6   3.2e+03      16      36 ..     601     621 ..     591     637 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00066
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHTS CS
                     PSK_trans_fac  15 reLarltgeskteAvrrAleerlerlrreraepllerllallrraaak 62 
                                       + La++ g sk e + + +  +le     +ae++l+r++al +++ + 
  gi|313127079|ref|YP_004037349.1| 402 EALAAAVGCSKEELIGTSIGDQLESA---DAEESLQRIMALSDEESDS 446
                                       579*********************98...79************99883 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                                       X...XX--HHHHHHHHHHHHHTS--SS-SS CS
                     PSK_trans_fac  43 e...raepllerllallrraaakaekedrs 69 
                                       e   +a ++le+l + +rr++a +++++ s
  gi|313127079|ref|YP_004037349.1| 535 EtilEAGESLESLSESARRFKASTHPNQSS 564
                                       233478899999999999999966555544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.6
                                       XXXXXXXXXXXXXXXXXXXXX CS
                     PSK_trans_fac  16 eLarltgeskteAvrrAleer 36 
                                       e+ ++    +te v+ A+++ 
  gi|313127079|ref|YP_004037349.1| 601 EVHEAFELALTELVENAIRHS 621
                                       667777778999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (709 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 4952.46
//
Query:       gi|313127080|ref|YP_004037350.1|  [L=151]
Description: hypothetical protein Hbor_23450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.5   0.1      0.037   14.4   0.1    1.5  1  CopD      Copper resistance protein D


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.1e-06     0.037       4      29 ..       1      27 [.       1      37 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-06
                              CopD  4 lrrFsrlalaav.avvlvtGvvnallr 29
                                      +rrFsr + +av a+++v+Gv++++ +
  gi|313127080|ref|YP_004037350.1|  1 MRRFSRAVAVAVvAILIVSGVGPVAAQ 27
                                      69**9987777725556*****98777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1131.61
//
Query:       gi|313127081|ref|YP_004037351.1|  [L=131]
Description: methylglyoxal synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-14   52.2   0.0    6.2e-14   52.0   0.0    1.1  1  MGS       MGS-like domain
  ------ inclusion threshold ------
       0.22   10.1   0.0       0.27    9.9   0.0    1.1  1  SepSecS   O-phosphoseryl-tRNA(Sec) selenium transferase, SepS


Domain annotation for each model (and alignments):
>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   6.9e-18   6.2e-14       2      95 .]      15     107 ..      14     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 6.9e-18
                                       HHHHHHHHHHTT..CEEEEEHHHHHHHH.HTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHH CS
                               MGS   2 lvelakklkelg..fellATgGTakllk.eagipvtevvektgegerlggrveildaikngeidlvintlypfkatv 75 
                                       l+e+a++ ++ +   +l+ATg+T++ l  ++g++    +e+ ++g +lgg+++i+++i+++  + vi++ +p++a++
  gi|313127081|ref|YP_004037351.1|  15 LIEFAQNRQDDLehLDLMATGTTGQRLIdATGLD----IERKESG-PLGGDMQIGAEIASETCHGVIFLRDPLTAQP 86 
                                       788999888776679*********8877589***....9999999.******************************* PP

                                       H.CHHHHHHHHHHHTTSHEES CS
                               MGS  76 a.kdgykirraaenidIplpt 95 
                                       + +d  ++ r+++++d+pl+t
  gi|313127081|ref|YP_004037351.1|  87 HePDITALLRICDVHDVPLAT 107
                                       *99999*************98 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   3.1e-05      0.27     165     194 ..      83     111 ..      61     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.1e-05
                                       TTTTB----HHHHHHHHHCCT--EEEEGCC CS
                           SepSecS 165 ffaprspDdvkeiakiCaeydvPhlvNgAY 194
                                       + +p  pD + ++ +iC+ +dvP+  N A 
  gi|313127081|ref|YP_004037351.1|  83 TAQPHEPD-ITALLRICDVHDVPLATNLAS 111
                                       56899***.***************999774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 986.59
//
Query:       gi|313127082|ref|YP_004037352.1|  [L=640]
Description: universal archaeal kh-domain/beta-lactamase-domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-32  110.5   1.0    3.1e-30  103.9   0.3    2.7  2  KH_7           KH domain
    9.5e-22   77.4   0.0    1.8e-21   76.5   0.0    1.5  1  Beta-Casp      Beta-Casp domain
      4e-16   58.7   0.0    1.3e-15   57.0   0.0    1.9  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
      2e-12   47.0   0.0    3.3e-12   46.2   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    4.6e-12   46.4   2.4    2.4e-11   44.0   2.4    2.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    8.2e-09   35.3   0.1    1.4e-08   34.5   0.1    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.6e-08   34.3   0.2      7e-07   29.0   0.0    2.6  2  KH_2           KH domain
     0.0008   19.3   0.4     0.0016   18.4   0.0    1.6  2  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.095   12.5   0.0    2.2  2  KH_1           KH domain
      0.037   13.9   0.0      0.085   12.7   0.0    1.6  1  KH_4           KH domain


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   0.3   1.7e-33   3.1e-30       2      68 .]       6      72 ..       5      72 .. 0.98
   2 ?    4.4   0.0      0.02        36       6      42 ..      77     115 ..      75     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 1.7e-33
                              KH_7  2 evleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                      ++leelk++i+++lP++++++dv++EGPelV+Yt++pk+fa+ngdlirklA++lrkRi++RpDp+vl
  gi|313127082|ref|YP_004037352.1|  6 KQLEELKAEITNELPSDISVSDVKYEGPELVVYTRDPKKFAQNGDLIRKLASKLRKRITVRPDPDVL 72
                                      799**************************************************************97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.02
                              KH_7   6 elkekieeklPkevkitdveF..EGPelViYtknpklfa 42 
                                       e +e++ + +P+e+ +td++F     e+Vi +  p  ++
  gi|313127082|ref|YP_004037352.1|  77 EAEERVLSVIPEEAGVTDLDFheDTGEVVIEASKPGMVI 115
                                       67899***************9422456666666555555 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0     1e-24   1.8e-21       2     110 .]     423     547 ..     422     547 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1e-24
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.........................E-SHH....H CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.........................veakslewme 53 
                                       qe++++Lee+++++k  ++++p+ ld+ ++ +at+++++y+e                         +     +  e
  gi|313127082|ref|YP_004037352.1| 423 QEIMLVLEEAMRSGK--IPSMPVHLDG-MIWEATAIHTTYPEylrddlrdrifhedenpfladefnhI-----DGGE 491
                                       9**********9955..6789******.************9999999888888877777765443322.....2223 PP

                                       HHH..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  54 skkeelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       +++++   ++gp++il++sgm++gG++  +l+++ +dp++ +++vgyqa+gTlgr++
  gi|313127082|ref|YP_004037352.1| 492 DERQD-VADDGPAIILSTSGMVTGGPIMSWLRHVGPDPKSRLVFVGYQAQGTLGRRI 547
                                       33322.3679*********************************************97 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.6   6.5e+03      22      36 ..     517     534 ..     506     535 .. 0.72
   2 !   57.0   0.0   7.4e-19   1.3e-15       2      62 .]     568     631 ..     567     631 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.6
                             RMMBL  22 llelirklkprn...vil 36 
                                       ++ ++r++ p +   +++
  gi|313127082|ref|YP_004037352.1| 517 IMSWLRHVGPDPksrLVF 534
                                       789*****9998777555 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 7.4e-19
                             RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                       + +k+ +e++d fSgHad+++l +++++++pr+  v  vHG+e++ ++l ++l  +++ ++f+P
  gi|313127082|ref|YP_004037352.1| 568 LQLKMDVETVDgFSGHADRAGLENFVKTMNPRPekVLCVHGDERSVQDLSSALYHNYNMRTFAP 631
                                       678**************************************************99999999987 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   1.9e-15   3.3e-12       1     173 [.     199     365 ..     199     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.9e-15
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdes..kvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpv 75 
                                       +L+  +++iL+D+G +    +v + ++ + l + ++++d+++L+ha l+h +  + l+  f  k++ + p+y+t p+
  gi|313127082|ref|YP_004037352.1| 199 ILSTPETRILIDCGDKPGsdDVPYLQVPEALGSGANSLDAVILTHAHLDHSALIP-LL--F--KYGYDGPIYTTEPT 270
                                       5777799*******996511444555666666679***************88433.33..3..47889********* PP

                     Lactamase_B_6  76 vkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti..Wkis 150
                                         L  +++ld+   +  +g +     e e ++ea +++++l Y   +++     ++ +t +naGh lG ++  ++i 
  gi|313127082|ref|YP_004037352.1| 271 RDLMGLLTLDYLDVAAKEGRTP--PYESEMVREAIKHCIPLEYGDVTDIAP---DVKLTFHNAGHILGSAVshFHIG 342
                                       *********9998887766554..5577889**************999985...899***********976558888 PP

                     Lactamase_B_6 151 kesekivYavdwnhakeshLnga 173
                                       +++ ++ +  d++ +  ++ nga
  gi|313127082|ref|YP_004037352.1| 343 DGLYNVAFSGDIHYEDTRLFNGA 365
                                       99999988888887777777775 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   2.4   1.3e-14   2.4e-11       7     163 ..     196     379 ..     191     415 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.3e-14
                                       EEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   7 nsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                        s+++ ++++ iLiD+G  +  ++  +   + alg + + +davilTH+HlDH +  + l +     +++  e ++ 
  gi|313127082|ref|YP_004037352.1| 196 ASFILSTPETRILIDCGDKPGSDDVPYlqVPEALGSGANSLDAVILTHAHLDHSALIPLLFKYGYDGPIYTTEPTRD 272
                                       5788889******************999************************************************9 PP

                                       CHCHHHHHHHHHCCHH.........TTCHCGCCEEEEETTTEECCCTEEEEEHE...CTTSTSCCEEEEEETTCCEE CS
                       Lactamase_B  82 lfmeeaddaasrkgll.........lagvsadkpdvdeeeldgnaggrralyvt...ggpghghghgvveygggkvl 146
                                       l +    d+      +           ++ +++ ++ e ++ ++ ++++ l ++   ++ g+  +h+++++g  +v+
  gi|313127082|ref|YP_004037352.1| 273 LMGLLTLDYLDVAAKEgrtppyeseMVREAIKHCIPLEYGDVTDIAPDVKLTFHnagHILGSAVSHFHIGDGLYNVA 349
                                       999999888887777799*******66666666777777766666666666654333999***************** PP

                                       EECTTTSSHHCCCCCC.............. CS
                       Lactamase_B 147 ftGDallagetgridl.............t 163
                                       f+GD  ++  ++  +               
  gi|313127082|ref|YP_004037352.1| 350 FSGDIHYEDTRLFNGAvndfprvetlvleS 379
                                       *******88887777766666666665552 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1     8e-12   1.4e-08       1     150 [.     205     361 ..     205     391 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 8e-12
                                       SEEEES--TTHHHHHTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH....... CS
                     Lactamase_B_2   1 rriLiDagpdlrqqalral.qPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla....... 68 
                                       +riLiD+g        ++l  P +l +  +++daV+lthaH DH a ++ l + ++  + p+y ++ +++       
  gi|313127082|ref|YP_004037352.1| 205 TRILIDCGDKPGSDDVPYLqVPEALGSGANSLDAVILTHAHLDHSALIPLLFKyGY--DGPIYTTEPTRDlmglltl 279
                                       79******996555667775677799999****************99999999443..4799999999888888877 PP

                                       ......HCCTTCGHHHCHTT.....TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTT CS
                     Lactamase_B_2  69 ......vleanfvylaleee.....pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrieggg 134
                                               e ++++           ++ ++ +l+ g+ ++++ +++++t++ a h  g         +  + i++g 
  gi|313127082|ref|YP_004037352.1| 280 dyldvaAKEGRTPPYE---SemvreAIKHCIPLEYGDVTDIA-PDVKLTFHNAGHILGS-------AVSHFHIGDGL 345
                                       7665332222333333...1455888999999*********9.699*****99999999.......8999******* PP

                                       EEEEEESS-S---HHH CS
                     Lactamase_B_2 135 krvyyigDtgyipeei 150
                                        +v+++gD  y + ++
  gi|313127082|ref|YP_004037352.1| 346 YNVAFSGDIHYEDTRL 361
                                       ********99877543 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.075   1.3e+02      42      59 ..      47      64 ..       7      71 .. 0.78
   2 !   29.0   0.0   3.9e-10     7e-07      10      73 ..      86     149 ..      80     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.075
                                      GGGHHHHHHHHHHHHHHH CS
                              KH_2 42 kgGsnikkigkelrkdie 59
                                      ++G  i+k+ ++lrk+i 
  gi|313127082|ref|YP_004037352.1| 47 QNGDLIRKLASKLRKRIT 64
                                      68999**********995 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 3.9e-10
                                       T.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEE.EE CS
                              KH_2  10 i.kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklniv.kV 73 
                                       i ++agv +++   +++  ++vi +s+pg+vIG+ Gs++++i+ke++   e+++  +++   v +V
  gi|313127082|ref|YP_004037352.1|  86 IpEEAGVTDLDF--HEDTGEVVIEASKPGMVIGRHGSTLREITKEVGWTPEVVRTPPIESSTVsNV 149
                                       448899999999..44999***************************98888888888776655555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.9e-07    0.0016       6      52 ..     194     251 ..     192     258 .. 0.77
   2 ?   -3.7   0.2       5.4   9.8e+03      98     118 ..     338     358 ..     326     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.9e-07
                     Lactamase_B_3   6 ghnsflletagarilvDPf..........kanlgyeppa.........eeaDlvlisqaledHahl 52 
                                       g +sf l+t+++ril+D +                   +          + D+v++++a+ dH +l
  gi|313127082|ref|YP_004037352.1| 194 GRASFILSTPETRILIDCGdkpgsddvpyL--------QvpealgsgaNSLDAVILTHAHLDHSAL 251
                                       89***************9944333333320........2557777777***************976 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.4
                     Lactamase_B_3  98 gflleqdgltiyhlGhlahel 118
                                        f++ ++ +++++ G++++e 
  gi|313127082|ref|YP_004037352.1| 338 HFHIGDGLYNVAFSGDIHYED 358
                                       577777788899999999865 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.4   2.5e+03      18      48 ..      48      83 ..      47      90 .. 0.67
   2 ?   12.5   0.0   5.3e-05     0.095       4      28 ..     104     128 ..     101     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                                      GGHHHHHHHHHHT-EEEEESSTT..........T.-EE CS
                              KH_1 18 gGsnIkeIreetgakIkvpksedeg.......sderev 48
                                      +G  I+++ ++   +I+v  +++ +        +er++
  gi|313127082|ref|YP_004037352.1| 48 NGDLIRKLASKLRKRITVR-PDP-DvlsppreAEERVL 83
                                      7888999999668889976.333.33555555555555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.3e-05
                                       EEEGGGHHHHHHTGGGHHHHHHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIree 28 
                                       + + +s+ g +IG+ Gs+++eI +e
  gi|313127082|ref|YP_004037352.1| 104 VVIEASKPGMVIGRHGSTLREITKE 128
                                       667778889*************986 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.8e-05     0.085      26      52 ..      97     123 ..      81     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                              KH_4  26 eeeveielnvegedlGrvIGkrGrtld 52 
                                        +e++ e+ +e ++ G vIG++G tl+
  gi|313127082|ref|YP_004037352.1|  97 FHEDTGEVVIEASKPGMVIGRHGSTLR 123
                                       45666778889999***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4336.42
//
Query:       gi|313127083|ref|YP_004037353.1|  [L=161]
Description: hypothetical protein Hbor_23480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0044   16.5   0.1     0.0078   15.7   0.1    1.4  1  DUF1155   Protein of unknown function (DUF1155)
  ------ inclusion threshold ------
       0.23   11.5   1.2       0.57   10.2   1.2    1.8  1  PgpA      Phosphatidylglycerophosphatase A


Domain annotation for each model (and alignments):
>> DUF1155  Protein of unknown function (DUF1155)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   8.7e-07    0.0078       6      30 ..      96     120 ..      93     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.7e-07
                           DUF1155   6 STTLSFEPPLSLLAEPGTWFADTmD 30 
                                       + T++   PLSLLA     FADTm 
  gi|313127083|ref|YP_004037353.1|  96 AATIAGGQPLSLLAQATFHFADTMT 120
                                       56777778****************5 PP

>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.2   6.4e-05      0.57      64     105 ..      77     118 ..      33     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.4e-05
                                       -.HHT-TT--HHHHTTHHHHH........TTHHHHHHHHHHHH CS
                              PgpA  64 g.ekDpgeiviDEvvgqwiallllpatllalllafilFrlfDi 105
                                       + ++D  ++v+DEv+g  +a  ++       lla ++F + D 
  gi|313127083|ref|YP_004037353.1|  77 DvRDDYPGFVVDEVLGRELAATIAGG-QPLSLLAQATFHFADT 118
                                       3468899*************966644.4555999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1225.78
//
Query:       gi|313127084|ref|YP_004037354.1|  [L=186]
Description: hypothetical protein Hbor_23490 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   11.5   2.1        1.2    9.0   0.1    2.5  2  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5


Domain annotation for each model (and alignments):
>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1     7e-05       1.2      15      28 ..      96     109 ..      94     110 .. 0.94
   2 ?    1.2   0.2      0.02   3.6e+02      12      24 ..     157     169 ..     156     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 7e-05
                             RHH_5  15 eLeewAdeegRsvS 28 
                                       +L++wA + gRsvS
  gi|313127084|ref|YP_004037354.1|  96 RLQRWAWQHGRSVS 109
                                       8************9 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.02
                             RHH_5  12 lleeLeewAdeeg 24 
                                       l e+Le +A+ e+
  gi|313127084|ref|YP_004037354.1| 157 LTERLETLAERER 169
                                       579*******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1306.95
//
Query:       gi|313127085|ref|YP_004037355.1|  [L=488]
Description: prolyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-23   82.8   0.5    1.4e-23   82.8   0.5    1.8  2  HGTP_anticodon  Anticodon binding domain
    9.9e-21   74.5   0.0    2.1e-20   73.5   0.0    1.5  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      5e-20   71.5   0.1    1.3e-19   70.1   0.1    1.8  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
      0.046   14.3   0.3        7.7    7.2   0.0    2.7  2  TIR_2           TIR domain
       0.15   12.3   0.1       0.23   11.7   0.1    1.3  1  PHF5            PHF5-like protein


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.5     4e-27   1.4e-23       1      93 [.     295     390 ..     295     391 .. 0.97
   2 ?   -2.4   0.1       1.5   5.4e+03      29      50 ..     394     416 ..     393     418 .. 0.82

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 4e-27
                                       SEEEEESSSS..HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET CS
                    HGTP_anticodon   1 qvvviplnek..aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdr 74 
                                       qvv++p+ +   +e+++eya+++ eeL++agirveldd +++++g+k++e++l+g+p+++++G++e+++++vtv +r
  gi|313127085|ref|YP_004037355.1| 295 QVVIVPIWQAdtQEKVLEYAESISEELEDAGIRVELDDrDERNPGFKFNEWELKGVPVRFEIGPNEVDDDVVTVVHR 371
                                       8******9999999999************************************************************ PP

                                       TTCEEEEEETTHHHHHHHH CS
                    HGTP_anticodon  75 dtreqervsldelveklke 93 
                                        ++e+ +v++++++e ++e
  gi|313127085|ref|YP_004037355.1| 372 PDGETKEVAREDIAETVRE 390
                                       ****************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                                       TSEEEEES.SSSTHHHHHHHHHH CS
                    HGTP_anticodon  29 girveldd.snesigkkireadl 50 
                                       +++++l+   +e++ + +read 
  gi|313127085|ref|YP_004037355.1| 394 EVYAKLYAaAEENLEENVREADS 416
                                       57788888899999999999985 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   5.8e-24   2.1e-20       5     176 ..     105     276 ..      98     279 .. 0.90
   2 ?   -4.1   0.0       3.6   1.3e+04      73      97 ..     303     327 ..     294     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 5.8e-24
                                       ETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                      tRNA-synt_2b   5 drndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easldds 79 
                                       d+ +++++++Pt+e  ++  ++++ +rs ++LPl++ q  ++ R E+ ++++ +R +eF +++g+  ha ++ ++d+
  gi|313127085|ref|YP_004037355.1| 105 DELEERLAVRPTSESIIAPYMSQW-VRShRDLPLRVNQWASVVRWEATETKPFFRTKEFLWQEGHTAHAtAEAAWDE 180
                                       78899**********999999977.***555****************99********************8899**** PP

                                       HHHHHHHHHHHHHHTT.SCEEEEEE..GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  80 lrdlikaisriferlglefraiiel..msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldenn 154
                                           + +++ ++e+l+    ++++    ++k + ++ ++ +ea+++  +k ++ +t + lgt+++e++++t+ de++
  gi|313127085|ref|YP_004037355.1| 181 TMTRLDQYESVYEDLLA-IPVLRGAkpEHDKFPGANTTTTVEALMP-DGKSVQGATSHDLGTSFAEAFDLTYTDEDE 255
                                       **************974.35667767777777999999********.9***************************** PP

                                       SEEEEEEEEEEEEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 155 reksvimicaaigveRllsail 176
                                       +++  +++  +++  R l+a++
  gi|313127085|ref|YP_004037355.1| 256 ESQVAHTTSWGLS-WRALGALI 276
                                       *****99999998.77777765 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.6
                                       GGGHHHHHHHHHHHHHHHHHHTT.S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  73 easlddslrdlikaisriferlgle 97 
                                       +a+ ++++ ++ + is+ +e+ g+ 
  gi|313127085|ref|YP_004037355.1| 303 QADTQEKVLEYAESISEELEDAGIR 327
                                       6777888888888888888888876 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.1   3.7e-23   1.3e-19       6      69 .]     422     488 .]     418     488 .] 0.91

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3.7e-23
                                       HHHHTT-.EEEEEESSGHHHHHHHHHHHS-EEEEEESSB..-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                         ProRS-C_1   6 ealekkg.fvlapWcgeeecEekIkeetgakslcipfdq..epseegtkCivcgkpakkwvlfgrsY 69 
                                        ++ ++g +v+apWcg+e+cE +Ik++++a+++++p+++   + ++g+ C++cg +a+++++f++sY
  gi|313127085|ref|YP_004037355.1| 422 GTIGQHGgYVKAPWCGDEDCETEIKDQIAAEIVMVPLNDeeAEVHDGEDCAICGDDADETAYFAKSY 488
                                       56777777*****************************97667789********************** PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0021       7.7      11      39 ..     312     341 ..     306     350 .. 0.79
   2 ?    4.3   0.0     0.016        57       8      76 ..     375     445 ..     366     471 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0021
                             TIR_2  11 ewaeklaeaLeaagirvwldrwdl.kpged 39 
                                       e+ae + e+Le+agirv ld +d   pg +
  gi|313127085|ref|YP_004037355.1| 312 EYAESISEELEDAGIRVELDDRDErNPGFK 341
                                       789**************8888774356655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                             TIR_2   8 edkewa.eklaeaLeaagirvwldrwdlkpgedweeeieeaiessdvvlvvlspa..ylesewcree.leaal 76 
                                       e ke+a e++ae+ +++  +v+ + +   + e++ee+++ea  ++d +l  ++++  y++ +wc +e  e+ +
  gi|313127085|ref|YP_004037355.1| 375 ETKEVArEDIAETVREEFDEVYAKLYA-AAEENLEENVREADSRAD-ILGTIGQHggYVKAPWCGDEdCETEI 445
                                       567888788*****9996669988764.889999999999999999.777777777999****8886333333 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.5e-05      0.23      20      73 ..     433     486 ..     416     488 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                              PHF5  20 gklcekcdgkcpicdslvkpatkvricdecsfgkleekciicgskgvsdayycl 73 
                                       +  c   d    i d    ++  v + de +  +  e c icg  + ++ay+ +
  gi|313127085|ref|YP_004037355.1| 433 APWCGDEDCETEIKDQIAAEIVMVPLNDEEAEVHDGEDCAICGDDADETAYFAK 486
                                       55699999999999*999*********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3521.20
//
Query:       gi|313127086|ref|YP_004037356.1|  [L=1510]
Description: glutamate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.3e-157  523.1   0.0   5.9e-157  522.7   0.0    1.2  1  GATase_2         Glutamine amidotransferases class-II
   1.8e-150  501.2   0.1   2.6e-149  497.4   0.0    2.2  2  Glu_synthase     Conserved region in glutamate synthase
   3.2e-116  387.7   0.0     1e-115  386.0   0.0    1.8  2  Glu_syn_central  Glutamate synthase central domain
    9.6e-80  266.7  10.0    1.7e-79  265.8  10.0    1.4  1  GXGXG            GXGXG motif
    3.1e-05   23.5   1.1    7.2e-05   22.3   1.1    1.5  1  NMO              Nitronate monooxygenase
    0.00098   18.2  12.5     0.0045   16.1   2.0    3.4  3  FMN_dh           FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.048   12.7   3.0      0.093   11.7   1.2    2.3  3  IMPDH            IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  522.7   0.0  2.3e-160  5.9e-157       1     420 []      25     440 ..      25     440 .. 0.98

  Alignments for each domain:
  == domain 1  score: 522.7 bits;  conditional E-value: 2.3e-160
                                       -EEEEEE-SSS--BSHHHHHHHHHHHHGGGGS-B-TTSSSBSEEEEEEE--HHHHHHHHHHTT-----GGG-EEEEE CS
                          GATase_2   1 CGvgfiaelkgkkshkivekalealenleHRGavgadektGDGaGillqiPdeflrkeakekgielpeageyavgml 77 
                                       CGvg +++l+g   h+ v+++le+lenleHRG++ga+++tGDGaGi++q Pdef+ +++   + elpe  +yavg +
  gi|313127086|ref|YP_004037356.1|  25 CGVGAVIDLDGGVCHETVSDGLELLENLEHRGTTGAEADTGDGAGIMIQRPDEFFDAVV---DAELPE--SYAVGSI 96 
                                       *********************************************************99...889987..9****** PP

                                       EE-SSHHHHHHHHHHHHHHHHHTT-EEEEEEE--B-GGGS-HHHHHH--EEEEEEEE-TT---HHHHHHHHHHHHHH CS
                          GATase_2  78 flpkdeekaeeakkileeiveeeglevlgwRevpvdksvlgeaakesePsieqvfvekkedlseeelerklyviRkr 154
                                       f+p+d++ +e   +++e+++ ++gl+v+ wR+vp+++  lg++a++seP + q fv  +ed+se+ ++r ly++R+ 
  gi|313127086|ref|YP_004037356.1|  97 FMPTDDAVREMLVDVFERELGAHGLDVVHWRDVPTNNADLGATALDSEPDVWQAFVVPSEDMSEDGFDRALYIARRA 173
                                       ***************************************************************************** PP

                                       HGGG.......-BTTBEEEEEESSEEEEEESS-GGGHHHHBHGGGSTT--BSEEEEEE---SSSS--GGGSSS-SSE CS
                          GATase_2 155 iekeiakkk..aekefYicslssrtivYkglltseqlkefykdlkdeelesalalvHsRfstntfPsWelaqPlRll 229
                                       +e+++++ +  ++ +fY+csls++t+vYkgll+ eql  +y+dl+de+l+++l+lvH Rfstnt+  W+la+P+R +
  gi|313127086|ref|YP_004037356.1| 174 VENAVSELDepETARFYVCSLSRKTLVYKGLLKGEQLAGYYPDLQDERLKTTLTLVHARFSTNTLGAWHLAHPYRHI 250
                                       *****9988788999************************************************************** PP

                                       EEEE--TTHHHHHHHHHHHCTT--BT-HH.HHHTC--S--TTS-HHHHHHHHHHHHHHTT--HHHHHHHHS----TT CS
                          GATase_2 230 aHnGEintlrGnknwmkareaelksellgdelekllPivneegsDsasldnvlellvlsgrslaealmlliPeawen 306
                                        HnGEint+rGn+nwm+are+ l+++ +gd++e ++P++++++sD+as+dn++ell+++gr+l++ l++liPe+++ 
  gi|313127086|ref|YP_004037356.1| 251 IHNGEINTIRGNVNWMRARETDLEHPDFGDDIEAVKPVTKADQSDTASVDNAVELLLQGGRELPHVLRMLIPESFRG 327
                                       ***************************************************************************** PP

                                       -GGGTHHHHHHHHHHTTT-----SSEEEEEE-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEEEE CS
                          GATase_2 307 nksldkekkafyeyasalmepWDGPalivftdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevvek 383
                                       ++++d+e++++y+y+++l+epWDGPal++ tdG  v+avLDRnGLRP+Ry vt+d+++v+asEvG ld +++e+ e+
  gi|313127086|ref|YP_004037356.1| 328 DDAMDEERREWYDYHASLVEPWDGPALVAATDGDRVAAVLDRNGLRPCRYDVTTDNTLVMASEVGALDTDPAEIRER 404
                                       ***************************************************************************** PP

                                       EE--TT-EEEEETTTTEEEEHHHHHHHHHTTS-HHHH CS
                          GATase_2 384 grlqPGrmllvdleegriledeeikkkiaskkpykew 420
                                       grlqPG++++ d eegr++ dee+ +++++ + y+ew
  gi|313127086|ref|YP_004037356.1| 405 GRLQPGQLFVADPEEGRVIPDEEVFDSLTD-EKYGEW 440
                                       ************************999875.568888 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.053   1.4e+02     250     282 ..     632     664 ..     625     685 .. 0.80
   2 !  497.4   0.0    1e-152  2.6e-149       2     368 .]     803    1167 ..     802    1167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.053
                                       HB---HHHHHHHHHHHHHHTT-GGG-EEEEESS CS
                      Glu_synthase 250 haGlPlelalaevdqtlkeeglrdrvsliadGg 282
                                        a +P +la  +v++ l+++glr++  l ++ g
  gi|313127086|ref|YP_004037356.1| 632 RAAVPSLLATGAVHHNLVRNGLRNHAGLVVESG 664
                                       5789*********************99988644 PP

  == domain 2  score: 497.4 bits;  conditional E-value: 1e-152
                                        SS-HHHHHHHHHHHHH---HHHHHHHHHHHTS..-S-SGGGGEEE--SS--.--GGGS--HHHHHTTEE---B-T CS
                      Glu_synthase    2 rneievikllqkavqveskesidkyrekleer.evlkakrdlleldaaeealikleevepalkikkriltsamSy 75  
                                        + ++++  +lq+av+++++e+++++++ ++++ e l+++r lle+d+++++ ++++evep++ i++r+ t+amS+
  gi|313127086|ref|YP_004037356.1|  803 QWNPKTVGTLQQAVRSGNYEKYQEFAQLINDQsEELQTLRGLLEFDSDRDP-VPIAEVEPVEDIVERFSTAAMSL 876 
                                        56788999*******************99875267999*************.79********************* PP

                                        TTS-HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHHH-SEEEEE---TTSTTS CS
                      Glu_synthase   76 GalseeahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLnnakaleikiaQGakpge 150 
                                        G+ls eahe  ++amnr+g+ksntGEGGe++er+ t+k+  +kQvasgrFGvt++yL+ a++l+ik+aQG+kpge
  gi|313127086|ref|YP_004037356.1|  877 GSLSPEAHENNSIAMNRIGGKSNTGEGGEPPERFGTEKECNVKQVASGRFGVTSHYLSAADELQIKMAQGSKPGE 951 
                                        *************************************************************************** PP

                                        --EE-GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHH CS
                      Glu_synthase  151 GgqlpgeKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevnkeakvsvKlvaeagvetiaagvak 225 
                                        Gg+lpg+Kv e+ia++R  +pgv+liSP+p hdiysiedl+qli+dLk++n+ea + vKlv+eag++tiaagvak
  gi|313127086|ref|YP_004037356.1|  952 GGHLPGKKVNEMIAHVRFATPGVGLISPPPLHDIYSIEDLKQLIHDLKTANPEADINVKLVSEAGIGTIAAGVAK 1026
                                        *************************************************************************** PP

                                        TT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEE CS
                      Glu_synthase  226 anadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdav 300 
                                        anad++ i+G++GGTGAspk+sik+aGlP+el+lae++q+l++++lr+r++++adGg+ktg+d+++a++lGA+++
  gi|313127086|ref|YP_004037356.1| 1027 ANADVVHISGHDGGTGASPKTSIKNAGLPWELGLAEANQMLRATNLRSRIRVTADGGMKTGRDIAVAALLGAEEY 1101
                                        *************************************************************************** PP

                                        E-SHHHHHHTT--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT-S CS
                      Glu_synthase  301 gigtaalialgCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgin 368 
                                         +gta+l++ gC+mar+Ch ntCpvGvatq+++Lr   ++ +++++v+ny++++a+e+re++a+lg++
  gi|313127086|ref|YP_004037356.1| 1102 VFGTASLVTSGCVMARQCHENTCPVGVATQREDLR--RRFPGEPDHVINYMTFMAQELREIMAELGFR 1167
                                        ***********************************..99***************************85 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.0   0.0    4e-119    1e-115       2     279 .]     469     746 ..     468     746 .. 0.96
   2 ?   -1.7   0.0      0.64   1.6e+03     166     264 ..    1051    1169 ..    1038    1172 .. 0.55

  Alignments for each domain:
  == domain 1  score: 386.0 bits;  conditional E-value: 4e-119
                                       HHHHTT--HHHHHHTHHHHHHHSS--EE-S---S--TTT-SS---GGGGEEE----SSS----TTTTGGG-B--EEE CS
                   Glu_syn_central   2 rqkafgyteedlelllepmakegkeaigsmGdDtplavLsekprllydYFkqlfAqVTNPpiDpiREelvmsletll 78 
                                       rq+afgyt+++l++l+epma++gk+++gsmGdDtpl+vLs+ +r+l++YFkqlfAqVTNPp+D+iREelv+sle++l
  gi|313127086|ref|YP_004037356.1| 469 RQAAFGYTQDQLNHLVEPMAEQGKDPVGSMGDDTPLSVLSDFDRPLFTYFKQLFAQVTNPPLDYIREELVTSLESRL 545
                                       799************************************************************************** PP

                                       S----SSS--GGGG-EEEESSSB--HHHHHHH....HHSSS-EEEEESEE....SHHHHHHHHHHHHHHHHHTT-SE CS
                   Glu_syn_central  79 GkegnlleeeeeqakrlklesPiLteeeleklkklkekkefkaktlditfeae.aleealerlceeaeeavregaei 154
                                       G+++nll+e++e+a++l+l+sPiL+++e++++k+l+   +++++++ditfe+e +l+ea+er++e+a++a+++ga+i
  gi|313127086|ref|YP_004037356.1| 546 GPQRNLLDETPEHARQLVLDSPILSDAETAAIKDLD-G-DMTSAVVDITFETEtSLQEAVERVREDAKAAIEDGADI 620
                                       ********************************9995.3.7**********88856********************** PP

                                       EEEESS--STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEEEHHHHHHHHHHHT CS
                   Glu_syn_central 155 lvLsDrkvseervpipslLavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavnPylaletieklve 231
                                       +vLsDr+++ er+++pslLa+gavhh+Lvr+glr++++lvvesge+ evhh+a+l+gyGa av+Pyla++ti+++v+
  gi|313127086|ref|YP_004037356.1| 621 VVLSDRNLDPERAAVPSLLATGAVHHNLVRNGLRNHAGLVVESGEPSEVHHMATLIGYGAGAVTPYLAYQTISDIVA 697
                                       **************************************************************************998 PP

                                       TTS-.----HHHHHHHHHHHHHHHHHHHTT--BHHHHHHS--EEESSB- CS
                   Glu_syn_central 232 egal.aeeeleknyrkavekGllKimskmGistlqSYkgaqifeavGls 279
                                         +  +e+e+ ++y+ka+e+G+lK+m+kmGist++SY+gaqifeavGl+
  gi|313127086|ref|YP_004037356.1| 698 GPDGaDEKEAIAAYTKALENGVLKTMAKMGISTIASYQGAQIFEAVGLD 746
                                       77663455556************************************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.64
                                        EEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SE.EEEHHHHHHH....HHHHTTT.. CS
                   Glu_syn_central  166 rvpipslLavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGada.vnPylaleti....eklveeg.. 233 
                                        ++ +p  L ++  ++ L +++lr+++ +  + g +++  ++av   +Ga+  v     l t     +    ++  
  gi|313127086|ref|YP_004037356.1| 1051 NAGLPWELGLAEANQMLRATNLRSRIRVTADGG-MKTGRDIAVAALLGAEEyVFGTASLVTSgcvmA----RQch 1120
                                        566677777788888888888888888777655.666777777777777531322222222211221....1122 PP

                                        ..S-................----HHHHHHHHHHHHHHHHHHHTT--BH CS
                   Glu_syn_central  234 ..al................aeeeleknyrkavekGllKimskmGistl 264 
                                          ++                 e ++  ny++ + + l  im+ +G  t+
  gi|313127086|ref|YP_004037356.1| 1121 enTCpvgvatqredlrrrfpGEPDHVINYMTFMAQELREIMAELGFRTV 1169
                                        2211233333222223333222233367777777777777777777666 PP

>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.8  10.0   6.8e-83   1.7e-79       3     186 ..    1245    1428 ..    1243    1432 .. 0.97

  Alignments for each domain:
  == domain 1  score: 265.8 bits;  conditional E-value: 6.8e-83
                                        E-TT--STTHHHHHHHHHHHTTT---.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE- CS
                             GXGXG    3 irnldrsvgtilsneiakrygeeglpedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikp 77  
                                        ++n+dr+vg++lsnei++ryg egl++dti+ +++G+aGqs+gafla+G+t++l+G +ndyvGkglsgGk+v+++
  gi|313127086|ref|YP_004037356.1| 1245 LSNVDRAVGAMLSNEISTRYGGEGLADDTINCEFSGVAGQSFGAFLANGVTMRLNGASNDYVGKGLSGGKVVVTT 1319
                                        68************************************************************************* PP

                                        -TT-SS-GGGSB-S-SSTTTT--SEEEEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S-B-SSBT CS
                             GXGXG   78 skeskfkaeeniivGnvvlygatgGklfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgktgrnfa 152 
                                        +k++ ++a+en+++Gnv++ygat+G+++i+g ageRf+vrnsg++avvegvgdhgceYmtGGvv vLg+tgrnfa
  gi|313127086|ref|YP_004037356.1| 1320 PKTAGYEADENVLIGNVAFYGATQGEAYINGVAGERFCVRNSGVKAVVEGVGDHGCEYMTGGVVAVLGDTGRNFA 1394
                                        *************************************************************************** PP

                                        TT--EEEEEEE-SSSTHHHHB-TTT-EEEES-SH CS
                             GXGXG  153 aGmsgGiayvldedekfekklnkelvelekvede 186 
                                        aGmsgG+ayv+d d++fe+k n+ +v+l++  d+
  gi|313127086|ref|YP_004037356.1| 1395 AGMSGGVAYVYDPDDEFEAKANTGMVSLSDTLDD 1428
                                        ***************************9875444 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   1.1   2.8e-08   7.2e-05     149     287 ..    1021    1172 ..     995    1199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.8e-08
                               NMO  149 arkvearGaDalivqGpeaG.GhqGtpevgd.....kglfaLvpqvldavd....iPviAaGGiidrrgvaaaLa 213 
                                        a  v+++ aD++ + G ++G G  ++ ++++     +  +a  +q+l a +    i v A GG+ ++r++a a  
  gi|313127086|ref|YP_004037356.1| 1021 AAGVAKANADVVHISGHDGGtGASPKTSIKNaglpwELGLAEANQMLRATNlrsrIRVTADGGMKTGRDIAVAAL 1095
                                        44577888*********9997777766666544653333445689999999999********************* PP

                               NMO  214 lGAsgvqigtrfLltkesd.akdahkkk.lleaklddteltsavsGrpaRalatelleelee.akiatlalpeah 285 
                                        lGA+    gt+ L+t+ +  a++ h++  ++    ++  l +++ G p  +++       e    +a l++++++
  gi|313127086|ref|YP_004037356.1| 1096 LGAEEYVFGTASLVTSGCVmARQCHENTcPVGVATQREDLRRRFPGEPDHVINYMTFMAQELrEIMAELGFRTVE 1170
                                        *****************9625566654424556666777888888888888776555444442344455666665 PP

                               NMO  286 el 287 
                                        e+
  gi|313127086|ref|YP_004037356.1| 1171 EM 1172
                                        55 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   1.6    0.0028       7.1     228     340 ..     608     733 ..     605     740 .. 0.65
   2 !   16.1   2.0   1.7e-06    0.0045     233     304 ..    1024    1108 ..    1018    1116 .. 0.71
   3 ?    0.5   0.0     0.096   2.5e+02     315     341 ..    1146    1172 ..    1141    1180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0028
                                       HHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHH........HHHH..SS-EEEESS-.-SHHHHHHHHHTT-S CS
                            FMN_dh 228 edakraveaGvdgivvSNHGGRqldgapatidvLpei........veavggrievlvDgGi.rrGsDvlkAlalGAd 295
                                       edak a+e G+d++v+S+   R+ld   a++  L +         ++ +++++ ++v +G  ++  +++  +  GA 
  gi|313127086|ref|YP_004037356.1| 608 EDAKAAIEDGADIVVLSD---RNLDPERAAVPSLLATgavhhnlvRNGLRNHAGLVVESGEpSEVHHMATLIGYGAG 681
                                       9****************9...99999999999997764444444355556677777777751344556666677777 PP

                                       EEE..ESHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHH CS
                            FMN_dh 296 avl..lGRpflygl.....aagGeeGvervleilraelertmallGvksvae 340
                                       av   l+ +++  +      a+ +e ++ +++ l++ + +tma +G++++a+
  gi|313127086|ref|YP_004037356.1| 682 AVTpyLAYQTISDIvagpdGADEKEAIAAYTKALENGVLKTMAKMGISTIAS 733
                                       7752233333333211111344455666777777777778888888877776 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.7e-06
                                        HHHTTESEEEE--GGGTSSTT---HHHCH........HHH.....HHHH..SS-EEEESS--SHHHHHHHHHTT- CS
                            FMN_dh  233 aveaGvdgivvSNHGGRqldgapatidvL........pei.....veavggrievlvDgGirrGsDvlkAlalGA 294 
                                        +++a +d + +S H G    +  ++i+           e      + ++++ri v +DgG ++G D++ A  lGA
  gi|313127086|ref|YP_004037356.1| 1024 VAKANADVVHISGHDGGTGASPKTSIKNAglpwelglAEAnqmlrATNLRSRIRVTADGGMKTGRDIAVAALLGA 1098
                                        567788888888888855555555555443343333333333334455677************************ PP

                                        SEEEESHHHH CS
                            FMN_dh  295 davllGRpfl 304 
                                        +  ++G + l
  gi|313127086|ref|YP_004037356.1| 1099 EEYVFGTASL 1108
                                        9988887665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.096
                                        HHHHHHHHHHHHHHHHHHHT-SBHHHH CS
                            FMN_dh  315 vervleilraelertmallGvksvael 341 
                                        v +++  + +el++ ma lG+++v+e+
  gi|313127086|ref|YP_004037356.1| 1146 VINYMTFMAQELREIMAELGFRTVEEM 1172
                                        55788899****************986 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.1   2.7e+03     297     329 ..     706     738 ..     701     743 .. 0.79
   2 ?   11.7   1.2   3.6e-05     0.093     160     237 ..    1022    1105 ..     988    1114 .. 0.77
   3 ?   -1.7   0.0      0.43   1.1e+03     300     326 ..    1147    1173 ..    1136    1186 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.1
                                       B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 297 gsvkevveqlvgglrsgmgylGaktieelkeka 329
                                         ++++ + l +g+ ++m ++G +ti++ +  +
  gi|313127086|ref|YP_004037356.1| 706 EAIAAYTKALENGVLKTMAKMGISTIASYQGAQ 738
                                       567777888999999**********99887655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.6e-05
                                        HHHHHTT-SEEEE.-S..S-STTBHHHHHCSB---HHHHHHHHHHHHCTCT....-EEEEES---SHHHHHHHHH CS
                                        xxxxxxxxxxxxx.xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  160 kaLieagadavkv.Gi..GpGsiCttrvvagvGvpqltAvaevaeaakkag....vpviaDGGikysgdivkAla 227 
                                        + +++a ad+v++ G   G+G+   t  ++ +G p    +ae+ ++ + ++    ++v aDGG+k+ +di+ A  
  gi|313127086|ref|YP_004037356.1| 1022 AGVAKANADVVHIsGHdgGTGASPKT-SIKNAGLPWELGLAEANQMLRATNlrsrIRVTADGGMKTGRDIAVAAL 1095
                                        55678888888884332244444444.56788999999999999988888777779******************* PP

                                        TT-SEEEESC CS
                                        xxxxxxxxxx RF
                             IMPDH  228 aGadavmlGs 237 
                                        +Ga+  + G 
  gi|313127086|ref|YP_004037356.1| 1096 LGAEEYVFGT 1105
                                        ***9988885 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.43
                                        HHHHHHHHHHHHHHHHHHT-SSHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  300 kevveqlvgglrsgmgylGaktieelk 326 
                                         ++++ ++++lr+ m +lG +t+ee+ 
  gi|313127086|ref|YP_004037356.1| 1147 INYMTFMAQELREIMAELGFRTVEEMI 1173
                                        456677899****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.96u 0.33s 00:00:01.29 Elapsed: 00:00:00.54
# Mc/sec: 8460.14
//
Query:       gi|313127087|ref|YP_004037357.1|  [L=330]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-28   98.1   0.3    3.6e-15   56.1   0.0    2.1  2  Epimerase       NAD dependent epimerase/dehydratase family
    8.3e-09   35.3   0.1    0.00047   19.7   0.1    2.1  2  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
    2.2e-06   26.9   0.1     0.0008   18.5   0.1    2.2  1  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
    6.6e-06   26.1   0.1    1.6e-05   24.9   0.1    1.6  1  NAD_binding_10  NAD(P)H-binding
     0.0033   16.6   0.1       0.36    9.9   0.0    2.1  2  RmlD_sub_bind   RmlD substrate binding domain
  ------ inclusion threshold ------
      0.012   14.8   0.0        1.2    8.2   0.0    2.2  2  NAD_binding_4   Male sterility protein
      0.027   13.9   0.0      0.042   13.3   0.0    1.3  1  adh_short       short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   6.6e-14   1.7e-10       1      79 [.       5      81 ..       5      93 .. 0.89
   2 !   56.1   0.0   1.4e-18   3.6e-15     106     241 .]      92     225 ..      83     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6.6e-14
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHH CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaa 79
                                      +lV+G+t fiG+++v+ ll++gy v  ++r ++++++a +++++ ve+d +d+ +l+++  + +pd+vi + a    +a
  gi|313127087|ref|YP_004037357.1|  5 ALVIGGTRFIGRHTVEDLLDHGYAVAIFNRGNHENPFADDDRVTHVEGDRKDEMDLKAAKLSIEPDIVIDCVA--YQPA 81
                                      59*********************************************************************55..3333 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 1.4e-18
                                       TCTEEEEEEEGGGGTSCSSSS.BSTCSTTS--.......--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEES CS
                         Epimerase 106 gvkrllflsSsevYGkdaeqp.keettltgpl.......kpnspYaaaKlageklveayaaqyglnaiilrlfnlyG 174
                                       +v+ ++++sS + YG+ +  p +e +t    +        +   Y+  K+ g+++v ++a + g+na+++r++ +yG
  gi|313127087|ref|YP_004037357.1|  92 DVDAYVYISSGAAYGREEI-PkREGETPLCDCtpeqaasDSDASYGPRKAEGDRIVFDAAMD-GVNAMSIRPCIVYG 166
                                       68899**********7766.653333311111222445678889*************98655.5************* PP

                                       TTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
                         Epimerase 175 prngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                                       p     + +  + ++i ++ +    v++ gdgt+++   yv+Dva a+  v+e+   g +ge yn+G
  gi|313127087|ref|YP_004037357.1| 167 PD----DYTERLDYWIHRVETYD-RVVVPGDGTNVWHRAYVKDVASALRVVAER---GTPGESYNVG 225
                                       *9....9**************99.******************************...999******9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.8e-07   0.00047       1      81 [.       6      74 ..       6      94 .. 0.80
   2 !   13.9   0.0   1.1e-05     0.027     126     282 ..      98     259 ..      84     291 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
                                      EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEE CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdev 79
                                      L+ G++ fiG +++e Ll+ gy v ++       n g+ e+   d     +++++ ++gD +D+  l+ +  +++pd v
  gi|313127087|ref|YP_004037357.1|  6 LVIGGTRFIGRHTVEDLLDHGYAVAIF-------NRGNHENPFAD-----DDRVTHVEGDRKDEMDLKAAKLSIEPDIV 72
                                      899*********************764.......44444444432.....45778899999999999999999999888 PP

                                      EE CS
                     GDP_Man_Dehyd 80 yn 81
                                      + 
  gi|313127087|ref|YP_004037357.1| 73 ID 74
                                      76 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.1e-05
                                       EEEEGGGG-S-S......SSSB-....TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTS CS
                     GDP_Man_Dehyd 126 qaStsEvYGkvq......evpqt....EttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetf 192
                                        +S+   YG+ +      e+p      E+   +    Y+  K+  d iv +     g+ a++ +    ++p      
  gi|313127087|ref|YP_004037357.1|  98 YISSGAAYGREEipkregETPLCdctpEQAASDSDASYGPRKAEGDRIVFDAA-MDGVNAMSIRPCIVYGPDD---- 169
                                       56777777765322222234422111234444556788888888888888754.4788888888888888884.... PP

                                       CCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS-.--EEE-TT-EEECHHCHHCCHHCCCH CS
                     GDP_Man_Dehyd 193 vtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkp.edyviatgethsvrefvelaflelgk 268
                                        t+ +   ++r++     v++ G++ ++    +vkD+++a++ + ++++p e y++++ + ++++e+ve  + ++  
  gi|313127087|ref|YP_004037357.1| 170 YTERLDYWIHRVETYD-RVVVPGDGTNVWHRAYVKDVASALRVVAERGTPgESYNVGDRRLVTLEEMVECIADAADT 245
                                       4455566888888765.67778******999*****************9956799**************99988888 PP

                                       HHHHH......... CS
                     GDP_Man_Dehyd 269 tiewegkgeeevgr 282
                                       ++e    ge+e ++
  gi|313127087|ref|YP_004037357.1| 246 SVEVVHAGERELAA 259
                                       88877777776654 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   3.1e-07    0.0008       1     229 [.       6     214 ..       6     218 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.1e-07
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +v+Gg+ F+Gr+ v+ L++ +    v ++   ++++    +   ++ + +egD +d+ +l++a  +++  i++ ++ 
  gi|313127087|ref|YP_004037357.1|   6 LVIGGTRFIGRHTVEDLLDHGY--AVAIFNRGNHENP---FADDDRVTHVEGDRKDEMDLKAAKLSIEPDIVIDCVA 77 
                                       6999999999999999999995..7888876665555...4555555577999999999999988888888885554 PP

                         3Beta_HSD  78 dvagkltedeimkvnvkGTrnvleacvk..agvrvlvYtSsaevvgpnslgeeilngd.Eeleyesl.......hqd 144
                                            +  d             +ea+v+  a+v + vY Ss  + g     eei + + E+   + +         +
  gi|313127087|ref|YP_004037357.1|  78 ----YQPAD-------------VEAAVDifADVDAYVYISSGAAYGR----EEIPKREgETPLCDCTpeqaasdSDA 133
                                       ....44455.............223322117999*******999887....23322220222222221111122556 PP

                         3Beta_HSD 145 aypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegd..kllvpllkqlaklglalfkigdeevlsdrvYvg 219
                                        y   Ka  +++v  a      +g  ++  ++Rp ++yG+ d  ++l   ++++      ++  gd  ++  r Yv 
  gi|313127087|ref|YP_004037357.1| 134 SYGPRKAEGDRIVFDAAM----DG--VNAMSIRPCIVYGPDDytERLDYWIHRVETYD-RVVVPGDGTNVWHRAYVK 203
                                       688889999999998876....77..8999*********9763245666666666665.99999************* PP

                         3Beta_HSD 220 Nvawa.hilAa 229
                                        va a  ++A 
  gi|313127087|ref|YP_004037357.1| 204 DVASAlRVVAE 214
                                       **987246665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   6.2e-09   1.6e-05       1      82 [.       9      90 ..       9     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.2e-09
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-..SEEEES---TCCHHHH CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkga..daVvsalggggkdeeg 77
                                      G+t  +Gr+ v+ ll++ g++v ++ R  ++ + ++++++++ vegd  d+ dl++a   +  d+V+ +++ +  d e+
  gi|313127087|ref|YP_004037357.1|  9 GGTRFIGRHTVEDLLDH-GYAVAIFNRGNHENP-FADDDRVTHVEGDRKDEMDLKAAKLSIepDIVIDCVAYQPADVEA 85
                                      99***************.5***99999888888.8999***************99987655337999888888777666 PP

                                      HHHHH CS
                    NAD_binding_10 78 akniv 82
                                      a+ i 
  gi|313127087|ref|YP_004037357.1| 86 AVDIF 90
                                      66655 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00014      0.36       3      65 ..       5      82 ..       3      96 .. 0.91
   2 !    4.7   0.0    0.0055        14     123     240 ..     133     252 ..     124     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                                      EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE------HH CS
                     RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAytavD 65
                                       lv+G++  +G++ ++ l  +g++v  ++r                e d +d+  ++++  +++pd+v+++ Ay+  D
  gi|313127087|ref|YP_004037357.1|  5 ALVIGGTRFIGRHTVEDLLDHGYAVAIFNRGnhenpfadddrvthvEGDRKDEMDLKAAKLSIEPDIVIDCVAYQPAD 82
                                      5899******************9999999989999********99999999***********************9776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0055
                                       SHHHHHHHHHHHHHHH...H-SSEEEEEE-SEESS.SSS-HHHHHHHHHHH-SEEEEESS-EE..--EEHHHHHHHH CS
                     RmlD_sub_bind 123 nvYGrtKlaGEqavla...agkkalivRtswvyge.kgknfvktmlrlakereelkvvaDqlg..sPTsardlAevl 193
                                         YG  K++G + v +   +g +a+ +R   vyg     + +   ++++++ +++ v  D +      +++d+A++l
  gi|313127087|ref|YP_004037357.1| 133 ASYGPRKAEGDRIVFDaamDGVNAMSIRPCIVYGPdDYTERLDYWIHRVETYDRVVVPGDGTNvwHRAYVKDVASAL 209
                                       57************98656677999********98455677888899999999999999965411678999999999 PP

                                       HHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEE CS
                     RmlD_sub_bind 194 lqllekaaeekelagvyHlanegetswlefArailkeagadseevkp 240
                                         ++e+ +      + y ++ ++ ++  e+ + i+++a+++ e v++
  gi|313127087|ref|YP_004037357.1| 210 RVVAERGTP----GESYNVGDRRLVTLEEMVECIADAADTSVEVVHA 252
                                       999999987....7778888888888888888888888887766655 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0066        17       3      25 ..       9      31 ..       7      68 .. 0.83
   2 ?    8.2   0.0   0.00048       1.2     130     209 ..      95     172 ..      88     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0066
                                      -TTSHHHHHHHHHHHHHS-.TEE CS
                     NAD_binding_4  3 GaTGFLGkvLlekLLrttpevki 25
                                      G+T F+G++ +e+LL+   +v i
  gi|313127087|ref|YP_004037357.1|  9 GGTRFIGRHTVEDLLDHGYAVAI 31
                                      9**************99876555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00048
                                       -EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EE CS
                     NAD_binding_4 130 vllhvSTayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsii 206
                                       +++++S+++++g +e   +e     ge +   d + ++   +    Y   Ka+++++v +a+   g++++ +Rp i+
  gi|313127087|ref|YP_004037357.1|  95 AYVYISSGAAYGREEIPKRE-----GE-TPLCDCTPEQAASDSDASYGPRKAEGDRIVFDAAMD-GVNAMSIRPCIV 164
                                       67888885555544422212.....22.222344444445556679****************66.************ PP

                                       E-.....- CS
                     NAD_binding_4 207 tg.....e 209
                                       +g     e
  gi|313127087|ref|YP_004037357.1| 165 YGpddytE 172
                                       99654443 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.7e-05     0.042       2      36 ..       4      38 ..       3      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseek 36
                                      ++lv+G+++ IGr +++ l+  G+ v++++r + +
  gi|313127087|ref|YP_004037357.1|  4 TALVIGGTRFIGRHTVEDLLDHGYAVAIFNRGNHE 38
                                      79**************************9887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2349.35
//
Query:       gi|313127088|ref|YP_004037358.1|  [L=229]
Description: hypothetical protein Hbor_23530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-16   61.1   0.5    2.3e-16   60.1   0.5    1.5  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.5   1.3e-20   2.3e-16       1     120 [.      50     150 ..      50     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.3e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld 77 
                                       r++H+l+V  la  +ae++g  +d++++++aaL+HDi+k   ++            + H+++ga+++re++  +g+ 
  gi|313127088|ref|YP_004037358.1|  50 RFNHILNVVDLASNIAEREG--ADVDVVRVAALFHDIAKLEAEQ------------EVHAEEGARVAREYLSTHGDF 112
                                       79******************..*******************554............57****************998 PP

                                       ....HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHH CS
                                HD  78 ....ledvaklirehheswegkkrprglaerqlslearivklaDrla 120
                                           +e v+++++ h+ + + +         + +le r++  aD l+
  gi|313127088|ref|YP_004037358.1| 113 pqsfIEQVCQVVADHSYQGPLS---------DVTLETRCLIEADILD 150
                                       ********************77.........9********9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1544.14
//
Query:       gi|313127089|ref|YP_004037359.1|  [L=351]
Description: hypothetical protein Hbor_23540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-82  276.4   0.0    3.2e-82  276.1   0.0    1.0  1  DUF3179   Protein of unknown function (DUF3179)


Domain annotation for each model (and alignments):
>> DUF3179  Protein of unknown function (DUF3179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.1   0.0   1.8e-86   3.2e-82       2     280 ..      24     340 ..      23     349 .. 0.93

  Alignments for each domain:
  == domain 1  score: 276.1 bits;  conditional E-value: 1.8e-86
                           DUF3179   2 DgIPaidnPefasaeeasksldddepVigvelngearaYPlrilvwheiVNdtlggepvavTYCpLcgtalaferri 78 
                                       D+IP++dnP+f +a+e +   d++++Vi+ve+ g+araYP r+l++heiVNd++g++pvavT+CpLcg+a++++rr+
  gi|313127089|ref|YP_004037359.1|  24 DAIPSVDNPTFGPADEYDG--DGSDDVIVVEIAGDARAYPVRFLHYHEIVNDEFGSVPVAVTWCPLCGSAVVYDRRV 98 
                                       9***************999..******************************************************** PP

                           DUF3179  79 d.............ggelefgvsGkLvnsnlvmyDreteslwqQllgeaiaGklegteLeelpvvtttwekwkeahp 142
                                       +             +++le+gvsGkL++++lvmyDret+s w+Q++g++++G +eg++L++lp++ttt e+++++++
  gi|313127089|ref|YP_004037359.1|  99 AeaapadddadvpdHAVLELGVSGKLADDDLVMYDRETGSEWKQSSGACLSGVHEGMRLAVLPAATTTAEAFARDYD 175
                                       ***************************************************************************** PP

                           DUF3179 143 dtkVlseetgssr...........dYgrdPygsye.p.............asdrplfpvekrddrlppkerVvgvev 194
                                       d+++l+ ++g+s+           +Y++dPy++y+ +             ++d+   p + + + ++pk++V+g+e 
  gi|313127089|ref|YP_004037359.1| 176 DGAMLRPPGGESEaasdsdepasiEYDADPYEAYFeMpgyglgahrgtggRDDW---PQSLSTAGVEPKSIVAGLER 249
                                       *****99999999999999****************659********98876666...444444569*********** PP

                           DUF3179 195 gddavaypkaelkee.gvvedtvgdkevvvvldadaesaldakrv.......vldees.....gtlwdlangealdg 258
                                       ++da+ +p++ ++++ gvv++tvgd+e vv+++ad+ +a++a+++            +     gt+w+  +g+a+dg
  gi|313127089|ref|YP_004037359.1| 250 DEDALGIPLEVAEATgGVVRVTVGDDEAVVFATADGIHAFEAPSFeleptdeE----GmfvgdGTTWHGGTGRADDG 322
                                       ************9999***************************9976644440....366666799***99***999 PP

                           DUF3179 259 klkgarlervaaaeafWFawaa 280
                                       +    +l+r++ ++ f+Faw  
  gi|313127089|ref|YP_004037359.1| 323 R----TLDRLPVRRLFAFAWRD 340
                                       9....79*************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2558.86
//
Query:       gi|313127090|ref|YP_004037360.1|  [L=147]
Description: mn-dependent transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-17   62.5   0.2      8e-17   61.2   0.1    1.7  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    9.3e-11   41.7   0.1    4.7e-10   39.4   0.1    1.9  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    3.9e-05   23.5   0.0    8.8e-05   22.3   0.0    1.5  1  MarR_2          MarR family
    6.1e-05   22.9   0.0    0.00011   22.1   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00016   21.2   0.0     0.0015   18.0   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00025   20.9   0.0     0.0012   18.7   0.0    2.0  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00028   21.3   0.0    0.00046   20.6   0.0    1.3  1  HTH_27          Winged helix DNA-binding domain
     0.0021   18.0   0.0     0.0039   17.1   0.0    1.4  1  MarR            MarR family
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.016   14.9   0.0    1.3  1  DUF4423         Domain of unknown function (DUF4423)
      0.047   13.8   0.0       0.11   12.6   0.0    1.5  1  HTH_20          Helix-turn-helix domain
      0.081   12.8   0.0       0.15   12.0   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.084   12.5   0.0       0.26   11.0   0.0    1.8  2  GntR            Bacterial regulatory proteins, gntR family
       0.13   12.7   0.0       0.24   11.8   0.0    1.5  1  Rrf2            Transcriptional regulator


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.1   5.8e-20     8e-17       4      60 .]       2      59 ..       1      59 [. 0.97
   2 ?   -1.6   0.0       2.3   3.2e+03      20      32 ..      99     111 ..      79     113 .. 0.55

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 5.8e-20
                                      HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  4 estEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +++++Y ++IY l+e e +++ t  la  L+vsp+s+ em+ kLe+ G+ e+ekykg+
  gi|313127090|ref|YP_004037360.1|  2 NTADQYVKAIYLLQEmEDGPAATGALADMLDVSPASANEMIGKLEDRGLAEHEKYKGV 59
                                      67899***************************************************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                                       HSSB-HHHHHHHH CS
                    Fe_dep_repress  20 kkvvktkdlaerL 32 
                                        ++v    +aerL
  gi|313127090|ref|YP_004037360.1|  99 LEPVIDDTVAERL 111
                                       3444445566666 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0         1   1.4e+03      22      41 ..      27      46 ..      24      48 .. 0.86
   2 !   39.4   0.1   3.4e-13   4.7e-10       1      64 [.      62     123 ..      62     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1
                                      HHHHCT--CCCHHHHCCCCG CS
                     Fe_dep_repr_C 22 LvdvlgvdweeaheeAerlE 41
                                      L+d+l+v++  a e   +lE
  gi|313127090|ref|YP_004037360.1| 27 LADMLDVSPASANEMIGKLE 46
                                      88999999999999887777 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 3.4e-13
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TT CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPh 64 
                                       T++G   A++ ++ + ++erfL++vl+v  ee   eA +lE ++++ ++erld++++  +ecP+
  gi|313127090|ref|YP_004037360.1|  62 TDEGIIRARDALQTYCIIERFLANVLDV--EEFRSEARELEPVIDDTVAERLDTIIDRNSECPD 123
                                       9*************************98..9********************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   6.4e-08   8.8e-05      11      54 ..      14      54 ..       9      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.4e-08
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      L +  ++p    + g+la+ l++s+++++ ++ +L+++GL e +
  gi|313127090|ref|YP_004037360.1| 14 LQEMEDGP---AATGALADMLDVSPASANEMIGKLEDRGLAEHE 54
                                      55555565...69***************************9987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     8e-08   0.00011      25      62 ..      25      64 ..      10      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8e-08
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES-H CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rgrr.irildl 62
                                        lA+ml +++ + + ++++L+++gl +  +++ +r++d 
  gi|313127090|ref|YP_004037360.1| 25 GALADMLDVSPASANEMIGKLEDRGLAEhEKYKgVRLTDE 64
                                      569*************************644334999986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.1e-06    0.0015      12      46 ..      14      50 ..       9      52 .. 0.88
   2 ?    0.8   0.0      0.27   3.7e+02      40      48 .]      60      68 ..      60      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                            HTH_24 12 Lqk..nprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                      Lq+  ++      LA++l++Sp+  n+ + +Le+ Gl
  gi|313127090|ref|YP_004037360.1| 14 LQEmeDGPAATGALADMLDVSPASANEMIGKLEDRGL 50
                                      5556588899999**********************97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.27
                            HTH_24 40 rLeeeGlIk 48
                                      rL++eG+I+
  gi|313127090|ref|YP_004037360.1| 60 RLTDEGIIR 68
                                      89******7 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.8e-07    0.0012      19      57 ..      18      56 ..      11      79 .. 0.88
   2 ?   -0.5   0.0      0.84   1.2e+03       8      24 ..     128     144 ..     127     147 .] 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.8e-07
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      + gpa +  +a +l+v+ ++++e++ +Led+Gl e ek 
  gi|313127090|ref|YP_004037360.1| 18 EDGPAATGALADMLDVSPASANEMIGKLEDRGLAEHEKY 56
                                      7899*******************************9975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.84
                                       HHCCCHCHHHHHHCCCH CS
                              TrmB   8 eyEakvYlaLlklgpat 24 
                                       e++a +Yl L ++ + +
  gi|313127090|ref|YP_004037360.1| 128 ETDACCYLELASEPEEK 144
                                       78999*****9877655 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.3e-07   0.00046      13      68 .]      12      65 ..       3      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.3e-07
                            HTH_27 13 r....hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +    +++++++  +l+++l+v+ +++ +++ kL+ +GL       +  ++k vrlTd+G
  gi|313127090|ref|YP_004037360.1| 12 YllqeMEDGPAATGALADMLDVSPASANEMIGKLEDRGLA------EHEKYKGVRLTDEG 65
                                      3334688999999***************************......445668******99 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.8e-06    0.0039      16      46 ..      20      50 ..       8      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.8e-06
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGl 46
                                      gp+    La++l vs++++ +++ +Le++Gl
  gi|313127090|ref|YP_004037360.1| 20 GPAATGALADMLDVSPASANEMIGKLEDRGL 50
                                      5566679***********************9 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.2e-05     0.016      22      83 ..       7      66 ..       3      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                           DUF4423 22 yypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteksl 83
                                      y  +i+ l +++d+ a + +la++l   +s + +++ +  L++ gl++ ++ + +r t++ +
  gi|313127090|ref|YP_004037360.1|  7 YVKAIYLLQEMEDGPAATGALADMLD--VSPASANEMIGKLEDRGLAEHEKYKGVRLTDEGI 66
                                      677999999*****************..**********************999999998765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.7e-05      0.11      16      57 ..      14      54 ..      11      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-05
                                      HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      l++  +++++  ++la+ ld+s+++++  + +Le+ gL e +
  gi|313127090|ref|YP_004037360.1| 14 LQEM-EDGPAATGALADMLDVSPASANEMIGKLEDRGLAEHE 54
                                      5555.899******************************9876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.15       8      45 ..      11      51 ..       8      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      HHHHTT...SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  8 LklLae...gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      ++lL+e   g++  + la++l++s++   +   kL++ GL 
  gi|313127090|ref|YP_004037360.1| 11 IYLLQEmedGPAATGALADMLDVSPASANEMIGKLEDRGLA 51
                                      555555555*****************999999999999886 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.26      29      63 ..      26      60 ..      23      61 .. 0.93
   2 ?   -1.5   0.0       1.5   2.1e+03      47      57 ..      60      70 ..      59      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEE CS
                              GntR 29 eLaaefgVsrttvReALrrLeaeglverrqgrGtf 63
                                      +La++++Vs  + +e + +Le +gl+e ++ +G++
  gi|313127090|ref|YP_004037360.1| 26 ALADMLDVSPASANEMIGKLEDRGLAEHEKYKGVR 60
                                      7**************************99999976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                      HHHHTTSEEEE CS
                              GntR 47 rLeaeglverr 57
                                      rL+ eg++ +r
  gi|313127090|ref|YP_004037360.1| 60 RLTDEGIIRAR 70
                                      899***99987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.24      15      58 ..      11      54 ..       2      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      +yL +e e++p+++ ++a++ ++sp  +  ++ kL+  gl + +
  gi|313127090|ref|YP_004037360.1| 11 IYLLQEMEDGPAATGALADMLDVSPASANEMIGKLEDRGLAEHE 54
                                      45666666678****************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1003.43
//
Query:       gi|313127091|ref|YP_004037361.1|  [L=165]
Description: rubrerythrin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0004   20.6   2.5      0.014   15.6   0.7    2.3  2  DUF4226       Domain of unknown function (DUF4226)
    0.00041   20.8   7.8    0.00057   20.3   6.8    1.7  1  Rubrerythrin  Rubrerythrin
      0.007   16.6   3.5       0.51   10.5   1.2    2.1  2  Ferritin_2    Ferritin-like domain
  ------ inclusion threshold ------
      0.017   14.9   0.4      0.022   14.6   0.4    1.3  1  DUF445        Protein of unknown function (DUF445)
      0.032   12.8   0.4        3.6    6.1   0.0    2.0  2  FapA          Flagellar Assembly Protein A
      0.042   13.7   0.0      0.059   13.2   0.0    1.3  1  AAA_lid_11    Dynein heavy chain AAA lid domain
      0.048   13.7   1.7      0.097   12.7   1.7    1.6  1  PspB          Phage shock protein B
       0.12   12.4   5.9          1    9.3   5.5    2.3  1  DUF892        Domain of unknown function (DUF892)
       0.23   12.0   1.5       0.64   10.5   1.5    1.7  1  PP2C_C        Protein serine/threonine phosphatase 2C, C-term
       0.26   11.4   4.1       0.63   10.1   2.3    2.3  3  Nup54         Nucleoporin complex subunit 54
       0.36   10.8   4.3        9.8    6.2   1.2    2.7  2  T2SSF         Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> DUF4226  Domain of unknown function (DUF4226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.7   8.8e-06     0.014      23      57 ..      38      76 ..      21      91 .. 0.79
   2 ?    4.8   0.0     0.021        34      25      58 ..     116     149 ..     104     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.8e-06
                           DUF4226 23 ta....elDrqlaevlrsahakaaegrrrLdalqaeidq 57
                                       +    elD+++++ l +a++++ae r+rL+ +  e+d+
  gi|313127091|ref|YP_004037361.1| 38 LSdeerELDEEIEDLLEHAAEESAEHRERLERIIDELDA 76
                                      3333369****************************9986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.021
                           DUF4226  25 elDrqlaevlrsahakaaegrrrLdalqaeidqa 58 
                                       ++ ++l+++++  +a+  ++r+rL  l ++i++ 
  gi|313127091|ref|YP_004037361.1| 116 KFYDDLINAIAASDAQFGVDRERLVRLLTDIREE 149
                                       566789999999999999********99999875 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   6.8   3.5e-07   0.00057      10     106 ..      28     121 ..      26     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.5e-07
                                       HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHH CS
                      Rubrerythrin  10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLe 86 
                                       E  a+  Y++l+++ +e  ++i+ l+e  Aee +eH+++l++++++l+ e    + e++ + +ea+   +t++++ +
  gi|313127091|ref|YP_004037361.1|  28 EARAYHHYQSLSDEERELDEEIEDLLEHAAEESAEHRERLERIIDELDAESI--PFEDIETLVEAQ-YGKTKPDDFD 101
                                       889999****************************************999999..333333333332.2335666777 PP

                                       HHHHHHHHHHHCHHHHHHHH CS
                      Rubrerythrin  87 eaiegayaeeeemyrfyeel 106
                                        ++    ++ee++y+fy +l
  gi|313127091|ref|YP_004037361.1| 102 GILYDQLCNEETAYKFYDDL 121
                                       77778888888888888776 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   1.2   0.00031      0.51       4      62 ..      15      72 ..      12      95 .. 0.83
   2 !    6.5   0.0    0.0057       9.3      13      61 ..     111     161 ..     102     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                        Ferritin_2  4 diLnfAlnl.EyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaale 62
                                      ++L++ + l E +ea +Y++  +    d++  ld+e+ +++e +a++ ++H+e l++ + 
  gi|313127091|ref|YP_004037361.1| 15 RLLQIGVVLeEVVEARAYHHYQSLS--DEERELDEEIEDLLEHAAEESAEHRERLERIID 72
                                      5788888885678******999854..3499************************99985 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0057
                        Ferritin_2  13 EyleaafYtaalegasldd..kalldaevrevaeeiakheeaHveflkaal 61 
                                       E ++ +fY   ++++ ++d   +   ++ ++++++i+++e++ ve+ ++  
  gi|313127091|ref|YP_004037361.1| 111 EETAYKFYDDLINAIAASDaqFGVDRERLVRLLTDIREEEAEGVEAVTKIM 161
                                       88999****999998888776777778889***************998865 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.4   1.4e-05     0.022      67     174 ..      44     150 ..      12     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                            DUF445  67 evasklaewlknptnkeslaaiveellkeiledlddesik.ellkknlkkkleevipepllgkllellleeerhkkl 142
                                       e+++++ ++l++ + +   +a+ +e l++i+++ld esi+ e ++++++ +  +  p  ++g l ++l +ee ++k+
  gi|313127091|ref|YP_004037361.1|  44 ELDEEIEDLLEHAAEE---SAEHRERLERIIDELDAESIPfEDIETLVEAQYGKTKPDDFDGILYDQLCNEETAYKF 117
                                       5556666666633333...4689999*************94569********************************* PP

                            DUF445 143 lddlldriknllkdeevk.ekikelidelieee 174
                                        ddl++ i +  +++ v+ e++ +l+ + +eee
  gi|313127091|ref|YP_004037361.1| 118 YDDLINAIAASDAQFGVDrERLVRLLTDIREEE 150
                                       *****9988766665543145555555555555 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0033       5.3     314     366 ..      17      73 ..       3      98 .. 0.64
   2 ?    6.1   0.0    0.0022       3.6      26      58 ..     117     149 ..      89     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0033
                              FapA 314 kklGselgtkteievgldepelkeklkeleeeleel....eeeleklkkkikklpkl 366
                                        ++G  l++  e ++  ++++l ++ +el+ee+e+l     ee  +++++++++ ++
  gi|313127091|ref|YP_004037361.1|  17 LQIGVVLEEVVEARAYHHYQSLSDEERELDEEIEDLlehaAEESAEHRERLERIIDE 73 
                                       478888888888888777788888888888888888766655555555554444442 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0022
                              FapA  26 tleeileaLkkagivfgidkealekilksakeg 58 
                                       + +++++a++++   fg+d+e l ++l+  +e+
  gi|313127091|ref|YP_004037361.1| 117 FYDDLINAIAASDAQFGVDRERLVRLLTDIREE 149
                                       789************************999888 PP

>> AAA_lid_11  Dynein heavy chain AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.6e-05     0.059      69     122 ..      66     118 ..      53     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHCSSGGS-HHHHHHHHHHTTTSTT--SHHHHHHHHHHHHHHSSGGGG CS
                        AAA_lid_11  69 vlkmyldeyeekevpwealkyligeinYGGrvtDdwDrrllktyleeffseevl 122
                                        l++++de +++++p+e++++l+ e++YG    Dd+D  l + +++e    + +
  gi|313127091|ref|YP_004037361.1|  66 RLERIIDELDAESIPFEDIETLV-EAQYGKTKPDDFDGILYDQLCNEETAYKFY 118
                                       57889999999***********9.9************99998888875554444 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.7   5.9e-05     0.097      24      67 ..      34      77 ..      12      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
                              PspB 24 HYrskkkrskglsaedekrLeellekAekleeRietLEriLdae 67
                                      HY s + ++++l++e e+ Le+ +e++ + +eR+e + + Ldae
  gi|313127091|ref|YP_004037361.1| 34 HYQSLSDEERELDEEIEDLLEHAAEESAEHRERLERIIDELDAE 77
                                      *****************************9*9977666666666 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.5   0.00063         1      32      77 ..      45      88 ..      26     165 .] 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00063
                                      SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------.-HHHHTT CS
                            DUF892 32 espeLkaaleqHleeTegqierLeqvferlgesasekkcdamegli 77
                                       ++e+++ le+  ee  ++ erLe+++++l+++   ++   +e l+
  gi|313127091|ref|YP_004037361.1| 45 LDEEIEDLLEHAAEESAEHRERLERIIDELDAESIPFE--DIETLV 88
                                      45999*************************98765554..455555 PP

>> PP2C_C  Protein serine/threonine phosphatase 2C, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.5    0.0004      0.64      19      60 ..      40      80 ..      34      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                            PP2C_C 19 kkEkeldekleervkeiiekeekkeeldlekvlkvLasedip 60
                                      ++E+elde++e  ++ + e e+ +++  le+++ +L +e+ip
  gi|313127091|ref|YP_004037361.1| 40 DEERELDEEIEDLLEHAAE-ESAEHRERLERIIDELDAESIP 80
                                      6899********9999999.88888999**********9997 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.3   0.00039      0.63      86     136 ..      14      70 ..       5      78 .. 0.76
   2 ?    3.0   0.1     0.063     1e+02      41      61 ..      56      76 ..      51      96 .. 0.73
   3 ?    0.0   0.0      0.51   8.3e+02      29      77 ..     116     163 ..     113     165 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHH.HHTT-SS....---SSHHHHHHHHHHHHHHHS-H.HH.HHHHHHH CS
                             Nup54  86 hRllrllrkle.ilrsrgy....aldaeEeelrarletleaqlndp.aqlkgrvnel 136
                                        Rll++ + le +++ r+y    +l+ eE+el +++e+l ++  ++ a+ + r++ +
  gi|313127091|ref|YP_004037361.1|  14 ARLLQIGVVLEeVVEARAYhhyqSLSDEERELDEEIEDLLEHAAEEsAEHRERLERI 70 
                                       699999999997888887767779*************99998886445555555554 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.063
                                      HHHHHHHHHHHHHHHHHHHHH CS
                             Nup54 41 Qqkevaqhrerlkeisdrlee 61
                                       ++e+a+hrerl+ i d+l++
  gi|313127091|ref|YP_004037361.1| 56 AAEESAEHRERLERIIDELDA 76
                                      6789999******99998864 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.51
                                       ECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  29 kGFedLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrleka 77 
                                       k ++dL +  +a +++  + rerl  + ++++e e ++ +e+ +++ + 
  gi|313127091|ref|YP_004037361.1| 116 KFYDDLINAIAASDAQFGVDRERLVRLLTDIREEE-AEGVEAVTKIMET 163
                                       56788888888889999999999999999999988.8888888887765 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3    0.0098        16       3      39 ..      11      53 ..      11      58 .. 0.69
   2 ?    6.2   1.2     0.006       9.8      15     103 ..      49     161 ..      48     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0098
                                      HHHHHHHHTT--HHHHHH.HHHHHHS.....SHHHHHHHHHHH CS
                             T2SSF  3 rqlatllsaGvplveaLe.llaeeae.....ngplaeelkria 39
                                      +qla+ll+ Gv l+e++e ++ ++ +     +++l ee+++++
  gi|313127091|ref|YP_004037361.1| 11 HQLARLLQIGVVLEEVVEaRAYHHYQslsdeERELDEEIEDLL 53
                                      59****************4444444466666666666666555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC..........................T-TT.TS.-HHH CS
                             T2SSF  15 lveaLellaeeaengplaeelkriarrlraGgslseale..........................rtpssef.pelv 64 
                                       +++ Le++aee+   + +e+l+ri+++l+a + + e +e                          +t   +f ++l+
  gi|313127091|ref|YP_004037361.1|  49 IEDLLEHAAEES--AEHRERLERIIDELDAESIPFEDIEtlveaqygktkpddfdgilydqlcneETAY-KFyDDLI 122
                                       567888888888..9999999999999999887777777777777777666666677777777755554.5547777 PP

                                       HHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             T2SSF  65 vqlirageeggnLaevLerlaeyleeerelrrkllaall 103
                                        ++ ++  + g   e L rl ++++ee++   +  ++++
  gi|313127091|ref|YP_004037361.1| 123 NAIAASDAQFGVDRERLVRLLTDIREEEAEGVEAVTKIM 161
                                       777777777777777777777777777777666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1810  (0.100954); expected 358.6 (0.02)
Passed bias filter:                     1033  (0.0576162); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1098.71
//
Query:       gi|313127092|ref|YP_004037362.1|  [L=402]
Description: iron ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-62  209.9   0.6    4.4e-62  209.6   0.6    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.6   0.6   2.5e-66   4.4e-62       3     218 .]     151     376 ..     149     376 .. 0.97

  Alignments for each domain:
  == domain 1  score: 209.6 bits;  conditional E-value: 2.5e-66
                           UPF0051   3 fertlivveegaevtiieey......agc.....gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklel 68 
                                       f +tl+v ee ++vti+e++      +         vei  gen+ ++y ++qn +ed+++++ kr + +   ++++
  gi|313127092|ref|YP_004037362.1| 151 FSHTLVVTEESSSVTILERIdsgasaE-GaryfsNLVEIATGENSYVQYGSLQNLDEDTYHYTLKRGDADVYGTINW 226
                                       78***************9999776652.056677*********************************99999***** PP

                           UPF0051  69 ttvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvr 145
                                       +++++g++ltr+++++el+g+ +e+++ g+++++++qhld++ +v hn++nt+++++++gvl+d+ar+v++g  +v 
  gi|313127092|ref|YP_004037362.1| 227 IEGNIGSRLTRSDVETELNGDSSETQIVGAFFGHEDQHLDLNARVWHNAENTTADLVTRGVLDDDARSVYEGVQDVG 303
                                       ***************************************************************************** PP

                           UPF0051 146 kgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       ++a +t+++q++++L+lsd+++ad+ P+l i+++d +asH AtvG++d+e lfY+ sR +++ +Ar+++v+gf
  gi|313127092|ref|YP_004037362.1| 304 RDAWNTSSYQRENTLMLSDESEADASPKLIIHNHDTEASHSATVGQVDKEDLFYMISRSVPQLQARNMLVEGF 376
                                       ************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2755.89
//
Query:       gi|313127093|ref|YP_004037363.1|  [L=476]
Description: iron-regulated ABC transporter membrane component sufb [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-73  244.7   0.7    1.1e-72  244.3   0.7    1.2  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.3   0.7   6.2e-77   1.1e-72       2     218 .]     222     447 ..     221     447 .. 0.97

  Alignments for each domain:
  == domain 1  score: 244.3 bits;  conditional E-value: 6.2e-77
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       qfe+tli++eeg+ev++i   +gc            g ve+fvge+A+++y++vqnws++++nl+tkra ++++ ++
  gi|313127093|ref|YP_004037363.1| 222 QFEHTLIIAEEGSEVHYI---EGCsapkysafnlhsGGVEVFVGEDAHVQYSTVQNWSKNTYNLNTKRAIVEKNGRM 295
                                       89****************...666666777777777*********************************999***** PP

                           UPF0051  67 elttvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkik 143
                                       e++++s+g+k t+ +p + lkg+ga+ +  ++++a+++q++dt+ kv hn+pnt+s+i sk+++kd++r+ +rg ++
  gi|313127093|ref|YP_004037363.1| 296 EWISGSMGSKATMLYPCSILKGRGASDNHITIAFAGEGQNIDTGAKVYHNAPNTKSTIESKSISKDGGRTNYRGLVH 372
                                       ***************************************************************************** PP

                           UPF0051 144 vrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       +++ga+++++ +e+++L++++++++dt+P++ei++  v + H+AtvGki +e +fYL+sRGl+ ++A+++iv gf
  gi|313127093|ref|YP_004037363.1| 373 ISEGAENSSTAVECDALMFDNESTSDTMPYMEINESTVDVAHEATVGKIGDEDIFYLQSRGLDDDDAKQMIVSGF 447
                                       **************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3454.47
//
Query:       gi|313127094|ref|YP_004037364.1|  [L=305]
Description: fes assembly ATPase sufc [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-15   57.2   0.0    9.8e-15   55.3   0.0    1.9  1  ABC_tran  ABC transporter
    4.4e-06   26.3   0.8       0.02   14.4   0.1    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
    0.00019   21.3   0.2      0.079   12.8   0.0    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00024   21.5   0.1       0.21   12.0   0.0    2.3  2  AAA       ATPase family associated with various cellular acti
     0.0018   18.3   0.2        1.6    8.7   0.0    2.7  3  AAA_5     AAA domain (dynein-related subfamily)
     0.0037   17.0   0.1     0.0067   16.1   0.1    1.3  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.033   14.4   0.0       0.52   10.5   0.0    2.4  2  AAA_28    AAA domain
      0.043   14.4   0.0       0.16   12.5   0.0    1.9  1  AAA_18    AAA domain
      0.059   13.7   0.1       0.94    9.8   0.0    2.2  2  AAA_22    AAA domain
      0.064   13.2   0.0       0.11   12.4   0.0    1.3  1  Rad17     Rad17 P-loop domain
      0.069   13.6   4.4       0.29   11.6   0.0    2.3  2  AAA_23    AAA domain
      0.085   12.4   0.0       0.18   11.3   0.0    1.5  1  AAA_27    AAA domain
       0.14   12.3   0.0        0.2   11.8   0.0    1.3  1  AAA_33    AAA domain
       0.18   11.5   1.3       0.56    9.8   1.3    1.9  1  AAA_15    AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   7.7e-18   9.8e-15       1     134 [.      22     223 ..      22     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 7.7e-18
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEE..........................EETTCEG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx..........................xxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGei..........................lldgkdl 49 
                                       l+ v+l++k ge++a++G+nG+GKSt +k++ag+     t Gei                          l      
  gi|313127094|ref|YP_004037364.1|  22 LRGVDLEVKSGEIHALMGPNGSGKSTTAKVIAGHPAYevTDGEIllhleddefgddfeipedkrtwnlldL------ 92 
                                       6789*****************************865555*****775555555555555444443333330...... PP

                                       GGB-HHHCCHCEEEE-SS--S-TTSBHHHH............................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                          ABC_tran  50 keqeleslrkeigvlpqepqlfpeltvren............................................... 79 
                                         ++ e++   i   +q p   +++t+ +                                                
  gi|313127094|ref|YP_004037364.1|  93 --EPNERAALGIFLGFQYPAEIEGVTMTNFlrtalnakieereelfededeaddaeeeddsgyetspmegpadegev 167
                                       ..444444444444444444444444433366666666666666666666666666666777777777766655554 PP

                                       ...HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                          e ++ +++ +++l+++e  +  +++  + +SgG+k+  ++ +a + +p++ +lDE
  gi|313127094|ref|YP_004037364.1| 168 gvaEFQKLLKEKMEQLDMDE--KFMQRYLNAGFSGGEKKQNEVLQAAILEPSIAVLDE 223
                                       44333333555555555555..44444455***************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00021      0.27      25      41 ..      33      49 ..      24      53 .. 0.81
   2 !   14.4   0.1   1.5e-05      0.02     136     204 ..     197     263 ..     115     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      ++ a++GpNGSGKs   
  gi|313127094|ref|YP_004037364.1| 33 EIHALMGPNGSGKSTTA 49
                                      5789**********765 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.5e-05
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlek 204
                                        +SgGek+   + L  Ai +    ++ +lDeid+ LD  + + v++ +++ +++  + ++ i++ +++le 
  gi|313127094|ref|YP_004037364.1| 197 GFSGGEKKQNEV-LQAAILE---PSIAVLDEIDSGLDIDRLQDVSKGINALRDEqgTGVLQITHYQRILEY 263
                                       578888886654.4445543...4689*********************97776534778888888888775 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   6.1e-05     0.079       2      53 ..      35      71 ..      34     102 .. 0.68
   2 !    6.7   0.1    0.0042       5.4     255     297 ..     214     256 ..     118     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlyd 53
                                       +l GpNgsGKS+  + + +                +  + ++ + ll l d
  gi|313127094|ref|YP_004037364.1| 35 HALMGPNGSGKSTTAKVIAGH---------------PAYEVTDGEILLHLED 71
                                      6899*********99999765...............3334444444444444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0042
                            AAA_21 255 lkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                       l++ s+ ++DE+++gL+  +l  + + +++l++  g+ v+  TH
  gi|313127094|ref|YP_004037364.1| 214 LEP-SIAVLDEIDSGLDIDRLQDVSKGINALRDeQGTGVLQITH 256
                                       233.99***********998877775554444444455555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00016      0.21       3      21 ..      37      55 ..      35      74 .. 0.87
   2 !    7.3   0.1    0.0045       5.8      36      74 ..     195     231 ..     170     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                      EESSTTSSHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavake 21
                                      l+Gp G GK+++ak +a +
  gi|313127094|ref|YP_004037364.1| 37 LMGPNGSGKSTTAKVIAGH 55
                                      89**************986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0045
                                       SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                               AAA  36 skyvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                       +  ++ +ekk +e++++a   + psi ++DEid+    +
  gi|313127094|ref|YP_004037364.1| 195 NAGFSGGEKKQNEVLQAA-ILE-PSIAVLDEIDSGLDID 231
                                       446777899999999886.444.9*********976655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0054         7       4      20 ..      37      53 ..      35      87 .. 0.92
   2 ?   -2.2   0.1       2.9   3.7e+03      84     108 ..     124     148 ..     112     151 .. 0.75
   3 !    8.7   0.0    0.0012       1.6      41      76 ..     189     226 ..     169     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0054
                                      EE--SSSSHHHHHHHGG CS
                             AAA_5  4 LvGppGtgKselaerla 20
                                      L Gp G+gKs+ a+ +a
  gi|313127094|ref|YP_004037364.1| 37 LMGPNGSGKSTTAKVIA 53
                                      89***********9987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                                       HHHHHHHSSEEE..-SSSEEE---. CS
                             AAA_5  84 sLlslleerrllleeggelvkaknd 108
                                       +L+  +eer+ l+e+ +e  +a+++
  gi|313127094|ref|YP_004037364.1| 124 ALNAKIEEREELFEDEDEADDAEEE 148
                                       5777888888888888888877765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0012
                                       HH--B--...........--------G-SEEEEESGGG CS
                             AAA_5  41 lkgrreik..ngttslvdsplvraaregeilvlDEver 76 
                                       + +r+  +  +g+++ ++ +l  a+ e++i+vlDE++ 
  gi|313127094|ref|YP_004037364.1| 189 FMQRYLNAgfSGGEKKQNEVLQAAILEPSIAVLDEIDS 226
                                       333333336789999999****9999**********95 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.3e-06    0.0067      14      37 ..      24      47 ..      19      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKST 37
                                      g ++e++  +++ l+Gp+GsGKST
  gi|313127094|ref|YP_004037364.1| 24 GVDLEVKSGEIHALMGPNGSGKST 47
                                      5677888666*************9 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0004      0.52       3      47 ..      36      82 ..      34     143 .. 0.83
   2 ?    1.5   0.0      0.24   3.1e+02      11      30 ..     281     301 ..     279     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                            AAA_28  3 vitGgestGKTtlleaLaar.gypvv.pEaareileeklakgedalp 47
                                      +++G+ ++GK+t+++ +a +  y+v   E+   + +++  +++++ +
  gi|313127094|ref|YP_004037364.1| 36 ALMGPNGSGKSTTAKVIAGHpAYEVTdGEILLHLEDDEFGDDFEIPE 82
                                      799***************99889988788877777777777666444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.24
                            AAA_28  11 GKTtlleaLaargypvv.pEa 30 
                                       G  +l+e L+++gy +v +E+
  gi|313127094|ref|YP_004037364.1| 281 GDASLAETLEDKGYDWVrEEV 301
                                       556899***********6665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.16       3      67 ..      37      95 ..      36     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleen 67
                                      l+G+ G+GK+t ak ++ +        +v   + ll  +d+e + +  ++ edk+  +l  le n
  gi|313127094|ref|YP_004037364.1| 37 LMGPNGSGKSTTAKVIAGH-----PAYEVTDGEILLHLEDDE-FGDDFEIPEDKRTWNLLDLEPN 95
                                      89**************766.....566666666666666666.5666666666666666555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00073      0.94       5      24 ..      32      51 ..      27      72 .. 0.87
   2 ?    1.7   0.1      0.23   2.9e+02      85     113 ..     207     237 ..     133     262 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00073
                            AAA_22  5 agilvvtGesGtGKTtllrr 24
                                        i +++G+ G+GK+t+++ 
  gi|313127094|ref|YP_004037364.1| 32 GEIHALMGPNGSGKSTTAKV 51
                                      667899***********985 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.23
                            AAA_22  85 alrarav..ielliiDEaqh.lrseealeeLr 113
                                        + ++a   +++ ++DE++  l+  + l++++
  gi|313127094|ref|YP_004037364.1| 207 EVLQAAIlePSIAVLDEIDSgLD-IDRLQDVS 237
                                       33333336788999999999995.33333333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.6e-05      0.11      32      74 ..      19      61 ..       9      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.6e-05
                             Rad17 32 kewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklr 74
                                      ++ l+   Le +  +i  + GP G gkst+ kv++   ++++ 
  gi|313127094|ref|YP_004037364.1| 19 EQILRGVDLEVKSGEIHALMGPNGSGKSTTAKVIAGHPAYEVT 61
                                      677888889999999******************9987777765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.29      17      37 ..      29      50 ..       4      54 .. 0.78
   2 ?    1.4   3.2      0.31     4e+02     125     167 ..      80     181 ..      57     246 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_23 17 F.skgltlItGpNGaGKTTild 37
                                        s  + ++ GpNG+GK+T   
  gi|313127094|ref|YP_004037364.1| 29 VkSGEIHALMGPNGSGKSTTAK 50
                                      4445688999*********765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                            AAA_23 125 lgskkiilnlilflgqer...................................feefelkdkke............. 153
                                       +  +k+  nl+++ + er                                   +e fe++d+ +             
  gi|313127094|ref|YP_004037364.1|  80 IPEDKRTWNLLDLEPNERaalgiflgfqypaeiegvtmtnflrtalnakieerEELFEDEDEADdaeeeddsgyets 156
                                       44555555555555555555555555555555555553332222222111111222222111113333333334444 PP

                            AAA_23 154 ...........rleelekeleeled 167
                                                   ++e++k l+e+ +
  gi|313127094|ref|YP_004037364.1| 157 pmegpadegevGVAEFQKLLKEKME 181
                                       4444444444433333333333322 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.18      19      45 ..      25      51 ..      18      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrA 45
                                      +d++ ++ ++h ++GpN +GKst+ + 
  gi|313127094|ref|YP_004037364.1| 25 VDLEVKSGEIHALMGPNGSGKSTTAKV 51
                                      78888999***************9875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016       0.2       4      29 ..      37      62 ..      34     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                            AAA_33  4 lvGlpGsGKstlaerllkklgavlls 29
                                      l G++GsGKst a+ ++ + ++++ +
  gi|313127094|ref|YP_004037364.1| 37 LMGPNGSGKSTTAKVIAGHPAYEVTD 62
                                      78************999887766644 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.3   0.00044      0.56      24      43 ..      32      52 ..      22     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00044
                            AAA_15 24 e.ltvliGkNnsGKSsileal 43
                                        +  l G+N+sGKS+ ++++
  gi|313127094|ref|YP_004037364.1| 32 GeIHALMGPNGSGKSTTAKVI 52
                                      348899************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1964.85
//
Query:       gi|313127095|ref|YP_004037365.1|  [L=909]
Description: DNA polymerase elongation subunit (family b) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-47  159.7   0.0    3.1e-46  158.0   0.0    1.7  1  DNA_pol_B       DNA polymerase family B
      4e-31  108.4   0.0    2.4e-30  105.8   0.0    2.1  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
     0.0036   17.3   0.1       0.17   12.0   0.0    2.4  2  ELK             ELK domain
      0.007   15.3   0.0       0.31    9.9   0.0    2.2  2  DNA_pol_B_2     DNA polymerase type B, organellar and viral


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0   0.0     7e-50   3.1e-46      28     379 ..     460     790 ..     446     802 .. 0.82

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 7e-50
                                       BE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT...TEE CS
                         DNA_pol_B  28 filpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeeakeleaedeyleve 104
                                       f lp ++ ++++e+  Y+G+ V++P++g+ +++v+vlD +SLYP  ++  N +++t v  e+ + +         + 
  gi|313127095|ref|YP_004037365.1| 460 FALP-SKGQQESED--YEGGAVFDPITGV-KENVTVLDLKSLYPMCMVTINASPETKVDPESYDGD---------MF 523
                                       5667.555544445..************8.678***********************9988877553.........33 PP

                                       E-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HH..HHHHHHHHHHHHHHHHHHHHHHHTSTTSTT-- CS
                         DNA_pol_B 105 veprlvefvkksvregllpklLkdllakRkaikkelkeekdef..ekalldkqQlalKvtaNsvYGftGvansrlpc 179
                                        +p++ +f   ++  g++ +++ +lla+R++ kk+l++++d+     +++d qQ+a+Kv++Ns+YG++G    rl+ 
  gi|313127095|ref|YP_004037365.1| 524 QAPNGTHF--RKEPDGIIREMVDELLAEREE-KKRLRNDHDPGtsAYEQFDRQQQAVKVIMNSLYGVLGWDRFRLYD 597
                                       45777888..66778**************98.78899998885226789**************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-.SSHHHHHHHHHHHHHH CS
                         DNA_pol_B 180 lalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkv.kdveellkigkelaee 255
                                       +++ a vT++GRe++  t+++  ++                 +++v YGDTDSv++el+   + ee+++   e++e+
  gi|313127095|ref|YP_004037365.1| 598 KEMGAAVTATGREVIDFTDQTAGEM-----------------GYSVAYGDTDSVMLELGPdVSKEEAIEQSFEIEER 657
                                       ***********************99.................9***************8767788888888888888 PP

                                       HHT...TS.............TTT--EEEEEEEEEEEEE.ETTEEEEEEEEESSTTS.EEEEESSGGGSTTS-HHHH CS
                         DNA_pol_B 256 vsek..lf.............kkplklefekvykkllLi.sKKkYaglkvektskan.klliKGvdlvRrdncklvk 315
                                       ++e+  +f             ++ +++efek y +     +KK+Yag +v k+ k    ++i G +  R d ++++k
  gi|313127095|ref|YP_004037365.1| 658 INEAydNFardelgvdvdggeEHRFQIEFEKLYRRFFQAgTKKRYAGHIVWKEGKDVdDIDITGFEYKRSDIAQITK 734
                                       8873222322222222222224679*********9986548******887765554427****************** PP

                                       HHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGC CS
                         DNA_pol_B 316 evikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksk 379
                                       ev k+v++++++     ++++++ +++++++    ++++e++ pl++  +   + k  e+y+++
  gi|313127095|ref|YP_004037365.1| 735 EVQKNVIDMIVHG----EDTDDIKDYVHEVI----TDFQEGNLPLDEVGIPGGIGKRLEAYDTA 790
                                       *************....99999999999999....89999999999888888888887777554 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.0   5.4e-34   2.4e-30       2     337 .]      84     376 ..      83     376 .. 0.81

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 5.4e-34
                                       ECTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESS CS
                    DNA_pol_B_exo1   2 teegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsn 78 
                                       t+e+k+  v+v gf+pyfY+ + + ++   + + +   ++e +++++              g e     ++k+ +++
  gi|313127095|ref|YP_004037365.1|  84 TRENKTEHVRVLGFEPYFYAPTDSLDDD-LLDKDVITRTDEGYESIR--------------GEE-----LTKICTQT 140
                                       67899999***********999966665.777777777766665555..............555.....55****** PP

                                       TCHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTTC CS
                    DNA_pol_B_exo1  79 pnelkkirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpkes 155
                                       p+++ +ir+e+       + ye+d+ +  r+lid++i+++ +   +        +++  +  i++ +d++++++ + 
  gi|313127095|ref|YP_004037365.1| 141 PRDVGQIRDEF-------EHYEADILFPNRLLIDKDIESGICVPAR--------RLDDEEGTIQIPHDEVVPIDVD- 201
                                       **********9.......48********************996666........9999999999999999996544. PP

                                       CS-EEEEEEEEEETEETTSEETTTT..--EEEEEEEE.CCTC..SS.SEE...EEEEECCCTSS----EE--SSTCS CS
                    DNA_pol_B_exo1 156 epplrvlsFDIeckskkgkfpdaensedpiiqIscvl.dglg.ekepear...klftlrecaseeeedfeltpkpey 227
                                        ++lrv  FDIe++ + g fp+  +  +pii  ++++ d++  e         +    +  +++  +  +++p  e+
  gi|313127095|ref|YP_004037365.1| 202 -ADLRVNTFDIEVDDRSG-FPEEGE--EPII--CLTShDSYRdEYI---AwlyNAPEAGDGVESPTDLGDYEPLDED 269
                                       .*****************.******..***6..5566455552333...2444677778888888889999999999 PP

                                       TTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCS..CTCEECCCCESEE CS
                    DNA_pol_B_exo1 228 pgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrln..kggrskvseigfs 302
                                       ++ ++ +fd+E ++L af+++i + dPdv+tg+N d+FD+pY l+R++ ++   +s +   +     +++v++ g +
  gi|313127095|ref|YP_004037365.1| 270 TDIEIRSFDREGAMLDAFVTYIEETDPDVLTGWNFDDFDMPYFLDRLDVVN--PTSEYDLDPdrLSRVNEVWRGGWG 344
                                       999*********************************************333..333333332323334566777766 PP

                                       EEEECEEEETTSEEEEHHHHHHHH..SSSSG-SHHHH CS
                    DNA_pol_B_exo1 303 kqarekvkisgrihlDlyrvvkrk..lklpsYkLnav 337
                                               ++gr+++Dl+  +kr+  + l+sY L+av
  gi|313127095|ref|YP_004037365.1| 345 -----GPDVKGRVVFDLLYAYKRTqfTELESYRLDAV 376
                                       .....999****************555555*****98 PP

>> ELK  ELK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   3.9e-05      0.17       7      19 ..     385     397 ..     385     397 .. 0.92
   2 ?    3.0   0.0     0.026   1.2e+02       7      15 ..     699     707 ..     699     707 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.9e-05
                               ELK   7 LrKYsGyLssLRk 19 
                                       + +YsG++++L++
  gi|313127095|ref|YP_004037365.1| 385 KERYSGSIGDLWE 397
                                       689*********7 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.026
                               ELK   7 LrKYsGyLs 15 
                                       +++Y+G+++
  gi|313127095|ref|YP_004037365.1| 699 KKRYAGHIV 707
                                       89*****96 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   6.9e-05      0.31     212     245 ..     472     504 ..     402     520 .. 0.86
   2 !    3.1   0.0    0.0075        34     370     384 ..     573     587 ..     527     596 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 6.9e-05
                       DNA_pol_B_2 212 ayrGGrc.ypsvlgiyeeniyvyDvnSlYPsamth 245
                                        y GG +  p+ +g ++en+ v D +SlYP +m+ 
  gi|313127095|ref|YP_004037365.1| 472 DYEGGAVfDPI-TG-VKENVTVLDLKSLYPMCMVT 504
                                       68999997777.55.57****************85 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0075
                       DNA_pol_B_2 370 krsiaKlllNsLYGr 384
                                       +++  K ++NsLYG 
  gi|313127095|ref|YP_004037365.1| 573 QQQAVKVIMNSLYGV 587
                                       57889*********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (909 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 5632.27
//
Query:       gi|313127096|ref|YP_004037366.1|  [L=62]
Description: hypothetical protein Hbor_23620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 503.08
//
Query:       gi|313127097|ref|YP_004037367.1|  [L=131]
Description: hypothetical protein Hbor_23630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 922.96
//
Query:       gi|313127098|ref|YP_004037368.1|  [L=142]
Description: hypothetical protein Hbor_23640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.079   12.9   1.2       0.12   12.3   0.3    1.8  2  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.32   5.8e+03      36      47 ..      53      64 ..      51      65 .. 0.78
   2 ?   12.3   0.3   6.5e-06      0.12       9      55 ..      73     117 ..      70     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.32
                                      HHHHHHHHHHHH CS
                            MarR_2 36 savsrilkrLva 47
                                      s vs  l+r+v 
  gi|313127098|ref|YP_004037368.1| 53 SGVSEPLRRAVT 64
                                      778999999886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.5e-06
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                        +L +L +r+   ++v el ++ +l  s ++ +l ++ aaGL+++++
  gi|313127098|ref|YP_004037368.1|  73 GLLVELVDRDA--VSVVELLAAYDLCESDLHGLLSEFRAAGLITETT 117
                                       5899******9..******************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1167.21
//
Query:       gi|313127099|ref|YP_004037369.1|  [L=894]
Description: DNA repair ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-24   87.7   0.0    1.4e-24   87.7   0.0    5.9  1  AAA_23           AAA domain
    2.7e-15   57.0   0.0    1.3e-11   44.9   0.0    3.0  2  AAA_15           AAA ATPase domain
    4.2e-11   42.7  48.2    6.1e-10   38.9  48.2    2.2  1  SMC_N            RecF/RecN/SMC N terminal domain
    4.4e-09   35.9  68.7     0.0042   16.2  12.0    5.3  5  Atg14            Vacuolar sorting 38 and autophagy-related su
    3.3e-07   28.3  98.5    0.00064   17.4  42.3    4.0  4  DUF3584          Protein of unknown function (DUF3584)
    1.9e-06   26.9  52.7    0.00011   21.1   3.5    4.6  5  AAA_13           AAA domain
    3.2e-06   27.2  18.4    0.00049   20.0   6.8    3.6  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    7.6e-06   25.6   0.0    1.3e-05   24.8   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
    0.00049   19.1 100.1      0.085   11.7  16.3    5.7  5  Spc7             Spc7 kinetochore protein
    0.00064   20.1  22.6       0.33   11.5   0.1    8.5  6  NPV_P10          Nucleopolyhedrovirus P10 protein
     0.0053   17.3  11.5     0.0053   17.3  11.5    7.6  4  Syntaxin-6_N     Syntaxin 6, N-terminal
  ------ inclusion threshold ------
      0.023   14.9  41.2        1.9    8.7   4.6    5.8  6  Fib_alpha        Fibrinogen alpha/beta chain family
      0.035   14.1 109.1       0.43   10.6  11.3    7.3  6  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.078   13.4  39.4        1.5    9.3   0.7    7.9  6  Snapin_Pallidin  Snapin/Pallidin
      0.079   13.0  45.5       0.42   10.7   0.7    7.7  9  DUF1664          Protein of unknown function (DUF1664)
       0.12   12.5 109.6       0.16   12.0  17.1    7.8  7  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.21   11.6   0.4       0.81    9.8   0.4    2.1  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.23   11.5  21.5        5.1    7.1   0.1    6.4  6  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.23   11.2  76.3        1.2    8.9   7.8    7.7  7  DUF4201          Domain of unknown function (DUF4201)
       0.33   11.5   0.0       0.33   11.5   0.0    5.4  1  ABC_tran         ABC transporter
       0.53   10.4  75.5       0.21   11.7   5.5    6.7  6  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.99    9.2   7.3        1.2    8.9   0.0    3.8  4  MukB             MukB N-terminal
        1.2    9.2   0.0        1.2    9.2   0.0    4.9  5  AAA_33           AAA domain
        1.5    8.4  98.5        2.9    7.4  43.1    6.5  3  Filament         Intermediate filament protein
        1.7    8.8 112.3        1.9    8.7  10.7    6.3  4  ATG16            Autophagy protein 16 (ATG16)
        2.9    7.9  52.6       0.11   12.6   5.9    6.5  7  Laminin_II       Laminin Domain II
        4.2    5.9  57.0        0.6    8.7   6.1    5.5  6  FapA             Flagellar Assembly Protein A
        4.2    6.2  63.2        1.1    8.2   8.2    5.8  6  IFT57            Intra-flagellar transport protein 57
        4.7    6.5  88.0        2.8    7.2   4.2    5.2  5  DUF4407          Domain of unknown function (DUF4407)
        6.8    7.1  94.1        3.3    8.1  18.1    5.2  5  Fez1             Fez1
        7.2    5.9  82.4       0.51    9.7  11.8    5.6  4  GAS              Growth-arrest specific micro-tubule binding


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   2.4e-27   1.4e-24       1     195 [.       5     263 ..       5     268 .. 0.74

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 2.4e-27
                            AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvel 77 
                                       +++++nf+++ ++++d+ +g+t+I+G NG+GK+++l+A+ +aLyg  + l+       + +dv   + g+ +a +el
  gi|313127099|ref|YP_004037369.1|   5 RIRLQNFKPYAETDLDLTDGVTVIHGLNGSGKSSLLEACFFALYGA-RALD------ENLEDVM--TTGTEEAEIEL 72 
                                       79*******************************************4.2222......3567777..45688899*** PP

                            AAA_23  78 tfenkdgrytrsiererelskkkgkttkkaklellei.....deleqfisellgskkiilnlilflgqerfeefelk 149
                                        f++++g   + i+r+  +s +  ++t k  le+ ++     ++ + f+ +ll  + + + ++++  q++ +++ ++
  gi|313127099|ref|YP_004037369.1|  73 WFTHDGGS--YHIHRRLRKSGD-RVQTAKCLLEGPDVsvdgaRDVRGFVADLLRMDAEAFVNCAYVRQGEVNKLINA 146
                                       *****996..566555554444.445555555555556677899999999999999999999999999996666665 PP

                            AAA_23 150 dkke........................................................rleelekeleeledekk 170
                                       ++++                                                        rl++le+el e  d+++
  gi|313127099|ref|YP_004037369.1| 147 TPSQrqdtiddllqlgkleeyrvragkarlgvedvlterrgalskvesqieakedaglheRLNALETELGEVDDQIE 223
                                       555555666688888888889999999999999999999999999999999999999***88888888888888888 PP

                            AAA_23 171 llekl...............eqekekekeleeleeeleei 195
                                         e++               e   ek++el+el e++ ++
  gi|313127099|ref|YP_004037369.1| 224 RYEDQrekavetrenaeevlETYREKRAELDELAEDIADL 263
                                       7777776666555222222322233333555555555555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   2.2e-14   1.3e-11       1     249 [.       1     372 [.       1     409 [. 0.66
   2 ?    4.9   3.7     0.032        19     113     271 ..     526     686 ..     472     857 .. 0.44

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.2e-14
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdi 77 
                                       M+ ++i+++NF+ + ++++dl + +tv+ G N+sGKSs+lea   F+         +  ++++  +++  +    + 
  gi|313127099|ref|YP_004037369.1|   1 MRFDRIRLQNFKPYAETDLDLTDGVTVIHGLNGSGKSSLLEAC--FFALY-----GARALDENLEDVM--TTGTEEA 68 
                                       88899*************************************9..66533.....4555666666666..5666667 PP

                            AAA_15  78 kIdvef....................................................................... 83 
                                       +I+++f                                                                       
  gi|313127099|ref|YP_004037369.1|  69 EIELWFthdggsyhihrrlrksgdrvqtakcllegpdvsvdgardvrgfvadllrmdaeafvncayvrqgevnklin 145
                                       77777777889999999999999999999999999999999999999999999999999999999999999999999 PP

                            AAA_15  84 ...............................................aekekakeyektlkskekkkadlllkkkes 113
                                                                                      +                      +  k++ 
  gi|313127099|ref|YP_004037369.1| 146 atpsqrqdtiddllqlgkleeyrvragkarlgvedvlterrgalskvE--------------------SQIEAKEDA 202
                                       999999999999999999999999888777776666655443332221....................122223334 PP

                            AAA_15 114 dlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkid..kedlkklikkleeslkkee.... 184
                                        l+++++  +++l + +++ e+++++ +k+    ++ +e  ++ +++  ++d   ed+ +l +++e+   k e    
  gi|313127099|ref|YP_004037369.1| 203 GLHERLNALETELGEVDDQIERYEDQREKAVETRENAEEVLETYREKRAELDelAEDIADLRETIESDERKREtlrs 279
                                       45556666666666666666666666666655555555555555555555554466666666666666555555556 PP

                            AAA_15 185 .......................elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl.... 234
                                                              +          +++ i a+R+  de++ +++s l+ + e+  + ++q k     
  gi|313127099|ref|YP_004037369.1| 280 evgeardsveeirdriekkraetT------LDEVTSDAIAARRDELDEREAEIRSDLTDVRERRTMLSNQAKKlrer 350
                                       555555555555554332212221......22234667888888888888888888888888888877775555555 PP

                            AAA_15 235 ..............eeelteklkeiqekl 249
                                                             +e++++ 
  gi|313127099|ref|YP_004037369.1| 351 aeefesraaekrsrA-------DELDDDA 372
                                       555544433222221.......2222222 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.032
                            AAA_15 113 sdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee..... 184
                                       +d  +t++++ ++ ++ +   +k ++e ++++    +   e +e   e+++   +dl+++           +     
  gi|313127099|ref|YP_004037369.1| 526 EDARETVEERRTEAETLREAADKLEAEADEKRTAATTQ-AEAAEDAAETVEGLESDLESV-----------Aeaesr 590
                                       33333333333333333333333333333332221111.111222222222222222222...........133334 PP

                            AAA_15 185 .....elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkkl 256
                                             l ++l +   +++  +++R++  e++++ ++ l ++ ++ +e  l+++ +e++ e++k  +ek ++  +++
  gi|313127099|ref|YP_004037369.1| 591 ldtlsDLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSE--LADEVDESTVEEAKAKKEKAENYLEQV 665
                                       444444444444444455555555555555555555555555555544..334444444444444444444444444 PP

                            AAA_15 257 aeelk......kilkkkidki 271
                                       +eel+      ++l+++i  +
  gi|313127099|ref|YP_004037369.1| 666 DEELAtlrekrDSLQSDIGGV 686
                                       444443333332222222222 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9  48.2   1.1e-12   6.1e-10       3     213 ..       4     868 ..       2     874 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.1e-12
                                       EEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   3 krleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaev 79 
                                        r++++nFk ya  +++l++++++t+i G NGSGKs+ll+A  F L    a++l  e+l+d+++       +++ae+
  gi|313127099|ref|YP_004037369.1|   4 DRIRLQNFKPYA--ETDLDLTDGVTVIHGLNGSGKSSLLEACFFALY--GARAL-DENLEDVMTT-----GTEEAEI 70 
                                       689********5..99****************************997..34445.7899***998.....899**** PP

                                       EEEEEETTEESSSSSSCEEEEEEEETTSE....EEEEETTEEE-H...HHHHHHHHCTT-STT.............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx...xxxxxxxxxxxxxxx.............. RF
                             SMC_N  80 eitfdnedkklkiekeevsisrrvkrkge....seykingkevtk...kevsellesagiske.............. 135
                                       e+ f++++ +       + i rr+ ++g+     +  ++g +v+    ++v+ ++++  + ++              
  gi|313127099|ref|YP_004037369.1|  71 ELWFTHDGGS-------YHIHRRLRKSGDrvqtAKCLLEGPDVSVdgaRDVRGFVAD-LLRMDaeafvncayvrqge 139
                                       ****999999.......6666666666665554777788877776333455544443.334444588899******* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127099|ref|YP_004037369.1| 140 vnklinatpsqrqdtiddllqlgkleeyrvragkarlgvedvlterrgalskvesqieakedaglherlnaletelg 216
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127099|ref|YP_004037369.1| 217 evddqieryedqrekavetrenaeevletyrekraeldelaediadlretiesderkretlrsevgeardsveeird 293
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127099|ref|YP_004037369.1| 294 riekkraettldevtsdaiaarrdeldereaeirsdltdvrerrtmlsnqakklreraeefesraaekrsradeldd 370
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127099|ref|YP_004037369.1| 371 daedaeeeleqrsarleeleaelesltaefedapvelgeaashrdevretltdvraeltetnaegenvrdrlteare 447
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127099|ref|YP_004037369.1| 448 lrdegkcpecgqpvedsphvdsigeyearieeleatlsdlrerretlnsrleraeslvetenrigelrnsrelfeqr 524
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127099|ref|YP_004037369.1| 525 iedaretveerrteaetlreaadkleaeadekrtaattqaeaaedaaetveglesdlesvaeaesrldtlsdlrskl 601
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127099|ref|YP_004037369.1| 602 teteseierleerresiaelnderrerlaekrdrrseladevdestveeakakkekaenyleqvdeelatlrekrds 678
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127099|ref|YP_004037369.1| 679 lqsdiggvngeleqlealredrdelaarvdaleslhaeteeleamygdlraelrqrnvetlermlnetfdlvygnda 755
                                       ***************************************************************************** PP

                                       .........................CS-HHHHHHHHHHHHHH........HHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       .........................xxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 .........................lLSgGektLvalaLlfA........iqkvkpaplyllDeidaaLDeknvkkv 179
                                                                +LSgGe++L  l+L+ A        i+ + p p  +lDe    LD  +v+++
  gi|313127099|ref|YP_004037369.1| 756 ysrirldgeyeltvfqkdgtaldpeQLSGGERALFNLSLRCAiyrllaegIEGAAPMPPLILDEPTVFLDSGHVSRL 832
                                       ******************************************99999999999************************ PP

                                       HHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 180 aellkekskn..aQfivislreemlekadklvgvtk 213
                                       ++l++e ++    Q+i++s+++e++  ad+lv v k
  gi|313127099|ref|YP_004037369.1| 833 VDLVDEMRDLgvRQIIIVSHDDELVGAADELVTVEK 868
                                       *****99986669*******************9987 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  12.0   7.2e-06    0.0042      21     118 ..     205     302 ..     185     321 .. 0.86
   2 !   10.4   9.8   0.00042      0.24      37     130 ..     322     412 ..     312     450 .. 0.75
   3 !    9.8  11.5   0.00067      0.39      20     142 ..     464     583 ..     417     595 .. 0.71
   4 ?    5.4  11.6     0.014       8.1      48     126 ..     580     656 ..     561     661 .. 0.68
   5 !   12.9   1.7   7.3e-05     0.042      42     143 ..     652     749 ..     644     767 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.2e-06
                             Atg14  21 perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                        erl+ l ++l  +  + e  + + eka+e++e+ae+  +  + k+a l+el  +iadlre ++  + k+++l++e+
  gi|313127099|ref|YP_004037369.1| 205 HERLNALETELGEVDDQIERYEDQREKAVETRENAEEVLETYREKRAELDELAEDIADLRETIESDERKRETLRSEV 281
                                       578888888899999999999999999999999******************************************** PP

                             Atg14  98 eekkkklaklsdklkkRrsdl 118
                                        e++  +++ +d + k+r++ 
  gi|313127099|ref|YP_004037369.1| 282 GEARDSVEEIRDRIEKKRAET 302
                                       **************9999883 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00042
                             Atg14  37 ekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkk 113
                                       + +++++ +++  e+++    l++++k++++++ee  s+ a++r+r  el d+ +   +e+e+++++l++l ++l  
  gi|313127099|ref|YP_004037369.1| 322 REAEIRSDLTDVRERRT---MLSNQAKKLRERAEEFESRAAEKRSRADELDDDAEDAEEELEQRSARLEELEAELES 395
                                       44455555555555555...89999***************************************************9 PP

                             Atg14 114 Rrsdleslqneleerrk 130
                                        +++ e +  el e+  
  gi|313127099|ref|YP_004037369.1| 396 LTAEFEDAPVELGEAAS 412
                                       99999999999987532 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00067
                             Atg14  20 g.........perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelk 87 
                                       +         + r++el   l +l++++e+l +++e+a++  e           + +++ el++ +++ ++r++  +
  gi|313127099|ref|YP_004037369.1| 464 SphvdsigeyEARIEELEATLSDLRERRETLNSRLERAESLVE-----------TENRIGELRNSRELFEQRIEDAR 529
                                       2555555555679999999999999999999999999988888...........55666666666666666666666 PP

                             Atg14  88 dklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikr 142
                                       +++++++ e e  ++   kl ++    +++++ +q e +e  ++ +++l +++  
  gi|313127099|ref|YP_004037369.1| 530 ETVEERRTEAETLREAADKLEAEAD-EKRTAATTQAEAAEDAAETVEGLESDLES 583
                                       6666666666666666666666653.33333566666666666666666665554 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.014
                             Atg14  48 alegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqne 124
                                        le+  eae++ d +  ++ kl e+ s+i++l+er + + +  ++++++++ek+ + ++l d++    s+ e ++ +
  gi|313127099|ref|YP_004037369.1| 580 DLESVAEAESRLDTLSDLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSELADEVD--ESTVEEAKAK 654
                                       33333466667777888888888888888888888888888888888888888888888888886..4444444444 PP

                             Atg14 125 le 126
                                        e
  gi|313127099|ref|YP_004037369.1| 655 KE 656
                                       33 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 7.3e-05
                             Atg14  42 kkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdl 118
                                       k k eka++     eq ++++ ++++k ++l+s+i   + +l++l++ l++ ++e++++   l++l +++ +  +  
  gi|313127099|ref|YP_004037369.1| 652 KAKKEKAENYL---EQVDEELATLREKRDSLQSDIGGVNGELEQLEA-LREDRDELAARVDALESLHAETEELEAMY 724
                                       33334444444...47779*************************986.788899999999***********999999 PP

                             Atg14 119 eslqneleerrkkqiaklqdaikri 143
                                         l+ el++r  + +++++++++  
  gi|313127099|ref|YP_004037369.1| 725 GDLRAELRQRNVETLERMLNETFDL 749
                                       99*****************999854 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.01       5.9      14      35 ..      19      41 ..      14      54 .. 0.78
   2 !   17.4  42.3   1.1e-06   0.00064     316     534 ..     203     429 ..     163     434 .. 0.83
   3 !    6.6  18.7    0.0019       1.1     430     533 ..     478     581 ..     430     587 .. 0.89
   4 !   10.9  22.9    0.0001      0.06     245     402 ..     582     745 ..     570     766 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.01
                           DUF3584 14 ldld.ghtnieGtNaaGKTtLlr 35
                                      ldl+ g t i G N++GK +Ll 
  gi|313127099|ref|YP_004037369.1| 19 LDLTdGVTVIHGLNGSGKSSLLE 41
                                      6665156789***********95 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.1e-06
                           DUF3584 316 aakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeel 392
                                        +++ l+a e el ++++q ++yed++ ek+ +  ++++++ + ++e  +eld l e + d+ e  + ++ k++  l
  gi|313127099|ref|YP_004037369.1| 203 GLHERLNALETELGEVDDQIERYEDQR-EKAVETRENAEEVLETYREKRAELDELAEDIADLRETIESDERKRET-L 277
                                       4578899******************98.999999***********************************999865.6 PP

                           DUF3584 393 eeeleklkerleaireekdrl..kaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEel 467
                                         e+ + ++++e+ir+  +++   ++ +e+ +   ++ r++l++ ++e++ +  ++++r   l  ++++     Ee 
  gi|313127099|ref|YP_004037369.1| 278 RSEVGEARDSVEEIRDRIEKKraETTLDEVTSDAIAARRDELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEF 354
                                       66777777888999998888744566788888888999999999999999999999998888888888887777766 PP

                           DUF3584 468 eqie........eadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqaleeleeqls 534
                                       e  +        e d+  e a+eele+++a+ e+l+ae+e l ++++ a   l +a+    ++r+ l +++  l+
  gi|313127099|ref|YP_004037369.1| 355 ESRAaekrsradELDDDAEDAEEELEQRSARLEELEAELESLTAEFEDAPVELGEAASHRDEVRETLTDVRAELT 429
                                       54431111111156788999************************************************9988775 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0019
                           DUF3584 430 kqleaqkeelneeekelesrlselklrldsatateEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrd 506
                                       ++lea  ++l+e+++ l+srl++++ +++      E+    e +++++e a+e++e+++ e e l ++  +l+++ d
  gi|313127099|ref|YP_004037369.1| 478 EELEATLSDLRERRETLNSRLERAESLVETENRIGELRNSRELFEQRIEDARETVEERRTEAETLREAADKLEAEAD 554
                                       3789999********************************************************99999999999999 PP

                           DUF3584 507 eadealqkaerrleqlrqaleeleeql 533
                                       e  +a +  ++++e+ ++ +e le  l
  gi|313127099|ref|YP_004037369.1| 555 EKRTAATTQAEAAEDAAETVEGLESDL 581
                                       999999999999999999988888765 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.0001
                           DUF3584 245 peieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaideln.qelsaakak 320
                                       +++++ + +  +l  l  +L     e+++++erl+e++e ++e + e +++l++++d  +e +de+  + +++akak
  gi|313127099|ref|YP_004037369.1| 582 ESVAEAESRLDTLSDLRSKLT----ETESEIERLEERRESIAELNDERRERLAEKRDRRSELADEVDeSTVEEAKAK 654
                                       333333333333333333333....4445555555555555566666666666666665555555531334555555 PP

                           DUF3584 321 laakeselealeeq......kkkyedadieklkadldqlpsirseleeleeeldaltekh...qdvqekydrrkqki 388
                                        +++e+ le+++e+      k++ +++di  ++ +l+ql+++r++  el +++dal++ h   +++++ y  +++++
  gi|313127099|ref|YP_004037369.1| 655 KEKAENYLEQVDEElatlreKRDSLQSDIGGVNGELEQLEALREDRDELAARVDALESLHaetEELEAMYGDLRAEL 731
                                       55555555555543111111455678899999999999999999999999999988876522257888899999999 PP

                           DUF3584 389 keeleeeleklker 402
                                        +++ e le++ ++
  gi|313127099|ref|YP_004037369.1| 732 RQRNVETLERMLNE 745
                                       99998888876554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.08        46      19      32 ..      26      39 ..      11      47 .. 0.86
   2 !    5.9  10.5    0.0072       4.2     340     456 ..     178     298 ..     173     308 .. 0.82
   3 ?    4.7  22.9     0.017       9.7     287     455 ..     238     402 ..     234     442 .. 0.73
   4 ?    3.1  22.5      0.05        29     320     460 ..     355     560 ..     317     566 .. 0.53
   5 !   21.1   3.5   1.9e-07   0.00011     282     573 ..     571     856 ..     563     876 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.08
                            AAA_13 19 NliYGwNGaGKTtL 32
                                       +i G NG+GK++L
  gi|313127099|ref|YP_004037369.1| 26 TVIHGLNGSGKSSL 39
                                      58**********98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0072
                            AAA_13 340 lqraleaKrkepfksvelesvkaki......esikklvaeineliakhNekvanleeekeeakkklelhlveelese 410
                                       ++++l+++r  ++k  ++ ++k+++      ++++ ++ e+ ++i+++  + ++  e +e+a++ le ++ +  ++e
  gi|313127099|ref|YP_004037369.1| 178 VEDVLTERRGALSKVESQIEAKEDAglherlNALETELGEVDDQIERYEDQREKAVETRENAEEVLETYREK--RAE 252
                                       56777888877777555555555554554446888999999999****999999999999999999997766..679 PP

                            AAA_13 411 ldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrde 456
                                       lde+ +++++l ++ie+ e++ +   +e+ ++++ ++e++ +++++
  gi|313127099|ref|YP_004037369.1| 253 LDELAEDIADLRETIESDERKRETLRSEVGEARDSVEEIRDRIEKK 298
                                       9999*************99999999999999999999999998765 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.017
                            AAA_13 287 rLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvka 362
                                       + e+ +e++ +k++el e  ++++d  +  +  e+++e+l++e  + +++ +++++++e+Kr e    +v+ + ++a
  gi|313127099|ref|YP_004037369.1| 238 NAEEVLETYREKRAELDELAEDIADLRETIESDERKRETLRSEVGEARDSVEEIRDRIEKKRAETTLdEVTSDAIAA 314
                                       557889999999987766667777777777779999**************************887654888888888 PP

                            AAA_13 363 kiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeael 439
                                       + +++ +  aei    ++  e+ ++l ++++++++  e ++   +e+      +  ++l++++e++e+el++ +a+l
  gi|313127099|ref|YP_004037369.1| 315 RRDELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAEKR-----SRADELDDDAEDAEEELEQRSARL 386
                                       889999999999999999999999999998888888888775444333.....445555556666666666666666 PP

                            AAA_13 440 kkleeeikeLekqlrd 455
                                       ++le+e + L ++ +d
  gi|313127099|ref|YP_004037369.1| 387 EELEAELESLTAEFED 402
                                       6666655555555443 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.05
                            AAA_13 320 eedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkakie.............................. 365
                                       e+  +e +++a++l++  + ++++le++  ++ + ++eles++a+ e                              
  gi|313127099|ref|YP_004037369.1| 355 ESRAAEKRSRADELDDDAEDAEEELEQRSARLEElEAELESLTAEFEdapvelgeaashrdevretltdvraeltet 431
                                       33333333333333333333333333333333333333333333333333333333333334444444444444455 PP

                            AAA_13 366 .................................sikklvaeineliakhNekvanleeekeeakkklelhl.veele 408
                                                                           +++ e ++ i++  ++ ++l e++e++++ le+ + + e e
  gi|313127099|ref|YP_004037369.1| 432 naegenvrdrltearelrdegkcpecgqpvedsPHVDSIGEYEARIEELEATLSDLRERRETLNSRLERAEsLVETE 508
                                       55555555555555555555555556666666566677777788888888888888888888888887776567788 PP

                            AAA_13 409 seldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaa 460
                                       + + e+ +  + +e+ ie++ + ++e  +e+++l+e +  Le++  +++ aa
  gi|313127099|ref|YP_004037369.1| 509 NRIGELRNSRELFEQRIEDARETVEERRTEAETLREAADKLEAEADEKRTAA 560
                                       8888888888888888888888888888888888888888887766655555 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 1.9e-07
                            AAA_13 282 eekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvele 358
                                       +e +e Le+++e+v++++s    +l+++sd  s+  ++e+++e l+++ e ++e  ++ +++l +Kr++ ++ +  +
  gi|313127099|ref|YP_004037369.1| 571 AETVEGLESDLESVAEAES----RLDTLSDLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSE-L-AD 641
                                       4566777777777777765....89999**************************99***********88777.3.34 PP

                            AAA_13 359 svkaki.esikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelke 434
                                       +v++ + e++k + +++++  ++  e  a l e++ ++++++     e   ++l+++ ++ ++l++ +     +l+ 
  gi|313127099|ref|YP_004037369.1| 642 EVDESTvEEAKAKKEKAENYLEQVDEELATLREKRDSLQSDIGGVNGE--LEQLEALREDRDELAARVD----ALES 712
                                       454444499999999********************9999999983333..3556666666666555554....5557 PP

                            AAA_13 435 eeaelkkleeeikeLekqlrdekpaaeeinkeLka....fGlgeleLkfeeekkgYrivr..kggsqaa.etLSeGE 504
                                         ae+++le+   +L+++lr+    +e +++ L++    +  g++  + +  +  Y+++   k+g   + e+LS GE
  gi|313127099|ref|YP_004037369.1| 713 LHAETEELEAMYGDLRAELRQR--NVETLERMLNEtfdlV-YGNDAYSRIRLDGEYELTVfqKDGTALDpEQLSGGE 786
                                       7777777888888888888764..4444444444411115.346666666668888876522455444469****** PP

                            AAA_13 505 ktaIaf...lYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnlef 573
                                       + +  +   +  + +l e ++        ++D P   LDs+++   + l+++    +  ++Q++i  H  e+
  gi|313127099|ref|YP_004037369.1| 787 RALFNLslrCAIYRLLAEGIEGAAPMPPLILDEPTVFLDSGHVSRLVDLVDEMR--DLGVRQIIIVSHDDEL 856
                                       *99887555566777778888887788899999999999999999999998875..8899999999997655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   5.9e-05     0.034       1      22 [.      25      46 ..      25      71 .. 0.84
   2 !   20.0   6.8   8.6e-07   0.00049     219     302 ..     713     857 ..     471     858 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      ++v+ G NgsGKS+LL+a  ++
  gi|313127099|ref|YP_004037369.1| 25 VTVIHGLNGSGKSSLLEACFFA 46
                                      69***************97665 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 8.6e-07
                            AAA_21 219 r...................................................gvvflengdgqelparelSdGtkrl 244
                                                                                           +  ++  +dg  l++ +lS G + l
  gi|313127099|ref|YP_004037369.1| 713 LhaeteeleamygdlraelrqrnvetlermlnetfdlvygndaysrirldgeYELTVFQKDGTALDPEQLSGGERAL 789
                                       0233333334444444444445555666666666666666666666666666999999******************* PP

                            AAA_21 245 lalltallralkkg.........sllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       + l + ++  +  +         + l++DEp  +L+   ++rl++l++e ++ +  Q+i+++H+ +l+
  gi|313127099|ref|YP_004037369.1| 790 FNLSLRCAIYRLLAegiegaapmPPLILDEPTVFLDSGHVSRLVDLVDEMRDlGVRQIIIVSHDDELV 857
                                       *999988888888888*******************************999888889********9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.3e-08   1.3e-05       3      51 ..       5      52 ..       3      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.3e-08
                            AAA_29  3 rlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakk 51
                                      r++l N   + +++++++ +g+t++ G +GsGKS+ll A  + L++a+ 
  gi|313127099|ref|YP_004037369.1|  5 RIRLQNFKPYAETDLDLT-DGVTVIHGLNGSGKSSLLEACFFALYGARA 52
                                      788999999999999997.77************************9985 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7  16.3   0.00015     0.085     157     262 ..     188     293 ..     175     308 .. 0.77
   2 !   11.3  20.3    0.0002      0.11     142     254 ..     317     432 ..     297     453 .. 0.58
   3 ?    1.9  14.0      0.14        83     173     254 ..     474     557 ..     466     570 .. 0.43
   4 !    9.3  24.6   0.00082      0.48     142     282 ..     568     714 ..     563     717 .. 0.81
   5 !    7.5   9.6    0.0027       1.6     160     233 ..     653     735 ..     646     746 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                              Spc7 157 lLekqeeel.dellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleel 232
                                        L+k e+++  +    l+e+ ++le el +  ++ e  e+ ++e+  e+re+ +e+ ++++ek++el+el e++++l
  gi|313127099|ref|YP_004037369.1| 188 ALSKVESQIeAKEDAGLHERLNALETELGEVDDQIERYED-QREKAVETRENAEEVLETYREKRAELDELAEDIADL 263
                                       4566666663334455777777777777777776666555.567777899*************************** PP

                              Spc7 233 eekieelkeqkseleeeiaeaervleeckg 262
                                       +e+ie+ + ++++l++e+ ea++ +ee ++
  gi|313127099|ref|YP_004037369.1| 264 RETIESDERKRETLRSEVGEARDSVEEIRD 293
                                       *****99999999*****999999998776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0002
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..id.keeLeelreelaelkaei 215
                                       ++l+e+ +++++d + + +++  l++  ++l+e+ +e e+++++ +++a+el++   d +eeLe+   +l+el+ae+
  gi|313127099|ref|YP_004037369.1| 317 DELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAEKRSRADELDDdaEDaEEELEQRSARLEELEAEL 393
                                       44555555556666666666666666666666666666666666666666555544333555555555555555555 PP

                              Spc7 216 eekkkelaelqeqleeleekieelkeqkseleeeiaeae 254
                                       e++ +e ++   +l e ++  +e++e  +++++e+ e +
  gi|313127099|ref|YP_004037369.1| 394 ESLTAEFEDAPVELGEAASHRDEVRETLTDVRAELTETN 432
                                       555555555555555555555555555555555555544 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.14
                              Spc7 173 eeekaeleeeleklqeaaeeles..idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksele 247
                                       e++ +ele++l +l+e++e l+s     e+L e+ +++ el +  e +++++++ +e +ee +++ e+l+e  ++le
  gi|313127099|ref|YP_004037369.1| 474 EARIEELEATLSDLRERRETLNSrlERAESLVETENRIGELRNSRELFEQRIEDARETVEERRTEAETLREAADKLE 550
                                       44555555555555555555444322233444444444444444444444444444444444444444444444433 PP

                              Spc7 248 eeiaeae 254
                                       +e  e++
  gi|313127099|ref|YP_004037369.1| 551 AEADEKR 557
                                       3333322 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00082
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkae. 214
                                       e + e++egle+d e +++ e+ ld+l  +l+++ +e e+e+e+l+e++e++++     +e+L+e r++ +el  e 
  gi|313127099|ref|YP_004037369.1| 568 EDAAETVEGLESDLESVAEAESRLDTL-SDLRSKLTETESEIERLEERRESIAElndERRERLAEKRDRRSELADEv 643
                                       567899******************975.78*****************777666632255899999998888876661 PP

                              Spc7 215 ....ieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleelt 282
                                           +ee k++ ++ ++ le+++e++++l+e++++l+++i   +  le+ +  + ++ ++l ++v+ale+l+
  gi|313127099|ref|YP_004037369.1| 644 destVEEAKAKKEKAENYLEQVDEELATLREKRDSLQSDIGGVNGELEQLEALR-EDRDELAARVDALESLH 714
                                       111256778888888899999999999***********9999999999766655.56699999999999887 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.0027
                              Spc7 160 kqeeeldellpeleeekaeleeeleklqe.......aaeeles..idkeeLeelreelaelkaeieekkkelaelqe 227
                                       +++e+++++l++++ee a+l+e+ ++lq+       + e+le+   d++eL++  ++l++l+ae ee+++++ +l++
  gi|313127099|ref|YP_004037369.1| 653 AKKEKAENYLEQVDEELATLREKRDSLQSdiggvngELEQLEAlrEDRDELAARVDALESLHAETEELEAMYGDLRA 729
                                       45666677777777777777777777777444432244444444455666666666666666666666666666666 PP

                              Spc7 228 qleele 233
                                       +l + +
  gi|313127099|ref|YP_004037369.1| 730 ELRQRN 735
                                       665443 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   3.7       1.1   6.4e+02      30      30 ..     232     232 ..     178     356 .. 0.63
   2 ?    3.3   1.3       0.2   1.2e+02      28      61 ..     366     396 ..     324     457 .. 0.72
   3 ?    1.3   0.0      0.84   4.9e+02      15      46 ..     472     500 ..     462     517 .. 0.49
   4 ?   -1.4   0.0       5.8   3.4e+03      19      49 ..     524     554 ..     519     565 .. 0.79
   5 ?    5.4   0.2     0.043        25      25      62 ..     572     609 ..     562     623 .. 0.80
   6 !   11.5   0.1   0.00057      0.33       4      66 ..     660     744 ..     658     750 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.1
                           NPV_P10  30 v 30 
                                        
  gi|313127099|ref|YP_004037369.1| 232 A 232
                                       2 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.2
                           NPV_P10  28 ddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                       d+++++ +d    +e+L++ sa L+ele+++e+ 
  gi|313127099|ref|YP_004037369.1| 366 DELDDDAED---AEEELEQRSARLEELEAELESL 396
                                       555555555...3466777777777777666654 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.84
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLda 46 
                                       + + +++ l++ + d++e  ++   ln++L++
  gi|313127099|ref|YP_004037369.1| 472 EYEARIEELEATLSDLRERRET---LNSRLER 500
                                       3333444444444444443333...4444443 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 5.8
                           NPV_P10  19 kVdalqqqvddvqenlpdvtelnekLdaqsa 49 
                                       +++   + v++ +++ +++ e  +kL+a ++
  gi|313127099|ref|YP_004037369.1| 524 RIEDARETVEERRTEAETLREAADKLEAEAD 554
                                       5566667888889999999999999999776 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.043
                           NPV_P10  25 qqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                       + v+ ++++l+ v e +++Ld +s+   +l ++ ++I+
  gi|313127099|ref|YP_004037369.1| 572 ETVEGLESDLESVAEAESRLDTLSDLRSKLTETESEIE 609
                                       56889999999999999999999987777777666654 PP

  == domain 6  score: 11.5 bits;  conditional E-value: 0.00057
                           NPV_P10   4 niLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet......................kv 58 
                                       n L ++ ++ + + +k d+lq+ +  v+ +l++++ l e  d+++a +++le+                      +v
  gi|313127099|ref|YP_004037369.1| 660 NYLEQVDEELATLREKRDSLQSDIGGVNGELEQLEALREDRDELAARVDALESlhaeteeleamygdlraelrqrNV 736
                                       678899999999**************************999999999999998888888888888888888888888 PP

                           NPV_P10  59 enIqdiLn 66 
                                       e+ + +Ln
  gi|313127099|ref|YP_004037369.1| 737 ETLERMLN 744
                                       88888888 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3  11.5   9.1e-06    0.0053      12      97 ..     213     297 ..     177     299 .. 0.87
   2 ?    2.0   3.9      0.53     3e+02      34      84 ..     307     357 ..     297     364 .. 0.56
   3 ?    5.9   7.1     0.034        19      12      95 ..     342     424 ..     335     427 .. 0.81
   4 ?   -0.0   5.4       2.3   1.3e+03      35      88 ..     476     532 ..     423     543 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.1e-06
                      Syntaxin-6_N  12 kslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrra 86 
                                        +l ++   ++r+e+ +e++ +  ++ ee+ et +e r++l+++ +d+ dL+et+   e++++k +   +e+ + r+
  gi|313127099|ref|YP_004037369.1| 213 TELGEVDDQIERYEDQREKAVEtrENAEEVLETYREKRAELDELAEDIADLRETI---ESDERKRETLRSEVGEARD 286
                                       556666677778864444444434589****************************...******************* PP

                      Syntaxin-6_N  87 fveevreevke 97 
                                        vee+r+++++
  gi|313127099|ref|YP_004037369.1| 287 SVEEIRDRIEK 297
                                       ********985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.53
                      Syntaxin-6_N  34 stseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrr 84 
                                        ts+ +   r+eL +   +i+ dl d +e   +++++ +k + +++e ++r
  gi|313127099|ref|YP_004037369.1| 307 VTSDAIAARRDELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEFESR 357
                                       345666666666666666666666666666656655555555555555555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.034
                      Syntaxin-6_N  12 kslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrra 86 
                                       ++++k+++  +++e+    + +  s+ +eld+  ++ +++l++ +  le+Le   + + ++ ++  ++  e +++r+
  gi|313127099|ref|YP_004037369.1| 342 NQAKKLRERAEEFES---RAAEkrSRADELDDDAEDAEEELEQRSARLEELEAELESLTAEFEDAPVELGEAASHRD 415
                                       556666666666654...333323689*******************************9999999***********9 PP

                      Syntaxin-6_N  87 fveevreev 95 
                                        v+e+   v
  gi|313127099|ref|YP_004037369.1| 416 EVRETLTDV 424
                                       999987766 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 2.3
                      Syntaxin-6_N  35 tseeldetrteLrkalrsiewdledLeetvrivek...npskfkidekelsrrrafv 88 
                                       + eel+ t ++Lr+  ++++  le  e  v++ ++    ++  ++ e+ ++  r+ v
  gi|313127099|ref|YP_004037369.1| 476 RIEELEATLSDLRERRETLNSRLERAESLVETENRigeLRNSRELFEQRIEDARETV 532
                                       344444444444444444444444444444111111111122223333333333333 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.6    0.0033       1.9      30     130 ..     201     300 ..     186     302 .. 0.67
   2 ?    8.0   3.1    0.0054       3.1      24      95 ..     317     388 ..     315     399 .. 0.94
   3 ?    4.9   0.0     0.048        28      33     127 ..     417     507 ..     410     511 .. 0.62
   4 ?    7.6   4.4    0.0069         4      26     124 ..     514     614 ..     511     624 .. 0.84
   5 ?    3.9   2.6     0.096        55      47     122 ..     629     711 ..     613     719 .. 0.53
   6 ?    3.1   0.0      0.17        97      25      94 ..     671     739 ..     669     749 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0033
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                                       +  ++++l+ le el e+ ++ +  e+  ++  ++ +++++  +   +   ++ +el e+i++l+eti + e++ + 
  gi|313127099|ref|YP_004037369.1| 201 DAGLHERLNALETELGEVDDQIERYEDQREKAVETRENAEEVLETYREKRAEL-DELAEDIADLRETIESDERKRET 276
                                       44556666666666666665555555444444444333333333333333333.35666****************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 107 LqnvlesneqkiqkLeqdidqker 130
                                       L++ + + + ++++++  i++k++
  gi|313127099|ref|YP_004037369.1| 277 LRSEVGEARDSVEEIRDRIEKKRA 300
                                       *****************9999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0054
                                       HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH CS
                         Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlke 95 
                                       d l++ e +++ dl++++++ + +sn+ k+ +e  +e ++  +ek + +++ d   ++ ++ele++ +rl+e
  gi|313127099|ref|YP_004037369.1| 317 DELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAEKRSRADELDDDAEDAEEELEQRSARLEE 388
                                       78999*********************************************99**************999987 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.048
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHCCCHHHHHHHCCHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn....dnvikksskeleeeilrlketidaqesnir 105
                                       v+++       l++++ + +e++   ++++d l+e+ +  ++          + s +++  i +++++i + e ++ 
  gi|313127099|ref|YP_004037369.1| 417 VRET-------LTDVRAELTETNAEGENVRDRLTEARELRDEGkcpeCGQPVEDSPHVD-SIGEYEARIEELEATLS 485
                                       4444.......444444444444444444444444444433322211223334456788.9999************* PP

                                       HHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 106 vLqnvlesneqkiqkLeqdidq 127
                                        L++  e++++++++ e+ +++
  gi|313127099|ref|YP_004037369.1| 486 DLRERRETLNSRLERAESLVET 507
                                       *********9999999988876 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0069
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH. CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe. 101
                                       l + ++ +++++e+ ++++ee + + ++ +e   +++    ek + ++ + ++ ++ ++++e   ++l+    a+  
  gi|313127099|ref|YP_004037369.1| 514 LRNSRELFEQRIEDARETVEERRTEAETLREAADKLEAEADEKRTAATTQAEAAEDAAETVEGLESDLESVAEAESr 590
                                       5667778999***********************************99999999999999999666666655444334 PP

                                       .HHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 .snirvLqnvlesneqkiqkLeqd 124
                                         ++  L++ l + e++i++Le+ 
  gi|313127099|ref|YP_004037369.1| 591 lDTLSDLRSKLTETESEIERLEER 614
                                       4788899999***********975 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.096
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHH...HHCCCHHHHHH...HCCHHHHHHHHHHHHHHHH CS
                         Fib_alpha  47 isnstkeaeelvkeikdslrekqkskkdn.dnvikksskel...eeeilrlketi...daqesnirvLqnvlesneq 116
                                       ++++    +el  e+++s+ e+ k kk++ +n+++++ +el   +e+   l+  i   + + +++++L++  +++  
  gi|313127099|ref|YP_004037369.1| 629 LAEKRDRRSELADEVDESTVEEAKAKKEKaENYLEQVDEELatlREKRDSLQSDIggvNGELEQLEALREDRDELAA 705
                                       55555666666667776666666666655577777776664111344444554442212333555555555555555 PP

                                       HHHHHH CS
                         Fib_alpha 117 kiqkLe 122
                                       ++  Le
  gi|313127099|ref|YP_004037369.1| 706 RVDALE 711
                                       555555 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.17
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlk 94 
                                       +l +++ +++ d+  ++ ele+++   ++ +el  +++     + ++++  + ++ +++ el+++ ++  
  gi|313127099|ref|YP_004037369.1| 671 TLREKRDSLQSDIGGVNGELEQLEALREDRDELAARVDALESLHAETEE-LEAMYGDLRAELRQRNVETL 739
                                       577888899999999******************9999776555555554.799*********98765433 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  16.1     0.033        19      20      99 ..     202     291 ..     190     301 .. 0.53
   2 ?    3.9  13.8     0.087        50      47     131 ..     300     386 ..     296     387 .. 0.89
   3 ?   10.6  11.3   0.00075      0.43      14      93 ..     360     446 ..     357     451 .. 0.77
   4 ?    5.7   6.1     0.024        14      65     112 ..     474     527 ..     466     533 .. 0.50
   5 ?    1.4  20.3       0.5   2.9e+02       7     100 ..     527     622 ..     521     631 .. 0.70
   6 ?   10.3  16.0   0.00093      0.54      31     137 ..     625     733 ..     618     736 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.033
                    CENP-F_leu_zip  20 dsLkdkvenLerel.......emseenqekvileaEtskaevet...lkeeieelaeelreleldLvalrsekeeLe 86 
                                       + L+++ ++Le el       e  e ++ek++   E++ + +et    ++e++elae   +l+  +++  + +e+L 
  gi|313127099|ref|YP_004037369.1| 202 AGLHERLNALETELgevddqiERYEDQREKAVETRENAEEVLETyreKRAELDELAEDIADLRETIESDERKRETLR 278
                                       44666666666665111111133334444444444444444444221234455555555556666666567788888 PP

                    CENP-F_leu_zip  87 kelqkkqervseL 99 
                                        e+ + ++ v+e 
  gi|313127099|ref|YP_004037369.1| 279 SEVGEARDSVEEI 291
                                       8888888888775 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.087
                    CENP-F_leu_zip  47 aEtskaevet..lkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmk 121
                                       aEt   ev +  + +  +el e+  e+++dL+++r+ +  L ++ +k +er +e es+  + ++   e+ ++    +
  gi|313127099|ref|YP_004037369.1| 300 AETTLDEVTSdaIAARRDELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAEKRSRADELDDDAEDAE 376
                                       677777776555888999******************************************************99999 PP

                    CENP-F_leu_zip 122 eeskaaveeL 131
                                       ee +++   L
  gi|313127099|ref|YP_004037369.1| 377 EELEQRSARL 386
                                       9999988766 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00075
                    CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEtskaevet.......lkeeieelaeelreleldLvalrseke 83 
                                       e +++ad L d +e  e ele+  + +e+++ e E+  ae e          ++ +e +e+l++ +++L+++  e e
  gi|313127099|ref|YP_004037369.1| 360 EKRSRADELDDDAEDAEEELEQRSARLEELEAELESLTAEFEDapvelgeAASHRDEVRETLTDVRAELTETNAEGE 436
                                       6788999******9999999998888888888888888888885555444666777788888888888888888888 PP

                    CENP-F_leu_zip  84 eLekelqkkq 93 
                                       ++   l + +
  gi|313127099|ref|YP_004037369.1| 437 NVRDRLTEAR 446
                                       8877777665 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.024
                    CENP-F_leu_zip  65 aeelreleldLvalrsekeeLekelq......kkqervseLeslnsslenllee 112
                                       +++ +ele+ L++lr+ +e+L+  l+      +  +r+ eL ++++ +e+ +e+
  gi|313127099|ref|YP_004037369.1| 474 EARIEELEATLSDLRERRETLNSRLEraeslvETENRIGELRNSRELFEQRIED 527
                                       444555555555555555555554441111113445555555555555555544 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.5
                    CENP-F_leu_zip   7 hvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelae......elreleldLva 77 
                                        ++e   e + +a+ L++ +++Le+e  +     +     aE++ ++ve+l++ +e  ae      +l++l+++L++
  gi|313127099|ref|YP_004037369.1| 527 DARETVEERRTEAETLREAADKLEAEADEKRTAATTQAEAAEDAAETVEGLESDLESVAEaesrldTLSDLRSKLTE 603
                                       56677788889999999999999999988888888888888888889999999999988722222234455555555 PP

                    CENP-F_leu_zip  78 lrsekeeLekelqkkqervseLe 100
                                       + se e L    ++ +e + eL+
  gi|313127099|ref|YP_004037369.1| 604 TESEIERL----EERRESIAELN 622
                                       55555554....67777777775 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00093
                    CENP-F_leu_zip  31 relemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnssle 107
                                       r    +e+   + +l  E    +ve+ k+++e+ ++ l++   +L++lr+ +++L+ ++   + + ++Le+l+++  
  gi|313127099|ref|YP_004037369.1| 625 RRERLAEKRDRRSELADEVDESTVEEAKAKKEKAENYLEQVDEELATLREKRDSLQSDIGGVNGELEQLEALREDRD 701
                                       555667788888899999999*****************************************************999 PP

                    CENP-F_leu_zip 108 nlleekEqe..kvqmkeeskaaveeLqtqlke 137
                                       +l  +  +      + ee +a    L+++l++
  gi|313127099|ref|YP_004037369.1| 702 ELAARVDALesLHAETEELEAMYGDLRAELRQ 733
                                       88777665433445667777777778877776 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.1     0.019        11      19      88 ..     229     297 ..     208     297 .. 0.93
   2 ?    0.6   0.2       1.3   7.6e+02      65      88 ..     330     353 ..     318     359 .. 0.82
   3 ?    6.8   0.3     0.015       8.8      18      87 ..     375     443 ..     363     444 .. 0.86
   4 ?    4.7   2.8     0.072        42      11      89 ..     473     549 ..     467     550 .. 0.68
   5 ?    4.8   0.2     0.066        38      34      82 ..     572     618 ..     557     622 .. 0.84
   6 ?    9.3   0.7    0.0026       1.5      14      51 ..     661     698 ..     656     733 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.019
                   Snapin_Pallidin  19 deklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaek 88 
                                       +ek  e+r++ ee+le+ ++ +++L+el+e+   ++ +++++  +K  +++ ++ +  ++++++++R+ek
  gi|313127099|ref|YP_004037369.1| 229 REKAVETRENAEEVLETYREKRAELDELAEDIA-DLRETIESDERKRETLRSEVGEARDSVEEIRDRIEK 297
                                       5678899*********************99887.99*******************************986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.3
                   Snapin_Pallidin  65 LvnikkrmsslnerlqklkkRaek 88 
                                       L+ ++ r + l+++ +kl++Rae+
  gi|313127099|ref|YP_004037369.1| 330 LTDVRERRTMLSNQAKKLRERAEE 353
                                       667788888888899999988875 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.015
                   Snapin_Pallidin  18 ldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                        +e+l++  +  eeL ++l++l+++++++  +   e+ +  +e ++ L+ ++ ++++ n   +++++R++
  gi|313127099|ref|YP_004037369.1| 375 AEEELEQRSARLEELEAELESLTAEFEDAPVELG-EAASHRDEVRETLTDVRAELTETNAEGENVRDRLT 443
                                       566666666777899***********99998888.8999999**************************96 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.072
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                       +e  ++el+++l++lr+  e L+++l+r  + ++  +++ e  + +  +   +++  ++  +++  +  ++l++ a+
  gi|313127099|ref|YP_004037369.1| 473 YEARIEELEATLSDLRERRETLNSRLERAESLVETENRIGE--LRNSRELFEQRIEDARETVEERRTEAETLREAAD 547
                                       67778888888888888888888888887666654444444..5666666667777777777777777777777666 PP

                   Snapin_Pallidin  88 kL 89 
                                       kL
  gi|313127099|ref|YP_004037369.1| 548 KL 549
                                       66 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.066
                   Snapin_Pallidin  34 eqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                       e+++ l ++L++++ea++   l +l   + KL++ + ++++l+er +++
  gi|313127099|ref|YP_004037369.1| 572 ETVEGLESDLESVAEAES--RLDTLSDLRSKLTETESEIERLEERRESI 618
                                       788889999999999999..77788888999999999999999987665 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.0026
                   Snapin_Pallidin  14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                        l+++de+l+ lr++ + L++++   n +L++le + e
  gi|313127099|ref|YP_004037369.1| 661 YLEQVDEELATLREKRDSLQSDIGGVNGELEQLEALRE 698
                                       699*****************************999887 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.1     0.019        11      42     121 ..     188     271 ..     178     274 .. 0.80
   2 ?    7.8   2.0    0.0056       3.2      59     105 ..     251     297 ..     234     306 .. 0.83
   3 ?    3.8   2.5     0.098        57      68     116 ..     309     357 ..     274     361 .. 0.59
   4 ?    4.8   1.3     0.048        28      54     105 ..     309     360 ..     298     378 .. 0.67
   5 ?    5.1   0.4     0.039        23      43     110 ..     372     442 ..     365     448 .. 0.74
   6 ?    5.4   1.7      0.03        18      49     115 ..     479     551 ..     468     556 .. 0.63
   7 ?    4.0   2.9     0.083        48      47     114 ..     522     592 ..     512     615 .. 0.56
   8 ?    1.9   2.6      0.38   2.2e+02      49     105 ..     590     645 ..     573     659 .. 0.74
   9 ?   10.7   0.7   0.00073      0.42      48     117 ..     663     731 ..     647     738 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                           DUF1664  42 avesvskqleqvs.eslaatkrhLssridrvdkkld...eqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       a+++v +q+e    + l++  + L+ ++ +vd++++   +q e + e++e+ +ev e  +e + +++++ e + +l 
  gi|313127099|ref|YP_004037369.1| 188 ALSKVESQIEAKEdAGLHERLNALETELGEVDDQIEryeDQREKAVETRENAEEVLETYREKRAELDELAEDIADLR 264
                                       67788888887762468888899999999999998722256667778999999999999999999999999999999 PP

                           DUF1664 115 sklerie 121
                                       +++e+ e
  gi|313127099|ref|YP_004037369.1| 265 ETIESDE 271
                                       9998755 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0056
                           DUF1664  59 atkrhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                       a  ++L+++i+ + +++++ ++  + +++ev e+r+ ++ei++ +e+
  gi|313127099|ref|YP_004037369.1| 251 AELDELAEDIADLRETIESDERKRETLRSEVGEARDSVEEIRDRIEK 297
                                       44468999*********************************999875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.098
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                        d + ++ de  e  +ei++++t+vre  + ++++ ++++e  e++es+
  gi|313127099|ref|YP_004037369.1| 309 SDAIAARRDELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEFESR 357
                                       2455566677777777777777777777777777777777777766654 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.048
                           DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                       s+++aa +++L +r +++ + l ++ e  + ++++ +++re  +e+++   +
  gi|313127099|ref|YP_004037369.1| 309 SDAIAARRDELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAE 360
                                       4667777777777777777777777777777777777777777777666555 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.039
                           DUF1664  43 vesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                        e+  ++leq s   e+l+a  + L+++ +    +l e +    e++e +t+vr +l+e++ + e+v++  
  gi|313127099|ref|YP_004037369.1| 372 AEDAEEELEQRSarlEELEAELESLTAEFEDAPVELGEAASHRDEVRETLTDVRAELTETNAEGENVRDRL 442
                                       55566777777733344455556667778888889999999999999999999999999999999888765 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.03
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkei......skeikeevtevredlseigedvesvkeavegles 115
                                       +le   ++l++ ++ L+sr++r ++ ++  ++i       +  ++ ++++re ++e +++ e+++ea  +le+
  gi|313127099|ref|YP_004037369.1| 479 ELEATLSDLRERRETLNSRLERAESLVETENRIgelrnsRELFEQRIEDARETVEERRTEAETLREAADKLEA 551
                                       5666667777777777777777665555444331111114556667777777777777777777777777765 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.083
                           DUF1664  47 skqleqvseslaatkrh...Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                        +++e+  e++++ + +   L +  d+++++ de   +++  +e  +++ e ++ +++d+esv ea + l+
  gi|313127099|ref|YP_004037369.1| 522 EQRIEDARETVEERRTEaetLREAADKLEAEADEKRTAATTQAEAAEDAAETVEGLESDLESVAEAESRLD 592
                                       55555555555544432222555556666666665555555555555666666666666666665555444 PP

  == domain 8  score: 1.9 bits;  conditional E-value: 0.38
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                       +l+++s +l++   + +s+i+r++++ ++ +e+  e +e ++e r+  se+ ++v++
  gi|313127099|ref|YP_004037369.1| 590 RLDTLS-DLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSELADEVDE 645
                                       344333.35555566678999999999999999999999999999999999998874 PP

  == domain 9  score: 10.7 bits;  conditional E-value: 0.00073
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       +q+++  ++l++ ++ L+s+i  v+ +l++ +++ +  ++e+++  + l++++ + e+++++  +l ++l
  gi|313127099|ref|YP_004037369.1| 663 EQVDEELATLREKRDSLQSDIGGVNGELEQLEALRE-DRDELAARVDALESLHAETEELEAMYGDLRAEL 731
                                       344444566778888999999999999988766655.577888888899999999999999988887766 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.7    0.0052         3      54     116 ..     203     264 ..     195     265 .. 0.89
   2 ?   12.0  17.1   0.00028      0.16       2     116 ..     252     369 ..     251     371 .. 0.95
   3 ?    9.2  11.9     0.002       1.2       7      92 ..     362     447 ..     358     453 .. 0.83
   4 ?   10.9   4.2   0.00064      0.37      55     116 ..     466     529 ..     459     531 .. 0.84
   5 ?    1.7  25.9      0.45   2.6e+02       4     103 ..     533     638 ..     530     650 .. 0.78
   6 ?    2.0   9.1      0.34     2e+02      63     117 ..     626     681 ..     625     682 .. 0.89
   7 ?    0.3  12.1       1.1   6.6e+02      18      84 ..     652     714 ..     644     745 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0052
                        TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedln 116
                                          + l+al +el e+ ++i+  ++++e+a ++ e++ee +e+ +e+ + el+el + i dl 
  gi|313127099|ref|YP_004037369.1| 203 GLHERLNALETELGEVDDQIERYEDQREKAVETRENAEEVLETYREK-RAELDELAEDIADLR 264
                                       556899***********************************999987.889999999999996 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00028
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYer...elvkhaedvkelqalreelnelkaeiae 75 
                                       el++l e+i++l+e +e+ e+k ++l++++ + +++++e  ++ e+   e ++ + ++++++a r+el+e +aei++
  gi|313127099|ref|YP_004037369.1| 252 ELDELAEDIADLRETIESDERKRETLRSEVGEARDSVEEIRDRIEKkraETTLDEVTSDAIAARRDELDEREAEIRS 328
                                       899***************************************9996555899999********************** PP

                        TPR_MLP1_2  76 lkaeaesakaeleeseesweeqkeelekelselekriedln 116
                                         +++ + ++ l+++ +++ e+ ee+e++ +e ++r ++l+
  gi|313127099|ref|YP_004037369.1| 329 DLTDVRERRTMLSNQAKKLRERAEEFESRAAEKRSRADELD 369
                                       ***************************************98 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.002
                        TPR_MLP1_2   7 eeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesa 83 
                                       ++ +++l++++e+ae++l++    le+ +++++     +e   v+  e++    ++re l +++ae++e +ae e++
  gi|313127099|ref|YP_004037369.1| 362 RSRADELDDDAEDAEEELEQRSARLEELEAELESLTAEFEDAPVELGEAASHRDEVRETLTDVRAELTETNAEGENV 438
                                       66778888999999999999999999999999999999999999999999999999999999999999999999999 PP

                        TPR_MLP1_2  84 kaeleesee 92 
                                       +  l e++e
  gi|313127099|ref|YP_004037369.1| 439 RDRLTEARE 447
                                       988888876 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00064
                        TPR_MLP1_2  55 dvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqk..eelekelselekriedln 116
                                        v+++ ++ ++++el+a++++l++++e++++ le++e+  e++    el++  + +e+ried  
  gi|313127099|ref|YP_004037369.1| 466 HVDSIGEYEARIEELEATLSDLRERRETLNSRLERAESLVETENriGELRNSRELFEQRIEDAR 529
                                       57788899999************************99876655512799************986 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.45
                        TPR_MLP1_2   4 ksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYe......relvkhaedvkelqalreelnelkaeia 74 
                                       ++ ++e+++l+e ++++ea++ + ++  ++qae a++a +  e      + + + ++ +++l++lr++l e+++ei+
  gi|313127099|ref|YP_004037369.1| 533 EERRTEAETLREAADKLEAEADEKRTAATTQAEAAEDAAETVEglesdlESVAEAESRLDTLSDLRSKLTETESEIE 609
                                       5667889999999999999999999999999999988888766444333345555567999**************** PP

                        TPR_MLP1_2  75 elkaeaesakaeleeseesweeqkeelek 103
                                        l++++es  + ++e +e ++e++++  +
  gi|313127099|ref|YP_004037369.1| 610 RLEERRESIAELNDERRERLAEKRDRRSE 638
                                       ********************998876443 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.34
                        TPR_MLP1_2  63 reelnelkaeiaelkaeae.sakaeleeseesweeqkeelekelselekriedlne 117
                                       re+l+e +++++el +e++ s+ +e ++++e+ e+  e+ ++el+ l+++++ l++
  gi|313127099|ref|YP_004037369.1| 626 RERLAEKRDRRSELADEVDeSTVEEAKAKKEKAENYLEQVDEELATLREKRDSLQS 681
                                       78999999******99996156688999999*********************9986 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 1.1
                        TPR_MLP1_2  18 eeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesak 84 
                                       ++ ++k++++ e++ ++ + ++e  ++ ++ +   + ++++l+alre+ +el a++  l++    ++
  gi|313127099|ref|YP_004037369.1| 652 KAKKEKAENYLEQVDEELATLREKRDSLQSDIGGVNGELEQLEALREDRDELAARVDALES----LH 714
                                       3333333333333333333344444444446666666666666666666666666555443....22 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4    0.0014      0.81       1      11 [.     453     463 ..     453     476 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP+CG++v+ 
  gi|313127099|ref|YP_004037369.1| 453 KCPECGQPVED 463
                                       6********94 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0088       5.1      34     100 ..     202     266 ..     163     270 .. 0.66
   2 ?    1.7   0.7      0.41   2.4e+02      25      97 ..     326     396 ..     271     399 .. 0.59
   3 ?    5.5   0.2     0.028        16      40      93 ..     379     434 ..     363     445 .. 0.57
   4 ?    0.7   2.7      0.84   4.9e+02      47      94 ..     574     608 ..     456     631 .. 0.67
   5 ?    6.1   0.5     0.019        11      22     109 ..     594     691 ..     592     696 .. 0.46
   6 ?    1.7   0.1      0.42   2.4e+02      47      79 ..     693     727 ..     669     750 .. 0.38

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0088
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlss 100
                                       a l + l+a+et+L+++++++++  ++++++  ++ +n ++ l +   + r eL+ l  ++++L   
  gi|313127099|ref|YP_004037369.1| 202 AGLHERLNALETELGEVDDQIER-YEDQREKAVETRENAEEVLETYR-EKRAELDELAEDIADLRET 266
                                       45666777777777777777777.55555555566666666666666.4578888888888888655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.41
                      Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnL 97 
                                       ir+ ++ +  +  t+l + +++L + +e+++s  ae ++r d+l +  +da  +l+ + + +L+ l+++l +L
  gi|313127099|ref|YP_004037369.1| 326 IRSDLTDV-RERRTMLSNQAKKLRERAEEFESRAAEKRSRADELDDDAEDAEEELE-QRSARLEELEAELESL 396
                                       33333333.23333333344444444444444444444454444444444544444.2234444444444444 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.028
                      Baculo_PEP_C  40 ldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsi 93 
                                       l++   +L++l+++l+sl ae+++   +l +++++ ++   +l+ ++r eLt +n++
  gi|313127099|ref|YP_004037369.1| 379 LEQRSARLEELEAELESLTAEFEDapvELGEAASHRDEVRETLT-DVRAELTETNAE 434
                                       44445566666666666666666655545555554444444444.455555555544 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.84
                      Baculo_PEP_C  47 LnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnlnsil 94 
                                       ++ l++dl+s +ae ++              +l    +lr++Lt ++s++
  gi|313127099|ref|YP_004037369.1| 574 VEGLESDLES-VAEAES--------------RLDtlSDLRSKLTETESEI 608
                                       2233333333.222222..............2222223333333333333 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.019
                      Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...........dtlrneL 87 
                                       L+++r++++++ +++++l +  e ++ +l+++ ++ lae ++r ++l+++++++  + +           +++++eL
  gi|313127099|ref|YP_004037369.1| 594 LSDLRSKLTETESEIERLEERRE-SIAELNDERRERLAEKRDRRSELADEVDESTVEEAkakkekaenylEQVDEEL 669
                                       55555555555555555444333.35555555555555555543444444333222211233422222224566666 PP

                      Baculo_PEP_C  88 tnlnsiltnLlssvtNinstLn 109
                                        +l  +  +L+s+++++n  L+
  gi|313127099|ref|YP_004037369.1| 670 ATLREKRDSLQSDIGGVNGELE 691
                                       6666666666666666666655 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.42
                      Baculo_PEP_C  47 Lnalsedlksllaeldt..rldtlltnLtdalnal 79 
                                       L+al ed  +l a +d+   l++ +++L++    l
  gi|313127099|ref|YP_004037369.1| 693 LEALREDRDELAARVDAleSLHAETEELEAMYGDL 727
                                       22222222222222222222222222222222222 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.8     0.002       1.2      99     170 ..     200     269 ..     181     273 .. 0.86
   2 ?    6.3   5.2     0.013       7.3      60     138 ..     248     326 ..     248     329 .. 0.92
   3 ?    8.0   7.5    0.0038       2.2      79     140 ..     330     391 ..     327     401 .. 0.92
   4 ?    4.9   7.2     0.033        19      45     175 ..     373     498 ..     369     500 .. 0.85
   5 ?    0.9   8.8      0.55   3.2e+02      54     133 ..     473     558 ..     468     586 .. 0.72
   6 ?    5.9  10.8     0.017       9.7      59     130 ..     588     659 ..     583     665 .. 0.93
   7 ?    6.3   0.5     0.013       7.4      78     140 ..     668     729 ..     666     741 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                           DUF4201  99 elkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvki 170
                                       e   ++erl++l+ el +v  + +++++q+ek  +  ++  ++++l+ Y ++ ++++e+ + ++ Lr+++++
  gi|313127099|ref|YP_004037369.1| 200 EDAGLHERLNALETELGEVDDQIERYEDQREKAVETREN--AEEVLETYREKRAELDELAEDIADLRETIES 269
                                       44567899**************************99999..8999999*********************997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                           DUF4201  60 ernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg 136
                                       e+ +eL +l + +++   +++    k+ +l+se+ e++++ +e+ +r++k r+e++  +   d + +++++l ++ +
  gi|313127099|ref|YP_004037369.1| 248 EKRAELDELAEDIADLRETIESDERKRETLRSEVGEARDSVEEIRDRIEKKRAETTLDEVTSDAIAARRDELDEREA 324
                                       799999999999999999999999*********************************99999999999999998877 PP

                           DUF4201 137 ll 138
                                       ++
  gi|313127099|ref|YP_004037369.1| 325 EI 326
                                       65 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0038
                           DUF4201  79 lthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrv 140
                                       lt+++e+++ml+++ ++l+++ +e e r a+ r +  ++  + + ++++ e+ ++++++l++
  gi|313127099|ref|YP_004037369.1| 330 LTDVRERRTMLSNQAKKLRERAEEFESRAAEKRSRADELDDDAEDAEEELEQRSARLEELEA 391
                                       899*********************************************99999999998865 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.033
                           DUF4201  45 eqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkler 121
                                       e ++ e ++ + ++ee ++eL+ l     +   +l +    +++++++l + + el e +++ + +r++l+++++ r
  gi|313127099|ref|YP_004037369.1| 373 EDAEEELEQRSARLEELEAELESLTAEFEDAPVELGEAASHRDEVRETLTDVRAELTETNAEGENVRDRLTEARELR 449
                                       6778999999***************************************************************9999 PP

                           DUF4201 122 dklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemrl 175
                                       d    +  ++ q  ++   P++     ++++++ee+++++  Lr++ + l++rl
  gi|313127099|ref|YP_004037369.1| 450 DE--GKCPECGQPVED--SPHVDS-IGEYEARIEELEATLSDLRERRETLNSRL 498
                                       85..445566666666..777766.77788888888888888888888888877 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.55
                           DUF4201  54 lnkkIeernkeLkrlkkk...ttktvhalthlkeklh...mleselselkkelkekeerlaklrkelykvklerdkl 124
                                       ++ +Iee ++ L+ l+++    ++ + + + l e ++   +l++  +  ++++++  e+ ++ r e + +++  dkl
  gi|313127099|ref|YP_004037369.1| 473 YEARIEELEATLSDLRERretLNSRLERAESLVETENrigELRNSRELFEQRIEDARETVEERRTEAETLREAADKL 549
                                       67778888887777776511144455555555555556668888889999999999999999999999999999999 PP

                           DUF4201 125 rkqneklkq 133
                                       +++ ++ ++
  gi|313127099|ref|YP_004037369.1| 550 EAEADEKRT 558
                                       988887666 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.017
                           DUF4201  59 eernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnek 130
                                       e+r + L+ l++k t t  +++ l e++  +++ + e++++l ek +r+ +l +e+ +   e +k++k++++
  gi|313127099|ref|YP_004037369.1| 588 ESRLDTLSDLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSELADEVDESTVEEAKAKKEKAE 659
                                       889999******************************************************999999999876 PP

  == domain 7  score: 6.3 bits;  conditional E-value: 0.013
                           DUF4201  78 althlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrv 140
                                       +l++l+ek++ l+s     + el+++e+ +++ r+el       + l+++ e+l++  g+lr+
  gi|313127099|ref|YP_004037369.1| 668 ELATLREKRDSLQSDIGGVNGELEQLEALRED-RDELAARVDALESLHAETEELEAMYGDLRA 729
                                       58899999999999999999999999999888.777777777888899999999888888775 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00056      0.33      13      30 ..      25      42 ..      16      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00056
                                      EEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkl 30
                                      +++i G nG+GKS+Ll++
  gi|313127099|ref|YP_004037369.1| 25 VTVIHGLNGSGKSSLLEA 42
                                      689************986 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.9     0.026        15      45      90 ..     210     259 ..     179     264 .. 0.70
   2 ?    3.5   0.5      0.12        71      49      84 ..     267     302 ..     257     325 .. 0.67
   3 ?    1.6  13.8      0.46   2.6e+02       7     120 ..     329     444 ..     304     456 .. 0.69
   4 ?    5.7   8.9     0.026        15       7      87 ..     483     556 ..     470     571 .. 0.53
   5 ?    7.2   7.8    0.0089       5.1       6      72 ..     579     645 ..     577     654 .. 0.91
   6 ?   11.7   5.5   0.00036      0.21      12      88 ..     652     728 ..     645     747 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                             Mod_r  45 laeknlslep....eleelrselqekleelkelekefeekeqeldellqk 90 
                                        +e  l + +    ++e++r++  e++e+++e+ ++++ek +eldel ++
  gi|313127099|ref|YP_004037369.1| 210 ALETELGEVDdqieRYEDQREKAVETRENAEEVLETYREKRAELDELAED 259
                                       33433333224555899999999999999999999999999999998765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                             Mod_r  49 nlslepeleelrselqekleelkelekefeekeqel 84 
                                         s+e + e lrse+ e++++++e++++ e+k +e 
  gi|313127099|ref|YP_004037369.1| 267 IESDERKRETLRSEVGEARDSVEEIRDRIEKKRAET 302
                                       233366777778888888888888888777776664 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.46
                             Mod_r   7 eLqelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeq 82 
                                       +L ++ e    l++ +k+l ++ ++ +++  e +    +l ++  + e+ele+ +++l+e   el++l +efe+   
  gi|313127099|ref|YP_004037369.1| 329 DLTDVRERRTMLSNQAKKLrERAEEFESRAAEKRSRADELDDDAEDAEEELEQRSARLEELEAELESLTAEFEDAPV 405
                                       45555555555555555554444444444444444444444444455778888888888888888888888888888 PP

                             Mod_r  83 el.dellqkfspdallarLqtavaeaeeeSealaeefle 120
                                       el ++++ +     +l+ ++++++e++ e e++ +++ e
  gi|313127099|ref|YP_004037369.1| 406 ELgEAASHRDEVRETLTDVRAELTETNAEGENVRDRLTE 444
                                       884444466666688888999999999999998888765 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.026
                             Mod_r   7 eLqelledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqe 83 
                                        L +l e  e l+++++ ++++ + +++  el    ++l e+      ++e+ r+ ++e++ e+++l+++ +++e+e
  gi|313127099|ref|YP_004037369.1| 483 TLSDLRERRETLNSRLERAESLVETENRIGEL-RNSRELFEQ------RIEDARETVEERRTEAETLREAADKLEAE 552
                                       34444445555555555555555555555555.233444444......55555555555555555555555555555 PP

                             Mod_r  84 ldel 87 
                                        de+
  gi|313127099|ref|YP_004037369.1| 553 ADEK 556
                                       5443 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.0089
                             Mod_r   6 eeLqelledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelke 72 
                                       ++L+ + e e+ l+ l +  +++ + ++e e l++  es+ae n +++++l e+r++ +e  +e++e
  gi|313127099|ref|YP_004037369.1| 579 SDLESVAEAESRLDTLSDLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSELADEVDE 645
                                       689999999******9966699***********************************9999998765 PP

  == domain 6  score: 11.7 bits;  conditional E-value: 0.00036
                             Mod_r  12 ledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldel 87 
                                         ++ek e++++++ +e+ +l+e++++l ++ +   +  l++ + l+e r+el+++ + l++l++e ee+e+ + +l
  gi|313127099|ref|YP_004037369.1| 652 KAKKEKAENYLEQVdEELATLREKRDSL-QSDIGGVNGELEQLEALREDRDELAARVDALESLHAETEELEAMYGDL 727
                                       567899********888**********9.9999999**********************************9987665 PP

                             Mod_r  88 l 88 
                                        
  gi|313127099|ref|YP_004037369.1| 728 R 728
                                       5 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0021       1.2       7      51 ..       4      48 ..       1      97 [. 0.85
   2 ?   -3.1   0.2       9.5   5.5e+03     124     151 ..     266     293 ..     233     305 .. 0.65
   3 ?    0.6   0.2      0.73   4.2e+02     121     153 ..     593     625 ..     577     645 .. 0.67
   4 ?    0.8   0.1      0.63   3.6e+02     114     161 ..     675     722 ..     646     729 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                                      EEEEEEEETTEEEEEE-HHHHHHHHHS--SHHHHHHHHHHHHHHS CS
                              MukB  7 ksltlinWnGffartfdldelvttlsGgnGaGksttmaafvtali 51
                                        + l n++ +     dl + vt + G nG+Gks  + a + al 
  gi|313127099|ref|YP_004037369.1|  4 DRIRLQNFKPYAETDLDLTDGVTVIHGLNGSGKSSLLEACFFALY 48
                                      5667778888888889999*****************999998886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.5
                                       S--TT--HHHHHEE--SSS--EE--HHH CS
                              MukB 124 gleedvkltdvlleklddkkarvrelne 151
                                        +e+d +  + l +++++ ++ v e+ +
  gi|313127099|ref|YP_004037369.1| 266 TIESDERKRETLRSEVGEARDSVEEIRD 293
                                       4556666666777777776666655544 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.73
                                       EEES--TT--HHHHHEE--SSS--EE--HHHHH CS
                              MukB 121 alqgleedvkltdvlleklddkkarvrelnelk 153
                                       +l++l ++++ t+  +e+l+++++ + eln+ +
  gi|313127099|ref|YP_004037369.1| 593 TLSDLRSKLTETESEIERLEERRESIAELNDER 625
                                       466777777777777777777777777777643 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.63
                                       -EEEEEEEEES--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT CS
                              MukB 114 kvdikpfalqgleedvkltdvlleklddkkarvrelnelkekleeleg 161
                                       k d     + g++ +++  + l e  d+  arv +l+ l+++ eele+
  gi|313127099|ref|YP_004037369.1| 675 KRDSLQSDIGGVNGELEQLEALREDRDELAARVDALESLHAETEELEA 722
                                       4555556788999999999999******************99999887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0022       1.2       1      24 [.      25      48 ..      25     161 .. 0.80
   2 ?   -1.0   1.2         3   1.8e+03     107     138 ..     287     317 ..     244     322 .. 0.74
   3 ?   -2.4   1.9       8.7     5e+03     116     142 ..     362     388 ..     330     389 .. 0.73
   4 ?   -1.9   1.5       5.9   3.4e+03     111     139 ..     625     654 ..     620     673 .. 0.72
   5 ?   -2.3   0.0       7.5   4.4e+03      55      55 ..     798     798 ..     704     857 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg 24
                                      +++++Gl+GsGKs l+e    +l 
  gi|313127099|ref|YP_004037369.1| 25 VTVIHGLNGSGKSSLLEACFFALY 48
                                      6799***********998765554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                            AAA_33 107 deetlkeRlakRaangddrsevpeealdrqka 138
                                       + e++++R++k+ a+++   ev+  a+ + ++
  gi|313127099|ref|YP_004037369.1| 287 SVEEIRDRIEKKRAETT-LDEVTSDAIAARRD 317
                                       56889999998888643.33666666666555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8.7
                            AAA_33 116 akRaangddrsevpeealdrqkarfer 142
                                       + Ra++ dd++e  ee l++  ar+e+
  gi|313127099|ref|YP_004037369.1| 362 RSRADELDDDAEDAEEELEQRSARLEE 388
                                       345555588888888888888888886 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.9
                            AAA_33 111 lkeRlakRaang.ddrsevpeealdrqkar 139
                                        +eRla++ +++ + + ev+e+++++ ka+
  gi|313127099|ref|YP_004037369.1| 625 RRERLAEKRDRRsELADEVDESTVEEAKAK 654
                                       567776666655344557888888887775 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 7.5
                            AAA_33  55 l 55 
                                       +
  gi|313127099|ref|YP_004037369.1| 798 I 798
                                       3 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  43.1     0.005       2.9      35     278 ..     194     442 ..     180     450 .. 0.74
   2 ?    3.4   0.9     0.083        48     217     255 ..     469     507 ..     464     511 .. 0.84
   3 ?   -0.2  44.0         1     6e+02      24     284 ..     492     737 ..     491     765 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.005
                                       XXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  35 eeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkd 111
                                       ++ e k+ a  ++  ++ e+el e+ +q+++ + +r++++  ++n++e le++r    ++ ++ +e+ +++++lr  
  gi|313127099|ref|YP_004037369.1| 194 SQIEAKEDAGLHERLNALETELGEVDDQIERYEDQREKAVETRENAEEVLETYR----EKRAELDELAEDIADLRET 266
                                       344444455667777889999999999999999999998877666666666555....55667789999******99 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXX CS
                          Filament 112 ldeatlarvdLekkvesLkeelafl.....kkvheeEvkelqkqvseqvlvevdaarkldLteilkeiraq...yee 180
                                       ++    +r  L ++v + ++ ++       kk  e+ ++e+++ + + +  e+d +r+ ++ + l ++r+      +
  gi|313127099|ref|YP_004037369.1| 267 IESDERKRETLRSEVGEARDSVEEIrdrieKKRAETTLDEVTSDAIAARRDELD-EREAEIRSDLTDVRERrtmLSN 342
                                       999999999999888888777765500011555555666666666666666777.7788888888888876111556 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHH CS
                          Filament 181 laeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaele...erle 254
                                       +a+k re ae  ++s+ +e ++ a++ +++++ a+ee+++   ++++le+elesl ++ +    +l e+    +++ 
  gi|313127099|ref|YP_004037369.1| 343 QAKKLRERAE-EFESRAAEKRSRADELDDDAEDAEEELEQRSARLEELEAELESLTAEFEDAPVELGEAAshrDEVR 418
                                       6666666665.6*******************************************9999999888888751114556 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 255 aeleklqeklseleeelaeireem 278
                                       + l++++++l+e ++e +++r+++
  gi|313127099|ref|YP_004037369.1| 419 ETLTDVRAELTETNAEGENVRDRL 442
                                       677777888888888888887766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.083
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 217 eitelrrqiqsleieleslkkqkasleaqlaeleerlea 255
                                        i e+  +i++le+ l++l++ +++l+++l+ +e  +e+
  gi|313127099|ref|YP_004037369.1| 469 SIGEYEARIEELEATLSDLRERRETLNSRLERAESLVET 507
                                       578999999999999999999999999999988876665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXXXXX.XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  24 EqenkeLeakieeleekk.saevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkre 99 
                                       E+ n++Le   +  e ++   e ++ +el+e+ +e++r++++e  +e + l+   d+l++e+++ r+   ++++  e
  gi|313127099|ref|YP_004037369.1| 492 ETLNSRLERAESLVETENrIGELRNSRELFEQRIEDARETVEERRTEAETLREAADKLEAEADEKRTAATTQAEAAE 568
                                       667888887766666555367888999************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 100 evEaelkalrkdldeatlarvdLekkvesLkeelaflkkvheeEvkelqkqvseqvlvevdaarkldLteilkeira 176
                                       ++ +++++l  dl+      ++ e+++++L + l+   +  e E++ l+++   + + e++++r+  L+e     r+
  gi|313127099|ref|YP_004037369.1| 569 DAAETVEGLESDLESV----AEAESRLDTLSD-LRSKLTETESEIERLEERR--ESIAELNDERRERLAE----KRD 634
                                       **********999976....699*******85.8888889999*****9998..7788888777765554....444 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 177 qyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerl 253
                                          el       a+e+ +s +ee++ + ek ++ l+++ ee++ lr + +sl++++  + ++ ++lea  ++ +e  
  gi|313127099|ref|YP_004037369.1| 635 RRSEL-------ADEVDESTVEEAKAKKEKAENYLEQVDEELATLREKRDSLQSDIGGVNGELEQLEALREDRDELA 704
                                       33333.......34444556777777777777777777777777777777777777777777666665555444433 PP

                                       HH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 254 ea..eleklqeklseleeelaeireemarqlre 284
                                       ++  +le+l+++ +ele+   ++r+e+ +++ e
  gi|313127099|ref|YP_004037369.1| 705 ARvdALESLHAETEELEAMYGDLRAELRQRNVE 737
                                       322256777777777777777777777665544 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  17.3     0.055        32      67     151 ..     202     300 ..     177     318 .. 0.75
   2 ?    7.1  26.6      0.01       5.9      73     177 ..     313     417 ..     297     453 .. 0.65
   3 ?   -1.8  22.1       5.1     3e+03     109     181 ..     592     660 ..     555     660 .. 0.79
   4 ?    8.7  10.7    0.0032       1.9      66     149 ..     652     734 ..     644     741 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.055
                             ATG16  67 q..............snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaele 129
                                       +              +  +q ++ +++ +k +++re  +e++ +  e    l el e +++l+e++++de++ + l+
  gi|313127099|ref|YP_004037369.1| 202 AglherlnaletelgEVDDQIERYEDQREKAVETRENAEEVLETYREKRAELDELAEDIADLRETIESDERKRETLR 278
                                       222223333444455778889999999999*********************************************** PP

                             ATG16 130 aeraaletklkdreeelrekek 151
                                       +e+ + ++ +++ +++++ k++
  gi|313127099|ref|YP_004037369.1| 279 SEVGEARDSVEEIRDRIEKKRA 300
                                       ***9999999999999988875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.01
                             ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                       +a+  +l+++ a++r++l+++  +r+ l+++ ++l e  ++ e+++ e+++r +el ++ ++ e++l++r ++l+e+
  gi|313127099|ref|YP_004037369.1| 313 AARRDELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAEKRSRADELDDDAEDAEEELEQRSARLEEL 389
                                       34455666666777777777777777777777777777777777777777777777777777777777777777777 PP

                             ATG16 150 eklvqdlqDElsaLqlqlnqaEeklrkl 177
                                       e+ ++ l  E +   ++l  a + ++++
  gi|313127099|ref|YP_004037369.1| 390 EAELESLTAEFEDAPVELGEAASHRDEV 417
                                       7777766666666665555555444443 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.1
                             ATG16 109 eelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekEN 181
                                       ++l++l++kl+e e+++++le++r+++ +  ++r+e+l+ek+    +l DE++  +++    E+k +k ++EN
  gi|313127099|ref|YP_004037369.1| 592 DTLSDLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSELADEVDESTVE----EAKAKKEKAEN 660
                                       57889***********************************************977665....55556666655 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0032
                             ATG16  66 sqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdr 142
                                       +++++k ++++++ +++la+lre    l+   g  +  l +l+ +l++++++l ++  +l++l+ae ++le  + d+
  gi|313127099|ref|YP_004037369.1| 652 KAKKEKAENYLEQVDEELATLREKRDSLQSDIGGVNGELEQLE-ALREDRDELAARVDALESLHAETEELEAMYGDL 727
                                       1223456677777777777777777777777777777777775.58888889999999******************* PP

                             ATG16 143 eeelrek 149
                                       ++elr++
  gi|313127099|ref|YP_004037369.1| 728 RAELRQR 734
                                       **99976 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   5.9   0.00018      0.11      17     104 ..     206     293 ..     195     301 .. 0.89
   2 ?    6.1   4.4     0.018        10       6      79 ..     324     397 ..     318     405 .. 0.82
   3 ?    2.4   1.8      0.24   1.4e+02       7      48 ..     409     450 ..     405     516 .. 0.57
   4 ?    2.1   2.6      0.31   1.8e+02      22      72 ..     500     550 ..     467     559 .. 0.66
   5 ?    4.4   6.0     0.061        36      16      95 ..     529     611 ..     518     620 .. 0.73
   6 ?    2.2   3.7      0.29   1.7e+02      37      87 ..     567     617 ..     550     646 .. 0.41
   7 ?    4.5   2.3     0.058        34       1      50 [.     651     700 ..     638     746 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnis 93 
                                       e l++l+++l ++ +++++ +++ e+  e  ++a ++++  r++  +L++la+++ d  ++++  e ++++l  ++ 
  gi|313127099|ref|YP_004037369.1| 206 ERLNALETELGEVDDQIERYEDQREKAVETRENAEEVLETYREKRAELDELAEDIADLRETIESDERKRETLRSEVG 282
                                       67999******************999999999*************************99*******99999888888 PP

                                       HHHHHHHHHHH CS
                        Laminin_II  94 eikelIaqARk 104
                                       e +  ++  R+
  gi|313127099|ref|YP_004037369.1| 283 EARDSVEEIRD 293
                                       88877777776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelk 79 
                                       ae+ + ++ v e  + ls++ ++++e ++e+++ ++e    ++++    +dA+++  +    +++L++ l++l 
  gi|313127099|ref|YP_004037369.1| 324 AEIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAEKRSRADELDDDAEDAEEELEQRSARLEELEAELESLT 397
                                       57778888999999999999999999999999998888888888888888888888888888888888888875 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.24
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvk 48 
                                       ea +   ev e l+++ ++l +t+++ +++++ + e  e+ +
  gi|313127099|ref|YP_004037369.1| 409 EAASHRDEVRETLTDVRAELTETNAEGENVRDRLTEARELRD 450
                                       666777788888888888888888888888887777665443 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.31
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II  22 lsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLl 72 
                                        ++ l +t++ + e+++s e  ++ ++da +++++ r++  +L + a++L+
  gi|313127099|ref|YP_004037369.1| 500 RAESLVETENRIGELRNSRELFEQRIEDARETVEERRTEAETLREAADKLE 550
                                       344555666677777777777777777777777777777777777777765 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.061
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG...GHHHHHHHHHH...HH CS
                        Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld...klkelkqleeasssls 89 
                                        e +++  ++ e ++e + +++++++e    +    +a +dA + v  Le  ++ + +   +l +l  l+++     
  gi|313127099|ref|YP_004037369.1| 529 RETVEERRTEAETLREAADKLEAEADEKRTAATTQAEAAEDAAETVEGLESDLESVAEaesRLDTLSDLRSKLTETE 605
                                       56677777888899999999999999999999999999999999999999999988651115555555555544444 PP

                                       HHHHHH CS
                        Laminin_II  90 dnisei 95 
                                        +i+++
  gi|313127099|ref|YP_004037369.1| 606 SEIERL 611
                                       455544 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.29
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH... CS
                        Laminin_II  37 nrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss 87 
                                       +++++et e +++  + +++A++   +L  l  +L +  +e++ lee ++s
  gi|313127099|ref|YP_004037369.1| 567 AEDAAETVEGLESDLESVAEAESRLDTLSDLRSKLTETESEIERLEERRES 617
                                       223333333333333333333333333333333333333333333333332 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.058
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkda 50 
                                       +k++ ++a++ +++v e la l ++ + +++++ ++n+++e+ +++ +d 
  gi|313127099|ref|YP_004037369.1| 651 AKAKKEKAENYLEQVDEELATLREKRDSLQSDIGGVNGELEQLEALREDR 700
                                       45566667777777777777777777777777777777776666655533 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   7.6    0.0041       2.3     338     412 ..     201     273 ..     178     304 .. 0.68
   2 ?    8.7   6.1     0.001       0.6     327     410 ..     325     402 ..     302     412 .. 0.57
   3 ?    5.2   0.3     0.012       6.8     331     411 ..     413     501 ..     405     512 .. 0.56
   4 ?    4.2   5.8     0.024        14     333     414 ..     478     559 ..     446     575 .. 0.62
   5 ?   -0.2   7.0       0.5   2.9e+02     340     417 ..     575     651 ..     558     661 .. 0.48
   6 ?    7.0   5.0    0.0032       1.8     315     425 ..     638     757 ..     627     772 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0041
                              FapA 338 klkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk..k 412
                                         + l e+l++le el +++++i++ ++   + +   e +e  +++let+ + + el el e++++l e +es   k
  gi|313127099|ref|YP_004037369.1| 201 D-AGLHERLNALETELGEVDDQIERYED---QREKAVETRENAEEVLETYREKRAELDELAEDIADLRETIESDerK 273
                                       2.56777777777777777777777777...3333467778888888888888888888888888888888877322 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.001
                              FapA 327 evgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelke 403
                                       e+  d  +++e+++ l ++ ++l+e+ e+ +++ ++ ++         e  ++ + ++e++e+ + +leele+el++
  gi|313127099|ref|YP_004037369.1| 325 EIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAEKRS------RADELDDDAEDAEEELEQRSARLEELEAELES 395
                                       333333445555555555555555555555555333333......12344566666666666666666666666666 PP

                              FapA 404 lkeeles 410
                                       l +e+e+
  gi|313127099|ref|YP_004037369.1| 396 LTAEFED 402
                                       6666665 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.012
                              FapA 331 depelkeklkeleeeleeleeeleklkkkikklpklkaekq.lesekkeqlkklletk.......eklkeeleelee 399
                                       ++ e++e l++++ el e+++e e++++++++ ++l+ e++  e+ +  +      +        e+l+  l++l+e
  gi|313127099|ref|YP_004037369.1| 413 HRDEVRETLTDVRAELTETNAEGENVRDRLTEARELRDEGKcPECGQPVEDSPHVDSIgeyeariEELEATLSDLRE 489
                                       45789999999999999999999999999666666666443022222222222223330001222455555555555 PP

                              FapA 400 elkelkeelesk 411
                                       ++++l+++le+ 
  gi|313127099|ref|YP_004037369.1| 490 RRETLNSRLERA 501
                                       555555555544 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.024
                              FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                        el + l++l+e+ e l+++le+ ++ ++  + +++  +  + +++ ++ ++et e+ ++e e l+e  ++l++e +
  gi|313127099|ref|YP_004037369.1| 478 EELEATLSDLRERRETLNSRLERAESLVETENRIGELRNSRELFEQRIEDARETVEERRTEAETLREAADKLEAEAD 554
                                       33344444444444444444444444444444444444455667777888888888888888888888888888887 PP

                              FapA 410 skkee 414
                                       +k+ +
  gi|313127099|ref|YP_004037369.1| 555 EKRTA 559
                                       77333 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.5
                              FapA 340 keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeeak 416
                                       + le +le++ e   +l+   ++ +kl +++   ++ +e  +++ e   + +e+l+e ++++ el +e+++++  ++
  gi|313127099|ref|YP_004037369.1| 575 EGLESDLESVAEAESRLDTLSDLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSELADEVDEST-VEE 650
                                       4444444444333333333333333333333334444555555555556666667777777777777766662.222 PP

                              FapA 417 i 417
                                        
  gi|313127099|ref|YP_004037369.1| 651 A 651
                                       2 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0032
                              FapA 315 klGselgtkteievgldepelkeklkeleeeleeleeeleklkkk.......ikklpklkaekqlesekkeqlkkll 384
                                       +l+ e ++ t  e+  ++ ++ + l++++eel  l+e+ + l+++       +++l++l+++ +  + + + l++l+
  gi|313127099|ref|YP_004037369.1| 638 ELADEVDESTVEEAKAKKEKAENYLEQVDEELATLREKRDSLQSDiggvngeLEQLEALREDRDELAARVDALESLH 714
                                       56667778888888888677777779999999999999999988866666667777777777766777777777777 PP

                              FapA 385 etkeklkeeleeleeelkelk.eeleskkeea.kikvnkeiyp 425
                                        + e+l+  + +l++el + + e le++ +e+  ++ ++ +y+
  gi|313127099|ref|YP_004037369.1| 715 AETEELEAMYGDLRAELRQRNvETLERMLNETfDLVYGNDAYS 757
                                       7777777777777777774441444444555555555555555 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   8.2    0.0019       1.1     243     323 ..     204     290 ..     187     298 .. 0.77
   2 ?    6.7   7.7    0.0051         3     229     327 ..     288     385 ..     278     388 .. 0.83
   3 ?    8.0   0.1    0.0021       1.2     267     323 ..     388     444 ..     383     449 .. 0.91
   4 ?    4.9   8.5     0.019        11     240     331 ..     477     563 ..     465     584 .. 0.73
   5 ?    0.4   3.7      0.42   2.4e+02     253     323 ..     576     645 ..     564     648 .. 0.73
   6 ?   -1.9  12.0       2.2   1.3e+03     240     350 ..     601     719 ..     585     731 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                             IFT57 243 tksqlkklhedisktlekie....srEkyl..nsqleellqeyreaqeelsevkekykqlsegvseltrelaeisee 313
                                       +++ l+ l++++ ++ ++ie    +rEk +   ++ ee l+ yre+++el+e+ e++ +l e++++ +r+ +++  e
  gi|313127099|ref|YP_004037369.1| 204 LHERLNALETELGEVDDQIEryedQREKAVetRENAEEVLETYREKRAELDELAEDIADLRETIESDERKRETLRSE 280
                                       456777788888888888763334699999434578999999*************************9999999999 PP

                             IFT57 314 lekvkqemee 323
                                       + ++   +ee
  gi|313127099|ref|YP_004037369.1| 281 VGEARDSVEE 290
                                       9888887776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0051
                             IFT57 229 mkkhkksieeslpetksqlkklhed.isktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvselt 304
                                       +++ ++ ie++   +++ l+++ +d i+   +++ +rE  + s l +  +    ++++ ++++e+ ++ +++  e++
  gi|313127099|ref|YP_004037369.1| 288 VEEIRDRIEKKR--AETTLDEVTSDaIAARRDELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAEKR 362
                                       344444444443..457899987663677889********************************************* PP

                             IFT57 305 relaeiseelekvkqemeergss 327
                                          +e++++ e++++e+e+r+++
  gi|313127099|ref|YP_004037369.1| 363 SRADELDDDAEDAEEELEQRSAR 385
                                       ********************987 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0021
                             IFT57 267 ylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemee 323
                                        l+ +le+l++e+++a  el e+  + +++ e++++ + el+e++ e e+v  ++ e
  gi|313127099|ref|YP_004037369.1| 388 ELEAELESLTAEFEDAPVELGEAASHRDEVRETLTDVRAELTETNAEGENVRDRLTE 444
                                       68899*********************************************9988766 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.019
                             IFT57 240 lpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelek 316
                                       ++e++  l++l e  +   +++e  E+ +++  e+ + e+r   ++ + ++++++++ e+v+e+++e +++ e  +k
  gi|313127099|ref|YP_004037369.1| 477 IEELEATLSDLRERRETLNSRLERAESLVET--ENRIGELR---NSRELFEQRIEDARETVEERRTEAETLREAADK 548
                                       4455555666666666666666666666654..44555555...5556678899*********************** PP

                             IFT57 317 vkqemeergssmtDg 331
                                       ++ e +e+ + +t +
  gi|313127099|ref|YP_004037369.1| 549 LEAEADEKRTAATTQ 563
                                       *******99888755 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.42
                             IFT57 253 disktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemee 323
                                        ++  le + + E++l++ l++l +++ e++ e++ ++e+ + + e + e+++ lae  ++ +++  e++e
  gi|313127099|ref|YP_004037369.1| 576 GLESDLESVAEAESRLDT-LSDLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSELADEVDE 645
                                       566677777777888764.7888888888888888888888888888888888888877777777777766 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 2.2
                             IFT57 240 lpetksqlkklhedisktlekiesrEkylnsqleellqe...................yreaqeelsevkekykqls 297
                                       l           ++ + ++e++e+r + + + ++e  +                     +ea+++ +++++ ++q+ 
  gi|313127099|ref|YP_004037369.1| 601 L-----------TETESEIERLEERRESIAELNDERRERlaekrdrrseladevdestVEEAKAKKEKAENYLEQVD 666
                                       3...........33334444444444444444444444400000000000000000223344455555555555555 PP

                             IFT57 298 egvseltrelaeiseelekvkqemeergssmtDgsplvkikkaltklkkEikq 350
                                       e++  l+++ ++++ ++  v  e+e+ ++   D + l    +al++l  E ++
  gi|313127099|ref|YP_004037369.1| 667 EELATLREKRDSLQSDIGGVNGELEQLEALREDRDELAARVDALESLHAETEE 719
                                       55555555555555555555555555555555555555555555555555555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  16.7     0.025        14     138     246 ..     192     315 ..     137     319 .. 0.55
   2 ?    0.4  23.8      0.58   3.3e+02     107     218 ..     290     413 ..     289     451 .. 0.49
   3 ?    7.2   4.2    0.0048       2.8     120     236 ..     410     528 ..     405     531 .. 0.73
   4 ?    5.9  21.2     0.012       7.1     125     239 ..     522     638 ..     508     647 .. 0.80
   5 ?    5.2   9.7      0.02        12     120     230 ..     640     735 ..     630     750 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.025
                           DUF4407 138 leaqia.....alqaeidaaearldalraeaqkeldgtk...gtgttgvaGkgpaakekkaqldaaqaelaelkakl 206
                                        e+qi+      l + ++a+e++l +  ++ ++  d+      t++ + +   + ++ek+a+ld++ +++a+l++++
  gi|313127099|ref|YP_004037369.1| 192 VESQIEakedaGLHERLNALETELGEVDDQIERYEDQREkavETRE-NAEEVLETYREKRAELDELAEDIADLRETI 267
                                       2222222222333333333333332222222222222112213332.25667899*********************9 PP

                           DUF4407 207 d...............atarlaalraelaeleaerakeraasqaaaaaddGllar 246
                                       +               a++ +++ r+++++ +ae++ ++ +s+a       ++ar
  gi|313127099|ref|YP_004037369.1| 268 EsderkretlrsevgeARDSVEEIRDRIEKKRAETTLDEVTSDA-------IAAR 315
                                       9*999999955554444444444444444444444444444444.......4443 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.58
                           DUF4407 107 eIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk......gtgttg 177
                                       eI+ +++++++e++ +    + +a  a+ +el+++ a++++ ++  ++r++ l ++a+k  + +        ++ ++
  gi|313127099|ref|YP_004037369.1| 290 EIRDRIEKKRAETTLDE--VTSDAIAARRDELDEREAEIRSDLTDVRERRTMLSNQAKKLRERAEefesraAEKRSR 364
                                       67777777777765444..4444577777777777777777777777777777777776666543332222112222 PP

                           DUF4407 178 vaGkgpaakekkaqldaaqaelaelkakld...............atarlaalrae 218
                                            + a+ ++++l++++a+l+el+a+l+               a        + 
  gi|313127099|ref|YP_004037369.1| 365 ADELDDDAEDAEEELEQRSARLEELEAELEsltaefedapvelgeA-------ASH 413
                                       2222223333444444444444444444445555555533332221.......222 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0048
                           DUF4407 120 akelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...gtgttgvaGkgpaakekkaqld 193
                                       a++++++++++lt+  ael ++++a  ++++   +++++lr+e ++   g++   +     +  ++++ +e +a l 
  gi|313127099|ref|YP_004037369.1| 410 AASHRDEVRETLTDVRAEL-TETNAEGENVRDRLTEARELRDEGKCPECGQPvedSPHVDSIGEYEARIEELEATLS 485
                                       5556666666665444444.445555666777777778888888888888887775555556677778888999999 PP

                           DUF4407 194 aaqaelaelkakldatarlaalraelaeleaerakeraasqaa 236
                                       +++++ ++l+++l++++ l + ++++ el++ r+  +++ ++a
  gi|313127099|ref|YP_004037369.1| 486 DLRERRETLNSRLERAESLVETENRIGELRNSRELFEQRIEDA 528
                                       9999999999999999999999999999999988888777665 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.012
                           DUF4407 125 eqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..gtgttgvaGkgpaakekkaqldaaqael 199
                                       eq  ++++++++e +++ + l+++ d++ea++d++r++a+ +++ +    ++ +g + + ++  e+++ ld+++   
  gi|313127099|ref|YP_004037369.1| 522 EQRIEDARETVEERRTEAETLREAADKLEAEADEKRTAATTQAEAAEdaAETVEGLESDLESVAEAESRLDTLSDLR 598
                                       44445689999999999999999999999999999999999888877775555677778888888999999998888 PP

                           DUF4407 200 aelkakldatarlaalraelaeleaerakeraasqaaaaa 239
                                        +l+++ ++ +rl+++r+ +ael++er+++ a++++++++
  gi|313127099|ref|YP_004037369.1| 599 SKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSE 638
                                       8888888889999999999999999999998888877665 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.02
                           DUF4407 120 akelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaq 196
                                       a+e++e++ ++++a+ +++e+ +++ ++e+++++++    r+ +        ++ + gv+G+ +  ++ +++ d++ 
  gi|313127099|ref|YP_004037369.1| 640 ADEVDESTVEEAKAKKEKAENYLEQVDEELATLREK----RDSL--------QSDIGGVNGELEQLEALREDRDELA 704
                                       333322222222222222222222222222222222....2222........3444458888888888888888888 PP

                           DUF4407 197 aelaelkakldatarlaalraelaeleaeraker 230
                                       a++++l++     a++++l+a + +l+ae+++++
  gi|313127099|ref|YP_004037369.1| 705 ARVDALESL---HAETEELEAMYGDLRAELRQRN 735
                                       888888777...7777888888888877776655 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7  14.8      0.53     3e+02      39     164 ..     188     287 ..     164     299 .. 0.39
   2 ?    3.0  17.0      0.22   1.3e+02      28     147 ..     248     361 ..     242     369 .. 0.42
   3 ?    8.1  18.1    0.0057       3.3      37     157 ..     355     497 ..     333     502 .. 0.66
   4 ?    4.1  22.6     0.099        57      42     168 ..     499     631 ..     494     633 .. 0.71
   5 ?    5.1  24.4     0.047        27      22     152 ..     583     735 ..     580     746 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.53
                              Fez1  39 qlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaal 115
                                        l  +++++e+ke+    l+e+l+  ++el +++++++r +++ e   e+ e++ee l+  re+             
  gi|313127099|ref|YP_004037369.1| 188 ALSKVESQIEAKED--AGLHERLNALETELGEVDDQIERYEDQREKAVETRENAEEVLETYREK------------- 249
                                       22222333333222..233344444444444444444444333333333333333333333332............. PP

                              Fez1 116 esdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqERrt 164
                                                  + el+el ++++ lr+ ++ +++k+e+ +s+  + R  
  gi|313127099|ref|YP_004037369.1| 250 -----------RAELDELAEDIADLRETIESDERKRETLRSEVGEARDS 287
                                       ...........33333333444444444443333333333333333322 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.22
                              Fez1  28 qklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk.......kseaellrekvekleeelk 97 
                                       +k  e+ +l  ++ +lr+++e+ e++ ++l++++ e  +++e++ +++++k       + +++ +  + ++l+e  +
  gi|313127099|ref|YP_004037369.1| 248 EKRAELDELAEDIADLRETIESDERKRETLRSEVGEARDSVEEIRDRIEKKraettldEVTSDAIAARRDELDEREA 324
                                       33444444555555555555555555555555555555555555555555534433333333333333333333334 PP

                              Fez1  98 elreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkee 147
                                       e+r++l+++ ++++               ++++++l+++ e+ +++ +e+
  gi|313127099|ref|YP_004037369.1| 325 EIRSDLTDVRERRTML-------------SNQAKKLRERAEEFESRAAEK 361
                                       4444444433332222.............223333333333333333333 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0057
                              Fez1  37 kaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeea 113
                                        ++  e r++ +e ++ ++++ee+le++++ le++e+el+  ++e e    +++++ +   e+re+l+++ +e +e+
  gi|313127099|ref|YP_004037369.1| 355 ESRAAEKRSRADELDDDAEDAEEELEQRSARLEELEAELESLTAEFEDAPVELGEAASHRDEVRETLTDVRAELTET 431
                                       34445666666777777777777777777777777777777766665555555555555555555555555554444 PP

                              Fez1 114 a.......lesdeakaqrqe...............aeeleelkreverlraeLkeerqkkeeqass 157
                                       +        + +ea++ r+e                ++++e ++++e+l+a L+  r+++e+ +s 
  gi|313127099|ref|YP_004037369.1| 432 NaegenvrDRLTEARELRDEgkcpecgqpvedsphVDSIGEYEARIEELEATLSDLRERRETLNSR 497
                                       42222222444444444444888899999999998999********************99987665 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.099
                              Fez1  42 elrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa.... 114
                                       e  ++l e+e++i el++s+e  ++ +e   + ++++++eae+lre ++kle+e  e r++++++++ +e+aa    
  gi|313127099|ref|YP_004037369.1| 499 ERAESLVETENRIGELRNSRELFEQRIEDARETVEERRTEAETLREAADKLEAEADEKRTAATTQAEAAEDAAetve 575
                                       55678999999*********999********************************9999988887666666556667 PP

                              Fez1 115 .....lesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqERrtWqee 168
                                            l  +++ + +++ ++l++l++++ + ++e++  ++++e+  ++ ++ERr    e
  gi|313127099|ref|YP_004037369.1| 576 glesdL--ESVAEAESRLDTLSDLRSKLTETESEIERLEERRESI-AELNDERRERLAE 631
                                       755331..2222333334566666666666666666666665554.5566777665555 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.047
                              Fez1  22 sqaevtqklseivalkaqlrelrakleeke...eeikeleesleektlelevcenelqrk.........kseaellr 86 
                                       s ae  ++l+ +  l+++l e+++++e+ e   e+i el+++++e+ +e     +el+ +         k+++e  +
  gi|313127099|ref|YP_004037369.1| 583 SVAEAESRLDTLSDLRSKLTETESEIERLEerrESIAELNDERRERLAEKRDRRSELADEvdestveeaKAKKEKAE 659
                                       66899999999999******999887665511156778888888888885555555544433222222233333333 PP

                              Fez1  87 ekvekleeelkelreelselsleeeeaa..........lesdeakaqrqe.......aeeleelkreverlraeLke 146
                                       + +e+++eel+ lre+  +l       +          ++ ++ ++ r+e        e+l+++++e+e + + L+ 
  gi|313127099|ref|YP_004037369.1| 660 NYLEQVDEELATLREKRDSL-------QsdiggvngelEQLEALREDRDElaarvdaLESLHAETEELEAMYGDLRA 729
                                       33334444444444333332.......22333334444223333333333444433344555555555555557777 PP

                              Fez1 147 erqkke 152
                                       e ++++
  gi|313127099|ref|YP_004037369.1| 730 ELRQRN 735
                                       766654 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  11.8   0.00088      0.51      37     132 ..     203     298 ..     195     313 .. 0.87
   2 ?    6.7  15.1    0.0071       4.1      76     192 ..     318     434 ..     295     442 .. 0.78
   3 ?    1.7  10.9      0.25   1.4e+02      52     125 ..     473     556 ..     464     587 .. 0.47
   4 ?    2.0  22.4      0.19   1.1e+02      23     127 ..     589     695 ..     585     747 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00088
                               GAS  37 elkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleq 113
                                        l ++ ++ e el e+  + +r++++ +ka e +e+ ++ l++y++++++l++l + + +l + +++ + + e l+ 
  gi|313127099|ref|YP_004037369.1| 203 GLHERLNALETELGEVDDQIERYEDQREKAVETRENAEEVLETYREKRAELDELAEDIADLRETIESDERKRETLRS 279
                                       56788899999999999999999999999999999999999999999999999999999999999999999999999 PP

                               GAS 114 rfekvekerdelykkfeaa 132
                                       ++ ++ ++ +e++++ e++
  gi|313127099|ref|YP_004037369.1| 280 EVGEARDSVEEIRDRIEKK 298
                                       9988888888888877765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0071
                               GAS  76 qlknye.kdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekkl 151
                                       +l + e + +++l+ +++r ++l ++ k+l++ +e  e r ++  +  del +  e+a +e+ q++  +   Le  l
  gi|313127099|ref|YP_004037369.1| 318 ELDEREaEIRSDLTDVRERRTMLSNQAKKLRERAEEFESRAAEKRSRADELDDDAEDAEEELEQRSA-RLEELEAEL 393
                                       4444441457889999999999999999999999999999999999999999999999999999986.555689999 PP

                               GAS 152 kalqeelEkkeaqleevlaaanldpaalsavsekleevles 192
                                       ++l++e E + ++l e+ ++ +   ++l+ v+++l+e+ ++
  gi|313127099|ref|YP_004037369.1| 394 ESLTAEFEDAPVELGEAASHRDEVRETLTDVRAELTETNAE 434
                                       99999999999999999999998899999999999887655 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.25
                               GAS  52 isqenkrlkepLkkaeeeveeLrkqlknye..........kdkqslknlkarlkelekelkdlkwehevleqrfekv 118
                                       ++++ ++l+ +L  ++e +e L+ +l++ e          + ++s +  ++r++++ + +++ + e+e l++  +k+
  gi|313127099|ref|YP_004037369.1| 473 YEARIEELEATLSDLRERRETLNSRLERAEslvetenrigELRNSRELFEQRIEDARETVEERRTEAETLREAADKL 549
                                       33444444444444444444444433333300000000002223333334555555555555555566666666666 PP

                               GAS 119 ekerdel 125
                                       e+e de 
  gi|313127099|ref|YP_004037369.1| 550 EAEADEK 556
                                       5555553 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.19
                               GAS  23 nNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlk..nyekdkqslknlkarlkel 97 
                                       + L++   l+++++e + + er e + + i++ n + +e L + +  + eL  ++   + e+ k++ +++++ l+++
  gi|313127099|ref|YP_004037369.1| 589 SRLDTLSDLRSKLTETESEIERLEERRESIAELNDERRERLAEKRDRRSELADEVDesTVEEAKAKKEKAENYLEQV 665
                                       579999*********************************************9977511678999999999999**** PP

                               GAS  98 ekelkdlkwehevleqrfekvekerdelyk 127
                                       ++el +l+++ ++l+  +  v  e ++l++
  gi|313127099|ref|YP_004037369.1| 666 DEELATLREKRDSLQSDIGGVNGELEQLEA 695
                                       **************9888777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (894 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2489  (0.138825); expected 358.6 (0.02)
Passed bias filter:                      808  (0.0450667); expected 358.6 (0.02)
Passed Vit filter:                       284  (0.0158403); expected 17.9 (0.001)
Passed Fwd filter:                       181  (0.0100954); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 3.94u 0.42s 00:00:04.36 Elapsed: 00:00:00.93
# Mc/sec: 2900.87
//
Query:       gi|313127100|ref|YP_004037370.1|  [L=476]
Description: DNA repair exonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-11   42.7   1.9    9.1e-11   42.2   0.6    1.9  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.4e-10   41.2   1.5    3.6e-10   40.7   1.5    1.4  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.6     1e-14   9.1e-11       2     164 ..       3     221 ..       2     222 .. 0.75
   2 ?   -3.3   0.0      0.98   8.8e+03      17      48 ..     249     284 ..     247     296 .. 0.62

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1e-14
                     Metallophos_2   2 klaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeep.........evleellela.pv 54 
                                       ++++  D+H             + lda e+v++++ + +vda++haGDl  ++ p         ++l++l + + p+
  gi|313127100|ref|YP_004037370.1|   3 RVIHTGDTHigyqqyhsperrrDFLDAFEQVVADAIADDVDAVVHAGDLfHDRRPelrdllgtiSILRQLDDAEiPF 79 
                                       578899999999999999999999999*******99999*********88777776666666556888888877*** PP

                     Metallophos_2  55 laVrGNnD...........eev.veedvlreaaelgtdl.......peeaelel........agekvlliHgdpl.. 102
                                       laV GN++           e+  ++e++++ ++ +g+         p++++ +l        a   +l+ Hg     
  gi|313127100|ref|YP_004037370.1|  80 LAVVGNHEstrggqwldlfENLgLAERLGDDPHVVGDTAfygldhvPKARRDDLaydfephdAAHAALVGHGL-Ftp 155
                                       *************999998555677777777777766666777778544444444343443344449999998.336 PP

                     Metallophos_2 103 ..gvkdalaellke...aeegsd..vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe..tyaildtde 164
                                         +     a+   e   +e++++   ++ G  H p+ e+ +g++v + Gs ++++ +++e  +y +++ d+
  gi|313127100|ref|YP_004037370.1| 156 faH-----ADWETEtvlGESNVAfdAFLIGDNHAPGTEQVDGTWVTYCGSTERASAAETEarGYNLVTFDD 221
                                       532.....22222222233444448*****************************99998888777777665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.98
                     Metallophos_2  17 eavlealkevgvdaiihaGDl....eeeepevleel 48 
                                       e+v e++++++vd  +   ++    e ++p ++ee+
  gi|313127100|ref|YP_004037370.1| 249 ERVREQVRQHDVDDAVAIVEItgegEPVTPASIEEF 284
                                       567777777777777766666532233344455555 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   1.5     4e-14   3.6e-10       2     108 ..       3     104 ..       2     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4e-14
                                       EEEEEESBTB....TTCCTHHHHHHHHHHHH....HHHTTESEEEEESTSSSSS......HHHHHHHHH.HHHHHHH CS
                       Metallophos   2 rilvigDlHl....algggqlddllkllddl....lreekpdlvllaGDlvdrg......dlekellel.laalvky 63 
                                       r++++gD+H+     + +++ +d+l++++++    +++ ++d+v++aGDl+++                 ++ l ++
  gi|313127100|ref|YP_004037370.1|   3 RVIHTGDTHIgyqqYHSPERRRDFLDAFEQVvadaIAD-DVDAVVHAGDLFHDRrpelrdL------LGtISILRQL 72 
                                       89************666666666666666664442555.************9995655431......2223333333 PP

                                       ...TSEEEEEC-TTS.........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEE CS
                       Metallophos  64 ...pipvylllGNHe.........gfeeellnkygylgifsepwrsdaevfnnlpla 108
                                           ip+ ++ GNHe                                   f+nl la
  gi|313127100|ref|YP_004037370.1|  73 ddaEIPFLAVVGNHEstrggqwldL-------------------------FENLGLA 104
                                       44488**********6655433332.........................3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2940.17
//
Query:       gi|313127101|ref|YP_004037371.1|  [L=105]
Description: hypothetical protein Hbor_23670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 789.91
//
Query:       gi|313127102|ref|YP_004037372.1|  [L=87]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-06   26.9   0.0    3.9e-06   26.3   0.0    1.2  1  HTH_24        Winged helix-turn-helix DNA-binding
    9.2e-05   22.3   0.1    0.00012   21.9   0.1    1.2  1  MarR_2        MarR family
    0.00035   20.6   0.0    0.00047   20.2   0.0    1.3  1  HTH_20        Helix-turn-helix domain
      0.001   18.7   0.1     0.0014   18.2   0.1    1.2  1  GntR          Bacterial regulatory proteins, gntR family
     0.0041   17.0   0.0     0.0062   16.4   0.0    1.2  1  MarR          MarR family
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.035   14.0   0.0    1.2  1  HTH_5         Bacterial regulatory protein, arsR family
      0.025   14.2   0.0      0.054   13.2   0.0    1.5  1  Sigma70_r4_2  Sigma-70, region 4
      0.034   14.5   0.0      0.044   14.1   0.0    1.2  1  Rrf2          Transcriptional regulator
      0.035   14.0   0.0      0.041   13.7   0.0    1.1  1  TFIIE_alpha   TFIIE alpha subunit
      0.039   14.1   0.0       0.12   12.5   0.0    1.8  2  HTH_28        Helix-turn-helix domain
      0.083   12.7   0.1       0.14   12.0   0.1    1.3  1  HTH_IclR      IclR helix-turn-helix domain
      0.089   12.7   0.0       0.11   12.3   0.0    1.2  1  TrmB          Sugar-specific transcriptional regulator TrmB
       0.14   12.1   0.1       0.18   11.7   0.1    1.2  1  HTH_11        HTH domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.8e-09   3.9e-06      11      44 ..      33      66 ..      31      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.8e-09
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeee 44
                                      +L  n  ++q++LAe++ l+p tv++ l rLee+
  gi|313127102|ref|YP_004037372.1| 33 VLDYNETLTQSQLAEETLLPPRTVRYALSRLEEA 66
                                      5777999*************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   8.8e-08   0.00012      10      54 ..      30      72 ..      21      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.8e-08
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      v  +L  ++   lt+++la+++ l++ +v ++l rL++a  v  r
  gi|313127102|ref|YP_004037372.1| 30 VAKVLDYNET--LTQSQLAEETLLPPRTVRYALSRLEEADAVNSR 72
                                      5556677777..***************************988666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.4e-07   0.00047      19      57 ..      34      72 ..      25      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.4e-07
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      L  +e lt s+lae+  l++ t++y L  Leea++v ++
  gi|313127102|ref|YP_004037372.1| 34 LDYNETLTQSQLAEETLLPPRTVRYALSRLEEADAVNSR 72
                                      567899999******99*******************987 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1     1e-06    0.0014      12      56 ..      28      71 ..      26      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1e-06
                                      HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                      ++++++l  +++L ++++La+e      tvR AL+rLe+++ v +
  gi|313127102|ref|YP_004037372.1| 28 KLVAKVLDYNETL-TQSQLAEETLLPPRTVRYALSRLEEADAVNS 71
                                      688889999****.*************************999976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.5e-06    0.0062      12      57 ..      34      79 ..      30      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.5e-06
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                      l++++ l++s+La+   + + tv  +l rLe+++ ++++ s +D R
  gi|313127102|ref|YP_004037372.1| 34 LDYNETLTQSQLAEETLLPPRTVRYALSRLEEADAVNSRFSFSDAR 79
                                      78999*********************************99999999 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.5e-05     0.035      15      47 .]      38      71 ..      28      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                                      S.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 15 e.lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      e l+ ++laee+ l++ tv++ L++L+ea+ V++
  gi|313127102|ref|YP_004037372.1| 38 EtLTQSQLAEETLLPPRTVRYALSRLEEADAVNS 71
                                      44899************************98875 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.9e-05     0.054      21      49 ..      34      62 ..      33      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                                      HHHTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrlsR 49
                                      l y e l++ + Ae++ ++++tV+++lsR
  gi|313127102|ref|YP_004037372.1| 34 LDYNETLTQSQLAEETLLPPRTVRYALSR 62
                                      6677889********************99 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.2e-05     0.044      23      58 ..      37      72 ..      27      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      +e+++ +++ae++ ++p+ ++  l++L++a+ v+s+
  gi|313127102|ref|YP_004037372.1| 37 NETLTQSQLAEETLLPPRTVRYALSRLEEADAVNSR 72
                                      556999***************************996 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     3e-05     0.041      14      60 ..      26      72 ..      20      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkyk 60
                                      +a+lv +vL  +  +t  +la+e+ + +  +r +L rL ea  v+ +
  gi|313127102|ref|YP_004037372.1| 26 SAKLVAKVLDYNETLTQSQLAEETLLPPRTVRYALSRLEEADAVNSR 72
                                      6889999*********************************9888765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.9   2.6e+03      20      32 ..       5      17 ..       2      19 .. 0.83
   2 ?   12.5   0.0   8.6e-05      0.12      11      38 ..      38      65 ..      27      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                            HTH_28 20 relgisrrtvyrW 32
                                      + +g+++ t  rW
  gi|313127102|ref|YP_004037372.1|  5 EVVGTDEGTTDRW 17
                                      6789999999999 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.6e-05
                            HTH_28 11 aGhsvreaArelgisrrtvyrWikryee 38
                                      +  +++++A+e  + +rtv+  ++r+ee
  gi|313127102|ref|YP_004037372.1| 38 ETLTQSQLAEETLLPPRTVRYALSRLEE 65
                                      34499*********************99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0001      0.14      16      46 ..      37      67 ..      30      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelG 46
                                      ++ lt s+lA++t lp+ tv+  L+ L+e  
  gi|313127102|ref|YP_004037372.1| 37 NETLTQSQLAEETLLPPRTVRYALSRLEEAD 67
                                      67899**********************9976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.3e-05      0.11      18      54 ..      34      71 ..      27      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.3e-05
                                      H.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 18 l.klgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      l  ++ +t +++aee+ +p  +v  +L++Le+++ V+ 
  gi|313127102|ref|YP_004037372.1| 34 LdYNETLTQSQLAEETLLPPRTVRYALSRLEEADAVNS 71
                                      457899*****************************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00013      0.18       4      42 ..      28      66 ..      26      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      +++  +l+ +++++ ++LAee+ +  rtvr  + +Lee+
  gi|313127102|ref|YP_004037372.1| 28 KLVAKVLDYNETLTQSQLAEETLLPPRTVRYALSRLEEA 66
                                      56666779999*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 655.00
//
Query:       gi|313127103|ref|YP_004037373.1|  [L=405]
Description: proteasome-activating nucleotidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-46  156.2   1.4    1.1e-45  155.3   0.0    2.1  2  AAA              ATPase family associated with various cellul
    3.1e-12   46.1   0.5    1.1e-11   44.3   0.5    2.0  1  AAA_lid_3        AAA+ lid domain
    2.9e-09   37.3   0.0    1.1e-08   35.4   0.0    2.0  1  AAA_2            AAA domain (Cdc48 subfamily)
    1.5e-07   31.5   0.2    1.4e-06   28.4   0.2    2.5  1  AAA_5            AAA domain (dynein-related subfamily)
    6.6e-07   29.2   0.0    1.6e-06   28.0   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      7e-06   26.5   4.4    0.00024   21.6   0.0    3.4  3  AAA_16           AAA ATPase domain
    1.6e-05   24.7   0.2    3.5e-05   23.7   0.2    1.6  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    3.1e-05   24.3   3.1    0.00058   20.1   0.0    2.8  2  AAA_22           AAA domain
    9.2e-05   21.7   0.0    0.00021   20.6   0.0    1.7  1  DUF815           Protein of unknown function (DUF815)
    0.00017   21.6   0.2      0.002   18.2   0.0    2.2  2  AAA_14           AAA domain
    0.00019   21.9   5.2      0.044   14.2   0.0    2.6  2  AAA_17           AAA domain
    0.00022   21.8   1.3     0.0032   18.0   0.0    2.7  2  AAA_18           AAA domain
    0.00064   19.2   0.2     0.0036   16.7   0.1    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00087   19.0   7.1    0.00087   19.0   7.1    1.7  1  GrpE             GrpE
     0.0013   18.5   0.1      0.025   14.3   0.1    2.6  1  Sigma54_activat  Sigma-54 interaction domain
     0.0026   17.0   2.6     0.0045   16.2   0.1    2.4  2  TIP49            TIP49 P-loop domain
      0.003   17.3   4.2     0.0046   16.7   0.1    2.8  2  AAA_24           AAA domain
     0.0035   17.1   0.0       0.01   15.6   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
     0.0041   17.5   0.0      0.011   16.1   0.0    1.8  1  RNA_helicase     RNA helicase
     0.0056   16.9   0.8      0.014   15.7   0.0    2.2  1  AAA_28           AAA domain
     0.0059   16.5   0.7      0.072   12.9   0.0    2.9  2  AAA_3            ATPase family associated with various cellul
     0.0079   16.1   0.1       0.09   12.7   0.0    2.4  2  NACHT            NACHT domain
      0.009   16.1  10.9      0.031   14.4  10.9    1.9  1  Cep57_CLD_2      Centrosome localisation domain of PPC89
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.029   14.5   0.0    1.9  1  AAA_33           AAA domain
      0.017   14.6   1.6      0.033   13.7   0.1    2.2  2  AAA_7            P-loop containing dynein motor region
      0.019   14.1   2.8      0.027   13.6   2.8    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.02   15.4   4.3      0.066   13.7   4.3    1.9  1  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
      0.022   14.8   0.0      0.043   13.8   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.03   13.7   0.0          1    8.7   0.0    2.6  2  TniB             Bacterial TniB protein
       0.03   13.4   0.0      0.059   12.4   0.0    1.4  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.031   14.2   3.1       0.88    9.5   0.1    3.2  4  NTPase_1         NTPase
      0.032   13.6   7.1       0.18   11.1   0.0    3.3  3  ATPase           KaiC
      0.034   14.0   2.5       0.72    9.7   0.0    2.9  3  ATPase_2         ATPase domain predominantly from Archaea
      0.039   12.6   6.7        4.7    5.7   0.0    2.2  2  AAA_13           AAA domain
      0.044   13.9   0.2       0.18   12.0   0.0    2.1  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.051   13.2   0.1      0.087   12.5   0.1    1.4  1  DUF2334          Uncharacterized protein conserved in bacteri
      0.054   13.2   0.2       0.19   11.5   0.2    2.0  1  AAA_30           AAA domain
      0.057   14.2   1.8        1.1   10.1   2.1    2.5  2  Occludin_ELL     Occludin homology domain
      0.069   12.5   6.0       0.14   11.5   6.0    1.4  1  DUF4407          Domain of unknown function (DUF4407)
      0.075   11.9   6.6       0.12   11.2   6.6    1.3  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
      0.078   12.4   0.0       0.15   11.5   0.0    1.4  1  Creatininase     Creatinine amidohydrolase
      0.098   12.8  12.0       0.28   11.3   1.5    2.8  2  bZIP_1           bZIP transcription factor
       0.11   12.3   2.9       0.32   10.8   2.9    1.8  1  DUF724           Protein of unknown function (DUF724)
       0.11   12.2   9.7        0.2   11.4   9.7    1.4  1  SHE3             SWI5-dependent HO expression protein 3
       0.12   11.9  10.9       0.21   11.2   0.1    3.9  4  AAA_25           AAA domain
       0.13   12.4   8.0       0.33   11.0   8.0    1.6  1  ADIP             Afadin- and alpha -actinin-Binding
       0.16   12.6   6.5         61    4.3   7.8    2.8  2  YabA             Initiation control protein YabA
       0.16   11.7   0.1       0.16   11.7   0.1    2.3  2  AAA_11           AAA domain
       0.35   11.4   0.0       0.35   11.4   0.0    2.6  1  ABC_tran         ABC transporter
       0.55    9.9  11.0       0.79    9.4  10.3    1.6  1  DUF4201          Domain of unknown function (DUF4201)
        0.6    9.3   3.7         10    5.2   0.0    2.8  3  KAP_NTPase       KAP family P-loop domain
        1.3    9.5   5.6         29    5.1   0.0    3.4  3  FlaC_arch        Flagella accessory protein C (FlaC)
        2.2    7.2   6.4        2.8    6.8   4.6    1.9  2  DUF3987          Protein of unknown function (DUF3987)
        5.7    6.2  16.2        3.2    7.0  14.1    1.7  1  GAS              Growth-arrest specific micro-tubule binding
        6.2    7.3  15.4       0.32   11.5   9.4    1.9  1  APG6_N           Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3       8.2   2.7e+03      58      93 ..      69     109 ..      22     136 .. 0.58
   2 !  155.3   0.0   3.4e-48   1.1e-45       1     131 [.     186     318 ..     186     319 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 8.2
                                       TSEEEEEETGGGHHHHH.....TTCCCHHHHHHHHHHHHHH CS
                               AAA  58 kpsilfiDEidalaksr.....sgseseeeervvnqLltel 93 
                                       k+s lf+  + +++ +      +g+++e  ++v ++L + l
  gi|313127103|ref|YP_004037373.1|  69 KQSPLFVATVQEITDEGviikqHGNNQEALTEVTDELREDL 109
                                       34555555555554444433334444444445555554444 PP

  == domain 2  score: 155.3 bits;  conditional E-value: 3.4e-48
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vllyGppGtGKT+lakava++++++f+++ gsel+ k++ge++k +r+lf+ a+e++ p ++fiDEida+a++r   
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQTNASFIKMAGSELVHKFIGEGAKLVRDLFEVARENE-PAVIFIDEIDAIASKRtds 261
                                       79******************************************************8.****************986 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++s + e +r++ qLl+e+dg++++ +++ +i+atnr d+ldpa+lr gRfdr ie++
  gi|313127103|ref|YP_004037373.1| 262 KTSGDAEVQRTMMQLLSEMDGFEER-GDIRIIAATNRFDMLDPAILRpGRFDRLIEVP 318
                                       666888999***************7.66***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.5   3.3e-14   1.1e-11       1      43 [.     341     383 ..     341     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.3e-14
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                       dvd+++LAe+ +  SGAD +a+c eA++ A+r++++ei m df
  gi|313127103|ref|YP_004037373.1| 341 DVDFHQLAEMADEASGADVKAICTEAGMFAIRDDRTEIYMGDF 383
                                       9****************************************99 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   3.4e-11   1.1e-08       4     104 ..     184     278 ..     181     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3.4e-11
                                       --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGG CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEid 78 
                                       + +ll gp g+Gkt+laka+a+  ++    ++i +  sel      e ++lv  l        + +e  ++++DEid
  gi|313127103|ref|YP_004037373.1| 184 SGVLLYGPPGTGKTMLAKAVANQTNA----SFIKMAGSELVHkfIGEGAKLVRDL----FEVARENEPAVIFIDEID 252
                                       567999******************95....8999999999882222333333333....3344556677******** PP

                                       G-------------HHHHHHHHHHHH CS
                             AAA_2  79 KihpkessgadvSregVqrdLLqile 104
                                        i++k++ ++     +Vqr ++q+l 
  gi|313127103|ref|YP_004037373.1| 253 AIASKRTDSKTSGDAEVQRTMMQLLS 278
                                       ****87777777888*********96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.2   4.3e-09   1.4e-06       1     133 [.     185     304 ..     185     308 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.3e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL GppGtgK++la+ +a  +n+++  +++++      l+ +    +g +  +d   v   +e++++++DE++ +
  gi|313127103|ref|YP_004037373.1| 185 GVLLYGPPGTGKTMLAKAVANQTNASFIKMAGSE------LVHKFI-GEGAKLVRDLFEVARENEPAVIFIDEIDAI 254
                                       59************************99888876......666666.23444445544444445************9 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE.---........-EEEEEESS--.-TT-TTHH CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvk.aknddller..frviatanpldrslnelspa 133
                                        s+ ++s  s   e ++ ++++  +++ +++     r  +r+ia++n+ d     l+pa
  gi|313127103|ref|YP_004037373.1| 255 ASKRTDSKTSGDAEVQRTMMQLLSEMDgFEE-----RgdIRIIAATNRFD----MLDPA 304
                                       9666666555544444444555555540333.....33499999999887....55555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   4.8e-09   1.6e-06      34      98 ..     184     256 ..     156     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4.8e-09
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl......eekdvlfideihrlsr 98 
                                         vllyGpPG Gkt lak +a++ ++++   +g  l ++  g+ a l+ +l      +e  v+fidei  +++
  gi|313127103|ref|YP_004037373.1| 184 SGVLLYGPPGTGKTMLAKAVANQTNASFIKMAGSELVHKfiGEGAKLVRDLfevareNEPAVIFIDEIDAIAS 256
                                       569**********************997666665544332355555544442223223446*******98765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.0       4.9   1.6e+03     103     103 ..      60      60 ..       4     136 .. 0.53
   2 !   21.6   0.0   7.2e-07   0.00024      15      51 ..     174     210 ..     153     228 .. 0.82
   3 ?    4.3   0.0      0.14        46     122     149 ..     230     256 ..     226     283 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4.9
                            AAA_16 103 e 103
                                       +
  gi|313127103|ref|YP_004037373.1|  60 R 60 
                                       1 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 7.2e-07
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                       ++++v  + p+ vll+G++G+GK+ l+++++++ +++
  gi|313127103|ref|YP_004037373.1| 174 MFDQVGIQPPSGVLLYGPPGTGKTMLAKAVANQTNAS 210
                                       45666666679*******************9876655 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.14
                            AAA_16 122 llkrllallsrderplvlvlDdlqwade 149
                                       l+++l++ +++  +p v+++D+++ + +
  gi|313127103|ref|YP_004037373.1| 230 LVRDLFEVARE-NEPAVIFIDEIDAIAS 256
                                       45666788888.777*********6554 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.2   1.1e-07   3.5e-05       1      48 [.      75     120 ..      75     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.1e-07
                                       EEEEEEE-TTSSEEEEE-TT.S-EEEEEE-GGGSSST--TTEEEEEETT CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktss.deevvvslagavpremLrpgDlVavdkd 48 
                                       VatV E+ d+  ++i+k+++  +e +  +++ ++ e+L p  +Vav+++
  gi|313127103|ref|YP_004037373.1|  75 VATVQEITDE--GVIIKQHGnNQEALTEVTDELR-EDLEPDSRVAVNNS 120
                                       9*******75..******99788**********9.88**********85 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.8e-06   0.00058       8      43 ..     186     212 ..     181     235 .. 0.80
   2 ?    3.9   0.1      0.19        62      86     125 ..     238     291 ..     224     297 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.8e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                                       ++++G++GtGKT+l++ +++q          +++++
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQT---------NASFI 212
                                       689******************8.........33333 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.19
                            AAA_22  86 lraravielliiDEaqhlr.....s.........eealeeLrsllnl.srkgvql 125
                                       +r+   ++++ iDE++ +      s          ++++ L+++  + +r ++++
  gi|313127103|ref|YP_004037373.1| 238 ARENE-PAVIFIDEIDAIAskrtdSktsgdaevqRTMMQLLSEMDGFeERGDIRI 291
                                       33333.58*********98665541556666676777777766665565666655 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   6.4e-07   0.00021      15     116 ..     136     251 ..     124     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.4e-07
                            DUF815  15 alepveevdevklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallneyaeegL 82 
                                       ++  ve+   v+ +d+ g+++q +++ e +e  le          +p + vLL+G  GtGK  l ka+ n+++++ +
  gi|313127103|ref|YP_004037373.1| 136 RVMQVEHSPDVSYADIGGLEQQMQEVRETVEMPLESpemfdqvgiQPPSGVLLYGPPGTGKTMLAKAVANQTNASFI 212
                                       57789999999999999999999999998876554322222222378899*************************98 PP

                            DUF815  83 rli..evekedlkelpklvellr...erperfilfvDDL 116
                                       ++   e+ ++ + e  klv+ l    +++e  ++f+D +
  gi|313127103|ref|YP_004037373.1| 213 KMAgsELVHKFIGEGAKLVRDLFevaRENEPAVIFIDEI 251
                                       886448888888888888876541226677889999975 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2       1.4   4.7e+02      53     121 ..      59     141 ..      19     144 .. 0.54
   2 !   18.2   0.0   6.2e-06     0.002       5      77 ..     186     255 ..     184     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.4
                            AAA_14  53 lelileklkeekktylflDEiqev..............pewekalkslvdeg..knldvivtGSnskllskeiatsl 113
                                       ++l  e+ k+ k++ lf   +qe+              + + ++  +l + +  ++ +v v  S+s ++  + +t++
  gi|313127103|ref|YP_004037373.1|  59 ERLTHEN-KKLKQSPLFVATVQEItdegviikqhgnnqEALTEVTDELRE-DlePDSRVAVNNSLSIVKRLDNETDV 133
                                       2333332.223444566666666666666666665443222222222332.22466788888888888888888888 PP

                            AAA_14 114 agrvaeie 121
                                       + rv ++e
  gi|313127103|ref|YP_004037373.1| 134 RARVMQVE 141
                                       88877766 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 6.2e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       +++ G+  +GKT+l+k ++++      s++ ++  +   k + + +kl + ++e ++e++  ++f+DEi  + 
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQTN---ASFIKMAGSELVHKFIGEGAKLVRDLFEVARENEPAVIFIDEIDAIA 255
                                       6799**************98777...99999999887776666666888888887666799********9875 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.6     0.015       4.8      35     128 ..      50     137 ..      20     143 .. 0.74
   2 !   14.2   0.0   0.00013     0.044       1      68 [.     189     257 ..     189     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.015
                                       HTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE-- CS
                            AAA_17  35 krgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevleelkpdaiillead 111
                                       ++   +k ++++++l +e kk  q  +  +  +e  ++gv+++ h    +++++l ++++e  e+l+pd  + ++ +
  gi|313127103|ref|YP_004037373.1|  50 EN---NKYQQKLERLTHENKKLKQSPLFVATVQEITDEGVIIKQHG---NNQEALTEVTDELREDLEPDSRVAVNNS 120
                                       33...344566666666666665655555555556789*******9...57889********************999 PP

                                       HHHHHHHHHHH.TTST-T CS
                            AAA_17 112 peeilerrlkd.rtrgrd 128
                                          i++r+ ++ + r r 
  gi|313127103|ref|YP_004037373.1| 121 LS-IVKRLDNEtDVRARV 137
                                       96.888887763336654 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00013
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklpleekkelqkeaaekiaee 68 
                                       +G+PG GK+ +++ ++ + + +++ + G+ l      +g++  rd ++ + ++e   +    +++ia +
  gi|313127103|ref|YP_004037373.1| 189 YGPPGTGKTMLAKAVANQTNASFIKMaGSELVHKFIGEGAKLVRDLFEVARENEPAVIFIDEIDAIASK 257
                                       7***********************877999998888888877888887655555544444444445544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.1       2.3   7.6e+02      52      69 ..      36      53 ..       2      99 .. 0.52
   2 !   18.0   0.0   9.7e-06    0.0032       1      45 [.     186     258 ..     186     296 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.3
                            AAA_18 52 ldedkldklldaleenss 69
                                       +e+++dkllda+ en++
  gi|313127103|ref|YP_004037373.1| 36 QNEEMRDKLLDANAENNK 53
                                      233333333333333333 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 9.7e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......a 45 
                                       +ll G+pG+GKt lak++++ ++                      ++ l +va+en++   + +e        
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQTNAsfikmagselvhkfigegaklVRDLFEVARENEPAVIFIDEidaiaskR 258
                                       799***************9998445888898888877788877777777777777777776666665554442 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.1     1e+03      47      94 ..     107     154 ..      90     161 .. 0.72
   2 !   16.7   0.1   1.1e-05    0.0036      25      43 ..     186     204 ..     178     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.1
                      Mg_chelatase  47 pplseeealevakiasvagkkeeekllkrrpfraphhsaskaalvGgg 94 
                                        +l+ +  + v++  s++++ ++e+ +++r ++  h    + a +Gg 
  gi|313127103|ref|YP_004037373.1| 107 EDLEPDSRVAVNNSLSIVKRLDNETDVRARVMQVEHSPDVSYADIGGL 154
                                       456666777788888888888888888888888888877777777775 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.1e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKtmlak+++
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVA 204
                                       79*************9975 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   7.1   2.7e-06   0.00087       5      68 ..      14      77 ..       9     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.7e-06
                                      ..CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE  5 eeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdL 68
                                      e+ +++++++++l+e+l+ le++ +e+ +kll ++ae  ++++++e+   e kk + + ++ + 
  gi|313127103|ref|YP_004037373.1| 14 EDAASQQEKIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQSPLFVAT 77
                                      67899*******************************************9999998888776554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   7.8e-05     0.025      21      56 ..     182     214 ..     153     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.8e-05
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvav 56 
                                        ++ vl+ G  GtGK++la+a+ ++++   ++f+++
  gi|313127103|ref|YP_004037373.1| 182 PPSGVLLYGPPGTGKTMLAKAVANQTN---ASFIKM 214
                                       3488*****************987655...555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.7   8.8e+02     235     263 ..      82     110 ..      59     119 .. 0.76
   2 !   16.2   0.1   1.4e-05    0.0045      52      89 ..     185     220 ..     182     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.7
                                       XXXXXXXXX....XXXXXXXXXXXXXXXX CS
                             TIP49 235 rpqdllslllqllkskkteiteklreein 263
                                         ++++   + +++   te+t++lre+++
  gi|313127103|ref|YP_004037373.1|  82 TDEGVIIKQHGNNQEALTEVTDELREDLE 110
                                       446777777778889999*******9875 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevy 89 
                                       +vLl Gp+gtGkt la a++++ +    f++++gse+ 
  gi|313127103|ref|YP_004037373.1| 185 GVLLYGPPGTGKTMLAKAVANQTN--ASFIKMAGSELV 220
                                       79******************9976..78*******986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.77   2.5e+02      98     189 ..      44     144 ..      23     147 .. 0.59
   2 !   16.7   0.1   1.4e-05    0.0046       5      77 ..     186     254 ..     183     292 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.77
                            AAA_24  98 kgdgkG.ygelaeefrrllkklqelrknvifiahektrkdedpegeakytrlepklgkktanelkeevDlvlranlk 173
                                         d+++   ++++++ rl    ++l++   f+a  ++ +de           ++k++   +++l+e  D++ + +l+
  gi|313127103|ref|YP_004037373.1|  44 LLDANAeNNKYQQKLERLTHENKKLKQSPLFVATVQEITDEGV---------IIKQHGNNQEALTEVTDELRE-DLE 110
                                       5556666667778888888888888888888888888888755.........444444444555555555443.333 PP

                            AAA_24 174 red..................kvgervlktskse 189
                                         +                  +v  rv++ ++s+
  gi|313127103|ref|YP_004037373.1| 111 PDSrvavnnslsivkrldnetDVRARVMQVEHSP 144
                                       2223344444444444444447777777777765 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.4e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                       +l+yGp+g+GKT+lak    + ++ fi + ++    +++     e+ + ++d ++  +++++   +++iD id +
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVanQTNASFIKMAGSELVHKFIG----EGAKLVRDLFEVARENEP--AVIFIDEIDAI 254
                                       79**************997777777776655433322222....244555555555544444..67777777765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.1e-05      0.01      48      71 ..     184     207 ..     173     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.1e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                        +++l Gp+G+GK+ la a++ ++
  gi|313127103|ref|YP_004037373.1| 184 SGVLLYGPPGTGKTMLAKAVANQT 207
                                       6799***************99875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.5e-05     0.011       1      64 [.     186     240 ..     186     273 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.5e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkde 64 
                                       ++lyGp+g+GK++lak +a+         +++  +++ + ++ ++++ g+ + ++ D+ +v  e
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVAN---------QTNASFIKMAGSELVHKFIGEGAKLVRDLFEVARE 240
                                       689**************444.........44455556666677777776666666666666655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.3e-05     0.014       2      36 ..     186     221 ..     185     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.3e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareile 36 
                                       + + G+++tGKT l++a a++ + + ++ a+ e++ 
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQtNASFIKMAGSELVH 221
                                       6799***************87677777766666664 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.1   6.7e+02      16      51 ..     124     161 ..     118     178 .. 0.66
   2 !   12.9   0.0   0.00022     0.072       2      30 ..     186     214 ..     185     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.1
                             AAA_3  16 vkalakaldl..efkriqftpdllPsdilGtevfeeke 51 
                                       vk l +  d+  ++ ++   pd+  +di G e   ++ 
  gi|313127103|ref|YP_004037373.1| 124 VKRLDNETDVraRVMQVEHSPDVSYADIGGLEQQMQEV 161
                                       56666555550045566779********9987654443 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00022
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++kt+l+ka+a++ +++f ++
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQTNASFIKM 214
                                       7999******************9999664 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00028      0.09       3      23 ..     186     206 ..     184     223 .. 0.89
   2 ?    0.4   0.0       1.6   5.3e+02      75     114 ..     236     278 ..     216     281 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00028
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT+L++ +a +
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQ 206
                                       799*************99976 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                                       HHCCSCCCEEEEEE-STT-SS-TCH............HHHHHC CS
                             NACHT  75 vllelperlLlilDglDelvtdlgq...kekqpvrtlLselir 114
                                       ++++  e +++ +D +D ++++      ++ ++v++ + +l++
  gi|313127103|ref|YP_004037373.1| 236 EVARENEPAVIFIDEIDAIASKRTDsktSGDAEVQRTMMQLLS 278
                                       3455666677778999999987766667777777777777765 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4  10.9   9.5e-05     0.031       4      52 ..      22      70 ..      20      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.5e-05
                       Cep57_CLD_2  4 evktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLka 52
                                       +++Lq+rLd+l++++++  + l + n+E++ + ++L +   e+ +Lk+
  gi|313127103|ref|YP_004037373.1| 22 KIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQ 70
                                      689********************************************97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   8.9e-05     0.029       2      28 ..     186     212 ..     186     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.9e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavll 28 
                                       vll G+pG+GK+ la+ +++++ a ++
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQTNASFI 212
                                       7899***************99876554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       5.2   1.7e+03     106     121 ..       5      20 ..       2      32 .. 0.73
   2 ?   13.7   0.1    0.0001     0.033      34      59 ..     184     209 ..     173     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.2
                             AAA_7 106 vDDlnmpakekygaqp 121
                                       vDD+++p  e+  +q+
  gi|313127103|ref|YP_004037373.1|   5 VDDVDLPYDEDAASQQ 20 
                                       9******998877665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.0001
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldk 59 
                                         vll+Gp GtGKt+++k + ++ + 
  gi|313127103|ref|YP_004037373.1| 184 SGVLLYGPPGTGKTMLAKAVANQTNA 209
                                       569****************9998883 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.8   8.2e-05     0.027      61     117 ..      15      71 ..       8     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.2e-05
                             Atg14  61 kiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsd 117
                                       ++ ++++k++ l+ +  +l+++++e++dkl   ++e+++ ++kl++l +++kk +++
  gi|313127103|ref|YP_004037373.1|  15 DAASQQEKIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQS 71 
                                       556788888999999999999999999999999999999999999999998855443 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.3    0.0002     0.066       3      52 ..      20      70 ..      18      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0002
                       Fungal_TACC  3 nkrlqelaedLYvqYSsKHEqKVkllkkgye.akyqkkldklelenkslkq 52
                                      ++++q l e L +  S+  E + kll ++ e +kyq+kl++l+ enk+lkq
  gi|313127103|ref|YP_004037373.1| 20 QEKIQALQERLDILESQNEEMRDKLLDANAEnNKYQQKLERLTHENKKLKQ 70
                                      689************************9987369**************997 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   0.00013     0.043      21      59 ..     178     223 ..     154     256 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00013
                                       E.......EEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEE CS
                              TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeY 59 
                                       v       +lL+G+ G+GKT+l++++a++ + + +k     lv+++
  gi|313127103|ref|YP_004037373.1| 178 VgiqppsgVLLYGPPGTGKTMLAKAVANQTNASFIKMAGSELVHKF 223
                                       144455559*******************998876666666666666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0032         1      33      61 ..     181     209 ..     157     220 .. 0.83
   2 ?    1.9   0.0      0.38   1.2e+02     106     136 ..     229     259 ..     221     278 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0032
                              TniB  33 krmpnlllvGdsnnGKtmivekFarlhpp 61 
                                       + ++ +ll+G++ +GKtm+++  a++ ++
  gi|313127103|ref|YP_004037373.1| 181 QPPSGVLLYGPPGTGKTMLAKAVANQTNA 209
                                       556789**************998887665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.38
                              TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsa 136
                                       kl ++  ++ re ++ v+ iDEi+ + + + 
  gi|313127103|ref|YP_004037373.1| 229 KLVRDLFEVARENEPAVIFIDEIDAIASKRT 259
                                       6667778999999***********9986554 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018     0.059     117     137 ..     186     206 ..     171     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++yGp+ tGkt+la+a a+ 
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQ 206
                                       89***************9986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       8.2   2.7e+03     122     162 ..      68     108 ..      53     115 .. 0.71
   2 ?    2.9   0.1      0.27        89      94     125 ..     142     172 ..     113     176 .. 0.77
   3 ?    9.5   0.1    0.0027      0.88       2      33 ..     186     217 ..     185     259 .. 0.76
   4 ?   -0.2   0.0       2.5   8.1e+02      93     104 ..     239     251 ..     218     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 8.2
                                       HTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE--TTTTTT CS
                          NTPase_1 122 Lksekpvlavihrrkdlalveeirerkdvkvfevteenrda 162
                                       Lk+++ ++a++++ +d+ ++ + + +++  + evt e r+ 
  gi|313127103|ref|YP_004037373.1|  68 LKQSPLFVATVQEITDEGVIIKQHGNNQEALTEVTDELRED 108
                                       66677778888887766666665555666777777777765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.27
                                       HHH-EEEE---STTGGG-HHHHHHHHHHHTTT CS
                          NTPase_1  94 seadviviDEiGkmElkskkfkeaveevLkse 125
                                       +++dv   D iG +E ++++++e+ve  L+s 
  gi|313127103|ref|YP_004037373.1| 142 HSPDVSYAD-IGGLEQQMQEVRETVEMPLESP 172
                                       567777776.***************9988864 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0027
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf 33 
                                       v++ GppG+GKt l k v+++ + s +k++G 
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQTNASFIKMAGS 217
                                       6788****************999998888885 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.5
                                       H.HHH-EEEE--- CS
                          NTPase_1  93 l.seadviviDEi 104
                                         +e+ vi iDEi
  gi|313127103|ref|YP_004037373.1| 239 ReNEPAVIFIDEI 251
                                       236778999**99 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.2       1.1   3.6e+02      62     146 ..      53     139 ..      15     143 .. 0.62
   2 ?   11.1   0.0   0.00055      0.18      13      37 ..     177     201 ..     153     211 .. 0.87
   3 ?    3.6   0.1      0.11        36     106     151 ..     229     280 ..     216     285 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                            ATPase  62 dlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeika.krvviDsitgl.ayeek 136
                                       + +++ ++l ++ +kl+++ +++      ++e+ + +++ ++ e+l+e   e  ++++  +rv + +  ++ ++ ++
  gi|313127103|ref|YP_004037373.1|  53 KYQQKLERLTHENKKLKQSPLFVATVQEITDEGVIIKQHGNNQEALTEVTDELREDLEPdSRVAVNNSLSIvKRLDN 129
                                       44455566666666666666555555555555555555555555555555555555555555555433333366666 PP

                            ATPase 137 eavaReilrq 146
                                       e  +R+ ++q
  gi|313127103|ref|YP_004037373.1| 130 ETDVRARVMQ 139
                                       6666666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00055
                            ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                       + Gi   + vl++G pGtGKt++a+
  gi|313127103|ref|YP_004037373.1| 177 QVGIQPPSGVLLYGPPGTGKTMLAK 201
                                       458999999**************97 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.11
                            ATPase 106 elieelaeaikeikakrvviDsitgl.ayeek.....eavaReilrqlvrvl 151
                                       +l+++l e+ +e +   + iD i+++ +++++     +a++ ++++ql++++
  gi|313127103|ref|YP_004037373.1| 229 KLVRDLFEVARENEPAVIFIDEIDAIaSKRTDsktsgDAEVQRTMMQLLSEM 280
                                       78899999999************99954433311111234555566665555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.7       3.1     1e+03      63     115 ..      52     107 ..      16     117 .. 0.53
   2 ?    9.7   0.0    0.0022      0.72      22      44 ..     185     207 ..     177     215 .. 0.84
   3 ?    2.2   0.0      0.43   1.4e+02      35      82 ..     229     273 ..     225     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.1
                          ATPase_2  63 skldefie.eeeekkklekal.......giavpkaeleeilk.....eksklvfkaielllekikk 115
                                       +k+++++e            +       ++++  a+++ei +     ++  + ++a++++ +++++
  gi|313127103|ref|YP_004037373.1|  52 NKYQQKLErL----------ThenkklkQSPLFVATVQEITDegviiKQHGNNQEALTEVTDELRE 107
                                       2222222221..........1222222244444444444444444444444446666666666655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0022
                          ATPase_2  22 iyfiYGpegsGKtaLlkeiienl 44 
                                        +++YGp g GKt L k ++++ 
  gi|313127103|ref|YP_004037373.1| 185 GVLLYGPPGTGKTMLAKAVANQT 207
                                       5789*************999986 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.43
                          ATPase_2  35 aLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal 82 
                                       +L++ + e  ++ +  vi+++++  ++++++d++      + ++++++
  gi|313127103|ref|YP_004037373.1| 229 KLVRDLFEVARENEPAVIFIDEIDAIASKRTDSKTS---GDAEVQRTM 273
                                       577888888888888889999988888888888833...333333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   7.1     0.037        12     321     455 ..      14     167 ..       2     177 .. 0.67
   2 ?    5.7   0.0     0.014       4.7      20      43 ..     187     210 ..     186     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                            AAA_13 321 edkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkakie................sikklvaeineliak 380
                                       ed +  +++++al+e+L+ l+++ e+ r+++   ++e +++++k+e                +  +++++   +i++
  gi|313127103|ref|YP_004037373.1|  14 EDAASQQEKIQALQERLDILESQNEEMRDKLLDaNAENNKYQQKLErlthenkklkqsplfvATVQEITDEGVIIKQ 90 
                                       44444455555555555555555555444444334455555555544555555566666555888888889999999 PP

                            AAA_13 381 hNekvanleeekeeakkklelhlveeleseldeyk..kkykklekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                       h +  + l+e + e++++le +    +++ l+  k  ++  ++ + + ++e++ + ++a++  le++++e +++++ 
  gi|313127103|ref|YP_004037373.1|  91 HGNNQEALTEVTDELREDLEPDSRVAVNNSLSIVKrlDNETDVRARVMQVEHSPDVSYADIGGLEQQMQEVRETVEM 167
                                       99999999999999999999888777777766444335666677888888888888899999999888888887765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                            AAA_13  20 liYGwNGaGKTtLSrllrslelge 43 
                                       l+YG  G+GKT L+++ +++++ +
  gi|313127103|ref|YP_004037373.1| 187 LLYGPPGTGKTMLAKAVANQTNAS 210
                                       68****************987654 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00054      0.18      22      81 ..     184     254 ..     175     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00054
                                       S-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H........HHHHHHT...TTSEEEEEE-TT- CS
                   Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhknsgpwleifvverlaklp........ldlleqa...kggtLylkdiadl 81 
                                       + v+l G++G+gk++ A++ +++       +   +l++           dl+e a   +++++++ +i+ +
  gi|313127103|ref|YP_004037373.1| 184 SGVLLYGPPGTGKTMLAKAVANQTNASFIKMAGSELVHKFigegaklvRDLFEVArenEPAVIFIDEIDAI 254
                                       679*****************998766322222223333223444444477777665557788888888766 PP

>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00027     0.087      44      82 ..      61      99 ..      14     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00027
                           DUF2334 44 ktgskvnlsenpefvevLkylqakGgeialHGYtHqygt 82
                                       t+++++l+++p fv++++++ ++G +i +HG + +  t
  gi|313127103|ref|YP_004037373.1| 61 LTHENKKLKQSPLFVATVQEITDEGVIIKQHGNNQEALT 99
                                      567789**************************9988874 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00057      0.19      21      45 ..     186     210 ..     173     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00057
                            AAA_30  21 avltGpAGtGKttalkalreaweaa 45 
                                       ++l Gp+GtGKt++ ka+++  +a+
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAVANQTNAS 210
                                       6789*************99877665 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.1    0.0033       1.1      18      80 ..      17      79 ..       7      83 .. 0.87
   2 ?    0.4   0.0       3.4   1.1e+03      43      85 ..     257     301 ..     247     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0033
                      Occludin_ELL 18 nkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkk 80
                                       ++ ++ ++l+++l+ ++++ +e++++l +++ ++++y++  e++ +e kklk++p + ++ +
  gi|313127103|ref|YP_004037373.1| 17 ASQQEKIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQSPLFVATVQ 79
                                      56667778999*********************************************9987766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 3.4
                      Occludin_ELL  43 relkelkegskeykkieeeilqeykklkk..dpeyqekkkrceyL 85 
                                       +++++ + g+ e+++++ ++l+e   +++  d +  ++ +r++ L
  gi|313127103|ref|YP_004037373.1| 257 KRTDSKTSGDAEVQRTMMQLLSEMDGFEErgDIRIIAATNRFDML 301
                                       445555666679999999999999999886677777788887776 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   6.0   0.00042      0.14     117     224 ..      13     135 ..       7     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                           DUF4407 117 qeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk........gtgttgvaGkgpaa 185
                                        e+a++++e+++ al+++l+ le+q+++++ ++  a+a+ ++ ++++++ ++ +k         ++ + +  +g + 
  gi|313127103|ref|YP_004037373.1|  13 DEDAASQQEKIQ-ALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKklkqsplfVATVQEITDEGVII 88 
                                       566777777766.799*******************************99999988999*****4445568889**** PP

                           DUF4407 186 kekkaqldaaqaelaelkakld........atarlaalraelaelea 224
                                       k+  ++ +a+++  +el+++l+        ++  + ++ ++ ++++a
  gi|313127103|ref|YP_004037373.1|  89 KQHGNNQEALTEVTDELREDLEpdsrvavnNSLSIVKRLDNETDVRA 135
                                       ********************997755555533333333333333333 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   6.6   0.00038      0.12     169     242 ..      19      88 ..      12     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                        Fmp27_WPPW 169 ervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkesees 242
                                       ++ + + l+eRl+ le+q e++++kl +++ +++k    +++++e+l++e k+lk++  f+ t+ e ++e    
  gi|313127103|ref|YP_004037373.1|  19 QQEKIQALQERLDILESQNEEMRDKLLDANAENNK----YQQKLERLTHENKKLKQSPLFVATVQEITDEGVII 88 
                                       45567889**********************99999....9*****************99999887766665543 PP

>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00046      0.15     104     136 ..      86     126 ..      78     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00046
                      Creatininase 104 vlvngHggnsaalkeaarelraehdaaavrvt........a 136
                                       v++  Hg n++al e+ +elr++ +++  +++        +
  gi|313127103|ref|YP_004037373.1|  86 VIIKQHGNNQEALTEVTDELREDLEPDSRVAVnnslsivkR 126
                                       89*********************966554444455544331 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   0.00085      0.28      25      49 ..      20      44 ..      18      48 .. 0.93
   2 ?    5.6   3.3     0.053        17      40      61 ..      49      70 ..      46      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00085
                                      HHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 25 qaeieeLerrvkaLekeNksLksel 49
                                      q++i++L++r + Le++N++++++l
  gi|313127103|ref|YP_004037373.1| 20 QEKIQALQERLDILESQNEEMRDKL 44
                                      899*******************987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.053
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 40 keNksLkseleelkkevekLks 61
                                      +eN +++++le+l+ e++kLk+
  gi|313127103|ref|YP_004037373.1| 49 AENNKYQQKLERLTHENKKLKQ 70
                                      7999999*********999998 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.9   0.00099      0.32     129     186 ..      13      70 ..       6      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00099
                            DUF724 129 eeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeavas 186
                                       +e+ +  ++ki+ l+++l+ l +++e++  ++ + ++e++k++++le+  +e ++++ 
  gi|313127103|ref|YP_004037373.1|  13 DEDAASQQEKIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQ 70 
                                       67778899****************************************9999887765 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   9.7   0.00061       0.2      10     101 ..      21     114 ..      17     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00061
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  10 eqiDaLtktnlqLtqqsqeLleklelaqkkeskflenlaslkhENdnL..sslLkRKerrlkdlekelselkesvee 84 
                                       e+i aL + +  L  q++e+ +kl  a++ ++k+ ++l  l hEN +L  s l+    + + d    ++++ ++ e 
  gi|313127103|ref|YP_004037373.1|  21 EKIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLkqSPLFVATVQEITDEGVIIKQHGNNQEA 97 
                                       789999999999************************************444699999999***9999********** PP

                                       HHHHHHHHHHHHHHCCC CS
                              SHE3  85 lklekkqlkkrlenssa 101
                                       l++ +++l+++le  s 
  gi|313127103|ref|YP_004037373.1|  98 LTEVTDELREDLEPDSR 114
                                       *********99997664 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.73   2.4e+02      80     138 ..      48     110 ..      31     132 .. 0.68
   2 ?   11.2   0.1   0.00064      0.21      36      53 ..     186     203 ..     179     209 .. 0.87
   3 ?    4.3   0.1     0.083        27     129     165 ..     230     267 ..     210     294 .. 0.76
   4 ?   -1.1   0.1       3.6   1.2e+03     126     178 ..     340     393 ..     316     395 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.73
                            AAA_25  80 EdsedelrrRlravgeal.rd.darllvldlagv.eslpLfakdrggtl..ltadvdaleaaie 138
                                          ++  +++l+++ +++ ++ ++ l+v ++ ++ ++  ++ k++g+++  lt+++d+l++++e
  gi|313127103|ref|YP_004037373.1|  48 NAENNKYQQKLERLTHENkKLkQSPLFVATV-QEiTDEGVIIKQHGNNQeaLTEVTDELREDLE 110
                                       4444558888888887776441444555555.44455555555555555559999999999887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00064
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll+G+pgtGKt+la  +
  gi|313127103|ref|YP_004037373.1| 186 VLLYGPPGTGKTMLAKAV 203
                                       69************9665 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.083
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralgg..densnsdv 165
                                        v++l ++++e ++++++ iD ++++ +   d++ + d+
  gi|313127103|ref|YP_004037373.1| 230 LVRDLFEVARE-NEPAVIFIDEIDAIASKrtDSKTSGDA 267
                                       578899999**.88***********88886655555442 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.6
                            AAA_25 126 ltadvdaleaaieevegvrlvviDplsralgg.densnsdvgalvealeriarr 178
                                        + d+++l++ ++e+ g+++  i + + +++  d   +  +g +v+a+e+i+++
  gi|313127103|ref|YP_004037373.1| 340 DDVDFHQLAEMADEASGADVKAICTEAGMFAIrDDRTEIYMGDFVSAWEKIQAE 393
                                       566777777777777777776666666666664444444568888888888765 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   8.0     0.001      0.33      67     123 ..      14      70 ..      10      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.001
                              ADIP  67 aeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkn 123
                                        + +++q ki+ l+++l  le++++    k+ ++++++ + +qkl +++ e+++lk+
  gi|313127103|ref|YP_004037373.1|  14 EDAASQQEKIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQ 70 
                                       677889999999999999999999999999999999999999999999999999885 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   7.8      0.19        61       5      53 ..      25      80 ..      15     111 .. 0.67
   2 ?    4.2   0.0      0.21        68       3      53 ..     130     200 ..     127     250 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.19
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......X CS
                              YabA  5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl.......e 53
                                       l ++l+ le+q ee+ ++l + ++e ++  ++ ++L+ en+kl++         e
  gi|313127103|ref|YP_004037373.1| 25 ALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQSPlfvatvqE 80
                                      56677777788888888888888888888888888888888888886555555440 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....................X CS
                              YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl.....................e 53 
                                       ++++ ++++++e++ +  +++++ l+++++e+  e  e+ le  ++ +++                     +
  gi|313127103|ref|YP_004037373.1| 130 ETDVRARVMQVEHSPDVSYADIGGLEQQMQEVR-ETVEMPLESPEMFDQVgiqppsgvllygppgtgktmlA 200
                                       56788999*********************9975.55677777666666555555555555555555555443 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   6.0       2.3   7.5e+02      69     107 ..      39      75 ..       9     178 .. 0.55
   2 ?   11.7   0.1    0.0005      0.16      19      42 ..     185     208 ..     155     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.3
                            AAA_11  69 ellerllrglldsegekykpkivRvgneeeriseavksv 107
                                       e+ ++ll+   ++e +ky+ k+ R+ +e+++ +++   v
  gi|313127103|ref|YP_004037373.1|  39 EMRDKLLD--ANAENNKYQQKLERLTHENKKLKQSPLFV 75 
                                       34445555..55556666666666666663333333333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0005
                            AAA_11  19 itliqGPPGtgKTktivellsqll 42 
                                        +l+ GPPGtgKT    ++ +q +
  gi|313127103|ref|YP_004037373.1| 185 GVLLYGPPGTGKTMLAKAVANQTN 208
                                       5799*********88888888875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0011      0.35       7      37 ..     179     209 ..     176     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0011
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkp 37 
                                        +++ + v + G+ G+GK+ L+k++a++++ 
  gi|313127103|ref|YP_004037373.1| 179 GIQPPSGVLLYGPPGTGKTMLAKAVANQTNA 209
                                       567777899****************999864 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  10.3    0.0024      0.79      74     127 ..      18      71 ..      13     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0024
                           DUF4201  74 ktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkq 127
                                       ++  +++ l+e+l++les+++e++++l + +++ +k++++l+++ +e++kl++ 
  gi|313127103|ref|YP_004037373.1|  18 SQQEKIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQS 71 
                                       566789999*****************************************9975 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5       3.3   1.1e+03     252     301 ..      36      70 ..      17     138 .. 0.49
   2 ?    5.2   0.0     0.032        10      17      45 ..     180     208 ..     163     215 .. 0.82
   3 ?    3.8   0.1     0.086        28     167     190 ..     237     259 ..     226     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.3
                        KAP_NTPase 252 glrevkkvlmeaveaseettesesrdetlgnsasksnlqlaldlskillt 301
                                        ++e++++l  a               +  n+  +++l++  +++k l++
  gi|313127103|ref|YP_004037373.1|  36 QNEEMRDKLLDA---------------NAENNKYQQKLERLTHENKKLKQ 70 
                                       333333333333...............22222222222222222222222 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.032
                        KAP_NTPase  17 latpivvgLygkWGsGKssllnkledelk 45 
                                        ++p+ v Lyg+ G+GK+ l + + ++ +
  gi|313127103|ref|YP_004037373.1| 180 IQPPSGVLLYGPPGTGKTMLAKAVANQTN 208
                                       39999**************9998877665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.086
                        KAP_NTPase 167 tLdalqkrlVvviDdLDrceteev 190
                                         + ++ + V++iD++D + ++++
  gi|313127103|ref|YP_004037373.1| 237 VAR-ENEPAVIFIDEIDAIASKRT 259
                                       333.5999*********9888876 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.7      0.11        35       7      30 ..      21      44 ..      18      51 .. 0.89
   2 ?   -1.1   0.1       7.9   2.6e+03      12      35 ..      54      70 ..      46      72 .. 0.49
   3 ?    5.1   0.0     0.089        29      15      32 ..     150     167 ..     136     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.11
                         FlaC_arch  7 nklsklsteletvkkeneelsksv 30
                                      +k++ l+ +l+ ++++nee+++++
  gi|313127103|ref|YP_004037373.1| 21 EKIQALQERLDILESQNEEMRDKL 44
                                      7999999*************9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 7.9
                         FlaC_arch 12 lsteletvkkeneelsksveelke 35
                                       + +le +  en++l+       +
  gi|313127103|ref|YP_004037373.1| 54 YQQKLERLTHENKKLK-------Q 70
                                      3334444444444444.......3 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.089
                         FlaC_arch  15 eletvkkeneelsksvee 32 
                                        ++ ++++++e++++ve+
  gi|313127103|ref|YP_004037373.1| 150 DIGGLEQQMQEVRETVEM 167
                                       7899************98 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.6    0.0087       2.8      69     152 ..      17     105 ..      11     107 .. 0.73
   2 ?   -0.9   0.0         2   6.4e+02      41      58 ..     188     205 ..     185     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0087
                           DUF3987  69 eeyeeelkeyeaekkaweaelealekkaakak..eakaeealaeleaee...peePklprllvddvTpeaLl.elLa 139
                                       ++ +e++++ +++ +++e+++e+++ k+ +a+  + k +++l+ l+ e+   ++ P l   +v+++T e+++ ++  
  gi|313127103|ref|YP_004037373.1|  17 ASQQEKIQALQERLDILESQNEEMRDKLLDANaeNNKYQQKLERLTHENkklKQSP-LFVATVQEITDEGVIiKQHG 92 
                                       556789999999***************99998884444444444444444436666.678888******97615666 PP

                           DUF3987 140 engggililsdEg 152
                                       +n++ ++ ++dE+
  gi|313127103|ref|YP_004037373.1|  93 NNQEALTEVTDEL 105
                                       6669999999997 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                           DUF3987  41 vvapsGerKSpvdklvlr 58 
                                         +p+G++K+ ++k+v++
  gi|313127103|ref|YP_004037373.1| 188 LYGPPGTGKTMLAKAVAN 205
                                       569*********999875 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  14.1    0.0099       3.2      35      93 ..      16      74 ..      12     119 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0099
                               GAS 35 ieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkar 93
                                       +  ++k ++ + +l+ ++++n++++++L  a++e+++ +++l++  ++ ++lk++   
  gi|313127103|ref|YP_004037373.1| 16 AASQQEKIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQSPLF 74
                                      45555666666666666666666666666666666666666666666666666665544 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   9.4     0.001      0.32      44      96 ..      18      70 ..       7      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.001
                            APG6_N 44 kqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96
                                      +q+e++++l+e+l+ le++ ee+  +L ++ +e+ + +++l+ l+ e ++l++
  gi|313127103|ref|YP_004037373.1| 18 SQQEKIQALQERLDILESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQ 70
                                      257899*******************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1855  (0.103464); expected 358.6 (0.02)
Passed bias filter:                      954  (0.0532099); expected 358.6 (0.02)
Passed Vit filter:                       196  (0.010932); expected 17.9 (0.001)
Passed Fwd filter:                        64  (0.00356964); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              55  [number of targets reported over threshold]
# CPU time: 0.81u 0.35s 00:00:01.16 Elapsed: 00:00:00.49
# Mc/sec: 2501.21
//
Query:       gi|313127104|ref|YP_004037374.1|  [L=42]
Description: hypothetical protein Hbor_23700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 296.89
//
Query:       gi|313127105|ref|YP_004037375.1|  [L=227]
Description: endonuclease iii; DNA-(apurinic or apyrimidinic site) lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-22   80.3   0.0    1.9e-22   79.7   0.0    1.3  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    9.2e-10   37.9   0.0    1.2e-08   34.4   0.0    2.5  2  HHH            Helix-hairpin-helix motif
      3e-05   24.5   0.0      0.036   14.7   0.0    2.4  2  HHH_5          Helix-hairpin-helix domain
    4.9e-05   23.5   4.8    7.9e-05   22.9   4.8    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
      0.001   19.3   1.8      0.043   14.1   0.5    2.6  2  PqqD           Coenzyme PQQ synthesis protein D (PqqD)


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.0   5.4e-26   1.9e-22       1     106 [.      40     174 ..      40     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 5.4e-26
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       ++++ls+q++der+n+++++lfe+++  tped a+ad e+L++ i+++ f+++Ka y++++ + lv           
  gi|313127105|ref|YP_004037375.1|  40 IAVVLSAQCTDERVNEVTAELFEKYQ--TPEDYAAADVEELADDIYGITFHNNKAGYLQSIGETLVeehdgevpdtm 114
                                       689*********************97..************************************************* PP

                                       ....................S-SS.S--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHH CS
                                       ....................xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ....................gkpd.vlivvDvhvrrilkrlrsikekktkkkvekkleell 106
                                                           g+   ++ivvD+hvrr+ +rl++++e + ++k+e++l+ ++
  gi|313127105|ref|YP_004037375.1| 115 seltdlsgvgrktanvvlqhGHDVvEGIVVDTHVRRLSRRLGITEE-ERPEKIEQDLMPVV 174
                                       ********************6555689*****************99.7*******997655 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.25   9.1e+02       7      15 ..      72      80 ..      71      85 .. 0.80
   2 !   34.4   0.0   3.2e-12   1.2e-08       1      29 [.     105     133 ..     105     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.25
                                      TSSHHHHHT CS
                               HHH  7 pasreeLla 15
                                      +a++eeL++
  gi|313127105|ref|YP_004037375.1| 72 AADVEELAD 80
                                      6999**985 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 3.2e-12
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIls 29 
                                       +++g++p+++ eL++l+GVG+ktA+++l+
  gi|313127105|ref|YP_004037375.1| 105 EHDGEVPDTMSELTDLSGVGRKTANVVLQ 133
                                       589************************97 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0018       6.3      18      43 ..      60      85 ..      53      86 .. 0.82
   2 !   14.7   0.0     1e-05     0.036       3      44 ..     116     158 ..     114     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                                      HHTTT--SHHHHHHS-HHHHHT.STTS CS
                             HHH_5 18 llsaGiesvedlaaadveeLak.ipGi 43
                                      l ++ + ++ed aaadveeLa+ i Gi
  gi|313127105|ref|YP_004037375.1| 60 LFEK-YQTPEDYAAADVEELADdIYGI 85
                                      5666.89*************9866665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1e-05
                                       HHHTSTT--HHHHHHHHTTT--SHHHH.HHS-HHHHHTSTTS- CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedl.aaadveeLakipGiG 44 
                                       eL+++sG+G+ktA  +l +G + ve + ++  v +L++  Gi 
  gi|313127105|ref|YP_004037375.1| 116 ELTDLSGVGRKTANVVLQHGHDVVEGIvVDTHVRRLSRRLGIT 158
                                       89*****************999999772466788888876766 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   4.8   2.2e-08   7.9e-05       1      17 []     194     210 ..     194     210 .. 0.99

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.2e-08
                     EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                       C AR+P C++C+L DlC
  gi|313127105|ref|YP_004037375.1| 194 CDARNPDCDECVLEDLC 210
                                       99*************** PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.022        81      26      45 ..       5      26 ..       3      31 .. 0.77
   2 !   14.1   0.5   1.2e-05     0.043      26      60 ..      48      81 ..      40      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.022
                                      -SSSS-.HHHHHHHHHHHC.T- CS
                              PqqD 26 ldgers.veeivaalaeey.dv 45
                                      ld +   veei ++l e y d 
  gi|313127105|ref|YP_004037375.1|  5 LDTREAqVEEILDRLYEAYpDT 26
                                      6664447***********9554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.2e-05
                                      -SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHH CS
                              PqqD 26 ldgersveeivaalaeeydvdeeeaeadvlafldq 60
                                      + +   v e+ a+l+e+y+ +e+ a+adv+++ d+
  gi|313127105|ref|YP_004037375.1| 48 CTD-ERVNEVTAELFEKYQTPEDYAAADVEELADD 81
                                      655.469***********************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1630.42
//
Query:       gi|313127106|ref|YP_004037376.1|  [L=146]
Description: hypothetical protein Hbor_23720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.032   14.1   1.0      0.032   14.1   1.0    2.1  2  DUF5337         Family of unknown function (DUF5337)
       0.68   10.1   5.0       0.14   12.3   0.7    2.0  2  Cytochrom_B561  Eukaryotic cytochrome b561


Domain annotation for each model (and alignments):
>> DUF5337  Family of unknown function (DUF5337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.0   3.5e-06     0.032      22      72 ..      43      92 ..      37      93 .. 0.86
   2 ?    0.9   0.2     0.047   4.2e+02      18      34 ..     120     136 ..     108     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-06
                           DUF5337 22 vtmllwlgaqwigeqlglsnRyalLfdLaAlAaliwalvvtyqlwraRqns 72
                                      v +++w++  ++ +  g s+ +a+ + L A A l++al  ++++ +a++n+
  gi|313127106|ref|YP_004037376.1| 43 VPVVFWMAPRLLDQLGGFSALHAV-LGLQAYALLAFALTGIIRIYQAKRNA 92
                                      55899***9999988889887766.59********************9986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.047
                           DUF5337  18 lviavtmllwlgaqwig 34 
                                       + + + ++lw++a ++g
  gi|313127106|ref|YP_004037376.1| 120 IGVFGYVILWILAWFLG 136
                                       556778999**999988 PP

>> Cytochrom_B561  Eukaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7   1.5e-05      0.14      36      96 ..      28      87 ..       3     114 .. 0.83
   2 ?   -0.2   0.5      0.12     1e+03      79      95 ..     125     141 ..      94     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHT--SS-SHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                    Cytochrom_B561 36 llHlilqllalilavvgllavfksknekeianlyslHswlGlvtvilfllqlvlGfvlfll 96
                                      + Hl + + +lil++v +++ +  +   +   ++ lH++lGl + +l+++ l +G++ ++ 
  gi|313127106|ref|YP_004037376.1| 28 IYHLKFIVPGLILTTVPVVFWMAPRLLDQLGGFSALHAVLGLQAYALLAFAL-TGIIRIYQ 87
                                      4588888889999999999999999999******************999865.67766664 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHT CS
                    Cytochrom_B561  79 tvilfllqlvlGfvlfl 95 
                                        vil +l ++lG++ ++
  gi|313127106|ref|YP_004037376.1| 125 YVILWILAWFLGIYQYV 141
                                       56777888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1055.29
//
Query:       gi|313127107|ref|YP_004037377.1|  [L=273]
Description: hypothetical protein Hbor_23730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2002.98
//
Query:       gi|313127108|ref|YP_004037378.1|  [L=223]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-14   53.3   0.1    5.3e-14   52.5   0.1    1.5  1  Copper-bind     Copper binding proteins, plastocyanin/azurin 
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.28   11.3   0.0    1.4  1  Cupredoxin_1    Cupredoxin-like domain
        6.2    6.9  24.2        1.1    9.4  19.1    1.9  2  Keratin_2_head  Keratin type II head


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.1   8.9e-18   5.3e-14       7      98 ..      77     163 ..      71     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 8.9e-18
                                       ETTETSEEES...SEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEE CS
                       Copper-bind   7 vesgdlqFet...keitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtY 80 
                                       + ++dl+F++   + +++++g++v+fv+ ++  HN+v++++   +g++ +      ++++  +G +++ tf++ g+Y
  gi|313127108|ref|YP_004037378.1|  77 GPGNDLVFSPgtgEPLEIAPGTTVEFVW-DSNNHNIVVESQP--DGANWQ-----GHESIENEGFTYTHTFETLGEY 145
                                       5567799998333459************.999******9865..344333.....25567789************** PP

                                       EEEETTTTTTTSEEEEEE CS
                       Copper-bind  81 kffCsPHaaagMkgkvtv 98 
                                       ++fC+PH++agM+g+++v
  gi|313127108|ref|YP_004037378.1| 146 SYFCQPHKSAGMVGTIVV 163
                                       ****************98 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.6e-05      0.28      71     104 .]     130     163 ..      71     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
                      Cupredoxin_1  71 apgktttitiaplkpGeYeftcdmhm.d.akGkliV 104
                                       + g t+t t+  ++ GeY+++c+ h+   + G+++V
  gi|313127108|ref|YP_004037378.1| 130 NEGFTYTHTF--ETLGEYSYFCQPHKsAgMVGTIVV 163
                                       5788999999..899********9984589999998 PP

>> Keratin_2_head  Keratin type II head
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  19.1   0.00018       1.1      63     129 ..      17      80 ..       7      98 .. 0.42
   2 ?    0.3   0.2      0.11   6.7e+02      92     109 ..     158     175 ..     126     218 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00018
                    Keratin_2_head  63 agggsragsgfgfgggggggfglGfggGvglgfgagggvGggfGggggl.vGgggfGgggfGg..gGfGg 129
                                       a+ ++ ag+g+ +++g++ + g+G+++G       g+g+G+g G g  + +Gggg Ggg   +  +G G 
  gi|313127108|ref|YP_004037378.1|  17 ATASAAAGVGAAQETGNSTSSGTGTATG----T--GTGTGTGTGTGNETaTGGGGSGGGPTKTvtVGPGN 80 
                                       2222323333333333333333333333....3..33333333333333245566665333332356653 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                    Keratin_2_head  92 glgfgagggvGggfGggg 109
                                        + +++    Ggg Ggg 
  gi|313127108|ref|YP_004037378.1| 158 VGTIVVTENPGGGEGGGE 175
                                       222222222223333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1664.12
//
Query:       gi|313127109|ref|YP_004037379.1|  [L=128]
Description: hypothetical protein Hbor_23750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.3   7.5      0.081   13.0   2.1    2.1  2  VMA21     VMA21-like domain


Domain annotation for each model (and alignments):
>> VMA21  VMA21-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.0    0.0046        82      41      61 ..      19      39 ..       8      41 .. 0.85
   2 ?   13.0   2.1   4.5e-06     0.081      20      57 ..      37      73 ..      35      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0046
                             VMA21 41 tlysgvlAVivvnlvlasYii 61
                                         ++++A++++ ++ +++++
  gi|313127109|ref|YP_004037379.1| 19 ESTAAAIAIVLLTIIEVIFVF 39
                                      5679999*********99997 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.5e-06
                             VMA21 20 sfftskhllfegvfglsnssatlysgvlAVivvnlvla 57
                                        f++ + l++g  gls+  +++ ++vlAVi+v l+ +
  gi|313127109|ref|YP_004037379.1| 37 FVFLFSYGLVSG-WGLSDTGNMFLGAVLAVIFVDLAFI 73
                                      567778888886.6*******************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 824.70
//
Query:       gi|313127110|ref|YP_004037380.1|  [L=268]
Description: cytochrome b subunit of the bc complex [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-45  153.6  17.8    7.4e-45  153.1  17.8    1.2  1  Cytochrome_B     Cytochrome b/b6/petB
    6.3e-43  146.7  11.5    2.9e-42  144.5  10.9    1.9  2  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    3.4e-05   24.3   3.1    3.4e-05   24.3   3.1    2.9  2  DUF4405          Domain of unknown function (DUF4405)
  ------ inclusion threshold ------
       0.17   11.3   6.2       0.28   10.6   6.2    1.5  1  DUF373           Domain of unknown function (DUF373)
       0.19   11.3  21.8      0.034   13.8   6.6    2.3  2  Ni_hydr_CYTB     Prokaryotic cytochrome b561


Domain annotation for each model (and alignments):
>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1  17.8   2.1e-48   7.4e-45      13     185 ..      78     259 ..      70     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 2.1e-48
                      Cytochrome_B  13 iynlGsllllvlvlqiltGvalafyytptv........tlaflsvqyilrdvnfGwlirsvhangasllflllylhi 81 
                                       +y+lG   +l  v+  ++G +l fyy+p+         t a+ ++++i++d++fG+++rs+h+++a +++  ++lh+
  gi|313127110|ref|YP_004037380.1|  78 LYTLGLFSTLAYVVAAISGALLGFYYSPSSaagteaagTVAYEQIAFIMTDLQFGFMLRSIHRWAAQVMVAAVFLHM 154
                                       699***********************9864222222226789999******************************** PP

                      Cytochrome_B  82 frglllgglkktrelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPviGstlvellwgsvsvdda 158
                                        r++++g++k++rel W++G+il+ l++v++++Gy Lpwdq+++Wa ++  ++  +iP+iG+++ +ll+g+++++++
  gi|313127110|ref|YP_004037380.1| 155 LRVYFTGAYKEPRELNWLLGIILISLTMVFGYTGYLLPWDQLAFWAGQIGVEMSLSIPLIGEWIAQLLFGGFTLSQS 231
                                       ***************************************************************************** PP

                      Cytochrome_B 159 tLtrffslh.fllPflllillllhllll 185
                                       tL+r++ lh fllPf++++l+ +h+ ++
  gi|313127110|ref|YP_004037380.1| 232 TLQRMYILHvFLLPFVVTTLIAIHIGIV 259
                                       ************************8665 PP

>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.15   5.5e+02     121     156 ..      57      94 ..      44     110 .. 0.57
   2 !  144.5  10.9   8.1e-46   2.9e-42       2     122 ..     145     265 ..     144     268 .] 0.96

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.15
                   Cytochrom_B_N_2 121 qtpsrrkeknvvgeplvpvnavkml.llflvl.valli 156
                                       q+p+ ++e+    ++++  + +++l l++++  v+++i
  gi|313127110|ref|YP_004037380.1|  57 QMPKSHTEQYNLDNKFWYWYPLYTLgLFSTLAyVVAAI 94 
                                       56666566655556666666666662444444233333 PP

  == domain 2  score: 144.5 bits;  conditional E-value: 8.1e-46
                   Cytochrom_B_N_2   2 imiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvel 78 
                                       +m++++++Hmlrv+ftGaYk+pRelnW++G++l+ lt++ g++Gy+Lp+d+l+++a ++g ++  s+P++g+w+++l
  gi|313127110|ref|YP_004037380.1| 145 VMVAAVFLHMLRVYFTGAYKEPRELNWLLGIILISLTMVFGYTGYLLPWDQLAFWAGQIGVEMSLSIPLIGEWIAQL 221
                                       8**************************************************************************** PP

                   Cytochrom_B_N_2  79 lfGgelpgeallsrlyalHilllpalllalivahlllvekkgqt 122
                                       lfGg + ++ +l+r+y+lH++llp+++ +li++h+ +v  +g++
  gi|313127110|ref|YP_004037380.1| 222 LFGGFTLSQSTLQRMYILHVFLLPFVVTTLIAIHIGIVWVQGIA 265
                                       ***********************************998766665 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   3.1   9.4e-09   3.4e-05       4      62 ..      83     154 ..      80     157 .. 0.88
   2 ?   -4.7   8.2         5   1.8e+04      50      66 .]     244     260 ..     172     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 9.4e-09
                           DUF4405   4 lllllsflvlaiSGillsfavlpsgrgaywa.................flglskhqwrdiHeilgllflilvvlHl 62 
                                       l+ +l+ +v+aiSG ll f ++ps+ ++ +a                 f      ++r iH++++ +++++v lH+
  gi|313127110|ref|YP_004037380.1|  83 LFSTLAYVVAAISGALLGFYYSPSSAAGTEAagtvayeqiafimtdlqF----GFMLRSIHRWAAQVMVAAVFLHM 154
                                       5667899*****************9999999********9988666651....557*******************7 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 5
                           DUF4405  50 lgllflilvvlHlglhw 66 
                                       l ++   l+++H+g+ w
  gi|313127110|ref|YP_004037380.1| 244 LPFVVTTLIAIHIGIVW 260
                                       44777889999999988 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   6.2   7.9e-05      0.28     219     320 ..      84     200 ..      66     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.9e-05
                            DUF373 219 itfvtyvvalll.lligiisgyislesvss.asvssglltlila.....fiyg.avewlalailtaslgkiideylk 287
                                       ++ ++yvva+++ +l+g++++ +s++ +++ ++v+++ +  i++     f+   +  w a ++++a++ +++  y+ 
  gi|313127110|ref|YP_004037380.1|  84 FSTLAYVVAAISgALLGFYYSPSSAAGTEAaGTVAYEQIAFIMTdlqfgFMLRsIHRWAAQVMVAAVFLHMLRVYFT 160
                                       56788888888878888888888877776664555555555554444443333477899999**************9 PP

                            DUF373 288 reekdiarllllpflvlaiglvlygasaylls.......l 320
                                       + +k+  +l  l+ ++l+  ++++g ++yll        +
  gi|313127110|ref|YP_004037380.1| 161 GAYKEPRELNWLLGIILISLTMVFGYTGYLLPwdqlafwA 200
                                       98888877777777777778888*******9855544440 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   6.6   9.3e-06     0.034      83     171 ..      52     163 ..      25     174 .. 0.68
   2 ?    3.6   7.4     0.012        44     102     169 ..     171     263 ..     162     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.3e-06
                                       SSS----------------TT........THHHHHHHHHHHHHHHHHHHT....HHHHHHHH..............H CS
                      Ni_hydr_CYTB  83 ltlllrgrkpeagknnplqkl........vhlllyvllvvliltGlllsf....aatagfpll...........ldd 136
                                       +   l+ +k + +++n  +k         ++l+  ++ vv++++G ll f    +++ag + +            +d
  gi|313127110|ref|YP_004037380.1|  52 YRVNLQMPKSHTEQYNLDNKFwywyplytLGLFSTLAYVVAAISGALLGFyyspSSAAGTEAAgtvayeqiafiMTD 128
                                       455555555555566666665677777664444445555666666666555555666666666777788888889** PP

                                       TS-THHHHHHH.HHHHHHHHHHHHHHHHHHHHHH- CS
                      Ni_hydr_CYTB 137 kggaqlarelHellaaallafvvlHiaaallhgpv 171
                                        ++   +r++H ++a +++a v+lH + + + g+ 
  gi|313127110|ref|YP_004037380.1| 129 LQFGFMLRSIHRWAAQVMVAAVFLHMLRVYFTGAY 163
                                       *************************9988777665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
                                       TTTHHHHHHHHHHHHHHHHHHHT....HHHHHHHH.......................HTS-THHHHHHH.HHHHHH CS
                      Ni_hydr_CYTB 102 klvhlllyvllvvliltGlllsf....aatagfpll....................lddkggaqlarelHellaaal 154
                                       +l++++l+ l+ v   tG+ll +     ++ ++++                       +    q +  lH +l  ++
  gi|313127110|ref|YP_004037380.1| 171 WLLGIILISLTMVFGYTGYLLPWdqlaFWAGQIGVEmslsipligewiaqllfggfTLSQSTLQRMYILHVFLLPFV 247
                                       457778888888888899998666666323333333566666777777777777777799**********9999999 PP

                                       H.HHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB 155 l.afvvlHiaaallhg 169
                                       +  ++++Hi+ + + g
  gi|313127110|ref|YP_004037380.1| 248 VtTLIAIHIGIVWVQG 263
                                       99*******9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1882.27
//
Query:       gi|313127111|ref|YP_004037381.1|  [L=254]
Description: cytochrome b subunit of the bc complex [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-09   36.5   0.7    7.5e-09   35.8   0.2    1.7  2  Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
  ------ inclusion threshold ------
       0.16   11.4   0.0       0.22   10.9   0.0    1.1  1  VP4_helical    Rotavirus VP4 helical domain


Domain annotation for each model (and alignments):
>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.1   9.7e+03      27      40 ..      83      96 ..      72      98 .. 0.55
   2 !   35.8   0.2   8.4e-13   7.5e-09       1      84 [.     105     203 ..     105     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.1
                                      SSSHHHHHHHHHHH CS
                     Cytochrom_B_C 27 ipakllGvvamgaa 40
                                      i + ++G+++++ a
  gi|313127111|ref|YP_004037381.1| 83 IASFFVGMILFLSA 96
                                      35666666666554 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 8.4e-13
                                       B--TTC--TT----GGGHHHHHHHHCSS...............SHHHHHHHHHHHHHGGGCHHHH---SSSSSTT-. CS
                     Cytochrom_B_C   1 panplktPahIaPeWYflpfYaiLraip...............akllGvvamgaaivilfllpwldrskvksiryrk 62 
                                       panp +tPa I P WY+ + + +L+  p               ++  Gv+a ++ +  ++++p+l++ + +    ++
  gi|313127111|ref|YP_004037381.1| 105 PANPSSTPAIILPDWYLYWSFGLLKLGPlnpelsilggqkllaDRPYGVLANVVVVGAIAIVPFLNKGSARRPVEQP 181
                                       7*************************65555666666666666999******************************9 PP

                                       HHHHHHHHHHHHHHHHHHHHHT CS
                     Cytochrom_B_C  63 plakvllallvvsfvvLgylGv 84 
                                        +a++ +  +v++f +  y ++
  gi|313127111|ref|YP_004037381.1| 182 FWASIGVGGVVFAFTISVYSAK 203
                                       9999999999999988777655 PP

>> VP4_helical  Rotavirus VP4 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.5e-05      0.22     198     252 ..     184     241 ..     167     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.5e-05
                       VP4_helical 198 feigidgkffaykvdtleei...nfdvdkfadlvsdspvisaivdfktlkalrdnyGi 252
                                         ig+ g  fa+ +  +  +   ++dv+ + dl+  +p+++ +v ++ lk++r+ y  
  gi|313127111|ref|YP_004037381.1| 184 ASIGVGGVVFAFTISVYSAKnlvPMDVHLLFDLTFLAPLVAGVVTYAVLKTMREGYMY 241
                                       56899999******99977512268*****************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1717.15
//
Query:       gi|313127112|ref|YP_004037382.1|  [L=128]
Description: hypothetical protein Hbor_23780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        4.5    7.8   7.7         14    6.2   7.7    1.8  1  DUF202           Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   7.7   0.00076        14       9      63 ..      42     106 ..      27     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00076
                            DUF202   9 TfLaWlRtslalialglallrffl..........tgepsalgkilglilivlgiltllvglvryl 63 
                                       T++a +++ +++++l++a l++            t + s +  +l++il+v+g++++++g+  y+
  gi|313127112|ref|YP_004037382.1|  42 TLIAVISVVVGFMFLDAATLNVSFvgalitdlrtTLGISIADDVLSTILAVAGLAIIGFGAGVYI 106
                                       6666677777777777777774335677766665666666689999*************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 842.03
//
Query:       gi|313127113|ref|YP_004037383.1|  [L=89]
Description: hypothetical protein Hbor_23790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 661.57
//
Query:       gi|313127114|ref|YP_004037384.1|  [L=151]
Description: hypothetical protein Hbor_23800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1102.32
//
Query:       gi|313127115|ref|YP_004037385.1|  [L=252]
Description: sugar kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-11   44.6   0.2    1.3e-11   44.3   0.2    1.2  1  NAD_kinase  ATP-NAD kinase


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.2   7.2e-16   1.3e-11     162     274 ..     117     227 ..      40     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 7.2e-16
                                       EEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS- CS
                        NAD_kinase 162 iensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPhsls 238
                                          ++l +v++++  ++ ++e ++    e ++++++dg++v+tP Gs +y+ + Ggp++ P+    + vpi P + +
  gi|313127115|ref|YP_004037385.1| 117 LAGTALADVTLMTDEPARISEYAVSTPAERVDSFRADGVVVATPLGSHGYARGVGGPILAPETGV-VAVPISPYTTR 192
                                       4457899*******************************************************999.88********* PP

                                       ---EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-T CS
                        NAD_kinase 239 srpiVvssssklrirvasrseallaldGseelelsp 274
                                       s+  V   + +l+++  +++++ l+ld +e+ +++ 
  gi|313127115|ref|YP_004037385.1| 193 SDSWVHRLPVTLSVE-RDEASVTLILDDEEARDVPA 227
                                       ******999999966.47777888887777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1739.04
//
Query:       gi|313127116|ref|YP_004037386.1|  [L=435]
Description: aminopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-30  105.9   0.1    4.3e-30  104.9   0.1    1.5  2  Peptidase_M28  Peptidase family M28
    1.2e-13   50.9   0.0    2.3e-13   50.0   0.0    1.5  1  PA             PA domain
    3.4e-05   23.6   1.2    0.00068   19.4   0.5    2.4  2  Peptidase_M20  Peptidase family M20/M25/M40
     0.0026   16.8   0.1     0.0047   16.0   0.1    1.3  1  Peptidase_M42  M42 glutamyl aminopeptidase
  ------ inclusion threshold ------
       0.19   10.6   0.0       0.29   10.0   0.0    1.3  1  DUF4910        Domain of unknown function (DUF4910)


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.1   7.5e+03      18      27 ..      52      61 ..      50      73 .. 0.74
   2 !  104.9   0.1   1.2e-33   4.3e-30       1     197 [.     208     395 ..     208     396 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.1
                                      EEE--B-TTT CS
                     Peptidase_M28 18 gAHyDsvgvg 27
                                      +AH+D+  ++
  gi|313127116|ref|YP_004037386.1| 52 NAHIDTFEIQ 61
                                      69***99875 PP

  == domain 2  score: 104.9 bits;  conditional E-value: 1.2e-33
                                       EEEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHH CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllG 77 
                                       Nv a+l +++ +  ll+++H+D + +  ++   GA Dn+sg+a+++elar+la+++ +++ +vrf++f+aEE gl+G
  gi|313127116|ref|YP_004037386.1| 208 NVHAELGPDT-EDELLVTSHLDAHDI--AE---GAWDNGSGTAMVVELARILAEREDELETRVRFIAFGAEEVGLVG 278
                                       9*****9999.889***********9..99...***********************99******************* PP

                                       HHHHHHHHC..CCTTEEEEEEECS-SSSS--EEEHHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHH CS
                     Peptidase_M28  78 Skafakakp..elkkiaavlnlDmvgsggkellfesgdkssselekelkalakpvgraaaedpfdersgrgrsDhsp 152
                                       S +   ++   e++ i+av+n D v  g++  +    + + ++le+ ++++ +++ + +   +    +   +sDh+p
  gi|313127116|ref|YP_004037386.1| 279 SGHES-DRLgdEREHIKAVVNNDGVVFGRTLKF---DTHGFDALEAAAESVGDQFDHPV--SI--VPELVPHSDHWP 347
                                       *****.54456***************9999888...44555556666666666665543..22..2234578***** PP

                                       HHTTT--EEEE..CTSSS-TTT.TSTTSSGGGB-HHHHHHHHHHHHHH CS
                     Peptidase_M28 153 flkagvpvldl..aetgfpevy.HtprDtldnidkdtlariaelvlel 197
                                       f++ gvp+  +  ++ g ++ + Ht +Dtld+++ ++l++ a l+++l
  gi|313127116|ref|YP_004037386.1| 348 FTQWGVPGYMIscETAGRGRGWgHTFADTLDKLEVRNLREQAILLAQL 395
                                       *********998888999******************999988777765 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   6.4e-17   2.3e-13       2      89 .]      91     184 ..      89     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 6.4e-17
                                PA   2 tgplVyscfagygisadfegvdvkGkivLvqr.......tf...aeKarnAqaaGAagviiv..ndge.lgaatgas 65 
                                       +g+ V   + gyg ++df + d++Gk+v+v++        f   +eK+++A +aGA++++++  +  e   ++tg+ 
  gi|313127116|ref|YP_004037386.1|  91 SGEFV---DLGYGLPEDF-EADLSGKVVMVSStvpdhyeRFihrREKYYHAVEAGAEAFVFAnhV--EgCLPPTGSV 161
                                       58889...99*******9.799********65444444412666******************543..4324444455 PP

                                PA  66 gnegepdgitiPavgvsredgeal 89 
                                       g+e++p   +iPavgvs+e+g +l
  gi|313127116|ref|YP_004037386.1| 162 GTEESP-VGDIPAVGVSKEVGTRL 184
                                       555555.89************987 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.5   1.9e-07   0.00068      33      95 ..     234     297 ..     225     310 .. 0.90
   2 ?    2.3   0.0     0.032   1.1e+02     132     183 ..     311     371 ..     301     398 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.9e-07
                                       TTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHH.TTTCESEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                     Peptidase_M20  33 rGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegle.erekvdavf 95 
                                        Ga d+  g ++++e++r l+++  +++  ++++++++EE+g  G+++  + l  ere+++av+
  gi|313127116|ref|YP_004037386.1| 234 EGAWDNGSGTAMVVELARILAEREDELETRVRFIAFGAEEVGLVGSGHESDRLGdEREHIKAVV 297
                                       6999************************************9889**999998888999999977 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.032
                                       CHHHHHHHHHHHHHHHTSC...EEEEEES..SSBHTHHHH.TTTEEEEE....EESSGGCTT CS
                                       xxxxxxxxxxxxxxxxxxx...xxxxxxx..xxxxxxxxx.xxxxxxxx....xxxxxxxxx RF
                     Peptidase_M20 132 dsplvkalaeaaeelfgek...velivsg..pggtdarff.agiptvmi....fgpgsglaH 183
                                       d + ++al++aae++ g +   +  iv+   p +   +f  +g+p +mi     g+g g  H
  gi|313127116|ref|YP_004037386.1| 311 DTHGFDALEAAAESV-GDQfdhPVSIVPElvPHSDHWPFTqWGVPGYMIscetAGRGRGWGH 371
                                       477789999999998.7665434444666888899999999***999885333333323333 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.3e-06    0.0047     123     174 ..     227     280 ..     220     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                                       ETTECEEETTHHHHHHHHHHHHHHHHHCTSS-S..SEEEEEEESTCTTTSHHHH CS
                     Peptidase_M42 123 langkivskalDdragvavllellkelkeeele..atvylvatvqEEvGlrGak 174
                                       l+ + i+  a+D+  g a+++el++ l+e+e e  ++v ++a   EEvGl G+ 
  gi|313127116|ref|YP_004037386.1| 227 LDAHDIAEGAWDNGSGTAMVVELARILAEREDEleTRVRFIAFGAEEVGLVGSG 280
                                       566778889******************988755559999************985 PP

>> DUF4910  Domain of unknown function (DUF4910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   8.2e-05      0.29      65     113 ..     216     266 ..     133     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 8.2e-05
                                       SSS-EEEEEEE----S-TT...TTHHHHHHHHHHHHHHTTS--.SSEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4910  65 eteeevllsahvChPslan...dnlsGiavatalakalaerkerrysyrllf 113
                                       +te+e+l+++h+    +a    dn sG a+++ la+ laer++ ++  r+ f
  gi|313127116|ref|YP_004037386.1| 216 DTEDELLVTSHLDAHDIAEgawDNGSGTAMVVELARILAERED-ELETRVRF 266
                                       7899*******976666543449****************9876.56555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3290.95
//
Query:       gi|313127117|ref|YP_004037387.1|  [L=388]
Description: acetyl-CoA acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-25   89.2   2.4    3.4e-24   85.6   1.1    2.4  2  Thiolase_N       Thiolase, N-terminal domain
    4.7e-10   39.5   6.0    2.2e-08   34.0   3.9    3.2  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    6.8e-09   35.4   0.1    1.4e-08   34.4   0.1    1.5  1  Thiolase_C       Thiolase, C-terminal domain
     0.0065   16.5   1.4       0.09   12.8   1.4    2.5  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   1.1   7.7e-28   3.4e-24       3     259 ..       6     222 ..       4     223 .. 0.86
   2 ?   -3.4   0.0       1.1   4.8e+03      28      46 ..     261     279 ..     256     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 7.7e-28
                                       EEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEE CS
                        Thiolase_N   3 ivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpav 79 
                                       i++   tp+g+      + + ++L aea+ a+ e+agv+ ++ + v+ Gn + a+++++ ++   ++     + pa+
  gi|313127117|ref|YP_004037387.1|   6 IAGVGLTPFGE----QPERTGRDLFAEAALAAREEAGVPRDAYEGVHYGNFMGAFAERQGHQGPLMAEAAGLDCPAM 78 
                                       66666788888....7788899********************************999997776555555555***** PP

                                       EEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHH CS
                        Thiolase_N  80 tvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmG 156
                                       + + +c+S+  av +a++si+age dv++agG+E+m+n +t+  t   ++l + ++++ ++ + +           +
  gi|313127117|ref|YP_004037387.1|  79 RHESACASAGIAVRQAVRSIRAGEHDVLLAGGMERMTNLSTSRVT---ESLAIAADELFEVRSGM-----NFPGAYA 147
                                       ***************************************999864...45666666665555555.....2223679 PP

                                       HHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSS CS
                        Thiolase_N 157 ltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaF 233
                                       l a+ + ++y+ sRe++++ Avk+h++a+ +  a+ +++ei              + ++a++s  +a +L+      
  gi|313127117|ref|YP_004037387.1| 148 LMARAYFEEYGGSREDLAHIAVKNHANAVPNEYAQ-YRREI--------------TVEQAMESLPVATPLHLF---- 205
                                       9**********************************.*****..............778889999999****99.... PP

                                       STTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 234 kkeGtvtAgnasqisDGaaavllmse 259
                                                +a++i+DGa+av+l+s 
  gi|313127117|ref|YP_004037387.1| 206 ---------DACPITDGASAVVLVSD 222
                                       .........**************986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHTS-GGGCC CS
                        Thiolase_N  28 aealkallekagvdpeevd 46 
                                       ++a++a+ e+ag+ p++vd
  gi|313127117|ref|YP_004037387.1| 261 EKAATAAYEDAGIGPDDVD 279
                                       5788999999999999998 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   3.9   4.9e-12   2.2e-08     159     218 ..      68     127 ..      21     135 .. 0.91
   2 ?    0.5   0.0     0.084   3.8e+02      94     115 ..     262     283 ..     247     343 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.9e-12
                                       HHHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT CS
                     ketoacyl-synt 159 syalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag 218
                                       + a gl+ p++  ++AC+S+  av +av+s+r+ge dv laGG+e +++ ++ ++ ++++
  gi|313127117|ref|YP_004037387.1|  68 AEAAGLDCPAMRHESACASAGIAVRQAVRSIRAGEHDVLLAGGMERMTNLSTSRVTESLA 127
                                       5668999*****************************************999988887776 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.084
                                       HHHHHHHHHHTS-HHTCTTGGE CS
                     ketoacyl-synt  94 eaawealedagltpeeldgsrv 115
                                       +aa  a edag+ p+++d  +v
  gi|313127117|ref|YP_004037387.1| 262 KAATAAYEDAGIGPDDVDVAEV 283
                                       67889999***99999876554 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1   3.1e-12   1.4e-08      20     102 ..     254     356 ..     245     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.1e-12
                                       GGGHHH..HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HH CS
                        Thiolase_C  20 lglgPa..yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGai 76 
                                       +  +Pa   a++++ ++ag+  +d+d+ E+++ F+   + ++++l+l                      vN+ GG  
  gi|313127117|ref|YP_004037387.1| 254 FSRTPAaeKAATAAYEDAGIGPDDVDVAEVHDCFTIAEVLALESLGLFDhgeaitaaregkttrdgsLPVNLSGGLK 330
                                       55555522588999*********************99999999999877799************99889******** PP

                                       HH-B-TTTHHHHHHHHHHHHHHHCTT CS
                        Thiolase_C  77 alGHPlGasGaRivvtllselkkegg 102
                                       a GHP+Ga+G  +vv +++ l+ +++
  gi|313127117|ref|YP_004037387.1| 331 AKGHPVGATGGAQVVEMTKLLRGDHA 356
                                       ****************9999987665 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   1.4     2e-05      0.09      23      55 ..     257     289 ..     235     357 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSH CS
                   Ketoacyl-synt_C  23 geaqaraiekalaeagvdpedvdyveahgtgtp 55 
                                         a+++a ++a+++ag+ p+dvd+ e h+  t 
  gi|313127117|ref|YP_004037387.1| 257 TPAAEKAATAAYEDAGIGPDDVDVAEVHDCFTI 289
                                       5678899*********************97664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2632.47
//
Query:       gi|313127118|ref|YP_004037388.1|  [L=127]
Description: nucleic-acid-binding protein containing a zn-ribbon [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-09   35.9   0.5    7.4e-09   35.5   0.5    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    3.1e-05   23.8   0.9    4.6e-05   23.2   0.9    1.3  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
       0.12   12.5   1.6       0.16   12.1   0.5    1.8  2  Zn-ribbon_8    Zinc ribbon domain
       0.12   12.3   0.3       0.21   11.6   0.3    1.3  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.5   1.6e-12   7.4e-09       3      63 ..      48     110 ..      46     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.6e-12
                                       EE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES.....TT-B-EEE CS
                     OB_aCoA_assoc   3 elsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpde...vriGmrVrav 63 
                                       +l+  Gtv++f+ +h a p fa ++Pyv+++  +d  vr+++ l gv +++     +Gm V++ 
  gi|313127118|ref|YP_004037388.1|  48 PLPESGTVETFSEIHVAGPDFASQTPYVTAIASFDA-VRLTGVLRGVLDEDgpdPSVGMSVEVH 110
                                       78999*******************************.9988888887777777766******96 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.9     1e-08   4.6e-05      10      34 ..      19      42 ..      11      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1e-08
                           DUF35_N 10 vgqrCpdCGtvqfPPravCphCgsd 34
                                       +  Cpd G+   PPr+ CphCg+ 
  gi|313127118|ref|YP_004037388.1| 19 YYLACPD-GHGSLPPRRTCPHCGAM 42
                                      5667**9.**************964 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.54   2.4e+03      28      34 ..      22      28 ..      17      34 .. 0.76
   2 ?   12.1   0.5   3.7e-05      0.16      24      38 ..      31      46 ..      26      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.54
                       Zn-ribbon_8 28 aCPeCgs 34
                                      aCP+ ++
  gi|313127118|ref|YP_004037388.1| 22 ACPDGHG 28
                                      5999887 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.7e-05
                       Zn-ribbon_8 24 apltaCPeCgs.evrr 38
                                      +p  +CP+Cg+ e+++
  gi|313127118|ref|YP_004037388.1| 31 PPRRTCPHCGAmELEK 46
                                      56677******99998 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   4.7e-05      0.21      16      28 ..      31      43 ..      27      48 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                     Zn_Tnp_IS1595 16 pngfvCPhCgsrk 28
                                      p +++CPhCg ++
  gi|313127118|ref|YP_004037388.1| 31 PPRRTCPHCGAME 43
                                      6789******775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 938.02
//
Query:       gi|313127119|ref|YP_004037389.1|  [L=307]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-19   71.1   1.7      2e-19   71.1   1.7    1.5  2  Abhydrolase_6  Alpha/beta hydrolase family
      7e-11   42.3   0.0    1.3e-06   28.3   0.0    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold
    1.8e-06   27.4   0.0    2.9e-05   23.5   0.0    2.1  1  Hydrolase_4    Serine aminopeptidase, S33


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1   6.7e+03     112     123 ..      24      43 ..       8      58 .. 0.43
   2 !   71.1   1.7   3.4e-23     2e-19       1     217 [.      62     295 ..      62     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                       HHHHHHTT-C........CC CS
                     Abhydrolase_6 112 llallallrl........la 123
                                       l +++++l +        ++
  gi|313127119|ref|YP_004037389.1|  24 LSRRTPPLEPalsgeqhtYR 43 
                                       33333322221222222222 PP

  == domain 2  score: 71.1 bits;  conditional E-value: 3.4e-23
                                       EEEE--..GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT..TTSEEEEEETCH CS
                     Abhydrolase_6   1 vlllHG..agssassWlvapLaallaagvhvlapDlpGhGrsdpppldledladlaalldelaagggpvvlvGHSlG 75 
                                       +lllHG  a +s + ++  ++   la+++hv+apDlpG+G sd+ppl +++ a +++++ e++a  +++ +v+ Sl 
  gi|313127119|ref|YP_004037389.1|  62 LLLLHGvnAAASNGEFR--EVFDELAEDYHVIAPDLPGFGMSDRPPLRYSA-ALYEDFIGEFVAEFDDPAVVASSLT 135
                                       79****77666677776..888888************************99.666666666666669999******* PP

                                       HHHHHHHHHCC..EE..EEES-..----TTT..S----TTHHHHHH.........TT-CCCCHCCH.......S-HS CS
                     Abhydrolase_6  76 Galalaaaplalvvg..vlldppptalpagl..laaalelllalla.........llrllawlsre.......plpr 132
                                       +++  a   + ++v+  +l++p   + + g     +++el++a+           + ++ ++++++        +++
  gi|313127119|ref|YP_004037389.1| 136 ASYLIA---ADPDVSrlILVCP---SERGGPepKEWLRELIRAPVIgeavfnligSKPSIRYFNADhgyadpsRVSD 206
                                       998888...77555569*****...5555554544444444444443323322223333666654455444433333 PP

                                       CCCCHHHCCCCHCHCCCGHHHHCCHHC....HTT.....CCHHTT-TTGCEEECTT-C.HHHHCHHCCCH.STTEEE CS
                     Abhydrolase_6 133 lfladedadaawrarlarlaallaglg....llp.....aaawadlpvpllvlggeDp.lvprllerlla.qagarl 198
                                       ++++     ++wr++++  a+++++ +    l +      +++ad+ vp+ +++g+D  lvp    r la +a+++l
  gi|313127119|ref|YP_004037389.1| 207 EWID-----YEWRTAHQQNARFAPASFisgyL-NedidlETELADVDVPVTLVWGRDSdLVPLKRGRELAeAADCKL 277
                                       7777.....***************77766541.12344477*********777877775777445566669999999 PP

                                       TCE...SSS-HHHHSHHHH CS
                     Abhydrolase_6 199 pvvlpgaGHlphleepdev 217
                                        vv+ ++  lph e p+++
  gi|313127119|ref|YP_004037389.1| 278 -VVFDDTKLLPHVEFPEQF 295
                                       .*****9999999999887 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   2.2e-10   1.3e-06       1      75 [.      60     129 ..      60     173 .. 0.73
   2 !   12.0   0.0   1.9e-05      0.12     206     248 ..     222     283 ..     185     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.2e-10
                                       SEEEEE-STTT..CGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSE CS
                     Abhydrolase_1   1 pvlvilhGlpg..ssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkl 75 
                                       p l++lhG  +  s + ++e  +++ La+ +++vi++Dl+G+g S+++p      y+ a ++d++  +++ ++d  +
  gi|313127119|ref|YP_004037389.1|  60 PNLLLLHGVNAaaSNGEFRE--VFDELAE-DYHVIAPDLPGFGMSDRPPLR----YSAALYEDFIGEFVAEFDDPAV 129
                                       569********654455999..*******.*******************85....7776666666666666666555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.9e-05
                                       C....................THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETC CS
                     Abhydrolase_1 206 e....................lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisda 248
                                       +                    l +v +p+ +++g++  lvp k +++la++    +lvv++d+
  gi|313127119|ref|YP_004037389.1| 222 RfapasfisgylnedidleteLADVDVPVTLVWGRDSDLVPLKRGRELAEAADC-KLVVFDDT 283
                                       24445555556668888999999****************************999.99999987 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.8e-09   2.9e-05       6     220 ..      61     276 ..      56     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.8e-09
                       Hydrolase_4   6 vvvlvHGlaehs..gryaelaeaLaaqGfavyalDhrGhGrse..gkrghvpsfddyvdDlaafvekvkeehpelpl 78 
                                        ++l+HG++  +  g + e++++La ++++v+a D  G+G s+  + r   + ++d++        ++++e  +   
  gi|313127119|ref|YP_004037389.1|  61 NLLLLHGVNAAAsnGEFREVFDELA-EDYHVIAPDLPGFGMSDrpPLRYSAALYEDFIG-------EFVAEFDDP-- 127
                                       6899***987553389********8.58**************86666664444444444.......334444333.. PP

                       Hydrolase_4  79 fllGhSmGGliallyllrypdkvaglilsaPalkikaklkappllkl..llkllgkllpklqv...........snn 142
                                        +++ S    ++++yl    ++v++lil++P  +  ++  ++++l+    + ++g+++ +l             ++ 
  gi|313127119|ref|YP_004037389.1| 128 AVVASS----LTASYLIAADPDVSRLILVCPSERGGPE--PKEWLREliRAPVIGEAVFNLIGskpsiryfnadHGY 198
                                       567766....566777666666**********999987..5555544333344444444444466666669888777 PP

                       Hydrolase_4 143 lkadslsrdpevvaayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgs 219
                                        +++ +s++    +   a++   +   ++++ + l+   +le++ a++++P+ l+ G +  +v+ +  rel+e++  
  gi|313127119|ref|YP_004037389.1| 199 ADPSRVSDEWIDYEWRTAHQQNARFAPASFISGYLNEDIDLETELADVDVPVTLVWGRDSDLVPLKRGRELAEAADC 275
                                       888888888888888888888899999*********************************************99875 PP

                       Hydrolase_4 220 k 220
                                       k
  gi|313127119|ref|YP_004037389.1| 276 K 276
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2324.27
//
Query:       gi|313127120|ref|YP_004037390.1|  [L=374]
Description: lao/ao transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-91  305.5   3.4    2.8e-91  305.2   3.4    1.1  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
    5.1e-06   26.2   2.0    4.3e-05   23.2   2.0    2.2  1  cobW            CobW/HypB/UreG, nucleotide-binding domain
    4.3e-05   24.0   0.4    0.00032   21.1   0.0    2.3  2  AAA_16          AAA ATPase domain
      7e-05   22.8   0.6    0.00017   21.5   0.1    1.9  1  NTPase_1        NTPase
    0.00012   21.9   0.2    0.00039   20.2   0.1    1.9  2  AAA_30          AAA domain
    0.00014   21.5   0.6    0.00048   19.8   0.6    1.8  1  SRP54           SRP54-type protein, GTPase domain
    0.00043   20.3   0.0     0.0006   19.9   0.0    1.5  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00067   19.5   0.6     0.0022   17.8   0.1    2.0  3  ATP_bind_1      Conserved hypothetical ATP binding protein
    0.00085   19.9   0.0     0.0017   18.9   0.0    1.5  1  ABC_tran        ABC transporter
     0.0025   18.4   0.2     0.0096   16.5   0.1    2.0  2  AAA_18          AAA domain
     0.0025   17.5   0.2      0.005   16.5   0.2    1.4  1  AAA_29          P-loop containing region of AAA domain
     0.0029   17.2   0.1        1.5    8.3   0.1    2.3  2  GTP_EFTU        Elongation factor Tu GTP binding domain
     0.0031   17.4   0.1     0.0098   15.8   0.0    1.9  2  MobB            Molybdopterin guanine dinucleotide synthesis 
     0.0059   16.5   0.2        0.1   12.5   0.1    2.4  2  NACHT           NACHT domain
  ------ inclusion threshold ------
      0.011   15.9   0.1      0.029   14.7   0.0    1.7  1  AAA_22          AAA domain
      0.016   15.4   1.1      0.035   14.3   0.1    2.0  2  AAA_28          AAA domain
      0.017   14.9   0.0      0.029   14.1   0.0    1.3  1  PRK             Phosphoribulokinase / Uridine kinase family
      0.017   15.0   0.0      0.095   12.6   0.0    2.2  2  RsgA_GTPase     RsgA GTPase
      0.024   15.0   1.1      0.082   13.3   0.1    2.3  2  AAA_17          AAA domain
      0.024   13.9   0.1      0.047   13.0   0.1    1.4  1  Zeta_toxin      Zeta toxin
      0.025   14.0   0.1      0.054   12.9   0.0    1.5  2  KTI12           Chromatin associated protein KTI12
      0.027   13.7   0.0      0.036   13.3   0.0    1.5  1  KAP_NTPase      KAP family P-loop domain
       0.03   14.4   0.4      0.096   12.8   0.1    2.0  2  MMR_HSR1        50S ribosome-binding GTPase
      0.031   14.2   0.0      0.077   12.9   0.0    1.6  1  Ploopntkinase3  P-loop Nucleotide Kinase3
      0.032   14.4   0.3      0.094   12.9   0.1    1.8  2  AAA_33          AAA domain
      0.044   13.0   0.0      0.088   12.0   0.0    1.4  1  NB-ARC          NB-ARC domain
      0.072   12.2   0.0       0.12   11.6   0.0    1.2  1  DUF815          Protein of unknown function (DUF815)
        0.2   12.1   0.0       0.36   11.2   0.0    1.4  1  RNA_helicase    RNA helicase


Domain annotation for each model (and alignments):
>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.2   3.4   4.4e-94   2.8e-91       1     264 [.      28     331 ..      28     334 .. 0.98

  Alignments for each domain:
  == domain 1  score: 305.2 bits;  conditional E-value: 4.4e-94
                                       HHHHHHHHH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------ CS
                              MeaB   1 LaraitlveserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsil 77 
                                       Larait +e++ p  ++l++rl a++G a v+G+tG+PGaGkstlv++l+  +r+ G  v+v+ vDPssp+tGG++l
  gi|313127120|ref|YP_004037390.1|  28 LARAITKIENRSPGYRDLVSRLHAHTGDADVIGITGSPGAGKSTLVDKLAKAYRDDGLTVGVIGVDPSSPYTGGAVL 104
                                       8**************************************************************************** PP

                                       ------HCCCTSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESST CS
                              MeaB  78 GDklRleelavdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpea 154
                                       GD++R+++   d +vf+Rs+++rG+lGGl+++t ++v+ l+a+G D++++etvG+Gq evd+++ +dt+ vl+ p++
  gi|313127120|ref|YP_004037390.1| 105 GDRIRMASNVGDMDVFFRSMSARGQLGGLSTATSDAVKALDAFGKDKIIVETVGAGQNEVDIVRTADTVTVLVQPGS 181
                                       ***************************************************************************** PP

                                       TTTTTT--CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCST................................. CS
                              MeaB 155 GDelqgikkGileiaDiivvnkaDkkeaekaarelraaleleee................................. 198
                                       GD++q +k+Gilei+D++vvnkaD  +++++ +el+ +++l ++                                 
  gi|313127120|ref|YP_004037390.1| 182 GDDVQMLKAGILEIGDVFVVNKADMDGVNRTVAELEEMIHLRDNpgakldtghhgvdtslpagvseangqangtdad 258
                                       ******************************************999******************************** PP

                                       .......TBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              MeaB 199 .......kekeWrpkvlktsavegeGidelvdaieehrevlkktGllekrrrerakeelrelvedellkrvka 264
                                              ++ eW+p++++t+a++g+G+delv+++  h+e+l+++G++e++ r r +ee+r+l +++  + +k+
  gi|313127120|ref|YP_004037390.1| 259 epddaadDDPEWKPAIVETVATTGDGVDELVETLGAHAEFLTESGMREQKARTRYAEEIRQLLRNDANELLKE 331
                                       ****997799******************************************************998877765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   2.0   6.8e-08   4.3e-05       2     167 ..      58     221 ..      57     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.8e-08
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT...........EEEET.TTTECCH. CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve..........ivele.nGciCct. 64 
                                       v+++tG++G+GK+tL+ +l    + +gl + vi  + ++    +++l ++  +            +++  G +    
  gi|313127120|ref|YP_004037390.1|  58 VIGITGSPGAGKSTLVDKLAkaYRDDGLTVGVIGVDPSSPYTGGAVLGDRIRMasnvgdmdvfFRSMSaRGQLGGLs 134
                                       789*****************8778899*********99877777777444222334556688844443134443331 PP

                                       .CTT-HHHHHHHHHHHHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHH CS
                              cobW  65 .lredllkelealeereerldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqla 140
                                          +d++k+l+a+ +     d i++Et+G  +               t+d+v ++v       ++++ + +    l+
  gi|313127120|ref|YP_004037390.1| 135 tATSDAVKALDAFGK-----DKIIVETVGAGQNEVD--------IVRTADTVTVLVQP----GSGDDVQMLKAGILE 194
                                       135556555555555.....55*******7665443........25667777777777....78999999999999* PP

                                       TSSEEEEE-HHHHCHC..HHHHHHHHH CS
                              cobW 141 aadllvlnKtDlldeeallekleerlr 167
                                         d++v+nK+D+   ++++++lee+++
  gi|313127120|ref|YP_004037390.1| 195 IGDVFVVNKADMDGVNRTVAELEEMIH 221
                                       ***********9888888888888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     5e-07   0.00032      13      55 ..      46      87 ..      38     150 .. 0.82
   2 ?    0.5   0.1       1.1   6.9e+02      95     128 ..     268     322 ..     252     362 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5e-07
                            AAA_16 13 lsalervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                       s l+ +++g+  ++ ++G +G GKs+lv++l++a+++dg  +
  gi|313127120|ref|YP_004037390.1| 46 VSRLH-AHTGDADVIGITGSPGAGKSTLVDKLAKAYRDDGLTV 87
                                      33343.4556669999******************999995443 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                            AAA_16  95 eawrekleeala.....................avpelagaea.srllellkrlla 128
                                       ++w+ ++ e++a                     +++  + + a +r +e++++ll+
  gi|313127120|ref|YP_004037390.1| 268 PEWKPAIVETVAttgdgvdelvetlgahaefltESGMREQK-ArTRYAEEIRQLLR 322
                                       55555555555544454444444444444444211111122.13444444444442 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   2.7e-07   0.00017       2      31 ..      59      88 ..      58     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.7e-07
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                      + iTG+pG GK+Tlv+k++++ +++g++vg
  gi|313127120|ref|YP_004037390.1| 59 IGITGSPGAGKSTLVDKLAKAYRDDGLTVG 88
                                      78************************9986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   6.1e-07   0.00039      12      51 ..      50      89 ..      44     114 .. 0.84
   2 ?   -1.8   0.0       3.3   2.1e+03      51      74 ..     277     300 ..     270     340 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.1e-07
                            AAA_30 12 alltsgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                      +++t+++ v  +tG +G+GK+t++ +l++a++++g +v +
  gi|313127120|ref|YP_004037390.1| 50 HAHTGDADVIGITGSPGAGKSTLVDKLAKAYRDDGLTVGV 89
                                      56677778999***********************966533 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.3
                            AAA_30  51 glAptgkaAkvLaeelgieastia 74 
                                        +A tg   ++L e lg++a+ + 
  gi|313127120|ref|YP_004037390.1| 277 TVATTGDGVDELVETLGAHAEFLT 300
                                       556666666666666666555433 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.6   7.4e-07   0.00048       3     112 ..      58     177 ..      56     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.4e-07
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST...SSTTHH..HHHHHHHHHTTEEEEE...SSTTS..CHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt...fRaaAv..eQLktlaeklgvpvik...kkeea..dpa 69 
                                       vi + G  GaGK t + KLa+ ++++g +v ++ +D    +  +Av  + +++  +  +++v+    + +++     
  gi|313127120|ref|YP_004037390.1|  58 VIGITGSPGAGKSTLVDKLAKAYRDDGLTVGVIGVDPsspYTGGAVlgDRIRMASNVGDMDVFFrsmSARGQlgGLS 134
                                       6778999*****************************63347778986677777666666666543453333333567 PP

                                       HHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH CS
                             SRP54  70 avakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvv 112
                                       + +++av++ ++ + d ++v T G  qn+ ++++  +++   v
  gi|313127120|ref|YP_004037390.1| 135 TATSDAVKALDAFGKDKIIVETVGAGQNEVDIVRTADTVTVLV 177
                                       888999*******************999999988777776665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.4e-07    0.0006       6      66 ..      63     216 ..      58     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.4e-07
                                       SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx........................... RF
                              CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep........................... 54 
                                       ++ G+GK+tl+ +La+a  ++gl V ++ +Dp ++ +   + g++++ +                            
  gi|313127120|ref|YP_004037390.1|  63 GSPGAGKSTLVDKLAKAYRDDGLTVGVIGVDPSSPYTGGaVLGDRIRMASnvgdmdvffrsmsargqlgglstatsd 139
                                       5669*****************************99998455555555555889888899999988888888888888 PP

                                       .................................................................CCHCCCHHHHHH CS
                                       .................................................................xxxxxxxxxxxx RF
                              CbiA  55 .................................................................dlkrllelleal 66 
                                                                                                        d++ + +++++l
  gi|313127120|ref|YP_004037390.1| 140 avkaldafgkdkiivetvgagqnevdivrtadtvtvlvqpgsgddvqmlkagileigdvfvvnkaDMDGVNRTVAEL 216
                                       88888888888888888888888887777777777777777777777777777777777777766555555555555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.5e-06    0.0022       1      36 [.      61      96 ..      61     100 .. 0.95
   2 ?   -2.4   0.0         5   3.2e+03     157     170 ..     195     208 ..     190     229 .. 0.59
   3 ?   -2.6   0.0       5.9   3.7e+03     190     234 ..     303     345 ..     283     348 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-06
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                      ++G +G+GK+t+v +l++ +++ g +v v+  DP +
  gi|313127120|ref|YP_004037390.1| 61 ITGSPGAGKSTLVDKLAKAYRDDGLTVGVIGVDPSS 96
                                      68********************************75 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                        ATP_bind_1 157 lPhvvvlnkfDllk 170
                                       +  v v+nk+D+  
  gi|313127120|ref|YP_004037390.1| 195 IGDVFVVNKADMDG 208
                                       56678888888733 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.9
                        ATP_bind_1 190 lekeeekykklaeaiaelleefalvlrflplssekeesiedllsl 234
                                          e++++ + ae+i++ll + a    +l  + +++ ++e l ++
  gi|313127120|ref|YP_004037390.1| 303 GMREQKARTRYAEEIRQLLRNDANE--LLKEELDRHGGVESLAAA 345
                                       3334466677788888888776655..666666666666666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.6e-06    0.0017      12      45 ..      57      93 ..      47     169 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.6e-06
                                      SEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEET CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkp...teGeilld 45
                                       +++i+G+ GaGKStL+  la+ +++   t G i +d
  gi|313127120|ref|YP_004037390.1| 57 DVIGITGSPGAGKSTLVDKLAKAYRDdglTVGVIGVD 93
                                      689*********************9945555555444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.5e-05    0.0096       1      21 [.      59      79 ..      59     109 .. 0.88
   2 ?   -1.9   0.0       7.3   4.7e+03      46      67 ..     198     219 ..     134     237 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                      I++tG pG+GK+tl + L+k 
  gi|313127120|ref|YP_004037390.1| 59 IGITGSPGAGKSTLVDKLAKA 79
                                      89****************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.3
                            AAA_18  46 ldeskrldedkldklldaleen 67 
                                       +   +++d+d +++ + +lee 
  gi|313127120|ref|YP_004037390.1| 198 VFVVNKADMDGVNRTVAELEEM 219
                                       3445566666666666666665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   7.8e-06     0.005      20      41 ..      57      75 ..      46      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.8e-06
                            AAA_29 20 dlkgatlltGpsGsGKSTllDA 41
                                      d   ++ +tG  G+GKSTl+D 
  gi|313127120|ref|YP_004037390.1| 57 D---VIGITGSPGAGKSTLVDK 75
                                      3...556**************5 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0024       1.5       6      26 ..      59      79 ..      56      86 .. 0.88
   2 !    6.6   0.0    0.0079       5.1     121     191 ..     193     295 ..     162     297 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0024
                                      EEEEESTTSSHHHHHHHHHHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyk 26
                                      igi g   +GK+TL+d+L ++
  gi|313127120|ref|YP_004037390.1| 59 IGITGSPGAGKSTLVDKLAKA 79
                                      899**************9865 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0079
                                       TTTEEEEEEESCGST..HHHHHHHHHHHHHHHHHH...................................HHHHHHH CS
                          GTP_EFTU 121 egvpiivfiNKmDrl..kaelkeiveevkqklsrk...................................eekleky 160
                                       +++  ++++NK+D+   + ++ e+ e+++  l+++                                   +      
  gi|313127120|ref|YP_004037390.1| 193 LEIGDVFVVNKADMDgvNRTVAELEEMIH--LRDNpgakldtghhgvdtslpagvseangqangtdadepD------ 261
                                       5566799****999865666666666666..6555788889999999999888888776666655553332...... PP

                                       HHTTT.......TTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 161 gekge.......kevpvvfgSalkgegvktllealvel 191
                                           +        +  +v + a +g+gv++l+e+l  +
  gi|313127120|ref|YP_004037390.1| 262 ----DaadddpeWKPAIVETVATTGDGVDELVETLGAH 295
                                       ....0444444456789999999999999999998666 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.5e-05    0.0098       1      33 [.      58      90 ..      58      96 .. 0.95
   2 ?   -2.4   0.0       6.5   4.1e+03      42      60 ..     144     162 ..     136     188 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrvgti 33
                                      v+gi+g  g+GK tL+ kl ++ ++ gl+vg+i
  gi|313127120|ref|YP_004037390.1| 58 VIGITGSPGAGKSTLVDKLAKAYRDDGLTVGVI 90
                                      799****************************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.5
                              MobB  42 vdkpgkDsyrhrkAGAkev 60 
                                       +d  gkD   ++  GA + 
  gi|313127120|ref|YP_004037390.1| 144 LDAFGKDKIIVETVGAGQN 162
                                       5666777766666555443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00016       0.1       2      27 ..      58      83 ..      57      88 .. 0.86
   2 ?    1.3   0.0      0.46   2.9e+02      88     114 ..     283     322 ..     281     329 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaeg 27
                                      ++ ++G +G GK+tL+ kla a +++
  gi|313127120|ref|YP_004037390.1| 58 VIGITGSPGAGKSTLVDKLAKAYRDD 83
                                      6779****************998766 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.46
                                       E-STT-SS-TCH......................HHHHHC CS
                             NACHT  88 DglDelvtdlgq.............kekqpvrtlLselir 114
                                       Dg+Delv+ lg+             k +++  + +++l+r
  gi|313127120|ref|YP_004037390.1| 283 DGVDELVETLGAhaefltesgmreqKARTRYAEEIRQLLR 322
                                       9**********99999999996665555555566666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.5e-05     0.029       5      51 ..      56      98 ..      51     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsst 51
                                      a ++ +tG +G+GK+tl+ +l++ +       +   ++v+ v+++s+ 
  gi|313127120|ref|YP_004037390.1| 56 ADVIGITGSPGAGKSTLVDKLAKAYRD-----DgLTVGVIGVDPSSPY 98
                                      667889****************99842.....2346666666666665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   5.5e-05     0.035       2      22 ..      59      79 ..      58      90 .. 0.83
   2 ?   -1.4   0.1       3.9   2.5e+03     122     144 ..     300     324 ..     288     337 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar 22
                                      i itG +++GK+tl+ +La+ 
  gi|313127120|ref|YP_004037390.1| 59 IGITGSPGAGKSTLVDKLAKA 79
                                      569****************65 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.9
                            AAA_28 122 dddgeRre..dleereaiderlrea 144
                                       ++ g R++  + +++e+i ++lr+ 
  gi|313127120|ref|YP_004037390.1| 300 TESGMREQkaRTRYAEEIRQLLRND 324
                                       5566665412444555555555544 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.5e-05     0.029       1      29 [.      58      86 ..      58     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvk 29
                                      vIg++gs GaGk+t+  kl k+ +  +++
  gi|313127120|ref|YP_004037390.1| 58 VIGITGSPGAGKSTLVDKLAKAYRDDGLT 86
                                      8********************99987776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015     0.095      89     122 ..      45      79 ..      13      95 .. 0.78
   2 ?   -1.6   0.0       3.5   2.2e+03      73     104 ..     268     299 ..     255     304 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                        +++l+++  d +++ + G+ G+GKStL+++l+  
  gi|313127120|ref|YP_004037390.1|  45 LVSRLHAHTGDaDVIGITGSPGAGKSTLVDKLAKA 79 
                                       45566666666678889**************9874 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.5
                                       HHTTSEEEE--TTTHTTHHHHHHHCTTSEEEE CS
                       RsgA_GTPase  73 ealgyevllvsaktkegleelkellkdktsvl 104
                                        ++  +++ + a+t++g++el e l  +  +l
  gi|313127120|ref|YP_004037390.1| 268 PEWKPAIVETVATTGDGVDELVETLGAHAEFL 299
                                       567778888999999******99998766544 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00013     0.082       1      20 [.      62      81 ..      62      91 .. 0.82
   2 ?   -1.0   0.1       3.5   2.3e+03      47      69 ..     311     333 ..     277     351 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                                      EE-TTSSHHHHHHHHHHHHT CS
                            AAA_17  1 lGgPGsGKgtqceklvekyg 20
                                      +G PG+GK+t+++kl++ y 
  gi|313127120|ref|YP_004037390.1| 62 TGSPGAGKSTLVDKLAKAYR 81
                                      699**************994 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.5
                                       CTSHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17  47 rklpleekkelqkeaaekiaeea 69 
                                        +  +e+++ l+  a e ++ee 
  gi|313127120|ref|YP_004037390.1| 311 TRYAEEIRQLLRNDANELLKEEL 333
                                       23344555556666666555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.3e-05     0.047      18      44 ..      58      84 ..      46      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqg 44
                                      +i + G+pGAGKs+l ++l+++ + +g
  gi|313127120|ref|YP_004037390.1| 58 VIGITGSPGAGKSTLVDKLAKAYRDDG 84
                                      66789**************99986554 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.4e-05     0.054       5      36 ..      60      91 ..      57      98 .. 0.90
   2 ?   -3.4   0.0       8.2   5.2e+03      53      70 ..     306     323 ..     291     331 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-05
                                      EEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                             KTI12  5 vltGlPssGKstrakeLakaleeekrsvvvid 36
                                       +tG P +GKst++++Laka ++ + +v vi 
  gi|313127120|ref|YP_004037390.1| 60 GITGSPGAGKSTLVDKLAKAYRDDGLTVGVIG 91
                                      59************************999986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.2
                                       HHHHHHHHHHHHHHHHTT CS
                             KTI12  53 ekalRsslrsavkrdLsk 70 
                                       e+++R++  +++++ L +
  gi|313127120|ref|YP_004037390.1| 306 EQKARTRYAEEIRQLLRN 323
                                       555555555555555444 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.7e-05     0.036      18      47 ..      54      83 ..      39     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                        KAP_NTPase 18 atpivvgLygkWGsGKssllnkledelkef 47
                                      ++  v+g++g  G+GKs+l+ kl +++++ 
  gi|313127120|ref|YP_004037390.1| 54 GDADVIGITGSPGAGKSTLVDKLAKAYRDD 83
                                      66779********************99887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00015     0.096       2      22 ..      59      79 ..      58      90 .. 0.88
   2 ?   -1.8   0.1       5.1   3.3e+03      70      70 ..     192     192 ..     136     233 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      ++i G p +GKStL+ +l ++
  gi|313127120|ref|YP_004037390.1| 59 IGITGSPGAGKSTLVDKLAKA 79
                                      89**************99875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.1
                                       H CS
                          MMR_HSR1  70 f 70 
                                       +
  gi|313127120|ref|YP_004037390.1| 192 I 192
                                       2 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.077       5      30 ..      58      83 ..      55     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                    Ploopntkinase3  5 liylvGqPGaGkstlmaeltkgfdrs 30
                                      +i + G+PGaGkstl+ +l+k++   
  gi|313127120|ref|YP_004037390.1| 58 VIGITGSPGAGKSTLVDKLAKAYRDD 83
                                      67799****************99765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00015     0.094       4      22 ..      61      79 ..      58      92 .. 0.84
   2 ?   -2.2   0.0       6.5   4.2e+03      78      89 ..     303     314 ..     282     337 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                            AAA_33  4 lvGlpGsGKstlaerllkk 22
                                      + G pG+GKstl+++l+k+
  gi|313127120|ref|YP_004037390.1| 61 ITGSPGAGKSTLVDKLAKA 79
                                      68**************987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.5
                            AAA_33  78 tnlsrrerarfl 89 
                                       +++++++r r+ 
  gi|313127120|ref|YP_004037390.1| 303 GMREQKARTRYA 314
                                       333333332222 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014     0.088      11      42 ..      48      78 ..      42      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                      HHHC.TTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 11 kLle.kdelqslvvalvGmgGvGKttlakqiln 42
                                      +L    ++ +  v+++ G +G GK+tl+ +  +
  gi|313127120|ref|YP_004037390.1| 48 RLHAhTGDAD--VIGITGSPGAGKSTLVDKLAK 78
                                      5553244555..***************998766 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.12      53      84 ..      56      87 ..      31      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                            DUF815 53 annvLLwGarGtGKSslvkallneyaeegLrl 84
                                      a  + ++G+ G+GKS+lv  l ++y+++gL +
  gi|313127120|ref|YP_004037390.1| 56 ADVIGITGSPGAGKSTLVDKLAKAYRDDGLTV 87
                                      5556689**********************864 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00056      0.36       3      23 ..      61      81 ..      59      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                      RNA_helicase  3 lyGpsgeGKStlakeLakall 23
                                      ++G++g GKStl+++Laka  
  gi|313127120|ref|YP_004037390.1| 61 ITGSPGAGKSTLVDKLAKAYR 81
                                      79**************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2595.57
//
Query:       gi|313127121|ref|YP_004037391.1|  [L=143]
Description: methylmalonyl-CoA mutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-22   79.9   0.2    1.7e-22   79.7   0.2    1.1  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.24   11.2   0.0    1.5  1  Staph_haemo  Staphylococcus haemolytic protein
       0.14   11.1   0.0       0.18   10.8   0.0    1.1  1  IMPDH        IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.2   2.8e-26   1.7e-22       2     117 ..      15     129 ..      14     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 2.8e-26
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkri 78 
                                       + l+a+vg d h++G+ v+a+a+rdagfeV++ g+   +e+iv+a+ +e++dv+g+S+l++++ + v ++++ lk++
  gi|313127121|ref|YP_004037391.1|  15 RCLIAKVGLDGHDRGAHVIARAFRDAGFEVIYSGLHRAPEEIVQAAVQEDVDVLGISILSGAHNTLVPKIIDGLKEY 91 
                                       6899*********************************************************************8877 PP

                       B12-binding  79 rp..rvkvvvGGahpsldpeetleaklgiddvvvgegedal 117
                                       ++  ++ ++vGG++p  d  e l++ +g +  v+g g+   
  gi|313127121|ref|YP_004037391.1|  92 DAfeDTLILVGGIVPDEDRPE-LKE-MG-VSEVFGPGTPMQ 129
                                       6555**************999.555.**.888****98655 PP

>> Staph_haemo  Staphylococcus haemolytic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.1e-05      0.24       5      28 ..      50      73 ..      47      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                       Staph_haemo  5 feAikntVeAaikqDwveLGtsIv 28
                                        A   +V+Aa+++D   LG sI 
  gi|313127121|ref|YP_004037391.1| 50 HRAPEEIVQAAVQEDVDVLGISIL 73
                                      556678****************96 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     3e-05      0.18     104     170 ..      52     121 ..      35     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3e-05
                                       THHHHHHHHHHTT-SEEEEE-STS.SSHHHHHHHHHHHH..HTTTSEEEEEEE-SHHHHHHHHHTT-SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 104 dalervkalveagvdvlvvdsahg.hsekvleavkeikk..kveeveviaGnvataegakaLieagadav 170
                                         +e v+a v+++vdvl + +  g h++ v + ++ +k+  ++e+  +++G ++  e   +L e+g+  v
  gi|313127121|ref|YP_004037391.1|  52 APEEIVQAAVQEDVDVLGISILSGaHNTLVPKIIDGLKEydAFEDTLILVGGIVPDEDRPELKEMGVSEV 121
                                       55778999***********986652778888999999963256678889999*************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 956.83
//
Query:       gi|313127122|ref|YP_004037392.1|  [L=403]
Description: gaf domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-17   62.0   0.5    1.8e-16   60.7   0.1    1.9  2  GAF_2     GAF domain
    1.4e-10   41.6   0.2    3.3e-10   40.4   0.0    1.7  2  GAF_3     GAF domain
    1.4e-05   25.8   0.2    4.5e-05   24.1   0.1    2.0  2  GAF       GAF domain
  ------ inclusion threshold ------
      0.082   13.6   1.3       0.84   10.3   1.1    2.6  2  SnoaL_2   SnoaL-like domain
      0.083   12.9   0.4       0.27   11.3   0.4    1.8  1  DUF834    Domain of unknown function (DUF834)


Domain annotation for each model (and alignments):
>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.9   3.2e+03      14      38 ..      49      81 ..      44     128 .. 0.53
   2 !   60.7   0.1   5.1e-20   1.8e-16       2     137 ..     144     268 ..     143     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.9
                                      HHHHSS....EEEEEEE-TTS-EEEE.......E CS
                             GAF_2 14 elvelg..aalgyillvdddgglrla.......a 38
                                      +++elg  ++ + ++l ddd+ ++l+       +
  gi|313127122|ref|YP_004037392.1| 49 YVHELGptID-CALVLSDDDELVELLveasngvP 81
                                      5666653233.44444444444332243333330 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 5.1e-20
                                       HHHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG- CS
                             GAF_2   2 adleelldlvldelve.lgaalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleed 77 
                                        +++e+ +++l ++v+ l ++++ ++lv+dd+  + +a++ a++  ++++   ++eg++g+ +rtg+  +++d++ d
  gi|313127122|ref|YP_004037392.1| 144 ESVSEVCEETLAAAVDaLAFTFCTVALVEDDRI-VPRASTLAPDDYRSCH---VSEGIAGRTYRTGKTQLVDDIALD 216
                                       5899************889**********8775.4447777776666666...89******************7775 PP

                                       S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  78 pdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +d     +  ++ rs+++vP+   g ++Gv+ +++n p+afde+d e+Le la+  a a+
  gi|313127122|ref|YP_004037392.1| 217 DDT----LFSEARRSTVSVPF---G-PYGVIQVVSNSPNAFDERDAEFLEILADYTAEAL 268
                                       554....344578999*****...9.*******************************998 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.7   1.3e+04      15      39 ..     105     129 ..     101     137 .. 0.55
   2 !   40.4   0.0   9.1e-14   3.3e-10       2     129 .]     146     270 ..     145     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.7
                             GAF_3  15 kllgaevgalllldedgnklqvaag 39 
                                       +ll++ ++a+   +++ + + ++a+
  gi|313127122|ref|YP_004037392.1| 105 RLLNCLSAAIAADQRESELVEANAK 129
                                       5556666666555544444454444 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 9.1e-14
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvsepsfaee.dg 77 
                                       + e++e++l ++v++l ++++ + l+++d  +++++a++ + ++  +s+   +  a r++ +g  + + + a   d+
  gi|313127122|ref|YP_004037392.1| 146 VSEVCEETLAAAVDALAFTFCTVALVEDD--RIVPRASTLAPDDY-RSCHVSEGIAGRTYRTGKTQLVDDIALDdDT 219
                                       6799***********************88..999***99555655.59*****************999998664144 PP

                             GAF_3  78 lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                       l ++a     + ++ +++Gv+ + s++p afd++d+e+le lA+++a a++r
  gi|313127122|ref|YP_004037392.1| 220 LFSEARRS-TVSVPFGPYGVIQVVSNSPNAFDERDAEFLEILADYTAEALSR 270
                                       44444433.2568889*********************************987 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.2   7.9e+03      38      97 ..      75      84 ..      48     121 .. 0.55
   2 !   24.1   0.1   1.2e-08   4.5e-05       2     132 ..     146     267 ..     145     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.2
                                      EEECCEEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEE CS
                               GAF 38 qasrwlfmkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvn 97
                                      +as+                                                  +vP+v+
  gi|313127122|ref|YP_004037392.1| 75 EASN--------------------------------------------------GVPVVV 84
                                      2222..................................................233332 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECCEEEET......TSHHHHHHHHHSSSEEESTGG..TS CS
                               GAF   2 leelldtvveelrellgadrvalylpdydGlhydipqasrwlfmkn......grgicgqvlatgqplvipdst..pd 70 
                                       + e+++++++ + ++l+   +++ l + d     +p as+   + +       +gi+g++++tg++ +++d++  +d
  gi|313127122|ref|YP_004037392.1| 146 VSEVCEETLAAAVDALAFTFCTVALVEDDR--I-VPRASTL-APDDyrschvSEGIAGRTYRTGKTQLVDDIAldDD 218
                                       679********************8843444..3.5555555.3333244555777999*************663366 PP

                                       TTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHH CS
                               GAF  71 prfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvava 132
                                         f++            rs ++vP       +G++++++ sp  f++ + e+l+ lad  a a
  gi|313127122|ref|YP_004037392.1| 219 TLFSE----------ARRSTVSVPFG----PYGVIQVVSNSPnAFDERDAEFLEILADYTAEA 267
                                       66777..........55799****99....6********99989*************987766 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.43   1.6e+03      79     100 ..     156     177 ..     128     178 .. 0.82
   2 ?   10.3   1.1   0.00023      0.84       6      76 ..     247     317 ..     242     395 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.43
                                       TTSSEEEEEEEEEEEEETTEEE CS
                           SnoaL_2  79 atgrgvtvrgvdvfrvrdGkiv 100
                                       a  +++ +++++v  v+d++iv
  gi|313127122|ref|YP_004037392.1| 156 AAVDALAFTFCTVALVEDDRIV 177
                                       5556778899999999999997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00023
                                       HHHHTTCHHHHHHT..EEEEEEEEET.TSE.EESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE CS
                           SnoaL_2   6 aalnagdldalaal..fapdvvwedp.gge.lrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt 76 
                                       +a++++d++ l+ l  +++++  +    ++ ++ r+++raff +     p   +++++v+a gdrv  e +  ++
  gi|313127122|ref|YP_004037392.1| 247 NAFDERDAEFLEILadYTAEALSRLDrEAAlRQERDRLRAFFDSH----PVPVVSVEEVTAPGDRVRCETNHAYE 317
                                       588888887665441133333333222333689999999999999....9999**************99888776 PP

>> DUF834  Domain of unknown function (DUF834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   7.6e-05      0.27      11      32 ..      73      94 ..      69      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.6e-05
                            DUF834 11 rvdgdgGvpavfggnepaAGll 32
                                      +v   +Gvp+v+ g+++a+G++
  gi|313127122|ref|YP_004037392.1| 73 LVEASNGVPVVVYGEGRADGVE 94
                                      67788****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2947.22
//
Query:       gi|313127123|ref|YP_004037393.1|  [L=601]
Description: dipeptidyl aminopeptidase/acylaminoacyl peptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-43  146.9   0.0    8.9e-43  146.2   0.0    1.3  1  Peptidase_S9    Prolyl oligopeptidase family
    6.2e-13   48.3  11.8    8.4e-05   22.4   0.2    6.6  6  PD40            WD40-like Beta Propeller Repeat
    6.9e-13   48.6   0.0    2.3e-12   47.0   0.0    1.8  1  DLH             Dienelactone hydrolase family
    1.6e-12   47.2   0.1    8.1e-08   31.8   0.1    2.2  2  Hydrolase_4     Serine aminopeptidase, S33
    5.9e-12   45.7   0.0    5.8e-08   32.7   0.1    2.3  2  Peptidase_S15   X-Pro dipeptidyl-peptidase (S15 family)
    2.7e-10   40.3   0.2    1.4e-05   24.9   0.1    2.2  2  Abhydrolase_1   alpha/beta hydrolase fold
    4.2e-08   32.2   0.0    3.2e-06   26.1   0.0    2.2  1  AXE1            Acetyl xylan esterase (AXE1)
      5e-06   27.3   4.8    0.00011   22.9   1.4    3.2  2  Abhydrolase_6   Alpha/beta hydrolase family
    3.2e-05   23.9   0.0     0.0059   16.5   0.0    2.3  1  BAAT_C          BAAT / Acyl-CoA thioester hydrolase C termina
    6.8e-05   21.8   0.1       0.97    8.1   0.0    4.2  4  DPPIV_N         Dipeptidyl peptidase IV (DPP IV) N-terminal r
    9.9e-05   21.3   0.8      0.059   12.2   0.4    2.7  2  Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propel
    0.00052   19.4   0.0       0.14   11.4   0.0    2.3  2  Lactonase       Lactonase, 7-bladed beta-propeller
     0.0027   17.6   0.1      0.023   14.5   0.1    2.1  1  Abhydrolase_3   alpha/beta hydrolase fold
      0.004   17.4   0.0        1.8    8.9   0.0    3.6  3  ANAPC4_WD40     Anaphase-promoting complex subunit 4 WD40 dom
     0.0098   15.7   0.0        1.8    8.3   0.0    2.2  2  Abhydrolase_2   Phospholipase/Carboxylesterase
  ------ inclusion threshold ------
       0.01   16.1   0.1         16    6.0   0.0    4.4  4  Kelch_6         Kelch motif
       0.03   13.1   0.0      0.044   12.6   0.0    1.1  1  Peptidase_S28   Serine carboxypeptidase S28
      0.031   13.9   0.0       0.19   11.3   0.0    2.2  1  Esterase        Putative esterase
       0.07   13.7   0.7        3.2    8.4   0.1    3.2  3  PepSY           Peptidase propeptide and YPEB domain
      0.092   12.2   0.0       0.33   10.4   0.0    1.8  2  Esterase_phd    Esterase PHB depolymerase
      0.093   12.7   0.0        6.6    6.8   0.0    2.8  2  PQQ             PQQ enzyme repeat
        0.1   12.7   0.0       0.21   11.7   0.0    1.5  1  Abhydrolase_4   TAP-like protein


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.2   0.0   1.1e-45   8.9e-43       1     208 [.     394     600 ..     394     601 .] 0.95

  Alignments for each domain:
  == domain 1  score: 146.2 bits;  conditional E-value: 1.1e-45
                                       ----HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHH CS
                      Peptidase_S9   1 psfsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyl 77 
                                       psf+ + q++ ++Gy+v+ +n+rGs+gyG+a+ +  + ++   +++D+ aa+e+l ++  vd++r++++GgSyGG++
  gi|313127123|ref|YP_004037393.1| 394 PSFNAVKQYFLANGYAVFEPNVRGSAGYGKAYGHLDDVENRMDSVADIEAAVEWLHDHPAVDPDRIVAMGGSYGGFM 470
                                       68997777777****************************************************************** PP

                                       HHHHHHH-GGG-SEEEEESE---CCCHHCSTTS.THH.HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEET CS
                      Peptidase_S9  78 tgaalnqrpdlFkaavaevpvvdvlrydsdtdl.lte.eymewgnpeeneegykelspyspldnvkaypplLlihGl 152
                                       ++a +++ pdl++a++  v++++ +++  +t     e +  e+g  e+++e  + +sp+++ ++  + +pl+++hG+
  gi|313127123|ref|YP_004037393.1| 471 VLASMTEYPDLWAAGIDTVGIANFVTFLENTGDwRRElREAEYGSLEDDREFLESISPINNIEK--IRAPLFVLHGE 545
                                       ******************************9886566899999999999999999999999999..99********* PP

                                       T-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHH CS
                      Peptidase_S9 153 aDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkea 208
                                       +D rvp++ea ++v++  + +++v+ lif degHg+ k ++++e ++ +++Fl+e+
  gi|313127123|ref|YP_004037393.1| 546 NDPRVPVSEAHQIVEKAGE-HVPVRELIFEDEGHGFTKLENRIEAYEAIVEFLDEH 600
                                       ***************9876.899******************************998 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0086         7      11      38 .]      15      41 ..       6      41 .. 0.87
   2 !   22.4   0.2     1e-07   8.4e-05      14      38 .]     109     134 ..     104     134 .. 0.93
   3 ?    0.8   0.1      0.62   5.1e+02      16      24 ..     159     167 ..     157     169 .. 0.86
   4 ?    3.6   0.1     0.083        68      16      38 .]     206     228 ..     205     228 .. 0.85
   5 ?    5.8   0.0     0.017        14      14      35 ..     250     270 ..     246     271 .. 0.85
   6 !   10.6   0.1   0.00053      0.44      12      31 ..     296     315 ..     292     322 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0086
                                      EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
                              PD40 11 egaPsfSPDGkrlaFsSdRgsGkpdIyv 38
                                       ++ sf PDG rl F  d + G p++++
  gi|313127123|ref|YP_004037393.1| 15 AYGASFGPDGERLSFLMDTT-GVPQVWT 41
                                      67899***************.*****95 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1e-07
                                       EEE-TTSSEEEEEEECT..TCEEEEE CS
                              PD40  14 PsfSPDGkrlaFsSdRg.sGkpdIyv 38 
                                         +S+DG r+aF+S+R  +  +d+yv
  gi|313127123|ref|YP_004037393.1| 109 GGWSNDGDRFAFTSNRRdEAVFDVYV 134
                                       57***********************8 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.62
                                       E-TTSSEEE CS
                              PD40  16 fSPDGkrla 24 
                                       +SPD ++l+
  gi|313127123|ref|YP_004037393.1| 159 WSPDDSMLV 167
                                       ****99987 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.083
                                       E-TTSSEEEEEEECT.TCEEEEE CS
                              PD40  16 fSPDGkrlaFsSdRgsGkpdIyv 38 
                                       + PDG   + +SdR+s + d+++
  gi|313127123|ref|YP_004037393.1| 206 WGPDGENVYLVSDRDSDTLDLWR 228
                                       77*************66666886 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.017
                                       EEE-TTSSEEEEEEECT.TCEE CS
                              PD40  14 PsfSPDGkrlaFsSdRgsGkpd 35 
                                        +++ D +r+++s + + G+++
  gi|313127123|ref|YP_004037393.1| 250 VAVDHDSRRIVYSTNVD-GYTE 270
                                       57899***********9.9986 PP

  == domain 6  score: 10.6 bits;  conditional E-value: 0.00053
                                       EEEEE-TTSSEEEEEEECT. CS
                              PD40  12 gaPsfSPDGkrlaFsSdRgs 31 
                                       g+ sfSPDG r+a + +R+s
  gi|313127123|ref|YP_004037393.1| 296 GGVSFSPDGDRFAVTVSRSS 315
                                       7789*********9999983 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   2.8e-15   2.3e-12      27     195 ..     394     586 ..     362     596 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.8e-15
                               DLH  27 dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksvpevstkkvgvv 103
                                         ++ +++ ++ +GY+++ P++    +          +a+ +l++ ++  + ++d++aav++l+  p v++++++++
  gi|313127123|ref|YP_004037393.1| 394 PSFNAVKQYFLANGYAVFEPNVRGSAG--------YGKAYGHLDDVENRMDSVADIEAAVEWLHDHPAVDPDRIVAM 462
                                       566789999999999999999966555........4555556665555567888999******************** PP

                               DLH 104 GfCmGGalalllaaev.pevdaavafYG................................lspekeleeaakikapi 147
                                       G   GG ++l++ +e  +  +a +   G                                l+  +++++++ki ap+
  gi|313127123|ref|YP_004037393.1| 463 GGSYGGFMVLASMTEYpDLWAAGIDTVGianfvtflentgdwrrelreaeygsleddrefLESISPINNIEKIRAPL 539
                                       **************99677788999999******************************999999************* PP

                               DLH 148 lalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre 195
                                       ++l+ge+D+ +p +e++++ e+   ++v+++  ++++ gH+F++ +++
  gi|313127123|ref|YP_004037393.1| 540 FVLHGENDPRVPVSEAHQIVEKA-GEHVPVRELIFEDEGHGFTKLENR 586
                                       **********************9.99****************998876 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   9.9e-11   8.1e-08       6     103 ..     380     484 ..     377     492 .. 0.85
   2 !   13.1   0.0   5.2e-05     0.042     186     219 ..     531     564 ..     521     580 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 9.9e-11
                       Hydrolase_4   6 vvvlvHGlaehsgr..yaelaeaLaaqGfavyalDhrG...hGrsegkrghvpsfddyvdDlaafvekvkeehpel. 76 
                                       v+v +HG  e+ +r  ++ + +++ a+G+av+  + rG   +G+  g+  +v++  d v+D++a+ve +  +hp   
  gi|313127123|ref|YP_004037393.1| 380 VIVDIHGGPESQRRpsFNAVKQYFLANGYAVFEPNVRGsagYGKAYGHLDDVENRMDSVADIEAAVEWLH-DHPAVd 455
                                       678899999999876578899***************97222566669999999999**********9998.555555 PP

                       Hydrolase_4  77 ..plfllGhSmGGliallyllrypdkvag 103
                                         +++ +G S GG+++l+ +++ypd +a+
  gi|313127123|ref|YP_004037393.1| 456 pdRIVAMGGSYGGFMVLASMTEYPDLWAA 484
                                       7899*********************8875 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.2e-05
                       Hydrolase_4 186 raakitlPllllhGeaDkvvdpeasrelyerlgs 219
                                       + +ki++Pl++lhGe+D+ v+ +++++++e++g 
  gi|313127123|ref|YP_004037393.1| 531 NIEKIRAPLFVLHGENDPRVPVSEAHQIVEKAGE 564
                                       6789**************************9996 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   7.1e-11   5.8e-08       1     140 [.     358     496 ..     358     508 .. 0.75
   2 !   10.9   0.0   0.00032      0.26     204     267 ..     512     578 ..     498     579 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.1e-11
                                       TS-EEEEEEEEE...TTSSSEEEEEEEESS-CCT.CCCCHTTCHHCCHGGGHHHHHTT-EEEEEE-TTS...TTS-S CS
                     Peptidase_S15   1 DGvrLavdiyrP.etkskeklPvlltrtPYgkndelasdkalaleelelqdkvfvarGYavVvqdvrGt...ggSeG 73 
                                       DG ++ +   +P ++++++ +Pv++      ++  +++ + +        ++ f+a+GYav   +vrG+   g+  G
  gi|313127123|ref|YP_004037393.1| 358 DGREIPAFFSLPdDDAGEGDTPVIVDIHGGPES--QRRPSFN------AVKQYFLANGYAVFEPNVRGSagyGKAYG 426
                                       566666666677777777777777776543322..2223332......33345**************9833246778 PP

                                       ---TT..TTTHHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCC CS
                     Peptidase_S15  74 eftvg..dsdeaedgadvidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyd 140
                                         +      d ++d  ++++Wl+ +     +++ ++G SY+G++ l+  ++ ++  +a + +++i+++++
  gi|313127123|ref|YP_004037393.1| 427 HLDDVenRMDSVADIEAAVEWLHDHpAVDPDRIVAMGGSYGGFMVLASMTEYPDLWAAGIDTVGIANFVT 496
                                       8887789999***************89999*****************99988887777777777777665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00032
                                       CCCC--SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EEEEECECT CS
                     Peptidase_S15 204 elletgdydafWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..klilgpwtH 267
                                       e+ + +d ++f +++++ ++++k++ap+++++G nD  v   +a ++ e++ ++    +li+    H
  gi|313127123|ref|YP_004037393.1| 512 EYGSLEDDREFLESISPINNIEKIRAPLFVLHGENDPRVPvSEAHQIVEKAGEHVPvrELIFEDEGH 578
                                       5556788999**************************8888888888888887775577777776666 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.7e-08   1.4e-05       1      96 [.     379     480 ..     379     506 .. 0.82
   2 !   13.4   0.0   5.6e-05     0.046     206     250 ..     518     578 ..     487     582 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-08
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTS.TTSSSTTTGB.CHH.....SHHHHHHHHHHH..HHH CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGv.gySspapacinddy.....gtasvaddldri..lda 69 
                                       pv+v +hG+p+s   +  +++ +++  +g+ v+ +++rG+ gy+++      dd      + a++++ ++++    a
  gi|313127123|ref|YP_004037393.1| 379 PVIVDIHGGPESQRRPSFNAVKQYFLANGYAVFEPNVRGSaGYGKAYGHL--DDVenrmdSVADIEAAVEWLhdHPA 453
                                       78999******999988889*******************74666666666..3333344556666677779977778 PP

                                       CTTSSEEEEEETHHHHHHHHHHHHHGG CS
                     Abhydrolase_1  70 lgddkltlvGhSmGGmialayaaeype 96 
                                        + d+++ +G+S+GG+++la   eyp+
  gi|313127123|ref|YP_004037393.1| 454 VDPDRIVAMGGSYGGFMVLASMTEYPD 480
                                       9*******************9999998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.6e-05
                                       C.............THHHHSEEEEEEETTCSSSCHHHHHHHHHC.HTS..EEEEEEETCSS CS
                     Abhydrolase_1 206 e.............lknvlaptlvisgtsDplvppkaledlaql.lpk..krlvvisdagH 250
                                                     + ++ ap +v++g++Dp vp ++  ++ ++   +  +r+++++d+gH
  gi|313127123|ref|YP_004037393.1| 518 DdreflesispinnIEKIRAPLFVLHGENDPRVPVSEAHQIVEKaGEHvpVRELIFEDEGH 578
                                       24445555555555666777***************6666666663444777********** PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   3.9e-09   3.2e-06      59     191 ..     352     474 ..     343     483 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.9e-09
                                       EEEEEGGGEEEEEEEEEES.S..SSSEEEEEEEE-TT--GGGHH.HHH..HHHHTT-EEEEEE-TTTS..SSB-SSC CS
                              AXE1  59 ltfegvrgarikaklvlPkek..eeklPavvefhGYegsrgeih.dll..nyaaaGyavvvmdvRGqggesedkvgs 130
                                       + + ++ g +i a + lP++   e+  P++v  hG  +s+  ++ + +   + a+Gyav+  +vRG  g+       
  gi|313127123|ref|YP_004037393.1| 352 VHYPTFDGREIPAFFSLPDDDagEGDTPVIVDIHGGPESQRRPSfNAVkqYFLANGYAVFEPNVRGSAGYG------ 422
                                       78999*************976226789*******987774443314442158899***********99664...... PP

                                       CSS-SSSSTTTTTTSTTT-HHHHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHH CS
                              AXE1 131 kgnkakGfiirGlldkeklyyrrvflDavrlveivaslpevDeeRvavlGasqGGalalav 191
                                          ka G++    +d e+ +  +   D+  +ve ++++p vD++R++++G+s GG + la 
  gi|313127123|ref|YP_004037393.1| 423 ---KAYGHL----DDVENRM--DSVADIEAAVEWLHDHPAVDPDRIVAMGGSYGGFMVLAS 474
                                       ...456774....4544432..4568*****************************999985 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.5   1.2e+03      99     127 ..      35      67 ..      10     200 .. 0.53
   2 !   22.9   1.4   1.4e-07   0.00011       4     208 ..     384     580 ..     381     595 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.5
                                       ---TTT.S----TTHHHHHH...TT-C.CCCHCC CS
                     Abhydrolase_6  99 alpagl.laaalelllalla...llrl.lawlsr 127
                                       ++p  + l+ +++++++++    +  + + w+ +
  gi|313127123|ref|YP_004037393.1|  35 GVPQVWtLDGPAAWPEQRTFydeRV-TfASWSPE 67 
                                       3333333333333333222211111.12344332 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.4e-07
                                       E--GC.......GCHHHH.HHHHCCTCEEEEE--TTS...TS-GGCS--HHH....CHHHHHHHCCTT......TTS CS
                     Abhydrolase_6   4 lHGagss..assWlvapL.aallaagvhvlapDlpGh...Grsdpppldled....ladlaalldelaa....gggp 66 
                                       +HG++ s  + s+    + +++la g++v+ p  +G    G + ++ +d+e+    +ad++a+++ l +    ++++
  gi|313127123|ref|YP_004037393.1| 384 IHGGPESqrRPSFN--AVkQYFLANGYAVFEPNVRGSagyGKAYGHLDDVENrmdsVADIEAAVEWLHDhpavDPDR 458
                                       68877655566664..334667899*999******887335555555555556666788877777776678889*** PP

                                       EEEEEETCHHHHHHHHHHCC..EEEEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHCCCC CS
                     Abhydrolase_6  67 vvlvGHSlGGalalaaaplalvvgvlldppptalpagllaaalelllallallrllawlsreplprlfladedadaa 143
                                       +v++G S+GG+++la          + +     + ++ + + + ++  ++ l+ +  w++      ++ +     a+
  gi|313127123|ref|YP_004037393.1| 459 IVAMGGSYGGFMVLA---------SMTEY---PDLWAAGIDTVGIANFVTFLENTGDWRR------ELRE-----AE 512
                                       ***********9999.........66666...3344444444444444444555556663......5555.....55 PP

                                       HCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH...STTEEET...CE...SSS.- CS
                     Abhydrolase_6 144 wrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerlla...qagarlp...vvlpgaGH.l 208
                                       ++   ++   l +        +++ +++pl+vl g++Dp vp  + ++++   +ag+++p    ++++ GH +
  gi|313127123|ref|YP_004037393.1| 513 YGSLEDDREFLESISP---INNIEKIRAPLFVLhGENDPRVP--VSEAHQiveKAGEHVPvreLIFEDEGHgF 580
                                       5555555544444333...55999999999888679999999..88888888888888888888888999943 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.2e-06    0.0059       7     162 ..     442     579 ..     441     582 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.2e-06
                                       HHHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-E CS
                            BAAT_C   7 eeainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdeskvlpelklsmeklk 83 
                                       e a+++l +hp v  d+i  +G S Gg ++l+  + +++  a+ + + + +++            l++ +   ++l 
  gi|313127123|ref|YP_004037393.1| 442 EAAVEWLHDHPAVDPDRIVAMGGSYGGFMVLASMTEYPDLWAAGIDTVGIANF-----VT----FLENTGDWRRELR 509
                                       789****************************9889999876654444444443.....22....3344444555555 PP

                                       E-TTS-EE-TT-B--TTTGGGCCCB--GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB- CS
                            BAAT_C  84 vnknglldivdvlallkeklaekalipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaG 160
                                       + + g+l++ + + +  +      + ++ek+++p+ ++ ge+D  +p +e      +  +kag++v v+ l++++ G
  gi|313127123|ref|YP_004037393.1| 510 EAEYGSLEDDREFLESISP-----INNIEKIRAPLFVLHGENDPRVPVSEAH----QIVEKAGEHVPVRELIFEDEG 577
                                       5555655555555444322.....3457899999999999999888876665....345678888888888888888 PP

                                       S- CS
                            BAAT_C 161 Hl 162
                                       H 
  gi|313127123|ref|YP_004037393.1| 578 HG 579
                                       85 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.73   5.9e+02     104     128 ..      16      39 ..      12      54 .. 0.85
   2 ?   -1.8   0.0       1.2     1e+03      42      61 ..      56      75 ..      38      77 .. 0.78
   3 !    8.1   0.0    0.0012      0.97      20      64 ..     174     220 ..     160     247 .. 0.80
   4 !    5.7   0.0    0.0066       5.4     189     224 ..     298     332 ..     270     367 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.73
                                       BEEEE-TTSSEEEEEEEECTTS-EE CS
                           DPPIV_N 104 savwWspdgsrlaylrfdeseVpei 128
                                        +  + pdg+rl++l +d ++Vp++
  gi|313127123|ref|YP_004037393.1|  16 YGASFGPDGERLSFL-MDTTGVPQV 39 
                                       677899*******99.799999875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                      TT.BSEEEEESSTTEEEEEE CS
                           DPPIV_N 42 eeklqlakwSPagdklafvr 61
                                      +e++++a wSP++  l+f  
  gi|313127123|ref|YP_004037393.1| 56 DERVTFASWSPENPELVFGM 75
                                      67899999***999999965 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0012
                                       EETTEEEEEETTTEECEEEETT..TT.BSEEEEESSTTEEEEEETTE CS
                           DPPIV_N  20 sytaeyyiydletneveelspg..eeklqlakwSPagdklafvrnnn 64 
                                       ++ +++ + d+et+e+++l+p+  + + q a+w P+g++++ v +++
  gi|313127123|ref|YP_004037393.1| 174 NFDQDVSVLDVETGELTHLTPHegTVRFQSAEWGPDGENVYLVSDRD 220
                                       57788999999999999999997777889999999999999998875 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0066
                                       EEECTTSCCEEEEEEETTSTEEEEEEEETTTCCEEE CS
                           DPPIV_N 189 vkWtsdeksllvqwlnRsqnrlkvvlvdaetgravv 224
                                       v++++d++   +++++Rs+++++v++vda+tg+++ 
  gi|313127123|ref|YP_004037393.1| 298 VSFSPDGD-RFAVTVSRSSDTANVYVVDAKTGEVTQ 332
                                       55666666.445566777777777777777655443 PP

>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.4   7.2e-05     0.059     116     350 ..      47     271 ..      37     290 .. 0.78
   2 !    6.1   0.0     0.005       4.1     233     265 ..     297     329 ..     282     339 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.2e-05
                                       GGSTTS-.EE..EEEEEE-TTSSEEEEEEEETTSSEEEEEEEE.TTTTEEEEEEEEEEESEEEEECTTSSEEEEEES CS
                    Peptidase_S9_N 116 tlsedgtfva..lgefavsedgkllAyslsksGsdwytirvkd.ietgedlpdeledvkfsgivWaadekgffYtry 189
                                       +++e+ tf++  ++  + s+++  l ++++++G++++++  +d i+ g +   e+ d+k     W +d++ f +t+ 
  gi|313127123|ref|YP_004037393.1|  47 AWPEQRTFYDerVTFASWSPENPELVFGMDEGGNERQQLLRYDpISGGISNLTEMPDAKHRWGGWSNDGDRFAFTSN 123
                                       5666777775224445599*****************998888725555777888999999999************** PP

                                       S-SSS-TSTSB-S-BEEEEEETTS-GGG-EEEES-TTGTTBEEEEEE-TTSSEEEEEEESSSS--EEEEEEGGGTSS CS
                    Peptidase_S9_N 190 dkedersdtdtnlnqkvyrhkLGtaqseDelvfeeeeepkwllgaersedgkylfissasgtdtnelyvldlekesk 266
                                       ++++ + d        vy    ++  + +e+v+e    + wl+    s d++ l++s a +  ++++ vld+e ++ 
  gi|313127123|ref|YP_004037393.1| 124 RRDEAVFD--------VYVQGRDETGDAAEMVHE---GDGWLTVGGWSPDDSMLVVSEAYSNFDQDVSVLDVETGE- 188
                                       *9999999........999944555555666766...888999899999999999986655559*********995. PP

                                       --EEEEESSSSS-EEEEEE..ETTEEEEEE-TT-TT-EEEEEETTSSSGGGEEEEE--.SSCEEEEEEECTT..EEE CS
                    Peptidase_S9_N 267 kvlklvdnrfdaeysvehn..egdrfliltndgapnfrlvsvdlndpspsewkelvperekvvleeitvfkn..ylv 339
                                         + l + +   +++   +  +g++ ++ +++++    l +v++++ +      lv+e+++  +++++v+ +  ++v
  gi|313127123|ref|YP_004037393.1| 189 -LTHLTPHEGTVRFQSAEWgpDGENVYLVSDRDSDTLDLWRVNVESGE----FSLVAEDDEWEIDGVAVDHDsrRIV 260
                                       .88888885555888888878899******************999997....3599999999999777766511444 PP

                                       EEEEETTEEEE CS
                    Peptidase_S9_N 340 vsyrkdvlsrv 350
                                        s   d+ +++
  gi|313127123|ref|YP_004037393.1| 261 YSTNVDGYTEL 271
                                       44445555555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.005
                                       EEEE-TTSSEEEEEEESSSS--EEEEEEGGGTS CS
                    Peptidase_S9_N 233 gaersedgkylfissasgtdtnelyvldlekes 265
                                       g+++s dg    +++++++dt+++yv d++ ++
  gi|313127123|ref|YP_004037393.1| 297 GVSFSPDGDRFAVTVSRSSDTANVYVVDAKTGE 329
                                       555566666666666666666666666555543 PP

>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0098         8     252     333 ..     160     242 ..     154     249 .. 0.69
   2 !   11.4   0.0   0.00017      0.14     245     295 ..     294     344 ..     261     350 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0098
                                       -TTSSEEEEEETS...STEEEEEEE-TTT--EEEEEEEE-SSS.--EEEE-TTSSEEE.EEETTTTEEEEEEEETTT CS
                         Lactonase 252 spdgkflyvSnRg...adsiavfavdeadgtltlveevstegkfPRdfaldpsgklll.vanqksdnvtvferdaet 324
                                       spd++ l+vS+     +  ++v++v  ++g+lt+ +  + + +   + ++ p+g+ ++ v++++sd++ + +++ e+
  gi|313127123|ref|YP_004037393.1| 160 SPDDSMLVVSEAYsnfDQDVSVLDV--ETGELTHLTPHEGTVR-FQSAEWGPDGENVYlVSDRDSDTLDLWRVNVES 233
                                       5677777777766665666777777..4566666544433333.245567788877753788999999999999999 PP

                                       TEEEEESEE CS
                         Lactonase 325 GkLtelgkd 333
                                       G+ + + +d
  gi|313127123|ref|YP_004037393.1| 234 GEFSLVAED 242
                                       998877665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00017
                                       -EEEEEE-TTS.SEEEEEETSSTEEEEEEE-TTT--EEEEEEEE-SSS.--E CS
                         Lactonase 245 saaeIrlspdg.kflyvSnRgadsiavfavdeadgtltlveevstegkfPRd 295
                                        a+ +  spdg +f ++ +R++d+  v+ vd+++g++t+ ++++t g  PRd
  gi|313127123|ref|YP_004037393.1| 294 VAGGVSFSPDGdRFAVTVSRSSDTANVYVVDAKTGEVTQWTHAATAGI-PRD 344
                                       567788888875677888899999999999999999999999999888.997 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   2.8e-05     0.023      49      90 ..     438     476 ..     435     582 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHH CS
                     Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaaval 90 
                                       v d+ aa++wl+++    ++dp+riv +G S GG +++a + 
  gi|313127123|ref|YP_004037393.1| 438 VADIEAAVEWLHDHP---AVDPDRIVAMGGSYGGFMVLASMT 476
                                       67999*********5...8****************9998765 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.73   5.9e+02      29      60 ..      39      78 ..      26      82 .. 0.81
   2 !    8.9   0.0    0.0022       1.8      45      88 ..     158     205 ..     145     209 .. 0.78
   3 ?    2.4   0.0      0.23   1.9e+02      43      75 ..     297     333 ..     287     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.73
                       ANAPC4_WD40 29 vwtl........eedkedsevrsLaWkpdgklLavaysdg 60
                                      vwtl        +++  d++v+  +W+p++  L++++++g
  gi|313127123|ref|YP_004037393.1| 39 VWTLdgpaawpeQRTFYDERVTFASWSPENPELVFGMDEG 78
                                      566666666655888899************9999999887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0022
                       ANAPC4_WD40  45 aWkpdgklLavays....dgevrlldaesgkvvhslsvksekavtclg 88 
                                        W+pd+++L+v+ +    d  v++ld+e+g++ h  + + + + ++ +
  gi|313127123|ref|YP_004037393.1| 158 GWSPDDSMLVVSEAysnfDQDVSVLDVETGELTHLTPHEGTVRFQSAE 205
                                       6*********97653344679***********9988777665555555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.23
                       ANAPC4_WD40  43 sLaWkpdgklLavaysdg....evrlldaesgkvvhs 75 
                                       +++++pdg  +av +s +    +v ++da++g+v + 
  gi|313127123|ref|YP_004037393.1| 297 GVSFSPDGDRFAVTVSRSsdtaNVYVVDAKTGEVTQW 333
                                       6899********9986442334899999999998765 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0023       1.8      85     129 ..     436     481 ..     427     501 .. 0.80
   2 ?    5.1   0.0     0.021        17     156     199 ..     536     578 ..     522     598 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHHHHHTT.--GGGEEEEEETHHHHHHHHHHHT-SS- CS
                     Abhydrolase_2  85 ksaekleelidaelkkg.ipssriiigGFSqGaalalylaltlpkk 129
                                       +s+  +e+ ++   +++ ++ +ri+ +G S G+ ++l+++  +p  
  gi|313127123|ref|YP_004037393.1| 436 DSVADIEAAVEWLHDHPaVDPDRIVAMGGSYGGFMVLASMTEYPDL 481
                                       5566667777766677689**********************99974 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                                       G-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--S CS
                     Abhydrolase_2 156 klpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaH 199
                                         p + +Hge Dp vp++ + +  e   + +  v   ++e+ +H
  gi|313127123|ref|YP_004037393.1| 536 RAPLFVLHGENDPRVPVSEAHQIVEKAGEHVP-VRELIFEDEGH 578
                                       46999*************99988877666666.55556666665 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.019        16      18      48 ..      78     103 ..      71     106 .. 0.81
   2 ?    0.6   0.0      0.98     8e+02      28      45 ..     177     194 ..     157     197 .. 0.80
   3 ?    0.9   0.0      0.76   6.2e+02      26      44 ..     222     240 ..     210     243 .. 0.83
   4 ?    1.1   0.0      0.64   5.2e+02      10      25 ..     455     470 ..     453     476 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.019
                           Kelch_6  18 GGytdsspylnkvwvydpetksWeqlpplpv 48 
                                       GG+        ++++ydp+++ ++ l+ +p 
  gi|313127123|ref|YP_004037393.1|  78 GGNER-----QQLLRYDPISGGISNLTEMPD 103
                                       44444.....689**************9995 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.98
                           Kelch_6  28 nkvwvydpetksWeqlpp 45 
                                        +v v+d+et+  ++l+p
  gi|313127123|ref|YP_004037393.1| 177 QDVSVLDVETGELTHLTP 194
                                       5899**********9987 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.76
                           Kelch_6  26 ylnkvwvydpetksWeqlp 44 
                                        + ++w+ ++e++ ++ ++
  gi|313127123|ref|YP_004037393.1| 222 DTLDLWRVNVESGEFSLVA 240
                                       4689**********99886 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.64
                           Kelch_6  10 vggkiYifGGytdssp 25 
                                         ++i+++GG++++++
  gi|313127123|ref|YP_004037393.1| 455 DPDRIVAMGGSYGGFM 470
                                       5699*******98755 PP

>> Peptidase_S28  Serine carboxypeptidase S28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.4e-05     0.044      91     142 ..     436     486 ..     427     500 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                     Peptidase_S28  91 qaLaDlasfikalkqkfklsssskwitfGgSYsgsLaawarkkyPelvvgav 142
                                        ++aD+ ++++ l+  +   +  +++++GgSY+g ++      yP+l ++++
  gi|313127123|ref|YP_004037393.1| 436 DSVADIEAAVEWLH-DHPAVDPDRIVAMGGSYGGFMVLASMTEYPDLWAAGI 486
                                       5789*********9.566666777**********************988876 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024      0.19     103     140 ..     445     482 ..     356     492 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                       HHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTC CS
                          Esterase 103 lplldanfrtapdgravaGqSmGGlgALilalkhpdrF 140
                                       + +l ++  ++pd+ +++G S GG++ L   +++pd++
  gi|313127123|ref|YP_004037393.1| 445 VEWLHDHPAVDPDRIVAMGGSYGGFMVLASMTEYPDLW 482
                                       579999******************************87 PP

>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.51   4.2e+02      29      58 ..     209     235 ..     180     238 .. 0.78
   2 ?    8.4   0.1    0.0039       3.2      46      61 ..     319     332 ..     303     334 .. 0.72
   3 ?   -1.6   0.0       5.1   4.2e+03       6      20 ..     557     571 ..     551     578 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.51
                                       TTEEEEEEE.EE.EE.TTEEEEEEEETTT-- CS
                             PepSY  29 dgrlvYeve.lstaepegpeyevfiDAkTGk 58 
                                       dg  vY v+  ++  ++   +   ++ ++G+
  gi|313127123|ref|YP_004037393.1| 209 DGENVYLVSdRDS--DTLDLWR--VNVESGE 235
                                       8899999994443..5555599..9999998 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0039
                                       EEEEEEEETTT--EEE CS
                             PepSY  46 peyevfiDAkTGkvlk 61 
                                         y   +DAkTG+v  
  gi|313127123|ref|YP_004037393.1| 319 NVYV--VDAKTGEVTQ 332
                                       3455..********86 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.1
                                       HHHHHHHHHSTTEEE CS
                             PepSY   6 qAlaiAlaavpgkii 20 
                                       q++++A ++vp+ ++
  gi|313127123|ref|YP_004037393.1| 557 QIVEKAGEHVPVREL 571
                                       788888888998774 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0004      0.33      13     125 ..     375     485 ..     365     512 .. 0.80
   2 ?   -1.6   0.0       1.9   1.5e+03     171     192 ..     538     559 ..     526     563 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                      Esterase_phd  13 rgamplvvmlhGct..qsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwykdtdraGrGeaavvvalvda 87 
                                        g  p++v +hG    q    f a  +   la   G++v+ p+    a   k +   +d +++     a + a v+ 
  gi|313127123|ref|YP_004037393.1| 375 EGDTPVIVDIHGGPesQRRPSFNA-VKQYFLA--NGYAVFEPNVRGSAGYGKAYGHLDDVENRMDS-VADIEAAVEW 447
                                       577888899998751144445554.4445566..59999999999999999999999988887655.456788899* PP

                      Esterase_phd  88 lvdehrvdaarvyvaGlsaGaaladllalhypdvfaav 125
                                       l d+  vd+ r+   G s G+ +       ypd +aa 
  gi|313127123|ref|YP_004037393.1| 448 LHDHPAVDPDRIVAMGGSYGGFMVLASMTEYPDLWAAG 485
                                       **********************99999999*****984 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                      Esterase_phd 171 palvvqGdadtvvavknaeslv 192
                                       p +v++G+ d  v v +a+++v
  gi|313127123|ref|YP_004037393.1| 538 PLFVLHGENDPRVPVSEAHQIV 559
                                       8899**************9987 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.2   1.6e+02       9      21 ..     176     188 ..     173     189 .. 0.85
   2 ?    6.8   0.0    0.0081       6.6       8      22 ..     316     330 ..     311     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.2
                                       TSEEEEEETTTCC CS
                               PQQ   9 dGylyAlDadTGk 21 
                                       d  +  lD++TG+
  gi|313127123|ref|YP_004037393.1| 176 DQDVSVLDVETGE 188
                                       777999******9 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0081
                                       TTSEEEEEETTTCCE CS
                               PQQ   8 adGylyAlDadTGkv 22 
                                       +  ++y +Da+TG+v
  gi|313127123|ref|YP_004037393.1| 316 DTANVYVVDAKTGEV 330
                                       5669*********97 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.21      34      79 ..     536     584 ..     524     599 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                     Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalgg...avlvtvegeGHgalaag 79 
                                        ap  +l +e+Dp +P + a ++ ++ g+    + ++ e+eGHg+ + +
  gi|313127123|ref|YP_004037393.1| 536 RAPLFVLHGENDPRVPVSEAHQIVEKAGEhvpVRELIFEDEGHGFTKLE 584
                                       47999*********************999544489999*****998733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3625.96
//
Query:       gi|313127124|ref|YP_004037394.1|  [L=87]
Description: hypothetical protein Hbor_23900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-29  101.6   0.2    1.7e-29  101.4   0.2    1.0  1  MTH865    MTH865-like family


Domain annotation for each model (and alignments):
>> MTH865  MTH865-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.2   9.4e-34   1.7e-29       1      70 []       7      79 ..       7      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 9.4e-34
                                      HHHHHHHHHHTTSSSTTBHHHHHHHH-TTSS-----BTT..B---TTTTGGGS.-GGGSB-SHHHHHHHHHHH CS
                            MTH865  1 elkeqivealegadFPikspeeLlaalPkGaettceagd..vevtagelgkkl.kdsdFPyksaedladdive 70
                                      el+eq++ea+++a+FP+k++++L++alP+G++t++eagd  v++ta+e+++kl ++++FPy++ae+l+dd++e
  gi|313127124|ref|YP_004037394.1|  7 ELREQFTEAFSDAEFPVKNQMDLVPALPNGPGTRFEAGDgeVSFTAMEMAAKLgSHQEFPYDDAESLVDDVIE 79
                                      79************************************988999**************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 600.11
//
Query:       gi|313127125|ref|YP_004037395.1|  [L=351]
Description: peptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-91  307.0   6.4    1.3e-91  306.7   6.4    1.1  1  Peptidase_M42  M42 glutamyl aminopeptidase
    1.7e-07   31.2   0.6     0.0015   18.2   0.1    2.4  2  Peptidase_M28  Peptidase family M28
    1.8e-07   31.1   0.5      4e-07   29.9   0.5    1.6  1  Peptidase_M20  Peptidase family M20/M25/M40
    0.00045   19.1   0.6        0.1   11.4   0.0    2.1  2  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.7   6.4   2.8e-95   1.3e-91       1     292 []      48     335 ..      48     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 306.7 bits;  conditional E-value: 2.8e-95
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGC CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHll 77 
                                       Gn++++++g  ++++v++aAHmDeiGfmV++++++Gf++++++GG+d+++l++qrv+i+t +g+++Gvigs ppH+l
  gi|313127125|ref|YP_004037395.1|  48 GNVVGTIEG-TSDYSVAVAAHMDEIGFMVRHVTDEGFVQLDALGGWDARILKAQRVQIHTGAGDVTGVIGSPPPHTL 123
                                       9********.999**************************************************************** PP

                                       HHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS- CS
                     Peptidase_M42  78 keeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeel 154
                                       +ee+++k  e+k+l++Dig+ + e a+e  ++vGd v++++++ve++++ +++kalDdr+++  +le++k++++ + 
  gi|313127125|ref|YP_004037395.1| 124 SEEQKEKDDEVKDLYVDIGL-DAETAKET-VNVGDLVTMEQTTVEMGDH-VTGKALDDRICLFSILEAAKRVEDPD- 196
                                       *******************8.88889998.*******************.************************98. PP

                                       SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETTCCSHHHHHHHH CS
                     Peptidase_M42 155 eatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDasgiyhpklrkkl 229
                                        +tv+++atvqEEvGlrGa ++  +++pd+aia+Dvt+a+d pg +  ++   lg G++i++kD s+i++pk+ ++l
  gi|313127125|ref|YP_004037395.1| 197 -VTVHFAATVQEEVGLRGATALGVDLNPDLAIALDVTVANDVPGFDAGDHVteLGAGTAIKLKDGSVITNPKVHRRL 272
                                       .*********************************************9998889************************ PP

                                       HHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 230 lelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       +++A++++++yq+evl+ ggtD++ ++ t +  p+++isiptry+H+  e ah+ d++at++L
  gi|313127125|ref|YP_004037395.1| 273 RDVAESEGVEYQYEVLPAGGTDTAGFQNTHGAKPVGAISIPTRYLHTVTESAHVADVDATIDL 335
                                       ************************************************************998 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   5.4e-05      0.24       1      27 [.      49      74 ..      49     111 .. 0.83
   2 !   18.2   0.1   3.5e-07    0.0015      35     188 ..     175     333 ..     163     342 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.4e-05
                                      EEEEEESTTCESEEEEEEEE--B-TTT CS
                     Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgvg 27
                                      Nv++t+eg++ d  ++++AH+D +g+ 
  gi|313127125|ref|YP_004037395.1| 49 NVVGTIEGTS-DYSVAVAAHMDEIGFM 74
                                      9*********.************9985 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.5e-07
                                       TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH.HHC.CCTTEEEEEEECS-SSSS--EEE CS
                     Peptidase_M28  35 AdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak.akp.elkkiaavlnlDmvgsggkellf 109
                                       A D+  +  ++Le a+ +++    p+ +v f+++  EE gl G++a+    +p  + + ++ +  D  g      ++
  gi|313127125|ref|YP_004037395.1| 175 ALDDRICLFSILEAAKRVED----PDVTVHFAATVQEEVGLRGATALGVdLNPdLAIALDVTVANDVPGFDAGDHVT 247
                                       8899999999******9997....9**********************965444455556666666666666666666 PP

                                       .......HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT..--EEEECTSSS-TTT.TSTT CS
                     Peptidase_M28 110 .......esgdkssselekelkalakpvgraaaedpfdersgrgrsDhspflkag..vpvldlaetgfpevy.Htpr 176
                                                 +++s   + +++++ + v++++  +++ e   +g +D + f++ +   pv  +     p++y Ht  
  gi|313127125|ref|YP_004037395.1| 248 elgagtaIKLKDGSVITNPKVHRRLRDVAESEGVEYQYEVLPAGGTDTAGFQNTHgaKPVGAI---SIPTRYlHTVT 321
                                       777777433444444445567788888888777788777778888999999955433444444...67777778888 PP

                                       SSGGGB-HHHHH CS
                     Peptidase_M28 177 Dtldnidkdtla 188
                                         +   d d++ 
  gi|313127125|ref|YP_004037395.1| 322 ESAHVADVDATI 333
                                       777776666665 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.5     9e-11     4e-07      35     206 ..     175     341 ..     156     342 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 9e-11
                                       TTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEE...EESSSBTCHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                     Peptidase_M20  35 addmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelh...ieepgileag 108
                                       a d+   ++++lea+++++d     + t+++++++ EE+g +Ga al      + ++d +++l     ++ ++ +ag
  gi|313127125|ref|YP_004037395.1| 175 ALDDRICLFSILEAAKRVEDP----DVTVHFAATVQEEVGLRGATALGV----DLNPDLAIALDvtvANDVPGFDAG 243
                                       667888888999999887777....79***********76677777766....344444443331112333333434 PP

                                       TETEEEE......EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTT.EEEEEE CS
                                       xxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx.xxxxxx RF
                     Peptidase_M20 109 klaigvv......kvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpggtdarff...agi.ptvmif 175
                                            v+      +++++      +v +n +++ + l+++ae+  g++++ +v + ggtd++ f   +g  p   i 
  gi|313127125|ref|YP_004037395.1| 244 D---HVTelgagtAIKLK----DGSVITN-PKVHRRLRDVAESE-GVEYQYEVLPAGGTDTAGFqntHGAkPVGAIS 311
                                       4...33344443223333....4445555.9************8.99977775555888888884444445555555 PP

                                       ESSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 176 gpgsglaHspnEyvdledlekgikvlarlle 206
                                        p     H++ E  +++d+ + i++la++l+
  gi|313127125|ref|YP_004037395.1| 312 IPT-RYLHTVTESAHVADVDATIDLLAAFLD 341
                                       588.9**********************9986 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1   0.00079       3.5     202     277 ..     148     214 ..     102     225 .. 0.63
   2 !   11.4   0.0   2.3e-05       0.1     332     431 ..     244     339 ..     225     340 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00079
                                       -CCCCCCCEEEEEE-S--EEETTTT-EEEESSHHHHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-ST CS
                     Peptidase_M18 202 evedivdlelilvdaqkakivGiekeflfaprlDnkvscfaaleallesaedsleeedkvrivalfDnEEvGStsa 277
                                       + e +   +l+++++ + +++    + ++++ lD++++ f++lea  + ++    ++ +v+ +a + +EEvG  +a
  gi|313127125|ref|YP_004037395.1| 148 AKETVNVGDLVTMEQTTVEMG----DHVTGKALDDRICLFSILEAAKRVED----PDVTVHFAATV-QEEVGLRGA 214
                                       444444445555554443332....46899*************99877743....45455555554.788987665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.3e-05
                                       TTS--TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEE.EE-EEB CS
                     Peptidase_M18 332 nhapllnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaaktGirtiD.lGaaql 407
                                       +h  +l++G+ ik++ +    tn + +  l+ va+  +v+ Q+ v+    p+G+t  + ++   G++ +  + ++  
  gi|313127125|ref|YP_004037395.1| 244 DHVTELGAGTAIKLKDG-SVITNPKVHRRLRDVAESEGVEYQYEVL----PAGGTDTAGFQNTHGAKPVGaISIPTR 315
                                       68999********9865.6899999*****************9765....99**************99854899*** PP

                                       STTSSSEEEECCHHHHHHHHHHHC CS
                     Peptidase_M18 408 smHSireltgskdveeavklfkaF 431
                                        +H + e +  +dv  ++ l+ aF
  gi|313127125|ref|YP_004037395.1| 316 YLHTVTESAHVADVDATIDLLAAF 339
                                       *********************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2411.17
//
Query:       gi|313127126|ref|YP_004037396.1|  [L=224]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-15   55.7   0.2      1e-14   54.8   0.2    1.5  1  Copper-bind  Copper binding proteins, plastocyanin/azurin fam
  ------ inclusion threshold ------
      0.048   13.5  10.6      0.048   13.5  10.6    3.5  3  TAT_signal   TAT (twin-arginine translocation) pathway signal
      0.084   12.2   7.4       0.32   10.4   7.4    2.1  1  UCR_Fe-S_N   Ubiquitinol-cytochrome C reductase Fe-S subunit 
        5.1    5.2  15.9        7.5    4.6  15.9    1.2  1  SSP160       Special lobe-specific silk protein SSP160


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.2   2.3e-18     1e-14       6      98 ..      86     173 ..      81     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.3e-18
                                       EETTETSEEES...SEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEE CS
                       Copper-bind   6 gvesgdlqFet...keitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagt 79 
                                        + +gdl+F++   ++++v +g++v+fv+ ++  HN+v+d++      d    k   ++++  +G +++ tf++ g+
  gi|313127126|ref|YP_004037396.1|  86 VGPDGDLVFSPgtnEALQVTPGTTVKFVW-ESDNHNIVVDSQP-----DGASWK--GHESIENSGFTYKHTFETLGE 154
                                       5668899998744468*************.9999*****9866.....222333..36778899************* PP

                                       EEEEETTTTTTTSEEEEEE CS
                       Copper-bind  80 YkffCsPHaaagMkgkvtv 98 
                                       Y++fC+PH++agM+g+++v
  gi|313127126|ref|YP_004037396.1| 155 YEYFCQPHKSAGMVGTIEV 173
                                       *****************98 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  10.6   1.1e-05     0.048       1      26 []       7      32 ..       7      32 .. 0.91
   2 ?   -2.6   2.8       1.3     6e+03      13      19 ..      74      80 ..      70      85 .. 0.47
   3 ?   -2.4   0.1       1.1   4.9e+03       7      12 ..     213     218 ..     213     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalggcaaa 26
                                      ++SRR FL ++A++aA a++ g+aaa
  gi|313127126|ref|YP_004037396.1|  7 EMSRRAFLTTAAGTAAVAGATGAAAA 32
                                      69*****************9998875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                        TAT_signal 13 AaaAAaa 19
                                      +++ ++a
  gi|313127126|ref|YP_004037396.1| 74 GGGGGGA 80
                                      2222222 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.1
                        TAT_signal   7 FLKgsA 12 
                                       FLK ++
  gi|313127126|ref|YP_004037396.1| 213 FLKYGG 218
                                       9**987 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   7.4   7.1e-05      0.32       5      31 ..       4      30 ..       1      32 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.1e-05
                        UCR_Fe-S_N  5 esdeptRRDFLyiATgavgaVGaaaaa 31
                                       + e +RR FL +A+g +++ Ga  aa
  gi|313127126|ref|YP_004037396.1|  4 GNAEMSRRAFLTTAAGTAAVAGATGAA 30
                                      567889********9999888887665 PP

>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  15.9    0.0017       7.5     273     320 ..      22      69 ..      12      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0017
                            SSP160 273 lealasssasanstssststststttststtttnsttstnstsssnss 320
                                         a a+++a+a+ t + tst +st++ +st+t nst++   t +s  s
  gi|313127126|ref|YP_004037396.1|  22 AVAGATGAAAAQETGTGTSTGNSTAAGNSTATGNSTATGTPTGTSGES 69 
                                       345678899999999999999999999999999999887777666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1392.98
//
Query:       gi|313127127|ref|YP_004037397.1|  [L=352]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-18   67.1   0.2    6.2e-18   65.4   0.2    1.9  1  Glyco_transf_4   Glycosyltransferase Family 4
    3.6e-18   66.5   9.1    2.4e-17   63.9   3.9    2.3  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.9e-14   53.6   0.0    2.7e-14   53.1   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    8.3e-12   45.7   0.0    1.5e-11   44.8   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    3.5e-06   27.1   0.0    1.2e-05   25.3   0.0    1.9  2  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.077   13.6   1.0       0.71   10.5   0.1    2.4  2  MgtE_N           MgtE intracellular N domain


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.2   2.1e-21   6.2e-18       2     169 ..      16     167 ..      15     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 2.1e-21
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                        G+ r +++++++La+ Gh+V+v++ ++ + +  e     +   v++      +  + f++++  +l+r kpDv+Ha
  gi|313127127|ref|YP_004037397.1|  16 DGATRRMRRVSERLAASGHDVSVLCAQWWEGEVPE----FEQNDVNYIRVTETPSAPKFASKVPFALRRVKPDVIHA 88 
                                       69**********************66655555555....3566666666777778999*****************96 PP

                    Glyco_transf_4  79 h.spaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygv 154
                                         sp++ + ++  ++r l++p+V+                  +       +r++r  +rvia+S+ ++ ++re yg 
  gi|313127127|ref|YP_004037397.1|  89 TnSPPTQVTGAKTAARFLRVPVVVDWWAER------------EGDSSSACKRAARGPKRVIAPSQMVKTDVRE-YGA 152
                                       51566667777777779*****99644443............334444566688*******************.*** PP

                    Glyco_transf_4 155 ppekitVipnGvDle 169
                                       ++e ++V+p  +D e
  gi|313127127|ref|YP_004037397.1| 153 SEEAVRVVPESIDFE 167
                                       **********99976 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   3.9   7.9e-21   2.4e-17       2     158 ..      17     161 ..      16     162 .. 0.79
   2 !    5.2   0.2    0.0085        25      12     103 ..     200     295 ..     197     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 7.9e-21
                   Glyco_trans_4_4   2 GigryvaelaraLaarGheVtvltpapapg.apeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       G++r++++++++Laa Gh+V vl++++ +g  pe e++ v ++r+   ++      ++++  +  +l  rr +pdv+
  gi|313127127|ref|YP_004037397.1|  17 GATRRMRRVSERLAASGHDVSVLCAQWWEGeVPEFEQNDVNYIRVTETPS-----APKFASKVPFAL--RRVKPDVI 86 
                                       99**********************998777477899*****999864433.....357777777777..888***** PP

                   Glyco_trans_4_4  78 hahs.ptaglaa.rlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelralgvpad 152
                                       ha + p++   + + a+r  ++p+vv++++    + s+a+        +r++r+  +v+++s+ +  ++r++g+  +
  gi|313127127|ref|YP_004037397.1|  87 HATNsPPTQVTGaKTAARFLRVPVVVDWWAEREGDSSSAC--------KRAARGPKRVIAPSQMVKTDVREYGASEE 155
                                       **995555444424444366*********95322223333........5667999********************** PP

                   Glyco_trans_4_4 153 rvvvvp 158
                                        v+vvp
  gi|313127127|ref|YP_004037397.1| 156 AVRVVP 161
                                       *****9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0085
                   Glyco_trans_4_4  12 raLaarGheVtvltpapapgapeleedgvrvh.rlp....vprrpspladlaalralrrllrqrrerpdvvhahspt 83 
                                       ++L++  ++  v+ ++p +++ e++++ +r+  r+     +p+++  ++ ++ ++ ++++ +++ +  d+++a  + 
  gi|313127127|ref|YP_004037397.1| 200 AELRDKDWRAAVIGDGPERAEAEQTAADLRIDdRVEflgeLPPEE-FVPIMKGAHVFAQTAAVEPFANDLLWALASG 275
                                       6899999*************9999999999976676322344443.5566666666666665699999999998876 PP

                   Glyco_trans_4_4  84 .aglaarlarrrrgiplvvtl 103
                                         g++  +ar      lvv++
  gi|313127127|ref|YP_004037397.1| 276 cVGIVEYQAR-SSAHELVVNC 295
                                       5888888888.7777777776 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   8.9e-18   2.7e-14       8     153 ..     170     312 ..     163     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 8.9e-18
                                       HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
                   Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsre 84 
                                       ++++++++  il++  l+ + +v+ +  a+a+l+   +++++  ++G+g+e++e ++ a+ l + d+v+flge+++e
  gi|313127127|ref|YP_004037397.1| 170 REAEADDRADILYSRHLDQYANVESFFLALAELR---DKDWRAAVIGDGPERAEAEQTAADLRIDDRVEFLGELPPE 243
                                       567789999************************8...56************************************** PP

                                       SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET..TTTHCHHCHTTTSEEEE-TT-HHHHHHHHH CS
                   Glycos_transf_1  85 dleellknadifvlpsisEgfGivllEAmaaglpviasn..aggpaevvkdgetGllvkpnnaealaeair 153
                                       +   ++k a++f++++  E+f+  ll A+a+g+  i+     + + e+v++ + G+ v ++  ++la++i 
  gi|313127127|ref|YP_004037397.1| 244 EFVPIMKGAHVFAQTAAVEPFANDLLWALASGCVGIVEYqaRSSAHELVVNCDRGARVTSP--QELADEIS 312
                                       ********************************99777433689999999999999988888..88888775 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   5.1e-15   1.5e-11       3     129 ..     179     312 ..     177     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 5.1e-15
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaad 74 
                                       +il+   l +++ +v+ +  a+++lr+kd+r  ++Gdgp r +e e+ aa  ++++rvef+G++  e+  ++++ a+
  gi|313127127|ref|YP_004037397.1| 179 DILYSRHL-DQYANVESFFLALAELRDKDWRAAVIGDGPeR-AEAEQTAAdlRIDDRVEFLGELppEEFVPIMKGAH 253
                                       67888888.6679*************99***********55.5888766558899*********9888********* PP

                                       EEEE--..---SHHHHHHHHTT-EEEE-TG.G.GTTT--..TTSSEE--TT-HHHHHHHHH CS
                   Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdv.g.giaevv..gengllvppgdpealaeail 129
                                       vf  +   e f + ll a+a+g+  ++       + e+v   + g  v   +p++la++i 
  gi|313127127|ref|YP_004037397.1| 254 VFAQTAavEPFANDLLWALASGCVGIVEYQaRsSAHELVvnCDRGARVT--SPQELADEIS 312
                                       ****9999****************9999541225788888536677777..8999999986 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   4.1e-09   1.2e-05      13     107 ..      22     115 ..      13     138 .. 0.76
   2 ?   -2.6   0.0       1.7   4.9e+03      18      40 ..     200     223 ..     185     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.1e-09
                   Glyco_trans_4_2  13 tlrlakeLakrgyeVhvitp..kkgakdeleaegihvhrlkvdrkgpleylk.afklkklikkikPDvvhahyakpy 86 
                                       ++r+ + La+ g++V+v++    +g+  e e+++++ +r++ ++ ++    k a k+   +++ kPDv+ha + +p 
  gi|313127127|ref|YP_004037397.1|  22 MRRVSERLAASGHDVSVLCAqwWEGEVPEFEQNDVNYIRVT-ETPSAP---KfASKVPFALRRVKPDVIHATNSPPT 94 
                                       4567788*************443444555556677777776.333322...3234555556788*********9998 PP

                   Glyco_trans_4_2  87 .gllgslaarlsgvipvvlsvw 107
                                        ++ ++ aar+++ +pvv++ w
  gi|313127127|ref|YP_004037397.1|  95 qVTGAKTAARFLR-VPVVVDWW 115
                                       788899*******.****9998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                   Glyco_trans_4_2  18 keLakrgyeVhvitpkkga.kdel 40 
                                        eL++++++ +vi  ++++ + e+
  gi|313127127|ref|YP_004037397.1| 200 AELRDKDWRAAVIGDGPERaEAEQ 223
                                       589999999999998777634444 PP

>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.25   7.5e+02      56      70 ..     167     181 ..     152     193 .. 0.75
   2 ?   10.5   0.1   0.00024      0.71      50      77 ..     217     244 ..     189     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.25
                                       HHHCCS-HHHHHHHH CS
                            MgtE_N  56 elleeldsDdaadll 70 
                                       el+ e ++Dd+ad+l
  gi|313127127|ref|YP_004037397.1| 167 ELVREAEADDRADIL 181
                                       567777788888876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00024
                                       -HHHHHHHHCCS-HHHHHHHHCCCHHHH CS
                            MgtE_N  50 sdeelaelleeldsDdaadlleelpeek 77 
                                       +++e+++  ++l  Dd++++l elp+e+
  gi|313127127|ref|YP_004037397.1| 217 ERAEAEQTAADLRIDDRVEFLGELPPEE 244
                                       5679999******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2606.61
//
Query:       gi|313127128|ref|YP_004037398.1|  [L=208]
Description: hypothetical protein Hbor_23940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-33  114.4   8.7    4.3e-33  114.4   8.7    1.8  2  DUF420       Protein of unknown function (DUF420)
     0.0034   17.6   4.0     0.0034   17.6   4.0    2.4  2  DUF2306      Predicted membrane protein (DUF2306)
  ------ inclusion threshold ------
       0.11   12.2   7.6      0.014   15.1   3.3    1.7  2  Orai-1       Mediator of CRAC channel activity
       0.18   12.5   2.7       0.45   11.2   0.1    2.4  2  DUF4029      Protein of unknown function (DUF4029)
        1.4    9.4  13.9      0.043   14.2   4.3    2.8  3  DUF2231      Predicted membrane protein (DUF2231)
        6.2    5.0   8.9        7.2    4.8   8.9    1.3  1  DUF2070      Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.57   1.7e+03      81      99 ..      13      31 ..       9      35 .. 0.56
   2 !  114.4   8.7   1.4e-36   4.3e-33       2     132 .]      54     187 ..      53     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.57
                            DUF420 81 HivLavvvvplvlvtlvla 99
                                      H + a+vv+ +v ++lv +
  gi|313127128|ref|YP_004037398.1| 13 HPLAATVVLSIVGYALVIG 31
                                      5555555555555555544 PP

  == domain 2  score: 114.4 bits;  conditional E-value: 1.4e-36
                            DUF420   2 palnavlnalaavllllglvaikkgkieaHrklmllafvlsalFlvlYllkhalagetkfggpeeegvirpvYlaiL 78 
                                       ++++a++na+ ++++++g+++i+++++++H ++m+++f+l+++Flv+Yl+k+  +g++k + p    ++ + Yla+L
  gi|313127128|ref|YP_004037398.1|  54 SDAIAAVNAVNVIVIAAGWRWIRRDEVKKHATAMVTSFALILVFLVMYLAKIGGGGTKKMVAPW---FAYYPYLAML 127
                                       6889*******************************************************99666...699******* PP

                            DUF420  79 itHivLavvvvplvlvtlvlalkg......kfekHrkiaritvpiwlyvavtGvvvYllL 132
                                       ++Hi+L++v+vp+vl++lvl+l++      + + H k++r+++  wl+++ +Gv++YllL
  gi|313127128|ref|YP_004037398.1| 128 AIHIILSIVAVPVVLYALVLGLTHsptelrRETPHLKVGRLAAGSWLLSLSLGVITYLLL 187
                                       *****************************99***************************98 PP

>> DUF2306  Predicted membrane protein (DUF2306)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   4.0   1.1e-06    0.0034      33     140 ..      23     124 ..      16     128 .. 0.78
   2 ?    4.5   1.9     0.012        37       2      45 ..     128     176 ..     127     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                           DUF2306  33 laGrvyvlavllaalsglflsvyatgg.lvlllgflllallwlvftvlalvairrrdfaaHrawmirsYalalaavt 108
                                       ++G+++v+  +l  + g +   +++    +l+  +++++ + +++++++++ irr ++++H  +m+ s+a       
  gi|313127128|ref|YP_004037398.1|  23 IVGYALVIGTFLGFVPGSVFPELSLSQvNLLSDAIAAVNAVNVIVIAAGWRWIRRDEVKKHATAMVTSFA------- 92 
                                       689999999999999999998888855344555566667788999999**********************....... PP

                           DUF2306 109 lrlvllvlillvgedfetayavlsllawvpnl 140
                                       l lv+lv+ l +++   t   v+ ++a+ p l
  gi|313127128|ref|YP_004037398.1|  93 LILVFLVMYLAKIGGGGTKKMVAPWFAYYPYL 124
                                       44555666666777777777888888877765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                           DUF2306   2 vlHialalvalllGalqlvkrlr.....akrpklHrlaGrvyvlavlla 45 
                                       ++Hi l++va+++ + +lv +l       +r   H  +Gr+ + + ll+
  gi|313127128|ref|YP_004037398.1| 128 AIHIILSIVAVPVVLYALVLGLThspteLRRETPHLKVGRLAAGSWLLS 176
                                       89***********999999998877766455666888888887777765 PP

>> Orai-1  Mediator of CRAC channel activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.6   4.7e+03      61      76 ..      17      32 ..      11      36 .. 0.57
   2 ?   15.1   3.3   4.7e-06     0.014      21     132 ..      83     193 ..      75     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.6
                            Orai-1 61 tavlvavhllallist 76
                                      ++v++++   al+i t
  gi|313127128|ref|YP_004037398.1| 17 ATVVLSIVGYALVIGT 32
                                      4455555555555555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.7e-06
                            Orai-1  21 rtsALlsgFamvamvel..qlkeseekeeeisealliafsvvtavlvavhllallistliLpnieavskienledee 95 
                                       + +A++++Fa++ +  +    k +   ++++ +++++ +  ++ +++ + l +++   ++L ++   + +++ + e+
  gi|313127128|ref|YP_004037398.1|  83 HATAMVTSFALILVFLVmyLAKIGGGGTKKMVAPWFAYYPYLAMLAIHIIL-SIVAVPVVLYALV-LGLTHSPT-EL 156
                                       56899****986544440033444445566888888888888877766544.4555555555554.44555555.68 PP

                            Orai-1  96 veesphekleeyiekaWlfatalGillFLvevallsw 132
                                        +e+ph k+ +    +Wl++ +lG++ +L+   + sw
  gi|313127128|ref|YP_004037398.1| 157 RRETPHLKVGRLAAGSWLLSLSLGVITYLLLNHVFSW 193
                                       88***************************98888888 PP

>> DUF4029  Protein of unknown function (DUF4029)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00015      0.45       8      81 ..      27     100 ..      20     112 .. 0.84
   2 ?    0.8   0.1      0.26   7.8e+02      42      58 ..     180     196 ..     140     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                           DUF4029   8 alflgyvfifsnlnriqeqsileiclfsisielfsivsivllnelflrihsfelmkfgnvvlqvicayivfvvl 81 
                                       al++g  + f       e s+ ++ l+s +i  +  v ++++   +++i   e+ k    ++   +  +vf+v+
  gi|313127128|ref|YP_004037398.1|  27 ALVIGTFLGFVPGSVFPELSLSQVNLLSDAIAAVNAVNVIVIAAGWRWIRRDEVKKHATAMVTSFALILVFLVM 100
                                       6666766667777778899999****************************************999999999985 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.26
                           DUF4029  42 sivsivllnelflrihs 58 
                                        +++ +lln +f + +s
  gi|313127128|ref|YP_004037398.1| 180 GVITYLLLNHVFSWEYS 196
                                       46788999999999776 PP

>> DUF2231  Predicted membrane protein (DUF2231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.3   1.5e-05     0.043      38      95 ..      50     107 ..      15     115 .. 0.79
   2 ?    0.5   0.4      0.28   8.3e+02      72      94 ..     126     148 ..     119     152 .. 0.77
   3 ?   -0.8   1.7       0.7   2.1e+03      76      94 ..     130     148 ..     126     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                           DUF2231  38 ktallHavggvlllalivaltvWrfvlrlreeeqvsplylalslvvvvlllvqgwlGa 95 
                                         +l  a+ +v ++ +iv+ + Wr++ r + +++++++   ++l++v+l+++ + +G+
  gi|313127128|ref|YP_004037398.1|  50 VNLLSDAIAAVNAVNVIVIAAGWRWIRRDEVKKHATAMVTSFALILVFLVMYLAKIGG 107
                                       5556667888888888888899***********9999999999999999999888886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.28
                           DUF2231  72 vsplylalslvvvvlllvqgwlG 94 
                                       + + +++ls+v+v ++l++  lG
  gi|313127128|ref|YP_004037398.1| 126 MLAIHIILSIVAVPVVLYALVLG 148
                                       55677888888888888888887 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.7
                           DUF2231  76 ylalslvvvvlllvqgwlG 94 
                                       +++ls+v+v ++l++  lG
  gi|313127128|ref|YP_004037398.1| 130 HIILSIVAVPVVLYALVLG 148
                                       4555666665555555555 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   8.9    0.0024       7.2      71     164 ..      50     147 ..       9     203 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0024
                           DUF2070  71 s.lflalltelivviisllaillsall...qalvllalvlslalvfalrllvlvavsdesllkavlpaliq.pllai 142
                                         l+  +++++ +v ++++a+   ++     +    a+v s+al++++ ++ l  +++  ++k+v+p +++ p+la+
  gi|313127128|ref|YP_004037398.1|  50 VnLLSDAIAAVNAVNVIVIAAGWRWIRrdeVKKHATAMVTSFALILVFLVMYLAKIGGGGTKKMVAPWFAYyPYLAM 126
                                       22333333344444444444444444476655566677777888888888888888888888888776654144444 PP

                           DUF2070 143 lllvlyfspesfllllllslif 164
                                       l++ ++  +  +++++l+ l++
  gi|313127128|ref|YP_004037398.1| 127 LAIHII-LSIVAVPVVLYALVL 147
                                       444444.344444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1374.54
//
Query:       gi|313127129|ref|YP_004037399.1|  [L=348]
Description: glycerol dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-61  207.0   2.0    4.7e-61  206.7   2.0    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    7.8e-21   74.3   5.7    6.7e-20   71.2   5.7    1.9  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    4.3e-11   42.5   0.1    1.3e-10   40.9   0.1    1.6  1  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.7   2.0   7.8e-65   4.7e-61       3     250 .]      17     269 ..      15     269 .. 0.91

  Alignments for each domain:
  == domain 1  score: 206.7 bits;  conditional E-value: 7.8e-65
                          Fe-ADH_2   3 gegaleklgellkelelk.kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdl 78 
                                       g+g++++l++ + el l+ + +lv++ + +++ag++v+ ++++ + +v+ +    e+a++e+ve++v+a++++++  
  gi|313127129|ref|YP_004037399.1|  17 GHGVVDELADAVDELYLTgRPFLVTSPTPNDIAGDAVRTQFDDIA-SVT-I----ETASFESVERVVDAAEAADAGY 87 
                                       7999***********98669*********************9884.553.5....4899****************** PP

                          Fe-ADH_2  79 vvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrlla 155
                                       ++a+GgG++iD+ak++s +l++ +vsvpTaaS+DG+ s  +s+ +   + +v  a  Plav+aD+++laeAP +l++
  gi|313127129|ref|YP_004037399.1|  88 LIALGGGKVIDTAKMASDSLDCGFVSVPTAASHDGIVSGRSSIPEGDTRHSV-AADPPLAVVADTTILAEAPWELTT 163
                                       **********************************************99***9.9*********************** PP

                          Fe-ADH_2 156 sGvGDllgkytaladwklan........evseplaklsaamvqeaaeklvedkke..tealeellea.lalsgigis 221
                                       +G++D++++yta++dw+la+        e++  l++++a+m++++ae++  + +e    ++++ll++ +a+s++ +s
  gi|313127129|ref|YP_004037399.1| 164 AGCADIISNYTAVKDWQLAHrlknaeysEYAGALSQMTAEMLVDNAESIKPNLEEsaWVVVKALLSSgVAMSIADSS 240
                                       ********************9988877777779***************9876554224444555544279999999* PP

                          Fe-ADH_2 222 rpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       rpaSG+EHl+SH ld+l + +alHG qVG
  gi|313127129|ref|YP_004037399.1| 241 RPASGAEHLFSHQLDRLVPGRALHGHQVG 269
                                       ****************************9 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   5.7   1.1e-23   6.7e-20       1     339 [.      11     312 ..      11     331 .. 0.79

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.1e-23
                                       -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTT CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklgak.ralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaal 76 
                                       P+++++g g+++el++ +++l ++ r+++vt++    +  + d v++++   +i+ +++    +  + e+ve+++++
  gi|313127129|ref|YP_004037399.1|  11 PRNVLMGHGVVDELADAVDELYLTgRPFLVTSPTP--NDIAGDAVRTQF--DDIASVTI----ETASFESVERVVDA 79 
                                       899******************7555********94..555777777777..55555544....4579********** PP

                                       S-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  77 areegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegek 153
                                       a++++a ++ia+GGG+viDtAK+++  l                   + ++ +PT a+ +  v++ + i  e + ++
  gi|313127129|ref|YP_004037399.1|  80 AEAADAGYLIALGGGKVIDTAKMASDSLD------------------CGFVSVPTAASHDGIVSGRSSIP-EGDTRH 137
                                       *****************************..................88*********************.666455 PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSS.B--HHHHHHHHHHHHHHHHHH. CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsda.laleairliaknleravadge. 228
                                        + +dp   P +++ D+++++ +P ++t a+ +D+++ +      + a+ l +a ++++a  l     e +v+++e 
  gi|313127129|ref|YP_004037399.1| 138 SVAADP---PLAVVADTTILAEAPWELTTAGCADIISNYTAVKDWQLAHRLKNAeYSEYAGALSQMTAEMLVDNAEs 211
                                       555565...7789************************9988877777777777667777777777777777777665 PP

                                       ...HHHHHHHHHHHHHH.HHHHHHSS---.....HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHH CS
                            Fe-ADH 229 ...dleareqmllastl.aglafsnaglg.....avHalahalgalfgiphglanaillpavlrfnaeaaperlaql 296
                                          +le  + ++  ++l +g+a+s a  +     a H ++h+l  l  +p  ++++  +  +              +
  gi|313127129|ref|YP_004037399.1| 212 ikpNLEESAWVVVKALLsSGVAMSIADSSrpasgAEHLFSHQLDRL--VPGRALHGHQVGVGS------------IV 274
                                       5568899999999999999999998887777788**********95..555555555544444............11 PP

                                       HHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT-HH CS
                            Fe-ADH 297 aralggesdeeaaeeliealrellkelglptsLselgvdeedl 339
                                        + l     +++ + + + +r+ l+e+g+pt+ +elg+d+e +
  gi|313127129|ref|YP_004037399.1| 275 IEYL-----HSGEKGEWRDIRNALDEVGAPTTAAELGIDAETV 312
                                       2221.....2466677888888888888888888888888633 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1   2.2e-14   1.3e-10      15     256 ..      69     317 ..      64     322 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.2e-14
                                       HHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEE CS
                      DHQ_synthase  15 tlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGa 91 
                                       ++e++ +++ +a++    +lialGGG v D a  ++  +  G  fv vPt+  a  D  v g+ +i     +  + a
  gi|313127129|ref|YP_004037399.1|  69 SFESVERVVDAAEAADAGYLIALGGGKVIDTAKMASDSLDCG--FVSVPTA--ASHDGIVSGRSSIPEGDTRHSVAA 141
                                       4556666666677777889*******************9988..9****97..999******************966 PP

                                       E---SEEEEEGGGGGGS-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC...............TTTHHHHH CS
                      DHQ_synthase  92 faqPkavlidlevLktLperelraGlaEvi.Kyalikdeelfelleenaeallk...............eeeeeale 152
                                          P av++d+++L+  p + ++aG+a++i  y+++kd +l ++l++ + +  +               e       
  gi|313127129|ref|YP_004037399.1| 142 -DPPLAVVADTTILAEAPWELTTAGCADIIsNYTAVKDWQLAHRLKNAEYSEYAgalsqmtaemlvdnaE------- 210
                                       .89*************************995699*************99998887777666544432221....... PP

                                       HHHHHHHHHHHHHHHHCCTTTTGGGG........GGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS CS
                      DHQ_synthase 153 eliarsievkaevveeDekekglral........LnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgll 221
                                         i+  +e  a vv +    +g+ +             H ++H++++l+   + lHG+ V +G ++  +l +     
  gi|313127129|ref|YP_004037399.1| 211 -SIKPNLEESAWVVVKALLSSGVAMSiadssrpaSGAEHLFSHQLDRLVPG-RALHGHQVGVGSIVIEYLHS----G 281
                                       .3344444444444444444444333122222117788*********9988.***********887766653....2 PP

                                       -HHHHHHHHHHHHHTT---STTTT..-HHHHHHHHT CS
                      DHQ_synthase 222 kkeeverllkllkklglpvslkel.leveellealk 256
                                       +k e +++++ l+++g p++  el +++e++leal+
  gi|313127129|ref|YP_004037399.1| 282 EKGEWRDIRNALDEVGAPTTAAELgIDAETVLEALT 317
                                       3556789************99988789999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2217.00
//
Query:       gi|313127130|ref|YP_004037400.1|  [L=250]
Description: threonine efflux protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-26   92.6   2.3    3.9e-24   85.2   2.3    2.2  1  LysE      LysE type translocator


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   2.3   2.2e-28   3.9e-24       2     129 ..      17     164 ..      16     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 2.2e-28
                              LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlal 78 
                                       +l+++pGp n+++ ++++ +g+ +g+ ++lg++ +da++++l++lG+ ++l+ +p ++++++ +Gg+ Ll++++ a+
  gi|313127130|ref|YP_004037400.1|  17 ALAAPPGPMNAIIAEESVIHGWLAGFKAGLGAMSADAIFFVLAALGVVTFLQGSPTLHAVMMGVGGVLLLYFAYGAV 93 
                                       7899************************************************************************* PP

                              LysE  79 rdakekkveae....................ksve..aslvkpflkglllslsNPkailfwlsvisallakae 129
                                       +da ++                         +     +     f k+++l l+NP+ ilfw+ ++  +l+++ 
  gi|313127130|ref|YP_004037400.1|  94 QDAQSSFQPDDssdrpndpgeqsndptdqpnN--PseRPTGTGFTKAFVLALTNPYQILFWITIGVKMLDPGT 164
                                       *9998876555555666666666665555543..056999**************************9999742 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1848.35
//
Query:       gi|313127131|ref|YP_004037401.1|  [L=235]
Description: hypothetical protein Hbor_23970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-26   92.4  15.4    1.3e-15   57.4   2.6    2.3  2  UPF0016   Uncharacterized protein family UPF0016


Domain annotation for each model (and alignments):
>> UPF0016  Uncharacterized protein family UPF0016
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   5.1   1.3e-14   2.3e-10       7      75 .]      15      83 ..       9      83 .. 0.92
   2 !   57.4   2.6   7.4e-20   1.3e-15       3      75 .]     134     207 ..     132     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.3e-14
                           UPF0016  7 iflaElGDkTqlaaalLaarykplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75
                                       ++   G k q+++a L++ry+pl V+++a  A+a  t+l +l+G+++ + lp+  ++ ++a+lFl f+
  gi|313127131|ref|YP_004037401.1| 15 QLAVLPGEKVQFIIAGLSTRYNPLVVVAAAGSAFAGWTALEILFGQAIRSALPPIALNAITAALFLTFA 83
                                      55555699**********************************************************997 PP

  == domain 2  score: 57.4 bits;  conditional E-value: 7.4e-20
                           UPF0016   3 aflliflaElGDkTqlaaalLaary.kplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75 
                                        f+++++ E+GDkTq++++ La  y +  ++++G +lA++ +++  ++l +++++r+++r ++l++a+lF +fG
  gi|313127131|ref|YP_004037401.1| 134 IFVMMAAGEFGDKTQMVTIGLAIDYgATSAIWFGEMLAIIPVSLANAYLFHKFSHRFDMRKVHLLSAALFCFFG 207
                                       69***********************77777*******************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1722.24
//
Query:       gi|313127132|ref|YP_004037402.1|  [L=239]
Description: mn-dependent transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-29   99.5   1.1    1.7e-28   98.5   1.1    1.5  1  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
      1e-19   70.5   0.1    2.3e-19   69.3   0.1    1.7  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    1.9e-15   56.9   0.8    4.1e-15   55.8   0.1    1.9  2  FeoA             FeoA domain
    3.5e-07   30.0   0.0    1.1e-06   28.4   0.0    1.8  2  MarR_2           MarR family
    5.6e-07   29.4   0.0    1.2e-06   28.3   0.0    1.6  1  MarR             MarR family
    3.1e-06   27.1   0.0    6.4e-06   26.0   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    5.1e-06   26.0   0.0    9.7e-06   25.1   0.0    1.5  1  Crp              Bacterial regulatory proteins, crp family
    5.9e-06   26.1   0.1    6.3e-05   22.8   0.1    2.6  2  HTH_12           Ribonuclease R winged-helix domain
    2.2e-05   24.2   0.1    0.00022   21.0   0.0    2.4  2  HTH_IclR         IclR helix-turn-helix domain
    0.00036   20.0   0.0      0.001   18.6   0.0    1.8  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00036   20.5   0.1     0.0077   16.3   0.0    2.9  3  HTH_20           Helix-turn-helix domain
    0.00082   19.2   0.0     0.0017   18.2   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.001   18.8   0.0     0.0028   17.5   0.0    1.8  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0019   18.1   0.1      0.011   15.7   0.0    2.2  2  HTH_1            Bacterial regulatory helix-turn-helix protei
     0.0036   17.4   0.1     0.0077   16.3   0.1    1.6  1  DUF2250          Uncharacterized protein conserved in archaea
     0.0038   17.6   0.0     0.0087   16.4   0.0    1.6  1  Rrf2             Transcriptional regulator
     0.0043   17.5   0.0     0.0094   16.4   0.0    1.6  1  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.019   14.6   0.0    1.3  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
      0.012   15.9   0.0      0.038   14.3   0.0    1.8  2  Penicillinase_R  Penicillinase repressor
      0.015   14.9   0.0      0.079   12.6   0.0    2.2  3  GntR             Bacterial regulatory proteins, gntR family
      0.037   14.1   0.0      0.092   12.8   0.0    1.6  1  FeoC             FeoC like transcriptional regulator
       0.04   14.0   0.0      0.076   13.1   0.0    1.4  1  HTH_13           HTH DNA binding domain
      0.044   13.2   0.0         27    4.3   0.0    3.3  3  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
        0.1   11.6   0.0       0.15   11.1   0.0    1.1  1  Topoisom_bac     DNA topoisomerase


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   1.1   2.2e-31   1.7e-28       1      69 [.      64     132 ..      64     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 2.2e-31
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                       Te+G+ +A++++r+hrlle +L+++l+++w+e+h+eA +lEh++see+++r+ e lg+p+++Phgdpip
  gi|313127132|ref|YP_004037402.1|  64 TEEGETVALEVLRHHRLLEAYLAEHLDYSWSEVHDEADALEHHISEEFERRVAEALGNPTVDPHGDPIP 132
                                       9*******************************************************************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.1     3e-22   2.3e-19       1      60 []       1      61 [.       1      61 [. 0.98

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 3e-22
                                      X--HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  1 dLvestEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +L++++EdYL++IY+++  ++ +v+t+ +ae L+  p++V+ ml kLe+ G+v+ ekykg+
  gi|313127132|ref|YP_004037402.1|  1 MLSDVMEDYLKAIYQIQAtSGPPVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNREKYKGV 61
                                      89****************9999*************************************97 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         5   3.8e+03       7      30 ..      65      87 ..      62      88 .. 0.78
   2 !   55.8   0.1   5.5e-18   4.1e-15       2      74 .]     146     218 ..     145     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5
                                      -TT-EEEEEEE-TT.SSHHHHHHH CS
                              FeoA  7 keGergeiarisdedpellrrLre 30
                                      +eGe++  + ++++ + l+++L+e
  gi|313127132|ref|YP_004037402.1| 65 EEGETVALEVLRHH-RLLEAYLAE 87
                                      67888888888888.888888887 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 5.5e-18
                                       EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEET.TEEEEE-HHHHTTEEEEE CS
                              FeoA   2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvg.dtrvaLgreeAqaIlVea 74 
                                       +Lsd + G++++++r+sd+d+e l +L++ G++pG+++evv+ apf g+++vr + d + +L+ ++A++I V++
  gi|313127132|ref|YP_004037402.1| 146 TLSDHPVGDHVVVTRVSDRDEEELEYLADAGVTPGTKLEVVDVAPF-GMVTVRTEdDGEQSLPESVAASIRVKP 218
                                       7*********************************************.9******9788899***********85 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.5e-09   1.1e-06      19      55 ..      21      57 ..      11      62 .. 0.87
   2 ?   -2.7   0.0       7.6   5.7e+03      22      33 ..      80      91 ..      69     104 .. 0.57

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.5e-09
                                      TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      g++++ +++a++lg ++++v+ +l +L+++GLv r++
  gi|313127132|ref|YP_004037402.1| 21 GPPVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNREK 57
                                      4449*****************************9985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.6
                                      EEHHHHHHHHTS CS
                            MarR_2 22 ltvgelarrlgl 33
                                      l  + la++l++
  gi|313127132|ref|YP_004037402.1| 80 LLEAYLAEHLDY 91
                                      344455555555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.6e-09   1.2e-06      16      51 ..      22      57 ..      12      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.6e-09
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      +p s s +a+ lg +++tvt +l +Le++Gl++R+k
  gi|313127132|ref|YP_004037402.1| 22 PPVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNREK 57
                                      678999****************************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   8.6e-09   6.4e-06      20      59 ..      22      63 ..       8      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 8.6e-09
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET.EE.EEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrg.rr.iri 59
                                       p++   +A++lG t+ tv+ +l++L+++gl+ r+ ++ +++
  gi|313127132|ref|YP_004037402.1| 22 PPVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNREkYKgVEL 63
                                      589999***************************642333665 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.3e-08   9.7e-06       2      31 ..      23      52 ..      23      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.3e-08
                                      E--HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                               Crp  2 pmSRqdIAdylGlTrETVSRlLtrLrekGL 31
                                      p+S  +IA+ylG T+ TV+ +L++L+e+GL
  gi|313127132|ref|YP_004037402.1| 23 PVSTSAIAEYLGKTPPTVTSMLGKLEERGL 52
                                      678899***********************9 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   8.4e-08   6.3e-05       3      64 ..      13      69 ..      11      71 .. 0.84
   2 ?   -1.1   0.0       2.6   1.9e+03      10      28 ..     148     167 ..     147     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.4e-08
                            HTH_12  3 ILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGle 64
                                      I +i a s  p++  +iae L k+        v   L kleergl++r  y g eltE G++
  gi|313127132|ref|YP_004037402.1| 13 IYQIQATSGPPVSTSAIAEYLGKTPPT-----VTSMLGKLEERGLVNREKYKGVELTEEGET 69
                                      666777888899999999999887554.....46789***********************86 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                            HTH_12  10 sdkpigakeiaeeLkkr.gy 28 
                                       sd+p+g + + + + +r ++
  gi|313127132|ref|YP_004037402.1| 148 SDHPVGDHVVVTRVSDRdEE 167
                                       689***99999999999555 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.9e-07   0.00022      14      50 ..      19      55 ..      15      57 .. 0.91
   2 ?    0.2   0.0       0.9   6.7e+02      24      44 ..      85     105 ..      72     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.9e-07
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      + +++++ s +A+ +g +++tv  +L  L+e+G+v +
  gi|313127132|ref|YP_004037402.1| 19 TSGPPVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNR 55
                                      56778999***************************87 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.9
                                       HHHHHTS-HHHHHHHHHHHHH CS
                          HTH_IclR  24 lArrtglpkStvhRlLqtLve 44 
                                       lA++++ + S vh     L++
  gi|313127132|ref|YP_004037402.1|  85 LAEHLDYSWSEVHDEADALEH 105
                                       788888888888866666666 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.3e-06     0.001      16      47 ..      22      53 ..      10      54 .. 0.90
   2 ?   -2.4   0.0         5   3.7e+03      23      35 ..      85      97 ..      84      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                            HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      p  s + +Ae lg +p+tv+  l +Lee Gl+
  gi|313127132|ref|YP_004037402.1| 22 PPVSTSAIAEYLGKTPPTVTSMLGKLEERGLV 53
                                      678999************************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                            HTH_24 23 LAerlglSpstvn 35
                                      LAe+l+ S s v+
  gi|313127132|ref|YP_004037402.1| 85 LAEHLDYSWSEVH 97
                                      89****9998776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     1e-05    0.0077      20      58 ..      19      57 ..       6      58 .. 0.87
   2 ?   -1.7   0.2       4.2   3.1e+03      30      49 ..      85     104 ..      72     106 .. 0.61
   3 ?    0.2   0.0       1.1   7.9e+02       2      11 ..     114     123 ..     113     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                                      STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 20 araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +++ +++ s++ae l+ ++ t+   L +Lee gLv +++
  gi|313127132|ref|YP_004037402.1| 19 TSGPPVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNREK 57
                                      5889*******************************9875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.2
                                       HHHHHTS-HHHHHHHHHHHH CS
                            HTH_20  30 laerldlskntlsyHLrvLe 49 
                                       lae ld s +++++  ++Le
  gi|313127132|ref|YP_004037402.1|  85 LAEHLDYSWSEVHDEADALE 104
                                       56666666666666666665 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.1
                                       HHHHHHS-HH CS
                            HTH_20   2 qiaeALahPv 11 
                                       ++aeAL++P+
  gi|313127132|ref|YP_004037402.1| 114 RVAEALGNPT 123
                                       69*******8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.2e-06    0.0017      22      56 ..      23      57 ..      13      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-06
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      p +++ iae lg   ++v ++L +Le++GlV+rek
  gi|313127132|ref|YP_004037402.1| 23 PVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNREK 57
                                      677899***************************98 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.8e-06    0.0028      17      46 ..      25      54 ..      10      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLVe 46
                                      + + +ae+lg++++tv   L kL+e GLV+
  gi|313127132|ref|YP_004037402.1| 25 STSAIAEYLGKTPPTVTSMLGKLEERGLVN 54
                                      6799*************************8 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05     0.011      17      60 .]      27      68 ..      24      68 .. 0.87
   2 ?   -0.7   0.1         2   1.5e+03      20      43 ..      86     109 ..      73     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSS.EEEE-HHHH CS
                             HTH_1 17 trAAeeLglsqpavsrqikrLEeelgvpLfeRtgr.glrLTeaGe 60
                                      ++ Ae Lg ++p+v+ ++ +LEe+    L++R +  g++LTe+Ge
  gi|313127132|ref|YP_004037402.1| 27 SAIAEYLGKTPPTVTSMLGKLEER---GLVNREKYkGVELTEEGE 68
                                      56699*****************96...7****77548*******7 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                                       HHHHTS-HHHHHHHHHHHHHHHTS CS
                             HTH_1  20 AeeLglsqpavsrqikrLEeelgv 43 
                                       Ae+L +s + v +   +LE+++ +
  gi|313127132|ref|YP_004037402.1|  86 AEHLDYSWSEVHDEADALEHHISE 109
                                       788888888888888888888765 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     1e-05    0.0077      27      78 ..      28      79 ..       7      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                           DUF2250 27 siakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhHt 78
                                       ia++l +    v+++l kLee GL++r + k +  te     + ev +hH 
  gi|313127132|ref|YP_004037402.1| 28 AIAEYLGKTPPTVTSMLGKLEERGLVNREKYKGVELTEEGETVALEVLRHHR 79
                                      578899999999***************************************6 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0087       4      76 ..       3      72 ..       1      77 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                                      -HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCCSBH CS
                              Rrf2  4 sskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeItl 76
                                      s  +e  l+a++ +++ ++  pvs+++iae  +  p+ +  +l kL++ glv+ ++ k  G+ L+++ e++ l
  gi|313127132|ref|YP_004037402.1|  3 SDVMEDYLKAIYQIQATSGP-PVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNREKYK--GVELTEEGETVAL 72
                                      56666778888888888884.6******************************988766..7888877777665 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05    0.0094      15      68 .]      20      67 ..       9      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                            HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                       + +++ ++++++l  +  ++ ++l kL+e+GLv r+      ++k v+lT++G
  gi|313127132|ref|YP_004037402.1| 20 SGPPVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNRE------KYKGVELTEEG 67
                                      5667788***************************555......45799999998 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.5e-05     0.019       1      54 [.       1      54 [.       1      58 [. 0.95

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                      HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLve 54
                                      +L++v ++ l+a+ +++  ++ +v +  iAe l++ + tv  +l  L   gLv+
  gi|313127132|ref|YP_004037402.1|  1 MLSDVMEDYLKAIYQIQATSGPPVSTSAIAEYLGKTPPTVTSMLGKLEERGLVN 54
                                      699********************************************9999996 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.1e-05     0.038      16      56 ..      21      58 ..       9      63 .. 0.80
   2 ?   -2.6   0.0       9.5   7.1e+03      62      76 ..      93     107 ..      73     120 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.1e-05
                                      S-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEE CS
                   Penicillinase_R 16 ge.atvkevveeleeekelaysTVktllrrLvkKgllsreke 56
                                      g+ ++++ + e l ++    + TV+++l++L+++gl++rek 
  gi|313127132|ref|YP_004037402.1| 21 GPpVSTSAIAEYLGKT----PPTVTSMLGKLEERGLVNREKY 58
                                      5557777777777777....99******************96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.5
                                       EE----XXXXXXXXX CS
                   Penicillinase_R  62 Ysplvseeeavasav 76 
                                       +s +++e +a+++  
  gi|313127132|ref|YP_004037402.1|  93 WSEVHDEADALEHHI 107
                                       333344444443333 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.079      16      62 ..      16      61 ..       4      63 .. 0.87
   2 ?   -3.0   0.0         8     6e+03      22      39 ..      79      94 ..      71      97 .. 0.65
   3 ?   -3.0   0.0       8.2   6.1e+03      18      27 ..     177     185 ..     171     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      TSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 16 gelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                       + + G +  s +++a+ +g + +tv   L +Le++glv r++ +G+
  gi|313127132|ref|YP_004037402.1| 16 IQATSGPPV-STSAIAEYLGKTPPTVTSMLGKLEERGLVNREKYKGV 61
                                      556677778.8999****************************99997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8
                                      SB---HHHHHHHHTS-HH CS
                              GntR 22 dkLPsereLaaefgVsrt 39
                                        L  e  La+ ++ s++
  gi|313127132|ref|YP_004037402.1| 79 RLL--EAYLAEHLDYSWS 94
                                      334..7778888877776 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.2
                                       S-TTSB---H CS
                              GntR  18 lrpGdkLPse 27 
                                       ++pG+kL ++
  gi|313127132|ref|YP_004037402.1| 177 VTPGTKL-EV 185
                                       7899999.55 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012     0.092      14      49 ..      23      58 ..       9      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                              FeoC 14 rvslkeLsrhfkaspealeamLeqwvrkGrvekvaa 49
                                       vs + ++ ++  +p ++ +mL  ++ +G v++++ 
  gi|313127132|ref|YP_004037402.1| 23 PVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNREKY 58
                                      5999***************************99875 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.076      10      50 ..      20      60 ..      18      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                            HTH_13 10 srPlVsagmvakeLkvtpraalklvkelglRElTGRgrfrA 50
                                      s P Vs++ +a+ L  tp  +++++  l+ R l  R+++++
  gi|313127132|ref|YP_004037402.1| 20 SGPPVSTSAIAEYLGKTPPTVTSMLGKLEERGLVNREKYKG 60
                                      5689***********************************95 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.037        27      28      47 ..      24      43 ..      13      44 .. 0.84
   2 ?    1.5   0.0      0.26   1.9e+02      34      46 ..      86      98 ..      85     103 .. 0.84
   3 ?    3.1   0.0     0.082        61      10      30 ..     105     124 ..     104     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.037
                      HTH_Tnp_ISL3 28 rsvkavArqlgvSwtTVwri 47
                                       s +a+A+ lg ++ TV  +
  gi|313127132|ref|YP_004037402.1| 24 VSTSAIAEYLGKTPPTVTSM 43
                                      5889*************876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                      HTH_Tnp_ISL3 34 ArqlgvSwtTVwr 46
                                      A++l+ Sw+ V++
  gi|313127132|ref|YP_004037402.1| 86 AEHLDYSWSEVHD 98
                                      99*********97 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.082
                      HTH_Tnp_ISL3  10 sriTlrleayilelllesrsv 30 
                                       ++i++ +e+ ++e+l +  +v
  gi|313127132|ref|YP_004037402.1| 105 HHISEEFERRVAEALGNP-TV 124
                                       689***********9987.65 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0002      0.15     342     395 ..      36      90 ..      28     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                      Topoisom_bac 342 tpaTraeiieklvergYverkk.kslvptelGkalvellekfkdlvspelTaele 395
                                       tp T  +++ kl erg v+r+k k +  te G++++  + + ++l +  l  +l 
  gi|313127132|ref|YP_004037402.1|  36 TPPTVTSMLGKLEERGLVNREKyKGVELTEEGETVALEVLRHHRLLEAYLAEHLD 90 
                                       899********************************97774457777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1816.62
//
Query:       gi|313127133|ref|YP_004037403.1|  [L=391]
Description: l-threonine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-61  208.4   3.7    1.8e-61  208.1   3.7    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1   3.7     1e-65   1.8e-61       2     293 ..      71     372 ..      70     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 1e-65
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       t  +g+TPlv++  l++elg++ l +K+E+ nptg + dRg++ ++++++e+ +a+ v+ as+GN+g+++A +a+++
  gi|313127133|ref|YP_004037403.1|  71 TANEGGTPLVASAELAAELGIKsLSIKDEGRNPTGTVLDRGLSPAVTAAREA-DAELVALASAGNAGQSAASYASMA 146
                                       5679************************************************.************************ PP

                                       T-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHT CS
                              PALP  78 GlkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileql 154
                                        l+++ +vp+ a+ +++a+   +G e+++vgg y +a++  +e +++  +++ ++ fdnp++ +g +t+++E++e l
  gi|313127133|ref|YP_004037403.1| 147 DLRSYAFVPSRAPFSNKAMVNVHGGEMRVVGGRYPDAEDGLHEQLQS--DWFTLQEFDNPYRHDGIKTLAFEVAESL 221
                                       ****************************************9998888..9************************999 PP

                                       T.TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT....-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCS CS
                              PALP 155 g.gkpdavvvpvGgGgliaGiaaglke....rrpd....vrvigvepegsdalarslragrrvtvpvs..dtiadgl 220
                                       +  +pdav+vp+++G  ++G+a g+++    +       + +++++++g++++++++++g+r+  p +  dti+  l
  gi|313127133|ref|YP_004037403.1| 222 DwSVPDAVIVPTSTGEVVTGVANGFRQlrelG--LidepPSIYAAQASGCAPIYAAHERGERDVEPWEhpDTIVGEL 296
                                       99*************************76652..14478*********************9999888888******* PP

                                       TCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE- CS
                              PALP 221 avg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvvilt 293
                                       +++  + ++ a+ +++++ ++i +++de++le ++  a+++g+ v+ +++aa+aa+ +l+e+g ++e d+vvv+ t
  gi|313127133|ref|YP_004037403.1| 297 EIPdpKGGAAAVHAVEQTDGDILAIDDEDILESAVVAAQTAGVEVGTAGGAAMAAAwQLAEDGVVGETDDVVVVNT 372
                                       ***988899999999***********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2631.85
//
Query:       gi|313127134|ref|YP_004037404.1|  [L=425]
Description: udp-galactopyranose mutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-47  161.6   0.5    4.9e-47  161.2   0.5    1.1  1  Amino_oxidase   Flavin containing amine oxidoreductase
    1.8e-16   60.1   0.1    4.2e-16   58.9   0.1    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.9e-12   46.8   1.6    2.4e-05   24.1   0.7    2.1  2  DAO             FAD dependent oxidoreductase
    2.4e-09   36.9   1.7    9.5e-05   21.8   0.0    2.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    8.3e-08   31.3   0.1    9.1e-05   21.3   0.0    2.1  2  HI0933_like     HI0933-like protein
    7.1e-07   29.7   1.6    0.00011   22.7   0.3    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    9.4e-07   28.3   1.4    1.4e-06   27.7   0.4    1.7  2  FAD_binding_2   FAD binding domain
    3.3e-06   26.6   0.5    0.00012   21.5   0.1    2.2  2  FAD_binding_3   FAD binding domain
    1.2e-05   24.7   0.4      0.058   12.6   0.0    2.3  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.5e-05   23.0   0.5    4.5e-05   23.0   0.5    2.0  3  FAD_oxidored    FAD dependent oxidoreductase
     0.0001   21.7   0.2    0.00021   20.7   0.2    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00018   21.9   0.5      0.005   17.2   0.0    2.7  2  NAD_binding_7   Putative NAD(P)-binding
    0.00055   19.2   0.8    0.00089   18.5   0.3    1.6  2  CoA_transf_3    CoA-transferase family III
     0.0007   18.9   0.1     0.0013   18.0   0.1    1.4  1  Thi4            Thi4 family
     0.0013   18.7   2.6      0.098   12.6   0.2    2.5  2  NAD_binding_9   FAD-NAD(P)-binding
     0.0037   16.4   0.4     0.0037   16.4   0.4    1.7  2  GIDA            Glucose inhibited division protein A
      0.004   16.8   0.9      0.084   12.5   0.1    2.6  3  ApbA            Ketopantoate reductase PanE/ApbA
     0.0075   16.2   0.7      0.022   14.7   0.2    1.9  2  YjeF_N          YjeF-related protein N-terminus
  ------ inclusion threshold ------
      0.047   13.9   0.5          1    9.6   0.0    2.5  2  TrkA_N          TrkA-N domain
      0.064   13.3   0.0       0.16   12.1   0.0    1.7  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.071   12.1   3.1       0.41    9.6   0.4    2.1  2  Lycopene_cycl   Lycopene cyclase protein
      0.098   12.5   1.0       0.19   11.6   0.1    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.12   11.8   0.0        2.7    7.4   0.0    2.2  2  Epimerase       NAD dependent epimerase/dehydratase family
       0.13   10.7   0.0       0.19   10.1   0.0    1.2  1  FMO-like        Flavin-binding monooxygenase-like
       0.16   12.5   0.2        0.9   10.0   0.0    2.3  2  XdhC_C          XdhC Rossmann domain
       0.67   10.0   3.5         14    5.7   0.2    2.4  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
          1    8.1   3.0       0.65    8.8   0.5    1.8  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.2   0.5   7.4e-50   4.9e-47       1     451 [.      13     420 ..      13     421 .. 0.82

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 7.4e-50
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHHTTCCCCEEEESCCGCEE CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellkelgledslslpdpgapkr 77 
                                       laGL+aAr+L++aG dVtv+E r+ vGGR+rt ++dG++++ G+++++ +++++ + l+   l+ + + p      +
  gi|313127134|ref|YP_004037404.1|  13 LAGLVAARHLADAGADVTVFERRPEVGGRVRTQKRDGFTFDRGFQVLFTKYPAVRRELDLSALDVRYFAPG-----A 84 
                                       79********************************************************9988887766333.....4 PP

                                       EEETTEECC.TTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHH CS
                     Amino_oxidase  78 vlskggref.pgdlspvpaewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgd 153
                                       v+ + g++    d  + p++  a l+      +++++++klr    +++ +  +e +     ++  +  l + ++++
  gi|313127134|ref|YP_004037404.1|  85 VIARPGQRStLSDPIRDPRATVASLQ-----NDEVTTTDKLRTLALRQHVGSMTENEIFGSEDDSIRDYLREWGFSE 156
                                       56666666558888888999999999.....8*****************4444444555555555556677777888 PP

                                       HHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHHHHHHH..TTTTEEEETS CS
                     Amino_oxidase 154 vevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlpealae..elrgldirln 228
                                        +  ++++ p       f +g+ +   ++ls +   ++  + +  +gs+ +p gG++++pe+la+  ++ g +i ++
  gi|313127134|ref|YP_004037404.1| 157 -DYIEHFVAP-------FYGGITLD--RSLSTSKRVFEYTFKMLSEGSIGVPAGGMQAVPEQLAAnaRKAGARIVTE 223
                                       .88******9.......99999887..99************************************************ PP

                                       EEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEES..CCSHHHHHHHHHSEEEEEEEEEEEESSGGSG CS
                     Amino_oxidase 229 trVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsP..plpdekaeairnlgfgsvnkvilefdrkfwe 303
                                       + V  i+ +gd  t+t++  +v +aD Vvv++++  ++   ++   + p  +++ + +  +       le+++k   
  gi|313127134|ref|YP_004037404.1| 224 SGVEHIDDNGDSATITTVEETV-DADFVVVATDPKEAR--RLTDvnQIPTNARSCVTQ-SYRLPKGTKLETRKKL-- 294
                                       ***************9876665.***************..333322444433333333.4444444446777776.. PP

                                       CSTSECECECCCEEETTTEEEEECC..ECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHHHHHHHHHHT...G CS
                     Amino_oxidase 304 dnalgqgvlvseltttlgeafissd..fpsrappgkglvllvyvggdaaneleslsdeelvqavlrdLrklfg...e 375
                                                + +  ++++++++ ++   p++ap++  lv  +++g  a ++    + +el++ +++ L+++++   +
  gi|313127134|ref|YP_004037404.1| 295 ---------LLNAADDAPNTVVPMSevAPEYAPDDAELVNATFLGTSALDR----DASELAEMTRKTLESWYPdrmF 358
                                       .........555555555555555555***********9999999888888....9*****************5555 PP

                                       TSSTCSEEEEEECCTETTTSSSEEE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 376 evpepkatlvtrWhtdplargsysyvsvgpghedydplakpegdprlffAGehtsreypgtvegAilSGlraAari 451
                                       +  ep        htd++  +++      pg +d  p +++ + +r ++AG+ t+   +++++gA++SG++aA+++
  gi|313127134|ref|YP_004037404.1| 359 DGLEP-------IHTDRIEFAQF---DQPPGVHDALPTNRE-PGGRTYLAGDFTA---WSSIQGAMQSGRNAAEAV 420
                                       55555.......56788886666...888899999999999.9************...799************997 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.1   6.4e-19   4.2e-16       1      63 [.       8      68 ..       8      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 6.4e-19
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHH CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrr 63
                                      + GaGl+GlvaA++La+ag+dv+++e+r+ +GGr+++ +++g+++d g +++++  +yp+vrr
  gi|313127134|ref|YP_004037404.1|  8 VAGAGLAGLVAARHLADAGADVTVFERRPEVGGRVRTQKRDGFTFDRGFQVLFT--KYPAVRR 68
                                      56****************************************************..6999986 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.7   3.6e-08   2.4e-05       2      35 ..       6      40 ..       5      50 .. 0.93
   2 !   21.8   0.0   1.8e-07   0.00012     151     238 ..     208     292 ..     172     410 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.6e-08
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                      vv+ G+G +Gl +A++La +g  Vt++e+++++g g
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADAGadVTVFERRPEVG-G 40
                                      9*****************9999********9998.4 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.8e-07
                                       HHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHH.HTT..CTTTSEEEEEEEE CS
                               DAO 151 alaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdll.gll..keldlpispvrgq 223
                                        la+ a+++G++i++++ v+++++ +g+ +++  tt +e+ da d vV+a+ +   ++ +l+  ++++   + +  q
  gi|313127134|ref|YP_004037404.1| 208 QLAANARKAGARIVTESGVEHIDD-NGDSATI--TTVEETvDA-DFVVVATDPK--EArRLTdvNQIPTNARSCVTQ 278
                                       58888999**************55.4566777..555555244.77*******9..562222333333344556666 PP

                                       EEEEEECCTHSTGSG CS
                               DAO 224 vlvlkplseklvspa 238
                                       +++l p+  kl+ ++
  gi|313127134|ref|YP_004037404.1| 279 SYRL-PKGTKLETRK 292
                                       6666.4444443333 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.4e-07   9.5e-05       3      34 ..       6      36 ..       4     121 .. 0.86
   2 !   14.2   0.2   2.9e-05     0.019     187     235 ..     207     254 ..     200     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
                                      EEEE--SHHHHHHHHHHHHHTS-EEEEETTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  3 vvviGgGpAGlaaaltlaqagakvtlvelegt 34
                                      vvv G+G AGl aa++la aga+vt++e ++ 
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADAGADVTVFE-RRP 36
                                      7888888888888888888888888885.322 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 187 aaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvav 235
                                       ++l++  +k G ++++++ v+ id+ng+   ++++ +e++dad vvva+
  gi|313127134|ref|YP_004037404.1| 207 EQLAANARKAGARIVTESGVEHIDDNGD-SATITTVEETVDADFVVVAT 254
                                       6677889999*****************9.6699999***********98 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.4e-07   9.1e-05       2      40 ..       5      43 ..       4      71 .. 0.92
   2 !    7.9   0.0    0.0016       1.1     112     162 ..     206     254 ..     199     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.4e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                      +v+v G+G AGl aA ++a++g++V+++e+ +++g +++
  gi|313127134|ref|YP_004037404.1|  5 TVVVAGAGLAGLVAARHLADAGADVTVFERRPEVGGRVR 43
                                      69********************************98876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 112 vdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAt 162
                                        + l +++++ag ++ +e+ v++++ + d+  +++t  ee++ ad +v+At
  gi|313127134|ref|YP_004037404.1| 206 PEQLAANARKAGARIVTESGVEHIDDNGDS-ATITT-VEETVDADFVVVAT 254
                                       5678999*****************888888.88888.8************8 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3   1.6e-07   0.00011       2      35 ..       6      39 ..       5      47 .. 0.93
   2 ?    5.3   0.0     0.044        29      45      76 ..     208     238 ..     203     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.6e-07
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      vvv G+G+ gl +A  la+ g++Vtv+er++++ 
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADAGADVTVFERRPEVG 39
                                      8******************************997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.044
                                       HHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox  45 ilqeklekngievllntkveeiegsedgvesv 76 
                                        l+ + +k g ++++++ ve i+ ++d  + +
  gi|313127134|ref|YP_004037404.1| 208 QLAANARKAGARIVTESGVEHIDDNGDSAT-I 238
                                       577889999**************9999644.3 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.4   2.1e-09   1.4e-06       2      36 ..       6      40 ..       5      52 .. 0.90
   2 ?   -1.8   0.0       1.9   1.3e+03     139     180 ..     201     242 ..     176     282 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.1e-09
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      v+V G+GlAGL+AA  +a+aG++v+v e  +e+gg
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADAGADVTVFERRPEVGG 40
                                      9*******************************999 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEE CS
                     FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedgrvtGavve 180
                                         +a+ + l+++arkag ++ ++  ++++  +++ +t  +ve
  gi|313127134|ref|YP_004037404.1| 201 GMQAVPEQLAANARKAGARIVTESGVEHIDDNGDSATITTVE 242
                                       556666677777777777777777777773333344433333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   1.7e-07   0.00012       3      35 ..       5      37 ..       4      52 .. 0.90
   2 ?    3.4   0.0     0.054        36     107     161 ..     205     253 ..     121     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      +V++ GaG+aGl++a+ L+ aG +v++ e+r +
  gi|313127134|ref|YP_004037404.1|  5 TVVVAGAGLAGLVAARHLADAGADVTVFERRPE 37
                                      599***************************976 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE- CS
                     FAD_binding_3 107 leriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGa 161
                                       +   L+++a+++g+++  +  ve  + d++g +a+++  e    etv+a+++v a
  gi|313127134|ref|YP_004037404.1| 205 VPEQLAANARKAGARIVTESGVE--HIDDNGDSATITTVE----ETVDADFVVVA 253
                                       55678999999999999999999..788888899999885....79*****9865 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00045       0.3     164     201 ..       3      40 ..       1      48 [. 0.77
   2 !   12.6   0.0   8.7e-05     0.058      85     132 ..     207     254 ..     194     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiek 201
                                       g+ vvV G++  +  aA +l+++ga+Vtv+ r+ e+  
  gi|313127134|ref|YP_004037404.1|   3 GETVVVAGAGLAGLVAARHLADAGADVTVFERRPEVGG 40 
                                       67788888888888888888888888888888877655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.7e-05
                       Pyr_redox_3  85 eYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAt 132
                                       e+l++ a++   +i +++ Ve ++ ++++ +++t +et+ A++v++At
  gi|313127134|ref|YP_004037404.1| 207 EQLAANARKAGARIVTESGVEHIDDNGDSATITTVEETVDADFVVVAT 254
                                       6677778889999**********************************9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.5   6.7e-08   4.5e-05       2      38 ..       6      42 ..       5      54 .. 0.94
   2 ?   -2.8   0.0       4.4   2.9e+03     279     299 ..     144     162 ..      96     167 .. 0.70
   3 ?   -1.5   0.1       1.9   1.2e+03     154     154 ..     265     265 ..     201     374 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.7e-08
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38
                                      vvV G+g+aG++AA   a aGa v + e+r+ +GG +
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADAGADVTVFERRPEVGGRV 42
                                      9**********************************75 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.4
                      FAD_oxidored 279 gllkylqteewgfekaelegl 299
                                       ++++yl   ewgf+++++e++
  gi|313127134|ref|YP_004037404.1| 144 SIRDYLR--EWGFSEDYIEHF 162
                                       4555555..899999999876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.9
                      FAD_oxidored 154 v 154
                                       v
  gi|313127134|ref|YP_004037404.1| 265 V 265
                                       0 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   3.1e-07   0.00021      30      68 ..       5      43 ..       2      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.1e-07
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqle 68
                                      +v+v G+G aGl A++  +  ga+Vtv++ rp++  +++
  gi|313127134|ref|YP_004037404.1|  5 TVVVAGAGLAGLVAARHLADAGADVTVFERRPEVGGRVR 43
                                      69******************************9876665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.6e-06     0.005       5      54 ..       1      48 [.       1     163 [. 0.84
   2 ?    2.1   0.3       0.4   2.6e+02      57      75 ..     242     260 ..     201     309 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.6e-06
                     NAD_binding_7  5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee 54
                                      ++g++v+v+G+G  ++  +r+l++aga+vtv   +  +e+ ++v+ ++++
  gi|313127134|ref|YP_004037404.1|  1 MDGETVVVAGAGLAGLVAARHLADAGADVTVFERR--PEVGGRVRTQKRD 48
                                      5799***************************9888..5666666665544 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.4
                     NAD_binding_7  57 kdlegadlviaatddreln 75 
                                       ++  +ad+v++atd +e +
  gi|313127134|ref|YP_004037404.1| 242 EETVDADFVVVATDPKEAR 260
                                       3344788999999665543 PP

>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   1.3e-06   0.00089       1      46 [.       1      47 [.       1      66 [. 0.85
   2 ?   -2.6   0.0       3.5   2.3e+03     229     262 ..     237     270 ..     205     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                      CoA_transf_3  1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppk.kgDpaRkvgp 46
                                      ++G +V+ ++  laG +a+++LAd GA+V+  E++   g  +R++++
  gi|313127134|ref|YP_004037404.1|  1 MDGETVVVAGAGLAGLVAARHLADAGADVTVFERRPeVGGRVRTQKR 47
                                      58999****************************97657777777654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                      CoA_transf_3 229 apygvyrtkdgwvaiaaatdkqwaalckalgrpe 262
                                        + +v +t d  ++++a+++k+ ++l ++   p+
  gi|313127134|ref|YP_004037404.1| 237 TITTVEETVDADFVVVATDPKEARRLTDVNQIPT 270
                                       4455556677777788888888888887766664 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     2e-06    0.0013      20      56 ..       6      41 ..       2      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                      vv+ GaG +GL aa+ la + +  v+++er+  +GG 
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADA-GADVTVFERRPEVGGR 41
                                      9*******************.**********999995 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.2   0.00015     0.098       1      44 [.       7      45 ..       7      51 .. 0.83
   2 ?    5.6   0.2     0.021        14     104     153 ..     206     254 ..     202     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrt 44
                                      ++ GaG +Gl ++++L++        ++t+f++++   grv  +
  gi|313127134|ref|YP_004037404.1|  7 VVAGAGLAGLVAARHLADA-----GADVTVFERRPEVGGRVRTQ 45
                                      578**************99.....59*******99853777554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                     NAD_binding_9 104 feellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAl 153
                                        e+l+a++++     v ++ v+ +++++d++++ ++ +++++ad Vv+A+
  gi|313127134|ref|YP_004037404.1| 206 PEQLAANARKAGARIVTESGVEHIDDNGDSATI-TTVEETVDADFVVVAT 254
                                       56667777544444456779999**99999866.88999*********98 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   5.6e-06    0.0037       1      29 [.       5      35 ..       5      51 .. 0.81
   2 ?   -2.0   0.1       2.2   1.5e+03     116     150 ..     224     256 ..     220     294 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.6e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE..E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..t 29
                                      +v+V G+G+AG+ AA ++a +Ga+v+ +   
  gi|313127134|ref|YP_004037404.1|  5 TVVVAGAGLAGLVAARHLADAGADVTVFerR 35
                                      599**********************998440 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                       S-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 116 eeveeliveekkvkgvvtedgetikakavviatGt 150
                                         ve++++  +  ++ +t+ +et+ a+ vv+at +
  gi|313127134|ref|YP_004037404.1| 224 SGVEHIDD--NGDSATITTVEETVDADFVVVATDP 256
                                       55666644..3334456677889999999999988 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00013     0.084       1      31 [.       6      36 ..       6      58 .. 0.87
   2 ?   -1.6   0.0       2.8   1.9e+03      90     103 ..      98     111 ..      94     140 .. 0.75
   3 ?    1.5   0.1       0.3     2e+02      33      76 ..     210     254 ..     204     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      ++++GaG  G + a +La agadvt+  r++
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADAGADVTVFERRP 36
                                      689************************9997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                                       GGECTCEEEEEESS CS
                              ApbA  90 plldpntvvlllqN 103
                                       p+ dp+++v +lqN
  gi|313127134|ref|YP_004037404.1|  98 PIRDPRATVASLQN 111
                                       77799999999999 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.3
                                       HHHHHHHCEEEEETTCEEEEEECEEECCH.SCCCCS-ESEEEE-S CS
                              ApbA  33 lealkknGlrltseggeeilrppealsae.ekselepidlvivtv 76 
                                       +++ +k+G r+ +e+g e++ ++   ++  + +e  ++d v+v++
  gi|313127134|ref|YP_004037404.1| 210 AANARKAGARIVTESGVEHIDDNGDSATItTVEETVDADFVVVAT 254
                                       445899999999999888887776666656678999999999987 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   3.3e-05     0.022      39      74 ..      12      45 ..       3      50 .. 0.78
   2 ?   -1.6   0.0       3.3   2.2e+03      74     107 ..     209     246 ..     197     274 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                            YjeF_N 39 GgdglaaArhLaqegakVtvllleeeekldedaera 74
                                      G  gl+aArhLa +ga+Vtv  +e++++  + ++++
  gi|313127134|ref|YP_004037404.1| 12 GLAGLVAARHLADAGADVTV--FERRPEVGGRVRTQ 45
                                      6679****************..57777666666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                            YjeF_N  74 alellkkaggkvveekpeedleekls....apvdlviD 107
                                         ++++kag ++v+e+ +e  +++      ++v+  +D
  gi|313127134|ref|YP_004037404.1| 209 LAANARKAGARIVTESGVEHIDDNGDsatiTTVEETVD 246
                                       55566777777776666555443222344444444444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0016         1       1      37 [.       6      42 ..       6      53 .. 0.82
   2 ?    1.9   0.1      0.38   2.5e+02      22      39 ..     247     264 ..     212     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveel 37
                                      ++++G+G  G   a+ L ++g dv+v ++++e+  ++
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADAGADVTVFERRPEVGGRV 42
                                      79*****************6668*******9974444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.38
                                       EEEEEEESSHHHHHHHHH CS
                            TrkA_N  22 kdvvvidkdeerveelre 39 
                                        d+vv+ +d++ +++l++
  gi|313127134|ref|YP_004037404.1| 247 ADFVVVATDPKEARRLTD 264
                                       357888888888777765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.16      12      49 ..       3      39 ..       1      51 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                                      T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHH CS
                      Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlera 49
                                      +++v++ GaG  +  +a+hL+++g++ v+v+ R  e  
  gi|313127134|ref|YP_004037404.1|  3 GETVVVAGAGLAGLVAARHLADAGAD-VTVFERRPEVG 39
                                      689**********************9.******98765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   0.00061      0.41       2      31 ..       6      33 ..       5      45 .. 0.78
   2 ?    2.9   0.1     0.068        45     100     146 ..     217     260 ..     203     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00061
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlie 31
                                      vvv GaG+Agl  A +l++a  g  v++ e
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADA--GADVTVFE 33
                                      89***************555..55555555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.068
                     Lycopene_cycl 100 ngvklleakvesveeeeageslvvleggrkirarlvvdarglaslkk 146
                                       ++++ +e+ ve++ ++ +  s  ++  +++++a +vv+a+  +++ +
  gi|313127134|ref|YP_004037404.1| 217 GARIVTESGVEHIDDNGD--SATITTVEETVDADFVVVATD-PKEAR 260
                                       456788999999988777..778888899**********98.55543 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00028      0.19       1      39 [.       5      43 ..       5      54 .. 0.88
   2 ?   -2.1   0.1       4.7   3.1e+03      69      82 ..     237     250 ..     204     256 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekal 39
                                      +v v GaG+ G   a  +a ag +V+++++++e   +++
  gi|313127134|ref|YP_004037404.1|  5 TVVVAGAGLAGLVAARHLADAGADVTVFERRPEVGGRVR 43
                                      5899**************************998766655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.7
                                       EES-HHHHHC-SEE CS
                           3HCDH_N  69 fttdleeavdadlv 82 
                                       + t +ee vdad+v
  gi|313127134|ref|YP_004037404.1| 237 TITTVEETVDADFV 250
                                       23344444444444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.004       2.7       2      67 ..       7      77 ..       6      99 .. 0.77
   2 ?    2.1   0.0      0.17   1.1e+02     207     223 ..     147     163 ..     108     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.004
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SE CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpda 67
                                      +V+Ga G+ G   +++l+++g +v+++ r+++ + + r ++       +  ++ +t+  a++r ++  + d+
  gi|313127134|ref|YP_004037404.1|  7 VVAGA-GLAGLVAARHLADAGADVTVFERRPEVGGRVRTQKRdgftfdRGFQVLFTKYPAVRRELDLSALDV 77
                                      56766.************************998888887777777777666777777777777666656555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.17
                                       T-EEEEEEHHHHHHHHH CS
                         Epimerase 207 talRdflyveDvaeail 223
                                       + lR+++++eD++e ++
  gi|313127134|ref|YP_004037404.1| 147 DYLREWGFSEDYIEHFV 163
                                       568**********9876 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00028      0.19       3      43 ..       5      45 ..       3      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00028
                          FMO-like  3 kvaviGaGvsGlasikccleegleptcfersddiGGlwrfk 43
                                       v v GaG++Gl++ +   + g + t fer  ++GG  r +
  gi|313127134|ref|YP_004037404.1|  5 TVVVAGAGLAGLVAARHLADAGADVTVFERRPEVGGRVRTQ 45
                                      58999*******************************77755 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0014       0.9       1      45 [.       6      55 ..       6     168 .. 0.70
   2 ?   -0.4   0.0       2.4   1.6e+03      37      51 ..     239     254 ..     201     309 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.....- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.....t 45
                                      +v+ Gag  +   ar +a +g +vtv++ r+e+  + r ++ d       
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADAGADVTVFERRPEVGGRVRTQKRDGftfdrG 55
                                      689****************************9774444443322555553 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.4
                                       GG-TT-SE.-EEEE-- CS
                            XdhC_C  37 erfpeade.tavvvlt 51 
                                       + ++e+ + ++vvv+t
  gi|313127134|ref|YP_004037404.1| 239 TTVEETVDaDFVVVAT 254
                                       3333222223333333 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.021        14      22      55 ..       2      35 ..       1      42 [. 0.92
   2 ?    4.8   0.1     0.041        27      33     106 ..     204     274 ..     186     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.021
                                      TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S- CS
                     AdoHcyase_NAD 22 aGkvavvaGyGdvGkGcaaslkglGarvivtevd 55
                                       G ++vvaG G  G  +a+ l  +Ga v+v e  
  gi|313127134|ref|YP_004037404.1|  2 DGETVVVAGAGLAGLVAARHLADAGADVTVFERR 35
                                      699**************************98865 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HHHHCCS-TTEEE CS
                     AdoHcyase_NAD  33 dvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtttGnkdiitlehlkkmkddaiv 106
                                        v    aa  +++Gar+ vte   +  +    +   ++t+ee v+ ad+vv +t  k+  +l +++++  +a  
  gi|313127134|ref|YP_004037404.1| 204 AVPEQLAANARKAGARI-VTE-SGVEHIDDNGDSATITTVEETVD-ADFVVVATDPKEARRLTDVNQIPTNARS 274
                                       56666788899999996.788.468889999999********985.8999999999999999998888877755 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.5   0.00099      0.65       2      33 ..       6      34 ..       5      40 .. 0.89
   2 ?   -1.3   0.1       1.1   7.4e+02     158     205 ..     207     252 ..     203     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00099
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlves 33
                                      +v++G+G aG +aA +la a+   ++vt+ e 
  gi|313127134|ref|YP_004037404.1|  6 VVVAGAGLAGLVAARHLADAG---ADVTVFER 34
                                      9*******************9...88998875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE CS
                    Trp_halogenase 158 kfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiD 205
                                       + L ++a ++G ++v    ve ++d++g+ + +++  +++v+ad+++ 
  gi|313127134|ref|YP_004037404.1| 207 EQLAANARKAGARIVTESGVE-HIDDNGDSATITT-VEETVDADFVVV 252
                                       568888999998877665544.4555666666665.456799999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2742.28
//
Query:       gi|313127135|ref|YP_004037405.1|  [L=253]
Description: phosphoesterase, icc [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-10   41.1   0.1    2.8e-10   40.7   0.1    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    6.4e-09   36.6   0.0    1.4e-08   35.5   0.0    1.6  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.1   3.1e-14   2.8e-10       4     131 ..      28     173 ..      26     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.1e-14
                     Metallophos_2   4 aiiSDlH..............snldaleavlealkevgvdaiihaGD.......leeeep....evleellela... 52 
                                       +++SDlH              ++ d+ +++ + +++ ++  +++aGD       +         + l+el  ++   
  gi|313127135|ref|YP_004037405.1|  28 LVVSDLHvgraeasdvafplgERSDLRDRLSALVEAFDPAEVVFAGDvlhrfdtA----TtaaeSGLDELVGVCrna 100
                                       89******************95555555555555555556*******55554431....122223555555555666 PP

                     Metallophos_2  53 ..pvlaVrGNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsd..vvvcG 125
                                         + + VrGN+D           +  +++++  ++ + ++  +v ++Hg+  ++++a +e+ ++a+++ d  ++v G
  gi|313127135|ref|YP_004037405.1| 101 gvKPILVRGNHD--------TVLESAWDGKV-FDQYVIAESPSVVVCHGH--AAPAAESEVESSATSETDasLYVIG 166
                                       9*9*********........44567788888.55555558999*******..77777777777766665568***** PP

                     Metallophos_2 126 HtHvp.e 131
                                       H H + +
  gi|313127135|ref|YP_004037405.1| 167 HVHPAiT 173
                                       ***7654 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   1.6e-12   1.4e-08       3     124 ..      27     144 ..      25     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.6e-12
                                       EEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH....TSE CS
                       Metallophos   3 ilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvky....pip 66 
                                        lv++DlH+        a   g  +dl++ l+ l +  +p  v++aGD+ +r d  +  +e  l++lv      +++
  gi|313127135|ref|YP_004037405.1|  27 TLVVSDLHVgraeasdvAFPLGERSDLRDRLSALVEAFDPAEVVFAGDVLHRFDTATTAAESgLDELVGVcrnaGVK 103
                                       69***************999999999999999999999***************999999999899999988866666 PP

                                       EEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE..C CS
                       Metallophos  67 vylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg..s 124
                                        +l++GNH+     +l++ ++           ++vf+ + +a+  s    v+++hG+  +
  gi|313127135|ref|YP_004037405.1| 104 PILVRGNHD----TVLESAWD-----------GKVFDQYVIAE--SP--SVVVCHGHaaP 144
                                       6********....77777665...........77889999999..77..88999999431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1806.21
//
Query:       gi|313127136|ref|YP_004037406.1|  [L=264]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-10   38.8   0.0    2.1e-09   36.8   0.0    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
    5.4e-09   35.8   0.2    1.7e-08   34.2   0.2    1.9  1  MarR_2          MarR family
    1.2e-06   28.3   0.0    3.1e-06   27.0   0.0    1.6  1  MarR            MarR family
      4e-06   27.2   4.8    0.00014   22.3   0.1    3.5  4  HTH_27          Winged helix DNA-binding domain
    0.00017   21.3   0.0    0.00042   20.1   0.0    1.7  1  HTH_IclR        IclR helix-turn-helix domain
    0.00022   21.1   0.0    0.00054   19.9   0.0    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0017   18.2   0.2     0.0039   17.1   0.2    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0018   18.1   0.0     0.0032   17.3   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0025   17.3   0.1      0.077   12.4   0.1    2.1  2  NMD3            NMD3 family
     0.0028   17.9   0.0      0.011   16.1   0.0    2.0  2  Rrf2            Transcriptional regulator
     0.0032   17.6   0.1     0.0087   16.2   0.1    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0049   16.9   0.1      0.011   15.7   0.1    1.6  1  HTH_20          Helix-turn-helix domain
     0.0089   16.0   0.0      0.028   14.4   0.0    1.9  2  HTH_45          Winged helix-turn-helix
     0.0096   16.2   0.2      0.025   14.9   0.2    1.7  1  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.025   14.6   0.0    1.6  1  HTH_13          HTH DNA binding domain
      0.022   15.0   0.1      0.073   13.4   0.0    1.9  1  Mnd1            Mnd1 HTH domain
      0.056   13.2   0.0      0.094   12.5   0.0    1.3  1  DUF4364         Domain of unknown function (DUF4364)
       0.07   13.0   0.1       0.18   11.7   0.1    1.7  1  P22_Cro         DNA-binding transcriptional regulator Cro
      0.081   12.8   0.2        1.3    8.9   0.1    2.5  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.095   12.7   0.0       0.18   11.8   0.0    1.4  1  HTH_11          HTH domain
       0.11   12.4   0.0       0.28   11.1   0.0    1.7  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
       0.12   12.4   0.1       0.41   10.7   0.1    1.9  2  HTH_3           Helix-turn-helix
       0.14   12.3   0.3       0.63   10.2   0.0    2.3  2  Mrr_N           Mrr N-terminal domain
       0.17   11.7   0.2          1    9.2   0.0    2.2  2  LexA_DNA_bind   LexA DNA binding domain
       0.29   11.3   1.4       0.59   10.3   0.1    2.2  2  HTH_28          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   2.9e-12   2.1e-09       3      48 .]      11      57 ..       9      57 .. 0.90
   2 ?   -1.6   0.0       2.8     2e+03       8      24 ..      92     108 ..      91     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.9e-12
                            HTH_24  3 etdrkIL.elLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       t+++IL e+  ++p  sq e+Ae++g+++++v+++ ++L+e+G+++
  gi|313127136|ref|YP_004037406.1| 11 ATRLRILvEIANRQPAVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVE 57
                                      799****566666********************************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                            HTH_24   8 ILelLqknprisqreLA 24 
                                       +Le +q+++ i   eL+
  gi|313127136|ref|YP_004037406.1|  92 VLENVQEDAAIATEELS 108
                                       79999****99998887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.2   2.4e-11   1.7e-08       4      54 ..      10      59 ..       8      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.4e-11
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      t + +r+L ++++r +  +++ge+a++ g++ +avs   + Lv+ G+ve++
  gi|313127136|ref|YP_004037406.1| 10 TATRLRILVEIANRQPA-VSQGEVAEAVGVTSQAVSEYTRQLVEDGYVEKE 59
                                      78999**********96.9******************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   4.4e-09   3.1e-06       2      50 ..      10      59 ..      10      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.4e-09
                                      -HHHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  2 tltqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      t+t+++iL+ +++++p  s+ e a+++gv++ +v++ +++L+++G++e++
  gi|313127136|ref|YP_004037406.1| 10 TATRLRILVEIANRQPaVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVEKE 59
                                      7899*******9998879999**************************985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   1.9e-07   0.00014       9      68 .]      17      70 ..      11      70 .. 0.83
   2 ?   -1.7   0.0       5.9   4.2e+03      42      66 ..     116     139 ..     105     140 .. 0.70
   3 ?    4.6   0.0     0.065        46      20      47 ..     182     209 ..     175     216 .. 0.88
   4 ?   -0.5   0.1       2.6   1.9e+03      46      67 ..     238     259 ..     233     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.9e-07
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      L  i+ r+  +++ ++++++ v+++++s+  ++L+e G+ve++      +++r+ +T +G
  gi|313127136|ref|YP_004037406.1| 17 LVEIANRQPAVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVEKE------GRSRYHVTKEG 70
                                      4445568888889***************************444......44688899887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.9
                            HTH_27  42 LtekGLvertgdeadrrekrvrlTd 66 
                                        ++ GL++ t+ e ++ ++ v+ Td
  gi|313127136|ref|YP_004037406.1| 116 TVRDGLLHATPGE-SGPATGVATTD 139
                                       5778999888885.66556666666 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.065
                            HTH_27  20 kladlcgrlnvedshisyslkkLtekGL 47 
                                       +la+ c+  +v ++++++++  L ++++
  gi|313127136|ref|YP_004037406.1| 182 TLAEMCDDADVVAATGIEAIVSLRKADV 209
                                       7899********************9985 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.6
                            HTH_27  46 GLvertgdeadrrekrvrlTdk 67 
                                       +Lv r +d   ++++++++T++
  gi|313127136|ref|YP_004037406.1| 238 DLVGRVTDVLRDGDVLYEVTEA 259
                                       7888888888889999***997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.9e-07   0.00042       6      51 ..      14      59 ..      13      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.9e-07
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      l+iL  +a ++++++  e+A++ g++  +v+ +++ Lve Gyve++
  gi|313127136|ref|YP_004037406.1| 14 LRILVEIANRQPAVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVEKE 59
                                      6888889999**********************************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   7.5e-07   0.00054       7      59 ..      17      66 ..       8      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.5e-07
                                      HHHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEE CS
                         HTH_Crp_2  7 LlrlaeraggeielpltqeelAsmlGltretvsrilseLkreglis.rgrr.iri 59
                                      L+++a+r+       ++q e A+ +G+t + vs   ++L ++g+++  gr   ++
  gi|313127136|ref|YP_004037406.1| 17 LVEIANRQ-----PAVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVEkEGRSrYHV 66
                                      45555553.....469******************************545422555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   5.4e-06    0.0039      25      59 ..      29      63 ..      15      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.4e-06
                                      HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                        e+ae++gv  + v e+ r+L++ G+Ve+e +++
  gi|313127136|ref|YP_004037406.1| 29 QGEVAEAVGVTSQAVSEYTRQLVEDGYVEKEGRSR 63
                                      569***************************97653 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.4e-06    0.0032       3      47 .]      12      58 ..      10      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.4e-06
                                      HHHHHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  3 tRlkILklLae.ge.lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      tRl+IL   a+ ++  + +e ae++g++  +vS++ ++L e G+Vek
  gi|313127136|ref|YP_004037406.1| 12 TRLRILVEIANrQPaVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVEK 58
                                      9**********888667789*************************97 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   0.00011     0.077     162     233 ..      40     112 ..      30     118 .. 0.84
   2 ?    2.9   0.0      0.09        64     124     158 ..     177     210 ..     162     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                              NMD3 162 hkrtfelleqlilkhd.ahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkksgke 233
                                        +++ e+ +ql++ +   ++  s++  +keG+D  f++ ++ r++++ +++ v  +v+e   +++e+ +sg+ 
  gi|313127136|ref|YP_004037406.1|  40 SQAVSEYTRQLVEDGYvEKEGRSRYHVTKEGVDWLFQEAKDLRRFADHVTDDVLENVQEDAAIATEELSSGET 112
                                       667888999999666547778899999*********************************9999997776654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.09
                              NMD3 124 evevkvkrqqCprCsriaggyyeaivQvRqkrelt 158
                                        v +++  ++C++   +a+   eaiv +R+  +++
  gi|313127136|ref|YP_004037406.1| 177 AVDLETLAEMCDDADVVAATGIEAIVSLRKA-DVE 210
                                       567777889********************99.333 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.5e-05     0.011       5      56 ..       8      57 ..       6      62 .. 0.91
   2 ?   -2.5   0.0       9.5   6.8e+03      51      63 ..     118     130 ..      97     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  5 skteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      ++t   l++l+++a+++    vs  e+ae +++  + ++  +++L + g+v+
  gi|313127136|ref|YP_004037406.1|  8 KRTATRLRILVEIANRQP--AVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVE 57
                                      5677789********999..59*****************************8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.5
                                       HTTSEEEETTT-T CS
                              Rrf2  51 kaglvksvrGkgG 63 
                                       + gl++++ G +G
  gi|313127136|ref|YP_004037406.1| 118 RDGLLHATPGESG 130
                                       6788888888876 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.2e-05    0.0087      19      57 ..      23      61 ..      10      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                       +  v++ ++ae+ +v    Vse  + L +dGyve e++
  gi|313127136|ref|YP_004037406.1| 23 RQPAVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVEKEGR 61
                                      566799****************************98875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.6e-05     0.011      11      60 ..      12      62 ..      10      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 11 vRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      +R+ril ++ +r  +++ +e+ae+++++ + +s   r+L+e g+ve ++ +
  gi|313127136|ref|YP_004037406.1| 12 TRLRILVEIaNRQPAVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVEKEGRS 62
                                      899******999999*******************************99876 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.9e-05     0.028      19      73 ..      26      82 ..       8      86 .. 0.72
   2 ?   -1.6   0.0       3.7   2.7e+03       2      23 ..      83     104 ..      82     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
                            HTH_45 19 eakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlell.eklkele 73
                                        ++ ++  ++  + + +++Y  +Lve g+++k   + Y +T++G + l ++ k+l+
  gi|313127136|ref|YP_004037406.1| 26 AVSQGEVAEAVGVTSQAVSEYTRQLVEDGYVEKeGRSRYHVTKEGVDWLfQEAKDLR 82
                                      5556666677777888999************6648899*******986525555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                            HTH_45   2 RskleIiadILeaisegeakkT 23 
                                       R    ++ d+Le+++e+ a  T
  gi|313127136|ref|YP_004037406.1|  83 RFADHVTDDVLENVQEDAAIAT 104
                                       555678889*****98888776 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   3.5e-05     0.025      17      91 ..     154     225 ..     153     227 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                                       EEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHH.TT-SEEEESSSCHHHHHHHCTTTSEEEES.-SSBHHHHHH CS
                     Nitro_FeMo-Co  17 iyeveegevkivenrveeaadaegggggklaqllae.egvdvvivgkiGpralakleaagievykg.aggtveealk 91 
                                       i+e+++g+v++v+++    ++++g++   l+ l+++  ++dvv + +i  +a+  l++a +e+ +  a+g+v+ea +
  gi|313127136|ref|YP_004037406.1| 154 IIEIDPGSVTVVQVP---PTRSGGSRAVDLETLAEMcDDADVVAATGI--EAIVSLRKADVEMETSwAAGDVAEAAA 225
                                       89*************...9999********************998876..99*************99******9975 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.5e-05     0.025       4      49 ..      17      65 ..      14      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
                            HTH_13  4 LvelvlsrPlVsagmvakeLkvtpraalklvkel...glRElTGRgrfr 49
                                      Lve+  ++P Vs g va++  vt +a+ +  ++l   g  E  GR r+ 
  gi|313127136|ref|YP_004037406.1| 17 LVEIANRQPAVSQGEVAEAVGVTSQAVSEYTRQLvedGYVEKEGRSRYH 65
                                      8999999********************9988887444668999999995 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0    0.0001     0.073      24      48 ..      35      59 ..      29      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                              Mnd1 24 ekgivsqsVkdvlqsLvdDglveve 48
                                      + g++sq V ++  +Lv+Dg ve+e
  gi|313127136|ref|YP_004037406.1| 35 AVGVTSQAVSEYTRQLVEDGYVEKE 59
                                      579*******************987 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013     0.094      36      90 ..      43      94 ..      37     120 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                           DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketlelfenripksirekideylk 90
                                      ++++  +Lve+g++e+   e++++y++T++G + l +  +++     + +d+ l+
  gi|313127136|ref|YP_004037406.1| 43 VSEYTRQLVEDGYVEK---EGRSRYHVTKEGVDWLFQEAKDLRRFADHVTDDVLE 94
                                      678999*********7...9***********987755555443322222222222 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00025      0.18      12      29 ..      29      46 ..      28      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                                      HHHHHHHHTS-HHHHHHH CS
                           P22_Cro 12 vekvAkalgvtksAVsqW 29
                                      +  vA+a+gvt +AVs+ 
  gi|313127136|ref|YP_004037406.1| 29 QGEVAEAVGVTSQAVSEY 46
                                      678*************87 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0018       1.3      14      36 ..      23      45 ..      14      50 .. 0.77
   2 ?    0.9   0.0      0.56     4e+02       9      24 ..      93     108 ..      91     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                     HTH_AsnC-type 14 edaRisyaeLAervGlSestvlr 36
                                      +++  s  e+Ae+vG++ ++v +
  gi|313127136|ref|YP_004037406.1| 23 RQPAVSQGEVAEAVGVTSQAVSE 45
                                      44888999************986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.56
                     HTH_AsnC-type   9 LeaLqedaRisyaeLA 24 
                                       Le  qeda i  +eL+
  gi|313127136|ref|YP_004037406.1|  93 LENVQEDAAIATEELS 108
                                       6678**********97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.18       2      47 ..      13      57 ..      12      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                            HTH_11  2 llqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIe 47
                                      +l il  + ++r+p +s  e Ae  +v+ ++v  + ++L e g  +e
  gi|313127136|ref|YP_004037406.1| 13 RLRILVEI-ANRQPaVSQGEVAEAVGVTSQAVSEYTRQLVEDG-YVE 57
                                      56788888.778888******************9999998888.555 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00038      0.28      10      29 ..      28      47 ..      22      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWl 29
                                      +q ++Aea+gv++qaVs   
  gi|313127136|ref|YP_004037406.1| 28 SQGEVAEAVGVTSQAVSEYT 47
                                      899**************874 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00057      0.41      11      30 ..      28      47 ..      11      50 .. 0.92
   2 ?   -2.8   0.0       9.9   7.1e+03      32      45 ..     174     187 ..     174     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00057
                                      HHHHHHHHHTSSHHHHHHHH CS
                             HTH_3 11 sqeeLAeklGvsrstisriE 30
                                      sq e+Ae++Gv+ +++s + 
  gi|313127136|ref|YP_004037406.1| 28 SQGEVAEAVGVTSQAVSEYT 47
                                      99***************996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.9
                                       TSSCSBHHHHHHHH CS
                             HTH_3  32 GernPsletlkkla 45 
                                       G r+ +letl +++
  gi|313127136|ref|YP_004037406.1| 174 GSRAVDLETLAEMC 187
                                       56778888887765 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00088      0.63      58      85 ..      47      74 ..       4      76 .. 0.84
   2 ?   -1.2   0.1       3.2   2.3e+03      19      38 ..      88     107 ..      81     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00088
                             Mrr_N 58 rtyLkkagllespkrgvwkiTekGrevl 85
                                        +L++ g++e++ r+ + +T++G ++l
  gi|313127136|ref|YP_004037406.1| 47 TRQLVEDGYVEKEGRSRYHVTKEGVDWL 74
                                      66899********************998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.2
                             Mrr_N  19 rlkeirervaerfglseeer 38 
                                        ++++ e v+e++ +  ee+
  gi|313127136|ref|YP_004037406.1|  88 VTDDVLENVQEDAAIATEEL 107
                                       45799999999999998886 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0014         1      18      64 ..      19      63 ..       8      64 .. 0.85
   2 ?   -0.9   0.0         2   1.4e+03      19      38 ..     162     181 ..     154     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                      HHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG-CC CS
                     LexA_DNA_bind 18 sieetgypPsireiaralglkSpsaveehLkaLerKGyierdpgkpR 64
                                      +i +++ + s  e+a+a+g++ ++av e  + L   Gy+e  +g++R
  gi|313127136|ref|YP_004037406.1| 19 EIANRQPAVSQGEVAEAVGVT-SQAVSEYTRQLVEDGYVEK-EGRSR 63
                                      577788888999*********.689**************95.56666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                                       HHHHSS---HHHHHHHHTS- CS
                     LexA_DNA_bind  19 ieetgypPsireiaralglk 38 
                                       ++  + pP++   +ra+ l+
  gi|313127136|ref|YP_004037406.1| 162 VTVVQVPPTRSGGSRAVDLE 181
                                       66678999999888888875 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00082      0.59       2      40 ..      13      54 ..      12      63 .. 0.77
   2 ?   -1.3   0.1       3.5   2.5e+03      15      25 ..     220     230 ..     218     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00082
                            HTH_28  2 RleiikllaaGh...svreaArelgisrrtvyrWikryeegG 40
                                      Rl+i+ ++a+     s+ e+A+++g++++ v+   +++ e G
  gi|313127136|ref|YP_004037406.1| 13 RLRILVEIANRQpavSQGEVAEAVGVTSQAVSEYTRQLVEDG 54
                                      8999999996533449***************98888777744 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.5
                            HTH_28  15 vreaArelgis 25 
                                       v+eaA++ g+s
  gi|313127136|ref|YP_004037406.1| 220 VAEAAAARGLS 230
                                       799***99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1826.26
//
Query:       gi|313127137|ref|YP_004037407.1|  [L=202]
Description: dnaj-class molecular chaperone with c-terminal zn finger domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-08   34.1   0.2      4e-08   33.3   0.2    1.4  1  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.2   2.3e-12     4e-08       3      59 ..     146     198 ..     144     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.3e-12
                                       HHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHH CS
                              DnaJ   3 YeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekR 59 
                                       ++ L ++++as +e+k aYr++++  HPD       ++ +F++++eAy + ++  +R
  gi|313127137|ref|YP_004037407.1| 146 FDHLDLPRTASPAEVKVAYRDKVKTAHPDHG----GSQAEFQRLQEAYATAKEHAER 198
                                       788**************************99....77899********998777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1580.95
//
Query:       gi|313127138|ref|YP_004037408.1|  [L=765]
Description: phosphoenolpyruvate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.6e-109  365.0   0.2   5.4e-109  364.4   0.2    1.2  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    7.2e-80  268.2   0.0    1.1e-79  267.7   0.0    1.2  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    7.4e-28   96.1   2.7    1.8e-27   94.9   2.7    1.7  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
     0.0029   17.7   1.7        5.7    7.1   0.0    3.7  3  PEP-utilisers_N  PEP-utilising enzyme, N-terminal


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.4   0.2  1.2e-112  5.4e-109       3     322 ..      16     325 ..      14     330 .. 0.97

  Alignments for each domain:
  == domain 1  score: 364.4 bits;  conditional E-value: 1.2e-112
                            PPDK_N   3 lvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPe 79 
                                       +vGGKga+L+el ++ag+pvP gf++ta ++r+f+e++g++e++ ++++ +d +d ++l++a ++++eli+++++Pe
  gi|313127138|ref|YP_004037408.1|  16 TVGGKGASLGEL-TSAGLPVPTGFVVTAGTYRSFIEDAGIDEELFDAVD-VDHEDSAALKEAHERAHELIMETPVPE 90 
                                       69**********.77*******************************999.8************************** PP

                            PPDK_N  80 eleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrk 156
                                       ++ e+i +ay+e+g+   d+e  vaVRSSataEDlp+asfaGqq+t+Lnv+ ++++++ +k+++aSlf++rAi+Yr+
  gi|313127138|ref|YP_004037408.1|  91 SVGEEILAAYDEVGE--SDDEAFVAVRSSATAEDLPDASFAGQQETFLNVQ-KDDLIHRVKECWASLFSQRAIYYRN 164
                                       *************98..66679****************************6.899********************** PP

                            PPDK_N 157 ekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilekk 233
                                       +kg++h+ev++avvvq+mv+++  +sGV+f+ +p+tG + +++i+a++GlGeaVV+G v+pd++vv++++ +++ ++
  gi|313127138|ref|YP_004037408.1| 165 RKGFPHHEVDIAVVVQEMVDAE--KSGVMFTSHPSTG-EPRIIIEAAWGLGEAVVSGSVSPDNYVVDRDSGEVETAT 238
                                       **********************..*************.*************************************** PP

                            PPDK_N 234 igekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpet 310
                                       +++k++++v d+++ +t+e +v++++r++ +L+++e+ +L e+++++e+hyg+p+d+E+ai   e+++y+lQ+Rp+t
  gi|313127138|ref|YP_004037408.1| 239 VADKKVMMVKDSETGETVERDVEDDKRSARVLDEDEIARLVELGERVEDHYGEPQDVEWAIY--EDDVYMLQSRPIT 313
                                       ************9988**********************************************..************* PP

                            PPDK_N 311 rtsekkekkaae 322
                                       + s++++++a++
  gi|313127138|ref|YP_004037408.1| 314 TISDDEKDAATQ 325
                                       ***998877665 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.7   0.0   2.4e-83   1.1e-79      12     293 ..     467     756 ..     457     757 .. 0.94

  Alignments for each domain:
  == domain 1  score: 267.7 bits;  conditional E-value: 2.4e-83
                                       CCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH...........HHHHHHHHHHHTTT CS
                   PEP-utilizers_C  12 avtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee...........qaeaykkvleamng 77 
                                       +++k++++++v +N++ pe+ae+a+++ga+G+GLlR+E++ ++  ++p               ++e +++v+e +++
  gi|313127138|ref|YP_004037408.1| 467 TPVKPMTATEVKVNVSIPEAAERAAATGADGVGLLRIEHMVLSLGKTPDKYIadngerayveeLVEGIRGVAEEFYP 543
                                       67889999**********************************998865443346888999999************** PP

                                       SEEEEEXXXSSCC..GGSGGCHHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCCCC..EEEEEESSXXSHHH CS
                   PEP-utilizers_C  78 rpvvvRtlDiggd..kelpelkeepeevNPmlGfRgirlglsepelfetqlrAllrasaag..kleimlPmvasvee 150
                                       rpv vR lD+++d  ++l+ +++ep+e NPmlG+Rgir++l++pelf+ +l A+ r  ++g  ++e+m+P+v+ +e+
  gi|313127138|ref|YP_004037408.1| 544 RPVRVRSLDAPTDefRQLEGGEDEPREHNPMLGYRGIRRSLDKPELFKHELEAFRRLFEMGydNVEMMFPLVNDAED 620
                                       *************9999*****************************************96666************** PP

                                       HHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTT.SSEEEEXHHHHHHHHHTXXCCCHCHHHHS CS
                   PEP-utilizers_C 151 leeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklake.vdFfSiGtNDLtQytlavdRdneevakly 226
                                       + ++k++++ +  +         +k ++G+MiE+p+ al ++++a    dF+S+GtNDLtQytlavdR+ne+va  +
  gi|313127138|ref|YP_004037408.1| 621 VLRTKELMQGAGIDP--------EKREWGVMIETPASALSVEEMADAgLDFVSFGTNDLTQYTLAVDRNNENVAGRF 689
                                       *********993333........3569******************998***************************** PP

                                       XTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                   PEP-utilizers_C 227 dplepavlrlikevikaaeekglkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqve 293
                                       d+l+pavl+li+ +i++++e g+k++iCG++a++p++v++lv+ G+ ++S++ ++v  +++++++ve
  gi|313127138|ref|YP_004037408.1| 690 DELHPAVLKLIGDTIETCREVGVKTSICGQAASKPQMVQFLVNEGISSISANIDAVRDVQHEVKRVE 756
                                       ************************************************************9999875 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   2.7   3.9e-31   1.8e-27       2      73 .]     373     444 ..     372     444 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 3.9e-31
                                       --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       +++g+I+v+e+t p++++++++a+Givt++GGmtSHaAiv+relg+PaVvg+g+at+e++eg+ it+Dg++G
  gi|313127138|ref|YP_004037408.1| 373 VSDGDIIVTEMTMPDMVPAMKRASGIVTDEGGMTSHAAIVSRELGVPAVVGTGSATREIEEGQPITIDGDKG 444
                                       6789******************************************************************99 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.12   5.4e+02      21      47 ..      56      83 ..      24     126 .. 0.59
   2 !    6.3   0.1    0.0024        11      58     112 ..     235     289 ..     220     291 .. 0.83
   3 !    7.1   0.0    0.0013       5.7       1      16 [.     348     368 ..     348     398 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                                      ----G.GGHHHHH.HHHHHHHHHHHHHH CS
                   PEP-utilisers_N 21 eeeveaedveael.erleeAlekvreel 47
                                      ee  +a dv++e  + l+eA e+++e +
  gi|313127138|ref|YP_004037408.1| 56 EELFDAVDVDHEDsAALKEAHERAHELI 83
                                      3333344444332133444444444333 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHHHHHT-HHHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHTT-HH CS
                   PEP-utilisers_N  58 eeaaifeahlmlleDpelleeveerIregglnaeaAveevveefaaqfealddey 112
                                       e a + +   m+++D+e  e ve+ +++++ +a    e+ ++++++  e+++d+y
  gi|313127138|ref|YP_004037408.1| 235 ETATVADKKVMMVKDSETGETVERDVEDDKRSARVLDEDEIARLVELGERVEDHY 289
                                       3577999999********************9998877888888888877777766 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0013
                                       E-EEEE-SEEEEEEE.....- CS
                   PEP-utilisers_N   1 kGiaaspGiaiGkav.....e 16 
                                       +G++aspGia G+a      +
  gi|313127138|ref|YP_004037408.1| 348 RGLGASPGIAAGNARivtklD 368
                                       69************9754431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4867.68
//
Query:       gi|313127139|ref|YP_004037409.1|  [L=353]
Description: plp-dependent enzyme, glutamate decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-29  101.2   0.0    7.4e-29  100.6   0.0    1.3  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    2.5e-11   43.1   0.0    2.9e-11   42.9   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    7.8e-05   22.1   0.0    0.00012   21.4   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0014   17.3   0.0      0.002   16.8   0.0    1.2  1  SHMT             Serine hydroxymethyltransferase
  ------ inclusion threshold ------
       0.04   13.2   1.0      0.058   12.7   1.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   2.1e-32   7.4e-29      76     300 ..      44     241 ..      32     302 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 2.1e-32
                                       HHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEET CS
                     Pyridoxal_deC  76 altelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlytsd 152
                                        ++ele   ++ l+++ gl       +  g +++g++e++  a+ Aar++ + ++               +++++ +
  gi|313127139|ref|YP_004037409.1|  44 EVAELEADAVETLGKITGLA------DPHGYITSGGTEANVQAVRAARNRSRDRVS-------------DPNIVAPE 101
                                       5789***************9......35699*****************99988874.............3789**** PP

                                       TS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT- CS
                     Pyridoxal_deC 153 qahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydl 229
                                        ah s +kaa vl+v+lr++p+de ++  ++a ++a+   +e     + vv  +Gtt  g  d + el+ i +  + 
  gi|313127139|ref|YP_004037409.1| 102 SAHFSFNKAADVLDVELRLVPTDETHRADVDAVRAAVD--DET----VLVVGVAGTTEFGRVDPIPELAAIAHDAGA 172
                                       ************************99998988888874..444....469999************************ PP

                                       EEEEE-TTGGGGGGSGGGGG.GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TT CS
                     Pyridoxal_deC 230 wlHvDAAyaGsaficpeirh.llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehed 300
                                         HvDAA++G  f+ p+  h + +    +dS+t+ phK + + + ++ l+++d++ l +   +e  YLe ++
  gi|313127139|ref|YP_004037409.1| 173 FCHVDAAWGG--FLLPFTDHaWNFAHAPVDSLTIDPHKCGQACIPAGGLLFRDRNGLDSLA-VETPYLESTS 241
                                       **********..*********************************************8765.9*****9554 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   8.2e-15   2.9e-11      65     177 ..      68     179 ..      40     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 8.2e-15
                                       EEESSHHHHHHHHHHHCCCC...-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--T CS
                       Aminotran_5  65 iftsGtteainlvalslars...lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllne 138
                                       + tsG+tea+  ++++++++      + +iv  e+ h +      ++a+   ++++ +p de+ + d+d++++++++
  gi|313127139|ref|YP_004037409.1|  68 YITSGGTEANVQAVRAARNRsrdRVSDPNIVAPESAHFSFN----KAADVLDVELRLVPTDETHRADVDAVRAAVDD 140
                                       679*****777776666554354445567777777777766....6777788************************* PP

                                       TEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 139 ktklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                       +t lv   +  ++ G ++p++e++++a+++ga+ +vDaa
  gi|313127139|ref|YP_004037409.1| 141 ETVLVVGVAGTTEFGRVDPIPELAAIAHDAGAFCHVDAA 179
                                       **************************************9 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.5e-08   0.00012      13     238 ..      26     292 ..      15     339 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.5e-08
                                       HHHHHHHCS----CC.CT--HHHHHHHHHHHHHTT-SEEEE......ES-HHHHHHHHHHHH--TTEEEEEETT... CS
                   Beta_elim_lyase  13 amsdaqaaamlGdes.YgedktvnrLedavaelfgkeaalf......vpqGtaAnsillkillqrgeevivtep... 79 
                                       a  ++  a + Gd + Y+   +v +Le+ + e +gk  +l       +  Gt An  ++++  +r    + + +   
  gi|313127139|ref|YP_004037409.1|  26 AAAERFLATNPGDPAtYE---EVAELEADAVETLGKITGLAdphgyiTSGGTEANVQAVRAARNRSRDRVSDPNiva 99 
                                       444555666667753254...577777777777777777755566657789********999888777666665666 PP

                                       ...-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHH CS
                   Beta_elim_lyase  80 ...ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrev 153
                                          ah+ f  +  +  + +v+lr ++++e+   d+++++aa+++     e + ++ ++ T++   G+v   + + e+
  gi|313127139|ref|YP_004037409.1| 100 pesAHFSFNKA--A-DVLDVELRLVPTDETHRADVDAVRAAVDD-----ETVLVVGVAGTTEF--GRV---DPIPEL 163
                                       64477776644..4.34678899999***99*************.....7899999******9..887...556778 PP

                                       HHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHH.TTSSEEEEESSS..TT--SS-EEEEE-HH.............. CS
                   Beta_elim_lyase 154 aaiakkygiplhlDgARfanaakslgeivkemf.syvDsvtmslkK..dllanvGgvlafrddel............ 215
                                       aaia++ g   h+D+A +         ++ + + + vDs+t+   K   ++++ Gg+l+ ++++l            
  gi|313127139|ref|YP_004037409.1| 164 AAIAHDAGAFCHVDAA-WGGFLLPFTDHAWNFAhAPVDSLTIDPHKcgQACIPAGGLLFRDRNGLdslavetpyles 239
                                       999************9.444445555555555547799999998884345678888888888877777777666666 PP

                                       .................................HHHHHHHHHHHHT---SSTHH CS
                   Beta_elim_lyase 216 ...............................edylaerveqrkylggglrqagv 238
                                                                      ++y ++   ++   +g+lr  g+
  gi|313127139|ref|YP_004037409.1| 240 tsqatltgtrsgagvasaaaaldelwpdgyrHEY-DRVSDLASWFAGELRTRGF 292
                                       6666666666666666666666666666555555.5555555555555555555 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.7e-07     0.002     151     325 ..     124     296 ..     112     312 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.7e-07
                                       TTTSSB-HHHHHHHHHHH--SEE.EEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEE CS
                              SHMT 151 ketglidydelekkakefkPkli.vaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvv 226
                                        et+  d d+++    +    ++ vaGt+ + r+     l  ia++ ga+  vd a    l+    ++  f +a v 
  gi|313127139|ref|YP_004037409.1| 124 DETHRADVDAVRAAVDDETVLVVgVAGTTEFGRVDPIPELAAIAHDAGAFCHVDAAWGGFLLPFTDHAWNFAHAPVD 200
                                       4788999999998888777665569*******************************99999999**********886 PP

                                       EEE..SSSTT-S..-S-EEEEEC-.SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHH CS
                              SHMT 227 ttt..thktlrG..prgglillrk.gvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepef 298
                                       + t   hk  +   p ggl++  + g+ s+   +  v+  + +   +a + g++ G     +a+ a al e   + +
  gi|313127139|ref|YP_004037409.1| 201 SLTidPHKCGQAciPAGGLLFRDRnGLDSL---A--VETPYLESTSQATLTGTRSGA---GVASAAAALDELWPDGY 269
                                       555226998776336788888752133333...3..334445556667777776665...689999*********** PP

                                       HHHHHHHHHHHHHHHHHHHHTT-EEGG CS
                              SHMT 299 kvyqkqvlknakalaealkekgyklvs 325
                                       +    +v + a+++a +l  +g+++v 
  gi|313127139|ref|YP_004037409.1| 270 RHEYDRVSDLASWFAGELRTRGFDVVD 296
                                       ************************995 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   1.6e-05     0.058      38     146 ..      64     179 ..      24     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                       -SEEEEESSHHHHHHHHHHHTTTT.....TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG-- CS
                   DegT_DnrJ_EryC1  38 vkhaiavssGtaAlhlaLralgvg.....pgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaait 109
                                       + h   +s Gt+A+  a ra          +  ++ p    ++  +a+  l  +  +v  d +t+  d++a++aa+ 
  gi|313127139|ref|YP_004037409.1|  64 DPHGYITSGGTEANVQAVRAARNRsrdrvSDPNIVAPESAHFSFNKAADVLDVELRLVPTD-ETHRADVDAVRAAVD 139
                                       4567779999**********66662333345567888889999989988888888899888.9************** PP

                                       TTEEEEEEB...-GGGB---HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1 110 ertkaIlpV...hlyGqvadmdalkaiaakhglkvieDaA 146
                                        +t  ++ V     +G+v  +++l aia++ g     DaA
  gi|313127139|ref|YP_004037409.1| 140 DETVLVVGVagtTEFGRVDPIPELAAIAHDAGAFCHVDAA 179
                                       ***7777662225689999*************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2479.72
//
Query:       gi|313127140|ref|YP_004037410.1|  [L=205]
Description: hypothetical protein Hbor_24060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-09   36.1   5.5    3.8e-08   33.8   5.5    1.9  1  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   5.5   2.1e-12   3.8e-08      15     116 ..      88     196 ..      34     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.1e-12
                       SNARE_assoc  15 glllgtlvtslgallGaslayllgrylgrkalrrkllsekrvka...lerlv....erygflallllrllpivPrdl 84 
                                       +l l ++++ +g  +G+++a+++g+ + ++ + +k l + r++     er+     ++ g l l  +  +p++P++l
  gi|313127140|ref|YP_004037410.1|  88 HLGLIMVISGAGKAAGSVFAFHIGQEAKESGFIEKRLRQSRFDImewTERKTleiaQKWGYLGLAAALCVPGFPDTL 164
                                       567799**********************99999999999999855552222244448888888************** PP

                       SNARE_assoc  85 vnyvaGltrvsfkrFflatfiGsipwalvyay 116
                                       + y++++++  + +F++atf Gsi +++v+++
  gi|313127140|ref|YP_004037410.1| 165 SIYAFSILEKDYLKFAVATFTGSIGRLVVTTV 196
                                       ************************99988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1423.92
//
Query:       gi|313127141|ref|YP_004037411.1|  [L=133]
Description: alkylhydroperoxidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-14   51.8   0.5    9.9e-14   51.2   0.5    1.4  1  CMD             Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
       0.02   14.9   0.4      0.032   14.2   0.4    1.3  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
      0.021   15.3   0.0      0.029   14.8   0.0    1.3  1  Thioredoxin_2   Thioredoxin-like domain
      0.042   13.2   0.1       0.05   13.0   0.1    1.1  1  TatD_DNase      TatD related DNase
       0.11   12.5   1.3       0.18   11.8   1.3    1.4  1  GvpG            Gas vesicle protein G
       0.13   12.4   0.1        0.2   11.8   0.1    1.3  1  THUMP           THUMP domain


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.5   3.3e-17   9.9e-14      10      81 ..      36     106 ..      27     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 3.3e-17
                                       HHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHH CS
                               CMD  10 lreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAla 81 
                                       +r+ +l+ e +L+p+e+ L+al+++aa++c yCv++H ++A+   vte e+ae+   aa   ++  +++  +
  gi|313127141|ref|YP_004037411.1|  36 VRDLELE-ETELPPREKALVALGAAAAMNCPYCVHFHREEAKLEDVTETELAEATNLAATVRYFSTVLHGSE 106
                                       5566676.899**************************************************99999888765 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   1.1e-05     0.032      41      94 ..      73     128 ..      68     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                    CENP-F_leu_zip  41 ekvile..aEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqe 94 
                                       e+++le   Et+ ae+ +l + ++  ++ l+  e+dL+++++e  e+ + ++++q 
  gi|313127141|ref|YP_004037411.1|  73 EEAKLEdvTETELAEATNLAATVRYFSTVLHGSEADLDEFKRETSEIVEYIEEQQA 128
                                       455554337***************************************99999997 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   9.6e-06     0.029      14      41 ..      61      88 ..      49     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.6e-06
                     Thioredoxin_2 14 dpdCpyCkklkkelkelddvtvrvllfp 41
                                      + +CpyC  +++e  +l+dvt++ l+ +
  gi|313127141|ref|YP_004037411.1| 61 AMNCPYCVHFHREEAKLEDVTETELAEA 88
                                      569******************9966544 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.7e-05      0.05     117     168 ..      56     116 ..      37     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                       HHHHHHTTEEEEEEEES........-HHHHHHHHHHCG.GCCSEEEETT--S-HHHHHHHH CS
                        TatD_DNase 117 lrlAkelklplviHlrk........aeedlleilkeaa.eakakvvlHsfsgsaeeakkfl 168
                                       l +A+ +++p+ +H  +        +e++l e+++ aa  ++++ vlH  + + +e k+ +
  gi|313127141|ref|YP_004037411.1|  56 LGAAAAMNCPYCVHFHReeakledvTETELAEATNLAAtVRYFSTVLHGSEADLDEFKRET 116
                                       56899*********99989999999999********9966666******999998887766 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.3   6.1e-05      0.18      18      73 ..      76     131 ..      74     133 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
                              GvpG  18 qvqeraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLealerlea 73 
                                       ++++ +e++l + +nl +        L   e d +eF r+ +e+ + +e+ ++++a
  gi|313127141|ref|YP_004037411.1|  76 KLEDVTETELAEATNLAATVRYFSTVLHGSEADLDEFKRETSEIVEYIEEQQATAA 131
                                       688999*******************************************8876655 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   6.6e-05       0.2      26      80 ..      77     125 ..      62     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-05
                                       EECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHH CS
                             THUMP  26 velkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfe 80 
                                       +e         e +l ea+  a+++  ++ v+++ eadl+++++ ++eiv+   e
  gi|313127141|ref|YP_004037411.1|  77 LEDV------TETELAEATNLAATVRYFSTVLHGSEADLDEFKRETSEIVEYIEE 125
                                       4444......4578999999999**************************996554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1001.75
//
Query:       gi|313127142|ref|YP_004037412.1|  [L=39]
Description: hypothetical protein Hbor_24080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       151  (0.00842211); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.28s 00:00:00.59 Elapsed: 00:00:00.42
# Mc/sec: 278.46
//
Query:       gi|313127143|ref|YP_004037413.1|  [L=688]
Description: methionyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.2e-145  484.3   0.0     3e-145  483.9   0.0    1.2  1  tRNA-synt_1g  tRNA synthetases class I (M)
    1.9e-23   82.4   0.2    6.6e-23   80.6   0.1    1.9  2  tRNA_bind     Putative tRNA binding domain
    2.3e-15   55.9   1.5    8.9e-09   34.1   0.1    3.0  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    3.3e-10   39.8   0.0    1.3e-06   28.0   0.0    2.2  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    4.2e-08   33.3   0.0      1e-07   32.1   0.0    1.6  2  Anticodon_1   Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
      0.024   13.6   0.7       0.82    8.5   0.2    2.8  2  tRNA-synt_1f  tRNA synthetases class I (K)
      0.071   12.9   0.0       0.84    9.5   0.0    2.2  2  YL1_C         YL1 nuclear protein C-terminal domain
      0.087   11.8   0.0        1.1    8.1   0.0    2.5  3  tRNA-synt_1d  tRNA synthetases class I (R)
       0.16   12.1   0.0       0.39   10.9   0.0    1.6  1  Mpt_N         Methylene-tetrahydromethanopterin dehydrogenase
       0.25   11.6   0.2       0.51   10.6   0.2    1.5  1  DUF2423       Protein of unknown function (DUF2423)


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.9   0.0  1.6e-148    3e-145       2     390 ..      13     401 ..      12     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 483.9 bits;  conditional E-value: 1.6e-148
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelf 78 
                                       +vt++lpYang+lH+Ghl++++ +Di++R  +  g+e+ fv+g+D+hGtp++++Aekegvtpe ++ + he++ke+f
  gi|313127143|ref|YP_004037413.1|  13 VVTCGLPYANGDLHIGHLRTYVGGDIYSRALKRLGQETAFVSGSDMHGTPVAVNAEKEGVTPESFALRHHEKYKETF 89 
                                       79*************************************************************************** PP

                                       HHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE.-T CS
                      tRNA-synt_1g  79 kklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc.ee 154
                                        k++i+fd+yg+t++e+++el+qe++++l+++g++y+k+i ++y+p+++++lpdryvegtCP+c+ e+argd+c e 
  gi|313127143|ref|YP_004037413.1|  90 PKFEIEFDNYGHTHDETNTELTQELVRTLEDEGYVYKKQIPVAYDPDADQWLPDRYVEGTCPYCG-EHARGDECdEG 165
                                       *****************************************************************.99******999 PP

                                       TSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS- CS
                      tRNA-synt_1g 155 cgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdl 231
                                       cg++lep e+++p+sai+g+ +e+++++h ff++ +++++l+e+i++   e ++n++++ +ew++ +L+d++i+rd+
  gi|313127143|ref|YP_004037413.1| 166 CGRHLEPGEIEDPVSAITGNPAEYRDRNHRFFRVTELQEYLQEFIDRL--EGTSNAQNQPREWIEGELQDWCITRDM 240
                                       *********************************************554..59************************* PP

                                       SSS-EET..TECCEEE-HHHHHHHHHHHTTTTT-...TTSG.GGG.G--S......EEEEEGGGHHHHHTHHHHHHH CS
                      tRNA-synt_1g 232 dwGipvP..gaekkvlYVWldAligYisatkelakkkgeee.kwkeyWakdkevelvhfigkdiikFHtifwPaill 305
                                       dwGi++P   +++ vlYVW+dA+i+Yis+tk++++++g++  +w++ W  ++  ++vh+ig+dii++Ht+fwPa+l 
  gi|313127143|ref|YP_004037413.1| 241 DWGIDYPgeTEDDLVLYVWVDAPIEYISSTKQYTERAGADTfDWEKAW--KESGDIVHIIGRDIIQHHTVFWPAMLR 315
                                       *******8767899********************99999999******..5699*********************** PP

                                       HTT----S-EEEE--EEE--------------HHHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCC CS
                      tRNA-synt_1g 306 gaelklpkkvvaheyltvegkKlSkSrgvvvkakealer.ldadllRYylaaeapekkDldfswedfvervNseLad 381
                                       ++++  p++v+a++++t++gk +S+Sr+++v+a+e+l++ +d+ l+RYyla+++ +++D+dfswe+f +rvN+eL++
  gi|313127143|ref|YP_004037413.1| 316 ATDHVEPRAVMASGFITLNGKGFSTSRNRAVWADEYLDEgFDPALIRYYLATNGGFQQDVDFSWEKFRNRVNNELVG 392
                                       ***************************************************************************** PP

                                       HHHHHHHHH CS
                      tRNA-synt_1g 382 klgnlvnRv 390
                                       ++gn+++R+
  gi|313127143|ref|YP_004037413.1| 393 TVGNFLYRS 401
                                       *******97 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.8   3.1e+03      22      42 ..     466     485 ..     465     496 .. 0.78
   2 !   80.6   0.1   3.7e-26   6.6e-23       1      95 [.     596     685 ..     596     686 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.8
                                       EEEESSSSEEEEEESCTTTST CS
                         tRNA_bind  22 kvdvGeeeprqivsgaknvye 42 
                                       k+d+G e+ rq++   +++++
  gi|313127143|ref|YP_004037413.1| 466 KLDDGAEK-RQVIRDCVQIAK 485
                                       7899****.**9977766665 PP

  == domain 2  score: 80.6 bits;  conditional E-value: 3.7e-26
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       lrv+++++ae +++adkL +l+vd+G ee rqiv+g+k+    +el +kkv+vvanl+ ++l GveS+GM+l+a   
  gi|313127143|ref|YP_004037413.1| 596 LRVAEIIDAEGIEGADKLAKLTVDIGVEE-RQIVAGIKQLHDLDELPGKKVIVVANLEKAELFGVESNGMVLAAG-- 669
                                       79***************************.*********************************************.. PP

                                       ESSCEEEEEESST--TTC CS
                         tRNA_bind  78 dekevgilelpadveaGe 95 
                                         ++ ++l+  +d+e+G+
  gi|313127143|ref|YP_004037413.1| 670 --DQADLLTTYEDAEPGT 685
                                       ..6889999999999998 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1     5e-12   8.9e-09      26     173 ..      13     141 ..       3     148 .. 0.88
   2 !   18.0   0.1   3.9e-07    0.0007     355     432 ..     170     247 ..     163     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5e-12
                       tRNA-synt_1  26 ilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefre 102
                                       +++ g Py++G lHiGh  + +  di  r  +  G+e+ +v G D++G ++  + ek+ g + +             
  gi|313127143|ref|YP_004037413.1|  13 VVTCGLPYANGDLHIGHLRTYVGGDIYSRALKRLGQETAFVSGSDMHGTPVAVNAEKE-GVTPE------------- 75 
                                       567889*********************************************9999998.44443............. PP

                       tRNA-synt_1 103 kvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktal 173
                                          +++ + +e++++++ ++   + fd+   T d+  +e ++e    l d+g +y+ + +v +++++   l
  gi|313127143|ref|YP_004037413.1|  76 ---SFALRHHEKYKETFPKF--EIEFDNYGHTHDETNTELTQELVRTLEDEGYVYKKQIPVAYDPDADQWL 141
                                       ...57888899999999997..688999999*********************************9987666 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.9e-07
                       tRNA-synt_1 355 aekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswle.niqdWciSRqrwWGhr 430
                                        e+ e + p++  +++p +yr  +  f rv+el++ + + +++ + + + + ++  +w+e + qdWci R+  WG  
  gi|313127143|ref|YP_004037413.1| 170 LEPGEIEDPVSAITGNPAEYRDRNHRFFRVTELQEYLQEFIDRLEGTSNAQ-NQPREWIEgELQDWCITRDMDWGID 245
                                       56667777999999***************************9999888765.55677886489************87 PP

                       tRNA-synt_1 431 ip 432
                                        p
  gi|313127143|ref|YP_004037413.1| 246 YP 247
                                       66 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   7.3e-10   1.3e-06      14     125 ..      15     128 ..       7     140 .. 0.84
   2 !    9.5   0.0   0.00032      0.57     211     297 ..     296     383 ..     286     387 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 7.3e-10
                                       EEE.EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1e  14 vCG.ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdlea 89 
                                       +CG p +  + h+Gh R++v  Di  r l+ lg + +fv+        +  +a++e+ + +++a ++ e++k+ + +
  gi|313127143|ref|YP_004037413.1|  15 TCGlPYANGDLHIGHLRTYVGGDIYSRALKRLGQETAFVSGSDMHGTPVAVNAEKEGVTPESFALRHHEKYKETFPK 91 
                                       68834567799****************************9865555678899************************* PP

                                       TT----SB--BGGGGHHHH.HHHHHHHHHTTSEEE-T CS
                      tRNA-synt_1e  90 Lnvlkptleprvsekvdei.ielvekliekgyaYavs 125
                                        ++   ++     e+ +e+  elv +l ++gy Y+ +
  gi|313127143|ref|YP_004037413.1|  92 FEIEFDNYGHTHDETNTELtQELVRTLEDEGYVYKKQ 128
                                       ****988877666666665268************987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00032
                                       EEEEGGGTTTHHHHHHHHHHHHSSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTT.S-HHHHHHHHHSS.-T CS
                      tRNA-synt_1e 211 hsGGiDLafPhhenelaqseaafdkqlvkyflhnghlkiegekmsksLknfitikdvlkk.fdprqlRllllsa.hy 285
                                       h  G D++  hh         a+d+   +  + +g+++++g+  s s +  +   + l + fdp+ +R++l+++  +
  gi|313127143|ref|YP_004037413.1| 296 HIIGRDIIQ-HHTVFWPAMLRATDHVEPRAVMASGFITLNGKGFSTSRNRAVWADEYLDEgFDPALIRYYLATNgGF 371
                                       666666654.44444333334455555678899*************************765**********875279 PP

                                       TS-EEE-HHHHH CS
                      tRNA-synt_1e 286 rsqldfkeelle 297
                                       ++ +df+ e+++
  gi|313127143|ref|YP_004037413.1| 372 QQDVDFSWEKFR 383
                                       999**9987765 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         6   1.1e+04     107     134 ..      89     119 ..      78     129 .. 0.54
   2 !   32.1   0.0   5.6e-11     1e-07       6     108 ..     423     518 ..     419     565 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6
                       Anticodon_1 107 wpe.kaeelekele......eeevellkeivkair 134
                                       +p+ + e+     +      e+  el +e+v++++
  gi|313127143|ref|YP_004037413.1|  89 FPKfEIEFD----NyghthdETNTELTQELVRTLE 119
                                       332222222....1222345778888888887776 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 5.6e-11
                       Anticodon_1   6 selnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmP 82 
                                        +++++++e+++  ++y+ +++ +++  +   ++ + y++ ++p+  ++ a +kr++ + +  +++++  l++P++P
  gi|313127143|ref|YP_004037413.1| 423 ERIYDAIEEFEAGVNDYSVREVGNSVVRL--AQFGNEYIQGHEPWKLDDGA-EKRQVIRDCVQIAKAIAVLFEPVAP 496
                                       689*************************8..99*************88766.4445667788899************ PP

                       Anticodon_1  83 fitEelwqreeeelgkkesimlaewp 108
                                         +E+lw    + l+++ +++    +
  gi|313127143|ref|YP_004037413.1| 497 GKAEKLW----DDLNEDGDVHAVGVE 518
                                       *******....777777777665544 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2   0.00046      0.82      23      70 ..      10      58 ..       2     159 .. 0.80
   2 ?   -1.2   0.0      0.41   7.4e+02     225     309 ..     283     366 ..     260     382 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00046
                      tRNA-synt_1f 23 devvvesGis.pSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70
                                      +  vv  G+  + G +HiG lr  + +d+  ral+++g+e+ ++  sD 
  gi|313127143|ref|YP_004037413.1| 10 NPAVVTCGLPyANGDLHIGHLRTYVGGDIYSRALKRLGQETAFVSGSDM 58
                                      55677777752579***************************99998875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.41
                      tRNA-synt_1f 225 dwamrWaalgVdfEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwl.evae 300
                                       dw   W+  g  +  +G+D+++    +    ++ +  +  +P  v+   ++  +g+  s S+   +  ++ l e   
  gi|313127143|ref|YP_004037413.1| 283 DWEKAWKESGDIVHIIGRDIIQ--HHTVFWPAMLRATDHVEPRAVMASGFITLNGKGFSTSRNRAVWADEYLdEGFD 357
                                       5555555555555555555555..22223333335555555555555444444444566666666655555522345 PP

                      tRNA-synt_1f 301 pevlrflil 309
                                       p ++r++++
  gi|313127143|ref|YP_004037413.1| 358 PALIRYYLA 366
                                       556666555 PP

>> YL1_C  YL1 nuclear protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.24   4.4e+02      17      22 ..      17      22 ..      14      24 .. 0.81
   2 ?    9.5   0.0   0.00047      0.84       2      13 ..     180     191 ..     179     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.24
                             YL1_C 17 gLpYan 22
                                      gLpYan
  gi|313127143|ref|YP_004037413.1| 17 GLPYAN 22
                                      9****9 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00047
                             YL1_C   2 CdITGlpAkYrD 13 
                                       ++ITG pA YrD
  gi|313127143|ref|YP_004037413.1| 180 SAITGNPAEYRD 191
                                       78*********9 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00063       1.1      23      59 ..      13      49 ..       5      54 .. 0.84
   2 ?   -0.2   0.0      0.22   3.9e+02     261     303 ..     321     360 ..     286     364 .. 0.69
   3 ?   -2.4   0.0      0.97   1.7e+03     167     199 ..     422     456 ..     418     459 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00063
                                      EEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-E CS
                      tRNA-synt_1d 23 vvdfssPniakemhvGhLrstiiGdavsrlleflGyd 59
                                      vv    P    ++h+GhLr+ + Gd  sr l  lG +
  gi|313127143|ref|YP_004037413.1| 13 VVTCGLPYANGDLHIGHLRTYVGGDIYSRALKRLGQE 49
                                      555666777789*******************999965 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                                       TTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHH CS
                      tRNA-synt_1d 261 eskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeral 303
                                       e   +   +f  +   ++k+f+t +   v  ++ Lde+ + al
  gi|313127143|ref|YP_004037413.1| 321 EPRAVMASGFITL---NGKGFSTSRNRAVWADEYLDEGFDPAL 360
                                       4445555555444...89********************99775 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.97
                                       CCCHHHHHHHHHC..TT-EEECTTCEEEEECCCTS CS
                      tRNA-synt_1d 167 keslneivkelkk..kglvkesdGalvvfldefgk 199
                                       ke++ ++++e+++  +++ + + G  vv l +fg+
  gi|313127143|ref|YP_004037413.1| 422 KERIYDAIEEFEAgvNDYSVREVGNSVVRLAQFGN 456
                                       78888999999865578999999999999999987 PP

>> Mpt_N  Methylene-tetrahydromethanopterin dehydrogenase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022      0.39      23      57 ..      27      61 ..      18      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                                      TTTHHHHHHHHHSSS-GGGGGGEEEEEE-S-HHHH CS
                             Mpt_N 23 leevealvqdaiFsRgpkdlkrtaiFigGrdvala 57
                                        + + +v + i+sR+ k+l +   F+ G+d++ +
  gi|313127143|ref|YP_004037413.1| 27 IGHLRTYVGGDIYSRALKRLGQETAFVSGSDMHGT 61
                                      56778899***********************9865 PP

>> DUF2423  Protein of unknown function (DUF2423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00029      0.51      22      41 ..     535     554 ..     532     557 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                           DUF2423  22 FgpvedaRteRLsaKLkela 41 
                                       F++++d+R e L++KL++ +
  gi|313127143|ref|YP_004037413.1| 535 FEKIDDERVEELNEKLQARV 554
                                       9****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 4288.83
//
Query:       gi|313127144|ref|YP_004037414.1|  [L=586]
Description: pyruvate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.4e-108  361.0   3.8     8e-108  360.4   3.8    1.2  1  PK             Pyruvate kinase, barrel domain
    3.4e-31  107.9   0.1    7.4e-31  106.8   0.1    1.6  1  PK_C           Pyruvate kinase, alpha/beta domain
    7.7e-09   35.2   0.2    9.7e-08   31.6   0.0    3.0  3  PEP-utilizers  PEP-utilising enzyme, mobile domain
     0.0027   16.9   2.4     0.0054   15.9   1.1    2.0  2  HpcH_HpaI      HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.4   3.8  1.8e-111    8e-108       1     341 [.       1     331 [.       1     337 [. 0.96

  Alignments for each domain:
  == domain 1  score: 360.4 bits;  conditional E-value: 1.8e-111
                                       ---SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--B CS
                                PK   1 lrrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgll 77 
                                       +r++kivctlGPas+++ ++++l +aG+ v+rln shG+ e+++e+i+++r++ +++++ +a ++D++Gpe+rt  +
  gi|313127144|ref|YP_004037414.1|   1 MRNAKIVCTLGPASDDQATIRALSDAGMSVARLNASHGTPEHRAEVIDRIRTVDDATTEPLAAMVDLQGPEVRTAPI 77 
                                       5899***********************************************************************99 PP

                                       TTCSSSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-E CS
                                PK  78 kdgkkdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventg 154
                                       ++    i+l +g+++++   ++ +    +  + +  ++ ++  e G+til+dDG+++ +v+ v+  + ++  +  +g
  gi|313127144|ref|YP_004037414.1|  78 DE---PIHLDTGSEVRFIEGDEAT----PAEVGV--SHPIDAAEKGDTILLDDGRIEATVERVEGGA-VVAYIDSGG 144
                                       88...7**********76554443....445555..556999*********************9999.999****** PP

                                       EE-SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHH CS
                                PK 155 vlgskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegve 231
                                       +lgs+kgvnlpg+k+d++ ++e D+++l+++++++ d++aasfvr+a+Dv ++ + le+ g +i ++akie++ +ve
  gi|313127144|ref|YP_004037414.1| 145 ELGSRKGVNLPGVKLDIDLITEGDRRELEVAAEKNADFVAASFVRSAEDVYTISDALENLGADIPVVAKIERAGAVE 221
                                       ***************************************************************************** PP

                                       THHHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT CS
                                PK 232 nldeileasDgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDG 308
                                       nl+ei+eas g+mvarGDlG+e+p e+v+++qk++i++c ++g pvitat+ml+sm+++ rptrae+sDvanavlDG
  gi|313127144|ref|YP_004037414.1| 222 NLEEIIEASYGVMVARGDLGVEMPLEEVPIIQKRIIRRCHATGTPVITATEMLDSMVHSRRPTRAEASDVANAVLDG 298
                                       ***************************************************************************** PP

                                       -SEEEESHHHHTSS-HHHHHHHHHHHHHHHHHT CS
                                PK 309 tDavmLsgetakGkyPveavkamaevaleaeka 341
                                       tDavmLsgeta G+ Pv+ v++m ++ ++ e++
  gi|313127144|ref|YP_004037414.1| 299 TDAVMLSGETAIGDNPVRVVETMDSIVRQVESS 331
                                       **************************9999875 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.1   1.7e-34   7.4e-31       1     117 []     352     467 ..     352     467 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.7e-34
                                       HHHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSH CS
                              PK_C   1 eaiakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdel 77 
                                       ea+a++a++++++++a+aIv+++esG+tAr+ +k+rp+vp++a tpn+++ rqlal++Gv+p +++       +d++
  gi|313127144|ref|YP_004037414.1| 352 EALARSARYLSRDVNASAIVAASESGYTARKTAKFRPGVPVVATTPNDRVRRQLALSWGVIPKYADY---RAGIDDI 425
                                       799************************************************************9775...579**** PP

                                       HHHHHHHHHHTTSS-STSEEEEEE-SSSS..SS..--EEEEE CS
                              PK_C  78 lreavkvakeaglvkkgdevvvtaGtpkgesgt..tNtlrVv 117
                                       +++av++a++a ++++gd++vv++G+ ++ +gt  tN+l+V+
  gi|313127144|ref|YP_004037414.1| 426 MDDAVDAALDADVADSGDTLVVLSGMMTELEGTntTNMLKVH 467
                                       ***************************96544444*****97 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.41   1.8e+03      48      69 ..      99     120 ..      97     122 .. 0.84
   2 ?   -3.4   0.0       1.8   8.3e+03      46      57 ..     207     218 ..     205     227 .. 0.70
   3 !   31.6   0.0   2.2e-11   9.7e-08      20      73 .]     518     570 ..     498     570 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.41
                                       -EEE--SSHH.HH--TEEEEEE CS
                     PEP-utilizers  48 PaVvgvgeatielkegdlitvD 69 
                                       Pa vgv++    +++gd+i +D
  gi|313127144|ref|YP_004037414.1|  99 PAEVGVSHPIDAAEKGDTILLD 120
                                       7779999999888888***999 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                                       T--EEE--SSHH CS
                     PEP-utilizers  46 giPaVvgvgeat 57 
                                       +iP+V++++ a 
  gi|313127144|ref|YP_004037414.1| 207 DIPVVAKIERAG 218
                                       799999999885 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 2.2e-11
                                       TS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers  20 gldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                         +k+ Gi+ +r Gmt   A+vArel++P+V+g++  + +++ g+++t+ +++G
  gi|313127144|ref|YP_004037414.1| 518 DAKKLGGIIDARPGMTGYPALVARELDLPMVSGAPLPE-SIEPGTELTLHAERG 570
                                       4559********************************99.99999*****99998 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.1   1.2e-06    0.0054      78     158 ..     172     244 ..     164     295 .. 0.81
   2 ?   -1.0   0.0      0.18     8e+02      14      33 ..     291     310 ..     284     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                                       GG.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEEEE-HH CS
                         HpcH_HpaI  78 le.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgvflGae 152
                                       le ++++ a+ v   +v +ae++ ++  al++         + ++++a iE a +v+n+eeI+ a+ g++   ++  
  gi|313127144|ref|YP_004037414.1| 172 LEvAAEKNADFVAASFVRSAEDVYTISDALENLG-------ADIPVVAKIERAGAVENLEEIIeASYGVM---VARG 238
                                       5667889999999999***************999.......99********************6666655...4556 PP

                                       HHHHHT CS
                         HpcH_HpaI 153 Dlsadl 158
                                       Dl +++
  gi|313127144|ref|YP_004037414.1| 239 DLGVEM 244
                                       666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.18
                                       HHHHCTC--SEEEEESSTSS CS
                         HpcH_HpaI  14 aekaaiagaDsvliDlEdav 33 
                                       + +a + g D+v++ +E a 
  gi|313127144|ref|YP_004037414.1| 291 VANAVLDGTDAVMLSGETAI 310
                                       66778889999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 3586.57
//
Query:       gi|313127145|ref|YP_004037415.1|  [L=76]
Description: hypothetical protein Hbor_24120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 553.09
//
Query:       gi|313127146|ref|YP_004037416.1|  [L=606]
Description: hypothetical protein Hbor_24130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        4.1    7.5  16.4        0.4   10.7   6.5    2.3  2  PGF-CTERM        PGF-CTERM motif


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   2.3     0.012   2.1e+02       9      20 ..       6      17 ..       6      18 .. 0.89
   2 ?   10.7   6.5   2.2e-05       0.4       7      22 ..     583     599 ..     582     599 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.012
                         PGF-CTERM  9 AlaGLLaaalLa 20
                                      +l++L+a++lL+
  gi|313127146|ref|YP_004037416.1|  6 TLTALAAVVLLV 17
                                      589*******98 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.2e-05
                         PGF-CTERM   7 vlAlaGLLaaa.lLaRR 22 
                                       ++A+++LLaaa lL+RR
  gi|313127146|ref|YP_004037416.1| 583 AVAVVALLAAAgLLVRR 599
                                       79*********777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3964.76
//
Query:       gi|313127147|ref|YP_004037417.1|  [L=394]
Description: telomeric repeat-binding factor 2./restriction endonuclease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-08   32.4   0.0    1.2e-07   31.8   0.0    1.3  1  Mrr_cat   Restriction endonuclease
    1.6e-05   25.2   0.0    3.1e-05   24.3   0.0    1.4  1  DUF4352   Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   1.3e-11   1.2e-07       3     112 ..       6     111 ..       4     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.3e-11
                                       TT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS..S CS
                           Mrr_cat   3 kmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrgad 79 
                                       +++p  F +++++l+ + G+   + ++++ D+    i+ k++ g++ +l      ++ v++k+ ++++g   k+g d
  gi|313127147|ref|YP_004037417.1|   6 ELEPDAFVSFLEDLWNERGWD--TSVKQRPDETFF-IIGKRGDGKRGVLYVFPTVESHVKEKHMKQFVGFCRKKGID 79 
                                       6899****************9..466678999995.55556668776666677778********************* PP

                                       EEEEEESS-B-HHHHHHHHTT--EEEE-HHHHH CS
                           Mrr_cat  80 kgifvttsdftkaAreeaeelnkieLldgdeLa 112
                                        g++ t + ++++ r+ ae+ ++i+Lld+++La
  gi|313127147|ref|YP_004037417.1|  80 VGVVATQGAYADPSRQIAES-KGIHLLDRETLA 111
                                       ********************.**********98 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.4e-09   3.1e-05      20     114 ..     279     370 ..     264     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.4e-09
                                       EEEEEETTS-CEETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB--EEEE-TT-EEE CS
                           DUF4352  20 eytksvgkneylqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskaddlflgtlnpGkkvt 96 
                                       ++t++v  ++y++p+  ++f++v+++v+N+ ++++++ +s+  L+   g++y ++      +  + +g  +p+   +
  gi|313127147|ref|YP_004037417.1| 279 TKTLTVNGTTYTAPE-NETFVLVRMNVTNHNESPMSFGQSSLALE-VAGERYGYQPLNGTTGF-AEGGLFAPNDPRE 352
                                       445555646666665.59**************************7.66677766665544442.567888******* PP

                                       EEEEEEESTT-CGEEEEE CS
                           DUF4352  97 GklvFdvpkgkkkleLey 114
                                        +l+F vpk+++  +L++
  gi|313127147|ref|YP_004037417.1| 353 VWLAFTVPKDATSGTLVL 370
                                       ***********9988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.38s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 2110.16
//
Query:       gi|313127148|ref|YP_004037418.1|  [L=211]
Description: membrane protease regulatory membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-06   27.4   0.0    6.6e-06   26.4   0.0    1.5  1  NfeD             NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
       0.12   12.5   0.7        0.2   11.8   0.7    1.3  1  YtpI             YtpI-like protein
       0.21   11.6   1.1       0.33   11.0   0.1    1.8  2  PUA              PUA domain


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.1e-09   6.6e-06       6      75 ..      70     154 ..      65     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.1e-09
                                       XXXXXXXXXXXS---SSS--S.........S---.GGTTSEEEEEE-B..S-EEEEET.....TEEEEEE-.SS.B- CS
                              NfeD   6 svlllvllrplllkklkkkek........ktnae.aliGkegvvledi..gtGrvkvd.....GeeWsarsege.ie 65 
                                       +vl+lv++   l  ++ +  +        kt  + +l G++++v+e++  ++G+vk+d     + ++ ars ++ i+
  gi|313127148|ref|YP_004037418.1|  70 GVLVLVFGALALYGYR-EF-DlyggkgsgKTSDSaSLKGRTARVTERVtpTQGEVKLDegggfNPYYAARSVSGeIP 144
                                       4444444442222222.11.1123334444554457************8647*******998889******7555** PP

                                       TT-EEEEEEE CS
                              NfeD  66 kgerVrVvev 75 
                                       +g++V Vv+ 
  gi|313127148|ref|YP_004037418.1| 145 EGSEVMVVDP 154
                                       *******985 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   3.4e-05       0.2      35      83 ..      42      90 ..      31      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                              YtpI 35 sialGlflilfginqllllestvalvvgavflvlGlanlfaGiraykhy 83
                                       i+lG+ l++ g+  lll  s  + +v  v++++  a +++G+r++  y
  gi|313127148|ref|YP_004037418.1| 42 LIVLGVALLAAGLIGLLLGPSLAGPIVLGVLVLVFGALALYGYREFDLY 90
                                      699***********999999999988887777777778899***99877 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.91   5.4e+03      11      24 ..      34      47 ..      31      54 .. 0.65
   2 ?   11.0   0.1   5.5e-05      0.33      26      53 ..     138     182 ..     135     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.91
                                      HHHHTT-EEEGGGE CS
                               PUA 11 kallsgasLlapGv 24
                                      +al+ ga+L + Gv
  gi|313127148|ref|YP_004037418.1| 34 EALAPGAHLIVLGV 47
                                      56666777766665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.5e-05
                                       EEETT--TTSEEEEEETTS.................CEEEEEEES CS
                               PUA  26 evegdfeegdvVaivdedg.................elvavGlan 53 
                                       +v g++ eg +V +vd++g                 +++a+G++n
  gi|313127148|ref|YP_004037418.1| 138 SVSGEIPEGSEVMVVDPGGgnvitvesfegtlddidRELARGRSN 182
                                       799**************8679999999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1474.92
//
Query:       gi|313127149|ref|YP_004037419.1|  [L=405]
Description: spfh domain, band 7 family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-38  130.1   4.2    8.6e-38  130.1   4.2    2.4  3  Band_7    SPFH domain / Band 7 family
    0.00077   19.2   0.6     0.0022   17.8   0.2    1.9  2  Band_7_1  SPFH domain-Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   4.2   9.6e-42   8.6e-38      12     178 .]      46     206 ..      36     206 .. 0.97
   2 ?   -3.9   0.7       1.3   1.2e+04     159     178 .]     209     228 ..     208     228 .. 0.84
   3 ?    0.5   0.3     0.057   5.1e+02      98     136 ..     310     348 ..     253     386 .. 0.71

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 9.6e-42
                            Band_7  12 vrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaaveresan 88 
                                       + fG++++ lepG+ fi Pf+++++ +++r+qtldv++ ++++t+D+ pvt d++v+++v  da+k++++v    ++
  gi|313127149|ref|YP_004037419.1|  46 TVFGEYRKLLEPGINFIPPFVSRTYAFDMRTQTLDVPR-QEAITRDNSPVTADAVVYIKV-MDARKAFLEV----DD 116
                                       44************************************.*********************.**********....** PP

                            Band_7  89 ldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaaea 165
                                       +++ ++++++ +lr+v+++m+l++ l++r+e+++++++el e  +++Gv v++v +++++p+++v+qa+++   ae+
  gi|313127149|ref|YP_004037419.1| 117 YKKAVSNLAQTTLRAVLGDMELDDTLNKRQEINARIRKELDEPTDEWGVRVESVEVREVNPSQDVQQAMEQQTSAER 193
                                       ***************************************************************************** PP

                            Band_7 166 eaqaeiaraeaea 178
                                       +++a i +a++e+
  gi|313127149|ref|YP_004037419.1| 194 RRRAMILEAQGER 206
                                       **********985 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.3
                            Band_7 159 akqaaeaeaqaeiaraeaea 178
                                       a+ +ae e+q  i ra++e+
  gi|313127149|ref|YP_004037419.1| 209 AVEQAEGEKQSNIIRAQGEK 228
                                       57889999999999999985 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.057
                            Band_7  98 esalrevisemtleellsnreelaeelknelneqlrkyG 136
                                       ++++re+i+  ++ee+l+  +e ae   +el ++++ + 
  gi|313127149|ref|YP_004037419.1| 310 DEETRELIGLDDIEEILGQIDEAAEMNVEELEQEAQAIK 348
                                       566677776666666666655555555555555555544 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   2.4e-07    0.0022     130     209 ..     114     191 ..      92     193 .. 0.80
   2 ?   -1.5   0.0      0.19   1.7e+03     131     191 ..     238     299 ..     233     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-07
                          Band_7_1 130 teeiseqlkslivtrlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkr 206
                                        ++ ++ + +l +t+l  vl++ +  + d   k +e+ +++++ l+e  +e G+ +e++e+++++  ++v++a++++
  gi|313127149|ref|YP_004037419.1| 114 VDDYKKAVSNLAQTTLRAVLGDME--LDDTLNKRQEINARIRKELDEPTDEWGVRVESVEVREVNPSQDVQQAMEQQ 188
                                       555566666666666777776544..557888999*****************************************9 PP

                          Band_7_1 207 asm 209
                                       +s+
  gi|313127149|ref|YP_004037419.1| 189 TSA 191
                                       986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.19
                          Band_7_1 131 eeiseqlkslivtrlsd.vlaeskipvldlaakseelaeklkealkeelaeyGlelekleie 191
                                       + is+ l+ + ++++++ ++ e+++  l+  ++ e+ +  l + l++ + +yG +l++  ++
  gi|313127149|ref|YP_004037419.1| 238 DAISTVLRAKSAESMGErAIIEKGMETLEHIGQGESTTFVLPQELTSLVGRYGRQLTDSDVQ 299
                                       66777888887777754278899999999999999999999999999999999988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1583  (0.0882927); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2710.67
//
Query:       gi|313127150|ref|YP_004037420.1|  [L=206]
Description: hypothetical protein Hbor_24170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-10   40.1   0.4    8.5e-05   22.5   0.3    2.3  2  HTH_20          Helix-turn-helix domain
    1.1e-09   38.0   0.6    4.2e-06   26.5   0.3    2.5  2  MarR_2          MarR family
    1.5e-08   34.3   0.0      4e-05   23.4   0.0    2.2  2  HTH_5           Bacterial regulatory protein, arsR family
    1.8e-07   30.6   0.0    0.00014   21.3   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
    1.5e-06   27.9   0.9    0.00031   20.5   0.2    3.1  3  HTH_IclR        IclR helix-turn-helix domain
    6.8e-06   25.9   0.0    1.4e-05   25.0   0.0    1.5  1  HTH_11          HTH domain
    1.2e-05   25.4   0.0       0.17   12.1   0.0    2.2  2  HTH_34          Winged helix DNA-binding domain
      2e-05   24.4   0.0    0.00066   19.5   0.0    2.2  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00018   21.4   0.0      0.001   19.0   0.0    2.0  2  MarR            MarR family
    0.00025   20.8   0.1       0.38   10.4   0.0    2.3  2  RP-C            Replication protein C N-terminal domain
    0.00063   19.7   0.0     0.0021   18.0   0.0    1.9  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0008   19.2   0.2     0.0018   18.0   0.2    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
     0.0014   18.8   0.1     0.0056   16.8   0.0    2.0  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0023   18.4   0.1       0.15   12.5   0.0    2.6  2  HTH_27          Winged helix DNA-binding domain
     0.0029   17.3   0.0     0.0068   16.2   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.005   16.8   0.1       0.02   14.9   0.0    1.9  2  HTH_29          Winged helix-turn helix
     0.0077   15.9   0.1      0.075   12.7   0.0    2.2  2  GntR            Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.049   13.4   0.2       0.36   10.7   0.0    2.4  3  HTH_10          HTH DNA binding domain
       0.06   13.4   0.0       0.12   12.4   0.0    1.5  1  HTH_3           Helix-turn-helix
      0.096   12.7   0.0       0.18   11.8   0.0    1.4  1  HTH_6           Helix-turn-helix domain, rpiR family
       0.14   12.3   0.0       0.27   11.4   0.0    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.15   12.3   0.0       0.63   10.3   0.0    2.1  2  HTH_17          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.8e-05     0.015      11      60 ..      44      93 ..      41      94 .. 0.83
   2 !   22.5   0.3     1e-07   8.5e-05      11      56 ..     119     164 ..     112     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      +R +i  ++a+  g+ +s + + l+l   +  yHLr L+e ++ve +r g
  gi|313127150|ref|YP_004037420.1| 44 TRDAIVGYIASTPGAHFSKVRDDLQLGTGETQYHLRRLVEDDIVEYRRDG 93
                                      5666777777777788888888999999999****************987 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1e-07
                                       HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56 
                                       + r++l aL r+  +t sela++ld+s++t+s+  r+L e+gL+ +
  gi|313127150|ref|YP_004037420.1| 119 TARGMLVALLRDPDATGSELAAALDVSRATVSNYARKLDEVGLLSR 164
                                       66778888889999*****************************987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0014       1.1      13      58 ..      51      94 ..      47      97 .. 0.82
   2 !   26.5   0.3   5.2e-09   4.2e-06       7      54 ..     120     165 ..     110     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                      +++  pg     + + + l+l  + ++++l+rLv+   ve+r++ +
  gi|313127150|ref|YP_004037420.1| 51 YIASTPG--AHFSKVRDDLQLGTGETQYHLRRLVEDDIVEYRRDGD 94
                                      6677777..7788888899999999*****************9865 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 5.2e-09
                                       HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                        +  L aL r p+   t +ela++l++s+++vs+  ++L + GL+ r 
  gi|313127150|ref|YP_004037420.1| 120 ARGMLVALLRDPD--ATGSELAAALDVSRATVSNYARKLDEVGLLSRD 165
                                       5667888888888..9****************************9875 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0013       1.1      23      47 .]      65      89 ..      42      89 .. 0.80
   2 !   23.4   0.0   4.9e-08     4e-05       5      46 ..     121     163 ..     117     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                                      HHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 23 eelglsqstvShHLkkLreaGLVek 47
                                      ++l+l  + + +HL++L e ++Ve+
  gi|313127150|ref|YP_004037420.1| 65 DDLQLGTGETQYHLRRLVEDDIVEY 89
                                      67888888899************96 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 4.9e-08
                                       HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   5 lkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       + +L +L + + ++ +ela++l++s++tvS + +kL e GL++
  gi|313127150|ref|YP_004037420.1| 121 RGMLVALLRDPdATGSELAAALDVSRATVSNYARKLDEVGLLS 163
                                       556777777776*****************************86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0043       3.5      19      48 .]      59      88 ..      43      88 .. 0.71
   2 !   21.3   0.0   1.7e-07   0.00014       6      45 ..     121     160 ..     116     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0043
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                        + + + l l  + + ++l+rL+e+ +++
  gi|313127150|ref|YP_004037420.1| 59 HFSKVRDDLQLGTGETQYHLRRLVEDDIVE 88
                                      55555555566667789***********96 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.7e-07
                            HTH_24   6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45 
                                       r  L +L ++p+ + +eLA +l++S++tv+ + ++L e G
  gi|313127150|ref|YP_004037420.1| 121 RGMLVALLRDPDATGSELAAALDVSRATVSNYARKLDEVG 160
                                       667889*****************************97765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.21   1.7e+02       8      50 ..      48      89 ..      47      91 .. 0.87
   2 ?    3.1   0.1     0.099        81      30      43 ..     115     128 ..     111     130 .. 0.87
   3 !   20.5   0.2   3.7e-07   0.00031      14      52 .]     129     166 ..     124     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.21
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      i  ++a++p++  +s + + + l    +  +L+ Lve  +ve+
  gi|313127150|ref|YP_004037420.1| 48 IVGYIASTPGA-HFSKVRDDLQLGTGETQYHLRRLVEDDIVEY 89
                                      66788999997.899999999999999**********999997 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.099
                                       S-HHHHHHHHHHHH CS
                          HTH_IclR  30 lpkStvhRlLqtLv 43 
                                       l +St++++L  L 
  gi|313127150|ref|YP_004037420.1| 115 LRRSTARGMLVALL 128
                                       569*******9996 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 3.7e-07
                                       TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR  14 eapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52 
                                       + p + t selA++++++++tv+++ + L e G++ +d+
  gi|313127150|ref|YP_004037420.1| 129 RDPDA-TGSELAAALDVSRATVSNYARKLDEVGLLSRDD 166
                                       45554.889***************************995 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.7e-08   1.4e-05      12      43 ..     129     160 ..     122     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
                            HTH_11  12 argpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                        +++ +g+eLA  L+vSr+tv ++ ++L e g
  gi|313127150|ref|YP_004037420.1| 129 RDPDATGSELAAALDVSRATVSNYARKLDEVG 160
                                       34459***********************9988 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0    0.0002      0.17       4      49 ..      47      92 ..      44     106 .. 0.89
   2 !   11.2   0.0   0.00039      0.32       6      61 ..     124     179 ..     122     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                            HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                      a++ y as+  a f+++++ l++ +g+   hl+ L + + +e++ +
  gi|313127150|ref|YP_004037420.1| 47 AIVGYIASTPGAHFSKVRDDLQLGTGETQYHLRRLVEDDIVEYRRD 92
                                      8999*******************************99988888765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00039
                            HTH_34   6 lsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllri 61 
                                       l  L+ +  a+ +el +al ++ +  s  ++kL + g +++d ++   +p t++++
  gi|313127150|ref|YP_004037420.1| 124 LVALLRDPDATGSELAAALDVSRATVSNYARKLDEVGLLSRDDGYAIAQPETVITL 179
                                       677889999*************************************9999999875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.15   1.2e+02      26      61 ..      61      97 ..      51     103 .. 0.74
   2 !   19.5   0.0   8.1e-07   0.00066      14      56 ..     124     166 ..     122     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.15
                                      CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTE CS
                              TrmB 26 deiaeelgvprskvYevLrsLedkGlVerekgr.pkl 61
                                      +++  +l +     +  Lr+L++ ++Ve ++   +k+
  gi|313127150|ref|YP_004037420.1| 61 SKVRDDLQLGTGETQYHLRRLVEDDIVEYRRDGdYKR 97
                                      56667777777778889**********9888543554 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 8.1e-07
                                       CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                        +aLl+   at +e+a +l+v+r++v ++ r+L + Gl  r +
  gi|313127150|ref|YP_004037420.1| 124 LVALLRDPDATGSELAAALDVSRATVSNYARKLDEVGLLSRDD 166
                                       589***********************************98876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.4   1.1e+03      36      52 ..      76      92 ..      52      97 .. 0.77
   2 !   19.0   0.0   1.2e-06     0.001      12      49 ..     127     164 ..     123     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                                      HHHHHHHHTTSEEEEEE CS
                              MarR 36 rvldrLekkGlieRsks 52
                                        l+rL++++ +e +++
  gi|313127150|ref|YP_004037420.1| 76 YHLRRLVEDDIVEYRRD 92
                                      67999999999987776 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.2e-06
                                       HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49 
                                       l + ++++ seLa +l vs++tv++ +++L + Gl++R
  gi|313127150|ref|YP_004037420.1| 127 LLRDPDATGSELAAALDVSRATVSNYARKLDEVGLLSR 164
                                       5667888999**************************99 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00047      0.38      81     119 ..      67     105 ..      61     114 .. 0.83
   2 !    8.2   0.0    0.0021       1.7      76     105 ..     137     166 ..     133     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                              RP-C  81 lglsestlrrhlaaLveaGliirrDspngkRyarrdreG 119
                                       l+l +   ++hl++Lve  ++ +r   ++kR+   +r  
  gi|313127150|ref|YP_004037420.1|  67 LQLGTGETQYHLRRLVEDDIVEYRRDGDYKRFFSAGRFT 105
                                       567788899***********************8777655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0021
                              RP-C  76 qLsralglsestlrrhlaaLveaGliirrD 105
                                       +L+ al++s++t+++  ++L e+Gl+ r D
  gi|313127150|ref|YP_004037420.1| 137 ELAAALDVSRATVSNYARKLDEVGLLSRDD 166
                                       7999**********************9988 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.3   3.5e+03      42      54 ..      78      91 ..      75      95 .. 0.80
   2 !   18.0   0.0   2.6e-06    0.0021      21      61 ..     132     172 ..     111     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.3
                                      HHHHHHTTSEE.ET CS
                         HTH_Crp_2 42 lseLkreglis.rg 54
                                      l++L ++ +++ r+
  gi|313127150|ref|YP_004037420.1| 78 LRRLVEDDIVEyRR 91
                                      89999999999543 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.6e-06
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET.EEEEES- CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglisrg.rririld 61 
                                       + t  elA+ l ++r tvs   ++L + gl+sr  +   i +
  gi|313127150|ref|YP_004037420.1| 132 DATGSELAAALDVSRATVSNYARKLDEVGLLSRDdG-YAIAQ 172
                                       67889***************************7523.66655 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   2.2e-06    0.0018       7      36 ..     122     151 ..     119     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                     HTH_AsnC-type   7 kILeaLqedaRisyaeLAervGlSestvlr 36 
                                         L aL +d+ ++ +eLA+++ +S++tv +
  gi|313127150|ref|YP_004037420.1| 122 GMLVALLRDPDATGSELAAALDVSRATVSN 151
                                       5799************************76 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       3.8   3.1e+03      43      56 ..      78      91 ..      75      93 .. 0.85
   2 !   16.8   0.0   6.9e-06    0.0056      25      53 ..     135     163 ..     132     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.8
                                      HHHHHHTTSEEEET CS
                    Fe_dep_repress 43 lkkLekdGyveyek 56
                                      l++L +d  vey  
  gi|313127150|ref|YP_004037420.1| 78 LRRLVEDDIVEYRR 91
                                      899*******9986 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6.9e-06
                                       HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  25 tkdlaerLnvspssVsemlkkLekdGyve 53 
                                        ++la +L+vs ++Vs   +kL++ G++ 
  gi|313127150|ref|YP_004037420.1| 135 GSELAAALDVSRATVSNYARKLDEVGLLS 163
                                       589***********************985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.17   1.4e+02      22      58 ..      61      94 ..      51     101 .. 0.73
   2 !   12.5   0.0   0.00019      0.15      16      56 ..     129     165 ..     121     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.17
                            HTH_27 22 adlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                      + +++ l+++   + y l++L+e + ve     +d+ 
  gi|313127150|ref|YP_004037420.1| 61 SKVRDDLQLGTGETQYHLRRLVEDDIVEYR---RDGD 94
                                      56666677777778899**********444...4444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00019
                            HTH_27  16 rrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdead 56 
                                       r++++  ++l+ +l+v+ +++s+  +kL e GL+      +d
  gi|313127150|ref|YP_004037420.1| 129 RDPDATgSELAAALDVSRATVSNYARKLDEVGLLS-----RD 165
                                       6788888***************999*********2.....23 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.3e-06    0.0068      10      42 ..     124     157 ..     117     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.3e-06
                            HTH_23  10 illllae.GlsvreIAreLgvsrrTvyrwlkryr 42 
                                        + ll++  ++ +e A++L+vsr Tv+++ ++  
  gi|313127150|ref|YP_004037420.1| 124 LVALLRDpDATGSELAAALDVSRATVSNYARKLD 157
                                       56677779999*****************988865 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.6   2.9e+03      32      42 ..      13      23 ..      11      28 .. 0.80
   2 !   14.9   0.0   2.4e-05      0.02       3      41 ..     123     161 ..     121     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.6
                            HTH_29 32 wlkrfeegGla 42
                                      +l+rf + G+a
  gi|313127150|ref|YP_004037420.1| 13 TLRRFAALGAA 23
                                      78999999976 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.4e-05
                            HTH_29   3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41 
                                       + ++ll++   t s++A++l++sr tv ++ +  +e Gl
  gi|313127150|ref|YP_004037420.1| 123 MLVALLRDPDATGSELAAALDVSRATVSNYARKLDEVGL 161
                                       5566666666699**********************9995 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.63   5.1e+02      45      58 ..      78      91 ..      77      93 .. 0.87
   2 !   12.7   0.0   9.2e-05     0.075      28      60 ..     136     168 ..     134     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.63
                                      HHHHHHTTSEEEET CS
                              GntR 45 LrrLeaeglverrq 58
                                      LrrL+++++ve r+
  gi|313127150|ref|YP_004037420.1| 78 LRRLVEDDIVEYRR 91
                                      89********9875 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.2e-05
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR  28 reLaaefgVsrttvReALrrLeaeglverrqgr 60 
                                       +eLaa+++Vsr tv    r+L + gl+ r +g 
  gi|313127150|ref|YP_004037420.1| 136 SELAAALDVSRATVSNYARKLDEVGLLSRDDGY 168
                                       69**************************99885 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.4     2e+03      40      46 ..      74      80 ..      65      84 .. 0.82
   2 ?   -2.7   0.0       6.6   5.4e+03      38      48 ..     109     119 ..     108     121 .. 0.75
   3 ?   10.7   0.0   0.00044      0.36      23      46 ..     132     155 ..     130     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
                            HTH_10 40 lsehLrk 46
                                      +++hLr+
  gi|313127150|ref|YP_004037420.1| 74 TQYHLRR 80
                                      799***9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.6
                            HTH_10  38 stlsehLrkae 48 
                                       +t++ +Lr+++
  gi|313127150|ref|YP_004037420.1| 109 QTALGYLRRST 119
                                       68888999875 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00044
                            HTH_10  23 rvtlkeLAkelGIskstlsehLrk 46 
                                       ++t +eLA +l++s++t+s++ rk
  gi|313127150|ref|YP_004037420.1| 132 DATGSELAAALDVSRATVSNYARK 155
                                       5899***************99887 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015      0.12      13      31 ..     136     154 ..     134     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                       HHHHHHHTSSHHHHHHHHT CS
                             HTH_3  13 eeLAeklGvsrstisriEn 31 
                                        eLA++l+vsr+t+s++ +
  gi|313127150|ref|YP_004037420.1| 136 SELAAALDVSRATVSNYAR 154
                                       59**************976 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00023      0.18      38      60 ..     136     158 ..     127     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                                       HHHHHHTT--HHHHHHHH---S- CS
                             HTH_6  38 kalAkaaavSeativrfakkLGf 60 
                                       ++lA+a+ vS+at+   a+kL+ 
  gi|313127150|ref|YP_004037420.1| 136 SELAAALDVSRATVSNYARKLDE 158
                                       79*******************86 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00033      0.27      28      62 ..     138     172 ..     130     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                           DUF2250  28 iakeleipleevrellkkLeelGLlervegktikr 62 
                                       +a  l++++  v+++ +kL e+GLl r +g +i +
  gi|313127150|ref|YP_004037420.1| 138 LAAALDVSRATVSNYARKLDEVGLLSRDDGYAIAQ 172
                                       6788999*********************9988865 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.7   7.9e+03      15      22 ..      11      18 ..      10      30 .. 0.75
   2 ?   10.3   0.0   0.00077      0.63       5      24 ..     136     155 ..     134     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.7
                            HTH_17 15 rstvyrli 22
                                      r+t++r++
  gi|313127150|ref|YP_004037420.1| 11 RATLRRFA 18
                                      78999887 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00077
                            HTH_17   5 eEaAelLgvsrstvyrlirr 24 
                                       +E+A+ L+vsr+tv +++r+
  gi|313127150|ref|YP_004037420.1| 136 SELAAALDVSRATVSNYARK 155
                                       699**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1305.35
//
Query:       gi|313127151|ref|YP_004037421.1|  [L=82]
Description: hypothetical protein Hbor_24180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.009   15.8   0.1      0.012   15.3   0.1    1.2  1  LexA_DNA_bind  LexA DNA binding domain
  ------ inclusion threshold ------
      0.044   14.4   0.0      0.054   14.2   0.0    1.1  1  RPA_C          Replication protein A C terminal
      0.045   13.3   0.2         10    5.7   0.0    2.6  3  HTH_24         Winged helix-turn-helix DNA-binding
      0.054   13.4   0.0      0.068   13.0   0.0    1.1  1  DUF3263        Protein of unknown function (DUF3263)
      0.064   12.8   0.1       0.56    9.8   0.1    2.0  1  GerE           Bacterial regulatory proteins, luxR family
       0.17   11.8   0.1        1.1    9.2   0.1    2.2  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   4.1e-06     0.012       2      42 ..      12      50 ..      11      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.1e-06
                                      X---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHH CS
                     LexA_DNA_bind  2 kkLTerQrevldlikasieetgypPsireiaralglkSpsa 42
                                      ++L+e+Qr++l++++ +  e+ y  s r ia++lgl+ ++ 
  gi|313127151|ref|YP_004037421.1| 12 TDLSEKQRNILQYLRTNAPEQTYFKS-RLIAQELGLS-AKE 50
                                      68*********************988.68*******7.555 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.8e-05     0.054      38      86 ..       6      53 ..       1      60 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                                      XXXXXXX.XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHH CS
                             RPA_C 38 nqaklankgltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkq 86
                                      ++a  ++  l++ ++ +l+++++++ ++   + + iaq+l+ls ++v  
  gi|313127151|ref|YP_004037421.1|  6 SNAAPTT-DLSEKQRNILQYLRTNAPEQTYFKSRLIAQELGLSAKEVGA 53
                                      3333444.69**********************************99976 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0035        10       1      16 [.      14      29 ..      14      35 .. 0.88
   2 ?    5.0   0.0    0.0059        18      21      36 ..      38      53 ..      36      60 .. 0.79
   3 ?   -2.0   0.0      0.92   2.7e+03      28      35 ..      71      78 ..      68      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0035
                            HTH_24  1 ldetdrkILelLqknp 16
                                      l+e++r+IL++L+ n+
  gi|313127151|ref|YP_004037421.1| 14 LSEKQRNILQYLRTNA 29
                                      6799********9986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0059
                            HTH_24 21 reLAerlglSpstvnr 36
                                      r +A++lglS   v +
  gi|313127151|ref|YP_004037421.1| 38 RLIAQELGLSAKEVGA 53
                                      569*******976655 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.92
                            HTH_24 28 glSpstvn 35
                                      g S++t++
  gi|313127151|ref|YP_004037421.1| 71 GYSSGTTW 78
                                      8899*998 PP

>> DUF3263  Protein of unknown function (DUF3263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05     0.068       2      48 ..      14      61 ..      13      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                           DUF3263  2 LserdraiLaferqw.wrhagakeeaireelglsptrYyqlLnaLidd 48
                                      Lse++r+iL+  r+   +++  k + i +elgls+ +    + a+id 
  gi|313127151|ref|YP_004037421.1| 14 LSEKQRNILQYLRTNaPEQTYFKSRLIAQELGLSAKEVGANMRAIIDG 61
                                      99*******977665379999**************9999999888885 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00019      0.56       3      41 ..      14      58 ..      12      60 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
                                      S-HHHHHHHHHHCTT......S-HHHHHHHHTS-HHHHHHHHHHH CS
                              GerE  3 LskRErevLrllaeG......ksnkeIAeelniSekTVkvhksni 41
                                      Ls+++r +L++l +       +++  IA+el++S+k V + ++ i
  gi|313127151|ref|YP_004037421.1| 14 LSEKQRNILQYLRTNapeqtyFKSRLIAQELGLSAKEVGANMRAI 58
                                      78888888888866522222256788**********998887766 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00037       1.1       6      36 ..      19      53 ..      14      57 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00037
                     HTH_AsnC-type  6 rkILeaLqed.aRisy...aeLAervGlSestvlr 36
                                      r IL+ L+ + +  +y   + +A+++GlS+ +v +
  gi|313127151|ref|YP_004037421.1| 19 RNILQYLRTNaPEQTYfksRLIAQELGLSAKEVGA 53
                                      5566666666422222333669*********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 641.78
//
Query:       gi|313127152|ref|YP_004037422.1|  [L=610]
Description: hypothetical protein Hbor_24190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-39  135.4  31.7    4.2e-39  134.9  31.7    1.2  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
      5e-29  101.3   0.0    8.7e-29  100.5   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    7.4e-13   48.9   0.3    7.4e-13   48.9   0.3    1.7  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00031   20.3   0.0    0.00047   19.7   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.025   15.1   0.1      0.051   14.1   0.1    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.048   13.8   2.3       0.24   11.5   0.2    2.6  2  MLTR_LBD         MmyB-like transcription regulator ligand bin


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.9  31.7   1.4e-42   4.2e-39       2     299 ..     258     576 ..     257     578 .. 0.92

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 1.4e-42
                   LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayligl 78 
                                       ++g +l++l l+l++  ++++++ + + ++dp ++ +a l+++ls+ lr+lr+r +l++lg++ + + l+ a++i++
  gi|313127152|ref|YP_004037422.1| 258 VAGGVLTILALLLMTQYINFEQVLEKMGNADPVLVGVATLIYALSWPLRGLRYRDILSELGFHEKASFLTGAVFISQ 334
                                       678888999999999************************************************************** PP

                   LPG_synthase_TM  79 fvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa........... 144
                                         n v P++l G+++ray++k ++g+++++ +as+ +er++dll++ +l +++l+  +++ ++              
  gi|313127152|ref|YP_004037422.1| 335 TGNLVFPARL-GDFIRAYVVKARRGIPYASGFASLAAERVFDLLTITALAGIVLIGYTATGQTAELaqtvvgakgae 410
                                       **********.*****************************************99977777655444899******** PP

                   LPG_synthase_TM 145 .vllllalallllavlalllllllrrrlarlarvlkrlarllarfarklasakr.....klvlasprrlllafllsl 215
                                        v++l+a++++l+a++a++++ ++ r   ++a  l r a+  +   +     +r     + v++ +r ++++   sl
  gi|313127152|ref|YP_004037422.1| 411 qVAVLVAIVVALAAIVAVVTIVASARSDSNIAGSLVRRASSDSYAEFVAGIVERfvgdlQSVAGTRRGFVRISVSSL 487
                                       **************************************998765555555555599***999999999********* PP

                   LPG_synthase_TM 216 liwllealtlylllralgvdvslalll....lillaltlvgalpplPgGlGvrEaalalllall.Gvsaaealaaal 287
                                       +iw l+++t++l+l+a+   + +++l+    +++ + +l+ +lp++PgG+G++E+a++ll+  l  v+   a+ aa+
  gi|313127152|ref|YP_004037422.1| 488 AIWTLDVVTAMLVLAAFEPGLATVELVsvsfFAVSVGNLAKVLPLSPGGVGLYEGAFTLLVIGLtPVGYQVAIGAAI 564
                                       *************************999999999999********************77776666************ PP

                   LPG_synthase_TM 288 lyrlitlyllll 299
                                       l++++  +++++
  gi|313127152|ref|YP_004037422.1| 565 LDHAVKNIVTVI 576
                                       *******66665 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.0   2.9e-32   8.7e-29       1     169 [.      15     184 ..      15     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 2.9e-32
                                       EEEEEESS-TTTHHHHHHHHHHH....GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq....dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalna 73 
                                       svv p+yNe++t++ t+e  l+      p+  fe+iv+ Dg  D+t+e++e+ a+ d r+r ++ + + G +gal +
  gi|313127152|ref|YP_004037422.1|  15 SVVLPAYNEANTIEDTVETTLQTlssfLPAGTFEVIVAEDGCDDRTPELAEQMAADDSRIRHFHSDDRLGRGGALEH 91 
                                       8********999999999999999999************************************************** PP

                                       HHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCC CS
                   Glycos_transf_2  74 glraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgn 150
                                       +++aa+gd ++++D D++ d d+le+lve+   +++dv+ g+r   +   d+  ++      +r+y+   + +l+ +
  gi|313127152|ref|YP_004037422.1|  92 AFAAADGDTLVYFDTDLATDMDHLEELVERVRSGEYDVATGSRWMPGNVADRPAKRG---VPSRGYNLLVRTFLDSS 165
                                       ***********************************************9999999985...79*************** PP

                                       STTCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 151 lsfeigsaallrrealeel 169
                                       l +  +++ +++re++e+l
  gi|313127152|ref|YP_004037422.1| 166 LRDHQCGFKAFSREVFEDL 184
                                       ****************986 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.3   2.5e-16   7.4e-13       4     208 ..      14     217 ..      11     245 .. 0.84
   2 ?   -3.2   0.2       2.1   6.2e+03       7      43 ..     431     473 ..     411     481 .. 0.61

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.5e-16
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesll.aqe.y.pr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       ++v+ p++ne+ ++++++e +l + +   p+  +ev+v  d++d+ t e ae++aa+ +  r+r  + +++lg++g+
  gi|313127152|ref|YP_004037422.1|  14 VSVVLPAYNEANTIEDTVETTLqTLSsFlPAgtFEVIVAEDGCDDRTPELAEQMAADDS--RIRHFHSDDRLGRGGA 88 
                                       89****************999944454465566********************987765..5788899998997776 PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfl......lnrstlvsalgalefaerhl 146
                                          l++a+ a+++d ++ +D D  ++ d l+ l+  +++ +++++++++++      +  ++ v+  g+  + +++l
  gi|313127152|ref|YP_004037422.1|  89 ---LEHAFAAADGDTLVYFDTDLATDMDHLEELVERVRSGEYDVATGSRWMpgnvadRPAKRGVPSRGYNLLVRTFL 162
                                       ...66********************************999*********9976544222223366666667789*** PP

                   Glyco_tranf_2_3 147 rflaarralgvltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaa 208
                                       + +++++  g+        ++ rev+++l + d   ++ + D e+ +r+ rag+r++ +p + 
  gi|313127152|ref|YP_004037422.1| 163 DSSLRDHQCGFK-------AFSREVFEDL-REDVeDNHWFWDTEMLVRAQRAGYRVDEFPVRW 217
                                       **********98.......59********.7777789999****************9888774 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.1
                   Glyco_tranf_2_3   7 lVptfneed.vlgevlesllaqeypr.....vevvvvvdesda 43 
                                       +V++++ ++   g++++ +++++y +     ve +v++ +s a
  gi|313127152|ref|YP_004037422.1| 431 IVASARSDSnIAGSLVRRASSDSYAEfvagiVERFVGDLQSVA 473
                                       4555555556667777777777764422334555555555555 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.6e-07   0.00047       1     104 [.      15     120 ..      15     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-07
                   Glyco_tranf_2_2   1 svviplraseerhyieerv...lqkakyy..deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaa 72 
                                       svv+p +++ ++  ie++v   lq  + +     +e+iv +dg  + + e  +++ +   ++   +  d   + + a
  gi|313127152|ref|YP_004037422.1|  15 SVVLPAYNEANT--IEDTVettLQTLSSFlpAGTFEVIVAEDGCDDRTPELAEQMAADDSRIRHFHS-DDRLGRGGA 88 
                                       79******9999..***99998777777768889*************99999999999999987788.556899999 PP

                   Glyco_tranf_2_2  73 rNrGaskaesdlvlFlDaDcfissDkfekilk 104
                                           +  a +d +++ D+D     D++e +++
  gi|313127152|ref|YP_004037422.1|  89 LEHAFAAADGDTLVYFDTDLATDMDHLEELVE 120
                                       9**************************99876 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.7e-05     0.051       9      81 ..      36     107 ..      21     122 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                   Glyco_tranf_2_4   9 eflahhlalgfdrilvydndstDgtrailkelpe....vkllhvdksyederrqvellkallaryaeadwvlvvDaD 81 
                                       ++l   l +g  +++v++++++D+t ++ +++++    ++++h+d+      r+ +l +a++  +a++d ++++D+D
  gi|313127152|ref|YP_004037422.1|  36 QTLSSFLPAGTFEVIVAEDGCDDRTPELAEQMAAddsrIRHFHSDDRLG---RGGALEHAFA--AADGDTLVYFDTD 107
                                       2333444455668****************99633232255666666553...5555555555..3478888888887 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4      0.13   3.9e+02      82     150 ..      51     119 ..      44     131 .. 0.87
   2 ?   11.5   0.2     8e-05      0.24      41      85 ..     147     191 ..     112     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.13
                          MLTR_LBD  82 aarrpddpalaalvaeLsaaspefarlwarhdvaarrsgrkrlrhpevgeltldsetlgtpddptlelv 150
                                       +a++  d++  +l ++++a + + +   +++  ++ ++    +   ++ +l  + + l+t +d   elv
  gi|313127152|ref|YP_004037422.1|  51 VAEDGCDDRTPELAEQMAADDSRIRHFHSDDRLGRGGALEHAFAAADGDTLVYFDTDLATDMDHLEELV 119
                                       67788899999********99999999999999999999999999999999999999999998877665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8e-05
                          MLTR_LBD  41 aalpeperNllrlvfldpglrpliedweevaralvarLraeaarr 85 
                                         +p+++ Nll ++fld  lr+     ++++r++ ++Lr ++  +
  gi|313127152|ref|YP_004037422.1| 147 RGVPSRGYNLLVRTFLDSSLRDHQCGFKAFSREVFEDLREDVEDN 191
                                       5689999********************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4127.44
//
Query:       gi|313127153|ref|YP_004037423.1|  [L=168]
Description: hypothetical protein Hbor_24200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.7e-48  163.1   0.0    5.2e-48  162.9   0.0    1.0  1  NTPase_I-T  Protein of unknown function DUF84


Domain annotation for each model (and alignments):
>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.9   0.0   2.9e-52   5.2e-48       1     163 []       6     164 ..       6     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 2.9e-52
                                       S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET.... CS
                        NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleek 77 
                                       gS NpvK +A+ ++f+++    +v++  vpsgv++qP+g++et++GA+nRa+++l   + +d+gvG+EgGv+++e++
  gi|313127153|ref|YP_004037423.1|   6 GSGNPVKRDATARVFSEA----SVVAEPVPSGVAEQPTGHDETRTGAENRAAACLGIGP-YDLGVGIEGGVARFEGG 77 
                                       89*********9999955....79*********************************99.****************9 PP

                                       ..TEEEEEE.EEEESS-EEEEE---EE--HHHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHH CS
                        NTPase_I-T  78 ..lldvawaavvdkegrvsvgrsasfelPeevveevkegeelgevmdelfgtenikqkeGaigllTkglvtRedlye 152
                                          + v+waav+d+ +r++ g+++s++lP+ v++++ +geelg+vmd+++gte++++k+Ga g++T g++tR+d++e
  gi|313127153|ref|YP_004037423.1|  78 sdPFLVMWAAVTDG-DRWGRGSGPSLRLPDAVADRIAAGEELGPVMDDVLGTEDVAKKQGAAGAFTGGRLTRTDALE 153
                                       99************.8************************************************************* PP

                                       HHHHHHTHHHH CS
                        NTPase_I-T 153 qavilAlipfl 163
                                       +av+ A +pfl
  gi|313127153|ref|YP_004037423.1| 154 SAVVSAAAPFL 164
                                       *********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1258.94
//
Query:       gi|313127154|ref|YP_004037424.1|  [L=261]
Description: Fe3+-hydroxamate ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-17   62.5   0.0    7.6e-17   61.7   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   4.2e-21   7.6e-17       1     200 [.      12     197 ..      12     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 4.2e-21
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       ++sl+ps+t++l a+Ga d +vgv + + +         + ++vg+  ++++++la+l+PDlv  s +l + +  +e
  gi|313127154|ref|YP_004037424.1|  12 VVSLAPSSTATLTAMGAGDCLVGVTAHCDF---------DAPVVGGWLNPNYDRLAELDPDLVCTSDDL-QSEIRDE 78 
                                       89*********************9876655.........35779*************************.999999* PP

                                       HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE..EEE CS
                      Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvfggadeggyvv 153
                                       l++ g+ ++ +e+     ++ e+++ lg ++g+++++e+l++    +l+ + ++++s+ + +p+++  ++ + ++  
  gi|313127154|ref|YP_004037424.1|  79 LRERGYAVYHDEPERL-TDVVESFESLGSAVGRPAAGEQLAEASRARLETVATRVPSDsDSRPIVYCEEWSD-PP-- 151
                                       **************96.*****************************************77777777777776.44.. PP

                                       E-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEE CS
                      Peripla_BP_2 154 agsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvs 200
                                       ++ ++++ d + a+g++  +    ++ + e+s+E +  ++pd ++ +
  gi|313127154|ref|YP_004037424.1| 152 MAAGNWVPDAVAAAGGRCPFVKP-GERSREVSREVVEGAAPDHVVLH 197
                                       45567899*********997775.9*****************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1877.42
//
Query:       gi|313127155|ref|YP_004037425.1|  [L=321]
Description: transcription initiation factor iib (tfiib) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-40  134.7   0.2    1.3e-20   73.2   0.0    2.2  2  TFIIB            Transcription factor TFIIB repeat
    3.4e-16   58.5   3.5    6.8e-16   57.5   3.5    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00041   19.8   0.6       0.55    9.8   0.0    4.0  4  Sigma70_r4       Sigma-70, region 4
    0.00046   19.8   0.7    0.00071   19.2   0.7    1.3  1  A2L_zn_ribbon    A2L zinc ribbon domain
  ------ inclusion threshold ------
      0.015   15.3   0.3      0.026   14.6   0.3    1.3  1  DZR              Double zinc ribbon
       0.02   15.0   0.1        6.5    6.9   0.1    2.3  2  Cyclin_C         Cyclin, C-terminal domain
      0.026   14.9   0.6      0.026   14.9   0.6    2.0  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.027   14.4   1.2      0.066   13.1   1.2    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.027   14.4   0.5      0.052   13.5   0.5    1.4  1  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
       0.07   12.6   4.1        1.2    8.7   4.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.16   12.2   1.8       0.29   11.3   1.8    1.4  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.55   10.4   4.0        1.1    9.4   0.4    2.3  2  Zn-ribbon_8      Zinc ribbon domain
       0.56   10.2   2.1        1.8    8.6   2.1    1.8  1  Nudix_N_2        Nudix N-terminal
        1.3    9.4   4.2       0.56   10.5   0.5    2.1  2  zinc_ribbon_9    zinc-ribbon
        4.2    7.6   5.7        6.6    6.9   0.2    3.0  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.0   1.1e-23   1.3e-20       1      71 []     140     210 ..     140     210 .. 0.98
   2 !   59.7   0.1   1.7e-19   2.1e-16       1      71 []     234     304 ..     234     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.1e-23
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+a+al+Lpe V++ A  ++++al++++l Grs +g+a +c+y A+r+++v r++ eis+v++V++ ++
  gi|313127155|ref|YP_004037425.1| 140 IDRMASALGLPENVRETASVIYRRALDDDLLPGRSIEGVATSCVYAAARMAGVPRSLDEISEVSRVEKSEV 210
                                       789***************************************************************99875 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 1.7e-19
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf ++l+L+++ + +A +l+k+a+e++v++G+sp g+aAA++y A+++ ++k tq+ +s+v+ +se+ti
  gi|313127155|ref|YP_004037425.1| 234 VPRFGSELGLSDESKMRARQLLKNAKEKGVHSGKSPVGLAAAAVYAAALLTNEKTTQAAVSDVADISEVTI 304
                                       689******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   3.5   5.6e-19   6.8e-16       2      43 .]      25      65 ..      24      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 5.6e-19
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+Cg+  +v+D e+ge+vC dCGlV+ ++s+d gpewr+f
  gi|313127155|ref|YP_004037425.1| 25 TCPECGGN-VVVDDEHGETVCADCGLVVTEDSVDRGPEWRAF 65
                                      8******5.9******************************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.34   4.1e+02      34      46 ..     154     166 ..     144     167 .. 0.89
   2 ?   -1.0   0.0       1.1   1.3e+03      20      29 ..     193     202 ..     184     222 .. 0.70
   3 ?    4.1   0.0     0.028        33      33      47 ..     247     261 ..     238     261 .. 0.86
   4 !    9.8   0.0   0.00046      0.55      18      46 ..     285     313 ..     276     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAlr 46 
                                       re+++ i +rAl+
  gi|313127155|ref|YP_004037425.1| 154 RETASVIYRRALD 166
                                       89*********96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                       T--HHHHHHH CS
                        Sigma70_r4  20 glTleEIger 29 
                                       +++l EI+e+
  gi|313127155|ref|YP_004037425.1| 193 PRSLDEISEV 202
                                       6778888776 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.028
                                       -HHHHHHHHHHHHHH CS
                        Sigma70_r4  33 SrerVrqiekrAlrk 47 
                                       S++r+rq++k+A +k
  gi|313127155|ref|YP_004037425.1| 247 SKMRARQLLKNAKEK 261
                                       899********9876 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00046
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlr 46 
                                        e+ T++ ++++ +iS+ ++r + ++ l+
  gi|313127155|ref|YP_004037425.1| 285 NEKTTQAAVSDVADISEVTIRNRYHELLE 313
                                       5889********************99876 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.7     6e-07   0.00071       5      30 ..      25      50 ..      21      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6e-07
                     A2L_zn_ribbon  5 vCsvCggngilnseqgylvCieCgas 30
                                      +C  Cggn+++  e+g+ vC +Cg++
  gi|313127155|ref|YP_004037425.1| 25 TCPECGGNVVVDDEHGETVCADCGLV 50
                                      8999********************86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   2.2e-05     0.026       7      40 ..      18      53 ..      14      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                               DZR  7 elppdarfCseCgtklkavaa..edrCpsCgekvdp 40
                                      e+++++ +C+eCg ++    +  e++C  Cg  v++
  gi|313127155|ref|YP_004037425.1| 18 ENTSEDLTCPECGGNVVVDDEhgETVCADCGLVVTE 53
                                      7899999********75333367*******988765 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.012        14      47      90 ..     178     221 ..     174     235 .. 0.90
   2 ?    6.9   0.1    0.0054       6.5      47      89 ..     272     314 ..     264     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                       +A++++++a ++ + p   +++ ++++++k+++   ++ i+  l
  gi|313127155|ref|YP_004037425.1| 178 VATSCVYAAARMAGVPRSLDEISEVSRVEKSEVARTYRYIAREL 221
                                       7*********************************9999888655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0054
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                                       +Aaaa+++a    n+++ + ++  +  +s+  +++ ++ +le+
  gi|313127155|ref|YP_004037425.1| 272 LAAAAVYAAALLTNEKTTQAAVSDVADISEVTIRNRYHELLEA 314
                                       8*********999******999999999999999999988875 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.6   2.2e-05     0.026       5      49 ..      25      63 ..      22      75 .. 0.75
   2 ?   -2.6   0.3       6.1   7.3e+03      55      61 ..     116     122 ..     107     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga.stpwfkiaedeae 49
                                       CP Cgg  v+  +++ +        CadCg  +t +   +++e +
  gi|313127155|ref|YP_004037425.1| 25 TCPECGGNVVVDDEHGET-------VCADCGLvVTEDSVDRGPEWR 63
                                      7*************9888.......5******75555555555544 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.1
                   Lar_restr_allev  55 ieaWNrR 61 
                                         +WN R
  gi|313127155|ref|YP_004037425.1| 116 LRKWNER 122
                                       578**98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.2   5.6e-05     0.066      25      59 ..      18      54 ..       9      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.6e-05
                    OrfB_Zn_ribbon 25 ayTSk..tCseCgsknkealsgrtfkCpnCgfeadrD 59
                                      ++TS   tC+eCg ++  ++++ + +C +Cg++   D
  gi|313127155|ref|YP_004037425.1| 18 ENTSEdlTCPECGGNVVVDDEHGETVCADCGLVVTED 54
                                      45776448*********99************987655 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   4.3e-05     0.052      21      49 ..      14      42 ..       8      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                                      EETTE......E-TTTTTSSEEE-HHHHH CS
                         Anti-TRAP 21 kiepeeprasleCPkCsGkglipTaqGqk 49
                                      + e+e+    l CP+C+G+ ++  ++G++
  gi|313127155|ref|YP_004037425.1| 14 ESESENTSEDLTCPECGGNVVVDDEHGET 42
                                      4567788889************9999987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.5    0.0019       2.2      13      24 ..      20      31 ..      17      33 .. 0.82
   2 ?    8.7   4.1   0.00096       1.2       4      25 ..      25      50 ..      24      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0019
                       zf-ribbon_3 13 ssddnvCpyCGt 24
                                      +s+d +Cp CG+
  gi|313127155|ref|YP_004037425.1| 20 TSEDLTCPECGG 31
                                      688999999997 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00096
                       zf-ribbon_3  4 rCPnCGa.p.lss..ddnvCpyCGtk 25
                                      +CP+CG  + +++  + +vC+ CG +
  gi|313127155|ref|YP_004037425.1| 25 TCPECGGnVvVDDehGETVCADCGLV 50
                                      6****997756654468*******85 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.8   0.00024      0.29      17      40 .]      25      48 ..      23      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                     Auto_anti-p27 17 tCpvC.gvPLmrdrkggkvyCvaCd 40
                                      tCp+C g + + d + g+++C+ C+
  gi|313127155|ref|YP_004037425.1| 25 TCPECgGNVVVDD-EHGETVCADCG 48
                                      8****88888888.56999*****6 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4   0.00092       1.1      23      36 ..      20      33 ..       8      36 .. 0.70
   2 ?    2.1   0.2      0.19   2.2e+02      23      34 ..      38      49 ..      33      54 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00092
                       Zn-ribbon_8 23 dapltaCPeCgsev 36
                                       +++ +CPeCg++v
  gi|313127155|ref|YP_004037425.1| 20 TSEDLTCPECGGNV 33
                                      345778*****987 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.19
                       Zn-ribbon_8 23 dapltaCPeCgs 34
                                      +  +t+C +Cg 
  gi|313127155|ref|YP_004037425.1| 38 EHGETVCADCGL 49
                                      445677999985 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.1    0.0015       1.8       3      31 ..      26      50 ..      26      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                                      -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                      C++CG+ v      +D++   vC++Cg +
  gi|313127155|ref|YP_004037425.1| 26 CPECGGNVVV----DDEHGETVCADCGLV 50
                                      ******9654....6777778******87 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.5   0.00047      0.56      16      30 ..      18      32 ..      13      36 .. 0.78
   2 ?   -0.2   0.3         1   1.2e+03      17      28 ..      37      48 ..      32      49 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00047
                     zinc_ribbon_9 16 pdedsdvlCPhCggg 30
                                      +++++d +CP+Cgg 
  gi|313127155|ref|YP_004037425.1| 18 ENTSEDLTCPECGGN 32
                                      56677789*****96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                     zinc_ribbon_9 17 dedsdvlCPhCg 28
                                      de+ +++C +Cg
  gi|313127155|ref|YP_004037425.1| 37 DEHGETVCADCG 48
                                      3444455****7 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0055       6.6      11      32 ..      18      39 ..       8      42 .. 0.80
   2 ?    2.8   0.2       0.1   1.2e+02      14      26 ..      39      51 ..      36      56 .. 0.80
   3 ?   -0.9   0.1       1.5   1.8e+03      39      52 ..     108     121 ..     106     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0055
                          zf-Mss51 11 apkhvdfeCpdCGiptycseeh 32
                                      ++ + d++Cp+CG  + ++ eh
  gi|313127155|ref|YP_004037425.1| 18 ENTSEDLTCPECGGNVVVDDEH 39
                                      6778899******999888888 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.1
                          zf-Mss51 14 hvdfeCpdCGipt 26
                                      h +  C dCG+++
  gi|313127155|ref|YP_004037425.1| 39 HGETVCADCGLVV 51
                                      66789*****987 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.5
                          zf-Mss51  39 ahleicdtLrqvne 52 
                                       ++++ +++Lr+ ne
  gi|313127155|ref|YP_004037425.1| 108 NQRQKMQRLRKWNE 121
                                       478999*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2174.28
//
Query:       gi|313127156|ref|YP_004037426.1|  [L=225]
Description: 3-dehydroquinate dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-43  149.0   0.1      3e-43  148.7   0.1    1.0  1  DHquinase_I    Type I 3-dehydroquinase
  ------ inclusion threshold ------
      0.025   14.1   1.0       0.17   11.4   0.3    2.0  2  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.7   0.1   3.3e-47     3e-43      19     227 ..      22     220 ..      10     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 3.3e-47
                                       HTT.S-SEEEEEGGG-.TT.THHHHHHHHHHHHHH.TTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT-.SE CS
                       DHquinase_I  19 gke.kaDlvElRlDllketseaedvseeleelrst.sdlpliftlrtkaeggrfkrkseeeylellrtaielga.dy 92 
                                       +++ +aD+vE+R+Dl  ++         l+el    ++lpl++t r ++egg+ ++ +ee +l  l++a++  a   
  gi|313127156|ref|YP_004037426.1|  22 AAReHADVVEFRMDLA-DD--------PLAELDDYdGTLPLLVTNRASWEGGE-SEADEEGRLASLERAARYDAvVA 88 
                                       44448*********77.33........4788888867****************.59***************9999** PP

                                       EEEEGG-.HHG.HHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHH CS
                       DHquinase_I  93 vDvElteapee.skkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrllsl 168
                                       vDvEl +a e+ +  + +e  re+++ vI+S hdfe+tp+  el +ll++++++g D+ K+av+a+s+ D lrll++
  gi|313127156|ref|YP_004037426.1|  89 VDVEL-NALETtRGVTAAERLRESNVAVIASVHDFERTPATSELRRLLHEAATVG-DVGKVAVTANSRHDALRLLEA 163
                                       *****.6776675668888999*********************************.********************* PP

                                       HHHHHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHH CS
                       DHquinase_I 169 tseakeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelre 227
                                       t+ a++      + +m mGe+Gk +R +++v+Gs + +a + +++++apGq +++ l +
  gi|313127156|ref|YP_004037426.1| 164 THAATA--WGDTVATMGMGEAGKHTRAVAPVYGSKIGYAPVHAGEETAPGQYDLESLAH 220
                                       *64444..4689******************************************99865 PP

>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   1.9e-05      0.17      54     101 ..      75     121 ..      68     125 .. 0.92
   2 ?    1.5   0.0     0.022     2e+02      47      89 ..     126     168 ..     120     190 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHTT-EEEEEES--SSS--HHHHHHHHHHHHHT-EEEE--TT CS
                     PP_kinase_C_1  54 kaLieAaengkqvtvlvElkArfdeenNiewakkleeagvkvvygvvg 101
                                       ++L +Aa+ +  v+v vEl+A ++ ++ ++ a++l+e+ v v+ +v++
  gi|313127156|ref|YP_004037426.1|  75 ASLERAARYDAVVAVDVELNA-LETTRGVTAAERLRESNVAVIASVHD 121
                                       6899****************9.899******************99976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.022
                                       -S--HHHHHHHHHHHTT-EEEEEES--SSS--HHHHHHHHHHH CS
                     PP_kinase_C_1  47 akdskivkaLieAaengkqvtvlvElkArfdeenNiewakkle 89 
                                        ++s++ + L eAa+ g    v v  ++r d  + +e +++ +
  gi|313127156|ref|YP_004037426.1| 126 PATSELRRLLHEAATVGDVGKVAVTANSRHDALRLLEATHAAT 168
                                       5566666666666666666666666666666554444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1679.38
//
Query:       gi|313127157|ref|YP_004037427.1|  [L=144]
Description: hypothetical protein Hbor_24240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0011   18.4   0.0     0.0015   18.0   0.0    1.2  1  TMEM126         Transmembrane protein 126
     0.0014   18.0   0.9     0.0022   17.3   0.9    1.3  1  zf-ribbon_3     zinc-ribbon domain
     0.0022   18.0   0.5     0.0031   17.5   0.5    1.2  1  DZR             Double zinc ribbon
     0.0074   16.0   0.9      0.011   15.4   0.9    1.3  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.016   16.0   1.2      0.022   15.5   0.7    1.5  2  zinc_ribbon_15  zinc-ribbon family
      0.032   14.0   0.6        1.5    8.7   0.0    2.2  2  DUF4538         Domain of unknown function (DUF4538)
      0.055   13.3   1.2       0.75    9.7   1.2    2.1  1  Prok-RING_4     Prokaryotic RING finger family 4
      0.055   13.4   0.5      0.078   12.9   0.5    1.2  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.094   12.5   0.1      0.094   12.5   0.1    1.7  2  DUF3953         Protein of unknown function (DUF3953)
       0.11   12.3   2.9       0.33   10.8   0.5    2.1  2  Rad50_zn_hook   Rad50 zinc hook motif
       0.13   12.2   0.1       0.23   11.4   0.1    1.4  1  UCR_6-4kD       Ubiquinol-cytochrome C reductase complex, 6.4
       0.42   10.9   2.3        7.7    6.9   0.1    2.2  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.59   10.3   3.8          1    9.5   3.8    1.4  1  UPF0547         Uncharacterised protein family UPF0547
        4.2    7.8   7.7         18    5.8   7.7    1.9  1  TM2             TM2 domain


Domain annotation for each model (and alignments):
>> TMEM126  Transmembrane protein 126
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.2e-06    0.0015      50      97 ..      66     110 ..      32     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                           TMEM126  50 VkqaalksslplavlPflstvvaykalvtdpllsgdlncevcaviRgg 97 
                                       + +  +  ++p++vl flst+ ay ++ ++p  s++l c+vc   Rg 
  gi|313127157|ref|YP_004037427.1|  66 IDEVPVEVTAPMFVLFFLSTFDAYYVASRKPQESDSLRCPVC---RGK 110
                                       5566778889********************************...765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.9   1.7e-06    0.0022       4      22 ..     103     121 ..     102     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyC 22 
                                       rCP C  +l++++++Cp+C
  gi|313127157|ref|YP_004037427.1| 103 RCPVCRGKLDPQVTFCPWC 121
                                       8****6655********** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   2.4e-06    0.0031      30      48 ..     103     121 ..      88     133 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                               DZR  30 rCpsCgekvdpearfCpeC 48 
                                       rCp C  k+dp+ +fCp C
  gi|313127157|ref|YP_004037427.1| 103 RCPVCRGKLDPQVTFCPWC 121
                                       5666666666666666665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.9   8.7e-06     0.011       1      22 [.     103     124 ..     103     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.7e-06
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtp 22 
                                       +Cp C  +l++ ++FCp C t+
  gi|313127157|ref|YP_004037427.1| 103 RCPVCRGKLDPQVTFCPWCATE 124
                                       6******************886 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.9     5e+03      18      30 ..      75      87 ..      67      99 .. 0.74
   2 ?   15.5   0.7   1.7e-05     0.022      58      85 ..      94     121 ..      82     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
                    zinc_ribbon_15 18 kkvlklffipvfk 30
                                        ++ lff+ +f+
  gi|313127157|ref|YP_004037427.1| 75 APMFVLFFLSTFD 87
                                      5678888888775 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.7e-05
                    zinc_ribbon_15  58 ekkessekkeCknCgkeveeefkyCpkC 85 
                                       +k ++s++ +C+ C+ ++++++++Cp C
  gi|313127157|ref|YP_004037427.1|  94 RKPQESDSLRCPVCRGKLDPQVTFCPWC 121
                                       455667799******************* PP

>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3     0.047        60       6      18 ..      10      22 ..       2      25 .. 0.56
   2 ?    8.7   0.0    0.0011       1.5       1      30 [.      31      60 ..      31      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.047
                           DUF4538  6 yvllvggvvglig 18
                                      +++++ggv + +g
  gi|313127157|ref|YP_004037427.1| 10 VAAFIGGVGASVG 22
                                      4455555555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
                           DUF4538  1 lrglkyvllvggvvgliglalYPiiiaPll 30
                                      lr ++ +++  ++v  igl l +++ +P++
  gi|313127157|ref|YP_004037427.1| 31 LREWRRAVAWFTFVLGIGLVLLSVFTDPMS 60
                                      699*************************97 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.2   0.00058      0.75      28      46 .]      99     117 ..      94     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00058
                       Prok-RING_4  28 kdlssCPlCqrrisksdpf 46 
                                       +d+ +CP+C+ +++++ +f
  gi|313127157|ref|YP_004037427.1|  99 SDSLRCPVCRGKLDPQVTF 117
                                       5566999999999988666 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   6.1e-05     0.078       6      29 ..     103     124 ..      98     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-05
                       Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgtp 29 
                                       +CpvC+ +l+++  +  Cp C t 
  gi|313127157|ref|YP_004037427.1| 103 RCPVCRGKLDPQ--VTFCPWCATE 124
                                       7***********..*******995 PP

>> DUF3953  Protein of unknown function (DUF3953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4       6.8   8.7e+03      30      38 ..       9      17 ..       9      20 .. 0.62
   2 ?   12.5   0.1   7.4e-05     0.094      17      40 ..      30      54 ..      28      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.8
                           DUF3953 30 laalfvlfV 38
                                      l+a+f+  V
  gi|313127157|ref|YP_004037427.1|  9 LVAAFIGGV 17
                                      567776555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.4e-05
                           DUF3953 17 fkke.nkfsGillilaalfvlfVsi 40
                                      + +e ++++++++++ ++ +++ s+
  gi|313127157|ref|YP_004037427.1| 30 YLREwRRAVAWFTFVLGIGLVLLSV 54
                                      78999****************9997 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   0.00026      0.33      17      31 ..      98     113 ..      94     115 .. 0.84
   2 ?    1.5   0.1       0.2   2.6e+02      22      31 ..     118     127 ..     116     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                                       T-SE.E-TTT--EE-H CS
                     Rad50_zn_hook  17 eakg.cCPlCgRelde 31 
                                       e++  +CP+C  +ld+
  gi|313127157|ref|YP_004037427.1|  98 ESDSlRCPVCRGKLDP 113
                                       566679********97 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                                       -TTT--EE-H CS
                     Rad50_zn_hook  22 CPlCgRelde 31 
                                       CP C  e+++
  gi|313127157|ref|YP_004037427.1| 118 CPWCATEFES 127
                                       *******986 PP

>> UCR_6-4kD  Ubiquinol-cytochrome C reductase complex, 6.4kD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00018      0.23      10      49 ..       6      45 ..       4      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHCT-HHHHTTSSS-- CS
                         UCR_6-4kD 10 yaelaknwvpsavawgavggvalvyltDWrliLdYvPyin 49
                                        +l+++++  ++a   ++g +  yl +Wr  + ++ ++ 
  gi|313127157|ref|YP_004037427.1|  6 RRALVAAFIGGVGASVGIAGAGHAYLREWRRAVAWFTFVL 45
                                      5678999*******99********************9985 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.006       7.7      26      41 ..      96     111 ..      89     117 .. 0.75
   2 ?    4.1   0.4     0.046        59       4      13 ..     117     126 ..     114     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.006
                           zf-Di19  26 rveskevvCPvCaekv 41 
                                       ++es +  CPvC  k+
  gi|313127157|ref|YP_004037427.1|  96 PQESDSLRCPVCRGKL 111
                                       5678888899998776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.046
                           zf-Di19   4 tCPyCgkelt 13 
                                        CP+C  e++
  gi|313127157|ref|YP_004037427.1| 117 FCPWCATEFE 126
                                       5999988776 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.8   0.00079         1       2      26 .]     103     127 ..     103     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00079
                           UPF0547   2 vCPeCeakvPvaaqfCphCGyvFqa 26 
                                       +CP C+ k+   + fCp C ++F++
  gi|313127157|ref|YP_004037427.1| 103 RCPVCRGKLDPQVTFCPWCATEFES 127
                                       6**********************85 PP

>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   7.7     0.014        18      15      44 ..      21      49 ..       6      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                               TM2 15 LGglGvHRFYlGktgsGvlqlltfvGglgi 44
                                       G+ G+ + Yl  +  +v+++ + +G+ g+
  gi|313127157|ref|YP_004037427.1| 21 VGIAGAGHAYLREWRRAVAWFTFVLGI-GL 49
                                      699******************888633.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 907.31
//
Query:       gi|313127158|ref|YP_004037428.1|  [L=393]
Description: 3-dehydroquinate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.9e-148  494.1   1.5   2.2e-148  493.9   1.5    1.0  1  DHQS       3-dehydroquinate synthase II
     0.0012   18.4   0.0      0.031   13.8   0.0    2.2  2  Hint       Hint module
  ------ inclusion threshold ------
       0.01   16.1   2.3          1    9.6   0.1    3.3  4  Hint_2     Hint domain
      0.037   13.8   0.3       0.32   10.8   0.1    2.3  2  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.9   1.5  4.8e-152  2.2e-148       1     352 []       3     393 .]       3     393 .] 0.97

  Alignments for each domain:
  == domain 1  score: 493.9 bits;  conditional E-value: 4.8e-152
                              DHQS   1 kevwikade..eeweerkelvtaaleagvdavlveeedaekvkelgkikviakeed....................d 55 
                                       ++vw+kad+  ++we+rk+++ta+le+gvd++lv+e+d+e+v++lg+++v+a+++d                    d
  gi|313127158|ref|YP_004037428.1|   3 RSVWLKADDsvGDWETRKRRITAGLESGVDWILVDESDVERVRSLGDVNVAAFRTDadaslidnveeaessdpdvaD 79 
                                       689*****9999******************************************88778888777777777777777 PP

                              DHQS  56 avlvgkd.................dleklkka..kkvaalveikskeeeeeaaeaakeadyvivelkdwtvIPlEnl 113
                                       a++vgk+                 d+++l+++  ++ aa+v+i sk++e++a++aa++ad++iv ++dwt+IPlEnl
  gi|313127158|ref|YP_004037428.1|  80 AYVVGKNgegdgtvdlpgdfsgsaDMTTLRREddRANAAYVRILSKDHEAFAEAAADDADFTIVVGEDWTIIPLENL 156
                                       7777777*****************9999999888999**************************************** PP

                              DHQS 114 iAalqgeetkiiaavksaeeAklaletLEkGadgvllktedveeikelaelleeaeeekleLkeaevtkveevgmgd 190
                                       iA++ geet++ia+v++aeeA++a+etLE G+dgvll+t+d++ei++++e++e+ae+e+l+L++aevt+ve++gm+d
  gi|313127158|ref|YP_004037428.1| 157 IARI-GEETDLIAGVTTAEEARTAFETLELGSDGVLLDTDDPDEIRRTVEVREAAERESLDLQWAEVTAVERTGMAD 232
                                       **99.999********************************************************************* PP

                              DHQS 191 RvcvDtcslmkegeGmLvGsssrglfLvhsEtlespYvasRPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvd 267
                                       RvcvDt +lm+++eGmLvGs+ rglf+vh+Et+espYvasRPFRVNAGavhaYv++p+g TkYLseLk+Gdev+v+d
  gi|313127158|ref|YP_004037428.1| 233 RVCVDTGNLMEHDEGMLVGSMGRGLFFVHAETAESPYVASRPFRVNAGAVHAYVRTPEGGTKYLSELKSGDEVQVID 309
                                       ***************************************************************************** PP

                              DHQS 268 kkGktreavvGRvKiEkRPlllveaeaegkkvstilQnaetirlvtedgkaisvteLkeGdevlvyleekaRHfGik 344
                                       ++G+trea+vGRvKiEkRP+++veae +g++v+t+lQnaeti++ t+dg +++vt+L++Gdevl+y+e++aRHfG +
  gi|313127158|ref|YP_004037428.1| 310 TDGRTREAIVGRVKIEKRPMFRVEAELDGDRVETLLQNAETIKVQTRDG-RTAVTDLEPGDEVLLYYEDTARHFGEA 385
                                       *************************************************.9************************** PP

                              DHQS 345 ieEtiiEk 352
                                       +eE+iiEk
  gi|313127158|ref|YP_004037428.1| 386 VEESIIEK 393
                                       *******8 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   6.9e-06     0.031      17      47 ..     284     314 ..     281     322 .. 0.91
   2 ?    2.0   0.0     0.027   1.2e+02      19      40 ..     353     373 ..     347     384 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint  17 stvtvedgeqkslseLepGdkVlavdesgev 47 
                                       + v++ +g++k lseL+ Gd+V+ +d++g++
  gi|313127158|ref|YP_004037428.1| 284 AYVRTPEGGTKYLSELKSGDEVQVIDTDGRT 314
                                       7899**********************99985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.027
                                       XXXXXXXXXXXXXXXXXXXXXX CS
                              Hint  19 vtvedgeqkslseLepGdkVla 40 
                                       v++ dg + ++ +LepGd+Vl 
  gi|313127158|ref|YP_004037428.1| 353 VQTRDG-RTAVTDLEPGDEVLL 373
                                       666666.7899*********96 PP

>> Hint_2  Hint domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.91   4.1e+03     106     128 ..     106     129 ..     103     136 .. 0.72
   2 ?    4.5   0.1    0.0087        39       8      34 ..     285     312 ..     281     335 .. 0.76
   3 ?   -2.1   0.0      0.96   4.3e+03      17      37 ..     331     351 ..     321     353 .. 0.82
   4 ?    9.6   0.1   0.00023         1       8      30 ..     352     374 ..     347     382 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.91
                            Hint_2 106 asir.eeeaeevtyvhllldrhev 128
                                       ++ r e+++ ++ yv +l ++he 
  gi|313127158|ref|YP_004037428.1| 106 TTLRrEDDRANAAYVRILSKDHEA 129
                                       566525567789999999999986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0087
                            Hint_2   8 liatpeG.evaveeLrvGdlVvtadggl 34 
                                        ++tpeG +  + eL+ Gd+V++ d+  
  gi|313127158|ref|YP_004037428.1| 285 YVRTPEGgTKYLSELKSGDEVQVIDTDG 312
                                       689998725679**********998654 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.96
                            Hint_2  17 aveeLrvGdlVvtadgglqpv 37 
                                       +ve+   Gd+V t  ++++++
  gi|313127158|ref|YP_004037428.1| 331 RVEAELDGDRVETLLQNAETI 351
                                       677778899999998888877 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00023
                            Hint_2   8 liatpeGevaveeLrvGdlVvta 30 
                                        ++t +G  av +L++Gd+V+  
  gi|313127158|ref|YP_004037428.1| 352 KVQTRDGRTAVTDLEPGDEVLLY 374
                                       589*****************865 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.11   5.1e+02      94     117 ..      24      47 ..      14      73 .. 0.80
   2 ?   10.8   0.1   7.1e-05      0.32      87     126 ..     170     212 ..     152     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.11
                                       HHHHHHT-SEEEEES--HHHHHHH CS
                         QRPTase_C  94 eevleaeadiimLDnfsveelkka 117
                                       ++ le ++d i++D+ +ve +++ 
  gi|313127158|ref|YP_004037428.1|  24 TAGLESGVDWILVDESDVERVRSL 47 
                                       556788999999999999999875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.1e-05
                                       ESSHHHHHHHHH...HT-SEEEEES--HHHHHHHHHHHHHHST CS
                         QRPTase_C  87 vesleeleevle...aeadiimLDnfsveelkkaveelkeknk 126
                                       v + ee++ + e    + d+++LD+ +++e++++ve+++++++
  gi|313127158|ref|YP_004037428.1| 170 VTTAEEARTAFEtleLGSDGVLLDTDDPDEIRRTVEVREAAER 212
                                       56667776665532278*******************7765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2587.35
//
Query:       gi|313127159|ref|YP_004037429.1|  [L=135]
Description: hypothetical protein Hbor_24260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-07   29.7   2.4    5.6e-07   29.1   2.4    1.3  1  SHOCT            Short C-terminal domain
    0.00015   21.7   1.9    0.00026   21.0   1.9    1.3  1  DUF1707          Domain of unknown function (DUF1707)
     0.0032   17.2   5.6     0.0036   17.0   5.6    1.1  1  Yip1             Yip1 domain
  ------ inclusion threshold ------
      0.055   13.5   6.5      0.074   13.1   6.5    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.092   12.3   0.1       0.11   12.0   0.1    1.2  1  DUF533           Protein of unknown function (DUF533)
        3.6    7.6   8.0        1.6    8.7   2.1    2.2  2  Apq12            Nuclear pore assembly and biogenesis


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   2.4   1.9e-10   5.6e-07       2      27 ..     107     132 ..     106     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.9e-10
                             SHOCT   2 aLekLkeLyarGeIteEEFeakKakL 27 
                                       aLe+L+  yarG +t+EE+e +++ L
  gi|313127159|ref|YP_004037429.1| 107 ALEELRVAYARGDLTDEEYEDRRKTL 132
                                       9**********************977 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.9   8.8e-08   0.00026       9      33 ..     105     129 ..     101     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.8e-08
                           DUF1707   9 eravelLrealaeGrLtldEfdeRl 33 
                                       +ra+e Lr a+a+G Lt +E+++R 
  gi|313127159|ref|YP_004037429.1| 105 DRALEELRVAYARGDLTDEEYEDRR 129
                                       79*********************96 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   5.6   1.2e-06    0.0036      20      93 ..      24      99 ..       3     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-06
                              Yip1 20 rapdlallllalltlllgllaslnlgqtlasg..eevqgltlssllgaiiggylglllgllllalllhliakllgg 93
                                      + ++ al  l+ll+ l++ ++++ +g ++++g  ++++g+++  +++++++g++++l+ l++++++ +l+ k+  g
  gi|313127159|ref|YP_004037429.1| 24 ALVLIALGALILLPTLFMGFGTMGYGPMMGGGmwGQMWGTGGTVPMWVPLAGLVMQLVFLAVIGGVAYLVYKAITG 99
                                      344566666666777777777778888888888888888999999999*********************9998765 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   6.5   2.5e-05     0.074      32     106 ..      20     112 ..      10     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                   Phage_holin_3_6  32 ragsgagllgaagvlallalllllvala...............lala.a....lwlaalivaavllvlagvlalvgl 88 
                                       r +++++l++++++++l +l++ + ++                   + +      la l++ +v+l++ g +a++ +
  gi|313127159|ref|YP_004037429.1|  20 RRLIALVLIALGALILLPTLFMGFGTMGygpmmgggmwgqmwgT--GgTvpmwVPLAGLVMQLVFLAVIGGVAYLVY 94 
                                       55677777777777788887777777745777787776665331..2224656778999999*************** PP

                   Phage_holin_3_6  89 kklkkakplpertieelk 106
                                       k++ + +++ +r++eel+
  gi|313127159|ref|YP_004037429.1|  95 KAITGPERTGDRALEELR 112
                                       *****8888888888887 PP

>> DUF533  Protein of unknown function (DUF533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.8e-05      0.11       4      53 ..      49     102 ..      46     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                            DUF533   4 ggaaaggllglllGskkgr....klgkkalklGglAalGglAykayqnwqanqq 53 
                                       g+++ gg+ g++ G++++      l++ +++l  lA++Gg+Ay  y++++  ++
  gi|313127159|ref|YP_004037429.1|  49 GPMMGGGMWGQMWGTGGTVpmwvPLAGLVMQLVFLAVIGGVAYLVYKAITGPER 102
                                       678899**********9444566999*********************8755444 PP

>> Apq12  Nuclear pore assembly and biogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4     0.053   1.6e+02      32      51 ..      15      34 ..       8      36 .. 0.81
   2 ?    8.7   2.1   0.00055       1.6      28      53 ..      70      95 ..      66      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.053
                             Apq12 32 vrllvrlvfwlavvlvgayv 51
                                      + ++ r+++ l+++++ga +
  gi|313127159|ref|YP_004037429.1| 15 TNTTNRRLIALVLIALGALI 34
                                      67888999999999999976 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00055
                             Apq12 28 vlfwvrllvrlvfwlavvlvgayvyn 53
                                      +  +  l++ lvf++++ +v++ vy+
  gi|313127159|ref|YP_004037429.1| 70 WVPLAGLVMQLVFLAVIGGVAYLVYK 95
                                      666677999****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 993.76
//
Query:       gi|313127160|ref|YP_004037430.1|  [L=264]
Description: 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-44  152.8   0.1    1.4e-44  152.5   0.1    1.1  1  DeoC          DeoC/LacD family aldolase
    0.00063   19.3   0.1    0.00095   18.7   0.1    1.3  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.011   15.3   0.2      0.017   14.7   0.2    1.3  1  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
      0.043   14.0   0.0      0.058   13.6   0.0    1.4  1  DHquinase_I   Type I 3-dehydroquinase
      0.061   12.5   0.0      0.089   11.9   0.0    1.2  1  DUF561        Protein of unknown function (DUF561)
      0.097   12.8   0.0        1.6    8.9   0.0    2.2  2  UvrA_inter    UvrA interaction domain
       0.12   11.7   0.5        5.5    6.4   0.0    2.9  3  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.5   0.1   5.3e-48   1.4e-44       3     235 .]      20     231 ..      18     231 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.5 bits;  conditional E-value: 5.3e-48
                                       EEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEE CS
                              DeoC   3 ilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrd 79 
                                       ++++D+++ ++++++        dl+++v++++++ga+avl+++gv+++++ +++   +++v+l+ +t + ++++++
  gi|313127160|ref|YP_004037430.1|  20 VVPMDHGITLGPVKGL------VDLETTVDAITRGGADAVLTQKGVARRVHPKKN-GKGYIVHLNGSTVIGPDSNDK 89 
                                       79**************......9****************************9999.88*******999999999888 PP

                                       EETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHH CS
                              DeoC  80 vdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeA 156
                                        +   sveea++ GAdav++++++   gse e  ++ ++++  e++h  glp++++ y r+++i+  + d+++ a+A
  gi|313127160|ref|YP_004037430.1|  90 RL-TGSVEEALRVGADAVSFHMNV---GSEFEPDQMTQLGELTEKAHRFGLPVLAMNYARGQDID-SQ-DAENLAHA 160
                                       88.*********************...************************************84.44.7******* PP

                                       HHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS..SHHHHHHHHHHHHHHHTHCEEEESHH CS
                              DeoC 157 arvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv..seedfletvedAvkeagasGvlsGRa 231
                                        r++ elGaD++K++++        + ae+f++v +a+++p vv++GG+  ++++  e+v+ A+ + ga+Gv++GR+
  gi|313127160|ref|YP_004037430.1| 161 VRLAEELGADVVKTSYT--------GEAETFERVCEATRLP-VVIAGGSrgTDRQTIEMVRGAM-DGGAAGVSMGRS 227
                                       *****************........99**************.********99999*********.************ PP

                                       HHTT CS
                              DeoC 232 ifqk 235
                                       ifq+
  gi|313127160|ref|YP_004037430.1| 228 IFQH 231
                                       **97 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   3.7e-07   0.00095       2     111 ..      96     188 ..      95     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.7e-07
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraiel 78 
                                       ++a + G+d+v +++  +  + +++ ++l el + + + gl + ++++  +   + +     +     ++l +a++l
  gi|313127160|ref|YP_004037430.1|  96 EEALRVGADAVSFHMNVGSEFEPDQMTQLGELTEKAHRFGLPVLAMNYARGQDIDSQ-----D----AENLAHAVRL 163
                                       78999*****************99************************999999766.....6....899******* PP

                                       HHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHH CS
                      AP_endonuc_2  79 aaaLGapllvlhpGtagagpkgseeeawerlae 111
                                       a++LGa+++ +           +e+e++er+ e
  gi|313127160|ref|YP_004037430.1| 164 AEELGADVVKTSYT--------GEAETFERVCE 188
                                       *********99844........66666666655 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   6.7e-06     0.017      85     223 ..     101     239 ..      91     241 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.7e-06
                                       TTESEEEEEGTGH....HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEEC CS
                         OMPdecase  85 ewadivtvhavaG....kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfva 157
                                        +ad+v  h+ +G     + +++l e  ek   r  l +  m+ + +++  + + ++++++a+r ++ e    G+ +
  gi|313127160|ref|YP_004037430.1| 101 VGADAVSFHMNVGsefePDQMTQLGELTEKAH-RFGLPVLAMNYARGQDIDS-QDAENLAHAVRLAE-E---LGADV 171
                                       57888888888883333457888888888887.5555555555555555555.37777777777777.5...57777 PP

                                       CCHTHHHHHHTTCSCEEEHHHTT....EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHH CS
                         OMPdecase 158 qetlnateedaddfihltpgigl....eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeae 223
                                        +t   t e a++f  + +  +l    + g+ g + q  ++   + + ga  + +GR+I++ +dp++ ++
  gi|313127160|ref|YP_004037430.1| 172 VKTSY-TGE-AETFERVCEATRLpvviAGGSRGTDRQTIEMVRGAMDGGAAGVSMGRSIFQHDDPEAITR 239
                                       77755.334.48999999999999987777888888887777778889*****************99776 PP

>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.3e-05     0.058      72     155 ..      85     177 ..      10     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                       SS-HHHHHHHHHHHHHCT-SEEEEEGG.....-.HHG...HHHHHHHHHHHTT-EEEEEEE....ESS----HHHHH CS
                       DHquinase_I  72 rkseeeylellrtaielgadyvDvElt.....eapee...skkrlieekreggtkvIvSyh....dfegtpsaeelk 136
                                       + +++     +++a+++gad v + +      e  ++   +  +l+e++++ g  v + +     d ++++ ae+l 
  gi|313127160|ref|YP_004037430.1|  85 DSNDKRLTGSVEEALRVGADAVSFHMNvgsefE--PDqmtQLGELTEKAHRFGLPVLAMNYargqDIDSQD-AENLA 158
                                       566666677789999999999999997777443..444587789**********99988776665555443.559** PP

                                       HHHHHHHHTT-SEEEEEE- CS
                       DHquinase_I 137 allekmqalgaDivKiavm 155
                                       + ++ +++lgaD+vK   +
  gi|313127160|ref|YP_004037430.1| 159 HAVRLAEELGADVVKTSYT 177
                                       ***************8766 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.5e-05     0.089     166     235 ..     170     246 ..     148     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                            DUF561 166 dliekslstlastye.iskkvslPvicasG...lsdvtvpl...alslgasGiGigsavsklndeeemvallseikk 235
                                       d++++s +  a t+e + ++++lPv+ a G       t+++   a+  ga+G+ +g+++ + +d e++  ++s +++
  gi|313127160|ref|YP_004037430.1| 170 DVVKTSYTGEAETFErVCEATRLPVVIAGGsrgTDRQTIEMvrgAMDGGAAGVSMGRSIFQHDDPEAITRAVSAVIH 246
                                       66667777667777548999*****98765111667899887778999*********************99998876 PP

>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00061       1.6      82     106 ..      85     109 ..      60     111 .. 0.86
   2 ?    1.3   0.0      0.14   3.5e+02      80     105 ..     149     174 ..     124     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00061
                        UvrA_inter  82 keersrlaesvetAlklgeglvivs 106
                                       +++++rl+ sve+Al++g + v ++
  gi|313127160|ref|YP_004037430.1|  85 DSNDKRLTGSVEEALRVGADAVSFH 109
                                       5689***************999875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                        UvrA_inter  80 vkkeersrlaesvetAlklgeglviv 105
                                       +++++ + la +v+ A +lg ++v  
  gi|313127160|ref|YP_004037430.1| 149 IDSQDAENLAHAVRLAEELGADVVKT 174
                                       56778899************999875 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.059   1.5e+02     146     168 ..      34      56 ..      30      59 .. 0.91
   2 ?   -0.6   0.0       0.3   7.6e+02     153     166 ..      94     107 ..      91     110 .. 0.90
   3 ?    6.4   0.0    0.0022       5.5     101     169 ..     153     226 ..     146     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.059
                                       SS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 146 GLietkedveealkaGaiavsts 168
                                       GL++ + +v+++ + Ga+av t 
  gi|313127160|ref|YP_004037430.1|  34 GLVDLETTVDAITRGGADAVLTQ 56 
                                       9*******************885 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.3
                                       HHHHHCTT.SSEEE CS
                      G3P_antiterm 153 dveealkaGaiavs 166
                                        veeal+ Ga+avs
  gi|313127160|ref|YP_004037430.1|  94 SVEEALRVGADAVS 107
                                       699**********9 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0022
                                       SHHHHHHHHHHHHHHT-SEEEEESGGGHHHHCTSTTS...EE.EEESS-....-SHHHHHHHCTT.SSEEEE-- CS
                      G3P_antiterm 101 DssalekalkqiekskpdavevlPglvpkvikeikkelkipi.iaGGLi....etkedveealkaGaiavstsn 169
                                       D + l +a++ +e+  +d+v       +++ +++++++++p+ iaGG      +t e v+ a++ Ga +vs ++
  gi|313127160|ref|YP_004037430.1| 153 DAENLAHAVRLAEELGADVVKTSYTGEAETFERVCEATRLPVvIAGGSRgtdrQTIEMVRGAMDGGAAGVSMGR 226
                                       77788889999999999999999888899*********999637888752222455778889999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1795.56
//
Query:       gi|313127161|ref|YP_004037431.1|  [L=294]
Description: tryptophan synthase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-94  313.5   0.0    8.5e-94  313.2   0.0    1.1  1  Trp_syntA     Tryptophan synthase alpha chain
      8e-05   22.2   0.2    0.00014   21.4   0.2    1.4  1  His_biosynth  Histidine biosynthesis protein
     0.0041   16.6   0.7      0.077   12.4   0.7    2.1  2  PcrB          PcrB family


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.2   0.0   1.4e-97   8.5e-94       7     250 ..      11     255 ..       6     280 .. 0.94

  Alignments for each domain:
  == domain 1  score: 313.2 bits;  conditional E-value: 1.4e-97
                                       TTB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHH CS
                         Trp_syntA   7 enraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrk 83 
                                       en aafvpy++agdpd+e+s+e+++ale++gadviElGlpfs+P+a+GP+Iq+a++r+L++g+t+++++e+vee++ 
  gi|313127161|ref|YP_004037431.1|  11 ENGAAFVPYLAAGDPDYESSIEYVEALERGGADVIELGLPFSEPIAEGPTIQNAVVRSLESGMTPDRFFEFVEELD- 86 
                                       799*************************************************************************. PP

                                       HCSSS-EEEEE-CHHHCCC-HHH....HCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHH CS
                         Trp_syntA  84 kevevPivlltylnlvlsygeer....flaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderl 156
                                         v+vP+v++ty+nl++++g+e+    f+++++e+g  g++vpDlP+eea++l+ea++++gl+lvf+vaptt+++rl
  gi|313127161|ref|YP_004037431.1|  87 --VDVPLVCMTYYNLIYRFGDESgprpFVEKAAEVGLSGFVVPDLPAEEADPLREACDEFGLDLVFIVAPTTQGDRL 161
                                       ..********************99999************************************************** PP

                                       HHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 157 kevveqaegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                       ++++eq++g+vYv++r GvTga++ v+ ++++++er+ +++  P+avGFGi+t +++++++ ++adG+ivGSalv++
  gi|313127161|ref|YP_004037431.1| 162 DRIMEQVSGYVYVQARLGVTGAQDDVSGQTESSLERVAEYD-IPKAVGFGIKTGDHAERIVaAGADGIIVGSALVDI 237
                                       ****************************************8.*****************999*************** PP

                                       HHCTTTSHHHHHHHHHHH CS
                         Trp_syntA 233 ieeeaeekeqalekleel 250
                                       ++e a+ ++q+ ++ ++ 
  gi|313127161|ref|YP_004037431.1| 238 VAEGASAPRQMQSNDAAA 255
                                       **9777777766554444 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   2.4e-08   0.00014      59     107 ..     189     236 ..     178     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.4e-08
                                       HHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                      His_biosynth  59 eanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                       ++  + +e++ae  +ip  vG GI++ +++e+++ agad +i+g+a v+
  gi|313127161|ref|YP_004037431.1| 189 GQTESSLERVAEY-DIPKAVGFGIKTGDHAERIVAAGADGIIVGSALVD 236
                                       4555677888877.********************************986 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.022   1.3e+02       8      37 ..      19      48 ..      14      53 .. 0.88
   2 !   12.4   0.7   1.3e-05     0.077     182     212 ..     204     235 ..     163     244 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.022
                                      EEEEE-TTSS-CHHHHHHHHCTT-SEEEEE CS
                              PcrB  8 hltklDPeeenpdEiveiviesgtDavmig 37
                                      +l   DP+ e   E ve++ ++g+D + +g
  gi|313127161|ref|YP_004037431.1| 19 YLAAGDPDYESSIEYVEALERGGADVIELG 48
                                      56667********************99765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.3e-05
                                       EEEEESS--SHHHHHHHHCC.SSEEEE-CHHH CS
                              PcrB 182 rlivGGGirsaEkAkevvea.ADvivvGnvve 212
                                          vG Gi+ +++A+++v a AD i+vG ++ 
  gi|313127161|ref|YP_004037431.1| 204 PKAVGFGIKTGDHAERIVAAgADGIIVGSALV 235
                                       3369************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2081.78
//
Query:       gi|313127162|ref|YP_004037432.1|  [L=415]
Description: tryptophan synthase subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-37  128.7   0.9    3.6e-37  128.4   0.9    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.9     2e-41   3.6e-37       4     294 .]      56     384 ..      53     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 2e-41
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                       g +pTP   ++rls+++ ++++ K+E+l ++g++K++ a   ++ +k   + + v+e+++G+hg a+A+aaa+l ++
  gi|313127162|ref|YP_004037432.1|  56 GGRPTPTQYAERLSERYDCDVYMKREDLVHGGAHKLNNALGQVLLAKYMGKERIVAETGAGQHGTATAMAAAHLDMP 132
                                       789*************************************99999888879999999999***************** PP

                                       EEEEEETTS-H...HHHHHHHHTT-EEEEE...CCHHHHHHHH.HHHHHHH.......STTCEE--TTTSHH...HH CS
                              PALP  81 vtivvpadasp...ekvallrllGaevvev...ggdydeavaa.aaelaae.......gegaylvsqfdnpt...vi 140
                                       +++++ + + +    +v ++rl G ev  v    g+ +ea +  +++ a +       +++++  ++        v 
  gi|313127162|ref|YP_004037432.1| 133 CEVYMGERDINrqrPNVFRMRLNGSEVNPVtvgRGTLKEAISEtMRDWATNventhyvIGSIVGPHP----FpvmVR 205
                                       *********95556****************9887888888888666777775333443333333344....244366 PP

                                       HHHHTHHHHHH....HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B. CS
                              PALP 141 egygtiglEil....eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs 213
                                       + ++ i  E      eq g+ pd v++++GgG++ +G  a + + + dv +++ve+ gs    +  +   + + +  
  gi|313127162|ref|YP_004037432.1| 206 DFQSVISEEARkqmrEQAGTLPDSVLACAGGGSNTMGAFAEFVA-DEDVSLYAVEAGGSTLEVDEEAGVAPNSAS-L 280
                                       66********877889999*************999999999997.6789*****888777666666222333333.2 PP

                                       ..........................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B- CS
                              PALP 214 ..........................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivve 264
                                                                 ++  +gl+   ++++   l+d+    +v + d++al a  +l + eg+++ 
  gi|313127162|ref|YP_004037432.1| 281 stgsegvlhgartkllqdrdgqimesHSVSSGLDYAGVGPELAHLVDEDRVLAVNIGDDDALTAFHRLSQLEGVIPA 357
                                       477777888889999999**888888888888888899999999********************************* PP

                                       HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 265 pssaaalaalklreagelkegdrvvviltg 294
                                         +a+a+a l  ++ +el++   v+v ++g
  gi|313127162|ref|YP_004037432.1| 358 LETAHAFAYL-EEHHEELGDT--VLVNVSG 384
                                       **********.7777777766..9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2917.24
//
Query:       gi|313127163|ref|YP_004037433.1|  [L=260]
Description: indole-3-glycerol phosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-70  236.0   0.0      4e-70  235.9   0.0    1.0  1  IGPS           Indole-3-glycerol phosphate synthase
    2.4e-07   30.1   1.0      1e-06   28.0   1.2    1.7  2  FMN_dh         FMN-dependent dehydrogenase
    0.00029   20.1   0.5     0.0056   15.9   0.2    2.6  2  NanE           Putative N-acetylmannosamine-6-phosphate epime
    0.00071   19.4   0.1     0.0022   17.8   0.0    1.8  3  QRPTase_C      Quinolinate phosphoribosyl transferase, C-term
     0.0015   18.0   0.0      0.029   13.8   0.0    2.4  2  His_biosynth   Histidine biosynthesis protein
     0.0025   17.1   0.1     0.0051   16.1   0.0    1.5  2  DHO_dh         Dihydroorotate dehydrogenase
     0.0081   15.6   0.0      0.018   14.5   0.0    1.5  1  PcrB           PcrB family
  ------ inclusion threshold ------
        0.1   11.8   0.2        2.6    7.2   0.1    2.3  2  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
       0.18   11.1   2.3       0.33   10.2   0.7    2.3  2  ThiG           Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.9   0.0     2e-73     4e-70      31     250 ..      30     245 ..       6     249 .. 0.93

  Alignments for each domain:
  == domain 1  score: 235.9 bits;  conditional E-value: 2e-73
                                       SS-SS-HHHHCHCH..TTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHH CS
                              IGPS  31 akpkrsfaeaLres..ekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrevr 105
                                       a  +rsf++a++ +  + ++ ++aEvK +SP++   r+d dp+e+A+++ ++gA+a+SVLte+++F Gs+e+Lr++r
  gi|313127163|ref|YP_004037433.1|  30 AVTARSFPDAVAATeaAGRIPVVAEVKPTSPTTAGERTD-DPVELAREMVAGGATALSVLTEPDHFGGSVESLRRIR 105
                                       6789*******9988899***************999999.************************************* PP

                                       HH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEE CS
                              IGPS 106 qavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeeeleralklgakii 182
                                       +av++pvlrKdF+++e+q++   a+ +d++LLi+++l d++ ++l++aak+ g+++LvEvhd++el ral++ga+ii
  gi|313127163|ref|YP_004037433.1| 106 EAVDVPVLRKDFVVNESQLD---AVESDLVLLIARFLGDDL-SDLVTAAKERGFQPLVEVHDRDELGRALDAGADII 178
                                       ********************...89*************987.9********************************** PP

                                       EEESEETTTTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHH CS
                              IGPS 183 GvNnRnLktlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedveka 250
                                       GvNnR+L tl vdl+t+e++a++vp+dv+l aeSG++++ed+++++++g++a+L+G+++m+  dv+++
  gi|313127163|ref|YP_004037433.1| 179 GVNNRDLATLAVDLETFESVAPHVPDDVTLLAESGVTSAEDARRMRAAGADALLIGTAIMDG-DVRAN 245
                                       ************************************************************98.56655 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.26   5.2e+02     202     229 ..      92     122 ..      32     131 .. 0.66
   2 !   28.0   1.2   5.2e-10     1e-06     224     306 ..     161     240 ..     149     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.26
                                       C-...-HHHHHHHHHHHSSEEEEEEE-SHHH CS
                            FMN_dh 202 sl...twddikwlreqtklplvvKGvltaed 229
                                       +    + ++++++re++++p++ K  +  e 
  gi|313127163|ref|YP_004037433.1|  92 DHfggSVESLRRIREAVDVPVLRKDFVVNES 122
                                       3344467888888888888888776655555 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 5.2e-10
                                       E-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEES CS
                            FMN_dh 224 vltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllG 300
                                       v + ++  ra++aG+d+i v N   R l +    +++  +++ +v++++++l+ +G+++ +D+ +  a GAda l+G
  gi|313127163|ref|YP_004037433.1| 161 VHDRDELGRALDAGADIIGVNN---RDLATLAVDLETFESVAPHVPDDVTLLAESGVTSAEDARRMRAAGADALLIG 234
                                       66778889*************9...9*************************************************** PP

                                       HHHHHH CS
                            FMN_dh 301 Rpflyg 306
                                        +++ g
  gi|313127163|ref|YP_004037433.1| 235 TAIMDG 240
                                       998766 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.47   9.3e+02     144     168 ..      48      72 ..      38      90 .. 0.64
   2 !   15.9   0.2   2.8e-06    0.0056      80     178 ..     142     239 ..      71     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.47
                                       T--EEEES---SHHHHHHHHTT--S CS
                              NanE 144 glkviaeGrintPekakkaieiGvd 168
                                        + v+ae +  +P  a + ++  v+
  gi|313127163|ref|YP_004037433.1|  48 RIPVVAEVKPTSPTTAGERTDDPVE 72 
                                       4678888888888888776665543 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.8e-06
                                       -HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SH CS
                              NanE  80 tieelikkikekyqllmaDistleeglvakklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrintP 156
                                       ++ +l+ + ke++   + ++   +e   a ++G+di+G      ++ + +  + f+ v   + ++++++ae  + + 
  gi|313127163|ref|YP_004037433.1| 142 DLSDLVTAAKERGFQPLVEVHDRDELGRALDAGADIIGVNNRDLATLAVD-LETFESVAPHVPDDVTLLAESGVTSA 217
                                       677889999999999999999999999***********998887776655.556999999999************** PP

                                       HHHHHHHTT--SEEEE-HHHH- CS
                              NanE 157 ekakkaieiGvdavvvGsaitr 178
                                       e a+++   G+da+ +G+ai  
  gi|313127163|ref|YP_004037433.1| 218 EDARRMRAAGADALLIGTAIMD 239
                                       *******************975 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   2.8e+03      66     100 ..      12      46 ..       7      87 .. 0.64
   2 ?   -2.9   0.0       2.5     5e+03      63      81 ..      94     112 ..      92     134 .. 0.67
   3 !   17.8   0.0   1.1e-06    0.0022      84     159 ..     158     238 ..     135     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHT CS
                         QRPTase_C  66 iveavksvreavdkevkievevesleeleevleae 100
                                       ++++++++re  +   ++ v ++s  ++ ++ ea 
  gi|313127163|ref|YP_004037433.1|  12 VRSILDAARERPGGDEPVAVTARSFPDAVAATEAA 46 
                                       55566666666655545666666666666666654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                                       HSSHHHHHHHHHHHHTTTS CS
                         QRPTase_C  63 agsiveavksvreavdkev 81 
                                       +g+ ve ++++reavd  v
  gi|313127163|ref|YP_004037433.1|  94 FGGSVESLRRIREAVDVPV 112
                                       6777788888888876544 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 1.1e-06
                                       EEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT.....SEEEEESS--TTTHHHHHCTT-SEEEEC CS
                         QRPTase_C  84 evevesleeleevleaeadiimLDnfsveelkkaveelkeknkr.....vlievSGgvtlenveeyaksgvdvisvg 155
                                        vev+  +el ++l a+adii + n +  +l+  +e+ ++ +++      l+  SG  + e+ + ++  g d++ +g
  gi|313127163|ref|YP_004037433.1| 158 LVEVHDRDELGRALDAGADIIGVNNRDLATLAVDLETFESVAPHvpddvTLLAESGVTSAEDARRMRAAGADALLIG 234
                                       69*****************************99999999999988889777788999999***************** PP

                                       HHCH CS
                         QRPTase_C 156 alth 159
                                       +++ 
  gi|313127163|ref|YP_004037433.1| 235 TAIM 238
                                       9875 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.073   1.5e+02      26      49 ..      65      88 ..      51     114 .. 0.70
   2 !   13.8   0.0   1.5e-05     0.029     179     227 ..     191     241 ..     162     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.073
                                      EETTSHHHHHHHHHHHT-SEEEEE CS
                      His_biosynth 26 ryagdpvelakryeeegadelhvv 49
                                      +  +dpvela++  + ga+ l v+
  gi|313127163|ref|YP_004037433.1| 65 ERTDDPVELAREMVAGGATALSVL 88
                                      667899999999999999999886 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
                                       -HHHHHHHHHHH..SSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTS CS
                      His_biosynth 179 dleltkelaeav..kipviasGGvgsledlkelksegvdavivgsalyege 227
                                       dle  +++a +v  +++++a  Gv+s ed ++++++g+da+++g+a+ +g+
  gi|313127163|ref|YP_004037433.1| 191 DLETFESVAPHVpdDVTLLAESGVTSAEDARRMRAAGADALLIGTAIMDGD 241
                                       666666666666666777777777777777777777777777777777665 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.3   4.6e+03     259     275 ..      74      90 ..      72     100 .. 0.80
   2 !   16.1   0.0   2.6e-06    0.0051     231     279 ..     192     240 ..     174     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.3
                                       HHHHHHHTECEEEESHH CS
                            DHO_dh 259 alekieaGAslvqvyta 275
                                       a e++  GA+++ v t+
  gi|313127163|ref|YP_004037433.1|  74 AREMVAGGATALSVLTE 90 
                                       56899999999999886 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHH CS
                            DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfe 279
                                       l++  +++ ++ +++ +++  G++s+eDa  +  aGA ++ ++ta++  
  gi|313127163|ref|YP_004037433.1| 192 LETFESVAPHVPDDVTLLAESGVTSAEDARRMRAAGADALLIGTAIMDG 240
                                       5677888999999********************************9544 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     9e-06     0.018     178     215 ..     203     241 ..     189     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9e-06
                                       HSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                              PcrB 178 lekarlivGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                        ++ +l+   G+ saE+A+++  a AD++++G+++ + d
  gi|313127163|ref|YP_004037433.1| 203 PDDVTLLAESGVTSAEDARRMRAAgADALLIGTAIMDGD 241
                                       578899999**************9**********99876 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.047        93     140     175 ..     145     180 ..     143     194 .. 0.90
   2 ?    7.2   0.1    0.0013       2.6     152     179 ..     210     237 ..     201     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.047
                     PEP_hydrolase 140 elikkAheldllttayvfneeearamaeaGadviva 175
                                       +l+ +A+e+++  +  v +++e  +  +aGad+i +
  gi|313127163|ref|YP_004037433.1| 145 DLVTAAKERGFQPLVEVHDRDELGRALDAGADIIGV 180
                                       5788999999999999*****************976 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                     PEP_hydrolase 152 ttayvfneeearamaeaGadvivahlGl 179
                                       + + v+++e+ar+m +aGad++ +   +
  gi|313127163|ref|YP_004037433.1| 210 AESGVTSAEDARRMRAAGADALLIGTAI 237
                                       5556899**************9987655 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.25     5e+02     136     178 ..      73     112 ..      36     127 .. 0.63
   2 ?   10.2   0.7   0.00017      0.33     165     209 ..     193     239 ..     102     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.25
                                       HHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-B CS
                              ThiG 136 larrleevGcaavmPlaapiGsglGllnkealkiiieeakvPv 178
                                       lar +   G++a+  l+ p   g    + e l+ i+e ++vPv
  gi|313127163|ref|YP_004037433.1|  73 LAREMVAGGATALSVLTEPDHFGG---SVESLRRIREAVDVPV 112
                                       344444444444444444422221...2344555555556665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                                       HHHHHHHHH-..SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
                              ThiG 165 ealkiiieea..kvPvivDAGigspsdaaqamelGadavllntavae 209
                                       e+++ +  ++  +v ++ + G+ s++da      Gada+l+ ta+  
  gi|313127163|ref|YP_004037433.1| 193 ETFESVAPHVpdDVTLLAESGVTSAEDARRMRAAGADALLIGTAIMD 239
                                       45555666666689999***************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1867.88
//
Query:       gi|313127164|ref|YP_004037434.1|  [L=150]
Description: methylated-DNA--protein-cysteine methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-08   34.2   0.0    3.2e-08   33.6   0.0    1.3  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.8e-12   3.2e-08       4      64 ..      74     138 ..      72     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.8e-12
                                       HHHHHHHTTS-TT-BEEHHHHHHHTT.....TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCT CS
                     DNA_binding_1   4 qrVwellrqIpyGkvttYgeiAkllgk....pkaaraVgqalaanplailvPcHRVvgadgklgg 64 
                                       +rV++++r+IpyG+++    + +++g+    +  +    +al++np+++++P HRV  a g++ +
  gi|313127164|ref|YP_004037434.1|  74 RRVLDAVRNIPYGETIALRRVIRMAGMdpedEDDVATARSALRENPVPLFIPDHRVDDAPGAIPE 138
                                       79************************887777777888889***************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 974.02
//
Query:       gi|313127165|ref|YP_004037435.1|  [L=324]
Description: metal-dependent membrane protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-10   41.8  10.1      1e-10   41.8  10.1    2.3  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.02   3.6e+02      40      75 ..     137     187 ..     117     197 .. 0.66
   2 !   41.8  10.1   5.6e-15     1e-10       5      91 ..     220     309 ..     214     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHCSGGGHHH.H..............HHHHHHHHHHHHHHHH CS
                              CPBP  40 ailissilFglaHlpngps.v..............llaalaGlvlgylylk 75 
                                        +++s  lF+la l  +++                +  +++G++lg++ + 
  gi|313127165|ref|YP_004037435.1| 137 NVAFSQGLFALALLGGAWYtQvpasafgagteafsVSGLFVGVALGLALYA 187
                                       567788888888888877743455555555555555555566666655554 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 5.6e-15
                                       HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH...S-HHHHHHHHHHHHHCSGGGHHH.HHHHHHHHHHHHHHHHHTT- CS
                              CPBP   5 llvfllalllapllEEllfRglllqllqer..gsstlailissilFglaHlpngps.vllaalaGlvlgylylktgs 78 
                                       ++++l++l + + +EEllfRg l+  +++    s++l  +iss++F+l H ++g   v+++ ++G+vl++ ++ t s
  gi|313127165|ref|YP_004037435.1| 220 VALLLVILPIIAGFEELLFRGALVGVFAAGfgISPWLLAVISSLAFALGHGAQGRLgVVVTGALGFVLAAGFILTES 296
                                       3344445555556**************999774448*****************8888******************** PP

                                       HHHHHHHHHHHHH CS
                              CPBP  79 llaaillHallnl 91 
                                       l++++++H l+n+
  gi|313127165|ref|YP_004037435.1| 297 LFVVVVAHYLVNA 309
                                       ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2035.92
//
Query:       gi|313127166|ref|YP_004037436.1|  [L=696]
Description: lon-b peptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-33  114.1   2.8      1e-32  113.4   2.8    1.3  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    1.4e-29  103.3   0.0    7.1e-22   77.9   0.0    2.2  2  AAA_32           AAA domain
    5.1e-18   65.2   0.1    9.7e-11   41.4   0.1    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    7.8e-15   55.0   0.0    1.8e-08   34.3   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    2.2e-10   40.7   0.0    0.00072   19.6   0.0    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
    1.7e-09   37.6   0.3      4e-09   36.4   0.3    1.6  1  ChlI             Subunit ChlI of Mg-chelatase
    1.5e-07   31.9   0.0      0.023   15.1   0.0    2.7  2  AAA              ATPase family associated with various cellul
    1.6e-07   30.7   0.1     0.0077   15.3   0.0    2.3  2  MCM              MCM P-loop domain
    2.8e-06   27.2   0.1      0.004   16.9   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.3e-05   24.6   0.1       0.06   12.6   0.0    2.4  2  TIP49            TIP49 P-loop domain
    8.1e-05   22.9   0.0     0.0024   18.2   0.0    2.3  2  AAA_22           AAA domain
     0.0002   20.9   0.1    0.00057   19.4   0.0    1.7  2  AAA_7            P-loop containing dynein motor region
    0.00031   20.9   0.0       0.44   10.7   0.0    2.3  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00033   21.0   0.5    0.00099   19.5   0.0    2.0  2  MCM_lid          MCM AAA-lid domain
    0.00042   20.2   0.1       0.54   10.1   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00085   18.3   0.0      0.065   12.1   0.0    2.2  2  AAA_PrkA         PrkA AAA domain
     0.0011   19.3   0.0       0.62   10.4   0.0    2.6  2  AAA_19           AAA domain
     0.0018   18.0   0.0      0.075   12.7   0.0    2.3  2  AAA_30           AAA domain
     0.0046   17.1   0.0          1    9.5   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.025   14.1   0.0    1.5  1  PhoH             PhoH-like protein
      0.018   15.2   0.0      0.063   13.4   0.0    2.0  1  AAA_33           AAA domain
      0.022   13.9   0.0      0.041   13.0   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
      0.032   14.8   0.0      0.088   13.3   0.0    1.7  1  ABC_tran         ABC transporter
      0.043   14.2   0.0       0.35   11.2   0.0    2.3  2  AAA_16           AAA ATPase domain
      0.048   12.6   0.0      0.079   11.9   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.051   13.9   0.1      0.088   13.1   0.1    1.3  1  TctB             Tripartite tricarboxylate transporter TctB f
      0.054   13.2   0.0       0.12   12.1   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.079   13.5   0.0       0.34   11.5   0.0    2.1  1  AAA_18           AAA domain
        0.1   12.5   0.0        0.2   11.6   0.0    1.5  1  NACHT            NACHT domain
       0.12   11.5   0.0       0.21   10.6   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.12   11.2   0.0       0.22   10.4   0.0    1.3  1  AAA_10           AAA-like domain


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   2.8   1.7e-35     1e-32       7     204 ..     468     662 ..     462     663 .. 0.84

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 1.7e-35
                                       THHHH-S-SS--SSSSS--BSSEEEEEEEE.TTEEEEEEEEEEEES..S-S-EEEEES--HHHHHHHHHHHHHHTSS CS
                             Lon_C   7 leellGkkrfrseeaekedqvGvvtGlawt.evGGdlltieavllp..gkgklkltGklgdvmkesaqaalsyvrsr 80 
                                        ++++ +++  + ++    q G v Gla   e  G +l + a ++p  g g+++ tG+l+++ +e++    +++++ 
  gi|313127166|ref|YP_004037436.1| 468 ADDYIQRRKDYELQVADGYQAGRVNGLAVMgEDSGIMLPVMAEVTPsqGPGEVIATGQLKEMAQEAVDNVSAIIKKF 544
                                       556665555444455577899******975277899999977776633778********999999888777776643 PP

                                       -GGGSS-SS-TTT-EEEEE.E-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHH CS
                             Lon_C  81 aeelgidkevfekkdihih.vPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekll 156
                                             ++e+ +++dihi  v +G    dG sa +t+ata++s+l ++ v++ +amtG +++rG vlp+GG+  k+ 
  gi|313127166|ref|YP_004037436.1| 545 ------SDENISERDIHIQfVQAGQGGVDGDSASITVATAVISALEEVGVDQSLAMTGSLSVRGDVLPVGGVTHKIE 615
                                       ......33456789****636789999************************************************** PP

                                       HHHHTT-SBEEEEGGGGGGTTTS-HHHHTS-B--EESBHHHHHHHHB- CS
                             Lon_C 157 aakragikkvilPkenekdlediPeevreeleiilveevdevlkaalv 204
                                       aa ++g +++i+P++n +d+  i +e +e +eii+v++++evl+ al+
  gi|313127166|ref|YP_004037436.1| 616 AAAKSGCERIIIPQANMQDVM-IEDEYKEMVEIIPVSHISEVLDIALE 662
                                       *******************96.99*********************996 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.9e-08   2.8e-05       8      92 ..      91     170 ..      84     180 .. 0.83
   2 !   77.9   0.0   1.2e-24   7.1e-22     280     507 ..     230     456 ..     227     462 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.9e-08
                            AAA_32   8 eeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpaG 84 
                                       +++igqe A + +   +k  k+  ++ ++G++gtG+++l+k + e    k +  +D++  +n d+ ++Pk+  +paG
  gi|313127166|ref|YP_004037436.1|  91 DQVIGQEHARDVV---MKAAKQRRHVMMIGSPGTGKSMLAKAMSELLP-K-EELQDVLVYHNPDDGNNPKVRTVPAG 162
                                       7899999998766...66677888*************99998876654.4.446788888***************** PP

                            AAA_32  85 kGkelkkd 92 
                                       kG++  + 
  gi|313127166|ref|YP_004037436.1| 163 KGEQIVEA 170
                                       **998665 PP

  == domain 2  score: 77.9 bits;  conditional E-value: 1.2e-24
                            AAA_32 280 vnvlvdnsetegaPVvvednptyanLfGkieyesemg..alvtdftlIkaGaLhkAnGGyLildaedlLeeplaWea 354
                                        n++v+n++t+ aP    +  +   L+G + ++  +   + +  + ++++Ga+hkAn G+L +d  + L    + ++
  gi|313127166|ref|YP_004037436.1| 230 PNLVVNNADTTTAPFEDATGAHAGALLGDVRHDPFQSggMETPSHDRVEPGAIHKANKGVLFIDEINTLD-IRSQQH 305
                                       59*****************************9975433588889********************999996.6788** PP

                            AAA_32 355 LkraLrskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteen 431
                                       L  a++++e +i       + +s    + ep+p d   i  G+ +  + ++ +     k +  ++ +dd++e t+e 
  gi|313127166|ref|YP_004037436.1| 306 LMTAIQEGEFSITGQ---SERSSGAMVQTEPVPTDFIMIAAGNLDAMENMHPALRSRIKGYGYEVYMDDTIEDTPEM 379
                                       *************53...4467888999*******9999999888777777777777778889************** PP

                            AAA_32 432 ekkyarfiasivkkek.llpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekA 507
                                        +ky rf+a+ v+k++ l+ f+++a++++i ++ r a+++ +l+++++++  l+r +  +a+ e+a+ v+++hV +A
  gi|313127166|ref|YP_004037436.1| 380 RRKYTRFVAQEVQKDGrLPAFNAEAIEEVILEARRRAGRKGHLTLELRNLGGLVRVSGDIARAENADFVTRDHVLQA 456
                                       *********99988763888******************************************************999 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   1.7e-13   9.7e-11       3      55 ..      91     143 ..      89     149 .. 0.93
   2 !   21.3   0.0   2.5e-07   0.00014      96     158 ..     276     346 ..     266     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.7e-13
                      Mg_chelatase   3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55 
                                        +v+Gqe+a+ ++  aa  + +++++G+pG+GK+mlak++++llp+ + +++l
  gi|313127166|ref|YP_004037436.1|  91 DQVIGQEHARDVVMKAAKQRRHVMMIGSPGTGKSMLAKAMSELLPKEELQDVL 143
                                       689******************************************99988876 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.5e-07
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtis....rakakv....efparfqlvaamNp 158
                                       +++pG+i +a++GvLf+DE+  ++ +  + L + +++ge +i+    r++  +      p++f ++aa N+
  gi|313127166|ref|YP_004037436.1| 276 RVEPGAIHKANKGVLFIDEINTLDIRSQQHLMTAIQEGEFSITgqseRSSGAMvqtePVPTDFIMIAAGNL 346
                                       789************************************99972222332222111146777777777775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.3e-06    0.0019      11      49 ..      99     137 ..      91     150 .. 0.84
   2 !   34.3   0.0   3.1e-11   1.8e-08      85     130 ..     278     323 ..     264     355 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTT CS
                   Sigma54_activat  11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrk 49 
                                       +++ + k+ak++ +v++ G  GtGK++la+a+ e  +++
  gi|313127166|ref|YP_004037436.1|  99 ARDVVMKAAKQRRHVMMIGSPGTGKSMLAKAMSELLPKE 137
                                       567788999***********************9876654 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 3.1e-11
                                       BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                   Sigma54_activat  85 kkGlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       + G+++ka++G+lf+Dei++l+++ Q++L++++qege++  G+s+ 
  gi|313127166|ref|YP_004037436.1| 278 EPGAIHKANKGVLFIDEINTLDIRSQQHLMTAIQEGEFSITGQSER 323
                                       45*************************************9998765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-06   0.00072       1      28 [.     112     140 ..     112     149 .. 0.85
   2 !   18.0   0.0   3.8e-06    0.0022      65     137 ..     286     359 ..     257     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nreve 28 
                                       +v+++G pGtgKs+la+ ++++l + e++
  gi|313127166|ref|YP_004037436.1| 112 HVMMIGSPGTGKSMLAKAMSELLpKEELQ 140
                                       79*********************765555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.8e-06
                                       G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---..........-EEEEEESS--.-TT-TTHHHHTT CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller....frviatanpldrslnelspalrsR 137
                                       ++ +l++DE+++++   ++ L++ + e ++++    e+ + +  + +e+    f  ia++n      +++ palrsR
  gi|313127166|ref|YP_004037436.1| 286 NKGVLFIDEINTLDIRSQQHLMTAIQEGEFSITGQSERSSGAMVQ-TEPvptdFIMIAAGNLDA--MENMHPALRSR 359
                                       788****************************88888887777643.3337899*****999888..78889*****9 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.3   6.9e-12     4e-09       2     121 .]     510     631 ..     509     631 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 6.9e-12
                              ChlI   2 evdvskglpkftivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadl.kkeGsafDLpiAigilaaleqi 76 
                                       ev+ s+g  ++  +G +++  +e+ + v +++k+ s+ ++ ++ i +    a     +G + ++++A ++++ale++
  gi|313127166|ref|YP_004037436.1| 510 EVTPSQGPGEVIATGQLKEMAQEAVDNVSAIIKKfSDENISERDIHIQFVQAGQgGVDGDSASITVATAVISALEEV 586
                                       67778888889999*******************989999*********9888652689******************* PP

                              ChlI  77 eaeeetlflGeLsldGslrpvkgvlpialaakkegikkvivpken 121
                                        +++++ + G Ls  G++ pv gv+  + aa+k+g++++i+p++n
  gi|313127166|ref|YP_004037436.1| 587 GVDQSLAMTGSLSVRGDVLPVGGVTHKIEAAAKSGCERIIIPQAN 631
                                       ******************************************998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0    0.0001      0.06       1      22 [.     113     134 ..     113     185 .. 0.83
   2 !   15.1   0.0   3.9e-05     0.023      55     125 ..     284     361 ..     270     364 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                                       EEEESSTTSSHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel 22 
                                       v+++G pGtGK++laka+ + l
  gi|313127166|ref|YP_004037436.1| 113 VMMIGSPGTGKSMLAKAMSELL 134
                                       6899*************97765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.9e-05
                                       HTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS.. CS
                               AAA  55 ekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr.. 111
                                       +  ++ +lfiDEi  l  ++           +++L+t++++ + +                    ++i+i+a+n   
  gi|313127166|ref|YP_004037436.1| 284 KA-NKGVLFIDEINTLDIRS-----------QQHLMTAIQEGEFSitgqserssgamvqtepvPTDFIMIAAGNLda 348
                                       23.469**********6666...........8999999998888888999999999*******788*********** PP

                                       GGGSTHHHHSTTSS CS
                               AAA 112 pdkldpallrgRfd 125
                                       ++++ pal+ +R++
  gi|313127166|ref|YP_004037436.1| 349 MENMHPALR-SRIK 361
                                       *********.9975 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   7.7e-05     0.045      51      84 ..     104     137 ..      85     142 .. 0.77
   2 !   15.3   0.0   1.3e-05    0.0077     112     153 ..     277     318 ..     242     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-05
                                       SSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSE CS
                               MCM  51 ktklrgdinvllvgdpgtaKsqlLkyveklapra 84 
                                        +  + + +v+++g pgt+Ks l k++++l+p+ 
  gi|313127166|ref|YP_004037436.1| 104 MKAAKQRRHVMMIGSPGTGKSMLAKAMSELLPKE 137
                                       34477889********************999975 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.3e-05
                                       EEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEE CS
                               MCM 112 leaGalvladkGvcciDefdkmkeedrsalhEamEqqtisia 153
                                       +e Ga+  a+kGv+ iDe++  + + ++ l+ a+ + + si+
  gi|313127166|ref|YP_004037436.1| 277 VEPGAIHKANKGVLFIDEINTLDIRSQQHLMTAIQEGEFSIT 318
                                       79********************************99999986 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     7e-06     0.004       5      55 ..      89     132 ..      85     140 .. 0.85
   2 !    7.7   0.0    0.0048       2.8      84     119 ..     286     321 ..     281     361 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7e-06
                            RuvB_N   5 sleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiak 55 
                                        +++ igqe+ ++   ++++aak+r+    hv+++G+PG Gk+ lak +++
  gi|313127166|ref|YP_004037436.1|  89 LVDQVIGQEHARD---VVMKAAKQRR----HVMMIGSPGTGKSMLAKAMSE 132
                                       4578899999885...899*****97....9***************98876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0048
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigk 119
                                       +k vlfidei  l+   ++ l +a+++ ++ i+ ++
  gi|313127166|ref|YP_004037436.1| 286 NKGVLFIDEINTLDIRSQQHLMTAIQEGEFSITGQS 321
                                       678**********************99888886433 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0    0.0001      0.06      19      75 ..      86     135 ..      52     143 .. 0.78
   2 !    9.3   0.0     0.001      0.58     279     303 ..     287     311 ..     278     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  19 aekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelg 75 
                                       +++  + ++Gq++ar+   v+++  k++    r v++ G +gtGk+ la a+s+ l 
  gi|313127166|ref|YP_004037436.1|  86 PDRLVDQVIGQEHARD---VVMKAAKQR----RHVMMIGSPGTGKSMLAKAMSELLP 135
                                       3444568999999996...666666665....689*****************98775 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.001
                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhmlDiecfsylnrale 303
                                       +GvlfiDe++ lDi +  +l  a+ 
  gi|313127166|ref|YP_004037436.1| 287 KGVLFIDEINTLDIRSQQHLMTAIQ 311
                                       7***************999999885 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.1e-06    0.0024       3      38 ..     108     148 ..     104     190 .. 0.79
   2 ?    2.0   0.0       0.4   2.3e+02      86     111 ..     282     308 ..     269     318 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.1e-06
                            AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaee.....e 38 
                                       k++++++ +G +GtGK++l++ + e l++e+ ++      +
  gi|313127166|ref|YP_004037436.1| 108 KQRRHVMMIGSPGTGKSMLAKAMSELLPKEELQDVlvyhnP 148
                                       5899***********************98887655555440 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.4
                            AAA_22  86 lraravielliiDEaqhlr..seealee 111
                                       ++++ + ++l iDE+  l+  s+++l +
  gi|313127166|ref|YP_004037436.1| 282 IHKANK-GVLFIDEINTLDirSQQHLMT 308
                                       556666.**********98875666654 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   9.9e-07   0.00057      26      64 ..     103     141 ..      89     147 .. 0.88
   2 ?   -2.6   0.0       5.6   3.3e+03     100     111 ..     286     297 ..     283     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.9e-07
                             AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkldkekyls 64 
                                       + +  k++++v+++G+ GtGK++++k + + l+ke+++ 
  gi|313127166|ref|YP_004037436.1| 103 VMKAAKQRRHVMMIGSPGTGKSMLAKAMSELLPKEELQD 141
                                       556789***************************999875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.6
                             AAA_7 100 kklvvFvDDlnm 111
                                       +k v+F+D++n 
  gi|313127166|ref|YP_004037436.1| 286 NKGVLFIDEINT 297
                                       6789******96 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0063       3.7      14      44 ..     103     133 ..      97     150 .. 0.85
   2 !   10.7   0.0   0.00076      0.44      65      97 ..     282     314 ..     261     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0063
                                       HHHHHT-SS-EEEEEETT--HHHHHHCC--T CS
                   Sigma54_activ_2  14 LeqaaqsklpvfltGekGsgkelvArlLhkn 44 
                                       + +aa++   v ++G +G+gk++ A+++++ 
  gi|313127166|ref|YP_004037436.1| 103 VMKAAKQRRHVMMIGSPGTGKSMLAKAMSEL 133
                                       5688999999****************99875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00076
                                       HHHTTTSEEEEEE-TT--HHHHHHHHHHHHHHT CS
                   Sigma54_activ_2  65 leqakggtLylkdiadlskaeqkeLlellakae 97 
                                       + +a+ g+L++ +i+ l+   q++L+ +++++e
  gi|313127166|ref|YP_004037436.1| 282 IHKANKGVLFIDEINTLDIRSQQHLMTAIQEGE 314
                                       56899*************************976 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.7e-06   0.00099      17      79 ..     396     456 ..     379     458 .. 0.85
   2 ?   -2.1   0.1       9.4   5.4e+03      22      37 ..     463     478 ..     460     487 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.7e-06
                                       BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHH CS
                           MCM_lid  17 klseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveea 79 
                                       +l    +e+++e+ +e R+++  + + +++   R+L  l+R+s  +A+ +  ++vt+++v +a
  gi|313127166|ref|YP_004037436.1| 396 RLPAFNAEAIEEVILEARRRAG-R-KGHLTLELRNLGGLVRVSGDIARAENADFVTRDHVLQA 456
                                       57777889999999*****994.4.799********************************887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.4
                                       HHHHHHHHHHHHHHHH CS
                           MCM_lid  22 akeklseaYvelRkee 37 
                                        +++l++ Y++ Rk+ 
  gi|313127166|ref|YP_004037436.1| 463 IEQQLADDYIQRRKDY 478
                                       678999*******976 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0063       3.6       1      23 [.     112     134 ..     112     143 .. 0.91
   2 !   10.1   0.0   0.00093      0.54      64      99 ..     288     323 ..     270     355 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0063
                             AAA_3   1 hvllegvPGlaktllvkalakal 23 
                                       hv++ g PG++k +l+ka+++ l
  gi|313127166|ref|YP_004037436.1| 112 HVMMIGSPGTGKSMLAKAMSELL 134
                                       9******************9987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00093
                             AAA_3  64 nllladeinrappktqsalleameerqvtvegethk 99 
                                        +l+ dein    ++q  l+ a++e + +++g++ +
  gi|313127166|ref|YP_004037436.1| 288 GVLFIDEINTLDIRSQQHLMTAIQEGEFSITGQSER 323
                                       5899***********************999987654 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.038        22      76     115 ..      98     137 ..      86     151 .. 0.78
   2 !   12.1   0.0   0.00011     0.065     227     267 ..     280     320 ..     253     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.038
                          AAA_PrkA  76 yfraaaqrleerkqilyllGPvggGksslverlkklleaa 115
                                       + r   ++  ++++ ++++G  g+Gks l++++ +ll ++
  gi|313127166|ref|YP_004037436.1|  98 HARDVVMKAAKQRRHVMMIGSPGTGKSMLAKAMSELLPKE 137
                                       556677888888999999**************99888654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00011
                          AAA_PrkA 227 GalnranrGllefvemfkadikvlhplltatqegnykstek 267
                                       Ga+ +an+G+l   e+   di+   +l+ta qeg+++ t++
  gi|313127166|ref|YP_004037436.1| 280 GAIHKANKGVLFIDEINTLDIRSQQHLMTAIQEGEFSITGQ 320
                                       99**********************************98876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0011      0.62       7      37 ..     107     137 ..     100     147 .. 0.79
   2 ?    5.9   0.0     0.025        15     102     129 ..     285     313 ..     233     324 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvel 37 
                                       a +++++++++ pGtGK+ + k++ +ll ++
  gi|313127166|ref|YP_004037436.1| 107 AKQRRHVMMIGSPGTGKSMLAKAMSELLPKE 137
                                       678999************9988888777665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.025
                            AAA_19 102 eee.llivDEfqdvd.elqyrLlkallgek 129
                                       +++ +l++DE+  +d   q++L+ a+  e+
  gi|313127166|ref|YP_004037436.1| 285 ANKgVLFIDEINTLDiRSQQHLMTAIQ-EG 313
                                       34459******************9998.44 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00013     0.075       9      46 ..     102     138 ..      95     148 .. 0.77
   2 ?    2.7   0.0      0.16        93      87     115 ..     285     313 ..     244     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                            AAA_30   9 avealltsgdrvavltGpAGtGKttalkalreaweaag 46 
                                       +v ++++++ r +++ G +GtGK+++ ka+ e++ +++
  gi|313127166|ref|YP_004037436.1| 102 VVMKAAKQR-RHVMMIGSPGTGKSMLAKAMSELLPKEE 138
                                       555565555.599999***************9998874 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
                            AAA_30  87 epgtllivDEagmvdtkqlaallkaaeka 115
                                       +++ +l +DE+  +d+++ ++l++a+++ 
  gi|313127166|ref|YP_004037436.1| 285 ANKGVLFIDEINTLDIRSQQHLMTAIQEG 313
                                       456899******************99984 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.046        26       5      28 ..     112     135 ..     108     154 .. 0.86
   2 !    9.5   0.0    0.0018         1      60     136 ..     278     353 ..     273     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.046
                                       -EEEE--TTSSHHHHHHHHHHHTT CS
                             AAA_2   5 silllgptgvGktelakalaellf 28 
                                        ++++g+ g+Gk++laka++ell 
  gi|313127166|ref|YP_004037436.1| 112 HVMMIGSPGTGKSMLAKAMSELLP 135
                                       57999***************9997 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0018
                                       TTT-HHHHTTSEEEEETGGG-------------HHHHHHHHHHHH--EE-......------EE-T....T-EEEEE CS
                             AAA_2  60 ppgyvgaeegGivllDEidKihpkessgadvSregVqrdLLqileggtlt......dkqgrkvdtk....nilfImt 126
                                       +pg + ++++G++++DEi                  q+ L+  + +g+ +       ++g +v+t+    + ++I++
  gi|313127166|ref|YP_004037436.1| 278 EPGAIHKANKGVLFIDEINTLDI-----------RSQQHLMTAIQEGEFSitgqseRSSGAMVQTEpvptDFIMIAA 343
                                       689999************99888...........5688888888888888888887777777777533335688888 PP

                                       E--TTHHHHT CS
                             AAA_2 127 gafgsskisd 136
                                       g++++ +   
  gi|313127166|ref|YP_004037436.1| 344 GNLDAMENMH 353
                                       8888777665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.3e-05     0.025       8      52 ..      99     142 ..      92     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEE CS
                              PhoH   8 eQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkri 52 
                                       + + +++a k+   v++iG+ GtGK++la a+   +l k++++ +
  gi|313127166|ref|YP_004037436.1|  99 ARDVVMKAAKQRRHVMMIGSPGTGKSMLAKAMSE-LLPKEELQDV 142
                                       4556788888999****************99974.4444444443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.063       2      23 ..     113     134 ..     113     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            AAA_33   2 vllvGlpGsGKstlaerllkkl 23 
                                       v+++G pG+GKs la+ + + l
  gi|313127166|ref|YP_004037436.1| 113 VMMIGSPGTGKSMLAKAMSELL 134
                                       89**************987554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.1e-05     0.041      51      83 ..     108     140 ..      81     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLr 83 
                                       ++ ++v+++G+ GtGKS l ka+ + + +e+L+
  gi|313127166|ref|YP_004037436.1| 108 KQRRHVMMIGSPGTGKSMLAKAMSELLPKEELQ 140
                                       45689******************9988888876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00015     0.088       9      39 ..     108     138 ..     101     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00015
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpte 39 
                                       k+ + v ++G+ G+GKS L+k++++ll ++e
  gi|313127166|ref|YP_004037436.1| 108 KQRRHVMMIGSPGTGKSMLAKAMSELLPKEE 138
                                       5667899*****************9987654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0006      0.35      19      52 ..     106     138 ..      94     185 .. 0.68
   2 ?   -0.6   0.0       2.7   1.5e+03     137     158 ..     288     309 ..     280     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0006
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdg 52 
                                       ++++r + v+ +G +G+GKs l+++  + l k++
  gi|313127166|ref|YP_004037436.1| 106 AAKQR-RHVMMIGSPGTGKSMLAKAMSELLPKEE 138
                                       33344.899***************9998888873 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.7
                            AAA_16 137 lvlvlDdlqwadeaslqllaaL 158
                                        vl++D++  +d  s+q l + 
  gi|313127166|ref|YP_004037436.1| 288 GVLFIDEINTLDIRSQQHLMTA 309
                                       59***********999987555 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014     0.079       7      35 ..     102     130 ..      97     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                     TrwB_AAD_bind   7 vplpkeretqhilivGttGsGKtqalekl 35 
                                       v ++  + ++h++++G+ G+GK+  ++++
  gi|313127166|ref|YP_004037436.1| 102 VVMKAAKQRRHVMMIGSPGTGKSMLAKAM 130
                                       66888999**************9876665 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00015     0.088      53     101 ..     171     220 ..     156     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                              TctB  53 ekeekearedwrkllklvlallaalllyalllep...lGfilatalflllll 101
                                       +kee  +r + r++l  +++++a++l yall+e    lG + a +++l++ +
  gi|313127166|ref|YP_004037436.1| 171 HKEEARKRNQMRSFL--MWIIIAIVLGYALLIEGavlLGILAAGVIYLAFRY 220
                                       444444444555555..5555578888******9777899999998886655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021      0.12      45      69 ..     108     132 ..      80     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgv 69 
                                       +++  ++++G +G+GKs la a++ 
  gi|313127166|ref|YP_004037436.1| 108 KQRRHVMMIGSPGTGKSMLAKAMSE 132
                                       5677899***************975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00059      0.34       2      45 ..     114     161 ..     113     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00059
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpe.....a 45 
                                       +  G pG+GK+ lak+ s++  +  ++l+dv+  +++ ++++p+     a
  gi|313127166|ref|YP_004037436.1| 114 MMIGSPGTGKSMLAKAMSEL--LpKEELQDVLVYHNPDDGNNPKvrtvpA 161
                                       6689**************99..4478889998888888888888444441 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00034       0.2       2      39 ..     112     145 ..     111     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEE CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFf 39 
                                        v++ G +G GK++L++ + +++ +++l+     ++ +
  gi|313127166|ref|YP_004037436.1| 112 HVMMIGSPGTGKSMLAKAMSELLPKEELQD----VLVY 145
                                       6899****************9999998665....4444 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00037      0.21     106     139 ..     102     135 ..      92     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                         Parvo_NS1 106 wlskqlgkrntvwfyGpantGktnlaeaIakavp 139
                                       +++k   +r  v+++G++ tGk++la+a+ + +p
  gi|313127166|ref|YP_004037436.1| 102 VVMKAAKQRRHVMMIGSPGTGKSMLAKAMSELLP 135
                                       5667788999*******************99887 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00039      0.22      17      44 ..     106     133 ..      96     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                            AAA_10  17 sktnasasliiGdlGnGKSvlakllvly 44 
                                       + ++  ++++iG++G GKS+lak +   
  gi|313127166|ref|YP_004037436.1| 106 AAKQRRHVMMIGSPGTGKSMLAKAMSEL 133
                                       55666789***************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.44
# Mc/sec: 4746.88
//
Query:       gi|313127167|ref|YP_004037437.1|  [L=178]
Description: nicotinamide-nucleotide adenylyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-14   51.7   0.0    1.9e-13   50.8   0.0    1.5  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0     1e-17   1.9e-13       1     141 [.       4     130 ..       4     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1e-17
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       ++ G+F+p H+GH r++e+++++++e l+ g+ s+  +++  +++++a eR+ m+ +     e++ v  + +  e l
  gi|313127167|ref|YP_004037437.1|   4 FYIGRFQPYHNGHHRMVEEIADEVDE-LVLGIGSAGDSHSP-RNPFTAGERIMMVTKS---VEAFDVTTYAVPIEDL 75 
                                       589***********************.************99.*************988...3346666666665444 PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                       ++      ++v   ++++      +++  ++n++lv++ ++e   +v   ++ ++    +t++r
  gi|313127167|ref|YP_004037437.1|  76 ERN--S--VWVSHVQSMSP-----AFDVAYSNNPLVIQLFKEAGVEVRQSPMFNRDVLEGTELR 130
                                       444..5..78888877777.....4888888888888888877766667777777666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1212.65
//
Query:       gi|313127168|ref|YP_004037438.1|  [L=216]
Description: hypothetical protein Hbor_24350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-40  135.1  29.0      2e-20   72.4  10.6    2.3  2  UPF0126   UPF0126 domain


Domain annotation for each model (and alignments):
>> UPF0126  UPF0126 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5  10.5   1.9e-23   3.4e-19       2      76 ..      10      82 ..       9      84 .. 0.92
   2 !   72.4  10.6   1.1e-24     2e-20       2      76 ..     100     172 ..      99     174 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.9e-23
                                      HHHHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHH CS
                           UPF0126  2 ildaiGlaafavsGalvAlkkgldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvll 76
                                      +++++Gl afav+G l+A+++gld++gv+vlGv+TA+gGG++RDvl++r +P+ l + ++ +++al+g+++++ll
  gi|313127168|ref|YP_004037438.1| 10 VMNVVGLLAFAVAGSLKAADAGLDAFGVAVLGVITALGGGTTRDVLVNR-PPASLAT-TWDMSVALVGVALAILL 82
                                      799*********************************************7.7777765.59999***999999987 PP

  == domain 2  score: 72.4 bits;  conditional E-value: 1.1e-24
                                       HHHHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHH CS
                           UPF0126   2 ildaiGlaafavsGalvAlkkgldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvll 76 
                                       + da+Glaafa++Galv++++gl + g+vvl++vTAvgGG l D+l+gr +Pvvl ++ +yat+allg+++++++
  gi|313127168|ref|YP_004037438.1| 100 VSDAVGLAAFAATGALVGAQAGLTPYGIVVLATVTAVGGGSLADLLIGR-IPVVLRED-FYATPALLGGIAFWVA 172
                                       68**********************************************6.*****666.************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1544.97
//
Query:       gi|313127169|ref|YP_004037439.1|  [L=524]
Description: thermosome subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.2e-152  507.2  12.0   4.7e-152  507.0  12.0    1.0  1  Cpn60_TCP1      TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.023   14.7   0.1       0.12   12.4   0.1    2.3  1  SIS_2           SIS domain
      0.025   14.9   1.6       0.41   11.0   0.0    3.2  3  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor
      0.092   13.1   0.2       0.36   11.2   0.2    2.0  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.0  12.0  1.1e-155  4.7e-152       1     489 [.      35     523 ..      35     524 .] 0.97

  Alignments for each domain:
  == domain 1  score: 507.0 bits;  conditional E-value: 1.1e-155
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v+ttlGP+GmdKmlv++ g+vv+TnDGatil+e++iehPaa+++ve+ae+q+e vGDGTtt+++L+geLl  a
  gi|313127169|ref|YP_004037439.1|  35 VASAVRTTLGPRGMDKMLVDSSGTVVITNDGATILEEMDIEHPAAQMIVEVAETQEEAVGDGTTTAAVLTGELLAHA 111
                                       5899************************************************************************* PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXS.THHHHHHHHHHHH.HC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltsk.eaeelsklvvdAv.kl 152
                                       e+l+++++hpt+i+egy +a+e a ea+++    ++++  d+++L+kva++s+++k t + +a+ l+k vv+Av ++
  gi|313127169|ref|YP_004037439.1| 112 EDLLEQDLHPTVIVEGYTEAAELAQEAIDAQ--IFDVD-LDDDRLQKVAESSMTGKGTGDvTADALAKHVVKAVrMV 185
                                       ****************************988..78887.67899************66552789**********888 PP

                                       HCCCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCH CS
                        Cpn60_TCP1 153 ieenekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaee 229
                                       +e+n++++d + ++v++ +g s++ +elveG+v+dk+ ++ +mpk++e+a v++ld +L+  k e++t+ ++++a++
  gi|313127169|ref|YP_004037439.1| 186 YEDNDGRFDSDDVRVLTHTGASSSATELVEGVVIDKDRVNDTMPKSVEDATVAVLDAKLDVRKGEADTEYNITSADQ 262
                                       88899************************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGC CS
                        Cpn60_TCP1 230 leklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltp 306
                                       l++  kae ++l+   +  ++++v+vv+c+k+i+d +  +lak+gila + v+ +d + +a+atGa+ + +++d+++
  gi|313127169|ref|YP_004037439.1| 263 LDAAIKAEDEELRGYAKTFADADVDVVFCTKAISDRVAGYLAKEGILAFKSVSDSDARAIANATGAKRLGTPSDIDE 339
                                       ***************************************************************************** PP

                                       GC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHH CS
                        Cpn60_TCP1 307 eelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelel 383
                                       +++G+a++v+ +k+g++++t+ie+ + +k++t+ lrg t++v+de+era++dA++vv +a+++++vvpG+G te+++
  gi|313127169|ref|YP_004037439.1| 340 SDFGHADSVSLQKYGDDELTFIEGGAASKAVTLFLRGGTEHVVDELERAVNDAIDVVVAALDKGGVVPGAGGTEIAI 416
                                       ***************************************************************************** PP

                                       HHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEE..ETTTTCEEECCCCT CS
                        Cpn60_TCP1 384 akklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgi..dvesgeiidlveag 458
                                       a +++++a  ++g++qla+eafa+A e++p+tLaeN G+dpi+ l +lra h k+e ++gi  + ++gei d+ve+g
  gi|313127169|ref|YP_004037439.1| 417 ADHIRAEAAGIEGRKQLAVEAFADAVESLPRTLAENTGMDPIDALVDLRA-HFKKEGTAGIisNGRTGEIGDPVEHG 492
                                       **************************************************.544443555544999*********** PP

                                       XEEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 459 vvDplkvkrqalksAteaastiLrideiika 489
                                       ++Dp++vkr a++s teaa++i rid++i a
  gi|313127169|ref|YP_004037439.1| 493 ILDPAAVKREAVESGTEAATMIVRIDDVIAA 523
                                       *****************************87 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.6e-05      0.12      11      72 ..     379     439 ..     374     463 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                                       HHHHHHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHH.HHHHTSSSTT-BTTEEEE--GGGS CS
                             SIS_2  11 erivetqaeaiekaaeliadslenggkvlvfGsGhSaa.laeelaaragglaeferialpala 72 
                                       e++v++ + a++ a+++++++l +gg+v   G+G+ ++ +a ++ a+a g+ +++++a +a a
  gi|313127169|ref|YP_004037439.1| 379 EHVVDELERAVNDAIDVVVAALDKGGVV--PGAGGTEIaIADHIRAEAAGIEGRKQLAVEAFA 439
                                       78999*********************98..588888752688999999999999998887765 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         4   1.8e+04      16      28 ..      81      93 ..      78     104 .. 0.59
   2 ?    1.1   0.1      0.11   4.9e+02      16      58 ..     142     182 ..     137     190 .. 0.86
   3 ?   11.0   0.0   9.2e-05      0.41      28      85 ..     258     318 ..     249     326 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4
                                      EEEEESSSCEEEE CS
                     Nitro_FeMo-Co 16 aiyeveegevkiv 28
                                      +i+ev e +++ v
  gi|313127169|ref|YP_004037439.1| 81 MIVEVAETQEEAV 93
                                      4555555555444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                                       EEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEE CS
                     Nitro_FeMo-Co  16 aiyeveegevkivenrveeaadaegggggklaqllaeegvdvv 58 
                                       +i++v+ ++ ++ ++   e++ +++g g+ +a+ la++ v++v
  gi|313127169|ref|YP_004037439.1| 142 QIFDVDLDDDRLQKVA--ESSMTGKGTGDVTADALAKHVVKAV 182
                                       5899998888888888..7888999999999*99999988887 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 9.2e-05
                                       EEEE.E.GCCCTSSCSSTHHHHHHHHTT-SEEEESS.SCHHHHHHHCTTTSEEEES.-SSB CS
                     Nitro_FeMo-Co  28 venr.veeaadaegggggklaqllaeegvdvvivgk.iGpralakleaagievykg.aggt 85 
                                        + +  ++a +ae ++ +  a++ a+++vdvv++ k i  r +  l+++gi ++k  ++ +
  gi|313127169|ref|YP_004037439.1| 258 TSADqLDAAIKAEDEELRGYAKTFADADVDVVFCTKaISDRVAGYLAKEGILAFKSvSDSD 318
                                       5555556667777788888999***********97538****************9744444 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   8.1e-05      0.36      24      75 ..     379     425 ..     364     446 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.1e-05
                    GHMP_kinases_C  24 elkavvgilppeleelleal.selGalgaklsGaGgGptvfalfkdkdeaeqv 75 
                                       e   vv++l +++ ++++    +l+  g++++Ga  G+t +a++ d+ +ae++
  gi|313127169|ref|YP_004037439.1| 379 EH--VVDELERAVNDAIDVVvAALD-KGGVVPGA--GGTEIAIA-DHIRAEAA 425
                                       44..999999999999999988888.99******..*******9.66555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3400.58
//
Query:       gi|313127170|ref|YP_004037440.1|  [L=276]
Description: tim-barrel fold metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-08   32.8   1.1      9e-08   32.2   1.0    1.4  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   1.0     5e-12     9e-08      80     288 ..      94     267 ..      24     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5e-12
                                       HCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE....CHHH CS
                      Amidohydro_2  80 rpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdihtGpspewl 156
                                       + +r++ + ++ +++++d  +++  a  + +f G+ l p+v g ++ +       +  le  glp  +h+G      
  gi|313127170|ref|YP_004037440.1|  94 ASARLRNLTTSRDESHADPEDIEQYAY-DDRFHGFTLAPAVDGLPDEET------LDQLENVGLPTLVHVG------ 157
                                       556677777777777777777666666.888888888777777666665......555***********99...... PP

                                       CHHHHHHHHHHHHHHHCCHH..HHCTTSEEEESGGGTT...TTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHH CS
                      Amidohydro_2 157 fggpqettraiqplllsgva..rkfPnlkivlaHgGgp...serlraalellarrpnvyvklsglytellyfdspla 228
                                               +a+ p ++ + +  r+fP   +++a +Gg           + ll++++ +yv++s            + 
  gi|313127170|ref|YP_004037440.1| 158 --------EAFTPDDAVETLldRDFP---VIFAGFGGYplnRDLMHRSIDLLDEYDDLYVDTSY-----------VR 212
                                       ........888888888888567777...9********88888888889999999999999965...........89 PP

                                       CHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHH CS
                      Amidohydro_2 229 dppalarlieavgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNAarl 288
                                       ++ +++r++ +  pdr++fGs  P  ++   + +l  ld     s+++ ++ +++NAar+
  gi|313127170|ref|YP_004037440.1| 213 FRGVMERALLEH-PDRVMFGSGAPEAHPNVGVMELLTLDV----SEDAMRRAFSKNAARV 267
                                       ************.**************************9....***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1872.81
//
Query:       gi|313127171|ref|YP_004037441.1|  [L=300]
Description: glycosyl transferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-13   51.5   1.0    3.8e-13   49.6   0.5    2.2  2  Glycos_transf_2  Glycosyl transferase family 2
    7.6e-07   29.2   2.9    3.6e-06   27.0   2.9    1.9  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00063   19.3   0.0      0.015   14.8   0.0    2.0  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0013   18.1   0.1       0.45    9.8   0.0    2.4  2  LysR_substrate   LysR substrate binding domain
  ------ inclusion threshold ------
      0.056   13.4   0.0      0.077   12.9   0.0    1.2  1  Glyco_trans_2_3  Glycosyl transferase family group 2
      0.068   12.6   0.0       0.36   10.3   0.0    2.0  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.5   1.3e-16   3.8e-13       1     114 [.       4     109 ..       4     153 .. 0.81
   2 ?   -2.7   0.0       1.5   4.6e+03      75     114 ..     227     237 ..     209     252 .. 0.57

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.3e-16
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       svv+pt N  + l+ +l++l++   +p+ e++vv+  S D+t  ++++     ++v v+     + +  a+nag++a
  gi|313127171|ref|YP_004037441.1|   4 SVVVPTLNGRDRLATSLDALAEA--APEAEVVVVNGPSADGTTGMVRDR----DDVDVLIELSDRTLNVARNAGIEA 74 
                                       8*****************99999..************************....5788877777889*********** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEE CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlg 114
                                       a+gd i+f+  D++++++wl  + + l++  a vv g
  gi|313127171|ref|YP_004037441.1|  75 ASGDAIAFVRYDVAVEEQWLDGVTAGLDE-AA-VVTG 109
                                       **********************9999999.44.3433 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                                       HHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEE CS
                   Glycos_transf_2  75 lraatgdyilflDaDdepdpdwleklvealekdgadvvlg 114
                                       l++a++d                              ++ 
  gi|313127171|ref|YP_004037441.1| 227 LKHARTDA-----------------------------IAT 237
                                       33333333.............................444 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   2.9   1.2e-09   3.6e-06       3     213 ..       2     190 ..       1     206 [. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.2e-09
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       dl+v+Vpt+n  d+l   l++l+  + p+ evvvv  +s ++t  +++      +  +v+v++       ++   a 
  gi|313127171|ref|YP_004037441.1|   2 DLSVVVPTLNGRDRLATSLDALAE-AAPEAEVVVVNGPSADGTTGMVRD----RD--DVDVLIELS---DRTLNVAR 68 
                                       489*****************9997.58******************9987....44..567775533...34555667 PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralg 156
                                       n +++a+++d +++v  D+ ve   l+ +++ +  +++++v++p +   r  +++ +      +r +        ++
  gi|313127171|ref|YP_004037441.1|  69 NAGIEAASGDAIAFVRYDVAVEEQWLDGVTAGL--DEAAVVTGPSHQTLRAGMTTETLE----RRTI-------CGR 132
                                       8***************************99999..7899******99999999993322....3333.......344 PP

                   Glyco_tranf_2_3 157 .vltlnGsgslirrevlkelegldplflltdDy.elglrlrragfrtayvpgaavrevf 213
                                        v+++nG  +++ r+ l+el+g+d+  l t ++ + + rl ++g+ + ++p   vr++ 
  gi|313127171|ref|YP_004037441.1| 133 dVTYFNGDNVAFHRDALEELDGFDE-YLQTGGArDAAHRLAETGYGVTWQPTMSVRTEY 190
                                       5999*********************.444444448899*************99999874 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.1e-06     0.015       1      92 [.       4      87 ..       4      97 .. 0.84
   2 ?    2.6   0.0     0.026        78     164     192 ..     138     166 ..     114     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                   Glyco_tranf_2_2  1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGask 79
                                      svv+p  ++++r  +   +   a    +e e++vv++ S++ +   v+   d   l+ l+d      +l  arN G++ 
  gi|313127171|ref|YP_004037441.1|  4 SVVVPTLNGRDR--LATSLDALAEA-APEAEVVVVNGPSADGTTGMVRDRDDVDVLIELSDR-----TLNVARNAGIEA 74
                                      567777777766..55555444444.689*****************************9*99.....8999******** PP

                   Glyco_tranf_2_2 80 aesdlvlFlDaDc 92
                                      a +d + F+  D 
  gi|313127171|ref|YP_004037441.1| 75 ASGDAIAFVRYDV 87
                                      ********98775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.026
                   Glyco_tranf_2_2 164 ssssilinrraflevGGyDErfrGhgaED 192
                                       +++++  +r a+ e+ G+DE ++  ga D
  gi|313127171|ref|YP_004037441.1| 138 NGDNVAFHRDALEELDGFDEYLQTGGARD 166
                                       57888899**************9888877 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0019       5.6       8      57 ..       3      52 ..       1      73 [. 0.82
   2 !    9.8   0.0   0.00015      0.45     140     201 ..     166     227 ..      80     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0019
                                      EEEEEECCCHHHHHHHHHHHHHHHSTTEEEEEEEESH.HHHHHHHHTTSSS CS
                    LysR_substrate  8 LrigapptlaryllppllarfraryPevelelvegds.eelldllaegelD 57
                                      L++ +p+  +r +l+  l +++++ Pe e+ +v g+s +    +++++  D
  gi|313127171|ref|YP_004037441.1|  3 LSVVVPTLNGRDRLATSLDALAEAAPEAEVVVVNGPSaDGTTGMVRDR-DD 52
                                      88999999***************************9955555666655.44 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00015
                                       HHHHHHHHTTS-BEEEEGGGHHCCC.HTTTEEEEEESSTTCE.EEEEEEEETTCCCHHHHHHHH CS
                    LysR_substrate 140 eallalvaaGlGiallprsavrdel.adgrlvalplpepplp.relylvyrkgrelspavrafi 201
                                       +a+ +l++ G G+++ p++ vr e  adg+++ +++    ++   + l+ + g  ++  vr+ +
  gi|313127171|ref|YP_004037441.1| 166 DAAHRLAETGYGVTWQPTMSVRTEYeADGGMKERDWGW-KYRaLGYRLAKNYGL-RPTVVRRTL 227
                                       68889*****************9999999999888877.777677777766665.555555555 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.6e-05     0.077      68     125 ..     133     189 ..     116     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                   Glyco_trans_2_3  68 rvvpsvGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkek 125
                                       +v+ + G +++++r+al+e+ g+d     ++   d + rl++ Gy v + p   v+++
  gi|313127171|ref|YP_004037441.1| 133 DVTYFNGDNVAFHRDALEELDGFD-EYLQTGGARDAAHRLAETGYGVTWQPTMSVRTE 189
                                       577899******************.445899999*************99876545444 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.36      24     122 ..      70     158 ..      58     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                   Glyco_transf_21  24 qaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqaklsglgf 100
                                        ++eaa  d + +   dv+v+++ L+ + a l +  +++Vt+++  + ++g++++       tl +++      +  
  gi|313127171|ref|YP_004037441.1|  70 AGIEAASGDAIAFVRYDVAVEEQWLDGVTAGLDE--AAVVTGPSHQTLRAGMTTE-------TLERRTIC-GRDVTY 136
                                       578889999999999999999******9999996..9999999998888888874.......45555555.567778 PP

                   Glyco_transf_21 101 avGksmalrreaLeaiGGfeal 122
                                        +G  +a++r+aLe++ Gf + 
  gi|313127171|ref|YP_004037441.1| 137 FNGDNVAFHRDALEELDGFDEY 158
                                       89**************999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1951.29
//
Query:       gi|313127172|ref|YP_004037442.1|  [L=238]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-24   85.2   0.1    6.5e-24   84.5   0.1    1.3  1  Methyltransf_25  Methyltransferase domain
      8e-24   84.1   0.1    2.1e-23   82.8   0.1    1.6  1  Methyltransf_11  Methyltransferase domain
    3.8e-17   62.5   0.0    5.3e-17   62.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    6.8e-16   58.3   0.0    3.1e-15   56.2   0.0    1.8  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.1e-13   50.8   0.0    3.3e-13   50.2   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    4.4e-12   46.1   0.0    5.5e-12   45.8   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.7e-06   27.9   0.0      1e-05   25.3   0.0    2.2  2  UPF0020          Putative RNA methylase family UPF0020
     0.0001   21.3   0.0    0.00015   20.8   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
    0.00013   21.6   0.0     0.0002   21.0   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00031   20.1   0.0    0.00044   19.6   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00033   19.8   0.0    0.00042   19.5   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0005   19.6   0.0    0.00071   19.1   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
    0.00062   19.0   0.0     0.0021   17.3   0.0    1.8  2  Methyltransf_20  Putative methyltransferase
     0.0013   18.4   0.0     0.0017   18.0   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0021   18.1   0.0     0.0028   17.6   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0031   17.1   0.0      0.004   16.8   0.0    1.1  1  NodS             Nodulation protein S (NodS)
     0.0033   17.0   0.0     0.0045   16.5   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0035   16.4   0.0     0.0055   15.7   0.0    1.3  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
  ------ inclusion threshold ------
      0.015   14.7   0.0      0.022   14.2   0.0    1.2  1  TehB             Tellurite resistance protein TehB
      0.017   14.8   0.0      0.022   14.4   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
      0.024   14.4   0.0      0.035   13.9   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.025   14.7   0.0      0.029   14.5   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
       0.03   13.5   0.0      0.044   12.9   0.0    1.2  1  Methyltransf_3   O-methyltransferase
       0.07   12.3   0.0      0.097   11.8   0.0    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
      0.076   12.8   0.0        0.1   12.4   0.0    1.1  1  Met_10           Met-10+ like-protein
       0.11   12.4   0.0       0.16   11.9   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
       0.12   13.4   0.2       0.26   12.3   0.2    1.7  1  Methyltransf_24  Methyltransferase domain
       0.19   11.4   0.0       0.46   10.2   0.0    1.7  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.1     1e-26   6.5e-24       1      94 [.      48     139 ..      48     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 1e-26
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       vL+++cGtGr+t +la+r+  a+++g+Dis +m+++ re+a+++g+  +vef++gda +lpf+d++fD+v++ + + 
  gi|313127172|ref|YP_004037442.1|  48 VLEIACGTGRFTVMLAERG--ADIVGLDISRAMMQQGREKARRAGVadHVEFLRGDAARLPFPDDHFDAVFA-MRFF 121
                                       9*****************5..***************************************************.5755 PP

                                       GSSHHHHHHHHHHHHHHEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLk 94 
                                       hl d   +k+l+e+arv k
  gi|313127172|ref|YP_004037442.1| 122 HLAD-TPAKFLAEMARVSK 139
                                       5553.5579*******977 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.1   3.2e-26   2.1e-23       1      89 [.      49     139 ..      49     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 3.2e-26
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       L+++cGtGr++  la+rga++vg+D+s +m+++ +eka+++g+  +vef+++da +lpf+d+ fD+v++  ++h  +
  gi|313127172|ref|YP_004037442.1|  49 LEIACGTGRFTVMLAERGADIVGLDISRAMMQQGREKARRAGVadHVEFLRGDAARLPFPDDHFDAVFAMRFFHLAD 125
                                       89*************************************************************************** PP

                                       CHHHHHHHHHHHEE CS
                   Methyltransf_11  76 dpekalkeiaRvLk 89 
                                        p+k+l+e+aRv k
  gi|313127172|ref|YP_004037442.1| 126 TPAKFLAEMARVSK 139
                                       ************77 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0   8.3e-20   5.3e-17       4     103 ..      45     140 ..      42     151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 8.3e-20
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlil 79 
                                       ++ vl+++CGtG++t  lae+   +a++vG+Dis  + ++ re+a++ g+   veF +gd+  l+  + d+ fD ++
  gi|313127172|ref|YP_004037442.1|  45 DKDVLEIACGTGRFTVMLAER---GADIVGLDISRAMMQQGREKARRAGVAdHVEFLRGDAARLP--FPDDHFDAVF 116
                                       789****************66...799***********************99*************..********** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkp 103
                                       +  ++++   p+k+l e+ rv k+
  gi|313127172|ref|YP_004037442.1| 117 AMRFFHLADTPAKFLAEMARVSKD 140
                                       ********************9875 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   4.8e-18   3.1e-15      36     144 ..      33     139 ..      10     147 .. 0.84
   2 ?   -0.3   0.0      0.88   5.6e+02     188     216 ..     156     184 ..     146     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 4.8e-18
                                       HHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-T CS
                   Ubie_methyltran  36 kkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLp 111
                                       k+ v + v++ + ++vl++a+Gtg +++ l++   +  ++v+lDi+  m+++g++k+++ g+  ++efl ++a +Lp
  gi|313127172|ref|YP_004037442.1|  33 KQAVLDAVGPVEDKDVLEIACGTGRFTVMLAE---RGADIVGLDISRAMMQQGREKARRAGVAdHVEFLRGDAARLP 106
                                       67899999********************9976...4568***********************989************ PP

                                       TS-T-EEEEEEES-GGG-..S-H.HHHHHHHHHHEE CS
                   Ubie_methyltran 112 feddsfDvvtvsfGlrnv..tDk.lkaLkeayrvlk 144
                                       f dd fD v   f +r +  +D+  k L e+ rv k
  gi|313127172|ref|YP_004037442.1| 107 FPDDHFDAV---FAMRFFhlADTpAKFLAEMARVSK 139
                                       *******98...555543114542578999999977 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.88
                                       HHHHHHHHHHS--HHHHHHHHHHTTEEEE CS
                   Ubie_methyltran 188 yryLvesirafPdqetlkeliedaGfksv 216
                                       y++L     +  ++e+++ l+ daG+k  
  gi|313127172|ref|YP_004037442.1| 156 YNWLLPMGSRLYGEEEVDGLLSDAGLKLT 184
                                       88998888889999***********9865 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   5.2e-16   3.3e-13       1      94 [.      49     139 ..      49     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 5.2e-16
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       Lei cGtG+++ +l+e+  +++++g+Dis++++   + + ++r++  +++ve+   d++ l+ + ++fD+v+a  ++
  gi|313127172|ref|YP_004037442.1|  49 LEIACGTGRFTVMLAER--GADIVGLDISRAMM--QQGREKARRAGVADHVEFLRGDAARLPFPdDHFDAVFAMRFF 121
                                       8****************..**************..5555556666688999999999988877799*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLk 94 
                                       h  ++++++l++++++ k
  gi|313127172|ref|YP_004037442.1| 122 HLADTPAKFLAEMARVSK 139
                                       ************999855 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   8.5e-15   5.5e-12      20     162 ..      42     183 ..      16     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 8.5e-15
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                         +++ vL+i+cGtG+++  l+e+g++++g D+s+++ +  +        a+  ++   d+   ++p+++fd + ++
  gi|313127172|ref|YP_004037442.1|  42 PVEDKDVLEIACGTGRFTVMLAERGADIVGLDISRAMMQQGRekarragVADHVEFLRGDAARLPFPDDHFDAVFAM 118
                                       45788******************************9988777778766666666666666667777*********** PP

                   Methyltransf_23  90 evlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlev 162
                                        +++  + p++ l+ +a+  k+  ++++ +++    ++r + +wl++      ++++ ++++  ll +aGl++
  gi|313127172|ref|YP_004037442.1| 119 RFFHLADTPAKFLAEMARVSKD--VVFFDTFND--TSARVVYNWLLPM----GSRLYGEEEVDGLLSDAGLKL 183
                                       ******************9885..899999964..6788888888766....458999999999999999986 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.6e-08     1e-05      75     125 ..      65     115 ..      36     117 .. 0.91
   2 ?   -0.7   0.0       1.5   9.7e+02     122     137 ..     211     226 ..     202     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.6e-08
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125
                                       + + ++g+D+ r+++q++re+a++agv+d +ef   daa L+ +++ +d++
  gi|313127172|ref|YP_004037442.1|  65 RGADIVGLDISRAMMQQGREKARRAGVADHVEFLRGDAARLPFPDDHFDAV 115
                                       55679*************************************998899987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                       --EEEE---------- CS
                           UPF0020 122 vdvivtnpPYGerlgs 137
                                       +d+ v++ P Gerl s
  gi|313127172|ref|YP_004037442.1| 211 FDTSVGDTPLGERLAS 226
                                       789999******9976 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.3e-07   0.00015     105     203 ..      34     132 ..      29     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.3e-07
                                       HHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.- CS
                    Methyltransf_9 105 drvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.l 180
                                       + vl  + +++++ +l++ cg+G +   m++e  + +vG+d s+  + q +   +  g   ++  l     +lp   
  gi|313127172|ref|YP_004037442.1|  34 QAVLDAVGPVEDKDVLEIACGTGRFTV-MLAERGADIVGLDISRAMMQQGREKARRAGVADHVEFLRGDAARLPFpD 109
                                       67889999***************9875.888888889************9988888888888889989999***878 PP

                                       --EEEEEEES-GGG-S-HHHHHH CS
                    Methyltransf_9 181 eafdtvfsmGvlyhrrsPldhll 203
                                       + fd+vf+m  ++   +P   l 
  gi|313127172|ref|YP_004037442.1| 110 DHFDAVFAMRFFHLADTPAKFLA 132
                                       99*******98877777776665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.1e-07    0.0002      15     112 ..      46     147 ..      31     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.1e-07
                              MetW  15 srvldlGcGdGellellkeekqvdgrGleldeegvaecvak....Glsviqgdldkdle..nfedksfdyvvlsqtl 85 
                                         vl++ cG G +  +l+e ++ d  Gl+++++ +++  +k    G++ + + l  d +   f+d+ fd v   + +
  gi|313127172|ref|YP_004037442.1|  46 KDVLEIACGTGRFTVMLAE-RGADIVGLDISRAMMQQGREKarraGVADHVEFLRGDAArlPFPDDHFDAVFAMRFF 121
                                       57************99976.9*********998887654432222665554444444431169************** PP

                              MetW  86 qatrnpkevldellrigrraivsfPnf 112
                                            p++ l e+ r+++ ++  f  f
  gi|313127172|ref|YP_004037442.1| 122 HLADTPAKFLAEMARVSKDVV-FFDTF 147
                                       ****************98864.55555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.9e-07   0.00044      62     137 ..      44     121 ..      29     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.9e-07
                                       TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEEEES CS
                              CMAS  62 pGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvvsvg 135
                                       + + +L+i cG G  ++  +er ++++vgl +S+  +++ +++  +++++++ve +  d   l+    ++d+v ++ 
  gi|313127172|ref|YP_004037442.1|  44 EDKDVLEIACGTGRFTVMLAER-GADIVGLDISRAMMQQGREKARRAGVADHVEFLRGDAARLPFpddHFDAVFAMR 119
                                       55789*****************.******************************999888877743224777776665 PP

                                       -G CS
                              CMAS 136 af 137
                                        f
  gi|313127172|ref|YP_004037442.1| 120 FF 121
                                       55 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.5e-07   0.00042      19      93 ..      33     110 ..      19     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.5e-07
                                       HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHHHH CS
                            RrnaAD  19 ineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls...kdeklkvvhqDflkfetpe 92 
                                        + +ld++ + e++ vlei+ G+G +T+ La+r    v l + +++++  ++k +    +  ++ +  D+    +p 
  gi|313127172|ref|YP_004037442.1|  33 KQAVLDAVGPVEDKDVLEIACGTGRFTVMLAERGADIVGLDISRAMMQQGREKARragVADHVEFLRGDAARLPFPD 109
                                       56788888999*****************************************9998888888888888888887777 PP

                                       H CS
                            RrnaAD  93 e 93 
                                       +
  gi|313127172|ref|YP_004037442.1| 110 D 110
                                       5 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.1e-06   0.00071       3      62 ..      46     104 ..      44     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                                       EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTT.SSEEEEES-CCC CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealel.kNlrilrgdalk 62 
                                       + vlei cG G+f+v lA++ +d  ++G++i++ ++++  +k+++ ++   ++ lrgda +
  gi|313127172|ref|YP_004037442.1|  46 KDVLEIACGTGRFTVMLAERGAD--IVGLDISRAMMQQGREKARRAGVaDHVEFLRGDAAR 104
                                       5799****************987..79*****************99762569999999943 PP

>> Methyltransf_20  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.2e-06    0.0021     133     195 ..      44     102 ..      21     114 .. 0.85
   2 ?   -1.2   0.0       1.4   9.1e+02     273     294 ..     165     186 ..     150     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                   Methyltransf_20 133 rpvrildiaaGhGryvldalekaeervesillrdyselnveqGraliaekglediarfekgda 195
                                       ++  +l+ia+G Gr+ +      +er  +i+  d s + ++qGr+ +++ g++d ++f +gda
  gi|313127172|ref|YP_004037442.1|  44 EDKDVLEIACGTGRFTVM----LAERGADIVGLDISRAMMQQGREKARRAGVADHVEFLRGDA 102
                                       45679**********863....44556789999*****************************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                   Methyltransf_20 273 rrrsqaemdelveaaGfrkleq 294
                                       r    +e+d l+ +aG++ ++ 
  gi|313127172|ref|YP_004037442.1| 165 RLYGEEEVDGLLSDAGLKLTDA 186
                                       5556899*********987665 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-06    0.0017       4      61 ..      48     126 ..      45     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                   Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe.................... 60 
                                       +l + +G+G  ++ +a+ +  +++++i++  +++  + a+  gv+d++ +  gd                       
  gi|313127172|ref|YP_004037442.1|  48 VLEIACGTGRFTVMLAERGADIVGLDISRAMMQQGREKARRAGVADHVEFLRGDAARlpfpddhfdavfamrffhla 124
                                       7999**************************************************98877777766666666666555 PP

                   Methyltransf_15  61 .l 61 
                                        +
  gi|313127172|ref|YP_004037442.1| 125 dT 126
                                       51 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.4e-06    0.0028      25      90 ..      44     103 ..      31     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
                   Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsie 90 
                                       ++++v+++++G g  + +la      +  +vg+d++++++++ ++ a++ g  ++++++f  ++ +
  gi|313127172|ref|YP_004037442.1|  44 EDKDVLEIACGTGRFTVMLAE----RGADIVGLDISRAMMQQGREKARRAG--VADHVEFLRGDAA 103
                                       6789****************9....59************************..9899999988765 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.3e-06     0.004      44     111 ..      45     116 ..      24     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.3e-06
                              NodS  44 iadalevGcaaGalterlapyckrltvvdvveeaiararervke...sshiswivsdvqqfs.tdekfdliv 111
                                         d+le+ c +G +t++la     +  +d+    +++ re+ ++   + h+ ++  d  ++   d++fd + 
  gi|313127172|ref|YP_004037442.1|  45 DKDVLEIACGTGRFTVMLAERGADIVGLDISRAMMQQGREKARRagvADHVEFLRGDAARLPfPDDHFDAVF 116
                                       468**************************9887777777654441116899999999999963578888765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.1e-06    0.0045      30     102 ..      43     116 ..      28     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.1e-06
                                       CTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT.TSTTS-EEEEE CS
                               MTS  30 elsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle.eveekkfdliv 102
                                        ++++vl ++cG+G  +++la++  +  ++ +d++ + ++  +e +++ +++  ve++  d+    +++++fd++ 
  gi|313127172|ref|YP_004037442.1|  43 VEDKDVLEIACGTGRFTVMLAERGAD--IVGLDISRAMMQQGREKARRAGVAdhVEFLRGDAARlPFPDDHFDAVF 116
                                       46789*****************9988..9********************999999999999876255688888875 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.7e-06    0.0055     201     243 ..      44      86 ..      21     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.7e-06
                   tRNA_U5-meth_tr 201 skgdllelycGnGnfslalarnfekvlateiakssveaaqyni 243
                                       +++d+le+ cG G f++ la++   ++  +i+++ ++  +   
  gi|313127172|ref|YP_004037442.1|  44 EDKDVLEIACGTGRFTVMLAERGADIVGLDISRAMMQQGREKA 86 
                                       467*****************************99988766555 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.4e-05     0.022      20      62 ..      34      76 ..      21      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                                      HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-H CS
                              TehB 20 sevveavkivkpgkvldlgcgqgrnslylsllgydvtawdkne 62
                                        v++av  v+   vl++ cg gr ++ l+  g d+  +d   
  gi|313127172|ref|YP_004037442.1| 34 QAVLDAVGPVEDKDVLEIACGTGRFTVMLAERGADIVGLDISR 76
                                      5799********************************9998654 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.5e-05     0.022      42      77 ..      49      84 ..      33     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-05
                                      EEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHH CS
                              TPMT 42 lvPlCGkaldlvwlAeqgrevvGvelselAvekffe 77
                                      l   CG +   v lAe+g ++vG+++s + +++  e
  gi|313127172|ref|YP_004037442.1| 49 LEIACGTGRFTVMLAERGADIVGLDISRAMMQQGRE 84
                                      5557***********************988887433 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.4e-05     0.035      73     133 ..      44     102 ..      33     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-G CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDG 133
                                       + + vLe+ +G+G  t++la+   + + +v+++ ++ ++++ +++ ++ +++ +v +  gD 
  gi|313127172|ref|YP_004037442.1|  44 EDKDVLEIACGTGRFTVMLAE---RGADIVGLDISRAMMQQGREKARRAGVAdHVEFLRGDA 102
                                       5678**********9998885...66789*******************99876999999996 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.6e-05     0.029      21      71 ..      44     103 ..      13     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-05
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS........HHH....TTEEEECS-CC CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm........apl....pgvttiqgdit 71 
                                       ++k v+++++++G ++ +l++r g  + +v++D+ + m        + +    ++v++++gd  
  gi|313127172|ref|YP_004037442.1|  44 EDKDVLEIACGTGRFTVMLAER-G--ADIVGLDIsRAMmqqgrekaR-RagvaDHVEFLRGDAA 103
                                       4467******************.6..69******6666898888641.2344689999999984 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.9e-05     0.044      47     110 ..      44     104 ..      33     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-05
                                       T--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHH CS
                    Methyltransf_3  47 nakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalk 110
                                       + k vlei   tG   +++a        i+ +di r  ++ +++  ++agva+ +e+ +gda +
  gi|313127172|ref|YP_004037442.1|  44 EDKDVLEIACGTGRFTVMLAER---GADIVGLDISRAMMQQGREKARRAGVADHVEFLRGDAAR 104
                                       5689999999999877776643...447*********************************975 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015     0.097     122     171 ..      43      91 ..      11     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                   Methyltrans_SAM 122 akdknvlnlfaytcgfsvaaiaggaskvvnvdmargslnkgrdnhrlngh 171
                                        +dk+vl++ + t  f+v     ga+ +v +d++r+ +++gr++ r  g 
  gi|313127172|ref|YP_004037442.1|  43 VEDKDVLEIACGTGRFTVMLAERGAD-IVGLDISRAMMQQGREKARRAGV 91 
                                       5799*****999999**987777775.89**************9987664 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016       0.1      89     193 ..      31     140 ..      21     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                       HHHHHHHTT--T..T-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG- CS
                            Met_10  89 aErerlaklvee..gevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrev 163
                                        E++ +   v +  ++ V+++  G G f++ +a   ++  +++ d+  + ++  +e  ++  v++ v+ + +D++ +
  gi|313127172|ref|YP_004037442.1|  31 REKQAVLDAVGPveDKDVLEIACGTGRFTVMLAE--RGADIVGLDISRAMMQQGREKARRAGVADHVEFLRGDAARL 105
                                       566666666654114579***************9..9999**********************************998 PP

                                       --.TT-EEEE.EE-...-TTTGGGGHHHHHHHEEE CS
                            Met_10 164 ir.eqladrv.vmn...lpksaieFldkvlaalkd 193
                                          ++ +d v  m    l ++  +Fl ++ ++ kd
  gi|313127172|ref|YP_004037442.1| 106 PFpDDHFDAVfAMRffhLADTPAKFLAEMARVSKD 140
                                       76566666431454111445556787777766665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.16      15      75 ..      45     103 ..      34     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                   Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGl 75 
                                       ++ v+ i +  g  +++l+++g    ++  Di++  +++ +e++++ag+ d++e+  +d  
  gi|313127172|ref|YP_004037442.1|  45 DKDVLEIACGTGRFTVMLAERGA--DIVGLDISRAMMQQGREKARRAGVADHVEFLRGDAA 103
                                       568999************98875..69****************************999875 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00041      0.26       3      80 ..      53     149 ..      49     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00041
                   Methyltransf_24   3 iGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikads.................... 58 
                                       +G   G+ t++l+   +r +   +v +d  ++  ++ ++ ar+ag++d+v+++++d+                    
  gi|313127172|ref|YP_004037442.1|  53 CG--TGRFTVMLA---ERGA--DIVGLDISRAmMQQGREKARRAGVADHVEFLRGDAarlpfpddhfdavfamrffh 122
                                       55..999999999...4444..599999988654455667788**************99999999988888888888 PP

                   Methyltransf_24  59 .....eealaslaagsiDllfiDggha 80 
                                             + la++a+ s D++f+D   +
  gi|313127172|ref|YP_004037442.1| 123 ladtpAKFLAEMARVSKDVVFFDTFND 149
                                       866665566666688889999996433 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00071      0.46      17      46 ..      36      65 ..      30     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00071
                            DUF938 17 vLksylakttervLEiasGtGqHAvffApa 46
                                      vL  + + + + vLEia GtG+  v +A++
  gi|313127172|ref|YP_004037442.1| 36 VLDAVGPVEDKDVLEIACGTGRFTVMLAER 65
                                      555555666668*************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1739.65
//
Query:       gi|313127173|ref|YP_004037443.1|  [L=133]
Description: hypothetical protein Hbor_24400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-18   64.6   0.0    9.4e-18   64.2   0.0    1.1  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
    3.4e-06   27.1   0.1    3.7e-06   27.0   0.1    1.1  1  Pyridox_ox_2     Pyridoxamine 5'-phosphate oxidase
    0.00036   20.2   0.0    0.00039   20.0   0.0    1.2  1  Pyrid_ox_like    Pyridoxamine 5'-phosphate oxidase like
  ------ inclusion threshold ------
      0.054   13.6   0.1      0.075   13.2   0.1    1.3  1  F420H2_quin_red  F420H(2)-dependent quinone reductase
      0.056   13.4   0.0       0.12   12.3   0.0    1.7  1  TRAM             TRAM domain


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   2.6e-21   9.4e-18       2      87 ..       6      91 ..       5      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.6e-21
                                      HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEEE CS
                    Putative_PNPOx  2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.lgrgvrieG 79
                                      +e +r+++++++++ +AT  +dG+P+v+pv+  + +g+ + ++ +++ +rk+ n+e++p+v++++ d++  +r+v+++G
  gi|313127173|ref|YP_004037443.1|  6 PESHRDIFEKESFAQVATNMPDGTPQVTPVWVDHENGE-YVLLNSARGRRKVTNIERDPKVGVSVTDPDdPYRYVSVRG 83
                                      578999********************************.**************************************** PP

                                      EEEEESCH CS
                    Putative_PNPOx 80 taelvsdg 87
                                      +ael+ dg
  gi|313127173|ref|YP_004037443.1| 84 EAELIGDG 91
                                      *****997 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1     1e-09   3.7e-06       7     108 ..      11     103 ..       6     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1e-09
                                       HHHHC-SEEEEEEEE.TTEEEEEEEEEEEE.TTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEEEEE CS
                      Pyridox_ox_2   7 alLdegevgrlafvd.dgepvilPvnyvvd.gdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnslnyr 80 
                                       ++ ++++++ +a+++ dg p ++Pv +  + g+ +++ +a+g r++  ++  p v v+vt+ d+           yr
  gi|313127173|ref|YP_004037443.1|  11 DIFEKESFAQVATNMpDGTPQVTPVWVDHEnGEYVLLNSARGRRKVTNIERDPkVGVSVTDPDD-----P-----YR 77 
                                       67889999******97777*****97666656669999************6667*********9.....4.....88 PP

                                       EEEEEEEEEEE--HHHHHHHCCCHHHHH CS
                      Pyridox_ox_2  81 SVvvrGraeevtdeeekaealellveki 108
                                        V vrG+ae++ d +  ++++++l++++
  gi|313127173|ref|YP_004037443.1|  78 YVSVRGEAELIGDGA--DAHVDKLARQY 103
                                       8**********4333..33334444444 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.1e-07   0.00039      11      90 ..      14      93 ..       7     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-07
                     Pyrid_ox_like 11 kdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdesk.kkyvsvsGtaevvedr 88
                                      ++ ++a ++t+  dg+ ++ P  + + e+ + +   +++  +kv++i++d++v + + d+++   yvsv+G+ae+  d 
  gi|313127173|ref|YP_004037443.1| 14 EKESFAQVATNMPDGTPQVTPVWVDH-ENGEYVLLNSARGRRKVTNIERDPKVGVSVTDPDDpYRYVSVRGEAELIGDG 91
                                      55566666666667777777766543.445556667888999*****************987357**********9997 PP

                     Pyrid_ox_like 89 ak 90
                                      a 
  gi|313127173|ref|YP_004037443.1| 92 AD 93
                                      65 PP

>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.1e-05     0.075      36      87 ..      28      75 ..      22     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                                      -SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEETTEEEE CS
                   F420H2_quin_red 36 gkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevqvgakkld 87
                                      g p+ tp+   +++++y++  s  G  k    + N++ +P+v v v     +
  gi|313127173|ref|YP_004037443.1| 28 GTPQVTPVWVDHENGEYVLLNSARGRRK----VTNIERDPKVGVSVTDPDDP 75
                                      899*****************99997766....79**********99876555 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.5e-05      0.12      29      56 ..      76     103 ..      38     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
                                       TEEEEETT--T...TEEEEEEEEEE-SSE CS
                              TRAM  29 gkvvfvpgdlpg.IGdfVeVkItkvkrqy 56 
                                       +++v v+g +++ IGd ++++++k  rqy
  gi|313127173|ref|YP_004037443.1|  76 YRYVSVRG-EAElIGDGADAHVDKLARQY 103
                                       89******.6666**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 1080.43
//
Query:       gi|313127174|ref|YP_004037444.1|  [L=83]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-06   28.2   0.0    2.9e-06   26.7   0.0    1.6  2  HTH_24         Winged helix-turn-helix DNA-binding
      5e-05   23.1   0.1    6.4e-05   22.8   0.1    1.2  1  MarR_2         MarR family
    0.00011   22.2   1.0     0.0016   18.4   0.3    2.0  2  HTH_20         Helix-turn-helix domain
    0.00087   18.9   0.7     0.0016   18.0   0.7    1.6  1  GntR           Bacterial regulatory proteins, gntR family
     0.0021   17.9   0.9      0.018   15.0   0.2    2.5  2  HTH_12         Ribonuclease R winged-helix domain
     0.0048   16.8   0.0     0.0069   16.3   0.0    1.3  1  MarR           MarR family
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.021   14.7   0.0    1.1  1  TFIIE_alpha    TFIIE alpha subunit
      0.038   13.9   0.0       0.24   11.4   0.0    2.0  1  HTH_36         Helix-turn-helix domain
       0.04   13.8   0.1      0.052   13.4   0.1    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.071   13.3   0.0        0.1   12.7   0.0    1.3  1  HTH_28         Helix-turn-helix domain
      0.073   12.9   0.3       0.85    9.5   0.1    2.1  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.075   12.8   0.2       0.12   12.2   0.2    1.3  1  HTH_IclR       IclR helix-turn-helix domain
      0.084   12.9   0.0       0.11   12.5   0.0    1.3  1  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.094   13.1   0.0       0.12   12.7   0.0    1.2  1  Rrf2           Transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2   1.6e+03      29      41 ..       7      19 ..       6      19 .. 0.84
   2 !   26.7   0.0   2.2e-09   2.9e-06      11      47 ..      29      65 ..      27      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                            HTH_24 29 lSpstvnrrlkrL 41
                                      lS +  ++rl++L
  gi|313127174|ref|YP_004037444.1|  7 LSEGEFRERLREL 19
                                      7888889999998 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 2.2e-09
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +L+ ++ +sq eLAe++ l+  tv++ l+rLee +l+
  gi|313127174|ref|YP_004037444.1| 29 VLEGDAPLSQGELAEESLLPDRTVRYALNRLEETELV 65
                                      7899*****************************9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1     5e-08   6.4e-05      14      54 ..      30      68 ..      15      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5e-08
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      L    +  l++gela++  l+  +v ++l+rL++  Lv  r
  gi|313127174|ref|YP_004037444.1| 30 LEGDAP--LSQGELAEESLLPDRTVRYALNRLEETELVSSR 68
                                      444555..******************************776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11   1.5e+02      21      38 ..       3      21 ..       2      25 .. 0.77
   2 !   18.4   0.3   1.3e-06    0.0016      19      57 ..      30      68 ..      23      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                      TCTTB-HHHHHHHH.TS-H CS
                            HTH_20 21 raegltaselaerl.dlsk 38
                                      r++ l+ +e+ erl +l++
  gi|313127174|ref|YP_004037444.1|  3 REDSLSEGEFRERLrELPP 21
                                      6889999999999944665 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.3e-06
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      L ++++l+ +elae+  l++ t++y L+ Lee +Lv ++
  gi|313127174|ref|YP_004037444.1| 30 LEGDAPLSQGELAEESLLPDRTVRYALNRLEETELVSSR 68
                                      6789***********99*******************876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.7   1.3e-06    0.0016      12      57 ..      24      68 ..       4      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-06
                                      HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                      ++++++l+  ++L s+ eLa+e      tvR AL+rLe+  lv +r
  gi|313127174|ref|YP_004037444.1| 24 KLVAKVLEGDAPL-SQGELAEESLLPDRTVRYALNRLEETELVSSR 68
                                      678888999999*.****************************9876 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.23   2.9e+02      26      51 ..       3      29 ..       1      37 [. 0.70
   2 !   15.0   0.2   1.4e-05     0.018       9      49 ..      31      66 ..      23      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.23
                            HTH_12 26 rgydigeravRyrLrkleerg.ltrrv 51
                                      r+  ++e   R rLr l     l+ +v
  gi|313127174|ref|YP_004037444.1|  3 REDSLSEGEFRERLRELPPSAkLVAKV 29
                                      677888888899999886443366555 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.4e-05
                            HTH_12  9 esdkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                                      e d+p++ +e+aee       + +r+vRy L  lee +l+ 
  gi|313127174|ref|YP_004037444.1| 31 EGDAPLSQGELAEE-----SLLPDRTVRYALNRLEETELVS 66
                                      67999999999986.....45678**************985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.4e-06    0.0069      17      58 ..      35      76 ..      20      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.4e-06
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      pls+ eLa+ + +   tv  +l rLe+ +l++++ s +D R+
  gi|313127174|ref|YP_004037444.1| 35 PLSQGELAEESLLPDRTVRYALNRLEETELVSSRYSFKDARK 76
                                      7999******************************99999995 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.6e-05     0.021      14      69 ..      22      78 ..      13      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE.EETTTEE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr.rdeeksw 69
                                      +a+lv +vL  ++ ++  +la+e  +    +r +LnrL e  lv+ + + +d  k++
  gi|313127174|ref|YP_004037444.1| 22 SAKLVAKVLEGDAPLSQGELAEESLLPDRTVRYALNRLEETELVSSRYSfKDARKQV 78
                                      578899999999999******************************987635566665 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.24      27      54 ..      37      64 ..      17      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGy 54
                                      sq  la+ + l ++Tv+ a++ Le++ +
  gi|313127174|ref|YP_004037444.1| 37 SQGELAEESLLPDRTVRYALNRLEETEL 64
                                      8999********************9865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.1e-05     0.052      22      56 ..      35      69 ..      23      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      p++  e+aee+ +p  +v  +L++Le+  lV  + 
  gi|313127174|ref|YP_004037444.1| 35 PLSQGELAEESLLPDRTVRYALNRLEETELVSSRY 69
                                      677789*************************8775 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.2e-05       0.1       5      39 ..      25      62 ..      23      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.2e-05
                            HTH_28  5 iikllaaGh...svreaArelgisrrtvyrWikryeeg 39
                                       +  +++G+   s+ e+A+e  +  rtv+  ++r+ee 
  gi|313127174|ref|YP_004037444.1| 25 LVAKVLEGDaplSQGELAEESLLPDRTVRYALNRLEET 62
                                      5677888988889999********************95 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.26   3.3e+02      29      41 ..       7      19 ..       6      19 .. 0.90
   2 ?    9.5   0.1   0.00066      0.85      11      42 .]      29      60 ..      28      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.26
                     HTH_AsnC-type 29 lSestvlrRvrrL 41
                                      lSe + ++R+r L
  gi|313127174|ref|YP_004037444.1|  7 LSEGEFRERLREL 19
                                      89********987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00066
                     HTH_AsnC-type 11 aLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                       L+ da +s  eLAe+  l   tv+  ++rLe
  gi|313127174|ref|YP_004037444.1| 29 VLEGDAPLSQGELAEESLLPDRTVRYALNRLE 60
                                      5888***************************8 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2     9e-05      0.12      14      49 ..      31      66 ..      25      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      e++ +l+  elA+++ lp  tv+  L+ L+e  +v 
  gi|313127174|ref|YP_004037444.1| 31 EGDAPLSQGELAEESLLPDRTVRYALNRLEETELVS 66
                                      67889**************************99986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.4e-05      0.11      19      54 ..      33      68 ..      11      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisrg 54
                                      + pl+q elA+   l   tv  +l++L++  l+s +
  gi|313127174|ref|YP_004037444.1| 33 DAPLSQGELAEESLLPDRTVRYALNRLEETELVSSR 68
                                      579******************************954 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.5e-05      0.12      20      58 ..      30      68 ..      23      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-05
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                       e++ p+s  e+ae+  ++++ ++  l++L++ +lv s+
  gi|313127174|ref|YP_004037444.1| 30 LEGDAPLSQGELAEESLLPDRTVRYALNRLEETELVSSR 68
                                      5678899*****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 625.40
//
Query:       gi|313127175|ref|YP_004037445.1|  [L=258]
Description: zn-dependent hydrolase, glyoxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-13   49.1   7.7    1.3e-12   48.2   7.7    1.5  1  Lactamase_B  Metallo-beta-lactamase superfamily
    0.00069   19.6   0.2     0.0015   18.5   0.2    1.6  1  BLACT_WH     Beta-lactamase associated winged helix domain
  ------ inclusion threshold ------
      0.053   13.5   0.1       0.14   12.1   0.0    1.8  2  RMMBL        Zn-dependent metallo-hydrolase RNA specificity d


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   7.7   2.1e-16   1.3e-12       4     197 .]      16     174 ..      13     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 2.1e-16
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       + +n+yl+ g ++++L+D+ + t++ +++       +   +v+++ +TH H+DH+ +++  + atd+ v++ +  ++
  gi|313127175|ref|YP_004037445.1|  16 GATNAYLV-GTERALLVDPAGRTDELDEL-------VAESNVEHIAVTHTHPDHTDAVAAYAAATDATVWCRRGRKR 84 
                                       689*****.9*****************86.......***************************************** PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHC CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallaget 157
                                        +++  +                    +++    +++    + +vt+  ++gh + +v ++g   +++GD+  a+  
  gi|313127175|ref|YP_004037445.1|  85 RFIDATGI-------------------EPDRTFVEGDVIPAGHGVTVLDTPGHAPDHVAFEGNFGVICGDLAVAEGS 142
                                       *******3...................344444444444445566677777777777778888889*********** PP

                                       CCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 158 gridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       + ++         + ++ + yl +l++l + ++ +l+pgH
  gi|313127175|ref|YP_004037445.1| 143 VVVGA--------PEGSIRAYLVALRRLHARDPPTLFPGH 174
                                       *****........*************************** PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   2.5e-07    0.0015      15      41 ..     223     249 ..     210     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.5e-07
                          BLACT_WH  15 eslhpaAergvlahLeKLeeeGkVkre 41 
                                         ++  A+ +v+ah eKL +eG+V  +
  gi|313127175|ref|YP_004037445.1| 223 SGVRDLARATVVAHIEKLAAEGRVHYD 249
                                       567889******************876 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05      0.14      20      52 ..      38      70 ..      36      93 .. 0.88
   2 ?   -3.9   0.1       2.3   1.4e+04      31      39 ..     167     175 ..     163     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                             RMMBL 20 nellelirklkprnvilvHGeeeatsalarllk 52
                                      +el el++  + +++++ H ++++t+a a++++
  gi|313127175|ref|YP_004037445.1| 38 DELDELVAESNVEHIAVTHTHPDHTDAVAAYAA 70
                                      6999**************************994 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.3
                             RMMBL  31 prnvilvHG 39 
                                       p+ +++ HG
  gi|313127175|ref|YP_004037445.1| 167 PPTLFPGHG 175
                                       666999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1659.01
//
Query:       gi|313127176|ref|YP_004037446.1|  [L=248]
Description: Fe-S oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-14   52.4   0.0    1.4e-13   51.3   0.0    1.6  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   7.6e-18   1.4e-13       1      84 [.      33     183 ..      33     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 7.6e-18
                          CxxCxxCC   1 eCkeCgaCCk.........elkvklteedlerlkaaevaeeeeeskkiak.........................ad 43 
                                       eC++CgaCCk          +++++ +++++ +++a + +e+ +++++a+                         a+
  gi|313127176|ref|YP_004037446.1|  33 ECTRCGACCKghgpaddrePHTATVFPDEVRAVQDATE-TESYDWRDVARpmpygltegddgpegetfewalqtdAC 108
                                       7****************999999***********9999.788889999999************************** PP

                          CxxCxxCC  44 grCvfldeetk......lCkiYeeRpkicrlfpas............................ekeellaraetC 84 
                                       g+Cvf++e ++       C+i+++Rp+ic+++p+s                            ++e++++ra++C
  gi|313127176|ref|YP_004037446.1| 109 GDCVFYEESEGadgttgACSIHSDRPLICETYPFSvalggtsqpmgeavdsvalgdqqdpdetDDEAMTVRAHEC 183
                                       *******9988889999*****************98888888888887777777777777777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1897.00
//
Query:       gi|313127177|ref|YP_004037447.1|  [L=140]
Description: RNA-binding protein, contains tram domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-14   52.6   3.1    3.4e-14   52.6   3.1    2.1  2  TRAM      TRAM domain
  ------ inclusion threshold ------
      0.035   13.8   0.7       0.12   12.2   0.6    1.9  2  Hexapep   Bacterial transferase hexapeptide (six repeats)
       0.15   12.1   1.4        2.2    8.3   1.2    2.0  2  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       0.2   1.2e+03      37      37 ..      34      34 ..       2      52 .. 0.50
   2 !   52.6   3.1   5.7e-18   3.4e-14       2      62 .]      79     136 ..      78     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.2
                                      - CS
                              TRAM 37 d 37
                                       
  gi|313127177|ref|YP_004037447.1| 34 R 34
                                      3 PP

  == domain 2  score: 52.6 bits;  conditional E-value: 5.7e-18
                                       XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                       +++G+   V++e+ + ++g+gi+r+++g+v++vpg++   Gd+V++++t+vk++++ Ge++
  gi|313127177|ref|YP_004037447.1|  79 VEIGELRYVEIEDIG-KQGDGIARVERGYVIIVPGAEV--GDRVKIEVTEVKSNFAVGEVI 136
                                       56889999*******.*******************999..******************985 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.51     3e+03      18      24 ..      77      83 ..      76      83 .. 0.79
   2 ?   12.2   0.6   1.9e-05      0.12      12      29 ..     105     122 ..      97     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.51
                                      TTEEE-T CS
                           Hexapep 18 gnVkIGd 24
                                      ++V+IG+
  gi|313127177|ref|YP_004037447.1| 77 PPVEIGE 83
                                      7899996 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.9e-05
                                       TTEEEETTEEE-TTEEEE CS
                           Hexapep  12 pfaviggnVkIGdnvkIg 29 
                                        +++i +++++Gd+vkI+
  gi|313127177|ref|YP_004037447.1| 105 GYVIIVPGAEVGDRVKIE 122
                                       599**************7 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.2   0.00037       2.2      34      56 ..      38      61 ..      21      70 .. 0.85
   2 ?    1.9   0.0     0.035   2.1e+02      97     116 ..      74      94 ..      63     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00037
                                      EEECBTTSHHHHHHH.HHHHHHHS CS
                             NUDIX 34 gGkvepgEtpeeAAr.REleEEtG 56
                                       G+vepgEt++ A++ RE+ EE+ 
  gi|313127177|ref|YP_004037447.1| 38 SGTVEPGETYRVALIsREAVEEAE 61
                                      69*********99877******86 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.035
                                       SSTSTTTEEEEEEEEHHHH.H CS
                             NUDIX  97 epndenevsevrwvpleel.l 116
                                       ep+ + e+ e+r+v++e++ +
  gi|313127177|ref|YP_004037447.1|  74 EPQPPVEIGELRYVEIEDIgK 94 
                                       5667899***********932 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 979.96
//
Query:       gi|313127178|ref|YP_004037448.1|  [L=575]
Description: hypothetical protein Hbor_24450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-12   48.6   0.1    3.8e-12   46.9   0.1    2.0  1  Radical_SAM  Radical SAM superfamily
    2.5e-05   24.4   0.0    6.6e-05   23.1   0.0    1.7  1  HHH_3        Helix-hairpin-helix motif
    3.2e-05   23.6   0.0    0.00012   21.8   0.0    2.0  1  HHH          Helix-hairpin-helix motif
     0.0034   17.9   0.0      0.011   16.3   0.0    1.9  1  HHH_5        Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.074   13.0   0.0       0.41   10.7   0.0    2.2  2  PsbU         Photosystem II 12 kDa extrinsic protein (PsbU)
       0.11   12.9   0.0       0.35   11.3   0.0    1.8  1  HHH_8        Helix-hairpin-helix domain
       0.12   12.5   0.0       0.43   10.7   0.0    1.9  1  HHH_2        Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.1   1.5e-15   3.8e-12       2     141 ..     193     345 ..     192     395 .. 0.73

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.5e-15
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE........SSTGGGS.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxx.......... RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg........ggeplly.......... 60 
                                       +++rgC++rCsfC+ p    ++g +++++ e++++ev+ l+  +g+k++ lg        gg+  +           
  gi|313127178|ref|YP_004037448.1| 193 ETSRGCAYRCSFCTEP----MYGNPAFRTAESVVREVENLS-ARGAKHFRLGrqadilafGGDGEAPnpdalrrlyg 264
                                       789*************....69******************6.778*******9888888844333312223333333 PP

                                       ..TTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHH CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 ..pdfvellerlaklavpgiritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlea 133
                                         ++ + +l  l+    +   itv+  + +  +e ++ ++e +   d+ ++gle+ad+  v++ +  + t +e  ea
  gi|313127178|ref|YP_004037448.1| 265 giREVAPDLQTLHLD--NMNPITVVKWPEKA-RECIRIIAEHNtpGDTAAFGLESADPV-VQEANTLNVTADECFEA 337
                                       333333333333333..34444444444443.*********99***************8.9*999999********* PP

                                       HHHHHHTT CS
                                       xxxxxxxx RF
                       Radical_SAM 134 leklreag 141
                                       +++ +e  
  gi|313127178|ref|YP_004037448.1| 338 VKIVNEEA 345
                                       **999865 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.6e-08   6.6e-05       5      45 ..     517     553 ..     515     557 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.6e-08
                             HHH_3   5 gvdiNtAsaeeLqklpGlgpklAknIvayReknGpfksree 45 
                                       + d N As +eL+ +pG+g+++A  Iv  R    p++s +e
  gi|313127178|ref|YP_004037448.1| 517 PLDPNEASMDELTSIPGIGKRTAGDIVINR----PYASADE 553
                                       6799**************************....9999887 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   4.7e-08   0.00012       6      27 ..     521     542 ..     521     543 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.7e-08
                                       HTSSHHHHHTSTT-SHHHHHHH CS
                               HHH   6 ipasreeLlalPGVGpktAeaI 27 
                                       ++as++eL+++PG+G+ tA+ I
  gi|313127178|ref|YP_004037448.1| 521 NEASMDELTSIPGIGKRTAGDI 542
                                       58******************99 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.3e-06     0.011      32      52 ..     523     543 ..     499     560 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.3e-06
                                       S-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  32 adveeLakipGiGkktAerii 52 
                                       a+ +eL++ipGiGk+tA  i+
  gi|313127178|ref|YP_004037448.1| 523 ASMDELTSIPGIGKRTAGDIV 543
                                       555777778888877777765 PP

>> PsbU  Photosystem II 12 kDa extrinsic protein (PsbU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.9   4.8e+03      32      52 ..     134     154 ..     128     180 .. 0.76
   2 ?   10.7   0.0   0.00016      0.41      10      52 ..     513     555 ..     504     563 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                                       TTHHHHHHHHS---SSGGGGG CS
                              PsbU  32 yPtlakkivknaPYdsvedvl 52 
                                       y +la   v+ a Yd v+  l
  gi|313127178|ref|YP_004037448.1| 134 YDYLAMADVEAAAYDLVDSGL 154
                                       677888889999999998655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                                       GGGTSEETTTS-GGGGGGSTTTTTHHHHHHHHS---SSGGGGG CS
                              PsbU  10 elgekvDlnnanvrafrqlrGlyPtlakkivknaPYdsvedvl 52 
                                        + + +D n a++ +   ++G+    a+ iv n PY+s ++v 
  gi|313127178|ref|YP_004037448.1| 513 GVPHPLDPNEASMDELTSIPGIGKRTAGDIVINRPYASADEVS 555
                                       45577999********************************997 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.35      43      63 ..     523     542 ..     509     543 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                       HHHTTHCTTSTT--HHHHHHH CS
                             HHH_8  43 tsleeeltklpgiGkkiaaki 63 
                                       +s++e lt++pgiGk++a  i
  gi|313127178|ref|YP_004037448.1| 523 ASMDE-LTSIPGIGKRTAGDI 542
                                       46677.************876 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00017      0.43      31      52 ..     522     543 ..     521     544 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                             HHH_2  31 kasleeLlevddiGeeiAqsiv 52 
                                       +as++eL+++++iG+++A +iv
  gi|313127178|ref|YP_004037448.1| 522 EASMDELTSIPGIGKRTAGDIV 543
                                       79****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3705.98
//
Query:       gi|313127179|ref|YP_004037449.1|  [L=425]
Description: hypothetical protein Hbor_24460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-39  133.3  10.7    3.8e-10   39.9   0.0    7.4  7  FG-GAP_2  FG-GAP repeat


Domain annotation for each model (and alignments):
>> FG-GAP_2  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   7.7e-05       1.4      11      35 ..      52      76 ..      41      85 .. 0.86
   2 !   19.9   0.0   3.6e-08   0.00065       1      49 []      97     145 ..      97     145 .. 0.88
   3 !    9.7   0.0   5.4e-05      0.97       1      35 [.     152     193 ..     152     207 .. 0.71
   4 !   39.9   0.0   2.1e-14   3.8e-10       1      49 []     214     262 ..     214     262 .. 0.92
   5 !    6.0   1.7   0.00081        15       1      49 []     269     318 ..     269     318 .. 0.74
   6 !   25.6   0.0   5.9e-10   1.1e-05       1      47 [.     328     371 ..     328     373 .. 0.93
   7 !   22.2   0.1   6.9e-09   0.00012       1      49 []     380     423 ..     380     423 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 7.7e-05
                          FG-GAP_2 11 DgaagDyFGssVaisgdtlvVGAyg 35
                                      D  ++ ++G s a++g+ + VGA+g
  gi|313127179|ref|YP_004037449.1| 52 DPDEDTFYGLSSALDGNRAFVGAPG 76
                                      77778899***************96 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.6e-08
                          FG-GAP_2   1 WteeakLtAsDgaagDyFGssVaisgdtlvVGAygddd.ngsnsGaaYvf 49 
                                       Wt+ + L++s   + D FG++ + ++  lvV+A++++  +   +G++Yv+
  gi|313127179|ref|YP_004037449.1|  97 WTQ-QPLIPSPNDSIDLFGYDLDAEDRHLVVSAPFAKVgDVEHAGEVYVY 145
                                       666.88999*************************8887555578*****8 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 5.4e-05
                          FG-GAP_2   1 WteeakLtAsDgaagDyFGssVaisgdtlvVGAy.......g 35 
                                       W    +L A    ++  FG++Va+s   ++V          +
  gi|313127179|ref|YP_004037449.1| 152 WELRHRLHAPTPRENASFGQAVALSFPRIAVTESplwlrdpV 193
                                       88889999999**************88877765555544443 PP

  == domain 4  score: 39.9 bits;  conditional E-value: 2.1e-14
                          FG-GAP_2   1 WteeakLtAsDgaagDyFGssVaisgdtlvVGAygdddngsnsGaaYvf 49 
                                       W+  + L ++Dga +D FG +V+i++  +vVGA+++ +++   Gaa+vf
  gi|313127179|ref|YP_004037449.1| 214 WSFLTELEPDDGAPDDLFGHAVDIEQQRVVVGAPRAENDDHPVGAAFVF 262
                                       999999****************************888866667*****9 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.00081
                          FG-GAP_2   1 WteeakLtAsDgaagDyFGssVaisgdtlvVGAy..gdddngsns.GaaYvf 49 
                                       W+++ +L+  D a g   G +Va + + ++VG+     ++ +s+  G++ v+
  gi|313127179|ref|YP_004037449.1| 269 WRQTGRLVGADDAPGV--GAAVATDRNIVLVGSDqfATGRSSSDVpGSVSVY 318
                                       9999999999999986..9*************98532222333434777775 PP

  == domain 6  score: 25.6 bits;  conditional E-value: 5.9e-10
                          FG-GAP_2   1 WteeakLtAsDgaagDyFGssVaisgdtlvVGAygdddngsnsGaaY 47 
                                       W  + +L+   g+ gD+FG ++++ +d  v+GA+g +++    G+aY
  gi|313127179|ref|YP_004037449.1| 328 WIFQERLVGPSGEPGDRFGAAIDMLNDHTVIGAPGVGED---GGEAY 371
                                       8899******************************99994...49999 PP

  == domain 7  score: 22.2 bits;  conditional E-value: 6.9e-09
                          FG-GAP_2   1 WteeakLtAsDgaagDyFGssVaisgdtlvVGAygdddngsnsGaaYvf 49 
                                       W+  a+L      ++ +FG+sVa++  +++VGA++  +     G+a++f
  gi|313127179|ref|YP_004037449.1| 380 WVRRATLAGTSPTEDKQFGRSVAVDSRFAIVGAPFFPG-----GSAFIF 423
                                       8888888888889999******************9988.....899888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2789.47
//
Query:       gi|313127180|ref|YP_004037450.1|  [L=63]
Description: hypothetical protein Hbor_24470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 470.04
//
Query:       gi|313127181|ref|YP_004037451.1|  [L=190]
Description: molecular chaperone [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-07   29.8   0.0      1e-06   28.8   0.0    1.6  1  HSP20       Hsp20/alpha crystallin family
  ------ inclusion threshold ------
      0.028   14.0   0.1      0.067   12.8   0.0    1.6  2  ArsA_HSP20  HSP20-like domain found in ArsA


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.2e-10     1e-06       2      93 ..      36     130 ..      35     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.2e-10
                                       --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--ST..TB-TTT-EEEE CS
                             HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPe..nvdadkvkasl 76 
                                         e+++++ v +d pg+++++++v   +++v v+  +    +++  ++   +  + +   +LP+   vda+  +a+l
  gi|313127181|ref|YP_004037451.1|  36 LLESDDAYLVVFDAPGVQRSDVQVRFLNGEVQVRIDRFRDFHEGFEMRFPGRGLSLDGGAELPDdaAVDATGASATL 112
                                       6789*******************************999555666666665666788899*****44478999999** PP

                                       .ETTEEEEEEEBSS--.. CS
                             HSP20  77 .kdGvLtvtvpkkepekk 93 
                                        ++G L+v++pk e++++
  gi|313127181|ref|YP_004037451.1| 113 tANGTLRVEIPKDEQAHD 130
                                       ************999855 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.4e-06     0.067       1      35 [.      40      74 ..      40      75 .. 0.96
   2 ?   -3.2   0.0      0.72   6.4e+03      55      62 ..     113     121 ..     101     122 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.4e-06
                        ArsA_HSP20  1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkignfr 35
                                      dd y ++ d P+v++++++++  + e  ++i++fr
  gi|313127181|ref|YP_004037451.1| 40 DDAYLVVFDAPGVQRSDVQVRFLNGEVQVRIDRFR 74
                                      789*****************************998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.72
                        ArsA_HSP20  55 e.dgvLeIr 62 
                                         +g L+++
  gi|313127181|ref|YP_004037451.1| 113 TaNGTLRVE 121
                                       348888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1335.63
//
Query:       gi|313127182|ref|YP_004037452.1|  [L=409]
Description: glycine/d-amino acid oxidase, deaminating [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-53  181.9   9.5    2.9e-53  181.7   9.5    1.0  1  DAO             FAD dependent oxidoreductase
    8.9e-11   41.6   3.1    0.00017   21.0   0.6    2.2  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.9e-09   35.8   5.7    7.2e-09   35.2   5.7    1.3  1  FAD_binding_2   FAD binding domain
    5.7e-07   29.7   1.6    1.9e-06   28.0   1.6    2.0  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.2e-05   25.7   0.0    3.4e-05   24.2   0.0    1.7  1  NAD_binding_7   Putative NAD(P)-binding
    3.1e-05   22.9   1.2    0.00066   18.5   1.2    2.1  2  HI0933_like     HI0933-like protein
    6.2e-05   22.7   0.7    0.00071   19.2   0.3    2.4  3  ApbA            Ketopantoate reductase PanE/ApbA
    0.00012   22.6   1.2     0.0028   18.2   1.5    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00035   20.0   0.9      0.089   12.1   0.2    2.2  2  Amino_oxidase   Flavin containing amine oxidoreductase
    0.00052   19.4   0.1     0.0016   17.8   0.1    1.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00069   19.0   0.8     0.0015   17.8   0.8    1.5  1  FAD_binding_3   FAD binding domain
     0.0042   16.4   0.9     0.0075   15.5   0.9    1.3  1  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.015   15.2   0.6      0.015   15.2   0.6    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.019   14.1   2.0      0.038   13.1   1.5    1.7  2  GIDA            Glucose inhibited division protein A
      0.025   13.9   0.0      0.045   13.1   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.037   13.4   0.0      0.072   12.4   0.0    1.4  1  ThiF            ThiF family
      0.053   12.8   2.1      0.094   12.0   2.1    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.061   12.9   0.1        0.1   12.2   0.1    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.099   12.0   5.3       0.15   11.3   5.3    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
       0.15   11.6   0.3        0.3   10.6   0.3    1.5  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
       0.25   11.3   2.5          2    8.4   0.1    2.6  3  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   9.5   3.4e-56   2.9e-53       1     352 []      41     378 ..      41     378 .. 0.84

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 3.4e-56
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       +v+++G+G +Gl++A++La++g  Vt++e+g ++gsg+Sgr+sg+l+ ++++  +a    r++++al+++re++++ 
  gi|313127182|ref|YP_004037452.1|  41 RVAVVGAGAVGLTAAFDLAEAGasVTVYERG-DVGSGSSGRASGILYDAYAEDVDA----RMAARALARFREFDGTG 112
                                       59*****************************.9999************88655555....***************98 PP

                                       SSTTSEEEEEEEEEES..SHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.ST..TTSEEEEETTEEEEEHHH CS
                               DAO  76 gididyrrtGllslaa..deeelealdkllallleagldaelldaeevrelepa.lp..gllgalfypdtgqvdpak 147
                                       g  + + ++ ++ +a+  de+  ea+++ +++ + +g d+   d++ + e++   l+  ++  a+  +++ + dpa 
  gi|313127182|ref|YP_004037452.1| 113 G--FSVTPCPHVAVAHesDEKTAEAIAETAERMRVHGRDVTTTDGAGLTERFGEtLRtdDVGTAVIADNAMWTDPAS 187
                                       8..89**********96666778889999999888999999999999*****87733559999999*********** PP

                                       HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTT.CTTTSEEEEEE CS
                               DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgll.keldlpispvr 221
                                       ++ a+a +++++Gv+++++tev g++ +     ++  +++ ge++++dav +aaGa+++  l+ +     +p++p r
  gi|313127182|ref|YP_004037452.1| 188 YVEAMAPRVREAGVDLRTETEV-GIRTD---PPEI--VSDdGETERYDAVLVAAGAHTKhVLADAgV--SIPMKPYR 256
                                       *******************998.89554...3344..2333777667************54444434..4599**** PP

                                       EEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGG CS
                               DAO 222 gqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPq 298
                                        q lv +++ +           p+  d   g y++p ++g +l+G    ee   d+ + d +  d++ e +  ++ +
  gi|313127182|ref|YP_004037452.1| 257 VQALVSDQPYD----------GPICYDATEGAYFRPHPEG-LLAGDGT-EEVEADPDRWDRDGDDWFVEDVTGVLDN 321
                                       ******65544..........345889999********99.8886655.4444444488888888888888888866 PP

                                       ....GCGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 299 ....lgdvlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                           ++dv+r+waGl + +pd++pl+ge    +++y+atG+ ghG++ +pa+G+++a +
  gi|313127182|ref|YP_004037452.1| 322 ragyDADVSRAWAGLCTaTPDRNPLLGEI--EDDVYVATGWHGHGFMWSPASGEAVAAM 378
                                       44456*********99967*********6..79***********************975 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.6   1.9e-07   0.00017     143     175 ..      40      72 ..       5     136 .. 0.72
   2 !   19.7   1.0   4.7e-07    0.0004       2      33 ..      41      72 ..      40     180 .. 0.85
   3 !   20.6   0.0   2.6e-07   0.00022     187     252 ..     190     250 ..     177     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.9e-07
                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveard 175
                                       +r++vvG+G++G+  A  la++g+ vt+ e++d
  gi|313127182|ref|YP_004037452.1|  40 RRVAVVGAGAVGLTAAFDLAEAGASVTVYERGD 72 
                                       566666666666666666666666666544443 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 4.7e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      +v+v+G+G+ Gl+aa +la+aga vt++e+++
  gi|313127182|ref|YP_004037452.1| 41 RVAVVGAGAVGLTAAFDLAEAGASVTVYERGD 72
                                      79999999999999999999999999996443 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 187 aaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglel 252
                                       +a++ ++++ Gv+++++t+v  i+ ++   e v +dge++ +d v+va+G   ++ l+  ++g+ +
  gi|313127182|ref|YP_004037452.1| 190 EAMAPRVREAGVDLRTETEV-GIRTDPP--EIVSDDGETERYDAVLVAAGAHTKHVLA--DAGVSI 250
                                       5667788999**********.9999998..9***********************9996..555544 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   5.7   8.4e-12   7.2e-09       2     164 ..      42     209 ..      41     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 8.4e-12
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-E.E-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgi.davlspeqkkagikdspelhrtdtlkaldela 77 
                                       v V+G+G+ GL+AA  +aeaG++v+v e +++ +g++  ++G + da+++  ++++     + l+r+  + + ++ +
  gi|313127182|ref|YP_004037452.1|  42 VAVVGAGAVGLTAAFDLAEAGASVTVYERGDVGSGSSGRASGILyDAYAEDVDARMAA---RALARFREFDGTGGFS 115
                                       89******************************999*******8637777677766655...6677766666665555 PP

                                       .-HHHHHHHHHTHHHHHHHHHHT...T----B....CCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHH CS
                     FAD_binding_2  78 .dqplveafveaapeavdeLeel...gvpfsr....tedgpvdvrelGglsatartlhdaadarretlvtghallar 146
                                         +    a+++++ e+ +e  +     +++++    t+dg+    ++G++ +t  ++  a  a +  +++    +++
  gi|313127182|ref|YP_004037452.1| 116 vTPCPHVAVAHESDEKTAEAIAEtaeRMRVHGrdvtTTDGAGLTERFGETLRTDDVGT-AVIADNAMWTDPASYVEA 191
                                       34444444444666666666666444333333445558889999999****9976666.33333499999999**** PP

                                       HHHHHHTCTEEEEESEEE CS
                     FAD_binding_2 147 lvesarkagvdfqertea 164
                                       ++ ++r+agvd++++te+
  gi|313127182|ref|YP_004037452.1| 192 MAPRVREAGVDLRTETEV 209
                                       ***************987 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   1.6   2.2e-09   1.9e-06       1      35 [.      44      78 ..      44     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.2e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      +vGaG+ Gl+aA  La+ag++v+++e++d  +G +
  gi|313127182|ref|YP_004037452.1| 44 VVGAGAVGLTAAFDLAEAGASVTVYERGDVGSGSS 78
                                      8**************************98755543 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     4e-08   3.4e-05       6      87 ..      38     145 ..      35     155 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4e-08
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapev...keele.............elvklaeeelekd........ 58 
                                       +g++v vvG+G v+++ +  l+eaga vtv+           +             e       ++++         
  gi|313127182|ref|YP_004037452.1|  38 SGRRVAVVGAGAVGLTAAFDLAEAGASVTVYERGDvgsG---SsgrasgilydayaE-------DVDARmaaralar 104
                                       689***************************877743330...133333433333331.......2221122222222 PP

                     NAD_binding_7  59 ...leg.........adlviaatddrelneriaeaakarri 87 
                                          ++g          ++++a  +d++  e+iae+a++ r+
  gi|313127182|ref|YP_004037452.1| 105 freFDGtggfsvtpcPHVAVAHESDEKTAEAIAETAERMRV 145
                                       22222233444444466999999999999999999986655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.2   7.8e-07   0.00066       2      32 ..      41      71 ..      40      77 .. 0.93
   2 ?    2.2   0.0     0.067        57     109     164 ..     186     237 ..     160     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.8e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +v+v+G+Ga Gl aA  +a++g++V+++e++
  gi|313127182|ref|YP_004037452.1| 41 RVAVVGAGAVGLTAAFDLAEAGASVTVYERG 71
                                      69***************************97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.067
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       ++ v+a+  +++eagv+lr+etev  ++++  +   v+  ++e+ + d++++A G 
  gi|313127182|ref|YP_004037452.1| 186 ASYVEAMAPRVREAGVDLRTETEVG-IRTDPPE--IVSD-DGETERYDAVLVAAGA 237
                                       45689999***************95.5455555..4444.8899999999999996 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   8.3e-07   0.00071       1      31 [.      42      72 ..      42      94 .. 0.93
   2 ?   -2.1   0.0       3.2   2.8e+03      82     136 ..     133     187 ..     131     201 .. 0.72
   3 ?    0.7   0.0      0.44   3.7e+02      35      76 ..     195     235 ..     188     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.3e-07
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      +a++GaGa+G + a  La+aga vt++ r++
  gi|313127182|ref|YP_004037452.1| 42 VAVVGAGAVGLTAAFDLAEAGASVTVYERGD 72
                                      69************************99976 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                                       HHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTE CS
                              ApbA  82 eealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpge 136
                                       +ea++e ++++  +   +++  G g  e++ e l+++ v  +v+  +a  ++p  
  gi|313127182|ref|YP_004037452.1| 133 AEAIAETAERMRVHGRDVTTTDGAGLTERFGETLRTDDVGTAVIADNAMWTDPAS 187
                                       5666666666666666677788888888888888888888888888777777665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.44
                                       HHHHHCEEEEETT..CEEEEEECEEECCHSCCCCS-ESEEEE-S CS
                              ApbA  35 alkknGlrltseg..geeilrppealsaeekselepidlvivtv 76 
                                       +++++G++l++e+  g ++ +p+ + ++    e e +d v+v+ 
  gi|313127182|ref|YP_004037452.1| 195 RVREAGVDLRTETevGIRTDPPEIVSDDG---ETERYDAVLVAA 235
                                       58999999999997555555555555555...99*******985 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.5   3.3e-06    0.0028       1      32 [.      41      72 ..      41      77 .. 0.96
   2 ?    0.9   0.0      0.82     7e+02      44      63 ..     190     209 ..     176     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.3e-06
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversd 32
                                      +v+vvG+G +gl +A  lae g++Vtv er+d
  gi|313127182|ref|YP_004037452.1| 41 RVAVVGAGAVGLTAAFDLAEAGASVTVYERGD 72
                                      79***************************987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.82
                                       HHHHHHHHHTTEEEECSEEE CS
                         Pyr_redox  44 kilqeklekngievllntkv 63 
                                       ++++ ++++ g++++++t+v
  gi|313127182|ref|YP_004037452.1| 190 EAMAPRVREAGVDLRTETEV 209
                                       5678899**********997 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.2    0.0001     0.089       3      24 ..      51      72 ..      50      87 .. 0.94
   2 !    6.4   0.0    0.0053       4.5     212     264 ..     188     239 ..     181     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHHTTEEEEEEESSS CS
                     Amino_oxidase  3 GLaaArqLlsaGfdVtvlEard 24
                                      GL+aA  L++aG +Vtv+E  d
  gi|313127182|ref|YP_004037452.1| 51 GLTAAFDLAEAGASVTVYERGD 72
                                      9******************998 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0053
                                       HHHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHH CS
                     Amino_oxidase 212 lpealae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgv 264
                                        +ea+a   ++ g+d+r++t+V  i++++ +  +   dge+ ++DaV+v++   +
  gi|313127182|ref|YP_004037452.1| 188 YVEAMAPrvREAGVDLRTETEV-GIRTDPPE--IVSDDGETERYDAVLVAAGAHT 239
                                       6899999888899999999777.57775555..5557*************98765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.8e-06    0.0016     163     198 ..      38      73 ..      15     101 .. 0.74
   2 ?   -2.0   0.0         2   1.7e+03     247     274 ..     218     244 ..     187     253 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                       Pyr_redox_3 163 agqkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                       +g++v+V+G++  +  aA++l+++ga+Vtv+ rg+ 
  gi|313127182|ref|YP_004037452.1|  38 SGRRVAVVGAGAVGLTAAFDLAEAGASVTVYERGDV 73 
                                       677788888888888888888888888888877764 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                       Pyr_redox_3 247 vktedgkkvevkddvvlatGykpdlsfl 274
                                       + ++dg ++e +d v++a G + ++ + 
  gi|313127182|ref|YP_004037452.1| 218 IVSDDG-ETERYDAVLVAAGAHTKHVLA 244
                                       444555.568889999999999887655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.8   1.8e-06    0.0015       4      45 ..      42      84 ..      40      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EE CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radgl 45
                                      V++VGaG +Gl++a  L+eaG +v++ e+ +  +  + ra+g+
  gi|313127182|ref|YP_004037452.1| 42 VAVVGAGAVGLTAAFDLAEAGASVTVYERGDVGSGSSgRASGI 84
                                      99***************************98877776688765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.9   8.8e-06    0.0075      20      64 ..      42      86 ..      36     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.8e-06
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEES.SSS--TTTTTTSTTB CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailer.svspGGGawlGGqlf 64
                                      v++vGaG+ GLtaa+ la++ +  v++ er  v  G      G l+
  gi|313127182|ref|YP_004037452.1| 42 VAVVGAGAVGLTAAFDLAEA-GASVTVYERgDVGSGSSGRASGILY 86
                                      89******************.9******983455555444556555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.6   1.8e-05     0.015       2      30 ..      42      70 ..      41     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      vav+GaG +G   a  +a+ag +V+++++
  gi|313127182|ref|YP_004037452.1| 42 VAVVGAGAVGLTAAFDLAEAGASVTVYER 70
                                      9*************************997 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.5   4.5e-05     0.038       2      28 ..      42      68 ..      41      94 .. 0.90
   2 ?   -1.6   0.0       1.2   1.1e+03      96     150 ..     187     237 ..     168     251 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi 28
                                      v V+G+G  G+ AA+ +a++Ga+v+ +
  gi|313127182|ref|YP_004037452.1| 42 VAVVGAGAVGLTAAFDLAEAGASVTVY 68
                                      89**********************988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA  96 lyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                        y +++  ++++   +++++e+   + +       +v +dget + +av +a+G+
  gi|313127182|ref|YP_004037452.1| 187 SYVEAMAPRVRE-AGVDLRTETEVGIRT---DPPEIVSDDGETERYDAVLVAAGA 237
                                       444455555544.445555554444443...334456666666666666666666 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.2e-05     0.045      32      67 ..      35      70 ..      14      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                                      S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                      2-Hacid_dh_C 32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydr 67
                                       + sg++v+++G+G++G ++a  l++ g+ v++y+r
  gi|313127182|ref|YP_004037452.1| 35 PDGSGRRVAVVGAGAVGLTAAFDLAEAGASVTVYER 70
                                      56689*****************************98 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.4e-05     0.072      19      42 ..      40      63 ..      20      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.4e-05
                                      SEEEEE--SHHHHHHHHHHHHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 19 skvllvGaGglGsellknLalsGv 42
                                       +v++vGaG++G  ++ +La +G 
  gi|313127182|ref|YP_004037452.1| 40 RRVAVVGAGAVGLTAAFDLAEAGA 63
                                      69*******************996 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.1   0.00011     0.094      29      59 ..      40      70 ..      33      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDv 59
                                       +v v+G+G +Gl A+   ++ ga+Vtv++ 
  gi|313127182|ref|YP_004037452.1| 40 RRVAVVGAGAVGLTAAFDLAEAGASVTVYER 70
                                      589************************9985 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012       0.1       2      28 ..      41      67 ..      40      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                      EEEEE--STTHHHHHHHHHHCTSEEEE CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevig 28
                                      +++v+G+G vGl+ a  lae+g  v++
  gi|313127182|ref|YP_004037452.1| 41 RVAVVGAGAVGLTAAFDLAEAGASVTV 67
                                      89*********************9987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.3   0.00018      0.15       2      69 ..      42     107 ..      41     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq 69 
                                       v VvG+g+ G++AA   a+aGa+v + e+ +v  G +++ + + +   +ae+ v  ++a + l+r r+
  gi|313127182|ref|YP_004037452.1|  42 VAVVGAGAVGLTAAFDLAEAGASVTVYERGDVGSG-SSGRASGILYDAYAED-VDARMAARALARFRE 107
                                       89***********************9999887433.3444444444445344.666666666666666 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00036       0.3       4      49 ..      39      84 ..      38      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                                      TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT- CS
                              IlvN  4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegf 49
                                      g+++av+G G+ G + a  l ++g  v+v  r +  s ++ +++g+
  gi|313127182|ref|YP_004037452.1| 39 GRRVAVVGAGAVGLTAAFDLAEAGASVTVYERGDVGSGSSGRASGI 84
                                      789*************************988877766666666665 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0024         2       1      40 [.      43      77 ..      43     106 .. 0.89
   2 ?   -2.8   0.1       6.3   5.4e+03     116     125 ..     142     151 ..     122     174 .. 0.51
   3 ?    2.3   0.0      0.17   1.4e+02     126     154 ..     210     236 ..     187     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0024
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                      a+vGaG+ Gl+++  L++        ++t++++   g+g+
  gi|313127182|ref|YP_004037452.1| 43 AVVGAGAVGLTAAFDLAEA-----GASVTVYERGDVGSGS 77
                                      89**************999.....5999999998888765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.3
                     NAD_binding_9 116 tvevhraevv 125
                                       +++vh  +v+
  gi|313127182|ref|YP_004037452.1| 142 RMRVHGRDVT 151
                                       2222322222 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.17
                     NAD_binding_9 126 dleeradgqavlladgaslaadaVvLAlG 154
                                        ++++    +++ +dg++ ++daV +A G
  gi|313127182|ref|YP_004037452.1| 210 GIRTD--PPEIVSDDGETERYDAVLVAAG 236
                                       44444..446899**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2802.46
//
Query:       gi|313127183|ref|YP_004037453.1|  [L=260]
Description: luciferase-like monooxygenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0032   17.0   4.1     0.0033   16.9   3.3    1.4  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.078   12.5   0.0    2.0  3  PrpR_N          Propionate catabolism activator


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   3.3   3.7e-07    0.0033     213     313 ..     159     245 ..     133     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-07
                    Bac_luciferase 213 agrdpadirvgisltvivadteeeAraearaliagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelva 289
                                        g    d ++++ +++++ d+e+e ++ + a+           ++ +  a+a  ++ e d+n+ ++a d++  + v+
  gi|313127183|ref|YP_004037453.1| 159 TGY---DGEIAVYAPTVLSDDEDEILDAVGAYA----------ARRRPVAKALPEGAETDSNAADRARDVL-GAAVR 221
                                       444...678999*****************9888..........4444444455666777777777776665.899** PP

                    Bac_luciferase 290 atalvGtpeqvaerlaayaeagvd 313
                                         alvG+ e v+e++ +++eag+d
  gi|313127183|ref|YP_004037453.1| 222 DYALVGSVERVREQVSTLKEAGAD 245
                                       **********************97 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.43   3.8e+03     131     156 ..       6      31 ..       3      37 .. 0.73
   2 ?   -1.4   0.0      0.16   1.5e+03     121     155 ..     122     157 ..      97     162 .. 0.68
   3 ?   12.5   0.0   8.7e-06     0.078      78     125 ..     201     249 ..     178     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.43
                            PrpR_N 131 dlAekaGlksvlltsgkesvrqAiee 156
                                       + +++ G+ +v l+  +  vr+A+e+
  gi|313127183|ref|YP_004037453.1|   6 RSVSQTGIDAVALKPKECDVRMALET 31 
                                       56678888888888877778888776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.16
                            PrpR_N 121 evvvGdgvvadlAekaG.lksvlltsgkesvrqAie 155
                                       ++ vG + ++++A + G  ++ ll+   es  +A++
  gi|313127183|ref|YP_004037453.1| 122 DAWVGTEGIERVALAVGgTQYELLSRRTESNLRALR 157
                                       466777777777777543677777777777777764 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 8.7e-06
                            PrpR_N  78 gfeniikglktlselldldieiytin.seeeaeaavkelkaegvevvvG 125
                                       g e+ ++++++ +++l+  ++ y++  s e ++++v +lk++g +v+vG
  gi|313127183|ref|YP_004037453.1| 201 GAETDSNAADRARDVLGAAVRDYALVgSVERVREQVSTLKEAGADVIVG 249
                                       56778899999*********99987725566****************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1699.78
//
Query:       gi|313127184|ref|YP_004037454.1|  [L=199]
Description: nudix family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-16   59.2   0.1    5.5e-16   58.8   0.1    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.1   3.1e-20   5.5e-16       2     125 ..      19     142 ..      18     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 3.1e-20
                                       EEEEEEEEEEETTSE..EEEEEES..SSSTTT.EESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEE CS
                             NUDIX   2 lrravgvvllnekge..vLlvrrs..kkpfpg.WelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhyla 72 
                                       +++av++ +l ++ge  vL ++r+     +pg  ++PgG  ep + +++++A+RE+ EE+Gl+ +++e++g+l++ +
  gi|313127184|ref|YP_004037454.1|  19 RQAAVIAPVLTRRGEdhVLFTKRAdhLGEHPGqMSFPGGSREPSDgDLRATALREAYEEIGLRSNEVEFFGCLDDIK 95 
                                       67788888777777779*******88444444479***************************99*******998877 PP

                                       EEEEEEEEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHH CS
                             NUDIX  73 pydgpygdeheilyvfleevegelepndenevsevrwvpleellkeklaaesr 125
                                       +++++       + ++++ ++ e ep+ e ev+e+  + + +l   + +++ +
  gi|313127184|ref|YP_004037454.1|  96 TVTDYSV-----TPFVARVPDREYEPD-EREVAEIAVLAVSDLTNLDNYESEE 142
                                       7765555.....355558888888888.**************95544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1330.22
//
Query:       gi|313127185|ref|YP_004037455.1|  [L=160]
Description: hypothetical protein Hbor_24520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0096   16.1   0.5      0.027   14.6   0.5    1.8  1  FANC_SAP  Fanconi anemia-associated nuclease SAP domain


Domain annotation for each model (and alignments):
>> FANC_SAP  Fanconi anemia-associated nuclease SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.5   1.5e-06     0.027       6      24 ..      16      33 ..      14      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-06
                          FANC_SAP  6 eLFaLltkpELlqaFaavl 24
                                      +LF++lt++EL +a+ + l
  gi|313127185|ref|YP_004037455.1| 16 DLFGVLTRAELERALDE-L 33
                                      8*************988.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1045.09
//
Query:       gi|313127186|ref|YP_004037456.1|  [L=365]
Description: hypothetical protein Hbor_24530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2668.76
//
Query:       gi|313127187|ref|YP_004037457.1|  [L=398]
Description: arabinose efflux permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-44  152.2  57.5      6e-36  124.1  37.1    2.2  2  MFS_1       Major Facilitator Superfamily
    7.9e-09   34.8  16.1    2.8e-08   33.0   8.9    2.1  2  MFS_1_like  MFS_1 like family
    9.6e-05   21.8  33.3    9.6e-05   21.8  33.3    1.3  2  MFS_4       Uncharacterised MFS-type transporter YbfB


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1  37.1     1e-39     6e-36       7     348 ..       4     328 ..       1     332 [. 0.83
   2 !   41.8  12.4     1e-14   6.1e-11      28     166 ..     223     362 ..     219     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 1e-39
                             MFS_1   7 lsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfa 82 
                                       l+ lar +++p+l   l + + i + ++gl++tl+ +g+a+  +p+G++ +r+ r r vl +g++l+a++++ ++ a
  gi|313127187|ref|YP_004037457.1|   4 LVNLARIVFAPLLE-QLISVFSIGEGTAGLIVTLVWVGSALPRIPTGWVLTRVPRHRvVLGTGVILTAASAFTAA-A 78 
                                       66678889999999.5678999***********************************9************44444.3 PP

                             MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslgWravfyila 158
                                        s+ +++v+ +l+Gl +ga+f a++ l+++++p+ + gra+g+ +++++l+a+++ p +  +l+  + W +vf+ l+
  gi|313127187|ref|YP_004037457.1|  79 DSVAMVAVGALLMGLSSGAYFVAANPLVSELYPE-RVGRAMGIHGMASQLAAVIAaPFVTLALTLFVEWYVVFVCLG 154
                                       6666*****************************9.*****************8885777778889999********* PP

                             MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw..illialllfffgfsglltllply 233
                                       i++++a v   +++++ ++++ ++++ e+         +++++a l++  +    ++i  ++ +f+++gl+ +  ly
  gi|313127187|ref|YP_004037457.1| 155 IAAFVATV---VFYYTAKRTNLPEAGGED---------RNLLRAALNQWRIIalGIVILGFT-GFVWQGLFNFYELY 218
                                       ******99...555555555555556666.........133444444444433223333333.45************ PP

                             MFS_1 234 lqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl 309
                                        +++ +++ +   +   l l++++g+++++++g+l+drl+r ++ll +l+++++++l+l ++      + ll++ +l
  gi|313127187|ref|YP_004037457.1| 219 -MQTKNIAdATAKNM--LTLIFAAGVPAFFISGKLADRLPRVPYLLSILVAFVIGVLALTVTRGL---IPLLVLTAL 289
                                       .99999998557777..8889999999999***********************************...555566777 PP

                             MFS_1 310 iGfglgfvfpsllalasdlappeeagtasglfntagslg 348
                                       iG      fp+l +++ d +p e++++a+++++    ++
  gi|313127187|ref|YP_004037457.1| 290 IGYVIHSLFPALDTYLLDTLPDENRASAYAVYSAGMMVV 328
                                       88866667************************9877665 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 1e-14
                             MFS_1  28 gispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfp 104
                                       +i+ +++  +ltl +++ + a ++ G l+dr+ r ++ll  l++f++g+l+l+++ +l +llvl +l G    +lfp
  gi|313127187|ref|YP_004037457.1| 223 NIADATAKNMLTLIFAAGVPAFFISGKLADRLPRVPYLLSILVAFVIGVLALTVTRGLIPLLVLTALIGYVIHSLFP 299
                                       56667777789999999***************7777888888889999566665466668***************** PP

                             MFS_1 105 agaaliadwfpkeergraigllsagfslGailgpllggllasslg.Wravfyilaivsllafv 166
                                       a  +++ d  p+e+r++a++++sag+ +  + g  + g+l + +g ++ +  + a+v +++++
  gi|313127187|ref|YP_004037457.1| 300 ALDTYLLDTLPDENRASAYAVYSAGMMVVQASGSSVVGALREGGGtYEFIRAATAVVPFVGIL 362
                                       ****************************************97777755555555555555544 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.7   0.00058       3.4     280     356 ..      49     123 ..      23     129 .. 0.75
   2 !   33.0   8.9   4.7e-12   2.8e-08     176     375 ..     143     341 ..     126     351 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00058
                        MFS_1_like 280 aeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsg 356
                                       +  l++   h+++l ++++++++  +  a+ +++ +v +  +L g+s g++++aa   vs++ p+++ ++ +g+  +
  gi|313127187|ref|YP_004037457.1|  49 GWVLTRVPRHRVVLGTGVILTAASAFT-AAADSVAMVAVGALLMGLSSGAYFVAANPLVSELYPERV-GRAMGIHGM 123
                                       445666677899999999998887654.5668888888899***********************986.566666655 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 4.7e-12
                        MFS_1_like 176 llp.ysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllval.ilgmswgiienFlfl 250
                                       +++ y++++++ +a +v+++++ ++ + t+  ++ +     + l + l++ ++i++ +v+l + g++w  + nF++l
  gi|313127187|ref|YP_004037457.1| 143 FVEwYVVFVCLGIAAFVATVVFYYTAKRTNLPEAGGEDR--NLLRAALNQWRIIALGIVILgFTGFVWQGLFNFYEL 217
                                       333687888888888888888888888888888888774..5566889999999996554449************** PP

                        MFS_1_like 251 YLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisf 327
                                       Y++ ++    ++  +++l  +a +p ff++ kl ++l  v  l+  l+a+++  l + +++ +  +l++ +L g+ +
  gi|313127187|ref|YP_004037457.1| 218 YMQTKNIADATAKNMLTLIFAAGVPAFFISGKLADRLPRVPYLLSILVAFVIGVLALTVTRGLIPLLVLTALIGYVI 294
                                       ***************************************************************************** PP

                        MFS_1_like 328 gllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwd 375
                                       + l+ a+ +y  +  p++ +a   +++s+ +  + +a+Gs + G+l +
  gi|313127187|ref|YP_004037457.1| 295 HSLFPALDTYLLDTLPDENRASAYAVYSAGM-MVVQASGSSVVGALRE 341
                                       ***************************9764.4668888888887755 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8  33.3   1.6e-08   9.6e-05       7     359 ..       7     361 ..       1     364 [. 0.86
   2 ?   -4.2   0.3       1.3   7.7e+03     287     300 ..     376     389 ..     371     394 .. 0.42

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-08
                             MFS_4   7 iGRFsytpiLPallaegqlslsqagllaaaNylGYLvGallaafalsag.aeRlrllagllatvllllamaltesfa 82 
                                       ++R +++p+L +l+   ++  + agl+ +  ++G  +  +     l +  ++R++l  g+++t++++++ a+++s+a
  gi|313127187|ref|YP_004037457.1|   7 LARIVFAPLLEQLISVFSIGEGTAGLIVTLVWVGSALPRIPTGWVLTRVpRHRVVLGTGVILTAASAFT-AAADSVA 82 
                                       89********************************99888877555544416677788888888877776.56799** PP

                             MFS_4  83 aflliRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsa 159
                                       ++++  +l G++s++ +v++  lv +   + r +r ++++     l  ++++  v+l+l+l++++ ++ + l++ ++
  gi|313127187|ref|YP_004037457.1|  83 MVAVGALLMGLSSGAYFVAANPLVSEL-YPERVGRAMGIHGMASQLAAVIAAPFVTLALTLFVEWYVVFVCLGIAAF 158
                                       *******************99999777.8999999999*999999999***************************** PP

                             MFS_4 160 vllllvalllpraalreas.aa.aeaakaeqkslpllalllaYglaGfGYiitatFlvaiardgaggalleallWll 234
                                       v++++   +++r++l ea  ++    ++a+++ + +   ++  g+ Gf +     F  ++ +++  + + ++ + +l
  gi|313127187|ref|YP_004037457.1| 159 VATVVFYYTAKRTNLPEAGgEDrNLLRAALNQWRIIALGIVILGFTGFVWQGLFNFYELYMQTKNIADATAKNMLTL 235
                                       *********99666555441330334444444444444556778888888889999999999999999999999999 PP

                             MFS_4 235 vGlaaivgvlvwlrvakrsglrralaaallieavgvllsllspsplglivssvllGltflaitalvlqlarelappa 311
                                       +  a +++ +++ ++a+r    + l  +l+  ++gvl+ ++  +++ l+v   l+G       +   ++     p++
  gi|313127187|ref|YP_004037457.1| 236 IFAAGVPAFFISGKLADRLPRVPYLLSILVAFVIGVLALTVTRGLIPLLVLTALIGYVIHSLFPALDTYLLDTLPDE 312
                                       999*******************************************************9999998888888899988 PP

                             MFS_4 312 t.rrllglmTasfgigQilGpllasllaeatgslalallvaaaalvlaa 359
                                       +   + ++  a   + Q+ G  ++++l e  g+++   ++ a++ ++++
  gi|313127187|ref|YP_004037457.1| 313 NrASAYAVYSAGMMVVQASGSSVVGALREGGGTYEFIRAATAVVPFVGI 361
                                       846788999***********************99999999998888876 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 1.3
                             MFS_4 287 vllGltflaitalv 300
                                       + lGl+ +++t l 
  gi|313127187|ref|YP_004037457.1| 376 LALGLAVIVTTLLL 389
                                       33333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 2593.53
//
Query:       gi|313127188|ref|YP_004037458.1|  [L=49]
Description: hypothetical protein Hbor_24550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00079   19.4   0.3      0.001   19.1   0.3    1.2  1  DZR              Double zinc ribbon
     0.0086   16.0   2.2       0.09   12.8   0.3    2.1  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0096   16.0   1.9       0.23   11.6   0.1    2.1  2  UPF0547          Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
      0.018   15.0   2.5       0.15   12.1   0.2    2.2  2  ADK_lid          Adenylate kinase, active site lid
      0.021   14.7   1.4      0.032   14.1   1.4    1.3  1  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
      0.034   13.5   0.4          6    6.4   0.0    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.038   14.0   0.6      0.038   14.0   0.6    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.038   14.0   1.6      0.095   12.7   1.6    1.6  1  zinc-ribbons_6   zinc-ribbons
       0.08   13.3   2.5        2.8    8.4   0.1    2.1  2  Arc_trans_TRASH  Archaeal TRASH domain
      0.085   12.8   2.9       0.16   11.9   2.9    1.5  1  Prok-RING_1      Prokaryotic RING finger family 1
       0.12   12.5   3.3       0.23   11.6   3.3    1.5  2  Zn-ribbon_8      Zinc ribbon domain
       0.18   11.8   4.2       0.86    9.6   0.2    1.9  2  Nudix_N_2        Nudix N-terminal
       0.21   11.2   1.7        1.2    8.8   0.1    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.92    9.6   5.5        1.1    9.4   0.3    2.4  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   7.9e-07     0.001      12      37 ..      13      44 ..       6      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.9e-07
                               DZR 12 arfCseCgtklkavaa......edrCpsCgek 37
                                        +C eCg++lk+ ++       + Cp C+++
  gi|313127188|ref|YP_004037458.1| 13 RLTCAECGESLKKRNDpdevfsVRICPTCETE 44
                                      458********98777*************987 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.065        83      20      26 ..      14      20 ..      11      22 .. 0.82
   2 !   12.8   0.3     7e-05      0.09      21      29 ..      37      45 ..      33      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.065
                    PhnA_Zn_Ribbon 20 lvCpeCa 26
                                      l C eC+
  gi|313127188|ref|YP_004037458.1| 14 LTCAECG 20
                                      67****8 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7e-05
                    PhnA_Zn_Ribbon 21 vCpeCahEw 29
                                      +Cp+C  Ew
  gi|313127188|ref|YP_004037458.1| 37 ICPTCETEW 45
                                      9******** PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.037        47      17      21 ..      16      20 ..      13      22 .. 0.88
   2 !   11.6   0.1   0.00018      0.23      13      26 .]      34      47 ..      33      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.037
                           UPF0547 17 CphCG 21
                                      C++CG
  gi|313127188|ref|YP_004037458.1| 16 CAECG 20
                                      99999 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00018
                           UPF0547 13 aaqfCphCGyvFqa 26
                                      ++++Cp C +++++
  gi|313127188|ref|YP_004037458.1| 34 SVRICPTCETEWKE 47
                                      689*********86 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00012      0.15      23      36 .]      15      28 ..      10      28 .. 0.91
   2 ?    3.2   0.2      0.07        89       2       8 ..      36      42 ..      36      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                      B-TTT--.-B--GG CS
                           ADK_lid 23 lCDkCGepLvqRsD 36
                                       C +CGe L +R D
  gi|313127188|ref|YP_004037458.1| 15 TCAECGESLKKRND 28
                                      699*********99 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.07
                                      EE-TTT- CS
                           ADK_lid  2 rvCpkCG 8 
                                      r+Cp C 
  gi|313127188|ref|YP_004037458.1| 36 RICPTCE 42
                                      89**996 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.4   2.5e-05     0.032      25      49 ..      15      47 ..      11      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                                      E-HHHHHHHHH........TT-B-TTT--B--E CS
                        zf-C3HC4_3 25 lCeeCaekllk........rkkkCpiCrrpiek 49
                                      +C eC e+l+k        + + Cp C ++ ++
  gi|313127188|ref|YP_004037458.1| 15 TCAECGESLKKrndpdevfSVRICPTCETEWKE 47
                                      8********9999**999999*******99765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0047         6      18      24 ..      15      21 ..      12      27 .. 0.60
   2 ?    5.7   0.1    0.0082        10      16      24 ..      35      43 ..      33      44 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0047
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C+ CG+
  gi|313127188|ref|YP_004037458.1| 15 TCAECGE 21
                                      4666654 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0082
                       zf-ribbon_3 16 dnvCpyCGt 24
                                      +++Cp C t
  gi|313127188|ref|YP_004037458.1| 35 VRICPTCET 43
                                      567887765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6     3e-05     0.038      70      95 ..      13      44 ..       3      49 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
                                      EEEETTTS-EEECHHH.HH.....S-TTTSSS CS
                              HypA 70 kvrCreCgkefeleek.al.....rCpkCgsa 95
                                      +++C eCg++ +++++ ++      Cp+C+++
  gi|313127188|ref|YP_004037458.1| 13 RLTCAECGESLKKRNDpDEvfsvrICPTCETE 44
                                      689********98774433467789****986 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.6   7.4e-05     0.095      15      41 ..      12      47 ..       3      49 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.4e-05
                                      SEEE-TTT--.........EEEEEEE-SSS-S---E CS
                    zinc-ribbons_6 15 eqyhCeaCqe.........dlkkealCpeCeqelev 41
                                      ++++C +C e         ++  + +Cp+Ce e + 
  gi|313127188|ref|YP_004037458.1| 12 DRLTCAECGEslkkrndpdEVFSVRICPTCETEWKE 47
                                      677888888877777777777778888888877665 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3     0.017        22      26      36 ..      16      26 ..       6      27 .. 0.88
   2 ?    8.4   0.1    0.0022       2.8      26      35 ..      38      47 ..      35      49 .] 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
                   Arc_trans_TRASH 26 CktCkselkkk 36
                                      C  C + lkk+
  gi|313127188|ref|YP_004037458.1| 16 CAECGESLKKR 26
                                      99*******97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0022
                   Arc_trans_TRASH 26 CktCkselkk 35
                                      C+tC++e k+
  gi|313127188|ref|YP_004037458.1| 38 CPTCETEWKE 47
                                      *******998 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.9   0.00012      0.16       2      29 ..      11      44 ..      10      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                       Prok-RING_1  2 ytgkkCpvCgkelkeedD......iVvCpeCgtp 29
                                      y    C  Cg+ lk+ +D      + +Cp+C t 
  gi|313127188|ref|YP_004037458.1| 11 YDRLTCAECGESLKKRNDpdevfsVRICPTCETE 44
                                      66779*********9966555555679****995 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0044       5.6      27      38 ..      14      25 ..       5      27 .. 0.72
   2 ?   11.6   3.3   0.00018      0.23       7      34 ..      15      43 ..      10      48 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0044
                       Zn-ribbon_8 27 taCPeCgsevrr 38
                                       +C eCg+ +++
  gi|313127188|ref|YP_004037458.1| 14 LTCAECGESLKK 25
                                      459999888877 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00018
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgs 34
                                       C eCg+   ++   ++   +  CP+C  
  gi|313127188|ref|YP_004037458.1| 15 TCAECGESLKKRNDPDEVFSVRiCPTCET 43
                                      5*****77776665554447778****86 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00067      0.86      16      29 ..       7      20 ..       5      23 .. 0.89
   2 ?    9.5   4.0   0.00072      0.92       3      30 ..      16      43 ..      16      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00067
                                      TT-SS-EEEETTTT CS
                         Nudix_N_2 16 dgDnreRlvCpaCg 29
                                      + D+  Rl+C+ Cg
  gi|313127188|ref|YP_004037458.1|  7 EKDTYDRLTCAECG 20
                                      579999*******9 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00072
                                      -TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgt 30
                                      C +CG+ ++ r  +++     +Cp C+t
  gi|313127188|ref|YP_004037458.1| 16 CAECGESLKKRNDPDEVFSVRICPTCET 43
                                      9***********999999999*****86 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00093       1.2       2      13 ..      13      24 ..      12      30 .. 0.84
   2 ?    2.0   0.2      0.13   1.6e+02       4      10 ..      37      43 ..      35      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00093
                            zf_UBZ  2 tylCerCgkeip 13
                                        +C++Cg+++ 
  gi|313127188|ref|YP_004037458.1| 13 RLTCAECGESLK 24
                                      579*****9975 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                            zf_UBZ  4 lCerCgk 10
                                      +C+ C +
  gi|313127188|ref|YP_004037458.1| 37 ICPTCET 43
                                      6****86 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.1   7.8e+03      15      19 ..       5       9 ..       5      11 .. 0.73
   2 ?    9.4   0.3   0.00087       1.1       4      14 ..      16      26 ..      14      27 .. 0.88
   3 ?    3.0   0.3     0.088   1.1e+02      22      26 .]      37      41 ..      34      43 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.1
                            zf-ACC 15 eLern 19
                                      eLe++
  gi|313127188|ref|YP_004037458.1|  5 ELEKD 9 
                                      78986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00087
                            zf-ACC  4 CpsCgemlykk 14
                                      C +Cge+l k+
  gi|313127188|ref|YP_004037458.1| 16 CAECGESLKKR 26
                                      ********987 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.088
                            zf-ACC 22 VCPkC 26
                                      +CP C
  gi|313127188|ref|YP_004037458.1| 37 ICPTC 41
                                      67777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 340.37
//
Query:       gi|313127189|ref|YP_004037459.1|  [L=364]
Description: oxidoreductase, aryl-alcohol dehydrogenase like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-29  102.4   0.0    3.6e-23   82.2   0.0    2.4  2  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.0     2e-27   3.6e-23       2     145 ..      34     213 ..      33     302 .. 0.77
   2 !   17.8   0.0   8.3e-08    0.0015     238     281 ..     309     354 ..     297     362 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 2e-27
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE........ CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv........ 70 
                                       +g+Gt  lg+++  +++   e+l +ale G+n++DtA  Y+  +se+++Geal ++   reev++atK+        
  gi|313127189|ref|YP_004037459.1|  34 IGIGTY-LGDPTDAADARYREALTAALESGVNLVDTAINYRCQRSERVVGEALREADIAREEVVVATKGgfvpfdgs 109
                                       889998.777677778888899*****************************************************99 PP

                                       ................--SSSTTSSSS-HH....HHHHHHHHHHHHHT-S-EEEEEE-S--TTS-..........HH CS
                      Aldo_ket_red  71 ................dlrdaeiksglske....niresleeslkrLgtdyvDllllHrpdpslp.........sie 118
                                                       +  d++  +++s++     +++ +++sl +Lg+d+vD +++H+p+ +l          ++e
  gi|313127189|ref|YP_004037459.1| 110 rpedpgayvrdefvrtGIVDGAELARGSHAiapgYLDALFDRSLDNLGLDTVDCYYVHNPETQLAvrsredvydQLE 186
                                       9999999999999999444444444444445555******************************************* PP

                                       HHHHHHHHHHHTTSEEEEEEES--HHH CS
                      Aldo_ket_red 119 evldaleelvkeGkiraiGvSnfsveq 145
                                        ++++lee + +G +  +Gv+ + + +
  gi|313127189|ref|YP_004037459.1| 187 AAFEVLEERRLAGELGVYGVATWKAFR 213
                                       *********************887543 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 8.3e-08
                                       H.TT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG-.-- CS
                      Aldo_ket_red 238 e.hgvslaqlalryalsqpavgivipgasnieqlednldalel.kl 281
                                       +  g++ aq al++a s+p+v+++++g+ ++e++ +n++a  + +l
  gi|313127189|ref|YP_004037459.1| 309 QlSGETAAQRALNFARSAPGVTCALVGTGSPEHVAENVAAGTFePL 354
                                       44689**********************************9977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2374.44
//
Query:       gi|313127190|ref|YP_004037460.1|  [L=388]
Description: exopolyphosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-10   40.7   0.1    3.4e-10   40.1   0.1    1.3  1  DHH       DHH family
    4.5e-08   33.6   0.2    8.4e-08   32.7   0.2    1.3  1  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   3.7e-14   3.4e-10       2     101 .]      60     216 ..      59     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.7e-14
                                       EEEE-ECSSSHHHHHHHHHHHH...............................................CECS--TC CS
                                       xxxxxxxxxxxxxxxxxxxxxx...............................................xxxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialan...............................................llvDhnek 31 
                                       +++++h npD D++++ai++a                                                +lvDhn++
  gi|313127190|ref|YP_004037460.1|  60 VAVLMHPNPDPDAMAAAIGVAClaeqvgtdsyiqysgqirhqenrafetvldldldaidhvtdlaaehvVLVDHNQP 136
                                       78999*****************777777666666666666666666666666666666666666666666******* PP

                                       GGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHH................TT----HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxx RF
                               DHH  32 sqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaellee................kkeeiske 92 
                                          + +   +      i+DHH  + + e+++    +++++g++a+ivae++++                ++ +++++
  gi|313127190|ref|YP_004037460.1| 137 RGFAGA---DGILPFAIVDHHPGEGTGERFT---DVRTDYGACASIVAEYFRDigakpvppdrhasevgSEYTVPST 207
                                       *99976...9999**********87666664...56789************99888777777777666666666666 PP

                                       HHHHHHHHH CS
                                       xxxxxxxxx RF
                               DHH  93 iaellllgi 101
                                       ia+ ll gi
  gi|313127190|ref|YP_004037460.1| 208 IATGLLYGI 216
                                       666666665 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.2   9.3e-12   8.4e-08      21     124 ..     258     358 ..     244     365 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 9.3e-12
                                       HHHHHHHHHHHHTCEEEC..TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHSS CS
                             DHHA1  21 alaklkaeellekaeevk..gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkdgv 94 
                                       +  +lka ++       +    +++v+ +g+  + +a+ +aad+l +   + +++v+v +e++ + ++s+rs++d+v
  gi|313127190|ref|YP_004037460.1| 258 EVLELKARAIAG-----RdvRGPFAVSDIGTLSNVDAIPQAADELIQ--LEgVTAVVVCGERDGTLYLSGRSRDDRV 327
                                       333333333333.....145999******999999************..887888887777777*********99** PP

                                       -HHHHHHHHHHHTTCCE.EEETCEEEEEEEH CS
                             DHHA1  95 dagelakeaaaklgggG.GGHdlAaGagipa 124
                                       ++g  + +a + + g   GGH+ + G+++p+
  gi|313127190|ref|YP_004037460.1| 328 HMGRTLGHALDNVPGASaGGHARMGGGQVPQ 358
                                       *************99888*********9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2545.14
//
Query:       gi|313127191|ref|YP_004037461.1|  [L=308]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-12   48.2   0.1    1.5e-12   47.7   0.1    1.2  1  NAD_binding_10   NAD(P)H-binding
    1.1e-11   44.6   0.0    2.2e-11   43.7   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    8.9e-06   26.0   0.1    2.2e-05   24.7   0.0    1.7  2  TrkA_N           TrkA-N domain
    4.6e-05   22.6   0.0    0.00011   21.3   0.0    1.6  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00023   20.9   0.0    0.00049   19.8   0.0    1.5  2  ApbA             Ketopantoate reductase PanE/ApbA
    0.00025   20.8   0.0    0.00062   19.6   0.0    1.6  1  DUF1731          Domain of unknown function (DUF1731)
    0.00054   20.5   0.2     0.0013   19.2   0.2    1.7  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00065   19.3   0.0     0.0011   18.5   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
  ------ inclusion threshold ------
       0.01   15.0   0.0      0.031   13.4   0.0    1.7  1  RmlD_sub_bind    RmlD substrate binding domain
      0.021   14.1   0.1      0.036   13.3   0.1    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.042   13.3   0.0        4.5    6.6   0.0    2.1  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.052   13.8   0.0      0.099   12.9   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.077   13.6   0.0       0.18   12.4   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   1.1e-15   1.5e-12       4     176 ..      10     197 ..       8     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.1e-15
                                       SHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC...HHHH CS
                    NAD_binding_10   4 GkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk...deeg 77 
                                       G vG +l ++l+++ gh+vt + R+ + la++e ++g +   +dvtd+++la  l +ad  v+a+++gg+      +
  gi|313127191|ref|YP_004037461.1|  10 GYVGLELGRQLAES-GHDVTGVRRSDDGLAAVE-SAGFSPARADVTDPDSLAP-LPDADWLVFAASSGGRgaeA--A 81 
                                       89************.5***************98.7***************998.67777666666555553441..2 PP

                                       .......HHHHHHHH..HHCT--EEEEEEETTTTSGCGCHHHHHHHH........CCHHHHHHHHHHHHHHHHSSSE CS
                    NAD_binding_10  78 .......aknivdaa..keagvkRfvlvsaigvgdevpgefgewnke........llkaylaakraaeellrasgld 137
                                               +n++d    ++++  R+v+ s+ gv+ ++ g   ++++e          +  ++a r a e   a g+d
  gi|313127191|ref|YP_004037461.1|  82 rrvyvegLQNVIDEYggRASQPDRLVYTSSTGVYGDHGGG--WVDEEtsldpttdKTRVLAEAERVAVEDASAAGID 156
                                       45677779****97644899*************9754442..22222211111112344456666777777889*** PP

                                       EEEEEE-CEE-ST--SEEEEETTSS----..EEEHHHHHHH CS
                    NAD_binding_10 138 wTivrpggLtdepttkyrvvekgepfkgg..sisradVAdv 176
                                        T+ r +gL   ++ +      g+  +g+   + r+d A +
  gi|313127191|ref|YP_004037461.1| 157 GTVARFAGLYGPDRYRLDRYLTGPVTEGYlnMVHRDDAAGA 197
                                       **********9999888888888877774448899988765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   1.6e-14   2.2e-11       2     179 ..       5     172 ..       4     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.6e-14
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       lV+G  G++G  l ++l+e g++v+g+ r  ++ +  + +  +  ++d+td+++l+ l +   +d  + +A  gg +
  gi|313127191|ref|YP_004037461.1|   5 LVLGC-GYVGLELGRQLAESGHDVTGVRRSDDGLAAVESAGFSPARADVTDPDSLAPLPD---ADWLVFAASSGGRG 77 
                                       78887.************************888888888888****************99...799999999***** PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHH..TCTEEEEEEEGGGGTSCSSSS.BSTCSTTS----SSHHHHHHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarka..gvkrllflsSsevYGkdaeqp.keettltgplkpnspYaaaKlagekl 152
                                       a++ ++ +     ++g +n++++   +  +++rl++ sS+ vYG+      +eet+    l p++   +  + +e++
  gi|313127191|ref|YP_004037461.1|  78 AEAARRVY-----VEGLQNVIDEYGGRasQPDRLVYTSSTGVYGDHGGGWvDEETS----LDPTTDKTRVLAEAERV 145
                                       *9999888.....99*******9975523777************999943255555....55555555555566677 PP

                                       HHHHHHHHT-EEEEEEESEEESTTS-T CS
                         Epimerase 153 veayaaqyglnaiilrlfnlyGprnge 179
                                       + + a + g++ ++ r   lyGp ++ 
  gi|313127191|ref|YP_004037461.1| 146 AVEDASAAGIDGTVARFAGLYGPDRYR 172
                                       666677789**************9544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.6e-08   2.2e-05       2      71 ..       5      72 ..       4      96 .. 0.87
   2 ?   -3.0   0.0       6.1   8.4e+03      55      69 ..     201     215 ..     195     221 .. 0.52

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.6e-08
                                      EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SS CS
                            TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatg 71
                                      +++G+G vG +l ++L e g+ dv+++ ++++ ++ ++  g+    +d+td++ L  a + +ad+++ a++
  gi|313127191|ref|YP_004037461.1|  5 LVLGCGYVGLELGRQLAEsGH-DVTGVRRSDDGLAAVESAGFSPARADVTDPDSL--APLPDADWLVFAAS 72
                                      79****************555.8******************************99..56677777777665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.1
                                       HHHTTGGGESEEEE- CS
                            TrkA_N  55 Leeagiekadaviaa 69 
                                       L ea++++ d+v+++
  gi|313127191|ref|YP_004037461.1| 201 LLEADAARDDVVLVV 215
                                       444444444444443 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   8.1e-08   0.00011       5     143 ..       8     134 ..       4     193 .. 0.76
   2 ?   -1.6   0.0      0.79   1.1e+03     240     272 ..     206     237 ..     196     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.1e-08
                         3Beta_HSD   5 gaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag 81 
                                       g+G++G +l ++L + ++     v  +r s+  l  +++ +      +Dvtd d+l   l ++d +++ as      
  gi|313127191|ref|YP_004037461.1|   8 GCGYVGLELGRQLAESGH----DVTGVRRSDDGLAAVESAGFS-PARADVTDPDSLA-PLPDADWLVFAASSGGRG- 77 
                                       89*************997....567788888888899999998.99*********97.588999999886654433. PP

                         3Beta_HSD  82 kltedeimkvnvkGTrnvlea..cvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhq 143
                                           +   +v v+G +nv++    + ++  +lvYtSs +v g+  +g   +  dEe+ ++++  
  gi|313127191|ref|YP_004037461.1|  78 ---AEAARRVYVEGLQNVIDEygGRASQPDRLVYTSSTGVYGD--HGGGWV--DEETSLDPTTD 134
                                       ...466789**********97336788899*************..666666..67776666543 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.79
                         3Beta_HSD 240 svagqayfisddsPvesyddfnltllkelglel 272
                                       +++ ++  + dd+Pv   + f+  l  e g+++
  gi|313127191|ref|YP_004037461.1| 206 AARDDVVLVVDDEPVD-KWSFADWLADECGVSH 237
                                       5566677899*****9.999*999999999876 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.5e-07   0.00049       2      43 ..       5      47 ..       4      70 .. 0.89
   2 ?   -3.2   0.0       4.2   5.8e+03      20      46 ..     207     233 ..     201     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.5e-07
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEE CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrl 43
                                      ++lG+G +G  l+ +La+ g+dvt + rs+  l+a++++G++ 
  gi|313127191|ref|YP_004037461.1|  5 LVLGCGYVGLELGRQLAESGHDVTGVRRSDdGLAAVESAGFSP 47
                                      69************************************99875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                                       HTHCEEEE-SCHHHHHHHHHCEEEEET CS
                              ApbA  20 agadvtlilrsrrlealkknGlrltse 46 
                                       a  dv+l++ ++ +++++ ++   +++
  gi|313127191|ref|YP_004037461.1| 207 ARDDVVLVVDDEPVDKWSFADWLADEC 233
                                       445688888888787776665555555 PP

>> DUF1731  Domain of unknown function (DUF1731)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   4.5e-07   0.00062      12      39 ..     254     282 ..     252     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.5e-07
                           DUF1731  12 emae.llLegqrVlPkrLleaGFqFrypd 39 
                                       e a+  +L++ r +  rL e+G++F yp+
  gi|313127191|ref|YP_004037461.1| 254 EAARrRILTSKRCSNDRLRELGYEFAYPT 282
                                       7788889*********************9 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   9.5e-07    0.0013       1      35 [.       3      37 ..       3      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.5e-07
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      +++v+G Gy+glEl+  lae g++Vt v rsd  l
  gi|313127191|ref|YP_004037461.1|  3 HALVLGCGYVGLELGRQLAESGHDVTGVRRSDDGL 37
                                      689***************************99765 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   8.3e-07    0.0011       5      34 ..       6      35 ..       2      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.3e-07
                                      EE--STTHHHHHHHHHHCTSEEEEE-S-HH CS
                    UDPG_MGDP_dh_N  5 viGlGYvGlvtaavlaeighevigvDidee 34
                                      v+G GYvGl  +  lae gh+v+gv  ++ 
  gi|313127191|ref|YP_004037461.1|  6 VLGCGYVGLELGRQLAESGHDVTGVRRSDD 35
                                      89**********************977665 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.2e-05     0.031       7     154 ..       8     168 ..       2     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                                       STTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                     RmlD_sub_bind   7 GanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                       G  G +G eL +qlae+g++v+++ r+               ++d+td++++a l ++   d++v aA         
  gi|313127191|ref|YP_004037461.1|   8 G-CGYVGLELGRQLAESGHDVTGVRRSddglaavesagfspaRADVTDPDSLAPLPDA---DWLVFAAS-SGGRG-- 77 
                                       4.599*******************9999*************************99988...88887664.44444.. PP

                                       HSHHHHHHHHTHHHHHHHHHHHHCT-...EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHH.HHHH... CS
                     RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavga...lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEq.avla... 138
                                          eaa +v +e+ +++ ++   + +    L++ S+  V+  +      e+   +P +   r  ++ E+ av++   
  gi|313127191|ref|YP_004037461.1|  78 --AEAARRVYVEGLQNVIDEYGGRASqpdRLVYTSSTGVYGDHGGGWVDEETSLDPTTDKTRVLAEAERvAVEDasa 152
                                       ..45778899999998877654333312269********97776666678888999999999999999834554444 PP

                                       H-SSEEEEEE-SEESS CS
                     RmlD_sub_bind 139 agkkalivRtswvyge 154
                                       ag + ++ R++ +yg 
  gi|313127191|ref|YP_004037461.1| 153 AGIDGTVARFAGLYGP 168
                                       5568899999999986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.6e-05     0.036     144     178 ..       3      37 ..       2      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrll 178
                                       +++v G Gy+G+El  +la+ g++vt v + d  l
  gi|313127191|ref|YP_004037461.1|   3 HALVLGCGYVGLELGRQLAESGHDVTGVRRSDDGL 37 
                                       789***********************999988766 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0      0.01        14       5      33 ..       8      36 ..       5      61 .. 0.80
   2 ?    6.6   0.0    0.0032       4.5     120     151 ..     102     133 ..      77     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.01
                                      TTSHHHHHHHHHHHHCT-CCEEEEEEESS CS
                     GDP_Man_Dehyd  5 iaGfiGsylaelLlekgyevhgivrrsss 33
                                      + G++G  l ++L e g++v+g+ r ++ 
  gi|313127191|ref|YP_004037461.1|  8 GCGYVGLELGRQLAESGHDVTGVRRSDDG 36
                                      57********************8776654 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0032
                                       TTSEEEEEEEGGGG-S-SSSSB-TTS-----S CS
                     GDP_Man_Dehyd 120 kkvrfyqaStsEvYGkvqevpqtEttpfyPrs 151
                                       +  r++ +S+  vYG+     ++E+t ++P+ 
  gi|313127191|ref|YP_004037461.1| 102 QPDRLVYTSSTGVYGDHGGGWVDEETSLDPTT 133
                                       567999************************86 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.2e-05     0.099       2      66 ..       5      61 ..       4      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-05
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal 66
                                      l++G+G+vG  + + la++++    +t + rs+++l+a+     +  f+++  d+ ++++ La+l
  gi|313127191|ref|YP_004037461.1|  5 LVLGCGYVGLELGRQLAESGHD---VTGVRRSDDGLAAV----ESAGFSPARADVTDPDS-LAPL 61
                                      89*****************985...**********9888....5789*************.9986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013      0.18       4      45 ..       6      43 ..       4      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                      EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHH CS
                     F420_oxidored  4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaee 45
                                      ++G+G +g  l ++l+++g   h+++ + +r+ + +++ +++
  gi|313127191|ref|YP_004037461.1|  6 VLGCGYVGLELGRQLAESG---HDVT-GVRRSDDGLAAVESA 43
                                      68*****************...****.889999999887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2133.12
//
Query:       gi|313127192|ref|YP_004037462.1|  [L=143]
Description: hypothetical protein Hbor_24590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 940.51
//
Query:       gi|313127193|ref|YP_004037463.1|  [L=1004]
Description: hypothetical protein Hbor_24600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1004 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 7134.52
//
Query:       gi|313127194|ref|YP_004037464.1|  [L=294]
Description: hypothetical protein Hbor_24610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 2431.06
//
Query:       gi|313127195|ref|YP_004037465.1|  [L=143]
Description: hypothetical protein Hbor_24620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1164.42
//
Query:       gi|313127196|ref|YP_004037466.1|  [L=159]
Description: hypothetical protein Hbor_24630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1040.42
//
Query:       gi|313127197|ref|YP_004037467.1|  [L=575]
Description: hypothetical protein Hbor_24640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.5   5.0      0.051   14.0   5.0    1.8  1  DUF2231   Predicted membrane protein (DUF2231)
      0.078   12.9   4.8       0.49   10.4   1.8    3.1  2  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> DUF2231  Predicted membrane protein (DUF2231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   5.0   5.7e-06     0.051       4      99 ..     480     575 .]     478     575 .] 0.95

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-06
                           DUF2231   4 vglwnlvaalvigflaalaGlvelllaepsirakktallHavggvlllalivaltvWrfvlrlreeeqvsplylals 80 
                                       ++l++ +++ ++ ++aa +G  ++ l+e  ++a    ll +++g+ +l+l+v+lt     l    ++++    + l+
  gi|313127197|ref|YP_004037467.1| 480 AALFAPLVGGATVAMAARMGAADTALVEDGAQALGPELLGTAVGAYVLVLAVVLTTLATGLDRGLDRTLVGYRVGLA 556
                                       678888999999*********************************************99999999999********* PP

                           DUF2231  81 lvvvvlllvqgwlGaeLvy 99 
                                       l+ ++  +++++ Ga Lv+
  gi|313127197|ref|YP_004037467.1| 557 LLSATAAYLAAFRGAALVF 575
                                       ***************9986 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.023     2e+02      15      70 ..     126     181 ..     120     241 .. 0.60
   2 ?   10.4   1.8   5.4e-05      0.49       8     120 ..     368     487 ..     344     491 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC.T-TT.TS-HHHHHHHHH CS
                             T2SSF  15 lveaLellaeeaengplaeelkriarrlraGg.slseale.rtpssefpelvvqlira 70 
                                       +++a + +a++a +gpla+ l++ +rr r    s  e+++ ++ +++fp l ++++ +
  gi|313127197|ref|YP_004037467.1| 126 PERAASFAAHTA-DGPLADSLAEHVRRARGTPnSGFESFArEW-RDHFPALERAISLL 181
                                       566666677777.999999988888888877632245555433.33555555544433 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.4e-05
                                       HHHTT--HHHHHHHHHHHHS..SHHHHHHHHHHHHHHHTTSSHHHHHC.......T-TT.TS-HHHHHHHHHHHHHT CS
                             T2SSF   8 llsaGvplveaLellaeeae..ngplaeelkriarrlraGgslseale.......rtpssefpelvvqlirageegg 75 
                                        +saG +++ aLe++a+  +   g++    + ++rrlr   s++ea+          ps+  +  ++ l+ a+ eg 
  gi|313127197|ref|YP_004037467.1| 368 RVSAGDSVEVALESAADAVStpAGAVFADAAGVRRRLRV--SVREAFLgrygvlaDVPSPRTRAAAALLSVAATEGR 442
                                       578889999999999999975555555555555555554..568888888888878888999*************** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXX CS
                             T2SSF  76 nLaevLerlaeyleeerelrrkllaallepllllvvallvllill 120
                                       + +++  + a++l e r+ + + + +l+++  +l  +++++++l+
  gi|313127197|ref|YP_004037467.1| 443 PAGHAVVATADHLSELRRVESEARRELASVTGTLSNTAALFAPLV 487
                                       *****************************9999998888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 4056.15
//
Query:       gi|313127198|ref|YP_004037468.1|  [L=647]
Description: ATPase, type iv secretory pathway virb11 component like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-36  124.4   0.0    6.3e-36  123.8   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.014   15.7   0.9      0.043   14.2   0.1    2.2  2  AAA_16    AAA ATPase domain
      0.046   14.2   0.0      0.091   13.3   0.0    1.4  1  ABC_tran  ABC transporter
       0.17   11.7   0.1       0.38   10.5   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0   1.4e-39   6.3e-36       4     247 ..     276     533 ..     273     551 .. 0.90

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 1.4e-39
                             T2SSE   4 lleallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlp...ek 76 
                                       +l+ l++d++v+d++ + p +   vr  +dg ++r+  +l+++ +++l+sr+ +++++  s+ +p +da++    ++
  gi|313127198|ref|YP_004037468.1| 276 VLDDLFADPRVTDVVASAPVAsNPVRVAIDGERIRTNVRLTPDGAAALASRFRHASGRGFSRASPALDAAIDapnGS 352
                                       678899***********9999899999****9***************************************998888 PP

                             T2SSE  77 gvrlrvvllPvvagealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                        vr+ +v++P++ g  ++ R ++ ++ tl  l+a+++l+++ a++l+ av++  + lv+G+ g GKttll +ll e+
  gi|313127198|ref|YP_004037468.1| 353 RVRVAGVTAPASDGIGFAFRAHDGRAWTLPGLVASGTLSAETAAFLSFAVERGATGLVAGTRGAGKTTLLGSLLWEL 429
                                       899999*********************************************************************** PP

                             T2SSE 154 nksderivtvEDpvEiqle.....ganqvqlnak...kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnT 222
                                       ++   r+vtvED+ E+ ++     g ++  l+++   +++    d++r+aLRl    ++vGE+R+ e+ ++ +A+  
  gi|313127198|ref|YP_004037468.1| 430 PAA-TRLVTVEDTPELPVAalrdgGRDVQPLHTDlgeDGSFSPTDAVRTALRLGDGALVVGEVRGDEASALYEAMRV 505
                                       ***.***********9886121214556667777999999******************************9999975 PP

                             T2SSE 223 ...GHlgslsTlHansaagalerL.eqlg 247
                                          GH + l+T+H +s+a + er+ ++lg
  gi|313127198|ref|YP_004037468.1| 506 gahGHAV-LGTIHGDSPAAVRERVvSDLG 533
                                       2227***.***********9999625666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   9.6e-06     0.043      25     123 ..     406     503 ..     392     506 .. 0.59
   2 ?   -3.6   0.1       2.8   1.2e+04     138     145 ..     608     615 ..     592     636 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.6e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.......aesael 94 
                                          l+ G +G GK++l+ +ll +l ++  +++ +++ +l       ++a + +  + ++ l+++       +     
  gi|313127198|ref|YP_004037468.1| 406 ATGLVAGTRGAGKTTLLGSLLWELPAATRLVTVEDTPEL-------PVAALRDGGRDVQPLHTDlgedgsfS---PT 472
                                       34699****************999999555544444444.......34444444455566665533222221...22 PP

                            AAA_16  95 eawrekleeala......avpelagaeasrllell 123
                                       +a     ++al+       v+e++g+eas+l+e++
  gi|313127198|ref|YP_004037468.1| 473 DA----VRTALRlgdgalVVGEVRGDEASALYEAM 503
                                       22....22222233445567777777777777765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
                            AAA_16 138 vlvlDdlq 145
                                         vlD l+
  gi|313127198|ref|YP_004037468.1| 608 ADVLDALD 615
                                       22333333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     2e-05     0.091       4      36 ..     398     430 ..     396     449 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllk 36 
                                       +s+ +++g +  + G  GaGK+tLl  l+ +l 
  gi|313127198|ref|YP_004037468.1| 398 LSFAVERGATGLVAGTRGAGKTTLLGSLLWELP 430
                                       699**********************98876665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   8.4e-05      0.38      20      41 ..     403     424 ..     394     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.4e-05
                            AAA_29  20 dlkg.atlltGpsGsGKSTllDA 41 
                                       + +g + l++G+ G+GK+Tll +
  gi|313127198|ref|YP_004037468.1| 403 E-RGaTGLVAGTRGAGKTTLLGS 424
                                       4.45588*************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 4058.51
//
Query:       gi|313127199|ref|YP_004037469.1|  [L=156]
Description: hypothetical protein Hbor_24660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1129.84
//
Query:       gi|313127200|ref|YP_004037470.1|  [L=157]
Description: hypothetical protein Hbor_24670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.012   15.9   2.4      0.014   15.7   2.4    1.1  1  MutS_III      MutS domain III
      0.028   14.9   2.5      0.049   14.1   2.5    1.4  1  DUF3209       Protein of unknown function (DUF3209)
      0.028   14.9   0.5       0.43   11.1   0.0    2.3  2  NPV_P10       Nucleopolyhedrovirus P10 protein
      0.039   14.6   1.5       0.16   12.6   0.3    2.4  2  SlyX          SlyX
      0.054   13.9   0.5       0.12   12.7   0.1    1.9  2  CLZ           C-terminal leucine zipper domain of cyclic nucl
      0.061   13.7   0.2      0.098   13.1   0.2    1.4  1  DUF4094       Domain of unknown function (DUF4094)
      0.092   13.0   2.9       0.88    9.9   0.6    2.6  2  ABC_tran_CTD  ABC transporter C-terminal domain
       0.16    9.9   0.1        0.2    9.6   0.1    1.0  1  Prominin      Prominin
       0.34   11.3   1.8       0.82   10.0   0.2    2.2  3  BLOC1_2       Biogenesis of lysosome-related organelles compl
        2.9    7.2   8.3        3.7    6.8   8.3    1.3  1  DUF4407       Domain of unknown function (DUF4407)
        3.9    5.9   9.4        4.7    5.6   9.4    1.2  1  FUSC          Fusaric acid resistance protein family


Domain annotation for each model (and alignments):
>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   2.4   8.4e-06     0.014      46     125 ..       6     111 ..       5     157 .] 0.49

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.4e-06
                                       S-HHHHHHHHHHHHH.T......................TT.HHHHHHHHTT.---HHHHHHHHHTT---HHHHHHH CS
                                       xxxxxxxxxxxxxxx.xx....................xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III  46 tdleeInaRldaVee.le....................neelreelrellrr.lpDleRllsrislgkakardlkal 100
                                       tdl+++ aRldaVe+ l+                     e+l+e+  ++l++ +  l+R +s++s+   + + ++ l
  gi|313127200|ref|YP_004037470.1|   6 TDLTTLAARLDAVERaLTdddrdqpsndasgtdtdteaAEALSETTVADLEQsIAALDRRVSELSA---ELEAVRGL 79 
                                       899***********9888777777777666655433332222333333344333444444444444...22234446 PP

                                       HHHHHHHHTTTTT---SSTHHHHH.......H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.......x RF
                          MutS_III 101 lealkaleelvallekeklaesee.......e 125
                                       l  ++a++e+v+ + +  la  e+       +
  gi|313127200|ref|YP_004037470.1|  80 LGGVQAVNESVERRADLALAIAEQlaaahdeD 111
                                       66666666655555544443333322222220 PP

>> DUF3209  Protein of unknown function (DUF3209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.5     3e-05     0.049      49     115 ..      39     109 ..      12     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                                       -SHHHHHHHHHHHHHHHHHHHHH........STT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF3209  49 kdlaelerhldaalvdLeeevaktded....dpeldYlRgrlvavrdaeralkrlveeleallddleelHd 115
                                       +d ++ e + +++++dLe+ +a+ d+      +el+ +Rg+l  v++++++++r ++ + a+ ++l ++Hd
  gi|313127200|ref|YP_004037470.1|  39 TDTEAAEALSETTVADLEQSIAALDRRvselSAELEAVRGLLGGVQAVNESVERRADLALAIAEQLAAAHD 109
                                       5667777788899999999999887642222678899*********************************9 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.19   3.2e+02      35      53 ..       6      24 ..       2      33 .. 0.70
   2 ?   11.1   0.0   0.00026      0.43      11      49 ..      57      95 ..      47     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.19
                           NPV_P10 35 pdvtelnekLdaqsaqLae 53
                                       d+t l ++Lda   +L++
  gi|313127200|ref|YP_004037470.1|  6 TDLTTLAARLDAVERALTD 24
                                      4666677777777776664 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00026
                           NPV_P10 11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsa 49
                                      + i+a+d +V+ l+++++ v+  l  v+ +ne +++ ++
  gi|313127200|ref|YP_004037470.1| 57 QSIAALDRRVSELSAELEAVRGLLGGVQAVNESVERRAD 95
                                      667888888888888888888888888888877776655 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.56   9.2e+02      40      58 ..       8      26 ..       4      40 .. 0.51
   2 ?   12.6   0.3    0.0001      0.16      12      55 ..      45      88 ..      39     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.56
                                      HHHHHHT-XXXXXXXXXXX CS
                              SlyX 40 lrllaerlkeleessgase 58
                                      l  la rl ++e +  +++
  gi|313127200|ref|YP_004037470.1|  8 LTTLAARLDAVERALTDDD 26
                                      4444455544444444333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX 12 lafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55
                                       a  e t+ +L + +a+ ++++++l ++l++++  l  +++ ++
  gi|313127200|ref|YP_004037470.1| 45 EALSETTVADLEQSIAALDRRVSELSAELEAVRGLLGGVQAVNE 88
                                      57889999999999999999999999999999988865555444 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.5   7.3e+03      61      69 ..      11      19 ..       5      23 .. 0.44
   2 ?   12.7   0.1   7.5e-05      0.12      24      57 ..      43      76 ..      33      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.5
                               CLZ 61 LkqRitkLE 69
                                      L +R+ ++E
  gi|313127200|ref|YP_004037470.1| 11 LAARLDAVE 19
                                      333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.5e-05
                               CLZ 24 aeqkeleekverLessLeaLqtrlarLlaeyess 57
                                      a +   e+ v  Le+s+ aL+ r+  L ae+e++
  gi|313127200|ref|YP_004037470.1| 43 AAEALSETTVADLEQSIAALDRRVSELSAELEAV 76
                                      445567999**********************986 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2     6e-05     0.098      55      86 ..      45      77 ..       6      79 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-05
                           DUF4094 55 kdilg.evskthkaiqtLdktissLemeLaaar 86
                                      + + +  v + ++ i +Ld+++s+L  eL+a r
  gi|313127200|ref|YP_004037470.1| 45 EALSEtTVADLEQSIAALDRRVSELSAELEAVR 77
                                      233345788899******************987 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.092   1.5e+02      39      57 ..       4      22 ..       1      25 [. 0.82
   2 ?    9.9   0.6   0.00054      0.88      11      37 ..      53      79 ..      42     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.092
                      ABC_tran_CTD 39 dpeklaelsaeleeleaeL 57
                                      d + l+ l a+l+++e +L
  gi|313127200|ref|YP_004037470.1|  4 DKTDLTTLAARLDAVERAL 22
                                      55889999*****999988 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00054
                      ABC_tran_CTD 11 eeleaeIeaLEeeiaeleaeladpely 37
                                      + le+ I+aL+ + +el ael++    
  gi|313127200|ref|YP_004037470.1| 53 ADLEQSIAALDRRVSELSAELEAVRGL 79
                                      468999999999999999998876555 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00012       0.2     623     703 ..       5      92 ..       3     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00012
                          Prominin 623 kvnletlaekleelanelsngk....knlkqslkneaqdlraiqqelvlplessvkklkksvkklde...ensdlqe 692
                                       k++l+tla++l+++ ++l+       +n  + + ++ +  +a+ +++v  le+s++ l ++v +l++     ++l  
  gi|313127200|ref|YP_004037470.1|   5 KTDLTTLAARLDAVERALTDDDrdqpSNDASGTDTDTEAAEALSETTVADLEQSIAALDRRVSELSAeleAVRGLLG 81 
                                       799***************77766666555566666777777777777777777777777777777775544455555 PP

                          Prominin 693 sikkllaaver 703
                                        ++ + ++ver
  gi|313127200|ref|YP_004037470.1|  82 GVQAVNESVER 92 
                                       56666555554 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.6   2.6e+03      75      91 ..       6      22 ..       3      24 .. 0.77
   2 ?   10.0   0.2    0.0005      0.82      71      94 ..      49      72 ..      45      74 .. 0.90
   3 ?    0.3   0.0      0.52   8.5e+02      12      41 ..      70      99 ..      68     109 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                           BLOC1_2 75 teLeeavseLDeyskeL 91
                                      t+L++++++LD+  ++L
  gi|313127200|ref|YP_004037470.1|  6 TDLTTLAARLDAVERAL 22
                                      67889999999876655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0005
                           BLOC1_2 71 ekqvteLeeavseLDeyskeLEak 94
                                      e++v++Le+ +++LD  ++eL a 
  gi|313127200|ref|YP_004037470.1| 49 ETTVADLEQSIAALDRRVSELSAE 72
                                      689******************876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.52
                           BLOC1_2 12 eaeleatvedyklLeklNeaasekykklkd 41
                                      +aelea++  +  ++++Ne+++++ +    
  gi|313127200|ref|YP_004037470.1| 70 SAELEAVRGLLGGVQAVNESVERRADLALA 99
                                      678888888888888888888877665555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.3    0.0023       3.7     109     248 ..      19     154 ..       5     157 .] 0.66

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0023
                           DUF4407 109 daelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaa 185
                                       ++ l + ++++ +   + ++++ +a  a  e+ +a+l++ i+a+++r+++l ae++  + g  g    gv+   ++ 
  gi|313127200|ref|YP_004037470.1|  19 ERALTDDDRDQPSNDASGTDTDTEAAEALSETTVADLEQSIAALDRRVSELSAELE-AVRGLLG----GVQAVNESV 90 
                                       45555555555555555555556666666677777777777777777777777776.3344222....466666666 PP

                           DUF4407 186 kekkaqldaaqaelaelkakld..atarlaalraelaeleaerakeraasqaaaaaddGllarle 248
                                       +++ + + a+ ++la+++++ d    +rl+++ ++  +++++r++++ +++   +a d l+arl+
  gi|313127200|ref|YP_004037470.1|  91 ERRADLALAIAEQLAAAHDEDDglVVERLPDDAETVGDVADRRDDTACDTDG-DEAEDSLAARLR 154
                                       6666666777777777777755777789999999999988888777777776.666788888875 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   9.4    0.0029       4.7     179     288 ..      41     155 ..       4     157 .] 0.72

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0029
                              FUSC 179 geegaeareaararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpe 255
                                        e +++ +e++ a+l + i+al+  +s +++e + +r   + +++ +  + +   l+ ++a++la+ ++e+++ v  
  gi|313127200|ref|YP_004037470.1|  41 TEAAEALSETTVADLEQSIAALDRRVSELSAELEAVRGLLGGVQAVNESVERRADLALAIAEQLAAAHDEDDGLV-- 115
                                       233344448999999999***************************************************999998.. PP

                              FUSC 256 laallaelaal.......eaaaaaealeaalaalrarlra 288
                                       ++ l ++++++       +++a   + ++a ++l arlr+
  gi|313127200|ref|YP_004037470.1| 116 VERLPDDAETVgdvadrrDDTACDTDGDEAEDSLAARLRE 155
                                       5555555555555566674444444445555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1176.89
//
Query:       gi|313127201|ref|YP_004037471.1|  [L=361]
Description: cell division GTPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.5e-25   89.3   0.0    9.9e-25   87.9   0.0    1.7  1  Tubulin    Tubulin/FtsZ family, GTPase domain
    9.1e-05   21.8   0.2     0.0002   20.7   0.2    1.5  1  Tubulin_2  Tubulin like
  ------ inclusion threshold ------
      0.043   13.2   0.2      0.072   12.4   0.2    1.3  1  HEM4       Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.0   1.7e-28   9.9e-25       2     192 ..       3     168 ..       2     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 1.7e-28
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE- CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklll 78 
                                       ++ igvGq+G+++  el++ + +  +                 +  +  +va++  + +l+ i  +       ++l+
  gi|313127201|ref|YP_004037471.1|   3 TVLIGVGQAGGKLTRELVD-FDERMEF----------------GAVL-DAVAVNSAKADLRDIPFE-------TILI 54 
                                       689****************.4333232................4444.788**********99999.......**** PP

                                       -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE...SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEE CS
                           Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcds..lqgffitaslgGGTGSGlgpvilevlkeeypkalvvtv 153
                                       g++  +++g+gg++e+g+e++++ ++e+  ++++  +  ++++f++a+lgGGTGSG +pv++  l++ y ++++++ 
  gi|313127201|ref|YP_004037471.1|  55 GQDRVKGHGVGGDNELGAEVMQADKREVLSALDGRITaeAEAIFVVAGLGGGTGSGGAPVLVNELQQIY-DVPIYAL 130
                                       *********************************988755789**************************9.99***** PP

                                       EEE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHH CS
                           Tubulin 154 vvlPsefsevvvepynailalkelieesdavividNdaL 192
                                        +lP +  e+  ++ na  +lk++ +e+d+++++dNda+
  gi|313127201|ref|YP_004037471.1| 131 GILPGDS-EGAMYQVNAGRSLKTVAREADSLLLVDNDAF 168
                                       ****877.*****************************97 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   3.4e-08    0.0002     154     227 ..      93     166 ..      68     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.4e-08
                         Tubulin_2 154 eglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkELna.... 226
                                       e   +fVv +L GGTGSG +  ++  l++i+      v i++l +lP       ++g  ++ Na ++Lk +++    
  gi|313127201|ref|YP_004037471.1|  93 EAEAIFVVAGLGGGTGSGGAPVLVNELQQIY----D-VPIYALGILPGD-----SEGAMYQVNAGRSLKTVAReads 159
                                       4467**************9876655555555....3.679*******95.....5699***********99996666 PP

                         Tubulin_2 227 ......l 227
                                              
  gi|313127201|ref|YP_004037471.1| 160 lllvdnD 166
                                       5544443 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.2e-05     0.072      45     126 ..     191     273 ..     173     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                       EEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHHHHHHHHHTT---SEE-..SSSHHHH..GGGS-.---E.E CS
                              HEM4  45 wliftSanavealfealkreeedvkalaslkvaavGpaTaraLeelglrvdlvpseegtaegL..aeelaeslag.k 118
                                       +l+f S +ave ++e + +++e+++ l+s  + a G a+a+++ + + ++  v s +   ++L    +l+e++ + +
  gi|313127201|ref|YP_004037471.1| 191 GLLFASGEAVEGVAESVVDSSEVINTLRSGGISALGYAAAESADSSEGNINTVMS-TTR-RSLltGTSLPEATTAdS 265
                                       689********************************************99999999.444.55624559999777746 PP

                                       EEEE-SS. CS
                              HEM4 119 rvlllrge 126
                                        +l+++ge
  gi|313127201|ref|YP_004037471.1| 266 ALLVVAGE 273
                                       66667765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2622.98
//
Query:       gi|313127202|ref|YP_004037472.1|  [L=449]
Description: hypothetical protein Hbor_24710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-59  202.2   0.1    1.9e-59  202.0   0.1    1.0  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
  ------ inclusion threshold ------
      0.031   13.6   0.0       0.17   11.3   0.0    2.0  2  Metalloenzyme  Metalloenzyme superfamily
       0.14   12.4   0.2       0.29   11.4   0.2    1.5  1  DUF2063        Putative DNA-binding domain
       0.96    8.8   4.2       0.91    8.8   1.2    2.3  2  Sulfatase      Sulfatase


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.0   0.1   4.3e-63   1.9e-59       1     356 [.      15     402 ..      15     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 4.3e-63
                                       EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEE CS
                      Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyv 77 
                                       v +i++DG++++ll +  ++ pn+a La++g+ ++ +++++P+++ +++ +l TG +Pge+G++g  f dr++g+y 
  gi|313127202|ref|YP_004037472.1|  15 VAFIGIDGVPFSLLADNPDEFPNMADLAETGSAGA-IESIVPPESSACWPALTTGVNPGETGVYG--FQDRENGSYE 88 
                                       578*************547****************.*****************************..88******** PP

                                       EEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC..........TBHHSBTCT.CSTTS... CS
                      Phosphodiest  78 vfvtededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs.........etppryleddfnakv... 142
                                       ++v+  +d    +q  +iwd+++ a g+ka ++++p + ++ ++ +++vs               + ddf++++   
  gi|313127202|ref|YP_004037472.1|  89 TYVPMGRD----VQATRIWDRVTDA-GRKATVMNVPVTFPPQRNVQRMVSgflspsvdkA----AYPDDFRDHLess 156
                                       *****999....9************.************************9888854442....3334555555555 PP

                                       ..........CHHHHHHHHHHHHH...HHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-.......TTSHHHHH CS
                      Phosphodiest 143 ..........pledkvdkavlqtw...ldaafakvvlekelekpdlllvyleetDtvgHkfG.......pdspeved 199
                                                 ++ d++++ + ++    ld+ f++ +  ++++++dl++++++ tD+v H +         d++++ +
  gi|313127202|ref|YP_004037472.1| 157 gyiidvnaklGHKDDKTE-FVENAnktLDRRFEAFSHYLQQDDWDLFFGVFMTTDRVNHFLFkdyenetSDKEKFMA 232
                                       555544442255555544.6656644466666555555555********************7444333223555*** PP

                                       HHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGHGEEEEECBHHS.SSE........ CS
                      Phosphodiest 200 alrrvDkaigdLlealderglsaetniilvSDHGmadvsddkvielndlleekgllhlkdegkggakal........ 268
                                        +r+vD+++g+++e l+e+     +++++++DHG++++  d+ ++ n+lle++g+l+ +d+  ++ +++        
  gi|313127202|ref|YP_004037472.1| 233 FYRKVDDYLGQIREMLPED-----VTLVIAADHGFTSL--DYEVHCNTLLEQEGWLSYEDDDHEQLEDIsddtlays 302
                                       *******************.....**************..**************77777777666666677777788 PP

                                       .....EEEEESTEE.E.CCCTTHHHHHHHHHHTCHHCCHST.HTT..TEEEEEGG.GS-GGGCHSTTS-SEEEEE-T CS
                      Phosphodiest 269 .....iainpkare.lnrvaeaeaeevyaelkakleelrkk.ege..alavylke.aipkrlhykkrapdlvlvadp 335
                                             +in+++re +++v++ e++e ++elk++le l  + +g+  a +v +ke a+++ +   + apdlv+v+++
  gi|313127202|ref|YP_004037472.1| 303 lipgrFYINLEGREpRGAVPQDEYQERRDELKEMLENLE-GpNGRkvADRVVEKEdAFRGNHD--DIAPDLVIVPNH 376
                                       88999*****************************77776.44777779999999989***998..************ PP

                                       TEEEESSTTCS.....SBS-SEE--S CS
                      Phosphodiest 336 gwsitskdkpd.....eyeikgthGy 356
                                       g+ + s+ k++     +    g+h++
  gi|313127202|ref|YP_004037472.1| 377 GFDLKSGFKGKddvfgQGPRNGMHSF 402
                                       ********999877776667777766 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.7e-05      0.17     142     186 ..     218     261 ..     162     268 .. 0.88
   2 ?   -0.5   0.0      0.14   6.5e+02     227     247 ..     415     435 ..     406     436 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 142 aDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHg 186
                                        D    t d e+ +a   ++D  +++i + + ++  +lv+ ADHg
  gi|313127202|ref|YP_004037472.1| 218 KDYENETSDKEKFMAFYRKVDDYLGQIREMLPEDV-TLVIAADHG 261
                                       4666778999999**************98776655.********9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.14
                                       HHTT-TTEEEEGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 227 frekggLanvaatllnllgle 247
                                       + e++ L ++a+t+l+l+ +e
  gi|313127202|ref|YP_004037472.1| 415 TIEDADLYDIAPTILDLMEVE 435
                                       567999***********9887 PP

>> DUF2063  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   6.6e-05      0.29      32      77 ..     175     220 ..     172     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHHHTTTGGGGS-HHHHHHHHHHHHHSGGGG-S-GGGH CS
                           DUF2063  32 vfnnlieaLaaaFpvlrallGeerfdalarayirahpsrspllrey 77 
                                       +++n  ++L++ F++  ++l ++ +d +   ++ + +  + l+++y
  gi|313127202|ref|YP_004037472.1| 175 FVENANKTLDRRFEAFSHYLQQDDWDLFFGVFMTTDRVNHFLFKDY 220
                                       78999**************************************998 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.2    0.0002      0.91     150     252 ..     180     263 ..      26     291 .. 0.73
   2 ?    0.1   0.1     0.093   4.2e+02     294     308 ..     419     433 ..     411     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0002
                                       TCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-T.TSSSTCTCGGHTCCGSTTTTCCCCCCHHHHHHHHHHHHHHHHHH CS
                         Sulfatase 150 ggysddrlldealefllarndkpfflylatla.pHappeapdeyakkyatffddgseaarqlleaylnsveyvDdli 225
                                       ++++d+r+ + +  +l++ + + ff +++t   +   ++ +++y++++            +  e++ ++ + vDd +
  gi|313127202|ref|YP_004037472.1| 180 NKTLDRRF-EAFSHYLQQDDWDLFFGVFMTTDrVN--HFLFKDYENET------------SDKEKFMAFYRKVDDYL 241
                                       33444433.33333333333333333333332122..46777777765............8999************* PP

                                       HHHHHHHHHTTTGGGEEEEEEESSSSC CS
                         Sulfatase 226 grvlaaLeenglldntlvvftSDhgas 252
                                       g++ + L      +++++v+ +Dhg  
  gi|313127202|ref|YP_004037472.1| 242 GQIREML-----PEDVTLVIAADHGFT 263
                                       *******.....9999999******75 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.093
                                       EEGGGHHHHHHHHTT CS
                         Sulfatase 294 vshiDlfptildlag 308
                                       +++ D++ptildl+ 
  gi|313127202|ref|YP_004037472.1| 419 ADLYDIAPTILDLME 433
                                       5678*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3186.72
//
Query:       gi|313127203|ref|YP_004037473.1|  [L=147]
Description: hypothetical protein Hbor_24720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.036   14.6   1.0      0.056   14.0   0.6    1.5  1  FAM104      Family 104
        2.6    7.9   7.0       0.58   10.0   1.0    2.4  2  SNN_linker  Stannin unstructured linker


Domain annotation for each model (and alignments):
>> FAM104  Family 104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   6.2e-06     0.056       2      72 ..      45     118 ..      44     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.2e-06
                            FAM104   2 KRrrngneednhllpqpkRskrnsvl...qdswdtEsssSdsesssssinspdrasgpesslnqivaesspntp 72 
                                       KRr    e ++ ++ q+k++ r + l   q+  d+E+s+ + ++   si   dra  +   l +   e+++  +
  gi|313127203|ref|YP_004037473.1|  45 KRRDTVPEGEKDRVEQAKKNLRRERLqrlQQIEDNEVSYEEGQRLVESIVGIDRALNALEQLRPANLEQESQLQ 118
                                       8999889999999999997766544434499999***********99********9999999998888887654 PP

>> SNN_linker  Stannin unstructured linker
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.0   6.5e-05      0.58       4      15 ..      69      80 ..      68      86 .. 0.93
   2 ?    0.4   0.5     0.062   5.6e+02      15      19 ..      91      95 ..      90      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.5e-05
                        SNN_linker  4 RLQklSQsEDEE 15
                                      RLQ+l Q ED E
  gi|313127203|ref|YP_004037473.1| 69 RLQRLQQIEDNE 80
                                      9*********99 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.062
                        SNN_linker 15 ESIVG 19
                                      ESIVG
  gi|313127203|ref|YP_004037473.1| 91 ESIVG 95
                                      9***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1235  (0.0688828); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 996.61
//
Query:       gi|313127204|ref|YP_004037474.1|  [L=582]
Description: DNA polymerase iv (family x) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-24   84.3   0.0    1.5e-23   82.7   0.0    2.0  1  DNA_pol_B_thumb  DNA polymerase beta thumb
    3.3e-21   75.4   2.6    4.2e-16   59.1   0.1    3.5  3  HHH_8            Helix-hairpin-helix domain
    6.6e-15   55.5   3.1    8.1e-13   48.8   0.1    3.2  2  HHH_5            Helix-hairpin-helix domain
    1.3e-07   31.6   0.4     0.0049   16.9   0.1    3.3  2  HHH_2            Helix-hairpin-helix motif
    4.8e-07   30.2   0.0      1e-06   29.1   0.0    1.6  1  PHP              PHP domain
    2.3e-05   24.1   0.0    0.00013   21.7   0.0    2.3  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    0.00015   21.9   0.1     0.0014   18.8   0.0    2.2  2  DNA_pol_B_palm   DNA polymerase beta palm
     0.0006   19.6   0.5      0.027   14.4   0.1    3.2  2  HHH              Helix-hairpin-helix motif
     0.0098   16.1   0.1         47    4.3   0.0    3.5  3  HHH_3            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.058   12.3   0.1        0.6    9.0   0.1    2.1  2  DUF3363          Protein of unknown function (DUF3363)
      0.063   13.6   0.1         11    6.5   0.0    2.9  2  IMS_HHH          IMS family HHH motif
       0.15   12.7   1.3         33    5.2   0.1    3.1  2  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold


Domain annotation for each model (and alignments):
>> DNA_pol_B_thumb  DNA polymerase beta thumb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.0     1e-26   1.5e-23       1      70 []     254     326 ..     254     326 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 1e-26
                                       HHHHHHS-HHHHHHHHHHHHCTTEEEETTEEE..........ETCCCEEEC-SSHHHHHHHCTS----GGGTT CS
                   DNA_pol_B_thumb   1 allyfTGsktFnrdlRrlakkkglkLnssglrdek...gkaeddddgelvevetErdvfelLglpyipPeeRe 70 
                                       al+yfTGsk++n++lR++a +kglk+n++g++d+    + ++d+++ge++++etE++++e+Lglp+ipPe+Re
  gi|313127204|ref|YP_004037474.1| 254 ALQYFTGSKDHNVALRNIAIEKGLKMNEYGVFDVSdveDPETDQRAGEKIAGETEASMYEALGLPFIPPELRE 326
                                       89******************************8334557889******************************7 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.1   2.8e-19   4.2e-16       1      68 []       4      74 ..       4      74 .. 0.93
   2 ?    4.1   0.0     0.039        58      36      63 ..      82     109 ..      78     114 .. 0.67
   3 !   10.6   0.1   0.00039      0.58      32      65 ..     115     146 ..     112     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.8e-19
                                      HHHHHHHHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHH..TT..HCTTSTT--HHHHHHHHHHHH CS
                             HHH_8  1 NkeiadaLeeladllelkgedpfrvraYrrAaraiealpeeitsl..ee..eltklpgiGkkiaakieeile 68
                                      N+e+a+++ee adll+ k + +++ + YrrAa++i+++p++i++l  ++  ++ +++g+G++i aki e+ e
  gi|313127204|ref|YP_004037474.1|  4 NDEVASLFEEFADLLDAK-DVSYKPNTYRRAAENIREYPHPIEELaaDGadAVGEIQGVGDAISAKIIEYFE 74
                                      99****************.899***********************7533878899**************975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.039
                                       CC-SS-HHHHTT.HCTTSTT--HHHHHHH CS
                             HHH_8  36 ealpeeitslee.eltklpgiGkkiaaki 63 
                                       eal  e+   e  +lt++ g+G+k+  k+
  gi|313127204|ref|YP_004037474.1|  82 EALRAELPV-EMaTLTSVEGVGPKTVGKL 109
                                       555554444.22359**********9887 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00039
                                       HCCCCC-SS-HHHHTTHCTTSTT--HHHHHHHHH CS
                             HHH_8  32 araiealpeeitsleeeltklpgiGkkiaakiee 65 
                                       ++++++l+++ ++ e+ +++++g+G+k+ a i+e
  gi|313127204|ref|YP_004037474.1| 115 ITTLDELERAAEE-EQ-IREVKGFGPKTEANIRE 146
                                       7899999999999.88.***************98 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.011        17      15      53 ..      34      71 ..      14      84 .. 0.82
   2 !   48.8   0.1   5.4e-16   8.1e-13       3      53 ..      94     146 ..      92     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                                      HHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5 15 AlallsaGiesvedlaaadveeLakipGiGkktAeriil 53
                                      A ++ +     +e+laa  ++++ +i+G+G     +ii+
  gi|313127204|ref|YP_004037474.1| 34 AENIREY-PHPIEELAADGADAVGEIQGVGDAISAKIIE 71
                                      4445555.556899999999**********999999997 PP

  == domain 2  score: 48.8 bits;  conditional E-value: 5.4e-16
                                       HHHTSTT--HHHHHHHHTT.T--SHHHHHHS-H.HHHHTSTTS-HHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsa.Giesvedlaaadv.eeLakipGiGkktAeriil 53 
                                        L+sv+G+Gpkt+ +l++a Gi+++++l +a++ e++ +++G+G+kt  +i +
  gi|313127204|ref|YP_004037474.1|  94 TLTSVEGVGPKTVGKLYDAlGITTLDELERAAEeEQIREVKGFGPKTEANIRE 146
                                       69*****************99*******98765278*************9976 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   3.3e-06    0.0049      15      62 ..      33      80 ..      31      82 .. 0.86
   2 !   11.1   0.0   0.00022      0.33       8      53 ..      98     146 ..      91     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.3e-06
                             HHH_2 15 tAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFeneknre 62
                                      +A+++ +  + +++L++  ++   e++++G+ i+++i+e+Fe+ + +e
  gi|313127204|ref|YP_004037474.1| 33 AAENIREYPHPIEELAADGADAVGEIQGVGDAISAKIIEYFETGEIEE 80
                                      566666666789******************************987766 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00022
                             HHH_2   8 IrhVGektAklLakrFk..sldaLkka.sleeLlevddiGeeiAqsive 53 
                                       +  VG kt  +L  + +  +ld+L++a ++e++ ev++ G+++ ++i+e
  gi|313127204|ref|YP_004037474.1|  98 VEGVGPKTVGKLYDALGitTLDELERAaEEEQIREVKGFGPKTEANIRE 146
                                       6689999999999999888*****97615678**********9888876 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0     7e-10     1e-06       1      72 [.     351     432 ..     351     538 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7e-10
                                       EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT..............HHHHHHHHHHHHTTTTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxx RF
                               PHP   1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf..............gyvefykaakkkykagikpiiG 63 
                                       dlH+H++ s    +  i+e+v++a+e+g++ +a+TDh+                 + ++++  +    + +++++ G
  gi|313127204|ref|YP_004037474.1| 351 DLHTHSDWSDGRYS--ISEMVAAAEERGYDYYAVTDHATGPgmvggvgldddelrDQMDAVADI--AAETDLELLHG 423
                                       89******944355..5**********************99999*******9776455555555..45568999*** PP

                                       EE....... CS
                                       xxxxxxxxx RF
                               PHP  64 leayvadds 72 
                                       +ea++  ++
  gi|313127204|ref|YP_004037474.1| 424 VEANIDAEG 432
                                       999998776 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.1   4.6e+03       6      19 ..      58      71 ..      57      88 .. 0.69
   2 !   21.7   0.0   8.5e-08   0.00013       2      30 ..      94     123 ..      93     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.1
                   DNA_pol_lambd_f  6 vyGVGpktAkkwya 19
                                      + GVG ++  k ++
  gi|313127204|ref|YP_004037474.1| 58 IQGVGDAISAKIIE 71
                                      77999988877664 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 8.5e-08
                   DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwyak.Girtledlra 30 
                                       ++t+v GVGpkt  k+y++ Gi+tl++l +
  gi|313127204|ref|YP_004037474.1|  94 TLTSVEGVGPKTVGKLYDAlGITTLDELER 123
                                       5899************************98 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   9.5e-07    0.0014      12      54 ..     168     210 ..     162     228 .. 0.83
   2 ?    0.2   0.0      0.56   8.4e+02      39      71 ..     440     471 ..     403     476 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.5e-07
                                       HHHHHHHHHH-TT-EEEE-HHHHTT-SEESSEEEEEEBTTBST CS
                    DNA_pol_B_palm  12 alvkkaakeldpevevivcGSYRRgaessGDvDvlitkkdaks 54 
                                       + v + ++e d    + v+GS RR +++ GDvDvl+  + ++s
  gi|313127204|ref|YP_004037474.1| 168 DDVLAYLREADTVQAAEVAGSIRRWRDTIGDVDVLVAAESGDS 210
                                       5667777888888999********************9998877 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.56
                                       EESSEEEEEEBTTBSTTSS--HHHHHHHHHHHH CS
                    DNA_pol_B_palm  39 ssGDvDvlitkkdakseskklkklleklvkklk 71 
                                          D+Dv++  ++a+  + ++++ +++lv++++
  gi|313127204|ref|YP_004037474.1| 440 VLADLDVVVASPHAALGQ-DRETATDRLVAAVE 471
                                       5579*********99954.68888899888776 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.8e-05     0.027      10      28 ..      92     110 ..      78     112 .. 0.84
   2 ?    1.9   0.0      0.16   2.4e+02       6      23 ..     123     140 ..     117     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                                       HHHHHTSTT-SHHHHHHHH CS
                               HHH  10 reeLlalPGVGpktAeaIl 28 
                                       ++ L++++GVGpkt ++ +
  gi|313127204|ref|YP_004037474.1|  92 MATLTSVEGVGPKTVGKLY 110
                                       678***********99876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                                       HTSSHHHHHTSTT-SHHH CS
                               HHH   6 ipasreeLlalPGVGpkt 23 
                                       ++a +e++ +++G Gpkt
  gi|313127204|ref|YP_004037474.1| 123 RAAEEEQIREVKGFGPKT 140
                                       677789***********9 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.037        55      19      46 ..      58      84 ..      52      86 .. 0.81
   2 ?    3.1   0.0     0.078   1.2e+02      44      60 ..      93     109 ..      90     113 .. 0.78
   3 ?    4.3   0.0     0.032        47      44      62 ..     128     146 ..     120     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.037
                             HHH_3 19 lpGlgpklAknIvayReknGpfksreeL 46
                                      + G+g++++ +I++y  + G ++ +e L
  gi|313127204|ref|YP_004037474.1| 58 IQGVGDAISAKIIEYF-ETGEIEELEAL 84
                                      78*************8.66677666666 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.078
                             HHH_3  44 eeLlkvkglgpktfeql 60 
                                         L++v+g+gpkt+ +l
  gi|313127204|ref|YP_004037474.1|  93 ATLTSVEGVGPKTVGKL 109
                                       67999999999998776 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.032
                             HHH_3  44 eeLlkvkglgpktfeqlag 62 
                                       e+  +vkg+gpkt   +++
  gi|313127204|ref|YP_004037474.1| 128 EQIREVKGFGPKTEANIRE 146
                                       79999*******9877776 PP

>> DUF3363  Protein of unknown function (DUF3363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0004       0.6     212     298 ..      97     184 ..      76     192 .. 0.83
   2 ?    0.7   0.0      0.13     2e+02     292     334 ..     323     365 ..     319     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0004
                           DUF3363 212 avevksalslekqvtargatWLDrelvsgekedlada.GFGkevrealarRrqflveqglaeeeqgrvvlrrnllat 287
                                       +ve  ++  + k+ +a g t LD+   + e+e++++  GFG ++++ +++   f +e +  e+ ++   l+ ++la 
  gi|313127204|ref|YP_004037474.1|  97 SVEGVGPKTVGKLYDALGITTLDELERAAEEEQIREVkGFGPKTEANIRENIPFAREAQKRERLGNARPLADDVLAY 173
                                       455555667899999*********99999999998866*******************999777777778******** PP

                           DUF3363 288 Lrrrelervak 298
                                       Lr+ +  ++a+
  gi|313127204|ref|YP_004037474.1| 174 LREADTVQAAE 184
                                       ****9999886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.13
                           DUF3363 292 elervakelaaetglsfreaeegekveGvlrrsvelasGrfAl 334
                                       el++  +e++a ++ +  e+ e++ v+G l+ + + + Gr+ +
  gi|313127204|ref|YP_004037474.1| 323 ELRENTGEVEAAQAGTLPEVVEMGDVRGDLHTHSDWSDGRYSI 365
                                       677777888888888999***********************86 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.051        76      13      32 .]      95     115 ..      94     115 .. 0.81
   2 ?    6.5   0.0    0.0076        11      13      27 ..     130     144 ..     129     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.051
                           IMS_HHH  13 itkipGiGgklgekLek.lGi 32 
                                       +t++ G+G+k+  kL + lGi
  gi|313127204|ref|YP_004037474.1|  95 LTSVEGVGPKTVGKLYDaLGI 115
                                       57777*********7665887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0076
                           IMS_HHH  13 itkipGiGgklgekL 27 
                                       i+++ G+G+k+++ +
  gi|313127204|ref|YP_004037474.1| 130 IREVKGFGPKTEANI 144
                                       89**********974 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.03        44      12      40 ..      47      75 ..      42      93 .. 0.82
   2 ?    5.2   0.1     0.022        33      21      63 ..      96     147 ..      91     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.03
                        5_3_exonuc 12 LvGDssDnipGvpgiGektAakLlkeygs 40
                                      L+ D +D +  ++g+G+   ak+++ +++
  gi|313127204|ref|YP_004037474.1| 47 LAADGADAVGEIQGVGDAISAKIIEYFET 75
                                      777999******************98854 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                        5_3_exonuc  21 pGvpgiGektAakLlkeyg..sleeilenld..elke.....kklkekLeen 63 
                                         v+g+G+kt  kL    g  +l+e+ ++++  +++e     +k++++++en
  gi|313127204|ref|YP_004037474.1|  96 TSVEGVGPKTVGKLYDALGitTLDELERAAEeeQIREvkgfgPKTEANIREN 147
                                       6799*********988764337777777665322222333554555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4180.72
//
Query:       gi|313127205|ref|YP_004037475.1|  [L=177]
Description: hypothetical protein Hbor_24740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-41  141.1   0.0      3e-41  140.9   0.0    1.0  1  Mut7-C           Mut7-C RNAse domain
    1.9e-05   24.3   0.0    3.2e-05   23.6   0.0    1.4  1  DUF5615          Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
       0.03   14.6   1.0          6    7.2   0.0    2.4  2  RNA_pol_N        RNA polymerases N / 8 kDa subunit
       0.11   13.0   0.0       0.17   12.4   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
       0.12   12.7   0.3        0.2   12.0   0.3    1.3  1  zf-UBP           Zn-finger in ubiquitin-hydrolases and other 


Domain annotation for each model (and alignments):
>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9   0.0   8.4e-45     3e-41       2     145 ..      13     155 ..      12     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 8.4e-45
                            Mut7-C   2 rfllDamlgklakyLRllGydalyasdv....edeellalaakekrillTrdreLlkraklkkgvlltsrdveeqlr 74 
                                       r+llDamlgkl++yLR++Gyda+ya d      d++ll++a++e+r+l+Trd +L++ra +   vl+t+r + +qlr
  gi|313127205|ref|YP_004037475.1|  13 RLLLDAMLGKLTTYLRMCGYDAAYALDDgpdpGDDALLERAREENRTLVTRDERLARRAPDG--VLVTTRAITDQLR 87 
                                       99**********************998778889**************************988..************* PP

                            Mut7-C  75 eviarlglklslkpelsrCvaCngeleevekeevkervpekvyeeade.ftrCekCrkvfWkGshwerveel 145
                                       e  + +g++++l+    rC +Cng++e+v  +e    vpe++++  ++ ++rC +C++v+WkGshw++v+++
  gi|313127205|ref|YP_004037475.1|  88 EF-SSAGYAVELRGGPVRCSTCNGQVERVGTDEP---VPEYAPDPGEQpLWRCLDCGQVYWKGSHWDDVAKR 155
                                       **.99***************************99...**********99*******************9986 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   8.8e-09   3.2e-05       2      56 ..      13      65 ..      12      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.8e-09
                           DUF5615  2 klllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDk 56
                                      +lllD+ l  +l + lr  g+d+ +  + g +   D++ le+A+ee+r++vT+D+
  gi|313127205|ref|YP_004037475.1| 13 RLLLDAMLG-KLTTYLRMCGYDAAYALDDG-PDPGDDALLERAREENRTLVTRDE 65
                                      7999*9999.999*************9999.5679*******************4 PP

>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2    0.0055        20       4      14 ..     102     112 ..     101     116 .. 0.84
   2 ?    7.2   0.0    0.0017         6       6      32 ..     135     163 ..     133     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0055
                                       -SS-TTT--B- CS
                         RNA_pol_N   4 PVrCFtCGkvi 14 
                                       PVrC tC+  +
  gi|313127205|ref|YP_004037475.1| 102 PVRCSTCNGQV 112
                                       9******8665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0017
                                       S-TTT--B-..STHHHHHHHHHHTT--HH CS
                         RNA_pol_N   6 rCFtCGkvi..gekweeylellekgeepk 32 
                                       rC  CG+v   g++w++++++++++e+++
  gi|313127205|ref|YP_004037475.1| 135 RCLDCGQVYwkGSHWDDVAKRIDAKENER 163
                                       9******9755789********9998876 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05      0.17       6      52 ..      19      67 ..      16      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                   Glyco_tranf_2_4  6 iLpeflahhlalgfdrilvydndstDgtrailkel..pevkllhvdksy 52
                                      +L++  ++++  g+d+ + +d+++++g +a+l++   ++ +l++ d+  
  gi|313127205|ref|YP_004037475.1| 19 MLGKLTTYLRMCGYDAAYALDDGPDPGDDALLERAreENRTLVTRDERL 67
                                      7889999*************************99621334444444443 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   5.6e-05       0.2       1      21 [.     105     143 ..     105     153 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
                                       -TTTH.......--.SS..............EEEETTT--EE CS
                            zf-UBP   1 CseCn.......senkn..............lWlCLkCghvg 21 
                                       Cs+Cn       +   +              lW CL+Cg+v 
  gi|313127205|ref|YP_004037475.1| 105 CSTCNgqvervgT---DepvpeyapdpgeqpLWRCLDCGQVY 143
                                       9999955555550...055555555555555********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1164.87
//
Query:       gi|313127206|ref|YP_004037476.1|  [L=321]
Description: ribonuclease bn-like family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-06   25.3   3.2    9.9e-06   25.3   3.2    1.7  2  Virul_fac_BrkB  Virulence factor BrkB
  ------ inclusion threshold ------
      0.075   11.9   3.3      0.091   11.6   3.3    1.0  1  Apt1            Golgi-body localisation protein domain
        0.1   12.4   0.4        0.1   12.4   0.4    2.6  3  HCV_NS4a        Hepatitis C virus non-structural protein NS4a


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   3.2   1.7e-09   9.9e-06      94     206 ..       2     104 ..       1     110 [. 0.76
   2 ?   -1.2   0.0      0.21   1.3e+03     160     188 ..     125     153 ..     111     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.7e-09
                    Virul_fac_BrkB  94 ralnkiygv.eesrsflrkrllsllllllllvllllslvlsvflqslllasapllglglelsell.llqllrwlval 168
                                       ++l ++y+  e+  + l+++ll l+++ll+++l+++ +v+ +      +      g+      l+ + +l+++ +a 
  gi|313127206|ref|YP_004037476.1|   2 TSLSEAYHKgERAGPGLQRLLLGLGMFLLGVLLVVAGIVVATTSVL--RGD----GMS-----LGdVRELGGI-LAG 66 
                                       6789999996666689999999999999998777777666665544..322....222.....2235677777.577 PP

                    Virul_fac_BrkB 169 lllvlafallYrvlpnvkvrlraalpGallaallwllv 206
                                       + + l+f+ +++v+p+ + +  aa++Ga +a +++ l+
  gi|313127206|ref|YP_004037476.1|  67 VGVPLVFLGIFTVTPSGRLTKAAAIVGAGIALAGVALF 104
                                       777799*************************9998876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.21
                    Virul_fac_BrkB 160 qllrwlvallllvlafallYrvlpnvkvr 188
                                        ll++ v +l ++++f  l+  + n k+r
  gi|313127206|ref|YP_004037476.1| 125 TLLTVSVYFLGTLTTFWCLFVGVANFKTR 153
                                       45556677788888888888888887766 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.3   1.5e-05     0.091     319     384 ..     200     272 ..     172     311 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.5e-05
                              Apt1 319 esdeesessssss....ssssssassssssssrssslelrlkpt....sstssssssessssssskkrsseess 384
                                       +++  ++++++ s       ++ as +s + ++++s++++++p+     +++ssss++s+s+s  ++++se+ s
  gi|313127206|ref|YP_004037476.1| 200 TQTARQSQTGQ-SgtvsDGGTDAASITSPQGTGTQSQSRSRSPQspsgPQSQSSSSPQSQSQSRGSRSQSERGS 272
                                       22222222222.23566677777777777777777777776655444322222222222222222222222222 PP

>> HCV_NS4a  Hepatitis C virus non-structural protein NS4a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5      0.34   2.1e+03       6      32 ..      37      48 ..      21      60 .. 0.62
   2 ?   -1.8   0.3      0.47   2.8e+03       6      13 ..      60      67 ..      55      71 .. 0.86
   3 ?   12.4   0.4   1.7e-05       0.1       2      28 ..      90     121 ..      89     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.34
                          HCV_NS4a  6 vGlalAglAiyalttGSvvvvtrwsvn 32
                                      +                +vv t+ ++ 
  gi|313127206|ref|YP_004037476.1| 37 A---------------GIVVATTSVLR 48
                                      2...............34555555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.47
                          HCV_NS4a  6 vGlalAgl 13
                                       G++lAg+
  gi|313127206|ref|YP_004037476.1| 60 LGGILAGV 67
                                      59****98 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 1.7e-05
                          HCV_NS4a   2 pvvlvGlalAglAiy.....alttGSvvvvtr 28 
                                       ++v +G+alAg+A++     +++ GS++ ++r
  gi|313127206|ref|YP_004037476.1|  90 AIVGAGIALAGVALFwhaypCQWSGSLCRRGR 121
                                       69***********9877778999***996665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1278  (0.0712812); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 2157.08
//
Query:       gi|313127207|ref|YP_004037477.1|  [L=93]
Description: hypothetical protein Hbor_24760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 636.02
//
Query:       gi|313127208|ref|YP_004037478.1|  [L=198]
Description: caax amino terminal protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-06   28.1   0.2    3.9e-06   27.2   0.2    1.7  1  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   2.2e-10   3.9e-06      11      88 ..      90     167 ..       9     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.2e-10
                                       HHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGGHHH.HHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                              CPBP  11 alllapllEEllfRglllqllqergsstlailissilFglaHlpngps.vllaalaGlvlgylylktgsllaaillH 86 
                                         l++ ++ E ++Rgll+  ++e ++ + +++is ++++l H+   p+ ++l     +++g++ + ++s+l++i++H
  gi|313127208|ref|YP_004037478.1|  90 QQLVVVIAAETYYRGLLCVGVSEEFG-FKSVFISPVVYALHHVGKPPIeLVLSGPTDVLFGAVDYDSNSILPSIVAH 165
                                       557888999***************77.89****************9999**************************** PP

                                       HH CS
                              CPBP  87 al 88 
                                       +l
  gi|313127208|ref|YP_004037478.1| 166 GL 167
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1300.08
//
Query:       gi|313127209|ref|YP_004037479.1|  [L=150]
Description: hypothetical protein Hbor_24780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-15   57.3   0.0    1.6e-15   56.7   0.0    1.3  1  DUF302    Domain of unknown function DUF302


Domain annotation for each model (and alignments):
>> DUF302  Domain of unknown function DUF302
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   9.1e-20   1.6e-15       4      61 ..      51     110 ..      48     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 9.1e-20
                                       HHHHHCTT-S--S-EEEEEEE-HHHHHHHHCC-.GGGGGG-SEEEEEEE.ETTEEEEEEE CS
                            DUF302   4 qatlkkklgedlrpykilgaCnPklatealqad.peiglllPcrvvVye.kdgkttvsyv 61 
                                       ++ l++k+++d +py++lgaCnP +a++al+a+ +++g l Pc+v+++e + g+ tv+ v
  gi|313127209|ref|YP_004037479.1|  51 SELLNEKVDADRDPYYVLGACNPSMADRALDASeKKMGGLFPCNVIIWEeEPGVQTVYHV 110
                                       67899**************************9989**************777**999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1102.86
//
Query:       gi|313127210|ref|YP_004037480.1|  [L=218]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-17   63.3   0.0      2e-17   62.7   0.0    1.3  1  HTH_10         HTH DNA binding domain
    1.1e-12   48.1   0.4    1.8e-12   47.4   0.4    1.4  1  BAT            GAF and HTH_10 associated domain
    0.00065   19.2   0.0     0.0013   18.3   0.0    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0023   17.8   0.1     0.0079   16.1   0.1    2.0  2  MarR_2         MarR family
     0.0036   17.1   0.4     0.0087   15.9   0.2    1.7  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.042   13.4   0.1       0.14   11.7   0.0    1.9  2  Sigma70_r4     Sigma-70, region 4
       0.08   12.6   0.2       0.17   11.6   0.1    1.6  2  Sigma70_r4_2   Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   7.9e-21     2e-17       1      52 [.     156     207 ..     156     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 7.9e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT  q+e+l +A+e+GY+d PRr+t+ eLA+ l+Is+++++e+Lr+a+  l+
  gi|313127210|ref|YP_004037480.1| 156 LTAIQRETLLVAVEAGYYDIPRRCTTVELAEMLDISDQAVTERLRRAIVSLV 207
                                       9**********************************************98776 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.4   7.2e-16   1.8e-12      11     132 ..       8     133 ..       1     153 [. 0.86

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 7.2e-16
                               BAT  11 rdeddvlv...alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltv 84 
                                       r +++++    al+ +++ r+ele +vp +   ++ ff++ +    ++++aa d+++v ++  v++ dd+tl+ l +
  gi|313127210|ref|YP_004037480.1|   8 RLPSSAFElgrALSVQTGERIELETMVPLGAA-AIPFFWLYHSGENAFVSAANDHPSVRNIATVDTFDDRTLFALDW 83 
                                       4444444333589***************9876.88*******999******************************98 PP

                               BAT  85 s..gpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeer 132
                                       +   + l+ t++++ g+v +a+   +++rl +++P+  ++ ++ +a++++
  gi|313127210|ref|YP_004037480.1|  84 DpeADGLFDTIVDCRGRVLDATGAHDEWRLELRFPSHDELSAFRSACQDE 133
                                       644788999*************************************9975 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     5e-07    0.0013      17      40 ..     178     201 ..     176     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5e-07
                            HTH_24  17 risqreLAerlglSpstvnrrlkr 40 
                                       r++  eLAe+l++S ++v++rl+r
  gi|313127210|ref|YP_004037480.1| 178 RCTTVELAEMLDISDQAVTERLRR 201
                                       79*********************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.6   9.3e+03       9      19 ..     100     110 ..      99     112 .. 0.85
   2 !   16.1   0.1   3.1e-06    0.0079      19      45 ..     176     202 ..     154     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.6
                                       HHHHHHHCTTT CS
                            MarR_2   9 rvLaaLgrrpg 19 
                                       rvL a g++++
  gi|313127210|ref|YP_004037480.1| 100 RVLDATGAHDE 110
                                       89999999985 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.1e-06
                                       TSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2  19 grdltvgelarrlglsksavsrilkrL 45 
                                       +r++t  ela+ l++s +av+ +l+r+
  gi|313127210|ref|YP_004037480.1| 176 PRRCTTVELAEMLDISDQAVTERLRRA 202
                                       2379*********************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.3   1.1e+04      22      29 ..      15      22 ..      14      25 .. 0.77
   2 !   15.9   0.2   3.4e-06    0.0087      17      40 ..     178     201 ..     174     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.3
                     HTH_AsnC-type 22 eLAervGl 29
                                      eL++++ +
  gi|313127210|ref|YP_004037480.1| 15 ELGRALSV 22
                                      78999876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.4e-06
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrr 40 
                                       R +  eLAe++ +S ++v +R+rr
  gi|313127210|ref|YP_004037480.1| 178 RCTTVELAEMLDISDQAVTERLRR 201
                                       77899******************9 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   3.4e+03      30      39 ..     135     144 ..     133     145 .. 0.74
   2 ?   11.7   0.0   5.6e-05      0.14      22      48 ..     180     206 ..     168     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                                       HTS-HHHHHH CS
                        Sigma70_r4  30 lgiSrerVrq 39 
                                       + ++ erV++
  gi|313127210|ref|YP_004037480.1| 135 YPLTVERVSR 144
                                       5678999986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.6e-05
                                       -HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  22 TleEIgerlgiSrerVrqiekrAlrkL 48 
                                       T  E++e+l+iS  +V  +++rA+  L
  gi|313127210|ref|YP_004037480.1| 180 TTVELAEMLDISDQAVTERLRRAIVSL 206
                                       788********************9765 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.9   7.4e+03      11      24 ..     156     169 ..     156     172 .. 0.70
   2 ?   11.6   0.1   6.7e-05      0.17      28      51 ..     180     203 ..     178     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.9
                                       S-HHHHHHHHHHHT CS
                      Sigma70_r4_2  11 Lperqreifllryl 24 
                                       L+ +qre +l   +
  gi|313127210|ref|YP_004037480.1| 156 LTAIQRETLLVAVE 169
                                       77889998876555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.7e-05
                                       -HHHHHHHHT--HHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRAr 51 
                                       ++ E Ae+l+is+++V  rl+RA 
  gi|313127210|ref|YP_004037480.1| 180 TTVELAEMLDISDQAVTERLRRAI 203
                                       56699*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1583.29
//
Query:       gi|313127211|ref|YP_004037481.1|  [L=106]
Description: hypothetical protein Hbor_24800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0006   19.8   0.5      0.015   15.3   0.2    2.2  2  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.7   0.1       0.02   15.1   0.1    1.3  1  DUF4777   Domain of unknown function (DUF4777)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.7e-06     0.015       2      37 ..       6      42 ..       5      54 .. 0.84
   2 ?    2.7   0.0     0.015   1.4e+02      44      55 ..      67      78 ..      65      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-06
                                      HHHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHHTS- CS
                            HTH_20  2 qiaeALahPvRrrilraL.araegltaselaerldls 37
                                      +++++L+++ R+ +l+ L  r+e+ t+ ela +++++
  gi|313127211|ref|YP_004037481.1|  6 EQFRLLSQRRRLVVLSVLrERDEPTTLDELATEVGVR 42
                                      6899****************************99643 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.015
                                      HHHHHHHCTTEE CS
                            HTH_20 44 HLrvLeeagLve 55
                                      H+ +L +a+Lve
  gi|313127211|ref|YP_004037481.1| 67 HIPKLIDADLVE 78
                                      999********9 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   2.2e-06      0.02       8      42 ..      18      53 ..      11      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-06
                           DUF4777  8 lvlealkvlnrPaTldEiverv.aerydlseeelkk 42
                                      +vl++l++ ++P TldE+++ v  + +d++ eel +
  gi|313127211|ref|YP_004037481.1| 18 VVLSVLRERDEPTTLDELATEVgVRELDVPREELTD 53
                                      79********************65778999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 763.93
//
Query:       gi|313127212|ref|YP_004037482.1|  [L=421]
Description: hypothetical protein Hbor_24810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.7e-100  336.3   0.0   2.1e-100  336.1   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    4.5e-36  123.1   0.0    7.8e-36  122.3   0.0    1.4  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.1   0.0  2.3e-104  2.1e-100       1     270 []      21     298 ..      21     298 .. 0.98

  Alignments for each domain:
  == domain 1  score: 336.1 bits;  conditional E-value: 2.3e-104
                             Nre_N   1 Lcglkkcpileklravekakkki.sskeleGsspPsvfVGrygYPkVsvgplvppveg.dasvldspekwl..glsl 73 
                                       L+++k+++ile+l++++++++++ ++++l+Gs +Ps+fVG+++YP+Vs+g+l p  ++ da+++++++ w+  g+s+
  gi|313127212|ref|YP_004037482.1|  21 LAQEKSYDILEHLEDFQNRFEETvQGDSLFGSVSPSIFVGQSNYPNVSTGILSPVGHEdDAAKFETSAGWYdeGVSI 97 
                                       7899*****************999**************************887777779*************9**** PP

                             Nre_N  74 ediiklrlslvrgekkvkvkkak..edklleeiqelalsekpvdvevelekkp..kaklkfdevlaPvGpsaelekl 146
                                       +d++++r+sl+++++ ++v++++  +d +l+ ++e+a++++pv+ve+ l+++p  ++++++d+v++PvGp+a+++++
  gi|313127212|ref|YP_004037482.1|  98 NDVFQRRTSLLNSNRPTEVQNVNdaWDGFLGVQREVAIADRPVSVEIGLDSRPdiDFDVSLDDVATPVGPRARAQSA 174
                                       *********************9999*************************99656999******************* PP

                             Nre_N 147 kvaenpkvprkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkk 223
                                       ++aenp+vpr+v+k++eD+d++A+ a+ +Lyr+g+dvy+i+++LS+G+LG+ ++rrlVPTrWsITAvdd+vg+ l+ 
  gi|313127212|ref|YP_004037482.1| 175 DLAENPHVPRPVQKTLEDDDWNAQGAMNYLYRRGFDVYDINTILSAGALGQGDNRRLVPTRWSITAVDDTVGQFLRG 251
                                       ***************************************************************************** PP

                             Nre_N 224 eikdlpeidevevfsgeylgNrflviLaPgkwsfelvEawapgslwn 270
                                       +i+++p+i++ve++++e+lgN f+viLaPg+w+felvE++apgs+wn
  gi|313127212|ref|YP_004037482.1| 252 RIQTNPSINTVEIHRNEFLGNAFWVILAPGNWEFELVEMKAPGSVWN 298
                                       **********************************************8 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   0.0   8.7e-40   7.8e-36       1     110 []     312     420 ..     312     420 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 8.7e-40
                             Nre_C   1 egyegrkeyse.iaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleea 76 
                                       eg+egr++y+e +aGaY+a+rl+vle+L++++rqak+++lr+++++Yw P GvWqvRe+vr+a++++ +e+e++ +a
  gi|313127212|ref|YP_004037482.1| 312 EGFEGRTGYVEeTAGAYHASRLGVLEYLDQQGRQAKALILRHVSDDYWGPAGVWQVRESVRNAFDGERAEAETFAAA 388
                                       6899************************************************************************* PP

                             Nre_C  77 leevseklklplkkllkkskllkelkkqktLddF 110
                                       +++v+e l+++l +l++ks+++++l  q +L+dF
  gi|313127212|ref|YP_004037482.1| 389 VRQVTEYLPVSLGDLRRKSTMASGL--QMNLRDF 420
                                       *************************..9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2926.67
//
Query:       gi|313127213|ref|YP_004037483.1|  [L=327]
Description: transcription initiation factor iib (tfiib) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-46  154.5   1.7    8.7e-25   86.6   0.1    2.2  2  TFIIB         Transcription factor TFIIB repeat
     0.0012   18.4   0.1     0.0028   17.1   0.1    1.6  1  TF_Zn_Ribbon  TFIIB zinc-binding
  ------ inclusion threshold ------
      0.047   13.8   0.0       0.34   11.0   0.0    2.1  2  Cyclin_C      Cyclin, C-terminal domain
      0.053   13.9   0.0        1.5    9.3   0.1    2.4  2  HARE-HTH      HB1, ASXL, restriction endonuclease HTH domain
       0.38   10.3   0.1       0.38   10.3   0.1    3.5  5  Sigma70_r4    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.1   2.4e-22   8.7e-19       1      71 []     148     218 ..     148     218 .. 0.98
   2 !   86.6   0.1   2.4e-28   8.7e-25       1      71 []     242     312 ..     242     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.4e-22
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+a+al+ p  V++ A  ++++al+e+++ Grs +g+a ++ly Acrke+  r+++eis+v++V+ k+i
  gi|313127213|ref|YP_004037483.1| 148 IDRMASALGVPRSVREVASVIYRRALNEDLIRGRSIEGVATSALYAACRKEGIPRSLEEISDVSRVERKEI 218
                                       789****************************************************************9997 PP

  == domain 2  score: 86.6 bits;  conditional E-value: 2.4e-28
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf+++l+L+++V+++A+e++++++e+++l+G+sp+g+aAA++y A++++++k+tq+e+++v+qV+e+ti
  gi|313127213|ref|YP_004037483.1| 242 VPRFSSELDLSKEVQSKANEIIETTAEKGLLSGKSPTGYAAAAIYAASLLCNEKKTQREVADVAQVTEVTI 312
                                       689******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   7.8e-07    0.0028      26      43 .]      56      73 ..      56      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.8e-07
                                      SBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon 26 GlVlednsidegpewref 43
                                      G V+e+++id+gpewr+f
  gi|313127213|ref|YP_004037483.1| 56 GIVVEEEQIDPGPEWRAF 73
                                      67**************98 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.24   8.6e+02      47      84 ..     186     223 ..     184     234 .. 0.75
   2 ?   11.0   0.0   9.4e-05      0.34       3      86 ..     238     319 ..     236     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.24
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcve 84 
                                       +A++al++a++  + p   e++  +++++ +++   ++
  gi|313127213|ref|YP_004037483.1| 186 VATSALYAACRKEGIPRSLEEISDVSRVERKEIGRTYR 223
                                       799*****999867777777777777777777666655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.4e-05
                                       HHHHHHHHHCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHH CS
                          Cyclin_C   3 plsFlrrflkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedl 79 
                                       p  ++ rf+    +  ++e+++ a+ ++e+t+    + + +p   Aaaa+++a+   n+++ ++++  + ++++  +
  gi|313127213|ref|YP_004037483.1| 238 PKKYVPRFSSEL-DL-SKEVQSKANEIIETTAEKGLLSGKSPTGYAAAAIYAASLLCNEKKTQREVADVAQVTEVTI 312
                                       566777884442.33.3599999******9999999999*******************************9999999 PP

                                       HHHHHHH CS
                          Cyclin_C  80 kpcveli 86 
                                       ++ ++  
  gi|313127213|ref|YP_004037483.1| 313 RNRYQEQ 319
                                       8877765 PP

>> HARE-HTH  HB1, ASXL, restriction endonuclease HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.087   3.1e+02      19      53 ..     160     196 ..     152     211 .. 0.79
   2 ?    9.3   0.1   0.00041       1.5      19      51 ..     258     288 ..     255     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.087
                                       EHHHHHHHHHHHTTS-....GGHHGCHHH.HHHHHHH CS
                          HARE-HTH  19 tvkeIwekiqekgliklt..gktpeatlaaqlytdik 53 
                                       +v+e++ +i ++ l +    g++ e    ++ly+ ++
  gi|313127213|ref|YP_004037483.1| 160 SVREVASVIYRRALNEDLirGRSIEGVATSALYAACR 196
                                       67777777777777776677*************9998 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00041
                                       EHHHHHHHHHHHTTS-..GGHHGCHHH.HHHHH CS
                          HARE-HTH  19 tvkeIwekiqekglikltgktpeatlaaqlytd 51 
                                       +++eI e+  ekgl++  gk+p    aa++y+ 
  gi|313127213|ref|YP_004037483.1| 258 KANEIIETTAEKGLLS--GKSPTGYAAAAIYAA 288
                                       579*************..***********9975 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.7       1.2   4.2e+03      37      50 .]     113     126 ..     112     126 .. 0.88
   2 ?   -2.2   0.0      0.83     3e+03      34      45 ..     162     173 ..     152     175 .. 0.61
   3 ?   -1.1   0.0       0.4   1.4e+03      20      29 ..     201     210 ..     195     223 .. 0.78
   4 ?   -1.5   0.0       0.5   1.8e+03      18      32 ..     217     231 ..     213     231 .. 0.74
   5 ?   10.3   0.1   0.00011      0.38      18      42 ..     293     317 ..     284     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHH CS
                        Sigma70_r4  37 VrqiekrAlrkLRk 50 
                                       ++++++  +++LRk
  gi|313127213|ref|YP_004037483.1| 113 ISSRKRSQMHRLRK 126
                                       8999999999**97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAl 45 
                                       re ++ i +rAl
  gi|313127213|ref|YP_004037483.1| 162 REVASVIYRRAL 173
                                       355666777776 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.4
                                       T--HHHHHHH CS
                        Sigma70_r4  20 glTleEIger 29 
                                       +++leEI+++
  gi|313127213|ref|YP_004037483.1| 201 PRSLEEISDV 210
                                       6789999875 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.5
                                       TTT--HHHHHHHHTS CS
                        Sigma70_r4  18 geglTleEIgerlgi 32 
                                       + g+T+  I+++lg+
  gi|313127213|ref|YP_004037483.1| 217 EIGRTYRYISQELGL 231
                                       557888889999885 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00011
                                       TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiek 42 
                                        e+ T+ E++++ ++++ ++r +  
  gi|313127213|ref|YP_004037483.1| 293 NEKKTQREVADVAQVTEVTIRNRYQ 317
                                       5899*****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2364.18
//
Query:       gi|313127214|ref|YP_004037484.1|  [L=197]
Description: ribonuclease hi [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-28   97.4   0.0    1.2e-27   96.2   0.0    1.6  2  RVT_3     Reverse transcriptase-like
    4.3e-13   49.7   0.0      1e-12   48.4   0.0    1.6  1  RNase_H   RNase H
  ------ inclusion threshold ------
       0.02   15.1   0.2      0.043   14.0   0.2    1.6  1  Mac       Maltose acetyltransferase


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.59   3.5e+03       7      25 ..      50      68 ..      46      71 .. 0.76
   2 !   96.2   0.0     2e-31   1.2e-27       2     124 .]      73     193 ..      72     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.59
                             RVT_3  7 kkksgaggagvvirdsnGe 25
                                       ++s+ + + +++rd+ G+
  gi|313127214|ref|YP_004037484.1| 50 VQGSRPTDLLALLRDHSGR 68
                                      5677778888999999997 PP

  == domain 2  score: 96.2 bits;  conditional E-value: 2e-31
                             RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllng 78 
                                       fdga + + g +++g++i++s+G +++ g+e+  g +++  AE++AL+r+L++a+++g+ ++ v gDs+ +v++++g
  gi|313127214|ref|YP_004037484.1|  73 FDGASRGNPGPAAIGWAIVNSEG-IVGEGSET-IGETTNNRAEYEALIRALEAADEYGFDEVDVRGDSELIVKQVHG 147
                                       89*99******************.77777777.67789*************************************** PP

                             RVT_3  79 rekvksselanlldeirkllksfesvsvehipReqNrvAdalAkra 124
                                       + + +++el+     +r+ll++f++ s+eh+pRe N  Ad+lA++a
  gi|313127214|ref|YP_004037484.1| 148 EYDTNNPELRERRVRVRELLERFDRWSLEHVPREINDRADSLANEA 193
                                       ********************************************86 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   1.7e-16     1e-12       5     141 ..      70     193 ..      66     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.7e-16
                                       EEEEEEEEECTTTCEEEEE.EECTT..E.EEEEEECCCCHHHHHHHHHHHHHHHTT.SC..SEEEEEES-HHHHHHH CS
                           RNase_H   5 vvYtDGsclgnpgeggaga.vlykegar.nisapleeaqtnnraELsAvieaLkalksd..ekvniytDSkYvvkgi 77 
                                        vY DG+++gnpg++ +g  ++++eg   + s+++ +++tnnraE +A+i aL+a+++    +v ++ DS+ +vk  
  gi|313127214|ref|YP_004037484.1|  70 HVYFDGASRGNPGPAAIGWaIVNSEGIVgEGSETI-GETTNNRAEYEALIRALEAADEYgfDEVDVRGDSELIVKQ- 144
                                       69*************99997778785333555555.69****************87777899*********99994. PP

                                       HCCCHHHHHTTSSSETTSSBHTTHHHHHHHHHCHCSSEEEEEE-SCCSSSTHHHHHHHHHHHHH CS
                           RNase_H  78 tqwvhrwkknawkttseqkpvknkdlaellkelakkkkvqlkwvkgHaGvpkgNemaDrlAkea 141
                                          vh+    +++   e + v  ++l e++       + +l++v+      + N +aD+lA+ea
  gi|313127214|ref|YP_004037484.1| 145 ---VHGEYDTNNPELRERR-VRVRELLERF------DRWSLEHVP----R-EINDRADSLANEA 193
                                       ...5554444444444443.4444555554......456777776....3.4577777777776 PP

>> Mac  Maltose acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   7.3e-06     0.043       8      31 ..     149     171 ..     147     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.3e-06
                                       BETTTSHHHHHHHHHHHHHHHHHH CS
                               Mac   8 YdafsDpeLvaeRlrarelcrryN 31 
                                       Yd ++ peL ++R r rel+ r+ 
  gi|313127214|ref|YP_004037484.1| 149 YDTNN-PELRERRVRVRELLERFD 171
                                       99975.****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1358.37
//
Query:       gi|313127215|ref|YP_004037485.1|  [L=212]
Description: hypothetical protein Hbor_24840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1627.92
//
Query:       gi|313127216|ref|YP_004037486.1|  [L=118]
Description: transcriptional regulator, padr family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-17   63.0   0.4    2.6e-17   62.5   0.4    1.2  1  PadR      Transcriptional regulator PadR-like family
    4.1e-05   24.0   0.0      6e-05   23.5   0.0    1.3  1  HTH_27    Winged helix DNA-binding domain
     0.0035   17.3   0.1     0.0053   16.7   0.1    1.3  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.016   15.4   0.0    1.2  1  FUR       Ferric uptake regulator family
       0.02   14.6   0.0      0.025   14.3   0.0    1.2  1  DUF4364   Domain of unknown function (DUF4364)
      0.052   14.2   0.1      0.074   13.7   0.1    1.3  1  RTP       Replication terminator protein
      0.092   12.9   0.1       0.21   11.8   0.0    1.7  2  HTH_34    Winged helix DNA-binding domain
       0.13   12.1   0.0       0.24   11.3   0.0    1.4  1  DUF1495   Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.4   1.2e-20   2.6e-17       1      72 [.      23      88 ..      23      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.2e-20
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                      iL +l+e+p+yG++i+++le++++  +e+++G+lYp+L++L + +lve+++ +    ++++ Y+lT++G+++
  gi|313127216|ref|YP_004037486.1| 23 ILVILAEEPMYGLAIKRNLEDYYQ--TEVNHGRLYPNLDDLVEMDLVEKSELD----KRTNQYELTEKGHDA 88
                                      899*******************97..5***********************998....59**********986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.7e-08     6e-05      21      68 .]      38      85 ..      17      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.7e-08
                            HTH_27 21 ladlcgrlnvedshis..yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ++ l +++++e  h+    +l+ L+e++Lv  +++e d+r+ +++lT+kG
  gi|313127216|ref|YP_004037486.1| 38 KRNLEDYYQTEVNHGRlyPNLDDLVEMDLV--EKSELDKRTNQYELTEKG 85
                                      47777777777777776348**********..667889***********9 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.4e-06    0.0053      27      65 ..      45      88 ..      36      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.4e-06
                            HTH_45 27 ykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlel 65
                                      y+ + +  +l   Ld Lve +l+     +k++++Y+lTekG + 
  gi|313127216|ref|YP_004037486.1| 45 YQTEVNHGRLYPNLDDLVEMDLVekselDKRTNQYELTEKGHDA 88
                                      7778888899999*********9888888999*********864 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   7.1e-06     0.016      38      82 ..      47      90 ..      15     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
                                      TT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSEEEEE CS
                               FUR 38 peislaTVYrtLklleeaglvkelefedgesryelakkehhdhli 82
                                       e+    +Y +L+ l e++lv++ e+++ +++yel+ ++ hd + 
  gi|313127216|ref|YP_004037486.1| 47 TEVNHGRLYPNLDDLVEMDLVEKSELDKRTNQYELT-EKGHDAVL 90
                                      56777789****************************.57777765 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-05     0.025      39      85 ..      57     105 ..      35     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                           DUF4364  39 alseLvesglieee.ekenktlykiTekGke.tlelfenripksireki 85 
                                        l++Lve +l+e++  ++ +++y++TekG + +l+ f   ++k + +++
  gi|313127216|ref|YP_004037486.1|  57 NLDDLVEMDLVEKSeLDKRTNQYELTEKGHDaVLNRFAWMLSKFVTDET 105
                                       589*********996668999********86267889988888887765 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.3e-05     0.074      14      88 ..      23      88 ..      12     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                                      HHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHH CS
                               RTP 14 litlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkek 88
                                      ++ +++++++ygl +  +l + +++   + nh  +y  l++lve  ++++ +  k          Y+lt++G+++
  gi|313127216|ref|YP_004037486.1| 23 ILVILAEEPMYGLAIKRNLEDYYQT---EVNHGRLYPNLDDLVEMDLVEKSELDK------RTNQYELTEKGHDA 88
                                      6677888999*********998765...88****************998876554......34457777777776 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         2   4.5e+03      23      40 ..       4      21 ..       1      27 [. 0.74
   2 ?   11.8   0.0   9.4e-05      0.21      23      76 ..      46      96 ..      38     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2
                            HTH_34 23 aleatdgnLsvhlkkLek 40
                                      a  ++d+ L+  l+++++
  gi|313127216|ref|YP_004037486.1|  4 AQTVNDSGLARDLTAFQQ 21
                                      556788888888888876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.4e-05
                            HTH_34 23 aleatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaL 76
                                      ++e++ g+L+ +l+ L + + +e  k+  +k +   +++T++G++a  + ++++
  gi|313127216|ref|YP_004037486.1| 46 QTEVNHGRLYPNLDDLVEMDLVE--KSELDK-RTNQYELTEKGHDAVLNRFAWM 96
                                      68999999999999999999765..666555.7889**********99988887 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.24      53      87 ..      55      89 ..      49      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                           DUF1495 53 ynsessLielGLveeeeeseglklYklteeGieiv 87
                                      y + + L+e+ Lve+ e ++ ++ Y+lte+G   v
  gi|313127216|ref|YP_004037486.1| 55 YPNLDDLVEMDLVEKSELDKRTNQYELTEKGHDAV 89
                                      666678*******99999*************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 882.44
//
Query:       gi|313127217|ref|YP_004037487.1|  [L=177]
Description: inorganic pyrophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-50  169.3   1.3    6.1e-50  169.2   1.3    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   1.3   3.4e-54   6.1e-50       1     159 [.      20     172 ..      20     173 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 3.4e-54
                                       EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEE CS
                   Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkv 77 
                                       +vvE  +g+++Kye+dk+   ++ldrvl++ ++yp +YGf+pqT+ d     D+DP D+lvl+e++++pg+v+e+++
  gi|313127217|ref|YP_004037487.1|  20 AVVECLKGERNKYEYDKDIPGVVLDRVLHSNVHYPSDYGFMPQTYYD-----DEDPFDILVLVEDQTFPGCVIEARP 91 
                                       59*********************************************.....***********999*********** PP

                                       EEEEEEEETTEEEEEEEEEETTSGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHH CS
                   Pyrophosphatase  78 lGvlamiDegetDdKiiavpvkdprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekviee 154
                                       ++++ m D+ge+DdK+iavp++dpr+++++d++dl ++ ++ei +fFetyk+le  +k+v+  +w+++++A++ ie+
  gi|313127217|ref|YP_004037487.1|  92 VALMGMDDDGEKDDKVIAVPTEDPRYDHVQDVDDLTDQQKDEIAEFFETYKNLE-AGKEVETLGWEGADAAKDAIEH 167
                                       ******************************************************.56999***************** PP

                                       HHHHH CS
                   Pyrophosphatase 155 ahery 159
                                       a++ y
  gi|313127217|ref|YP_004037487.1| 168 AMDLY 172
                                       99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1156.62
//
Query:       gi|313127218|ref|YP_004037488.1|  [L=40]
Description: hypothetical protein Hbor_24870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       146  (0.00814323); expected 358.6 (0.02)
Passed bias filter:                       95  (0.00529868); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.26s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 321.87
//
Query:       gi|313127219|ref|YP_004037489.1|  [L=301]
Description: hypothetical protein Hbor_24880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-29  100.4  13.4    8.9e-29  100.4  13.4    1.5  2  Rhomboid  Rhomboid family
      2e-12   47.1   9.5    2.8e-12   46.6   9.5    1.2  1  zf-AN1    AN1-like Zinc finger
     0.0088   16.6   1.2      0.021   15.4   0.7    1.9  1  DUF1751   Eukaryotic integral membrane protein (DUF1751)
  ------ inclusion threshold ------
      0.055   13.6   1.9      0.083   13.0   1.9    1.3  1  FYVE      FYVE zinc finger
       0.52   10.2   4.6       0.84    9.6   4.6    1.3  1  zf-HIT    HIT zinc finger
        1.8    8.3   5.3         15    5.3   0.8    2.4  2  zf_UBZ    Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3       1.9   5.8e+03      82      95 ..      88     101 ..      80     117 .. 0.49
   2 !  100.4  13.4     3e-32   8.9e-29       3     146 ..     121     278 ..     119     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHCCCC CS
                          Rhomboid  82 llgallvlvprnrk 95 
                                       +lg+++v++  +++
  gi|313127219|ref|YP_004037489.1|  88 FLGLMWVTFALEWI 101
                                       34444444433333 PP

  == domain 2  score: 100.4 bits;  conditional E-value: 3e-32
                                       GCC-TTHHHHGGG--..SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S.......-EE CS
                          Rhomboid   3 krgelwrlltsmflH..agwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses....plv 73 
                                        +  +w+++ts+f H  ++++H+++N+++l++fG+ +er +Gs +f ll+l sg++++l ++ +    e      ++
  gi|313127219|ref|YP_004037489.1| 121 DPFYVWTWVTSIFAHsrFSFFHIVGNSIVLYFFGPLVERYIGSRKFTLLFLGSGMLAGLSHVGVGMLLEPgvrtGVL 197
                                       56789**********6669*********************************99998887766665555555559** PP

                                       SSHHHHHHHHHHHHHHHHCCCCGS----HC.....CCCCCCCCCCHHHCTSS......STTTHHHHHHHHHHHHHHH CS
                          Rhomboid  74 GaSGaifgllgallvlvprnrkllrkliia..llllllfillnlvlgllpra......ggvsnlAHlgGllaGlllg 142
                                       GaSGaif++lg+l+vl p+ +++l +li++  +l+ l f+ l++v+ l p+a      g+v+++AHl+Gl++Gl++g
  gi|313127219|ref|YP_004037489.1| 198 GASGAIFAILGVLTVLNPNLKIYLYFLIPIplWLFTLGFAGLSIVFFLQPGAaasvgqGEVAHFAHLIGLIIGLAYG 274
                                       **************************9999999*****************99************************9 PP

                                       HHHC CS
                          Rhomboid 143 llll 146
                                         + 
  gi|313127219|ref|YP_004037489.1| 275 QRVK 278
                                       7665 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   9.5   9.2e-16   2.8e-12       1      39 [.       4      40 ..       3      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 9.2e-16
                            zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkHrlpedHdCkkla 39
                                      C+  +C+k++++p++Cr+Cg++FC++Hrlpe+H+C++l+
  gi|313127219|ref|YP_004037489.1|  4 CD--ECGKHENMPYQCRRCGQTFCAEHRLPENHNCPGLS 40
                                      66..7*******************************975 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.7     7e-06     0.021       6      65 ..     123     184 ..     117     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7e-06
                           DUF1751   6 pypwtlltasfveq..nvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvll 65 
                                       +y+wt +t+ f  +  ++++++ + + l+++g ++Er+ gs+ +   +l  +++++l  v +
  gi|313127219|ref|YP_004037489.1| 123 FYVWTWVTSIFAHSrfSFFHIVGNSIVLYFFGPLVERYIGSRKFTLLFLGSGMLAGLSHVGV 184
                                       59*********9973357999*********************99988887777777776665 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.9   2.8e-05     0.083      10      39 ..       2      28 ..       1      64 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                      SB-TTT--B--SSS--EE-TTT--EE-STT CS
                              FYVE 10 kkCeiCakkFsllrrrhhCrlCGkvvCekC 39
                                      ++C++C k+ ++    + Cr CG+ +C+++
  gi|313127219|ref|YP_004037489.1|  2 ATCDECGKHENM---PYQCRRCGQTFCAEH 28
                                      579999988766...899*********654 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.6   0.00028      0.84       4      24 ..       3      25 ..       1      26 [. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                                      B-TTT-S..B-SEE-TTT--EES CS
                            zf-HIT  4 lCgvCgf..pakYkCpkCntryC 24
                                       C  Cg+     Y C++C++ +C
  gi|313127219|ref|YP_004037489.1|  3 TCDECGKheNMPYQCRRCGQTFC 25
                                      6999***99999**********9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3    0.0067        20       4      11 ..       3      10 ..       1      12 [. 0.90
   2 ?    5.3   0.8    0.0051        15       3      12 ..      15      24 ..      14      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0067
                            zf_UBZ  4 lCerCgke 11
                                      +C++Cgk+
  gi|313127219|ref|YP_004037489.1|  3 TCDECGKH 10
                                      8*****97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0051
                            zf_UBZ  3 ylCerCgkei 12
                                      y+C rCg+++
  gi|313127219|ref|YP_004037489.1| 15 YQCRRCGQTF 24
                                      99******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2007.28
//
Query:       gi|313127220|ref|YP_004037490.1|  [L=255]
Description: endonuclease V [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-53  181.9   0.0    1.3e-53  181.6   0.0    1.0  1  Endonuclease_5  Endonuclease V


Domain annotation for each model (and alignments):
>> Endonuclease_5  Endonuclease V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.6   0.0   7.2e-58   1.3e-53      16     196 ..      54     244 ..      40     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 181.6 bits;  conditional E-value: 7.2e-58
                                       G-SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC-SS--SEEEE CS
                    Endonuclease_5  16 klklvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkaleklkqkpdvllv 92 
                                       +  lvaGvD +f +++    v+a+vv +    +vve+ +av++l++pYipg+L+FRE  ++++a+ekl+ +pd+l++
  gi|313127220|ref|YP_004037490.1|  54 DRPLVAGVDQAFLDDRG---VSAIVVAR--GDTVVERVHAVTDLEIPYIPGLLSFREGGPIVAAFEKLSCDPDLLVF 125
                                       3679********55444...99999998..6789******************************************* PP

                                       EC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE-..---SSTTEEEEEE........ETTEEEEEEEESSTTS CS
                    Endonuclease_5  93 DGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkve..epekekgsvvplv........segevigaalrtkknv 159
                                       DG+G +H r++GlA+hlGv++d p++GvaKsll+g+ +    ++ +g  ++++        ++g+ ig+a+++++  
  gi|313127220|ref|YP_004037490.1| 126 DGSGRIHFRQAGLATHLGVVFDKPSVGVAKSLLCGHPTedVDGRPEGWRAEILaddsvenaDSGDPIGHAFQSRQYD 202
                                       **********************************854421233334444444445444443559*********9987 PP

                                       .....--EEEEEECSS-HHHHHHHHHHCS-T-SS-HHHHHHH CS
                    Endonuclease_5 160 .....kpiyvSvGhrisletalelvlallkkyrlPepirqAd 196
                                            +p+yvS+Ghr+s+ ta++lv +l+ +y+lPep+rqAd
  gi|313127220|ref|YP_004037490.1| 203 tepiiNPLYVSPGHRVSVPTATTLVSQLCGGYKLPEPTRQAD 244
                                       78899************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1716.89
//
Query:       gi|313127221|ref|YP_004037491.1|  [L=280]
Description: hypothetical protein Hbor_24900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-49  167.7   0.0    2.5e-49  167.4   0.0    1.1  1  adh_short        short chain dehydrogenase
    1.3e-38  132.9   0.0    1.8e-38  132.4   0.0    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    4.2e-13   49.6   0.0      7e-13   48.9   0.0    1.4  1  KR               KR domain
    5.8e-06   25.9   0.0    1.2e-05   24.9   0.0    1.7  1  Epimerase        NAD dependent epimerase/dehydratase family
    8.2e-06   25.4   0.0    1.1e-05   25.0   0.0    1.1  1  DUF1776          Fungal family of unknown function (DUF1776)
    1.7e-05   24.8   0.0    3.3e-05   23.9   0.0    1.7  1  NAD_binding_10   NAD(P)H-binding
    0.00017   20.8   0.0    0.00026   20.2   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.043   13.6   0.0    1.4  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.4   0.0   1.1e-52   2.5e-49       1     192 [.       4     189 ..       4     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.4 bits;  conditional E-value: 1.1e-52
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k+vl+tG+ssGIGra+a ++++e+++v++++r+++++e++ ++          +++Dvtd ++ve+++++++++ g+
  gi|313127221|ref|YP_004037491.1|   4 KTVLITGCSSGIGRATALAFLEEDWRVYATARNPADIETLGEKG------CELATLDVTDGDDVERVIDRIIEEEGH 74 
                                       79**********************************95555553......6789*********************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       l ++vnNAG  ++gp +++  e++ r ++vN+ g+  l+ra+lp+m +q  G+IvnvsSvag+ +++g+ +Ys sK+
  gi|313127221|ref|YP_004037491.1|  75 LTCVVNNAGYGQFGPLEDVPTEQVHRQFDVNVYGPHRLIRAALPHMRRQGDGTIVNVSSVAGQISFPGGGVYSGSKF 151
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                       a+ ++t++l++e++++g+  + v PG+v+T++++++++
  gi|313127221|ref|YP_004037491.1| 152 ALGAMTDALRNEVSEYGVDAVLVEPGPVATNFTERVEA 189
                                       *******************************9998766 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   0.0   8.2e-42   1.8e-38       1     185 [.      10     190 ..      10     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 8.2e-42
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnna 77 
                                       G  sgIGra+A a+ ee ++v +t +n ++   +e+l e+ g e+  +DVtd ++ve++++++ e+ g+l ++vnna
  gi|313127221|ref|YP_004037491.1|  10 GCSSGIGRATALAFLEEDWRVYATARNPAD---IETLGEK-GCELATLDVTDGDDVERVIDRIIEEEGHLTCVVNNA 82 
                                       6789*************************9...9999986.999********************************* PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                       g+ +   gp+++++ e+++r +dvn+y+ ++l++aalp+m+++  g ivn+ssv++++++p+  +y+ +K al a+t
  gi|313127221|ref|YP_004037491.1|  83 GYGQF--GPLEDVPTEQVHRQFDVNVYGPHRLIRAALPHMRRQgdGTIVNVSSVAGQISFPGGGVYSGSKFALGAMT 157
                                       *****..*******************************9998889******************************** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTH CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikgf 185
                                        +l +e+ ++g+    v pgp++T+ +++++ +
  gi|313127221|ref|YP_004037491.1| 158 DALRNEVSEYGVDAVLVEPGPVATNFTERVEAE 190
                                       **************************9998754 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   3.1e-16     7e-13       2     177 ..       5     178 ..       4     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 3.1e-16
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78 
                                       t+litG+  g+G+++a   +e+   ++  ++R+        a i++l ++g+e   + +Dv+d d+ve+++++i +e
  gi|313127221|ref|YP_004037491.1|   5 TVLITGCSSGIGRATALAFLEED-WRVYATARN-------PADIETLGEKGCEL--ATLDVTDGDDVERVIDRIIEE 71 
                                       78***************999986.568999999.......35899******975..6789***************** PP

                                       SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--S.EEEEEEEHHHHH--TT-HHHHH CS
                                KR  79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esld.ffvlfSSiagllgsagqanYaa 151
                                       e+ ++ v++ Ag  + ++le++ +e++++ +   v G + L ++  +   ++ d  +v +SS+ag +  +g + Y+ 
  gi|313127221|ref|YP_004037491.1|  72 EGHLTCVVNNAGYGQFGPLEDVPTEQVHRQFDVNVYGPHRLIRAALPhmrRQGDgTIVNVSSVAGQISFPGGGVYSG 148
                                       **************************************999988766577566647899****************96 PP

                                       H....HHHHHHHHHHHHHHHHTEEEEEE-- CS
                                KR 152 a....NaflDalaeyrrsqglpavsinwgl 177
                                             a+ Dal ++ ++ g  av ++ g+
  gi|313127221|ref|YP_004037491.1| 149 SkfalGAMTDALRNEVSEYGVDAVLVEPGP 178
                                       511115666777777777777777776666 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   5.4e-09   1.2e-05       1     115 [.       6     133 ..       6     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.4e-09
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHH....HH.T-SEEEE-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfk....ee.qpdavihlA 72 
                                       +l+tG +  iG+a++ a+le++++v + +r++ + +t  ++  el +ld+td++++er+++    ee + ++v++ A
  gi|313127221|ref|YP_004037491.1|   6 VLITGCSSGIGRATALAFLEEDWRVYATARNPADIETLGEKGCELATLDVTDGDDVERVIDriieEEgHLTCVVNNA 82 
                                       79*****************************999999999888***********77766542221677899999999 PP

                                       S---HHHHHHSH....HHHHHHHTHHHHHHHHHHHHHTCT....EEEEEEE CS
                         Epimerase  73 avggvaassedp....adfieknlqgtlnlleaarkagvk....rllflsS 115
                                       ++g  +   + p     + ++ n+ g  +l+ aa  +  +     ++++sS
  gi|313127221|ref|YP_004037491.1|  83 GYGQFGPLEDVPteqvHRQFDVNVYGPHRLIRAALPHMRRqgdgTIVNVSS 133
                                       866554444444000044566788888888888874433223336666666 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.7e-09   1.1e-05     101     296 .]      82     270 ..      75     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.7e-09
                           DUF1776 101 lsy.ptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsa 176
                                         y ++gp+e +p ++++ ++  ++  p  ++ a lp+++    q   +iv   s+  +++ p  ++ +    al a
  gi|313127221|ref|YP_004037491.1|  82 AGYgQFGPLEDVPTEQVHRQFDVNVYGPHRLIRAALPHMRR---QGDGTIVNVSSVAGQISFPGGGVYSGSKFALGA 155
                                       56889***********************************7...99999**************************** PP

                           DUF1776 177 lfevLkrelrphnidvtqikLGnldlangsqsnskiasvagsevlsWsesaralygpnyvsilskaisaksirrgss 253
                                       ++ +L++e++++++d + +  G +     +  +   a+v gse l+   +   +y++ y+  +  +   + ++   s
  gi|313127221|ref|YP_004037491.1| 156 MTDALRNEVSEYGVDAVLVEPGPVAT---NFTERVEAEVEGSEELPG-VERSGAYESFYELLSDTQLLGGGGPAAIS 228
                                       **********************9766...577778899999995554.34556899888888887666666669999 PP

                           DUF1776 254 lreLhnalfdllegsskkrvvyvGkgarlyslvgkllpeglve 296
                                         ++ + ++d+  ++ + + +y G+ ar++  ++++lp+++v+
  gi|313127221|ref|YP_004037491.1| 229 PERVAEDIVDAASSTKPRARYYPGTPARIAA-LARVLPNSWVD 270
                                       9************9999999********975.78999999985 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.5e-08   3.3e-05       3     102 ..      12     137 ..      10     243 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.5e-08
                                       TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT......T-S.EEEES---TC CS
                    NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealk......gad.aVvsalgggg 72 
                                       + ++Gr+ +   l++ +++v a +Rnp++++ l  e+g+e+ ++dvtd +d++++++      g+   Vv ++g g+
  gi|313127221|ref|YP_004037491.1|  12 SSGIGRATALAFLEE-DWRVYATARNPADIETLG-EKGCELATLDVTDGDDVERVIDriieeeGHLtCVVNNAGYGQ 86 
                                       6789***********.7**************997.7*******************9866655544314555553332 PP

                                       C.......HHHH................HHHHHHHHHHCT--EEEEEEETTTT CS
                    NAD_binding_10  73 k.......deeg................aknivdaakeagvkRfvlvsaigvg 102
                                               +                    ++++  ++++g   +v vs++  +
  gi|313127221|ref|YP_004037491.1|  87 FgpledvpT--EqvhrqfdvnvygphrlIRAALPHMRRQGDGTIVNVSSVAGQ 137
                                       244333331..033445555556666666666666777777777777766544 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.2e-07   0.00026       2      89 ..       5     116 ..       4     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-07
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHH.....HHH--SEEEE- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaell.....keakpdvvvna 58 
                                       ++l+tG +  +G++ a ++ ee++ v+a+ r+               +ld+td + v++++     +e +  +vvn 
  gi|313127221|ref|YP_004037491.1|   5 TVLITGCSSGIGRATALAFLEEDWRVYATARNpadietlgekgcelaTLDVTDGDDVERVIdriieEEGHLTCVVNN 81 
                                       69*****************************9**************************999666555556779**** PP

                                       -----HHHHHHSH....HHHHHHHTHHHHHHHHHH CS
                     RmlD_sub_bind  59 AAytavDkaEsee....eaayavnaeavealAeaa 89 
                                       A y +    E+ +    ++++ vn+ ++++l +aa
  gi|313127221|ref|YP_004037491.1|  82 AGYGQFGPLEDVPteqvHRQFDVNVYGPHRLIRAA 116
                                       ******9999875111146789*******999887 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.043      40      59 ..       3      22 ..       1      27 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                      -SEEEEESTSSHHHHHHHHH CS
                   Eno-Rase_NADH_b 40 pkkvLviGaStGYGLAsria 59
                                      pk+vL+ G+S+G G A+ +a
  gi|313127221|ref|YP_004037491.1|  3 PKTVLITGCSSGIGRATALA 22
                                      9*************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1828.11
//
Query:       gi|313127222|ref|YP_004037492.1|  [L=414]
Description: arsenite efflux ATP-binding protein arsa [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-78  264.2   0.0    1.9e-53  181.7   0.0    2.6  2  ArsA_ATPase  Anion-transporting ATPase
    1.1e-07   32.0   0.0    1.9e-07   31.2   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
      2e-06   27.9   0.0    9.8e-06   25.6   0.0    1.9  2  AAA_31       AAA domain
    0.00032   20.2   1.4     0.0028   17.2   0.0    2.5  3  ParA         NUBPL iron-transfer P-loop NTPase
     0.0032   16.9   0.0     0.0058   16.1   0.0    1.4  1  PhoH         PhoH-like protein
     0.0038   16.8   1.2      0.037   13.6   0.1    2.8  3  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.013   15.1   0.3        0.8    9.3   0.5    2.3  2  SRP54        SRP54-type protein, GTPase domain
      0.028   13.7   0.1      0.065   12.5   0.1    1.6  1  Zeta_toxin   Zeta toxin
      0.054   12.9   0.0        0.1   12.0   0.0    1.4  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
       0.07   13.6   1.7       0.13   12.7   1.7    1.4  1  NPF          Rabosyn-5 repeating NPF sequence-motif
       0.12   11.9   0.0       0.19   11.2   0.0    1.2  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   0.0   1.7e-25   2.8e-22       2      74 ..      54     128 ..      53     138 .. 0.92
   2 !  181.7   0.0   1.2e-56   1.9e-53      92     303 ..     185     413 ..     163     414 .] 0.89

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.7e-25
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSS..EEEEE--HHHHHH CS
                       ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeN..LsavEidpevele 74 
                                       +++l gGKGGVGKtt++aata+  + +g  +l++stDPAhslsD +  ++ ++p +v+e   L+a+Eidp++ +e
  gi|313127222|ref|YP_004037492.1|  54 EYVLYGGKGGVGKTTMAAATALSSAATGTATLVVSTDPAHSLSDTLGVEVPADPSRVREDipLYAAEIDPDEVIE 128
                                       5899******************************************************65449*******97655 PP

  == domain 2  score: 181.7 bits;  conditional E-value: 1.2e-56
                                       HHHHHHHHHH..TSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHHHHH CS
                       ArsA_ATPase  92 eledvlaeel..aslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklkeklspla 166
                                       ++edvl + +   s+PG de++++++l+ y+++  +d vv+DtaPTGhtlrll+lpe ++++l ++ ++++k+s ++
  gi|313127222|ref|YP_004037492.1| 185 GMEDVLGDMMgpGSMPGADEAAAMQQLVAYLDDPRFDRVVVDTAPTGHTLRLLELPELMDSMLGRIARMRQKFSGMM 261
                                       56677777663359*************************************************************** PP

                                       HHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                       ArsA_ATPase 167 kqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivN 243
                                        ++++++g+g+ +    + +l+e  e+i++++++l dp++t fr+V+ipE++s+ E++R+i  L  ygi v++++vN
  gi|313127222|ref|YP_004037492.1| 262 DNIKGMFGAGNPNQA-GMGDLDELRERIERLRAVLRDPQQTDFRVVMIPEEMSVVESKRLIDRLDGYGIPVQTLVVN 337
                                       ******999998877.8999********************************************************* PP

                                       EE-TTCSSS................TSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHHH CS
                       ArsA_ATPase 244 kllpeeeqe................nCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklsell 303
                                       +++++  +                 +Cef+++r+ +q++ l++  +lf+  +v+++pll++Ev G ++l+ +++ l
  gi|313127222|ref|YP_004037492.1| 338 RVMENLADVtttpvdsewvvspnldECEFCQRRWTVQQNALQRATDLFRGRNVKRVPLLADEVSGEDALRVVAACL 413
                                       *9876332122233345667777779********************************************999876 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.2e-10   1.9e-07       3      69 ..      57     294 ..      55     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.2e-10
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep......................... 54 
                                       + ++kGGvGKTt+aa+ a + a  g  +l+v +Dp  +++    g+e   +p                         
  gi|313127222|ref|YP_004037492.1|  57 LYGGKGGVGKTTMAAATALSSAATGTATLVVSTDPAHSLSD-TLGVEVPADPsrvrediplyaaeidpdeviegpfa 132
                                       569*********************************99999.7888888887999999999999999999******* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|313127222|ref|YP_004037492.1| 133 sdegtggfdavdldaddnpfeddtddgfgdetatdnpfggqngqnpfgmdmggmedvlgdmmgpgsmpgadeaaamq 209
                                       ********999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ......................................................................CCHCCCH CS
                                       ......................................................................xxxxxxx RF
                              CbiA  55 ......................................................................dlkrlle 61 
                                                                                                             dl+ l e
  gi|313127222|ref|YP_004037492.1| 210 qlvaylddprfdrvvvdtaptghtlrllelpelmdsmlgriarmrqkfsgmmdnikgmfgagnpnqagmgDLDELRE 286
                                       99999999999999999999999998888888888888888877777777777777777777777777775555555 PP

                                       HHHHHCHC CS
                                       xxxxxxxx RF
                              CbiA  62 llealgkk 69 
                                        +e+l+ +
  gi|313127222|ref|YP_004037492.1| 287 RIERLRAV 294
                                       55555544 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0     6e-09   9.8e-06       9      51 ..      60     102 ..      56     128 .. 0.86
   2 ?   -0.7   0.0      0.72   1.2e+03     108     128 ..     209     230 ..     184     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6e-09
                            AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgie 51 
                                        KGGvGKTT + + a + a +g  +L+v  Dp  +++ +lg+e
  gi|313127222|ref|YP_004037492.1|  60 GKGGVGKTTMAAATALSSAATGTATLVVSTDPAHSLSDTLGVE 102
                                       6***********************************9999886 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.72
                            AAA_31 108 kellekvkd.eYDyiiiDcpPs 128
                                       ++l+  ++d ++D +++D+ P+
  gi|313127222|ref|YP_004037492.1| 209 QQLVAYLDDpRFDRVVVDTAPT 230
                                       45555555426*********97 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.7e-06    0.0028       8      54 ..      57     102 ..      53     122 .. 0.77
   2 ?   -1.9   0.0       1.1   1.8e+03      94     121 ..     202     229 ..     191     236 .. 0.85
   3 ?    0.8   0.1      0.16   2.7e+02     138     173 ..     302     337 ..     292     350 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-06
                              ParA   8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgve 54 
                                          gKGGVGK+t+a+  Al+ a++g+++ ++ +D   +s+ + lgve
  gi|313127222|ref|YP_004037492.1|  57 LYGGKGGVGKTTMAAATALSSAATGTATLVVSTDP-AHSLSDTLGVE 102
                                       578**********************9999998884.46666666665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                              ParA  94 pmkskaikqllkdvewgelDyLiiDlPP 121
                                       +  ++a++ql++  +    D +++D+ P
  gi|313127222|ref|YP_004037492.1| 202 ADEAAAMQQLVAYLDDPRFDRVVVDTAP 229
                                       556789999999999999999****988 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.16
                              ParA 138 gaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                       +  +V  p+e+++ + k+ i+ ++   ++v  +v N
  gi|313127222|ref|YP_004037492.1| 302 DFRVVMIPEEMSVVESKRLIDRLDGYGIPVQTLVVN 337
                                       5568999***********************999988 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.6e-06    0.0058       2      67 ..      36     101 ..      35     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.6e-06
                                       ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----S CS
                              PhoH   2 ikpktkeQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGf 67 
                                       ++++t+  +++ + +++ + v   G+ G GKt +a a+a++    ++ + ++ t pa +  + lG+
  gi|313127222|ref|YP_004037492.1|  36 VEARTTDETDLPDRVDAPEYVLYGGKGGVGKTTMAAATALSSAATGTATLVVSTDPAHSLSDTLGV 101
                                       677788888888888999999************************************999888886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   2.3e-05     0.037      28      62 ..      48      83 ..      30      95 .. 0.83
   2 ?   -0.5   0.0      0.48   7.9e+02     126     150 ..     204     227 ..     178     234 .. 0.82
   3 ?   -0.6   0.0      0.51   8.3e+02      82     106 ..     280     304 ..     276     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                            AAA_25 28 gllpagelallaGapgtGKttlaldlalava.tGkp 62
                                      + + a e +l  G +g+GKtt+a   al+ a tG  
  gi|313127222|ref|YP_004037492.1| 48 DRVDAPEYVLYGGKGGVGKTTMAAATALSSAaTGTA 83
                                      55577788999*****************99988875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.48
                            AAA_25 126 ltadvdaleaaieevegvrlvviDp 150
                                        +a++++l a +++ ++ + vv+D+
  gi|313127222|ref|YP_004037492.1| 204 EAAAMQQLVAYLDD-PRFDRVVVDT 227
                                       46789999999999.9999*****9 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.51
                            AAA_25  82 sedelrrRlravgealrddarllvl 106
                                       + delr+R++++++ lrd+++ ++ 
  gi|313127222|ref|YP_004037492.1| 280 DLDELRERIERLRAVLRDPQQTDFR 304
                                       5678999999988888777776654 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5   0.00049       0.8       3      38 ..      55      90 ..      53      93 .. 0.90
   2 ?    3.2   0.0     0.035        58      64      93 ..     200     229 ..     189     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00049
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      ++l  G  G+GKTt +a  a    + g+ +l+v++D
  gi|313127222|ref|YP_004037492.1| 55 YVLYGGKGGVGKTTMAAATALSSAATGTATLVVSTD 90
                                      567778899*************************99 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.035
                                       TTSCHHHHHHHHHHHHHHTTSSEEEEEE-- CS
                             SRP54  64 eeadpaavakeavekakeekidvvlvDTaG 93 
                                        +ad+aa +++ v   ++ ++d v+vDTa 
  gi|313127222|ref|YP_004037492.1| 200 PGADEAAAMQQLVAYLDDPRFDRVVVDTAP 229
                                       57899999********************94 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     4e-05     0.065       6      51 ..      42      89 ..      37      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                        Zeta_toxin  6 kdkkypsq.erPklillgGqpGAGKselaellkdele.rqgnvvrldp 51
                                      +++  p++ + P  +l gG  G GK+++a++++ + + ++   +++++
  gi|313127222|ref|YP_004037492.1| 42 DETDLPDRvDAPEYVLYGGKGGVGKTTMAAATALSSAaTGTATLVVST 89
                                      3334677779********************999888744444455555 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.2e-05       0.1       6      41 ..      58      94 ..      54     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.2e-05
                         Fer4_NifH  6 y.GkGGiGksttsqnlsaalaemgkkvlivGCDPkaD 41
                                      y GkGG+Gk+t ++ ++ + a++g   l+v  DP + 
  gi|313127222|ref|YP_004037492.1| 58 YgGKGGVGKTTMAAATALSSAATGTATLVVSTDPAHS 94
                                      527*******************************874 PP

>> NPF  Rabosyn-5 repeating NPF sequence-motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.7   8.3e-05      0.13     136     173 ..     148     182 ..     123     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                               NPF 136 apNPFeeedenpfqkpasppvpgNPFeeatstNPFevd 173
                                         NPFe++ +  f ++++     NPF +  + NPF +d
  gi|313127222|ref|YP_004037492.1| 148 DDNPFEDDTDDGFGDETA---TDNPFGGQNGQNPFGMD 182
                                       579999998888877765...78************998 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.19       5      45 ..      56      96 ..      53     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                          CBP_BcsQ  5 alqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLr 45
                                      +l G +GGvG+t+++aa a +  + g   lv+ + p+  L 
  gi|313127222|ref|YP_004037492.1| 56 VLYGGKGGVGKTTMAAATALSSAATGTATLVVSTDPAHSLS 96
                                      68899***************************999887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2535.14
//
Query:       gi|313127223|ref|YP_004037493.1|  [L=173]
Description: competence/damage-inducible protein cina-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-60  201.0   0.1    8.5e-60  200.8   0.1    1.0  1  CinA      Competence-damaged protein


Domain annotation for each model (and alignments):
>> CinA  Competence-damaged protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.8   0.1   4.7e-64   8.5e-60       4     154 ..      10     167 ..       7     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 200.8 bits;  conditional E-value: 4.7e-64
                              CinA   4 laeevvkllkkkgltlatAEScTGGllaaaltsvpGaSavfeggvvtYsneaKeelLgvseetleehgavSeevaee 80 
                                       ++++v+++l+++g+tla+AEScTGGl+++ lt+vpG+S++f+++vvtYs +aK   L vs+e l+ehgavSe+va++
  gi|313127223|ref|YP_004037493.1|  10 VEARVGSALRESGETLAAAESCTGGLIGSFLTDVPGSSDYFDRSVVTYSYDAKLTELAVSRESLDEHGAVSEPVARQ 86 
                                       7899************************************************************************* PP

                              CinA  81 maegarerlgadiavavtGiAGpsggteekpvGtvyialagkgg.......veveklefegdreeireaavkaALel 150
                                       ma g+r+++g+d+ava+tGiAGp+ggt+ekpvGtvyi+la +g+       ++ve++ef+gdr++i+e+++++ALe 
  gi|313127223|ref|YP_004037493.1|  87 MATGVRDTAGTDWAVATTGIAGPDGGTDEKPVGTVYIGLAYRGEwgtqesyATVERHEFDGDRTQIKEQIARQALET 163
                                       ******************************************999999998999**********************9 PP

                              CinA 151 lrel 154
                                       ++++
  gi|313127223|ref|YP_004037493.1| 164 VLDA 167
                                       9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1188.10
//
Query:       gi|313127224|ref|YP_004037494.1|  [L=177]
Description: membrane-bound metal-dependent hydrolase (duf457) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.6e-12   44.7   4.4    1.2e-10   41.0   4.4    2.2  1  YdjM         LexA-binding, inner membrane-associated putative
  ------ inclusion threshold ------
      0.027   14.5   0.2      0.058   13.4   0.2    1.4  1  Zn_dep_PLPC  Zinc dependent phospholipase C


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   4.4   1.3e-14   1.2e-10       1     160 [.       1     148 [.       1     165 [. 0.80

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.3e-14
                              YdjM   1 MdgltHallGaalglalaallgaake....................avllavavlgAllPDiDhpsstlgrklglls 57 
                                       M    H+l Ga+l+l+l+  l+ ++                      +l + ++lgAl+PD+D        ++g   
  gi|313127224|ref|YP_004037494.1|   1 MNKEGHVLNGALLALGLGLILAVDPTagplitesssalaleagrrvVELSLPVILGALFPDVD-------TAFGK-- 68 
                                       77779*********999999999888999***************9999999999*********.......55555.. PP

                              YdjM  58 kklaklvgHRgftHSllflallalvlllllrlfgrsalrlglllllgvlsHlllDlltk.yGvpllwPfskkkvrls 133
                                               HR   H l++la++ ++  ++ +l           +++gv++H +lD++ + +G+ l++P+s++++ l+
  gi|313127224|ref|YP_004037494.1|  69 --------HRKTLHNLPVLAIFLAFPPIFGNLQY---------VWVGVATHYVLDMVGSkRGIALFYPLSSQEYDLP 128
                                       ........**********9999888777777666.........56************877***************** PP

                              YdjM 134 llfiiidplltllsrrglvalelvllv 160
                                       + + + ++++       +v   +v +v
  gi|313127224|ref|YP_004037494.1| 129 TGVATSSKWAN------PV-TFVVTAV 148
                                       99996666443......33.2222222 PP

>> Zn_dep_PLPC  Zinc dependent phospholipase C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.5e-06     0.058      29     106 ..      53     108 ..      38     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-06
                                       HHHHHHGGGG..-TT-GGG--BTTTTB-HHHHS-HHHHHHHHHHHHHHHHHC.....T-HHHHHHHHHHHHHHHHHH CS
                       Zn_dep_PLPC  29 lllGsvaPDleylfnasshsykthtkagllgedhhweetgkfllllikklrelyksegslklaafllGvlsHyvaDv 105
                                       ++lG+ +PD+  ++ +++h   +h+           + + + +l+++  +          +l+  + Gv++Hyv D+
  gi|313127224|ref|YP_004037494.1|  53 VILGALFPDV--DTAFGKHRKTLHN-----------LPVLAIFLAFPPIF-G--------NLQYVWVGVATHYVLDM 107
                                       589*******..6666888888888...........89999999999999.4........68**************8 PP

                                       T CS
                       Zn_dep_PLPC 106 f 106
                                       +
  gi|313127224|ref|YP_004037494.1| 108 V 108
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1183.23
//
Query:       gi|313127225|ref|YP_004037495.1|  [L=35]
Description: hypothetical protein Hbor_24950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 260.57
//
Query:       gi|313127226|ref|YP_004037496.1|  [L=270]
Description: metal-dependent phosphoesterase, php family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-17   61.8   0.0    7.5e-17   60.8   0.0    1.5  1  PHP_C     PHP-associated


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   4.2e-21   7.5e-17       3      55 ..     158     210 ..     156     211 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 4.2e-21
                             PHP_C   3 aNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegr 55 
                                       +Nr  r+f +++++pg+g+S+AH  + +G+a+Tef+++i+++++l++a+reg+
  gi|313127226|ref|YP_004037496.1| 158 QNRPGREFSAEFDIPGFGSSYAHLRGSIGEAWTEFDREIESAEDLVAALREGA 210
                                       79999**********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1819.52
//
Query:       gi|313127227|ref|YP_004037497.1|  [L=100]
Description: hypothetical protein Hbor_24970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.9   0.2      0.025   14.7   0.2    1.3  1  FYVE      FYVE zinc finger


Domain annotation for each model (and alignments):
>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   1.4e-06     0.025      15      37 ..      11      43 ..       2      90 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-06
                                      T--B--..........SSS--EE-TTT--EE-S CS
                              FYVE 15 CakkFs..........llrrrhhCrlCGkvvCe 37
                                      C+ +F+          + + rh C++CG +v e
  gi|313127227|ref|YP_004037497.1| 11 CDGRFEevedaiihqtVEHERHECKVCGTIVPE 43
                                      77777434444444434589**********974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 699.52
//
Query:       gi|313127228|ref|YP_004037498.1|  [L=151]
Description: 50S ribosomal protein L24a [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-23   80.9   0.1    7.3e-23   80.3   0.1    1.3  1  Spt5-NGN         Early transcription elongation factor of RNA
    5.1e-08   32.6   1.0    9.5e-08   31.7   0.4    1.8  2  KOW              KOW motif
  ------ inclusion threshold ------
      0.031   14.8   0.0       0.13   12.7   0.0    1.9  1  NusG             Transcription termination factor nusG
      0.047   13.6   0.5      0.098   12.6   0.5    1.5  1  Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal dom


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.1   1.6e-26   7.3e-23       2      84 .]       6      84 ..       5      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.6e-26
                          Spt5-NGN  2 iwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvv...qglvpi 77
                                      i+avk+ta+qE++va++++        +e+ eI++v+apd+l++y++vEAd++a+++r+le+ip++rg+v   q ++++
  gi|313127228|ref|YP_004037498.1|  6 IFAVKTTARQEQTVADMIAT-------REEAEIHAVLAPDSLTSYVMVEADNNAVINRVLEEIPHARGLVgdgQATSSM 77
                                      9*****************55.......56779**************************************866688*** PP

                          Spt5-NGN 78 kEvedll 84
                                      +Eve++l
  gi|313127228|ref|YP_004037498.1| 78 AEVEHFL 84
                                      *****98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.4   2.1e-11   9.5e-08       1      32 []      95     126 ..      95     126 .. 0.97
   2 ?   -2.3   0.0       1.1   4.9e+03       1       8 [.     139     146 ..     139     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.1e-11
                                       TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                       +Gd+V+ v+Gp+kG++++V ++d+ k+ V+v+
  gi|313127228|ref|YP_004037498.1|  95 EGDIVELVAGPFKGEKARVQRIDETKDQVTVE 126
                                       59****************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                       TTSEEEES CS
                               KOW   1 pGdhVkVv 8  
                                       +Gd  +V+
  gi|313127228|ref|YP_004037498.1| 139 RGDQIRVL 146
                                       69999997 PP

>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     3e-05      0.13      44      85 ..      19      76 ..       3      84 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                                      E..................CSSTTEEEEEE---CHHHHHHHCSTTEEEE-EETTSSCC-E CS
                                      x..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              NusG 44 k..................klfpgyifikadmndkllmairktpgVtgfvrvggeskpvp 85
                                                           + +y++++ad n    ++++++p+  g+v  g+      
  gi|313127228|ref|YP_004037498.1| 19 VadmiatreeaeihavlapDSLTSYVMVEADNNAVINRVLEEIPHARGLVGDGQ--ATSS 76
                                      355555566677777777788899*********9999999**********5444..3333 PP

>> Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.5   2.2e-05     0.098      23      51 .]     116     145 ..     112     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                                       EEEESSEEEEEEESSS.TEEEEETTEEEEE CS
                   Glyco_hydro_65C  23 Vrvtpeevtvtlesge.pltievyGeevtL 51 
                                       ++ t+++vtv+l +++ p++++v+G ++++
  gi|313127228|ref|YP_004037498.1| 116 IDETKDQVTVELYEATvPIPVTVRGDQIRV 145
                                       56689********9777********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1041.03
//
Query:       gi|313127229|ref|YP_004037499.1|  [L=57]
Description: protein translocase subunit sece/sec61 gamma [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-05   22.9   0.0    7.6e-05   22.5   0.0    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   4.3e-09   7.6e-05       7      49 ..      10      52 ..       7      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.3e-09
                                      HHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE  7 vkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfsk 49
                                       ++ lkK + P+++E+ ++ ++  ++++++g+ +f++  ++s+
  gi|313127229|ref|YP_004037499.1| 10 YVRVLKKASTPSWDEFSQIGLIAGAGIFLIGFMGFVIFALMSF 52
                                      6889********************************9777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 386.56
//
Query:       gi|313127230|ref|YP_004037500.1|  [L=386]
Description: cell division protein ftsz [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-42  144.1   0.5    8.4e-42  143.6   0.5    1.2  1  Tubulin         Tubulin/FtsZ family, GTPase domain
    2.5e-36  123.9   2.8    3.8e-36  123.3   1.3    2.1  2  FtsZ_C          FtsZ family, C-terminal domain
     0.0093   15.2   7.9      0.037   13.2   2.2    2.6  2  Tubulin_2       Tubulin like
  ------ inclusion threshold ------
       0.01   15.7   2.3      0.022   14.6   0.1    2.4  3  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.5   1.9e-45   8.4e-42       2     195 ..      53     211 ..      52     213 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 1.9e-45
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE- CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklll 78 
                                       i v+g+G++G++++n+++e    e gi             +g ++++    a++td q+l ei+a+      +k+l+
  gi|313127230|ref|YP_004037500.1|  53 ITVVGCGGAGGNTVNRMHE----E-GI-------------KG-AKLV----AANTDVQHLVEIDAD------TKILM 100
                                       89*****************....8.**.............88.7777....***************......***** PP

                                       -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEE CS
                           Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvv 155
                                       g++++++ gag+ p+vg+eaa e++eei +++e++d+   +f+ta+lgGGTG+G +pv++++++e   +al++++v+
  gi|313127230|ref|YP_004037500.1| 101 GEQKTQGRGAGSLPQVGEEAALESQEEIYDAIEGSDM---VFVTAGLGGGTGTGSAPVVAKAAREC--GALTIAIVT 172
                                       *************************************...**************************..********* PP

                                       E--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
                           Tubulin 156 lPsefsevvvepynailalkelieesdavividNdaLlki 195
                                       +P++  e+ v+  na+ +l++l++ +d+viv++Nd+Ll+ 
  gi|313127230|ref|YP_004037500.1| 173 TPFTA-EGEVRRTNAEAGLERLRDVADTVIVVPNDRLLDA 211
                                       ***99.*******************************986 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.4   1.1e+04      74      85 ..      35      46 ..      23      57 .. 0.74
   2 !  123.3   1.3   8.5e-40   3.8e-36       1      95 []     260     354 ..     260     354 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                                      EEEE-TT--SEE CS
                            FtsZ_C 74 Gavideeledei 85
                                      G++ deel++++
  gi|313127230|ref|YP_004037500.1| 35 GTMTDEELKNVL 46
                                      777777777765 PP

  == domain 2  score: 123.3 bits;  conditional E-value: 8.5e-40
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvAm+g+Ge++++++a++++++a++spLLdvd+sgA+++lvn+tggsd++++E+e v+e+i++++d++a++i+G+++
  gi|313127230|ref|YP_004037500.1| 260 GVAMIGLGESDSDSKAQDSVKSALRSPLLDVDISGANSALVNVTGGSDMSIEEAEGVVEEIYDRIDPDARIIWGTSV 336
                                       99*************************************************************************** PP

                                       -TT--SEEEEEEEEES-X CS
                            FtsZ_C  78 deeledeirvtvvatglk 95 
                                       deel++++r+++v+tg++
  gi|313127230|ref|YP_004037500.1| 337 DEELDGTMRTMIVVTGVE 354
                                       ****************95 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.4    0.0026        12       2      41 ..      55      95 ..      54     106 .. 0.66
   2 !   13.2   2.2   8.3e-06     0.037     114     181 ..     103     161 ..      77     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0026
                         Tubulin_2  2 viGLGGtGgkvlaelrrrlreel.gslelpdkvqFlyiDtd 41
                                      v+G+GG Gg++++++ +   +   + + + d  + + iD d
  gi|313127230|ref|YP_004037500.1| 55 VVGCGGAGGNTVNRMHEEGIKGAkLVAANTDVQHLVEIDAD 95
                                      7*************987644433233444444445556655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.3e-06
                         Tubulin_2 114 s....eGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllr 181
                                       +    +GAG +++vG  a +++ eei++a++        s        vfV  +L GGTG G++  va   r
  gi|313127230|ref|YP_004037500.1| 103 QktqgRGAGSLPQVGEEAALESQEEIYDAIEG-------S------DMVFVTAGLGGGTGTGSAPVVAKAAR 161
                                       233349**********9999999999988864.......3......48**************9877766555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.18   8.2e+02      51      94 ..      39      90 ..      24     106 .. 0.59
   2 ?   14.6   0.1     5e-06     0.022      46     102 ..     120     177 ..     112     200 .. 0.79
   3 ?   -2.2   0.0      0.71   3.2e+03       6      54 ..     212     255 ..     211     282 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.18
                                      CCHHHHHHT..T-S.EEEES---TCC.....HHHHHHHHHHHHHHCT--EEE CS
                    NAD_binding_10 51 vedlaealk..gad.aVvsalggggk.....deegaknivdaakeagvkRfv 94
                                       e+l+++l+  ++d +Vv ++g+gg+      eeg k +  +a +++v+++v
  gi|313127230|ref|YP_004037500.1| 39 DEELKNVLQdlQTDiTVVGCGGAGGNtvnrmHEEGIKGAKLVAANTDVQHLV 90
                                      4566666662222333666666655544443333344444445556666665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5e-06
                                       --TT-CCHHHHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEEEETTTT CS
                    NAD_binding_10  46 gdvtdvedlaealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlvsaigvg 102
                                       + ++++e++ +a++g d V++++g gg++ +g a  +++aa+e g   + +v++  + 
  gi|313127230|ref|YP_004037500.1| 120 AALESQEEIYDAIEGSDMVFVTAGLGGGTGTGsAPVVAKAARECGALTIAIVTTPFTA 177
                                       66899******************87777555658888899999999999999885443 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.71
                                       HHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHH CS
                    NAD_binding_10   6 vGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedl 54 
                                       vG+l v+++ + +  e  +l+R+ + ++el    +  +v +d+ dv+++
  gi|313127230|ref|YP_004037500.1| 212 VGKLPVRQAFKVS-DE--VLMRSVKGITELIT--KPGLVNLDFADVKTV 255
                                       6777777777775.45..47788888888874..445677777665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2665.45
//
Query:       gi|313127231|ref|YP_004037501.1|  [L=445]
Description: hypothetical protein Hbor_25010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-62  209.2   0.0    6.5e-62  208.7   0.0    1.2  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase
  ------ inclusion threshold ------
          1    9.7   7.1      0.088   13.1   1.6    2.2  2  Halo_GVPC       Halobacterial gas vesicle protein C (GVPC) re


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.7   0.0   7.3e-66   6.5e-62       2     205 .]      69     267 ..      68     267 .. 0.97

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 7.3e-66
                                       T---SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS CS
                    tRNA_deacylase   2 gedvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHG 78 
                                       +e++++i+f+SrHs+e+g plLT+H+tGn+g+ae+GG+ + +a+++P+++ka+++a++++a  ++ ++v +E+tHHG
  gi|313127231|ref|YP_004037501.1|  69 SESPEFIAFVSRHSGETG-PLLTAHFTGNFGPAEYGGDSGAFARSCPNAQKAVVEAFDRHA--PDAYDVGVECTHHG 142
                                       6789**************.******************************************..************** PP

                                       -----S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GG CS
                    tRNA_deacylase  79 PtelkvPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilsky 155
                                       Pt+  +P++FvE+GS e+eW+d++ a+ava++vl+l +   ++e++lvg+GGgHYaprf+++v+et++avGhi +++
  gi|313127231|ref|YP_004037501.1| 143 PTDPGAPAMFVELGSGEDEWEDPAGARAVAQSVLDLSGVTADRERHLVGFGGGHYAPRFERIVRETDWAVGHIGAEW 219
                                       ************************************99999************************************ PP

                                       GGGG--HH.....HHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EEE CS
                    tRNA_deacylase 156 aleelkee.....vikqaleksegadvalidkkslkseqkeaieelleelgievl 205
                                        l+++ +      vi++a+e+s  a++a+i+       +++++ e++e+lg++v+
  gi|313127231|ref|YP_004037501.1| 220 PLDAMGSPaenrdVIRRAFEAS-AAEYAVIE------GDRPELVEVVESLGYRVV 267
                                       8888877777788*********.********......89************9985 PP

>> Halo_GVPC  Halobacterial gas vesicle protein C (GVPC) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       1.4   1.3e+04      20      24 ..     236     240 ..     235     245 .. 0.59
   2 ?   13.1   1.6   9.8e-06     0.088       1      21 [.     384     404 ..     384     404 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                         Halo_GVPC  20 daFea 24 
                                        aFea
  gi|313127231|ref|YP_004037501.1| 236 RAFEA 240
                                       56665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.8e-06
                         Halo_GVPC   1 VsaLlaaIaafreefdatqda 21 
                                       V+++++a+ a+re+fda ++a
  gi|313127231|ref|YP_004037501.1| 384 VRHKQTAVVATRESFDAAAAA 404
                                       89***************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.20s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3414.27
//
Query:       gi|313127232|ref|YP_004037502.1|  [L=439]
Description: ca2+/na+ antiporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-22   80.3  22.3    7.9e-12   45.4   6.0    2.8  3  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   6.0   4.4e-16   7.9e-12       4     150 ..      38     199 ..      10     200 .. 0.86
   2 !   42.0   6.3     5e-15   8.9e-11       3     149 ..     229     374 ..     227     376 .. 0.86
   3 ?   -2.0   0.0      0.18   3.2e+03     107     120 ..     396     409 ..     382     423 .. 0.51

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 4.4e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHT.....TTHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaalt.....gevdlaignvlGsn 75 
                                       +++++s l++  ++++l + ae   k  +++   ++l +lA    +pE++++   a++      +++la++n++G+n
  gi|313127232|ref|YP_004037502.1|  38 GTVVVSGLAVLGASFLLAWGAETAEK--DVPR-AFALAVLAVLAVAPEYAVDALYAWQaatdpSKANLAVANMTGAN 111
                                       67888999999999999999999995..7776.77899*******************86666555************ PP

                                       HHHHHTHHHHHHHHHH.........BTTSSCE...........CCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHH CS
                          Na_Ca_ex  76 ifnlllviGlialigs.........lkvdses...........lkldlgllllvallllllvlllllplfvpgrltv 132
                                        + ++l+++ ial++                s           ++ld ++   +++l++++v+++++p      +++
  gi|313127232|ref|YP_004037502.1| 112 RILIGLGWSGIALFSIfkairgrddT-----SvvnrdgylrdaVTLDPSISTEILFLFIATVYAFFVPIG--AGIDW 181
                                       **************887765555540.....045555666888899999999999999999999998885..9**** PP

                                       HHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex 133 leglvllllYalylvlsl 150
                                       ++ +vl++lY+ y+++ +
  gi|313127232|ref|YP_004037502.1| 182 VDTVVLVGLYVTYIAIII 199
                                       **************9976 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 5e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       ++lf++s +li ++ + +   +ee++  +gi++ ++  ++ +l++ +pEli++ + + +   + a +++++s +  +
  gi|313127232|ref|YP_004037502.1| 229 LGLFAYSAFLIFTAVEPFAHGLEELGLQFGIPEFFMIQWIAPLASESPELIVTAYLVNKARSTAAFNALISSKLNQW 305
                                       689************************9************************************************* PP

                                       HTHHHHHHHHHH...BTTSSCECCHHH..HHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigs...lkvdseslkldl..gllllvallllllvlllllplfvpgrltvleglvllllYalylvls 149
                                       +l iG+ +++ s    ++ ++ ++l+   +++l++a  +++l++l+        +++v e+++ll+l++  +v+ 
  gi|313127232|ref|YP_004037502.1| 306 TLLIGTLVVVYSislGQYGKLPFDLKQeaEIWLTAAQSFFALTVLV------NFQIDVREAVTLLVLFVSQVVVE 374
                                       **********995543666666555553366666666665555543......49***************999875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHT CS
                          Na_Ca_ex 107 llvallllllvlll 120
                                        ++a++ll+ v+ll
  gi|313127232|ref|YP_004037502.1| 396 AYTAIYLLIGVVLL 409
                                       33333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2890.88
//
Query:       gi|313127233|ref|YP_004037503.1|  [L=319]
Description: k+dependent na+ exchanger related-protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-45  154.3  37.8    5.7e-24   84.8  13.1    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7  16.7   2.1e-25   3.7e-21       4     150 ..      12     150 ..      10     151 .. 0.93
   2 !   84.8  13.1   3.2e-28   5.7e-24       4     146 ..     180     315 ..     178     319 .] 0.93

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 2.1e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       +l+++++++++++a+flv++a+ +a  +gi  +v+G+t++A+++++pEl++ + +  + +++l++g+++Gsni+n++
  gi|313127233|ref|YP_004037503.1|  12 ALLLVGVVALYAGAEFLVRAASRLAIGFGIRAAVVGVTVVAFATTAPELAVVLLSGFSYSTNLGLGAIVGSNIANIG 88 
                                       6899*********************889************************************************* PP

                                       THHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       lv+Gl+al+ +l vd++ l++++++++ +a ll   vll +     +gr+  ++g+vll++ a+++ ++l
  gi|313127233|ref|YP_004037503.1|  89 LVLGLSALVRPLNVDESVLIRHVPFMFAAAGLL---VLLGM-----DGRIGTFDGVVLLAVLAVFTSYLL 150
                                       ***********************8888877777...45545.....5******************98865 PP

  == domain 2  score: 84.8 bits;  conditional E-value: 3.2e-28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       v+++++l l+ +++ +l++    + k  g  ++++Glt+lA+g+slpEl++si++a++ge++ +ignv+Gsni n+l
  gi|313127233|ref|YP_004037503.1| 180 VILLAGLGLLLLGSRWLIQGGQGVLKAYGFGERFIGLTVLAFGTSLPELAASIVSAAKGEAQFSIGNVVGSNIYNIL 256
                                       8999************************************************************************* PP

                                       THHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalyl 146
                                        viG+ a++ ++ v  e+l+ld+++l+++++++++ ++++       +++++ +g+vl++ Y+ + 
  gi|313127233|ref|YP_004037503.1| 257 AVIGVLAVLVPVGVPAETLALDFPALVVFTVVVVA-LMAYG------RTVSRADGAVLVVGYLGFF 315
                                       *********9*9999999*****999999999944.55556......9**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2383.07
//
Query:       gi|313127234|ref|YP_004037504.1|  [L=268]
Description: shikimate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-28   96.2   0.0    2.2e-27   95.1   0.0    1.6  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
      4e-13   48.9   0.7    8.7e-13   47.8   0.7    1.6  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
    8.1e-09   35.7   0.1    1.4e-08   34.9   0.1    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0016   17.6   4.7     0.0016   17.6   4.7    1.5  2  FAD_binding_2    FAD binding domain
     0.0028   17.0   0.1      0.018   14.3   0.1    2.0  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
     0.0085   15.3   1.3      0.013   14.7   1.3    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0087   16.3   0.4      0.019   15.2   0.4    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
       0.01   15.1   0.1      0.015   14.6   0.1    1.3  1  Thi4             Thi4 family
      0.014   15.0   0.2      0.024   14.2   0.2    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.019   14.3   0.1      0.027   13.7   0.1    1.2  1  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
      0.019   14.1   2.2      0.024   13.7   2.2    1.1  1  GIDA             Glucose inhibited division protein A
      0.024   14.1   1.4      0.044   13.2   1.4    1.5  1  adh_short        short chain dehydrogenase
      0.042   13.5   0.4      0.068   12.8   0.4    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.056   13.9   0.2       0.11   13.0   0.2    1.4  1  NAD_binding_7    Putative NAD(P)-binding
      0.078   13.1   0.1       0.14   12.3   0.1    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.079   12.3   0.0       0.12   11.7   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.21   10.2   1.7       0.28    9.8   1.7    1.1  1  HI0933_like      HI0933-like protein


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.0   2.1e-30   2.2e-27       1      83 []       8      89 ..       8      89 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 2.1e-30
                                      EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT- CS
                    Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigA 79
                                      +iGnp+ hSlSP +h+aa++++g++++y++fe +++++ +ave++ alg++GlnvTiPfK++v+++++  +e A++igA
  gi|313127234|ref|YP_004037504.1|  8 LIGNPVGHSLSPPMHEAAYDHCGIDARYVTFEPAPEDIGTAVEGADALGITGLNVTIPFKQDVLEHVE-PDELAARIGA 85
                                      79*****************************************************************7.********** PP

                                      -SEE CS
                    Shikimate_dh_N 80 vNti 83
                                      vNti
  gi|313127234|ref|YP_004037504.1| 86 VNTI 89
                                      ***8 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.7   8.3e-16   8.7e-13       1      31 []     234     264 ..     234     264 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 8.3e-16
                                       HHHHHHHHHHHHHHHHHS----HHHHHHHHH CS
                             SDH_C   1 GLgMLveQgaeqFelWTGrepPvevMreall 31 
                                       G +ML+ Qg+e+Fe+WTGr++Pve+M +al+
  gi|313127234|ref|YP_004037504.1| 234 GAWMLLFQGVEAFERWTGRDAPVEAMNDALR 264
                                       789**************************97 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.3e-11   1.4e-08       9      84 ..     116     187 ..     109     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.3e-11
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisata 84 
                                        l+++ ++++GaG  ++ +a +L+++++  v vaNRt era ela+++ g+  +   l  l+  +++adv++ at+
  gi|313127234|ref|YP_004037504.1| 116 ALADRDAVVVGAGGAGRAAAFALADAEAS-VHVANRTAERATELADDVPGA--TGGGLGTLD-QVRDADVLVNATS 187
                                       578999*********************99.******************888..677777776.6789999999997 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.2   4.4e+03     318     341 ..      72      94 ..      67     115 .. 0.71
   2 !   17.6   4.7   1.5e-06    0.0016       1      34 [.     121     154 ..     121     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.2
                                       TT.SSHHHHHHHSHHHHHHHHHCC CS
                     FAD_binding_2 318 shgldaegleatleaineeaangl 341
                                        h ++++ l+a++ a+n++a +++
  gi|313127234|ref|YP_004037504.1|  72 EH-VEPDELAARIGAVNTIAFTDE 94 
                                       56.777888888888777765544 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.5e-06
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGG CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqef 34 
                                       D++V+G+G+AG aAA ++a+a ++v v + + e+
  gi|313127234|ref|YP_004037504.1| 121 DAVVVGAGGAGRAAAFALADAEASVHVANRTAER 154
                                       89*************************9998874 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.7e-05     0.018      16      79 ..      99     158 ..      85     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                       --HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCC CS
                     THF_DHG_CYH_C  16 lpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitre 79 
                                           ++gv +  +++++ l+++++vvvG++   g++ a+ L+ ++a V v+++ ++  +e    
  gi|313127234|ref|YP_004037504.1|  99 YNTDAAGVRRSFTHHDVALADRDAVVVGAGG-AGRAAAFALADAEASVHVANRTAERATE---L 158
                                       556689999999****************997.5****************99987755444...3 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.3   1.3e-05     0.013       2      31 ..     121     152 ..     120     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE..T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve..l 31 
                                       d vv+G+G AG aaa  la a+a v++ +  +
  gi|313127234|ref|YP_004037504.1| 121 DAVVVGAGGAGRAAAFALADAEASVHVANrtA 152
                                       679**********************9996432 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   1.8e-05     0.019       2      98 ..     123     233 ..     122     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..................TTTCEEEEE--TTTHH CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..................lgvrfeaialdaenye 60 
                                       +++GaG+ G+a+a  la+ +     ++va r+ e++ +la+++                    v+++++ +  ++ +
  gi|313127234|ref|YP_004037504.1| 123 VVVGAGGAGRAAAFALADAEA---SVHVANRTAERATELADDVpgatggglgtldqvrdadVLVNATSVGMESDDTP 196
                                       79****************986...5***************9998888877777777777655555566666666666 PP

                                       HHHHHHHTTSSEEEE-SSGGGHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  61 avLaallkegdlvvnlsppissldvlkaCietgvhyvd 98 
                                           ++l +  +v++++ +     +l+ ++++g+  +d
  gi|313127234|ref|YP_004037504.1| 197 V-PRKYLHDDLAVLDAVYSPIETRLLRDAAAAGATTID 233
                                       5.667777777777777777777777777777777777 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.4e-05     0.015       6      46 ..     107     147 ..     103     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                       HHHHHHH.HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEE CS
                              Thi4   6 eryfedl.lkyaesDvvivGaGssGLtaayylakkpdlkvai 46 
                                       +r+f++  + +a+ D v+vGaG +G +aa+ la + +  v +
  gi|313127234|ref|YP_004037504.1| 107 RRSFTHHdVALADRDAVVVGAGGAGRAAAFALADA-EASVHV 147
                                       5555544157899********************98.444443 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   2.3e-05     0.024       2      46 ..     117     161 ..     116     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAke 46 
                                       l ++  +v+G G  G+a a  l d+   v v++r+ ++ ++ A +
  gi|313127234|ref|YP_004037504.1| 117 LADRDAVVVGAGGAGRAAAFALADAEASVHVANRTAERATELADD 161
                                       7789999****************************9999888865 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.6e-05     0.027     160     202 ..     115     157 ..      95     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                       Pyr_redox_3 160 hkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseieke 202
                                         +a+++ vV+G++  +  aA+ l++++a+V+v+ r++e+ +e
  gi|313127234|ref|YP_004037504.1| 115 VALADRDAVVVGAGGAGRAAAFALADAEASVHVANRTAERATE 157
                                       367899******************************9987665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.2   2.3e-05     0.024       1      34 [.     121     154 ..     121     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34 
                                       d +V+G+G AG +AA+a+a + a+v       ++
  gi|313127234|ref|YP_004037504.1| 121 DAVVVGAGGAGRAAAFALADAEASVHVANRTAER 154
                                       579**********************988544444 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.4   4.2e-05     0.044       3      46 ..     122     164 ..     120     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHH CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelke 46 
                                       ++v+Ga+ G Gra a +la + a+v v++r++e++ e+a+ +  
  gi|313127234|ref|YP_004037504.1| 122 AVVVGAG-GAGRAAAFALADAEASVHVANRTAERATELADDVPG 164
                                       7888887.*****************************9998765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   6.4e-05     0.068       2      36 ..     123     158 ..     122     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.4e-05
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHH CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rleal 36 
                                       +++GaG+ G+  a  La a a v++ +r++ r+ +l
  gi|313127234|ref|YP_004037504.1| 123 VVVGAGGAGRAAAFALADAEASVHVANRTAeRATEL 158
                                       69***************************9887766 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2    0.0001      0.11       5      46 ..     117     184 ..     115     233 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele..........................e 46 
                                       l ++  +vvG+G  +   +  l++a+a v+v   + ++++e                          +
  gi|313127234|ref|YP_004037504.1| 117 LADRDAVVVGAGGAGRAAAFALADAEASVHVANRTAERATEladdvpgatggglgtldqvrdadvlvN 184
                                       78999**************************8777433333444555555555544433333332220 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00013      0.14       4      42 ..     124     162 ..     121     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg 42 
                                       ++G G  G+  a  l++a+ +v+v nrt+e+++el+++ 
  gi|313127234|ref|YP_004037504.1| 124 VVGAGGAGRAAAFALADAEASVHVANRTAERATELADDV 162
                                       79*********************************9875 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.12      27      76 ..     110     159 ..      86     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHH CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeee 76 
                                        +++   l+++   ++G+G  G+a+a  l+  ++ v + +r+ ++ +e +
  gi|313127234|ref|YP_004037504.1| 110 FTHHDVALADRDAVVVGAGGAGRAAAFALADAEASVHVANRTAERATELA 159
                                       455556899999******************************98776333 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.7   0.00026      0.28       2      33 ..     121     152 ..     120     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00026
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                       d +v+G+G AG  aA ++a+++++V + +++ 
  gi|313127234|ref|YP_004037504.1| 121 DAVVVGAGGAGRAAAFALADAEASVHVANRTA 152
                                       78***********************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2104.28
//
Query:       gi|313127235|ref|YP_004037505.1|  [L=207]
Description: hypothetical protein Hbor_25050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-10   41.8   0.4    2.5e-10   40.8   0.0    1.7  2  HHH_5            Helix-hairpin-helix domain
    0.00023   21.4   0.0     0.0008   19.6   0.0    1.8  1  DUF4332          Domain of unknown function (DUF4332)
    0.00073   19.7   0.0     0.0012   19.0   0.0    1.3  1  Cdd1             Pathogenicity locus
      0.002   17.9   0.0     0.0036   17.1   0.0    1.4  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
      0.074   12.5   0.1       0.12   11.8   0.1    1.4  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
       0.17   12.0   0.0       0.27   11.3   0.0    1.3  1  TfoX_C           TfoX C-terminal domain


Domain annotation for each model (and alignments):
>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       4.2   1.3e+04      48      55 ..      52      59 ..      49      60 .. 0.77
   2 !   40.8   0.0   8.4e-14   2.5e-10       5      56 ..     152     203 ..     149     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.2
                                      HHHHHHHH CS
                             HHH_5 48 Aeriilel 55
                                      Ae +i+e+
  gi|313127235|ref|YP_004037505.1| 52 AEAVIEEA 59
                                      88999997 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 8.4e-14
                                       HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                         v+GiGp++A +l + Gie+v+dl +ad+e++ +  ++++k+++r+i+ + 
  gi|313127235|ref|YP_004037505.1| 152 ENVKGIGPAYAERLSDVGIETVDDLSSADAETVGEQIDVSEKRVQRWIDRAN 203
                                       579********************************88***********9875 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.7e-07    0.0008       2      54 ..     156     203 ..     155     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-07
                           DUF4332   2 gigkeeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanlAd 54 
                                       gig+++ae+L  +Gi+t++dL ++ ++  g+     +  +se++v++++ +A+
  gi|313127235|ref|YP_004037505.1| 156 GIGPAYAERLSDVGIETVDDLSSADAETVGE-----QIDVSEKRVQRWIDRAN 203
                                       899*********************9999888.....99999*******99985 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.1e-07    0.0012       9      46 ..     152     189 ..     145     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.1e-07
                              Cdd1   9 qdiPniGkalaedlvelGirsveelkgedpeelyekle 46 
                                       +++ +iG+a ae l ++Gi++v++l   d+e + e++ 
  gi|313127235|ref|YP_004037505.1| 152 ENVKGIGPAYAERLSDVGIETVDDLSSADAETVGEQID 189
                                       68899*************************99877764 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.2e-06    0.0036       5      30 ..     153     178 ..     151     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                   DNA_pol_lambd_f   5 kvyGVGpktAkkwyakGirtledlra 30 
                                       +v G+Gp+ A+++ + Gi t++dl  
  gi|313127235|ref|YP_004037505.1| 153 NVKGIGPAYAERLSDVGIETVDDLSS 178
                                       799*********************87 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.1e-05      0.12      32      51 ..     183     202 ..     176     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.1e-05
                      HTH_Tnp_ISL3  32 avArqlgvSwtTVwrildry 51 
                                       +v +q +vS+++V+r++dr+
  gi|313127235|ref|YP_004037505.1| 183 TVGEQIDVSEKRVQRWIDRA 202
                                       7999**************96 PP

>> TfoX_C  TfoX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.2e-05      0.27       6      40 ..     152     186 ..     147     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.2e-05
                            TfoX_C   6 kdLpNlglklerlLkkaGIktveeLrelGaveayl 40 
                                       ++++ +g++ ++ L+ +GI+tv++L +  a+ +  
  gi|313127235|ref|YP_004037505.1| 152 ENVKGIGPAYAERLSDVGIETVDDLSSADAETVGE 186
                                       677889*******************9988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1431  (0.0798148); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.80u 0.36s 00:00:01.16 Elapsed: 00:00:00.49
# Mc/sec: 1262.64
//
Query:       gi|313127236|ref|YP_004037506.1|  [L=543]
Description: aminodeoxychorismate synthase subunit i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.3e-101  338.2   0.0   4.4e-101  337.8   0.0    1.2  1  Chorismate_bind  chorismate binding enzyme
      6e-14   52.4   0.0    1.1e-13   51.5   0.0    1.4  1  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.8   0.0    5e-105  4.4e-101       2     258 .]     243     496 ..     242     496 .. 0.99

  Alignments for each domain:
  == domain 1  score: 337.8 bits;  conditional E-value: 5e-105
                                       HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEE CS
                   Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkve 78 
                                       r++++++v++vk++ir+gd++++++s+rl a+  a v+p+a+yralr+ npapys+l+e+++ +l++aSPEll++ve
  gi|313127236|ref|YP_004037506.1| 243 RAAFRDRVSAVKRYIRDGDTFQANVSQRLVAP--AVVHPVAAYRALRQVNPAPYSGLVEFPEADLVSASPELLVHVE 317
                                       6799****************************..99***************************************** PP

                                       TTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEE CS
                   Chorismate_bind  79 ggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhl 155
                                       g+ r++tepiaGTr+rg+t++ed ale++l++deKeraEh+m+vdl rndLgkv++ gsv+v+e+++v+rysev+hl
  gi|313127236|ref|YP_004037506.1| 318 GD-RLVTEPIAGTRPRGATEAEDDALERDLTSDEKERAEHAMLVDLERNDLGKVSEYGSVEVSEYRRVDRYSEVMHL 393
                                       77.************************************************************************** PP

                                       EEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETT CS
                   Chorismate_bind 156 vstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdk 232
                                       vs +eg+ ++dvs++d+++a+fP+g++tGaPk r+meii+e+E++rRg+Y+G++ ++++d++a+l++vIRt+v++d+
  gi|313127236|ref|YP_004037506.1| 394 VSVVEGQRRPDVSVADAVAAVFPGGTITGAPKPRTMEIIEEVESTRRGPYTGSIAAFGFDDRATLNIVIRTLVHHDD 470
                                       ****************************************************************************9 PP

                                       EEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 233 elrlgaGaGIvadSdpeaEyeEtlaK 258
                                       e++l++GaGIv+dSdp+aEy+Et+aK
  gi|313127236|ref|YP_004037506.1| 471 EYHLRVGAGIVHDSDPDAEYDETMAK 496
                                       ************************98 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   1.3e-17   1.1e-13       4     131 ..      39     167 ..      36     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.3e-17
                     Anth_synt_I_N   4 tplsvylklaeee.hkflLeSaeneggegrySfigldpflelkskngeveveg...pegeeleeeepldalreller 76 
                                       +p  +y++ ++e+ + f+Le     gg++ +S+ g+dp  +l + +++ ++       g +++++++l++l++ le+
  gi|313127236|ref|YP_004037506.1|  39 DPFDAYRRARDEGgDGFFLETT---GGQSGWSYFGMDPVERLCVGSDAETLAAadtGRGPNANTSSSLSTLDAALES 112
                                       7999*******99*********...89999********7775533333333333333444445555*********88 PP

                     Anth_synt_I_N  77 frsaedseptelpfvgGlvGylgYDlvreieklpksakddlnlpdarlilydtli 131
                                          +  +   e+p  +Gl+G ++YD+ re+e lp+ a dd+nlp +rl l+d++ 
  gi|313127236|ref|YP_004037506.1| 113 ESLVRGETGVEVPYPCGLFGWFSYDVARELESLPELADDDRNLPHLRLGLFDRVA 167
                                       8878888899*****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3841.71
//
Query:       gi|313127237|ref|YP_004037507.1|  [L=195]
Description: aminodeoxychorismate synthase, glutamine amidotransferase subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-45  154.5   0.0      3e-45  154.4   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    6.7e-07   29.3   0.1    2.6e-06   27.4   0.1    1.8  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.4   0.0   3.3e-49     3e-45       2     188 ..       6     188 ..       5     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 3.3e-49
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGI 77 
                                       ++Dnyds+ +nlv+++ ++  +v v+++da +   +    +pdgi+vs+Gpg+p+ ++ ++ + + +     P LG+
  gi|313127237|ref|YP_004037507.1|   6 VVDNYDSFAYNLVQYVGAFADEVVVRRNDAVDTADI-RSLDPDGIVVSPGPGTPAeAGVSVPVFRDLSY---PTLGV 78 
                                       89***************************9666665.489***************9******9999766...***** PP

                                       THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTE.E CS
                            GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtaksedde.e 153
                                       CLG+Q+l+ ++g +v ++  +  hg+ + + +d++++++gl++++++ ++H+++v++ e  p +l+ ta+++dd   
  gi|313127237|ref|YP_004037507.1|  79 CLGHQALCAALGSPVKRAP-EVVHGKPSLVSHDGEGIFEGLPDRFEVGRYHSLAVER-EDIPGELVETAWTDDDRrV 153
                                       *******************.9***********************************9.8889999999999888768 PP

                                       EEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHH CS
                            GATase 154 lmeiiekknpfvgvQFHPEststpegpellfnfli 188
                                       +m+++++++p vgvQFHPEs++t++g++l++nf+ 
  gi|313127237|ref|YP_004037507.1| 154 VMGVRRRNRPHVGVQFHPESILTENGKQLVANFVA 188
                                       999999999***********************965 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   2.9e-10   2.6e-06     105     216 .]      72     172 ..      67     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.9e-10
                     Peptidase_C26 105 gvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike. 180
                                       + P lg+C+G+q l  alG  + ++ e    ++ h ++        v+ + +++++ l    ++ev  +H+ a+++ 
  gi|313127237|ref|YP_004037507.1|  72 SYPTLGVCLGHQALCAALGSPVKRAPE----VV-HGKP------SLVSHDGEGIFEGLPD--RFEVGRYHSLAVERe 135
                                       67************9988866544433....33.3222......3466778899999988..************997 PP

                     Peptidase_C26 181 .laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        +  el  +A+++D+    + +++++ + +gvQ+HPE
  gi|313127237|ref|YP_004037507.1| 136 dIPGELVETAWTDDDRRVVMGVRRRNRPHVGVQFHPE 172
                                       788899999*999886666666666678********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1559.27
//
Query:       gi|313127238|ref|YP_004037508.1|  [L=301]
Description: branched chain amino acid aminotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-55  188.1   0.0    2.4e-55  187.8   0.0    1.1  1  Aminotran_4  Amino-transferase class IV


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.8   0.0   1.3e-59   2.4e-55       2     223 .]      43     272 ..      42     272 .. 0.96

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 1.3e-59
                       Aminotran_4   2 lfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglg...aats 75 
                                       lfEt+r+y g if++++H++RL+++ae+l+l+  ++  el++ ++e+l+an+ + ++++l v+rg        ++++
  gi|313127238|ref|YP_004037508.1|  43 LFETLRAYGGDIFRWEAHANRLAEGAEILELDHGLSNAELKRRVDETLAANELSDAYVKLSVTRGVQPGKlnpDPEV 119
                                       9***************************************************************99666688***** PP

                       Aminotran_4  76 epsvavyvsalppgpeseke.....lplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgnv 147
                                       +p+v+++v++lp g    ++      +l t + +r++ +   ++aKt nyl+ +lar+e + ++ade++++d dg +
  gi|313127238|ref|YP_004037508.1| 120 DPTVVIQVKPLPRGGRGSDPvwdapATLQTVKTRRVPDRAIPSRAKTHNYLNGILARLELRVTDADEAVMLDGDGAL 196
                                       **************9999999**986666667788899999999********************************* PP

                       Aminotran_4 148 tEgstsNvfivkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvrsi 223
                                        Eg+tsN+f+v++++l tP+l++ +LpGitr+ +l++a+++g++v+e+++ ++dl++a eaf+tn++ +++pv s+
  gi|313127238|ref|YP_004037508.1| 197 AEGATSNLFFVRNNALHTPSLDGPVLPGITRAEVLDIARDEGIPVREGRYKPDDLRDATEAFVTNSTWELRPVASV 272
                                       *************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2151.96
//
Query:       gi|313127239|ref|YP_004037509.1|  [L=139]
Description: ferredoxin subunit of nitrite reductase and ring-hydroxylating dioxygenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-09   36.5   0.0    4.4e-09   36.2   0.0    1.2  1  Rieske    Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
      0.079   12.9   0.0        0.1   12.5   0.0    1.2  1  Rieske_2  Rieske-like [2Fe-2S] domain
       0.11   12.6   0.0       0.15   12.2   0.0    1.1  1  DUF2318   Predicted membrane protein (DUF2318)


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   7.3e-13   4.4e-09       6      84 ..       8      94 ..       4     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 7.3e-13
                                      EEGGGC-.TTC.EEEEEETTEE..EEEEE-TTS-EEEEESC-TT.TT-BCGGSEE..ETT.EEE-TTT--EEE.TTSBE CS
                            Rieske  6 akesdvp.egd.pltvkvggep..lvvlrdedgevyAlsdvCtH.rgaplsegki..dekgvleCpcHgwayd.adGkv 76
                                       ++++vp +g+   t + g e+  +++ +  d+e++A+++ C+H   ++l++g++  + +g+l+C  Hg++++  +G +
  gi|313127239|ref|YP_004037509.1|  8 IAADEVPsDGTvLFTAQNGSETteVILTKLADDEIVAFENFCPHwTDIRLDKGSGayVRNGELVCEKHGATFQrDTGYC 86
                                      5677888656543333334333226666666*************44677977555336999************999999 PP

                                      EE-TTHHH CS
                            Rieske 77 ikgPaprp 84
                                        gP++ +
  gi|313127239|ref|YP_004037509.1| 87 DFGPCKGS 94
                                      99999876 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05       0.1      21     102 ..      27     109 ..       5     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                                       ETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS..-TTSB-BEE-EE CS
                          Rieske_2  21 vdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecle..deevslkvypvr 95 
                                        + ++v+l  l+++e+ A +n++p  +   l +G  +  ++   +++  ++ +f+ +tG c     +   l++++v 
  gi|313127239|ref|YP_004037509.1|  27 SETTEVILTKLADDEIVAFENFCPHWTDIRLDKGSGAYVRNGE-LVCEKHGATFQRDTGYCDFgpCKGSVLSTFDVA 102
                                       36788999999**********************9977774444.445679**********97644566889****** PP

                                       ESTSEEE CS
                          Rieske_2  96 vedgkve 102
                                       v+dg v 
  gi|313127239|ref|YP_004037509.1| 103 VQDGDVF 109
                                       ***9996 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.5e-05      0.15       9      94 ..      21     115 ..      14     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                           DUF2318   9 yeyeadgkevrflvvkksdgklrvaldaCevC......ekkgYvqegeelvCknCgvrfaldsigekkGGCnpipl. 78 
                                       ++ ++ +++ ++++ k  d+++++  + C         +++g + ++ elvC++ g +f+ d+     G C+   l 
  gi|313127239|ref|YP_004037509.1|  21 FTAQNGSETTEVILTKLADDEIVAFENFCPHWtdirldKGSGAYVRNGELVCEKHGATFQRDTGYCDFGPCKGSVLs 97 
                                       445556778999999999***9999999987667778877888889999*************999899***999987 PP

                           DUF2318  79 ..eytvkgdkiviskael 94 
                                         +  v+++++ ++++ l
  gi|313127239|ref|YP_004037509.1|  98 tfDVAVQDGDVFLTEEAL 115
                                       778899999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1190.73
//
Query:       gi|313127240|ref|YP_004037510.1|  [L=150]
Description: hypothetical protein Hbor_25110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-15   55.3   8.7    9.7e-15   54.8   8.7    1.2  1  GtrA      GtrA-like protein


Domain annotation for each model (and alignments):
>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   8.7   5.4e-19   9.7e-15       1     117 []      17     145 ..      17     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 5.4e-19
                              GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakl....lkqflkFvlvsll 73 
                                       +F+ vG++g++ d+++ ++l+ ll +   +A++++ +vai++ F++n++wtF d+  ++     l+++l   +v+  
  gi|313127240|ref|YP_004037510.1|  17 KFASVGAVGAVFDMTTTTALIVLLDVLNEYAKLVGAEVAIVVMFFINEHWTFADAGASEGvvptLRRLLTSNVVRSG 93 
                                       7********************99*********************************9998999************** PP

                              GtrA  74 glllnllilwllveklgleall....aklv....giivalvlnyvlsklfvF 117
                                       gl++++l++ ++ e    ++++    ++l+    +i++ ++lnyv++++f++
  gi|313127240|ref|YP_004037510.1|  94 GLAVQFLVVRAFREAGFSFFVFgfdvWELLpiplAIAASMFLNYVAESIFTW 145
                                       **********999998887777999955555556999999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 980.23
//
Query:       gi|313127241|ref|YP_004037511.1|  [L=264]
Description: family 2 glycosyl transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-07   29.1   0.1    1.9e-06   27.8   0.1    1.6  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1     1e-10   1.9e-06       2     121 ..       7     122 ..       6     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1e-10
                                       EEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   2 vviptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       vv+p+y   ++ l+  + +l++    +  ++ +  D+ + +  + l +l     + +v + + ++Gk++a+ ag++a
  gi|313127241|ref|YP_004037511.1|   7 VVVPAYRPdSERLADYVSALRSH--LSPATVRIELDAPRPGVLDRLADL-----PATVNTVDTRRGKGAAITAGFEA 76 
                                       78888888888888888877777..777777777888877777777777.....999999***************** PP

                                       --SS..EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEEC CS
                   Glycos_transf_2  78 atgd..yilflDaDdepdpdwleklvealekdgadvvlgqrprifg 121
                                          d  +++f DaD   +   +  +v+    ++ad+++g+r++  +
  gi|313127241|ref|YP_004037511.1|  77 IADDvdVLAFADADGSTPAASFASVVKSVAGGDADLAVGSRRHPAS 122
                                       *****************************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2001.66
//
Query:       gi|313127242|ref|YP_004037512.1|  [L=795]
Description: hypothetical protein Hbor_25130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-142  476.4  36.2   1.4e-142  476.0  36.2    1.2  1  DUF2298   Uncharacterized membrane protein (DUF2298)


Domain annotation for each model (and alignments):
>> DUF2298  Uncharacterized membrane protein (DUF2298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.0  36.2  7.7e-147  1.4e-142       1     497 []      46     556 ..      46     556 .. 0.95

  Alignments for each domain:
  == domain 1  score: 476.0 bits;  conditional E-value: 7.7e-147
                           DUF2298   1 lvalvaWllgslgllkftrllvllvllvlaalgllalvrkrkalaa..a.erlrailevellFlaaFlflvllRaln 74 
                                       +++++a+++g++ ++  ++l++++vllv++al++++  + r+ + +  +   +ra+ +++++F + F+flv+lRa++
  gi|313127242|ref|YP_004037512.1|  46 VLTVPAYWVGQVTFGLPALLAGVVVLLVASALAAADHDALRAGRLElgIdIPRRALGDAAAVFGLSFAFLVVLRAFD 122
                                       57899*******************************999999888764444************************** PP

                           DUF2298  75 PdlwhpagEkpmdfgfLnailrsptlPPeDpWfAggsinYYYfGyllvallakltgtapevaYnLalatlfAllvta 151
                                       P++ ++agEk++d+g+L++++r+ptlPPeD+WfAg++++YYY+G+l+++l+a+lt+t+p++aYnLala+++A+lvta
  gi|313127242|ref|YP_004037512.1| 123 PAVFPIAGEKFLDYGLLKSLQRAPTLPPEDMWFAGEPVKYYYGGHLVTTLFAWLTATPPRFAYNLALAGFYATLVTA 199
                                       ***************************************************************************** PP

                           DUF2298 152 afglaynlaaargrkesralvaGvlaallvllagnlatavrlllasllaglssalasaaalteera........... 217
                                       af+la ++ +++g   sr++ +G laa++v++a+nl ta rl l  l++gl++++a+++a +++++           
  gi|313127242|ref|YP_004037512.1| 200 AFELAATVGESHG--LSRRV-SGALAAFFVGIASNLVTAGRLALTLLPSGLQRQVAEMVAARTDYSvtkllqgvssf 273
                                       *************..88998.**************************************99999999*********6 PP

                           DUF2298 218 WfwdasRviksedetInEFPlFsfllgDlHaHvialpllllalalllallrrpaskrrrrrsllllllalvlGalaa 294
                                        +wdasRvi   ++tInEFPlF++l+gDlHaH++a+p+llla+a+ +a++r+p+++ rrrr  ll+ l++v+G++a+
  gi|313127242|ref|YP_004037512.1| 274 HYWDASRVI---PGTINEFPLFAWLNGDLHAHMTATPFLLLAAAIGYAYYRTPEADIRRRRL-LLASLPVVAGWQAV 346
                                       388******...********************************************999987.6************* PP

                           DUF2298 295 tNtWdfptyllllllalllaaarpatllp............srvlallkrlllallaavavlvlalllalPFlls.. 357
                                        NtW+fp++++l++lal++a+a p+tl+p            sr+ ++l+r+++al++++a +vl++l+a+PF+    
  gi|313127242|ref|YP_004037512.1| 347 NNTWSFPSVIALGTLALIFAPAAPWTLVPglsgvgdrlaarSRLSEELTRVAAALVVTAAGAVLTILVAAPFFFGta 423
                                       *****************************************99******************************9954 PP

                           DUF2298 358 faasvggiallp..ersslselllvhGlflvlllaylvllrvsrlsarralallaallllagvllalalalaallll 432
                                       ++ s+++++ll   +rss++ ll+vhG+f+v++ ayl+    srl++rr + l+a+ll++    + l+++laa+++ 
  gi|313127242|ref|YP_004037512.1| 424 VSGSERTVELLGpeMRSSFGGLLFVHGAFVVTFGAYLL----SRLRVRRPAYLVAGLLAAG--YVGLEIGLAAFAVS 494
                                       45588888888799************************....4688888888888887665..567999999***** PP

                           DUF2298 433 lpllllalallrrslaaeagfalvlalaglglvllvElvylrdaleeseRmNTvFKfyyqaWvLl 497
                                       +pll++++++lr++  +++g+++vl++ag+glv+lvElvy+++++ +s+RmNTvFK+y+q+WvL+
  gi|313127242|ref|YP_004037512.1| 495 IPLLVFGWVALRSD--RPVGYETVLIIAGAGLVTLVELVYVNEQA-GSGRMNTVFKTYMQVWVLW 556
                                       *************9..9****************************.******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 5112.44
//
Query:       gi|313127243|ref|YP_004037513.1|  [L=87]
Description: hypothetical protein Hbor_25140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 626.07
//
Query:       gi|313127244|ref|YP_004037514.1|  [L=63]
Description: hypothetical protein Hbor_25150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 464.73
//
Query:       gi|313127245|ref|YP_004037515.1|  [L=93]
Description: 50S ribosomal protein L44e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-24   83.8   2.0      1e-23   83.6   2.0    1.1  1  Ribosomal_L44   Ribosomal protein L44
     0.0099   15.3   1.2        3.7    7.1   0.0    2.2  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
       0.04   13.4   0.9        6.9    6.3   0.1    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.21   11.3   4.8        2.3    8.0   1.0    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.31   11.2   2.7         16    5.7   0.1    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.32   10.9   3.6        6.2    6.8   0.1    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.43   10.8   7.3        4.9    7.4   2.3    2.1  2  zf-B_box        B-box zinc finger
       0.43   10.7   5.6       0.98    9.6   5.7    1.6  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   2.0   4.6e-27     1e-23       2      76 .]      17      92 ..      16      92 .. 0.99

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 4.6e-27
                                      EEEEEEEE-------SSSHHHHHHHH.H-SSS..GGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                     Ribosomal_L44  2 HtehkveqykkgkdselaqgkRrydrkqsgyg..GqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                      H+eh+ve++++g+ + +++++R  +r +s +g  G++++v+++ +K+tKK++l++ C++C+k+++++++Ra+++e++
  gi|313127245|ref|YP_004037515.1| 17 HHEHEVEKVRSGRPTGMKWDARAQKRGKSTIGnaGRFSKVPGG-DKPTKKTHLKYICSDCGKAHMREGWRAGRLEFQ 92
                                      9******************************************.*******************************95 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.4    0.0018       3.9       3       9 ..       9      15 ..       7      18 .. 0.82
   2 !    7.1   0.0    0.0016       3.7       3      17 ..      70      85 ..      68      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0018
                       zf-ribbon_3  3 vrCPnCG 9 
                                      ++CPnC+
  gi|313127245|ref|YP_004037515.1|  9 TYCPNCD 15
                                      7999995 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0016
                       zf-ribbon_3  3 vrCPnCGa.plssddn 17
                                      + C+ CG+ + +++++
  gi|313127245|ref|YP_004037515.1| 70 YICSDCGKaHMREGWR 85
                                      789****999888876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0041       9.3       2       8 ..      10      16 ..       4      24 .. 0.68
   2 ?    6.3   0.1    0.0031       6.9      19      26 ..      69      76 ..      65      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0041
                                      EETTTTC CS
                      TF_Zn_Ribbon  2 kCPnCgs 8 
                                       CPnC +
  gi|313127245|ref|YP_004037515.1| 10 YCPNCDG 16
                                      4666654 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0031
                                      CEEESSSS CS
                      TF_Zn_Ribbon 19 elvCtdCG 26
                                       ++C+dCG
  gi|313127245|ref|YP_004037515.1| 69 KYICSDCG 76
                                      69*****9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.0     0.001       2.3      13      21 ..       8      17 ..       7      18 .. 0.81
   2 ?    4.9   0.2    0.0099        22       2       8 ..      72      78 ..      71      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.001
                     zinc_ribbon_2 13 akFCpyC.Gt 21
                                      +++Cp+C G+
  gi|313127245|ref|YP_004037515.1|  8 NTYCPNCdGH 17
                                      5899999887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0099
                     zinc_ribbon_2  2 CpnCGae 8 
                                      C+ CG+ 
  gi|313127245|ref|YP_004037515.1| 72 CSDCGKA 78
                                      9999985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4    0.0086        19      26      34 ..       8      16 ..       1      25 [. 0.71
   2 ?    5.7   0.1     0.007        16       6      13 ..      70      77 ..      60      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0086
                       Zn-ribbon_8 26 ltaCPeCgs 34
                                      +t CP+C +
  gi|313127245|ref|YP_004037515.1|  8 NTYCPNCDG 16
                                      566999976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.007
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      Y C +Cg+
  gi|313127245|ref|YP_004037515.1| 70 YICSDCGK 77
                                      77777775 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.8     0.015        34       6      17 ..      10      18 ..       5      20 .. 0.79
   2 ?    6.8   0.1    0.0028       6.2       4      17 ..      69      79 ..      69      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.015
                    Zn_ribbon_SprT  6 rCtgCgreythh 17
                                      +C++C+   +hh
  gi|313127245|ref|YP_004037515.1| 10 YCPNCD---GHH 18
                                      788888...776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0028
                    Zn_ribbon_SprT  4 vYrCtgCgreythh 17
                                      +Y C +Cg   ++h
  gi|313127245|ref|YP_004037515.1| 69 KYICSDCG---KAH 79
                                      7*******...776 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.3    0.0022       4.9      25      41 ..      10      24 ..       8      25 .. 0.86
   2 ?    6.2   0.2     0.005        11      13      23 ..      67      77 ..      63      80 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0022
                          zf-B_box 25 lCeeCstgeHrgHevvp 41
                                       C++C +g+H+ Hev++
  gi|313127245|ref|YP_004037515.1| 10 YCPNC-DGHHE-HEVEK 24
                                      5****.99997.**987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.005
                          zf-B_box 13 patlfCedCqq 23
                                      ++++ C dC++
  gi|313127245|ref|YP_004037515.1| 67 HLKYICSDCGK 77
                                      66666766664 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.7   0.00044      0.98       1      25 [.      10      78 ..      10      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00044
                          zf-Mss51  1 lCPvpkhkqt............................................apkhvdfeCpdCGip 25
                                      +CP ++ +++                                            ++ h ++ C dCG  
  gi|313127245|ref|YP_004037515.1| 10 YCPNCDGHHEhevekvrsgrptgmkwdaraqkrgkstignagrfskvpggdkptKKTHLKYICSDCGKA 78
                                      69999888888999**************************************999************64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 672.72
//
Query:       gi|313127246|ref|YP_004037516.1|  [L=61]
Description: 30S ribosomal protein S27e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-19   68.8   0.6    2.6e-19   68.7   0.6    1.0  1  Ribosomal_S27e  Ribosomal protein S27
  ------ inclusion threshold ------
      0.022   14.8   0.3      0.041   14.0   0.3    1.4  1  Zn-ribbon_8     Zinc ribbon domain
      0.043   13.5   0.9       0.06   13.1   0.9    1.2  1  A2L_zn_ribbon   A2L zinc ribbon domain
       0.12   13.1   0.5       0.15   12.8   0.5    1.1  1  MRNIP           MRN-interacting protein
       0.15   12.0   1.4       0.19   11.6   1.4    1.1  1  eIF-5_eIF-2B    Domain found in IF2B/IF5


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.6   7.3e-23   2.6e-19       2      54 ..       2      54 ..       1      55 [. 0.94

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 7.3e-23
                                      S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                    Ribosomal_S27e  2 rskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                       ++F  v+C dC ne+vvF++a++v++C  Cg++L++PtGG a +  +++e +
  gi|313127246|ref|YP_004037516.1|  2 AGNFYLVQCTDCDNEQVVFGKASSVINCAVCGTTLATPTGGDAEIHGEVVETV 54
                                      68999*****************************************9999876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   1.1e-05     0.041       4      36 ..       6      36 ..       5      38 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                       Zn-ribbon_8  4 YeYrCeeCghefevlqsisdapltaCPeCgsev 36
                                      Y  +C++C++e  v+ ++s  + + C  Cg ++
  gi|313127246|ref|YP_004037516.1|  6 YLVQCTDCDNEQVVFGKAS--SVINCAVCGTTL 36
                                      6779*****9999999877..3555*****854 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.9   1.7e-05      0.06       5      30 ..       9      35 ..       7      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                     A2L_zn_ribbon  5 vCsvCggngiln.seqgylvCieCgas 30
                                       C+ C+++ ++  ++++  +C  Cg++
  gi|313127246|ref|YP_004037516.1|  9 QCTDCDNEQVVFgKASSVINCAVCGTT 35
                                      6************************87 PP

>> MRNIP  MRN-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   4.2e-05      0.15       2      28 ..       8      34 ..       7      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                             MRNIP  2 lrCysCetfqvkqvkKskkwkCkvCne 28
                                      ++C  C   qv   k s+  +C vC++
  gi|313127246|ref|YP_004037516.1|  8 VQCTDCDNEQVVFGKASSVINCAVCGT 34
                                      8************************96 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.4   5.4e-05      0.19      88     116 ..       8      34 ..       5      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                                       TSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  88 VlCkeCkspetelekeerllvlkCkaCga 116
                                       V+C+ C++ ++ + k ++++  +C  Cg 
  gi|313127246|ref|YP_004037516.1|   8 VQCTDCDNEQVVFGKASSVI--NCAVCGT 34 
                                       99********9999988777..*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 476.99
//
Query:       gi|313127247|ref|YP_004037517.1|  [L=265]
Description: translation initiation factor 2 subunit alpha (aeif-2a) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-26   92.8   0.1    2.7e-26   91.9   0.1    1.4  1  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    8.8e-13   48.4   0.9    8.8e-13   48.4   0.9    1.8  2  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.086   12.7   0.0       0.16   11.8   0.0    1.4  1  DUF1494      Protein of unknown function (DUF1494)


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.1   4.5e-30   2.7e-26       2     116 .]     118     229 ..     117     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 4.5e-30
                                       HHCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHH CS
                       EIF_2_alpha   2 yeevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIke 77 
                                       y e+++ + ++y+++yd+F ++ai++ ++l++++++e+  ea+v++++++++++ v+++++i+++c t dGv+ Ike
  gi|313127247|ref|YP_004037517.1| 118 YSEIANAVLAEYETLYDGFeQAAIHGVSALEDVDLDEDEVEAIVDTARQNVSVPYVNVTGYIDIRCPTGDGVDDIKE 194
                                       8999************************************************************************* PP

                                       HHHHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  78 aLkageeasneeeveeeeevkikliapPeYvltvetldk 116
                                       aLka+e+    ++v ee++++++++++PeY+++v+++d+
  gi|313127247|ref|YP_004037517.1| 195 ALKAAEG----DDVPEEIQLEVTYVGAPEYRIKVRAPDY 229
                                       ***8888....56888********************997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.9   1.5e-16   8.8e-13       4      75 .]       9      81 ..       7      81 .. 0.97
   2 ?   -2.2   0.1      0.95   5.7e+03       6      32 ..     155     179 ..     149     182 .. 0.62

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.5e-16
                                      TTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  4 kgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                       ge v G+V ++t++G+fV+l+  ++ +g++++se+++   +++  +++++G++v +kvl+vd     i+lsik
  gi|313127247|ref|YP_004037517.1|  9 SGELVVGKVDEITDFGVFVDLEeyEDTRGLCHISEVASG-WIKNVRDHVREGQTVVAKVLDVDTGSQQIDLSIK 81
                                      7999**********************************9.9*******************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.95
                                       CEEEEEEEEEETTEEEEEETTTEEEEE CS
                                S1   6 evveGeVtsvtkgGafVelgngvegfv 32 
                                       ++ve+ +++  + ++ V ++ +v+g++
  gi|313127247|ref|YP_004037517.1| 155 DEVEA-IVDTARQNVSVPYV-NVTGYI 179
                                       55666.55666666666666.666665 PP

>> DUF1494  Protein of unknown function (DUF1494)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.7e-05      0.16      90     126 ..      61      97 ..      54     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                           DUF1494  90 GevaGtlhydtirkelelivaslkeeakqekivlldh 126
                                        +va +l  dt  ++++l+++  +e++++eki  ++ 
  gi|313127247|ref|YP_004037517.1|  61 TVVAKVLDVDTGSQQIDLSIKDVNEHQRKEKIQEWKN 97 
                                       579999**************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1257  (0.0701099); expected 358.6 (0.02)
Passed bias filter:                      732  (0.0408277); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.58
# Mc/sec: 1385.79
//
Query:       gi|313127248|ref|YP_004037518.1|  [L=60]
Description: zn-ribbon RNA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-24   85.6   0.2    1.9e-24   85.5   0.2    1.0  1  Nop10p       Nucleolar RNA-binding protein, Nop10p family
  ------ inclusion threshold ------
       0.03   14.4   0.1      0.046   13.8   0.1    1.3  1  Zn-ribbon_8  Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.2   2.1e-28   1.9e-24       1      51 [.       1      57 [.       1      58 [. 0.99

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 2.1e-28
                                      .----EE-TTT-......-EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHCHHH CS
                            Nop10p  1 mksylrkcgkcr......vYTLkkvcpecggptksahPaRFSPdDkyskyRralKkr 51
                                      mks++r+c +++      vYTL+++cpecg+++++++Pa+F P+D+y++yRralK+r
  gi|313127248|ref|YP_004037518.1|  1 MKSDIRVCDAWQnaherpVYTLSDTCPECGADAVNSAPAPFNPEDPYGEYRRALKRR 57
                                      9*******************************************************9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.1e-06     0.046      16      36 ..       9      33 ..       5      36 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-06
                       Zn-ribbon_8 16 evlqsisdap...lta.CPeCgsev 36
                                      +++q ++++p   l + CPeCg+++
  gi|313127248|ref|YP_004037518.1|  9 DAWQNAHERPvytLSDtCPECGADA 33
                                      67888888888886666*****954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 367.65
//
Query:       gi|313127249|ref|YP_004037519.1|  [L=251]
Description: hypothetical protein Hbor_25200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-53  182.3   0.2    1.4e-53  182.1   0.2    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.1   0.2   7.7e-58   1.4e-53       1     212 [.      19     232 ..      19     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: 182.1 bits;  conditional E-value: 7.7e-58
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEETTT.SEEEEEEE. CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyakdsgsrdllvlqg. 74 
                                       L++G+pg+G+Vg+lav++L+e+l+ e+v +i+ d+ +p     p+v+++++   +l   +++a d+g+rdllvl+g 
  gi|313127249|ref|YP_004037519.1|  19 LVEGLPGVGHVGKLAVEHLLEELDSEPVRYIYADE-FP-----PQVTLNDDsvAQLARAEFHAVDAGDRDLLVLTGd 89 
                                       89*********************************.**.....********9999999999999999*********9 PP

                                       ...E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH........CT-C CS
                              PAC2  75 ...repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele........esey 140
                                           + +++y  +++a ld+aee+gv+e + Lgg+++ge+     ++p +v ga+tde+ +e+le        ++++
  gi|313127249|ref|YP_004037519.1|  90 hqaQTNSGHYH-LTDAFLDIAEEFGVEEGYALGGVPTGELV----DEP-SVLGAVTDEDDVERLEavdvefreDEPA 160
                                       88888888888.**************************997....689.9**************76776665434** PP

                                       EEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 141 ggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                       ggivg++glLl+++++rg+++++l++e+++yl+dP++a+++le+l++++++ev  e+Lee+aee++e + ++
  gi|313127249|ref|YP_004037519.1| 161 GGIVGVSGLLLGLGERRGLSVACLMGETSGYLVDPQSAQVVLEVLQDVIDFEVGFESLEERAEEMKEVVGKI 232
                                       *******************************************************************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1684.36
//
Query:       gi|313127250|ref|YP_004037520.1|  [L=106]
Description: hypothetical protein Hbor_25210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.1   1.4       0.17   11.8   0.0    2.2  2  HTH_5     Bacterial regulatory protein, arsR family
     0.0024   17.9   0.4     0.0044   17.0   0.4    1.5  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   1.9e-05      0.17       1      28 [.      16      43 ..      16      44 .. 0.90
   2 !    5.4   0.3    0.0018        16      32      46 ..      64      78 ..      63      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS- CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelgls 28
                                      d  R+++L++L++++  + e+a e+ +s
  gi|313127250|ref|YP_004037520.1| 16 DVVRRRLLYYLCSSSSDANEIAFETLVS 43
                                      567********************99777 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHHTTSEE CS
                             HTH_5 32 vShHLkkLreaGLVe 46
                                      v  HL kL++a+L+e
  gi|313127250|ref|YP_004037520.1| 64 VHVHLPKLEQANLIE 78
                                      567**********97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   4.9e-07    0.0044       4      57 ..      11      80 ..       8      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.9e-07
                                      HHHHS-HHHHHHHHHH....STCTTB-HHHHHHHH..T..........S-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  4 aeALahPvRrrilraL....araegltaselaerl..d..........lskntlsyHLrvLeeagLvevv 57
                                      + A+a+ vRrr+l +L    ++a +  ++ l  rl  d          ++ n ++ HL +Le+a L+e  
  gi|313127250|ref|YP_004037520.1| 11 FVAFADVVRRRLLYYLcsssSDANEIAFETLVSRLadDdtfgshtraqMRLNLVHVHLPKLEQANLIEHD 80
                                      779*************99999999999999999998626777888888*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 674.37
//
Query:       gi|313127251|ref|YP_004037521.1|  [L=299]
Description: phenazine biosynthesis protein phzf family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-63  213.5   0.1    4.6e-63  213.3   0.1    1.0  1  PhzC-PhzF      Phenazine biosynthesis-like protein
     0.0073   15.4   0.0      0.011   14.8   0.0    1.2  1  Pro_racemase   Proline racemase
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.051   13.8   0.1    1.9  2  DAP_epimerase  Diaminopimelate epimerase


Domain annotation for each model (and alignments):
>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.3   0.1   7.6e-67   4.6e-63       1     283 []       9     284 ..       9     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: 213.3 bits;  conditional E-value: 7.6e-67
                                       EEET-SSTTSSEEEEEEESTTCS-HHHHHHHHHHHTSSEEEEEE--SSTTSSEEEEEE-SSSEES--HHHHHHHHHH CS
                         PhzC-PhzF   1 vdaFtespfkGNpaaVvldadelddeelqsiAaelnlseTaFllkpsdekarfrlRyFTPvaEvdlcGHatlasaha 77 
                                       vdaF+++p+ GN a+Vv d  +l++ ++qs+A+el +seTaF+  +   +a+ rlR+FTP++E+dlcGHat+a++  
  gi|313127251|ref|YP_004037521.1|   9 VDAFATEPLSGNAAGVVPDG-DLTESQMQSVASELAVSETAFVQSS--GSADRRLRFFTPTREIDLCGHATIATHAH 82 
                                       8****************985.7*********************996..689************************** PP

                                       HHHHCT-S-SCEEEEEETTEEEEE.EEEEETCEECCEEEEE-SEEEEEE-HHHHHHHHHHCCTSGG...-TTS-BEE CS
                         PhzC-PhzF  78 laekglvasaetveletkaGilpvkslkekddgeellielkfPvikteevssedlallakllklaa...qkalpiav 151
                                       l   g + +a t  +et++G l v    e + +  + + +++P+++ +++++++l +++++   a+    +a+p+av
  gi|313127251|ref|YP_004037521.1|  83 LYRDGVI-DAGTHTVETNVGVLDV----EVEADGIVWMTQESPTVESVDLDYARLGEALGIDPAAFrdvGEAVPPAV 154
                                       ****987.***************9....466677788899******************9999999888888****** PP

                                       EESSSEEEEEEBSTCCHHHH----H...HHHHHHCT-EEEEEEEETTTSSCCEEEEEEEEGGGTEEEESS-HHHHHH CS
                         PhzC-PhzF 152 kstglekvivplsseeavaelspdl...aeeikkcpkkgvivtaaaeagskkdfhsRmFaPklGivEDpvtGsAsga 225
                                       +stgl  ++vp++  e++ +++pd+   ++   + + +g+ v+++ + ++++ +h+RmFaP +Gi EDpvtG+Asga
  gi|313127251|ref|YP_004037521.1| 155 ASTGLPFLVVPVNFLEHLGNADPDFtavEKLTDEYDVAGLYVFTFDALEADTTLHARMFAPGIGIPEDPVTGTASGA 231
                                       *************************77777777888999************************************** PP

                                       HHHHHHHCC-S..SSEEEEEEEE-GGGT--EEEEEEEE.E-TTCEEEEEEEE-EEEEEEE CS
                         PhzC-PhzF 226 Laaylseklnl..eesakikieqgqalgrsgtlevevevkvdkekervkvtGkAvtvmeg 283
                                        +ayl++   +  e  +k+ +eqg+ l r+g+++v+v        ++v+v G Avt  +g
  gi|313127251|ref|YP_004037521.1| 232 CGAYLRHVDAFdgELPEKMVFEQGHFLDRPGRVHVRVG-------TEVRVGGFAVTALDG 284
                                       ********9996666799****************7774.......5799*****998765 PP

>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.9e-06     0.011      69     126 ..      58     111 ..      45     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-06
                                       EEEEEEESSSB-SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTS CS
                      Pro_racemase  69 lgvifletsgylpmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrd 126
                                         + f+ ++     cG++ti++ + l   G++ + +++    +et +G+++v++e ++
  gi|313127251|ref|YP_004037521.1|  58 RRLRFFTPTREIDLCGHATIATHAHLYRDGVIDAGTHT----VETNVGVLDVEVEADG 111
                                       5556888899999************************9....9*********999876 PP

>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   8.5e-06     0.051      43     112 ..      47     113 ..      18     121 .. 0.79
   2 ?   -1.8   0.0      0.57   3.4e+03       4      24 ..     156     176 ..     154     239 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.5e-06
                                       EEEEEEEETTEEEEEEEETTTEEESTTHCC.HHHHHHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSSEE CS
                     DAP_epimerase  43 vlfvkpsgeediklryfnrdgseaemCGnG.vrvfaaylreggletkkevtvetlgGeleievkddgekvk 112
                                         fv+ sg++d +lr+f     e   CG + ++  a+ +r+g ++   + tvet  G l +ev+ dg   +
  gi|313127251|ref|YP_004037521.1|  47 TAFVQSSGSADRRLRFFTPTR-EIDLCGHAtIATHAHLYRDGVID-AGTHTVETNVGVLDVEVEADGI--V 113
                                       578888899999999888765.6688****999999999999888.*******************983..3 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.57
                                       ECSSEEEEEEECCTTCSSHHH CS
                     DAP_epimerase   4 shGnpndvvvvddveaelvle 24 
                                       s+G+p +vv v+ +e+     
  gi|313127251|ref|YP_004037521.1| 156 STGLPFLVVPVNFLEHLGNAD 176
                                       677888888887777644333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2033.86
//
Query:       gi|313127252|ref|YP_004037522.1|  [L=51]
Description: hypothetical protein Hbor_25230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00012   21.6   0.8       0.11   12.2   0.0    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
     0.0014   18.7   0.6     0.0018   18.3   0.6    1.2  1  Zn-ribbon_8      Zinc ribbon domain
     0.0016   17.8   0.7       0.04   13.3   0.0    2.2  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
       0.11   12.8   3.1        2.3    8.5   3.1    2.1  1  zinc_ribbon_9    zinc-ribbon
       0.12   12.3   1.7       0.39   10.7   1.7    1.8  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.37   10.5   3.7        1.3    8.8   0.5    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.4    0.0007       2.1       7      17 ..       2      12 ..       1      13 [. 0.89
   2 !   12.2   0.0   3.6e-05      0.11       5      23 ..      25      43 ..      22      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0007
                                      EE-TTT--EEE CS
                   Desulfoferrod_N  7 YkCevCGniVe 17
                                      Y C+ CG+ V+
  gi|313127252|ref|YP_004037522.1|  2 YTCNNCGEFVT 12
                                      99*****9995 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.6e-05
                                      -EEE-TTT--EEEECC--S CS
                   Desulfoferrod_N  5 evYkCevCGniVeVleaGg 23
                                      ev+ C  C n+ eV+++G+
  gi|313127252|ref|YP_004037522.1| 25 EVFGCPSCMNMREVMNGGA 43
                                      9*****************7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.6   6.1e-07    0.0018       6      34 ..       2      33 ..       1      39 [. 0.66

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.1e-07
                       Zn-ribbon_8  6 YrCeeCghefe..vlqsis.dap.lta.CPeCgs 34
                                      Y C++Cg ef    +++++ d++ ++  CP+C  
  gi|313127252|ref|YP_004037522.1|  2 YTCNNCG-EFVtrDFVRVFgDSDdEVFgCPSC-M 33
                                      99*****.77769444555554415559****.4 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.3e-05      0.04       2      14 ..       1      13 [.       1      15 [. 0.81
   2 ?    2.9   0.2     0.025        74       5       8 ..      29      32 ..      22      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                       zf-ribbon_3  2 tvrCPnCGaplss 14
                                      +++C+nCG+ ++ 
  gi|313127252|ref|YP_004037522.1|  1 MYTCNNCGEFVTR 13
                                      799******6565 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.025
                       zf-ribbon_3  5 CPnC 8 
                                      CP+C
  gi|313127252|ref|YP_004037522.1| 29 CPSC 32
                                      6666 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.1   0.00077       2.3       9      28 ..      13      33 ..       1      35 [. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00077
                     zinc_ribbon_9  9 drfVsvspdedsdv.lCPhCg 28
                                      + fV+v  d+d++v  CP+C 
  gi|313127252|ref|YP_004037522.1| 13 RDFVRVFGDSDDEVfGCPSCM 33
                                      5799999999999999****5 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.7   0.00013      0.39      30      52 ..       3      32 ..       1      37 [. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                    OrfB_Zn_ribbon 30 tCseCgsknke.......alsgrtfkCpnC 52
                                      tC++Cg+ +++       + ++++f Cp+C
  gi|313127252|ref|YP_004037522.1|  3 TCNNCGEFVTRdfvrvfgDSDDEVFGCPSC 32
                                      677777777777777777777777777777 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.5   0.00044       1.3       1       7 [.       2       8 ..       2      13 .. 0.89
   2 ?    2.9   0.1      0.03        91      17      20 ..      29      32 ..      26      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00044
                      Rubredoxin_2 1 YvCsqCG 7
                                     Y C++CG
  gi|313127252|ref|YP_004037522.1| 2 YTCNNCG 8
                                     99****9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.03
                      Rubredoxin_2 17 CpsC 20
                                      CpsC
  gi|313127252|ref|YP_004037522.1| 29 CPSC 32
                                      **** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.47
# Mc/sec: 328.21
//
Query:       gi|313127253|ref|YP_004037523.1|  [L=237]
Description: phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-16   58.7   0.0    6.9e-16   58.2   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0092   15.4   0.0      0.012   15.0   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   7.7e-20   6.9e-16       8     153 ..      15     157 ..      10     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 7.7e-20
                                       ---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE..........EE- CS
                      Pribosyltran   8 npaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes..rll 82 
                                       ++ i+ ++++ + +     ++ pdvvv+ argG+  +  + d L+  l+++ + k ++ +++ ++ g  + +   ++
  gi|313127253|ref|YP_004037523.1|  15 WEYIYGRCRDVSDQVKGA-EFDPDVVVALARGGWFAGRCICDFLG--LDDLTSLKMEHYVGTAQKSGEPEVRypMPE 88 
                                       555666777777777777.999**********************9..6666666666666666654433333669** PP

                                       ---TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS......EEEEEEE- CS
                      Pribosyltran  83 edpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfsls.pdnfvavvg 153
                                       ++++gk Vli+DDi dtGg++++a e + e+++ evr+a+l    ++e+e+d+   ++  l+  ++ v +++
  gi|313127253|ref|YP_004037523.1|  89 GSVEGKDVLIIDDIADTGGSIERAYEYVTERDAGEVRTATLQLLQTSEFEPDF---VGERLEeWTWVVYPWN 157
                                       *****************************************999999999976...5555565667776666 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.4e-06     0.012     102     162 ..      74     134 ..      26     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-06
                           UPRTase 102 eeetlepveyynkLPkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlas 162
                                        +++ ep+  y  +P+   + + vl++D +  TGgs+  a + ++er++ge +   l++l+ 
  gi|313127253|ref|YP_004037523.1|  74 AQKSGEPEVRYP-MPEGSvEGKDVLIIDDIADTGGSIERAYEYVTERDAGEVRTATLQLLQT 134
                                       345577777775.666666999****************************999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1735.13
//
Query:       gi|313127254|ref|YP_004037524.1|  [L=214]
Description: hd superfamily hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-27   93.9   0.0    1.2e-26   93.5   0.0    1.2  1  HD_3      HD domain
    6.3e-13   48.9   0.0    1.1e-12   48.1   0.0    1.4  2  HD_2      HD containing hydrolase-like enzyme
    1.2e-07   32.0   0.0    2.3e-07   31.0   0.0    1.5  1  HD        HD domain
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.17   11.4   0.0    1.2  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.0   2.8e-30   1.2e-26       3     139 ..      23     159 ..      21     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 2.8e-30
                              HD_3   3 kLKfqkRqgwlqtgrvreesvaeHmwrvalmalllseelkekvdiarvikmfLiHDlvEiltgDiispd.....ela 74 
                                        LK   R+gw   ++ ++esva H+w va + l++++++ ++vd + +++++++HD++E+ tgD ++ +     +++
  gi|313127254|ref|YP_004037524.1|  23 ALKDERRTGWQLREVSDPESVASHSWGVAYLCLCFADDV-PDVDPDEALRLAVLHDVAEARTGDKPTRAdpdaeTVD 98 
                                       59*************************************.6************************998889996699 PP

                              HD_3  75 keekeeeekeaaerilkllpeelaeellalweEFeeretkeakfakdlDklepllqalekegdsl 139
                                         eke++e++a +++l++ + +    l++ we +e r t+ a+f+kd+D ++++lqa+++e++  
  gi|313127254|ref|YP_004037524.1|  99 PDEKEQRERAAVSELLAPFDAH----LRDDWEAYESRGTPTAQFVKDMDLVDMCLQAVIYEREAR 159
                                       9***************998888....9999******************************98764 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   2.5e-16   1.1e-12      15     142 ..      32     152 ..      22     172 .. 0.87
   2 ?   -3.3   0.0       1.4   6.5e+03      89     115 ..     179     205 ..     173     212 .. 0.63

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.5e-16
                              HD_2  15 walmrntreenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpeir.eayk 90 
                                       w+l + + +e+va Hs+ va+++ ++a  ++     ++d+++++ la++HD++E+ tGD pt      +++  ++ +
  gi|313127254|ref|YP_004037524.1|  32 WQLREVSDPESVASHSWGVAYLCLCFA--DDV---PDVDPDEALRLAVLHDVAEARTGDKPTRADPDAETVDpDEKE 103
                                       99*******************976555..454...49****************************999999746778 PP

                              HD_2  91 evEeeaeekllelLpeelreeyeelladeeaeeeekklvkaaDklsalikcl 142
                                       + E++a ++ll+  +++lr+++e + ++ +    + ++vk  D ++  ++++
  gi|313127254|ref|YP_004037524.1| 104 QRERAAVSELLAPFDAHLRDDWEAYESRGT---PTAQFVKDMDLVDMCLQAV 152
                                       89999******************9974333...589*********9999875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                              HD_2  89 ykevEeeaeekllelLpeelreeyeel 115
                                       +++ E + ++ l + L e l+++ye+ 
  gi|313127254|ref|YP_004037524.1| 179 FATAEPRLRTDLGRRLFEALQRRYETA 205
                                       555566666666667777777777655 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   5.2e-11   2.3e-07       2     118 ..      44     144 ..      43     148 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 5.2e-11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH. CS
                                HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld. 77 
                                       + Hs++Va+l+ ++a+d+  + d++ +l  a lHD+++ ++gd+  ++           +  ae +   ek +++  
  gi|313127254|ref|YP_004037524.1|  44 ASHSWGVAYLCLCFADDVP-DVDPDEALRLAVLHDVAEARTGDKPTRA-----------DPDAETVDPDEKEQRERa 108
                                       68*****************.***********************66654...........444444444444444444 PP

                                       ..HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHH CS
                                HD  78 ..ledvaklirehheswegkkrprglaerqlslearivklaDr 118
                                          e++a   ++ +++we        +e   ++ a+ vk++D 
  gi|313127254|ref|YP_004037524.1| 109 avSELLAPFDAHLRDDWE-------AYESRGTPTAQFVKDMDL 144
                                       433333333333334444.......455566666666666665 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.7e-05      0.17      89     133 ..      37      81 ..      21     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                                       SS-HHHHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHH CS
                              HDOD  89 gadlkklwehslavAlvarelaeelgledpeeaflaGLLhdiGkl 133
                                         d +++++hs  vA+++   a+ +   dp+ea+  + Lhd+ + 
  gi|313127254|ref|YP_004037524.1|  37 VSDPESVASHSWGVAYLCLCFADDVPDVDPDEALRLAVLHDVAEA 81 
                                       56778999*********************************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1495.17
//
Query:       gi|313127255|ref|YP_004037525.1|  [L=318]
Description: permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.1e-24   84.4  23.7    7.2e-14   51.0   2.1    2.0  2  Mem_trans  Membrane transport protein


Domain annotation for each model (and alignments):
>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   2.1     4e-18   7.2e-14       3     145 ..       9     145 ..       7     153 .. 0.84
   2 !   39.1  14.0   1.6e-14   2.9e-10     243     385 ..     161     307 ..     155     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 4e-18
                         Mem_trans   3 leavvplyvimllgYgsvkwvkiftpdqcsginrfVvlfavPllifhfisqnnpyemllrfiladvlvklivlilll 79 
                                        +a++p++v+ ++g++ ++     ++  +  +n++Vv++  P+l+fh+++++   e+  +++ +   v +  l++++
  gi|313127255|ref|YP_004037525.1|   9 ATAILPILVVGAVGFVLGRA----KDIDTDPLNTVVVYILAPALVFHSLATTTLAES--TLVQVAGAVTVYHLVMIV 79 
                                       689*****************....5556679*******************9877763..334444444455556666 PP

                         Mem_trans  80 lgallskifkgslewtitlfslstlpNtlvlgipllkalygeygvslmvqvvvlqciiiytlllfl 145
                                       +   + + f+      + l+++s++pN+++ g+p+    +ge+g + +v++  +q ++iyt+++ +
  gi|313127255|ref|YP_004037525.1|  80 VAEGVGRAFSERDPLLSALVLVSAFPNSGNYGVPVSNFAFGETGRATAVLFLSVQGVLIYTVGVYI 145
                                       67778888899999***********************************************99854 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 1.6e-14
                         Mem_trans 243 lirnPntyssllglilslvsfkwnvimpkiiqksisilgdaglpmalfslGlfLalqpkkiacgnsvatfa..lavR 317
                                        +r P +y+++ +l  +  ++  +    ++ + ++++ gda++p++l++lG  La+++    +g+  +t+   + ++
  gi|313127255|ref|YP_004037525.1| 161 VFRIPLVYAVIAALLARGLGIVPP--ADATSMATLKLVGDASIPVMLIILGIQLARTD----VGATLRTVGvvTTLK 231
                                       567788888888888777766654..448999***********************886....5555555444499** PP

                         Mem_trans 318 lilgPlvmlvavlavgLrgs.lllvaivqaAlPqgivlfviAkey......nvhe.relstllifgmlialpitlv 385
                                       +i+ P+++++++l+vg     + + ++++ A+P ++ + ++  e+      +v   + +st++++++l+++pi++ 
  gi|313127255|ref|YP_004037525.1| 232 MIVAPVIGVGVALVVGFSDPaVAKTFVLESAMPAAVTPLILVAEFaegkvaGVPVaEFVSTAVFVTTLVSIPILTA 307
                                       ****************88767999**************999888733322244442568**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2352.88
//
Query:       gi|313127256|ref|YP_004037526.1|  [L=286]
Description: methylthioadenosine phosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-44  150.8   0.0    4.3e-44  150.5   0.0    1.1  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.5   0.0   2.4e-48   4.3e-44       1     233 [.       2     243 ..       2     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 2.4e-48
                                       CEEEEESSH.HHHHHHHHH..EEEEEEEEEE..TTEEEEEEEETTEEEEEEE--....SSHHHHHHHHHHHHHHHC- CS
                         PNP_UDP_1   1 kiaiivgsp.gevellaes..pleetpfgre.grgfkfvtGtlkgkpvvivstG....iGkpnaavvaeirllkefg 69 
                                       +i++i+gs+ +++ +l ++   + etp+g++        +G  ++++v++ ++G     +++ + + a+i +lke+g
  gi|313127256|ref|YP_004037526.1|   2 TIGFIGGSGiYDALPLQDTrtVEVETPYGNPsAPPTVGEFGDTGREVVFVPRHGpdhqRSPTAIPYCANIFALKELG 78 
                                       5899*****9777777777799*********666677777777**************99999999************ PP

                                       -SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTT.TTEEE CS
                         PNP_UDP_1  70 vkaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealg.ikvhr 145
                                       v ++++++++G+l+++l++ ++vipd++ + +  +++++++e+++ + +++++ ++ el ++l eaae+   +kv+r
  gi|313127256|ref|YP_004037526.1|  79 VTHVLASNAVGSLREELPPQTLVIPDQIFDRTKHRDSTFFDEDIVVHQPFAEP-YCTELNEILTEAAEEATdAKVVR 154
                                       ******************************************97777777777.***********555544599999 PP

                                       .EEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHH CS
                         PNP_UDP_1 146 .GvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqea 221
                                        G++++ +g++++t+ae++++r++g+d+++M+t ++a lAre+++ +a++ +v+d+ +   d e t eev ++a+++
  gi|313127256|ref|YP_004037526.1| 155 gGTYVCIEGPQYSTRAESEFYREQGWDIIGMTTIPEAKLAREAEMAYATVTGVTDYDVWKEDSEVTLEEVLKNAEKN 231
                                       9******************************************************999899999999********** PP

                                       HHHHHHHHHHHH CS
                         PNP_UDP_1 222 aknaaalllall 233
                                       ++++++ ++a++
  gi|313127256|ref|YP_004037526.1| 232 ETAIKETVEAAI 243
                                       ******999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2060.02
//
Query:       gi|313127257|ref|YP_004037527.1|  [L=411]
Description: ferrichrome ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-14   53.1   0.0    5.2e-14   52.4   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   2.9e-18   5.2e-14       3     232 ..      85     348 ..      83     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.9e-18
                                       E-SHHHHHHHHHTT-GGGEEEB...-GGG--GGGGGGT..TS-BSBESSSB-H.......HHHHHH--SEEEE-GGG CS
                      Peripla_BP_2   3 slspsvteillalGatdkvvgv...dtttsdpldadkleeaivevgadgeidv.......EklaalkPDlvilskgl 69 
                                       +++p ++++ +alG+ d + +v   + +  +++ ++  + + v++   +  d        E+l++l+ D+ ++++ +
  gi|313127257|ref|YP_004037527.1|  85 TVYPQYADMAVALGHGDALNSVyvpEMSGTTMNQYYHHL-DGVSFEWQNLTDPlsdglhkEQLLELDSDVHLADPAW 160
                                       678888888888866665443311133444555555444.66666666666656666777***************** PP

                                       ...GGGHHHHHHHS-EEE----TTS....................HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                      Peripla_BP_2  70 gltdedeellksgiptvivessntg....................eslkeqiralgellgledeaeklvaeidskla 126
                                         ++ ++  ++ ++  ++ +  +++                    + l e +  ++ ++++  ++e+l + +++ + 
  gi|313127257|ref|YP_004037527.1| 161 --VSTQDTWDAGDVAEIESQVAPWFgnfysgthaeapdgyddygyYTLWELFGHVADVFQERTRYEALNEVHQNLVS 235
                                       ..8888888888888888888888888888889*********999899999999999999***************** PP

                                       HHHHTS-TT..-EEE..EEEEETTE..EEEE-TTS.TTTHHHHTS--EESTTT--.STT-EEE-HHHHHHH--SEEE CS
                      Peripla_BP_2 127 aaksaidse.kpkpv..lvfggadeggyvvagsns.yigdlldalgieniaaesk.kseyeeisaEqilasdpdvif 198
                                        ++s ++ + +++ v  ++f++++e ++++  + + y+ + ++ lg+++++ae+  ++ ++++++E+++++dpdvi+
  gi|313127257|ref|YP_004037527.1| 236 TIRSNLPPKeDRPSVirATFSESNEIFWTYHLNEPgYWLADTRPLGANDAFAEQDwGGLWGSVDFEAVAEADPDVIL 312
                                       *********95555511566666666665554433255555666*********99********************** PP

                                       EEEH..HHHT-S--HHHHT-SHHHHTSHHHHTT-EE CS
                      Peripla_BP_2 199 vsgr..aeadnktgleflkenpllaelpAvkngrVy 232
                                         +   +  + + + ++l ++p+ +el+Av++ rVy
  gi|313127257|ref|YP_004037527.1| 313 HLWGmtPNYQMSDVRAALDSHPVGSELTAVQEDRVY 348
                                       999988889999999********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3125.99
//
Query:       gi|313127258|ref|YP_004037528.1|  [L=145]
Description: hypothetical protein Hbor_25290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00087   19.6   2.1      0.016   15.6   0.1    2.1  2  DUF1924   Domain of unknown function (DUF1924)


Domain annotation for each model (and alignments):
>> DUF1924  Domain of unknown function (DUF1924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.3    0.0041        74      15      37 ..      68      90 ..      60     103 .. 0.83
   2 !   15.6   0.1   8.7e-07     0.016      20      52 ..     110     142 ..      98     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0041
                                      HH---SSS-TT-SSTHHHH-SST CS
                           DUF1924 15 fkkkvktkkgkelsCasCHgedp 37
                                      ++++ ++++++ +sC+ C g+d 
  gi|313127258|ref|YP_004037528.1| 68 YRRTLEAQSAHVTSCTVCEGSDD 90
                                      6777788888889*****99875 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 8.7e-07
                                       SSS-TT-SSTHHHH-SSTTS-EE.-TTS-EE-- CS
                           DUF1924  20 ktkkgkelsCasCHgedptkegkhaktgkaiep 52 
                                       +t++g+++ CasCH+ +  + g  a+ ++++ep
  gi|313127258|ref|YP_004037528.1| 110 TTEDGENWYCASCHAVEHGDGGSTAAGERVVEP 142
                                       6889*******************9999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1117.64
//
Query:       gi|313127259|ref|YP_004037529.1|  [L=311]
Description: condensin subunit scpa [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-13   51.1   0.0    1.2e-09   38.4   0.0    2.3  2  SMC_ScpA  Segregation and condensation protein ScpA
  ------ inclusion threshold ------
       0.55   10.8   5.6        3.9    8.0   0.2    3.0  2  Rnk_N     Rnk N-terminus


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.4e-13   1.2e-09       1      66 [.      35      96 ..      35     105 .. 0.88
   2 !   10.4   0.0   4.8e-05      0.43     209     239 ..     247     277 ..     207     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.4e-13
                                      HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXX CS
                          SMC_ScpA  1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeed 66
                                      L+ ++e+d++d++v++vtd fl+ + t     +l  s+ +l  as l+++K++ Ll+ +  eee +
  gi|313127259|ref|YP_004037529.1| 35 LAEDGEIDPWDIDVVEVTDAFLERLDTA----DLRTSGRALFYASVLLRMKSDALLEPDAAEEEPE 96
                                      67899*********************99....************************9887777433 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 4.8e-05
                                       HHHHHHHHHHHHHTT-EEEEESSTTS-EEEE CS
                          SMC_ScpA 209 lvgvFlAlLeLiknqavaleQeeflddLqvs 239
                                        v+++l lL L++  +v l+Q + ++dL v+
  gi|313127259|ref|YP_004037529.1| 247 PVTTYLSLLFLSHRGVVRLQQDDLFGDLWVQ 277
                                       59**************************998 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2   0.00043       3.9      24      37 ..     120     133 ..     109     133 .. 0.64
   2 ?    3.4   1.3     0.012   1.1e+02      19      39 ..     138     158 ..     135     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00043
                                       SSTTHHHHHHHHHC CS
                             Rnk_N  24 dppaaeaLeaELdR 37 
                                        ++ ++aLeaE+dR
  gi|313127259|ref|YP_004037529.1| 120 GFDPVDALEAEMDR 133
                                       44556********9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.012
                                       CTTTTSSTTHHHHHHHHHCSE CS
                             Rnk_N  19 sladrdppaaeaLeaELdRAe 39 
                                       ++a+++p+++++L +EL  Ae
  gi|313127259|ref|YP_004037529.1| 138 KHARGNPETLDELVRELREAE 158
                                       34555************8665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2157.82
//
Query:       gi|313127260|ref|YP_004037530.1|  [L=1198]
Description: condensin subunit smc [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-46  157.7  57.4    6.7e-46  156.5  57.4    1.9  1  SMC_N            RecF/RecN/SMC N terminal domain
    4.2e-28   98.0   0.0    1.2e-27   96.6   0.0    1.8  1  SMC_hinge        SMC proteins Flexible Hinge Domain
    1.4e-11   43.9 138.0    0.00088   18.2  17.1    8.3  8  Spc7             Spc7 kinetochore protein
    5.6e-11   43.3  23.8    5.6e-11   43.3  23.8    8.4  2  AAA_23           AAA domain
    1.9e-10   40.9 153.1      2e-05   24.7  16.7    8.9  8  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    4.9e-10   38.7  99.1     0.0029   16.4  31.0    6.0  6  AAA_13           AAA domain
    7.6e-09   35.8  17.5    7.4e-06   26.0   0.1    5.4  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.2e-06   27.9  96.2     0.0047   16.1  20.4    5.8  6  Atg14            Vacuolar sorting 38 and autophagy-related su
    1.5e-05   25.0  84.3    0.00082   19.4   6.0    9.6 11  DUF1664          Protein of unknown function (DUF1664)
    2.5e-05   24.3  30.1       0.01   15.8   1.8    7.2  7  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    3.8e-05   23.2 102.3      0.017   14.5  13.2    6.7  6  DUF4407          Domain of unknown function (DUF4407)
    4.1e-05   24.1 124.6      0.058   13.8  13.3    6.6  6  Fez1             Fez1
    4.2e-05   23.2   0.0     0.0001   22.0   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
    5.5e-05   23.0 101.4     0.0067   16.2   3.3    8.4  8  DUF4201          Domain of unknown function (DUF4201)
    6.1e-05   22.5 117.6      0.051   12.9  25.1    7.0  6  GAS              Growth-arrest specific micro-tubule binding
    0.00012   22.6 176.1     0.0047   17.5  23.7   10.0  8  APG6_N           Apg6 coiled-coil region
    0.00017   20.7  12.2    0.00017   20.7  12.2    5.3  2  IFT57            Intra-flagellar transport protein 57
    0.00021   20.9  13.9    0.00021   20.9  13.9    6.4  6  Leu_zip          Leucine zipper
    0.00047   17.9  50.3    0.00047   17.9  50.3    4.7  3  DUF3584          Protein of unknown function (DUF3584)
    0.00049   19.8  70.6      0.085   12.4  10.1    6.2  3  Exonuc_VII_L     Exonuclease VII, large subunit
    0.00091   18.8  17.5    0.00091   18.8  17.5    5.8  5  MscS_porin       Mechanosensitive ion channel porin domain
    0.00097   18.1  26.8    0.00097   18.1  26.8    5.8  4  DUF812           Protein of unknown function (DUF812)
     0.0012   19.0  27.1     0.0039   17.4  12.4   13.4 10  ABC_tran_CTD     ABC transporter C-terminal domain
     0.0018   18.5  17.8     0.0018   18.5  17.8    8.4  9  ATG16            Autophagy protein 16 (ATG16)
     0.0019   18.3  18.7     0.0019   18.3  18.7    8.6  6  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
     0.0019   16.5 117.6      0.027   12.7  19.3    5.8  6  FPP              Filament-like plant protein, long coiled-coi
     0.0021   17.8  18.9     0.0021   17.8  18.9    5.0  3  AAA_15           AAA ATPase domain
     0.0022   17.4   4.8     0.0022   17.4   4.8    9.3  9  DUF3450          Protein of unknown function (DUF3450)
     0.0026   18.0   8.9     0.0026   18.0   8.9    7.2  7  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0048   16.9  82.3      0.029   14.4   4.8    9.0 10  Laminin_II       Laminin Domain II
     0.0053   16.0  76.2       0.11   11.8   5.6    6.9  7  TMPIT            TMPIT-like protein
     0.0061   16.1 123.3      0.012   15.1  24.1    4.7  4  HMMR_N           Hyaluronan mediated motility receptor N-term
     0.0082   16.4   6.2     0.0082   16.4   6.2    8.5  9  FliJ             Flagellar FliJ protein
  ------ inclusion threshold ------
      0.011   15.9 122.8      0.013   15.8   6.7   10.3 11  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.013   15.7   4.0      0.013   15.7   4.0   10.7  9  DUF5082          Domain of unknown function (DUF5082)
      0.036   13.6 129.7       0.13   11.8  54.5    7.0  5  Filament         Intermediate filament protein
      0.062   13.8  63.0       0.02   15.3   4.7   10.7 10  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.12   10.8 127.2      0.011   14.2  13.1    4.3  4  MAD              Mitotic checkpoint protein
       0.14   12.0 112.5      0.012   15.5  10.3    8.3  6  DUF724           Protein of unknown function (DUF724)
       0.15   11.6   0.0       0.15   11.6   0.0    6.2  6  AAA_27           AAA domain
       0.59   10.5 141.1      0.049   14.0  12.5    9.7  9  DUF4200          Domain of unknown function (DUF4200)
       0.91    9.1 119.2       0.38   10.3   6.4    8.5  7  PspA_IM30        PspA/IM30 family
        1.1    9.6   5.8         13    6.1   0.0    4.1  3  AAA_22           AAA domain
        1.9    8.2  71.5       0.27   11.0  14.9    6.3  7  DUF745           Protein of unknown function (DUF745)
        2.4    8.5  87.0       0.67   10.3   5.9   10.6 12  BLOC1_2          Biogenesis of lysosome-related organelles co
        2.9    8.7  37.4        7.4    7.3   2.0    8.9  6  FliD_N           Flagellar hook-associated protein 2 N-termin
        5.1    7.2 134.3       0.25   11.4  19.8    7.0  7  UPF0242          Uncharacterised protein family (UPF0242) N-t
        6.9    6.8  71.1       0.47   10.6   1.7    9.7 10  DUF2730          Protein of unknown function (DUF2730)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.5  57.4   1.8e-48   6.7e-46       1     219 [.       2    1176 ..       2    1177 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 1.8e-48
                                        EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.......B CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......x RF
                             SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.......s 68  
                                        ++k+l++++Fks+ g+++ +pf + ft+++GpNGSGKsn++d +lF LG + ++ +r+ekl+dli++       s
  gi|313127260|ref|YP_004037530.1|    2 HIKELVLDGFKSF-GRKTRIPFYEDFTVVTGPNGSGKSNIIDGVLFALGLARTRGIRAEKLTDLIYNpghadaeS 75  
                                        599**********.5****************************************************99999877 PP

                                        TTCSSTTEEEEEEEEEETTEE.............SSSSSSCEEEEEEEETTSE...EEEEETTEEE-HHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                             SMC_N   69 kekasvkkaeveitfdnedkk.............lkiekeevsisrrvkrkge...seykingkevtkkevsell 127 
                                        ++   +k+a+v++++dn+d k              + + +e+ ++rrvk+++e   s y++ng++++ +++++ll
  gi|313127260|ref|YP_004037530.1|   76 ERAGGTKEASVTVILDNSDGKldrsqvinaagsdDVGDVSEIRVKRRVKETDEnyySYYYLNGRSCNLSDIQDLL 150 
                                        788899*************9999999999988776778899*******99998888999**************** PP

                                        HCTT-STT................................................................... CS
                                        xxxxxxxx................................................................... RF
                             SMC_N  128 esagiske................................................................... 135 
                                        ++agi++e                                                                   
  gi|313127260|ref|YP_004037530.1|  151 AQAGITPEgynvvmqgdvteiinmtpyqrrgiideiagvaefdakkedafgelesveerieeadlrieekesrld 225 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  226 qlederetalkyqslreereeyegylkaaeledkradlerteskaetkaekleslreeldtrqgrvsrleaelde 300 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  301 lskeierkgedeqlrikseiesvkgeidrlenaieaaedrideaeterrkafveldrkqemiddveddiravkve 375 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  376 kasvkseiktketelaeveaeidsvdtefdelkdelaakksqleelkterndlqrekdrllddtrrrsseisetq 450 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  451 ekisevreelptlkaklsdlhseldkaeknkqkidgviedlredrsdlksdldevedelrskqseyaelearagk 525 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  526 dgdtswpravttilnsgqsgvhgtvgqlgsvpgeyatacetaaggrlahvvvdddgvgsscidylksrnagratf 600 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  601 lpitkmddrglprkpsdpgvvdfarniveydaeyepifsyvlgstlvvedmqtarslmgdyrmvtldgdlversg 675 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  676 amtggsgggsrysfsksgsgrlerlaveisdleddrreieqeirdiesqlddarekasdaadrvrsveadidrae 750 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  751 edveekkaeieqledrieelrekraevdeemqsldtdidaltadiddvqseideleseladskipeltaqadeir 825 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  826 aeieekedrmdeldgrlnelqlekeyaedaiedlnetvesaqdrkadardvirekeqaieekeavleekreavsd 900 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  901 leaelkelkaersdlredvreakserdeqrdkvervesrvenlresaerlaweideleaevgeydpeeipdhdev 975 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  976 qeniqqltgkmeslepvnmlaideydevqadledlqdgrdvlaeerqgiqdrieqfeaqkketfmeafdaindnf 1050
                                        *************************************************************************** PP

                                        ..........................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                        ..........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 ..........................................lLSgGektLvalaLlfAiqkvkpaplyllDeid 168 
                                                                                  ++SgGek+L+ala++fAiq+ +pap+y lDe+d
  gi|313127260|ref|YP_004037530.1| 1051 tdiferlsngtgelhlenpedpfeegltmkaqpgdkpiqrldAMSGGEKSLTALAFIFAIQRHNPAPFYALDEVD 1125
                                        *************************************************************************** PP

                                        TTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  169 aaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkvengvs 219 
                                        a LD++n ++v e+++    +aQf+v+s+r+ +le++++ +gvt++ ++vs
  gi|313127260|ref|YP_004037530.1| 1126 AFLDAANAERVGEMVDDLAGRAQFVVVSHRSALLERSERAIGVTMQGDNVS 1176
                                        *********************************************877765 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   3.1e-30   1.2e-27       2     116 ..     544     657 ..     543     658 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 3.1e-30
                         SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns 78 
                                       +gv+G++++l +v+ +y +A e+a+g+rl ++vv+d+ +  ++i++lk++nagratflp+ +++++  + ++ d + 
  gi|313127260|ref|YP_004037530.1| 544 SGVHGTVGQLGSVPGEYATACETAAGGRLAHVVVDDDGVGSSCIDYLKSRNAGRATFLPITKMDDRGLPRKPSDPG- 619
                                       69**********************************************************************9999. PP

                         SMC_hinge  79 gavplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                        + ++ ++ve+d+e+++++ y+lg tlvv+++++A+ l
  gi|313127260|ref|YP_004037530.1| 620 VVDFARNIVEYDAEYEPIFSYVLGSTLVVEDMQTARSL 657
                                       ***********************************987 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6  26.0    0.0005      0.18     154     282 ..     206     334 ..     197     343 .. 0.74
   2 !    8.1  19.7    0.0029       1.1     145     258 ..     321     426 ..     312     434 .. 0.40
   3 !   14.4  19.6   3.5e-05     0.013     145     253 ..     349     456 ..     338     461 .. 0.91
   4 !   14.3  20.6   3.8e-05     0.014     146     261 ..     395     513 ..     393     526 .. 0.83
   5 !   18.2  17.1   2.4e-06   0.00088     144     258 ..     700     810 ..     695     815 .. 0.68
   6 !   13.3  17.7   7.4e-05     0.028     156     262 ..     761     868 ..     757     873 .. 0.54
   7 !    9.6  17.8     0.001      0.38     203     284 ..     872     952 ..     865     961 .. 0.62
   8 ?    3.8   7.3      0.06        23     144     259 ..     936    1037 ..     931    1049 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                              Spc7 154 dkelLekqeeeldellpeleeeka..eleeeleklqeaaeeles.idkeeLeelreelaelkaeieekkkelaelqe 227
                                        +e++e+    ++e   +l++ ++  e   ++++l+e++ee e  ++ +eLe  r +l++ +++ e k ++l++l+e
  gi|313127260|ref|YP_004037530.1| 206 VEERIEEADLRIEEKESRLDQLEDerETALKYQSLREEREEYEGyLKAAELEDKRADLERTESKAETKAEKLESLRE 282
                                       333333333333333333332222113333456677777777774569***************************** PP

                              Spc7 228 qleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleelt 282
                                       +l++ + +++ l+++ +el +ei+   r  e ++   +se++++k e ++le+  
  gi|313127260|ref|YP_004037530.1| 283 ELDTRQGRVSRLEAELDELSKEIE---RKGEDEQLRIKSEIESVKGEIDRLENAI 334
                                       ***********************9...77788889999*************9865 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0029
                              Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                       e+   ++++ ++ +e+ e+ +de+  e ++ + el ++ e++ +         ++++++++ e a++k+ei+ k++e
  gi|313127260|ref|YP_004037530.1| 321 ESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDD--------VEDDIRAVKVEKASVKSEIKTKETE 389
                                       33333333333333333333333333333333333333333333........2344455555555555555555555 PP

                              Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervle 258
                                       lae+++++++++++++elk++ +  +++++e +  ++
  gi|313127260|ref|YP_004037530.1| 390 LAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERN 426
                                       5555555444444444444444444444444443332 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 3.5e-05
                              Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                       ++ + +l++ +e++++ e+ + +++ e  + k+e++ + ++l e ++e++s+d +e  el++ela+ k+++ee+k+e
  gi|313127260|ref|YP_004037530.1| 349 RKAFVELDRKQEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDSVD-TEFDELKDELAAKKSQLEELKTE 424
                                       56677889999999999999999999999999999999999999999999988.689******************** PP

                              Spc7 222 laelqeqleeleekieelkeqkseleeeiaea 253
                                        ++lq+++++l ++    ++++se++e+i+e 
  gi|313127260|ref|YP_004037530.1| 425 RNDLQREKDRLLDDTRRRSSEISETQEKISEV 456
                                       *****************************985 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 3.8e-05
                              Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqe..aaeeles.idkeeLeelreelaelkaeieekk 219
                                        ++++++++ ++L+++ +  ++ l+el++e+++l++e ++l +  ++++ e   ++e++ e+reel +lka+++ + 
  gi|313127260|ref|YP_004037530.1| 395 AEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLDdtRRRSSEIsETQEKISEVREELPTLKAKLSDLH 471
                                       5678888999999999999999999999999999999999877442233332246********************** PP

                              Spc7 220 kelaelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                        el++ ++++++++  ie+l+e +s+l++++ e e+ l+ ++
  gi|313127260|ref|YP_004037530.1| 472 SELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRSKQ 513
                                       ********************************9998776443 PP

  == domain 5  score: 18.2 bits;  conditional E-value: 2.4e-06
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkk 220
                                       l  ++++le+d++++e++   +++ l++ +e+ ++  +++++ ++  +      +e++ee + e+++l+  iee+++
  gi|313127260|ref|YP_004037530.1| 700 LAVEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDR----AEEDVEEKKAEIEQLEDRIEELRE 772
                                       5556666666666666655555555555555555544444444443332....477888999999999999999999 PP

                              Spc7 221 elaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                       + ae+ e++++l+++i++l++ ++++++ei e e+ l 
  gi|313127260|ref|YP_004037530.1| 773 KRAEVDEEMQSLDTDIDALTADIDDVQSEIDELESELA 810
                                       99999999999999999999999999999988887665 PP

  == domain 6  score: 13.3 bits;  conditional E-value: 7.4e-05
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeeles.idkeeLeelreelaelkaeieekkkelaelqeqlee 231
                                       e+Le++ eel e   e++ee ++l   ++ l +  ++++s id+ e e + +++ el a+ +e ++e++e++++++e
  gi|313127260|ref|YP_004037530.1| 761 EQLEDRIEELREKRAEVDEEMQSLDTDIDALTADIDDVQSeIDELESELADSKIPELTAQADEIRAEIEEKEDRMDE 837
                                       44444444444444444444444444444444444444444455555555555566666666666666666666666 PP

                              Spc7 232 leekieelkeqkseleeeiaeaervleeckg 262
                                       l+ +++el+ +k+ +e++i+  ++++e  ++
  gi|313127260|ref|YP_004037530.1| 838 LDGRLNELQLEKEYAEDAIEDLNETVESAQD 868
                                       6666666666666666666666666665554 PP

  == domain 7  score: 9.6 bits;  conditional E-value: 0.001
                              Spc7 203 elreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkale 279
                                        +r+ ++e ++ ieek++ l+e++e + +le++++elk+++s+l+e+++ea++ ++e+++   + v++  e++++  
  gi|313127260|ref|YP_004037530.1| 872 DARDVIREKEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDK-VERVESRVENLRESA 947
                                       5677777788888888888888888888888888888888888888888887777776653.223333333333333 PP

                              Spc7 280 eltgw 284
                                       e + w
  gi|313127260|ref|YP_004037530.1| 948 ERLAW 952
                                       33334 PP

  == domain 8  score: 3.8 bits;  conditional E-value: 0.06
                              Spc7  144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqe.....aaeelesid..keeLeelreelael 211 
                                        +e+++e+l+e +e+                     l  e+++l++       ee+ + d  +e++++l  ++++l
  gi|313127260|ref|YP_004037530.1|  936 VESRVENLRESAER---------------------LAWEIDELEAevgeyDPEEIPDHDevQENIQQLTGKMESL 989 
                                        33333444444433.....................3333333333222112233333333344444444444444 PP

                              Spc7  212 kaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259 
                                        +       +e++e+q++le+l++  + l+e+++ ++++i++ e  ++e
  gi|313127260|ref|YP_004037530.1|  990 EPVNMLAIDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEAQKKE 1037
                                        444444445555555555555555555555555555555555444443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3  23.8   1.5e-13   5.6e-11       2     196 ..       6     267 ..       5     347 .. 0.73
   2 ?   -0.7  13.4       4.5   1.7e+03     143     198 ..     713     773 ..     684     782 .. 0.57

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.5e-13
                            AAA_23   2 Lkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLyget.prlsrks....grgfeksdveiese.gkv 71 
                                       L + +f+sf r++ i F   +t++tGpNG+GK+ i+d + +aL+    ++ + ++      +  ++d e e   g++
  gi|313127260|ref|YP_004037530.1|   6 LVLDGFKSFgRKTRIPFYEDFTVVTGPNGSGKSNIIDGVLFALGLARtRGIRAEKltdlIYNPGHADAESERAgGTK 82 
                                       889******55666*****************************8744144455448776556667777766665677 PP

                            AAA_23  72 kayveltfenkdgry..................trsiererelskkkgkttkkaklelleideleqfise....... 123
                                       +a+v++ + n dg+                     +++r+ ++++++  +++  ++++++ ++ ++++ +       
  gi|313127260|ref|YP_004037530.1|  83 EASVTVILDNSDGKLdrsqvinaagsddvgdvsEIRVKRRVKETDENYYSYYYLNGRSCNLSDIQDLLAQagitpeg 159
                                       777**********99***************98888888888888888888899999999999999999999988888 PP

                            AAA_23 124 .llgskkiilnlilflgqer..................feefel....kdkkerleelekeleeledekkllekl.. 175
                                        ++  + +  ++i + + +r                            ++ +er+ee+   +ee+e + ++le++  
  gi|313127260|ref|YP_004037530.1| 160 yNVVMQGDVTEIINMTPYQRrgiideiagvaefdakkeD----AfgelESVEERIEEADLRIEEKESRLDQLEDEre 232
                                       888888889999999999998888888887765433321....0222333334555555555555555555555555 PP

                            AAA_23 176 ...........eqekekek.........eleeleeeleeil 196
                                                         +         ele+++ +le ++
  gi|313127260|ref|YP_004037530.1| 233 talkyqslreeR------EeyegylkaaELEDKRADLERTE 267
                                       554443333220......12334444443333333333333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.5
                            AAA_23 143 feefelkdkkerleelekeleeledekkllekl.....eqekekekeleeleeeleeilke 198
                                       + e+e  d +++l++++++  ++ d+ + +e+      e+ +ek++e+e+le+++ee+ ++
  gi|313127260|ref|YP_004037530.1| 713 EIEQEIRDIESQLDDAREKASDAADRVRSVEADidraeEDVEEKKAEIEQLEDRIEELREK 773
                                       1111113333344444444444444444444448888777777777888888888887765 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1  22.7    0.0033       1.2      31     131 ..     254     362 ..     251     365 .. 0.89
   2 !    9.1  12.7    0.0033       1.2      35     107 ..     357     429 ..     353     431 .. 0.73
   3 !   17.6  17.1   7.9e-06     0.003      27     123 ..     419     515 ..     419     523 .. 0.92
   4 ?    5.4   2.9     0.047        17      61     116 ..     697     752 ..     694     755 .. 0.62
   5 !   24.7  16.7   5.3e-08     2e-05       4     105 ..     717     811 ..     708     814 .. 0.77
   6 !   10.3  19.5    0.0015      0.54      52     139 ..     819     909 ..     808     910 .. 0.81
   7 !   11.6  22.6   0.00056      0.21      31     136 ..     878     987 ..     873     991 .. 0.84
   8 ?    3.7  16.9      0.16        59       7     118 ..     914    1036 ..     911    1044 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0033
                    CENP-F_leu_zip  31 relemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr........sekeeLekelqkkqervseL 99 
                                       +ele+  +++e+++  aEt+ +++e+l+ee+++ + + ++le++L++l+         e+  ++ e++  + +++ L
  gi|313127260|ref|YP_004037530.1| 254 AELEDKRADLERTESKAETKAEKLESLREELDTRQGRVSRLEAELDELSkeierkgeDEQLRIKSEIESVKGEIDRL 330
                                       69999*******************************************97777776556667899999999****** PP

                    CENP-F_leu_zip 100 eslnsslenlleekEqekvqmkeeskaaveeL 131
                                       e++ +  e  + e+E e+++   e +++ e++
  gi|313127260|ref|YP_004037530.1| 331 ENAIEAAEDRIDEAETERRKAFVELDRKQEMI 362
                                       ****************9999888888887776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0033
                    CENP-F_leu_zip  35 mseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnssle 107
                                         +e  ++v+ +    k e  ++k+ei++ ++el e e++++++  e +eL+ el  k+++ +eL++ + +l+
  gi|313127260|ref|YP_004037530.1| 357 RKQEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQ 429
                                       4555555666666667777788888888888888888888888888888888888888888888888777765 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 7.9e-06
                    CENP-F_leu_zip  27 enLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLesln 103
                                       e+L+ e ++++++++++  +      e+++ +e+i e +eel  l+++L++l se ++ ek+ qk    +++L + +
  gi|313127260|ref|YP_004037530.1| 419 EELKTERNDLQREKDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDR 495
                                       679999*********************************************************************** PP

                    CENP-F_leu_zip 104 sslenlleekEqekvqmkee 123
                                       s+l++ l e E+e +  + e
  gi|313127260|ref|YP_004037530.1| 496 SDLKSDLDEVEDELRSKQSE 515
                                       *************5444433 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.047
                    CENP-F_leu_zip  61 ieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqe 116
                                       +e+la e ++le d  ++ +e  ++e +l + +e+ s+   +  s+e  + ++E++
  gi|313127260|ref|YP_004037530.1| 697 LERLAVEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEED 752
                                       45666666666666666666666666666666666666666666666666666654 PP

  == domain 5  score: 24.7 bits;  conditional E-value: 5.3e-08
                    CENP-F_leu_zip   4 kklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrs 80 
                                       + + ++++L  +++ka+   d+v + e+++        +++ ++E++kae+e+l++ ieel+e++ e   ++++l  
  gi|313127260|ref|YP_004037530.1| 717 EIRDIESQLDDAREKASDAADRVRSVEADID-------RAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLDT 786
                                       3334555555555555555555555555555.......555579********************************* PP

                    CENP-F_leu_zip  81 ekeeLekelqkkqervseLeslnss 105
                                       + + L+ ++ + q++++eLes   +
  gi|313127260|ref|YP_004037530.1| 787 DIDALTADIDDVQSEIDELESELAD 811
                                       ********************97766 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.0015
                    CENP-F_leu_zip  52 aevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqe...kvqmkeesk 125
                                       a++ ++++eiee + ++ el   L++l+ eke  e  +++ +e+v++ + ++ + + +++ekEq    k  + ee  
  gi|313127260|ref|YP_004037530.1| 819 AQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAieeKEAVLEEKR 895
                                       344556666666666666677777777778888888888889999999999************9877799999**** PP

                    CENP-F_leu_zip 126 aaveeLqtqlkeln 139
                                       +av+ L+++lkel+
  gi|313127260|ref|YP_004037530.1| 896 EAVSDLEAELKELK 909
                                       ************96 PP

  == domain 7  score: 11.6 bits;  conditional E-value: 0.00056
                    CENP-F_leu_zip  31 relemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnssle 107
                                       re+e++ e++e+v    E+++++v+ l++e++el++e+++l+ d+ + +se++e   +++   +rv++L ++ + l 
  gi|313127260|ref|YP_004037530.1| 878 REKEQAIEEKEAV---LEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLA 951
                                       4555555555444...57889999***************************************************** PP

                    CENP-F_leu_zip 108 nlleekEqe.......kvqmkeeskaaveeLqtqlk 136
                                         + e+E+e       ++  ++e ++++++L+  ++
  gi|313127260|ref|YP_004037530.1| 952 WEIDELEAEvgeydpeEIPDHDEVQENIQQLTGKME 987
                                       *********877777667777777777777776665 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 0.16
                    CENP-F_leu_zip    7 hvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevet...........lkeeieelaeelre 70  
                                         ++e  +e++++ d  +dkve+ e+ +e++ e+ e++  e ++  aev +           ++e+i++l+ +++ 
  gi|313127260|ref|YP_004037530.1|  914 DLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELEAEVGEydpeeipdhdeVQENIQQLTGKMES 988 
                                        5678999*********************************99999999997777666666666666666666666 PP

                    CENP-F_leu_zip   71 leldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekv 118 
                                        le        e +e++ +l++ q+  + L + +  ++  +e+ E++k+
  gi|313127260|ref|YP_004037530.1|  989 LEPVNMLAIDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEAQKK 1036
                                        654333333677777777777777777777777777777777776654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   2.8      0.26        96     101     156 ..     199     254 ..     184     266 .. 0.78
   2 !   16.4  31.0   7.7e-06    0.0029     284     470 ..     220     414 ..     204     430 .. 0.73
   3 !   10.2   5.5   0.00057      0.21     400     470 ..     442     512 ..     426     527 .. 0.85
   4 !   14.7  15.0   2.5e-05    0.0094     357     470 ..     697     812 ..     690     832 .. 0.77
   5 !   10.5  18.2   0.00046      0.17     332     467 ..     816     961 ..     810     968 .. 0.51
   6 !    7.7   0.3    0.0031       1.2     416     511 ..     998    1105 ..     967    1115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.26
                            AAA_13 101 lkkeikkleekleaaeaqlqkaekekkklekeledeawkkivkkknsalsealkgl 156
                                       + +e++++ee++e+a+  ++++e+++++le+e e+ ++ + ++++++++++ lk  
  gi|313127260|ref|YP_004037530.1| 199 AFGELESVEERIEEADLRIEEKESRLDQLEDERETALKYQSLREEREEYEGYLKAA 254
                                       45688899999999999999999999999999999998888888888887766554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.7e-06
                            AAA_13 284 kqerLekliekveskkselleklkavsde......asensafeedkeelkaeaealeeqLkglqraleaKrkepfk. 353
                                       k +rL++l ++ e++ + + ++l +  +e      a e +  + d e  +++ae+ +e+L++l+++l+ +  ++++ 
  gi|313127260|ref|YP_004037530.1| 220 KESRLDQLEDERETALK-Y-QSLREEREEyegylkAAELEDKRADLERTESKAETKAEKLESLREELDTRQGRVSRl 294
                                       44555555555444432.2.222222222233222333444556677777799999999999999999999999999 PP

                            AAA_13 354 svelesvkaki.esikklvaeineliakhNekvanleeekeeakkklelhlveeles..eldeykkkykklekaiek 427
                                       ++el++++++i  ++++++ +i+  i++    +++le++ e+a++ +   + e+ ++  eld+ ++ ++++e++i  
  gi|313127260|ref|YP_004037530.1| 295 EAELDELSKEIeRKGEDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAfvELDRKQEMIDDVEDDIRA 371
                                       99999999999667888888888888888888888888888888888888776555422667888999999999999 PP

                            AAA_13 428 lekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                       ++ e++  ++e+k++e e +e e+++ ++    +e+ +eL+a 
  gi|313127260|ref|YP_004037530.1| 372 VKVEKASVKSEIKTKETELAEVEAEIDSVDTEFDELKDELAAK 414
                                       9999999999999999999999999999999999999999987 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00057
                            AAA_13 400 elhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                       + ++++e +++++e  +++  l++++++l  el+++e++++k+++ i++L++  +d k   +e+++eL++ 
  gi|313127260|ref|YP_004037530.1| 442 RSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRSK 512
                                       456799**************************************************************875 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 2.5e-05
                            AAA_13 357 lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaiekleke 431
                                       le+++ +i+ ++++  ei++ i++   + ++  e++++a++ ++  +  + ++e++++e k ++++le+ ie+l ++
  gi|313127260|ref|YP_004037530.1| 697 LERLAVEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEadIDRAEEDVEEKKAEIEQLEDRIEELREK 773
                                       56666777778888888888888888888888888888888888877445788888888888888888888888888 PP

                            AAA_13 432 lkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                        +e  +e++ l+ +i +L + + d++  ++e+++eL++ 
  gi|313127260|ref|YP_004037530.1| 774 RAEVDEEMQSLDTDIDALTADIDDVQSEIDELESELADS 812
                                       888888888888888888888888888888888888765 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00046
                            AAA_13 332 aleeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv.... 404
                                       +l++q ++++ ++e+K +       ++++++++++++ + + +++ i++ Ne+v++ +++k++a++ ++  +     
  gi|313127260|ref|YP_004037530.1| 816 ELTAQADEIRAEIEEKED------RMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQaiee 886
                                       344444444444444443......24455555556666666666666666666666666666666666665543333 PP

                            AAA_13 405 ............eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeL 467
                                                   ++le+el+e+k + ++l +++ +++ e +e+ ++++ +e ++++L+++ +     ++e++ e+
  gi|313127260|ref|YP_004037530.1| 887 keavleekreavSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELEAEV 961
                                       333442222222445555555555556666666666666666666666666666666666655555555555555 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0031
                            AAA_13  416 kkykklekaieklekelkeeeaelkkleeeikeLekqlrde.kpaaeeinkeLka....f..GlgeleLkfeee. 482 
                                        ++y+++++++e+l++  +  ++e + ++++i++ e+q ++   +a + in+  ++       G gel L+  e+ 
  gi|313127260|ref|YP_004037530.1|  998 DEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEAQKKETfMEAFDAINDNFTDiferLsnGTGELHLENPEDp 1072
                                        788999*****************************9998762677788888776522223356777777777778 PP

                            AAA_13  483 .kkgYrivrkggsqaa...etLSeGEktaIafl 511 
                                         ++g ++  + g+++    + +S GEk++ a+ 
  gi|313127260|ref|YP_004037530.1| 1073 fEEGLTMKAQPGDKPIqrlDAMSGGEKSLTALA 1105
                                        878888877777766512345699999876665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1     2e-08   7.4e-06       1      62 [.      26      88 ..      26     147 .. 0.64
   2 ?   -1.8   1.1       5.8   2.2e+03      68     121 ..     241     290 ..     182     361 .. 0.43
   3 ?   -2.2   5.3       7.8   2.9e+03      86     219 ..     361     494 ..     345     511 .. 0.69
   4 !   20.3  14.3   1.1e-06    0.0004     169     302 ..     882    1159 ..     671    1160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl..drdvegltdelsggggirkipslldlydpeipfefei 62
                                      ++v++GpNgsGKSn++d   ++ +l     +++     + + +++  + ++ +   ++++  ++
  gi|313127260|ref|YP_004037530.1| 26 FTVVTGPNGSGKSNIIDGVLFALGLarT-RGIRAEKLTDLIYNPGHADAESERAGGTKEASVTV 88
                                      89********************999953.44444444444444444444444444444444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.8
                            AAA_21  68 qgvryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirgg 121
                                       ++ r +y+  l+   +     +++ +le+++ + +  +e+      e ++  g 
  gi|313127260|ref|YP_004037530.1| 241 REEREEYEGYLKAAEL----EDKRADLERTESKAETKAEKLESLREELDTRQGR 290
                                       3333333333333333....2222222222222222222222222222222222 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.8
                            AAA_21  86 klssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglr 162
                                       ++ +ve++ +     + +++ e++ +  e  +  + +++    + +++++ + +++++  + t+r++  ++ ++ l 
  gi|313127260|ref|YP_004037530.1| 361 MIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLD 437
                                       55555555555666666666666666666666666666666666666666666666666666666665555555555 PP

                            AAA_21 163 kerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer 219
                                       + r +  +i+    + +++++ l  l  +l++ ++el++ ++ +++i+ v+e+lre 
  gi|313127260|ref|YP_004037530.1| 438 DTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLRED 494
                                       559999999999999999999999999999999999999999999999999988874 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 1.1e-06
                            AAA_21  169 lnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer........................ 219 
                                        + i  +++   ++++ +++l+ +lk+  +e sdl+e +++ +s+ + +r++                        
  gi|313127260|ref|YP_004037530.1|  882 QAIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKvervesrvenlresaerlaweide 956 
                                        444444444444444444444444444444444444444444444444444444444444444444444444444 PP

                            AAA_21  220 ........................................................................... 219 
                                                                                                                   
  gi|313127260|ref|YP_004037530.1|  957 leaevgeydpeeipdhdevqeniqqltgkmeslepvnmlaideydevqadledlqdgrdvlaeerqgiqdrieqf 1031
                                        444444444444444444444455555555555567777777777777777777777788888888888888888 PP

                            AAA_21  220 .............................................gvvflengdgqelparelSdGtkrl.l.al 247 
                                                                                      ++   +gd     ++ +S G k+l + a+
  gi|313127260|ref|YP_004037530.1| 1032 eaqkketfmeafdaindnftdiferlsngtgelhlenpedpfeegLTMKAQPGDKPIQRLDAMSGGEKSLtAlAF 1106
                                        888888888888888888888888888888888888888888887888888888888888999*******63255 PP

                            AAA_21  248 ltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302 
                                        + a+ r ++  +++++DE++++L+ +  +r+ e++++l+  +aQ+++++H   ll
  gi|313127260|ref|YP_004037530.1| 1107 IFAIQRHNPA-PFYALDEVDAFLDAANAERVGEMVDDLAG-RAQFVVVSHRSALL 1159
                                        5555544444.***************************99.*********88877 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1  20.6      0.11        42      23     154 ..     216     341 ..     193     355 .. 0.55
   2 ?    6.1   8.2     0.014       5.1      30     125 ..     290     397 ..     287     401 .. 0.84
   3 !   16.1  20.4   1.3e-05    0.0047      22     167 ..     360     515 ..     355     534 .. 0.78
   4 !   15.7  10.3   1.7e-05    0.0063      18     129 ..     691     806 ..     687     811 .. 0.76
   5 !    8.2   5.8    0.0031       1.1      27     119 ..     784     874 ..     779     882 .. 0.80
   6 !    8.3  12.1     0.003       1.1      43     145 ..     879     981 ..     867     994 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                             Atg14  23 rlyelrerlaklksekeslkkkiekalegke........eaeqledkiknkkakleelksliadlrerlqelkdkls 91 
                                       r++e+  rl +l  e+e        al+ ++        e+  ++++++ k+a+le++ s+ + + e+l+ l++ l+
  gi|313127260|ref|YP_004037530.1| 216 RIEEKESRLDQLEDERE-------TALKYQSlreereeyEGYLKAAELEDKRADLERTESKAETKAEKLESLREELD 285
                                       45555555555555555.......55544443222222366666666666666666666666666666666666666 PP

                             Atg14  92 qlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslsskt 154
                                       +++ ++    ++l +ls+++ ++ +d        + r k++i+++  +i r e+ +++ ++ +
  gi|313127260|ref|YP_004037530.1| 286 TRQGRVSRLEAELDELSKEIERKGED-------EQLRIKSEIESVKGEIDRLENAIEAAEDRI 341
                                       66666666666666666666433333.......333444444444444444444444444443 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                             Atg14  30 rlaklksekeslkkkiekalegke............eaeqledkiknkkakleelksliadlrerlqelkdklsqlk 94 
                                       r+ +l +e ++l k+ie++ e ++            e ++le++i+   ++++e  +++++   +l + ++ ++   
  gi|313127260|ref|YP_004037530.1| 290 RVSRLEAELDELSKEIERKGEDEQlrikseiesvkgEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVE 366
                                       7899*****************99988888888888888888888888888888888888888888888888888888 PP

                             Atg14  95 keieekkkklaklsdklkkRrsdleslqnel 125
                                       + i++ k + a+ ++++k++  +l+ ++ e+
  gi|313127260|ref|YP_004037530.1| 367 DDIRAVKVEKASVKSEIKTKETELAEVEAEI 397
                                       9999988888888888888888887777665 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.3e-05
                             Atg14  22 erlyelrerlaklksekeslkkkiekalegke...........eaeqledkiknkkakleelksliadlrerlqelk 87 
                                       e++ +   +++ +k ek+s+k++i+ ++++             e ++l+d++  kk +leelk+++ dl++++ +l 
  gi|313127260|ref|YP_004037530.1| 360 EMIDDVEDDIRAVKVEKASVKSEIKTKETELAeveaeidsvdtEFDELKDELAAKKSQLEELKTERNDLQREKDRLL 436
                                       555566667788899999999999987777777889999**9999******************************** PP

                             Atg14  88 dklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslssktlesrsslcse 164
                                       d+ +++ +ei e+++k+++ +++l + +++l+ l++el +++k+  +k+   i   ++  s+l+s++ e   +l s 
  gi|313127260|ref|YP_004037530.1| 437 DDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKN-KQKIDGVIEDLREDRSDLKSDLDEVEDELRSK 512
                                       ********************************9**999987764.34455455545555555555555554444444 PP

                             Atg14 165 lak 167
                                        ++
  gi|313127260|ref|YP_004037530.1| 513 QSE 515
                                       444 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 1.7e-05
                             Atg14  18 rngperlyelrerlaklksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrerlqelkdkl 90 
                                       ++g+ rl++l +++ +l  ++ +++++i +++++ +    +a++++d++++  a++++   +++++++++++l+d++
  gi|313127260|ref|YP_004037530.1| 691 KSGSGRLERLAVEISDLEDDRREIEQEIRDIESQLDdareKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRI 767
                                       567889************************99999977776666677777777777777777777777777777777 PP

                             Atg14  91 sqlkkeieekkkklaklsdklkkRrsdleslqneleerr 129
                                       ++l+++ +e  +++++l+ ++   ++d++ +q+e+ e +
  gi|313127260|ref|YP_004037530.1| 768 EELREKRAEVDEEMQSLDTDIDALTADIDDVQSEIDELE 806
                                       777777777777777777777788888877777777655 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0031
                             Atg14  27 lrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkk 103
                                       l +++  l ++ + ++++i++++++       ++ki  ++a+++e++++i+++++r+ el  +l +l+ e e +   
  gi|313127260|ref|YP_004037530.1| 784 LDTDIDALTADIDDVQSEIDELESELA-----DSKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDA 855
                                       555666666677777777776666555.....99******************************************* PP

                             Atg14 104 laklsdklk...kRrsdle 119
                                       ++ l++++    +R++d++
  gi|313127260|ref|YP_004037530.1| 856 IEDLNETVEsaqDRKADAR 874
                                       *****99987777777744 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.003
                             Atg14  43 kkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdle 119
                                       +k ++++e++   e++++++  + a l+elk++++dlre ++e k  ++++++++e    +++ l+++  +   +++
  gi|313127260|ref|YP_004037530.1| 879 EKEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEID 955
                                       33333333333444555555566666666666666666666666666666666666666666666666667777777 PP

                             Atg14 120 slqneleerrkkqiaklqdaikrieq 145
                                        l+ e+ e+  ++i  + +   +i+q
  gi|313127260|ref|YP_004037530.1| 956 ELEAEVGEYDPEEIPDHDEVQENIQQ 981
                                       77777777777776554444444444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       8.1     3e+03     103     119 ..     203     219 ..     187     239 .. 0.50
   2 !    9.2   4.1    0.0032       1.2      54     122 ..     274     346 ..     256     348 .. 0.79
   3 ?    4.2   2.7      0.11        41      66     115 ..     360     409 ..     351     413 .. 0.71
   4 !    9.3   5.6    0.0029       1.1      43     123 ..     397     480 ..     393     481 .. 0.82
   5 ?    4.3   0.4      0.11        40      48      80 ..     482     514 ..     477     523 .. 0.81
   6 !   19.4   6.0   2.2e-06   0.00082      55     123 ..     705     773 ..     690     774 .. 0.92
   7 !   11.3   3.9   0.00072      0.27      37     121 ..     782     867 ..     775     870 .. 0.87
   8 ?    4.6   7.8     0.081        30      65     120 ..     895     950 ..     853     960 .. 0.73
   9 ?    6.6   5.3      0.02       7.3      71     120 ..     901     950 ..     891     993 .. 0.52
  10 ?    3.0   1.5      0.26        98      62     122 ..     973    1033 ..     967    1038 .. 0.86
  11 ?    2.1   0.2       0.5   1.9e+02      45      98 ..    1002    1059 ..     996    1065 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 8.1
                           DUF1664 103 vesvkeavegleskler 119
                                       +esv+e +e+ + ++e+
  gi|313127260|ref|YP_004037530.1| 203 LESVEERIEEADLRIEE 219
                                       33333333333333322 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0032
                           DUF1664  54 seslaatkrhL...ssridrvdkklde.qkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                        e+l++ +++L   + r+ r++++lde +kei ++ ++e  ++++++++++ +++ +++a+e  e ++++ e+
  gi|313127260|ref|YP_004037530.1| 274 AEKLESLREELdtrQGRVSRLEAELDElSKEIERKGEDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEAET 346
                                       566666777772224578888899988346788888899999*************************998775 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
                           DUF1664  66 sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       + id v++ + ++k  ++++k+e+++ + +l+e++ +++sv++ + +l+ 
  gi|313127260|ref|YP_004037530.1| 360 EMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDSVDTEFDELKD 409
                                       45777777777777777777777777777777777777777777777665 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0029
                           DUF1664  43 vesvskqleqvseslaatkrhLss...ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       ++sv ++ ++++++laa k +L++   + + ++++ d   + ++  ++e++e +e++se++e++ ++k+  ++l s+
  gi|313127260|ref|YP_004037530.1| 397 IDSVDTEFDELKDELAAKKSQLEElktERNDLQREKDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSE 473
                                       68899999999999999998765421166677777888888888888999999********************9999 PP

                           DUF1664 117 lerieek 123
                                       l++ e++
  gi|313127260|ref|YP_004037530.1| 474 LDKAEKN 480
                                       9998876 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.11
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqke 80 
                                       ++++ v e+l++ + +L+s++d+v+++l + + 
  gi|313127260|ref|YP_004037530.1| 482 QKIDGVIEDLREDRSDLKSDLDEVEDELRSKQS 514
                                       789999999999999999999999999976654 PP

  == domain 6  score: 19.4 bits;  conditional E-value: 2.2e-06
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                                       ++l++ +r+++++i  ++++ld+  e +++ ++ v +v+ d+++ +edve+ k+ +e+le ++e++ ek
  gi|313127260|ref|YP_004037530.1| 705 SDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREK 773
                                       678999***********************************************************9876 PP

  == domain 7  score: 11.3 bits;  conditional E-value: 0.00072
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLs.sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                       +sl   ++ ++ ++++v++++ +   +L+ s+i ++ ++ de  + ++e ++ ++e+ + l+e++ + e  ++a+e+
  gi|313127260|ref|YP_004037530.1| 782 QSLDTDIDALTADIDDVQSEIDELESELAdSKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIED 858
                                       57788889999999999999999999996468999999999999999999999999999999999999999999999 PP

                           DUF1664 113 lesklerie 121
                                       l++++e+ +
  gi|313127260|ref|YP_004037530.1| 859 LNETVESAQ 867
                                       999988765 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.081
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                        + +  ++++l+e k+  ++++e+v e++++ +e +++ve v++ ve+l ++ er+
  gi|313127260|ref|YP_004037530.1| 895 REAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERL 950
                                       34566777888888888888888888888888888888888888888887776665 PP

  == domain 9  score: 6.6 bits;  conditional E-value: 0.02
                           DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       ++++l+e k+  ++++e+v e++++ +e +++ve v++ ve+l ++ er+
  gi|313127260|ref|YP_004037530.1| 901 LEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERL 950
                                       44444444444444444444444444444444444444444444433333 PP

  == domain 10  score: 3.0 bits;  conditional E-value: 0.26
                           DUF1664   62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122 
                                        ++ +++i+++  k+++ + +     +e +ev+ dl+++++  + + e  +g++ ++e+ e+
  gi|313127260|ref|YP_004037530.1|  973 DEVQENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEA 1033
                                        5778999999999999999999999999999999999999999999888888888888875 PP

  == domain 11  score: 2.1 bits;  conditional E-value: 0.5
                           DUF1664   45 svskqleqvs...eslaatkrhLssridrvdkk.ldeqkeiskeikeevtevredlse 98  
                                        +v  +le+++   + la+ ++ +++ri++ +++  +  +e+  +i+++ t++ e ls+
  gi|313127260|ref|YP_004037530.1| 1002 EVQADLEDLQdgrDVLAEERQGIQDRIEQFEAQkKETFMEAFDAINDNFTDIFERLSN 1059
                                        5666666666444779999999999999998651566789999999998888877776 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.039        15      35      91 ..     279     338 ..     266     346 .. 0.79
   2 ?    7.2   0.7     0.013       4.8      24      87 ..     368     428 ..     361     435 .. 0.67
   3 ?    7.4   0.3     0.011       4.2      22      95 ..     436     517 ..     431     523 .. 0.67
   4 !   15.8   1.8   2.8e-05      0.01      35     129 ..     720     823 ..     696     831 .. 0.64
   5 ?    6.9   1.8     0.017       6.2      26      80 ..     782     846 ..     780     891 .. 0.56
   6 ?    2.2   0.7      0.46   1.7e+02      35     110 ..     900     956 ..     858    1011 .. 0.58
   7 ?    1.1   0.2         1   3.8e+02      49     103 ..    1002    1059 ..     973    1064 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.039
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnln 91 
                                        l + ld+ +++++ l+++l +l++e++++ ++   ++++ + +++   d l+n++++ +
  gi|313127260|ref|YP_004037530.1| 279 SLREELDTRQGRVSRLEAELDELSKEIERKGEDEQLRIKSEIESVKgeiDRLENAIEAAE 338
                                       577788888999999999999999999998888888888888888877777777777655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                      Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneL 87 
                                       +ir+ +v+  a +++ +++ et+L ++++++ s    +dt++d+l ++L ++  +l+  +t rn+L
  gi|313127260|ref|YP_004037530.1| 368 DIRAVKVEK-ASVKSEIKTKETELAEVEAEIDS----VDTEFDELKDELAAKKSQLEelKTERNDL 428
                                       666666666.77777777777777777777776....77777777777777777776444444444 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.011
                      Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq...dtlrneLtn 89 
                                       L++ r  +++i ++ ++ + ++ ++L +l+++l++l +eld+      ++d +++ L +    l+   d+++ eL +
  gi|313127260|ref|YP_004037530.1| 436 LDDTRRRSSEI-SETQEKISEVREELPTLKAKLSDLHSELDKaeknkqKIDGVIEDLREDRSDLKsdlDEVEDELRS 511
                                       67777777788.77888888889999999999999998888755555555555555555555555555555555555 PP

                      Baculo_PEP_C  90 lnsilt 95 
                                        +s+ +
  gi|313127260|ref|YP_004037530.1| 512 KQSEYA 517
                                       555554 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 2.8e-05
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvt 102
                                       +++++ld+  ++ ++ +++++s+ a++d+      + ++ +++L+d + +l     ++++e+++l++++  L++++ 
  gi|313127260|ref|YP_004037530.1| 720 DIESQLDDAREKASDAADRVRSVEADIDRaeedveEKKAEIEQLEDRIEELRekrAEVDEEMQSLDTDIDALTADID 796
                                       33333333333333333333333333333444333335667888888888887777899999999999999999999 PP

                      Baculo_PEP_C 103 NinstLnnllqalnnldlgalsqeled 129
                                        ++s +  l + l+  +  +l++++++
  gi|313127260|ref|YP_004037530.1| 797 DVQSEIDELESELADSKIPELTAQADE 823
                                       999999988888887777777666665 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.017
                      Baculo_PEP_C  26 rlqnvqilaqlatlldaietqLnalsedlksl.laeldt..........rldtlltnLtdalnalq 80 
                                       +++ + i  +l++++d++++++++l+++l ++ ++el++          + ++ +++L+  ln+lq
  gi|313127260|ref|YP_004037530.1| 782 QSLDTDI-DALTADIDDVQSEIDELESELADSkIPELTAqadeiraeieEKEDRMDELDGRLNELQ 846
                                       4555555.6666666666666666666665421444444222233322222223333333333333 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.46
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstL 108
                                       +l++ l++++ + ++                      L + + + +   d+ r + + ++s + nL  s   +   +
  gi|313127260|ref|YP_004037530.1| 900 DLEAELKELKAERSD----------------------LREDVREAKserDEQRDKVERVESRVENLRESAERLAWEI 954
                                       333333333333333......................3333333334444444444444444444444333333333 PP

                      Baculo_PEP_C 109 nn 110
                                         
  gi|313127260|ref|YP_004037530.1| 955 DE 956
                                       33 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 1
                      Baculo_PEP_C   49 alsedlksllaeldtrldtlltnLtdalnalq....dtlrneLtnlnsiltnLlssvtN 103 
                                        ++++dl++ l++ ++ l++  + ++d + +++    +t+ ++ +++n + t++   + N
  gi|313127260|ref|YP_004037530.1| 1002 EVQADLED-LQDGRDVLAEERQGIQDRIEQFEaqkkETFMEAFDAINDNFTDIFERLSN 1059
                                        44555555.34444567777777777777777767777777777777777777665555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1  15.1       1.3   4.7e+02     131     235 ..     199     300 ..     182     315 .. 0.52
   2 !   12.8  16.1   0.00015     0.055     107     236 ..     300     435 ..     298     441 .. 0.71
   3 !   11.2  17.2   0.00045      0.17     113     242 ..     384     518 ..     366     552 .. 0.62
   4 !   14.5  13.2   4.4e-05     0.017     132     235 ..     701     804 ..     687     813 .. 0.75
   5 !    6.9  20.3    0.0094       3.5     109     232 ..     806     932 ..     798     939 .. 0.45
   6 !    7.3  14.2    0.0069       2.6     117     247 ..     887    1057 ..     879    1065 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.3
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.gtgttgvaGkgpaakekkaqldaaqaelaelkakl 206
                                       +  el+  e++i++++  i+++e+rld+l++e +  l+ ++     + ++ ++ + k+++ + ++a+ e +e ka+ 
  gi|313127260|ref|YP_004037530.1| 199 AFGELESVEERIEEADLRIEEKESRLDQLEDERETALKYQSlR---EEREEYEGYLKAAELEDKRADLERTESKAE- 271
                                       4466777777778888888888888888888777777764443...334444444444222222222222222222. PP

                           DUF4407 207 datarlaalraelaeleaerakeraasqa 235
                                       +++++l++lr+el++ + + ++ +a+ ++
  gi|313127260|ref|YP_004037530.1| 272 TKAEKLESLREELDTRQGRVSRLEAELDE 300
                                       23444444444444444444444443332 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00015
                           DUF4407 107 eIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.........gtg 174
                                       e+ +e++++ ++e+ ++k++++ + + e+++le+ i+a++  id+ae++++++  e++++ +            +  
  gi|313127260|ref|YP_004037530.1| 300 ELSKEIERKGEDEQLRIKSEIE-SVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDdveddiravK-- 373
                                       6667777777777777777777.6789999999999999999999999999999999877665335655553221.. PP

                           DUF4407 175 ttgvaGkgpaakekkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqaa 236
                                          +a    + k+k+++l++ +ae+++++++ d  +++laa++++l+el++er++ ++++++ 
  gi|313127260|ref|YP_004037530.1| 374 -VEKASVKSEIKTKETELAEVEAEIDSVDTEFDeLKDELAAKKSQLEELKTERNDLQREKDRL 435
                                       .22444555555566666666666666666666988999999999999999999888887764 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00045
                           DUF4407 113 aeeqqeeakelkeqlaaa......ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..gtgttgvaGk 181
                                       ++ ++ e +e               ++e +el++++aa +++++++++++++l++e ++ ld t+  +++++ ++ k
  gi|313127260|ref|YP_004037530.1| 384 KT-KETELAE-------VeaeidsVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLDDTRrrSSEISETQEK 452
                                       22.2222233.......144445589999********************************9987774444444444 PP

                           DUF4407 182 gpaake....kkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqaaaaaddG 242
                                         + +e     ka+l ++  el++++++ +  +  +++lr+ +++l++++++ +++ ++++++ + 
  gi|313127260|ref|YP_004037530.1| 453 ISEVREelptLKAKLSDLHSELDKAEKNKQkIDGVIEDLREDRSDLKSDLDEVEDELRSKQSEYAE 518
                                       444444444455555555555555555544544444444444444444444444444444443333 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 4.4e-05
                           DUF4407 132 taelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld. 207
                                         e+++le++++++++ei+  e++ld++r++a + +d  ++ +   + + ++  +ekka++++++ +++el++k+  
  gi|313127260|ref|YP_004037530.1| 701 AVEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVE-ADIDRAEEDVEEKKAEIEQLEDRIEELREKRAe 776
                                       568999*****************************99866444.558889999999999999999999999999888 PP

                           DUF4407 208 atarlaalraelaeleaerakeraasqa 235
                                        ++++++l++ ++ l+a++++ +++ ++
  gi|313127260|ref|YP_004037530.1| 777 VDEEMQSLDTDIDALTADIDDVQSEIDE 804
                                       4555555555555555555544444333 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0094
                           DUF4407 109 daelaeeqqeeakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkg 182
                                       ++ela+ +  e +++ ++++a+    +++++el+ ++++lq e + ae+++++l++++++  d +  ++   ++ k+
  gi|313127260|ref|YP_004037530.1| 806 ESELADSKIPELTAQADEIRAEieeKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADAR-DVIREKE 881
                                       222222222222222223232244455666666666666666666666666666666666666544222.2344444 PP

                           DUF4407 183 paakekkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraa 232
                                       +a +ek+a l+++++++ +l+a+l+  +a++++lr+   e+++er+++r++
  gi|313127260|ref|YP_004037530.1| 882 QAIEEKEAVLEEKREAVSDLEAELKeLKAERSDLREDVREAKSERDEQRDK 932
                                       444444444444444444444444444444444444444444444444444 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0069
                           DUF4407  117 qeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.............gtgttgv 178 
                                        +e++ e k++  ++l+ael+el+a++++l++ +++a++++d++r+++++  +                       
  gi|313127260|ref|YP_004037530.1|  887 KEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVEnlresaerlaweiD------ 955 
                                        334444444444558888888888888888888888888888888887555543344444444433330...... PP

                           DUF4407  179 aGkgpaake.......................................kkaqldaaqaelaelkakld.atarla 213 
                                                e                                       + +++d+ qa+l++l++ +d  +++++
  gi|313127260|ref|YP_004037530.1|  956 --------EleaevgeydpeeipdhdevqeniqqltgkmeslepvnmlAIDEYDEVQADLEDLQDGRDvLAEERQ 1022
                                        ........1333444444444444444444555555555555556666777777777777777777668777888 PP

                           DUF4407  214 alraelaeleaera.keraasqaaaaaddGllarl 247 
                                          ++++++ ea+++ +  +a++a +++++++ +rl
  gi|313127260|ref|YP_004037530.1| 1023 GIQDRIEQFEAQKKeTFMEAFDAINDNFTDIFERL 1057
                                        88888888777655155788888888888888886 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5  20.2       1.9   7.2e+02      41     153 ..     197     307 ..     189     310 .. 0.67
   2 ?    6.2  33.3     0.035        13       7     173 ..     286     436 ..     251     441 .. 0.53
   3 !   10.3  16.5    0.0019       0.7      11     121 ..     410     520 ..     409     541 .. 0.84
   4 !   13.8  13.3   0.00016     0.058      32     145 ..     703     810 ..     696     816 .. 0.63
   5 ?    4.7  12.1       0.1        37      35      99 ..     816     891 ..     810     899 .. 0.71
   6 !   10.0  21.4    0.0023      0.87      40     162 ..     884    1035 ..     870    1043 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.9
                              Fez1  41 relrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaales 117
                                        ++  +le+ ee+i+e++ ++eek+  l+++e+e + + + +  lre+ e++e  lk    e +++ le++e+++e+
  gi|313127260|ref|YP_004037530.1| 197 EDAFGELESVEERIEEADLRIEEKESRLDQLEDERETALKYQ-SLREEREEYEGYLKAAELEDKRADLERTESKAET 272
                                       5667799**************************999887555.5666677777655554433333333333333333 PP

                              Fez1 118 deakaqrqeaeeleelkreverlraeLkeerqkkee 153
                                       ++ k +   +eel++ + +v rl+aeL e  ++ e+
  gi|313127260|ref|YP_004037530.1| 273 KAEKLESL-REELDTRQGRVSRLEAELDELSKEIER 307
                                       33333332.467888888888888888887777665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.035
                              Fez1   7 QksGEislLKqQLkdsqaevtqkls.eivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkksea 82 
                                        ++G +s L   L +  +e+ +k++ e + +k+++  ++ ++++ e++i+ +e++++e ++e  +   el+rk++  
  gi|313127260|ref|YP_004037530.1| 286 TRQGRVSRLEAELDELSKEIERKGEdEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMI 362
                                       34455555555555555555555432455555555555555555555555555555555555555555555555444 PP

                              Fez1  83 ellrekvekleeelkelreelselsleeeeaalesdeakaqrqe....aeeleelkreverlraeLkeerqkkeeqa 155
                                       + +++ +++++ e +++++e++++++                 e    + e+++ + e ++l+ eL+ ++    +q 
  gi|313127260|ref|YP_004037530.1| 363 DDVEDDIRAVKVEKASVKSEIKTKET-----------------ElaevEAEIDSVDTEFDELKDELAAKK----SQL 418
                                       44444444444444444444444211.................111112345555666666666665555....556 PP

                              Fez1 156 ssFeqERrtWqeeKekVi 173
                                       ++ ++ER+  q+eK++ +
  gi|313127260|ref|YP_004037530.1| 419 EELKTERNDLQREKDRLL 436
                                       6779***********987 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0019
                              Fez1  11 EislLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellre 87 
                                       E++  K+QL + ++e +    e   l  ++r  +++++e++e+i+e++e+l + +++l  +++el++++++++ ++ 
  gi|313127260|ref|YP_004037530.1| 410 ELAAKKSQLEELKTERNDLQREKDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDG 486
                                       78888999999999999999999999999999999999999999999999999999999999999999999999999 PP

                              Fez1  88 kvekleeelkelreelselsleeeeaalesdeak 121
                                        +e l e+ ++l+++l e++ e +++++e  e +
  gi|313127260|ref|YP_004037530.1| 487 VIEDLREDRSDLKSDLDEVEDELRSKQSEYAELE 520
                                       9999999999999999998766555554444433 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 0.00016
                              Fez1  32 eivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsl 108
                                       ei  l  + re+++++++ e+++++++e++++ ++ +  +e++++r+++++e ++ ++e+le+ ++elre+ +e+ +
  gi|313127260|ref|YP_004037530.1| 703 EISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDE 779
                                       56666667777777777777777777777777777777777777777777777777777777777777776666554 PP

                              Fez1 109 eeeeaalesdeakaqrqeaeeleelkreverlraeLk 145
                                       e ++  ++ d+       + ++++ ++e+++l++eL+
  gi|313127260|ref|YP_004037530.1| 780 EMQSLDTDIDA------LTADIDDVQSEIDELESELA 810
                                       43333333332......23456666666666666665 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.1
                              Fez1  35 alkaqlrelrakleekeeeikeleesleektle...........levcenelqrkkseaellrekvekleeelkel 99 
                                       +l aq  e+ra++eeke++++el+ +l+e +le           +e++e+  +rk +  +++rek +++ee+ + l
  gi|313127260|ref|YP_004037530.1| 816 ELTAQADEIRAEIEEKEDRMDELDGRLNELQLEkeyaedaiedlNETVESAQDRKADARDVIREKEQAIEEKEAVL 891
                                       6889999*************************96666666666556666666666666666666666666554443 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.0023
                              Fez1   40 lrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa 114 
                                        + e +a leek e++++le++l+e ++e   + ++++++kse +  r+kve++e+ +++lre++++l+ e +e +
  gi|313127260|ref|YP_004037530.1|  884 IEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELE 958 
                                        233334444444444444444444444444444444444555555555555555555555555555444444433 PP

                              Fez1  115 ....................lesdeakaqrqe...............aeeleelkreverlra...eLkeerqkk 151 
                                                            +         q+                +e +e ++++e l+     L+eerq  
  gi|313127260|ref|YP_004037530.1|  959 aevgeydpeeipdhdevqenI---------QQltgkmeslepvnmlaIDEYDEVQADLEDLQDgrdVLAEERQGI 1024
                                        677777776664433332221.........3355566666688888867777777777777655559*******9 PP

                              Fez1  152 eeqassFeqER 162 
                                        +++ ++Fe  +
  gi|313127260|ref|YP_004037530.1| 1025 QDRIEQFEAQK 1035
                                        99999999765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.8e-07    0.0001      13      46 ..      15      48 ..       8      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.8e-07
                            AAA_29 13 dg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                       + ++i++  +++t++tGp+GsGKS ++D + + L
  gi|313127260|ref|YP_004037530.1| 15 GRkTRIPFY-EDFTVVTGPNGSGKSNIIDGVLFAL 48
                                      554667776.458****************998765 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4  20.6       8.8   3.3e+03      21     126 ..     209     332 ..     192     352 .. 0.47
   2 ?    6.5  10.7     0.016       6.1      94     173 ..     349     430 ..     338     434 .. 0.85
   3 !   16.2   3.3   1.8e-05    0.0067      71     134 ..     445     508 ..     437     515 .. 0.90
   4 !    8.7   9.7    0.0035       1.3      93     174 ..     697     773 ..     694     776 .. 0.78
   5 !    7.8   0.5    0.0066       2.5      79     120 ..     767     808 ..     765     813 .. 0.91
   6 !    7.4   1.6    0.0089       3.3      87     133 ..     815     861 ..     811     868 .. 0.90
   7 !   12.8  11.0    0.0002     0.075      56     165 ..     882     990 ..     877     994 .. 0.96
   8 ?   -0.2   0.2       1.9   7.1e+02      98     141 ..     998    1041 ..     993    1044 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.8
                           DUF4201  21 qlakiqeklekkeelgegL.....tlidFeqlqienqaln.....kkIeernkeLkrlkkkttktvhalthlkeklh 87 
                                       ++++ + ++e+ke   ++L     t+  +++l+ e ++++      ++e++ ++L+r  +k+ ++  +l+ l+e l+
  gi|313127260|ref|YP_004037530.1| 209 RIEEADLRIEEKESRLDQLedereTALKYQSLREEREEYEgylkaAELEDKRADLERTESKAETKAEKLESLREELD 285
                                       33333334444444333332211223345555555555532222235555555555555555555555555555555 PP

                           DUF4201  88 .......mleselselkkelkekee.rlaklrkelykvklerdklrk 126
                                               le+el el ke+++k e ++ +++ e+++vk e d+l++
  gi|313127260|ref|YP_004037530.1| 286 trqgrvsRLEAELDELSKEIERKGEdEQLRIKSEIESVKGEIDRLEN 332
                                       44444444444444444444333220222344444444444443333 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.016
                           DUF4201  94 selkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrv..PaLlkDYdktkekveekrksvkkLrrkv 168
                                       +++  el++k+e+++++++ +  vk e++ ++ + +  +++++++++   ++ +++d+ k++++ k++++++L+++ 
  gi|313127260|ref|YP_004037530.1| 349 RKAFVELDRKQEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAeiDSVDTEFDELKDELAAKKSQLEELKTER 425
                                       455568999********************9999999999999988762269************************99 PP

                           DUF4201 169 kilem 173
                                       ++l++
  gi|313127260|ref|YP_004037530.1| 426 NDLQR 430
                                       99986 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.8e-05
                           DUF4201  71 kttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqq 134
                                        +  t  ++++++e l +l+++ls+l++el++ e++++k++  ++ ++++r+ l+ + ++++++
  gi|313127260|ref|YP_004037530.1| 445 EISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDE 508
                                       5667788999**********************************************99998765 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0035
                           DUF4201  93 lselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvk 169
                                       l++l  e++++e++++++++e+   + + d +r++ ++  ++       ++  D d+ +e+veek++++++L+ +++
  gi|313127260|ref|YP_004037530.1| 697 LERLAVEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVR-----SVEADIDRAEEDVEEKKAEIEQLEDRIE 768
                                       56666777888888888888888888888888877777666555.....5899999999999999999999999999 PP

                           DUF4201 170 ilemr 174
                                       +l ++
  gi|313127260|ref|YP_004037530.1| 769 ELREK 773
                                       99875 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0066
                           DUF4201  79 lthlkeklhmleselselkkelkekeerlaklrkelykvkle 120
                                       +++l+ek+ ++++e++ l ++++ +++++++++ e+ +++ e
  gi|313127260|ref|YP_004037530.1| 767 IEELREKRAEVDEEMQSLDTDIDALTADIDDVQSEIDELESE 808
                                       6789********************************999877 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0089
                           DUF4201  87 hmleselselkkelkekeerlaklrkelykvklerdklrkqneklkq 133
                                        +l+++  e + e++eke+r ++l+ +l++++le++ +++  e+l++
  gi|313127260|ref|YP_004037530.1| 815 PELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNE 861
                                       578999999******************************99999986 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 0.0002
                           DUF4201  56 kkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklk 132
                                       + Iee+++ L++ ++ + +   +l++lk  ++ l++ ++e+k+e +e+ ++ ++++ +++++++  ++l  + ++l+
  gi|313127260|ref|YP_004037530.1| 882 QAIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELE 958
                                       57*************************************************************************** PP

                           DUF4201 133 qqggllrvPaLlkDYdktkekveekrksvkkLr 165
                                       ++ g+++ +++  D d+ +e+++++  + ++L+
  gi|313127260|ref|YP_004037530.1| 959 AEVGEYDPEEIP-DHDEVQENIQQLTGKMESLE 990
                                       *****9999995.8***********99999987 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 1.9
                           DUF4201   98 kelkekeerlaklrkelykvklerdklrkqneklkqqggllrvP 141 
                                        +e++e +++l++l++    + +er+ ++++ e++++q+ + +++
  gi|313127260|ref|YP_004037530.1|  998 DEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEAQKKETFME 1041
                                        57788888888888888899999999999999999988887776 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  27.5      0.19        71      30     168 ..     205     344 ..     198     368 .. 0.88
   2 !    7.7  15.7    0.0054         2      28     137 ..     320     440 ..     318     443 .. 0.72
   3 !    8.5  12.4    0.0032       1.2      31     120 ..     428     521 ..     424     527 .. 0.70
   4 ?    4.5   1.5     0.053        20      93     136 ..     696     739 ..     691     757 .. 0.64
   5 !   12.9  25.1   0.00014     0.051      27     159 ..     759     902 ..     754     912 .. 0.78
   6 !    7.9   9.7    0.0048       1.8      30     129 ..     914    1014 ..     910    1058 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.19
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrk..qlknyekdkqslknlkarlkelekelkdl 104
                                       s  e iee + + e++e +l++++ e +    + + ++ee+ee +   ++++ e ++++l++++++ ++  ++l++l
  gi|313127260|ref|YP_004037530.1| 205 SVEERIEEADLRIEEKESRLDQLEDERET-ALKYQSLREEREEYEGylKAAELEDKRADLERTESKAETKAEKLESL 280
                                       7789999****************998665.556788888888888744556677889******************** PP

                               GAS 105 kwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqleev 168
                                       ++e +  + r++++e+e del+k+ e++ ++ q +++ +   ++  +++l++++E++e +++e+
  gi|313127260|ref|YP_004037530.1| 281 REELDTRQGRVSRLEAELDELSKEIERKGEDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEA 344
                                       **********************************************************999987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0054
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqs...........lknlkar 93 
                                       I+s K ei +l++  e++e +++e+++e ++   +L + +e ++  + +++  + +k+s           l++++a+
  gi|313127260|ref|YP_004037530.1| 320 IESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEKASvkseiktketeLAEVEAE 396
                                       88999999999999999999999999999999999999999988888877665555443111111111116667777 PP

                               GAS  94 lkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevq 137
                                       + +++ e+ +lk e   ++ ++e+++ er++l+++ ++ +++++
  gi|313127260|ref|YP_004037530.1| 397 IDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLDDTR 440
                                       77777778888888888888888888899998888888877766 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0032
                               GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslk....nlkarlkelekelkd 103
                                       l  e  +l    +r + e+se++++ ++ +e+L ++++++  L+ +l + ek kq+++     l++  ++l++ l +
  gi|313127260|ref|YP_004037530.1| 428 LQREKDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDgvieDLREDRSDLKSDLDE 504
                                       66666777777888999999999999999999999999999999999999999998651111445555555555555 PP

                               GAS 104 lkwehevleqrfekvek 120
                                       ++ e ++++ +++++e+
  gi|313127260|ref|YP_004037530.1| 505 VEDELRSKQSEYAELEA 521
                                       55555555555555553 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.053
                               GAS  93 rlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqev 136
                                       rl++l  e++dl+ + +  eq++  +e++ d+ ++k  +a + v
  gi|313127260|ref|YP_004037530.1| 696 RLERLAVEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRV 739
                                       55666666777777777777777777777777766666665444 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 0.00014
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknye..kdkqslknlkarlkelekel 101
                                        I++l + ieel++k ++ + e++ + ++   l+  +  ++ e++eL+ +l++ +  +  ++ ++++a+++e e+ +
  gi|313127260|ref|YP_004037530.1| 759 EIEQLEDRIEELREKRAEVDEEMQSLDTDIDALTADIDDVQSEIDELESELADSKipELTAQADEIRAEIEEKEDRM 835
                                       599***********************************************998763345566677777777777777 PP

                               GAS 102 kdlkwehevleqrfekvekerdelykkfeaa..........iqevqqktglknllLekklkalqeelE 159
                                        +l    + l+ + e +e+++++l+++ e+a          i+e  q ++ k+ +Le k +a+++ lE
  gi|313127260|ref|YP_004037530.1| 836 DELDGRLNELQLEKEYAEDAIEDLNETVESAqdrkadardvIREKEQAIEEKEAVLEEKREAVSD-LE 902
                                       77777777777777777777777777777776665555777888899999999999998887764.33 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0048
                               GAS   30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknye.kdkqslknlkarlkelekelkd 103 
                                         l+e++ e k + ++++ +++ ++++ ++l+e  +++  e++eL++++ +y+ ++  +++++++++++l+ ++++
  gi|313127260|ref|YP_004037530.1|  914 DLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELEAEVGEYDpEEIPDHDEVQENIQQLTGKMES 988 
                                        79*************************************************9345679***************** PP

                               GAS  104 lkwehevleqrfekvekerdelykkf 129 
                                        l+  +    +++++v+++ ++l++  
  gi|313127260|ref|YP_004037530.1|  989 LEPVNMLAIDEYDEVQADLEDLQDGR 1014
                                        ******************99999865 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   8.9      0.63   2.4e+02      56     102 ..     189     235 ..     178     239 .. 0.86
   2 ?    7.9  21.7     0.012       4.3      17      93 ..     236     314 ..     232     324 .. 0.67
   3 !   17.5  23.7   1.3e-05    0.0047      15     118 ..     317     438 ..     315     445 .. 0.77
   4 !   14.5  13.0    0.0001     0.038      37     117 ..     441     521 ..     433     524 .. 0.82
   5 ?    4.2  26.5      0.15        57      18     121 ..     704     811 ..     697     824 .. 0.53
   6 ?    1.8  28.9      0.85   3.2e+02      12     131 ..     747     868 ..     746     869 .. 0.86
   7 ?    4.4  19.6      0.13        49      14     125 ..     901    1020 ..     900    1028 .. 0.87
   8 ?    2.3   5.2      0.62   2.3e+02      60     102 ..     997    1039 ..     963    1048 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.63
                            APG6_N  56 leklekeeeelleeLkelekereeleaelaaleeelealeeeeerfw 102
                                       +++ ++++e+++ eL+ +e+  ee +  +++ e+ l++le+e e  +
  gi|313127260|ref|YP_004037530.1| 189 VAEFDAKKEDAFGELESVEERIEEADLRIEEKESRLDQLEDERETAL 235
                                       56778899999999999999999999999999999999999988765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.012
                            APG6_N  17 qleqaekerdaYeeflkklkkekkeeek..qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeel 91 
                                       +++++++er++Ye +lk  + e+k ++   ++++ e   e+le l++e ++ +    +le+e +el +e++   e +
  gi|313127260|ref|YP_004037530.1| 236 KYQSLREEREEYEGYLKAAELEDKRADLerTESKAETKAEKLESLREELDTRQGRVSRLEAELDELSKEIERKGEDE 312
                                       78999*************99997775444455555555555666666666666666666666666666666665555 PP

                            APG6_N  92 ea 93 
                                       + 
  gi|313127260|ref|YP_004037530.1| 313 QL 314
                                       44 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.3e-05
                            APG6_N  15 dkqleqaekerdaYeeflkklkkekkeeek..................qdeeleeleeeleklekeeeelleeLkel 73 
                                       ++++e+++ e+d +e+  +  +++ +e+e+                   ++++++ + e + +++e +++++eL+e+
  gi|313127260|ref|YP_004037530.1| 317 KSEIESVKGEIDRLENAIEAAEDRIDEAETerrkafveldrkqemiddVEDDIRAVKVEKASVKSEIKTKETELAEV 393
                                       66777777777777777777777777766677777888888666666667788888888888888888888888888 PP

                            APG6_N  74 ekereeleaelaaleeelealeeeeerfwreynelqlelleleee 118
                                       e+e ++++ e  +l+ el+a++ + e+  +e+n+lq+e+ +l ++
  gi|313127260|ref|YP_004037530.1| 394 EAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLDD 438
                                       888888888888888888888888888888888888888877765 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 0.0001
                            APG6_N  37 kekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlell 113
                                       ++++e ++++e++ e +eel +l+++ ++l +eL+++ek++++++  +++l+e  ++l+ + ++   e +++q e +
  gi|313127260|ref|YP_004037530.1| 441 RRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRSKQSEYA 517
                                       33344444688999999999999999999999999999999999999999999999999999999999999999988 PP

                            APG6_N 114 elee 117
                                       ele 
  gi|313127260|ref|YP_004037530.1| 518 ELEA 521
                                       8875 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.15
                            APG6_N  18 leqaekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleee 90 
                                       ++++e++r++ e+  + ++++ +++++      + +++ e ++++ e++ ee+ +e+++le+  eel++++a+  ee
  gi|313127260|ref|YP_004037530.1| 704 ISDLEDDRREIEQEIRDIESQLDDAREkasdAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEE 780
                                       55555555555555555544433333233333345555555555555555555555555555555555555555555 PP

                            APG6_N  91 lealeeeeerfwreynelqlelleleeelds 121
                                        + l+ + ++   +  + q e  ele el+ 
  gi|313127260|ref|YP_004037530.1| 781 MQSLDTDIDALTADIDDVQSEIDELESELAD 811
                                       5555555555555555555555555555544 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.85
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekeree.....leae 83 
                                       ++ ++ +e+ ++e++++e+  ++l++++ e    dee+++l+ ++++l ++ ++ ++e++ele+e ++     l a+
  gi|313127260|ref|YP_004037530.1| 747 DRAEEDVEEKKAEIEQLEDRIEELREKRAEV---DEEMQSLDTDIDALTADIDDVQSEIDELESELADskipeLTAQ 820
                                       6667888999999999999999999996664...6899999999999999999999999999999985333338999 PP

                            APG6_N  84 laaleeelealeeeeerfwreynelqlelleleeeldsleaqyehaqn 131
                                         ++++e e++e+  ++   + nelqle++  e+  + l+  +e aq+
  gi|313127260|ref|YP_004037530.1| 821 ADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQD 868
                                       999999999999999999999***************999999999886 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.13
                            APG6_N   14 ldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkeleke...........r 77  
                                        l+ +l+++++er +++e  ++ k+e++e+   ++++e+ e ++e+l++  e+l  e++ele+e           +
  gi|313127260|ref|YP_004037530.1|  901 LEAELKELKAERSDLREDVREAKSERDEQ---RDKVERVESRVENLRESAERLAWEIDELEAEvgeydpeeipdH 972 
                                        7899*********************8775...5899999999999999999999999999998665555555556 PP

                            APG6_N   78 eeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaq 125 
                                        +e+++ +++l+ + e le  +   + ey e q +l++l++ +d l+ +
  gi|313127260|ref|YP_004037530.1|  973 DEVQENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDVLAEE 1020
                                        8999************************************99988765 PP

  == domain 8  score: 2.3 bits;  conditional E-value: 0.62
                            APG6_N   60 ekeeeelleeLkelekereeleaelaaleeelealeeeeerfw 102 
                                         +e +e ++ L++l++ r+ l++e++ ++   e+ e+++++ +
  gi|313127260|ref|YP_004037530.1|  997 IDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEAQKKETF 1039
                                        3444555556666666666666666666666666665555554 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9  23.8      0.47   1.7e+02     162     323 ..     362     518 ..     337     528 .. 0.42
   2 !   20.7  12.2   4.6e-07   0.00017     227     349 ..     705     829 ..     701     830 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.47
                             IFT57 162 dedeedeeeelklesekkeekekekeeeiieskvdaaeWklEleRvlpqLkvtikadakdWrahleqmkkhkksiee 238
                                        +d ed+ +++k+e+ + +++ k+ke+e++e + +     +E+     +L ++ k++ ++ +++ + +++ k+ + +
  gi|313127260|ref|YP_004037530.1| 362 IDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDSVDTEFDELKDELAAK-KSQLEELKTERNDLQREKDRLLD 437
                                       12222222333333333333333333333333333333333333333333332.22333333333333333333333 PP

                             IFT57 239 slpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseele 315
                                       ++ + +s++++ +e+is++ e++ +    l  +l++l +e+ +a+++ +++   +++l e  s+l+ +l+e+++el+
  gi|313127260|ref|YP_004037530.1| 438 DTRRRSSEISETQEKISEVREELPT----LKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELR 510
                                       3333333333333333333333332....455666666666666666666666666666666666666666666666 PP

                             IFT57 316 kvkqemee 323
                                       + ++e  e
  gi|313127260|ref|YP_004037530.1| 511 SKQSEYAE 518
                                       65555554 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4.6e-07
                             IFT57 227 eqmkkhkksieeslpetksqlkklhedisktlekiesrEkyl...nsqleellqeyreaqeelsevkekykqlsegv 300
                                         +++ +++ie+++ +++sql++  e+ s + +++ s E  +   ++ +ee  +e ++++++++e++ek  ++ e++
  gi|313127260|ref|YP_004037530.1| 705 SDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIdraEEDVEEKKAEIEQLEDRIEELREKRAEVDEEM 781
                                       55667789**********************************66678999*************************** PP

                             IFT57 301 seltrelaeiseelekvkqemeergssmtDgsplvkikkaltklkkEik 349
                                       ++l ++ + ++ ++++v++e++e +s+++D++ + +++ + ++++ Ei+
  gi|313127260|ref|YP_004037530.1| 782 QSLDTDIDALTADIDDVQSEIDELESELADSK-IPELTAQADEIRAEIE 829
                                       ******************************76.4788888888888886 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3  14.4       1.7   6.3e+02     145     247 ..     213     309 ..     195     313 .. 0.60
   2 ?    0.3  29.6       1.1   3.9e+02      94     257 ..     252     419 ..     242     431 .. 0.62
   3 ?    6.1  17.0     0.019         7     132     242 ..     401     515 ..     395     525 .. 0.77
   4 !   20.9  13.9   5.7e-07   0.00021     125     275 ..     694     843 ..     690     844 .. 0.87
   5 ?   -2.2  18.6       6.2   2.3e+03     132     239 ..     825     936 ..     817     949 .. 0.48
   6 ?    4.8   1.1     0.047        17     137     204 ..     974    1042 ..     968    1060 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                           Leu_zip 145 LkerlkelEkqatsaleeksklekalkelqkelgekkdekenskeiskleeklaelkldlektleektasaksleed 221
                                          r++e E+++ ++ +e    e+alk +  +l e+++e e   + ++le+k a+l+   e++ e+k+++ +sl+e+
  gi|313127260|ref|YP_004037530.1| 213 ADLRIEEKESRLDQLEDE---RETALKYQ--SLREEREEYEGYLKAAELEDKRADLER-TESKAETKAEKLESLREE 283
                                       222222222222222222...22222222..233333344445567788888888875.45566777888999**** PP

                           Leu_zip 222 lastkhelLkvqeqLelaekeLekkf 247
                                       l + + ++ +++++L+   ke+e+k 
  gi|313127260|ref|YP_004037530.1| 284 LDTRQGRVSRLEAELDELSKEIERKG 309
                                       ***********************995 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                           Leu_zip  94 kiaefEekefkssnkkeseelkkkkLePlneg.....GgaeLLkkeierLkeene.kLkerlkelEkqatsaleeks 164
                                       k ae+E+k +  + +++++e+k++kLe l e      G +  L+ e+++L +e e k ++   ++ ++++s+  e  
  gi|313127260|ref|YP_004037530.1| 252 KAAELEDKRADLERTESKAETKAEKLESLREEldtrqGRVSRLEAELDELSKEIErKGEDEQLRIKSEIESVKGEID 328
                                       45788999999988999999999999999987666679999999999999777551566777788999999999999 PP

                           Leu_zip 165 klekalkelqkelgekkdekenskeiskleeklaelkldlektleektasaksleedlastkhelLkvqeqLelaek 241
                                       +le+a+++++++++e+++e++  k + +l++k +e+  d+e   ++ + +++s+++++ +   el +v+++++  + 
  gi|313127260|ref|YP_004037530.1| 329 RLENAIEAAEDRIDEAETERR--KAFVELDRK-QEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDSVDT 402
                                       999999999888877765554..444444333.33444444444444455555555554444444444444444444 PP

                           Leu_zip 242 eLekkfqqtaayk.nlk 257
                                       e +   ++ aa k  l 
  gi|313127260|ref|YP_004037530.1| 403 EFDELKDELAAKKsQLE 419
                                       44332222222111222 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.019
                           Leu_zip 132 kkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldlekt 207
                                       ++e ++Lk+e    k++l+el ++ +++ +ek +l  + ++  +e++e++++ +   +e+ +l++kl++l+++l+k 
  gi|313127260|ref|YP_004037530.1| 401 DTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLDDTRRRSSEISETQEKISeVREELPTLKAKLSDLHSELDKA 477
                                       57888999999999999999999999999999999999888887777765554437889999999999999999886 PP

                           Leu_zip 208 leektas...aksleedlastkhelLkvqeqLelaeke 242
                                        ++k++     ++l+ed  + k +l +v+++L  +++e
  gi|313127260|ref|YP_004037530.1| 478 EKNKQKIdgvIEDLREDRSDLKSDLDEVEDELRSKQSE 515
                                       66665441115788888888888888888888887776 PP

  == domain 4  score: 20.9 bits;  conditional E-value: 5.7e-07
                           Leu_zip 125 gGgaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgek.kdekenskeiskleeklael 200
                                       +G  e L  ei+ L+++ + +++ ++++E+q+ +a e+ s  +  +++++++++ + +d++e+++ei++le++++el
  gi|313127260|ref|YP_004037530.1| 694 SGRLERLAVEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAeEDVEEKKAEIEQLEDRIEEL 770
                                       688899*******************************************9988765266677899999999999887 PP

                           Leu_zip 201 kldlektleektasaksleedlastkhelLkvqeqLelaekeL.ekkfqq.taayknlkemltkkneqikelRkrLs 275
                                       +     +  e  ++ +sl++d+     ++  vq++++  e+eL + k+ + ta+   ++  + +k + + el  rL+
  gi|313127260|ref|YP_004037530.1| 771 RE----KRAEVDEEMQSLDTDIDALTADIDDVQSEIDELESELaDSKIPElTAQADEIRAEIEEKEDRMDELDGRLN 843
                                       65....556667788899999999999***************95567765499999****************99996 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 6.2
                           Leu_zip 132 kkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleekla...elkldl 204
                                       + eie+ ++  + L  rl+el  + + a +  + l+++++++q++  +++d+ + +++ i++ e+ l+   e  +dl
  gi|313127260|ref|YP_004037530.1| 825 RAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIReKEQAIEEKEAVLEekrEAVSDL 901
                                       44555555555555555555544444444444444444444444433333322223444444443333000334455 PP

                           Leu_zip 205 ektleektasaksleedlastkhelLkvqeqLela 239
                                       e +l+e +a+ ++l+ed+ ++k e  + ++++e  
  gi|313127260|ref|YP_004037530.1| 902 EAELKELKAERSDLREDVREAKSERDEQRDKVERV 936
                                       55666666666666666666666555555555555 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.047
                           Leu_zip  137 rLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldl 204 
                                        +++e+ ++L  ++++lE   + a++e  +++++l++lq+  +   +e++  + +i++ e++ +e  ++ 
  gi|313127260|ref|YP_004037530.1|  974 EVQENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDVLAEERQgIQDRIEQFEAQKKETFMEA 1042
                                        56888899*****************************99887776666646677888887777766654 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  54.9     0.043        16     239     535 ..     216     504 ..     195     511 .. 0.55
   2 !   17.9  50.3   1.2e-06   0.00047     285     529 ..     707     950 ..     696     952 .. 0.69
   3 ?    4.2   6.1     0.017       6.4     324     430 ..     950    1052 ..     945    1098 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.043
                           DUF3584 239 aiekvrpeieklqeefeql...eslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnq 312
                                       +ie+ + ++++l+ e e+    +sl ++    +g lka+e + ++   e+ e+kae     +++ + l e+ d++++
  gi|313127260|ref|YP_004037530.1| 216 RIEEKESRLDQLEDERETAlkyQSLREEREEYEGYLKAAELEDKRADLERTESKAE---TKAEKLESLREELDTRQG 289
                                       23333333333333333220002222222222222222222222111111111111...112222334444444555 PP

                           DUF3584 313 elsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkik 389
                                       ++s ++a+l++ ++e+e+  e+++   +++ie++k + d+l+   + +e++e ++d  +++ ++   ++dr++  i+
  gi|313127260|ref|YP_004037530.1| 290 RVSRLEAELDELSKEIERKGEDEQLRIKSEIESVKGEIDRLE---NAIEAAEDRIDEAETERRKAFVELDRKQEMID 363
                                       555555555555555555555555555555555555554443...34445555555555555555555554444443 PP

                           DUF3584 390 eeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEe 466
                                        + e++++  k +++ ++ e +++    e +l ++e++     + +  el++e +  +s+l+elk+ +++ + +++ 
  gi|313127260|ref|YP_004037530.1| 364 -DVEDDIRAVKVEKASVKSEIKTK----ETELAEVEAEID-SVDTEFDELKDELAAKKSQLEELKTERNDLQREKDR 434
                                       .34444444444444444444442....333444444444.456677789999999999*************99997 PP

                           DUF3584 467 leq.ieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqaleeleeqlsP 535
                                       l++  +   +++++ qe++ + ++e   l+a++  l ++ d+a++  qk+   +e+lr++ ++l+  l+ 
  gi|313127260|ref|YP_004037530.1| 435 LLDdTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDE 504
                                       76516678899****************************************************9988765 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.2e-06
                           DUF3584 285 vqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldql....psir 357
                                        +   +e++q++r  e++l      ++++ s+a + +   e++++++ee+ ++ ++a+ie+l+   ++l     ++ 
  gi|313127260|ref|YP_004037530.1| 707 LEDDRREIEQEIRDIESQLD----DAREKASDAADRVRSVEADIDRAEEDVEE-KKAEIEQLEDRIEELrekrAEVD 778
                                       33333444444444333333....33333444444555555555555555444.44455555444444411115677 PP

                           DUF3584 358 seleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqlea 434
                                       +e++ l+ ++dalt  + dvq++ d++++++ +++  el    ++  a  eek+ +  + +  l++l+ + +   e 
  gi|313127260|ref|YP_004037530.1| 779 EEMQSLDTDIDALTADIDDVQSEIDELESELADSKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKE-YAED 854
                                       89999*************************999999988888888555555555557788888877765554.4577 PP

                           DUF3584 435 qkeelneeekelesr.lselklrldsatateEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeade 510
                                       ++e+lne  +  + r ++  ++ +++ +a eE+   +ee+ ea++  ++el++ +ae+++l ++ ++++++rde+ +
  gi|313127260|ref|YP_004037530.1| 855 AIEDLNETVESAQDRkADARDVIREKEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRD 931
                                       7888888777776651555666777777788888889**************************************** PP

                           DUF3584 511 alqkaerrleqlrqaleel 529
                                       + ++ e r+e+lr+ +e l
  gi|313127260|ref|YP_004037530.1| 932 KVERVESRVENLRESAERL 950
                                       *************998866 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.017
                           DUF3584  324 keselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeelek 398 
                                           e+++le++  +y+ ++i+   + ++++ ++  ++e le    + +++  +vq+ ++ ++  ++  l+ee ++
  gi|313127260|ref|YP_004037530.1|  950 LAWEIDELEAEVGEYDPEEIPDHDEVQENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDV-LAEERQG 1023
                                        5569******************************************************999876654.5666677 PP

                           DUF3584  399 lkerleaireekdrlkaaieealealesqlrk 430 
                                        +++r   i + ++++k+++ ea++a++ ++ +
  gi|313127260|ref|YP_004037530.1| 1024 IQDR---IEQFEAQKKETFMEAFDAINDNFTD 1052
                                        7777...7777777788999999999888764 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4  10.1   0.00023     0.085     140     260 ..     709     846 ..     703     853 .. 0.71
   2 !    8.5  11.3    0.0034       1.3     146     266 ..     853     996 ..     842     997 .. 0.56
   3 ?    3.8   0.0     0.095        36     187     291 ..     995    1099 ..     973    1107 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                      Exonuc_VII_L 140 pdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq...lkkkrer 213
                                        d++e+e++++++e++l++a +++  +++ r+++++ ++ ++ee +e+k+ ++++le+r+e+ l+++   ++++ + 
  gi|313127260|ref|YP_004037530.1| 709 DDRREIEQEIRDIESQLDDAREKAS-DAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEE-LREKraeVDEEMQS 783
                                       5788999999999999999876655.577899999999999999999999999999999999.44441333333333 PP

                      Exonuc_VII_L 214 leelkerlkekleekkerlkklkerle................lleekkerleeleekleals 260
                                       l++  ++l++++++ ++++++l+++l+                ++eek++r++el  +l+ l+
  gi|313127260|ref|YP_004037530.1| 784 LDTDIDALTADIDDVQSEIDELESELAdskipeltaqadeiraEIEEKEDRMDELDGRLNELQ 846
                                       333333333666677766666666666666666666555655568889999999988888876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0034
                      Exonuc_VII_L 146 eeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq.......lkkkrerle 215
                                       e+ +e+l++ +e+a +r+ + ++  +++ +++++++e++le+kr+++++le++l++ lk +       +++++++ +
  gi|313127260|ref|YP_004037530.1| 853 EDAIEDLNETVESAQDRKAD-ARDVIREKEQAIEEKEAVLEEKREAVSDLEAELKE-LKAErsdlredVREAKSERD 927
                                       45555666666666555554.45566666777777777777777777777777777.44441232222333333322 PP

                      Exonuc_VII_L 216 elkerlkekleekkerlkklkerle...................lleekkerleeleeklealsplkvLk 266
                                       e ++++ e++e++ e+l++ +erl+                     +e +e++++l+ k+e+l+p ++L+
  gi|313127260|ref|YP_004037530.1| 928 EQRDKV-ERVESRVENLRESAERLAweideleaevgeydpeeipDHDEVQENIQQLTGKMESLEPVNMLA 996
                                       222222.222222222233333333555555566667777666669999999999999999999999985 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.095
                      Exonuc_VII_L  187 rkrqrldeleerleralkkq...lkkkrerleelkerlkekleekkerl..kklkerlelleekkerleeleekl 256 
                                         + +++de++++le  l+     l+++r+ ++   e++    e++k+++  ++  +  +++++  erl++ + +l
  gi|313127260|ref|YP_004037530.1|  995 LAIDEYDEVQADLED-LQDGrdvLAEERQGIQDRIEQF----EAQKKETfmEAFDAINDNFTDIFERLSNGTGEL 1064
                                        333444444445544.2222122444444444444333....2222222223332233379999999999***** PP

                      Exonuc_VII_L  257 ealsplkvLkrGyaivrkedgkvvtsakdlkkgde 291 
                                        ++ +p+   + G ++  +  +k++++ ++++ g++
  gi|313127260|ref|YP_004037530.1| 1065 HLENPEDPFEEGLTMKAQPGDKPIQRLDAMSGGEK 1099
                                        *************9999988999999998888876 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  26.1     0.078        29      37     215 ..     201     377 ..     190     396 .. 0.86
   2 ?    5.2  18.9     0.037        14      31     171 ..     382     520 ..     378     525 .. 0.63
   3 !   18.8  17.5   2.4e-06   0.00091      81     213 ..     712     848 ..     708     849 .. 0.87
   4 !   15.9  32.8   1.9e-05    0.0071       8     206 ..     749     946 ..     746     977 .. 0.88
   5 ?    1.5   1.6      0.47   1.8e+02      31     121 ..     999    1034 ..     971    1049 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.078
                        MscS_porin  37 kkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqt 113
                                        ++e  +++i++a  +++e + +l++l  ++e +++ ++++l  e  e +     ++l++ +++l   +s++ +   
  gi|313127260|ref|YP_004037530.1| 201 GELESVEERIEEADLRIEEKESRLDQL--EDERETALKYQSLREEREEYEGYLKAAELEDKRADLERTESKAETKAE 275
                                       56788899*******************..777777777777777777777778899********************* PP

                        MscS_porin 114 rperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllk 190
                                        +e ++++l + + r + ++++L++++++ e+  ++++   + e ++ + +i+ le + + +  r++ ++ +r  + 
  gi|313127260|ref|YP_004037530.1| 276 KLESLREELDTRQGRVSRLEAELDELSKEIERKGEDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAF 352
                                       **************************88888******************************************9999 PP

                        MscS_porin 191 lriqqleqelqaLqellnekRlaea 215
                                        ++++ ++ +++++  + + + ++a
  gi|313127260|ref|YP_004037530.1| 353 VELDRKQEMIDDVEDDIRAVKVEKA 377
                                       9999999999988887776665554 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.037
                        MscS_porin  31 kidkskkkaeelqkaiddaPkelrelqqeleal.qkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlns 106
                                       +i+  + +++e +  id+   e +el+ el+a  ++ +e +++ ++ +   + L      +ss+ +e+qe++++  +
  gi|313127260|ref|YP_004037530.1| 382 EIKTKETELAEVEAEIDSVDTEFDELKDELAAKkSQLEELKTERNDLQREKDRLLDDTRRRSSEISETQEKISEVRE 458
                                       56777777777777777777777777777777744444555555555566677777777777777777777777777 PP

                        MscS_porin 107 qlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqieeleqe 171
                                       +l +l   ++ ++++l +a +  q+i   +++++   e+ s+ + ++ ++e ++++ q e+ e+e
  gi|313127260|ref|YP_004037530.1| 459 ELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLR---EDRSDLKSDLDEVEDELRSKQSEYAELE 520
                                       7777777777777777777777777765555552...2333333444445555555555555555 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 2.4e-06
                        MscS_porin  81 eeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrL.....nstaaage.alsqaqr 151
                                       +e+eq++ + +sql +++e+ +++ +++++ +  ++ra +   e + +++++++r+     +  + ++e +  ++  
  gi|313127260|ref|YP_004037530.1| 712 REIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIeelreKRAEVDEEmQSLDTDI 788
                                       699***************************************************99555533333344488888888 PP

                        MscS_porin 152 talqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqellnekRla 213
                                       +al a     +++i+ele el+ +   +  l++q+d+ +++i++ e +++ L  +lne  l+
  gi|313127260|ref|YP_004037530.1| 789 DALTADIDDVQSEIDELESELADS--KIPELTAQADEIRAEIEEKEDRMDELDGRLNELQLE 848
                                       999999999999999999999765..567799*************************99886 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 1.9e-05
                        MscS_porin   8 akldeaeqkallqdLeqalnlL.dkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeL 83 
                                       a++d +e+ka +++Le+ ++ L +k+++ +++++ l + id  ++ ++++q e+++l +++ ++sk    +   +e+
  gi|313127260|ref|YP_004037530.1| 749 AEEDVEEKKAEIEQLEDRIEELrEKRAEVDEEMQSLDTDIDALTADIDDVQSEIDEL-ESELADSKIPELTAQADEI 824
                                       4567799**********997662678899****************************.44444444444466789** PP

                        MscS_porin  84 eqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaa 160
                                         ++++ ++++ el  +l++l+ +   +++++e + ++  +a+ r ++ r+ + ++   ++a+++ + ++ + ++a 
  gi|313127260|ref|YP_004037530.1| 825 RAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREK---EQAIEEKEAVLEEKREAV 898
                                       ***************************************************88666...449999999999999999 PP

                        MscS_porin 161 leaqieeleqellsnnnrqeL..lklqrdllklriqqleqelqaLqel 206
                                        +++ e+ e+ ++ ++ r +   +k++rd+ + ++++ e+++++L+e 
  gi|313127260|ref|YP_004037530.1| 899 SDLEAELKELKAERSDLREDVreAKSERDEQRDKVERVESRVENLRES 946
                                       999***************9995567789*****************985 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.47
                        MscS_porin   31 kidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqln 105 
                                        +                                                       +++++++l++lq  +  l 
  gi|313127260|ref|YP_004037530.1|  999 E-------------------------------------------------------YDEVQADLEDLQDGRDVLA 1018
                                        3.......................................................4455555555555555555 PP

                        MscS_porin  106 sqlvelqtrperaqqq 121 
                                        ++ + +q+r+e+  +q
  gi|313127260|ref|YP_004037530.1| 1019 EERQGIQDRIEQFEAQ 1034
                                        5555555555555544 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1  14.5      0.78   2.9e+02     383     488 ..     195     293 ..     189     296 .. 0.88
   2 !    8.2  33.1    0.0027      0.99     319     486 ..     307     481 ..     294     483 .. 0.84
   3 ?    3.3  11.1     0.083        31     313     390 ..     442     518 ..     423     525 .. 0.61
   4 !   18.1  26.8   2.6e-06   0.00097     316     473 ..     702     867 ..     680     880 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.78
                            DUF812 383 lkkktlellpdaeeniekLqalveasaqrlvelakqWekhRvplieeyrelkesksekekeaerkleeikklrekmk 459
                                       +k+ ++  l++ ee ie+    +e++++rl +l+++ e        +y++l+e+ +e   e   k +e++  r+ ++
  gi|313127260|ref|YP_004037530.1| 195 KKEDAFGELESVEERIEEADLRIEEKESRLDQLEDERET----A-LKYQSLREEREE--YEGYLKAAELEDKRADLE 264
                                       68899999**********************988776554....3.58****998765..5667899*********** PP

                            DUF812 460 evaeelrqkeellkqLvaeleklpkdvsR 488
                                        +++++ +k+e+l+ L +el++++  vsR
  gi|313127260|ref|YP_004037530.1| 265 RTESKAETKAEKLESLREELDTRQGRVSR 293
                                       ***************************99 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0027
                            DUF812 319 eteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneeleke...vklkkk.tlell 391
                                       ++ e+ + + + e+e+++ +i++le+ ie+ e+ i++ e++ +++  el++++e     e++   vk++k  + + +
  gi|313127260|ref|YP_004037530.1| 307 RKGEDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDiraVKVEKAsVKSEI 383
                                       455666777788999**************************************998777766111555554155688 PP

                            DUF812 392 pdaeeniekLqalveasaqrlvelakqWekhRvplie...eyrelkesksekekeaerkleeikklrekmkevaeel 465
                                       ++ e+ +++ +a++++   +  el+++  +++++l e   e  +l+ +k++  ++++r+ +ei +++ek+ ev eel
  gi|313127260|ref|YP_004037530.1| 384 KTKETELAEVEAEIDSVDTEFDELKDELAAKKSQLEElktERNDLQREKDRLLDDTRRRSSEISETQEKISEVREEL 460
                                       ******************************999864321155567777777778*********************** PP

                            DUF812 466 rqkeellkqLvaeleklpkdv 486
                                        + + +l+ L +el+k++k++
  gi|313127260|ref|YP_004037530.1| 461 PTLKAKLSDLHSELDKAEKNK 481
                                       *****************9976 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.083
                            DUF812 313 elakkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktle 389
                                       + ++ +et+e + + re el +l+ ++++l+s++++ e++ +k++  i+ + e    +k+   e e+e++ k+  ++
  gi|313127260|ref|YP_004037530.1| 442 RSSEISETQEKISEVRE-ELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRSKQSEYA 517
                                       22244555555555555.77777777777777777777777777777777777777777777777777777766555 PP

                            DUF812 390 l 390
                                        
  gi|313127260|ref|YP_004037530.1| 518 E 518
                                       5 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 2.6e-06
                            DUF812 316 kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevk.lkkk...tl 388
                                        + ++ e+ + + e+e++++++q++++++k++  ++ ++++e++i ++ee +ee+k+e e+le+ ++ l++k   + 
  gi|313127260|ref|YP_004037530.1| 702 VEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEeLREKraeVD 778
                                       456678888999999**********************************************9987642344411144 PP

                            DUF812 389 ellpdaeeniekLqalveasaqrlvelakqWekhRvpli....eeyrelkesksekekeaerkleeikklrekmkev 461
                                       e +++ ++ i +L a++++ ++++ el+++    ++p +    +e+r+  e+k+++++e   +l+e++  +e  +++
  gi|313127260|ref|YP_004037530.1| 779 EEMQSLDTDIDALTADIDDVQSEIDELESELADSKIPELtaqaDEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDA 855
                                       56788999999999999999999999999999999886533336889999999999999999999999999999888 PP

                            DUF812 462 aeelrqkeellk 473
                                       +e+l +  e+ +
  gi|313127260|ref|YP_004037530.1| 856 IEDLNETVESAQ 867
                                       888877666554 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6  12.6       8.7   3.3e+03       9      60 ..     202     254 ..     200     257 .. 0.78
   2 ?    0.9  10.1       1.4   5.4e+02      19      68 ..     255     302 ..     250     311 .. 0.57
   3 !    9.4   3.7    0.0033       1.2       7      54 ..     317     366 ..     314     372 .. 0.73
   4 !    8.0   9.1    0.0092       3.4      13      60 ..     379     421 ..     370     438 .. 0.75
   5 ?   -0.9  12.2       5.4     2e+03      10      68 ..     453     520 ..     424     522 .. 0.65
   6 !   11.5   5.0   0.00073      0.27       9      65 ..     696     754 ..     693     755 .. 0.89
   7 !   17.4  12.4     1e-05    0.0039       6      62 ..     756     807 ..     754     808 .. 0.93
   8 !   17.0   6.8   1.4e-05    0.0054      10      67 ..     788     838 ..     782     840 .. 0.91
   9 ?   -0.5   5.5         4   1.5e+03      11      54 ..     948     990 ..     943    1020 .. 0.76
  10 ?    0.6   0.6       1.8   6.6e+02      10      26 ..    1021    1037 ..    1017    1059 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 8.7
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdp.eklaelsaeleeleaeLeel 60 
                                       ele +e++Ie+ + +i+e e +l + e       k + l +e ee e  L+++
  gi|313127260|ref|YP_004037530.1| 202 ELESVEERIEEADLRIEEKESRLDQLEDERETaLKYQSLREEREEYEGYLKAA 254
                                       89*******************99988744333366888888888887777766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.4
                      ABC_tran_CTD  19 aLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeLe 68 
                                       +LE + a+le   +++e  ++ ekl  l +el++ +    +l+++  eL+
  gi|313127260|ref|YP_004037530.1| 255 ELEDKRADLERTESKAE--TKAEKLESLREELDTRQGRVSRLEAELDELS 302
                                       55666666666666665..5555555555555555555555555555554 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0033
                      ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleele 54 
                                       + e+e +  eI++LE+ i++ e+++ ++e   +    +l + ++ ++++e
  gi|313127260|ref|YP_004037530.1| 317 KSEIESVKGEIDRLENAIEAAEDRIDEAETERRKafVELDRKQEMIDDVE 366
                                       679999********************999552222455555555555555 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0092
                      ABC_tran_CTD  13 leaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60 
                                       + +eI   E+e+ae+eae+ + +     +++ el  el++ +++Leel
  gi|313127260|ref|YP_004037530.1| 379 VKSEIKTKETELAEVEAEIDSVD-----TEFDELKDELAAKKSQLEEL 421
                                       56778888888888888888777.....77788888888888888776 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 5.4
                      ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpek....laelsae...........leeleaeLeelyerWeeLe 68 
                                       + e+ +e+  L +++++l+ el ++e  ++ +k    +                 l+e+e+eL  + +++ eLe
  gi|313127260|ref|YP_004037530.1| 453 ISEVREELPTLKAKLSDLHSELDKAE--KNKQKidgvIE----DlredrsdlksdLDEVEDELRSKQSEYAELE 520
                                       45555555555555555555555555..44444333322....1222344444449999999999999999998 PP

  == domain 6  score: 11.5 bits;  conditional E-value: 0.00073
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelyerWe 65 
                                       +le+l  eI  LE +  e+e+e+ d e   d+  ek +++  +   +ea++++++e  e
  gi|313127260|ref|YP_004037530.1| 696 RLERLAVEISDLEDDRREIEQEIRDIESQLDDarEKASDAADRVRSVEADIDRAEEDVE 754
                                       58999999**************999999955559********************99755 PP

  == domain 7  score: 17.4 bits;  conditional E-value: 1e-05
                      ABC_tran_CTD   6 eqreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62 
                                       ++ e+e+le++Ie+L e+ ae+++e+++ +     + + +l+a ++++++e++el++
  gi|313127260|ref|YP_004037530.1| 756 KKAEIEQLEDRIEELREKRAEVDEEMQSLD-----TDIDALTADIDDVQSEIDELES 807
                                       6899***********************888.....789****************987 PP

  == domain 8  score: 17.0 bits;  conditional E-value: 1.4e-05
                      ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeL 67 
                                       +++l a+I+  + ei ele elad        k+ el+a+ +e++ae+ee+++r  eL
  gi|313127260|ref|YP_004037530.1| 788 IDALTADIDDVQSEIDELESELADS-------KIPELTAQADEIRAEIEEKEDRMDEL 838
                                       6889999****************87.......599*******************9998 PP

  == domain 9  score: -0.5 bits;  conditional E-value: 4
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaelea.eladpelysdpeklaelsaeleele 54 
                                       e+l  eI++LE+e  e +  e+ d +  + +e +++l+ ++e le
  gi|313127260|ref|YP_004037530.1| 948 ERLAWEIDELEAEVGEYDPeEIPDHD--EVQENIQQLTGKMESLE 990
                                       67777899999999999853666666..55577888888888887 PP

  == domain 10  score: 0.6 bits;  conditional E-value: 1.8
                      ABC_tran_CTD   10 leeleaeIeaLEeeiae 26  
                                         + + ++Ie+ E++++e
  gi|313127260|ref|YP_004037530.1| 1021 RQGIQDRIEQFEAQKKE 1037
                                        4568999****999987 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   7.2       9.6   3.6e+03     103     138 ..     202     237 ..     189     255 .. 0.65
   2 ?    3.9  18.5      0.15        56     100     181 ..     266     348 ..     251     350 .. 0.63
   3 ?    2.7  11.6      0.33   1.2e+02     102     180 ..     318     396 ..     310     398 .. 0.80
   4 !    8.3  14.4    0.0067       2.5     110     186 ..     354     437 ..     351     439 .. 0.77
   5 !   11.3  24.0   0.00081       0.3      74     184 ..     409     519 ..     405     523 .. 0.96
   6 !   18.5  17.8   4.9e-06    0.0018      73     175 ..     708     810 ..     685     814 .. 0.91
   7 ?    6.6   6.0     0.021         8     103     158 ..     813     868 ..     810     873 .. 0.93
   8 ?    1.6  22.8      0.73   2.7e+02      70     149 ..     885     964 ..     871    1028 .. 0.61
   9 ?   -0.3   0.7       2.9   1.1e+03     139     180 ..     979    1020 ..     962    1046 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.6
                             ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletk 138
                                        l +++e +++ + +++e+e+rl++le+er++  + 
  gi|313127260|ref|YP_004037530.1| 202 ELESVEERIEEADLRIEEKESRLDQLEDERETALKY 237
                                       456677777777777777777777777777665433 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                             ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdr..eeelrekeklvqdlqDElsaLqlqlnqaEekl 174
                                       ++++  ++ e+l+ l+e+l +++ r+ +leae  +l+++++++  +e+lr k   ++ ++ E++ L+ + + aE++ 
  gi|313127260|ref|YP_004037530.1| 266 TESKAETKAEKLESLREELDTRQGRVSRLEAELDELSKEIERKgeDEQLRIKS-EIESVKGEIDRLENAIEAAEDRI 341
                                       33444455566666666666666666666666666666654432134444433.456******************** PP

                             ATG16 175 rklekEN 181
                                       ++ e+E 
  gi|313127260|ref|YP_004037530.1| 342 DEAETER 348
                                       9999985 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.33
                             ATG16 102 qrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrkle 178
                                       + + +++ e+++le+ +++ e r++e+e+er++   +l++++e + + e  + +++ E ++ + + +  E +l ++e
  gi|313127260|ref|YP_004037530.1| 318 SEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVE 394
                                       56677778888888888888888888888888888888888888888888888888888888888888888888888 PP

                             ATG16 179 kE 180
                                       +E
  gi|313127260|ref|YP_004037530.1| 395 AE 396
                                       87 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0067
                             ATG16 110 elqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq.......dlqDElsaLqlqlnqaEeklrklek 179
                                       el++++e +   e  +++++ e+a+++ ++k +e el+e e+ ++       +l+DEl+a + ql+ +  ++++l++
  gi|313127260|ref|YP_004037530.1| 354 ELDRKQEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDsvdtefdELKDELAAKKSQLEELKTERNDLQR 430
                                       56677777777777777777777777777777777777777777766666669999999999999999999999999 PP

                             ATG16 180 ENkeLve 186
                                       E   L++
  gi|313127260|ref|YP_004037530.1| 431 EKDRLLD 437
                                       9999987 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00081
                             ATG16  74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelreke 150
                                       +++++ +++l +l++e  +l++++  l +  ++ ++e+++ +ek++e +e+l  l+a+ ++l  +l++ e++ +  +
  gi|313127260|ref|YP_004037530.1| 409 DELAAKKSQLEELKTERNDLQREKDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKID 485
                                       67889999********************************************************************* PP

                             ATG16 151 klvqdlqDElsaLqlqlnqaEeklrklekENkeL 184
                                        +++dl+++ s L+  l  +E++lr  + E +eL
  gi|313127260|ref|YP_004037530.1| 486 GVIEDLREDRSDLKSDLDEVEDELRSKQSEYAEL 519
                                       *******************************999 PP

  == domain 6  score: 18.5 bits;  conditional E-value: 4.9e-06
                             ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                       +++  + eq++  + ++l ++  + ++ a+r++++++ +++ ee  +e+++++++le+++++l++k+++ +ee++ +
  gi|313127260|ref|YP_004037530.1| 708 EDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSL 784
                                       56667899********************************************************************* PP

                             ATG16 150 eklvqdlqDElsaLqlqlnqaEeklr 175
                                       ++ +++l  +++  q +   +E++l 
  gi|313127260|ref|YP_004037530.1| 785 DTDIDALTADIDDVQSEIDELESELA 810
                                       *****999999999999999999876 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.021
                             ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqD 158
                                       ++ el+++ ++ +++++e+e r++el  + ++l+ + +  e+++++++++v+  qD
  gi|313127260|ref|YP_004037530.1| 813 KIPELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQD 868
                                       6789999**********************************************999 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.73
                             ATG16  70 skqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeel 146
                                       ++++a +++  ++++ l +el+el  +r++l + ++e+++e +++++k ++ e+r+++l+++ ++l  +++++e+e+
  gi|313127260|ref|YP_004037530.1| 885 EEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELEAEV 961
                                       23445555555566666666666666666666666666666666666666666666666666666666666666665 PP

                             ATG16 147 rek 149
                                        e 
  gi|313127260|ref|YP_004037530.1| 962 GEY 964
                                       554 PP

  == domain 9  score: -0.3 bits;  conditional E-value: 2.9
                             ATG16  139 lkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekE 180 
                                        +++++ +++ +e ++    DE++  q  l+ + + ++ l +E
  gi|313127260|ref|YP_004037530.1|  979 IQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDVLAEE 1020
                                        333333333333333333333333333333333333333222 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7  16.3   0.00013     0.049       2     105 ..     326     432 ..     325     442 .. 0.89
   2 !    8.8   3.1    0.0044       1.7      58     116 ..     445     499 ..     439     500 .. 0.55
   3 ?    2.3   0.3      0.45   1.7e+02      91     115 ..     704     728 ..     696     730 .. 0.57
   4 !   18.3  18.7   5.1e-06    0.0019       2     116 ..     724     839 ..     723     844 .. 0.97
   5 ?    7.5  26.5     0.011         4       3     110 ..     842     949 ..     840     963 .. 0.85
   6 ?    0.4   1.2       1.7   6.3e+02      61     110 ..    1002    1033 ..     967    1041 .. 0.40

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00013
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       e+++le+ i++++++++eae++ +k+  +l  ++e   + +++     v++a+   e+++  +el+e++aei ++ +
  gi|313127260|ref|YP_004037530.1| 326 EIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDSVDT 402
                                       7899************************************************************************* PP

                        TPR_MLP1_2  79 eaesakaeleeseesweeqkee...lekel 105
                                       e +++k el+++++++ee k+e   l++e+
  gi|313127260|ref|YP_004037530.1| 403 EFDELKDELAAKKSQLEELKTErndLQREK 432
                                       *************99988654401155544 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0044
                        TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedln 116
                                       e++++ e+++e+++e+ +lka++ ++++el+++e    + k++++  +++l++ + dl+
  gi|313127260|ref|YP_004037530.1| 445 EISETQEKISEVREELPTLKAKLSDLHSELDKAE----KNKQKIDGVIEDLREDRSDLK 499
                                       4444455555555555555555555555554443....456677777777777777765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.45
                        TPR_MLP1_2  91 eesweeqkeelekelselekriedl 115
                                        + +e  + e+e+e++++e++++d 
  gi|313127260|ref|YP_004037530.1| 704 ISDLEDDRREIEQEIRDIESQLDDA 728
                                       3445566666666666666666665 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 5.1e-06
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       +l+ ++e+++++ ++  + ea++  ++ed+e+++++ ++ +++ e+   k ae  +e+q+l ++++ l+a+i ++++
  gi|313127260|ref|YP_004037530.1| 724 QLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLDTDIDALTADIDDVQS 800
                                       788999*********************************************************************** PP

                        TPR_MLP1_2  79 eaesakaeleesee.sweeqkeelekelselekriedln 116
                                       e +++++el+ s+  +++ q +e++ e++e e r+++l+
  gi|313127260|ref|YP_004037530.1| 801 EIDELESELADSKIpELTAQADEIRAEIEEKEDRMDELD 839
                                       ***********996589********************97 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.011
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       l++l+ e++ +++ +e+++++++++q+     ++  +e +q  e+     +e  +++++l +el+elkae+++l+++
  gi|313127260|ref|YP_004037530.1| 842 LNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDLRED 918
                                       68999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelselek 110
                                       + +ak+e +e++ + e+ +++ e+  +++e+
  gi|313127260|ref|YP_004037530.1| 919 VREAKSERDEQRDKVERVESRVENLRESAER 949
                                       9999999999999998888777665555544 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.7
                        TPR_MLP1_2   61 alreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselek 110 
                                        ++ ++l++l+                    +  ++e+++ ++++++++e+
  gi|313127260|ref|YP_004037530.1| 1002 EVQADLEDLQ------------------DGRDVLAEERQGIQDRIEQFEA 1033
                                        2222222222..................2222223333333333333322 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  20.3     0.015       5.4     698     815 ..     190     311 ..     176     314 .. 0.82
   2 !   12.7  19.3   7.3e-05     0.027     691     811 ..     307     434 ..     303     442 .. 0.85
   3 !    8.2  17.9    0.0017      0.62     688     801 ..     409     522 ..     405     526 .. 0.95
   4 !   11.7  12.1   0.00014     0.052     687     792 ..     708     813 ..     688     815 .. 0.85
   5 !    9.8  20.6   0.00054       0.2     713     817 ..     816     919 ..     811     935 .. 0.85
   6 ?   -2.2   7.0       2.4   8.8e+02     734     813 ..     907     990 ..     905    1019 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                               FPP 698 eelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesy.esletratelea. 772
                                        e +++ke+   el+s +e++e++ ++++e+E  l++l+ e e++ + +sl e+  + +  ++  +le + ++le  
  gi|313127260|ref|YP_004037530.1| 190 AEFDAKKEDAFGELESVEERIEEADLRIEEKESRLDQLEDERETALKYQSLREEREEYEGYLKaAELEDKRADLERt 266
                                       577899************************************99999999999987776554425687776666550 PP

                               FPP 773 ..elnelkqkieaLeveLeeekksheeleakckelqeqlervekk 815
                                         + +   +k+e+L +eL++++     lea+  el + +er+ ++
  gi|313127260|ref|YP_004037530.1| 267 esKAETKAEKLESLREELDTRQGRVSRLEAELDELSKEIERKGED 311
                                       0044445567778889************************98765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.3e-05
                               FPP 691 kllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesl.... 763
                                       ++ ++e  ++kse e ++ e+ + ++ +e++  ++ e E    +   eL++ +e    +e++++  k+ + s+    
  gi|313127260|ref|YP_004037530.1| 307 RKGEDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEKASVksei 383
                                       56689999******************************************************997765544432222 PP

                               FPP 764 ...etrateleaelnelkqkieaLeveLeeekksheeleakckelqeqler 811
                                          et ++e+eae+ ++ +++++L+ eL  +k+  eel+++ ++lq   +r
  gi|313127260|ref|YP_004037530.1| 384 ktkETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDR 434
                                       2225667778999999999***************************98777 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0017
                               FPP 688 eenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesle 764
                                       +e   +k +leelk e+++l+ e  +  ++     + ++e+ ++++e+++eL +lk   s + ++l++ +  +++++
  gi|313127260|ref|YP_004037530.1| 409 DELAAKKSQLEELKTERNDLQREKDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKID 485
                                       566778999******************************************************************** PP

                               FPP 765 trateleaelnelkqkieaLeveLeeekksheeleak 801
                                          ++l+++ + lk+ ++++e eL ++++ + elea+
  gi|313127260|ref|YP_004037530.1| 486 GVIEDLREDRSDLKSDLDEVEDELRSKQSEYAELEAR 522
                                       **********************************998 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00014
                               FPP 687 keenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesl 763
                                       ++ ++  ++e+++++s+ ++   + ++a +++ s+ a +   E+ ++e k+e+e+l++  + + ++  +  e  +sl
  gi|313127260|ref|YP_004037530.1| 708 EDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSL 784
                                       456778899***********************************************98765555555555566677* PP

                               FPP 764 etrateleaelnelkqkieaLeveLeeek 792
                                       +t    l+a++  ++++i++Le+eL + k
  gi|313127260|ref|YP_004037530.1| 785 DTDIDALTADIDDVQSEIDELESELADSK 813
                                       *************************9976 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00054
                               FPP 713 satenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLe 789
                                       + t++ +++ a ++e+E  ++el   L++l+  k+ ae+ ++  +e+ es + r++++++ ++e +q ie+ e+ Le
  gi|313127260|ref|YP_004037530.1| 816 ELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLE 892
                                       66889999********************************************************************* PP

                               FPP 790 eekksheeleakckelqeqlervekkev 817
                                       e++++  +lea+ kel+      ++ +v
  gi|313127260|ref|YP_004037530.1| 893 EKREAVSDLEAELKELKAERSDLRE-DV 919
                                       ****************976554442.22 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 2.4
                               FPP 734 elkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLee....ekksheeleakckelq 806
                                       elk+e + l+e  + a ++ +++    e +e+r ++l++  ++l  +i++Le+e+ e    e   h e + ++++l 
  gi|313127260|ref|YP_004037530.1| 907 ELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELEAEVGEydpeEIPDHDEVQENIQQLT 983
                                       55555555555555555555566666666666666666666666666666666665311114445666666666666 PP

                               FPP 807 eqlerve 813
                                        ++e+ e
  gi|313127260|ref|YP_004037530.1| 984 GKMESLE 990
                                       6666665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8  18.9   5.7e-06    0.0021       1     278 [.       1     414 [.       1     419 [. 0.53
   2 ?   -1.0   6.5         3   1.1e+03     201     272 ..     716     806 ..     693     831 .. 0.40
   3 ?   -0.4  21.1       1.9   7.1e+02      63     364 ..     744    1154 ..     724    1159 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.7e-06
                            AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...................... 54 
                                       M Ik++ +  F+s+   + i++ e++tv+ G+N+sGKS+i++   + l    +                        
  gi|313127260|ref|YP_004037530.1|   1 MHIKELVLDGFKSFGRkTRIPFYEDFTVVTGPNGSGKSNIIDGVLFALG-LARTRgiraekltdliynpghadaese 76 
                                       99************777**************************944444.434446788899999999999888888 PP

                            AAA_15  55 ...........................................kkvikiekedleifeniseskdikIdvef..... 83 
                                                                                  k                                 
  gi|313127260|ref|YP_004037530.1|  77 raggtkeasvtvildnsdgkldrsqvinaagsddvgdvseirvK---------------------------Rrvket 126
                                       88888888888888885555555444444444444444444440...........................355555 PP

                            AAA_15  84 ....................................................................aekekakey 92 
                                                                                                           +  +++   
  gi|313127260|ref|YP_004037530.1| 127 denyysyyylngrscnlsdiqdllaqagitpegynvvmqgdvteiinmtpyqrrgiideiagvaefdaK--KEDAFG 201
                                       555666666666666666666667777777777888888888888888888888888888888765330..333333 PP

                            AAA_15  93 ektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedl 169
                                       e ++ ++++++adl +++kes+l+++  +++++lk + l  e+ ++e   ++    + k+ +le  + + +++ e+l
  gi|313127260|ref|YP_004037530.1| 202 ELESVEERIEEADLRIEEKESRLDQLEDERETALKYQSLREEREEYEGYLKAA-ELEDKRADLERTESKAETKAEKL 277
                                       44455566677777777777777777777777776444433333322222222.22233333333444444444444 PP

                            AAA_15 170 kklikkleeslkkee..............elknvlksaiiklllisakRnvsd.edsekkssllgklkekileealq 231
                                       ++l ++l       +              el++ ++ + ++ +l  +    s   + +  +++++++ ++i e    
  gi|313127260|ref|YP_004037530.1| 278 ESLREEL-------DtrqgrvsrleaeldELSKEIERKGEDEQLRIKSEIESVkGEIDRLENAIEAAEDRIDEA-ET 346
                                       4444433.......222233445666666444444444444444333333333122222222222222222222.11 PP

                            AAA_15 232 ekl...................eeelteklkeiqeklkeidkklaeelk..kilkkkidkikkfnykg 278
                                       e+                    +  ++ +  ++++++k+++ +lae ++  ++++  +d++k++ + +
  gi|313127260|ref|YP_004037530.1| 347 ERRkafveldrkqemiddveddIRAVKVEKASVKSEIKTKETELAEVEAeiDSVDTEFDELKDELAAK 414
                                       11123333333333322222221111222222222222222222222223355555555555554444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                            AAA_15 201 sakRnvsdedsekkssllgklkekileealqekl......eeelteklkeiqeklkeidkklaeelk.......... 261
                                       ++ R++++++++  +++ +++++  + ea  +++      ++  +e+l++  e+l+e+  +++ee +          
  gi|313127260|ref|YP_004037530.1| 716 QEIRDIESQLDDAREKASDAADRVRSVEADIDRAeedveeKKAEIEQLEDRIEELREKRAEVDEEMQsldtdidalt 792
                                       33333333333333333333333333332222222232222222222222222222222222222223333332222 PP

                            AAA_15 262 ...kilkkkidkik 272
                                          +++++ id+++
  gi|313127260|ref|YP_004037530.1| 793 adiDDVQSEIDELE 806
                                       23333333333333 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.9
                            AAA_15   63 edleifeniseskdikIdvef..aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdek 135 
                                         d++  e++ e+k+ +I+  +  +e+  +k  e+ ++++  + +   l+  ++d ++ i + + +l  +++   +
  gi|313127260|ref|YP_004037530.1|  744 ADIDRAEEDVEEKKAEIEQLEdrIEELREKRAEVDEEMQSLDTDIDALTADIDDVQSEIDELESELADSKIPELT 818 
                                        555666666666666666555331223344444444444444555556667778888888888888888888899 PP

                            AAA_15  136 isvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee.......................... 184 
                                         +++++ ++ e ++ + ++l+ + +el+++ke +++ i++l+e +++ +                          
  gi|313127260|ref|YP_004037530.1|  819 AQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQdrkadardvirekeqaieekeavlee 893 
                                        99999999999999999999*************************999999******999999999988888888 PP

                            AAA_15  185 .......elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl..............eeel 238 
                                               +  ++ + +++ ++l +++R++++e++e+ +++     +  +   ++e+l              + e 
  gi|313127260|ref|YP_004037530.1|  894 kreavsdLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLaweideleaevgeyDPEE 968 
                                        888888544455555677788888888888877777665543333333333344555889999999999997777 PP

                            AAA_15  239 teklkeiqeklkeidkklaeelk............................kilkkkidkikkfnykgkkneeie 285 
                                        + + +e+qe+++++ +k+ e+l+                            ++ + + d i++f++++k+ +   
  gi|313127260|ref|YP_004037530.1|  969 IPDHDEVQENIQQLTGKM-ESLEpvnmlaideydevqadledlqdgrdvlaEERQGIQDRIEQFEAQKKETFMEA 1042
                                        777788888888888887.44445777777888777777777777777777444444444444444444333333 PP

                            AAA_15  286 ik........................................ddeelplnknGsGvqrllllillileaekkdek 320 
                                        +                                         d+  + l+ ++ G ++l  l++  +  + +   
  gi|313127260|ref|YP_004037530.1| 1043 FDaindnftdiferlsngtgelhlenpedpfeegltmkaqpgDKPIQRLDAMSGGEKSLTALAFIFAIQRHN--- 1114
                                        225556667777777777777888888888889999999999999999999999999988888755444444... PP

                            AAA_15  321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364 
                                          +  +++++E +a L   + + + +   +la     Q ++ +H
  gi|313127260|ref|YP_004037530.1| 1115 --PAPFYALDEVDAFLDAANAERVGEMVDDLAGRA--QFVVVSH 1154
                                        ..888999999888887777777777777777777..7777777 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   4.5     0.092        34      41      98 ..     308     369 ..     288     372 .. 0.72
   2 ?    5.5   7.7     0.025       9.2      19      90 ..     363     434 ..     351     441 .. 0.64
   3 !    9.1   8.8     0.002      0.73      20      98 ..     378     460 ..     371     461 .. 0.85
   4 !   17.4   4.8   5.8e-06    0.0022      21      92 ..     435     506 ..     429     511 .. 0.91
   5 !    9.7   3.3    0.0013      0.48      38      90 ..     703     755 ..     698     758 .. 0.94
   6 !    9.6   6.7    0.0014      0.51      17      82 ..     745     810 ..     743     818 .. 0.63
   7 ?    2.2  11.8      0.25        95      15      93 ..     818     896 ..     811     908 .. 0.74
   8 ?    4.4   8.9     0.052        19      25      93 ..     891     959 ..     882     966 .. 0.77
   9 ?    1.4   3.2      0.44   1.6e+02      34      97 ..     974    1037 ..     966    1047 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.092
                           DUF3450  41 klddekqellaeyralkeeleslevyneqlerlvasqeqeia....sleeqieeieeierel 98 
                                       k +de+  +++e++++k e+++le   e  e+ ++++e+e+     +l++++e i+ +e+++
  gi|313127260|ref|YP_004037530.1| 308 KGEDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRkafvELDRKQEMIDDVEDDI 369
                                       45788889999999999999999999999999999998886522225677777777766665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                           DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       d++++  ++   ++a++ ++i+  + e +e++ae+ ++ +e ++l+ + +  +++++++++e+++l++++++
  gi|313127260|ref|YP_004037530.1| 363 DDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDR 434
                                       555555555566666666666666666666666666666666666666666666666666666666666654 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.002
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqle....rlvasqeqeiasleeqieeie 92 
                                       ++++e +   ++ a+++++id++d e +el++e+ a k++le+l+ +++ l+    rl+++ +++ +++ e +e+i+
  gi|313127260|ref|YP_004037530.1| 378 SVKSEIKTKETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQrekdRLLDDTRRRSSEISETQEKIS 454
                                       567777888888999*******************************9988872222588999999999999999999 PP

                           DUF3450  93 eierel 98 
                                       e+++el
  gi|313127260|ref|YP_004037530.1| 455 EVREEL 460
                                       999886 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 5.8e-06
                           DUF3450  21 alkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       +l+ +++  ++ +++q+ki+++ +e  +l+a++ +l++el+++e+ +++ + +++++++++++l+ +++e+e
  gi|313127260|ref|YP_004037530.1| 435 LLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVE 506
                                       56666677777899********************************************************98 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0013
                           DUF3450  38 kidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       +i++l+d+++e+++e+r+++++l++++ + +  ++ v+s+e++i++ ee+ ee
  gi|313127260|ref|YP_004037530.1| 703 EISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEE 755
                                       6999******************************************9998876 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0014
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeia 82 
                                       ++d a++  e+  a+ +q + +i++l ++++e+ +e+++l + +++l++  + +++ ++++e+e+a
  gi|313127260|ref|YP_004037530.1| 745 DIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLDTDIDALTADIDDVQSEIDELESELA 810
                                       555666666666666666666666666666666666666666666666666666666666666665 PP

  == domain 7  score: 2.2 bits;  conditional E-value: 0.25
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                        a++d++++e e+  +   +   + ++l+ ek+  ++ +++l+e +es++  ++  ++++++ eq i++ e  +ee 
  gi|313127260|ref|YP_004037530.1| 818 TAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLEEK 894
                                       56788888888888888888888888888888888888888888888888888888888888888888877666654 PP

                           DUF3450  92 ee 93 
                                       +e
  gi|313127260|ref|YP_004037530.1| 895 RE 896
                                       44 PP

  == domain 8  score: 4.4 bits;  conditional E-value: 0.052
                           DUF3450  25 aekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                        e+  +a ++ +++ ++l+ e+++l +++r++k+e ++ + + e++e+ v++++++ ++l  +i+e+e+
  gi|313127260|ref|YP_004037530.1| 891 LEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELEA 959
                                       455555666677788888888899999999999999999999999999999999988888888888875 PP

  == domain 9  score: 1.4 bits;  conditional E-value: 0.44
                           DUF3450   34 qsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeiere 97  
                                        ++q++i++l+ + ++l+     + +e ++ ++  e l++  + + +e++ ++ +ie++e+ ++e
  gi|313127260|ref|YP_004037530.1|  974 EVQENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEAQKKE 1037
                                        6788888888888888888888888888888888888888888888888888888888776665 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   5.1      0.89   3.3e+02      38     129 ..     204     302 ..     190     307 .. 0.60
   2 !    8.9   7.5    0.0044       1.6      31     130 ..     314     416 ..     308     421 .. 0.91
   3 ?    3.4   5.3      0.21        78      41     107 ..     450     512 ..     416     523 .. 0.43
   4 !   18.0   8.9     7e-06    0.0026      26     125 ..     707     809 ..     703     814 .. 0.84
   5 ?    6.7   9.1     0.021       7.7      32     128 ..     830     929 ..     819     932 .. 0.83
   6 ?    6.5   8.5     0.024       9.1      32     124 ..     851     946 ..     845     967 .. 0.72
   7 ?    5.4   3.3     0.052        19      34     122 ..     895     990 ..     890     998 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.89
                                       CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHH..HHHHH...HCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdn..dnvikks..skele...eeilrlketidaqesnirvL 107
                                       e++e+++ee+  + +e e+   +++d  + + k ++     + ++ +  + ele    + +r + +  ++ ++++ L
  gi|313127260|ref|YP_004037530.1| 204 ESVEERIEEADLRIEEKESRLDQLEDERETALKYQSLReeREEYEGYlkAAELEdkrADLERTESKAETKAEKLESL 280
                                       5555555555555555555555555555444443332112222222211223330003556777888899999**** PP

                                       HHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 108 qnvlesneqkiqkLeqdidqke 129
                                       ++ l++ + ++++Le + d++ 
  gi|313127260|ref|YP_004037530.1| 281 REELDTRQGRVSRLEAELDELS 302
                                       ***************9988876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0044
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...CCCHHHHHHHCCHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee...eilrlketidaqesni 104
                                         +k ++e+++ e+++++n  + ae+ + e ++  r++  + + ++++i +++++++    e + +k +i+++e+++
  gi|313127260|ref|YP_004037530.1| 314 LRIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDIRAvkvEKASVKSEIKTKETEL 390
                                       568999*************************************99********99985333678899********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 105 rvLqnvlesneqkiqkLeqdidqker 130
                                        +    ++s + +  +L+ + ++k++
  gi|313127260|ref|YP_004037530.1| 391 AEVEAEIDSVDTEFDELKDELAAKKS 416
                                       *******************9999876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.21
                                       CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  41 eneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                       +++++e++++  + +   +++++ l +++k    n++ i  + ++l+e+ ++lk  +d+ e ++r  
  gi|313127260|ref|YP_004037530.1| 450 QEKISEVREELPTLKAKLSDLHSELDKAEK----NKQKIDGVIEDLREDRSDLKSDLDEVEDELRSK 512
                                       222222222222222222222222222222....233444444444444455555555544444444 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 7e-06
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HCCCHHHHHHHC CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskele...eeilrlketida 99 
                                       l++ +++++++++++e++l++++++ ++a + v++++  + ++++  ++++  i+++++++e   e+ ++++e++++
  gi|313127260|ref|YP_004037530.1| 707 LEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEelrEKRAEVDEEMQS 783
                                       56678999*******************************99999999999999999887655111566667777777 PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 100 qesnirvLqnvlesneqkiqkLeqdi 125
                                         + i +L+  +++ +++i +Le++ 
  gi|313127260|ref|YP_004037530.1| 784 LDTDIDALTADIDDVQSEIDELESEL 809
                                       7778999***************9875 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.021
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH...HHCCHHHHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlket...idaqesnir 105
                                       + ++++++l  +l+e++ +++ ae+ +++++++++++q  k+d   vi++ ++ +ee+ + l+e+   +++ e +++
  gi|313127260|ref|YP_004037530.1| 830 EKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLEEKreaVSDLEAELK 906
                                       5678999*************************************************998888765333777778889 PP

                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 106 vLqnvlesneqkiqkLeqdidqk 128
                                       +L+   +++++++ + +++ d++
  gi|313127260|ref|YP_004037530.1| 907 ELKAERSDLREDVREAKSERDEQ 929
                                       99888888888887777766666 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.024
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...CCCHHHHHHHCCHHHHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee...eilrlketidaqesnir 105
                                         ++ +e+l++++e++++++ +a+++++e ++ ++ek++  +++ +++++++ el+e   e ++l+e + +  s+  
  gi|313127260|ref|YP_004037530.1| 851 YAEDAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLEEKREAVSDLEAELKElkaERSDLREDVREAKSERD 927
                                       457789********************************999998888877776554211155555555555555555 PP

                                       HHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 106 vLqnvlesneqkiqkLeqd 124
                                       + ++ +e+ e+++++L++ 
  gi|313127260|ref|YP_004037530.1| 928 EQRDKVERVESRVENLRES 946
                                       5555555555555555544 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.052
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHCCH.HHH.. CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketidaqe.sni.. 104
                                       ++ +++le el+e++ + ++ +e v+e k+   e+  + +      + +++s+++l  ei +l++++ +   ++i  
  gi|313127260|ref|YP_004037530.1| 895 REAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVesrVENLRESAERLAWEIDELEAEVGEYDpEEIpd 971
                                       578999***************99999999887776666665422355566777888889999999999887777744 PP

                                       .HHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 105 .rvLqnvlesneqkiqkLe 122
                                         + q++++++  k++ Le
  gi|313127260|ref|YP_004037530.1| 972 hDEVQENIQQLTGKMESLE 990
                                       4689999999999999998 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2       2.1   7.8e+02       6      49 ..     197     239 ..     194     249 .. 0.83
   2 !    9.0   5.6    0.0036       1.4      24     100 ..     254     328 ..     251     341 .. 0.82
   3 ?    1.7   6.0      0.64   2.4e+02      13      73 ..     377     437 ..     358     445 .. 0.65
   4 !   12.5   3.5   0.00031      0.11      10      77 ..     444     511 ..     438     521 .. 0.86
   5 !   14.4   4.8   7.9e-05     0.029      15      82 ..     707     774 ..     697     776 .. 0.84
   6 !   10.1   4.3    0.0016      0.61       5      68 ..     746     809 ..     742     819 .. 0.90
   7 ?    3.8   6.1      0.14        54      13     102 ..     775     866 ..     772     869 .. 0.65
   8 ?    3.3   8.8      0.21        77       4      96 ..     820     909 ..     812     911 .. 0.84
   9 !    7.9   1.0    0.0079         3       3      71 ..     917     989 ..     915     995 .. 0.79
  10 ?    0.1   0.1       1.9   7.2e+02      12      60 ..    1000    1049 ..     993    1058 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.1
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkd 49 
                                       ++a   +++v+e +++ + ++e+ ++ l +++++ +et  k ++
  gi|313127260|ref|YP_004037530.1| 197 EDAFGELESVEERIEEADLRIEEKESRLDQLEDE-RETALKYQS 239
                                       5677788999999************999999999.888766665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0036
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....HHHHHHHHHHHH CS
                        Laminin_II  24 qnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.lsdniseikelI 99 
                                       ++le  +++l++ ++++e   ek++++ + ++  +  v+ Le ++++L +    ++ + e ++  ++ +i+ +k  I
  gi|313127260|ref|YP_004037530.1| 254 AELEDKRADLERTESKAETKAEKLESLREELDTRQGRVSRLEAELDELSKE---IERKGEDEQLrIKSEIESVKGEI 327
                                       689999**********99999**************************9877...66666665556777777777555 PP

                                       H CS
                        Laminin_II 100 a 100
                                        
  gi|313127260|ref|YP_004037530.1| 328 D 328
                                       4 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.64
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG CS
                        Laminin_II  13 kevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld 73 
                                       ++v++ ++  +++l ++++++ +++++ +e ++++ +++ ++++ +++  +L+++ ++Lld
  gi|313127260|ref|YP_004037530.1| 377 ASVKSEIKTKETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLD 437
                                       3455555555666677777777777777777777777777777777777777777777776 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00031
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklke 77 
                                       + ++e++e++ ++ ++l+ +k+kls +++++++ +++ ++   +i+d r+  ++L+  +++++d l++
  gi|313127260|ref|YP_004037530.1| 444 SEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRS 511
                                       55789999999999999999999999999999999999999999999999999999999999998875 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 7.9e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                        +++  +++q++  ++++l  +++++    + v++    i+ A++ v + + +++qL+d+++el++++
  gi|313127260|ref|YP_004037530.1| 707 LEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKR 774
                                       56777888999999999999999999999999999999999999999999999999999999999887 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.0016
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TT CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekla 68 
                                       ++ a+e ++e ++ +++l+ ++e+++ek  e++++++  + ++++++  i+d+++++ +Le ++
  gi|313127260|ref|YP_004037530.1| 746 IDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLDTDIDALTADIDDVQSEIDELESEL 809
                                       67889999999999999999***************************************99876 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.14
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  13 kevleqlaplsqnlentkeklseinrsveetnekvk.....dankairdArrsvkkLeklapqLldklkelkqleea 84 
                                       +ev e ++ l+++++ + +++  ++++++e + ++      +++ + ++ r ++ + e  +++L  +l+el+  +e 
  gi|313127260|ref|YP_004037530.1| 775 AEVDEEMQSLDTDIDALTADIDDVQSEIDELESELAdskipELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEY 851
                                       67778888888888888888888888877777666633222556666666677777777777777777777655544 PP

                                       ...HHHHHHHHHHHHHHH CS
                        Laminin_II  85 ssslsdniseikelIaqA 102
                                            d i+ + e ++ A
  gi|313127260|ref|YP_004037530.1| 852 ---AEDAIEDLNETVESA 866
                                       ...467777777777666 PP

  == domain 8  score: 3.3 bits;  conditional E-value: 0.21
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                        a+e+   ++e ++ + +l+ +l++++ + + +++ +e  ne v++a+   +dAr+ +++ e+    +++k   l++
  gi|313127260|ref|YP_004037530.1| 820 QADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQA---IEEKEAVLEE 893
                                       467777777777888999999**********************************999987765...5566666899 PP

                                       HHHH...HHHHHHHHH CS
                        Laminin_II  81 leeassslsdniseik 96 
                                       ++ea s l ++++e+k
  gi|313127260|ref|YP_004037530.1| 894 KREAVSDLEAELKELK 909
                                       9999888999999888 PP

  == domain 9  score: 7.9 bits;  conditional E-value: 0.0079
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXX--TTTTT CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdanka....irdArrsvkkLeklapqL 71 
                                       e ++ea++   e  ++++ ++ ++en++e++++++ +++e +++v ++        +++++++++L+ +++ L
  gi|313127260|ref|YP_004037530.1| 917 EDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELEAEVGEYDPEeipdHDEVQENIQQLTGKMESL 989
                                       6789999999*********************************999554321111466777777777766665 PP

  == domain 10  score: 0.1 bits;  conditional E-value: 1.9
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX CS
                        Laminin_II   12 akevleqlaplsqnlentkeklseinrsveetnekvk.dankairdArrs 60  
                                          ev+++l++l+   + + e+ ++i++ +e+ +++ k  +++a +  +++
  gi|313127260|ref|YP_004037530.1| 1000 YDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEAQKKeTFMEAFDAINDN 1049
                                        57899999999999999999999999999998877664566666665555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.6         2   7.5e+02      21      83 ..     192     252 ..     187     263 .. 0.73
   2 ?    5.6   5.4     0.022       8.3       4      86 ..     256     338 ..     250     345 .. 0.68
   3 ?    6.0   7.0     0.016       5.9       2      94 ..     318     416 ..     317     423 .. 0.89
   4 !   11.8   8.1   0.00029      0.11       5      98 ..     419     518 ..     415     520 .. 0.63
   5 !   11.8   5.6   0.00028      0.11       4      88 ..     697     780 ..     695     788 .. 0.89
   6 !   11.6   4.0   0.00032      0.12       3      92 ..     794     880 ..     788     890 .. 0.86
   7 !    7.5   3.6    0.0055       2.1       2      86 ..     903     987 ..     895     996 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2
                             TMPIT  21 ykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                       + +k e+ +   +++ ++i++   r++e +s+l++l+ +  +e++ ++++l+ee +e + +lk
  gi|313127260|ref|YP_004037530.1| 192 FDAKKEDAFGELESVEERIEEADLRIEEKESRLDQLEDE--RETALKYQSLREEREEYEGYLK 252
                                       556677777777888888888888888888888888877..5677777777777777666665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       +e+ + ++++ e++a++  +kle+l +  ++ + ++++ + +l el++++++  ++ + + ++e+e++k e+++ ++
  gi|313127260|ref|YP_004037530.1| 256 LEDKRADLERTESKAETKAEKLESLREELDTRQGRVSRLEAELDELSKEIERKGEDEQLRIKSEIESVKGEIDRLEN 332
                                       33444455556666666666777777777777778888888888888888888877777777778888888877777 PP

                             TMPIT  81 vlkeve 86 
                                        ++  e
  gi|313127260|ref|YP_004037530.1| 333 AIEAAE 338
                                       777655 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.016
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelk 72 
                                       +e+e+++ e+++le++ +  + +++e ++   k   e++++++++ +++++++ +k ++       + +e+e++e++
  gi|313127260|ref|YP_004037530.1| 318 SEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEKAsvkseiKTKETELAEVE 394
                                       689999***********************************************999985567777778888999999 PP

                             TMPIT  73 eelkerkkvlkevesllpkkng 94 
                                       +e+++ ++ ++e+++ l +k++
  gi|313127260|ref|YP_004037530.1| 395 AEIDSVDTEFDELKDELAAKKS 416
                                       9999999999999999998866 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00029
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeel 75 
                                       eel++e ++l+ +++++  ++++ s+ +s+++++i++ +++l  lk++l++l+++++      ++ +  +e+l+e+ 
  gi|313127260|ref|YP_004037530.1| 419 EELKTERNDLQREKDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDkaeknkQKIDGVIEDLREDR 495
                                       56666666666666666666666666666666666666666666666665555554433211145556788888888 PP

                             TMPIT  76 kerkkvlkevesllpkknglylk 98 
                                       ++ k+ l+eve+ l +k++ y +
  gi|313127260|ref|YP_004037530.1| 496 SDLKSDLDEVEDELRSKQSEYAE 518
                                       88889999*********999865 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00028
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       +e+l+ e+ +le+  +e++q++++++++ ++ +++++    r++++++++++ +++v ee++ e+e+l+++++e ++
  gi|313127260|ref|YP_004037530.1| 697 LERLAVEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDV-EEKKAEIEQLEDRIEELRE 772
                                       578899999*********************************************997.6899999****99999888 PP

                             TMPIT  81 vlkevesl 88 
                                         +ev++ 
  gi|313127260|ref|YP_004037530.1| 773 KRAEVDEE 780
                                       77776654 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00032
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       +++++++e++ele++     +k+ el+++ ++++ ei++++ r+ el+ +l++l+ + ke  e+++e+l+e++++++
  gi|313127260|ref|YP_004037530.1| 794 DIDDVQSEIDELESEL--ADSKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQLE-KEYAEDAIEDLNETVESAQ 867
                                       6778888888888877..7899*********************************99.5788899999999999999 PP

                             TMPIT  80 kvlkevesllpkk 92 
                                          ++  +++ +k
  gi|313127260|ref|YP_004037530.1| 868 DRKADARDVIREK 880
                                       8888877776665 PP

  == domain 7  score: 7.5 bits;  conditional E-value: 0.0055
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                        e++el+ e  +l+e  +e k++ +e     +++ +++++ ++ +++l  ++++l+++v+e + ee+ + +e  +++
  gi|313127260|ref|YP_004037530.1| 903 AELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELEAEVGEYDPEEIPDHDEVQENI 979
                                       35556666666666666666666666666666666666666666666666666666665544444443333333333 PP

                             TMPIT  79 kkvlkeve 86 
                                       ++   ++e
  gi|313127260|ref|YP_004037530.1| 980 QQLTGKME 987
                                       33333333 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6  26.0   9.6e-05     0.036     181     330 ..     193     343 ..     189     348 .. 0.85
   2 ?    6.1  28.2     0.018       6.7     161     314 ..     371     519 ..     358     523 .. 0.61
   3 !   15.1  24.1   3.2e-05     0.012     159     319 ..     697     850 ..     689     871 .. 0.71
   4 ?   -2.7  22.5       8.3   3.1e+03     187     324 ..     880     996 ..     861    1038 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.6e-05
                            HMMR_N 181 svkQedmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnv..seqlekykldiaqlee 255
                                        +k ed  ++l+++++ +ee+  ++ + + +l +le+e  e+  + + l e+ ee +    + +le  + d++  e+
  gi|313127260|ref|YP_004037530.1| 193 DAKKEDAFGELESVEERIEEADLRIEEKESRLDQLEDE-RETALKYQSLREEREEYEGYlkAAELEDKRADLERTES 268
                                       57888888999999999999999999999999999998.66666666777766666654114567899********* PP

                            HMMR_N 256 llkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvreeeekeqtlsaEleelkeklklkeqeaqk 330
                                        +++k++++esL+++L+ ++  +s+   +l+e  k++e++ e++  + +   ++++ E++ l+++++  e+ + +
  gi|313127260|ref|YP_004037530.1| 269 KAETKAEKLESLREELDTRQGRVSRLEAELDELSKEIERKGEDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDE 343
                                       ***************************************999999999999999999****99999998887665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.018
                            HMMR_N 161 sLsleLmklrnkleakekevsvkQedmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieels 237
                                       +  +e   +++++++ke e+     ++ea++ +++++++e k ++a+ k +l +l+ e+++ + e ++ll+ + + s
  gi|313127260|ref|YP_004037530.1| 371 AVKVEKASVKSEIKTKETEL----AEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLDDTRRRS 443
                                       44444455555555555555....66777777777777777777777777777777777777777777777776666 PP

                            HMMR_N 238 nvseqlekykldiaqleellkekndeiesLkssLe...ekeqelskqvkdlnekckllekekeelvreeeekeqtls 311
                                       +++ +    +++i +++e l + + ++++L s+L+   +++q+++  ++dl e  + l ++++e+  e + k++++ 
  gi|313127260|ref|YP_004037530.1| 444 SEISET---QEKISEVREELPTLKAKLSDLHSELDkaeKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRSKQSEY- 516
                                       666666...6667777777766666666666666411134555666667777777777766665555555554443. PP

                            HMMR_N 312 aEl 314
                                       aEl
  gi|313127260|ref|YP_004037530.1| 517 AEL 519
                                       444 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 3.2e-05
                            HMMR_N 159 lnsLsleLmklrnkleakekevsvkQedmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyiee 235
                                       l+ L +e+  l + +   e+e+    +d+e++l  + ++  ++  +v+ ++  +   e++ +e+k+e+e+l++ iee
  gi|313127260|ref|YP_004037530.1| 697 LERLAVEISDLEDDRREIEQEI----RDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEE 769
                                       6666666666666666666666....899999999999999999999999999999999999999999999999999 PP

                            HMMR_N 236 lsnvseqlekykldiaqleellkekndeiesLkssLeekeqel.skqvkdlnekckllekekeelvreeeekeqtls 311
                                       l++ + ++    +++++l   +++   +i +++s+++e e el + ++ +l+++ +++ +e ee+  +  e + +l 
  gi|313127260|ref|YP_004037530.1| 770 LREKRAEV---DEEMQSLDTDIDALTADIDDVQSEIDELESELaDSKIPELTAQADEIRAEIEEKEDRMDELDGRL- 842
                                       99999998...77888888888888888888888888777666245778888888888877775555555444333. PP

                            HMMR_N 312 aEleelke 319
                                        El+  ke
  gi|313127260|ref|YP_004037530.1| 843 NELQLEKE 850
                                       34443333 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 8.3
                            HMMR_N 187 meaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkeknde 263
                                        e  +++ ++ Lee +++v+ L+  l++l+ e+ + ++++++   + +e    ++++e+ + ++++l+e ++  + e
  gi|313127260|ref|YP_004037530.1| 880 KEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDE---QRDKVERVESRVENLRESAERLAWE 953
                                       3444555555555555555555555555554444444444433333332...3344444455555555555555555 PP

                            HMMR_N 264 iesLkssLeekeqelskqvkdlnekckllekekeelvreeeekeqtlsaEleelkeklklk 324
                                       i +L  ++ e + e     ++ +e++++l                     +e+l+    l 
  gi|313127260|ref|YP_004037530.1| 954 IDELEAEVGEYDPEEIPDHDEVQENIQQLT------------------GKMESLEPVNMLA 996
                                       555555555544444444444444444444..................3333333322222 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   8.7      0.16        60      45     113 ..     201     269 ..     189     270 .. 0.88
   2 !   14.6   5.8   7.5e-05     0.028       2      89 ..     272     355 ..     271     373 .. 0.89
   3 !   16.4   6.2   2.2e-05    0.0082       4      97 ..     401     489 ..     398     500 .. 0.89
   4 !    8.4   1.7    0.0064       2.4      12      93 ..     444     520 ..     439     524 .. 0.89
   5 !   10.1   8.5    0.0019       0.7      11      94 ..     708     786 ..     696     811 .. 0.87
   6 ?    7.7   6.6     0.011       4.1       1      72 [.     747     813 ..     747     834 .. 0.79
   7 ?    1.2  16.3       1.1     4e+02       9     113 ..     823     923 ..     815     931 .. 0.65
   8 ?    2.6   6.6      0.41   1.5e+02       2      74 ..     886     960 ..     885     965 .. 0.68
   9 ?   -0.5   2.0       3.7   1.4e+03      59     112 ..     977    1030 ..     972    1045 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.16
                              FliJ  45 aelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkkle.kLkerekkeeqkeenrrEqk 113
                                        el  +++ i+  d +i++ ++ l+q+e ++e+a  ++q+ r er+ +e +Lk+ e ++ ++ ++r E k
  gi|313127260|ref|YP_004037530.1| 201 GELESVEERIEEADLRIEEKESRLDQLEDERETAL-KYQSLREEREEYEgYLKAAELEDKRADLERTESK 269
                                       688889999999********************997.689999999999879*****************98 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.5e-05
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqveka 78 
                                       + a++L++ + el+  + ++ +le +++e++k+++ ++      e+  +++ i++++ +i++++++++ ae ++++a
  gi|313127260|ref|YP_004037530.1| 272 TKAEKLESLREELDTRQGRVSRLEAELDELSKEIERKG----EDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEA 344
                                       56899*********************************....7888889999************************9 PP

                              FliJ  79 reewqearqer 89 
                                       + e  +a  e+
  gi|313127260|ref|YP_004037530.1| 345 ETERRKAFVEL 355
                                       99888877766 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 2.2e-05
                              FliJ   4 areLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                        +e+ e + el++++++leel+ +r+++q ++          + r +++ is  +e+i++ ++el  ++++++   +
  gi|313127260|ref|YP_004037530.1| 401 DTEFDELKDELAAKKSQLEELKTERNDLQREKDRLL-----DDTRRRSSEISETQEKISEVREELPTLKAKLSDLHS 472
                                       57889999********************99999999.....999999999999999999999999999999999999 PP

                              FliJ  81 ewqearqerkklekLke 97 
                                       e+ +a++ ++k++ ++e
  gi|313127260|ref|YP_004037530.1| 473 ELDKAEKNKQKIDGVIE 489
                                       99999999999987776 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0064
                              FliJ  12 relqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqe 88 
                                        e+ + +ek+ e+++++  ++ +ls+       +el + ++ ++++d  i+ ++++ ++++ ++++ ++e+ +++ e
  gi|313127260|ref|YP_004037530.1| 444 SEISETQEKISEVREELPTLKAKLSDLH-----SELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRSKQSE 515
                                       6788999999999999999999999999.....99999999999999999999999999999999999999999999 PP

                              FliJ  89 rkkle 93 
                                       +  le
  gi|313127260|ref|YP_004037530.1| 516 YAELE 520
                                       98776 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0019
                              FliJ  11 qrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearq 87 
                                       +  +++ e+++  +e+++++ ++++s++a      + r ++a i++ +e +++ k e++q+e ++e+ re+  e   
  gi|313127260|ref|YP_004037530.1| 708 EDDRREIEQEIRDIESQLDDAREKASDAA-----DRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDE 779
                                       55677888899999999999988888888.....9***********************************9999999 PP

                              FliJ  88 erkklek 94 
                                       e ++l++
  gi|313127260|ref|YP_004037530.1| 780 EMQSLDT 786
                                       9999886 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.011
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqae 72 
                                       d a++ ++e ++e++q e ++eel++ r+e  +++++        ++ ++ a i+ ++++i+++++ela+++
  gi|313127260|ref|YP_004037530.1| 747 DRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLD-----TDIDALTADIDDVQSEIDELESELADSK 813
                                       678999999999999999999999999999999999999.....8888888888888888888888887765 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 1.1
                              FliJ   9 eaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqea 85 
                                       e+++e++++e +++el   ++e+q +++++       ++  +++  ++ +++ a ++ ++  +e+++e++++ + e+
  gi|313127260|ref|YP_004037530.1| 823 EIRAEIEEKEDRMDELDGRLNELQLEKEYAE-----DAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLEEK 894
                                       7888999999999999999999988888888.....66666666666666666666666666666666666666666 PP

                              FliJ  86 rqerkklek.LkerekkeeqkeenrrEqk 113
                                       r  +  le  Lke ++++   +e+ rE k
  gi|313127260|ref|YP_004037530.1| 895 REAVSDLEAeLKELKAERSDLREDVREAK 923
                                       66666655325555555555555555554 PP

  == domain 8  score: 2.6 bits;  conditional E-value: 0.41
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekq 74 
                                       e +  L+e + ++ + e++l el+ +r+++++  +++  +   +  +   +++  ++l+e  +++  e++ +e++
  gi|313127260|ref|YP_004037530.1| 886 EKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKsErDEQRDKVERVESRVENLRESAERLAWEIDELEAE 960
                                       667789999999999999999999999999999999984444445555555555555555555555555555544 PP

  == domain 9  score: -0.5 bits;  conditional E-value: 3.7
                              FliJ   59 eaiaqqkqelaqaekqvekareewqearqerkklekLkerekkeeqkeenrrEq 112 
                                        e i+q++ + + +e +   a +e+ e +  ++ l+  ++  ++e+q  ++r Eq
  gi|313127260|ref|YP_004037530.1|  977 ENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQ 1030
                                        555555555555555555555555555555555555555555555555555555 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   2.4       1.4   5.2e+02      63     101 ..     195     235 ..     185     237 .. 0.80
   2 ?   10.7  13.0    0.0013      0.47      18      99 ..     263     343 ..     250     353 .. 0.78
   3 ?    7.6   7.6     0.011       4.2      29     100 ..     339     407 ..     339     414 .. 0.71
   4 ?    9.7  11.3    0.0025      0.93      33     100 ..     406     477 ..     401     485 .. 0.55
   5 ?    2.4   2.3      0.49   1.8e+02      64      96 ..     481     515 ..     476     522 .. 0.58
   6 ?    8.8  11.3    0.0049       1.8      30      99 ..     710     783 ..     696     784 .. 0.85
   7 ?   15.8   6.7   3.4e-05     0.013      29     102 ..     772     847 ..     765     848 .. 0.92
   8 ?   -1.0  12.4       5.5   2.1e+03      31      96 ..     856     925 ..     848     929 .. 0.53
   9 ?    3.7  14.2      0.19        73       7      93 ..     877     964 ..     873     976 .. 0.73
  10 ?    5.7   3.7     0.046        17      15      87 ..     920     990 ..     916     993 .. 0.85
  11 ?    5.2   1.4     0.064        24      10      97 ..     978    1064 ..     971    1066 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.4
                                       CCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  63 kkkk..edaeeliaevkelkeelkaleaelkeleaelekll 101
                                       kk++   + e++ ++++e   +++++e +l++le+e e++l
  gi|313127260|ref|YP_004037530.1| 195 KKEDafGELESVEERIEEADLRIEEKESRLDQLEDERETAL 235
                                       33334678888999999999999999999999999988876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0013
                                       HCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  18 lkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkel 93 
                                       l++ + +++ + ++l +l e+  + q ++  l ae  elskeI+++ +++    +++ e++++k e+++le++ +++
  gi|313127260|ref|YP_004037530.1| 263 LERTEsKAETKAEKLESLREELDTRQGRVSRLEAELDELSKEIERKGEDE--QLRIKSEIESVKGEIDRLENAIEAA 337
                                       443334778899********************************999864..5567777777777777777777777 PP

                                       HHHHHH CS
                      Seryl_tRNA_N  94 eaelek 99 
                                       e+++++
  gi|313127260|ref|YP_004037530.1| 338 EDRIDE 343
                                       777665 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                       d++ e++++rr++ vel+  q+    +   I   k +k   ++++ e+k+  +el+++eae + +++e+++l
  gi|313127260|ref|YP_004037530.1| 339 DRIDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEK---ASVKSEIKTKETELAEVEAEIDSVDTEFDEL 407
                                       6788999****************************987...4455555555555555555555555555443 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  33 eldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                       el ++  + +++leel++erN l++e  ++ ++      +++e  ++++e+ eel +l+a+l++l +el+k+
  gi|313127260|ref|YP_004037530.1| 406 ELKDELAAKKSQLEELKTERNDLQREKDRLLDDTrrrsSEISETQEKISEVREELPTLKAKLSDLHSELDKA 477
                                       555555556666666666666666665555555555555555555555555555555555555555555543 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.49
                                       CTT..S-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  64 kkk..edaeeliaevkelkeelkaleaelkeleae 96 
                                       k+k    +e+l+++ ++lk +l+++e+el+  ++e
  gi|313127260|ref|YP_004037530.1| 481 KQKidGVIEDLREDRSDLKSDLDEVEDELRSKQSE 515
                                       33334556666666666666666666666666655 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelek 99 
                                       +  e++++ r ++++l++++++   ++  + +  ++     ed ee +ae+++l +++++l ++ +e+++e+++
  gi|313127260|ref|YP_004037530.1| 710 DRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIdraeEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQS 783
                                       45678888899999999999999999988887776657778******************************996 PP

  == domain 7  score: 15.8 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkk..edaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       ++  e+de++++l +++++l a    ++ eI ++  +    ++ el a+++e+ +e++++e++++el+ +l++l l
  gi|313127260|ref|YP_004037530.1| 772 EKRAEVDEEMQSLDTDIDALTADIDDVQSEIDELESELadSKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQL 847
                                       566799*****************************99888999****************************99876 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 5.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  31 lleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleae 96 
                                       + +l+e  +++q +  +++    e  ++I+++ +      e  ++l ae kelk+e ++l ++++e+++e
  gi|313127260|ref|YP_004037530.1| 856 IEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLeekrEAVSDLEAELKELKAERSDLREDVREAKSE 925
                                       4444444444444444444444444444444443323234666666666677777777776666666666 PP

  == domain 9  score: 3.7 bits;  conditional E-value: 0.19
                                       HHH-HHHHHHH...HCCCTCCCHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHH CS
                      Seryl_tRNA_N   7 irenpeavkek...lkkRgedkadvd.elleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkel 79 
                                       ire  +a++ek   l++++e+++d++ el el ++r  l+ ++ e+++er e   ++++   +    e l+++++ l
  gi|313127260|ref|YP_004037530.1| 877 IREKEQAIEEKeavLEEKREAVSDLEaELKELKAERSDLREDVREAKSERDEQRDKVERVESR---VENLRESAERL 950
                                       666555555542225556666666643789999999999999999999999999999998875...67788888888 PP

                                       HHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  80 keelkaleaelkel 93 
                                         e+++leae+ e 
  gi|313127260|ref|YP_004037530.1| 951 AWEIDELEAEVGEY 964
                                       88888888887665 PP

  == domain 10  score: 5.7 bits;  conditional E-value: 0.046
                                       HHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHH CS
                      Seryl_tRNA_N  15 keklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkale 87 
                                       +e+  +R   +++ d++  ++++ ++l+  +e l  e  el +e+g+   ++  d +e+ + +++l  +++ le
  gi|313127260|ref|YP_004037530.1| 920 REAKSER---DEQRDKVERVESRVENLRESAERLAWEIDELEAEVGEYDPEEiPDHDEVQENIQQLTGKMESLE 990
                                       5554444...68889999999999999999*******************9999999999999999999999887 PP

  == domain 11  score: 5.2 bits;  conditional E-value: 0.064
                                        -HHHHHHHHCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHH CS
                      Seryl_tRNA_N   10 npeavkeklkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeel 83  
                                        n++++  k+++ + +  + +de+ e+++  + lq   + l +er  ++  I++  ++k  +e  ++  +++++++
  gi|313127260|ref|YP_004037530.1|  978 NIQQLTGKMESLEpVNMLAIDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEAQK--KETFMEAFDAINDNF 1050
                                        5555555555544566788999999999999************************998..889999999999999 PP

                                        HHHHHHHHHHHHHH CS
                      Seryl_tRNA_N   84 kaleaelkeleael 97  
                                         ++ ++l++ + el
  gi|313127260|ref|YP_004037530.1| 1051 TDIFERLSNGTGEL 1064
                                        99988888766665 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  10.7         1   3.9e+02       9     113 ..     257     343 ..     236     348 .. 0.42
   2 ?    5.7  13.1     0.047        18       2     107 ..     317     425 ..     314     439 .. 0.85
   3 ?    5.4  14.7     0.055        21       3     122 ..     395     520 ..     393     521 .. 0.75
   4 ?    5.2   0.4     0.066        25      92     120 ..     699     727 ..     695     731 .. 0.84
   5 ?   15.7   4.0   3.6e-05     0.013       4      50 ..     745     791 ..     742     793 .. 0.92
   6 ?    7.0   0.9     0.019         7      85     120 ..     776     811 ..     772     814 .. 0.79
   7 ?    3.7  12.8      0.19        72       3     116 ..     812     924 ..     810     927 .. 0.86
   8 ?    2.2  10.2      0.55     2e+02       9     104 ..     867     961 ..     864     965 .. 0.47
   9 ?   -0.6   0.9         4   1.5e+03      21      40 ..    1002    1021 ..     971    1059 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1
                           DUF5082   9 qaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvdk 85 
                                       + + a+l+ + ++ e k e+L++ +++l++ + +++  + +l +                     ++e + +  + +
  gi|313127260|ref|YP_004037530.1| 257 EDKRADLERTESKAETKAEKLESLREELDTRQGRVSRLEAELDELSK------------------EIERKGEDEQLR 315
                                       33333333333333334444444444444444333333333333222..................333333333333 PP

                           DUF5082  86 ldelidaieeEIerLenqiseaqgvldt 113
                                       +++ i +++ EI rLen i+ a+  +d 
  gi|313127260|ref|YP_004037530.1| 316 IKSEIESVKGEIDRLENAIEAAEDRIDE 343
                                       3333344444444444444444433333 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.047
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLk....eaktklsdekeslkqkkkklekplnssesWkGkeennydgirsn 74 
                                       k++i++++ +i+ l++ i+a e+ I + +    +a  +l+ ++e +++ + +++   ++++s k +e ++ ++++++
  gi|313127260|ref|YP_004037530.1| 317 KSEIESVKGEIDRLENAIEAAEDRIDEAEterrKAFVELDRKQEMIDDVEDDIRAVKVEKASVK-SEIKTKETELAE 392
                                       7899*********************99996666777789*********************8876.566666788899 PP

                           DUF5082  75 lessyqtyvdkldelidaieeEIerLenqisea 107
                                       +e +++ + ++ del+d++  + ++Le+ ++e 
  gi|313127260|ref|YP_004037530.1| 393 VEAEIDSVDTEFDELKDELAAKKSQLEELKTER 425
                                       ********************9999998866654 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.055
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekesl.kqkkkklekplnssesWkGkeen..nydgirs... 73 
                                       ++i ++  + +el+ e+aa  +++e+Lk+ +  l+ ek +l +++++ ++++  ++e     +e+  + + ++s   
  gi|313127260|ref|YP_004037530.1| 395 AEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLlDDTRRRSSEISETQEKISEVREElpTLKAKLSdlh 471
                                       68999999***************************999987255566666666666643333222113444444333 PP

                           DUF5082  74 nlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                       +  ++ ++ ++k+d +i  + e+ ++L++++ e +  l ++qs+  +l+
  gi|313127260|ref|YP_004037530.1| 472 SELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRSKQSEYAELE 520
                                       4455666778999999999999999999999999999999999988875 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.066
                           DUF5082  92 aieeEIerLenqiseaqgvldtlqsqlns 120
                                       ++  EI++Le ++ e ++ +  ++sql++
  gi|313127260|ref|YP_004037530.1| 699 RLAVEISDLEDDRREIEQEIRDIESQLDD 727
                                       78889999999999999999999999886 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 3.6e-05
                           DUF5082   4 kisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkkl 50 
                                        i +++++++e+++ei++le+ Ie+L+e + ++++e +sl++++ +l
  gi|313127260|ref|YP_004037530.1| 745 DIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLDTDIDAL 791
                                       68999***********************************9987665 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.019
                           DUF5082  85 kldelidaieeEIerLenqiseaqgvldtlqsqlns 120
                                       ++de +++++++I  L  +i + q+ +d l+s+l +
  gi|313127260|ref|YP_004037530.1| 776 EVDEEMQSLDTDIDALTADIDDVQSEIDELESELAD 811
                                       678888888888888888888888888888888765 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.19
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessy 79 
                                       +ki +l aq++e r+ei+  e+   +L     +l+ eke +++++++l+++  s +  k  +++   ++++ +e+  
  gi|313127260|ref|YP_004037530.1| 812 SKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEE-K 887
                                       68999**********************************************999977666666666666656665.5 PP

                           DUF5082  80 qtyvdkldelidaieeEIerLenqiseaqgvldtlqs 116
                                       +++ ++ +e+++ +e E ++L+ ++s++  ++   +s
  gi|313127260|ref|YP_004037530.1| 888 EAVLEEKREAVSDLEAELKELKAERSDLREDVREAKS 924
                                       88999999999*************9999888877665 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.55
                           DUF5082   9 qaqiaelrseiaaleekIer.......LkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnless 78 
                                       q ++a++r  i+  e+ Ie+        +ea + l++e ++lk+++++l++   + +s + +++        +  + 
  gi|313127260|ref|YP_004037530.1| 867 QDRKADARDVIREKEQAIEEkeavleeKREAVSDLEAELKELKAERSDLREDVREAKSERDEQR--------DKVER 935
                                       4555555555555555555511110004455555555555555555555555555544444444........44444 PP

                           DUF5082  79 yqtyvdkldelidaieeEIerLenqi 104
                                       ++  v++l+e   ++ +EI +Le ++
  gi|313127260|ref|YP_004037530.1| 936 VESRVENLRESAERLAWEIDELEAEV 961
                                       44445555555566666666666655 PP

  == domain 9  score: -0.6 bits;  conditional E-value: 4
                           DUF5082   21 aleekIerLkeaktklsdek 40  
                                         ++ ++e L+  ++ l +e 
  gi|313127260|ref|YP_004037530.1| 1002 EVQADLEDLQDGRDVLAEER 1021
                                        33333444443333333333 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0  25.7       1.4   5.2e+02     144     281 ..     210     344 ..     190     351 .. 0.82
   2 ?    4.6  13.5     0.056        21     197     290 ..     341     437 ..     338     441 .. 0.51
   3 ?   10.1  10.6    0.0011      0.42     201     288 ..     429     519 ..     422     521 .. 0.61
   4 ?   11.8  54.5   0.00036      0.13      29     284 ..     699     953 ..     690     957 .. 0.75
   5 ?    3.9   4.5      0.09        34      19     119 ..     939    1042 ..     938    1047 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.4
                                       XXXXXXXXX..XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHH CS
                          Filament 144 vkelqkqvs..eqvlvevdaarkldLt.eilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrsakee 217
                                       ++e   +++  e++l +++++r++ L+ + l+e r++ye   +    e+e+  ++ le+ +++ae++ e+l+s +ee
  gi|313127260|ref|YP_004037530.1| 210 IEEADLRIEekESRLDQLEDERETALKyQSLREEREEYEGYLKAA--ELEDK-RADLERTESKAETKAEKLESLREE 283
                                       4444444444355566666777777764789********998865..55555.689********************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 218 itelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemarq 281
                                       +   + ++ +le+el++l k    +e++ ++ + r+++e+e+++ ++++le++++ + ++++  
  gi|313127260|ref|YP_004037530.1| 284 LDTRQGRVSRLEAELDELSK---EIERKGEDEQLRIKSEIESVKGEIDRLENAIEAAEDRIDEA 344
                                       ****************9876...689999*************************9988877655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.056
                                       XXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHH CS
                          Filament 197 leelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleer...leaeleklqeklseleee 270
                                       ++e++++ +k   +l + +e i ++   i + ++e +s+k++ ++ e++lae+e++   +++e ++l+++l+++ ++
  gi|313127260|ref|YP_004037530.1| 341 IDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEidsVDTEFDELKDELAAKKSQ 417
                                       44444444555555555555555555555555555555555555555555555544111334555555555555555 PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                          Filament 271 laeireemarqlreYqeLLd 290
                                       l+e++ e +   re ++LLd
  gi|313127260|ref|YP_004037530.1| 418 LEELKTERNDLQREKDRLLD 437
                                       55555555555555555554 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0011
                                       XXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 201 qeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaele...erleaeleklqeklseleeelaei 274
                                       q++ ++  ++ r+  +ei+e++ +i + + el  lk++ + l+++l  +e   ++++  +e+l+e  s+l ++l e+
  gi|313127260|ref|YP_004037530.1| 429 QREKDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEknkQKIDGVIEDLREDRSDLKSDLDEV 505
                                       44555555555555555555555555555555555555555555554444111556667888888888888888888 PP

                                       HHHHHHHHHHHHHH CS
                          Filament 275 reemarqlreYqeL 288
                                        +e+  + +eY eL
  gi|313127260|ref|YP_004037530.1| 506 EDELRSKQSEYAEL 519
                                       88888888888887 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00036
                                       XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXX CS
                          Filament  29 eLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyeke.......lnkr 98 
                                       +L ++i++le+  ++e+++  +  e++l+++r++  +++     +++++d+++e++e+ ++ +e+         +kr
  gi|313127260|ref|YP_004037530.1| 699 RLAVEISDLEDD-RREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLedrieelREKR 774
                                       577788888777.6666666677788888888777777776666777777766666655554444334444448999 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  99 eevEaelkalrkdldeatlarvdLekkvesLkeelaflkkvheeEvkelqkqvs.eqvlvevdaarkldLteilkei 174
                                        ev++e+++l  d+d++t    d+++++++L+ ela         + el++q+   ++ +e ++ r  +L+  l+e+
  gi|313127260|ref|YP_004037530.1| 775 AEVDEEMQSLDTDIDALTADIDDVQSEIDELESELAD------SKIPELTAQADeIRAEIEEKEDRMDELDGRLNEL 845
                                       9999999999999999999999999999999999985......5588888888434555566666777799999998 PP

                                       X..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 175 r..aqyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlael 249
                                       +  ++y e a +  +e  e  + + +++++ ++++++a+++ +  ++e r  +  le+el++lk++++ l++ ++e+
  gi|313127260|ref|YP_004037530.1| 846 QleKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREA 922
                                       6335565555555556556667778889999999999999999999999999************9999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 250 eerleaeleklqeklseleeelaeireemarqlre 284
                                       + +    +++ ++k++++e+ ++++re  +r   e
  gi|313127260|ref|YP_004037530.1| 923 KSE----RDEQRDKVERVESRVENLRESAERLAWE 953
                                       865....5555667778888888888888877666 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.09
                                        XXXXXXXXXXXXXXXXXXXXXXX...XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament   19 kVraLEqenkeLeakieeleekk...saevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkk 90  
                                        +V  L ++ ++L  +i ele +     +e+  +++  ++++++l  ++++l+  +  +  e+d+++++ledl+  
  gi|313127260|ref|YP_004037530.1|  939 RVENLRESAERLAWEIDELEAEVgeyDPEEIPDHDEVQENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDG 1013
                                        78999999999*****999988655678888899999************************************** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament   91 yekelnkreevEaelkalrkdldeatlar 119 
                                         +  +++r+ + + ++++  + +e+ ++ 
  gi|313127260|ref|YP_004037530.1| 1014 RDVLAEERQGIQDRIEQFEAQKKETFMEA 1042
                                        99999******999999998888877765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2       1.1   4.1e+02      16      47 ..     266     301 ..     253     308 .. 0.42
   2 ?    0.8   1.0       1.8   6.8e+02       8      58 ..     315     369 ..     313     375 .. 0.62
   3 ?    7.5   2.1     0.015       5.6       9      60 ..     379     427 ..     377     430 .. 0.85
   4 ?    8.9   1.6    0.0055       2.1      10      65 ..     436     488 ..     433     520 .. 0.85
   5 ?    0.8   0.4       1.9     7e+02      18      47 ..     709     735 ..     697     755 .. 0.50
   6 ?   15.3   4.7   5.5e-05      0.02      11      73 ..     758     817 ..     751     819 .. 0.89
   7 ?    5.1   0.6     0.085        32       9      56 ..     824     868 ..     822     887 .. 0.80
   8 ?    6.0   0.6     0.044        16       5      62 ..     890     944 ..     887     963 .. 0.85
   9 ?    1.3   0.2       1.3   4.8e+02      20      56 ..     954     991 ..     944    1022 .. 0.68
  10 ?    0.5   0.1       2.3   8.6e+02      23      58 ..    1024    1057 ..     996    1070 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.1
                           NPV_P10  16 vddkVdalqqqvddvqenlpd....vtelnekLdaq 47 
                                       +++k +   +++++++e+l +    v+ l+++Ld++
  gi|313127260|ref|YP_004037530.1| 266 TESKAETKAEKLESLREELDTrqgrVSRLEAELDEL 301
                                       444443334444444443333111133333333333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.8
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnek....LdaqsaqLaeletkv 58 
                                        I+++i+ v+  +d l+++++  ++ + + +    k    Ld+ ++ ++++e+ +
  gi|313127260|ref|YP_004037530.1| 315 RIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKafveLDRKQEMIDDVEDDI 369
                                       6889999999999999999966666555533222212222666666666666655 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.015
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       ++++ik  ++ +  +++++d+v++++ +   l+++L a   qL+el+t+ ++
  gi|313127260|ref|YP_004037530.1| 379 VKSEIKTKETELAEVEAEIDSVDTEFDE---LKDELAAKKSQLEELKTERND 427
                                       5788999999999999******997655...99*************997655 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0055
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                       ++d +  ++ ++  q+++ +v+e+lp+   l++kL ++  +L++ e++ ++I+ + 
  gi|313127260|ref|YP_004037530.1| 436 LDDTRRRSSEISETQEKISEVREELPT---LKAKLSDLHSELDKAEKNKQKIDGVI 488
                                       677777888899999999999999999...88999999999999988878777665 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.9
                           NPV_P10  18 dkVdalqqqvddvqenlpdvtelnekLdaq 47 
                                       d    ++q++ d++++l d     ek  + 
  gi|313127260|ref|YP_004037530.1| 709 DDRREIEQEIRDIESQLDDA---REKASDA 735
                                       44444444444444444442...2333333 PP

  == domain 6  score: 15.3 bits;  conditional E-value: 5.5e-05
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpdevPdl 73 
                                       a+i++++d+++ l ++ ++v+e+++    l + +da++a ++++++++++ ++ L   ++P+l
  gi|313127260|ref|YP_004037530.1| 758 AEIEQLEDRIEELREKRAEVDEEMQS---LDTDIDALTADIDDVQSEIDELESELADSKIPEL 817
                                       67889999999999999999998888...88*************************767**98 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.085
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                       Ira+i++ +d++d l+ +++++q + +     ++ ++++++++++ ++
  gi|313127260|ref|YP_004037530.1| 824 IRAEIEEKEDRMDELDGRLNELQLEKEY---AEDAIEDLNETVESAQD 868
                                       9********************9987666...45777777777776665 PP

  == domain 8  score: 6.0 bits;  conditional E-value: 0.044
                           NPV_P10   5 iLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                       +L   r+++++++  ++ l+++  d++e++++    +++ d+q ++++ +e+ ven  
  gi|313127260|ref|YP_004037530.1| 890 VLEEKREAVSDLEAELKELKAERSDLREDVRE---AKSERDEQRDKVERVESRVENLR 944
                                       66677999999999999999999999996655...77899999999999999999875 PP

  == domain 9  score: 1.3 bits;  conditional E-value: 1.3
                           NPV_P10  20 Vdalqqqvddvq.enlpdvtelnekLdaqsaqLaelet 56 
                                       +d l+++v + + e++pd +e++e++++++ ++++le 
  gi|313127260|ref|YP_004037530.1| 954 IDELEAEVGEYDpEEIPDHDEVQENIQQLTGKMESLEP 991
                                       56666666555425677777777777777777777764 PP

  == domain 10  score: 0.5 bits;  conditional E-value: 2.3
                           NPV_P10   23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkv 58  
                                        +q+++++ +++ ++     e +da++++ +++ + +
  gi|313127260|ref|YP_004037530.1| 1024 IQDRIEQFEAQKKE--TFMEAFDAINDNFTDIFERL 1057
                                        56666666666666..56667777777766665555 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4  24.1       5.9   2.2e+03     111     244 ..     201     334 ..     188     338 .. 0.71
   2 ?    0.4  32.1      0.43   1.6e+02      59     242 ..     329     507 ..     317     523 .. 0.58
   3 ?   14.2  13.1   2.8e-05     0.011      85     183 ..     711     809 ..     697     816 .. 0.84
   4 ?   14.0  40.3   3.2e-05     0.012      27     246 ..     812    1037 ..     798    1041 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.9
                               MAD 111 nelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqsqeddsl 187
                                       +el+  ++ ie+++l ++ekes l +l+ + +    k++ l + ++++e   k  ae e++  +Le+  ++ e +++
  gi|313127260|ref|YP_004037530.1| 201 GELESVEERIEEADLRIEEKESRLDQLEDERE-TALKYQSLREEREEYEGYLKA-AELEDKRADLERTESKAETKAE 275
                                       57777788888888888888888888876654.556788888888888888775.4555566788888888888888 PP

                               MAD 188 ivknsksel....aripelekelerlreenkklnelkenkelLkEevedlkkkLereEkar 244
                                        +++ ++el     r+++le+el++l +e+++  + +++++ +k e+e +k  ++r E+a 
  gi|313127260|ref|YP_004037530.1| 276 KLESLREELdtrqGRVSRLEAELDELSKEIER--KGEDEQLRIKSEIESVKGEIDRLENAI 334
                                       78777777653224788888888888888774..455556667888888888888888765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.43
                               MAD  59 llekreeekeealreqiElarlkkknlealnkkekekesklaearevi...salknelaelkrqiekqelelsekes 132
                                       +le+  e++e+   +++E +r  +k   +l++k++  ++ + ++r v+    ++k e++  ++++ + e e+ + ++
  gi|313127260|ref|YP_004037530.1| 329 RLENAIEAAEDRI-DEAETER--RKAFVELDRKQEMIDDVEDDIRAVKvekASVKSEIKTKETELAEVEAEIDSVDT 402
                                       4444333333332.3344444..455555666665555555555555411134556666666666666666666666 PP

                               MAD 133 eleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqs.qeddslivknskselaripelekeler 208
                                       e  el+ +l  +k +l+el+  +++l+ +++ l +   r    + ei++ qe+ s++ ++     a++++l +el++
  gi|313127260|ref|YP_004037530.1| 403 EFDELKDELAAKKSQLEELKTERNDLQREKDRLLDDTRRR---SSEISEtQEKISEVREELPTLKAKLSDLHSELDK 476
                                       6666666666666666666666666666666555554442...3344443444444444444444888999999999 PP

                               MAD 209 lreenkklnelkenkelLkEevedlkkkLereEk 242
                                        +++ +k+  ++e+   L+E+  dlk+ L+ +E+
  gi|313127260|ref|YP_004037530.1| 477 AEKNKQKIDGVIED---LREDRSDLKSDLDEVED 507
                                       88888888888877...88999999999998886 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.8e-05
                               MAD  85 lealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekk 161
                                         +++++ ++ es+l +are  s   ++++  +  i ++e +++ek+ e+e+l+ r ++l++k +e+++ +q+l++ 
  gi|313127260|ref|YP_004037530.1| 711 RREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLDTD 787
                                       46789999999***************************************************************999 PP

                               MAD 162 qkelaeaeqrikeLefeiqsqe 183
                                        + l++  + ++  + e++s  
  gi|313127260|ref|YP_004037530.1| 788 IDALTADIDDVQSEIDELESEL 809
                                       9999887766654444444433 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 3.2e-05
                               MAD   27 rarielekkasalkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklae 101 
                                        +   el ++a + + ++ee+ dr+ el+ r+++l+ + e++e+a ++  E + + +  ++ +    +eke+  +e
  gi|313127260|ref|YP_004037530.1|  812 SKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEE 886 
                                        4456899999999********************998888888777777777776667778888999********* PP

                               MAD  102 arevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLe 176 
                                         + v +++++ +++l+ ++++ + e s  +++++e + + d+++ k++ +e ++++l ++ + la     i eLe
  gi|313127260|ref|YP_004037530.1|  887 KEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAW---EIDELE 958 
                                        **********************************************************99999885...689999 PP

                               MAD  177 feiqs.....qeddslivknskselaripelek....elerlreenkklnelkenkelLkEevedlkkkLereEk 242 
                                         e+ +       d  ++ +n+++   ++  le      +++  e  + l++l++   +L Ee ++++ ++e++E 
  gi|313127260|ref|YP_004037530.1|  959 AEVGEydpeeIPDHDEVQENIQQLTGKMESLEPvnmlAIDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEA 1033
                                        99999555443455666677777667887777522224688889999***************************9 PP

                               MAD  243 aree 246 
                                         ++e
  gi|313127260|ref|YP_004037530.1| 1034 QKKE 1037
                                        9887 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   4.8       3.3   1.2e+03     113     179 ..     191     256 ..     186     260 .. 0.77
   2 ?   15.5  10.3   3.1e-05     0.012      96     185 ..     319     408 ..     312     411 .. 0.94
   3 ?    9.6  12.2    0.0019      0.72     101     186 ..     415     514 ..     407     516 .. 0.67
   4 ?    5.9  17.7     0.028        10      77     181 ..     704     809 ..     697     844 .. 0.78
   5 ?    5.6  16.1     0.035        13      97     180 ..     842     925 ..     835     943 .. 0.92
   6 ?   -2.2   5.8       8.4   3.1e+03     106     155 ..     974    1023 ..     923    1056 .. 0.44

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.3
                            DUF724 113 klekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveq 179
                                       +++ k e++  e +++ee i+e + +i e e +l++l  ++e+a  +  +l+ e e++e +l+++e 
  gi|313127260|ref|YP_004037530.1| 191 EFDAKKEDAFGELESVEERIEEADLRIEEKESRLDQLEDERETA-LKYQSLREEREEYEGYLKAAEL 256
                                       56777778888889999999999999999999999888666554.5667788888888887777776 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.1e-05
                            DUF724  96 kLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaeklee 172
                                       ++ s+k e ++l+++++++e +i e+e+e+rk+  e+d +++ i ++e    ++k +k + ++ei++ ++e +++e 
  gi|313127260|ref|YP_004037530.1| 319 EIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEA 395
                                       666899*********************************************************************** PP

                            DUF724 173 eledveqeFeava 185
                                       e+++v +eF++++
  gi|313127260|ref|YP_004037530.1| 396 EIDSVDTEFDELK 408
                                       *********9875 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0019
                            DUF724 101 kdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk..............ekkeaadkeiarl 163
                                       k++ ++l++er++l+++     ++ r+ ++ei+e+++ki+e++++l +lk              ++k++ d  i +l
  gi|313127260|ref|YP_004037530.1| 415 KSQLEELKTERNDLQREKDRLLDDTRRRSSEISETQEKISEVREELPTLKaklsdlhseldkaeKNKQKIDGVIEDL 491
                                       45555555666666666666666666666666666666666666666666555555555555559999999999999 PP

                            DUF724 164 kseaekleeeledveqeFeavas 186
                                       + + ++l+ +l++ve+e ++ +s
  gi|313127260|ref|YP_004037530.1| 492 REDRSDLKSDLDEVEDELRSKQS 514
                                       99999999999999999888765 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.028
                            DUF724  77 laeLekhGFdVkalqsrl.nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkek 152
                                       +++Le +  ++++    + ++L   +++ + ++++ + +e +i  +e++ ++ ++ei++le +i el++++a + e+
  gi|313127260|ref|YP_004037530.1| 704 ISDLEDDRREIEQEIRDIeSQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEE 780
                                       55555555555555555534455677788888888888888888888888888888888888888888888888888 PP

                            DUF724 153 keaadkeiarlkseaekleeeledveqeF 181
                                       +++ d +i +l ++ ++++ e+++ e+e 
  gi|313127260|ref|YP_004037530.1| 781 MQSLDTDIDALTADIDDVQSEIDELESEL 809
                                       88888888888888888888888888776 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.035
                            DUF724  97 Llslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleee 173
                                       L +l+ e++ +++++++l++ +e ++++k+ + + i+e+e++i e e  l+ ++e  ++ ++e+++lk+e ++l+e+
  gi|313127260|ref|YP_004037530.1| 842 LNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDLRED 918
                                       55678889999999*************************************************************** PP

                            DUF724 174 ledveqe 180
                                       ++++++e
  gi|313127260|ref|YP_004037530.1| 919 VREAKSE 925
                                       9999986 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 8.4
                            DUF724  106 klleerkklekkieeeesekrkleeeidelekkilelerqlallkekkea 155 
                                        +++e++++l  k+e  e  +  + +e de++    +l+  +++l e+++ 
  gi|313127260|ref|YP_004037530.1|  974 EVQENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDVLAEERQG 1023
                                        22333333333333333333333333333333333333333333344444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00041      0.15       1      46 [.       1      44 [.       1      54 [. 0.85
   2 ?    6.2   1.3     0.018       6.9     142     199 ..     405     462 ..     398     470 .. 0.87
   3 ?   -1.9   0.0       5.4     2e+03     161     200 ..     696     735 ..     690     746 .. 0.75
   4 ?   -0.7   0.2       2.4   8.9e+02     160     200 ..     758     798 ..     737     815 .. 0.63
   5 ?   -0.9   0.3       2.7     1e+03     156     178 ..     789     811 ..     759     852 .. 0.47
   6 ?    0.3   2.4       1.2   4.4e+02     152     203 ..     888     939 ..     854     944 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                            AAA_27  1 MrlerLdLeryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAi 46
                                      M +++L L+ + +f  + ++ f    +d++++ GpN +GKs +++++
  gi|313127260|ref|YP_004037530.1|  1 MHIKELVLDGFKSFGRKtRIPFY---EDFTVVTGPNGSGKSNIIDGV 44
                                      99999999999999644268887...8**************998765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.018
                            AAA_27 142 gelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       +el   L + ++ l++l++ +++L++e+d+l +++++++ +i e++e+++e+++el +
  gi|313127260|ref|YP_004037530.1| 405 DELKDELAAKKSQLEELKTERNDLQREKDRLLDDTRRRSSEISETQEKISEVREELPT 462
                                       56667788889999************************99***********9999865 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.4
                            AAA_27 161 vleaLeaeadelfkprkskkrainealeeleeakkelrea 200
                                        le+L  e ++l ++r++ +++i++ +++l++a+++  +a
  gi|313127260|ref|YP_004037530.1| 696 RLERLAVEISDLEDDRREIEQEIRDIESQLDDAREKASDA 735
                                       5677888888888888888888888888888888877665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.4
                            AAA_27 160 evleaLeaeadelfkprkskkrainealeeleeakkelrea 200
                                       + +e+Le++ +el ++r++ +++++   ++++++++ + + 
  gi|313127260|ref|YP_004037530.1| 758 AEIEQLEDRIEELREKRAEVDEEMQSLDTDIDALTADIDDV 798
                                       44555555555555555555555555555555555554444 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 2.7
                            AAA_27 156 aslrevleaLeaeadelfkprks 178
                                         l++ ++++++e del ++ + 
  gi|313127260|ref|YP_004037530.1| 789 DALTADIDDVQSEIDELESELAD 811
                                       33333333333333333333333 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 1.2
                            AAA_27 152 saGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelreaqvr 203
                                       +a l++ re + +Leae +el ++r+  ++ ++ea++e +e++ ++++ + r
  gi|313127260|ref|YP_004037530.1| 888 EAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESR 939
                                       5556667788889999999999999999999999999999999888776655 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   7.8       2.1   7.8e+02      56     114 ..     191     252 ..     189     254 .. 0.77
   2 ?    5.5  22.6     0.059        22       2     105 ..     227     336 ..     227     346 .. 0.70
   3 ?    6.5  18.1     0.029        11       7     107 ..     312     415 ..     309     423 .. 0.84
   4 ?    6.7  17.5     0.025       9.2       4     105 ..     386     483 ..     384     486 .. 0.88
   5 ?    3.5  14.3      0.23        87      13     107 ..     419     513 ..     417     519 .. 0.93
   6 ?   14.0  12.5   0.00013     0.049      34     107 ..     698     771 ..     692     774 .. 0.92
   7 ?    8.7   0.3    0.0059       2.2      69     106 ..     775     812 ..     771     816 .. 0.79
   8 ?    3.0  23.5      0.33   1.2e+02      14     103 ..     823     912 ..     812     923 .. 0.75
   9 ?   -1.1  14.7       6.5   2.4e+03      30      93 ..     902     965 ..     900    1043 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.1
                           DUF4200  56 endakraralkkaeeerklkkekeaeikklkaeietlkseie...kleekleeykkYeefLe 114
                                       e dak+++a  + e+ +++++e +  i++ ++ +++l+ e+e   k++   ee ++Ye +L+
  gi|313127260|ref|YP_004037530.1| 191 EFDAKKEDAFGELESVEERIEEADLRIEEKESRLDQLEDEREtalKYQSLREEREEYEGYLK 252
                                       67888888888888888888888888888888888888877766677777777777888876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.059
                           DUF4200   2 lekkremfevqealeakkeeiqr..leealkqreeelekkeqeleedllkfdkflkendakraralkkaee...erk 73 
                                       le++re  +  ++l + +ee++   +  +l++++++le++e++ e +++k++   +e d ++ r  +  +e    +k
  gi|313127260|ref|YP_004037530.1| 227 LEDERETALKYQSLREEREEYEGylKAAELEDKRADLERTESKAETKAEKLESLREELDTRQGRVSRLEAEldeLSK 303
                                       57788888888888888888885437777888888888888888888888888888888887666554444000444 PP

                           DUF4200  74 lkkek.eaeikklkaeietlkseiekleeklee 105
                                       ++++k e e  ++k+eie +k ei++le+++e 
  gi|313127260|ref|YP_004037530.1| 304 EIERKgEDEQLRIKSEIESVKGEIDRLENAIEA 336
                                       444442446677888888888888888887764 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.029
                           DUF4200   7 emfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdk...flkendakraralkkaeeerklkkekea 80 
                                       e+ +++ ++e  k ei rle+a++ +e+ ++++e e ++ ++++d+   ++ + ++  +    + ++ + ++k ke 
  gi|313127260|ref|YP_004037530.1| 312 EQLRIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRkqeMIDDVEDDIRAVKVEKASVKSEIKTKET 388
                                       66778999*********************************9998622256666666555555667778899999** PP

                           DUF4200  81 eikklkaeietlkseiekleekleeyk 107
                                       e+++ +aei+ + +e ++l+++l+  k
  gi|313127260|ref|YP_004037530.1| 389 ELAEVEAEIDSVDTEFDELKDELAAKK 415
                                       ******************999998766 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.025
                           DUF4200   4 kkremfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekea 80 
                                       k+ e+ ev+ +++    e+ +l+++l+ ++ +le+ + e ++   + d+ l +  +++     ++ e ++++ e  +
  gi|313127260|ref|YP_004037530.1| 386 KETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLDDTRRRS----SEISETQEKISEVRE 458
                                       7889999999999999999999999999999999999999999999999998876666....567888999999*** PP

                           DUF4200  81 eikklkaeietlkseiekleeklee 105
                                       e+  lka++++l+se++k e++ ++
  gi|313127260|ref|YP_004037530.1| 459 ELPTLKAKLSDLHSELDKAEKNKQK 483
                                       ******************9998665 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.23
                           DUF4200  13 ealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaei 89 
                                       e+l++ ++++qr +++l +  +    + +e +e++ ++ + l   +ak ++   + ++ +k+k++ +  i++l+++ 
  gi|313127260|ref|YP_004037530.1| 419 EELKTERNDLQREKDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDR 495
                                       58999999999999999999999999999************************************************ PP

                           DUF4200  90 etlkseiekleekleeyk 107
                                       ++lks++++ e++l++ +
  gi|313127260|ref|YP_004037530.1| 496 SDLKSDLDEVEDELRSKQ 513
                                       ************998765 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 0.00013
                           DUF4200  34 eelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleekleeyk 107
                                       e l  + + le+d  + ++ +++++++  +a++ka + +++ ++ ea+i ++++++e+ k+eie+le+++ee++
  gi|313127260|ref|YP_004037530.1| 698 ERLAVEISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELR 771
                                       5566667899*************************************************************986 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0059
                           DUF4200  69 eeerklkkekeaeikklkaeietlkseiekleekleey 106
                                       +e  ++ ++ + +i  l+a+i++++sei++le +l++ 
  gi|313127260|ref|YP_004037530.1| 775 AEVDEEMQSLDTDIDALTADIDDVQSEIDELESELADS 812
                                       44456678899999999999999999999999999876 PP

  == domain 8  score: 3.0 bits;  conditional E-value: 0.33
                           DUF4200  14 aleakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeie 90 
                                       ++ a  ee + ++++l+ r +el+ ++++ e+ ++ +++ +++ ++++a+a+  + e++++++ekea +++ ++ ++
  gi|313127260|ref|YP_004037530.1| 823 EIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLEEKREAVS 899
                                       34444445556888888899999999999999999999999999999999999999999999999988888777777 PP

                           DUF4200  91 tlkseiekleekl 103
                                       +l++e+++l+++ 
  gi|313127260|ref|YP_004037530.1| 900 DLEAELKELKAER 912
                                       7777777776654 PP

  == domain 9  score: -1.1 bits;  conditional E-value: 6.5
                           DUF4200  30 kqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlk 93 
                                       + + +el+++++ l+ed+ + +    e  +k +r + ++e+ r+  ++ + ei +l+ae+ +  
  gi|313127260|ref|YP_004037530.1| 902 EAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERLAWEIDELEAEVGEYD 965
                                       5566888888888888888888888888888888888888888888888888888888887766 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8  19.6         5   1.9e+03     106     215 ..     202     314 ..     189     319 .. 0.84
   2 ?    5.3  14.7     0.034        13      38     141 ..     312     424 ..     310     433 .. 0.90
   3 ?    4.1   1.6     0.082        31      93     137 ..     432     476 ..     427     486 .. 0.69
   4 ?    2.8   3.5       0.2        74      12      68 ..     468     524 ..     463     526 .. 0.85
   5 ?    8.5  27.5    0.0037       1.4      18     141 ..     704     827 ..     700     868 .. 0.71
   6 ?   -0.6  20.7       2.2   8.3e+02     109     214 ..     816     922 ..     810     930 .. 0.53
   7 ?   10.3   6.4     0.001      0.38     102     207 ..     928    1037 ..     917    1047 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5
                         PspA_IM30 106 qlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqeavqkslgklstesatdslerieeKieer.eara 181
                                       +l+ +++ +e++   +e+ e ++++l++++e+ +  ++    +e+ +  l++++ e+  + ler e K e   e  +
  gi|313127260|ref|YP_004037530.1| 202 ELESVEERIEEADLRIEEKESRLDQLEDERETALKYQSLREEREEYEGYLKAAELEDKRADLERTESKAETKaEKLE 278
                                       67889999999***********************99*********************************98625567 PP

                         PspA_IM30 182 daaaelaesaqd....ldakleaagiqkevseqvlarl 215
                                       ++++el  ++q+    l+a+l+++ ++ e  + ++++l
  gi|313127260|ref|YP_004037530.1| 279 SLREELD-TRQGrvsrLEAELDELSKEIER-KGEDEQL 314
                                       7888888.6666666799999999998888.5555554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.034
                         PspA_IM30  38 elakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkg.........eeeLArealaeikslekqaealet 105
                                       e+ + + ++++v+++  +le+ +e++++++ + e + ++A+ +           e+ +r++  e++s +++++ +et
  gi|313127260|ref|YP_004037530.1| 312 EQLRIKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELdrkqemiddVEDDIRAVKVEKASVKSEIKTKET 388
                                       55677889999************************99999877778899**999999******************** PP

                         PspA_IM30 106 qlaqqrsaveqlrkqlealetkieelkakkellkar 141
                                       +la++++ ++ + ++ ++l+  ++++k++ e+lk  
  gi|313127260|ref|YP_004037530.1| 389 ELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTE 424
                                       ******************************999975 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.082
                         PspA_IM30  93 ikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkel 137
                                       + +l +++++ + + ++ ++ + ++r++l  l++k+++l ++ ++
  gi|313127260|ref|YP_004037530.1| 432 KDRLLDDTRRRSSEISETQEKISEVREELPTLKAKLSDLHSELDK 476
                                       556667777777777777777777777777777777777777654 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.2
                         PspA_IM30  12 aniselldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqak 68 
                                       + +++ ldkae  ++ ++  i+d++++  +++  l +v  + ++ + +++e +++a 
  gi|313127260|ref|YP_004037530.1| 468 SDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRSKQSEYAELEARAG 524
                                       778999999999999999999999999999999999999988888888888888876 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0037
                         PspA_IM30  18 ldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkgeeeLAr...eala 91 
                                       ++ +eD  + +eq+ird++s+l++ar+++ ++  r +++e ++++++e++++ +++ ++ L+   eeL +   e+ +
  gi|313127260|ref|YP_004037530.1| 704 ISDLEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQ-LEDRIEELREkraEVDE 779
                                       57899999******************************************998888776.45555555431114445 PP

                         PspA_IM30  92 eikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkar 141
                                       e++sl  ++ al +  + ++s +++l+ +l++   ki el a+ +++ a 
  gi|313127260|ref|YP_004037530.1| 780 EMQSLDTDIDALTADIDDVQSEIDELESELAD--SKIPELTAQADEIRAE 827
                                       67777777777777777777777777766653..4566666665555544 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 2.2
                         PspA_IM30 109 qqrsaveqlrkqlealetkieelkakkellkarekaak.aqeavqkslgkls..tesatdslerieeKieerearad 182
                                       ++ ++++++r+++e+ e +++el    ++l++ ++ a  a e++++++++++   ++a d   + e+ iee ea   
  gi|313127260|ref|YP_004037530.1| 816 ELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEdAIEDLNETVESAQdrKADARDVIREKEQAIEEKEA--- 889
                                       44556666666666666666666666666666555443266666666666664444444444444444444443... PP

                         PspA_IM30 183 aaaelaesaqdldakleaagiqkev.seqvlar 214
                                         +e +e ++dl+a+l++++++ +   e+v+++
  gi|313127260|ref|YP_004037530.1| 890 VLEEKREAVSDLEAELKELKAERSDlREDVREA 922
                                       333334345556666666666665533555444 PP

  == domain 7  score: 10.3 bits;  conditional E-value: 0.001
                         PspA_IM30  102 aletqlaqqrsaveqlrkqlealetkieelkakkellkare..kaakaqeavqkslgkls..tesatdsleriee 172 
                                        + + ++++++s ve+lr++ e+l+  i+el+a++ ++   e       qe++q+ +gk++   + ++ + ++  e
  gi|313127260|ref|YP_004037530.1|  928 EQRDKVERVESRVENLRESAERLAWEIDELEAEVGEYDPEEipDHDEVQENIQQLTGKMEslEPVNMLAIDEYDE 1002
                                        566788999999***********************99998844678899**********9987888888899999 PP

                         PspA_IM30  173 Kieerearadaaaelaesaqdldakleaagiqkev 207 
                                         ++++e+ +d++  lae++q+ +  +e+ ++qk+ 
  gi|313127260|ref|YP_004037530.1| 1003 VQADLEDLQDGRDVLAEERQGIQDRIEQFEAQKKE 1037
                                        99999999999999998888888888888888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.034        13       5      21 ..      24      40 ..      19      50 .. 0.86
   2 ?   -0.4   4.0       3.5   1.3e+03      37     116 ..     926    1014 ..     873    1025 .. 0.54
   3 ?   -1.7   0.0       8.9   3.3e+03      87     118 ..    1111    1142 ..    1065    1155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.034
                            AAA_22  5 agilvvtGesGtGKTtl 21
                                      + ++vvtG+ G+GK+  
  gi|313127260|ref|YP_004037530.1| 24 EDFTVVTGPNGSGKSNI 40
                                      6799**********965 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.5
                            AAA_22   37 e..erpevvfvtlpsst..sskdllrellralglelka.......erlsseellealeqalraravielliiDEa 100 
                                        +  +r++v +v+  +++  +s++ l +   +l+ e  +         ++ +e +++l+  +++   + +l iDE 
  gi|313127260|ref|YP_004037530.1|  926 RdeQRDKVERVESRVENlrESAERLAWEIDELEAEVGEydpeeipDHDEVQENIQQLTGKMESLEPVNMLAIDEY 1000
                                        233333333443333333322222222222333322224555554444444555555555555555888999998 PP

                            AAA_22  101 qhlrseealeeLrsll 116 
                                        + +  ++ le+L +  
  gi|313127260|ref|YP_004037530.1| 1001 DEV--QADLEDLQDGR 1014
                                        888..66666665544 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 8.9
                            AAA_22   87 raravielliiDEaqh.lrseealeeLrsllnl 118 
                                        +++   ++  +DE++  l  +++ e + +++++
  gi|313127260|ref|YP_004037530.1| 1111 QRHNPAPFYALDEVDAfL-DAANAERVGEMVDD 1142
                                        44444689999****966.44444444444443 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   9.4      0.49   1.8e+02      64     164 ..     203     307 ..     201     313 .. 0.84
   2 ?    6.6   2.2     0.015       5.8     100     163 ..     321     384 ..     315     396 .. 0.85
   3 ?   10.3   8.8    0.0012      0.44      55     165 ..     353     463 ..     342     468 .. 0.85
   4 ?    4.5   1.2     0.066        25      69     139 ..     444     514 ..     439     525 .. 0.79
   5 ?    5.5   6.7     0.033        12      67     146 ..     707     786 ..     700     814 .. 0.49
   6 ?   11.0  14.9   0.00071      0.27      66     174 ..     816     924 ..     813     933 .. 0.94
   7 ?    4.8   6.2     0.057        21      91     156 ..     883     948 ..     877     960 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.49
                            DUF745  64 veqleqelreaeavvqeekkslqsseanakaaakaak..qaqqqle.alkal.lkaakenlenaeqvaagaqqelae 136
                                       +e++e+ ++ea+  ++e ++ l + e   ++a k ++  + ++++e  lka+ l+  ++ le++e+ a+  +++l++
  gi|313127260|ref|YP_004037530.1| 203 LESVEERIEEADLRIEEKESRLDQLEDERETALKYQSlrEEREEYEgYLKAAeLEDKRADLERTESKAETKAEKLES 279
                                       68999********************999999987654113334443267765588899999**************** PP

                            DUF745 137 ktqlleaAkkRveeLkkqlkearkdlek 164
                                        ++ l++ + Rv +L+ +l+e  k+ e+
  gi|313127260|ref|YP_004037530.1| 280 LREELDTRQGRVSRLEAELDELSKEIER 307
                                       *********************9999876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                            DUF745 100 kqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdle 163
                                       ++++ ++++l+++++aa++++++ae+   +a  el+ k++++++ +  +  +k + ++++++ +
  gi|313127260|ref|YP_004037530.1| 321 ESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEKASVKSEIK 384
                                       567788999**********************************999988888877777777654 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0012
                            DUF745  55 AaLaGKqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaq 131
                                         L+ Kq +++ +e+++r  +    ++k+++++ e+ ++ +++  +++ ++++ lk+ l+a k++le++++  +  q
  gi|313127260|ref|YP_004037530.1| 353 VELDRKQEMIDDVEDDIRAVKVEKASVKSEIKTKETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQ 429
                                       56889********************************************************9999999988888887 PP

                            DUF745 132 qelaektqlleaAkkRveeL...kkqlkearkdlekt 165
                                       +   ek  ll++ ++R  e+   +++++e+r++l   
  gi|313127260|ref|YP_004037530.1| 430 R---EKDRLLDDTRRRSSEIsetQEKISEVREELPTL 463
                                       5...7***********998822234566677776655 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.066
                            DUF745  69 qelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektq 139
                                       +e++e+++ ++e+ ++l + +a+++  ++  ++a+++ + +  +++  +e  +++++  ++++ el++k++
  gi|313127260|ref|YP_004037530.1| 444 SEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSDLDEVEDELRSKQS 514
                                       67888888888888888888888888888888888888888888888888888888888888888888875 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.033
                            DUF745  67 leqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqllea 143
                                       le++ re e+ +++++++l  + ++a+ aa+ ++++++ +++ ++ +++ k+++e++e+  ++  ++ ae  + +++
  gi|313127260|ref|YP_004037530.1| 707 LEDDRREIEQEIRDIESQLDDAREKASDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQS 783
                                       55555555555555555555555555555555555555555555555555555555554444444433333333333 PP

                            DUF745 144 Akk 146
                                         +
  gi|313127260|ref|YP_004037530.1| 784 LDT 786
                                       333 PP

  == domain 6  score: 11.0 bits;  conditional E-value: 0.00071
                            DUF745  66 qleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlle 142
                                       +l+++  e  a ++e ++ + +    ++  +  ++ a+  +e l++++++a+++ ++a++v  + +q ++ek++ le
  gi|313127260|ref|YP_004037530.1| 816 ELTAQADEIRAEIEEKEDRMDELDGRLNELQLEKEYAEDAIEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLE 892
                                       6899999********************************************************************** PP

                            DUF745 143 aAkkRveeLkkqlkearkdlektkkaAykAac 174
                                       + ++ v  L+ +lke +++  + ++  + A++
  gi|313127260|ref|YP_004037530.1| 893 EKREAVSDLEAELKELKAERSDLREDVREAKS 924
                                       ******************99999999988875 PP

  == domain 7  score: 4.8 bits;  conditional E-value: 0.057
                            DUF745  91 nakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlk 156
                                       +++  +++ ++ ++ ++ l+a lk+ k++ +++++   +a++e +e+++ +e  ++Rve+L++  +
  gi|313127260|ref|YP_004037530.1| 883 AIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAE 948
                                       444445555556666666666666666666666666666666666666666666666666665544 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.9    0.0018      0.67      34      94 ..     251     308 ..     231     310 .. 0.92
   2 ?    2.4   0.4       0.5   1.9e+02      11      61 ..     316     366 ..     312     381 .. 0.68
   3 ?    4.5   2.9      0.11        42      10      67 ..     378     435 ..     370     441 .. 0.86
   4 ?    6.6   1.4     0.026       9.6      40      91 ..     440     491 ..     434     496 .. 0.75
   5 ?   -0.0   0.2         3   1.1e+03      46      75 ..     700     726 ..     690     746 .. 0.54
   6 ?    6.5   7.4     0.027        10      32      93 ..     728     786 ..     707     789 .. 0.81
   7 ?    6.5   7.8     0.028        11      32      91 ..     749     809 ..     738     813 .. 0.79
   8 ?    2.7   3.0      0.41   1.5e+02      38      92 ..     790     846 ..     785     849 .. 0.76
   9 ?    1.8   1.4      0.79     3e+02      34      68 ..     812     846 ..     808     864 .. 0.63
  10 ?    2.6   4.0      0.44   1.6e+02      25      79 ..     856     910 ..     848     915 .. 0.90
  11 ?    6.9   9.0      0.02       7.6       8      94 ..     874     960 ..     870     962 .. 0.89
  12 ?    8.1   0.6    0.0089       3.3      11      67 ..     975    1031 ..     972    1040 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0018
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                        k ++l+d+ a+le++ +k + k e+l+++ +++d  + +v++Le+   eLDe ske+E k
  gi|313127260|ref|YP_004037530.1| 251 LKAAELEDKRADLERTESKAETKAEKLESLREELDTRQGRVSRLEA---ELDELSKEIERK 308
                                       57789****************************************6...9********987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.5
                           BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelq 61 
                                       +++e+e+++ +++ Le+  eaa+ ++++ +++  ++ ++l++ +e+ + ++
  gi|313127260|ref|YP_004037530.1| 316 IKSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVE 366
                                       677788888888888888888888887777776666666666555555444 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.11
                           BLOC1_2  10 yleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqi 67 
                                        +++e++   +++  +e+   ++ +++++lkd++a  +++le+l+ + + lq  ++++
  gi|313127260|ref|YP_004037530.1| 378 SVKSEIKTKETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRL 435
                                       5788999999999999999999999999999999999999999999999999888765 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.026
                           BLOC1_2  40 kdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                       +++ ++++++ ek++e  eel  ++ ++ +++ ++++ e++ +++D  + +L
  gi|313127260|ref|YP_004037530.1| 440 RRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDL 491
                                       5667777888888888888888888888888888888888888888777766 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 3
                           BLOC1_2  46 lekkleklnekyeelqpylqqidqiekqvt 75 
                                       l++++++l+      ++  q+i +ie q++
  gi|313127260|ref|YP_004037530.1| 700 LAVEISDLED---DRREIEQEIRDIESQLD 726
                                       3333334433...33333344444444444 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.027
                           BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       a ek  + +d++ s+e+++++ +e    +++++ +i+q+e++++eL e  +e+De +++L  
  gi|313127260|ref|YP_004037530.1| 728 AREKASDAADRVRSVEADIDRAEE---DVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLDT 786
                                       666777777777777777777777...**********************9999999988865 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.028
                           BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLDeyskeL 91 
                                       a+e +++ k ++++le+ +e+l+ek +e+++ +q++d +i++ ++++ ++ se+De  +eL
  gi|313127260|ref|YP_004037530.1| 749 AEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLDtDIDALTADIDDVQSEIDELESEL 809
                                       5666777788889999999999999999999998887568888888888888888877777 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.41
                           BLOC1_2  38 klkdvaaslekkleklnekye..elqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       +l+  ++++++++++l+++ +  ++ ++  q d+i ++++e e+  +eLD    eL+
  gi|313127260|ref|YP_004037530.1| 790 ALTADIDDVQSEIDELESELAdsKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQ 846
                                       566667778888888877655457888889999999999999999999998888885 PP

  == domain 9  score: 1.8 bits;  conditional E-value: 0.79
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqid 68 
                                       +k+ +l+ +a+++++++e+ + + +el+  l++++
  gi|313127260|ref|YP_004037530.1| 812 SKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQ 846
                                       55666677777777777777777777766666654 PP

  == domain 10  score: 2.6 bits;  conditional E-value: 0.44
                           BLOC1_2  25 LeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       +e lNe++++  +  +d+ + +++k ++++ek++ l+++ + + ++e++++eL++
  gi|313127260|ref|YP_004037530.1| 856 IEDLNETVESAQDRKADARDVIREKEQAIEEKEAVLEEKREAVSDLEAELKELKA 910
                                       7889999999999999999999999999***********************9975 PP

  == domain 11  score: 6.9 bits;  conditional E-value: 0.02
                           BLOC1_2   8 skyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseL 84 
                                       +++++++ +a  e+  +Le+  ea+s   ++lk+  a+ ++  e+++e + e +++ ++++++e +v+ L e +++L
  gi|313127260|ref|YP_004037530.1| 874 RDVIREKEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDVREAKSERDEQRDKVERVESRVENLRESAERL 950
                                       677888888888889999999999999999999999999999999999999************************** PP

                           BLOC1_2  85 DeyskeLEak 94 
                                          + eLEa 
  gi|313127260|ref|YP_004037530.1| 951 AWEIDELEAE 960
                                       *999999986 PP

  == domain 12  score: 8.1 bits;  conditional E-value: 0.0089
                           BLOC1_2   11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqi 67  
                                        ++++++  + +++ Le +N  a+ +y++++  +++l++  + l e+ + +q  ++q 
  gi|313127260|ref|YP_004037530.1|  975 VQENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQF 1031
                                        6788889999***********************************999998877764 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.6      0.54     2e+02      21      54 ..     261     294 ..     250     320 .. 0.59
   2 ?    4.5   2.3      0.15        56      13      60 ..     372     418 ..     361     435 .. 0.75
   3 ?    4.0   2.1      0.21        79      17      54 ..     440     477 ..     427     545 .. 0.68
   4 ?    4.1   1.0       0.2        73      23      55 ..     746     778 ..     723     876 .. 0.69
   5 ?    7.3   2.0      0.02       7.4      17      54 ..     878     915 ..     858     964 .. 0.82
   6 ?   -0.4   0.0         5   1.9e+03      33      50 ..     996    1013 ..     974    1051 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.54
                                       XXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHH CS
                            FliD_N  21 dkleqkktklewkqsayrelnsklsnlksalsal 54 
                                         le+ ++k e+k +++++l+ +l++ +  +s l
  gi|313127260|ref|YP_004037530.1| 261 ADLERTESKAETKAEKLESLREELDTRQGRVSRL 294
                                       4566666666666666666666666655544333 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.15
                                       XXXXXXXXXX.XXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXXGGGG CS
                            FliD_N  13 mkaerakldk.leqkktklewkqsayrelnsklsnlksalsalsksstf 60 
                                       +k+e+a ++  +++k+t+l +  +++ ++ +++++lk++l+  +k+s++
  gi|313127260|ref|YP_004037530.1| 372 VKVEKASVKSeIKTKETELAEVEAEIDSVDTEFDELKDELA--AKKSQL 418
                                       78889966666999999999999999999999999999763..223333 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.21
                                       XXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHH CS
                            FliD_N  17 rakldkleqkktklewkqsayrelnsklsnlksalsal 54 
                                       r++  ++ + ++k+++ ++++ +l+ kls+l s+l++ 
  gi|313127260|ref|YP_004037530.1| 440 RRRSSEISETQEKISEVREELPTLKAKLSDLHSELDKA 477
                                       45555566666666667777777777777776655311 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.2
                                       XXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHX CS
                            FliD_N  23 leqkktklewkqsayrelnsklsnlksalsals 55 
                                       ++++++++e+k++++++l+  +++l+++ +++ 
  gi|313127260|ref|YP_004037530.1| 746 IDRAEEDVEEKKAEIEQLEDRIEELREKRAEVD 778
                                       555666666666666666666666666442221 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHH CS
                            FliD_N  17 rakldkleqkktklewkqsayrelnsklsnlksalsal 54 
                                       r k + +e+k++ le+k++a+++l+ +l++lk + s+l
  gi|313127260|ref|YP_004037530.1| 878 REKEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDL 915
                                       55677899999999999999999999999999966555 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 5
                                        XHHHHHHHHHHHHHHHHH CS
                            FliD_N   33 kqsayrelnsklsnlksa 50  
                                         +++y e++ +l++l++ 
  gi|313127260|ref|YP_004037530.1|  996 AIDEYDEVQADLEDLQDG 1013
                                        578899999999999983 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  21.4     0.022       8.4      79     186 ..     191     305 ..     168     308 .. 0.76
   2 ?    0.8  20.1       1.2   4.4e+02      67     189 ..     317     435 ..     306     439 .. 0.68
   3 ?   11.4  19.8   0.00068      0.25      74     182 ..     380     491 ..     363     492 .. 0.83
   4 ?    8.7  11.6    0.0044       1.7      80     155 ..     439     520 ..     430     525 .. 0.73
   5 ?   10.1  24.3    0.0017      0.63      71     185 ..     733     848 ..     697     850 .. 0.82
   6 ?    6.4  19.7     0.023       8.7      66     167 ..     880     988 ..     849     995 .. 0.85
   7 ?    1.6   5.0      0.67   2.5e+02      77     145 ..     972    1040 ..     954    1057 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.022
                           UPF0242  79 eldeglktkee...aleelqeeeeeLkeeldakeeelerlkeenq.qLqek.leaiaedfeelklele.....eqLa 145
                                       e d   ++ke+   +le ++e+ ee   ++++ke+ l +l+ e +  L+ + l +  e++e +++++e     + L+
  gi|313127260|ref|YP_004037530.1| 191 EFD---AKKEDafgELESVEERIEEADLRIEEKESRLDQLEDEREtALKYQsLREEREEYEGYLKAAEledkrADLE 264
                                       444...333334556777777777777779999999999998887677766245556688888876653333357** PP

                           UPF0242 146 ekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEi 186
                                       + + + ++ +e++e++r++l+ rq ++++Le+    l+ Ei
  gi|313127260|ref|YP_004037530.1| 265 RTESKAETKAEKLESLREELDTRQGRVSRLEAELDELSKEI 305
                                       *************************************9998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
                           UPF0242  67 kskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeq 143
                                       ks++e+ +  +  l++ ++  e+ + e++ e ++   eld k+e +   + +   +++++  ++ ++    +  e +
  gi|313127260|ref|YP_004037530.1| 317 KSEIESVKGEIDRLENAIEAAEDRIDEAETERRKAFVELDRKQEMIDDVEDDIRAVKVEKASVKSEI----KTKETE 389
                                       3444444444455555555555566666666666666677777777776666666665555544444....556788 PP

                           UPF0242 144 LaekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEiktL 189
                                       Lae +  ++    ++ e++ +l  ++ q e+L +  +Dl+ E   L
  gi|313127260|ref|YP_004037530.1| 390 LAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRL 435
                                       9999999*******************************99886555 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00068
                           UPF0242  74 eaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklel...eeqLaek 147
                                       ++ ++ ++ +l++ e ++  +  e +eLk+el+ak+++le+lk e + Lq ++     d  + + e+   +e++ e 
  gi|313127260|ref|YP_004037530.1| 380 KSEIKTKETELAEVEAEIDSVDTEFDELKDELAAKKSQLEELKTERNDLQREKDRLLDDTRRRSSEIsetQEKISEV 456
                                       3334444456888889**********************************999999998888776551116789999 PP

                           UPF0242 148 qellqeyqetieeqrsvlekrqdqieqLeskVrDl 182
                                       +e l ++++++++++s+l+k +++ ++++  ++Dl
  gi|313127260|ref|YP_004037530.1| 457 REELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDL 491
                                       **********************9999999999998 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0044
                           UPF0242  80 ld...eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkl...eleeqLaekqel 150
                                       ++    ++++ +e++ e++ee   Lk +l+  ++el + ++++q++    e+  ed ++lk    e+e++L+ kq  
  gi|313127260|ref|YP_004037530.1| 439 TRrrsSEISETQEKISEVREELPTLKAKLSDLHSELDKAEKNKQKIDGVIEDLREDRSDLKSdldEVEDELRSKQSE 515
                                       44444677888899999999999999999999999999999999998888888886666554111667778888877 PP

                           UPF0242 151 lqeyq 155
                                         e++
  gi|313127260|ref|YP_004037530.1| 516 YAELE 520
                                       77665 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0017
                           UPF0242  71 eekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklelee.qLae 146
                                       +     + + + +++  ee +ee ++e e+L++++++  e+ ++  ee q+L     a  +d+++++ e++e + + 
  gi|313127260|ref|YP_004037530.1| 733 SDAADRVRSVEADIDRAEEDVEEKKAEIEQLEDRIEELREKRAEVDEEMQSLDTDIDALTADIDDVQSEIDElESEL 809
                                       33333444444789999********************************************9999999887622333 PP

                           UPF0242 147 kqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyE 185
                                          ++ e+ ++  e r+++e+++d+  +L+ + + l+ E
  gi|313127260|ref|YP_004037530.1| 810 ADSKIPELTAQADEIRAEIEEKEDRMDELDGRLNELQLE 848
                                       56899***************************9999876 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.023
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkee.......ldakeeelerlkeenqqLqekleaiaedfee 135
                                       +++ +eekea+l e++e ++  e +l+el++e  +L+e         d++  ++er + + ++L+e +e  a +++e
  gi|313127260|ref|YP_004037530.1| 880 KEQAIEEKEAVLEEKREAVSDLEAELKELKAERSDLREDvreakseRDEQRDKVERVESRVENLRESAERLAWEIDE 956
                                       5677999999999999999999999999999999999997777777677777788888888899999999999**** PP

                           UPF0242 136 lkleleeqLaekqellqeyqetieeqrsvlek 167
                                       l  e+ e   e+   ++e qe+i+++   +e+
  gi|313127260|ref|YP_004037530.1| 957 LEAEVGEYDPEEIPDHDEVQENIQQLTGKMES 988
                                       ********99999************9998885 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.67
                           UPF0242   77 lteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLa 145 
                                          e +e++++   ++e l+  ++   +e+d+ +  le l+     L e+ + i+  +e++  + +e+  
  gi|313127260|ref|YP_004037530.1|  972 HDEVQENIQQLTGKMESLEPVNMLAIDEYDEVQADLEDLQDGRDVLAEERQGIQDRIEQFEAQKKETFM 1040
                                        233336666666677777777777777788888888888888888888888888866666666666554 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.4      0.24        88      34      65 ..     202     233 ..     193     265 .. 0.79
   2 ?   10.6   1.7    0.0013      0.47      30      90 ..     272     338 ..     264     343 .. 0.81
   3 ?    6.2   5.5     0.029        11      32      99 ..     373     438 ..     368     441 .. 0.91
   4 ?    2.7   3.6      0.35   1.3e+02      30      86 ..     441     502 ..     435     520 .. 0.61
   5 ?    6.8   0.1     0.018       6.8      65      94 ..     697     726 ..     693     727 .. 0.93
   6 ?    9.7   3.9    0.0023      0.86      31      85 ..     756     808 ..     743     818 .. 0.58
   7 ?   -0.9   1.8       4.9   1.8e+03      39      64 ..     825     850 ..     812     894 .. 0.69
   8 ?    0.7   3.4       1.5   5.5e+02      41      89 ..     876     922 ..     844     927 .. 0.76
   9 ?    5.2   1.1     0.061        23      32      83 ..     916     965 ..     915     982 .. 0.89
  10 ?   -1.6   0.1       7.6   2.8e+03      34      75 ..     971    1010 ..     968    1029 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.24
                           DUF2730  34 dleklaekveendkrlteletkvenLPtakdl 65 
                                       +le+++e +ee d r++e e+++++L  +++ 
  gi|313127260|ref|YP_004037530.1| 202 ELESVEERIEEADLRIEEKESRLDQLEDERET 233
                                       68999********************9776664 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0013
                           DUF2730  30 akredleklaekveendkrlteletkvenLPta......kdlekLkllladlrgelkaleaevrqls 90 
                                       +k e le+l e++++ + r+++le+++++L  +      ++  ++k +++ ++ge++ le+ +++ +
  gi|313127260|ref|YP_004037530.1| 272 TKAEKLESLREELDTRQGRVSRLEAELDELSKEierkgeDEQLRIKSEIESVKGEIDRLENAIEAAE 338
                                       688999************************875222222455688999***********99998766 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.029
                           DUF2730  32 redleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvdLLLen 99 
                                       + + ++++ +++++++ l+e+e++++++ t  ++++Lk +la  + +l++l+ e + l++  d LL++
  gi|313127260|ref|YP_004037530.1| 373 KVEKASVKSEIKTKETELAEVEAEIDSVDT--EFDELKDELAAKKSQLEELKTERNDLQREKDRLLDD 438
                                       66788999*******************976..688*************************99999976 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.35
                           DUF2730  30 akredleklaekveendkrlteletkvenLPtakd.....lekLkllladlrgelkaleaev 86 
                                        + +++++ +ek++e ++ l +l++k+++L ++ d      +k++  ++dlr + ++l+ ++
  gi|313127260|ref|YP_004037530.1| 441 RRSSEISETQEKISEVREELPTLKAKLSDLHSELDkaeknKQKIDGVIEDLREDRSDLKSDL 502
                                       45577888888888888888888888888865433100002334444444444444444444 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.018
                           DUF2730  65 lekLkllladlrgelkaleaevrqlshqvd 94 
                                       le+L ++++dl+ + +++e+e+r ++ q+d
  gi|313127260|ref|YP_004037530.1| 697 LERLAVEISDLEDDRREIEQEIRDIESQLD 726
                                       89************************9976 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.0023
                           DUF2730  31 kredleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleae 85 
                                       k+ ++e+l++ +ee +++ +e++ ++++L t  d+++L  ++ d++ e+++le e
  gi|313127260|ref|YP_004037530.1| 756 KKAEIEQLEDRIEELREKRAEVDEEMQSLDT--DIDALTADIDDVQSEIDELESE 808
                                       5555555555555555555555555555543..4555555555555555555555 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 4.9
                           DUF2730  39 aekveendkrlteletkvenLPtakd 64 
                                         ++ee++ r++el+ ++++L  +k+
  gi|313127260|ref|YP_004037530.1| 825 RAEIEEKEDRMDELDGRLNELQLEKE 850
                                       44556666666666666665554444 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 1.5
                           DUF2730  41 kveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrql 89 
                                       +++e+++ ++e e+ +e+   ++ +++L+ +l++l++e ++l+++vr+ 
  gi|313127260|ref|YP_004037530.1| 876 VIREKEQAIEEKEAVLEE--KREAVSDLEAELKELKAERSDLREDVREA 922
                                       366666666666666665..57778999999999999999998888765 PP

  == domain 9  score: 5.2 bits;  conditional E-value: 0.061
                           DUF2730  32 redleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkale 83 
                                       red+ + + + +e++ +++++e++venL  ++  e+L  ++ +l++e+ + +
  gi|313127260|ref|YP_004037530.1| 916 REDVREAKSERDEQRDKVERVESRVENL--RESAERLAWEIDELEAEVGEYD 965
                                       78999999999999**************..566789*********9998876 PP

  == domain 10  score: -1.6 bits;  conditional E-value: 7.6
                           DUF2730   34 dleklaekveendkrlteletkvenLPtakdlekLkllladl 75  
                                        d+ +++e++++   ++++le  v n+   ++ ++++ +l+dl
  gi|313127260|ref|YP_004037530.1|  971 DHDEVQENIQQLTGKMESLEP-V-NMLAIDEYDEVQADLEDL 1010
                                        667777777777777777774.2.333444555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2521  (0.14061); expected 358.6 (0.02)
Passed bias filter:                      785  (0.0437838); expected 358.6 (0.02)
Passed Vit filter:                       330  (0.0184059); expected 17.9 (0.001)
Passed Fwd filter:                       250  (0.0139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              48  [number of targets reported over threshold]
# CPU time: 6.01u 0.32s 00:00:06.33 Elapsed: 00:00:01.09
# Mc/sec: 3311.24
//
Query:       gi|313127261|ref|YP_004037531.1|  [L=157]
Description: hypothetical protein Hbor_25320 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00027   21.0   0.2    0.00034   20.7   0.2    1.2  1  GerPC       Spore germination protein GerPC
  ------ inclusion threshold ------
      0.067   13.8   1.2      0.067   13.8   1.2    2.3  2  SlyX        SlyX
      0.093   12.8   2.1       0.15   12.1   2.1    1.4  1  bZIP_1      bZIP transcription factor
       0.13   12.7   2.6       0.32   11.4   2.6    1.7  1  FlaC_arch   Flagella accessory protein C (FlaC)
       0.48   10.2   3.2       0.27   11.0   0.8    1.6  2  ATP-synt_D  ATP synthase subunit D
       0.75   10.4  13.5        5.5    7.6  13.5    1.9  1  Striatin    Striatin family
        3.4    8.2   8.6         85    3.7   8.6    2.3  1  ZapB        Cell division protein ZapB
        3.7    6.8   8.4        4.4    6.6   8.4    1.2  1  DUF4407     Domain of unknown function (DUF4407)
        5.9    6.7   7.4       0.23   11.2   1.2    1.8  2  DivIC       Septum formation initiator
          8    4.5  21.0        9.7    4.3  21.0    1.1  1  Nop14       Nop14-like family


Domain annotation for each model (and alignments):
>> GerPC  Spore germination protein GerPC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   1.9e-07   0.00034       2     108 ..       2     107 ..       1     125 [. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.9e-07
                             GerPC   2 qklekqleelqeeleelkkkpatsiekieYkFDqLKvekLeGTLNiGlnPsdlg.ksiedfaveqaktvapeneaes 77 
                                       ++le++++elq  ++ l ++   + e++    Dq  v+   G   +G +P++++ +s  + +v+ a + ++e++a++
  gi|313127261|ref|YP_004037531.1|   2 EELESKVAELQAAVNGLTEELVETKERVRLLEDQVEVDLTAGSRPVGHAPAQPDvESDAEPEVQAADQ-SDETTAQA 77 
                                       68***************************************************655555566666665.44455555 PP

                             GerPC  78 elfqeiqeeveayLeeeapelleelekqyev 108
                                       e  +e +++ +++L e+  + ++++e+  + 
  gi|313127261|ref|YP_004037531.1|  78 ES-DEQTDDSNSHLRESPAQAMSRAETSAQP 107
                                       54.67778889************99998765 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.2   3.7e-05     0.067       6      41 ..       2      37 ..       1      43 [. 0.93
   2 ?   -0.1   0.5      0.85   1.5e+03      22      49 ..      69      96 ..      58     112 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  6 eeLEiklafqedtieeLndvvaeqqqqidrlqrqlr 41
                                      eeLE+k+a ++ +++ L ++++e  +++  l+ q++
  gi|313127261|ref|YP_004037531.1|  2 EELESKVAELQAAVNGLTEELVETKERVRLLEDQVE 37
                                      89*****************************99986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.85
                                      HHHHHHHHHHHHHHHHHHHHHHHHT-XX CS
                              SlyX 22 Lndvvaeqqqqidrlqrqlrllaerlke 49
                                       +d+ ++q++  ++      +l+e  ++
  gi|313127261|ref|YP_004037531.1| 69 QSDETTAQAESDEQTDDSNSHLRESPAQ 96
                                      4555555655555555555566555533 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.1   8.6e-05      0.15      28      63 ..       1      36 [.       1      37 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.6e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 28 ieeLerrvkaLekeNksLkseleelkkevekLkskv 63
                                      +eeLe++v++L++    L +el e k+ v  L+++v
  gi|313127261|ref|YP_004037531.1|  1 MEELESKVAELQAAVNGLTEELVETKERVRLLEDQV 36
                                      69***************************9988876 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.6   0.00018      0.32       2      38 ..       1      37 [.       1      41 [. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                         FlaC_arch  2 idelEnklsklsteletvkkeneelsksveelkenVk 38
                                      ++elE+k+ +l+  ++ + +e+ e ++ v  l+++V+
  gi|313127261|ref|YP_004037531.1|  1 MEELESKVAELQAAVNGLTEELVETKERVRLLEDQVE 37
                                      79********************************994 PP

>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.8   0.00015      0.27     135     163 ..       6      34 ..       2      36 .. 0.90
   2 ?   -1.9   0.1       1.4   2.5e+03     114     129 ..      77      92 ..      59     113 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        ATP-synt_D 135 velasletslelLdeeikktnrRvNaLek 163
                                        ++a+l+ +++ L ee+ +t+ Rv +Le 
  gi|313127261|ref|YP_004037531.1|   6 SKVAELQAAVNGLTEELVETKERVRLLED 34 
                                       589************************96 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                                       SSSTCHHHHHHHHCHH CS
                        ATP-synt_D 114 lrtgaqldeavealre 129
                                       +++ +q d+  + lre
  gi|313127261|ref|YP_004037531.1|  77 AESDEQTDDSNSHLRE 92 
                                       3333333333222222 PP

>> Striatin  Striatin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  13.5     0.003       5.5      29     118 ..       3     129 ..       1     154 [. 0.54

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.003
                          Striatin  29 EmkarIakLegerrgaenlkkdlvrrikmLEyalkqerakylkl.................kegtsaakenkkkeke 88 
                                       E+ +++a+L+   +g  +   + + r+++LE +++   +   +                   +++++++e++ ++++
  gi|313127261|ref|YP_004037531.1|   3 ELESKVAELQAAVNGLTEELVETKERVRLLEDQVEVDLTAGSRPvghapaqpdvesdaepeVQAADQSDETTAQAES 79 
                                       9********************************99997653333565555544433322211122222111222222 PP

                          Striatin  89 eeeaeeeekseeeskskekksakeslkks...................................e 118
                                       +e++++++++ +e               s                                   +
  gi|313127261|ref|YP_004037531.1|  80 DEQTDDSNSHLRE---------------SpaqamsraetsaqpsddaslidadandstvsdpteS 129
                                       2222222222112...............1222233333334555666676666665555544440 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   8.6     0.048        85       7      42 ..       2      37 ..       1     103 [. 0.63

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.048
                              ZapB  7 eqLEskiqkaidtitlLqmeieeLkeeneelkeenr 42
                                      e+LEsk+ ++   +  L +e+ e ke+++ l+++ +
  gi|313127261|ref|YP_004037531.1|  2 EELESKVAELQAAVNGLTEELVETKERVRLLEDQVE 37
                                      677777777777777777777777777777776654 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   8.4    0.0025       4.4     131     235 ..       4     106 ..       1     152 [. 0.57

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0025
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake..kkaqldaaqaelaelkak 205
                                       l++++ael+a ++ l +e+ + ++r++ l+++++  l+   g++  g a   p  ++    +  +a q + ++++a+
  gi|313127261|ref|YP_004037531.1|   4 LESKVAELQAAVNGLTEELVETKERVRLLEDQVEVDLTA--GSRPVGHAPAQPDVESdaEPEVQAADQSDETTAQAE 78 
                                       567888888888888888888888888888888877776..333222222233333321333333333333333333 PP

                           DUF4407 206 ldatarlaalraelaeleaerakeraasqa 235
                                         +++++++ ++ l e  a++ +++++s++
  gi|313127261|ref|YP_004037531.1|  79 --SDEQTDDSNSHLRESPAQAMSRAETSAQ 106
                                       ..5555555555444444443333333333 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.2   0.00013      0.23      20      57 ..       2      38 ..       1      42 [. 0.88
   2 ?   -3.2   0.6       4.3   7.7e+03      35      55 ..     133     153 ..     128     155 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXX CS
                             DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedyi 57
                                       +l++++a+lqa ++ l++e  e +++v++L  d+  +
  gi|313127261|ref|YP_004037531.1|  2 EELESKVAELQAAVNGLTEELVETKERVRLL-EDQVEV 38
                                      68999**************************.577555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.3
                                       HHHHHHHHHHHHHCC-XXXXX CS
                             DivIC  35 klkaeneeLeaevkdLksded 55 
                                       ++k ++ e ++e +  ++d d
  gi|313127261|ref|YP_004037531.1| 133 EVKSDESESDDEAESAEDDSD 153
                                       566666777777777766655 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  21.0    0.0054       9.7     300     395 ..      57     151 ..      18     155 .. 0.47

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0054
                             Nop14 300 eeeeeekkkkkkkeasaDdldddfvleeeeeeeefglgkglka..taeee.eeededdfeedddlveseseeeeeee 373
                                       e++ e + +      + D+   + + +e++++++  l ++ ++  +++e   +  +d + +d+d+++s+ ++ + e+
  gi|313127261|ref|YP_004037531.1|  57 ESDAEPEVQAA---DQSDETTAQAESDEQTDDSNSHLRESPAQamSRAETsAQPSDDASLIDADANDSTVSDPT-ES 129
                                       33333222222...346777777777777777777776666334533344255555555666655555544443.33 PP

                             Nop14 374 eedeeeeedeeeeeeeeededd 395
                                       e+de +++++e+++e+e+ edd
  gi|313127261|ref|YP_004037531.1| 130 EDDEVKSDESESDDEAESAEDD 151
                                       3333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1754  (0.0978303); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 1039.63
//
Query:       gi|313127262|ref|YP_004037532.1|  [L=272]
Description: esterase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-19   68.8   0.8    1.5e-18   67.5   0.8    1.6  1  Abhydrolase_3  alpha/beta hydrolase fold
    5.4e-10   39.1   0.0    9.4e-08   31.8   0.0    2.4  2  Peptidase_S9   Prolyl oligopeptidase family
    1.3e-07   31.2   0.2     0.0013   18.1   0.0    2.8  2  Hydrolase_4    Serine aminopeptidase, S33
    1.5e-07   30.7   0.0    3.8e-07   29.3   0.0    1.5  1  COesterase     Carboxylesterase family
      1e-06   28.7   0.0       0.11   12.3   0.0    3.0  3  Abhydrolase_2  Phospholipase/Carboxylesterase
     0.0034   17.0   0.0      0.025   14.2   0.0    2.2  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
      0.053   13.1   0.0       0.95    9.0   0.0    2.4  2  DLH            Dienelactone hydrolase family
      0.088   12.0   0.0       0.13   11.4   0.0    1.2  1  DUF2099        Uncharacterized protein conserved in archaea (
        0.2   11.1   6.9       0.62    9.5   3.7    2.7  3  Esterase_phd   Esterase PHB depolymerase
       0.21   11.4   0.1       0.44   10.3   0.1    1.5  1  Imm27          Immunity protein 27


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.8   8.2e-22   1.5e-18       1     209 [.      44     251 ..      44     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 8.2e-22
                                       EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEE CS
                     Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaG 77 
                                       +v +HGGG+ +g+ +  ++++ +la++ + v+  +d+rl+ e+ fPaa+ d+ aa+rw +++a + g+ p+ri+ +G
  gi|313127262|ref|YP_004037532.1|  44 VVLLHGGGWHAGDRSDLTQVALSLAER-RFVCAVPDFRLSREATFPAAIRDVKAAIRWCRANADAVGVAPDRIATFG 119
                                       6899********************986.89999*****************************99************* PP

                                       ETHHHHHHHHHHHHHHHTT.---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGST CS
                     Abhydrolase_3  78 dSaGGnlaaavalrardeg.epkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylpeadrddp 153
                                        S G++la  +al   d    p +a++      t      +++      ++ +++  ra+l +f+    +e   +  
  gi|313127262|ref|YP_004037532.1| 120 PSTGAHLAVLAALTGNDPRlAPDPAHVSDAVANTSD--AVTATVGVGGLYNFEHTPDRAELTAFLGGSRNEVPERYE 194
                                       *********999999987534445555555554322..222222222222222333455555555555556666667 PP

                                       TTSGGGCS-SST---EE.EEEETT-TTHH.HHHHHHHHHHHTT--EEEEEETTEETTG CS
                     Abhydrolase_3 154 laspllaedlsglpptl.vvvaefDplrd.egeayaerlraagvevelieyegmvHgf 209
                                       lasp  + d    pptl +  ++ D+l    +e +++ l++ag ++e+++ +g+ H +
  gi|313127262|ref|YP_004037532.1| 195 LASPSSHLDDG-GPPTLlLHGGDDDVLPAmASELFYDGLEEAGIDAECVVADGVGHHV 251
                                       89988663444.5565505556667776514577899*******************86 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0078        14      46      83 ..      92     132 ..      59     139 .. 0.74
   2 !   31.8   0.0   5.2e-11   9.4e-08      91     192 ..     156     255 ..     149     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0078
                                       HHHHHHHHHH...HHTTS--GGGEEEEEETHHHHHHHHHHH CS
                      Peptidase_S9  46 dDfiaaaeal...akegyvdserlaitGgSyGGyltgaaln 83 
                                       +D+ aa+++    a+   v ++r+a +G S G  l+  a+ 
  gi|313127262|ref|YP_004037532.1|  92 RDVKAAIRWCranADAVGVAPDRIATFGPSTGAHLAVLAAL 132
                                       45555555551114555799************988766554 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 5.2e-11
                                       EEEEESE---CCCHHCSTTS..THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHH CS
                      Peptidase_S9  91 aavaevpvvdvlrydsdtdl..lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealkl 165
                                       a+ a v+v  + ++  ++d   lt+ + + g  +e +e y+ +sp s+ld     pp+Ll+hG  Dd  p   ++ +
  gi|313127262|ref|YP_004037532.1| 156 AVTATVGVGGLYNFEHTPDRaeLTA-FLG-GSRNEVPERYELASPSSHLDD--GGPPTLLLHGGDDDVLPAMASELF 228
                                       6778888888888888887755555.444.555579***************..************************ PP

                                       HHHHH--S-SEEEEEETTS-SSTTSSH CS
                      Peptidase_S9 166 vaaLqkkgknvlllifpdegHgvgkpr 192
                                       ++ L+++g +++ ++  + gH v +++
  gi|313127262|ref|YP_004037532.1| 229 YDGLEEAGIDAECVVADGVGHHVLDEQ 255
                                       *********************887654 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00024      0.43       3      94 ..      40     131 ..      38     142 .. 0.65
   2 !   18.1   0.0   7.2e-07    0.0013     193     238 ..     208     255 ..     195     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00024
                       Hydrolase_4   3 pkavvvlvHGlaehsgryae...laeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpel 76 
                                        +a+vvl+HG + h+g  ++   +a  La++ f ++  D r    s     + + f   ++D++a+++  +++    
  gi|313127262|ref|YP_004037532.1|  40 RRALVVLLHGGGWHAGDRSDltqVALSLAERRFVCAVPDFR---LS-----REATFPAAIRDVKAAIRWCRANADAV 108
                                       79*************98766222566788888888888877...33.....23455566666666665555444443 PP

                       Hydrolase_4  77 .....plfllGhSmGGliallyl 94 
                                            ++  +G S+G+ +a+l++
  gi|313127262|ref|YP_004037532.1| 109 gvapdRIATFGPSTGAHLAVLAA 131
                                       44555667777777777776666 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 7.2e-07
                       Hydrolase_4 193 PllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHellnEp 238
                                       P+lllhG++D v +  as+ +y+ l  +  d +  + +g  H +l E+
  gi|313127262|ref|YP_004037532.1| 208 PTLLLHGGDDDVLPAMASELFYDGLEEAgiDAECVVADGVGHHVLDEQ 255
                                       9*************************9999**************9996 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   2.1e-10   3.8e-07      88     204 ..      26     132 ..      23     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.1e-10
                                       -EEEEEEESSSSSTTSSEEEEEEE--STTTS-BGCG..S-THHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HH CS
                        COesterase  88 LyLnvytPkekkeakkklPVlVwihGggfqtgsase..ydgsaLaaegnvivVtinYRlGvlGFlstgdeeapGNvG 162
                                       L L+vy P+    +  ++  +V +hGgg   g+ s+    + +La++ + +     +Rl         ++ea+  ++
  gi|313127262|ref|YP_004037532.1|  26 LRLDVYRPAGG--SGARRALVVLLHGGGWHAGDRSDltQVALSLAER-RFVCAVPDFRL---------SREATFPAA 90 
                                       99******976..555558*****************54445667777.9*********9.........46888889* PP

                                       HHHHHHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHH CS
                        COesterase 163 llDqvlALrWVkenIasFGGdpervtlfGesAGaasvsllll 204
                                       + D+ +A+rW + n  + G  p+r+  fG s Ga ++ l  l
  gi|313127262|ref|YP_004037532.1|  91 IRDVKAAIRWCRANADAVGVAPDRIATFGPSTGAHLAVLAAL 132
                                       **********************************99877655 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.016        29      12      48 ..      39      75 ..      34      78 .. 0.84
   2 !    8.7   0.0   0.00075       1.4      77     126 ..      81     134 ..      75     140 .. 0.86
   3 !   12.3   0.0     6e-05      0.11     158     208 ..     208     258 ..     189     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                                      ---EEEEEE--TT--SHHHHHHHH.TT--TTEEEEEE CS
                     Abhydrolase_2 12 kaqavviflHGlGdsghawaeaakteaalpnikfifp 48
                                      + +a+v++lHG G  +   ++ +++   l +  f++ 
  gi|313127262|ref|YP_004037532.1| 39 ARRALVVLLHGGGWHAGDRSDLTQVALSLAERRFVCA 75
                                      5789********9999888888888888888888885 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00075
                                       -B-HHHHHHHHHHHHHHHHHHHHTT....--GGGEEEEEETHHHHHHHHHHHT- CS
                     Abhydrolase_2  77 kedeagikksaekleelidaelkkg....ipssriiigGFSqGaalalylaltl 126
                                        ++ea ++++++ +++ i+   ++     +  +ri+ +G S Ga la+ +alt 
  gi|313127262|ref|YP_004037532.1|  81 LSREATFPAAIRDVKAAIRWCRANAdavgVAPDRIATFGPSTGAHLAVLAALTG 134
                                       689999************97777767778*******************999986 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 6e-05
                                       EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--HHHHHH CS
                     Abhydrolase_2 158 pilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsideeemqd 208
                                       p l++Hg +D v+p + +++++  l+++  + e ++  g++H    e++  
  gi|313127262|ref|YP_004037532.1| 208 PTLLLHGGDDDVLPAMASELFYDGLEEAGIDAECVVADGVGHHVLDEQFDW 258
                                       7899**************************************998887765 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.4e-05     0.025      76     123 ..      84     135 ..      24     140 .. 0.72
   2 ?   -1.3   0.0      0.71   1.3e+03     219     256 ..     197     235 ..     185     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                       -TTTTTHHHHHHHHHHHHHH....CTTEEEEEEEEEECHHHHHHHHHCTT-- CS
                     Peptidase_S15  76 tvgdsdeaedgadvidWlak....qpwsnGkVgmtGiSYlGttqllaaatgv 123
                                       + +++  ++d++++i+W ++       + ++++++G S ++ +++laa tg 
  gi|313127262|ref|YP_004037532.1|  84 EATFPAAIRDVKAAIRWCRAnadaVGVAPDRIATFGPSTGAHLAVLAALTGN 135
                                       44578999************5553356899*****************99875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.71
                                       -HHHHHCT--S-EEEEEECCSSTTCCHHHHH.HHHHCCT CS
                     Peptidase_S15 219 nlsedadkvkapvllvgGwnDwnvkngaikl.yealkap 256
                                       ++s+++d  + p+ll++G  D+     a++l y+ l+++
  gi|313127262|ref|YP_004037532.1| 197 SPSSHLDDGGPPTLLLHGGDDDVLPAMASELfYDGLEEA 235
                                       567788888899999999999555565555514555555 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.084   1.5e+02      78     115 ..      90     130 ..      30     140 .. 0.60
   2 ?    9.0   0.0   0.00053      0.95     134     188 ..     196     250 ..     146     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.084
                               DLH  78 vlddlkaavaylksvpe...vstkkvgvvGfCmGGalalll 115
                                         +d+kaa+++ +++ +   v +++++  G   G+ la+l 
  gi|313127262|ref|YP_004037532.1|  90 AIRDVKAAIRWCRANADavgVAPDRIATFGPSTGAHLAVLA 130
                                       33444555555544432111455666666666666666655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00053
                               DLH 134 ekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHa 188
                                        ++ ++ ++   p l l+g+ D + pa + e +   l++a++d+e +v +g+gH 
  gi|313127262|ref|YP_004037532.1| 196 ASPSSHLDDGGPPTLLLHGGDDDVLPAMASELFYDGLEEAGIDAECVVADGVGHH 250
                                       566777788899******************************************5 PP

>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.2e-05      0.13      71     106 ..     218     253 ..     214     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.2e-05
                           DUF2099  71 dfvsfGasEilstalkeglidaavivcdgaGtvivt 106
                                       d++   asE++ ++l+e  ida  +v+dg+G  +++
  gi|313127262|ref|YP_004037532.1| 218 DVLPAMASELFYDGLEEAGIDAECVVADGVGHHVLD 253
                                       6677789************************88766 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.7   0.00034      0.62       5     142 ..      30     159 ..      26     166 .. 0.80
   2 ?   -2.0   0.0       1.1     2e+03     169     184 ..     206     221 ..     199     239 .. 0.76
   3 ?   -3.5   0.0       3.2   5.8e+03     102     120 ..     235     253 ..     220     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00034
                      Esterase_phd   5 lylpp...GarrgamplvvmlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwykdtdraGrGea 78 
                                       +y p    Garr    lvv+lhG   ++ + ++ t++ l   +  +v   p+  l  +a            a r + 
  gi|313127262|ref|YP_004037532.1|  30 VYRPAggsGARR---ALVVLLHGGGWHAGDRSDLTQVALSLAERRFVCAVPDFRLSREATF--------PAAIR-DV 94 
                                       677774446666...9**********************999999999999*9988777752........23334.34 PP

                      Esterase_phd  79 avvvalvdalvdehrvdaarvyvaGlsaGaaladllalhypd.vfaavalhsGlalGeaadvisa 142
                                       ++ +   +a +d+ +v + r+   G s+Ga la l al+  d ++a    h   a+ +++d+++a
  gi|313127262|ref|YP_004037532.1|  95 KAAIRWCRANADAVGVAPDRIATFGPSTGAHLAVLAALTGNDpRLAPDPAHVSDAVANTSDAVTA 159
                                       45557889999999999999999999999999999999887757787888888888888888877 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                      Esterase_phd 169 glpalvvqGdadtvva 184
                                       g p+l+++G  d v+ 
  gi|313127262|ref|YP_004037532.1| 206 GPPTLLLHGGDDDVLP 221
                                       6799999998777654 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.2
                      Esterase_phd 102 aGlsaGaaladllalhypd 120
                                       aG+ a + +ad +++h  d
  gi|313127262|ref|YP_004037532.1| 235 AGIDAECVVADGVGHHVLD 253
                                       7888888888888888655 PP

>> Imm27  Immunity protein 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00025      0.44      47      63 ..     194     210 ..     190     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                             Imm27  47 eLaYpeselqgGGpPrl 63 
                                       eLa p s+l +GGpP+l
  gi|313127262|ref|YP_004037532.1| 194 ELASPSSHLDDGGPPTL 210
                                       7999***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1869.24
//
Query:       gi|313127263|ref|YP_004037533.1|  [L=496]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   5.2e-100  334.3   0.0   7.9e-100  333.7   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    2.2e-41  141.2   0.0    4.4e-41  140.2   0.0    1.5  1  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.7   0.0  8.8e-104  7.9e-100       1     269 [.      13     308 ..      13     311 .. 0.94

  Alignments for each domain:
  == domain 1  score: 333.7 bits;  conditional E-value: 8.8e-104
                                       EEEEEEEEEEB--SB-SSSSSBSSS.SCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N   1 lviGlEiHaqlktksKlFssastee.egeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRK 76 
                                       +viGlE+H+ql+t++K+F+++st + e+eepn+++++v+l+lPG+lPvln+ ave a+k+++al++++ae+++f+RK
  gi|313127263|ref|YP_004037533.1|  13 TVIGLEVHVQLETDTKIFCGCSTDAaEDEEPNTRTCPVCLGLPGALPVLNEGAVEAAVKVGKALDATVAEHTRFHRK 89 
                                       59********************88646667*********************************************** PP

                                       E-TCTTCTTSEEEEESSS.SEEEEEEEE.....TEEEEEEEEEEEE---EEEE.....EETTEEEEETTSTT-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxx RF
                            GatB_N  77 nyfypdlpkgyQitqkeeplakeGslel.....ekkvrierihlEeDaaksvh.....eekeeslvdlnRaGvpLiE 143
                                       ny+ypdlpk++Qitq+++p++ +G+le+     +++v+ier+hlEeD +   h     ++++++lv++nRaG+pL+E
  gi|313127263|ref|YP_004037533.1|  90 NYYYPDLPKNFQITQYDAPICADGTLEVsvegeRREVGIERAHLEEDPGSLQHkggsiDTADYTLVNYNRAGTPLME 166
                                       ***************************9999999999****************999987788*************** PP

                                       EEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSE........TTSSS...--EEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxx..xxxxxxxxxxx RF
                            GatB_N 144 ivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreee........kgeee..gtrvEiKnlns 210
                                       ivt+pd+rsp+e ra++ kl+e+l++lgv d+   +GslR+D+N+S+  ++        ++e+    +r+E+Kn++s
  gi|313127263|ref|YP_004037533.1| 167 IVTKPDFRSPQETRAFLAKLEEVLEYLGVFDATR-DGSLRIDANISMVPADevgddgsiADETLaaANRTEVKNISS 242
                                       ********************************98.8**********9977447777665233324699********* PP

                                       HHHHHHHHHHHHHHHHHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--H CS
                                       xxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 211 lksiekaieyeierqiell.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleise 269
                                        k  eka++ye++rq +++       qeTr++de++g tvs+Rskee++dYryf e+dlpple+ +
  gi|313127263|ref|YP_004037533.1| 243 HKGAEKALAYEVTRQKNAIsrgraieQETRHWDESRGITVSMRSKEEEKDYRYFREADLPPLEVAD 308
                                       **************************************************************9875 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.2   0.0   4.9e-45   4.4e-41       1     148 []     348     494 ..     348     494 .. 0.97

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 4.9e-45
                                       HHHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHH.HHHHHHTXXH CS
                         GatB_Yqey   1 dffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevl.eelleegksp 76 
                                       df+e v+++  d+ laa+w++++llgeln+++++i+e+  + +++++l++l++ g+I+ k a+ev+ + +l++g+sp
  gi|313127263|ref|YP_004037533.1| 348 DFYEDVADKF-DPSLAATWVADNLLGELNYRDMQITEITHRLDEFTRLVELVDAGDITTKNAEEVVlRRMLDDGESP 423
                                       799******9.**************************99999********************9987699******** PP

                                       HHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  77 eeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       ++i+e +gL ++ d +e+  +v e+i+enp+avedy++g+  a++flvGqvM+kt G adp  vn++l+++L
  gi|313127263|ref|YP_004037533.1| 424 DDIVEAEGLGAADD-DEVVTAVTEAIEENPDAVEDYHAGEGGAINFLVGQVMQKTGGSADPGDVNQMLRDEL 494
                                       ************99.99999*************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3360.22
//
Query:       gi|313127264|ref|YP_004037534.1|  [L=61]
Description: hypothetical protein Hbor_25350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0091   16.4   1.2        0.3   11.6   0.1    2.2  2  zf-H2C2_2    Zinc-finger double domain
  ------ inclusion threshold ------
       0.06   13.3   1.4        6.8    6.7   0.1    2.5  3  Nudix_N_2    Nudix N-terminal
      0.067   13.1   2.0       0.24   11.3   0.3    2.0  2  DUF35_N      Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.068   13.3   2.1       0.14   12.3   2.1    1.5  1  Zn-ribbon_8  Zinc ribbon domain
       0.08   12.9   0.1       0.23   11.5   0.1    1.7  1  ADK_lid      Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.021        76       8      20 ..       2      16 ..       1      21 [. 0.83
   2 !   11.6   0.1   8.3e-05       0.3       8      23 ..      30      45 ..      27      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.021
                         zf-H2C2_2  8 kHtgekp..yeCplC 20
                                      +Ht++ p  y C+ C
  gi|313127264|ref|YP_004037534.1|  2 SHTPDIPeqYVCKGC 16
                                      599888888****99 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.3e-05
                         zf-H2C2_2  8 kHtgekpyeCplCdka 23
                                      +H+ e p eC++C+ +
  gi|313127264|ref|YP_004037534.1| 30 THHFEAPAECSACGST 45
                                      6************976 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0019       6.8      20      31 ..       8      19 ..       3      20 .. 0.80
   2 ?   -3.2   0.0       2.4   8.7e+03      16      20 ..      27      31 ..      24      32 .. 0.70
   3 ?    5.4   0.1    0.0048        17       3       9 ..      39      45 ..      39      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0019
                                      S-EEEETTTTEE CS
                         Nudix_N_2 20 reRlvCpaCgti 31
                                       e +vC+ C++i
  gi|313127264|ref|YP_004037534.1|  8 PEQYVCKGCQAI 19
                                      5669******98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.4
                                      TT-SS CS
                         Nudix_N_2 16 dgDnr 20
                                       gD++
  gi|313127264|ref|YP_004037534.1| 27 RGDTH 31
                                      68987 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0048
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      Cs+CG++
  gi|313127264|ref|YP_004037534.1| 39 CSACGST 45
                                      9999986 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.082   2.9e+02      13      19 ..      12      18 ..       8      20 .. 0.67
   2 ?   11.3   0.3   6.7e-05      0.24      18      36 ..      29      47 ..      26      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.082
                           DUF35_N 13 rCpdCGt 19
                                       C+ C++
  gi|313127264|ref|YP_004037534.1| 12 VCKGCQA 18
                                      4777766 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.7e-05
                           DUF35_N 18 GtvqfPPravCphCgsddl 36
                                      +t++f + a C+ Cgs+++
  gi|313127264|ref|YP_004037534.1| 29 DTHHFEAPAECSACGSTAF 47
                                      799*************987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.1   3.9e-05      0.14       5      35 ..      10      45 ..      10      48 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                       Zn-ribbon_8  5 eYrCeeCghefe..vlqsis..daplta.CPeCgse 35
                                      +Y C+ C+  +   vl + +    + +a C +Cgs+
  gi|313127264|ref|YP_004037534.1| 10 QYVCKGCQAIYAgtVLKRGDthHFEAPAeCSACGST 45
                                      59*********998555544323336677*****95 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   6.3e-05      0.23       3      29 ..      12      44 ..      11      48 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.3e-05
                                      E-TTT--EE..........ETTTB--SSTTB-TTT-- CS
                           ADK_lid  3 vCpkCGrsY..........hvvfnpPkveglCDkCGe 29
                                      vC+ C+++Y          h  f    ++  C  CG+
  gi|313127264|ref|YP_004037534.1| 12 VCKGCQAIYagtvlkrgdtH-HF---EAPAECSACGS 44
                                      9********88888877775.56...44455666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 457.81
//
Query:       gi|313127265|ref|YP_004037535.1|  [L=474]
Description: efflux protein, mate family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-59  198.8  35.8    4.7e-38  130.4  10.1    2.6  3  MatE             MatE
    6.6e-09   36.0   5.9    6.6e-09   36.0   5.9    4.6  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4  10.1   5.2e-42   4.7e-38       1     161 []      25     185 ..      25     185 .. 0.99
   2 !   80.1  11.2   1.5e-26   1.3e-22       1     160 [.     250     410 ..     250     411 .. 0.95
   3 ?   -3.6   0.4      0.87   7.8e+03      74      90 ..     421     437 ..     420     442 .. 0.79

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 5.2e-42
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P++  nll+++++l+d+++vgr+g+ka+Aavs+ ++++++++++++g+ +a+ +lv+q +Ga++ ++a++++ q+l+
  gi|313127265|ref|YP_004037535.1|  25 PLVAGNLLQTFYNLADMFWVGRVGPKAVAAVSLMFPTAWMFVSVAMGVTAAAVALVSQHVGAGDDRAAERVVGQSLL 101
                                       8999************************************************************************* PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l++++++++a++++l ++q+l l+++   v   a  y ++l++++p+ +++++++++lrgag+t++++ ++++s+ l
  gi|313127265|ref|YP_004037535.1| 102 LAIGVGVLLAIIGYLGRHQLLTLIGAQGRVYTEALAYAEVLFVTLPFTFVFFAFRAVLRGAGDTRTAMWLVVVSAGL 178
                                       ***************************************************************************** PP

                              MatE 155 niplnyl 161
                                       n++l++l
  gi|313127265|ref|YP_004037535.1| 179 NVILDPL 185
                                       ****985 PP

  == domain 2  score: 80.1 bits;  conditional E-value: 1.5e-26
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+ l  l+ s+   ++  lv+r+gs+a Aa++i+l++ s+  +++ +++ a++t vgq+lGa+ ++ra+e++ +++ 
  gi|313127265|ref|YP_004037535.1| 250 PATLDGLARSFAAVALAALVARFGSVATAAYGIGLRLMSVSWTVSGAVGQAAATGVGQNLGANTPDRAAEVTWKATA 326
                                       56666677788889999******************************************************999999 PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.l 153
                                        ++++  ++  +v++f+  ++++f +d+ v++++ ++l i++++  +l+ ++v++g++rgag+t+v++++slis  +
  gi|313127265|ref|YP_004037535.1| 327 GTMAILGAVGGVVWAFPAVFMRVFIDDAPVVAAGVEMLTIIAPFWAFLGGLMVIQGAFRGAGRTRVSMVLSLISRwV 403
                                       9999999999999**************************************************************** PP

                              MatE 154 lniplny 160
                                       +++p ++
  gi|313127265|ref|YP_004037535.1| 404 VRFPAAF 410
                                       **99887 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 0.87
                              MatE  74 qglilllllsliiallv 90 
                                       +gl+++l ls i++++v
  gi|313127265|ref|YP_004037535.1| 421 TGLWWGLSLSGIVTFVV 437
                                       68899999998888875 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.6     0.011        97      88     136 ..      59     113 ..      24     118 .. 0.57
   2 !   36.0   5.9   7.3e-13   6.6e-09       4      74 ..     141     217 ..     138     224 .. 0.87
   3 ?   -2.5   6.0      0.54   4.8e+03      64     142 ..     265     348 ..     241     349 .. 0.54
   4 !   12.9   6.6   9.3e-06     0.083       1      78 [.     363     444 ..     363     451 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.011
                   Polysacc_synt_C  88 lrrllkpllaalvmgiv..vylllllllglllla........alalllavlvgalvYll 136
                                       + + +  ++++++mg+   +++l+++ +g+            + +llla++vg+l+ ++
  gi|313127265|ref|YP_004037535.1|  59 FPTAW--MFVSVAMGVTaaAVALVSQHVGAG--DdraaervvGQSLLLAIGVGVLLAII 113
                                       33444..566666666622333444444444..35589986422777777777665544 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 7.3e-13
                   Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavlnl 74 
                                       +l ++++f++++  + ++L g g +++a++ +v++a +++il  l+i        +g+ Gaa+at++a +v+a+  l
  gi|313127265|ref|YP_004037535.1| 141 VLFVTLPFTFVFFAFRAVLRGAGDTRTAMWLVVVSAGLNVILDPLFIlgygpfSAMGTRGAAVATLVARIVAAAAGL 217
                                       788999*****************************************55543335577*************998765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.54
                   Polysacc_synt_C  64 lallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllglllla.........al.alllavlvg 130
                                       la lv+ +  +  +   +g++l+ + +++  ++  ++  +v    ++l  +++            +  ++++ ++vg
  gi|313127265|ref|YP_004037535.1| 265 LAALVARFGSVATAAYGIGLRLMSVSWTVSGAVGQAAATGV---GQNLGANTP--DraaevtwkaTAgTMAILGAVG 336
                                       44444444444444444444443233332222222222222...222222222..1335566665335777777899 PP

                   Polysacc_synt_C 131 alvYlllllllr 142
                                       ++v+++ ++++r
  gi|313127265|ref|YP_004037535.1| 337 GVVWAFPAVFMR 348
                                       999998888877 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 9.3e-06
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvig.alvklilnllli..plfgivGaaiatvlallvvavln. 73 
                                       +L i+a+   fl+  +v ++ + g gr++  ++ ++i+  +v +   ++l    ++g++G  ++  l+ +v++v+  
  gi|313127265|ref|YP_004037535.1| 363 MLTIIAPFWAFLGGLMVIQGAFRGAGRTRVSMVLSLISrWVVRFPAAFVLAytLSWGVTGLWWGLSLSGIVTFVVGc 439
                                       5899***************************9988887478999999999976799****************99875 PP

                   Polysacc_synt_C  74 lyalr 78 
                                       l++l+
  gi|313127265|ref|YP_004037535.1| 440 LWFLH 444
                                       66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3201.29
//
Query:       gi|313127266|ref|YP_004037536.1|  [L=850]
Description: DNA topoisomerase i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.8e-125  416.9   0.0   1.1e-124  416.6   0.0    1.1  1  Topoisom_bac     DNA topoisomerase
    1.5e-18   66.3  10.3    4.5e-11   42.3   0.1    4.1  4  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
    1.5e-17   63.7   0.0      3e-17   62.7   0.0    1.5  1  Toprim           Toprim domain
    5.6e-12   46.1   0.3    2.2e-11   44.2   0.3    2.1  1  HHH_5            Helix-hairpin-helix domain
    2.9e-05   23.7   1.8    0.00045   19.9   0.2    2.7  2  HHH              Helix-hairpin-helix motif
    0.00011   22.0   0.1      0.015   15.1   0.0    3.1  4  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0013   18.9   0.0     0.0057   16.9   0.0    2.1  1  Cdd1             Pathogenicity locus
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.024   14.9   0.0    1.6  1  DUF4332          Domain of unknown function (DUF4332)
      0.021   15.1   0.1      0.097   13.0   0.1    2.2  2  IMS_HHH          IMS family HHH motif
      0.059   13.9   0.0       0.18   12.3   0.0    1.9  1  Toprim_4         Toprim domain
      0.082   13.3   0.3       0.98    9.8   0.3    2.7  2  HHH_8            Helix-hairpin-helix domain
      0.089   13.0   0.1       0.24   11.6   0.1    1.7  1  HEXIM            Hexamethylene bis-acetamide-inducible protei
       0.11   12.8   0.0       0.24   11.7   0.0    1.6  1  HHH_3            Helix-hairpin-helix motif
        0.2   11.8   0.2        1.9    8.7   0.0    2.2  2  HHH_2            Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.6   0.0  8.6e-128  1.1e-124       2     411 ..     154     565 ..     153     567 .. 0.95

  Alignments for each domain:
  == domain 1  score: 416.6 bits;  conditional E-value: 8.6e-128
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkke 76 
                                       +++nl++a+eaR+++D+++G++l+r+l++++++  ++++s+GRVq ptL+liv+Rereie+F pe+ywe+ a+l+k+
  gi|313127266|ref|YP_004037536.1| 154 LDFNLAAAGEARQIVDLVWGAALTRFLSLSARQlgDDFISVGRVQGPTLKLIVDREREIEAFDPEDYWELFADLQKD 230
                                       589**************************5555559**************************************888 PP

                      Topoisom_bac  77 kkeke......kkkkkkkerikdkeeaeaileklkk.keakvesvekkekkkppplpfdtttLqkeasrklglsakk 146
                                       ++++e      ++   + er++d ++ae+++e+l++ + a+v+sv+++++++ pp pf+tt++ ++a + lg+sa++
  gi|313127266|ref|YP_004037536.1| 231 SESFEaqyfylDEDGNEAERVWDGDDAEEAYETLRNvEAATVDSVRRRTRTDDPPAPFNTTQFIRAAGS-LGYSAQR 306
                                       888888*****99999******************99659***************************999.6****** PP

                      Topoisom_bac 147 tlsiaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPt 223
                                       ++sia++LY+  g+itYpRTd+t+++e+ + +++l+a++ +   ++ + a++ll++++ + +++++++++H++I+Pt
  gi|313127266|ref|YP_004037536.1| 307 AMSIAEDLYTA-GYITYPRTDNTVYPEDLDPRELLDAFTAN--RTFGDDAQNLLEQEEIEPTAGDNETTDHPPIHPT 380
                                       **********5.****************668********97..6689999999987776668999999********* PP

                      Topoisom_bac 224 eelpklkelsddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelp 300
                                       +elp++++l++de+++Yel+vrrf+a+++++ak+e+ +v  ++++ ++ka+gk+++++G+++vy++ + +e+   +p
  gi|313127266|ref|YP_004037536.1| 381 GELPSRSDLTEDEWDVYELVVRRFFATVAESAKWEHLRVVADAGGLSLKANGKRLVKAGYHEVYPYFNSSES--FVP 455
                                       ****99**********************************************************99999876..5** PP

                      Topoisom_bac 301 elkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalve 377
                                       +++ege++ v++ e+eek+T+pp ry +++Li++mek giGt+aTr+++i+kl++r+Y+e++    +pt+l++a+ve
  gi|313127266|ref|YP_004037536.1| 456 DVAEGESLAVTDTEIEEKQTQPPRRYGQSRLIETMEKMGIGTKATRHDVIQKLYDRNYIESDP--PRPTRLARAVVE 530
                                       *************************************************************76..89********** PP

                      Topoisom_bac 378 llekf.kdlvspelTaeleekLdeIaegkadakev 411
                                       + e+f + +vs+e+Ta+le ++++Ia+g a+ ++v
  gi|313127266|ref|YP_004037536.1| 531 ASEEFaELIVSEEMTAQLEADMQAIARGDASLDDV 565
                                       *****888**********************99988 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.1   3.5e-14   4.5e-11       2      38 ..     602     639 ..     601     640 .. 0.94
   2 ?   -2.1   0.3       2.8   3.5e+03       4       9 ..     671     676 ..     668     677 .. 0.78
   3 ?    3.6   0.6     0.046        59       2       9 ..     688     695 ..     687     697 .. 0.83
   4 !   24.8   0.0     1e-08   1.3e-05       9      38 ..     714     744 ..     712     745 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 3.5e-14
                                       EE-SSS--EEEEEE-SSS.EEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                       + CP+   dLv++++++G  F+GC+ YP+C++t +l++
  gi|313127266|ref|YP_004037536.1| 602 GACPESDHDLVVRKSRRGsYFIGCDGYPDCTYTLPLPS 639
                                       78********************************9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                                       -SSS-- CS
                    zf-C4_Topoisom   4 CPkCgg 9  
                                       CP C++
  gi|313127266|ref|YP_004037536.1| 671 CPLCKA 676
                                       ****86 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.046
                                       EE-SSS-- CS
                    zf-C4_Topoisom   2 ekCPkCgg 9  
                                       ++CP+Cg+
  gi|313127266|ref|YP_004037536.1| 688 GDCPECGA 695
                                       79****95 PP

  == domain 4  score: 24.8 bits;  conditional E-value: 1e-08
                                       -EEEEEE-SSS.EEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   9 gdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                       g+L +kr + G + vGC++YP+C++  +l++
  gi|313127266|ref|YP_004037536.1| 714 GELAIKRLRSGsRLVGCTRYPDCDYSLPLPR 744
                                       7899**********************99986 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   2.3e-20     3e-17       1     103 []       6     139 ..       6     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 2.3e-20
                                       EEEEESSHHHHHHHHHTHT................STEEEEEEESSSSEEEHSTTEEEEE................E CS
                            Toprim   1 elvivEgpsdaktiakalg................sgfqavtaslGhildletefkpvye................e 45 
                                       el+i E++++a+ ia +l+                 g+++++ ++Gh++ +++  +p+y+                +
  gi|313127266|ref|YP_004037536.1|   6 ELIITEKDNAARRIADILSgesaeadringvnvykWGGKRCIGLSGHVVGVDF--PPEYNdwrdvepvelidapidK 80 
                                       69********************************9999**************9..5555555556666666666669 PP

                                       CTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEESSS CS
                            Toprim  46 iedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefsei 103
                                        ++++++++al++la++a ++++atD DreGe i++e++e++++ +e+  + rv+fs+i
  gi|313127266|ref|YP_004037536.1|  81 HPTQENIVAALRRLARNARRVVIATDYDREGELIGKEAYELVRDVNEDvPVDRVRFSSI 139
                                       99999999************************************************987 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.3   1.7e-14   2.2e-11       2      55 ..     795     849 ..     794     850 .] 0.96

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.7e-14
                                       HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHT.STTS-HHHHHHHHHHH CS
                             HHH_5   2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLak.ipGiGkktAeriilel 55 
                                       +eL+sv+GiG+ktA +l  aGie v  l++a++++La+ + G+G++t++++  ++
  gi|313127266|ref|YP_004037536.1| 795 DELQSVKGIGEKTAEKLKAAGIEDVPSLKEAEPDALADlVDGVGPDTVRKWQSAA 849
                                       58************************************99***********8876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   3.5e-07   0.00045      10      28 ..     794     812 ..     790     814 .. 0.87
   2 ?    2.2   0.1      0.15     2e+02       4      24 ..     821     842 ..     818     844 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.5e-07
                                       HHHHHTSTT-SHHHHHHHH CS
                               HHH  10 reeLlalPGVGpktAeaIl 28 
                                        +eL++++G+G+ktAe+  
  gi|313127266|ref|YP_004037536.1| 794 GDELQSVKGIGEKTAEKLK 812
                                       69**************975 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                                       HHHTSSHHHHHT.STT-SHHHH CS
                               HHH   4 glipasreeLla.lPGVGpktA 24 
                                       +l++a ++ L++ + GVGp t 
  gi|313127266|ref|YP_004037536.1| 821 SLKEAEPDALADlVDGVGPDTV 842
                                       6778889999999******775 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.4   1.1e+04      13      22 ..     310     319 ..     309     321 .. 0.83
   2 ?   -3.1   0.0       5.7   7.3e+03      19      30 ..     556     567 ..     555     573 .. 0.79
   3 !   15.1   0.0   1.2e-05     0.015       2      30 ..     796     824 ..     795     832 .. 0.88
   4 ?    3.2   0.0     0.064        82       8      18 ..     836     846 ..     833     848 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.4
                   DNA_pol_lambd_f  13 tAkkwyakGi 22 
                                       +A+++y +G+
  gi|313127266|ref|YP_004037536.1| 310 IAEDLYTAGY 319
                                       69*****998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.7
                   DNA_pol_lambd_f  19 akGirtledlra 30 
                                       a+G  +l+d+ a
  gi|313127266|ref|YP_004037536.1| 556 ARGDASLDDVTA 567
                                       678889***988 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.2e-05
                   DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwyakGirtledlra 30 
                                       ++++v G+G ktA+k+ a+Gi ++  l++
  gi|313127266|ref|YP_004037536.1| 796 ELQSVKGIGEKTAEKLKAAGIEDVPSLKE 824
                                       699*********************99998 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.064
                   DNA_pol_lambd_f   8 GVGpktAkkwy 18 
                                       GVGp t +kw 
  gi|313127266|ref|YP_004037536.1| 836 GVGPDTVRKWQ 846
                                       9*********6 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.4e-06    0.0057       6      43 ..     795     832 ..     790     837 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.4e-06
                              Cdd1   6 kelqdiPniGkalaedlvelGirsveelkgedpeelye 43 
                                       +elq++ +iG+++ae+l + Gi++v  lk+ +p++l +
  gi|313127266|ref|YP_004037536.1| 795 DELQSVKGIGEKTAEKLKAAGIEDVPSLKEAEPDALAD 832
                                       79********************************9976 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.9e-05     0.024       2      54 ..     802     850 .]     797     850 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                           DUF4332   2 gigkeeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanlAd 54 
                                       gig++ aekLk+aGi+++ +L e++++  +   l++       +v+k++ +Ad
  gi|313127266|ref|YP_004037536.1| 802 GIGEKTAEKLKAAGIEDVPSLKEAEPDALAD--LVDGV--GPDTVRKWQSAAD 850
                                       7888889999999999999999988888888..77654..6778888888876 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         6   7.7e+03      15      28 ..     190     203 ..     189     204 .. 0.83
   2 ?   13.0   0.1   7.5e-05     0.097      13      32 .]     797     816 ..     796     816 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6
                           IMS_HHH  15 kipGiGgklgekLe 28 
                                       ++  +G+++g  L+
  gi|313127266|ref|YP_004037536.1| 190 DFISVGRVQGPTLK 203
                                       7889****998876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.5e-05
                           IMS_HHH  13 itkipGiGgklgekLeklGi 32 
                                       + ++ GiG k++ekL++ Gi
  gi|313127266|ref|YP_004037536.1| 797 LQSVKGIGEKTAEKLKAAGI 816
                                       6799**************98 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.18      47      85 ..      91     131 ..      75     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                          Toprim_4  47 lveaekkvkevilaldgDaeGeataerlaelll..eegvkv 85 
                                       l++   ++++v++a+d D eGe   ++++el++  +e+v v
  gi|313127266|ref|YP_004037536.1|  91 LRRLARNARRVVIATDYDREGELIGKEAYELVRdvNEDVPV 131
                                       33345567**************9999999944312555555 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00077      0.98      43      64 ..     792     812 ..     783     815 .. 0.77
   2 ?   -0.4   0.0       1.2   1.6e+03      47      64 ..     824     846 ..     813     849 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00077
                                       HHHTTHCTTSTT--HHHHHHHH CS
                             HHH_8  43 tsleeeltklpgiGkkiaakie 64 
                                       + ++e l++++giG+k+a+k++
  gi|313127266|ref|YP_004037536.1| 792 AGGDE-LQSVKGIGEKTAEKLK 812
                                       33366.*************985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                                       T....HCTT.STT--HHHHHHHH CS
                             HHH_8  47 e....eltk.lpgiGkkiaakie 64 
                                       e    +l + ++g+G+++ +k++
  gi|313127266|ref|YP_004037536.1| 824 EaepdALADlVDGVGPDTVRKWQ 846
                                       22344566779*******99986 PP

>> HEXIM  Hexamethylene bis-acetamide-inducible protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00018      0.24      19      46 ..     268     294 ..     256     300 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                             HEXIM  19 ekqrasrvraemfakgqpvAPyNtTQFL 46 
                                       e++ +  vr++ +    p+AP+NtTQF+
  gi|313127266|ref|YP_004037536.1| 268 EAATVDSVRRRTR-TDDPPAPFNTTQFI 294
                                       5555555666444.56899********7 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.24      42      61 ..     793     812 ..     780     814 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                             HHH_3  42 sreeLlkvkglgpktfeqla 61 
                                         +eL++vkg+g+kt e+l+
  gi|313127266|ref|YP_004037536.1| 793 GGDELQSVKGIGEKTAEKLK 812
                                       5589*************997 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0015       1.9      31      51 ..     791     811 ..     789     814 .. 0.88
   2 ?    8.3   0.1    0.0019       2.4       8      46 ..     800     840 ..     798     844 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                             HHH_2  31 kasleeLlevddiGeeiAqsi 51 
                                       +a  +eL++v++iGe++A++ 
  gi|313127266|ref|YP_004037536.1| 791 QAGGDELQSVKGIGEKTAEKL 811
                                       78889*************976 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0019
                             HHH_2   8 IrhVGektAklL.akrFksldaLkkasleeLle.vddiGee 46 
                                       ++ +GektA++L a   +++  Lk+a+ + L+  vd++G+ 
  gi|313127266|ref|YP_004037536.1| 800 VKGIGEKTAEKLkAAGIEDVPSLKEAEPDALADlVDGVGPD 840
                                       688*********667799*************8658999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (850 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.41
# Mc/sec: 6217.36
//
Query:       gi|313127267|ref|YP_004037537.1|  [L=242]
Description: geranylgeranylglyceryl diphosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-57  194.2   0.2    2.5e-57  194.0   0.2    1.0  1  PcrB      PcrB family


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.0   0.2   1.4e-61   2.5e-57       3     224 ..       5     228 ..       3     230 .. 0.94

  Alignments for each domain:
  == domain 1  score: 194.0 bits;  conditional E-value: 1.4e-61
                                       GGGTSEEEEE-TTSS-CH.HHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TT..SS CS
                              PcrB   3 ileerhltklDPeeenpd.EiveiviesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvry..aD 76 
                                       ++ ++h+ k+DP+++++d E  e v++ gtDa+ igG+  +t d+ +r++    ++++P+  epsn+  v  +  +D
  gi|313127267|ref|YP_004037537.1|   5 WTDWNHVLKVDPDKDLIDgETFEDVCQTGTDAIEIGGTLDITADKMQRVVDACAEYDVPLYQEPSNPGVVIDDdaLD 81 
                                       899**************9899*********************************************98887644478 PP

                                       EEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-B-TTHHHHHHHHHHHHHHTT CS
                              PcrB  77 alFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteakvdlnkediaayallaakllg 153
                                        + +++++n+++a Wi+gah++ + ++++ ++     +e+Y+v++P++ va++t+a++d+  +d+a+ya +a++++g
  gi|313127267|ref|YP_004037537.1|  82 GYLIPTVFNAKDAFWITGAHKEWV-RIENGMDWGRTHTEAYIVLNPEASVAQLTDANCDQSADDVASYASVAERMFG 157
                                       99******************8866.677777799******************************************* PP

                                       -SEEEEE-TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHHCHHHHHHH CS
                              PcrB 154 lrliYlEasGaledveevialkkklekarlivGGGirsaEkAkevveaADvivvGnvveekderkidaile 224
                                         ++Y+E+sG  +d e+v+a +  l++a+l++GGGir+ + A+e+ ++ Dv+vvG+++++++ +++++ +e
  gi|313127267|ref|YP_004037537.1| 158 QEIVYVEYSGMFGDTEKVQAAHDALDDATLFYGGGIRDYDAAYEMGQHTDVVVVGDLLHDEGVDAVRETVE 228
                                       ************************************************************99666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1858.12
//
Query:       gi|313127268|ref|YP_004037538.1|  [L=254]
Description: hypothetical protein Hbor_25390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-15   57.3  11.9    3.6e-15   56.2  11.9    1.6  1  DUF4013         Protein of unknown function (DUF4013)
  ------ inclusion threshold ------
       0.12   12.6   0.4       0.24   11.6   0.4    1.5  1  Arch_flagellin  Archaebacterial flagellin
       0.58    9.5   1.0       0.89    8.9   1.0    1.3  1  TMEM43          Transmembrane protein 43
        1.2    8.6   6.6          2    7.9   6.6    1.2  1  SseC            Secretion system effector C (SseC) like famil


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2  11.9   8.1e-19   3.6e-15       1     166 [.      25     186 ..      25     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 8.1e-19
                           DUF4013   1 llsllliiaivlslvllGYlvrvlrdtirgddelPefddwgkllvdGlkafvvslvYllipliialltllvalasla 77 
                                       llsl+ + a+v+ ++llGY vr +r ++rg d +P fd w   ++dGl+++v +  +   p++  ++t+++   +l 
  gi|313127268|ref|YP_004037538.1|  25 LLSLATVSAPVVGVLLLGYAVRAIRYRVRG-DGVPAFDGWHSIFRDGLRVAVTTGPLH-APAVA-IITVVGYDRMLR 98 
                                       589999************************.667***************977777755.99999.665556555555 PP

                           DUF4013  78 agdsaa..gallvlallglllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialill 152
                                       +++s+a  g +++   +g+++al++v++l l+ g+l++++l+++a +++++  + +  +++++++  +++ ++++l+
  gi|313127268|ref|YP_004037538.1|  99 GASSLAyiGHYAFSPDYGAVAALVAVAFLELAGGFLSVATLVALASSDTMGRHL-LTDVVAVARR--RRFHRVFGLV 172
                                       55555544555555555************************************5.5556665655..59******** PP

                           DUF4013 153 lvigivlsllaill 166
                                       l +g+++ ++ ++l
  gi|313127268|ref|YP_004037538.1| 173 LGVGVAARFARLAL 186
                                       *******9998877 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   5.3e-05      0.24       5      28 ..     196     219 ..     191     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                    Arch_flagellin   5 igtlIvfIAmVlVAAvaagvlint 28 
                                       +g+++ f+A+V++A+++agv+   
  gi|313127268|ref|YP_004037538.1| 196 LGAVVSFVALVVAASALAGVVSRD 219
                                       89******************8665 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.0    0.0002      0.89     189     242 ..     163     216 ..     125     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0002
                            TMEM43 189 lRllGfllmflglllllsplsvlvslipllgelvglglalvalllslslsllvi 242
                                        R+  ++ ++lg+ ++++  +  + +ip++ge +g+++++val++++s    v+
  gi|313127268|ref|YP_004037538.1| 163 RRFHRVFGLVLGVGVAARFARLALGVIPFVGEPLGAVVSFVALVVAASALAGVV 216
                                       455557778889999999999*************************99887776 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.6   0.00045         2      80     156 ..     118     216 ..     115     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00045
                              SseC  80 gaslll.aavgvAgglmdaalgiadevvaaattkslideemqpimdvv..........................dka 129
                                       +a+l++ a +++Agg + + ++ + ++++ + +  l      ++++v+                          + +
  gi|313127268|ref|YP_004037538.1| 118 VAALVAvAFLELAGGFLSV-ATLVALASSDTMGRHLL----TDVVAVArrrrfhrvfglvlgvgvaarfarlalGVI 189
                                       5566666667777777776.33333333333333333....33444558999999********************** PP

                              SseC 130 qlageivgavvaavavvaavvavgsaa 156
                                        ++ge +gavv +va+v a++a+++++
  gi|313127268|ref|YP_004037538.1| 190 PFVGEPLGAVVSFVALVVAASALAGVV 216
                                       *****************9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1923.01
//
Query:       gi|313127269|ref|YP_004037539.1|  [L=434]
Description: aspartyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-85  284.7   0.0    9.6e-85  284.4   0.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    3.6e-14   52.5   0.2      6e-14   51.8   0.2    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.011   15.2   0.4      0.065   12.7   0.1    2.2  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)
       0.15   12.2   0.1       0.72   10.0   0.1    2.1  2  BOF              Bacterial OB fold (BOF) protein


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.4   0.0   2.1e-88   9.6e-85       3     313 ..     115     428 ..     113     429 .. 0.96

  Alignments for each domain:
  == domain 1  score: 284.4 bits;  conditional E-value: 2.1e-88
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aL 75 
                                        +rl+nr ldlr+++v++v+++r++++++vr+ +   + +ei+tP ++ + te+g +lF +       ++f    ++
  gi|313127269|ref|YP_004037539.1| 115 STRLDNRTLDLRKDEVKAVFEIRAEILRSVRDAFRGLNATEINTPKIVATGTEGGTELFPI-------TYFgqeaFM 184
                                       589**********************************************************.......566666679 PP

                                       -S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  76 tqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakd 152
                                       +qspql+++l++ +g++rvf++++ FRaE+++t rhl+E t+i++e +f ++ + m+  e+++k   + v e+++++
  gi|313127269|ref|YP_004037539.1| 185 NQSPQLFKQLMVGSGLERVFEVGPIFRAEEHNTPRHLNEATSIDFESAFFDHTEAMDACEHVVKAAYEGVAENCQRE 261
                                       ***************************************************************************** PP

                                       CCHTTTTTSEE-SSS.-EEEEHHHHHHHHHTS.........-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBB CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 153 iefvirrnskdlkkp.fkrltykeaieklnei.........gkdldkaderalvkkeknepvfvtdfPaelkpFyar 219
                                       +e+    ++ ++++  f+rlty+eaie++n +         g+dl ++ eral + +  e +f+td+P+e+kpFy +
  gi|313127269|ref|YP_004037539.1| 262 LETLGLAEEFEVPEGeFPRLTYEEAIERINATgeldeqlvwGDDLPTEGERALGE-DVGEHYFITDWPSEIKPFYIK 337
                                       9998877776666666************9999***********************.9999***************** PP

                                       BSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 220 keeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvm 296
                                       +++dd++l+ ++D++ + +Elv+G +R+++ e l + ++++gld   +++f+ y+++++yG+pph+G+glG +Rlvm
  gi|313127269|ref|YP_004037539.1| 338 DHDDDETLSTGFDMMHPRMELVSGGQREHRFEHLVAGFEQQGLD---PDQFEYYTKMFKYGMPPHAGWGLGGERLVM 411
                                       ********************************************...****************************** PP

                                       HHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 297 lllgsesIrdviaFPkl 313
                                       ++lg+++Ir++++FP+ 
  gi|313127269|ref|YP_004037539.1| 412 TMLGLDNIREAVLFPRD 428
                                       ***************96 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.2   1.3e-17     6e-14       1      74 [.      16      93 ..      16      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.3e-17
                                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkvee 72
                                      VtvaG+v+ +  r+ g+++f++lrD++g+iq+ l +    ee  ++  ++ +++vv v+G vk+    p+g +e++ e+
  gi|313127269|ref|YP_004037539.1| 16 VTVAGWVHEV--RDLGGIAFLILRDKSGKIQIKLEKdemdEELVETGLDVARESVVSVSGDVKEEpraPTG-VEVVPED 91
                                      9*********..************************9999999999999****************888999.9999999 PP

                                      EE CS
                   tRNA_anti-codon 73 ie 74
                                      i 
  gi|313127269|ref|YP_004037539.1| 92 ID 93
                                      85 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.93   4.2e+03      20      43 ..     138     161 ..     128     164 .. 0.82
   2 ?   -0.8   0.0      0.19   8.6e+02     102     128 ..     201     228 ..     186     262 .. 0.67
   3 ?   12.7   0.1   1.4e-05     0.065     212     234 ..     400     422 ..     390     432 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.93
                                       HHHHHHHHHHHHCTTCEESSTTSE CS
                      tRNA-synt_2d  20 tkvleeikeiflelgfeevegpev 43 
                                       +++l+ +++ f+ l+ +e++ p++
  gi|313127269|ref|YP_004037539.1| 138 AEILRSVRDAFRGLNATEINTPKI 161
                                       678899999999999999999887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.19
                                       EEEEEEEEEEBSST.-SSSB-SEEEEEE CS
                      tRNA-synt_2d 102 ikiisigrvfRrda.vDathlaeFhqve 128
                                        +++ +g +fR ++    +hl e ++++
  gi|313127269|ref|YP_004037539.1| 201 ERVFEVGPIFRAEEhNTPRHLNEATSID 228
                                       5899999999999855667877766664 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 1.4e-05
                                       EEEEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 212 fafGlGveRlamlkygieDiRel 234
                                       +++GlG eRl m ++g+++iRe 
  gi|313127269|ref|YP_004037539.1| 400 AGWGLGGERLVMTMLGLDNIREA 422
                                       68*******************84 PP

>> BOF  Bacterial OB fold (BOF) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00016      0.72      37      90 ..      16      78 ..       6      92 .. 0.69
   2 ?   -1.9   0.0       0.8   3.6e+03      79      91 ..     288     300 ..     271     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                                      EEEEEEE..EEEEETTEE.EEEETTEEEEEE--GGGST......T----TTSEEEEEEEEEEE CS
                               BOF 37 vslrGni..vkriddDey.vFrDasGeikveiddrvfn......glevqpkdkvkiqGkvDke 90
                                      v++ G +  v+  ++  + + rD+sG+i++++++ + +      gl+v  +  v ++G+v +e
  gi|313127269|ref|YP_004037539.1| 16 VTVAGWVheVRDLGGIAFlILRDKSGKIQIKLEKDEMDeelvetGLDVARESVVSVSGDVKEE 78
                                      555665533444445455268**********99988764444447888999999999999854 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.8
                                       SEEEEEEEEEEET CS
                               BOF  79 dkvkiqGkvDkel 91 
                                       ++++ +G++D++l
  gi|313127269|ref|YP_004037539.1| 288 ERINATGELDEQL 300
                                       78999*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3238.40
//
Query:       gi|313127270|ref|YP_004037540.1|  [L=132]
Description: hypothetical protein Hbor_25410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-08   34.6   3.9      2e-08   33.7   3.9    1.5  1  SHOCT            Short C-terminal domain
    4.3e-06   26.7   1.9    7.5e-06   25.9   1.9    1.4  1  DUF1707          Domain of unknown function (DUF1707)
      7e-06   26.0   1.1      1e-05   25.4   1.1    1.3  1  GvpG             Gas vesicle protein G
     0.0082   16.1   0.1      0.015   15.2   0.1    1.4  1  SLATT_1          SMODS and SLOG-associating 2TM effector doma
     0.0084   16.1   0.1      0.014   15.4   0.1    1.3  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
      0.016   14.5   0.0       0.02   14.3   0.0    1.1  1  DUF4191          Domain of unknown function (DUF4191)
      0.017   15.0   2.8       0.26   11.2   1.6    2.4  2  VbhA             Antitoxin VbhA
      0.027   14.3   0.2      0.037   13.9   0.2    1.2  1  CdvA             CdvA-like coiled-coil domain
      0.069   12.9   0.0      0.088   12.6   0.0    1.1  1  DUF4018          Domain of unknown function (DUF4018)
      0.071   13.0   0.8      0.084   12.7   0.1    1.4  2  sCache_2         Single Cache domain 2


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   3.9   1.1e-11     2e-08       1      28 []      81     108 ..      81     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.1e-11
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakLL 28 
                                       +aLe+L+++ya GeI+e+EFe++ ++LL
  gi|313127270|ref|YP_004037540.1|  81 EALETLRRRYATGEIDEAEFERRVERLL 108
                                       69*************************8 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.9   4.2e-09   7.5e-06       7      45 ..      78     116 ..      75     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.2e-09
                           DUF1707   7 dReravelLrealaeGrLtldEfdeRleaalaArtrgeL 45 
                                       + e+a+e Lr+ +a G ++ +Ef++R+e+ l  +t ++ 
  gi|313127270|ref|YP_004037540.1|  78 ETEEALETLRRRYATGEIDEAEFERRVERLLGTETVEDA 116
                                       5589****************************9999885 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.1   5.7e-09     1e-05      21      63 ..      67     109 ..      58     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.7e-09
                              GvpG  21 eraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLd 63 
                                       ++ ++ +d++ + +  L +L ++   GeIde+eF+rr e+lL 
  gi|313127270|ref|YP_004037540.1|  67 QKQNTHADKPSETEEALETLRRRYATGEIDEAEFERRVERLLG 109
                                       5669999**********************************95 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   8.4e-06     0.015      30     116 ..      22     121 ..      12     126 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.4e-06
                           SLATT_1  30 llillellalllaalr.afgelsv..dlvgvlaavaaallaWlelkqyeel.aaaYslaaeeLeiiraalea..... 97 
                                       +++l+ l+a +l al   f  + +   + gvl  +a  ++ W e +q +++ a + s ++e Le++r++ ++     
  gi|313127270|ref|YP_004037540.1|  22 VIALVLLIAFTLLALDvSFFWVAFpvGFGGVL-PAAIGITKWYEQRQKQNThADKPSETEEALETLRRRYATgeide 97 
                                       55556666666666664444444431334444.45567899999988776516789***************995555 PP

                           SLATT_1  98 .....eateeewaklVadaEeais 116
                                            ++++    + V+daE+ +s
  gi|313127270|ref|YP_004037540.1|  98 aeferRVERLLGTETVEDAESYVS 121
                                       444322222223345666666665 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   7.7e-06     0.014      41     106 ..      18      84 ..      10      90 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.7e-06
                   Phage_holin_3_6  41 gaagvlallalllllvalalala.a.lwlaali.vaavllvlagvlalvglkklkkakp.lpertieelk 106
                                       ++++v+al+ l+++++   lal+    w+a+ +  ++vl ++ g+  +   ++ ++ ++ +p +t e l+
  gi|313127270|ref|YP_004037540.1|  18 VGGVVIALVLLIAFTL---LALDvSfFWVAFPVgFGGVLPAAIGITKWYEQRQKQNTHAdKPSETEEALE 84 
                                       3444444444444444...444433579999996667776777777777777777777778888877665 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-05      0.02      30     102 ..      18      94 ..       8     111 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                           DUF4191  30 laaflvvvvvfvvlglllgs...lilllilgillgllvalivlt.rraekaayaqiegqpGaaaavlenlrrgwrv. 101
                                       ++ +++++v++++++ll+ +    ++  ++g   g+l a i +t +  +++  +   ++p  ++ +le+lrr++ + 
  gi|313127270|ref|YP_004037540.1|  18 VGGVVIALVLLIAFTLLALDvsfFWVAFPVGFG-GVLPAAIGITkWYEQRQKQNTHADKPSETEEALETLRRRYATg 93 
                                       444555555555555555433025555555544.45555555550566778888899****************9985 PP

                           DUF4191 102 e 102
                                       e
  gi|313127270|ref|YP_004037540.1|  94 E 94 
                                       3 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.6   0.00014      0.26      23      45 ..      83     105 ..      77     106 .. 0.81
   2 ?    2.8   0.0     0.061   1.1e+02      21      31 ..     110     120 ..     108     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                              VbhA  23 tvadleayvrGeIdadElvrrvr 45 
                                       ++ +  +y+ GeId +E  rrv 
  gi|313127270|ref|YP_004037540.1|  83 LETLRRRYATGEIDEAEFERRVE 105
                                       5556679*************996 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.061
                              VbhA  21 aetvadleayv 31 
                                       +etv+d+e yv
  gi|313127270|ref|YP_004037540.1| 110 TETVEDAESYV 120
                                       69********8 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.1e-05     0.037      50      87 ..      70     107 ..      64     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                              CdvA  50 keledqikslekalanlkisyasGEidEeaYksaieai 87 
                                       ++  d+ +++e+al +l+ +ya+GEidE ++++  e +
  gi|313127270|ref|YP_004037540.1|  70 NTHADKPSETEEALETLRRRYATGEIDEAEFERRVERL 107
                                       5556777899*********************9988765 PP

>> DUF4018  Domain of unknown function (DUF4018)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.9e-05     0.088     104     162 ..      17      80 ..      13      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                           DUF4018 104 aiGvvsflivlllPyirlilsyilyvval..GfGyalepllki...aelkdaeevveklGygek 162
                                       a+G v + +vll+ +  l+l   + +va+  GfG +l + + i    e+++ +++ +++   ++
  gi|313127270|ref|YP_004037540.1|  17 AVGGVVIALVLLIAFTLLALDVSFFWVAFpvGFGGVLPAAIGItkwYEQRQKQNTHADKPSETE 80 
                                       7888899999******************844666789888888444445555555555555544 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         4   7.1e+03      82      97 ..       4      19 ..       3      21 .. 0.76
   2 ?   12.7   0.1   4.7e-05     0.084      14      63 ..      77     126 ..      63     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4
                          sCache_2 82 nlkDanGkyiirelvk 97
                                      ++ D +G++ +++ v 
  gi|313127270|ref|YP_004037540.1|  4 DVDDGDGETALQKAVG 19
                                      6788999998888775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.7e-05
                          sCache_2  14 etaislieavykqvesgkiteeeaqeevkelvnglkfgdGkgYffvlded 63 
                                       +++ +++e +++++++g+i+e+e  ++v+ l+ + + +d + Y+   +e+
  gi|313127270|ref|YP_004037540.1|  77 SETEEALETLRRRYATGEIDEAEFERRVERLLGTETVEDAESYVSTPTEQ 126
                                       678999*************************************9887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1481  (0.0826036); expected 358.6 (0.02)
Passed bias filter:                      913  (0.0509231); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 965.57
//
Query:       gi|313127271|ref|YP_004037541.1|  [L=300]
Description: pantothenate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-10   38.8   3.3    3.6e-09   36.7   1.4    2.3  2  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.015   15.1   0.2      0.032   14.0   0.2    1.5  1  FAD_binding_4   FAD binding domain
        0.2   12.1   1.6       0.21   11.9   0.0    1.9  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   1.4   6.1e-13   3.6e-09       4      66 .]     103     165 ..     100     165 .. 0.92
   2 ?    1.8   0.0      0.05     3e+02      38      65 ..     235     268 ..     204     269 .. 0.54

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 6.1e-13
                                       EEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   4 ikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                        ++ +P+g+G+G S+A+a+++++A++a ++ + +e++l  +a+r+ + + ++ gDv a + Gg
  gi|313127271|ref|YP_004037541.1| 103 AETPLPLGSGFGVSGAMALGTAYAANAVFDAEHSENELVTVAHRAEVEAGTGLGDVVAQARGG 165
                                       56789************************877777********99999***********9998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.05
                                       H.....HHH.HHHHHHHHHHHHHHSHHHHHHHHS CS
                    GHMP_kinases_N  38 e.....akl.aleaerlaqggngsggDvaasvyG 65 
                                             a+l + + e  ++ ++  ggD++ +++G
  gi|313127271|ref|YP_004037541.1| 235 RqfareADLtTDRVESVIADVRAAGGDASMAMLG 268
                                       1444445553344555567788999999999998 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   5.4e-06     0.032      43     103 ..     126     183 ..      98     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-06
                                       CCEEEEEETT.S--EEEEETTTTEEEEETTSBHHHHHHHHHHHTTECSSGGGTTCGSBHHHT CS
                     FAD_binding_4  43 tggvvldlsr.lnrileideeegtatveaGvtlgdlvealaakglllglepgsgipgtvGGa 103
                                           v d ++  n   e+   +++a+veaG+ lgd+v+++ + gl ++lepg+   gt+ G+
  gi|313127271|ref|YP_004037541.1| 126 AANAVFDAEHsEN---ELVTVAHRAEVEAGTGLGDVVAQA-RGGLPIRLEPGAPGHGTMDGV 183
                                       4445566644222...4444579*****************.*************99998776 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.5         3   1.8e+04      49      56 ..     111     118 ..     108     126 .. 0.70
   2 ?   11.9   0.0   3.6e-05      0.21      10      67 ..     227     276 ..     217     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3
                    GHMP_kinases_C  49 lgaklsGa 56 
                                        g+++sGa
  gi|313127271|ref|YP_004037541.1| 111 SGFGVSGA 118
                                       46777777 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.6e-05
                    GHMP_kinases_C  10 lellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfk 67 
                                       ++++  l ++++r     +++  ++++e+++   +++G   +  s+a++G tvfa+++
  gi|313127271|ref|YP_004037541.1| 227 ADRFLSLSRQFAR-----EADLTTDRVESVIADVRAAG---GDASMAMLGETVFAFGT 276
                                       6778888899999.....9*******************...**************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2029.57
//
Query:       gi|313127272|ref|YP_004037542.1|  [L=249]
Description: pantothenate synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-75  252.9   3.5    1.5e-75  252.6   3.5    1.1  1  PPS_PS    Phosphopantothenate/pantothenate synthetase


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.6   3.5   8.2e-80   1.5e-75       1     176 []      68     243 ..      68     243 .. 0.99

  Alignments for each domain:
  == domain 1  score: 252.6 bits;  conditional E-value: 8.2e-80
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseR 77 
                                       llla++pv+svNGN+aaLv+ e+veLaea++a+levNlf+rteeR+++ia++l+e+gae+v+gl++d rip+l++eR
  gi|313127272|ref|YP_004037542.1|  68 LLLAEHPVLSVNGNVAALVPGEMVELAEAVDADLEVNLFNRTEERMRAIADHLREHGAEDVKGLTADGRIPNLDHER 144
                                       79*************************************************************************** PP

                            PPS_PS  78 akvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkske 154
                                       akv+++Gi +aDvvlvplEDGDRaeaL++mgK  i++DLNP+sR+a++a+i+ivdn++Ra+pn+t+++++l+++++e
  gi|313127272|ref|YP_004037542.1| 145 AKVDADGIGAADVVLVPLEDGDRAEALAAMGKVEIVVDLNPMSRSAQSAAIPIVDNIIRAVPNVTDHARDLTDATEE 221
                                       ***************************************************************************** PP

                            PPS_PS 155 eleeivkefdnkkvlkealkei 176
                                       e e+iv+efd++++l+ea ++i
  gi|313127272|ref|YP_004037542.1| 222 EREKIVREFDREAALREAEDAI 243
                                       *****************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1859.00
//
Query:       gi|313127273|ref|YP_004037543.1|  [L=373]
Description: sulfite oxidase-like oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-27   95.1   0.0    5.5e-27   94.5   0.0    1.2  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain
     0.0095   15.5   7.9      0.086   12.4   0.5    2.4  2  Ni_hydr_CYTB    Prokaryotic cytochrome b561
  ------ inclusion threshold ------
        0.2   11.2   0.8       0.36   10.4   0.8    1.4  1  DUF2632         Protein of unknown function (DUF2632)


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   9.2e-31   5.5e-27       7     172 .]     226     364 ..     220     364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 9.2e-31
                                       .GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHHH CS
                    Oxidored_molyb   7 vdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvLe 83 
                                       vd e+wrl+v glve+pl+ls + L a   + + + l+C++              +w     +   W+Gv l dvL+
  gi|313127273|ref|YP_004037543.1| 226 VDSESWRLRVGGLVESPLELSAEALTADADTDRRVLLDCTS--------------GW----YAERDWRGVHLGDVLD 284
                                       5899***********************8889**********..............8*....9*************** PP

                                       HTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEEE CS
                    Oxidored_molyb  84 kagvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlkr 160
                                       +ag + +  r+v++++        +y  s p ++a   ++lLA+++ ge+L+  hG+P+Rlv p   g++++Kw+++
  gi|313127273|ref|YP_004037543.1| 285 AAGTT-EAGRWVTVRSVT------GYRWSFPTDEAR--EMLLATHVGGERLTHGHGFPCRLVAPDRRGFQWIKWVDS 352
                                       ****7.99********86......6***********..9************************************** PP

                                       EEEESS---SHH CS
                    Oxidored_molyb 161 ievsdeesegyw 172
                                       iev +++ + +w
  gi|313127273|ref|YP_004037543.1| 353 IEVRRRRDPAQW 364
                                       ****99998887 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.5   1.4e-05     0.086       7      61 ..      18      68 ..      12      88 .. 0.82
   2 !    6.5   1.6   0.00095       5.7      13      73 ..      91     150 ..      87     168 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                                      THHHHHHHHHHHHHHHHHHHHHS------S-GGG-HHHHHHHHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB  7 rllHWlnallvvllllsgllianlhprlywgdsgkaralHklaGlvllalllfrl 61
                                      rl+ W + ++v+  + sg+l + +  +++w      ++lH ++Gl+l++ll + +
  gi|313127273|ref|YP_004037543.1| 18 RLVDWSILACVLFEVGSGVLSFGAGAPSHWPL----FELHTVVGLTLVFLLCYKF 68
                                      6777****************999999999996....9*************96544 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00095
                                       HHHHHHHHHHHHHHHHS------S-GGG-HHHHHHHHHHHHHHHHHHHHHHH--------- CS
                      Ni_hydr_CYTB  13 nallvvllllsgllianlhprlywgdsgkaralHklaGlvllalllfrllwlkkakkpspr 73 
                                       +a++ v  l++g++      ++ ++  +++++lH+ +Gl+l+ l+l+ l  ++  + + ++
  gi|313127273|ref|YP_004037543.1|  91 TAAVAVSSLATGVWWVL-GGNVRVTSYWTLLNLHIGLGLALVPLVLLHLSTRFRTPTRADF 150
                                       66666777777776443.2333333344479*****************9999444444444 PP

>> DUF2632  Protein of unknown function (DUF2632)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.8     6e-05      0.36      56     110 ..      73     132 ..      44     151 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6e-05
                           DUF2632  56 palhwspiw...rglenfwlflslaslaiaywwl..psmtftgywaltiiatilglimli 110
                                         +  s +w    gl  +   ++++sla   ww+   ++ +t yw+l  +   lgl ++ 
  gi|313127273|ref|YP_004037543.1|  73 RRVTDSDLWdraTGLSALTAAVAVSSLATGVWWVlgGNVRVTSYWTLLNLHIGLGLALVP 132
                                       3344567774334899999999***********83346899******9998888886543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2304.92
//
Query:       gi|313127274|ref|YP_004037544.1|  [L=331]
Description: glutathione s-transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-24   84.3   0.1    4.3e-23   81.4   0.0    2.2  2  GST_N_2         Glutathione S-transferase, N-terminal domain
    4.2e-11   42.7   0.2    8.6e-11   41.7   0.2    1.5  1  GST_C_2         Glutathione S-transferase, C-terminal domain
    1.7e-08   34.6   0.1    4.1e-08   33.3   0.0    1.6  2  GST_C           Glutathione S-transferase, C-terminal domain
    2.2e-06   27.8   0.0    3.8e-06   27.0   0.0    1.3  1  GST_C_3         Glutathione S-transferase, C-terminal domain
    5.3e-06   26.7   0.0    5.8e-05   23.4   0.0    2.5  1  GST_N_3         Glutathione S-transferase, N-terminal domain
    0.00048   19.9   0.1    0.00082   19.1   0.1    1.3  1  GST_C_6         Glutathione S-transferase, C-terminal domain
  ------ inclusion threshold ------
      0.033   13.5   0.0      0.049   13.0   0.0    1.2  1  SF-assemblin    SF-assemblin/beta giardin
      0.043   13.0   0.2        3.8    6.6   0.0    2.1  2  Baculo_ODV-E27  Baculovirus occlusion-derived virus envelope 


Domain annotation for each model (and alignments):
>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.0   1.9e-26   4.3e-23       1      70 []      54     147 ..      54     147 .. 0.86
   2 ?    0.3   0.0      0.41   9.1e+02      13      48 ..     264     299 ..     251     299 .. 0.67

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 1.9e-26
                                       S-HHHHHHHHHHHHCT--EEEEEE....H...-TTSHHHHH..................HHHCTTTSSSEEE-CTTE CS
                           GST_N_2   1 aCPwahRvlialalkglediisvv....vlepkgfekseef..................prlnprgtVPvLwdkdgq 55 
                                       aCPwahR+ ++++lkgled+is +    v  ++g+e s+e+                   ++++r+tVPvLwdk+  
  gi|313127274|ref|YP_004037544.1|  54 ACPWAHRTAMTRRLKGLEDAISLSvvepVRINDGWEFSAEYpdplygedylrdiytradDEFTGRVTVPVLWDKERE 130
                                       7**********************734444555666666666****************9999************9655 PP

                                       ..EEESHHHHHHHHHHH CS
                           GST_N_2  56 ..vineSseIlrylete 70 
                                         v+neS+eI+r+l+te
  gi|313127274|ref|YP_004037544.1| 131 tiVNNESREIMRMLDTE 147
                                       67*************95 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.41
                                       HHCT--EEEEEE..H...-TTSHHHHHHHHCTTTSSSE CS
                           GST_N_2  13 alkglediisvv..vlepkgfekseefprlnprgtVPv 48 
                                       +l +l+ + + +  ++ + +++ s    ++np+  VPv
  gi|313127274|ref|YP_004037544.1| 264 ELAQLPGVAETIniDHITRHYYMS--HGDVNPKRLVPV 299
                                       456666665554334444444444..689999999998 PP

>> GST_C_2  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.2   3.8e-14   8.6e-11       2      67 ..     192     262 ..     191     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 3.8e-14
                                       HHHCHHHHHCCHCHHHCTTT---SS.CTTCS--HHHHHHHHHHHHHHHHHHS-...---...TT-HHHHHHH CS
                           GST_C_2   2 aaveraleqldaaldaleahLadspflfGdqptlaDialapflvrlraagpgf...dir...eaypnlraWl 67 
                                        a+++a ++l+ ald +e+ L+d++f+ Gd +t aDia +++l+r++ +++ +   + r   ++ypnl+ + 
  gi|313127274|ref|YP_004037544.1| 192 DAYDEAITELFDALDHWESVLEDQRFVVGDVLTEADIAMFVTLIRFDHVYHTHfkcN-RraiHEYPNLWNYT 262
                                       6899*********************************************98775552.0566*******995 PP

>> GST_C  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.8   8.6e+03      14      36 ..     124     145 ..     115     153 .. 0.71
   2 !   33.3   0.0   1.8e-11   4.1e-08      18      93 .]     188     269 ..     163     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.8
                                       STTHHHHHHHHHHHHHHHHHHHH CS
                             GST_C  14 vkaeekkeelvdealekvaevls 36 
                                        ++ + +e+ v +++++++++l+
  gi|313127274|ref|YP_004037544.1| 124 LWD-KERETIVNNESREIMRMLD 145
                                       555.3566688888888888776 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 1.8e-11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTSSSSSTTSSCHHHHHHHHHHH...HHHHHTTTTT...TTTSHHHHHHHHH CS
                             GST_C  18 ekkeelvdealekvaevlsaleeelkkqdylvGdkltlADialvpiln...wlqrlglafg...qekfpnlkawler 88 
                                       + ++ ++dea ++++ +l+  e +l++q ++vGd lt ADia++  l    +++++ +++      ++pnl  ++++
  gi|313127274|ref|YP_004037544.1| 188 ADSQDAYDEAITELFDALDHWESVLEDQRFVVGDVLTEADIAMFVTLIrfdHVYHTHFKCNrraIHEYPNLWNYTKE 264
                                       557889***********************************9887765567999999999999999*********** PP

                                       HHTSH CS
                             GST_C  89 imarp 93 
                                       ++++p
  gi|313127274|ref|YP_004037544.1| 265 LAQLP 269
                                       99987 PP

>> GST_C_3  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.7e-09   3.8e-06      27      94 ..     199     273 ..     172     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.7e-09
                                       HHHHCHHHHHHHHHHCHGTSSSSTTS--HHHHHHHHHHHHHHHH......TCC....CC-HHHHHHHHHHHTSHHHH CS
                           GST_C_3  27 erlpkflkyfekvlkkkgggylvgdklTyADlalfqvldgleea......eal....kkfpklkalyervearpkik 93 
                                       ++l + l+++e vl+   + ++vgd lT AD+a+f  l  + ++        +     ++p+l ++ ++++++p+++
  gi|313127274|ref|YP_004037544.1| 199 TELFDALDHWESVLE--DQRFVVGDVLTEADIAMFVTLIRFDHVyhthfkC-NrraiHEYPNLWNYTKELAQLPGVA 272
                                       344456788888998..899****************999999999999961.3445799****************99 PP

                                       H CS
                           GST_C_3  94 a 94 
                                       +
  gi|313127274|ref|YP_004037544.1| 273 E 273
                                       7 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.6e-08   5.8e-05       1      72 [.      49     149 ..      49     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.6e-08
                                       EES-TTSHHHHHHHHHHHHHT--.......EEEE---..............TTTT..HHHHHHH-....TT--SSEE CS
                           GST_N_3   1 LygfpaSpyarrvrlaLnekglp.......vevvevt..............pgeh..deellakn....plgkvPvL 50 
                                       Ly ++a+p+a r +++ ++kgl+       ve v ++              + e   ++ + + +    ++ +vPvL
  gi|313127274|ref|YP_004037544.1|  49 LYISRACPWAHRTAMTRRLKGLEdaislsvVEPVRINdgwefsaeypdplyG-EDylRDIYTRADdeftGRVTVPVL 124
                                       89********************845554444445555899999999999962.3334444433334666******** PP

                                       ETTS-...EEESHHHHHHHHHHHH- CS
                           GST_N_3  51 eddge...altdSlaIidyLeelyp 72 
                                        d ++   +  +S++I++ L+++++
  gi|313127274|ref|YP_004037544.1| 125 WDKERetiVNNESREIMRMLDTEFD 149
                                       88744455667***********997 PP

>> GST_C_6  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   3.6e-07   0.00082       4      62 ..     204     263 ..     202     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.6e-07
                           GST_C_6   4 dleaLselLgdkkyFfGdkPtslDAlvFGhlaqilytplesp..elrellkeypNLvayce 62 
                                       +l+   ++L+d+ +  Gd  t++D ++F  l  + +  ++++    r+ ++eypNL +y++
  gi|313127274|ref|YP_004037544.1| 204 ALDHWESVLEDQRFVVGDVLTEADIAMFVTLIRF-DHVYHTHfkCNRRAIHEYPNLWNYTK 263
                                       56777899*********99************887.4455666655699999********87 PP

>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05     0.049      32     116 ..     126     220 ..     110     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                      SF-assemblin  32 ektrvklikeaiakleksveaEvkkRaesdkdi.....qeefkkeikklqekikee.....vddlalelkkaveeln 98 
                                       +k+r  ++ +    + + +++E    a++d d+     +ee++++i+ ++e i++      + d + +  +a+ el 
  gi|313127274|ref|YP_004037544.1| 126 DKERETIVNNESREIMRMLDTEFDAHAKHDVDLwpegyREEVDESIDSIYEPINNGvyragFADSQDAYDEAITELF 202
                                       7888899999999999999***99999999887666669**************996222225899************ PP

                      SF-assemblin  99 ekinnveanvenekakrr 116
                                       + +   e+ +e+++    
  gi|313127274|ref|YP_004037544.1| 203 DALDHWESVLEDQRFVVG 220
                                       *************97655 PP

>> Baculo_ODV-E27  Baculovirus occlusion-derived virus envelope protein EC27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0082        18     140     162 ..     135     157 ..     111     160 .. 0.81
   2 ?    6.6   0.0    0.0017       3.8     204     238 ..     223     256 ..     216     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0082
                    Baculo_ODV-E27 140 vdrasilkilekevdveakfend 162
                                        ++ +i+++l+ e+d  ak + d
  gi|313127274|ref|YP_004037544.1| 135 NESREIMRMLDTEFDAHAKHDVD 157
                                       57889*************99887 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                    Baculo_ODV-E27 204 itevevtqyltlllivenaylglyklkrsdvfeyf 238
                                       +te++++ ++tl+  +++ y   +k  r  ++ey 
  gi|313127274|ref|YP_004037544.1| 223 LTEADIAMFVTLI-RFDHVYHTHFKCNRRAIHEYP 256
                                       79*********86.79***************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2236.65
//
Query:       gi|313127275|ref|YP_004037545.1|  [L=308]
Description: thiazole-adenylate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-60  203.7   1.0    8.2e-48  162.7   0.2    2.5  3  Thi4            Thi4 family
    1.5e-09   37.9   0.1    3.8e-09   36.6   0.1    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.5e-09   36.5   0.3    4.9e-09   36.0   0.3    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
    7.5e-09   35.2   1.8      2e-06   27.1   0.2    2.3  2  FAD_binding_2   FAD binding domain
    2.2e-08   34.1   2.9    1.9e-05   24.4   0.4    2.5  2  DAO             FAD dependent oxidoreductase
      3e-08   33.3   0.1    6.4e-08   32.2   0.1    1.5  2  FAD_binding_3   FAD binding domain
    1.2e-07   31.2   0.1      2e-07   30.6   0.1    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.7e-07   29.2   0.0    5.1e-07   28.8   0.0    1.2  1  HI0933_like     HI0933-like protein
    2.3e-05   24.8   0.2    9.6e-05   22.9   0.2    2.1  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.6e-05   23.5   0.1    0.00011   22.3   0.1    1.6  1  NAD_binding_9   FAD-NAD(P)-binding
    8.2e-05   21.6   0.2     0.0088   14.9   0.1    2.2  2  Trp_halogenase  Tryptophan halogenase
    0.00019   20.8   0.0    0.00031   20.1   0.0    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0013   18.1   0.0     0.0021   17.4   0.0    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0061   15.7   0.9      0.018   14.1   0.2    1.9  2  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.013   14.6   0.2      0.019   14.1   0.2    1.2  1  GIDA            Glucose inhibited division protein A
      0.021   15.1   0.5      0.054   13.7   0.1    1.9  2  TrkA_N          TrkA-N domain
      0.038   14.4   0.1      0.079   13.4   0.1    1.6  1  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7   0.2   7.8e-51   8.2e-48       1     183 [.      16     198 ..      16     217 .. 0.94
   2 !   39.0   0.0   4.8e-13   5.1e-10     190     235 .]     228     273 ..     221     273 .. 0.95
   3 ?   -1.9   0.0       1.5   1.6e+03     160     175 ..     285     300 ..     279     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 7.8e-51
                                       HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHH CS
                              Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelL 77 
                                       ++ai +   e++++ ++++v+ivG+G+sGL aa+ la++ d+ v+i+e++  +GGG wlGG l +++ vr+pa+e+L
  gi|313127275|ref|YP_004037545.1|  16 TQAIASDWTEEFMDRIDTEVIIVGGGPSGLVAAKELAER-DVDVTIVEKNNYLGGGFWLGGFLMNKVTVRDPAQEIL 91 
                                       579999999******************************.************************************* PP

                                       HHTT---EEESS..EEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.- CS
                              Thi4  78 delgikyedegd..yvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscv 152
                                       delg++ye+ +d  +++v+d   + s l+ ++++ a++ + n +   D++vre+++v Gvv+nwt v+    + +cv
  gi|313127275|ref|YP_004037545.1|  92 DELGVPYEEAEDveGLYVADGPHACSALIKAACD-AGASVQNMTEFTDVVVREDHRVGGVVLNWTPVHALPRELTCV 167
                                       ********98763389******************.***********************************999**** PP

                                       B-EEEEEEEEEE--GSSSTTTTHHHHHHHHC CS
                              Thi4 153 DPlvirakvvvdatGhdgeivavvvkkikle 183
                                       DP  +++ +v+datGhd+ +++ +  + +l+
  gi|313127275|ref|YP_004037545.1| 168 DPVAVESDLVLDATGHDAVVISKLSERGVLN 198
                                       *******************998877776555 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 4.8e-13
                                       ---ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
                              Thi4 190 kgeksldaekaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                                       +g  s+++ ++ed+iv++t  v p+++++Gm+va v+g++RmGp+f
  gi|313127275|ref|YP_004037545.1| 228 PGHDSMWVAESEDKIVEQTGVVHPGVVASGMAVATVHGLPRMGPTF 273
                                       6889*****************************************9 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
                                       EEEEE--GSSSTTTTH CS
                              Thi4 160 kvvvdatGhdgeivav 175
                                       +  +d  Ghd++ v++
  gi|313127275|ref|YP_004037545.1| 285 QSCIDELGHDAPAVDF 300
                                       5578899999998876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   3.6e-12   3.8e-09       1      33 [.      37      69 ..      37      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.6e-12
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                      IvG+G sGlvaA +La++++dv+++ek+++lGG
  gi|313127275|ref|YP_004037545.1| 37 IVGGGPSGLVAAKELAERDVDVTIVEKNNYLGG 69
                                      9*******************************9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.3   4.6e-12   4.9e-09       1     125 [.      34     152 ..      34     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 4.6e-12
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrggarlkk 77 
                                       +v++vGGgp+G++AA   a+++  v +ve++++lGG +  g+   +++nk     v+  a+e+l++l     +++++
  gi|313127275|ref|YP_004037545.1|  34 EVIIVGGGPSGLVAAKELAERDVDVTIVEKNNYLGGGFWLGG---FLMNK---VTVRDPAQEILDELGV--PYEEAE 102
                                       59**********************************886555...88888...79999*********55..443334 PP

                      FAD_oxidored  78 rskw..ntfepevakavleemlaeagvtvllntrlvevek.egkriesvtv 125
                                       + +   ++  p++  a++++ ++  g  v  +t++++v++ e++r+ +v++
  gi|313127275|ref|YP_004037545.1| 103 DVEGlyVADGPHACSALIKAACDA-GASVQNMTEFTDVVVrEDHRVGGVVL 152
                                       444444478899999999999977.99********9999944667777765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.2   1.9e-09     2e-06       2      36 ..      35      69 ..      34      78 .. 0.93
   2 !    7.2   0.0    0.0023       2.4     136     183 ..     108     165 ..      93     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.9e-09
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      vi++G+G +GL+AA e+ae+  +v++vek ++ gg
  gi|313127275|ref|YP_004037545.1| 35 VIIVGGGPSGLVAAKELAERDVDVTIVEKNNYLGG 69
                                      9*****************************99887 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0023
                                       ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEE.CTTEEEEEEEEET.........T CS
                     FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLiv.edgrvtGavvenp.........e 183
                                        +++g++ + +l+++a +ag  +q+ te ++++v ed rv G+v++           +
  gi|313127275|ref|YP_004037545.1| 108 YVADGPHACSALIKAACDAGASVQNMTEFTDVVVrEDHRVGGVVLNWTpvhalprelT 165
                                       567999**************************994566****9998556664443333 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.4   1.8e-08   1.9e-05       2      35 ..      35      69 ..      34      77 .. 0.92
   2 !    9.0   0.1    0.0009      0.95     143     204 ..     110     185 ..     104     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-08
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                      v+i+GGG  Gl +A eLa+r   Vt++ek++ +g g
  gi|313127275|ref|YP_004037545.1| 35 VIIVGGGPSGLVAAKELAERDvdVTIVEKNNYLG-G 69
                                      9*******************999*******9998.3 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0009
                                       EEHHHHHHHHHHHHHHTT-EEEESECEEEE.EEEETCEEEEE.EECT.EEE.E..........EEEEEEE--GGGH CS
                               DAO 143 vdpakltaalaraaealGveilegtevtgl.eeedgkvwgve.rttp.gen.d..........aadavVnaaGaws 204
                                       +d  +++ al +aa ++G+ + + te t++  +ed +v+gv  + tp ++  +          + d v  a+G+ +
  gi|313127275|ref|YP_004037545.1| 110 ADGPHACSALIKAACDAGASVQNMTEFTDVvVREDHRVGGVVlNWTPvHALpReltcvdpvavESDLVLDATGHDA 185
                                       578899***********************646678999**999666656554355555666553355888888775 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.1   6.1e-11   6.4e-08       1      34 [.      32      65 ..      32      68 .. 0.95
   2 ?   -3.6   0.0       4.6   4.9e+03     110     131 ..     118     139 ..     113     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 6.1e-11
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      +t+V+IVG+Gp+Gl++a++L+e+ v+v++vek +
  gi|313127275|ref|YP_004037545.1| 32 DTEVIIVGGGPSGLVAAKELAERDVDVTIVEKNN 65
                                      69*****************************975 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.6
                                       HHHHHHHHHTEEETCSEEEECC CS
                     FAD_binding_3 110 iLvehaeerglqvrfktevesl 131
                                       +L+++a  +g++v+  te++ +
  gi|313127275|ref|YP_004037545.1| 118 ALIKAACDAGASVQNMTEFTDV 139
                                       5778888888999998887754 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1   1.9e-10     2e-07       2      74 ..      34     105 ..      33     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.9e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgee 74 
                                       +v+++GgGp Gl aa++la+  ++vt+v ++++ l+gg +l   l +    ++ a+e +++l+  +e   ++e
  gi|313127275|ref|YP_004037545.1|  34 EVIIVGGGPSGLVAAKELAERDVDVTIV-EKNNYLGGGFWLGGFLMNKVTVRDPAQEILDELGVPYEEAEDVE 105
                                       69**************************.77777788877777777777777777766666655555555544 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   4.8e-10   5.1e-07       2      42 ..      34      74 ..      33     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 4.8e-10
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilis 42
                                      +vi++GgG++Gl aA ++a+r+ +V+++ek++ lg  + + 
  gi|313127275|ref|YP_004037545.1| 34 EVIIVGGGPSGLVAAKELAERDVDVTIVEKNNYLGGGFWLG 74
                                      79******************************999766665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   9.1e-08   9.6e-05       2      35 ..      35      68 ..      34      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.1e-08
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v++vGgG +gl +A++lae   +Vt+ve ++ l 
  gi|313127275|ref|YP_004037545.1| 35 VIIVGGGPSGLVAAKELAERDVDVTIVEKNNYLG 68
                                      89**************************999876 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1     1e-07   0.00011       2      43 ..      37      73 ..      36      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1e-07
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwr 43
                                      ivG+Gp+Gl ++++L++r     ++++t+++++++ g g+ w 
  gi|313127275|ref|YP_004037545.1| 37 IVGGGPSGLVAAKELAER-----DVDVTIVEKNNYlG-GGFWL 73
                                      9****************9.....6********88856.99995 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   8.3e-06    0.0088       2      34 ..      35      64 ..      34      68 .. 0.91
   2 ?    4.7   0.0      0.01        11     190     217 ..     164     191 ..     114     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.3e-06
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      ++ivGGG++G +aA  la+     ++vt+ve++
  gi|313127275|ref|YP_004037545.1| 35 VIIVGGGPSGLVAAKELAERD---VDVTIVEKN 64
                                      99***************9888...9******97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                                       EEETTS-EEE-SEEEE-SGGG-IIIIII CS
                    Trp_halogenase 190 lrledgreveadlfiDcsGfrgllieqa 217
                                       l+  d   ve dl++D++G+ + +i++ 
  gi|313127275|ref|YP_004037545.1| 164 LTCVDPVAVESDLVLDATGHDAVVISKL 191
                                       444457789**************99985 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.9e-07   0.00031       1      31 [.      36      65 ..      15      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.9e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      iI+G+GP Gl aa el + ++ d++i+Ek+n
  gi|313127275|ref|YP_004037545.1| 36 IIVGGGPSGLVAAKELAERDV-DVTIVEKNN 65
                                      788888888888888888888.688888876 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     2e-06    0.0021       2      28 ..      43      69 ..      42      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                                      HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                      +GL+aA++L+++ +dVt++E ++ +GG
  gi|313127275|ref|YP_004037545.1| 43 SGLVAAKELAERDVDVTIVEKNNYLGG 69
                                      9*************************9 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   1.7e-05     0.018       2      33 ..      35      64 ..      34      70 .. 0.91
   2 ?   -0.6   0.0       0.5   5.3e+02     109     142 ..     151     184 ..     136     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieas 33
                                      v+++G+Gp gl  A++l  a+ ++ v+++e  
  gi|313127275|ref|YP_004037545.1| 35 VIIVGGGPSGLVAAKEL--AERDVDVTIVEKN 64
                                      9****************..9999*****9865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.5
                     Lycopene_cycl 109 vesveeeeageslvvleggrkirarlvvdargla 142
                                       v + ++++a  +  ++ + + +++ lv+da+g  
  gi|313127275|ref|YP_004037545.1| 151 VLNWTPVHALPRELTCVDPVAVESDLVLDATGHD 184
                                       5556667777788999999************943 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.8e-05     0.019       1      31 [.      34      64 ..      34      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                      +vi++GgG +G+ AA ++a++ ++v+++ ++
  gi|313127275|ref|YP_004037545.1| 34 EVIIVGGGPSGLVAAKELAERDVDVTIVEKN 64
                                      59***********************999443 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.2e-05     0.054       1      30 [.      35      64 ..      35      67 .. 0.92
   2 ?   -2.0   0.0         4   4.2e+03      44      64 ..     186     206 ..     170     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-05
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkd 30
                                      +ii+G G  G   a+eL e+  dv++++k+
  gi|313127275|ref|YP_004037545.1| 35 VIIVGGGPSGLVAAKELAERDVDVTIVEKN 64
                                      79*****************7768*****98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                                       EEES-TTSHHHHHHTTGGGES CS
                            TrkA_N  44 vvvgdatdeevLeeagiekad 64 
                                       vv+   +++ vL + gie+a+
  gi|313127275|ref|YP_004037545.1| 186 VVISKLSERGVLNAPGIEHAK 206
                                       666777777888888888876 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.5e-05     0.079       7      40 ..      32      65 ..      27     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.5e-05
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                      + +v++vGgG+ ++  ++ l+e + +vt+v ++ 
  gi|313127275|ref|YP_004037545.1| 32 DTEVIIVGGGPSGLVAAKELAERDVDVTIVEKNN 65
                                      789***************************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2064.79
//
Query:       gi|313127276|ref|YP_004037546.1|  [L=236]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-14   52.8   0.1    7.5e-14   52.2   0.1    1.3  1  Methyltransf_11  Methyltransferase domain
    1.7e-13   51.0   0.0    2.8e-13   50.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    7.3e-13   48.6   0.0    7.9e-13   48.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    9.5e-12   45.1   0.0    1.3e-11   44.7   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.2e-11   45.2   0.0    1.9e-11   44.6   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.2e-10   41.1   0.0    1.6e-10   40.8   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      4e-10   39.8   0.0    5.5e-10   39.3   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.7e-05   25.0   0.0    2.4e-05   24.5   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
    0.00079   18.9   0.0     0.0012   18.3   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
     0.0013   18.1   0.1     0.0019   17.5   0.1    1.2  1  Methyltransf_2   O-methyltransferase domain
     0.0033   16.6   0.0     0.0042   16.2   0.0    1.1  1  Fibrillarin      Fibrillarin
     0.0057   16.3   0.0     0.0079   15.9   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0092   15.7   0.0      0.012   15.3   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
     0.0096   15.2   0.0      0.013   14.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.036   14.1   0.0    1.3  1  Pyr_excise       Pyrimidine dimer DNA glycosylase
      0.024   14.2   0.0      0.036   13.6   0.0    1.2  1  MTS              Methyltransferase small domain
      0.044   13.8   0.0      0.064   13.2   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.054   13.0   0.3       0.73    9.3   0.3    2.0  1  Methyltransf_19  S-adenosyl methyltransferase
       0.18   10.9   0.0       0.24   10.4   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.1   7.9e-17   7.5e-14       2      95 ..      50     145 ..      49     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 7.9e-17
                                       EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       ++GcGtG+++++l +r+   ++vvgvD+++ +l++a++++++++  +v +v++da++ p++    D+vv+++v   +
  gi|313127276|ref|YP_004037546.1|  50 EMGCGTGANFAYLRDRVgseGTVVGVDFTPGVLAVARDRIRKKEWeNVHVVRGDATRPPVAA--ADAVVATFVSGML 124
                                       79************7777*************************99************88776..9************ PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                        dp++a++ +a ++  gG+l+
  gi|313127276|ref|YP_004037546.1| 125 SDPAAAVRTWAELVGSGGRLA 145
                                       ******************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0     3e-16   2.8e-13       1      97 []      48     142 ..      48     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 3e-16
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       ++++GcGtG + ++l +r+g +++v+gvD++++ l+ ar r++++++ nv++v+gda++ p ++   D+vv++++  
  gi|313127276|ref|YP_004037546.1|  48 IVEMGCGTGANFAYLRDRVGsEGTVVGVDFTPGVLAVARDRIRKKEWeNVHVVRGDATRPPVAA--ADAVVATFVSG 122
                                       799****************779**********************999************99886..9*****98877 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       +lsd   ++a++ +a+++  gG
  gi|313127276|ref|YP_004037546.1| 123 MLSD--PAAAVRTWAELVGSGG 142
                                       8885..5589999999988887 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   8.4e-16   7.9e-13       4     113 ..      45     150 ..      42     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 8.4e-16
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g ++++ GCGtG+    l +++g++++vvG+D+++ ++ +Ar + +k++ +nv++ +gd++  +  ++    D +++
  gi|313127276|ref|YP_004037546.1|  45 GDTIVEMGCGTGANFAYLRDRVGSEGTVVGVDFTPGVLAVARDRIRKKEWENVHVVRGDATRPP--VA--AADAVVA 117
                                       67899*********************************************************88..44..69***** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedpr 113
                                         v   l+dp+++ +   +++ +gg+l+++d  
  gi|313127276|ref|YP_004037546.1| 118 TFVSGMLSDPAAAVRTWAELVGSGGRLALADLG 150
                                       988899*********************999875 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   1.4e-14   1.3e-11      65     135 ..      36     106 ..      26     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.4e-14
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGG CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrk 135
                                       + + l l++g+ ++e+G+G+G + a l   vg++g+vv+++ ++ + + a+ +++k++ env+vv gD + 
  gi|313127276|ref|YP_004037546.1|  36 VADALALTPGDTIVEMGCGTGANFAYLRDRVGSEGTVVGVDFTPGVLAVARDRIRKKEWENVHVVRGDATR 106
                                       567899**************************************************************865 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0     2e-14   1.9e-11       1      99 []      49     144 ..      49     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2e-14
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       +e GcGtG++ ++l+++  ++ +++gvD+ p +++ a+ +++k+e +n+++v+ +a+        ++ D+vva +v 
  gi|313127276|ref|YP_004037546.1|  49 VEMGCGTGANFAYLRDRVgSEGTVVGVDFTPGVLAVARDRIRKKEWENVHVVRGDATRPP----VAAADAVVATFVS 121
                                       599***************9**************************999999999988865....46*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                         l d++++++  ++l+  gGrl
  gi|313127276|ref|YP_004037546.1| 122 GMLSDPAAAVRTWAELVGSGGRL 144
                                       *********************97 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   1.6e-13   1.6e-10      30     161 ..      28     156 ..       5     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.6e-13
                                       TTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE-- CS
                   Ubie_methyltran  30 gihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan 106
                                       g+h l ++ v +  a  +g +++++ +Gtg   + l d vg++g+vv++D+ + +L v++++++++   n++ + ++
  gi|313127276|ref|YP_004037546.1|  28 GVHGL-RRAVADALALTPGDTIVEMGCGTGANFAYLRDRVGSEGTVVGVDFTPGVLAVARDRIRKKEWENVHVVRGD 103
                                       66766.5678899999************************************************************* PP

                                       TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHH CS
                   Ubie_methyltran 107 aeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpl 161
                                       a + p    + D v  +f    ++D   a+++    +  GGrl   ++ + + + 
  gi|313127276|ref|YP_004037546.1| 104 ATRPPVA--AADAVVATFVSGMLSDPAAAVRTWAELVGSGGRLALADLGRTTRTP 156
                                       **99986..66777777777789********************998888777655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   5.8e-13   5.5e-10      10     125 ..      33     154 ..      24     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 5.8e-13
                   Methyltransf_23  10 sdklerllpklraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae....kakkaqkdqfdeqeaaep 79 
                                       +++++ +l+ l +g  ++++GcGtG +  +lr++ g   +v+gvD  p   + a+    k+   + + ++ +  ++p
  gi|313127276|ref|YP_004037546.1|  33 RRAVADALA-LTPGDTIVEMGCGTGANFAYLRDRvGSegTVVGVDFTPGVLAVARdrirKKEWENVHVVRGDATRPP 108
                                       455555555.78899****************988466899******9987777767666333333333333456889 PP

                   Methyltransf_23  80 qgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslk 125
                                        +  d +v+++v + + dp++++r+ a+l+  gG+l l + ++   
  gi|313127276|ref|YP_004037546.1| 109 VAAADAVVATFVSGMLSDPAAAVRTWAELVGSGGRLALADLGRTTR 154
                                       99************************************99988754 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.5e-08   2.4e-05      19      95 ..      42     127 ..      29     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.5e-08
                                       S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...........HHHTTEEEECS-CCCSSHHHHHCHCHH CS
                              FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...........aplpgvttiqgditdpetiekikeals 84 
                                       ++pg+t+v+ g+++G+   +l  r+g +g vv+vD  p+           +  ++v++++gd t+p ++ +  +a+ 
  gi|313127276|ref|YP_004037546.1|  42 LTPGDTIVEMGCGTGANFAYLRDRVGSEGTVVGVDFTPGvlavardrirkKEWENVHVVRGDATRPPVAAA--DAVV 116
                                       689***********************9**************9999776533449***********988772..2333 PP

                                       HSSEEEEEE-- CS
                              FtsJ  85 erkvdlvvsDg 95 
                                          v+ ++sD 
  gi|313127276|ref|YP_004037546.1| 117 ATFVSGMLSDP 127
                                       33455555554 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.3e-06    0.0012       4      61 ..      47     105 ..      45     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                                       EEEEET-TTSHHHHHHHHHS.TTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CC CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkkn.PdknflGiEirvkvvakvlkkiealelkNlrilrgdal 61 
                                       +++e+GcG G     l  +   + +++G++    v+a + ++i+++e +N++++rgda+
  gi|313127276|ref|YP_004037546.1|  47 TIVEMGCGTGANFAYLRDRVgSEGTVVGVDFTPGVLAVARDRIRKKEWENVHVVRGDAT 105
                                       689********99999887526789********************************96 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1     2e-06    0.0019      56     134 ..      38     118 ..      30     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                                       HSS-GGG-SEEEEET-TTSHHHHHHHHH-TT.-EEEEEE-.HHHHHHHHHHS-----TTEEEEES-TTTS-----SE CS
                    Methyltransf_2  56 eafdleglkslvDvGGGtGalakaivsayPt.ikvivfDl.peVveaAkehlsageeervefvgGdffkdslPeaDa 130
                                        a +l++  ++v++G GtGa+ +       +  +v+  D+ p V + A++++  +e e+v++v Gd  + ++  aDa
  gi|313127276|ref|YP_004037546.1|  38 DALALTPGDTIVEMGCGTGANFAYLRDRVGSeGTVVGVDFtPGVLAVARDRIRKKEWENVHVVRGDATRPPVAAADA 114
                                       5667888899***********9999877654144555675599********************************** PP

                                       EEEE CS
                    Methyltransf_2 131 illk 134
                                       ++ +
  gi|313127276|ref|YP_004037546.1| 115 VVAT 118
                                       9855 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.5e-06    0.0042      65     131 ..      39     107 ..      24     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.5e-06
                                       --S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH...HHHHHHHTTSTTEEEEES-TTSG CS
                       Fibrillarin  65 elpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl...relievakkRknivPileDArkP 131
                                        l + +g+ ++ +G ++G   +++ D vg+eg+v +v+f+p vl   r+ i+  k+ +n+  + +DA++P
  gi|313127276|ref|YP_004037546.1|  39 ALALTPGDTIVEMGCGTGANFAYLRDRVGSEGTVVGVDFTPGVLavaRDRIR-KKEWENVHVVRGDATRP 107
                                       56799***********************************987511155443.45678999999999998 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.3e-06    0.0079       3      77 ..      39     113 ..      37     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.3e-06
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg 77 
                                       +La+ +++ti+++ ++ G+  +++ + + ++gtvv vd     l    + +++   +n+ v+++Da++++   ++
  gi|313127276|ref|YP_004037546.1|  39 ALALTPGDTIVEMGCGTGANFAYLRDRVGSEGTVVGVDFTPGVLAVARDRIRKKEWENVHVVRGDATRPPVAAAD 113
                                       799999*************************************************************99876665 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-05     0.012      33     106 ..      37     109 ..      34     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                             GCD14  33 imkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGf 106
                                          L l+pG  +ve G G+g+   ++   v+  G +  ++f       ar+  r++e  ++v+v   D+ +   
  gi|313127276|ref|YP_004037546.1|  37 ADALALTPGDTIVEMGCGTGANFAYLRDRVGSEGTVVGVDFTPGVLAVARDRIRKKEW-ENVHVVRGDATRPPV 109
                                       56899**************************************************997.578888888876655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.4e-05     0.013      53     116 ..      35     100 ..      31     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--..EEEEEES-HHHHHHHHHHHHTS-SSS-EEE CS
                              CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydv..kvvglTlSkeqaklakkrvdeldlerkvev 116
                                        + + l l pG+t++++GcG G+ + +  +r +    vvg+ +     ++a++r+ + + e+ + v
  gi|313127276|ref|YP_004037546.1|  35 AVADALALTPGDTIVEMGCGTGANFAYLRDRVGSegTVVGVDFTPGVLAVARDRIRKKEWENVHVV 100
                                       56799*****************99988888876522699999999999999999999887766555 PP

>> Pyr_excise  Pyrimidine dimer DNA glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.8e-05     0.036       7      36 ..     182     212 ..     180     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                                       S-GGGS-HHHHHHHHHHTHHH.HHHHHH-GG CS
                        Pyr_excise   7 eliseLpdqhLlaeyrElpri.nalakkerg 36 
                                       ++++ L dq L+a +rEl ++ + + +++r 
  gi|313127276|ref|YP_004037546.1| 182 VPPTVLLDQRLVAAHRELEAVcEDVRRETRA 212
                                       68999****************8888887554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.8e-05     0.036      25     102 ..      38     116 ..      33     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EE CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleeveekkfd 99 
                                       ++l  +  ++++ +GcG+G+  a l ++  +   v+ vd     l++a+  +++++ e v+vv  d++     +  d
  gi|313127276|ref|YP_004037546.1|  38 DALALTPGDTIVEMGCGTGANFAYLRDRVGSEGtVVGVDFTPGVLAVARDRIRKKEWEnVHVVRGDATRPPV-AAAD 113
                                       5566667889*********988888887765444************************9********99988.8888 PP

                                       EEE CS
                               MTS 100 liv 102
                                       ++v
  gi|313127276|ref|YP_004037546.1| 114 AVV 116
                                       877 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.7e-05     0.064      20      84 ..      39      99 ..      28     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.7e-05
                   Methyltransf_32 20 lakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsf 84
                                      + + ++  t+v++G+G g     l + ++  +  vvg+d    + + a++r +k +  + ++++ 
  gi|313127276|ref|YP_004037546.1| 39 ALALTPGDTIVEMGCGTGANFAYLRD-RVGSEGTVVGVDFTPGVLAVARDRIRKKE--W-ENVHV 99
                                      34457789*********943333433.55679*****************9999988..7.55544 PP

>> Methyltransf_19  S-adenosyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.3   0.00077      0.73      57     139 ..      32     112 ..      24     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00077
                   Methyltransf_19  57 lrRavrvlaeeaGirqflDiGtGlPtednvHqvaqrvaPesRvvYvDnDPivlaharallestpeGatdyieaDlrd 133
                                       lrRav+   + +  + ++++G G  t  n   +  rv  e  vv vD  P vla ar  +++++  + +++++D  +
  gi|313127276|ref|YP_004037546.1|  32 LRRAVADALALTPGDTIVEMGCG--TGANFAYLRDRVGSEGTVVGVDFTPGVLAVARDRIRKKEWENVHVVRGDATR 106
                                       66777655444455777777777..88999999999*********************99999999999999999988 PP

                   Methyltransf_19 134 peeile 139
                                       p    +
  gi|313127276|ref|YP_004037546.1| 107 PPVAAA 112
                                       864444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00025      0.24      22      85 ..      36     104 ..      32     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                                       HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
                            RrnaAD  22 IldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqDf 85 
                                       + d+l l++ +t++e+g G+G+  + L +r+     vv +   +  +++ +++++  + e++ vv  D+
  gi|313127276|ref|YP_004037546.1|  36 VADALALTPGDTIVEMGCGTGANFAYLRDRVgseGTVVGVDFTPGVLAVARDRIRkkEWENVHVVRGDA 104
                                       678999****************99999999986556666666677888888877765567777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1570.26
//
Query:       gi|313127277|ref|YP_004037547.1|  [L=302]
Description: hypothetical protein Hbor_25480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-51  173.2   0.0    4.6e-51  172.7   0.0    1.2  1  ThiP_synth      Thiamine-phosphate synthase
    8.5e-07   28.9   0.1    1.8e-06   27.9   0.1    1.6  1  HTH_3           Helix-turn-helix
    0.00011   21.9   0.3     0.0006   19.5   0.0    2.3  2  HTH_23          Homeodomain-like domain
    0.00015   22.1   0.2    0.00015   22.1   0.2    2.1  1  HTH_31          Helix-turn-helix domain
    0.00015   21.2   1.2     0.0062   16.0   0.0    2.7  2  Sigma70_r4      Sigma-70, region 4
    0.00027   20.8   0.0    0.00055   19.8   0.0    1.4  1  HTH_37          Helix-turn-helix domain
    0.00034   20.6   0.0    0.00065   19.7   0.0    1.5  1  HTH_19          Helix-turn-helix domain
    0.00075   19.3   0.4     0.0049   16.7   0.0    2.6  2  MarR_2          MarR family
     0.0011   19.4   0.0     0.0021   18.5   0.0    1.4  1  HTH_26          Cro/C1-type HTH DNA-binding domain
     0.0014   18.1   0.0     0.0067   16.0   0.0    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0045   16.7   0.0      0.054   13.3   0.0    2.4  2  HTH_38          Helix-turn-helix domain
     0.0079   16.3   0.0      0.014   15.4   0.0    1.4  1  RepB            RepB plasmid partitioning protein
  ------ inclusion threshold ------
      0.012   15.5   0.2      0.039   13.8   0.0    2.0  1  P22_Cro         DNA-binding transcriptional regulator Cro
      0.013   15.3   0.0      0.028   14.3   0.0    1.5  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
       0.05   13.2   0.0       0.12   12.1   0.0    1.7  1  HTH_50          Helix-turn-helix domain
      0.053   13.2   0.4        0.2   11.4   0.0    2.2  2  Sigma70_r4_2    Sigma-70, region 4
      0.061   13.7   0.1      0.098   13.1   0.1    1.4  1  DUF3486         Protein of unknown function (DUF3486)
      0.069   13.1   0.0         18    5.4   0.0    3.1  3  MarR            MarR family
      0.074   13.7   0.0       0.14   12.7   0.0    1.4  1  HNF-1_N         Hepatocyte nuclear factor 1 (HNF-1), N termin
      0.091   13.0   0.0       0.29   11.4   0.0    1.9  1  Phage_CII       Bacteriophage CII protein
      0.098   12.8   0.1          1    9.5   0.0    2.6  3  HTH_28          Helix-turn-helix domain
       0.12   12.4   0.1       0.77    9.8   0.0    2.4  2  HTH_35          Winged helix-turn-helix DNA-binding
       0.13   12.1   0.0       0.32   10.8   0.0    1.6  1  HTH_10          HTH DNA binding domain
       0.66    9.8   5.6        2.3    8.1   0.0    3.2  3  HTH_IclR        IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.7   0.0   6.2e-54   4.6e-51       1     164 [.     139     297 ..     139     298 .. 0.94

  Alignments for each domain:
  == domain 1  score: 172.7 bits;  conditional E-value: 6.2e-54
                                       HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC CS
                        ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkf 77 
                                       +++r+l++l+++++fa liP+vgsN+a++lp++++ieDvaa+pGRI++vkg+++v+++pefg+s+hva+vll+a+++
  gi|313127277|ref|YP_004037547.1| 139 SVRRGLRTLTNASGFAGLIPNVGSNLAECLPEPSGIEDVAAIPGRIFDVKGQATVPSDPEFGVSEHVASVLLSAREA 215
                                       589************************************************************************** PP

                                       -TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC...S-ECEEEE--BCTB--EEEE CS
                        ThiP_synth  78 dpevraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel...evpdviydeGgvGkEpmiyv 151
                                       +++v++a+niryd++i+++le+ g++++efd+++ ++         + +a++++   +   ++y+ G++G+E+++yv
  gi|313127277|ref|YP_004037547.1| 216 GRDVHSAVNIRYDPDIIASLEDSGYDAIEFDPDAPTDP--------IVAALSDRddlTDTFALYQSGAYGIEAITYV 284
                                       **********************************9999........5666666655534678*************** PP

                                       EESSHHHHHHHHH CS
                        ThiP_synth 152 lgkdaeevvekvl 164
                                       lg+da +v++ v+
  gi|313127277|ref|YP_004037547.1| 285 LGPDAPTVARAVR 297
                                       *********9987 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   2.4e-09   1.8e-06       3      33 ..      22      52 ..      20      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.4e-09
                                      HHHHHTTHHHHHHHHHHTSSHHHHHHHHTTS CS
                             HTH_3  3 elRkqlglsqeeLAeklGvsrstisriEnGe 33
                                      e +  +g +q+e+A++lG+s+s++s++  Ge
  gi|313127277|ref|YP_004037547.1| 22 EELRDRGFTQREVADALGISQSAVSKYAHGE 52
                                      455569*********************9995 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   8.1e-07    0.0006      13      37 ..      24      48 ..      19      55 .. 0.85
   2 ?   -1.2   0.1       2.7     2e+03      31      49 ..     137     156 ..     129     157 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.1e-07
                            HTH_23 13 llaeGlsvreIAreLgvsrrTvyrw 37
                                      l ++G ++re+A++Lg+s++ v+++
  gi|313127277|ref|YP_004037547.1| 24 LRDRGFTQREVADALGISQSAVSKY 48
                                      3455******************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.7
                            HTH_23  31 rrTvyrwlkry.reeGlegl 49 
                                       r+ v+r l++  +++G++gl
  gi|313127277|ref|YP_004037547.1| 137 RSSVRRGLRTLtNASGFAGL 156
                                       45555555555235888887 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2     2e-07   0.00015      12      45 ..      26      58 ..      18      87 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-07
                            HTH_31 12 raGLsqeevAerlgvsestlsrlEqGrrgrpspa 45
                                       +G +q+evA++lg+s+s +s++  G+   + + 
  gi|313127277|ref|YP_004037547.1| 26 DRGFTQREVADALGISQSAVSKYAHGEVS-RNET 58
                                      689***********************995.6443 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.3e-06    0.0062      18      39 ..      26      47 ..      16      50 .. 0.90
   2 ?    2.9   0.4       0.1        77      33      48 ..     132     147 ..     131     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.3e-06
                                      TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 18 geglTleEIgerlgiSrerVrq 39
                                      ++g T+ E+++ lgiS+++V+ 
  gi|313127277|ref|YP_004037547.1| 26 DRGFTQREVADALGISQSAVSK 47
                                      6899****************85 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.1
                                       -HHHHHHHHHHHHHHH CS
                        Sigma70_r4  33 SrerVrqiekrAlrkL 48 
                                       + erVr+  +r+lr L
  gi|313127277|ref|YP_004037547.1| 132 TAERVRSSVRRGLRTL 147
                                       679**********987 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   7.3e-07   0.00055      22      58 ..      19      55 ..      16      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.3e-07
                                      HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT CS
                            HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsrllrgklsr 58
                                      ++ae +++r+ +q+e+a +lgi+q+ vs+   g++sr
  gi|313127277|ref|YP_004037547.1| 19 MLAEELRDRGFTQREVADALGISQSAVSKYAHGEVSR 55
                                      7999*************************99888876 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   8.7e-07   0.00065       8      44 ..      24      64 ..      18      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.7e-07
                            HTH_19  8 ReelgltqeelaerlgisrskisaiEng...kkdvps.ael 44
                                       + +g+tq+e+a+ lgis+s  s++ +g   +++++   e+
  gi|313127277|ref|YP_004037547.1| 24 LRDRGFTQREVADALGISQSAVSKYAHGevsRNETLLeDER 64
                                      6789**********************998874434332555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.5e-06    0.0049      12      40 ..      22      47 ..      14      55 .. 0.87
   2 ?   -2.2   0.0       5.3   3.9e+03      32      45 ..     286     299 ..     280     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.5e-06
                                      HHHHCTTTSEEEHHHHHHHHTSSHHHHHH CS
                            MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsr 40
                                       +L++r+   +t++e+a++lg+s+savs+
  gi|313127277|ref|YP_004037547.1| 22 EELRDRG---FTQREVADALGISQSAVSK 47
                                      4689998...9****************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.3
                                       TSSHHHHHHHHHHH CS
                            MarR_2  32 glsksavsrilkrL 45 
                                       g + ++v r+++ L
  gi|313127277|ref|YP_004037547.1| 286 GPDAPTVARAVRSL 299
                                       55778999999987 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.7e-06    0.0021       2      37 ..      20      55 ..      19      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.7e-06
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkper 37
                                      L e ++drg t+ e+a ++gis++ +s++ +g+++r
  gi|313127277|ref|YP_004037547.1| 20 LAEELRDRGFTQREVADALGISQSAVSKYAHGEVSR 55
                                      77889***************************9876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.9e-06    0.0067      15      37 ..      26      48 ..      22      49 .. 0.88
   2 ?   -2.6   0.0       5.7   4.3e+03      32      41 ..     290     299 ..     288     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.9e-06
                            HTH_24 15 nprisqreLAerlglSpstvnrr 37
                                      + + +qre+A++lg+S+s+v+++
  gi|313127277|ref|YP_004037547.1| 26 DRGFTQREVADALGISQSAVSKY 48
                                      55669***************987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.7
                            HTH_24  32 stvnrrlkrL 41 
                                       +tv r ++ L
  gi|313127277|ref|YP_004037547.1| 290 PTVARAVRSL 299
                                       89*****988 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   7.2e-05     0.054      14      39 ..      22      47 ..      19      56 .. 0.91
   2 ?    0.3   0.0      0.79   5.9e+02      15      42 ..     269     297 ..     268     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-05
                            HTH_38 14 erllaeGlslreIArrLgrspsTIsR 39
                                      e l+++G ++re+A  Lg s s +s+
  gi|313127277|ref|YP_004037547.1| 22 EELRDRGFTQREVADALGISQSAVSK 47
                                      789*******************9986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.79
                            HTH_38  15 rllaeG.lslreIArrLgrspsTIsRElk 42 
                                       +l++ G +++ +I   Lg +  T++R ++
  gi|313127277|ref|YP_004037547.1| 269 ALYQSGaYGIEAITYVLGPDAPTVARAVR 297
                                       5899999999999999**9*******987 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-05     0.014      12      60 ..      19      62 ..      16      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                              RepB 12 rfaarleerGvdreeiasalgldkqtvskmva.raipegicaeevaLLkd 60
                                      + a  l++rG++++e+a+alg+++++vsk+   +  ++++      LL+d
  gi|313127277|ref|YP_004037547.1| 19 MLAEELRDRGFTQREVADALGISQSAVSKYAHgEVSRNET------LLED 62
                                      56889**********************9994442222222......4444 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.2e-05     0.039      12      29 ..      31      48 ..      29      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.2e-05
                                      HHHHHHHHTS-HHHHHHH CS
                           P22_Cro 12 vekvAkalgvtksAVsqW 29
                                      ++ vA alg+++sAVs+ 
  gi|313127277|ref|YP_004037547.1| 31 QREVADALGISQSAVSKY 48
                                      789*************98 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.7e-05     0.028      10      33 ..      30      53 ..      29      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkk 33
                                      +q+++A+alg+sq+aVs+ ++g+ 
  gi|313127277|ref|YP_004037547.1| 30 TQREVADALGISQSAVSKYAHGEV 53
                                      5999***************99854 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.12      26      41 ..      31      46 ..       8      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                            HTH_50 26 tRklAkrLGvShtaia 41
                                       R +A +LG+S++a+ 
  gi|313127277|ref|YP_004037547.1| 31 QREVADALGISQSAVS 46
                                      599***********95 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027       0.2      26      48 ..      28      50 ..      23      50 .. 0.91
   2 ?   -2.0   0.2       4.1   3.1e+03      43      54 .]     136     147 ..     132     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                      ---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksrls 48
                                      g++++E+A  lgis ++V ++ +
  gi|313127277|ref|YP_004037547.1| 28 GFTQREVADALGISQSAVSKYAH 50
                                      89****************98865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHH CS
                      Sigma70_r4_2  43 VksrlsRArkkL 54 
                                       V+s ++R+++ L
  gi|313127277|ref|YP_004037547.1| 136 VRSSVRRGLRTL 147
                                       9999****9976 PP

>> DUF3486  Protein of unknown function (DUF3486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00013     0.098      12      89 ..      14      81 ..       9     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                           DUF3486 12 eevreeLdeaLrekgftqdeIyeelnallaerGeykiSkSalnryaqrleevaeklresreiaealveelgdeedddv 89
                                      +  r+ L+e+Lr++gftq    +e++   ++ G   iS Sa+ +ya    ++ e l e + + e++ + ++  +++d+
  gi|313127277|ref|YP_004037547.1| 14 PTFRSMLAEELRDRGFTQ----REVA---DALG---ISQSAVSKYAHGEVSRNETLLEDERVQELVERVADGLSTGDM 81
                                      567999***********9....4444...4557...*********998777777776666665555555555555555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.08        60      19      36 ..      30      47 ..      25      50 .. 0.87
   2 ?   -1.0   0.0       2.3   1.8e+03       6      21 ..     100     115 ..      98     124 .. 0.80
   3 ?    5.4   0.0     0.024        18      12      42 ..     270     300 ..     268     302 .] 0.93

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.08
                                      EHHHHHHHHTS-HHHHHH CS
                              MarR 19 svseLakklgvskstvtr 36
                                      ++ e a++lg+s+s+v++
  gi|313127277|ref|YP_004037547.1| 30 TQREVADALGISQSAVSK 47
                                      78899***********97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                                       HHHHHHHHHSTTEEHH CS
                              MarR   6 fviLrilyeqgplsvs 21 
                                        ++L++l+eq+ + +s
  gi|313127277|ref|YP_004037547.1| 100 GDLLATLHEQQMPELS 115
                                       579******9877766 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.024
                                       HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHH CS
                              MarR  12 lyeqgplsvseLakklgvskstvtrvldrLe 42 
                                       ly++g+  +  +   lg + +tv r+++ L 
  gi|313127277|ref|YP_004037547.1| 270 LYQSGAYGIEAITYVLGPDAPTVARAVRSLL 300
                                       99**************************997 PP

>> HNF-1_N  Hepatocyte nuclear factor 1 (HNF-1), N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00019      0.14     150     173 ..      25      48 ..       6      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                           HNF-1_N 150 qqhrIsQrevvdvTGlsQShlSqw 173
                                         +   Qrev+d+ G+sQS +S++
  gi|313127277|ref|YP_004037547.1|  25 RDRGFTQREVADALGISQSAVSKY 48 
                                       567789****************98 PP

>> Phage_CII  Bacteriophage CII protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00039      0.29      25      77 ..      30      75 ..      20      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
                                      HHHHHHHHHTSSTTTHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHHHHHHHH CS
                         Phage_CII 25 gqrkvaeaiGvdeskisrwktDwipkasvLlavlefGvaddelarlakkvadl 77
                                      +qr+va+a+G+ +s +s++    + +   Ll        d+ + +l+ +vad+
  gi|313127277|ref|YP_004037547.1| 30 TQREVADALGISQSAVSKYAHGEVSRNETLLE-------DERVQELVERVADG 75
                                      8*****************87655555544443.......55555555555555 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0014         1      10      30 ..      26      46 ..      20      51 .. 0.83
   2 ?   -2.3   0.0       6.8   5.1e+03      31      40 ..      92     100 ..      91     107 .. 0.77
   3 ?   -1.1   0.0         3   2.2e+03      37      47 ..     149     159 ..     137     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                            HTH_28 10 aaGhsvreaArelgisrrtvy 30
                                       +G ++re+A +lgis++ v+
  gi|313127277|ref|YP_004037547.1| 26 DRGFTQREVADALGISQSAVS 46
                                      3677**************997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.8
                            HTH_28  31 rWikryeegG 40 
                                       ++i+++ee G
  gi|313127277|ref|YP_004037547.1|  92 VLIRQFEE-G 100
                                       689****9.5 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3
                            HTH_28  37 eegGiagLvpr 47 
                                       ++ G+agL p 
  gi|313127277|ref|YP_004037547.1| 149 NASGFAGLIPN 159
                                       6789****986 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0     0.001      0.77      10      46 ..      23      59 ..      18      63 .. 0.92
   2 ?   -2.2   0.0       5.8   4.3e+03       8      31 ..     137     160 ..     133     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.001
                            HTH_35 10 aLrkrgttLaalsreaglssstlsnaltrpwpkgEal 46
                                      +Lr rg t ++++ ++g+s+s++s+  +  + ++E+l
  gi|313127277|ref|YP_004037547.1| 23 ELRDRGFTQREVADALGISQSAVSKYAHGEVSRNETL 59
                                      79*************************9999999987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.8
                            HTH_35   8 iAaLrkrgttLaalsreaglssst 31 
                                        +++r+   tL++ s  agl ++ 
  gi|313127277|ref|YP_004037547.1| 137 RSSVRRGLRTLTNASGFAGLIPNV 160
                                       567777788999999999997765 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00043      0.32      21      43 ..      26      48 ..      25      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                            HTH_10 21 PRrvtlkeLAkelGIskstlseh 43
                                      +R  t +e+A++lGIs+s++s++
  gi|313127277|ref|YP_004037547.1| 26 DRGFTQREVADALGISQSAVSKY 48
                                      588899*************9986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0031       2.3      16      39 ..      26      49 ..      19      51 .. 0.84
   2 ?    3.1   0.2      0.11        81      32      44 ..     137     149 ..     132     151 .. 0.92
   3 ?   -2.0   0.0       4.2   3.2e+03      28      43 ..     285     300 ..     272     302 .] 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0031
                                      BSS-BHHHHHHHHTS-HHHHHHHH CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlL 39
                                      +++ t +e+A+++g++ S+v+ + 
  gi|313127277|ref|YP_004037547.1| 26 DRGFTQREVADALGISQSAVSKYA 49
                                      4567899*************9876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHH CS
                          HTH_IclR  32 kStvhRlLqtLve 44 
                                       +S+v+R L+tL++
  gi|313127277|ref|YP_004037547.1| 137 RSSVRRGLRTLTN 149
                                       8**********86 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.2
                                       HTS-HHHHHHHHHHHH CS
                          HTH_IclR  28 tglpkStvhRlLqtLv 43 
                                       +g   +tv R +++L 
  gi|313127277|ref|YP_004037547.1| 285 LGPDAPTVARAVRSLL 300
                                       5667789999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2197.87
//
Query:       gi|313127278|ref|YP_004037548.1|  [L=207]
Description: dCTP deaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-16   60.6   0.0    1.3e-11   43.9   0.0    2.1  2  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)
    9.2e-15   54.5   0.0    1.3e-14   54.0   0.0    1.2  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   9.3e-07    0.0084       4      42 ..       2      41 ..       1      52 [. 0.69
   2 !   43.9   0.0   1.5e-15   1.3e-11     223     353 ..      53     178 ..      41     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.3e-07
                               DCD  4 ilpdqeiealieegai.kaeepleeeqiqPaslDLrLgkk 42
                                      il+d +i + +++g +     +  + q+qPas+DLrLg++
  gi|313127278|ref|YP_004037548.1|  2 ILSDADILERLSDGDLvVEPLDDIDMQVQPASIDLRLGEE 41
                                      56666665544444440444445569************86 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 1.5e-15
                               DCD 223 ldkigalevedfweplkakegeklildpdeFYilasreavkvppdlaaemvpfdalvGefRv..h.YaGffDpGFGl 296
                                       ++  ++ ev+++  + + +eg+++il p++F + +++e+v++ppdl a + +  +++G + +  h  aG +DpG+  
  gi|313127278|ref|YP_004037548.1|  53 IHPNREDEVSKYVTETYVEEGDEFILHPGDFVLGTTKERVEIPPDLLATV-EGRSSLGRLAIviHaTAGIVDPGYHG 128
                                       5556778899************************************9975.56778888764226369******953 PP

                               DCD 297 aeaggegsravLevRsr.evPFiledgqivgrlvyermaekpealYGeelgsnYqgqg 353
                                               +  Le+     +P  l+ g  v++lv+ +m++ +++ YG e gs+Yq q+
  gi|313127278|ref|YP_004037548.1| 129 --------QITLELSNLgTAPVALSPGMRVSQLVFTEMKNPADRPYGVERGSKYQDQK 178
                                       ........456888765279************************************96 PP

>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   1.5e-18   1.3e-14      21     107 ..      73     161 ..      70     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.5e-18
                                       SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEE..EEEETTBTSEEEEEEEE-SSS-EEE-TT-E CS
                           dUTPase  21 akdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvp..gvidsdyrGevkvvlfnltkkdvkikkgdR 95 
                                        +++++ pg+ vl +t+  +++p +l a++ +RS+l ++ ++++   g++d  y G++ + l nl+ ++v +  g R
  gi|313127278|ref|YP_004037548.1|  73 GDEFILHPGDFVLGTTKERVEIPPDLLATVEGRSSLGRLAIVIHAtaGIVDPGYHGQITLELSNLGTAPVALSPGMR 149
                                       6899****************************************99******************************* PP

                                       EEEEEEEEBECG CS
                           dUTPase  96 iAqLifarilta 107
                                       + qL+f++++++
  gi|313127278|ref|YP_004037548.1| 150 VSQLVFTEMKNP 161
                                       *******99983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1317.26
//
Query:       gi|313127279|ref|YP_004037549.1|  [L=112]
Description: peptidyl-tRNA hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-41  139.8   0.0    5.1e-41  139.6   0.0    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2
  ------ inclusion threshold ------
      0.027   14.4   0.1       0.68    9.8   0.1    2.1  1  DUF2000   Protein of unknown function (DUF2000)
      0.058   12.1   0.0      0.071   11.8   0.0    1.0  1  WEMBL     Weak chloroplast movement under blue light


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   0.0   8.5e-45   5.1e-41       1     117 []       1     112 []       1     112 [] 0.97

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 8.5e-45
                                       EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-S CS
                              PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglp 77 
                                       +k+++v r DL+m++Gk+aaq+ahA++++++++ ++ ++    +eW+ +gqkk+vlk++ e++L +la++a+++glp
  gi|313127279|ref|YP_004037549.1|   1 MKQAIVARADLGMGRGKLAAQVAHASLSAYEDADRK-AK----NEWKGSGQKKVVLKANGEDKLFRLADEAERQGLP 72 
                                       69*******************************998.44....69******************************** PP

                                       EEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                              PTH2  78 aalirDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                       +a+irDag+tq+epgt+T+la+gP+ +++v+kvtg+L l+
  gi|313127279|ref|YP_004037549.1|  73 HAIIRDAGHTQLEPGTVTCLAVGPGRDDLVNKVTGDLSLY 112
                                       *************************************997 PP

>> DUF2000  Protein of unknown function (DUF2000)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00011      0.68      27      84 ..      18      77 ..       1     112 [] 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                                      HHHH-GGGB-S-EE-TTS-EE---..BSS-EEEEEE.-HHHHHHHHHHHHHT.T---EEEE CS
                           DUF2000 27 lgaaapelvgedyaDadgeahagi..selPvpvlka.ssekLrelrekaleregltvvdFt 84
                                      l+a++ ++   +y+Dad +a ++   s++  +vlka  ++kL +l ++a  + gl ++   
  gi|313127279|ref|YP_004037549.1| 18 LAAQVAHASLSAYEDADRKAKNEWkgSGQKKVVLKAnGEDKLFRLADEAERQ-GLPHAIIR 77
                                      55568888999999999988876533778889****6678999999997777.98887655 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.2e-05     0.071     440     491 ..      18      69 ..      13      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.2e-05
                             WEMBL 440 aseklAlaaikALqesessaeakeqedsersvtLsleeYeeLskraheaEel 491
                                        ++++A a+++A ++ +++a+++ +++ +++v+L+++  ++L + a eaE +
  gi|313127279|ref|YP_004037549.1|  18 LAAQVAHASLSAYEDADRKAKNEWKGSGQKKVVLKANGEDKLFRLADEAERQ 69 
                                       67899************99*******************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 776.45
//
Query:       gi|313127280|ref|YP_004037550.1|  [L=466]
Description: pas domain s-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-20   71.6   0.4    5.4e-09   36.3   0.1    2.7  2  PAS_9        PAS domain
    5.2e-17   61.9   1.1    1.5e-09   37.9   0.0    3.0  3  PAS          PAS fold
    1.6e-15   57.3   3.3    7.5e-10   39.0   0.1    2.8  3  PAS_4        PAS fold
    1.7e-15   57.5   0.0    4.7e-15   56.1   0.0    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.9e-13   49.9   0.1    3.1e-08   33.8   0.1    3.0  2  PAS_3        PAS fold
    2.2e-12   46.8   2.3    4.9e-12   45.7   0.3    2.6  3  HisKA        His Kinase A (phospho-acceptor) domain
    1.7e-10   40.7   0.7    2.4e-05   24.2   0.1    3.3  3  PAS_8        PAS domain
    7.7e-05   22.8   1.3       0.12   12.5   0.0    2.9  3  PAS_7        PAS fold
    0.00014   21.8   0.0    0.00039   20.4   0.0    1.7  1  HATPase_c_2  Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.8e-11   5.6e-08       3     104 .]      23     125 ..      21     125 .. 0.89
   2 !   36.3   0.1   2.7e-12   5.4e-09       2     104 .]     145     250 ..     144     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.8e-11
                             PAS_9   3 gili.dnpdgrilyaNeaalrllGyspeevlgksitdlf.....vtdpeanerlraaleqgrkkerevevvlirkng 73 
                                        i + d + g+ l ++ a+++++Gy+pee+    i+        +t+++a+e +++a e+g+    ++e    r +g
  gi|313127280|ref|YP_004037550.1|  23 VITVrDAETGETLAVSGAVEEMYGYTPEEFSELTIEAYSanhveYTEERAQELIADARERGE---ASFEWKAKRADG 96 
                                       55667889999******************999998888898888888888888888888887...************ PP

                             PAS_9  74 etfwvlltaspvkdddgelvgiivilrDite 104
                                        +fw+++++s    +++++     ++rDit+
  gi|313127280|ref|YP_004037550.1|  97 AEFWTEISISKTELEERTVLV--NVVRDITD 125
                                       ************999888877..******96 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 2.7e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetf 76 
                                       d+++ ++++ ri y+N+a   l+Gys+ee++ +++++l ++ +  + +l+a+    ++     + e +++r++g++ 
  gi|313127280|ref|YP_004037550.1| 145 DPVFTIDENDRIDYVNDATVGLTGYSREELVETDFEELSADISLVQGDLDAIHGLQDTeeDSIRLEGTITRPDGTER 221
                                       7889888********************************4444444444444444444777789************* PP

                             PAS_9  77 wvlltaspv.kdddgelvgiivilrDite 104
                                        ++ +++ +   ++g++ g+++++rDit+
  gi|313127280|ref|YP_004037550.1| 222 TIETNLALLpPTEEGTFGGAVGVSRDITQ 250
                                       *********5555***************7 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1     1e-07    0.0002       4     113 .]      14     123 ..      11     123 .. 0.78
   2 !   37.9   0.0   7.3e-13   1.5e-09       2      94 ..     135     228 ..     134     248 .. 0.90
   3 ?   -1.0   0.0      0.84   1.7e+03      27      62 ..     274     308 ..     271     319 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1e-07
                                       HHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   4 raileslpdpifvvD.edgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                        ++le+  d i v+D e g+ l v+ a ee+ G+++ee +  ++  +   ++ +++ e+ ++l+++++e+      +
  gi|313127280|ref|YP_004037550.1|  14 LRVLENVNDVITVRDaETGETLAVSGAVEEMYGYTPEEFSELTIEAYS-ANHVEYTEERAQELIADARERGEASFEW 89 
                                       589***********************************9998887555.4444456666666666666666666666 PP

                                       EC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 kl..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       k    dg +++ e+  s++  ++ +   ++ v+rdi
  gi|313127280|ref|YP_004037550.1|  90 KAkrADGAEFWTEISISKTELEERT--VLVNVVRDI 123
                                       66666************99988654..677777776 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 7.3e-13
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesragei 77 
                                       +++++++ + dp+f +De+ ri yvN+a+  l+G+sree++   + +l    +    + ++++ l  + e+s   e 
  gi|313127280|ref|YP_004037550.1| 135 RFERLVSLISDPVFTIDENDRIDYVNDATVGLTGYSREELVETDFEELSADISLVqGDLDAIHGLQDTEEDSIRLEG 211
                                       799******************************************988876655599******************** PP

                                       EEECTTSSEEEEEEEEE CS
                               PAS  78 sfklrdgrpihlevras 94 
                                       +++++dg+++ +e++ +
  gi|313127280|ref|YP_004037550.1| 212 TITRPDGTERTIETNLA 228
                                       ************99875 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.84
                                       CHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHH CS
                               PAS  27 NaaaeellGlsreevlgkslldliheeddaelaell 62 
                                       Naa+++++ l++ e + + ++d + + +++ +ae++
  gi|313127280|ref|YP_004037550.1| 274 NAAMAQITLLREIEGCDSEYVDTLENLTNR-MAEII 308
                                       999999999999999999999988777665.55555 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3     1e-06    0.0021       1     110 []      17     128 ..      17     128 .. 0.88
   2 !   39.0   0.1   3.8e-13   7.5e-10       4     110 .]     143     253 ..     140     253 .. 0.94
   3 ?   -4.0   0.0       8.7   1.7e+04       2      12 ..     387     397 ..     387     398 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1e-06
                             PAS_4   1 ldslpdalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpee...daarleralrrvlegeepiefleell 73 
                                       l++++d+++v   + g  l+++ a +e++g++pee+   t + +   +     +r ++ ++ + e +e+ +++   +
  gi|313127280|ref|YP_004037550.1|  17 LENVNDVITVRdAETGETLAVSGAVEEMYGYTPEEFSELTIEAYSANHveyTEERAQELIADARERGEASFEWKAKR 93 
                                       689999999994457999************************655555566************************** PP

                             PAS_4  74 lpgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        +g+e + e++++  + e+ +   ++ ++rDiT+r++
  gi|313127280|ref|YP_004037550.1|  94 ADGAEFWTEISISKTELEERT--VLVNVVRDITDRKE 128
                                       ************887555555..899********985 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 3.8e-13
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee..daarleralrrvlegeepiefleelll.pge 77 
                                       ++d+++ +d++ r+ y+N a   l g+++eel+   ++el  +   ++++l+++     ++e++i+ + + ++ +g 
  gi|313127280|ref|YP_004037550.1| 143 ISDPVFTIDENDRIDYVNDATVGLTGYSREELVETDFEELSADIslVQGDLDAIHGLQDTEEDSIRLEGTITRpDGT 219
                                       79*************************************88888*99999*9999999999*****9999999**** PP

                             PAS_4  78 erhyelrl..lPlrdesGevigvlvisrDiTerrr 110
                                       er++e++l  lP   e+G+  g++++srDiT+r+r
  gi|313127280|ref|YP_004037550.1| 220 ERTIETNLalLPP-TEEGTFGGAVGVSRDITQRKR 253
                                       ********98888.79*****************97 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 8.7
                             PAS_4   2 dslpdalavld 12 
                                       ++lpd++a++d
  gi|313127280|ref|YP_004037550.1| 387 ERLPDGFAICD 397
                                       579******99 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   2.4e-18   4.7e-15       1     106 [.     358     454 ..     358     459 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 2.4e-18
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSH CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGl 76 
                                       gd +r+r+++ nl +Nav++   +++i+v+i++      + + D+G+Gip+++++++fe  +s+       + gtG+
  gi|313127280|ref|YP_004037550.1| 358 GDRQRVRRLLENLFSNAVRH--GGDDISVRIERL--PDGFAICDDGPGIPPDERNEVFEyGYST------ATDGTGF 424
                                       7999***************9..79********52..467999*****************99999......789**** PP

                                       HHHHHHHHHHHTTTEEEEEEETTTEEEEEE CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftf 106
                                       Gl iv+++++ ++ +i + +++ +G +f +
  gi|313127280|ref|YP_004037550.1| 425 GLNIVEEIADAHDWNIVIAESDSGGARFEI 454
                                       ******************999999999986 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   1.6e-11   3.1e-08       3      75 ..      36     108 ..      34     140 .. 0.88
   2 !   12.9   0.0     5e-05       0.1       3      87 ..     158     243 ..     156     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.6e-11
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvi 75 
                                        vs++vee++Gy+pee+ +   + +++ h e   er++e +++a ++ge  ++e++ +r+dG  +w e +++ +
  gi|313127280|ref|YP_004037550.1|  36 AVSGAVEEMYGYTPEEFSELTIEAYSANHVEYtEERAQELIADARERGE-ASFEWKAKRADGAEFWTEISISKT 108
                                       699*****************************77777777777777777.89***************9988765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5e-05
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkge.pyegeyRirrkdGeyrwveararvi.r 76 
                                       yv+++   ++Gys+eel ++  ++ +l       +   +a++ + ++ e ++  e  i r+dG+ r +e+    +  
  gi|313127280|ref|YP_004037550.1| 158 YVNDATVGLTGYSREELVET--DFEELSADISlVQGDLDAIHGLQDTEEdSIRLEGTITRPDGTERTIETNLALLpP 232
                                       99******************..888876544434444566666667777799*****************99988877 PP

                             PAS_3  77 dengkpvrvig 87 
                                        e+g     +g
  gi|313127280|ref|YP_004037550.1| 233 TEEGTFGGAVG 243
                                       77777766666 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.3   8.5e+03      48      58 ..      69      79 ..      53      84 .. 0.60
   2 !   45.7   0.3   2.5e-15   4.9e-12       2      65 ..     258     318 ..     257     319 .. 0.93
   3 ?   -1.3   0.0       1.2   2.3e+03      44      58 ..     356     370 ..     347     376 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.3
                                      HHHHHHHHHHH CS
                             HisKA 48 arrldhlvedl 58
                                      ++r ++l+ d 
  gi|313127280|ref|YP_004037550.1| 69 EERAQELIADA 79
                                      34555555544 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 2.5e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l+rf++ ++H+Lr+PL+a ++ + +L++         ey++t+e+ ++r+ ++++d+L+l+r++
  gi|313127280|ref|YP_004037550.1| 258 LERFASVLSHDLRNPLNAAMAQITLLRE---IEGCDSEYVDTLENLTNRMAEIIDDVLTLTREG 318
                                       78************************99...4588999**********************9975 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHH CS
                             HisKA  44 iesearrldhlvedl 58 
                                       +e   +r+++l+e+l
  gi|313127280|ref|YP_004037550.1| 356 VEGDRQRVRRLLENL 370
                                       555567888888887 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   4.5e-05      0.09       5      62 ..      15      75 ..      11      81 .. 0.80
   2 !   24.2   0.1   1.2e-08   2.4e-05       2      52 ..     135     182 ..     134     201 .. 0.80
   3 ?   -1.1   0.0         1     2e+03       8      20 ..     387     399 ..     384     407 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-05
                             PAS_8  5 alfesspdgiavvd..lgdrivdvNqaalellGys.adlkgellg.qllpvlrplledaeql 62
                                       ++e+++d i v d  +g+  + v  a +e++Gy+ +++++ ++  +  +++++ +e+a++l
  gi|313127280|ref|YP_004037550.1| 15 RVLENVNDVITVRDaeTGE-TLAVSGAVEEMYGYTpEEFSELTIEaYSANHVEYTEERAQEL 75
                                      699*********9976666.***************999999888767777776666666665 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.2e-08
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvl 52 
                                       r++ l+  ++d+++ +d++dri +vN+a+  l+Gys ++l + ++     +l
  gi|313127280|ref|YP_004037550.1| 135 RFERLVSLISDPVFTIDENDRIDYVNDATVGLTGYSrEELVETDFE----EL 182
                                       99***************6666*************996666555553....33 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                             PAS_8   8 esspdgiavvdlg 20 
                                       e +pdg a++d+g
  gi|313127280|ref|YP_004037550.1| 387 ERLPDGFAICDDG 399
                                       668******9954 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.2    0.0013       2.7       1     114 [.      17     130 ..      17     131 .. 0.62
   2 !   12.5   0.0   6.2e-05      0.12       4     115 .]     143     256 ..     140     256 .. 0.83
   3 ?   -2.0   0.0         2   3.9e+03      75      98 ..     369     392 ..     347     395 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                             PAS_7   1 lenmsqGisvfDad.lrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkph 76 
                                       len+++ i+v Da+ ++ +a+   + e++++++e +    +  ++ +y a++ e++++++++ ++       ++ + 
  gi|313127280|ref|YP_004037550.1|  17 LENVNDVITVRDAEtGETLAVSGAVEEMYGYTPEEF----SELTIEAYSANHVEYTEERAQELIADAR----ERGEA 85 
                                       677777777777762466777777888888877766....2334556778888888555555555555....54444 PP

                             PAS_7  77 sfer..erpdg....rvievrgnplpdgG.fVttytDiTerrrae 114
                                       sfe   +r+dg    + i++ +++l+++  +V +  DiT+r+++e
  gi|313127280|ref|YP_004037550.1|  86 SFEWkaKRADGaefwTEISISKTELEERTvLVNVVRDITDRKEHE 130
                                       44431134444223345777788887765278999*******987 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.2e-05
                             PAS_7   4 msqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellryn.aergefg..agdveaeverrlaaaragkphs 77 
                                       +s+ +  +D+++r+  +N+  + l ++++e + v + +eel + +   +g+++  +g ++ e + +  + +  +p+ 
  gi|313127280|ref|YP_004037550.1| 143 ISDPVFTIDENDRIDYVNDATVGLTGYSREEL-VETDFEELSADIsLVQGDLDaiHGLQDTEEDSIRLEGTITRPDG 218
                                       56667889**********************99.99*****9765548999999765555555445444566788999 PP

                             PAS_7  78 fererpdgrvievrgnplpdgGfVttytDiTerrraee 115
                                       +er+ +++  +   +++   gG V +  DiT+r+r ee
  gi|313127280|ref|YP_004037550.1| 219 TERTIETNLALLPPTEEGTFGGAVGVSRDITQRKRREE 256
                                       99999999999999999999**************9986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2
                             PAS_7  75 phsfererpdgrvievrgnplpdg 98 
                                       + + +  r+ g  i+vr ++lpdg
  gi|313127280|ref|YP_004037550.1| 369 NLFSNAVRHGGDDISVRIERLPDG 392
                                       445566778888999999999997 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     2e-07   0.00039      26     114 ..     357     438 ..     340     452 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2e-07
                       HATPase_c_2  26 eelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGl 102
                                       e +++++r  +e +++Nav+h+ +     +++vr+e+ ++ + +   D+Gpg +p ++++  e ++++  +  G+Gl
  gi|313127280|ref|YP_004037550.1| 357 EGDRQRVRRLLENLFSNAVRHGGD-----DISVRIERLPDGFAI--CDDGPGIPPDERNEVFEYGYSTATDGTGFGL 426
                                       66778888899999********95.....677888899998875..9*************999999*********** PP

                       HATPase_c_2 103 alikglvDevey 114
                                        ++++++D  ++
  gi|313127280|ref|YP_004037550.1| 427 NIVEEIADAHDW 438
                                       ********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3296.44
//
Query:       gi|313127281|ref|YP_004037551.1|  [L=462]
Description: hypothetical protein Hbor_25520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-163  544.8   0.0   1.4e-163  544.6   0.0    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.6   0.0  7.5e-168  1.4e-163       2     416 .]      11     454 ..      10     454 .. 0.97

  Alignments for each domain:
  == domain 1  score: 544.6 bits;  conditional E-value: 7.5e-168
                              TruD   2 lgielyvtdtegigGrlrespeDFiVeEieefsge.eeadegey..lvlrvekrnwdtldlvrelaralgisrkrvg 75 
                                       +gie+yv+d+eg+gGrlr+ peDF+V+E+e++++  +++d+g+y  l+lrv++r+wdt+d++r+l++algisr+rv+
  gi|313127281|ref|YP_004037551.1|  11 VGIEHYVSDAEGTGGRLRDAPEDFRVREVEAMDAVdVDEDPGDYpsLLLRVTLREWDTNDFARRLSDALGISRERVS 87 
                                       8******************************9665599*************************************** PP

                              TruD  76 faGtKDkrAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeile 152
                                       +aGtKDk+AvTtQl+s+r+++p+e++  +i+++++ev+gr +r+l +GdLaGN+F++rvrd+    +a+++a+ +++
  gi|313127281|ref|YP_004037551.1|  88 WAGTKDKYAVTTQLFSVRDASPDEIP--AINNADIEVLGRIGRDLGFGDLAGNDFDVRVRDA----DASANAATVTA 158
                                       **************************..899******************************4....45679999999 PP

                              TruD 153 eleekg..................gvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtrear 211
                                       +l+++                   +vPNyfG+QRFGsrrpvth+vG+++v+g++ eAv +yvg+p+++e++ t++ar
  gi|313127281|ref|YP_004037551.1| 159 QLQAFLtdedavdgaategetaavAVPNYFGHQRFGSRRPVTHEVGLHVVRGEWCEAVLSYVGNPASAEPDGTQAAR 235
                                       9999888999*************9***************************************************** PP

                              TruD 212 eav.....aetgdleealeelpkslryErallkrLae....kpkdykkAlealpknLqrlFvhAyqSylFNrvlseR 279
                                       ++v     +++ d+++ale++p++lryEr++l+rLae    + +d+++Alea+p+nLqrlFv+A+qSy+FNr+lseR
  gi|313127281|ref|YP_004037551.1| 236 RFVdeqaaSDDPDWHAALETMPNRLRYERSMLHRLAEdgdeSAEDWRHALEAVPRNLQRLFVNAAQSYVFNRILSER 312
                                       ***77777779**************************99989999******************************** PP

                              TruD 280 lerglpldepveGDvvifaeer......lpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeie 350
                                       l+rglpl++p+eGDvv+fa+++      ++d+dr+q++t ++ve ++r++ergrafvtaplvGtetelaege+geie
  gi|313127281|ref|YP_004037551.1| 313 LDRGLPLTRPIEGDVVCFADRDvpdrlyRADPDRTQVATGRRVEVMSRHCERGRAFVTAPLVGTETELAEGEAGEIE 389
                                       *******************88899999999*********************************************** PP

                              TruD 351 revleeegleledFklpklpelsskGtrRaillrve.dlelsaeedeltleFsLpkGsYATvvlrEi 416
                                       r+vl+e +le++dF+lp+  e++s+GtrRa+llr++ +++++ + d+++l+FsLp+GsYAT++lrE+
  gi|313127281|ref|YP_004037551.1| 390 RAVLNELDLEPADFDLPG--EFDSTGTRRAVLLRTDvETTVDSDADTYELTFSLPSGSYATALLREY 454
                                       ******************..****************999999999*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2877.97
//
Query:       gi|313127282|ref|YP_004037552.1|  [L=439]
Description: hypothetical protein Hbor_25530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3278.77
//
Query:       gi|313127283|ref|YP_004037553.1|  [L=240]
Description: metal-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-38  130.8   0.1    3.9e-38  129.4   0.1    1.7  2  DUF2103        Predicted metal-binding protein (DUF2103)
  ------ inclusion threshold ------
       0.76    9.5   3.8        1.6    8.4   3.8    1.6  1  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> DUF2103  Predicted metal-binding protein (DUF2103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.43   3.9e+03       7      25 ..      49      67 ..      44      72 .. 0.66
   2 !  129.4   0.1   4.3e-42   3.9e-38       2      98 .]     135     231 ..     134     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.43
                           DUF2103  7 ggsHstiiggreGkkllek 25
                                      g++  t i++ eG  ++ +
  gi|313127283|ref|YP_004037553.1| 49 GKTTVTTIPESEGEAMVVE 67
                                      5555677777777776655 PP

  == domain 2  score: 129.4 bits;  conditional E-value: 4.3e-42
                           DUF2103   2 pkeklggsHstiiggreGkkllekiakhpevkkviPgvikakgsssggglrvkvtraderGnlrlllrdgssvQevf 78 
                                       p+ek+gg+Hst+ig+reG++++  +a+hp+vkk+iPg+i+a+g+ s++ lr+kvtrad +Gn+rlllrdgssvQe++
  gi|313127283|ref|YP_004037553.1| 135 PREKMGGTHSTLIGDREGRRAIGVVADHPHVKKIIPGPIDAGGMGSQKSLRAKVTRADANGNVRLLLRDGSSVQENR 211
                                       89*************************************************************************** PP

                           DUF2103  79 ivttakdreegeriaeeLne 98 
                                       ivtta+d+e+ge ++++Lne
  gi|313127283|ref|YP_004037553.1| 212 IVTTAMDTETGEFVRDDLNE 231
                                       ******************96 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.8   0.00018       1.6       6      29 ..       3      27 ..       3      29 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00018
                     zf-NADH-PPase  6 CgrCGaptepaeggwarvC..paCgl 29
                                      CgrCG+p e ++g++++ C  ++C++
  gi|313127283|ref|YP_004037553.1|  3 CGRCGTPLE-KPGDYCLTCstANCDT 27
                                      *******98.5888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1629.73
//
Query:       gi|313127284|ref|YP_004037554.1|  [L=93]
Description: 50S ribosomal protein L37ae [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-22   77.5   0.9    7.1e-22   77.3   0.9    1.1  1  Ribosomal_L37ae  Ribosomal L37ae protein family


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.9     4e-26   7.1e-22       2      83 ..       6      83 ..       5      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 4e-26
                                      XXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH-X CS
                   Ribosomal_L37ae  2 tkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksai 80
                                       +k+g+aG++g+rYG+ +r+rvk+ie+++++    ++++ ++v R ++giw  +++g++++Gg+y pet+ +k v+++i
  gi|313127284|ref|YP_004037554.1|  6 ARKTGSAGRFGARYGRVARRRVKEIEADMRD----AKVDGDSVTRIGTGIWMNEETGEKFTGGTYRPETPGGKQVQRSI 80
                                      689****************************....599***************************************** PP

                                      XXX CS
                   Ribosomal_L37ae 81 rrl 83
                                      r +
  gi|313127284|ref|YP_004037554.1| 81 RAA 83
                                      975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 725.38
//
Query:       gi|313127285|ref|YP_004037555.1|  [L=44]
Description: DNA-directed RNA polymerase subunit p [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-10   40.4   6.8      2e-10   40.1   6.8    1.1  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
    2.1e-05   23.8   0.2     0.0016   17.8   0.0    2.1  2  zf-ribbon_3      zinc-ribbon domain
    0.00059   19.4   1.5       0.18   11.4   0.4    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
    0.00075   19.5   0.3    0.00075   19.5   0.3    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0018   17.9   1.0       0.03   14.0   2.1    1.9  2  A2L_zn_ribbon    A2L zinc ribbon domain
     0.0034   17.4   0.5     0.0061   16.6   0.5    1.4  1  zf-CHCC          Zinc-finger domain
      0.006   16.5   4.9        0.1   12.6   0.2    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0077   16.2   0.7      0.015   15.3   0.7    1.5  1  DZR              Double zinc ribbon
     0.0077   15.9   0.4       0.37   10.5   0.1    2.0  2  YacG             DNA gyrase inhibitor YacG
     0.0089   15.7   2.3       0.17   11.6   0.3    2.2  2  zinc_ribbon_2    zinc-ribbon domain
  ------ inclusion threshold ------
      0.017   15.1   0.3       0.02   14.8   0.3    1.2  1  zinc-ribbons_6   zinc-ribbons
       0.03   14.3   0.3       0.03   14.3   0.3    1.1  1  RNHCP            RNHCP domain
       0.03   13.9   1.9        1.4    8.5   0.2    2.1  2  Sgf11            Sgf11 (transcriptional regulation protein)
      0.035   14.0   0.8       0.13   12.1   0.1    1.9  2  Cys_rich_CPXG    Cysteine-rich CPXCG
      0.039   13.9   0.1      0.046   13.7   0.1    1.2  1  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
      0.041   14.0   3.8      0.081   13.1   3.8    1.5  1  Zn-ribbon_8      Zinc ribbon domain
      0.057   13.3   2.1      0.091   12.7   2.1    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.061   13.7   0.9       0.32   11.4   0.1    1.9  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.063   12.8   3.9       0.16   11.5   4.1    1.5  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.088   12.7   0.3          4    7.4   0.0    2.0  2  DUF951           Bacterial protein of unknown function (DUF95
       0.16   12.3   1.1       0.59   10.5   0.1    1.9  2  DUF3268          zinc-finger-containing domain
        0.2   11.7   1.2       0.62   10.1   0.2    1.9  2  CpXC             CpXC protein
       0.35   10.8   5.5         13    5.8   5.5    2.1  1  zinc_ribbon_4    zinc-ribbon domain
        0.7   10.0   1.9       0.88    9.7   0.0    1.9  2  Thioredoxin_4    Thioredoxin


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   6.8   2.7e-13     2e-10       1      32 []       3      34 ..       3      34 .. 0.99

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.7e-13
                                      -B-SSS--B----SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevslkkgdpiRCkeCGhRilYKkR 32
                                      Y+C +C+ +v+l++   +RC +CGhR+l K+R
  gi|313127285|ref|YP_004037555.1|  3 YKCSRCKRDVELDEYGGVRCPYCGHRVLLKER 34
                                      9******************************9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.027        20       3      10 ..       3      10 ..       1      16 [. 0.78
   2 !   17.8   0.0   2.1e-06    0.0016       3      17 ..      20      36 ..      18      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.027
                       zf-ribbon_3  3 vrCPnCGa 10
                                      ++C++C+ 
  gi|313127285|ref|YP_004037555.1|  3 YKCSRCKR 10
                                      68****85 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.1e-06
                       zf-ribbon_3  3 vrCPnCGa.p.lssddn 17
                                      vrCP+CG+ + l+++++
  gi|313127285|ref|YP_004037555.1| 20 VRCPYCGHrVlLKERAP 36
                                      89*******98888875 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.4   0.00024      0.18       2      16 ..       2      16 ..       1      18 [. 0.87
   2 !    7.6   0.0    0.0037       2.7       3      17 ..      20      34 ..      18      35 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                            zf_UBZ  2 tylCerCgkeipese 16
                                      +y C+rC++ ++ +e
  gi|313127285|ref|YP_004037555.1|  2 SYKCSRCKRDVELDE 16
                                      69*******999887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0037
                            zf_UBZ  3 ylCerCgkeipesel 17
                                      + C+ Cg++++  e+
  gi|313127285|ref|YP_004037555.1| 20 VRCPYCGHRVLLKER 34
                                      67********98776 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3     1e-06   0.00075      70      95 ..       2      28 ..       1      43 [. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1e-06
                                      EEEETTTS-EEECHHH.HHS-TTTSSS CS
                              HypA 70 kvrCreCgkefeleek.alrCpkCgsa 95
                                      +++C++C++++el+e+  +rCp Cg++
  gi|313127285|ref|YP_004037555.1|  2 SYKCSRCKRDVELDEYgGVRCPYCGHR 28
                                      689*********9997789******86 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   2.1   4.1e-05      0.03       4      28 ..       3      26 ..       2      27 .. 0.96
   2 !    7.9   0.0    0.0033       2.5       6      19 ..      22      34 ..      19      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                     A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieCg 28
                                      ++Cs C+++++l  e g+  C+ Cg
  gi|313127285|ref|YP_004037555.1|  3 YKCSRCKRDVEL-DEYGGVRCPYCG 26
                                      89**********.***********9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0033
                     A2L_zn_ribbon  6 CsvCggngilnseq 19
                                      C +Cg+ ++l +e+
  gi|313127285|ref|YP_004037555.1| 22 CPYCGHRVLL-KER 34
                                      99*******9.886 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.5   8.2e-06    0.0061      21      36 ..      13      28 ..      12      28 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.2e-06
                                      E--TTSEEEETTTTEE CS
                           zf-CHCC 21 eldkkgpvdCgYCglr 36
                                      eld+ g v+C+YCg r
  gi|313127285|ref|YP_004037555.1| 13 ELDEYGGVRCPYCGHR 28
                                      799***********87 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.9     0.013       9.5      38      45 ..       3      10 ..       1      11 [. 0.87
   2 !   12.6   0.2   0.00014       0.1      18      30 ..      19      31 ..      17      38 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                     Zn_Tnp_IS1595 38 fqCkeCrk 45
                                      ++C++C++
  gi|313127285|ref|YP_004037555.1|  3 YKCSRCKR 10
                                      9*****97 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkay 30
                                      g++CP+Cg+r + 
  gi|313127285|ref|YP_004037555.1| 19 GVRCPYCGHRVLL 31
                                      789*****99654 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.7     2e-05     0.015      15      41 ..       5      32 ..       1      37 [. 0.61

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                               DZR 15 CseCgtklkavaa..edrCpsCgekvdpe 41
                                      Cs+C+ +++   +    rCp Cg+ v ++
  gi|313127285|ref|YP_004037555.1|  5 CSRCKRDVEL-DEygGVRCPYCGHRVLLK 32
                                      7777777652.223567777777766555 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.053        40       2      14 ..       4      16 ..       3      18 .. 0.84
   2 !   10.5   0.1    0.0005      0.37       1      17 [.      20      36 ..      20      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.053
                              YacG  2 kCPtCkkevewse 14
                                      kC  Ck++ve +e
  gi|313127285|ref|YP_004037555.1|  4 KCSRCKRDVELDE 16
                                      7999*99999875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0005
                              YacG  1 vkCPtCkkevewseenp 17
                                      v+CP C+++v  +e+ p
  gi|313127285|ref|YP_004037555.1| 20 VRCPYCGHRVLLKERAP 36
                                      89********9998765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.055        41       1       9 [.       4      12 ..       4      17 .. 0.75
   2 !   11.6   0.3   0.00023      0.17      16      22 ..      22      28 ..      20      29 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.055
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +C++C + +
  gi|313127285|ref|YP_004037555.1|  4 KCSRCKRDV 12
                                      799997766 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00023
                     zinc_ribbon_2 16 CpyCGtp 22
                                      CpyCG+ 
  gi|313127285|ref|YP_004037555.1| 22 CPYCGHR 28
                                      9999996 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   2.7e-05      0.02       2      30 ..       4      33 ..       1      41 [. 0.61

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                                      --SSS-S--E.E-SSEEE-TTT--EEEEEE CS
                    zinc-ribbons_6  2 kCpeCqqele.krgeqyhCeaCqedlkkea 30
                                      kC +C++ +e  +   ++C  C +++  + 
  gi|313127285|ref|YP_004037555.1|  4 KCSRCKRDVElDEYGGVRCPYCGHRVLLKE 33
                                      466666666655556666666666665555 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   4.1e-05      0.03       3      31 ..       2      27 ..       1      40 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                             RNHCP  3 sftCeeCgkeveklaagsakrnHCpsCLl 31
                                      s++C++C+++ve +++g      Cp+C +
  gi|313127285|ref|YP_004037555.1|  2 SYKCSRCKRDVELDEYGG---VRCPYCGH 27
                                      689**************9...67999965 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0019       1.4       5      14 ..       3      12 ..       1      14 [. 0.87
   2 ?    5.3   0.1     0.019        14       5      13 ..      20      28 ..      18      30 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
                                      EE-TTTSSEE CS
                             Sgf11  5 vtCpnCgRqi 14
                                      ++C  C+R++
  gi|313127285|ref|YP_004037555.1|  3 YKCSRCKRDV 12
                                      79******99 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                                      EE-TTTSSE CS
                             Sgf11  5 vtCpnCgRq 13
                                      v+Cp+Cg  
  gi|313127285|ref|YP_004037555.1| 20 VRCPYCGHR 28
                                      79****965 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.79   5.9e+02       2      11 ..       4      13 ..       3      18 .. 0.60
   2 ?   12.1   0.1   0.00018      0.13       1      10 [.      20      29 ..      20      32 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.79
                     Cys_rich_CPXG  2 qCPyCgeeie 11
                                      +C  C   +e
  gi|313127285|ref|YP_004037555.1|  4 KCSRCKRDVE 13
                                      5666665554 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                     Cys_rich_CPXG  1 iqCPyCgeei 10
                                      + CPyCg+++
  gi|313127285|ref|YP_004037555.1| 20 VRCPYCGHRV 29
                                      68******86 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.2e-05     0.046      12      45 ..       4      33 ..       1      39 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.2e-05
                                      E-TTTTTTSEETTE......E-TTTTTSSEEE-H CS
                         Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCsGkglipTa 45
                                      kC  C++  + +     +++ CP C G+ +++ +
  gi|313127285|ref|YP_004037555.1|  4 KCSRCKRDVELDE---YGGVRCPYC-GHRVLLKE 33
                                      7888888666655...5********.77777755 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.8   0.00011     0.081       6      36 ..       3      29 ..       2      32 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsev 36
                                      Y+C +C+++ e l    +   + CP Cg++v
  gi|313127285|ref|YP_004037555.1|  3 YKCSRCKRDVE-LD---EYGGVRCPYCGHRV 29
                                      ***********.43...444788*****965 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.1   0.00012     0.091      28      55 ..       2      28 ..       1      30 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                    OrfB_Zn_ribbon 28 SktCseCgsknkealsgrtfkCpnCgfe 55
                                      S +Cs+C + ++  ++   ++Cp Cg++
  gi|313127285|ref|YP_004037555.1|  2 SYKCSRCKRDVEL-DEYGGVRCPYCGHR 28
                                      779****999999.9999*******986 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1       0.5   3.8e+02       4      19 ..       3      18 ..       2      21 .. 0.74
   2 ?   11.4   0.1   0.00043      0.32       6      23 ..      22      39 ..      20      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.5
                   Lar_restr_allev  4 kpCPfCggravlersq 19
                                      + C  C+ + +l + +
  gi|313127285|ref|YP_004037555.1|  3 YKCSRCKRDVELDEYG 18
                                      6788899888887765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00043
                   Lar_restr_allev  6 CPfCggravlersqrvva 23
                                      CP Cg+r  l+++  +v+
  gi|313127285|ref|YP_004037555.1| 22 CPYCGHRVLLKERAPTVK 39
                                      **********99977776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.1   0.00021      0.16       1      27 [.       3      27 ..       3      29 .. 0.87
   2 ?    8.4   0.3     0.002       1.5       2      10 ..      21      29 ..      20      35 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                                      EEETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGl 27
                                      ykC  C+  ++++D e g ++C+ CG 
  gi|313127285|ref|YP_004037555.1|  3 YKCSRCKR-DVELD-EYGGVRCPYCGH 27
                                      89*****6.58999.66*********5 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.002
                                      EETTTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn 10
                                      +CP+Cg++ 
  gi|313127285|ref|YP_004037555.1| 21 RCPYCGHRV 29
                                      7****9974 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.057        43      32      42 ..       4      14 ..       1      17 [. 0.84
   2 ?    7.4   0.0    0.0054         4      31      43 ..      20      32 ..      18      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.057
                            DUF951 32 kClgcgrevml 42
                                      kC++c+r v l
  gi|313127285|ref|YP_004037555.1|  4 KCSRCKRDVEL 14
                                      9******9976 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0054
                            DUF951 31 lkClgcgrevmlp 43
                                      ++C  cg+ v+l+
  gi|313127285|ref|YP_004037555.1| 20 VRCPYCGHRVLLK 32
                                      69*********86 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.57   4.2e+02      29      42 ..       1      14 [.       1      19 [. 0.78
   2 ?   10.5   0.1   0.00079      0.59       3      16 ..      20      33 ..      18      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.57
                           DUF3268 29 llylCpkCdayvgv 42
                                      + y C +C   v +
  gi|313127285|ref|YP_004037555.1|  1 MSYKCSRCKRDVEL 14
                                      67999999887765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00079
                           DUF3268  3 trCpyCGekvilvs 16
                                      +rCpyCG++v l++
  gi|313127285|ref|YP_004037555.1| 20 VRCPYCGHRVLLKE 33
                                      69*******99876 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.19   1.4e+02      37      50 ..       2      15 ..       1      17 [. 0.76
   2 ?   10.1   0.2   0.00082      0.62      32      50 ..      14      32 ..       6      40 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.19
                              CpXC 37 eatCpkCgatakle 50
                                      +++C +C ++++l+
  gi|313127285|ref|YP_004037555.1|  2 SYKCSRCKRDVELD 15
                                      67899998887765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00082
                              CpXC 32 dgslfeatCpkCgatakle 50
                                       +++  ++Cp+Cg+++ l+
  gi|313127285|ref|YP_004037555.1| 14 LDEYGGVRCPYCGHRVLLK 32
                                      56677789******99886 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.5     0.017        13       4      33 ..       4      27 ..       1      29 [. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                     zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCgh 33
                                       C +Ck   e+d+       + vrC+ Cgh
  gi|313127285|ref|YP_004037555.1|  4 KCSRCKRDVELDE------YGGVRCPYCGH 27
                                      6777776666666......4679******9 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.5       0.7   5.2e+02      21      30 ..       1      10 [.       1      13 [. 0.86
   2 ?    9.7   0.0    0.0012      0.88      15      29 ..      12      26 ..       9      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.7
                                      E-TT-HHHHH CS
                     Thioredoxin_4 21 edlrCphCak 30
                                      ++++C+ C++
  gi|313127285|ref|YP_004037555.1|  1 MSYKCSRCKR 10
                                      589*****86 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                                      EEEEEEE-TT-HHHH CS
                     Thioredoxin_4 15 vtvieyedlrCphCa 29
                                      v ++ey  +rCp+C 
  gi|313127285|ref|YP_004037555.1| 12 VELDEYGGVRCPYCG 26
                                      7899**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 320.68
//
Query:       gi|313127286|ref|YP_004037556.1|  [L=83]
Description: transcription factor pcc1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-10   38.6   1.3    9.6e-10   38.5   1.3    1.0  1  Pcc1      Transcription factor Pcc1
  ------ inclusion threshold ------
      0.036   13.8   0.0      0.036   13.8   0.0    1.1  1  GP40      Glycoprotein GP40 of Cryptosporidium


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   1.3   1.1e-13   9.6e-10       2      72 ..       7      78 ..       6      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.1e-13
                                      EEEEEE-SSHHHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1  2 ltisvpfpterlAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfleslglvlet 72
                                      +t+++++ +er A+++ ++++ ++    ++ + ++++ ++++++v+++A ++ +LR+ vn++ + + ++ ++
  gi|313127286|ref|YP_004037556.1|  7 ITLTFSYADERRARTVAESIRIEEGEIADDrSAVTVERDDQTVRVRVAAADLVALRAGVNTWTRFVAVAERI 78
                                      6999*******************88888888***********************************999876 PP

>> GP40  Glycoprotein GP40 of Cryptosporidium
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     4e-06     0.036      47      89 ..      33      75 ..      10      83 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-06
                              GP40 47 isgevtsvtfeksdntvkikvngqdfstlsansssptenggsa 89
                                      i+ + ++vt+e+ d+tv+++v   d+ +l a   + t     a
  gi|313127286|ref|YP_004037556.1| 33 IADDRSAVTVERDDQTVRVRVAAADLVALRAGVNTWTRFVAVA 75
                                      5566789**********************99888777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 572.56
//
Query:       gi|313127287|ref|YP_004037557.1|  [L=133]
Description: prefoldin subunit beta, archaeal [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-25   87.8  19.4    4.5e-25   87.7  19.4    1.0  1  Prefoldin_2      Prefoldin subunit
     0.0004   20.7   8.1    0.00048   20.4   8.1    1.1  1  DUF5082          Domain of unknown function (DUF5082)
    0.00046   19.6   8.0    0.00056   19.3   8.0    1.0  1  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
     0.0015   18.9   3.3     0.0015   18.9   3.3    2.4  2  CLZ              C-terminal leucine zipper domain of cyclic n
     0.0019   18.1  15.5      0.022   14.6  15.5    2.2  1  Prefoldin        Prefoldin subunit
     0.0054   16.3  11.3       0.16   11.5   0.6    2.0  2  PspA_IM30        PspA/IM30 family
     0.0087   15.5   0.2     0.0087   15.5   0.2    2.0  2  TraF_2           F plasmid transfer operon, TraF, protein
     0.0089   15.9   2.3     0.0089   15.9   2.3    2.3  2  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
  ------ inclusion threshold ------
      0.014   14.9  10.5      0.017   14.7  10.5    1.0  1  Leu_zip          Leucine zipper
      0.014   15.5   5.4       0.58   10.3   0.3    2.1  2  RasGAP_C         RasGAP C-terminus
      0.016   14.9   2.6      0.032   13.9   0.4    2.0  2  DUF4988          Domain of unknown function
      0.021   14.9   9.9      0.042   13.9   1.7    2.3  2  BRE1             BRE1 E3 ubiquitin ligase
      0.026   14.6   2.1      0.026   14.6   2.1    2.2  2  bZIP_1           bZIP transcription factor
      0.036   13.9   9.0      0.048   13.5   9.0    1.1  1  DUF724           Protein of unknown function (DUF724)
      0.036   14.3   1.0      0.036   14.3   1.0    2.7  2  XhlA             Haemolysin XhlA
      0.045   13.7   3.2      0.045   13.7   3.2    2.1  2  FlxA             FlxA-like protein
      0.056   13.9   4.6      0.056   13.9   4.6    2.2  2  ZapB             Cell division protein ZapB
      0.063   13.6  11.2      0.055   13.8   1.8    2.1  2  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.09   12.7  13.0       0.16   11.9   2.9    2.1  2  Sec34            Sec34-like family
        0.1   12.4  18.8       0.19   11.5  18.8    1.3  1  ERM              Ezrin/radixin/moesin family
        0.1   11.9  19.6       0.05   12.9   4.6    2.0  2  DUF3450          Protein of unknown function (DUF3450)
       0.11   12.3   8.5      0.088   12.6   1.2    2.0  2  Lectin_N         Hepatic lectin, N-terminal domain
       0.11   12.3  12.6      0.059   13.2   2.0    2.1  2  Sigma70_ner      Sigma-70, non-essential region
       0.14   12.0   2.9       0.24   11.2   0.3    2.3  2  DASH_Dam1        DASH complex subunit Dam1
       0.15   11.4   9.6        2.6    7.3   9.6    2.0  1  DUF4407          Domain of unknown function (DUF4407)
       0.15   11.9   8.5       0.26   11.1   1.4    2.1  2  Sec8_exocyst     Sec8 exocyst complex component specific doma
       0.17   12.5   4.4       0.25   12.0   4.4    1.2  1  Hemerythrin      Hemerythrin HHE cation binding domain
       0.19   12.0  10.0        2.5    8.4   1.4    2.7  2  WXG100           Proteins of 100 residues with WXG
       0.21   11.7  11.2      0.097   12.8   1.8    2.0  2  ADIP             Afadin- and alpha -actinin-Binding
       0.22   12.0  10.0       0.55   10.7   2.7    2.3  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.25   11.6   7.6       0.73   10.0   2.4    2.1  2  DUF2379          Protein of unknown function (DUF2379)
       0.27   10.9  15.6        1.6    8.4   3.6    2.1  2  Laminin_I        Laminin Domain I
       0.34   10.7  14.5        1.1    9.0  14.5    1.6  1  TACC_C           Transforming acidic coiled-coil-containing p
       0.49   10.7  11.0       0.43   10.9   1.1    2.3  2  DUF4164          Domain of unknown function (DUF4164)
        0.5   10.8  15.7        0.9    9.9   5.4    2.1  2  DUF4200          Domain of unknown function (DUF4200)
       0.61   10.1  13.6       0.15   12.1   0.6    2.3  2  Bap31_Bap29_C    Bap31/Bap29 cytoplasmic coiled-coil domain
       0.76   10.2  16.7      0.099   13.1   3.5    2.1  2  DUF4140          N-terminal domain of unknown function (DUF41
       0.88    9.6  20.3       0.53   10.4   3.5    2.1  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        1.1    7.4  15.0        1.8    6.7  15.0    1.3  1  EzrA             Septation ring formation regulator, EzrA
        1.1    9.3   9.5        2.9    7.9   9.5    1.7  1  Laminin_II       Laminin Domain II
        1.1    8.9   9.1        1.4    8.5   9.1    1.1  1  LUC7             LUC7 N_terminus
        1.2    9.2   7.8        4.8    7.2   7.9    1.8  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
        1.2    9.2  11.9       0.34   11.0   2.6    2.0  2  COG2             COG (conserved oligomeric Golgi) complex com
        1.3    7.9  18.0        1.8    7.4   5.4    1.9  1  Spc7             Spc7 kinetochore protein
        1.3    9.3  14.0       0.55   10.4   5.8    2.6  2  JIP_LZII         JNK-interacting protein  leucine zipper II
        1.3    8.5   5.9        1.8    8.1   5.9    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
        1.7    8.8  10.6         11    6.1  10.6    2.0  1  Nup54            Nucleoporin complex subunit 54
        1.9    8.6  10.8    1.2e+02    2.8  10.9    2.1  1  DUF1664          Protein of unknown function (DUF1664)
          2    8.6  20.6         46    4.2  20.6    2.0  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
          2    6.2   5.9        2.5    5.9   5.9    1.2  1  Prominin         Prominin
        2.1    8.8  11.3       0.26   11.7   4.4    2.4  2  FlaC_arch        Flagella accessory protein C (FlaC)
        2.3    8.7   9.5        5.2    7.6   0.5    2.3  2  DASH_Dad2        DASH complex subunit Dad2
        2.4    8.3  11.2        3.5    7.8   2.0    2.1  2  GCN5L1           GCN5-like protein 1 (GCN5L1)
        2.4    9.0  13.7        1.3    9.9   3.2    2.3  2  Rho_Binding      Rho Binding
        2.8    8.1  12.5        2.5    8.3   2.1    2.3  2  Cnn_1N           Centrosomin N-terminal motif 1
        2.9    8.0  22.1    2.4e+02    1.8   7.7    2.2  1  DHR10            Designed helical repeat protein 10 domain
        3.3    8.0   9.1         11    6.4   0.6    2.4  3  DUF948           Bacterial protein of unknown function (DUF94
        3.4    7.9  16.9        1.2    9.4   3.7    2.1  2  Spc24            Spc24 subunit of Ndc80
        3.5    6.9  19.0         18    4.6   6.0    2.0  1  GAS              Growth-arrest specific micro-tubule binding
        3.5    6.0   4.9        5.2    5.5   4.9    1.3  1  FUSC             Fusaric acid resistance protein family
        3.7    6.4  13.5          1    8.3   3.0    1.9  2  IFT57            Intra-flagellar transport protein 57
        3.8    8.1  25.8        1.1    9.8   8.6    2.1  2  APG6_N           Apg6 coiled-coil region
          4    7.9  13.4        1.8    9.0   3.9    2.2  2  Snapin_Pallidin  Snapin/Pallidin
        4.3    7.9  13.9         24    5.5  13.9    1.9  1  DUF16            Protein of unknown function DUF16
        4.5    7.2  10.0        1.2    9.1   2.0    2.1  2  DUF4446          Protein of unknown function (DUF4446)
        4.5    6.8  16.7         54    3.3  16.6    1.9  1  DUF4795          Domain of unknown function (DUF4795)
        4.7    7.5  14.1          2    8.7   2.0    2.2  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        5.1    7.3  10.1         25    5.0  10.2    1.8  1  Fib_alpha        Fibrinogen alpha/beta chain family
        5.7    6.4   8.9        1.4    8.5   0.7    2.1  2  SseC             Secretion system effector C (SseC) like fami
        7.4    7.4   9.4        3.9    8.3   2.0    2.1  2  Occludin_ELL     Occludin homology domain
        7.9    6.9  13.7        2.9    8.3   4.2    2.1  2  eIF3_N           eIF3 subunit 6 N terminal domain
        8.5    7.0  11.8        3.3    8.3   2.6    2.2  2  bZIP_Maf         bZIP Maf transcription factor
          9    6.1  14.0         20    5.0  14.0    1.5  1  PCRF             PCRF domain


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7  19.4   1.8e-27   4.5e-25       1     105 [.      14     118 ..      14     119 .. 0.99

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 1.8e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketleke 77 
                                       qe+++++q+lq++ q++a+q++q+e  l+e+e++l++le++dedt +y+ vG++lv++d e+++e+L ++ ++le +
  gi|313127287|ref|YP_004037557.1|  14 QEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDEDTVMYREVGELLVETDYETAHEDLTDKVDSLEVR 90 
                                       89*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelqkklqq 105
                                       +++l+kq+e++++++e l++elq++lq+
  gi|313127287|ref|YP_004037557.1|  91 VEQLKKQEERVQEQFESLQSELQQMLQG 118
                                       *************************996 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   8.1     2e-06   0.00048      22     121 ..      13     115 ..       5     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2e-06
                           DUF5082  22 leekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirs...nlessyqtyvdkldelidaiee 95 
                                        +ek+e+L+   ++ +++ ++ +q+++ l++ +   +++    e+++   +     +e++y+t +++l + +d++e 
  gi|313127287|ref|YP_004037557.1|  13 AQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDEDTVMYREVgelLVETDYETAHEDLTDKVDSLEV 89 
                                       79*******9999999999999999999999999999*****77777666666899********************* PP

                           DUF5082  96 EIerLenqiseaqgvldtlqsqlnsl 121
                                        +e+L++q +  q   ++lqs+l+++
  gi|313127287|ref|YP_004037557.1|  90 RVEQLKKQEERVQEQFESLQSELQQM 115
                                       ***********************987 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   8.0   2.3e-06   0.00056       2     113 ..       9     117 ..       8     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.3e-06
                    ALIX_LYPXL_bnd   2 lPpsllekaeevrsqgglqrlekllqdlqelkerneeiLdeieklLdeEe..sedeklrakygtrWtrqpSseltae 76 
                                       lPp+  ek ee++      +l++  q++   k+++e++L+e e+ Ld+ e  +ed  + ++ g+    ++ +++++ 
  gi|313127287|ref|YP_004037557.1|   9 LPPEAQEKLEELQ------DLQETAQKVAAQKQQAESTLTESETALDALEdiDEDTVMYREVGELLVETDYETAHED 79 
                                       7777778888877......9**************************8655459************************ PP

                    ALIX_LYPXL_bnd  77 lraelqkyreileeAsesDkivrqklqenkedlelL.s 113
                                       l +++++++  +e+ ++ ++ v++++++ +++l+ + +
  gi|313127287|ref|YP_004037557.1|  80 LTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMlQ 117
                                       *******************************9988745 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.0      0.39        95      15      44 ..      23      52 ..       6      54 .. 0.72
   2 !   18.9   3.3     6e-06    0.0015      22      64 ..      73     115 ..      65     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.39
                               CLZ 15 LDeeaakagaeqkeleekverLessLeaLq 44
                                      L e+a+k  a+++++e+ +++ e++L+aL+
  gi|313127287|ref|YP_004037557.1| 23 LQETAQKVAAQKQQAESTLTESETALDALE 52
                                      334445555788888888888888888875 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 6e-06
                               CLZ  22 agaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqR 64 
                                        ++ +++l +kv++Le ++e+L+++ +r+ +++es q++L+q 
  gi|313127287|ref|YP_004037557.1|  73 YETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       457899**********************************995 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6  15.5   9.1e-05     0.022      16     119 ..      14     117 ..      12     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.1e-05
                                       HHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  16 keaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiellkkkleelekq 92 
                                       +e++eel+++ et +++ ++++ +e +   ++++    e +d d v+     +  ve ++e A e l +k+++le  
  gi|313127287|ref|YP_004037557.1|  14 QEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDEDTVMYREVGELLVETDYETAHEDLTDKVDSLEVR 90 
                                       78999**************8888888887778888777778888888877779************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  93 lekleeeleklkdqittleanlaqlyq 119
                                       +e+l+++ e  ++q ++l+ +l+q  q
  gi|313127287|ref|YP_004037557.1|  91 VEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       ***********************9866 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   4.3    0.0029      0.72      86     125 ..      13      52 ..       5      58 .. 0.92
   2 !   11.5   0.6   0.00065      0.16     111     148 ..      74     109 ..      61     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0029
                         PspA_IM30  86 Arealaeikslekqaealetqlaqqrsaveqlrkqleale 125
                                       A+e l+e+++l+++a++  +q +q++s+  + +++l+ale
  gi|313127287|ref|YP_004037557.1|  13 AQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALE 52 
                                       88999*******************************9998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00065
                         PspA_IM30 111 rsaveqlrkqlealetkieelkakkellkarekaakaq 148
                                       ++a e+l+ +++ le+++e+lk++ e ++ + +  + q
  gi|313127287|ref|YP_004037557.1|  74 ETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFE--SLQ 109
                                       566777777777777777777777776654332..233 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.8      0.15        36      35      86 ..      12      62 ..       2      68 .. 0.64
   2 !   15.5   0.2   3.5e-05    0.0087      29      82 ..      60     119 ..      58     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.15
                            TraF_2 35 nlvDkiDdlsdildgleaavnaasadetqvdeaaddlnalLedlggdgylka 86
                                      ++ +k+++l+d  ++++++++++++ e  ++e  ++  ++Led+++d+ ++ 
  gi|313127287|ref|YP_004037557.1| 12 EAQEKLEELQDLQETAQKVAAQKQQAESTLTES-ETALDALEDIDEDTVMYR 62
                                      566788888888887777766644443224444.444457899999986655 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.5e-05
                            TraF_2  29 evgdvdnlvDkiD......dlsdildgleaavnaasadetqvdeaaddlnalLedlggdg 82 
                                       ++++v +l+ + D      dl+d++d+le  v++++++e  v+e+++ l+++L+++ + g
  gi|313127287|ref|YP_004037557.1|  60 MYREVGELLVETDyetaheDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQGG 119
                                       67777777777777788889999999999999999988766*************997766 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.3      0.81     2e+02      44      62 ..      18      36 ..      12      49 .. 0.82
   2 !   15.9   2.3   3.6e-05    0.0089      23      57 ..      82     116 ..      77     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.81
                            GIT_CC 44 delrlLQskvqkLqaeNaq 62
                                      +el+ LQ+  qk +a  +q
  gi|313127287|ref|YP_004037557.1| 18 EELQDLQETAQKVAAQKQQ 36
                                      7899999999998877665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.6e-05
                            GIT_CC  23 kalaaseakiqqLlkvNtslsdelrlLQskvqkLq 57 
                                        ++   e++++qL+k  +  +++ + LQs++q++ 
  gi|313127287|ref|YP_004037557.1|  82 DKVDSLEVRVEQLKKQEERVQEQFESLQSELQQML 116
                                       577889*************************9975 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7  10.5   6.9e-05     0.017     142     248 ..      14     117 ..       4     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.9e-05
                           Leu_zip 142 nekLkerlkelEkqatsaleeksklekalkelqkelgekkdekenskeiskleeklaelkldlektleektasaksl 218
                                        ekL+  l++l + a+++  +k++ e++l e +++l++ +d  e++    ++ e    +++d+e   e+ t++ +sl
  gi|313127287|ref|YP_004037557.1|  14 QEKLE-ELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDEDTVMYREVGE--LLVETDYETAHEDLTDKVDSL 87 
                                       56665.58899999**************************99996655555555..45778999999********** PP

                           Leu_zip 219 eedlastkhelLkvqeqLelaekeLekkfq 248
                                       e  + + k++  +vqeq e  ++eL++ +q
  gi|313127287|ref|YP_004037557.1|  88 EVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       *************************98776 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.8     0.015       3.6      46      81 ..      14      49 ..       8      63 .. 0.87
   2 ?   10.3   0.3    0.0023      0.58      46      85 ..      78     117 ..      71     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.015
                          RasGAP_C 46 ekrkeElesleetlktLseknnylesqlesYkayie 81
                                      ++  eEl+ l+et +++  ++++ es l + ++ ++
  gi|313127287|ref|YP_004037557.1| 14 QEKLEELQDLQETAQKVAAQKQQAESTLTESETALD 49
                                      67789********************99998887776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0023
                          RasGAP_C  46 ekrkeElesleetlktLseknnylesqlesYkayienvle 85 
                                       e  +  ++sle  +++L+++++ +++q es+++ ++++l+
  gi|313127287|ref|YP_004037557.1|  78 EDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       55666788999999***********************987 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       1.2   2.9e+02     133     154 ..      22      40 ..      14      62 .. 0.62
   2 ?   13.9   0.4   0.00013     0.032       1      31 [.      80     110 ..      80     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.2
                           DUF4988 133 kildekGepvkAvgdkssedsf 154
                                       ++ +e+ ++v+A+++++  +s 
  gi|313127287|ref|YP_004037557.1|  22 DL-QETAQKVAAQKQQA--EST 40 
                                       44.66677777777766..222 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00013
                           DUF4988   1 leddvndlkdrvaaleeqvkelndniealkk 31 
                                       l d+v++l+ rv+ l++q + +++++e+l+ 
  gi|313127287|ref|YP_004037557.1|  80 LTDKVDSLEVRVEQLKKQEERVQEQFESLQS 110
                                       78***************************86 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.7   0.00017     0.042      18      58 ..      12      52 ..       8      54 .. 0.94
   2 ?    5.5   1.4      0.07        17      54      80 ..      84     110 ..      69     118 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00017
                              BRE1 18 qlskkvkeltileekklrleaekakadqkyfaamrskdale 58
                                      ++++k++el++l+e  +++ a+k++a+    + + + dale
  gi|313127287|ref|YP_004037557.1| 12 EAQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALE 52
                                      689*******************************9999997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.07
                              BRE1  54 kdalenelkkLnkllsKsselieqLke 80 
                                        d+le  + +L+k+ ++ +e  e L+ 
  gi|313127287|ref|YP_004037557.1|  84 VDSLEVRVEQLKKQEERVQEQFESLQS 110
                                       333444444444444443333333332 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   2.3       2.1   5.1e+02      23      59 ..      15      51 ..      14      55 .. 0.78
   2 ?   14.6   2.1   0.00011     0.026      28      60 ..      84     116 ..      76     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2.1
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 23 RKqaeieeLerrvkaLekeNksLkseleelkkevekL 59
                                       K +e + L++ +++  ++ ++  s+l e +   + L
  gi|313127287|ref|YP_004037557.1| 15 EKLEELQDLQETAQKVAAQKQQAESTLTESETALDAL 51
                                      5889999999999999999888888888877666655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLk 60 
                                       ++ Le rv++L+k+ +  +++ e+l+ e ++++
  gi|313127287|ref|YP_004037557.1|  84 VDSLEVRVEQLKKQEERVQEQFESLQSELQQML 116
                                       566777777777777777777777777777776 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   9.0   0.00019     0.048      91     186 ..      14     110 ..       8     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00019
                            DUF724  91 qsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk..ekkeaadkeiarlks 165
                                       q++l++L  l++  +k++ +++++e+ ++e e++   l e+ide     +e+ + l+ +   + +e+   ++ +l++
  gi|313127287|ref|YP_004037557.1|  14 QEKLEELQDLQETAQKVAAQKQQAESTLTESETALDAL-EDIDEDTVMYREVGELLVETDyeTAHEDLTDKVDSLEV 89 
                                       78899999999999999999999999999999988854.4455444444444444433335578889999******* PP

                            DUF724 166 eaekleeeledveqeFeavas 186
                                        +e+l+++ e+v+++Fe+++s
  gi|313127287|ref|YP_004037557.1|  90 RVEQLKKQEERVQEQFESLQS 110
                                       *****************9987 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   3.6      0.61   1.5e+02       4      46 ..      15      56 ..      12      59 .. 0.56
   2 ?   14.3   1.0   0.00015     0.036      11      44 ..      82     115 ..      69     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.61
                              XhlA  4 erlerietkldnleervdkleekaaeaeekiknleedlkkles 46
                                      e+le+++  l +  ++v   ++ a+ ++++++ + + l+++ +
  gi|313127287|ref|YP_004037557.1| 15 EKLEELQD-LQETAQKVAAQKQQAESTLTESETALDALEDIDE 56
                                      44444432.2223335666677777777777777777777766 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00015
                              XhlA  11 tkldnleervdkleekaaeaeekiknleedlkkl 44 
                                        k+d+le rv++l++ +++++e+ ++l+ +l ++
  gi|313127287|ref|YP_004037557.1|  82 DKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       6899999999************999999999876 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   5.0      0.61   1.5e+02      45      71 ..      14      40 ..       2      57 .. 0.62
   2 ?   13.7   3.2   0.00018     0.045      27      68 ..      74     115 ..      68     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.61
                              FlxA 45 eekkkqqqliqaQIqqlqaQIaqlqqq 71
                                      +ek +  q +q+  q++ aQ +q ++ 
  gi|313127287|ref|YP_004037557.1| 14 QEKLEELQDLQETAQKVAAQKQQAEST 40
                                      455555555555555555555555444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00018
                              FlxA  27 knlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaql 68 
                                       +++ + L +  +s e   e+ kkq++ +q+Q ++lq++++q+
  gi|313127287|ref|YP_004037557.1|  74 ETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       5666667666677778899**********************8 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.0      0.12        28      38      61 ..      17      40 ..       7      58 .. 0.48
   2 ?   13.9   4.6   0.00023     0.056      15      51 ..      79     115 ..      73     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.12
                              ZapB 38 keenreleeeneqlkeereawqer 61
                                       ee + l+e  ++  +++++ ++ 
  gi|313127287|ref|YP_004037557.1| 17 LEELQDLQETAQKVAAQKQQAEST 40
                                      222333333333333333333332 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00023
                              ZapB  15 kaidtitlLqmeieeLkeeneelkeenreleeeneql 51 
                                        + d++++L  ++e+Lk++ e  +e+ + l++e++q+
  gi|313127287|ref|YP_004037557.1|  79 DLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       6789999999999999999999999999999999986 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.9      0.12        29      34      73 ..      18      57 ..       8      64 .. 0.72
   2 ?   13.8   1.8   0.00022     0.055      37      68 ..      78     109 ..      54     117 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.12
                           BLOC1_2 34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekq 73
                                      e+ ++l++ a++++++ ++ +++  e +  l+ +++i+++
  gi|313127287|ref|YP_004037557.1| 18 EELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDED 57
                                      5566777777777777777777777777778888887765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00022
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqid 68 
                                       ++l+d+++sle+ +e+l++++e +q+++++++
  gi|313127287|ref|YP_004037557.1|  78 EDLTDKVDSLEVRVEQLKKQEERVQEQFESLQ 109
                                       57777777777777777777777777777665 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.6      0.03       7.4      19      74 ..      13      64 ..       5      70 .. 0.73
   2 ?   11.9   2.9   0.00064      0.16       8      52 ..      73     117 ..      68     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.03
                             Sec34 19 tdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeel 74
                                      ++e le+L++l+e  ++v+++    ++++e+ l+e +   +  e+i+e+  +++e+
  gi|313127287|ref|YP_004037557.1| 13 AQEKLEELQDLQETAQKVAAQ----KQQAESTLTESETALDALEDIDEDTVMYREV 64
                                      556666677777766666666....5677888888888888889999998888876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00064
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlle 52 
                                       +e   ++l +++d+++  +e+l+++ ++v+e+ +sl+++ +q+l+
  gi|313127287|ref|YP_004037557.1|  73 YETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       5677899**********************************9986 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  18.8   0.00076      0.19      97     201 ..      12     115 ..       5     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00076
                               ERM  97 eserkeeeaerLkeeleeareaeeeakekllealstpskseseenveeseteeee..enseeesaeletdeveklsl 171
                                       e ++k ee + L+e ++++ +++++a++ l e  ++       e  +e++  + e  e   e+ +e  +++    + 
  gi|313127287|ref|YP_004037557.1|  12 EAQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDAL---EDIDEDTVMYREvgELLVETDYETAHEDL-TDKV 84 
                                       77899999***********999999999999988888432...22222222222201222334555555554.3367 PP

                               ERM 172 eieeeRvtyleks.krlqeqLkeLkseleql 201
                                       ++ e Rv+ l+k+ +r+qeq + L+sel+q+
  gi|313127287|ref|YP_004037557.1|  85 DSLEVRVEQLKKQeERVQEQFESLQSELQQM 115
                                       8888999999886279************997 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   7.3     0.043        11      44      86 ..      11      53 ..       5      71 .. 0.75
   2 ?   12.9   4.6    0.0002      0.05      48      93 ..      72     117 ..      68     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.043
                           DUF3450 44 dekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86
                                       e+qe l+e+++l+e +++ +++++q e+ +++ e+ ++ le 
  gi|313127287|ref|YP_004037557.1| 11 PEAQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALED 53
                                      5788888888888888888888888888888888888887764 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0002
                           DUF3450  48 ellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       +++   ++l+++++slev  eql+++ + ++++++sl+ +++++ +
  gi|313127287|ref|YP_004037557.1|  72 DYETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       5667778999*****************************9999765 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.1      0.14        35      68     105 ..      13      50 ..       3      56 .. 0.86
   2 ?   12.6   1.2   0.00036     0.088      55      99 ..      71     115 ..      66     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.14
                          Lectin_N  68 ssstlaeiqalssqggslsekvtsleaklekkqqdlka 105
                                       +++ l e+q+l+  ++++  + +  e++l + + +l+a
  gi|313127287|ref|YP_004037557.1|  13 AQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDA 50 
                                       5677899***********************99999987 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00036
                          Lectin_N  55 reLetLketfsnfssstlaeiqalssqggslsekvtsleaklekk 99 
                                        + et +e++++   s ++ +++l+ q ++++e+ +sl+++l++ 
  gi|313127287|ref|YP_004037557.1|  71 TDYETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       688999999*********************************975 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.0   0.00024     0.059      64     104 ..       4      44 ..       1      54 [. 0.77
   2 ?    3.7   4.6      0.21        51      46      89 ..      74     117 ..      43     124 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00024
                       Sigma70_ner  64 adeeelkeealekfeelreqyeklrkalkkkgrkskkyeka 104
                                        +++ l++ea ek+eel+++ e+++k+ ++k++++  + + 
  gi|313127287|ref|YP_004037557.1|   4 SMQGNLPPEAQEKLEELQDLQETAQKVAAQKQQAESTLTES 44 
                                       6899**********************888886655444433 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.21
                       Sigma70_ner  46 eeeeeeeddd.eeeseseaadeeelkeealekfeelreqyeklrk 89 
                                       e   e+   d  ++ e   +++++ +e++ e+fe l++ ++++ +
  gi|313127287|ref|YP_004037557.1|  74 ETAHEDLT-DkVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       22222211.124466777888888889999999999988888865 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       2.1   5.2e+02       5      14 ..      17      26 ..      13      57 .. 0.65
   2 ?   11.2   0.3   0.00097      0.24       6      38 ..      78     110 ..      74     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.1
                         DASH_Dam1  5 faeLaDslet 14
                                      ++eL+D  et
  gi|313127287|ref|YP_004037557.1| 17 LEELQDLQET 26
                                      4444433332 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00097
                         DASH_Dam1   6 aeLaDsletLdknledLqqihesLsdfNeSFas 38 
                                       ++L+D+++ L+ ++e+L++ +e++++  eS+ s
  gi|313127287|ref|YP_004037557.1|  78 EDLTDKVDSLEVRVEQLKKQEERVQEQFESLQS 110
                                       79**********************997788766 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   9.6     0.011       2.6     109     178 ..      27     127 ..       4     133 .] 0.63

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                           DUF4407 109 daelaeeqqeeakelkeqlaaa...............................ltaelaeleaqiaalqaeidaaea 154
                                       ++++a+++q+++++l+e+ +a                                lt++++ le ++++l+++ +  ++
  gi|313127287|ref|YP_004037557.1|  27 AQKVAAQKQQAESTLTESETALdaledidedtvmyrevgellvetdyetahedLTDKVDSLEVRVEQLKKQEERVQE 103
                                       34444444444444444444446666677777777777777777776666666777777777777777777777777 PP

                           DUF4407 155 rldalraeaqkeldgtkgtgttgv 178
                                       +++ l+ e+q+ l+g  g g  g 
  gi|313127287|ref|YP_004037557.1| 104 QFESLQSELQQMLQGGAGGGPMGP 127
                                       777777777777777665554444 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4    0.0011      0.26      78     130 ..      20      72 ..      16      87 .. 0.87
   2 ?    5.5   1.5     0.061        15      74     114 ..      77     117 ..      71     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0011
                      Sec8_exocyst  78 lssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLdaie 130
                                       l+ +qe ++kv++ K++ e++ ++ +t  + L+++ +++++y+ev e+L + +
  gi|313127287|ref|YP_004037557.1|  20 LQDLQETAQKVAAQKQQAESTLTESETALDALEDIDEDTVMYREVGELLVETD 72 
                                       67899****************************************99998754 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.061
                      Sec8_exocyst  74 YskilssiqesqekvselKesleeakkklstkkkeLkelna 114
                                       ++ + +++++ + +v++lK++ e  +++++  ++eL+++ +
  gi|313127287|ref|YP_004037557.1|  77 HEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       556667777778899***********************976 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.4     0.001      0.25      15     119 ..      18     115 ..      12     125 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHH.HHHHCCC...HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH...........CCC.HHHHHHHH CS
                       Hemerythrin  15 allerlralada.aaevhga...lrklaelldelvdeleaHhaaEEellfPlle..........drpggravldvle 77 
                                       ++l++l++ a++ aa  ++a   l++ +++ld+l+d       +E+++++ ++           ++++ ++ +d+le
  gi|313127287|ref|YP_004037557.1|  18 EELQDLQETAQKvAAQKQQAestLTESETALDALEDI------DEDTVMYREVGellvetdyetAHEDLTDKVDSLE 88 
                                       45555666666643333333688*************8......***********66655555554444444444444 PP

                                       HHHHHHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHH CS
                       Hemerythrin  78 reHdeirelleelrellkgleepsaaafaelleeladllreH 119
                                          +++ ++ e+++               e++e l+++l ++
  gi|313127287|ref|YP_004037557.1|  89 VRVEQLKKQEERVQ---------------EQFESLQSELQQM 115
                                       44444444444444...............4444444444444 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.4      0.01       2.5       7      38 ..      21      52 ..       9      54 .. 0.82
   2 ?    7.7   1.3     0.017       4.1       7      38 ..      92     117 ..      84     122 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.01
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCG CS
                            WXG100  7 eelrqaaarfqkqaeeledelqrlkaevdalq 38
                                      ++l+++a+++++q+++ e+ l++ +  +dal+
  gi|313127287|ref|YP_004037557.1| 21 QDLQETAQKVAAQKQQAESTLTESETALDALE 52
                                      67889999999999999999888888877775 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.G CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdal.q 38 
                                       e       +++kq+e+++++ ++l++e++++ q
  gi|313127287|ref|YP_004037557.1|  92 E-------QLKKQEERVQEQFESLQSELQQMlQ 117
                                       3.......4556666666666666666666644 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.3      0.15        38      81     113 ..      18      50 ..       3      57 .. 0.58
   2 ?   12.8   1.8    0.0004     0.097      45      92 ..      68     114 ..      59     118 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.15
                              ADIP  81 tqleqlerelalvqakerqlekklktleqklkn 113
                                       ++l++l+  ++ v a+++q+e +l++ e++l  
  gi|313127287|ref|YP_004037557.1|  18 EELQDLQETAQKVAAQKQQAESTLTESETALDA 50 
                                       345555555555555555555555555555544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0004
                              ADIP  45 lqardrdleqreslnetirkleaeierlqskierlktqleqlerelal 92 
                                       l+ +d + +  e l++++ +le   e+l+++ er+++q e+l++el++
  gi|313127287|ref|YP_004037557.1|  68 LVETDYETA-HEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQ 114
                                       444444433.35566667777777777777777777777777776664 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.8     0.093        23      34      63 ..      20      53 ..       5      61 .. 0.51
   2 ?   10.7   2.7    0.0023      0.55      15      53 ..      79     114 ..      74     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.093
                           NPV_P10 34 lpdvtelnekLdaqsaq....LaeletkvenIqd 63
                                      l+d++e  +k+ aq +q    L+e et++++ +d
  gi|313127287|ref|YP_004037557.1| 20 LQDLQETAQKVAAQKQQaestLTESETALDALED 53
                                      3333333333333333311114444445544444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0023
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLae 53 
                                       ++ dkVd+l+ +v++++++ + v+   e++++++ +L++
  gi|313127287|ref|YP_004037557.1|  79 DLTDKVDSLEVRVEQLKKQEERVQ---EQFESLQSELQQ 114
                                       689***************999977...666666666654 PP

>> DUF2379  Protein of unknown function (DUF2379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.4     0.003      0.73      32      63 ..      23      54 ..      14      58 .. 0.89
   2 ?    4.6   0.3      0.14        35      24      83 ..      60     117 ..      55     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.003
                           DUF2379 32 LrrtarevaiseadaeeaLateesAlaLlrei 63
                                      L+ ta++va ++++ae++L ++e+Al  l++i
  gi|313127287|ref|YP_004037557.1| 23 LQETAQKVAAQKQQAESTLTESETALDALEDI 54
                                      899***********************999887 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.14
                           DUF2379  24 LtdevralLrrtarevaiseadaeeaLateesAlaLlreiarRiregskrLvdallrmlr 83 
                                       + +ev +lL  t  e a +  d ++ + + e   + l++ ++R++e  + L++ l++ml+
  gi|313127287|ref|YP_004037557.1|  60 MYREVGELLVETDYETAHE--DLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       5678888999998888865..888999999999999999999999999999999988876 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.9    0.0072       1.8     187     222 ..      18      53 ..       8      60 .. 0.86
   2 ?    8.4   3.6    0.0066       1.6      31      68 ..      80     117 ..      51     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0072
                         Laminin_I 187 akLsDlrelleeAaaktrdanrlnlanqanlreiek 222
                                       ++L+Dl+e  ++ aa+ ++a+  + + + +l+++e+
  gi|313127287|ref|YP_004037557.1|  18 EELQDLQETAQKVAAQKQQAESTLTESETALDALED 53 
                                       579999999999999999999999999999998775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0066
                         Laminin_I  31 klskesakkskieilekelesLaqeteeLqkkatqvla 68 
                                          k ++ ++++e l+k+ e +++++e+Lq +++q+l+
  gi|313127287|ref|YP_004037557.1|  80 LTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       45566677888899999999999999999999999986 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  14.5    0.0045       1.1      16     123 ..      12     116 ..       5     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0045
                            TACC_C  16 eveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsveksfs 92 
                                       e++ek ee+q+l+++ ++  +++q+ + ++ e e+++  l + +  + +   +e+ ++l e +  +a+  ++  +++
  gi|313127287|ref|YP_004037557.1|  12 EAQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALEDID--EDTVMYREVGELLVETDYETAHE-DLTDKVD 85 
                                       78899999*************************99998887766..45568889999998777665554.4445567 PP

                            TACC_C  93 dlfkryekqkevlegykkneeslkkcaeeyl 123
                                        l  r+e++k+  e  +++ esl+++ +++l
  gi|313127287|ref|YP_004037557.1|  86 SLEVRVEQLKKQEERVQEQFESLQSELQQML 116
                                       7777777777777777777777777777776 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.1      0.16        40      29      72 ..      15      58 ..      11      61 .. 0.85
   2 ?   10.9   1.1    0.0017      0.43       4      44 ..      71     115 ..      68     118 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.16
                           DUF4164 29 eaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEv 72
                                      e+ ++ ++l+++ +++++ +++ +  L+++e  + +le++ +++
  gi|313127287|ref|YP_004037557.1| 15 EKLEELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDEDT 58
                                      56677789999999999999999999999999999999988775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0017
                           DUF4164   4 keleaaltrLeaaldsLEkavdrrleaerkr....deleaeieal 44 
                                       ++ e a ++L+ ++dsLE +v++  ++e+      ++l++e++++
  gi|313127287|ref|YP_004037557.1|  71 TDYETAHEDLTDKVDSLEVRVEQLKKQEERVqeqfESLQSELQQM 115
                                       567788889999999999999875555554455556666666554 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.6     0.037         9      76     108 ..      14      46 ..      11      59 .. 0.65
   2 ?    9.9   5.4    0.0037       0.9      10      56 ..      68     114 ..      62     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.037
                           DUF4200  76 kekeaeikklkaeietlkseiekleekleeykk 108
                                       +ek +e+++l++  +++ +++++ e +l e ++
  gi|313127287|ref|YP_004037557.1|  14 QEKLEELQDLQETAQKVAAQKQQAESTLTESET 46 
                                       566667777777777777777777776666544 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0037
                           DUF4200  10 evqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflke 56 
                                       +v+  +e++ e++  + ++l+ r e+l+k+e++ +e+++ ++  l++
  gi|313127287|ref|YP_004037557.1|  68 LVETDYETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQ 114
                                       6889999999****************************999988876 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   6.6      0.69   1.7e+02       5      28 ..      16      41 ..      13      52 .. 0.83
   2 ?   12.1   0.6    0.0006      0.15       9      44 ..      83     119 ..      76     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.69
                     Bap31_Bap29_C  5 kLkk..eLkkkkkDlealKkQaegla 28
                                      kL++   L+++ + + a K+Qae++ 
  gi|313127287|ref|YP_004037557.1| 16 KLEElqDLQETAQKVAAQKQQAESTL 41
                                      555555799999***********985 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0006
                     Bap31_Bap29_C   9 eLkkkkkDlealKkQaeglakEYDrLadehskl.des 44 
                                       + ++ +  +e lKkQ e ++  +  L  e +++ +++
  gi|313127287|ref|YP_004037557.1|  83 KVDSLEVRVEQLKKQEERVQEQFESLQSELQQMlQGG 119
                                       55555566899*********************98433 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   6.0       0.7   1.7e+02      58      97 ..      11      50 ..       2      56 .. 0.71
   2 ?   13.1   3.5    0.0004     0.099      53      96 ..      70     113 ..      52     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.7
                           DUF4140 58 pnreaeeeelkalraeleeledelaaledelaaaearlaf 97
                                      p+ +++ eel+ l+++ +++ ++++++e++l+  e+ l++
  gi|313127287|ref|YP_004037557.1| 11 PEAQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDA 50
                                      3344444468888888888888888888888877777665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0004
                           DUF4140  53 qvervpnreaeeeelkalraeleeledelaaledelaaaearla 96 
                                       +++ ++  e  ++++++l+ ++e+l+++ ++++++ ++++++l+
  gi|313127287|ref|YP_004037557.1|  70 ETDYETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQ 113
                                       33333333333446999***********************9986 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   8.0     0.065        16      55      89 ..      16      50 ..       8      63 .. 0.57
   2 ?   10.4   3.5    0.0021      0.53       2      34 ..      83     115 ..      82     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.065
                        TPR_MLP1_2 55 dvkelqalreelnelkaeiaelkaeaesakaelee 89
                                       ++elq+l e ++++ a+ +++++ + + +++l++
  gi|313127287|ref|YP_004037557.1| 16 KLEELQDLQETAQKVAAQKQQAESTLTESETALDA 50
                                      44444444444444444444444444444444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0021
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekq 34 
                                       +++sle  +++lk+++e+ ++++++lq++l+++
  gi|313127287|ref|YP_004037557.1|  83 KVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       68899*************************986 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  15.0    0.0072       1.8     326     426 ..      14     115 ..       8     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0072
                                       GGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHH..HHHHHHHHHHHHHHHH CS
                              EzrA 326 keeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleel..eekleeieekqeeile 400
                                       +e+l++l++  e +++   + ++ e+ l e e+ ++ l e+++e++v Y e+ e l e+  e   e++ +k+++++ 
  gi|313127287|ref|YP_004037557.1|  14 QEKLEELQDLQETAQKVAAQKQQAESTLTESETALDAL-EDIDEDTVMYREVGELLVETdyETAHEDLTDKVDSLEV 89 
                                       55666666666666777777888888888888888877.569999********99976511566799********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 401 slkslrkdEkrAreqldeikkelkei 426
                                        +++l+k+E+r +eq + +++el+++
  gi|313127287|ref|YP_004037557.1|  90 RVEQLKKQEERVQEQFESLQSELQQM 115
                                       ***********************986 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   9.5     0.012       2.9       5      92 ..      20     112 ..       4     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXX--TTTTTGGGHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdank..airdArrsvkkLeklapqLldklkelk 79 
                                       +++ +eta++v +q+++ +  l + +  l  +++  +e +   ++  +  +  d +++  +L+ +++ L+ ++++lk
  gi|313127287|ref|YP_004037557.1|  20 LQDLQETAQKVAAQKQQAESTLTESETALDALEDI-DEDTVMYREVGEllVETDYETAHEDLTDKVDSLEVRVEQLK 95 
                                       56778889999999888888888877777766655.44444444444411455778888899999999999999999 PP

                                       HHHHH.......HHHHH CS
                        Laminin_II  80 qleeasss....lsdni 92 
                                       ++ee  +     l  ++
  gi|313127287|ref|YP_004037557.1|  96 KQEERVQEqfesLQSEL 112
                                       98888554444454444 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   9.1    0.0058       1.4      84     181 ..      15     111 ..       9     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0058
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                              LUC7  84 eflrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeae.elgeeGkVdeaqklmk 159
                                       e l++l++ l++  +k++ +kq+ e t +e+e++ +a  +  ++   + +++ +ll e + e + e+  d+  +l  
  gi|313127287|ref|YP_004037557.1|  15 EKLEELQD-LQETAQKVAAQKQQAESTLTESETALDA-LEDIDEDTVMYREVGELLVETDyETAHEDLTDKVDSLEV 89 
                                       55666666.6788899999999999998888766665.467777778888899998888835566777788888999 PP

                                       XXXXXXXXXXXXXXXXXXX..X CS
                              LUC7 160 eveelkeekeeleqqyeaaaan 181
                                       +ve+lk++ e++++q e+ +++
  gi|313127287|ref|YP_004037557.1|  90 RVEQLKKQEERVQEQFESLQSE 111
                                       9*************99987543 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.9      0.02       4.8      17      97 ..      22     115 ..       6     118 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.02
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt......................rldtlltn 71 
                                       dL ++ + + +q+ q  + l++  +a++  L++++           +                      +l++ ++ 
  gi|313127287|ref|YP_004037557.1|  22 DLQETAQKVAAQKQQAESTLTESETALDA-LEDID-----------EdtvmyrevgellvetdyetaheDLTDKVDS 86 
                                       45555555555555555555555555554.55555...........3333333444455555335555555555555 PP

                      Baculo_PEP_C  72 Ltdalnalq...dtlrneLtnlnsiltnL 97 
                                       L+  + +l+   + ++++ ++l+s+l ++
  gi|313127287|ref|YP_004037557.1|  87 LEVRVEQLKkqeERVQEQFESLQSELQQM 115
                                       55555555566666666666666666554 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.2      0.26        64      68     110 ..      14      55 ..       5      67 .. 0.55
   2 ?   11.0   2.6    0.0014      0.34      49      97 ..      68     117 ..      62     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.26
                              COG2  68 qeeleevesplaaarkkvesvreklsereeeveskleeakele 110
                                       qe+lee++ +l+++ +kv + +++ + + +e e  l++ +++ 
  gi|313127287|ref|YP_004037557.1|  14 QEKLEELQ-DLQETAQKVAAQKQQAESTLTESETALDALEDID 55 
                                       44444443.3444444555555555555555555555444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0014
                              COG2  49 lvnedyad.FvslSghLvglqeeleevesplaaarkkvesvreklseree 97 
                                       lv++dy++   +l ++  +l+ ++e+++++ +++++++es++++l+++ +
  gi|313127287|ref|YP_004037557.1|  68 LVETDYETaHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       799*******************************************9976 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.4    0.0071       1.8     222     268 ..      13      59 ..       7      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0071
                              Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesev 268
                                        +e+ e+l++l+e+ +++++qk+++e+ + e+e  l++ ++++e+ v
  gi|313127287|ref|YP_004037557.1|  13 AQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDEDTV 59 
                                       67888999999999999999999999999999999999888888766 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.1      0.35        85      47      70 ..      18      41 ..      10      49 .. 0.72
   2 ?   10.4   5.8    0.0023      0.55      26      66 ..      75     115 ..      58     118 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.35
                          JIP_LZII 47 eEleslqkakerlesrikelEeel 70
                                      eEl+ lq++ +++  + +++E +l
  gi|313127287|ref|YP_004037557.1| 18 EELQDLQETAQKVAAQKQQAESTL 41
                                      577777777777777777777655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0023
                          JIP_LZII  26 vvkddLIarvdeLtsereiLreEleslqkakerlesrikel 66 
                                       ++ +dL  +vd L  + e L++  e++q++ e+l+s+++++
  gi|313127287|ref|YP_004037557.1|  75 TAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       55666666666666666666666666666666666666554 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.9    0.0072       1.8     169     258 ..      18     110 ..       2     120 .. 0.41

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0072
                      Exonuc_VII_L 169 qrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k....ekleekkerlkklkerle 240
                                       ++l+ l+++ ++  ++ +++++ l+e e+ l++   + +++ +  ++e+ e l +    +  e+ ++++++l+ r+e
  gi|313127287|ref|YP_004037557.1|  18 EELQDLQETAQKVAAQKQQAESTLTESETALDA--LEDIDEDTVMYREVGELLvEtdyeTAHEDLTDKVDSLEVRVE 92 
                                       222222222222222222222223333333322..222333333333333333333333333333344455556666 PP

                      Exonuc_VII_L 241 lleekkerleeleeklea 258
                                       +l++++er++e+ e+l++
  gi|313127287|ref|YP_004037557.1|  93 QLKKQEERVQEQFESLQS 110
                                       777777777777666654 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  10.6     0.044        11      34     125 ..      26     114 ..      12     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHH CS
                             Nup54  34 LakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEe 110
                                        a++v+aQ+++++      ++  d le++   +++ +  ++ ++   ++  ++    l+ k++ l+ r  +l+++Ee
  gi|313127287|ref|YP_004037557.1|  26 TAQKVAAQKQQAESTLTESETALDALEDID--EDTVMYREVGELL-VETDYETAHEDLTDKVDSLEVRVEQLKKQEE 99 
                                       345555555555555555555555555555..3444444444332.2333444445789999999999********* PP

                                       HHHHHHHHHHHHHS- CS
                             Nup54 111 elrarletleaqlnd 125
                                       ++++++e+l+++l++
  gi|313127287|ref|YP_004037557.1| 100 RVQEQFESLQSELQQ 114
                                       *************96 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  10.9      0.47   1.2e+02      57      98 ..      73     114 ..      12     117 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.47
                           DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredlse 98 
                                        +++ ++L++++d+++ ++++ k+  + ++e+ ++++++l++
  gi|313127287|ref|YP_004037557.1|  73 YETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQ 114
                                       344555666666666666666666666666666666666555 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  20.6      0.19        46      51     129 ..      12     115 ..       3     120 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.19
                     Jnk-SapK_ap_N  51 eleelreeleqLeteyerekelrkrae.......................eel..eeiedqweeerkelqekveqle 102
                                       e++e  eel++L++  ++ ++++++ae                       +e+  +++e+ +e  +++l +kv +le
  gi|313127287|ref|YP_004037557.1|  12 EAQEKLEELQDLQETAQKVAAQKQQAEstltesetaldaledidedtvmyREVgeLLVETDYETAHEDLTDKVDSLE 88 
                                       55666666666666666666666666655555555555555555555555222114567777777777777777777 PP

                     Jnk-SapK_ap_N 103 eenrelelkaknaadqlsrleekeael 129
                                        ++++l+++ + +++q ++l+++ +++
  gi|313127287|ref|YP_004037557.1|  89 VRVEQLKKQEERVQEQFESLQSELQQM 115
                                       777777766666777777776665554 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.9      0.01       2.5     570     669 ..      14     116 ..       1     120 [. 0.58

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.01
                          Prominin 570 eeiqkelenlkvdlsnlelLteeerkdLeklres..glskihsslyl.eqlckkltkvnletlaekleelanelsng 643
                                       +e+ +el+ l++  +++   ++++++ L++ +++   l++i+ ++++  ++ + l++++ et +e+l ++ ++l+ +
  gi|313127287|ref|YP_004037557.1|  14 QEKLEELQDLQETAQKVAAQKQQAESTLTESETAldALEDIDEDTVMyREVGELLVETDYETAHEDLTDKVDSLEVR 90 
                                       34445555555555555555555566665554432256666666654256777777777777777777777777666 PP

                          Prominin 644 kknlkqslkneaqdlraiqqelvlpl 669
                                        ++lk++ ++ +++++++q+el + l
  gi|313127287|ref|YP_004037557.1|  91 VEQLKKQEERVQEQFESLQSELQQML 116
                                       66666666666666666666665555 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.6       2.5   6.1e+02      19      20 ..      30      31 ..      11      60 .. 0.52
   2 ?   11.7   4.4    0.0011      0.26       4      41 ..      79     116 ..      77     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2.5
                         FlaC_arch 19 vk 20
                                      v 
  gi|313127287|ref|YP_004037557.1| 30 VA 31
                                      22 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0011
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenVkdll 41 
                                       +l  k+++l++++e +kk+ e ++++ e l+ + +++l
  gi|313127287|ref|YP_004037557.1|  79 DLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQML 116
                                       678899************************99999988 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.9      0.13        31       8      48 ..      14      54 ..      11      60 .. 0.84
   2 ?    7.6   0.5     0.021       5.2      13      41 ..      90     118 ..      72     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.13
                         DASH_Dad2  8 raELeaLkqlrdlsdslakqleeLeeklstladgteavasV 48
                                      ++ Le+L+ l++ ++++a q ++ e  l++ ++  +a +++
  gi|313127287|ref|YP_004037557.1| 14 QEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALEDI 54
                                      67899999999999999999999999988888887777665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.021
                         DASH_Dad2  13 aLkqlrdlsdslakqleeLeeklstladg 41 
                                         +ql+++ +++++q e+L+ +l+++ +g
  gi|313127287|ref|YP_004037557.1|  90 RVEQLKKQEERVQEQFESLQSELQQMLQG 118
                                       35677777777777777777777777666 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.0     0.051        12      49      91 ..      14      55 ..      12      60 .. 0.87
   2 ?    7.8   2.0     0.014       3.5      33      66 ..      82     115 ..      57     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.051
                            GCN5L1 49 qkklekeakalqanvakfakqtdqWlalvesfnsalkeiGDve 91
                                      q+kle e+++lq++++k+a q +q  ++  + ++al+ + D+ 
  gi|313127287|ref|YP_004037557.1| 14 QEKLE-ELQDLQETAQKVAAQKQQAESTLTESETALDALEDID 55
                                      56665.8999**************9999999999999999986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.014
                            GCN5L1  33 alvdklnsgvaeayanqkklekeakalqanvakf 66 
                                         vd+l+ +v+++ ++++++ +++ +lq++++++
  gi|313127287|ref|YP_004037557.1|  82 DKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       3479999999999999999999999999999886 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.8      0.23        57      20      48 ..      14      42 ..       5      52 .. 0.56
   2 ?    9.9   3.2    0.0054       1.3       3      32 ..      82     111 ..      71     118 .. 0.47

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.23
                       Rho_Binding 20 kkleeelekakeeeeeieklkasyekqLk 48
                                      ++  eel+ ++e++++++  k++ e++L 
  gi|313127287|ref|YP_004037557.1| 14 QEKLEELQDLQETAQKVAAQKQQAESTLT 42
                                      44445555555555555555555555554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0054
                       Rho_Binding   3 kdvenlakekeelnkklkkleeelekakee 32 
                                        +v+ l+   e+l+k+ + ++e++e +++e
  gi|313127287|ref|YP_004037557.1|  82 DKVDSLEVRVEQLKKQEERVQEQFESLQSE 111
                                       444444444444444444444444444322 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.0     0.079        19      33      72 ..       8      47 ..       1      48 [. 0.82
   2 ?    8.3   2.1      0.01       2.5      36      71 ..      75     110 ..      49     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.079
                            Cnn_1N 33 lseeqkeellkenielkveveslqkelkekkkllreaeka 72
                                      + + + +e l+e+ +l+++ ++   ++++ +  l+e+e+a
  gi|313127287|ref|YP_004037557.1|  8 NLPPEAQEKLEELQDLQETAQKVAAQKQQAESTLTESETA 47
                                      445567777888************************9987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.01
                            Cnn_1N  36 eqkeellkenielkveveslqkelkekkkllreaek 71 
                                       + +e+l ++   l+v+ve+l+k+ ++ +++ +++++
  gi|313127287|ref|YP_004037557.1|  75 TAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQS 110
                                       566777777777888888888888888877776665 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   7.7      0.96   2.4e+02      62      95 ..      16      49 ..      11      58 .. 0.45

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.96
                             DHR10 62 lrdaleekeielrelerkeerlqrqlenaeekle 95
                                        ++l++++++++++ +++++ +  l   e  l+
  gi|313127287|ref|YP_004037557.1| 16 KLEELQDLQETAQKVAAQKQQAESTLTESETALD 49
                                      3344444444444444444444444444444443 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.2     0.079        19      28      62 ..      23      57 ..      12      70 .. 0.84
   2 ?    3.9   3.7      0.26        64      25      85 ..      38     102 ..      35     110 .. 0.66
   3 ?    6.4   0.6     0.045        11      25      61 ..      81     117 ..      73     120 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.079
                            DUF948 28 ldeaaatieelekqvdpilkevedllakvnelled 62
                                      l+e+a+ ++  ++q++++l+e+e++l+  +++ ed
  gi|313127287|ref|YP_004037557.1| 23 LQETAQKVAAQKQQAESTLTESETALDALEDIDED 57
                                      67888888888999999999999999988887666 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.26
                            DUF948  25 kktldeaaatieele..kqvdpilkevedllakvne..lledvneklekvdplteavadlgesvs 85 
                                       ++tl+e +++++ le  ++ + + +ev +ll ++      ed+++k+++++  +e++++  e v+
  gi|313127287|ref|YP_004037557.1|  38 ESTLTESETALDALEdiDEDTVMYREVGELLVETDYetAHEDLTDKVDSLEVRVEQLKKQEERVQ 102
                                       56777777777777755444556677777777765433667778888888777777777777665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.045
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelle 61 
                                       ++ +d+++ ++e+l+kq + + ++ e l ++ +++l+
  gi|313127287|ref|YP_004037557.1|  81 TDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       4556666666777776666666666666666666665 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   5.5      0.15        36      10      53 ..      17      59 ..       8      77 .. 0.64
   2 ?    9.4   3.7    0.0049       1.2       8      43 ..      79     114 ..      72     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.15
                             Spc24 10 akelsdleselesleselaelkeeleeleeeseekeservedet 53
                                       +el+dl+++++++ +++++ +++l+e e+   + e ++ ed++
  gi|313127287|ref|YP_004037557.1| 17 LEELQDLQETAQKVAAQKQQAESTLTESETALDALE-DIDEDTV 59
                                      456777777777777777777777777777666611.1123443 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0049
                             Spc24   8 riakelsdleselesleselaelkeeleeleeesee 43 
                                       +++ ++++le  +e+l+++ ++ +e++e l++e ++
  gi|313127287|ref|YP_004037557.1|  79 DLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQ 114
                                       67889999999****************999999887 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   6.0     0.073        18      65     106 ..      12      53 ..       4      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.073
                               GAS  65 kaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                       +a+e++eeL+   ++ +k  ++ +++++ l+e+e  l +l+ 
  gi|313127287|ref|YP_004037557.1|  12 EAQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALED 53 
                                       789999999999999999999999999999999999999875 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   4.9     0.021       5.2     235     316 ..      23     117 ..       7     121 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.021
                              FUSC 235 lsslarllarlraeeaaavpelaallaelaal.................eaaaaaealeaalaalrarlralrrale 294
                                       l+++a+  a+ +++ + +  e ++ l++l+++                 + + a+e+l++++++l+ r+++l++++e
  gi|313127287|ref|YP_004037557.1|  23 LQETAQKVAAQKQQAESTLTESETALDALEDIdedtvmyrevgellvetDYETAHEDLTDKVDSLEVRVEQLKKQEE 99 
                                       33333333333333333333356666666666777888888887788776677889999999999999999999999 PP

                              FUSC 295 adadtaalllarlaellaelaq 316
                                           + ++ +++l+++l++++q
  gi|313127287|ref|YP_004037557.1| 100 ----RVQEQFESLQSELQQMLQ 117
                                       ....666666666666666655 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   2.9       0.1        26     273     312 ..      14      53 ..       8      62 .. 0.82
   2 ?    8.3   3.0    0.0041         1     237     282 ..      70     115 ..      62     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.1
                             IFT57 273 eellqeyreaqeelsevkekykqlsegvseltrelaeise 312
                                       +e l+e++++qe+ ++v  + +q++++++e ++ l+ +++
  gi|313127287|ref|YP_004037557.1|  14 QEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALED 53 
                                       6788899999999999999999999999999988887754 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0041
                             IFT57 237 eeslpetksqlkklhedisktlekiesrEkylnsqleellqeyrea 282
                                       e++++++++ l++  + ++  +e+++++E+++++q+e+l +e++++
  gi|313127287|ref|YP_004037557.1|  70 ETDYETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       5666777777777777778888888888888888888888777765 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  10.3      0.37        92      62      96 ..      12      46 ..       7      60 .. 0.74
   2 ?    9.8   8.6    0.0045       1.1      40      79 ..      73     114 ..      48     118 .. 0.49

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.37
                            APG6_N 62 eeeelleeLkelekereeleaelaaleeelealee 96
                                      e +e+leeL++l+++ ++++a+ +++e++l + e 
  gi|313127287|ref|YP_004037557.1| 12 EAQEKLEELQDLQETAQKVAAQKQQAESTLTESET 46
                                      66788888888888888888888888877766554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0045
                            APG6_N  40 keeek..qdeeleeleeeleklekeeeelleeLkelekeree 79 
                                        e+ +    +++++le ++e+l+k+ee+ +e+ + l++e ++
  gi|313127287|ref|YP_004037557.1|  73 YETAHedLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQ 114
                                       332223334444444444555555555555555555544444 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.0       0.2        50      14      51 ..      19      56 ..       5      65 .. 0.62
   2 ?    9.0   3.9    0.0075       1.8      12      48 ..      81     117 ..      78     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.2
                   Snapin_Pallidin 14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51
                                      +l++l+e+ +++ ++ ++  ++l++  ++L+ le+++e
  gi|313127287|ref|YP_004037557.1| 19 ELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDE 56
                                      45556666666666666666666666666666666555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0075
                   Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkelee 48 
                                         k+d l+ ++++l+++ e ++eq ++l+++L+++ +
  gi|313127287|ref|YP_004037557.1|  81 TDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       5789*****************************9875 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  13.9     0.098        24      25      90 ..      30     117 ..       6     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.098
                                       HHHB-..BHHHHHHHHHHHH.........................HHHHHHHHHHHHHHHHHHHHHHHHHHHHH... CS
                             DUF16  25 lnefkdsnkqrLkkieakvd......................klgeqinkleqkvekqgekikelkveqkaqgeeln 79 
                                           k++ +  L+++e+ +d                        +   + l++kv+ ++ ++++lk++ +  +e+++
  gi|313127287|ref|YP_004037557.1|  30 VAAQKQQAESTLTESETALDaledidedtvmyrevgellvetDYETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFE 106
                                       44468889999999999999999**********99999999878888899999999999999999999999999999 PP

                                       ....HHHHHHH CS
                             DUF16  80 kvdetlelile 90 
                                       ++++ l+ +l+
  gi|313127287|ref|YP_004037557.1| 107 SLQSELQQMLQ 117
                                       88888877665 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.2       0.3        74      42      77 ..       8      43 ..       1      59 [. 0.71
   2 ?    9.1   2.0    0.0048       1.2      38      80 ..      75     117 ..      58     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.3
                           DUF4446 42 sleellkekleeveelkeeseelekeieeleeklkk 77
                                      +l    +eklee+++l+e+ +++ ++ ++ e++l++
  gi|313127287|ref|YP_004037557.1|  8 NLPPEAQEKLEELQDLQETAQKVAAQKQQAESTLTE 43
                                      555566777777778877777777777777766655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0048
                           DUF4446  38 kdgksleellkekleeveelkeeseelekeieeleeklkkslq 80 
                                       + +++l +++ +   +ve+lk+++e++++++e+l+++l+++lq
  gi|313127287|ref|YP_004037557.1|  75 TAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQ 117
                                       3456777777777778888888888888888888888888876 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  16.6      0.22        54      85     153 ..      22     116 ..      10     122 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.22
                           DUF4795  85 qfDeakkeLekmleellekleeqeealkkaldtLq......................eelkekld..rlelepLkeq 137
                                       +++e++++   + +++ + l+e e al+ al+++                       e+l+ k+d  ++ +e+Lk+q
  gi|313127287|ref|YP_004037557.1|  22 DLQETAQKVAAQKQQAESTLTESETALD-ALEDIDedtvmyrevgellvetdyetahEDLTDKVDslEVRVEQLKKQ 97 
                                       2333344444344444444444443333.233333566666666666666666666688888888666666777776 PP

                           DUF4795 138 le...erlkelqkelqeam 153
                                        e   e++++lq elq+++
  gi|313127287|ref|YP_004037557.1|  98 EErvqEQFESLQSELQQML 116
                                       4444488888888888765 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   4.6      0.17        41      65      98 ..      15      49 ..       4      53 .. 0.62
   2 ?    8.7   2.0    0.0081         2      68     100 ..      83     115 ..      56     118 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.17
                                      TT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N 65 kk.edaeeliaevkelkeelkaleaelkeleaele 98
                                      +k e+ ++l + ++++ ++ +++e +l+e e++l+
  gi|313127287|ref|YP_004037557.1| 15 EKlEELQDLQETAQKVAAQKQQAESTLTESETALD 49
                                      23366666666666666666666666666666665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0081
                                       -TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  68 daeeliaevkelkeelkaleaelkeleaelekl 100
                                       + ++l  +v++lk++ ++++++ + l++el+++
  gi|313127287|ref|YP_004037557.1|  83 KVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       344455555555555555555555555555555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  10.2       0.1        25      22     127 ..       5     114 ..       4     118 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.1
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHCCCHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikks.....skeleeeilrl 93 
                                       +q+ l    ++  ++l++l+++ ++++ ++++ae++ +e ++ l + +  ++d + +++++     +++ e+ +++l
  gi|313127287|ref|YP_004037557.1|   5 MQGNLPPEAQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDED-TVMYREVgellvETDYETAHEDL 80 
                                       66777777788889999999999999999999999999999999888888876.55555541111144556667777 PP

                                       HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  94 ketidaqesnirvLqnvlesneqkiqkLeqdidq 127
                                        +++d+ e ++++L++  e+ +++ + L+++ +q
  gi|313127287|ref|YP_004037557.1|  81 TDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQ 114
                                       7777777777777777777777777777776665 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   2.0      0.41     1e+02      18      40 ..      14      36 ..       4      53 .. 0.52
   2 ?    8.5   0.7    0.0055       1.4     265     299 ..      84     118 ..      71     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.41
                              SseC 18 eskqkllkelqekqeklrqeqve 40
                                      + k+++l++lqe+++k + ++++
  gi|313127287|ref|YP_004037557.1| 14 QEKLEELQDLQETAQKVAAQKQQ 36
                                      33333333333333332222221 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0055
                              SseC 265 tkllravleqlqkvldeaaeeikellesiqellks 299
                                       ++ l+  +eql+k+ ++++e++ +l++  q++l+ 
  gi|313127287|ref|YP_004037557.1|  84 VDSLEVRVEQLKKQEERVQEQFESLQSELQQMLQG 118
                                       45566789999999999999999999999998875 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.0       0.5   1.2e+02      19      60 ..      15      56 ..      10      66 .. 0.64
   2 ?    8.3   2.0     0.016       3.9      31      69 ..      77     115 ..      70     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.5
                      Occludin_ELL 19 keYkeYkelhaeleevskkfseLerelkelkegskeykkiee 60
                                      ++ +e ++l++  ++v+++ ++ e+ l e+++  +  ++i e
  gi|313127287|ref|YP_004037557.1| 15 EKLEELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDE 56
                                      556666777777777777777777777666666555555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.016
                      Occludin_ELL  31 leevskkfseLerelkelkegskeykkieeeilqeykkl 69 
                                        e++++k+  Le ++++lk++++++++  e++++e++++
  gi|313127287|ref|YP_004037557.1|  77 HEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       467788999999999999999999999999888888877 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.8      0.14        34      50      90 ..      13      53 ..       1      65 [. 0.59
   2 ?    8.3   4.2     0.012       2.9      27      89 ..      54     116 ..      46     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.14
                            eIF3_N 50 aadlykelegeeevpeelekkreevleeleeleeeaekvle 90
                                      a++  +el++ +e++++++++++++ ++l+e e++ +++ +
  gi|313127287|ref|YP_004037557.1| 13 AQEKLEELQDLQETAQKVAAQKQQAESTLTESETALDALED 53
                                      34444555566666666666666666666666555554444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.012
                            eIF3_N  27 iydeeellkaklellkkTnmvdyaadlykelegeeevpeelekkreevleeleeleeeaekvl 89 
                                       i++++ + +   ell +T+  ++ +dl  ++   e   e+l+k++e v e++e+l++e +++l
  gi|313127287|ref|YP_004037557.1|  54 IDEDTVMYREVGELLVETDYETAHEDLTDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQML 116
                                       4555556666779999***************99999999*******************99986 PP

>> bZIP_Maf  bZIP Maf transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.9       0.3        73      49      83 ..      16      50 ..      10      58 .. 0.56
   2 ?    8.3   2.6     0.014       3.3      57      91 ..      81     115 ..      74     120 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.3
                          bZIP_Maf 49 rlqqkeelekekeeleeelerlqqelsrlrqekda 83
                                      +l++ ++l++  ++ + ++++ + +l++ +  +da
  gi|313127287|ref|YP_004037557.1| 16 KLEELQDLQETAQKVAAQKQQAESTLTESETALDA 50
                                      45555555555555555555555555555555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.014
                          bZIP_Maf  57 ekekeeleeelerlqqelsrlrqekdalkrkneql 91 
                                        ++  +le ++e+l+++ +r++++ ++l+++ +q+
  gi|313127287|ref|YP_004037557.1|  81 TDKVDSLEVRVEQLKKQEERVQEQFESLQSELQQM 115
                                       55555555555555555555555555555555554 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  14.0     0.082        20       5     105 ..      17     116 ..      11     123 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.082
                                       HTTTTTST.-GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT............-S-..-.GGGT CS
                              PCRF   5 leelekklsdpevwedqekakklskelaeleeivealeeleealedleeakelle........edeelaela.eeel 72 
                                       le         e+++ qe+a+k++ + ++ e+++++ e++ +aled++e + +++        +d e a++   +++
  gi|313127287|ref|YP_004037557.1|  17 LE---------ELQDLQETAQKVAAQKQQAESTLTESETALDALEDIDEDTVMYRevgellveTDYETAHEDlTDKV 84 
                                       33.........344445555555555555555555555555555555555444421222222355444422213334 PP

                                       HHHHHHHHHH..HHHHHT-..SSSTTSEEEEEE CS
                              PCRF  73 eelekeleeleeelkklLlpkdendeknailei 105
                                       ++le ++e+l++  ++    + e  +++    +
  gi|313127287|ref|YP_004037557.1|  85 DSLEVRVEQLKK-QEERVQEQFESLQSELQQML 116
                                       444444444422.22222223333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2729  (0.152212); expected 358.6 (0.02)
Passed bias filter:                     1100  (0.0613531); expected 358.6 (0.02)
Passed Vit filter:                       203  (0.0113224); expected 17.9 (0.001)
Passed Fwd filter:                       102  (0.00568911); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              73  [number of targets reported over threshold]
# CPU time: 0.91u 0.31s 00:00:01.22 Elapsed: 00:00:00.46
# Mc/sec: 873.32
//
Query:       gi|313127288|ref|YP_004037558.1|  [L=89]
Description: hypothetical protein Hbor_25590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-06   26.8   4.5    6.9e-06   26.3   4.5    1.2  1  DUF3194   Protein of unknown function (DUF3194)


Domain annotation for each model (and alignments):
>> DUF3194  Protein of unknown function (DUF3194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   4.5   3.9e-10   6.9e-06      11      82 ..       6      75 ..       4      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.9e-10
                                      HHHHHHHHHHHHHHHTTS-TTTEEEEEEEEEEEESSSEEEEEEEEEEE-TT----TT.HHHHHHHHHHHHHHH CS
                           DUF3194 11 eiseflaeviekkifkkvskkevldlditvevkeneeLdvdveveleldelskldqe.lideavdeayeeldk 82
                                      ++ e +ae++e  if +  +++v+d+d+tv ++ +    +dv+v+++ ++  ++d +  +dea+  a  ++d+
  gi|313127288|ref|YP_004037558.1|  6 TVVETAAEAAEGVIFARYKQSDVKDFDVTVTFEDG---ILDVDVYINAPDDADADADdVADEAARTAQDAVDE 75
                                      78899**************************9776...47778899999999999997899****99999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 620.35
//
Query:       gi|313127289|ref|YP_004037559.1|  [L=66]
Description: hypothetical protein Hbor_25600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0001   22.1   4.8     0.0099   15.8   0.4    2.3  2  Nudix_N_2       Nudix N-terminal
    0.00012   21.5   0.3       0.41   10.2   0.1    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0023   18.0   0.9       0.23   11.6   0.2    2.1  2  Ribosomal_L37e  Ribosomal protein L37e
     0.0054   16.8   1.9        1.6    8.8   0.4    2.2  2  UPF0547         Uncharacterised protein family UPF0547
      0.008   16.3   1.8        1.6    8.9   0.1    2.1  2  DUF2387         Probable metal-binding protein (DUF2387)
  ------ inclusion threshold ------
      0.019   15.2   1.1       0.86    9.9   0.0    2.1  2  Ribosomal_L32p  Ribosomal L32p protein family
      0.039   14.4   1.6        4.7    7.8   0.1    2.3  2  zf-H2C2_2       Zinc-finger double domain
      0.048   13.7   2.0        1.6    8.8   2.2    2.0  1  DZR             Double zinc ribbon
        0.1   12.5   5.3       0.19   11.7   0.3    2.4  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        0.1   12.1   3.1        1.6    8.3   0.5    2.2  2  zf-ribbon_3     zinc-ribbon domain
       0.11   12.6   3.3       0.59   10.2   3.3    1.9  1  Rubredoxin      Rubredoxin
       0.11   12.5   3.1       0.18   11.8   3.1    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.17   12.1   3.6        1.7    8.9   3.7    2.0  2  Zn-ribbon_8     Zinc ribbon domain
        0.2   11.4   3.7        3.7    7.4   0.4    2.2  2  zinc_ribbon_2   zinc-ribbon domain
       0.24   11.4   0.2       0.24   11.4   0.2    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.28   11.0   2.8       0.39   10.5   0.2    2.0  2  zf-CCHC_4       Zinc knuckle
       0.33   10.7   3.6        7.3    6.4   0.2    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
          4    7.5   7.6        7.7    6.6   1.2    2.5  2  DUF1610         Domain of unknown function (DUF1610)


Domain annotation for each model (and alignments):
>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4     1e-05    0.0099      19      31 ..      20      32 ..      10      33 .. 0.85
   2 !    8.2   0.4    0.0023       2.3      23      30 ..      51      58 ..      51      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                                      SS-EEEETTTTEE CS
                         Nudix_N_2 19 nreRlvCpaCgti 31
                                      +r+R +C+aCg++
  gi|313127289|ref|YP_004037559.1| 20 ERTRKRCTACGYV 32
                                      8***********9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
                                      EEETTTTE CS
                         Nudix_N_2 23 lvCpaCgt 30
                                      +vCp+Cg+
  gi|313127289|ref|YP_004037559.1| 51 HVCPSCGY 58
                                      8*****98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00057      0.57      15      31 ..      19      35 ..      12      38 .. 0.83
   2 !   10.2   0.1   0.00041      0.41      17      27 ..      48      58 ..      45      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00057
                                      TSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon 15 pergelvCtdCGlVled 31
                                      +er+  +Ct+CG+V  d
  gi|313127289|ref|YP_004037559.1| 19 YERTRKRCTACGYVDTD 35
                                      6777779*******876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00041
                                      TTCEEESSSSB CS
                      TF_Zn_Ribbon 17 rgelvCtdCGl 27
                                      + e+vC++CG+
  gi|313127289|ref|YP_004037559.1| 48 TYEHVCPSCGY 58
                                      689*******6 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2   0.00023      0.23      25      41 ..      17      33 ..      15      40 .. 0.82
   2 ?    5.3   0.0     0.023        23      31      41 ..      50      60 ..      47      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                    Ribosomal_L37e 25 rsyhvqkktCascGyps 41
                                      + y   +k+C +cGy +
  gi|313127289|ref|YP_004037559.1| 17 KHYERTRKRCTACGYVD 33
                                      679999*********65 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.023
                    Ribosomal_L37e 31 kktCascGyps 41
                                      +++C scGy +
  gi|313127289|ref|YP_004037559.1| 50 EHVCPSCGYAD 60
                                      578******65 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0039       3.9      15      24 ..      24      33 ..      23      35 .. 0.86
   2 !    8.8   0.4    0.0016       1.6      16      24 ..      52      60 ..      51      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0039
                           UPF0547 15 qfCphCGyvF 24
                                      ++C  CGyv+
  gi|313127289|ref|YP_004037559.1| 24 KRCTACGYVD 33
                                      68*88***97 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0016
                           UPF0547 16 fCphCGyvF 24
                                      +Cp CGy +
  gi|313127289|ref|YP_004037559.1| 52 VCPSCGYAD 60
                                      6*****975 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0016       1.6      28      42 ..      21      35 ..      12      50 .. 0.76
   2 !    7.4   0.1    0.0048       4.8      10      21 ..      52      63 ..      50      66 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                           DUF2387 28 veyrECvsCgftdel 42
                                      +  + C++Cg++d+ 
  gi|313127289|ref|YP_004037559.1| 21 RTRKRCTACGYVDTD 35
                                      45567*******985 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0048
                           DUF2387 10 vCPrCsemDkir 21
                                      vCP C   D+i+
  gi|313127289|ref|YP_004037559.1| 52 VCPSCGYADRIV 63
                                      899999999886 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.048        48      33      49 ..      17      33 ..      13      36 .. 0.81
   2 ?    9.9   0.0   0.00086      0.86      33      49 ..      44      60 ..      39      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.048
                                      CCEECTTC-BTTTTBSS CS
                    Ribosomal_L32p 33 gelklpHrvcpscGyYk 49
                                      +++ + +  c++cGy +
  gi|313127289|ref|YP_004037559.1| 17 KHYERTRKRCTACGYVD 33
                                      67888888999999975 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00086
                                      CCEECTTC-BTTTTBSS CS
                    Ribosomal_L32p 33 gelklpHrvcpscGyYk 49
                                      g+ +   +vcpscGy +
  gi|313127289|ref|YP_004037559.1| 44 GSEITYEHVCPSCGYAD 60
                                      55566779*****9875 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.017        17       7      22 ..      16      31 ..       8      32 .. 0.84
   2 ?    7.8   0.1    0.0047       4.7      15      23 ..      51      59 ..      43      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
                         zf-H2C2_2  7 rkHtgekpyeCplCdk 22
                                      rkH   ++  C +C++
  gi|313127289|ref|YP_004037559.1| 16 RKHYERTRKRCTACGY 31
                                      778888888*****99 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0047
                         zf-H2C2_2 15 yeCplCdka 23
                                      + Cp+C++a
  gi|313127289|ref|YP_004037559.1| 51 HVCPSCGYA 59
                                      89*****96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.2    0.0016       1.6      28      49 .]      23      57 ..       9      57 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                               DZR 28 edrCpsCgek.vdpearf............CpeCG 49
                                       +rC +Cg+  +d +++             Cp+CG
  gi|313127289|ref|YP_004037559.1| 23 RKRCTACGYVdTDGRWTAattgseityehvCPSCG 57
                                      55666666654444444455555555555555555 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.8      0.11   1.1e+02       6      11 ..      25      30 ..      25      32 .. 0.87
   2 ?   11.7   0.3   0.00019      0.19       2      15 ..      48      58 ..      48      66 .] 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.11
                    Zn_ribbon_SprT  6 rCtgCg 11
                                      rCt Cg
  gi|313127289|ref|YP_004037559.1| 25 RCTACG 30
                                      8****9 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00019
                    Zn_ribbon_SprT  2 kyvYrCtgCgreyt 15
                                      +y+++C++Cg   +
  gi|313127289|ref|YP_004037559.1| 48 TYEHVCPSCG---Y 58
                                      7*********...3 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.028        28      19      25 ..      26      32 ..      23      37 .. 0.77
   2 ?    8.3   0.5    0.0016       1.6      18      24 ..      52      58 ..      50      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.028
                       zf-ribbon_3 19 CpyCGtk 25
                                      C+ CG++
  gi|313127289|ref|YP_004037559.1| 26 CTACGYV 32
                                      7777764 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                       zf-ribbon_3 18 vCpyCGt 24
                                      vCp+CG+
  gi|313127289|ref|YP_004037559.1| 52 VCPSCGY 58
                                      6888886 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.3   0.00059      0.59       3      42 ..      25      58 ..      23      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00059
                                      EETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB- CS
                        Rubredoxin  3 eCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgv 42
                                      +C++Cgyv      d d   ++ T  +++  + vCP+Cg 
  gi|313127289|ref|YP_004037559.1| 25 RCTACGYV------DTDGRWTAATTGSEITYEHVCPSCGY 58
                                      79999999......7888899999**************85 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.1   0.00018      0.18      26      55 ..      20      59 ..      11      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                    OrfB_Zn_ribbon 26 y.TSktCseCgsknke.........alsgrtfkCpnCgfe 55
                                        T k+C  Cg+++++         +  + +++Cp+Cg+ 
  gi|313127289|ref|YP_004037559.1| 20 ErTRKRCTACGYVDTDgrwtaattgSEITYEHVCPSCGYA 59
                                      25889***************99998888999*******85 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.019        19      23      33 ..      20      30 ..       9      38 .. 0.64
   2 ?    8.9   3.7    0.0017       1.7       7      34 ..      25      58 ..      18      64 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                       Zn-ribbon_8 23 dapltaCPeCg 33
                                      ++  + C +Cg
  gi|313127289|ref|YP_004037559.1| 20 ERTRKRCTACG 30
                                      55555566666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0017
                       Zn-ribbon_8  7 rCeeCghefe......vlqsisdap.ltaCPeCgs 34
                                      rC++Cg   +      +  + s+   + +CP+Cg 
  gi|313127289|ref|YP_004037559.1| 25 RCTACGY-VDtdgrwtAATTGSEITyEHVCPSCGY 58
                                      6999995.554885543333333333666****85 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.017        17      15      21 ..      25      31 ..      17      32 .. 0.75
   2 ?    7.4   0.4    0.0037       3.7       2       7 ..      53      58 ..      49      59 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                     zinc_ribbon_2 15 FCpyCGt 21
                                       C+ CG+
  gi|313127289|ref|YP_004037559.1| 25 RCTACGY 31
                                      5777776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0037
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp+CG+
  gi|313127289|ref|YP_004037559.1| 53 CPSCGY 58
                                      666663 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.6      0.21   2.1e+02      35      45 ..      21      31 ..      12      32 .. 0.64
   2 ?   11.4   0.2   0.00024      0.24      19      33 ..      51      65 ..      34      66 .] 0.69

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.21
                     Zn_Tnp_IS1595 35 rglfqCkeCrk 45
                                      r + +C +C++
  gi|313127289|ref|YP_004037559.1| 21 RTRKRCTACGY 31
                                      45567777765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00024
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayrik 33
                                      +vCP Cg++  + i+
  gi|313127289|ref|YP_004037559.1| 51 HVCPSCGYADRIVIQ 65
                                      89*****99766665 PP

>> zf-CCHC_4  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00039      0.39      26      40 ..      18      32 ..      14      33 .. 0.89
   2 ?    0.5   0.2      0.51     5e+02      32      39 ..      51      58 ..      46      59 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                         zf-CCHC_4 26 kYErLrsfCyiCgvl 40
                                       YEr r+ C+ Cg++
  gi|313127289|ref|YP_004037559.1| 18 HYERTRKRCTACGYV 32
                                      7************86 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.51
                         zf-CCHC_4 32 sfCyiCgv 39
                                       +C +Cg+
  gi|313127289|ref|YP_004037559.1| 51 HVCPSCGY 58
                                      46999986 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0073       7.3       2       9 ..      25      32 ..      25      38 .. 0.84
   2 ?    5.4   0.4     0.015        15       2       8 ..      52      58 ..      51      61 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0073
                      Rubredoxin_2  2 vCsqCGfe 9 
                                      +C +CG++
  gi|313127289|ref|YP_004037559.1| 25 RCTACGYV 32
                                      7*****97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                      Rubredoxin_2  2 vCsqCGf 8 
                                      vC +CG+
  gi|313127289|ref|YP_004037559.1| 52 VCPSCGY 58
                                      5666665 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.7     0.036        36       1       6 [.      26      31 ..      26      34 .. 0.89
   2 ?    6.6   1.2    0.0077       7.7      16      23 ..      50      57 ..      42      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.036
                           DUF1610  1 CtSCGa 6 
                                      Ct+CG 
  gi|313127289|ref|YP_004037559.1| 26 CTACGY 31
                                      *****6 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0077
                           DUF1610 16 vFpCPNCG 23
                                      ++ CP CG
  gi|313127289|ref|YP_004037559.1| 50 EHVCPSCG 57
                                      699****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 492.35
//
Query:       gi|313127290|ref|YP_004037560.1|  [L=636]
Description: hypothetical protein Hbor_25610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     9e-211  701.0   0.6     1e-210  700.9   0.6    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  700.9   0.6  5.7e-215    1e-210       1     564 []       8     629 ..       8     629 .. 0.99

  Alignments for each domain:
  == domain 1  score: 700.9 bits;  conditional E-value: 5.7e-215
                           DUF2070   1 leklskyifrlPswkvsllliillalligllaflssk...............lfgillfglpalvaflltlpvlril 62 
                                       l++ls++ifr+Psw++sl+++il+a+++g+ af+s++               ++gi+++g+p++va++ t+ v+r++
  gi|313127290|ref|YP_004037560.1|   8 LAGLSRFIFRAPSWYTSLTFAILIAAMAGVGAFDSGEsmqtwrglffigkdaWEGIFFIGVPTVVAAVGTSGVDRYV 84 
                                       689************************************************************************** PP

                           DUF2070  63 ggrltykrslflalltelivviisllaillsall...qalvllalvlslalvfalrllvlvavsdesllkavlpali 136
                                       gg+lt +rs +lal++e+i+v i+++a+++s+++   q++v++alv++la+vfa+rllv++avs++sll a++pa++
  gi|313127290|ref|YP_004037560.1|  85 GGTLTPNRSSLLALVCEIIIVTIVTIAATISVFTglgQRFVFDALVVALASVFAFRLLVVMAVSRSSLLVAAIPASL 161
                                       ***************************************************************************** PP

                           DUF2070 137 qpllailllvly..................................fspesfllllllslifalavylfivvvdrpl 179
                                       q+l+a++ll++y                                  +sp++f+ll ++++i+al+vy+fivvvdrp+
  gi|313127290|ref|YP_004037560.1| 162 QTLAAAVLLFIYsgtltflsdggpilnaylrpylvradrapaelsaISPDHFALLGVTCVIYALGVYAFIVVVDRPW 238
                                       ***************************************************************************** PP

                           DUF2070 180 krnlgvsaldllsaFlahilegskelEeffeeigeeadvpvkvlsfrredgekallvvPniHPGPlgeiGGsnLpki 256
                                       +r+lgvs+ld++++F++h++egs+elEeffe++geea vpv+vlsfr   geka++++P+iHPGP+geiGG+n+p++
  gi|313127290|ref|YP_004037560.1| 239 RRSLGVSVLDFIRGFIGHLAEGSRELEEFFEQLGEEAIVPVTVLSFRSSAGEKARFILPMIHPGPMGEIGGGNFPER 315
                                       ***************************************************************************** PP

                           DUF2070 257 laerldelvlvlHgtatHdfNlvserevekiveavkealeeleysskaskpvrvesgdvkllgqrfgdslllvitra 333
                                       +a+r d+l++++H+ta+HdfNlv+erev++i+ea++ a+e++ey s+a+++++v+sg++k+lgq fgd+++lv+t+a
  gi|313127290|ref|YP_004037560.1| 316 VASRSDGLAFPPHATAGHDFNLVTEREVDTILEAADAAHEQIEYGSEATQSIQVQSGEAKMLGQGFGDDAVLVSTYA 392
                                       ***************************************************************************** PP

                           DUF2070 334 pegiDDiplsvglsimaeakaegfedvllVDaHNsfseeage....vlpgsedaeeliraaekalekleaaeeselk 406
                                       p+++DD++++vgls+++ea+++g+e+vllVDaHNs+++ +g+    ++pgs++++++i+aa   +e+l++a++++l+
  gi|313127290|ref|YP_004037560.1| 393 PNFADDVEYAVGLSAATEARTAGIENVLLVDAHNSNNGLDGPdlghITPGSKRSFDMITAAGLGGEALTSASRGDLS 469
                                       ***************************************************************************** PP

                           DUF2070 407 vgvarsetpkltpeeglGdlgiqvlvlevdgqktayvliDgNNmepglreeirealkevdl....evevmTTDtHvv 479
                                       +gva++et+ + p+eg+G+lgi+v+v+ev gq+tayvliDgNNmepglr++i++ l +++      +e mTTDtH+v
  gi|313127290|ref|YP_004037560.1| 470 MGVAWDETE-WVPREGIGPLGIRVAVTEVAGQTTAYVLIDGNNMEPGLRDDIVSDLTGGENpladVAEAMTTDTHIV 545
                                       *********.8899*******************************************84446999************ PP

                           DUF2070 480 ngvslgynpvGekvskdelielvlelvekAiadlepvevgyatervevkvfgedrfeelvstvnsvvsvakilaaal 556
                                       n+v+ + n+vG+++++ e+ el+ el+++A++d+epve+g+a+er+ev+vfg+dr+e+l+s++n+vv++++++a+ +
  gi|313127290|ref|YP_004037560.1| 546 NTVE-ADNQVGAAIDQGEIRELIVELTREALSDVEPVEAGMAVERAEVTVFGNDRTETLASHANAVVAMGGAFAVSV 621
                                       ****.************************************************************************ PP

                           DUF2070 557 lllaills 564
                                        l+a+++s
  gi|313127290|ref|YP_004037560.1| 622 TLAAMAVS 629
                                       ****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4314.42
//
Query:       gi|313127291|ref|YP_004037561.1|  [L=183]
Description: GMP synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-36  123.4   0.0      1e-35  123.3   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.8e-12   47.5   2.7    6.8e-11   42.3   0.6    2.9  2  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.3   0.0   1.1e-39     1e-35       1     187 [.       5     178 ..       5     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 1.1e-39
                                       EEEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEE CS
                            GATase   1 lliDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGI 77 
                                       ++iDn+ ++t+  ++al+ lg+++e+v +d++ eei     ++dgi++sgGp    ++++++ ++     ++P+LGI
  gi|313127291|ref|YP_004037561.1|   5 VVIDNHGQFTHLEHRALRDLGIDTELVDNDTPPEEI-----DADGIVLSGGPDMDRIGNCPDYLE----LDVPVLGI 72 
                                       58*********************************9.....79***********99999998765....69****** PP

                                       THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEE CS
                            GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeel 154
                                       CLGmQ++a e+g+ v + +  ++   t  + d++  l+  l +e +++ +H +ev++   +pag++ t+ s d +++
  gi|313127291|ref|YP_004037561.1|  73 CLGMQIIASELGGRVGSGEYGGYADVTVGVLDESDPLIGSLAPETRVWASHADEVKE---VPAGFTHTGSS-DVCSI 145
                                       ********************************999**********************...***********.66778 PP

                                       EEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 155 meiiekknpfvgvQFHPEststpegpellfnfl 187
                                       +++   ++ ++gvQ+HPE+ +t++g+e+++nfl
  gi|313127291|ref|YP_004037561.1| 146 EAMSDPDRDLYGVQWHPEVAHTENGEEVFENFL 178
                                       888777778**********************96 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.036   3.2e+02      59      71 ..      42      54 ..      38      57 .. 0.88
   2 !   42.3   0.6   7.6e-15   6.8e-11     102     216 .]      63     163 ..      59     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.036
                     Peptidase_C26 59 ldgllltGgqdve 71
                                       dg++l+Gg+d++
  gi|313127291|ref|YP_004037561.1| 42 ADGIVLSGGPDMD 54
                                      59********976 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 7.6e-15
                     Peptidase_C26 102 lergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqai 178
                                       le +vP+lgiC+G+q+++  lGG++ +  +   g+ d         +  v  e++ l+ +l+   e++v   H   +
  gi|313127291|ref|YP_004037561.1|  63 LELDVPVLGICLGMQIIASELGGRVGSGEYG--GYAD--------VTVGVLDESDPLIGSLAP--ETRVWASHADEV 127
                                       6889*******************99876663..3332........244566678888888888..9*********** PP

                     Peptidase_C26 179 kelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       ke+  ++  +  ++   iEa++ ++++  ++gvQwHPE
  gi|313127291|ref|YP_004037561.1| 128 KEVPAGFTHTGSSDVCSIEAMSDPDRD--LYGVQWHPE 163
                                       *************************88..********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1267.12
//
Query:       gi|313127292|ref|YP_004037562.1|  [L=382]
Description: hypothetical protein Hbor_25630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-31  108.7  39.7    4.7e-31  108.4  39.7    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
        6.6    7.2   7.9        1.1    9.8   0.4    3.0  2  DUF3357          Domain of unknown function (DUF3357)


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4  39.7   5.2e-35   4.7e-31       2     300 ..      52     368 ..      51     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 5.2e-35
                   LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllral.r.Wrlllrslgarislrrllrayli 76 
                                       ++g+al++++l+++++ ++ +++  a++++d +++++ ++  +++  ++++    r+ l++  ++++ + +  ay  
  gi|313127292|ref|YP_004037562.1|  52 VVGIALAIVVLVIFISLTGGREVVVAVARADLRLVAVGCI--AGVAAISSWgEsLRQALST-AKPVGGLHYRLAYRS 125
                                       689999988888888999*************777777777..3333344443225888877.8************** PP

                   LPG_synthase_TM  77 glfvnnvtPgalg.Gevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa..vlllla 150
                                       g f+ +v+P++   G +++ y ++r  g+ +++ala+v+v  ll+ll+ v +  l+ll+l+  ++ g +  +++ l+
  gi|313127292|ref|YP_004037562.1| 126 GDFARQVLPMGHLsGSAIASYAVSRPFGLQYEEALAAVTVADLLNLLSAVTISTLGLLFLLLDSDIGDVrtFVAGLL 202
                                       **********************************************************9999887775554344444 PP

                   LPG_synthase_TM 151 lallllavlalllllllrrrlarlarvlkrlarllarfarklasakr....................klvlasprrl 207
                                       +al+++ ++ +l+ ++++  ++++  v+   +rl+ar++ ++                          +v+++++r+
  gi|313127292|ref|YP_004037562.1| 203 GALTVASAIFVLVTRRRDLLERAVVTVIAVGHRLAARLGIST----AerllrpdsveqriesyfrtlDTVAENRKRV 275
                                       444444444444444444444444444444444444444444....34467************************** PP

                   LPG_synthase_TM 208 llafllslliwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllall.Gvsaaeal 283
                                       +la  + +l w++++ +l +++ al+v+++la++l++ +a+ lvg  +plPgG+G++E+a+++ l++  Gv+ ++a+
  gi|313127292|ref|YP_004037562.1| 276 ALAGVFAALGWVAFGTALAVAATALDVEIPLAAALFVAPASGLVG-WSPLPGGSGGVEVAVTAGLVATaGVPVSTAA 351
                                       *********************************988888888887.5889***********99999999******** PP

                   LPG_synthase_TM 284 aaallyrlitlylllll 300
                                       a+allyr++ +++++++
  gi|313127292|ref|YP_004037562.1| 352 AVALLYRVCGYWVVVAV 368
                                       **************986 PP

>> DUF3357  Domain of unknown function (DUF3357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4   0.00012       1.1       4      47 ..      31      73 ..      28     103 .. 0.80
   2 ?    1.0   0.4     0.064   5.7e+02      13      48 ..     266     301 ..     246     332 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00012
                           DUF3357  4 pL.Peddeaaaaaaararrpllaavliasalvvlvvlvalagvrl 47
                                      pL P+ ++   ++++r r ++ a+v ia a+vvlv+++ l g r+
  gi|313127292|ref|YP_004037562.1| 31 PLqPDVASP--RTRTRLRPAVRAVVGIALAIVVLVIFISLTGGRE 73
                                      676777666..7788888899999999*******99999988754 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.064
                           DUF3357  13 aaaaararrpllaavliasalvvlvvlvalagvrla 48 
                                       ++ a++++r +la v++a + v++  ++a+a   l+
  gi|313127292|ref|YP_004037562.1| 266 DTVAENRKRVALAGVFAALGWVAFGTALAVAATALD 301
                                       567888999889999999999999999998866544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2437.27
//
Query:       gi|313127293|ref|YP_004037563.1|  [L=195]
Description: hypothetical protein Hbor_25640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.17   12.1   1.6       0.24   11.5   0.4    1.8  2  RecA_dep_nuc  Recombination enhancement, RecA-dependent nucle


Domain annotation for each model (and alignments):
>> RecA_dep_nuc  Recombination enhancement, RecA-dependent nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.14   2.5e+03      29      39 ..      92     108 ..      74     120 .. 0.56
   2 ?   11.5   0.4   1.3e-05      0.24      30      60 ..     122     152 ..     112     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.14
                                       -......EEEEESS-SS CS
                      RecA_dep_nuc  29 e......velhhiagrt 39 
                                       e       e hh+  ++
  gi|313127293|ref|YP_004037563.1|  92 EtgarplLEEHHLSYGG 108
                                       23334446778876443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.3e-05
                                       EEEEESS-SSSTTGGGSEEEEEHHHHT---- CS
                      RecA_dep_nuc  30 velhhiagrtkpdahkktlpLcawhhqaaap 60 
                                        + h  ++     +h+ t+ Lc+w h ++  
  gi|313127293|ref|YP_004037563.1| 122 SSSHRTQSDDDEPSHEITVALCRWCHTKVHK 152
                                       6778899999999*************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1249.64
//
Query:       gi|313127294|ref|YP_004037564.1|  [L=115]
Description: hypothetical protein Hbor_25650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-21   73.9   0.0      1e-20   73.6   0.0    1.0  1  DUF192    Uncharacterized ACR, COG1430


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   5.8e-25     1e-20       2      95 ..      17     112 ..      16     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 5.8e-25
                                       EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT-......E CS
                            DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpqs......v 72 
                                       +vevAdt+ ++arGLm+r+++p+d++++f+fd+ ++++++M ++ +++d+++l a +++++ ++ l+ ++      +
  gi|313127294|ref|YP_004037564.1|  17 DVEVADTFLTKARGLMFRRRIPDDYALVFEFDEVDKRNLHMVFVPFDIDALWL-AGEEVTKKKR-LSGWTgigfglA 91 
                                       69***************************************************.8899999885.768955556668 PP

                                       CEEEEEETTHHHHHT--TT-EEE CS
                            DUF192  73 ryvLElpaGaakklgikpGdrle 95 
                                       + ++ElpaGaa+  gi+ Gd+++
  gi|313127294|ref|YP_004037564.1|  92 DRIIELPAGAAD--GIERGDTVR 112
                                       88*********8..******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 762.85
//
Query:       gi|313127295|ref|YP_004037565.1|  [L=523]
Description: isopropylmalate/homocitrate/citramalate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-65  220.7   2.5    2.4e-65  220.7   2.5    1.8  2  HMGL-like     HMGL-like
    2.2e-32  111.7   1.2    4.3e-32  110.8   1.2    1.5  1  LeuA_dimer    LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
      0.035   13.6   1.4      0.072   12.5   0.2    2.1  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.11   12.7   0.1       0.29   11.4   0.1    1.7  1  SusE          SusE outer membrane protein


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.7   2.5   5.3e-69   2.4e-65       2     262 ..      23     275 ..      22     277 .. 0.96
   2 ?   -2.4   0.0      0.61   2.7e+03      93     125 ..     466     499 ..     452     519 .. 0.48

  Alignments for each domain:
  == domain 1  score: 220.7 bits;  conditional E-value: 5.3e-69
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       v+++dttLRDGeqa++ +ls eek  ia+aLd+a v++iE+g +  +++++e +r + + + +a+i++ +r +++d+
  gi|313127295|ref|YP_004037565.1|  23 VQLLDTTLRDGEQAPGISLSPEEKADIARALDRANVQYIEAGSACTGQGERETIRRVTDLGLDATITSFARGVQRDV 99 
                                       89*************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       + a +    + ++ v +++++s+ h++ k++ +reev++ + ++v++a+++g  ve+  ed sr+dlefl++++eaa
  gi|313127295|ref|YP_004037565.1| 100 DLALD----CDVDGVTIVVPASDKHVEGKVGTTREEVVETTGDLVAYAKDHGLWVEVIGEDGSRADLEFLVDIAEAA 172
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                        +aGa+r   aDtvG ++P+  +e +sal+e  +    +s+H+H+dlGlA+ n +a + aGad+v gtvnG+GeraG
  gi|313127295|ref|YP_004037565.1| 173 LDAGADRSCYADTVGHASPETTYEYVSALAELGP----VSTHTHDDLGLAMTNVYASLAAGADVVHGTVNGIGERAG 245
                                       ******************************9988....*************************************** PP

                                       B-BHHHHHHHHHHTT-B----HHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealgvdtgldlqklrsiaa 262
                                       n+alee+++al +       +l +l+++a+
  gi|313127295|ref|YP_004037565.1| 246 NVALEEVAIALSHCYDVETAKLDELYALAQ 275
                                       ***********9987555567777776665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.61
                                       EEEEEES-HHHHHHHHSSTHHHH.HHHHHHHHHH CS
                         HMGL-like  93 vhvfiatselhlkaklkkdreev.akkaeeavka 125
                                       v v + +s   +++ +  +  ++ ++++e++v+a
  gi|313127295|ref|YP_004037565.1| 466 VTVEVEMSHGDRSVTVATSDSDItRASVEAMVEA 499
                                       4444444444444433333333202233333433 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   1.2   9.6e-36   4.3e-32       2     133 .]     373     504 ..     372     504 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 9.6e-36
                                       XXXXXXXXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T CS
                        LeuA_dimer   2 vtdedlealvkdelleae.erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..d 75 
                                       vtd+dl a+++d+ ++++ +r++l++l+  sg + ++ta+v+l+v ++ee++as++G+GpvdA+++A+r+alg   d
  gi|313127295|ref|YP_004037565.1| 373 VTDADLLAIAEDVQGRERdRRVELLDLTAASGGG-TPTASVRLRV-NDEERVASGTGSGPVDAAVKAVRSALGPdaD 447
                                       9***************999************997.**********.99999**********************9666 PP

                                       -EEEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHHS CS
                        LeuA_dimer  76 ikLldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrll 133
                                       ++L++Y+v+ait+gtda ++v Ve++ +++++v+    dsdi++AS++A+++al+rll
  gi|313127295|ref|YP_004037565.1| 448 AQLDSYHVDAITGGTDAVVTVEVEMS-HGDRSVTVATSDSDITRASVEAMVEALDRLL 504
                                       6*************************.777779999******************9985 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.6e-05     0.072      22     127 ..      33     150 ..      21     179 .. 0.71
   2 ?   -1.8   0.1      0.39   1.8e+03     118     152 ..     333     364 ..     324     378 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                       HHHC.....HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC......HTTCS......HHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  22 vsel.....sdeelrelrkaldelglriaslslftrfgypded......erear......reesvdalkraielaaa 81 
                                         ++     s+ee +++++ald+++++   +++ +  ++ +e+          +         + + ++r ++la +
  gi|313127295|ref|YP_004037565.1|  33 GEQApgislSPEEKADIARALDRANVQ--YIEAGSACTGQGERetirrvT---DlgldatITSFARGVQRDVDLALD 104
                                       444455566999999**********99..333333333333434454440...155555689999999********* PP

                                       HTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEE CS
                      AP_endonuc_2  82 LGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvkl 127
                                       ++++ +++ +   + + +g   +++e ++e   +l++ya+++g ++
  gi|313127295|ref|YP_004037565.1| 105 CDVDGVTIVVPASDKHVEGKVGTTREEVVETTGDLVAYAKDHGLWV 150
                                       9999988887766888888888*********************654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.39
                                       HHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHT CS
                      AP_endonuc_2 118 dyaekegvklalEtlagsgvelgdeelarlldavd 152
                                       ++a ++gv  al  ++ + +   d+ela+++++v+
  gi|313127295|ref|YP_004037565.1| 333 KHAGRAGVAAALDEHDVDVT---DDELAAVVERVK 364
                                       55555555555555544442...255555555554 PP

>> SusE  SusE outer membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   6.4e-05      0.29      44      99 ..     460     515 ..     431     517 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.4e-05
                              SusE  44 ygvpaavtYtvqfdkkgedFskpvdatgttetslsitvkeLNtalldlglepgetg 99 
                                        g++a+vt +v+++  + + + +++ ++ t  s++  v+ L+++l++ + +p+ t+
  gi|313127295|ref|YP_004037565.1| 460 GGTDAVVTVEVEMSHGDRSVTVATSDSDITRASVEAMVEALDRLLVAVDGTPDDTA 515
                                       4899*************9999999999999*****************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3348.10
//
Query:       gi|313127296|ref|YP_004037566.1|  [L=58]
Description: hypothetical protein Hbor_25670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.043   14.0   0.2      0.053   13.7   0.2    1.2  1  Pentapeptide_3  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     3e-06     0.053      30      47 ..      29      46 ..      15      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-06
                    Pentapeptide_3 30 sadFsgarFtgdvdFsga 47
                                       ad +++rF+gdv+F+++
  gi|313127296|ref|YP_004037566.1| 29 VADYARTRFDGDVRFERC 46
                                      5888999********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 397.84
//
Query:       gi|313127297|ref|YP_004037567.1|  [L=43]
Description: hypothetical protein Hbor_25680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        58  (0.00323498); expected 358.6 (0.02)
Passed bias filter:                       54  (0.00301188); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 322.27
//
Query:       gi|313127298|ref|YP_004037568.1|  [L=529]
Description: sulfite oxidase-like oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-29  101.0   0.0    8.6e-29  100.3   0.0    1.2  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain
    3.6e-12   46.5   0.1    6.8e-12   45.6   0.1    1.4  1  Mo-co_dimer     Mo-co oxidoreductase dimerisation domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   9.6e-33   8.6e-29       6     172 .]     260     402 ..     253     402 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 9.6e-33
                                       -.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHH CS
                    Oxidored_molyb   6 kvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvL 82 
                                       ++++++w+l+v+g+ve++ ++++d+L a+  +++ +tl+C+++             +++ + + +  WtGv+++ +L
  gi|313127298|ref|YP_004037568.1| 260 NLRASDWTLSVTGSVEQEATYTYDELTAMGDEQRFVTLRCVSD-------------KINGTLMDTDLWTGVPISRIL 323
                                       567889************************************6.............4555578999*********** PP

                                       HHTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEE CS
                    Oxidored_molyb  83 ekagvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlk 159
                                       ++++++     +v++++ad       y ++ p+e +   d +LAy   g pLp+ hG P+R+++pg++g  +vKw++
  gi|313127298|ref|YP_004037568.1| 324 DEVNPQ---GAFVMLRAAD------DYFEEFPVEALE--DGFLAYGKRGGPLPRAHGHPVRALIPGHWGEINVKWVT 389
                                       ***996...69*******9......5*******8666..99************************************ PP

                                       EEEEESS---SHH CS
                    Oxidored_molyb 160 rievsdeesegyw 172
                                       ++e+ d +++g+w
  gi|313127298|ref|YP_004037568.1| 390 EMEILDGPEKGFW 402
                                       ***********99 PP

>> Mo-co_dimer  Mo-co oxidoreductase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.1   7.6e-16   6.8e-12      26     117 ..     424     510 ..     412     514 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 7.6e-16
                                       ...EEEEEEEEEE-STT--EEEEEEESSTTSS-EE-EEESSSSS---..SSTTS-TTS-EEEEEEEEESS...E.EE CS
                       Mo-co_dimer  26 eaeetytikGyaysGgGrritrvevsldkGksWklaeieyeedkereakeesretafcwvfweldvevselakekei 102
                                         +++++  G+ay+G  r i+rvevs+d+G++W  a+++ +       +e+ + +  +w  we + e   +   + +
  gi|313127298|ref|YP_004037568.1| 424 RRDGQIQAAGHAYAGT-RGIERVEVSIDGGETWADATLSDRLPAGT--DESGEAAEDAWRQWEHTYENPGR--RHTV 495
                                       347899********86.89******************998744433..345677788*******9999986..667* PP

                                       EEEEEETT--B--SH CS
                       Mo-co_dimer 103 lvravDealnvqPee 117
                                       +vra D++ ++qP+e
  gi|313127298|ref|YP_004037568.1| 496 VVRATDSTGTLQPRE 510
                                       *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2979.29
//
Query:       gi|313127299|ref|YP_004037569.1|  [L=252]
Description: hypothetical protein Hbor_25700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-64  218.0   4.3    1.5e-64  217.8   4.3    1.0  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.8   4.3   8.1e-69   1.5e-64       2     239 ..      11     243 ..      10     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 8.1e-69
                      Creatininase   2 eltwpeveealked.dvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTi 77 
                                        +tw+eve al+++ ++a+++vG++EqHGphlpl +Dtl++++la+r+aeklg +a+ +Pt+  G+s +h++fpGTi
  gi|313127299|ref|YP_004037569.1|  11 ACTWTEVESALESGmRTAVVAVGAIEQHGPHLPLIMDTLAGDELARRIAEKLG-DAFAAPTIRPGCSGHHMEFPGTI 86 
                                       68********666659************************************8.57********************* PP

                      Creatininase  78 slspetliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaae.a 153
                                       ++ petl++v+r +++sl +hGf++i lv  Hggn a+++ +a e+++e da++v v    +e+      +++a  +
  gi|313127299|ref|YP_004037569.1|  87 TVPPETLMDVIRSYCRSLDEHGFEHIALVPTHGGNFAPVNTVAPEIGREIDANVVAVA-DLHEYMD----RQKAGlH 158
                                       **************************************************66665433.2222222....3444445 PP

                      Creatininase 154 aeeseeeegggHAgelEtSlmlalrpelVrmdraedpeeaklakegvstaedaeelspsGvlGdpskataekGeall 230
                                       a   e ee  +HAg +Et+++la+++ lVr+d+++ ++e + +++    + ++ +++++GvlGdp++atae+Ge+++
  gi|313127299|ref|YP_004037569.1| 159 AGGVEYEESVIHAGAVETAMVLAVDEGLVRTDELAVGHEGEVSTA-RLLSDGFASITENGVLGDPRAATAEAGEEIF 234
                                       6666667788************************99999988887.8999999************************ PP

                      Creatininase 231 eaaveelae 239
                                       ea++++ +e
  gi|313127299|ref|YP_004037569.1| 235 EAVADAYVE 243
                                       *****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1542.96
//
Query:       gi|313127300|ref|YP_004037570.1|  [L=316]
Description: moxr-like ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-66  222.2   0.2    3.6e-66  221.0   0.0    1.7  2  AAA_3            ATPase family associated with various cellul
    4.4e-20   71.3   1.5    9.5e-20   70.2   1.5    1.6  1  AAA_lid_2        AAA lid domain
    4.8e-14   52.5   0.0    1.6e-13   50.9   0.0    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
    2.9e-06   27.8   0.0    5.4e-06   26.9   0.0    1.5  1  AAA              ATPase family associated with various cellul
    1.6e-05   24.7   0.0    0.00016   21.4   0.0    2.1  1  Sigma54_activat  Sigma-54 interaction domain
     0.0036   16.7   0.2        2.8    7.3   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0082   15.9   0.0       0.11   12.2   0.0    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0089   15.1   0.0      0.014   14.5   0.0    1.4  1  MCM              MCM P-loop domain
  ------ inclusion threshold ------
      0.095   12.8   0.0       0.35   11.0   0.0    2.0  2  AAA_2            AAA domain (Cdc48 subfamily)


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.0   0.0   1.8e-69   3.6e-66       1     130 [.      40     169 ..      40     170 .. 0.99
   2 ?   -2.4   0.0         2   3.9e+03      28      47 ..     284     303 ..     272     311 .. 0.74

  Alignments for each domain:
  == domain 1  score: 221.0 bits;  conditional E-value: 1.8e-69
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvlle+vPG++ktl ++++a+al+l+f+r+qftpdllPsd++Gt++f+e+e++fef++Gp+fan++ladeinrappk
  gi|313127300|ref|YP_004037570.1|  40 HVLLEDVPGTGKTLSARSVATALGLSFSRVQFTPDLLPSDVTGTNIFNEREQSFEFSEGPIFANVVLADEINRAPPK 116
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                       tq+alleamee qvtv+geth+lp+pf+v+atqnP+e+eGt+plpeaq+drf+
  gi|313127300|ref|YP_004037570.1| 117 TQAALLEAMEEGQVTVDGETHELPKPFFVIATQNPVESEGTFPLPEAQIDRFV 169
                                       ****************************************************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                             AAA_3  28 kriqftpdllPsdilGtevf 47 
                                       +r+ +tpd    d+  ++v+
  gi|313127300|ref|YP_004037570.1| 284 HRLVLTPDAQVNDVAKADVV 303
                                       67888888888888776665 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   1.5   4.8e-23   9.5e-20       2      72 ..     234     305 ..     233     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 4.8e-23
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeivee 72 
                                       +tr+++++ +gvs+r +++ ll+a+rA+A l gr++Vtp+Dvk++ p VLaHRl+  ++++ +++ + ++v++
  gi|313127300|ref|YP_004037570.1| 234 TTRNDRRVDVGVSPR-GTQRLLEASRARAVLSGREFVTPDDVKRVSPAVLAHRLVltPDAQVNDVAKADVVSD 305
                                       89*************.****************************************99999999999998876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   7.9e-17   1.6e-13       1     138 []      40     168 ..      40     168 .. 0.92
   2 ?   -1.4   0.0       1.1   2.1e+03      58      83 ..     257     283 ..     226     294 .. 0.65

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 7.9e-17
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vlL   pGtgK+  a+++a al+ ++  vq+t d+ ++d++g   ++  ++  +++++p+      + +++ DE++
  gi|313127300|ref|YP_004037570.1|  40 HVLLEDVPGTGKTLSARSVATALGLSFSRVQFTPDLLPSDVTGTNIFNerEQSFEFSEGPIF-----ANVVLADEIN 111
                                       6888889*************************************999988888999999999.....9********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra+++++++Ll  +ee ++   +g + +  k+      f viat np++  +  +l +a ++Rf
  gi|313127300|ref|YP_004037570.1| 112 RAPPKTQAALLEAMEEGQVT-VDGETHELPKP------FFVIATQNPVEsEGTFPLPEAQIDRF 168
                                       ********************.55555555666......99*********999999999999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                       -------G-.SEEEEESGGG--HHHHH CS
                             AAA_5  58 plvraareg.eilvlDEveraesevln 83 
                                       +  ra+ +g e +  D+v+r++++vl+
  gi|313127300|ref|YP_004037570.1| 257 SRARAVLSGrEFVTPDDVKRVSPAVLA 283
                                       444455544134555888888888875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.7e-09   5.4e-06       2     112 ..      42     152 ..      41     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.7e-09
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SS.....STTHHHHHHHHHHHHHHHTS.......TSEEEEE CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisg.sell.sk.....yvgesekkirelfkeakeka.......kpsilfi 64 
                                       ll   pGtGKTl a++va+ lg +f +++  ++ll s+     ++ e+e++                      +++ 
  gi|313127300|ref|YP_004037570.1|  42 LLEDVPGTGKTLSARSVATALGLSFSRVQFtPDLLpSDvtgtnIFNEREQS-----------FefsegpiFANVVLA 107
                                       67778*******************999986267774443332233333333...........12223334348**** PP

                                       ETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESSG CS
                               AAA  65 DEidalaksrsgseseeeervvnqLlteldgvkkk........eskvivigatnrp 112
                                       DEi +  ++            +++Ll+++++ +           ++++vi++ n +
  gi|313127300|ref|YP_004037570.1| 108 DEINRAPPKT-----------QAALLEAMEEGQVTvdgethelPKPFFVIATQNPV 152
                                       ******9999...........**********9999999999986668888887763 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   8.2e-08   0.00016      11     142 ..      27     150 ..      17     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.2e-08
                                       HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEH CS
                   Sigma54_activat  11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkG 87 
                                        le+i   + ++ +vl++   GtGK+l ar++ +a   +  + v++    +p+++  +++F  ++ +F  +e    G
  gi|313127300|ref|YP_004037570.1|  27 FLERIMLGVLSRGHVLLEDVPGTGKTLSARSVATALGLS-FSRVQFTPDLLPSDVTGTNIFNEREQSFEFSE----G 98 
                                       556666666777889999999999999999988766533.23456666677888888888888888886553....4 PP

                                       HHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  88 lfekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                        +      +++ Dei++ p+++Q+ Ll++++eg+v+  G+++e +  + +ia+ n
  gi|313127300|ref|YP_004037570.1|  99 PIF---ANVVLADEINRAPPKTQAALLEAMEEGQVTVDGETHELPKPFFVIATQN 150
                                       332...246888*******************************999887776544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0015       2.9      17      46 ..      33      62 ..      19      69 .. 0.78
   2 !    7.3   0.0    0.0014       2.8     109     160 ..     104     153 ..     100     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
                      Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlpsll 46
                                      + +  + ++ll   pG+GKt+ a+ +++ l
  gi|313127300|ref|YP_004037570.1| 33 LGVLSRGHVLLEDVPGTGKTLSARSVATAL 62
                                      555566789**************9988765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcp 160
                                       v++ DE+     k+  +L e +e+g+vt+   ++  e p  f ++a+ Np  
  gi|313127300|ref|YP_004037570.1| 104 VVLADEINRAPPKTQAALLEAMEEGQVTVDGETH--ELPKPFFVIATQNPVE 153
                                       6778*************************87665..56899********976 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   5.7e-05      0.11      34     114 ..      39     131 ..      34     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.7e-05
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaa..lltnleek..........dvlfideihrls 97 
                                        hvll   PG Gkt  a+ +a+ lg ++ ++  +P l  ++d+++  ++++ e++          +v++ dei r  
  gi|313127300|ref|YP_004037570.1|  39 GHVLLEDVPGTGKTLSARSVATALGLSFsRVQFTPDLL-PSDVTGtnIFNEREQSfefsegpifaNVVLADEINRAP 114
                                       6************************9973455567654.44444311555444322222223333788999999999 PP

                            RuvB_N  98 raveevlysamedfrld 114
                                       ++++  l  ame+ ++ 
  gi|313127300|ref|YP_004037570.1| 115 PKTQAALLEAMEEGQVT 131
                                       99999999999987765 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     7e-06     0.014     124     175 ..     104     153 ..      32     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7e-06
                                       EEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                               MCM 124 vcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                       v++ De+++   +++ al+EamE+ ++++   G +  L+    v+a  np++
  gi|313127300|ref|YP_004037570.1| 104 VVLADEINRAPPKTQAALLEAMEEGQVTVD--GETHELPKPFFVIATQNPVE 153
                                       8999***********************997..55688888888888888875 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.35       7     113 ..      42     135 ..      37     155 .. 0.66
   2 ?   -3.0   0.1       3.3   6.6e+03      86     101 ..     293     308 ..     288     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                       EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..........EEE CS
                             AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..........ivl 73 
                                       ll +  g+Gkt+ a+++a  l +    ++ r+  +  l      + v+   + ++  ++               +vl
  gi|313127300|ref|YP_004037570.1|  42 LLEDVPGTGKTLSARSVATALGL----SFSRVQFTPDLL----PSDVTGTNIFNEREQS----FefsegpifanVVL 106
                                       56666677777777777777776....677766666666....3333333333333222....22222357777*** PP

                                       EETGGG-------------HHHHHHHHHHHH--EE----- CS
                             AAA_2  74 lDEidKihpkessgadvSregVqrdLLqileggtltdkqg 113
                                        DEi ++ p             q +LL  +e+g++t   +
  gi|313127300|ref|YP_004037570.1| 107 ADEINRAPP-----------KTQAALLEAMEEGQVTVDGE 135
                                       *********...........99*************96655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.3
                                       -------HHHHHHHHH CS
                             AAA_2  86 sgadvSregVqrdLLq 101
                                       + +dv + +V+ d L 
  gi|313127300|ref|YP_004037570.1| 293 QVNDVAKADVVSDVLE 308
                                       5689999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1911.93
//
Query:       gi|313127301|ref|YP_004037571.1|  [L=177]
Description: hypothetical protein Hbor_25730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1198.20
//
Query:       gi|313127302|ref|YP_004037572.1|  [L=423]
Description: hypothetical protein Hbor_25740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-23   81.2   1.2    1.1e-22   80.1   1.2    1.6  1  DUF58        Protein of unknown function DUF58
    5.5e-10   39.4   1.8    8.2e-10   38.9   0.4    2.0  2  DUF11        Domain of unknown function DUF11
     0.0054   16.1   0.0     0.0085   15.5   0.0    1.2  1  TRAP_beta    Translocon-associated protein beta (TRAPB)
     0.0098   16.1   0.8      0.028   14.6   0.3    2.0  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
       0.17   12.1   0.1       0.39   11.0   0.1    1.6  1  CARDB        CARDB


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   1.2     3e-26   1.1e-22       1      86 []     194     281 ..     194     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 3e-26
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg..dekletavsaaaslar 75 
                                       gl+f+++ReY++gDpl+rIdW+  ARtge+ + ef +era+tv+l++d+++e++ ++++  ++++e++v+aa+    
  gi|313127302|ref|YP_004037572.1| 194 GLEFYSTREYRRGDPLNRIDWNRRARTGEMATLEFREERAATVVLLIDARSEAYVATDEgeQNAVERSVDAATRAFS 270
                                       689****************************************************999999**************** PP

                             DUF58  76 qlldegdrvgl 86 
                                       +lld+gdrvg+
  gi|313127302|ref|YP_004037572.1| 271 SLLDSGDRVGV 281
                                       *********96 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.4   2.3e-13   8.2e-10       1      80 [.      57     128 ..      57     133 .. 0.92
   2 ?   -2.6   0.0       1.9   6.9e+03      75      81 ..     164     170 ..     141     198 .. 0.54

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.3e-13
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvr 77 
                                       +t+  ++++++ G+ v++t+tv+N g+++++++++ D +P++l+   +sa+ g        + L +g+ at+s++v+
  gi|313127302|ref|YP_004037572.1|  57 ITRELSNQTPDTGEDVRVTVTVRNVGATPLTDLRLIDGVPPALEVTDGSARIG--------TALRPGKAATFSYSVE 125
                                       68889999*******************************************44........46*************9 PP

                             DUF11  78 vtr 80 
                                       + r
  gi|313127302|ref|YP_004037572.1| 126 AVR 128
                                       987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                             DUF11  75 tvrvtrt 81 
                                       t++  +t
  gi|313127302|ref|YP_004037572.1| 164 TPSLEAT 170
                                       3222222 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-06    0.0085      22      94 ..      57     126 ..      37     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                         TRAP_beta  22 vkKkilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvep 94 
                                       +  ++ n+ +  ged+ v++t+ NvG ++ +d++l D    + a ev  gs+ +    l pg+  ++s+ ve+
  gi|313127302|ref|YP_004037572.1|  57 ITRELSNQTPDTGEDVRVTVTVRNVGATPLTDLRLIDGV--PPALEVTDGSARIGT-ALRPGKAATFSYSVEA 126
                                       66789999****************************964..336788888777654.5788888888877775 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   7.9e-06     0.028       3      61 ..      68     126 ..      67     142 .. 0.90
   2 ?   -2.7   0.0         2   7.3e+03      34      66 ..     214     245 ..     213     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.9e-06
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtp 61 
                                        Ge+v++t+tv n g +++t+++l   +P+  +v+  s + +++l+pG+++++   V +
  gi|313127302|ref|YP_004037572.1|  68 TGEDVRVTVTVRNVGATPLTDLRLIDGVPPALEVTDGSARIGTALRPGKAATFSYSVEA 126
                                       599******************************9999999999*********9998876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                       NPCBM_assoc  34 WtvvevspasaaslapGetveatvkVtppagaa 66 
                                       W+ + + + ++a+l+  e+  atv + + a+ +
  gi|313127302|ref|YP_004037572.1| 214 WN-RRARTGEMATLEFREERAATVVLLIDARSE 245
                                       77.778888889999999999998887766655 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00011      0.39       2      36 ..      53      87 ..      52     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                      --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EE CS
                             CARDB  2 pDLtvtntlnpseafvgeentitvtvkNqGtaasg 36
                                      p L +t +l+ +++ +ge++++tvtv+N G    +
  gi|313127302|ref|YP_004037572.1| 53 PALDITRELSNQTPDTGEDVRVTVTVRNVGATPLT 87
                                      77899999*********************986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2976.50
//
Query:       gi|313127303|ref|YP_004037573.1|  [L=188]
Description: hypothetical protein Hbor_25750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1351.39
//
Query:       gi|313127304|ref|YP_004037574.1|  [L=310]
Description: hypothetical protein Hbor_25760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-11   42.0   1.4    2.1e-10   40.7   1.4    1.7  1  DUF4129   Domain of unknown function (DUF4129)


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   1.4   1.2e-14   2.1e-10       3      69 .]     233     299 ..     231     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.2e-14
                           DUF4129   3 rallraLaergldrrpgeTprEyarrvriapspaaalaalaelfeearYGgrpasaeeyrrlvealr 69 
                                       ra  ++ a   ++ + + Tp+E+a ++  a+  ++ +++l+ lfee+rYGg+ a+ +  +r+v alr
  gi|313127304|ref|YP_004037574.1| 233 RAWSEMTALLDIPNPQTSTPGEFASAAVDAGMTREDVDELTHLFEEVRYGGQSATTDREERAVTALR 299
                                       554455554499************99988899********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2091.99
//
Query:       gi|313127305|ref|YP_004037575.1|  [L=266]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.1   0.0    2.5e-10   40.3   0.0    1.4  1  DUF1724   Domain of unknown function (DUF1724)
     0.0068   16.9   0.1      0.019   15.5   0.0    1.8  2  HTH_27    Winged helix DNA-binding domain
     0.0079   16.1   0.0      0.014   15.2   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.03   14.2   0.0      0.064   13.1   0.0    1.6  1  HTH_5     Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   5.7e-14   2.5e-10       9      62 .]     203     256 ..     197     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 5.7e-14
                           DUF1724   9 eikplsltvtDkflslslfdkdgkydhk.dlisfdesAlkWGeeLFeyYlkrSep 62 
                                       +i  ++l+v++ ++ lsl + dg+yd + +li ++e+A  +G +LFe+++++++p
  gi|313127305|ref|YP_004037575.1| 203 DI-SFGLAVANGITFLSLPQLDGTYDPRtELIADSEAAAAFGDDLFEWFWRDATP 256
                                       45.789***********************************************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.1e-06     0.019       4      65 ..      19      71 ..      17      74 .. 0.90
   2 ?   -2.8   0.0       2.1   9.2e+03      56      66 ..     167     177 ..     160     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.1e-06
                            HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlT 65
                                       qa+vL l+    ++k+ ++lc +ln + s i  + + L  +G++e t+de      ++rlT
  gi|313127305|ref|YP_004037575.1| 19 RQAVVLALAS---EPKTTRELCTKLNASESGIYGATNNLRDNGVLEGTEDE------HFRLT 71
                                      5777887777...9************************************9......88888 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.1
                            HTH_27  56 drrekrvrlTd 66 
                                       d+r+ r+ +Td
  gi|313127305|ref|YP_004037575.1| 167 DDRPGRLLVTD 177
                                       77888888887 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.2e-06     0.014      18      56 ..      26      64 ..      21      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-06
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      l+++p+t++e+  +l+ ++s +Y + ++L d G+ e  +
  gi|313127305|ref|YP_004037575.1| 26 LASEPKTTRELCTKLNASESGIYGATNNLRDNGVLEGTE 64
                                      4799*****************************988665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.064       3      33 ..      18      48 ..      16      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHH CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvS 33
                                      tR  ++ +La+++++  el+ +l+ s+s + 
  gi|313127305|ref|YP_004037575.1| 18 TRQAVVLALASEPKTTRELCTKLNASESGIY 48
                                      78889**********************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1924.59
//
Query:       gi|313127306|ref|YP_004037576.1|  [L=587]
Description: na+ antiporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-58  197.8  38.0      3e-58  197.5  38.0    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
       0.13   12.7   0.7        1.2    9.6   0.1    2.2  2  STAT_int        STAT protein, protein interaction domain


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.5  38.0   3.3e-62     3e-58       4     380 ..      15     401 ..      12     402 .. 0.91

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 3.3e-62
                                       HHHHHHHHHHH.HHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHH CS
                    Na_H_Exchanger   4 lillallvgll.arrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksi 79 
                                       ++l+a  vg+l a+  ++p++++l++aG      gl  i+ + +  ++++ ++l++llF+ +  +d++e+r+n+  +
  gi|313127306|ref|YP_004037576.1|  15 VFLIAGGVGALlAKIGRVPYTIALLLAGFAASIAGLE-IDIT-LTHDIILLVVLPPLLFEGAATTDIDEFRSNFSVM 89 
                                       44445555666488888********************.8998.********************************** PP

                                       HHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCC CS
                    Na_H_Exchanger  80 lllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavav 156
                                       l la++g+++++v++G++     +lg++ll +llfg+i+ +tdpv vla++ ++   perl  l++ges+lnD+vav
  gi|313127306|ref|YP_004037576.1|  90 LTLATVGLAASIVVVGVVSTR--LLGYSLLLGLLFGTIILPTDPVSVLALF-KQVGAPERLSVLVEGESLLNDGVAV 163
                                       **************9997665..79**************************.************************* PP

                                       CCCHHHHHHTX.....XXXXTSSSTS......XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHH CS
                    Na_H_Exchanger 157 vllavllalak.....eeaggetsll......lllliflvvavgglllglvigwllrlitrftdddrelevllvlll 222
                                       v+++ llal++            +l+       l++ +++ a+gg ++gl+ g+l  ++ + + d+  +e++l+++l
  gi|313127306|ref|YP_004037576.1| 164 VIFSALLALVEagdsaA------DLAtlegiaELAGGIIFSAGGGAIVGLAAGYLIYRLMANL-DEHMTEIILTVVL 233
                                       **********5542222......22255566699999*****************998888886.************* PP

                                       HHHHHHHHHTS.XXXHHHHHHHHHHHHHHHHHHTTHHHH....HHHHHH...HHHHHHHHHHHHHHSXHHHHHXXHH CS
                    Na_H_Exchanger 223 allaallaell.gvsgilgaflaGlvlseyefsnklsek....lesfre...glfnplfFvlvGlsldlkvlnnhls 291
                                       a++a+l+ae+  +vsg+++ ++aGl++++ +++  +s +    + +++e    ++n+++F+l+G+++++  +   + 
  gi|313127306|ref|YP_004037576.1| 234 AYGAFLVAEHYlHVSGVIATVAAGLLIGNRGREYAMSPQtktaVFNTWEtaaYVVNTFIFLLLGVKTPIRQI---IA 307
                                       *********988****************555555555554444999999*******************9999...9* PP

                                       HHHHHHHHHHHHHTHHHHHHHHHTTTX......SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTC CS
                    Na_H_Exchanger 292 vlilvllilvaillgrilavflllrll......glslrealiigfgglqrgavalalaalgpalgllarelyalliv 362
                                          l+l ++v++l++r++av++l+ +       +++++ ++++++ggl  g++ +al++ +p +  + ++l  l+++
  gi|313127306|ref|YP_004037576.1| 308 EAELLLPAVVLVLVARAVAVYPLTEIAnrfsdaNVPRNYQHVLVWGGL-HGSIPIALVLGLPEAVGPRQQLRVLVFG 383
                                       *************************99*********************.***************9999999****** PP

                                       STSXHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 363 vvlftvlvqGlslkpllk 380
                                       ++ f++++qGls k +l+
  gi|313127306|ref|YP_004037576.1| 384 IAAFSLVIQGLSMKRFLR 401
                                       **************9987 PP

>> STAT_int  STAT protein, protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00013       1.2      72     121 ..     426     477 ..     402     479 .. 0.72
   2 ?    1.0   0.0     0.063   5.6e+02      47      81 ..     495     529 ..     485     547 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                          STAT_int  72 srlseeenflqklklre..iaknlqkkyqenPleLariikeiLeeEkkivqe 121
                                       ++  +e++ l + +l +  + +++q++y ++  eL ++i+++Le E  ++++
  gi|313127306|ref|YP_004037576.1| 426 DEALDESERLHERNLIRtdVYERFQREYGREKEELNTVIRDLLEAEPALLKQ 477
                                       33334555666666654116799************************99987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.063
                          STAT_int  47 pdnpedeslatalleelleeleekasrlseeenfl 81 
                                       +d + + +l+t+l+e+l+ e+++k  rl + e+ +
  gi|313127306|ref|YP_004037576.1| 495 TDAELSGQLSTELAEDLIAEVHQKQARLDRGETTV 529
                                       4666788999**************99998666333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3992.10
//
Query:       gi|313127307|ref|YP_004037577.1|  [L=31]
Description: hypothetical protein Hbor_25790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   13.5  10.2      0.062   12.9  10.2    1.3  1  PT        PT repeat


Domain annotation for each model (and alignments):
>> PT  PT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  10.2   3.5e-06     0.062       9      34 ..       3      28 ..       2      30 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-06
                                PT  9 qPTvqPTgqPtaqPTdqPtaqPtdaP 34
                                      +PT++ T  Pt++ Td Pt++ td P
  gi|313127307|ref|YP_004037577.1|  3 EPTDEVTDTPTDEVTDTPTDEVTDTP 28
                                      56666677777777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       103  (0.00574488); expected 358.6 (0.02)
Passed bias filter:                       45  (0.0025099); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.26s 00:00:00.56 Elapsed: 00:00:00.40
# Mc/sec: 235.42
//
Query:       gi|313127308|ref|YP_004037578.1|  [L=338]
Description: hypothetical protein Hbor_25800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2456.31
//
Query:       gi|313127309|ref|YP_004037579.1|  [L=108]
Description: hypothetical protein Hbor_25810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.1   0.1       0.29   11.2   0.1    1.5  1  PqqA      PqqA family


Domain annotation for each model (and alignments):
>> PqqA  PqqA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   1.6e-05      0.29       3      17 ..       5      19 ..       5      20 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.6e-05
                              PqqA  3 tkPkfvElrvGmEVT 17
                                      t P+ +++ v+mE+T
  gi|313127309|ref|YP_004037579.1|  5 TEPDAEDVQVSMEIT 19
                                      66************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 733.48
//
Query:       gi|313127310|ref|YP_004037580.1|  [L=474]
Description: subtilisin-like serine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-37  128.6   9.6    2.9e-37  128.6   9.6    1.8  2  Peptidase_S8     Subtilase family
  ------ inclusion threshold ------
      0.014   15.6   1.7      0.072   13.4   1.7    2.3  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.32   2.9e+03     146     194 ..      21      63 ..       5      87 .. 0.64
   2 !  128.6   9.6   3.2e-41   2.9e-37       1     284 [.     111     447 ..     111     458 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.32
                                       HHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 146 ainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayt 194
                                        +++  +++g+ vv S G ++        +  +g+ s  + v +v++++
  gi|313127310|ref|YP_004037580.1|  21 GVRKRLEREGFEVVKSIGDDS------VHLVIGGSKSAIQRVSGVKSAD 63 
                                       555556678888888888888......5666666666666666666666 PP

  == domain 2  score: 128.6 bits;  conditional E-value: 3.2e-41
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG..............................GGEETT-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................xxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag.............................fngadset 48 
                                       g+g  va++DtG++++hpdl  t + + kl+  +     g                             +++  +++
  gi|313127310|ref|YP_004037580.1| 111 GSGRRVAIIDTGIETDHPDLT-TATADGKLFRAD-----GissptgtptvagdttiqarlppeseeiesYTYLGAPK 181
                                       67888***************9.666667775333.....13345578899999999999999999988866666666 PP

                                       S-TT-SC-SSS....HHHHHHHHHH-B..SSSSSB-SSTTSEEE.........................EEE-SSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxx RF
                      Peptidase_S8  49 tstnwarddngnsieHGthvAGiaaanapeegekngvapgakil.........................svkvldts 100
                                         t+ a+dd ++s  HGth+AGi  +n   + ++ g ap+a+                              v  t 
  gi|313127310|ref|YP_004037580.1| 182 LRTQAAADD-VDS--HGTHCAGISTGNNTGTTGIAGMAPDAEAVplrvfywkkvenfpwdkdgdgeaeeH--VTVTT 253
                                       666666666.333..*****************************99******999999999999976332..33223 PP

                                       SB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH....HHHHHH.CCT-EEEEE--SS-T-HHEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 101 ggsmetgteliraieeaaedkvdvinmslgestslpktgrsieal....ainravnkkgvlvviSaGNngktgsslq 173
                                          ++t  ++++aie+a e ++d+ nmslg++  +++  +s e +    +i++av k+g++v +SaGN +   s+lq
  gi|313127310|ref|YP_004037580.1| 254 --LATTDFDILSAIEYAPETNADAANMSLGGGVIKGSAHKSGEHVayqtVIQNAV-KRGTVVTASAGNAS---SNLQ 324
                                       ..3444599999******************6666666666655557789******.9*************...5567 PP

                                       -TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-...CCCCCCCCCHHHTTTHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx....... RF
                      Peptidase_S8 174 agspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgn...ivstwsrqsnnsaglss....... 240
                                       +g  +  p +  +++++ a+ + ++ a +S+ G s d    +d+ apGg    + +t   ++       +       
  gi|313127310|ref|YP_004037580.1| 325 QGGYYTLPNSVPGAMSITATGPGNERAFYSNDGTS-D----VDVGAPGGGyetVEKTLAPDT-------Ewpyplnl 389
                                       8888888**************************97.4....9*******9554333333334.......23345556 PP

                                       ..............EEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE CS
                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 241 ..............yqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdl 284
                                                     y    GTSmA+P +ag +Al+++  p+lt+++v+ ++++tA+  
  gi|313127310|ref|YP_004037580.1| 390 vyssvpadlndgsqYAWYAGTSMAAPQVAGLVALVREVAPDLTAKQVQNVIERTARFS 447
                                       9999***************************************************754 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.7     8e-06     0.072      16      65 ..     309     354 ..     288     376 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8e-06
                   CarboxypepD_reg  16 gatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatre 65 
                                       g  Vt++      +as    + G+++l++  pg  s+t++ pG + a ++
  gi|313127310|ref|YP_004037580.1| 309 GTVVTAS----AGNASSNLQQGGYYTLPNSVPGAMSITATGPGNERAFYS 354
                                       4455555....678888889***********************9998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3401.74
//
Query:       gi|313127311|ref|YP_004037581.1|  [L=761]
Description: ATPase, type iv secretory pathway virb11 component like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-24   84.2   0.0    1.9e-23   82.9   0.0    1.6  1  T2SSE        Type II/IV secretion system protein
     0.0018   17.9   0.0     0.0029   17.1   0.0    1.3  1  AAA_7        P-loop containing dynein motor region
     0.0049   16.8   0.0     0.0092   15.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
     0.0093   15.7   0.0      0.018   14.8   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   16.2   0.0       0.02   15.4   0.0    1.3  1  AAA_23       AAA domain
      0.045   14.1   0.0       0.14   12.5   0.0    1.9  2  AAA_16       AAA ATPase domain
      0.048   13.8   0.0        0.3   11.2   0.0    2.3  2  AAA_33       AAA domain
       0.18   12.2   0.1       0.56   10.6   0.0    1.9  2  AAA          ATPase family associated with various cellular a


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   8.3e-27   1.9e-23      34     250 ..     370     594 ..     327     607 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 8.3e-27
                             T2SSE  34 ielreveelekaalerlisriaalakldiseerplqdarlp....ekgvrlrvvllPvvag..ealviRkksakelt 104
                                        +  ++++ ++     ++ ++aa+ + +++ +rp    +l     e+ +r  v +lPv+ +  ++++iRk+sa  +t
  gi|313127311|ref|YP_004037581.1| 370 RVPTNLAFEDETSFVNVVTQLAAADGVELNASRPSAKVNLRpegiEETIRCAV-ALPVISEggPHVSIRKQSADPMT 445
                                       45666777788889999***********************9986555555554.56777666999************ PP

                             T2SSE 105 lddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlna 181
                                         dl+   al  ++ ++l    +++ ++l+sG+Tg GKttl++a + +i+ +++ + + E ++E++l ++  ++l +
  gi|313127311|ref|YP_004037581.1| 446 PVDLVHLDALPIELVALLWMLYEHHRVVLFSGPTGVGKTTLMNAHMPFIPYDHRPVSIDEGSREVRLPHETGISLTT 522
                                       *********************9******************************9999999****************** PP

                             T2SSE 182 k.....kakvtfadllraaLRlrPDrimvGEiRdketlei.lkAvnTGHlgslsTlHansaagalerLeqlgaev 250
                                       +      ++v +adl+ +a  l+PD+ ++ E+    ++e   + +nTGH + ++T Ha++    ++r+ + g  +
  gi|313127311|ref|YP_004037581.1| 523 RdheseFKRVSMADLMTEANYLNPDVEVIAEVNTPASFETfAEVLNTGHGV-IGTTHAEDIETLVNRVVEQG--L 594
                                       *99998899******************************999*********.********999999987766..5 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-06    0.0029      24      55 ..     461     492 ..     456     504 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                             AAA_7  24 yllelllknkkpvllvGptGtGKtviikdllk 55 
                                        ll +l ++++ vl+ GptG+GKt++++  + 
  gi|313127311|ref|YP_004037581.1| 461 ALLWMLYEHHRVVLFSGPTGVGKTTLMNAHMP 492
                                       6788999********************98765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.1e-06    0.0092      99     122 ..     470     493 ..     448     523 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.1e-06
                                       TSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpe 122
                                       ++++++ G++GvGK+tL+na +p 
  gi|313127311|ref|YP_004037581.1| 470 HRVVLFSGPTGVGKTTLMNAHMPF 493
                                       48999**************98775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   7.8e-06     0.018      23      43 ..     470     491 ..     462     495 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.8e-06
                            AAA_29  23 g.atlltGpsGsGKSTllDAiq 43 
                                         ++l++Gp+G+GK+Tl+ A++
  gi|313127311|ref|YP_004037581.1| 470 HrVVLFSGPTGVGKTTLMNAHM 491
                                       3389**************9986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   9.1e-06      0.02      18      38 ..     469     489 ..     453     524 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.1e-06
                            AAA_23  18 skgltlItGpNGaGKTTildA 38 
                                       ++ ++l++Gp+G GKTT+++A
  gi|313127311|ref|YP_004037581.1| 469 HHRVVLFSGPTGVGKTTLMNA 489
                                       57899**************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       6.5   1.4e+04      93      93 ..     279     279 ..     251     329 .. 0.51
   2 ?   12.5   0.0   6.4e-05      0.14      25      43 ..     471     489 ..     458     534 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.5
                            AAA_16  93 e 93 
                                       +
  gi|313127311|ref|YP_004037581.1| 279 N 279
                                       1 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.4e-05
                            AAA_16  25 elvllsGesGvGKsslvre 43 
                                       ++vl+sG+ GvGK++l+++
  gi|313127311|ref|YP_004037581.1| 471 RVVLFSGPTGVGKTTLMNA 489
                                       78**************986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014       0.3       1      20 [.     472     491 ..     472     567 .. 0.88
   2 ?   -1.2   0.1      0.89     2e+03     103     126 ..     728     751 ..     699     757 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                            AAA_33   1 lvllvGlpGsGKstlaerll 20 
                                       +vl+ G+ G+GK+tl   ++
  gi|313127311|ref|YP_004037581.1| 472 VVLFSGPTGVGKTTLMNAHM 491
                                       89*************99998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.89
                            AAA_33 103 vvetdeetlkeRlakRaangddrs 126
                                       +++tde+   eR+++++a++ d++
  gi|313127311|ref|YP_004037581.1| 728 DLRTDEAATVERVRRQMAESADET 751
                                       456777777777777777765544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025      0.56       1      17 [.     473     489 ..     473     504 .. 0.93
   2 ?   -3.5   0.0       5.6   1.3e+04      76     114 ..     524     559 ..     518     562 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                                       EEEESSTTSSHHHHHHH CS
                               AAA   1 vllyGppGtGKTllaka 17 
                                       vl++Gp G+GKT+l++a
  gi|313127311|ref|YP_004037581.1| 473 VLFSGPTGVGKTTLMNA 489
                                       79************987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.6
                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGG CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdk 114
                                       ++ese+++  ++ L+te + ++    +v vi+  n+p +
  gi|313127311|ref|YP_004037581.1| 524 DHESEFKRVSMADLMTEANYLNP---DVEVIAEVNTPAS 559
                                       46777777777777777776666...5777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (761 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 5202.75
//
Query:       gi|313127312|ref|YP_004037582.1|  [L=636]
Description: flagella assembly protein j [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-22   77.8   2.9    3.3e-10   40.0   0.0    3.5  3  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0     0.062   1.1e+03      46      79 ..      90     127 ..      84     137 .. 0.79
   2 !   35.0   1.0   6.5e-13   1.2e-08       3     124 ..     157     284 ..     155     285 .. 0.87
   3 !   40.0   0.0   1.8e-14   3.3e-10       1     124 [.     420     552 ..     420     553 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.062
                                       SSHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-HHH CS
                             T2SSF  46 gslseale....rtpssefpelvvqlirageeggnLae 79 
                                        +++e++     r p + +p+l+  +++a+  gg +  
  gi|313127312|ref|YP_004037582.1|  90 VAFAESVVpfagRLPIPRIPRLFLGIVAAAAVGGAVKR 127
                                       5555666677778888899***************9865 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 6.5e-13
                                       HHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHHHH CS
                             T2SSF   3 rqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirageeg 74 
                                       r+l +l s+  +  + L+++a+++ +g+ a  l+++++  ++ g+++e l+     tp +   ++++  + + +++g
  gi|313127312|ref|YP_004037582.1| 157 RYLHVLASGSDGRRTMLRRVADTDAYGETAVSLRKALNTAAMTGNINEGLRrvarDTPAENTlAPFLLKFREHADQG 233
                                       6666666666677789***********************************77775555555588888888888887 PP

                                       T-.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  75 gn.LaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                       ++ L  +L+  +++l  +++++r+++  +le l++++++llvl++ll+i+l
  gi|313127312|ref|YP_004037582.1| 234 SDaLRNYLRMESRMLGHQQDRARRRAEGFLELLAEIFIVLLVLPALLVIIL 284
                                       6449*********************************************98 PP

  == domain 3  score: 40.0 bits;  conditional E-value: 1.8e-14
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.......SHH.HHHC.....T-TT.TS-HHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.......sls.eale.....rtpssefpelv 64 
                                       f++ ++ ++s G p+ ea+e++a+e e gpl++ ++++a +lr  +       +l+ +a       r +++   +++
  gi|313127312|ref|YP_004037582.1| 420 FVHAISGHVSLGRPFPEAVEHVAREVELGPLSDDVADLALNLRLTSpntgtdeDLRtAA-LdrfveRVGTPMAEQTI 495
                                       78999****************************************97666555444244.3588876666566**** PP

                                       HHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  65 vqlirageeggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                         +i a ++g++ + v+e l++++ + ++ +r l++ +l   ++++v++  +l++++i++
  gi|313127312|ref|YP_004037582.1| 496 GLVIGALDAGSDTGTVFETLQSEVGRLYHEKRALRSGML---VYVAVGWTTALLVVGITV 552
                                       ***************************************...777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 4156.36
//
Query:       gi|313127313|ref|YP_004037583.1|  [L=250]
Description: flagellin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0017   19.2   1.7     0.0036   18.2   1.7    1.6  1  Pilin_N       Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
       0.33   10.9   1.0       0.53   10.2   1.0    1.3  1  Borrelia_P13  Borrelia membrane protein P13


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.7   4.1e-07    0.0036       2      69 ..      16      87 ..      15     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.1e-07
                           Pilin_N  2 AVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgkna...vslehkgGdsidt 69
                                      A S ++Gv L++ +tv+ ++++ a ++ + ++ +++a+ +++   +d+  +tg+ a    +++ +gG +  t
  gi|313127313|ref|YP_004037583.1| 16 AQSAIVGVALLLGLTVVGIGILTAAAGTVvQEGASTAATTRVAGGLDDALDTGTAAeteATIRLSGGTMRVT 87
                                      6699*************************7777777777777555555555544445568999999876555 PP

>> Borrelia_P13  Borrelia membrane protein P13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.0   5.9e-05      0.53      29      71 ..      16      58 ..      14      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.9e-05
                      Borrelia_P13 29 vqGdyiGGglllGfdvlGlililaGvikaldgivkkaeaavis 71
                                      +q  ++G +lllG  v+G+++++a + +  +  +  a+++ ++
  gi|313127313|ref|YP_004037583.1| 16 AQSAIVGVALLLGLTVVGIGILTAAAGTVVQEGASTAATTRVA 58
                                      68899*****************998876666555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1660.76
//
Query:       gi|313127314|ref|YP_004037584.1|  [L=187]
Description: hypothetical protein Hbor_25860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0091   16.9   0.3      0.022   15.7   0.3    1.7  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   1.2e-06     0.022       1      45 [.      22      67 ..      22      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-06
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievk 45
                                      +A SpV+G  L + i+v+ +A++ +   g       +++ a++ ++
  gi|313127314|ref|YP_004037584.1| 22 RALSPVVGKALELGIVVLFIALVTTTFYGDvIPGYRTTAAAEVAER 67
                                      699********************99888775555666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1320.26
//
Query:       gi|313127315|ref|YP_004037585.1|  [L=224]
Description: hypothetical protein Hbor_25870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   13.5   0.0       0.13   12.1   0.0    1.7  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     7e-06      0.13      30      58 ..      84     111 ..      76     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-06
                                       EE-HHHH.CT----TT-EEEEEE-TT-TTE CS
                            eIF-1a  30 eipgkfR.nkiwikrGdyVlVelspydltk 58 
                                       ++++  R + i+i+ Gd VlVe    d++k
  gi|313127315|ref|YP_004037585.1|  84 RLAPSVRnRSIRIRLGDEVLVER--GDPEK 111
                                       6778899999************8..55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1680.66
//
Query:       gi|313127316|ref|YP_004037586.1|  [L=135]
Description: hypothetical protein Hbor_25880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 955.22
//
Query:       gi|313127317|ref|YP_004037587.1|  [L=164]
Description: hypothetical protein Hbor_25890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.47    9.2   2.4       0.69    8.6   2.4    1.2  1  Sulfate_transp  Sulfate permease family


Domain annotation for each model (and alignments):
>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.4   3.9e-05      0.69       5      25 ..       3      23 ..       2      26 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 3.9e-05
                    Sulfate_transp  5 liaGitvallaiPqalayall 25
                                      l+a+++va+ ++P+alaya+l
  gi|313127317|ref|YP_004037587.1|  3 LLAAVVVAVALVPMALAYAQL 23
                                      689****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1240.89
//
Query:       gi|313127318|ref|YP_004037588.1|  [L=361]
Description: serine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-07   31.3   0.3    6.8e-07   29.3   0.3    1.9  1  Trypsin    Trypsin
    1.2e-06   29.5   0.6    1.2e-05   26.3   0.1    2.5  2  Trypsin_2  Trypsin-like peptidase domain


Domain annotation for each model (and alignments):
>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.3   7.5e-11   6.8e-07      24     201 ..     165     330 ..     143     335 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 7.5e-11
                                       EEEEEEEEEETTEEEEEGGGTTTGGGEEEEESESBTTSCTTT.EEEEEEEE.EEEETTEBTTTTTTTEEEEEESSSS CS
                           Trypsin  24 khlCgGslisenwvlTAaHCvsnasdvkvvlgehnlkksegk.eqklkvek.vivhpnynpstldnDiallklkepv 98 
                                        +  +G+l++ n vlTA H+v    d ++++ +     ++g+    ++v   v   ++y+   +  D+a+lkl +p 
  gi|313127318|ref|YP_004037588.1| 165 AWSGTGALVGRNVVLTASHVVPW--DSDPWMMRFVPAYWDGSsRLGGSVNSyVQAYRGYENHSQGDDMAVLKLYTP- 238
                                       66779*****************8..55555555444444444122233333444456777777889**********. PP

                                       TSBSSBHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHH.HHHHHTTTTSTTTEEEEESTTSSS CS
                           Trypsin  99 klgdtvrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsre.tcksaykgkvtenmlcagakeggk 174
                                        lgdt   + + +  +s + g+  + +G++   ++g ++  + +  p+++++ +             +     e+ +
  gi|313127318|ref|YP_004037588.1| 239 -LGDTFGYFGYKTYHDSWEDGDYWTKVGYPGAVASG-QRPSRVTWYPIIDDDnDGAG----------VEL---EYRA 300
                                       .************88866777666666666655555.33334445788777422222..........222...3466 PP

                                       BCTTTTTTSEEEETTT...EEEEEEEEESS CS
                           Trypsin 175 dacqGDSGGPlvcsdg...elvGivswgkg 201
                                       d+  G SGGP++       ++vG +s+g++
  gi|313127318|ref|YP_004037588.1| 301 DSSGGGSGGPVFGWWSgspYVVGTHSGGEE 330
                                       9999*******95444458*******9964 PP

>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.09   8.1e+02      48      73 ..      60      84 ..      32     166 .. 0.55
   2 !   26.3   0.1   1.3e-09   1.2e-05       1     141 [.     168     312 ..     168     323 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.09
                         Trypsin_2 48 vvaadpelDlAllkvssderaglppl 73
                                      v ++d + D+A+ +v  +++ +++p+
  gi|313127318|ref|YP_004037588.1| 60 VARVDLDEDMAVGRV-GQAGEAVDPP 84
                                      555666668888888.3333333333 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.3e-09
                         Trypsin_2   1 GsGflvgsdglilTnaHvv................dsadgaavkaikkkveeagadgrevpakvvaadpelDlAllk 61 
                                       G+G lvg +  +lT+ Hvv                d          +    ++ +  +++++   +++ + D+A+lk
  gi|313127318|ref|YP_004037588.1| 168 GTGALVGRNV-VLTASHVVpwdsdpwmmrfvpaywD--------GSSRLGGSVNSYVQAYRGYENHSQ-GDDMAVLK 234
                                       8*********.********66555544444443331........333344455777777777777777.77****** PP

                         Trypsin_2  62 vssderaglpplplgp.sealkggepvyvvGyplggeksgsvssGivsgvvesesaasgegesflqtdaatspGsSG 137
                                       +    ++ +++   ++  ++ + g+  + vGyp+ + +       +v+ +    + ++      l++ a+ s+G+SG
  gi|313127318|ref|YP_004037588.1| 235 LYTPLGDTFGYFGYKTyHDSWEDGDYWTKVGYPGAVAS--GQRPSRVTWYPI-IDDDNDGAGVELEYRADSSGGGSG 308
                                       *666666677776666556999999*******866666..344445555444.33344455555599999999**** PP

                         Trypsin_2 138 Gplf 141
                                       Gp+f
  gi|313127318|ref|YP_004037588.1| 309 GPVF 312
                                       ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2547.64
//
Query:       gi|313127319|ref|YP_004037589.1|  [L=164]
Description: hypothetical protein Hbor_25910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1158.34
//
Query:       gi|313127320|ref|YP_004037590.1|  [L=520]
Description: Na+/proline symporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-46  157.7  37.8    4.9e-46  157.4  37.8    1.1  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.4  37.8   2.7e-50   4.9e-46       1     406 []      45     447 ..      45     447 .. 0.91

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 2.7e-50
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpd 73 
                                       + + g+s++ +vl+l++++   s+  fvG++ +v+  G   +++ + a l++++ ++lla+r+r       ++Tl+d
  gi|313127320|ref|YP_004037590.1|  45 FLITGKSIGTWVLALTAFSVIQSGFGFVGGPELVYSFGTTALWIFFTAPLGFIVTWVLLAKRMRlladIRDVMTLAD 121
                                       6789************************************************************9998899****** PP

                               SSF  74 ylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiq 150
                                        ++ R++++  ++ l  + +l+ ++++l+ +l +    ++ ++Gl +  +++++aa++ lY ++GG++A v+td +q
  gi|313127320|ref|YP_004037590.1| 122 GMFVRYESSW-MRGLTGVGVLIGVVAYLATNLAALQYVMRAIFGLPVIWGLFIGAAILLLYSMLGGMIAGVWTDFVQ 197
                                       **********.****************************************************************** PP

                               SSF 151 avlmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRfla 227
                                       a+ m+vg++++  ++l+  Gg+ ++ ++l++a+p +v  + + s         al  w+++ +G ag+ph + +f+ 
  gi|313127320|ref|YP_004037590.1| 198 ALTMIVGSVLVFAFALSFGGGMTNISQNLASADPALVSPFGAMSG-ATATIFVALGWWILFSIGAAGQPHLITKFYM 273
                                       ***************99989**************77555544442.334555567789******************* PP

                               SSF 228 akdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAa 304
                                         + k ++ g  ++ +  ++  ++++s +l   +++ a ++++ +  + + ++ p  v +  p ++aGl+la+ lAa
  gi|313127320|ref|YP_004037590.1| 274 SRNLKILRWGAPIAAVTYAVSSLLAFSTGLSMRAMVEA-GQTAAP--KSASVVGPVFVLEHTPGVVAGLILAALLAA 347
                                       ******************************99999998.665555..5678999*********************** PP

                               SSF 305 imstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasav 381
                                       imst +s l+++++a+++D+  ++ r  ++ ++el      + l    +a  l+v   +  v  l  + ++ +a+a+
  gi|313127320|ref|YP_004037590.1| 348 IMSTSDSFLNIGAAAVSRDIPRALGRPIEDDQTELR--VTQAALAGLTIASTLIVYYSDALVGILGTIGWGFFAAAF 422
                                       **************************9976666653..3345566777777777777777455666667******** PP

                               SSF 382 lavillalfwkrvneqGAlagliiG 406
                                       +a+  l+l wk ++++GA a++ iG
  gi|313127320|ref|YP_004037590.1| 423 FAIAALGLNWKGATREGAVAAIAIG 447
                                       ********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3276.59
//
Query:       gi|313127321|ref|YP_004037591.1|  [L=172]
Description: hypothetical protein Hbor_25930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1258.24
//
Query:       gi|313127322|ref|YP_004037592.1|  [L=268]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-15   55.0   0.0      9e-15   54.2   0.0    1.5  1  HTH_10          HTH DNA binding domain
     0.0014   18.8   0.1     0.0024   18.1   0.1    1.6  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13
  ------ inclusion threshold ------
      0.013   15.5   0.1      0.055   13.5   0.0    1.9  2  DNA_photolyase  DNA photolyase
      0.029   14.6   0.3       0.19   12.0   0.1    2.4  3  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.034   14.0   0.0       0.12   12.2   0.0    1.9  1  MarR_2          MarR family
      0.058   13.3   0.0       0.13   12.2   0.0    1.6  1  PuR_N           Bacterial purine repressor, N-terminal
      0.063   13.2   0.0       0.21   11.6   0.0    1.8  2  HTH_11          HTH domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   3.5e-18     9e-15       4      52 ..     174     222 ..     171     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 3.5e-18
                            HTH_10   4 kqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                        + e+l +A+++GYF++PR+++l  LA+e+++sk+++s+ Lr+ e+k++
  gi|313127322|ref|YP_004037592.1| 174 VEQETLSKAVKAGYFETPRDASLTTLAEEFDVSKTSVSKNLRRGEKKVL 222
                                       6889*******************************************97 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   9.2e-07    0.0024      32      65 ..     192     226 ..     149     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.2e-07
                           UPF0122  32 dDlSlsEiAeefnvsrqavydnikrtek.llekyE 65 
                                        D Sl+ +Aeef+vs+++v+ n++r ek +l +  
  gi|313127322|ref|YP_004037592.1| 192 RDASLTTLAEEFDVSKTSVSKNLRRGEKkVLGSVV 226
                                       699**********************9861455555 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.1e-05     0.055      41      97 ..      42      99 ..      25     103 .. 0.83
   2 ?   -1.0   0.1      0.61   1.6e+03      80     101 ..     225     246 ..     187     267 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                      G..S-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHCTECEEEEE-- CS
                    DNA_photolyase 41 l..rvgaarvdfllesLadLdeeLrelgirLvvrrgdpadvlpelakelgasavvanre 97
                                      +   v  a++  l e+L +L+e+   +g +L+ r+g++a v++++++e++a +v+ +++
  gi|313127322|ref|YP_004037592.1| 42 TriLVTGASRGALTEGLSSLKEQPGMRGFDLLSRQGESA-VIKSFIHETNAMRVIREHD 99
                                      245678899999************************986.6**********99987765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.61
                                       HHHHHHHCTECEEEEE---SHH CS
                    DNA_photolyase  80 lpelakelgasavvanreyepd 101
                                       ++e +++++ +a+++ re   +
  gi|313127322|ref|YP_004037592.1| 225 VVETLETIDETALTTGREKPHE 246
                                       3333333333444443333333 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.7   4.4e+03       6      13 ..     148     155 ..     146     168 .. 0.68
   2 ?   -1.0   0.0      0.84   2.2e+03      40      54 ..     176     190 ..     175     196 .. 0.84
   3 ?   12.0   0.1   7.3e-05      0.19      24      48 ..     195     219 ..     189     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
                                       HHHHHHHH CS
                    Fe_dep_repress   6 tEdYLetI 13 
                                        EdYL ++
  gi|313127322|ref|YP_004037592.1| 148 LEDYLDVV 155
                                       57787765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.84
                                       HHHHHHHHHTTSEEE CS
                    Fe_dep_repress  40 semlkkLekdGyvey 54 
                                       +e+l+k  k+Gy e+
  gi|313127322|ref|YP_004037592.1| 176 QETLSKAVKAGYFET 190
                                       68999999****887 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 7.3e-05
                                       -HHHHHHHHTS-HHHHHHHHHHHHH CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVsemlkkLek 48 
                                       + + lae+ +vs+ sVs+ l++ ek
  gi|313127322|ref|YP_004037592.1| 195 SLTTLAEEFDVSKTSVSKNLRRGEK 219
                                       6789****************99666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.9e-05      0.12      19      47 ..     191     219 ..     186     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                                       TSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  19 grdltvgelarrlglsksavsrilkrLva 47 
                                       +rd + + la+++++sk +vs+ l+r ++
  gi|313127322|ref|YP_004037592.1| 191 PRDASLTTLAEEFDVSKTSVSKNLRRGEK 219
                                       5688999******************9666 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.2e-05      0.13      21      42 ..     194     215 ..     182     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.2e-05
                             PuR_N  21 isltyfaerfeaAKSsiSeDla 42 
                                        slt++ae+f+++K+s+S  l+
  gi|313127322|ref|YP_004037592.1| 194 ASLTTLAEEFDVSKTSVSKNLR 215
                                       69****************9876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.9   7.5e+03       6      18 ..      92     104 ..      89     105 .. 0.79
   2 ?   11.6   0.0   8.1e-05      0.21      13      36 ..     191     214 ..     185     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.9
                            HTH_11   6 lelLleargpisg 18 
                                       ++ ++e++g+i+g
  gi|313127322|ref|YP_004037592.1|  92 MRVIREHDGYITG 104
                                       5678899999998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.1e-05
                            HTH_11  13 rgpisgeeLAeeLnvSrrtvrrdI 36 
                                         + s  +LAee++vS++ v + +
  gi|313127322|ref|YP_004037592.1| 191 PRDASLTTLAEEFDVSKTSVSKNL 214
                                       4558999*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1800.93
//
Query:       gi|313127323|ref|YP_004037593.1|  [L=291]
Description: hypothetical protein Hbor_25950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-36  124.5   0.5      7e-36  124.0   0.5    1.2  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.1e-31  109.9   0.3    1.4e-31  109.5   0.3    1.1  1  adh_short     short chain dehydrogenase
     0.0017   18.3   0.4      0.003   17.5   0.4    1.4  1  KR            KR domain
      0.009   15.9   0.3      0.015   15.2   0.3    1.4  1  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do
  ------ inclusion threshold ------
      0.025   14.0   0.4      0.037   13.5   0.4    1.2  1  Epimerase     NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   0.5   1.9e-39     7e-36       1     234 []      40     287 ..      40     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 1.9e-39
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTT..SEE..EE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelg..aev..lecDVtdeeqvealveevvekfgklDil 73 
                                       Ga sgIGra+A a+a++G +v++td++ e+  +++e a+e++   +v  +e+D +d++++e +ve+++++ g++ +l
  gi|313127323|ref|YP_004037593.1|  40 GAGSGIGRATALACAANGLTVAATDVDGEGLTDTQEKAAEHDlsGTVvtVEADLADDDELEGIVETAADH-GTVRYL 115
                                       889***************************7777777777664344459****************98765.9***** PP

                                       EE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC....CEEEEEEEGGGTSBSTTTTHHHHHHH CS
                      adh_short_C2  74 vnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg....gsivnlssvgaervvpnynaygaaKa 146
                                        n ag  +    p++e++ e++d ++dv l++ ++l+k ++p+++++    g + n++sv+++ v+ +   y+++K 
  gi|313127323|ref|YP_004037593.1| 116 ANVAGLQHI--DPIEEFPMEQYDLMHDVMLRAPLYLSKLVVPHIRATddgvGVVGNMASVHGHYVTGDKVGYNVSKF 190
                                       ********9..*******************************6665556799999********************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEE--BHCTG.GGGSTTHHH.........HHHHHHHHSTTSS-B-HHHHHHHHHH CS
                      adh_short_C2 147 alealtrylAvelgpkgiRvNavspgpikTla.asgikgfde.........lleelearaplgrlgtpeevaeaalf 213
                                       +l +lt+++A+e      R  +vs g++kT++ +++i+++ e         +++ +  ++  ++++tp eva++ +f
  gi|313127323|ref|YP_004037593.1| 191 GLRGLTQSIAAEGDG-SLRSFSVSTGYVKTPLvTNQIPDTAEqrgisvdevIENVMLGQSRTKEMMTPGEVANLFVF 266
                                       ************766.9**************98888998444344433333566666777888999*********** PP

                                       HCSGGGTT--SEEEEESTTGG CS
                      adh_short_C2 214 LasdeasyitGqtlvvDgGlt 234
                                        +s++a+  +G +l  DgG+t
  gi|313127323|ref|YP_004037593.1| 267 GFSKHAKHLNGGDLRFDGGMT 287
                                       *******************98 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.3   3.9e-35   1.4e-31       1     190 [.      34     225 ..      34     230 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 3.9e-35
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHH CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkkl 75 
                                       +v+++tGa+sGIGra+a ++a++G +v+++d   e l  + ++  e+  + +++++++D++d +e+e +ve+a +++
  gi|313127323|ref|YP_004037593.1|  34 NVAVITGAGSGIGRATALACAANGLTVAATDVDGEGLTDTQEKAAEHdlSGTVVTVEADLADDDELEGIVETA-ADH 109
                                       69*****************************************9999999**********************9.889 PP

                                       SSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH..HCTTEEEEEEEEGGGTSB-TTBHHHH CS
                         adh_short  76 gkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml..kqssGrIvnvsSvagkvpvagvaaYs 150
                                       g++  L n AG+++  p++e+  e+++ + +v l +++ l+++v+p++   +   G + n++Sv+g++     + Y 
  gi|313127323|ref|YP_004037593.1| 110 GTVRYLANVAGLQHIDPIEEFPMEQYDLMHDVMLRAPLYLSKLVVPHIRatDDGVGVVGNMASVHGHYVTGDKVGYN 186
                                       ***********************************************8888999999******************** PP

                                       HHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 151 AsKaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                        sK++++glt+s+a e   +  r  +v +G+v+T++++++
  gi|313127323|ref|YP_004037593.1| 187 VSKFGLRGLTQSIAAEGDGS-LRSFSVSTGYVKTPLVTNQ 225
                                       ****************9997.**************99876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.4   8.4e-07     0.003       3     109 ..      36     139 ..      34     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.4e-07
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        +itG+  g+G+++a   a++g + ++ +  +++   d +++ ae      +v +v+aD++d d++e ++e++  ++
  gi|313127323|ref|YP_004037593.1|  36 AVITGAGSGIGRATALACAANGLT-VAATDVDGEGLTDTQEKAAEHDL-SGTVVTVEADLADDDELEGIVETAA-DH 109
                                       58*************999999864.55555665666666666665544.446778899*************997.67 PP

                                       S---EEEE---------TTT--HHHHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvl 109
                                       ++++   + Ag+ + +++ee  +e+++ + 
  gi|313127323|ref|YP_004037593.1| 110 GTVRYLANVAGLQHIDPIEEFPMEQYDLMH 139
                                       7*************9999999998887655 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   4.3e-06     0.015       2      56 ..      35      92 ..      34     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.3e-06
                                      EEEE.--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH.HHHCCTTTTSS- CS
                           3HCDH_N  2 vavi.GaGt.mGagiaavfasagleVvlvdiseealekalekiek.sleklvekgklk 56
                                      vavi GaG  +G+  a ++a++gl+V  +d++ e l++ +ek+++  l+  v   +++
  gi|313127323|ref|YP_004037593.1| 35 VAVItGAGSgIGRATALACAANGLTVAATDVDGEGLTDTQEKAAEhDLSGTVVTVEAD 92
                                      66665999769***********************999999888775565555444444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4     1e-05     0.037       2      76 ..      37     120 ..      36     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHH.T-SEEE CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkee.qpdavi 69 
                                       ++tGa   iG+a++ a++++g +v + d + ++    +++ +          ve+dl d+++le ++++  +  +v 
  gi|313127323|ref|YP_004037593.1|  37 VITGAGSGIGRATALACAANGLTVAATDVDGEGLTDTQEKAAehdlsgtvVTVEADLADDDELEGIVETAaDHGTVR 113
                                       79*************************9986655544444446778**9999************9999765555555 PP

                                       E--S--- CS
                         Epimerase  70 hlAavgg 76 
                                        lA v+g
  gi|313127323|ref|YP_004037593.1| 114 YLANVAG 120
                                       5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1899.15
//
Query:       gi|313127324|ref|YP_004037594.1|  [L=148]
Description: ester cyclase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-27   93.6   0.3    8.9e-27   93.4   0.3    1.0  1  SnoaL     SnoaL-like polyketide cyclase
    3.3e-22   79.0   0.7    4.5e-22   78.6   0.7    1.3  1  SnoaL_2   SnoaL-like domain
  ------ inclusion threshold ------
      0.044   14.0   0.0      0.053   13.8   0.0    1.2  1  SnoaL_3   SnoaL-like domain


Domain annotation for each model (and alignments):
>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.3   1.5e-30   8.9e-27       4     125 ..      19     140 ..      16     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1.5e-30
                                       HHHHHHHHHTT-HHHHHGTEEEEEEETCCTT.TCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEE CS
                             SnoaL   4 lrfyeevwnsgdldaldelvaedvvdhnpee.eparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftG 79 
                                       +r+y e+  +g l+a+de++ae+vv h + + e+++G+e+fr+++++  + f+ ++ve++d+va+ d  a+r+t++G
  gi|313127324|ref|YP_004037594.1|  19 IRRYHEI-TEGGLAAADEVLAEEVVVHGAFDgEETHGIEAFRERLTDIHDSFSGFSVEIHDIVAQADGGASRWTVSG 94 
                                       5899999.999******************99********************************************** PP

                                       EESSEBTTBE-TT-EEEEEEEEEEEEETTEEEEEEEEECHHHHHHH CS
                             SnoaL  80 thtgeflGipptGkkvkfeeitllrvedGkIveewdviDllgllrQ 125
                                       t+++++ Gi p G + +  +i ++r+edGkIve wd +D  ++l+Q
  gi|313127324|ref|YP_004037594.1|  95 TFEEPYDGIEPDGERKTNPGISMFRFEDGKIVEIWDREDTHSALQQ 140
                                       *********************************************9 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.7   7.5e-26   4.5e-22       5     101 ..      22     127 ..       6     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 7.5e-26
                                       HHHHHTTCHHHHHHTEEEEEEEEET..TSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE... CS
                           SnoaL_2   5 laalnagdldalaalfapdvvwedp..ggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt... 76 
                                       ++ +++g l+a+++++a++vv++++  g e++G+ea+r+ ++  +++f+++ +eihd+va+ d  a +wtv+gt   
  gi|313127324|ref|YP_004037594.1|  22 YHEITEGGLAAADEVLAEEVVVHGAfdGEETHGIEAFRERLTDIHDSFSGFSVEIHDIVAQADGGASRWTVSGTfee 98 
                                       5567899******************95555*********************************************** PP

                                       ....EETTSSEEEEEEEEEEEEETTEEEE CS
                           SnoaL_2  77 ....ipatgrgvtvrgvdvfrvrdGkive 101
                                           i+++g++ t++g+++fr++dGkive
  gi|313127324|ref|YP_004037594.1|  99 pydgIEPDGERKTNPGISMFRFEDGKIVE 127
                                       ****************************9 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.9e-06     0.053      12      73 ..      25      86 ..      17     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.9e-06
                           SnoaL_3 12 aaegdfdalfalwaddivfigtgadelltgreevrrslkqifakgegisfeltdvrvtesgd 73
                                      ++eg ++a  +++a+++v  g  ++e  +g e++r+ l +i + + g+s e++d+ ++++g 
  gi|313127324|ref|YP_004037594.1| 25 ITEGGLAAADEVLAEEVVVHGAFDGEETHGIEAFRERLTDIHDSFSGFSVEIHDIVAQADGG 86
                                      567788999**********************************************9998763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1094.06
//
Query:       gi|313127325|ref|YP_004037595.1|  [L=468]
Description: Na+/proline symporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-30  106.7  35.5    7.4e-30  104.1  35.5    2.1  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1  35.5   4.1e-34   7.4e-30       1     406 []      37     417 ..      37     417 .. 0.85

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 4.1e-34
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGla.GavaasGlavvllelgalllvlllllllaerlrnagalTlpdyls 76 
                                       ++lagr l+ + ++ +l a+ ++++s+ G    +++ +Gl  ++l+    l+ + +l++l  r r + ++T+p++l 
  gi|313127325|ref|YP_004037595.1|  37 FMLAGRGLGTVIIAGTLLATWMGSGSITGSTnSLAYSYGLWPAVLSGTSALVGIGVLWFLSSRIRGYDKYTIPEILG 113
                                       78***************************8626799****999999877777777788999**************** PP

                               SSF  77 kRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavl 153
                                          +++   + +  +++ ++ +  +s ++ g +  ++ + G+ +et+ l++aal++++  +GGl++v ytd i a+l
  gi|313127325|ref|YP_004037595.1| 114 DGIGKEA--KAIGLVTIAAAYVGIVSYQFTGFGFVLNVTTGIPVETGTLIGAALIIILATTGGLMSVAYTDAISALL 188
                                       ***9998..9999999999999******************************************************* PP

                               SSF 154 mlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRflaakd 230
                                       m vg+++ l + l+++Gg+e++++++ + +p     lt+ +      +l     w+  +l +   + + +R++a  +
  gi|313127325|ref|YP_004037595.1| 189 MAVGLIVGLPFILSSAGGVETVTSNVSS-SP--FGSLTGLQ------FLG---YWAPALLLILADQNMYQRIVAGGS 253
                                       ********************99987665.44..24444444......444...44444444567899********** PP

                               SSF 231 akailkgvlkltivlilvligmis.iilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaim 306
                                        ++  +g+  +++++++ +  +i+ +i fa+       +   ++  ++ +a++  +  ++p ++ G+lla++ A ++
  gi|313127325|ref|YP_004037595.1| 254 NEETDHGI--GIWFIGVAVTSTIIpVIAFAA-------RSLFPD-IEPGMAMIA-MTTVIPTWIGGILLAAAAAFVI 319
                                       *****996..566777766665531333333.......333333.467788887.6789****************** PP

                               SSF 307 stltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavla 383
                                        t ts llsas+ +++DlY  ++  + a++k++ ++ r++v+v+++ a++l + ++    l l  la    ++ +++
  gi|313127325|ref|YP_004037595.1| 320 TTGTSYLLSASTNISQDLYRGFINPN-ASDKQVFWMTRVTVVVLGAFAFVLGQYFPTI--LSLQMLAYTAYGATITP 393
                                       **************************.*************************999976..88888888888887776 PP

                               SSF 384 villalfwkr..vneqGAlagliiG 406
                                         l+a+f  r  +++ G  +g+++G
  gi|313127325|ref|YP_004037595.1| 394 -ALFAVFLMRghLTKLGGVSGMVAG 417
                                       .478888876558999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3369.92
//
Query:       gi|313127326|ref|YP_004037596.1|  [L=245]
Description: hypothetical protein Hbor_25980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1946.47
//
Query:       gi|313127327|ref|YP_004037597.1|  [L=185]
Description: hypothetical protein Hbor_25990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1394.89
//
Query:       gi|313127328|ref|YP_004037598.1|  [L=257]
Description: septum site-determining protein mind [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.4e-18   64.7   0.0    1.4e-17   63.9   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    3.1e-12   46.8   0.0    4.5e-12   46.2   0.0    1.2  1  AAA_31       AAA domain
    7.2e-12   45.3   0.4    2.2e-06   27.3   0.4    2.4  2  ParA         NUBPL iron-transfer P-loop NTPase
    4.1e-08   33.0   0.0    7.2e-05   22.4   0.0    2.0  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    8.4e-06   25.4   0.0    1.3e-05   24.8   0.0    1.2  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
      3e-05   23.4   0.9     0.0052   16.0   0.8    2.1  2  ArsA_ATPase  Anion-transporting ATPase
    0.00052   19.4   2.1     0.0077   15.5   2.1    2.0  1  MipZ         ATPase MipZ
    0.00061   19.7   0.3     0.0094   15.8   0.0    2.5  2  AAA_26       AAA domain
  ------ inclusion threshold ------
      0.027   14.2   0.0      0.037   13.8   0.0    1.2  1  AAA_24       AAA domain
      0.043   13.4   2.8       0.11   12.0   2.8    1.8  1  AAA_25       AAA domain
      0.052   12.8   0.5      0.082   12.2   0.5    1.3  1  VirC1        VirC1 protein
      0.079   12.1   0.1       0.12   11.6   0.1    1.2  1  PIF1         PIF1-like helicase
       0.24   11.1   2.0       0.24   11.1   0.2    1.9  2  AAA_30       AAA domain
       0.35    9.8   0.3        0.5    9.3   0.3    1.1  1  AAA_6        Hydrolytic ATP binding site of dynein motor regi


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   1.1e-20   1.4e-17       2     127 ..       6     213 ..       5     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.1e-20
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       a+as+kGG+GKTt +++L+ ala+  ++V ++DaD+ + nl    gl     +                        
  gi|313127328|ref|YP_004037598.1|   6 AVASGKGGTGKTTSTLALGMALAE-TYDVTVIDADTGMANLLFHTGLDDADVTlhdllveghdasvedavydrfgms 81 
                                       89**********************.*************999854444444444999********************* PP

                                       ....................................................................CCHCCCHHH CS
                                       ....................................................................xxxxxxxxx RF
                              CbiA  55 ....................................................................dlkrllell 63 
                                                                                                           d  ++ e +
  gi|313127328|ref|YP_004037598.1|  82 vvpcgtslaafeaadparlrevvaelaadtdvllldspaalgsksavlpvvladrvvvvlqptvpslsDGLKVQEYA 158
                                       *******************************************************9999999888888666777788 PP

                                       HHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  64 ealgkkkalllkiagvvlnrvdgeneetllkealeelkqry.gvpvlgviprdeavaeapargep 127
                                       ++ g++       agv++nrv++++ ++++ e+      ry g   l+++p+++av  a   gep
  gi|313127328|ref|YP_004037598.1| 159 RSYGTE------TAGVLFNRVRPDEDTENIAEQA----SRYfGGTTLASVPESDAVRAARRAGEP 213
                                       777766......79*********95555555444....4555**************888777776 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   3.5e-15   4.5e-12       4     154 ..       5     148 ..       2     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.5e-15
                            AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQ.anattglgiekneiektlyevli..eeknikeaiiktk 77 
                                        a+a  KGG GKTT++++l++ala++ + v ++D+D+  an+ +++g+  ++++ tl+++l+  +++++++a++  +
  gi|313127328|ref|YP_004037598.1|   5 FAVASGKGGTGKTTSTLALGMALAET-YDVTVIDADTGmANLLFHTGL--DDADVTLHDLLVegHDASVEDAVY--D 76 
                                       589999******************86.779******962688888887..566679***997567899999999..5 PP

                            AAA_31  78 venldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLgllt.enaLvasdsviipvqaeaya 153
                                          ++++p  ++La++e           +l+e++ ++  + D+ ++D p +Lg    +  +v +d v++++q++  +
  gi|313127328|ref|YP_004037598.1|  77 RFGMSVVPCGTSLAAFEAA------DPARLREVVAELAADTDVLLLDSPAALGSKSaVLPVVLADRVVVVLQPTVPS 147
                                       5678**********99864......567899*********************98651567999*********98766 PP

                            AAA_31 154 l 154
                                       l
  gi|313127328|ref|YP_004037598.1| 148 L 148
                                       5 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.4   1.7e-09   2.2e-06       5      42 ..       4      40 ..       1      69 [. 0.87
   2 !   15.4   0.0   7.2e-06    0.0093     111     245 ..     110     234 ..      99     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.7e-09
                              ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDi 42
                                       +av+SgKGG GK+t +  l +aLa + ++v ++DaD 
  gi|313127328|ref|YP_004037598.1|  4 AFAVASGKGGTGKTTSTLALGMALA-ETYDVTVIDADT 40
                                      579*********************7.579********5 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.2e-06
                              ParA 111 elDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekte 187
                                       + D+L++D P   g  +  v+  +  + +v+V  p   +l+d  k  e +++  ++  Gv+ N    v p+ + +  
  gi|313127328|ref|YP_004037598.1| 110 DTDVLLLDSPAALGSKSA-VLPVVLADRVVVVLQPTVPSLSDGLKVQEYARSYGTETAGVLFNR---VRPDED-T-- 179
                                       68*********9998775.55556689*********************************9885...444422.2.. PP

                              ParA 188 ifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                          ++ +e++++ +g ++l+++p + ++r a  +g+pl++++pe++aa+a+ e a+++
  gi|313127328|ref|YP_004037598.1| 180 ---ENIAEQASRYFGGTTLASVPESDAVRAARRAGEPLLAHAPEDPAADAFYEAAANL 234
                                       ...3557899999**************************************9988765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0007      0.89       6      53 ..       9      53 ..       4      96 .. 0.65
   2 !   22.4   0.0   5.6e-08   7.2e-05     164     244 ..     153     234 ..     101     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0007
                         Fer4_NifH  6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqe 53
                                       GkGG Gk+t++  l +alae+   v ++  D  +  ++ll+++ + +
  gi|313127328|ref|YP_004037598.1|  9 SGKGGTGKTTSTLALGMALAETYD-VTVIDAD--TGMANLLFHTGLDD 53
                                      59******************9865.5555444..44455666655444 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 5.6e-08
                         Fer4_NifH 164 giekyaksggvrlgGliinsrkvddereliek.faeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyre 239
                                        +++ya+s g + +G++ n  + d+++e i +   +  g   l+ vP ++ vr a+ + + +  +ape + a+ + e
  gi|313127328|ref|YP_004037598.1| 153 KVQEYARSYGTETAGVLFNRVRPDEDTENIAEqASRYFGGTTLASVPESDAVRAARRAGEPLLAHAPEDPAADAFYE 229
                                       489****************87778777766550556789************************************99 PP

                         Fer4_NifH 240 larki 244
                                        a ++
  gi|313127328|ref|YP_004037598.1| 230 AAANL 234
                                       99876 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0     1e-08   1.3e-05      10     149 ..      11     145 ..       3     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1e-08
                          CBP_BcsQ  10 RGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqre.gwaraeldgapwrqa.aleyapgldllPf 84 
                                       +GG+G+t+ + aL++al e  + v viD+ +  + +l F++ +++++ ++   +++g++ +   a+  + g++++P 
  gi|313127328|ref|YP_004037598.1|  11 KGGTGKTTSTLALGMALAET-YDVTVIDADT-GMANLLFHTGLDDADvTLHDLLVEGHDASVEdAVYDRFGMSVVPC 85 
                                       7****************875.6777887654.455555666666554167777778777654403444679****** PP

                          CBP_BcsQ  85 GelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrel.laladlvllvvepda 149
                                       G+  ++ +      a+++ +l + ++el+++ + +llD pa   +    l + lad+v+ v++p +
  gi|313127328|ref|YP_004037598.1|  86 GTSLAAFE------AADPARLREVVAELAADTDVLLLDSPAALGSKSAVLpVVLADRVVVVLQPTV 145
                                       *7544433......478999*********************76555444325669*******9975 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.8     4e-06    0.0052       5      35 ..       7      36 ..       3      43 .. 0.82
   2 !    5.3   0.0    0.0075       9.6     209     254 ..     137     182 ..     131     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4e-06
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvlli 35
                                      + +GKGG GKtt+  a+++ l+e+     +i
  gi|313127328|ref|YP_004037598.1|  7 VASGKGGTGKTTSTLALGMALAETYDV-TVI 36
                                      679*******************97544.444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0075
                                       EEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCSSSTS CS
                       ArsA_ATPase 209 frlVvipEklslkEteRaikeLkkygikvdavivNkllpeeeqenC 254
                                       +++V++p   sl +  +  ++  +yg ++  v+ N++ p+e++en 
  gi|313127328|ref|YP_004037598.1| 137 VVVVLQPTVPSLSDGLKVQEYARSYGTETAGVLFNRVRPDEDTENI 182
                                       78999999*********************************99864 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.1     6e-06    0.0077       5     127 ..       7     139 ..       3     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6e-06
                                       E--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EE............E- CS
                              MipZ   5 lgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpea............la 69 
                                       ++  kGG+Gk+t ++ + +aL+++   v++id d+  + l  + +   a ++ ++l ++  +a             +
  gi|313127328|ref|YP_004037598.1|   7 VASGKGGTGKTTSTLALGMALAET-YDVTVIDADTGMANLLFHTGLDDADVTLHDLLVEGHDAsvedavydrfgmSV 82 
                                       7889****************9875.89*******9988776665555555555555444433300100001111012 PP

                                       SSS-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS-.-HHHHHHHHT-SEEEE CS
                              MipZ  70 lseaeeaeveeeeeaevaeleelvadleaeldfividtPGsd.salsrlahsladtlvt 127
                                       ++ +  +++   e a+ a+l+e+va+l+a++d++++d+P    s+ + l   lad +v 
  gi|313127328|ref|YP_004037598.1|  83 VPCG--TSLAAFEAADPARLREVVAELAADTDVLLLDSPAALgSKSAVLPVVLADRVVV 139
                                       2222..2334445566679********************76413344455667777765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.26   3.3e+02       5      30 ..       7      31 ..       3      42 .. 0.77
   2 !   15.8   0.0   7.3e-06    0.0094     130     197 ..     136     207 ..      84     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.26
                            AAA_26  5 vtgtdtgvGKTvvslgLvralkrkgv 30
                                      v++   g GKT+ +l+L  al ++++
  gi|313127328|ref|YP_004037598.1|  7 VASGKGGTGKTTSTLALGMAL-AETY 31
                                      677777899999999999888.5555 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 7.3e-06
                            AAA_26 130 pvilVargglgtinqllltiealrqknvrvlGvilNkvrnpenvetlekksgi....pvlGvvPylpdleap 197
                                        v++V++++  ++ + l   e++r+ + + +Gv +N+vr++e+ e++ ++ +     + l++vP ++ ++a+
  gi|313127328|ref|YP_004037598.1| 136 RVVVVLQPTVPSLSDGLKVQEYARSYGTETAGVLFNRVRPDEDTENIAEQASRyfggTTLASVPESDAVRAA 207
                                       69999999999***************************9998666666665533455*******99988775 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.9e-05     0.037       8      44 ..       9      51 ..       5     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                            AAA_24  8 yGpsgiGKTtlakel......gpkplfidtekGlksldadkfp 44
                                       G+ g+GKTt+ + l      ++++ +id + G+++l ++ + 
  gi|313127328|ref|YP_004037598.1|  9 SGKGGTGKTTSTLALgmalaeTYDVTVIDADTGMANLLFHTGL 51
                                      599********999999******************99888765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.8   8.8e-05      0.11      34     107 ..       4      78 ..       2     126 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                            AAA_25  34 elallaGapgtGKttlaldlalavatGkpwlg.pvapeqgkVlyvsaEdsedelrrRlravgealrddarllvld 107
                                       ++a+  G +gtGKtt +l l+ a+a+   ++  +  +  ++ l+  + d++d +   l   g++++  + ++   
  gi|313127328|ref|YP_004037598.1|   4 AFAVASGKGGTGKTTSTLALGMALAETYDVTViDADTGMANLLFHTGLDDADVTLHDLLVEGHDASVEDAVYDRF 78 
                                       688999*****************9965555444444455555555555555555555555556664444444444 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   6.4e-05     0.082       5      39 ..       6      39 ..       2      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.4e-05
                             VirC1  5 tfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                      +++s kGG+Gktt+ ++l  ala     v++ +ad
  gi|313127328|ref|YP_004037598.1|  6 AVASGKGGTGKTTSTLALGMALAET-YDVTVIDAD 39
                                      67999**************999865.568888888 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   9.1e-05      0.12      28      69 ..       9      50 ..       3      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-05
                                      EESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC.TS CS
                              PIF1 28 tGsgGtgKtflwkallkklrsegkivlavAssGvAalllegG 69
                                      +G gGtgKt    al  +l ++ ++++  A +G+A ll + G
  gi|313127328|ref|YP_004037598.1|  9 SGKGGTGKTTSTLALGMALAETYDVTVIDADTGMANLLFHTG 50
                                      7*************************************9998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00019      0.24      20      77 ..       5      62 ..       2     127 .. 0.76
   2 ?   -1.2   0.1       1.1   1.4e+03      40      64 ..     205     229 ..     201     250 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakll 77
                                      +av+ G  GtGKtt+  al  a+++     ++ A tg a     ++l+ +  t++ ll
  gi|313127328|ref|YP_004037598.1|  5 FAVASGKGGTGKTTSTLALGMALAETYDVTVIDADTGMANLLFHTGLDDADVTLHDLL 62
                                      68999**********9999777776633344557777776556666666666777776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                            AAA_30  40 eaweaaggrviglAptgkaAkvLae 64 
                                       +a+++ag+++++ Ap+  aA++  e
  gi|313127328|ref|YP_004037598.1| 205 RAARRAGEPLLAHAPEDPAADAFYE 229
                                       5566666677777777777665443 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.3   0.00039       0.5      35      66 ..       6      37 ..       2      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00039
                             AAA_6 35 gapaGpagtGKtEtvkdLakalakqvvvfncs 66
                                      +  +G  gtGKt ++  L+ ala++  v+ ++
  gi|313127328|ref|YP_004037598.1|  6 AVASGKGGTGKTTSTLALGMALAETYDVTVID 37
                                      56789******************987666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1541.98
//
Query:       gi|313127329|ref|YP_004037599.1|  [L=227]
Description: hypothetical protein Hbor_26010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.17   12.5   0.0       0.25   11.9   0.0    1.3  1  Elf-1_N     Transcription factor protein N terminal


Domain annotation for each model (and alignments):
>> Elf-1_N  Transcription factor protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.4e-05      0.25      71     111 .]      79     119 ..      61     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                           Elf-1_N  71 eeqeietedvelaveasvhgsvecsdktieAaeaLLnmesp 111
                                       +e    t++ve+   +   ++++++  t+eA ea+L +esp
  gi|313127329|ref|YP_004037599.1|  79 NEGGCRTRTVETPDCKVGGDREHAFRYTVEAGEAILAVESP 119
                                       5555667777774444444599******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1900  (0.105974); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                       176  (0.0098165); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1420.49
//
Query:       gi|313127330|ref|YP_004037600.1|  [L=61]
Description: hypothetical protein Hbor_26020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 480.92
//
Query:       gi|313127331|ref|YP_004037601.1|  [L=223]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-15   54.9   0.2    8.8e-15   54.2   0.2    1.4  1  HTH_10         HTH DNA binding domain
    1.2e-08   35.0   0.1    1.8e-08   34.4   0.1    1.2  1  BAT            GAF and HTH_10 associated domain
    0.00011   21.7   0.0    0.00024   20.6   0.0    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0037   17.3   0.0      0.013   15.5   0.0    2.0  2  HTH_3          Helix-turn-helix
     0.0076   16.3   0.0      0.015   15.3   0.0    1.5  1  Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix do
  ------ inclusion threshold ------
       0.01   15.3   0.1      0.025   14.1   0.1    1.6  1  Sigma70_r4     Sigma-70, region 4
      0.035   14.0   0.1       0.12   12.3   0.1    2.0  1  MarR_2         MarR family
      0.041   13.7   0.1       0.11   12.3   0.1    1.8  1  HTH_8          Bacterial regulatory protein, Fis family
      0.051   13.7   0.2       0.24   11.6   0.3    2.0  2  HTH_28         Helix-turn-helix domain
       0.07   13.0   1.0       0.14   12.0   0.1    1.9  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.12   12.1   0.0       0.12   12.1   0.0    2.3  4  Sigma70_r4_2   Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.2   5.4e-18   8.8e-15       1      52 [.     160     211 ..     160     212 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 5.4e-18
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+ q e+l+ Ay++ Y+d PR ++ k+LA+elGIs++++  +Lr+  ++li
  gi|313127331|ref|YP_004037601.1| 160 LTPEQAEALRRAYKSEYYDDPRGIDQKALAEELGISRQAFASRLRRGYRNLI 211
                                       9*********************************************999998 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1   1.1e-11   1.8e-08       7     143 ..       6     148 ..       5     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.1e-11
                               BAT   7 eleirdeddvlvalaae.ldcrveleglvprsdgevlvfftvdgadpee....vrdaaedldavedvrvvseeddgt 78 
                                       e+++  +d++l ++ ++  ++++el+++vp  d++v+ +f+v+   +++    +r+ ++ l    ++ +++e +d+ 
  gi|313127331|ref|YP_004037601.1|   6 EFTLPAPDFPLGRIFERwPEATLELDRVVP-NDDTVMPYFWVTVPNADGdlaaIREEFDGLAELRSAVLMEELGDKG 81 
                                       678888888898875542799*********.6889*****9998554444444999999999999999********* PP

                               BAT  79 lleltvsgp..slastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarre 143
                                       l++++++ +   ++++++  G+tv sa+ + +++++ ++  + ++  ++  +++e+  +v+L +  +
  gi|313127331|ref|YP_004037601.1|  82 LFRAEWEPEymGIMRAISVTGVTVLSATGSADGWTFELRAMEAEQFSQFHHYCTEHDINVTLARLSQ 148
                                       *****9544224566***************************************9999999987666 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.5e-07   0.00024      13      40 ..     177     205 ..     174     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.5e-07
                            HTH_24  13 qknpr.isqreLAerlglSpstvnrrlkr 40 
                                       +++pr i q+ LAe+lg+S+++   rl+r
  gi|313127331|ref|YP_004037601.1| 177 YDDPRgIDQKALAEELGISRQAFASRLRR 205
                                       689999*********************98 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.9   3.1e+03      25      39 ..     148     163 ..     139     173 .. 0.50
   2 !   15.5   0.0   8.2e-06     0.013       7      25 ..     180     198 ..     175     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
                                       HHHHHHTT.SSCSBHH CS
                             HTH_3  25 tisriEnG.ernPsle 39 
                                       ++s    G e   ++e
  gi|313127331|ref|YP_004037601.1| 148 QLSEATTGsEYDLTPE 163
                                       3333344444445555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 8.2e-06
                                       HTTHHHHHHHHHHTSSHHH CS
                             HTH_3   7 qlglsqeeLAeklGvsrst 25 
                                        +g++q+ LAe+lG+sr++
  gi|313127331|ref|YP_004037601.1| 180 PRGIDQKALAEELGISRQA 198
                                       68**************986 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.5e-06     0.015      14      53 ..     184     220 ..     182     223 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.5e-06
                                       SCHHHHCCTT--HHHHHHHHHSSS--HHHHHHHHHHH--- CS
                     Phage_CI_repr  14 mqkeLAdlLgiakssvstwvrRdffPgdvvvtcaletdts 53 
                                       +qk+LA++Lgi+++ ++ + rR++     +++c l +dt+
  gi|313127331|ref|YP_004037601.1| 184 DQKALAEELGISRQAFASRLRRGY---RNLIRCTLIRDTR 220
                                       589*******************98...7788888888875 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.5e-05     0.025       5      48 ..     160     210 ..     159     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L++++ e l+  +        +g  ++ ++e+lgiSr +  ++++r+ r+L
  gi|313127331|ref|YP_004037601.1| 160 LTPEQAEALRRAYkseyyddPRGIDQKALAEELGISRQAFASRLRRGYRNL 210
                                       99**************998888999**************999999999887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.2e-05      0.12       3      44 ..     160     205 ..     158     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.2e-05
                                       --HHHHHHHHHHHCTTTS....EEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2   3 ltpaqarvLaaLgrrpgr....dltvgelarrlglsksavsrilkr 44 
                                       ltp qa +L   + ++ +     + +++la++lg+s++a   +l+r
  gi|313127331|ref|YP_004037601.1| 160 LTPEQAEALRRAYKSEYYddprGIDQKALAEELGISRQAFASRLRR 205
                                       5555555555555555335444679**************9999987 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.9e-05      0.11      21      41 ..     185     205 ..     182     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHHTS-HHHHHHHHHH CS
                             HTH_8  21 kskAArlLGisRrtLyrKLkk 41 
                                       +++ A++LGisR+ +  +L++
  gi|313127331|ref|YP_004037601.1| 185 QKALAEELGISRQAFASRLRR 205
                                       7889*************9997 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.7e+03      20      38 ..     156     174 ..     151     182 .. 0.86
   2 ?   11.6   0.3   0.00014      0.24      14      36 ..     184     207 ..     163     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                            HTH_28  20 relgisrrtvyrWikryee 38 
                                        e+ +++++   ++++y +
  gi|313127331|ref|YP_004037601.1| 156 SEYDLTPEQAEALRRAYKS 174
                                       5789999999999999976 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
                            HTH_28  14 svreaArelgisrrtv.yrWikry 36 
                                        ++++A+elgisr+   +r+++ y
  gi|313127331|ref|YP_004037601.1| 184 DQKALAEELGISRQAFaSRLRRGY 207
                                       6899***********955555555 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.1   3.4e+03      22      33 ..     142     153 ..     140     155 .. 0.77
   2 ?   12.0   0.1   8.9e-05      0.14      21      40 ..     186     205 ..     183     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.1
                     HTH_AsnC-type  22 eLAervGlSest 33 
                                        LA+   lSe+t
  gi|313127331|ref|YP_004037601.1| 142 TLARLSQLSEAT 153
                                       688888899887 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.9e-05
                     HTH_AsnC-type  21 aeLAervGlSestvlrRvrr 40 
                                       ++LAe++G+S+++ + R+rr
  gi|313127331|ref|YP_004037601.1| 186 KALAEELGISRQAFASRLRR 205
                                       79****************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.2   3.6e+03       3      19 ..      57      73 ..      55      77 .. 0.76
   2 ?   -3.5   0.0       5.4   8.8e+03      22      28 ..     144     150 ..     141     154 .. 0.47
   3 ?   -3.3   0.1       4.8   7.7e+03      11      20 ..     160     169 ..     160     172 .. 0.72
   4 ?   12.1   0.0   7.1e-05      0.12      28      54 .]     184     210 ..     182     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.2
                                      HHHHHHTTS-HHHHHHH CS
                      Sigma70_r4_2  3 alrealaeLperqreif 19
                                      a+re  + L e +++++
  gi|313127331|ref|YP_004037601.1| 57 AIREEFDGLAELRSAVL 73
                                      78888888888888877 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.4
                                       HHTS--- CS
                      Sigma70_r4_2  22 rylegls 28 
                                        +l +ls
  gi|313127331|ref|YP_004037601.1| 144 ARLSQLS 150
                                       4444443 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.8
                                       S-HHHHHHHH CS
                      Sigma70_r4_2  11 Lperqreifl 20 
                                       L+++q e++ 
  gi|313127331|ref|YP_004037601.1| 160 LTPEQAEALR 169
                                       7888888875 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 7.1e-05
                                       -HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArkkL 54 
                                       ++k  Ae+lgis ++  srl+R+ + L
  gi|313127331|ref|YP_004037601.1| 184 DQKALAEELGISRQAFASRLRRGYRNL 210
                                       57889*****************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1642.22
//
Query:       gi|313127332|ref|YP_004037602.1|  [L=513]
Description: NADH dehydrogenase subunit f [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-22   79.4   0.6    4.5e-22   77.9   0.5    1.9  2  NADH_4Fe-4S   NADH-ubiquinone oxidoreductase-F iron-sulfur bi
    3.9e-12   46.3   0.0      6e-12   45.7   0.0    1.3  1  Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subu
     0.0013   18.6   0.1      0.006   16.4   0.1    2.2  2  SLBB          SLBB domain
  ------ inclusion threshold ------
      0.081   12.8   0.0       0.21   11.5   0.0    1.7  1  ADH_N         Alcohol dehydrogenase GroES-like domain


Domain annotation for each model (and alignments):
>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.5   1.1e+04      64      83 ..     236     255 ..     234     256 .. 0.82
   2 !   77.9   0.5     1e-25   4.5e-22       7      85 .]     422     497 ..     417     497 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHHHHHH CS
                       NADH_4Fe-4S  64 gdsaanpvlsalrkFreefe 83 
                                       g +aa+ +  a  ++r+e+ 
  gi|313127332|ref|YP_004037602.1| 236 GSMAAERLSAAASRYRDEYG 255
                                       77888889999999999986 PP

  == domain 2  score: 77.9 bits;  conditional E-value: 1e-25
                                       HHHHHHH--S--HHHHIIIIHHHHHHHHHTBT---HHHHHHHHHHHHHHSS--SSTHHHHHHHHHHHHHHHHHHHHH CS
                       NADH_4Fe-4S   7 lefyaaesCGkCtpCreGtkrllelleriaagegteedldlleelaetikgtslCalgdsaanpvlsalrkFreefe 83 
                                       ++f+++e+CG+C+pCreGt++l +ll++i ag+ +    d+l+el++t+++ts C +g+saa+ v++a+  F++efe
  gi|313127332|ref|YP_004037602.1| 422 ARFASEENCGRCVPCREGTTQLTDLLRDIYAGDYD---DDTLRELTRTMRNTSTCDFGRSAARTVETAMAAFEAEFE 495
                                       79******************************998...489************************************ PP

                                       H. CS
                       NADH_4Fe-4S  84 ah 85 
                                       ah
  gi|313127332|ref|YP_004037602.1| 496 AH 497
                                       98 PP

>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   1.3e-15     6e-12       2     150 ..     154     315 ..     153     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.3e-15
                      Complex1_51K   2 keagivGrGGa....gfPthvKlkakakkkk.kylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgv 73 
                                       ++ g+ GrG +      P++  + +++k++  ++l+vNa+  +   ++D +l++ ++  +++++ ++a++++ae ++
  gi|313127332|ref|YP_004037602.1| 154 HRIGLLGRGRGdaraDRPVAEGWATARKTDGdTVLVVNANDADERNRTDSTLVEGDAGGVVDAAMAVAHLVEAEDVI 230
                                       66778777753223378**********97668999****************************************** PP

                      Complex1_51K  74 igvrdekpeaiealekalaeakaaglldievvklagkYpaGeekaLiesltgr.evprg.kpp..advgv.....vv 141
                                       ++ +     a+e+l++a++  +++     +v+ ++++Y+aGe ++ +esl+g+ +++++ +pp   + g+     v+
  gi|313127332|ref|YP_004037602.1| 231 MYAQTG-SMAAERLSAAASRYRDEYGDAPQVAVGPERYIAGEPTMALESLEGNdRLEARlRPPgpETHGLygrptVI 306
                                       **9988.7889999999999887554889************************855444255565666667777777 PP

                      Complex1_51K 142 nNveTlaav 150
                                       +   Tl++v
  gi|313127332|ref|YP_004037602.1| 307 HTPRTLLQV 315
                                       777777766 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.9   8.5e+03      19      37 ..      22      40 ..      20      42 .. 0.82
   2 !   16.4   0.1   1.3e-06     0.006       1      25 [.     336     360 ..     336     366 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                                      T-BHHHHHHTTT-SBSS.. CS
                              SLBB 19 gttlsdlieqaGGltddad 37
                                       t +s ++++a   t++a 
  gi|313127332|ref|YP_004037602.1| 22 RTDVSAVVDAAREATETAT 40
                                      6889999999999999886 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.3e-06
                                       EEEEESSBSS-EEEEEETT-BHHHH CS
                              SLBB   1 vVtVtGeVkrPgnyevpigttlsdl 25 
                                       vVtVtG+V  P ++e++ g++l+ +
  gi|313127332|ref|YP_004037602.1| 336 VVTVTGDVDSPATVELTTGAPLRAA 360
                                       7*********************987 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.7e-05      0.21      40      81 ..     402     444 ..     370     475 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.7e-05
                                       EEEEEEESTT-CS.--TT-EEEE-SEEE-SSSHHHHTT-GGG- CS
                             ADH_N  40 vGeveevgpevkk.lkvGdrVvvepliscgeCaaCkegeenlC 81 
                                        G+ve +g++     +vG+r       +cg+C  C+eg ++l 
  gi|313127332|ref|YP_004037602.1| 402 EGVVELFGDDRCAlATVGSRARFASEENCGRCVPCREGTTQLT 444
                                       4889999966544389**********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3679.77
//
Query:       gi|313127333|ref|YP_004037603.1|  [L=82]
Description: hypothetical protein Hbor_26050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 599.45
//
Query:       gi|313127334|ref|YP_004037604.1|  [L=606]
Description: aldehyde:ferredoxin oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-89  298.3   0.0    1.1e-88  297.8   0.0    1.2  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
      4e-62  209.6   0.0    5.7e-62  209.1   0.0    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.8   0.0   1.3e-92   1.1e-88      10     382 .]     223     601 ..     214     601 .. 0.89

  Alignments for each domain:
  == domain 1  score: 297.8 bits;  conditional E-value: 1.3e-92
                                       HHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE.... CS
                            AFOR_C  10 iksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrevkveeg 86 
                                       + ++  + ++lr+ GT e++++a+e+g+lpt+ ++ g+f+++++++ ea++     ++ + +s     + ++++e +
  gi|313127334|ref|YP_004037604.1| 223 FSREG-PGEWLRAGGTLETIDFADEMGVLPTRGWESGSFDGVDDVGIEAVQAAAVAREYDDVSVVSDGRGDFRIEVS 298
                                       44444.5559****************************************996555554455555556666666655 PP

                                       ...ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-T CS
                            AFOR_C  87 kk.vkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgda 162
                                       ++  + ++p+   + +lG+ l idd++a+++l  +cd+lG+D+isaG+++a+am++  +Gll++      +l+fgda
  gi|313127334|ref|YP_004037604.1| 299 DEqKPESVPRGAAPISLGAGLAIDDFDAVATLGATCDRLGVDVISAGTAVAWAMRAADEGLLER------DLSFGDA 369
                                       5534499*******************************************************98......99***** PP

                                       HHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-.................GGG--EETTEE--SS-GGG-HHHHHH CS
                            AFOR_C 163 eallellekiAkreg.igdllAeGvkrlaeklga.................eelamhvkGlelpaydprgakgmala 221
                                       + + +l+ +iA+r+g ++d+lA+Gv ++a+++g                    l+ +vk + lp ydprg+++mala
  gi|313127334|ref|YP_004037604.1| 370 ASAQALVSRIARRDGeLADTLADGVDAAANRFGNderrshtsaqqtpsgdgDSLVPTVKSMALPSYDPRGSPAMALA 446
                                       *********************************445677888889999998************************** PP

                                       HHH-TTSS-SGGG-THHHH.S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT-- CS
                            AFOR_C 222 YatsnrGacHlrayliale.ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGid 297
                                       Yats+rGacH ra ++  e  ++++ ++e +a++v+  q ++a+++sl++ +f+ e    +  +  a++lsa +G+d
  gi|313127334|ref|YP_004037604.1| 447 YATSDRGACHRRARPVVEEvFATEEWSPERRAAAVAEEQITRAVLWSLVVDDFAGE----VIRDYGASWLSA-VGLD 518
                                       ***************99998777788889**************************2....333446666666.9*** PP

                                       --HHHHHHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---H CS
                            AFOR_C 298 vteeellkaGeRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtk 374
                                       +t+ el+++GeR+++l+Rlfn+reG++r+dd lp+ l+  p+ +g ++g    + +e+ ld+yY + GWde+G+Pt+
  gi|313127334|ref|YP_004037604.1| 519 YTPAELRRVGERVWTLTRLFNVREGFDRDDDALPDILT-RPQVQGGHDGLDR-EAFERTLDAYYDRLGWDEDGRPTP 593
                                       *************************************9.7888888887663.55********************** PP

                                       HHHHHCT- CS
                            AFOR_C 375 etlkrLgL 382
                                       +  +rLg+
  gi|313127334|ref|YP_004037604.1| 594 DLCERLGI 601
                                       ******97 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.1   0.0   6.3e-66   5.7e-62       2     197 ..      11     203 ..      10     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 209.1 bits;  conditional E-value: 6.3e-66
                                       EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE- CS
                            AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaks 78 
                                       ++lrvdLs+g+++  +lp+e+ ++++Gg+glaa+ll+++++pg+dplsp+n++++a Gpl+g+ apg  r++vv+ks
  gi|313127334|ref|YP_004037604.1|  11 RLLRVDLSDGTVTHDSLPAEWRRQFVGGKGLAARLLYEKLDPGTDPLSPSNVVILALGPLSGI-APGEDRFAVVTKS 86 
                                       78************************************************************9.************* PP

                                       TTTSSEEEEEEETCHHHHHHHCT-S..EEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTSEEE CS
                            AFOR_N  79 PltgtlgesnaGgrfgaelkraGyd..aivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgdkva 153
                                       Pl+gt+ +s+aGg+f + l+ a  d   + ieG+a++p+ lvied+++++e  +d wgldt et++++       va
  gi|313127334|ref|YP_004037604.1|  87 PLSGTFLDSYAGGSFPPTLAGALPDhlLVAIEGQADEPTRLVIEDGDARLER-SDCWGLDTVETDDRVDG----AVA 158
                                       ***********************99556789*******************99.89*************98....79* PP

                                       EE-HHHHTT-TTB-E.EE.TTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 154 viGpaGenlvrfAsisvd.dgraagrgGlGavmgsKnlkaivvrg 197
                                       +iGpaGenlvr+A+++ d  +++agrgG+Gav+gsK+lk +v+rg
  gi|313127334|ref|YP_004037604.1| 159 CIGPAGENLVRYATLASDgGDHHAGRGGVGAVFGSKQLKSVVARG 203
                                       ***************88887789********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 4022.78
//
Query:       gi|313127335|ref|YP_004037605.1|  [L=559]
Description: adenosylcobyric acid synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-41  142.2   0.0    2.3e-41  141.6   0.0    1.3  1  GATase_3     CobB/CobQ-like glutamine amidotransferase domain
    3.6e-22   78.8   0.0    8.3e-22   77.6   0.0    1.6  2  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    5.9e-17   62.2   0.0    1.1e-09   38.4   0.0    2.2  2  AAA_26       AAA domain
     0.0046   16.3   0.1      0.055   12.7   0.0    2.4  2  DUF1611      Domain of unknown function (DUF1611_C) P-loop do
     0.0089   15.8   0.0      0.017   14.9   0.0    1.4  1  DJ-1_PfpI    DJ-1/PfpI family
  ------ inclusion threshold ------
       0.16   11.2   0.0       0.57    9.5   0.0    1.9  3  CTP_synth_N  CTP synthase N-terminus
       0.17   11.7   0.0       0.31   10.9   0.0    1.3  1  SNO          SNO glutamine amidotransferase family
       0.22   11.0   0.1        0.5    9.8   0.1    1.5  2  ParA         NUBPL iron-transfer P-loop NTPase


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.0     1e-44   2.3e-41       1     195 [.     299     508 ..     299     509 .. 0.83

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 1e-44
                          GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                       +iav+rlp++sn tdl+pL+aep vrv++vp  d +l + ad+v+lpG+k+t++dl + re gl + ++e++   gp
  gi|313127335|ref|YP_004037605.1| 299 TIAVPRLPRVSNATDLEPLAAEPGVRVEYVP-LDADLSS-ADAVVLPGSKNTADDLRACREAGLHDRLHEFS---GP 370
                                       69*****************************.9999*66.******************************87...8* PP

                          GATase_3  78 vlgiCGGlqmLGeeiedpegvegeag..eveglglLdietefekekltgqvegevel....aaegeevkGyEiHsGr 148
                                       ++g CGG+q+LGe++++  g e+ +g  e++g glL++et+f+ ek++  v+ + +      +   +v+GyEiH G+
  gi|313127335|ref|YP_004037605.1| 371 IVGLCGGYQLLGERLRNV-GAESVRGgdELPGFGLLPVETRFSTEKRVAPVRWRFDGtgpfDEFAGTVSGYEIHTGE 446
                                       ***************997.677855557********************999999777986533349**********9 PP

                          GATase_3 149 tilkekakpllkvkv..ggn.....ng......ekdGavk...ksedgnvlGtYlHglfdnrn 195
                                       t+l ++a++l   +   +        g       +dG      + ++g+vlGtYlHglf+n++
  gi|313127335|ref|YP_004037605.1| 447 TSLVADADTLSGADAspN-AdtlsdAGtpvapfVADGRADatlGIARGRVLGTYLHGLFENDE 508
                                       999999999998877542.23455411455667555555200023456************987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.0   3.7e-25   8.3e-22       1     116 [.      18     267 ..      18     275 .. 0.95
   2 ?   -3.3   0.0         4   8.9e+03      31      55 ..     328     377 ..     318     415 .. 0.61

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 3.7e-25
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i++a+t + vGK+t+aa+L r+la+rg+ V++++a++++nn++        i+p                       
  gi|313127335|ref|YP_004037605.1|  18 ILVAGTASHVGKSTVAAGLSRLLADRGFSVAPFKAQNMSNNARA-----VPIAPavagssaerggdagdadtvtdaa 89 
                                       79***************************************994.....44444555566667778888888***** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|313127335|ref|YP_004037605.1|  90 fgeigvsqyvqaraarvtpttdhnpvllkprgegesqlvvngrpagnhaasdyyeegwhrardaaeaaharlgrqhd 166
                                       ***************************************************************************** PP

                                       .....................................CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS... CS
                                       .....................................xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx RF
                              CbiA  55 .....................................dlkrllellealgkkkall.....lkiagvvlnrvdgene 89 
                                                                            d++r ++++++l+++++l       +iag v+++++g+  
  gi|313127335|ref|YP_004037605.1| 167 vviaegagsiaeinlhhrdlanvettrfadadvllvaDIER-GGVFASLVGTLELVpddvrDRIAGAVITKFRGD-- 240
                                       *****************************************.**********9988*******************.. PP

                                       -TTCHHHHHHHHHHCTS-EEEEEE--C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  90 etllkealeelkqrygvpvlgviprde 116
                                       e ll+++l+  ++r+gvpvlgv+p+d+
  gi|313127335|ref|YP_004037605.1| 241 ESLLSDGLDAFEERTGVPVLGVLPYDD 267
                                       *************************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4
                                       EEEEEEESSCCCCHHTTEB-HHHH.........................C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.........................x RF
                              CbiA  31 llvDaDpqannlaileglendiep.........................d 55 
                                       +++DaD  +  + +l g++n  +                          +
  gi|313127335|ref|YP_004037605.1| 328 VPLDADLSSADAVVLPGSKNTADDlracreaglhdrlhefsgpivglcgG 377
                                       56666666555555666666555555555555555555555555555554 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.2e-08   0.00016       1      36 [.      16      51 ..      16      88 .. 0.92
   2 !   38.4   0.0   4.9e-13   1.1e-09      93     191 ..     159     266 ..     134     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.2e-08
                            AAA_26  1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                                      rti+v+gt  +vGK++v++gL r l ++g++v+ fK
  gi|313127335|ref|YP_004037605.1| 16 RTILVAGTASHVGKSTVAAGLSRLLADRGFSVAPFK 51
                                      79*****************************99888 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 4.9e-13
                            AAA_26  93 kelekdadivvVEGagglgvp..iteellnadiaknlgapvilVarggl.gtinqllltiealrq.knvrvlGvilN 165
                                        +l  ++d+v+ EGag++ +     ++l n++  +  +a+v+lVa +++ g ++ l+ t+e++ +    r++G ++ 
  gi|313127335|ref|YP_004037605.1| 159 ARLGRQHDVVIAEGAGSIAEInlHHRDLANVETTRFADADVLLVADIERgGVFASLVGTLELVPDdVRDRIAGAVIT 235
                                       58999**************7722445599******************994589**********7515779******* PP

                            AAA_26 166 kvrnpe.....nvetlekksgipvlGvvPyl 191
                                       k+r +e      ++++e+ +g+pvlGv+Py+
  gi|313127335|ref|YP_004037605.1| 236 KFRGDEsllsdGLDAFEERTGVPVLGVLPYD 266
                                       *****555555******************97 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   2.5e-05     0.055      10      46 ..      13      49 ..       5      59 .. 0.87
   2 ?    0.6   0.1      0.13   2.9e+02      75     101 ..     154     180 ..     149     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                           DUF1611 10 vkakrvlvvGTdcavGKrttaleleealeerGlkaaf 46
                                      ++++ +lv GT + vGK t a  l + l +rG+ +a 
  gi|313127335|ref|YP_004037605.1| 13 HSTRTILVAGTASHVGKSTVAAGLSRLLADRGFSVAP 49
                                      56789***************************99875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                           DUF1611  75 veglvkkaaeeeepdlilveGQgsLt..h 101
                                       +e++  ++ + ++ d+++ eG gs+   +
  gi|313127335|ref|YP_004037605.1| 154 AEAAHARLGR-QH-DVVIAEGAGSIAeiN 180
                                       5666666665.67.999999999998552 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.6e-06     0.017      51     108 ..     326     382 ..     292     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.6e-06
                                       SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHH CS
                         DJ-1_PfpI  51 daslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLa 108
                                       +++  d++ ++ Da+vlpG ++ +++lr++ +   l  + +e  ++++ +C g qlL 
  gi|313127335|ref|YP_004037605.1| 326 EYVPLDADLSSADAVVLPGSKNTADDLRAC-REAGLHDRLHEFSGPIVGLCGGYQLLG 382
                                       44445789999*******************.5556889999*************9996 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00025      0.57       3      39 ..      18      53 ..      16      67 .. 0.86
   2 ?   -2.7   0.0       1.3   2.8e+03      17      61 ..      85     129 ..      80     133 .. 0.84
   3 ?   -3.4   0.0       2.2   4.9e+03     131     148 ..     163     180 ..     153     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00025
                                      EEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE CS
                       CTP_synth_N  3 ilvtGGvvSglGkGiiaaslgallksrglkvtlikiD 39
                                      ilv+ G +S +Gk  +aa l++ll  rg++v+  k  
  gi|313127335|ref|YP_004037605.1| 18 ILVA-GTASHVGKSTVAAGLSRLLADRGFSVAPFKAQ 53
                                      6665.578***********************988865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-T CS
                       CTP_synth_N  17 iiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvld 61 
                                       ++ a+ g++  s+ ++ ++ ++ P  + ++  l+p   GE  ++ 
  gi|313127335|ref|YP_004037605.1|  85 VTDAAFGEIGVSQYVQARAARVTPTTDHNPVLLKPRGEGESQLVV 129
                                       677889999999999999999999999999999999999976655 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.2
                                       CT-SEEEEEE-S-TTSGG CS
                       CTP_synth_N 131 veadvviveigGtvgdie 148
                                        ++dvvi e  G++++i+
  gi|313127335|ref|YP_004037605.1| 163 RQHDVVIAEGAGSIAEIN 180
                                       368999999999999885 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00014      0.31      28      87 ..     331     387 ..     315     395 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                       GGGGCC-SEEEE-SS-HHHHHHHHHH.TT-HHHHHHHHHTT.--EEEETHHHHHHCCEETT CS
                               SNO  28 kedlaevdaliiPGGestamsklier.tglyedllefvknsekvvlGtCaGlillskelen 87 
                                         dl   da+++PG   ta  + + r  gl + l+ef    + ++ G C G  ll ++l n
  gi|313127335|ref|YP_004037605.1| 331 DADLSSADAVVLPGSKNTADDLRACReAGLHDRLHEF----SGPIVGLCGGYQLLGERLRN 387
                                       6799***************987665515655555555....679*******9999888765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00022       0.5       4      36 ..      16      48 ..      13      52 .. 0.90
   2 ?   -3.5   0.0       2.6   5.8e+03     192     213 ..     246     267 ..     241     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                              ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvg 36
                                      ++i+v+ +   VGKStva+ l+  La++g++v+
  gi|313127335|ref|YP_004037605.1| 16 RTILVAGTASHVGKSTVAAGLSRLLADRGFSVA 48
                                      67899999999*******************996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                              ParA 192 gggeklaeelgvpllgeipldp 213
                                       +g +++ e++gvp+lg +p d 
  gi|313127335|ref|YP_004037605.1| 246 DGLDAFEERTGVPVLGVLPYDD 267
                                       5677788999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3961.30
//
Query:       gi|313127336|ref|YP_004037606.1|  [L=231]
Description: cob(i)yrinic acid a,c-diamide adenosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-55  186.0   0.0    7.6e-55  185.8   0.0    1.0  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
  ------ inclusion threshold ------
      0.032   14.3   0.0      0.044   13.8   0.0    1.4  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.8   0.0   8.4e-59   7.6e-55       2     172 .]      36     231 .]      35     231 .] 0.91

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 8.4e-59
                    CobA_CobO_BtuR   2 kglihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKg.eke....sgElaalkkl.eielerlgkegfv.kmee 71 
                                        gl++ ++GdGKGKttAAlG+a+Ra+g+g++v+++qFlKg +++     gE++++++l +i++e++g++g+  +m+ 
  gi|313127336|ref|YP_004037606.1|  36 FGLVQAWWGDGKGKTTAALGMAFRAAGHGYRVHLLQFLKGgADSvesvRGEYNVIAALpTISYENTGHYGWKgRMDG 112
                                       699*************************************544367779*********66*************9*** PP

                    CobA_CobO_BtuR  72 eekeedaaaakealekakealas.eeyd................lvvlDEinyalklglldeeevlellkkkpekle 131
                                       ++++e+aa+a++a++++ke++a+ +e+d                ++vlDEi+ya+++glld +evlel+++kpe+le
  gi|313127336|ref|YP_004037606.1| 113 SDDDEHAAKAQAAFDRTKELVAAaGEADltaplpsdgnaedgvhMLVLDEILYAVEMGLLDADEVLELVESKPENLE 189
                                       ********************988455556666666666666666********************************* PP

                    CobA_CobO_BtuR 132 lvlTG.rnapeelleaADlvtemkkvkHpydkgikarkGiey 172
                                       lvlTG +++p+ ll+aADlv+e++kv+Hp+d+g +arkG ey
  gi|313127336|ref|YP_004037606.1| 190 LVLTGgHEEPTFLLDAADLVSEVRKVNHPFDDGTRARKGTEY 231
                                       ****9899*********************************8 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     5e-06     0.044       9      33 ..      46      70 ..      44     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-06
                                      TSSHHHHHHHHHHHHHHTT--EEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrVllv 33
                                      G GKTt a+++a+  a +g+rV l+
  gi|313127336|ref|YP_004037606.1| 46 GKGKTTAALGMAFRAAGHGYRVHLL 70
                                      88********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1681.94
//
Query:       gi|313127337|ref|YP_004037607.1|  [L=137]
Description: hypothetical protein Hbor_26090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 933.27
//
Query:       gi|313127338|ref|YP_004037608.1|  [L=523]
Description: hypothetical protein Hbor_26100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.13   12.8   0.3       0.26   11.8   0.3    1.5  1  Acyl-thio_N  Acyl-ATP thioesterase


Domain annotation for each model (and alignments):
>> Acyl-thio_N  Acyl-ATP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   1.5e-05      0.26      69     107 ..      38      75 ..       8      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                       Acyl-thio_N  69 gladseekvkedeevsssaPrtfinqLPDWslLlaaitt 107
                                       + +++e +++++++v   +P tf    PDWs +++a tt
  gi|313127338|ref|YP_004037608.1|  38 TSTATETETNTSNDVG-RPPETFPEARPDWSQVITAETT 75 
                                       3344455555555555.89*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3922.85
//
Query:       gi|313127339|ref|YP_004037609.1|  [L=445]
Description: hydrogenobyrinic acid a,c-diamide synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-35  122.6   0.0      2e-35  122.2   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    8.1e-11   42.1   0.0    4.4e-05   23.4   0.0    2.2  2  AAA_26         AAA domain
      7e-08   32.6   0.0    1.1e-07   31.9   0.0    1.3  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00035   20.5   0.0    0.00057   19.8   0.0    1.2  1  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.036   13.7   0.0      0.059   13.0   0.0    1.2  1  Peptidase_S51  Peptidase family S51


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   0.0   5.7e-39     2e-35       1     194 [.     245     434 ..     245     436 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 5.7e-39
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       ++av+ ++a+ + +    + L+a+++v   f+p+ +++l +d+d+v+lpGg+++++  a++++      i+e a++g
  gi|313127339|ref|YP_004037609.1| 245 TVAVATDDAFRFVYpsVREHLAARATV-EPFAPVAGDDL-PDCDAVYLPGGYPERHTEAIAES-PALSTIAERAADG 318
                                       589999999999998555788887755.589999*****.56****************99999.666789999**** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel......aaegeevkGyEiHs 146
                                        pv+g+CGGl++LGe+++++eg+     ++e+ g+L+++t++++ + +g  ++ +++      a+ege+v+G+E+H+
  gi|313127339|ref|YP_004037609.1| 319 LPVFGECGGLMVLGESLTTAEGE-----TYEMAGVLPVSTHLTE-RPVGLDHVGLRArrdsilASEGETVRGHEFHY 389
                                       **********************9.....****************.9996666555558999998899********** PP

                          GATase_3 147 Grtilkekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglfdnr 194
                                       +  + +++a+ +++v++g + +  +dG+ +     ++lGtY+H+++++ 
  gi|313127339|ref|YP_004037609.1| 390 SAATAAPDARYAFEVVRGAGLDgANDGLTEY----RTLGTYTHFHAESG 434
                                       ***************8755555599999977....**********9875 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.5e-06    0.0054       3      29 ..      13      39 ..      11      43 .. 0.92
   2 !   23.4   0.0   1.2e-08   4.4e-05      96     191 ..      86     185 ..      65     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkg 29
                                      ++++gt  gvGKTv +l+++ral+r+g
  gi|313127339|ref|YP_004037609.1| 13 LVLAGTASGVGKTVATLAVCRALEREG 39
                                      899********************9876 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.2e-08
                            AAA_26  96 ekdadivvVEGagglgvpiteellnadiaknlgapvilVargglg..tinqllltiealrqk...nvrvlGvilNkv 167
                                       + d d+ vVEG+ gl ++ +   ++a +a++l++p++lV+ +++g  +i++++l   a+ ++   +v v+G+ + + 
  gi|313127339|ref|YP_004037609.1|  86 ATDGDVCVVEGMMGLYDGDV---STAAVAAKLDLPIVLVVDATTGmeSIAATALGFRAYADRmgyDVDVAGLLAARA 159
                                       55889*********999955...6799*************99775338***********98777799*********9 PP

                            AAA_26 168 rnpenvetlekksgi..pvlGvvPyl 191
                                       r  +  e +++++++    +G+ P l
  gi|313127339|ref|YP_004037609.1| 160 RGGRHEEGIKNAIPVelHYVGRTPPL 185
                                       99999999999999833445666655 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   3.1e-11   1.1e-07       2     102 ..      14     177 ..      13     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.1e-11
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx....................... RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep....................... 54 
                                       ++a+t +GvGKT+ +++ +ral r+g+  ++ +a+p+    ++ +  + ++  +                       
  gi|313127339|ref|YP_004037609.1|  14 VLAGTASGVGKTVATLAVCRALEREGHTPVAAKAGPDFIDPSHhA-ATLGRPSRtldpwlagddglertyargatdg 89 
                                       789**********************************98888852.33333333467799999999999******** PP

                                       .................................CCHCCCHHHHHHCHCHHHH.........EEEEEEEEESS...-T CS
                                       .................................xxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .................................dlkrllellealgkkkall.......lkiagvvlnrvdgeneet 91 
                                                                        d+  + e+++a   +++         +++ag+++ r +g ++e+
  gi|313127339|ref|YP_004037609.1|  90 dvcvvegmmglydgdvstaavaakldlpivlvvDATTGMESIAATALGFRAYadrmgydVDVAGLLAARARGGRHEE 166
                                       *********************************66666666666666655555668999**************9999 PP

                                       TCHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                              CbiA  92 llkealeelkq 102
                                        +k+a+  +++
  gi|313127339|ref|YP_004037609.1| 167 GIKNAIPVELH 177
                                       99988866654 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.6e-07   0.00057      17      94 ..     268     344 ..     258     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.6e-07
                                       HTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS-SS CS
                               SNO  17 kclaenktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelenelvktl 93 
                                       ++ +e       +dl ++da+ +PGG     +  i +   + ++ e ++++ ++v+G C Gl++l + l++ + +t 
  gi|313127339|ref|YP_004037609.1| 268 RATVEPFAPVAGDDLPDCDAVYLPGGYPERHTEAIAESPALSTIAERAADG-LPVFGECGGLMVLGESLTTAEGETY 343
                                       5566666666779*************9988877777777799********9.*************999987755554 PP

                                       - CS
                               SNO  94 e 94 
                                       e
  gi|313127339|ref|YP_004037609.1| 344 E 344
                                       4 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05     0.059      80     137 ..     282     339 ..     273     350 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                       HHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGT CS
                     Peptidase_S51  80 lleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesietts 137
                                       l + d++y+ GG   r  ++++e  + + + e+ ++gl+++G   G +v ges++t +
  gi|313127339|ref|YP_004037609.1| 282 LPDCDAVYLPGGYPERHTEAIAESPALSTIAERAADGLPVFGECGGLMVLGESLTTAE 339
                                       56789*************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3043.30
//
Query:       gi|313127340|ref|YP_004037610.1|  [L=250]
Description: hypothetical protein Hbor_26120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-42  143.9   4.1    7.4e-42  143.6   4.1    1.1  1  CbiZ      Adenosylcobinamide amidohydrolase
  ------ inclusion threshold ------
      0.086   13.1   0.0       0.21   11.8   0.0    1.7  1  MoaE      MoaE protein
        0.2   11.5   2.1       0.33   10.8   0.1    2.4  3  TetR_N    Bacterial regulatory proteins, tetR family
        1.5    9.1   4.9          2    8.7   1.2    2.7  3  CnrY      Anti-sigma factor CnrY


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   4.1   1.6e-45   7.4e-42       2     191 ..      17     201 ..      16     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 1.6e-45
                              CbiZ   2 feeprrvlssavlngGlrelravlnhqvpegyeredpeeyleeyleelglppektvgllTaadmenaaiaeeefedl 78 
                                       +++p + + s+ + gG ++  +++n++vpeg++++d ++y+e++l+++g+  ek+++llT+++m++a+ a+ +    
  gi|313127340|ref|YP_004037610.1|  17 LSRPETRWLSTGHAGGESRGPVAYNVSVPEGWDEMDVDGYVERRLDAAGF-DEKGPTLLTGVSMRHARRARLG---- 88 
                                       678889999999**************************************.5*********************.... PP

                              CbiZ  79 evtavvTaGvesnavragd.........edeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlgvrsr 146
                                        v++v+TaGv sn++++           ++++++++GT+N++v ++++L+ +al++++++a+EAKta+l++ +    
  gi|313127340|ref|YP_004037610.1|  89 PVEVVATAGV-SNPAALPVadsahstahSRTDDPPAGTVNVFVGTTRDLAAGALANLVAVAAEAKTATLLAQTG--- 161
                                       **********.*****99999******966899*************************************9999... PP

                              CbiZ 147 ysegatGTgTDaiavaadkegeeeltyaGkhtklGeliaraVyeA 191
                                           ++GT+TDai+ a+d+ ge+   y+G++t++G++++++V++A
  gi|313127340|ref|YP_004037610.1| 162 ----FPGTTTDAIIAACDPAGET-TLYSGSATEVGAATRACVRDA 201
                                       ....9*****************6.*******************99 PP

>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.8e-05      0.21      11      36 ..     114     139 ..     104     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                                       HHHHH--TT--EEEEEEEE------T CS
                              MoaE  11 iealvaspkaGAvvlFvGtvRdsfdg 36 
                                       + +   +p aG v +FvGt+Rd   g
  gi|313127340|ref|YP_004037610.1| 114 AHSRTDDPPAGTVNVFVGTTRDLAAG 139
                                       445556999************86554 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.42   1.9e+03      21      32 ..      91     102 ..      90     103 .. 0.86
   2 ?   -3.5   0.0       2.1   9.5e+03      18      26 ..     132     140 ..     131     140 .. 0.79
   3 ?   10.8   0.1   7.3e-05      0.33       5      27 ..     153     175 ..     150     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.42
                                       HHHHHHTSSHHH CS
                            TetR_N  21 eIAkrAGvskga 32 
                                       e+++ AGvs +a
  gi|313127340|ref|YP_004037610.1|  91 EVVATAGVSNPA 102
                                       78999***9876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.1
                                       -HHHHHHHH CS
                            TetR_N  18 tvreIAkrA 26 
                                       t+r++A+ A
  gi|313127340|ref|YP_004037610.1| 132 TTRDLAAGA 140
                                       799999865 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHHTTT--HHHHHHHHT CS
                            TetR_N   5 ArelfaerGydattvreIAkrAG 27 
                                       ++ l+a+ G+ +tt+++I +++ 
  gi|313127340|ref|YP_004037610.1| 153 TATLLAQTGFPGTTTDAIIAACD 175
                                       6789***************9985 PP

>> CnrY  Anti-sigma factor CnrY
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.74   3.3e+03      61      85 ..       6      30 ..       4      33 .. 0.80
   2 ?    8.7   1.2   0.00045         2      47      75 ..     133     161 ..     118     179 .. 0.85
   3 ?   -0.0   0.5      0.24   1.1e+03      32      57 ..     183     208 ..     165     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.74
                                      XXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CnrY 61 fvainrvatlmlekaaptwlaspsa 85
                                      f a  r   l l ++   wl++  a
  gi|313127340|ref|YP_004037610.1|  6 FDATVRDDVLQLSRPETRWLSTGHA 30
                                      5666778889999999999998766 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00045
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CnrY  47 qraivcaalaalvafvainrvatlmleka 75 
                                        r +  +ala lva +a  ++atl+ +  
  gi|313127340|ref|YP_004037610.1| 133 TRDLAAGALANLVAVAAEAKTATLLAQTG 161
                                       68899******************987655 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.24
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CnrY  32 dkemaqivlvarrdaqraivcaalaa 57 
                                           a  v +a r   r   ca+l +
  gi|313127340|ref|YP_004037610.1| 183 YSGSATEVGAATRACVRDALCASLES 208
                                       55667788899999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1601.29
//
Query:       gi|313127341|ref|YP_004037611.1|  [L=335]
Description: l-threonine o-3-phosphate decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-33  115.2   0.0    5.1e-33  114.7   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
     0.0021   17.4   0.0     0.0034   16.8   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   0.0   5.7e-37   5.1e-33      35     362 ..      46     331 ..      21     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 5.7e-37
                                       TSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH CS
                     Aminotran_1_2  35 gtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr 111
                                        t ++y+  d + +++ a a+++        ++   v+ + G  a++ +++ ++ + pgd++l+p+p++++y++ +r
  gi|313127341|ref|YP_004037611.1|  46 ATSTRYPADD-YVDFRVAAAEYVD------CDPH-DVIPTAGGMAALRLAFGVT-VGPGDDVLLPEPSFGEYDREIR 113
                                       5667788878.8999999999999......9999.8999999999999999999.89******************** PP

                                       HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                     Aminotran_1_2 112 lsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                       l g++ v ++              +e l+++p + +     +v++p+NPtG +a+++el++ l+ ++    +l+vDe
  gi|313127341|ref|YP_004037611.1| 114 LQGATPVAVA-------------HDEILETDPRDYA---AAVVCNPNNPTGEAADPDELRAYLEDCRDADTVLIVDE 174
                                       *****99999.............2344444454455...779*********************************** PP

                                       TTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                     Aminotran_1_2 189 aYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaals 265
                                       a+ +f  +        + ++ ep +++++sl K fGl+G+R G++++++a+ + l  + +++  s++++ +    ++
  gi|313127341|ref|YP_004037611.1| 175 AFLDFTDD--------PSLAGEPGVIVARSLTKMFGLPGLRAGFAVATEALGEKLDAARQAWSLSTPAADVGEFCMR 243
                                       *******9........68999************************************9999999***9999998888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTT CS
                     Aminotran_1_2 266 dallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftvpg 342
                                        +     +++e++ r+  +r+++r++L ++ ++v++s++ ++ll +      +el    +e+   +  + t +t+ +
  gi|313127341|ref|YP_004037611.1| 244 QQV----FVTETKVRVRIERERMRERL-SDAFEVYPSDAPFLLLGVEGDV--DELLSYARERGFALRDARTFPTLDS 313
                                       866....99******************.88********999999665555..99********7777777777888** PP

                                       EEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 343 rlRitvAglteeeleelvea 362
                                       ++R+ v    ++e+++lv+ 
  gi|313127341|ref|YP_004037611.1| 314 HVRVAV--RRPQENDKLVRT 331
                                       ******..999999999976 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.8e-07    0.0034      27     108 ..      58     139 ..      40     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.8e-07
                                       HHHHHHHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-G CS
                   DegT_DnrJ_EryC1  27 eFEkafaaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidp 101
                                       +F  a a+y+    + +i+++ G aAl la  +  vgpgd V+ p  +F      ++  ga+pv v  d + +  dp
  gi|313127341|ref|YP_004037611.1|  58 DFRVAAAEYVDcdPHDVIPTAGGMAALRLAFGV-TVGPGDDVLLPEPSFGEYDREIRLQGATPVAVAHD-EILETDP 132
                                       68889999988634569************9975.799****************************9877.6666676 PP

                                       GGCGGG- CS
                   DegT_DnrJ_EryC1 102 aaieaai 108
                                        + +aa+
  gi|313127341|ref|YP_004037611.1| 133 RDYAAAV 139
                                       6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 2346.71
//
Query:       gi|313127342|ref|YP_004037612.1|  [L=324]
Description: namn:dmb phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2387.71
//
Query:       gi|313127343|ref|YP_004037613.1|  [L=189]
Description: adenosylcobinamide-phosphate guanylyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-18   67.8   3.4    1.7e-18   67.5   3.3    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    2.5e-09   37.4   0.0    2.9e-09   37.2   0.0    1.1  1  CTP_transf_3     Cytidylyltransferase
    4.7e-05   23.2   3.2    5.9e-05   22.9   1.1    1.9  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    0.00064   19.4   0.0    0.00096   18.8   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.019   14.8   0.3      0.039   13.8   0.2    1.6  2  DUF2064          Uncharacterized protein conserved in bacteri
      0.025   13.8   0.0       0.04   13.1   0.0    1.3  1  CofC             Guanylyl transferase CofC like


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   3.3   5.8e-22   1.7e-18       5     117 ..       2     114 ..       1     160 [. 0.88

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 5.8e-22
                                       EESS-TTTTT..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHH CS
                      NTP_transf_3   5 AGGrSsRmgg..dKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplasla 77 
                                       +GG+++R+gg  +K+l++++g p+++rv+ alr++ v+ v  v+ +  +e ++++++++++vve +  g+g ++ l 
  gi|313127343|ref|YP_004037613.1|   2 CGGQGTRLGGetEKPLVRVCGVPMVDRVATALRQSRVETVHAVVSPdaPETAQHVREKRLSVVETA--GEGYVSDLT 76 
                                       8********999************************99888777664589999************8..9******** PP

                                       HHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSS CS
                      NTP_transf_3  78 aalraaadadavlvlacDmPlltpelverllaaaaasgad 117
                                        al+a+   ++v+ +a+D+Pll +e+v+  ++ a a+g++
  gi|313127343|ref|YP_004037613.1|  77 DALEAV--GKPVVTVAADLPLLAAEHVDSAIETANAAGEQ 114
                                       ****98..7***********************99877744 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   9.6e-13   2.9e-09      15     131 ..      14     123 ..       7     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 9.6e-13
                                       TGGGSEETTEEHHHHHHHHHHHTTTTSE.EEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHHHHHHHTTT.TT CS
                      CTP_transf_3  15 gKnlldlggkpliayvleaalkskafek.vivaTDseeiknvakefgasvlvtrsslesdterflevvkaflmsene 90 
                                       +K+l +  g p++++v  a+++s + +   +v+ D  e+++++ e + sv+ t ++     + ++++++a+      
  gi|313127343|ref|YP_004037613.1|  14 EKPLVRVCGVPMVDRVATALRQSRVETVhAVVSPDAPETAQHVREKRLSVVETAGEGY--VSDLTDALEAVGKP--- 85 
                                       7**********************9966568*********************9999864..45589999999999... PP

                                       SEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEETT CS
                      CTP_transf_3  91 eiivnlqGdnPllqeevikkaietlkenqedylstlvkkvg 131
                                         +v + +d Pll  e+++ aiet + ++e +++ ++ ++ 
  gi|313127343|ref|YP_004037613.1|  86 --VVTVAADLPLLAAEHVDSAIETANAAGE-QMDGIASVTV 123
                                       ..**************************98.6665555444 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.1     2e-08   5.9e-05       8     119 ..       3     110 ..       1     145 [. 0.78
   2 ?    0.2   0.0      0.18   5.3e+02     188     215 ..     157     184 ..     139     186 .. 0.57

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2e-08
                                       TTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE.--SSHHHHHHH CS
                              IspD   8 AGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlva.GGdeRaesVln 83 
                                        G+G+R++ +++K ++ + g +++ +  +al + ++v+++  vvs+d  e+++++   k++ +v+  G+      + 
  gi|313127343|ref|YP_004037613.1|   3 GGQGTRLGGETEKPLVRVCGVPMVDRVATALRQ-SRVETVHAVVSPDAPETAQHVRE-KRLSVVEtAGEGYVSDLTD 77 
                                       59**********************997666665.89***********9555555555.5688887257777888999 PP

                                       HHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHT CS
                              IspD  84 glkalegeakfVLvHDaARpllkaadiaellaaaeq 119
                                       +l+a+ +    V+   a  pll+a+++++ +++a+ 
  gi|313127343|ref|YP_004037613.1|  78 ALEAVGKP---VVTVAADLPLLAAEHVDSAIETANA 110
                                       99997665...5555678899999999999987764 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                                       HHTT--EEEEE--TTG----SHHHHHHH CS
                              IspD 188 ekiGlsvkvVeGeednlKittpeDlalA 215
                                         +  +v++   ++ ++ + +p+Dl lA
  gi|313127343|ref|YP_004037613.1| 157 AGATDTVQLTYDDRIAVNVNRPTDLELA 184
                                       3333344555555555555566666555 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.2e-07   0.00096       5      92 ..       1      77 [.       1     136 [. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.2e-07
                                      E--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS- CS
                   NTP_transferase  5 LaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepeg 83
                                      ++GG+GtRL     ++ k+lv v g  ++++ ++++l +s++e+ +  + + ++++ +++++e+  ++     ++e+ g
  gi|313127343|ref|YP_004037613.1|  1 MCGGQGTRLG---GETEKPLVRVCGV-PMVDRVATALRQSRVET-VHAVVSPDAPETAQHVREKR-LS-----VVETAG 68
                                      89******86...5778*********.*****************.55555677788888999775.66.....344444 PP

                                      -BGGHHHHH CS
                   NTP_transferase 84 kgtAdAval 92
                                      +g    ++ 
  gi|313127343|ref|YP_004037613.1| 69 EGYVSDLTD 77
                                      444433333 PP

>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.3e-05     0.039       8      89 ..      36     111 ..      27     128 .. 0.79
   2 ?   -1.7   0.0      0.79   2.3e+03      48      62 ..     132     146 ..     109     169 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                                       TSSSEEEEEE----TTHHHHHHHH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHHHHHHHH CS
                           DUF2064   8 adaaevvlaldgaldkalaeqlalakglevlpQqggdlgeRlarafdrafeageepvlliGsDcpqltaalleqAfe 84 
                                       +++  v+ +++++ +++++    ++k+l+v++  g+     l +a++++    ++pv+ + +D+p l a+++++A+e
  gi|313127343|ref|YP_004037613.1|  36 SRVETVHAVVSPDAPETAQH--VREKRLSVVETAGEGYVSDLTDALEAV----GKPVVTVAADLPLLAAEHVDSAIE 106
                                       44445555666666666665..788899999999999999999999999....88*********************9 PP

                                       HTTT- CS
                           DUF2064  85 aLeea 89 
                                       + ++a
  gi|313127343|ref|YP_004037613.1| 107 TANAA 111
                                       87765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHTT-S CS
                           DUF2064  48 Rlarafdrafeagee 62 
                                       Rl   +d +fe+++e
  gi|313127343|ref|YP_004037613.1| 132 RLGVSVDTTFEHEGE 146
                                       333333333333322 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.3e-05      0.04      58     114 ..      54     109 ..       9     116 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                              CofC  58 yaldelgvevvkekekdlntavekafeeieekeviiipsdiPlikkedvkdllelek 114
                                           e+++ vv+   ++  + +  a+e    k+v+ + +d+Pl+  e+v+  +e+++
  gi|313127343|ref|YP_004037613.1|  54 QHVREKRLSVVETAGEGYVSDLTDALE-AVGKPVVTVAADLPLLAAEHVDSAIETAN 109
                                       444456666666665555555555533.34799******************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1436.27
//
Query:       gi|313127344|ref|YP_004037614.1|  [L=260]
Description: cobalamin-5'-phosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-39  136.1  20.2    2.1e-39  135.9  20.2    1.0  1  CobS      Cobalamin-5-phosphate synthase
  ------ inclusion threshold ------
      0.073   13.2   0.1       0.14   12.3   0.1    1.4  1  PUMA      Bcl-2-binding component 3, p53 upregulated modulato


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.9  20.2   2.3e-43   2.1e-39       2     203 ..      10     250 ..       9     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 2.3e-43
                              CobS   2 lsflTrlPvp.......elaralaffPlvGlllGlll.llallllllllllaallavaalvlltgglHlDGlaDtaD 70 
                                       l flTrlPv        +++r   +fPlvG+ lG+l+ +++ll   +  + aa+l++aal++ltg+ H+DGlaD++D
  gi|313127344|ref|YP_004037614.1|  10 LVFLTRLPVGvdeaswdAFRRTPVAFPLVGYGLGALAaIPFLLPVPV--PTAAALYMAALYVLTGVTHVDGLADVGD 84 
                                       67*******777776666699***************65555544443..678999999999**************** PP

                              CobS  71 glgsgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala..........lllapvlsRlaallaiallpyaee 137
                                       + + ++d e+rl+++kDs++G++G+lal l+l+   +  +++a          +++a+v ++++++++++++++a+e
  gi|313127344|ref|YP_004037614.1|  85 AAAVHGDAEERLAVLKDSQTGVGGALALGLALVTLGLGALSVAgtapqvafplVVAAEVGAKTGMATLVCTGESAHE 161
                                       **8888************************999888774344455677788877899******************99 PP

                              CobS 138 glgalfaeaqkk.........lvllal..................avlllllalllaall....valllrrlarrkl 183
                                       glg+++++ ++          l    +                  a++++++a+     +    va+l+ r+ +++l
  gi|313127344|ref|YP_004037614.1| 162 GLGSALIDVNDVsnlvpvavsL----VllpallitpvagvagvttAAFAAVAAAS----FapvaVAVLAGRWGNEHL 230
                                       *******855555665543331....13344455666655543321111111122....13444778899******* PP

                              CobS 184 ggvtGDvlGavieltellvl 203
                                       ggv+GDvlG ++el++++ l
  gi|313127344|ref|YP_004037614.1| 231 GGVSGDVLGTANELGRVAGL 250
                                       ****************9865 PP

>> PUMA  Bcl-2-binding component 3, p53 upregulated modulator of apoptosis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.6e-05      0.14      25      76 ..     172     224 ..     156     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                              PUMA  25 plgrlvpsavscglceaglsprvaa.dsllpapaaalaapsllpvavsllsqr 76 
                                        +++lvp avs  l  a l + va+  ++  a+ aa+aa+s +pvav++l++r
  gi|313127344|ref|YP_004037614.1| 172 DVSNLVPVAVSLVLLPALLITPVAGvAGVTTAAFAAVAAASFAPVAVAVLAGR 224
                                       5789***********9998777777256888999**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1767.05
//
Query:       gi|313127345|ref|YP_004037615.1|  [L=307]
Description: adenosylcobinamide-phosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-76  256.5  11.5    3.1e-76  256.2  11.5    1.0  1  CobD_Cbib  CobD/Cbib protein
  ------ inclusion threshold ------
      0.039   13.3   1.7      0.051   12.9   0.7    1.5  2  AmpE       Regulatory signalling modulator protein AmpE


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.2  11.5   3.4e-80   3.1e-76       2     275 ..      10     289 ..       9     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 256.2 bits;  conditional E-value: 3.4e-80
                         CobD_Cbib   2 llAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvalllllla..laallglvl 76 
                                       +lA+ lD+++ +p++++hPv+l+g+l+s  +++++   + rl Gv+lal+++l+++ va +++++a  l++++g ++
  gi|313127345|ref|YP_004037615.1|  10 VLAAGLDVAVAEPPARVHPVALLGRLVSHADRTWS---HPRLVGVVLALAAPLGFAGVAGGVVAAAetLSPWVGALF 83 
                                       89******************************775...4689********************9988866668899** PP

                         CobD_Cbib  77 ealllkltlalrsLleevrkvakalkgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyfll 153
                                       ++l+l+++++lr+Ll++vr+v +a ++dl+aaR++++ + gRd s+ld++++++AavEsvaENlsDg+vaPlf f++
  gi|313127345|ref|YP_004037615.1|  84 ASLVLFAATSLRMLLDAVRDVTQAAETDLDAARTELRALAGRDASALDAAHVRSAAVESVAENLSDGLVAPLFAFAV 160
                                       *************************99************************************************99 PP

                         CobD_Cbib 154 l.......glpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala......aalriarrd 217
                                               ++++a+++k vnTlDsm+GY+    + +Gwa+ArlDD+++++PARl+++lla++       + +++r  
  gi|313127345|ref|YP_004037615.1| 161 CapfslplAAAAAAWVKGVNTLDSMFGYR---SKPIGWAPARLDDVVMWLPARLAGVLLAVSvaefslPFSSRVRTL 234
                                       877777766688999**************...799**************************7444444348999*** PP

                         CobD_Cbib 218 arkhpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrpleaedieralrl 275
                                       ar+ pSpNsgwp+a++A++l  rL +p+vY l+   ++ t   ++r ++++d  +a+r+
  gi|313127345|ref|YP_004037615.1| 235 ARRPPSPNSGWPMATMAAVLPARLVKPGVYdLD-PASD-TA--NTRLPTTADAMQAVRV 289
                                       ******************************555.3322.32..3456689999999987 PP

>> AmpE  Regulatory signalling modulator protein AmpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.27   2.4e+03     202     211 ..      47      56 ..      37     123 .. 0.63
   2 ?   12.9   0.7   5.7e-06     0.051     145     210 ..     152     218 ..     104     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.27
                              AmpE 202 rlagvayall 211
                                       rl+gv+ al 
  gi|313127345|ref|YP_004037615.1|  47 RLVGVVLALA 56 
                                       5555555542 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.7e-06
                              AmpE 145 laplfwfvvagpyg.pvalvgyavlrayqt...wlarrktpleraqsgvdallhvldwipvrlagvayal 210
                                       +aplf f v+ p+  p+a ++ a +++ +t   ++  r+ p+  a + +d    v+ w+p+rlagv  a+
  gi|313127345|ref|YP_004037615.1| 152 VAPLFAFAVCAPFSlPLAAAAAAWVKGVNTldsMFGYRSKPIGWAPARLDD---VVMWLPARLAGVLLAV 218
                                       79***********779*******9999877222566778888888888886...5679********9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2191.33
//
Query:       gi|313127346|ref|YP_004037616.1|  [L=219]
Description: had superfamily hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-08   33.8   0.2    1.1e-07   32.3   0.2    1.6  1  Hydrolase       haloacid dehalogenase-like hydrolase
      3e-05   24.2   0.0    3.8e-05   23.8   0.0    1.2  1  HAD_2           Haloacid dehalogenase-like hydrolase
      4e-05   23.6   0.0    9.1e-05   22.5   0.0    1.6  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
       0.11   12.6   0.0        1.5    9.0   0.0    2.1  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.2   2.5e-11   1.1e-07       4     202 ..       3     178 ..       1     183 [. 0.72

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2.5e-11
                                       EEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH.HHHHHETTTEHHHHTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   4 vvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgal.tgfatfigrgayaigkpewlta 79 
                                       + fD+ GTL+  e    +  + a                 +a++a+  +r+ a+ ++++      aya+   +  + 
  gi|313127346|ref|YP_004037616.1|   3 ISFDLFGTLVAVE----RPADPA-----------------AAVAAELRDRGVAVpDDWGD-----AYAELHIDAPDG 53 
                                       6677777777444....333333.................44556777776666655555.....555444444444 PP

                                       HHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHH.HHHHHHHHTTEEEEEEESSEH.HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase  80 ldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaa.eavasLkaagievvlltgdnp.etaeraanq 154
                                          +  l a +++a +     a  +a  +av+++ dp    pe a +av +  ++g  v+ll++ +  e + r++ +
  gi|313127346|ref|YP_004037616.1|  54 A--EVPLPAHVSAALRSRDVDAPANAARRAVVAAFDPEVRTPEGAvDAVSAAAERGP-VALLSNCSVpELVARTLIR 127
                                       4..2224444444444444444447788999999999999999888**********9.*****86652555577777 PP

                                       TT..GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.H CS
                                       xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                         Hydrolase 155 lG..ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.D 202
                                        +  +d+fd+ ++s   +  kp+pe+++ ++ +L + pe  ++VGD +n D
  gi|313127346|ref|YP_004037616.1| 128 SDldRDAFDVMVSSVACGWRKPHPEAFETVAGRLDVAPETLVHVGDDPNtD 178
                                       77769999****************************************966 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   8.6e-09   3.8e-05     120     164 ..     133     178 ..      75     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.6e-09
                             HAD_2 120 syFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsp.tD 164
                                       + Fdv+v+s  ++ +KP+pe +e++  +l++ +e  + vGD p tD
  gi|313127346|ref|YP_004037616.1| 133 DAFDVMVSSVACGWRKPHPEAFETVAGRLDVAPETLVHVGDDPnTD 178
                                       79***************************************99665 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     2e-08   9.1e-05       2      34 ..     146     178 ..     145     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2e-08
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTH CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatD 34 
                                       ++KP+pe+++  + +l+++pe  + +GD+++tD
  gi|313127346|ref|YP_004037616.1| 146 WRKPHPEAFETVAGRLDVAPETLVHVGDDPNTD 178
                                       69******************************9 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00033       1.5       2      69 ..       4     143 ..       3     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00033
                                       EEESTTTSEETTEE-TTHHHHHHHHHHTT................................................ CS
                       Hydrolase_6   2 lfDidGvLwrgdkaipgaaealnalraag................................................ 30 
                                        fD+ G+L+  +++ + aa +   lr++g                                                
  gi|313127346|ref|YP_004037616.1|   4 SFDLFGTLVAVERPADPAAAVAAELRDRGvavpddwgdayaelhidapdgaevplpahvsaalrsrdvdapanaarr 80 
                                       59999****99999999999999999999777777777777777777777777777777777777777777777777 PP

                                       ..........................-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHH CS
                       Hydrolase_6  31 ..........................kpvvllTNnsskseeeyakkleklgvditeeqvvtsata 69 
                                                                  pv+ll+N s    e +a  l + ++d ++ +v+ s++a
  gi|313127346|ref|YP_004037616.1|  81 avvaafdpevrtpegavdavsaaaerGPVALLSNCSVP--ELVARTLIRSDLDRDAFDVMVSSVA 143
                                       77777777777777777777777777788888886643..4677777777777777666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1583.11
//
Query:       gi|313127347|ref|YP_004037617.1|  [L=301]
Description: 3-methyladenine DNA glycosylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00074   19.9   0.0     0.0013   19.2   0.0    1.4  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.1e-08    0.0013       3      89 ..     133     261 ..     131     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.1e-08
                                       HHHHTTS-HHHHHHHHHHHHHHHS............HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                           HhH-GPD   3 ailsqqtsderanriierlferfg............fptpedladadeekLrelirelGfyrrKakyikelArilv. 66 
                                       a lsqqt++ +a+++   l++++g            fptp ++ +a ++++r++   +G   rK k + ++A++++ 
  gi|313127347|ref|YP_004037617.1| 133 AALSQQTPIRVATELRDALVRAVGrvavvdgtavslFPTP-AMVRARPDEIRDA---IGNE-RKTKTLLAAAEAFLe 204
                                       679********************************99998.688999*******...8976.*************99 PP

                                       ..................................S-SSS--TTSHHHHHHHHHHTTS CS
                                       ..................................xxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ..................................gkpdvlivvDvhvrrilkrlrsi 89 
                                                                         g++ +l+     +  +++ +++i
  gi|313127347|ref|YP_004037617.1| 205 hdlanlttddlltqladvwgfgswsaefialrgfGRMSILPSEESRLCTAVGDVYGI 261
                                       888888888887777777777777777777777766666666555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2227.93
//
Query:       gi|313127348|ref|YP_004037618.1|  [L=399]
Description: xaa-pro aminopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-34  120.1   1.4    1.3e-34  119.7   1.4    1.2  1  Peptidase_M24  Metallopeptidase family M24
    6.8e-12   46.2   0.0    1.4e-11   45.2   0.0    1.6  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   1.4   1.5e-38   1.3e-34       2     209 .]     153     380 ..     152     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 1.5e-38
                                       HHHHHHHHHHHHHHHHHHHHHTTC........BHHHHHHHHHHHHHHHTT........TCEESSSSEEEEGGGGGST CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgv........terelaaeieattlkrhg........arglafppivasgenaavl 62 
                                       lir++a+ a+  ++++ +  + g          ++e+ +++ +t     g        + g+ +     sg ++a++
  gi|313127348|ref|YP_004037618.1| 153 LIRESAKWANLGHRYLTDYTEVGAhpatvsqrASMEASRAMLDT----LGdrysvrvrGSGPVHA-GYISGRETALP 224
                                       57788888888888887776665422222221233333333333....22333444333333333.334799***** PP

                                       TTBCSSSB--TTEEEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHH CS
                     Peptidase_M24  63 hytpndrvlkegdlvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarev 139
                                       h++  +++l egd+++  a a++dgy+s   rT++vG++t e    +e++leaq  ai+a+ pGv+l+ +d+ + ++
  gi|313127348|ref|YP_004037618.1| 225 HGHTPNERLSEGDVLITGASANVDGYHSELERTMFVGEPTSEDVHYFELMLEAQTIAIDALGPGVELAYVDEQVNDY 301
                                       **7779***********************************9999******************************** PP

                                       HHHTTBCCGBSSCSEEEESSSSSEEEEEESS............STTCSSB--TTBEEEEEEEEEEETTTEEEEEBEE CS
                     Peptidase_M24 140 lesaglakffphglGHgvGlevhdegpsvsr............esndgrkleeGmvftiEpgiyfapgeggvriedt 204
                                       +e++g+ +   h++GH +Gl  h+  p++ +             + ++ ++++G+v+tiEpg+y  ++  g r  dt
  gi|313127348|ref|YP_004037618.1| 302 FEEQGVLDLAQHHVGHNIGLGGHEP-PYIDTgwdehcasehteMTETDATMAPGHVYTIEPGLY-TERA-GYRHSDT 375
                                       *****88999*************98.99988999***999876444899***************.4444.******* PP

                                       EEEES CS
                     Peptidase_M24 205 vlvte 209
                                       v vte
  gi|313127348|ref|YP_004037618.1| 376 VAVTE 380
                                       ****7 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   1.5e-15   1.4e-11       1     105 [.      13     128 ..      13     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.5e-15
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEEST. CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveydd. 76 
                                       Rl+++r +++++++da++ +  ++++YltGf++   +r+++l vt ++  + v++l++++++    + +ev+ y d 
  gi|313127348|ref|YP_004037618.1|  13 RLDAIRGRLADTDADAAVWFGATSIEYLTGFHHIQTERPVVLAVTDARVEITVPRLEVERVQDNP-RIDEVRHYFDy 88 
                                       99*******************************************9999****************.*********** PP

                                       ....HSSHHHHHHHHHHHHT.........-EEEE-TTSSBHH CS
                      Creatinase_N  77 ....pvealadllkellese.........krvgveldaltva 105
                                           p ++ a++l+el+ ++         +++g e  a  ++
  gi|313127348|ref|YP_004037618.1|  89 pggdPIKTAASMLSELGVDSvvadsdgapGTMGYEGPA--LS 128
                                       ***************98877666667777777777765..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2432.43
//
Query:       gi|313127349|ref|YP_004037619.1|  [L=160]
Description: peroxiredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-19   69.9   0.0    2.1e-19   69.7   0.0    1.1  1  AhpC-TSA  AhpC/TSA family
    1.2e-18   67.3   0.0    1.4e-18   67.0   0.0    1.0  1  Redoxin   Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   2.3e-23   2.1e-19       2     123 ..       5     130 ..       4     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 2.3e-23
                                       TSB----EEESTTCEEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCH.HHCCCTTEEEEEEESSSCHHHHHH CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdy.kgkpvvlffypkdwcpvCttelpalakly.eefkergvevigvsvdspeshkkf 76 
                                       g  apdf+l  ++g +v+ls+   + p+v+++ ++ wc +C ++l+ +++   +   + gv+++ + +d+   + + 
  gi|313127349|ref|YP_004037619.1|   5 GTDAPDFTLASTNGADVTLSKTlDDGPTVILINRGHWCSFCAEQLQTFSEISyDLWFHDGVDILPIVTDPIGPVTEM 81 
                                       789****************8886557***********************9752666699****************** PP

                                       HHH-H.SSEEEE-TTSHHHHHTT-EETT..TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  77 iekeslnfpllsDeegkvakaygvlkee..kglalratfvidkegkiry 123
                                        ++++l ++ll+D++g+va++y    +     + + at+v+d+eg+++y
  gi|313127349|ref|YP_004037619.1|  82 RDRYDLGIQLLADPDGTVAEQYSGTEQTshGLTGISATYVVDEEGVVQY 130
                                       **********************988666888999**************9 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   1.6e-22   1.4e-18       3     137 ..       5     138 ..       3     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 1.6e-22
                                       TSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTH.HHHHHCSTTTEEEEEESSSHHHH CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpylekl.aellkekgvdvvavvadndafvk 77 
                                       g  aPdftl  a t+g +v+ls+ + ++++v+ + +g +c  C +++  + ++ ++l    gvd++ +v+d   +v+
  gi|313127349|ref|YP_004037619.1|   5 GTDAPDFTL--ASTNGADVTLSKtLDDGPTVILINRGHWCSFCAEQLQTFSEIsYDLWFHDGVDILPIVTDPIGPVT 79 
                                       888*****8..56***********************************9999989999******************* PP

                                       HHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEEEESSSCH CS
                           Redoxin  78 efwgkeglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvylevepepe 137
                                       e+ ++++l + +l+D+++ +++++    +e+ s g  ++ ++ v+de+g+v y +v + p 
  gi|313127349|ref|YP_004037619.1|  80 EMRDRYDLGIQLLADPDGTVAEQYS--GTEQTSHGlTGISATYVVDEEGVVQYEQVADHPA 138
                                       *************************..8899999999*****************9999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1079.65
//
Query:       gi|313127350|ref|YP_004037620.1|  [L=194]
Description: hypothetical protein Hbor_26230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-10   37.9  14.6    1.3e-06   27.9   5.7    2.5  2  zinc_ribbon_2   zinc-ribbon domain
    1.1e-07   31.7  11.4    1.9e-07   31.0  11.4    1.4  1  DZR             Double zinc ribbon
    7.1e-07   28.4  14.3    3.3e-05   23.1   4.4    2.4  2  zf-ribbon_3     zinc-ribbon domain
    1.1e-06   29.3   9.1    7.1e-05   23.5   1.2    2.3  2  zinc_ribbon_15  zinc-ribbon family
    0.00015   21.6   6.0     0.0014   18.5   0.6    3.3  2  RHH_1           Ribbon-helix-helix protein, copG family
     0.0017   18.6   3.7     0.0031   17.7   3.7    1.5  1  YwqJ-deaminase  YwqJ-like deaminase
  ------ inclusion threshold ------
       0.06   13.3  11.2        3.2    7.7   2.3    3.8  3  Nudix_N_2       Nudix N-terminal
      0.071   13.1   8.6        1.3    9.0   8.6    2.2  1  zinc-ribbons_6  zinc-ribbons
       0.12   11.9   6.1        1.8    8.3   0.4    3.4  3  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.14   12.1  10.9       0.23   11.4   6.9    2.3  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.14   12.0   6.3        1.7    8.5   6.3    2.1  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.15   11.8   8.0       0.86    9.3   0.6    3.3  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.16   11.9   6.6       0.56   10.1   0.8    2.5  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.17   12.0  11.3       0.49   10.6   3.7    3.3  3  Zn-ribbon_8     Zinc ribbon domain
       0.36   10.9  11.6       0.34   10.9   2.1    2.6  3  HypA            Hydrogenase/urease nickel incorporation, meta
        1.4    9.0   3.0         15    5.7   0.1    2.3  2  DUF2752         Protein of unknown function (DUF2752)
        2.3    8.2  12.0          5    7.1   0.4    3.5  4  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        2.3    8.1   7.3        7.1    6.5   0.1    2.7  2  Cys_rich_KTR    Cysteine-rich KTR
        4.4    7.5  12.5         19    5.5   5.8    3.0  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        6.9    6.8   8.9         34    4.6   8.9    2.2  1  Zn_Tnp_IS91     Transposase zinc-binding domain
        7.5    6.6  11.9         95    3.0  10.4    2.8  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   5.7   1.6e-09   1.3e-06       2      22 ..     138     158 ..     137     158 .. 0.96
   2 !   14.9   1.6   1.8e-05     0.016       4      21 ..     166     183 ..     163     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.6e-09
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                                       C +CG+el++++++Cp+CG++
  gi|313127350|ref|YP_004037620.1| 138 CEKCGEELSPDDVYCPNCGEK 158
                                       *******************86 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.8e-05
                     zinc_ribbon_2   4 nCGaelqdnakFCpyCGt 21 
                                       +CG e+  +  FCp CG 
  gi|313127350|ref|YP_004037620.1| 166 ECGDEVRSDWAFCPGCGR 183
                                       7****************5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0  11.4   2.2e-10   1.9e-07       1      49 []     138     182 ..     138     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.2e-10
                               DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49 
                                       C +Cgeel+pd+ +C++Cg+k +   +  +C +Cg +v ++++fCp CG
  gi|313127350|ref|YP_004037620.1| 138 CEKCGEELSPDDVYCPNCGEKAN---HRVFC-ECGDEVRSDWAFCPGCG 182
                                       **********************9...57888.7***************9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   4.4   3.9e-08   3.3e-05       1      25 [.     134     158 ..     134     158 .. 0.90
   2 !   10.6   2.3   0.00034      0.29       7      23 ..     166     182 ..     165     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.9e-08
                       zf-ribbon_3   1 stvrCPnCGa.plssddnvCpyCGtk 25 
                                       +++ C +CG+ + s+dd+ Cp+CG+k
  gi|313127350|ref|YP_004037620.1| 134 QEKPCEKCGEeL-SPDDVYCPNCGEK 158
                                       5899******66.***********86 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00034
                       zf-ribbon_3   7 nCGa.plssddnvCpyCG 23 
                                       +CG  + +sd+ +Cp CG
  gi|313127350|ref|YP_004037620.1| 166 ECGDeV-RSDWAFCPGCG 182
                                       59**67.**********9 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   1.2   8.3e-08   7.1e-05      54      86 .]     117     156 ..      97     156 .. 0.73
   2 !   10.4   1.5     0.001      0.87      67      86 .]     164     182 ..     157     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.3e-08
                    zinc_ribbon_15  54 gkeiekkesse.......kkeCknCgkeveeefkyCpkCg 86 
                                        ++i+k+++++       +k C++Cg+e++++  yCp+Cg
  gi|313127350|ref|YP_004037620.1| 117 DSKIRKTNDEDasgvhtqEKPCEKCGEELSPDDVYCPNCG 156
                                       3333333333355667779********************9 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                    zinc_ribbon_15  67 eCknCgkeveeefkyCpkCg 86 
                                        C +Cg ev ++ ++Cp Cg
  gi|313127350|ref|YP_004037620.1| 164 FC-ECGDEVRSDWAFCPGCG 182
                                       46.8***************9 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.6   1.6e-06    0.0014       2      38 ..       4      36 ..       3      37 .. 0.90
   2 ?    3.3   0.5     0.097        83       4      21 ..      52      69 ..      51      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.6e-06
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                      +++r d+el+erL+     ++ S+Se++R+Alr yl+
  gi|313127350|ref|YP_004037620.1|  4 ITFRADDELVERLE----GLETSKSEVMRDALRVYLD 36
                                      79999999999996....78*************9997 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.097
                                      EEEEHHHHHHHHHHHHHH CS
                             RHH_1  4 irldeellerLdelarrr 21
                                      +++d+ l  rLdel+++r
  gi|313127350|ref|YP_004037620.1| 52 VTVDDVLQSRLDELIEER 69
                                      899999999*****9987 PP

>> YwqJ-deaminase  YwqJ-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   3.7   3.7e-06    0.0031       5     129 ..      17     145 ..      13     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.7e-06
                    YwqJ-deaminase   5 kgkllsksrlppaqagaldlrtGevitavnkakekppkdlHPlvqsrLdeliveakreraae.....gaglhAEvaa 76 
                                        g + sks++  ++  ++ ++ +e  + +n+++e p++++  ++qsrLdeli e++  + a+     g+++ A +  
  gi|313127350|ref|YP_004037620.1|  17 EGLETSKSEVMRDALRVYLDE-AERSSEANETDE-PEVTVDDVLQSRLDELIEERVDAVLAKrlgavGHSTLAPPRD 91 
                                       667788999996666565555.799999999888.*****************955555555566699********** PP

                    YwqJ-deaminase  77 vsdaLydleaeageskarkaldgarimvltvrlpkkpekG..taappCpnCtaiL 129
                                       v+  +  +e    e  +++  dg+++     +++ +++ G  t+  pC+ C + L
  gi|313127350|ref|YP_004037620.1|  92 VNVNIA-VESATDETSVNATEDGSKSDSKIRKTNDEDASGvhTQEKPCEKCGEEL 145
                                       *****9.777755554444445555444444444455555115568999998766 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.085        72       3      11 ..     138     146 ..     136     148 .. 0.85
   2 ?    7.7   2.3    0.0038       3.2       2      14 ..     151     163 ..     151     172 .. 0.88
   3 ?    5.9   0.1     0.015        12       2      11 ..     177     186 ..     176     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.085
                                       -TTT--B-E CS
                         Nudix_N_2   3 CsqCGtpve 11 
                                       C++CG++++
  gi|313127350|ref|YP_004037620.1| 138 CEKCGEELS 146
                                       99***9986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0038
                                       B-TTT--B-EEE- CS
                         Nudix_N_2   2 FCsqCGtpvelri 14 
                                       +C++CG++ ++r+
  gi|313127350|ref|YP_004037620.1| 151 YCPNCGEKANHRV 163
                                       9*******99987 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.015
                                       B-TTT--B-E CS
                         Nudix_N_2   2 FCsqCGtpve 11 
                                       FC+ CG +++
  gi|313127350|ref|YP_004037620.1| 177 FCPGCGRRTS 186
                                       9*****9876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.6    0.0016       1.3       3      39 ..     138     171 ..     116     189 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                                       -SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S-- CS
                    zinc-ribbons_6   3 CpeCqqelekrgeqyhCeaCqedlkkealCpeCeqel 39 
                                       C++C +el+ ++  + C +C e+ +   +C eC++e+
  gi|313127350|ref|YP_004037620.1| 138 CEKCGEELSPDD--VYCPNCGEKANHRVFC-ECGDEV 171
                                       666666665554..5555555555555555.344443 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0021       1.8       3      16 ..     136     149 ..     134     151 .. 0.86
   2 ?    2.4   0.4      0.14   1.2e+02       2      11 ..     149     158 ..     148     160 .. 0.82
   3 ?    3.5   0.0     0.062        53       4      19 ..     177     192 ..     174     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                            zf_UBZ   3 ylCerCgkeipese 16 
                                        +Ce+Cg+e+++++
  gi|313127350|ref|YP_004037620.1| 136 KPCEKCGEELSPDD 149
                                       58********9987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                            zf_UBZ   2 tylCerCgke 11 
                                        + C+ Cg++
  gi|313127350|ref|YP_004037620.1| 149 DVYCPNCGEK 158
                                       678*****85 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.062
                            zf_UBZ   4 lCerCgkeipeselqE 19 
                                       +C+ Cg++ + +++ E
  gi|313127350|ref|YP_004037620.1| 177 FCPGCGRRTSAADVLE 192
                                       8******999888776 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.9   0.00027      0.23       3      28 ..     134     157 ..     132     169 .. 0.81
   2 ?    1.4   0.9      0.36     3e+02      10      27 ..     167     182 ..     164     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                       Prok-RING_1   3 tgkkCpvCgkelkeedDiVvCpeCgt 28 
                                       ++k C+ Cg+el+++d  V Cp+Cg 
  gi|313127350|ref|YP_004037620.1| 134 QEKPCEKCGEELSPDD--VYCPNCGE 157
                                       6899*********984..9*****95 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.36
                       Prok-RING_1  10 CgkelkeedDiVvCpeCg 27 
                                       Cg+e+++  D   Cp Cg
  gi|313127350|ref|YP_004037620.1| 167 CGDEVRS--DWAFCPGCG 182
                                       5555544..578899998 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.3     0.002       1.7       2      46 ..     135     184 ..     134     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                                       GSB-TTTSSS..BS-EEETTEE....EEEE-HHHHHHHHHTT-B-TTT--B CS
                        zf-C3HC4_3   2 deeCviCler..prnvvllpCg....HlvlCeeCaekllkrkkkCpiCrrp 46 
                                       +++C  C e+  p +v + +Cg    H v+C eC +++++  + Cp C r 
  gi|313127350|ref|YP_004037620.1| 135 EKPCEKCGEElsPDDVYCPNCGekanHRVFC-ECGDEVRSDWAFCPGCGRR 184
                                       6789999997668888888896666699999.5999999999999999876 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.92   7.8e+02      24      30 ..     138     144 ..     135     145 .. 0.85
   2 ?    5.1   0.1     0.021        18       5      12 ..     151     158 ..     150     162 .. 0.75
   3 ?    9.3   0.6     0.001      0.86       5      16 ..     177     188 ..     175     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.92
                     zf-NADH-PPase  24 CpaCgle 30 
                                       C+ Cg+e
  gi|313127350|ref|YP_004037620.1| 138 CEKCGEE 144
                                       9999986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                     zf-NADH-PPase   5 FCgrCGap 12 
                                       +C+ CG +
  gi|313127350|ref|YP_004037620.1| 151 YCPNCGEK 158
                                       78888865 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.001
                     zf-NADH-PPase   5 FCgrCGaptepa 16 
                                       FC+ CG +t  a
  gi|313127350|ref|YP_004037620.1| 177 FCPGCGRRTSAA 188
                                       *********876 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00066      0.56      14      34 ..     138     158 ..     138     161 .. 0.86
   2 ?    4.2   0.6     0.047        40      26      34 ..     176     184 ..     175     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00066
                           DUF35_N  14 CpdCGtvqfPPravCphCgsd 34 
                                       C +CG    P   +Cp+Cg +
  gi|313127350|ref|YP_004037620.1| 138 CEKCGEELSPDDVYCPNCGEK 158
                                       99*****87777******975 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.047
                           DUF35_N  26 avCphCgsd 34 
                                       a+Cp+Cg++
  gi|313127350|ref|YP_004037620.1| 176 AFCPGCGRR 184
                                       689999876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.8     0.046        39      26      36 ..     135     145 ..     118     147 .. 0.70
   2 ?   10.6   3.7   0.00057      0.49       8      39 ..     138     163 ..     136     164 .. 0.75
   3 ?    4.0   0.7     0.066        57      28      35 ..     176     184 ..     165     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.046
                       Zn-ribbon_8  26 ltaCPeCgsev 36 
                                       +++C +Cg+e+
  gi|313127350|ref|YP_004037620.1| 135 EKPCEKCGEEL 145
                                       55599998765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00057
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.evrrv 39 
                                       Ce+Cg   e+l +    +++ CP+Cg+ + +rv
  gi|313127350|ref|YP_004037620.1| 138 CEKCG---EELSP----DDVYCPNCGEkANHRV 163
                                       999**...77753....3667*****9666665 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.066
                       Zn-ribbon_8  28 a.CPeCgse 35 
                                       a CP Cg +
  gi|313127350|ref|YP_004037620.1| 176 AfCPGCGRR 184
                                       55****985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.3   6.2e+03      38      57 ..      25      44 ..      21      59 .. 0.62
   2 ?   10.9   2.1    0.0004      0.34      72      96 ..     137     159 ..     131     163 .. 0.82
   3 ?    6.3   1.3     0.011       9.1      67      95 ..     159     184 ..     157     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.3
                                      T--HHHHHHHHHHHHCC.TT CS
                              HypA 38 gvepeaLefafellaegtvl 57
                                      +v  +aL+ +++ +++++ +
  gi|313127350|ref|YP_004037620.1| 25 EVMRDALRVYLDEAERSSEA 44
                                      45566666666665555443 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0004
                                       EETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  72 rCreCgkefeleekalrCpkCgsad 96 
                                        C++Cg+e + +  ++ Cp+Cg++ 
  gi|313127350|ref|YP_004037620.1| 137 PCEKCGEELSPD--DVYCPNCGEKA 159
                                       5*********88..468*****975 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.011
                                       E--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  67 vpvkvrCreCgkefeleekalrCpkCgsa 95 
                                        + +v C+ Cg e++++  a+ Cp Cg++
  gi|313127350|ref|YP_004037620.1| 159 ANHRVFCE-CGDEVRSD-WAF-CPGCGRR 184
                                       667899*5.*****987.445.****986 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4     0.092        79       9      15 ..     150     156 ..     149     157 .. 0.90
   2 ?    5.7   0.1     0.018        15      11      22 ..     178     189 ..     176     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.092
                           DUF2752   9 ipCPGCG 15 
                                       ++CP CG
  gi|313127350|ref|YP_004037620.1| 150 VYCPNCG 156
                                       79****9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.018
                           DUF2752  11 CPGCGltRavha 22 
                                       CPGCG  +++ +
  gi|313127350|ref|YP_004037620.1| 178 CPGCGRRTSAAD 189
                                       *****7666655 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.3   1.1e+03      27      35 ..     138     146 ..     137     149 .. 0.82
   2 ?    6.9   0.4    0.0069       5.9       6      17 ..     151     162 ..     151     163 .. 0.91
   3 ?   -0.7   3.5       1.6   1.4e+03       7      30 ..     165     181 ..     164     181 .. 0.58
   4 ?    7.1   0.4    0.0058         5       3      13 ..     174     184 ..     172     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                    Zn_ribbon_SprT  27 CrrCkgtLr 35 
                                       C +C+++L+
  gi|313127350|ref|YP_004037620.1| 138 CEKCGEELS 146
                                       889999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0069
                    Zn_ribbon_SprT   6 rCtgCgreythh 17 
                                       +C++Cg++ +h+
  gi|313127350|ref|YP_004037620.1| 151 YCPNCGEKANHR 162
                                       7*******9998 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.6
                    Zn_ribbon_SprT   7 CtgCgreythhlsirrhnYrCrrC 30 
                                       C  Cg+e     +++++   C+ C
  gi|313127350|ref|YP_004037620.1| 165 C-ECGDE----VRSDWAF--CPGC 181
                                       6.66643....5666666..6666 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0058
                    Zn_ribbon_SprT   3 yvYrCtgCgre 13 
                                        ++ C+gCgr+
  gi|313127350|ref|YP_004037620.1| 174 DWAFCPGCGRR 184
                                       6899*****65 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.016        14       4      17 ..     150     163 ..     148     168 .. 0.84
   2 ?    6.5   0.1    0.0083       7.1       2      13 ..     174     185 ..     173     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.016
                      Cys_rich_KTR   4 vlcPvCgnkTRlki 17 
                                       v+cP Cg k  +++
  gi|313127350|ref|YP_004037620.1| 150 VYCPNCGEKANHRV 163
                                       78999999988776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0083
                      Cys_rich_KTR   2 eWvlcPvCgnkT 13 
                                       +W +cP Cg +T
  gi|313127350|ref|YP_004037620.1| 174 DWAFCPGCGRRT 185
                                       7********998 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   5.8     0.022        19      11      43 ..     138     169 ..     130     174 .. 0.76
   2 ?    2.5   3.0      0.19   1.6e+02      24      33 ..     176     185 ..     165     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                      NOB1_Zn_bind  11 ChaCfkvtkdmtkkFCpkCGnktLkrvavsvde 43 
                                       C  C +  +  + ++Cp+CG+k  +rv +   +
  gi|313127350|ref|YP_004037620.1| 138 CEKCGEELS-PDDVYCPNCGEKANHRVFCECGD 169
                                       555555443.5679*********9999987765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.19
                      NOB1_Zn_bind  24 kFCpkCGnkt 33 
                                        FCp CG +t
  gi|313127350|ref|YP_004037620.1| 176 AFCPGCGRRT 185
                                       7******987 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   8.9     0.039        34      24      69 ..     135     187 ..     104     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.039
                       Zn_Tnp_IS91  24 vekilrCrtaalGfaryeCeeCghe..kivyfsCksr......hCpsCqkkate 69 
                                        +  ++C++ +l    + C++Cg++  + v++ C++       +Cp C++++++
  gi|313127350|ref|YP_004037620.1| 135 EKPCEKCGE-ELSPDDVYCPNCGEKanHRVFCECGDEvrsdwaFCPGCGRRTSA 187
                                       455678888.78889999999985544889999987433444479999998875 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.15   1.3e+02      40      56 ..     126     145 ..      95     150 .. 0.64
   2 ?    3.0  10.4      0.11        95      31      57 ..     138     160 ..     135     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.15
                    OrfB_Zn_ribbon  40 e...alsgrtfkCpnCgfea 56 
                                       e    +++++  C++Cg e+
  gi|313127350|ref|YP_004037620.1| 126 EdasGVHTQEKPCEKCGEEL 145
                                       25555666677788887765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                    OrfB_Zn_ribbon  31 CseCgsknkealsgrtfkCpnCgfead 57 
                                       C +Cg+++++    + ++CpnCg +a+
  gi|313127350|ref|YP_004037620.1| 138 CEKCGEELSP----DDVYCPNCGEKAN 160
                                       7778777766....8888888888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1311.67
//
Query:       gi|313127351|ref|YP_004037621.1|  [L=59]
Description: transcriptional regulator, copg family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-08   33.4   0.2    3.6e-08   33.0   0.2    1.2  1  RHH_1          Ribbon-helix-helix protein, copG family
    7.1e-05   23.0   0.0    7.5e-05   22.9   0.0    1.0  1  RHH_8          Ribbon-Helix-Helix transcriptional regulator f
  ------ inclusion threshold ------
      0.036   14.8   0.7      0.052   14.3   0.7    1.3  1  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.2   6.1e-12   3.6e-08       1      37 [.       3      40 ..       3      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 6.1e-12
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                      rv++r++++ +e+++++++ ++ ++rSe+IR A+re l
  gi|313127351|ref|YP_004037621.1|  3 RVTLRIPKQQIEEVERMVETGEfPNRSEAIRSAVREML 40
                                      9**********************************966 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.3e-08   7.5e-05       4      57 ..       2      55 ..       1      58 [. 0.90

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-08
                             RHH_8  4 ekvtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakhddalkqavkrks 57
                                      e+vt+ +    + +++ +ve G + nR++ ir+a+r+ L++++ + +++ +++ 
  gi|313127351|ref|YP_004037621.1|  2 ERVTLRIPKQQIEEVERMVETGEFPNRSEAIRSAVREMLNEQQVEGRESSTKRG 55
                                      89**************************************99988777777665 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.7   8.7e-06     0.052      21      51 ..      22      54 ..      10      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.7e-06
                                      XXX..XXXXXXXXXXXXXXXXXXXXXX--HHHH CS
                     PSK_trans_fac 21 tge..skteAvrrAleerlerlrreraepller 51
                                      tge  +  eA+r A++e l++ + e +e++++r
  gi|313127351|ref|YP_004037621.1| 22 TGEfpNRSEAIRSAVREMLNEQQVEGRESSTKR 54
                                      77777899*************998866666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 390.89
//
Query:       gi|313127352|ref|YP_004037622.1|  [L=402]
Description: cell division protein ftsz [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-37  128.8   3.5    8.3e-37  127.3   3.5    1.9  1  Tubulin   Tubulin/FtsZ family, GTPase domain
    1.6e-35  121.3   0.7    1.6e-35  121.3   0.7    2.7  3  FtsZ_C    FtsZ family, C-terminal domain
  ------ inclusion threshold ------
      0.058   12.7   0.0       0.13   11.6   0.0    1.5  1  ThiF      ThiF family
       0.09   12.6   0.0       0.32   10.9   0.0    1.9  1  Csm1_B    Csm1 subunit domain B
        3.6    8.3   9.6        9.1    7.0   9.6    1.6  1  IMUP      Immortalisation up-regulated protein


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3   3.5   2.3e-40   8.3e-37       1     195 [.      32     190 ..      32     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 2.3e-40
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +i+++g+G++Gn+++n+l++      g+             +g +e++    ai+td+q+l+ i+a+      +k+l
  gi|313127352|ref|YP_004037622.1|  32 RIVIVGCGGAGNNTVNRLYN-----IGV-------------DG-AETV----AINTDKQHLKMIEAD------TKIL 79 
                                       59******************.....488.............66.7777....***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       +gk+ ++++gagg+p++g++a+e  +  +++ + ++d+   +f+ta++gGGTG+G++pv+ +++ke+  +a+vv++v
  gi|313127352|ref|YP_004037622.1|  80 VGKSLTQGLGAGGDPSMGERATEMAQGTVKEVLGNADL---VFVTAGMGGGTGTGAAPVVSKIAKEQ--GAIVVGMV 151
                                       **************************************...**************************..******** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlki 195
                                        +P++   +  +  +a+++l++l++e+d++iv+dN++Ll+ 
  gi|313127352|ref|YP_004037622.1| 152 STPFNV--ERARTVKAEEGLEKLRNEADSIIVLDNNRLLDY 190
                                       ****98..899***************************986 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.82   2.9e+03      27      56 ..      48      76 ..      42      85 .. 0.75
   2 ?   -1.1   0.1      0.68   2.4e+03      40      40 ..     117     117 ..      87     161 .. 0.59
   3 !  121.3   0.7   4.4e-39   1.6e-35       1      95 []     239     333 ..     239     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.82
                                      GGGT--GGG-SEEEEEEEE-TT--HHHHHH CS
                            FtsZ_C 27 pLLdvdlsgAkgvlvnitggsdltlkEvee 56
                                       L ++ ++gA++v +n t  + l++ E+++
  gi|313127352|ref|YP_004037622.1| 48 RLYNIGVDGAETVAIN-TDKQHLKMIEADT 76
                                      5677888899998888.5667777777765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.68
                                       E CS
                            FtsZ_C  40 l 40 
                                       l
  gi|313127352|ref|YP_004037622.1| 117 L 117
                                       2 PP

  == domain 3  score: 121.3 bits;  conditional E-value: 4.4e-39
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvA+m vGe++++++++e++++a+++pLLdvd++gA+g lv+itgg+dltlkE+e +a++i+e+++ +anvi+Ga+i
  gi|313127352|ref|YP_004037622.1| 239 GVAVMLVGETQDKNKTQEVVNDAMNHPLLDVDYRGASGGLVHITGGPDLTLKEAEGIANNITERLEASANVIWGARI 315
                                       99*************************************************************************** PP

                                       -TT--SEEEEEEEEES-X CS
                            FtsZ_C  78 deeledeirvtvvatglk 95 
                                       ++e+++++rv++++tg++
  gi|313127352|ref|YP_004037622.1| 316 QDEYKGKVRVMAIMTGVQ 333
                                       ****************96 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.5e-05      0.13      12      43 ..      24      55 ..      15      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                                      HHHHHHTSEEEEE--SHHHHHHHHHHHHHTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 12 gqekLrdskvllvGaGglGsellknLalsGvg 43
                                      ++e+  + ++++vG+Gg G++ +  L  +Gv 
  gi|313127352|ref|YP_004037622.1| 24 DDEEFGNPRIVIVGCGGAGNNTVNRLYNIGVD 55
                                      56777889**********************96 PP

>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     9e-05      0.32      20      73 ..     214     267 ..     210     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9e-05
                                       HHHHHHHHHHHHTT--CCCEEEEETTEEEEEEE--HHHHHHHHHHHHHHHHHCC CS
                            Csm1_B  20 lleeivdelleklelsranllYagGGhfylLlpntekvkekleeiekelnewll 73 
                                       ++e i +  l +l+  +++ +++ GG +++L+ +t++ +++ e +++++n+ ll
  gi|313127352|ref|YP_004037622.1| 214 ISETITQPSLINLDYADMSTIMNQGGVAVMLVGETQDKNKTQEVVNDAMNHPLL 267
                                       67899999999*************************999999999999998876 PP

>> IMUP  Immortalisation up-regulated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   9.6    0.0025       9.1      31      76 ..     336     380 ..     331     394 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                              IMUP  31 kvqGaseagaaekprhg.hgkssssdsssssssssdsdaeakphaag 76 
                                       +v G s ++ a+k r++ +g+ss+ d+ssssssss   +   p ++g
  gi|313127352|ref|YP_004037622.1| 336 QVLGPSTQKQADKSRQSiQGTSSEFDTSSSSSSSS--RQPQAPSSTG 380
                                       68899999999999987356666667777665444..4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 2999.78
//
Query:       gi|313127353|ref|YP_004037623.1|  [L=707]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-13   50.8   0.1    5.8e-13   49.1   0.1    1.9  1  Copper-bind  Copper binding proteins, plastocyanin/azurin fam
  ------ inclusion threshold ------
       0.12   12.2   1.8       0.42   10.6   1.8    2.0  1  TAT_signal   TAT (twin-arginine translocation) pathway signal


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.1   6.5e-17   5.8e-13       8      98 ..      80     169 ..      73     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 6.5e-17
                                       TTETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEE CS
                       Copper-bind   8 esgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffC 84 
                                         g+++F ++ + v++g++v +   ++m+H v   ++  ++     +     +     +G +++ tf+++g Y+++C
  gi|313127353|ref|YP_004037623.1|  80 GAGKFVFTPAVVWVESGTTVSWSI-EGMAHSVTAYHEDNDKPHRVPEGASAFDSGTLEAGTTFEHTFETPGVYNYYC 155
                                       4567******************98.*******998855433333333322224445789****************** PP

                                       TTTTTTTSEEEEEE CS
                       Copper-bind  85 sPHaaagMkgkvtv 98 
                                       +PH ++gM+g v+v
  gi|313127353|ref|YP_004037623.1| 156 TPHEGLGMVGLVVV 169
                                       ************98 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.8   4.6e-05      0.42       4      25 ..       5      25 ..       4      26 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.6e-05
                        TAT_signal  4 RRdFLKgsAAaaAAaalggcaa 25
                                      RR+FLK   +++  a ++gcaa
  gi|313127353|ref|YP_004037623.1|  5 RRQFLK-LTGVGLTASFAGCAA 25
                                      9*****.555557888999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (707 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 5124.26
//
Query:       gi|313127354|ref|YP_004037624.1|  [L=322]
Description: hypothetical protein Hbor_26270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-15   54.8   0.0    1.7e-14   54.0   0.0    1.5  1  ATP_bind_3     PP-loop family
    1.7e-05   24.9   0.0    2.4e-05   24.5   0.0    1.2  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
     0.0003   20.0   0.0    0.00055   19.1   0.0    1.4  1  NAD_synthase   NAD synthase
     0.0016   17.9   1.6     0.0016   17.9   1.6    2.1  2  zn-ribbon_14   Zinc-ribbon
     0.0051   15.6   0.0      0.007   15.2   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.051   13.1   0.0      0.079   12.5   0.0    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
       0.56    9.8   8.0       0.76    9.4   2.4    3.2  3  RecR           RecR protein


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   6.8e-18   1.7e-14       2     124 ..      56     190 ..      55     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 6.8e-18
                                       EEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv......... 68 
                                       +++++SgG DS++L+++l +   k    +++a++++ g+    +e  e++ el++ l++++e  + +          
  gi|313127354|ref|YP_004037624.1|  56 WVIGLSGGKDSVVLTHILDETFGKDPRiEMMALTIHEGIEGYRDESVEACVELSDDLQMRHELVTYEEefgvqmddv 132
                                       69****************9987766555*********************************9999987777777666 PP

                                       HHCTTSTCCCHH..HHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CC CS
                        ATP_bind_3  69 akkkgknleeaA..RelRYevlkealkkegievlllAhhadDqaEtfllrlargsgla 124
                                       a++  +n+   A    +R ++l++++++ +++ ll++h+ dD aEt+l+++  g  ++
  gi|313127354|ref|YP_004037624.1| 133 AREDPENMAPCAycGVFRRDLLESYAEEFSADKLLTGHNLDDEAETALMNILEGDVKQ 190
                                       44444444443311469*********************************99987764 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   9.3e-09   2.4e-05       3     155 ..      57     237 ..      55     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.3e-09
                                       EEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHT.T-EEEEEE-SCHHHHHHHHHH-S-THH CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleery.glrlkvyepeeevaekinaekhgssly 78 
                                       v+  sgGkds+Vl h++ ++f + p + ++    ++ +  ++de +e   +l   + + ++e    +++++   +++
  gi|313127354|ref|YP_004037624.1|  57 VIGLSGGKDSVVLTHILDETFGKDPRIEMMALTIHEGIEGYRDESVEACvEL-SDDLQMRHELVTYEEEFGVQMDDV 132
                                       6778******************985555555555555555555555555211.233333344444444444444444 PP

                                       HC.........HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S................. CS
                       PAPS_reduct  79 ee.........aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek................. 129
                                        +         a++ + + + l+   e++++d lltG   d++++ a ++i+e d ++ +                 
  gi|313127354|ref|YP_004037624.1| 133 ARedpenmapcAYCGVFRRDLLESYAEEFSADKLLTGHNLDDEAETALMNILEGDVKQMAkhfdaslgpfdernpsd 209
                                       44444445556********************************************9988899*************** PP

                                       ..CEEE-CCCT--HHHHHHHHHHCT--B CS
                       PAPS_reduct 130 ..slrvfPllnWteedvwqyilrenipy 155
                                         + r  Pl +  e++v  y+  +++p 
  gi|313127354|ref|YP_004037624.1| 210 dfVPRAKPLRDIPEKEVALYAHLKDLPA 237
                                       *999999**************9999986 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.1e-07   0.00055      19     123 ..      54     164 ..      46     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.1e-07
                                       SEEEEEE-SSHHHHHHHHHHHHHHTCG...EEEEEE--..SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHH CS
                      NAD_synthase  19 kgvvlGlSGGvDSslvaalavkalgke...nvlalllP..ssvsseedvedalalaenlgievktidikpivrafeq 90 
                                       +  v+GlSGG DS +   +  + +gk+   +++al +    +   +e+ve+ ++l ++l+++ + +  ++   +  +
  gi|313127354|ref|YP_004037624.1|  54 ERWVIGLSGGKDSVVLTHILDETFGKDpriEMMALTIHegIEGYRDESVEACVELSDDLQMRHELVTYEEEFGVQMD 130
                                       5679********************9984445778888742234578999*****************99998877666 PP

                                       .HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEE CS
                      NAD_synthase  91 .elkeakedlakgNlkaRiRmailyaianklnll 123
                                         ++e+ e++a    +   R  +l ++a++++  
  gi|313127354|ref|YP_004037624.1| 131 dVAREDPENMAPCAYCGVFRRDLLESYAEEFSAD 164
                                       2555666999999999999999988888877644 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       1.3   3.2e+03       2       7 ..       2       7 ..       1       7 [. 0.81
   2 !   17.9   1.6   6.3e-07    0.0016       2      23 ..     297     318 ..     296     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                      zn-ribbon_14 2 kCerCG 7
                                      C +C+
  gi|313127354|ref|YP_004037624.1| 2 ECDKCD 7
                                     6****5 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 6.3e-07
                      zn-ribbon_14   2 kCerCGylSSqkiCkACvLLeg 23 
                                        CerCG  +  ++C+ C LLe+
  gi|313127354|ref|YP_004037624.1| 297 DCERCGSKTARDVCRKCRLLES 318
                                       7*******************97 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.7e-06     0.007       4     128 ..      57     174 ..      54     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-06
                     tRNA_Me_trans   4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfe 80 
                                       v++lSgG DS v  ++l e + +  ++ +   + ++  g e   +e ++   + ++ l++++e v +e+e+  ++  
  gi|313127354|ref|YP_004037624.1|  57 VIGLSGGKDSVVLTHILDETFGKDPRIEMMALTIHE--GIEGYRDESVEACVELSDDLQMRHELVTYEEEFGVQMD- 130
                                       799*****************9998888877776633..334688999999*********************98864. PP

                     tRNA_Me_trans  81 efleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHYarv 128
                                       ++ +e    +   P++ C    + ++l ++a+ e  ad+l tGH    
  gi|313127354|ref|YP_004037624.1| 131 DVARED--PENMAPCAYCGVF-RRDLLESYAE-EFSADKLLTGHNLDD 174
                                       444443..344579****753.4455555555.59*********6554 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05     0.079       7     129 ..      57     183 ..      53     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                              ThiI   7 laLlSgGiDSpVaayll...lkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeil 80 
                                       +  lSgG DS V +++l   + +  r++++ l+ + g +    e ve  +el  + q  +e+  +  +f   ++++ 
  gi|313127354|ref|YP_004037624.1|  57 VIGLSGGKDSVVLTHILdetFGKDPRIEMMALTIHEGIEGYRDESVEACVELSDDLQMRHELVTYEEEFGVQMDDVA 133
                                       55689999999999986333556778999999989999999999************98666666666899999**** PP

                              ThiI  81 ekvkekltivl.lkrkmlriAekvaeeegakalvtGesLgqVaSqtleNl 129
                                       ++ +e++     +      + e +aee+ a+ l+tG +L   a   l N+
  gi|313127354|ref|YP_004037624.1| 134 REDPENMAPCAyCGVFRRDLLESYAEEFSADKLLTGHNLDDEAETALMNI 183
                                       *9999987554044444458899*****************9999999998 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.094   2.4e+02      16      39 ..     140     151 ..     134     152 .. 0.57
   2 ?   -1.2   0.0      0.61   1.6e+03       6      20 ..     229     243 ..     227     244 .. 0.81
   3 ?    9.4   2.4    0.0003      0.76      18      35 ..     297     314 ..     294     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.094
                                       -EE-TTT--EESSSS-CCCCSTTS CS
                              RecR  16 vrhCsrCgnlteedlCaICsdprR 39 
                                       +             +Ca C   rR
  gi|313127354|ref|YP_004037624.1| 140 MA------------PCAYCGVFRR 151
                                       44............5555555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.61
                                       HHHHHHHHHH-EE-T CS
                              RecR   6 aeaLqeakekvrhCs 20 
                                          L+++  +++ C+
  gi|313127354|ref|YP_004037624.1| 229 YAHLKDLPAHITECP 243
                                       567999999*****7 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0003
                                       E-TTT--EESSSS-CCCC CS
                              RecR  18 hCsrCgnlteedlCaICs 35 
                                        C+rCg  t +d+C+ C+
  gi|313127354|ref|YP_004037624.1| 297 DCERCGSKTARDVCRKCR 314
                                       6**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2417.21
//
Query:       gi|313127355|ref|YP_004037625.1|  [L=214]
Description: hypothetical protein Hbor_26280 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1455.53
//
Query:       gi|313127356|ref|YP_004037626.1|  [L=54]
Description: hypothetical protein Hbor_26290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.17   12.1   0.0        0.2   11.9   0.0    1.1  1  Chordopox_A13L  Chordopoxvirus A13L protein


Domain annotation for each model (and alignments):
>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.1e-05       0.2       5      43 ..       8      47 ..       4      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.1e-05
                    Chordopox_A13L  5 lllliiCvaivglivYgiYnrkketqttnpst.veeyeee 43
                                      ++l+++ ++   l++Yg  +++++ q+t  ++  e+  ++
  gi|313127356|ref|YP_004037626.1|  8 FVLFMLLAIGAPLVLYGFIRKETSDQQTMDRSdAERAAQK 47
                                      6677777777789***********9999998855555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 418.73
//
Query:       gi|313127357|ref|YP_004037627.1|  [L=71]
Description: nucleic-acid-binding protein containing a zn-ribbon domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-26   91.1   0.3    4.1e-26   90.9   0.3    1.0  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
     0.0015   18.2   2.0       0.14   12.0   0.0    2.2  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.002   17.5   1.6       0.68    9.4   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0028   17.6   2.8       0.71    9.9   0.4    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0036   17.3   0.2     0.0049   16.9   0.2    1.2  1  DZR              Double zinc ribbon
      0.004   17.5   0.2     0.0054   17.1   0.2    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.012   15.7   0.8      0.028   14.5   0.8    1.6  1  CpXC             CpXC protein
      0.017   15.2   0.7       0.63   10.2   0.6    2.1  2  DUF2387          Probable metal-binding protein (DUF2387)
      0.024   14.7   0.4        1.5    9.0   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
      0.044   13.5   3.5        1.1    9.1   0.5    2.2  2  zinc_ribbon_2    zinc-ribbon domain
      0.053   13.7   1.0       0.64   10.2   0.1    2.1  2  Ribosomal_L37e   Ribosomal protein L37e
      0.055   13.3   1.0        1.4    8.8   0.0    2.2  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
      0.065   13.2   4.0        2.2    8.3   0.4    2.1  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.082   12.4   4.1        1.1    8.8   4.1    2.1  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.093   12.4   1.1       0.31   10.7   1.1    1.8  1  DUF2225          Uncharacterized protein conserved in bacteri
        0.1   12.5   5.4        1.3    8.9   0.3    2.5  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.11   12.3   3.7        3.7    7.3   1.2    2.3  2  Ribosomal_S27e   Ribosomal protein S27
       0.14   12.0   2.2        2.3    8.2   0.2    2.2  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.17   11.9   1.9        1.3    9.1   0.2    2.1  2  Zn_Tnp_IS91      Transposase zinc-binding domain
       0.23   11.0   0.8       0.39   10.3   0.1    1.7  2  zf_C2H2_10       C2H2 type zinc-finger
       0.82    9.6   4.0         15    5.6   0.9    2.2  2  zinc_ribbon_4    zinc-ribbon domain
       0.91    9.7   6.5        7.1    6.8   0.3    2.2  2  UPF0547          Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.3     5e-29   4.1e-26       1      63 []      11      71 .]      11      71 .] 0.97

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 5e-29
                    zinc_ribbon_13  1 kCpKCgnteaevkevaatGsglskifdvqnkkfitvsCknCgYtelYkaetsegknilDlllg 63
                                      +CpKCg+te+e++++a++G+glsk+fdvqn+ f++v+C +CgY+elY++++s   n+ Dl+lg
  gi|313127357|ref|YP_004037627.1| 11 GCPKCGHTETEMDSIATSGTGLSKFFDVQNRSFTVVTCASCGYSELYRKKSSG--NLADLFLG 71
                                      5*************************************************998..9****987 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.6     0.014        11       2       8 ..      10      16 ..       9      19 .. 0.80
   2 !   12.0   0.0   0.00017      0.14       1      23 [.      45      71 .]      45      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                                      EE-SSS- CS
                    zf-C4_Topoisom  2 ekCPkCg 8 
                                      + CPkCg
  gi|313127357|ref|YP_004037627.1| 10 RGCPKCG 16
                                      56****9 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00017
                                      -EE-SSS-.-EEEEEE-SSS...EEEE CS
                    zf-C4_Topoisom  1 vekCPkCg.gdLvlkrgkkG...kFvG 23
                                      v++C +Cg ++L +k++  +    F+G
  gi|313127357|ref|YP_004037627.1| 45 VVTCASCGySELYRKKSSGNladLFLG 71
                                      579**************9997777776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2   0.00083      0.68      18      24 ..      11      17 ..       5      22 .. 0.68
   2 !    7.4   0.1    0.0036       2.9      16      24 ..      45      53 ..      42      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00083
                       zf-ribbon_3 18 vCpyCGt 24
                                       Cp+CG+
  gi|313127357|ref|YP_004037627.1| 11 GCPKCGH 17
                                      5666664 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0036
                       zf-ribbon_3 16 dnvCpyCGt 24
                                      +++C++CG+
  gi|313127357|ref|YP_004037627.1| 45 VVTCASCGY 53
                                      689*****7 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.4   0.00087      0.71      17      29 ..       7      22 ..       4      41 .. 0.73
   2 !    8.4   0.1    0.0025         2      19      33 ..      46      60 ..      39      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00087
                     Zn_Tnp_IS1595 17 ng.fvCPhCgsr..ka 29
                                      ng + CP+Cg++  + 
  gi|313127357|ref|YP_004037627.1|  7 NGdRGCPKCGHTetEM 22
                                      45345*****986555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayrik 33
                                      ++C  Cg++++yr k
  gi|313127357|ref|YP_004037627.1| 46 VTCASCGYSELYRKK 60
                                      67**********966 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2     6e-06    0.0049       6      37 ..       3      54 ..       2      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6e-06
                               DZR  6 eelppdarfCseCgtklkavaa....................edrCpsCgek 37
                                      +e ++++r C++Cg++  ++ +                      +C sCg++
  gi|313127357|ref|YP_004037627.1|  3 HEARNGDRGCPKCGHTETEMDSiatsgtglskffdvqnrsftVVTCASCGYS 54
                                      677899*********977766688899***********************97 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   6.7e-06    0.0054       6      37 ..      12      54 ..      10      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.7e-06
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigq...........cvyCadCgas 37
                                      CP Cg+ ++   s  ++  +             +v+Ca Cg+s
  gi|313127357|ref|YP_004037627.1| 12 CPKCGHTETEMDSIATSGTGLSkffdvqnrsftVVTCASCGYS 54
                                      **********9999888766669******************92 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   3.4e-05     0.028       3      49 ..      12      57 ..      10      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                              CpXC  3 CpaCgkefeaeiwtsidadedpelkeklldgslfeatCpkCgatakl 49
                                      Cp+Cg++ e+e+  + +  +      ++ + s++ +tC +Cg++  +
  gi|313127357|ref|YP_004037627.1| 12 CPKCGHT-ETEMDSIATSGTGLSKFFDVQNRSFTVVTCASCGYSELY 57
                                      ****985.5566666666666666779***************98765 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1      0.01       8.1      31      45 ..      10      24 ..       2      40 .. 0.78
   2 ?   10.2   0.6   0.00077      0.63      11      45 ..      12      60 ..      11      68 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                           DUF2387 31 rECvsCgftdelsek 45
                                      r C +Cg+t++  ++
  gi|313127357|ref|YP_004037627.1| 10 RGCPKCGHTETEMDS 24
                                      779999999987665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00077
                           DUF2387 11 CPrC....semD........kirmweede..veyrECvsCgftdelsek 45
                                      CP+C     emD          + ++ ++    ++ C sCg+++  ++k
  gi|313127357|ref|YP_004037627.1| 12 CPKCghteTEMDsiatsgtgLSKFFDVQNrsFTVVTCASCGYSELYRKK 60
                                      888833333677444443322245666664567899******9988777 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0019       1.5      28      36 ..      11      20 ..       1      28 [. 0.68
   2 ?    4.6   0.0     0.045        37      28      35 ..      47      55 ..      33      64 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                       Zn-ribbon_8 28 aCPeCgs.ev 36
                                       CP+Cg+ e+
  gi|313127357|ref|YP_004037627.1| 11 GCPKCGHtET 20
                                      3888887554 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.045
                       Zn-ribbon_8 28 aCPeCgs.e 35
                                      +C +Cg  e
  gi|313127357|ref|YP_004037627.1| 47 TCASCGYsE 55
                                      466666444 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.5    0.0013       1.1      16      21 ..      12      17 ..       3      18 .. 0.72
   2 ?    5.4   0.1     0.019        16      13      21 ..      45      53 ..      39      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                     zinc_ribbon_2 16 CpyCGt 21
                                      Cp+CG+
  gi|313127357|ref|YP_004037627.1| 12 CPKCGH 17
                                      777776 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                     zinc_ribbon_2 13 akFCpyCGt 21
                                      ++ C  CG+
  gi|313127357|ref|YP_004037627.1| 45 VVTCASCGY 53
                                      677999997 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.23   1.9e+02      33      43 ..      11      21 ..       6      26 .. 0.71
   2 ?   10.2   0.1   0.00078      0.64      32      45 ..      46      60 ..      37      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.23
                    Ribosomal_L37e 33 tCascGypsak 43
                                       C +cG+ ++ 
  gi|313127357|ref|YP_004037627.1| 11 GCPKCGHTETE 21
                                      47788876655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00078
                    Ribosomal_L37e 32 ktCascGy.psaklr 45
                                       tCascGy    +++
  gi|313127357|ref|YP_004037627.1| 46 VTCASCGYsELYRKK 60
                                      48******6666665 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.091        74      15      20 ..      10      16 ..       2      18 .. 0.74
   2 ?    8.8   0.0    0.0017       1.4       4      20 ..      36      52 ..      35      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.091
                         zf-C2H2_3 15 q.CkeCg 20
                                      + C++Cg
  gi|313127357|ref|YP_004037627.1| 10 RgCPKCG 16
                                      35****9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                         zf-C2H2_3  4 LdlgqksfgasqCkeCg 20
                                       d+ ++sf+ ++C+ Cg
  gi|313127357|ref|YP_004037627.1| 36 FDVQNRSFTVVTCASCG 52
                                      588899**********9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0078       6.4      31      40 ..      12      21 ..       5      35 .. 0.81
   2 ?    8.3   0.4    0.0027       2.2      21      40 ..      38      57 ..      33      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0078
                    OrfB_Zn_ribbon 31 CseCgsknke 40
                                      C++Cg++ +e
  gi|313127357|ref|YP_004037627.1| 12 CPKCGHTETE 21
                                      999*999988 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0027
                    OrfB_Zn_ribbon 21 evnpayTSktCseCgsknke 40
                                      + n+++T  tC+ Cg+   +
  gi|313127357|ref|YP_004037627.1| 38 VQNRSFTVVTCASCGYSELY 57
                                      568889*********97655 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.1    0.0014       1.1       3      26 ..      12      52 ..      10      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                                      ETTTTCEEC.................HEETSTTCEEESSSS CS
                      TF_Zn_Ribbon  3 CPnCgstnl.................veDpergelvCtdCG 26
                                      CP+Cg+t++                 v + + + ++C +CG
  gi|313127357|ref|YP_004037627.1| 12 CPKCGHTETemdsiatsgtglskffdVQNRSFTVVTCASCG 52
                                      *******9978888888888888333333443444788888 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00038      0.31      35      60 ..      32      57 ..      10      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                           DUF2225 35 nakYeevnplfYevvvCpkCgYaalk 60
                                        k+ +v+ + + vv+C +CgY+ l 
  gi|313127357|ref|YP_004037627.1| 32 LSKFFDVQNRSFTVVTCASCGYSELY 57
                                      5688899999************9875 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3    0.0016       1.3       3      11 ..      12      20 ..      10      23 .. 0.89
   2 ?    5.3   0.8     0.021        17      27      36 ..      44      53 ..      34      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                           TFIIS_C  3 CpkCgsrea 11
                                      CpkCg++e+
  gi|313127357|ref|YP_004037627.1| 12 CPKCGHTET 20
                                      ******997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.021
                           TFIIS_C 27 vfykCtkCgh 36
                                      + ++C++Cg+
  gi|313127357|ref|YP_004037627.1| 44 TVVTCASCGY 53
                                      7789999997 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.02        16      10      23 ..      12      25 ..       9      29 .. 0.80
   2 ?    7.3   1.2    0.0046       3.7      21      33 ..      40      52 ..      34      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.02
                                      -TTTS-EEEEESS- CS
                    Ribosomal_S27e 10 CpdCenetvvFsha 23
                                      Cp+C+++ +  ++ 
  gi|313127357|ref|YP_004037627.1| 12 CPKCGHTETEMDSI 25
                                      ******99877665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0046
                                      SS-SS-EEESSST CS
                    Ribosomal_S27e 21 shaatvvkCisCg 33
                                      +++ tvv+C sCg
  gi|313127357|ref|YP_004037627.1| 40 NRSFTVVTCASCG 52
                                      5788********9 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.07        57       4       8 ..      12      16 ..       5      21 .. 0.91
   2 ?    8.2   0.2    0.0028       2.3      21      31 ..      45      55 ..      37      55 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.07
                                      ESTTT CS
                    RNA_POL_M_15KD  4 CpkCg 8 
                                      CpkCg
  gi|313127357|ref|YP_004037627.1| 12 CPKCG 16
                                      99998 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0028
                                      EEEESSSS-EE CS
                    RNA_POL_M_15KD 21 nfeCrqCgYee 31
                                      ++ C++CgY e
  gi|313127357|ref|YP_004037627.1| 45 VVTCASCGYSE 55
                                      378******75 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0016       1.3      56      69 ..       8      21 ..       3      38 .. 0.87
   2 ?    3.1   0.1      0.12        94      36      50 ..      42      56 ..      32      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                       Zn_Tnp_IS91 56 ksrhCpsCqkkate 69
                                      ++r Cp+C++ +te
  gi|313127357|ref|YP_004037627.1|  8 GDRGCPKCGHTETE 21
                                      5799******9987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                       Zn_Tnp_IS91 36 GfaryeCeeCgheki 50
                                       f+++ C +Cg +++
  gi|313127357|ref|YP_004037627.1| 42 SFTVVTCASCGYSEL 56
                                      578889999997765 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00048      0.39       5      17 ..      12      24 ..       9      26 .. 0.86
   2 ?   -1.6   0.1       2.5   2.1e+03       5      10 ..      48      53 ..      46      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                        zf_C2H2_10  5 CPKCqeklPDiDt 17
                                      CPKC+     +D+
  gi|313127357|ref|YP_004037627.1| 12 CPKCGHTETEMDS 24
                                      *****99999998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                        zf_C2H2_10  5 CPKCqe 10
                                      C  C++
  gi|313127357|ref|YP_004037627.1| 48 CASCGY 53
                                      888998 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.9     0.018        15      28      34 ..      12      18 ..      10      18 .. 0.90
   2 ?    5.0   0.1     0.029        24      25      33 ..      45      53 ..      40      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.018
                     zinc_ribbon_4 28 CskCghv 34
                                      C+kCgh+
  gi|313127357|ref|YP_004037627.1| 12 CPKCGHT 18
                                      999*996 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                     zinc_ribbon_4 25 kvrCskCgh 33
                                       v+C+ Cg 
  gi|313127357|ref|YP_004037627.1| 45 VVTCASCGY 53
                                      588999985 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.5      0.02        16      17      22 ..      12      17 ..      10      18 .. 0.78
   2 ?    6.8   0.3    0.0087       7.1      15      23 ..      46      54 ..      44      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.02
                           UPF0547 17 CphCGy 22
                                      Cp CG+
  gi|313127357|ref|YP_004037627.1| 12 CPKCGH 17
                                      999998 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0087
                           UPF0547 15 qfCphCGyv 23
                                      + C+ CGy+
  gi|313127357|ref|YP_004037627.1| 46 VTCASCGYS 54
                                      57******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 494.69
//
Query:       gi|313127358|ref|YP_004037628.1|  [L=267]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-17   63.7   0.1    7.3e-17   61.9   0.0    2.0  1  Methyltransf_25  Methyltransferase domain
      5e-17   62.3   0.0    1.4e-16   60.9   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
      2e-13   50.4   0.0    3.5e-13   49.6   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    1.8e-11   44.1   0.0    2.5e-11   43.7   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    4.6e-09   36.9   0.0    1.7e-08   35.1   0.0    2.0  2  Methyltransf_12  Methyltransferase domain
    1.9e-06   27.4   0.0    3.2e-06   26.7   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.1e-06   26.9   0.0    5.3e-06   26.1   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
    7.8e-06   25.5   0.0    1.9e-05   24.2   0.0    1.6  2  MTS              Methyltransferase small domain
    4.8e-05   23.4   0.0    8.5e-05   22.6   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
    9.9e-05   21.9   0.0    0.00014   21.4   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.008   15.9   0.0      0.022   14.5   0.0    1.7  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.043   12.4   0.0      0.063   11.8   0.0    1.2  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.051   12.6   0.0      0.077   12.1   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.087   12.1   0.1       0.25   10.6   0.0    1.7  2  CMAS             Mycolic acid cyclopropane synthetase
       0.21   11.4   0.1       0.34   10.7   0.1    1.3  1  Methyltransf_8   Hypothetical methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   6.1e-20   7.3e-17       1      91 [.      35     117 ..      35     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 6.1e-20
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd+GcGtG+l++ l ++   ++v+++D ++e+l+ are a     ++  v+gda++lpf+d++fDlvv++  l  l
  gi|313127358|ref|YP_004037628.1|  35 VLDVGCGTGELSRVLDAET-PGEVVCLDADPELLRVAREAA-----DLPTVVGDATRLPFPDDTFDLVVCQALLVNL 105
                                       9*****************8.5********************.....899*********************7557766 PP

                                       SHHHHHHHHHHHHH CS
                   Methyltransf_25  78 sdedlekalkeiar 91 
                                       +++   +a++ + r
  gi|313127358|ref|YP_004037628.1| 106 PRP--TDAIESFTR 117
                                       644..355655554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   1.2e-19   1.4e-16       1      86 [.      36     117 ..      36     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.2e-19
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhved 76 
                                       LdvGcGtG l++ l     ++vv++D ++e+l++a+e+a  +      vv+da++lpf+d++fDlvv++  l ++++
  gi|313127358|ref|YP_004037628.1|  36 LDVGCGTGELSRVLDAETpGEVVCLDADPELLRVAREAADLPT-----VVGDATRLPFPDDTFDLVVCQALLVNLPR 107
                                       8**************5556********************9998.....***************************** PP

                                       HHHHHHHHHH CS
                   Methyltransf_11  77 pekalkeiaR 86 
                                       p +a++ + R
  gi|313127358|ref|YP_004037628.1| 108 PTDAIESFTR 117
                                       **99998887 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   2.9e-16   3.5e-13       5     100 ..      33     118 ..      30     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 2.9e-16
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                        rvlD+GCGtGel+ +l  e  + +evv +D ++e +++Are a+      +   +gd++ l+  + d++fDl++++
  gi|313127358|ref|YP_004037628.1|  33 SRVLDVGCGTGELSRVLDAE--TPGEVVCLDADPELLRVAREAAD------LPTVVGDATRLP--FPDDTFDLVVCQ 99 
                                       58***************965..579*****************655......55579*******..************ PP

                   Methyltransf_31  82 evlnaladpdkileeierv 100
                                       ++l  l+ p +++e+ +r+
  gi|313127358|ref|YP_004037628.1| 100 ALLVNLPRPTDAIESFTRA 118
                                       *************998876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   2.1e-14   2.5e-11      10     108 ..      21     118 ..       8     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 2.1e-14
                   Methyltransf_23  10 sdklerllpklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdl 85 
                                       +d+l+ l+  l+ ++rvLd+GcGtG+l++vl ++   +v+  D++pe+   a++a   + +  d+   ++p+++fdl
  gi|313127358|ref|YP_004037628.1|  21 RDALQDLS--LPDRSRVLDVGCGTGELSRVLDAETPgEVVCLDADPELLRVAREAADLPTVVGDATRLPFPDDTFDL 95 
                                       34555555..899******************887777****************9999999999999*********** PP

                   Methyltransf_23  86 Ivlrevlehvpdppellrqiatl 108
                                       +v+  +l ++p p+ ++ ++ + 
  gi|313127358|ref|YP_004037628.1|  96 VVCQALLVNLPRPTDAIESFTRA 118
                                       **************999988774 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   1.4e-11   1.7e-08       1      91 [.      36     117 ..      36     122 .. 0.87
   2 ?   -2.1   0.0       5.6   6.7e+03      32      32 ..     229     229 ..     195     262 .. 0.48

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.4e-11
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcGtG+l+r+l ++  + e++++D +p+ + + +++ a+      +  +l   d+       +fDlvv+  +l 
  gi|313127358|ref|YP_004037628.1|  36 LDVGCGTGELSRVLDAE-TPGEVVCLDADPELL-RVAREAADLPTVVGDATRLPFPDD-------TFDLVVCQALLV 103
                                       8**************99.9**************.888888888876666666666654.......9*********** PP

                   Methyltransf_12  78 hlkdirevldnirk 91 
                                       +l+ + ++++++ +
  gi|313127358|ref|YP_004037628.1| 104 NLPRPTDAIESFTR 117
                                       **999999998876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.6
                   Methyltransf_12  32 a 32 
                                       a
  gi|313127358|ref|YP_004037628.1| 229 A 229
                                       1 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.6e-09   3.2e-06      49     138 ..      33     114 ..      15     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.6e-09
                                       TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES- CS
                   Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfG 125
                                       ++vlDv +Gtg+l+  l   +++ g+vv lD ++++L+v+++ +      ++  ++++a +Lpf dd+fD+v     
  gi|313127358|ref|YP_004037628.1|  33 SRVLDVGCGTGELSRVLD--AETPGEVVCLDADPELLRVAREAA------DLPTVVGDATRLPFPDDTFDLVVCQAL 101
                                       589*********997774..6889**************998755......68889****************998877 PP

                                       GGG-S-HHHHHHH CS
                   Ubie_methyltran 126 lrnvtDklkaLke 138
                                       l n++  + a+++
  gi|313127358|ref|YP_004037628.1| 102 LVNLPRPTDAIES 114
                                       7777766666655 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   4.5e-09   5.3e-06      11     102 ..      29     119 ..      21     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.5e-09
                              MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaec.vakGlsviqgdldkdlenfedksfdyvvlsqtlq 86 
                                       ++++srvld+GcG Gel ++l  e   +   l+ d e +  +  a  l  + gd+ +    f+d++fd+vv +  l 
  gi|313127358|ref|YP_004037628.1|  29 LPDRSRVLDVGCGTGELSRVLDAETPGEVVCLDADPELLRVArEAADLPTVVGDATR--LPFPDDTFDLVVCQALLV 103
                                       689******************887766666676666655433134456677777654..57**********998888 PP

                              MetW  87 atrnpkevldellrig 102
                                       ++ +p+  ++   r +
  gi|313127358|ref|YP_004037628.1| 104 NLPRPTDAIESFTRAS 119
                                       8888888777777665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.6e-08   1.9e-05      25      79 ..      25      78 ..      18      99 .. 0.78
   2 ?   -3.3   0.0       4.8   5.7e+03      50      68 ..     212     230 ..     202     254 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.6e-08
                                      HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTT CS
                               MTS 25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleank 79
                                      + l+   + +vlD+GcG+G l+ +l +e+p  ev+++d+d + l++a+e +    
  gi|313127358|ref|YP_004037628.1| 25 QDLSLPDRSRVLDVGCGTGELSRVLDAETPG-EVVCLDADPELLRVAREAADLPT 78
                                      5555556788********************9.9**************99876655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                                       HHHTTC.EEEEEESBHHHH CS
                               MTS  50 akespeaevtlvdvdarAl 68 
                                       a+++ e++ tl d ++ Al
  gi|313127358|ref|YP_004037628.1| 212 AAHETELRRTLSDDEYDAL 230
                                       3444444445555555554 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   7.1e-08   8.5e-05      26      71 ..      32      74 ..      21      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.1e-08
                   Methyltransf_32 26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekra 71
                                      + +v+DvG+G g Ls+vl     e + +vv++da  el + a++ a
  gi|313127358|ref|YP_004037628.1| 32 RSRVLDVGCGTGELSRVLDA---ETPGEVVCLDADPELLRVAREAA 74
                                      678*****************...99**************9999877 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.2e-07   0.00014     155     251 ..      24     117 ..      20     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-07
                              PrmA 155 leklvkege.evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvi 230
                                       l++l  +++ +vlDvG+G+G L+ +       +vv +D D+  ++va+e a+l  v       +    ++  ++d++
  gi|313127358|ref|YP_004037628.1|  24 LQDLSLPDRsRVLDVGCGTGELSRVLDAETPGEVVCLDADPELLRVAREAADLPTVVGDA---TRLPFPD-DTFDLV 96 
                                       66666666549************99999999**********************9998877...3445666.8899** PP

                              PrmA 231 vaNILaevlielaedikklvk 251
                                       v+  L   l + ++ i ++ +
  gi|313127358|ref|YP_004037628.1|  97 VCQALLVNLPRPTDAIESFTR 117
                                       *99887777776666666655 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.8e-05     0.022      66     116 ..      24      72 ..      21      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHH CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakr 116
                                       l+ l+l + +rvL+vG+G+G l+ vl    ++ g vv ++  +el + a++
  gi|313127358|ref|YP_004037628.1|  24 LQDLSLPDRSRVLDVGCGTGELSRVLDA--ETPGEVVCLDADPELLRVARE 72 
                                       66788999*************9999985..677889999999999988876 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.2e-05     0.063     120     194 ..      34     105 ..      21     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                   Methyltransf_29 120 tvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeR.gvpailavlgtkrlpyPsrsfdlihCsrCridw 194
                                        vlDvGCg   ++ +l + +     +   D   + + +a e   +p++++   ++rlp+P  +fdl+ C   +++ 
  gi|313127358|ref|YP_004037628.1|  34 RVLDVGCGTGELSRVL-DAETPG-EVVCLDADPELLRVAREAaDLPTVVG--DATRLPFPDDTFDLVVCQALLVNL 105
                                       5899999999987655.555544.34456888889999998636898888..478**************9988875 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.4e-05     0.077      22      71 ..      23      73 ..      20      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                                      HHHHH-GGTTSEEEEES-TTTCCHHHH.HCC-SEEEEE-S-HHHHHHHHCH CS
                            RrnaAD 22 IldklnleekltvleigpGkGilTeeL.akrakqvvvlElderLakllqkk 71
                                      +l+ l l +   vl++g G+G l++ L a+   +vv l  d++L+ + +++
  gi|313127358|ref|YP_004037628.1| 23 ALQDLSLPDRSRVLDVGCGTGELSRVLdAETPGEVVCLDADPELLRVAREA 73
                                      67778888999****************88888*************999884 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.25      53      82 ..      22      51 ..      14      75 .. 0.80
   2 ?   -1.7   0.0       1.2   1.4e+03      92     132 ..     221     262 ..     218     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                                      HHHTTTT--TT-EEEEES-TTSHHHHHHHH CS
                              CMAS 53 lileklelkpGmtlLdiGcGWGslvrrave 82
                                       +l+ l+l + +++Ld+GcG G+l r   +
  gi|313127358|ref|YP_004037628.1| 22 DALQDLSLPDRSRVLDVGCGTGELSRVLDA 51
                                      578899999**************9886555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                       ES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEE CS
                              CMAS  92 TlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvv 132
                                       TlS++++   ++   e++ +  ++++   y+  +  ++d vv
  gi|313127358|ref|YP_004037628.1| 221 TLSDDEYDALRRDWREMGRTVVEQMQDERYRRAEVvPFDVVV 262
                                       899999999999999999888888888888887777888776 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00028      0.34      71     133 ..      30     102 ..      21     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                                       -TTS-EEEES-TT-HHH..HH--S-..EEEEE....S.....S-SSTTEEES-TTS-S--TT-EEEEEEES--- CS
                    Methyltransf_8  71 kdnlvvadlGcGeakia..eavrekekvrsfd....l.....vavnervvacdlakvPledesvdvavfclslm 133
                                       +d   v d+GcG   ++     + + +v ++d    l      a +   v+ d +++P  d++ d++v+  +l+
  gi|313127358|ref|YP_004037628.1|  30 PDRSRVLDVGCGTGELSrvLDAETPGEVVCLDadpeLlrvarEAADLPTVVGDATRLPFPDDTFDLVVC-QALL 102
                                       677889*******99994444566779****933332121111233345788999**********9885.4544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1818.18
//
Query:       gi|313127359|ref|YP_004037629.1|  [L=471]
Description: hypothetical protein Hbor_26320 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-10   39.0   0.4    1.4e-09   37.8   0.4    1.6  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
  ------ inclusion threshold ------
      0.028   14.3   7.4      0.028   14.3   7.4    2.7  2  TAT_signal     TAT (twin-arginine translocation) pathway sign


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.4   1.6e-13   1.4e-09      16     233 .]      83     358 ..      50     358 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.6e-13
                                       HHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH................TTCEEEEECCH............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxx............ RF
                     Exo_endo_phos  16 srrsdrladlltaydaDvlgLQEvdddelsriplllal................ggflgasstsp............ 64 
                                       s+r++++ad+l+++++Dv+g+QE         +                               +            
  gi|313127359|ref|YP_004037629.1|  83 SARMRAIADELARTRPDVVGVQE-------AALIR--TetpgdggedgldaeavS---------Fdfldeltaalde 141
                                       578********************.......22111..022223333333333320.........1333333344444 PP

                                       ........................ECSSSTTSSEEEEEECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE.. CS
                                       ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                     Exo_endo_phos  65 ........................tgggggggnggavlsrfpltslfrrtfiefndlvaalrreplaakleqlni.. 115
                                                                ++    ++  + l+r   +  + ++  +++d+ +++   ++ +  +   +  
  gi|313127359|ref|YP_004037629.1| 142 tgtpyevaqvkttadaefpglvddERIDVRLTDRDVFLVRSDADVTVSDSSAGTFDEALEIPVGDDRTFRVERGYgv 218
                                       44444444444455555555555555555555555555555555554444444444444444444444444444489 PP

                                       ...........CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SSSTSGGGBSCGHHHHHHCTTTHH.... CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                     Exo_endo_phos 116 ...........ashrdhdlvrdlqllalllqvealnadrgapvivaGDfNarpsdddsrvlrtrglalapapv.... 177
                                                  a ++    + +  +  + ++++   +d +++ +++GD+N  p        +   ++++ +      
  gi|313127359|ref|YP_004037629.1| 219 isatadgreftAVNTHLEASSESVRGSQADELASVLDDIDGRTVLLGDLNDGPAYKNGAYETLTSNLADAWKQarsd 295
                                       999999999999999999999999999999999999999999999******66666666666666666666647889 PP

                                       SSCESCETTTTTTTTTTTEB-BEEEEEECHHHCCEEEEEEECCHHEEC.......TSSCSSSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxx RF
                     Exo_endo_phos 178 glyllgggptptyvtraggsrlDrilaspalalfrsgvlppplalvrr.......ealtlSDH 233
                                       +   ++   ++    ++ + r+D++l+++++a  ++      + ++ +       + l++SDH
  gi|313127359|ref|YP_004037629.1| 296 ADGFTCCRSATLDGEESMPKRVDHVLVRSGVAATDAKLIGAGAESRLHttvngssRTLWPSDH 358
                                       99999999************************9999999999999999*************** PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   7.4   3.1e-06     0.028       2      26 .]       9      33 ..       8      33 .. 0.93
   2 ?   -0.3   1.2      0.12   1.1e+03      14      24 ..     453     463 ..     452     464 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaaa 26
                                      lSRR+ L+++AAa+ ++++++++aa
  gi|313127359|ref|YP_004037629.1|  9 LSRRSVLRAGAAAGLGLTVPSVGAA 33
                                      7*******************99875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.12
                        TAT_signal  14 aaAAaalggca 24 
                                       ++A+++l+g+a
  gi|313127359|ref|YP_004037629.1| 453 VGALGVLAGVA 463
                                       79999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3158.73
//
Query:       gi|313127360|ref|YP_004037630.1|  [L=281]
Description: endonuclease iv [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-25   90.3   1.0    1.8e-25   89.7   0.4    1.6  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.4   9.8e-30   1.8e-25      12     209 ..      33     236 ..      26     237 .. 0.85
   2 ?   -2.2   0.0      0.13   2.4e+03     124     145 ..     253     276 ..     240     280 .. 0.70

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 9.8e-30
                                       EEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS...HHHHHHHHHHHHHHHHHHT CS
                      AP_endonuc_2  12 vElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear...reesvdalkraielaaaLG 83 
                                        ++f+ +++ +++   sd+e++ +r+  +      ++++ ++  +        ++   r++s+d ++ ++++aa+LG
  gi|313127360|ref|YP_004037630.1|  33 GQIFTTSPQVWRDPdiSDAEAELFREETAGKLDGPWVIHSSYLVNLCT-----PKddlRQKSLDSMQTEVDMAAKLG 104
                                       566666666666666677777777766666555555555554444432.....224688999*************** PP

                                       BSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTTEEE CS
                      AP_endonuc_2  84 apllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspnvgv 158
                                       ++++++h G   a+ + +ee+ +++++++l+el d+  + +v++++E  agsg+ +gd  e+la++l++ +++ + +
  gi|313127360|ref|YP_004037630.1| 105 IEYVNVHLG---AHTGAGEEQGLDNAVSVLDEL-DI--PDDVTVLIESDAGSGTKMGDefEHLAYVLEQSEQD-LDI 174
                                       *********...********************9.88..89*****************************9987.*** PP

                                       EEEHHHHHHH......TTTHHHHHHHHHGG.....EEEEEE.EESSTTTTSSTTEESTTSSS CS
                      AP_endonuc_2 159 clDtgHllia......eedvddalraladr.....ikhvHikDakgdlgagrdrhvpigeGe 209
                                       clDt+H+++a       + v++++++l+d      ++ vH++D+k ++g ++d+h+ igeG 
  gi|313127360|ref|YP_004037630.1| 175 CLDTAHAFAAgydlstSDGVEETVAELDDVvglehLACVHLNDSKHECGTNKDEHAHIGEGL 236
                                       ************************************************************95 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.13
                                       TSEEEEE--TTTTSSSTC..HHHH CS
                      AP_endonuc_2 124 gvklalEtlagsgvelgd..eela 145
                                       +v l+lEt ++ g  + +  e ++
  gi|313127360|ref|YP_004037630.1| 253 DVPLVLETPTENGKGFAWniERVR 276
                                       688999999999988887664444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2179.18
//
Query:       gi|313127361|ref|YP_004037631.1|  [L=176]
Description: peroxiredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-21   75.3   0.0    4.4e-21   75.1   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    8.1e-16   58.1   0.0    1.2e-15   57.4   0.0    1.3  2  Redoxin     Redoxin
  ------ inclusion threshold ------
       0.12   12.6   0.1       0.39   10.9   0.1    1.8  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   7.4e-25   4.4e-21       1     124 []       8     139 ..       8     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 7.4e-25
                                       TTSB----EEE....STTCEEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHH CS
                          AhpC-TSA   1 vgdkapdfelk....nadgetvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspes 72 
                                       vg+ +pd++      +++ et sls++ + +pv+l+fy+ d++p C  e++++++         v+v+g s   +  
  gi|313127361|ref|YP_004037631.1|   8 VGETVPDVQQSlvqpDGETETASLSELvEEQPVLLNFYTVDFSPDCISEWCEFRDFDWFASGDAVQVVGASKSGERL 84 
                                       6888999888888789999********888**************************99999**************** PP

                                       HHHHHHH-H.SSEEEE-TTSHHHHHTT-EETT...TTECSCEEEEE-TTSBEEEE CS
                          AhpC-TSA  73 hkkfiekeslnfpllsDeegkvakaygvlkee...kglalratfvidkegkirya 124
                                       h+kfi + +l fpl++D++ ++a+a+gv  ++   +  a r+ f++d+e+++ry+
  gi|313127361|ref|YP_004037631.1|  85 HRKFISQFDLGFPLFADTTLELADAFGVRYKAfglSHRAHRSCFLVDEEMTVRYK 139
                                       *****************************999999999999************95 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   2.1e-19   1.2e-15       2     133 ..       8     142 ..       7     162 .. 0.91
   2 ?   -2.6   0.0      0.66   3.9e+03      37      54 ..     148     166 ..     146     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2.1e-19
                                       TTSBB---E..CCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH CS
                           Redoxin   2 agdkaPdft..lplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf 75 
                                       +g+++Pd++  l + + + ++ slse +++++v++nf++  f+P C  e +++++++ +++  +v+vv+ + + + +
  gi|313127361|ref|YP_004037631.1|   8 VGETVPDVQqsLVQPDGETETASLSElVEEQPVLLNFYTVDFSPDCISEWCEFRDFDWFASGDAVQVVGASKSGERL 84 
                                       899******7755555777899******************************************************* PP

                                       HHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEES CS
                           Redoxin  76 vkefwgkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvyleve 133
                                        ++f+++ +l fp+++D + +++ a+G+r+++   +  + ++ +++de+  v+y+  +
  gi|313127361|ref|YP_004037631.1|  85 HRKFISQFDLGFPLFADTTLELADAFGVRYKAFGLSHRAHRSCFLVDEEMTVRYKWIG 142
                                       *****************************99988888899999******999997655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.66
                                       STTT-HHHHHTHH.HHHTH CS
                           Redoxin  37 pgafcPtCsaehp.ylekl 54 
                                       p+ ++P+ s+ h   +++l
  gi|313127361|ref|YP_004037631.1| 148 PTRDTPPVSEIHEaIVDEL 166
                                       6779999999988666555 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   6.5e-05      0.39      14      55 ..      72     114 ..      60     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.5e-05
                        AhpC-TSA_2  14 vklvaigigdps.akkFvkltgfpfelyvDpsaklyqalglkr 55 
                                       v++v+ ++  +   +kF+++ +  f+l++D + +l +a+g++ 
  gi|313127361|ref|YP_004037631.1|  72 VQVVGASKSGERlHRKFISQFDLGFPLFADTTLELADAFGVRY 114
                                       444444444443689*************************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1371.27
//
Query:       gi|313127362|ref|YP_004037632.1|  [L=274]
Description: lipoate-protein ligase A [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-09   36.8   0.0    5.1e-09   36.1   0.0    1.3  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   2.8e-13   5.1e-09      22     127 ..      74     187 ..      63     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.8e-13
                                       -TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHH..HHHHHHHHHHHH...........HHTT-T CS
                     BPL_LplA_LipB  22 esgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlely..vsllvlavlealg....y.rdskpgiegi 91 
                                       e +++ v+rrqtgG  ++h+ +g+++ys++  +     + + +e y   ++ +l+++  lg    +  +s p+i   
  gi|313127362|ref|YP_004037632.1|  74 ERENVTVTRRQTGGGGIYHDYDGDISYSIVAPKAE--LPGDLMESYhlLCEPILDAFARLGvaadFvEESMPEIWHP 148
                                       67899**************************9665..77778888888*************8765355577887777 PP

                                       TEEEE...TTTEEEETTEEEEEEEEEEEETTS-EEEEEE CS
                     BPL_LplA_LipB  92 pvfik...wpnDlyvngrKlaGiavtstrgktlhhivig 127
                                        ++ +      D+++ng+K++G a+ ++  + ++h+++ 
  gi|313127362|ref|YP_004037632.1| 149 ACYLRelhPAHDVVANGKKVSGNAQYRRNDAVIQHGSLT 187
                                       78777652346************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1941.77
//
Query:       gi|313127363|ref|YP_004037633.1|  [L=247]
Description: hypothetical protein Hbor_26360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-35  121.4   0.0    4.1e-35  121.0   0.0    1.1  1  adh_short       short chain dehydrogenase
    6.7e-24   84.7   0.2      8e-24   84.5   0.2    1.1  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    8.5e-09   35.6   0.2    1.1e-08   35.2   0.2    1.3  1  NAD_binding_10  NAD(P)H-binding
    6.9e-08   32.6   0.1    1.4e-07   31.6   0.1    1.4  1  KR              KR domain
    1.8e-07   30.9   0.0    2.7e-07   30.3   0.0    1.3  1  Epimerase       NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.082   12.2   0.0       0.34   10.2   0.0    1.9  3  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
       0.11   12.4   0.1       0.18   11.6   0.1    1.3  1  DFP             DNA / pantothenate metabolism flavoprotein
       0.14   11.9   0.0        0.3   10.7   0.0    1.8  2  MoCF_biosynth   Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.0   0.0   1.8e-38   4.1e-35       2     188 ..      11     194 ..      10     200 .. 0.95

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 1.8e-38
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       +++v+GassGIGra+a ela +G++v +++r+ +kle + + l  +    +++++Dv+d +e+++ +++ ++ ++++
  gi|313127363|ref|YP_004037633.1|  11 TAVVVGASSGIGRALASELADAGYEVGLAARRLSKLESLGADLPTK---SYVARMDVSDPDEARDRMDRLADAMDGV 84 
                                       79**********************************9999999975...9*************************** PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHH CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaa 155
                                       d++v  AG+   ++  el  e  +++++vN+ g   l+   ++++ ++ +G+ v +sSva + ++++ +aY AsKa+
  gi|313127363|ref|YP_004037633.1|  85 DLVVLSAGV--GHENRELAWEPERDTVDVNVRGFAALATWSMEHFESRGGGHLVGISSVAEFFGNPVAPAYNASKAF 159
                                       *********..6888899999999***************************************************** PP

                                       HHHHHHHHHHHHGGGT..EEEEEEEESSBSSHHHH CS
                         adh_short 156 vagltrslakelaptg..irvnavaPGlvdTdmak 188
                                       v  + + l+     ++  i+v+ v PG+vdT+ma 
  gi|313127363|ref|YP_004037633.1| 160 VSRYLDGLRSRAVASEadITVTDVIPGFVDTEMAI 194
                                       ********9987776668***************85 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.2   3.6e-27     8e-24       1     181 [.      16     195 ..      16     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 3.6e-27
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae..vlecDVtdeeqvealveevvekfgklDilvn 75 
                                       Ga sgIGra+A +la++G+ev l+ ++ ++   +e+l ++l+++  v ++DV+d+++ ++ ++++++ ++++D +v 
  gi|313127363|ref|YP_004037633.1|  16 GASSGIGRALASELADAGYEVGLAARRLSK---LESLGADLPTKsyVARMDVSDPDEARDRMDRLADAMDGVDLVVL 89 
                                       899*********************988887...99999999977657****************************** PP

                                       -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalea 150
                                       +ag+ ++  ++  e+ +e  ++++dvn++++++la   +++++++  g +v +ssv+   + p   ay+a+Ka +  
  gi|313127363|ref|YP_004037633.1|  90 SAGVGHE--NR--ELAWEPERDTVDVNVRGFAALATWSMEHFESRggGHLVGISSVAEFFGNPVAPAYNASKAFVSR 162
                                       ******9..54..8999999********************8876658****************************98 PP

                                       HH...HHHHHHHGGGTEEEEEEEE--BHCTGGGG CS
                      adh_short_C2 151 lt...rylAvelgpkgiRvNavspgpikTlaasg 181
                                            r+ Av   +  i+v  v pg+++T++a g
  gi|313127363|ref|YP_004037633.1| 163 YLdglRSRAVASEA-DITVTDVIPGFVDTEMAIG 195
                                       75222777776665.9***************755 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.2     5e-12   1.1e-08       1     100 [.      16     142 ..      16     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5e-12
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT..TTCEEEE--TT-C.......CHHHHHHTT-SEEEES- CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleae..eglevvegdvtdv.......edlaealkgadaVvsal 68 
                                       GA+ ++Gr+l++el+++ g+ev + +R+ +kl++l a+   +  v  +dv+d+       + la+a++g+d Vv ++
  gi|313127363|ref|YP_004037633.1|  16 GASSGIGRALASELADA-GYEVGLAARRLSKLESLGADlpTKSYVARMDVSDPdeardrmDRLADAMDGVDLVVLSA 91 
                                       9****************.5**************99866546777889***997222333357899999***776666 PP

                                       --TCCHHHH...................HHHHHHHHHHCT--EEEEEEETT CS
                    NAD_binding_10  69 ggggkdeeg...................aknivdaakeagvkRfvlvsaig 100
                                       g g++++e                    a   ++  +  g  ++v +s++ 
  gi|313127363|ref|YP_004037633.1|  92 GVGHENRELaweperdtvdvnvrgfaalATWSMEHFESRGGGHLVGISSVA 142
                                       555543333344444545556566655455557777777777777777754 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   6.3e-11   1.4e-07       3     165 ..      12     169 ..      11     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 6.3e-11
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-....EEEE----TT-HHHHHHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga....evevvaaDvsdkdavealleei 75 
                                        +++G+  g+G++la  la+ g  ++ l +R+          +++le+lga    +  v+++Dvsd+d+ +  ++++
  gi|313127363|ref|YP_004037633.1|  12 AVVVGASSGIGRALASELADAGY-EVGLAARR----------LSKLESLGAdlptKSYVARMDVSDPDEARDRMDRL 77 
                                       589*****************996.58899999..........3334444432222788999**************** PP

                                       HHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HH CS
                                KR  76 kaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqan 148
                                        + ++ +  v+ +Agv +++   e+  e  +  +   v+G   L + + +    +   ++v +SS+a ++g++   +
  gi|313127363|ref|YP_004037633.1|  78 ADAMDGVDLVVLSAGVGHENR--ELAWEPERDTVDVNVRGFAALATWSMEhfesRGGGHLVGISSVAEFFGNPVAPA 152
                                       *****************9886..55555557788888999988876554444448999******************* PP

                                       HHHHHHHHHHHHHHHHH CS
                                KR 149 YaaaNaflDalaeyrrs 165
                                       Y a  af+  + +  rs
  gi|313127363|ref|YP_004037633.1| 153 YNASKAFVSRYLDGLRS 169
                                       ****9998776665555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.2e-10   2.7e-07       2     121 ..      13     147 ..      12     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.2e-10
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HH....HHHHHHHHH.T-SEEE CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrs....alerlfkee.qpdavi 69 
                                       +V+Ga+  iG+al+ +l+++gyev   +r+ s+ + ++ +dl     + ++d+ d++    +++rl +   ++d v+
  gi|313127363|ref|YP_004037633.1|  13 VVVGASSGIGRALASELADAGYEVGLAARRLSKLE-SLGADLptksYVARMDVSDPDeardRMDRLADAMdGVDLVV 88 
                                       79*********************877777733333.23333478999999****999777766777776669***** PP

                                       E--S---HHHH..HHSHHHHHHHHTHHHHHHHHHHHHH....TCTEEEEEEE.GGGGTS CS
                         Epimerase  70 hlAavggvaas..sedpadfieknlqgtlnlleaarka....gvkrllflsS.sevYGk 121
                                       + A+vg+ +++  +e   d+++ n++g   l+ ++ ++    g   l+ +sS +e +G+
  gi|313127363|ref|YP_004037633.1|  89 LSAGVGHENRElaWEPERDTVDVNVRGFAALATWSMEHfesrGGGHLVGISSvAEFFGN 147
                                       ****99988752278999****************9988744444499999996666665 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00015      0.34      37      74 ..      10      47 ..       4      52 .. 0.86
   2 ?   -2.8   0.0       1.5   3.4e+03      72      92 ..      76      96 ..      72     116 .. 0.71
   3 ?   -1.9   0.0      0.82   1.8e+03      74      97 ..     170     192 ..     132     196 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                                      -EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHH CS
                     THF_DHG_CYH_C 37 kkvvvvGrsnivgkplallLleknatVtvchsktkdla 74
                                      +++vvvG+s+ +g++la  L+ ++  V ++ ++ ++l+
  gi|313127363|ref|YP_004037633.1| 10 RTAVVVGASSGIGRALASELADAGYEVGLAARRLSKLE 47
                                      689********************999998887766665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.5
                                      CHHHHHCCSSEEEE-SS-TT- CS
                     THF_DHG_CYH_C 72 dlaeitreadivvvavGkpel 92
                                       la+ +   d+vv ++G+ + 
  gi|313127363|ref|YP_004037633.1| 76 RLADAMDGVDLVVLSAGVGHE 96
                                      567777888999998887665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.82
                                       HHHHCCSSEEEE-SS-TT-B-GGG CS
                     THF_DHG_CYH_C  74 aeitreadivvvavGkpelikaem 97 
                                       +++ +eadi v+ v  p++++ em
  gi|313127363|ref|YP_004037633.1| 170 RAVASEADITVTDV-IPGFVDTEM 192
                                       56678888888776.566666665 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   8.2e-05      0.18      26      92 ..      17      93 ..       9      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.2e-05
                                      ----HHHHHHHHHHHHTT-EEEEEE-S.-SS--.......-TT-EEEE--SHHHHHHHHHHHHTT-...SEEEE---S CS
                               DFP 26 rSSGkmGyalAeaaaarGaeVtlvsgp.vslet.......pegvevvkvesaeemleaveealkea...divimaAAv 92
                                       SSG  G alA+++a++G eV l +   ++le        ++ v +++v++ +e ++ +++ ++++   d+v+ +A v
  gi|313127363|ref|YP_004037633.1| 17 ASSG-IGRALASELADAGYEVGLAARRlSKLESlgadlptKSYVARMDVSDPDEARDRMDRLADAMdgvDLVVLSAGV 93
                                      5777.6******************998446553344443256789999998888888877666444344999999977 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.8   8.5e+03      20      33 ..      23      36 ..      22      37 .. 0.84
   2 ?   10.7   0.0   0.00013       0.3      40     109 ..      67     135 ..      45     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.8
                                      HHHHHHHHTTSEEE CS
                     MoCF_biosynth 20 pllaellkelgvev 33
                                        la++l+++g+ev
  gi|313127363|ref|YP_004037633.1| 23 RALASELADAGYEV 36
                                      67999999999997 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00013
                                       -SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGG CS
                     MoCF_biosynth  40 pDdeeeikeallaaleeadviittGGtGptpdDvtpealaklfekelegfeeafrrvslkpgkpvgvapg 109
                                       pD+  +  + l++a++++d+++++ G+G   + +  e  ++  +  + gf+++      ++++  g +++
  gi|313127363|ref|YP_004037633.1|  67 PDEARDRMDRLADAMDGVDLVVLSAGVGHENRELAWEPERDTVDVNVRGFAALATWSMEHFES-RGGGHL 135
                                       455555555667777999*****************9999999999999998876555555543.233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1848.25
//
Query:       gi|313127364|ref|YP_004037634.1|  [L=119]
Description: hypothetical protein Hbor_26370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 996.69
//
Query:       gi|313127365|ref|YP_004037635.1|  [L=154]
Description: hypothetical protein Hbor_26380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-29  101.6   0.4      3e-29  101.4   0.4    1.1  1  DUF4112      Domain of unknown function (DUF4112)
  ------ inclusion threshold ------
      0.079   13.2   0.2       0.13   12.5   0.2    1.3  1  CRAL_TRIO_N  CRAL/TRIO, N-terminal domain


Domain annotation for each model (and alignments):
>> DUF4112  Domain of unknown function (DUF4112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.4   3.3e-33     3e-29       2     101 ..      26     124 ..      25     128 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 3.3e-33
                           DUF4112   2 lkkvrklayllDkalripgcglrfGldpiigliPvvGdvisallslylvleakkaeglpkslllrmlvnialDllig 78 
                                       ++++r++ay+lD  ++ipg++ r+G+dp++g +PvvGdv+sa++sly+vle+ ++ g++ ++ll m++n+a+D++ g
  gi|313127365|ref|YP_004037635.1|  26 VERMRSVAYVLDDLVGIPGTNSRVGIDPVLGTVPVVGDVVSAAFSLYIVLES-ARLGVSYKTLLVMIANVAIDTAGG 101
                                       5799************************************************.9999******************** PP

                           DUF4112  79 lvPvvGdlfdvlfkantrNaall 101
                                         P vG lfd+++kan+ N+++ 
  gi|313127365|ref|YP_004037635.1| 102 SLPYVGVLFDAVWKANKWNVEMA 124
                                       ********************985 PP

>> CRAL_TRIO_N  CRAL/TRIO, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.5e-05      0.13      39      54 .]     115     130 ..     115     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                       CRAL_TRIO_N  39 RArkwdvekAikrLed 54 
                                       +A+kw+ve+A + L+d
  gi|313127365|ref|YP_004037635.1| 115 KANKWNVEMALAELTD 130
                                       7**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1156.11
//
Query:       gi|313127366|ref|YP_004037636.1|  [L=228]
Description: hypothetical protein Hbor_26390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1680.28
//
Query:       gi|313127367|ref|YP_004037637.1|  [L=445]
Description: hypothetical protein Hbor_26400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2775.20
//
Query:       gi|313127368|ref|YP_004037638.1|  [L=236]
Description: hypothetical protein Hbor_26410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.089   12.6   0.3       0.13   12.1   0.3    1.3  1  GBR_NSP5  Group B Rotavirus Non-structural protein 5


Domain annotation for each model (and alignments):
>> GBR_NSP5  Group B Rotavirus Non-structural protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   7.3e-06      0.13      36      79 ..     129     172 ..      99     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.3e-06
                          GBR_NSP5  36 dcetdslisesvssthsyedyskaykeltletpadvndsastiv 79 
                                        c t sl   s s t  + dy  +y+++ +    d +ds s ++
  gi|313127368|ref|YP_004037638.1| 129 SCHTLSLCNVSWSDTDIHADYGSTYRDVDVRCEVDTKDSVSMLI 172
                                       59**************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1694.55
//
Query:       gi|313127369|ref|YP_004037639.1|  [L=303]
Description: serine/threonine protein kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-47  160.4   0.1    5.6e-47  159.8   0.1    1.2  1  RIO1      RIO1 family
    3.3e-26   91.3   0.0    6.5e-26   90.4   0.0    1.5  1  Rio2_N    Rio2, N-terminal


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.8   0.1   6.2e-51   5.6e-47       2     182 ..     108     276 ..     107     281 .. 0.95

  Alignments for each domain:
  == domain 1  score: 159.8 bits;  conditional E-value: 6.2e-51
                                       EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpiel 78 
                                       V++++s   k +a+K+++ ++t+F+++ + ++++++    +++ +++++++ +ae+E++ L+ l+   v+vP+pi+ 
  gi|313127369|ref|YP_004037639.1| 108 VFEVQS--YKPLALKFHREGYTNFREVMREREYTSD----NQHVSWLYTARKAAEREYEVLEDLYPD-VSVPRPIDQ 177
                                       777754..7899**********************99....6799**********************9.********* PP

                                       ETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEET CS
                              RIO1  79 krhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQavel 155
                                       +rh++vme +g  gv++ + k  +  ++   +++ vl+e++++y +ag+vHaD+SeyNv v e++v+i+D++Qav++
  gi|313127369|ref|YP_004037639.1| 178 NRHAIVMEKLG--GVELDRAKLED--DQVVGVLDLVLNEVAAAY-DAGYVHADMSEYNVAVGEQGVIIFDWPQAVST 249
                                       ***********..99999999888..89****************.******************************** PP

                                       TSTTHHHHHHHHHHHHHHHHHTTC--- CS
                              RIO1 156 dhpnalefLerDveniikfFrrkgvek 182
                                       dh+na+e+LerDv+n+  +Frrk+ ++
  gi|313127369|ref|YP_004037639.1| 250 DHDNARELLERDVKNVLGYFRRKYPAS 276
                                       ***********************9874 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   7.2e-30   6.5e-26       1      82 []       9      90 ..       9      90 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 7.2e-30
                            Rio2_N  1 lryLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktl 79
                                      +++L++edf +L++vE+gmr  e+V + ++  +s+l+ e+v++rl+r+++++l++rkt++y+GYkL  eGyD+LAL+t+
  gi|313127369|ref|YP_004037639.1|  9 MAELESEDFYLLSGVEQGMRFGEWVNRGKLPDLSGLTPENVEYRLNRCMRRDLVERKTIQYEGYKLAVEGYDALALRTF 87
                                      789**************************************************************************** PP

                            Rio2_N 80 vkr 82
                                      +kr
  gi|313127369|ref|YP_004037639.1| 88 SKR 90
                                      *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2355.51
//
Query:       gi|313127370|ref|YP_004037640.1|  [L=350]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-62  209.6   0.0    4.6e-62  209.3   0.0    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    8.7e-16   57.6   0.0    2.8e-15   56.0   0.0    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.002   18.0   0.0     0.0057   16.5   0.0    1.8  1  MarR_2          MarR family
     0.0047   16.8   0.0     0.0073   16.2   0.0    1.3  1  PLDc_2          PLD-like domain
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.028   14.8   0.0    1.5  1  Rrf2            Transcriptional regulator
      0.016   15.2   0.6        2.1    8.3   0.0    2.5  2  HTH_11          HTH domain
      0.026   15.1   0.4        1.5    9.4   0.0    2.6  2  MerR-DNA-bind   MerR, DNA binding
      0.061   13.3   0.0       0.12   12.3   0.0    1.5  1  MarR            MarR family
      0.078   12.4   0.0       0.23   10.9   0.0    1.8  2  Glu_dehyd_C     Glucose dehydrogenase C-terminus


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.3   0.0   2.3e-65   4.6e-62       2     231 ..     109     347 ..     108     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 209.3 bits;  conditional E-value: 2.3e-65
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S- CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvrr 78 
                                       ++vvksr tv++ri+elI+ A++e+++ +p++l+ e+ +el++a++rgv+Vll++++ + +++l+l + a+++r+++
  gi|313127370|ref|YP_004037640.1| 109 FEVVKSRVTVLKRIAELIDRANSEVTLGVPYSLVDEMADELRDAVDRGVLVLLIVTGVSPTDDLELSGLASVARAWE 185
                                       789************************************************************************** PP

                                       --S.EEEEETTTEEEEE-SSS-.EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-HHHHH CS
                    Regulator_TrmB  79 sgapllvivDrkrgvvaprevl.rdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssirlav 154
                                       +++p+++ vD++ g+vap+e+l r+++  +ai+  +++l  vl+++Fl+++W ++ + +t + +e+p+t+ ++r+av
  gi|313127370|ref|YP_004037640.1| 186 EPMPTMLSVDQEAGIVAPTEMLtRSNSAAQAIVLAQEQLGPVLVGSFLGNYWPMAAETYTCDLDELPATYDDFRHAV 262
                                       ***************************************************************************** PP

                                       HHHHHHT.TTS-EEEEEEEEETT.T--EEEEEEEEEEEE.......EETTTTEEEEEEEETTEEEEEE-TT--SSSE CS
                    Regulator_TrmB 155 edikkllraglkveaeveGrdte.tgeevtieGrvveat.......lnstpgvaslvvetedgevtVGGlgAvlEDi 223
                                        +++   r g++++a v+Gr +  ++++ +++G++v+++       +ns+p +++lv+et+dg++++GG+gA++ED+
  gi|313127370|ref|YP_004037640.1| 263 LQATLRARTGTDLVAHVTGRPVHvENGPSELSGTIVDIRqgllepsTNSFPVENTLVIETDDGTFSIGGKGAFIEDF 339
                                       *************************************99************************************** PP

                                       EEEEEEEE CS
                    Regulator_TrmB 224 eaeeitle 231
                                       ea++++l+
  gi|313127370|ref|YP_004037640.1| 340 EADTVELR 347
                                       *****996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   1.4e-18   2.8e-15       1      67 [.      10      77 ..      10      78 .. 0.95
   2 ?   -2.5   0.0       2.4   4.8e+03      32      48 ..     135     151 ..     132     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.4e-18
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravdp 67
                                      Lq +G+s+ E+++Yl++l+lg+a+a++iaee++v++  vY++ ++L ++G+Ve+++   p+  ra +p
  gi|313127370|ref|YP_004037640.1| 10 LQRFGFSDKEIDTYLTILELGEAKASTIAEEADVSKRYVYSIAEKLQSRGFVEVNDHAvPTTIRAQPP 77
                                      899****************************************************9877999998887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                                       TTSSCHCHHHHHHHHHH CS
                              TrmB  32 lgvprskvYevLrsLed 48 
                                       lgvp+s v e+  +L d
  gi|313127370|ref|YP_004037640.1| 135 LGVPYSLVDEMADELRD 151
                                       899**999998877765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.9e-06    0.0057      22      53 ..      32      63 ..       5      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                                      EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLver 53
                                        ++ +a++ ++sk +v  i ++L+++G+ve 
  gi|313127370|ref|YP_004037640.1| 32 AKASTIAEEADVSKRYVYSIAEKLQSRGFVEV 63
                                      5799**************************96 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.7e-06    0.0073       2      48 ..     123     168 ..     122     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.7e-06
                            PLDc_2   2 iqliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkd 48 
                                        +li++A++++ + ++y    +e++d+l++a +rgv v +++    +
  gi|313127370|ref|YP_004037640.1| 123 AELIDRANSEVTLGVPYS-LVDEMADELRDAVDRGVLVLLIVTGVSP 168
                                       689***************.99999*****************988444 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.4e-05     0.028      22      57 ..      29      63 ..      20      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvks 57
                                       +e +++++iae+ ++s++y+  i +kL+  g+v++
  gi|313127370|ref|YP_004037640.1| 29 LGE-AKASTIAEEADVSKRYVYSIAEKLQSRGFVEV 63
                                      444.7899**************************86 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0011       2.1      16      43 ..      32      59 ..      19      66 .. 0.83
   2 ?    4.7   0.1     0.014        29      23      39 ..     107     125 ..     106     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                            HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                        ++++Aee +vS+r v+   ++L++ g
  gi|313127370|ref|YP_004037640.1| 32 AKASTIAEEADVSKRYVYSIAEKLQSRG 59
                                      5799**************9999998888 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.014
                            HTH_11  23 eeLnv..SrrtvrrdIkaL 39 
                                       e+++v  Sr tv ++I++L
  gi|313127370|ref|YP_004037640.1| 107 ERFEVvkSRVTVLKRIAEL 125
                                       7888889**********99 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00077       1.5       5      45 ..       5      48 ..       4      57 .. 0.70
   2 ?    3.0   0.1     0.074   1.5e+02      17      50 ..      88     121 ..      86     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00077
                                      HHHHHHHHTT--HHHHHHHH...HHHHSTTTBHHHHHHHHHHHH CS
                     MerR-DNA-bind  5 kfIrrarrlGFsLdeIrelL...alyddrappcqdvrallarkl 45
                                      ++I  ++r+GFs +eI + L   +l + +a++ ++  ++++r +
  gi|313127370|ref|YP_004037640.1|  5 ALIELLQRFGFSDKEIDTYLtilELGEAKASTIAEEADVSKRYV 48
                                      58999**************9544444446666666666666655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHHSTTTBHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  17 LdeIrelLalyddrappcqdvrallarklaelee 50 
                                       L+e+r  L+ + +ra+p+ ++ ++++ ++  l +
  gi|313127370|ref|YP_004037640.1|  88 LEEMRPALESRFSRAAPRSERFEVVKSRVTVLKR 121
                                       99******999999*******99**999988864 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     6e-05      0.12      10      49 ..      24      63 ..      15      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6e-05
                                      HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                       ++ e g+++ s +a+   vsk +v  ++ +L  +G++e 
  gi|313127370|ref|YP_004037640.1| 24 LTILELGEAKASTIAEEADVSKRYVYSIAEKLQSRGFVEV 63
                                      578899********************************96 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   2.8e+03      90     133 ..     193     236 ..     190     246 .. 0.77
   2 ?   10.9   0.0   0.00012      0.23      76     140 ..     248     312 ..     239     348 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                       Glu_dehyd_C  90 pvdeipeaseemdlvvEaTGsakhafeaiealapnGvaaLlGvp 133
                                       +vd+ + +  + +++  +  +a++++ a e+l+p  v   lG +
  gi|313127370|ref|YP_004037640.1| 193 SVDQEAGIVAPTEMLTRSNSAAQAIVLAQEQLGPVLVGSFLGNY 236
                                       67777888888888888888888888888888888888888765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
                       Glu_dehyd_C  76 veelGatYvdsretpvdeipeaseemdlvvEaTGsakhafeaiealapnGvaaLlGvpedsevev 140
                                       ++el atY d r++ ++    a +  dlv   TG + h+ +  ++l+ + v + +G+ e+s+ ++
  gi|313127370|ref|YP_004037640.1| 248 LDELPATYDDFRHAVLQATLRARTGTDLVAHVTGRPVHVENGPSELSGTIVDIRQGLLEPSTNSF 312
                                       489************************************99999999999988888888775444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2609.54
//
Query:       gi|313127371|ref|YP_004037641.1|  [L=686]
Description: glycosidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-47  160.5   0.0    1.1e-46  160.0   0.0    1.2  1  Alpha-amylase    Alpha amylase, catalytic domain
      7e-09   35.9   0.0    2.2e-08   34.3   0.0    1.9  1  DUF3459          Domain of unknown function (DUF3459)
    0.00013   22.0   0.0    0.00039   20.5   0.0    1.8  1  Malt_amylase_C   Maltogenic Amylase, C-terminal domain
    0.00097   19.6   0.1      0.015   15.8   0.0    2.9  3  Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
     0.0041   17.5   0.1       0.14   12.6   0.0    2.5  2  Lipase_GDSL_2    GDSL-like Lipase/Acylhydrolase family


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.0   0.0   3.1e-50   1.1e-46       6     334 ..     290     574 ..     286     582 .. 0.86

  Alignments for each domain:
  == domain 1  score: 160.0 bits;  conditional E-value: 3.1e-50
                                       HHCTCCCCCCCT-SCEEE-B-CE-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--TTSC CS
                     Alpha-amylase   6 iiekLdYlkeLGvtaiwlsPifkspqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsdehe 82 
                                       i  +++Yl+ LGv+ +wl+P+ ksp   hgY+i+d   + +  Gt ++++ L++++he gi+v++DlV+NHts +h 
  gi|313127371|ref|YP_004037641.1| 290 IERRVPYLEHLGVDTVWLTPVCKSP-THHGYHITDLFDTADDLGTRAAFESLVDRLHESGIRVVFDLVINHTSRDHP 365
                                       77899********************.9************************************************** PP

                                       CCHCCHHSTTSGGGCCC-E......ESS-STTC-TTTTCSCEECTTTTCEEESSS-TTS-BB-TTTCCCCCCCCCCC CS
                     Alpha-amylase  83 wfkeslkkkgepkrdyyiwkegkeekeppnnwkslfdgsaweydekaqeyylhlflkklpdLnteneevrkelkdvv 159
                                         + + +   e ++d y        +  +  +    +  +w+ d   +   ++ + ++ p+Ln+++  vr+ + dvv
  gi|313127371|ref|YP_004037641.1| 366 AYQLHEA-GVEGYEDLYE-------RVSDGRNV---SDIDWSADGAPG---VYFNWWQIPNLNYDSLRVREWMLDVV 428
                                       8776666.4446888887.......22333332...456677777665...6888889******************* PP

                                       CCCCTTT-SEEEETTCCCTTTCCCCHCCHCCHHHHHHHHHHHTCCGTT-EEEEE-TT-SCCCHCCCC-CGG-SICEC CS
                     Alpha-amylase 160 kfwlekgidGfRlDvvkhvskvealesngeflheftqalnetvasrkevmtvgEvssdasedlrvyttearlelemv 236
                                         w    +dGfR Dv+  v++         f++e ++ l++++    ++ +++E+             e++++l+  
  gi|313127371|ref|YP_004037641.1| 429 DEWAP-LVDGFRCDVAWGVPH--------GFWKEVRARLKREY---PDFLLLDETVPRRP-----AFRENEFDLH-- 486
                                       ***85.59*************........***********886...********998554.....5677777777.. PP

                                       CITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-CCCTTCEEES--TTS--HHHHTTSSTTTTHHHHHHHHHC CS
                     Alpha-amylase 237 ldfphldvaqkakikeqlksisakklkellkkwlkaleeaaeeavtflgnHDqeRilsrlgddsaeaekklklaail 313
                                        d   +d+ +++    ++++   + +++l ++ +  +++ +   + +++nHD  R l  +g d+      l++a+++
  gi|313127371|ref|YP_004037641.1| 487 YDTDLYDALRDIG---NGEKSATAIFDALDASARLGYPD-EAVHMRYVENHDEDRYLDECGADA------LRAAVAV 553
                                       5566677777777...55554556666666777889998.9999********************......9****** PP

                                       CCTSSSEEEEETTCCCT---- CS
                     Alpha-amylase 314 lltlrGvpviYyGeEigmtgg 334
                                       ++tl+G+p iYyG+E g+t++
  gi|313127371|ref|YP_004037641.1| 554 TFTLPGTPLIYYGQERGVTEQ 574
                                       ******************987 PP

>> DUF3459  Domain of unknown function (DUF3459)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   6.2e-12   2.2e-08       1      69 [.     590     659 ..     590     683 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 6.2e-12
                                       HHHHHHHHHHHHCCCTT-..-CGGEEEEEEECTCEEEEEEEETTEEEEEEEE-SSCGCCS-SS---SEEEE CS
                           DUF3459   1 lyrdLLaLRreePaLada..rrgglevavlgdgallvrwrlgdgrllrllaNLgdepvtlppegaagkllf 69 
                                       ++r+L  LR+ ePaL+    ++ ++ v+  ++ +++++ r ++++ l++++N+g++ +t++  + + +l  
  gi|313127371|ref|YP_004037641.1| 590 FHRRLVGLRQSEPALRSGsvEPVSCSVSGADASTVVAYERTAGDDSLLVVVNFGADDATVS-FDGEVDLSA 659
                                       7****************9445556666666677899**********************999.333333333 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.1e-07   0.00039       9      57 ..     620     669 ..     615     678 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-07
                                       S-TTEEEEEEEETTEEEEEEEESS-EEEEE--G.GGTT-EEEETTTTEE- CS
                    Malt_amylase_C   9 dnrkvlaYlReyedetilvvaNrsaqaveldls.elagrvpvelfggeef 57 
                                       d   v aY+R+ +d+ +lvv+N+ a ++++++  e+  + +++l++ +++
  gi|313127371|ref|YP_004037641.1| 620 DASTVVAYERTAGDDSLLVVVNFGADDATVSFDgEVDLSAATDLISTANV 669
                                       5678******************9999999999988888888888887665 PP

>> Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.78   2.8e+03      21      50 ..     139     167 ..     119     202 .. 0.58
   2 ?   -2.5   0.0         2   7.2e+03      25      51 ..     356     381 ..     352     393 .. 0.68
   3 !   15.8   0.0   4.1e-06     0.015       9      57 ..     622     670 ..     617     682 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.78
                                       EEEEEEE-SSSSEEECEEESSSSSEEEEET CS
                   Alpha-amylase_C  21 kllvvfNfhpsnsrqdyrvgvpaagkyrdv 50 
                                       +++++f  ++ +++ + +v+v+ +g+ r  
  gi|313127371|ref|YP_004037641.1| 139 DAIFAFD-DDFDTFATTEVTVEGPGRPRLR 167
                                       3555555.4555566666666555555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                                       EEE-SSSSEEECEEESSSSSEE..EEETT CS
                   Alpha-amylase_C  25 vfNfhpsnsrqdyrvgvpaagk..yrdvl 51 
                                       v+N+++   ++ y++    ag   y+d++
  gi|313127371|ref|YP_004037641.1| 356 VINHTS-RDHPAYQLHE--AGVegYEDLY 381
                                       899777.7778898833..3333477766 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 4.1e-06
                                       SSEEEEEECTTT.EEEEEEE-SSSSEEECEEESSSSSEEEEETTCTTSGC CS
                   Alpha-amylase_C   9 nkviaFeRgdge.kllvvfNfhpsnsrqdyrvgvpaagkyrdvlntdaee 57 
                                       + v+a+eR +g+ +llvv+Nf+ ++ ++ +   v+     +d+++t ++ 
  gi|313127371|ref|YP_004037641.1| 622 STVVAYERTAGDdSLLVVVNFGADDATVSFDGEVD-LSAATDLISTANVG 670
                                       689*****997779*********999998888777.45567888777764 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   3.8e-05      0.14      74     151 ..     323     398 ..     317     419 .. 0.85
   2 ?    2.1   0.1     0.061   2.2e+02      39      77 ..     614     649 ..     577     671 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                                       CCCTT--HHHHHHH..HHHHHHHHCCC...GEEECEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHCT-EEE-H CS
                     Lipase_GDSL_2  74 DlgrgvpaaaaaandnleelidalraaapgarilvlgplpptpeaaadarelnaviaaynealrevaaeegvpfvDl 150
                                       Dl+  +++  ++a+  +e+l+d+l++   g+r++   +++ t+++++  +  +a ++ y +++++v +  +v  +D 
  gi|313127371|ref|YP_004037641.1| 323 DLFDTADDLGTRAA--FESLVDRLHES--GIRVVFDLVINHTSRDHPAYQLHEAGVEGYEDLYERVSDGRNVSDIDW 395
                                       56666666666777..***********..*****9**************************************9998 PP

                                       ..H CS
                     Lipase_GDSL_2 151 ..h 151
                                         +
  gi|313127371|ref|YP_004037641.1| 396 saD 398
                                       442 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.061
                                       EEHCCH-H..HHHHHHHHCTGGG-TSEEEEE--CCCCCT CS
                     Lipase_GDSL_2  39 lgvsGattallrllerlrdllrlkpdlvtiliGtNDlgr 77 
                                        +vsGa  +     e   + +  ++ lv++++G+ D+  
  gi|313127371|ref|YP_004037641.1| 614 CSVSGADASTVVAYE---RTAGDDSLLVVVNFGADDATV 649
                                       566777431122222...234567789*********543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 4467.35
//
Query:       gi|313127372|ref|YP_004037642.1|  [L=685]
Description: hypothetical protein Hbor_26450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00077   18.4   0.3       0.01   14.7   0.0    2.3  2  Glyco_hydro_15  Glycosyl hydrolases family 15
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.28   11.0   0.0    1.5  1  DUF1391         Protein of unknown function (DUF1391)


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4     0.017   1.5e+02      25      53 ..     301     334 ..     281     362 .. 0.73
   2 !   14.7   0.0   1.1e-06      0.01     318     446 ..     382     666 ..     368     668 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.017
                                       -B-S-S-BSSS......B--SEEHHHHHHHHHHHH CS
                    Glyco_hydro_15  25 lliASpstsdp......DYrytWvRDsvyvilavw 53 
                                       l iA p+  dp      +Y ytW RD + +   + 
  gi|313127372|ref|YP_004037642.1| 301 LRIAGPD-FDPyyaysgGYGYTWFRDDAEISRFLF 334
                                       5555555.3444666669********987666555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.1e-06
                                       --SBTT--CG......................................SSSBSCT--BHHHHHH............. CS
                    Glyco_hydro_15 318 vrRysedvkp......................................dklglsGrpyylctlw............. 343
                                       ++R+++ +                                        d l ++Grp   +++w             
  gi|313127372|ref|YP_004037642.1| 382 NGRLESGSDVdyqadqtgsvvaylarylndtgddrvietleralaglnDTLASDGRPITCQNAWenmsgrfthtaat 458
                                       55555444334455555566666666666666688888888888888899********9999999999999999999 PP

                                       ............................................................................. CS
                    Glyco_hydro_15 344 ............................................................................. 343
                                                                                                                    
  gi|313127372|ref|YP_004037642.1| 459 flegyaalaatdsdlaaeakaradevyeaiddfwapsrgiyalreyaddheesglddrcdsatlalvdahrtyaevg 535
                                       999999*********************************************************************** PP

                                       ............HHHHHHHHHHHHHHHTE-EEEECCCHHHHHHHTTT............TTGGGSSEEE.TCHHHHH CS
                    Glyco_hydro_15 344 ............tvetlldelyekagkgrlwglvryalglleklves............kqltvGlppe.resvisa 395
                                                    vet+ dely+   ++++ gl+ry+ + ++ + ++             +++++l++   +s    
  gi|313127372|ref|YP_004037642.1| 536 eidverierlvsHVETVIDELYHDPAESSVEGLIRYEGDDWRMREQDhekiwtvstawgAHAAASLSALlADSDDAR 612
                                       ******************************************99999**9999999998666666666665555555 PP

                                       HHHHHHHHHHHHHHH...HH.S-TTS---SEE-TTT--EESSTT-HHHHHHHHHH CS
                    Glyco_hydro_15 396 plpveeladliveav...ee.dnslgvLteevdvylgeliraqpllfsealllri 446
                                        ++ +e a+ ++  v   ++ + ++g+L e+v + +g++++a+pl + +al+l +
  gi|313127372|ref|YP_004037642.1| 613 NEAFAETARDLLALVlpdGPlTTEGGYLPEQVFD-DGTPDSATPLGWPHALRLAT 666
                                       5666666666666663334567899*******98.9****************975 PP

>> DUF1391  Protein of unknown function (DUF1391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.1e-05      0.28      12      36 ..     221     245 ..     215     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.1e-05
                           DUF1391  12 vCGvfPnqDGtftamtytksktfkt 36 
                                       v Gv P  DGt t  ty  s+   t
  gi|313127372|ref|YP_004037642.1| 221 VVGVVPTTDGTATVATYLTSRSEHT 245
                                       89***************99987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 4483.09
//
Query:       gi|313127373|ref|YP_004037643.1|  [L=374]
Description: carbohydrate ABC transporter ATP-binding protein, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-35  120.2   0.0    1.5e-34  119.4   0.0    1.4  1  ABC_tran         ABC transporter
    1.4e-09   38.6   0.0    6.3e-09   36.5   0.0    2.2  1  OB_MalK          MalK OB fold domain
    1.6e-09   37.8   0.5    5.8e-09   36.0   0.5    2.1  1  TOBE_2           TOBE domain
    6.2e-07   29.5   0.1     0.0034   17.3   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      4e-06   27.0   0.1    9.9e-06   25.8   0.1    1.7  1  TOBE             TOBE domain
    6.7e-05   22.4   0.1    0.00021   20.8   0.1    1.7  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0042   17.6   0.5        0.1   13.2   0.0    3.1  3  CysA_C_terminal  CysA C-terminal regulatory domain
      0.005   17.1   0.3     0.0089   16.3   0.3    1.7  1  AAA_22           AAA domain
     0.0051   17.2   0.2      0.008   16.6   0.2    1.5  1  AAA_16           AAA ATPase domain
     0.0093   15.9   0.0      0.013   15.4   0.0    1.3  1  Rad17            Rad17 P-loop domain
     0.0097   15.1   0.0      0.013   14.7   0.0    1.1  1  G-alpha          G-protein alpha subunit
  ------ inclusion threshold ------
      0.017   15.6   0.2      0.076   13.4   0.0    2.0  2  AAA              ATPase family associated with various cellul
       0.02   15.5   0.0      0.043   14.4   0.0    1.8  1  AAA_18           AAA domain
      0.023   14.4   0.8       0.11   12.3   0.0    2.5  4  AAA_29           P-loop containing region of AAA domain
      0.024   14.6   0.0      0.051   13.5   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
      0.034   13.4   0.0       0.07   12.4   0.0    1.5  1  Zeta_toxin       Zeta toxin
       0.05   13.3   0.2       0.19   11.4   0.0    2.1  3  AAA_30           AAA domain
        0.2   12.1   0.0        1.2    9.6   0.0    2.2  2  RNA_helicase     RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.0   1.5e-37   1.5e-34       2     136 ..      22     164 ..      21     165 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 1.5e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++vs++++ ge v +vG++G+GKSt l+++agl++pt G+i++ g+d+++   +  ++ +++++q+  l p++tvr+
  gi|313127373|ref|YP_004037643.1|  22 DDVSFEVEDGEFVTVVGPSGCGKSTTLRMIAGLESPTGGSIRIGGEDVTD--VHARKRDVAMVFQNYALYPHKTVRQ 96 
                                       89************************************************..9999********************* PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              e+++++e+ ++ +++++l d++     ++LSgGqkqrval ra++++p+++l+DEp 
  gi|313127373|ref|YP_004037643.1|  97 NmafglrmstdlskaERNRRVEETAEMMDIEDLLDDKP----NELSGGQKQRVALGRAIVREPDVFLFDEPL 164
                                       ************99999999999999999999888888....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   6.3e-12   6.3e-09       1      52 [.     238     292 ..     238     293 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 6.3e-12
                           OB_MalK   1 GSPaMNflpatveedg...vlvegggvtlplpeeqklalklyagkevilGiRPEh 52 
                                       GSP+MNf++++v+++g   +l++++g++  l+++ + + ++   k+  lG+RPE+
  gi|313127373|ref|YP_004037643.1| 238 GSPSMNFVDVEVTGSGgsvTLANDDGFDYSLTGDVAQRVSESGSKTARLGVRPED 292
                                       9************999***9***********9999667777788**********9 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.5   5.8e-12   5.8e-09       1      76 []     286     354 ..     286     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.8e-12
                            TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       l++RPE++++   +g+ g++ tV+ ve  Gs+  +++++  g+++++r+++      +++Gdt+e+++d  +++++
  gi|313127373|ref|YP_004037643.1| 286 LGVRPEDVTV--VTGGAGIPTTVDVVEPIGSDNYLHLDV--GTDFIARVDSDV---EPTVGDTIEITFDQSAVHLF 354
                                       79********..35466****************999666..666788888888...9*****************98 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00055      0.54       2      22 ..      34      54 ..      33      74 .. 0.78
   2 !   17.3   0.0   3.4e-06    0.0034     220     298 ..     120     196 ..      97     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                        ++Gp g+GKS+ L+ + +l
  gi|313127373|ref|YP_004037643.1| 34 VTVVGPSGCGKSTTLRMIAGL 54
                                      679***************998 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.4e-06
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQvilt 295
                                       +   ++ +d  +  ++elS G+k+  al  a+ r +   +++l+DEp ++L+ kl ++  + + ++ ++ g+  i +
  gi|313127373|ref|YP_004037643.1| 120 TAEMMDIEDLLDDKPNELSGGQKQRVALGRAIVREP---DVFLFDEPLSNLDAKLRTTMRTEIqRIQNELGITSIYV 193
                                       555556666666678999*******9********99...9********************99955555589999*** PP

                            AAA_21 296 THS 298
                                       TH+
  gi|313127373|ref|YP_004037643.1| 194 THD 196
                                       *98 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   9.9e-09   9.9e-06       6      64 .]     301     353 ..     297     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9.9e-09
                              TOBE   6 qlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                        +p tV+vvep gs+ ++++d+g     +Arv+ +  +     +G+++ +++++++vhl
  gi|313127373|ref|YP_004037643.1| 301 GIPTTVDVVEPIGSDNYLHLDVGTDF--IARVDSDVEPT----VGDTIEITFDQSAVHL 353
                                       689*******************9876..****9999999....***************7 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   2.1e-07   0.00021      24     205 ..      31     203 ..      19     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.1e-07
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                        +f  +vGp G+GKs  l  i   L   +  ++r    +d+     + ++ + a v   +    +k++ ++  + ++
  gi|313127373|ref|YP_004037643.1|  31 GEFVTVVGPSGCGKSTTLRMIA-GLESPTGGSIRIGG-EDVTDV--HARKRDVAMVFQNYALYPHKTVRQNMAFGLR 103
                                       46999***********999994.44444555676543.344333..3456677777777777778888888889999 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                        +   ++  + +  +++++  ++++ll +   ++++LSgG+k+ val    Ai  v+   ++l+De  ++LD+k ++
  gi|313127373|ref|YP_004037643.1| 104 MSTDLSKAERNRRVEETAEMMDIEDLLDD---KPNELSGGQKQRVALG--RAI--VREPDVFLFDEPLSNLDAKLRT 173
                                       99999988888888999999999999999...589*******977664..455..4556689*************** PP

                                       HHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkekskn..aQfivislreemleka 205
                                        + + +++ +++     i +++++e    +
  gi|313127373|ref|YP_004037643.1| 174 TMRTEIQRIQNElgITSIYVTHDQEEAMTM 203
                                       **9999988877334556677766554444 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.1   4.1e+03       8      22 ..      14      29 ..      13      36 .. 0.68
   2 ?    0.7   0.0      0.81   8.1e+02       9      22 ..      59      73 ..      58      83 .. 0.72
   3 !   13.2   0.0    0.0001       0.1      15      43 .]     270     295 ..     253     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.1
                   CysA_C_terminal  8 edGk.lriGglalpvP 22
                                      ++G+ + +++++++v+
  gi|313127373|ref|YP_004037643.1| 14 DNGRiVAVDDVSFEVE 29
                                      5787455588888887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.81
                   CysA_C_terminal  9 dGklriGglalp.vP 22
                                      +G +riGg ++  v+
  gi|313127373|ref|YP_004037643.1| 59 GGSIRIGGEDVTdVH 73
                                      699*****8887454 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.0001
                   CysA_C_terminal  15 GglalpvPelagadgqevvayVRPhDlei 43 
                                       G++a  v  + g+  + ++++VRP+D+++
  gi|313127373|ref|YP_004037643.1| 270 GDVAQRVS-ESGS--KTARLGVRPEDVTV 295
                                       66666776.5666..9**********987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   8.9e-06    0.0089       4      26 ..      30      52 ..      27     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.9e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                      +  +++v+G+sG+GK+t+lr+++
  gi|313127373|ref|YP_004037643.1| 30 DGEFVTVVGPSGCGKSTTLRMIA 52
                                      56799***************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   8.1e-06     0.008      24      50 ..      31      56 ..      21     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.1e-06
                            AAA_16 24 pelvllsGesGvGKsslvrellralek 50
                                      +e v ++G+sG+GKs+ +r+++  le 
  gi|313127373|ref|YP_004037643.1| 31 GEFVTVVGPSGCGKSTTLRMIAG-LES 56
                                      3789***************9983.444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05     0.013      46      66 ..      32      52 ..      19     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                             Rad17 46 riLLisGPsGCgkstvvkvLs 66
                                      + + + GPsGCgkst++++++
  gi|313127373|ref|YP_004037643.1| 32 EFVTVVGPSGCGKSTTLRMIA 52
                                      567799***********9987 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.3e-05     0.013      28     148 ..      36     193 ..      27     231 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                       EEESTTSSHHHHHHHHHHHCS--..........--HHHH.HCCHHHHHHHHHHHHHHHHHHHHHTT.......HHHC CS
                           G-alpha  28 llGqseSGKsTilkqlkllykkg..........fseeel.atwraviqlnivrsiktilealesleselsesfelqe 93 
                                       ++G s++GKsT+l+ +  l+ ++          +++  + +   a++++n     ++ +++ + ++ ++s +++++e
  gi|313127373|ref|YP_004037643.1|  36 VVGPSGCGKSTTLRMIAGLESPTggsiriggedVTDVHArKRDVAMVFQNYALYPHKTVRQNMAFGLRMSTDLSKAE 112
                                       79******************99999***9999944444414466788888888888888888888999988887777 PP

                                       -SS-SCCC...S-HCHHHH.................................HHCCHHC..........-HCHHHHH CS
                           G-alpha  94 lkerldpl...kkveasliaklssateee.......................qeiefnp..........raevgedi 134
                                       +++r+++    +++e+ l +k +     e                             +          r+ ++++i
  gi|313127373|ref|YP_004037643.1| 113 RNRRVEETaemMDIEDLLDDKPN-----ElsggqkqrvalgraivrepdvflF-----DeplsnldaklRTTMRTEI 179
                                       77777766211555555544333.....2234546667777666666544442.....1233335555555666677 PP

                                       HHHCCSHHHHHHHC CS
                           G-alpha 135 kaLwndpgiqelye 148
                                       +++ n+ gi ++y 
  gi|313127373|ref|YP_004037643.1| 180 QRIQNELGITSIYV 193
                                       77777777777765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.7e-05     0.076       2      52 ..      35      85 ..      34      94 .. 0.79
   2 ?   -0.5   0.1       1.5   1.5e+03      58      89 ..     154     186 ..     116     203 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.7e-05
                                      EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfke 52
                                       ++Gp G+GK+++ + +a   +     ++i g +++   v +++++++++f++
  gi|313127373|ref|YP_004037643.1| 35 TVVGPSGCGKSTTLRMIAGLESptGGSIRIGGEDVT--DVHARKRDVAMVFQN 85
                                      689***************975422346888888888..678888888888876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                                       TSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHH CS
                               AAA  58 kpsilfiDEidalaksr.sgseseeeervvnqL 89 
                                       +p ++++DE  +   ++ +++ ++e +r++n+L
  gi|313127373|ref|YP_004037643.1| 154 EPDVFLFDEPLSNLDAKlRTTMRTEIQRIQNEL 186
                                       478888888555544443344555555555554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.3e-05     0.043       1      56 [.      34      98 ..      34     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.........gvnlrdvakenglllevdpe.aldeskrldedk 56
                                      + + G++G+GK+t  + ++ ++ +         g+ ++dv++ ++ + +v+++ al ++k +++++
  gi|313127373|ref|YP_004037643.1| 34 VTVVGPSGCGKSTTLRMIAGLE-SptggsirigGEDVTDVHARKRDVAMVFQNyALYPHKTVRQNM 98
                                      6799**************7774.456778999*999999999999999999998777777666654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.11      14      39 ..      23      48 ..      19      57 .. 0.81
   2 ?   -2.9   0.0       5.9   5.9e+03      44      57 ..      86      99 ..      84      99 .. 0.83
   3 ?   -2.6   0.0         5   4.9e+03      18      32 ..     287     301 ..     281     303 .. 0.78
   4 ?   -2.7   0.0       5.1   5.1e+03      11      30 ..     345     366 ..     344     367 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                      + ++e++  +++ ++GpsG GKST l
  gi|313127373|ref|YP_004037643.1| 23 DVSFEVEDGEFVTVVGPSGCGKSTTL 48
                                      5667777445999***********76 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.9
                            AAA_29 44 alLvpakkvrfNka 57
                                      + L+p+k+vr N a
  gi|313127373|ref|YP_004037643.1| 86 YALYPHKTVRQNMA 99
                                      689****9999976 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5
                            AAA_29  18 eidlkgatlltGpsG 32 
                                        ++++++t++tG  G
  gi|313127373|ref|YP_004037643.1| 287 GVRPEDVTVVTGGAG 301
                                       56778899***9877 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 5.1
                            AAA_29  11 tfdg.htieidlkg.atlltGp 30 
                                       tfd+  ++ +d  g   ll+G+
  gi|313127373|ref|YP_004037643.1| 345 TFDQsAVHLFDATGgDALLSGA 366
                                       6788777777877778899886 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.1e-05     0.051      90     122 ..      21      54 ..      12      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +++++ +++d +++++vG+SG GKSt + ++++ 
  gi|313127373|ref|YP_004037643.1|  21 VDDVSFEVEDgEFVTVVGPSGCGKSTTLRMIAGL 54 
                                       6677788888799*************99999875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     7e-05      0.07      18      60 ..      33      75 ..      21     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                       + ++G +G+GKs+++++++    ++g+ +r+ + d+   h +
  gi|313127373|ref|YP_004037643.1| 33 FVTVVGPSGCGKSTTLRMIAGLESPTGGSIRIGGEDVTDVHAR 75
                                      57899***************99889********9999888855 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.19      19      48 ..      32      61 ..      25     130 .. 0.86
   2 ?   -2.8   0.0       4.4   4.4e+03      32      67 ..     173     208 ..     172     214 .. 0.73
   3 ?   -2.4   0.0       3.4   3.3e+03      18      28 ..     291     301 ..     258     302 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggr 48
                                       +++++Gp G GK+t+l+ ++ +    gg+
  gi|313127373|ref|YP_004037643.1| 32 EFVTVVGPSGCGKSTTLRMIAGLESPTGGS 61
                                      4889***************99887766654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.4
                            AAA_30  32 ttalkalreaweaaggrviglAptgkaAkvLaeelg 67 
                                       tt+ ++++++ ++ g + i +++ ++ A ++++ l 
  gi|313127373|ref|YP_004037643.1| 173 TTMRTEIQRIQNELGITSIYVTHDQEEAMTMGDRLA 208
                                       666666777777778888888888888888887665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.4
                            AAA_30  18 drvavltGpAG 28 
                                       + v+v+tG+AG
  gi|313127373|ref|YP_004037643.1| 291 EDVTVVTGGAG 301
                                       33666777766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0012       1.2       2      18 ..      35      51 ..      34      80 .. 0.87
   2 ?   -0.8   0.0         2     2e+03      23      58 ..     215     247 ..     206     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                      RNA_helicase  2 wlyGpsgeGKStlakeL 18
                                       ++Gpsg+GKSt+ + +
  gi|313127373|ref|YP_004037643.1| 35 TVVGPSGCGKSTTLRMI 51
                                      689*********99874 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2
                      RNA_helicase  23 lkklklkkkdsvysrnpeddfwdgYtgqevvvidDf 58 
                                       l+++   k ++vy  np+++f+ g+ g + + + D+
  gi|313127373|ref|YP_004037643.1| 215 LQQV--GKPKDVY-ENPTNKFVGGFVGSPSMNFVDV 247
                                       4444..4556787.599*****99999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2388.67
//
Query:       gi|313127374|ref|YP_004037644.1|  [L=428]
Description: carbohydrate ABC transporter substrate-binding protein, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-34  120.3   7.5      2e-34  119.7   7.5    1.2  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.9e-16   60.9   7.6    1.9e-16   60.9   7.6    1.7  2  SBP_bac_1   Bacterial extracellular solute-binding protein
     0.0017   18.1   0.1     0.0033   17.2   0.1    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   7.5   3.4e-38     2e-34       6     277 ..      82     371 ..      77     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 3.4e-38
                                       HHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG.GS.TTHHH-HH.HHHTT- CS
                         SBP_bac_8   6 fekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladls.dl.dnlddltd.alaavg 79 
                                       f+++t+ ++    ++   l  k+++a++ag++p+ + +wa +d+ + + +++ ++d s  l   ld +td a +a +
  gi|313127374|ref|YP_004037644.1|  82 FNDQTKHTLDG--SDISNLKKKTTSAIPAGQGPTTF-EWA-HDWGGDYYQRNFVVDKSdALsVSLDTFTDgATEAIQ 154
                                       55555555554..45567899************965.666.8****************544689999999555555* PP

                                       -TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHH....HHH-SEGG---G..GGGGGTHHETTEE-- CS
                         SBP_bac_8  80 ydgklygvPyasetpyvliynkdllekaedpktwdellaaakkl....kgkfglpdpasg..wlqaallakdgksld 150
                                       +dg++ g+P  +et  +liyn+++++ a  p+t++e++++ +++     g +gl+ p +g  +  +a+ + +g+++d
  gi|313127374|ref|YP_004037644.1| 155 FDGATIGLPHSAET-VALIYNTEMVDSA--PETVSEMKSVMEEYhdpeSGMYGLSCPFDGyfVSAWAQAF-GGYYFD 227
                                       *************9.7**********75..**************77666*****8777763255999999.999998 PP

                                       -H..HHH.........HHHHHH.HHHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE.--.. CS
                         SBP_bac_8 151 ddggkdgl........kealel.lkklkdngktydtgadavsefanGevaftingswdiaaaqkagkklgai.vp.. 215
                                         +  +++        ++ +++ l++l++++   +t+  + ++fa+G++  +ing+w + +++++g ++g+  +p  
  gi|313127374|ref|YP_004037644.1| 228 HEK--ETQlginidatVKGFQFaLDNLVPYMPNDPTYGPQAAAFAEGNAPLAINGPWYLSTLNEKGIDYGVSkLPap 302
                                       874..3334445544455554427778888876677766669******************************97766 PP

                                       ...S--EEEEEEEEEEBT..TS-HHHH.HHHHHHHHHTTSH.HHHHHHHHH---BS-S-TTTHHHHHH- CS
                         SBP_bac_8 216 ...kqgsfaggkglavpk..naknedl.aAldFlkwltspe.nqaalaektgyipvnksaalspevkkd 277
                                          k+++ +g++ ++ +k   a+n+   aAldF++w+t++e      a+ +g +pv+   a+s+e+ ++
  gi|313127374|ref|YP_004037644.1| 303 eggKPTPYTGITMWYFSKamEADNASTqAALDFIEWYTTNEdILLRNAKEQGAVPVLERIATSDELPDA 371
                                       877788*********9995558888888*********86555**********************98876 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   7.6   3.2e-20   1.9e-16      13     312 ..      77     343 ..      68     345 .. 0.84
   2 ?   -1.1   0.1      0.24   1.4e+03      45      95 ..     362     408 ..     358     420 .. 0.72

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.2e-20
                                       HHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCT CS
                         SBP_bac_1  13 lvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkda 89 
                                        + + f+      k +++ ++ ++l+ k t ai aG+gp   + +++dw +++ + +++ + ++ +   l + ++  
  gi|313127374|ref|YP_004037644.1|  77 EALQTFND-Q--TKHTLDGSDISNLKKKTTSAIPAGQGP-TTFEWAHDWGGDYYQRNFVVDKSDALSVSLDTFTD-- 147
                                       44466655.3..444555555699***************.****************9999999999999766643.. PP

                                       EEEEHHHHTHHHHCEEE...ES.EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEH CS
                         SBP_bac_1  90 adklsssvlpkildskv...ly.vPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsa 161
                                          +++          +      +P  a + +liYN+  ++    ++p+t +e   + ++  ++  +      +g  
  gi|313127374|ref|YP_004037644.1| 148 --GATEAI-------QFdgaTIgLPHSAeTVALIYNTEMVD----SAPETVSEMKSVMEEYHDPESGM-----YGLS 206
                                       ..322222.......33446677****77************....4567*************988877.....7777 PP

                                       HHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEE CS
                         SBP_bac_1 162 sgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaama 238
                                           +yf +a+a+ +gg++fd +       e +  ++     ++++++ ++l ++ + + +    +a+f++G+a++a
  gi|313127374|ref|YP_004037644.1| 207 CPFDGYFVSAWAQAFGGYYFDHE------KETQLGINIDATVKGFQFALDNLVPYMPNDPTYGPQAAAFAEGNAPLA 277
                                       778889**************965......45566777777777779999**************************** PP

                                       EEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHH.......HHHHHHHH CS
                         SBP_bac_1 239 ivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpea.......AkkFldfl 308
                                       i+g+w+               +  ++++++gv  lPa +ggkp+   + g+++++ sk +ea       A +F++++
  gi|313127374|ref|YP_004037644.1| 278 INGPWY-------------LSTLNEKGIDYGVSKLPAPEGGKPT--PYTGITMWYFSKAMEAdnastqaALDFIEWY 339
                                       ******.............99999999****************7..77779999999999999999999******** PP

                                       TSHH CS
                         SBP_bac_1 309 lspe 312
                                       +++e
  gi|313127374|ref|YP_004037644.1| 340 TTNE 343
                                       **98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.24
                                       HHTTS.SSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHH CS
                         SBP_bac_1  45 iaaGd.gpaDviavdndwiarlakaglllpldpyvkaylapgvkdaadklss 95 
                                       ia++d  p D +++    +++ +++g+++p  p ++a + p+++  ++ +++
  gi|313127374|ref|YP_004037644.1| 362 IATSDeLP-DAVQG----FSQAVQQGVPMPAHPKMNAVWTPVKDALTKAFNG 408
                                       66666555.88888....6788888999999999999987776655555544 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   5.5e-07    0.0033       2      25 ..       3      26 ..       2      27 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR+ LK  ++++  +al+gc++
  gi|313127374|ref|YP_004037644.1|  3 MDRRSVLKHLGGVGVIGALAGCVG 26
                                      99********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2929.85
//
Query:       gi|313127375|ref|YP_004037645.1|  [L=321]
Description: carbohydrate ABC transporter membrane protein 1, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-16   59.6  14.2    3.2e-16   59.6  14.2    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.22   11.7   1.3       0.42   10.8   0.4    1.9  2  TM_PBP2_N     N-terminal of TM subunit in PBP-dependent ABC t


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.4   8.0         2   1.8e+04      33      64 ..      37     112 ..      21     122 .. 0.56
   2 !   59.6  14.2   3.6e-20   3.2e-16       4     171 ..     115     303 ..     108     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: -6.4 bits;  conditional E-value: 2
                      BPD_transp_1  33 fvlaillvlvf.........................................vilsilghlilpv...iillllsa 64 
                                       f l+++l+lv                                          ++++++g ++l v   +++ + ++
  gi|313127375|ref|YP_004037645.1|  37 FMLFPVLYLVGisftnarpanlfagetaldvltfgqaefvglqnyvsaltdpAFWNSFGVTWLFVgtsVTAKIAFS 112
                                       2244444444366666677777777777777777777777777777777777666666666665412233333444 PP

  == domain 2  score: 59.6 bits;  conditional E-value: 3.6e-20
                      BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfvlaillvlvf....................vilsilghlilpviill 60 
                                       +++++ ++ + +++++lr lii++++lP + ++ ++  +f                    ++ls  ++++l+  ++ 
  gi|313127375|ref|YP_004037645.1| 115 IALVV-TSDRVRGKRFLRSLIIIPMGLPAIFVVTVWRGIFstaefglanqilreigfesvAWLSQRWTAFLAYNVTE 190
                                       34444.4788999*******************999999999999********************************* PP

                      BPD_transp_1  61 llsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG. 136
                                       ++ a p+++li+ +al+ +p++l eaa ++Ga++  +f +v+lP++++p++   il++++++ ++++++ + ++++ 
  gi|313127375|ref|YP_004037645.1| 191 VWLAYPFMVLITVSALQDVPEELHEAAMVDGAGYVSRFLHVTLPAIKRPVMFASILTAAASFQAFLIPYVFNQGGPa 267
                                       ******************************************************************99999977778 PP

                      BPD_transp_1 137 .lgtllleailgydyseisnggvlalviavlllnlv 171
                                         + l++       +++ ++g  +a+ ++ ++++ +
  gi|313127375|ref|YP_004037645.1| 268 rANELIVVYGYREAFTFSQYGEGAAISLLAVAFIGA 303
                                       877777777777777777733333333333333333 PP

>> TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   4.7e-05      0.42       4      22 ..      35      53 ..      31      69 .. 0.88
   2 ?   -1.9   0.0      0.42   3.8e+03      10      26 ..     273     291 ..     272     294 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.7e-05
                         TM_PBP2_N  4 lvfqvfpvlyTistafTNy 22
                                       +f +fpvly + ++fTN 
  gi|313127375|ref|YP_004037645.1| 35 SAFMLFPVLYLVGISFTNA 53
                                      589***************5 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.42
                         TM_PBP2_N  10 pvlyTistafT..NyGdGh 26 
                                       +v+y  + afT   yG+G 
  gi|313127375|ref|YP_004037645.1| 273 IVVYGYREAFTfsQYGEGA 291
                                       5778888887744688875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 2007.41
//
Query:       gi|313127376|ref|YP_004037646.1|  [L=360]
Description: carbohydrate ABC transporter membrane protein 2, cut1 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-16   59.5  14.4    3.5e-16   59.5  14.4    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2     0.022   3.9e+02      23      36 ..      58      71 ..      17     125 .. 0.67
   2 !   59.5  14.4   1.9e-20   3.5e-16      25     180 ..     155     350 ..     150     354 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.022
                      BPD_transp_1 23 liivllslPsfvla 36
                                      ++ +ll +P+++++
  gi|313127376|ref|YP_004037646.1| 58 VVVALLLFPVYWIL 71
                                      22333333444433 PP

  == domain 2  score: 59.5 bits;  conditional E-value: 1.9e-20
                      BPD_transp_1  25 ivllslPsfvlaillvlvf........................................vilsilghlilpviilll 61 
                                        ++ s+P++++a+ l+  +                                        +++ +l ++ l++++ ++
  gi|313127376|ref|YP_004037646.1| 155 SLTVSIPTVIIAMCLIIPAsyalsrrkfifrrkilftyvlltqvggglgialliglytvYVQVGLNNSKLALAVYYA 231
                                       67889*********998889***************************************9999************** PP

                      BPD_transp_1  62 lsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlg 138
                                        +a+p+++++ + +++ +p +++eaa ++Ga++w+++  v+lP+++  ++t +i++f   ++++v++ +l+   G  
  gi|313127376|ref|YP_004037646.1| 232 ATAVPFNTWLLKTYMDGIPVSYEEAAVVDGAPPWRVVTEVILPLSAAGLATVFIFTFLTGWTEFVVAQTLL---GTE 305
                                       ***********************************************************************...778 PP

                      BPD_transp_1 139 tllleailgydyseis...nggvlalviavlllnlvadilqrlld 180
                                       + +l + l++ ++e s   +  +++++++  +l+lv+++ qr+++
  gi|313127376|ref|YP_004037646.1| 306 NYTLPVGLYSLVDEYSipwARFSAFALVFASPLMLVYFFAQRYIE 350
                                       8888888888888888887779999999999***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2498.83
//
Query:       gi|313127377|ref|YP_004037647.1|  [L=165]
Description: cupin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-13   48.6   0.0    8.2e-13   47.9   0.0    1.3  1  Cupin_2          Cupin domain
    3.1e-06   27.2   0.0    4.3e-06   26.7   0.0    1.2  1  AraC_binding     AraC-like ligand binding domain
    7.4e-05   22.5   0.0    0.00011   22.0   0.0    1.3  1  EutQ             Ethanolamine utilisation protein EutQ
    0.00045   19.9   0.0    0.00071   19.2   0.0    1.2  1  DMSP_lyase       Dimethlysulfonioproprionate lyase
     0.0056   16.3   0.0       0.01   15.5   0.0    1.4  1  Cupin_3          Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.034   13.8   0.1      0.038   13.7   0.1    1.2  1  AraC_binding_2   AraC-binding-like domain
       0.05   13.2   0.0      0.088   12.4   0.0    1.5  1  Cupin_1          Cupin
      0.071   13.0   0.0        0.1   12.5   0.0    1.2  1  MannoseP_isomer  Mannose-6-phosphate isomerase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   3.7e-16   8.2e-13      10      62 ..      53     105 ..      48     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.7e-16
                                       EEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SS CS
                           Cupin_2  10 sapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgd 62 
                                       ++p h+H+  de+ yVl+Ge+el +dge    e+Gd+++ p ++pH++r + d
  gi|313127377|ref|YP_004037647.1|  53 VTPLHVHRSDDELWYVLDGEMELFIDGELLSAEPGDTAFAPQNVPHALRIAAD 105
                                       6799*******************************************987665 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.9e-09   4.3e-06      11      78 ..      48     116 ..      41     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.9e-09
                                       STT-SE.EEETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE-- CS
                      AraC_binding  11 ypdhsf.pphvhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfeg 78 
                                       + + ++ p hvh    +++yv++G+  l+++g+   ++pGd  + p+++pH ++ +++ g +y +l+ +g
  gi|313127377|ref|YP_004037647.1|  48 DENRVVtPLHVHRsDDELWYVLDGEMELFIDGELLSAEPGDTAFAPQNVPHALRIAAD-GTRYLVLRTPG 116
                                       444444277***9999***************************************996.88888887666 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     5e-08   0.00011      96     134 ..      63     101 ..      55     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5e-08
                              EutQ  96 deidyvieGrldvlidGrkvvaeaGdviliPkgskiefs 134
                                       de+ yv++G++++ idG  ++ae+Gd  + P++    + 
  gi|313127377|ref|YP_004037647.1|  63 DELWYVLDGEMELFIDGELLSAEPGDTAFAPQNVPHALR 101
                                       9******************************99755554 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.2e-07   0.00071     107     157 ..      53     103 ..      51     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.2e-07
                        DMSP_lyase 107 rYPdHhhaa.eelYlvlsggaefrqgeaewlsrgiGevifnepgikhamrsa 157
                                         P H h+  +el++vl g +e+   ++e ls + G++ f++++++ha+r a
  gi|313127377|ref|YP_004037647.1|  53 VTPLHVHRSdDELWYVLDGEMELFI-DGELLSAEPGDTAFAPQNVPHALRIA 103
                                       569**99998**********99955.5669*******************976 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.7e-06      0.01      20      62 ..      57      98 ..      54     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.7e-06
                                      EECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEE CS
                           Cupin_3 20 rltyeedEfcyileGevkvtpeggetvelraGDlvvlpkglsg 62
                                      +++   dE+ y+l Ge+++   +ge    ++GD ++ p++   
  gi|313127377|ref|YP_004037647.1| 57 HVHRSDDELWYVLDGEMELFI-DGELLSAEPGDTAFAPQNVPH 98
                                      667788***************.****************98755 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.7e-05     0.038      43     114 ..      54     124 ..      20     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                    AraC_binding_2  43 aavsirpselddfylvqlplsGraeveqggrevvlgpgdavvldpgrpyrlrwsa.dceqlvlrip..ralLerp 114
                                       ++ ++++s+++    + + l G++e+  +g+ + ++pgd++++  + p  lr++a +++ lvlr p   +l+++ 
  gi|313127377|ref|YP_004037647.1|  54 TPLHVHRSDDE----LWYVLDGEMELFIDGELLSAEPGDTAFAPQNVPHALRIAAdGTRYLVLRTPgnKSLFGAV 124
                                       55566666655....67789****************************99998775899*****99876666554 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.9e-05     0.088      45      99 ..      53     100 ..      37     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                                       EEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEE CS
                           Cupin_1  45 lllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfq 99 
                                       + ++h+h +  e+ yvl+Ge+   f+  +          ++Gd+   P++++h+ 
  gi|313127377|ref|YP_004037647.1|  53 VTPLHVHRSDDELWYVLDGEME-LFIDGE------LLSAEPGDTAFAPQNVPHAL 100
                                       6799*****************9.454444......35578************985 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.4e-05       0.1      75     123 ..      51     101 ..      41     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                   MannoseP_isomer  75 klslqkhhhra..ehWvvvkGtakvtvddevlllkenestyiplgaihrle 123
                                       +++   h hr+  e W v+ G  ++ +d e l  +  ++ + p+++ h+l 
  gi|313127377|ref|YP_004037647.1|  51 RVVTPLHVHRSddELWYVLDGEMELFIDGELLSAEPGDTAFAPQNVPHALR 101
                                       566667999985578*********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1226.56
//
Query:       gi|313127378|ref|YP_004037648.1|  [L=196]
Description: 50S ribosomal protein L15e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-83  277.0   4.8      8e-83  276.9   4.8    1.0  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
       0.14   11.9   0.1        0.9    9.3   0.1    2.0  1  YjbF            Group 4 capsule polysaccharide lipoprotein gf


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.9   4.8     9e-87     8e-83       1     189 [.       4     189 ..       4     191 .. 0.99

  Alignments for each domain:
  == domain 1  score: 276.9 bits;  conditional E-value: 9e-87
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       ++y++++++wk++ +  l el+++r +++r+e a+vr++rptrld+Ar+LGYkakqGivv+rv+vr+Gg++k  +++
  gi|313127378|ref|YP_004037648.1|   4 SFYSHIKDAWKNPGDGKLGELQWQRKQDWRDEGAIVRIDRPTRLDKARELGYKAKQGIVVARVSVRKGGARK--QRF 78 
                                       68**********************************************************************..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGG CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkv 154
                                       k+gr++krqgvn++ ++ks+q+iaeer++rk+pnlrvLnSYwvgeDg++k++E+i+vDp+h+ai++d+++nwic+++
  gi|313127378|ref|YP_004037648.1|  79 KAGRRTKRQGVNRIGRRKSIQRIAEERAARKYPNLRVLNSYWVGEDGSQKWHEIIMVDPEHPAIESDDDLNWICSDD 155
                                       ***************************************************************************** PP

                                       GTTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-TG CS
                    Ribosomal_L15e 155 hkhRelrGltsagkksRGlrkkglkgaekirgsrr 189
                                       hk+R++rGlt+agk +RGl+++g kg+e++r+s+r
  gi|313127378|ref|YP_004037648.1| 156 HKGRTFRGLTNAGKSNRGLTTRG-KGSEHTRPSIR 189
                                       ***********************.*********98 PP

>> YjbF  Group 4 capsule polysaccharide lipoprotein gfcB, YjbF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0001       0.9      87     166 ..      10     125 ..       3     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0001
                                       G-GGGGGGG--.TT-EEEEEEEE........................................EETTEEEEEEEEEE CS
                              YjbF  87 adplalallalsragswqrildw........................................qekyrygyladstf 123
                                       +d+++++   + +  +wqr+ dw                                        +  ++ +++a    
  gi|313127378|ref|YP_004037648.1|  10 KDAWKNPGDGKLGELQWQRKQDWrdegaivridrptrldkarelgykakqgivvarvsvrkggA--RKQRFKAGR-- 82 
                                       5777777777777888888888888888888888888888887777777777777665533211..112222333.. PP

                                       EEEEEEEEEETTEEEEEEEEEEEEEETT.TTEEEEEEEEEETTT CS
                              YjbF 124 rragketvtilektvettrieEsvevpa.leaefqNqYwvdsqs 166
                                        r+++++v+  +++  ++ri E+ +  +  + ++ N+Ywv ++ 
  gi|313127378|ref|YP_004037648.1|  83 -RTKRQGVNRIGRRKSIQRIAEERAARKyPNLRVLNSYWVGEDG 125
                                       .334444555577777777766666555589*********6544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 1319.07
//
Query:       gi|313127379|ref|YP_004037649.1|  [L=270]
Description: caax amino terminal protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-10   41.2  17.1    8.9e-10   38.8  17.1    2.3  1  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8  17.1   4.9e-14   8.9e-10      10      90 ..     152     256 ..      19     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 4.9e-14
                                       HHHHHHHHHHHHHHTTCHHHHHHHH.S-.............HHHHHHHHHHHHHCSGGG...........HHH.HHH CS
                              CPBP  10 lalllapllEEllfRglllqllqergss.............tlailissilFglaHlpn...........gps.vll 61 
                                       + +l+++l+EEll R+ l++ l++ g++             + ai+++s++Fg++Hlp             +  vll
  gi|313127379|ref|YP_004037649.1| 152 VRFLYGGLTEELLLRWGLMSFLAWVGWRaaggirrpgsdvmWPAIVLTSVVFGIVHLPAlaglaslsfatMIRtVLL 228
                                       47899********************9999******************************9999988887544468** PP

                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              CPBP  62 aalaGlvlgylylktgsllaaillHalln 90 
                                        ++ G+v+g+ +++   l aa+l+Ha+++
  gi|313127379|ref|YP_004037649.1| 229 NSIGGIVYGWFFWRWH-LEAAMLAHAGTH 256
                                       ****************.*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1935.52
//
Query:       gi|313127380|ref|YP_004037650.1|  [L=106]
Description: rhodanese-related sulfurtransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-14   52.9   0.0    8.5e-14   52.0   0.0    1.4  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   4.8e-18   8.5e-14       2     105 ..       7      97 ..       6      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 4.8e-18
                         Rhodanese   2 akelkellekgkva..llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgg 76 
                                       ++ l++ le+++    ++D+R+p  Y++ghI+gAvn+             p   l  +  +   d ++ vvv c  g
  gi|313127380|ref|YP_004037650.1|   7 PETLVAKLEDDDSEttVVDIRDPSSYAAGHIEGAVNL-------------PASRLSLSTVDT--DWGDDVVVACYVG 68 
                                       6778888866665568*********************.............666666666666..789********** PP

                         Rhodanese  77 graaaaaallkk.lGyknvsvldGGfkawk 105
                                       ++++++a ll + l   +vs l+GGf+aw 
  gi|313127380|ref|YP_004037650.1|  69 QSSRRVASLLDShLD-ADVSSLRGGFDAWD 97 
                                       **9999999996477.88***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 795.22
//
Query:       gi|313127381|ref|YP_004037651.1|  [L=269]
Description: dinucleotide-utilizing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-69  232.8   0.0    4.8e-69  232.4   0.0    1.0  1  ThiF             ThiF family
      0.005   17.1   1.0      0.021   15.1   1.0    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
       0.01   15.9   0.1      0.019   15.0   0.0    1.5  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.014   16.0   0.1      0.026   15.2   0.1    1.5  1  PglD_N           PglD N-terminal domain


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.4   0.0   1.1e-72   4.8e-69       1     240 [.      13     244 ..      13     251 .. 0.95

  Alignments for each domain:
  == domain 1  score: 232.4 bits;  conditional E-value: 1.1e-72
                                       THHHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHH CS
                                       xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   1 ysrqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKae 75 
                                       ysr++ +  +g+ gq++L d++vl+vGaGglGs+++++La++Gvg+l +vD+D++e sNl+Rq+ +r++d+G+pK+e
  gi|313127381|ref|YP_004037651.1|  13 YSRHIIMdeVGPPGQKRLLDASVLVVGAGGLGSPVIQYLAAAGVGHLGIVDDDVVERSNLQRQVVHRDDDVGTPKVE 89 
                                       788987788999***************************************************************** PP

                                       HHHHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  76 vaaealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvvi 152
                                       +aa++++ +npdv ve+++ r+++e+v   +l ++D+Vvda+Dn+++r+lvn++c+ ++ip+ +++   fegqv++ 
  gi|313127381|ref|YP_004037651.1|  90 SAAAFVHGLNPDVTVETYETRLEKENV--GVLADYDVVVDASDNFPTRYLVNDFCRINEIPVAHGAIYKFEGQVTTL 164
                                       ************************984..79********************************************** PP

                                       EECCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHH.TTBCGGGCCEEEECCTTTTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                              ThiF 153 ipgktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkll.sgkeklenslltqvdllesr 228
                                          + +cy+Cl+p   e p++ +vp c ++ g   +++ +++ v++++a+e++kl+ ++ ++l ++ll ++d+ +++
  gi|313127381|ref|YP_004037651.1| 165 T-PDGPCYRCLFP---EAPEPGTVPDC-ATTG---VLGVLPGTVGCIQATEAVKLVlDEGDPLVGRLL-FYDAMDMT 232
                                       7.59*********...***********.****...*********************766666666666.******** PP

                                       EEEECCEEEEEE CS
                                       xxxxxxxxxxxx RF
                              ThiF 229 fenvelerakks 240
                                       fe+v+++r++++
  gi|313127381|ref|YP_004037651.1| 233 FETVPYRRNSDC 244
                                       ******998865 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.0   4.8e-06     0.021       1      98 [.      35     151 ..      35     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.8e-06
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.....................TTTCEEEEE--T CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.....................lgvrfeaialda 56 
                                       vl++GaG+ G++v+++la+ +    ++ ++d +  +  +l  ++                     l+++++ ++   
  gi|313127381|ref|YP_004037651.1|  35 VLVVGAGGLGSPVIQYLAAAGVG--HLGIVDDDVVERSNLQRQVvhrdddvgtpkvesaaafvhgLNPDVTVETYET 109
                                       89*****************9976..8999998888877777777888999999999999999988777777777777 PP

                                       TTHHHHHHHHHTTSSEEEE-SSGG.GHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  57 enyeavLaallkegdlvvnlsppi.ssldvlkaCietgvhyvd 98 
                                         +++  + +l+++d+vv++s ++     v ++C+ + + +  
  gi|313127381|ref|YP_004037651.1| 110 RLEKE-NVGVLADYDVVVDASDNFpTRYLVNDFCRINEIPVAH 151
                                       77777.77889999********997777888888877766655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   4.2e-06     0.019       9      52 ..      29      72 ..      25      95 .. 0.84
   2 ?   -3.6   0.0       2.5   1.1e+04      71      82 ..     117     128 ..     102     130 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.2e-06
                                      ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHH CS
                      Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakel 52
                                      +l ++ vl++GaG +++ v+++L+a+gv ++ ++  ++   ++l
  gi|313127381|ref|YP_004037651.1| 29 RLLDASVLVVGAGGLGSPVIQYLAAAGVGHLGIVDDDVVERSNL 72
                                      566899**********************9999987666555555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.5
                                       HHHHT-SEEEE- CS
                      Shikimate_DH  71 ellaeadvvisa 82 
                                        +la++dvv+ a
  gi|313127381|ref|YP_004037651.1| 117 GVLADYDVVVDA 128
                                       567888888765 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   5.8e-06     0.026       2      36 ..      35      68 ..      34      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
                            PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflDdnkkt 36
                                      ++++GaGG g  v++ + a g    +g++Dd+  +
  gi|313127381|ref|YP_004037651.1| 35 VLVVGAGGLGSPVIQYLAAAG-VGHLGIVDDDVVE 68
                                      789******************.9********8633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1992.75
//
Query:       gi|313127382|ref|YP_004037652.1|  [L=601]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-39  134.7  44.3    1.8e-37  128.8  27.7    3.0  4  MCPsignal      Methyl-accepting chemotaxis protein (MCP) sign
    7.8e-06   25.9   0.0    2.3e-05   24.4   0.0    1.8  1  PAS            PAS fold
    8.7e-06   26.0   5.8    1.6e-05   25.1   0.2    3.7  3  PAS_4          PAS fold
    3.6e-05   24.0   0.1    0.00021   21.5   0.0    2.4  2  PAS_9          PAS domain
     0.0024   16.9  14.8      0.021   13.8  14.3    2.2  1  Kre28          Spindle pole body component
  ------ inclusion threshold ------
       0.02   15.1  26.2       0.76   10.1   4.1    5.2  5  DUF948         Bacterial protein of unknown function (DUF948)
      0.043   13.5  30.3      0.019   14.6   7.5    3.1  3  TMP_2          Prophage tail length tape measure protein
      0.049   13.7   8.9        2.9    8.0   4.7    2.4  2  UPF0242        Uncharacterised protein family (UPF0242) N-ter
      0.093   13.1  15.1        5.8    7.4   0.5    5.7  4  HAMP           HAMP domain
       0.11   11.8  27.1        0.7    9.2  10.5    3.2  3  DUF3450        Protein of unknown function (DUF3450)
       0.23   11.2  38.4       0.48   10.1   9.2    3.4  3  DUF745         Protein of unknown function (DUF745)
       0.23   10.1   6.9        1.5    7.4   0.6    2.4  2  Dor1           Dor1-like family
       0.26   11.1   3.6         29    4.6   0.1    4.4  4  DASH_Dam1      DASH complex subunit Dam1
        0.4    9.5  24.6       0.73    8.7   4.7    2.4  3  Spc7           Spc7 kinetochore protein
        0.4   10.7   7.8        3.1    7.8   0.1    2.4  2  DUF489         Protein of unknown function (DUF489)
       0.55    9.4  17.7       0.16   11.2   2.2    2.4  2  ISG65-75       Invariant surface glycoprotein
       0.62   10.2   5.0        3.1    8.0   0.0    3.5  4  PAS_7          PAS fold
       0.73    9.1  15.7       0.24   10.7   5.4    2.6  2  CorA           CorA-like Mg2+ transporter protein
        1.5    9.0  22.8       0.55   10.4   9.4    2.5  2  ATG16          Autophagy protein 16 (ATG16)
        1.5    7.8  20.4       0.63    9.1  10.4    2.2  2  AIP3           Actin interacting protein 3
        1.8    8.4   5.7          4    7.4   0.9    2.8  2  CoatB          Bacteriophage coat protein B
        2.4    7.9   5.0         13    5.5   4.5    2.4  2  Sec5           Exocyst complex component Sec5
        2.7    8.0  27.5        2.7    8.0   9.7    4.1  4  Laminin_II     Laminin Domain II
        2.8    8.2  26.3       0.34   11.2   7.1    3.5  3  I_LWEQ         I/LWEQ domain
          3    7.0   9.9        6.9    5.8   5.2    2.2  2  TMPIT          TMPIT-like protein
        3.1    7.6  12.1        6.5    6.5   0.3    2.3  2  SKA1           Spindle and kinetochore-associated protein 1
        5.2    7.4  29.0        1.6    9.0   0.6    5.8  6  WXG100         Proteins of 100 residues with WXG
        8.2    4.2  11.1         13    3.6   9.5    1.8  2  Prominin       Prominin
        8.7    7.0   6.0        3.2    8.4   1.3    2.5  2  DUF4665        Domain of unknown function (DUF4665)
        9.3    6.5  17.3       0.41   10.9   6.0    3.1  2  TMF_TATA_bd    TATA element modulatory factor 1 TATA binding


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.3   3.2e+03      36      53 ..     206     223 ..     190     231 .. 0.77
   2 !   13.3   7.8   8.8e-05     0.053      74     163 ..     268     357 ..     247     366 .. 0.83
   3 !  128.8  27.7     3e-40   1.8e-37       4     169 ..     348     524 ..     347     527 .. 0.93
   4 ?   -3.1   0.0       9.9   5.9e+03     145     166 ..     535     556 ..     529     559 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHHHHHHHHH CS
                         MCPsignal  36 sdiieVideiadQTNlLA 53 
                                        ++++V++ i d T ++A
  gi|313127382|ref|YP_004037652.1| 206 DEVVAVVETIYDRTDVVA 223
                                       578889999999988887 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  74 AdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaa 150
                                         E  ++Aer    a e+++  +++ k i++++++    +++v   sel ++ ++++++++++++e+a++ +++a++
  gi|313127382|ref|YP_004037652.1| 268 VPEFNAMAERFERLADEVDQKAVHLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEEIAATSDQVASS 344
                                       45788999999999999999988999999999999999999999999999999999999999999999998888887 PP

                                       HHHHHHHHHHHHH CS
                         MCPsignal 151 seeqsasieevnq 163
                                       +++  +++e+   
  gi|313127382|ref|YP_004037652.1| 345 AAQAQTAAESARG 357
                                       7766665555544 PP

  == domain 3  score: 128.8 bits;  conditional E-value: 3e-40
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHH CS
                         MCPsignal   4 aeeaseeAeeggkevanvvkqmeeieks...........skeisdiieVideiadQTNlLALNAaiEAARAGeqGrG 69 
                                       a++a e+A+  g+ v  + +++ +i++               i++++eVi e+ad TNlLALNA iEAARAGe+G+G
  gi|313127382|ref|YP_004037652.1| 348 AQTAAESARGAGESVRSATDNVIDISDDlldsvielqerMGSIEEVVEVIAEVADRTNLLALNANIEAARAGEAGEG 424
                                       67777888888888888888777777777777888888799************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  70 FaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqe 146
                                       F+VVAdEV++LA+++ + ++ei++ i++iq++ +++v + e+++++++++s ++e+   +l+ei++a++  ad + e
  gi|313127382|ref|YP_004037652.1| 425 FSVVADEVKQLANQTHEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQATDAAADGIGE 501
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 147 iaaaseeqsasieevnqaveeva 169
                                       +a+a++ q++ ieev+++++  +
  gi|313127382|ref|YP_004037652.1| 502 VARATDSQATNIEEVTTTIQTAQ 524
                                       *****************998765 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 9.9
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 145 qeiaaaseeqsasieevnqave 166
                                       +ei+ a+++q+ +++e ++ v+
  gi|313127382|ref|YP_004037652.1| 535 TEITDATADQTMALDELTDRVA 556
                                       5677777777777777666665 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   3.8e-08   2.3e-05       4     101 ..      97     207 ..      94     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.8e-08
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       ++ile   +p+f+++  g ++ +N+ +e+l+  +++ ++g+    + + +d    +++ + + ++ e +++ +++f 
  gi|313127382|ref|YP_004037652.1|  97 SQILEGVGAPTFILNDEGTVVAWNKQIERLTAVPASVAVGSEHASEAFYPD---GRRAKTLADKVLEAPSNADKTFG 170
                                       689*******************************************99999...66666666666666666666666 PP

                                       C................TTSSEEEEEEEEEEEEETTE CS
                               PAS  81 l................rdgrpihlevraspvrdagg 101
                                       +                 dg ++h++  a+p++++++
  gi|313127382|ref|YP_004037652.1| 171 VattgdggfedsstmvtGDGVERHIRFVAKPIFEGDE 207
                                       6666666998899998889999999999999988875 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   2.7e-08   1.6e-05       1     108 [.     100     221 ..     100     223 .. 0.84
   2 ?   -0.1   0.1       1.8   1.1e+03      48      85 ..     292     329 ..     257     360 .. 0.76
   3 ?    0.3   0.1       1.3   7.9e+02      47      71 ..     449     473 ..     392     491 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.7e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelll.. 74 
                                       l+ + +++++l+++g+v+++N+++++l ++p+  ++G+  a e + + d++r  +  ++vle    ++ +  + +  
  gi|313127382|ref|YP_004037652.1| 100 LEGVGAPTFILNDEGTVVAWNKQIERLTAVPASVAVGSEHAsEAFYP-DGRRAKTLADKVLEAPSNADKTFGVATtg 175
                                       577889***********************************865555.67777777777777777766666665566 PP

                             PAS_4  75 .............pgeerhyelrllPlrdesGe.vigvlvisrDiTer 108
                                                    +g erh+ + + P+++  G+ v++v+++++D T+ 
  gi|313127382|ref|YP_004037652.1| 176 dggfedsstmvtgDGVERHIRFVAKPIFE--GDeVVAVVETIYDRTDV 221
                                       699999999999***************86..777***********986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                             PAS_4  48 daarleralrrvlegeepiefleelllpgeerhyelrl 85 
                                       ++ ++era +++++ e  ++++ ell+ g+++  +l++
  gi|313127382|ref|YP_004037652.1| 292 LGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSA 329
                                       67788888888888888888888888888877766654 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.3
                             PAS_4  47 edaarleralrrvlegeepieflee 71 
                                       +  +  e+a++ v+++e+++e+ ++
  gi|313127382|ref|YP_004037652.1| 449 SIEQIQEQADETVMASEQSHEQIQV 473
                                       3666777888888888888887765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.5e-07   0.00021       3     104 .]     106     220 ..     104     220 .. 0.76
   2 ?   -2.1   0.0         8   4.8e+03      45      67 ..     441     461 ..     424     481 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.5e-07
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgks.itdlf...............vtdpeanerlraaleqgrk.... 59 
                                       +++i n++g+++ +N++ +rl+   +   +g    ++ f               +              + ++    
  gi|313127382|ref|YP_004037652.1| 106 PTFILNDEGTVVAWNKQIERLTAVPASVAVGSEhASEAFypdgrraktladkvlE--------------APSNadkt 168
                                       578999****************988666666544888885333333333333333..............33336666 PP

                             PAS_9  60 ........kerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                                 +e+  ++++ +g + ++++ a p+++ ++e+v+++ ++ D t+
  gi|313127382|ref|YP_004037652.1| 169 fgvattgdGGFEDSSTMVTGDGVERHIRFVAKPIFE-GDEVVAVVETIYDRTD 220
                                       666666667*************************96.679999*******996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8
                             PAS_9  45 eanerlraaleqgrkkerevevv 67 
                                       e+ e++++ +eq++  e+++e+v
  gi|313127382|ref|YP_004037652.1| 441 EHTEEIAQSIEQIQ--EQADETV 461
                                       34444444444444..4444433 PP

>> Kre28  Spindle pole body component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8  14.3   3.5e-05     0.021     118     229 ..     421     531 ..     318     566 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                             Kre28 118 sDpkyvsleeeVseLedetltekeseieqikgeIkekgkelaekqdqinelyLettneideCwelLnEleelrdrrn 194
                                       + + +  +++eV++L ++t  e+ +ei q  ++I+e++ e  ++ +q  e    +++ei++  ++L+E+ +++d   
  gi|313127382|ref|YP_004037652.1| 421 AGEGFSVVADEVKQLANQTH-EHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQATDAAA 496
                                       56678899*******99875.67889***********************************************9888 PP

                             Kre28 195 kvekqtseekdteddlveetYeeWkslqkslqeke 229
                                       +   +++  +d +   +ee+ +  ++ q++  + +
  gi|313127382|ref|YP_004037652.1| 497 DGIGEVARATDSQATNIEEVTTTIQTAQSHAFDAR 531
                                       88889999999999999999888888776555444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0028       1.7      26      87 ..     273     334 ..     264     336 .. 0.84
   2 ?    5.7   0.6     0.029        17      35      82 ..     324     374 ..     306     379 .. 0.66
   3 ?    4.6   0.5     0.064        38      29      83 ..     349     403 ..     334     408 .. 0.64
   4 ?   10.1   4.1    0.0013      0.76      22      83 ..     430     491 ..     424     497 .. 0.80
   5 ?    2.8   2.8      0.24   1.5e+02      24      80 ..     502     558 ..     493     565 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0028
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                        +++++++  +e+ +++  + k +e++ + + ++ ++v++++e +d+  ++++dl++s++e+
  gi|313127382|ref|YP_004037652.1| 273 AMAERFERLADEVDQKAVHLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEEI 334
                                       456677777888888888999999999999999999*********************99887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.029
                            DUF948  35 ieele...kqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                       +++l    +++ +++++v+   a++++ +e  ++  e+v + t++v d+++
  gi|313127382|ref|YP_004037652.1| 324 MQDLSasmEEIAATSDQVASSAAQAQTAAESARGAGESVRSATDNVIDISD 374
                                       333332225666777777777777777777777788888888888877776 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.064
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                       + aa++ ++ ++ v++ +++v d+ +   + + +++e++ ++++++e +a++++ 
  gi|313127382|ref|YP_004037652.1| 349 QTAAESARGAGESVRSATDNVIDISDDLLDSVIELQERMGSIEEVVEVIAEVADR 403
                                       4455555555566666666666666666666666777777777777777777665 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0013
                            DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                        ++k++++++ ++ ee+ + +++i +++++++  +++  e+++  + +++ + +++++++++
  gi|313127382|ref|YP_004037652.1| 430 DEVKQLANQTHEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQA 491
                                       56788888888999999999999999999999999999999999888888888888888776 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.24
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                       +++  d+ a+ iee++  ++     + d+ + + e+++   +++ ++d+lt+ va l
  gi|313127382|ref|YP_004037652.1| 502 VARATDSQATNIEEVTTTIQTAQSHAFDARDASTEITDATADQTMALDELTDRVARL 558
                                       556667777778888888888888888888888889999999999999999999875 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   7.5   3.2e-05     0.019      80     196 ..     289     407 ..     281     412 .. 0.85
   2 ?    4.5   1.5      0.04        24     115     188 ..     390     463 ..     387     471 .. 0.82
   3 ?    5.3  11.6     0.022        13      88     195 ..     451     557 ..     447     564 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
                             TMP_2  80 vgalalAyykgakearefnkaliltGnaaGlTasqLeamaesiaeagg...tqaaaaealaalastGkiggeqlerv 153
                                       ++ l++A+ ++a+ a +++++++  ++  ++ a++++++++s++e++    ++a+ a+++++ a++++ +ge+++++
  gi|313127382|ref|YP_004037652.1| 289 AVHLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEEIAAtsdQVASSAAQAQTAAESARGAGESVRSA 365
                                       67899***********************************998887762124455566677789999********** PP

                             TMP_2 154 akaaaelekatGqsvdetakelaklakdPvkaaeklneqlhfL 196
                                       +  ++++++ +  sv e+ + +++++ + v+ +++++++ ++L
  gi|313127382|ref|YP_004037652.1| 366 TDNVIDISDDLLDSVIELQERMGSIE-EVVEVIAEVADRTNLL 407
                                       *********99999999999999985.5677777777777766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.04
                             TMP_2 115 Leamaesiaeagg.tqaaaaealaalastGkiggeqlervakaaaelekatGqsvdetakelaklakdPvkaaek 188
                                       +e++ e iae++  t+  a +a  + a++G+ g+  ++ va  +++l++ t + ++e+a++++++++++ + + +
  gi|313127382|ref|YP_004037652.1| 390 IEEVVEVIAEVADrTNLLALNANIEAARAGEAGEG-FSVVADEVKQLANQTHEHTEEIAQSIEQIQEQADETVMA 463
                                       56667778888888888888888999999987665.999**************************9999887665 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.022
                             TMP_2  88 ykgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekat 164
                                        + +++a+e+  a  ++ +++ + ++++e++ +s++e+++ + aaa+ + ++a++    ++++e+v+++ +++++  
  gi|313127382|ref|YP_004037652.1| 451 EQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQATDAAADGIGEVARATDSQATNIEEVTTT-IQTAQSH 526
                                       5778999999999999999***********************************************976.5666678 PP

                             TMP_2 165 GqsvdetakelaklakdPvkaaeklneqlhf 195
                                         ++ ++  e+ ++++d + a+++l++++  
  gi|313127382|ref|YP_004037652.1| 527 AFDARDASTEITDATADQTMALDELTDRVAR 557
                                       999**********************998765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0062       3.7     101     167 ..     260     333 ..     231     345 .. 0.84
   2 ?    8.0   4.7    0.0048       2.9      81     150 ..     417     488 ..     379     552 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0062
                           UPF0242 101 Lkee.......ldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlek 167
                                       L ee       ++a+ e  erl  e  q  + l ++ e  ++    +e+q+  + ell++ + +++++ +++e+
  gi|313127382|ref|YP_004037652.1| 260 LPEEalsvvpeFNAMAERFERLADEVDQKAVHLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEE 333
                                       44445555555999999999999999999999999999999999999999999999999999999999999987 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0048
                           UPF0242  81 d.....eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqel 150
                                       +     eg+++ ++++++l ++++e  ee+++  e++++   e    +   e++ e+++  + e+e+ La  +e 
  gi|313127382|ref|YP_004037652.1| 417 RageagEGFSVVADEVKQLANQTHEHTEEIAQSIEQIQEQADETVMAS---EQSHEQIQVASGEIEDVLASLEEI 488
                                       244455899999999999999999999998888888887777766444...333445555555555555443333 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.7     0.015       8.9      10      29 ..     232     256 ..     228     287 .. 0.69
   2 ?    7.4   0.5    0.0096       5.8      10      46 ..     296     333 ..     292     337 .. 0.86
   3 ?   -0.4   0.1       2.6   1.5e+03       9      38 ..     389     422 ..     387     423 .. 0.74
   4 ?    4.0   0.1      0.11        64       6      24 ..     481     505 ..     480     532 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHTTTBTSST.....C CS
                              HAMP  10 LrrLaraarriaaGdldtr.....l 29 
                                       + +L +++ ++a+Gdl++r      
  gi|313127382|ref|YP_004037652.1| 232 IDELLDTVGALANGDLSARiefedE 256
                                       67899999***********554440 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0096
                                       HHHHHHHHHHHTTTBTSST.CCTTSSSHHHHHHHHHHH CS
                              HAMP  10 LrrLaraarriaaGdldtr.lpvsgrDEiGeLarafNa 46 
                                       ++r a+aa ri +   d++ l ++g DE+ +L +++++
  gi|313127382|ref|YP_004037652.1| 296 IERAADAAMRIESQVTDQSeLLDKGADEMQDLSASMEE 333
                                       8999*********8777778999**********99876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHTTT....BTSSTCCTTSSSHHH CS
                              HAMP   9 PLrrLaraarriaaG....dldtrlpvsgrDEiG 38 
                                       ++++++++++++a+      l++ ++  +  E G
  gi|313127382|ref|YP_004037652.1| 389 SIEEVVEVIAEVADRtnllALNANIEAARAGEAG 422
                                       689999*******755566777777777777766 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.11
                                       THHHHHHHHHHHHHHTTT......B CS
                              HAMP   6 ilrPLrrLaraarriaaG......d 24 
                                       +l++L+++a+a+++ a+G       
  gi|313127382|ref|YP_004037652.1| 481 VLASLEEIAQATDAAADGigevarA 505
                                       6899************986655551 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.7    0.0023       1.4      20     100 ..     263     343 ..     257     399 .. 0.91
   2 ?    0.6   0.3      0.49   2.9e+02      15      70 ..     342     397 ..     341     435 .. 0.80
   3 ?    9.2  10.5    0.0012       0.7      14      92 ..     446     524 ..     438     531 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeier 96 
                                       +al++  + +a a++ ++  d++d+++  l + ++++ + + ++e +   +++l+++   e+++l  ++eei ++++
  gi|313127382|ref|YP_004037652.1| 263 EALSVVPEFNAMAERFERLADEVDQKAVHLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEEIAATSD 339
                                       666777788999999999*********************************************************99 PP

                           DUF3450  97 elvp 100
                                       ++  
  gi|313127382|ref|YP_004037652.1| 340 QVAS 343
                                       9875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.49
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneql 70 
                                       a++++qa+ +ae+a  a +++ +  d++ d +++ll+ + +l+e+  s+e   e  
  gi|313127382|ref|YP_004037652.1| 342 ASSAAQAQTAAESARGAGESVRSATDNVIDISDDLLDSVIELQERMGSIEEVVEVI 397
                                       56788899999999999999999999999999999999888888877776655554 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0012
                           DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       +a++++q++++a ++v a++qs+++i+  + e +++la ++++ + +++++    +++r  +sq ++i+++++ i+ 
  gi|313127382|ref|YP_004037652.1| 446 IAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQATDAAADGIGEVARATDSQATNIEEVTTTIQT 522
                                       5899*********************************************************************9998 PP

                           DUF3450  91 ie 92 
                                       ++
  gi|313127382|ref|YP_004037652.1| 523 AQ 524
                                       76 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   9.2   0.00081      0.48     115     180 ..     291     356 ..     262     358 .. 0.87
   2 ?    5.7  13.4     0.018        11      45     133 ..     410     498 ..     391     503 .. 0.89
   3 ?    9.1   4.5    0.0017         1      70     152 ..     477     559 ..     474     570 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00081
                            DUF745 115 aakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektkkaAykAacAAqeAk 180
                                       +  +++e+a ++a+  ++++ ++++ll++    ++ L+  ++e  +  +++ ++A +A++AA+ A+
  gi|313127382|ref|YP_004037652.1| 291 HLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEEIAATSDQVASSAAQAQTAAESAR 356
                                       5567889999999***************************************************97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.018
                            DUF745  45 kA.lqAakAAeAaLaGKqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenl 120
                                        A ++Aa+A eA  +G +++ ++++q  + +++  +e+ +s+++ +++a+ + +a++q ++q+++ +  ++ + ++l
  gi|313127382|ref|YP_004037652.1| 410 NAnIEAARAGEAG-EGFSVVADEVKQLANQTHEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASL 485
                                       4426899999986.9************************************************************** PP

                            DUF745 121 enaeqvaagaqqe 133
                                       e++ q+ + a+  
  gi|313127382|ref|YP_004037652.1| 486 EEIAQATDAAADG 498
                                       *****99998865 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0017
                            DUF745  70 elreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkk 146
                                       e+++  a ++e+ +++ ++   +  +a+a ++  +++e +++++++a++ + +a++++++     a++t+ l++   
  gi|313127382|ref|YP_004037652.1| 477 EIEDVLASLEEIAQATDAAADGIGEVARATDSQATNIEEVTTTIQTAQSHAFDARDASTEITDATADQTMALDELTD 553
                                       566777788899999999999999999999999999***************************************** PP

                            DUF745 147 RveeLk 152
                                       Rv++L 
  gi|313127382|ref|YP_004037652.1| 554 RVARLC 559
                                       **9986 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.9    0.0085       5.1      54     152 ..     270     400 ..     261     413 .. 0.56
   2 ?    7.4   0.6    0.0026       1.5      51     106 ..     432     488 ..     427     543 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0085
                              Dor1  54 elediraqledLvlkl....pkLteectrfskkaeeisekrkenkllldkheqllellelPqlmd............ 114
                                       e++++++ +e+L++++      L ++++r  ++a +i ++  + + lldk ++  e+ +l   m+            
  gi|313127382|ref|YP_004037652.1| 270 EFNAMAERFERLADEVdqkaVHLGKAIERAADAAMRIESQVTDQSELLDKGAD--EMQDLSASMEeiaatsdqvass 344
                                       56666666666666552222336666666666666666665555555555444..3344445555555566666667 PP

                              Dor1 115 ...............rcirng...yydealeLeayvsrLkqristnpviqsiaaev 152
                                                      +++r +     d  ++L   v  L++r+++++ + +++aev
  gi|313127382|ref|YP_004037652.1| 345 aaqaqtaaesargagESVRSAtdnVIDISDDLLDSVIELQERMGSIEEVVEVIAEV 400
                                       77777777777777744443333256667777777777777777744444444444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0026
                              Dor1  51 irqelediraqledLvlklpkLteectrfskkaeeisek.rkenkllldkheqllel 106
                                       + q+ ++  +++e++++++++++e++ + + ++e++ e+ +  +  ++d+ + l e+
  gi|313127382|ref|YP_004037652.1| 432 VKQLANQTHEHTEEIAQSIEQIQEQADETVMASEQSHEQiQVASGEIEDVLASLEEI 488
                                       56777888999***********************99999766666677776666665 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.6   9.5e+02       2      13 ..     275     286 ..     269     293 .. 0.83
   2 ?    4.6   0.1     0.048        29       9      30 ..     321     342 ..     314     346 .. 0.87
   3 ?    2.1   0.0      0.29   1.7e+02       7      31 ..     375     399 ..     373     403 .. 0.85
   4 ?    0.5   0.1      0.89   5.3e+02       4      31 ..     424     452 ..     422     456 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.6
                         DASH_Dam1   2 epafaeLaDsle 13 
                                       +++f++LaD+++
  gi|313127382|ref|YP_004037652.1| 275 AERFERLADEVD 286
                                       678999999987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.048
                         DASH_Dam1   9 aDsletLdknledLqqihesLs 30 
                                       aD++++L++ +e++  ++++++
  gi|313127382|ref|YP_004037652.1| 321 ADEMQDLSASMEEIAATSDQVA 342
                                       79************99998876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.29
                         DASH_Dam1   7 eLaDsletLdknledLqqihesLsd 31 
                                       +L Ds+ +L++++  ++++ e +++
  gi|313127382|ref|YP_004037652.1| 375 DLLDSVIELQERMGSIEEVVEVIAE 399
                                       689***********99999887765 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.89
                         DASH_Dam1   4 afaeLaDsletLdknl.edLqqihesLsd 31 
                                        f+  aD++++L +++ e+ ++i +s+++
  gi|313127382|ref|YP_004037652.1| 424 GFSVVADEVKQLANQThEHTEEIAQSIEQ 452
                                       58899999999987762467777777776 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.7    0.0012      0.73     172     281 ..     267     375 ..     230     401 .. 0.81
   2 ?    7.3   8.7    0.0032       1.9     159     283 ..     363     493 ..     352     499 .. 0.75
   3 ?    6.9  11.3    0.0042       2.5     163     282 ..     430     552 ..     420     560 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                              Spc7 172 leeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkselee 248
                                       ++ e++++ e++e+l +++++ +    + +e + ++  ++++++  +++ l++  +++++l++++ee+++  +++ +
  gi|313127382|ref|YP_004037652.1| 267 VVPEFNAMAERFERLADEVDQKAVHLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEEIAATSDQVAS 343
                                       45566777777777777777744444889999999999*************************************** PP

                              Spc7 249 eiaeaervleeckgwsesevsrlkeevkaleel 281
                                         a+a+   e  +g  es v++ +++v ++ + 
  gi|313127382|ref|YP_004037652.1| 344 SAAQAQTAAESARGAGES-VRSATDNVIDISDD 375
                                       ******999999987654.77777766666655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0032
                              Spc7 159 ekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelael.....kaeieekkkelaelqeql 229
                                        +  +++ ++ ++l     el+e++ +++e +e ++++  +++L +l  +++++      +  +   +e+++l +q 
  gi|313127382|ref|YP_004037652.1| 363 RSATDNVIDISDDLLDSVIELQERMGSIEEVVEVIAEVAdRTNLLALNANIEAArageaGEGFSVVADEVKQLANQT 439
                                       455566666667777777777777777777666666643377777777777654111114556677999999999*9 PP

                              Spc7 230 eeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltg 283
                                        e +e+i++  eq++e  +e+  a +  +e+ ++ + e++ + ++++++ + t+
  gi|313127382|ref|YP_004037652.1| 440 HEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQATD 493
                                       999999999999999999999999999999999*******99999999998886 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0042
                              Spc7 163 eeldellpeleeekaeleeeleklqeaaee..lesid.keeLeelreelaelkaeieekkkelaelqeqleeleeki 236
                                       +e+++l ++++e+ +e+ + +e++qe+a+e  ++s + +e+++ +  e++++ a +ee  + ++   + + e++ + 
  gi|313127382|ref|YP_004037652.1| 430 DEVKQLANQTHEHTEEIAQSIEQIQEQADEtvMASEQsHEQIQVASGEIEDVLASLEEIAQATDAAADGIGEVARAT 506
                                       67788888888888888888888888766622334445888888888888888888888888888888888888888 PP

                              Spc7 237 eelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleelt 282
                                       ++ +++++e+ + i+ a++     ++ s++  ++  ++  al+elt
  gi|313127382|ref|YP_004037652.1| 507 DSQATNIEEVTTTIQTAQSHAFDARDASTEITDATADQTMALDELT 552
                                       8888888888888888888777777776665556666666665554 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0052       3.1      43     129 ..     262     348 ..     258     356 .. 0.89
   2 ?    4.7   3.2     0.044        26      12     113 ..     428     528 ..     423     546 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0052
                                       SSHHHHTTSGGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHTTS-TTS CS
                            DUF489  43 estedvygglanlklGletlleqlekekkkkdaeltryalsllalerkLsknkealaklgerieqierqlehfdllh 119
                                       e++++v  + +++++ +e l + +++++ +    + r a + +++e++++ ++e+l+k +++++ ++  +e+   ++
  gi|313127382|ref|YP_004037652.1| 262 EEALSVVPEFNAMAERFERLADEVDQKAVHLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEEIAATS 338
                                       5566666677778888999999999999999999******************************************* PP

                                       HHHHHHHHHH CS
                            DUF489 120 envlanlasi 129
                                       ++v ++ a+ 
  gi|313127382|ref|YP_004037652.1| 339 DQVASSAAQA 348
                                       ****998875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHS---HHHHHHHHHHHH--S-SSHHHHTTSGGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHH CS
                            DUF489  12 aaklvqqlArtGqadeealetllkslletdpestedvygglanlklGletlleqlekekkkkdaeltryalsllale 88 
                                        a+ v+qlA++ + ++e+++++++ + e+ +e++ +  +++++++++   ++++l + ++   + +   a ++ +++
  gi|313127382|ref|YP_004037652.1| 428 VADEVKQLANQTHEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEE-IAQATDAAADGIGEVA 503
                                       577899999999999999999999998888888888888889999988888888888777.3333444455566677 PP

                                       HHHHHSTTHHHHHHHHHHTTHHHHT CS
                            DUF489  89 rkLsknkealaklgerieqierqle 113
                                       r   ++ + ++++++ i+++++++ 
  gi|313127382|ref|YP_004037652.1| 504 RATDSQATNIEEVTTTIQTAQSHAF 528
                                       7777777777777777777776655 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.2   0.00026      0.16      26     139 ..     257     368 ..     237     372 .. 0.82
   2 ?    3.4   7.8     0.061        36      78     158 ..     430     516 ..     382     545 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                          ISG65-75  26 dkkLnkeaakaLCalkkladkvreetadyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklk 102
                                        ++L +ea++++    ++a++  e  ad++ +++ +  + ie a ++  +  +++ + +e    kg  +++d    +
  gi|313127382|ref|YP_004037652.1| 257 SGRLPEEALSVVPEFNAMAERF-ERLADEVDQKAVHLGKAIERAADAAMRIESQVTDQSEL-LDKGADEMQDLSASM 331
                                       6789999999999999999999.88888888888888888888888888888888888888.467888888888889 PP

                          ISG65-75 103 kaceeAkaknkkarekakkalekaekaskkakeaakk 139
                                       ++++++ ++++++ ++a+ a+e a+ a + + +a+ +
  gi|313127382|ref|YP_004037652.1| 332 EEIAATSDQVASSAAQAQTAAESARGAGESVRSATDN 368
                                       9999999999999999999999998888877777765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.061
                          ISG65-75  78 ekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaeka......skkakeaakkAlGeeleee 148
                                       +++++l ++ +e ++  ++ +e+++++++e+  + ++++e+ + a  ++e++      + +a++aa++ +Ge +  +
  gi|313127382|ref|YP_004037652.1| 430 DEVKQLANQTHEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVlasleeIAQATDAAADGIGEVARAT 506
                                       44555555555566666666677777777777777777777777777776642222224566666677777766666 PP

                          ISG65-75 149 nsnstGLlkv 158
                                       +s++t + +v
  gi|313127382|ref|YP_004037652.1| 507 DSQATNIEEV 516
                                       6666665555 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0053       3.1      10      39 ..     109     137 ..     101     157 .. 0.87
   2 ?   -2.4   0.1       8.4     5e+03      74      74 ..     328     328 ..     272     372 .. 0.59
   3 ?    1.2   1.3      0.66   3.9e+02      56      97 ..     439     480 ..     415     496 .. 0.76
   4 ?   -1.2   0.0       3.8   2.3e+03      56      86 ..     506     536 ..     476     546 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0053
                             PAS_7  10 vfDadlrLvawNrrylelldlpeelvqvgv 39 
                                       +++ ++ +vawN+++ +l  +p++++ vg 
  gi|313127382|ref|YP_004037652.1| 109 ILNDEGTVVAWNKQIERLTAVPASVA-VGS 137
                                       678999*****************998.554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.4
                             PAS_7  74 k 74 
                                       +
  gi|313127382|ref|YP_004037652.1| 328 S 328
                                       1 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.66
                             PAS_7  56 agdveaeverrlaaaragkphsfererpdgrvievrgnplpd 97 
                                       +++  +e+++ ++++++++ +++  ++++++ i+v + +++d
  gi|313127382|ref|YP_004037652.1| 439 THEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIED 480
                                       355667788888899999999999999999999998877765 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 3.8
                             PAS_7  56 agdveaeverrlaaaragkphsfererpdgr 86 
                                       +++++  +e++++ +++ ++h+f+ + ++ +
  gi|313127382|ref|YP_004037652.1| 506 TDSQATNIEEVTTTIQTAQSHAFDARDASTE 536
                                       3335555777777777778887777666555 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   3.8      0.13        77     118     222 ..     287     401 ..     271     415 .. 0.59
   2 ?   10.7   5.4    0.0004      0.24     105     225 ..     421     544 ..     401     557 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.13
                              CorA 118 eivdrlfellekleeeldeledel.....edstkkeilrelaqlrrrlvklrralapnrevlkrlla.....kaddk 184
                                       + + +l +++e   +   ++e+++       ++ ++++++l++  ++++   +++a + +  ++  +      +   
  gi|313127382|ref|YP_004037652.1| 287 QKAVHLGKAIERAADAAMRIESQVtdqseLLDKGADEMQDLSASMEEIAATSDQVASSAAQAQTAAEsargaGESVR 363
                                       44555566666777777777777766555556666777777776666666666666666666555554422222333 PP

                              CorA 185 llddedkeylrdlldelerllemlealrerleslqdty 222
                                         +d   +  +dlld +  l+e + ++ e++e++ +  
  gi|313127382|ref|YP_004037652.1| 364 SATDNVIDISDDLLDSVIELQERMGSIEEVVEVIAEVA 401
                                       33333333344555555558888888888887777665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0004
                              CorA 105 pkspgellyrlldeivdrlfellekleeeldeledel......edstkkeilrelaqlrrrlvklrralapnrevlk 175
                                           +++++  + +++++ +e +e++ + +++++++       +++++++i     +++  l+ l++++ ++ ++ +
  gi|313127382|ref|YP_004037652.1| 421 AGEGFSVVADEVKQLANQTHEHTEEIAQSIEQIQEQAdetvmaSEQSHEQIQVASGEIEDVLASLEEIAQATDAAAD 497
                                       55556777777888999999999999999999999998777766666666666666777778888888888888884 PP

                              CorA 176 rllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssl 225
                                        +    +  + +d ++ +++++   ++ ++ ++   r+  + + d+ + +
  gi|313127382|ref|YP_004037652.1| 498 GIG---EVARATDSQATNIEEVTTTIQTAQSHAFDARDASTEITDATADQ 544
                                       444...599999999999*************************9998765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   4.7      0.04        24      19     155 ..     266     392 ..     262     395 .. 0.66
   2 ?   10.4   9.4   0.00092      0.55      19     157 ..     392     524 ..     389     532 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.04
                             ATG16  19 eliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyk 95 
                                       +++  +n +++r + l++e  +   +  +a +          ++a a+ + ++q ++ ++l +k a   ++l+++  
  gi|313127382|ref|YP_004037652.1| 266 SVVPEFNAMAERFERLADEVDQKAVHLGKAIE----------RAADAAMRIESQVTDQSELLDKGADEMQDLSASME 332
                                       67788888899999888888777333333222..........11111111122223334444444444555666666 PP

                             ATG16  96 srgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqd 155
                                       + + +++++ +  ++ q+  e+++   e+++++++++ ++++ l d   el+e+   +++
  gi|313127382|ref|YP_004037652.1| 333 EIAATSDQVASSAAQAQTAAESARGAGESVRSATDNVIDISDDLLDSVIELQERMGSIEE 392
                                       666677899999999999999999999999999999999999999999999998777765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00092
                             ATG16  19 eliqaynrLldrtsaleaenaklekaaasaks.sksskksakekeasasqsnskqsakiqsleqklaqlreelaely 94 
                                       e+++   + +drt++l+   a++e+a a +     s  +++ +++a++      +++++++ +q + q++e+  e+ 
  gi|313127382|ref|YP_004037652.1| 392 EVVEVIAEVADRTNLLALN-ANIEAARAGEAGeGFSVVADEVKQLANQ------THEHTEEIAQSIEQIQEQADETV 461
                                       6777888899999999655.5554433333334455555566666654......5599******************* PP

                             ATG16  95 ksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlq 157
                                        + +++ ++++ ++ e+++  ++l+e +++ +++ + + ++ ++ ++++ +++e ++++q+ q
  gi|313127382|ref|YP_004037652.1| 462 MASEQSHEQIQVASGEIEDVLASLEEIAQATDAAADGIGEVARATDSQATNIEEVTTTIQTAQ 524
                                       ************************************************************998 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.0     0.036        21     147     214 ..     316     387 ..     250     395 .. 0.65
   2 ?    9.1  10.4    0.0011      0.63      56     217 ..     395     558 ..     381     560 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.036
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 147 lrqlysefkseikeslselrekakkvk....easlastkkssnrayiekgkkkLseesdklvtkvddLqDlv 214
                                       l    ++ ++++++s++e+ ++ ++v     +a++a  +  ++ + + ++ +++ + sd+l+  v +Lq  +
  gi|313127382|ref|YP_004037652.1| 316 LLDKGADEMQDLSASMEEIAATSDQVAssaaQAQTAAESARGAGESVRSATDNVIDISDDLLDSVIELQERM 387
                                       444456777888888888888888888533333333333344445666666666666777777776666655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                                       XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXX.XXXXXXXXXXXXXXXXXX.... CS
                              AIP3  56 edlsdvkdrs.vLsLniepldevkkhideslaslskelkelkssiesqkaslqe.vserqeeaakekaseslakkel 130
                                       e + +v dr+ +L Ln +       +  e+++ +++e+k+l ++++++++++++ +++ qe+a ++ + + +++++ 
  gi|313127382|ref|YP_004037652.1| 395 EVIAEVADRTnLLALNANIEAARAGEAGEGFSVVADEVKQLANQTHEHTEEIAQsIEQIQEQADETVMASEQSHEQI 471
                                       55788988875788998877777778999999999*****9998877776666514444555555555555667888 PP

                                       .....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 131 kaqlkevqslrrdLavlrqlysefkseikeslselrekakkvkeaslastkkssnrayiekgkkkLseesdklvtkv 207
                                       +    e++++   L+ + q  ++  + i e   +  ++a++++e++++ ++ +s+     ++ +++ + + +    +
  gi|313127382|ref|YP_004037652.1| 472 QVASGEIEDVLASLEEIAQATDAAADGIGEVARATDSQATNIEEVTTTIQTAQSHAFDARDASTEITDATADQTMAL 548
                                       89999**************************************777754444555555778889999999999999* PP

                                       HHHHHHHHHH CS
                              AIP3 208 ddLqDlvedl 217
                                       d+L D v  l
  gi|313127382|ref|YP_004037652.1| 549 DELTDRVARL 558
                                       *****98765 PP

>> CoatB  Bacteriophage coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.4     0.043        26       3      19 ..     508     524 ..     506     525 .. 0.87
   2 ?    7.4   0.9    0.0067         4       1      23 [.     523     545 ..     523     547 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.043
                             CoatB   3 asgvdvsaVttaittAk 19 
                                       +++   ++Vtt+i tA+
  gi|313127382|ref|YP_004037652.1| 508 SQATNIEEVTTTIQTAQ 524
                                       678889*********96 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0067
                             CoatB   1 AgasgvdvsaVttaittAkadia 23 
                                       A++++ d  ++ t+it+A ad +
  gi|313127382|ref|YP_004037652.1| 523 AQSHAFDARDASTEITDATADQT 545
                                       89******************965 PP

>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   4.5     0.022        13      19     125 ..     335     462 ..     298     495 .. 0.66
   2 ?    0.3   1.6      0.89   5.3e+02      13     165 ..     441     470 ..     428     527 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                              Sec5  19 kdtldqiykefseskteaqed.slveeLeeslneairkttllfkpvlenkekadklraaleviernk...flFnLPk 91 
                                        +t dq+ +   + +t+a++     e+++++ +++i+ ++ l++ v+e +e++ +++ ++evi +      l+ L  
  gi|313127382|ref|YP_004037652.1| 335 AATSDQVASSAAQAQTAAESArGAGESVRSATDNVIDISDDLLDSVIELQERMGSIEEVVEVIAEVAdrtNLLALNA 411
                                       455666666666666663333477799***********************************998761114555555 PP

                              Sec5  92 sLkesiakgdydklindYkkakslfestrqslv.................e 125
                                       +++ + a +  + +    +++k+l ++t +  +                 +
  gi|313127382|ref|YP_004037652.1| 412 NIEAARAGEAGEGFSVVADEVKQLANQTHEHTEeiaqsieqiqeqadetvM 462
                                       555554444433333333555555555533333333444444444444441 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.89
                              Sec5  13 tkfvkvkdtldqiykefseskteaqedslveeLeeslneairkttllfkpvlenkekadklraaleviernkflFnL 89 
                                       ++  ++ ++++qi+++ +e                                                          
  gi|313127382|ref|YP_004037652.1| 441 EHTEEIAQSIEQIQEQADE---------------------------------------------------------- 459
                                       3333344444444444433.......................................................... PP

                              Sec5  90 PksLkesiakgdydklindYkkakslfestrqslveedkkqvkvfkkvwsevekiieeyrkklwekLleldesqee 165
                                                                                                          + +++s e+
  gi|313127382|ref|YP_004037652.1| 460 -----------------------------------------------------------------TVMASEQSHEQ 470
                                       .................................................................22222222222 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.1     0.056        33       7      72 ..     270     335 ..     264     349 .. 0.64
   2 ?    4.0   5.2     0.078        47      12      95 ..     317     397 ..     298     417 .. 0.52
   3 ?    8.0   9.7    0.0045       2.7       4     106 ..     428     527 ..     424     528 .. 0.72
   4 ?    5.3   3.0     0.031        18       3      59 ..     469     525 ..     467     560 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.056
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLl 72 
                                       e n  a+  ++   +++q+  ++ + ++++++ + +++ +v d ++ ++   +++++L   ++++ 
  gi|313127382|ref|YP_004037652.1| 270 EFNAMAERFERLADEVDQKAVHLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEEIA 335
                                       555556666666666666666666666666666666666677777777777777777666666554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.078
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGG.HHHHHHHHHH... CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldk.lkelkqleeasss 87 
                                       + +  + +++ls+ +e++ +   ++++s+++ +     a +  r A++sv+  + ++ ++ d  l ++ +l+e  +s
  gi|313127382|ref|YP_004037652.1| 317 LDKGADEMQDLSASMEEIAATSDQVASSAAQAQ----TAAESARGAGESVRSATDNVIDISDDlLDSVIELQERMGS 389
                                       334444555555555555555555555544333....3444444445555555555555544313445555555444 PP

                                       HHHHHHHH CS
                        Laminin_II  88 lsdnisei 95 
                                       + + ++ i
  gi|313127382|ref|YP_004037652.1| 390 IEEVVEVI 397
                                       55444444 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0045
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                       +a+e+++ a+++ e +++++q +e+++e++ e     e+ +e+++ a+  i+d+  s  ++ +  +   d + e+  
  gi|313127382|ref|YP_004037652.1| 428 VADEVKQLANQTHEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQATDAAADGIGEVAR 504
                                       46777777777777777777777777777776666667777777777777777777777777777777777777766 PP

                                       HHHH...HHHHHHHHHHHHHHHHHHH CS
                        Laminin_II  81 leeassslsdniseikelIaqARkaA 106
                                         +       ni+e+   I+ A + A
  gi|313127382|ref|YP_004037652.1| 505 ATDS---QATNIEEVTTTIQTAQSHA 527
                                       6666...4589999999998887766 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.031
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArr 59 
                                       e ++ a+  ++ vl+ l++++q ++   + + e++r  +    ++++ +++i+ A++
  gi|313127382|ref|YP_004037652.1| 469 EQIQVASGEIEDVLASLEEIAQATDAAADGIGEVARATDSQATNIEEVTTTIQTAQS 525
                                       667778888888888888888888888888888888777766677777777766654 PP

>> I_LWEQ  I/LWEQ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   3.5     0.014       8.6      17      61 ..     309     353 ..     302     370 .. 0.84
   2 ?   11.2   7.1   0.00056      0.34      13     121 ..     364     469 ..     356     486 .. 0.75
   3 ?    1.6   8.5      0.49   2.9e+02      17     120 ..     445     546 ..     443     556 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.014
                            I_LWEQ  17 aVaaaanlLveaadavvqgkakeeeLivaakevaastaqLvvasr 61 
                                       +V+++ +lL + ad++    a+ ee+ +++++va+s+aq ++a++
  gi|313127382|ref|YP_004037652.1| 309 QVTDQSELLDKGADEMQDLSASMEEIAATSDQVASSAAQAQTAAE 353
                                       57777888888899999999999*************999999876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00056
                            I_LWEQ  13 sAAkaVaaaanlLveaadavvqgkakeeeLivaakevaastaqLvvasrvKadknskslkrLeaaskaVkkatkelv 89 
                                       sA  +V +  + L ++  ++ +  ++ ee++ +  eva  t  L   +++ a + +++ +  + ++ +Vk+ +++  
  gi|313127382|ref|YP_004037652.1| 364 SATDNVIDISDDLLDSVIELQERMGSIEEVVEVIAEVADRTNLLALNANIEAARAGEAGEGFSVVADEVKQLANQTH 440
                                       455555555666666666666666*************************************9999999999999999 PP

                            I_LWEQ  90 kavkeakekqeeeeseeeeldisklslvqakr 121
                                       ++++e++++ e+    +e+ d + +   q++ 
  gi|313127382|ref|YP_004037652.1| 441 EHTEEIAQSIEQI---QEQADETVMASEQSHE 469
                                       9999999888885...4444443333333333 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.49
                            I_LWEQ  17 aVaaaanlLveaa.davvqgkakeeeLivaakevaastaqLvvasrvKadknskslkrLeaaskaVkkatkelvkav 92 
                                       ++a++++ + e+a + v+ +++++e++ va+ e+    a L   +++  d+  +   ++ +a  + ++ ++e+  ++
  gi|313127382|ref|YP_004037652.1| 445 EIAQSIEQIQEQAdETVMASEQSHEQIQVASGEIEDVLASLEEIAQAT-DAAADGIGEVARATDSQATNIEEVTTTI 520
                                       567777778888844455566888888888888777777665444442.3333444555666666666666666666 PP

                            I_LWEQ  93 keakekqeeeeseeeeldisklslvqak 120
                                       ++a++++ +++  + +++i++ ++ q++
  gi|313127382|ref|YP_004037652.1| 521 QTAQSHAFDAR--DASTEITDATADQTM 546
                                       66665555543..345555555555555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.056        34      31      87 ..     281     343 ..     258     403 .. 0.58
   2 ?    5.8   5.2     0.012       6.9       3      84 ..     442     529 ..     429     545 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.056
                             TMPIT  31 lqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeelkerkkvlkeves 87 
                                       l +++ +++ +  k +++  ++  +++++v+      ++ ++e+++l+++++e+ ++ ++v+s
  gi|313127382|ref|YP_004037652.1| 281 LADEVDQKAVHLGKAIERAADAAMRIESQVTdqsellDKGADEMQDLSASMEEIAATSDQVAS 343
                                       333333333333333333333333333333222222234444444444444444444444333 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelke 73 
                                       + ee+++++++++e+a+e    +e+ +++++  s ei+     l+e+ ++ +     ++      +++++++ee+++
  gi|313127382|ref|YP_004037652.1| 442 HTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQATDAAADGIGevaratDSQATNIEEVTT 518
                                       34444555555555555555555555555444444444444444444444444444422555555666667777777 PP

                             TMPIT  74 elkerkkvlke 84 
                                       +++++++  ++
  gi|313127382|ref|YP_004037652.1| 519 TIQTAQSHAFD 529
                                       77777666665 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3     0.011       6.5      27     102 ..     291     366 ..     276     402 .. 0.82
   2 ?    4.4   6.2      0.05        30      18     110 ..     436     531 ..     426     552 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  27 kieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaeeskssspeeee 102
                                        ++++++   +   +++ ++ +++e+++k  +e++    + e++  +++++ s   + ++a ++ + + +s  +++
  gi|313127382|ref|YP_004037652.1| 291 HLGKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASMEEIAATSDQVASSAAQAQTAAESARGAGESVRSAT 366
                                       566777777788889***********************99999999999999998888887777776666655554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.05
                                       ......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  18 pallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaeesk 94 
                                        + ++e  ++i +++++++e+ ++  ++ ++  e+i+ +  eie  l + e++ +  +   +++ +  +a+ ++ ++
  gi|313127382|ref|YP_004037652.1| 436 ANQTHEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQATDAAADGIGEVARATDSQATN 512
                                       44557888999999999999999999999999999999999999999999999999999999999999999888888 PP

                                       XXXXXXXXXXXXXXX...X CS
                              SKA1  95 ssspeeeeeteskke...k 110
                                        ++ + + +t ++++   +
  gi|313127382|ref|YP_004037652.1| 513 IEEVTTTIQTAQSHAfdaR 531
                                       8888777766666555441 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.5      0.16        94      43      82 ..     293     332 ..     270     335 .. 0.62
   2 ?    5.3   1.5     0.039        23       2      37 ..     334     369 ..     333     372 .. 0.91
   3 ?    9.0   0.6    0.0027       1.6      42      80 ..     418     456 ..     382     460 .. 0.88
   4 ?    6.6   0.4     0.015       9.2      45      79 ..     463     497 ..     462     502 .. 0.90
   5 ?   -1.3   0.0       4.5   2.7e+03      12      32 ..     502     522 ..     497     529 .. 0.64
   6 ?   -0.8   0.2       3.1   1.8e+03       5      35 ..     519     549 ..     510     558 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.16
                                       HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  43 GaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82 
                                       G+a ++ +++ +++  ++++  ++L++ +++++  ++++e
  gi|313127382|ref|YP_004037652.1| 293 GKAIERAADAAMRIESQVTDQSELLDKGADEMQDLSASME 332
                                       6666666666667777777777777777777666666666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.039
                                       HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100   2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdal 37 
                                       i ++ ++++++aa++q++ae+ +++ +++++  d++
  gi|313127382|ref|YP_004037652.1| 334 IAATSDQVASSAAQAQTAAESARGAGESVRSATDNV 369
                                       8899**********************9999998876 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0027
                                       THHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  42 sGaaadafqaefeewkqaaqklvdaLeeisealkqaana 80 
                                        G+a++ f  + +e+kq a++ ++  eei+++++q+ ++
  gi|313127382|ref|YP_004037652.1| 418 AGEAGEGFSVVADEVKQLANQTHEHTEEIAQSIEQIQEQ 456
                                       699******************************999875 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.015
                                       HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  45 aadafqaefeewkqaaqklvdaLeeisealkqaan 79 
                                       a+++ +++++    +++++ + Leei++a+++aa+
  gi|313127382|ref|YP_004037652.1| 463 ASEQSHEQIQVASGEIEDVLASLEEIAQATDAAAD 497
                                       88999999999999******************997 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  12 aaarfqkqaeeledelqrlka 32 
                                       +a++ ++qa+++e++ ++++ 
  gi|313127382|ref|YP_004037652.1| 502 VARATDSQATNIEEVTTTIQT 522
                                       566666666666666666554 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   5 dpeelrqaaarfqkqaeeledelqrlkaevd 35 
                                       + +  +++a +++++++e++d+ ++    +d
  gi|313127382|ref|YP_004037652.1| 519 TIQTAQSHAFDARDASTEITDATADQTMALD 549
                                       5566677777777777777776665555544 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   9.5     0.022        13     204     410 ..     278     470 ..     260     495 .. 0.44
   2 ?    2.6   2.7     0.043        25     197     289 ..     433     512 ..     421     568 .. 0.40

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.022
                          Prominin 204 yeelekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvk 280
                                       +e    ++ d++d+   hlg++++++ +++ ++  ++++   e l +  ++++ ++++ +e+  +++q  ++  +++
  gi|313127382|ref|YP_004037652.1| 278 FE----RLADEVDQKAVHLGKAIERAADAA-MRIESQVTDQSELLDKGADEMQDLSASMEEIAATSDQVASSAAQAQ 349
                                       33....556777777778888887776666.3333444444444444444455555555555555444444444443 PP

                          Prominin 281 rdlnqalsnlCqseeCskilssleiekldtskcl.dqlpnvdevlealeevletnlssivkeglarlneipekvknq 356
                                       +  ++a          ++++s +++  +d s +l d++ +++e + ++eev+e    ++   + ++l +++  ++  
  gi|313127382|ref|YP_004037652.1| 350 TAAESARG------AGESVRSATDN-VIDISDDLlDSVIELQERMGSIEEVVEVIA-EV--ADRTNLLALNANIEAA 416
                                       33333322......23344444333.445555544444444444444444432211.11..1233333444444444 PP

                          Prominin 357 taevvpdlkkalakgreqikklakkiprealdavisdle.nterssktfddvvek 410
                                        a+   + ++ +a++ +q+ +++++  +e + + i++++ +  +++ + ++ +e+
  gi|313127382|ref|YP_004037652.1| 417 RAGEAGEGFSVVADEVKQLANQTHEH-TEEIAQSIEQIQeQADETVMASEQSHEQ 470
                                       44444444444444444444444444.3333333333333333333333333333 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.043
                          Prominin 197 dhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLr 273
                                       +++++q  e +            +++ + +++  e++  +++ + e+  e+++ a+ ++e v ++++e+ + ++   
  gi|313127382|ref|YP_004037652.1| 433 KQLANQTHEHT------------EEIAQSIEQIQEQA-DETVMASEQSHEQIQVASGEIEDVLASLEEIAQATDAAA 496
                                       22222222222............22222222222222.222222222223333333333333333333333333333 PP

                          Prominin 274 dglrgvkrdlnqalsn 289
                                       dg+ +v r  ++ ++n
  gi|313127382|ref|YP_004037652.1| 497 DGIGEVARATDSQATN 512
                                       3333332222222222 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       3.1   1.9e+03      58      94 ..     331     367 ..     276     372 .. 0.63
   2 ?    8.4   1.3    0.0053       3.2      32      86 ..     428     482 ..     426     497 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.1
                           DUF4665  58 qkdlkslskklkletkkkekvkkkkekekvnvdeaae 94 
                                        ++++++s ++++ + + +++ ++ +   ++v +a++
  gi|313127382|ref|YP_004037652.1| 331 MEEIAATSDQVASSAAQAQTAAESARGAGESVRSATD 367
                                       2344455555555555666555666666666666655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0053
                           DUF4665  32 VttnLKkinavkkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekek 86 
                                       V  + K++ ++++e +e++ +++++iq++  ++   +++ +++ ++++ + e+  
  gi|313127382|ref|YP_004037652.1| 428 VADEVKQLANQTHEHTEEIAQSIEQIQEQADETVMASEQSHEQIQVASGEIEDVL 482
                                       67789***********************998877655555555555544444333 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   3.4       1.4   8.6e+02      31      69 ..     306     344 ..     268     406 .. 0.64
   2 ?   10.9   6.0   0.00068      0.41      18      91 ..     429     503 ..     413     526 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                       TMF_TATA_bd  31 lkeelerleaerdeareeivklmkeneelkelkkeleel 69 
                                       ++++++  ++  d+ ++e+ +l++++ee +++++++++ 
  gi|313127382|ref|YP_004037652.1| 306 IESQVTDQSELLDKGADEMQDLSASMEEIAATSDQVASS 344
                                       444444444444444455555555555555555444444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00068
                       TMF_TATA_bd  18 sseirrlEgElaslkeeler.leaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeks 91 
                                         e+++l ++ ++  ee+++ +e+ +++a e +++  ++ e+ + +++e+e++ ++lee+ +  +++   +Ge +
  gi|313127382|ref|YP_004037652.1| 429 ADEVKQLANQTHEHTEEIAQsIEQIQEQADETVMASEQSHEQIQVASGEIEDVLASLEEIAQATDAAADGIGEVA 503
                                       67899********999998726667777777788888999***********************999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2059  (0.114842); expected 358.6 (0.02)
Passed bias filter:                      922  (0.0514251); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        68  (0.00379274); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 1.29u 0.39s 00:00:01.68 Elapsed: 00:00:00.55
# Mc/sec: 3273.25
//
Query:       gi|313127383|ref|YP_004037653.1|  [L=208]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-13   50.6   0.0    2.1e-13   49.9   0.0    1.4  1  HTH_10        HTH DNA binding domain
    7.5e-05   22.7   2.0    0.00051   20.0   0.0    2.6  3  BAT           GAF and HTH_10 associated domain
  ------ inclusion threshold ------
      0.025   14.3   0.5       0.74    9.5   0.2    2.8  2  Sigma70_r4_2  Sigma-70, region 4
      0.053   13.6   0.0       0.11   12.6   0.0    1.5  1  HTH_20        Helix-turn-helix domain
       0.08   12.5   0.0       0.16   11.5   0.0    1.5  1  Sigma70_r4    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   5.7e-17   2.1e-13       1      52 [.     146     197 ..     146     198 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 5.7e-17
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       L+++q+ +l +A+e+GY+  PR+++++++A++l+ s  t+ ehLrkae  ++
  gi|313127383|ref|YP_004037653.1| 146 LSPRQRDALVVAVELGYYGNPREASVSAVADRLDCSTGTAAEHLRKAEAAVF 197
                                       789*********************************************9876 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.4e-07   0.00051      35      86 ..      21      71 ..      10      94 .. 0.82
   2 ?    0.6   0.1      0.13   4.5e+02      52      77 ..     111     138 ..      98     160 .. 0.69
   3 ?   -0.5   0.0      0.27   9.7e+02      11      27 ..     165     181 ..     152     197 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-07
                               BAT 35 prsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsg 86
                                      p  d++ + +f+vdg+dpe+ +da+e+ +++ d+++ +++d    + l+v++
  gi|313127383|ref|YP_004037653.1| 21 PLVDDRNTFLFHVDGDDPETYTDALEASPSILDYEISQTDDR-PGFYLAVQE 71
                                      5669999***************************99886665.555555554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                               BAT  52 peevrdaaedldav..edvrvvseeddg 77 
                                       +e+++da+e+l+    +dvr ++e+d++
  gi|313127383|ref|YP_004037653.1| 111 AEALTDAFESLPPSieADVREIHEYDGR 138
                                       4667777776654322467777777763 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.27
                               BAT  11 rdeddvlvalaaeldcr 27 
                                       + +++ ++a+a++ldc 
  gi|313127383|ref|YP_004037653.1| 165 NPREASVSAVADRLDCS 181
                                       44556666777777775 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.34   1.2e+03       2      13 ..     112     123 ..     111     124 .. 0.89
   2 ?    9.5   0.2   0.00021      0.74       9      52 ..     144     194 ..     143     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.34
                                       HHHHHHHTTS-H CS
                      Sigma70_r4_2   2 qalrealaeLpe 13 
                                       +al +a ++Lp+
  gi|313127383|ref|YP_004037653.1| 112 EALTDAFESLPP 123
                                       68999******8 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00021
                                       TTS-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHH CS
                      Sigma70_r4_2   9 aeLperqreifllrylegl.......sykEIAellgisegtVksrlsRArk 52 
                                       a+L++rqr +++   + g+       s   +A +l++s gt   +l++A +
  gi|313127383|ref|YP_004037653.1| 144 AALSPRQRDALVVAVELGYygnpreaSVSAVADRLDCSTGTAAEHLRKAEA 194
                                       679999999999999999888888889999999********9999999965 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     3e-05      0.11      23      47 ..     167     191 ..     153     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                                       TTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  23 egltaselaerldlskntlsyHLrv 47 
                                       +++++s++a+rld+s  t+  HLr+
  gi|313127383|ref|YP_004037653.1| 167 REASVSAVADRLDCSTGTAAEHLRK 191
                                       789********************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.5e-05      0.16       4      44 ..     145     192 ..     144     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrA 44 
                                        L++r+r+ l+           ++ + + +++rl+ S +++  ++++A
  gi|313127383|ref|YP_004037653.1| 145 ALSPRQRDALVVAVelgyygnPREASVSAVADRLDCSTGTAAEHLRKA 192
                                       79*********99999999998999***************98888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1428.33
//
Query:       gi|313127384|ref|YP_004037654.1|  [L=550]
Description: NADH dehydrogenase subunit d; NADH dehydrogenase subunit c [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-82  276.0   0.0    5.9e-81  271.5   0.0    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    1.8e-34  118.9   0.1    4.5e-34  117.7   0.1    1.7  2  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.5   0.0   6.6e-85   5.9e-81       5     271 .]     300     550 .]     296     550 .] 0.94

  Alignments for each domain:
  == domain 1  score: 271.5 bits;  conditional E-value: 6.6e-85
                                       HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---T...THHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   5 ltvflyafreRekildlleevtGaRltasyiriGGvarDlpe...gllekikeflkelekkldeleklltknrifkk 78 
                                       +++f+ya+r+Re+i ++le+vtG+Rl+ +y+r+GGv +Dlpe   +++ek+++f++ l++kl+e+++llt n++++ 
  gi|313127384|ref|YP_004037654.1| 300 TATFMYAIRDREQIQNILEDVTGQRLMFNYFRLGGVVWDLPEpreEFFEKVYNFVDGLPQKLAEYHDLLTGNEVLQL 376
                                       4579*************************************98889******************************* PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                       R ++ g+l +e a ++g+tGpv+R+sG++yDlR+++pY  Y+eld++v+++ +gD ++R+lvr++E+++S++I+eq+
  gi|313127384|ref|YP_004037654.1| 377 RSVDTGILPAEVAKSYGCTGPVARGSGIEYDLRRDDPYGYYNELDWNVVTEPDGDNFSRLLVRMREIEESARIVEQC 453
                                       ***************************************************************************** PP

                                       HHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEE CS
                    Complex1_49kDa 156 leklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlki 232
                                        e l + p   +d+++    +++v ++++                + evy+avE +kGelg+y+ sdg++kp r+ki
  gi|313127384|ref|YP_004037654.1| 454 AELLADWP--EDDRTI----QSNVPRTIRP-------------DDDTEVYRAVEGAKGELGIYIRSDGTEKPARFKI 511
                                       ****8644..455444....3455555533.............3568****************************** PP

                                       E-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 233 rapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       r psf nlqal+e+++g l+ D++a lgsld ++gevDR
  gi|313127384|ref|YP_004037654.1| 512 RGPSFSNLQALPEIAEGGLIPDLIASLGSLDTIMGEVDR 550
                                       **************************************9 PP

>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.1     5e-38   4.5e-34       2     119 ..      40     155 ..      39     158 .. 0.91
   2 ?   -3.4   0.0       1.6   1.4e+04       5      46 ..     310     354 ..     303     360 .. 0.60

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 5e-38
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--...S-.-EEEEEE....-S-BEE--TTT-S CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllsl...eknerirvkvevdeeepevpSvtdlfp 75 
                                       vv+p++++e+++ l+d  e gfd+ls++ta ++ e+r+e +yh+ s+   +   ++++ v +++++p+ +S +++f+
  gi|313127384|ref|YP_004037654.1|  40 VVRPDNVQETLRRLRD--EAGFDHLSCVTAQEY-EDRYETIYHMKSYddpT--DEVSIVVPTPSNAPVSESGAPVFE 111
                                       799*************..599***********9.7************6333..55555555599************* PP

                                       THHHHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-TTSTTS--- CS
                    Complex1_30kDa  76 gadwyEREayDmfGivfeghpdlrrillpedfeghPLRkdfpls 119
                                       +a w+EREayD++Gi++++hpdlrrillpe+++ghPL +d++ +
  gi|313127384|ref|YP_004037654.1| 112 TAGWHEREAYDLVGIEYDDHPDLRRILLPETWQGHPLSRDYDQD 155
                                       *****************************************876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHH...TT--EEEEEEEEETT.....SSSEEEEEEEE CS
                    Complex1_30kDa   5 pedllevakflkdeeelgfdvlsdltavDek.....eerfevvyhll 46 
                                       +e+++++++ +   ++l f+++    +v ++     ee fe vy+++
  gi|313127384|ref|YP_004037654.1| 310 REQIQNILEDVTG-QRLMFNYFRL-GGVVWDlpeprEEFFEKVYNFV 354
                                       5555666666665.4555666643.3333334455677778888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3476.13
//
Query:       gi|313127385|ref|YP_004037655.1|  [L=923]
Description: DNA mismatch repair protein muts [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-88  294.2   0.0    8.6e-88  293.3   0.0    1.5  1  MutS_V    MutS domain V
    4.5e-39  134.7   3.2    9.6e-39  133.6   3.2    1.6  1  MutS_III  MutS domain III
    1.4e-26   92.9   0.0    3.1e-26   91.8   0.0    1.6  1  MutS_I    MutS domain I
    1.5e-24   86.1   2.0    4.1e-24   84.7   2.0    1.8  1  MutS_IV   MutS family domain IV
    9.3e-22   77.8   0.0    3.1e-21   76.1   0.0    1.9  2  MutS_II   MutS domain II
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.49   10.4   0.0    2.0  1  AAA_14    AAA domain
       0.16   12.4   0.1        5.6    7.4   0.0    2.4  2  AAA_23    AAA domain
       0.23   11.2   0.0       0.23   11.2   0.0    2.2  3  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.3   0.0   3.8e-91   8.6e-88       1     187 [.     607     793 ..     607     794 .. 0.99

  Alignments for each domain:
  == domain 1  score: 293.3 bits;  conditional E-value: 3.8e-91
                                       EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                            MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                       l++tGpnm+Gksty+rq alivllaq+Gsfvpa++aei++vd i+tRvga D+la+g+stFmvEm+E+++il++ate
  gi|313127385|ref|YP_004037655.1| 607 LIVTGPNMSGKSTYMRQAALIVLLAQVGSFVPARSAEIGVVDGIYTRVGALDELAQGRSTFMVEMQELSNILHSATE 683
                                       59*************************************************************************** PP

                                       TSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEE CS
                            MutS_V  78 kslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykvk 154
                                       +slvilDE+GRGt+tydG++ia+a +eyl+++++aktlfatHyhelt+la++l++v+n+h+a++e++ d++fl++v+
  gi|313127385|ref|YP_004037655.1| 684 DSLVILDEVGRGTATYDGISIAWAATEYLHNEVRAKTLFATHYHELTSLADHLDRVANVHVAAEERDGDVTFLRTVQ 760
                                       ***************************************************************************** PP

                                       ES--SS--HHHHHHHTT--HHHHHHHHHHHHHT CS
                            MutS_V 155 egaaeksyGikvaklaglPesvverArevlkel 187
                                       +g +++syGi+va lag+P+ vv+rA++vl++l
  gi|313127385|ref|YP_004037655.1| 761 DGPTDRSYGIHVADLAGVPKPVVSRADNVLEKL 793
                                       *****************************9998 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   3.2   4.3e-42   9.6e-39       1     191 []     264     558 ..     264     558 .. 0.93

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 4.3e-42
                                       HHHHHTTSSS-TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          MutS_III   1 aTlrnLeilenlrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVee.leneelreelrellrr 76 
                                       +T+rnLe++e+++g +++g+L+ ++d+TvT+ G RlLrewl++P +d++e+++RldaV+    ++  re++r++l  
  gi|313127385|ref|YP_004037655.1| 264 TTQRNLELTETMHG-ETDGTLVDAIDHTVTSPGGRLLREWLTRPRRDRAELERRLDAVTAlAREALSRERVRDTLDG 339
                                       599*******9997.779*****************************************966667779999999*** PP

                                       ---HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH..............HHHHHHHHHHB-SS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxx RF
                          MutS_III  77 lpDleRllsrislgkakardlkallealkaleelvallekeklaesee..............eslaelleeaideep 139
                                       ++DleRl +r ++g+a a+dl++++++l  l++ +++ e++ l  se+              ++l++ l +a+ ++p
  gi|313127385|ref|YP_004037655.1| 340 VYDLERLAARAASGSAGASDLLSVRDTLAVLPAVAEAIEESPL--SESplsdvvarpdreaaAALHDELADALADDP 414
                                       ***********************9*****99988887754443..333678999999887655577899999***** PP

                                       -SSGGGS--B-T................................................................. CS
                                       xxxxxxxxxxxx................................................................. RF
                          MutS_III 140 lalekegedlra................................................................. 151
                                       ++  ++g+  ++                                                                 
  gi|313127385|ref|YP_004037655.1| 415 PKTVRQGGLFKHgyddeldelidsheeaqrwidtladrekrqhslshvtvdrnktdgyyiqvgksvadqvpehyrei 491
                                       *********999***************************************************************** PP

                                       ...........................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 ...........................iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                                                  + +le+elf+el+e+v++++e l+++ ++lae+Dvl SlA
  gi|313127385|ref|YP_004037655.1| 492 ktlknskrfvteeleerereilrleesRGELEYELFCELRERVAAHAELLQDVGRVLAEIDVLSSLA 558
                                       ***********************999888888**********************************9 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   1.4e-29   3.1e-26       5     111 ..       8     109 ..       4     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.4e-29
                                       HHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC.EEEEEEEHHHHHHHHHHHHHTT-EEE CS
                            MutS_I   5 kqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkkssekeipmagvPehalekylrkLvekgykVa 81 
                                         +l+lk++ +  vl +++GdfYe+fg+DA+++a+el++++++++ s+++++pmagvP   l  yl+ Lve+gy+Va
  gi|313127385|ref|YP_004037655.1|   8 GEFLSLKSETDADVLTMQCGDFYEFFGDDAEFVAEELDLKVSQKS-SHGSSYPMAGVPVDDLTPYLKVLVERGYRVA 83 
                                       5799**************************************665.56666************************** PP

                                       EEEE-S-HHHHS.S--EEEEEEEBTTC-TT CS
                            MutS_I  82 vveqtetpaekkgvvkrevvrviTpGtltd 111
                                       v++q + ++     + r+++rv+TpGtl++
  gi|313127385|ref|YP_004037655.1|  84 VADQFDGED----GHYRKITRVATPGTLLE 109
                                       *****7744....578***********987 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   2.0   1.8e-27   4.1e-24       1      91 [.     427     517 ..     427     518 .. 0.99

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1.8e-27
                                       TTSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECC CS
                           MutS_IV   1 gfdeeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknserytta 77 
                                       g+d+eLdel d++ee+++++++l+++e+++++++++ v++nk++Gyy++v +s a++vp+++++++tlkns+r++t+
  gi|313127385|ref|YP_004037655.1| 427 GYDDELDELIDSHEEAQRWIDTLADREKRQHSLSHVTVDRNKTDGYYIQVGKSVADQVPEHYREIKTLKNSKRFVTE 503
                                       8**************************************************************************** PP

                                       CHHHHHHHHHHHHH CS
                           MutS_IV  78 elkkleaelleaee 91 
                                       el++ e+e+l++ee
  gi|313127385|ref|YP_004037655.1| 504 ELEEREREILRLEE 517
                                       ***********997 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   1.4e-24   3.1e-21       2     130 ..     117     242 ..     116     248 .. 0.87
   2 ?   -4.0   0.0       7.2   1.6e+04      18      31 ..     812     825 ..     810     827 .. 0.81

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.4e-24
                                       EEEEEEEETTTSEEEEEEEETTTTEEEEEEEEE-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTTT-EEEEE CS
                           MutS_II   2 ylaAisekregrrvGlafiDlstgefvvsefedfeeleaeLsrlsPkElllpedlsestaeeessklrelrsrvgvr 78 
                                       y+a+ ++  ++  vGlaf+D++tg+f+v+e+ d +   +eL+r+sP+E+l ++++  ++  + s   +++   ++ +
  gi|313127385|ref|YP_004037655.1| 117 YIASMVAPDDDEGVGLAFADVTTGQFFVTETDDADAAYSELYRFSPVEILPGPTVRGDDD-FLSRLRQDTDASLSLF 192
                                       9999666556666*****************************************966653.5666666666678888 PP

                                       SCCCCSHCCHHHHCHHHB--STTTTTTTGGG-HHHHHHHHHHHHHCCCCCSC CS
                           MutS_II  79 etvefesekaserleedfsvedldgfglekekklalaAlgalisYleetqke 130
                                       e+  f+   a++ + ++f+ e+l+++gl  +++la++A+ga+++Y+eet   
  gi|313127385|ref|YP_004037655.1| 193 EADAFAPGRAKHVVRDQFGRETLESVGL--NSDLAVRAAGAVLRYVEETGTG 242
                                       999999999******************8..9*****************9665 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 7.2
                                       EEEETTTTEEEEEE CS
                           MutS_II  18 afiDlstgefvvse 31 
                                       a+ Dls+gef+  e
  gi|313127385|ref|YP_004037655.1| 812 AVFDLSSGEFSSGE 825
                                       678*******8666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00022      0.49       3      75 ..     605     694 ..     603     713 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell.........vkkesilyinldderd...kkladpe....kllelileklke. 62 
                                         l++tG+  +GK+t+++q +   l         +++ +i  ++    r    +   + +    +++ +++e+ ++ 
  gi|313127385|ref|YP_004037655.1| 605 GFLIVTGPNMSGKSTYMRQAALIVLlaqvgsfvpARSAEIGVVDGIYTRVgalD---ELAqgrsTFMVEMQEL-SNi 677
                                       579****************98555577878876655555655555555553331...2222223333333332.123 PP

                            AAA_14  63 ....ekktylflDEiqe 75 
                                            ++++++lDE+ +
  gi|313127385|ref|YP_004037655.1| 678 lhsaTEDSLVILDEVGR 694
                                       33456888999999865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.12   2.6e+02     137     187 ..     438     517 ..     406     537 .. 0.55
   2 ?    7.4   0.0    0.0025       5.6      18      36 ..     603     621 ..     587     633 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.12
                            AAA_23 137 flgqerfeefelkdkke............................rleelekeleeledekkllekleqekekek.e 184
                                        + + + +   l+d+++                            ++ e  +e+++l++ k+++ ++++e e+e  +
  gi|313127385|ref|YP_004037655.1| 438 SHEEAQRWIDTLADREKrqhslshvtvdrnktdgyyiqvgksvadQVPEHYREIKTLKNSKRFVTEELEEREREIlR 514
                                       33333333333322222333333333344444445555555555577777777777777777777665443322123 PP

                            AAA_23 185 lee 187
                                       lee
  gi|313127385|ref|YP_004037655.1| 515 LEE 517
                                       333 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0025
                            AAA_23  18 skgltlItGpNGaGKTTil 36 
                                       ++g+ ++tGpN +GK+T +
  gi|313127385|ref|YP_004037655.1| 603 ERGFLIVTGPNMSGKSTYM 621
                                       78999************77 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.1   6.9e+03      37      44 ..     282     289 ..     281     295 .. 0.76
   2 ?   11.2   0.0    0.0001      0.23      20      45 ..     602     628 ..     594     636 .. 0.75
   3 ?   -3.6   0.9       4.5     1e+04      28      37 ..     827     836 ..     823     845 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.1
                            AAA_29  37 TllDAiqa 44 
                                       Tl+DAi  
  gi|313127385|ref|YP_004037655.1| 282 TLVDAIDH 289
                                       9****975 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0001
                            AAA_29  20 dlkgatlltGpsGsGKSTll.DAiqal 45 
                                       d++g+ ++tGp+ sGKST +  A  ++
  gi|313127385|ref|YP_004037655.1| 602 DERGFLIVTGPNMSGKSTYMrQAALIV 628
                                       45678999**********873344444 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.5
                            AAA_29  28 tGpsGsGKST 37 
                                       +G+ GsG +T
  gi|313127385|ref|YP_004037655.1| 827 SGQAGSGQTT 836
                                       6999***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (923 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.47
# Mc/sec: 5852.79
//
Query:       gi|313127386|ref|YP_004037656.1|  [L=134]
Description: ADP-ribose pyrophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-17   64.2   0.3    1.4e-17   64.0   0.3    1.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.3   7.8e-22   1.4e-17       8     125 ..      14     122 ..       7     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 7.8e-22
                                       EEEEETTSEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE.EEE CS
                             NUDIX   8 vvllnekgevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd.ehe 83 
                                        vl+ ++g vL+vrr+  +  gWelPgG++ + E++ e ++RE++EEtGl++el + +      a  ++   d +  
  gi|313127386|ref|YP_004037656.1|  14 GVLFAPDGDVLVVRRT--TDEGWELPGGRLGAYEDASEGVQREIAEETGLNVELGQPVH---AIAWRND---DdDGR 82 
                                       68999***********..9999***************************9665555554...3333332...13445 PP

                                       EEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHH CS
                             NUDIX  84 ilyvfleevegelepndenevsevrwvpleellkeklaaesr 125
                                       + +++ + v+++     ++e+ e++wv+++ + +++l ++++
  gi|313127386|ref|YP_004037656.1|  83 FGVYYYGTVTEQTVSL-SHEHIEYEWVSPQSA-EDRLSEPQA 122
                                       5566666777776666.8**************.666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 993.16
//
Query:       gi|313127387|ref|YP_004037657.1|  [L=787]
Description: DNA mismatch repair protein mutl [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-38  130.3   0.0    7.1e-38  129.7   0.0    1.3  1  MutL_C          MutL C terminal dimerisation domain
      2e-35  121.0   0.0    3.1e-35  120.4   0.0    1.3  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    3.5e-12   46.3   0.1    7.7e-12   45.2   0.1    1.5  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
      2e-07   31.5   0.2    4.3e-07   30.4   0.2    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
  ------ inclusion threshold ------
      0.084   12.2   0.0       0.14   11.5   0.0    1.2  1  Aldose_epim     Aldose 1-epimerase


Domain annotation for each model (and alignments):
>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7   0.0     2e-41   7.1e-38       4     147 .]     588     734 ..     585     734 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 2e-41
                                       EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHSSB-EEEEEEEEEEE--HHHHHHHHHCHHHHHHCT CS
                            MutL_C   4 kalgqvhgtyilaenedglvlvDqhaAherilyeklkeqlkeeelksQpLliPlvlelspeeaalleehkeeLaklG 80 
                                       ++lgq+ +tyi+ae++dg+vl+DqhaA+er++ye+l+++l+   +++Q+L  P+++el+++eaal+ee++++La+ G
  gi|313127387|ref|YP_004037657.1| 588 RVLGQLLDTYIVAETADGMVLIDQHAADERVNYERLQRELAG-DVTTQALADPVEMELTAREAALFEEYQDALAQTG 663
                                       79***************************************9.58******************************** PP

                                       -EEEE-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS....-H-HCCHHHHHHHHCTTSSSSSS--- CS
                            MutL_C  81 feleefgpnslivravPallrqqnleelirelleelaekgk....esleekleellatmachssvkagrrl 147
                                       f+  + g++++ vr+vPa++ ++  +el+r+ l+ + ++g+    e++++  +ella +ac  sv  +++l
  gi|313127387|ref|YP_004037657.1| 664 FHAGRTGERTVEVRSVPAVFAEALRPELLRDALTAFVSEGEdggrETVDAVADELLADLACYPSVTGNTSL 734
                                       *************************************99999996669*****************999876 PP

>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   8.5e-39   3.1e-35       3     118 ..     228     346 ..     226     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 8.5e-39
                                       HHHHHHHHCCEEEEEEEETT...EEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EE CS
                    DNA_mis_repair   3 avlgkevaenlleiekeeeq...lkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgrypvv 76 
                                       +v+g+evae++ ++e+e ++    +++G++s+pe++rs rd+ ++fvN R+v+ + l++a+ +aY  +l+++ryp++
  gi|313127387|ref|YP_004037657.1| 228 SVYGREVAESMTRVEHEPDDgpvASVTGLVSHPETTRSARDYLSTFVNDRYVTARVLREAVLDAYGGQLATDRYPFA 304
                                       79*************999989******************************************************** PP

                                       EEEEEESSGGEE-TSSTT----EETTHHCHHHHHHHHHHHHH CS
                    DNA_mis_repair  77 vLnleidpeevDvNvhPtKreVrfqdeeevieaieealkeal 118
                                       vL+++++p++vDvNvhP+K+eVrf de+ v +a+e+a+++al
  gi|313127387|ref|YP_004037657.1| 305 VLFVDVPPNTVDVNVHPRKMEVRFDDESGVKSAVESAVESAL 346
                                       ***************************************998 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1   2.1e-15   7.7e-12       4      96 ..      30     123 ..      26     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.1e-15
                       HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeak..rkstslGkkGi.Gl 77 
                                        +++ elv+NsldAda+++++ v+     t+ ++++DdG Gm++e+l+ a + +t+sk ++    +  +G  G+ G 
  gi|313127387|ref|YP_004037657.1|  30 ASVVKELVENSLDADANRISVAVDSG--GTEGVRVRDDGVGMDREDLQMAVEEHTTSKISDinDLESGVGTLGFrGE 104
                                       689*********************95..68*********************99999998652223555777777676 PP

                       HATPase_c_3  78 klAslslgkkltvitkkeg 96 
                                        l ++s  ++ltv +k +g
  gi|313127387|ref|YP_004037657.1| 105 ALHTISAVSRLTVRSKPRG 123
                                       6777788888888888665 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.2   1.2e-10   4.3e-07       5      81 ..      28     101 ..      24     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.2e-10
                                       HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                       r   ++++lv+N++++  +a++i+v ++ s ++  ++v+D+G G+++edl++  e +++++ ++++   +G+G    
  gi|313127387|ref|YP_004037657.1|  28 RPASVVKELVENSLDA--DANRISVAVD-SGGTEGVRVRDDGVGMDREDLQMAVEEHTTSKISDINDLESGVGTLGF 101
                                       66789**********6..99********.55799*****************99997777466666666666655444 PP

>> Aldose_epim  Aldose 1-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.8e-05      0.14     170     239 ..     138     213 ..     132     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                                       GGEEEEEEEEEEEECTTSGEEEEEEECTTCCCCCCSSEEHCSSET.EEEEEEEESSC.....SEEEEEETTTTEEE CS
                       Aldose_epim 170 shelqieadeylevdeeliptgelkdvkgtpfdfrqpkaigedlk.glDhayllksk.....lkaviidpdkksgi 239
                                       ++el++e+ e+++v  ++ p g +++v++  +++ ++k++ +++  ++Dh+ +  ++     ++ +i + ++++++
  gi|313127387|ref|YP_004037657.1| 138 GTELRVEGGEVTDVRPAGCPEGTVVEVEDLFYNTPARKKFLKTTAtEFDHVNTVVTQyalanPEVAISLEHDDREV 213
                                       789*******************************999999999889999998888877777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.45
# Mc/sec: 5237.84
//
Query:       gi|313127388|ref|YP_004037658.1|  [L=319]
Description: 2-keto-3-deoxygluconate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-56  191.4   0.0    2.6e-56  191.2   0.0    1.0  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.2   0.0   1.4e-60   2.6e-56       1     291 [.       1     293 [.       1     302 [. 0.96

  Alignments for each domain:
  == domain 1  score: 191.2 bits;  conditional E-value: 1.4e-60
                                       EEEEEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   1 mtkvvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                       mt++v +Ge++  l++   +    l + +t+  +aGGa  NvAva++rlg ++++++++ d+++G+++++el+++gv
  gi|313127388|ref|YP_004037658.1|   1 MTDIVTFGETMLRLSPPRGD---RLERTRTLDVQAGGAESNVAVAASRLGSNAVWLSKLPDSPLGRRVISELQSHGV 74 
                                       789**************866...888*************************************************** PP

                                       EETTEEEESS.SEEEEEEEEETTT.SEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES...EECTTSHHHHHH CS
                              PfkB  78 dtdyvkided.trtglalivvded.gertivfnrgaaadltkeeleededlleeadllyisg...llsselpeavle 149
                                       +td    d + tr+g+++++  +    ++++++r++aa  t+++ e ++d++ +ad++y sg   +ls+ l e++ +
  gi|313127388|ref|YP_004037658.1|  75 ETDVAWDDSGeTRMGTYYLEPGGSpRGTNVIYDRSDAAVTTTTPGELPQDAVRAADVFYTSGitpALSATLAETTAT 151
                                       ***99888878**************99************************************************** PP

                                       HHHHHHHHTTE..EEEEECESSSHH..HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.S CS
                              PfkB 150 elaeaaknggt..fdpnlldplgaq..fkeallellaladllkpneeElealtgekledieealaalhklkakga.k 221
                                       +l++a ++g+t  fd+n++++l+    +k  +++ll+ +d+l++ e+++e ++g+ +e  + a +++ +    +  +
  gi|313127388|ref|YP_004037658.1| 152 LLETAQEAGTTtaFDLNYRSKLWTPaeAKAGYETLLPNVDVLIGAERDIETCLGKRGEPADVARELADE----YDfE 224
                                       ***********************99*******************************9888888888888....7779 PP

                                       EEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHT CS
                              PfkB 222 tvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvq 291
                                       tv+vtl+++G+l+  +dg+++ + v+  +  D +G+GD+fvggfla  l+g ++ e+l+++ a+A+l  +
  gi|313127388|ref|YP_004037658.1| 225 TVIVTLSEKGSLAL-HDGKVYEQGVYDADTFDAIGTGDAFVGGFLARRLDGGDVPESLAYGAATASLKRT 293
                                       **************.999999999******************************************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2330.81
//
Query:       gi|313127389|ref|YP_004037659.1|  [L=421]
Description: hypothetical protein Hbor_26620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-06   27.5   3.3    4.4e-06   26.5   3.3    1.6  1  PGF-CTERM        PGF-CTERM motif
  ------ inclusion threshold ------
       0.26   11.2   1.8       0.36   10.8   0.2    2.1  2  Gram_pos_anchor  LPXTG cell wall anchor motif
       0.84    7.7   5.3          1    7.4   5.3    1.3  1  Hid1             High-temperature-induced dauer-formation pro
        2.1    8.7   5.3        3.4    8.1   0.2    3.3  4  Pirin_C          Pirin C-terminal cupin domain
        2.4    6.6  16.0        3.1    6.2  16.0    1.3  1  Utp14            Utp14 protein
        4.1    8.3   6.0       0.63   10.9   0.5    2.4  2  Ntox50           Bacterial toxin 50


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   3.3   1.5e-09   4.4e-06       1      23 []     398     420 ..     398     421 .] 0.93

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.5e-09
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       tPGFG+  Al++L+++alL+ Rr
  gi|313127389|ref|YP_004037659.1| 398 TPGFGVTAALVALAGSALLIARR 420
                                       9****************888887 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       4.7   1.4e+04      10      15 ..      12      17 ..      12      20 .. 0.63
   2 ?   10.8   0.2   0.00012      0.36      14      39 ..     395     420 ..     392     421 .] 0.90

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.7
                                      XXXXXX CS
                   Gram_pos_anchor 10 PkTGen 15
                                      P TG++
  gi|313127389|ref|YP_004037659.1| 12 PATGAA 17
                                      778854 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  14 engnifltaaGllallggllLlvkrR 39 
                                       e++++++ + ++l++l+g++Ll+ rR
  gi|313127389|ref|YP_004037659.1| 395 ESSTPGFGVTAALVALAGSALLIARR 420
                                       889********999999999999998 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.3   0.00033         1     589     656 ..     330     396 ..     191     412 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00033
                              Hid1 589 sarldsideeeeenssessrieesrsesrspslsevpelksslaitddeskaereksatessssqavs 656
                                       + ++++ ++ ++e+  es+++e++++   + + +e ++ ++s a+t+d+++a++++sate+ s+ ++s
  gi|313127389|ref|YP_004037659.1| 330 TMQSADNESTTTETATESTETETNTTA-TESTDTETETDTDSTATTSDDTSATENESATEHGSETTES 396
                                       222223333333333344444443333.3333444455566777777777888888888887777555 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.73   2.2e+03      56      84 ..      87     116 ..      25     130 .. 0.57
   2 ?    8.1   0.2    0.0011       3.4       4      75 ..     133     210 ..     130     215 .. 0.83
   3 ?   -2.3   0.0         2   5.9e+03      22      48 ..     241     259 ..     224     282 .. 0.45
   4 ?    0.9   0.1       0.2   5.9e+02       5      57 ..     283     341 ..     279     350 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.73
                                       EE--S.S-EEEEEEEE----S--EEETTEE CS
                           Pirin_C  56 vkaee.kgarvlLlaGePlgepvvqyGpfV 84 
                                       ++a++ ++a v   +G+ l  +    G++V
  gi|313127389|ref|YP_004037659.1|  87 ISATAeASADVTTESGATLTAHDTPNGNLV 116
                                       333322444444444444444444444444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                                       EEE-TT-EEEEE--TT-EEEEEEEES-EEESSTT.....EEE-TTEEEEE-.SSSEEEEE--SS-EEEEEEEE---- CS
                           Pirin_C   4 ltleagaelelplpegleaavyvleGelevgger.....seieeeqlavlg.dgdslvvkaeekgarvlLlaGePlg 74 
                                       +t++++ e ++ +++g ++ v++  G+++v +++      ++e +  +v++  g++ + + ++++a+ l+  G +  
  gi|313127389|ref|YP_004037659.1| 133 ATVTEDGEARVVVENGNTTGVFIAVGNASVAKNDdgdvsARVESDGRVVFRsYGENEERTENDREAERLVANGTATA 209
                                       5778888999999*******************999999999999999999964444444444599999999998876 PP

                                       S CS
                           Pirin_C  75 e 75 
                                       e
  gi|313127389|ref|YP_004037659.1| 210 E 210
                                       5 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2
                                       EEEEEEES-EEESSTTEEE-TTEEEEE CS
                           Pirin_C  22 aavyvleGelevggerseieeeqlavl 48 
                                        +v +   +        +++e+ ++++
  gi|313127389|ref|YP_004037659.1| 241 ETVNITVER--------AVSEGAVVLT 259
                                       333332222........2333333333 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.2
                                       EE-TT-EEEEE--TT-EEEEEEEES-EEESSTT......EEE-TTEEEEE-SSSEEEEE CS
                           Pirin_C   5 tleagaelelplpegleaavyvleGelevgger......seieeeqlavlgdgdslvvk 57 
                                       ++e  +el+ + + g + a ++ +G++  + e+      ++++e+++ + ++ ++ + +
  gi|313127389|ref|YP_004037659.1| 283 EVESTSELRTAADGGNQSAYMIADGSADADAETdvyvalNHFSERKVTMQSADNESTTT 341
                                       66777778877555555566666899988888888888888999999888844444433 PP

>> Utp14  Utp14 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  16.0    0.0011       3.1     388     594 ..     182     385 ..      56     412 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0011
                             Utp14 388 FmkraearkkeendeeieelrrelekgdeeeedeeeeeeeekesknvGrrvfgpskkskkkekkkkkkeskakkekr 464
                                       F +  e++++ end+e+e+l  +  +  e   ++e       ++++++   +g++ + + +e+++++ + +++++ +
  gi|313127389|ref|YP_004037659.1| 182 FRSYGENEERTENDREAERLVANGTATAEVYVTDE---G---DNRSSEVVHYGSNTTVNVTEQSTETVNITVERAVS 252
                                       66667788888888888888444333322222222...1...22234445566666555544444444444444444 PP

                             Utp14 465 eeeeedeskaaeekakke..........kskksekkkkkkkeesakeeeeeeeenpwlae.e.............ek 517
                                       e +   +s ++++ ++ +          +     +++ ++++e +++++  ++++ ++a+ +             ++
  gi|313127389|ref|YP_004037659.1| 253 EGAVVLTSVSEKALNA-SdslevtvdgqA-----AAEVESTSELRTAADGGNQSAYMIADgSadadaetdvyvalNH 323
                                       4333333333222222.135544333220.....1111112222222222333333333331322111112221122 PP

                             Utp14 518 kkskkeevaaekssskakkskakakkkkkksskkkeaake.kkkkdeeidlkkk....etlkekektlkkkkkedke 589
                                        +++k+++++ +++s++++ +            ++ +++e ++ + e++d++++     t++++++t        ++
  gi|313127389|ref|YP_004037659.1| 324 FSERKVTMQSADNESTTTETA------------TESTETEtNTTATESTDTETEtdtdSTATTSDDT--------SA 380
                                       222222222222221111111............1111111122222222222210000111111111........11 PP

                             Utp14 590 eesdd 594
                                       +e+++
  gi|313127389|ref|YP_004037659.1| 381 TENES 385
                                       11111 PP

>> Ntox50  Bacterial toxin 50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   0.00021      0.63      26      82 ..     194     247 ..     181     253 .. 0.84
   2 ?   -1.9   0.7         2   6.1e+03      43      43 ..     352     352 ..     320     390 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                            Ntox50  26 dskeaqellkkyagtgevvkdrkgkwrnkevvdfgevigvvvdketgeeteTklgkI 82 
                                       ++ ea+ l+ +  +t+ev  +++g +r+ evv++g+   v    +t++ teT ++++
  gi|313127389|ref|YP_004037659.1| 194 NDREAERLVANGTATAEVYVTDEGDNRSSEVVHYGSNTTVN---VTEQSTETVNITV 247
                                       67899*******************************99874...5788888888776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                            Ntox50  43 v 43 
                                        
  gi|313127389|ref|YP_004037659.1| 352 T 352
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2359  (0.131575); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                       138  (0.00769703); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.89u 0.38s 00:00:01.27 Elapsed: 00:00:00.51
# Mc/sec: 2479.64
//
Query:       gi|313127390|ref|YP_004037660.1|  [L=467]
Description: pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-41  140.2   0.3    1.2e-40  139.6   0.3    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.1e-10   40.1   0.0    4.1e-10   40.1   0.0    2.1  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.1e-06   28.8   0.0    2.4e-06   27.8   0.0    1.5  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    5.1e-05   23.3   0.6     0.0099   15.9   0.5    3.2  2  NAD_binding_9   FAD-NAD(P)-binding
    7.1e-05   22.2   0.3    0.00034   20.0   0.0    2.0  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00062   20.0   0.4      0.019   15.3   0.0    2.8  2  TrkA_N          TrkA-N domain
  ------ inclusion threshold ------
      0.024   14.2   0.0      0.055   13.0   0.0    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.027   13.6   0.0       0.27   10.3   0.0    2.1  2  GIDA            Glucose inhibited division protein A
      0.039   13.2   0.5        4.6    6.4   0.0    3.3  4  Amino_oxidase   Flavin containing amine oxidoreductase
      0.058   13.8   1.3        1.5    9.3   0.1    3.6  5  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
       0.12   11.6   4.1        9.7    5.3   0.0    4.0  4  FAD_binding_3   FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   0.3   7.2e-44   1.2e-40       2     292 ..       3     324 ..       2     326 .. 0.87

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 7.2e-44
                                       SEEEE--.SHHHHHHHHHHHHH.TS-E...EEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH............ CS
                                       xxxxxxx.xxxxxxxxxxxxxx.xxxx...xxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                       Pyr_redox_2   2 dvvviGg.GpAGlaaaltlaqa.gakv...tlve....legtclnggcllskallgvaedaeias............ 57 
                                       +v+++G+ G AG+a+a +l ++ ga++   tlv+     +g c ++gc++sk++l++a+++ +++            
  gi|313127390|ref|YP_004037660.1|   3 HVAIVGAyGSAGVAVADRLVEHvGAEIdrlTLVDdgepGGGLCILRGCMPSKEVLSTAAHRYQMRhdhrlvgeppem 79 
                                       79****99*************66666522277767889999***********99999999999999*********** PP

                                       ..............HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC. CS
                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ..............evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGva 120
                                                     +  +  ++ ++++ ++e+v++ ++ +++++  +     e+i++d++v+AtGss +++++pG  
  gi|313127390|ref|YP_004037660.1|  80 dleavvetknehtsNFASHRRTAVHRMEEREGVAFRHETARFVDDRTLLVGDERIEADYVVVATGSSLNIPDLPGI- 155
                                       *****999996665222334445777777899999999999999666667779***********************. PP

                                       TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2 121 envgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke. 196
                                          g+ v++ +sa+ l    lp++ vv G GyiG+El  +l+++g++ t++e+ +r++ + d+e ++++    ++e 
  gi|313127390|ref|YP_004037660.1| 156 ---GD-VDYNTSADVLDATTLPDSGVVMGFGYIGLELVPYLSEAGVDLTVIEHDERPVDEGDPEYGDEILSMYREEf 228
                                       ...44.4999************************************************9999999999888888888 PP

                                       TEEEEESCEEEEEEETTE..EEEEEETTSCE.EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBES.S CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.x RF
                       Pyr_redox_2 197 Gvevklgtsvkeidgnge..klevvledgee.idadlvvvavGvrpstelle.eklglelderggivvdeflrtn.v 268
                                       Gve++++t+  ++++ ++  +l+v+  dge  ida+ +++ +G+rp  ++le e++g+  +++g   v  +++t  +
  gi|313127390|ref|YP_004037660.1| 229 GVEIRTETRERRVERTDDgvRLHVEGPDGEDaIDAEALFLFTGRRPTLDGLElEAAGI--TPTGEEWVRNTMQTRaD 303
                                       ****************9966666999999999*************************9..569999********98* PP

                                       TTEEE-GGGCTECCSS--HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 269 pgiyaiGDvaggkggpelaqaAvq 292
                                       +++y++GD     g+    ++A +
  gi|313127390|ref|YP_004037660.1| 304 DNVYVVGDAN---GKEPILHVAKE 324
                                       ********88...55555555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       9.2   1.5e+04       1      18 [.       3      21 ..       3      35 .. 0.69
   2 ?   -2.4   0.0       4.7   7.6e+03      41      61 ..      98     118 ..      84     119 .. 0.58
   3 !   40.1   0.0   2.5e-13   4.1e-10       2      78 ..     176     250 ..     175     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.2
                                      EEEEECS.SHHHHHHHHHH CS
                         Pyr_redox  1 kvvvvGg.GyiglElAgal 18
                                      +v++vG+ G  g+ +A  l
  gi|313127390|ref|YP_004037660.1|  3 HVAIVGAyGSAGVAVADRL 21
                                      6888887666677766666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.7
                                       HHHHHHHHHHHHTTEEEECSE CS
                         Pyr_redox  41 easkilqeklekngievllnt 61 
                                         ++++++  e++g+ ++++t
  gi|313127390|ref|YP_004037660.1|  98 HRRTAVHRMEEREGVAFRHET 118
                                       445555555566688888765 PP

  == domain 3  score: 40.1 bits;  conditional E-value: 2.5e-13
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvk 77 
                                        vv+G GyiglEl  +l+e g + tv+e  +++    D+e ++++    +++ g+e++++t+  ++e ++dg   v+
  gi|313127390|ref|YP_004037660.1| 176 GVVMGFGYIGLELVPYLSEAGVDLTVIEHDERPVDEGDPEYGDEILSMYREEfGVEIRTETRERRVERTDDG---VR 249
                                       69********************************9999999999999998888******************9...55 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       l
  gi|313127390|ref|YP_004037660.1| 250 L 250
                                       5 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.5e-09   2.4e-06       9     105 ..     360     454 ..     353     458 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.5e-09
                                       SEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHHHHHT CS
                     Pyr_redox_dim   9 pevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelavaika 85 
                                       +++a vG +  +A++ag++++ ++ + ++ g  +++   +g + lv+   +g vlG++ + ++a+ + + ++va+++
  gi|313127390|ref|YP_004037660.1| 360 YPYARVGHSVSSAEEAGLNYVAVHREASDDGVFKTKLAPRGRATLVVGT-DGAVLGFQGLHYHADVMAKTMQVAVEN 435
                                       789**************777777777777777777777*******8876.*************************** PP

                                       TSBHHHHHTSBSSSSSTGGG CS
                     Pyr_redox_dim  86 gltvedladtihihPtlsea 105
                                       ++ v+++ d  ++hPt  e 
  gi|313127390|ref|YP_004037660.1| 436 EMDVRKIPD-RAYHPTTPEI 454
                                       *****9865.5899998875 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.5   6.1e-06    0.0099       1      67 [.       5      79 ..       5     146 .. 0.64
   2 ?   -0.8   0.0      0.82   1.3e+03     113     154 ..     226     271 ..     215     273 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.1e-06
                     NAD_binding_9  1 aivGa.GprGlavlerLlarakkkspleitlfdpsep.gagrvwrtdqseelllNvpasemslftddp.......p 67
                                      aivGa G +G+av++rL+++   ++  ++tl+d+ ep g   + r   ++   l ++a++ ++ +d+         
  gi|313127390|ref|YP_004037660.1|  5 AIVGAyGSAGVAVADRLVEHV-GAEIDRLTLVDDGEPgGGLCILRGCMPSKEVLSTAAHRYQMRHDHRlvgeppeM 79
                                      89**88**************8.777789******8884545566777799999********999996555555442 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.82
                     NAD_binding_9 113 egvtvevh.raevvdleeradgqavll..adg.aslaadaVvLAlG 154
                                       e++ ve+  +++  ++e+++dg++++    dg + ++a+a++L +G
  gi|313127390|ref|YP_004037660.1| 226 EEFGVEIRtETRERRVERTDDGVRLHVegPDGeDAIDAEALFLFTG 271
                                       3444444313355578888888766553345625579999998888 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3       0.3   4.9e+02     165     190 ..       2      29 ..       1      39 [. 0.75
   2 !   20.0   0.0   2.1e-07   0.00034     121     305 .]     132     310 ..      85     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.3
                       Pyr_redox_3 165 qkvvViGgknSa.vDaAlelvrk.gaeV 190
                                       ++v+++G++ Sa v +A  lv++ gae+
  gi|313127390|ref|YP_004037660.1|   2 THVAIVGAYGSAgVAVADRLVEHvGAEI 29 
                                       5789999999974777888888766666 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2.1e-07
                       Pyr_redox_3 121 etyeAkkviiAtGefdkPnklnipGeek.lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrg 196
                                       e +eA++v++AtG     n ++ pG  +     ++ v +++ +  +  vV G +  + +    l ++g + tv+ ++
  gi|313127390|ref|YP_004037660.1| 132 ERIEADYVVVATGS--SLNIPDLPGIGDvDYNTSADVLDAT-TLPDSGVVMGFGYIGLELVPYLSEAGVDLTVIEHD 205
                                       689**********8..7777788888752233334444553.336678899***********************998 PP

                       Pyr_redox_3 197 se.iekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdls 272
                                       +  +++ + ++  ++  ++++++        i+ +++++  e +++ ++ +v+ +dg+     +  +l tG +p+l+
  gi|313127390|ref|YP_004037660.1| 206 ERpVDEGDPEYGDEILSMYREEFGVE-----IRTETRERRVERTDDGVRLHVEGPDGEDAIDAEALFLFTGRRPTLD 277
                                       74134444444446666666666543.....4444444444445567788999******9999999999******** PP

                       Pyr_redox_3 273 flkkslfeldedgrpvlteeteetnvpglflaG 305
                                        l+ +   ++ +g+  + +  +    ++++++G
  gi|313127390|ref|YP_004037660.1| 278 GLELEAAGITPTGEEWVRNTMQTRADDNVYVVG 310
                                       999876667667776665544444457888887 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       0.2   3.3e+02       2      28 ..       5      36 ..       4      39 .. 0.76
   2 !   15.3   0.0   1.1e-05     0.019       2      36 ..     177     211 ..     176     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.2
                                      EEES.-SHHHHHHHHHHHHTT....EEEEEEE CS
                            TrkA_N  2 iiiG.lGrvGrslaeeLsegg....kdvvvid 28
                                      +i+G +G  G ++a++L e+     ++ +++d
  gi|313127390|ref|YP_004037660.1|  5 AIVGaYGSAGVAVADRLVEHVgaeiDRLTLVD 36
                                      677779***********995446775577776 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.1e-05
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeervee 36 
                                       +++G+G +G +l+ +Lse+g d +vi++de+ v+e
  gi|313127390|ref|YP_004037660.1| 177 VVMGFGYIGLELVPYLSEAGVDLTVIEHDERPVDE 211
                                       79****************7768********99987 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.4e-05     0.055       5      38 ..     178     211 ..     176     218 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                                       EE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH CS
                    UDPG_MGDP_dh_N   5 viGlGYvGlvtaavlaeighevigvDideekvdk 38 
                                       v+G GY+Gl     l+e+g++++++  de+ vd+
  gi|313127390|ref|YP_004037660.1| 178 VMGFGYIGLELVPYLSEAGVDLTVIEHDERPVDE 211
                                       89***************************99986 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.13   2.1e+02     133     151 ..     128     146 ..      97     187 .. 0.83
   2 ?   10.3   0.0   0.00017      0.27     346     390 ..     294     339 ..     286     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                                       ETTS-EEEECEEEE--TT- CS
                              GIDA 133 tedgetikakavviatGtf 151
                                       +  +e i+a+ vv+atG+ 
  gi|313127390|ref|YP_004037660.1| 128 LVGDERIEADYVVVATGSS 146
                                       5668899**********94 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00017
                                       B-TTSBBSSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHHHHHHCT CS
                              GIDA 346 llntLetkkvkgLflAGqinGteGYeEaaa..qGllAGinaarkakg 390
                                       + nt++t++ +++++ G+ nG e  +  +a  qG +A+ n+ ++++g
  gi|313127390|ref|YP_004037660.1| 294 VRNTMQTRADDNVYVVGDANGKEPILH-VAkeQGHVAAENILADVNG 339
                                       568*******************96554.4447*********999887 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.058        95     244     262 ..     127     145 ..      77     148 .. 0.75
   2 ?   -1.2   0.0      0.57   9.2e+02       9      25 ..     191     207 ..     190     208 .. 0.91
   3 ?    6.4   0.0    0.0028       4.6     217     249 ..     224     258 ..     210     266 .. 0.82
   4 ?   -0.4   0.0      0.34   5.6e+02     404     451 ..     288     333 ..     283     334 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.058
                                       EETTSTEEEESEEEE-S-H CS
                     Amino_oxidase 244 tledgevveaDaVvvTvpl 262
                                        l+  e +eaD+Vvv++  
  gi|313127390|ref|YP_004037660.1| 127 LLVGDERIEADYVVVATGS 145
                                       23344555********875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.57
                                       HHHHTTEEEEEEESSSS CS
                     Amino_oxidase   9 qLlsaGfdVtvlEardr 25 
                                       +L++aG+d+tv+E ++r
  gi|313127390|ref|YP_004037660.1| 191 YLSEAGVDLTVIEHDER 207
                                       699**********9998 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0028
                                       HHTTTTEEEETSEEEEEEEEETTCEEEEET..TST CS
                     Amino_oxidase 217 aeelrgldirlntrVkeikregdgvtvtle..dge 249
                                        +e+ g++ir++tr ++++r +dgv++++e  dge
  gi|313127390|ref|YP_004037660.1| 224 YREEFGVEIRTETRERRVERTDDGVRLHVEgpDGE 258
                                       456779**********************9944444 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.34
                                       THHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 404 gpghedydplakpegdprlffAGehtsreypgtvegAilSGlraAari 451
                                        +g+e+ ++ ++++ d+++++ G++        ++ A + G  aA+ i
  gi|313127390|ref|YP_004037660.1| 288 PTGEEWVRNTMQTRADDNVYVVGDANG--KEPILHVAKEQGHVAAENI 333
                                       46899999999999**********955..3334777777777777666 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00091       1.5       2      31 ..       4      33 ..       3      41 .. 0.90
   2 ?   -1.6   0.0       2.2   3.5e+03      57      77 ..     130     146 ..      84     150 .. 0.60
   3 ?   -1.6   0.0       2.1   3.4e+03       8      21 ..     181     194 ..     176     208 .. 0.78
   4 ?   -1.3   0.0       1.7   2.8e+03      86     110 ..     286     309 ..     217     318 .. 0.61
   5 ?   -0.7   0.0       1.1   1.8e+03      23      54 ..     361     390 ..     358     406 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00091
                                      EEEETTTSHHHHHHHHHHHCTSSEEEEEEE CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvll 31
                                      vaivGa G  G +++ +L eh  +e+ +l+
  gi|313127390|ref|YP_004037660.1|  4 VAIVGAYGSAGVAVADRLVEHVGAEIDRLT 33
                                      9********************999987765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                                       EEGGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh  57 edvdeeelkevdivflalpag 77 
                                            +e  e+d+v+ a++++
  gi|313127390|ref|YP_004037660.1| 130 G----DERIEADYVVVATGSS 146
                                       2....3445889999999876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.1
                                       TSHHHHHHHHHHHC CS
                    Semialdhyde_dh   8 tGyvGqellrlLee 21 
                                        Gy+G el+ +L+e
  gi|313127390|ref|YP_004037660.1| 181 FGYIGLELVPYLSE 194
                                       69******999987 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.7
                                       HHHTTSEEEESSSTTTTSTTSEBE- CS
                    Semialdhyde_dh  86 laeagvkviDlssdfRlkddavyvl 110
                                       +  +g  ++ ++ + R +d+ vyv+
  gi|313127390|ref|YP_004037660.1| 286 ITPTGEEWVRNTMQTRADDN-VYVV 309
                                       34455577888888887644.4555 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1.1
                                       SSEEEEEEEESTTTTTSBHHHHSGGGTTTECE CS
                    Semialdhyde_dh  23 pevelvvllsssrsaGkklaeavkaleegkdl 54 
                                       p++ + + +ss+++aG ++ ++++  e   d 
  gi|313127390|ref|YP_004037660.1| 361 PYARVGHSVSSAEEAGLNYVAVHR--EASDDG 390
                                       67778888999999*****99987..444444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       0.3     5e+02       2      23 ..       2      24 ..       1      37 [. 0.86
   2 ?    1.1   0.1      0.12   1.9e+02     120     163 ..      95     144 ..      49     149 .. 0.55
   3 ?    5.3   0.0    0.0059       9.7       6      38 ..     178     210 ..     175     214 .. 0.89
   4 ?    2.8   0.0     0.035        57     109     149 ..     219     258 ..     215     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.3
                                      EEEEEE--.SHHHHHHHHHHHHT CS
                     FAD_binding_3  2 tdVlIVGa.GpaGlmlallLsea 23
                                      t V+IVGa G aG+  a  L e+
  gi|313127390|ref|YP_004037660.1|  2 THVAIVGAyGSAGVAVADRLVEH 24
                                      78******9******99999877 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                                       EEETCSEEEECCEECC....CCCCCEEEECCT...TEEEEEEEEEEEE--G CS
                     FAD_binding_3 120 lqvrfktevesleqde....egvtaevrdket...geeetvrakYlvGaDG 163
                                       +  ++ t v+ +e+ e     ++ta++ d +t   g +e+++a+Y+v a G
  gi|313127390|ref|YP_004037660.1|  95 FASHRRTAVHRMEEREgvafRHETARFVDDRTllvG-DERIEADYVVVATG 144
                                       444444444433332211113455555544442213.34788888877766 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0059
                                       EE--SHHHHHHHHHHHHTTHHEEEEESSSSSCC CS
                     FAD_binding_3   6 IVGaGpaGlmlallLseaGvrvvlvekrsttvv 38 
                                       + G G  Gl l   LseaGv+ +++e  ++ v+
  gi|313127390|ref|YP_004037660.1| 178 VMGFGYIGLELVPYLSEAGVDLTVIEHDERPVD 210
                                       7899999*******************9998876 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.035
                                       HHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTE CS
                     FAD_binding_3 109 riLvehaeerglqvrfktevesleqdeegvtaevrdketge 149
                                        iL+  +ee g+++r +t+ + +e++++gv+  v + + ge
  gi|313127390|ref|YP_004037660.1| 219 EILSMYREEFGVEIRTETRERRVERTDDGVRLHVEGPD-GE 258
                                       6899999***********************98888663.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3113.19
//
Query:       gi|313127391|ref|YP_004037661.1|  [L=394]
Description: histidine kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-10   41.5   0.0    2.8e-10   40.7   0.0    1.3  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      6e-10   38.9   2.4      1e-09   38.2   2.4    1.4  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
    2.7e-06   27.4   0.1    4.1e-06   26.8   0.1    1.3  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0035   17.4   0.4     0.0071   16.4   0.4    1.5  1  HisKA        His Kinase A (phospho-acceptor) domain
  ------ inclusion threshold ------
      0.021   14.5   1.4      0.039   13.6   1.4    1.4  1  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain
      0.051   13.5   0.0       0.08   12.9   0.0    1.3  1  HATPase_c_5  GHKL domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   9.3e-14   2.8e-10       9     111 ..     264     361 ..     258     362 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 9.3e-14
                                       HHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHH CS
                         HATPase_c   9 iisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkkl 84 
                                       ++  l +Nav ++  +++ ++v++++++d++ ++v DnG+Gip+ ++  +fe+ ++    +     +GlGl +v+  
  gi|313127391|ref|YP_004037661.1| 264 VVELLAENAVIHNDrDEPLVSVRVRTDDDHVILRVADNGPGIPETERA-VFESGTE----TPLRHSEGLGLWVVEWA 335
                                       55567899**9944455556666666779*******************.8884444....4556899*********7 PP

                                       HHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  85 velmgGeiwvesepgrGttftftlple 111
                                       v+  gG++ +++++  Gt + +tlp +
  gi|313127391|ref|YP_004037661.1| 336 VNEAGGDLDFRNRE-VGTVVSVTLPRT 361
                                       777*******7766.9********976 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   2.4   3.4e-13     1e-09      66     162 ..      75     178 ..      15     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 3.4e-13
                         HisKA_4TM  66 vlvwslgGavvvgavigltvlvrllegrtiaePvfvvlvaaevGavaGllaGylaara.......radasrakrisd 135
                                       +  w  +Gav+ + +  ltv+   l+g ++ e    v   +  G+vaG l G + ara       r + +r     +
  gi|313127391|ref|YP_004037661.1|  75 IGRWVAVGAVASAFLGVLTVIYFRLNGVVLPEQAHFVSNVTTGGTVAGSLVGVYDARAarvsnrlRHERRRVSLLNQ 151
                                       334777888877777778999999********99999889999*************993322222234445555678 PP

                         HisKA_4TM 136 alafvndlirhdlrndlvvirgyaeai 162
                                        l  +n ++rhdlrnd++v++gya  +
  gi|313127391|ref|YP_004037661.1| 152 RLHVLNRVLRHDLRNDVNVVHGYASLL 178
                                       89999*******************865 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   1.4e-09   4.1e-06      40     123 ..     269     356 ..     223     358 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.4e-09
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvDev... 112
                                         Nav+h+ +++p   v+vr++ d++ + ++vaD+Gpg  ++e  +  +  + +  + ++G+Gl +++  v+e    
  gi|313127391|ref|YP_004037661.1| 269 AENAVIHNDRDEP--LVSVRVRTDDDHVILRVADNGPGiPETER-AVFESGTETPLRHSEGLGLWVVEWAVNEAggd 342
                                       45********999..77778889***************655554.44444445699************999998664 PP

                       HATPase_c_2 113 .ey..dgegnvvtm 123
                                        ++  ++ g+vv++
  gi|313127391|ref|YP_004037661.1| 343 lDFrnREVGTVVSV 356
                                       45576777888876 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   2.4e-06    0.0071       7      61 ..     158     210 ..     152     221 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA   7 agvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdl 61 
                                         + H+Lr+ ++++ g+a++L +    ++ + e  e+i++ ++ l +l e+ + l
  gi|313127391|ref|YP_004037661.1| 158 RVLRHDLRNDVNVVHGYASLLADF--PDPVVSERGEIIREKSEALISLSERARHL 210
                                       5789*****************996..44555555555555555444443333333 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.4   1.3e-05     0.039       3      36 ..     143     177 ..     141     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                            SPOB_a   3 keeikelkeliklL.rsqRHDflNhLQvIsGylqL 36 
                                       +++++ l++ + +L r++RHD  N+  v++Gy  L
  gi|313127391|ref|YP_004037661.1| 143 RRRVSLLNQRLHVLnRVLRHDLRNDVNVVHGYASL 177
                                       5677889999999999****************877 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.7e-05      0.08      15     100 ..     270     358 ..     260     359 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                       HATPase_c_5  15 dNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkkle..sskskkeehGiGlksireivkkykgnl 85 
                                       +NA+   +   ++++ +++ vr++++++i+++  +  g    e   +e  +++  ++ +G+Gl  ++  v++ +g+l
  gi|313127391|ref|YP_004037661.1| 270 ENAVIHND---RDEPLVSVRVRTDDDHVILRVADNGPGipetERAVFEsgTETPLRHSEGLGLWVVEWAVNEAGGDL 343
                                       55554433...3589****************9988655443333444444556778999****************** PP

                       HATPase_c_5  86 sieaedglFtlsvll 100
                                       ++++ +    +sv+l
  gi|313127391|ref|YP_004037661.1| 344 DFRNREVGTVVSVTL 358
                                       *99988776777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2592.62
//
Query:       gi|313127392|ref|YP_004037662.1|  [L=509]
Description: transporter, nhac family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-53  182.5  41.3    5.2e-46  157.3  19.8    2.1  2  Na_H_antiporter  Na+/H+ antiporter family


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4  13.5   2.3e-14     4e-10     133     264 ..      58     187 ..      27     187 .. 0.89
   2 !  157.3  19.8   2.9e-50   5.2e-46       1     303 []     173     486 ..     173     486 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2.3e-14
                   Na_H_antiporter 133 aglivatllelaslseidkllnrGiksmlgaililllAwgiggvlealgvteslvsslakgvvskgllplilflval 209
                                       +g++  +  +   ++++ + +++G+ + ++aili+++ + + +     g + sl+   ++ + +  +lp++++l a+
  gi|313127392|ref|YP_004037662.1|  58 TGIVGRYWYGT-TWAKMYEGIVDGLRMGMQAILIIFVIYMLISTWTGAGTIPSLIYYGLELLSPSIFLPIATIL-AA 132
                                       44444444444.788888999****************************************9999999988865.77 PP

                   Na_H_antiporter 210 lvafatGtswgtigIilpiavplaaklgisllalvraveaggtlgdhlsPisdtt 264
                                       +vafa+G+sw t g ++  ++ ++  lgi ++ +++av++g+  gd  sP+sdtt
  gi|313127392|ref|YP_004037662.1| 133 VVAFAIGSSWTTAGTLGVAFIGIGTGLGIPEPMTAGAVLTGAYTGDKVSPLSDTT 187
                                       9*****************************************************8 PP

  == domain 2  score: 157.3 bits;  conditional E-value: 2.9e-50
                   Na_H_antiporter   1 vavfgdkssplsdtvgliagilktdlieeiaalgmlvqsipanvysifallvvglvvl...llrdigamlraeaear 74 
                                       +a+ gdk splsdt++l+a++++tdl+++++  +m v + +a ++s+++++ +gl +        i ++++a  +++
  gi|313127392|ref|YP_004037662.1| 173 GAYTGDKVSPLSDTTNLAAAVTNTDLMTHVR--TMRVGTGIAMLLSLALYTYLGLTATgniPPGRIAEIQTAISGTY 247
                                       6999***************************..4************************7777778888888888888 PP

                   Na_H_antiporter  75 eleekeltklpiavliiltlskmpytgalalvaivkafivalafqntdvatalv...vgalaglivatllela.... 144
                                       ++++ +++  p++ +++l+l+++p+++a++ ++++ ++++++++q+  + +++v     a++g++   + +la    
  gi|313127392|ref|YP_004037662.1| 248 TVSPLTFA--PLVLTFALALRGYPALPAITSGVFA-GVATQIFVQGPISIEGFVramEVAQSGTAAGSGAGLAaefk 321
                                       99999999..**********************999.*******9997766655411137888888888888889665 PP

                   Na_H_antiporter 145 slseidk..llnrGiksmlgaililllAwgiggvlealgvteslvsslakgvvskgllplilflvallvafatGtsw 219
                                         sei +  l+++G+ +  ++i+++++A+++gg+le++gv++++  ++ ++++s+g+l++ + l+a+ +++ +++++
  gi|313127392|ref|YP_004037662.1| 322 TGSEIVNnlLFTEGLIGSSWTITVVVAALALGGILERTGVLAVIAYHIGESLHSVGSLTAGTALSAFGMNILAAEQY 398
                                       3334433236799**************************************************************** PP

                   Na_H_antiporter 220 gtigIilpiavplaaklgisllalvraveaggtlgdhlsPisdttilsstglnadhidhvs....ytqlpyallvap 292
                                       ++i+++++ ++ l++ +++++++l+ravea+gt +++l+P++++++++ + l +   +  +    y +++++ + +p
  gi|313127392|ref|YP_004037662.1| 399 MSIVVPGMSLRGLYDDFDLDSRNLSRAVEAAGTTTSALIPWNAGGVYMVSVLDVPVCSGAWcldgYAPFYFLGFFSP 475
                                       ****************************************************65555555577789*********** PP

                   Na_H_antiporter 293 itailllvfGi 303
                                       +++il++v+G+
  gi|313127392|ref|YP_004037662.1| 476 TILILMGVTGW 486
                                       **********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 3014.17
//
Query:       gi|313127393|ref|YP_004037663.1|  [L=237]
Description: hypothetical protein Hbor_26660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1630.77
//
Query:       gi|313127394|ref|YP_004037664.1|  [L=142]
Description: transcriptional regulator, copg family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-21   76.5   0.3    2.1e-21   75.9   0.3    1.3  1  NikR_C           NikR C terminal nickel binding domain
    3.3e-08   33.2   0.0    5.6e-08   32.4   0.0    1.4  1  RHH_1            Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.019   15.1   0.0    1.4  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
      0.023   14.5   0.0        0.3   10.9   0.0    2.2  2  GP57             Phage Tail fiber assembly helper gene produc
      0.085   12.2   0.0      0.094   12.0   0.0    1.1  1  DUF1978          Domain of unknown function (DUF1978)
        0.1   12.8   0.0       0.17   12.1   0.0    1.3  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.3   6.9e-25   2.1e-21       1      76 [.      54     129 ..      54     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 6.9e-25
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                       ++v+t+v+d++++ ++er+++++hey+  + s++h h+ +++c+e++vl+Ge ++i++++ k+ra++   +v++++
  gi|313127394|ref|YP_004037664.1|  54 MAVVTVVFDYETTSVEERMMKLRHEYEGFVASNFHSHVGEHYCMELFVLEGELADISTFVGKIRATRDTLSVDYSV 129
                                       79*****************************************************************999999876 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   1.9e-11   5.6e-08       2      38 ..       4      41 ..       3      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.9e-11
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      vs++++eeller+d  a + g   rSe++ReA+r++l 
  gi|313127394|ref|YP_004037664.1|  4 VSVSMPEELLERIDNFAGEHGyTGRSEVVREAARNLLG 41
                                      9**********************************985 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   6.3e-06     0.019      92     123 .]       4      36 ..       1      36 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.3e-06
                   HicB_lk_antitox  92 iNitlpervlkriDaavkaag.esRSgflakaa 123
                                       + +++pe++l+riD+++ ++g + RS  + +aa
  gi|313127394|ref|YP_004037664.1|   4 VSVSMPEELLERIDNFAGEHGyTGRSEVVREAA 36 
                                       789******************557999887776 PP

>> GP57  Phage Tail fiber assembly helper gene product 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.098   2.9e+02      49      74 ..      20      45 ..       9      46 .. 0.75
   2 ?   10.9   0.0    0.0001       0.3      36      75 .]     100     142 .]      94     142 .] 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.098
                              GP57 49 vGitGdtikveeiveavknltaesad 74
                                       G  G t + e + ea +nl  e  d
  gi|313127394|ref|YP_004037664.1| 20 AGEHGYTGRSEVVREAARNLLGEFED 45
                                      56677888889999999999888655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                              GP57  36 kilqGtlaeiaravG...itGdtikveeiveavknltaesade 75 
                                        +l+G la+i+  vG    t dt+ v+  v  v ++ta +a+e
  gi|313127394|ref|YP_004037664.1| 100 FVLEGELADISTFVGkirATRDTLSVDYSVMPVDDFTAIAAEE 142
                                       589**********99644599*****************99987 PP

>> DUF1978  Domain of unknown function (DUF1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.1e-05     0.094      97     146 ..      48      95 ..      22     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                           DUF1978  97 leeaekellkalkdlkdqeierveeRlkelealYpevseskeeteaqekv 146
                                       le+   +l+ +++ ++d e   veeR+ +l+  Y + + s+   +  e  
  gi|313127394|ref|YP_004037664.1|  48 LED--RKLMAVVTVVFDYETTSVEERMMKLRHEYEGFVASNFHSHVGEHY 95 
                                       222..456778999*********************999887766665555 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.6e-05      0.17      15      74 ..      13      72 ..       3      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                             RHH_8 15 LgqiDlLveeGfYsnRtDlirtairaqLakhddalkqavkrkslvlGvtklsraeleevq 74
                                      L +iD    e  Y+ R++++r+a r+ L + +d+  +  k  ++v  v +++ +++ee  
  gi|313127394|ref|YP_004037664.1| 13 LERIDNFAGEHGYTGRSEVVREAARNLLGEFEDKRLEDRKLMAVVTVVFDYETTSVEERM 72
                                      789999999999*****************9999877777777777778888888887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1139.39
//
Query:       gi|313127395|ref|YP_004037665.1|  [L=349]
Description: signal transduction histidine kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-12   45.3   0.1    4.4e-11   42.9   0.0    2.1  3  Response_reg  Response regulator receiver domain
      8e-07   29.0   0.1    1.9e-06   27.8   0.1    1.7  1  HisKA         His Kinase A (phospho-acceptor) domain
     0.0021   17.7   0.4     0.0036   16.9   0.4    1.4  1  HisKA_4TM     Archaeal 4TM region of histidine kinase
     0.0032   18.0   0.0     0.0081   16.7   0.0    1.7  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
  ------ inclusion threshold ------
      0.037   14.0   0.1        0.1   12.5   0.1    1.8  1  HATPase_c_2   Histidine kinase-like ATPase domain
      0.079   12.7   0.0       0.14   11.8   0.0    1.4  1  SPOB_a        Sensor_kinase_SpoOB-type, alpha-helical domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.5e-14   4.4e-11      38      99 ..      37      98 ..      28     105 .. 0.93
   2 ?   -1.6   0.1      0.97   2.9e+03      41      41 ..     150     150 ..     107     190 .. 0.56
   3 ?   -1.5   0.0      0.94   2.8e+03      28      42 ..     171     186 ..     150     206 .. 0.57

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.5e-14
                                      HHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEEEE CS
                      Response_reg 38 llkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddfls 99
                                       l++ ++d+++++  + + dG+el+ e+r+ +p+lp+i++ta ++e++a +al+aga d+++
  gi|313127395|ref|YP_004037665.1| 37 RLDSGAYDCVVCNYVLATRDGVELTAELRDSHPTLPIIVYTAMGDETVARDALRAGATDYVV 98
                                      567788******************************************************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.97
                                       H CS
                      Response_reg  41 e 41 
                                       +
  gi|313127395|ref|YP_004037665.1| 150 T 150
                                       1 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.94
                                       EESSHHHHHHHH.HHH CS
                      Response_reg  28 eaedgkealell.kee 42 
                                       ++edg+e+le + ++ 
  gi|313127395|ref|YP_004037665.1| 171 VTEDGEEVLERIlDNG 186
                                       3445555544432222 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   6.5e-10   1.9e-06       2      56 ..     142     194 ..     141     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 6.5e-10
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlve 56 
                                       l++++  + H++r+ Ls+i g a++L++  + te+ +e le+i +++r  ++l +
  gi|313127395|ref|YP_004037665.1| 142 LEKLTRVLTHDIRNDLSVIVGWADILRN--SVTEDGEEVLERILDNGRKTLELTD 194
                                       6789999*********************..699**************98887765 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   1.2e-06    0.0036     126     163 ..     128     168 ..     113     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                         HisKA_4TM 126 dasrakrisdalafvndlir...hdlrndlvvirgyaeaie 163
                                       +++r +r+++a + +++l r   hd+rndl vi g a++++
  gi|313127395|ref|YP_004037665.1| 128 ESQRIERTAEAATQLEKLTRvltHDIRNDLSVIVGWADILR 168
                                       34566677776666665544444**************9987 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.7e-06    0.0081       6     108 ..     252     345 ..     248     348 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsi 80 
                                       L  +++nl+  a+ + +++++ +v+i+a+   d ++++v+D+  G   + ++     f +   ++ g+  t +++ +
  gi|313127395|ref|YP_004037665.1| 252 LSAVFRNLLNDALSH-QSGDDPSVHISAERagDVVQVRVTDDS-GAADARREAA---FNN---AELGSPDTDISVFL 320
                                       67799**********.7788888888864456899******87.6666666744...555...444678999***** PP

                                       HHHHHHHTTTEEEEEEETTTEEEEEEEE CS
                         HATPase_c  81 vkklvelmgGeiwvesepgrGttftftl 108
                                       v+ lv+ +gG++wv ++   G  f+++l
  gi|313127395|ref|YP_004037665.1| 321 VETLVDAYGGDVWV-ED--DGAVFVVEL 345
                                       **************.33..477777766 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.5e-05       0.1      45     118 ..     265     338 ..     255     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.5e-05
                       HATPase_c_2  45 ehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDev..ey..dge 117
                                        h   ++p  +v++++e++++ ++v+v+D+  + d++  +  +    +   +  ++ ++l+++lvD +  ++  +++
  gi|313127395|ref|YP_004037665.1| 265 SHQSGDDP--SVHISAERAGDVVQVRVTDDSGAADARREAAFNNA--ELGSPDTDISVFLVETLVDAYggDVwvEDD 337
                                       45555544..8999**************97777666544444333..4889999************98664445555 PP

                       HATPase_c_2 118 g 118
                                       g
  gi|313127395|ref|YP_004037665.1| 338 G 338
                                       5 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.8e-05      0.14       8      49 ..     137     182 ..     130     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                            SPOB_a   8 elkeliklL.rsqRHDflNhLQvIsGylqLgk...ydkaeeyieev 49 
                                       e+ + ++ L r++ HD  N+L vI G  ++ +    ++ ee++e++
  gi|313127395|ref|YP_004037665.1| 137 EAATQLEKLtRVLTHDIRNDLSVIVGWADILRnsvTEDGEEVLERI 182
                                       5555555555****************99986633346666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2638.31
//
Query:       gi|313127396|ref|YP_004037666.1|  [L=276]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-20   72.2   0.0    7.8e-20   70.5   0.0    1.9  2  HxlR          HxlR-like helix-turn-helix
    5.6e-13   49.0   0.0    9.3e-13   48.3   0.0    1.4  1  Response_reg  Response regulator receiver domain
    0.00014   21.7   0.0    0.00046   20.0   0.0    1.9  2  MarR_2        MarR family
    0.00017   21.6   0.1     0.0065   16.5   0.0    2.6  2  HTH_20        Helix-turn-helix domain
    0.00019   21.3   0.1    0.00073   19.4   0.0    2.0  2  TrmB          Sugar-specific transcriptional regulator TrmB
    0.00044   20.1   0.0     0.0011   18.8   0.0    1.6  1  MarR          MarR family
    0.00076   19.3   0.0     0.0019   18.0   0.0    1.7  1  HTH_5         Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
       0.05   13.6   0.0       0.11   12.4   0.0    1.6  1  PadR          Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   3.5e-23   7.8e-20       1      89 [.      17     105 ..      17     107 .. 0.97
   2 ?   -1.9   0.0       1.4   3.1e+03      56      72 ..     208     224 ..     161     239 .. 0.57

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 3.5e-23
                                       HHHSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                              HxlR   1 liggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76 
                                       ++g+kW+  ++++l++ g+  fs+l+r+l +is k+L+++L  L  dglier+++++ P +veY+ t +G++l+ +l
  gi|313127396|ref|YP_004037666.1|  17 VVGKKWHPAVVYSLVSnGPAGFSDLERRL-DISSKVLSETLADLVDDGLIERNELQTSPLRVEYTPTTAGHELASIL 92 
                                       79************988************.*********************************************** PP

                                       HHHHHHHHHHHHC CS
                              HxlR  77 qelkkwgeeylee 89 
                                         l  w e+y ++
  gi|313127396|ref|YP_004037666.1|  93 GDLGRWTERYHDN 105
                                       **********987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                                       SSS-EEEEEE-TCGGGG CS
                              HxlR  56 evPpkveYsltekGrsl 72 
                                       e  + ve  lt++ + +
  gi|313127396|ref|YP_004037666.1| 208 ELTETVEALLTPRSEVV 224
                                       22333444444444444 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   4.1e-16   9.3e-13       1     111 [.     110     213 ..     110     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 4.1e-16
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vl+vdDd  + el +++l   ++ ev++a+dg+e l +++e  vd +llD +mp+++G ++++ i +e p+++v +l
  gi|313127396|ref|YP_004037666.1| 110 VLVVDDDARLTELYTSMLS--EF-EVRTANDGTEGLSKVDET-VDAVLLDRKMPDVSGEHVAQCIAAEYPSIRVALL 182
                                       8*****************9..88.99*************987.*******************************999 PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                        ++      ++ l++  d ++ Kp++ +eL++ +
  gi|313127396|ref|YP_004037666.1| 183 ASAR---LDEQTLSVPFDRYVRKPVTATELTETV 213
                                       8555...568999*****************9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     2e-07   0.00046      17      54 ..      33      68 ..      25      74 .. 0.85
   2 ?   -3.5   0.0       4.6     1e+04      18      29 ..     202     211 ..     199     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2e-07
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +++     ++l+rrl++s   +s +l++Lv+ GL+er 
  gi|313127396|ref|YP_004037666.1| 33 NGP--AGFSDLERRLDISSKVLSETLADLVDDGLIERN 68
                                      555..5689***************************96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.6
                                       TTSEEEHHHHHH CS
                            MarR_2  18 pgrdltvgelar 29 
                                        +  +t++el++
  gi|313127396|ref|YP_004037666.1| 202 KP--VTATELTE 211
                                       44..89999987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.9e-06    0.0065      17      56 ..      29      67 ..      23      70 .. 0.89
   2 ?    2.3   0.0      0.08   1.8e+02      21      40 ..     200     222 ..     180     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                                      HHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 17 raLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ++  +++++ +s+l +rld+s + ls  L+ L++ gL+e+
  gi|313127396|ref|YP_004037666.1| 29 SLV-SNGPAGFSDLERRLDISSKVLSETLADLVDDGLIER 67
                                      555.8889999***************************98 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.08
                                       TCTTB-HHHHHHHHT...S-HHH CS
                            HTH_20  21 raegltaselaerld...lsknt 40 
                                        ++++ta+el e+++   +++++
  gi|313127396|ref|YP_004037666.1| 200 VRKPVTATELTETVEallTPRSE 222
                                       589********998666566665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.3e-07   0.00073      16      60 ..      29      75 ..      25      83 .. 0.85
   2 ?   -3.1   0.0       3.4   7.6e+03      21      33 ..     202     214 ..     201     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.3e-07
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TT CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pk 60
                                       L+++gpa  +++ ++l+++     e+L  L+d Gl+er++ +  p 
  gi|313127396|ref|YP_004037666.1| 29 SLVSNGPAGFSDLERRLDISSKVLSETLADLVDDGLIERNELQtsPL 75
                                      69*************************************98544544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.4
                                       CCCHHCHHCCCTT CS
                              TrmB  21 gpatadeiaeelg 33 
                                       +p ta+e+ e ++
  gi|313127396|ref|YP_004037666.1| 202 KPVTATELTETVE 214
                                       5778888887765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     5e-07    0.0011       8      50 ..      26      68 ..      25      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5e-07
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++++l ++gp+  s+L ++l +s+  ++++l  L+++GlieR 
  gi|313127396|ref|YP_004037666.1| 26 VVYSLVSNGPAGFSDLERRLDISSKVLSETLADLVDDGLIERN 68
                                      56788899**********************************6 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.6e-07    0.0019       9      46 ..      28      66 ..      25      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.6e-07
                                      HHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  9 klLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++L + g++ +++l + l++s   +S+ L+ L + GL+e
  gi|313127396|ref|YP_004037666.1| 28 YSLVSnGPAGFSDLERRLDISSKVLSETLADLVDDGLIE 66
                                      555555*******************************97 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.1e-05      0.11      36      71 ..      54      87 ..      40      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                                      HHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR 36 paLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                       +L++L ++gl+e+++ ++  +p r  Y+ T aG++
  gi|313127396|ref|YP_004037666.1| 54 ETLADLVDDGLIERNELQT--SPLRVEYTPTTAGHE 87
                                      689************9985..9************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1824.88
//
Query:       gi|313127397|ref|YP_004037667.1|  [L=144]
Description: tm2 domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0005   20.0   0.3    0.00076   19.4   0.3    1.2  1  DZR             Double zinc ribbon
     0.0012   18.1   0.7      0.002   17.5   0.7    1.4  1  zf-ribbon_3     zinc-ribbon domain
     0.0049   16.5   1.7      0.021   14.5   1.8    1.9  3  zinc_ribbon_2   zinc-ribbon domain
      0.009   16.3   0.2      0.015   15.6   0.2    1.3  1  TM2             TM2 domain
  ------ inclusion threshold ------
      0.019   15.7   0.2      0.025   15.3   0.2    1.2  1  zinc_ribbon_15  zinc-ribbon family
      0.062   13.3   0.2       0.12   12.4   0.2    1.4  1  zinc-ribbons_6  zinc-ribbons


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.3   2.6e-07   0.00076       1      23 [.     104     126 ..      95     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.6e-07
                               DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                       Cp Cg+el+ d  fC++C t+l+
  gi|313127397|ref|YP_004037667.1| 104 CPYCGKELDGDLDFCQWCTTELD 126
                                       99999999999999999999986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.7   6.7e-07     0.002       3      22 ..     102     121 ..     101     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.7e-07
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyC 22 
                                       ++CP+CG+ + + d  +C +C
  gi|313127397|ref|YP_004037667.1| 102 THCPYCGKeL-DGDLDFCQWC 121
                                       59******66.********** PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.4   0.00012      0.34      15      23 .]     102     111 ..      95     111 .. 0.67
   2 !   14.5   1.8   7.1e-06     0.021       2      23 .]     104     125 ..     103     125 .. 0.93
   3 ?    3.5   0.1     0.022        64       1      11 [.     117     127 ..     117     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                     zinc_ribbon_2  15 F.CpyCGtpl 23 
                                         CpyCG +l
  gi|313127397|ref|YP_004037667.1| 102 ThCPYCGKEL 111
                                       4499999876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7.1e-06
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtpl 23 
                                       Cp CG+el+ +  FC  C t+l
  gi|313127397|ref|YP_004037667.1| 104 CPYCGKELDGDLDFCQWCTTEL 125
                                       ******************9986 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.022
                     zinc_ribbon_2   1 fCpnCGaelqd 11 
                                       fC  C +el+d
  gi|313127397|ref|YP_004037667.1| 117 FCQWCTTELDD 127
                                       78888888776 PP

>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   4.9e-06     0.015       3      44 ..       7      48 ..       5      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                               TM2  3 ksklvaylLwffLGglGvHRFYlGktgsGvlqlltfv..Gglgi 44
                                      k  ++a++L  +  + G+ ++Yl +++ ++ +  t    G+l++
  gi|313127397|ref|YP_004037667.1|  7 KRPWLAAVLGAL--ATGAGHIYLRRWKRAFGWVATAMatGILFV 48
                                      455555555554..78*******************977777665 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   8.5e-06     0.025      64      85 ..      93     121 ..      75     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.5e-06
                    zinc_ribbon_15  64 e.......kkeCknCgkeveeefkyCpkC 85 
                                       +        ++C+ Cgke++ + ++C  C
  gi|313127397|ref|YP_004037667.1|  93 RtvnpdgtITHCPYCGKELDGDLDFCQWC 121
                                       1233446699*****************99 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   3.9e-05      0.12      11      42 ..      96     128 ..      85     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                                       EE-SSEEE-TTT--EEE.EEEE-SSS-S---EE CS
                    zinc-ribbons_6  11 ekrgeqyhCeaCqedlk.kealCpeCeqelevl 42 
                                       + +g+ +hC  C ++l+    +C+ C  el+ +
  gi|313127397|ref|YP_004037667.1|  96 NPDGTITHCPYCGKELDgDLDFCQWCTTELDDF 128
                                       3556899*******99835689*****999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1008.48
//
Query:       gi|313127398|ref|YP_004037668.1|  [L=213]
Description: pyroglutamyl peptidase i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-52  176.8   0.0    6.7e-52  176.6   0.0    1.0  1  Peptidase_C15  Pyroglutamyl peptidase


Domain annotation for each model (and alignments):
>> Peptidase_C15  Pyroglutamyl peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.6   0.0   3.7e-56   6.7e-52       1     199 [.       1     209 [.       1     212 [. 0.95

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 3.7e-56
                                       -EEEEEEE---TT-S--HHHHHHHHHTT-EETTEEEEEEEE-SSTTHHHHHHHHHHHHH--SEEEEEEE-TT--SEE CS
                     Peptidase_C15   1 mkvLvtGfdPfgkekinPaleavkeLdgaeiaeativkrevPtvfkksadvlkkaiaeikpdivlaiGqagGrsait 77 
                                       m v+vtG++Pfg+ + nP+ +++ eLdg+++a+  +v  ++P+ f +++d l+  +ae++p + ++ G a G  a+ 
  gi|313127398|ref|YP_004037668.1|   1 MTVVVTGYEPFGELDTNPTAHVAAELDGETVAGESVVGAVLPVAFDSVTDRLESLLAEHDPTVFVSTGVARGSAAVR 77 
                                       789************************************************************************** PP

                                       EE-EEES-BE-.SS--TTS---ESB-SSTTS-SEEE--S-HHHHHHHHHHTT--EEEES---SSHHHHHHHHHHHHH CS
                     Peptidase_C15  78 vervainldDa.ripDnegkqlidepispdgeaaYfstlPvkamvkalkeaGvPaavsntaGtfvCnhllYqvlyll 153
                                       +erv +n++Da   pDn g  + +e + +dg+aaYfstlPv  +v+ l ++G+Pa +sntaGt++Cn  lY+v + +
  gi|313127398|ref|YP_004037668.1|  78 IERVGVNVADAvTTPDNVGADPRNERL-ADGPAAYFSTLPVESVVTDLLDEGIPACLSNTAGTHLCNDALYTVRHAV 153
                                       ***********669*********9987.79*********************************************** PP

                                       HHHS--SEEEEEEE-B-GGGTHHHHHT..........-B--HHHHHHHHHHHHHHH CS
                     Peptidase_C15 154 dkklpevraGfihiPylpeqvidkpet..........pslsldkevagvkaaieai 199
                                       ++   e+r+Gf+h+P+ p+ ++               ps++l +++++v+ aie+ 
  gi|313127398|ref|YP_004037668.1| 154 ERDDRETRSGFVHLPFSPSLAAAAAREneatrggsvpPSMALTTQTRAVRLAIETT 209
                                       *****************9987654433347999********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1531.29
//
Query:       gi|313127399|ref|YP_004037669.1|  [L=313]
Description: divalent heavy-metal cations transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-16   60.3  18.3    3.5e-14   52.8  18.3    2.3  1  Zip       ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8  18.3     2e-18   3.5e-14       9     332 ..      25     308 ..      17     309 .. 0.76

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2e-18
                               Zip   9 iaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleeehthplagllvllG 85 
                                       i   ++ ++ llg++lv  i +++ ++ l  +l fa+Gv+l+ +f +Ll +++   +++        p++ + + l+
  gi|313127399|ref|YP_004037669.1|  25 I---VIAFMNLLGAVLVL-IWRNPTERSLDGALGFAAGVMLSASFTSLLLPGIDFASDPAY-R----PFTPGGIELA 92 
                                       4...45555555555555.34578999****************************999863.3....8999999999 PP

                               Zip  86 flllllveklltmivekksshkektpkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqek 162
                                        ++  l+ + l  i               + ++  ++++  +s + ++  e +     +++td+     +r + + +
  gi|313127399|ref|YP_004037669.1|  93 GITPVLIGFGLGVILLD------------QGERWVQYVGPLISGELTDRAESD----GGEGTDDW----QRSSDSVS 149
                                       99999999999888887............333333333333333333333333....22222222....22222223 PP

                               Zip 163 sesekeqaseeedkeklaslkvraiilllglilHsfidGLAlG...vssssstgislfiAvllHelpeelglgaiLl 236
                                       ++ +k++    +  e++ s+ v ++++++++ lH+ ++GLA+G    s +++ +i l++A+ + ++pe+l++ +  +
  gi|313127399|ref|YP_004037669.1| 150 DGGIKRA---GAMVEQADSRVVGVLLFTVAITLHNMPEGLAVGvgfGSGDVTNAIGLMLAIGIQNIPEGLAVSVAAI 223
                                       3333333...3467788899999********************9966888999************************ PP

                               Zip 237 kaglsrkkav.llnllfalta.plGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgsss 311
                                       +agl r +   ++ +  +++  pl+++ +++         a  + ++ ++++aG++lYv   e++p E +++ +   
  gi|313127399|ref|YP_004037669.1| 224 NAGLGRTYYAaVAGIRAGIVEiPLAVFGAWA------VVAAAPLLPYAMGFAAGGMLYVLGDEIIP-ETHAHGH--- 290
                                       ******9988688888888862666666666......89999************************.6555553... PP

                               Zip 312 lkqsllqllglllGfalmlll 332
                                          + l+ l ++ G+++ml l
  gi|313127399|ref|YP_004037669.1| 291 ---ERLATLTMMGGAIVMLTL 308
                                       ...9**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2248.72
//
Query:       gi|313127400|ref|YP_004037670.1|  [L=59]
Description: hypothetical protein Hbor_26730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.057   12.7   2.3      0.059   12.7   2.3    1.0  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.3   3.3e-06     0.059     169     214 ..      10      54 ..       6      59 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-06
                   ABC2_membrane_2 169 vlllllvvflalglllSsvarssreaaalalglfvvlailvpivly 214
                                       v+++ ++ f al l++ +v+ s + a+ +a++l+++l++++p + +
  gi|313127400|ref|YP_004037670.1|  10 VIVAGTG-FSALVLGVGVVTESIVLALGAAFFLLLALVLVYPFARF 54 
                                       4444444.7999*****************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 419.12
//
Query:       gi|313127401|ref|YP_004037671.1|  [L=551]
Description: nuclease-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-30  103.6   0.0    6.7e-14   52.3   0.0    2.4  2  SNase     Staphylococcal nuclease homologue
  ------ inclusion threshold ------
        0.1   12.5   2.1         11    5.9   0.2    2.7  2  Tudor_3   DNA repair protein Crb2 Tudor domain
       0.19   11.5   1.4       0.99    9.2   0.1    2.3  2  DUF1654   Protein of unknown function (DUF1654)
          1    9.6   6.0         10    6.4   1.0    2.4  2  Clavanin  Clavanin


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   1.5e-17   6.7e-14       2     107 ..     186     303 ..     185     304 .. 0.94
   2 !   49.1   0.0   1.5e-16   6.7e-13       2     107 ..     361     479 ..     360     480 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.5e-17
                                       EEETTEE-STSSBTTT.............TTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEETTE CS
                             SNase   2 vrLvgidaPetakpkk.............tvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvylnkk 63 
                                       v+Lvg+daP  +   +              +  + ++A++f++++v +++v++ ++++  ++D++grll y+   ++
  gi|313127401|ref|YP_004037671.1| 186 VKLVGVDAPDGQYDDSdfegmptedggdaWLDGWVSNATDFTREKVGGEEVTIRVDSTtdRRDSQGRLLVYLESRGE 262
                                       89********99777799**********999*********************99999999***************** PP

                                       EHHHHHHHTTSSEE---BTTSTTTHHHHHHHHHHHHHTT-GGGC CS
                             SNase  64 nineeLvkeGlArvyevyekneekkkellkaeeeAkkkrkglWs 107
                                        +ne+Lv++G A+   v ++ + ++  +++ae +A++   glW+
  gi|313127401|ref|YP_004037671.1| 263 TLNEQLVQQGHAQ---VSDRSFVERSSYESAETNAQQGYTGLWQ 303
                                       *************...55567889*******************6 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 1.5e-16
                                       EEETTEE-STSSBTTT.............TTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEET.T CS
                             SNase   2 vrLvgidaPetakpkk.............tvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvyln.k 62 
                                       v+Lvg+d+P                     ++++  +A+ f++++v++++v++ +++k  ++D++grll yv +   
  gi|313127401|ref|YP_004037671.1| 361 VQLVGVDTPDGDYDSDdfhgmaaedggeeWLNEWDGKAESFTSDKVSGEEVTIRVDSKadRRDSQGRLLVYVDYGaS 437
                                       78********9966669999*******9999************************999**************99988 PP

                                       EEHHHHHHHTTSSEE---BTTSTTTHHHHHHHHHHHHHTT-GGGC CS
                             SNase  63 knineeLvkeGlArvyevyekneekkkellkaeeeAkkkrkglWs 107
                                         +ne+L+++G+A+   v ++ + + ++++ ae  A +   glW+
  gi|313127401|ref|YP_004037671.1| 438 DTLNEKLIQQGYAQ---VSDRTFSEVEAFEDAETGASQGYSGLWE 479
                                       99************...55667899*******************6 PP

>> Tudor_3  DNA repair protein Crb2 Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0025        11      31      48 ..     173     190 ..     163     192 .. 0.81
   2 ?    5.3   0.1     0.004        18      26      46 ..     345     363 ..     337     366 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0025
                                       EEEEEETTS-EEEEETTS CS
                           Tudor_3  31 rykVrFdDgtpeevdskq 48 
                                       +++V+F Dg++eev+  +
  gi|313127401|ref|YP_004037671.1| 173 TITVKFADGSIEEVKLVG 190
                                       789***********9765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.004
                                       E-SSSEEEEEETTS-EEEEET CS
                           Tudor_3  26 ssgsqrykVrFdDgtpeevds 46 
                                       +++  r++V F+Dg +e v+ 
  gi|313127401|ref|YP_004037671.1| 345 AGD--RLEVTFEDGHTEVVQL 363
                                       344..9********9998875 PP

>> DUF1654  Protein of unknown function (DUF1654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00022      0.99      30      61 ..     153     183 ..     146     186 .. 0.87
   2 ?    0.2   0.1      0.14   6.1e+02      33      57 ..     331     355 ..     327     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00022
                           DUF1654  30 ledeseddWerlleeiaeteevelafrdDgsv 61 
                                        +d ++ +W   ++ei e + ++++f  Dgs+
  gi|313127401|ref|YP_004037671.1| 153 SDDAKQTEWTVTVDEIVEADTITVKFA-DGSI 183
                                       5788899*******************7.5776 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.14
                           DUF1654  33 eseddWerlleeiaeteevelafrd 57 
                                       e++  W   +e++   + +e++f+d
  gi|313127401|ref|YP_004037671.1| 331 ENRSSWTVTVENVVAGDRLEVTFED 355
                                       78999******************97 PP

>> Clavanin  Clavanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3    0.0051        23      48      76 ..     189     217 ..     177     219 .. 0.87
   2 ?    6.4   1.0    0.0023        10      44      77 ..     360     393 ..     351     396 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0051
                          Clavanin  48 isvvlgddqqdngkfygyyaedngkhwyd 76 
                                       ++v   d q d+  f g  +ed g  w d
  gi|313127401|ref|YP_004037671.1| 189 VGVDAPDGQYDDSDFEGMPTEDGGDAWLD 217
                                       66777899*******************98 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0023
                          Clavanin  44 lvygisvvlgddqqdngkfygyyaedngkhwydt 77 
                                       +v  ++v   d + d   f+g  aed g  w + 
  gi|313127401|ref|YP_004037671.1| 360 VVQLVGVDTPDGDYDSDDFHGMAAEDGGEEWLNE 393
                                       67777888889999*****************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 3669.16
//
Query:       gi|313127402|ref|YP_004037672.1|  [L=383]
Description: multicopper oxidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-30  103.9  13.5    7.2e-19   67.9   2.2    3.2  2  Cu-oxidase_2    Multicopper oxidase
    3.5e-25   88.3   5.8    1.8e-20   73.1   0.6    2.7  2  Cu-oxidase_3    Multicopper oxidase
    1.4e-16   61.0   0.5    1.2e-15   58.0   0.1    2.2  2  Cu-oxidase      Multicopper oxidase
    7.5e-06   26.3   1.5     0.0053   17.2   0.2    2.6  2  Copper-bind     Copper binding proteins, plastocyanin/azurin 
     0.0009   19.3   0.0        1.4    9.1   0.0    2.8  2  Cupredoxin_1    Cupredoxin-like domain
  ------ inclusion threshold ------
      0.099   12.9   0.0        3.1    8.1   0.0    2.7  2  CBM_4_9         Carbohydrate binding domain
        0.2   12.2   0.0       0.45   11.1   0.0    1.6  1  Self-incomp_S1  Plant self-incompatibility protein S1


Domain annotation for each model (and alignments):
>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   3.6   2.6e-13   6.8e-10      27     136 ..     110     206 ..      79     207 .. 0.83
   2 !   67.9   2.2   2.8e-22   7.2e-19      10     127 ..     237     351 ..     232     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.6e-13
                                       CTTTSSEEEEEETTEEEEEEEEE-SSS.-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEE CS
                      Cu-oxidase_2  27 efsentnvitlpkgevveiviqnntkl.pHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwva 102
                                       + s   +++++++ge+  ++++n+++  pH++H HG +    +                +  +    ++v++g++ +
  gi|313127402|ref|YP_004037672.1| 110 TPSVPGPILRIQEGETFTVTLDNSGMDmPHTLHVHGLRKTWEN----------------DGVPTTTGITVEAGEKHT 170
                                       455678999****************999********9544432................2234467799999***** PP

                                       EEEES.S-EEEEEEESSH..HHHHTT-EEEEEEECH CS
                      Cu-oxidase_2 103 irfkadnpGvwllHCHil..wHldqGmalqfvvrpd 136
                                       ++f+a+ +G  l+HCH +   H+d+Gm + + v+p+
  gi|313127402|ref|YP_004037672.1| 171 YEFTANVAGTHLYHCHYQtpRHMDMGMFGILRVEPK 206
                                       ******************99********99999875 PP

  == domain 2  score: 67.9 bits;  conditional E-value: 2.8e-22
                                       CCCEEEEEEEEEEE...ETCCTT.TSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSS CS
                      Cu-oxidase_2  10 lqltsgneeaseit...ngeefs.entnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksy 82 
                                       +++t++ +++ +i+    +++f+ e+ ++i ++ g++v++   n +   HP+HlH h+f+v++++++         +
  gi|313127402|ref|YP_004037672.1| 237 YDITNRMMDTFTINgksAPATFHpETGSPIIVDPGDTVRVHWVNAGFHSHPMHLHNHRFKVVEKDGSA--------I 305
                                       567766666666667766665555899***********************************999999........4 PP

                                       GCCGSSCBSEEEE-TTEEEEEEEES..S-EEEEEEESSHHHHHTT- CS
                      Cu-oxidase_2  83 nlenpvrrdtvqvppggwvairfkad.npGvwllHCHilwHldqGm 127
                                         + +  +d+v++ p ++ +++f+ad +pG +l+HCH   H+ +G 
  gi|313127402|ref|YP_004037672.1| 306 PEQMQLLQDVVNIAPAERYTVEFTADaDPGIYLMHCHKVDHVRNGS 351
                                       44456699*****************98***************9996 PP

>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.6   6.9e-24   1.8e-20      23     117 ..     112     206 ..     109     207 .. 0.96
   2 !   16.7   0.5   2.1e-06    0.0054      26     103 ..     263     346 ..     233     358 .. 0.79

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 6.9e-24
                                       SSBS-EEEEETT-EEEEEEEE-S.SS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE CS
                      Cu-oxidase_3  23 qfpgptievregdtvvvnvtNkl.dentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhs 98 
                                       ++pgp ++++eg+t +v++ N+  d + ++h+hGl+  ++   DGvp  t   +++ge+ ty+ft++  agt++Yh 
  gi|313127402|ref|YP_004037672.1| 112 SVPGPILRIQEGETFTVTLDNSGmDMPHTLHVHGLRKTWE--NDGVPTTTGITVEAGEKHTYEFTANV-AGTHLYHC 185
                                       68*******************9879***********9999..**************************.******** PP

                                       --TT.HHH.TT-EEEEEEE-H CS
                      Cu-oxidase_3  99 hlsl.qqa.aGlaGaiiiedk 117
                                       h+++ +++ +G++G++ +e+k
  gi|313127402|ref|YP_004037672.1| 186 HYQTpRHMdMGMFGILRVEPK 206
                                       ****97777*********987 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.1e-06
                                       S-EEEEETT-EEEEEEEE-S..SS-B-EEEET--S-GG.....GSCSGGG-.......B-TT-EEEEEEE--S-SEE CS
                      Cu-oxidase_3  26 gptievregdtvvvnvtNkl..dentsihwhGlqqrktswmDGvpgvtqcp.......iqpgesftyrftvkqqagt 93 
                                       g  i v+ gdtv+v+ +N+   ++++ +h h +++ ++   DG +   q +       i+p e++t +ft++   g 
  gi|313127402|ref|YP_004037672.1| 263 GSPIIVDPGDTVRVHWVNAGfhSHPMHLHNHRFKVVEK---DGSAIPEQMQllqdvvnIAPAERYTVEFTADADPGI 336
                                       66799**************9667777777777777777...**88765542333334499***************** PP

                                       EEEEE--TTH CS
                      Cu-oxidase_3  94 lwYhshlslq 103
                                       ++ h h   +
  gi|313127402|ref|YP_004037672.1| 337 YLMHCHKVDH 346
                                       ****997664 PP

>> Cu-oxidase  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.59   1.5e+03      57      78 ..     156     178 ..     124     188 .. 0.67
   2 !   58.0   0.1   4.6e-19   1.2e-15       3     148 ..     215     350 ..     213     363 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.59
                                       TTSGGGEEEEETTEEEEEE.EES CS
                        Cu-oxidase  57 aslatltvepgktyrlrii.nvs 78 
                                         ++ +tve+g+++   +  nv+
  gi|313127402|ref|YP_004037672.1| 156 PTTTGITVEAGEKHTYEFTaNVA 178
                                       34778999999998888876665 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 4.6e-19
                                       EEEEEEEETCBCTTSCBC.HSSCHCHHHHH.TT--SEEEETTBSS.......CTTTTSGGGEEEEETTEEEEEEEES CS
                        Cu-oxidase   3 yvitlsDwyhkdakelekellasgkapadt.ppvpdavlingkggfnatladkdgaslatltvepgktyrlriinvs 78 
                                       y++t+++w ++  + ++  ++a+   +  +   + d+++ingk+ ++ t  +        + v+pg+t+r++ +n++
  gi|313127402|ref|YP_004037672.1| 215 YYMTVKEW-DTRLSRQYGGQDAT---YD-ItNRMMDTFTINGKSAPA-TFHP---ETGSPIIVDPGDTVRVHWVNAG 282
                                       55556666.22222222222222...22.246789*******77766.4343...4578999*************98 PP

                                       SS-BEEEEETSB-EEEEEETCETTS...EEEESCEEE-TTEEEEEEEEE-SSSEEEEEEEEGSSSCHHHHTTS CS
                        Cu-oxidase  79 addslnfsIeGHkltVvevDgvyve...pvevdsldIavGqrysvlvtanqapgnYwivasgrsnlieafeng 148
                                         +s+++ +++H+++Vve Dg+ +    ++ +d ++Ia+++ry+v +ta+++pg Y +++    ++ ++++ng
  gi|313127402|ref|YP_004037672.1| 283 F-HSHPMHLHNHRFKVVEKDGSAIPeqmQLLQDVVNIAPAERYTVEFTADADPGIYLMHC----HKVDHVRNG 350
                                       5.689******************99889999*****************************....445666655 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   2.1e-06    0.0053      20      99 .]     119     204 ..     114     204 .. 0.75
   2 !    7.6   0.1     0.002       5.1      19      85 ..     266     342 ..     247     351 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                                       EEETTEEEEEEEE....SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEET...T. CS
                       Copper-bind  20 tvkkgekvtfvnl....avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffCs...P. 86 
                                       ++++ge+ t + l     +m+H ++++  g+ +  ++d v  +     + +Gek + +f+   agt  ++C    P 
  gi|313127402|ref|YP_004037672.1| 119 RIQEGETFTVT-LdnsgMDMPHTLHVH--GLRKTWENDGVPTT-TGITVEAGEKHTYEFTanVAGTHLYHCHyqtPr 191
                                       67777765433.335678899999886..55667788887775.5566788999999999768899999995557** PP

                                       TTTTTSEEEEEEE CS
                       Copper-bind  87 HaaagMkgkvtve 99 
                                       H  +gM g + ve
  gi|313127402|ref|YP_004037672.1| 192 HMDMGMFGILRVE 204
                                       ********99885 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                                       EEEETTEEE..EEEEESSSSBEEEEETTSSTTTGGGTTSCTTC....EEEE.BSTTEEEEEEEE...SSEEEEEEET CS
                       Copper-bind  19 itvkkgekv..tfvnlavmgHNvvldkdgvpagvdkdkvkaed....etkl.iggGekdsvtfd...eagtYkffCs 85 
                                       i v++g++v   +vn    +H ++l++   +  +++    +e+    ++ + i++ e ++v+f+   ++g Y  +C 
  gi|313127402|ref|YP_004037672.1| 266 IIVDPGDTVrvHWVNAGFHSHPMHLHNHRFKVVEKDGSAIPEQmqllQDVVnIAPAERYTVEFTadaDPGIYLMHCH 342
                                       6788888752268887777888888886665433333332223466655543799*********7655666**9997 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00054       1.4      37      96 ..     118     189 ..     115     196 .. 0.72
   2 !    7.0   0.0    0.0024       6.1      22      93 ..     273     342 ..     244     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00054
                      Cupredoxin_1  37 ievkagekvklkiknkdkt.peefesed...........lgeekvlapgktttitiaplkpGeYeftcdmhm 96 
                                       + +++ge ++++++n +   p+++ ++              +  +++ g+++t ++++  +G++ ++c ++ 
  gi|313127402|ref|YP_004037672.1| 118 LRIQEGETFTVTLDNSGMDmPHTLHVHGlrktwendgvpTTTGITVEAGEKHTYEFTANVAGTHLYHCHYQT 189
                                       679999999999999998853666666644444444444333357888999999999999999999998875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0024
                      Cupredoxin_1  22 tveitvkdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiap.lkpGeYeftcd 93 
                                       tv++   + gf    ++++  +   +k++ kd ++   +++ l+   ++ap + +t+++++  +pG Y ++c 
  gi|313127402|ref|YP_004037672.1| 273 TVRVHWVNAGFHSHPMHLHNHR---FKVVEKDGSAIPEQMQLLQDVVNIAPAERYTVEFTAdADPGIYLMHCH 342
                                       5666667777777777777665...8888888887666777788889***********976258********6 PP

>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.11   2.9e+02      40      73 ..     142     177 ..     117     188 .. 0.67
   2 ?    8.1   0.0    0.0012       3.1      33      74 ..     291     333 ..     227     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                                       EEESCSSTTCEEEEEEE..CCS-TT-EEEEEEEEEE CS
                           CBM_4_9  40 kvsgrgetwdgqaidit..irlekgktYtvsfwvka 73 
                                       +v g  +tw +  + +t  i++e g++ t +f++  
  gi|313127402|ref|YP_004037672.1| 142 HVHGLRKTWENDGVPTTtgITVEAGEKHTYEFTANV 177
                                       555555556555555554599999887777777654 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0012
                                       SSSSEEEEEESCSS.TTCEEEEEEECCS-TT-EEEEEEEEEES CS
                           CBM_4_9  33 yngtyslkvsgrge.twdgqaiditirlekgktYtvsfwvkas 74 
                                       +n ++++   ++++ + + q++++  ++ + ++Ytv+f++ a+
  gi|313127402|ref|YP_004037672.1| 291 HNHRFKVVEKDGSAiPEQMQLLQDVVNIAPAERYTVEFTADAD 333
                                       7777888666666699999********************9987 PP

>> Self-incomp_S1  Plant self-incompatibility protein S1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.45      28      83 ..     161     224 ..     132     244 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                    Self-incomp_S1  28 htlkpgeefsfsfkenffgttlffCefrwgk.kes.sfdvfkdkr.dskkcgkl.....csWev 83 
                                        t++ ge+ +++f+ n+ gt l++C+ +         f + +++   +++ +k+      +W+ 
  gi|313127402|ref|YP_004037672.1| 161 ITVEAGEKHTYEFTANVAGTHLYHCHYQTPRhMDMgMFGILRVEPkGYERADKEyymtvKEWDT 224
                                       578899*********************9955233357777777763344444434444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2890.44
//
Query:       gi|313127403|ref|YP_004037673.1|  [L=345]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-19   69.6   0.1    6.8e-11   42.5   0.0    3.4  2  Copper-bind  Copper binding proteins, plastocyanin/azurin fam


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   3.8e-15   6.8e-11       2      98 ..      59     144 ..      58     145 .. 0.89
   2 !   22.1   0.0   8.4e-09   0.00015       3      98 ..     213     297 ..     210     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3.8e-15
                                       EEEEEETTETSEEESSEEEEETTEEEEEEEE.SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESS CS
                       Copper-bind   2 evklgvesgdlqFetkeitvkkgekvtfvnl.avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdea 77 
                                       ev + +++gd+ F+++ ++v++ ++vt++++ ++ +HNvv + +      ++++ +         +G ++ +t++++
  gi|313127403|ref|YP_004037673.1|  59 EVGTAGNGGDFGFSPAVVRVSPETTVTWKWTgKGGSHNVVAEDGTF----ESEYYSD--------AGATFAQTVSTS 123
                                       5667788999********************999999***9987775....6677776........59********** PP

                                       EEEEEEETTTTTTTSEEEEEE CS
                       Copper-bind  78 gtYkffCsPHaaagMkgkvtv 98 
                                       +   + C+PH+a+gM+g+++v
  gi|313127403|ref|YP_004037673.1| 124 DVIPYACAPHSAMGMRGALVV 144
                                       ******************998 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 8.4e-09
                                       EEEEETTETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEE CS
                       Copper-bind   3 vklgvesgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagt 79 
                                       v +++++g+++Fe+++i++++g+ v + +          ++++  + +d++   a  +++l g+G ++ + fd  g 
  gi|313127403|ref|YP_004037673.1| 213 VGATGNGGEFAFEPAAIHIDPGTVVRWEWV--------GTAGAY-DVMDEQVGYA--SDQLRGTGHEYALAFDGDGL 278
                                       556788899******************983........333333.4455555555..478999************** PP

                                       EEEEETTTTTTTSEEEEEE CS
                       Copper-bind  80 YkffCsPHaaagMkgkvtv 98 
                                        k+ C+     gM+g v v
  gi|313127403|ref|YP_004037673.1| 279 SKYECTKYGDKGMRGVVLV 297
                                       *******999******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2772.64
//
Query:       gi|313127404|ref|YP_004037674.1|  [L=211]
Description: hypothetical protein Hbor_26770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1619.43
//
Query:       gi|313127405|ref|YP_004037675.1|  [L=454]
Description: tRNA adenylyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-43  147.3   0.0    3.2e-43  146.6   0.0    1.4  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    5.6e-15   55.4   0.0      1e-14   54.6   0.0    1.4  1  NTP_transf_2     Nucleotidyltransferase domain
    8.8e-05   22.7   0.0    0.00099   19.3   0.0    2.1  1  SMODS            Second Messenger Oligonucleotide or Dinucleo


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0   5.3e-47   3.2e-43       2     113 .]     160     269 ..     159     269 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 5.3e-47
                                       HHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEETT CS
                   tRNA_NucTransf2   2 evrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDPv 78 
                                       evr++K+flkgig+YGs+l+++GfsGYl+Ellvleyg+fe+++ aaa+w+p+v++d+e++ +  ++fd+plvviDP+
  gi|313127405|ref|YP_004037675.1| 160 EVRVFKRFLKGIGAYGSNLRTQGFSGYLTELLVLEYGGFESLICAAADWHPPVELDPEDHGS--RSFDDPLVVIDPT 234
                                       8***********************************************************99..9************ PP

                                       EEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGGS CS
                   tRNA_NucTransf2  79 DpkRNvaaalsleklaefilaareflkkpseefff 113
                                       Dp+RNvaa++s+e++a+++++are+l++p+ ++ff
  gi|313127405|ref|YP_004037675.1| 235 DPTRNVAAVCSAENVARLQHYARELLDDPRVDLFF 269
                                       ********************************996 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   1.7e-18     1e-14       3      93 ..      40     143 ..      38     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.7e-18
                                       HHHHHHHHHTTTSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH............HHHEHHHHHHHHCCCEEEC CS
                      NTP_transf_2   3 klleelkelepvakvvlfGSyarGtalkg.SDiDllvvlpeevsre............kkeegleklaeiikfleel 66 
                                       ++ +el  l+ +a+v  +GS+arGt+l+g  DiDl++ +p++ +re            + +eg e++ae+++++ e+
  gi|313127405|ref|YP_004037675.1|  40 RVEDELAALSVDADVLRVGSTARGTWLSGdRDIDLFIRFPDDLDREsleryglaignaVLPEGHEEYAEHPYVVGEF 116
                                       77889999999***********************************************9999*************** PP

                                       TTEEEEEECEEECCCCTEEEEEECEEE CS
                      NTP_transf_2  67 lglevdlvtrekledpllvksileerp 93 
                                        g  vdlv++  + d +  +s+++++p
  gi|313127405|ref|YP_004037675.1| 117 DGFDVDLVPCFDVDDGSSLRSAVDRTP 143
                                       **************9999999988876 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.6e-07   0.00099      14     137 ..      20     133 ..      10     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-07
                             SMODS  14 ielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegdeps 90 
                                       i + + +++ + +  +++t+r++ +     s  a+ l vGS ar+T + +  d d+  +++ dl        +++ +
  gi|313127405|ref|YP_004037675.1|  20 IDPDEAEQTALRETAATLTSRVEDEL-AALSVDADVLRVGSTARGTWLSGDRDIDLFIRFPDDLD-------RESLE 88 
                                       78888999999999999*****9999.4455677899************9999999999999843.......34445 PP

                             SMODS  91 dlleklkkalkktyksseirqdrqvvvvelneikidvvPavenkdgs 137
                                       ++  ++ +a+  +  +  +  +++ vv e++++++d+vP++  +dgs
  gi|313127405|ref|YP_004037675.1|  89 RYGLAIGNAVLPEGHE--EYAEHPYVVGEFDGFDVDLVPCFDVDDGS 133
                                       5555666666333333..5688*******************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3144.90
//
Query:       gi|313127406|ref|YP_004037676.1|  [L=338]
Description: deacetylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-83  278.7   0.0    8.9e-83  278.3   0.0    1.2  1  Hist_deacetyl  Histone deacetylase domain
    0.00017   22.0   0.6       0.38   11.1   0.0    2.9  3  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.3   0.0   9.9e-87   8.9e-83       1     305 [.      18     305 ..      18     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 278.3 bits;  conditional E-value: 9.9e-87
                                       SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskll 77 
                                       hpe+++Rl+ai  +la+  g+       +++ +a+++ +++vH++ Y+++++s ++e + +               +
  gi|313127406|ref|YP_004037676.1|  18 HPETADRLRAIRRALAKRHGVE-----YVEADPADDAAVAAVHEEGYVDEIRSFCEEGGGN---------------W 74 
                                       89***************86742.....4788**********************99775543...............7 PP

                                       SSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSS..SEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHH..CC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                     Hist_deacetyl  78 dddtpvspktlkaallavgavleavdavlsgsv..kaafvlvrPpgHHakaseasGFClvNnvaiaikylqa..khe 150
                                       d dt++s++t++aal+++g +  a++a ++g    ++ f l rPpgHHa +++a+GFC++Nn+a+a++++ +  +  
  gi|313127406|ref|YP_004037676.1|  75 DPDTVASEDTWDAALVSAGLAQWAARAAVEGADerDTPFSLGRPPGHHAVENDAMGFCFINNAAVAAQTVIDddELD 151
                                       899**************************8854336679999****************************8833555 PP

                                       SS-EEEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 151 lkrvailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfe 227
                                       ++rvai+D+DvHhGnGt+++fy++ dv+++S+H+  g++yPgtg+++++geg+g+g++lnvple+g gd++y  v++
  gi|313127406|ref|YP_004037676.1| 152 AERVAIFDWDVHHGNGTQDIFYDRGDVFYASLHE--GGLYPGTGEIDEIGEGDGEGTTLNVPLEAGAGDADYELVIS 226
                                       77********************************..999************************************** PP

                                       HCHHHHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G..EEEEE-S---HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 228 eilrpvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvk.kvvllleGGYnlealaravtav 303
                                       e+lrp+le+f+Pdli++saGfDa+++dp++++++s+egy++lt++++++a++v+  + ++leGGY l++l+++v+ v
  gi|313127406|ref|YP_004037676.1| 227 EVLRPALEQFDPDLIIISAGFDAHRHDPISRMRVSTEGYAQLTDSVRAIANDVDaGLAFVLEGGYGLDTLSEGVAIV 303
                                       ***************************************************9955*****************99887 PP

                                       HH CS
                                       xx RF
                     Hist_deacetyl 304 ls 305
                                        +
  gi|313127406|ref|YP_004037676.1| 304 HE 305
                                       65 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00037       3.3     117     151 ..      10      49 ..       2      82 .. 0.73
   2 ?   -0.2   0.0      0.13   1.1e+03     108     142 ..      70     104 ..      48     131 .. 0.63
   3 !   11.1   0.0   4.2e-05      0.38      53     104 ..     227     279 ..     202     336 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00037
                                       T-TTSTCCHHHHHHHHHHHHHHHHHHCT-EEE-H.....H CS
                     Lipase_GDSL_2 117 eaaadarelnaviaaynealrevaaeegvpfvDl.....h 151
                                        a++  ++  +++++++++ r++a+++gv++v +     +
  gi|313127406|ref|YP_004037676.1|  10 LAHDTGKRHPETADRLRAIRRALAKRHGVEYVEAdpaddA 49 
                                       5666667778999********************9666541 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.13
                                       CEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHH CS
                     Lipase_GDSL_2 108 vlgplpptpeaaadarelnaviaaynealrevaae 142
                                       + g++ p + a++d+ +++ v a ++++++++a e
  gi|313127406|ref|YP_004037676.1|  70 GGGNWDPDTVASEDTWDAALVSAGLAQWAARAAVE 104
                                       45566666666666666666666666666666554 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4.2e-05
                                       HHHH.CTGGG-TSEEEEE--CCCCCTT--HHHHHHH...HHHHHHHHCCC...G CS
                     Lipase_GDSL_2  53 erlr.dllrlkpdlvtiliGtNDlgrgvpaaaaaand.nleelidalraaapga 104
                                       e lr +l++++pdl++i++G  D+ r++p ++ +  + ++++l d +ra a ++
  gi|313127406|ref|YP_004037676.1| 227 EVLRpALEQFDPDLIIISAGF-DAHRHDPISRMRVSTeGYAQLTDSVRAIANDV 279
                                       44446899**********996.66666666666666669*********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2475.54
//
Query:       gi|313127407|ref|YP_004037677.1|  [L=143]
Description: histone-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-27   94.1   0.9    7.3e-14   51.8   0.1    2.1  2  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    9.1e-14   51.9   2.6    4.7e-10   39.9   0.5    2.0  2  Histone        Core histone H2A/H2B/H3/H4
    3.9e-07   30.2   1.9    7.5e-05   22.8   0.2    2.1  2  CENP-T_C       Centromere kinetochore component CENP-T histon
    0.00034   21.0   1.0     0.0014   19.1   0.4    2.0  2  TFIID_20kDa    Transcription initiation factor TFIID subunit 
    0.00054   19.9   0.3      0.075   13.1   0.0    2.2  2  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
      0.002   18.3   3.1       0.23   11.6   0.2    2.2  2  TAF            TATA box binding protein associated factor (TA
     0.0027   18.0   1.4     0.0055   17.1   0.5    1.9  2  CENP-S         CENP-S protein
     0.0074   16.4   3.4      0.041   14.0   0.2    2.1  2  DUF1931        Domain of unknown function (DUF1931)


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.1   6.2e-14   1.4e-10       2      60 ..       4      62 ..       3      69 .. 0.96
   2 !   51.8   0.1   3.3e-17   7.3e-14       2      62 ..      75     136 ..      74     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 6.2e-14
                                      XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHH CS
                     CBFD_NFYB_HMF  2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaeh 60
                                      eLP a+v++I++   +  +++ dA e +a+ ++   +ela  Aae++ +++rKt++ae+
  gi|313127407|ref|YP_004037677.1|  4 ELPFAPVDTIIRRNAGSLRVSADAAEELARRIQRHGSELAIDAAERAREDGRKTLMAED 62
                                      8*********************************************************9 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 3.3e-17
                                       XXXHHHHHHHHHCC.TTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHH CS
                     CBFD_NFYB_HMF   2 eLPiarvkkImksd.pdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehik 62 
                                       eLP+a+v++I +   +d  +++ dA++ +a+++e ++  +a++Aa+++ +++r+ti+ae+i+
  gi|313127407|ref|YP_004037677.1|  75 ELPVAPVDRIARLRiDDRYRVSMDARIALADILEDYADNVADAAAKLARHADRRTIQAEDIE 136
                                       8*************999999*****************************************7 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   6.8e-05      0.15      65     123 ..       5      62 ..       2      67 .. 0.87
   2 !   39.9   0.5   2.1e-13   4.7e-10      56     127 ..      70     138 ..      64     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                                       HHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHH CS
                           Histone  65 lpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkD 123
                                       lpfa v + i+ ++  +lr+sa+a + l+  +  +  el+ +A+  a++  R+T++++D
  gi|313127407|ref|YP_004037677.1|   5 LPFAPVDTIIR-RNAGSLRVSADAAEELARRIQRHGSELAIDAAERAREDGRKTLMAED 62 
                                       56666444455.5899*****************************************99 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 2.1e-13
                                       HXXSXXSXHHHHHHHHH.HHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHH CS
                           Histone  56 kstdlliqklpfaRvvr.eivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlA 127
                                       ++ +l+ + +p++R+ r  i    ++ +r+s +a  al+ +lE++   ++  A++la+ha R+Ti+++Di+++
  gi|313127407|ref|YP_004037677.1|  70 SRAELELPVAPVDRIARlRI----DDRYRVSMDARIALADILEDYADNVADAAAKLARHADRRTIQAEDIETY 138
                                       6778999999****777445....56********************************************986 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0023       5.2      20      70 ..      13      63 ..       5      72 .. 0.89
   2 !   22.8   0.2   3.3e-08   7.5e-05       8      72 ..      76     137 ..      69     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0023
                          CENP-T_C 20 fakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDv 70
                                      + ++++ + +++++a + l +  +++ + ++ D +  a+  gRKt+ ++D 
  gi|313127407|ref|YP_004037677.1| 13 IIRRNAGSLRVSADAAEELARRIQRHGSELAIDAAERAREDGRKTLMAEDF 63
                                      567778999************************************988874 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.3e-08
                          CENP-T_C   8 lPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvil 72 
                                       lP+a v ++a+        + +++ +a  al  +++++ + v++  +  a+Ha R+ti+++D+++
  gi|313127407|ref|YP_004037677.1|  76 LPVAPVDRIARLRID---DRYRVSMDARIALADILEDYADNVADAAAKLARHADRRTIQAEDIET 137
                                       899999999987644...589*****************************************986 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.5   1.1e+03      12      40 ..      44      71 ..      29      74 .. 0.74
   2 !   19.1   0.4   6.2e-07    0.0014      13      60 ..      90     137 ..      86     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.5
                                      C-SS----HHHHHHHHHHHHHH.HHHHHHH CS
                       TFIID_20kDa 12 vdsetkldedvedlLleiaddF.vesvtkf 40
                                      +d+ ++  ed++  L  +a+dF ve+v+++
  gi|313127407|ref|YP_004037677.1| 44 IDAAERAREDGRKTL--MAEDFdVEQVVSR 71
                                      566666666666665..5788878888876 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 6.2e-07
                                       -SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHH CS
                       TFIID_20kDa  13 dsetkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiql 60 
                                       d   ++  d +  L++i +d+ ++v ++a+kla+h    ++++ Di+ 
  gi|313127407|ref|YP_004037677.1|  90 DDRYRVSMDARIALADILEDYADNVADAAAKLARHADRRTIQAEDIET 137
                                       55555666666779********************************85 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.1      0.01        22      37      60 ..      40      63 ..      21      68 .. 0.85
   2 !   13.1   0.0   3.4e-05     0.075      27      61 ..     102     136 ..      91     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.01
                                      HHHHHHHHC-XXXX...XXXXXXX CS
                       TFIID-18kDa 37 iellqqaakvaklrgsrkitlEDl 60
                                       el + aa+ a+++g++ +  ED+
  gi|313127407|ref|YP_004037677.1| 40 SELAIDAAERAREDGRKTLMAEDF 63
                                      69999******************8 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXX CS
                       TFIID-18kDa  27 lledlvrgyliellqqaakvaklrgsrkitlEDll 61 
                                        l d++++y  ++   aak+a++ ++r i+ ED+ 
  gi|313127407|ref|YP_004037677.1| 102 ALADILEDYADNVADAAAKLARHADRRTIQAEDIE 136
                                       5789*****************************94 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.2    0.0024       5.4      20      62 ..      22      64 ..       8      66 .. 0.91
   2 !   11.6   0.2    0.0001      0.23      25      62 ..      99     136 ..      93     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0024
                                      -B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHH CS
                               TAF 20 nLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvd 62
                                       +s++aa++La  ++    e + +aa   r   R++L ++D+d
  gi|313127407|ref|YP_004037677.1| 22 RVSADAAEELARRIQRHGSELAIDAAERAREDGRKTLMAEDFD 64
                                      5689*************************************98 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHH CS
                               TAF  25 aaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvd 62 
                                       a  +La+ +e    +++  aak  rh+ R+++ ++D++
  gi|313127407|ref|YP_004037677.1|  99 ARIALADILEDYADNVADAAAKLARHADRRTIQAEDIE 136
                                       5556666666667789999******************8 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.63   1.4e+03      39      65 ..      36      62 ..      11      72 .. 0.71
   2 !   17.1   0.5   2.5e-06    0.0055      21      66 ..      90     135 ..      63     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.63
                            CENP-S 39 ykqlenlakDLeaFakHAkRstittdD 65
                                       ++ ++la D    a+  +R+t  ++D
  gi|313127407|ref|YP_004037677.1| 36 QRHGSELAIDAAERAREDGRKTLMAED 62
                                      455566777777778888888888887 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.5e-06
                            CENP-S  21 ekeveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDv 66 
                                       + + +++ ++  al+++  + ++n+a+     a+HA R ti+++D+
  gi|313127407|ref|YP_004037677.1|  90 DDRYRVSMDARIALADILEDYADNVADAAAKLARHADRRTIQAEDI 135
                                       566778888889999999999************************7 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   1.8e-05     0.041       6      55 ..      16      65 ..      11      72 .. 0.92
   2 ?    3.4   0.3     0.033        74      21      53 ..     103     135 ..      86     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                      HHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-- CS
                           DUF1931  6 reaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPi 55
                                      r+a +L v  + ++++   ++++  +L++ a e+A+++gr++ + +D  +
  gi|313127407|ref|YP_004037677.1| 16 RNAGSLRVSADAAEELARRIQRHGSELAIDAAERAREDGRKTLMAEDFDV 65
                                      77889**************************************9999865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS CS
                           DUF1931  21 isdfVekklydLllvaeenAkangrdviepaDL 53 
                                       + d++e+  ++++ +a + A+   r +i+ +D+
  gi|313127407|ref|YP_004037677.1| 103 LADILEDYADNVADAAAKLARHADRRTIQAEDI 135
                                       578888888889999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 987.04
//
Query:       gi|313127408|ref|YP_004037678.1|  [L=486]
Description: single-stranded DNA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-32  110.3  11.3    3.3e-14   52.6   0.3    4.3  4  tRNA_anti-codon  OB-fold nucleic acid binding domain
    1.3e-13   51.2   0.2    7.3e-06   25.8   0.0    3.1  3  CDC24_OB3        Cell division control protein 24, OB domain 
    3.2e-11   43.0   3.1    2.7e-05   24.0   0.3    3.4  3  REPA_OB_2        Replication protein A OB domain
    0.00014   21.8   0.8       0.16   12.0   0.0    3.4  3  DUF4539          Domain of unknown function (DUF4539)
     0.0017   18.4   0.4      0.054   13.5   0.0    3.3  4  SSB              Single-strand binding protein family
  ------ inclusion threshold ------
      0.028   14.6   0.1        4.4    7.6   0.0    3.2  4  tRNA_anti_2      OB-fold nucleic acid binding domain
      0.081   12.7   0.2         25    4.6   0.0    3.1  3  Rep_fac-A_C      Replication factor-A C terminal domain
       0.18   11.4   0.1        8.7    6.0   0.0    2.9  3  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.3   1.5e-17   3.3e-14       1      75 [.      66     148 ..      66     149 .. 0.95
   2 !   45.3   0.3   2.8e-15   6.4e-12       1      70 [.     174     250 ..     174     256 .. 0.97
   3 !   17.1   0.4   1.8e-06    0.0041       3      61 ..     283     347 ..     281     356 .. 0.83
   4 ?   -0.9   0.0      0.77   1.7e+03      40      59 ..     453     472 ..     441     477 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.5e-17
                                       EEEEEEEEEEE.........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsis.........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelel 68 
                                       V++ G+v+si          + + g+v+++++ D+tgri+++l+++ a++  enl++G+v+r+ Gr+k  ++g +e+
  gi|313127408|ref|YP_004037678.1|  66 VKFLGKVMSIGelrtferddEDEDGRVVNVEVADETGRIRISLWDGMAEEATENLEVGQVLRIAGRPKDGYNG-VEV 141
                                       677799999999999999988889*************************************************.*** PP

                                       EEEEEEE CS
                   tRNA_anti-codon  69 kveeiel 75 
                                       +v+++e+
  gi|313127408|ref|YP_004037678.1| 142 SVNKVEP 148
                                       *****96 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 2.8e-15
                                       EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelel 68 
                                       V+++Grv s+         d+s+g+v++++l D tgri+v+l++ ++ +la +++ +  v+v  G+v++r+g  lel
  gi|313127408|ref|YP_004037678.1| 174 VNLKGRVLSTDsvrtfdrdDGSEGRVANLTLGDSTGRIRVTLWD-DKADLAAEFDTDITVEVVdGYVRERDGS-LEL 248
                                       789*****************************************.**************************99.*** PP

                                       EE CS
                   tRNA_anti-codon  69 kv 70 
                                       +v
  gi|313127408|ref|YP_004037678.1| 249 HV 250
                                       98 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.8e-06
                                       EEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEEC CS
                   tRNA_anti-codon   3 vaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrr 61 
                                       +aG v+ +         d+s+g v +i ++D+tg i+v l+    +k   +++  d+v +t  ++k+ 
  gi|313127408|ref|YP_004037678.1| 283 IAGGVIETDpkrtfdrdDGSEGQVRNIRVKDDTGDIRVALWG---EKADTDVDLADYVVITdAEIKEG 347
                                       666677777777778889************************...89999999999999998888775 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.77
                                       HHHHTTS-TTSEEEEEEEEE CS
                   tRNA_anti-codon  40 tklaenlkeGdvvrvtGrvk 59 
                                        ++ e+l+ G  v v+G v+
  gi|313127408|ref|YP_004037678.1| 453 VETSESLQLGAEVTVRGPVR 472
                                       577899999**9*9999886 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   3.3e-09   7.3e-06       1      67 [.      58     128 ..      58     132 .. 0.85
   2 !   10.3   0.0   0.00019      0.43       2      55 ..     167     223 ..     166     239 .. 0.75
   3 !   11.6   0.0   7.5e-05      0.17      18      69 ..     290     341 ..     275     358 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.3e-09
                         CDC24_OB3   1 DLrekmlnvtLlGrvvai.....freknsekkkmdryslrieDttGaidatlweeagklhfkrlrvGhlvll 67 
                                       D+++ m +v  lG+v+ i     f e+++e++  ++ +++++D+tG i++ lw+ +++++  +l+vG+++ +
  gi|313127408|ref|YP_004037678.1|  58 DIEPGMDDVKFLGKVMSIgelrtF-ERDDEDEDGRVVNVEVADETGRIRISLWDGMAEEATENLEVGQVLRI 128
                                       89999***************9865.4444444555559*********************9999*****9866 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                         CDC24_OB3   2 LrekmlnvtLlGrvvai.....freknsekkkmdryslrieDttGaidatlweeagklh 55 
                                       L    ++v L Grv        f ++++++ + ++ +l++ D+tG i++tlw+  + l+
  gi|313127408|ref|YP_004037678.1| 167 LSLGLSDVNLKGRVLSTdsvrtF-DRDDGS-EGRVANLTLGDSTGRIRVTLWDDKADLA 223
                                       55566789999999988886655.444444.344459****************987665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 7.5e-05
                         CDC24_OB3  18 i.....freknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvllsg 69 
                                             f+ +++++  +++  ++r++D+tG+i+++lw e   ++++++ + ++v+++ 
  gi|313127408|ref|YP_004037678.1| 290 TdpkrtFD-RDDGSeGQVR--NIRVKDDTGDIRVALWGE---KADTDVDLADYVVITD 341
                                       35554343.3333424555..9**************988...5555688999999875 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00055       1.2      15      89 ..      68     143 ..      56     147 .. 0.84
   2 !    8.6   0.0   0.00077       1.7      32      63 ..     192     222 ..     174     239 .. 0.73
   3 !   24.0   0.3   1.2e-08   2.7e-05       2      63 ..     270     329 ..     269     347 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00055
                         REPA_OB_2  15 vigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfe..sseepvvalkgvkvsdFggrslsl 89 
                                        +g v s++e++++ + ++ ++ +  ++++ De+g+ +++ lW+  ae+ +   +  +v+ + g     ++g ++s+
  gi|313127408|ref|YP_004037678.1|  68 FLGKVMSIGELRTFERDDEDEDGRVVNVEVADETGR-IRISLWDGMAEEATenLEVGQVLRIAGRPKDGYNGVEVSV 143
                                       578889999999999988888888899*******96.9******98888764468999**99999999999999987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00077
                         REPA_OB_2  32 stekelkkreltlvDesgasvevtlWgkeaek 63 
                                       +++ e +  +ltl D++g+ ++vtlW+++a+ 
  gi|313127408|ref|YP_004037678.1| 192 DDGSEGRVANLTLGDSTGR-IRVTLWDDKADL 222
                                       44447777899**999885.9*******8764 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 1.2e-08
                         REPA_OB_2   2 selenvekdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaek 63 
                                       +++ ++e +++vD+ g v ++++ +++ + +++ e + r++ ++D++g  ++v+lWg++a++
  gi|313127408|ref|YP_004037678.1| 270 ADIASLELGQTVDIAGGVIETDPKRTFDRDDGS-EGQVRNIRVKDDTG-DIRVALWGEKADT 329
                                       58999*****************99999888888.*************9.69*******9876 PP

>> DUF4539  Domain of unknown function (DUF4539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   7.3e-05      0.16      21      59 ..      86     140 ..      71     154 .. 0.75
   2 !    5.5   0.0    0.0079        18      21      52 ..     196     233 ..     180     235 .. 0.72
   3 ?    0.5   0.0      0.29   6.5e+02      23      37 ..     308     322 ..     297     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-05
                           DUF4539  21 d......alvtlkDptGeidgtihrkvleeygkdlsvGavllLk..........q 59 
                                       +      + v ++D+tG i+ ++   + ee +++l+vG vl +           +
  gi|313127408|ref|YP_004037678.1|  86 EdedgrvVNVEVADETGRIRISLWDGMAEEATENLEVGQVLRIAgrpkdgyngvE 140
                                       234477799*******************************977655555555555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0079
                           DUF4539  21 d...alvtlkDptGeidgtihrkvl...eeygkdlsvG 52 
                                       +   a +tl D+tG i+ t+  +      e+  d++v 
  gi|313127408|ref|YP_004037678.1| 196 EgrvANLTLGDSTGRIRVTLWDDKAdlaAEFDTDITVE 233
                                       1445899************9877665557777777765 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.29
                           DUF4539  23 lvtlkDptGeidgti 37 
                                        + +kD tG i+ ++
  gi|313127408|ref|YP_004037678.1| 308 NIRVKDDTGDIRVAL 322
                                       578999999998776 PP

>> SSB  Single-strand binding protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   2.4e-05     0.054      42      77 ..      96     131 ..      75     153 .. 0.90
   2 ?    0.1   0.0      0.38   8.5e+02      47      64 ..     208     225 ..     199     236 .. 0.77
   3 ?   -2.0   0.0       1.6   3.6e+03      43      60 ..     311     328 ..     298     330 .. 0.76
   4 ?   -1.8   0.0       1.5   3.3e+03      63      77 ..     456     470 ..     428     484 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                                       CEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEEE CS
                               SSB  42 ekdeetewhrvvvfgklaevvaeylkkGslvyveGr 77 
                                       e  +et  +r+++++ +ae ++e+l++G+ + + Gr
  gi|313127408|ref|YP_004037678.1|  96 EVADETGRIRISLWDGMAEEATENLEVGQVLRIAGR 131
                                       55688999***************************9 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.38
                                       EEEEEEEEEHHHHHHHHH CS
                               SSB  47 tewhrvvvfgklaevvae 64 
                                       t  +rv+++++ a+++ae
  gi|313127408|ref|YP_004037678.1| 208 TGRIRVTLWDDKADLAAE 225
                                       556788888888887765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.6
                                       EEEEEEEEEEEEEHHHHH CS
                               SSB  43 kdeetewhrvvvfgklae 60 
                                        ++ t  +rv+++g+ a+
  gi|313127408|ref|YP_004037678.1| 311 VKDDTGDIRVALWGEKAD 328
                                       556667789999999886 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.5
                                       HHH--TT-EEEEEEE CS
                               SSB  63 aeylkkGslvyveGr 77 
                                       +e+l+ G++v v G 
  gi|313127408|ref|YP_004037678.1| 456 SESLQLGAEVTVRGP 470
                                       455556666666665 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.002       4.4      21      78 ..      71     132 ..      58     143 .. 0.81
   2 ?    2.9   0.0     0.056   1.2e+02      40      74 ..     201     234 ..     170     252 .. 0.73
   3 ?   -2.2   0.0       2.1   4.8e+03      43      59 ..     311     327 ..     303     343 .. 0.75
   4 ?   -2.6   0.0       2.9   6.6e+03      63      78 ..     456     471 ..     446     472 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.002
                       tRNA_anti_2  21 avwvrGeisnlk...rkasg.hvYftLkDekakisavifrsraaklkftledGmkVlvkgrl 78 
                                       +v+  Ge+  ++   + + g  v ++  De+ +i++ ++ + a++ + +le G+ + ++gr+
  gi|313127408|ref|YP_004037678.1|  71 KVMSIGELRTFErddEDEDGrVVNVEVADETGRIRISLWDGMAEEATENLEVGQVLRIAGRP 132
                                       5666677777764432234447889999*******************************997 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.056
                       tRNA_anti_2  40 YftLkDekakisavifrsraaklkftledGmkVlv 74 
                                        +tL D++ +i+++++  +a  l ++++ + +V v
  gi|313127408|ref|YP_004037678.1| 201 NLTLGDSTGRIRVTLWDDKA-DLAAEFDTDITVEV 234
                                       5899999999******9776.56666666666644 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.1
                       tRNA_anti_2  43 LkDekakisavifrsra 59 
                                        kD++  i+++++ ++a
  gi|313127408|ref|YP_004037678.1| 311 VKDDTGDIRVALWGEKA 327
                                       68888889999998665 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.9
                       tRNA_anti_2  63 kftledGmkVlvkgrl 78 
                                       + +l+ G++V v+g +
  gi|313127408|ref|YP_004037678.1| 456 SESLQLGAEVTVRGPV 471
                                       3458889999998865 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.011        25      55      78 ..      92     115 ..      85     124 .. 0.91
   2 ?    3.0   0.0     0.034        76      57      77 ..     201     221 ..     198     229 .. 0.89
   3 ?    0.7   0.0      0.17   3.9e+02      57      77 ..     308     328 ..     305     343 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                                       EEEEEEE-SS-EEEEEEEHHHHHH CS
                       Rep_fac-A_C  55 ilsikvsDstgqlwvtlFneaaek 78 
                                       +++++v+D+tg+++++l++  ae+
  gi|313127408|ref|YP_004037678.1|  92 VVNVEVADETGRIRISLWDGMAEE 115
                                       689****************99986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.034
                                       EEEEE-SS-EEEEEEEHHHHH CS
                       Rep_fac-A_C  57 sikvsDstgqlwvtlFneaae 77 
                                       ++ + Dstg+++vtl++++a 
  gi|313127408|ref|YP_004037678.1| 201 NLTLGDSTGRIRVTLWDDKAD 221
                                       67899*************996 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.17
                                       EEEEE-SS-EEEEEEEHHHHH CS
                       Rep_fac-A_C  57 sikvsDstgqlwvtlFneaae 77 
                                       +i+v+D tg+++v l+ e+a 
  gi|313127408|ref|YP_004037678.1| 308 NIRVKDDTGDIRVALWGEKAD 328
                                       689**************9996 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0039       8.7     100     133 ..      96     133 ..      40     134 .. 0.77
   2 ?   -1.5   0.0      0.75   1.7e+03      68     115 ..     173     218 ..     157     225 .. 0.51
   3 ?    1.7   0.0     0.082   1.8e+02      55     101 ..     268     315 ..     263     328 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0039
                           DUF4131 100 ktkpvsgrvlvtvpkspae....glrpGdrlrltgrlk 133
                                       + ++ +gr+++++ ++ ae    +l+ G++lr+ gr+k
  gi|313127408|ref|YP_004037678.1|  96 EVADETGRIRISLWDGMAEeateNLEVGQVLRIAGRPK 133
                                       457789*******99999999**************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.75
                           DUF4131  68 eviveGvvaslpelt..gsgtrfvlevervlsagktkpvsgrvlvtvpks 115
                                       +v ++G+v+s+  ++  ++ +  + +    + +    + +gr++vt+ ++
  gi|313127408|ref|YP_004037678.1| 173 DVNLKGRVLSTDSVRtfDRDDGSEGR----VANLTLGDSTGRIRVTLWDD 218
                                       46666666554433311222233333....23334445677777777665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.082
                           DUF4131  55 nandlsqllesgqeviveG.vvaslpeltgsgt.rfvlevervlsagkt 101
                                       ++ d+++l   gq+v + G v+++ p++t +++   + +v+++  +++t
  gi|313127408|ref|YP_004037678.1| 268 ETADIASLEL-GQTVDIAGgVIETDPKRTFDRDdGSEGQVRNIRVKDDT 315
                                       5556666665.9****9999********998887777776666554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3014.92
//
Query:       gi|313127409|ref|YP_004037679.1|  [L=165]
Description: hypothetical protein Hbor_26840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1275.12
//
Query:       gi|313127410|ref|YP_004037680.1|  [L=73]
Description: hypothetical protein Hbor_26870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.028   14.6   0.1      0.028   14.6   0.1    1.1  1  FYVE_2       FYVE-type zinc finger
      0.034   14.2   0.6      0.038   14.0   0.6    1.2  1  Zn_Tnp_IS91  Transposase zinc-binding domain


Domain annotation for each model (and alignments):
>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.2e-06     0.028      51      81 ..       3      34 ..       1      59 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-06
                            FYVE_2 51 klgethCilCleefkllvnsk.rqCldCklnv 81
                                      ++++  Ci+C +++ +  + k + C dC+ + 
  gi|313127410|ref|YP_004037680.1|  3 RIQHPVCIRCGDTYLFTNSYKgNYCRDCHDEW 34
                                      567789***********9998799****9765 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   4.2e-06     0.038      41      68 ..       8      35 ..       3      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-06
                       Zn_Tnp_IS91 41 eCeeCghekivyfsCksrhCpsCqkkat 68
                                       C  Cg++ ++ +s k + C  C+ + +
  gi|313127410|ref|YP_004037680.1|  8 VCIRCGDTYLFTNSYKGNYCRDCHDEWS 35
                                      799********************97644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.31s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 473.20
//
Query:       gi|313127411|ref|YP_004037681.1|  [L=407]
Description: hypothetical protein Hbor_26880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-28   97.7   0.4    3.2e-15   55.7   0.1    2.5  2  TrkA_C         TrkA-C domain
    1.6e-18   66.9   8.4    3.4e-09   37.1   2.8    2.5  2  PhoU           PhoU domain
     0.0002   20.7   1.7       0.25   10.6   0.1    2.2  2  PhoU_div       Protein of unknown function DUF47
  ------ inclusion threshold ------
      0.033   14.5   3.9        1.3    9.4   0.0    2.5  2  CLZ            C-terminal leucine zipper domain of cyclic nuc
      0.061   13.3   2.9        1.6    8.7   0.2    2.3  2  Ribosomal_L34  Ribosomal protein L34
      0.079   13.6   5.3       0.68   10.6   0.0    3.4  4  KfrA_N         Plasmid replication region DNA-binding N-term
       0.29   11.2   0.8        1.9    8.6   0.0    2.3  2  bZIP_2         Basic region leucine zipper


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.1   1.3e-18   3.2e-15       1      67 [.     122     195 ..     122     197 .. 0.94
   2 !   39.8   0.1   1.2e-13     3e-10       1      69 [.     327     399 ..     327     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.3e-18
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T......-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRg......geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       lv+ t +a+s + G++l+++n++++ gv+v+airR+       ++++p+ +t+L+e+Dvll+ g++++++++ e
  gi|313127411|ref|YP_004037681.1| 122 LVRATAAADSDYTGRSLADINMETEtGVRVIAIRRQsvtgkrRWILNPNRETTLQENDVLLLRGPQAGIQTVFE 195
                                       689999***************************9888888888**************************99875 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 1.2e-13
                                       CEEEEEE--GGGTTSBHHHHTHHHH..S-EEEEEE-T...-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar..gvlvvairRg...geliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       +v++ v++g+ l++ tl++ ++ +   g +v+a+rR    ++++ p+++t+L+++Dv++  g++++ ++l ell
  gi|313127411|ref|YP_004037681.1| 327 IVRLHVGPGCSLANETLGD-RMVKTetGMRVIAVRRAdgrEWVVQPGPTTELKPDDVIIAKGTRAGAERLGELL 399
                                       5899***************.5555559*******999999**************************99998876 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   2.8   1.3e-12   3.4e-09       1      88 [.      17     100 ..      17     101 .. 0.89
   2 !   32.7   0.3     3e-11   7.6e-08       3      87 ..     224     304 ..     222     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.3e-12
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlER 77 
                                       l +m++++e  +d++ +a+ ++ +++arev+e+++++d l  + + sll a+  r+ +  d ++l+s+l ++   E 
  gi|313127411|ref|YP_004037681.1|  17 LAEMKDTAELLIDLSFSAVLNESDDIAREVLELEERMDVLKLQGRMSLLMAA--RSTE--DAEQLSSVLGVVGAAEK 89 
                                       679***************999988****************999999976665..3333..6789999********** PP

                                       HHHHHHHHHHH CS
                              PhoU  78 igDhavniaer 88 
                                       i+  a +ia+ 
  gi|313127411|ref|YP_004037681.1|  90 IANAAGDIAKV 100
                                       *********97 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 3e-11
                                       HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak.rqplaedlrellsllriardlERi 78 
                                        m++++e ++d+a+ ++  + ++ a+ev e++ e+d+l  ++e  +l+a+++ ++p+  +lr    l++ia+  E i
  gi|313127411|ref|YP_004037681.1| 224 LMKDMSELAVDLAYGSVLFDSEDVAEEVKELEAEVDALKSRFEAWVLRAAGRvDDPV--QLRG---LVHIASATEVI 295
                                       6***************777777****************************8878888..4666...999******** PP

                                       HHHHHHHHH CS
                              PhoU  79 gDhavniae 87 
                                       +D a +i+e
  gi|313127411|ref|YP_004037681.1| 296 SDAALEISE 304
                                       *******98 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.3   0.00025      0.64     144     206 ..      31      99 ..      10     103 .. 0.70
   2 !   10.6   0.1   9.9e-05      0.25     117     206 ..     212     304 ..     195     308 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00025
                          PhoU_div 144 alskk.....diveeieslEdeiDqlqrklikklfs.redasnplevlllveiieklenvsdraedvad 206
                                       ++s       di+ e+ +lE+++D l+ + +  l+    + +   +   +   +   e+++++a d+a+
  gi|313127411|ref|YP_004037681.1|  31 SFSAVlnesdDIAREVLELEERMDVLKLQGRMSLLMaARSTEDAEQLSSVLGVVGAAEKIANAAGDIAK 99 
                                       33322556779****************998888777466666777777788888888899999888886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9.9e-05
                          PhoU_div 117 lallkktveaiealaevieeleklleta..lskkdiveeieslEdeiDqlqrklikklfs.redasnplevlllvei 190
                                       ++ l++ v++i +++++ e    l  ++  ++ +d++ee+++lE e+D l+ +     +     +  p++   lv+i
  gi|313127411|ref|YP_004037681.1| 212 IEDLERAVDSIILMKDMSELAVDLAYGSvlFDSEDVAEEVKELEAEVDALKSRFEAWVLRaAGRVDDPVQLRGLVHI 288
                                       5555555555555555554443333333224555*****************99987666636667899999999999 PP

                          PhoU_div 191 ieklenvsdraedvad 206
                                           e++sd+a ++++
  gi|313127411|ref|YP_004037681.1| 289 ASATEVISDAALEISE 304
                                       9999999999987775 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.4     0.013        33      14      52 ..      27      67 ..      20      77 .. 0.80
   2 ?    9.4   0.0   0.00051       1.3      24      48 ..     242     266 ..     222     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                               CLZ 14 lLDeeaakagaeqkeleekverLessLeaL..qtrlarLla 52
                                      l+D ++ +  +e +++ + v +Le+++++L  q r+  L+a
  gi|313127411|ref|YP_004037681.1| 27 LIDLSFSAVLNESDDIAREVLELEERMDVLklQGRMSLLMA 67
                                      78999878889*****************8622667777776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00051
                               CLZ  24 aeqkeleekverLessLeaLqtrla 48 
                                        + +++ e v++Le++++aL+ r++
  gi|313127411|ref|YP_004037681.1| 242 FDSEDVAEEVKELEAEVDALKSRFE 266
                                       57899******************97 PP

>> Ribosomal_L34  Ribosomal protein L34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.012        32      22      36 ..     143     157 ..     142     167 .. 0.90
   2 ?    8.7   0.2   0.00064       1.6      23      39 ..     349     365 ..     345     368 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                                       HHSHHHHHHHHHHHT CS
                     Ribosomal_L34  22 mstknGrkvLkrRra 36 
                                       m+t +G +v++ Rr+
  gi|313127411|ref|YP_004037681.1| 143 METETGVRVIAIRRQ 157
                                       99***********97 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00064
                                       HSHHHHHHHHHHHTTSS CS
                     Ribosomal_L34  23 stknGrkvLkrRraKGR 39 
                                       +t +G +v++ Rra GR
  gi|313127411|ref|YP_004037681.1| 349 KTETGMRVIAVRRADGR 365
                                       7***************9 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.59   1.5e+03      64     105 ..      14      57 ..       3      64 .. 0.62
   2 ?    3.2   0.2     0.055   1.4e+02      56      83 ..     103     133 ..      66     147 .. 0.80
   3 ?   10.6   0.0   0.00027      0.68      57     110 ..     213     267 ..     184     269 .. 0.78
   4 ?   -3.1   0.1         5   1.3e+04      58      81 ..     301     325 ..     289     330 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.59
                            KfrA_N  64 aeal..laalwqaaleeaeeelaaaraelqaaraaleaeraeae 105
                                       +++l  +++ ++ + ++  +++  + ++++++  +le++ + ++
  gi|313127411|ref|YP_004037681.1|  14 KDVLaeMKDTAELLIDLSFSAVLNESDDIAREVLELEERMDVLK 57 
                                       44444446666666666666777777777777777777666554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.055
                            KfrA_N  56 a.pelPealaeal..laalwqaaleeaeeel 83 
                                       +  +lP+a+  al  +a++  +a ++a++++
  gi|313127411|ref|YP_004037681.1| 103 EdIGLPDAIRSALpeAAEMLVRATAAADSDY 133
                                       1458999999999998899989998888765 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00027
                            KfrA_N  57 pelPealaeal.laalwqaaleeaeeelaaaraelqaaraaleaeraeaearvee 110
                                       ++l  a+   + ++++ + a+++a  ++    ++++++ ++leae++++++r e+
  gi|313127411|ref|YP_004037681.1| 213 EDLERAVDSIIlMKDMSELAVDLAYGSVLFDSEDVAEEVKELEAEVDALKSRFEA 267
                                       3444445444499************************************999875 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5
                            KfrA_N  58 elPealaeal.laalwqaaleeaee 81 
                                       e++e + + + ++ + +aa+ee +e
  gi|313127411|ref|YP_004037681.1| 301 EISEGVLRGIdAHPVVAAAVEESDE 325
                                       5555555555677778888888776 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2      0.36   9.3e+02      28      45 ..      40      57 ..      37      65 .. 0.80
   2 ?    8.6   0.0   0.00073       1.9      28      49 ..     245     266 ..     242     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.36
                                      HHHHHHHHHHHHHHHHHH CS
                            bZIP_2 28 eeleervkeLeeeNaqLr 45
                                       +++++v eLee+ + L+
  gi|313127411|ref|YP_004037681.1| 40 DDIAREVLELEERMDVLK 57
                                      578899999999998884 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00073
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  28 eeleervkeLeeeNaqLrqkve 49 
                                       e+ +e+vkeLe+e ++L+ + e
  gi|313127411|ref|YP_004037681.1| 245 EDVAEEVKELEAEVDALKSRFE 266
                                       7899*************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2809.67
//
Query:       gi|313127412|ref|YP_004037682.1|  [L=105]
Description: hypothetical protein Hbor_26890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 702.80
//
Query:       gi|313127413|ref|YP_004037683.1|  [L=442]
Description: major facilitator superfamily transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-15   55.7  59.3    6.4e-09   35.2  18.7    3.0  3  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5  16.6   1.1e-08   0.00019     206     317 ..      24     140 ..       4     144 .. 0.76
   2 !    4.1  21.0     0.001        18      85     222 ..     133     277 ..     110     293 .. 0.56
   3 !   35.2  18.7   3.6e-13   6.4e-09      14     173 ..     267     434 ..     254     440 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-08
                             MFS_1 206 dpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllall 282
                                       d    +l ++++ f++gf+++  ++p y ++vlg +g + +gl+ +++ l++a+    +g++sdr+g+r +l+ +++
  gi|313127413|ref|YP_004037683.1|  24 DVL--VLSVSMFAFSLGFQMTGRYMPRY-MSVLGAGG-VAIGLYGSFGNLISAVYPYPGGAFSDRVGSRVALTAFGF 96 
                                       332..4889999999*************.*******8.99999********************************** PP

                             MFS_1 283 llllaalglallavt........ssavllll.......vlvliGfglgfv 317
                                       + ++++l+++++ ++        +      +       vl+ +G+++g+ 
  gi|313127413|ref|YP_004037683.1|  97 ASTVGFLIWLFADAFgvltvpgfT------VgpltidsVLLPVGIFVGLL 140
                                       ***********9999553333221......13333333333366665554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.001
                             MFS_1  85 lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsa....gfslGailgpllggllasslgWravfyil 157
                                       + +++ l + q++  ++++ a  a++ + +p+ + + +++   +    +f +G+++++++ +++a   g+r++  ++
  gi|313127413|ref|YP_004037683.1| 133 VGIFVGLLFAQAW-KSFGLGATFAIVKQSVPPGRLATGFASTETfrrtAFFIGPLFAAGVLAVFAFETGFRVILAVA 208
                                       3345666666666.59**********************977776333367777777777777777777899999999 PP

                             MFS_1 158 aivsllafv.lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw..............illialllf 219
                                       a+++++a v   +l+   e++  k + ++             +++ l++ p+ +               ++++++++
  gi|313127413|ref|YP_004037683.1| 209 AAFAAVATVaQHVLYDASEDSIGKSFGGIST-----------VLSDLRSMPPALrpllvgdtlvrfanGMVYVFFVI 274
                                       9999999883222333333333333333333...........34445555544221112111222234444444444 PP

                             MFS_1 220 ffg 222
                                        ++
  gi|313127413|ref|YP_004037683.1| 275 VVV 277
                                       433 PP

  == domain 3  score: 35.2 bits;  conditional E-value: 3.6e-13
                             MFS_1  14 ilgpalplalaedlg..........ispse.igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       ++++++ + + e l           +sp++ +g ll++ +++a+v+++p++ ls+rfG ++v+ lg++++a++ +ll
  gi|313127413|ref|YP_004037683.1| 267 MVYVFFVIVVVEFLEvgvtlpvvgsLSPDAfFGVLLAVEMAVALVTMVPVAKLSQRFGLKPVVALGFAVYAVFPVLL 343
                                       4444444222222223344444444333334999***************************************4444 PP

                             MFS_1  80 lfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                       + a+ +  +l+vl +++Gl   a++pa  ali+  + ++  gr++g +++  ++ +i  +++gg+l+ s     +f+
  gi|313127413|ref|YP_004037683.1| 344 INAPDSAlVLAVLFAFSGLRF-AGLPAHKALIVGPAEENAGGRVVGSYYLVRNVVTIPSAVVGGWLY-SNDPKTAFL 418
                                       435777778999999999986.9********************************************.669****** PP

                             MFS_1 156 ilaivsllafvlfllllp 173
                                       ++++v+l++     +l++
  gi|313127413|ref|YP_004037683.1| 419 LATAVGLIGTGY--FLVF 434
                                       *********554..4443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3051.26
//
Query:       gi|313127414|ref|YP_004037684.1|  [L=318]
Description: deacylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-58  195.9   0.0    8.5e-58  195.7   0.0    1.0  1  AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase f


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.7   0.0   4.7e-62   8.5e-58       1     289 [.      42     312 ..      42     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: 195.7 bits;  conditional E-value: 4.7e-62
                                       SS-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSSTT-S-CTTTTTCCCCCSSTC CS
                         AstE_AspA   1 sgpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyipidredLNRaFpgrslgrsld 77 
                                       +g++++++A+ +G+El+Gv ++++l  ql++ +++g+i++v ++N+ A++ ++++ pid++ +NRa+pg+++g    
  gi|313127414|ref|YP_004037684.1|  42 DGKTLYLQAASDGDELNGVGVIQRLFPQLDPTELSGQILIVGIVNYHAFQVAQHRNPIDDTKMNRAYPGDENG---- 114
                                       59***********************************************************************.... PP

                                       HHHHHHHHHHHHHHHCHCTCCCGCEEEEEEEESSTBCCSSEEEE---SSHHHH...HHHHHHTTTSEEEEEESS--S CS
                         AstE_AspA  78 ealrateaerladalfaaalpeadivlDLHtgtrglkhllfaeadiaeaqlqs...lallkalglpavllldekesa 151
                                            t+ er+a a f+aa  +ad++lDLH+g ++ +++  +++++ +++  +   l+l+k++g ++vl  d+k+++
  gi|313127414|ref|YP_004037684.1| 115 -----TSSERIAAATFDAA-RRADLILDLHQGSTS-QMIDEVRVRCGRHHRLHsecLQLAKTFGCGYVL--DQKGPD 182
                                       .....***********999.7*********98765.699999999998887777***************..****** PP

                                       SHHHHHHHHCTSEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT-SCC.CEEEEEEEEEEGGSCCCSSCSE CS
                         AstE_AspA 152 gfletaaeelgalaftlElGgagrlgaedisrtakgvlnvlahigvvagqeavepaklyrvlreldeprdiraeeaG 228
                                       g+l++aa   g++++ +ElGg+  +++e+i++ ++gv nvl+ +g+++g+     ++  r+   ++  +++ a+ +G
  gi|313127414|ref|YP_004037684.1| 183 GQLARAAPDEGIPTVDPELGGCVGWDEESIQKGVRGVYNVLRGYGFIDGS-----VETERQ-TRAKGFDQYGAPTGG 253
                                       **************************************************.....444554.457788889****** PP

                                       EECCCCSTTTTETCTEEEETTEEEEECTSTEEEEESSSSEEEESCCTSCCTTTTEEEEEEE CS
                         AstE_AspA 229 lvefkvklgddveagellakalvldslggekvelrapqdgvivfineaalvekgaalvkva 289
                                       lv fk  lg++v ag+++  + ++d +gg k++++a+ +g+++  ++ ++v+ g+ ++ v+
  gi|313127414|ref|YP_004037684.1| 254 LVRFKKSLGEQVSAGDVV--FEITDVFGGLKARVTADNTGIFWRSRRLPQVATGEYVCSVG 312
                                       ******************..**************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2354.82
//
Query:       gi|313127415|ref|YP_004037685.1|  [L=363]
Description: l-threonine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-59  202.0   1.5    1.5e-59  201.8   1.5    1.0  1  PALP          Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
        1.1    9.0   6.1        2.1    8.1   6.1    1.5  1  Rubredoxin_2  Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.8   1.5   1.7e-63   1.5e-59       1     294 []      68     358 ..      68     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 201.8 bits;  conditional E-value: 1.7e-63
                                       GGGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   1 ltlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       +tlg+g TPlv++p           +KlE+  ptgSfKdRga+  l+ ++e  g + vve ssGN+g+a+A +aa++
  gi|313127415|ref|YP_004037685.1|  68 VTLGEGMTPLVDAPEWD------AAFKLEYVFPTGSFKDRGATTTLSVATEL-GIEKVVEDSSGNAGAAIATYAARA 137
                                       5899***********98......889**************************.************************ PP

                                       T-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHT CS
                              PALP  78 GlkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileql 154
                                       G+++ i+vpa+++++k++++++ Ga+ v+v+g+ ++  +a+ e+ ++g+g+y  + + np+ ++g +t ++E++ q 
  gi|313127415|ref|YP_004037685.1| 138 GIDADIYVPASVKAAKLRAIERAGATPVRVEGSREDVTDACLEAVEDGDGWYASHAW-NPAFFAGTATFAYEVAYQR 213
                                       ***********************************************8888888888.9***************999 PP

                                       T.TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS. CS
                              PALP 155 g.gkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarslragrrvtvpvsdtiadglavg. 223
                                       g  +pdavv p+G G l+ G ++g+++    ++ d  ++++g++++g +++a+ l    + +++ ++  adg++++ 
  gi|313127415|ref|YP_004037685.1| 214 GwSAPDAVVTPLGHGTLFLGAYRGFRAlrdaGWIDemPKLLGAQAAGYAPVAEEL----HGPTEGTNDVADGIQIRd 286
                                       99*************************7665555599******************....77888889*********8 PP

                                       .CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 224 .spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                        +  ++ ++++d++ +++++++++++   + +l+ r g  +ep++a+a aal + re+g l+++d+vvv ltg
  gi|313127415|ref|YP_004037685.1| 287 pTRLDQILDAVDATDGDAIALTEDAVETELDRLH-RRGFYTEPTCAVAPAALgEYRERGVLSDDDDVVVPLTG 358
                                       88888899**************************.9**********************************998 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.1   0.00024       2.1       2      18 ..       9      26 ..       9      29 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00024
                      Rubredoxin_2  2 vCsqCGfes.akwfGrCp 18
                                      +Cs+CG ++  +w +rC 
  gi|313127415|ref|YP_004037685.1|  9 RCSACGETYeTAWAWRCD 26
                                      8*******9357*****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2647.90
//
Query:       gi|313127416|ref|YP_004037686.1|  [L=82]
Description: hypothetical protein Hbor_26930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-14   52.1   6.6    8.9e-13   48.1   6.6    2.0  1  DUF2892          Protein of unknown function (DUF2892)
  ------ inclusion threshold ------
      0.026   14.8   0.6      0.028   14.7   0.6    1.0  1  DUF1772          Domain of unknown function (DUF1772)
       0.99    9.4   2.5        1.1    9.2   2.5    1.1  1  DUF1676          Protein of unknown function (DUF1676)
          3    7.3   6.1        3.1    7.3   6.1    1.0  1  SseC             Secretion system effector C (SseC) like fami


Domain annotation for each model (and alignments):
>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   6.6     2e-16   8.9e-13       1      64 [.       1      75 [.       1      77 [. 0.93

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2e-16
                           DUF2892  1 MkkNvgtldRilrivvGlvllllallglsggw...........gwllglvGavllltgltgfCplyallgintck 64
                                      M+kNvg+ dRi+r+vvG +l+++++++++g +           +  +++vGavll tglt  Cpl  ++g++t +
  gi|313127416|ref|YP_004037686.1|  1 MEKNVGGYDRIARLVVGPLLVIVGAAAVAGLFtiaagtlglvlAGGALVVGAVLLTTGLTQKCPLNDVIGMDTYR 75
                                      9***************************99999******9888666789*********************99965 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.6   6.3e-06     0.028      37      85 ..      15      60 ..       7      80 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-06
                           DUF1772 37 avfpplallsalafaylaaraasrgarllylaaaallllsivpyTllvm 85
                                      +v p+l+++ a+a+a l+    ++g+ +l+ +a+++l+++ v++T  + 
  gi|313127416|ref|YP_004037686.1| 15 VVGPLLVIVGAAAVAGLF--TIAAGTLGLV-LAGGALVVGAVLLTTGLT 60
                                      345668888999999677..5677888888.668888889898887766 PP

>> DUF1676  Protein of unknown function (DUF1676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.5   0.00025       1.1     122     162 ..      13      55 ..       3      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00025
                           DUF1676 122 kkmllplllalk.lklklLlplalgllal.lagKALllgklaL 162
                                       +  ++pll+++  + ++ L+ +a g l+l lag AL++g ++L
  gi|313127416|ref|YP_004037686.1|  13 RLVVGPLLVIVGaAAVAGLFTIAAGTLGLvLAGGALVVGAVLL 55 
                                       46789****9999**************9746999****99987 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.1    0.0007       3.1      62     112 ..      15      66 ..      11      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0007
                              SseC  62 IfGwilaiv..svvagalkvgaslllaavgvAgglmdaa.lgiadevvaaattk 112
                                       ++G +l iv  + vag ++++a+ l   + +Agg+++++ +  +    +++  +
  gi|313127416|ref|YP_004037686.1|  15 VVGPLLVIVgaAAVAGLFTIAAGTLG--LVLAGGALVVGaVLLTTGLTQKCPLN 66 
                                       66777777633679*********999..9999999***9755555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 641.17
//
Query:       gi|313127417|ref|YP_004037687.1|  [L=251]
Description: protein-l-isoaspartate carboxylmethyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-35  120.3   0.0    1.1e-34  120.0   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.6e-06   27.8   0.1    2.5e-06   27.1   0.1    1.2  1  MTS              Methyltransferase small domain
      8e-06   26.5   0.0    1.6e-05   25.5   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    0.00014   21.6   0.0     0.0002   21.2   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0025   17.0   0.1     0.0036   16.5   0.1    1.1  1  Fibrillarin      Fibrillarin
     0.0041   16.6   0.1     0.0056   16.1   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.005   17.6   0.0       0.01   16.6   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.023   14.4   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.039   13.0   0.0       0.05   12.7   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.042   13.3   0.0      0.065   12.6   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
      0.063   13.0   0.0       0.08   12.7   0.0    1.2  1  Met_10           Met-10+ like-protein
        0.1   11.9   0.1       0.18   11.1   0.1    1.4  1  HEM4             Uroporphyrinogen-III synthase HemD
       0.13   12.2   0.0       0.21   11.6   0.0    1.2  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   0.0     8e-38   1.1e-34      12     202 ..      15     195 ..       6     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 8e-38
                                       HTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHH CS
                              PCMT  12 kkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGylt 88 
                                       ++g+ + + va a+++v+R+efv++    ++Y++ + + + ++t+ +p  va++l  l+ ++ + vL vG+G Gy +
  gi|313127417|ref|YP_004037687.1|  15 EHGMDVAESVALAMRTVPRHEFVED----APYQNRASKFE-GSTVLSPANVARLLTALSAEPDEDVLIVGAGVGYTA 86 
                                       5788999******************....9******9765.789999****************************** PP

                                       HHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTEEE CS
                              PCMT  89 avlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQLke 165
                                       a++a++vg++  v +++  ++lv +a+ nl+  +++ v v + DG  G +e+aP+d+i+v aaa e P+ l+ QL++
  gi|313127417|ref|YP_004037687.1|  87 ALVAEIVGDTH-VHAVDIDRRLVYAARSNLQSVESAAVLVDCRDGADGLPEYAPFDRILVEAAAIEPPNRLVSQLEP 162
                                       ********987.99999999********************************************************* PP

                                       EEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE-- CS
                              PCMT 166 GGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrf 202
                                        Grlv P+g   +Q+l  vd  +  +v ++k   v+f
  gi|313127417|ref|YP_004037687.1| 163 DGRLVFPMG-GPKQTLVSVDAAG--EV-VEKHGPVAF 195
                                       *********.9*****9999776..33.344455555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   1.8e-09   2.5e-06      23      94 ..      63     135 ..      58     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.8e-09
                                       HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST CS
                               MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve 94 
                                       Ll++l++e +++vl +G+G+G+ +a +a+   +++v++vd+d r + +a+ nl++ + + v v  +d+ + ++
  gi|313127417|ref|YP_004037687.1|  63 LLTALSAEPDEDVLIVGAGVGYTAALVAEIVGDTHVHAVDIDRRLVYAARSNLQSVESAaVLVDCRDGADGLP 135
                                       8999****99********************************************9888745555667776665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.2e-08   1.6e-05       1      72 [.      75     147 ..      75     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.2e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.TTTTEEEEESBCCGBSSSTTTEEEEEEES CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee.eglnvefvqgdaedlpfedgsfDlvvssg 72 
                                       vL +G+G G +++ +a+ +g+ +v++vDi+ +++ aar+++++ e++ v + + d  d   e + fD +++  
  gi|313127417|ref|YP_004037687.1|  75 VLIVGAGVGYTAALVAEIVGDTHVHAVDIDRRLVYAARSNLQSvESAAVLVDCRDGADGLPEYAPFDRILVEA 147
                                       789**************99**********************875555777777777774457789**999843 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.5e-07    0.0002       6      83 ..      74     148 ..      69     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.5e-07
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81 
                                        vl +G+G G+ +   a e+  + +v+ +Di+ + +  Ar+n+q+ ++  v +   d  + l++    ++fD il  
  gi|313127417|ref|YP_004037687.1|  74 DVLIVGAGVGYTAALVA-EIVGDTHVHAVDIDRRLVYAARSNLQSVESAAVLVDCRDGADgLPEY---APFDRILVE 146
                                       56779************.88889****************************************63...68**99886 PP

                   Methyltransf_31  82 ev 83 
                                       ++
  gi|313127417|ref|YP_004037687.1| 147 AA 148
                                       54 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.6e-06    0.0036      58     107 ..      59     107 ..      52     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-06
                                       HHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                       Fibrillarin  58 ailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                        + + l+ l  ++++ vL +Ga+ G t++ v++ivg +  v+av+   r 
  gi|313127417|ref|YP_004037687.1|  59 NVARLLTALSAEPDEDVLIVGAGVGYTAALVAEIVG-DTHVHAVDIDRRL 107
                                       566778889999************************.899****988775 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1     4e-06    0.0056     160     211 ..      70     122 ..      60     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-06
                              PrmA 160 kegeevlDvGtGSGiL.aiaaakLgakkvvavDiDevAvkvakeNaelNkvea 211
                                       +++e vl vG+G G   a++a  +g  +v+avDiD   v +a++N++  + +a
  gi|313127417|ref|YP_004037687.1|  70 EPDEDVLIVGAGVGYTaALVAEIVGDTHVHAVDIDRRLVYAARSNLQSVESAA 122
                                       67899*********75279999***********************98765555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.4e-06      0.01       1      70 [.      76     143 ..      76     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.4e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlv 70 
                                       L +G+G+G +++ ++e   d+++++vDi+++ + +a+  l++ e      v ++ +d +d  ++ + fD +
  gi|313127417|ref|YP_004037687.1|  76 LIVGAGVGYTAALVAEIVGDTHVHAVDIDRRLVYAARSNLQSVES-A--AVLVDCRDGADGLPEyAPFDRI 143
                                       569***********9999***************777777777664.3..3333444444444444566655 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.6e-05     0.023       2      87 ..      65     147 ..      64     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg. 77 
                                       ++L  +++e +l + a+ G   +++ae++    +v Avd++++ + +  +nl+ +    + v + D+      l + 
  gi|313127417|ref|YP_004037687.1|  65 TALSAEPDEDVLIVGAGVGYTAALVAEIVG-DTHVHAVDIDRRLVYAARSNLQSVESAAVLVDCRDGADG---LPEy 137
                                       5789999*********************65.568********9999999****99999777766666654...3333 PP

                                       ..EEEEEEEE CS
                   Methyltr_RsmB-F  78 elfDriLlDa 87 
                                       + fDriL++a
  gi|313127417|ref|YP_004037687.1| 138 APFDRILVEA 147
                                       56******98 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.6e-05      0.05      16      74 ..      57     117 ..      43     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTTT CS
                            RrnaAD  16 kkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkklsk 74 
                                       +  +++ l +l  e++  vl +g+G+G + + +a+++   +v ++ +d+rL+   + +l++
  gi|313127417|ref|YP_004037687.1|  57 PANVARLLTALSAEPDEDVLIVGAGVGYTAALVAEIVgdTHVHAVDIDRRLVYAARSNLQS 117
                                       45566778888889************************88888*********998887774 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.7e-05     0.065      18      86 ..      71     134 ..      62     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.7e-05
                                       ST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEESTCHHHH CS
                    Spermine_synth  18 npkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgdgfkfl 86 
                                         ++vLi+G g G ++  v      ++++ vdiD+  +   +++l+s++        v +   dg   l
  gi|313127417|ref|YP_004037687.1|  71 PDEDVLIVGAGVGYTAALVAEIVGDTHVHAVDIDRRLVYAARSNLQSVESA-----AVLVDCRDGADGL 134
                                       4789*********9999999988889*******************998876.....4445555555555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.8e-05      0.08      97     146 ..      68     117 ..      56     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-05
                                       T--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHH CS
                            Met_10  97 lveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkenikl 146
                                        +e++e V+ v AG+G+ a  +a    +  v a+d++ + v   ++n++ 
  gi|313127417|ref|YP_004037687.1|  68 SAEPDEDVLIVGAGVGYTAALVAEIVGDTHVHAVDIDRRLVYAARSNLQS 117
                                       3899********************************98766666666544 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00013      0.18     129     204 ..       7      81 ..       4      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                       -HHHHHHHHHTTEEEEEE-SEEE..EE-HHHHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HHHHHCTSEEEEE CS
                              HEM4 129 rddlaegLeergaevdevevYet..vpaeeepeelkealkagevdavvftSpstvrnllellkdegdelkevkvaai 203
                                       r+d+++gL e+g++v e ++     vp++e++e++  + +a+++++ ++ Sp  v++ll +l+ e  + ++v ++  
  gi|313127417|ref|YP_004037687.1|   7 REDMVDGL-EHGMDVAESVALAMrtVPRHEFVEDAPYQNRASKFEGSTVLSPANVARLLTALSAE--PDEDVLIVGA 80 
                                       78999999.7999*999987655449999**********************************87..8888877765 PP

                                       S CS
                              HEM4 204 G 204
                                       G
  gi|313127417|ref|YP_004037687.1|  81 G 81 
                                       5 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.21      13      77 ..      60     121 ..      56     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                   Methyltransf_32  13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkk 77 
                                       va+ll+   +++++++v+ vGaG gY +  +a       ++v+++d+ ++lv +a+   + ++++
  gi|313127417|ref|YP_004037687.1|  60 VARLLTA-LSAEPDEDVLIVGAGVGYTAALVAE--IVGDTHVHAVDIDRRLVYAARSNLQSVESA 121
                                       5565665.46777889999*******9999998..5579*************9999988888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2086.26
//
Query:       gi|313127418|ref|YP_004037688.1|  [L=159]
Description: hypothetical protein Hbor_26960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1228.21
//
Query:       gi|313127419|ref|YP_004037689.1|  [L=218]
Description: hypothetical protein Hbor_26970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.011   15.8   1.2      0.023   14.8   1.2    1.5  1  DUF2387          Probable metal-binding protein (DUF2387)
        0.1   12.7   2.4       0.14   12.2   1.8    1.6  2  Elf1             Transcription elongation factor Elf1 like
       0.12   12.2   1.0       0.28   11.0   1.0    1.7  1  zinc_ribbon_5    zinc-ribbon domain
       0.13   12.2   4.5       0.56   10.2   4.6    2.0  1  zinc_ribbon_4    zinc-ribbon domain
       0.24   11.8   1.2        0.6   10.5   1.2    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.33   10.7   4.2        2.2    8.1   0.1    2.7  2  zf-CSL           CSL zinc finger
        0.7    9.7   3.8        2.7    7.8   2.6    2.3  2  Zn_Tnp_IS1       InsA N-terminal domain


Domain annotation for each model (and alignments):
>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.2     9e-06     0.023       9      59 ..      10      61 ..       7      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9e-06
                           DUF2387  9 avCPrCsemD.ki.rmweedeveyrECvsCgftdelsekgqsvakelktrvnk 59
                                      + CP Cs    ++  + +  ++  + C++C+++ + + + +++ +e +  v +
  gi|313127419|ref|YP_004037689.1| 10 VACPSCSPAEeTVhEVLKTGGQATVRCTECSHVHKVRIE-TEQEVEKQVIVSQ 61
                                      57*****88844424778888**************9999.5555555555544 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.8   5.6e-05      0.14      23      60 ..      11      48 ..       4      59 .. 0.83
   2 ?   -3.6   0.0       4.8   1.2e+04      32      44 ..     128     140 ..     125     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                              Elf1 23 dCpfCnheksvevkldkkekiaevsCkvCgesfetkvn 60
                                       Cp C+  +    ++ k+ + a+v+C+ C+   +++++
  gi|313127419|ref|YP_004037689.1| 11 ACPSCSPAEETVHEVLKTGGQATVRCTECSHVHKVRIE 48
                                      6****987776677788889**********98888775 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
                              Elf1  32 svevkldkkekia 44 
                                       sv+v+++ ke+++
  gi|313127419|ref|YP_004037689.1| 128 SVNVTVNPKEGTG 140
                                       7889998888876 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0   0.00011      0.28       3      36 ..      10      44 ..       8      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                     zinc_ribbon_5  3 irCpdCdtkFklvdsklKksg.kkVrCakCaevFd 36
                                      + Cp C      v + lK  g   VrC  C +v  
  gi|313127419|ref|YP_004037689.1| 10 VACPSCSPAEETVHEVLKTGGqATVRCTECSHVHK 44
                                      579999999999999999865168********975 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.6   0.00022      0.56       3      34 ..      10      42 ..       9      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                     zinc_ribbon_4  3 itCpsCkakyeiddeklp.akgvkvrCskCghv 34
                                      + CpsC+ + e   e l+ ++ + vrC+ C+hv
  gi|313127419|ref|YP_004037689.1| 10 VACPSCSPAEETVHEVLKtGGQATVRCTECSHV 42
                                      789***97777777778835666*********8 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.2   0.00023       0.6       5      54 ..      11      57 ..       9      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigq.cvyCadCgastpwfkiaedeaeaekea 54
                                       CP C  +++ +++ +++ +  q +v C++C     +  ++e e+e ek++
  gi|313127419|ref|YP_004037689.1| 11 ACPSCSPAEETVHEVLKTGG--QaTVRCTECSH--VHKVRIETEQEVEKQV 57
                                      5*****99999999888864..44*******99..4555555555655555 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.7     0.027        68      42      51 ..       7      16 ..       2      18 .. 0.81
   2 ?    8.1   0.1   0.00084       2.2      39      57 ..      27      46 ..      17      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.027
                                      --EEEETTSS CS
                            zf-CSL 42 evvvqCssCS 51
                                       + v C+sCS
  gi|313127419|ref|YP_004037689.1|  7 RIAVACPSCS 16
                                      57799****9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00084
                                      ....--EEEETTSSEEEEEE CS
                            zf-CSL 39 e.gaevvvqCssCSLwikVk 57
                                      + g++  v+C++CS + kV+
  gi|313127419|ref|YP_004037689.1| 27 KtGGQATVRCTECSHVHKVR 46
                                      2478999*******999997 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.6     0.001       2.7       5      34 ..       9      39 ..       7      40 .. 0.83
   2 ?   -0.2   0.0      0.34   8.7e+02      17      21 ..     185     189 ..     180     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                        Zn_Tnp_IS1  5 sihCPrCsstd.VyRhGkstagHeRfrCrdC 34
                                       + CP+Cs ++  + +   t g    rC +C
  gi|313127419|ref|YP_004037689.1|  9 AVACPSCSPAEeTVHEVLKTGGQATVRCTEC 39
                                      799*****99888888888888888888888 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.34
                        Zn_Tnp_IS1  17 yRhGk 21 
                                       yRhGk
  gi|313127419|ref|YP_004037689.1| 185 YRHGK 189
                                       9***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1590.88
//
Query:       gi|313127420|ref|YP_004037690.1|  [L=331]
Description: leucyl aminopeptidase (aminopeptidase t) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-11   41.2   0.2      2e-09   36.8   0.1    2.0  2  Peptidase_M29  Thermophilic metalloprotease (M29)


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   0.0    0.0029        53       2      46 ..      16      60 ..      15      72 .. 0.87
   2 !   36.8   0.1   1.1e-13     2e-09     200     348 ..     152     295 ..     134     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0029
                                      HHHHHHHHHHHHHTTT---TT-EEEEEEETT-HHHHHHHHHHHHH CS
                     Peptidase_M29  2 eeklekyAellvkvglnlqkgqevvinaevealelarlvaeeayk 46
                                      + +l+  Ae +v  ++nl ++++ v+ ++ + l   +++++ a +
  gi|313127420|ref|YP_004037690.1| 16 DAELRAAAETAVVQCMNLAPDESCVVVTDDKRLAIGEALYDVASE 60
                                      5689999**********************9999999999887766 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 1.1e-13
                                       HHTT-SEEEEE.ETTEEEEEEE-TTB--EESS---SSS----SBSS---EEE-EEEEEEEEEEE-SS-EEETTEEEB CS
                     Peptidase_M29 200 nelkfkeLhyksspgtdLtvglaeghiWiggaektkkgiefvaNiPteevftaPdkrgvnGvvratkPlsysGnlie 276
                                       +e   +e+++++  gtd+t +   ++ W++ ++   ++   ++N+P +evf++P+  ++nG+++ +  ++ +  l e
  gi|313127420|ref|YP_004037690.1| 152 TE--AEEIRVTTPSGTDITFEP-GSRDWLADTGIV-HEAGGFSNLPAGEVFVSPE--NANGTYVVDGTMMPHALLEE 222
                                       44..899**************9.999******996.8888999***********7..57899998887777766655 PP

                                       S..-EEEEETTEEEEEE-SB-HHHHHH.HTTSSSGGGSEEEEE---TTSHHHHHT-----HHHHHT..TS-EEEEE- CS
                     Peptidase_M29 277 g..irltFedGkvveakAekGeevLkk.lletDegarrLGEvALvpndspisqsgilfyntLfDen..ascHlAlGa 348
                                       g  +r+++edG v+e++ +   + +++   e+  +a  L E+ +++n   +++   l+ ++L+De+  +++H+A+G+
  gi|313127420|ref|YP_004037690.1| 223 GqeLRFEVEDGYVTEISDDDVRKQIEAgAEEVGRDAYNLAELGIGTNV-GVDE---LVGSVLLDEKaaGTVHIAIGD 295
                                       511666678*******987766666651557899*************9.9999...**********9999******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2460.35
//
Query:       gi|313127421|ref|YP_004037691.1|  [L=358]
Description: glyceraldehyde-3-phosphate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-19   67.9   0.0    1.2e-18   67.2   0.0    1.4  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
    1.8e-08   34.6   0.1    4.1e-08   33.4   0.1    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    4.9e-05   23.6   0.1     0.0011   19.3   0.0    2.7  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
    4.9e-05   24.0   0.0    0.00035   21.2   0.0    2.2  2  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
     0.0071   15.7   0.2      0.056   12.8   0.1    2.1  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.088   13.1   0.0       0.27   11.5   0.0    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.13   12.7   0.0       0.35   11.3   0.0    1.7  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
       0.13   12.4   0.0        0.2   11.8   0.0    1.3  1  DUF4143          Domain of unknown function (DUF4143)


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.0   5.5e-22   1.2e-18       1     157 [.     142     295 ..     142     296 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 5.5e-22
                                       HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEE CS
                           Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldgl 75 
                                       L +++  l +++g++k+++t+v++  ++          +  r++++   +n+i ++++++++v++++p+    +d+l
  gi|313127421|ref|YP_004037691.1| 142 LSRIIAPLREEYGVEKVRATLVRRGGDP---------GQNSRGPINDilPNPISIPSHHGPDVNTIFPD--LAIDTL 207
                                       6799************************.........7889*****999*******************7..5799** PP

                                       EEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEE CS
                           Gp_dh_C  76 AvrVPtpnvsvvdlvvelekevtveevnaalkeaae....galkgilsyteeelvssDlvgdph..ssifdaketiv 146
                                        ++VP + ++v++l v+le++vt++ v ++l+ +++     +  gi +  + + ++ D  + +    ++ ++ e+i+
  gi|313127421|ref|YP_004037691.1| 208 GLKVPATLMHVHSLNVTLEDDVTAAHVRQLLESESRvyviPEGLGIDGAGKLKDFALDAGRPRGdlWENCVWGESIA 284
                                       ************************************9998778899999999******99988778999******** PP

                                       ETTTEEEEEEE CS
                           Gp_dh_C 147 veenlvkvvaw 157
                                       ve+++++++++
  gi|313127421|ref|YP_004037691.1| 285 VEGRDLYLFQA 295
                                       *9999999886 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   1.8e-11   4.1e-08       4      91 ..       2      98 ..       1     118 [. 0.83

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.8e-11
                                      EEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH............HHSSSS--S-BEBSSHHHHHHH-SE CS
                            DapB_N  4 avvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag............ellglgklgvavtddleevlekadv 70
                                      +v+G+ G++Gk+v++av++++d+e+ ++ ++++ ++e++ a             ++  +++ g+ v+  ++e++++ad+
  gi|313127421|ref|YP_004037691.1|  2 GVNGY-GTIGKRVADAVDAQPDMEVIGVAKTQP-NFEAHTAVkrgypmyaaipeRMPLFSEAGIDVEGAVDEMVADADI 78
                                      79**9.*************************99.45544444555********5555555******************* PP

                                      EEE-S-HHHHHHHHHHHHHTT CS
                            DapB_N 71 liDFTtpeavlenlklalekg 91
                                      ++D T p+++ +  k+++e++
  gi|313127421|ref|YP_004037691.1| 79 VVDCT-PSGIGAENKALYESH 98
                                      *****.999888888888764 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.8e-07    0.0011       4      35 ..       2      33 ..       1      54 [. 0.85
   2 ?    1.0   0.1      0.23   5.2e+02      86      96 ..      74      84 ..      59      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.8e-07
                                      EEESTSHHHHHHHHHHHHHTTCEEEEEE-TS- CS
                           Gp_dh_N  4 ainGfGRIGrlvlralleekelevvaindltd 35
                                      ++nG+G IG+ v+ a+ +++++ev+ + ++  
  gi|313127421|ref|YP_004037691.1|  2 GVNGYGTIGKRVADAVDAQPDMEVIGVAKTQP 33
                                      89*************************99543 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.23
                                      HTSSEEEE-SS CS
                           Gp_dh_N 86 lgvdlVvestG 96
                                      +++d+Vv++t 
  gi|313127421|ref|YP_004037691.1| 74 ADADIVVDCTP 84
                                      589*******7 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.6e-07   0.00035       1      70 [.       5      86 ..       5      93 .. 0.88
   2 ?   -0.6   0.0       0.9     2e+03      76      95 ..     292     311 ..     287     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                      --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT................HHHHHT--CB---HHHHHHHHS-EE CS
                     NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd................rkallasealtldlddliahldpdv 62
                                      G+G+iG++v++++++q++   +e+ +va+ +   +++                 ++   a  ++   +d+++a  d+d+
  gi|313127421|ref|YP_004037691.1|  5 GYGTIGKRVADAVDAQPD---MEVIGVAKTQpNFEAHTavkrgypmyaaipermPLFSEAGIDVEGAVDEMVA--DADI 78
                                      9****************6...8*********555555599******999999887778888899999999999..**** PP

                                      EEE-S--H CS
                     NAD_binding_3 63 vVEcasse 70
                                      vV+c++s 
  gi|313127421|ref|YP_004037691.1| 79 VVDCTPSG 86
                                      *****975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.9
                                       HHHHHHTTEEEE-S--CGGG CS
                     NAD_binding_3  76 vlkaLkagkdvvtankgala 95 
                                       + +a+ +  dv+  n++a+ 
  gi|313127421|ref|YP_004037691.1| 292 LFQAIHQESDVIPENVDAIR 311
                                       46899999********9986 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   2.5e-05     0.056      39      73 ..       1      36 [.       1      49 [. 0.82
   2 ?    0.7   0.0      0.13     3e+02      77     100 ..      60      84 ..      37      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                      EEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlk.afgmkviaydrskkkee 73
                                      +G+ G+G IG++va+ +  + +m+vi++ +++ + e
  gi|313127421|ref|YP_004037691.1|  1 MGVNGYGTIGKRVADAVDaQPDMEVIGVAKTQPNFE 36
                                      699**************9788*******99966433 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.13
                                       HHTCEEC.SHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  77 elgvelv.sleellaesDivslhlp 100
                                       e g++++  ++e++a++Div+ ++p
  gi|313127421|ref|YP_004037691.1|  60 EAGIDVEgAVDEMVADADIVVDCTP 84 
                                       5566555589**********98877 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.27       5      79 ..       5      85 ..       1      91 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                      --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...........TTTCEEEEE--TTTHHHHHHHHHTTSSE CS
                   Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaaka...........lgvrfeaialdaenyeavLaallkegdl 72
                                      G+G +G+ va+ + ++ d+  e++ + +++ + ea  a +           + + f+ + +d+e     ++++++++d+
  gi|313127421|ref|YP_004037691.1|  5 GYGTIGKRVADAVDAQPDM--EVIGVAKTQPNFEAHTAVKrgypmyaaipeRMPLFSEAGIDVEGA---VDEMVADADI 78
                                      9*****************9..555555555555655555569999999877777777777777654...66******** PP

                                      EEE-SSG CS
                   Sacchrp_dh_NADP 73 vvnlspp 79
                                      vv+++p+
  gi|313127421|ref|YP_004037691.1| 79 VVDCTPS 85
                                      ****985 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.35       9      84 ..       7      93 ..       2     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                      SHHHHHHHHHHHCTSSEEEEEEEESTT..TTTSBHHHHSG.........GGTTTECEBEEEGGGGGCTT-SEEEE-SCH CS
                    Semialdhyde_dh  9 GyvGqellrlLeehpevelvvllsssr..saGkklaeavk.........aleegkdlkvedvdeeelkevdivflalpa 76
                                      G +G++++  ++ +p++e++ ++ ++   +a +++++ ++          l +++ + ve + +e ++++div+ ++p+
  gi|313127421|ref|YP_004037691.1|  7 GTIGKRVADAVDAQPDMEVIGVAKTQPnfEAHTAVKRGYPmyaaipermPLFSEAGIDVEGAVDEMVADADIVVDCTPS 85
                                      8899999999999999999999988888888899999998999999987667778888888889999************ PP

                                      HHHHHHHH CS
                    Semialdhyde_dh 77 gvskelap 84
                                      g+ +e  +
  gi|313127421|ref|YP_004037691.1| 86 GIGAENKA 93
                                      *9887655 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.9e-05       0.2      37     108 ..     238     305 ..     183     315 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.9e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  37 lrkspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvie 108
                                       l++  ++y++  GL +  +g+ k++ l+    +G l+En V  e ++   +eg +ly ++    +E D++ e
  gi|313127421|ref|YP_004037691.1| 238 LESESRVYVIPEGLGIDGAGKLKDFALDAGRPRGDLWENCVWGESIA---VEGRDLYLFQAI-HQESDVIPE 305
                                       788999***********99999*************************...8899***99974.789888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2696.97
//
Query:       gi|313127422|ref|YP_004037692.1|  [L=162]
Description: phosphoesterase, mj0936 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-34  119.8   0.6    1.5e-34  119.6   0.6    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.3e-07   31.5   4.9    0.00011   22.8   1.3    2.2  2  Metallophos    Calcineurin-like phosphoesterase
     0.0044   16.4   0.0       0.11   11.8   0.0    2.0  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.6   0.6   2.5e-38   1.5e-34       1     164 [.       1     154 [.       1     155 [. 0.91

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 2.5e-38
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaael 77 
                                       M+++i SD+H+nl++ + v+e ++++gv+++ih+GD+  ++p + + + + ++++aVrGNnD    e+ +++    +
  gi|313127422|ref|YP_004037692.1|   1 MRVGICSDTHDNLELARGVVETFESAGVETVIHCGDI--VSPFTANVFDADFDFHAVRGNND---GEWNLSNVVDSF 72 
                                       9************************************..***7777777777**********...8999******** PP

                     Metallophos_2  78 gtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGsvgeprdgd 153
                                       gt++ e a+++++g+ v+ +Hg+    ++ l + l e  +g++ +v+ GHtH+++ ek g++++vnPG +  p  +d
  gi|313127422|ref|YP_004037692.1|  73 GTYHGECATFDFDGTAVAAYHGT----SETLVDGLVE--SGDYdYVFRGHTHQRTYEKSGETVHVNPGGLPIPGADD 143
                                       **********************9....4555555555..33333********************************* PP

                     Metallophos_2 154 petyaildtde 164
                                       + ++a+ld+de
  gi|313127422|ref|YP_004037692.1| 144 TYHVALLDVDE 154
                                       *********98 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.3   1.8e-08   0.00011       1     103 [.       1      85 [.       1     103 [. 0.72
   2 !   11.0   0.1   7.5e-05      0.45     180     203 ..      96     119 ..      88     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.8e-08
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       +r+ +++D+H      +l+ ++ +++ + +  ++  v+++GD+v        +++ ++a ++    +++++GN +  
  gi|313127422|ref|YP_004037692.1|   1 MRVGICSDTH-----DNLELARGVVETFESA-GVETVIHCGDIVSPF-----TANVFDADFD----FHAVRGNND-G 61 
                                       89********.....*************999.**********99998.....6666777777....6********.3 PP

                                       HHHHHHHHHHHHHHHHHHEHHHCEEE CS
                       Metallophos  78 eeellnkygylgifsepwrsdaevfn 103
                                       e +l+n  +++g++ +     +  f+
  gi|313127422|ref|YP_004037692.1|  62 EWNLSNVVDSFGTYHGECA--TFDFD 85 
                                       4455555555554422222..22344 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.5e-05
                                       CHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 180 gdealedllkkygvdlvisGHtHv 203
                                       ++  ++ l + ++ d+v++GHtH+
  gi|313127422|ref|YP_004037692.1|  96 SETLVDGLVESGDYDYVFRGHTHQ 119
                                       455566889999***********7 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.012        72      11      45 ..       6      40 ..       1      49 [. 0.86
   2 !   11.8   0.0   1.9e-05      0.11     194     237 ..      92     136 ..      80     162 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.012
                                      EE--TT-GGGHHHHHHHHHHH--SEEEEES----- CS
                     Metallophos_3 11 isdlkgevellerlveviedkdpDllvlvGdlvka 45
                                       sd +++ el   +ve+ e  +++ ++  Gd+v++
  gi|313127422|ref|YP_004037692.1|  6 CSDTHDNLELARGVVETFESAGVETVIHCGDIVSP 40
                                      678899999999999999999***********986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.9e-05
                                       S---S-HHHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--BG CS
                     Metallophos_3 194 lkekgsevvaelvktlnPevvvvghavkeh.eelgktlvvnPGal 237
                                       ++  ++  v  lv + + + v+ gh++++  e+ g+t+ vnPG l
  gi|313127422|ref|YP_004037692.1|  92 YHGTSETLVDGLVESGDYDYVFRGHTHQRTyEKSGETVHVNPGGL 136
                                       45677888999***************99989************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1168.30
//
Query:       gi|313127423|ref|YP_004037693.1|  [L=403]
Description: phosphoglycerate kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.9e-104  349.0   0.1   3.4e-104  348.8   0.1    1.0  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.8   0.1  1.9e-108  3.4e-104       7     377 ..      12     391 ..       7     392 .. 0.88

  Alignments for each domain:
  == domain 1  score: 348.8 bits;  conditional E-value: 1.9e-108
                                       TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHTT-E CS
                               PGK   7 kgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellgkeV 83 
                                       +++rvlvR+D+N+p+++ g+++d++r++++++T+++l e+g++vvl++H+grp g ++ +sl+++a+ L++ +g++V
  gi|313127423|ref|YP_004037693.1|  12 ADQRVLVRLDLNSPVED-GEVQDNRRFERHAETVSELAEAGHRVVLMAHQGRP-GGDDFVSLEQHASILADHVGHDV 86 
                                       579************86.***********************************.689******************** PP

                                       EEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTT..T.....TT-HHHHHHHHHT-SEEEE--GGGTTS--TTTTH CS
                               PGK  84 kfvedvvgeeveeaiaelkegevllLeNvrfykeE..e.....kndeelakklasladvyVnDAFgtahrahaStvg 153
                                        fv d++g+++ +ai++l++g++llLeN+r+ ++E  e     k+d++++++la ++d+yVnDA+++ahr+haS+vg
  gi|313127423|ref|YP_004037693.1|  87 GFVADTFGDDAIDAIESLSAGNILLLENTRMCDDElpEedpevKADTAFVQTLAPYFDAYVNDAYSAAHRSHASLVG 163
                                       ********************************9995322233344558***************************** PP

                                       HHHCSEEEE-HHHHHHHHHHHHHH.HS--SSEEEEEEES-HHHCHHHHHHHTTT-SEEEEETCHHHHHHHHTT-B-T CS
                               PGK 154 iakvlsaaaGllmekElealskvl.enperplvailGGakvsdkikvienLlekvdkliigGgmantFlkaqgleig 229
                                       ++  l+a+aG++m++E+ea s++  ++ + ++++++GG+k  d i+v++nL ekvd++++gG     Fl+a+g+++g
  gi|313127423|ref|YP_004037693.1| 164 FPLELPAYAGRVMQTEYEANSAIAtREFDGQVTMVVGGTKATDVIDVMNNLGEKVDRFLLGGIAGELFLRAAGHDVG 240
                                       *****99*************9887256679**********************************************9 PP

                                       TSS-.....-GGGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-.EEEEE-HHHHHHHHHH CS
                               PGK 230 kslv.....eedklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipede.malDigpktielfaea 300
                                        ++      +++     + + +  +++g++i l vD+++++e+ e+     +ve+i+e++  +lDig++t+e++  +
  gi|313127423|ref|YP_004037693.1| 241 YDVGgmdlfDDQWEANHETIESLIEERGDQITLAVDLAYEDEADER--AEIAVEDIDEKDrAYLDIGTDTVEAYDPV 315
                                       6655222214433333444444556678************965433..34468888665559*************** PP

                                       HCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GG.GSSEEESSSHHHHHHHC CS
                               PGK 301 ikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklglad.kvshvStGGgAsLelLe 376
                                       i++++ v+++G++G+fe e+f++GT  +++a+ae+  +++s+vGGgd+ +a+e++g+++ ++ hvS +GgA++++L+
  gi|313127423|ref|YP_004037693.1| 316 IRDSEAVFVKGALGLFEDERFSEGTVGVLRAIAET--DCFSVVGGGDTSRAIEMYGMSEdDFGHVSIAGGAYIRALT 390
                                       **********************************7..47*****************96659***************9 PP

                                       T CS
                               PGK 377 g 377
                                       g
  gi|313127423|ref|YP_004037693.1| 391 G 391
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2637.44
//
Query:       gi|313127424|ref|YP_004037694.1|  [L=338]
Description: glyceraldehyde-3-phosphate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-58  195.3   0.0      6e-58  194.9   0.0    1.2  1  Gp_dh_C        Glyceraldehyde 3-phosphate dehydrogenase, C-te
    3.1e-32  110.9   0.0    5.6e-32  110.1   0.0    1.4  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
     0.0013   18.8   0.1     0.0032   17.6   0.1    1.7  1  DapB_N         Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
       0.15   11.9   0.0         43    4.1   0.0    3.0  3  PriA_3primeBD  3′ DNA-binding domain (3′BD)


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.9   0.0   1.3e-61     6e-58       2     158 .]     161     318 ..     160     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 194.9 bits;  conditional E-value: 1.3e-61
                                       HHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTTCSSEEEE-THHHHHHHHSGGGTTTEEEEEEE CS
                           Gp_dh_C   2 aplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaaeniiptstgaakavglVlpelkgkldglAvr 78 
                                       +p+akvl+++fgi++gl+ttvhayt+ Q+l+Dgp+  + rr+raaaeni+ptstgaa+a +++lp+l+gkldg+A+r
  gi|313127424|ref|YP_004037694.1| 161 TPVAKVLDEEFGIESGLLTTVHAYTGSQNLIDGPK-AKKRRGRAAAENIVPTSTGAAQAATEILPQLDGKLDGMAMR 236
                                       79********************************8.899************************************** PP

                                       ESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH.TTTTTTEEEEHSHHHGGGGTTGCSSEEEEGGGCEEET.TTEEE CS
                           Gp_dh_C  79 VPtpnvsvvdlvvelekevtveevnaalkeaae.galkgilsyteeelvssDlvgdphssifdaketivve.enlvk 153
                                       VP+pn+s+++lvv l+++ +vee n+a+++aa+ g+l g+l+yt++e+vssD+vg p ss++d ++t++v+ + l k
  gi|313127424|ref|YP_004037694.1| 237 VPVPNGSITELVVSLDETPSVEELNDAFRDAADsGPLAGVLGYTDDEVVSSDIVGLPFSSTVDLQSTNMVNdGGLYK 313
                                       *********************************9*********************************998868899* PP

                                       EEEEE CS
                           Gp_dh_C 154 vvawy 158
                                       +++wy
  gi|313127424|ref|YP_004037694.1| 314 ILTWY 318
                                       ****9 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   1.3e-35   5.6e-32       1     101 []       7     106 ..       7     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 1.3e-35
                                       CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHHHHHHHHEETTTEC-SS-EEEETTEEEETTEEEEEE--SS CS
                           Gp_dh_N   1 vkvainGfGRIGrlvlralleekelevvaindltdletlayllkyDsvhgrfkgeveaeeealvvngkkikvlaekd 77 
                                       v+v++nGfGRIGr+v+ra++e++++e+v ind++d e++ayl kyD+v+gr + ev+ ++++lv +++++ +++ ++
  gi|313127424|ref|YP_004037694.1|   7 VRVGLNGFGRIGRNVFRAVMENPKVELVGINDVMDFEDMAYLAKYDTVMGR-QDEVSLDGDELVAGDTSVPLFNIQS 82 
                                       69************************************************9.568********************** PP

                                       GGGS-CHHHTSSEEEE-SSS--SH CS
                           Gp_dh_N  78 peelpwkelgvdlVvestGvftdk 101
                                       p+elpw+el+vd+ +e+tG+f++k
  gi|313127424|ref|YP_004037694.1|  83 PAELPWDELNVDVALECTGIFRTK 106
                                       *********************985 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   7.1e-07    0.0032       1      34 [.       7      39 ..       7      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.1e-07
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEET CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdr 34
                                      ++v+++G+ Gr+G++v +av e++++elv+  d 
  gi|313127424|ref|YP_004037694.1|  7 VRVGLNGF-GRIGRNVFRAVMENPKVELVGINDV 39
                                      69******.********************98765 PP

>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.1   4.5e+02      48      75 ..     153     180 ..     132     186 .. 0.80
   2 ?    4.1   0.0    0.0095        43      20      51 ..     226     258 ..     217     274 .. 0.82
   3 ?    2.6   0.0     0.027   1.2e+02      42      80 ..     298     336 ..     295     337 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.1
                     PriA_3primeBD  48 seveeeklkpieevldeepllteellel 75 
                                       +++ ++++ p+ +vldee  +++ ll  
  gi|313127424|ref|YP_004037694.1| 153 ASCTTNSVTPVAKVLDEEFGIESGLLTT 180
                                       444578999********99999888766 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0095
                     PriA_3primeBD  20 levki.GsrVlVpfgkrklvGiVvalkeeseve 51 
                                       l+ k  G+ ++Vp+ + +++ +Vv+l+e+++ve
  gi|313127424|ref|YP_004037694.1| 226 LDGKLdGMAMRVPVPNGSITELVVSLDETPSVE 258
                                       455557**********************98855 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.027
                     PriA_3primeBD  42 valkeeseveeeklkpieevldeepllteellelaewla 80 
                                       v+l++++ v++  l +i+   d+e  +++++l++a+++ 
  gi|313127424|ref|YP_004037694.1| 298 VDLQSTNMVNDGGLYKILTWYDNEYGFSNRMLDMAHFIT 336
                                       5677888889999*********************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2411.99
//
Query:       gi|313127425|ref|YP_004037695.1|  [L=120]
Description: molecular chaperone [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-17   60.6   0.0    2.2e-16   59.2   0.0    1.6  2  ArsA_HSP20     HSP20-like domain found in ArsA
    1.8e-09   37.7   0.0    5.1e-08   33.0   0.0    2.0  1  HSP20          Hsp20/alpha crystallin family
    0.00054   20.1   1.1    0.00064   19.8   1.1    1.1  1  GvpH           GvpH
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.021   15.2   0.0    1.2  1  PIH1_CS        PIH1 CS-like domain
      0.027   14.6   0.0        1.4    9.1   0.0    2.2  1  Frataxin_Cyay  Frataxin-like domain


Domain annotation for each model (and alignments):
>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.25     9e+02      12      25 ..      31      44 ..      30      46 .. 0.86
   2 !   59.2   0.0     6e-20   2.2e-16       3      63 .]      45     108 ..      43     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.25
                        ArsA_HSP20 12 fvdkeeidlsrsgd 25
                                      f+++ +id++ +g+
  gi|313127425|ref|YP_004037695.1| 31 FASETHIDVYDEGE 44
                                      78999****99986 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 6e-20
                        ArsA_HSP20   3 eyvlkldLPfvdkeeidlsrsgdeLtIkignfrRq....itLPsvlarkevtsAkfedgvLeIrF 63 
                                        ++l++dLP+v+k+ idl ++g++Lt+++ ++rR+    i LP +++++ + +A+f++gvL ++F
  gi|313127425|ref|YP_004037695.1|  45 AIRLVADLPGVEKDAIDLKCDGKTLTVSAASDRREyderIRLPVRVDEHSA-DASFNNGVLQVTF 108
                                       689*******************************99999**********77.************9 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   1.4e-11   5.1e-08       2      89 ..      39     112 ..      38     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.4e-11
                                       --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEET CS
                             HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkd 78 
                                       + +e e++++ +d+pg++k+ +++k ++++++v++  +              +r+++ +++LP  vd+++ +as+++
  gi|313127425|ref|YP_004037695.1|  39 VYDEGEAIRLVADLPGVEKDAIDLKCDGKTLTVSAASD--------------RREYDERIRLPVRVDEHSADASFNN 101
                                       66788999****************************99..............379********************** PP

                                       TEEEEEEEBSS CS
                             HSP20  79 GvLtvtvpkke 89 
                                       GvL+vt +k+ 
  gi|313127425|ref|YP_004037695.1| 102 GVLQVTFEKTG 112
                                       ******99975 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.1   1.8e-07   0.00064      87     169 ..      32     114 ..       4     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.8e-07
                              GvpH  87 edsihvetrasddsdelvvvadlpGvtdedvdvaletdeqaltlrvddd...vverlvld.dpdvaitdltlrnqvl 159
                                           h++    d+++ + +vadlpGv  + +d   +   ++lt++   d     er+ l  + d   +d + +n vl
  gi|313127425|ref|YP_004037695.1|  32 ASETHIDV--YDEGEAIRLVADLPGVEKDAIDLKCD--GKTLTVSAASDrreYDERIRLPvRVDEHSADASFNNGVL 104
                                       44455554..58899999*************97665..899999998872224578888537788889999999999 PP

                              GvpH 160 elrlarseds 169
                                       ++   ++ ds
  gi|313127425|ref|YP_004037695.1| 105 QVTFEKTGDS 114
                                       9999888887 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   5.9e-06     0.021      33      87 ..      46     101 ..      32     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.9e-06
                           PIH1_CS  33 laieielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvk 87 
                                       +++  +lP++ +  +++l+ + ++l + + +   +y  +++Lp +vde +++A F++
  gi|313127425|ref|YP_004037695.1|  46 IRLVADLPGV-EKDAIDLKCDGKTLTVSAASdrREYDERIRLPVRVDEHSADASFNN 101
                                       5566689999.7789********99996655569*********************96 PP

>> Frataxin_Cyay  Frataxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00038       1.4      29      50 ..      91     112 ..       3     117 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00038
                                       -CTS.SEEEETTEEEEEETTS- CS
                     Frataxin_Cyay  29 eedeldveyssgvLtiefekkg 50 
                                       +e+ +d+++++gvL+++fek g
  gi|313127425|ref|YP_004037695.1|  91 DEHSADASFNNGVLQVTFEKTG 112
                                       3344589999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 836.56
//
Query:       gi|313127426|ref|YP_004037696.1|  [L=285]
Description: 30S ribosomal protein s6p modification protein'' [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-29  102.2   0.0    3.4e-29  101.8   0.0    1.1  1  RimK             RimK-like ATP-grasp domain
    4.6e-12   45.7   0.0    6.6e-12   45.2   0.0    1.1  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
    5.5e-08   33.0   0.0      1e-07   32.2   0.0    1.4  1  ATP-grasp_3      ATP-grasp domain
    4.6e-06   26.1   0.0       0.05   12.8   0.0    2.2  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    1.1e-05   25.0   0.0    2.2e-05   24.1   0.0    1.5  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00039   20.0   0.0     0.0005   19.6   0.0    1.2  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
     0.0052   16.4   0.0     0.0086   15.7   0.0    1.3  1  ATP-grasp        ATP-grasp domain
  ------ inclusion threshold ------
      0.031   14.6   0.0      0.051   13.9   0.0    1.3  1  Btz              CASC3/Barentsz eIF4AIII binding
      0.061   13.2   0.0       0.11   12.4   0.0    1.3  1  R2K_2            ATP-grasp domain, R2K clade family 2
       0.16   11.6   0.0       0.33   10.6   0.0    1.5  1  ATP-grasp_4      ATP-grasp domain


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.0   1.9e-32   3.4e-29       2     171 ..      81     263 ..      80     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 1.9e-32
                                       H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-..-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--. CS
                              RimK   2 rdKlkslklLakakikvpntalardeedaekliekik.lrfPvvvKsvegsqGikvvlakkeqklkqvlealkeai. 76 
                                       r+K+  ++ L +a+++vp+t+++ +++d e +i+ +  l+fP+vvK   ++ G++v    + ++l  v++ l+    
  gi|313127426|ref|YP_004037696.1|  81 RNKAGVIAALSRAGLPVPETRMVSNPVDEETVINAVAdLSFPLVVKPNSATRGVGVAKVSDVDSLLGVVDYLNLVHd 157
                                       89999*******************************99*******************************99443333 PP

                                       .........EEEEE--SS-SEEEEEEEETTEEEEEEEEE....--SSS----TTTT-EEEE----HHHHHHHHHHHH CS
                              RimK  77 .........lvqeyieeaenediRvlvvddevvaalrrv....skeGdFRsnlhrGgvaeklqlseeekelAikaak 140
                                                l+qe++   + +d R++v+d+evv++++r+      eG ++ n+hrG+ a +l++se  +elA+ +a+
  gi|313127426|ref|YP_004037696.1| 158 yratgdksyLIQEFVP--NARDYRIMVLDGEVVGGVERRlpesLDEGRWKHNVHRGAEATELTVSERHRELAVSVAE 232
                                       455566666*****97..568****************983332378******************************* PP

                                       HCT-SEEEEEEEEETTEEEEEEEESS--SHH CS
                              RimK 141 amelvvaGvDllrakrgllvlEvnsspglek 171
                                       a++++++GvDll + +  +v E n+ p +++
  gi|313127426|ref|YP_004037696.1| 233 ALGIDYLGVDLLVTGELTVVSETNARPTIDH 263
                                       **************************98865 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   3.7e-15   6.6e-12      20     157 ..     109     250 ..      95     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 3.7e-15
                                       -HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHH.....HHHHTTTTTS-EEEEE--GGGGG-EEEEEEE CS
                         GSH-S_ATP  20 dkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksi.....lellteegkepviaqrylpeikeGDkRillv 91 
                                       +++ i+a+++ +  +++KP + + G gv +v++ d+ l+++     +  + ++g +  ++q+++p+++  D Ri+++
  gi|313127426|ref|YP_004037696.1| 109 EETVINAVADLSFPLVVKPNSATRGVGVAKVSDVDSLLGVVdylnlVHDYRATGDKSYLIQEFVPNAR--DYRIMVL 183
                                       445678888888889******************999887643312156667788999********998..7****** PP

                                       TTEE-SEEEEEE--...SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEE.TTEEE CS
                         GSH-S_ATP  92 dGepigyalaRvpa...egevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvi.gdklt 157
                                       dGe +g   +R+p+   eg  + n++ g++a++ +++er+re+a ++a++L   G+ + G+D++  ++lt
  gi|313127426|ref|YP_004037696.1| 184 DGEVVGGVERRLPEsldEGRWKHNVHRGAEATELTVSERHRELAVSVAEAL---GIDYLGVDLLvTGELT 250
                                       ******77778998222455789*************************998...8889999975144444 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   5.7e-11     1e-07       3     159 ..      82     260 ..      80     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5.7e-11
                                       SHHHHHHHHTTT.S---..............-EESS--.........SSSEEEEESS-------B--SS--TTE... CS
                       ATP-grasp_3   3 dKlktykkLkeagvkvP..........tkleaeeleee.........ekklvvKprdGaggesvrvveekeeaeaai 60 
                                       +K  +  +L++ag++vP          +         e           +lvvKp ++  g +v +v + +++   +
  gi|313127426|ref|YP_004037696.1|  82 NKAGVIAALSRAGLPVPetrmvsnpvdE---------EtvinavadlSFPLVVKPNSATRGVGVAKVSDVDSLLGVV 149
                                       7889999**********85555433333.........344555666699**************************** PP

                                       .................EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET................TEEEEEEES- CS
                       ATP-grasp_3  61 eeve.............lvqefieGkplSvsllsdgekvlvlavnrqliekaeke............fvyaGnvtpi 112
                                       ++++             l+qef+           ++ + +++++  ++++  e++            +v +G  +  
  gi|313127426|ref|YP_004037696.1| 150 DYLNlvhdyratgdksyLIQEFV----------PNARDYRIMVLDGEVVGGVERRlpesldegrwkhNVHRGAEATE 216
                                       ****5555555555555555555..........44444444444444444444434444555555559999988765 PP

                                       ---HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS-- CS
                       ATP-grasp_3 113 etelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRlt 159
                                         + +e+ +ela +v e+l g   y+GvDl+++ e  +v E N+R+t
  gi|313127426|ref|YP_004037696.1| 217 L-TVSERHRELAVSVAEAL-G-IDYLGVDLLVTGELTVVSETNARPT 260
                                       4.678999***********.5.57**********999999*****97 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   2.8e-05      0.05       9      82 ..      70     142 ..      63     175 .. 0.86
   2 !   11.3   0.0   8.5e-05      0.15     227     269 ..     222     262 ..     206     269 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                       ATPgrasp_ST   9 kyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviter 82 
                                        +N r+++    +K  +   ++ragl+vp++ +v +  +e + ++a+     + +v+Kp+    G G+ +++++
  gi|313127426|ref|YP_004037696.1|  70 WVNGREAVLSSRNKAGVIAALSRAGLPVPETRMVSNPVDEETVINAVADLSFP-LVVKPNSATRGVGVAKVSDV 142
                                       578999999999999888888*********88888888888888877777656.**************999764 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8.5e-05
                       ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpgla 269
                                       ++ ela+++ae  +g+ ylG+D+ ++ e   ++ E Narp ++
  gi|313127426|ref|YP_004037696.1| 222 RHRELAVSVAE-ALGIDYLGVDLLVTGEL-TVVSETNARPTID 262
                                       5679*******.*****************.9********9876 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.2e-08   2.2e-05       3     176 ..      91     259 ..      89     272 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.2e-08
                                       HHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHH...HTT....- CS
                   Dala_Dala_lig_C   3 kaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieea...fky....d 72 
                                       ++aGlpv++  ++ +   +e+    + + ++ l++p++VKp  +   vGv+kv+ ++ l   ++       y    d
  gi|313127426|ref|YP_004037696.1|  91 SRAGLPVPETRMVSNPVDEET----VINAVADLSFPLVVKPNSATRGVGVAKVSDVDSLLGVVDYLnlvHDYratgD 163
                                       678899988888877655544....588999***********************99998766554311133333338 PP

                                       SCEEEEE--.ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHH CS
                   Dala_Dala_lig_C  73 ekvlvEeai.egreievavlgneklevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkayka 148
                                       ++ l+ e++ ++r+  + vl+    ev   +e+++ +++ +   k+    ++   +a  e  v+e+ +ela+ + +a
  gi|313127426|ref|YP_004037696.1| 164 KSYLIQEFVpNARDYRIMVLD---GEVVGGVERRLPESLDEGRWKHN---VHRGAEA-TELTVSERHRELAVSVAEA 233
                                       899*****************9...66666667776666655444442...2222222.2334555666777777777 PP

                                       TT--SEEEEEEEEETTTEEEEEEEESS- CS
                   Dala_Dala_lig_C 149 ldlrGlaRvDfflteegeivlnEvNtlP 176
                                       l++  l+ vD+++t  +  v++E N  P
  gi|313127426|ref|YP_004037696.1| 234 LGIDYLG-VDLLVT-GELTVVSETNARP 259
                                       7765444.777777.3344567777666 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.8e-07    0.0005       6     139 ..      87     223 ..      82     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.8e-07
                                       HHHHHHTT-BBSSEECSS.BSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHH.HHHHHHHHHHST CS
                       CPSase_L_D2   6 kealkkinvpvvpssaap.vetleealaiakeigyPviikaafglGGkGmrvarneeelaelvk.kalaeakaafgn 80 
                                        +al++++ pv +   +    ++e+++++++++++P ++k+  +  G G   +++ + l  +v    l +   a g+
  gi|313127426|ref|YP_004037696.1|  87 IAALSRAGLPVPETRMVSnPVDEETVINAVADLSFPLVVKPNSATRGVGVAKVSDVDSLLGVVDyLNLVHDYRATGD 163
                                       568889999999988876567889999****************************99999888624566667799** PP

                                       S-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCE.EEES-SS--HHHHH CS
                       CPSase_L_D2  81 kqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvi.evAPsqtLtdeerq 139
                                       k+ l+++++ + +++ + vl  +    +     e +++ r +  +   A +  Lt +er+
  gi|313127426|ref|YP_004037696.1| 164 KSYLIQEFVPNARDYRIMVLDGEVVGGVERRLPESLDEGRWKHNVhRGAEATELTVSERH 223
                                       ****************99997555444444444555555444333134555556555555 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.8e-06    0.0086       3     160 ..      92     259 ..      90     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.8e-06
                                       TTT--B-EEEEECCHH...HHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC.........GTTCEE CS
                         ATP-grasp   3 klglpvprflaveske...eleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal.........keekvi 67 
                                       ++glpvp+  +v++      + +a+++l +p+vvK +  +  G G   v + ++l  ++++l         ++++ +
  gi|313127426|ref|YP_004037696.1|  92 RAGLPVPETRMVSNPVdeeTVINAVADLSFPLVVK-PNSATRGVGVAKVSDVDSLLGVVDYLnlvhdyratGDKSYL 167
                                       67899999998886432338999************.9**********************999999****99999*** PP

                                       EEE----SEEEEEEEEE.ETTC-EEE--EEEEEEETTEEEEEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEE CS
                         ATP-grasp  68 vEefvpfekElsvlvvr.saeGetafypvvetvqedgilrlsvapaevsek.aqkkaeeiakkiveeLggvGvfavE 142
                                       + efvp  +   ++v   ++ G  +   + e + e    + +   ae++e    ++ +e+a  ++e+Lg+   ++v 
  gi|313127426|ref|YP_004037696.1| 168 IQEFVPNARDYRIMVLDgEVVG-GVERRLPESLDEGRWKHNVHRGAEATELtVSERHRELAVSVAEALGI-DYLGVD 242
                                       ********99999998855556.45556667777777777777777766653667777888888888875.578889 PP

                                       EEEETTCT.EEEEEEESS- CS
                         ATP-grasp 143 lFvledge.llvnElapRp 160
                                       l v+  ge  +v+E   Rp
  gi|313127426|ref|YP_004037696.1| 243 LLVT--GElTVVSETNARP 259
                                       8888..7756778877776 PP

>> Btz  CASC3/Barentsz eIF4AIII binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.8e-05     0.051      52     105 ..     155     212 ..     154     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                               Btz  52 lHDdRtaeteangvrefekssrvaglivaskv....arrklkdaaeedrWtHDrfeev 105
                                        HD R +++++   +ef  ++r + ++v +       +r+l ++ +e+rW+H  ++  
  gi|313127426|ref|YP_004037696.1| 155 VHDYRATGDKSYLIQEFVPNARDYRIMVLDGEvvggVERRLPESLDEGRWKHNVHRGA 212
                                       5***************999999999655444447777999999************973 PP

>> R2K_2  ATP-grasp domain, R2K clade family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     6e-05      0.11      17      79 ..     119     190 ..     109     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6e-05
                             R2K_2  17 eewpvFvkpasdaksftgavvedgedlpgl.........gsldedlpvlvsevvsfasEyRlfvldgeiitv 79 
                                        + p+ vkp s+++ +  a v d + l g+         +++  d + l++e v+ a+ yR+ vldge++++
  gi|313127426|ref|YP_004037696.1| 119 LSFPLVVKPNSATRGVGVAKVSDVDSLLGVvdylnlvhdYRATGDKSYLIQEFVPNARDYRIMVLDGEVVGG 190
                                       5566667777776666666666666666666777777779999**************************986 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00018      0.33       2      35 ..     120     153 ..     119     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                       ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaie 35 
                                       s+P+v+KP++ +  +GV k+++ + +  +v+ ++
  gi|313127426|ref|YP_004037696.1| 120 SFPLVVKPNSATRGVGVAKVSDVDSLLGVVDYLN 153
                                       79********************999888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1893.34
//
Query:       gi|313127427|ref|YP_004037697.1|  [L=176]
Description: 50S ribosomal protein L10ae [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-29  100.6   0.0    7.4e-29  100.4   0.0    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0   4.1e-33   7.4e-29       3     131 ..      14     165 ..      12     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 4.1e-33
                                       SSXXBSSSXXSSTSXX.XSXXXXXESX...........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEX CS
                     Ribosomal_L16   3 rkkyrKsrkryirgvs.tkgtklefgd...........ygLvalekgqltaealeaariainrylkkkrgk...klw 64 
                                       ++ y++++  yi+g + +k+ + ++g+           ++L+ +e++q+++  le+ar+ +nr + k+ g+   k+ 
  gi|313127427|ref|YP_004037697.1|  14 KPSYTRRE--YITGIPgSKIAQHNMGNlqtgpedypvqISLRLEEECQIRHGSLESARLSANRVMLKQVGQknyKMV 88 
                                       7899**99..**************************9999**************************99999999*** PP

                                       XSXXXXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE.TTXX.XSHHHHHHHHHHHHTSSSXEE CS
                     Ribosomal_L16  65 irvfphhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei.kagv.neeiakealrraasKlpiktk 130
                                       +r+fph++++++     ag+dR+++G+    Gk+ g++ar++ ++ +f+i   +v ++ iak+alrra +K++ +++
  gi|313127427|ref|YP_004037697.1|  89 LRKFPHQVLRENkqatgAGADRVSDGMrqsfGKVVGTAARIQRNDRVFTIyC-DVeDAPIAKDALRRAYNKMSPPCR 164
                                       **************************************************63.344899*************99999 PP

                                       E CS
                     Ribosomal_L16 131 i 131
                                       i
  gi|313127427|ref|YP_004037697.1| 165 I 165
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1209.01
//
Query:       gi|313127428|ref|YP_004037698.1|  [L=219]
Description: GMP synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-16   59.3   0.0    5.7e-16   58.8   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    2.4e-10   40.5   0.0    1.2e-08   35.0   0.0    2.5  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
       0.17   11.7   0.0        0.3   10.9   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   9.6e-20   5.7e-16      12     176 ..      19     180 ..      14     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 9.6e-20
                                       HHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.......TTTHHHHHHHHCTSTS-EEEETHHH CS
                            GATase  12 nlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.......vegkieaikearenkiPiLGICLGm 81 
                                        + ++l ++g++v  +p+ +   + +  l  +d++++sg    ++       ++   e+++e+  +k+P L +C+G+
  gi|313127428|ref|YP_004037698.1|  19 EIRRHLEAAGATVRSYPFAEHGGRPD-VLHAADAVVLSGSTAGVYetetypwMDDLRELVRELVAEKVPTLAVCFGH 94 
                                       57788888899999999887777774.6999********77777767799999999999999999************ PP

                                       HHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEE CS
                            GATase  82 QllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeii 158
                                       Ql+ +++g+ v++      h g  +++  +  l+ g +   ++   H+++v++   + ag+e +a+ +    + + +
  gi|313127428|ref|YP_004037698.1|  95 QLVNDALGGAVEHHG---LHAGIDPVRFADDPLFDGVGT--RVPLVHSDVVTE---LGAGMEAIAAADYY-PNLASR 162
                                       ***********9877...667777777767889***966..57789*******...**********9776.9***** PP

                                       EETTTEEEESSBTTSTTS CS
                            GATase 159 ekknpfvgvQFHPEstst 176
                                       +++ p++ vQ+HPE+t +
  gi|313127428|ref|YP_004037698.1| 163 HRDAPLWTVQYHPEFTEQ 180
                                       ***************976 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.9e-12   1.2e-08      54     216 .]      44     176 ..       5     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.9e-12
                     Peptidase_C26  54 aildkldgllltGgqdvePslygeepsekeeeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdi 130
                                       ++l++ d+++l+G+      +y+ e   +   +d  R      L+r+ ++++vP l++C G+ql+n alGG +  + 
  gi|313127428|ref|YP_004037698.1|  44 DVLHAADAVVLSGSTA---GVYETE---TYPWMDDLR-----ELVRELVAEKVPTLAVCFGHQLVNDALGGAVEHHG 109
                                       5566666666666654...334333...333344444.....599**************************976554 PP

                     Peptidase_C26 131 eeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikelaeelrveAvaeDgviEaieseeakaf 207
                                                      a    v++  + l+  +      +v  +H+  ++el+ +++ +A a+      + s++++a+
  gi|313127428|ref|YP_004037698.1| 110 L-------------HAGIDPVRFADDPLFDGVGT----RVPLVHSDVVTELGAGMEAIAAADY--YPNLASRHRDAP 167
                                       4.............2456799999**99999887....9***************998887764..445566666789 PP

                     Peptidase_C26 208 vlgvQwHPE 216
                                       ++ vQ+HPE
  gi|313127428|ref|YP_004037698.1| 168 LWTVQYHPE 176
                                       ********9 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     5e-05       0.3      61     107 ..      48      97 ..      41     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5e-05
                                       G-SEEEE--...BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHH CS
                         DJ-1_PfpI  61 eyDalvlpG...GragperlrenekvvelvkefaekgklvaaICagpqlL 107
                                       + Da+vl G   G    e+    + ++elv+e + ++ +  a+C g ql 
  gi|313127428|ref|YP_004037698.1|  48 AADAVVLSGstaGVYETETYPWMDDLRELVRELVAEKVPTLAVCFGHQLV 97 
                                       4799999993334334455555569*********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1508.16
//
Query:       gi|313127429|ref|YP_004037699.1|  [L=258]
Description: nuclease of the recb family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-66  221.7   0.0      1e-65  221.3   0.0    1.0  1  NucS            Endonuclease NucS
     0.0084   15.9   0.0      0.016   15.1   0.0    1.4  1  YhcG_C          YhcG PDDEXK nuclease domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.033   14.2   0.0    1.3  1  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.3   0.0   1.7e-69     1e-65       4     214 ..      27     237 ..      25     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 221.3 bits;  conditional E-value: 1.7e-69
                              NucS   4 vlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeeeL 80 
                                       ++ ++ rC+v+y Gra s L  gerl+v kpdG++lvh d k++PvnWqpp+++ +a v+dg l ++s r  p+e+L
  gi|313127429|ref|YP_004037699.1|  27 MVTMFGRCTVEYDGRASSSLGPGERLVVCKPDGTILVHTDEKRKPVNWQPPGCTHRASVRDGRLRVRSERSTPQEHL 103
                                       667889*********************************************************************** PP

                              NucS  81 kveieevehasayeledveelvldGseaelaeliiehpdLieeGfkpvareyavaiGivdiLgkdeegklvivelkr 157
                                        v  e +e++saye+ d  +l l+Gse +l + i+ +p L+e Gf p a e  +++G+vdi+g d +gk v+velkr
  gi|313127429|ref|YP_004037699.1| 104 DVAFERIEQVSAYEVTDRSDLQLRGSEEDLRQRILDDPALVEAGFVPQATERETTAGPVDIFGADADGKPVVVELKR 180
                                       ***************************************************************************** PP

                              NucS 158 rkaevdaveqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefkeldpp 214
                                       r+ + +a +qL+ryve l e+   ++vrG+lvaps+t   ++ll e+gl f   +p 
  gi|313127429|ref|YP_004037699.1| 181 RRVGPSAASQLQRYVEALDEEFPDEGVRGILVAPSVTDRTQELLAENGLSFVAAEPI 237
                                       ***************************************************999874 PP

>> YhcG_C  YhcG PDDEXK nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.6e-06     0.016      74     105 ..     174     205 ..     171     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-06
                            YhcG_C  74 vvieLKvgefkpedagklnlYlsaldeelkke 105
                                       vv+eLK +++ p+ a++l+ Y++aldee  +e
  gi|313127429|ref|YP_004037699.1| 174 VVVELKRRRVGPSAASQLQRYVEALDEEFPDE 205
                                       89************************987654 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.4e-06     0.033       9      94 ..     135     234 ..     130     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-06
                                       --STT-HHHHHH........HCTTSEEEEEEEE-HHHHTCG.......S-CHHHHHHHHHHHHHHHHHHHHTT--EE CS
                    DNA_photolyase   9 lRlhDNpALaaA........aasgepvipvfvldpekahkl.......rvgaarvdfllesLadLdeeLrelgirLv 70 
                                       +R+ D pAL +A        +++ +  + +f +d +  ++        rvg+  +  l + +++Ldee+ + g+r +
  gi|313127429|ref|YP_004037699.1| 135 QRILDDPALVEAgfvpqateRETTAGPVDIFGADAD-GKPVvvelkrrRVGPSAASQLQRYVEALDEEFPDEGVRGI 210
                                       5899******99888865333333335566666666.3333566677899*************************** PP

                                       EEESSHHHHHHHHHHHCTECEEEE CS
                    DNA_photolyase  71 vrrgdpadvlpelakelgasavva 94 
                                       ++  ++ d  +el++e+g s v a
  gi|313127429|ref|YP_004037699.1| 211 LVAPSVTDRTQELLAENGLSFVAA 234
                                       ***999999999999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1731.20
//
Query:       gi|313127430|ref|YP_004037700.1|  [L=151]
Description: flavin-nucleotide-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-19   68.7   0.0    5.4e-19   68.6   0.0    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    1.7e-06   28.1   0.0    2.1e-06   27.8   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   6.1e-23   5.4e-19       2     139 ..      19     146 ..      18     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 6.1e-23
                                       HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEET..TSHCCHCCCT--.ECEEEEEEEEEEE-SEGG CS
                      Pyridox_ox_2   2 reeilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgak..gsrlaaalrgap.vcvvvtevdglvlarsfn 75 
                                       +ee++a+L+e++vg+la++d+++ + +P+++++dgd+lyf   +  +sr+ + ++++  ++ +v++v g        
  gi|313127430|ref|YP_004037700.1|  19 DEEVDAFLREHGVGVLALTDGERAYGVPISFGYDGDNLYFVFLRgeTSRKEEFAEKTAgATLTVFDVAG-------- 87 
                                       79***********************************8887433347899999997777*******999........ PP

                                       EEEEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEEEEEEEE CS
                      Pyridox_ox_2  76 slnyrSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelkatsvlrlkieevsg 139
                                        ++++SV+v G++++v +++e+++++ ++  ++    w ++   + + ++ +  + l+i+e++g
  gi|313127430|ref|YP_004037700.1|  88 RYEWQSVIVSGTIRPV-EDDEWDAVVSAMEANA----WFPSLFSESEPMRGIGGWTLDIAEATG 146
                                       358*************.5566666666655444....444444555567777777777777776 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.3e-10   2.1e-06       2      88 .]      19     107 ..      17     107 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.3e-10
                                       HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT...GSEEE CS
                    Putative_PNPOx   2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde...lgrgv 75 
                                       dee+ +fl+e+ ++vlA  d +   +++p+++ ++ +  ++vf   + srk +  e+   ++l+++d +     ++v
  gi|313127430|ref|YP_004037700.1|  19 DEEVDAFLREHGVGVLALTDGER-AYGVPISFGYDGDNLYFVFLRGETSRKEEFAEKTAGATLTVFDVAgryEWQSV 94 
                                       6799**************98887.***********************************************99999* PP

                                       EEEEEEEEESCHH CS
                    Putative_PNPOx  76 rieGtaelvsdge 88 
                                        ++Gt++ v+d+e
  gi|313127430|ref|YP_004037700.1|  95 IVSGTIRPVEDDE 107
                                       ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1062.98
//
Query:       gi|313127431|ref|YP_004037701.1|  [L=125]
Description: vanz like family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-10   39.3   0.9    1.8e-09   38.3   0.9    1.4  1  VanZ      VanZ like family
     0.0011   19.7   0.1     0.0016   19.1   0.1    1.2  1  DUF2279   Predicted periplasmic lipoprotein (DUF2279)
  ------ inclusion threshold ------
      0.053   13.3   1.0      0.087   12.6   1.0    1.6  1  DUF2238   Predicted membrane protein (DUF2238)


Domain annotation for each model (and alignments):
>> VanZ  VanZ like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.9   2.9e-13   1.8e-09      55     125 ..      38     118 ..       8     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.9e-13
                              VanZ  55 i...vgnvalfvp...lGfllplllkkk....flkvlllgfllslsiElhQlfvpgRsfdvdDvilntlGallGill 121
                                       +   + +v++f      +fl  ++l+ +    +  +++++++l  ++El+Q  +p R+f++ D   nt+Ga++G++ 
  gi|313127431|ref|YP_004037701.1|  38 FglgLDKVVHFGAyavTAFLAGVALRARdvrgLALAVVVAVVLGSGVELMQAALPTRTFSLGDAAANTIGAVCGAAA 114
                                       234589*******7766788899997777554333999999************************************ PP

                              VanZ 122 ylll 125
                                       y+l+
  gi|313127431|ref|YP_004037701.1| 115 YRLV 118
                                       *985 PP

>> DUF2279  Predicted periplasmic lipoprotein (DUF2279)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   2.7e-07    0.0016      12      87 ..      40     112 ..      34     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.7e-07
                           DUF2279  12 gGaDklgHlyssYllaellsalierkgleksnaalaasllslalmlymElgDsfkessGFsyeDvianlsGaalal 87 
                                       +G Dk+ H+  +Y ++  l ++  r      +++ +a ++++ l + +El+ +   +  Fs+ D +an++Ga  ++
  gi|313127431|ref|YP_004037701.1|  40 LGLDKVVHF-GAYAVTAFLAGVALRAR--DVRGLALAVVVAVVLGSGVELMQAALPTRTFSLGDAAANTIGAVCGA 112
                                       89******6.78999999988765543..3689999999********************************97665 PP

>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.0   1.5e-05     0.087      59     103 ..      42      83 ..       2     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                           DUF2238  59 YDrlvHfaqGlllalvvrelllrkkklrkwllllavlvvlaisal 103
                                        D++vHf  + + + +++ ++lr +++r+++l+++v+vvl     
  gi|313127431|ref|YP_004037701.1|  42 LDKVVHFGAYAV-TAFLAGVALRARDVRGLALAVVVAVVLGS--G 83 
                                       59**********.666779999999*9987777777766654..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 826.19
//
Query:       gi|313127432|ref|YP_004037702.1|  [L=64]
Description: cold-shock DNA-binding protein family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-19   68.6   0.1    3.5e-19   68.4   0.1    1.0  1  CSD       'Cold-shock' DNA-binding domain
  ------ inclusion threshold ------
      0.041   13.6   2.4      0.055   13.2   2.4    1.3  1  OB_RNB    Ribonuclease B OB domain
        0.1   12.5   0.3       0.14   12.1   0.3    1.4  1  S1-like   S1-like


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.1   5.8e-23   3.5e-19       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 5.8e-23
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      +G+V  fn+  g+GFI++ed+d+dvF+H+ ++ g +   L+eg e+eFe+++  kgp+A+nVt+
  gi|313127432|ref|YP_004037702.1|  3 EGKVDFFNDTGGYGFIETEDHDEDVFFHMEDVGGPD---LEEGTEIEFEIEDAPKGPRAKNVTR 63
                                      69******************************9999...***********************97 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.4   9.1e-06     0.055       8      28 ..      13      33 ..       4      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.1e-06
                                      SS-EEEEECT.TEEEEE-HHH CS
                            OB_RNB  8 kGFGFlipdegkeDifippeq 28
                                       G+GF+++++ +eD+f + e+
  gi|313127432|ref|YP_004037702.1| 13 GGYGFIETEDHDEDVFFHMED 33
                                      59**************87766 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   2.3e-05      0.14      14      43 ..      14      48 ..      10      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                           S1-like 14 tfGfv.....DeevfFqrsvvkGrlpkvgdrVlve 43
                                       +Gf+     De+vfF+++ v G+  + g  +++e
  gi|313127432|ref|YP_004037702.1| 14 GYGFIetedhDEDVFFHMEDVGGPDLEEGTEIEFE 48
                                      688887777789*********99988888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 453.94
//
Query:       gi|313127433|ref|YP_004037703.1|  [L=234]
Description: hypothetical protein Hbor_27110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.5   0.0      0.017   15.4   0.0    2.2  1  ParBc     ParB-like nuclease domain


Domain annotation for each model (and alignments):
>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.5e-07     0.017      34      74 ..     157     196 ..     110     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.5e-07
                             ParBc  34 GllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivl 74 
                                         l+P++v +   g ++ + G +R+  a +l ++ vpv+vl
  gi|313127433|ref|YP_004037703.1| 157 HHLEPLVVIGRS-GDIYWTEGFHRFAIASLLDVEAVPVYVL 196
                                       5689*******8.**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1633.03
//
Query:       gi|313127434|ref|YP_004037704.1|  [L=126]
Description: hypothetical protein Hbor_27120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   11.8   0.4       0.19   11.4   0.4    1.2  1  TPR_21    Tetratricopeptide repeat-like domain


Domain annotation for each model (and alignments):
>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4     1e-05      0.19       4      52 ..      15      64 ..      10      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1e-05
                            TPR_21  4 Wkengklilvgvvlalvgla.GwqgwqdyqeeqaeeAsalYqqlqeavea 52
                                      W +++ ++++ vv+al+ +a G   ++d+  +++ e s +Y+  +++ e+
  gi|313127434|ref|YP_004037704.1| 15 WGRFAAVVVITVVVALGLVAgGLWLYTDHLYRTSYESSYTYDVALNTNET 64
                                      6777788889999999888736899****************998874443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 919.68
//
Query:       gi|313127435|ref|YP_004037705.1|  [L=191]
Description: hypothetical protein Hbor_27130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.4    5.9  13.2        1.4    8.1   1.4    2.3  2  CitMHS    Citrate transporter


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.4   7.7e-05       1.4     202     245 ..      13      47 ..       1      65 [. 0.81
   2 ?    3.0   4.6    0.0026        46     118     164 ..     117     175 ..      77     190 .. 0.43

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 7.7e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 202 tilllaykkveWsvlllfaGvfllvgaleqtGilealadllgag 245
                                       +++       ++++++lf++v+ +v ++  tG + +l+++l  +
  gi|313127435|ref|YP_004037705.1|  13 SLI-------SFGLYILFIAVVSMVLIFAITGGIGLLGAVL--S 47 
                                       444.......999**************************99..3 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0026
                                       xxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxx..xxxxxxxxxxx RF
                            CitMHS 118 iplalaaniggaltpiGtpttraa..........arpglslpnlll..lalllvgllpl 164
                                        p+ l+a+i  a+++  tp + a+          ++ +++l+ +++  +a++  g ++ 
  gi|313127435|ref|YP_004037705.1| 117 GPVPLIAGIPAAFVLLATPVVYAIhrrssawtpeTSKWPVLLQWVVflTAVVTLGTAIP 175
                                       22333333333344444443333355555555555555555555553333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1333.08
//
Query:       gi|313127436|ref|YP_004037706.1|  [L=243]
Description: sortase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-12   48.1   0.0    2.4e-12   47.1   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.5e-09   38.2   0.1      2e-09   37.8   0.1    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    7.5e-07   29.5   0.0    1.4e-06   28.6   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    9.1e-06   25.7   0.2    3.4e-05   23.9   0.0    2.0  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    2.3e-05   24.4   0.1    8.5e-05   22.6   0.1    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    5.3e-05   23.2   0.0    0.00011   22.1   0.0    1.5  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00017   21.3   0.0    0.00028   20.6   0.0    1.3  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
    0.00049   20.8   0.1    0.00099   19.8   0.1    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.039   14.1   3.9      0.073   13.2   0.2    2.8  2  Acetyltransf_6   Acetyltransferase (GNAT) domain
      0.073   12.9   0.0       0.22   11.4   0.0    1.8  1  UBA_4            UBA-like domain
      0.076   13.4   0.0       0.14   12.5   0.0    1.5  1  HAMP             HAMP domain
      0.096   12.1   0.0       0.14   11.7   0.0    1.3  1  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   1.6e-15   2.4e-12      32     114 ..     128     214 ..      95     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.6e-15
                                       TC....EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETT CS
                    Acetyltransf_1  32 ae....gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveed 104
                                       +      +++a +++ ++G+  l   + ek ++++   + V+++yrg+G+Gs+Lle ++e+a+ +g++k +  + + 
  gi|313127436|ref|YP_004037706.1| 128 NTvesrVFFMAAHNDDILGWTHLDLPQIEKLQNTVQVTVGVREAYRGRGIGSRLLERALEWAKANGYRKAYNSIPAI 204
                                       2223335555***********999999999999999*******************************8877766555 PP

                                       EHHHHHHHHH CS
                    Acetyltransf_1 105 ndaairlYek 114
                                       nd ai+++e 
  gi|313127436|ref|YP_004037706.1| 205 NDEAIAFLEA 214
                                       *******975 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.1   1.3e-12     2e-09       1     155 []      84     238 ..      84     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.3e-12
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyevssveefekfleal.dsekeyvflvaesdrivGyaylg..qfkkrak 74 
                                       ir a+ +D++++ ++  +  +  +    + +  +  +e  + ++   e + +f++a +d+i G   l   q++k   
  gi|313127436|ref|YP_004037706.1|  84 IRPARTDDFDQLIDTIRDVTESSEYVVAESIAEQLLYEDTIVRHnTVESRVFFMAAHNDDILGWTHLDlpQIEK--L 158
                                       8999***********988656555555445555555665555552566688888888*******9999556777..9 PP

                    Acetyltransf_4  75 dwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwi 151
                                       ++ + ++v + +++ + +g+g+ l++   + +k++++++ + +i + n+++i+f++a+ +  +gi ++++   g+  
  gi|313127436|ref|YP_004037706.1| 159 QNTVQVTVGV-REAYRGRGIGSRLLERALEWAKANGYRKAYNSIPAINDEAIAFLEAHDWHTEGIRRDHYTLDGTFV 234
                                       99********.589******************************99******************************* PP

                    Acetyltransf_4 152 Dmiw 155
                                       D+++
  gi|313127436|ref|YP_004037706.1| 235 DEVM 238
                                       *986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   9.4e-10   1.4e-06       4      68 ..     134     211 ..     131     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.4e-10
                                       EEEEEEETTEEEEEEEEEEES....TCTEE.....EEE-GGGTTSSHHHHHHH.H...TT.SEEEEEEEEE.....T CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld....aeitr.....laVdpeyrgkGiGraLle.a...ae.kgiileqlel.....n 61 
                                        +f a +++ i+G   l l +        +     + V+++yrg+GiG++Lle a   a+ +g++ + ++      n
  gi|313127436|ref|YP_004037706.1| 134 VFFMAAHNDDILGWTHLDLPQieklQ---NtvqvtVGVREAYRGRGIGSRLLErAlewAKaNGYR-K-AYNsipaiN 205
                                       689999*******7776666575541...25556799***************9544441145543.1.122112222 PP

                                       HHHHHHH CS
                    Acetyltransf_7  62 aekaikf 68 
                                       + +ai+f
  gi|313127436|ref|YP_004037706.1| 206 D-EAIAF 211
                                       2.56666 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.2e-08   3.4e-05      30      59 ..     166     195 ..     153     197 .. 0.91
   2 ?   -2.0   0.0       2.8   4.2e+03      22      34 ..     224     236 ..     204     238 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.2e-08
                   Acetyltransf_CG  30 TeVpeelrGkGiAkkLvkaalddareeglk 59 
                                       + V e++rG+Gi+++L ++al++a+++g++
  gi|313127436|ref|YP_004037706.1| 166 VGVREAYRGRGIGSRLLERALEWAKANGYR 195
                                       679************************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                   Acetyltransf_CG  22 egvldfthTeVpe 34 
                                        ++++++ T+V+e
  gi|313127436|ref|YP_004037706.1| 224 RDHYTLDGTFVDE 236
                                       3478888899887 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   5.7e-08   8.5e-05       2     111 ..      84     198 ..      83     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.7e-08
                                       EEEE-GGGHHHHHHHHHHHTT----H...........HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETT. CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespl.........eeireyfrklleesrvlgaedngelvgqlallplelnvpG. 68 
                                       ir+++++d+d+ ++  + + + +e  +         +e +   ++++e+  ++ a  n+++ g  +l      +p  
  gi|313127436|ref|YP_004037706.1|  84 IRPARTDDFDQLIDTIRDVTESSEYVVaesiaeqllYEDTIVRHNTVESRVFFMAAHNDDILGWTHL-----DLPQi 155
                                       99*****************99999999998888776334445678888889999999****997654.....55555 PP

                                       EEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEE CS
                    Acetyltransf_9  69 ktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsl 111
                                       ++l+    + V+v   +rgrg+ s+Ll+rale ++++g++ ++
  gi|313127436|ref|YP_004037706.1| 156 EKLQNTVQVTVGVREAYRGRGIGSRLLERALEWAKANGYRKAY 198
                                       5666666678****************************98776 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   7.3e-08   0.00011      19     109 ..     121     220 ..      99     231 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.3e-08
                   Acetyltransf_10  19 pealrerieegealllvaeeggkivGvielrdgs.......hisllfVdpeyrgqGigkaLleaveeeaekdgikl. 87 
                                       ++++ ++ + ++ ++++a  ++ i+G   l+  +           + V+++yrg+Gig++Lle+++e a+ +g+++ 
  gi|313127436|ref|YP_004037706.1| 121 EDTIVRHNTVESRVFFMAAHNDDILGWTHLDLPQieklqntVQVTVGVREAYRGRGIGSRLLERALEWAKANGYRKa 197
                                       45555555556666777778889998884432222334443333458****************************99 PP

                   Acetyltransf_10  88 eltvnasp.yavpfYeklGFkav 109
                                         ++ a + +a++f e + +++ 
  gi|313127436|ref|YP_004037706.1| 198 YNSIPAINdEAIAFLEAHDWHTE 220
                                       99999999999999999999876 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.9e-07   0.00028      30      90 ..     125     189 ..     116     223 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                              PanZ  30 leaalteegalfaarFNdRlLgAvkvel...edkeaels.dlcVRevTRrRGVgsyLleearrqa 90 
                                       ++++  e++ +f a  Nd  Lg  +++l   e+ + +++  + VRe  R RG+gs+Lle+a++ a
  gi|313127436|ref|YP_004037706.1| 125 VRHNTVESRVFFMAAHNDDILGWTHLDLpqiEKLQNTVQvTVGVREAYRGRGIGSRLLERALEWA 189
                                       455667888999***********999761114445555425779****************99866 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   6.6e-07   0.00099       4     133 ..      84     213 ..      82     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.6e-07
                    Acetyltransf_3   4 LrplteeDlealf.elrsdpevmrylpepltleeaeewlerawaeeseeegyg.waivlkdtgviGsvglrdleeed 78 
                                       +rp++ +D+++l   +r   e  +y+   ++ +e+  + +++ +  ++ e+   ++  ++d+ ++G+  l   + e 
  gi|313127436|ref|YP_004037706.1|  84 IRPARTDDFDQLIdTIRDVTESSEYVV-AESIAEQLLYEDTIVR-HNTVESRVfFMAAHNDD-ILGWTHLDLPQIEK 157
                                       89**********834655555666632.3455555444444444.44445544155544666.9****999777666 PP

                    Acetyltransf_3  79 ee..aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvle 133
                                        +  +++   ++++++g+G+++  ++ +le+a +  g+++ +  i + N   i+ le
  gi|313127436|ref|YP_004037706.1| 158 LQntVQVTVGVREAYRGRGIGSRLLERALEWA-KANGYRKAYNSIPAINDEAIAFLE 213
                                       66669999999999******************.555688888888777777777665 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4      0.31   4.6e+02      20      69 ..       7      54 ..       1      82 [. 0.66
   2 ?   13.2   0.2   4.9e-05     0.073      99     130 ..     165     196 ..      70     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.31
                    Acetyltransf_6 20 vrfrvatdpedleallelf..raqwarrpdvfadpltraflrdllaalaarg 69
                                       +f+++  + ++ +++e++  +a+++ r d+   +l+ + +r+ l++l   g
  gi|313127436|ref|YP_004037706.1|  7 PTFETE-ASKEIYQFVERHgtAARHRVR-DMV--ELPAEEFREELERLTTNG 54
                                      556553.466777788888666777777.776..566666666666665544 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.9e-05
                    Acetyltransf_6  99 lggydpelaklspgllllweliedaaeeGlrr 130
                                        +g+++++++ ++g  ll +++e+a+++G+r+
  gi|313127436|ref|YP_004037706.1| 165 TVGVREAYRGRGIGSRLLERALEWAKANGYRK 196
                                       5799*************************985 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.22      16      29 ..     206     219 ..     201     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                             UBA_4  16 ekArqlLeannWdL 29 
                                       ++A+ +Lea++W+ 
  gi|313127436|ref|YP_004037706.1| 206 DEAIAFLEAHDWHT 219
                                       89**********85 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.6e-05      0.14      16      48 ..      71     103 ..      69     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.6e-05
                                       HHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHH CS
                              HAMP  16 aarriaaGdldtrlpvsgrDEiGeLarafNaMl 48 
                                       +++r a+Gdl++++ + + D +++L+ ++++  
  gi|313127436|ref|YP_004037706.1|  71 SVERYASGDLTYSIRPARTDDFDQLIDTIRDVT 103
                                       57899**********************998876 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.1e-05      0.14      45     102 ..     121     190 ..      84     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.1e-05
                   Acetyltransf_15  45 keeLvasvfivkkkyyslvs.............silieknvleiYtlyvsekyrgkGlakklLeeslkelk 102
                                       ++ +v +  +   +++   +              i + +n +++ t+ v e yrg+G+  +lLe++l+  k
  gi|313127436|ref|YP_004037706.1| 121 EDTIVRHNTVESRVFFMAAHnddilgwthldlpQIEKLQNTVQV-TVGVREAYRGRGIGSRLLERALEWAK 190
                                       44444444444444444444777788888887666677777777.999******************87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1627.52
//
Query:       gi|313127437|ref|YP_004037707.1|  [L=299]
Description: hypothetical protein Hbor_27150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2282.60
//
Query:       gi|313127438|ref|YP_004037708.1|  [L=178]
Description: hypothetical protein Hbor_27170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      0.003   17.8   1.0      0.003   17.8   1.0    2.1  2  DUF11         Domain of unknown function DUF11
     0.0033   17.6   1.0     0.0033   17.6   1.0    2.3  3  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos
  ------ inclusion threshold ------
      0.053   13.7   0.1      0.089   13.0   0.1    1.3  1  Arteri_nsp7a  Arterivirus nonstructural protein 7 alpha


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.4   8.2e+03      30      39 ..      36      45 ..      31      68 .. 0.46
   2 !   17.8   1.0   5.1e-07     0.003      17      78 ..      88     141 ..      86     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                             DUF11 30 angvvvtDtl 39
                                      a+++ v D +
  gi|313127438|ref|YP_004037708.1| 36 AAQASVGDAP 45
                                      4555555533 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 5.1e-07
                             DUF11  17 tytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrv 78 
                                       ++t+t+tNtg   a++v+v+  l +g + v             sv +L  ges+t++ +v+v
  gi|313127438|ref|YP_004037708.1|  88 NVTITATNTGDEMAKDVTVQTQLETGDTVVWQGNE--------SVSELDSGESKTMTKRVQV 141
                                       59*********************999998877777........6689**********99987 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.1   6.4e+03      61      73 ..      35      47 ..      33      49 .. 0.78
   2 !   17.6   1.0   5.5e-07    0.0033       8      62 ..      88     142 ..      85     143 .. 0.96
   3 ?   -1.0   0.1      0.36   2.1e+03      53      66 ..     156     169 ..     151     178 .] 0.51

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                       NPCBM_assoc 61 ppagaaaGdyevt 73
                                      p a+a  Gd +vt
  gi|313127438|ref|YP_004037708.1| 35 PAAQASVGDAPVT 47
                                      6688999998887 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.5e-07
                       NPCBM_assoc   8 tltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtpp 62 
                                       ++t+t+tn+g++ a++v ++ +l  G tvv    +s+++l+ Ge+ + t +V+++
  gi|313127438|ref|YP_004037708.1|  88 NVTITATNTGDEMAKDVTVQTQLETGDTVVWQGNESVSELDSGESKTMTKRVQVG 142
                                       79************************************************99986 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.36
                       NPCBM_assoc  53 veatvkVtppagaa 66 
                                       v+a+ +Vt ++g +
  gi|313127438|ref|YP_004037708.1| 156 VTANTTVTWNSGNE 169
                                       45555555444433 PP

>> Arteri_nsp7a  Arterivirus nonstructural protein 7 alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.5e-05     0.089      74     108 ..     105     136 ..      92     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                      Arteri_nsp7a  74 gvskelkpGDvvvllGkkpvgelvdikvgdkelvl 108
                                       +v+++l++GD+vv  G+++v+el +   g+++++ 
  gi|313127438|ref|YP_004037708.1| 105 TVQTQLETGDTVVWQGNESVSELDS---GESKTMT 136
                                       899**************99777766...5544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1367.96
//
Query:       gi|313127439|ref|YP_004037709.1|  [L=40]
Description: hypothetical protein Hbor_27180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       119  (0.00663729); expected 358.6 (0.02)
Passed bias filter:                      105  (0.00585643); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.26s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 309.76
//
Query:       gi|313127440|ref|YP_004037710.1|  [L=145]
Description: hypothetical protein Hbor_27190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.5   0.1      0.074   13.0   0.1    1.2  1  LrgA      LrgA family


Domain annotation for each model (and alignments):
>> LrgA  LrgA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.2e-06     0.074       5      56 ..      90     141 ..      86     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-06
                              LrgA   5 ellsrllplpiPgsviGlllLlllLltkivklekveeaadfllkhlallFvP 56 
                                        ++ +l   p+P++v G ++L+ +L  ++++l +    a++++  l l +v 
  gi|313127440|ref|YP_004037710.1|  90 AFVRQLAAHPLPAAVAGAFVLVGALGDHFFQLPEAALSASIIVGSLGLAYVG 141
                                       57889999**********************************9999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1107.52
//
Query:       gi|313127441|ref|YP_004037711.1|  [L=224]
Description: hypothetical protein Hbor_27200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.53   10.5   2.4       0.59   10.3   0.1    2.5  4  TOBE_2    TOBE domain


Domain annotation for each model (and alignments):
>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0      0.79   1.4e+04      18      27 ..      14      23 ..       8      25 .. 0.72
   2 ?   -3.4   0.1      0.62   1.1e+04      17      23 ..      41      48 ..      29      49 .. 0.54
   3 ?   -3.1   0.0      0.52   9.3e+03       5      11 ..      69      75 ..      69      86 .. 0.63
   4 ?   10.3   0.1   3.3e-05      0.59       1      47 [.      93     141 ..      93     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.79
                            TOBE_2 18 glsGtVedve 27
                                      +++G+Ve+ve
  gi|313127441|ref|YP_004037711.1| 14 QATGQVEKVE 23
                                      5688888876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.62
                            TOBE_2 17 n.glsGtV 23
                                      + +++GtV
  gi|313127441|ref|YP_004037711.1| 41 GsTVNGTV 48
                                      23777777 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.52
                            TOBE_2  5 PEklrla 11
                                      P++++++
  gi|313127441|ref|YP_004037711.1| 69 PDHVQVH 75
                                      7888885 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 3.3e-05
                            TOBE_2   1 laiRPEklrla.aaggan.glsGtVedveylGsstryvvelaggqlvvv 47 
                                       + +R Ek++   ++g ++ +l+ t+e+ ++ G s r++v+l+ g+ +++
  gi|313127441|ref|YP_004037711.1|  93 VTVRAEKVEFIsGQGVGEgALELTIEHDIHGGQSERTRVKLPTGSTQTL 141
                                       579******9853333455************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1587.53
//
Query:       gi|313127442|ref|YP_004037712.1|  [L=167]
Description: hypothetical protein Hbor_27220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-30  104.1   0.0    4.1e-30  103.8   0.0    1.1  1  DUF192    Uncharacterized ACR, COG1430


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.0   2.3e-34   4.1e-30       2      96 .]      57     164 ..      56     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 2.3e-34
                                       EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT....-... CS
                            DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpq....s... 71 
                                       +v+vAdt e+r++GL+ +esl+++egmlfv+d+e e+s++M+++ +pLdi+f+dadg+i++i++a  p     +   
  gi|313127442|ref|YP_004037712.1|  57 NVRVADTYEKRYTGLSATESLGTNEGMLFVHDSEGEYSYVMRDMAFPLDIVFIDADGTITAIHHAELPPegtpDggl 133
                                       79**************************************************************9877756551556 PP

                                       ......ECEEEEEETTHHHHHT--TT-EEE. CS
                            DUF192  72 ......vryvLElpaGaakklgikpGdrlei 96 
                                              +yvLE+p G+++++g+++Gd+++i
  gi|313127442|ref|YP_004037712.1| 134 khytgtGKYVLEVPYGYTNETGVEVGDTVRI 164
                                       666666999*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1311.41
//
Query:       gi|313127443|ref|YP_004037713.1|  [L=96]
Description: hypothetical protein Hbor_27230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 683.25
//
Query:       gi|313127444|ref|YP_004037714.1|  [L=648]
Description: multidrug ABC transporter ATPase/permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-38  131.0   5.2    1.3e-37  129.9   5.2    1.5  1  ABC_membrane   ABC transporter transmembrane region
      2e-37  128.8   0.0    3.6e-37  127.9   0.0    1.4  1  ABC_tran       ABC transporter
    7.9e-05   23.0   0.1    0.00038   20.7   0.1    2.1  1  AAA_22         AAA domain
    0.00056   19.7   0.0     0.0012   18.6   0.0    1.5  1  AAA_24         AAA domain
     0.0021   17.4   0.0      0.004   16.4   0.0    1.4  1  Zeta_toxin     Zeta toxin
     0.0022   17.9   0.0     0.0067   16.3   0.0    1.7  1  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
     0.0024   18.4   0.0     0.0077   16.8   0.0    1.9  1  AAA_18         AAA domain
     0.0027   18.1   0.2     0.0065   16.9   0.2    1.6  1  AAA_16         AAA ATPase domain
     0.0031   17.4   0.0     0.0057   16.6   0.0    1.4  1  RsgA_GTPase    RsgA GTPase
     0.0057   16.4   0.1      0.015   15.0   0.1    1.7  1  AAA_29         P-loop containing region of AAA domain
      0.006   16.0   0.9       0.19   11.2   0.2    2.1  2  SMC_N          RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.085   13.3   0.0    2.2  1  AAA            ATPase family associated with various cellular
      0.025   14.3   0.3      0.069   12.9   0.3    1.7  1  AAA_30         AAA domain
       0.11   13.0   0.0       0.22   12.0   0.0    1.4  1  AAA_23         AAA domain
       0.14   11.8   0.1       0.65    9.7   0.1    2.0  1  Guanylate_kin  Guanylate kinase
       0.15   12.1   0.1        1.5    8.8   0.0    2.4  2  AAA_5          AAA domain (dynein-related subfamily)
       0.17   10.6   0.1       0.35    9.6   0.1    1.4  1  ABC_ATPase     Predicted ATPase of the ABC class


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   5.2   1.3e-40   1.3e-37       2     253 ..      38     303 ..      37     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.3e-40
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH...............HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpet...............ealnvysllllllglaqfilallqsy 63 
                                       ++++l++++a +l+++ p++l   +d+++  g+ ++                +l +   l+++++++ +++ + +++
  gi|313127444|ref|YP_004037714.1|  38 VIGLLSSVVARLLDLMPPVLLTLAVDSIFL-GERDFsiwlipdawlpttklGELYLSTGLIAFAFFGGAAFHWTRNW 113
                                       6899*************************7.888888999999***99887777777777777888888999***** PP

                                       HHHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHS CS
                      ABC_membrane  64 llnvtgerlskrlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylg 140
                                        +n  ++++ +++r+++++k+ r++m ff ++++Ge++s l+ndv++l+ +l++ +   f+  ++++g+ ++++y +
  gi|313127444|ref|YP_004037714.1| 114 GWNSFAQNIQHAVRTDTYDKMQRLNMDFFADKQTGEMMSILSNDVNRLERFLNDGMNSAFRLGVMVIGIAAILLYWN 190
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 141 wkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkag 217
                                       w+l++v+l ++pli ++++ + +++++   +  ++v++++s +e  l gi+++k  + e+++ ++ e+ ++++  a+
  gi|313127444|ref|YP_004037714.1| 191 WQLAIVTLLVVPLIGYFTYRFIQTIQPKYADVRSSVGRVNSRLENNLGGIQVIKTSNTESFESDRVEDVSQDYFDAN 267
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                      ABC_membrane 218 ikkaianglligitqllgllsyalalwfGttlvisg 253
                                       + ++ ++  +++++++++ + ++l++++G+++v++ 
  gi|313127444|ref|YP_004037714.1| 268 WDAIGTRIKFFPALRVMAGVGFVLTFVVGGVWVHTY 303
                                       ********************************9873 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9   0.0   3.4e-40   3.6e-37       2     137 .]     399     547 ..     398     547 .. 0.97

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 3.4e-40
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++s+++  ge++a+vG++GaGKSt+lkll+++++ +eG+i++dg+d+++ +++slr+ ig+++q++++f+++ v+e
  gi|313127444|ref|YP_004037714.1| 399 EDISFDVDGGETLALVGPTGAGKSTVLKLLMRMYDVDEGSIEIDGTDIRDVTIPSLRQAIGYVSQDTFMFYGT-VEE 474
                                       799**********************************************************************.*** PP

                                       H................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n                ++ +e+++++++l + +  dt +++++ +LSgGq+qr+++ara+lk+p++l+lDE+t+
  gi|313127444|ref|YP_004037714.1| 475 NirygtfdaaqedvveaAKAAEAHDFIQNLPDGY--DTEIGERGVKLSGGQRQRLSIARAILKDPEILVLDEATS 547
                                       ********99999998888888*******99999..9999*********************************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   3.6e-07   0.00038       7     103 ..     410     549 ..     405     577 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.6e-07
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee........................................erpevv 43 
                                        l+++G++G+GK+t+l+ l++ +d ++   e                                              
  gi|313127444|ref|YP_004037714.1| 410 TLALVGPTGAGKSTVLKLLMRMYDVDEGSIEidgtdirdvtipslrqaigyvsqdtfmfygtveenirygtF----D 482
                                       689*********************999988899999999999999999999988888888888766555442....0 PP

                            AAA_22  44 .....fvtlpsstsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.l 103
                                             v++++  +  d+ ++l   ++ e  +   +   l   + ++ + ara    +e+l++DEa   +
  gi|313127444|ref|YP_004037714.1| 483 aaqedVVEAAKAAEAHDFIQNLPDGYDTEIGE---RGVKLSgGQRQRLSIARAIlkdPEILVLDEATSdV 549
                                       33446677777778888888888888877777...55555534555555555446688899999998755 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0012       5      85 ..     411     556 ..     408     569 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie............swedfldevvel.......... 59 
                                       ++++Gp g+GK+t++k l     + d+++G+ ++d++++ d++            +          +          
  gi|313127444|ref|YP_004037714.1| 411 LALVGPTGAGKSTVLKLL---MRMYDVDEGSIEIDGTDIRDVTipslrqaigyvsQ----------Dtfmfygtvee 474
                                       789***************...99****************99977755555555540..........34444444444 PP

                            AAA_24  60 ........................................................aaeladyktlviDtideleel 80 
                                                                                               +a l+d ++lv+D ++  ++ 
  gi|313127444|ref|YP_004037714.1| 475 nirygtfdaaqedvveaakaaeahdfiqnlpdgydteigergvklsggqrqrlsiaRAILKDPEILVLDEATSDVDT 551
                                       45555555555555555777777777777777777777777777777777777777777777777777777766665 PP

                            AAA_24  81 claev 85 
                                        ++++
  gi|313127444|ref|YP_004037714.1| 552 ETEML 556
                                       55555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.8e-06     0.004      21      62 ..     413     455 ..     408     502 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-06
                        Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRel.hPeye 62 
                                       l+G +GAGKs++++ll +  + +++ +++d++d+R   +P  +
  gi|313127444|ref|YP_004037714.1| 413 LVGPTGAGKSTVLKLLMRMYDVDEGSIEIDGTDIRDVtIPSLR 455
                                       899********************************85256655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.4e-06    0.0067       3      77 ..     412     481 ..     411     495 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.4e-06
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       +l+Gp g+GKS++L++l  + +      ++++++ +g +ir+++  + + ++ + ++ ++ + ++ + ++ryg  
  gi|313127444|ref|YP_004037714.1| 412 ALVGPTGAGKSTVLKLLMRMYD-----VDEGSIEIDGTDIRDVTIPSLRQAIGYVSQDTFMFYGTVEENIRYGTF 481
                                       79***************88876.....577778888888888888888888888888888888888888888755 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.3e-06    0.0077       3     116 ..     413     566 ..     411     576 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.3e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf........................gvnlrdvakenglllevdpe...aldeskrl 52 
                                       l G+ G+GK+t+ k L ++  +                        g++++d++   g+++e+  +   +  +++++
  gi|313127444|ref|YP_004037714.1| 413 LVGPTGAGKSTVLKLLMRMYDVdegsieidgtdirdvtipslrqaiGYVSQDTFMFYGTVEENIRYgtfDAAQEDVV 489
                                       89**************9994557777899988999999999999998888888887777777777777777888888 PP

                            AAA_18  53 dedkldklldaleenss....aleegknlvidghlaeleseaakdikk..........vvLtaspeelleRlekRgy 115
                                       +  k ++++d +++ ++        +  + ++g   + +s a+ ++k             +++++e+l++R  +R +
  gi|313127444|ref|YP_004037714.1| 490 EAAKAAEAHDFIQNLPDgydtE-IGERGVKLSGGQRQRLSIARAILKDpeilvldeatSDVDTETEMLIQRSLDRLT 565
                                       8888889988888888887641.222223344444444444444444445555555556666666666666666665 PP

                            AAA_18 116 e 116
                                       e
  gi|313127444|ref|YP_004037714.1| 566 E 566
                                       5 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   6.2e-06    0.0065      24     163 ..     408     565 ..     397     573 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.2e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd............................ggiflrgkcdqlesaipysal 72 
                                       +e + l+G+ G GKs++++ l+r +  d                            + + ++g+ +++   i+y + 
  gi|313127444|ref|YP_004037714.1| 408 GETLALVGPTGAGKSTVLKLLMRMYDVDegsieidgtdirdvtipslrqaigyvsqDTFMFYGTVEEN---IRYGT- 480
                                       38899*****************9777775555555666666666666654433333233344444444...55533. PP

                            AAA_16  73 aqalareellrqlldeaesaeleawrekleeala.avpelagaeasrllellkrllallsrderplvlvlDdlq.wa 147
                                        +a+ +e+++++ +++++ +  +  ++  +++++  + +l+g   +r +  ++r++  l   ++p +lvlD++  ++
  gi|313127444|ref|YP_004037714.1| 481 FDAA-QEDVVEAAKAAEAHDFIQNLPDGYDTEIGeRGVKLSGG--QRQRLSIARAI--L---KDPEILVLDEATsDV 549
                                       3333.23555555555444444444444444444444444444..55555555666..2...456799999988888 PP

                            AAA_16 148 deaslqllaaLlrlle 163
                                       d+++ +l++  l++l+
  gi|313127444|ref|YP_004037714.1| 550 DTETEMLIQRSLDRLT 565
                                       8888888877666654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.4e-06    0.0057      88     129 ..     396     438 ..     365     453 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.4e-06
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                       + +e+++  +++ +t +lvG++G+GKSt+++ l+   ++  g+
  gi|313127444|ref|YP_004037714.1| 396 TIVEDISFDVDGgETLALVGPTGAGKSTVLKLLMRMYDVDEGS 438
                                       45688999999989*****************999876665555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.4e-05     0.015      16      39 ..     400     425 ..     394     430 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                            AAA_29  16 tieidlkg..atlltGpsGsGKSTll 39 
                                       +i++d++g  +  l+Gp+G+GKST+l
  gi|313127444|ref|YP_004037714.1| 400 DISFDVDGgeTLALVGPTGAGKSTVL 425
                                       5667777777889***********97 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.046        49      27      42 ..     411     426 ..     398     431 .. 0.84
   2 !   11.2   0.2   0.00018      0.19     136     210 ..     518     588 ..     426     594 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.046
                                       EEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlld 42 
                                        a+vGp G+GKs +l 
  gi|313127444|ref|YP_004037714.1| 411 LALVGPTGAGKSTVLK 426
                                       589*********9985 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00018
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvg 210
                                        LSgG+++ +++a   Ai   k   + +lDe  +  D +    + + l++ +++   + i++r  ++++ad+++ 
  gi|313127444|ref|YP_004037714.1| 518 KLSGGQRQRLSIAR--AI--LKDPEILVLDEATSDVDTETEMLIQRSLDRLTEDRTTFSIAHRLSTIKDADQIIV 588
                                       79****98666553..44..5566689********************************************9985 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     8e-05     0.085       2      47 ..     412     477 ..     411     583 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-05
                                       EEESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS..................STTHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakelgve..fleisgsellsk..................yvgesekkir 47 
                                        l+Gp G GK+++ k +++  +v+   +ei+g+++++                   + g  e++ir
  gi|313127444|ref|YP_004037714.1| 412 ALVGPTGAGKSTVLKLLMRMYDVDegSIEIDGTDIRDVtipslrqaigyvsqdtfmFYGTVEENIR 477
                                       599*****************9755337999999999656777777777777777774444444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   6.6e-05     0.069      19      48 ..     409     438 ..     403     567 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggr 48 
                                        + +l+Gp G+GK+t+lk l ++++ ++g+
  gi|313127444|ref|YP_004037714.1| 409 ETLALVGPTGAGKSTVLKLLMRMYDVDEGS 438
                                       46789***************9999877433 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021      0.22      15      38 ..     401     427 ..     391     431 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                            AAA_23  15 idF...skgltlItGpNGaGKTTildA 38 
                                       i F   +    +++Gp+GaGK+T+l  
  gi|313127444|ref|YP_004037714.1| 401 ISFdvdGGETLALVGPTGAGKSTVLKL 427
                                       4444444445589**********9975 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00062      0.65       4      94 ..     410     493 ..     407     497 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00062
                                       EEEEESTTTSSHHHHHHHHHHHSTTTEE.E--EEESS---TTS-TTTSEEE-.-HHHHHHHHHTTTEEEEEEETTEE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg.vsvshtTrdprkgevdGkdYyFv.skeemekdiskneflEaaefsgnl 78 
                                       ++ lvgp+gaGks++ k L++ +    g + +  t  d+r           + s ++    +s++ f+ ++++++n+
  gi|313127444|ref|YP_004037714.1| 410 TLALVGPTGAGKSTVLKLLMRMYDVDEGsIEIDGT--DIRD--------VTIpSLRQAIGYVSQDTFMFYGTVEENI 476
                                       788**************999998877763444433..4444........1123555555556777788888766664 PP

                                       .EEEEHHHHHHHHHTTS CS
                     Guanylate_kin  79 .ygtsveaieevlekgk 94 
                                        ygt  +a e v e +k
  gi|313127444|ref|YP_004037714.1| 477 rYGTFDAAQEDVVEAAK 493
                                       47777777777777766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0014       1.5       3      23 ..     412     432 ..     410     472 .. 0.89
   2 ?    0.1   0.0      0.69   7.3e+02      49      88 ..     520     556 ..     504     589 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                                       EEE--SSSSHHHHHHHGGGGB CS
                             AAA_5   3 lLvGppGtgKselaerlaaal 23 
                                        LvGp+G gKs++ + l +++
  gi|313127444|ref|YP_004037714.1| 412 ALVGPTGAGKSTVLKLLMRMY 432
                                       69***************9998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.69
                                       ........--------G-SEEEEESGGG--HHHHHHHHHH CS
                             AAA_5  49 ngttslvdsplvraaregeilvlDEveraesevlnsLlsl 88 
                                       +g+++ + s++    + +eilvlDE +   s+v  +  +l
  gi|313127444|ref|YP_004037714.1| 520 SGGQRQRLSIARAILKDPEILVLDEAT---SDVDTETEML 556
                                       5555555666666677999*****987...5554444444 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00033      0.35     300     352 ..     495     548 ..     482     594 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00033
                                       E--TTTB---CCC--ST.TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS- CS
                        ABC_ATPase 300 vDispFinnLPegkdtt.kfstedASGStsqAanimealeagakllLiDEDtsA 352
                                       ++   Fi+nLP g dt+      + SG   q  +i++a+  + ++l++DE ts 
  gi|313127444|ref|YP_004037714.1| 495 AEAHDFIQNLPDGYDTEiGERGVKLSGGQRQRLSIARAILKDPEILVLDEATSD 548
                                       56789************76677799*************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (648 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.43
# Mc/sec: 4562.53
//
Query:       gi|313127445|ref|YP_004037715.1|  [L=248]
Description: hypothetical protein Hbor_27250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-71  238.9   3.6      6e-71  238.7   3.6    1.0  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.7   3.6   3.3e-75     6e-71       2     240 ..       5     232 ..       4     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: 238.7 bits;  conditional E-value: 3.3e-75
                      Creatininase   2 eltwpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTis 78 
                                       e tw++v +++ e+++a+lPvGstEqHGph+plgtD+++aea+a++  e+++++++v+Ptlp+Gv++eh++fpGT++
  gi|313127445|ref|YP_004037715.1|   5 EATWTDVSDLAGETNLAFLPVGSTEQHGPHAPLGTDAFTAEAVADAGSEAYDGEVVVAPTLPIGVAAEHRQFPGTLW 81 
                                       78*********************************************9***999*********************** PP

                      Creatininase  79 lspetliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaae 155
                                       lsp+t+++ +r++++sla hGf+r+v+vngHggn++al+e+  ++++e da av +           ++      + 
  gi|313127445|ref|YP_004037715.1|  82 LSPDTFRDTVRETVASLASHGFDRVVVVNGHGGNTDALREVTGTITREDDAYAVAF-----------TWF-----EA 142
                                       *************************************************6665432...........222.....22 PP

                      Creatininase 156 eseeeegggHAgelEtSlmlalrpelVrmdraedpeeaklakeg.....vstaedaeelspsGvlGdpskataekGe 227
                                       + e+++++gH+g+lEt+l+ +++pe+Vr++r+e+++e  ++++g     v+ a+d  e++++Gv+Gdps+ +ae Ge
  gi|313127445|ref|YP_004037715.1| 143 VGEHSSKMGHGGPLETALLRHVAPESVREERIETAREGGADRWGdwvskVNLAHDSAEFTANGVVGDPSAGDAELGE 219
                                       34445599********************************************************************* PP

                      Creatininase 228 alleaaveelael 240
                                       +lle a ++la+l
  gi|313127445|ref|YP_004037715.1| 220 ELLELASASLARL 232
                                       ********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1583.24
//
Query:       gi|313127446|ref|YP_004037716.1|  [L=164]
Description: hypothetical protein Hbor_27260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      0.003   18.1   6.0       0.49   11.0   0.1    2.8  3  DUF883       Bacterial protein of unknown function (DUF883)
  ------ inclusion threshold ------
      0.012   15.7   3.9       0.16   12.1   1.0    2.3  2  TPR_MLP1_2   TPR/MLP1/MLP2-like protein
       0.02   15.0   0.1      0.037   14.1   0.1    1.5  1  Rap1_C       TRF2-interacting telomeric protein/Rap1 - C term
       0.17   12.5   5.1      0.085   13.5   2.3    1.9  2  SlyX         SlyX
       0.18   12.2   0.7       0.18   12.2   0.7    3.2  4  LPP          Lipoprotein leucine-zipper


Domain annotation for each model (and alignments):
>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00014      0.49      24      59 ..      12      47 ..       4      54 .. 0.84
   2 ?   -3.5   0.0       4.8   1.7e+04      37      44 ..      66      73 ..      61      79 .. 0.54
   3 !    7.7   2.5    0.0015       5.4       5      61 ..      89     140 ..      86     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                            DUF883 24 eageeaeelRerleerlerarerlrdaeeavaerak 59
                                        ge aee+R+++ee+l++are+l da     ++a+
  gi|313127446|ref|YP_004037716.1| 12 LFGEAAEEMRAEVEEHLDAAREELPDADTVWSAEAD 47
                                      56899*******************999877666665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.8
                            DUF883 37 eerlerar 44
                                      e++l++a+
  gi|313127446|ref|YP_004037716.1| 66 EDNLRQAK 73
                                      33344433 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0015
                            DUF883   5 aeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakea 61 
                                       ++le+ +a++eell++ +d     a +l  +l++++ ++r++l+da++av +  +ea
  gi|313127446|ref|YP_004037716.1|  89 DDLEEEIASVEELLETLGD-----AGDLVGELTSTMPQLRSQLQDAADAVDAAESEA 140
                                       7888888999999987776.....455556666666667777776666654443333 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0079        28      69     108 ..      17      56 ..      13      69 .. 0.80
   2 ?   12.1   1.0   4.3e-05      0.16      32     100 ..      78     146 ..      57     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0079
                        TPR_MLP1_2  69 lkaeiaelkaeaesakaeleeseesweeqkeelekelsel 108
                                       +++ +ae+++ +++a++el  +   w+ + +++   l+ l
  gi|313127446|ref|YP_004037716.1|  17 AEEMRAEVEEHLDAAREELPDADTVWSAEADNILGVLNGL 56 
                                       5677889999999999999999999999888776666555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.3e-05
                        TPR_MLP1_2  32 ekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkee 100
                                         q+++a +  ++ e+e+   +e +++l ++ + + el++++ +l++++++a  +++++e++ ++ +++
  gi|313127446|ref|YP_004037716.1|  78 IGQRAEAFDDADDLEEEIASVEELLETLGDAGDLVGELTSTMPQLRSQLQDAADAVDAAESEADTDEDT 146
                                       45666666667779*********************************************9998887765 PP

>> Rap1_C  TRF2-interacting telomeric protein/Rap1 - C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     1e-05     0.037      26      71 ..      20      73 ..      15      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                            Rap1_C 26 lanyvlealkr.gkglpknkrGiWteedDeaL..........kagderdlerlekkh 71
                                      +   v e+l++ +++lp +   +W++e D++L          + gd++d   l + +
  gi|313127446|ref|YP_004037716.1| 20 MRAEVEEHLDAaREELP-DADTVWSAEADNILgvlnglrsslDVGDAED--NLRQAK 73
                                      788999*****999***.9999**********99999876552233333..333333 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.5   5.3e+03      37      45 ..      25      33 ..      15      45 .. 0.52
   2 ?   13.5   2.3   2.4e-05     0.085       6      60 ..      89     146 ..      86     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                                      HHHHHHHHH CS
                              SlyX 37 qrqlrllae 45
                                      +++l++ +e
  gi|313127446|ref|YP_004037716.1| 25 EEHLDAARE 33
                                      233333333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXX CS
                              SlyX   6 eeLEiklafqedtieeLndv...vaeqqqqidrlqrqlrllaerlkeleessgaseae 60 
                                       ++LE+++a  e+++e+L d+   v e   ++ +l+ ql+  a+ + ++e+++ ++e+ 
  gi|313127446|ref|YP_004037716.1|  89 DDLEEEIASVEELLETLGDAgdlVGELTSTMPQLRSQLQDAADAVDAAESEADTDEDT 146
                                       79***************8654449*********************8888887766553 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.6   5.9e+03      26      30 ..      20      24 ..       3      34 .. 0.52
   2 ?   -2.2   0.0       1.6   5.6e+03      10      21 ..      89     100 ..      85     108 .. 0.56
   3 ?   12.2   0.7   4.9e-05      0.18       9      37 ..     112     140 ..     109     142 .. 0.94
   4 ?   -0.5   3.6      0.45   1.6e+03      21      38 ..     144     161 ..     141     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                               LPP 26 akaaa 30
                                      ++a++
  gi|313127446|ref|YP_004037716.1| 20 MRAEV 24
                                      33333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                               LPP  10 sqLkskvdqlss 21 
                                        +L+++++++++
  gi|313127446|ref|YP_004037716.1|  89 DDLEEEIASVEE 100
                                       445555555544 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 4.9e-05
                               LPP   9 VsqLkskvdqlssdvnsakaaaqaakeEA 37 
                                       V +L s + ql s++++a++a++aa  EA
  gi|313127446|ref|YP_004037716.1| 112 VGELTSTMPQLRSQLQDAADAVDAAESEA 140
                                       789*************************9 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.45
                               LPP  21 sdvnsakaaaqaakeEAa 38 
                                       +d++++ a+a+++ +EA+
  gi|313127446|ref|YP_004037716.1| 144 EDTEESDADADDTADEAE 161
                                       789999**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1440  (0.0803168); expected 358.6 (0.02)
Passed bias filter:                      729  (0.0406604); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1087.22
//
Query:       gi|313127447|ref|YP_004037717.1|  [L=114]
Description: hypothetical protein Hbor_27270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-42  142.6   0.0    6.7e-42  142.4   0.0    1.0  1  DHNA      Dihydroneopterin aldolase


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4   0.0   3.7e-46   6.7e-42       1     107 [.       3     109 ..       3     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 3.7e-46
                                       -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-S..TS-EE--TT CS
                              DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleeklee..fgYteLtge 75 
                                       td+++A+FEagik+g+lyHqf+GtPvs+esa+sl++aieesi +QP++e+v+v+i+r++le++le+   +YteLtg+
  gi|313127447|ref|YP_004037717.1|   3 TDAQNACFEAGIKFGSLYHQFAGTPVSPESADSLARAIEESIANQPYCEAVRVTIRRDELEAALEDatADYTELTGR 79 
                                       799************************************************************9997567******* PP

                                       TEEEEEEEEETTEEEEEEEEEETTTTEEEEEE CS
                              DHNA  76 mldveitvkyeeaevkarleyieeldYplmkv 107
                                       +ldve++++ye++ v++++e+  e++Yplmk+
  gi|313127447|ref|YP_004037717.1|  80 FLDVEMDIEYEGTAVQTKMEM--EDGYPLMKL 109
                                       *********************..*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.52
# Mc/sec: 663.73
//
Query:       gi|313127448|ref|YP_004037718.1|  [L=254]
Description: NAD dependent epimerase/dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-20   72.9   0.0    3.5e-20   72.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.8e-15   55.6   0.0    4.7e-15   55.3   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.8e-11   42.9   0.0    8.2e-11   42.1   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
    1.3e-10   40.9   0.2      1e-07   31.4   0.3    2.8  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    6.4e-10   38.9   0.0    1.2e-09   38.0   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.1e-09   37.0   0.0    1.2e-08   34.5   0.0    1.8  2  NAD_binding_4    Male sterility protein
    3.8e-05   23.4   0.0    5.3e-05   22.9   0.0    1.2  1  NmrA             NmrA-like family
    0.00017   20.8   0.0    0.00033   19.8   0.0    1.4  1  RmlD_sub_bind    RmlD substrate binding domain
    0.00041   20.6   0.0    0.00074   19.8   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
        0.2   11.1   0.0        0.5    9.8   0.0    1.6  2  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   1.9e-23   3.5e-20       1     172 [.       5     182 ..       5     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.9e-23
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihlAav 74 
                                       +l+tGa G +G+a++++l ++  e+  ldr+   ++++r + +   +++  d+td++a+e++++  ++ avihlA+ 
  gi|313127448|ref|YP_004037718.1|   5 VLLTGAGGRVGQAILRHLGDR-FEWRLLDRE-PLGAEKRPDGVgeeDVYVTDITDEEAVEAAMD--GVYAVIHLAGD 77 
                                       699****************97.699999998.44555566666899******************..9*******888 PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSS...SS......BSTCSTTS--.--SSH CS
                         Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdae...qp......keettltgpl.kpnsp 141
                                         ++a +++   ++++n+ gt +++eaa +agv+++ f+sS +  G+ ++   +p      +   ++ ++l +p++ 
  gi|313127448|ref|YP_004037718.1|  78 PRPEAPWDS---VLRNNIDGTHTIFEAAVDAGVEKIAFASSNHAVGAYETderTPemyrpeDGFRLDGTELpHPSNL 151
                                       888887777...899****************************99955554433445544544455555668***** PP

                                       HHHHHHHHHHHHHHHHHHHT-EEEEEEESEE CS
                         Epimerase 142 YaaaKlageklveayaaqyglnaiilrlfnl 172
                                       Y+++K++ge l ++y + ++l+++++r+ nl
  gi|313127448|ref|YP_004037718.1| 152 YGVSKATGEVLGRYYYDHHDLSVVNVRIGNL 182
                                       ****************************997 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   2.6e-18   4.7e-15       2     123 ..       7     122 ..       6     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.6e-18
                         3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvd 78 
                                       +tG++G +G+a+ ++L ++    e r lD +      ++   v+ ++v  +D+td++ +e+a++gv++vihl  + d
  gi|313127448|ref|YP_004037718.1|   7 LTGAGGRVGQAILRHLGDRF---EWRLLDREPLGAE-KRPDGVGEEDVYVTDITDEEAVEAAMDGVYAVIHL--AGD 77 
                                       79************997665...799***7665544.5678899999*************************..568 PP

                         3Beta_HSD  79 vagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpn 123
                                        + +   d++ + n+ GT+++ ea+v+agv+++ + Ss  +vg  
  gi|313127448|ref|YP_004037718.1|  78 PRPEAPWDSVLRNNIDGTHTIFEAAVDAGVEKIAFASSNHAVGAY 122
                                       89999*************************************983 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   4.6e-14   8.2e-11       1     155 [.       9     192 ..       9     197 .. 0.66

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.6e-14
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT.TTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleae.eglevvegdvtdvedlaealkgadaVvsalggggk... 73 
                                       GA G+vG++++++l +r  +e ++l R+p  +++ ++   + +v + d+td+e++++a++g+ aV+  +g  +    
  gi|313127448|ref|YP_004037718.1|   9 GAGGRVGQAILRHLGDR--FEWRLLDREPLGAEKRPDGvGEEDVYVTDITDEEAVEAAMDGVYAVIHLAGDPRPeap 83 
                                       9*************999..9********988887775537778999********************99988777667 PP

                                       .....HHHH....HHHHHHHHHHCT--EEEEEEE...TTTTSGCGCHHHHHHHH............CCHHHHHHHHH CS
                    NAD_binding_10  74 .....deeg....aknivdaakeagvkRfvlvsa...igvgdevpgefgewnke............llkaylaakra 126
                                            +       + +i +aa  agv+++ + s+   +g+++ ++++++e+++               ++ +   +a
  gi|313127448|ref|YP_004037718.1|  84 wdsvlR--NnidgTHTIFEAAVDAGVEKIAFASSnhaVGAYE-TDERTPEMYRPedgfrldgtelpHPSNLYGVSKA 157
                                       755652..04577********************843344553.3333333322112121112222222333433333 PP

                                       HHHHHHH.....SSSEEEEEEE-CEE-S.T--SEE CS
                    NAD_binding_10 127 aeellra.....sgldwTivrpggLtde.pttkyr 155
                                         e+l +      +l  + vr g Lt++ p+ +y+
  gi|313127448|ref|YP_004037718.1| 158 TGEVLGRyyydhHDLSVVNVRIGNLTEGhPPIDYE 192
                                       33333222333377777777777777763355665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.3   5.7e-11     1e-07       1     133 [.       5     120 ..       5     125 .. 0.83
   2 !    5.4   0.0    0.0046       8.3     133     171 ..     147     182 ..     145     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 5.7e-11
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vl+tGagG +G++++r++ ++   + +ll+r+ l   +  + +     ++++       ++d++d+e +e a++  +
  gi|313127448|ref|YP_004037718.1|   5 VLLTGAGGRVGQAILRHLGDR--FEWRLLDREPLGAEKRPDGV----GEEDV------YVTDITDEEAVEAAMD--G 67 
                                       789999999999999988765..45567777766554444333....33333......489*************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvn 133
                                       v +v+h A     P  e  + +++++N+ gt+++ eaa++agv+k+ + S+  Av 
  gi|313127448|ref|YP_004037718.1|  68 VYAVIHLAGD---PRPEAPWDSVLRNNIDGTHTIFEAAVDAGVEKIAFASSNHAVG 120
                                       ********86...999************************************9995 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0046
                                       S--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EE CS
                   Polysacc_synt_2 133 nPtnvmGatKrlaekllqalakeseekktkfvvvRfGNV 171
                                       +P n++G++K++ e l   + +++   +  +v vR GN 
  gi|313127448|ref|YP_004037718.1| 147 HPSNLYGVSKATGEVLGRYYYDHH---DLSVVNVRIGNL 182
                                       599***********9999988887...8999******96 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   6.8e-13   1.2e-09       1     182 [.       6     181 ..       6     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 6.8e-13
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L TG  G +G+ ++++L ++ +e   + +r+ + + +r + + ++          ++  D+tD++++e +++ v   
  gi|313127448|ref|YP_004037718.1|   6 LLTGAGGRVGQAILRHLGDR-FEW-RLLDREPLGAEKRPDGVGEE---------DVYVTDITDEEAVEAAMDGV--Y 69 
                                       56777777777777777766.444.34445555565666666532.........36779**************9..7 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-.TT......... CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqt.Et......... 144
                                       +v++LA+    +  +++   ++++n+ Gt++++ea+ ++g+e   ++ +aS+    G  +    t E          
  gi|313127448|ref|YP_004037718.1|  70 AVIHLAGDPRPEAPWDS---VLRNNIDGTHTIFEAAVDAGVE---KIAFASSNHAVGAYETDERTpEMyrpedgfrl 140
                                       ***************97...99******************97...7889********99754433131333335555 PP

                                       ...S-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-E CS
                     GDP_Man_Dehyd 145 ...tpfyPrsPYaaaKlyadwivvnyreayglfavngilfn 182
                                             +P + Y+++K++ + + + y++ ++l +vn ++ n
  gi|313127448|ref|YP_004037718.1| 141 dgtELPHPSNLYGVSKATGEVLGRYYYDHHDLSVVNVRIGN 181
                                       5525559*******************************999 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.18   3.3e+02       1      16 [.       7      22 ..       7      28 .. 0.90
   2 !   34.5   0.0   6.5e-12   1.2e-08      78     209 ..      58     186 ..      54     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.18
                                      EE-TTSHHHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekL 16
                                      lTGa G +G+ +l+ L
  gi|313127448|ref|YP_004037718.1|  7 LTGAGGRVGQAILRHL 22
                                      8************988 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 6.5e-12
                                       HHHHHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvye 153
                                       ee+++  ++ v ++ih a++ + ++p + +lr N++Gt+ ++e a        + + S+  +v  ++++e + ++y+
  gi|313127448|ref|YP_004037718.1|  58 EEAVEAAMDGVYAVIHLAGDPRPEAPWDSVLRNNIDGTHTIFEAAVDAGVE-KIAFASSnHAVGAYETDERTPEMYR 133
                                       6778888999***********************************987766.8999999855555555555566665 PP

                                       ......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.- CS
                     NAD_binding_4 154 egekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.e 209
                                           +e    ++ ++l   +n Y  sKa +E l r + ++++l vv vR++++t  +
  gi|313127448|ref|YP_004037718.1| 134 ----PEDGFRLDGTELPHPSNLYGVSKATGEVLGRYYYDHHDLSVVNVRIGNLTEgH 186
                                       ....55566677777888999******************************999753 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     3e-08   5.3e-05       1     114 [.       5     127 ..       5     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3e-08
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SEEEE---GG. CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelv.kgdlddkeslvealkgvdvvfsvtgfy. 75 
                                       +l +Ga Gr G+++ r+l  + ++ r l R++ + + k     G e v   d+ d+e +++a++gv++v+   g   
  gi|313127448|ref|YP_004037718.1|   5 VLLTGAGGRVGQAILRHLG-DRFEWRLLDREPLGAE-KRPDGVGEEDVyVTDITDEEAVEAAMDGVYAVIHLAGDPr 79 
                                       6889************976.57**********7765.45577788888899**********************9659 PP

                                       .........S-HHHHHHHHHHHHHHHS-SEEEEEE---GG.GT.SSS- CS
                              NmrA  76 .........skeiedgkklvdAakeaGvkhfiySslgddndrsnaeep 114
                                                +++i+   ++ +Aa+ aGv+++ ++s   ++ +++ +e 
  gi|313127448|ref|YP_004037718.1|  80 peapwdsvlRNNIDGTHTIFEAAVDAGVEKIAFASSNHAVGAYETDER 127
                                       99999***99*************************9999988877765 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.9e-07   0.00033       3     135 ..       5     162 ..       3     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-07
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.................T--TTSHHHHHHHHHHH--SEEEE----- CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre.................eldltdaeavaellkeakpdvvvnaAAyt 62 
                                       +l+tGa+G +G+++ + l  + +e   l+re                  +d+td+eav+++++     +v+++A   
  gi|313127448|ref|YP_004037718.1|   5 VLLTGAGGRVGQAILRHLGDR-FEWRLLDREplgaekrpdgvgeedvyVTDITDEEAVEAAMDG--VYAVIHLAGDP 78 
                                       79************9999866.688888898999999**********99**************9..567***99754 PP

                                       -HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEE.EEEEGGGS-S-.....TTS-B-TTS........----SSHH CS
                     RmlD_sub_bind  63 avDkaEseeeaayavnaeavealAeaaaavgalLi.hvStDyVFdGe.....kkrpYeedd........etsPlnvY 125
                                          + E   ++  + n ++++++ eaa  +g+  i + S+     +      +++ Y+++d         ++P n+Y
  gi|313127448|ref|YP_004037718.1|  79 ---RPEAPWDSVLRNNIDGTHTIFEAAVDAGVEKIaFASSNHAVGAYetderTPEMYRPEDgfrldgteLPHPSNLY 152
                                       ...56888999999*****************97551667766543334556566668877633333322689***** PP

                                       HHHHHHHHHH CS
                     RmlD_sub_bind 126 GrtKlaGEqa 135
                                       G +K+ GE  
  gi|313127448|ref|YP_004037718.1| 153 GVSKATGEVL 162
                                       ********75 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.1e-07   0.00074       1      96 [.       5      94 ..       5     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.1e-07
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsp 78
                                      vl+ Ga G+vGqa+++ l ++f    e+ + dr+  ++e+  +     + + +  d+ ++ea ++a++ +  +v++l++
  gi|313127448|ref|YP_004037718.1|  5 VLLTGAgGRVGQAILRHLGDRF----EWRLLDREPLGAEKRPD--GVGEEDVYVTDITDEEA-VEAAMDGVYAVIHLAG 76
                                      6889****************98....689********999997..44555667777888888.**************** PP

                                      GGGHHHHHHHHHHHT-EE CS
                   Sacchrp_dh_NADP 79 pissldvlkaCietgvhy 96
                                      +   ++ ++  +++ ++ 
  gi|313127448|ref|YP_004037718.1| 77 DPRPEAPWDSVLRNNIDG 94
                                      *98888887777776665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00028       0.5       3      71 ..       5      68 ..       3      76 .. 0.93
   2 ?   -2.2   0.0       1.3   2.3e+03     100     122 ..      82     105 ..      77     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00028
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealveka 71
                                      vl tGa++ +G+ai ++l  + ++  ++dr++  +e+  + ++ee     ++ +D+td+e+vea+++ +
  gi|313127448|ref|YP_004037718.1|  5 VLLTGAGGRVGQAILRHLGDR-FEWRLLDREPLGAEKRPDGVGEE----DVYVTDITDEEAVEAAMDGV 68
                                      89****************988.9********************96....8999************9987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                       H.HHHHHHHHTHHHHHHHHHHHHH CS
                         adh_short 100 e.wervievNltgvflltravlpa 122
                                       + w++v+  N+ g+  + +a+++a
  gi|313127448|ref|YP_004037718.1|  82 ApWDSVLRNNIDGTHTIFEAAVDA 105
                                       348899999998888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1580.84
//
Query:       gi|313127449|ref|YP_004037719.1|  [L=206]
Description: hypothetical protein Hbor_27290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-19   68.1   2.6    5.8e-19   67.5   2.6    1.3  1  DUF309    Domain of unknown function (DUF309)


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   2.6   3.3e-23   5.8e-19       2      58 ..       6      64 ..       5      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 3.3e-23
                            DUF309  2 eeaielfnegeffeaHEvlEelWkeagep..erkllqglIqlAvAlyhlrrgnvrgakr 58
                                      + +++ fn+g++++aH+++E+ W + +++  +++ll+glIq  +A++h+r++n++ga+ 
  gi|313127449|ref|YP_004037719.1|  6 RVGAAVFNAGDYHAAHDAWEDEWLALEDDtaDERLLHGLIQYTAAVHHVRNRNWSGAQG 64
                                      66899******************88888779999***********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1405.18
//
Query:       gi|313127450|ref|YP_004037720.1|  [L=379]
Description: citrate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   7.6e-126  420.0   0.0   8.7e-126  419.8   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.8   0.0  4.9e-130  8.7e-126       1     361 []       8     362 ..       8     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 419.8 bits;  conditional E-value: 4.9e-130
                                       GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHH CS
                      Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlea 77 
                                       gl+gv ++e+e+s++dg++g+l+YRG++ie+La +++s+eev+ylL++gelPt+e+l+ef+  +ae+r+l+++vl++
  gi|313127450|ref|YP_004037720.1|   8 GLEGVLVAESELSYIDGDAGQLVYRGHTIEDLA-RNASYEEVVYLLWHGELPTREQLDEFSTAMAEERELDDAVLDE 83 
                                       899******************************.8****************************************** PP

                                       HHCSS.TTS-HHHHHHHHHHHHHHHSTTCTCHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHH CS
                      Citrate_synt  78 lealp.kdahpmavlraavsalsaddeeseakee.seeaalrdalkliAklptiaaaiyrarlgreplepddklsya 152
                                       ++al  +d  pma+lr+ vs+lsa+d+++++++    +  +++ +++ Ak+pt++aa+ r r+g++ ++p+++ls+a
  gi|313127450|ref|YP_004037720.1|  84 IRALAaADEVPMAALRTIVSSLSAYDDDADHEDVtDLKTNIKKGCRITAKIPTALAAFNRLRNGEDVVHPRTDLSHA 160
                                       **9998999*****************9955555556677899999*******************8666***99**** PP

                                       HHHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHH CS
                      Citrate_synt 153 enflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmle 229
                                       +nflyml+g++pd+ +a+ +d+alvlhaDH+lnaSTf a v+aStl+dl+sa++++ig+l+G lhggan  v++ml+
  gi|313127450|ref|YP_004037720.1| 161 ANFLYMLNGEEPDDVLAETFDMALVLHADHGLNASTFSAMVTASTLSDLHSAVTSAIGTLAGSLHGGANANVMRMLK 237
                                       ***************************************************************************** PP

                                       HHSSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHH CS
                      Citrate_synt 230 eigsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklaeeleevapevlkeke 306
                                       ei++++++  +++e++l+++ +r+pGfGHrvy ++DpRakil e  e l e  g+ ++++ + ++e+ + e     e
  gi|313127450|ref|YP_004037720.1| 238 EIDESDKDPTQWVEDALESG-RRVPGFGHRVYNVKDPRAKILGEKSEALGEAAGDMKWYDYSVAIEDYIGE-----E 308
                                       **88888***********96.**************************************************.....8 PP

                                       GCT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------E CS
                      Citrate_synt 307 eknlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileqladnkiiRPr 361
                                        k+l pNvDfys+ +y+++gip +++t++fa+sRv Gw+Ah++eq +dn++iRPr
  gi|313127450|ref|YP_004037720.1| 309 -KGLAPNVDFYSASTYYQMGIPVDIYTPIFAMSRVGGWIAHVIEQFEDNRLIRPR 362
                                       .*******************************************99********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2755.92
//
Query:       gi|313127451|ref|YP_004037721.1|  [L=138]
Description: aig2-like family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-11   42.6   0.1      1e-10   42.2   0.1    1.1  1  GGACT     Gamma-glutamyl cyclotransferase, AIG2-like
  ------ inclusion threshold ------
      0.046   14.1   0.0       0.07   13.5   0.0    1.3  1  AIG2_2    AIG2-like family


Domain annotation for each model (and alignments):
>> GGACT  Gamma-glutamyl cyclotransferase, AIG2-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   1.2e-14     1e-10       1     105 [.       4      94 ..       4     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.2e-14
                                       EEESSTTSTTSCCCHHHHCSECEEEEEEEECCTBEEEE.ETTTEEEETTSSE.EEEEEEEE-HHHHHHHHHCT.TTT CS
                             GGACT   1 vFvYGtLkrgepnhqrlllgarflesgpatlkgyrlydlggkypalvpgdgekVkGelyevddeelarLDelEpeep 77 
                                       +FvYGtL   +++    ll++   +  +  l+g +++   g yp l p  g++V+G +++ d  ++a LDe+E+ + 
  gi|313127451|ref|YP_004037721.1|   4 FFVYGTLT--DAERVDSLLDDWSYGP-TVELDGLHRVE--GRYPTLAP--GGSVHGRILRTD--DVATLDEYEGVAS 71 
                                       6*******..4555455657344433.33799988875..89*****8..888******965..599******999* PP

                                       TSEEEEEEEEEC.TTS-EEEEEEEEETT CS
                             GGACT  78 seYereevkvevledgeqveawvYvyag 105
                                       ++Y+r+  +v+ +++g   ea+vYv + 
  gi|313127451|ref|YP_004037721.1|  72 GLYIRV--EVPRDDGG---EAFVYVGDA 94 
                                       ******..88883333...457888744 PP

>> AIG2_2  AIG2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.8e-06      0.07      10      34 ..      56      80 ..      49      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-06
                            AIG2_2 10 dlenlkdLDkqEgvedgiyrpievr 34
                                       + ++  LD++Egv+ g+y+++ev+
  gi|313127451|ref|YP_004037721.1| 56 RTDDVATLDEYEGVASGLYIRVEVP 80
                                      5678899*************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 949.65
//
Query:       gi|313127452|ref|YP_004037722.1|  [L=403]
Description: l-threonine ammonia-lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-86  288.7   5.4    6.1e-86  288.5   5.4    1.1  1  PALP             Pyridoxal-phosphate dependent enzyme
    3.8e-06   27.4   2.3      2e-05   25.1   0.1    2.9  4  ACT_4            ACT domain
    4.6e-05   23.1   0.5    0.00016   21.3   0.0    2.3  2  ACT              ACT domain
     0.0018   18.4   0.0     0.0036   17.4   0.0    1.4  1  CagE_TrbE_VirB   CagE, TrbE, VirB family, component of type I
     0.0036   16.6   0.1      0.014   14.7   0.1    1.9  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.5   5.4   1.7e-89   6.1e-86       3     294 .]      16     304 ..      14     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 288.5 bits;  conditional E-value: 1.7e-89
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGl 79 
                                       ++++ TPl  ++ +++ +g+ + lKlE+++ tgSfK+Rga +++++l e+++  +vv+as+GNh++++A+aa ++G+
  gi|313127452|ref|YP_004037722.1|  16 GVAKHTPLDYSHTFTEMTGASVHLKLENHQRTGSFKIRGAMNRITTLSEAEKEAGVVTASAGNHAQGVALAATRAGV 92 
                                       66789*********************************************9************************** PP

                                       EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTT CS
                              PALP  80 kvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlgg 156
                                       ++ +v+p++a+ +kv+++r++Gae v++g dydea+++a+e++ e e++++v+ fd+++v++g+gtiglEi++++ +
  gi|313127452|ref|YP_004037722.1|  93 DSKVVMPEHAPISKVKATRRYGAETVLYGADYDEAQQRAHEIEDE-ENRTYVHAFDDEYVMAGQGTIGLEIVDDC-P 167
                                       *********************************************.*****************************.6 PP

                                       TEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHH CS
                              PALP 157 kpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafell 233
                                       ++++vvvp+GgGgli+Gi++++ke+ +dvrvigve+eg++++a+sl++g+++++++ +tiadg+a+++++++ fe++
  gi|313127452|ref|YP_004037722.1| 168 DVETVVVPIGGGGLISGISTAVKEQLSDVRVIGVEAEGASSVATSLQKGSVHELDSVNTIADGIATRRVGDKPFEVI 244
                                       ***************************************************************************** PP

                                       SEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 234 drlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       +++vde+vtvsdee++ ++  l +r + +ve ++a+alaal l e+ ++ +++++v  l+g
  gi|313127452|ref|YP_004037722.1| 245 EKYVDEVVTVSDEEIAVTLTYLLERSKTLVEGAGAVALAAL-LFEKFDFTKDEVIVPALCG 304
                                       *****************************************.**********999988776 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.7   9.7e+03      29      50 ..      31      52 ..      27      65 .. 0.67
   2 ?   -2.5   0.0       2.2   7.9e+03      17      40 ..      53      77 ..      36      85 .. 0.68
   3 ?    0.4   0.1      0.28     1e+03      17      65 ..     179     227 ..     168     233 .. 0.65
   4 !   25.1   0.1   5.7e-09     2e-05       9      70 ..     329     393 ..     326     395 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.7
                             ACT_4 29 eekanivsvnaktrkkdglaei 50
                                      e++++ v+++++++++ g ++i
  gi|313127452|ref|YP_004037722.1| 31 EMTGASVHLKLENHQRTGSFKI 52
                                      5566666777777665655555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.2
                             ACT_4 17 kglLaditqvisee.kanivsvnak 40
                                      +g++++it++ ++e +a +v  +a 
  gi|313127452|ref|YP_004037722.1| 53 RGAMNRITTLSEAEkEAGVVTASAG 77
                                      4677777777666655666555555 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.28
                             ACT_4  17 kglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrv 65 
                                        gl++ i+++++e+  +++ + ++++ ++++a+   + +V+ ++ ++++
  gi|313127452|ref|YP_004037722.1| 179 GGLISGISTAVKEQLSDVRVIGVEAEGASSVATSLQKGSVHELDSVNTI 227
                                       6899999999999955555555555435556666655566666666555 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 5.7e-09
                             ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLr 70 
                                       ++ + +d++g+L d++++i+ee+ani +++ + +++    + +++++++e + ++h+++++ +Lr
  gi|313127452|ref|YP_004037722.1| 329 VRTVLKDQPGALHDLLTIIAEEQANIYAIRHDRTSReigMNETDVELDLETRGHDHVETLLSALR 393
                                       566789**************************9988899889*********************99 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.7   6.2e+03      31      55 ..     231     259 ..     229     263 .. 0.66
   2 !   21.3   0.0   4.5e-08   0.00016       3      59 ..     329     389 ..     328     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                                       EEEEEESTT....ECEEEEEEEEEEHHHH CS
                               ACT  31 ieqrssedk....vagivfvvivvdeedl 55 
                                       i +r+++dk    + ++v+ v++v++e++
  gi|313127452|ref|YP_004037722.1| 231 IATRRVGDKpfevIEKYVDEVVTVSDEEI 259
                                       67778888877776666666666666665 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 4.5e-08
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT....ECEEEEEEEEEEHHHHHHHH CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedk....vagivfvvivvdeedleevl 59 
                                       +r+ ++D+PG+L+++++++a+ + Ni  i + ++ ++      +     ++ +++++e++l
  gi|313127452|ref|YP_004037722.1| 329 VRTVLKDQPGALHDLLTIIAEEQANIYAIRHDRTSREigmnETDVELDLETRGHDHVETLL 389
                                       577899***********************99999998555444444444455555555555 PP

>> CagE_TrbE_VirB  CagE, TrbE, VirB family, component of type IV transporter system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     1e-06    0.0036      91     158 ..      20      87 ..      15      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-06
                    CagE_TrbE_VirB  91 dieliitesfskiskqkalsklkk.kqsrllsiedkaksqiteledlidevasgdvalGayhlslvlfa 158
                                       +++l+  ++f  ++ ++++ kl+  +++ +++i  +a++ it+l+++++e+++ +  +G++   ++l a
  gi|313127452|ref|YP_004037722.1|  20 HTPLDYSHTFTEMTGASVHLKLENhQRTGSFKI-RGAMNRITTLSEAEKEAGVVTASAGNHAQGVALAA 87 
                                       789999*****************9899999999.9**************************99999877 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   3.9e-06     0.014      38     105 ..      68     135 ..      60     141 .. 0.90
   2 ?   -1.9   0.0      0.43   1.5e+03      49      71 ..     280     302 ..     269     303 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-06
                                       -SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCG CS
                   DegT_DnrJ_EryC1  38 vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaie 105
                                       ++ +++ s G +A  +aL a  +g + +V++p +  ++ ++a ++ ga++v+   d d  +  +++ie
  gi|313127452|ref|YP_004037722.1|  68 EAGVVTASAGNHAQGVALAATRAGVDSKVVMPEHAPISKVKATRRYGAETVLYGADYDEAQQRAHEIE 135
                                       5668999*************999999**************************9999999888888887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.43
                                       HHHHHHHHH.TTTTTT-EEEEESS CS
                   DegT_DnrJ_EryC1  49 aAlhlaLra.lgvgpgdeVIvpsl 71 
                                        Al+ +L   ++ + +deVIvp+l
  gi|313127452|ref|YP_004037722.1| 280 VALAALLFEkFDFT-KDEVIVPAL 302
                                       44443333235555.9******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2785.06
//
Query:       gi|313127453|ref|YP_004037723.1|  [L=473]
Description: cytochrome bd quinol oxidase subunit 1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.3e-143  476.6  27.6     6e-143  476.4  27.6    1.0  1  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
     0.0036   17.2   0.0     0.0091   15.9   0.0    1.7  1  JSRP            Junctional sarcoplasmic reticulum protein


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.4  27.6  6.7e-147    6e-143       2     418 .]       8     451 ..       7     451 .. 0.95

  Alignments for each domain:
  == domain 1  score: 476.4 bits;  conditional E-value: 6.7e-147
                    Cyt_bd_oxida_I   2 aRlqfaltavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWsey 78 
                                       +Rlqfalt+++H++f+ +++Gla +l+++ ++ +r++d++y++l +fw+k+fa++F+vG+vtGivlef+fgtn++++
  gi|313127453|ref|YP_004037723.1|   8 SRLQFALTTIVHIIFPVMSMGLAPFLVYFTWREIRSDDPVYEQLRRFWTKIFAVSFVVGTVTGIVLEFEFGTNFAAF 84 
                                       8**************************************************************************** PP

                    Cyt_bd_oxida_I  79 srfvGdifgapLaiEgllAFflEstflglmlfgwdrvskklhllatwlvaigtllSalwIlaanswmqtPvGaelnp 155
                                       s+++G+ fg pLa Eg++AF+lE+tflg+++fg+++vs+ l+++++++v +gt+lSa+wIl+answmqtP G+e+++
  gi|313127453|ref|YP_004037723.1|  85 STVTGELFGGPLATEGMMAFMLEATFLGVFVFGREKVSDALYMVSAVAVGLGTWLSAVWILVANSWMQTPRGFEMVT 161
                                       ***************************************************************************98 PP

                    Cyt_bd_oxida_I 156 dtg..raeltdflavlfnpsalakflHtvlaalltaaffvagvsawyllr........rekefarkslkialvvalv 222
                                       ++g   + l+d++a+ +np +++ f+H+  aa+l  a+f+ag++a++++r        ++ +f++k+lkia+vv+++
  gi|313127453|ref|YP_004037723.1| 162 KNGqsIVSLVDPIAAYANPRFPWMFVHMQNAAVLSVALFMAGIAAYHVFRhyhweypvQNVAFWEKTLKIAIVVLVL 238
                                       8762245567********************************************99999999*************** PP

                    Cyt_bd_oxida_I 223 aallqallGdlsgkevaetqpaKlAAmeglwetee.aplslfgipde......eeeknefaieiPgllsllat.gsl 291
                                       +a++q+l Gd+ +++va+tqp+K+AAme+ wete+  p +++++p++       + k+ + + iPg +s+l++ g++
  gi|313127453|ref|YP_004037723.1| 239 TAPFQVLHGDAYARHVADTQPQKFAAMEAVWETESyVPEYIIAVPTNledltdPRAKELLGVGIPGGASWLVSgGDP 315
                                       ********************************************88844333224444488**********98689* PP

                    Cyt_bd_oxida_I 292 dgevkGlndlpkeevPpvalvfwsfrimvglgvlllllallalll.........rwllrllllaiplpfiaveaGWi 359
                                       +++++Gln++ + e Ppva+vfwsfr+mvglg+++++la++a+++          +l++ l+++ +l+++ave+GWi
  gi|313127453|ref|YP_004037723.1| 316 TATITGLNEF-ETEAPPVAIVFWSFRLMVGLGFWFIVLAFWAAYRwwrgelredDLLHKSLMVSSLLGILAVEVGWI 391
                                       **********.7789**************************9966679*****977********************* PP

                    Cyt_bd_oxida_I 360 vtevGRqPWivygllrtadavsp.vsagevllslilflllylvLlvvevylllklikkgp 418
                                       vtevGRqPW+v+g+++tad+vsp +s  + +++l++f+++yl Ll+++ y+++++i++gp
  gi|313127453|ref|YP_004037723.1| 392 VTEVGRQPWVVQGVMKTADGVSPgLSGFDATVTLVGFAVVYLGLLTLYGYVVARIIRAGP 451
                                       *********************************************************997 PP

>> JSRP  Junctional sarcoplasmic reticulum protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-06    0.0091       3      46 ..     217     260 ..     215     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-06
                              JSRP   3 lPWedvtL.NkCLvlAslvavLgsgfqllhdavrGeaeveeraPe 46 
                                        P  +v   +k L +A++v+vL+  fq+lh+   +++ ++ + P+
  gi|313127453|ref|YP_004037723.1| 217 YPVQNVAFwEKTLKIAIVVLVLTAPFQVLHGDAYARHVADTQ-PQ 260
                                       55556553378899****************988887776655.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3201.40
//
Query:       gi|313127454|ref|YP_004037724.1|  [L=337]
Description: cytochrome bd quinol oxidase subunit 2 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-73  247.9  33.1    1.6e-73  247.7  33.1    1.0  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
  ------ inclusion threshold ------
      0.021   13.8   0.7      0.021   13.8   0.7    2.3  3  TMEM144          Transmembrane family, TMEM144 of transporter
        3.3    6.4   7.5        7.3    5.3   0.5    2.8  3  PTR2             POT family


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.7  33.1   2.7e-77   1.6e-73       1     303 []      18     324 ..      18     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: 247.7 bits;  conditional E-value: 2.7e-77
                   Cyt_bd_oxida_II   1 lqliwflligvllagYvvldGfDlGvGillpllakkde.errlllnsigpvWdgnevWLvtaggalfaaFPlayatl 76 
                                       l+++wf+l++++l  +++ldGfD+GvG+++ +  ++de er++ll +igp+WdgnevWLv++ggalfaaFP++ya l
  gi|313127454|ref|YP_004037724.1|  18 LPEMWFALVFFILGTFLFLDGFDFGVGAIFAT--REDEdEREQLLSAIGPFWDGNEVWLVVFGGALFAAFPAVYANL 92 
                                       6899*************************999..77777************************************** PP

                   Cyt_bd_oxida_II  77 fsglylpllliLlglilRgvafefrskaeskrwrklwdlaffigSllaalllGvalgnllqGvpfdadeygflsdll 153
                                       fs  yl++++iL +li+Rg+a e+ +++++++w+++w  af++gS+la+++lGv  +n++ G+           +l+
  gi|313127454|ref|YP_004037724.1|  93 FSRNYLLMFAILGALIMRGLAPEMYEQRHDESWQRWWGRAFVAGSVLAPFFLGVFAANWFLGAT----------TLV 159
                                       ****************************999******************************988..........489 PP

                   Cyt_bd_oxida_II 154 npfallvglllvalflllGalylalktegelqerarrlalvlalvllvllvvvllwtll..............lvll 216
                                       ++ +++vg+++val+++ Ga++l lkt+g+l+++  r+   ++++ l l+vv++ ++ll              l l+
  gi|313127454|ref|YP_004037724.1| 160 SLASIVVGVAVVALTVVSGAAFLGLKTRGSLRDETVRYGPPALVAYLGLVVVAVGYLLLtrpamradllaapsLGLV 236
                                       9************************************9988887777666666644444566778887766555444 PP

                   Cyt_bd_oxida_II 217 llavlalllavlllrkkreglaflasaltvllvvlllavslfPyllpss.ltianaasseytlkvmlivalillplv 292
                                        l v++ ++ v+++r+++++ a++a+a++  ++v+l+a+ l+P+  p s lt+ +a  s+  l++m+i++++llplv
  gi|313127454|ref|YP_004037724.1| 237 GLSVVLGVAYVVTMRREQYVPALAAAAGLTYGLVTLVATLLYPFADPGSgLTVSTAIVSTLPLNLMSIASALLLPLV 313
                                       5666666666677888888889**********************999999*************************** PP

                   Cyt_bd_oxida_II 293 laytawlyrvf 303
                                       + y+++ly +f
  gi|313127454|ref|YP_004037724.1| 314 FSYFVVLYSTF 324
                                       ********987 PP

>> TMEM144  Transmembrane family, TMEM144 of transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1      0.46   2.7e+03     118     136 ..      59      84 ..      22      92 .. 0.54
   2 ?   -0.9   0.5      0.11   6.4e+02     111     130 ..     195     214 ..     140     221 .. 0.52
   3 ?   13.8   0.7   3.6e-06     0.021     229     302 ..     233     306 ..     215     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.46
                           TMEM144 118 lLnylG.......ivlvvvggvlflf 136
                                       lL  +G       + lvv+gg+lf+ 
  gi|313127454|ref|YP_004037724.1|  59 LLSAIGpfwdgneVWLVVFGGALFAA 84 
                                       44444433333335677777777765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.11
                           TMEM144 111 aqvpksdlLnylGivlvvvg 130
                                        ++    l+ ylG+v+v vg
  gi|313127454|ref|YP_004037724.1| 195 VRYGPPALVAYLGLVVVAVG 214
                                       33333345556666666665 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 3.6e-06
                           TMEM144 229 lgifltstvilliYsivkknkplveselvlPsllaGilwaiavtsffvanqkLsqvvsyPiiskaPgliaalws 302
                                       lg++ +s v+ ++Y+++++++ +v++ +   +l++G++  +a+ ++  a+     +vs  i+s++P  + ++ s
  gi|313127454|ref|YP_004037724.1| 233 LGLVGLSVVLGVAYVVTMRREQYVPALAAAAGLTYGLVTLVATLLYPFADPGSGLTVSTAIVSTLPLNLMSIAS 306
                                       67778899999*******************************************************77666555 PP

>> PTR2  POT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.5    0.0012       7.3     108     129 ..      14      35 ..       6      37 .. 0.94
   2 ?   -0.3   0.3     0.064   3.8e+02      73     121 ..     125     170 ..     112     177 .. 0.65
   3 ?    4.3   0.4    0.0025        15       4      50 ..     168     215 ..     156     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHCTTTS- CS
                              PTR2 108 FgipavlmiiallvFllGsrly 129
                                       Fg+p   m++al+ F+lG+ l+
  gi|313127454|ref|YP_004037724.1|  14 FGLPLPEMWFALVFFILGTFLF 35 
                                       9*****************9887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.064
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHH CS
                              PTR2  73 rsrfFsiFyfsiNvGSLlsliitpylqenvgyplgFgipavlmiiallv 121
                                        +r   ++  +  +GS l+++++++++ n     + +++ + ++++++v
  gi|313127454|ref|YP_004037724.1| 125 WQR---WWGRAFVAGSVLAPFFLGVFAANWFLGATTLVSLASIVVGVAV 170
                                       444...7777788999999999999998855555555555555555554 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHHHHCCCCTTTTSS--S--.TCHHHHHHHHHHHHHHHH CS
                              PTR2   4 IllgsiiyaiGhvvlalsaipslksaesa.gvrvallfigLalIalGt 50 
                                       ++++++ ++ G + l+l++  sl+++    g  +++ ++gL+++a+G+
  gi|313127454|ref|YP_004037724.1| 168 VAVVALTVVSGAAFLGLKTRGSLRDETVRyGPPALVAYLGLVVVAVGY 215
                                       45677778889999999999999998877766778************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2250.28
//
Query:       gi|313127455|ref|YP_004037725.1|  [L=126]
Description: endoribonuclease L-PSP [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-38  131.3   0.0    1.9e-38  131.2   0.0    1.0  1  Ribonuc_L-PSP    Endoribonuclease L-PSP
  ------ inclusion threshold ------
      0.062   13.4   0.0      0.074   13.2   0.0    1.3  1  YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endori


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.0   2.1e-42   1.9e-38       2     120 ..       8     124 ..       7     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 2.1e-42
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB..-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelv.egdveeqtrqalenlkavLaaagaslsdvVkvtvFladie 77 
                                       ++apaa+++Ysqa ++g +++++Gq+pl+p +gel  ++d++ qt+q+l+n+ a+L++ ga+ sdv+kv+vFl die
  gi|313127455|ref|YP_004037725.1|   8 DDAPAAVGAYSQATTNGSVLFTAGQIPLTP-DGELLdDEDIATQTKQSLDNVMAILESEGADASDVLKVSVFLDDIE 83 
                                       689**************************8.999998**************************************** PP

                                       GHHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  78 dfaevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       df e+ne ya++fde+   Parsa eVa+Lpkg+ vEIeaia 
  gi|313127455|ref|YP_004037725.1|  84 DFDEMNETYADYFDEEP--PARSALEVANLPKGVGVEIEAIAD 124
                                       ****************5..**********************95 PP

>> YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endoribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.3e-06     0.074      12      41 ..       8      37 ..       1      76 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.3e-06
                                      ------SSSS-SEEEETTEEEE--B--EET CS
                   YjgF_endoribonc 12 pkvaaalGayepyaivasflttsfqlpylq 41
                                       +++aa+Gay   +  +s l t++q+p   
  gi|313127455|ref|YP_004037725.1|  8 DDAPAAVGAYSQATTNGSVLFTAGQIPLTP 37
                                      5789***********************853 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 986.53
//
Query:       gi|313127456|ref|YP_004037726.1|  [L=68]
Description: hypothetical protein Hbor_27360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   14.1   1.8      0.083   13.2   1.7    1.6  2  DUF5493   Family of unknown function (DUF5493)


Domain annotation for each model (and alignments):
>> DUF5493  Family of unknown function (DUF5493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.7   4.6e-06     0.083      33      49 ..      13      29 ..       7      54 .. 0.86
   2 ?   -0.6   0.2     0.089   1.6e+03      28      38 ..      45      55 ..      28      61 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-06
                           DUF5493 33 iigtvaflvfvqgytdi 49
                                      ++gt+aflv+vqgy  +
  gi|313127456|ref|YP_004037726.1| 13 VVGTLAFLVLVQGYRLV 29
                                      79************765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.089
                           DUF5493 28 nlmafiigtva 38
                                       ++a ++g  a
  gi|313127456|ref|YP_004037726.1| 45 VVIAVVVGIAA 55
                                      33444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 451.94
//
Query:       gi|313127457|ref|YP_004037727.1|  [L=54]
Description: hypothetical protein Hbor_27380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       140  (0.00780858); expected 358.6 (0.02)
Passed bias filter:                      119  (0.00663729); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.26s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 425.53
//
Query:       gi|313127458|ref|YP_004037728.1|  [L=59]
Description: hypothetical protein Hbor_27390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 419.49
//
Query:       gi|313127459|ref|YP_004037729.1|  [L=554]
Description: thermosome subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.3e-166  554.3  15.6   2.6e-166  554.1  15.6    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
        5.3    7.1   6.9        2.2    8.3   1.2    2.6  2  DUF1451     Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.1  15.6  2.9e-170  2.6e-166       1     489 [.      37     525 ..      37     527 .. 0.97

  Alignments for each domain:
  == domain 1  score: 554.1 bits;  conditional E-value: 2.9e-170
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v++tlGPkGmdKmlv+++g+v++TnDG+tilke++i++P+a+++ve+ae+q++e+GDGTtt+v +ageLl++a
  gi|313127459|ref|YP_004037729.1|  37 VAEAVRSTLGPKGMDKMLVDSMGDVTITNDGVTILKEMDIDNPTAEMIVEVAETQESEAGDGTTTAVAIAGELLKNA 113
                                       689************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                       e+l+++++hpt+ii+g++ a +ka e+ + ia++++   +d+e ++kva+ts+++k ++ ++e l++l+vdAv +++
  gi|313127459|ref|YP_004037729.1| 114 EDLLEQDIHPTAIIKGFHLASQKAREEVDDIAEAVD--PDDEELVKKVAETSMTGKSSELNKELLAELIVDAVkQVT 188
                                       *******************************66666..5699*******************************7666 PP

                                       CCCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSC CS
                        Cpn60_TCP1 154 eene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsda 227
                                        e++   + +dl+++ +++ +g+s ++sel++G v+dk++++ dmp+++++a vlll+ ++e e+ +++t+v+++++
  gi|313127459|ref|YP_004037729.1| 189 VEADdgtYVVDLENVSIETQTGRSASESELLNGAVIDKDPVHDDMPTEFDEASVLLLNDPIEVEEADVDTQVNIESP 265
                                       666699999******************************************************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGG CS
                        Cpn60_TCP1 228 eeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledl 304
                                       ++l+k++++eekql+e++eki++++++vv+cqkgiddla+h+lak+gila+rr+kk+d++ l ++ G+++vs+l+++
  gi|313127459|ref|YP_004037729.1| 266 DQLQKFLDQEEKQLKEKVEKIAATDADVVFCQKGIDDLAQHYLAKEGILAVRRTKKSDIKFLKNVAGGNVVSDLDSV 342
                                       ***************************************************************************** PP

                                       GCGC-EEEEEEEECCETTCCEEEEECE.SSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHH CS
                        Cpn60_TCP1 305 tpeelGtakkveeekigsekttiieev.ksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGate 380
                                       t+++lG a+     + ++ +++++e+  ++ + +t+llrg+td+v+de+er +edAl+vv+ ++ d++v++GGGa+e
  gi|313127459|ref|YP_004037729.1| 343 TEDDLGVASIR---RDEEGELFYVEGLgDKTHGVTMLLRGSTDHVVDELERGVEDALDVVATTVSDGRVLAGGGAIE 416
                                       ******98765...4457889999965367788******************************************** PP

                                       HHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCC CS
                        Cpn60_TCP1 381 lelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlvea 457
                                       +ela++l++ya+svsg+eqla+eafa+ALe +p++LaeNaGld+i++l +lraah+ g++ +g++v +g+++d +ea
  gi|313127459|ref|YP_004037729.1| 417 VELASRLRNYADSVSGREQLAVEAFADALELVPRVLAENAGLDSIDTLVDLRAAHEDGDVRAGLNVFTGNVEDTFEA 493
                                       ***************************************************************************** PP

                                       TXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 458 gvvDplkvkrqalksAteaastiLrideiika 489
                                       g+v+p+++k+qa++sA eaa+++L+id+ii a
  gi|313127459|ref|YP_004037729.1| 494 GIVEPAHAKEQAISSAQEAANLVLKIDDIIAA 525
                                       ******************************97 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.2   0.00024       2.2      26      84 ..     131     188 ..     106     196 .. 0.88
   2 ?    0.6   0.3     0.058   5.2e+02       9      77 ..     263     332 ..     257     346 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00024
                           DUF1451  26 seaeeltkeelelvaeylkrDleeaarsleeskeeleewlsldlelieesllealasia 84 
                                       + a++  +ee++ +ae++  D ee+ ++++e++  + ++ +l+ el+ e +++a  +++
  gi|313127459|ref|YP_004037729.1| 131 HLASQKAREEVDDIAEAVDPDDEELVKKVAETSM-TGKSSELNKELLAELIVDAVKQVT 188
                                       56778899*************************9.689999************999998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.058
                           DUF1451   9 kseeeleelvekakeklsea.eeltkeelelvaeylkrDleeaarsleeske..eleewlsldlelieesll 77 
                                       +s ++l++ +++ +++l+e+ e++ + +++ v  + ++ + ++a+++ +++    ++ +++ d++ +++ + 
  gi|313127459|ref|YP_004037729.1| 263 ESPDQLQKFLDQEEKQLKEKvEKIAATDADVV--FCQKGIDDLAQHYLAKEGilAVRRTKKSDIKFLKNVAG 332
                                       66788888888888887765255555666554..77888888777666555556777777778777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3712.39
//
Query:       gi|313127460|ref|YP_004037730.1|  [L=336]
Description: l-alanine dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-99  331.4   0.8      5e-99  331.2   0.8    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.2   0.8  2.8e-103     5e-99       3     317 ..       6     320 ..       4     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 331.2 bits;  conditional E-value: 2.8e-103
                                       EEEE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTT..EEEEEEEEEETTT CS
                   OCD_Mu_crystall   3 kavltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagre..llgvKlvnshpen 77 
                                       + +l + +v+e+ ++ +l++a+eeaf++++ g +++pp+ + + ++++g+++ mpay+ + +  ++g+K+vn+hp+n
  gi|313127460|ref|YP_004037730.1|   6 TLLLNNDDVHENANMTELVPAIEEAFAAFERGDAQMPPKSYIDLPQYNGDFRSMPAYMDAGDwdAAGIKWVNVHPDN 82 
                                       6678899**************************************************98766679************ PP

                                       CCC.TSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS- CS
                   OCD_Mu_crystall  78 kks.glptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavld 153
                                       +++  lptv++++v ++pet +plalmd+t lt +RT+A++ava+ +La +das l+iiGaGvq++tqlea+  v+d
  gi|313127460|ref|YP_004037730.1|  83 EEQfDLPTVMGTMVYSSPETAFPLALMDGTELTMKRTGAAAAVATDHLAIEDASSLGIIGAGVQSYTQLEAIATVRD 159
                                       ***9************************************************************************* PP

                                       -SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT-- CS
                   OCD_Mu_crystall 154 ikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkt 230
                                       i+ev + d+dee  ++f+++ +  ef+v+a +  eea + +d++ tvT+ + pi++ + v+  +hina+gada+gk+
  gi|313127460|ref|YP_004037730.1| 160 IQEVIVSDLDEERVARFIDTFED-EFDVRAGS-IEEA-ASCDVLSTVTPVEDPIVSRDAVGDHTHINAMGADAEGKH 233
                                       **********************7.*****965.4444.57************************************* PP

                                       SB-HHHHHCCEEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHH CS
                   OCD_Mu_crystall 231 eLdddilkradifvdseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaa 307
                                       eL d++l+ a++++d+ +q++++Gei+v+ ++gvl++d+++a +ge++ G  +GRt++  i +fds+Gla++Dvaaa
  gi|313127460|ref|YP_004037730.1| 234 ELADEVLLDAKLVIDDHEQTTHSGEINVPYNEGVLSDDDIHAAIGEIVVGDEEGRTDEDGISVFDSTGLAIQDVAAA 310
                                       ***************************************************************************** PP

                                       HHHHHHHCCC CS
                   OCD_Mu_crystall 308 klvyeraeek 317
                                       ++vye+a+e+
  gi|313127460|ref|YP_004037730.1| 311 HIVYEHAREN 320
                                       ******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2331.32
//
Query:       gi|313127461|ref|YP_004037731.1|  [L=73]
Description: hypothetical protein Hbor_27420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   13.6   0.1      0.049   13.5   0.1    1.1  1  DUF2975   Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.7e-06     0.049       8      45 ..      27      64 ..      13      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-06
                           DUF2975  8 elypeaaglrvpvlllgvlallafvvalvqlwkLlrsi 45
                                      ++ + + +   +v+++ +++ll+f+va++++ kLl ++
  gi|313127461|ref|YP_004037731.1| 27 TEMNSLGWAMFLVMVALLVPLLPFAVAVWAVAKLLDYL 64
                                      4445555556669999999999************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 532.20
//
Query:       gi|313127462|ref|YP_004037732.1|  [L=962]
Description: leucyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-53  179.4   0.9    1.4e-39  135.8   0.1    2.7  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
      3e-22   78.9   4.8    2.2e-10   39.9   0.1    3.5  4  tRNA-synt_1g   tRNA synthetases class I (M)
    1.8e-21   76.7   0.1    4.4e-21   75.4   0.1    1.7  1  Anticodon_1    Anticodon-binding domain of tRNA
    1.2e-08   34.7   0.0    2.4e-08   33.7   0.0    1.4  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    0.00012   21.6   0.0       0.39   10.0   0.0    2.4  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    0.00055   19.0   0.0      0.012   14.5   0.0    2.4  2  tRNA-synt_1f   tRNA synthetases class I (K)
  ------ inclusion threshold ------
       0.34   10.9   1.1        1.2    9.1   0.0    2.2  2  FlxA           FlxA-like protein


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.1   5.6e-43   1.4e-39       2     307 ..      12     333 ..      11     354 .. 0.82
   2 !   40.7   0.1   3.6e-14   9.3e-11     320     600 ..     402     667 ..     394     669 .. 0.84

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 5.6e-43
                       tRNA-synt_1   2 lyekWeeedvfkke......lekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDha 72 
                                       + e+W e++ +++        +++ ++++  ++++ Py  G +HiGha + t+ d+  ry+r++G +vl+ + w   
  gi|313127462|ref|YP_004037732.1|  12 WRERWAETGRYEADpsdadsADHDSDEDPTFITVPYPYPSGGMHIGHARTYTVPDVYARYRRQQGDNVLFPIAWHVT 88 
                                       567899999998651111112233334446688999***************************************** PP

                       tRNA-synt_1  73 Glaieakvekklgakekk.....erkklgreefre..kvrewkaeyae.eirkqvkrlGvsvDfdreylTldkelee 141
                                       G +i  +ve+    +ek+     + ++++++  ++      ++ +++e +++k ++ lG s+D+ re  T d+ +++
  gi|313127462|ref|YP_004037732.1|  89 GTPIIGAVERLKKGEEKQlsvlrDTYNVSEDTLTDleTPMGFARHFIEeHYKKGMQSLGLSIDWRREFTTNDERYSK 165
                                       *********864333332111112344555555431134557777765157899*********************** PP

                       tRNA-synt_1 142 avkevfvrladkgliyrgkklvnwstklktalselEv.eykdkk.dalihvafpladkeevklviaTTtPeTllgdt 216
                                        +++ +  l d+gl+ +g ++v+++t+ + +++  +  e ++ + +  + v+f    +++  + +aT +PeT+ g t
  gi|313127462|ref|YP_004037732.1| 166 FITWQYETLKDRGLLEKGLHPVKYCTDEEQPVTTHDLlEGEEAEfQEYTLVRFGH--GDT-VVPMATLRPETVRGVT 239
                                       ********************************99877433333323345577754..333.6789************ PP

                       tRNA-synt_1 217 avavnpeldyv...itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtG 290
                                          ++p+ dyv   +++e++ +  a  ++l  + ++ ++++++ g+eL g +v +p+++ ++ ++  d+vd+e+ tG
  gi|313127462|ref|YP_004037732.1| 240 NAYIDPDADYVyadVDGEQWFVSAAAAEKLQLQAHDVTVERRVSGAELAGERVMNPVTGDEVLVLPADFVDAENATG 316
                                       ************9999*****9999999999999******************************************* PP

                       tRNA-synt_1 291 vVkiaPahdedDyevgk 307
                                       vV   Pah +dDy + +
  gi|313127462|ref|YP_004037732.1| 317 VVMSVPAHSPDDYVALQ 333
                                       *************8765 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 3.6e-14
                       tRNA-synt_1 320 dgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalka 394
                                        g+l +e +ef+g  v+d r    ++ +++g++ ++++++ +v +  r ++ +++  +++Wf r ++   +++a ++
  gi|313127462|ref|YP_004037732.1| 402 AGRLFDEYGEFAGELVEDVRTRFRDAHRDEGAFGTMQEFSEEVVC--RCGADVVVAEQDTWFLRYNDeaWKQKAHDV 476
                                       58888999*****************************99999854..77778888899******987679999**** PP

                       tRNA-synt_1 395 vekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakd 471
                                       v+++  +p+ ++ +y + +   ++W   R+   G+r+p + ++   e    +++ +     ++  + ++ l++  ++
  gi|313127462|ref|YP_004037732.1| 477 VSRMDAIPENTRGEYDHTIDWLNEWPCIRNYGLGTRLP-WDDDFVIEPLS-DSTIY-----MAYYTIAHRLQDVPVE 546
                                       **************************************.66666444444.22222.....2333444444444555 PP

                       tRNA-synt_1 472 klkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfk 548
                                       +l         d d +D  F  +       +   e ++e +  +p     +  D i   ++  ++   +l++++ + 
  gi|313127462|ref|YP_004037732.1| 547 EL---------DRDFFDALFYGADAVEDPDEKALELRKEWNYWYPVTYRFSANDLISNHLTFYLFHHAELFDQSNWP 614
                                       55.........899*******999999998889999999999******************************99886 PP

                       tRNA-synt_1 549 e.vlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdin 600
                                       e +++ g+    eG KmS s+g v+ p + i++ygad +R++l+ +++  +d +
  gi|313127462|ref|YP_004037732.1| 615 EgIVIMGMG-LLEGEKMSSSKGHVVLPGKAIEEYGADTVRFFLLnSAEPWQDYD 667
                                       625555654.468*******************************6667777765 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   3.1e-13     8e-10       2      57 ..      42      97 ..      41     125 .. 0.88
   2 ?    0.9   0.0     0.057   1.5e+02      72     128 ..     137     195 ..     125     205 .. 0.78
   3 ?   -4.1   0.0         2     5e+03     171     238 ..     447     514 ..     438     521 .. 0.61
   4 !   39.9   0.1   8.5e-14   2.2e-10     268     376 ..     573     678 ..     552     692 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 3.1e-13
                                      EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHH CS
                      tRNA-synt_1g  2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAe 57
                                      ++t++ pY++g +H+Gh++++   D++aRy+r++g++vlf  +    Gtpi  + e
  gi|313127462|ref|YP_004037732.1| 42 FITVPYPYPSGGMHIGHARTYTVPDVYARYRRQQGDNVLFPIAWHVTGTPIIGAVE 97
                                      89************************************************976555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.057
                                       HHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTE CS
                      tRNA-synt_1g  72 eeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkder 128
                                       e++k+ +++l++s d     +t++e+ +++    +++lk++gl++++   + yc+++e+
  gi|313127462|ref|YP_004037732.1| 137 EHYKKGMQSLGLSIDwrREFTTNDERYSKFITWQYETLKDRGLLEKGLHPVKYCTDEEQ 195
                                       5556667777777762223358888999999999********************99886 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 2
                                       ......EEE.EEEEEE-GGG..GHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 171 isgskpevketehlffklsk..fekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                        +g+  +v e++ +f++ ++  +++k ++ + ++    +en++    ++++  L+++   r+   G ++P
  gi|313127462|ref|YP_004037732.1| 447 RCGADVVVAEQDTWFLRYNDeaWKQKAHDVV-SRMDAIPENTRGEYDHTIDW-LNEWPCIRNYGLGTRLP 514
                                       5788888888889998876511455555566.33335666666666666655.66666666666666666 PP

  == domain 4  score: 39.9 bits;  conditional E-value: 8.5e-14
                                       TSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHH CS
                      tRNA-synt_1g 268 eeekwkeyWakdkevelvhfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakeal 342
                                         ++w+ ++        + f + d i  H  f+         + + p+ +v  ++  +eg+K+S+S+g vv + +a+
  gi|313127462|ref|YP_004037732.1| 573 LRKEWNYWY-----PVTYRFSANDLISNHLTFYLFHHAElfDQSNWPEGIVIMGMGLLEGEKMSSSKGHVVLPGKAI 644
                                       456888666.....34799**********9888666555779999******************************** PP

                                       HHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHH CS
                      tRNA-synt_1g 343 erldadllRYylaaeapekkDldfswedfvervN 376
                                       e++ ad++R++l+ +a+  +D d++ e++    N
  gi|313127462|ref|YP_004037732.1| 645 EEYGADTVRFFLLNSAEPWQDYDWRAEQVESVRN 678
                                       ************************9998876655 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.1   1.7e-24   4.4e-21       1     141 [.     706     829 ..     706     847 .. 0.74

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 1.7e-24
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       drw+ls+l+++v++vtea+e+ + + a +a+++ f +dl +wy + +  +l+   +    aa+++l +vlet lrll
  gi|313127462|ref|YP_004037732.1| 706 DRWLLSKLQHTVSDVTEAMEQSETRSASQAAFYNFEEDL-RWYRRRT--DLDR--P----AARWTLQHVLETRLRLL 773
                                       9**************************************.***9986..4532..2....377************** PP

                       Anticodon_1  78 aPfmPfitEelwqreeeel.gkkesimlaewpe.kaeelekele..eeevellkeivkairklrselk 141
                                       aPf+Pf+t el     e+l g +     a+wpe +++++ ++ e  e+++e+      + ++++++++
  gi|313127462|ref|YP_004037732.1| 774 APFIPFMTNELH----ERLtGTP--AEDAPWPEpDESFESAAVEasEAQIER------LTEDIKGIQQ 829
                                       ************....4542444..34699**95554443333223445554......4444444443 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   9.4e-12   2.4e-08      24     126 ..     226     329 ..     214     338 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 9.4e-12
                     tRNA-synt_1_2  24 evfttrpdtlfGvtfvalapehplvekl.aekkkelaafieevkkksesereletkekeGv.ftglkaihPitgeki 98 
                                        + t rp+t+ Gvt  ++ p+ + v +    ++  ++a  +e  + + ++  + +++ +G    g  +++P+tg+++
  gi|313127462|ref|YP_004037732.1| 226 PMATLRPETVRGVTNAYIDPDADYVYADvDGEQWFVSAAAAEKLQLQAHDV-TVERRVSGAeLAGERVMNPVTGDEV 301
                                       55689****************999877625555556655555555555554.555667788689************* PP

                     tRNA-synt_1_2  99 piwvanyvlmeygtgavmavPahdqrDf 126
                                        +  a++v +e  tg+vm+vPah   D+
  gi|313127462|ref|YP_004037732.1| 302 LVLPADFVDAENATGVVMSVPAHSPDDY 329
                                       ***********************99998 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00034      0.86      23      50 ..      54      81 ..      48     101 .. 0.93
   2 !   10.0   0.0   0.00015      0.39     231     295 ..     606     672 ..     587     678 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00034
                                      -BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e 23 shlGhaRslvafDilrrilqalgYdvqf 50
                                      +h+GhaR++ + D+ +r+ +++g +v f
  gi|313127462|ref|YP_004037732.1| 54 MHIGHARTYTVPDVYARYRRQQGDNVLF 81
                                      7********************9999977 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00015
                                       HHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS.-TTS-EEE-HHH CS
                      tRNA-synt_1e 231 aafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsa.hyrsqldfkeel 295
                                        +fd +++ +  +  g+  +egekms s + +++  ++++++ + ++R++ll+  +  +  d++ e+
  gi|313127462|ref|YP_004037732.1| 606 ELFDqSNWPEGIVIMGMGLLEGEKMSSSKGHVVLPGKAIEEYGADTVRFFLLNSaEPWQDYDWRAEQ 672
                                       55665567777778899999*****************************998641333445555555 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.045   1.2e+02      33      62 ..      50      79 ..      31      87 .. 0.85
   2 !   14.5   0.0   4.8e-06     0.012     266     337 ..     614     685 ..     602     712 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.045
                      tRNA-synt_1f 33 pSGliHiGnlrevltadlvaralrkrgeev 62
                                      pSG +HiG +r    +d+ ar  r++g++v
  gi|313127462|ref|YP_004037732.1| 50 PSGGMHIGHARTYTVPDVYARYRRQQGDNV 79
                                      9**********9999999988888888876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.8e-06
                      tRNA-synt_1f 266 PekvvYelillkggekmssSkGnvltledwlevaepevlrflilr.rkPkkakkldldleilrlvdeYdkler 337
                                       Pe++v   ++l +gekmssSkG+v+ + +++e +  +++rf++l+ ++P +  +   + ++ ++ ++ +++ +
  gi|313127462|ref|YP_004037732.1| 614 PEGIVIMGMGLLEGEKMSSSKGHVVLPGKAIEEYGADTVRFFLLNsAEPWQDYDWRAE-QVESVRNQLERFWN 685
                                       666666667778899****************999999999988762589898888888.66655555555444 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.48   1.2e+03      16      43 ..     670     700 ..     667     737 .. 0.56
   2 ?    9.1   0.0   0.00048       1.2       8      39 ..     806     837 ..     802     847 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.48
                              FlxA  16 asqiasLqkQiknlqkqLkelses...delt 43 
                                       a+q++s ++Q+++  +  +e+ +s   ++++
  gi|313127462|ref|YP_004037732.1| 670 AEQVESVRNQLERFWNRADEVINSdvpEAQP 700
                                       5678888888888888888887774432222 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00048
                              FlxA   8 ssssssgsasqiasLqkQiknlqkqLkelses 39 
                                       +s+  + s++qi++L++ ik +q++L +  e+
  gi|313127462|ref|YP_004037732.1| 806 ESAAVEASEAQIERLTEDIKGIQQSLANADED 837
                                       566667899*****************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (962 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.79u 0.26s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 6254.98
//
Query:       gi|313127463|ref|YP_004037733.1|  [L=150]
Description: molecular chaperone [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-20   73.6   0.3    1.6e-20   73.1   0.3    1.2  1  HSP20       Hsp20/alpha crystallin family
    1.1e-14   53.7   0.0    1.9e-14   53.0   0.0    1.4  1  ArsA_HSP20  HSP20-like domain found in ArsA
    1.2e-05   25.4   1.3    0.00013   22.1   1.3    2.1  2  GvpH        GvpH
  ------ inclusion threshold ------
      0.084   13.9   0.0       0.11   13.5   0.0    1.2  1  CS          CS domain
       0.13   12.4   0.0         13    5.9   0.0    2.3  2  FKBP26_C    FKBP26_C-terminal


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.3   4.4e-24   1.6e-20       1     101 [.      44     149 ..      44     150 .] 0.93

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 4.4e-24
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--........---TT----SS---EEEEEE--STTB-TTT CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe......eeeedekglikerssrkFsrkftLPenvdadk 71 
                                       d+++++eef v +d+pgl+k++++++v+++++++++ +e      + +e++++l++er+ ++  r+++LPenv ad+
  gi|313127463|ref|YP_004037733.1|  44 DVRDSDEEFVVVADLPGLEKDDIDLSVTERTLTISASREmneeteSDTESREFLRRERRHESMHRTIRLPENVIADD 120
                                       67899**********************************99877666788999************************ PP

                                       -EEEEETTEEEEEEEBSS--..-------- CS
                             HSP20  72 vkaslkdGvLtvtvpkkepekkkkerkiqi 101
                                        +as+ +GvL+vt+pk++ e++ ++ +i+i
  gi|313127463|ref|YP_004037733.1| 121 ATASYTNGVLSVTLPKRSVESD-DSHRINI 149
                                       *******************988.7777777 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   5.2e-18   1.9e-14       1      63 []      49     134 ..      49     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 5.2e-18
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig........................nfrRqitLPsvlarkevtsAk 53 
                                       d e+v+++dLP+++k++idls ++ +LtI++                         + +R+i LP+ + ++++  A+
  gi|313127463|ref|YP_004037733.1|  49 DEEFVVVADLPGLEKDDIDLSVTERTLTISASremneetesdtesreflrrerrheSMHRTIRLPENVIADDA-TAS 124
                                       679********************************************************************99.9** PP

                        ArsA_HSP20  54 fedgvLeIrF 63 
                                       + +gvL +++
  gi|313127463|ref|YP_004037733.1| 125 YTNGVLSVTL 134
                                       ********86 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.088   3.2e+02      10      42 ..       4      36 ..       2      45 .. 0.80
   2 !   22.1   1.3   3.5e-08   0.00013      97     138 ..      46      85 ..      35      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.088
                              GvpH 10 lsGlldqlsrlvevlaeleeegGerhessridr 42
                                       s  +d+++ + e +a   +e G++ + s++  
  gi|313127463|ref|YP_004037733.1|  4 RSPTFDEIESMFERMARQFDEMGHQFGGSNLMS 36
                                      56778999*****************99887755 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 3.5e-08
                              GvpH  97 sddsdelvvvadlpGvtdedvdvaletdeqaltlrvdddvve 138
                                        d+ +e+vvvadlpG+  +d+d ++   e++lt++   ++ e
  gi|313127463|ref|YP_004037733.1|  46 RDSDEEFVVVADLPGLEKDDIDLSVT--ERTLTISASREMNE 85 
                                       456679******************99..999***98877666 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.2e-05      0.11       9      76 .]      49     136 ..      43     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                       TTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECE....................BSS-BETTTEEE CS
                                CS   9 ldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliege....................LfgpIdpeessw 63 
                                       ++e vv   ++++  +k+d++++ +er+l+++  ++ ++++ ++                     L +++  ++++ 
  gi|313127463|ref|YP_004037733.1|  49 DEEFVVVADLPGL--EKDDIDLSVTERTLTISAsREmNEETESDTesreflrrerrhesmhrtirLPENVIADDATA 123
                                       5666777888888..*****************986656665554489****************************** PP

                                       EEETTEEEEEEEB CS
                                CS  64 tieskkveitLkK 76 
                                       + ++  + +tL K
  gi|313127463|ref|YP_004037733.1| 124 SYTNGVLSVTLPK 136
                                       *********9988 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0037        13      11      33 ..      56      78 ..      50      87 .. 0.85
   2 ?    4.1   0.0     0.014        49      15      37 ..     115     137 ..     106     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0037
                                      HH-TT--..--EEEEETTEEEEE CS
                          FKBP26_C 11 ryiPnidlekfkieiedktvtIe 33
                                        +P ++++++++++++ t+tI 
  gi|313127463|ref|YP_004037733.1| 56 ADLPGLEKDDIDLSVTERTLTIS 78
                                      458******************96 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.014
                                       T--..--EEEEETTEEEEE--TT CS
                          FKBP26_C  15 nidlekfkieiedktvtIelpee 37 
                                       n+ ++++  ++++++++++lp+ 
  gi|313127463|ref|YP_004037733.1| 115 NVIADDATASYTNGVLSVTLPKR 137
                                       566799999************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1117.69
//
Query:       gi|313127464|ref|YP_004037734.1|  [L=138]
Description: heat shock protein Hsp20 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-22   79.7   0.8    1.7e-22   79.5   0.8    1.1  1  HSP20       Hsp20/alpha crystallin family
    2.2e-17   62.3   0.0    3.1e-17   61.9   0.0    1.2  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0031   18.5   0.0     0.0041   18.1   0.0    1.2  1  CS          CS domain
  ------ inclusion threshold ------
      0.043   13.9   3.9       0.14   12.2   3.6    1.9  1  GvpH        GvpH
       0.34   12.0   2.4       0.67   11.0   2.4    1.5  1  FAM110_C    Centrosome-associated C terminus


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.8   4.8e-26   1.7e-22       1     101 [.      35     137 ..      35     138 .] 0.97

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 4.8e-26
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkas 75 
                                       d+ e+++ef+v +d+pg +k++++++  ++++++++e++  +ee++++++++er++++ +r++tLP++v +++ +a+
  gi|313127464|ref|YP_004037734.1|  35 DVSETDDEFTVVADLPGYEKDDIEISASGRELTIRAEQTaeTEESGDRYVRRERRQSNVRRSLTLPQEVVEEEASAT 111
                                       57899*********************************99999********************************** PP

                                       EETTEEEEEEEBSS--..-------- CS
                             HSP20  76 lkdGvLtvtvpkkepekkkkerkiqi 101
                                       +k+GvLtvt+pk+++e++ ++ +i++
  gi|313127464|ref|YP_004037734.1| 112 YKNGVLTVTLPKETSEEDDESTSIDV 137
                                       *****************999999987 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   8.8e-21   3.1e-17       1      63 []      40     121 ..      40     121 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 8.8e-21
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedg 57 
                                       dde+ +++dLP+ +k++i++s sg eLtI+++                    n rR+ tLP+ + ++e+ sA++++g
  gi|313127464|ref|YP_004037734.1|  40 DDEFTVVADLPGYEKDDIEISASGRELTIRAEqtaeteesgdryvrrerrqsNVRRSLTLPQEVVEEEA-SATYKNG 115
                                       799******************************************************************.******* PP

                        ArsA_HSP20  58 vLeIrF 63 
                                       vL++++
  gi|313127464|ref|YP_004037734.1| 116 VLTVTL 121
                                       ****96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0041       5      76 .]      36     123 ..      32     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                       EEEETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEETS.CEEEEECE.....................BSS-BETT CS
                                CS   5 WyQtldeVvvtiyvkkvnikkkdvkvefkerslkvkigk.eklliege.....................LfgpIdpe 59 
                                        ++t+de +v   ++++  +k+d++++ + r l++  ++  +     e                     L ++++ e
  gi|313127464|ref|YP_004037734.1|  36 VSETDDEFTVVADLPGY--EKDDIEISASGRELTIRAEQtAET----EesgdryvrrerrqsnvrrsltLPQEVVEE 106
                                       579*************9..*****************9443444....33455************************* PP

                                       TEEEEEETTEEEEEEEB CS
                                CS  60 esswtieskkveitLkK 76 
                                       e+s t ++  + +tL K
  gi|313127464|ref|YP_004037734.1| 107 EASATYKNGVLTVTLPK 123
                                       **************988 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.6   3.9e-05      0.14      94     133 ..      34      71 ..      18     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                              GvpH  94 trasddsdelvvvadlpGvtdedvdvaletdeqaltlrvd 133
                                          s+  de+ vvadlpG   +d++++     + lt+r +
  gi|313127464|ref|YP_004037734.1|  34 VDVSETDDEFTVVADLPGYEKDDIEISAS--GRELTIRAE 71 
                                       5568889**************99998766..667777765 PP

>> FAM110_C  Centrosome-associated C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.4   0.00019      0.67      17      79 ..       5      83 ..       2     111 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                          FAM110_C 17 lalselerFFnycGLdeevveelgker.f.ssasassdasr...............svsvsssesgfseasgeesdeeg 78
                                      +++ e+e+FF+++G + e+   lg+ r + ++ s+++d+++               s+s+ + +    +++++e+++ +
  gi|313127464|ref|YP_004037734.1|  5 NPFDEIEQFFKRMGREFEES-GLGSLRdIsVDVSETDDEFTvvadlpgyekddieiSASGRELTIRAEQTAETEESGDR 82
                                      6889**********776643.3433330203455555533345666677777665533333333333333333332222 PP

                          FAM110_C 79 l 79
                                       
  gi|313127464|ref|YP_004037734.1| 83 Y 83
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 966.34
//
Query:       gi|313127465|ref|YP_004037735.1|  [L=268]
Description: prephenate dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-46  159.0   0.2    1.3e-46  158.7   0.2    1.1  1  PDT       Prephenate dehydratase
    1.5e-06   27.8   0.0    4.9e-06   26.2   0.0    1.9  1  ACT       ACT domain
  ------ inclusion threshold ------
        0.1   12.5   0.2       0.27   11.1   0.2    1.6  1  TIP39     TIP39 peptide


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   0.2   2.2e-50   1.3e-46       3     180 ..       5     170 ..       3     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 2.2e-50
                                       EES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEEEE CS
                               PDT   3 ylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgEvv 79 
                                        lGp gtysh+Aa++v+     ++   +s++++++av++ge d +vvPiENs+eGsV+etlD +++  d+ +++E+v
  gi|313127465|ref|YP_004037735.1|   5 TLGPAGTYSHRAARAVA----DDVAFRESVSAIVDAVDSGEYDRGVVPIENSIEGSVTETLDAIAE-ADIAVTQEIV 76 
                                       69************999....56777899*************************************.99******** PP

                                       EE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHHT CS
                               PDT  80 lpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaaely 156
                                        pi+h+Lla++    ee + v Sh+qal+Qcr++Le+++p+v+ +av+sta+ +++  a++d+++a i++   a   
  gi|313127465|ref|YP_004037735.1|  77 TPIRHALLAQT----EEFSVVASHSQALAQCRSYLETEYPGVTLEAVASTARGVER--AREDDSVAGIGHPDNAGD- 146
                                       *******9775....56***************************************..999**********99976. PP

                                       T-EEEECS-SS-S--EEEEEEEEE CS
                               PDT 157 glkvleeniedkknntTRFlvlak 180
                                       +l+vl+e+i+d++ n TRF+v+a 
  gi|313127465|ref|YP_004037735.1| 147 DLRVLAEDIQDRSSNATRFFVVAP 170
                                       6********************975 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   8.2e-10   4.9e-06      11      49 ..     192     230 ..     188     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.2e-10
                                       TTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEE CS
                               ACT  11 PGlLarvfgaladrgiNidsieqrssedkvagivfvviv 49 
                                       PGlL +++ a+a+r+iN+ +ie+r+s+ +++++ f ++ 
  gi|313127465|ref|YP_004037735.1| 192 PGLLLELLEAFAERDINLSRIESRPSGNRLGDYLFHIDF 230
                                       9***************************87777665554 PP

>> TIP39  TIP39 peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   4.5e-05      0.27      10      26 ..      13      29 ..       7      35 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.5e-05
                             TIP39 10 lakRslvlADDAAFREk 26
                                        +   ++ADD AFRE 
  gi|313127465|ref|YP_004037735.1| 13 SHRAARAVADDVAFRES 29
                                      3344559********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1884.97
//
Query:       gi|313127466|ref|YP_004037736.1|  [L=220]
Description: imidazole glycerol phosphate synthase subunit HisH [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-24   86.8   0.0    1.8e-24   86.5   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    2.5e-09   37.0   0.0    5.3e-09   36.0   0.0    1.5  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      1e-07   32.0   0.0    0.00038   20.3   0.0    2.0  2  SNO            SNO glutamine amidotransferase family
      6e-06   26.2   0.3    5.1e-05   23.1   0.3    2.1  1  Peptidase_C26  Peptidase C26
    0.00017   21.5   0.0    0.00025   20.9   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   5.1e-28   1.8e-24       2     187 ..      17     214 ..      16     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 5.1e-28
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS- CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiP 73 
                                       ++D++ ++ ++  + l ++g++v+v      + e+     ++dgi+++ G+g+ +     ++   ea+ ea++++ P
  gi|313127466|ref|YP_004037736.1|  17 MVDYGLGNLRSARRGLERAGADVTVSD----DPETF---ADADGIVLP-GVGAFSegmenAGPFREALAEAADRGQP 85 
                                       799********************9987....45663...588999875.677777778888888999999999**** PP

                                       EEEETHHHHHHHHHTTT..................EEE..EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEE CS
                            GATase  74 iLGICLGmQllaiefgr..................kvv..kekekehhggtmrlgddetallyglknevierhrHry 130
                                       i+GICLGmQ+l+ ++ +                  +v   + ++ +h+g++    ++++ l+ g  +  ++++ H+y
  gi|313127466|ref|YP_004037736.1|  86 IFGICLGMQMLLTSSEEadhagegevegldfvpgrNVRfdEGQKVPHMGWNELHVQRDHPLVDGV-DGEYAYFVHSY 161
                                       ***************99999999977777666666444888888*******99999888888888.999******** PP

                                       EEESGCHHHTTEEEEEEEETTEEEEEEEEETT.TEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 131 evnpkelepaglevtakseddeelmeiiekkn.pfvgvQFHPEststpegpellfnfl 187
                                        + p    ++g +v a+++ + e+ +i+ ++  +++g+QFHPE++ ++ g ++l+nf+
  gi|313127466|ref|YP_004037736.1| 162 YAVP---DDDGAVV-ATTDYGVEFPAIVANEAgNVFGTQFHPEKSGET-GLQILRNFV 214
                                       ****...7788766.6666888**********66*********87665.599999984 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.5e-12   5.3e-09      26     188 ..      38     198 ..      16     202 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.5e-12
                          GATase_3  26 rvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegea 102
                                       +v +++   e++ +dad ++lpG      +  ++++  ++ea++eaa +g p++giC G+qmL ++ e++++    +
  gi|313127466|ref|YP_004037736.1|  38 DVTVSD-DPETF-ADADGIVLPGVGAF--SEGMENAGPFREALAEAADRGQPIFGICLGMQMLLTSSEEADHA--GE 108
                                       344444.44555.67********8755..556677777***************************99988876..88 PP

                          GATase_3 103 geveglglLdiete.fek.ekltgqvegevel......aaeg.eevkGyEiHsGrtilkekakpllkvkvggnng.e 169
                                       gevegl++++ + + f + +k+ +    e+++      + +g +  ++y +Hs   + +++    ++       g e
  gi|313127466|ref|YP_004037736.1| 109 GEVEGLDFVPGRNVrFDEgQKVPHMGWNELHVqrdhplV-DGvDGEYAYFVHSYYAVPDDDGAVVATT----DYGvE 180
                                       9********987551555667776666665556666532.3345566788887766655554444444....22335 PP

                          GATase_3 170 kdGavkksedgnvlGtYlH 188
                                          +v  +e gnv+Gt +H
  gi|313127466|ref|YP_004037736.1| 181 FPAIV-ANEAGNVFGTQFH 198
                                       55555.4588888888888 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.1e-07   0.00038       6      84 ..      23      99 ..      21     134 .. 0.81
   2 !   10.1   0.0   0.00014      0.52     146     186 ..     172     217 ..     135     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-07
                                      SSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT.-HHHHHHHHHTT.--EEEETHHHHHHCC CS
                               SNO  6 GaveehveaikkclaenktvkrkedlaevdaliiPGGestamskliertg.lyedllefvknsekvvlGtCaGlillsk 83
                                      G+++   + +++++a+  +  ++e +a+ d++++PG    a+s  +e+ g + e+l e + ++ ++++G C G+ +l  
  gi|313127466|ref|YP_004037736.1| 23 GNLRSARRGLERAGADVTVSDDPETFADADGIVLPGV--GAFSEGMENAGpFREALAEAADRG-QPIFGICLGMQMLLT 98
                                      6667778899**************************6..467777777773677777777777.9********977644 PP

                                      E CS
                               SNO 84 e 84
                                       
  gi|313127466|ref|YP_004037736.1| 99 S 99
                                      3 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
                                       EEEECTT....EEEEEEETTEEEESS-GGGS.TTHCHHHHHHHHHH CS
                               SNO 146 vlyeldg....eivvakqkkilatsfhPela.eddirvhdyfveev 186
                                       v++   g     iv+ + +++++t fhPe + e + ++   fve +
  gi|313127466|ref|YP_004037736.1| 172 VATTDYGvefpAIVANEAGNVFGTQFHPEKSgETGLQILRNFVELC 217
                                       3333333334367777799**********87467899999999876 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.3   1.4e-08   5.1e-05      99     216 .]      77     200 ..      72     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.4e-08
                     Peptidase_C26  99 raalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHh 175
                                       ++a +rg Pi+giC+G+q+l       l ++ e+ ++ +  +e  ++ + ++v++++g+ + ++   +e +v+  H 
  gi|313127466|ref|YP_004037736.1|  77 AEAADRGQPIFGICLGMQML-------LTSSEEADHAGEGEVEGLDFVPGRNVRFDEGQKVPHMGW-NELHVQRDHP 145
                                       68999***************.......443333323333334444688888888888888877776.7788877776 PP

                     Peptidase_C26 176 q..aike............laeelrveAvaeDgviEaies.eeakafvlgvQwHPE 216
                                          +++              +++  v+A+++ g +E+  +  ++   v+g Q+HPE
  gi|313127466|ref|YP_004037736.1| 146 LvdGVDGeyayfvhsyyavPDDDGAVVATTDYG-VEFPAIvANEAGNVFGTQFHPE 200
                                       422444477777777777678888888887665.6764440444589********9 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   6.9e-08   0.00025      49     109 ..      36      98 ..       9     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.9e-08
                                       E-SEEGGG..CTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                         DJ-1_PfpI  49 tvdasldd..vkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaa 109
                                        +d++++d   + a+ D +vlpG  a +e +++   ++e + e+a++g++++ IC g q+L+ 
  gi|313127466|ref|YP_004037736.1|  36 GADVTVSDdpETFADADGIVLPGVGAFSEGMENAGPFREALAEAADRGQPIFGICLGMQMLLT 98 
                                       4555555310134589*******9999*******************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1624.56
//
Query:       gi|313127467|ref|YP_004037737.1|  [L=348]
Description: phosphate ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-66  222.4   0.7    7.5e-66  222.2   0.7    1.1  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
    6.9e-05   22.5   1.6    6.9e-05   22.5   1.6    2.1  2  TAT_signal      TAT (twin-arginine translocation) pathway sig
    0.00034   20.6   0.1    0.00062   19.8   0.1    1.3  1  NMT1            NMT1/THI5 like
  ------ inclusion threshold ------
      0.045   13.3   0.0       0.08   12.5   0.0    1.4  1  OpuAC           Substrate binding domain of ABC-type glycine 


Domain annotation for each model (and alignments):
>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2   0.7   1.7e-69   7.5e-66       1     243 []      65     332 ..      65     332 .. 0.93

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 1.7e-69
                                       EEE--SS-HHHHHHHHHHHHHHHHHHHSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEE CS
                    Phosphonate-bd   1 igvlPsespaelkeayqpladyLseelGvevelvvatdyaavvealragqvDiaflgplayvqardqagveplatrv 77 
                                       ++++P+es+ +++++y+pl++y+++e+Gv+v+ +va+dyaav++a+++gq+Dia ++p+ ++q  +++ ++++++rv
  gi|313127467|ref|YP_004037737.1|  65 FALTPAESDVDVEKQYKPLFNYIESEVGVTVDSTVAADYAAVMQAMKSGQADIADASPSIAIQGGNEDVTKVIGIRV 141
                                       789************************************************************************** PP

                                       ETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HH.......HHSSEEEE--HH CS
                    Phosphonate-bd  78 rsdGsasyrsviivradsdiqsledLkgktiafvspsStsGylvpaalLvkeagldpe.......ddfsevfsgshd 147
                                       + +G+++y+s++++++ds+i++l+dLkgk++af+++ StsG+l+p+++L ++agld++       + fs++fs+ h+
  gi|313127467|ref|YP_004037737.1| 142 A-YGASRYFSLMTTTPDSGIEKLSDLKGKNVAFADRLSTSGSLFPLYML-SKAGLDTGgapdgkpKGFSAKFSD-HS 215
                                       8.***********************************************.8*****99999888889****997.99 PP

                                       HHHHHHH.TTSSSEEEEEHHHHHHHH..................HH-HHHH....TTEEEEEEEEEEE--EEEEETT CS
                    Phosphonate-bd 148 aavlavl.sgdadaaavsadaledlv..................aegpedk....delrviassppipndpvvvrke 201
                                       +a + ++ ++d+ aa++ a+ + +++                  +          +el+++a s+pip++p++ r+e
  gi|313127467|ref|YP_004037737.1| 216 TARETLInRDDVVAAGTGAFSTASHIpkdqfpkqfldisaendgD-----LgsesPELKLLAASDPIPRAPILGRAE 287
                                       999977658999999999999999996666666666665544433.....05555********************** PP

                                       S-HHHHHHHHHHHHH---S...HHHHHHHHHTTEEEEEE--GGGG CS
                    Phosphonate-bd 202 lseelkekiqdallslaet...eegkkllealgiegfvpaddsdy 243
                                       ++++l ++i++all+++++   ++++k  ++l+++g+++ + +dy
  gi|313127467|ref|YP_004037737.1| 288 MDQSLYSDIKTALLDVSKEdliNDDLKDDQQLWFTGVDKGSVDDY 332
                                       ******************99*********************9999 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.6   1.5e-08   6.9e-05       1      22 [.       1      22 [.       1      27 [. 0.81
   2 ?   -3.0   1.4       1.8   7.9e+03      17      22 ..     229     234 ..     227     238 .. 0.47

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.5e-08
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalgg 22
                                      + SRR FLK+++A++ A++++ 
  gi|313127467|ref|YP_004037737.1|  1 MPSRRKFLKTTGATGVAGLTAL 22
                                      57*************8888873 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                        TAT_signal  17 Aaalgg 22 
                                       Aa++g+
  gi|313127467|ref|YP_004037737.1| 229 AAGTGA 234
                                       333333 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   1.4e-07   0.00062      19     118 ..      91     195 ..      89     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-07
                                       TTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT-.-EE..EEEEEE-S--EEEEEECCC--SSGGGGT CS
                              NMT1  19 eGldVeivepadpsdatelvasgkadfgvsyqesllaarakgl.pvv..svaallqeplsglivlkdsgikspkDLk 92 
                                        G+ V+    ad + +++++ sg+ad++ +++   ++   +++ +v   +va    + +s +++  dsgi++++DLk
  gi|313127467|ref|YP_004037737.1|  91 VGVTVDSTVAADYAAVMQAMKSGQADIADASPSIAIQGGNEDVtKVIgiRVAYGASRYFSLMTTTPDSGIEKLSDLK 167
                                       68889999999****************987777666544443314542245666778888899999*********** PP

                                       TSEEEE-S..-TTHHHHHHHHHHHTT-- CS
                              NMT1  93 Gkrigyvg..spfekallkallakdggd 118
                                       Gk +++    s  ++ +   +l+k+g+d
  gi|313127467|ref|YP_004037737.1| 168 GKNVAFADrlSTSGSLFPLYMLSKAGLD 195
                                       *****99866666777777888888876 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.8e-05      0.08      23     113 ..      86     171 ..      83     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                       HHHHT.TEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEEEEEEESEEECEEEEEEHHHHH CS
                             OpuAC  23 llekk.GykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkglevlgplgagnteglavpkyvae 98 
                                       ++e+  G++v+ t ++ +a++++a++sG++D++  +    a +  ++ v++  g++     ++g+   +   + + +
  gi|313127467|ref|YP_004037737.1|  86 YIESEvGVTVDSTVAADYAAVMQAMKSGQADIAD-ASPSIAIQGGNEDVTKVIGIR----VAYGASRYFSLMTTTPD 157
                                       678888**8888888888**************98.665555555555555444444....44555555555555667 PP

                                       HHTTTBHHHHCTHHG CS
                             OpuAC  99 kygiksisDLkkpae 113
                                        +gi+++sDLk +++
  gi|313127467|ref|YP_004037737.1| 158 -SGIEKLSDLKGKNV 171
                                       .99999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2716.05
//
Query:       gi|313127468|ref|YP_004037738.1|  [L=251]
Description: phosphonate ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-34  117.7   0.0    7.3e-34  117.2   0.0    1.2  1  ABC_tran      ABC transporter
    5.6e-07   29.7   0.1     0.0054   16.6   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.2e-06   26.8   0.0    7.1e-06   26.0   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
    3.9e-05   24.1   0.1    6.1e-05   23.5   0.1    1.3  1  AAA_16        AAA ATPase domain
    0.00062   19.4   0.0     0.0013   18.5   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
    0.00074   19.0   0.0       0.11   11.9   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0032   16.8   0.0     0.0057   16.0   0.0    1.3  1  Zeta_toxin    Zeta toxin
     0.0034   17.5   0.2       0.16   12.0   0.1    2.5  2  MMR_HSR1      50S ribosome-binding GTPase
     0.0039   17.7   0.0     0.0073   16.8   0.0    1.4  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.011   16.0   0.2       0.03   14.6   0.2    1.9  1  AAA_22        AAA domain
      0.021   13.7   0.0      0.029   13.2   0.0    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
      0.029   14.0   0.0      0.055   13.0   0.0    1.4  1  AAA_25        AAA domain
      0.052   13.8   0.4        1.9    8.8   0.4    2.5  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.059   12.8   0.0      0.087   12.2   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.069   12.9   0.1       0.13   11.9   0.1    1.7  1  AAA_30        AAA domain
       0.11   11.6   0.0       0.11   11.6   0.0    1.2  1  G-alpha       G-protein alpha subunit
       0.12   12.7   0.2        0.3   11.5   0.1    1.9  1  Ret2_MD       RNA editing 3' terminal uridylyl transferase 2 
       0.15   11.9   0.1        0.4   10.6   0.1    1.7  1  NACHT         NACHT domain
       0.18   10.4   0.0        5.1    5.6   0.0    2.0  2  AAA_13        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.0   7.7e-37   7.3e-34       1     137 []      19     167 ..      19     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 7.7e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++vs+++  ge v+++G++GaGKStLl++l g ++pteG+i +dg+++        r  +++++q++ + +++++ 
  gi|313127468|ref|YP_004037738.1|  19 LDDVSFTIPDGEFVVLLGQSGAGKSTLLRCLNGITQPTEGSISIDGTEVLG-----PRDDVAMIFQQHYILEQMSAF 90 
                                       79***********************************************99.....9******************** PP

                                       HH.....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       +n                      +++e+ +al+++gl + +++++     ++SgGq+qrv +aral+++p+lll+D
  gi|313127468|ref|YP_004037738.1|  91 SNaltgalgrtsflrslfgrypdGDKQEALRALDTVGLLDEANQRA----GNMSGGQQQRVGIARALVQEPNLLLAD 163
                                       ********************999999999***********999999....*************************** PP

                                       STTT CS
                                       xxxx RF
                          ABC_tran 134 Epta 137
                                       Ep a
  gi|313127468|ref|YP_004037738.1| 164 EPVA 167
                                       **75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.7e-06    0.0054       1      24 [.      31      54 ..      31      91 .. 0.78
   2 !   11.3   0.0   0.00024      0.22     231     294 ..     133     194 ..      83     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      + vl G  g+GKS+LL++l ++ +
  gi|313127468|ref|YP_004037738.1| 31 FVVLLGQSGAGKSTLLRCLNGITQ 54
                                      689****************99864 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvil 294
                                       +  a ++S G+++  +++ al + +    lll DEp ++L+P+  +++++ ++++++ ++   i+
  gi|313127468|ref|YP_004037738.1| 133 NQRAGNMSGGQQQRVGIARALVQEP---NLLLADEPVASLDPASAETVMRYIRDAASeRNLTTIA 194
                                       5567889999999989999999888...89**********************5555544444443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   7.5e-09   7.1e-06      80     131 ..       9      61 ..       1      66 [. 0.80

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.5e-09
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       l  s  + ++l++++  + d +++vl+GqSG+GKStL+  l++ ++   g++s
  gi|313127468|ref|YP_004037738.1|   9 LSKSYGDVQALDDVSFTIPDgEFVVLLGQSGAGKSTLLRCLNGITQPTEGSIS 61 
                                       455566678899999999988********************998777777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   6.5e-08   6.1e-05      22     119 ..      27     177 ..      15     199 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.5e-08
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekd.................ggiflrgkcdqlesaipysa.laqalaree 80 
                                       +++e v+l G+sG GKs+l+r+l   +++                  ++  + ++   le+  ++s  l+ al r +
  gi|313127468|ref|YP_004037738.1|  27 PDGEFVVLLGQSGAGKSTLLRCLN-GITQPtegsisidgtevlgprdDVAMIFQQHYILEQMSAFSNaLTGALGRTS 102
                                       34489******************9.5666667666666665555554344444444444344566666888888888 PP

                            AAA_16  81 llrqllde.....aesaeleawrekleeala...............................avpelagaeasrl 119
                                       +lr l  +     +++a+++ +   l+++++                               +v++l++a+a+ +
  gi|313127468|ref|YP_004037738.1| 103 FLRSLFGRypdgdKQEALRALDTVGLLDEANqragnmsggqqqrvgiaralvqepnllladePVASLDPASAETV 177
                                       888888886655544444444444444444476666666666666666666666666666666666666655444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.3e-06    0.0013      13      39 ..      20      46 ..      15      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                            AAA_29 13 dghtieidlkg.atlltGpsGsGKSTll 39
                                      d+ +++i  +g +++l G+sG+GKSTll
  gi|313127468|ref|YP_004037738.1| 20 DDVSFTIP-DGeFVVLLGQSGAGKSTLL 46
                                      56677776.45599*************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.011        10      23      43 ..      28      48 ..       1      54 [. 0.71
   2 !   11.9   0.0   0.00012      0.11     135     195 ..     106     193 ..      52     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                                      TSSEEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnlldA 43
                                      + +f +++G+ G+GKs ll  
  gi|313127468|ref|YP_004037738.1| 28 DGEFVVLLGQSGAGKSTLLRC 48
                                      46799***********99865 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00012
                                       T...............................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                       x...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e...............................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                       +                               ++SgG+++ v +a       v+   l l De  a LD +  + v 
  gi|313127468|ref|YP_004037738.1| 106 SlfgrypdgdkqealraldtvglldeanqragNMSGGQQQRVGIARA----LVQEPNLLLADEPVASLDPASAETVM 178
                                       15555555555555555555555555666666*******99988754....467778999***************** PP

                                       HHHHHHCTTSEEEEE CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N 181 ellkeksknaQfivi 195
                                       ++++ + ++  +  i
  gi|313127468|ref|YP_004037738.1| 179 RYIRDAASERNLTTI 193
                                       ****76655443333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     6e-06    0.0057      19      53 ..      32      66 ..      24      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6e-06
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDd 53
                                      ++l Gq+GAGKs+l++ l+  ++++++ + +d+++
  gi|313127468|ref|YP_004037738.1| 32 VVLLGQSGAGKSTLLRCLNGITQPTEGSISIDGTE 66
                                      7889***************************9876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00017      0.16       2      21 ..      32      51 ..      31      69 .. 0.86
   2 ?    2.9   0.0      0.12   1.1e+02      46      65 ..     118     137 ..      88     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      v+++G++ +GKStL++ l g
  gi|313127468|ref|YP_004037738.1| 32 VVLLGQSGAGKSTLLRCLNG 51
                                      899************99865 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                                       EEEEEEECGGCSSHHHHHHH CS
                          MMR_HSR1  46 keielvDtpGliegaseekg 65 
                                       + ++ +Dt+Gl+++a+++ g
  gi|313127468|ref|YP_004037738.1| 118 EALRALDTVGLLDEANQRAG 137
                                       56888999999864444442 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.8e-06    0.0073      16      41 ..      23      51 ..      11      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.8e-06
                            AAA_23 16 dF...skgltlItGpNGaGKTTildAikl 41
                                       F   +  ++++ G+ GaGK+T+l+++  
  gi|313127468|ref|YP_004037738.1| 23 SFtipDGEFVVLLGQSGAGKSTLLRCLNG 51
                                      3444677799****************975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   3.2e-05      0.03       6      30 ..      30      54 ..      27     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                       ++v+ G+sG+GK+tllr l    +
  gi|313127468|ref|YP_004037738.1| 30 EFVVLLGQSGAGKSTLLRCLNGITQ 54
                                      6899**************9976654 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.1e-05     0.029      21      55 ..      25      59 ..      15      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                              DLIC 21 klPsgksvlvlGedgsGkttliaklqGveeekkGr 55
                                       +P g  v++lG++g+Gk+tl+  l G+ ++  G+
  gi|313127468|ref|YP_004037738.1| 25 TIPDGEFVVLLGQSGAGKSTLLRCLNGITQPTEGS 59
                                      5899*************************999886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.8e-05     0.055      30      50 ..      26      46 ..      21      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +p ge+++l G++g+GK+tl+
  gi|313127468|ref|YP_004037738.1| 26 IPDGEFVVLLGQSGAGKSTLL 46
                                      899****************98 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4     0.002       1.9      27      89 ..     133     182 ..     124     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.002
                           SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       ++++g++SGG++q +       ++a ++ +       + l++ DE  ++lD+ s++t++++++
  gi|313127468|ref|YP_004037738.1| 133 NQRAGNMSGGQQQRV-------GIARALVQ------EPNLLLADEPVASLDPASAETVMRYIR 182
                                       566777777777432.......22222333......4789999************99999986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.2e-05     0.087       2      61 ..       9      68 ..       8     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.2e-05
                      Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakia 61
                                      l++  G+ +a   +  ++  g  ++l+G +G+GK+ l ++l+++  p + + +++ +++ 
  gi|313127468|ref|YP_004037738.1|  9 LSKSYGDVQALDDVSFTIPDGEFVVLLGQSGAGKSTLLRCLNGITQPTEGSISIDGTEVL 68
                                      5555666666666677777777899*******************9998887777766654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00014      0.13      19      46 ..      30      58 ..      22     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g 46
                                       ++vl G  G+GK+t+l+ l+ + +   g
  gi|313127468|ref|YP_004037738.1| 30 EFVVLLGQSGAGKSTLLRCLNGITQPTeG 58
                                      4899**************99988877633 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.11      26      50 ..      32      56 ..      28     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHHHHCS-- CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkg 50
                                      ++llGqs+ GKsT+l+ l  + +++
  gi|313127468|ref|YP_004037738.1| 32 VVLLGQSGAGKSTLLRCLNGITQPT 56
                                      689*************999888887 PP

>> Ret2_MD  RNA editing 3' terminal uridylyl transferase 2 middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00032       0.3      69      92 ..     212     235 ..     177     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                           Ret2_MD  69 lPdGkiltkgmredytrdvldqrf 92 
                                       + dG i+  g red+t dv+d+ +
  gi|313127468|ref|YP_004037738.1| 212 MKDGEIVFDGYREDFTVDVIDEIY 235
                                       57*******************866 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00042       0.4       3      19 ..      32      48 ..      30      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                                      EEEEC-TTTCHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqk 19
                                      v+l G++G GK+tLl+ 
  gi|313127468|ref|YP_004037738.1| 32 VVLLGQSGAGKSTLLRC 48
                                      89*************85 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0054       5.1      21      76 ..      34      88 ..      29      99 .. 0.71
   2 ?    2.7   0.0     0.041        38     528     558 ..     158     187 ..     150     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0054
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsi.....eitngeeldirVfNrdFveenls 76
                                      + G+ GaGK+tL r l+ +++       ++gsi     e+   +    ++f + ++ e++s
  gi|313127468|ref|YP_004037738.1| 34 LLGQSGAGKSTLLRCLNGITQ-P-----TEGSIsidgtEVLGPRDDVAMIFQQHYILEQMS 88
                                      66999*************953.2.....344442233355555788889999999988877 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.041
                            AAA_13 528 kivviDDPvSSLDsnslfivfsliksrllkk 558
                                            D Pv SLD  s   v+ +i++ + ++
  gi|313127468|ref|YP_004037738.1| 158 NLLLADEPVASLDPASAETVMRYIRDAA-SE 187
                                       56677********************998.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 1703.58
//
Query:       gi|313127469|ref|YP_004037739.1|  [L=321]
Description: phosphonate ABC transporter permease phne [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2192.27
//
Query:       gi|313127470|ref|YP_004037740.1|  [L=200]
Description: uracil-DNA glycosylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-38  129.7   0.0    9.9e-38  129.6   0.0    1.0  1  UDG       Uracil DNA glycosylase superfamily
  ------ inclusion threshold ------
        0.1   12.4   0.9       0.27   11.0   0.9    1.8  1  DUF1127   Domain of unknown function (DUF1127)


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   0.0   1.1e-41   9.9e-38       2     146 ..      30     175 ..      29     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 1.1e-41
                                       HC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCT CS
                               UDG   2 gegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeik 78 
                                       g gp da++v++GeaPga+ed++g+pF+gr+g  l+++l ++gl+r      +v itn v+crpp+nr +pt+ e+ 
  gi|313127470|ref|YP_004037740.1|  30 GVGPDDADLVFLGEAPGANEDEQGEPFVGRSGSVLDDALRDVGLAR-----SDVRITNCVRCRPPENR-DPTKTELG 100
                                       89********************************************.....*****************.******** PP

                                       CCHHHHHHHHHHHHSSEEEEESHHHHHH....HHHHSCESCCCSCT......SEEEEES-SSTTTTTTTTSHHHH CS
                               UDG  79 acaplleeeiellkprlivllGktaakall..geklgklrgklleak.....irvlplphPsplnrnffksnpel 146
                                       +c+ +le+e+ell p l+v+lGk + ++ll     ++k  g +++ +      rvl + hP++ ++   +++ ++
  gi|313127470|ref|YP_004037740.1| 101 NCRGYLERELELLDPDLVVTLGKVPSEHLLdrSVAVTKEAGDVVDVRlgerlQRVLICVHPAATLYDRSQRDTFS 175
                                       ****************************998744666666666666555569**************944444444 PP

>> DUF1127  Domain of unknown function (DUF1127)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9     3e-05      0.27      23      37 .]      65      79 ..      65      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3e-05
                           DUF1127 23 DreLaDIGlsRsdir 37
                                      D  L+D+Gl Rsd+r
  gi|313127470|ref|YP_004037740.1| 65 DDALRDVGLARSDVR 79
                                      889**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1473.42
//
Query:       gi|313127471|ref|YP_004037741.1|  [L=195]
Description: hypothetical protein Hbor_27520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-58  197.3   0.1    1.8e-58  197.0   0.1    1.0  1  DUF99     Protein of unknown function DUF99
  ------ inclusion threshold ------
      0.034   14.8   0.1       0.05   14.3   0.1    1.4  1  Imm1      Immunity protein Imm1


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0   0.1     2e-62   1.8e-58       2     181 ..       8     185 ..       7     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 2e-62
                                       GSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETT CS
                             DUF99   2 eirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiag 78 
                                       ++r+lGi++s+   +  + +svl+G+v+radrv+dg+a+g++tv+GtD+t++i  l+ +l red+r+v++ G+++a+
  gi|313127471|ref|YP_004037741.1|   8 GTRALGIAESYTD-DGVEAESVLCGAVVRADRVIDGAAYGTCTVGGTDVTDVIRGLFSNLGREDVRLVFVAGVAPAW 83 
                                       68*********77.678************************************************************ PP

                                       TEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTH..HHHHHHHHHC.---EEETT....EEEEEESS-HH CS
                             DUF99  79 FNvvDlerlheetglPviavtreepdlgklekaLrkhfpde..eeRlelieklgerieevektgeelyvravGiele 153
                                       FN+vDl rl++++++Pv++v++e ++ g l++aL+ +f++e  ++Rl+++e+l++r+++++  + +++vr+vGi+ +
  gi|313127471|ref|YP_004037741.1|  84 FNLVDLRRLADAVDRPVLSVSFESSS-G-LRSALKAAFSGEelDTRLAVYESLPPRRRVTVG-DDTVFVRSVGISDD 157
                                       **************************.8.************888*********999999999.99************ PP

                                       HHHHHHHHC-SSSSS-HHHHHHHHHHHH CS
                             DUF99 154 eaaklvrkltlegriPEPlRvAhliAsa 181
                                       eaa++vr++t++g++PEPlRvA+l+A++
  gi|313127471|ref|YP_004037741.1| 158 EAARAVRAYTPTGGRPEPLRVARLLARS 185
                                       **************************95 PP

>> Imm1  Immunity protein Imm1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   5.6e-06      0.05      46     123 ..     101     177 ..      63     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.6e-06
                              Imm1  46 LevgvggdaglgglvylsgeddgpvsssngdppdseevvydyvggqtefPadsevpleqvraAlkeFlatgerPtcv 122
                                       L v++ + +gl + +  + + +    ++ +  ++ +++    vg++t f ++++++ +++ +A++++  tg rP+ +
  gi|313127471|ref|YP_004037741.1| 101 LSVSFESSSGLRSALKAAFS-GEELDTRLAVYESLPPRRRVTVGDDTVFVRSVGISDDEAARAVRAYTPTGGRPEPL 176
                                       66666666666666666665.3333333334466666677788*******************************976 PP

                              Imm1 123 r 123
                                       r
  gi|313127471|ref|YP_004037741.1| 177 R 177
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1423.62
//
Query:       gi|313127472|ref|YP_004037742.1|  [L=58]
Description: hypothetical protein Hbor_27530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.71    9.7   5.3       0.84    9.4   5.3    1.0  1  Tom22     Mitochondrial import receptor subunit Tom22


Domain annotation for each model (and alignments):
>> Tom22  Mitochondrial import receptor subunit Tom22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.3   4.7e-05      0.84       9      64 ..       7      57 ..       5      58 .] 0.48

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 4.7e-05
                             Tom22  9 deefqeeqegeeeelaeededeadetdsdseissdedddfdvedEtlldRivALkD 64
                                      de++qe+q+ ++ +l e+d      ++s+++ + + + +  +++E lldR+   kD
  gi|313127472|ref|YP_004037742.1|  7 DESEQESQDYDQ-DLDENDG----VATSENDHDGEVNFENGASNEELLDRLQEIKD 57
                                      444433332222.2222222....2233333332233444456********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 436.70
//
Query:       gi|313127473|ref|YP_004037743.1|  [L=208]
Description: zn-dependent hydrolase, glyoxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-16   61.5   6.8    9.2e-15   55.2   6.8    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
      6e-06   25.9   2.9    8.8e-06   25.4   2.7    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.018   14.5   0.0      0.035   13.6   0.0    1.5  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
      0.057   13.3   0.9       0.17   11.8   0.9    1.9  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   6.8     2e-18   9.2e-15       4     190 ..      13     164 ..      10     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 2e-18
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       + +n+yl+  +++++L+D+Gt +  +        +    +++dav+lTH H+DHiG l+ + +++d+  +a+ ++  
  gi|313127473|ref|YP_004037743.1|  13 FTCNAYLV-LGERNVLVDAGTMPGVETV------VADHTDELDAVVLTHQHTDHIGELDAVLDRFDADLYAYGDHP- 81 
                                       689*****.9*****************9......69********************************99876654. PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHC CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallaget 157
                                         +++ea                      +e++d+  +g ++++v+++pgh ++h+++   ++k +f+GD++  ++ 
  gi|313127473|ref|YP_004037743.1|  82 --RRDEA----------------------LEDGDVLQMGEETFEVVYTPGHASDHISLV--SEKRIFSGDVVVYNDG 132
                                       ..44444......................566999999999999999999999988776..6788*******98888 PP

                                       CCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCH CS
                       Lactamase_B 158 gridltlrgaevrdpsdaekyldsllklaglka 190
                                       + +     g +++ +++ e + +sl+ l +  +
  gi|313127473|ref|YP_004037743.1| 133 AFDNG-SFGRTDMSGQSRERLVESLRTLLDRIP 164
                                       77777.455555555555555555554444333 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   2.7     2e-09   8.8e-06       1      72 [.      24      89 ..      24     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2e-09
                                      SEEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEE.EEHHHHHHCCT CS
                     Lactamase_B_2  1 rriLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklply.apkgvlavlea 72
                                      r++L+Dag+      +         d+ +++daV+lth+H DH+  l+ +   + + +l  y  +++  + le+
  gi|313127473|ref|YP_004037743.1| 24 RNVLVDAGTMPGVE-T-VV-----ADHTDELDAVVLTHQHTDHIGELDAVLDrF-DADLYAYgDHPRRDEALED 89
                                      79999999883333.2.22.....455689**************9999999843.3345555233555555555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.7e-06     0.035       6      61 ..      23      72 ..      18      84 .. 0.76
   2 ?   -1.7   0.0      0.36   1.6e+03     157     189 ..      74     106 ..      69     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.7e-06
                     Lactamase_B_6  6 nvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfks 61
                                      + ++L+D G+    v+       + ++ +++d+++L+h  ++h+G +  ++ +f +
  gi|313127473|ref|YP_004037743.1| 23 ERNVLVDAGTMPG-VE-----TVVADHTDELDAVVLTHQHTDHIGELDAVLDRFDA 72
                                      6678999999885.42.....3467999*****************98877766654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.36
                     Lactamase_B_6 157 vYavdwnhakeshLngaalldssgkvleqllrp 189
                                       +Ya   + ++++ L+  ++l+   ++ e + +p
  gi|313127473|ref|YP_004037743.1|  74 LYAYGDHPRRDEALEDGDVLQMGEETFEVVYTP 106
                                       788888999999999999998777777777766 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.9   3.7e-05      0.17      15      50 ..      22      60 ..      14     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                     Lactamase_B_3 15 agarilvDPfka...nlgyeppaeeaDlvlisqaledHa 50
                                      ++ ++lvD ++    ++ ++  ++e D+v+++++++dH 
  gi|313127473|ref|YP_004037743.1| 22 GERNVLVDAGTMpgvETVVADHTDELDAVVLTHQHTDHI 60
                                      567899998855544666677789**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1613.69
//
Query:       gi|313127474|ref|YP_004037744.1|  [L=49]
Description: 50S ribosomal protein L40e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-08   33.8   7.2    2.8e-08   33.5   7.2    1.1  1  Ribosomal_L40e  Ribosomal L40e family
    9.9e-05   21.9   2.4    0.00014   21.4   2.4    1.2  1  zinc_ribbon_2   zinc-ribbon domain
    0.00076   19.5   1.5    0.00081   19.4   1.5    1.2  1  DZR             Double zinc ribbon
     0.0011   18.3   2.3     0.0013   18.1   2.3    1.2  1  zf-ribbon_3     zinc-ribbon domain
     0.0064   17.0   1.4     0.0067   16.9   1.4    1.1  1  zf-CHY          CHY zinc finger
  ------ inclusion threshold ------
      0.045   13.9   2.0      0.048   13.8   2.0    1.1  1  DHHC            DHHC palmitoyltransferase
      0.055   13.2   5.2       0.13   12.0   5.2    1.6  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        0.2   11.0   4.9       0.71    9.2   4.9    1.9  1  zf-RanBP        Zn-finger in Ran binding protein and others
       0.33   10.9   4.7       0.79    9.6   0.9    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.45   10.7   6.3       0.64   10.2   6.3    1.3  1  Ribosomal_L37e  Ribosomal protein L37e


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   7.2   1.5e-11   2.8e-08       9      49 ..       7      44 ..       4      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.5e-11
                    Ribosomal_L40e  9 AqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKKk 49
                                      A K   +K+iC +C Ar p rAt Cr  kCg  +nlrpK k
  gi|313127474|ref|YP_004037744.1|  7 ATKRTLEKQICMRCNARNPARATSCR--KCGY-KNLRPKSK 44
                                      8999**********************..9**7.67999965 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   2.4   7.9e-08   0.00014       2      22 ..      17      37 ..      16      38 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.9e-08
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C +C a ++ +a+ C +CG++
  gi|313127474|ref|YP_004037744.1| 17 CMRCNARNPARATSCRKCGYK 37
                                      *******************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.5   4.5e-07   0.00081      29      49 .]      15      35 ..       3      46 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.5e-07
                               DZR 29 drCpsCgekvdpearfCpeCG 49
                                      + C++C++ ++++a+ C +CG
  gi|313127474|ref|YP_004037744.1| 15 QICMRCNARNPARATSCRKCG 35
                                      556666666666666666665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.3   7.3e-07    0.0013       2      25 ..      14      37 ..      13      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.3e-07
                       zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCGtk 25
                                      ++ C +C+a +  ++++ C +CG+k
  gi|313127474|ref|YP_004037744.1| 14 KQICMRCNArN-PARATSCRKCGYK 37
                                      67899******.***********98 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.4   3.7e-06    0.0067      34      62 ..       7      36 ..       2      47 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                            zf-CHY 34 lerlevkevlcllCeteq.ekavlCkkCkk 62
                                      +++ + ++ +c++C++++   a+ C+kC+ 
  gi|313127474|ref|YP_004037744.1|  7 ATKRTLEKQICMRCNARNpARATSCRKCGY 36
                                      4455556667*******9445678****86 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.0   2.7e-05     0.048       3      26 ..      12      35 ..      10      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                              DHHC  3 kelkfCstcniykpprskHcrvCn 26
                                       e+++C  cn + p+r+  cr+C+
  gi|313127474|ref|YP_004037744.1| 12 LEKQICMRCNARNPARATSCRKCG 35
                                      5899*******************7 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   5.2   7.3e-05      0.13       2      26 ..      16      37 ..      16      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-05
                                      B-SSS--B----SSS----SSS--- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGhR 26
                                      iC++C+a++  +++    C++CG++
  gi|313127474|ref|YP_004037744.1| 16 ICMRCNARNPARAT---SCRKCGYK 37
                                      8*********9999...8*****98 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.9    0.0004      0.71       7      25 ..      17      35 ..      16      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0004
                                      -SSS--EEESSSSB-TTT- CS
                          zf-RanBP  7 CskClvqNfawstkCvaCq 25
                                      C  C+++N+a +t C  C+
  gi|313127474|ref|YP_004037744.1| 17 CMRCNARNPARATSCRKCG 35
                                      889************9996 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.028        51      23      33 ..      13      26 ..       1      29 [. 0.66
   2 ?    9.6   0.9   0.00044      0.79      23      30 ..      30      37 ..      26      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.028
                                      E...ESSSS-EEES CS
                    RNA_POL_M_15KD 23 e...CrqCgYeepa 33
                                      e   C  C +  pa
  gi|313127474|ref|YP_004037744.1| 13 EkqiCMRCNARNPA 26
                                      33339999999997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00044
                                      EESSSS-E CS
                    RNA_POL_M_15KD 23 eCrqCgYe 30
                                       Cr+CgY+
  gi|313127474|ref|YP_004037744.1| 30 SCRKCGYK 37
                                      4******8 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   6.3   0.00035      0.64      16      45 ..      14      42 ..       6      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00035
                    Ribosomal_L37e 16 HilCrrCgkrsyhvqkktCascGypsaklr 45
                                        +C rC+ r    + ++C +cGy++ + +
  gi|313127474|ref|YP_004037744.1| 14 KQICMRCNARN-PARATSCRKCGYKNLRPK 42
                                      568*****997.678999******987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 358.05
//
Query:       gi|313127475|ref|YP_004037745.1|  [L=88]
Description: thioredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-23   80.6   0.0    7.6e-23   80.5   0.0    1.0  1  Thioredoxin    Thioredoxin
    6.5e-08   33.0   0.4    4.1e-07   30.4   0.4    1.8  1  Thioredoxin_2  Thioredoxin-like domain
      6e-06   26.1   0.0    6.8e-06   25.9   0.0    1.1  1  Thioredoxin_9  Thioredoxin
    7.4e-06   26.2   0.0      0.011   16.0   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    0.00015   22.0   0.3     0.0004   20.5   0.1    1.7  2  Glutaredoxin   Glutaredoxin
    0.00019   21.2   0.4      0.011   15.5   0.0    2.0  2  Redoxin        Redoxin
    0.00022   21.2   0.0    0.00027   20.9   0.0    1.1  1  Thioredoxin_3  Thioredoxin domain
     0.0004   20.3   0.0    0.00043   20.2   0.0    1.1  1  TraF           F plasmid transfer operon protein
     0.0012   18.8   0.3      0.013   15.4   0.3    1.9  1  AhpC-TSA       AhpC/TSA family
     0.0015   18.4   0.2      0.089   12.6   0.0    2.0  2  DSBA           DSBA-like thioredoxin domain
     0.0045   17.4   0.2     0.0053   17.1   0.2    1.2  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.015   15.6   0.4      0.021   15.1   0.4    1.2  1  DUF1947        Domain of unknown function (DUF1947)
      0.056   13.1   0.2      0.091   12.4   0.1    1.5  2  Thioredoxin_5  Thioredoxin
      0.077   13.0   0.0      0.092   12.7   0.0    1.2  1  HyaE           Hydrogenase-1 expression protein HyaE
       0.17   11.2   0.0       0.17   11.2   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   6.3e-26   7.6e-23      23     102 ..       6      84 ..       2      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 6.3e-26
                                       EEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHH CS
                       Thioredoxin  23 veFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarekeklaa 99 
                                        +FyA+wCg+Ck   P l++l ee++ +v + kvdvde++d+a++y+v+++Ptl++ +++  v++++g  ++e+l++
  gi|313127475|ref|YP_004037745.1|   6 KDFYADWCGPCKTQDPILDELEEEYA-DVEFEKVDVDEEQDVANEYQVRSLPTLIIENDDGIVDRFVGVTQREDLED 81 
                                       59************************.***************************9999999**************99 PP

                                       HHH CS
                       Thioredoxin 100 flk 102
                                        l+
  gi|313127475|ref|YP_004037745.1|  82 ALQ 84 
                                       987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.4   3.5e-10   4.1e-07      11     109 .]       7      83 ..       4      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.5e-10
                     Thioredoxin_2  11 vftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfl 87 
                                       +f++++C+ Ck     l+el            ++ ++ ++++++ ++e           +++a++y+vr++Pt+++ 
  gi|313127475|ref|YP_004037745.1|   7 DFYADWCGPCKTQDPILDEL-----------EEEYADVEFEKVDVDEE-----------QDVANEYQVRSLPTLIIE 61 
                                       68999999999988877777...........22223333333333333...........3578************** PP

                     Thioredoxin_2  88 dgkeivarlpGyvpaeeleall 109
                                       + + iv+r +G +++e+le++l
  gi|313127475|ref|YP_004037745.1|  62 NDDGIVDRFVGVTQREDLEDAL 83 
                                       ******************9876 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   5.7e-09   6.8e-06      50     108 ..      10      65 ..       5      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.7e-09
                                       -TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT- CS
                     Thioredoxin_9  50 edwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildeeg 108
                                       +dwCg +    P+l+++ e+  ++e++ +  de++++ ++y+    r+ Ptlii +++g
  gi|313127475|ref|YP_004037745.1|  10 ADWCGPCKTQDPILDELEEEYADVEFEKVDVDEEQDVANEYQV---RSLPTLIIENDDG 65 
                                       79***************************************66...********99885 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.5e-06     0.011       7      45 ..       7      42 ..       3      45 .. 0.83
   2 !   10.6   0.0   0.00045      0.54      67      94 ..      39      66 ..      32      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.5e-06
                                      EE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS CS
                     Thioredoxin_8  7 yfgaswcppckaftpklkelyeklkkkkkveivyvsldk 45
                                       f+a+wc pck+  p l+el+e++    +ve+  v +d+
  gi|313127475|ref|YP_004037745.1|  7 DFYADWCGPCKTQDPILDELEEEYA---DVEFEKVDVDE 42
                                      59**********************7...66666666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00045
                                      -TT-HHHHTT-S--TT-SEEEEE-TT-B CS
                     Thioredoxin_8 67 ddkkrnklkkkynvkaiPtlvvldknge 94
                                      d ++ + ++++y+v ++Ptl++ + +g 
  gi|313127475|ref|YP_004037745.1| 39 DVDEEQDVANEYQVRSLPTLIIENDDGI 66
                                      3456899***************999885 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   3.3e-07    0.0004       7      57 ..      11      62 ..       2      66 .. 0.85
   2 ?   -0.6   0.0       1.4   1.6e+03      27      43 ..      69      85 ..      62      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.3e-07
                                      TSSHHHHHHHHHHHHTT.....GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETT CS
                      Glutaredoxin  7 ptCpyCkkakrlLkelg.....vkfeeidvdkdeeireelkelsgvrtvPqvfidg 57
                                       +C+ Ck    +L+el      v+fe +dvd+++++  e      vr++P++ i +
  gi|313127475|ref|YP_004037745.1| 11 DWCGPCKTQDPILDELEeeyadVEFEKVDVDEEQDVANEY----QVRSLPTLIIEN 62
                                      79***********99998888899*******997777777....999999999965 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                                      EEEEGCCSHHHHHHHHH CS
                      Glutaredoxin 27 eeidvdkdeeireelke 43
                                      +++ v++ e++ ++l++
  gi|313127475|ref|YP_004037745.1| 69 RFVGVTQREDLEDALQK 85
                                      67889999999999986 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.2e-06     0.011      35      66 ..       8      38 ..       4      41 .. 0.89
   2 ?    4.6   0.1      0.02        24      92     145 ..      41      81 ..      37      85 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.2e-06
                                      EESTTT-HHHHHTHHHHHTHHHHHHCSTTTEE CS
                           Redoxin 35 fvpgafcPtCsaehpyleklaellkekgvdvv 66
                                      f++  +c++C+++ p l++l+e++++  +++v
  gi|313127475|ref|YP_004037745.1|  8 FYAD-WCGPCKTQDPILDELEEEYADVEFEKV 38
                                      5666.********************9988876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.02
                                       -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                           Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepeteesnaea 145
                                       D++++++ ++ +r          +p + +i  d+ +v ++v++  +   +++e+
  gi|313127475|ref|YP_004037745.1|  41 DEEQDVANEYQVR---------SLP-TLIIENDDGIVDRFVGVTQR---EDLED 81 
                                       5666666666655.........455.55666666688999999884...44444 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.3e-07   0.00027      10      73 ..      13      81 ..       8      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.3e-07
                                      STTCHHHHHHHHHHCHCC.TCECEEECCTTHHHH.HHCT-SSSSEEECT...TCE.EEESS---CCHHHH CS
                     Thioredoxin_3 10 CakCpklekavkeaaaek.gikaevekvtdfeei.ekygVmsvPalvid...gkv.vvsGkvpseeeirk 73
                                      C  C++ + ++ e+ +e  ++++e ++v + +++ ++y+V+s P+l+i+   g v +++G v ++e+++ 
  gi|313127475|ref|YP_004037745.1| 13 CGPCKTQDPILDELEEEYaDVEFEKVDVDEEQDVaNEYQVRSLPTLIIEnddGIVdRFVG-VTQREDLED 81
                                      88888777777777777755888888899999999*************866444335888.888887776 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.6e-07   0.00043     136     201 ..       8      63 ..       5      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.6e-07
                              TraF 136 Fyrgkcpyceaqapilqafadky.glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdp 201
                                       Fy+  c+ c+ q pil++++++y   e   V+vd++++  ++n         +++v++ P+l++ + 
  gi|313127475|ref|YP_004037745.1|   8 FYADWCGPCKTQDPILDELEEEYaDVEFEKVDVDEEQD--VAN---------EYQVRSLPTLIIEND 63 
                                       9999*******************99***********99..999.........9********998665 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   1.1e-05     0.013      32      99 ..       8      72 ..       5      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                      EESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT CS
                          AhpC-TSA 32 fypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakayg 99
                                      fy+  wc +C+t+ p l +l ee++  +ve   v vd+++++++  +  sl+  ++   +g v +  g
  gi|313127475|ref|YP_004037745.1|  8 FYAD-WCGPCKTQDPILDELEEEYA--DVEFEKVDVDEEQDVANEYQVRSLPTLIIENDDGIVDRFVG 72
                                      7777.********************..88899999999999999998888888887777766665555 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.016        19       4      34 ..       8      37 ..       5      40 .. 0.84
   2 !   12.6   0.0   7.5e-05     0.089     151     193 .]      38      84 ..      36      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                                      EEEBTTBHHHHHHHHHHHHHHHHCCTEEEEE CS
                              DSBA  4 effDvlCPyCylgkerleklaarspdvkvvl 34
                                      ++ D  C+ C++ ++ l++l++ + dv++ +
  gi|313127475|ref|YP_004037745.1|  8 FYAD-WCGPCKTQDPILDELEEEYADVEFEK 37
                                      4444.59*****************9999875 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHHHHHHTT-SSSSEEEE.TTC....EEEESSSSHHHHHHHHH CS
                              DSBA 151 eavrentaaaqslgvtGvPtvvv.dgk....rmvfGadrldtladala 193
                                        +v+e+++ a++++v+ +Pt ++ +        ++G+++ + l+dal+
  gi|313127475|ref|YP_004037745.1|  38 VDVDEEQDVANEYQVRSLPTLIIeN-DdgivDRFVGVTQREDLEDALQ 84 
                                       579********************63.33567799***********997 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   4.4e-06    0.0053      10      57 ..      13      62 ..       8      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.4e-06
                                      -HHHHHHHHHHHHHCCCTT.EEEEEEETTT-CCCHCCCCTTT.TEEEECT CS
                            DUF836 10 ChlCeqakekLkelkleeg.leleviDIakdeeleakYglei.pvlaleg 57
                                      C+ C+    +L el++e   +e e++D++++++  ++Y++++ p l +e+
  gi|313127475|ref|YP_004037745.1| 13 CGPCKTQDPILDELEEEYAdVEFEKVDVDEEQDVANEYQVRSlPTLIIEN 62
                                      999*********98766656*******************97437777776 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.4   1.8e-05     0.021      11      53 ..      20      62 ..      17      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHTTT---TT--..-EEEE-S.S-EEEEETTEEEEEE.S CS
                           DUF1947 11 keileklkekyisislesdkiEieeek.keklYlingvpilfe.e 53
                                      + il++l+e+y ++++e+  ++++ee+  +  Y + + p l+  +
  gi|313127475|ref|YP_004037745.1| 20 DPILDELEEEYADVEFEK--VDVDEEQdVANEYQVRSLPTLIIeN 62
                                      5699*******99*9999..****999556778888888877644 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2   1.4e+03       7      27 ..      12      32 ..       8      40 .. 0.80
   2 ?   12.4   0.1   7.6e-05     0.091     140     167 ..      37      64 ..      23      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                     Thioredoxin_5  7 lcseCweiEpelkklkveyge 27
                                      +c  C   +p+l  l +ey +
  gi|313127475|ref|YP_004037745.1| 12 WCGPCKTQDPILDELEEEYAD 32
                                      799999999999999999864 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.6e-05
                     Thioredoxin_5 140 kkafqcDlklakemgvtevPtlvffnen 167
                                       k   ++ + +a+e++v+++Ptl++ n++
  gi|313127475|ref|YP_004037745.1|  37 KVDVDEEQDVANEYQVRSLPTLIIENDD 64 
                                       55567889****************9943 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.7e-05     0.092      49      98 ..      22      69 ..      16      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.7e-05
                                      HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEE CS
                              HyaE 49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgv 98
                                      +l El +++ ++    v    ++e+ +a++++v+  P+l++  d+ ++  
  gi|313127475|ref|YP_004037745.1| 22 ILDELEEEYADVEFEKVDV--DEEQDVANEYQVRSLPTLIIENDDGIVDR 69
                                      7889999999988888755..78889**************9888766554 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.17      71     101 ..      30      60 ..       8      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                         OST3_OST6  71 skklfFakvdfdegkdvFqklglnsaPhlll 101
                                         ++ F kvd+de +dv ++++++s+P l++
  gi|313127475|ref|YP_004037745.1|  30 YADVEFEKVDVDEEQDVANEYQVRSLPTLII 60 
                                       456679*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 653.32
//
Query:       gi|313127476|ref|YP_004037746.1|  [L=54]
Description: preprotein translocase subunit sec61beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-16   60.2   0.1      2e-16   59.7   0.1    1.2  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.1   1.1e-20     2e-16       1      41 []      12      53 ..      12      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.1e-20
                                      XXXXXXXXXX.----SS-B-THHHHHHHHHHHHHHHHHTSS- CS
                        Sec61_beta  1 SsaGLlryye.edapgikidPkvVlvlsvafiasVilLhila 41
                                      SsaGL+ry++ ed+++i++dPk +++++++f++ V++L+++a
  gi|313127476|ref|YP_004037746.1| 12 SSAGLVRYFDaEDRNAIRLDPKSIVAFGLLFGVGVLVLNVVA 53
                                      9**************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 371.23
//
Query:       gi|313127477|ref|YP_004037747.1|  [L=200]
Description: pyridoxal phosphate synthase yaae subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-55  185.8   0.0    7.8e-55  185.6   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    5.7e-11   42.4   0.0    1.2e-10   41.3   0.0    1.5  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    1.3e-06   28.2   0.0    1.7e-06   27.8   0.0    1.1  1  Peptidase_S51  Peptidase family S51
    0.00034   20.5   0.0    0.00051   19.9   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
     0.0053   16.5   0.0      0.033   14.0   0.0    1.9  1  GATase         Glutamine amidotransferase class-I
     0.0067   15.6   0.0      0.033   13.3   0.0    1.9  2  BPL_N          Biotin-protein ligase, N terminal
  ------ inclusion threshold ------
       0.16   11.7   0.0        0.2   11.3   0.0    1.2  1  ThiJ_like      ThiJ/PfpI family-like
       0.19   11.9   0.0       0.37   11.0   0.0    1.4  1  DUF4154        YfiR/HmsC-like


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.6   0.0   3.5e-58   7.8e-55       1     181 [.       6     188 ..       6     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 185.6 bits;  conditional E-value: 3.5e-58
                                       EESSSSSHHHHHHHHHHTTSEE......EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--E CS
                               SNO   1 vlalqGaveehveaikkclaen......ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvv 71 
                                       v+a+qG+v eh  ai+++  +         +++  ++ ++d l+iPGGesta+s+l+ r g+ e++++ v+ + k+v
  gi|313127477|ref|YP_004037747.1|   6 VVAVQGDVSEHAAAIRRAADAHgenvdvVEIRQSGHIPDCDVLLIPGGESTAISRLLRREGIDEEIRDHVAAG-KPV 81 
                                       79**************99876677788888899999***********************************99.*** PP

                                       EEETHHHHHHCCEETTBSS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEE CS
                               SNO  72 lGtCaGlillskelenelvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvly 148
                                       l tCaGli+ s++ + + v+tl+l++v+v rnafGrqvdsfe+ ld+ +++++f+avfiraP i+ +   + v+vl 
  gi|313127477|ref|YP_004037747.1|  82 LATCAGLIVSSRDAKDDRVETLDLIDVSVDRNAFGRQVDSFEAPLDIAGMDDPFPAVFIRAPLIDDVD--DGVEVLA 156
                                       ******************************************************************98..89***** PP

                                       ECTTEEEEEEETTEEEESS-GGGSTTHCHHHHH CS
                               SNO 149 eldgeivvakqkkilatsfhPelaeddirvhdy 181
                                       e dg  v+++q+ +++tsfhPel+ d  r+hd+
  gi|313127477|ref|YP_004037747.1| 157 EWDGTPVAVRQGPVVGTSFHPELTAD-SRLHDL 188
                                       ************************98.899986 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   5.5e-14   1.2e-10      25     115 ..      29     110 ..      15     127 .. 0.79
   2 ?   -2.5   0.0       1.5   3.3e+03     171     188 ..     159     176 ..     145     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 5.5e-14
                          GATase_3  25 vrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvege 101
                                       ++v +v+++++   +d+d++++pGg++t+ +  llr++g+de+i+++++ag+pvl+ C+Gl++ ++  +d+      
  gi|313127477|ref|YP_004037747.1|  29 ENVDVVEIRQSGHIPDCDVLLIPGGESTAISR-LLRREGIDEEIRDHVAAGKPVLATCAGLIVSSRDAKDD------ 98 
                                       4555666555555588***********98765.55566***********************9988877764...... PP

                          GATase_3 102 ageveglglLdiet 115
                                         +ve l+l+d+++
  gi|313127477|ref|YP_004037747.1|  99 --RVETLDLIDVSV 110
                                       ..567777777765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                          GATase_3 171 dGavkksedgnvlGtYlH 188
                                       dG     ++g v+Gt +H
  gi|313127477|ref|YP_004037747.1| 159 DGTPVAVRQGPVVGTSFH 176
                                       555555567899999999 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   7.5e-10   1.7e-06      41     137 ..       9      99 ..       4     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 7.5e-10
                                       GG-S--HHHHHHHHHHHHTT-EEEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT- CS
                     Peptidase_S51  41 vsgdddeyvekvrkaleklglevdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqgl 117
                                       v gd+ e  +++r+a   +g +vd++e+   ++  i +     dv+++ GG+   + +ll+++g+d+ +r++v++g+
  gi|313127477|ref|YP_004037747.1|   9 VQGDVSEHAAAIRRAADAHGENVDVVEIR--QSGHIPD----CDVLLIPGGESTAISRLLRREGIDEEIRDHVAAGK 79 
                                       55788888888888888899999999987..5667888....*********************************** PP

                                       EEEEETHHHHTTSSB-GGGT CS
                     Peptidase_S51 118 vyiGvSAGaivagesietts 137
                                       ++  + AG iv ++  + + 
  gi|313127477|ref|YP_004037747.1|  80 PVLATCAGLIVSSRDAKDDR 99 
                                       ***********999887665 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.3e-07   0.00051      61     106 ..      44      90 ..      11     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-07
                                       G-SEEEE--BHHHH.HHHHTSHHHHHHHHHHHHTT-EEEEETTTHHH CS
                         DJ-1_PfpI  61 eyDalvlpGGragp.erlrenekvvelvkefaekgklvaaICagpql 106
                                       + D+l++pGG++ +  rl + e + e +++++ +gk+v a Cag ++
  gi|313127477|ref|YP_004037747.1|  44 DCDVLLIPGGESTAiSRLLRREGIDEEIRDHVAAGKPVLATCAGLIV 90 
                                       68********997546788889**********************554 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.5e-05     0.033      12     183 ..      19     189 ..      13     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHH CS
                            GATase  12 nlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQl 83 
                                       ++ +a+ + g +v+vv+i +s ++      ++d +l++gG  +       +eg  e i+    +++P+L  C G+ +
  gi|313127477|ref|YP_004037747.1|  19 AIRRAADAHGENVDVVEIRQSGHIP-----DCDVLLIPGGESTAIsrllrREGIDEEIRDHVAAGKPVLATCAGLIV 90 
                                       6777888888899999999888888.....79999999998877678888777777777777789999999999988 PP

                                       HHHHTTT......EEEEEECEEEEEEEEEEEETTT......CGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEE CS
                            GATase  84 laiefgr......kvvkekekehhggtmrlgddet......allyglknevierhrHryevnpkelepaglevtaks 148
                                          +         +        +     +   ++         + g+++++ + +     +++   +++g+ev+a+ 
  gi|313127477|ref|YP_004037747.1|  91 SSRDAKDdrvetlD------LIDVSVDRNAFGRQVdsfeapLDIAGMDDPFPAVFIRAPLIDD---VDDGVEVLAEW 158
                                       88888885443331......2222222222222222233345788999999999999999999...9******9888 PP

                                       ETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHH CS
                            GATase 149 eddeelmeiiekknpfvgvQFHPEststpegpell 183
                                        d+ + +++++ +  +vg+ FHPE t   + + l 
  gi|313127477|ref|YP_004037747.1| 159 -DG-TPVAVRQGP--VVGTSFHPELTADSRLHDLA 189
                                       .55.788887655..9********99877665555 PP

>> BPL_N  Biotin-protein ligase, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.5e-05     0.033      48      96 ..      43      92 ..      29     104 .. 0.86
   2 ?   -0.2   0.0      0.18     4e+02     180     210 ..     152     168 ..     137     192 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                             BPL_N 48 stcallVlPgGaDlpYvrelngegn.rkikeyVekGGkylGlCAGaYygs 96
                                        c +l +PgG  ++  r l++eg+ ++i+++V +G   l+ CAG   +s
  gi|313127477|ref|YP_004037747.1| 43 PDCDVLLIPGGESTAISRLLRREGIdEEIRDHVAAGKPVLATCAGLIVSS 92
                                      6899*****************9997368*****************76665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                             BPL_N 180 vevLArYa.eeldvdsgeakkaAvvlckvgeG 210
                                       vevLA+++  +++v                +G
  gi|313127477|ref|YP_004037747.1| 152 VEVLAEWDgTPVAV---------------RQG 168
                                       77777766333333...............344 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.9e-05       0.2      82     137 ..      42      90 ..      26     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.9e-05
                         ThiJ_like  82 leeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvla 137
                                       + + d++l+pGG+  a+  ll  e + + +++++       +  k + a+c g ++
  gi|313127477|ref|YP_004037747.1|  42 IPDCDVLLIPGGESTAISRLLRREGIDEEIRDHV-------AAGKPVLATCAGLIV 90 
                                       55679**************************999.......344555566666554 PP

>> DUF4154  YfiR/HmsC-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.37      32      87 ..      11      64 ..       5      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                                      S-BSSTHHHHT-EE-TTS..-EEEEEEE-TT-TTHH-SEEEE-S--HHHHHHHHHH CS
                           DUF4154 32 gddpfaaaleallegkkvrgrpievrrlddsseaeechvlyigesearelaailka 87
                                      gd  + ++ +a+ + + ++g ++ v+++++s  + +c+vl+i  +e+++++++l++
  gi|313127477|ref|YP_004037747.1| 11 GD--VSEHAAAIRRAADAHGENVDVVEIRQSGHIPDCDVLLIPGGESTAISRLLRR 64
                                      44..5555555566677899**************99*********99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1345.86
//
Query:       gi|313127478|ref|YP_004037748.1|  [L=101]
Description: phosphoribosyl-ATP pyrophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-14   53.9   1.9    2.2e-14   53.7   1.9    1.1  1  PRA-PH         Phosphoribosyl-ATP pyrophosphohydrolase
  ------ inclusion threshold ------
       0.12   12.6   2.8       0.19   11.9   2.8    1.3  1  MazG           MazG nucleotide pyrophosphohydrolase domain
       0.15   12.5   0.1       0.15   12.5   0.1    1.9  2  Calpain_inhib  Calpain inhibitor


Domain annotation for each model (and alignments):
>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   1.9   3.6e-18   2.2e-14       4      82 ..      15     100 ..      12     101 .] 0.96

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 3.6e-18
                                       HHHHCT----SS----.-HHHHHH......HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CH CS
                            PRA-PH   4 fhrligerkpetPeas.taelasl......raaligEEavElleaasegdlaeladelaDllYvtygllvllGidld 73 
                                       +  +i+ rk+e Pe s t +l+++      ++++igEE +E + aa++++ +el  e aDl+Y++++ll  ++ +ld
  gi|313127478|ref|YP_004037748.1|  15 LFSTIESRKAELPEDSyTTTLFTHekgenyVLEKIGEETTEAILAAKDDETEELLAESADLVYHLLVLLSMKDASLD 91 
                                       6679************************************************************************* PP

                                       HHHHHHHHH CS
                            PRA-PH  74 avfeevhra 82 
                                       ++ +e++++
  gi|313127478|ref|YP_004037748.1|  92 DLRDELKER 100
                                       *****9986 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.8   3.2e-05      0.19       6      55 ..      45      90 ..      40     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---H CS
                              MazG  6 llaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidl 55
                                      +l+ + eE+ E + a k ++++el  E +D+ +++l l  +    ++ +l
  gi|313127478|ref|YP_004037748.1| 45 VLEKIGEETTEAILAAKDDETEELLAESADLVYHLLVLLSM----KDASL 90
                                      678899******************************99997....44444 PP

>> Calpain_inhib  Calpain inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.5e-05      0.15      60     109 ..       3      52 ..       1      56 [. 0.88
   2 ?    0.2   0.4      0.17   9.9e+02      62      77 ..      84      99 ..      59     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                     Calpain_inhib  60 kesmsddA.ldaLsdsLgkrepdpeepkkppedkVkeekakeekreklGer 109
                                       +e+ sddA ldaL  ++++r+++ +e + ++      ek  +  +ek+Ge+
  gi|313127478|ref|YP_004037748.1|   3 DEADSDDAvLDALFSTIESRKAELPE-DSYTTTLFTHEKGENYVLEKIGEE 52 
                                       4566777758****************.99999999999999999*****96 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.17
                     Calpain_inhib 62 smsddAldaLsdsLgk 77
                                      sm+d  ld L d L++
  gi|313127478|ref|YP_004037748.1| 84 SMKDASLDDLRDELKE 99
                                      6889999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 748.42
//
Query:       gi|313127479|ref|YP_004037749.1|  [L=175]
Description: hypothetical protein Hbor_27600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1219.52
//
Query:       gi|313127480|ref|YP_004037750.1|  [L=222]
Description: reduced coenzyme f420:NADp oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-22   78.2   0.0    9.6e-22   77.4   0.0    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    6.9e-05   23.1   0.0    0.00014   22.1   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0018   17.4   0.1     0.0022   17.1   0.1    1.2  1  PDH              Prephenate dehydrogenase
     0.0045   16.9   0.4      0.033   14.1   0.0    2.1  2  KR               KR domain
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.048   13.6   0.0    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.024   15.1   0.0      0.033   14.6   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.025   15.4   0.0      0.051   14.4   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.039   13.6   0.0      0.052   13.2   0.0    1.2  1  ApbA             Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   4.3e-25   9.6e-22       1      97 []       2     105 ..       2     105 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 4.3e-25
                                       EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE CS
                     F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvl 67 
                                       +i+++ G+G++ge+la++++ +   +h+iv++ sr+peka++ a+e++         vkvt+ +n+ aa++a +vvl
  gi|313127480|ref|YP_004037750.1|   2 RIALLgGTGDIGEGLALRWAYHT--DHDIVIG-SRDPEKARAKADEYEtelssrgrdVKVTGFENKMAADRARIVVL 75 
                                       79******************997..8****88.******************************************** PP

                                       -S-HHHHHHHHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  68 avkpedveevlselakdalkgklvisvlag 97 
                                       av+p++v+++++++ ++++++ ++++ +ag
  gi|313127480|ref|YP_004037750.1|  76 AVPPYHVADTIEAVEDSLSEDDVLVTPAAG 105
                                       **************************9987 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.4e-08   0.00014       1      88 [.       3      88 ..       3      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.4e-08
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS.SEEEE-S CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg.dlvvnls 77
                                      + ++G+ G +G+++a   a h d+  +i++ +r+ ek++a a++  +++++++  d++       ++ +++  +vv ++
  gi|313127480|ref|YP_004037750.1|  3 IALLGGtGDIGEGLALRWAYHTDH--DIVIGSRDPEKARAKADE-YETELSSRGRDVKVTGF-ENKMAADRaRIVVLAV 77
                                      5689999*****************..9**********9999877.67777777777666665.4455555559999999 PP

                                      SGGGHHHHHHH CS
                   Sacchrp_dh_NADP 78 ppissldvlka 88
                                      pp+  +d ++a
  gi|313127480|ref|YP_004037750.1| 78 PPYHVADTIEA 88
                                      99998888887 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   9.8e-07    0.0022      27      83 ..      53     108 ..      25     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.8e-07
                                       HHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT.-EEEE--S--C CS
                               PDH  27 alelglvdeatddieavkeadivvlavPvevilevlkelaphlked.alitDvgsvKe 83 
                                       ++++ +     ++  a+  a ivvlavP+  ++++++++   l+ed +l+t  ++vK 
  gi|313127480|ref|YP_004037750.1|  53 GRDVKVTG--FENKMAADRARIVVLAVPPYHVADTIEAVEDSLSEDdVLVTPAAGVKR 108
                                       44444432..222358999**********************99985278899999996 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.5e-05     0.033       5      58 ..       5      59 ..       3      77 .. 0.84
   2 ?    0.8   0.1      0.18   4.1e+02      47      94 ..     151     200 ..     121     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                      EETTTSHHHHHHHHHHHHHHS-EEEEE-SS...--HHHHHHHHHHHHTT-EEEE- CS
                                KR  5 itGGlGgLGlelarwlaekgarhlvllsRsa.aadedskaliaelealgaevevv 58
                                      + GG+G +G  la   a +  + +v+ sR++ +a++++++  +el+++g +v+v 
  gi|313127480|ref|YP_004037750.1|  5 LLGGTGDIGEGLALRWAYHTDHDIVIGSRDPeKARAKADEYETELSSRGRDVKVT 59
                                      57****************************73455556678889***99999986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.18
                                       HHHHT.T-EEEE----TT-HHHHHHHHHHHHHHS.S---EEEE------- CS
                                KR  47 eleal.gaevevvaaDvsdkdavealleeikaee.ppikGvihaAgvlrd 94 
                                       +l a  +++  vva D   kd v++l eei+        G+ +aA v   
  gi|313127480|ref|YP_004037750.1| 151 NLDAElDIDTLVVADDFDAKDTVSRLAEEIDGLRaLDAGGIANAAEVESV 200
                                       44443355666777788888888888888887665666788888877655 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.1e-05     0.048      62     109 ..      62     109 ..       2     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                                       -HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET. CS
                    NAD_Gly3P_dh_N  62 dlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGieeg 109
                                       + + a+++a+i+vl+vP  +++++++ +++ l+++ +lv  + G++++
  gi|313127480|ref|YP_004037750.1|  62 ENKMAADRARIVVLAVPPYHVADTIEAVEDSLSEDDVLVTPAAGVKRD 109
                                       4467999*********************************99999764 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-05     0.033       1      84 [.       2      87 ..       2     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG.GGTTTECEBEEE.GGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk.aleegkdlkved.vdeeelkevdivflalpag 77
                                      ++a++G+tG +G+ l+ + + h + ++v  +   ++a  k +e+     + g+d+kv+   ++ + +++ iv+la+p  
  gi|313127480|ref|YP_004037750.1|  2 RIALLGGTGDIGEGLALRWAYHTDHDIVIGSRDPEKARAKADEYETeLSSRGRDVKVTGfENKMAADRARIVVLAVPPY 80
                                      69************************9996666665555555554477788999999996666777*********9954 PP

                                      HHHHHHH CS
                    Semialdhyde_dh 78 vskelap 84
                                        ++  +
  gi|313127480|ref|YP_004037750.1| 81 HVADTIE 87
                                      4333333 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.3e-05     0.051       2      80 ..       2      87 ..       1      98 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                                      EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS........HHHHHTCTTESEEEE-S- CS
                      GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd........leelladpeidavivatp 71
                                      r+a+ G+ G ig+  +  +  ++++  v++  dp+++ra+  a++++ e  s         +e+ +a +++++v+ a+p
  gi|313127480|ref|YP_004037750.1|  2 RIALLGGtGDIGEGLALRWAYHTDHDIVIGSRDPEKARAK--ADEYETELSSRgrdvkvtgFENKMAADRARIVVLAVP 78
                                      66666665**************777777766666666666..7888888555556667677998888899********* PP

                                      GGGHHHHHH CS
                      GFO_IDH_MocA 72 ngtheelak 80
                                      +++ ++ ++
  gi|313127480|ref|YP_004037750.1| 79 PYHVADTIE 87
                                      *76655554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.3e-05     0.052       5     107 ..       8     108 ..       3     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                                       S-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHH.HHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                              ApbA   5 GaGaiGsllaakLak.agadvtlilrsr.rlea.lkknGlrltseggeeilrppealsaeekselepidlvivtvKa 78 
                                       G+G iG  la + a  + +d+++  r++ ++ a   +   +l+s+g  + ++++   ++     +  + +v+++v+ 
  gi|313127480|ref|YP_004037750.1|   8 GTGDIGEGLALRWAYhTDHDIVIGSRDPeKARAkADEYETELSSRG--RDVKVTGFENKM---AADRARIVVLAVPP 79 
                                       89***********999999999999999555554455555555555..444444444444...7789********** PP

                                       GGHHHHHHHHGGGECTCEEEEEESSSSCH CS
                              ApbA  79 yqteealeeikplldpntvvlllqNGlgh 107
                                       y++++ +e++++ l ++ v ++   G++ 
  gi|313127480|ref|YP_004037750.1|  80 YHVADTIEAVEDSLSEDDVLVTPAAGVKR 108
                                       ****************9988876666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1641.57
//
Query:       gi|313127481|ref|YP_004037751.1|  [L=63]
Description: hypothetical protein Hbor_27620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 490.08
//
Query:       gi|313127482|ref|YP_004037752.1|  [L=124]
Description: hypothetical protein Hbor_27630 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        1.7    8.4   3.7        2.7    7.8   0.7    2.2  2  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l


Domain annotation for each model (and alignments):
>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.7   0.00015       2.7      19      50 ..      15      47 ..      11      49 .. 0.87
   2 ?    1.0   0.1      0.02   3.6e+02      18      32 ..      94     109 ..      79     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00015
                   Phage_holin_2_4 19 gGavvsf.aGflasselialvGlavAliGlLvn 50
                                      +G +v++ +Gfl++ +  +lv la+A + +Lv+
  gi|313127482|ref|YP_004037752.1| 15 VGLIVAVpLGFLLAPDPTGLVPLALAAVAFLVS 47
                                      677788768**********************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.02
                   Phage_holin_2_4  18 ggGavvsf.aGflass 32 
                                         G  vsf aG++a+s
  gi|313127482|ref|YP_004037752.1|  94 FAGNLVSFgAGWIAAS 109
                                       5788899978999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 950.31
//
Query:       gi|313127483|ref|YP_004037753.1|  [L=290]
Description: haloacid dehalogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-09   38.5   0.3    6.3e-09   36.4   0.3    1.9  1  Hydrolase       haloacid dehalogenase-like hydrolase
    1.9e-08   34.6   0.0    8.8e-07   29.2   0.0    2.1  2  HAD_2           Haloacid dehalogenase-like hydrolase
    6.2e-05   23.0   0.7    0.00025   21.1   0.7    2.0  1  Hydrolase_like  HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.3     1e-12   6.3e-09       2     209 ..       4     239 ..       3     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1e-12
                                       SEEEEESBTTTBCHHHHHHHHHHHH.......CHHHHHHHHHH........HHCHHHHHHHHHHHHH.HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx........xxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa.......alalaaaletg........sehpigkalvaaakar.sgaltgfat 62 
                                       ++vv+D+dG+L++   s +++iv+        +++ + + ++          e  +++al   a++r ++++++f+ 
  gi|313127483|ref|YP_004037753.1|   4 DAVVLDVDGVLVDVADSYRRAIVESiarlydrTIDKSDVQQFKdaggfnndWELTYAAALYLLADDRePISIAEFTD 80 
                                       79*************99999999997777777444444444445567777788888888866666666888888887 PP

                                       .ETTTE....HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH...............TTHHHHHHHHHHTHHB CS
                                       .xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxx RF
                         Hydrolase  63 .figrg....ayaigkpewltaldippdlgaaigsaqsqgrtvall...............qaralavftiadplkv 119
                                        + +rg    a+    +  l+a     d++a  +++  +g  +a++               +    a   i+d+  +
  gi|313127483|ref|YP_004037753.1|  81 rIHERGggldAAEAVTEAHLDAD----DYDAVREAWDPEGLRAAFQalylgadlyrelegsEPPFEASGYIHDEPII 153
                                       44444466654444444444444....88888888888888888889999888888887764444444444555334 PP

                                       HTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 120 kpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyf.daviasdietvakpspegkvaaireLqgkpeeva 194
                                        ++  e++ +L ++  +v++ltg   + a+ a+ ++  +    ++ ++ d+ + +kp+p+++  ++++L+++   v+
  gi|313127483|ref|YP_004037753.1| 154 VEG--ETLDYLTSN-HRVGVLTGRPAAEADIALTRVRlA-VPeNHRFTMDDWEEGKPNPRALTTLADRLGAES--VV 224
                                       444..899999966.67*************888888832.3335555666666*****************999..** PP

                                       EEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxx RF
                         Hydrolase 195 mVGDgvnDaaalaaA 209
                                       +VGD++ D+  + +A
  gi|313127483|ref|YP_004037753.1| 225 FVGDTLDDVRTAVNA 239
                                       ********9988766 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.013        77       1      40 [.       6      45 ..       6      85 .. 0.75
   2 !   29.2   0.0   1.5e-10   8.8e-07      86     171 ..     157     239 ..     149     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.013
                             HAD_2  1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkl 40
                                      ++ D+Dg+l+d  + +  a+ e +++    ++++++++++
  gi|313127483|ref|YP_004037753.1|  6 VVLDVDGVLVDVADSYRRAIVESIARLYDRTIDKSDVQQF 45
                                      578********98877666655555553335555555544 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 1.5e-10
                             HAD_2  86 elLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsp 162
                                       e+L++L   ++++g+ T + +++++  l+++ +    ++  t++d e+ KP+p+ + ++ ++l++  e+v++vGD+ 
  gi|313127483|ref|YP_004037753.1| 157 ETLDYL-TSNHRVGVLTGRPAAEADIALTRVRLAVPENHRFTMDDWEEGKPNPRALTTLADRLGA--ESVVFVGDTL 230
                                       8999**.89****************************************************9986..78******** PP

                             HAD_2 163 tDieaakka 171
                                        D+ +a +a
  gi|313127483|ref|YP_004037753.1| 231 DDVRTAVNA 239
                                       ******987 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.7   4.1e-08   0.00025       3      74 ..     204     281 ..     203     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.1e-08
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT.......-EEEEESSSS.S-TTTHHHHH.HHHT---S CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaG.......wksvLVltGv.trpedleepe.hkptyvad 70 
                                       gKP+p ++   + +lg+  e v+++GD+  +D++ A na        +++v VltG  t++e +e+ e  ++++v+ 
  gi|313127483|ref|YP_004037753.1| 204 GKPNPRALTTLADRLGA--ESVVFVGDT-LDDVRTAVNAAeedpehtYHGVGVLTGGlTGDEGREKYEsVGAAAVVG 277
                                       9**************99..78*******.*******99876666666889999996624444444444367777887 PP

                                       EEES CS
                    Hydrolase_like  71 dlae 74 
                                       ++ +
  gi|313127483|ref|YP_004037753.1| 278 SVND 281
                                       7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2131.74
//
Query:       gi|313127484|ref|YP_004037754.1|  [L=139]
Description: hypothetical protein Hbor_27650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-19   70.1   0.0    2.2e-19   69.6   0.0    1.2  1  UPF0146   Uncharacterised protein family (UPF0146)


Domain annotation for each model (and alignments):
>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   1.2e-23   2.2e-19       8     125 ..      10     131 ..       4     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.2e-23
                                       HHHHS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS--HH.....HHTTEEEEEEES- CS
                           UPF0146   8 iaeenargkvvEvGiGrkldvaealakrgvdlvatDikekkakegvrivrDDvtdPnle.....iYkgadliYslRp 79 
                                       +a++++ + v E+G+Gr++ va ala  g+d+++tD++    + ++++v DDv+    +      Y  ad+iY+l  
  gi|313127484|ref|YP_004037754.1|  10 VARLSQYETVTEIGVGRRPSVAVALADAGCDVTVTDVHSFDLPSELHFVADDVVVASDRddpgpAY-HADAIYALNL 85 
                                       7899999*********************************************97433221222245.58******** PP

                                       -TTSHHHHHHHHHHHT-EEEEE-BTTB-----TT-EEEEETTEEEE CS
                           UPF0146  80 PaelqsaildvakkvgAaliikpLlgedvvvekelklvnykgalFy 125
                                       P+el++   dva +v+A+ + ++L+ + + v+ e+     + ++ y
  gi|313127484|ref|YP_004037754.1|  86 PPELHRPARDVAAAVDAEFLFTTLGFDSPTVPCETETIADGAETLY 131
                                       *****************************99999887777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 930.56
//
Query:       gi|313127485|ref|YP_004037755.1|  [L=173]
Description: zn-dependent protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-23   81.4   0.0    1.1e-22   81.0   0.0    1.2  1  Peptidase_M54  Peptidase family M54
    8.1e-06   25.6   0.0    9.9e-06   25.3   0.0    1.1  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
    4.6e-05   23.3   0.0    4.6e-05   23.3   0.0    1.2  1  Peptidase_M10  Matrixin
    0.00012   21.4   0.0    0.00017   20.9   0.0    1.2  1  DUF4953        Met-zincin
    0.00035   20.5   0.0    0.00039   20.4   0.0    1.1  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like
    0.00037   21.0   0.0    0.00044   20.8   0.0    1.2  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
    0.00041   20.5   0.1    0.00045   20.4   0.1    1.2  1  Reprolysin_5   Metallo-peptidase family M12
  ------ inclusion threshold ------
      0.022   13.4   0.3      0.029   13.0   0.3    1.2  1  Metallopep     Putative peptidase family
      0.023   14.3   1.0      0.058   13.0   0.4    1.8  2  Peptidase_M57  Dual-action HEIGH metallo-peptidase
       0.03   14.4   0.0      0.053   13.6   0.0    1.4  1  Zincin_1       Zincin-like metallopeptidase
      0.032   13.2   0.0      0.038   12.9   0.0    1.2  1  Peptidase_M66  Peptidase M66
      0.044   13.7   0.1      0.083   12.8   0.1    1.4  1  Peptidase_M43  Pregnancy-associated plasma protein-A
      0.059   13.3   0.0      0.079   12.9   0.0    1.2  1  Reprolysin     Reprolysin (M12B) family zinc metalloprotease


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   7.7e-26   1.1e-22      95     192 ..      67     172 ..      38     173 .] 0.87

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 7.7e-26
                                       ...EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T.....--.......SHHHHHHHHHHHHHHHHHHHTT----S- CS
                     Peptidase_M54  95 ittlplgsrdqyidiykkvlGievsiGnyavlals.....ike.fyte.dkeLflervvkevlhelGhlyGLshCke 164
                                          ++++ +d y    ++v+G++   Gn +v++        +    t+ + e+f +rv kev+he+Gh++GL hC++
  gi|313127485|ref|YP_004037755.1|  67 EKNIGITAQDLYYRRRNYVFGLAYLNGNGSVISTYrlqtsSDGgISTKpQSEVFSDRVRKEVVHEIGHTLGLEHCDN 143
                                       56799***************************9765333322213344699************************** PP

                                       .TSTTS--SSHHHHHHS-SS--HHHHHHH CS
                     Peptidase_M54 165 .dCvmnfsndlkdvDrkapkyCksClekl 192
                                        +Cvm+fs  +++vD k+ + C +C + +
  gi|313127485|ref|YP_004037755.1| 144 sKCVMSFSPTVREVDVKEEHLCGTCSRLV 172
                                       9************************9865 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   7.2e-09   9.9e-06      69     158 ..      45     147 ..      21     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 7.2e-09
                      Reprolysin_4  69 disgedlgnsslatltstrdskdyDlaallrdtrasqqn..vgvawvgalcls..arq..nkkasgvaas..rdey. 136
                                       d s ++   ++ + l s  +s ++ ++   +d    + n   g+a++++ ++   ++   +   +g++     + + 
  gi|313127485|ref|YP_004037755.1|  45 DRSRNQYRAEQFIELASRVGSGEKNIGITAQDLYYRRRNyvFGLAYLNGNGSVisTYRlqTSSDGGISTKpqSEVFs 121
                                       667777788889999999999999999988887644444469******99976765543144445555555322334 PP

                      Reprolysin_4 137 .di...fAHEiGHtfGaaHdlsdege 158
                                         +   + HEiGHt+G++H  ++++ 
  gi|313127485|ref|YP_004037755.1| 122 dRVrkeVVHEIGHTLGLEHCDNSKCV 147
                                       4334579************8888775 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   3.3e-08   4.6e-05     113     135 ..     128     150 ..      37     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.3e-08
                                       HHHHHHHHTTBESXSSTTSTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 113 aaHEiGHalGLeHssdkdalmyp 135
                                       ++HEiGH+lGLeH ++++ +m  
  gi|313127485|ref|YP_004037755.1| 128 VVHEIGHTLGLEHCDNSKCVMSF 150
                                       69****************99964 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.2e-07   0.00017       2      29 ..     113     140 ..     112     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.2e-07
                           DUF4953   2 eefpdelmgallrfvvaHEvGhtLGLrh 29 
                                       +++++e++ +++r  v HE+GhtLGL+h
  gi|313127485|ref|YP_004037755.1| 113 TKPQSEVFSDRVRKEVVHEIGHTLGLEH 140
                                       5678999********************9 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.8e-07   0.00039      79     146 ..      77     145 ..      18     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.8e-07
                      Reprolysin_2  79 llgtfsggvlGLayvg...qicqkeassrktntglsttansgsaveetkeidvvaHEvGHaFGatHdndgs 146
                                       l     + v GLay+    ++ ++   ++++  g+st  +s+ +   ++  + v HE+GH+ G  H ++++
  gi|313127485|ref|YP_004037755.1|  77 LYYRRRNYVFGLAYLNgngSVISTYRLQTSSDGGISTKPQSEVFS--DRVRKEVVHEIGHTLGLEHCDNSK 145
                                       4455566789*****7676676565555568889**666666666..55556678***********98865 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.2e-07   0.00044      75     123 ..      77     140 ..      31     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.2e-07
                      Reprolysin_3  75 e.....sgvgGlAyv....gsvcnsskkagvnsgssvlgkvga......dtvaHEiGHnfganH 123
                                               v GlAy+    + +++ + ++++  g s+  ++++      + v HEiGH +g++H
  gi|313127485|ref|YP_004037755.1|  77 LyyrrrNYVFGLAYLngngSVISTYRLQTSSDGGISTKPQSEVfsdrvrKEVVHEIGHTLGLEH 140
                                       3344457889999998875333333333333333333333333556677*************** PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   3.2e-07   0.00045     108     169 ..      86     146 ..      26     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.2e-07
                      Reprolysin_5 108 vGlAwl.........gqlcnsgsagsvstrveksnsvvvstatevqvvaHElGHnfGavHDcdsssesqsC 169
                                        GlA+l         + l++s+++g+ + +    +s v  ++   + v HE+GH++G +H  +s+     C
  gi|313127485|ref|YP_004037755.1|  86 FGLAYLngngsvistYRLQTSSDGGISTKP----QSEVF-SDRVRKEVVHEIGHTLGLEHCDNSK-----C 146
                                       567776544444444556666666666655....55666.667777788***********66654.....3 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   2.1e-05     0.029     318     339 ..     128     149 ..     127     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                        Metallopep 318 flHEiGHllglpHqedGvmlrd 339
                                       ++HEiGH+lgl H+ ++    +
  gi|313127485|ref|YP_004037755.1| 128 VVHEIGHTLGLEHCDNSKCVMS 149
                                       68************99544444 PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.56   7.7e+02       8      39 ..      30      62 ..      26      95 .. 0.72
   2 ?   13.0   0.4   4.2e-05     0.058     137     158 ..     128     149 ..     110     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.56
                     Peptidase_M57  8 vvtleasreml.qteeetkeqyrttnlvsssvk 39
                                       vt+++ + +   + +++++qyr ++ +  +++
  gi|313127485|ref|YP_004037755.1| 30 DVTVHNEQSIPeGAFDRSRNQYRAEQFIELASR 62
                                      555555555553456788999999988876655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.2e-05
                     Peptidase_M57 137 ithelGhtvGlRhsDyynrsis 158
                                       + he+Ght+Gl h D  +  +s
  gi|313127485|ref|YP_004037755.1| 128 VVHEIGHTLGLEHCDNSKCVMS 149
                                       78************97665555 PP

>> Zincin_1  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.8e-05     0.053      66      87 ..     118     139 ..      94     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                                       --HHHHHHHHHHHHHHHHHTT- CS
                          Zincin_1  66 eeleeevretllHEighhfGld 87 
                                       e + + vr+ ++HEigh +Gl+
  gi|313127485|ref|YP_004037755.1| 118 EVFSDRVRKEVVHEIGHTLGLE 139
                                       458999**************97 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.7e-05     0.038     189     209 ..     121     141 ..      69     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                     Peptidase_M66 189 datltgefiHEqGHalGLpHy 209
                                         ++ +e +HE GH lGL H 
  gi|313127485|ref|YP_004037755.1| 121 SDRVRKEVVHEIGHTLGLEHC 141
                                       46788999************4 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     6e-05     0.083      65      92 ..     121     148 ..     113     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                     Peptidase_M43  65 stnksstLthelGhfLgLihtfeggCer 92 
                                       s+  +  + he+Gh LgL+h  +  C  
  gi|313127485|ref|YP_004037755.1| 121 SDRVRKEVVHEIGHTLGLEHCDNSKCVM 148
                                       566778899**************99965 PP

>> Reprolysin  Reprolysin (M12B) family zinc metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.7e-05     0.079     114     155 ..     105     148 ..      81     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                                       TSTSEEEEE--SSSH..HHHHHHHHHHHHHHCT---GHHTTS-- CS
                        Reprolysin 114 keksggvaedkkknl..ealavilaqeLghnlGlthdeekeCkc 155
                                       ++++gg+++++++++  + +   +++e+gh lGl+h ++++C  
  gi|313127485|ref|YP_004037755.1| 105 TSSDGGISTKPQSEVfsDRVRKEVVHEIGHTLGLEHCDNSKCVM 148
                                       567889999887554115678889************99988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1204.98
//
Query:       gi|313127486|ref|YP_004037756.1|  [L=138]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-29  101.4   1.6    6.4e-29  101.3   1.6    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   1.6   3.6e-33   6.4e-29       6     140 ..       4     137 ..       1     138 [] 0.97

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 3.6e-33
                                       EEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEE CS
                               Usp   6 lVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkv 82 
                                       +VavDgse  +kAl++Al l  + +a l++++ ++pr  ++ ++ + ++  +++ +++++l ++a +++a+++gv v
  gi|313127486|ref|YP_004037756.1|   4 VVAVDGSEPGEKALDHALLLTTRLDASLTVVYSVEPRVVAEDGNDMYQEDPDAAGDRGDKLLEAA-AERAAEQGVPV 79 
                                       8**********************************************************999876.*********** PP

                                       EEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  83 evvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                        + +++gdpae+i  ++ e+d+d i+vG+rg+s   + ++GSv+++++++a++pV++V
  gi|313127486|ref|YP_004037756.1|  80 STALLWGDPAETIPSYVAENDVDGIIVGHRGLSQRVEGMVGSVAKSLVQNATVPVTIV 137
                                       *************************************9*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1034.36
//
Query:       gi|313127487|ref|YP_004037757.1|  [L=353]
Description: RNA 3''-phosphate cyclase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-67  225.1   0.0      8e-67  224.7   0.0    1.0  1  RTC            RNA 3'-terminal phosphate cyclase
    1.4e-11   44.8   0.9    4.3e-11   43.3   0.9    1.8  1  RTC_insert     RNA 3'-terminal phosphate cyclase (RTC), inser
  ------ inclusion threshold ------
       0.25   11.2   1.4        5.1    6.9   0.1    2.3  2  Fucose_iso_N1  L-fucose isomerase, first N-terminal domain


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.7   0.0   1.3e-70     8e-67       4     215 ..       9     331 ..       7     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 224.7 bits;  conditional E-value: 1.3e-70
                                       TSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   4 gGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikageyev 80 
                                       gGgq++Rtal+Lsa+tg+++ Ien+R +R++PGL++qh++a++ + + t+a+v+g e gs+++ F P+ +++g + v
  gi|313127487|ref|YP_004037757.1|   9 GGGQLVRTALSLSAVTGQAICIENVRGGRPNPGLKPQHVAAIETVGRATEATVSGVERGSERFSFAPEAVRGGAFAV 85 
                                       9**************************************************************************** PP

                                       EEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  81 digtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGgGe 157
                                       ++gtAGs++l+  ++ pl++  ++p+++tl+GgT+v+++p+vdyl++v lpll+ +g l++el +++rGfyp GgG+
  gi|313127487|ref|YP_004037757.1|  86 EVGTAGSVALVCDAVAPLAVALDRPLTVTLHGGTDVQWSPPVDYLREVKLPLLRAVG-LDAELAVHQRGFYPVGGGS 161
                                       *********************************************************.7****************** PP

                                       EEEEEE-.-S---EB.............................................................. CS
                                       xxxxxxxxxxxxxxx.............................................................. RF
                               RTC 158 velevepskklkpie.............................................................. 172
                                       ++l+++ps +l++++                                                              
  gi|313127487|ref|YP_004037757.1| 162 LTLTIRPS-SLTALRlrrrgpverlsvyalasdslesasvaerlaetvreriedgsegevvtetaeiettaeietta 237
                                       ******96.799999999*********************************************************** PP

                                       .....................................................BSS-HHHHHHHHHHHHHHT.-EEE CS
                                       .....................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 .....................................................acvDehlqdqlilfmaLakgksri 196
                                                                                            a+vDehl dql++++aLa g  ++
  gi|313127487|ref|YP_004037757.1| 238 tyaetdcpgavvtlvadcgtsragfdalgrrgvpaedvaeevvdafrawratgAPVDEHLGDQLLVWLALAGG--EV 312
                                       ***********************************************************************98..79 PP

                                       EESS--HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                               RTC 197 rvaeltlhtetairvieqf 215
                                       r  + t h+et++++i+ f
  gi|313127487|ref|YP_004037757.1| 313 RLPHSTAHVETNAELIRAF 331
                                       99**************988 PP

>> RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.9   7.1e-15   4.3e-11       2      98 ..     178     283 ..     177     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 7.1e-15
                                       S----SEEEEEEEEES..S-THHHHHHHHHHHHHHTTTSS........EEEEEEE..EE-CGGC-SS-EEEEEEEEE CS
                        RTC_insert   2 drGrvkrirGvafaar..vspsvanrmveaargvLnkllp........dvyiytdv.vkegkesgkspGfgisLvae 67 
                                        rG v+r +++a+a+    s+sva+r++e++r+++++           +++ +++  +  + ++   pG+ ++Lva 
  gi|313127487|ref|YP_004037757.1| 178 RRGPVERLSVYALASDslESASVAERLAETVRERIEDGSEgevvtetaEIETTAEIeTTATYAETDCPGAVVTLVAD 254
                                       69**************9889***************99877999999886666666534444456677********** PP

                                       -T.TS-EEEEEEEE-TT--HHHHHHHHHHHH CS
                        RTC_insert  68 tttegvllgaealgekgvppedvGeeaaeeL 98 
                                             + g++alg++gvp+edv+ee+++++
  gi|313127487|ref|YP_004037757.1| 255 CG--TSRAGFDALGRRGVPAEDVAEEVVDAF 283
                                       *5..59********************99876 PP

>> Fucose_iso_N1  L-fucose isomerase, first N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3     0.011        66      26      67 ..     198     237 ..     190     239 .. 0.81
   2 ?    6.9   0.1   0.00085       5.1     106     153 ..     240     278 ..     233     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.011
                     Fucose_iso_N1  26 mamakavaelleeklkyadgtevevviadttiggvaeaaaca 67 
                                         +a+++ae+++e+    dg+e evv+    i+  ae++ +a
  gi|313127487|ref|YP_004037757.1| 198 ASVAERLAETVRER--IEDGSEGEVVTETAEIETTAEIETTA 237
                                       45677788888887..68***********9999999988765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00085
                     Fucose_iso_N1 106 ngterPGaVylaAalaalaqkGlpafriyGkdvqdaddeeipedvkek 153
                                         t+ PGaV ++ a+ + +++G+ a +  G  v  +       dv+e 
  gi|313127487|ref|YP_004037757.1| 240 AETDCPGAVVTLVADCGTSRAGFDALGRRG--VPAE-------DVAEE 278
                                       5699*********************99999..4433.......33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2841.43
//
Query:       gi|313127488|ref|YP_004037758.1|  [L=611]
Description: ATPase, rnase l inhibitor (rli) like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-41  140.5   0.0      7e-20   71.9   0.0    2.8  2  ABC_tran      ABC transporter
    4.7e-15   55.6   1.5    0.00032   20.2   0.0    4.2  4  SMC_N         RecF/RecN/SMC N terminal domain
    2.7e-12   46.3   0.7    5.6e-12   45.3   0.7    1.5  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    6.9e-11   42.5   6.8      0.069   12.9   0.2    4.3  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.2e-08   32.6   0.3      0.012   16.0   0.0    3.3  3  AAA_16        AAA ATPase domain
    8.3e-07   29.7   1.4      0.057   13.9   0.9    2.5  2  AAA_23        AAA domain
    4.4e-06   27.2   0.0      0.035   14.5   0.0    2.7  2  AAA           ATPase family associated with various cellular 
    1.5e-05   25.3   0.0      0.015   15.5   0.0    2.8  2  AAA_22        AAA domain
    6.1e-05   22.3   0.0       0.21   10.8   0.0    2.3  2  NB-ARC        NB-ARC domain
    8.3e-05   22.4   0.5        0.1   12.3   0.1    2.5  2  AAA_24        AAA domain
    0.00011   21.9   0.2       0.43   10.4   0.0    2.4  2  AAA_29        P-loop containing region of AAA domain
    0.00015   21.8   0.1        1.5    8.9   0.0    3.5  4  AAA_14        AAA domain
    0.00026   21.4   0.0        1.4    9.3   0.0    2.6  2  RNA_helicase  RNA helicase
    0.00055   19.9   0.0       0.65    9.9   0.0    2.5  2  NACHT         NACHT domain
    0.00075   19.5   0.0       0.18   11.7   0.0    2.3  2  ATPase_2      ATPase domain predominantly from Archaea
    0.00084   19.1   0.1        1.5    8.4   0.0    3.0  3  AAA_15        AAA ATPase domain
    0.00087   19.0   2.4    0.00087   19.0   2.4    2.9  3  Fer4          4Fe-4S binding domain
    0.00088   19.2   0.0       0.73    9.7   0.0    2.4  2  RsgA_GTPase   RsgA GTPase
     0.0014   18.8   0.2        2.4    8.3   0.3    3.1  3  AAA_33        AAA domain
     0.0017   18.3   0.0       0.69    9.8   0.0    2.5  2  Rad17         Rad17 P-loop domain
     0.0022   18.3   1.6       0.36   11.0   0.0    3.2  3  AAA_28        AAA domain
     0.0043   16.9   0.4        4.6    7.0   0.2    2.7  3  MukB          MukB N-terminal
     0.0046   17.0  12.7      0.086   12.9   2.4    2.4  2  Fer4_6        4Fe-4S binding domain
  ------ inclusion threshold ------
      0.018   15.6   0.1        3.4    8.2   0.0    2.8  2  AAA_18        AAA domain
      0.023   14.4   0.1         12    5.6   0.0    2.9  3  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.025   14.5   1.1         13    5.6   0.0    3.5  4  NTPase_1      NTPase
       0.03   14.9   8.7      0.068   13.8   8.7    1.7  1  Fer4_7        4Fe-4S dicluster domain
      0.038   13.6   0.1        2.4    7.7   0.0    2.4  2  SRP54         SRP54-type protein, GTPase domain
      0.044   13.8   0.0        8.2    6.4   0.0    2.7  2  AAA_5         AAA domain (dynein-related subfamily)
      0.045   13.8   0.0         26    4.9   0.0    3.1  3  MMR_HSR1      50S ribosome-binding GTPase
      0.075   12.8   1.0        3.5    7.3   0.1    2.4  2  IstB_IS21     IstB-like ATP binding protein
       0.14   11.7   6.3         20    4.7   0.0    3.7  4  AAA_25        AAA domain
       0.14   11.7   0.0          6    6.4   0.0    2.4  2  AAA_27        AAA domain
       0.31   11.2  10.9       0.62   10.2   1.4    2.1  2  Fer4_10       4Fe-4S dicluster domain
       0.32   11.2   9.0       0.63   10.3   9.0    1.5  1  Fer4_9        4Fe-4S dicluster domain
       0.34   10.6   2.5        8.3    6.1   0.1    2.9  3  AAA_30        AAA domain
       0.84    9.9  11.7       0.24   11.6   1.2    2.4  2  Fer4_2        4Fe-4S binding domain
        1.4    9.1   6.8        2.8    8.1   6.8    1.5  1  Fer4_21       4Fe-4S dicluster domain
        1.9    9.5   8.9        1.1   10.3   1.5    2.1  2  Fer4_16       4Fe-4S double cluster binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   1.7e-20   7.7e-18       9     136 ..     112     255 ..     111     256 .. 0.88
   2 !   71.9   0.0   1.5e-22     7e-20       7     137 .]     380     501 ..     374     501 .. 0.84

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.7e-20
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGG......B-HHHCCHCEEEE-SS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx......xxxxxxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlke......qeleslrkeigvlpqep 68 
                                       ++g +++i+G+nG GK+t +++lag++ p+ G+            +++g++l++      +e+ s  ++ +++ q p
  gi|313127488|ref|YP_004037758.1| 112 EPGAVTGILGPNGIGKTTAVRALAGEMVPNLGTYdeeatweavldRYRGTELQNyiervrEEEVSIARKPQYVDQIP 188
                                       5899****************************999999999999999999999988888777777888888888889 PP

                                       -S-TTSBHHHH....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       + f+++t +      +++ ++++++++lg+  + d+++     +LSgG+ qrvala++l++++++++lDE t
  gi|313127488|ref|YP_004037758.1| 189 KQFDGITSE-LleatDERGKLDEYVERLGIAPVVDQPL----DTLSGGELQRVALAATLARDRDFYFLDEIT 255
                                       999999633.2454555556************999999....****************************87 PP

  == domain 2  score: 71.9 bits;  conditional E-value: 1.5e-22
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.... 79 
                                       +++++e+++ivG+nG GKStL+k++ag l+p+eGe+              +r  i++ pq  ++++ ++v       
  gi|313127488|ref|YP_004037758.1| 380 TIYQSEVLGIVGPNGIGKSTLAKMFAGGLEPDEGEL-------------DFRLDIAYKPQYIEIDQPMRVDAFlssi 443
                                       7999********************************.............6888999999998888888777777766 PP

                                       HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++d   + + +++ ++   +++++++   LSgG++qrva+a++l ++++l+++DEp+a
  gi|313127488|ref|YP_004037758.1| 444 TDDFGTSYWKTEVANPLQLNRIMERNLDDLSGGERQRVAIAATLSEDADLYVMDEPSA 501
                                       444446666666666666666776666*****************************75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.016       7.5      25      44 ..     115     134 ..     108     138 .. 0.87
   2 !   18.0   0.0   3.3e-06    0.0015     135     196 ..     220     283 ..     146     296 .. 0.74
   3 !    7.3   0.1    0.0062       2.9      23      41 ..     383     401 ..     365     405 .. 0.81
   4 !   20.2   0.0     7e-07   0.00032     121     203 ..     454     537 ..     444     551 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                                       SEEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAi 44 
                                        +t i+GpNG GK+  + A+
  gi|313127488|ref|YP_004037758.1| 115 AVTGILGPNGIGKTTAVRAL 134
                                       5799**********999887 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.3e-06
                                       T......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                       x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivis 196
                                              +LSgGe + vala  +A    + + +y+lDei   LD  ++   a+l++e  ++    v +
  gi|313127488|ref|YP_004037758.1| 220 VvdqpldTLSGGELQRVALAATLA----RDRDFYFLDEITPYLDIGQRVTAARLIRELAEDEDKAVLA 283
                                       15555558******9999998876....6678************************998876655555 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0062
                                       TSSEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnll 41 
                                       ++++  ivGpNG GKs l 
  gi|313127488|ref|YP_004037758.1| 383 QSEVLGIVGPNGIGKSTLA 401
                                       566788**********875 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 7e-07
                                       HHHHHHHHCTT-ST...TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEE CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                             SMC_N 121 kevsellesagisk...elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQf 192
                                       +ev++ l+  +i +   + LSgGe++ va+a  +     + a ly++De  a+LD +++ +  + +++  +n  a +
  gi|313127488|ref|YP_004037758.1| 454 TEVANPLQLNRIMErnlDDLSGGERQRVAIAATL----SEDADLYVMDEPSAHLDVEQRVQATTAIRRYAENhdATV 526
                                       66666666666654111569******99998765....57899***********************98777634777 PP

                                       EEE-SSHHHCC CS
                                       xxxxxxxxxxx RF
                             SMC_N 193 ivislreemle 203
                                       +vi ++  m+ 
  gi|313127488|ref|YP_004037758.1| 527 MVIDHDIYMID 537
                                       77777776665 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.7   1.2e-14   5.6e-12       3      35 .]       6      35 ..       5      35 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.2e-14
                                      EEEES---------TTHHHHHTTSEEEESS--S CS
                               RLI  3 lAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                      +A+vd d+C+P++C++ +ca +cp   +rtgk+
  gi|313127488|ref|YP_004037758.1|  6 IAVVDLDRCQPDRCSY-ECANYCPP--NRTGKE 35
                                      8***************.********..****96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   0.00015     0.069       1      20 [.     116     135 ..     116     162 .. 0.90
   2 !    7.3   0.0    0.0081       3.7     233     287 ..     224     275 ..     220     292 .. 0.73
   3 !   11.7   0.4   0.00035      0.16       3      35 ..     388     414 ..     386     451 .. 0.73
   4 !   12.2   0.0   0.00024      0.11     180     294 ..     411     528 ..     407     537 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                            AAA_21   1 lnvliGpNgsGKSnLLdald 20 
                                       ++++ GpNg GK++  +al 
  gi|313127488|ref|YP_004037758.1| 116 VTGILGPNGIGKTTAVRALA 135
                                       699***************95 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0081
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       p++ lS G ++  al++ l+r++   +++++DE+   L+     + ++l++el++
  gi|313127488|ref|YP_004037758.1| 224 PLDTLSGGELQRVALAATLARDR---DFYFLDEITPYLDIGQRVTAARLIRELAE 275
                                       7888999999999**********...9********99999555444444433333 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00035
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltde 35 
                                       +++GpNg GKS+L + +       + +e++  e
  gi|313127488|ref|YP_004037758.1| 388 GIVGPNGIGKSTLAKMFA------GGLEPDEGE 414
                                       79***********99884......444444444 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00024
                            AAA_21 180 kekrllqrlvrslklveielsdlgegeeliasvderlrer.....gvvflengdgqelparelSdGtkrllalltal 251
                                       +e++l +rl   +k++ ie++  + ++    s+ ++   +         l  ++  e+++++lS G ++  a+++ l
  gi|313127488|ref|YP_004037758.1| 411 DEGELDFRLDIAYKPQYIEIDQPMRVDAFLSSITDDFGTSywkteVANPLQLNRIMERNLDDLSGGERQRVAIAATL 487
                                       5566666666666666666666666666666666665555666553333344444478999**************** PP

                            AAA_21 252 lralkkgsllliDEpEngLHPkllrrllell.kelsrngaQvil 294
                                        +++   +l++ DEp ++L+ +      + + +++++++a v++
  gi|313127488|ref|YP_004037758.1| 488 SEDA---DLYVMDEPSAHLDVEQRVQATTAIrRYAENHDATVMV 528
                                       ****...9************955544444443444444555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0016      0.73      29      51 ..     119     141 ..     104     219 .. 0.72
   2 ?    2.3   0.1      0.43     2e+02      64      98 ..     252     286 ..     197     333 .. 0.75
   3 !   16.0   0.0   2.5e-05     0.012      24     143 ..     384     531 ..     374     533 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
                            AAA_16  29 lsGesGvGKsslvrellralekd 51 
                                       + G+ G+GK++ vr+l+ ++  +
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAGEMVPN 141
                                       89**************9877776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.43
                            AAA_16  64 esaipysalaqalareellrqlldeaesaeleawr 98 
                                       ++ +py+ + q  ++ +l+r+l++++++a l+  +
  gi|313127488|ref|YP_004037758.1| 252 DEITPYLDIGQRVTAARLIRELAEDEDKAVLAVEH 286
                                       5569999999999999******9995554444333 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2.5e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd........................ggiflrgkcdqlesaipy..salaq 74 
                                       +e++ ++G+ G+GKs+l+++++  le d                           fl+  +d++  +++y    +a+
  gi|313127488|ref|YP_004037758.1| 384 SEVLGIVGPNGIGKSTLAKMFAGGLEPDegeldfrldiaykpqyieidqpmrVDAFLSSITDDF--GTSYwkTEVAN 458
                                       477889*****************99999665544443333333333333221112233333333..23333111333 PP

                            AAA_16  75 alareellrqlldeaesaeleawrekleeala................................avpelagaea... 116
                                        l                             +                                 v +     +   
  gi|313127488|ref|YP_004037758.1| 459 PL-----------------------------QlnrimernlddlsggerqrvaiaatlsedadlYVMD-----Epsa 501
                                       33.............................2222222222222244444443333333445453333.....1344 PP

                            AAA_16 117 ....srllellkrllallsrderplvlvlDd 143
                                           ++  ++ +++ +++++ ++ +v+v+D+
  gi|313127488|ref|YP_004037758.1| 502 hldvEQRVQATTAIRRYAEN-HDATVMVIDH 531
                                       44777777777777788898.5559999995 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.9   0.00012     0.057      21      40 ..     116     135 ..     109     217 .. 0.85
   2 !   13.5   0.0   0.00017     0.077       9      39 ..     366     404 ..     364     465 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                            AAA_23  21 ltlItGpNGaGKTTildAik 40 
                                       +t I GpNG GKTT ++A+ 
  gi|313127488|ref|YP_004037758.1| 116 VTGILGPNGIGKTTAVRALA 135
                                       799*************9985 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00017
                            AAA_23   9 sfrdqeidF........skgltlItGpNGaGKTTildAi 39 
                                       s+++ e+ +         + +  I+GpNG GK+T+   +
  gi|313127488|ref|YP_004037758.1| 366 SYGEGEFSLdveagtiyQSEVLGIVGPNGIGKSTLAKMF 404
                                       67555555555666666667889***********98765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.7e-05     0.035       4      23 ..     120     139 ..     118     205 .. 0.73
   2 !    9.8   0.0    0.0022         1       3      22 ..     389     408 ..     387     449 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.7e-05
                                       ESSTTSSHHHHHHHHHHHHT CS
                               AAA   4 yGppGtGKTllakavakelg 23 
                                        Gp G+GKT++++a+a e+ 
  gi|313127488|ref|YP_004037758.1| 120 LGPNGIGKTTAVRALAGEMV 139
                                       7*****************83 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0022
                                       EESSTTSSHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel 22 
                                       ++Gp G+GK++lak  a  l
  gi|313127488|ref|YP_004037758.1| 389 IVGPNGIGKSTLAKMFAGGL 408
                                       68*************99876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.021       9.8      10      26 ..     119     135 ..     113     149 .. 0.88
   2 !   15.5   0.0   3.3e-05     0.015       8      86 ..     387     473 ..     382     530 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.021
                            AAA_22  10 vtGesGtGKTtllrrll 26 
                                       + G+ G+GKTt +r l+
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALA 135
                                       78************987 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.3e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsstsskdllrellralglelka....erlsse 76 
                                       l ++G+ G+GK+tl+++++  l+ ++   + r +++    ++++ +++  + +l+ +  ++g +  +    ++l++ 
  gi|313127488|ref|YP_004037758.1| 387 LGIVGPNGIGKSTLAKMFAGGLEPDEGELDFRLDIAykpqYIEIDQPMRVDAFLSSITDDFGTSYWKtevaNPLQLN 463
                                       569******************96554444444444446778888888889999999999999766667666555555 PP

                            AAA_22  77 ellealeqal 86 
                                       +++e+  + l
  gi|313127488|ref|YP_004037758.1| 464 RIMERNLDDL 473
                                       5543333333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0014      0.62      18      82 ..     113     176 ..     108     198 .. 0.82
   2 !   10.8   0.0   0.00045      0.21      19      39 ..     383     403 ..     377     468 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                       SCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEEESXXHHHHHHHXXHHHHHCCCTT CS
                            NB-ARC  18 lqslvvalvGmgGvGKttlakqilnksdevegrFd.svawvvvsktdkseeiletilkeLslsedd 82 
                                       ++  v ++ G  G+GKtt ++    ++    g++d    w  v + +   e+++ i ++  ++e  
  gi|313127488|ref|YP_004037758.1| 113 PG-AVTGILGPNGIGKTTAVRALAGEMVPNLGTYDeEATWEAVLDRYRGTELQNYIERV-REEEVS 176
                                       55.6789**************99999888889**98899************99977654.444454 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00045
                                       CSEEEEEEESTTSSHHHHHHH CS
                            NB-ARC  19 qslvvalvGmgGvGKttlakq 39 
                                       qs v+++vG  G+GK+tlak 
  gi|313127488|ref|YP_004037758.1| 383 QSEVLGIVGPNGIGKSTLAKM 403
                                       6779**************985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0044         2       5      22 ..     117     134 ..     114     157 .. 0.86
   2 !   12.3   0.1   0.00022       0.1       5      23 ..     387     409 ..     383     531 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0044
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                         i Gp+giGKTt ++ l
  gi|313127488|ref|YP_004037758.1| 117 TGILGPNGIGKTTAVRAL 134
                                       5799*********99887 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00022
                            AAA_24   5 iliyGpsgiGKTtlakel....g 23 
                                       + i+Gp+giGK+tlak++    +
  gi|313127488|ref|YP_004037758.1| 387 LGIVGPNGIGKSTLAKMFagglE 409
                                       679*************9965442 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00093      0.43      22      49 ..     113     141 ..     103     150 .. 0.84
   2 !    9.0   0.1    0.0024       1.1      24      38 ..     386     400 ..     370     403 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00093
                            AAA_29  22 kg.atlltGpsGsGKSTllDAiqalLvpa 49 
                                        g +t + Gp+G GK+T + A++  +vp+
  gi|313127488|ref|YP_004037758.1| 113 PGaVTGILGPNGIGKTTAVRALAGEMVPN 141
                                       456889**************999988887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
                            AAA_29  24 atlltGpsGsGKSTl 38 
                                       +  ++Gp+G GKSTl
  gi|313127488|ref|YP_004037758.1| 386 VLGIVGPNGIGKSTL 400
                                       5669**********8 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0078       3.6       4      49 ..     116     166 ..     114     209 .. 0.76
   2 ?    0.1   0.0       1.6   7.5e+02      63      78 ..     244     259 ..     221     284 .. 0.66
   3 !    8.9   0.0    0.0032       1.5       2      27 ..     384     409 ..     383     446 .. 0.78
   4 ?   -2.2   0.0       8.4   3.8e+03      31      82 ..     463     508 ..     446     529 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0078
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell.....vkkesilyinldderdkkladp 49 
                                       +  i G+  +GKTt ++ l+ e        ++e + +  ld+ r ++l+++
  gi|313127488|ref|YP_004037758.1| 116 VTGILGPNGIGKTTAVRALAGEMVpnlgtYDEEATWEAVLDRYRGTELQNY 166
                                       66799**************99888777777777777777777776666655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.6
                            AAA_14  63 ekktylflDEiqevpe 78 
                                       +++ + flDEi  + +
  gi|313127488|ref|YP_004037758.1| 244 RDRDFYFLDEITPYLD 259
                                       368899*****98743 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0032
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell 27 
                                       +++l i+G+  +GK+tl+k ++  l 
  gi|313127488|ref|YP_004037758.1| 384 SEVLGIVGPNGIGKSTLAKMFAGGLE 409
                                       57899*************99986655 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 8.4
                            AAA_14  31 esilyinldderdkkladpekllelileklkeekktylflDEiqevpeweka 82 
                                       ++i++ nldd +  +++       +i + l+e +  + ++DE +   ++e+ 
  gi|313127488|ref|YP_004037758.1| 463 NRIMERNLDDLSGGERQRV-----AIAATLSE-DADLYVMDEPSAHLDVEQR 508
                                       5666666666665443322.....22222333.4556777776665444433 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0033       1.5       3      31 ..     119     147 ..     118     178 .. 0.77
   2 !    9.3   0.0    0.0031       1.4       3      22 ..     389     408 ..     387     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0033
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkk 31 
                                       + Gp+g+GK+t+++ La ++  +l++  +
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAGEMVPNLGTYDE 147
                                       67**************9999877744443 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0031
                      RNA_helicase   3 lyGpsgeGKStlakeLakal 22 
                                       ++Gp+g+GKStlak +a  l
  gi|313127488|ref|YP_004037758.1| 389 IVGPNGIGKSTLAKMFAGGL 408
                                       78************988665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0081       3.7       5      22 ..     119     136 ..     115     140 .. 0.87
   2 !    9.9   0.0    0.0014      0.65       3      27 ..     387     411 ..     385     443 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0081
                                       EEC-TTTCHHHHHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlqklal 22 
                                       + G++G+GKTt ++ la 
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAG 136
                                       89************9985 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                                       EEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaeg 27 
                                       + + G++G+GK+tL++ +a  +  +
  gi|313127488|ref|YP_004037758.1| 387 LGIVGPNGIGKSTLAKMFAGGLEPD 411
                                       5699************999777655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0004      0.18      19      89 ..     113     190 ..     110     220 .. 0.73
   2 ?    5.4   0.0     0.034        16      21      42 ..     385     406 ..     380     428 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0004
                          ATPase_2  19 pneiyfiYGpegsGKtaLlk....eiienledkdkyviyyialreesiskldefie...eeeekkklekalgiavpk 88 
                                       p  +  i Gp g+GKt+ ++    e++ nl  +d++  +   l +++ ++l+++ie   eee++   + +  +++pk
  gi|313127488|ref|YP_004037758.1| 113 PGAVTGILGPNGIGKTTAVRalagEMVPNLGTYDEEATWEAVLDRYRGTELQNYIErvrEEEVSIARKPQYVDQIPK 189
                                       66677799********75553333889999**************************986555555545555666666 PP

                          ATPase_2  89 a 89 
                                       +
  gi|313127488|ref|YP_004037758.1| 190 Q 190
                                       3 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.034
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiie 42 
                                       e++ i Gp g+GK++L k ++ 
  gi|313127488|ref|YP_004037758.1| 385 EVLGIVGPNGIGKSTLAKMFAG 406
                                       677799***********98875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.021       9.6      25      43 ..     116     134 ..     109     136 .. 0.89
   2 !    8.4   0.0    0.0033       1.5      25      43 ..     386     404 ..     375     409 .. 0.86
   3 ?    0.7   0.0      0.74   3.4e+02     321     368 ..     488     535 ..     466     536 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.021
                            AAA_15  25 ltvliGkNnsGKSsileal 43 
                                       +t + G+N++GK+++++al
  gi|313127488|ref|YP_004037758.1| 116 VTGILGPNGIGKTTAVRAL 134
                                       67799************98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0033
                            AAA_15  25 ltvliGkNnsGKSsileal 43 
                                       +  ++G+N++GKS++++++
  gi|313127488|ref|YP_004037758.1| 386 VLGIVGPNGIGKSTLAKMF 404
                                       7779***********9986 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.74
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       +e+ ++++++EP ahL  ++  +   ++++ a++++  v++  H  ++
  gi|313127488|ref|YP_004037758.1| 488 SEDADLYVMDEPSAHLDVEQRVQATTAIRRYAENHDATVMVIDHDIYM 535
                                       56789***********88888888888888888887777776666666 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.3   2.9e+03       2       8 ..       8      14 ..       7      15 .. 0.87
   2 ?    1.0   0.9      0.94   4.3e+02      13      19 ..      22      28 ..      21      30 .. 0.84
   3 !   19.0   2.4   1.9e-06   0.00087      11      24 .]      69      82 ..      57      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.3
                                      EEETTTS CS
                              Fer4  2 videekC 8 
                                      v+d ++C
  gi|313127488|ref|YP_004037758.1|  8 VVDLDRC 14
                                      89***** PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.94
                                      HHHHHST CS
                              Fer4 13 aCvevCP 19
                                      +C++ CP
  gi|313127488|ref|YP_004037758.1| 22 ECANYCP 28
                                      6****** PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.9e-06
                                      -THHHHHSTTTEEE CS
                              Fer4 11 CGaCvevCPvgAIt 24
                                      CG+Cve CP++AI+
  gi|313127488|ref|YP_004037758.1| 69 CGICVEKCPFDAIE 82
                                      *************6 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.011       5.1     101     128 ..     116     143 ..     112     158 .. 0.84
   2 !    9.7   0.0    0.0016      0.73      98     124 ..     383     409 ..     344     420 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                                       EEEEECSTTSSHHHHHHHHCTT-----S CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelelktg 128
                                       ++ ++G+ G+GK+t + al++e+  + g
  gi|313127488|ref|YP_004037758.1| 116 VTGILGPNGIGKTTAVRALAGEMVPNLG 143
                                       67799***************99866555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
                                       TTSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpele 124
                                       ++++  +vG+ G+GKStL +++++ le
  gi|313127488|ref|YP_004037758.1| 383 QSEVLGIVGPNGIGKSTLAKMFAGGLE 409
                                       5577889***********999888765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.013       5.8       5      22 ..     120     137 ..     116     207 .. 0.79
   2 !    8.3   0.3    0.0052       2.4       4      20 ..     389     405 ..     386     532 .. 0.81
   3 ?   -1.3   0.0       4.9   2.3e+03      13      36 ..     512     542 ..     511     574 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                            AAA_33   5 vGlpGsGKstlaerllkk 22 
                                        G++G GK+t ++ l+ +
  gi|313127488|ref|YP_004037758.1| 120 LGPNGIGKTTAVRALAGE 137
                                       6************99865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0052
                            AAA_33   4 lvGlpGsGKstlaerll 20 
                                       +vG++G GKstla+  +
  gi|313127488|ref|YP_004037758.1| 389 IVGPNGIGKSTLAKMFA 405
                                       79***********9765 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.9
                            AAA_33  13 stlaerllkklg..avllssdt.....lrrr 36 
                                       +t ++r++++++  + +++ d+     l +r
  gi|313127488|ref|YP_004037758.1| 512 TTAIRRYAENHDatVMVIDHDIymidlLADR 542
                                       8999999999997777788888555543333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0015      0.69      50      73 ..     119     142 ..     112     152 .. 0.88
   2 ?    5.5   0.0     0.031        14      46      66 ..     385     405 ..     374     414 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                             Rad17  50 isGPsGCgkstvvkvLskelgikl 73 
                                       i GP G gk+t+v+ L+ e++++l
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAGEMVPNL 142
                                       78*****************99987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.031
                             Rad17  46 riLLisGPsGCgkstvvkvLs 66 
                                       ++L i GP G gkst  k+ +
  gi|313127488|ref|YP_004037758.1| 385 EVLGIVGPNGIGKSTLAKMFA 405
                                       5899***********999876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00079      0.36       4      40 ..     119     159 ..     117     182 .. 0.74
   2 ?    4.2   0.1       0.1        46       4      20 ..     389     405 ..     387     413 .. 0.90
   3 ?   -0.6   0.0         3   1.4e+03      60      85 ..     511     536 ..     472     573 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00079
                            AAA_28   4 itGgestGKTtlleaLaar...gypvv.pEaareileekla 40 
                                       i+G+ + GKTt ++aLa +   +  ++ +Ea  e + ++++
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAGEmvpNLGTYdEEATWEAVLDRYR 159
                                       89***************663555556666666666666554 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.1
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       i+G+ + GK+tl++ +a
  gi|313127488|ref|YP_004037758.1| 389 IVGPNGIGKSTLAKMFA 405
                                       89**********99776 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3
                            AAA_28  60 leeqleeeaaaaankvlfcDrglldt 85 
                                          +++++a++++  v+++D ++  +
  gi|313127488|ref|YP_004037758.1| 511 ATTAIRRYAENHDATVMVIDHDIYMI 536
                                       23455666666777777777766555 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2      0.01       4.6      28      57 ..     116     145 ..     113     155 .. 0.86
   2 ?   -2.1   0.0       6.1   2.8e+03     149     201 ..     163     213 ..     151     215 .. 0.71
   3 ?    6.7   0.0     0.012       5.5      28      60 ..     386     418 ..     380     421 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                                       HHHHHS--SHHHHHHHHHHHHHHS--TTT- CS
                              MukB  28 vttlsGgnGaGksttmaafvtaliPdlsll 57 
                                       vt + G nG Gk+t++ a+   ++P+l   
  gi|313127488|ref|YP_004037758.1| 116 VTGILGPNGIGKTTAVRALAGEMVPNLGTY 145
                                       9999*********************98765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.1
                                       HHHHHHHHHTSTT-EEEE-S-HHHHHHHHHHTTSBSS---SHHHHHHHHHHHH CS
                              MukB 149 lnelkekleelegvrlkkfnsvtdyhallfdlGvipkrlrssedrskfyrlie 201
                                       l++  e++ e e+v +++    +d     fd G+++  l+  ++r k+ + +e
  gi|313127488|ref|YP_004037758.1| 163 LQNYIERVRE-EEVSIARKPQYVDQIPKQFD-GITSELLEATDERGKLDEYVE 213
                                       4444445544.56666677777777777787.999999999999999988776 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.012
                                       HHHHHS--SHHHHHHHHHHHHHHS--TTT---- CS
                              MukB  28 vttlsGgnGaGksttmaafvtaliPdlsllhfr 60 
                                       v  + G nG Gkst    f   l Pd   l fr
  gi|313127488|ref|YP_004037758.1| 386 VLGIVGPNGIGKSTLAKMFAGGLEPDEGELDFR 418
                                       667889*************************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   2.8    0.0031       1.4       1      20 [.       6      28 ..       6      33 .. 0.87
   2 !   12.9   2.4   0.00019     0.086       3      24 .]      58      81 ..      57      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0031
                            Fer4_6  1 vveidpdkCi..gC.gdCvrvCP 20
                                      ++++d d+C    C ++C++ CP
  gi|313127488|ref|YP_004037758.1|  6 IAVVDLDRCQpdRCsYECANYCP 28
                                      689******9767*9******** PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00019
                            Fer4_6  3 eidpdkCig..CgdCvrvCPegai 24
                                      +i ++ C+g  Cg Cv  CP++ai
  gi|313127488|ref|YP_004037758.1| 58 RISEEVCLGetCGICVEKCPFDAI 81
                                      688899**999***********98 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0075       3.4       3      43 ..     119     157 ..     118     213 .. 0.67
   2 ?    4.4   0.0      0.11        51       3      18 ..     389     404 ..     387     516 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0075
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdp 43 
                                       + G+ G GKtt  ++L+ ++  + nl+ +  e  ++   d 
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAGEM--VPNLGTYDEEATWEAVLDR 157
                                       89**************8887..5555555444444443333 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                            AAA_18   3 ltGtpGvGKttlakeL 18 
                                       + G+ G GK+tlak  
  gi|313127488|ref|YP_004037758.1| 389 IVGPNGIGKSTLAKMF 404
                                       89***********976 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.037        17      38      61 ..     119     142 ..     116     176 .. 0.88
   2 ?   -1.8   0.0       5.1   2.3e+03      65      93 ..     229     254 ..     217     258 .. 0.65
   3 ?    5.6   0.0     0.027        12      38      57 ..     389     408 ..     374     414 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.037
                            RuvB_N  38 lyGpPGlGkttlakiiakelgvkl 61 
                                       + Gp G+Gktt  + +a e+  +l
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAGEMVPNL 142
                                       57*****************97765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.1
                            RuvB_N  65 sgPvlekagdlaalltnleekdvlfidei 93 
                                       sg  l++   laa l+  +++d  f+dei
  gi|313127488|ref|YP_004037758.1| 229 SGGELQRV-ALAATLA--RDRDFYFLDEI 254
                                       55555543.3555443..589999***99 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.027
                            RuvB_N  38 lyGpPGlGkttlakiiakel 57 
                                       ++Gp G+Gk+tlak+ a  l
  gi|313127488|ref|YP_004037758.1| 389 IVGPNGIGKSTLAKMFAGGL 408
                                       78************998765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.029        13       4      23 ..     119     138 ..     116     206 .. 0.83
   2 ?   -2.3   0.0         8   3.7e+03      94     133 ..     244     286 ..     231     296 .. 0.59
   3 ?    4.8   0.0     0.051        23       3      21 ..     388     406 ..     386     414 .. 0.82
   4 ?   -0.2   0.1       1.8   8.2e+02      93     104 ..     488     499 ..     471     542 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.029
                                       EE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlell 23 
                                       i Gp G+GKtT v+ ++ ++
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAGEM 138
                                       669**********9888766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8
                                       HHH-EEEE---STTGGG-HHH..HHHHHHHHT.TTSEEEEE-- CS
                          NTPase_1  94 seadviviDEiGkmElkskkf..keaveevLk.sekpvlavih 133
                                       ++ d + +DEi +     +++  ++ ++e+ + ++k vlav h
  gi|313127488|ref|YP_004037758.1| 244 RDRDFYFLDEITPYLDIGQRVtaARLIRELAEdEDKAVLAVEH 286
                                       5677777788776544444431134567777666666666655 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.051
                                       EEE--TTSSHHHHHHHHHH CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvle 21 
                                        i Gp G+GK+Tl k  + 
  gi|313127488|ref|YP_004037758.1| 388 GIVGPNGIGKSTLAKMFAG 406
                                       688**********987665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.8
                                       HHHH-EEEE--- CS
                          NTPase_1  93 lseadviviDEi 104
                                        ++ad++v+DE 
  gi|313127488|ref|YP_004037758.1| 488 SEDADLYVMDEP 499
                                       367788888873 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   8.7   0.00015     0.068       5      52 .]      19      80 ..       9      80 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00015
                            Fer4_7  5 Cg.aCvaaCpvkaield.........eeenek.....gtekveidpekClg..CgaCvavCPtga 52
                                      C   C+++Cp +    +         e   e+     g ++++i++e Clg  Cg Cv+ CP++a
  gi|313127488|ref|YP_004037758.1| 19 CSyECANYCPPNRTGKEcivtrgeyfE---EDepydgGPDQIRISEEVCLGetCGICVEKCPFDA 80
                                      6547*****966666443333343321...22234445599********9655*********997 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0053       2.4       6      25 ..     119     138 ..     115     202 .. 0.82
   2 ?    3.4   0.0      0.11        52       3      20 ..     386     402 ..     384     411 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0053
                                       EEESTTSSHHHHHHHHHHHH CS
                             SRP54   6 lvGlqGaGKTttlaKLaall 25 
                                       ++G++G+GKTt++  La  +
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAGEM 138
                                       79***********9999765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                                       EEEEEESTTSSHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaK 20 
                                       v+ +vG++G+GK t + K
  gi|313127488|ref|YP_004037758.1| 386 VLGIVGPNGIGKSTLA-K 402
                                       6669********9854.4 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.082        38       4      21 ..     119     136 ..     118     154 .. 0.88
   2 ?    6.4   0.0     0.018       8.2       4      21 ..     389     406 ..     387     443 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.082
                                       EE--SSSSHHHHHHHGGG CS
                             AAA_5   4 LvGppGtgKselaerlaa 21 
                                       ++Gp G+gK++ ++ la 
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAG 136
                                       58************9985 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.018
                                       EE--SSSSHHHHHHHGGG CS
                             AAA_5   4 LvGppGtgKselaerlaa 21 
                                       +vGp G+gKs+la+ +a 
  gi|313127488|ref|YP_004037758.1| 389 IVGPNGIGKSTLAKMFAG 406
                                       69***********99875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0       0.1        46       3      22 ..     118     137 ..     116     173 .. 0.85
   2 ?    4.9   0.0     0.057        26       3      20 ..     388     405 ..     386     437 .. 0.89
   3 ?    0.6   0.0       1.2   5.7e+02      44      85 ..     489     531 ..     448     560 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                                       EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                       +i+G    GK+t ++al ge
  gi|313127488|ref|YP_004037758.1| 118 GILGPNGIGKTTAVRALAGE 137
                                       799**************997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.057
                                       EEEESTTSSHHHHHHHHH CS
                          MMR_HSR1   3 aivGrpNvGKStLinalt 20 
                                       +ivG    GKStL +   
  gi|313127488|ref|YP_004037758.1| 388 GIVGPNGIGKSTLAKMFA 405
                                       8************87665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.2
                                       TTEEEEEEECGGCSS.HHHHHHHHHHHHHHHHC.TSEEEEEEET CS
                          MMR_HSR1  44 kgkeielvDtpGlie.gaseekglgkaflalee.adlillvvda 85 
                                       ++ +++++D p   + + +++ + + a+++  e  d+ ++v+d 
  gi|313127488|ref|YP_004037758.1| 489 EDADLYVMDEPS-AHlDVEQRVQATTAIRRYAEnHDATVMVIDH 531
                                       346788888888.5422333335555555544436889999983 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.12        54      52      72 ..     119     139 ..     112     145 .. 0.86
   2 ?    7.3   0.1    0.0076       3.5      45      68 ..     382     405 ..     374     409 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                         IstB_IS21  52 llGpsGvGKshlaialgveav 72 
                                       +lGp G+GK+    al+ e v
  gi|313127488|ref|YP_004037758.1| 119 ILGPNGIGKTTAVRALAGEMV 139
                                       89********99999987765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0076
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialg 68 
                                        ++e + ++Gp G+GKs la  ++
  gi|313127488|ref|YP_004037758.1| 382 YQSEVLGIVGPNGIGKSTLAKMFA 405
                                       5678889************98765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.044        20      33      58 ..     114     139 ..     109     153 .. 0.86
   2 ?   -2.4   0.1       6.3   2.9e+03     100     149 ..     245     292 ..     231     305 .. 0.44
   3 ?    3.6   0.1     0.091        42      29      50 ..     380     401 ..     375     407 .. 0.83
   4 ?    4.6   0.1     0.046        21      94     149 ..     484     530 ..     448     532 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.044
                            AAA_25  33 gelallaGapgtGKttlaldlalava 58 
                                       g+++ + G+ g GKtt++  la +++
  gi|313127488|ref|YP_004037758.1| 114 GAVTGILGPNGIGKTTAVRALAGEMV 139
                                       7889999***********99998876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.3
                            AAA_25 100 darllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviD 149
                                       d++ ++ld       l++ +  +   l+ +  ++ ++a+ +ve  +l ++D
  gi|313127488|ref|YP_004037758.1| 245 DRDFYFLDE--ItPYLDIGQRVTAARLIRELAEDEDKAVLAVE-HDLAILD 292
                                       455555542..11222222222222223333333444444433.5555555 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.091
                            AAA_25  29 llpagelallaGapgtGKttla 50 
                                        +   e+  ++G+ g GK+tla
  gi|313127488|ref|YP_004037758.1| 380 TIYQSEVLGIVGPNGIGKSTLA 401
                                       5666788889***********8 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.046
                            AAA_25  94 gealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviD 149
                                        ++l++da+l+v+d ++    +L    + +++++ ++ a+++ +e  +++ + viD
  gi|313127488|ref|YP_004037758.1| 484 AATLSEDADLYVMDEPSA---HL----DVEQRVQ-ATTAIRRYAEN-HDATVMVID 530
                                       344455666666664332...22....2333332.33455555555.566666666 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.013         6      25      47 ..     113     135 ..      90     192 .. 0.83
   2 ?    2.6   0.0      0.18        85      28      43 ..     386     401 ..     366     408 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                            AAA_27  25 eadlhliyGpNEAGKstalrAis 47 
                                          ++ i+GpN  GK+ta+rA+ 
  gi|313127488|ref|YP_004037758.1| 113 PGAVTGILGPNGIGKTTAVRALA 135
                                       4456779**************85 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.18
                            AAA_27  28 lhliyGpNEAGKstal 43 
                                       +  i+GpN  GKst+ 
  gi|313127488|ref|YP_004037758.1| 386 VLGIVGPNGIGKSTLA 401
                                       55599*********86 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  12.2      0.01       4.7       2      56 .]       7      77 ..       6      77 .. 0.83
   2 ?   10.2   1.4    0.0013      0.62       2      25 ..      57      82 ..      56     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.01
                           Fer4_10  2 vvidddtC..irCg.kCvkaCPadl...........tsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56
                                      +v+d d+C   rC  +C + CP +               + ++++ + +++r+  e C g  cg Cve+CP
  gi|313127488|ref|YP_004037758.1|  7 AVVDLDRCqpDRCSyECANYCPPNRtgkecivtrgeYFEEDEPYDGGPDQIRISEEVCLGetCGICVEKCP 77
                                      68899***6669999********99*******999966666677777777777778887777********9 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                           Fer4_10  2 vvidddtC..irCgkCvkaCPadlts 25
                                      ++i ++ C    Cg Cv+ CP+d+ +
  gi|313127488|ref|YP_004037758.1| 57 IRISEEVClgETCGICVEKCPFDAIE 82
                                      578889994448*********97633 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   9.0    0.0014      0.63       4      51 .]      18      81 ..      13      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0014
                            Fer4_9  4 gCga.CveaCpagvvvedaaerkarlraase.............eaCig..CgaCveaCpkgai 51
                                      +C + C + Cp + + +++  +  ++ +++e             e C+g  Cg Cve+Cp +ai
  gi|313127488|ref|YP_004037758.1| 18 RCSYeCANYCPPNRTGKECIVTRGEYFEEDEpydggpdqiriseEVCLGetCGICVEKCPFDAI 81
                                      5875699999*****99999999999887779************99*6445*********9987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.018       8.3      19      39 ..     115     135 ..     110     145 .. 0.85
   2 ?    3.0   0.0      0.16        74      19      40 ..     385     406 ..     377     422 .. 0.80
   3 ?   -1.6   0.1         4   1.8e+03      86     119 ..     487     526 ..     452     531 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.018
                            AAA_30  19 rvavltGpAGtGKttalkalr 39 
                                        v+ + Gp G GKtta++al+
  gi|313127488|ref|YP_004037758.1| 115 AVTGILGPNGIGKTTAVRALA 135
                                       588999************995 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.16
                            AAA_30  19 rvavltGpAGtGKttalkalre 40 
                                        v  ++Gp G GK+t+ k  + 
  gi|313127488|ref|YP_004037758.1| 385 EVLGIVGPNGIGKSTLAKMFAG 406
                                       38899**********9987765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4
                            AAA_30  86 lepg.tllivDEagmv.....dtkqlaallkaaekagakv 119
                                       l+++ +l++ DE +         + ++a+ + ae+++a+v
  gi|313127488|ref|YP_004037758.1| 487 LSEDaDLYVMDEPSAHldveqRVQATTAIRRYAENHDATV 526
                                       3344477888886654433322333344444444445555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   3.4      0.29   1.4e+02       3      21 ..       7      28 ..       5      29 .. 0.84
   2 ?   11.6   1.2   0.00053      0.24       5      21 ..      59      77 ..      56      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.29
                            Fer4_2  3 vvvdtdrC.i.gCg.aCvsaCP 21
                                      +vvd drC   +C+  C + CP
  gi|313127488|ref|YP_004037758.1|  7 AVVDLDRCqPdRCSyECANYCP 28
                                      68999***8448*779*****9 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00053
                            Fer4_2  5 vdtdrCig..CgaCvsaCP 21
                                      + ++ C+g  Cg+Cv  CP
  gi|313127488|ref|YP_004037758.1| 59 ISEEVCLGetCGICVEKCP 77
                                      56899**99********** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.8    0.0061       2.8      11      58 ..      19      82 ..       7      83 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0061
                           Fer4_21 11 Cg.kCliaCe..dtshqai.........eidakt.......vlkvvedeCvG..CnlCssvCPvedcie 58
                                      C  +C+  C+   t+ ++i         +    +       ++++ e+ C G  C +C++ CP  d+ie
  gi|313127488|ref|YP_004037758.1| 19 CSyECANYCPpnRTGKECIvtrgeyfeeD----EpydggpdQIRISEEVCLGetCGICVEKCPF-DAIE 82
                                      54268888853257899995555433220....1222333355899****9988*********7.9997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   9.0     0.019       8.7       4      66 ..      18      78 ..      14      79 .. 0.66
   2 ?   10.3   1.5    0.0024       1.1       4      18 ..      68      82 ..      63      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.019
                           Fer4_16  4 tCgk.CaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeai..tgCdiCqdvCPa 66
                                      +C   Ca+ CP n   ++   +i +r +  ++++  ++  +d+ +   +e +    C+iC++ CP+
  gi|313127488|ref|YP_004037758.1| 18 RCSYeCANYCPPNRTGKE---CIVTRGEYFEEDEPYDGG-PDQIRIS-EEVClgETCGICVEKCPF 78
                                      57766*********9999...776666655433333333.3333333.23333489*********8 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0024
                           Fer4_16  4 tCgkCaevCPtnaik 18
                                      tCg C+e CP +ai+
  gi|313127488|ref|YP_004037758.1| 68 TCGICVEKCPFDAIE 82
                                      89********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 3798.52
//
Query:       gi|313127489|ref|YP_004037759.1|  [L=108]
Description: hypothetical protein Hbor_27700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0068   16.5   3.2      0.011   15.8   3.2    1.5  1  DUF1634   Protein of unknown function (DUF1634)


Domain annotation for each model (and alignments):
>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.2   6.2e-07     0.011      48     101 ..      47     100 ..      13     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.2e-07
                           DUF1634  48 lelkglaiiqlGllvLiatPvlrVvlsliaFlkekdilyviitliVLliLllsl 101
                                       ++ +++++  lG +vL   P+lrVv   +  +  kd++yv++ ++ L  + +++
  gi|313127489|ref|YP_004037759.1|  47 AATNQQTLAVLGAFVLAQFPLLRVVGVDVGDFGVKDYIYVVFMTFTLWFISYGI 100
                                       567889999****************999999999*******9999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.53
# Mc/sec: 618.04
//
Query:       gi|313127490|ref|YP_004037760.1|  [L=96]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00079   19.9   0.0    0.00097   19.6   0.0    1.1  1  HTH_27         Winged helix DNA-binding domain
     0.0024   17.4   0.0     0.0033   17.0   0.0    1.2  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.021   14.5   0.0    1.3  1  GntR           Bacterial regulatory proteins, gntR family
      0.016   15.1   0.1      0.022   14.7   0.1    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.016   15.1   0.0      0.022   14.8   0.0    1.1  1  Dimerisation2  Dimerisation domain
      0.026   14.4   0.0      0.035   14.0   0.0    1.2  1  MarR_2         MarR family
      0.042   13.8   0.0      0.061   13.3   0.0    1.2  1  MarR           MarR family
      0.047   13.6   0.0      0.057   13.3   0.0    1.2  1  TFIIE_alpha    TFIIE alpha subunit
        0.1   12.5   0.0       0.14   12.1   0.0    1.2  1  HTH_11         HTH domain
       0.15   12.3   0.1       0.22   11.8   0.1    1.2  1  PaaX           PaaX-like protein


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.4e-07   0.00097      13      67 ..      23      77 ..      13      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.4e-07
                            HTH_27 13 rhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdk 67
                                       + +++ +++ +++  ++++ ++ y+l++L+  G+v +  + ad r+ +++lT++
  gi|313127490|ref|YP_004037760.1| 23 LEYNGPLTQKGIVQESMLSARTVRYALERLEGIGVVDEDVYFADARQNLYQLTEA 77
                                      45788889999999999************************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.8e-06    0.0033      10      47 ..      21      58 ..      17      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                            HTH_24 10 elLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++L+ n+ ++q+ + +++ lS  tv++ l+rLe  G++
  gi|313127490|ref|YP_004037760.1| 21 KVLEYNGPLTQKGIVQESMLSARTVRYALERLEGIGVV 58
                                      67899****************************99987 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.021      16      54 ..      21      58 ..       9      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                      TSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 16 gelrpGdkLPsereLaaefgVsrttvReALrrLeaeglv 54
                                      ++l+ + +L +++ +++e   s+ tvR AL rLe  g+v
  gi|313127490|ref|YP_004037760.1| 21 KVLEYNGPL-TQKGIVQESMLSARTVRYALERLEGIGVV 58
                                      567888899.9999**********************998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.2e-05     0.022      13      54 ..      19      60 ..      15      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      v+++L  +gp+t + i +e+ ++  +v  +L++Le  G+V+ 
  gi|313127490|ref|YP_004037760.1| 19 VFKVLEYNGPLTQKGIVQESMLSARTVRYALERLEGIGVVDE 60
                                      6667779********************************986 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-05     0.022      23      82 ..      19      80 ..      15      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                     Dimerisation2 23 vFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLere..kkeekkalYsntelast 82
                                      vF +L+ ++pl+ + + +e  +s++ ++  l+ + ++g    +    + +++lY+ te+a +
  gi|313127490|ref|YP_004037760.1| 19 VFKVLEYNGPLTQKGIVQESMLSARTVRYALERLEGIGVVDEDvyFADARQNLYQLTEAAPK 80
                                      9****************************************8865455578*******9965 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.9e-05     0.035       3      52 ..      12      59 ..      10      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      l+p+   v  +L  +++  lt++ ++++  ls  +v ++l+rL+  G v 
  gi|313127490|ref|YP_004037760.1| 12 LPPSAKLVFKVLEYNGP--LTQKGIVQESMLSARTVRYALERLEGIGVVD 59
                                      67777778888999999..************************9888776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.4e-05     0.061      11      47 ..      22      58 ..      14      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                                      HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                       l+++gpl+++ +   +++s  tv  +l rLe  G +
  gi|313127490|ref|YP_004037760.1| 22 VLEYNGPLTQKGIVQESMLSARTVRYALERLEGIGVV 58
                                      5899****************************99976 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.057      14      58 ..      15      59 ..      10      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                      +a+lv +vL  +g +t   + +e  +    +r +L rL ++++v+
  gi|313127490|ref|YP_004037760.1| 15 SAKLVFKVLEYNGPLTQKGIVQESMLSARTVRYALERLEGIGVVD 59
                                      5789***************************************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.9e-05      0.14       7      44 ..      20      57 ..      15      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                            HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                        +le +gp++ + + +e  +S rtvr  +++Le +gv
  gi|313127490|ref|YP_004037760.1| 20 FKVLEYNGPLTQKGIVQESMLSARTVRYALERLEGIGV 57
                                      445599****************************9994 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012      0.22      35      69 ..      40      77 ..      33      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                              PaaX 35 iseslvRaalsRlakaGwlvre...kegrrsfYrLsdk 69
                                      +s+++vR al Rl+  G +++    +++r+ +Y+L+++
  gi|313127490|ref|YP_004037760.1| 40 LSARTVRYALERLEGIGVVDEDvyfADARQNLYQLTEA 77
                                      689****************886444789999****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 685.16
//
Query:       gi|313127491|ref|YP_004037761.1|  [L=615]
Description: ATPase, pilt family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-13   49.4   0.4    1.9e-12   46.8   0.2    2.2  2  T2SSE            Type II/IV secretion system protein
    4.4e-05   23.2   0.1    0.00011   21.9   0.1    1.7  1  KH_1             KH domain
    5.5e-05   23.6   0.1    0.00027   21.3   0.0    2.1  2  AAA_16           AAA ATPase domain
    0.00037   20.2   0.0     0.0013   18.4   0.0    1.9  1  Thymidylate_kin  Thymidylate kinase
     0.0014   18.5   0.0     0.0037   17.2   0.0    1.7  1  NTPase_1         NTPase
      0.005   16.6   1.3      0.014   15.2   1.3    1.7  1  KH_2             KH domain
     0.0078   16.4   0.0      0.039   14.1   0.0    2.1  2  AAA_33           AAA domain
     0.0085   15.4   0.0      0.019   14.3   0.0    1.5  1  Zeta_toxin       Zeta toxin
     0.0089   15.8   0.0      0.031   14.0   0.0    1.9  1  AAA_29           P-loop containing region of AAA domain
     0.0093   15.7   0.1      0.026   14.2   0.0    1.8  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.022   14.2   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
      0.011   16.3   0.0      0.038   14.5   0.0    2.0  1  AAA_18           AAA domain
      0.011   15.7   1.4       0.44   10.6   0.1    3.0  3  FliMN_C          Type III flagellar switch regulator (C-ring)
      0.013   15.0   0.0      0.023   14.2   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.013   16.0   0.0      0.037   14.5   0.0    1.9  1  PIN              PIN domain
       0.02   14.9   0.0       0.05   13.6   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
      0.022   15.2   0.0      0.054   13.9   0.0    1.7  1  AAA              ATPase family associated with various cellul
      0.022   14.6   0.0      0.054   13.3   0.0    1.6  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.025   14.3   0.0      0.053   13.2   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.025   14.8   0.0       0.08   13.2   0.0    1.8  1  AAA_22           AAA domain
       0.05   13.9   0.0       0.15   12.4   0.0    1.9  1  PIN_4            PIN domain
      0.051   13.5   0.0      0.091   12.7   0.0    1.4  1  NACHT            NACHT domain
      0.053   13.5   0.0       0.11   12.4   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.054   13.5   0.0       0.12   12.4   0.0    1.6  1  AAA_14           AAA domain
      0.075   12.9   0.0       0.16   11.8   0.0    1.6  1  APS_kinase       Adenylylsulphate kinase
        0.1   12.3   0.0       0.23   11.1   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
       0.12   12.1   0.0       0.29   10.8   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.13   12.8   0.0       0.33   11.4   0.0    1.7  1  ABC_tran         ABC transporter
       0.15   12.5   0.0       0.38   11.2   0.0    1.8  1  RNA_helicase     RNA helicase
       0.19   11.6   2.1       0.38   10.7   0.6    2.4  2  KH_4             KH domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.2   3.2e-15   1.9e-12      75     247 ..     213     374 ..      69     403 .. 0.78
   2 ?    0.3   0.0      0.48   2.9e+02      46     105 ..     507     570 ..     470     612 .. 0.64

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 3.2e-15
                             T2SSE  75 ekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyall 150
                                        + +r+ ++ +P + g e  ++R   +   +ld++ ++ +l++     l++    +  +l+sG  g GK+t++ a+ 
  gi|313127491|ref|YP_004037761.1| 213 FRDYRIALARPPFSDGiEITAVRPIVKT--DLDEYEFADELRD----RLSER---QRGVLISGSPGAGKSTFAQAVA 280
                                       5678888888999998888888844443..5788876655554....45555...7789****************** PP

                             T2SSE 151 keinksderivtvEDpvEiql.eganqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlg 226
                                       +++n+sd  + t+E p+ +q+    + +q  a   + ++++   ++L  rPD  +  E+R ++ +e+   +     g
  gi|313127491|ref|YP_004037761.1| 281 EFLNESDYAVKTMEKPRDLQVgP--EITQYTAL--DGQMEKTADSLLLVRPDYTIYDEVRKTDDFEVFADMRLAGVG 353
                                       ********************942..34444333..3357788889999*******************6666655566 PP

                             T2SSE 227 slsTlHansaagalerLeqlg 247
                                        ++ +Ha  a++al+rL   +
  gi|313127491|ref|YP_004037761.1| 354 MVGVVHATRAIDALQRLVGRV 374
                                       699*************97543 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                             T2SSE  46 alerlisriaalakldiseerplqdarlp..ekgvrlrvvllPvvagealviR..kksakeltl 105
                                        ++ +  r+ +    +++ee+p q+a+ +  ++g +   ++ P v   ++v+R  ++  + +++
  gi|313127491|ref|YP_004037761.1| 507 RISDIEDRLGIDIDVRTHEENPSQSAASSgtSGGGDQGEIVTPEVTSRHVVVRmdDHVGETVEV 570
                                       5566667777778889999999999999988677777778889999999999976555555544 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.9e-07   0.00011       3      41 ..     489     528 ..     487     547 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-07
                                       EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT. CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sede 41 
                                       ++ v+ + ++++IGkgG +I +I+++ g  I+v   +e++
  gi|313127491|ref|YP_004037761.1| 489 TVYVDEDDISYVIGKGGGRISDIEDRLGIDIDVRThEENP 528
                                       689999*******************77*****98745544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.7   2.2e+03     119     145 ..      90     112 ..      32     151 .. 0.56
   2 !   21.3   0.0   4.6e-07   0.00027      14      77 ..     249     310 ..     244     378 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.7
                            AAA_16 119 llellkrllallsrderplvlvlDdlq 145
                                       + +l+++++   ++ ++ ++l+ D++q
  gi|313127491|ref|YP_004037761.1|  90 IDALIRDIA---EE-HEATLLTSDQVQ 112
                                       333333333...33.222555555555 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 4.6e-07
                            AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqala 77 
                                       + l++  s r + vl+sG +G GKs+ ++++++ l++++  + + +k ++l+ +    + ++q+ a
  gi|313127491|ref|YP_004037761.1| 249 DELRDRLSERQRGVLISGSPGAGKSTFAQAVAEFLNESDYAVkTMEKPRDLQVG----PeITQYTA 310
                                       556666677779************************997555577777777433....33444443 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.2e-06    0.0013       3      58 ..     266     321 ..     264     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.2e-06
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHH CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqtea 58 
                                       G  GaGK+t+a++++e l+e+ ++v +   p++ ++G  i ++     ++e+ +  
  gi|313127491|ref|YP_004037761.1| 266 GSPGAGKSTFAQAVAEFLNESDYAVKTMEKPRDLQVGPEITQYTALDGQMEKTADS 321
                                       778*********************999999************98867777766644 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.1e-06    0.0037       2      31 ..     262     291 ..     261     306 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.1e-06
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                       v+i+G+pG GK+T+ + v+e l++s++ v+
  gi|313127491|ref|YP_004037761.1| 262 VLISGSPGAGKSTFAQAVAEFLNESDYAVK 291
                                       78************************9997 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.3   2.3e-05     0.014       3      59 ..     463     520 ..     462     526 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHTECETEEEEEEECCS.CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2   3 peslaveikkagvskveIerta.nrviiviresqpgivIGkgGsnikkigkelrkdie 59 
                                       ++ +++ei++   ++v++e +  +++++ + e     vIGkgG +i  i+  l+ di+
  gi|313127491|ref|YP_004037761.1| 463 RQEIEREIRSIARGHVDVELQGqEKATVYVDEDDISYVIGKGGGRISDIEDRLGIDID 520
                                       678899996666666666654448999999*********************9998885 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.1     3e+03      16      38 ..      94     116 ..      92     141 .. 0.79
   2 !   14.1   0.0   6.5e-05     0.039       2      40 ..     262     297 ..     262     333 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.1
                            AAA_33  16 aerllkklgavllssdtlrrrlf 38 
                                       ++ +++++ a+ll+sd++   ++
  gi|313127491|ref|YP_004037761.1|  94 IRDIAEEHEATLLTSDQVQAEVA 116
                                       67788999999999999877665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.5e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg.t 40 
                                       vl+ G pG+GKst+a+ +++    +l +sd++ +++++ +
  gi|313127491|ref|YP_004037761.1| 262 VLISGSPGAGKSTFAQAVAE----FLNESDYAVKTMEKpR 297
                                       6789*************993....3334566666666652 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.1e-05     0.019      14      44 ..     257     287 ..     248     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqg 44 
                                       er   +l++G+pGAGKs+ a+++++ l++ +
  gi|313127491|ref|YP_004037761.1| 257 ERQRGVLISGSPGAGKSTFAQAVAEFLNESD 287
                                       5556699***************999886555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.1e-05     0.031      21      44 ..     259     281 ..     243     288 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-05
                            AAA_29  21 lkgatlltGpsGsGKSTllDAiqa 44 
                                       ++  +l++G  G+GKST+  A++ 
  gi|313127491|ref|YP_004037761.1| 259 QR-GVLISGSPGAGKSTFAQAVAE 281
                                       34.59************9988875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.4e-05     0.026      13      50 ..     254     291 ..     248     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                            AAA_30  13 lltsgdrvavltGpAGtGKttalkalreaweaaggrvi 50 
                                        l++++r +++ G +G+GK+t  +a++e ++++ + v 
  gi|313127491|ref|YP_004037761.1| 254 RLSERQRGVLISGSPGAGKSTFAQAVAEFLNESDYAVK 291
                                       567888899*********************99998875 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.7e-05     0.022       4      36 ..     262     294 ..     261     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvvid 36 
                                       v+++G P +GKst+a+ +a+ l+e++++v  ++
  gi|313127491|ref|YP_004037761.1| 262 VLISGSPGAGKSTFAQAVAEFLNESDYAVKTME 294
                                       89*************************998776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.4e-05     0.038       1      32 [.     262     289 ..     262     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.4e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdva 32 
                                       +l++G pG+GK+t+a+++++ l    n +d+a
  gi|313127491|ref|YP_004037761.1| 262 VLISGSPGAGKSTFAQAVAEFL----NESDYA 289
                                       79****************9976....444443 PP

>> FliMN_C  Type III flagellar switch regulator (C-ring) FliN C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.27   1.6e+02      15      66 ..     313     364 ..     308     369 .. 0.85
   2 ?   -1.8   0.0       5.3   3.2e+03      34      48 ..     481     493 ..     468     520 .. 0.52
   3 ?   10.6   0.1   0.00073      0.44      32      61 ..     557     586 ..     556     589 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.27
                                       EEEEEEHHHHHHHHTTSEEE--TTGGGCEEEEETTEEEEEEEEEEETTEEEE CS
                           FliMN_C  15 grtrltlrellnLkvGdvipLdkpadepvevyvngkpiarGelgvvggrlav 66 
                                       g+++ t   ll  +++ +i  + + +++ ev+++ ++ + G +gvv+  +a+
  gi|313127491|ref|YP_004037761.1| 313 GQMEKTADSLLLVRPDYTIYDEVRKTDDFEVFADMRLAGVGMVGVVHATRAI 364
                                       56666777777888888888888999********************998887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.3
                                       E--TTGGGCEEEEET CS
                           FliMN_C  34 pLdkpadepvevyvn 48 
                                       +L  + +e+ +vyv+
  gi|313127491|ref|YP_004037761.1| 481 EL--QGQEKATVYVD 493
                                       33..33356666665 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00073
                                       EEE--TTGGGCEEEEETTEEEEEEEEEEET CS
                           FliMN_C  32 vipLdkpadepvevyvngkpiarGelgvvg 61 
                                       v+++d +++e+vev+++g  ++++ +g+ g
  gi|313127491|ref|YP_004037761.1| 557 VVRMDDHVGETVEVRADGEYLFTATVGRGG 586
                                       7999***********************866 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.8e-05     0.023      26      68 ..     252     294 ..     240     322 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                             AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkldkekylsltin 68 
                                        + l ++++ vl+ G+ G GK++ ++ + + l++++y ++t++
  gi|313127491|ref|YP_004037761.1| 252 RDRLSERQRGVLISGSPGAGKSTFAQAVAEFLNESDYAVKTME 294
                                       5789999******************************999885 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.2e-05     0.037       3     121 ..       5     117 ..       3     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.2e-05
                                       E-HHHHHHHHTTSHHHHHHHHHHHTS...SEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                               PIN   3 lDTsvliallrgeekaeaarklleel...eelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpida 75 
                                        DTs++i   +g++  +     +e+     +++++++v+ El   ++    ++ e + el +l +l+++  +     
  gi|313127491|ref|YP_004037761.1|   5 PDTSAVI---DGRVSER-----VESGdaeTTVCVPEAVVGELESQANQgYDTGWEGLSELQRLTELADEGALTVEYV 73 
                                       5777777...4444332.....222223499*****************65566666677777777788888877788 PP

                                       HHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  76 eiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                       + + + +e    +  + +Dali   A+eh ++l+ t D   ++va+
  gi|313127491|ref|YP_004037761.1|  74 GRRTKPSEATGAH-EGDIDALIRDIAEEHEATLL-TSDQVQAEVAR 117
                                       8888888877777.8889****************.****9999985 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.4e-05      0.05       1      33 [.     261     294 ..     261     346 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-05
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE-- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqlt 33 
                                       +vl+ G pG gKs++a+ +a++l ++ + ++ + 
  gi|313127491|ref|YP_004037761.1| 261 GVLISGSPGAGKSTFAQAVAEFLnESDYAVKTME 294
                                       5899*******************64444444443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     9e-05     0.054       1      23 [.     262     284 ..     262     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-05
                                       EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelg 23 
                                       vl++G pG GK+++a+ava+ l+
  gi|313127491|ref|YP_004037761.1| 262 VLISGSPGAGKSTFAQAVAEFLN 284
                                       799****************9876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     9e-05     0.054       1      29 [.     264     292 ..     264     294 .. 0.89
   2 ?   -2.2   0.0       4.9   2.9e+03      55      97 ..     294     333 ..     289     333 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvav 29 
                                       + G +G+GK+tf +a++e+l+++ + v++
  gi|313127491|ref|YP_004037761.1| 264 ISGSPGAGKSTFAQAVAEFLNESDYAVKT 292
                                       579*******************9887765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.9
                        ATP_bind_1  55 dvmedlglgpngalvvaleflresldwldeelekeeddyllfD 97 
                                       +   dl++gp  +  +al+  +e+    +++l   + dy ++D
  gi|313127491|ref|YP_004037761.1| 294 EKPRDLQVGPEITQYTALDGQMEKT---ADSLLLVRPDYTIYD 333
                                       44456999*********99766666...444423356777776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.9e-05     0.053      44      85 ..     256     297 ..     236     340 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrved 85 
                                        e++ ++++ G +G+GKs +a a++    +++++v  +  ++
  gi|313127491|ref|YP_004037761.1| 256 SERQRGVLISGSPGAGKSTFAQAVAEFLNESDYAVKTMEKPR 297
                                       578899********************9999999998766543 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013      0.08       4      35 ..     258     289 ..     253     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeaka 35 
                                       +++ +++ G +G+GK+t ++ ++e l+e  +a
  gi|313127491|ref|YP_004037761.1| 258 RQRGVLISGSPGAGKSTFAQAVAEFLNESDYA 289
                                       577789*******************9876554 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00025      0.15       2     128 ..       4     124 ..       3     127 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                             PIN_4   2 VlDTnvlLhdpealksf...keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsae 75 
                                       V DT+ +++   + +++   + e+ v++P  V+ EL+++ ++   ++  +  ++ +r l el  +  g l+v+ +  
  gi|313127491|ref|YP_004037761.1|   4 VPDTSAVIDGR-VSERVesgDAETTVCVPEAVVGELESQANQGY-DTGWEGLSELQR-LTELADE--GALTVEYVGR 75 
                                       88999999765.3455555699*****************99998.333333344444.4455554..4444455544 PP

                             PIN_4  76 elpeeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgieae 128
                                       + +++e +    +  I a    ++ee+   + +L++ D+     A+a+gi++e
  gi|313127491|ref|YP_004037761.1|  76 RTKPSE-ATGAHEGDIDALIRDIAEEH---EATLLTSDQVQAEVARAKGIDVE 124
                                       445432.22456666667777777776...67899999999999999999876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015     0.091       3      29 ..     262     288 ..     260     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegkl 29 
                                       v++ G +G GK+t++q +a+ + e+++
  gi|313127491|ref|YP_004037761.1| 262 VLISGSPGAGKSTFAQAVAEFLNESDY 288
                                       89*****************99988875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019      0.11       9      45 ..     246     285 ..     239     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                                       HHHHHHHHCH...TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE   9 algkklakal...gdvilLeGdLGaGKTtlvrglakalgv 45 
                                       +++ +l + l   ++ +l++G  GaGK+t+++++a+ l+ 
  gi|313127491|ref|YP_004037761.1| 246 EFADELRDRLserQRGVLISGSPGAGKSTFAQAVAEFLNE 285
                                       5667776666544556*******************98865 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0002      0.12       4      82 ..     261     344 ..     258     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelileklke....ekktylflDE 72 
                                        ++i+G   +GK+t+++ ++ e l +++++   +++++rd +   pe    + l+  +ek  +     +  y + DE
  gi|313127491|ref|YP_004037761.1| 261 GVLISGSPGAGKSTFAQAVA-EFL-NESDYAVKTMEKPRDLQVG-PEitqyTALDGQMEKTADslllVRPDYTIYDE 334
                                       5899***********87776.666.7999***********6654.22122334444444422257777899****** PP

                            AAA_14  73 iqevpeweka 82 
                                       + + +++e +
  gi|313127491|ref|YP_004037761.1| 335 VRKTDDFEVF 344
                                       ****999865 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00027      0.16       5      36 ..     262     293 ..     258     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                        APS_kinase   5 vwltGlsgsGKstianalekkLvekgisvylL 36 
                                       v+++G  g+GKst a+a+++ L+e+ ++v+++
  gi|313127491|ref|YP_004037761.1| 262 VLISGSPGAGKSTFAQAVAEFLNESDYAVKTM 293
                                       789*********************99988765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.23      17      49 ..     254     286 ..     243     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                                       HHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTT CS
                   Sigma54_activat  17 kvaktdlsvlitGesGtGKellaraiheaskrk 49 
                                       ++ + +  vli G  G+GK+++a+a+ e  +++
  gi|313127491|ref|YP_004037761.1| 254 RLSERQRGVLISGSPGAGKSTFAQAVAEFLNES 286
                                       56677889*****************98865554 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00049      0.29      33      60 ..     259     286 ..     240     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvk 60 
                                          vl++G+PG Gk+t+a+ +a+ l+ +
  gi|313127491|ref|YP_004037761.1| 259 QRGVLISGSPGAGKSTFAQAVAEFLNES 286
                                       5569******************877654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00056      0.33      13      43 ..     261     291 ..     254     385 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00056
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeil 43 
                                        v i G+ GaGKSt+++++a+ l+     ++
  gi|313127491|ref|YP_004037761.1| 261 GVLISGSPGAGKSTFAQAVAEFLNESDYAVK 291
                                       57899**************999887665554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00064      0.38       1      25 [.     262     285 ..     262     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00064
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkk 25 
                                       ++++G++g GKSt+a+ +a+ l  +
  gi|313127491|ref|YP_004037761.1| 262 VLISGSPGAGKSTFAQAVAEFLN-E 285
                                       6799*************555444.3 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       7.6   4.6e+03      49      60 ..     362     373 ..     362     374 .. 0.81
   2 ?   10.7   0.6   0.00063      0.38      17      50 ..     477     507 ..     463     511 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.6
                              KH_4  49 rtldAlqylvsa 60 
                                       r +dAlq lv +
  gi|313127491|ref|YP_004037761.1| 362 RAIDALQRLVGR 373
                                       569****99976 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00063
                              KH_4  17 evevteeeeeeeveielnvegedlGrvIGkrGrt 50 
                                        v+v+++    +++ +++v+++d+  vIGk G  
  gi|313127491|ref|YP_004037761.1| 477 HVDVELQ---GQEKATVYVDEDDISYVIGKGGGR 507
                                       5666665...567899***************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.72u 0.26s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 3983.20
//
Query:       gi|313127492|ref|YP_004037762.1|  [L=549]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-41  140.7  52.6    8.9e-40  136.3  26.1    4.0  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    4.2e-15   55.9  14.4    4.9e-13   49.2   0.1    6.0  6  HAMP             HAMP domain
    4.7e-06   26.8  36.5    0.00049   20.3   5.4    6.6  6  DUF948           Bacterial protein of unknown function (DUF94
    6.7e-05   23.2   0.2          2    8.8   0.0    4.9  4  Syntaxin_2       Syntaxin-like protein
    0.00064   19.7  27.1      0.039   14.0   3.9    5.5  6  DUF1664          Protein of unknown function (DUF1664)
    0.00065   19.7  32.6       0.26   11.3   2.2    4.9  5  Laminin_II       Laminin Domain II
      0.002   18.4  23.0       0.51   10.7   0.9    4.9  4  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0055   17.2  12.0        3.8    8.0   0.6    4.5  4  DUF16            Protein of unknown function DUF16
     0.0058   16.4   3.5        9.6    6.1   0.0    5.5  6  DASH_Dam1        DASH complex subunit Dam1
  ------ inclusion threshold ------
      0.019   15.4  18.5      0.027   15.0   2.9    4.7  5  Spectrin         Spectrin repeat
      0.024   15.0   9.0        7.2    7.1   0.3    4.6  4  Snapin_Pallidin  Snapin/Pallidin
      0.025   14.8  24.0      0.026   14.7   0.8    4.6  5  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.032   14.8  26.4      0.034   14.7  10.6    4.0  3  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.033   14.2   5.2        2.2    8.4   0.0    4.9  4  HisKA            His Kinase A (phospho-acceptor) domain
       0.04   14.6   0.7       0.04   14.6   0.7    3.8  4  SnoaL_2          SnoaL-like domain
      0.042   13.7   9.3      0.075   12.9   4.0    2.5  2  SKA1             Spindle and kinetochore-associated protein 1
      0.046   12.7  13.7          1    8.3   0.4    2.7  2  IFT57            Intra-flagellar transport protein 57
       0.14   12.4  15.6        4.1    7.6   1.1    4.3  4  Fib_alpha        Fibrinogen alpha/beta chain family
       0.19   11.2  14.6        1.3    8.4   0.9    2.5  2  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.41   11.0   4.3        3.3    8.1   0.1    4.1  4  GAT              GAT domain
       0.51   10.7   2.0          1    9.8   0.1    2.6  1  DASH_Hsk3        DASH complex subunit Hsk3 like
       0.54    9.5  10.3       0.67    9.1   0.2    2.9  2  TMPIT            TMPIT-like protein
       0.55    9.7   6.7        5.5    6.5   0.2    2.7  2  TBK1_CCD1        TANK-binding kinase 1 coiled-coil domain 1
       0.85    9.4  19.6      0.042   13.7   5.6    3.7  4  Phage_GP20       Phage minor structural protein GP20
        1.6    8.0  18.0       0.94    8.7   5.7    3.8  4  CorA             CorA-like Mg2+ transporter protein
        1.6    7.8  11.1       0.37    9.9   2.0    3.2  3  BAR_2            Bin/amphiphysin/Rvs domain for vesicular tra
        1.7    9.1  24.4         10    6.7   0.8    5.9  6  NPV_P10          Nucleopolyhedrovirus P10 protein
        2.1    8.0  27.0      0.088   12.5   2.1    4.2  3  YkyA             Putative cell-wall binding lipoprotein
        2.1    9.1  26.6        5.7    7.7   1.2    4.9  5  DUF2203          Uncharacterized conserved protein (DUF2203)
        2.2    8.2   5.4        2.5    8.0   0.7    3.1  2  STAT_alpha       STAT protein, all-alpha domain
        2.6    8.1  18.8        1.7    8.7   2.3    4.1  5  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
        3.4    7.6  19.8      0.059   13.3   3.1    4.4  4  Ferritin         Ferritin-like domain
        5.1    4.9  17.5       0.94    7.3   1.8    2.5  3  V_ATPase_I       V-type ATPase 116kDa subunit family
        6.1    6.0  21.2         11    5.2   1.6    3.3  3  HAP1_N           HAP1 N-terminal conserved region
        6.2    4.5  12.9        2.4    5.8   0.3    2.5  3  Nup88            Nuclear pore component
        6.3    5.6  28.4        1.5    7.6   1.9    3.4  4  Spc7             Spc7 kinetochore protein
        6.4    6.9   7.9         20    5.3   0.2    3.4  2  Exonuc_VII_S     Exonuclease VII small subunit
          8    6.6  17.2       0.74    9.9   0.4    4.4  4  Mating_N         Mating-type protein beta 1


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   2.8    0.0071       3.4     105     170 ..     193     258 ..     159     260 .. 0.74
   2 !   10.6  12.0   0.00075      0.36      83     159 ..     227     303 ..     208     310 .. 0.54
   3 !  136.3  26.1   1.9e-42   8.9e-40       2     171 ..     314     483 ..     313     484 .. 0.97
   4 ?    1.7   0.3      0.43     2e+02       5      39 ..     492     526 ..     486     547 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0071
                                       .....HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 105 svesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevak 170
                                       ++  +ee+  + e  +e +++ +e ++e+++++aev++   e+++ s+e  +sie  n+a  +va+
  gi|313127492|ref|YP_004037762.1| 193 ALLPVEEVGGENERYVEVARSYNEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVAS 258
                                       33457888888889999999999999999999*****999****9999999999999999887765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00075
                                       HHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  83 rsaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasie 159
                                       + +  a e++++  e q  i+++ e+   + + v+e s+ ++e +e l++++++ + ++++v+eiaa++e+ + ++e
  gi|313127492|ref|YP_004037762.1| 227 EVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTVE 303
                                       23334445555555555555555555555555555555555556666666666666666666666666666666665 PP

  == domain 3  score: 136.3 bits;  conditional E-value: 1.9e-42
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHH CS
                         MCPsignal   2 dlaeeaseeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVr 78 
                                       d+a+ea +e +  + +++++ +++ ++ ++ +ei +i e id+++ QT lLA+NAaiEAA AGe+G+GF VVA+EV+
  gi|313127492|ref|YP_004037762.1| 314 DVATEAMDELDVVESQIDETASAVVALGERIEEIDEIAEFIDDVGSQTDLLAINAAIEAAHAGEAGDGFGVVAEEVK 390
                                       667778888888899************************************************************** PP

                                       HHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  79 kLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                       +LAe++ ++a e++ali+++++ ++++++++ et+++v+e++e+ve++ e+++ iv+av++v+++v+e++ a+++q+
  gi|313127492|ref|YP_004037762.1| 391 ALAEETRESADEVSALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEATDQQA 467
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHH CS
                         MCPsignal 156 asieevnqaveevakv 171
                                       +s+++v+  v+eva++
  gi|313127492|ref|YP_004037762.1| 468 SSSQDVAAHVDEVANI 483
                                       ************9987 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal   5 eeaseeAeeggkevanvvkqmeeieksskeisdii 39 
                                       ++a++ A+++ + v+++ +++++++++++ +++++
  gi|313127492|ref|YP_004037762.1| 492 DSAEDAATRQAESVDDIADRTRTLSERAAALERLV 526
                                       45666677777777777777777777777777665 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1     1e-15   4.9e-13       2      52 ..      76     127 ..      75     128 .. 0.95
   2 ?    0.0   0.0       2.5   1.2e+03      10      31 ..     126     147 ..     126     163 .. 0.73
   3 !    8.0   0.1     0.008       3.8      10      33 ..     176     200 ..     169     203 .. 0.76
   4 ?   -0.6   0.0       3.8   1.8e+03      39      52 ..     209     222 ..     209     223 .. 0.88
   5 ?    3.2   0.3      0.25   1.2e+02      13      50 ..     256     294 ..     254     297 .. 0.74
   6 ?   -1.9   0.2       9.6   4.5e+03      32      42 ..     398     408 ..     385     413 .. 0.60

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1e-15
                                       HHHTTHHHHHHHHHHHHHHTTTBTSSTCCT.TSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   2 larrilrPLrrLaraarriaaGdldtrlpv.sgrDEiGeLarafNaMldrLr 52 
                                       + r ++rPL+rL+++a ++aaGdl+t++p  +g+DEi++L + f++M+ +L+
  gi|313127492|ref|YP_004037762.1|  76 VRRDVVRPLERLSDSASAVAAGDLSTPPPSvEGDDEIARLTADFEDMHAHLQ 127
                                       67889**********************9998******************998 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHTTTBTSSTCCT CS
                              HAMP  10 LrrLaraarriaaGdldtrlpv 31 
                                       L+ ++++a ++a+ ++d ++ +
  gi|313127492|ref|YP_004037762.1| 126 LQTVSEQATALADREFDDPVLD 147
                                       56789999****9988888433 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.008
                                       HHHHHHHHHHHTTTBTSSTCCT.TS CS
                              HAMP  10 LrrLaraarriaaGdldtrlpv.sg 33 
                                       +   a+a++r aaGdl++ lpv + 
  gi|313127492|ref|YP_004037762.1| 176 VDAFAEATERAAAGDLTALLPVeEV 200
                                       55678999************99555 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHH CS
                              HAMP  39 eLarafNaMldrLr 52 
                                       e+ar++N+++++L 
  gi|313127492|ref|YP_004037762.1| 209 EVARSYNEFVRELS 222
                                       68********9985 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.25
                                       HHHHHHHHTTT......BTSSTCCTTSSSHHHHHHHHHHHHHHH CS
                              HAMP  13 LaraarriaaG......dldtrlpvsgrDEiGeLarafNaMldr 50 
                                       +a+a+ +i++G      +l t       DE+ +L +++++ + +
  gi|313127492|ref|YP_004037762.1| 256 VASAVSEISDGadeqteHLQT-----VADELSTLSATVEEIAAS 294
                                       688999999996555544444.....58******9999887665 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 9.6
                                       TSSSHHHHHHH CS
                              HAMP  32 sgrDEiGeLar 42 
                                       ++ DE+ +L++
  gi|313127492|ref|YP_004037762.1| 398 ESADEVSALIE 408
                                       35699988876 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2       1.1   5.3e+02      58      80 ..     156     182 ..      60     188 .. 0.58
   2 !   14.2   2.2   8.4e-05      0.04      22      87 ..     212     291 ..     204     293 .. 0.79
   3 ?    3.4   4.0       0.2        94      48      84 ..     266     302 ..     259     365 .. 0.63
   4 ?    0.9   0.0       1.1   5.4e+02      26      56 ..     345     375 ..     333     396 .. 0.71
   5 !   20.3   5.4     1e-06   0.00049      24      88 ..     396     460 ..     384     461 .. 0.92
   6 ?    6.0   2.5     0.031        15      25      87 ..     460     522 ..     457     524 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.1
                            DUF948  58 e....lledvneklekvdplteavadl 80 
                                       +    ++ d+  ++ ++++l++a+a++
  gi|313127492|ref|YP_004037762.1| 156 DaldrMAVDLAAHTRNLQRLVDAFAEA 182
                                       033335555555555555555555555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.4e-05
                            DUF948  22 lklkktldeaaatieele...kqvdpilkevedllakvne...........lledvneklekvdplteavadlgesv 84 
                                       ++ ++ ++e+++ti+e++    +v  +++e+++ ++ +ne           + ++  e++e+++++ +++ +l+++v
  gi|313127492|ref|YP_004037762.1| 212 RSYNEFVRELSSTIAEVQsfaAEVSTMSDEAQTSIERANEasgavasavseISDGADEQTEHLQTVADELSTLSATV 288
                                       55567788888888888877789999999999999999998888777777777777778888888888888888888 PP

                            DUF948  85 sel 87 
                                       +e+
  gi|313127492|ref|YP_004037762.1| 289 EEI 291
                                       776 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.2
                            DUF948  48 evedllakvnelledvneklekvdplteavadlgesv 84 
                                        +++ +++ ++++++++  +++v+++ ++++d++ +v
  gi|313127492|ref|YP_004037762.1| 266 GADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTV 302
                                       3333333333333333333333333333333333333 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.1
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakv 56 
                                       + +de+a++i+++++q+d +  +++   a++
  gi|313127492|ref|YP_004037762.1| 345 EEIDEIAEFIDDVGSQTDLLAINAAIEAAHA 375
                                       4578999999999999998877766555555 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 1e-06
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                        ++ +de++a ie+++++ +++l  v+++ ++v e +e v+  +e+ +++++av+d+ +sv+e++
  gi|313127492|ref|YP_004037762.1| 396 TRESADEVSALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVS 460
                                       577899*******************************************************9986 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.031
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       ++  d+ a++ +++  +vd++ + +e++ a +    +  +++ e+vd + +  ++l+e  ++l
  gi|313127492|ref|YP_004037762.1| 460 SEATDQQASSSQDVAAHVDEVANISEETAARTDSAEDAATRQAESVDDIADRTRTLSERAAAL 522
                                       4555666677777777777777777777777777777778899******99999999988877 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.48   2.2e+02      73      95 ..     113     135 ..     105     139 .. 0.90
   2 ?    3.4   0.0      0.21     1e+02      27      71 ..     234     278 ..     208     308 .. 0.66
   3 !    8.8   0.0    0.0042         2      12      93 ..     347     449 ..     342     456 .. 0.80
   4 ?    2.8   0.1      0.31   1.5e+02       5      79 ..     449     529 ..     429     533 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.48
                        Syntaxin_2  73 ekLkkdfkealqeFqkiqrqyae 95 
                                       ++L+ df++ + ++q + +q++ 
  gi|313127492|ref|YP_004037762.1| 113 ARLTADFEDMHAHLQTVSEQATA 135
                                       69***************999875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.21
                        Syntaxin_2  27 dteelreklhelieeinelikktnellkklsqldnsssdsqqklq 71 
                                       +   + ++++++ie++ne + ++ + ++++s  ++ +  + q ++
  gi|313127492|ref|YP_004037762.1| 234 EVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVA 278
                                       344556777777777777777777777777777776665555443 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0042
                        Syntaxin_2  12 vstleklvkqLgtkkdteelr...................eklhelieeinelikktnellkklsqldnsssds..q 67 
                                       + ++ ++++++g+++d   ++                   e+++ l ee++e + ++++l++++++ ++ ++     
  gi|313127492|ref|YP_004037762.1| 347 IDEIAEFIDDVGSQTDLLAINaaieaahageagdgfgvvaEEVKALAEETRESADEVSALIEDVTERSEETLATvrE 423
                                       677888888888888866666777788888888888888899***********************998888877654 PP

                        Syntaxin_2  68 qklqkekLkkdfkealqeFqkiqrqy 93 
                                        + q +  ++ +++a++eF+ i+  +
  gi|313127492|ref|YP_004037762.1| 424 TNRQVAESVETVETAIEEFEAIVAAV 449
                                       44488888889999999998887665 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.31
                        Syntaxin_2   5 lqkinsnvstleklvkq.Lgtkkd.......teelreklhelieeinelikktnellkklsqldnsssdsqqklqke 73 
                                       +  +n++v++  + ++q  ++++d         ++ e+    ++++ + +++  e++ +++  ++++s   +  + e
  gi|313127492|ref|YP_004037762.1| 449 VEDVNTSVREVSEATDQqASSSQDvaahvdeVANISEETAARTDSAEDAATRQAESVDDIADRTRTLS--ERAAALE 523
                                       55667777777777776444556633332223333333333333333333333333333333333332..4555677 PP

                        Syntaxin_2  74 kLkkdf 79 
                                       +L+ +f
  gi|313127492|ref|YP_004037762.1| 524 RLVGSF 529
                                       776666 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.5   1.7e+03      87     113 ..     110     136 ..     105     139 .. 0.68
   2 ?    1.5   0.0      0.59   2.8e+02      47     121 ..     155     229 ..     152     231 .. 0.84
   3 !   11.2   1.6   0.00062      0.29      37     112 ..     229     304 ..     221     310 .. 0.75
   4 ?    2.2   0.5      0.36   1.7e+02      90     121 ..     317     348 ..     296     362 .. 0.62
   5 !   14.0   3.9   8.4e-05     0.039      45     121 ..     384     460 ..     379     463 .. 0.93
   6 ?    4.1   0.7     0.094        44      64     121 ..     466     523 ..     457     530 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.5
                           DUF1664  87 eevtevredlseigedvesvkeavegl 113
                                       +e++++  d ++++  +++v+e  + l
  gi|313127492|ref|YP_004037762.1| 110 DEIARLTADFEDMHAHLQTVSEQATAL 136
                                       667777777777777777777766655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.59
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +  l+++  +laa  r+L++ +d   +  +  ++        v+ev ++ ++  e  +s +e v++l s++++++
  gi|313127492|ref|YP_004037762.1| 155 GDALDRMAVDLAAHTRNLQRLVDAFAEATERAAAGDLTALLPVEEVGGENERYVEVARSYNEFVRELSSTIAEVQ 229
                                       667888888999999999999999999998888888888888999999999999999999999999999998876 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00062
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                       +s++  v+++s + ++  e  +++    +s + ++ +  deq+e  + +++e+++++  ++ei    e v  +ve+
  gi|313127492|ref|YP_004037762.1| 229 QSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTVET 304
                                       4555566666666666666667777788888888888888888888888888888888888888888888888876 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.36
                           DUF1664  90 tevredlseigedvesvkeaveglesklerie 121
                                       te+ ++l+ +++++++  +av  l++++e+i+
  gi|313127492|ref|YP_004037762.1| 317 TEAMDELDVVESQIDETASAVVALGERIEEID 348
                                       45555555555555555555555555555554 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 8.4e-05
                           DUF1664  45 svskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                        v+++++ + e+ ++  ++ s+ i+ v ++ +e+ ++ +e++++v+e  e +++  e++e++ +ave++++++++++
  gi|313127492|ref|YP_004037762.1| 384 VVAEEVKALAEETRESADEVSALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVS 460
                                       6888999999999***********************************************************99986 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.094
                           DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                        +s  + v +++de+++is+e+++  +++++  ++  e v+ + +  ++l ++ + +e
  gi|313127492|ref|YP_004037762.1| 466 QASSSQDVAAHVDEVANISEETAARTDSAEDAATRQAESVDDIADRTRTLSERAAALE 523
                                       4455567777888888888888888888888888888888888887777777766665 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         6   2.8e+03      14      38 ..     114     138 ..     107     146 .. 0.63
   2 !    9.5   1.4     0.002      0.96       2      71 ..     215     281 ..     204     281 .. 0.88
   3 !   11.3   2.2   0.00055      0.26       4      97 ..     259     349 ..     253     360 .. 0.78
   4 !    9.7   5.0    0.0018      0.84       1      66 [.     389     454 ..     389     457 .. 0.86
   5 !    9.4   5.1    0.0021         1       9      85 ..     446     522 ..     439     542 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6
                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  14 evleqlaplsqnlentkeklseinr 38 
                                          ++ +++++ l+ ++e++  +++
  gi|313127492|ref|YP_004037762.1| 114 RLTADFEDMHAHLQTVSEQATALAD 138
                                       4445566666666666666666554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       +e+++e ++t++ev++  a++s+  ++ + +++++n+      +++++ +++ + A ++  +L+ +a++L
  gi|313127492|ref|YP_004037762.1| 215 NEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEA---SGAVASAVSEISDGADEQTEHLQTVADEL 281
                                       68999999999999999999999999999999999999...77778888888888999999999888876 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00055
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                        ++e+++ a e  e l+ ++ +l+ +++ ++ei++s+e +   v+ a +  rd r+   +   +++++++++ e   
  gi|313127492|ref|YP_004037762.1| 259 AVSEISDGADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTVETAAERGRDGRDVATEAMDELDVVESQIDETAS 335
                                       57788888888888888888999999999999999988888889988888888888888888888888888555555 PP

                                       HHHH...HHHHHHHHHH CS
                        Laminin_II  81 leeassslsdniseike 97 
                                         +a   l++ i+ei e
  gi|313127492|ref|YP_004037762.1| 336 AVVA---LGERIEEIDE 349
                                       5555...8888887765 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-- CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLek 66 
                                       +k+la+e  e+a ev + ++++ ++ e+t + + e nr+v+e  e v+ a +  +    +v +++ 
  gi|313127492|ref|YP_004037762.1| 389 VKALAEETRESADEVSALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNT 454
                                       599**************************************9999999777776666666666664 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0021
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                          ++ v   + ++s+ +++  ++ + ++++v+e+ +  ++    +++A+++     + ++++ d+ ++l ++  a 
  gi|313127492|ref|YP_004037762.1| 446 VAAVEDVNTSVREVSEATDQQASSSQDVAAHVDEVANISEETAARTDSAEDAATRQAESVDDIADRTRTLSERAAAL 522
                                       4567788899999999999999999***********9999*****************************99998873 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.9    0.0011      0.51       9      76 ..     230     297 ..     222     307 .. 0.60
   2 ?    4.8   0.3     0.072        34      48      85 ..     318     355 ..     301     362 .. 0.61
   3 ?    7.5   3.4     0.011       5.1      12      81 ..     394     463 ..     384     475 .. 0.65
   4 ?    7.3   0.3     0.012       5.7      40      91 ..     478     529 ..     465     531 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                           BLOC1_2   9 kyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvte 76 
                                       ++  +  +++ e    +e+ Nea+ +   +++++ +++ ++ e+l+   +el+ +   +++i ++ ++
  gi|313127492|ref|YP_004037762.1| 230 SFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADELSTLSATVEEIAASAED 297
                                       44444445555555666666666666666666666666666666666666666666666666666555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.072
                           BLOC1_2  48 kkleklnekyeelqpylqqidqiekqvteLeeavseLD 85 
                                       + +++l+  + ++++  + + ++ ++++e+ e+++ +D
  gi|313127492|ref|YP_004037762.1| 318 EAMDELDVVESQIDETASAVVALGERIEEIDEIAEFID 355
                                       33444444444666666666666666666666666666 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.011
                           BLOC1_2  12 eaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                       e++ e++ e   l+e + e+++e  + +++   ++++++e ++   ee++  +  +++++++v+e  ea 
  gi|313127492|ref|YP_004037762.1| 394 EETRESADEVSALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEAT 463
                                       3333444444456677777777777777777777777777777777777777777777777777766665 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.012
                           BLOC1_2  40 kdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                       ++va+  e+++ ++++ +++   + +++d+i +++++L e +++L+  + + 
  gi|313127492|ref|YP_004037762.1| 478 DEVANISEETAARTDSAEDAATRQAESVDDIADRTRTLSERAAALERLVGSF 529
                                       34444445555666666679999**********************9988765 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.021       9.8      16      95 ..     204     291 ..     198     298 .. 0.80
   2 ?    4.1   0.1      0.14        66      41      69 ..     321     349 ..     312     365 .. 0.73
   3 !    8.0   0.6    0.0081       3.8      25     102 ..     350     435 ..     346     443 .. 0.59
   4 ?    7.0   1.6     0.017       8.2      32     103 ..     424     495 ..     421     496 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.021
                                       XTTB-.BHHHHHHB-.....BHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......H CS
                             DUF16  16 kteYV.Trkqlnefkds...nkqrLkkieakvd....klgeqinkleqkvekqgekikelkveqkaqgeelnkvdet 84 
                                       +++YV   + +nef  +   + ++++ + a+v+      + +i++ +++  +    ++e++   + q e+l++v + 
  gi|313127492|ref|YP_004037762.1| 204 NERYVeVARSYNEFVRElssTIAEVQSFAAEVStmsdEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADE 280
                                       677883468899999875556667777777776655566778888999999999999999************99999 PP

                                       HHHHHHHHHHH CS
                             DUF16  85 leliletLqki 95 
                                       l  +  t+++i
  gi|313127492|ref|YP_004037762.1| 281 LSTLSATVEEI 291
                                       99999998877 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
                                       HHHH...HHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  41 akvdklgeqinkleqkvekqgekikelkv 69 
                                       +++d+ + qi++ + +v ++ge+i+e+ +
  gi|313127492|ref|YP_004037762.1| 321 DELDVVESQIDETASAVVALGERIEEIDE 349
                                       56777888888888888888888876654 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0081
                                       HHHB-....BHHHHHHHHHHHH........HHHHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHH CS
                             DUF16  25 lnefkds..nkqrLkkieakvd.....klgeqinkleqkvekqgekikelkveqkaqgeeln.kvdetleliletLq 93 
                                       + ef d+   +++L  i+a ++       g  + +++++v+++ e+ +e   e+ a  e++  + +etl  + et  
  gi|313127492|ref|YP_004037762.1| 350 IAEFIDDvgSQTDLLAINAAIEaahagEAGDGFGVVAEEVKALAEETRESADEVSALIEDVTeRSEETLATVRETNR 426
                                       56788888888999999999998888844455555555555555555555555555555554444444444444444 PP

                                       HHHHHHHHH CS
                             DUF16  94 kinkRlDsi 102
                                       ++ + +  +
  gi|313127492|ref|YP_004037762.1| 427 QVAESVETV 435
                                       433333333 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.017
                                       BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                             DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                       ++ ++ ++ ++v++  e+++++  +ve  +  ++e ++  ++q  + + v   ++ ++++ +++  R Ds e
  gi|313127492|ref|YP_004037762.1| 424 TNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEATDQQASSSQDVAAHVDEVANISEETAARTDSAE 495
                                       7778888889999999*****************************99*999999999999999999999876 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.1   5.4e+02      10      30 ..     110     130 ..     109     139 .. 0.50
   2 ?   -2.2   0.0       8.1   3.8e+03      14      28 ..     164     178 ..     156     184 .. 0.60
   3 ?    3.6   0.0      0.12        58       3      28 ..     272     297 ..     270     302 .. 0.84
   4 ?   -1.5   0.0       4.7   2.2e+03       3      31 ..     328     356 ..     326     358 .. 0.81
   5 ?    6.1   0.0      0.02       9.6       7      36 ..     427     456 ..     422     457 .. 0.93
   6 ?   -0.2   0.0       1.9   8.9e+02       4      25 ..     504     525 ..     501     530 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.1
                         DASH_Dam1  10 DsletLdknledLqqihesLs 30 
                                       D+++ L++ +ed++   +++s
  gi|313127492|ref|YP_004037762.1| 110 DEIARLTADFEDMHAHLQTVS 130
                                       555555555555544333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.1
                         DASH_Dam1  14 tLdknledLqqihes 28 
                                       +L +++++Lq++ ++
  gi|313127492|ref|YP_004037762.1| 164 DLAAHTRNLQRLVDA 178
                                       566666666666554 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.12
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihes 28 
                                       + ++  aD+l+tL++ +e++    e+
  gi|313127492|ref|YP_004037762.1| 272 EHLQTVADELSTLSATVEEIAASAED 297
                                       678999***********999876665 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.7
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLsd 31 
                                        ++ e a ++ +L +++e++++i e ++d
  gi|313127492|ref|YP_004037762.1| 328 SQIDETASAVVALGERIEEIDEIAEFIDD 356
                                       67788888999999999999999887765 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.02
                         DASH_Dam1   7 eLaDsletLdknledLqqihesLsdfNeSF 36 
                                       + a+s+et+++ +e+++ i  +++d+N S+
  gi|313127492|ref|YP_004037762.1| 427 QVAESVETVETAIEEFEAIVAAVEDVNTSV 456
                                       789************************995 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 1.9
                         DASH_Dam1   4 afaeLaDsletLdknledLqqi 25 
                                       +  ++aD  +tL+++   L+++
  gi|313127492|ref|YP_004037762.1| 504 SVDDIADRTRTLSERAAALERL 525
                                       4556677777777666666554 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.56   2.7e+02      45      73 ..     114     142 ..     109     178 .. 0.76
   2 ?    2.2   0.3      0.54   2.5e+02      30      97 ..     218     286 ..     208     291 .. 0.71
   3 ?    1.9   0.2      0.68   3.2e+02      38      68 ..     269     299 ..     264     325 .. 0.63
   4 ?    4.3   0.3      0.12        57      12     100 ..     339     425 ..     328     430 .. 0.81
   5 ?   15.0   2.9   5.7e-05     0.027       5      98 ..     427     521 ..     425     526 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTHT CS
                          Spectrin  45 aleaelaaqqervkalnelaeklldeghs 73 
                                       +l a+++++  +++++ e+a++l+d++ +
  gi|313127492|ref|YP_004037762.1| 114 RLTADFEDMHAHLQTVSEQATALADREFD 142
                                       67789999999999999999999887533 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.54
                                       SSSHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  30 gkdleevqallkkhkaleaelaa.qqervkalnelaeklldeghsaseeieerleelnerWeeLkelaa 97 
                                        ++l+++ a ++ + a   ++++ +q+ +++ ne + +++++  + s+   e++e+l++  +eL++l a
  gi|313127492|ref|YP_004037762.1| 218 VRELSSTIAEVQSFAAEVSTMSDeAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADELSTLSA 286
                                       555555566666666666666666788888888888888888888888888888888888888887766 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.68
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  38 allkkhkaleaelaaqqervkalnelaekll 68 
                                       ++ + ++++ +el++    v+++ + ae+++
  gi|313127492|ref|YP_004037762.1| 269 EQTEHLQTVADELSTLSATVEEIAASAEDVA 299
                                       4555666666666666666666666666663 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHH CS
                          Spectrin  12 eleeWieekeellssedlgkdleevqallkkhkaleaelaa.qqervkalnelaeklldeghsaseeieerleelne 87 
                                       +l e iee++e++   ++  d+ +  +ll    a+ea  a  + + +  + e  ++l++e  ++++e+++ +e+++e
  gi|313127492|ref|YP_004037762.1| 339 ALGERIEEIDEIA---EFIDDVGSQTDLLAINAAIEAAHAGeAGDGFGVVAEEVKALAEETRESADEVSALIEDVTE 412
                                       6677788888888...7779999999999999999999888788999999999999999999999999999999999 PP

                                       HHHHHHHHHHHHH CS
                          Spectrin  88 rWeeLkelaaerk 100
                                       r ee ++++ e+ 
  gi|313127492|ref|YP_004037762.1| 413 RSEETLATVRETN 425
                                       9887776666655 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 5.7e-05
                                       HHHHHHHHHHHHHHHHHHHH.CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHH CS
                          Spectrin   5 qfaqdadeleeWieekeell.ssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeiee 80 
                                       q a+ ++ +e  iee e+++ + ed+  ++ ev +  ++     +++aa+ ++v ++ e   + +d+ ++a+ +  e
  gi|313127492|ref|YP_004037762.1| 427 QVAESVETVETAIEEFEAIVaAVEDVNTSVREVSEATDQQASSSQDVAAHVDEVANISEETAARTDSAEDAATRQAE 503
                                       5677889999**********555666*************************************************** PP

                                       HHHHHHHHHHHHHHHHHH CS
                          Spectrin  81 rleelnerWeeLkelaae 98 
                                       +++++ +r + L+e+aa+
  gi|313127492|ref|YP_004037762.1| 504 SVDDIADRTRTLSERAAA 521
                                       ************999986 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.35   1.7e+02      47      87 ..     211     250 ..     198     252 .. 0.78
   2 ?    3.1   0.0      0.27   1.3e+02       8      83 ..     274     348 ..     261     354 .. 0.86
   3 ?    5.7   0.2     0.043        20       5      51 ..     401     447 ..     398     454 .. 0.87
   4 ?    7.1   0.3     0.015       7.2      11      89 ..     445     522 ..     442     523 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.35
                   Snapin_Pallidin  47 eeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                       ++   +e + +l + ++ ++++  ++s++++  q+  +Ra+
  gi|313127492|ref|YP_004037762.1| 211 ARSY-NEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERAN 250
                                       4433.478899999999999999999999999999999997 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.27
                   Snapin_Pallidin   8 lellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklk 83 
                                       l+++  +l +l ++++e+ +s e+++ ++++ +e+ ++ ++++  e++ +l+     + +    + +l er++++ 
  gi|313127492|ref|YP_004037762.1| 274 LQTVADELSTLSATVEEIAASAEDVAVTVETAAERGRDGRDVAT-EAMDELDVVESQIDETASAVVALGERIEEID 348
                                       56777889999999999999999999999999999999999888.8999999999999999999988888888775 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.043
                   Snapin_Pallidin   5 egllellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                       ++++ l+e + ++ +e+l+ +r++ ++++e++++  ++++e+e +  
  gi|313127492|ref|YP_004037762.1| 401 DEVSALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVA 447
                                       678899999******************************99988766 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.015
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                       ++ ++++++++++e+ +  ++ +++ +  ++ ++e++++ e e+ +++++  +  ++    +  + +r+++l +Ra 
  gi|313127492|ref|YP_004037762.1| 445 IVAAVEDVNTSVREVSEATDQQASSSQDVAAHVDEVANISE-ETAARTDSAEDAATRQAESVDDIADRTRTLSERAA 520
                                       67788999999999988888888888888888888888888.788*******************************9 PP

                   Snapin_Pallidin  88 kL 89 
                                        L
  gi|313127492|ref|YP_004037762.1| 521 AL 522
                                       88 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       7.1   3.4e+03      75      99 ..     111     135 ..     107     139 .. 0.65
   2 ?   14.7   0.8   5.5e-05     0.026      23     103 ..     220     301 ..     209     306 .. 0.91
   3 ?    2.8   0.5      0.28   1.3e+02      31      98 ..     274     345 ..     269     357 .. 0.66
   4 ?    2.0   0.6      0.51   2.4e+02      67      96 ..     387     416 ..     366     423 .. 0.70
   5 ?    9.6   4.8    0.0021         1      19      95 ..     424     499 ..     413     510 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.1
                                       CCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  75 evkelkeelkaleaelkeleaelek 99 
                                       e++ l ++++++ a l++++++ ++
  gi|313127492|ref|YP_004037762.1| 111 EIARLTADFEDMHAHLQTVSEQATA 135
                                       5666677777777777777766555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.5e-05
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaele 98 
                                       e +++++e+ +  ++  ++  e++   ++ Ne+s ++++a  +  + a+e  +  +++ +el++l+a+++e+ a  e
  gi|313127492|ref|YP_004037762.1| 220 ELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEIsDGADEQTEHLQTVADELSTLSATVEEIAASAE 296
                                       5678899999999999************************9998899***************************999 PP

                                       HHHCT CS
                      Seryl_tRNA_N  99 kllla 103
                                       +++ +
  gi|313127492|ref|YP_004037762.1| 297 DVAVT 301
                                       98765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  31 lleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaele 98 
                                       l  + ++  +l +++ee+ a    ++ +++ a +++    + a+e ++e + +  +++++  ++ +l +++e
  gi|313127492|ref|YP_004037762.1| 274 LQTVADELSTLSATVEEIAASAEDVAVTVETAAERGrdgrDVATEAMDELDVVESQIDETASAVVALGERIE 345
                                       445556666666667777777777777777777666666666667777777777777777776666666655 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.51
                                       S-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  67 edaeeliaevkelkeelkaleaelkeleae 96 
                                       e+ ++l +e++e  +e++al ++++e ++e
  gi|313127492|ref|YP_004037762.1| 387 EEVKALAEETRESADEVSALIEDVTERSEE 416
                                       566666777777777777776666665555 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0021
                                       CCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  19 kkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkelea 95 
                                        +R + ++ v+++  + e+ +++ +++e++++   e+s++  +   + +d ++ ++ev++++ee++a ++  +++ +
  gi|313127492|ref|YP_004037762.1| 424 TNR-QVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEATDQQASSSQDVAAHVDEVANISEETAARTDSAEDAAT 499
                                       345.57899*******************************************************9987776655544 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.7       0.1        49      19      84 ..     230     308 ..     213     357 .. 0.53
   2 ?   14.7  10.6   7.1e-05     0.034       1      96 [.     380     478 ..     380     516 .. 0.80
   3 ?    0.4   1.3         2   9.6e+02      10      60 ..     473     522 ..     457     542 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.1
                      Syntaxin-6_N  19 slyrrwerlledtsss.............tseeldetrteLrkalrsiewdledLeetvriveknpskfkidekels 82 
                                       s  ++ + + +++++s               +e+++  +e  + l+++  +l+ L  tv+ + ++ +++ ++ ++ +
  gi|313127492|ref|YP_004037762.1| 230 SFAAEVSTMSDEAQTSieraneasgavasAVSEISDGADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTVETAA 306
                                       44444444444444433344444444444556666666666666666666666666666544444444444333333 PP

                      Syntaxin-6_N  83 rr 84 
                                       +r
  gi|313127492|ref|YP_004037762.1| 307 ER 308
                                       33 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.1e-05
                      Syntaxin-6_N   1 DPFfevkeeVqkslnkaeslyrrwerlledtss.s..tseeldetrteLrkalrsiewdledLeetvriveknpskf 74 
                                       D F +v+eeV+  ++++++  ++ + l ed ++ s  t   ++et++++ ++++++e+ +e++e  v++ve  ++ +
  gi|313127492|ref|YP_004037762.1| 380 DGFGVVAEEVKALAEETRESADEVSALIEDVTErSeeTLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSV 456
                                       78999*******************9888777774244888999************************9999966664 PP

                      Syntaxin-6_N  75 kidekelsrrrafveevreevk 96 
                                       +  +++ +++ +  ++v  +v+
  gi|313127492|ref|YP_004037762.1| 457 REVSEATDQQASSSQDVAAHVD 478
                                       4444444555554444444444 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2
                      Syntaxin-6_N  10 VqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledL 60 
                                       V   +++++++ ++    ++d+ ++      e  +++    r++++    L
  gi|313127492|ref|YP_004037762.1| 473 VAAHVDEVANISEETAA-RTDSAEDAATRQAESVDDIADRTRTLSERAAAL 522
                                       33333333333333321.122222223333333344444444444444444 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.38   1.8e+02      29      58 ..     265     291 ..     235     297 .. 0.81
   2 ?    8.4   0.0    0.0046       2.2      20      62 ..     366     414 ..     360     419 .. 0.73
   3 ?    0.4   0.1       1.5     7e+02      37      55 ..     431     449 ..     411     461 .. 0.50
   4 ?    0.8   0.1       1.1     5e+02      33      50 ..     497     514 ..     472     527 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.38
                                       C..T-HSSCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  29 regklteelkeyletiesearrldhlvedl 58 
                                       +     +e+ e l+t+ +e   l++ ve++
  gi|313127492|ref|YP_004037762.1| 265 D---GADEQTEHLQTVADELSTLSATVEEI 291
                                       3...45899999*******99999999987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0046
                                       HHHHHHHHHC........T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHC CS
                             HisKA  20 ilgnaeaLkre......gklteelkeyletiesearrldhlvedlLdls 62 
                                       i +++ea          g   ee+k++ e  +++a+ +++l+ed+ + s
  gi|313127492|ref|YP_004037762.1| 366 INAAIEAAHAGeagdgfGVVAEEVKALAEETRESADEVSALIEDVTERS 414
                                       444444443333448895556***********************95544 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.5
                                       CHHHHHHHHHHHHHHHHHH CS
                             HisKA  37 lkeyletiesearrldhlv 55 
                                         e +et+++e + + + v
  gi|313127492|ref|YP_004037762.1| 431 SVETVETAIEEFEAIVAAV 449
                                       2224444444444444444 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.1
                                       -HSSCHHHHHHHHHHHHH CS
                             HisKA  33 lteelkeyletiesearr 50 
                                       +  +++e +++i + +r 
  gi|313127492|ref|YP_004037762.1| 497 AATRQAESVDDIADRTRT 514
                                       334444444444444443 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       3.6   1.7e+03      29      61 ..     102     130 ..      90     143 .. 0.69
   2 ?   -1.6   0.0       9.1   4.3e+03      22      22 ..     193     193 ..     163     262 .. 0.56
   3 ?   14.6   0.7   8.5e-05      0.04      33      99 ..     264     330 ..     252     333 .. 0.88
   4 ?   -0.7   1.7       4.9   2.3e+03      33      60 ..     432     459 ..     340     505 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.6
                                       TTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEE CS
                           SnoaL_2  29 pggelrGreairaffralfaafpdlrfeihdvv 61 
                                       p+++++G ++i++  + +    +d++ +++ v 
  gi|313127492|ref|YP_004037762.1| 102 PPPSVEGDDEIARLTADF----EDMHAHLQTVS 130
                                       555688889998887777....56666666553 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 9.1
                                       E CS
                           SnoaL_2  22 p 22 
                                       +
  gi|313127492|ref|YP_004037762.1| 193 A 193
                                       1 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 8.5e-05
                                       EESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEEEEEEEEEEEETTEE CS
                           SnoaL_2  33 lrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvtvrgvdvfrvrdGki 99 
                                        +G ++  ++++++ +++++l  ++++++a+ + vav ++  ++++++gr v  +++d ++v + +i
  gi|313127492|ref|YP_004037762.1| 264 SDGADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTVETAAERGRDGRDVATEAMDELDVVESQI 330
                                       67999999************************************************99988866665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 4.9
                                       EESHHHHHHHHHHHHHHEEEEEEEEEEE CS
                           SnoaL_2  33 lrGreairaffralfaafpdlrfeihdv 60 
                                       ++  e + + f+a  aa++d++ ++++v
  gi|313127492|ref|YP_004037762.1| 432 VETVETAIEEFEAIVAAVEDVNTSVREV 459
                                       4444555555555555666666666666 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2      0.13        62      22      85 ..     225     289 ..     197     340 .. 0.65
   2 ?   12.9   4.0   0.00016     0.075      17     105 ..     417     505 ..     402     540 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
                                       ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXX CS
                              SKA1  22 kedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqek.lqhlkenlpshlpkkt 85 
                                          ++ + aevs++ +  +   ++ +e + a  ++ +ei   +++q++ lq ++++l +     +
  gi|313127492|ref|YP_004037762.1| 225 IAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEhLQTVADELSTLSATVE 289
                                       44566677777777777777666677777777777777777777666667777776654433222 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00016
                                       .......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  17 dpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqek.lqhlkenlpshlpkktaassaee 92 
                                       + a+ +e+ +++ ++v+++e  +++++++++  e+++ +++ e+ +  +qq +  q +++++ +  ++++++    +
  gi|313127492|ref|YP_004037762.1| 417 TLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVR-EVSEATDQQASsSQDVAAHVDEVANISEETAARTD 492
                                       4556677888999****************************.777777777777********998877776666544 PP

                                       XXXXXXXXXXXXX CS
                              SKA1  93 skssspeeeeete 105
                                       s+++  + + e+ 
  gi|313127492|ref|YP_004037762.1| 493 SAEDAATRQAESV 505
                                       4444444333222 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0021         1     269     351 ..     204     284 ..     203     289 .. 0.90
   2 ?    8.2   5.7    0.0022       1.1     227     322 ..     398     495 ..     386     513 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                             IFT57 269 nsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDgsplvkikkaltklk 345
                                       n+++ e  + y+e  +els++  +++   ++vs +++e ++  e+ ++++  + +  s+++Dg+   ++++ l+++ 
  gi|313127492|ref|YP_004037762.1| 204 NERYVEVARSYNEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGAD--EQTEHLQTVA 278
                                       55666778899****************************9999********************99..9999999999 PP

                             IFT57 346 kEikqm 351
                                        E++++
  gi|313127492|ref|YP_004037762.1| 279 DELSTL 284
                                       998877 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0022
                             IFT57 227 eqmkkhkksieeslpetksqlkklhedisktlekiesrEkylns..qleellqeyreaqeelsevkekykqlsegvs 301
                                       e+  +++  ie+ ++++++ l+ + e   ++ e +e+ E+ +++   +   +++ ++  +e+se++++    s+ v 
  gi|313127492|ref|YP_004037762.1| 398 ESADEVSALIEDVTERSEETLATVRETNRQVAESVETVETAIEEfeAIVAAVEDVNTSVREVSEATDQQASSSQDVA 474
                                       45566667788888888889999999999999999999999974225556666777777788888888888888888 PP

                             IFT57 302 eltrelaeiseelekvkqeme 322
                                       +  +e a+isee  +     e
  gi|313127492|ref|YP_004037762.1| 475 AHVDEVANISEETAARTDSAE 495
                                       888888888888766555444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.052        24      30     100 ..     211     280 ..     205     286 .. 0.82
   2 ?    3.9   0.1      0.12        56      37     113 ..     274     346 ..     268     367 .. 0.51
   3 ?    6.1   0.9     0.025        12      40      99 ..     389     448 ..     384     451 .. 0.83
   4 ?    7.6   1.1    0.0088       4.1      30     107 ..     449     525 ..     444     534 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.052
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCC CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaq 100
                                        +++++ +++l ++++e+++   e+++++ e ++s++++++ +    ++++++s+  +e+ + l +t+ ++
  gi|313127492|ref|YP_004037762.1| 211 ARSYNEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHL-QTVADE 280
                                       6778889999************************999999999988999999999999555554.555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                                       HCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHH CS
                         Fib_alpha  37 lekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvles 113
                                       l+++ +el+++s + +e+    +++  +++ + +  +d   v ++  +el+     ++ +id++ s + +L + +e+
  gi|313127492|ref|YP_004037762.1| 274 LQTVADELSTLSATVEEIAASAEDVAVTVETAAERGRDGRDVATEAMDELD----VVESQIDETASAVVALGERIEE 346
                                       444444555555555554444444444444444444444444444444444....4455555555555554444443 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.025
                                       CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  40 leneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketida 99 
                                       ++   ee ++s  e++ l++++++  +e+ ++ +++++ + +s +++e+ i+++++ + a
  gi|313127492|ref|YP_004037762.1| 389 VKALAEETRESADEVSALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAA 448
                                       45556677888888999999999999999999999999**************99998876 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0088
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                                        +dv+++++++ +  ++ ++s++++  +v e+ ++ +e+ + ++  + + ++ +++++ +i++  +t+++    ++ 
  gi|313127492|ref|YP_004037762.1| 449 VEDVNTSVREVSEATDQQASSSQDVAAHVDEVANISEETAARTDSAEDAATRQAESVD-DIADRTRTLSERAAALER 524
                                       5799*******************************99999999988999999999999.999999999888887777 PP

                                       H CS
                         Fib_alpha 107 L 107
                                       L
  gi|313127492|ref|YP_004037762.1| 525 L 525
                                       6 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.9    0.0027       1.3     193     298 ..     241     346 ..     215     369 .. 0.88
   2 ?    7.2   6.9    0.0065       3.1     221     317 ..     388     483 ..     384     526 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
                            HMMR_N 193 vtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLks 269
                                       ++q+ +e++ ++  ++    +++ +   e+ ++ +   ++ + ls++ e++    +d+a+  e+++e+ ++  ++ +
  gi|313127492|ref|YP_004037762.1| 241 EAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTVETAAERGRDGRDVAT 317
                                       6788888888888888888888999989999999999999**********9999*********************99 PP

                            HMMR_N 270 sLeekeqelskqvkdlnekckllekekee 298
                                       +  ++ ++++ q+++  + +  l +  ee
  gi|313127492|ref|YP_004037762.1| 318 EAMDELDVVESQIDETASAVVALGERIEE 346
                                       99999999*******99999999888885 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0065
                            HMMR_N 221 eekseteklleyieelsnvseql.ekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekek 296
                                       e k+  e+  e  +e+s+++e + e+ ++ +a ++e+  + ++ +e++ +++ee e  + + v+d n+ ++++ + +
  gi|313127492|ref|YP_004037762.1| 388 EVKALAEETRESADEVSALIEDVtERSEETLATVRETNRQVAESVETVETAIEEFEA-IVAAVEDVNTSVREVSEAT 463
                                       5677788889999999*99999989999999**********************9999.9999***********9999 PP

                            HMMR_N 297 eelvreeeekeqtlsaEleel 317
                                       +++ + ++  +     E+ ++
  gi|313127492|ref|YP_004037762.1| 464 DQQASSSQDVAA-HVDEVANI 483
                                       976665554333.33455555 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       5.8   2.7e+03      15      47 ..     102     133 ..      98     150 .. 0.71
   2 ?   -1.1   0.0       5.3   2.5e+03      28      47 ..     164     183 ..     144     220 .. 0.57
   3 ?    0.6   0.1       1.5   7.1e+02      37      66 ..     253     283 ..     209     294 .. 0.58
   4 ?    8.1   0.1     0.007       3.3      24      68 ..     387     432 ..     381     441 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.8
                               GAT  15 epdeellenellkeLyetckamqpriqklieet 47 
                                       +p+ +++ ++ +  L    + m+  +q   e+ 
  gi|313127492|ref|YP_004037762.1| 102 PPP-SVEGDDEIARLTADFEDMHAHLQTVSEQA 133
                                       444.67778888888888888888888777764 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.3
                               GAT  28 eLyetckamqpriqklieet 47 
                                       +L+ + +++q+ +  ++e+t
  gi|313127492|ref|YP_004037762.1| 164 DLAAHTRNLQRLVDAFAEAT 183
                                       44444444444444444443 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.5
                               GAT  37 qpriqklieetadeed.llaelLqlNDeLnn 66 
                                       +  +   ++e++d  d  ++ l  + DeL++
  gi|313127492|ref|YP_004037762.1| 253 SGAVASAVSEISDGADeQTEHLQTVADELST 283
                                       3334444444433333356666666666665 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.007
                               GAT  24 ellkeLyetckamqpriqklieetadeed.llaelLqlNDeLnnvl 68 
                                       e +k L+e+ +++   +  lie+++++++ +la+  ++N ++ + +
  gi|313127492|ref|YP_004037762.1| 387 EEVKALAEETRESADEVSALIEDVTERSEeTLATVRETNRQVAESV 432
                                       8899*******************9555444*****99998876655 PP

>> DASH_Hsk3  DASH complex subunit Hsk3 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0022         1      10      34 ..     111     135 ..     109     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0022
                         DASH_Hsk3  10 qLaqLqaNLadteellevtseQaes 34 
                                       ++a+L+a  +d++ +l + seQa +
  gi|313127492|ref|YP_004037762.1| 111 EIARLTADFEDMHAHLQTVSEQATA 135
                                       6799******************975 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0014      0.67       8      87 ..     215     293 ..     197     309 .. 0.79
   2 ?    2.2   4.8      0.18        86      16      46 ..     440     470 ..     383     530 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlke 84 
                                       ++ ++el++t  e+++  +e+s++ ++ +++i++ ++   ++ s++++++  + +e+ e+++++++el++ +++++e
  gi|313127492|ref|YP_004037762.1| 215 NEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGA-DEQTEHLQTVADELSTLSATVEE 290
                                       44456777888888888888888888888888888888888888888888775.68888888888888888888888 PP

                             TMPIT  85 ves 87 
                                       +++
  gi|313127492|ref|YP_004037762.1| 291 IAA 293
                                       765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                             TMPIT  16 etakeykqkleelsklqskcskeikkqkkrl 46 
                                       e+++ + + +e+++++  ++s+++++q    
  gi|313127492|ref|YP_004037762.1| 440 EEFEAIVAAVEDVNTSVREVSEATDQQASSS 470
                                       1111112222222222222222222222222 PP

>> TBK1_CCD1  TANK-binding kinase 1 coiled-coil domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.012       5.5      40     125 ..     210     293 ..     207     321 .. 0.87
   2 ?    5.7   1.2      0.02       9.5      51     103 ..     410     466 ..     382     526 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                         TBK1_CCD1  40 mrkgvrwliellkedvnkllhkktevelkceiceetlekaekllevlmqanlepsEldeiselhkkllrlsssleri 116
                                       + ++++ ++  l +++ ++     ev+  ++  + ++e+a++   ++  a++e+   d + e  ++l++++ +l+++
  gi|313127492|ref|YP_004037762.1| 210 VARSYNEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEI--SDGADEQTEHLQTVADELSTL 284
                                       567888999999999999999999999999***********9999999999988..577899999999999999999 PP

                         TBK1_CCD1 117 eeslqeikn 125
                                       + +++ei  
  gi|313127492|ref|YP_004037762.1| 285 SATVEEIAA 293
                                       999999865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                         TBK1_CCD1  51 lkedvnkl....lhkktevelkceiceetlekaekllevlmqanlepsEldeiselh 103
                                       + e+ +++     + + +v  ++e  e  +e+ e ++ ++  +n++  E++e+++ +
  gi|313127492|ref|YP_004037762.1| 410 VTERSEETlatvRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEATDQQ 466
                                       333333332221344556666667777777777777777777777777777766543 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       7.3   3.4e+03      53      83 ..     114     143 ..     109     148 .. 0.64
   2 ?    4.2   0.6     0.073        35      31      73 ..     260     303 ..     225     311 .. 0.77
   3 ?   -1.0   0.0       2.9   1.4e+03      26      60 ..     322     356 ..     308     376 .. 0.48
   4 ?   13.7   5.6   8.8e-05     0.042       2      85 ..     399     483 ..     398     502 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.3
                        Phage_GP20  53 eLqkqieelqaknkkakaeyeakiadlkldn 83 
                                        L++++e++ a +++  +e ++ +ad+++d+
  gi|313127492|ref|YP_004037762.1| 114 RLTADFEDMHAHLQT-VSEQATALADREFDD 143
                                       566777777777766.444555567777765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.073
                        Phage_GP20  31 keqlkd.rdkqLedLkkkakdneeLqkqieelqaknkkakaeye 73 
                                        +++ d +d+q e L+++a +  +L +++ee+ a +++   + e
  gi|313127492|ref|YP_004037762.1| 260 VSEISDgADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTVE 303
                                       44444338999999999999999999999999999998776655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.9
                        Phage_GP20  26 erdtlkeqlkdrdkqLedLkkkakdneeLqkqiee 60 
                                       e d +++q+++  + +  L +  ++ +e+ + i++
  gi|313127492|ref|YP_004037762.1| 322 ELDVVESQIDETASAVVALGERIEEIDEIAEFIDD 356
                                       33333344444333333333333333333333333 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 8.8e-05
                        Phage_GP20   2 qikkvmkaengkdit...kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeak 75 
                                        +++v  a+  +d+t   ++ l++v e + ++ e++++ ++ +e++++ +  +e++++ + e+ ++ +++ + ++  
  gi|313127492|ref|YP_004037762.1| 399 SADEVS-ALI-EDVTersEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEATDQQASSSQDV 473
                                       577776.444.6787788999**********************************************9998887776 PP

                        Phage_GP20  76 iadlkldnai 85 
                                        a ++  + i
  gi|313127492|ref|YP_004037762.1| 474 AAHVDEVANI 483
                                       6666555555 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.95   4.5e+02     192     213 ..     117     138 ..      67     140 .. 0.70
   2 ?    4.9   0.6     0.029        13     117     218 ..     201     298 ..     165     308 .. 0.70
   3 ?    1.0   0.4      0.45   2.1e+02     132     226 ..     321     407 ..     310     418 .. 0.47
   4 ?    8.7   5.7     0.002      0.94     114     221 ..     391     497 ..     358     530 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.95
                              CorA 192 eylrdlldelerllemlealre 213
                                         ++d++ +l+ ++e+++al++
  gi|313127492|ref|YP_004037762.1| 117 ADFEDMHAHLQTVSEQATALAD 138
                                       2267777777777777776666 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.029
                              CorA 117 deivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvkl.rralapnrevlkrllakaddkllddedke 192
                                          ++r+ e+ +  +e ++el++++   + ++++ e++++  ++ +  +ra  ++ +v  + ++  + +   de+ e
  gi|313127492|ref|YP_004037762.1| 201 GGENERYVEVARSYNEFVRELSSTI--AEVQSFAAEVSTMSDEAQTSiERANEASGAVA-SAVS--EISDGADEQTE 272
                                       5567888888888888888888888..77777888888888775544155555555555.5555..67777778888 PP

                              CorA 193 ylrdlldelerllemlealrerlesl 218
                                       +l+++ del+ l+ ++e ++  +e +
  gi|313127492|ref|YP_004037762.1| 273 HLQTVADELSTLSATVEEIAASAEDV 298
                                       89999999999999999988887766 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.45
                              CorA 132 eeldeledeledstkkeilrelaqlrrrlvklrralapnrevlk..rllakaddkllddedkeylrdlldelerlle 206
                                       +eld +e+++     +e ++ +++l +r+ ++ +++    +v +  +l   a +  +++++     +  d +  ++e
  gi|313127492|ref|YP_004037762.1| 321 DELDVVESQI-----DETASAVVALGERIEEIDEIAEFIDDVGSqtDL--LAINAAIEAAH---AGEAGDGFGVVAE 387
                                       4444444444.....555666666666666666666555555542222..22333333333...4444444444444 PP

                              CorA 207 mlealrerleslqdtyssll 226
                                       +++al+e ++   d+ s+l+
  gi|313127492|ref|YP_004037762.1| 388 EVKALAEETRESADEVSALI 407
                                       44444444444444444443 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.002
                              CorA 114 rlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddklldd 188
                                       +l +e  ++ +e+   +e+ +++ e++l   ++t+++ ++++ ++++ + +++ ++a+ ++v +++    + ++ +d
  gi|313127492|ref|YP_004037762.1| 391 ALAEETRESADEVSALIEDVTERSEETLatVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVR---EVSEATD 464
                                       3334444444444444444455555555666667777777777777777777777777777773333...4666666 PP

                              CorA 189 edkeylrdlldelerllemlealrerleslqdt 221
                                       +++   +d+  +++ +++ +e ++ r++s  d+
  gi|313127492|ref|YP_004037762.1| 465 QQASSSQDVAAHVDEVANISEETAARTDSAEDA 497
                                       666667777777777777666666666666554 PP

>> BAR_2  Bin/amphiphysin/Rvs domain for vesicular trafficking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.43     2e+02     106     150 ..     138     175 ..     112     197 .. 0.66
   2 ?    9.9   2.0   0.00078      0.37      76     165 ..     210     299 ..     203     306 .. 0.89
   3 ?    0.5   1.1      0.55   2.6e+02      74     162 ..     433     471 ..     380     538 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                             BAR_2 106 keekesqatsallprtlaqalskaakdsslilqeleekdedlepL 150
                                       + e ++   +++lp ++  al ++a+d +    +l+       +L
  gi|313127492|ref|YP_004037762.1| 138 DREFDDPVLDESLPGSFGDALDRMAVDLAAHTRNLQ-------RL 175
                                       344445566788899999999999998886666664.......22 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00078
                             BAR_2  76 igaklkelknvssleedeivllgkkkkekskeekesqatsallprtlaqalskaakdsslilqeleekdedlepLik 152
                                       ++   +e+    s + +e+ +++ + +  s+e+++s +  ++ + + a+a+s+++ +++++ ++l+   ++l+ L+ 
  gi|313127492|ref|YP_004037762.1| 210 VARSYNEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADELSTLSA 286
                                       566678888888888889999********9**999999999************************999999*****9 PP

                             BAR_2 153 vleqvssaykeia 165
                                         e+++ + +++a
  gi|313127492|ref|YP_004037762.1| 287 TVEEIAASAEDVA 299
                                       9999999888876 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.55
                             BAR_2  74 ksigaklkelknvssleedeivllgkkkkekskeekesqatsallprtlaqalskaakdsslilqeleekdedlepL 150
                                       +++ + ++e++ +                                                  +  +e+ ++ + ++
  gi|313127492|ref|YP_004037762.1| 433 ETVETAIEEFEAI--------------------------------------------------VAAVEDVNTSVREV 459
                                       2222222222222..................................................33333333333333 PP

                             BAR_2 151 ikvleqvssayk 162
                                       +++ +q +s+ +
  gi|313127492|ref|YP_004037762.1| 460 SEATDQQASSSQ 471
                                       333333333332 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.4   1.1e+03      37      58 ..     112     133 ..     106     140 .. 0.47
   2 ?    6.7   0.8     0.021        10      35      61 ..     258     291 ..     215     301 .. 0.63
   3 ?    5.3   0.4     0.057        27      12      47 ..     322     357 ..     313     374 .. 0.60
   4 ?    6.0   2.8     0.034        16      22      63 ..     420     461 ..     385     468 .. 0.77
   5 ?    5.5   4.9     0.051        24      10      64 ..     429     483 ..     426     510 .. 0.77
   6 ?   -1.5   0.1       7.8   3.7e+03      25      45 ..     503     523 ..     477     535 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.4
                           NPV_P10  37 vtelnekLdaqsaqLaeletkv 58 
                                       +  l++ ++++ a L++++++ 
  gi|313127492|ref|YP_004037762.1| 112 IARLTADFEDMHAHLQTVSEQA 133
                                       3334444444444444444433 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.021
                           NPV_P10  35 pdvtelnekLdaqsaqLaelet.......kvenI 61 
                                         v+e+++  d+q++ L+++ +       +ve+I
  gi|313127492|ref|YP_004037762.1| 258 SAVSEISDGADEQTEHLQTVADelstlsaTVEEI 291
                                       3345555555555555555555111111166665 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.057
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaq 47 
                                       +   v++++d   ++v  + e +++++e+ e +d+ 
  gi|313127492|ref|YP_004037762.1| 322 ELDVVESQIDETASAVVALGERIEEIDEIAEFIDDV 357
                                       344555666666666666666666666666655554 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.034
                           NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                        + +   +v+e +++v+   e+++a+ a++++++t+v ++++
  gi|313127492|ref|YP_004037762.1| 420 TVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSE 461
                                       344444788888888888888999999999999999988765 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.051
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                        + ++ v++ ++  ++ v+ v++    v e++e  d+q+ + +++ ++v+++ +i
  gi|313127492|ref|YP_004037762.1| 429 AESVETVETAIEEFEAIVAAVEDVNTSVREVSEATDQQASSSQDVAAHVDEVANI 483
                                       5667777777777777777777777777777788888888888888888877776 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 7.8
                           NPV_P10  25 qqvddvqenlpdvtelnekLd 45 
                                       ++vdd+++  ++++e  + L+
  gi|313127492|ref|YP_004037762.1| 503 ESVDDIADRTRTLSERAAALE 523
                                       334444444444444333333 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.1   0.00019     0.088      34     112 ..     203     280 ..     198     298 .. 0.80
   2 ?    4.9   7.4     0.039        18      28     112 ..     390     465 ..     366     482 .. 0.63
   3 ?    3.2   3.7      0.13        63      42     110 ..     435     509 ..     433     528 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                              YkyA  34 eqelyeeiielgmde.fdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeaeeliea 109
                                       e+e y e+     +e   ++++ ++e+++ + e  ++ ++ ++sie+a+e+   + + ++ei d  + +++e l+++
  gi|313127492|ref|YP_004037762.1| 203 ENERYVEVARSY-NEfVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDG-ADEQTEHLQTV 277
                                       566677776544.44388999*****************************************776.66666666665 PP

                              YkyA 110 mee 112
                                        +e
  gi|313127492|ref|YP_004037762.1| 278 ADE 280
                                       554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.039
                              YkyA  28 telekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeae 104
                                       + l ++  e  +e+ +      +++++ s+e l++v e + ++++  e +e a eefe i + +e+++       + 
  gi|313127492|ref|YP_004037762.1| 390 KALAEETRESADEVSA-L---IEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNT-----SVR 457
                                       4444444444444433.2...234788888888888888888888888888888888888877777732.....233 PP

                              YkyA 105 elieamee 112
                                       e+ ea ++
  gi|313127492|ref|YP_004037762.1| 458 EVSEATDQ 465
                                       33333333 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.13
                              YkyA  42 ielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieei......edeelkkeaeelieam 110
                                       +e  ++ef++i++ ++++ ++v e  e  +++  s ++    ++++ ++ ee+       ++++  +ae++ ++ 
  gi|313127492|ref|YP_004037762.1| 435 VETAIEEFEAIVAAVEDVNTSVREVSEATDQQASSSQDVAAHVDEVANISEETaartdsAEDAATRQAESVDDIA 509
                                       667788999999999999999999999999988888888888888888877776665543444555565555443 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.25   1.2e+02      18      74 ..     161     233 ..     156     240 .. 0.54
   2 ?    5.0   0.3     0.083        39       9      70 ..     215     275 ..     190     280 .. 0.72
   3 ?    7.7   1.2     0.012       5.7       7      86 ..     276     353 ..     266     365 .. 0.65
   4 ?    7.4   3.5     0.015       7.2      14      80 ..     388     453 ..     384     458 .. 0.83
   5 ?    3.7   2.4      0.21        97       6      67 ..     450     517 ..     448     537 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.25
                           DUF2203  18 lleelralrkeleeleeeleeakaeaekse................aaeleaeleeleaeieelveeieelGv 74 
                                       +  +l+a +++l++l+++ +ea+++a++ +                + e +++++e   e++++++e++++ +
  gi|313127492|ref|YP_004037762.1| 161 MAVDLAAHTRNLQRLVDAFAEATERAAAGDltallpveevggenerYVEVARSYNEFVRELSSTIAEVQSFAA 233
                                       5555566666666666666666666655556667777763333333444444555555555555555554444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.083
                           DUF2203   9 nalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeie 70 
                                       n+ + +l+++++e+++ ++e+ ++++e +++ ++a++    + +++++e+++ ++e +e+++
  gi|313127492|ref|YP_004037762.1| 215 NEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEA-SGAVASAVSEISDGADEQTEHLQ 275
                                       56777888888888888888888888888777776543.44455555555555555555554 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.012
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekse......aaeleaeleeleaeieelveeieelGvevk 77 
                                       +  + L +l+ ++ee++a +++++ ++e  +e        +      a+e+  el+ +e++i+e+ + + +lG  + 
  gi|313127492|ref|YP_004037762.1| 276 TVADELSTLSATVEEIAASAEDVAVTVETAAER-------GrdgrdvATEAMDELDVVESQIDETASAVVALGERIE 345
                                       333445555555555555555555544444433.......33444569999999******************99999 PP

                           DUF2203  78 dleaglvDF 86 
                                       +++  + +F
  gi|313127492|ref|YP_004037762.1| 346 EID-EIAEF 353
                                       987.45555 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.015
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                                       ++k l ee r+ ++e+  l e+++e ++e+   + +e +++++e  + +e ++ee+e++ + v d++
  gi|313127492|ref|YP_004037762.1| 388 EVKALAEETRESADEVSALIEDVTERSEET-LATVRETNRQVAESVETVETAIEEFEAIVAAVEDVN 453
                                       688889999999999999999999888885.455899999999999999999999999999998886 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.21
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekse......aaeleaeleeleaeieelve 67 
                                       e+ n+ + +++e +++ ++  ++++  ++e++++++e+++++      a++++++++ ++++ + l e
  gi|313127492|ref|YP_004037762.1| 450 EDVNTSVREVSEATDQQASSSQDVAAHVDEVANISEETAARTdsaedaATRQAESVDDIADRTRTLSE 517
                                       67788888999999999999999999999999888887766666444444444444444444444444 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.1   5.4e+02      18      92 ..     217     287 ..     204     308 .. 0.57
   2 ?    8.0   0.7    0.0052       2.5       5      86 ..     415     532 ..     411     540 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                        STAT_alpha  18 teqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlnaLdqkRkelvdklkellnlleslqek 92 
                                        ++++++   e  +F+ ++++++ +  ++++ e++  +++   +++ ++++++   e  ++l+ + ++l++l ++
  gi|313127492|ref|YP_004037762.1| 217 FVRELSSTIAEVQSFAAEVSTMSDE--AQTSIERA--NEASGAVASAVSEISDGADEQTEHLQTVADELSTLSAT 287
                                       4444444444455777777777777..33333333..55555555555555555555555555555555555443 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0052
                        STAT_alpha   5 eqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl..................................eqera 47 
                                       e++l+++r++++++ ++++++e   eeF+  +  ++                                    +++r+
  gi|313127492|ref|YP_004037762.1| 415 EETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVntsvrevseatdqqasssqdvaahvdevaniseeTAART 491
                                       57788999999999999999999999999999999888777777777666666666666666777777777666666 PP

                        STAT_alpha  48 esekkelkkqkellqqmlna..LdqkRkelvdklkellnll 86 
                                       +s++   ++q e++++ + +     +R++ +++l  +++l+
  gi|313127492|ref|YP_004037762.1| 492 DSAEDAATRQAESVDDIADRtrTLSERAAALERLVGSFELV 532
                                       66666677777777776666666666777777776666665 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.7   7.9e+02      34      59 ..     113     138 ..     109     194 .. 0.52
   2 ?    8.7   2.3    0.0036       1.7      45     118 ..     219     305 ..     206     332 .. 0.63
   3 ?   -1.4   0.0       4.7   2.2e+03      29      49 ..     327     346 ..     314     374 .. 0.44
   4 ?    7.4   1.3    0.0092       4.3      38      96 ..     387     448 ..     381     463 .. 0.59
   5 ?    6.1   2.6     0.023        11      20      69 ..     416     467 ..     410     528 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.7
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlkslla 59 
                                       a l++++++++  L+++se+ ++l  
  gi|313127492|ref|YP_004037762.1| 113 ARLTADFEDMHAHLQTVSEQATALAD 138
                                       55555566666666666555555443 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0036
                      Baculo_PEP_C  45 tqLnalsedlksllaeldt..........rldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstL 108
                                       ++L++  ++++s  ae++t          r ++++ ++ +a+ +++   d+ +++L+++  +l++L + v  i ++ 
  gi|313127492|ref|YP_004037762.1| 219 RELSSTIAEVQSFAAEVSTmsdeaqtsieRANEASGAVASAVSEISdgaDEQTEHLQTVADELSTLSATVEEIAASA 295
                                       44444444444444444444555555666677778888888888887777777788888888888888888888888 PP

                      Baculo_PEP_C 109 nnllqalnnl 118
                                       + +  +++  
  gi|313127492|ref|YP_004037762.1| 296 EDVAVTVETA 305
                                       7777777765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.7
                      Baculo_PEP_C  29 nvqilaqlatlldaietqLna 49 
                                       ++qi  + a+++ a+ +++++
  gi|313127492|ref|YP_004037762.1| 327 ESQI-DETASAVVALGERIEE 346
                                       2222.2222222222222222 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0092
                      Baculo_PEP_C  38 tlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltn 96 
                                       + ++a++++  + ++++++l++++++r +++l+++ ++  +++   +t++++++  ++i++ 
  gi|313127492|ref|YP_004037762.1| 387 EEVKALAEETRESADEVSALIEDVTERSEETLATVRETNRQVAesvETVETAIEEFEAIVAA 448
                                       55566666666666677777777777666666666666666665555555555555555443 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.023
                      Baculo_PEP_C  20 nvLnairlqnvqilaqlatlldaietqLnalsedlks...llaeldtrldtll 69 
                                       ++L+++r  n q++  ++t  +aie+ ++a+ +++++   ++ e++++ d+++
  gi|313127492|ref|YP_004037762.1| 416 ETLATVRETNRQVAESVETVETAIEE-FEAIVAAVEDvntSVREVSEATDQQA 467
                                       68999999999998888888888886.55555544440004444444333333 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.5   7.1e+02      73     107 ..     149     183 ..     113     189 .. 0.59
   2 ?    1.1   2.3      0.74   3.5e+02      41     132 ..     267     354 ..     258     363 .. 0.58
   3 ?    0.7   0.1         1   4.7e+02      44      71 ..     343     365 ..     324     379 .. 0.68
   4 ?   13.3   3.1   0.00012     0.059      27     109 ..     379     466 ..     363     477 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.5
                                       -SSSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  73 eapkefgsveevleaalehekkvteslrelielae 107
                                         p +fg++++ ++ +l++++   ++l ++ + a 
  gi|313127492|ref|YP_004037762.1| 149 SLPGSFGDALDRMAVDLAAHTRNLQRLVDAFAEAT 183
                                       22444677777777777777777777766666665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS.CS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHH CS
                          Ferritin  41 aeeerehadklaerilalGgtpvltraeleeieapke.fg.sveevleaalehekkvteslrelielaeeegDpata 115
                                       a+e +eh + +a+ + +l +     ++  eei+a  e ++ +ve + e   +  + +te++ el  +  +    a+a
  gi|313127492|ref|YP_004037762.1| 267 ADEQTEHLQTVADELSTLSA-----TV--EEIAASAEdVAvTVETAAERGRDGRDVATEAMDELDVVESQIDETASA 336
                                       77888888888888888877.....22..222222222244666666666666666666666654444444455555 PP

                                       HHH.HHHHHHHHHHHHHH CS
                          Ferritin 116 dfl.edfleeqeehewel 132
                                         + ++ +ee +e ++++
  gi|313127492|ref|YP_004037762.1| 337 VVAlGERIEEIDEIAEFI 354
                                       555566666655555555 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHTTS....SHHHHHH CS
                          Ferritin  44 erehadklaerilalGgtpvltraelee 71 
                                         e +d++ae+i + G      + +l +
  gi|313127492|ref|YP_004037762.1| 343 RIEEIDEIAEFIDDVGS-----QTDLLA 365
                                       34677777777777776.....444444 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00012
                                       STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH.....C-SSSSCSSHHHHHHHHHHHHHHHHHH CS
                          Ferritin  27 gpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee.....ieapkefgsveevleaalehekkvtes 98 
                                       g g+  +ae+ +  aee re ad++   i +  +    t a++ e      e+++ ++++ e +ea++++ ++v++s
  gi|313127492|ref|YP_004037762.1| 379 GDGFGVVAEEVKALAEETRESADEVSALIEDVTERSEETLATVREtnrqvAESVETVETAIEEFEAIVAAVEDVNTS 455
                                       778999999999999999999999877777777755555555555655654444558899999************** PP

                                       HHHHHHHHHHT CS
                          Ferritin  99 lrelielaeee 109
                                       +re+ e ++++
  gi|313127492|ref|YP_004037762.1| 456 VREVSEATDQQ 466
                                       ****9999985 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.4   1.6e+03      65      98 ..     106     139 ..      86     141 .. 0.81
   2 ?    7.3   1.8     0.002      0.94      15     117 ..     204     307 ..     199     356 .. 0.73
   3 ?    1.7   8.8     0.096        45      40     131 ..     404     496 ..     343     535 .. 0.49

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.4
                        V_ATPase_I  65 apeekeldeleeelekleeelkelnenleklkke 98 
                                        + ++e+ +l++++e+++++l++++e++++l ++
  gi|313127492|ref|YP_004037762.1| 106 VEGDDEIARLTADFEDMHAHLQTVSEQATALADR 139
                                       5667889999999999999999999999888765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                        V_ATPase_I  15 nedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnen 91 
                                       ne   ++ r++ + vr +     +++ + +e++ ++++ +++ e +++ + + ++ ++e+++  ++ +e+l+++ ++
  gi|313127492|ref|YP_004037762.1| 204 NERYVEVARSYNEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADE 280
                                       56667889999999999999999999999999999999999999888999999999999999999999999999999 PP

                        V_ATPase_I  92 leklkkelnelvelka.vlekakefle 117
                                       l++l+++++e+    + v  ++++  e
  gi|313127492|ref|YP_004037762.1| 281 LSTLSATVEEIAASAEdVAVTVETAAE 307
                                       999999988876554414434433333 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.096
                        V_ATPase_I  40 rfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkel.nelvelkavlekakef 115
                                       + l e +++ ++++  + ++++++ a++ +++++  ee+e + + ++++n++ +++++ + +++   + v  +++e+
  gi|313127492|ref|YP_004037762.1| 404 SALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEATdQQASSSQDVAAHVDEV 480
                                       22222222222222222222333333333333333333333334444444444444333212333334444444444 PP

                        V_ATPase_I 116 leeeeeeeeeeeseee 131
                                        + +ee+++++ s e+
  gi|313127492|ref|YP_004037762.1| 481 ANISEETAARTDSAED 496
                                       4333222222222222 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.28   1.3e+02     255     304 ..     199     248 ..     194     252 .. 0.79
   2 ?    5.2   1.6     0.022        11     191     293 ..     233     335 ..     226     350 .. 0.81
   3 ?    3.9  11.3     0.054        26     184     262 ..     387     465 ..     384     510 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.28
                            HAP1_N 255 elgveneelkqhLaaskeaqrqLtaELqdlqekyaevegmLheaqeevke 304
                                       e+g ene   +  ++  e  r+L + + ++q+  aev +m  eaq+ +++
  gi|313127492|ref|YP_004037762.1| 199 EVGGENERYVEVARSYNEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIER 248
                                       56667777777778888888999999999999999999999999987765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                            HAP1_N 191 tetdtlEekEqqLvldcveqlseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhL 267
                                        e +t+ ++ q  +    e    + + ++e+s+  ++++e l++  +e s+L a + ++    + ++v  e   ++ 
  gi|313127492|ref|YP_004037762.1| 233 AEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTVETAAERG 309
                                       55566666666666665555566778899******************************************999999 PP

                            HAP1_N 268 aaskeaqrqLtaELqdlqekyaeveg 293
                                       +  +++ ++  +EL  ++++  e+ +
  gi|313127492|ref|YP_004037762.1| 310 RDGRDVATEAMDELDVVESQIDETAS 335
                                       99999999999999998888888655 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.054
                            HAP1_N 184 eeasqLktetdtlEekEqqLvldcveqlseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgven 260
                                       ee + L++et +  ++   L+ d++e  +e+ + + e + ++a+ +e++e+  ee + + a + d+++ ++e+++ +
  gi|313127492|ref|YP_004037762.1| 387 EEVKALAEETRESADEVSALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEAT 463
                                       68899*****************************************************************9987655 PP

                            HAP1_N 261 ee 262
                                       ++
  gi|313127492|ref|YP_004037762.1| 464 DQ 465
                                       54 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3    0.0052       2.4     593     674 ..     205     286 ..     198     351 .. 0.67
   2 ?    1.6   6.9     0.099        47     587     668 ..     392     476 ..     383     518 .. 0.52
   3 ?   -1.5   0.1      0.84     4e+02     582     612 ..     492     522 ..     474     530 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0052
                             Nup88 593 ekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklkslknalkqvkkkldkqrkqiakskeee 669
                                       e+y e+    +++vr +++ + +++s +  +s++  e +  +e+ +e+   ++ a++++    d+q ++++  ++e 
  gi|313127492|ref|YP_004037762.1| 205 ERYVEVARSYNEFVRELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADEL 281
                                       56666666666666666666666666666666666666666666666666666666666666666666666655554 PP

                             Nup88 670 kkssl 674
                                       ++ s 
  gi|313127492|ref|YP_004037762.1| 282 STLSA 286
                                       43333 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.099
                             Nup88 587 raeklAekyeeikdkQeklvrrvkkvl...krlnsklpvlseaeremkkelekikeklkslknalkqvkkkldkqrk 660
                                        ae+  e  +e++   e++++r ++ l   +++n ++  ++e+     +e+e+i  +++ +++++++v + +d+q++
  gi|313127492|ref|YP_004037762.1| 392 LAEETRESADEVSALIEDVTERSEETLatvRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEATDQQAS 468
                                       33333344444444444444555444411123334444444444444555555555555555555555555555555 PP

                             Nup88 661 qiakskee 668
                                         +  + +
  gi|313127492|ref|YP_004037762.1| 469 SSQDVAAH 476
                                       55444333 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.84
                             Nup88 582 kslseraeklAekyeeikdkQeklvrrvkkv 612
                                       +s +++a + Ae  ++i d+  +l +r+ ++
  gi|313127492|ref|YP_004037762.1| 492 DSAEDAATRQAESVDDIADRTRTLSERAAAL 522
                                       4456777888888888888888888887654 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         5   2.4e+03     214     237 ..     111     134 ..     107     142 .. 0.45
   2 ?    7.6   1.9    0.0032       1.5     198     278 ..     215     291 ..     148     293 .. 0.65
   3 ?    2.5   5.9      0.12        55     138     247 ..     261     348 ..     240     403 .. 0.52
   4 ?    5.8  11.6     0.012       5.6     135     255 ..     405     524 ..     394     536 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5
                              Spc7 214 eieekkkelaelqeqleeleekie 237
                                       ei+++ ++ +++ + l++++e+ +
  gi|313127492|ref|YP_004037762.1| 111 EIARLTADFEDMHAHLQTVSEQAT 134
                                       344444444444444444444333 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0032
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkee 274
                                       +e +    +el++  ae++++ +e++++ ++ +++ e+ +e++   +++ +ei+   + + e+ +  ++e+s+l ++
  gi|313127492|ref|YP_004037762.1| 215 NEFV----RELSSTIAEVQSFAAEVSTMSDEAQTSIERANEASGAVASAVSEISDGADEQTEHLQTVADELSTLSAT 287
                                       3333....345555555555555666666666666666666666666666666666666666666777777777777 PP

                              Spc7 275 vkal 278
                                       v+++
  gi|313127492|ref|YP_004037762.1| 288 VEEI 291
                                       7665 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.12
                              Spc7 138 egLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkae 214
                                       +++ +g++e+ e l++ +++L+   + ++e+  + e    ++e  +e+ ++  +++++   +eL  + ++++e  + 
  gi|313127492|ref|YP_004037762.1| 261 SEISDGADEQTEHLQTVADELSTLSATVEEIAASAEDVAVTVETAAERGRD-GRDVATEAMDELDVVESQIDETASA 336
                                       333344444444444444444444444444444433333333333333333.2223333344444444444444444 PP

                              Spc7 215 ieekkkelaelqeqleeleekieelkeqksele 247
                                       +                      +l e+++e+ 
  gi|313127492|ref|YP_004037762.1| 337 VV---------------------ALGERIEEID 348
                                       44.....................3333333332 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.012
                              Spc7 135 qllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..idkeeLeelreela 209
                                        l+e++ e+ ee+l++++e +++++++ e ++++ +e+e+  a++e+  ++ +e +e  ++  + ++++++  +e+a
  gi|313127492|ref|YP_004037762.1| 405 ALIEDVTERSEETLATVRETNRQVAESVETVETAIEEFEAIVAAVEDVNTSVREVSEATDQqaSSSQDVAAHVDEVA 481
                                       47778888888888888888888888888888888888888888888777777744443332255677777777777 PP

                              Spc7 210 elkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                                       ++++e +++ +     ++  ++++e++++++++ ++l e+ a+ er
  gi|313127492|ref|YP_004037762.1| 482 NISEETAARTDSA---EDAATRQAESVDDIADRTRTLSERAAALER 524
                                       7777777444444...444444444444444445555555554444 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.045        21       8      51 ..     288     331 ..     282     332 .. 0.93
   2 ?    5.3   0.2     0.043        20       2      27 ..     436     461 ..     436     465 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.045
                      Exonuc_VII_S   8 LeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdeaeqkve 51 
                                        eeI++  E+  +++e + +    G   + e++++Ld +e +++
  gi|313127492|ref|YP_004037762.1| 288 VEEIAASAEDVAVTVETAAERGRDGRDVATEAMDELDVVESQID 331
                                       79999999**********************************97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.043
                      Exonuc_VII_S   2 EealaeLeeIvekLEsgelsLeeslk 27 
                                       E+a++e e+Iv+  E+ ++s+ e  +
  gi|313127492|ref|YP_004037762.1| 436 ETAIEEFEAIVAAVEDVNTSVREVSE 461
                                       89**************9999988765 PP

>> Mating_N  Mating-type protein beta 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4       0.4   1.9e+02      59      78 ..     222     241 ..     201     251 .. 0.78
   2 ?    2.6   3.6      0.31   1.5e+02      35      94 ..     227     282 ..     215     283 .. 0.69
   3 ?    9.9   0.4    0.0016      0.74      55      93 ..     390     428 ..     382     430 .. 0.88
   4 ?   -1.7   0.3       6.6   3.1e+03      65      91 ..     439     465 ..     431     479 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.4
                          Mating_N  59 eeTleliysfssliatvssg 78 
                                       ++T+++++sf++ ++t s+ 
  gi|313127492|ref|YP_004037762.1| 222 SSTIAEVQSFAAEVSTMSDE 241
                                       47888999999888888875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.31
                          Mating_N  35 alstFlsawskfdellqschdsLseeTleliysfssliatvssgllelesekeaiedels 94 
                                       ++++F+ + s++++ +q       e + e++  ++s+++ +s+g  e++++ ++++dels
  gi|313127492|ref|YP_004037762.1| 227 EVQSFAAEVSTMSDEAQTSI----ERANEASGAVASAVSEISDGADEQTEHLQTVADELS 282
                                       45555555555555555533....556777888999999999999999999999999997 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0016
                          Mating_N  55 dsLseeTleliysfssliatvssgllelesekeaiedel 93 
                                       + L eeT+e ++++s+li+ v++   e+ ++  ++++++
  gi|313127492|ref|YP_004037762.1| 390 KALAEETRESADEVSALIEDVTERSEETLATVRETNRQV 428
                                       579**********************99999988888776 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 6.6
                          Mating_N  65 iysfssliatvssgllelesekeaied 91 
                                       i +f +++a+v +      + +ea+++
  gi|313127492|ref|YP_004037762.1| 439 IEEFEAIVAAVEDVNTSVREVSEATDQ 465
                                       555555555554443333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1993  (0.111161); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                       152  (0.00847788); expected 17.9 (0.001)
Passed Fwd filter:                        85  (0.00474092); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 1.63u 0.37s 00:00:02.00 Elapsed: 00:00:00.61
# Mc/sec: 2703.28
//
Query:       gi|313127493|ref|YP_004037763.1|  [L=374]
Description: acetylornithine deacetylase/succinyldiaminopimelate desuccinylase-like deacylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-31  108.8   4.1    3.6e-31  108.5   4.1    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.9e-13   49.7   0.1      1e-12   47.9   0.0    1.8  2  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   4.1     4e-35   3.6e-31       2     202 ..      70     365 ..      69     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 4e-35
                                       EEEES-BSS.TTCGGGSSS..TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT CS
                                       xxxxxxxxx.xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVp.eeetdgwtt..pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr 75 
                                       l +H DvVp +e +   +   +f  +e+dG+lyGrG++dmkg v+a + a+r  + +g     ++v++ ++ EE+g+
  gi|313127493|ref|YP_004037763.1|  70 LVGHHDVVPpDESQ--VEDsgEFVVEERDGRLYGRGTADMKGAVAASMLAFRDAAPAG-----ELVFASFVGEETGG 139
                                       779******55555..44449******************************9966665.....9**********999 PP

                                       THHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE..................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                     Peptidase_M20  76 gGakallegleerekvdavfelhieepgileagklaigvv..................................... 115
                                       +Ga+  ++   +++++d+   ++++e++ + +g  +++ v                                     
  gi|313127493|ref|YP_004037763.1| 140 EGARGAIA---DGFAPDY---AIVGEGSTNYSGA-DVTDVavahkgrrastvvahgsaahasepeaganavyracda 209
                                       ***77777...5899999...5699999988666.4444468999******************************** PP

                                       ................................................................EEEEEEEEEESHE CS
                                       ................................................................xxxxxxxxxxxxx RF
                     Peptidase_M20 116 ................................................................kvevelleggapv 128
                                                                                                        ve+  +++ +p+
  gi|313127493|ref|YP_004037763.1| 210 vdvirgldvpeaevfgerlsgsvvvteidggsawnvvpercavtvdertvpgeyaelerveaieGVEWVIEQDLPPM 286
                                       *************************************************************9964777777****** PP

                                       EECCHHHHHHHHHHHHHHH...TSC.EEEEEESSSBHTHHHH..TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx...xxx.xxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 129 tlndsplvkalaeaaeelf...gek.velivsgpggtdarff..agiptvmifgpgs.glaHspnEyvdledlekgi 198
                                       +++d+++++ + +aa++++   g + + +++++  +tda+ +  ag+ t++i+gp++ g aH+ +E v+l+ le+++
  gi|313127493|ref|YP_004037763.1| 287 RCDDADFADRVLDAARRVHdarGDEtPAQVTKP-HATDAGRLaeAGT-TCVIYGPSEpGEAHTKDESVSLDVLERCY 361
                                       ******************988776656666777.********65555.8899**9977******************* PP

                                       HHHH CS
                                       xxxx RF
                     Peptidase_M20 199 kvla 202
                                       +++ 
  gi|313127493|ref|YP_004037763.1| 362 ETYR 365
                                       9986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.24   2.1e+03      84     107 ..      25      48 ..      16      50 .. 0.79
   2 !   47.9   0.0   1.2e-16     1e-12       1      90 [.     174     264 ..     174     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHTSCCST CS
                         M20_dimer  84 llpgedpeevleeieeilekeape 107
                                       ++ +ed  ++ ++ie++l++e  +
  gi|313127493|ref|YP_004037763.1|  25 IPSHEDETACGDAIESWLREETDA 48 
                                       788999999*********998766 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 1.2e-16
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.......TCCTCCCCCEECCE-CCCCEESSE CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia..eerslprttlnvtgiegGsaknvipde 75 
                                       ++hkG    ++ ++g a+H++ p+agaNA++ ++++++ ++ ++ ++a   +++l+  ++ vt+i+gGsa nv+p++
  gi|313127493|ref|YP_004037763.1| 174 VAHKGRRASTVVAHGSAAHASEPEAGANAVYRACDAVDVIRGLDVPEAevFGERLS-GSVVVTEIDGGSAWNVVPER 249
                                       589*******************************************9965444444.4689**************** PP

                                       EEEEEEEEHHHHHHH CS
                         M20_dimer  76 aeakidiRllpgedp 90 
                                       + +++d R++pge +
  gi|313127493|ref|YP_004037763.1| 250 CAVTVDERTVPGEYA 264
                                       ***********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2551.38
//
Query:       gi|313127494|ref|YP_004037764.1|  [L=520]
Description: carboxypeptidase taq [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     2e-181  604.1   0.2   2.3e-181  603.9   0.2    1.0  1  Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
  ------ inclusion threshold ------
       0.06   13.9   0.0       0.29   11.7   0.0    2.1  2  DsrC           DsrC like protein


Domain annotation for each model (and alignments):
>> Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  603.9   0.2  2.5e-185  2.3e-181       2     488 .]      28     512 ..      27     512 .. 0.98

  Alignments for each domain:
  == domain 1  score: 603.9 bits;  conditional E-value: 2.5e-185
                     Peptidase_M32   2 lkellkkvsalesasallewDketvmpkkgaearaeqlatLselahelltseevaellekleeekeeldekekavve 78 
                                       l +++k+v ++++a +ll+wD++++mp++g+ ar++ql+tLs +ah+llt+e v+e l++le+ ++ +  +++avv+
  gi|313127494|ref|YP_004037764.1|  28 LLQTYKRVANVRNAGGLLSWDQQVMMPEGGTPARSQQLSTLSAVAHDLLTDEAVGEKLDELEDADLTD--EQAAVVR 102
                                       77899*********************************************************988865..49***** PP

                     Peptidase_M32  79 elkreykkakkvpaelvealakasakaeaaWreareandfalfepsLeevielkreiaelledlkkspYdaLldeye 155
                                       e++r+y++a +vp+elve+++  s++a  aW+ea++++df+ f+p+Le+ ielkre+ae++ d++k+pY++L++e+e
  gi|313127494|ref|YP_004037764.1| 103 EIRRQYDRAVSVPSELVEEISTTSSEALPAWEEAKAEDDFSVFAPYLEKHIELKREYAEHI-DPDKDPYEVLFEEFE 178
                                       *************************************************************.*************** PP

                     Peptidase_M32 156 pgltvekidalFeelkealvpllkkikeskekekkdksflereipeekqrelsrellkalgfdfdrgrldeseHPFt 232
                                       p l  e+ +++ +el+++lvp++++i+e+  +  +d  +++++++e+ q+el+r++l+ lg+ ++rgr+d+s+HPF+
  gi|313127494|ref|YP_004037764.1| 179 PCLPLEQAEEILSELRDTLVPMIEQIREEGDDIATDAFTSKGDYSEDGQEELCRDVLSTLGYPWERGRMDTSSHPFS 255
                                       *******************************999998899************************************* PP

                     Peptidase_M32 233 tsfsrkDvRittryeednllsslfsvlHEaGHalYeqnlpeelsktplgggvslgihEsqSrlyEniigrskeFwev 309
                                       ++ +  D+R+ttr++e++ l slfs++HE+GHa Y+++lp+e++ tplg+ ++l++hEsqSrl+En++grs++Fw+v
  gi|313127494|ref|YP_004037764.1| 256 SG-TMFDARVTTRFDETDPLGSLFSTVHEFGHATYNLGLPDEHYATPLGEDRNLSVHESQSRLWENHVGRSEAFWNV 331
                                       **.88************************************************************************ PP

                     Peptidase_M32 310 llpklkeafpeqlddvsleefyeavnkveps.liRveADEltYslHillRyelEkeliegklsvkdlpeaWnekyke 385
                                       llp++ke+f+++ d v+l+e yea+n+v    liRve+DEltY+lHi++R+e+E++li+g+++v+d+pe+Wn+ky+e
  gi|313127494|ref|YP_004037764.1| 332 LLPTFKEHFQKAED-VTLQEAYEAANQVYDDnLIRVESDELTYHLHIIIRFEIERALIAGDIDVEDVPEVWNDKYEE 407
                                       *********99666.*************7766********************************************* PP

                     Peptidase_M32 386 yLgidppddaeGvLQDvHWssgafGYFPtYalGniyaaqlfeamekdlpel..eiakgefseikkWLkenihqkGsl 460
                                       yLgi+p++d+eG+LQD+HWs+g fGYFPtY+lG+++aaql+ a+e+d+++l   i++g+f+++ +WL+en+hq+G++
  gi|313127494|ref|YP_004037764.1| 408 YLGIRPETDSEGCLQDIHWSHGNFGYFPTYSLGSVMAAQLYAAAEEDIDDLagHIEAGDFEPLHEWLTENVHQHGAR 484
                                       ************************************************9999*99********************** PP

                     Peptidase_M32 461 ysseellkkatgeslnaeyyidyLkeky 488
                                       y+++el+ +at e+++a+++idy++eky
  gi|313127494|ref|YP_004037764.1| 485 YETNELVVQATDEDFTADAFIDYVTEKY 512
                                       ***************************9 PP

>> DsrC  DsrC like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.2e-05      0.29      22      60 ..      78     116 ..      72     136 .. 0.86
   2 ?   -3.2   0.0       1.3   1.2e+04       7      21 ..     413     426 ..     408     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
                              DsrC  22 seevaealakeegieLteehwevikflreyyeeygvapa 60 
                                       +e+v e+l + e+ +Lt+e+  v++ +r++y++   +p+
  gi|313127494|ref|YP_004037764.1|  78 DEAVGEKLDELEDADLTDEQAAVVREIRRQYDRAVSVPS 116
                                       5789999*************************9988886 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                              DsrC   7 ieldeegfLkdledw 21 
                                        e+d+eg L+d+ +w
  gi|313127494|ref|YP_004037764.1| 413 PETDSEGCLQDI-HW 426
                                       589999999987.45 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 3079.30
//
Query:       gi|313127495|ref|YP_004037765.1|  [L=60]
Description: hypothetical protein Hbor_27760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0033   16.8   3.9      0.021   14.2   3.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
     0.0072   16.0   1.2     0.0072   16.0   1.2    1.5  2  zinc_ribbon_2   zinc-ribbon domain
      0.008   16.2   0.5      0.009   16.0   0.5    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.13   12.2   2.7       0.32   11.0   2.7    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.18   11.5   0.5       0.18   11.5   0.5    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.33   11.0   2.5       0.59   10.1   0.2    2.0  2  YhfH            YhfH-like protein


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   3.2   7.2e-06     0.021       2      23 ..      34      55 ..      33      57 .. 0.92
   2 !    7.3   0.3    0.0011       3.2       3      11 ..      49      58 ..      47      60 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-06
                       zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCG 23
                                      +++CP CGa + + +++ C  CG
  gi|313127495|ref|YP_004037765.1| 34 KKQCPDCGAlH-DRSAVDCSVCG 55
                                      689******88.**********9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      v C+ CG+ p
  gi|313127495|ref|YP_004037765.1| 49 VDCSVCGWdP 58
                                      67******88 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   4.9e+03       7      15 ..       4      12 ..       4      12 .. 0.73
   2 !   16.0   1.2   2.4e-06    0.0072       2      20 ..      37      55 ..      36      55 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                     zinc_ribbon_2  7 aelqdnakF 15
                                      a++ d+a F
  gi|313127495|ref|YP_004037765.1|  4 APNADEALF 12
                                      578898876 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.4e-06
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCG 20
                                      Cp CGa ++  a+ C+ CG
  gi|313127495|ref|YP_004037765.1| 37 CPDCGALHDRSAVDCSVCG 55
                                      ******************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.5     3e-06     0.009       1      22 [.      37      58 ..      17      60 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3e-06
                               DZR  1 CpqCgeelppdarfCseCgtkl 22
                                      Cp Cg+ ++ +a  Cs Cg ++
  gi|313127495|ref|YP_004037765.1| 37 CPDCGALHDRSAVDCSVCGWDP 58
                                      8888888888888888888766 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.7   0.00011      0.32      23      54 ..      29      56 ..      17      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                    OrfB_Zn_ribbon 23 npayTSktCseCgsknkealsgrtfkCpnCgf 54
                                      + +y  k+C+ Cg+ +++      + C+ Cg 
  gi|313127495|ref|YP_004037765.1| 29 ETSYNKKQCPDCGALHDR----SAVDCSVCGW 56
                                      45667799******9999....8899999985 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5     6e-05      0.18      21      31 ..      34      44 ..      20      44 .. 0.92
   2 ?    1.9   0.4     0.059   1.8e+02       6      10 ..      51      55 ..      47      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                     zf-NADH-PPase 21 arvCpaCgleh 31
                                      +++Cp+Cg+ h
  gi|313127495|ref|YP_004037765.1| 34 KKQCPDCGALH 44
                                      79******998 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.059
                     zf-NADH-PPase  6 CgrCG 10
                                      C+ CG
  gi|313127495|ref|YP_004037765.1| 51 CSVCG 55
                                      77777 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2    0.0002      0.59      13      20 ..      34      41 ..      30      45 .. 0.89
   2 ?    0.7   0.2      0.17   5.1e+02      16      20 ..      51      55 ..      49      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                              YhfH 13 kKkCteCG 20
                                      kK+C++CG
  gi|313127495|ref|YP_004037765.1| 34 KKQCPDCG 41
                                      8******* PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
                              YhfH 16 CteCG 20
                                      C+ CG
  gi|313127495|ref|YP_004037765.1| 51 CSVCG 55
                                      999*9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 432.76
//
Query:       gi|313127496|ref|YP_004037766.1|  [L=616]
Description: ATP-dependent DNA helicase, rep family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-25   90.5   1.2    5.7e-12   45.8   0.0    2.7  3  UvrD-helicase    UvrD/REP helicase N-terminal domain
      2e-23   83.4   0.0    4.8e-23   82.1   0.0    1.7  1  AAA_19           AAA domain
      7e-16   58.5   0.0    9.1e-10   38.4   0.0    2.3  2  UvrD_C           UvrD-like helicase C-terminal domain
    2.4e-09   36.9   0.2     0.0035   17.1   0.0    2.7  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    3.8e-07   30.0   0.0    0.00077   19.2   0.0    2.5  2  AAA_30           AAA domain
    2.3e-05   24.3   0.0        2.1    8.1   0.1    3.8  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00091   18.9   0.0     0.0075   15.9   0.0    2.4  3  AAA_12           AAA domain
     0.0022   18.3   0.1       0.45   10.8   0.0    2.9  3  AAA_22           AAA domain
     0.0036   15.5   0.0     0.0056   14.8   0.0    1.2  1  Herpes_ori_bp    Origin of replication binding protein
      0.004   17.0   0.0      0.028   14.2   0.0    2.2  2  AAA_11           AAA domain
  ------ inclusion threshold ------
      0.049   13.4   0.0        4.7    6.9   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
      0.086   12.4   0.2       0.58    9.7   0.0    2.4  2  AAA_25           AAA domain
       0.13   11.4   0.0        2.7    7.1   0.0    2.6  3  DUF2075          Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   4.2e-15   5.7e-12      19     106 ..      12      85 ..       3     134 .. 0.85
   2 !   42.7   0.2   3.5e-14   4.8e-11     255     313 ..     220     278 ..     203     280 .. 0.91
   3 ?   -2.2   0.0       1.6   2.2e+03     186     226 ..     402     440 ..     305     490 .. 0.64

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.2e-15
                                       EE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HHHHHHHHHCTTSEEE CS
                     UvrD-helicase  19 eAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdderlrlalqnlseanis 95 
                                         ++GsGKT+ l +r+ ++++   +++++ilvv +T++Aa+E++eR++e+l  + +              + + n+ 
  gi|313127496|ref|YP_004037766.1|  12 FGGPGSGKTTALLDRVEEMLEDDDVTIRDILVVSYTRAAAAEIRERLAERLDISPR--------------ALQGNVA 74 
                                       679**********************************************8887652..............3445677 PP

                                       EHHHHHHHHHH CS
                     UvrD-helicase  96 TlHsfcqkilk 106
                                       T+H+ ++++l 
  gi|313127496|ref|YP_004037766.1|  75 TMHAKAYELLD 85 
                                       77776666665 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 3.5e-14
                                       HHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-THHHHHHHHH CS
                     UvrD-helicase 255 erykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdielflkkkkd 313
                                        +++++ iDE+QD    Qy++ +    + e +++ GD++Q +Y+++gAd++l+l +++d
  gi|313127496|ref|YP_004037766.1| 220 PNVDYLVIDEFQDITTLQYDVYQEWLPHLEGVLIAGDDDQVVYAWQGADPNLLLDAERD 278
                                       56899************************99***********************99876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.6
                                       HHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHH CS
                     UvrD-helicase 186 vskakekqlspkelkkafekasdlqkkiaeflkeyqeqkke 226
                                       ++ ++ + l    +++     s++++++ + + e+qe+   
  gi|313127496|ref|YP_004037766.1| 402 INGLEARRLADMLQES--AFGSNERDDLFDYIDELQEETGV 440
                                       2222222222222222..33455555555555555555544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   3.5e-26   4.8e-23       9     144 ..       5     263 ..       1     265 [. 0.92

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 3.5e-26
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae...........atTiHr 74 
                                        +kv  + +GpG+GKT+ l  +v++++e  +v  ++il+v++t+ Aa e+rerla+   +             T+H+
  gi|313127496|ref|YP_004037766.1|   5 DAKVTRLFGGPGSGKTTALLDRVEEMLEDDDVTIRDILVVSYTRAAAAEIRERLAE---RldispralqgnVATMHA 78 
                                       678999**********************************************9933...234688999999*****9 PP

                            AAA_19  75 lal.......................................................................... 77 
                                        a                                                                           
  gi|313127496|ref|YP_004037766.1|  79 KAYelldlsrndvvgekdkkefceeygvefedeyggagrrtarsttignkiiatsqwlqrtrrdvadwydvpfnwnv 155
                                       9999************************************************************************* PP

                            AAA_19  78 .........................................ldfddlltealelleeaeeekklqeeellivDEfqd 113
                                                                                 + d+ l   + +le+ ++++ + + ++l++DEfqd
  gi|313127496|ref|YP_004037766.1| 156 eevrlppeidpnaqegnkytptwpsdddridvpgvirgwrkYKGDNGLVGFADMLERVRQRSLVPNVDYLVIDEFQD 232
                                       **************************************999555555556667777777777887777********* PP

                            AAA_19 114 vdelqyrLlkallgekkklllvGDpdQliyv 144
                                       ++ lqy + +++l++ + +l+ GD+dQ +y+
  gi|313127496|ref|YP_004037766.1| 233 ITTLQYDVYQEWLPHLEGVLIAGDDDQVVYA 263
                                       *************77799**********997 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-06    0.0016       2     108 ..     282     382 ..     281     406 .. 0.88
   2 !   38.4   0.0   6.6e-13   9.1e-10     284     344 ..     494     573 ..     384     576 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   2 vLekNyRStksLlkaankflenilnrralekek..ktvekgekivvleaeteeeEaekiaatikalleknekledia 76 
                                       vL   yR ++++l+++n+ +++i +r  +e  k   ++++g  ++   +++  + a+++  ti++      ++e+i 
  gi|313127496|ref|YP_004037766.1| 282 VLPNSYRLPSRILDVVNEEIRHIDKR--QE--KdlHPRKEGGVVEGVASPSMLDLARNVRYTIEEDE----DDESIM 350
                                       66777*******************99..33..3359999***9******************998876....9***** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  77 vLvRsnkdadkiskaLkkegipfnvvdeekfF 108
                                       vL+R  ++  ++ +++  +gipf v+ +++++
  gi|313127496|ref|YP_004037766.1| 351 VLFRARYQMFQFIDEFLPLGIPFSVLTDQRMW 382
                                       ************************99988766 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 6.6e-13
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxx RF
                            UvrD_C 284 kekipiiTiHqAKGlEFdvVflag.leegtfPsyrskk.....................ekrleEEkRlfYVaiTRA 338
                                        +++ + TiH+AKG E d Vf+   l+e+ +  +++ +                     +   + E+R+fYV+++RA
  gi|313127496|ref|YP_004037766.1| 494 PNRVRVGTIHSAKGREADHVFVSTdLTEKVVE-QMAASvddeevsgveefttstdpvpiL--TDNERRVFYVGMSRA 567
                                       389*******************8515555555.333334777788888888888999542..789************ PP

                                       xxxxxx RF
                            UvrD_C 339 kkrLfi 344
                                       ++rL+i
  gi|313127496|ref|YP_004037766.1| 568 RERLVI 573
                                       ****98 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.6e-06    0.0035       3      23 ..     498     517 ..     496     526 .. 0.82
   2 !   16.9   0.0   2.9e-06     0.004      34      51 ..     556     573 ..     542     574 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-06
                          UvrD_C_2   3 yaltihkaQGsefpaVivfdp 23 
                                        + tih a+G e+++V+v   
  gi|313127496|ref|YP_004037766.1| 498 RVGTIHSAKGREADHVFV-ST 517
                                       688**************9.44 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.9e-06
                          UvrD_C_2  34 rrrlLYtavTRAreklil 51 
                                        rr +Y++++RAre+l++
  gi|313127496|ref|YP_004037766.1| 556 ERRVFYVGMSRARERLVI 573
                                       5***************98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.6e-07   0.00077      16      67 ..       4      59 ..       1      98 [. 0.79
   2 !    8.2   0.0    0.0013       1.8      76     173 ..     209     305 ..     194     324 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.6e-07
                            AAA_30 16 sgdrvavltGpAGtGKttal.kalreaweaag...grviglAptgkaAkvLaeelg 67
                                      s+++v+ l G++G+GKttal   ++e++e++    +++++++ t +aA++++e l 
  gi|313127496|ref|YP_004037766.1|  4 SDAKVTRLFGGPGSGKTTALlDRVEEMLEDDDvtiRDILVVSYTRAAAAEIRERLA 59
                                      667899999********9862677999999988999999***********998665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                            AAA_30  76 llkrlkgrarlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdlveaagigtaeL 151
                                       +l+r ++  +l p+ + l++DE   + t q +   + + +    v+++GD++Q     +G+  ++l++a++ + + L
  gi|313127496|ref|YP_004037766.1| 209 MLERVRQ-RSLVPNvDYLVIDEFQDITTLQYDVYQEWLPH-LEGVLIAGDDDQVVYAWQGADPNLLLDAERDEDVVL 283
                                       5555555.4566666*************999988888877.88899*********************999******* PP

                            AAA_30 152 tevvRqkeseeraaalalregd 173
                                        + +R  +     + +++r+ d
  gi|313127496|ref|YP_004037766.1| 284 PNSYRLPSRILDVVNEEIRHID 305
                                       9999996665555556666555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0016       2.1       5      22 ..      13      30 ..      11      73 .. 0.78
   2 ?    3.0   0.0     0.053        72      62     141 ..     221     300 ..     206     342 .. 0.75
   3 !    8.1   0.1    0.0015       2.1     201     233 ..     551     574 ..     473     575 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                   Viral_helicase1  5 GvpGcGKStlirkllrts 22
                                      G pG+GK+t++ + +++ 
  gi|313127496|ref|YP_004037766.1| 13 GGPGSGKTTALLDRVEEM 30
                                      89**********999883 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.053
                   Viral_helicase1  62 kgkililDEylllhaGyill.laalskaklvilfGDplQipfhsrnasfllahlpsslshrvgrrttyllpsdvaei 137
                                       + ++l++DE++  ++ + ++    l++++ v++ GD  Q  +  + +  ++  l  + ++ v     y+lps   ++
  gi|313127496|ref|YP_004037766.1| 221 NVDYLVIDEFQDITTLQYDVyQEWLPHLEGVLIAGDDDQVVYAWQ-GADPNLLLDAERDEDVVLPNSYRLPSRILDV 296
                                       3789******9999766666334479999***********99964.4457777788888888888899999999999 PP

                   Viral_helicase1 138 lsak 141
                                        ++ 
  gi|313127496|ref|YP_004037766.1| 297 VNEE 300
                                       9887 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0015
                   Viral_helicase1 201 lvllketdlelisesrenllvAlTRhrkslvil 233
                                       ++++         ++r +++v+++R+r++lvil
  gi|313127496|ref|YP_004037766.1| 551 ILTD---------NERRVFYVGMSRARERLVIL 574
                                       2222.........46999*************97 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.52   7.2e+02      95     138 ..      23      65 ..      18      78 .. 0.81
   2 ?   -3.2   0.0       3.9   5.4e+03      15      38 ..     278     301 ..     272     316 .. 0.80
   3 !   15.9   0.0   5.4e-06    0.0075     128     195 ..     482     574 ..     347     577 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.52
                            AAA_12  95 vvklvekllkkgseeerkkigvitpYraqvellkkklkekeeek 138
                                       +++ ve++l++   +  ++i v++  ra +  ++++l+e+ + +
  gi|313127496|ref|YP_004037766.1|  23 LLDRVEEMLEDDDVT-IRDILVVSYTRAAAAEIRERLAERLDIS 65 
                                       566788888888888.89*******9**********99887665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.9
                            AAA_12  15 ekvvlLdtqYRmhpeIsrfpsklf 38 
                                        + v+L   YR  ++I++ +++++
  gi|313127496|ref|YP_004037766.1| 278 DEDVVLPNSYRLPSRILDVVNEEI 301
                                       567889999999999999988865 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 5.4e-06
                            AAA_12 128 kkklkekeeeksekeievntvdgfQGrekdviilslVRsn....ekk....................eigflkde.r 179
                                       +  ++ + +  + ++++v+t+ +  Gre d +++s+  ++    +                       + +l+d+ r
  gi|313127496|ref|YP_004037766.1| 482 EAYFAGEYQGMDPNRVRVGTIHSAKGREADHVFVSTDLTEkvveQ-MaasvddeevsgveefttstdPVPILTDNeR 557
                                       333333333333344*********************999655441.1455555667777777777655776766414 PP

                            AAA_12 180 r.lNValTRAkskliiv 195
                                       r + V ++RA+++l+i+
  gi|313127496|ref|YP_004037766.1| 558 RvFYVGMSRARERLVIL 574
                                       4368***********98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00033      0.45       4      70 ..       5      68 ..       2      92 .. 0.63
   2 ?    4.0   0.0      0.04        55      77     105 ..     208     237 ..     195     262 .. 0.73
   3 ?   -2.0   0.1       2.9     4e+03      23     101 ..     408     435 ..     374     458 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                            AAA_22  4 tagilvvtGesGtGKTtll.rrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka 70
                                      +a+++ ++G +G+GKTt l  r+ e l e+ + + ++  vv++t ++    ++++++l++ l+ +  a
  gi|313127496|ref|YP_004037766.1|  5 DAKVTRLFGGPGSGKTTALlDRVEEML-EDDDVTIRDILVVSYTRAA---AAEIRERLAERLDISPRA 68
                                      6788889********996615566665.4444444555555555554...458888888888877777 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.04
                            AAA_22  77 ellealeqalraravielliiDEaqhlr..s 105
                                       ++le+++q +    v   l+iDE+q ++  +
  gi|313127496|ref|YP_004037766.1| 208 DMLERVRQRSLVPNV-DYLVIDEFQDITtlQ 237
                                       455666666666666.*********995332 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.9
                            AAA_22  23 rrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDE 99 
                                       rrl++ l+e a+  +er++                                                    +  iDE
  gi|313127496|ref|YP_004037766.1| 408 RRLADMLQESAFGSNERDD---------------------------------------------------LFDYIDE 433
                                       2333333333332223333...................................................3334444 PP

                            AAA_22 100 aq 101
                                        q
  gi|313127496|ref|YP_004037766.1| 434 LQ 435
                                       44 PP

>> Herpes_ori_bp  Origin of replication binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.1e-06    0.0056      59     100 ..      16      60 ..       5      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-06
                     Herpes_ori_bp  59 GsGkttALiewLkevldsedls...vlvvsCRrsFtntlserfnr 100
                                       GsGkttAL++ ++e+l+++d+    +lvvs  r+ ++++ er+++
  gi|313127496|ref|YP_004037766.1|  16 GSGKTTALLDRVEEMLEDDDVTirdILVVSYTRAAAAEIRERLAE 60 
                                       9*******************863336***************9976 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.1e-05     0.028      18      76 ..       7      60 ..       2     107 .. 0.85
   2 ?   -0.6   0.0      0.66   9.1e+02      78     126 ..     484     528 ..     472     558 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                            AAA_11 18 eitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr 76
                                      ++t + G PG+gKT++++  ++++      e +  + + iLv + + aA  e+ erl++
  gi|313127496|ref|YP_004037766.1|  7 KVTRLFGGPGSGKTTALLDRVEEM-----LEDDDVTIRDILVVSYTRAAAAEIRERLAE 60
                                      477888999***************.....456899**********************99 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.66
                            AAA_11  78 lldsegekykpkivRvgneeeriseavksvsleekvekrlekeekaqla 126
                                        + +e++  +p+ vRvg   ++ ++++  v++++ + ++  +++    a
  gi|313127496|ref|YP_004037766.1| 484 YFAGEYQGMDPNRVRVGTIHSAKGREADHVFVSTDLTEKVVEQM----A 528
                                       5667899999*******999777888888888888887776643....3 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0034       4.7      24      77 ..      16      67 ..      11      95 .. 0.74
   2 ?    3.9   0.0      0.03        41     113     144 ..     215     243 ..     196     261 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0034
                                      TSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 24 GsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77
                                      GsGKT+a l   +++++e+++ t   +l+v+ tr+ a ++ ++l ++++ i+ r
  gi|313127496|ref|YP_004037766.1| 16 GSGKTTALLD-RVEEMLEDDDVTIRDILVVSYTRAAAAEIRERLAERLD-ISPR 67
                                      9******555.555666778999999******************99988.3323 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.03
                                       HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 113 stgklnlsqvrflVlDEadrlldqgfsdfinr 144
                                       ++    + +v +lV+DE + +    + d +++
  gi|313127496|ref|YP_004037766.1| 215 QRSL--VPNVDYLVIDEFQDITTL-QYDVYQE 243
                                       3333..889*********999887.4444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00042      0.58      34      91 ..       7      59 ..       4      97 .. 0.73
   2 ?   -1.1   0.0      0.83   1.1e+03     128     154 ..     208     233 ..     177     243 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
                            AAA_25 34 elallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds.edelrrRlr 91
                                      +++ l+G pg+GKtt++ld + ++++++ ++       +  l+vs   + ++e+r+Rl+
  gi|313127496|ref|YP_004037766.1|  7 KVTRLFGGPGSGKTTALLDRVEEMLEDDDVTI------RDILVVSYTRAaAAEIRERLA 59
                                      6899***************9999998886644......345555544443345666655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.83
                            AAA_25 128 advdaleaaieevegvrlvviDplsra 154
                                         +++++++   v++v+ +viD ++ +
  gi|313127496|ref|YP_004037766.1| 208 DMLERVRQRSL-VPNVDYLVIDEFQDI 233
                                       22333333333.377*******99976 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.002       2.7       8      55 ..      13      62 ..       7     100 .. 0.71
   2 ?   -2.2   0.0       1.4   1.9e+03      79     102 ..     212     235 ..     201     292 .. 0.74
   3 ?    0.8   0.0      0.17   2.3e+02     280     359 ..     498     573 ..     495     575 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.002
                           DUF2075  8 GvaGtGKtvvllnllaeleddeeertavyl..svNhplvlvlrealakke 55
                                      G++G+GKt  ll  + e+ +d++   + +l  s  ++  + +re+la++ 
  gi|313127496|ref|YP_004037766.1| 13 GGPGSGKTTALLDRVEEMLEDDDVTIRDILvvSYTRAAAAEIRERLAERL 62
                                      9****************944444444444400444566667777777776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                           DUF2075  79 kaeekkeepkedvvivDEAhrllt 102
                                       +  ++   p++d +++DE + ++t
  gi|313127496|ref|YP_004037766.1| 212 RVRQRSLVPNVDYLVIDEFQDITT 235
                                       455666677777788887766655 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.17
                           DUF2075 280 evgseytiQGleldyvgviiGpdlvyrkeedrikfrgkksedkeakskrkkkkeseekaqkllkNayrVLLtRGrkG 356
                                       +vg+++++ G e+d v+v  +    +  e+   +++ ++++ +e ++ ++   +     + + +  ++V ++R+r+ 
  gi|313127496|ref|YP_004037766.1| 498 RVGTIHSAKGREADHVFVSTDLTEKVV-EQMAASVDDEEVSGVEEFTTST---DPVPILTDNERRVFYVGMSRARER 570
                                       5999**********9999866544443.4556677777777777777763...333344444444566667777777 PP

                           DUF2075 357 lyi 359
                                       l+i
  gi|313127496|ref|YP_004037766.1| 571 LVI 573
                                       766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 3571.45
//
Query:       gi|313127497|ref|YP_004037767.1|  [L=388]
Description: xaa-pro aminopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-43  148.4   0.2    2.9e-43  148.0   0.2    1.2  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.0   0.2   1.6e-47   2.9e-43       2     209 .]     151     370 ..     150     370 .. 0.88

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 1.6e-47
                                       HHHHHHHHHHHHHHHHHHHHHTT.............CBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTB CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpg.............vterelaaeieattlkrhgarglafppivasgenaavlhyt 65 
                                       ++r+++r+a + ++++ e +                 +++ l + ++a+ l+  g+r+ + ++++++g+ +a lhyt
  gi|313127497|ref|YP_004037767.1| 151 CLRRVQRAAVRGMRRAEEILAAAepmddeliwqdapLSTERLRRQVNAE-LAVYGVRDAG-NTVIGAGPTCADLHYT 225
                                       899************9765443222233333333336999999999988.6667888877.89*************9 PP

                                       CSSSB--TTEEEEEEEEEEET.TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHH CS
                     Peptidase_M24  66 pndrvlkegdlvlidagaeyd.gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevle 141
                                          +vl++++ +l+d+ ++   gy++D +rT++v++    +r++y av++a++a++++++pG++++ei++ a + l+
  gi|313127497|ref|YP_004037767.1| 226 GM-DVLRPDETILLDISPRGPhGYYGDLSRTYVVDSNGGWERRAYVAVEAALKAGLAEIEPGAHANEIHREAAAELT 301
                                       95.9***************988************8777799************************************ PP

                                       HTTB.......CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                     Peptidase_M24 142 sagl.......akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                       ++g+       ++ f+hg+GHgvG+++h++ ps+     + ++le Gmvft+Epg+y  p++ggvr+e++v+vte
  gi|313127497|ref|YP_004037767.1| 302 AHGFdpnadegEAGFTHGTGHGVGISLHEG-PSLR----EPVELESGMVFTVEPGVY-DPEQGGVRLEELVVVTE 370
                                       ***********9999*************98.*987....589***************.8999************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2680.35
//
Query:       gi|313127498|ref|YP_004037768.1|  [L=80]
Description: hypothetical protein Hbor_27790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   14.4   2.7      0.048   13.9   2.7    1.2  1  DUF3017   Protein of unknown function (DUF3017)


Domain annotation for each model (and alignments):
>> DUF3017  Protein of unknown function (DUF3017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.7   2.7e-06     0.048       2      43 ..      11      52 ..      10      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-06
                           DUF3017  2 llvllvvavglllvaldhwRrGalllGvalllaAvlRlvlps 43
                                      l+++l++av + + +l+++  G  +lG++l++ Avl +vlp+
  gi|313127498|ref|YP_004037768.1| 11 LAATLIFAVPVGVYGLNAFLDGQQVLGGGLVVVAVLMVVLPQ 52
                                      5788999*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 554.25
//
Query:       gi|313127499|ref|YP_004037769.1|  [L=622]
Description: di-/tricarboxylate transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-58  198.6   3.0    1.3e-58  198.6   3.0    2.3  2  CitMHS         Citrate transporter
    9.6e-22   77.6  39.1    2.8e-14   53.1  17.2    2.8  3  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    1.2e-18   66.7   1.3    2.2e-09   37.0   0.1    2.5  2  TrkA_C         TrkA-C domain


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6   3.0   2.2e-62   1.3e-58       1     297 [.      32     564 ..      32     567 .. 0.88
   2 !    3.2   0.7    0.0068        41     113     159 ..     559     615 ..     556     621 .. 0.60

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 2.2e-62
                                       xxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll.......vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlagg 70 
                                       +vl+++e+++ dv+a+ v+v+l        ++  e lsg+++p+++++l++ i+++++++tG+++rl+  ++ l++g
  gi|313127499|ref|YP_004037769.1|  32 VVLFVTEAVSPDVTAIAVIVALvalepftKVSAAEGLSGFSNPATVTILAMYILSRGIQRTGVVRRLGVEVAHLTRG 108
                                       59*********************888887777888****************************************** PP

                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  71 krd.llvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpg 145
                                       +++ llv++++lt+ ++++v+n++vv+++ip+v +la++ ++ +p+ llipl++a+++ g+lt++Gt          
  gi|313127499|ref|YP_004037769.1| 109 SENrLLVAIIALTGPIAGIVNNTPVVAVFIPMVTDLANE-SGVSPSkLLIPLSYASMLAGTLTLFGTA--------- 175
                                       **************************************9.7777777*********************......... PP

                                       xxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            CitMHS 146 lslpnlll.....................lalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpv. 200
                                          +nl++                     ++++lvg+++l++++                          r+llp+ 
  gi|313127499|ref|YP_004037769.1| 176 ---TNLVAselsadllgrpfgvflltpvgIVAFLVGAAYLLTVG--------------------------RWLLPAr 223
                                       ...5555555555555555555555565599999999*******..........................8888888 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|313127499|ref|YP_004037769.1| 224 vppgsrteryemqpylarvlvtarspfvgnsaqtvaadahrdlgldvldvvrgadhfvatdsdrelasrdiltvrgn 300
                                       88888888888888888888888999999999999999999999999999999999999999999999999999999 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|313127499|ref|YP_004037769.1| 301 pptiqqfveygslrllpratvtdaeldnperstlvelivpadsslvgetvtgarlrerydatvlairraggelvrdd 377
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ......................................................................xxxxxxx RF
                            CitMHS 201 ......................................................................atillla 207
                                                                                                                   +
  gi|313127499|ref|YP_004037769.1| 378 igetqlhggdalllqttevsaeflaenddvvvtgevfdevmarvreggvsstaliafgilfgvvavaalgL-----L 449
                                       99999999999999999999999999999999999999999999999999888888888877666555550.....1 PP

                                       ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxxxx RF
                            CitMHS 208 ........................ykkveWsvlllfaGvfllvgaleqtGilealadllga...g.gplvalalvlg 256
                                                               y++v+Wsv++l+aG+++l+ al++tG + ++ad+++    g +plv+l+l+++
  gi|313127499|ref|YP_004037769.1| 450 pisvaaltgvlamfvtgvlspneaYDAVNWSVIFLLAGIIPLGIALRETGAAALVADAVSGvavGlPPLVVLVLFYL 526
                                       555555666667778999********************************9999999994458768999999***** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 257 liallsafisnvavaalmapialgmapalgllspsplalal 297
                                       l++++ ++i +va ++l++pia+++a+++g   ++p+ ++l
  gi|313127499|ref|YP_004037769.1| 527 LTGAFANVITPVASVVLFLPIAASTASSIG---ADPFSFVL 564
                                       ***************************999...88888877 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0068
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxx RF
                            CitMHS 113 ppllliplalaaniggaltpiGtpttraa...........arpglslpnllllalllv 159
                                       p ++++ + +aa +   +tp+G  t +++           +r+g  l+ ll+++  ++
  gi|313127499|ref|YP_004037769.1| 559 PFSFVLGVTFAATTAF-MTPVGYQTNLMVygpggytfsdyVRVGAPLQLLLAVVTSVA 615
                                       6678899999999999.*******6666655555555544333333333333333333 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1  12.8   8.4e-11     5e-07      26     210 ..      17     189 ..       9     190 .. 0.87
   2 !    6.5   2.6   0.00063       3.8     377     432 ..     126     180 ..     101     219 .. 0.83
   3 !   53.1  17.2   4.6e-18   2.8e-14     295     466 ..     453     620 ..     430     622 .] 0.93

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 8.4e-11
                     Na_sulph_symp  26 leskawrllaifiaaivglileplplavialialsllavligvlaakalsevlsgfssdttlLvfaalliaaavekt 102
                                       l++   +++a+++ a+v +++e+++  v+a++ +  l++l  +++ ++  e lsgfs+ +t+ ++a ++++++++ t
  gi|313127499|ref|YP_004037769.1|  17 LPVSVLVVFAVVLGAVVLFVTEAVSPDVTAIAVIVALVALEPFTK-VSAAEGLSGFSNPATVTILAMYILSRGIQRT 92 
                                       56667789************************9999999999999.9999*************************** PP

                     Na_sulph_symp 103 gLgkRiAlvlvkivGkrtliLgyalvladlllapatpsntAraggivfpvikslssafgsepekqserkigaylmlt 179
                                       g  +R+   + +    +  +L  a+++++  +a ++  n    +++  p++ +l++  g++p k         l++ 
  gi|313127499|ref|YP_004037769.1|  93 GVVRRLGVEVAHLTRGSENRLLVAIIALTGPIAGIV--NNTPVVAVFIPMVTDLANESGVSPSK---------LLIP 158
                                       ********9998887777778888877776665544..33445566669*****9999999988.........8899 PP

                     Na_sulph_symp 180 vvqsasitsiaflTamApNllllglinsilg 210
                                         +++++ ++ +l ++A Nl++++l +++lg
  gi|313127499|ref|YP_004037769.1| 159 LSYASMLAGTLTLFGTATNLVASELSADLLG 189
                                       999********************99888776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00063
                     Na_sulph_symp 377 lfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpiv 432
                                        +  +t  +a+++p++  +a+   g+ p  + ++l  a+ lag+l+ ++t+ n ++
  gi|313127499|ref|YP_004037769.1| 126 GIVNNTPVVAVFIPMVTDLANES-GVSPSKLLIPLSYASMLAGTLTLFGTATNLVA 180
                                       55678999**************9.999************************99885 PP

  == domain 3  score: 53.1 bits;  conditional E-value: 4.6e-18
                     Na_sulph_symp 295 tvaivvlvillllrvldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslf 371
                                       + a+ ++  ++++ vl+ +    +   W +++ll+g+i l   l ++g    +++++++      p +++++++ l+
  gi|313127499|ref|YP_004037769.1| 453 VAALTGVLAMFVTGVLSPN-EAYDAVNWSVIFLLAGIIPLGIALRETGAAALVADAVSGVAV-GLPPLVVLVLFYLL 527
                                       568889999********99.6778899*******************************9998.56778888999999 PP

                     Na_sulph_symp 372 vlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGf 448
                                         ++      +A ++ +lpi ++ a +i ga+p  ++l +++a   a f++p++   n +v+g g     dy r+G+
  gi|313127499|ref|YP_004037769.1| 528 TGAFANVITPVASVVLFLPIAASTASSI-GADPFSFVLGVTFAATTA-FMTPVGYQTNLMVYGPGGYTFSDYVRVGA 602
                                       999999999*******************.*****************9.***************************** PP

                     Na_sulph_symp 449 ilsiigllillllgalww 466
                                       +l+++  ++  +++al+w
  gi|313127499|ref|YP_004037769.1| 603 PLQLLLAVVTSVAIALYW 620
                                       ****************** PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1     2e-10   1.2e-06       1      67 [.     239     309 ..     239     310 .. 0.93
   2 !   37.0   0.1   3.6e-13   2.2e-09       1      61 [.     334     397 ..     334     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2e-10
                                       CEEEEEE--GGGTTSBHHHHTHHHH...S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar...gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       l++v v+a sp+vG + + +   a+   g  v+ ++Rg ++++  ++d +L ++D+l+v g+p +++++ e
  gi|313127499|ref|YP_004037769.1| 239 LARVLVTARSPFVGNSAQTVAADAHrdlGLDVLDVVRGaDHFVATDSDRELASRDILTVRGNPPTIQQFVE 309
                                       6899***************99999999***********888888888********************9976 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 3.6e-13
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--T.T-B--TT-EEEEEEEHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsg.dtvLeeGDvllvvgspsd 61 
                                       lve+ vpa+s lvG t+  ++lr+r +++v+airR  gel+  +  +t+L+ GD ll+ ++  +
  gi|313127499|ref|YP_004037769.1| 334 LVELIVPADSSLVGETVTGARLRERyDATVLAIRRAgGELVRDDIgETQLHGGDALLLQTTEVS 397
                                       699*******************************999777777767***********9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4211.91
//
Query:       gi|313127500|ref|YP_004037770.1|  [L=224]
Description: hypothetical protein Hbor_27810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-28   96.6   0.0    1.3e-27   95.8   0.0    1.4  1  DUF502    Protein of unknown function (DUF502)


Domain annotation for each model (and alignments):
>> DUF502  Protein of unknown function (DUF502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0   7.1e-32   1.3e-27       2     105 ..      76     179 ..      75     180 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 7.1e-32
                            DUF502   2 vvlllillvGllasnligrkllklgerllkriPlvksiYsalkqvvetfsseekksfrevvlveyprkglwalgFvt 78 
                                       ++ ++++l+G++as+ +gr+l++ +er ++ +Plv++iY  ++qv+e++ + +++ f++vvlveyprkg++++gFvt
  gi|313127500|ref|YP_004037770.1|  76 ILAIMLTLIGYVASRELGRRLFGGLERGVRLVPLVRTIYFGVRQVSESLTR-QSEGFDRVVLVEYPRKGIYSIGFVT 151
                                       567999*******************************************87.8888********************* PP

                            DUF502  79 get.egelatkgeedlvaVfvPtspnpt 105
                                       ++  ++ +a++++++l++Vf+P+spnpt
  gi|313127500|ref|YP_004037770.1| 152 THGpRAAVAATENDELLTVFLPHSPNPT 179
                                       ***8888877799**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1518.68
//
Query:       gi|313127501|ref|YP_004037771.1|  [L=203]
Description: riboflavin synthase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-45  151.1   0.3    3.5e-21   75.0   0.0    2.0  2  Lum_binding    Lumazine binding domain
  ------ inclusion threshold ------
      0.027   14.1   0.0      0.072   12.8   0.0    1.8  1  Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain


Domain annotation for each model (and alignments):
>> Lum_binding  Lumazine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.1   4.9e-25   4.4e-21       1      87 []       3      88 ..       3      88 .. 0.91
   2 !   75.0   0.0   3.9e-25   3.5e-21       1      87 []     101     185 ..     101     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 4.9e-25
                                      -S--SEEEEEEEEE.ECGCTTEETEESGGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG--TT CS
                       Lum_binding  1 tGiVeevgtvesiekeekledltielpelakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgelkvg 79
                                      tGiVe++g v++ ++++  ++l++  p+++   +++G+siav GvcLTV + +++e++f+v +++eT+e+t lg++++g
  gi|313127501|ref|YP_004037771.1|  3 TGIVEGTGVVVAATDDDGGRRLRL-SPDVTFEDLRHGQSIAVSGVCLTVEDYSTDEQWFDVFLAAETVEKTYLGDVSEG 80
                                      8************88887899999.55788888899*************8666779*********************** PP

                                      SEEEEEEE CS
                       Lum_binding 80 dkVNlEra 87
                                      d+VNlEra
  gi|313127501|ref|YP_004037771.1| 81 DRVNLERA 88
                                      ******96 PP

  == domain 2  score: 75.0 bits;  conditional E-value: 3.9e-25
                                       -S--SEEEEEEEEE.ECGCTTEETEES.GGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG- CS
                       Lum_binding   1 tGiVeevgtvesiekeekledltielp.elakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgel 76 
                                       +G+V+++ tv+ ie+ ++ + ++++lp el ky+v+kG s++++G++LTV+  + +e+ f v++ip+T++ ttl+e+
  gi|313127501|ref|YP_004037771.1| 101 QGHVDTTTTVTGIERVGDDWFFEFDLPeELGKYVVAKG-SVCLDGISLTVA--DRRESDFAVAIIPTTYDLTTLSEK 174
                                       8************9889999****999***********.***********9..67899******************* PP

                                       -TTSEEEEEEE CS
                       Lum_binding  77 kvgdkVNlEra 87 
                                       +vgd V +E++
  gi|313127501|ref|YP_004037771.1| 175 SVGDPVHVEVD 185
                                       *********97 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     8e-06     0.072      20      45 ..      20      43 ..       7      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8e-06
                     Prot_ATP_OB_N 20 ggrrmrVavsPlvdaeeLrpGqeVlL 45
                                      ggrr+r+  sP+v  e+Lr+Gq + +
  gi|313127501|ref|YP_004037771.1| 20 GGRRLRL--SPDVTFEDLRHGQSIAV 43
                                      6888887..*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1321.28
//
Query:       gi|313127502|ref|YP_004037772.1|  [L=334]
Description: hypothetical protein Hbor_27830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-45  153.2  10.5    5.7e-45  153.2  10.5    1.6  2  PrsW-protease  PrsW family intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> PrsW-protease  PrsW family intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.3      0.42   7.5e+03       5      23 ..      47      66 ..      44      80 .. 0.62
   2 !  153.2  10.5   3.2e-49   5.7e-45       1     184 [.      98     285 ..      98     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.42
                     PrsW-protease  5 lllaaflwgalvavl.lall 23
                                      +l+ a+++g lv++  +a++
  gi|313127502|ref|YP_004037772.1| 47 FLIIAVAFGLLVSIGgFAAI 66
                                      56666666666666633443 PP

  == domain 2  score: 153.2 bits;  conditional E-value: 3.2e-49
                     PrsW-protease   1 eplwlllaaflwgalvavllalllntvlqallraelgkfiaeflaaflvaglvEEllKalgvllllllrrrefdepl 77 
                                       epl ll+++fl+ +l+a + a++ln+++  ++  e  +f++++l++flv+g+vEE++K+l+v l+++  +++f++++
  gi|313127502|ref|YP_004037772.1|  98 EPLVLLVGTFLLSVLTASF-AAILNSLIGGYF--EILGFAGTLLSFFLVVGPVEESMKLLAVRLFAY-TDDRFNSVV 170
                                       7999***************.*********988..999*****************************6.********* PP

                     PrsW-protease  78 dGivygaavglGFavlEnllYyvqalpsaane....gqlgglqllilRillsvagHalftallGiglglaksrrraa 150
                                       dG vyga++glGFa++En++Y++++lp ++ +        g +++++R+l++ +gH++++a++G++lglak++r+  
  gi|313127502|ref|YP_004037772.1| 171 DGAVYGAMAGLGFAFIENAIYITRELPVQNLDlslgLLGMGGSITAARALAG-PGHVIYSAIAGYYLGLAKFNRE-- 244
                                       **************************999998666333334455******99.******************9998.. PP

                     PrsW-protease 151 rrvqilllglllavllHalwNllaslaelllav.......v 184
                                       +r +i+++gll+a+++Ha++N+++++++++  +        
  gi|313127502|ref|YP_004037772.1| 245 NRGPIIIKGLLIAAFVHAMYNVTVGFGTVAIDLftplsglW 285
                                       9***********************99554333345554431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2466.51
//
Query:       gi|313127503|ref|YP_004037773.1|  [L=125]
Description: hypothetical protein Hbor_27840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 862.92
//
Query:       gi|313127504|ref|YP_004037774.1|  [L=473]
Description: RNA-binding protein au-1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-16   58.9   1.2    7.6e-16   58.1   1.2    1.5  1  DUF402    Protein of unknown function (DUF402)
    0.00079   19.7   0.0     0.0023   18.3   0.0    1.8  1  S1        S1 RNA binding domain
     0.0032   17.6   0.0      0.024   14.8   0.0    2.2  2  MoeA_C    MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   1.2   1.3e-19   7.6e-16       3      68 .]     378     443 ..     376     443 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.3e-19
                                       EEEEE-TT-SEEEEEEEETTTEEEEEEEEEES--EE..E.EEE-EEEEEEESEEE......-HHHH CS
                            DUF402   3 elwllplglwynvfhfldgdgrlqglYvDiatppevgegawktiDlyLDlvvspdgevevlDedEL 68 
                                       +l+ +++g+w+  ++++ + g+l+g Yv+++tp e  +++++++Dl +D++ +pdg+ve++D dEL
  gi|313127504|ref|YP_004037774.1| 378 ALTKFREGRWWYPTVYRSAAGDLKGTYVNVCTPVECFPDEVRYVDLHVDVIKHPDGTVERVDDDEL 443
                                       677799******************************9999*************************8 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.8e-07    0.0023       4      62 ..      94     142 ..      92     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.8e-07
                                       TTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEE CS
                                S1   4 kgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlk 62 
                                        g+v+++ Vt+    Ga   lg ++egf+p +e  ++         + +Gd v+v+v +
  gi|313127504|ref|YP_004037774.1|  94 PGAVFDARVTDTKGSGAVCSLG-EAEGFLPFHETNDR---------IEEGDAVRVQVRE 142
                                       59********************.*********98865.........8888888888865 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     4e-06     0.024      31      70 ..     100     139 ..      94     140 .. 0.90
   2 ?   -0.6   0.0      0.27   1.6e+03       2      21 ..     152     171 ..     151     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-06
                                       EEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEE CS
                            MoeA_C  31 aeptgkqgSglLsslaeAnglivipegtegleaGeeVevi 70 
                                       a+ t ++gSg++ sl eA+g++   e ++++e+G+ V v+
  gi|313127504|ref|YP_004037774.1| 100 ARVTDTKGSGAVCSLGEAEGFLPFHETNDRIEEGDAVRVQ 139
                                       5556689******************************997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                                       EEESS-EE--SSS-EEEEEE CS
                            MoeA_C   2 arlaedlksdpgrreflRvi 21 
                                       a l++ +++d+g ++++R++
  gi|313127504|ref|YP_004037774.1| 152 ASLGTGIRADGGLATLVRGR 171
                                       789999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2988.78
//
Query:       gi|313127505|ref|YP_004037775.1|  [L=110]
Description: thioredoxin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-10   38.9   0.2      1e-09   38.4   0.2    1.3  1  NifU      NifU-like domain


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.2   5.8e-14     1e-09      11      67 .]      21      78 ..      12      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 5.8e-14
                                      GG--GG--EEEEEEEETT..EEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EEE CS
                              NifU 11 PaLasdGGdielvdvdeg..vVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeVe 67
                                      P ++++GGd  + + d +  +V v+l GaC+gC  s++t  + i++ L   +++v+ V+
  gi|313127505|ref|YP_004037775.1| 21 PIIQMHGGDSVVRKADPEtgEVVVELGGACAGCGISNITA-NNIKADLIMDFDDVTDVQ 78
                                      99*******88887776666********************.99*****99999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 690.13
//
Query:       gi|313127506|ref|YP_004037776.1|  [L=497]
Description: hypothetical protein Hbor_27870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-12   44.8   4.4    5.5e-06   25.6   0.0    6.0  7  LVIVD        LVIVD repeat
  ------ inclusion threshold ------
      0.016   15.0   1.0      0.016   15.0   1.0    2.6  2  TAT_signal   TAT (twin-arginine translocation) pathway signal
      0.027   13.3   0.0        2.3    7.0   0.0    3.5  5  Beta_propel  Beta propeller domain
      0.038   12.8   0.5        1.1    8.1   0.1    2.5  2  SBP56        56kDa selenium binding protein (SBP56)


Domain annotation for each model (and alignments):
>> LVIVD  LVIVD repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0024        11      14      35 ..      56      76 ..      48      82 .. 0.80
   2 !    6.6   0.0    0.0011       4.9      24      37 ..     126     139 ..     121     144 .. 0.79
   3 ?   -1.4   0.0      0.32   1.5e+03      20      27 ..     167     174 ..     156     177 .. 0.85
   4 !   25.6   0.0   1.2e-09   5.5e-06       6      40 ..     205     239 ..     201     241 .. 0.95
   5 ?   -3.2   0.0       1.2   5.3e+03      11      17 ..     263     269 ..     263     273 .. 0.80
   6 ?    0.4   0.0     0.089     4e+02      27      34 ..     310     317 ..     304     323 .. 0.86
   7 ?    1.2   0.1     0.052   2.3e+02      27      34 ..     363     370 ..     363     373 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0024
                             LVIVD 14 aYvAdqdngLvIvDISNpSspt 35
                                      aY A    g v vDIS p  p+
  gi|313127506|ref|YP_004037776.1| 56 AYLA-ATTGYVTVDISTPDRPS 76
                                      9999.55999******998876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0011
                             LVIVD  24 vIvDISNpSsptlk 37 
                                        +vD+S+p+ p  +
  gi|313127506|ref|YP_004037776.1| 126 LVVDVSDPADPERV 139
                                       69*******99755 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.32
                             LVIVD  20 dngLvIvD 27 
                                        n Lv++D
  gi|313127506|ref|YP_004037776.1| 167 ANALVVID 174
                                       489****9 PP

  == domain 4  score: 25.6 bits;  conditional E-value: 1.2e-09
                             LVIVD   6 dvavsGnYaYvAdqdngLvIvDISNpSsptlkgsy 40 
                                       dv v ++ aY A +d g  I+D+S p+ ptl gs+
  gi|313127506|ref|YP_004037776.1| 205 DVYVHEDTAYLAYWDAGTWILDVSEPADPTLLGSV 239
                                       99*******************************98 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 1.2
                             LVIVD  11 GnYaYvA 17 
                                       Gn  YvA
  gi|313127506|ref|YP_004037776.1| 263 GNHHYVA 269
                                       8999**9 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 0.089
                             LVIVD  27 DISNpSsp 34 
                                       D+S+p++p
  gi|313127506|ref|YP_004037776.1| 310 DVSDPAAP 317
                                       9*****99 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.052
                             LVIVD  27 DISNpSsp 34 
                                       D+S+p++p
  gi|313127506|ref|YP_004037776.1| 363 DVSDPTNP 370
                                       9******9 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.0   3.6e-06     0.016       2      18 ..       1      17 [.       1      23 [. 0.90
   2 ?   -1.6   0.7      0.66   2.9e+03      10      20 ..     440     450 ..     439     454 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAa 18
                                      + RRdFL+++A ++A +
  gi|313127506|ref|YP_004037776.1|  1 MHRRDFLRAGALLGASG 17
                                      78************976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                        TAT_signal  10 gsAAaaAAaal 20 
                                       gs++++AA ++
  gi|313127506|ref|YP_004037776.1| 440 GSLVGTAASGT 450
                                       78888888765 PP

>> Beta_propel  Beta propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.14   6.4e+02      93     112 ..      62      81 ..      39      87 .. 0.66
   2 ?    0.2   0.0     0.057   2.6e+02      96     133 ..     126     163 ..     102     217 .. 0.72
   3 ?   -2.7   0.0      0.43   1.9e+03     334     349 ..     224     239 ..     210     242 .. 0.77
   4 ?    7.0   0.0   0.00051       2.3     355     402 ..     265     323 ..     257     346 .. 0.75
   5 ?   -0.6   0.0       0.1   4.6e+02     389     408 ..     363     382 ..     359     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.14
                       Beta_propel  93 tkvliyDisdkenpkllrel 112
                                       t ++++Dis+++ p +l+e+
  gi|313127506|ref|YP_004037776.1|  62 TGYVTVDISTPDRPSVLAEV 81 
                                       66667777777777666665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.057
                       Beta_propel  96 liyDisdkenpkllreleldGsyvssRkigdklylvss 133
                                       l++D+sd+++p+ ++ +e +  +++  + ++++yl  +
  gi|313127506|ref|YP_004037776.1| 126 LVVDVSDPADPERVSFFETKYPIHNCFVRDEHAYLTRN 163
                                       55555555555555555555555555555555554444 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.43
                       Beta_propel 334 viDLsdpanPkilGeL 349
                                       ++D s+pa+P+ lG +
  gi|313127506|ref|YP_004037776.1| 224 ILDVSEPADPTLLGSV 239
                                       5677777777777754 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.00051
                       Beta_propel 355 SeYLhpydenhLlGiGke........adeegeee.........qglklslFDVsDpanpkevakv 402
                                         Y    + + LlGiGke               +             + l+DVsDpa+p   +++
  gi|313127506|ref|YP_004037776.1| 265 HHYVATDESGTLLGIGKEswaqriggN------DedsetrligGPSGIDLWDVSDPAAPEHRSTI 323
                                       55666667889*****99664444332......2556666988445689**********987765 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.1
                       Beta_propel 389 DVsDpanpkevakvvigdrg 408
                                       DVsDp+np ++  ++++d+ 
  gi|313127506|ref|YP_004037776.1| 363 DVSDPTNPEQLTWWRMPDEA 382
                                       99999999999888887776 PP

>> SBP56  56kDa selenium binding protein (SBP56)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.014        61     276     347 ..     161     240 ..     129     253 .. 0.73
   2 ?    8.1   0.1   0.00024       1.1     319     342 ..     350     372 ..     337     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.014
                             SBP56 276 keedekweaekvieipa.kkvegeelpel..........pglvtDillslDDrflyvsnWltGdlrqydisdpkkPk 341
                                       + +d++ +a  vi++++ + v +++l ++             + D+ +  D    y++ W  G  +  d+s+p++P 
  gi|313127506|ref|YP_004037776.1| 161 TRNDGEANALVVIDLESgEAVGEWSLTDVdevwgdvpseRRPLHDVYVHEDT--AYLAYWDAGT-WILDVSEPADPT 234
                                       4566667777888887624455778888844444444332223444444443..4778999996.789********* PP

                             SBP56 342 ltgqvr 347
                                       l g+v 
  gi|313127506|ref|YP_004037776.1| 235 LLGSVA 240
                                       999985 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00024
                             SBP56 319 lyvsnWltGdlrqydisdpkkPkl 342
                                       ly s+W  G ++++d+sdp++P++
  gi|313127506|ref|YP_004037776.1| 350 LY-SAWYRGGVKRHDVSDPTNPEQ 372
                                       44.89*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3444.52
//
Query:       gi|313127507|ref|YP_004037777.1|  [L=322]
Description: glucokinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-46  157.6   0.0    5.8e-46  157.3   0.0    1.0  1  ROK          ROK family
    3.1e-06   26.9   0.2    1.5e-05   24.7   0.2    1.9  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    6.8e-06   25.8   0.1    8.7e-06   25.4   0.1    1.5  1  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.047   14.1   0.0      0.064   13.7   0.0    1.3  1  FtsA         Cell division protein FtsA
        0.2   11.4   0.2       0.34   10.7   0.2    1.4  1  AAA_lid_4    RuvB AAA lid domain


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.3   0.0   1.6e-49   5.8e-46       1     289 [.       4     309 ..       4     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 1.6e-49
                                       EEEEEE-SSEEEEEEEETTS-EEEEEEEEEHCC....HHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCC CS
                               ROK   1 tigidiGgtkialalvdeegeilarekvetpte....tteetlvdaiaelvdeaerkadeliavgigspGlisdksg 73 
                                       ++g+d+G+t+i++ + de+g++ a+++  tp+      + e++  ++ e  +ea  + ++ +a g++s G+++  +g
  gi|313127507|ref|YP_004037777.1|   4 YVGVDLGATNIRAVVADEDGTVIASRSDGTPRGptgiAVTEAILRVVRETCSEAGIRPNQAVAAGVASIGPLDLAEG 80 
                                       68**********************9999666641122457888899999999999999******************* PP

                                       EBSSGGC.GCC.CCTTHHHHHHHHHTS-.EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE-- CS
                               ROK  74 kivstpn.itw.enfdlvekleerlnvp.vevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitG 147
                                        + +++n ++  + ++l + l+  l+ + v+++nD na   +E +   + + ++++yvt++ GvGaGv ++g++++G
  gi|313127507|ref|YP_004037777.1|  81 AVENPANlPDTiDRIPLTGPLSVLLDTErVYLHNDTNAGVIGERF-HSERNPDDMVYVTISSGVGAGVCVDGNVLSG 156
                                       *******76678*************99769**************9.88999************************** PP

                                       TTS-TT-GGGSBS-TTS-B.-TTS-BSBHHHCCSHHHHHHCHTC.............CGTTS-HHHHHHHHCTT-HH CS
                               ROK 148 rnGvagelGHiqldpegek.cgCGnqgClEtlasgralekraqq.............kgekleakeiiklaekgdev 210
                                         G+age+GH++ldp+g   cgCG  g +E+++sg+ + ++a+                 + +a++++++ae  de 
  gi|313127507|ref|YP_004037777.1| 157 WDGNAGEVGHMTLDPQGLLtCGCGHDGHWEAYCSGNNIPRYAEFlyeeddvetslpiDDPDFSAADVFNHAED-DEF 232
                                       *****************988*********************999999********999999**********99.*** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH--SEEEEEHCCC.TSTTHH.HHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHHH CS
                               ROK 211 aeevverlaeylakaiadlinlfdpqaivlgGgvs.eadkll.eairklvkkylnkklevpvveivaaklgdkagll 285
                                       a  vv++++++ a +ia+++ +++p  i +gG v  + ++l  ++ir+ + ++++ + ++    i    lgd+  ++
  gi|313127507|ref|YP_004037777.1| 233 ARYVVDQVGHWNAMGIANIVHAYAPLTIYVGGAVAlNNPDLTlDPIRERMDEMVMVNVPQ----IELTTLGDEVVVQ 305
                                       **********************************735566778*********99965443....6678899999999 PP

                                       HHHH CS
                               ROK 286 Gaaa 289
                                       Ga+a
  gi|313127507|ref|YP_004037777.1| 306 GALA 309
                                       9887 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.2   4.2e-09   1.5e-05       1      77 [.       3      71 ..       3      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.2e-09
                                      EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE CS
                            FGGY_N  1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisg 77
                                      +++g+D+G+t+++a+v de+g+v+as +   +      g       ++ +a+ +++r+++++agi ++q++a g+++
  gi|313127507|ref|YP_004037777.1|  3 YYVGVDLGATNIRAVVADEDGTVIASRSDGTPRGPT--GI------AVTEAILRVVRETCSEAGIRPNQAVAAGVAS 71
                                      89************************9988765544..22......3556788999999999999999999999986 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   2.4e-09   8.7e-06       1      62 [.       5      75 ..       5     316 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.4e-09
                                      EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGG...........E CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeead...........i 62
                                      vG+D+G+T ++av+ de+g v++    ++ +   +++ a+ + + ++++e +++ag  +++           +
  gi|313127507|ref|YP_004037777.1|  5 VGVDLGATNIRAVVADEDGTVIASRSDGTPRGP-TGI-AVTEAILRVVRETCSEAGIRPNQavaagvasigpL 75
                                      8*******************9998877665554.665.6889999************9998444444444440 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05     0.064       1      49 [.       5      58 ..       5     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                      EEEEE-SSSEEEEEEETTE.EEEEEEES-....-HHHHHHHHHHHHT--HHHHH CS
                                      xxxxxxxxxxxxxxxxxxx.xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  1 alvDiGagktdvavaedga.lvhlrvigv....ggngitkdiakalrtaveeAe 49
                                      ++vD+Ga+ + ++va++++ ++++r+ g+     g  +t+ i +++r+  +eA 
  gi|313127507|ref|YP_004037777.1|  5 VGVDLGATNIRAVVADEDGtVIASRSDGTprgpTGIAVTEAILRVVRETCSEAG 58
                                      69*************88653777999999999999999999****999999995 PP

>> AAA_lid_4  RuvB AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   9.5e-05      0.34      14      48 ..      11      51 ..       7      71 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.5e-05
                         AAA_lid_4 14 akilgveieeegaaeiarRsRGTPR......ianrLLrRvr 48
                                      a+ ++  + +e  + ia+Rs GTPR      +++ +Lr vr
  gi|313127507|ref|YP_004037777.1| 11 ATNIRAVVADEDGTVIASRSDGTPRgptgiaVTEAILRVVR 51
                                      556666777788889**********6666444556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2344.64
//
Query:       gi|313127508|ref|YP_004037778.1|  [L=152]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-19   68.5   0.8    1.1e-18   68.1   0.8    1.2  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.8     6e-23   1.1e-18       4     141 .]       5     148 ..       2     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 6e-23
                                       EEEEEE-.SSHHHH.HHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....HHHH CS
                               Usp   4 rIlVavD.gseesk.kAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....akaa 74 
                                        Il+av  g  +   ++++  ++ a  +ga+++l+hv   +++ ++ d  +   ++ ++++ + + +      + + 
  gi|313127508|ref|YP_004037778.1|   5 SILLAVGpGDADRLeRLADETIDVAGPTGARVVLAHVFTREEYNSALDNLDFDTTADEVSADDVAMRHStireLVDT 81 
                                       68888864333333478888888**************99998888776555555555555544443333569999** PP

                                       HHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  75 aeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++++gv+ ++  ++gd +e+i+ +a++ dad ++vG r+rs   ++++GSv++ v+ +apcpV+ Vr
  gi|313127508|ref|YP_004037778.1|  82 LDEAGVEYDIRGRVGDHGESIVSLANDVDADRVLVGGRKRSPAGKAVFGSVAQEVMLSAPCPVTFVR 148
                                       ****************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1200.60
//
Query:       gi|313127509|ref|YP_004037779.1|  [L=246]
Description: hypothetical protein Hbor_27900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-52  176.7   0.9    1.9e-51  174.9   0.9    1.7  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    1.9e-44  151.4   0.1    2.4e-44  151.2   0.1    1.0  1  adh_short       short chain dehydrogenase
    5.5e-06   26.4   0.2    8.3e-06   25.8   0.2    1.2  1  KR              KR domain
    0.00038   20.0   1.1    0.00096   18.7   0.1    2.0  3  Epimerase       NAD dependent epimerase/dehydratase family
      0.007   16.3   1.7      0.011   15.7   1.7    1.5  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.9   0.9   5.3e-55   1.9e-51       1     233 [.      15     241 ..      15     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 174.9 bits;  conditional E-value: 5.3e-55
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE...EE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev...lecDVtdeeqvealveevvekfgklDil 73 
                                       G a+g+GraiA ++a+ Ga v++++   ++ ++++++ a+elga +   ++ DVtd+++v+a++++v++++g++D l
  gi|313127509|ref|YP_004037779.1|  15 GSAHGVGRAIALRAAASGAAVAVHYHTSDDaAREAAAEARELGAPAattVQGDVTDPDSVDAMFDAVEAELGTVDLL 91 
                                       789***********************999989999999*****884468**************************** PP

                                       EE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSB..STTTTHHHHHHH CS
                      adh_short_C2  74 vnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaerv..vpnynaygaaKa 146
                                       vnn+g   +   + +e++   ++r++++n+y+++l++k+al  m+++  g+ivn+ + g+e++   p++  y +aK 
  gi|313127509|ref|YP_004037779.1|  92 VNNVGDFAP--VHWEEIDFGTWKRIIETNFYGTVLCSKRALAGMRDQswGRIVNIGYAGSEKAlvYPKNFPYFVAKT 166
                                       *****9999..899****************************9988889************985466666******* PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT-- CS
                      adh_short_C2 147 alealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyit 223
                                       ++  +tr lA++  ++g++vNavsp +++T             +e+ + ap gr++++e++a+a++f++ +++ yi+
  gi|313127509|ref|YP_004037779.1| 167 GVLMFTRMLAADTQDDGVTVNAVSPYVVDTS------------DEFPEDAPRGRWASVEDIAHAVAFFCHEDSGYIS 231
                                       *****************************74............456689**************************** PP

                                       SEEEEESTTG CS
                      adh_short_C2 224 GqtlvvDgGl 233
                                       G+++ +DgG+
  gi|313127509|ref|YP_004037779.1| 232 GENVEIDGGW 241
                                       *********6 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.2   0.1   6.6e-48   2.4e-44       2     185 ..      10     197 ..       9     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 6.6e-48
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklg 76 
                                       v+lvtG + G+Graia + a++Ga v+v +  s+++++e+a+e +e+ +  a+++q+Dvtd ++v+a++++++++lg
  gi|313127509|ref|YP_004037779.1|  10 VALVTGSAHGVGRAIALRAAASGAAVAVhYHTSDDAAREAAAEARELgAPAATTVQGDVTDPDSVDAMFDAVEAELG 86 
                                       89*********************************************8889************************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB..-TTBHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvp..vagvaaYsA 151
                                       ++d+LvnN+G   ++  +e++  +w+r+ie+N+ g++l+++ +l  m +qs+GrIvn++   ++++  ++   +Y  
  gi|313127509|ref|YP_004037779.1|  87 TVDLLVNNVGDFAPVHWEEIDFGTWKRIIETNFYGTVLCSKRALAGMRDQSWGRIVNIGYAGSEKAlvYPKNFPYFV 163
                                       **********************************************************8766655422789999*** PP

                                       HHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSH CS
                         adh_short 152 sKaavagltrslakelaptgirvnavaPGlvdTd 185
                                       +K +v ++tr la + +++g++vnav P +vdT 
  gi|313127509|ref|YP_004037779.1| 164 AKTGVLMFTRMLAADTQDDGVTVNAVSPYVVDTS 197
                                       ********************************95 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   2.3e-09   8.3e-06       3     117 ..      11     123 ..      10     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.3e-09
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-.EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga.evevvaaDvsdkdavealleeikae 78 
                                        l+tG + g+G+++a   a++ga+  v    s   d+++++  ae ++lga   ++v+ Dv+d+d+v a++++++ae
  gi|313127509|ref|YP_004037779.1|  11 ALVTGSAHGVGRAIALRAAASGAAVAVHYHTS---DDAAREAAAEARELGApAATTVQGDVTDPDSVDAMFDAVEAE 84 
                                       59********************9887777777...556666778888888867899********************* PP

                                       SS---EEEE---------TTT--HHHHHHHHTTTTHHHH CS
                                KR  79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGaw 117
                                        +++   ++  g ++    ee +  +++++++  + G+ 
  gi|313127509|ref|YP_004037779.1|  85 LGTVDLLVNNVGDFAPVHWEEIDFGTWKRIIETNFYGTV 123
                                       ***999999999999999999999999888888777775 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.7e-07   0.00096       1      65 [.      11      83 ..      11      93 .. 0.90
   2 ?   -2.0   0.0      0.56     2e+03     136     169 ..     155     188 ..     147     212 .. 0.68
   3 ?   -1.5   0.0       0.4   1.4e+03     212     228 ..     209     225 ..     199     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-07
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHHT- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkeeqp 65
                                      +lVtG +  +G+a++ + ++ g  v +  + s++ ++++ +++        + v++d+td+++++++f+ +++
  gi|313127509|ref|YP_004037779.1| 11 ALVTGSAHGVGRAIALRAAASGAAVAVHYHTSDDAAREAAAEArelgapaaTTVQGDVTDPDSVDAMFDAVEA 83
                                      59********************99888888888888777777789***********************97765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.56
                                       ---SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEE CS
                         Epimerase 136 lkpnspYaaaKlageklveayaaqyglnaiilrl 169
                                       ++ n pY +aK+ +   ++ +aa+ + + ++++ 
  gi|313127509|ref|YP_004037779.1| 155 YPKNFPYFVAKTGVLMFTRMLAADTQDDGVTVNA 188
                                       4678899999976666666666655555555544 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.4
                                       EEEHHHHHHHHHHHHHH CS
                         Epimerase 212 flyveDvaeaillvleh 228
                                       +  veD+a a+ ++  +
  gi|313127509|ref|YP_004037779.1| 209 WASVEDIAHAVAFFCHE 225
                                       889********998776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.7     3e-06     0.011       5     103 ..      19     151 ..      15     220 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3e-06
                                       HHHHHHHHHHHHC-T-EEEEEETTHHHCH........HHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-..... CS
                    NAD_binding_10   5 kvGrllvkellargghevtalvRnpekla........eleaeeglevvegdvtdvedlaealkgadaVvsal..... 68 
                                       +vGr+++ +++a+g  +v +   +++++a        el  ++++++v+gdvtd++++ + ++ ++a + ++     
  gi|313127509|ref|YP_004037779.1|  19 GVGRAIALRAAASG-AAVAVHYHTSDDAAreaaaearEL-GAPAATTVQGDVTDPDSVDAMFDAVEAELGTVdllvn 93 
                                       69999999999997.444444443333322222222255.479****************999866654444444443 PP

                                       ...........--TCCHHHH...................HHHHHHHHHHCT--EEEEEEETTTTS CS
                    NAD_binding_10  69 ...........ggggkdeeg...................aknivdaakeagvkRfvlvsaigvgd 103
                                                          +                    k++++ ++ +   R+v ++++g+++
  gi|313127509|ref|YP_004037779.1|  94 nvgdfapvhweE-------IdfgtwkriietnfygtvlcSKRALAGMRDQSWGRIVNIGYAGSEK 151
                                       333333222220.......1333444445555677777777788888888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1752.20
//
Query:       gi|313127510|ref|YP_004037780.1|  [L=126]
Description: hypothetical protein Hbor_27910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-29  103.4   0.2    1.2e-29  103.2   0.2    1.0  1  DUF5611   Domain of unknown function (DUF5611)


Domain annotation for each model (and alignments):
>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.2   6.5e-34   1.2e-29       1     103 []       1     117 [.       1     117 [. 0.97

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 6.5e-34
                                       -EEE---SSS--SH..HHHHHHHHHHT....-EEEEE.TTEEEE.E.....-TTBS-EEEEE..-SS-EEEEE--.B CS
                           DUF5611   1 mreYkiKrGfkkeee.erlkelleeyfg...geveee.gdllvv.s.....fgaikklevkisskkkklvvdteerd 66 
                                       m+eYk++rG++++++ +++++ +ee+fg   g++e++ +dl+vv +     f++i +++vk+s+kk+kl+v+++erd
  gi|313127510|ref|YP_004037780.1|   1 MKEYKMRRGETLDDRvPDMESYVEEMFGtitGTEEYKgSDLYVVgEpsnpvFERIIAGAVKYSGKKDKLAVEFTERD 77 
                                       9******************************9999999******669****************************** PP

                                       ......-TTS-HHHHHHHHHHHHHHHH---GGGHHHHH-- CS
                           DUF5611  67 aee...eddeaaldtvkkfndFLeeaTGydaKeRkkkakk 103
                                        +e   ++ eaa ++v+++n+FL eaTG+daK+R++++k+
  gi|313127510|ref|YP_004037780.1|  78 PTElgpDELEAAGEAVDAKNTFLLEATGRDAKSRRDSLKR 117
                                       *99**9*******************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 872.47
//
Query:       gi|313127511|ref|YP_004037781.1|  [L=399]
Description: hypothetical protein Hbor_27920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.017   14.5   1.5       0.46   10.0   0.1    2.6  2  zf-ribbon_3     zinc-ribbon domain
      0.044   13.9   3.6      0.087   13.0   1.2    2.3  2  Zn-ribbon_8     Zinc ribbon domain
      0.056   13.4   0.5      0.056   13.4   0.5    2.6  2  DUF1610         Domain of unknown function (DUF1610)
      0.064   13.2   0.5        0.2   11.6   0.5    1.8  1  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
      0.066   13.2   1.9        0.2   11.7   0.6    2.1  2  DZR             Double zinc ribbon
      0.086   13.3   0.3      0.086   13.3   0.3    2.4  2  DUF1660         Prophage protein (DUF1660)
      0.089   12.7   2.3        5.7    6.9   0.0    3.2  3  zinc_ribbon_4   zinc-ribbon domain
        0.2   11.6   0.8       0.49   10.4   0.1    1.8  2  ADD_DNMT3       Cysteine rich ADD domain in DNMT3
       0.38   11.5   1.6        8.5    7.2   0.2    2.3  2  zf-3CxxC_2      Zinc-binding domain
       0.59    9.9   2.4        2.2    8.1   0.0    2.9  4  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
        1.1    9.6   6.4        3.3    8.0   0.1    3.1  3  zinc_ribbon_9   zinc-ribbon
        2.1    8.5   3.7        1.3    9.1   0.5    2.0  2  Zn_Tnp_IS91     Transposase zinc-binding domain


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00031      0.46       2      10 ..     363     371 ..     362     378 .. 0.79
   2 ?    2.8   0.1     0.055        83       4      10 ..     385     391 ..     383     397 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                       zf-ribbon_3   2 tvrCPnCGa 10 
                                       + +CPnCG+
  gi|313127511|ref|YP_004037781.1| 363 EFYCPNCGH 371
                                       579*****9 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.055
                       zf-ribbon_3   4 rCPnCGa 10 
                                        CP+C++
  gi|313127511|ref|YP_004037781.1| 385 ICPECKQ 391
                                       5888876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.58   8.7e+02      22      34 ..      33      43 ..      24      48 .. 0.63
   2 ?   13.0   1.2   5.8e-05     0.087       5      34 ..     363     391 ..     362     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.58
                       Zn-ribbon_8 22 sdaplta.CPeCgs 34
                                          +++ C +C  
  gi|313127511|ref|YP_004037781.1| 33 R---EIQvCQRCED 43
                                      4...4455888865 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.8e-05
                       Zn-ribbon_8   5 eYrCeeCghefevlqsisdapltaCPeCgs 34 
                                       e+ C +Cgh  ++ +s+++ +   CPeC++
  gi|313127511|ref|YP_004037781.1| 363 EFYCPNCGHARTAGASSMR-AGDICPECKQ 391
                                       89*******9998887664.4456****86 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   3.8e-05     0.056      16      23 ..     363     370 ..     360     371 .. 0.92
   2 ?   -0.5   1.5      0.85   1.3e+03      18      22 ..     385     389 ..     385     389 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                           DUF1610  16 vFpCPNCG 23 
                                       +F+CPNCG
  gi|313127511|ref|YP_004037781.1| 363 EFYCPNCG 370
                                       6******9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.85
                           DUF1610  18 pCPNC 22 
                                       +CP+C
  gi|313127511|ref|YP_004037781.1| 385 ICPEC 389
                                       6**** PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00013       0.2       7      37 ..     360     390 ..     355     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                       HHCEEE-TTTTTTSEETTE......E-TTTT CS
                         Anti-TRAP   7 peLEtkCdaCngsGkiepeeprasleCPkCs 37 
                                       + +E  C++C  +  + +   ra+  CP+C+
  gi|313127511|ref|YP_004037781.1| 360 DRIEFYCPNCGHARTAGASSMRAGDICPECK 390
                                       668999****99988888899*********8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.68     1e+03      30      35 ..      37      42 ..      25      52 .. 0.67
   2 ?   11.7   0.6   0.00014       0.2      13      37 ..     364     392 ..     354     398 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.68
                               DZR 30 rCpsCg 35
                                      +C +C+
  gi|313127511|ref|YP_004037781.1| 37 VCQRCE 42
                                      444444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                               DZR  13 rfCseCgtklkavaa....edrCpsCgek 37 
                                        +C++Cg++  a a+     d Cp+C++ 
  gi|313127511|ref|YP_004037781.1| 364 FYCPNCGHARTAGASsmraGDICPECKQG 392
                                       48999999855333356669999999875 PP

>> DUF1660  Prophage protein (DUF1660)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   5.8e-05     0.086       1      49 [.       1      66 [.       1      72 [. 0.76
   2 ?   -3.4   0.2       9.7   1.4e+04      23      29 ..     364     370 ..     357     390 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-05
                           DUF1660  1 MKLlCKLfgHKwd.............enpaadseelyCeRCeivkekv..kcl..ekklnrsdLde 49
                                      M L+C+L gH +              e+ ++  e+++C+RCe +++    k++  +++ ++  Lde
  gi|313127511|ref|YP_004037781.1|  1 MGLKCRLLGHQYGdpeierereengdEVVVTIREIQVCQRCEDEHVVSenKEVtsIRDPQDVGLDE 66
                                      889*******99778888999888877888899999*****6664433223335678888888888 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.7
                           DUF1660  23 lyCeRCe 29 
                                        yC  C 
  gi|313127511|ref|YP_004037781.1| 364 FYCPNCG 370
                                       4777772 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.19   2.9e+02       4      18 ..      37      51 ..      35      55 .. 0.88
   2 ?    6.9   0.0    0.0038       5.7      18      33 ..     356     371 ..     353     372 .. 0.87
   3 ?    2.1   0.1      0.13   1.9e+02       5      12 ..     386     393 ..     385     399 .] 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.19
                     zinc_ribbon_4  4 tCpsCkakyeiddek 18
                                      +C++C+ ++ ++++k
  gi|313127511|ref|YP_004037781.1| 37 VCQRCEDEHVVSENK 51
                                      6*****999999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0038
                     zinc_ribbon_4  18 klpakgvkvrCskCgh 33 
                                        +p+++ +  C++Cgh
  gi|313127511|ref|YP_004037781.1| 356 DVPDDRIEFYCPNCGH 371
                                       5899999999*****9 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.13
                     zinc_ribbon_4   5 CpsCkaky 12 
                                       Cp+Ck  y
  gi|313127511|ref|YP_004037781.1| 386 CPECKQGY 393
                                       ****9887 PP

>> ADD_DNMT3  Cysteine rich ADD domain in DNMT3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.9   2.8e+03      39      46 ..      37      44 ..      34      47 .. 0.82
   2 ?   10.4   0.1   0.00033      0.49      14      47 ..     360     393 ..     349     396 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.9
                         ADD_DNMT3 39 lClkCkdn 46
                                      +C++C d+
  gi|313127511|ref|YP_004037781.1| 37 VCQRCEDE 44
                                      7****997 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00033
                         ADD_DNMT3  14 rniEdiClsCGslevetqHPLFeGglClkCkdnf 47 
                                        +iE  C  CG+ +++    +  G +C +Ck+ +
  gi|313127511|ref|YP_004037781.1| 360 DRIEFYCPNCGHARTAGASSMRAGDICPECKQGY 393
                                       57999**************************977 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.11   1.7e+02      26      44 ..      34      52 ..      31      71 .. 0.74
   2 ?    7.2   0.2    0.0057       8.5       7      35 ..     363     391 ..     362     397 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                        zf-3CxxC_2 26 eaQeCkkCkekvepyklre 44
                                      e+Q C++C+++ + ++ +e
  gi|313127511|ref|YP_004037781.1| 34 EIQVCQRCEDEHVVSENKE 52
                                      789*****99866555554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0057
                        zf-3CxxC_2   7 efkCekCgkeWsSanafaneaQeCkkCke 35 
                                       ef C++Cg+  + + + ++ +  C +Ck+
  gi|313127511|ref|YP_004037781.1| 363 EFYCPNCGHARTAGASSMRAGDICPECKQ 391
                                       699************************97 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.7   2.5e+03      20      29 ..      33      42 ..      25      54 .. 0.73
   2 ?   -3.4   0.0       5.6   8.4e+03      31      45 ..     321     335 ..     320     336 .. 0.74
   3 ?    8.1   0.0    0.0015       2.2      41      52 ..     360     371 ..     354     373 .. 0.87
   4 ?   -0.4   0.1      0.65   9.8e+02      24      29 ..     385     390 ..     379     392 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                    zinc_ribbon_10 20 ryalICskCh 29
                                      r   +C+ C 
  gi|313127511|ref|YP_004037781.1| 33 REIQVCQRCE 42
                                      5555899997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.6
                    zinc_ribbon_10  31 hnGlapkeeleevky 45 
                                       +nG+a  ++++e +y
  gi|313127511|ref|YP_004037781.1| 321 SNGQAADSDADEEEY 335
                                       699999777777666 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0015
                    zinc_ribbon_10  41 eevkyrCpkCga 52 
                                       ++++++Cp+Cg+
  gi|313127511|ref|YP_004037781.1| 360 DRIEFYCPNCGH 371
                                       579********8 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.65
                    zinc_ribbon_10  24 ICskCh 29 
                                       IC++C+
  gi|313127511|ref|YP_004037781.1| 385 ICPECK 390
                                       666665 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       3.4   5.1e+03      23      29 ..      37      43 ..      26      46 .. 0.66
   2 ?    3.8   0.4     0.047        70      18      29 ..     359     371 ..     350     375 .. 0.71
   3 ?    8.0   0.1    0.0022       3.3      17      33 ..     380     395 ..     372     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.4
                     zinc_ribbon_9 23 lCPhCgg 29
                                      +C +C+ 
  gi|313127511|ref|YP_004037781.1| 37 VCQRCED 43
                                      4999975 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.047
                     zinc_ribbon_9  18 edsdv.lCPhCgg 29 
                                       +d++  +CP+Cg 
  gi|313127511|ref|YP_004037781.1| 359 DDRIEfYCPNCGH 371
                                       3444359****96 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0022
                     zinc_ribbon_9  17 dedsdvlCPhCgggFVE 33 
                                       +   d+ CP+C++g + 
  gi|313127511|ref|YP_004037781.1| 380 MRAGDI-CPECKQGYIA 395
                                       556678.******9885 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2         1   1.5e+03      40      51 ..      36      47 ..      30      52 .. 0.76
   2 ?    9.1   0.5   0.00084       1.3      39      68 ..     363     394 ..     360     397 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1
                       Zn_Tnp_IS91 40 yeCeeCghekiv 51
                                        C+ C++e++v
  gi|313127511|ref|YP_004037781.1| 36 QVCQRCEDEHVV 47
                                      468888888876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00084
                       Zn_Tnp_IS91  39 ryeCeeCghekivyfsCksrh..CpsCqkkat 68 
                                       ++ C++Cgh ++   s  +    Cp+C++ + 
  gi|313127511|ref|YP_004037781.1| 363 EFYCPNCGHARTAGASSMRAGdiCPECKQGYI 394
                                       578*******9998888776667****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2586.95
//
Query:       gi|313127512|ref|YP_004037782.1|  [L=99]
Description: hypothetical protein Hbor_27930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0002   21.0   0.0    0.00026   20.6   0.0    1.2  1  GntR      Bacterial regulatory proteins, gntR family
    0.00027   20.8   0.0    0.00035   20.4   0.0    1.1  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0041   17.1   0.1     0.0059   16.7   0.1    1.2  1  HTH_20    Helix-turn-helix domain
     0.0049   17.1   0.1     0.0058   16.9   0.1    1.2  1  GGDEF_2   GGDEF-like domain
  ------ inclusion threshold ------
      0.012   16.3   0.0      0.015   15.9   0.0    1.1  1  RPA_C     Replication protein A C terminal
      0.019   14.9   0.1       0.03   14.2   0.1    1.2  1  MarR_2    MarR family
       0.17   12.3   0.0       0.22   11.9   0.0    1.1  1  Rrf2      Transcriptional regulator


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     1e-07   0.00026      20      59 ..      25      63 ..      15      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1e-07
                                      TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 20 pGdkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                      +++ + ++ eL+a+ + +  t+ eAL+ L+++gl+++ +g
  gi|313127512|ref|YP_004037782.1| 25 AEEGM-TVFELRAAVDADIDTIEEALSSLKSDGLITVDSG 63
                                      66777.899***************************9988 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.4e-07   0.00035       8      58 ..      12      64 ..      11      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.4e-07
                                      HHCCCHCHHHH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  8 eyEakvYlaLl..klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      + E++v  aL+  +++ +t+ e+  +++ +  ++ e+L+sL++ Gl+++  g+
  gi|313127512|ref|YP_004037782.1| 12 DVEVSVLDALVdrAEEGMTVFELRAAVDADIDTIEEALSSLKSDGLITVDSGE 64
                                      679********9999*********************************99887 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.3e-06    0.0059      14      57 ..      16      61 ..      10      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                                      HHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 14 rilraL..araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                       +l+aL  + +eg+t+ el +++d +  t+   L  L + gL++v 
  gi|313127512|ref|YP_004037782.1| 16 SVLDALvdRAEEGMTVFELRAAVDADIDTIEEALSSLKSDGLITVD 61
                                      6999***************************************985 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.3e-06    0.0058      26      85 ..      30      98 ..      10      99 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                           GGDEF_2 26 vvieleedaerllraleealralgpdalvavrgd.rlvlllp........aedeedaeallerlarrlg 85
                                       v+el+ + ++ ++++eeal++l+ d l++v+++   v++lp        +e++ed + +++++++r+g
  gi|313127512|ref|YP_004037782.1| 30 TVFELRAAVDADIDTIEEALSSLKSDGLITVDSGeDRVVILPddrvvpdpGEEPEDEQSFIDAIRDRFG 98
                                      5778888777889**********88888888776688999996777655555567777*******9997 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0     6e-06     0.015      47      97 ..      10      58 ..       2      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6e-06
                                      SXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 47 ltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                      + +++  vl+++ +  + eeG+ v e+ +++  +  ++++a+ +L ++G+i
  gi|313127512|ref|YP_004037782.1| 10 RRDVEVSVLDALVD--RAEEGMTVFELRAAVDADIDTIEEALSSLKSDGLI 58
                                      55667778888888..99*******************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.2e-05      0.03       7      59 ..      14      65 ..      12      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59
                                      +  vL aL +r ++ +tv el ++ + +  ++  +l  L + GL++   + eD
  gi|313127512|ref|YP_004037782.1| 14 EVSVLDALVDRAEEGMTVFELRAAVDADIDTIEEALSSLKSDGLITVD-SGED 65
                                      678*********999******************************754.4466 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.6e-05      0.22       8      61 ..      12      64 ..       6      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.6e-05
                                      HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2  8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                      ++ + +l  L  ++ee+ +++ e+ + ++     +e  l+ L+  gl+++  G 
  gi|313127512|ref|YP_004037782.1| 12 DVEVSVLDALVDRAEEG-MTVFELRAAVDADIDTIEEALSSLKSDGLITVDSGE 64
                                      55667777888888988.*******************************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 634.66
//
Query:       gi|313127513|ref|YP_004037783.1|  [L=364]
Description: glycine cleavage system protein T [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-39  135.5   0.1      3e-39  135.0   0.1    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
      4e-15   55.5   0.0    1.5e-14   53.6   0.0    2.1  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.1   3.3e-43     3e-39       3     244 ..       6     238 ..       4     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 3.3e-43
                             GCV_T   3 drhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkat 79 
                                       + h++ ga+f++ ag  +  +Y  + +++  +avr++a+++++   g + v+G+d+ ++++++++n++++ + g++ 
  gi|313127513|ref|YP_004037783.1|   6 EMHERYGATFETRAGRRVVRDY--GRPERTTRAVRNGAAVMEMG-YGVVVVEGDDRIEFVDNAVSNRVPDAD-GEGV 78 
                                       689*******************..*******************9.8***********************997.**** PP

                             GCV_T  80 ytlllnedGgvidDlivarldedefllvvnaankekdl.awlekaaekkdldvevedvteelallalqGPkarevls 155
                                       y+lll+++G+++ D++v++ + +++l  ++++++e ++ +w ek      +dv+++d+t++++++ + GP+++e ++
  gi|313127513|ref|YP_004037783.1|  79 YALLLDPQGRIETDMYVYNAG-ERLLCFTPPKRAEPLVeDWSEK-VF--IQDVSIRDATADFGVFGVHGPQSTEKVA 151
                                       *********************.6999999999999999677777.77..8************************888 PP

                             GCV_T 156 kll.gadlselkffsfaevelaggkkvlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtlR 231
                                        +l ga   e ++ sf++  + ++   +++  g +Ge+G+e++++a++a++++++Ll++g   ++ p+G++++d+l+
  gi|313127513|ref|YP_004037783.1| 152 SVLnGAAAPE-PALSFVRGSMGNAGVTVIAGDGLVGEEGYEVVCTADAAADVFDTLLTNGM--NAVPFGYATWDMLT 225
                                       8883555555.999999999884555677899************************99998..8************* PP

                             GCV_T 232 lEaglrlyghdld 244
                                        Eag +l++++l 
  gi|313127513|ref|YP_004037783.1| 226 AEAGTPLFDTELV 238
                                       **********985 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   1.7e-18   1.5e-14       2      80 .]     276     349 ..     275     349 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.7e-18
                           GCV_T_C   2 rlvglelddgapllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkpf 78 
                                       rlvgl++ ++  l++ g+++++++  vG+vT++  sp l+++ialA+++ +  +  ++v+v+v++k+v a vv+ pf
  gi|313127513|ref|YP_004037783.1| 276 RLVGLRP-EA--LPESGAAVFNGDSSVGEVTRAVESPMLESPIALALLDFDEDA--STVQVRVDEKEVTADVVSLPF 347
                                       899*999.33..58***********************************87777..9******************** PP

                           GCV_T_C  79 yD 80 
                                       +D
  gi|313127513|ref|YP_004037783.1| 348 VD 349
                                       *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2461.16
//
Query:       gi|313127514|ref|YP_004037784.1|  [L=360]
Description: geranylgeranyl reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-16   59.8   1.4      5e-11   42.4   0.0    3.0  3  FAD_binding_3   FAD binding domain
    1.3e-06   27.9   3.9    5.3e-05   22.6   2.3    2.8  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      3e-06   26.6   3.5     0.0082   15.2   2.4    2.7  2  Lycopene_cycl   Lycopene cyclase protein
    4.9e-06   26.4   0.6      0.034   13.7   0.0    2.3  2  DAO             FAD dependent oxidoreductase
    5.9e-05   22.3   0.9     0.0032   16.6   0.1    2.3  2  FAD_binding_2   FAD binding domain
    7.1e-05   22.3   0.2     0.0001   21.8   0.2    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0012   17.6   0.2      0.022   13.4   0.1    2.0  2  HI0933_like     HI0933-like protein
     0.0024   18.0   0.7      0.013   15.7   0.3    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.021   14.1   0.5       0.13   11.5   0.5    2.0  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.036   13.1   0.0       0.27   10.3   0.0    1.9  2  SE              Squalene epoxidase
      0.088   11.6   0.5       0.33    9.7   0.1    1.9  3  Trp_halogenase  Tryptophan halogenase
       0.16   12.2   0.0       0.45   10.7   0.0    1.7  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0031       4.6       3      34 ..       3      34 ..       1      47 [. 0.86
   2 !   42.4   0.0   3.4e-14     5e-11     100     176 ..      91     165 ..      53     206 .. 0.85
   3 !    8.8   0.0   0.00056      0.84     282     308 ..     251     277 ..     246     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0031
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      d ++VG GpaG+  a+  +eaG +vv  ek +
  gi|313127514|ref|YP_004037784.1|  3 DFAVVGVGPAGARFARRAAEAGYDVVAFEKGE 34
                                      5689*********************9999866 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 3.4e-14
                                       EE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGE CS
                     FAD_binding_3 100 tvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgief 176
                                        v+   el+r L++ a+ +g++vr+ + v+++e+  +gv+ +v     g e+t++ak ++G+DG  S+vr+++g++ 
  gi|313127514|ref|YP_004037784.1|  91 NVIDRVELDRTLAACARDAGADVRERHTVTNVEERHDGVELTVSAG--GDEQTIEAKMVAGCDGPVSRVRRQAGLDE 165
                                       5667789*******************************87766655..88889*********************983 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00056
                                       EETTEEE-GGGTEEE-STTSHHHHHHH CS
                     FAD_binding_3 282 rkgrvflaGDAaHihpPtgGqGlNtai 308
                                       +  rvfl GDAa  + P +G G+  ++
  gi|313127514|ref|YP_004037784.1| 251 TTRRVFLLGDAAAQTKPFTGGGILYGM 277
                                       566*****************9986666 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   2.3   3.5e-08   5.3e-05       1     102 [.       2     146 ..       2     147 .. 0.77
   2 !    6.6   0.3    0.0027         4     185     237 ..      98     153 ..      90     168 .. 0.81
   3 ?   -0.1   0.0      0.29   4.4e+02     255     280 ..     239     263 ..     225     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.5e-08
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias................. 57 
                                       +d +v+G GpAG ++a+++a+ag++v+ +e    ++ +   g + + +++ v+++a++ +                 
  gi|313127514|ref|YP_004037784.1|   2 YDFAVVGVGPAGARFARRAAEAGYDVVAFEkgeVGTPLACSGHVSTDIWAYVPDEAKTTLfqnriyganfhvggpns 78 
                                       5789*************************876677777777888888999999999888899999999999999999 PP

                                       ...........................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESE CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ...........................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydk 102
                                                                         +g +++ +++v+++++ +  v+l+ + +gde++i+++ 
  gi|313127514|ref|YP_004037784.1|  79 rdypfykneevsnvidrveldrtlaacA----RDAGADVRERHTVTNVEERHDGVELTVSAGGDEQTIEAKM 146
                                       9999999988887777666666654331....2334555555557777777777777666668888888875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHTTEEEEESCEEEEEEETTE..EEE.EEETTSCEEEESEEEE-S-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx.xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgnge..kle.vvledgeeidadlvvvavGv 237
                                       l ++l++  ++ G +v+ +++v++++++++  +l+    +d+++i+a++v  + G 
  gi|313127514|ref|YP_004037784.1|  98 LDRTLAACARDAGADVRERHTVTNVEERHDgvELTvSAGGDEQTIEAKMVAGCDGP 153
                                       566777888999*****************966555667788888*****9888775 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.29
                                       TTEEE--TTSBESSTTEEE-GGGCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 255 rggivvdeflrtnvpgiyaiGDvagg 280
                                        ggi + +  r++   ++++GD a  
  gi|313127514|ref|YP_004037784.1| 239 SGGIPIGPPDRVTTRRVFLLGDAA-A 263
                                       577777777899999*******99.2 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.4   5.5e-06    0.0082       1     148 [.       3     159 ..       3     188 .. 0.71
   2 !    8.8   0.0   0.00048      0.71     241     315 ..     240     313 ..     232     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.5e-06
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieasp..sllfpnny....vWsdefedlgaleecvehsWsgtivyldd 71 
                                       D +v+G GpAg + A r   a++g  vv  e ++   +l    +     W +   +++    + + +  g+  ++ +
  gi|313127514|ref|YP_004037784.1|   3 DFAVVGVGPAGARFARRA--AEAGYDVVAFEKGEvgTPLACSGHvstdIWAYVPDEAK--TTLFQNRIYGANFHVGG 75 
                                       889***************..999999****9987433444444422235888777777..56666666777777776 PP

                     Lycopene_cycl  72 gkkillg.....raYgrvsskrlkeellerlvengvk.lleakvesveeeeageslvvleggr..kirarlvvdarg 140
                                        ++++          + + + +l + l+    ++g+  + + +v++vee ++g  l v +gg   +i+a++v    g
  gi|313127514|ref|YP_004037784.1|  76 PNSRDYPfykneEVSNVIDRVELDRTLAACARDAGADvRERHTVTNVEERHDGVELTVSAGGDeqTIEAKMVAGCDG 152
                                       6666655322224445688999999988766688886155789*********76666666665589******99999 PP

                     Lycopene_cycl 141 laslkkar 148
                                        + ++  r
  gi|313127514|ref|YP_004037784.1| 153 -PVSRVRR 159
                                       .5444333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00048
                     Lycopene_cycl 241 gviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres....slsarawatlwprerk 313
                                       g iP+  g++ + +  +v+ +G aa  ++P TG  +   + +a+   + i      +      +++aw++   +e++
  gi|313127514|ref|YP_004037784.1| 240 GGIPI--GPPDRVTTRRVFLLGDAAAQTKPFTGGGILYGMTAADCAVDTIDPD---DpatlRDYESAWRSELSQEIA 311
                                       679**..9999999999*************************99555555322...122235566677777666666 PP

                     Lycopene_cycl 314 rq 315
                                       + 
  gi|313127514|ref|YP_004037784.1| 312 MG 313
                                       65 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00016      0.24       1      48 [.       3      53 ..       3      70 .. 0.80
   2 !   13.7   0.0   2.3e-05     0.034     147     205 ..      97     156 ..      88     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT..SSGGGSSEEEEESSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag..sgaSgrnsgllhsgl 48
                                      d +++G G +G+  A+ +a++g  V+ +ekg ++g   ++Sg+ s  +++++
  gi|313127514|ref|YP_004037784.1|  3 DFAVVGVGPAGARFARRAAEAGydVVAFEKG-EVGtpLACSGHVSTDIWAYV 53
                                      789****************************.87743477777766665544 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEE..EEE--GGGHH CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgve.rttp.gendaada..vVnaaGawsd 205
                                       +l + la+ a+++G++++e+++vt++ee+     gve ++++ g +++++a  v  + G+ s+
  gi|313127514|ref|YP_004037784.1|  97 ELDRTLAACARDAGADVRERHTVTNVEER---HDGVElTVSAgGDEQTIEAkmVAGCDGPVSR 156
                                       666789999*****************775...5666654444455555676668888888776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.1e-06    0.0032       1      43 [.       3      43 ..       3      60 .. 0.87
   2 ?    4.3   0.0     0.012        17     139     195 ..      94     147 ..      63     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                      D  V+G G AG + A +aaeaG +v+  ek+++  g+  +++G
  gi|313127514|ref|YP_004037784.1|  3 DFAVVGVGPAGARFARRAAEAGYDVVAFEKGEV--GTPLACSG 43
                                      778*****************************9..66666666 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEE CS
                     FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakav 195
                                       +  +l  +l++ ar+ag d++er+ ++++   ++r  G++++ +++g e++i+ak v
  gi|313127514|ref|YP_004037784.1|  94 DRVELDRTLAACARDAGADVRERHTVTNV---EERHDGVELTVSAGGDEQTIEAKMV 147
                                       5556667899999****************...77888999998899**999999977 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2     7e-08    0.0001       1     142 [.       3     150 ..       3     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7e-08
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrgga.... 73 
                                       D  VvG gpaG   A  Aa+aG  v+  e+ +v   l+ sg v+tdi  + ++++ t +++  +   + + g     
  gi|313127514|ref|YP_004037784.1|   3 DFAVVGVGPAGARFARRAAEAGYDVVAFEKGEVGTPLACSGHVSTDIWAYVPDEAKTTLFQNRIYGANFHVGGpnsr 79 
                                       779***************************9999999****************999999998777776633332433 PP

                      FAD_oxidored  74 rlk..krskw.ntfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDA 142
                                       ++   k+++  n+ +   + ++l +  ++ag +v   +++++ve +    ++v++  ++ g ++ti+Ak++  +
  gi|313127514|ref|YP_004037784.1|  80 DYPfyKNEEVsNVIDRVELDRTLAACARDAGADVRERHTVTNVEER---HDGVELTVSAgGdEQTIEAKMVAGC 150
                                       222433333345999999999999999****************975...5677776667578********9655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   1.5e-05     0.022       2      44 ..       3      44 ..       2      49 .. 0.92
   2 ?    2.1   0.0     0.041        62     113     156 ..     100     145 ..      94     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGG CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGg 44
                                      d +v+G G+AG   A +aa++g +V+ +ek+ ++g  ++ sG+
  gi|313127514|ref|YP_004037784.1|  3 DFAVVGVGPAGARFARRAAEAGYDVVAFEKG-EVGTPLACSGH 44
                                      789***************************9.89999999985 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE....TTEEEEES CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvkt...kseeelead 156
                                       ++l + +++ag ++r +++v++ve+++dg +++++    +e+++ea+
  gi|313127514|ref|YP_004037784.1| 100 RTLAACARDAGADVRERHTVTNVEERHDG-VELTVsagGDEQTIEAK 145
                                       578888999**************998888.55555213344555554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   8.5e-06     0.013       1      29 [.       6      34 ..       6      47 .. 0.95
   2 ?   -1.4   0.0       1.9   2.9e+03      26      53 ..     324     350 ..     314     359 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.5e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      +vG G +G+ +A+++a+ag+dv+ +ek++
  gi|313127514|ref|YP_004037784.1|  6 VVGVGPAGARFARRAAEAGYDVVAFEKGE 34
                                      8**************************85 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                                       -SSSSSSGGG-EECETTCEECTS---EE CS
                     NAD_binding_8  26 ekrdrlGGraasyevpgvrvdygahifh 53 
                                       e+ +++G r+ s e++ v  d + + f 
  gi|313127514|ref|YP_004037784.1| 324 ERVQHFGLRSLSGEIG-VHMDKPTSFFS 350
                                       7778999999999886.45566666655 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   8.5e-05      0.13       2      36 ..       6      39 ..       5     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgnignsi 36
                                      ++G GPaG  +a  + +ag  d++  Ekg++g+ +
  gi|313127514|ref|YP_004037784.1|  6 VVGVGPAGARFARRAAEAGY-DVVAFEKGEVGTPL 39
                                      8*******************.8********99754 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.18   2.7e+02       2      20 ..     144     162 ..     143     174 .. 0.81
   2 ?   10.3   0.0   0.00018      0.27     123     190 ..     246     320 ..     224     323 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.18
                                SE   2 AkltvvcDGifsklRkels 20 
                                       Ak+   cDG  s++R++  
  gi|313127514|ref|YP_004037784.1| 144 AKMVAGCDGPVSRVRRQAG 162
                                       889999*********9865 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00018
                                SE 123 pasknekkGlillGDalnmRHPltggGmtvalnDivllskllkpl..edlsdee.....kvleelksfyvkRkel 190
                                       p+++ +++ + llGDa     P tggG+  +++ +   ++++ p     l+d e     ++++e+   ++ R+++
  gi|313127514|ref|YP_004037784.1| 246 PPDRVTTRRVFLLGDAAAQTKPFTGGGILYGMTAADCAVDTIDPDdpATLRDYEsawrsELSQEIAMGHWIRRAY 320
                                       6677888999********************999999999999887554555544111115666666667776665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       2.6   3.9e+03       3      38 ..       5      37 ..       4      38 .. 0.75
   2 ?    9.7   0.1   0.00022      0.33     150     233 ..      92     178 ..      71     192 .. 0.82
   3 ?   -0.9   0.0      0.38   5.7e+02     312     371 ..     249     306 ..     217     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.6
                                      EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS-- CS
                    Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlveseeigt 38
                                       +vG G+aG   A   a+a+   ++v   e+ e+gt
  gi|313127514|ref|YP_004037784.1|  5 AVVGVGPAGARFARRAAEAG---YDVVAFEKGEVGT 37
                                      58999999977776666666...8888888888776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00022
                                       EE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT..S-EEE-SEEEE-SGGG-IIIIII.T---EE CS
                    Trp_halogenase 150 hldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled..greveadlfiDcsGfrgllieqa.Lktgfe 223
                                        +d+ ++++ L + a ++G +++e + v+ + + ++ ve    +   ++++ea ++  c G  +++  qa L+++ e
  gi|313127514|ref|YP_004037784.1|  92 VIDRVELDRTLAACARDAGADVRERHTVTNVEERHDGVELTVSAGgdEQTIEAKMVAGCDGPVSRVRRQAgLDEPEE 168
                                       58999*******************99888777777777765555434899***********9999998875777777 PP

                                       E-TTT----E CS
                    Trp_halogenase 224 dwsdvLltdr 233
                                         + vL  d 
  gi|313127514|ref|YP_004037784.1| 169 ILHGVLAFDE 178
                                       6666666665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.38
                                       -SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HHHHHHHHHHHHHHH CS
                    Trp_halogenase 312 qawvknvvalGlasgfvePlestsihliqaalrrLlallpdksdepaaiaefnrevarel 371
                                       ++  + v++lG+a++   P  + +i   ++a++  + ++    d+pa++  ++++ ++el
  gi|313127514|ref|YP_004037784.1| 249 RVTTRRVFLLGDAAAQTKPFTGGGILYGMTAADCAVDTID--PDDPATLRDYESAWRSEL 306
                                       5566789999***********9999999999988777774..458999999998888776 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.45       2      30 ..       4      32 ..       3      53 .. 0.91
   2 ?   -2.1   0.0       2.6   3.8e+03     127     140 ..     130     143 ..      95     157 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-S CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynr 30
                                      ++++G+G  G+ +a++ ++agy+v++++ 
  gi|313127514|ref|YP_004037784.1|  4 FAVVGVGPAGARFARRAAEAGYDVVAFEK 32
                                      79***********************9985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                                       -EEEEEEE-HHHHH CS
                     NAD_binding_2 127 tLsimvGGseeafe 140
                                       +L++ +GG+e+++e
  gi|313127514|ref|YP_004037784.1| 130 ELTVSAGGDEQTIE 143
                                       45555666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2528.59
//
Query:       gi|313127515|ref|YP_004037785.1|  [L=252]
Description: hypothetical protein Hbor_27960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1682.09
//
Query:       gi|313127516|ref|YP_004037786.1|  [L=330]
Description: bnr/asp-box hypothetical protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-14   52.8   0.0    8.8e-07   28.1   0.0    2.9  3  Sortilin-Vps10  Sortilin, neurotensin receptor 3,
    1.8e-08   34.0   4.5    0.00089   18.6   0.0    3.6  3  PSII_BNR        Photosynthesis system II assembly factor YCF4
    2.6e-06   26.6  25.9       0.15   12.2   0.2    6.1  6  BNR             BNR/Asp-box repeat
    0.00038   19.8   4.5      0.083   12.2   0.1    2.8  2  BNR_2           BNR repeat-like domain
  ------ inclusion threshold ------
       0.12   11.6   9.4        1.5    8.0   0.1    3.7  3  DUF4185         Domain of unknown function (DUF4185)


Domain annotation for each model (and alignments):
>> Sortilin-Vps10  Sortilin, neurotensin receptor 3,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.5e-10   8.8e-07       3      61 ..      49     107 ..      47     123 .. 0.91
   2 !   19.7   0.0   8.3e-08    0.0003      20     141 ..     124     237 ..     113     255 .. 0.79
   3 ?    1.7   0.0     0.024        88      25      63 ..     271     309 ..     252     320 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.5e-10
                                       EEEESSTTSS-EE-GGGGTTEEBE-EEE-STTS--EEEEEES-EEEEESSTTSSEEEEE CS
                    Sortilin-Vps10   3 vyiSeDeGktwkkvkeklkgeaiqeivvhpfdkkkaylltdskklyvttDrGktwkkfk 61 
                                       +++++D+G+tw++v +++  ++++++ v+p+d + +y+ t+ + +++++D+G+tw+k +
  gi|313127516|ref|YP_004037786.1|  49 LHRTDDAGETWHRVGKDTLPKSVTSVAVSPHDAEVVYAGTEPSAVFRSDDAGETWTKLN 107
                                       6799***********999999999********************************975 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 8.3e-08
                                       GTTEEBE-EEE-STTS--EEEEEES-EEEEESSTTSSEEEEE-SS-BS...S--EEESSETTEEEEE.......BTT CS
                    Sortilin-Vps10  20 lkgeaiqeivvhpfdkkkaylltdskklyvttDrGktwkkfklpfkpslsaeplsfhakdkdwlialgekkeskdck 96 
                                       ++ + ++ i ++p+d ++ y+  + + l+ t+D G+tw+    +++++  + ++++h + +d+  a           
  gi|313127516|ref|YP_004037786.1| 124 PHTHHVRWIEPDPHDPDHLYVSIEAGALIQTHDGGETWSDRVPSARRD--THSMATHTDAPDHAWAA--------AG 190
                                       4555666799****************************9975555555..899*********99888........46 PP

                                       S-EEEESSTTSSEEEEESSEEE.EEE-S......TT-EEEEE-SSS- CS
                    Sortilin-Vps10  97 kkayystdggkswkklqesvkk.cewakss.kkkeekilceekeees 141
                                       + +  ++dgg++w+  q+  ++ + w+++  +++ ++il+++ ++ +
  gi|313127516|ref|YP_004037786.1| 191 DGYAETSDGGETWTYPQKGLNHqYCWSVAVdAADPSRILVSAAQSAR 237
                                       678889***********999854778766557888888888877766 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.024
                                       BE-EEE-STTS--EEEEEES-EEEEESSTTSSEEEEE-S CS
                    Sortilin-Vps10  25 iqeivvhpfdkkkaylltdskklyvttDrGktwkkfklp 63 
                                       i ++v ++  +   +   +++ ly+t D G++++++ ++
  gi|313127516|ref|YP_004037786.1| 271 IVRAVLDRGRRGGEFYAVTNRGLYRTGDGGDSFERVGID 309
                                       445555555555555556689999999999999987665 PP

>> PSII_BNR  Photosynthesis system II assembly factor YCF48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.5e-07   0.00089      86     138 ..      51     104 ..      42     109 .. 0.83
   2 !   12.8   1.5   1.4e-05     0.052      27      95 ..     138     204 ..     110     303 .. 0.64
   3 ?   -0.2   0.0      0.13   4.8e+02      36      57 ..     289     310 ..     255     318 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-07
                                       EESSTTSS-EE----TT-SS-EEEEEEEETTEEEEE...ETT--EEEESSTTSSEE CS
                          PSII_BNR  86 httdgGksWerikLsekLPGePllitalgkkkaelv...tdvgaiYrtedagknWk 138
                                        t d+G++W+r+  +  LP + +  +a+ ++ ae+v   t+ +a++r++dag++W+
  gi|313127516|ref|YP_004037786.1|  51 RTDDAGETWHRVGKD-TLPKSVTS-VAVSPHDAEVVyagTEPSAVFRSDDAGETWT 104
                                       47899*******976.89987665.58899999987666889*************7 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.4e-05
                                       SSS-EEEEETTTEEEEESSTTSS-EE-----S--.--EEEEEEEETTEEEEEEETTEEEEESSTTSS-E CS
                          PSII_BNR  27 dekhGflvGtkatlletlDGGktWeersldleeevnyrlesvsfkgdegwivGkPslllhttdgGksWe 95 
                                       d++h ++  +  +l+ t+DGG+tW+ r  ++  + + ++++   + d +w +        t+dgG++W+
  gi|313127516|ref|YP_004037786.1| 138 DPDHLYVSIEAGALIQTHDGGETWSDRVPSARRD-THSMATHTDAPDHAWAAAGDG-YAETSDGGETWT 204
                                       7778888888888888888888888888666666.344444444555666554433.357778888776 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.13
                                       TTTEEEEESSTTSS-EE----- CS
                          PSII_BNR  36 tkatlletlDGGktWeersldl 57 
                                       t++ l+ t DGG+++e+  +d 
  gi|313127516|ref|YP_004037786.1| 289 TNRGLYRTGDGGDSFERVGIDW 310
                                       5666777777777777665555 PP

>> BNR  BNR/Asp-box repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00014      0.49       2      12 .]      51      61 ..      50      61 .. 0.88
   2 !   12.2   0.2   4.2e-05      0.15       1      12 []      94     105 ..      94     105 .. 0.90
   3 !    9.2   1.7   0.00041       1.5       3      11 ..     154     162 ..     154     163 .. 0.92
   4 !    8.9   0.3   0.00051       1.8       3      11 ..     196     204 ..     194     205 .. 0.88
   5 ?   -2.7   0.1       3.3   1.2e+04       8      11 ..     256     259 ..     256     260 .. 0.80
   6 ?    1.2   0.1      0.17     6e+02       3      11 ..     296     304 ..     294     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                                      EESSTTSS-EE CS
                               BNR  2 yStDgGktWsk 12
                                       ++D G+tW++
  gi|313127516|ref|YP_004037786.1| 51 RTDDAGETWHR 61
                                      59*******96 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.2e-05
                                       EEESSTTSS-EE CS
                               BNR   1 yyStDgGktWsk 12 
                                       + S+D G+tW+k
  gi|313127516|ref|YP_004037786.1|  94 FRSDDAGETWTK 105
                                       68********96 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00041
                                       ESSTTSS-E CS
                               BNR   3 StDgGktWs 11 
                                       ++DgG+tWs
  gi|313127516|ref|YP_004037786.1| 154 THDGGETWS 162
                                       79******8 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00051
                                       ESSTTSS-E CS
                               BNR   3 StDgGktWs 11 
                                       + DgG+tW+
  gi|313127516|ref|YP_004037786.1| 196 TSDGGETWT 204
                                       89******7 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 3.3
                                       SS-E CS
                               BNR   8 ktWs 11 
                                       +tW+
  gi|313127516|ref|YP_004037786.1| 256 ETWE 259
                                       6**8 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.17
                                       ESSTTSS-E CS
                               BNR   3 StDgGktWs 11 
                                       + DgG +++
  gi|313127516|ref|YP_004037786.1| 296 TGDGGDSFE 304
                                       55*****98 PP

>> BNR_2  BNR repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   2.3e-05     0.083     140     204 ..      49     110 ..      37     122 .. 0.59
   2 !   11.5   2.9   3.7e-05      0.13      85     209 ..      94     214 ..      92     261 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                                       EEEESSTTSS-EE----SSSEEEEEEEE.EEETTEEEEEEEE...EEEEEEESSTTSS-EEE-.EE CS
                             BNR_2 140 lelsddggktWkkgrvveqisgeiqpsilvekdgslvalaRsrkaaileseSedgGetWskve.lt 204
                                       l+ +dd g tW++++ + ++ +++  + +  +d ++v  a +  +  ++ +S d+GetW+k++ lt
  gi|313127516|ref|YP_004037786.1|  49 LHRTDDAGETWHRVGKD-TLPKSVTSVAVSPHDAEVVY-AGT--EPSAVFRSDDAGETWTKLNgLT 110
                                       66777777777777777.66566655555444433332.222..3344566777777777765233 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.7e-05
                                       EEESSTTSS----EHHHGG.EEEEEE-SS--..EE--T--EEEEEE......SS--EEEEEEEESSTTSS-EE---- CS
                             BNR_2  85 vtSkDdGktWsaprrlpks.pflnisgpvknkpiqladGrlilPsshe....lagkwrallelsddggktWkkgrvv 156
                                        +S+D G+tW++ + l++   +   s p +    ++++ r+i P  h       +  + +l  ++dgg tW+   ++
  gi|313127516|ref|YP_004037786.1|  94 FRSDDAGETWTKLNGLTDLsSASSWSFPPRP---HTHHVRWIEPDPHDpdhlYVSIEAGALIQTHDGGETWSDRVPS 167
                                       68***********966544122334444444...67788*****7776555433335667888999******99888 PP

                                       SSSEEEEEEEE.EEETTEEEEEEEE...EEEEEEESSTTSS-EEE-EEEEE-- CS
                             BNR_2 157 eqisgeiqpsilvekdgslvalaRsrkaaileseSedgGetWskveltslpnp 209
                                        + +++  ++  +++ +++ a a +       +e++dgGetW+ +++    ++
  gi|313127516|ref|YP_004037786.1| 168 -ARRDTHSMATHTDAPDHAWAAAGDG-----YAETSDGGETWTYPQKGLNHQY 214
                                       .6669999999999999999999884.....578*********9995333333 PP

>> DUF4185  Domain of unknown function (DUF4185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0033        12     126     165 ..      46      78 ..      40      91 .. 0.67
   2 ?    8.0   0.1   0.00041       1.5     124     149 ..      88     113 ..      71     123 .. 0.81
   3 ?    1.1   2.3     0.052   1.9e+02     131     154 ..     153     177 ..     142     259 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0033
                           DUF4185 126 ysaiaksdDngetWekvpesvrtnsdtagnenfqqvafvk 165
                                        +++ + dD getW++v +++ ++s t        va+  
  gi|313127516|ref|YP_004037786.1|  46 NTGLHRTDDAGETWHRVGKDTLPKSVT-------SVAVSP 78 
                                       578999***********9987666552.......234444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00041
                           DUF4185 124 tnysaiaksdDngetWekvpesvrtn 149
                                       t+ sa+++sdD getW+k ++ +  +
  gi|313127516|ref|YP_004037786.1|  88 TEPSAVFRSDDAGETWTKLNGLTDLS 113
                                       66799************998765555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.052
                           DUF4185 131 ksdDngetWekvpesvrtnsd.tag 154
                                       + +D+getW++   s+r ++  +a+
  gi|313127516|ref|YP_004037786.1| 153 QTHDGGETWSDRVPSARRDTHsMAT 177
                                       5566666665543333333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 2664.88
//
Query:       gi|313127517|ref|YP_004037787.1|  [L=67]
Description: hypothetical protein Hbor_27980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.8   5.5        1.3    9.5   0.3    2.2  2  HRG       Haem-transporter, endosomal/lysosomal, haem-respons


Domain annotation for each model (and alignments):
>> HRG  Haem-transporter, endosomal/lysosomal, haem-responsive gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.7    0.0017        30       4      23 ..       8      27 ..       6      37 .. 0.88
   2 ?    9.5   0.3   7.3e-05       1.3       6      25 ..      46      65 ..      44      67 .] 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0017
                               HRG  4 riaygifgsilglsaflvyl 23
                                      r a g +g+++g ++ + +l
  gi|313127517|ref|YP_004037787.1|  8 RYALGMCGLVVGGFWLAGFL 27
                                      6799***********98776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 7.3e-05
                               HRG  6 aygifgsilglsaflvylvl 25
                                      ++gif ++++lsa++  l++
  gi|313127517|ref|YP_004037787.1| 46 SVGIFSLAISLSAAVMLLAV 65
                                      58*************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 454.92
//
Query:       gi|313127518|ref|YP_004037788.1|  [L=982]
Description: excinuclease ABC subunit A [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-34  115.9   0.2      4e-33  113.7   0.0    2.4  1  UvrA_inter       UvrA interaction domain
    1.1e-29  102.9   0.8    6.9e-27   94.0   0.1    3.9  4  UvrA_DNA-bind    UvrA DNA-binding domain
    3.2e-22   79.5   0.0    5.8e-12   46.3   0.0    4.3  3  ABC_tran         ABC transporter
    2.5e-13   50.0   0.2     0.0033   16.9   0.2    4.2  3  SMC_N            RecF/RecN/SMC N terminal domain
    2.3e-08   33.7   0.0     0.0019   17.9   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
    7.4e-07   29.7   0.4      0.048   14.0   0.0    3.5  4  AAA_16           AAA ATPase domain
    1.9e-06   28.2   3.1      0.018   15.4   0.7    3.3  3  DnaJ_CXXCXGXG    DnaJ central domain
    2.7e-06   27.4   0.0      0.017   15.0   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
      6e-06   26.6   0.0       0.11   12.8   0.0    3.2  2  AAA_22           AAA domain
    2.6e-05   24.8   0.2       0.02   15.4   0.0    3.4  3  AAA_23           AAA domain
    8.1e-05   22.5   0.0       0.11   12.2   0.0    3.6  4  AAA_15           AAA ATPase domain
    0.00014   21.3   0.2      0.064   12.6   0.0    2.8  3  ATPase           KaiC
    0.00072   20.1   0.2       0.86   10.1   0.0    3.2  2  AAA_18           AAA domain
    0.00082   19.3   1.2        4.2    7.2   0.0    3.7  3  APS_kinase       Adenylylsulphate kinase
    0.00085   19.2  11.9       0.05   13.4   0.0    4.6  5  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0012   18.9   0.0       0.74    9.9   0.0    3.2  3  AAA_14           AAA domain
     0.0013   18.3   0.1        1.8    8.1   0.0    3.3  3  AAA_25           AAA domain
     0.0015   18.7   0.1          2    8.6   0.0    3.5  2  AAA_33           AAA domain
     0.0026   17.4   0.1       0.53    9.9   0.0    2.5  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0065   16.4   0.0       0.33   10.9   0.0    2.4  2  NACHT            NACHT domain
  ------ inclusion threshold ------
       0.01   15.6   0.1       0.45   10.2   0.0    2.6  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.011   15.0   0.0        3.6    6.7   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.02   14.8   0.0        6.3    6.6   0.0    2.5  2  ATPase_2         ATPase domain predominantly from Archaea
      0.034   13.5   0.5         20    4.4   0.0    3.4  3  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.034   13.9   1.3        2.1    8.0   0.1    3.2  3  AAA_30           AAA domain
      0.035   13.3   0.0       0.52    9.4   0.0    2.4  2  NB-ARC           NB-ARC domain
      0.036   14.5   0.0        1.3    9.4   0.0    2.4  2  RNA_helicase     RNA helicase
      0.048   13.7   0.2        3.1    7.9   0.0    3.4  3  MMR_HSR1         50S ribosome-binding GTPase
       0.11   12.2   1.4        5.3    6.7   0.0    3.3  4  AAA_24           AAA domain
       0.12   12.1   0.2        2.1    8.0   0.0    2.3  2  PRK              Phosphoribulokinase / Uridine kinase family
       0.13   12.4   5.6         22    5.3   0.4    3.5  3  Zn-ribbon_8      Zinc ribbon domain
       0.83   10.0   2.9        2.7    8.3   0.1    2.8  2  zinc_ribbon_9    zinc-ribbon
        3.4    7.7   5.8       0.76    9.8   0.0    2.8  2  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0   7.4e-36     4e-33       1     104 [.     132     236 ..     132     241 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 7.4e-36
                        UvrA_inter   1 QsveqIvdqilkleegtkllilaPvvrerkgefkkllenlkkkGfvrvriDgeiydlde.dieldknkkhsievvvD 76 
                                       Qs++++v+qil+l++gt++ i+aPvvr++kg f++l+++l  +G+ rv +Dge +dl+   ++ldkn  h+i+vvvD
  gi|313127518|ref|YP_004037788.1| 132 QSAQDMVTQILSLPDGTRAKIVAPVVRDQKGAFEDLFDELVADGYARVEVDGEAFDLTVnRPDLDKNYDHTIDVVVD 208
                                       9*******************************************************99669**************** PP

                        UvrA_inter  77 rlvvkkeersrlaesvetAlklgeglvi 104
                                       r++++ e+rsr+a+svetAl+ ++g++ 
  gi|313127518|ref|YP_004037788.1| 209 RVKIRPEDRSRIADSVETALTEADGVLK 236
                                       *************************986 PP

>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.23   1.3e+02      78     108 ..      37      67 ..      25      69 .. 0.85
   2 !   94.0   0.1   1.3e-29   6.9e-27       1     109 [.     313     418 ..     313     419 .. 0.96
   3 ?   -0.9   0.0       3.7     2e+03      24      70 ..     473     519 ..     461     526 .. 0.83
   4 ?    0.5   0.0       1.3   7.3e+02      75     105 ..     714     744 ..     698     747 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.23
                                       .......---HHHHHHHHHH-------HHHH CS
                     UvrA_DNA-bind  78 krsyektfeGvipnlerryreteSeavreel 108
                                       + + +  fe +  + +rry e+ S ++r+ l
  gi|313127518|ref|YP_004037788.1|  37 SGKSSLAFETIYAEGQRRYIESLSAYARNFL 67 
                                       5677789********************9865 PP

  == domain 2  score: 94.0 bits;  conditional E-value: 1.3e-29
                                       -S----.-----------GGG..TT-HHHHHHHHHHHTTTS------------S-THHHHH----............ CS
                     UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapwsskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikveyksggr 77 
                                       D+dlvv d s+ ++   ++pw s ++syyr+ +++va+h+++++dtpf+eL+e+++  +LyG++e +++++++ +++
  gi|313127518|ref|YP_004037788.1| 313 DEDLVVVDSSKPVK-HVFEPW-SYNRSYYRTRIDSVAAHFDVSVDTPFEELDEDVQRQFLYGTDE-QVVFKRQTRNG 386
                                       9************9.89****.88899*************************************7.788999999** PP

                                       .......---HHHHHHHHHH-------HHHHH CS
                     UvrA_DNA-bind  78 krsyektfeGvipnlerryreteSeavreele 109
                                       +r++ek+feGvipnlerr+ et+S+++re++e
  gi|313127518|ref|YP_004037788.1| 387 TRRKEKRFEGVIPNLERRHVETDSDSTREHIE 418
                                       ******************************98 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.7
                                       TT-HHHHHHHHHHHTTTS------------S-THHHHH----..... CS
                     UvrA_DNA-bind  24 kkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikv 70 
                                       +++++ +++l+++ +++g++ ++ ++ L+ +     L G ++++i+ 
  gi|313127518|ref|YP_004037788.1| 473 RERTIAEEILKEIRARLGFMEEVGLEYLTLDREASTLSGGESQRIRL 519
                                       56677899999999999999999999999999999999999888776 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.3
                                       ..........---HHHHHHHHHH-------H CS
                     UvrA_DNA-bind  75 ggrkrsyektfeGvipnlerryreteSeavr 105
                                       g++ rs  +t+ Gv  ++++ + et+  ++r
  gi|313127518|ref|YP_004037788.1| 714 GRTPRSNPATYTGVFDYIRELFAETKLSKQR 744
                                       6677888899***************987776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00053      0.29       1      28 [.      16      43 ..      16      59 .. 0.90
   2 !   15.9   0.0   2.6e-05     0.014      79     135 ..     459     537 ..     362     539 .. 0.70
   3 !   46.3   0.0   1.1e-14   5.8e-12       1     136 [.     643     880 ..     643     881 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00053
                                      EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                                      lk++++++ +   ++++G +G+GKS+L+
  gi|313127518|ref|YP_004037788.1| 16 LKDLDVQIPREAFTVVTGLSGSGKSSLA 43
                                      7999**********************95 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.6e-05
                                       H.................HHHTCHHHHHHHSTTGG...TTCBGESTTSGGS-HHHHHHHHHHHHHHHT..SSEEEEE CS
                                       x.................xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                          ABC_tran  79 n.................esdeeiekalsklglke...lkdtvvksspssLSgGqkqrvalarallkk..pkllllD 133
                                                          ++e +++++++lg  e   l+  ++++++s+LSgG+ qr+ la  + +     l++lD
  gi|313127518|ref|YP_004037788.1| 459 AlehfegleaelderertIAEEILKEIRARLGFMEevgLEYLTLDREASTLSGGESQRIRLATQVGSGlvGVLYVLD 535
                                       244444444433322224222335555566555555557778888888**************988765224688888 PP

                                       ST CS
                                       xx RF
                          ABC_tran 134 Ep 135
                                       Ep
  gi|313127518|ref|YP_004037788.1| 536 EP 537
                                       88 PP

  == domain 3  score: 46.3 bits;  conditional E-value: 1.1e-14
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHH.TTSS--.SEEEE....................EETTCEGGGB-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxx....................xxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkll.agllkp.teGei....................lldgkdlkeqele 55 
                                       lk+++++l  g+ +ai+G +G+GKStL+  + ++ l    +++                     l+d+ ++ +++++
  gi|313127518|ref|YP_004037788.1| 643 LKDLDVELPIGQFTAITGVSGSGKSTLMHEIlYKGLARtMNDNTsvhpgdhdaiegiehietvrLIDQSPIGRTPRS 719
                                       7999***********************97551544444233333558888888888888888888888888888888 PP

                                       HCCHCEEEE-SS--S-TTSBHHHH..................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..................................................... RF
                          ABC_tran  56 slrkeigvlpqepqlfpeltvren..................................................... 79 
                                             gv+    +lf e+++ ++                                                     
  gi|313127518|ref|YP_004037788.1| 720 NPATYTGVFDYIRELFAETKLSKQrgyekgrfsfnvkggrceacggqgtvkiemnflsdvyvpceecdgaryndatl 796
                                       8888888888888888888877768**************************************************** PP

                                       ........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTS...SE CS
                                       ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xx RF
                          ABC_tran  80 ........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkp...kl 129
                                                               es+++i + l+ l++++l   ++++  ++LSgG+ qrv+la+ l kk+   +l
  gi|313127518|ref|YP_004037788.1| 797 dvtykdktisdvldmevsealeffESNSQIRRRLQLLEDVGLGYMTLGQPSTTLSGGEAQRVKLAEELGKKQagdTL 873
                                       ***********************************************9999*****************99864447* PP

                                       EEEESTT CS
                                       xxxxxxx RF
                          ABC_tran 130 lllDEpt 136
                                       +llDEpt
  gi|313127518|ref|YP_004037788.1| 874 YLLDEPT 880
                                       ******9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   6.1e-06    0.0033      23     211 ..      25     582 ..      12     587 .. 0.88
   2 !   11.9   0.0   0.00021      0.11      17      46 ..     647     675 ..     634     684 .. 0.82
   3 !   13.4   0.0   7.3e-05     0.039     135     211 ..     803     924 ..     724     930 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.1e-06
                                       TSSEEEEEESTTSSHHHH.HHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEE....... CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx....... RF
                             SMC_N  23 sksftaivGpNGSGKsnl.ldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkk....... 89 
                                        + ft+++G  GSGKs+l ++ i +  G+r + +  s+ +++ + +  + + ++v+  + +i +d+++++       
  gi|313127518|ref|YP_004037788.1|  25 REAFTVVTGLSGSGKSSLaFETI-YAEGQRRYIESLSAYARNFLGQmdKPQVEAVEGLSPAISIDQKNAAnnprstv 100
                                       456**************934666.****9877555555555555553433333444334444444444443355543 PP

                                       SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                             SMC_N  90 lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske............................... 135
                                        ++++ + +++    r g++   + g+ev ++  ++++ +    ++                               
  gi|313127518|ref|YP_004037788.1| 101 GTVTELHDYLRLLYARVGTQYDPLTGEEVGEQSAQDMVTQILSLPDgtrakivapvvrdqkgafedlfdelvadgya 177
                                       33333444555555555555556899999999999999888888889****************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127518|ref|YP_004037788.1| 178 rvevdgeafdltvnrpdldknydhtidvvvdrvkirpedrsriadsvetalteadgvlklvvpdppedvpfgsntrs 254
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127518|ref|YP_004037788.1| 255 tgdlagegddrlvvqfseelgnpnsdfqfteietrsfsfnsphgacpaceglgqtkevdedlvvvdsskpvkhvfep 331
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127518|ref|YP_004037788.1| 332 wsynrsyyrtridsvaahfdvsvdtpfeeldedvqrqflygtdeqvvfkrqtrngtrrkekrfegvipnlerrhvet 408
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|313127518|ref|YP_004037788.1| 409 dsdstrehiedymavttcpdcdgtrlkeqsrhvlvadtsitevnrmsigdalehfegleaelderertiaeeilkei 485
                                       ***************************************************************************** PP

                                       ......................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT. CS
                                       ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                             SMC_N 136 ......................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn. 189
                                                             +LSgGe + + la  +   +     ly+lDe    L ++   ++ + l+  ++  
  gi|313127518|ref|YP_004037788.1| 486 rarlgfmeevgleyltldreasTLSGGESQRIRLATQVG--SGLVGVLYVLDEPSIGLHQRDNDRLLNTLEGLRDLg 560
                                       ****************************99877777644..445568************************888765 PP

                                       SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 190 aQfivislreemlekadklvgv 211
                                         +iv+ ++ee++++ad++v +
  gi|313127518|ref|YP_004037788.1| 561 NTLIVVEHDEETMRRADNVVDM 582
                                       889**************99865 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00021
                                       EEEEETTSSEEEEEESTTSSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  17 tvilpfsksftaivGpNGSGKsnlldAilF 46 
                                        v+lp+ + ftai+G  GSGKs l+  il+
  gi|313127518|ref|YP_004037788.1| 647 DVELPIGQ-FTAITGVSGSGKSTLMHEILY 675
                                       56666665.****************99987 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 7.3e-05
                                       T.............................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                       x.............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e.............................................lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                       +                                             +LSgGe + v la  +  ++     lyllDe
  gi|313127518|ref|YP_004037788.1| 803 KtisdvldmevsealeffesnsqirrrlqlledvglgymtlgqpstTLSGGEAQRVKLAEELGKKQ-AGDTLYLLDE 878
                                       04444444444455555555555555555555566666666666669***********99988655.5678****** PP

                                       TTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 167 idaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgv 211
                                           L ++  +k+ e+l++ ++n   ++v+ ++ +++++ad++v +
  gi|313127518|ref|YP_004037788.1| 879 PTTGLHKEDERKLIEVLQRLTDNgNTVVVVEHELDLVKNADNIVDL 924
                                       *******************999967889999**********99865 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00011      0.06      11      38 ..      15      42 ..       7      49 .. 0.83
   2 !   17.9   0.0   3.6e-06    0.0019      17      39 ..     648     670 ..     640     683 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTl 38
                                       +++ +++i ++ +t++tG sGsGKS+l
  gi|313127518|ref|YP_004037788.1| 15 NLKDLDVQIPREAFTVVTGLSGSGKSSL 42
                                      55666778877779************98 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.6e-06
                            AAA_29  17 ieidlkgatlltGpsGsGKSTll 39 
                                       +e+   ++t +tG sGsGKSTl+
  gi|313127518|ref|YP_004037788.1| 648 VELPIGQFTAITGVSGSGKSTLM 670
                                       55555569**************8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   8.8e-05     0.048      19      78 ..      21      83 ..       9     182 .. 0.61
   2 ?   -1.8   0.0       6.6   3.6e+03      72     116 ..     456     514 ..     395     566 .. 0.66
   3 !   11.3   0.0   0.00059      0.32      25      45 ..     654     674 ..     635     714 .. 0.81
   4 ?   -1.7   0.0       6.1   3.3e+03     106     129 ..     865     901 ..     783     919 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.8e-05
                            AAA_16 19 vrsgrpelvllsGesGvGKsslv.rellralekdggif..lrgkcdql..esaipysalaqalar 78
                                      v  +r+  ++++G sG+GKssl+ ++++   e+++ +   l++ ++ +  +++ p +  ++ l+ 
  gi|313127518|ref|YP_004037788.1| 21 VQIPREAFTVVTGLSGSGKSSLAfETIYA--EGQRRYIesLSAYARNFlgQMDKPQVEAVEGLSP 83
                                      566777889**************655554..4443444456666666666777776555555543 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.6
                            AAA_16  72 laqalareellrqlldeaesaeleawrekleeala..............avpelagaea 116
                                       + +al+  e l+++lde e + +e+  ++++++l+              +++ l+g e+
  gi|313127518|ref|YP_004037788.1| 456 IGDALEHFEGLEAELDERERTIAEEILKEIRARLGfmeevgleyltldrEASTLSGGES 514
                                       45555554555555555555555555555555555666666666655554444444444 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00059
                            AAA_16  25 elvllsGesGvGKsslvrell 45 
                                       + + ++G sG+GKs+l+ e+l
  gi|313127518|ref|YP_004037788.1| 654 QFTAITGVSGSGKSTLMHEIL 674
                                       56889************9987 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 6.1
                            AAA_16 106 a.............avpelagaeasrllellkrllal 129
                                       +             ++  l+ ++++ l e+l+rl + 
  gi|313127518|ref|YP_004037788.1| 865 GkkqagdtlylldePTTGLHKEDERKLIEVLQRLTDN 901
                                       3444444444444444444445555555555555532 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.051        27      16      29 ..     299     312 ..     286     324 .. 0.69
   2 ?    5.5   0.0      0.04        22      14      29 ..     423     439 ..     410     453 .. 0.66
   3 !   15.4   0.7   3.3e-05     0.018      15      50 ..     758     789 ..     745     794 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.051
                     DnaJ_CXXCXGXG  16 tCktCkGsGvvree 29 
                                        C++C+G G+++e 
  gi|313127518|ref|YP_004037788.1| 299 ACPACEGLGQTKEV 312
                                       58888888865443 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.04
                     DnaJ_CXXCXGXG  14 kktCktCkGsG.vvree 29 
                                       ++tC++C+G+  +++++
  gi|313127518|ref|YP_004037788.1| 423 VTTCPDCDGTRlKEQSR 439
                                       67888888887444333 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 3.3e-05
                     DnaJ_CXXCXGXG  15 ktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGt 50 
                                        +C++C+G+G+v+ e+    +f + +  +C+eC+G 
  gi|313127518|ref|YP_004037788.1| 758 GRCEACGGQGTVKIEM----NFLSDVYVPCEECDGA 789
                                       47********766665....36777889******97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0014      0.76      81     116 ..       7      43 ..       2      60 .. 0.83
   2 !   15.0   0.0   3.1e-05     0.017      79     139 ..     632     693 ..     622     700 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLi 116
                                        v+  ++++l++l  ++    ++v+ G SG GKS+L 
  gi|313127518|ref|YP_004037788.1|   7 EVRGAEEHNLKDLDVQIPReAFTVVTGLSGSGKSSLA 43 
                                       5566678899999999877699*************95 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.1e-05
                                       EEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S----------- CS
                       RsgA_GTPase  79 vllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkh 139
                                       +l+v+  ++++l++l  +l   +++++ G SG GKStL+ ++l +  ++t +  ++ + G h
  gi|313127518|ref|YP_004037788.1| 632 FLTVRGARQHNLKDLDVELPIgQFTAITGVSGSGKSTLMHEILYKGLARTMNDNTSVHPGDH 693
                                       5667777889999999999877******************9998877777666666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0016      0.84       5      38 ..      26      70 ..      24     151 .. 0.73
   2 !   12.8   0.0   0.00019      0.11       6      28 ..     654     676 ..     653     715 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0016
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee...........e 38
                                      + ++vvtG sG+GK+ l+ +  +   ++ ++e            +
  gi|313127518|ref|YP_004037788.1| 26 EAFTVVTGLSGSGKSSLAFETIYAEGQRRYIESlsayarnflgqM 70
                                      5699*************9888888877777776666655555551 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00019
                            AAA_22   6 gilvvtGesGtGKTtllrrlleq 28 
                                       +++++tG sG+GK+tl+ ++l++
  gi|313127518|ref|YP_004037788.1| 654 QFTAITGVSGSGKSTLMHEILYK 676
                                       689**************999876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.077        42      20      35 ..      27      42 ..      12      45 .. 0.85
   2 ?    0.2   0.0       1.6   8.8e+02     105     154 ..     345     433 ..     270     499 .. 0.49
   3 !   15.4   0.0   3.8e-05      0.02       2      41 ..     633     675 ..     633     835 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.077
                            AAA_23 20 gltlItGpNGaGKTTi 35
                                       +t++tG  G+GK+++
  gi|313127518|ref|YP_004037788.1| 27 AFTVVTGLSGSGKSSL 42
                                      589***********98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.6
                            AAA_23 105 kkaklelleideleqfisellgskki..ilnlilflgqerfeefelkdkke.......................... 153
                                       + a+ + +++d+  ++++e +++++     ++++f+ q r+   ++++++e                          
  gi|313127518|ref|YP_004037788.1| 345 SVAAHFDVSVDTPFEELDEDVQRQFLygTDEQVVFKRQTRNGTRRKEKRFEgvipnlerrhvetdsdstrehiedym 421
                                       44444444444444444444444433333344444444443222222222233333333333333333333333333 PP

                            AAA_23 154 ...........r 154
                                                  r
  gi|313127518|ref|YP_004037788.1| 422 avttcpdcdgtR 433
                                       333333333331 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 3.8e-05
                            AAA_23   2 Lkienfrsf..rdqeidF.skgltlItGpNGaGKTTildAikl 41 
                                       L++++ r++  +d ++++    +t+ItG  G+GK+T++  i +
  gi|313127518|ref|YP_004037788.1| 633 LTVRGARQHnlKDLDVELpIGQFTAITGVSGSGKSTLMHEILY 675
                                       6788889998888888888679***************977755 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.74     4e+02      14      39 ..      16      42 ..      14      45 .. 0.77
   2 ?   -1.7   0.0       3.4   1.9e+03     325     348 ..     530     553 ..     433     567 .. 0.73
   3 ?    4.6   0.0     0.042        23      14      43 ..     646     673 ..     641     719 .. 0.86
   4 !   12.2   0.0    0.0002      0.11     317     359 ..     859     906 ..     768     912 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.74
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsi 39
                                      lkd ++++  e +tv+ G  +sGKSs+
  gi|313127518|ref|YP_004037788.1| 16 LKDLDVQIPREaFTVVTGLSGSGKSSL 42
                                      455555555556**************8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                            AAA_15 325 villiEEPEahLHpqaqkvlikll 348
                                       v+++++EP + LH      l ++l
  gi|313127518|ref|YP_004037788.1| 530 VLYVLDEPSIGLHQRDNDRLLNTL 553
                                       577888888888876666666655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.042
                            AAA_15  14 lkdveidlseeltvliGkNnsGKSsileal 43 
                                       l+ ve+++   +t + G  +sGKS++++ +
  gi|313127518|ref|YP_004037788.1| 646 LD-VELPIGQ-FTAITGVSGSGKSTLMHEI 673
                                       44.8999999.***************9754 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.0002
                            AAA_15 317 k.....dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQv 359
                                       k      +k++   ++l++EP + LH +  + li+ l++l ++++t v
  gi|313127518|ref|YP_004037788.1| 859 KlaeelGKKQAGDTLYLLDEPTTGLHKEDERKLIEVLQRLTDNGNTVV 906
                                       04444567788899*****************************99544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.019        10      16      41 ..      23      48 ..      16      56 .. 0.86
   2 ?   -2.3   0.0       4.2   2.3e+03      61     112 ..     432     486 ..     420     503 .. 0.76
   3 !   12.6   0.0   0.00012     0.064      16      46 ..     650     680 ..     643     686 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.019
                            ATPase 16 ipegrvvlitGepGtGKtifalqFli 41
                                      ip+++ + +tG +G+GK+ +a + ++
  gi|313127518|ref|YP_004037788.1| 23 IPREAFTVVTGLSGSGKSSLAFETIY 48
                                      89****************99987666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
                            ATPase  61 edlrenakslGwdlekleeegklaiidasesaeesaee...kdkedleelieela 112
                                       + l+e+ +++ +  + + e +++ i da e+ e+ ++e   ++++ +ee+++e++
  gi|313127518|ref|YP_004037788.1| 432 TRLKEQSRHVLVADTSITEVNRMSIGDALEHFEGLEAEldeRERTIAEEILKEIR 486
                                       5677888887777788888899999999999999887776555556666666655 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00012
                            ATPase  16 ipegrvvlitGepGtGKtifalqFlikgaek 46 
                                       +p g+ + itG++G+GK+++  + l+kg+++
  gi|313127518|ref|YP_004037788.1| 650 LPIGQFTAITGVSGSGKSTLMHEILYKGLAR 680
                                       688999**********************876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.027        14       2      17 ..      30      45 ..      30      65 .. 0.91
   2 !   10.1   0.0    0.0016      0.86       3      18 ..     658     673 ..     657     706 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.027
                            AAA_18  2 lltGtpGvGKttlake 17
                                      ++tG +G+GK++la e
  gi|313127518|ref|YP_004037788.1| 30 VVTGLSGSGKSSLAFE 45
                                      59***********965 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0016
                            AAA_18   3 ltGtpGvGKttlakeL 18 
                                       +tG++G+GK+tl +e+
  gi|313127518|ref|YP_004037788.1| 658 ITGVSGSGKSTLMHEI 673
                                       9***********9998 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0077       4.2       6      21 ..      30      45 ..      25      58 .. 0.83
   2 ?    1.3   0.0      0.52   2.8e+02      82     117 ..     329     364 ..     316     383 .. 0.82
   3 ?    6.7   0.0     0.011         6       7      27 ..     658     679 ..     653     693 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0077
                                      EEESSTTSSHHHHHHH CS
                        APS_kinase  6 wltGlsgsGKstiana 21
                                       +tGlsgsGKs++a++
  gi|313127518|ref|YP_004037788.1| 30 VVTGLSGSGKSSLAFE 45
                                      58***********986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.52
                                       ---SHHHHHHHHHHHHCHTEEEEEEEE--HHHHHHH CS
                        APS_kinase  82 isPyreeReaarelleealkfievfvdtplevceer 117
                                         P++ +R+  r+ +++    ++v vdtp+e+  e 
  gi|313127518|ref|YP_004037788.1| 329 FEPWSYNRSYYRTRIDSVAAHFDVSVDTPFEELDED 364
                                       579999**********999***********987653 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.011
                                       EESSTTSSHHHHHHH.HHHHHH CS
                        APS_kinase   7 ltGlsgsGKstiana.lekkLv 27 
                                       +tG+sgsGKst+ ++ l k L 
  gi|313127518|ref|YP_004037788.1| 658 ITGVSGSGKSTLMHEiLYKGLA 679
                                       8**********98761445554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.8      0.18        99       1      15 [.      28      42 ..      28      43 .. 0.95
   2 ?   -2.7   0.0       7.5   4.1e+03     100     160 ..     158     218 ..     155     233 .. 0.78
   3 ?    1.8   0.2      0.31   1.7e+02     233     272 ..     505     543 ..     434     569 .. 0.78
   4 ?    5.7   0.1     0.021        11       1      16 [.     655     670 ..     655     689 .. 0.94
   5 !   13.4   0.0   9.2e-05      0.05     258     295 ..     870     908 ..     857     915 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                            AAA_21  1 lnvliGpNgsGKSnL 15
                                      ++v++G  gsGKS+L
  gi|313127518|ref|YP_004037788.1| 28 FTVVTGLSGSGKSSL 42
                                      89***********98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.5
                            AAA_21 100 ldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldg 160
                                       +d + ++e  ++  +a+g   ++ + ++  l+v+ p+ ++++++++d++ + +++++++++
  gi|313127518|ref|YP_004037788.1| 158 RDQKGAFEDLFDELVADGYARVEVDGEAFDLTVNRPDLDKNYDHTIDVVVDRVKIRPEDRS 218
                                       5666777777777777888888888899999999999999999999999999999999965 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.31
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHP 272
                                        a+ lS G  + ++l+t + + l    l+++DEp  gLH 
  gi|313127518|ref|YP_004037788.1| 505 EASTLSGGESQRIRLATQVGSGLVG-VLYVLDEPSIGLHQ 543
                                       4555688888888999999999988.89***********6 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.021
                            AAA_21   1 lnvliGpNgsGKSnLL 16 
                                       +++++G  gsGKS+L+
  gi|313127518|ref|YP_004037788.1| 655 FTAITGVSGSGKSTLM 670
                                       89************97 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 9.2e-05
                            AAA_21 258 g.sllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                       g +l+l+DEp +gLH +  r+l+e+l +l++ng  v+++
  gi|313127518|ref|YP_004037788.1| 870 GdTLYLLDEPTTGLHKEDERKLIEVLQRLTDNGNTVVVV 908
                                       149****************************99999875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.048        26       4      27 ..      28      51 ..      25      82 .. 0.81
   2 !    9.9   0.0    0.0014      0.74       4      30 ..     655     683 ..     653     731 .. 0.81
   3 ?   -1.5   0.0       4.3   2.4e+03      63      93 ..     869     904 ..     839     955 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.048
                            AAA_14  4 ilvitGaRrvGKTtllkqlikell 27
                                        v+tG+  +GK+ l+++ i+ + 
  gi|313127518|ref|YP_004037788.1| 28 FTVVTGLSGSGKSSLAFETIYAEG 51
                                      579***************998776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell..vkk 30 
                                         +itG+  +GK+tl+++++++ l  + +
  gi|313127518|ref|YP_004037788.1| 655 FTAITGVSGSGKSTLMHEILYKGLarTMN 683
                                       578****************9998865333 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.3
                            AAA_14  63 ekktylflDEiqev......pewekalkslvdegknl 93 
                                        ++t+ +lDE          +++ ++l++l d+g n 
  gi|313127518|ref|YP_004037788.1| 869 AGDTLYLLDEPTTGlhkedeRKLIEVLQRLTDNG-NT 904
                                       3566666666555445555555556666666655.32 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0034       1.8      30      52 ..      23      45 ..       9      50 .. 0.88
   2 ?    6.1   0.0     0.013       7.1      29      52 ..     650     672 ..     625     681 .. 0.79
   3 ?   -3.2   0.0       9.8   5.3e+03     163     188 ..     886     910 ..     883     911 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0034
                            AAA_25 30 lpagelallaGapgtGKttlald 52
                                      +p++++++++G +g+GK+ la +
  gi|313127518|ref|YP_004037788.1| 23 IPREAFTVVTGLSGSGKSSLAFE 45
                                      79******************976 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                            AAA_25  29 llpagelallaGapgtGKttlald 52 
                                       l p g +++++G +g+GK+tl  +
  gi|313127518|ref|YP_004037788.1| 650 L-PIGQFTAITGVSGSGKSTLMHE 672
                                       4.889***************9765 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9.8
                            AAA_25 163 sdvgalvealeriarrtgaavllvhH 188
                                       +d+++l+e l+r+ +  g +v++v H
  gi|313127518|ref|YP_004037788.1| 886 EDERKLIEVLQRL-TDNGNTVVVVEH 910
                                       5788999999999.666777777777 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.026        14       3      18 ..      30      45 ..      28      95 .. 0.86
   2 !    8.6   0.0    0.0037         2       5      21 ..     659     675 ..     656     745 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.026
                            AAA_33  3 llvGlpGsGKstlaer 18
                                      ++ Gl+GsGKs la +
  gi|313127518|ref|YP_004037788.1| 30 VVTGLSGSGKSSLAFE 45
                                      688*********9865 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0037
                            AAA_33   5 vGlpGsGKstlaerllk 21 
                                        G++GsGKstl +++l 
  gi|313127518|ref|YP_004037788.1| 659 TGVSGSGKSTLMHEILY 675
                                       7***********99874 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.033        18       2      24 ..      28      50 ..      27      57 .. 0.79
   2 !    9.9   0.0   0.00098      0.53       3      23 ..     656     676 ..     654     695 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.033
                                      EEEEEESTTCCHHHHHHHHHCT- CS
                              cobW  2 vtvltGflGsGKTtLlnhllenr 24
                                       tv+tG  GsGK++L  +++  +
  gi|313127518|ref|YP_004037788.1| 28 FTVVTGLSGSGKSSLAFETIYAE 50
                                      589************88887443 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00098
                                       EEEEESTTCCHHHHHHHHHCT CS
                              cobW   3 tvltGflGsGKTtLlnhllen 23 
                                       t +tG  GsGK+tL+ ++l +
  gi|313127518|ref|YP_004037788.1| 656 TAITGVSGSGKSTLMHEILYK 676
                                       78***************9933 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.16        85       3      19 ..      29      45 ..      27     100 .. 0.86
   2 !   10.9   0.0    0.0006      0.33       3      23 ..     656     676 ..     654     688 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                                      EEEEC-TTTCHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqk 19
                                       +++G +GsGK+ L+ +
  gi|313127518|ref|YP_004037788.1| 29 TVVTGLSGSGKSSLAFE 45
                                      5899**********855 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0006
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                        +++G +GsGK+tL++++  +
  gi|313127518|ref|YP_004037788.1| 656 TAITGVSGSGKSTLMHEILYK 676
                                       579**************9865 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       0.2   1.1e+02       1      15 [.      29      43 ..      29      81 .. 0.82
   2 ?   10.2   0.0   0.00082      0.45       2      30 ..     657     685 ..     656     712 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.2
                   Viral_helicase1  1 ivvhGvpGcGKStli 15
                                      +vv G  G+GKS+l 
  gi|313127518|ref|YP_004037788.1| 29 TVVTGLSGSGKSSLA 43
                                      69**********985 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00082
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrp 30 
                                        + Gv G+GKStl  ++l + l  t+n +
  gi|313127518|ref|YP_004037788.1| 657 AITGVSGSGKSTLMHEILYKGLARTMNDN 685
                                       589**************988755555555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.015       7.9       3      25 ..      28      50 ..      26     107 .. 0.79
   2 ?    6.7   0.0    0.0066       3.6       5      25 ..     657     677 ..     654     697 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                           DUF2075  3 vvlVtGvaGtGKtvvllnllael 25
                                        +VtG +G+GK+ ++++ +++ 
  gi|313127518|ref|YP_004037788.1| 28 FTVVTGLSGSGKSSLAFETIYAE 50
                                      579**************999876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0066
                           DUF2075   5 lVtGvaGtGKtvvllnllael 25 
                                        +tGv+G+GK+ ++ ++l++ 
  gi|313127518|ref|YP_004037788.1| 657 AITGVSGSGKSTLMHEILYKG 677
                                       59***************9986 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.026        14      20      47 ..      26      53 ..      13     118 .. 0.71
   2 ?    6.6   0.0     0.012       6.3      21      43 ..     654     676 ..     639     737 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledk 47
                                      + + +++G  gsGK++L  e i    + 
  gi|313127518|ref|YP_004037788.1| 26 EAFTVVTGLSGSGKSSLAFETIYAEGQR 53
                                      5789*************99998776443 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiien 43 
                                       ++  i+G  gsGK++L+ ei+ +
  gi|313127518|ref|YP_004037788.1| 654 QFTAITGVSGSGKSTLMHEILYK 676
                                       56789**************9865 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.54     3e+02      40      54 ..      27      41 ..       7      45 .. 0.80
   2 ?    3.9   0.0     0.052        28     101     156 ..     455     505 ..     442     538 .. 0.75
   3 ?    4.4   0.0     0.038        20      42      60 ..     656     674 ..     626     683 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.54
                                      .SEEEE--TTSSHHH CS
                      FtsK_SpoIIIE 40 shllvaGatgsGKSt 54
                                      + ++v G +gsGKS 
  gi|313127518|ref|YP_004037788.1| 27 AFTVVTGLSGSGKSS 41
                                      4799**********6 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.052
                                       SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-... CS
                      FtsK_SpoIIIE 101 dperalraleeLvkemeeryalfreagvrsiaaydgeiaedpldifgdvflvlDny 156
                                       ++ +al+ +e L++e++er++ ++e+  ++i+a  g ++e+ l+     +l lD  
  gi|313127518|ref|YP_004037788.1| 455 SIGDALEHFEGLEAELDERERTIAEEILKEIRARLGFMEEVGLE-----YLTLDRE 505
                                       68899**************************9966666665444.....4555554 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.038
                                       EEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE  42 llvaGatgsGKStalntLi 60 
                                       + + G +gsGKSt ++ ++
  gi|313127518|ref|YP_004037788.1| 656 TAITGVSGSGKSTLMHEIL 674
                                       689**********999876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.23   1.2e+02      19      34 ..      27      42 ..      22      64 .. 0.85
   2 ?    8.0   0.1    0.0039       2.1      19      38 ..     654     673 ..     651     684 .. 0.88
   3 ?   -0.8   0.0         2   1.1e+03      86     122 ..     867     908 ..     824     911 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.23
                            AAA_30 19 rvavltGpAGtGKtta 34
                                       ++v+tG  G+GK+ +
  gi|313127518|ref|YP_004037788.1| 27 AFTVVTGLSGSGKSSL 42
                                      589**********986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0039
                            AAA_30  19 rvavltGpAGtGKttalkal 38 
                                       +++++tG+ G+GK+t++ ++
  gi|313127518|ref|YP_004037788.1| 654 QFTAITGVSGSGKSTLMHEI 673
                                       4789*************987 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2
                            AAA_30  86 lepg.tllivDEagmv....dtkqlaallkaaekagakvilv 122
                                        ++g tl++ DE        d ++l ++l++++++g +v++v
  gi|313127518|ref|YP_004037788.1| 867 KQAGdTLYLLDEPTTGlhkeDERKLIEVLQRLTDNGNTVVVV 908
                                       234449999999765555779999999999999999999887 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.49   2.6e+02      21      39 ..      27      45 ..      15      55 .. 0.79
   2 ?    9.4   0.0   0.00096      0.52      21      43 ..     654     676 ..     642     688 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.49
                                      EEEEEEESTTSSHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakq 39
                                       +  + G  G+GK+ la +
  gi|313127518|ref|YP_004037788.1| 27 AFTVVTGLSGSGKSSLAFE 45
                                      567799*********9865 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00096
                                       EEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnk 43 
                                        + a+ G  G+GK+tl+++il k
  gi|313127518|ref|YP_004037788.1| 654 QFTAITGVSGSGKSTLMHEILYK 676
                                       4789****************876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.34   1.8e+02       2      17 ..      30      45 ..      29      69 .. 0.75
   2 ?    9.4   0.0    0.0025       1.3       3      48 ..     658     700 ..     656     723 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.34
                      RNA_helicase  2 wlyGpsgeGKStlake 17
                                      +++G sg GKS+la e
  gi|313127518|ref|YP_004037788.1| 30 VVTGLSGSGKSSLAFE 45
                                      6899*********988 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0025
                      RNA_helicase   3 lyGpsgeGKStlake.LakallkklklkkkdsvysrnpeddfwdgYt 48 
                                       ++G sg GKStl++e L k l++++    +d++ +++ ++d  +g +
  gi|313127518|ref|YP_004037788.1| 658 ITGVSGSGKSTLMHEiLYKGLARTM----NDNTSVHPGDHDAIEGIE 700
                                       7899***********5666677666....344455666666666666 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.6   3.2e+02       3      15 ..      30      42 ..      28      60 .. 0.88
   2 ?    7.9   0.0    0.0058       3.1       3      26 ..     657     681 ..     655     709 .. 0.81
   3 ?   -1.6   0.0         5   2.7e+03      44      84 ..     869     909 ..     844     925 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.6
                                      EEEESTTSSHHHH CS
                          MMR_HSR1  3 aivGrpNvGKStL 15
                                      ++ G + +GKS+L
  gi|313127518|ref|YP_004037788.1| 30 VVTGLSGSGKSSL 42
                                      789*********9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0058
                                       EEEESTTSSHHHHHHHHHTS.TEEE CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge.kaiv 26 
                                       ai G + +GKStL+  ++ +  a++
  gi|313127518|ref|YP_004037788.1| 657 AITGVSGSGKSTLMHEILYKgLART 681
                                       89*************9987655555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5
                                       TTEEEEEEECGGC.SSHHHHHHHHHHHHHHHHCTSEEEEEEE CS
                          MMR_HSR1  44 kgkeielvDtpGl.iegaseekglgkaflaleeadlillvvd 84 
                                        g+ ++l+D p   ++ +++e++l + +++l +    ++vv+
  gi|313127518|ref|YP_004037788.1| 869 AGDTLYLLDEPTTgLH-KEDERKLIEVLQRLTDNGNTVVVVE 909
                                       3456777775541133.3444466666666666555666665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.21   1.1e+02       5      22 ..      29      46 ..      25      55 .. 0.86
   2 ?   -2.8   0.0       8.3   4.5e+03     110     133 ..     548     571 ..     542     580 .. 0.65
   3 ?    6.7   0.0    0.0098       5.3       6      23 ..     657     674 ..     653     742 .. 0.85
   4 ?   -2.3   0.0       5.5     3e+03     109     131 ..     889     911 ..     881     917 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.21
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                       +++G sg+GK++la e 
  gi|313127518|ref|YP_004037788.1| 29 TVVTGLSGSGKSSLAFET 46
                                      5899**********9875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.3
                            AAA_24 110 efrrllkklqelrknvifiahekt 133
                                       ++ ++l+ l++l+++ i++ h ++
  gi|313127518|ref|YP_004037788.1| 548 RLLNTLEGLRDLGNTLIVVEHDEE 571
                                       444555556666668888888665 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0098
                            AAA_24   6 liyGpsgiGKTtlakelg 23 
                                       +i+G sg+GK+tl+ e+ 
  gi|313127518|ref|YP_004037788.1| 657 AITGVSGSGKSTLMHEIL 674
                                       79************9984 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 5.5
                            AAA_24 109 eefrrllkklqelrknvifiahe 131
                                       ++++++l++l++ +++v+++ he
  gi|313127518|ref|YP_004037788.1| 889 RKLIEVLQRLTDNGNTVVVVEHE 911
                                       45566666677777799999997 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.37     2e+02       4      16 ..      31      43 ..      28      63 .. 0.85
   2 ?    8.0   0.0    0.0039       2.1       3      19 ..     657     673 ..     655     727 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.37
                               PRK  4 vagsSGaGkttva 16
                                      v+g SG+Gk+++a
  gi|313127518|ref|YP_004037788.1| 31 VTGLSGSGKSSLA 43
                                      8*********986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0039
                               PRK   3 gvagsSGaGkttvarkl 19 
                                       +++g SG+Gk+t+++++
  gi|313127518|ref|YP_004037788.1| 657 AITGVSGSGKSTLMHEI 673
                                       8************9986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.12        65      18      34 ..     288     305 ..     278     312 .. 0.73
   2 ?    3.9   0.1      0.11        58      26      37 ..     423     435 ..     410     437 .. 0.76
   3 ?    5.3   0.4     0.041        22       7      34 ..     759     788 ..     759     792 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                       Zn-ribbon_8  18 lqsis.dapltaCPeCgs 34 
                                        +s+s  +p  aCP+C +
  gi|313127518|ref|YP_004037788.1| 288 TRSFSfNSPHGACPACEG 305
                                       455666888999****87 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                       Zn-ribbon_8  26 ltaCPeCgs.evr 37 
                                        t+CP+C + +++
  gi|313127518|ref|YP_004037788.1| 423 VTTCPDCDGtRLK 435
                                       567****997766 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.041
                       Zn-ribbon_8   7 rCeeCghefevlqsis.daplta.CPeCgs 34 
                                       rCe+Cg + +v  +++  ++  + C eC +
  gi|313127518|ref|YP_004037788.1| 759 RCEACGGQGTVKIEMNfLSDVYVpCEECDG 788
                                       8*********88888876666667****87 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.4   7.4e+02      23      29 ..     299     305 ..     286     307 .. 0.79
   2 ?    8.3   0.1    0.0049       2.7      10      32 ..     404     434 ..     403     436 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.4
                     zinc_ribbon_9  23 lCPhCgg 29 
                                       +CP C+g
  gi|313127518|ref|YP_004037788.1| 299 ACPACEG 305
                                       7****87 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0049
                     zinc_ribbon_9  10 rfVsvspdedsd........vlCPhCgggFV 32 
                                       r+V+  +d++++        ++CP+C+g  +
  gi|313127518|ref|YP_004037788.1| 404 RHVETDSDSTREhiedymavTTCPDCDGTRL 434
                                       6777666666668888888549*****9766 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.2   1.7e+03     136     172 ..     351     394 ..     330     487 .. 0.62
   2 ?    9.8   0.0    0.0014      0.76      17      45 ..     647     675 ..     644     688 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.2
                             DUF87 136 klssdepveklleelk............kekeelrklknqaiarlldkl 172
                                       ++s+d+p+e+l e+++                  +++ ++  +r+++++
  gi|313127518|ref|YP_004037788.1| 351 DVSVDTPFEELDEDVQrqflygtdeqvvF-----KRQTRNGTRRKEKRF 394
                                       66777777777777777777654333220.....222222222222222 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                             DUF87  17 dlnklvtrHlAilgsTGsGKSntvavLle 45 
                                       d++  + + +Ai g +GsGKS+++  +l 
  gi|313127518|ref|YP_004037788.1| 647 DVELPIGQFTAITGVSGSGKSTLMHEILY 675
                                       5555566778**************87764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (982 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.86u 0.30s 00:00:01.15 Elapsed: 00:00:00.47
# Mc/sec: 6226.30
//
Query:       gi|313127519|ref|YP_004037789.1|  [L=117]
Description: hypothetical protein Hbor_28000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-15   54.6   1.9    1.4e-14   54.1   1.9    1.2  1  SepF      Cell division protein SepF
  ------ inclusion threshold ------
      0.034   13.3   0.2      0.043   13.0   0.2    1.2  1  Lar_N     Lactate racemase N-terminal domain
      0.091   13.1   0.0       0.12   12.6   0.0    1.2  1  Rx_N      Rx N-terminal domain


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   1.9   2.3e-18   1.4e-14       1      72 []      38     111 ..      38     111 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.3e-18
                                       EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC..HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                              SepF   1 vvvveprsfedaqeiadalkegkiVilnledldk..eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                       v ++++ + +d+  i+da+++g+ Vi ++++  +  +++++ivd l++v+ ++dGdi++ g++ ++itP++v +
  gi|313127519|ref|YP_004037789.1|  38 VRIATIGDKQDVVSIKDAVYDGDLVIADITRHTTsdSTMEHIVDDLRQVAEEVDGDIVQKGDDQIIITPTGVAV 111
                                       678999999**********************99999***********************************976 PP

>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   7.1e-06     0.043      59      86 ..      61      87 ..      44      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-06
                             Lar_N 59 ivvsDiTRptpskiilpllleelkeagv 86
                                      +v+ DiTR t s+ +++++++ l+++ +
  gi|313127519|ref|YP_004037789.1| 61 LVIADITRHTTSDSTMEHIVDDLRQV-A 87
                                      6999********************94.3 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     2e-05      0.12      22      69 ..      44      91 ..      27      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                              Rx_N 22 gvkeeleklkdeLesiqavLedaeerqikdeavkeWlkelrdlaydae 69
                                      g k+++ ++kd     + v++d  +  + d+++++ +++lr++a +++
  gi|313127519|ref|YP_004037789.1| 44 GDKQDVVSIKDAVYDGDLVIADITRHTTSDSTMEHIVDDLRQVAEEVD 91
                                      77899999999999999***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 732.20
//
Query:       gi|313127520|ref|YP_004037790.1|  [L=230]
Description: hypothetical protein Hbor_28010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-68  229.1   0.3    4.5e-68  228.8   0.3    1.0  1  DUF1028   Family of unknown function (DUF1028)


Domain annotation for each model (and alignments):
>> DUF1028  Family of unknown function (DUF1028)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.8   0.3   2.5e-72   4.5e-68       1     193 []       2     204 ..       2     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 228.8 bits;  conditional E-value: 2.5e-72
                                       EEEEEEE-T.......TT--EEEEEEESSS-HHHHHEEEETTTEEEEEESS--HHHHHHHHHHHHTT--HHHHHHHH CS
                           DUF1028   1 TfSivardp.......etgelGvAvaskslaVgalvpfaragvGavatQaltnpelgekglelleagasaeealeal 70 
                                       TfSi++r++       e+ ++GvAv+++++aVgal+pfa+++ G+vatQ+l+n+elgekg+++l++g+++e+al+al
  gi|313127520|ref|YP_004037790.1|   2 TFSICVRETyddevgtEQTRFGVAVTTRLPAVGALCPFASEN-GVVATQSLVNVELGEKGIDYLDDGLAIEDALQAL 77 
                                       9******998999999999***********************.********************************** PP

                                       HHT-TTGGG-EEEEEETTS-EEEEE-TTS-S-EEEE.ETTEEEEEES-S-TCHHHHHHHHH......S-HHHHHHHH CS
                           DUF1028  71 laadegrelRQlavvdakgetaaftGeeclewaghrtgenyavaGNlLageevleamaeafeateg.epLaerLlaA 146
                                       l+adegre+RQl+ v+++g+ +af+G+ec++w ghr+ge+y+vaGNlL+geev++a a+a+e+ ++ +pLa rL++ 
  gi|313127520|ref|YP_004037790.1|  78 LNADEGREQRQLHGVGLDGT-FAFSGAECQGWFGHRVGEHYTVAGNLLTGEEVIDAAADAYESGNRdDPLAVRLIET 153
                                       *******************9.****************************************9877789********* PP

                                       HHHHHHT-------...-EEEEEEEE.....TTEEEEEEEE--SS-HHHHH CS
                           DUF1028 147 LeaGeaaGGDkrgr...qSAallVvr.esedeskpyvdLrvddhedpiaeL 193
                                       LeaG++aGGDkr++   qSAal+V++ e++  +  y dLrvd++++pi++L
  gi|313127520|ref|YP_004037790.1| 154 LEAGHEAGGDKREDltvQSAALVVTTtEDQAPTPYYNDLRVDATRTPISDL 204
                                       ************88888*********8777888999************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1631.63
//
Query:       gi|313127521|ref|YP_004037791.1|  [L=160]
Description: RNA-binding protein, containing pua domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   59.1   1.3    3.1e-16   59.1   1.3    1.8  2  PUA       PUA domain
  ------ inclusion threshold ------
      0.041   13.3   0.1      0.069   12.6   0.1    1.4  1  PIN_5     PINc domain ribonuclease
      0.043   14.1   0.0      0.079   13.3   0.0    1.4  1  DUF1947   Domain of unknown function (DUF1947)


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       0.5     3e+03      37      37 ..      46      46 ..      14      66 .. 0.65
   2 !   59.1   1.3   5.1e-20   3.1e-16       2      73 ..      79     151 ..      78     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.5
                                      E CS
                               PUA 37 V 37
                                      V
  gi|313127521|ref|YP_004037791.1| 46 V 46
                                      0 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 5.1e-20
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                        v+vd+gA+ +++ ga+++ pG+v++++d+e+gd V i  e  g+++avG+a+  ++e+    g++++ +++v
  gi|313127521|ref|YP_004037791.1|  79 VVTVDAGAISFVSDGADVMRPGIVDADDDIEPGDLVLIAEEThGKVLAVGRALEPGAEMVGDSGKVVESLHHV 151
                                       599**************************************88****************99988888888886 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.2e-05     0.069     147     188 ..      95     139 ..      71     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                             PIN_5 147 ealRkGilDsaeDl...dvllLAkELdaavvssDeGikkwaeklG 188
                                       + +R Gi+D+ +D+   d++l+A+E +++v++  + ++  ae +G
  gi|313127521|ref|YP_004037791.1|  95 DVMRPGIVDADDDIepgDLVLIAEETHGKVLAVGRALEPGAEMVG 139
                                       579***********7778*************98888777777665 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05     0.079       1      54 [.       5      60 ..       5      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                      --EE--HHHHHHHHHHHHTTT---TT--.....-EEEE-SS-EEEEETTEEEEEE.SS CS
                           DUF1947  1 kRHfLSkKeakeileklkekyisislesdk...iEieeekkeklYlingvpilfe.ee 54
                                      +RH L++ e+ e+ e+++     +++++d    +E++   ++ + l++g p+++  ++
  gi|313127521|ref|YP_004037791.1|  5 SRHHLRSDEISELEEEIAAQT-GVQMDGDAyemVELADA-DFDVVLVDGDPVVVYmDD 60
                                      6*****************999.99999987335555555.9999*******9998444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1131.55
//
Query:       gi|313127522|ref|YP_004037792.1|  [L=102]
Description: hypothetical protein Hbor_28030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.3   1.8       0.73    9.5   0.2    2.4  2  GATA      GATA zinc finger


Domain annotation for each model (and alignments):
>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   4.1e-05      0.73      11      28 ..       1      20 [.       1      22 [. 0.81
   2 ?    4.9   0.1    0.0011        19      11      26 ..      36      51 ..      31      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 4.1e-05
                              GATA 11 lWRrg..pdgnksLCnaCGl 28
                                      +WR+   +d ++ +C aCG+
  gi|313127522|ref|YP_004037792.1|  1 MWRSRtnRDRKTVVCLACGT 20
                                      6887777888888******7 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0011
                              GATA 11 lWRrgpdgnksLCnaC 26
                                       W+r +    +LC+ C
  gi|313127522|ref|YP_004037792.1| 36 RWNRQGKEFEHLCKEC 51
                                      69999888899***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1151  (0.0641977); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 686.99
//
Query:       gi|313127523|ref|YP_004037793.1|  [L=440]
Description: exoribonuclease R [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-82  275.3   0.1    1.3e-80  271.2   0.1    2.0  1  RNB       RNB domain
     0.0035   17.3   0.0     0.0099   15.9   0.0    1.7  1  DUF982    Protein of unknown function (DUF982)


Domain annotation for each model (and alignments):
>> RNB  RNB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.2   0.1   1.4e-84   1.3e-80       1     322 [.      71     373 ..      71     374 .. 0.91

  Alignments for each domain:
  == domain 1  score: 271.2 bits;  conditional E-value: 1.4e-84
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RNB   1 RkdlrdllvitIdpedakdlDdAisieklpngnyelgVhIADvshyvkegspldkearkratsvyLpekvvpMLPqe 77 
                                       R+dlrdl+++t dp da+d+DdAisi   +++ y+l+VhIADv+hyv++gs++++ea kr+++vyLp  +++MLP+ 
  gi|313127523|ref|YP_004037793.1|  71 RQDLRDLTTWTTDPIDAQDFDDAISIA-ENEETYTLWVHIADVTHYVHPGSEMWEEAVKRGNTVYLPAYTIHMLPPI 146
                                       9*************************5.55558******************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RNB  78 lsedlcSLnpgedrlalsvlidvdek.gevlsveiylsvIkskarltydevqdlleqkdekeekktaedLellyela 153
                                       l+e +cSL p+edrla +v++++d++  + ++ +iy+svI+s++rlty+++++ l+++        +e+ +l++ela
  gi|313127523|ref|YP_004037793.1| 147 LAETVCSLVPNEDRLAHTVEMEIDKEtLSFEEIDIYKSVIESDERLTYSQAEERLDDES----LPLHEECKLVFELA 219
                                       *************************98889*************************5443....46************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                               RNB 154 kalrkkRlkkgalefdspeikllldedkgnrielkveeetkahslveelmllANelvArfl.seleipailriheep 229
                                        +++++R+++g+l +         ++            ++ ah+++ee+ml AN++v++ l   ++++a++r+h++p
  gi|313127523|ref|YP_004037793.1| 220 DRMHEQRKEDGSLVL---------NP-----------SRDRAHTIIEECMLKANKAVTHELmWGRGVEAMYRVHPQP 276
                                       **********99888.........44...........3456*******************99*************** PP

                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                               RNB 230 snekledliklakklglk....lednsskknlqeslekleeeeaeqllselllrllkeakyssep.vgHfgLaleeY 301
                                       +++++++ ++   +l+       + ++ +k+++ +le+   +   + +++ +l+++++aky+ +p  gH +L++++Y
  gi|313127523|ref|YP_004037793.1| 277 TPDQWDKALREIMELDGVkipsAKFDDPRKAVNAALENSPGRA-LNKIQRAVLKVMPRAKYMNDPfGGHHALNFDIY 352
                                       *888877766666443335668777778888888888888777.8889**************999889********* PP

                                       xxxxxxxxxxxxxxxxxxxxx RF
                               RNB 302 thfTSPirRYpDlvvhrllka 322
                                        hfTSPirR +Dl++h+++++
  gi|313127523|ref|YP_004037793.1| 353 GHFTSPIRRLSDLINHWIVHE 373
                                       ******************996 PP

>> DUF982  Protein of unknown function (DUF982)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-06    0.0099      24      71 ..     363     410 ..     348     411 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-06
                                       HHHHH--S---SHHHHHHHHHHHHHHTT-S-HHHHHHHHHHHHHHHT- CS
                            DUF982  24 dfLleeWPvsrgpayeaAlkaCrdAldgdvpveeARraFiaAareagi 71 
                                         L ++W v+++   e+ ++ C++A d+++++e+A r   ++++e g+
  gi|313127523|ref|YP_004037793.1| 363 SDLINHWIVHENDVPEDLVELCDRASDRQKDAETAERLYKQFLEEVGL 410
                                       4578**************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2865.70
//
Query:       gi|313127524|ref|YP_004037794.1|  [L=77]
Description: hypothetical protein Hbor_28050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.084   12.8   0.6       0.16   11.9   0.6    1.4  1  Prok-RING_1  Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   8.8e-06      0.16       4      25 ..      30      48 ..      27      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.8e-06
                       Prok-RING_1  4 gkkCpvCgkelkeedDiVvCpe 25
                                        +Cp+C++++   dD+VvC e
  gi|313127524|ref|YP_004037794.1| 30 SIACPACEEPF---DDLVVCEE 48
                                      568*******9...799***86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 522.49
//
Query:       gi|313127525|ref|YP_004037795.1|  [L=134]
Description: signal-transduction protein containing camp-binding and cbs domains [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-27   95.8   4.7    5.4e-15   55.6   0.4    2.0  2  CBS              CBS domain
  ------ inclusion threshold ------
      0.099   12.6   0.0         14    5.6   0.0    2.1  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
       0.12   12.6   0.0         15    6.0   0.0    2.7  3  IF3_N            Translation initiation factor IF-3, N-termin


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.4   1.1e-14   6.8e-11       1      55 [.       6      60 ..       6      62 .. 0.92
   2 !   55.6   0.4     9e-19   5.4e-15       1      56 [.      71     126 ..      71     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.1e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V+ +m++ ++tv+ dt +e+a++lm e+gv+++++Vd+ ++l+Gi+t +D ++ +
  gi|313127525|ref|YP_004037795.1|  6 VARLMSTTLHTVSVDTLVEDAAKLMMENGVGSVLIVDDGNQLLGILTTTDFVQIV 60
                                      6789********************87999*******87779*********99876 PP

  == domain 2  score: 55.6 bits;  conditional E-value: 9e-19
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+++mt+dvvt + + ++ +++++m ++g++++PVVd+d+ ++Gi++ +Dl+++l+
  gi|313127525|ref|YP_004037795.1|  71 VSEYMTSDVVTTTAQVPIQDVADTMMQHGFHHVPVVDDDEGVIGIISTTDLASYLS 126
                                       899*********************88**********77777************985 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0033        20      15      50 ..      20      55 ..       6      61 .. 0.81
   2 ?    5.6   0.0    0.0024        14      19      50 ..      89     120 ..      70     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0033
                   Acetyltransf_10 15 efispealrerieegealllvaeeggkivGvielrd 50
                                      + + ++a + ++e+g   +l++++g++++G+++++d
  gi|313127525|ref|YP_004037795.1| 20 DTLVEDAAKLMMENGVGSVLIVDDGNQLLGILTTTD 55
                                      5566688889999******************98766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0024
                   Acetyltransf_10  19 pealrerieegealllvaeeggkivGvielrd 50 
                                       ++  + ++++g +++ v+++++ ++G+i+++d
  gi|313127525|ref|YP_004037795.1|  89 QDVADTMMQHGFHHVPVVDDDEGVIGIISTTD 120
                                       24445555899999**************8754 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.8   1.6e+04      50      55 ..       6      11 ..       3      13 .. 0.78
   2 ?    6.0   0.0    0.0024        15      10      35 ..      38      63 ..      24      71 .. 0.85
   3 ?    4.0   0.0      0.01        61       8      27 ..     101     120 ..      98     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.8
                                      EEEEE- CS
                             IF3_N 50 Vcrimd 55
                                      V+r+m+
  gi|313127525|ref|YP_004037795.1|  6 VARLMS 11
                                      899997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0024
                                      EEEE-SSS-EEEEEEHHHHHHHHHHH CS
                             IF3_N 10 vrlvdedGeqlGvistreAlrlaeek 35
                                      v +vd+ ++ lG+++t + +++  e+
  gi|313127525|ref|YP_004037795.1| 38 VLIVDDGNQLLGILTTTDFVQIVAER 63
                                      66776666778********9998776 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.01
                                       SEEEEE-SSS-EEEEEEHHH CS
                             IF3_N   8 revrlvdedGeqlGvistre 27 
                                        +v +vd+d   +G+ist +
  gi|313127525|ref|YP_004037795.1| 101 HHVPVVDDDEGVIGIISTTD 120
                                       6799***994469****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 967.94
//
Query:       gi|313127526|ref|YP_004037796.1|  [L=580]
Description: pre-peptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-08   33.7   3.0    7.9e-05   23.7   0.2    4.9  3  PPC       Bacterial pre-peptidase C-terminal domain


Domain annotation for each model (and alignments):
>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -15.1  16.9         1   1.8e+04      56      56 ..     245     245 ..      26     343 .. 0.69
   2 !   18.8   0.3   1.5e-07    0.0026       3      69 ..     381     443 ..     379     444 .. 0.88
   3 !   23.7   0.2   4.4e-09   7.9e-05       3      70 .]     492     564 ..     490     564 .. 0.76

  Alignments for each domain:
  == domain 1  score: -15.1 bits;  conditional E-value: 1
                                       E CS
                               PPC  56 f 56 
                                       f
  gi|313127526|ref|YP_004037796.1| 245 F 245
                                       1 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.5e-07
                                       EEEEEEE-TT-EEEEEES-TT..SE.EEEE-TT..-SS-EE-STT-TTS-TTS-EE-SSSEEEEEEE. CS
                               PPC   3 Dvysfevpagdsltididggtidld.LylldsngtsvaaydansapsgsdeyieftapqaGtYyvaVs 69 
                                       +vy+f+v  +  + i   gg  d+   +l+ ++gt++++++ ++  +   +++   ap++GtY + V+
  gi|313127526|ref|YP_004037796.1| 381 HVYTFSVDQDAYIRIPFGGGP-DTArATLYAPSGTELDTSVSYA--D-TIPFGA-QAPETGTYRIVVT 443
                                       79*******************.8887*************66666..4.459999.99********996 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 4.4e-09
                                       EEEEEEE-TT-EEEEEE...S-TT...SEEEEE-TT..-SS-EE-ST.T-TT.S-TTS-EE-SSSEEEEEEE.. CS
                               PPC   3 Dvysfevpagdsltidi...dggti.dldLylldsngtsvaaydans.apsg.sdeyieftapqaGtYyvaVss 70 
                                       D++  ++ +g ++t+d+   +++++ d+ + l  ++g+++a+ d +s   +  +   +++ta + GtYyv+Vs+
  gi|313127526|ref|YP_004037796.1| 492 DWFALDAQSGEQITVDLrrhSNNFGsDVAVALVAPDGSEIAS-DTSScGVGMcDPDDLTVTAATNGTYYVRVSG 564
                                       9***************977666664566699*****999998.55555333333345778999*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 4076.28
//
Query:       gi|313127527|ref|YP_004037797.1|  [L=90]
Description: hypothetical protein Hbor_28080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 611.89
//
Query:       gi|313127528|ref|YP_004037798.1|  [L=102]
Description: 30S ribosomal protein s10 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-26   90.5   0.0    6.6e-26   90.4   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   3.7e-30   6.6e-26       1      97 [.       5      98 ..       5      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 3.7e-30
                                      EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHH CS
                     Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketi 78
                                      r+rl ++++ +L+++++++ ++a+++g++++gp+plPtk+++v+ +ksp ++ + ++e++e+r+hkRlidi da+++ +
  gi|313127528|ref|YP_004037798.1|  5 RVRLAGTSPDDLDDICDDVREIANKTGVNLSGPIPLPTKTLEVPARKSPDGEgTATWEHWEMRVHKRLIDI-DADERAL 82
                                      799********************************************************************.8****** PP

                                      HHHS-...S---SS-EEEE CS
                     Ribosomal_S10 79 dtllkllqlnlpegVsvev 97
                                      ++l++   +++p+ Vs+e+
  gi|313127528|ref|YP_004037798.1| 83 RQLMR---IQVPSDVSIEI 98
                                      *****...*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 679.25
//
Query:       gi|313127529|ref|YP_004037799.1|  [L=421]
Description: translation elongation factor 1a (ef-1a/ef-tu) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.7e-57  191.6   0.1    1.3e-56  191.2   0.1    1.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.7e-37  126.0   0.1    1.9e-36  124.8   0.0    1.7  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    2.8e-17   62.9   3.1    2.8e-16   59.7   1.0    2.5  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.9e-06   27.9   0.1    2.4e-05   24.4   0.1    2.6  1  MMR_HSR1     50S ribosome-binding GTPase
    0.00035   20.5   0.1      0.017   15.1   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
    0.00041   19.8   0.1      0.061   12.7   0.0    2.3  2  Gtr1_RagA    Gtr1/RagA G protein conserved region
      0.008   16.1   0.5      0.022   14.7   0.5    1.7  1  GTP_EFTU_D4  Elongation factor Tu domain 4
  ------ inclusion threshold ------
      0.014   14.8   0.0       0.41   10.0   0.0    2.3  1  SRPRB        Signal recognition particle receptor beta subuni
      0.026   13.8   0.0      0.065   12.5   0.0    1.6  1  Septin       Septin
       0.08   12.7   0.2        1.2    8.9   0.1    2.3  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.13   11.8   0.1       0.62    9.6   0.1    1.9  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.13   12.3   0.0         12    5.9   0.0    2.5  2  Dynamin_N    Dynamin family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.2   0.1     9e-60   1.3e-56       1     189 [.       4     211 ..       4     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 191.2 bits;  conditional E-value: 9e-60
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHST.............HCHSHHHHHHTSCSSCEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka..eeerv.............lDtlkeErergiTiksaais 62 
                                       k++ n++iighvDhGK+TL++rLl++tg + ++  ++  e  ++             +D+l+eErerg+Ti++a+ +
  gi|313127529|ref|YP_004037799.1|   4 KPHQNLAIIGHVDHGKSTLVGRLLFETGSVPEHVIEQhrE--EAeekgkggfefayvMDNLAEERERGVTIDIAHQE 78 
                                       5799*************************99987777431..224568999************************** PP

                                       EETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST... CS
                          GTP_EFTU  63 leketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl... 135
                                       ++  t+++ ++++D+PGH+dF+k++i+g++++D avlvv+a++Gv pqt+e++ la+++g+  +i++iNKmD +   
  gi|313127529|ref|YP_004037799.1|  79 FD--TDEFYFTIVDCPGHRDFVKNMITGASQADNAVLVVAADDGVAPQTREHVFLARTLGIGeLIIAINKMDVVdys 153
                                       **..*********************************************************99***********996 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHHH CS
                          GTP_EFTU 136 kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllealv 189
                                       ++++k++ eev+ +l      l+++ ++++ + ++v++Sa++g+++             tlleal 
  gi|313127529|ref|YP_004037799.1| 154 EDTYKQVTEEVQ-NL------LKQVRFQSD-NATFVPISAFEGDNIAdasdntswydgkTLLEALN 211
                                       666777777777.66......688888875.99***********9997777777777777888775 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       9.5   1.4e+04      55      74 ..     271     290 ..     265     291 .. 0.68
   2 !  124.8   0.0   1.3e-39   1.9e-36       3     111 ..     312     418 ..     310     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 9.5
                                       B-BSS-SSCCSTT-CEEEEE CS
                       GTP_EFTU_D3  55 kvsekkpefvkpGdnvivev 74 
                                       + ++++ + + pGdnv ++v
  gi|313127529|ref|YP_004037799.1| 271 EMHHEEVDQAGPGDNVGFNV 290
                                       44456678888999987776 PP

  == domain 2  score: 124.8 bits;  conditional E-value: 1.3e-39
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCE CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikp 79 
                                       + +++f+Aqv+++++  ++ itagY+pv++++ta+v+++++++ +kld+ +++v+e++p+f+k+Gd+++v+v+++kp
  gi|313127529|ref|YP_004037799.1| 312 SVAETFKAQVVVMQH--PSVITAGYTPVFHAHTAQVACTIEAIDQKLDPASGEVAEENPDFIKSGDAAVVTVRPQKP 386
                                       56899**********..************************************************************ PP

                                       EEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  80 ialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       + +e   ++p+lG Fa+R++g+T+aaG+v e+
  gi|313127529|ref|YP_004037799.1| 387 LSIEPSGDIPELGSFAVRDMGQTIAAGKVLEV 418
                                       *****************************998 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.13   1.9e+02      14      53 ..       4      41 ..       4      49 .. 0.89
   2 !   59.7   1.0   1.8e-19   2.8e-16       1      73 [.     238     304 ..     238     305 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                                      ETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSE CS
                       GTP_EFTU_D2 14 kkGdevrilg.ndtskkeivtrissletfhededeavagan 53
                                      k+ +++ i+g +d +k+   t +++l+ + + + e v +++
  gi|313127529|ref|YP_004037799.1|  4 KPHQNLAIIGhVDHGKS---TLVGRLLFETGSVPEHVIEQH 41
                                      677899999*9**9999...************999987765 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 1.8e-19
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       Gtv  gr+++Gtl++Gd+v +  ++++     ++++ +e++he++d+a +g+n+G++v+++g +d i++Gd+ 
  gi|313127529|ref|YP_004037799.1| 238 GTVPVGRIETGTLNPGDNVSF--QPSDVG---GEVKTVEMHHEEVDQAGPGDNVGFNVRGVGKDD-IRRGDVC 304
                                       99*******************..666667...89*******************************.*****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   1.6e-08   2.4e-05       2      97 ..       9     128 ..       8     183 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.6e-08
                                       EEEEESTTSSHHHHHHHHH.....................T..........STEEESSSTTSSSSEEEEEEEETTEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt.....................g..........ekaivsdkpgtTrdinegrvklkgke 47 
                                        ai+G+   GKStL+ +l+                     g          ++   +++ g+T+di + ++++++  
  gi|313127529|ref|YP_004037799.1|   9 LAIIGHVDHGKSTLVGRLLfetgsvpehvieqhreeaeekGkggfefayvmDNLAEERERGVTIDIAHQEFDTDEFY 85 
                                       69****************988887777777777666665515566565544466678888************99999 PP

                                       EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHH CS
                          MMR_HSR1  48 ielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeel 97 
                                       +++vD+pG  +    +  +++ +    +ad ++lvv a  ++++p+ +e 
  gi|313127529|ref|YP_004037799.1|  86 FTIVDCPG--H----RDFVKNMITGASQADNAVLVVAAD-DGVAPQTREH 128
                                       ********..3....223444455555677777777655.4455554443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.052        78     101     122 ..       8      29 ..       3      53 .. 0.77
   2 !   15.1   0.0   1.1e-05     0.017      13      83 ..     105     175 ..      64     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.052
                                       EEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpe 122
                                         +++G+   GKStL+ +ll e
  gi|313127529|ref|YP_004037799.1|   8 NLAIIGHVDHGKSTLVGRLLFE 29 
                                       568999**********999866 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-05
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE-- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee.eleelkeelealgyevllvs 83 
                                       ++  d++++vv+++ + + +++ + +  la + gi e++i++nK+D+++ +e +++++ ee+++l  +v + s
  gi|313127529|ref|YP_004037799.1| 105 ASQADNAVLVVAAD-DGVAPQTREHVF-LARTLGIgELIIAINKMDVVDYSEdTYKQVTEEVQNLLKQVRFQS 175
                                       7889**********.777777766655.566667769***********9888789999999998877766655 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   4.1e-05     0.061      30      67 ..      67     103 ..      57     117 .. 0.82
   2 ?    4.7   0.0     0.011        17     116     158 ..     142     184 ..     137     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                         Gtr1_RagA  30 rlgatidveksevrflgnltlnlwDcgGqeafveeyls 67 
                                       + g+tid+ ++e+  +++ ++ ++Dc+G ++fv+++++
  gi|313127529|ref|YP_004037799.1|  67 ERGVTIDIAHQEF-DTDEFYFTIVDCPGHRDFVKNMIT 103
                                       5589*********.58899****************765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.011
                         Gtr1_RagA 116 vlihKmDliqedereeifeerkeeireeiekleke..eiqffaTS 158
                                       + i+KmD +  d  e+++++ +ee+++ +++++++  + +f   S
  gi|313127529|ref|YP_004037799.1| 142 IAINKMDVV--DYSEDTYKQVTEEVQNLLKQVRFQsdNATFVPIS 184
                                       679******..8889999999999999999887765544444444 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.5   1.5e-05     0.022      21      83 ..     242     302 ..     231     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT.S--TT- CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr.qikegd 83 
                                       vG ++ +G+++pg ++  +     Ge++ ++ +++++++a  G++v+  ++g  vG+ +i  gd
  gi|313127529|ref|YP_004037799.1| 242 VG-RIETGTLNPGDNVSFQPSDVGGEVKTVEMHHEEVDQAGPGDNVGFNVRG--VGKdDIRRGD 302
                                       78.99***********8877777789**********************9998..4552466666 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00028      0.41      44      88 ..      79     122 ..       4     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                                       ...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS- CS
                             SRPRB  44 ksekgskltliDfPGheklrqklleklkaksslkglvfvvDStid 88 
                                        +++++ +t++D PGh  + +++++   + ++   lv   D  + 
  gi|313127529|ref|YP_004037799.1|  79 FDTDEFYFTIVDCPGHRDFVKNMITGASQADN-AVLVVAADDGVA 122
                                       3678999***************9999444433.334444455555 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.3e-05     0.065       6      78 ..       8     100 ..       5     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-05
                                       EEEEEEBTTSSCCCCCCT.TSSSS----.....................--------------S-EEEEEEEEETTC CS
                            Septin   6 tlmvvGesglGkttlint.lfetdliee.....................ekleeasekkkktveikkkkvvieedgv 60 
                                       +l ++G+   Gk+tl+   lfet  ++e                       +++ +e+ ++ v+i+ ++++ + d  
  gi|313127529|ref|YP_004037799.1|   8 NLAIIGHVDHGKSTLVGRlLFETGSVPEhvieqhreeaeekgkggfefaYVMDNLAEERERGVTIDIAHQEFDTD-- 82 
                                       7899************76268888888889999***********9999866788888999999999999999998.. PP

                                       EEEEEEEE---BSSSSSH CS
                            Septin  61 klnltviDtpgfGdavdn 78 
                                       ++ +t++D pg+ d+v n
  gi|313127529|ref|YP_004037799.1|  83 EFYFTIVDCPGHRDFVKN 100
                                       7889***********998 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.19   2.8e+02       3      21 ..       8      26 ..       6      30 .. 0.85
   2 ?    8.9   0.1   0.00078       1.2      33     105 ..      81     153 ..      71     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.19
                         PduV-EutP  3 killiGkvgsGKttLtqal 21
                                      ++ +iG+v+ GK tL  +l
  gi|313127529|ref|YP_004037799.1|  8 NLAIIGHVDHGKSTLVGRL 26
                                      5679***********9776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00078
                         PduV-EutP  33 aiefsdeviDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGi......itkidlae 103
                                       + ef+ +++D+PG    +r + + +i+ + +ad  +lv++a++   v p++  +vf   ++Gi      i k+d+++
  gi|313127529|ref|YP_004037799.1|  81 TDEFYFTIVDCPG----HRDFVKNMITGASQADNAVLVVAADDG--VAPQTREHVFLARTLGIgeliiaINKMDVVD 151
                                       5689999******....79*******************999875..5566677777777777644433356666654 PP

                         PduV-EutP 104 de 105
                                        +
  gi|313127529|ref|YP_004037799.1| 152 YS 153
                                       33 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.71   1.1e+03       5      24 ..      11      30 ..       8      49 .. 0.75
   2 ?    9.6   0.1   0.00041      0.62     103     172 ..      99     170 ..      89     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.71
                                      EEESTTCCHHHHHHHHHCT- CS
                              cobW  5 ltGflGsGKTtLlnhllenr 24
                                      + G +  GK+tL+ +ll ++
  gi|313127529|ref|YP_004037799.1| 11 IIGHVDHGKSTLVGRLLFET 30
                                      6788888******9999444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00041
                                       SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEE.EE-HHHHCHC...HHHHHHHHHHHHTT CS
                              cobW 103 eeelksdltldavvavvDaknleaeeekieekaedqlaaadllv.lnKtDlldee.allekleerlrqlnpe 172
                                       ++ ++ + ++d  v vv a+   a +++++  + + l   +l++ +nK+D++d++ ++ ++++e++++l ++
  gi|313127529|ref|YP_004037799.1|  99 KNMITGASQADNAVLVVAADDGVAPQTREHVFLARTLGIGELIIaINKMDVVDYSeDTYKQVTEEVQNLLKQ 170
                                       5667778899999999999999999999999999*******99879*********77778888888777655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0081        12       1      19 [.       9      27 ..       9      34 .. 0.89
   2 ?    4.0   0.0     0.031        46      59     135 ..      49     115 ..      28     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0081
                                      EEEEEBTTTTHHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                      +a++G++ +GKS+++  Ll
  gi|313127529|ref|YP_004037799.1|  9 LAIIGHVDHGKSTLVGRLL 27
                                      589***********98887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.031
                                       T-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEE CS
                         Dynamin_N  59 ekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilav 135
                                        k   +f  v +++ +e+e+         ++ i ++ ++ ++   t+vD PG  +  k   ++++ + +  +++l+v
  gi|313127529|ref|YP_004037799.1|  49 GKGGFEFAYVMDNLAEERERGV-------TIDIAHQEFDTDEFYFTIVDCPGHRDFVK---NMITGASQADNAVLVV 115
                                       4444444444444444444444.......4578888899999999*******887433...3566655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2530.90
//
Query:       gi|313127530|ref|YP_004037800.1|  [L=318]
Description: homoserine dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-48  162.9   0.1      1e-47  162.3   0.1    1.3  1  Homoserine_dh  Homoserine dehydrogenase
      5e-08   33.6   0.2    9.2e-08   32.8   0.2    1.5  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
    6.1e-08   32.7   0.0    1.2e-07   31.7   0.0    1.5  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
     0.0095   15.3   0.1      0.015   14.6   0.1    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
  ------ inclusion threshold ------
      0.023   14.3   0.0       0.04   13.6   0.0    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.026   14.4   0.1      0.044   13.7   0.1    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.18   12.2   0.5        9.9    6.7   0.2    2.3  2  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.3   0.1     4e-51     1e-47       1     172 [.     141     314 ..     141     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 4e-51
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       P+++t+++ ls +++t+ +G+lngt n++l++m++eg ++++vl+eaq+lG+aeaDp++DveG+Daa K++il++++
  gi|313127530|ref|YP_004037800.1| 141 PVLSTIED-LSPEHVTAARGVLNGTANFVLSRMATEGLDYEHVLAEAQDLGVAEADPSFDVEGTDAALKCVILSNVL 216
                                       88888865.899***************************************************************99 PP

                                       C..TTT--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEEC..EEEEEEEEEETTSGGGHSSST-EEEEEEESSSE CS
                     Homoserine_dh  78 f..gleveledvevegiskltaedikeakeegkvlklvasav..earVkpelvpkshplasvkgsenavlvetdrlg 150
                                          + e++l+d +vegi++++   ++ a+e+g++++l+++++  ++rV+p+lvp++ +la v+g+ n+v++et+++g
  gi|313127530|ref|YP_004037800.1| 217 AegEREYTLADANVEGITNIPGSALELAAEDGQTVRLIGESTpdRVRVSPRLVPQNTALA-VSGTRNIVQLETKHAG 292
                                       9444566999******************************94559**************9.**************** PP

                                       EEEEEES-SSHHHHHHHHHHHH CS
                     Homoserine_dh 151 elviqGpgaGaepTAsavlsDl 172
                                       +l i+G+gaG+ +TAsavl+D+
  gi|313127530|ref|YP_004037800.1| 293 QLNISGRGAGGPETASAVLADI 314
                                       *********************8 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.2   3.6e-11   9.2e-08       1     117 []      10     133 ..      10     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.6e-11
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT.........HHHHHT--CB---HHHHHHHHS-EEEEE-S CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd.........rkallasealtldlddliahldpdvvVEca 67 
                                       G+Ga+G++v+e+ ++   +    + a+ad+    +++d          k + ++    ++  +l a  d dv+VE++
  gi|313127530|ref|YP_004037800.1|  10 GAGAVGGSVVELAESYGHT----VTAFADSAsAVVDADgidpasvlkQKHDEGRVGSADPESALHA--DYDVLVEAT 80 
                                       99*********99999986....7777777755555557777788776777777777777777777..********9 PP

                                       --HHHH.....TTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                     NAD_binding_3  68 sseava.....elvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                       + +        ++v  aL++g dvv ankg +a  ++y++L+++ ++n   +++e
  gi|313127530|ref|YP_004037800.1|  81 PTTLGDaepgfSHVRHALERGADVVLANKGPVA--ERYADLMALERENAGSVRFE 133
                                       976543223338*********************..************99888776 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   4.9e-11   1.2e-07      31      95 ..       2      66 ..       1      92 [. 0.88

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.9e-11
                                      TTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHH CS
                     ELFV_dehydrog 31 egkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieellelkeerksvkeykks 95
                                      +gkr+a+ G G vg  +++l+++ g++v+a  Ds  +++d +G+d +++l+ k++++ v + + +
  gi|313127530|ref|YP_004037800.1|  2 SGKRLAVLGAGAVGGSVVELAESYGHTVTAFADSASAVVDADGIDPASVLKQKHDEGRVGSADPE 66
                                      799**************************************************999998887755 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     6e-06     0.015      35      72 ..       2      39 ..       1      54 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6e-06
                                      TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C 35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72
                                      sgk+++++G+G++G +v +++++ g  v+a+  s ++ 
  gi|313127530|ref|YP_004037800.1|  2 SGKRLAVLGAGAVGGSVVELAESYGHTVTAFADSASAV 39
                                      79****************************99887644 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05      0.04       2     101 ..       7     107 ..       6     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                       EEES-SHHHHHHHHHHHH.HTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SS CS
                              ApbA   2 ailGaGaiGsllaakLak.agadvtlilrsrrlealkknGlrltseggeeilrppealsaeekselepidlvivtvK 77 
                                       a+lGaGa+G+ + ++La+  g++vt  + s+  + +  +G++  s+ ++++ + ++  +++e++  +++d+++ +++
  gi|313127530|ref|YP_004037800.1|   7 AVLGAGAVGGSV-VELAEsYGHTVTAFADSA-SAVVDADGIDPASVLKQKHDEGRVGSADPESALHADYDVLVEATP 81 
                                       79********98.678888************.8789*****999999888888888777777888899999999998 PP

                                       GG..GHHHHHHHHGGGECTCEEEEEE CS
                              ApbA  78 ay..qteealeeikplldpntvvlll 101
                                       ++  ++e   + ++++l++ + v+l 
  gi|313127530|ref|YP_004037800.1|  82 TTlgDAEPGFSHVRHALERGADVVLA 107
                                       85336666777788888887777765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.7e-05     0.044       2      64 ..       6      69 ..       5      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH.HHHHHHHCCTTTTSS-HHHHCCCH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekale.kieksleklvekgklkeeeveaal 64
                                      +av+GaG +G ++ +++ s g++V+ +  s++a+ +a     ++ l++ + +g++  ++ e+al
  gi|313127530|ref|YP_004037800.1|  6 LAVLGAGAVGGSVVELAESYGHTVTAFADSASAVVDADGiDPASVLKQKHDEGRVGSADPESAL 69
                                      69***********************998877777665541445578888888888877777766 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0039       9.9       5      40 ..       1      36 [.       1      83 [. 0.75
   2 ?    3.5   0.0     0.037        94      14      69 ..      85     146 ..      76     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0039
                     NAD_binding_7  5 lkgkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                      ++gk+  v G+G v+ + v+   ++g +vt  a   
  gi|313127530|ref|YP_004037800.1|  1 MSGKRLAVLGAGAVGGSVVELAESYGHTVTAFADSA 36
                                      5799**************************999884 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.037
                     NAD_binding_7  14 GgGevAarkvrklleagakvtvvapev.keeleelvklaeee.....lekdlegadlviaat 69 
                                       G  e + + vr+ le ga+v++  +   +e   +l+ l++e+     +e+ + ga  v+ ++
  gi|313127530|ref|YP_004037800.1|  85 GDAEPGFSHVRHALERGADVVLANKGPvAERYADLMALERENagsvrFEATVGGAIPVLSTI 146
                                       5556678899**********996666333334466666665533333356566655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 2394.77
//
Query:       gi|313127531|ref|YP_004037801.1|  [L=184]
Description: ACT binding domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-06   26.7   0.5    5.7e-05   22.8   0.0    2.6  3  ACT       ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.2e-09   5.7e-05       1      64 [.      19      84 ..      19      87 .. 0.86
   2 ?    1.5   0.1     0.014   2.5e+02      38      66 ..      96     122 ..      77     125 .. 0.71
   3 ?   -2.0   0.0      0.18   3.2e+03      34      56 ..     155     177 ..     150     182 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.2e-09
                                      EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT..ECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedk..vagivfvvivvdeedleevlealkk 64
                                      +++r++++D+PG L + ++ +a++g N+ si + +  ++  +   v v ++  +++ +++++al++
  gi|313127531|ref|YP_004037801.1| 19 HTIRLELADEPGQLLDALRPIAENGGNLLSIFHERGNRTprGRIPVEVDLECPPDRFDTIVDALRS 84
                                      789****************************99999888877777777777777777777777776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.014
                                       TTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  38 dkvagivfvvivvdeedleevlealkkle 66 
                                           +++ +vi+v++ +++++ ++l+++e
  gi|313127531|ref|YP_004037801.1|  96 Q--YSETLTVILVGHLVDSDLSDTLQRIE 122
                                       3..46777888888888888888887765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.18
                                       EEESTTECEEEEEEEEEEHHHHH CS
                               ACT  34 rssedkvagivfvvivvdeedle 56 
                                       +++ed +  i +v  + d  ++e
  gi|313127531|ref|YP_004037801.1| 155 GRTEDALDVIRTVAREKDLHVIE 177
                                       56666444455555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1181.99
//
Query:       gi|313127532|ref|YP_004037802.1|  [L=729]
Description: translation elongation factor 2 (ef-2/ef-g) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-65  219.0   0.8    6.7e-65  218.3   0.8    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.4e-24   86.0   0.1      3e-23   81.6   0.0    2.6  2  EFG_C        Elongation factor G C-terminus
    1.3e-22   79.7   0.5    1.3e-22   79.7   0.5    1.8  2  EFG_II       Elongation Factor G, domain II
      2e-21   76.0   0.0    8.1e-21   74.0   0.0    2.0  2  EFG_IV       Elongation factor G, domain IV
    1.2e-15   57.7   1.6    5.7e-15   55.5   1.6    2.3  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    8.3e-06   25.9   0.4    9.3e-05   22.5   0.1    2.6  2  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.063   13.5   0.0    2.1  1  DUF948       Bacterial protein of unknown function (DUF948)
      0.043   13.7   0.1       0.09   12.6   0.1    1.6  1  RF3_C        Class II release factor RF3, C-terminal domain
      0.065   12.7   0.1       0.19   11.1   0.1    1.8  1  SRPRB        Signal recognition particle receptor beta subuni
       0.18   11.4   0.0       0.44   10.1   0.0    1.6  1  Ras          Ras family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.3   0.8   3.7e-68   6.7e-65       2     193 ..      20     258 ..      19     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 218.3 bits;  conditional E-value: 3.7e-68
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEE CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliD 76 
                                       +irni+i++hvDhGKtTLtd+Ll+ +g+i+++ge +  + ++Dt ++E+ergiTi++a++s+ +  e +++linliD
  gi|313127532|ref|YP_004037802.1|  20 QIRNIAIAAHVDHGKTTLTDNLLAGAGMIADEGEAT--RLMMDTEEDEQERGITIDAANVSMTHeyEDNNHLINLID 94 
                                       79*****************************77755..589**********************44699********* PP

                                       ESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  77 tPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk 153
                                       tPGHvdF  +v+r++r++Dga++vvdaveG +pqte+v+r+al+egv++ +fiNK+Drl++el+e +ee++q+l+++
  gi|313127532|ref|YP_004037802.1|  95 TPGHVDFGGDVTRAMRAVDGALVVVDAVEGAMPQTETVVRQALREGVKPALFINKVDRLISELQEGPEEMQQRLTDV 171
                                       **************************************************************************888 PP

                                       ..............HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHH......................... CS
                          GTP_EFTU 154 ..............eeklekygekge.........kevpvvfgSalkgegvk......................... 182
                                                     +          +         ++ +v+fgSal ++gv+                         
  gi|313127532|ref|YP_004037802.1| 172 isdvnelirgmtedM----------DdvddwtvsvEDGTVAFGSALYKWGVSlpsmqatgmsfgdiieleradkrqe 238
                                       777766666665553..........14444444446889***********999999999999999999999999999 PP

                                       .........HHHHHHHHHSH CS
                          GTP_EFTU 183 .........tllealvellp 193
                                                 +l+++ e++p
  gi|313127532|ref|YP_004037802.1| 239 lhektplsdVVLDMVAEHFP 258
                                       99999998778999998887 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.2   3.6e+02      17      43 ..     167     193 ..     161     197 .. 0.82
   2 !   81.6   0.0   1.7e-26     3e-23       2      87 ..     622     706 ..     621     708 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.2
                                       CCCCHHHHHHH.CT-EEEEEEEE.TTEE CS
                             EFG_C  17 yvgkvisdlss.rrGeiedmeqdasgrv 43 
                                        + +visd+++  rG  edm+   ++++
  gi|313127532|ref|YP_004037802.1| 167 RLTDVISDVNElIRGMTEDMDDV-DDWT 193
                                       56799******99*******998.6665 PP

  == domain 2  score: 81.6 bits;  conditional E-value: 1.7e-26
                                       EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEE CS
                             EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgY 78 
                                       llEPi++v i+vp+e++g + ++++ rrG++ dm q+ ++ ++ie+ +P+ e+igf++++rs+T+G++s+++e +g+
  gi|313127532|ref|YP_004037802.1| 622 LLEPIQNVRIDVPSEHMGSASGEIQGRRGRVDDMYQE-GDLMVIEGIAPVEEMIGFSSDIRSATEGRASWNTENAGF 697
                                       9************************************.*************************************** PP

                                       EE--HHHHH CS
                             EFG_C  79 eevpgdkld 87 
                                       + +  ++++
  gi|313127532|ref|YP_004037802.1| 698 RVLSDNLQR 706
                                       *99988776 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.5     7e-26   1.3e-22       1      74 [.     388     461 ..     388     462 .. 0.97
   2 ?   -3.3   0.1       5.6     1e+04      41      53 ..     555     567 ..     551     568 .. 0.82

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 7e-26
                            EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                       ++ePvi+ ++e+k+ +d  kl + L+++++EDpt+rve +e+T+e ++sG GelHle++++r++++ ++ v +g
  gi|313127532|ref|YP_004037802.1| 388 ISEPVITKSVEAKNMDDLPKLIETLQQVAKEDPTIRVEINEDTGEHLISGQGELHLEVITQRIQKNQGIPVVTG 461
                                       689******************************************************************99987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.6
                            EFG_II  41 eeTketilsGmGe 53 
                                       +eT e++++G+ e
  gi|313127532|ref|YP_004037802.1| 555 NETMELVIEGLEE 567
                                       6999****99855 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.3     6e+03      97     117 ..     118     141 ..     111     144 .. 0.49
   2 !   74.0   0.0   4.5e-24   8.1e-21       2     120 ..     508     618 ..     507     619 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.3
                                       TTTC-HHHH...HHHHCHHHHHHH CS
                            EFG_IV  97 evdsseaaf...kpaarralkeal 117
                                        vd  e+a+   ++++r+al+e++
  gi|313127532|ref|YP_004037802.1| 118 VVDAVEGAMpqtETVVRQALREGV 141
                                       544444444111455566666655 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 4.5e-24
                                       CCESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TT CS
                            EFG_IV   2 qVayrEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGpl 78 
                                       +V+++    +p+ er+e l++ +g+d++ ++ +  i       +n+++d+tkg+q+++e++e+v +G++eal++Gpl
  gi|313127532|ref|YP_004037802.1| 508 EVSMD----MPELERREALQE-AGMDKDTSQNVEHIHG-----TNILIDDTKGIQHLNETMELVIEGLEEALDDGPL 574
                                       56666....788878888888.9************999.....8********************************* PP

                                       TS--EESEEEEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                            EFG_IV  79 agepvtdvkvtLldgslhe..vdsseaafkpaarralkeallkA 120
                                       a ep ++   +L+d++lhe  +++++a+++pa+r a++++l +A
  gi|313127532|ref|YP_004037802.1| 575 AAEPAQGSLLRLHDAKLHEdtIHRGPAQVIPAVRDAVHRSLIDA 618
                                       **************************************999877 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   1.6   3.2e-18   5.7e-15       1      73 [.     307     374 ..     307     375 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3.2e-18
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE.ETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea.vaganaGvivaikgledaiivGdtl 73 
                                       G++a+grv+sGt+kkG+e+++  ++t +k    r++s+  f++ e+e+   g++aG+i+a+ gl da i+G+t+
  gi|313127532|ref|YP_004037802.1| 307 GEIATGRVFSGTIKKGQELYV--SGTAGK---NRVQSVGIFMGGEREElDRGVPAGNIAAVTGLRDA-IAGSTV 374
                                       89*******************..9999**...***********9999946699*************8.****98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   5.2e-08   9.3e-05       2     107 ..      24     143 ..      23     150 .. 0.59
   2 ?   -0.0   0.0       0.5   8.9e+02      51     100 ..     511     561 ..     485     588 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.2e-08
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE......................EEEEECGGC CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke......................ielvDtpGl 56 
                                       +ai+ +   GK+tL   l+  +  ++d+  +Tr +   + +++  e                      i+l+DtpG 
  gi|313127532|ref|YP_004037802.1|  24 IAIAAHVDHGKTTLTDNLLAGAGMIADEGEATRLMMDTEEDEQ--ErgitidaanvsmtheyednnhlINLIDTPGH 98 
                                       778888899*********9866666666666666655543311..12333444444444444455556********6 PP

                                       SSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSE CS
                          MMR_HSR1  57 iegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkp 107
                                       ++    + ++++a+   + +d +l+vvda e+ + + +  + + l+e  kp
  gi|313127532|ref|YP_004037802.1|  99 VD---FGGDVTRAM---RAVDGALVVVDAVEGAMPQTETVVRQALREGVKP 143
                                       65...222344444...458********99554544444555555544444 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.5
                                       EECGGCSS..HHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHH CS
                          MMR_HSR1  51 vDtpGlie..gaseekglgkaflalee.adlillvvdaseeklkpldeeleel 100
                                       +D+p  +e  +a +e g+ k+  ++ e  +   +++d + +++++l+e++e +
  gi|313127532|ref|YP_004037802.1| 511 MDMPE-LErrEALQEAGMDKDTSQNVEhIHGTNILIDDT-KGIQHLNETMELV 561
                                       56666.443334444466666666666457777777733.5566666665544 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.5e-05     0.063      28      79 ..     147     198 ..     141     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavad 79 
                                       ++++ + i el++  +++ + ++d+++ vnel  +++e +++vd +t +v+d
  gi|313127532|ref|YP_004037802.1| 147 INKVDRLISELQEGPEEMQQRLTDVISDVNELIRGMTEDMDDVDDWTVSVED 198
                                       67888899999999999999999999999999999999*******9999987 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     5e-05      0.09      10      78 ..     392     460 ..     382     492 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-05
                                       SEEEEEEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEE CS
                             RF3_C  10 ElfarvrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrl 78 
                                        + ++v++k+     +l + l+q+a+E  +   + +e++ e +++  G+L +eV+++R+++  g++v +
  gi|313127532|ref|YP_004037802.1| 392 VITKSVEAKNMDDLPKLIETLQQVAKEDPTIRVEINEDTGEHLISGQGELHLEVITQRIQKNQGIPVVT 460
                                       5567899999999999***********97666666667888888889*************999988754 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00011      0.19       5      84 ..      23     120 ..      19     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                       EEEEE-STTSSHHHHHHHHHHS......................S---B---SS-EEETTG...GGTT-SEEEETT- CS
                             SRPRB   5 avllvGlsdsGKTslftrLttd......................svkktvtSqessaalkvksekgskltliDfPGh 59 
                                       ++ ++   d GKT+l   L+ +                      +   t  + + s+++++ +++++ ++liD PGh
  gi|313127532|ref|YP_004037802.1|  23 NIAIAAHVDHGKTTLTDNLLAGagmiadegeatrlmmdteedeqERGITIDAANVSMTHEY-EDNNHLINLIDTPGH 98 
                                       5667777788888888888877778888887777766666653222333334455666666.7788899******** PP

                                       GCCSHHHHHHHHHHGGEEEEEEEEE CS
                             SRPRB  60 eklrqklleklkaksslkglvfvvD 84 
                                       + +  +++  ++a +   g + vvD
  gi|313127532|ref|YP_004037802.1|  99 VDFGGDVTRAMRAVD---GALVVVD 120
                                       **9988887744444...4444444 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00024      0.44      26      82 ..      66     122 ..      55     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                                       SSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETT CS
                               Ras  26 eeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydit 82 
                                       +e   Ti +++ + + e+++++  +++ DT G  +f    +  +r ++g+l+v d  
  gi|313127532|ref|YP_004037802.1|  66 QERGITIDAANVSMTHEYEDNNHLINLIDTPGHVDFGGDVTRAMRAVDGALVVVDAV 122
                                       5566799999******************************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (729 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.76u 0.35s 00:00:01.10 Elapsed: 00:00:00.57
# Mc/sec: 3872.85
//
Query:       gi|313127533|ref|YP_004037803.1|  [L=256]
Description: hypothetical protein Hbor_28150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.7   1.0     0.0097   16.1   1.0    1.9  1  DUF4157   Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.0   5.4e-07    0.0097      52      77 ..      57      82 ..      17      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.4e-07
                           DUF4157 52 geyqpesaagrellaHELtHvvqqre 77
                                      ++++++sa grel+ HEL+H v+++e
  gi|313127533|ref|YP_004037803.1| 57 SRQAATSAMGRELVLHELAHMVRYEE 82
                                      677899****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1573.01
//
Query:       gi|313127534|ref|YP_004037804.1|  [L=204]
Description: 30S ribosomal protein S7 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-37  128.3   3.9    2.2e-37  128.0   3.9    1.1  1  Ribosomal_S7   Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
      0.036   13.9   0.0      0.071   13.0   0.0    1.4  1  DUF2185        Protein of unknown function (DUF2185)
      0.043   13.4   0.0      0.065   12.8   0.0    1.2  1  Peptidase_M13  Peptidase family M13
      0.058   13.4   0.3      0.092   12.7   0.3    1.3  1  PBECR3         phage-Barnase-EndoU-ColicinE5/D-RelE like nucl
       0.08   13.0   0.1       0.12   12.4   0.1    1.2  1  DUF2420        Protein of unknown function (DUF2420)
       0.11   12.7   0.0       0.21   11.8   0.0    1.4  1  PAS_9          PAS domain


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   3.9   7.4e-41   2.2e-37      13     149 .]      59     204 .]      50     204 .] 0.92

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 7.4e-41
                                       ---SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBE CS
                      Ribosomal_S7  13 lpdpkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGaty 85 
                                       ++ +k + ++ve+lin+lm+    +G+k++ +kiv++a++i++e+t+++p++vl++A+en++Pr+e+ ++++GG+++
  gi|313127534|ref|YP_004037804.1|  59 KQFQKSEISIVERLINRLMQsednTGHKQKTMKIVKDAFEIVHERTDENPIQVLVTAVENAAPREETVRLKYGGISV 135
                                       344558999**************9***************************************************** PP

                                       EEEEEE-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  86 qvpvevrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       +++v+v+p+Rr+++Al++++e++   + ++++s+ae+La++l+ A++ +   +a++++ee +r+Aea+r
  gi|313127534|ref|YP_004037804.1| 136 PQAVDVAPQRRVDQALKFLAEGTasgSYKTTTSAAEALAQQLVGASNYNveTYAINQKEERERVAEAAR 204
                                       **********************966667777788************99988****************97 PP

>> DUF2185  Protein of unknown function (DUF2185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.071      36      85 .]      13      63 ..      11      63 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                           DUF2185 36 desdeyindkenfgivdlntilniDpsiielle.apigsaferneegefkk 85
                                       +s+e   +++ fg++d+ +i   Dps   +++ +pi +++ r+ +++f+k
  gi|313127534|ref|YP_004037804.1| 13 ADSEEASANAQLFGVWDIVDIEYADPSTQRYINvTPIAHTMGRHASKQFQK 63
                                      5899999******************************************86 PP

>> Peptidase_M13  Peptidase family M13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.2e-05     0.065      17     107 ..      30     120 ..      21     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                     Peptidase_M13  17 ilqppffdleypeavNyggiGaviaHEltHgfddqgvqfdkegnlaswltdedaeefkekakcli.eqfsevtepek 92 
                                       i++  + d++ ++++N   i  +++   +  f+++++   + + +++ ++ ed+++ k+k+ +++ + f+ v+e+  
  gi|313127534|ref|YP_004037804.1|  30 IVDIEYADPSTQRYINVTPIAHTMGRHASKQFQKSEISIVERL-INRLMQSEDNTGHKQKTMKIVkDAFEIVHERTD 105
                                       55667889999***************************99999.99***********99887655278999999999 PP

                     Peptidase_M13  93 tkavngaltlgEniA 107
                                        + ++  +t  En+A
  gi|313127534|ref|YP_004037804.1| 106 ENPIQVLVTAVENAA 120
                                       99***********98 PP

>> PBECR3  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   3.1e-05     0.092      15      63 ..      31      77 ..      23     114 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                            PBECR3 15 lgldlsg..tkilidpgaikHilkrHgnqstekdrgqidianipdiiknPD 63
                                      +++++++  t ++i+ + i+H + rH      k++++ +i+ ++  i+   
  gi|313127534|ref|YP_004037804.1| 31 VDIEYADpsTQRYINVTPIAHTMGRH----ASKQFQKSEISIVERLINRLM 77
                                      5666777779****************....777888888888888888655 PP

>> DUF2420  Protein of unknown function (DUF2420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.1e-05      0.12      28      78 ..      57     107 ..      49     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                           DUF2420  28 gelvsaekElvLeipeL.dltltEdnvynkdislndilsifkiLkensksee 78 
                                        ++ ++++E+ +    +  l+ +Edn+  k+ +++ + + f+i +e++ +e+
  gi|313127534|ref|YP_004037804.1|  57 ASKQFQKSEISIVERLInRLMQSEDNTGHKQKTMKIVKDAFEIVHERT-DEN 107
                                       5567888899988777788999**************************.333 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.2e-05      0.21      19      83 ..      56     116 ..      44     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                             PAS_9  19 aalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltas 83 
                                       +a + ++ s+  ++ + i  l+ +++++   +++ ++  +    ++e+v+ r +++++ vl+ta+
  gi|313127534|ref|YP_004037804.1|  56 HASKQFQKSEISIVERLINRLM-QSEDNTGHKQKTMKIVK---DAFEIVHERTDENPIQVLVTAV 116
                                       5666677778888999999999.9***************9...****************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1137  (0.0634168); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 1601.90
//
Query:       gi|313127535|ref|YP_004037805.1|  [L=142]
Description: 30S ribosomal protein S12 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-50  169.9   0.6    1.5e-50  169.6   0.6    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.6   0.6   8.3e-55   1.5e-50       1     113 [.      27     140 ..      27     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.6 bits;  conditional E-value: 8.3e-55
                                       --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE- CS
                   Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGi 77 
                                       r+e+++++ksd+legapq+rG+vlekv++eak+PnsA+Rk+vrv+Likngk+vtaf+pg+ga++f+dEhdev+++Gi
  gi|313127535|ref|YP_004037805.1|  27 RRERGLRKKSDPLEGAPQARGIVLEKVGIEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAISFIDEHDEVTIAGI 103
                                       788999*********************************************************************** PP

                                       -......BTTSTTEEEEBETS---TSSSTTTTT---- CS
                   Ribosom_S12_S23  78 rrk.gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                       +++ g+a++Dl+Gv+ykv kv+gvs+ +l+++++ekp
  gi|313127535|ref|YP_004037805.1| 104 GGAkGRAMGDLSGVNYKVEKVNGVSMIELVRGNAEKP 140
                                       9988*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 857.28
//
Query:       gi|313127536|ref|YP_004037806.1|  [L=316]
Description: small-conductance mechanosensitive channel [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-32  112.3   0.0    2.3e-32  112.3   0.0    1.5  2  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   1.1      0.45     8e+03      34      53 ..      33      52 ..      32      55 .. 0.72
   2 !  112.3   0.0   1.3e-36   2.3e-32      28     204 ..     106     278 ..      81     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.45
                                      HHHHHHHHHCHHHHHHHHHH CS
                        MS_channel 34 lglalglalkdlisnlvaGi 53
                                      +g+alg++  +++  l++ +
  gi|313127536|ref|YP_004037806.1| 33 VGAALGFGIGSTVIYLFGRL 52
                                      79999999887776666655 PP

  == domain 2  score: 112.3 bits;  conditional E-value: 1.3e-36
                                       HHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS CS
                        MS_channel  28 lavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrttkirtfdgrivtiPnsslvts 104
                                         +++a+ l+ g a +++i +l++G++l+++  f++GD++ +++ eG+Ve + +r+t++rt ++++v +Pn +l+t+
  gi|313127536|ref|YP_004037806.1| 106 ALIVAAVTLVFGVAGQEVIGSLISGLFLVADPDFNVGDWIAWSGGEGIVEAVDFRVTRVRTINNETVAVPNTELTTN 182
                                       456789999*******************************************************************9 PP

                                       -EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE-SSSEEEEEEEEEET... CS
                        MS_channel 105 nieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldefgdsslnfevrvfvktvvp 181
                                       + +   + +++ r++ ++ v+y+ d   +e +l+el e+++ + ++l d+e++ ++ efgdss+ ++  +++ +   
  gi|313127536|ref|YP_004037806.1| 183 TLTRPYG-RDRYRVTERVAVAYDDD---VELALKELVEVIRTDDRILADPEPNSRIIEFGDSSIGLRAEFWLADPMD 255
                                       9998888.9****************...**********************************************555 PP

                                       TTHHHHHHHHHHHHHHHHHHHT- CS
                        MS_channel 182 eeylsvqseinlrikkileeegi 204
                                        +  +v+s++++r+k+ ++e g+
  gi|313127536|ref|YP_004037806.1| 256 VDLVDVRSSFRRRVKARFDEVGL 278
                                       6899****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 2350.33
//
Query:       gi|313127537|ref|YP_004037807.1|  [L=136]
Description: universal stress protein uspa-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   48.2   0.1    2.4e-12   47.6   0.1    1.3  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.1   1.3e-16   2.4e-12      23     141 .]      21     127 ..       4     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.3e-16
                                       HHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHH CS
                               Usp  23 lelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeileva 99 
                                       l++  +++++l +++v+++ a++ +s   +ea e+ +e  e            +   v+++   ++ +p +e++ +a
  gi|313127537|ref|YP_004037807.1|  21 LDQEVDSDDRLEIVNVLSSGADADESIKGREALEQLEERFE------------DRTSVTTHQFSRGQSPTDELIGYA 85 
                                       45556667777777776666555555555555555555554............466899****************** PP

                                       HHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp 100 eeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +e+dad iV++ r++s+ +r+++GSvs+++l++++ p+++V+
  gi|313127537|ref|YP_004037807.1|  86 DEIDADRIVIALRRHSRTERIIFGSVSHALLQRTTRPTTLVP 127
                                       ***************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 903.01
//
Query:       gi|313127538|ref|YP_004037808.1|  [L=139]
Description: nusa family kh domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-16   57.8   0.5    2.4e-07   30.4   0.0    2.1  2  KH_2      KH domain
      1e-11   44.7   0.3    2.2e-10   40.5   0.1    2.1  2  KH_5      NusA-like KH domain
    3.2e-09   36.5   0.1    6.2e-06   26.0   0.0    2.2  2  KH_4      KH domain
    0.00049   19.9   0.2      0.045   13.6   0.0    2.2  2  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   5.5e-11   2.4e-07       3      64 ..      12      71 ..      10      79 .. 0.92
   2 !   26.0   0.1   1.3e-09   5.8e-06      10      56 ..      82     129 ..      74     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 5.5e-11
                                      HHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTT CS
                              KH_2  3 peslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegk 64
                                      +++l++  ++a ++++ + +  +rv+i + ++q+g +IG +G+ + ++++++++ +e +e+ 
  gi|313127538|ref|YP_004037808.1| 12 YIALFEDETEAVARDCLVFD--DRVVILVAAGQMGQAIGPRGQHVHAVEEKIGRSVELVEDA 71
                                      678899889999******77..***********************************99986 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.3e-09
                                       TECETEEEEEEECCSCEEEEEEEE.SCHHHHHTGGGHHHHHHHHHHHH CS
                              KH_2  10 ikkagvskveIertanrviivire.sqpgivIGkgGsnikkigkelrk 56 
                                       ++ a v++v I ++ +rv +v+ e +  g++IGk+G+ni++ ++ +++
  gi|313127538|ref|YP_004037808.1|  82 LAPAAVRHVTISEQDDRVAYVEVEnADRGVAIGKEGRNIETARTLAER 129
                                       3678899****9999***999865289*****************9986 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   4.9e-14   2.2e-10       2      69 .]      31      92 ..      30      92 .. 0.98
   2 ?    2.4   0.0     0.036   1.6e+02      19      32 ..     109     122 ..      96     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 4.9e-14
                              KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69
                                      ++r+++ V +++     +G+++g +G+ ++av++++ g  +++ve  +  + f++++l+Pa v++V+i
  gi|313127538|ref|YP_004037808.1| 31 DDRVVILVAAGQ-----MGQAIGPRGQHVHAVEEKI-GRSVELVEDADTTEAFVESMLAPAAVRHVTI 92
                                      79**********.....*******************.****************************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.036
                              KH_5  19 vGaivgkkGsrika 32 
                                        G ++gk+G++i++
  gi|313127538|ref|YP_004037808.1| 109 RGVAIGKEGRNIET 122
                                       5999*******986 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00034       1.5      28      53 ..      31      56 ..       6      59 .. 0.73
   2 !   26.0   0.0   1.4e-09   6.2e-06       5      59 ..      75     128 ..      71     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00034
                              KH_4 28 eveielnvegedlGrvIGkrGrtldA 53
                                      ++++ + v+  ++G  IG rG+ + A
  gi|313127538|ref|YP_004037808.1| 31 DDRVVILVAAGQMGQAIGPRGQHVHA 56
                                      4688899999************9988 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.4e-09
                              KH_4   5 edilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvs 59 
                                       e ++++++ +p++v+  +  e+++++  ++ve  d G+ IGk+Gr++   ++l++
  gi|313127538|ref|YP_004037808.1|  75 EAFVESML-APAAVRHVTISEQDDRVAYVEVENADRGVAIGKEGRNIETARTLAE 128
                                       78999999.677776555557789999*********************9999986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0     1e-05     0.045       2      50 ..      34      92 ..      33     104 .. 0.75
   2 !    4.8   0.1    0.0057        25       4      23 ..     102     121 ..      99     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                                      EEEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT..............T.-EEEE CS
                              KH_1  2 lrilvPsslvgriIGkgGsnIkeIreetgakIkvpksedeg...........sderevti 50
                                      ++ilv + ++g  IG++G++++  +e+ g ++ ++ ++++               r vti
  gi|313127538|ref|YP_004037808.1| 34 VVILVAAGQMGQAIGPRGQHVHAVEEKIGRSVELV-EDADTteafvesmlapAAVRHVTI 92
                                      5789**********************55*999988.444334566666666666666666 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0057
                                       EEEGGGHHHHHHTGGGHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIk 23 
                                       ++v +   g  IGk G+nI 
  gi|313127538|ref|YP_004037808.1| 102 VEVENADRGVAIGKEGRNIE 121
                                       56777788999*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.62
# Mc/sec: 674.71
//
Query:       gi|313127539|ref|YP_004037809.1|  [L=417]
Description: DNA-directed RNA polymerase subunit a' [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-54  185.5   0.3    1.5e-54  185.2   0.3    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.064   13.2   0.1       0.81    9.7   0.0    2.5  2  HHH_4           Helix-hairpin-helix containing domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.2   0.3   1.7e-58   1.5e-54      45     265 ..      16     344 ..       6     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 185.2 bits;  conditional E-value: 1.7e-58
                                       ETTSEEEETTS-EEESSGGGTS....................B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSST CS
                                       xxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  45 kyddtvrnsggeivqflygedg....................lvepGeavGiiaaQSiGePgTQltlnTFHfaGvas 101
                                       + +d  r+ +++i+  ++ ++g                     v+p + vG+++aQSiGePgTQ+t+nTFH+aGva+
  gi|313127539|ref|YP_004037809.1|  16 EDRDIPRRLKIRIYDTIEEREGvspsqadeiaqavearyldtRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAE 92 
                                       55555555555555555555556666666666666666666699999****************************** PP

                                       SSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE............................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                    RNA_pol_Rpb1_5 102 knvtlGvprlkeilnvskniksksltvllvdeeakelekakkvkkaiek............................ 150
                                         vt+G+prl e++++ k+  ++++tv+l  e+a+e+e+a++v  ++e                             
  gi|313127539|ref|YP_004037809.1|  93 IDVTQGLPRLIELVDARKTPDTPMMTVFLEGEYATERERAHEVVWSMEAtkilalgdvstnvadmvvridlnedtlm 169
                                       *****************************************999888888899************************ PP

                                       ............................................................CBTTEEEEEEEEEEEEE CS
                                       ............................................................xxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 ............................................................gikkikrilvkeaekgk 167
                                                                                                   gi++i+r++++++e+ +
  gi|313127539|ref|YP_004037809.1| 170 erwptvnnvdtvaqeiaetiedalgvktrrsgtvvefgpespsyrrllqlveelrdivfkGIEDITRVVIRKEENDD 246
                                       *************************************************************************9999 PP

                                       EETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS.---HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 168 eeekelvletegvnlsevlkveevvdageilsndiaeileilgieaarkallkeiqevykvqgv.svndrHlelivd 243
                                       + e+e+vl teg ++ +vl++e+ vda++++sn+i+ei + lgieaar+a+++e  +++++qg+ +vn rHl+l++d
  gi|313127539|ref|YP_004037809.1| 247 TGEEEFVLYTEGSAFGDVLSIEG-VDASRTTSNNIHEIHRNLGIEAAREAIIDETMNTLREQGLdDVNVRHLMLVAD 322
                                       999********************.***************************************945*********** PP

                                       HHTTTSS---SSTTCHCCSSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 244 qmtkkgeivavnrsGinkaels 265
                                       +mt +gei +++r+Gi  ++ s
  gi|313127539|ref|YP_004037809.1| 323 IMTNRGEIESIGRHGISGSKDS 344
                                       ****************987765 PP

>> HHH_4  Helix-hairpin-helix containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   9.1e-05      0.81      32      66 ..      19      53 ..       8      60 .. 0.87
   2 ?   -0.1   0.0       0.1   9.4e+02      43      63 ..     218     238 ..     214     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.1e-05
                             HHH_4 32 ealeilkenPYrliedvegigFktaDkiakklgie 66
                                      +++++lk  +Y  ie+ eg++ ++aD+ia+ ++ +
  gi|313127539|ref|YP_004037809.1| 19 DIPRRLKIRIYDTIEEREGVSPSQADEIAQAVEAR 53
                                      478899999********************998755 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.1
                             HHH_4  43 rliedvegigFktaDkiakkl 63 
                                       +l+e++++i Fk +++i + +
  gi|313127539|ref|YP_004037809.1| 218 QLVEELRDIVFKGIEDITRVV 238
                                       799***********9998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 2481.14
//
Query:       gi|313127540|ref|YP_004037810.1|  [L=976]
Description: DNA-directed RNA polymerase subunit a' [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.5e-108  361.0   0.0   8.8e-108  360.3   0.0    1.3  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
      3e-69  232.5   0.3    4.9e-69  231.8   0.3    1.4  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    7.3e-32  109.5   0.0    1.5e-31  108.5   0.0    1.6  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    9.3e-30  103.6   0.0    1.6e-29  102.9   0.0    1.4  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    3.7e-27   95.4   0.1    6.7e-27   94.6   0.1    1.4  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    0.00038   20.4   0.0      0.001   19.1   0.0    1.8  1  HTH_3           Helix-turn-helix
  ------ inclusion threshold ------
       0.37   10.8   1.6        1.1    9.3   0.1    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.55   10.5   2.5        2.2    8.6   0.2    2.6  2  zf-RING_7       C4-type zinc ribbon domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.3   0.0  3.9e-111  8.8e-108       2     312 .]       5     383 ..       4     383 .. 0.93

  Alignments for each domain:
  == domain 1  score: 360.3 bits;  conditional E-value: 3.9e-111
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       k+i +iqfg+++pe++r++S+++v +a+t++++   P ++Gl+D+rlg+id  leC+tCg ++ +C+ghfGhieLa+
  gi|313127540|ref|YP_004037810.1|   5 KEIGAIQFGLMDPETYRDMSATKVITADTYDDDG-YPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAA 80 
                                       7999****************************95.9***************************************** PP

                                       EEE-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHH..HHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvckecskllldeekkkllsklk..krekleelkkrlkaieelckkinlcekCgavqpkl. 152
                                       Pv+h+gf+kli+++l+++c+ c++l l+ee+ + + +     +e  e++ + lk   +  +k + c +Cga q  + 
  gi|313127540|ref|YP_004037810.1|  81 PVIHVGFTKLIRRLLRSTCRDCGRLSLTEEEAEEFRDGLtrTEELGEDWTDVLKSAVRQARKASRCPHCGAPQHDIk 157
                                       *****************************988766665422334457788********************9555555 PP

                                       ...............EEETTEEEEEESSSST.............................................. CS
                                       ...............xxxxxxxxxxxxxxxx.............................................. RF
                    RNA_pol_Rpb1_1 153 ...............eeegeklkaalkkske.............................................. 168
                                                       +++e++ +a++++++                                              
  gi|313127540|ref|YP_004037810.1| 158 hekpttyyevqdvlaGDYSERIANAMQPDEDdeddtgmapseladqtgialqrvnqilsgefrpvgddrkklekald 234
                                       56666678888888988888899999888888999999999999999999999999999999999999999999999 PP

                                       .....SCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHH CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 169 .....eekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrd 240
                                            e+ +kl+++++++++++i+ded++ lg+++s++rPew+iltvlPVpP+++RPs++ld+g+rsedDlt+kl+d
  gi|313127540|ref|YP_004037810.1| 235 vdlteEDMNKLMPSDIRDWFEDIPDEDIVTLGIDPSRARPEWMILTVLPVPPVTARPSITLDNGQRSEDDLTHKLVD 311
                                       99997777********************************************************************* PP

                                       HHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 241 iikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                       ii++N+r+++++e+gap+liie+ +elLQ+hv+t++dneisg++pa+++s+rplk+lsqrLkGKeGrfRg+L
  gi|313127540|ref|YP_004037810.1| 312 IIRINQRFMENREAGAPQLIIEDLWELLQYHVTTFIDNEISGTPPARHRSGRPLKTLSQRLKGKEGRFRGSL 383
                                       **********************************************************************98 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.8   0.3   2.2e-72   4.9e-69       1     166 []     385     551 ..     385     551 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.8 bits;  conditional E-value: 2.2e-72
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrv++saR+vispdp+l+l+evgvP +va+ +t +  vte n ++ +++v+ngpe +Pga+yvkr dg++ k+++k
  gi|313127540|ref|YP_004037810.1| 385 GKRVNFSARTVISPDPTLSLNEVGVPERVAREMTQTMNVTERNLEQAQQYVRNGPEGHPGANYVKRPDGRRLKVTEK 461
                                       9**************************************************************************99 PP

                                       -S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SS CS
                    RNA_pol_Rpb1_2  78 kr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqs 153
                                       +  +la++++ g+ v+rh++dgd+v++NRqPsLh++simah+v v+++kt+rln++v+ +yNaDFDGDemn+h  q+
  gi|313127540|ref|YP_004037810.1| 462 NCeELAEKVQAGWEVNRHLIDGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQT 538
                                       9878************************************************************************* PP

                                       HHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 154 eearaEaeelllv 166
                                       eearaEa+ l+ v
  gi|313127540|ref|YP_004037810.1| 539 EEARAEARVLMRV 551
                                       **********975 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.0   6.7e-35   1.5e-31       2     108 .]     732     837 ..     731     837 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 6.7e-35
                                       HHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEB CS
                    RNA_pol_Rpb1_4   2 eeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnv 78 
                                       e +e  g+le+lpg++++e++e+ki++ l kard+ag+ia ++  ++N+ ++M++sGa+Gs++n++q+agc+Gqq+v
  gi|313127540|ref|YP_004037810.1| 732 EIYEA-GELESLPGRTVDETLEMKIMQQLGKARDSAGEIADDHFTDDNPAVVMARSGARGSMLNLTQMAGCVGQQAV 807
                                       66777.9*************************************977****************************** PP

                                       TTBSS--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  79 egkripkgfsgrtlphfkkidespesrGFv 108
                                       +g+ri++g++grtl h++k d s+e++GFv
  gi|313127540|ref|YP_004037810.1| 808 RGERINRGYEGRTLSHYQKEDLSAEAHGFV 837
                                       *****************************8 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.0   7.2e-33   1.6e-29       1     156 [.     554     705 ..     554     706 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 7.2e-33
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS..SEBEEHHHHHHCCC CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp..kelwtgkqtfsril 75 
                                       +ilsp+ g+ +ig +QD+++G yllT  +  +++ +a+ ll+  + +     +++pa      ++ wtg+q+fs +l
  gi|313127540|ref|YP_004037810.1| 554 QILSPRFGQNIIGAIQDHISGTYLLTNGNPHFTETQALDLLRATSID----TLPEPAGEEEdgQPYWTGRQLFSELL 626
                                       79******************************************553....35566655555455************ PP

                                       HCCCCEEEESSSSSTSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCEB- CS
                    RNA_pol_Rpb1_3  76 pneinyerkneekdgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyllqsgfti 152
                                       p+++n+  + +++ ++v+i++g+li+G+id+ +vg +  g+++++lak y+ ++ + f++ +  l+++ +++ gf+i
  gi|313127540|ref|YP_004037810.1| 627 PDDLNLSFT-SSTGDDVIIEDGQLIEGTIDEDAVG-AFGGEVVDTLAKVYSKTRSRVFINEVASLAMRAIMHFGFSI 701
                                       ********6.444699*******************.999************************************** PP

                                       TGGG CS
                    RNA_pol_Rpb1_3 153 gigD 156
                                       gi+D
  gi|313127540|ref|YP_004037810.1| 702 GIDD 705
                                       ***9 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.1     3e-30   6.7e-27       1      73 [.     844     920 ..     844     929 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 3e-30
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS....B--TT-B CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg....lvepGea 73 
                                       GL++ efffh+mggReGL+DtAv+T++sGYlqRrl++al ++  +yd+tvr+++g+ivqf +gedg     v+ Ge 
  gi|313127540|ref|YP_004037810.1| 844 GLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYDGTVRDTSGTIVQFEFGEDGtspvKVSSGEG 920
                                       9****************************************************************977776777765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.6e-07     0.001      12      54 ..     197     239 ..     193     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.6e-07
                                       HHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3  12 qeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54 
                                         eLA+ +G+  + +++i +Ge +P  +  kkl+kaL+v+l+e
  gi|313127540|ref|YP_004037810.1| 197 PSELADQTGIALQRVNQILSGEFRPVGDDRKKLEKALDVDLTE 239
                                       579*************************************986 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.5     0.042        93      70     105 ..      56     115 ..      49     119 .. 0.79
   2 ?    9.3   0.1    0.0005       1.1      70     100 ..      96     157 ..      89     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.042
                                       EEEETTTS-EEECHHHHH........................S-TTTSSS-EEEEESSSE CS
                              HypA  70 kvrCreCgkefeleekal........................rCpkCgsadveivsGeel 105
                                        ++Cr+Cg++  + + ++                        +C +Cg+ +++  + ee+
  gi|313127540|ref|YP_004037810.1|  56 GLECRTCGSHSGSCNGHFghielaapvihvgftklirrllrsTCRDCGRLSLTEEEAEEF 115
                                       578999997776554233556789999999999999999999999999999998888887 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0005
                                       EEEETTTS-EEECHHHHH...............................S-TTTSSS-EEEE CS
                              HypA  70 kvrCreCgkefeleekal...............................rCpkCgsadveiv 100
                                       + +Cr+Cg+   +ee+a+                               rCp+Cg+ + +i+
  gi|313127540|ref|YP_004037810.1|  96 RSTCRDCGRLSLTEEEAEefrdgltrteelgedwtdvlksavrqarkasRCPHCGAPQHDIK 157
                                       678*****55555443224699999*******************************999886 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.25   5.6e+02      24      32 ..      97     105 ..      88     105 .. 0.86
   2 ?    8.6   0.2   0.00097       2.2      15      31 ..     135     151 ..     133     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.25
                                       EE-TTT--E CS
                         zf-RING_7  24 vtCpeCGRI 32 
                                        tC  CGR+
  gi|313127540|ref|YP_004037810.1|  97 STCRDCGRL 105
                                       59******6 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00097
                                       HHHCCSTB-EE-TTT-- CS
                         zf-RING_7  15 selragdevvtCpeCGR 31 
                                       s++r++ +  +Cp+CG+
  gi|313127540|ref|YP_004037810.1| 135 SAVRQARKASRCPHCGA 151
                                       689999999******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (976 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.87u 0.36s 00:00:01.23 Elapsed: 00:00:00.55
# Mc/sec: 5371.98
//
Query:       gi|313127541|ref|YP_004037811.1|  [L=610]
Description: DNA-directed RNA polymerase subunit b' [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.1e-128  427.5   0.0   7.2e-128  427.0   0.0    1.2  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
      3e-25   88.4   0.0    5.3e-25   87.6   0.0    1.4  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    2.2e-23   82.3   0.7    1.4e-22   79.7   0.5    2.3  2  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    4.3e-09   36.8   5.6    1.3e-08   35.2   5.6    1.9  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.29   11.0   0.0    1.3  1  CAF1-p150_N     CAF1 complex subunit p150, region binding to 


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.0   0.0    2e-131  7.2e-128       2     390 .]     141     513 ..     140     513 .. 0.96

  Alignments for each domain:
  == domain 1  score: 427.0 bits;  conditional E-value: 2e-131
                                       HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SE CS
                    RNA_pol_Rpb2_6   2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalG 78 
                                       a  +p++eh+ spri++ a m kq+lg+ s+n+  r +++ +ll+++q  +vkt+ + e+++        ++e ++ 
  gi|313127541|ref|YP_004037811.1| 141 AGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQHLLHYPQLSMVKTQ-TTEQIG--------FDERPAA 208
                                       7789***************************************************.999999........******* PP

                                       EEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS-TTS CS
                    RNA_pol_Rpb2_6  79 qnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkLdedG 150
                                       qn++VAvmsyeG+niEDa+++n+ +vdr +++s+++++ye e r++++g+e+ ++ ++++     +e+a+++Ld+dG
  gi|313127541|ref|YP_004037811.1| 209 QNFTVAVMSYEGFNIEDALVMNKGSVDRAMARSHFFRTYEGEERRYPGGQEDRFEVPSQDvrgarGEDAYNHLDDDG 285
                                       **************************************************99999998889**************** PP

                                       B--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT-- CS
                    RNA_pol_Rpb2_6 151 ivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvn 227
                                       +v++++ v e+++l gk+  ++ ++ +e   +     +   + ++ts++++sge+gvVd+v++        + ++++
  gi|313127541|ref|YP_004037811.1| 286 LVNPETVVDENSVLLGKT--SPPRFLEEPDDMGGLSPQ---KRRETSVTMRSGENGVVDTVTL-------MEGEDGS 350
                                       *****************8..899999766666555555...5679******************.......6888999 PP

                                       EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSS CS
                    RNA_pol_Rpb2_6 228 klvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaale 304
                                       kl+kv v+++R +++GDKfasrhGqKGvv+ ++pqeDmPf++dG+v+D+v+NP+++PSRmt+g++lE+l gk++ale
  gi|313127541|ref|YP_004037811.1| 351 KLAKVSVRDQRIPELGDKFASRHGQKGVVGHLAPQEDMPFTADGVVPDLVINPHALPSRMTVGHVLEMLGGKVGALE 427
                                       ***************************************************************************** PP

                                       SS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT CS
                    RNA_pol_Rpb2_6 305 gkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpysllt 381
                                       g++vd+t+F+g++e+e++ +Lee+g+++sGkev+y+G+tGek+eaeifvG+i+y+kL+h+v++K+haRs+Gp+++lt
  gi|313127541|ref|YP_004037811.1| 428 GRRVDGTAFQGEDESELRGALEEHGFKSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLT 504
                                       ***************************************************************************** PP

                                       --B-SCGGG CS
                    RNA_pol_Rpb2_6 382 qQPlgGkaq 390
                                       +QP++G+a+
  gi|313127541|ref|YP_004037811.1| 505 RQPTEGRAR 513
                                       *******96 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   1.5e-28   5.3e-25       1      86 [.     515     606 ..     515     607 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 1.5e-28
                                       BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHH CS
                    RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklL 71 
                                       GGlr+GEMErd++i++Gaa++L+erl+++SD+ ev+v+ +++++a+++      + +++ +e++i+++ei++afklL
  gi|313127541|ref|YP_004037811.1| 515 GGLRLGEMERDTVIGHGAAMVLQERLLDSSDKEEVYVSADTGMVAVEDrdqrriYDPVTGDEDNIHEIEISYAFKLL 591
                                       9*********************************************99****99999******************** PP

                                       HHHHHHTTBEEEEES CS
                    RNA_pol_Rpb2_7  72 lqeLqslgialklll 86 
                                       l+e+ +lgi+++l l
  gi|313127541|ref|YP_004037811.1| 592 LDEMIALGIRPRLNL 606
                                       ***********9865 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.5   3.9e-26   1.4e-22       1      62 []      11      72 ..      11      72 .. 0.99
   2 ?   -0.5   0.0      0.43   1.5e+03      41      53 ..     545     557 ..     519     559 .. 0.74

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 3.9e-26
                                      EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                    RNA_pol_Rpb2_4  1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62
                                      V+vNG+l+G++ dpk+l+e++Re RR+g++s+ v+++++e+++ev i+ D+GR++RPli+Ve
  gi|313127541|ref|YP_004037811.1| 11 VYVNGSLVGTHPDPKQLAEQIREARRRGDVSQMVNVSVKERTREVIINADAGRARRPLIVVE 72
                                      9************************************************************7 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.43
                                       TT--EEEE-SSEE CS
                    RNA_pol_Rpb2_4  41 kqkevkiatDgGR 53 
                                       +++ev+++ D G 
  gi|313127541|ref|YP_004037811.1| 545 DKEEVYVSADTGM 557
                                       3889******995 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   5.6   3.7e-12   1.3e-08       1      58 []      93     133 ..      93     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3.7e-12
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIhP 58 
                                       ++dL++ g +E++DaeEEe++++a++++dl++                  +TH+EI+P
  gi|313127541|ref|YP_004037811.1|  93 FEDLIDRGYIEFIDAEEEEDIYVAVDEDDLNED-----------------HTHLEIDP 133
                                       89****************************887.................79999999 PP

>> CAF1-p150_N  CAF1 complex subunit p150, region binding to PCNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.2e-05      0.29     115     198 ..     374     459 ..     364     468 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.2e-05
                       CAF1-p150_N 115 gqsvviidlt..edsseqpdslvahsklnsaaspsreavngvreeagderGlpkaiqkdklalpeetlsdipcktee 189
                                       gq+ v+  l+  ed     d +v    +n+ a psr +v  v e  g++ G ++ ++ d  a++ e  s+++   ee
  gi|313127541|ref|YP_004037811.1| 374 GQKGVVGHLApqEDMPFTADGVVPDLVINPHALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGEDESELRGALEE 450
                                       6666666664225555667888888999************************************************* PP

                       CAF1-p150_N 190 egvdsgGae 198
                                       +g +s G e
  gi|313127541|ref|YP_004037811.1| 451 HGFKSSGKE 459
                                       *****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 3516.47
//
Query:       gi|313127542|ref|YP_004037812.1|  [L=523]
Description: DNA-directed RNA polymerase subunit b' [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-51  173.7   0.2    4.1e-51  173.4   0.2    1.1  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    3.2e-26   92.2   0.1    4.8e-26   91.6   0.1    1.2  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
      1e-24   86.5   0.0      2e-24   85.5   0.0    1.5  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
  ------ inclusion threshold ------
       0.28   11.4   1.3         27    5.0   0.0    3.2  3  DUF1359         Protein of unknown function (DUF1359)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.4   0.2   9.2e-55   4.1e-51       2     202 ..      19     401 ..      18     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 173.4 bits;  conditional E-value: 9.2e-55
                                       TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYs 78 
                                       L++ +  SFn+f+e  +++++ e+a+i ++   ++ +e +++++++ir++ P v+e+d+se+ ++P+earlrn+tY 
  gi|313127542|ref|YP_004037812.1|  19 LAEHHFRSFNNFLERGMQEVVSEKATIDTDIGDKEGEEPVYVELGDIRIETPRVREADGSEELLFPQEARLRNITYA 95 
                                       7899***************************99877777************************************** PP

                                       EEEEEEEEEEECCCC.TCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEE CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  79 aplyvklklvvyekd.nkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqe 154
                                       ap+++++  ++  ++ ++   + +e ++G++P+M+ s++c++s++++eelve++E+p d+GGyFi+nG+e+v++  e
  gi|313127542|ref|YP_004037812.1|  96 APVFMEMSIIRGGEEeEEVVVDTTETKVGRMPIMVGSSKCNISNLTDEELVEIGEDPVDPGGYFIVNGSERVLMTSE 172
                                       ********9997665477778899***************************************************** PP

                                       E............................................................................ CS
                                       x............................................................................ RF
                    RNA_pol_Rpb2_1 155 k............................................................................ 155
                                       +                                                                            
  gi|313127542|ref|YP_004037812.1| 173 Dlapnkilaeydtkygdeiqvaktfsqrrgyralvlcernregilevsfpsvsgsvefvtlvralglesdeeivhrv 249
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|313127542|ref|YP_004037812.1| 250 sddpeivkymlenleeaevqteaeaieslgkrvasgqgknyqlkranyvidryllphlhedgvdeedvrinkafylc 326
                                       ***************************************************************************** PP

                                       ............................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                       ............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 ............................laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                                                   + G+L+++lfr++l+kl+rdvk +l++   ++++l+++ +v+++ +t
  gi|313127542|ref|YP_004037812.1| 327 rmaeacfelalerrdsddkdhyankrlkVSGDLMKDLFRTALNKLARDVKYQLERANMRNRQLTVNTVVRSDVLT 401
                                       **********************************************************************99876 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.1   1.1e-29   4.8e-26      13     190 .]     176     354 ..     166     354 .. 0.86

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 1.1e-29
                                       SSSE.............SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSS CS
                    RNA_pol_Rpb2_2  13 knki.............satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericyd 76 
                                       +nki             +a+  s +  +r++vl +++ +++l ++ +s+   + +v + +Algl sd+eI+ r++  
  gi|313127542|ref|YP_004037812.1| 176 PNKIlaeydtkygdeiqVAKTFSQRRGYRALVLCERNREGILEVSFPSVSGSVEFVTLVRALGLESDEEIVHRVS-- 250
                                       55555555555555566677778888999999*******************************************.. PP

                                       STTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSST.C CS
                    RNA_pol_Rpb2_2  77 sedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglsesl.e 152
                                         d+  + +++ e+ e++e+qt++ea++ +gk+va ++g++ +l++a  ++         +r+ l+ hl  +    e
  gi|313127542|ref|YP_004037812.1| 251 --DDPEIVKYMLENLEEAEVQTEAEAIESLGKRVASGQGKNYQLKRANYVI---------DRYLLP-HLHEDGVDeE 315
                                       ..566777788888888999****************************996.........8*****.**88765404 PP

                                       HH...HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 153 nkr.lkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                         r  ka+++  m+++ ++l+l+rr+ DD+Dh++nkR++
  gi|313127542|ref|YP_004037812.1| 316 DVRiNKAFYLCRMAEACFELALERRDSDDKDHYANKRLK 354
                                       56789********************************96 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.0   4.4e-28     2e-24       1      65 [.     422     483 ..     422     486 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 4.4e-28
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLall 65 
                                       q++dr+ ++  lshlrr++s+   ls+++ ++e+Rdlh+++wGriCp+eTPEG+ncGlvk++a+ 
  gi|313127542|ref|YP_004037812.1| 422 QLVDRTDYMGVLSHLRRLRSP---LSRSQPHFEARDLHATQWGRICPSETPEGPNCGLVKNFAQA 483
                                       899******************...**************************************986 PP

>> DUF1359  Protein of unknown function (DUF1359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0061        27      23      60 ..     244     281 ..     240     289 .. 0.86
   2 ?   -1.6   0.1      0.74   3.3e+03      21      55 ..     368     402 ..     360     408 .. 0.76
   3 ?    3.3   0.0     0.021        94      79      97 ..     486     503 ..     481     507 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0061
                           DUF1359  23 dvihdvkdqtelvklleddlksneikkddkleleltdr 60 
                                       +++h v d  e+vk ++++l++ e++ +      l+ r
  gi|313127542|ref|YP_004037812.1| 244 EIVHRVSDDPEIVKYMLENLEEAEVQTEAEAIESLGKR 281
                                       799*********************99887766666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.74
                           DUF1359  21 lkdvihdvkdqtelvklleddlksneikkddklel 55 
                                       l ++  dvk q e  ++ + +l  n + ++d l  
  gi|313127542|ref|YP_004037812.1| 368 LNKLARDVKYQLERANMRNRQLTVNTVVRSDVLTE 402
                                       56677888888888888888888888888776655 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.021
                           DUF1359  79 lkdniedntaliselvkkl 97 
                                       l +nied+ al  el+  +
  gi|313127542|ref|YP_004037812.1| 486 LSQNIEDEQALKRELAS-M 503
                                       78************985.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 3105.35
//
Query:       gi|313127543|ref|YP_004037813.1|  [L=75]
Description: DNA-directed RNA polymerase subunit h [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-27   93.3   0.6    6.9e-27   93.1   0.6    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
  ------ inclusion threshold ------
      0.088   13.1   2.2        4.4    7.6   2.2    2.1  1  DUF3006         Protein of unknown function (DUF3006)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.6   7.7e-31   6.9e-27       1      73 []       2      73 ..       2      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 7.7e-31
                                      ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                      v++++H+lvP+h +l+eee++e+l+++++k+++LPki+++Dp+a   +++ Gdv+kI+r+s+t+++avtYRlV
  gi|313127543|ref|YP_004037813.1|  2 VDVSQHKLVPEHILLEEEEVEEMLDEYDVKRTNLPKIKRTDPAAP-DDAEAGDVIKIVRDSRTTDKAVTYRLV 73
                                      689*****************************************7.69************************9 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.2    0.0005       4.4      12      44 ..      15      61 ..       8      72 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0005
                           DUF3006 12 Vleled.getid...iprsdLp..........egakeGdvLeiedde 44
                                       le e+ +e++d   ++r++Lp          ++a+ Gdv++i  d 
  gi|313127543|ref|YP_004037813.1| 15 LLEEEEvEEMLDeydVKRTNLPkikrtdpaapDDAEAGDVIKIVRDS 61
                                      56666677777777766666661111111111566667776666443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 477.71
//
Query:       gi|313127544|ref|YP_004037814.1|  [L=123]
Description: camphor resistance protein crcb [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-19   69.3  10.8    3.4e-19   68.9  10.8    1.1  1  CRCB      CrcB-like protein, Camphor Resistance (CrcB)


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9  10.8   1.9e-23   3.4e-19       2      94 ..      15     116 ..      14     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1.9e-23
                                       HHHHHHHHHHHHHHHH.HHHHBEBHHHHHHHHHHHHHHHHHHH.........HHTTTHHHHHS-SHHHHHHHHHHHH CS
                              CRCB   2 lvalggalGallRyllssllnkrplgtlavNvlGsfllgllla.........llttGflGglTTfStfvlelvslle 69 
                                       lv++gg lGal Ry+++ +l +   +tlavNvlGs++lg+l+a         +++tGf+G++TTfS+f++ +++ ++
  gi|313127544|ref|YP_004037814.1|  15 LVGIGGTLGALSRYGVDLALSGGRRSTLAVNVLGSIALGALVAapisstaatVFGTGFCGAFTTFSSFAVSVAEDAS 91 
                                       799*************7777666559**************9998888877777************************ PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHH CS
                              CRCB  70 egellaallyvllsvvlgllavvlg 94 
                                       +g+ ++a+ y++ +++++l+ v+lg
  gi|313127544|ref|YP_004037814.1|  92 DGQRWRAVQYAVGTLLAALVGVALG 116
                                       ***9*************99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 877.71
//
Query:       gi|313127545|ref|YP_004037815.1|  [L=113]
Description: camphor resistance protein crcb [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-17   64.1  13.8    1.4e-17   63.8  13.8    1.0  1  CRCB            CrcB-like protein, Camphor Resistance (CrcB)
  ------ inclusion threshold ------
       0.11   10.8   8.6      0.053   11.8   1.8    2.0  2  SpecificRecomb  Site-specific recombinase


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8  13.8   1.5e-21   1.4e-17       2      94 ..       9     105 ..       8     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.5e-21
                                       HHHHHHHHHHHHHHHH.HHHHBEBHHHHHHHHHHHHHHHHHHH.........HHTTTHHHHHS-SHHHHHHHHHHHH CS
                              CRCB   2 lvalggalGallRyllssllnkrplgtlavNvlGsfllgllla.........llttGflGglTTfStfvlelvslle 69 
                                       lva+gg++Ga+lRy++ +++++ + gtlavNvlGsf+lg+lla         ll+tG+l+++TT+Stf++++++l  
  gi|313127545|ref|YP_004037815.1|   9 LVAAGGFIGAMLRYGV-DAAVPGVGGTLAVNVLGSFALGALLAvvrthrvriLLGTGLLSSFTTYSTFAVQTTALG- 83 
                                       79**************.55556656***************9998888888888*********************95. PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHH CS
                              CRCB  70 egellaallyvllsvvlgllavvlg 94 
                                           ++ l++v ++++lg++a++lg
  gi|313127545|ref|YP_004037815.1|  84 ---PTWGLANVGANYALGFAAALLG 105
                                       ...4567999**********99987 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.0    0.0019        17     585     616 ..      26      58 ..       8      61 .. 0.78
   2 ?   11.8   1.8   5.9e-06     0.053     330     370 ..      61     101 ..      57     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0019
                    SpecificRecomb 585 lavagvlligllNllVSFalAllvA.lrsrkvr 616
                                       +av gv  + ++N+l SFal  l+A +r ++vr
  gi|313127545|ref|YP_004037815.1|  26 AAVPGVGGTLAVNVLGSFALGALLAvVRTHRVR 58 
                                       6788999999**********8888835888887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.9e-06
                    SpecificRecomb 330 aggGliialtallKillaklhlapfvegllaslnYalsFvl 370
                                       +g Gl+ ++t++  +++++ +l p +    ++ nYal+F +
  gi|313127545|ref|YP_004037815.1|  61 LGTGLLSSFTTYSTFAVQTTALGPTWGLANVGANYALGFAA 101
                                       589************************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 887.55
//
Query:       gi|313127546|ref|YP_004037816.1|  [L=380]
Description: ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-09   36.3   0.1    5.1e-05   22.1   0.0    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
    2.6e-05   24.5   0.0    4.3e-05   23.7   0.0    1.3  1  DUF87          Helicase HerA, central domain
     0.0059   15.6   0.0          3    6.7   0.0    2.3  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
  ------ inclusion threshold ------
      0.073   13.5   1.0       0.33   11.3   0.5    2.4  2  AAA_16         AAA ATPase domain
      0.084   13.3   0.0         11    6.4   0.0    2.3  2  AAA            ATPase family associated with various cellular
        0.8    9.4   4.1        1.8    8.3   0.1    2.6  3  AAA_30         AAA domain


Domain annotation for each model (and alignments):
>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   1.7e-05      0.05      24      74 ..      61     112 ..      42     132 .. 0.82
   2 !   22.1   0.0   1.7e-08   5.1e-05     261     339 ..     245     318 ..     241     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                            DUF853  24 GliaGatGtGktvtLqvlaeslsea.GvpvfladvkGdLsgiakaGevkdkl 74 
                                        l+ G  G Gk  tL vlae++s+a Gv+ ++ d  G ++g++++  v ++l
  gi|313127546|ref|YP_004037816.1|  61 ALVVGKRGYGKSYTLGVLAEEVSRAsGVAPVVLDPMGVFAGLTESDAVPGRL 112
                                       599********************7559**9***********99887766665 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.7e-08
                            DUF853 261 fffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaad 337
                                       +f+deah++f++ ++  l     ++   r+ Gv +   tq P+ lP+  L+q   r+ h l a   +d +a+ aa  
  gi|313127546|ref|YP_004037816.1| 245 LFLDEAHVFFDGLAAPALR---TILTRGRAPGVSLVAATQRPSALPEVALSQSDLRIVHRLTA--GADVRALTAAEP 316
                                       79*********97776655...4667789999**9************************9987..567777777766 PP

                            DUF853 338 tf 339
                                       t+
  gi|313127546|ref|YP_004037816.1| 317 TY 318
                                       65 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.4e-08   4.3e-05      10      68 ..      47     103 ..      36     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.4e-08
                             DUF87  10 sevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal 68 
                                       ++ pv +dl+    +  +++g+ G+GKS+t +vL ee+ +  g+  ++lDp G ++ ++
  gi|313127546|ref|YP_004037816.1|  47 DGAPVAVDLDGP--HAALVVGKRGYGKSYTLGVLAEEVSRASGVAPVVLDPMGVFAGLT 103
                                       557888888666..455699*******************************99777666 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0     0.001         3      18      56 ..      61     100 ..      46     106 .. 0.80
   2 !    6.5   0.0    0.0011       3.3     243     288 ..     241     289 ..     218     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.001
                     TrwB_AAD_bind  18 ilivGttGsGKtqalekllrai.rargdraivlDltGafv 56 
                                       +l+vG  G GK+ +l  l +++ ra g   +vlD++G f 
  gi|313127546|ref|YP_004037816.1|  61 ALVVGKRGYGKSYTLGVLAEEVsRASGVAPVVLDPMGVFA 100
                                       4679***************99956778899*******985 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0011
                     TrwB_AAD_bind 243 rrlWfflDElpaL...grleelksllaegRkfGgavvlglqsiaqlrev 288
                                       r  W+flDE +      + ++l ++l++gR  G+ +v++ q  + l ev
  gi|313127546|ref|YP_004037816.1| 241 RLPWLFLDEAHVFfdgLAAPALRTILTRGRAPGVSLVAATQRPSALPEV 289
                                       446******766522235699********************99988765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   0.00011      0.33      22      53 ..      56      87 ..      49     278 .. 0.80
   2 ?   -0.2   0.0      0.38   1.1e+03     139     164 ..     245     271 ..     198     346 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdgg 53
                                      ++p++ l++G +G GKs  +  l+++++++ g
  gi|313127546|ref|YP_004037816.1| 56 DGPHAALVVGKRGYGKSYTLGVLAEEVSRASG 87
                                      568999*******************9999922 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.38
                            AAA_16 139 lvlDdlqwadeaslql.laaLlrlles 164
                                       l+lD+++ + ++ ++  l+++l+++ +
  gi|313127546|ref|YP_004037816.1| 245 LFLDEAHVFFDGLAAPaLRTILTRGRA 271
                                       455555544443333334444443333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.013        40       2      23 ..      62      83 ..      61     106 .. 0.83
   2 ?    6.4   0.0    0.0037        11      60     127 ..     243     297 ..     198     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                                      EEESSTTSSHHHHHHHHHHHHT CS
                               AAA  2 llyGppGtGKTllakavakelg 23
                                      l++G  G GK+++   +a+e++
  gi|313127546|ref|YP_004037816.1| 62 LVVGKRGYGKSYTLGVLAEEVS 83
                                      89****************9975 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0037
                                       EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                               AAA  60 silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                                         lf+DE++ ++             ++++L t l + +     v +++at+rp+ l++  l +  d +
  gi|313127546|ref|YP_004037816.1| 243 PWLFLDEAHVFFDGL----------AAPALRTILTRGRA--PGVSLVAATQRPSALPEVAL-SQSDLR 297
                                       679999999999888..........899*******9999..46*************99988.666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00059       1.8      20      55 ..      60      96 ..      51     123 .. 0.76
   2 ?   -1.3   0.1      0.51   1.5e+03      50      98 ..     152     213 ..     141     239 .. 0.68
   3 ?    1.5   0.1     0.068     2e+02      56      99 ..     296     342 ..     274     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00059
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.ggrviglApt 55
                                       a+++G  G GK+++l++l+e + +a g   ++l p 
  gi|313127546|ref|YP_004037816.1| 60 AALVVGKRGYGKSYTLGVLAEEVSRAsGVAPVVLDPM 96
                                      6899***************777666658555555554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.51
                            AAA_30  50 iglAptgkaAkvLaeelgieastiakllkrlk.............grarlepgtllivDEag 98 
                                         lA   + A+v a++++++ +t+  + +rl+             ++a+l  ++ ++ D ag
  gi|313127546|ref|YP_004037816.1| 152 ETLAEMRAFAEVPADSANVAPDTVRAVQNRLRraaswgvfdpdglDAAALCGSEAIVLDCAG 213
                                       45777777777777888888888888888888777777777777755566666777777666 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.068
                            AAA_30  56 gkaAkvLaeelgieastiakllkrlk...grarlepgtllivDEagm 99 
                                        +  ++L+++++++a t a+ ++  +   +r   +pg++l+vD ++ 
  gi|313127546|ref|YP_004037816.1| 296 LRIVHRLTAGADVRALTAAEPTYLSAgvaERIPTQPGDVLVVDDTAE 342
                                       5667788888889999999888877788866778899*****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2481.47
//
Query:       gi|313127547|ref|YP_004037817.1|  [L=150]
Description: hypothetical protein Hbor_28310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00018   21.7   2.4    0.00037   20.7   2.3    1.6  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0019   18.2   1.4     0.0041   17.1   1.4    1.5  1  Big_1            Bacterial Ig-like domain (group 1)
     0.0021   18.2   0.4     0.0058   16.8   0.4    1.8  1  MG4              Macroglobulin domain MG4
     0.0048   17.5   1.5      0.034   14.8   1.5    2.0  1  YtkA             YtkA-like


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   2.3   8.3e-08   0.00037       2      36 ..      67     100 ..      66     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.3e-08
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttda 36 
                                       is  V+d++g p++gatV+v++ +t    s++t++
  gi|313127547|ref|YP_004037817.1|  67 ISILVVDPDGDPVEGATVVVKD-GTADIESVVTNK 100
                                       8889*****************5.555566666664 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.4   9.1e-07    0.0041       9      52 ..      67     111 ..      64     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.1e-07
                             Big_1   9 ltatvkDangnpvagatVtfsvsggals.assgtTdanGkatvtl 52 
                                       +++ v+D +g pv+gatV ++   +++    + +T + G+atvt+
  gi|313127547|ref|YP_004037817.1|  67 ISILVVDPDGDPVEGATVVVKDGTADIEsVVTNKTREGGMATVTV 111
                                       6789*****************6667777899*************8 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   1.3e-06    0.0058      18      63 ..      67     112 ..      66     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                               MG4  18 ikVlvkdpdgspaknvpVkiealk.seteekeslttdedGtakfsin 63 
                                       i +lv+dpdg p+++ +V+++  +  + e+  + +t+e G+a +++ 
  gi|313127547|ref|YP_004037817.1|  67 ISILVVDPDGDPVEGATVVVKD-GtADIESVVTNKTREGGMATVTVA 112
                                       889******************9.4346888889999999**999985 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.5   7.5e-06     0.034       7      43 ..      51      87 ..      44     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.5e-06
                              YtkA  7 levelvspeepkagentivvt.vtqggkpVedadvkve 43
                                      l+v+   p+ ++ ge++i++  v+ +g+pVe+a+v v+
  gi|313127547|ref|YP_004037817.1| 51 LDVKPD-PDVMTPGEQDISILvVDPDGDPVEGATVVVK 87
                                      444444.346799*****9966***********97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1152.28
//
Query:       gi|313127548|ref|YP_004037818.1|  [L=436]
Description: tRNA(ile2) 2-agmatinylcytidine synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-36  124.8   0.0    2.8e-36  124.1   0.0    1.4  1  DUF1743         Domain of unknown function (DUF1743)
  ------ inclusion threshold ------
      0.073   13.0   0.2       0.14   12.0   0.2    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.12   12.4   1.0       0.28   11.2   1.0    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.21   11.6   1.1       0.49   10.4   1.1    1.6  1  zinc-ribbons_6  zinc-ribbons


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1   0.0   6.4e-40   2.8e-36       1     116 []     140     254 ..     140     254 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 6.4e-40
                                       TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEE CS
                           DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvl 76 
                                       grg iGA+aa+ga+ ale++tyE++aYre +r+g  r+vd esv++a++++ype +d+vD+ ++++v+vP++p p+l
  gi|313127548|ref|YP_004037818.1| 140 GRGRIGALAAVGAWAALEEWTYEHIAYREFDRCGtLRDVDIESVFDAAADHYPEAWDTVDTVEGQAVCVPNAPGPIL 216
                                       89*************************************************************************** PP

                                       EEEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  77 fGirgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                       +Girg+dp+a+++   +i+s  e++e+ a f tnqgtd h
  gi|313127548|ref|YP_004037818.1| 217 HGIRGDDPDAVRSLSAAIDS--EPVERRATFLTNQGTDIH 254
                                       ********************..***************987 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.2e-05      0.14      13      36 ..     366     390 ..     356     392 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                                       B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1  13 fCkhCgeflwg.kekqglkCswCkl 36 
                                       +C  C+  ++  ++ qg++C++C+ 
  gi|313127548|ref|YP_004037818.1| 366 TCPDCDRTMESaGRNQGYRCRDCRT 390
                                       7********888***********85 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   6.2e-05      0.28      19      45 ..     365     390 ..     357     391 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.2e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr..kayriktrglfqCkeCrk 45 
                                       ++CP C  +  +a r    + ++C++Cr+
  gi|313127548|ref|YP_004037818.1| 365 PTCPDCDRTmeSAGR---NQGYRCRDCRT 390
                                       89*****65533333...356******97 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.1   0.00011      0.49       2      24 ..     366     390 ..     365     398 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                                       --SSS-S--EE-S..SEEE-TTT-- CS
                    zinc-ribbons_6   2 kCpeCqqelekrg..eqyhCeaCqe 24 
                                       +Cp+C++ +e+ g  + y+C+ C++
  gi|313127548|ref|YP_004037818.1| 366 TCPDCDRTMESAGrnQGYRCRDCRT 390
                                       6*********5544499******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 3199.16
//
Query:       gi|313127549|ref|YP_004037819.1|  [L=325]
Description: XRE family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-09   35.4   0.0    1.4e-08   34.6   0.0    1.3  1  HTH_3           Helix-turn-helix
    2.7e-06   27.6   0.1    8.6e-06   26.0   0.1    1.8  1  HTH_31          Helix-turn-helix domain
     0.0001   22.3   0.0    0.00019   21.4   0.0    1.4  1  HTH_19          Helix-turn-helix domain
    0.00013   21.7   0.1    0.00027   20.7   0.1    1.6  1  HTH_25          Helix-turn-helix domain
    0.00028   20.6   0.5     0.0006   19.5   0.0    1.7  2  HTH_23          Homeodomain-like domain
    0.00048   20.0   0.0     0.0012   18.7   0.0    1.7  1  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.026   14.3   0.1       0.13   12.1   0.2    2.0  2  HTH_8           Bacterial regulatory protein, Fis family
      0.075   12.9   0.0       0.15   11.9   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.088   12.3   0.1       0.31   10.6   0.1    1.8  2  Sigma70_r4      Sigma-70, region 4
       0.13   12.1   0.0       0.25   11.2   0.0    1.5  1  HTH_38          Helix-turn-helix domain
       0.16   12.1   0.0       0.37   11.0   0.0    1.6  1  HTH_AraC        Bacterial regulatory helix-turn-helix protein


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   8.6e-12   1.4e-08       1      49 [.     132     179 ..     132     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 8.6e-12
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49 
                                       l+  R+++g+s+  LA +lGvsr+t+s++E G  n s+e+++ l++ ++
  gi|313127549|ref|YP_004037819.1| 132 LADEREKRGWSLGRLATELGVSRRTVSKYEDG-MNASIEVAIHLEELFD 179
                                       5678****************************.88*******9999987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   5.3e-09   8.6e-06       3      39 ..     129     165 ..     129     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.3e-09
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrr 39 
                                       G+lL++ Re++G+s+  +A  lgvs+ t+s++E G +
  gi|313127549|ref|YP_004037819.1| 129 GDLLADEREKRGWSLGRLATELGVSRRTVSKYEDGMN 165
                                       899******************************9965 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.2e-07   0.00019       2      42 ..     130     168 ..     129     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-07
                            HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEng.kkdvpsa 42 
                                       + L   Re++g+++  la +lg+sr+  s++E g +   +s+
  gi|313127549|ref|YP_004037819.1| 130 DLLADEREKRGWSLGRLATELGVSRRTVSKYEDGmN---ASI 168
                                       667777**************************9942...333 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   1.6e-07   0.00027       2      44 ..     132     174 ..     131     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.6e-07
                                       HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TTSS-HHHH CS
                            HTH_25   2 LraaRearglsleevaketkIrkdylealEeddfdalpepvyl 44 
                                       L  +Re+rg+sl  +a e+ ++ +++ + E+++ ++++ ++ l
  gi|313127549|ref|YP_004037819.1| 132 LADEREKRGWSLGRLATELGVSRRTVSKYEDGMNASIEVAIHL 174
                                       889******************************9999877665 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.7e-07    0.0006      14      37 ..     133     160 ..     131     166 .. 0.83
   2 ?   -3.5   0.1       6.2     1e+04       3      11 ..     259     267 ..     258     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.7e-07
                            HTH_23  14 lae....GlsvreIAreLgvsrrTvyrw 37 
                                       ++e    G+s  + A+eLgvsrrTv+++
  gi|313127549|ref|YP_004037819.1| 133 ADErekrGWSLGRLATELGVSRRTVSKY 160
                                       4545567******************986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.2
                            HTH_23   3 sereRlril 11 
                                       s+++R+ri+
  gi|313127549|ref|YP_004037819.1| 259 SAKKRARIM 267
                                       688999996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.6e-07    0.0012      12      35 ..     138     160 ..     132     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.6e-07
                            HTH_11  12 argpisgeeLAeeLnvSrrtvrrd 35 
                                       +rg +s  +LA eL+vSrrtv ++
  gi|313127549|ref|YP_004037819.1| 138 KRG-WSLGRLATELGVSRRTVSKY 160
                                       444.9****************997 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.5   2.5e+03      10      22 ..      10      22 ..      10      23 .. 0.88
   2 ?   12.1   0.2   8.1e-05      0.13      15      36 ..     137     158 ..     137     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                                      HHHHHHHTTT-HH CS
                             HTH_8 10 IeaALertgGnks 22
                                      I+a Le +g+++s
  gi|313127549|ref|YP_004037819.1| 10 ITAMLEDAGFVVS 22
                                      8899*****9997 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.1e-05
                                       HHTTT-HHHHHHHHTS-HHHHH CS
                             HTH_8  15 ertgGnkskAArlLGisRrtLy 36 
                                       e+ g+ + + A +LG+sRrt+ 
  gi|313127549|ref|YP_004037819.1| 137 EKRGWSLGRLATELGVSRRTVS 158
                                       5679****************85 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.2e-05      0.15      12      46 ..     144     177 ..     141     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.2e-05
                    YdaS_antitoxin  12 kaLAealgvsqqaVsqWlkgkkqvpaervpeIeka 46 
                                        +LA +lgvs+++Vs+  +g  ++++e  + +e++
  gi|313127549|ref|YP_004037819.1| 144 GRLATELGVSRRTVSKYEDG-MNASIEVAIHLEEL 177
                                       58***************876.77899999999986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.5   2.5e+03      14      23 ..      35      44 ..      34      47 .. 0.81
   2 ?   10.6   0.1   0.00019      0.31      19      39 ..     139     159 ..     134     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                                      HHHHTTT--H CS
                        Sigma70_r4 14 elrfgeglTl 23
                                        r+ge+lTl
  gi|313127549|ref|YP_004037819.1| 35 AARRGEDLTL 44
                                      6799*****9 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00019
                                       TT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4  19 eglTleEIgerlgiSrerVrq 39 
                                       +g++l  ++ +lg+Sr +V+ 
  gi|313127549|ref|YP_004037819.1| 139 RGWSLGRLATELGVSRRTVSK 159
                                       799****************97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.25      18      39 ..     138     159 ..     134     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                            HTH_38  18 aeGlslreIArrLgrspsTIsR 39 
                                       ++G+sl + A +Lg+s+ T+s+
  gi|313127549|ref|YP_004037819.1| 138 KRGWSLGRLATELGVSRRTVSK 159
                                       68******************96 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.37       4      27 ..     136     159 ..     134     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                                       CCSCT--HHHHHHHTTSSHHHHHH CS
                          HTH_AraC   4 nlstnltiediAdelgfSrsyFsr 27 
                                        ++++++++++A elg+Sr++ s+
  gi|313127549|ref|YP_004037819.1| 136 REKRGWSLGRLATELGVSRRTVSK 159
                                       56899***************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2289.73
//
Query:       gi|313127550|ref|YP_004037820.1|  [L=82]
Description: glutathione s-transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-13   48.7   0.0    8.2e-13   48.6   0.0    1.0  1  GST_N_3        Glutathione S-transferase, N-terminal domain
    1.6e-12   47.4   0.0    2.7e-12   46.7   0.0    1.4  2  Glutaredoxin   Glutaredoxin
    6.8e-10   39.1   0.0    7.8e-10   38.9   0.0    1.1  1  GST_N_2        Glutathione S-transferase, N-terminal domain
     0.0046   17.3   0.1     0.0054   17.1   0.1    1.4  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.013   15.6   0.3      0.022   14.8   0.3    1.4  1  Thioredoxin_3  Thioredoxin domain
      0.091   13.2   0.0       0.12   12.9   0.0    1.3  1  Thioredoxin_2  Thioredoxin-like domain
        0.1   12.7   0.1       0.88    9.7   0.0    1.9  2  Thioredoxin_4  Thioredoxin
       0.18   12.2   0.0        0.2   12.0   0.0    1.0  1  NTP_transf_3   MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   3.7e-16   8.2e-13       1      72 [.       6      81 ..       6      82 .] 0.90

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 3.7e-16
                                      EES-TTSHHHHHHHHHHHHHT--EEEE---TTTT.HHHHHHH-TT--SSEE...ETTS-EEESHHHHHHHHHHHH- CS
                           GST_N_3  1 LygfpaSpyarrvrlaLnekglpvevvevtpgeh.deellaknplgkvPvL...eddgealtdSlaIidyLeelyp 72
                                      Ly+  ++py+ +v   L e+gl++    v+  ++ + e+++++++  vPvL   e+d e + +S++I+ yLee+y+
  gi|313127550|ref|YP_004037820.1|  6 LYELDGCPYCAKVTDKLAELGLEYDSIMVPRSHSeRTEVKEVSGQTGVPVLvdeEHDVEGMPESDDIVAYLEETYG 81
                                      9************************999987776799**************554455669**************98 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.2e-15   2.7e-12       2      59 ..       5      61 ..       4      63 .. 0.95
   2 ?   -1.1   0.0         1   2.3e+03      27      43 ..      59      78 ..      58      81 .. 0.63

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.2e-15
                                      EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                      Glutaredoxin  2 vlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59
                                      +l+   +CpyC+k+ + L elg++++ i v   +++r e+ke+sg+  vP+++ d++h
  gi|313127550|ref|YP_004037820.1|  5 TLYELDGCPYCAKVTDKLAELGLEYDSIMVPRSHSERTEVKEVSGQTGVPVLV-DEEH 61
                                      789999********************************************998.7766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                                      EEEEGCCSH...HHHHHHHH CS
                      Glutaredoxin 27 eeidvdkde...eireelke 43
                                      ee+dv+ ++   +i ++l+e
  gi|313127550|ref|YP_004037820.1| 59 EEHDVEGMPesdDIVAYLEE 78
                                      57888888755555555555 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   3.5e-13   7.8e-10       2      69 ..      12      78 ..      11      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 3.5e-13
                                      -HHHHHHHHHHHHCT--EEEEEEH...-TTSHHHHHHHHCTTTSSSEEE-CTTEEEE..SHHHHHHHHHH CS
                           GST_N_2  2 CPwahRvlialalkglediisvvvlepkgfekseefprlnprgtVPvLwdkdgqvin..eSseIlrylet 69
                                      CP++ +v+  la++gle+  + v+    +++   e++++++++ VPvL+d++  v    eS +I+ yle+
  gi|313127550|ref|YP_004037820.1| 12 CPYCAKVTDKLAELGLEYDSIMVP---RSHSERTEVKEVSGQTGVPVLVDEEHDVEGmpESDDIVAYLEE 78
                                      *******************99994...45666679***************877754445*********98 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.4e-06    0.0054       2      28 ..       4      30 ..       3      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                                      EEEEE-TT-HHHHHHHHHHHHHCCCTT CS
                            DUF836  2 ltLyskpgChlCeqakekLkelkleeg 28
                                      ltLy  +gC+ C ++ +kL+el+le +
  gi|313127550|ref|YP_004037820.1|  4 LTLYELDGCPYCAKVTDKLAELGLEYD 30
                                      89*******************999876 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   9.7e-06     0.022       9      75 ..      11      76 ..       8      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.7e-06
                                      SSTTCHHHHHHHHHHCHCCT.CEC..EEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                     Thioredoxin_3  9 gCakCpklekavkeaaaekg.ika..evekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                      gC++C k++  ++e+  e + i +  +  + t+++e+   g + vP  ++d++  v+G +p+ ++i + l
  gi|313127550|ref|YP_004037820.1| 11 GCPYCAKVTDKLAELGLEYDsIMVprSHSERTEVKEV--SGQTGVPV-LVDEEHDVEG-MPESDDIVAYL 76
                                      8*****8777777777666537664444444666666..55589995.57********.9******9887 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.2e-05      0.12      10      52 ..       5      46 ..       3      76 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                     Thioredoxin_2 10 vvftdpdCpyCkklkkelkel.ddvtvrvllfp.lkpsfepkava 52
                                      ++++ ++CpyC+k  ++l el  ++ ++   +p    s  +++ +
  gi|313127550|ref|YP_004037820.1|  5 TLYELDGCPYCAKVTDKLAELgLEYDSI--MVPrS-HSERTEVKE 46
                                      5677899***********9996555555..55532.222444444 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00039      0.88      17      42 ..       4      29 ..       2      40 .. 0.86
   2 ?    1.5   0.0      0.13     3e+02     132     165 ..      43      77 ..      34      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00039
                                      EEEEE-TT-HHHHHHHHHHHHHHHHH CS
                     Thioredoxin_4 17 vieyedlrCphCakfeeeveklleey 42
                                      +++ye   Cp+Cak   ++ +l  ey
  gi|313127550|ref|YP_004037820.1|  4 LTLYELDGCPYCAKVTDKLAELGLEY 29
                                      57899999********9999887776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                                       HH.HHHT--SS-EEEETTEEE-TT--HHHHHHHHT CS
                     Thioredoxin_4 132 ea.kkagiestPtfiingekveepqtyeelkalid 165
                                       e+ + +g +++P ++  ++ ve+ ++ +++ a+++
  gi|313127550|ref|YP_004037820.1|  43 EVkEVSGQTGVPVLVDEEHDVEGMPESDDIVAYLE 77 
                                       55344577799988888888*********999998 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.8e-05       0.2      18      72 ..       6      66 ..       3      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                                      HHCCCCCCHHHHHHHHHCTT.-.CEEEEECSHC....HHHHHHTTCTS-EEE-TTSS.-SH CS
                      NTP_transf_3 18 llplggkpllervldalraagv.devvvvggde....evlaalarlgvrvvededpg.kgp 72
                                      l++l+g p  + v d+l+++g+  + ++v +++    ev++   ++gv+v++de+++ +g+
  gi|313127550|ref|YP_004037820.1|  6 LYELDGCPYCAKVTDKLAELGLeYDSIMVPRSHsertEVKEVSGQTGVPVLVDEEHDvEGM 66
                                      899*****************97435555555533444777788899*******99975776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 571.69
//
Query:       gi|313127551|ref|YP_004037821.1|  [L=462]
Description: arylsulfotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-11   43.2   7.2    8.7e-10   38.0   5.4    2.4  2  Arylsulfotrans   Arylsulfotransferase (ASST)
    8.8e-06   25.3   4.8    0.00012   21.6   3.6    2.5  2  Arylsulfotran_2  Arylsulfotransferase (ASST)
     0.0025   17.8   3.7        1.5    9.0   0.0    4.5  5  NHL              NHL repeat
     0.0062   16.4   2.3          5    7.2   0.1    3.7  3  PQQ              PQQ enzyme repeat


Domain annotation for each model (and alignments):
>> Arylsulfotrans  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   5.4   1.9e-13   8.7e-10      22     218 ..      57     238 ..      36     246 .. 0.80
   2 !    4.2   0.0    0.0037        17     119     140 ..     314     335 ..     297     354 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.9e-13
                    Arylsulfotrans  22 lewdekknnlivDtkGevrWyldqdkisdnk...lkrlkngkllilsg....qklaefdllGr.vikeyrlpggyid 90 
                                       ++ ++ ++ ++  ++G+ +W  + +  + +    +  + ng+ll+ s     + ++e++   +  + e++++   i+
  gi|313127551|ref|YP_004037821.1|  57 TNRKKPARLIAAGERGQTKWVHNDEVNNGAWffdVDPMPNGNLLVSSPrsgeTVVYELNPETQeRVWEKTFD---IE 130
                                       455666677778889999997766655554477789999999998877776666777776555333333444...44 PP

                    Arylsulfotrans  91 lhHdivelpngnllvlvaeenykrkdgkkvktveDtiievd.ktGkvvkewdlakiLdpyrdallkaakapfgdiag 166
                                         Hd+++l++++l+++       r+ +++  +  D i + + ++G+v++ew +++++ p                  
  gi|313127551|ref|YP_004037821.1| 131 DTHDVDVLSEDELVIANM-----REWNDSAGVSDDRIFVYNrTSGEVTWEWYFKNHF-PADT--------------D 187
                                       49********99999888.....5568999999************************.6644..............3 PP

                    Arylsulfotrans 167 vgagrdWlHiNsveydekddsiivSsRhqsavvkidyrtkkvkWilgdkegw 218
                                        g + dW H+N v+    dd++ +S R+ + vv +d +tk+++  lg+++ +
  gi|313127551|ref|YP_004037821.1| 188 GGYNDDWSHVNDVDPVG-DDKLALSPRNFDQVVVVDMETKNITHRLGSDDNY 238
                                       47899*********998.*****************************99876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0037
                    Arylsulfotrans 119 kvktveDtiievdktGkvvkew 140
                                        v+t++  +iev +tG+vv+e+
  gi|313127551|ref|YP_004037821.1| 314 IVDTLNHRVIEVTPTGEVVWEY 335
                                       5788999************998 PP

>> Arylsulfotran_2  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.033   1.5e+02     129     182 ..      72     126 ..      46     152 .. 0.68
   2 !   21.6   3.6   2.7e-08   0.00012     128     296 ..     179     335 ..     125     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.033
                   Arylsulfotran_2 129 plgdfgrdeskpedyfHlNsvekfedgdyLiSl.rel.sslflirpkegkvlWqlq 182
                                       ++++++++++ +  +    +v+ + +g++L+S+ r+  ++++ ++p++++ +W++ 
  gi|313127551|ref|YP_004037821.1|  72 GQTKWVHNDEVNNGAWF-FDVDPMPNGNLLVSSpRSGeTVVYELNPETQERVWEKT 126
                                       45555555555555443.36788888999998844432556778888888888775 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.7e-08
                   Arylsulfotran_2 128 aplgdfgrdeskpedyfHlNsvekfedgdyLiSlrelsslflirpkegkvlWqlqGpkggdfeldns.tfsrQHdar 203
                                       ++   +++d   ++d  H+N+v+ ++d  + +S r+++ ++++  ++++++ +l          dn      QH+++
  gi|313127551|ref|YP_004037821.1| 179 KNHFPADTDGGYNDDWSHVNDVDPVGDDKLALSPRNFDQVVVVDMETKNITHRLGSD-------DNYdVLNEQHNPD 248
                                       777888899999***************9****************9999999888766.......3331356799999 PP

                   Arylsulfotran_2 204 iveetedkivislfnNentdtnerepttglildvdlq.nkevtllrklkdaedeiss...vsqGsyqllpnghvlve 276
                                            + + ++ + +           ++++i+++  +  +e++     +++++ + +   ++   ++ lpng+ l+ 
  gi|313127551|ref|YP_004037821.1| 249 WMVSENGTPTLLVAD----------SGNNRIVEYAYEnRSETSHTDGEWVRTWTVGTgslKWPRDADRLPNGNTLIV 315
                                       874444445555544..........59999****99977788888888999999965333677899*********** PP

                   Arylsulfotran_2 277 egsigrveeydangkivlea 296
                                       ++ + rv+e++  g++v+e+
  gi|313127551|ref|YP_004037821.1| 316 DTLNHRVIEVTPTGEVVWEY 335
                                       ******************97 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.3     1e+04      11      17 ..      95     101 ..      91     102 .. 0.84
   2 ?    2.6   0.0     0.035   1.6e+02       5      19 ..     133     147 ..     133     152 .. 0.87
   3 ?   -2.6   0.1       1.6   7.1e+03      13      21 ..     216     226 ..     216     228 .. 0.71
   4 !    9.0   0.0   0.00033       1.5      15      27 ..     259     271 ..     258     272 .. 0.87
   5 ?    3.7   0.0     0.016        73       3      25 ..     300     322 ..     298     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.3
                                       TTTEEEE CS
                               NHL  11 snGdiyV 17 
                                       +nG+++V
  gi|313127551|ref|YP_004037821.1|  95 PNGNLLV 101
                                       7999999 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.035
                                       EEEEEETTTEEEEEE CS
                               NHL   5 hGvavdsnGdiyVaD 19 
                                       h+v v+s +++++a+
  gi|313127551|ref|YP_004037821.1| 133 HDVDVLSEDELVIAN 147
                                       89***********98 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.6
                                       TEEEEEE..CC CS
                               NHL  13 GdiyVaD..se 21 
                                       ++++V D  ++
  gi|313127551|ref|YP_004037821.1| 216 DQVVVVDmeTK 226
                                       58999995554 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00033
                                       EEEEECCCTEEEE CS
                               NHL  15 iyVaDsenhrvqv 27 
                                       ++VaDs+n+r++ 
  gi|313127551|ref|YP_004037821.1| 259 LLVADSGNNRIVE 271
                                       79*********85 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.016
                                       SEEEEEEETTTEEEEEECCCTEE CS
                               NHL   3 yPhGvavdsnGdiyVaDsenhrv 25 
                                       +P++   ++nG+ ++ D+ nhrv
  gi|313127551|ref|YP_004037821.1| 300 WPRDADRLPNGNTLIVDTLNHRV 322
                                       688999999*************9 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0024        11       7      25 ..     158     175 ..     155     186 .. 0.85
   2 ?   -1.1   0.0      0.48   2.2e+03      19      28 ..     295     304 ..     293     314 .. 0.79
   3 !    7.2   0.1    0.0011         5      19      32 ..     328     341 ..     321     344 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0024
                                       ETTSEEEEEETTTCCEEEE CS
                               PQQ   7 sadGylyAlDadTGkvlWr 25 
                                       s+d +++ +++++G+v W+
  gi|313127551|ref|YP_004037821.1| 158 SDD-RIFVYNRTSGEVTWE 175
                                       444.9***********996 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.48
                                       TCCEEEEEES CS
                               PQQ  19 TGkvlWrfkt 28 
                                       TG ++W  ++
  gi|313127551|ref|YP_004037821.1| 295 TGSLKWPRDA 304
                                       9*****8776 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0011
                                       TCCEEEEEESSSCG CS
                               PQQ  19 TGkvlWrfktggpv 32 
                                       TG+v+W++ + + +
  gi|313127551|ref|YP_004037821.1| 328 TGEVVWEYYATWGP 341
                                       9********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3593.12
//
Query:       gi|313127552|ref|YP_004037822.1|  [L=491]
Description: permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-36  123.6  45.5    1.9e-35  122.3  45.5    1.6  1  Xan_ur_permease  Permease family


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3  45.5     1e-39   1.9e-35       3     387 ..      23     444 ..      21     446 .. 0.89

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 1e-39
                                       HHHHHHHHHHHHHHHHHHHHHTTTS-......................H.HHHHHHHHHHHHHHHHHTTT-----EE CS
                   Xan_ur_permease   3 llllglQhllamfaalvvvPllvgda...........lgl.aeelr.qlisatllasGiatllqllifgirlpillg 66 
                                       ++++g++++l+m + +vv+P +++d+           +g   +e++ +l  +t++a+++at++++++++ +   + g
  gi|313127552|ref|YP_004037822.1|  23 EIVAGVTTFLTMSYIVVVNPSILTDQpfiegvdgiaiAGFsPAEVQsMLAVVTIVAAAVATFVMAIYANRPFGQAPG 99 
                                       79***********************9999998888874444455555****************************** PP

                                       E-GGGHHHHHGGG-....HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHT CS
                   Xan_ur_permease  67 ssfafvtalmialGsaedieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkv 143
                                       ++++++ a++++ +     ++  +++l a+++ g+lfil+ ++g r++++rl+p  v  +v ++iGl+l+ i+++ +
  gi|313127552|ref|YP_004037822.1| 100 LGLNAFFAFTVVGA----LGVPWQTALAAVVAEGILFILLTAVGAREYVIRLFPEPVKFAVGTGIGLFLTIIGLQAM 172
                                       *******9999999....5999******************************************************* PP

                                       TSS-..BTT.B---HHHHHHHHHHHHHHHHHHHS.SSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHH.......... CS
                   Xan_ur_permease 144 gggwaavegltvvslkllllavvvllvilllsvf.lkglfsqlpiLigiiagwllalfmgivnlspe.......... 209
                                       g++  + ++  ++++ + + +v++l v+ l+ +f l      ++i igi+++++l +++++                
  gi|313127552|ref|YP_004037822.1| 173 GLVVND-SATLITLGPVASDPVAILSVVGLFFTFaLYARGIPGSIIIGILGTAFLGWVLTVAGIVTPdaglvadass 248
                                       ***744.4458999999999****999999999988889999******************444333336799***** PP

                                       .......................HHS-SS-----------HH...H.HHHHTHHH.HHHHHHHHHHHHHHHHHHTS- CS
                   Xan_ur_permease 210 .......................vseapwfqlpsplkfgtpl.fnlgliltvlavalvavvesvGdiravakvvgrs 262
                                                               + +p++   + + +g+ + f++   l+v+++++v ++++ G++ +v++++g  
  gi|313127552|ref|YP_004037822.1| 249 mtlslpvlgtfdvlvpaagasatYNVTPLVGA-FVGGLGNVEaFSF--ALIVFTFFFVDFFDTAGTLVGVSQIAGFL 322
                                       **********9999999876555444555544.3444454446666..455667779******************77 PP

                                       TII..IIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHHHHHTB--HHHHHHHHHHHHHHT--HHHHHHHTTS-H CS
                   Xan_ur_permease 263 lkp..kpdlrralladGlatllsgllGalpvttyaeniGvvaltkvasrrvmvtagvilillglipklaallssIPe 337
                                       +++   pd+ + l+ad ++t+++g++G++ vtty+e++ +v+ +    +r+++ta ++ +l+ ++ ++ + +++IP+
  gi|313127552|ref|YP_004037822.1| 323 DDDgnLPDIDKPLMADAIGTTVGGMIGTSTVTTYVESASGVEEG----GRTGLTALTVSVLFLVSLAFVPVAAAIPQ 395
                                       77789***************************************....***************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTS-SHHHHHHHHHHHHHHHH----- CS
                   Xan_ur_permease 338 pvlgGvllvvfgmiaasgvsnlqtvdldsarnllivavslvlGlgvatvp 387
                                       ++ + ++lvv g++++ +v  ++++d++++  + ++ +++ ++ ++a+++
  gi|313127552|ref|YP_004037822.1| 396 YA-SHIALVVIGVVMLGNVIDIDWSDVTNTIPAGMTILVMPFTYSIAYGI 444
                                       **.99***************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3271.98
//
Query:       gi|313127553|ref|YP_004037823.1|  [L=239]
Description: prpp-binding protein, adenine/guanine phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-09   35.7   0.2    9.5e-09   35.0   0.2    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00054   20.1   0.5     0.0073   16.5   0.1    2.3  2  MOFRL         MOFRL family
     0.0056   16.7   0.0      0.011   15.8   0.0    1.4  1  HTH_3         Helix-turn-helix
  ------ inclusion threshold ------
      0.036   13.6   0.0      0.049   13.1   0.0    1.2  1  PRTase_2      Phosphoribosyl transferase
      0.055   13.8   0.3       0.11   12.9   0.3    1.5  1  HTH_31        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.2   2.6e-12   9.5e-09       9     111 ..      92     199 ..      86     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.6e-12
                                       --EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.............. CS
                      Pribosyltran   9 paildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...... 79 
                                       + +ld va  aa++l    ++pdvv++ a+ G++++ ++a+++++++ay  k+k  +      +r+    +      
  gi|313127553|ref|YP_004037823.1|  92 QSFLDLVAPVAANTLGF--ERPDVVLTAATDGITLGAAMASYFDARVAYAKKSKETAVEEFIESRQ----Rlasgie 162
                                       56677788888888777..9************************9999998877655433222222....1345688 PP

                                       .....EE----TTSEEEEE-SEESSSHHHHHHHHHHH CS
                      Pribosyltran  80 .....rlledpagkkVliVDDildtGgTllaalelLk 111
                                               ++  g+ VliVDD++ +G T +  l++  
  gi|313127553|ref|YP_004037823.1| 163 ltyylPTRALSSGENVLIVDDLIRSGETQELLLDIAL 199
                                       ****9999999*****************888887544 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.086   3.1e+02      39      53 ..     109     123 ..      85     159 .. 0.61
   2 !   16.5   0.1     2e-06    0.0073       4      57 ..     172     224 ..     169     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.086
                                       -TTEEEEEEETTS-- CS
                             MOFRL  39 aeevvllsagtDGiD 53 
                                       ++  v+l a+tDGi 
  gi|313127553|ref|YP_004037823.1| 109 ERPDVVLTAATDGIT 123
                                       455678999999984 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2e-06
                                       EEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS CS
                             MOFRL   4 lsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptd 57 
                                       ls+GE +  v    + G +qel+l +al+ ++   +  ++l+s+gt+GiD + +
  gi|313127553|ref|YP_004037823.1| 172 LSSGENVLIVDDLIRSGETQELLLDIALQSDAD-VTGVFALISVGTEGIDRARE 224
                                       899*******888***************55543.5666779*********8665 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.1e-06     0.011       7      44 ..      21      58 ..      17      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-06
                                      HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEnGernPsletlkkl 44
                                      +   +  eLAe++G++   ++r+ nG+  P +e++ ++
  gi|313127553|ref|YP_004037823.1| 21 KETRTYDELAELTGLPAGDLNRYVNGHVLPGIERAREV 58
                                      6778999**************************99876 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.049      38     141 ..      96     195 ..      55     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                          PRTase_2  38 aLaellaeakkeelpepvlvigfAEtAtaLghgvadaleeealylhtTRekvagveelleFeEeHSHAtdhllyaed 114
                                       +L + +a+ ++  +++p +v+  A   ++Lg+++a+ +++++ y +  +e+   vee++e +   +   + l y   
  gi|313127553|ref|YP_004037823.1|  96 DLVAPVAA-NTLGFERPDVVLTAATDGITLGAAMASYFDARVAYAKKSKETA--VEEFIESRQRLASGIE-LTYYLP 168
                                       44444442.334788999999*****************99999999888877..6666665555554444.445678 PP

                          PRTase_2 115 eellaaakelvLvDDEistGktalnli 141
                                       +++l++ +++++vDD i +G+t   l+
  gi|313127553|ref|YP_004037823.1| 169 TRALSSGENVLIVDDLIRSGETQELLL 195
                                       889999999************975544 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3     3e-05      0.11       4      57 ..      15      65 ..      12      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                            HTH_31  4 alLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57
                                      a Lr l e +  + +e+Ae++g+ +  l+r+ +G   +p  +  + +++++g d
  gi|313127553|ref|YP_004037823.1| 15 AVLRMLKETR--TYDELAELTGLPAGDLNRYVNGHV-LPGIERAREVVQGVGRD 65
                                      5789999998..************************.9*999999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.54
# Mc/sec: 1326.97
//
Query:       gi|313127554|ref|YP_004037824.1|  [L=178]
Description: orotate phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-13   49.0   2.4    6.2e-13   48.6   2.4    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00021   20.8   0.1    0.00026   20.5   0.1    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.011   15.3   1.1      0.014   15.0   0.2    1.6  2  PRTase_2      Phosphoribosyl transferase
      0.082   12.5   2.9       0.92    9.1   0.1    2.6  2  PikAIV_N      Narbonolide/10-deoxymethynolide synthase PikA4 
       0.12   12.0   0.1       0.16   11.6   0.1    1.1  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   2.4   1.7e-16   6.2e-13       6     138 ..      39     158 ..      36     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.7e-16
                                       TT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE- CS
                      Pribosyltran   6 lenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrll 82 
                                       ++np  l+ +a++ a  l+        ++g+a g+vp++  +a e + p+++ rk+ ++ +++  +           
  gi|313127554|ref|YP_004037824.1|  39 ETNPDCLRLIAEAFAAELDG----VEKLAGVALGAVPLVAVTAAETDTPYVIARKKAKEYGTAKRI---------EG 102
                                       56777777888888877777....899***************************************.........78 PP

                                       ---TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-T CS
                      Pribosyltran  83 edpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknak 138
                                       ++ +g+ V++ +Di +tG++ l a+e+L+e+g+ + r+ v+vd+ +++ e+ ++a+
  gi|313127554|ref|YP_004037824.1| 103 RLEEGEEVVVLEDIATTGNSALDAVEALREAGAVVNRVLVVVDRQEGAAERLAEAD 158
                                       999*********************************************99988876 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   7.3e-08   0.00026     112     176 ..      97     161 ..      70     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.3e-08
                           UPRTase 112 ynkLPkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegv.krlaeefpkv 176
                                        +++  ++ + ++v++l+ +  TG+sa +a++ L+e+g+ ++++lv  v+  +eg+ +rlae+  ++
  gi|313127554|ref|YP_004037824.1|  97 AKRIEGRLeEGEEVVVLEDIATTGNSALDAVEALREAGAVVNRVLV--VVDRQEGAaERLAEADVEL 161
                                       5566677766788**************************9998876..5666666535555554455 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.61   2.2e+03      28      65 ..      41      82 ..      38      86 .. 0.65
   2 ?   15.0   0.2   3.8e-06     0.014     113     177 ..      99     161 ..      87     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.61
                          PRTase_2 28 kpstvreagaaLaellaeakk....eelpepvlvigfAEtAt 65
                                      +p   r +++a a++l  ++k    +  + p++ +  AEt t
  gi|313127554|ref|YP_004037824.1| 41 NPDCLRLIAEAFAAELDGVEKlagvALGAVPLVAVTAAETDT 82
                                      566666666677776665555555445566778888888866 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.8e-06
                          PRTase_2 113 edeellaaakelvLvDDEistGktalnliralqeklpr.kryvvvslvdwrseedeaafaaleeel 177
                                       + e +l++ +e+v+  D ++tG++al+ ++al+e+    +r+ vv  vd ++ +  ++ a++  el
  gi|313127554|ref|YP_004037824.1|  99 RIEGRLEEGEEVVVLEDIATTGNSALDAVEALREAGAVvNRVLVV--VDRQEGA-AERLAEADVEL 161
                                       556789999*************************97764665554..5655444.44555555555 PP

>> PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00026      0.92       1      13 [.       1      13 [.       1      13 [. 0.88
   2 ?    3.0   0.5     0.021        75       7      12 ..     127     132 ..     122     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00026
                          PikAIV_N  1 tsdeklVeALRaS 13
                                      +++++l+eALRa+
  gi|313127554|ref|YP_004037824.1|  1 MANDELIEALRAA 13
                                      579********96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.021
                          PikAIV_N   7 VeALRa 12 
                                       VeALR+
  gi|313127554|ref|YP_004037824.1| 127 VEALRE 132
                                       9****7 PP

>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.4e-05      0.16      88     174 ..      89     171 ..      79     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHHHHHHHHT.T-EEEES---.-SS--HHHHHHHHHHTT-TTSSEEEEESSSSCHHHHHHTT-TTEEEE CS
                      Ribosomal_L4  88 kKvrrlAlrsaLsakakq.glllvvdnlepleesktkelvellkklglksksvLivvsekdenlvlaarnlpgvevi 163
                                       kK+++++ +  +  ++++ ++++v++++     +++ ++ve+l++ g+  ++vL+vv++       aa+ l++++v 
  gi|313127554|ref|YP_004037824.1|  89 KKAKEYGTAKRIEGRLEEgEEVVVLEDIA-TTGNSALDAVEALREAGAVVNRVLVVVDR----QEGAAERLAEADVE 160
                                       78999999999999999966899999998.899************************97....34566677777766 PP

                                       ESTT--CHHHH CS
                      Ribosomal_L4 164 eveslnvydll 174
                                           + ++dll
  gi|313127554|ref|YP_004037824.1| 161 LDSLVTAEDLL 171
                                       66666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:01.61
# Mc/sec: 333.94
//
Query:       gi|313127555|ref|YP_004037825.1|  [L=180]
Description: cdp-diglyceride synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-43  148.7   2.7    1.9e-43  148.5   2.7    1.0  1  CarS-like     CDP-archaeol synthase
    0.00071   19.4   4.5    0.00071   19.4   4.5    1.8  2  CTP_transf_1  Cytidylyltransferase family
     0.0069   16.4   0.0     0.0069   16.4   0.0    2.6  3  CcmD          Heme exporter protein D (CcmD)


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.5   2.7   3.1e-47   1.9e-43       2     175 .]       3     180 .]       2     180 .] 0.89

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 3.1e-47
                         CarS-like   2 ldlilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilal 78 
                                       ++l++ + + +lpayv+n+ avl GGG p+d G+t+    r++GdG+t+rGt++G+lvG   + +  ++      al
  gi|313127555|ref|YP_004037825.1|   3 IELVVGAFWAMLPAYVPNNAAVLAGGGAPIDGGRTWG-SSRVLGDGKTWRGTLVGTLVGFALAFVCNAVAGSVEAAL 78 
                                       789999****************************985.679**************************9966555666 PP

                         CarS-like  79 dssgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgallla....yp..vkllpieliil 149
                                          ++    v+ a+ lafGa+lGd+  sf+krr + erG  ++ ldqldfv+gal+la    +      +++ ++ +
  gi|313127555|ref|YP_004037825.1|  79 GIGLP-RFSVLGAFGLAFGAMLGDIGASFLKRRTGRERGAAFPGLDQLDFVVGALALAalldFAwfRGTFTLPVLGV 154
                                       66555.446778999*****************************************995443222235789999999 PP

                         CarS-like 150 ivlitlvlhlsaniiayklglkdvwy 175
                                       ++++t++lh+++ni ay lglk+ ++
  gi|313127555|ref|YP_004037825.1| 155 VLVLTPILHVGTNIAAYYLGLKNEPW 180
                                       **********************9988 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   4.5   1.2e-07   0.00071     170     231 ..      47     112 ..      34     138 .. 0.77
   2 ?   -0.4   0.4      0.13   8.1e+02     113     155 ..     136     174 ..     124     176 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-07
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS...---TTSHHHHHHH.HHHHHHHHHHHHHHHHHHHT CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskal...alsllhllllsll.lslvavfGDLveSglKRafg 231
                                       +KT+ G + G+++ +++++++  v+++      + l  + +l+++ l++ a++GD+ +S lKR+ g
  gi|313127555|ref|YP_004037825.1|  47 GKTWRGTLVGTLVGFALAFVCNAVAGSVEaalGIGLPRFSVLGAFgLAFGAMLGDIGASFLKRRTG 112
                                       7***********************9997777745555555555553678899***********987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.13
                                       HHHHTHHHH.TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      CTP_transf_1 113 allyvvlllqslllienikeglllvllllalvvaaDigaYffG 155
                                       all ++++     +++ +  g++lvl++++ v ++ i+aY  G
  gi|313127555|ref|YP_004037825.1| 136 ALLDFAWFR---GTFTLPVLGVVLVLTPILHVGTN-IAAYYLG 174
                                       333333333...56666667777777777776544.7777776 PP

>> CcmD  Heme exporter protein D (CcmD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-06    0.0069       5      31 ..      85     111 ..      85     115 .. 0.93
   2 ?   -1.0   1.2      0.33     2e+03      12      22 ..     128     138 ..     127     146 .. 0.67
   3 ?   -2.8   0.0       1.2   7.2e+03      14      23 ..     147     156 ..     145     159 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-06
                              CcmD   5 fYVWlsYgitllvlagLilwslrdrrr 31 
                                       f V++++g+++ +++g i +s ++rr+
  gi|313127555|ref|YP_004037825.1|  85 FSVLGAFGLAFGAMLGDIGASFLKRRT 111
                                       569**********************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.33
                              CcmD  12 gitllvlagLi 22 
                                        + +l+la+L+
  gi|313127555|ref|YP_004037825.1| 128 VVGALALAALL 138
                                       45677777775 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.2
                              CcmD  14 tllvlagLil 23 
                                       + l ++g++l
  gi|313127555|ref|YP_004037825.1| 147 FTLPVLGVVL 156
                                       4555665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1229.51
//
Query:       gi|313127556|ref|YP_004037826.1|  [L=279]
Description: l-proline dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-28   99.1   0.1    5.8e-28   98.3   0.1    1.4  1  Pro_dh    Proline dehydrogenase


Domain annotation for each model (and alignments):
>> Pro_dh  Proline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.1   3.2e-32   5.8e-28       3     293 ..      20     271 ..      18     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 3.2e-32
                                       HHHHHHHHTTEEEEEEES-SS--SHHHHHHHHHHHHHHHHHHHHHHCCS-TTCC-SEEE-GGGTT-SGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh   3 ktieklkkrgvrlsldllgeavlteedadryleayleaiksiekaskalkvleapgvsvklsaprletaeeeevmee 79 
                                       ++++k +k+gv+++l+llge + +++ ad+ ++ayle+i+++++++       +  vsvk+s+  ++    +ev   
  gi|313127556|ref|YP_004037826.1|  20 DHTRKVNKDGVKVILNLLGEHYHERAPADADAAAYLELIEDVGDSEL------DACVSVKPSQIGIDVG--DEV--- 85 
                                       577888878*********************************99987......778*****97544444..444... PP

                                       HHHHHHHHHHHHHHTT-EEEE----GGGHHHHHHHHHHHHHSCCTTT---EEEEEETTBTTHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh  80 lverlrtlakeakelgvrlliDaEeaklqeltlelfrklnkepelkdwevvgntyQaYlkdalevlqkllelAereg 156
                                       + e+  ++a++ +e++v ++ D+E+a+  ++tl++f++  +e +     +vg  +Qa lk++ ++l++l++      
  gi|313127556|ref|YP_004037826.1|  86 FRENYLRIAEKGAEHDVFVWCDMEDADTTDVTLDVFEEAAREYDG----GVGQCVQANLKRTGDDLERLAD------ 152
                                       46788899********************************87777....7*****************9975...... PP

                                       S-EEEEEE--S-HHHHHHHHHHTT-S-SB-SSHHHHHHHHHHHHHHHHHTTTTEEEEEE-S-HHHHHHHHHHHHHT. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh 157 frlgvkLVrGAYldsErkraqelgyespifdtkeeTDanYdavaelllenrdeiypavAsHNaesvakalalaeelg 233
                                       ++ +++LV+GAY +  ++           +++k +  ++Y++ +e+l+e+    ++av+sH  + +++a +la+e  
  gi|313127556|ref|YP_004037826.1| 153 VPGKIRLVKGAYDED-PE---------ISYKQKSKVNEKYEEYLEFLFEEY-VGRVAVGSHDPKMISAAEELANEY- 217
                                       6899********654.33.........2399*****************765.67899*******************. PP

                                       .T--GGGEEEEEETTSSHHHHHHHHHTTS-EEEEEEECEHHHHHHHHHHHHHHHH-TT-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh 234 qekeksevefqqLlGMadnlsfalakagynvrkYlPvGpveevlpYLvRRleENtanssf 293
                                           ++++e+q+L+G  d+ +++l+ +g++v  Y+P+G+  +  +Y  RR+ E ++n+ f
  gi|313127556|ref|YP_004037826.1| 218 ----DRDYEVQMLMGVRDDTQRELSAEGTEVWQYAPYGD--KWFSYFYRRARERKENALF 271
                                       ....**********************************6..89**********9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1778.14
//
Query:       gi|313127557|ref|YP_004037827.1|  [L=194]
Description: hypothetical protein Hbor_28410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-18   66.7   1.1      2e-18   66.2   0.1    1.7  2  DUF502     Protein of unknown function (DUF502)
     0.0066   16.4   4.2     0.0099   15.9   4.2    1.2  1  Colicin_V  Colicin V production protein
  ------ inclusion threshold ------
      0.045   13.7   3.8       0.07   13.1   3.8    1.3  1  DUF485     Protein of unknown function, DUF485
       0.11   12.8   3.6       0.16   12.4   3.6    1.2  1  MgtE       Divalent cation transporter


Domain annotation for each model (and alignments):
>> DUF502  Protein of unknown function (DUF502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.74   3.3e+03       4      24 ..      19      39 ..      14      45 .. 0.66
   2 !   66.2   0.1   4.5e-22     2e-18       1     106 []      52     148 ..      52     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.74
                            DUF502  4 lllillvGllasnligrkllk 24
                                      l++++++++l +++i   ++k
  gi|313127557|ref|YP_004037827.1| 19 LVILYVLSILYNSIIELPIIK 39
                                      566677777777777665555 PP

  == domain 2  score: 66.2 bits;  conditional E-value: 4.5e-22
                            DUF502   1 lvvlllillvGllasnligrkllklgerllkriPlvksiYsalkqvvetfsseekksfrevvlve.yprkglwalgF 76 
                                       +v+++l+l vG+l++++ gr + + ++++++r+Plv+ +Y+a+k  vet ++  +++++++v +e +  +g++++gF
  gi|313127557|ref|YP_004037827.1|  52 IVFMMLVLSVGYLMRTTAGRLFESGIDAAMNRLPLVRVLYNASKLAVETALT-GTEDLQKPVRLEvW--PGIRMTGF 125
                                       6899***********************************************8.8999********88..9******* PP

                            DUF502  77 vtgetegelatkgeedlvaVfvPtspnpts 106
                                        tg+t+       ++ + ++f+Pt+pn+t+
  gi|313127557|ref|YP_004037827.1| 126 KTGKTT-------QDGREVIFMPTAPNITT 148
                                       ****83.......46889**********96 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   4.2   2.2e-06    0.0099      60     121 ..       7      68 ..       2      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-06
                         Colicin_V  60 aiiaflllfllvllivsllgallsklvsktglglldrllGaifGllkglllvvllllllalv 121
                                        +++ l++++ +l+i+++l+ l +++++++ +++l++ +G+++ ++ ++ lv  + +l+ ++
  gi|313127557|ref|YP_004037827.1|   7 DFASGLVVLVPILVILYVLSILYNSIIELPIIKGLHQPFGFFVAIIVFMMLVLSVGYLMRTT 68 
                                       577889*******************************************9999777777666 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.8   1.6e-05      0.07      12      75 ..       4      67 ..       1      75 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                            DUF485 12 krrrfafpltaiflvvYfgfvllvafapdllatkvgeg.nitvglllgllqivltflltglYvrr 75
                                       rr fa  l++++ ++ +++vl + ++ ++ + ++++g + ++g+ ++++++++ +l +g+ +r 
  gi|313127557|ref|YP_004037827.1|  4 WRRDFASGLVVLVPILVILYVLSILYN-SIIELPIIKGlHQPFGFFVAIIVFMMLVLSVGYLMRT 67
                                      5899***********************.*************************999988877765 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.6   3.5e-05      0.16      35     113 ..       3      90 ..       1      95 [. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHH........HHHHHHHHHHHHHHH...HHHHHHHHHHTTS-G CS
                              MgtE  35 vllkelrvvlllgvilgllifllalllgwslllalv........vglalvlvllaaall.ilgvllplllwklglDP 102
                                        +++ ++ +l+++v + +++++l +l+ + + l ++        + +a+++++++++ + +l+ +++  l+  g+D 
  gi|313127557|ref|YP_004037827.1|   3 SWRRDFASGLVVLVPILVILYVLSILYNSIIELPIIkglhqpfgFFVAIIVFMMLVLSVgYLMRTTAGRLFESGIDA 79 
                                       56788888999999988888888888777444444455555544333334344444444578899989999****** PP

                                       GGSHHHHHHHH CS
                              MgtE 103 dnaaiPlltal 113
                                       ++  +Pl+ +l
  gi|313127557|ref|YP_004037827.1|  80 AMNRLPLVRVL 90 
                                       ******99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1381.88
//
Query:       gi|313127558|ref|YP_004037828.1|  [L=71]
Description: translation initiation inhibitor, yjgf family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-09   36.7   0.4    6.9e-09   35.8   0.4    1.4  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.4   3.8e-13   6.9e-09       6      53 ..      13      60 ..       9      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.8e-13
                                      TTSSS-BSEEEETTEEEEEEE-SB-TTTSCB..-SSHHHHHHHHHHHHH CS
                     Ribonuc_L-PSP  6 aaaapYsqavkagnlvyvsGqlpldpetgelv.egdveeqtrqalenlk 53
                                      ++ a Ys+av++g  v+vsG++ ++ ++ge+v egd++eqt+qal+ ++
  gi|313127558|ref|YP_004037828.1| 13 EPRAGYSRAVRVGPHVHVSGTTETN-DDGEIVgEGDAYEQTKQALQSVE 60
                                      5699******************999.69***99************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 509.90
//
Query:       gi|313127559|ref|YP_004037829.1|  [L=309]
Description: branched chain amino acid aminotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.9e-50  169.6   0.0    1.1e-49  169.4   0.0    1.1  1  Aminotran_4  Amino-transferase class IV


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.4   0.0   5.9e-54   1.1e-49       1     223 []      37     270 ..      37     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 169.4 bits;  conditional E-value: 5.9e-54
                       Aminotran_4   1 glfEtmrvy....ngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglgaa 73 
                                       g+fE++r y       if+++eHleRL  s +  ++e++f  eel++++ ell++++ +++++r++ + g ++lg +
  gi|313127559|ref|YP_004037829.1|  37 GVFEGVRCYdtekGPAIFRWEEHLERLYDSTKPYDMEISFEPEELTEATLELLRRQDLNEAYIRPIAFYGYESLGVS 113
                                       89*****998877778899********************************************************77 PP

                       Aminotran_4  74 tsepsvavyvsalppgpeseke.....lplvtssdvrrdapsplpgaKtln.yldnvlarreakergadevllvded 144
                                         +    v+++a+p+g++   +     +++++ss++++   ++ ++aKt+  y +++la +ea+++g+ e+++++++
  gi|313127559|ref|YP_004037829.1| 114 PGDCPTNVTIAAWPWGAYLGEDalengIEVMVSSWRKHASSQVPTNAKTTGlYVNSLLAGEEARRNGYREAIVLNKE 190
                                       7777778999******************************************************************* PP

                       Aminotran_4 145 gnvtEgstsNvfivkggelitPplssgiLpGitrrallelakalgleve.ereitlkdleeadeafltntlrgvlpv 220
                                       gnv Eg   N+f+v++gel+tP ls++iL+Gitr++l+ la+++g ev+  + i+ ++l+ ade+f+t+++++v+p+
  gi|313127559|ref|YP_004037829.1| 191 GNVAEGPGENIFLVRDGELYTPGLSESILDGITRNTLITLAEERGYEVHeNTSISRGELNTADELFFTGSAAEVTPI 267
                                       **********************************************9996789************************ PP

                       Aminotran_4 221 rsi 223
                                       r++
  gi|313127559|ref|YP_004037829.1| 268 RQV 270
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2301.26
//
Query:       gi|313127560|ref|YP_004037830.1|  [L=307]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-19   69.1   0.0    5.8e-19   68.5   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    9.9e-15   54.8   1.2    2.1e-11   43.8   0.2    2.7  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.2e-06   27.0   0.0    3.6e-06   26.3   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    4.7e-06   26.6   0.9    4.1e-05   23.5   0.3    2.1  2  NAD_binding_10   NAD(P)H-binding
      1e-05   24.7   0.0    1.6e-05   24.1   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00017   21.5   2.1      0.021   14.7   0.2    2.2  2  KR               KR domain
    0.00034   19.8   2.0       0.66    9.0   3.1    3.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0099   15.5   0.2      0.016   14.7   0.2    1.4  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.015   14.5   0.0       0.49    9.5   0.0    2.1  2  NAD_binding_4    Male sterility protein
      0.024   14.5   0.0      0.037   13.9   0.0    1.4  1  LpxI_N           LpxI N-terminal domain
      0.039   13.3   0.1      0.064   12.6   0.1    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.05   14.1   0.4       0.19   12.2   0.3    2.1  2  CoA_binding_2    CoA binding domain
      0.065   12.7   0.4       0.13   11.7   0.4    1.5  1  adh_short        short chain dehydrogenase
       0.12   12.5   0.1       0.22   11.6   0.1    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0   4.6e-22   5.8e-19       2     166 ..      22     185 ..      21     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 4.6e-22
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                        VtG+tG iG  +v al+++gy+v++++r   +++t++++d    ++d+td+ +   +f++ ++da++hl+  ++++
  gi|313127560|ref|YP_004037830.1|  22 AVTGGTGKIGPTVVAALQSAGYRVVNISRS--GGETEADAD---LRADMTDAGEAYGAFATADADAIVHLGMLSTPD 93 
                                       7*****************************..566666655...69************************9999999 PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSS.SS.......BSTCSTTS----SSHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdae.qp.......keettltgplkpnspYaaaKl 147
                                       +  +    ++e+n++ t+n+l+aa + +v+ ++ +sS +  G++ e  p        +e   + p+ p++ Y++ K+
  gi|313127560|ref|YP_004037830.1|  94 H--DPGHVVFESNAMSTYNVLQAAEALDVDTVVLASSLSAVGASFEpEPirlsylpLDE---SHPVSPSNSYGMGKH 165
                                       9..5666999***************************9999988874456554222333...3477*********** PP

                                       HHHHHHHHHHHHH.T-EEEE CS
                         Epimerase 148 ageklveayaaqy.glnaii 166
                                         e  +  +a+ + g ++i+
  gi|313127560|ref|YP_004037830.1| 166 VLEVTADGFAHRQnGPRTIA 185
                                       ***99998876553655555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.2   1.7e-14   2.1e-11       2     174 ..      23     181 ..      22     191 .. 0.81
   2 !    9.0   0.0   0.00064      0.83     290     324 ..     271     305 ..     202     307 .] 0.77

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.7e-14
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       +TG++G iG  ++  L + gy+v++i r   +++    +                 ++D+tD+ +   ++a ++ d+
  gi|313127560|ref|YP_004037830.1|  23 VTGGTGKIGPTVVAALQSAGYRVVNISRSGGETE--ADAD---------------LRADMTDAGEAYGAFATADADA 82 
                                       9************************987655543..2222...............479******************* PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-........SSSSB-TTS-- CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkv........qevpqtEttpf 147
                                       +++L+  s  d   +  + ++e n++ t+++L+a+ al ++    ++ aS+    G          +  p +E++p+
  gi|313127560|ref|YP_004037830.1|  83 IVHLGMLSTPDH--DPGHVVFESNAMSTYNVLQAAEALDVD---TVVLASSLSAVGASfepepirlSYLPLDESHPV 154
                                       *********998..666899*****************9985...4566777667777633222221245779***** PP

                                       ---SHHHHHHHHHHHHHHHHHHHH--- CS
                     GDP_Man_Dehyd 148 yPrsPYaaaKlyadwivvnyreayglf 174
                                       +P + Y++ K + +  +  + + ++ +
  gi|313127560|ref|YP_004037830.1| 155 SPSNSYGMGKHVLEVTADGFAHRQNGP 181
                                       ***********9999998888776655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00064
                                       CCCEECGG--SS--SB--B-THHHHHHH----SS- CS
                     GDP_Man_Dehyd 290 vvevdpkyfrpgevdlllgdaskakeeLgWkpkvs 324
                                        v  d +  r+ e  + l+ ++kak+ LgW+p+ s
  gi|313127560|ref|YP_004037830.1| 271 AVYPDVECKREFEGYEALISTEKAKRMLGWEPERS 305
                                       44456677788899999***************976 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.8e-09   3.6e-06       2     134 ..      20     169 ..      19     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.8e-09
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..........eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                       ++ vtG++G++G  ++++l+++g+ v+ ++r+          ++d+tda ++  +++ a+ d++v+++     D+  
  gi|313127560|ref|YP_004037830.1|  20 TVAVTGGTGKIGPTVVAALQSAGYRVVNISRSggeteadadlRADMTDAGEAYGAFATADADAIVHLGMLSTPDH-- 94 
                                       578****************************9******************************************7.. PP

                                       HSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-.........TTS-B-TTS----SSHHHHHHHHHHH CS
                     RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavgalLihvStDyVFdGe.........kkrpYeeddetsPlnvYGrtKlaGEq 134
                                       +  +  ++ na ++ ++ +aa+a ++  + + +     G+            p  e++++sP n YG  K+  E 
  gi|313127560|ref|YP_004037830.1|  95 DPGHVVFESNAMSTYNVLQAAEALDVDTVVLASSLSAVGAsfepepirlSYLPLDESHPVSPSNSYGMGKHVLEV 169
                                       678899999********99999999876655554433333355556655555667888889999***99998776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3   3.2e-08   4.1e-05       1     101 [.      25     131 ..      25     146 .. 0.75
   2 ?    1.2   0.0      0.22   2.9e+02       9      67 ..     236     291 ..     234     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.2e-08
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S..EEEES-..--TCC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgad..aVvsal..ggggk 73 
                                       G+tGk+G  +v+ l ++ g++v+ + R+  ++++   ++    + +d+td+ +   a++ ad  a+v  +  ++ + 
  gi|313127560|ref|YP_004037830.1|  25 GGTGKIGPTVVAALQSA-GYRVVNISRSGGETEA---DAD---LRADMTDAGEAYGAFATADadAIVHLGmlSTPDH 94 
                                       9****************.5*********999883...233...5789999999988887665115555444533333 PP

                                       ..HHHH.........HHHHHHHHHHCT--EEEEEEETTT CS
                    NAD_binding_10  74 ..deeg.........aknivdaakeagvkRfvlvsaigv 101
                                                      + n+++aa++ +v  +vl s++ +
  gi|313127560|ref|YP_004037830.1|  95 dpG--HvvfesnamsTYNVLQAAEALDVDTVVLASSLSA 131
                                       330..1455555578********************9876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.22
                                       HHHHHHHHC-..T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES CS
                    NAD_binding_10   9 llvkellarg..ghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsa 67 
                                       +lv+ +++++  ghe + ++  p+  a+++ ee +e+v  dv+     ++ ++g++a +s+
  gi|313127560|ref|YP_004037830.1| 236 ELVRLAVEADfeGHE-RFFASAPDTSADVPTEELVEAVYPDVE----CKREFEGYEALIST 291
                                       688999999886666.999999**9999998888888888876....78888888888887 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.2e-08   1.6e-05       1     130 [.      22     142 ..      22     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.2e-08
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdklee..alegvdvvihlas 75 
                                       +vtGg+G +G ++v +L +++     rv+ +  s    e       +  + +D+td+ +     a+ ++d+++hl +
  gi|313127560|ref|YP_004037830.1|  22 AVTGGTGKIGPTVVAALQSAGY----RVVNISRSGGETEAD----AD--LRADMTDAGEAYGafATADADAIVHL-G 87 
                                       59***************99995....999988777663333....33..567888877765411678999*****.8 PP

                         3Beta_HSD  76 lvdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeil 130
                                       +     ++    + + n   T nvl+a+   +v ++v  Ss+++vg  ++ e+i+
  gi|313127560|ref|YP_004037830.1|  88 MLSTPDHDPGHVVFESNAMSTYNVLQAAEALDVDTVVLASSLSAVGASFEPEPIR 142
                                       8899999***************************************999888876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.7e-05     0.021       2      52 ..      20      69 ..      19      83 .. 0.81
   2 !    6.5   0.1    0.0057       7.4      94     141 ..      86     133 ..      77     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                      EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT CS
                                KR  2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealg 52
                                      t+ +tGG+G++G +++  l + g r +v +sRs+ ++e++++l a +++ g
  gi|313127560|ref|YP_004037830.1| 20 TVAVTGGTGKIGPTVVAALQSAGYR-VVNISRSGGETEADADLRADMTDAG 69
                                      788****************999975.7899***988887777666666554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0057
                                       ---TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH CS
                                KR  94 dklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagll 141
                                        ++l++ + +  + v+++    + n+ ++ e  ++d +vl SS++++ 
  gi|313127560|ref|YP_004037830.1|  86 LGMLSTPDHDPGHVVFESNAMSTYNVLQAAEALDVDTVVLASSLSAVG 133
                                       5667777788888999999999**********************9975 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   3.1   0.00052      0.66      61     132 ..      63     132 ..      21     135 .. 0.63
   2 ?    2.5   0.0     0.051        65     132     168 ..     154     189 ..     149     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00052
                                       --TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHH.HHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS CS
                   Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlKhVPlveenple.aiktNvlgtenvieaaieagvkkvvliStDKAv 132
                                       +d++d+ +   a+ + + d+++h   l    + ++ p + +++ N ++t nv++aa + +v++vvl S+  Av
  gi|313127560|ref|YP_004037830.1|  63 ADMTDAGEAYGAFATADADAIVHLGML---STPDHDPGHvVFESNAMSTYNVLQAAEALDVDTVVLASSLSAV 132
                                       567777777777887888888887654...33455555415689**********************9987666 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.051
                                       SS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE CS
                   Polysacc_synt_2 132 vnPtnvmGatKrlaekllqalakeseekktkfvvvRf 168
                                       v+P n +G+ K + e ++  +a+++ +   +++ +Rf
  gi|313127560|ref|YP_004037830.1| 154 VSPSNSYGMGKHVLEVTADGFAHRQ-NGPRTIASIRF 189
                                       89**************999998887.55666777777 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.3e-05     0.016       1      32 [.      21      52 ..      21      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt 32
                                      ++v+G+TG++G  vv+al +ag++v  + R  
  gi|313127560|ref|YP_004037830.1| 21 VAVTGGTGKIGPTVVAALQSAGYRVVNISRSG 52
                                      79***********************9888876 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.033        43       1      46 [.      23      66 ..      23      78 .. 0.79
   2 ?    9.5   0.0   0.00038      0.49      86     200 ..      78     184 ..      70     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.033
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT- CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeele 46
                                      +TG+TG +G  +++ L +     +++   R+  +++a + l++ ++
  gi|313127560|ref|YP_004037830.1| 23 VTGGTGKIGPTVVAALQSAGY--RVVNISRSGGETEADADLRADMT 66
                                      7************99966655..77777887777777777766665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00038
                                       HH--EEEE--SS-S.ST.TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..GGGTTS-TTT--SSS-H...... CS
                     NAD_binding_4  86 eevdviihsaAtvnfde.pykellrvNveGtrevlelakklkklkvllhvST..ayvngeregeveekvyeegekee 159
                                       +  d+i+h +   + d+ p +++++ N ++t +vl+ a++l    +++  S+  a+ +  + + ++           
  gi|313127560|ref|YP_004037830.1|  78 ADADAIVHLGMLSTPDHdPGHVVFESNAMSTYNVLQAAEALDVD-TVVLASSlsAVGASFEPEPIRL---------- 143
                                       56789999988777666478889****************99999.8889998867777777766633.......... PP

                                       HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEE CS
                     NAD_binding_4 160 kldederaklkglpntYeqsKalaEklvrearrrsglpvvi 200
                                           +++++  + +n Y   K++ E      ++r++ p +i
  gi|313127560|ref|YP_004037830.1| 144 SYLPLDESHPVSPSNSYGMGKHVLEVTADGFAHRQNGPRTI 184
                                       35567778888889999999999998888777777776555 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.9e-05     0.037       2      82 ..      21      98 ..      20     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                            LpxI_N  2 igliAGsGrlPllvaeaakaagrevvvvalegeadeelekivdevaevsvgqlgklikaLkregvtevvmaGkvekpkl 80
                                      +++  G G++   v++a+++ag++vv ++ +g    e e+  d+  +  +++ g++  a+  ++++ +v +G ++ p+ 
  gi|313127560|ref|YP_004037830.1| 21 VAVTGGTGKIGPTVVAALQSAGYRVVNISRSGG---ETEA--DADLRADMTDAGEAYGAFATADADAIVHLGMLSTPDH 94
                                      67788************************9993...3333..3346789***********************9988776 PP

                            LpxI_N 81 l..d 82
                                         +
  gi|313127560|ref|YP_004037830.1| 95 DpgH 98
                                      6544 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     5e-05     0.064      36      87 ..      18      70 ..       4      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-05
                                      TSEEEEE.S-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHH CS
                      2-Hacid_dh_C 36 gktvGii.GlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvslee 87
                                       +tv++  G+G+IG +v   l++ g +v+ ++rs  ++e++++l++++++  e
  gi|313127560|ref|YP_004037830.1| 18 TSTVAVTgGTGKIGPTVVAALQSAGYRVVNISRSGGETEADADLRADMTDAGE 70
                                      456666537*************************9988877777776666555 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   0.00015      0.19       2      88 ..      20     128 ..      19     143 .. 0.76
   2 ?   -2.8   0.0       6.6   8.5e+03      58      76 ..     224     242 ..     198     248 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                       -EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--..................... CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvd..................... 57 
                                       t+aV G    +gk g  v++ l+++g++vv +   ++e +      +l +d    d                     
  gi|313127560|ref|YP_004037830.1|  20 TVAVTG---GTGKIGPTVVAALQSAGYRVVNISRSGGETEADA---DLRAD--MTDageaygafatadadaivhlgm 88 
                                       688999...899***********************99987744...33322..111222334666666777778888 PP

                                       .........EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT CS
                     CoA_binding_2  58 .........lvdvftppeatpeivkealalgakavwlqpg 88 
                                                 v++  ++  t +++++a+al++ +v+l ++
  gi|313127560|ref|YP_004037830.1|  89 lstpdhdpgHVVFESNAMSTYNVLQAAEALDVDTVVLASS 128
                                       8888888889999999999999999999999998888765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.6
                                       EEEE-S-HHHHGGGHHHHH CS
                     CoA_binding_2  58 lvdvftppeatpeivkeal 76 
                                       +v+ ++ +e+++e+v+ a+
  gi|313127560|ref|YP_004037830.1| 224 TVFAYLSQEDAAELVRLAV 242
                                       5555555556666655554 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4    0.0001      0.13       2      39 ..      20      57 ..      19      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseeklee 39
                                      +v vtG+++ IG  ++ +l ++G++vv ++rs  + e+
  gi|313127560|ref|YP_004037830.1| 20 TVAVTGGTGKIGPTVVAALQSAGYRVVNISRSGGETEA 57
                                      799***************************99887743 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00017      0.22       3      44 ..      21      61 ..      19     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                      EEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBH CS
                            DapB_N  3 vavvGasGrmGkevvkaveeaedlelvaavdrkeselegkda 44
                                      vav+G +G++G +vv a+++ +++++v    + +++  + d+
  gi|313127560|ref|YP_004037830.1| 21 VAVTGGTGKIGPTVVAALQS-AGYRVVNISRSGGETEADADL 61
                                      9****************999.899999887777654444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1972.29
//
Query:       gi|313127561|ref|YP_004037831.1|  [L=224]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-53  179.9   0.0    4.2e-53  179.7   0.0    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.7   0.0   2.4e-57   4.2e-53       2     191 ..      11     221 ..      10     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 179.7 bits;  conditional E-value: 2.4e-57
                                       HHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S...... CS
                     DHBP_synthase   2 eaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene...... 72 
                                       +a++al+aG++++v+D +dre+e+d++++A +v+p++va ++++a+Gl+cval++e+ +eL+Lp++           
  gi|313127561|ref|YP_004037831.1|  11 SALSALSAGEPILVHDFDDREGETDVVYPAGAVEPADVARLRNDAGGLVCVALSHEVSEELGLPFLDG--Vidhpta 85 
                                       689**************************************************************985..2335567 PP

                                       ......STT---BB--EEESST-SSS-SHHHHHHHHHHHH-T...........T--GGGEEEEEEEEEEEE-TTGGG CS
                     DHBP_synthase  73 ......dkhktaftvsvdaaegttTGIsaaDRalTirkladp...........kakpedfrrPGhvfplrareggvl 132
                                                +++f++ v+++ +t+TGI+++DRalTi++l ++           +  +++fr+PGhv +lr +++ + 
  gi|313127561|ref|YP_004037831.1|  86 adhelaYDDRSSFSLPVNHR-DTFTGITDEDRALTITELSAAaervpdgdygaDDFAAEFRSPGHVNLLRGAPNLLS 161
                                       7777774557**********.9*****************9966899999999855789******************* PP

                                       TS-SHHHHHHHHHHHTTS-SBEEEEEBB-TT.SCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                     DHBP_synthase 133 eRrghTEaavdLarlaglkpaavicellndd.gtmarrdeleefakkhglkiitiedlie 191
                                       +R+ghTE++++La  a+l+ a v+ce+l+d+ gt+++ + + ++a++h+l ++++ d++e
  gi|313127561|ref|YP_004037831.1| 162 DRQGHTELGLALAAEADLPAAVVVCEMLDDEsGTALSPAAALDYANRHDLVYVEGMDVVE 221
                                       ******************9988*******99899**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1691.49
//
Query:       gi|313127562|ref|YP_004037832.1|  [L=235]
Description: CTP-dependent riboflavin kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-47  158.1   0.0    1.3e-46  157.6   0.0    1.2  1  CTP-dep_RFKase  Domain of unknown function DUF120
    3.5e-06   26.8   0.1    6.9e-06   25.9   0.1    1.5  1  MarR_2          MarR family
    5.8e-06   26.3   0.0      1e-05   25.5   0.0    1.5  1  HTH_20          Helix-turn-helix domain
    0.00013   22.1   0.0    0.00024   21.2   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00015   21.3   0.0    0.00024   20.6   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0083   16.1   0.0      0.017   15.1   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.025   14.5   0.0    1.3  1  MarR            MarR family
      0.015   15.7   0.0      0.029   14.9   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
      0.017   15.1   0.0      0.028   14.4   0.0    1.4  1  HTH_11          HTH domain
      0.053   13.3   1.5      0.055   13.3   0.2    1.7  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.059   13.6   0.0       0.16   12.2   0.0    1.6  2  HTH_34          Winged helix DNA-binding domain
      0.061   13.1   0.0      0.093   12.5   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
       0.16   11.7   0.1       0.57   10.0   0.0    1.9  2  HTH_DeoR        DeoR-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.6   0.0   9.4e-50   1.3e-46       1     121 []     107     232 ..     107     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: 157.6 bits;  conditional E-value: 9.4e-50
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       V+sG+geG++y+sl+gy+eqfe++lg+ep+ GTLNv+ldees+++r+a+++l++++i+g+ede+rtfg +++y a++
  gi|313127562|ref|YP_004037832.1| 107 VTSGMGEGRHYISLPGYMEQFEDRLGYEPFAGTLNVELDEESVRTRAAMASLDAVPIDGWEDEDRTFGPATCYAATV 183
                                       89*************************************************************************** PP

                                       CCE.....EEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                    CTP-dep_RFKase  78 eki.....kaavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                       ++      + +++vperth++e+  EiiapekLR++l+l+dgdev++ v
  gi|313127562|ref|YP_004037832.1| 184 RHDgeafdTSHIIVPERTHHDESKAEIIAPEKLRDELDLDDGDEVTIVV 232
                                       75533334555***********************************976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1     5e-09   6.9e-06       7      53 ..      13      63 ..       6      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5e-09
                                      HHHHHHHHHCTTTS....EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  7 qarvLaaLgrrpgr....dltvgelarrlglsksavsrilkrLvaaGLver 53
                                      ++ +L +++ ++gr    +++ + la+rl+ s +++sr+l+rL +aG+v r
  gi|313127562|ref|YP_004037832.1| 13 ELAALKFVALEGGRtgpvKVSCSGLADRLDASAQTASRRLQRLDEAGYVDR 63
                                      56678888888999998999*****************************87 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   7.6e-09     1e-05      20      57 ..      27      64 ..      11      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.6e-09
                                      STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 20 araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +++  +++s la+rld s +t+s++L+ L eag+v++ 
  gi|313127562|ref|YP_004037832.1| 27 TGPVKVSCSGLADRLDASAQTASRRLQRLDEAGYVDRD 64
                                      567789*****************************986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.7e-07   0.00024      22      53 ..      31      62 ..      26      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.7e-07
                                      SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 22 vvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      +v+ + la rL+ s+ ++s  l++L+++Gyv+
  gi|313127562|ref|YP_004037832.1| 31 KVSCSGLADRLDASAQTASRRLQRLDEAGYVD 62
                                      688899*************************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.7e-07   0.00024      19      47 ..      33      61 ..      31      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-07
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      s + LA+rl+ S +t +rrl+rL e+G++
  gi|313127562|ref|YP_004037832.1| 33 SCSGLADRLDASAQTASRRLQRLDEAGYV 61
                                      6777************************8 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.017      21      53 ..      31      63 ..      14      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisr 53
                                      +++   lA++l ++ +t sr l++L ++g+++r
  gi|313127562|ref|YP_004037832.1| 31 KVSCSGLADRLDASAQTASRRLQRLDEAGYVDR 63
                                      5666779***********************995 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.8e-05     0.025      16      49 ..      28      63 ..      25      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                      TTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 16 gplsvs..eLakklgvskstvtrvldrLekkGlieR 49
                                      gp +vs   La++l  s  t++r l rL ++G+++R
  gi|313127562|ref|YP_004037832.1| 28 GPVKVScsGLADRLDASAQTASRRLQRLDEAGYVDR 63
                                      666676769*************************99 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.1e-05     0.029      22      50 ..      35      63 ..       9      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                            HTH_27 22 adlcgrlnvedshisyslkkLtekGLver 50
                                      + l++rl+ +++++s  l +L e+G+v r
  gi|313127562|ref|YP_004037832.1| 35 SGLADRLDASAQTASRRLQRLDEAGYVDR 63
                                      7899***********************44 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     2e-05     0.028      16      44 ..      32      60 ..      26      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                            HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      +s + LA++L+ S +t  r++++L e+g+
  gi|313127562|ref|YP_004037832.1| 32 VSCSGLADRLDASAQTASRRLQRLDEAGY 60
                                      89999**********************94 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2     4e-05     0.055      19      41 ..      33      55 ..      30      56 .. 0.91
   2 ?   -3.5   0.1       6.9   9.5e+03      27      37 ..     142     152 ..     142     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                     HTH_AsnC-type 19 syaeLAervGlSestvlrRvrrL 41
                                      s++ LA+r+  S++t+ rR++rL
  gi|313127562|ref|YP_004037832.1| 33 SCSGLADRLDASAQTASRRLQRL 55
                                      66779*****************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.9
                     HTH_AsnC-type  27 vGlSestvlrR 37 
                                       v l+e+ v+ R
  gi|313127562|ref|YP_004037832.1| 142 VELDEESVRTR 152
                                       57889999988 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.16      18      71 ..      35      84 ..      30      90 .. 0.87
   2 ?   -2.9   0.0         6   8.2e+03      16      29 ..     212     225 ..     207     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                            HTH_34 18 velkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71
                                      + l + l a++   s  l+ L +agY+ +d   +g+    ++ iT++G  a   
  gi|313127562|ref|YP_004037832.1| 35 SGLADRLDASAQTASRRLQRLDEAGYVDRDVVSDGQ----WVAITEDGEVALHH 84
                                      66778899999999******************9999....9*******988765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6
                            HTH_34  16 dfvelkealeatdg 29 
                                        +++l+++l + dg
  gi|313127562|ref|YP_004037832.1| 212 APEKLRDELDLDDG 225
                                       57899999999998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.7e-05     0.093      19      51 ..      32      64 ..      14      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-05
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      ++ s lA+r++ +  t++R Lq L e Gyv +d
  gi|313127562|ref|YP_004037832.1| 32 VSCSGLADRLDASAQTASRRLQRLDEAGYVDRD 64
                                      566789************************998 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00041      0.57      14      46 ..      31      63 ..      30      64 .. 0.91
   2 ?   -2.6   0.0       3.4   4.7e+03      29      34 ..     181     186 ..     180     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                          HTH_DeoR 14 klsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      k+s   l+++l+ S +T+ R L+ L+e+g + R
  gi|313127562|ref|YP_004037832.1| 31 KVSCSGLADRLDASAQTASRRLQRLDEAGYVDR 63
                                      5777889**********************9877 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.4
                          HTH_DeoR  29 aTiRRD 34 
                                       aT+R D
  gi|313127562|ref|YP_004037832.1| 181 ATVRHD 186
                                       799988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1666.26
//
Query:       gi|313127563|ref|YP_004037833.1|  [L=53]
Description: hypothetical protein Hbor_28470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       138  (0.00769703); expected 358.6 (0.02)
Passed bias filter:                      129  (0.00719505); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 415.68
//
Query:       gi|313127564|ref|YP_004037834.1|  [L=584]
Description: arginyl-tRNA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-41  140.1   0.1    1.1e-40  139.6   0.1    1.1  1  tRNA-synt_1d     tRNA synthetases class I (R)
    4.3e-37  126.9   0.2    1.2e-36  125.5   0.2    1.8  1  DALR_1           DALR anticodon binding domain
    5.7e-11   42.8   0.0    1.8e-10   41.3   0.0    1.8  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
     0.0037   16.2   0.0      0.073   12.0   0.0    2.2  2  tRNA-synt_1f     tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   0.1   2.5e-44   1.1e-40      17     349 .]     111     453 ..     100     453 .. 0.83

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 2.5e-44
                                       SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS--- CS
                      tRNA-synt_1d  17 rekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqe 93 
                                       +  k vv++++s n   ++hvG  r  i+Gda++r+lef+G dv r  +v D G+q  ++   +e  +de  l e+e
  gi|313127564|ref|YP_004037834.1| 111 ETGKDVVIEHTSANPTGPVHVGRARNPILGDAIARVLEFAGNDVDRHYYVNDAGRQVAVFTWAYET-FDESELPEPE 186
                                       55699****************************************************998766655.5555555555 PP

                                       --....SCCCHHHHHHH...HCCCSHCCCHHH..HHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC. CS
                      tRNA-synt_1d  94 lq....dLeafykeakk...dydeeeifaera..rnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie. 160
                                        +    dL  +y++ +    d de+e+ a +a   ++++ L++gde++ +    +vd +   +++  +rl  +  e 
  gi|313127564|ref|YP_004037834.1| 187 RDrsdyDLVRYYRKGNAyleDADEDEVEAAEAeiAEIMQGLEAGDEETYERVAVVVDQVLGGMRESLERLPAFFDEf 263
                                       43223389******9972225577888666552268999********888888888887777777777777776665 PP

                                       --CC..CCCCCHHHHHHHHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEE CS
                      tRNA-synt_1d 161 rGes..lykeslneivkelkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvl 235
                                         e+  + +   +++v+ lk+ ++++ ++ a  ++l+efg +  +v  +sDG++lytt+D+a    +    + d+++
  gi|313127564|ref|YP_004037834.1| 264 IKETkfIRNGDADDVVERLKDSEYAVYEEDAWQLDLSEFGFEKNLVFLRSDGTTLYTTRDLAHHEWKF--NNYDEAV 338
                                       34444489999**************************************************9766554..46899** PP

                                       EEEECCCHHHHHHHHHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCC CS
                      tRNA-synt_1d 236 yvidsrqslhlqqiflilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkd 312
                                        v+ +  +l  +q+ ++l  +g   ++ +l+ + +  v    + +++trkG  v L+dlLde+++ra++ ++e+   
  gi|313127564|ref|YP_004037834.1| 339 TVLGEDHKLQAEQLDAALEILGN--DTDQLRQTFYSWV-NLPEGGMSTRKGTGVDLDDLLDESVKRAREEVEERLDS 412
                                       **********************9..6667777777766.667889****************************9888 PP

                                       TS....-CCCCHCHHHHHHHHHHHHCCCCTS-TTS-EE--H CS
                      tRNA-synt_1d 313 kv....lqadelekvaeavgvgaikyaDlsknrindyifdw 349
                                       ++    l  ++ e++a  vg+ga++y  +sk+ ++   f+w
  gi|313127564|ref|YP_004037834.1| 413 RIrdddLDEEDIERIARQVGIGAVRYDIVSKQPTKGITFEW 453
                                       8733335567899*******************999999999 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.5   0.2   2.7e-40   1.2e-36       1     119 []     467     584 .]     467     584 .] 0.99

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 2.7e-40
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn 77 
                                       vqy haR++ il++a ++g+++++e ++l ++e+e eLl+ +a+fp v+e+aa++leph++a+y+ e a+tf++fY+
  gi|313127564|ref|YP_004037834.1| 467 VQYVHARCCGILNEASAAGIEAATEMSLL-DTEAEQELLRVIARFPAVVEQAADDLEPHVVATYVREFAETFNTFYR 542
                                       8********************99999988.*********************************************** PP

                                       HCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  78 kervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                       +++vl++++++ aaaRL Lv+a+++++an+L +LGieape m
  gi|313127564|ref|YP_004037834.1| 543 ECSVLNADDDDIAAARLGLVEAAQHTVANALYMLGIEAPESM 584
                                       ****************************************99 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0     4e-14   1.8e-10       2      84 ..       8      88 ..       6      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 4e-14
                                      HHHHHHHHHHHHHHSS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEEETT CS
                   Arg_tRNA_synt_N  2 elkeaiaealkkaagadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvevagp 78
                                      e+++a+++al+++   dl  +++ +e+p++   + +a+ va+++a++++ +P ++A++ia++++++++   e++e +gp
  gi|313127564|ref|YP_004037834.1|  8 EVEDAVEAALSSL---DLPTDDLGVEEPPEDVPATLASSVAFRMASEVGAPPPKVAADIADAIDATPYtyLERAEPQGP 83
                                      68999********...688889********************************************9999********* PP

                                      .EEEEE CS
                   Arg_tRNA_synt_N 79 GFiNff 84
                                       ++Nff
  gi|313127564|ref|YP_004037834.1| 84 -YVNFF 88
                                      .****9 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   1.6e-05     0.073      21      70 ..     113     162 ..      96     169 .. 0.85
   2 ?    1.7   0.0     0.022        97     240     297 ..     341     396 ..     328     401 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                      tRNA-synt_1f  21 ekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70 
                                       +kd v+  + + p G++H+G++r+ + +d++ar l+  g++v+  ++++d
  gi|313127564|ref|YP_004037834.1| 113 GKDVVIEHTSANPTGPVHVGRARNPILGDAIARVLEFAGNDVDRHYYVND 162
                                       67778888999***************************999766555555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.022
                      tRNA-synt_1f 240 aGkDhaaaGgSvdvsskiaeilgge..aPekvvYelillkggekmssSkGnvltledwle 297
                                        G Dh      +++ ++  eilg    +  +  Y ++ l +g  ms  kG+++ l+d+l+
  gi|313127564|ref|YP_004037834.1| 341 LGEDHKL---QAEQLDAALEILGNDtdQLRQTFYSWVNLPEG-GMSTRKGTGVDLDDLLD 396
                                       5666666...44455555566665411456889******999.8***********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4000.29
//
Query:       gi|313127565|ref|YP_004037835.1|  [L=483]
Description: chromosome partitioning ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-18   66.4   0.2    3.8e-18   65.8   0.2    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    8.9e-17   61.3   5.5    5.1e-11   42.5   1.9    3.0  2  ParA         NUBPL iron-transfer P-loop NTPase
    1.8e-16   60.6   0.0    2.9e-16   59.9   0.0    1.3  1  AAA_31       AAA domain
    6.1e-10   39.0   0.0    0.00041   19.9   0.0    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    1.5e-05   24.4   1.3    6.5e-05   22.4   1.2    1.9  1  MipZ         ATPase MipZ
    2.2e-05   24.1   1.5    0.00038   20.0   1.5    2.6  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    8.6e-05   22.4   2.8      0.018   14.8   0.0    2.5  2  AAA_26       AAA domain
     0.0021   17.3   3.0     0.0046   16.2   3.0    1.5  1  ArsA_ATPase  Anion-transporting ATPase
     0.0024   17.2   1.8     0.0053   16.1   0.7    1.9  2  VirC1        VirC1 protein
     0.0052   16.6   0.1     0.0089   15.8   0.1    1.3  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
     0.0066   16.1   2.6      0.073   12.7   0.8    2.5  2  SRP54        SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.024   14.2   1.9      0.051   13.2   0.6    2.2  2  AAA_25       AAA domain
       0.14   12.0   0.1       0.26   11.2   0.1    1.3  1  APS_kinase   Adenylylsulphate kinase


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.2   2.8e-21   3.8e-18       2     127 ..      17     220 ..      16     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.8e-21
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       a++s kGGvGKTt+++nLa+ala  g +V++vD D  + nla   g+ +                            
  gi|313127565|ref|YP_004037835.1|  17 AVVSAKGGVGKTTTTTNLAAALAASGADVAVVDGDLGMANLA---GSLGVDSSgatlhdvlageaeleaatrggphg 90 
                                       89**************************************99...555555556669******************** PP

                                       .....................................................................CCHCCCHH CS
                                       .....................................................................xxxxxxxx RF
                              CbiA  55 .....................................................................dlkrllel 62 
                                                                                                            d ++  ++
  gi|313127565|ref|YP_004037835.1|  91 mtvvpgsadldafaradpeglhdvlsalrenhdyvlldtgaglsndtvvpltyvdeillvsttgrdalgDTEKTRQV 167
                                       ************************************************************99988888888887777 PP

                                       HHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  63 lealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                       +++l+        +ag v++rvd++   + +++a+e ++      vl +ipr + v  a   gep
  gi|313127565|ref|YP_004037835.1| 168 AARLDV------PVAGAVITRVDPD---NPQQSAVESTL---DATVLSSIPRADVVRNAGDAGEP 220
                                       788885......59**********9...55677788887...99*********999999888887 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   1.9   3.7e-14   5.1e-11       4      55 ..      14      65 ..      11      82 .. 0.88
   2 !   17.2   0.1   1.9e-06    0.0026     111     245 ..     121     241 ..     112     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3.7e-14
                              ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee 55
                                      +v+av+S+KGGVGK+t+++nlA+aLa++g++v+++D D+   +++  lgv++
  gi|313127565|ref|YP_004037835.1| 14 RVYAVVSAKGGVGKTTTTTNLAAALAASGADVAVVDGDLGMANLAGSLGVDS 65
                                      799***********************************98777777777766 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.9e-06
                              ParA 111 elDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekte 187
                                       + Dy+++D+  G +    tv+    ++++++V+t  + al d++k+ +++ +++v+v G v      v p+      
  gi|313127565|ref|YP_004037835.1| 121 NHDYVLLDTGAGLSND--TVVPLTYVDEILLVSTTGRDALGDTEKTRQVAARLDVPVAGAVIT---RVDPDNP---- 188
                                       579999**97776655..677777889********************************9843...4445433.... PP

                              ParA 188 ifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                            + +++ ++l++++l++ip    +r+a+d+g+pl++ +p s+aa a++++a+++
  gi|313127565|ref|YP_004037835.1| 189 -----QQSAVESTLDATVLSSIPRADVVRNAGDAGEPLTTYAPGSSAAAAYRALAADL 241
                                       .....34567889999***********************************9998765 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   2.1e-19   2.9e-16       2     149 ..      14     153 ..      13     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2.1e-19
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp.Qanattglgiekneiektlyevlieeknikeaiiktk 77 
                                       +v a++  KGGvGKTTt++nlaaala +g  v +vD D   an++ +lg++++    tl++vl+ e++++ a     
  gi|313127565|ref|YP_004037835.1|  14 RVYAVVSAKGGVGKTTTTTNLAAALAASGADVAVVDGDLgMANLAGSLGVDSS--GATLHDVLAGEAELEAATR-GG 87 
                                       7889**********************************725899999998655..57************99998.45 PP

                            AAA_31  78 venldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqa 149
                                        + ++++p+s dL ++           e l+++l+++++++Dy+++D+   L+  t+  L+  d+++ +  +
  gi|313127565|ref|YP_004037835.1|  88 PHGMTVVPGSADLDAFAR------ADPEGLHDVLSALRENHDYVLLDTGAGLSNDTVVPLTYVDEILLVSTT 153
                                       6889********977543......3456678*********************************99988766 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   2.3e-06    0.0031       5      37 ..      19      51 ..      15      61 .. 0.89
   2 !   19.9   0.0     3e-07   0.00041     116     247 ..     122     244 ..      62     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.3e-06
                         Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                      +  kGG+Gk+tt++nl+aala+ g  v +v  D
  gi|313127565|ref|YP_004037835.1| 19 VSAKGGVGKTTTTTNLAAALAASGADVAVVDGD 51
                                      567*********************999988655 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3e-07
                         Fer4_NifH 116 lDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelmalyaanniakgiekyaksggvrlgGliinsrkvdderel 192
                                        D+vl+D  G        +P+   + +e+++v++++ +al    +     ++ a + +v ++G +i  r vd ++  
  gi|313127565|ref|YP_004037835.1| 122 HDYVLLDT-GAGLSNDTVVPLT--YVDEILLVSTTGRDALGDTEK----TRQVAARLDVPVAGAVIT-R-VDPDNPQ 189
                                       67777775.5566666777887..888888888888888866544....567888899********9.6.9999999 PP

                         Fer4_NifH 193 iekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                        ++  ++l+  vl  +Pr ++vr+a  + + ++ yap s+ a  yr+la +++ +
  gi|313127565|ref|YP_004037835.1| 190 QSAVESTLDATVLSSIPRADVVRNAGDAGEPLTTYAPGSSAAAAYRALAADLTGE 244
                                       9999*********************************************988755 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.2   4.7e-08   6.5e-05       5     112 ..      18     134 ..      14     150 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.7e-08
                                       E--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHH.....T------E......EE-S CS
                              MipZ   5 lgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerk.....glsLplpe......alal 70 
                                       +   kGG Gk+tt+  +a aL+++Ga va++d dl  + la  l+  +  a+ +     + +L+ ++      ++++
  gi|313127565|ref|YP_004037835.1|  18 VVSAKGGVGKTTTTTNLAAALAASGADVAVVDGDLGMANLAGSLGVDSSGATLHdvlagEAELEAATrggphgMTVV 94 
                                       4567******************************9999888877655544333300111334443321111112344 PP

                                       SS-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS-- CS
                              MipZ  71 seaeeaeveeeeeaevaeleelvadleaeldfividtPGsds 112
                                       + ++  ++   ++ e   l++++++l +++d++++dt    s
  gi|313127565|ref|YP_004037835.1|  95 PGSADLDAFARADPE--GLHDVLSALRENHDYVLLDTGAGLS 134
                                       444444555555444..8999999999999999999876555 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.5   2.7e-07   0.00038       9     149 ..      21     155 ..      14     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.7e-07
                          CBP_BcsQ   9 vRGGvGttsllaaLawalhelgesvlviD..lspdnlLrlhFnvdieqregwaraeldgapwrqaaleyapgldllP 83 
                                        +GGvG+t+ ++ La al + g  v v+D  l  +n L+ +  vd ++ +++   ++ +a++++a+    +g++++P
  gi|313127565|ref|YP_004037835.1|  21 AKGGVGKTTTTTNLAAALAASGADVAVVDgdLGMAN-LAGSLGVD-SSGATLHDVLAGEAELEAATRGGPHGMTVVP 95 
                                       68**************************83245555.55677777.5667788888888888888777777888888 PP

                          CBP_BcsQ  84 fGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepda 149
                                        G++  +        ++++e l + l++l+e+++++llD  ag s+ t   l+  d  llv ++  
  gi|313127565|ref|YP_004037835.1|  96 -GSADLDAF-----ARADPEGLHDVLSALRENHDYVLLDTGAGLSNDTVVPLTYVDEILLVSTTGR 155
                                       .55554444.....47899***********************999999988888999998877644 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.9    0.0037       5.1       4      34 ..      17      47 ..      14      48 .. 0.87
   2 !   14.8   0.0   1.3e-05     0.018     130     196 ..     146     213 ..     106     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0037
                            AAA_26  4 fvtgtdtgvGKTvvslgLvralkrkgvkvgy 34
                                       v++   gvGKT++++ L++al + g+ v++
  gi|313127565|ref|YP_004037835.1| 17 AVVSAKGGVGKTTTTTNLAAALAASGADVAV 47
                                      5899999***************999988876 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.3e-05
                            AAA_26 130 pvilVargglgtinqllltiealrqknvrvlGvilNkvrnpe.nvetlekksgipvlGvvPylpdlea 196
                                       +++lV ++g++++ ++  t +++ + +v+v+G ++ +v +++ +  ++e++   +vl ++P  + +++
  gi|313127565|ref|YP_004037835.1| 146 EILLVSTTGRDALGDTEKTRQVAARLDVPVAGAVITRVDPDNpQQSAVESTLDATVLSSIPRADVVRN 213
                                       79***********************9***********86665466778888999*******9887765 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   3.0   3.3e-06    0.0046       5      38 ..      18      51 ..      15      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.3e-06
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +v+ KGGVGKtt  + +a+ l+ +g +v ++  D
  gi|313127565|ref|YP_004037835.1| 18 VVSAKGGVGKTTTTTNLAAALAASGADVAVVDGD 51
                                      7899************************999877 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.7   3.8e-06    0.0053       5      39 ..      17      51 ..      14      55 .. 0.93
   2 ?   -1.1   0.0      0.67   9.2e+02      82     103 ..     120     139 ..     115     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.8e-06
                             VirC1  5 tfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                      +++s kGG Gktt+   l +ala+ g  va+ ++d
  gi|313127565|ref|YP_004037835.1| 17 AVVSAKGGVGKTTTTTNLAAALAASGADVAVVDGD 51
                                      57899***************************998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.67
                             VirC1  82 eGfdyaladtrgGsselnntii 103
                                       e +dy+l dt  G s+  +t++
  gi|313127565|ref|YP_004037835.1| 120 ENHDYVLLDTGAGLSN--DTVV 139
                                       5678999999888884..4443 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   6.5e-06    0.0089       4      37 ..      24      57 ..      22      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.5e-06
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvGqsei 37
                                       +GK+T +++L+  ++ +g  +++vD D+G  ++
  gi|313127565|ref|YP_004037835.1| 24 GVGKTTTTTNLAAALAASGADVAVVDGDLGMANL 57
                                      59****************************9886 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.8   5.3e-05     0.073      10      38 ..      23      51 ..      14      56 .. 0.86
   2 ?    2.1   0.0     0.093   1.3e+02      80     151 ..     118     184 ..     111     194 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.3e-05
                                      TTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54 10 qGaGKTttlaKLaallkkegkkvllvaaD 38
                                       G+GKTtt++ Laa l ++g +v++v  D
  gi|313127565|ref|YP_004037835.1| 23 GGVGKTTTTTNLAAALAASGADVAVVDGD 51
                                      48***********************9888 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.093
                                       HHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHH.....HSSCSEEEEESTT CS
                             SRP54  80 keekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFke.....avgitgviltklD 151
                                        +e++d+vl+DT   l nd+        +   +  de+llv  +ttg++a+  +++ ++      v ++g+++t++D
  gi|313127565|ref|YP_004037835.1| 118 LRENHDYVLLDTGAGLSNDT--------VVPLTYVDEILLV--STTGRDALGDTEKTRQvaarlDVPVAGAVITRVD 184
                                       56678888888855555553........2233333444444..2333333332222222000003456677777776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   3.7e-05     0.051      36      61 ..      17      43 ..       9      57 .. 0.87
   2 ?   -1.9   0.0       1.6   2.2e+03      85     137 ..     110     171 ..     104     180 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                            AAA_25 36 allaGapgtGKttlaldlalava.tGk 61
                                      a++ + +g+GKtt +++la+a+a +G 
  gi|313127565|ref|YP_004037835.1| 17 AVVSAKGGVGKTTTTTNLAAALAaSGA 43
                                      7899******************97775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                            AAA_25  85 elrrRlravgeal...........rddarllvldlagveslpLfakdrggtl.ltadvdaleaai 137
                                       +l+  l+a++e++           + d  +++++   v+++ L++++ +++l  t+++++++a++
  gi|313127565|ref|YP_004037835.1| 110 GLHDVLSALRENHdyvlldtgaglSNDTVVPLTY---VDEILLVSTTGRDALgDTEKTRQVAARL 171
                                       6777777777666556666665433333333333...3457777777777776677777777665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00019      0.26      11      53 ..      23      65 ..      15      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                      TTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSH CS
                        APS_kinase 11 sgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfse 53
                                       g GK+t +++l+ +L ++g  v ++dGd    +L   Lg ++
  gi|313127565|ref|YP_004037835.1| 23 GGVGKTTTTTNLAAALAASGADVAVVDGDLGMANLAGSLGVDS 65
                                      689**************************99999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.88u 0.30s 00:00:01.18 Elapsed: 00:00:00.46
# Mc/sec: 3152.64
//
Query:       gi|313127566|ref|YP_004037836.1|  [L=416]
Description: peptide chain release factor 1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-41  141.3   0.0    4.8e-41  140.2   0.0    1.6  1  eRF1_2          eRF1 domain 2
    6.8e-28   97.4   0.0    2.7e-27   95.5   0.1    2.0  2  eRF1_3          eRF1 domain 3
    4.6e-18   65.8   0.2    1.3e-17   64.3   0.1    1.7  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    2.1e-14   54.0   0.2    1.2e-13   51.5   0.0    2.3  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    2.1e-11   43.9   0.0    3.2e-11   43.3   0.0    1.3  1  eRF1_1          eRF1 domain 1
  ------ inclusion threshold ------
       0.02   15.0   1.9       0.02   15.0   1.9    1.8  2  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.2   0.0   1.6e-44   4.8e-41       2     133 .]     148     278 ..     147     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 1.6e-44
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       +glivld++eA++g+l+g+r+e +k+ ++ vP+K+++Ggqsa+rf+Rlr e++++f+++va +an+ f+  +++++ 
  gi|313127566|ref|YP_004037836.1| 148 FGLIVLDRREANVGWLRGKRVEPVKSASSLVPGKQRKGGQSAQRFARLRLEAIDNFYQEVAGMANDLFV-PERHEMG 223
                                       79*******************************************************************.59***** PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                       gi+++gp+++k+efld+d+l++el + v+  +dvsy++esgl +++++a+evl+d
  gi|313127566|ref|YP_004037836.1| 224 GILVGGPSPTKDEFLDGDYLHHELGDLVVGKFDVSYTDESGLYDLVDAAQEVLAD 278
                                       ****************************************************987 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.8   5.3e+03      70      98 ..     199     226 ..     150     229 .. 0.62
   2 !   95.5   0.1   8.9e-31   2.7e-27       1     112 [.     281     413 ..     281     414 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHTT-EEEEE-TTSHHHHHH CS
                            eRF1_3  70 lieelvenveesgakveiisseseeGeql 98 
                                       +i++++++v  +  ++ ++++++e G  l
  gi|313127566|ref|YP_004037836.1| 199 AIDNFYQEVAGMANDL-FVPERHEMGGIL 226
                                       5555555555554444.667777777665 PP

  == domain 2  score: 95.5 bits;  conditional E-value: 8.9e-31
                                       HHHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS................... CS
                            eRF1_3   1 liqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv................... 58 
                                       ++++k+ +eef+e+l ++ ++a+YG+  ++k l mg+v++LL+se+l+++ +++ ++                    
  gi|313127566|ref|YP_004037836.1| 281 VMKDKSQMEEFFEKLHTG-EQATYGFGPTRKNLIMGSVDRLLLSEDLRSDVVVYECPNgheeyevvdrrhgdpghdc 356
                                       5899************99.9******************************988888889****************** PP

                                       -HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                            eRF1_3  59 ketgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                       +e+gee+e+ +   +ie+l+e +e+ g++ ++is+++e+Geql++afgG+a+iLRy+
  gi|313127566|ref|YP_004037836.1| 357 TECGEEAEKTDredVIEHLMEIAEQRGTETKFISTDFEKGEQLYDAFGGVAGILRYS 413
                                       *********9999*******************************************7 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0         6   1.8e+04      80      94 ..     105     119 ..     100     126 .. 0.79
   2 !   64.3   0.1   4.2e-21   1.3e-17       4     118 ..     150     277 ..     148     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 6
                           acVLRF1  80 gGdrslvaevledar 94 
                                       gG+  +v +vl+++ 
  gi|313127566|ref|YP_004037836.1| 105 GGQTDMVTRVLDSPP 119
                                       788999999988865 PP

  == domain 2  score: 64.3 bits;  conditional E-value: 4.2e-21
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...v 77 
                                       +++l+rr +  vg ++g++++ +k  ++ v g+ ++GG+S qRfaR r + +d+ +++va+ a++l+ +e++e   +
  gi|313127566|ref|YP_004037836.1| 150 LIVLDRREA-NVGWLRGKRVEPVKSASSLVPGKQRKGGQSAQRFARLRLEAIDNFYQEVAGMANDLFVPERHEmggI 225
                                       589******.*********************************************************9999999*** PP

                           acVLRF1  78 vlgGdrslvaevledarlap...........latlareelldvpdprravLe 118
                                       ++gG+  + +e+l+   l++           ++   +  l+d+ d+ ++vL+
  gi|313127566|ref|YP_004037836.1| 226 LVGGPSPTKDEFLDGDYLHHelgdlvvgkfdVSYTDESGLYDLVDAAQEVLA 277
                                       ***************8766654444444443333333355555555555555 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   3.9e-17   1.2e-13       4     126 ..     136     261 ..     134     277 .. 0.89
   2 ?   -1.1   0.1      0.67     2e+03      69      91 ..     364     386 ..     338     403 .. 0.71

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 3.9e-17
                    baeRF_family10   4 apLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAell 80 
                                       +pL + l +   +g++++dr++a +   ++ ++e v+ +++ vpg++++gg+ s +rf+r + e ++ +++evA ++
  gi|313127566|ref|YP_004037836.1| 136 QPLEDMLSDKGLFGLIVLDRREANVGWLRGKRVEPVKSASSLVPGKQRKGGQ-SAQRFARLRLEAIDNFYQEVAGMA 211
                                       79**************************************************.************************ PP

                    baeRF_family10  81 aklleerg..verlvlgGdeeetaalld..rlpkalrarvvgtlplpvda 126
                                       ++l+ +++  +  +++gG+   ++++ld   l+ +l ++vvg+++++ ++
  gi|313127566|ref|YP_004037836.1| 212 NDLFVPERheMGGILVGGPSPTKDEFLDgdYLHHELGDLVVGKFDVSYTD 261
                                       ***9654434999******999999986337************9998855 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.67
                    baeRF_family10  69 aerhlkevAellaklleergver 91 
                                        +   ++v e+l++++e+rg+e 
  gi|313127566|ref|YP_004037836.1| 364 EKTDREDVIEHLMEIAEQRGTET 386
                                       44555677778888888877665 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   1.1e-14   3.2e-11       2     128 ..      19     141 ..      18     142 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.1e-14
                                       EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECT CS
                            eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdk 76 
                                       k++++  d+e++g+++vt++++dd++++++   +++++s ++++++k +r         ++v+ +Lt+   +++++ 
  gi|313127566|ref|YP_004037836.1|  19 KVIEEldDYEGSGTQLVTIYIPDDKQISDVVAHVTQEHSEASNIKSKQTR---------TNVQDALTSIKDRLRYYD 86 
                                       88888889***************************************999.........9**************999 PP

                                       T....SSEEEEEEEEEEGGGG--TTSEEEEEE-.TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  77 d....agvlrisGkvieenehvklgafhtldle.lkrpftiikee.wdsfalerLkea 128
                                       +    +g++ +sG v ++ +   ++ ++t  l+ +++p++ ++++ +++f +++L+++
  gi|313127566|ref|YP_004037836.1|  87 TfppdNGIVIFSGAVNSGGG---QTDMVTRVLDsPPEPIQSFRYHcDSNFLTQPLEDM 141
                                       88999***************...899******8789*******999999******987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1         5   1.5e+04       4      10 ..     125     131 ..     125     132 .. 0.76
   2 ?   15.0   1.9   6.6e-06      0.02       6      38 ..     333     365 ..     332     366 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5
                       Zn-ribbon_8   4 YeYrCee 10 
                                       + Y+C++
  gi|313127566|ref|YP_004037836.1| 125 FRYHCDS 131
                                       5799975 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.6e-06
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsevrr 38 
                                       Y+C + ++e+ev+ + + +p  +C eCg+e+++
  gi|313127566|ref|YP_004037836.1| 333 YECPNGHEEYEVVDRRHGDPGHDCTECGEEAEK 365
                                       9*************999778888******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      869  (0.048469); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2390.56
//
Query:       gi|313127567|ref|YP_004037837.1|  [L=83]
Description: hypothetical protein Hbor_28510 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 537.33
//
Query:       gi|313127568|ref|YP_004037838.1|  [L=261]
Description: hypothetical protein Hbor_28520 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1958.09
//
Query:       gi|313127569|ref|YP_004037839.1|  [L=131]
Description: hypothetical protein Hbor_28530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 990.81
//
Query:       gi|313127570|ref|YP_004037840.1|  [L=231]
Description: h(+)-transporting ATP synthase, vacuolar type subunit d [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-55  186.8  11.2    5.3e-55  186.3  11.2    1.2  1  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
          4    8.3  14.1        0.5   11.2   8.9    2.1  2  PAPA-1      PAPA-1-like conserved region


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.3  11.2   5.9e-59   5.3e-55       1     196 []      11     204 ..      11     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 186.3 bits;  conditional E-value: 5.9e-59
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       +L+++++r++l +rgh++L++Krd Li+ef++il+++++ r el+e+++ a++++ +a+a++g+ +++ a+++ ++ 
  gi|313127570|ref|YP_004037840.1|  11 NLMAIEDRIELSERGHDTLEQKRDGLIMEFMDILDQAQDVRSELNENYETAQSKINMARAMEGDVAVRGAAAALKE- 86 
                                       68999*****************************************************************996666. PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikk 153
                                         + +++++++n++GV vp++e ++  ks +++ ygll+++a++dea++a++elle ++ +a++et+++++ eei++
  gi|313127570|ref|YP_004037840.1|  87 --HPEITTQSKNIMGVVVPQIESSRVkKSLDQRGYGLLGSSARIDEAADAYEELLESIILAAEVETAMKKMLEEIET 161
                                       ..699****************9877677778889******************************************* PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 154 tnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                       t+rRvNaLe +++P l e+  yI+++L+Eqeree+frlkk+k+
  gi|313127570|ref|YP_004037840.1| 162 TKRRVNALEFKLLPDLYENKEYIEQKLEEQEREEIFRLKKIKA 204
                                       *****************************************95 PP

>> PAPA-1  PAPA-1-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       1.1   9.9e+03       7      14 ..     159     166 ..     149     172 .. 0.47
   2 ?   11.2   8.9   5.6e-05       0.5      14      57 ..     181     224 ..     180     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                       HHHHHHHH CS
                            PAPA-1   7 aEmarrRk 14 
                                        E+ +rR 
  gi|313127570|ref|YP_004037840.1| 159 IETTKRRV 166
                                       34555554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.6e-05
                                       HHHHHHHHHHHHHXHHHHHHXXXXXXXXXX..XXXXXXXXXXXX CS
                            PAPA-1  14 knqsekrleeekaeTInkLLkkqagkkkkkkkakaaaeaeeeee 57 
                                       k+ +e++lee++ e I +L k +a+k+++ k+++++++ae++ +
  gi|313127570|ref|YP_004037840.1| 181 KEYIEQKLEEQEREEIFRLKKIKAKKEEEAKAEAEEEAAEASAA 224
                                       7889***************9999999998854444333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2143  (0.119527); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1545.55
//
Query:       gi|313127571|ref|YP_004037841.1|  [L=471]
Description: ATP synthase, b subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-64  217.8   0.0    1.7e-64  217.4   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    1.1e-13   51.5   0.7    2.5e-13   50.3   0.7    1.7  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
      0.036   14.2   0.3       0.12   12.6   0.3    2.0  1  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.4   0.0   2.8e-68   1.7e-64       1     213 []     129     354 ..     129     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.4 bits;  conditional E-value: 2.8e-68
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS...........S.EEEEEEESEEHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x.xxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd...........d.aiiyvgiGergnevaevleefpe 65 
                                       G+ ++D + ++v+Gq++ i++a+g++++ ++ ++++q++             + a+++ ++G  ++e++e++++f++
  gi|313127571|ref|YP_004037841.1| 129 GVAAVDGMNTLVRGQKLPIFSASGLPHNDLALQIARQATVPeeaaeegeegsEfAVVFGAMGITAEEANEFMDDFER 205
                                       889**********************************86658999******878*********************** PP

                                       SSGGGGEEEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  66 gtimkrtvlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypayl 141
                                       +++++r+v+++n +++p+++r  ++++++t+AEy++  ++++vl+i++++++++eAlrei+++ +e+p+++gyp+y+
  gi|313127571|ref|YP_004037841.1| 206 TGALERSVVFMNLADDPAVERTVTPRMALTTAEYLAFeKDYHVLVILTDMTNYCEALREIGAAREEVPGRRGYPGYM 282
                                       ************************************9899************************************* PP

                                       HHHHHHHHTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 142 gaklaslyERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +++la+lyERag+++ r+Gsvt++++++++g+D ++p+++ t +it+g+i++d++l+++++ P++nvl S+S
  gi|313127571|ref|YP_004037841.1| 283 YTDLAQLYERAGRIEGREGSVTQIPILTMPGDDDTHPIPDLTGYITEGQIYVDRDLHSQGVQPPVNVLPSLS 354
                                       **********************************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.7   4.2e-17   2.5e-13       1      69 []       7      72 ..       7      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 4.2e-17
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i++++Gp+v +e ++   +g+++++e+e ++ g+  +g++l+ ++++V ++v+++t+G+++++ V+++G
  gi|313127571|ref|YP_004037841.1|  7 ISEISGPLVFAEVDEP--IGYDEIVEIETPQ-GETKRGQVLESSDGVVAIQVFEGTTGIDKNASVRFLG 72
                                      799********99999..**********888.***********************************98 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   1.9e-05      0.12       3      83 ..       2      67 ..       1      89 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                        HAS-barrel  3 evigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalate 80
                                      +++++ +  s++++++e ++++++ e Veie+p+ge   G+v+  +                        + ++++++e
  gi|313127571|ref|YP_004037841.1|  2 KEYQTISEiSGPLVFAEVDEPIGYDEIVEIETPQGETKRGQVLESSD-----------------------GVVAIQVFE 57
                                      689999999********************************998776.......................555555555 PP

                        HAS-barrel 81 dt.......g 83
                                      +t       +
  gi|313127571|ref|YP_004037841.1| 58 GTtgidknaS 67
                                      5555555542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3349.21
//
Query:       gi|313127572|ref|YP_004037842.1|  [L=585]
Description: ATP synthase, a subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-91  306.3   0.0    1.5e-91  305.8   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.2e-37  128.4   0.1    2.2e-37  127.6   0.1    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
      3e-12   46.9   3.7      3e-12   46.9   3.7    2.1  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
       0.13   12.3   0.4         26    5.0   0.0    3.0  3  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.8   0.0   3.4e-95   1.5e-91       1     213 []     217     438 ..     217     438 .. 0.97

  Alignments for each domain:
  == domain 1  score: 305.8 bits;  conditional E-value: 3.4e-95
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+r+lD lfpi++G++ +ipg fg Gktv +++l+k++++d +iiyvg+Gergne++ev+++fpe      g+ +m+
  gi|313127572|ref|YP_004037842.1| 217 GQRILDGLFPIAKGGTAAIPGPFGSGKTVTQHQLAKYADAD-IIIYVGCGERGNEMTEVIDDFPEledpstGNpLMA 292
                                       9************************************9888.***********************999865337*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       rt l+antsn+pvaare ++ytgit+AE++rd+g++v l+ads+srwaeA+reis rl+emp+++gypayl+a+l++
  gi|313127572|ref|YP_004037842.1| 293 RTSLIANTSNMPVAARESCVYTGITIAEFYRDMGYDVALMADSTSRWAEAMREISSRLEEMPGEEGYPAYLAARLSE 369
                                       ***************************************************************************** PP

                                       HHTTSEEE...TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka...pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yERag +   + ++Gsv+++ avsp+ggDfs+pvt++tl+i+++f+ Ld +la+r+hfP+in+  S+S
  gi|313127572|ref|YP_004037842.1| 370 FYERAGYFeniNGTEGSVSAIGAVSPPGGDFSEPVTQNTLRIVKTFWALDADLAERRHFPSINWNESYS 438
                                       *******9777777******************************************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.6   0.1   4.8e-41   2.2e-37       1     120 [.      91     207 ..      91     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 4.8e-41
                                       EETTS-BHHHHHHHHTS.BE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-.EEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgs.fierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkv.egkv 75 
                                       yDG+qrpL+ +++k+gs +++rGv++p ++ +k+w+f p+v++gd v++gd++G+v+et +i+hk+mvpp+   g+v
  gi|313127572|ref|YP_004037842.1|  91 YDGVQRPLDVLEDKMGSpYLDRGVDAPGIELDKEWDFDPEVAEGDVVEPGDVVGIVEETITIDHKVMVPPDSeGGEV 167
                                       9*********************************************************************773567* PP

                                       EEE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEE CS
                   ATP-synt_ab_Xtn  76 keiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkek 120
                                       +e++ +ge+tve+t+++++++e    e+ + q+wPvr++rp ++k
  gi|313127572|ref|YP_004037842.1| 168 TEVK-SGEFTVEETVVTLDNGE----EIAMRQEWPVREARPSETK 207
                                       ***8.**************776....8**************9987 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   3.7   6.7e-16     3e-12       1      69 []      14      75 ..      14      75 .. 0.94
   2 ?   -2.1   0.1       1.3   5.8e+03      25      45 ..     463     482 ..     449     485 .. 0.58

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 6.7e-16
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i +v+Gpvv + ++ +    +++++ v+  +  ++l+g+++++++d   ++v+++t+G+ +G++V++TG
  gi|313127572|ref|YP_004037842.1| 14 IASVSGPVVTA-RDLD--ARMNDVVYVG--D--EGLMGEVIEIEGDITTIQVYEETSGVGPGEPVENTG 75
                                      679********.5555..5*********..9..***********************************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                       EEECCETCSTEEEEEEEEEET CS
                     ATP-synt_ab_N  25 levelvefgtlllgvalnlge 45 
                                       +   l e +  l++ ++ +g 
  gi|313127572|ref|YP_004037842.1| 463 VVDVLDE-EAELQEIVQLVGK 482
                                       3333333.6666666666665 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.37   1.6e+03      25      78 ..       9      60 ..       3      63 .. 0.63
   2 ?    5.0   0.0    0.0057        26      45      68 ..     124     147 ..     116     150 .. 0.86
   3 ?    3.4   0.0     0.017        77      18      51 ..     301     332 ..     292     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.37
                                      SSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHH CS
                         QRPTase_N 25 keegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaE 78
                                      +e+g++a ++    + + l +++++  v  G++   g+ ++eieG++ ++  +E
  gi|313127572|ref|YP_004037842.1|  9 REDGIIASVSGPVVTARDL-DARMNDVVYVGDEGLMGE-VIEIEGDITTIQVYE 60
                                      6677777666666666666.666666666666666664.457888877777766 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0057
                                       TTEEEESS-TT-EEETTEEEEEEE CS
                         QRPTase_N  45 glevellvkDGervekgdvlleie 68 
                                       +  ++++v++G+ ve+gdv+  +e
  gi|313127572|ref|YP_004037842.1| 124 EWDFDPEVAEGDVVEPGDVVGIVE 147
                                       5678999************98775 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.017
                                       EEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEES CS
                         QRPTase_N  18 akaeiiakeegvvaGlevaeevfellpglevell 51 
                                       +++ + a+e++v+ G+++ae +++ + g+ v l+
  gi|313127572|ref|YP_004037842.1| 301 SNMPVAARESCVYTGITIAE-FYRDM-GYDVALM 332
                                       566789**********9986.56656.6666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3775.85
//
Query:       gi|313127573|ref|YP_004037843.1|  [L=109]
Description: archaeal/vacuolar-type h+-ATPase subunit f [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-16   58.7   0.0      6e-16   58.6   0.0    1.1  1  ATP-synt_F     ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
      0.042   14.8   0.0        2.7    9.0   0.0    2.2  2  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   6.6e-20     6e-16       1      89 [.       5      97 ..       5      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 6.6e-20
                                      EEEEESHHHHHHHHHTTCEEEE....CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEES CS
                        ATP-synt_F  1 iavIGdedtvtgfrlaGvgeve....vtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileIP 74
                                      iavIG+ d++tgfrlaGv+++e    ++++e++ ea+++ le+ed+gii++++  ++++++++++  e+   P+++++ 
  gi|313127573|ref|YP_004037843.1|  5 IAVIGSPDFTTGFRLAGVRKFEnvpdESKDEQLDEAVNRTLEDEDVGIIVMHDGDLDHLSRQVRQSVETsIEPTLVTLG 83
                                      8*********************99998889*******************************9999999889*****996 PP

                                      CSCCGGSHHCHHHHH CS
                        ATP-synt_F 75 skegpydeekdsvrk 89
                                      +  g  +  +d++++
  gi|313127573|ref|YP_004037843.1| 84 GGAGAGGL-RDKIKR 97
                                      66664433.666665 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0003       2.7      13      55 ..       3      46 ..       2      49 .. 0.71
   2 ?    3.8   0.0     0.013   1.1e+02      30      56 ..      50      77 ..      47      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0003
                                      EEEEEE-----TTS---EEEEEE---.-.--HHHHHHHHHHHHT- CS
                     AMP-binding_C 13 aeaaVvGvpdevkGealvafVvlkdg.s.ealeeeLkahvrkelg 55
                                      +e+aV+G pd ++G +l+++   + + + e+ +e+L + v+++l+
  gi|313127573|ref|YP_004037843.1|  3 QEIAVIGSPDFTTGFRLAGVRKFE-NvPdESKDEQLDEAVNRTLE 46
                                      69************8888876654.32222245777777777665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.013
                                      EEEEEE----.--HHHHHHHHHHHHT-T CS
                     AMP-binding_C 30 vafVvlkdgs.ealeeeLkahvrkelgp 56
                                      v+++v +dg  ++l +++++ v++ ++p
  gi|313127573|ref|YP_004037843.1| 50 VGIIVMHDGDlDHLSRQVRQSVETSIEP 77
                                      7899999886466889999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 714.80
//
Query:       gi|313127574|ref|YP_004037844.1|  [L=348]
Description: ATP synthase A1 subunit C [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-78  263.7   9.1    3.3e-78  263.6   9.1    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
       0.17   11.8   0.8        2.9    7.9   0.0    2.8  3  Inhibitor_I24   PinA peptidase inhibitor


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.6   9.1   3.6e-82   3.3e-78       1     335 [.      12     343 ..      12     344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 263.6 bits;  conditional E-value: 3.6e-82
                                       HHHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H CS
                    vATP-synt_AC39   1 leArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapg 77 
                                       ++Arvra++s l+++e+y++L+++   ++++r+++e++Y++++    s+ ++++ ie+ l+++la++fn+++++a+g
  gi|313127574|ref|YP_004037844.1|  12 VNARVRARQSALFSDEEYRKLVRM-GPAEIARFMEESEYEEEINALGSRFSGVDLIEYSLNKNLAKQFNDILKWADG 87 
                                       69*******************555.*****************66556****************************** PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHH CS
                    vATP-synt_AC39  78 psrefldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakylee 154
                                        +++++  +l+++d +Nvk+++rg++s d++ e++ ++l+ +ge++ + ld+l+ a+++ee+++ l gt +   le+
  gi|313127574|ref|YP_004037844.1|  88 RLYDLIARYLRKFDAWNVKTVIRGIYS-DAEREDVDSDLIRAGEFDDDFLDRLLDATTIEEVVDRLNGTMFDVDLEA 163
                                       *88************************.8999********************************************* PP

                                       HHCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS.......T...-- CS
                    vATP-synt_AC39 155 aldeleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkyg.elskedrkklli 230
                                       a++++eet  l ++ena+d+ay+e+ll+    ++++t + +re+l++eiD+rn +++lr+ ++g +  ++d+   +i
  gi|313127574|ref|YP_004037844.1| 164 AFEDYEETDVLVPLENAIDRAYYESLLEGLV-VDEAT-QQYREYLEAEIDFRNARNALRLARSGaDIDPADY---YI 235
                                       *****************************76.55555.66************************77778888...** PP

                                       SS-.S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT-...-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHH CS
                    vATP-synt_AC39 231 pgg.slypeglealaeaedveellaalkyteygelleealee...agslksledaldealvkllkk.afrqqfsvgv 302
                                       +gg  ++ ++l +la+    +el++++++++yg+ l++al++   a+sl  +e+al+ al+++++     +++sv +
  gi|313127574|ref|YP_004037844.1| 236 DGGsLFSASELVTLAQN--TDELVSKIRDSKYGNELSNALDAleaADSLIGFERALETALLEYAEGlGYVYPLSVSP 310
                                       ***999*********88..79****************99999998888***************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 303 fyaYlklkeqEirnlrwIaegiaqglpkekIre 335
                                       +++Y+++ke+E++n+r+Ia+g+++gl++++I+e
  gi|313127574|ref|YP_004037844.1| 311 VISYILAKEREVDNIRAIARGREAGLSEDEIEE 343
                                       *******************************98 PP

>> Inhibitor_I24  PinA peptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.18   1.6e+03     104     132 ..      66      97 ..      50     119 .. 0.63
   2 ?    0.7   0.1     0.054   4.8e+02      78     138 ..     142     209 ..     136     211 .. 0.52
   3 ?    7.9   0.0   0.00033       2.9      80     135 ..     245     300 ..     230     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.18
                     Inhibitor_I24 104 isyalaklaaqenndgy...egnlmqaaaeyi 132
                                       i y+l k  a++ nd     +g l +  a y+
  gi|313127574|ref|YP_004037844.1|  66 IEYSLNKNLAKQFNDILkwaDGRLYDLIARYL 97 
                                       66666666666666543111455555555554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.054
                     Inhibitor_I24  78 ngeieevvertnqvvqkp..kadfqgerisyalaklaaqenndgye....gnlm.qaaaeyiewletq 138
                                          ieevv+r n  +     +a f+    +  l  l    +   ye    g ++ +a+ +y e+le++
  gi|313127574|ref|YP_004037844.1| 142 ATTIEEVVDRLNGTMFDVdlEAAFEDYEETDVLVPLENAIDRAYYEslleGLVVdEATQQYREYLEAE 209
                                       56799999999977654311455555444555555544444444441111333323455677777665 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00033
                     Inhibitor_I24  80 eieevvertnqvvqkpkadfqgerisyalaklaaqenndgyegnlmqaaaeyiewl 135
                                       e+  + + t+++v k +    g+ +s al  l a +   g+e  l  a  ey e l
  gi|313127574|ref|YP_004037844.1| 245 ELVTLAQNTDELVSKIRDSKYGNELSNALDALEAADSLIGFERALETALLEYAEGL 300
                                       6667788999******************************************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2270.22
//
Query:       gi|313127575|ref|YP_004037845.1|  [L=193]
Description: archaeal/vacuolar-type h+-ATPase subunit e [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-44  149.6  14.0    1.2e-43  148.8  14.0    1.3  1  vATP-synt_E   ATP synthase (E/31 kDa) subunit
    0.00047   20.3  21.3     0.0005   20.2  19.0    2.0  2  ATP-synt_B    ATP synthase B/B' CF(0)
     0.0086   16.0  10.7        1.3    8.9   7.1    2.2  2  HrpE          HrpE/YscL/FliH and V-type ATPase subunit E
  ------ inclusion threshold ------
      0.018   14.4  21.1       0.42   10.0   3.6    1.9  2  DUF3552       Domain of unknown function (DUF3552)
      0.091   13.2  20.9       0.12   12.8  20.1    1.7  1  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
       0.18   11.7   8.3       0.27   11.1   8.3    1.2  1  Endonuc_Holl  Endonuclease related to archaeal Holliday junct
       0.51   10.4  12.5       0.14   12.3   8.4    2.0  1  DivIVA        DivIVA protein
       0.88   10.1  11.3       0.31   11.6   1.6    3.2  2  YtxH          YtxH-like protein
        1.2    7.0   3.4        1.3    6.8   3.4    1.0  1  V_ATPase_I    V-type ATPase 116kDa subunit family
        4.1    8.1  16.9        2.9    8.5   1.0    3.0  2  DUF883        Bacterial protein of unknown function (DUF883)
        6.4    5.8   7.5        8.4    5.4   7.5    1.1  1  Atg14         Vacuolar sorting 38 and autophagy-related subun


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.8  14.0   7.4e-47   1.2e-43       1     199 []       9     191 ..       9     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 7.4e-47
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   1 fIrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleev 77 
                                       +Ir+eA+++AeeI++++e+ +e++ ++++ ++ee +e+++ + e+q+e+++++a+S+a+++a++k+L+ar++vle+v
  gi|313127575|ref|YP_004037845.1|   9 DIRDEARARAEEIREDGEQRAEEIIEEAETDAEELLESRKTDVERQVEQEREQALSSAKLEAKQKRLEARRDVLEDV 85 
                                       69*************************************************************************** PP

                                       HHHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-.SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEE CS
                       vATP-synt_E  78 feeaekkLaeveedkdeYkellkkLivqalvkle.epevivrarkeDaelveealdkaaeeykaktkkktvevagde 153
                                       + ++e++La ++ d+  +++l+++L+++a+ ++  + +v+v++r+ D++l+e+    + ee ++      +e+ g+ 
  gi|313127575|ref|YP_004037845.1|  86 RGQVEEELAALSGDR--RETLTRSLLDEAADEFDdDADVVVYGRESDQSLIED----ILEEHDG------YEFGGTY 150
                                       ***************..****************96679***************....7888877......6777776 PP

                                       SSEBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 154 edfledvlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                            ++lGGvv+e+++++++vnnT++++Le v+e++l+e++ +LF
  gi|313127575|ref|YP_004037845.1| 151 -----ECLGGVVVESQQSRVRVNNTFDSVLEGVWEDNLKEVSSRLF 191
                                       .....****************************************9 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2  19.0   3.1e-07    0.0005      61     119 ..      12      70 ..       6      83 .. 0.90
   2 ?    0.2   0.7      0.45   7.4e+02      99     120 ..      70      90 ..      65     104 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.1e-07
                        ATP-synt_B  61 keAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqv 119
                                        eAra+A+ei+++++++ae++ ee+e++ae+ +e++k + + ++eqe+++al++ + ++
  gi|313127575|ref|YP_004037845.1|  12 DEARARAEEIREDGEQRAEEIIEEAETDAEELLESRKTDVERQVEQEREQALSSAKLEA 70 
                                       69**************************************************9866555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.45
                        ATP-synt_B  99 sAaaeIeqekdralaeLreqvv 120
                                       ++++++e+ +  +l+++r+qv 
  gi|313127575|ref|YP_004037845.1|  70 AKQKRLEA-RRDVLEDVRGQVE 90 
                                       34444443.3345666666654 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   7.1    0.0008       1.3      21      66 ..      16      63 ..       4      75 .. 0.48
   2 !    8.6   0.2   0.00096       1.6      32      85 ..      78     132 ..      66     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0008
                              HrpE 21 lrreqlae..slrarellaeArlqAeqllaqarekaeellevaveqAe 66
                                       r+e++ e  ++ra+e+++eA   Ae+ll+  +   e+ +e+  eqA+
  gi|313127575|ref|YP_004037845.1| 16 ARAEEIREdgEQRAEEIIEEAETDAEELLESRKTDVERQVEQEREQAL 63
                                      333444331134555555555555555555555444444444444444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00096
                              HrpE  32 arellaeArlqAeq.llaqarekaeellevaveqAeaqFWeqAnalLrglqqeRe 85 
                                        r++l++ r q e+ l a   +++e+l+    ++A  +F ++A+ ++ g   +  
  gi|313127575|ref|YP_004037845.1|  78 RRDVLEDVRGQVEEeLAALSGDRRETLTRSLLDEAADEFDDDADVVVYGRESDQS 132
                                       479*******987527778999**********************99888766655 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  12.6   0.00052      0.85      26      78 ..       8      60 ..       2      64 .. 0.89
   2 ?   10.0   3.6   0.00026      0.42     103     171 ..      58     124 ..      57     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00052
                           DUF3552 26 ekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelkerrn 78
                                      e   +eA+++A++i e+ ++ Ae++ +ea ++a e +   ++++e+ +++ r+
  gi|313127575|ref|YP_004037845.1|  8 EDIRDEARARAEEIREDGEQRAEEIIEEAETDAEELLESRKTDVERQVEQERE 60
                                      566689*****************************************998776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00026
                           DUF3552 103 kkeesleekekelkqkeqsleekeeeleelveeqrqeLerisgLtkeeAkeilleeveeelkheaAkmi 171
                                       ++e++l++   +l++k+++le++++ le++  + ++eL  +sg  +e     ll+e+ +e + +a +++
  gi|313127575|ref|YP_004037845.1|  58 EREQALSSA--KLEAKQKRLEARRDVLEDVRGQVEEELAALSGDRRETLTRSLLDEAADEFDDDADVVV 124
                                       678888765..5669*********************************************999987766 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  20.1   7.4e-05      0.12      22      96 ..      12      86 ..       2      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.4e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHH CS
                      V-ATPase_G_2 22 EaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkraearlqqAve 96
                                      ++Ar  ae+  e  e+ A+ i++eAe++a++l +  +  ++++v+++re+a + a+ ea++ r +a   + + v+
  gi|313127575|ref|YP_004037845.1| 12 DEARARAEEIREDGEQRAEEIIEEAETDAEELLESRKTDVERQVEQEREQALSSAKLEAKQKRLEARRDVLEDVR 86
                                      5899999999999************************************************99999887766665 PP

>> Endonuc_Holl  Endonuclease related to archaeal Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   8.3   0.00016      0.27      11      90 ..      16      95 ..      10     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                      Endonuc_Holl 11 lkiskiqkklekkarelfeewkkeeaeeleklk.eaeallkkeaevkleewkkkeekeiRedaikksksvilgkvtEel 88
                                      ++ ++i++  e++a+e+ ee +++  e le+ k  +e+++++e e+ l + k +  k+ R +a +   + ++g+v Eel
  gi|313127575|ref|YP_004037845.1| 16 ARAEEIREDGEQRAEEIIEEAETDAEELLESRKtDVERQVEQEREQALSSAKLEA-KQKRLEARRDVLEDVRGQVEEEL 93
                                      567899***************999988888877677************9988765.55699999999999********9 PP

                      Endonuc_Holl 89 iP 90
                                      + 
  gi|313127575|ref|YP_004037845.1| 94 AA 95
                                      85 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   8.4   8.4e-05      0.14      74     129 ..       5      61 ..       1      63 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX CS
                            DivIVA  74 etaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeie.elkrqarlfrqr 129
                                       +  e+++ +a++ ae i ++ e++ae+i+eeae +a+++ e  + +++rq ++ r++
  gi|313127575|ref|YP_004037845.1|   5 NVVEDIRDEARARAEEIREDGEQRAEEIIEEAETDAEELLESRKtDVERQVEQEREQ 61 
                                       678999999999999999999999999999999999998666555999999998875 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.6   0.00019      0.31      31      72 ..       4      45 ..       2      48 .. 0.90
   2 ?    0.7   3.1      0.48   7.9e+02      53      66 ..      79      92 ..      45     142 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                              YtxH 31 kekaddlkekakelleeakekakekaedlkekvkekadelke 72
                                       + ++d+++ a   +ee++e ++++ae++ e+++ +a+el e
  gi|313127575|ref|YP_004037845.1|  4 DNVVEDIRDEARARAEEIREDGEQRAEEIIEEAETDAEELLE 45
                                      56789999999999*************************987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.48
                              YtxH 53 kekaedlkekvkek 66
                                      ++  ed++ +v+e+
  gi|313127575|ref|YP_004037845.1| 79 RDVLEDVRGQVEEE 92
                                      44444444444443 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.4   0.00081       1.3      33     144 ..       8     117 ..       4     167 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00081
                        V_ATPase_I  33 demerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavl 109
                                       +++  + r   eei++ + +++ e e+ e+ e++ e+ l++ ++++e+  e+ +e+  ++ kl++++++l+  + vl
  gi|313127575|ref|YP_004037845.1|   8 EDIRDEARARAEEIRE-DGEQRAE-EIIEEAETDAEELLESRKTDVERQVEQEREQALSSAKLEAKQKRLEARRDVL 82 
                                       5566666666777777.4444333.3478888888889999999999999999999999****************** PP

                        V_ATPase_I 110 ekakefleee.eeeeeeeeseeeeeekeeeeeeese 144
                                       e ++  +eee ++ + +++++ + ++  +e ++e++
  gi|313127575|ref|YP_004037845.1|  83 EDVRGQVEEElAALSGDRRETLT-RSLLDEAADEFD 117
                                       *****999885554444333333.332233333443 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.0    0.0018       2.9      14      45 ..       3      34 ..       1      37 [. 0.75
   2 ?    2.5  10.8      0.13   2.2e+02       7      59 ..      33      86 ..      29     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                            DUF883 14 leellkeaadeageeaeelRerleerlerare 45
                                      l++++++  dea+  aee+Re  e+r+e+  e
  gi|313127575|ref|YP_004037845.1|  3 LDNVVEDIRDEARARAEEIREDGEQRAEEIIE 34
                                      67788888888888888888888888877654 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                            DUF883  7 leslladleellkeaadeageeaeelRerleerle..rarerlrdaeeavaerak 59
                                      +e++ +d+eell++ + + ++++e+ Re++ ++++  + ++rl+ a+++v e ++
  gi|313127575|ref|YP_004037845.1| 33 IEEAETDAEELLESRKTDVERQVEQEREQALSSAKleAKQKRLE-ARRDVLEDVR 86
                                      488999**********************9966543204445554.4444444333 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.5    0.0051       8.4      33     118 ..      17     104 ..      11     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0051
                             Atg14  33 klksekeslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakls 108
                                       +  + +e  +++ e+++e+ e +ae+l +  k++ ++  e+  ++a+++++l+  +++l+ +++ +e+ + ++++  
  gi|313127575|ref|YP_004037845.1|  17 RAEEIREDGEQRAEEIIEEAEtDAEELLESRKTDVERQVEQEREQALSSAKLEAKQKRLEARRDVLEDVRGQVEEEL 93 
                                       55566777788888888887756666777777777777788888999999999999999999999999999999988 PP

                             Atg14 109 dklk.kRrsdl 118
                                       ++l+ +Rr++l
  gi|313127575|ref|YP_004037845.1|  94 AALSgDRRETL 104
                                       88888777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2101  (0.117184); expected 358.6 (0.02)
Passed bias filter:                      848  (0.0472977); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1072.53
//
Query:       gi|313127576|ref|YP_004037846.1|  [L=79]
Description: ATP synthase subunit c [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-13   49.9  10.2    3.5e-13   49.7  10.2    1.1  1  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7  10.2     2e-17   3.5e-13       2      59 ..      21      78 ..      20      79 .] 0.98

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 2e-17
                                      HHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C  2 gaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivali 59
                                      +a+lavGl+a+g+G++   +g+a+++a+a++ +lf++ li+ +++e++ +++L+v +i
  gi|313127576|ref|YP_004037846.1| 21 AAALAVGLAAFGAGYAERGIGAAAMGAIAEDDSLFVNGLILTVLPETLVILALVVVFI 78
                                      8*******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 530.37
//
Query:       gi|313127577|ref|YP_004037847.1|  [L=742]
Description: archaeal/vacuolar-type h+-ATPase subunit i [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-19   69.8  16.3    1.1e-09   36.9   1.8    5.0  5  V_ATPase_I       V-type ATPase 116kDa subunit family
    0.00019   21.8   4.2     0.0097   16.3   0.3    2.7  2  FlaC_arch        Flagella accessory protein C (FlaC)
      0.003   17.8   3.1      0.018   15.3   0.1    2.3  2  Spc24            Spc24 subunit of Ndc80
  ------ inclusion threshold ------
      0.015   15.8   8.9       0.85   10.2   0.8    2.2  2  APG6_N           Apg6 coiled-coil region
      0.019   15.4   5.9       0.68   10.4   2.4    2.4  2  DUF4140          N-terminal domain of unknown function (DUF41
      0.027   14.1   1.0        2.4    7.8   0.1    2.3  2  TPD52            Tumour protein D52 family
       0.03   13.1   0.3       0.13   10.9   0.0    1.8  2  Tektin           Tektin family
       0.03   14.7   2.2        3.8    8.0   0.3    2.5  2  LPP              Lipoprotein leucine-zipper
      0.037   14.4   2.7        4.7    7.6   0.1    2.4  2  CCDC-167         Coiled-coil domain-containing protein 167
      0.081   12.8   1.8        0.2   11.6   1.8    1.5  1  Takusan          Takusan
      0.092   12.7   3.6       0.93    9.5   0.9    2.3  2  Prefoldin_2      Prefoldin subunit
        0.1   11.8   4.0        2.8    7.1   0.8    2.1  2  DLP_helical      Dynamin-like helical domain
       0.11   12.8   0.8       0.43   10.9   0.1    2.2  2  Imm7             Immunity protein 7
       0.12   13.0   2.1        1.9    9.1   0.2    2.5  2  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.12   12.6   0.2       0.31   11.2   0.1    1.7  2  Nmad5            Nucleotide modification associated domain 5
       0.12   12.4   6.3       0.46   10.5   0.3    2.4  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.13   12.7   5.9        4.9    7.7   0.5    2.3  2  Snapin_Pallidin  Snapin/Pallidin
       0.15   11.4   2.7        1.9    7.7   0.4    2.2  2  DUF3450          Protein of unknown function (DUF3450)
       0.17   10.7   0.1        2.3    6.9   0.0    2.0  2  BBS2_C           Ciliary BBSome complex subunit 2, C-terminal
       0.18   11.9   0.4        5.8    7.0   0.1    2.4  2  DUF1664          Protein of unknown function (DUF1664)
       0.18   12.2   1.1       0.69   10.3   0.1    2.2  2  E2F_CC-MB        E2F transcription factor CC-MB domain
        0.2   11.8   5.2       0.65   10.2   0.8    3.0  3  Cnn_1N           Centrosomin N-terminal motif 1
       0.23   11.9   1.6          1    9.8   0.2    2.1  2  DUF4600          Domain of unknown function (DUF4600)
        0.4   10.8   2.7         32    4.7   0.2    3.1  3  YojJ             Bacterial membrane-spanning protein N-termin
       0.44   10.2   2.7        1.2    8.8   0.4    2.1  2  DUF2968          Protein of unknown function (DUF2968)
        0.5   11.0   4.5        1.3    9.7   0.8    2.3  2  KfrA_N           Plasmid replication region DNA-binding N-ter
       0.57   10.0   5.0        1.7    8.4   1.6    2.2  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
        0.6   10.2   2.6         15    5.7   0.2    2.4  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        0.6    9.7   3.2        1.4    8.6   0.6    2.1  2  Med4             Vitamin-D-receptor interacting Mediator subu
       0.82   10.2   9.0        1.3    9.5   3.2    2.3  2  ZapB             Cell division protein ZapB
          1    9.2   6.5       0.38   10.6   0.8    2.3  2  DivIC            Septum formation initiator
          1    9.4   8.9        3.6    7.7   0.2    2.2  2  DHR10            Designed helical repeat protein 10 domain
        1.2    9.1   7.3        5.5    7.1   0.4    2.2  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        1.6    9.0   7.2        8.5    6.6   1.4    2.4  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.9    8.7   6.0         17    5.6   0.8    2.2  2  bZIP_1           bZIP transcription factor
          2    8.7   5.0        5.3    7.3   2.7    2.5  2  XhlA             Haemolysin XhlA
          3    7.8   5.1        3.8    7.5   0.7    2.2  2  DUF1640          Protein of unknown function (DUF1640)


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.052        25      72     106 ..      86     120 ..      56     130 .. 0.80
   2 !    5.8   0.0    0.0056       2.7     250     333 ..     218     299 ..     195     321 .. 0.61
   3 !   36.9   1.8   2.2e-12   1.1e-09     347     460 ..     349     453 ..     333     462 .. 0.84
   4 ?    0.7   0.3       0.2        97     515     560 ..     489     534 ..     487     538 .. 0.86
   5 !   30.3   0.2   2.2e-10   1.1e-07     761     812 ..     682     733 ..     659     734 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.052
                        V_ATPase_I  72 deleeelekleeelkelnenleklkkelnelvelk 106
                                       d leeele++ ++++el+++ ++l+++l++++e  
  gi|313127577|ref|YP_004037847.1|  86 DALEEELEEIRTQVNELDDERQELRQNLRDIEERI 120
                                       67899999999999999999999999999988865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0056
                        V_ATPase_I 250 eveeriedlekvleqteealkevleeiakeleewklkvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqka 326
                                       e+e++ +++++ l++ e++l+++  ++a  l + + k+     + +t   +++ +t++ +iaegW+p+++ +e ++a
  gi|313127577|ref|YP_004037847.1| 218 ELEHEQQQIRSDLDSVESELESLKLDAAGFLLAAEEKL--SIDVQKTEAPLSFATTENAFIAEGWIPASRFTEFKSA 292
                                       44444444444444444444333322222222111111..12344455556778999******************** PP

                        V_ATPase_I 327 lkeatee 333
                                       lke   e
  gi|313127577|ref|YP_004037847.1| 293 LKENIGE 299
                                       *997644 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 2.2e-12
                        V_ATPase_I 347 tketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkk 423
                                        +++pPT  +     + f  +v+a + ++Y E  p+++   tFP  F+ M GD+G Gl+ ++++ +l  + ++  + 
  gi|313127577|ref|YP_004037847.1| 349 RDDEPPTVQNNPGPIKPFEVLVQAVSRPSYYEFDPTVILFLTFPAFFGFMIGDLGYGLIYTAIGYFLYANFDDRPAF 425
                                       4589**************************************************************99876654443 PP

                        V_ATPase_I 424 kkdeilemlfsgRYiillmGlfsiYtGliYNdifsks 460
                                             +   s+  i +  Glf    G++Y +if++ 
  gi|313127577|ref|YP_004037847.1| 426 ------K---SMGGITIAAGLFTALFGILYGEIFGLH 453
                                       ......2...222355667888888888888888765 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.2
                        V_ATPase_I 515 lsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsifg 560
                                       +sv++Gv+++ ++ ++ ++++l  ++  + ++e    +l+l  + +
  gi|313127577|ref|YP_004037847.1| 489 VSVLVGVFHLNIAWIFDFFENLELHDAKHAVFESASWILMLNGLWI 534
                                       69********************999999999998887777777665 PP

  == domain 5  score: 30.3 bits;  conditional E-value: 2.2e-10
                        V_ATPase_I 761 lvilfavfavltvavLllmeglsafLHaLRLhWVEfqsKFykgdGykFepfs 812
                                        +++ +v +v+  + +l + ++sa L a+RL+ VEf +KFy+g G  +epf 
  gi|313127577|ref|YP_004037847.1| 682 AILGGLVILVVGHILVLALGVTSAGLQAVRLEYVEFFNKFYEGGGRDYEPFG 733
                                       44555555566666677899*******************************6 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3     2e-05    0.0097       3      38 ..      86     121 ..      86     142 .. 0.85
   2 ?    5.9   0.3     0.036        17       2      27 ..     216     241 ..     215     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2e-05
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVk 38 
                                       d lE++l+++ t+++ + +e +el++++ +++e++ 
  gi|313127577|ref|YP_004037847.1|  86 DALEEELEEIRTQVNELDDERQELRQNLRDIEERID 121
                                       679*******************************94 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.036
                         FlaC_arch   2 idelEnklsklsteletvkkeneels 27 
                                       + elE + +++ + l++v++e+e+l+
  gi|313127577|ref|YP_004037847.1| 216 VRELEHEQQQIRSDLDSVESELESLK 241
                                       67999999*************99986 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.6e-05     0.018      22      91 ..      87     174 ..      84     180 .. 0.79
   2 ?    2.4   0.4      0.36   1.8e+02      15      38 ..     218     241 ..     213     266 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-05
                             Spc24  22 sleselaelkeeleeleeeseekeserve.detllklklYrsLGiel................ekd.vnkvlirnke 80 
                                       +le+el+e +++++el++e++e ++++ + +e +  +  ++ LGi+l                ++d v++++++ ++
  gi|313127577|ref|YP_004037847.1|  87 ALEEELEEIRTQVNELDDERQELRQNLRDiEERIDTIAPFKDLGIDLdllsgydtlqvavgygKRDaVERAVVDADQ 163
                                       578888888999999988888855555677999**************888877777777777755578899999988 PP

                             Spc24  81 kgdvnvlnldd 91 
                                        gd ++l+ d+
  gi|313127577|ref|YP_004037847.1| 164 LGDYEILSGDR 174
                                       88888887665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.36
                             Spc24  15 dleselesleselaelkeeleele 38 
                                       +le e ++++s l++ ++ele l+
  gi|313127577|ref|YP_004037847.1| 218 ELEHEQQQIRSDLDSVESELESLK 241
                                       555555555555555555555554 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.8    0.0027       1.3      58      91 ..      87     120 ..      63     124 .. 0.75
   2 ?   10.2   0.8    0.0018      0.85      69     113 ..     215     260 ..     207     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0027
                            APG6_N  58 klekeeeelleeLkelekereeleaelaaleeel 91 
                                       +le+e ee  ++ +el++er+el++ l+++ee  
  gi|313127577|ref|YP_004037847.1|  87 ALEEELEEIRTQVNELDDERQELRQNLRDIEERI 120
                                       4677777777777777777777777777777654 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0018
                            APG6_N  69 eLkelekereeleaelaaleeelealeeeeerfwreyne.lqlell 113
                                         +ele+e+++++++l + e+ele l+ + + f+    e l+++++
  gi|313127577|ref|YP_004037847.1| 215 YVRELEHEQQQIRSDLDSVESELESLKLDAAGFLLAAEEkLSIDVQ 260
                                       5789***********************9999998776665555555 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.4    0.0014      0.68      49      93 ..      69     118 ..      53     123 .. 0.57
   2 ?    5.9   0.1     0.035        17      65      92 ..     213     241 ..     176     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                           DUF4140  49 ildvqvervpnreaeee.....elkalraeleeledelaaledelaaaea 93 
                                       ildv+ +    ++++++     el+++r +++el de+++l++ l+ +e+
  gi|313127577|ref|YP_004037847.1|  69 ILDVDEDDAGPTRIVTDdaleeELEEIRTQVNELDDERQELRQNLRDIEE 118
                                       66776666666666665333324555555555555555555555555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.035
                           DUF4140  65 ee.lkalraeleeledelaaledelaaae 92 
                                       +e +++l+ e ++++ +l+ +e+el++++
  gi|313127577|ref|YP_004037847.1| 213 QEyVRELEHEQQQIRSDLDSVESELESLK 241
                                       24488888888888888888888888876 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0049       2.4      12      46 ..      90     123 ..      67     152 .. 0.69
   2 ?    4.7   0.1     0.042        20      26      61 ..     220     260 ..     206     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0049
                             TPD52  12 daaesvsaseptlteeereeLkseLakleeeivtL 46 
                                       +  e+++++  +l ++er+eL+++L  +ee i t+
  gi|313127577|ref|YP_004037847.1|  90 EELEEIRTQVNEL-DDERQELRQNLRDIEERIDTI 123
                                       2223333322222.356777777777777777665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.042
                             TPD52  26 eeereeLkseLakleeeivtLrq.....vLaakekhlaelk 61 
                                       e e+++++s+L  +e e+ +L+      +Laa ek  ++++
  gi|313127577|ref|YP_004037847.1| 220 EHEQQQIRSDLDSVESELESLKLdaagfLLAAEEKLSIDVQ 260
                                       789*****************984333336777777766665 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.13     228     283 ..      67     122 ..      36     125 .. 0.74
   2 ?   -0.4   0.1      0.75   3.6e+02     260     285 ..     216     241 ..     212     247 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                            Tektin 228 dsilkqtandlraqaeavnealrkrieetedaknkleeqlkkvleeiaelekniee 283
                                       +sil   ++d    +  +++al++ +ee++   n+l ++++++++++ ++e+ i++
  gi|313127577|ref|YP_004037847.1|  67 ESILDVDEDDAGPTRIVTDDALEEELEEIRTQVNELDDERQELRQNLRDIEERIDT 122
                                       55555556666666677888888888888888888888888888888888888776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.75
                            Tektin 260 knkleeqlkkvleeiaeleknieeLe 285
                                        ++le+++++++ +++++e ++e+L+
  gi|313127577|ref|YP_004037847.1| 216 VRELEHEQQQIRSDLDSVESELESLK 241
                                       45566666666666666666666555 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.036        18       2      32 ..      92     122 ..      91     124 .. 0.87
   2 ?    8.0   0.3    0.0079       3.8       9      38 ..     216     245 ..     213     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.036
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                       l+e+ +qV++L ++ ++l +++ ++++ +++
  gi|313127577|ref|YP_004037847.1|  92 LEEIRTQVNELDDERQELRQNLRDIEERIDT 122
                                       68999****************9999887765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0079
                               LPP   9 VsqLkskvdqlssdvnsakaaaqaakeEAa 38 
                                       V +L+ +++q+ sd++s+++++++ k +Aa
  gi|313127577|ref|YP_004037847.1| 216 VRELEHEQQQIRSDLDSVESELESLKLDAA 245
                                       889********************9999986 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.6     0.028        14      38      64 ..      86     112 ..      64     121 .. 0.86
   2 ?    7.6   0.1    0.0097       4.7      37      62 ..     216     241 ..     205     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.028
                          CCDC-167  38 esleeEeaslkeqleenekeLksLrke 64 
                                       ++leeE++++++q++e + e ++Lr+ 
  gi|313127577|ref|YP_004037847.1|  86 DALEEELEEIRTQVNELDDERQELRQN 112
                                       578999999999999999999999875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0097
                          CCDC-167  37 ResleeEeaslkeqleenekeLksLr 62 
                                        ++le+E+++++++l++ e+eL+sL+
  gi|313127577|ref|YP_004037847.1| 216 VRELEHEQQQIRSDLDSVESELESLK 241
                                       57899999999999999999999886 PP

>> Takusan  Takusan
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.8   0.00041       0.2       6      43 ..      79     116 ..      77     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                           Takusan   6 ppailekeqakkklEeLkleLrkitreRdELrdiLaly 43 
                                       p +i++   ++++lEe+ ++   +  eR ELr+ L  +
  gi|313127577|ref|YP_004037847.1|  79 PTRIVTDDALEEELEEIRTQVNELDDERQELRQNLRDI 116
                                       5678888999***********************99865 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.9    0.0019      0.93      65      99 ..      86     120 ..      82     128 .. 0.68
   2 ?    3.3   0.1      0.16        78       8      32 ..     217     241 ..     205     254 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeel 99 
                                       + Lee++e++ +++++l ++ ++l+++l++++e +
  gi|313127577|ref|YP_004037847.1|  86 DALEEELEEIRTQVNELDDERQELRQNLRDIEERI 120
                                       56777777777777777777777777777666654 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   8 qqlqqqlqqlaqqikqletqlkele 32 
                                       ++l+ ++qq+ ++++++e +l+ l+
  gi|313127577|ref|YP_004037847.1| 217 RELEHEQQQIRSDLDSVESELESLK 241
                                       3445555555555555555555444 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.8    0.0058       2.8      68     106 ..      84     122 ..      79     125 .. 0.90
   2 ?    5.5   0.1     0.017       8.1      79     137 ..     205     263 ..     201     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0058
                       DLP_helical  68 irdvlerqlpeaeerleelekevekleesakriekelae 106
                                         d le++l+e++++++el+ e+++l++++++ie+++ +
  gi|313127577|ref|YP_004037847.1|  84 TDDALEEELEEIRTQVNELDDERQELRQNLRDIEERIDT 122
                                       5699******************************99876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.017
                       DLP_helical  79 aeerleelekevekleesakriekelaelkkeieearielreelkayfsdLilqvkgls 137
                                       + +++   ++ v++le+++++i+++l ++++e+e  + ++  +l a ++ L  +v+ ++
  gi|313127577|ref|YP_004037847.1| 205 VPDADGSPQEYVRELEHEQQQIRSDLDSVESELESLKLDAAGFLLAAEEKLSIDVQKTE 263
                                       55666677788999*************************************99999876 PP

>> Imm7  Immunity protein 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00088      0.43      10      73 ..      95     160 ..      92     165 .. 0.85
   2 ?   -1.0   0.1       4.3   2.1e+03      17      42 ..     220     245 ..     212     259 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00088
                              Imm7  10 iqesaee.dddeallesivkeieskideld.ysselvdLraknGeyylhlgglsnhrteeaeevid 73 
                                       i+ +++e dd++++l++++++ie++id ++ ++   +dL    G   l++++   +r ++  +v+d
  gi|313127577|ref|YP_004037847.1|  95 IRTQVNElDDERQELRQNLRDIEERIDTIApFKDLGIDLDLLSGYDTLQVAVGYGKRDAVERAVVD 160
                                       56666666888999**************984677789************99888888878888877 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.3
                              Imm7  17 dddeallesivkeieskideldysse 42 
                                       + ++++++s ++ +es++++l  + +
  gi|313127577|ref|YP_004037847.1| 220 EHEQQQIRSDLDSVESELESLKLDAA 245
                                       56677777777777777777766554 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2     0.004       1.9      34      59 ..      97     122 ..      56     126 .. 0.78
   2 ?    2.8   0.1      0.36   1.8e+02      36      61 ..     216     241 ..     200     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.004
                      Syntaxin-6_N  34 stseeldetrteLrkalrsiewdled 59 
                                       ++ +eld+ r+eLr++lr+ie+ ++ 
  gi|313127577|ref|YP_004037847.1|  97 TQVNELDDERQELRQNLRDIEERIDT 122
                                       25789999999999999999998875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.36
                      Syntaxin-6_N  36 seeldetrteLrkalrsiewdledLe 61 
                                         el++ ++++r+ l+s+e +le L+
  gi|313127577|ref|YP_004037847.1| 216 VRELEHEQQQIRSDLDSVESELESLK 241
                                       45777778888888888888888775 PP

>> Nmad5  Nucleotide modification associated domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00065      0.31     109     159 ..      68     116 ..       4     123 .. 0.65
   2 ?   -2.2   0.0         8   3.9e+03     126     157 ..     207     238 ..     199     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00065
                             Nmad5 109 svdeiaketkslpkvvleadnplvkrfdelekaqeelrekrkaikatVtav 159
                                       s+  +++++     + ++ d++l ++++e++ ++ el+++r++++++++ +
  gi|313127577|ref|YP_004037847.1|  68 SILDVDEDDAG--PTRIVTDDALEEELEEIRTQVNELDDERQELRQNLRDI 116
                                       33333333332..4699******************************9865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8
                             Nmad5 126 eadnplvkrfdelekaqeelrekrkaikatVt 157
                                       +ad   ++ + ele +q+++r++ + ++++++
  gi|313127577|ref|YP_004037847.1| 207 DADGSPQEYVRELEHEQQQIRSDLDSVESELE 238
                                       56666667777888888888888888777765 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00094      0.46      64      96 ..      88     120 ..      55     128 .. 0.61
   2 ?    4.9   0.2     0.051        25      55      79 ..     217     241 ..     209     276 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00094
                    CENP-F_leu_zip  64 laeelreleldLvalrsekeeLekelqkkqerv 96 
                                       l+eel+e+++++++l  e++eL ++l++  er+
  gi|313127577|ref|YP_004037847.1|  88 LEEELEEIRTQVNELDDERQELRQNLRDIEERI 120
                                       333333333333333333333333333333333 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.051
                    CENP-F_leu_zip  55 etlkeeieelaeelreleldLvalr 79 
                                        +l++e +++++ l   e++L++l+
  gi|313127577|ref|YP_004037847.1| 217 RELEHEQQQIRSDLDSVESELESLK 241
                                       2233333333333333333333332 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.5      0.01       4.9      11      47 ..      88     124 ..      86     134 .. 0.82
   2 ?    7.3   0.6     0.013       6.1      19      49 ..     213     243 ..     211     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.01
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkele 47 
                                       le +l+e++++++el ++ +eL+++l+   e+++ ++
  gi|313127577|ref|YP_004037847.1|  88 LEEELEEIRTQVNELDDERQELRQNLRDIEERIDTIA 124
                                       7889999999999999999999999998888877665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.013
                   Snapin_Pallidin  19 deklkelrqsQeeLleqldrlnekLkeleea 49 
                                       +e ++el+ +Q++ +++ld+  ++L++l+ +
  gi|313127577|ref|YP_004037847.1| 213 QEYVRELEHEQQQIRSDLDSVESELESLKLD 243
                                       5789*********************998755 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4    0.0039       1.9      31      63 ..      91     123 ..      82     128 .. 0.69
   2 ?    3.3   0.1     0.086        42      15      65 ..     192     242 ..     183     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0039
                           DUF3450  31 aaaqsqkkidklddekqellaeyralkeelesl 63 
                                       + +++ +++++ldde+qel +++r+++e+++ +
  gi|313127577|ref|YP_004037847.1|  91 ELEEIRTQVNELDDERQELRQNLRDIEERIDTI 123
                                       445666777788888888888888777777654 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.086
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslev 65 
                                       a+tl  a+ ++ +  +a+ + q+ + +l+ e+q++ +++ ++++elesl++
  gi|313127577|ref|YP_004037847.1| 192 ADTLVGADFTSLEVPDADGSPQEYVRELEHEQQQIRSDLDSVESELESLKL 242
                                       666666666777777778888999999999*************99999986 PP

>> BBS2_C  Ciliary BBSome complex subunit 2, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.21     1e+02     308     337 ..      90     119 ..      81     145 .. 0.67
   2 ?    6.9   0.0    0.0048       2.3      55     130 ..     208     278 ..     200     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.21
                            BBS2_C 308 eelkellekvdelnevrqkltaemadssnl 337
                                       eel+e+ ++v+el++ rq l++++ d  ++
  gi|313127577|ref|YP_004037847.1|  90 EELEEIRTQVNELDDERQELRQNLRDIEER 119
                                       445555555555555555555444444333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0048
                            BBS2_C  55 eeseeqealreLlqkKqnLlleLknleenlkakksaeaedgvipantklqvslsvnkeekhvelvvsttndtiira 130
                                       ++ + qe++reL++++q+    L+++e++l++ k  + +   + a+ kl++ ++++++     l+++tt++++i  
  gi|313127577|ref|YP_004037847.1| 208 ADGSPQEYVRELEHEQQQIRSDLDSVESELESLKLDA-AGFLLAAEEKLSIDVQKTEA----PLSFATTENAFIAE 278
                                       566789*************************999877.88889998888888777664....88888888888865 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.012       5.8      83     120 ..      86     123 ..      69     126 .. 0.74
   2 ?    2.4   0.0      0.32   1.6e+02      86     113 ..     213     240 ..     198     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                           DUF1664  83 keikeevtevredlseigedvesvkeavegleskleri 120
                                        +++ee++e+r +++e++++ +++++  +++e+++++i
  gi|313127577|ref|YP_004037847.1|  86 DALEEELEEIRTQVNELDDERQELRQNLRDIEERIDTI 123
                                       45667777777777777777777777777777777766 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.32
                           DUF1664  86 keevtevredlseigedvesvkeavegl 113
                                       +e v e++++ ++i++d++sv++  e+l
  gi|313127577|ref|YP_004037847.1| 213 QEYVRELEHEQQQIRSDLDSVESELESL 240
                                       5678888888888888888888777766 PP

>> E2F_CC-MB  E2F transcription factor CC-MB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1    0.0014      0.69       1      34 [.      88     121 ..      88     185 .. 0.72
   2 ?   -0.1   0.1       2.5   1.2e+03       3      29 ..     214     240 ..     200     262 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0014
                         E2F_CC-MB   1 lkqelesleeeeqkLDelieklteqlknltedek 34 
                                       l++ele+++ + ++LD+  ++l+++l++++e  +
  gi|313127577|ref|YP_004037847.1|  88 LEEELEEIRTQVNELDDERQELRQNLRDIEERID 121
                                       689**************************99433 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.5
                         E2F_CC-MB   3 qelesleeeeqkLDelieklteqlknl 29 
                                       + +++le e+q++ + +++++ +l++l
  gi|313127577|ref|YP_004037847.1| 214 EYVRELEHEQQQIRSDLDSVESELESL 240
                                       445666666666666666666666665 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8    0.0013      0.65      37      72 ..      84     119 ..      69     120 .. 0.90
   2 ?   -0.0   0.2         2   9.9e+02      36      62 ..     214     240 ..     207     244 .. 0.67
   3 ?    1.1   0.0       0.9   4.3e+02      39      58 ..     290     309 ..     272     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                            Cnn_1N  37 qkeellkenielkveveslqkelkekkkllreaeka 72 
                                       + ++l++e+ e++++v +l +e +e+++ lr+ e++
  gi|313127577|ref|YP_004037847.1|  84 TDDALEEELEEIRTQVNELDDERQELRQNLRDIEER 119
                                       568999**************************9986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2
                            Cnn_1N  36 eqkeellkenielkveveslqkelkek 62 
                                       e ++el+ e  +++ ++ s + el+++
  gi|313127577|ref|YP_004037847.1| 214 EYVRELEHEQQQIRSDLDSVESELESL 240
                                       666777777777777777777777665 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.9
                            Cnn_1N  39 eellkenielkveveslqke 58 
                                       +++lkeni  +++ve+l++ 
  gi|313127577|ref|YP_004037847.1| 290 KSALKENIGERIQVEELERA 309
                                       7899************9986 PP

>> DUF4600  Domain of unknown function (DUF4600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2    0.0021         1      52      81 ..      92     121 ..      51     124 .. 0.77
   2 ?    0.7   0.1       1.4   6.6e+02      57      81 ..     214     238 ..     207     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0021
                           DUF4600  52 eeelnqllkqLekekkslenqlkdlelrle 81 
                                        ee+++ +++L++e+++l ++l+d+e r++
  gi|313127577|ref|YP_004037847.1|  92 LEEIRTQVNELDDERQELRQNLRDIEERID 121
                                       4678888*********************98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.4
                           DUF4600  57 qllkqLekekkslenqlkdlelrle 81 
                                       +++++Le+e++++ ++l  +e  le
  gi|313127577|ref|YP_004037847.1| 214 EYVRELEHEQQQIRSDLDSVESELE 238
                                       7899***********9999998877 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.9   1.4e+03      16      52 ..      90     101 ..      86     105 .. 0.54
   2 ?    4.7   0.2     0.067        32      11      28 ..     106     123 ..      96     126 .. 0.85
   3 ?    4.4   0.0     0.084        41      26      62 ..     213     249 ..     204     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.9
                              YojJ  16 eeLeqiekeleevlkaldeedeClLcelesirekfae 52 
                                       eeLe+i+++++                         e
  gi|313127577|ref|YP_004037847.1|  90 EELEEIRTQVN-------------------------E 101
                                       55555555554.........................4 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.067
                              YojJ  11 keklkeeLeqiekeleev 28 
                                       +++l+++L++ie++++++
  gi|313127577|ref|YP_004037847.1| 106 RQELRQNLRDIEERIDTI 123
                                       89************9987 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.084
                              YojJ  26 eevlkaldeedeClLcelesirekfaeletlassyYL 62 
                                       +e +++l+ e++ + ++l+s+  +++ l+  a+ + L
  gi|313127577|ref|YP_004037847.1| 213 QEYVRELEHEQQQIRSDLDSVESELESLKLDAAGFLL 249
                                       778899999999999******9999999999998876 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4    0.0024       1.2     138     173 ..      87     122 ..      82     125 .. 0.88
   2 ?    1.1   0.1      0.55   2.7e+02     148     176 ..     214     242 ..     202     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0024
                           DUF2968 138 avaerQkqarkeaaaLeaqreaaqaqlralqrqirq 173
                                       a++e+ +++r++++ L+++r++++++lr+++++i++
  gi|313127577|ref|YP_004037847.1|  87 ALEEELEEIRTQVNELDDERQELRQNLRDIEERIDT 122
                                       566777899************************986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.55
                           DUF2968 148 keaaaLeaqreaaqaqlralqrqirqLqa 176
                                       + ++ Le++++++++ l++++ ++++L+ 
  gi|313127577|ref|YP_004037847.1| 214 EYVRELEHEQQQIRSDLDSVESELESLKL 242
                                       55678999999999999999999988875 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.8    0.0026       1.3      71     110 ..      83     122 ..      64     124 .. 0.85
   2 ?    2.1   0.1      0.61   2.9e+02      81     105 ..     217     241 ..     180     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0026
                            KfrA_N  71 lwqaaleeaeeelaaaraelqaaraaleaeraeaearvee 110
                                       + + alee  ee++++ +el+++r++l++ ++++e+r+++
  gi|313127577|ref|YP_004037847.1|  83 VTDDALEEELEEIRTQVNELDDERQELRQNLRDIEERIDT 122
                                       5678999999999999999999999999999999999876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.61
                            KfrA_N  81 eelaaaraelqaaraaleaeraeae 105
                                       +el++++++++++ +  e+e++ ++
  gi|313127577|ref|YP_004037847.1| 217 RELEHEQQQIRSDLDSVESELESLK 241
                                       3555555555555555555555544 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.6    0.0035       1.7      63      94 ..      86     117 ..      80     124 .. 0.80
   2 ?    2.5   0.1      0.24   1.1e+02      87     118 ..     213     244 ..     205     260 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0035
                          KASH_CCD  63 klleeEleelkalvkeleEkrarlkaqnkqle 94 
                                        +leeElee+++ v+el+++r++l ++ + +e
  gi|313127577|ref|YP_004037847.1|  86 DALEEELEEIRTQVNELDDERQELRQNLRDIE 117
                                       57999999999999999999998887766665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.24
                          KASH_CCD  87 kaqnkqlekenqsLiakiesLqeenikllaek 118
                                       + + ++le e+q++++ ++s + e++ l+ ++
  gi|313127577|ref|YP_004037847.1| 213 QEYVRELEHEQQQIRSDLDSVESELESLKLDA 244
                                       56678899999999999999999988877665 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2      0.03        15      99     133 ..      86     120 ..      59     130 .. 0.74
   2 ?    4.0   0.2     0.094        46     109     150 ..     213     254 ..     205     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.03
                           UPF0242  99 eeLkeeldakeeelerlkeenqqLqekleaiaedf 133
                                       + L+eel++  +++++l  e q+L++ l +i e +
  gi|313127577|ref|YP_004037847.1|  86 DALEEELEEIRTQVNELDDERQELRQNLRDIEERI 120
                                       45666666666777777777777776666666544 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.094
                           UPF0242 109 eeelerlkeenqqLqekleaiaedfeelkleleeqLaekqel 150
                                       +e +++l++e+qq+++ l  +  + e lkl++   L   +e+
  gi|313127577|ref|YP_004037847.1| 213 QEYVRELEHEQQQIRSDLDSVESELESLKLDAAGFLLAAEEK 254
                                       456677777777777777777777777777665544333333 PP

>> Med4  Vitamin-D-receptor interacting Mediator subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6    0.0029       1.4      28      62 ..      89     123 ..      81     134 .. 0.89
   2 ?    1.1   0.1      0.57   2.8e+02      38      62 ..     216     240 ..     210     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                              Med4  28 earilqLraeveslDekikeivksLkeyekeLkav 62 
                                       e++++++r +v++lD++ +e+ ++L ++e+ + + 
  gi|313127577|ref|YP_004037847.1|  89 EEELEEIRTQVNELDDERQELRQNLRDIEERIDTI 123
                                       799**************************999875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.57
                              Med4  38 veslDekikeivksLkeyekeLkav 62 
                                       v +l+ ++++i + L ++e+eL+++
  gi|313127577|ref|YP_004037847.1| 216 VRELEHEQQQIRSDLDSVESELESL 240
                                       7789999999999999999999986 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.2    0.0028       1.3      29      64 ..      87     122 ..      85     123 .. 0.88
   2 ?    3.6   0.3      0.19        93      40      65 ..     215     240 ..     211     258 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0028
                              ZapB  29 eLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                       +L+ee ee   + +el  e ++l+++   ++er+++
  gi|313127577|ref|YP_004037847.1|  87 ALEEELEEIRTQVNELDDERQELRQNLRDIEERIDT 122
                                       689999999999999999999999999999999986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.19
                              ZapB  40 enreleeeneqlkeereawqerlkkL 65 
                                         rele+e +q + +  ++++ l++L
  gi|313127577|ref|YP_004037847.1| 215 YVRELEHEQQQIRSDLDSVESELESL 240
                                       34555555555555555555555544 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   0.00078      0.38      20      60 ..      86     123 ..      77     125 .. 0.75
   2 ?    1.1   0.6      0.68   3.3e+02      24      51 ..     214     241 ..     211     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00078
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                             DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60 
                                        +l++e++++  ++++l +e++eL ++++d +   ++i+ +
  gi|313127577|ref|YP_004037847.1|  86 DALEEELEEIRTQVNELDDERQELRQNLRDIE---ERIDTI 123
                                       67888999999999999999999998888874...555555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.68
                                       HHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  24 qeiaalqaelaklkaeneeLeaevkdLk 51 
                                       + + +l++e ++++ + ++ e+e++ Lk
  gi|313127577|ref|YP_004037847.1| 214 EYVRELEHEQQQIRSDLDSVESELESLK 241
                                       5678899999999999999999999885 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   4.0      0.09        44      62      95 ..      88     121 ..      84     124 .. 0.82
   2 ?    7.7   0.2    0.0075       3.6      71     112 ..     214     255 ..     210     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.09
                             DHR10  62 lrdaleekeielrelerkeerlqrqlenaeekle 95 
                                       l+++lee +++++el+ +++ l++ l   ee+++
  gi|313127577|ref|YP_004037847.1|  88 LEEELEEIRTQVNELDDERQELRQNLRDIEERID 121
                                       7788889999999999999999999988888886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0075
                             DHR10  71 ielrelerkeerlqrqlenaeeklerlreqaeekreaakarl 112
                                       + +rele+++++++  l++ e +le l+ +a+    aa+++l
  gi|313127577|ref|YP_004037847.1| 214 EYVRELEHEQQQIRSDLDSVESELESLKLDAAGFLLAAEEKL 255
                                       678*************************99988888777776 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.5     0.045        22      29      64 ..      86     121 ..      83     124 .. 0.67
   2 ?    7.1   0.4     0.011       5.5      41      70 ..     215     244 ..     213     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.045
                        TMF_DNA_bd  29 lklnntikkLrkknkelekeikelkkkleklekele 64 
                                       ++l++ + + r +++el+ e +el + l++ e+ ++
  gi|313127577|ref|YP_004037847.1|  86 DALEEELEEIRTQVNELDDERQELRQNLRDIEERID 121
                                       566777777777777777777777777777776665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                        TMF_DNA_bd  41 knkelekeikelkkkleklekeleeleerl 70 
                                        ++ele e+++  + l+++e+ele+l+  +
  gi|313127577|ref|YP_004037847.1| 215 YVRELEHEQQQIRSDLDSVESELESLKLDA 244
                                       679***********************9766 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.4     0.018       8.5      24      58 ..      88     122 ..      86     128 .. 0.85
   2 ?    5.1   0.5     0.052        25      19      60 ..     214     255 ..     212     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.018
                       TMF_TATA_bd  24 lEgElaslkeelerleaerdeareeivklmkenee 58 
                                       lE El+++++++++l  er+e+r+ + ++ ++ ++
  gi|313127577|ref|YP_004037847.1|  88 LEEELEEIRTQVNELDDERQELRQNLRDIEERIDT 122
                                       89999999999999999999999999887777665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.052
                       TMF_TATA_bd  19 seirrlEgElaslkeelerleaerdeareeivklmkeneelk 60 
                                         +r+lE E ++++++l ++e+e ++++ + +  +   ee+ 
  gi|313127577|ref|YP_004037847.1| 214 EYVRELEHEQQQIRSDLDSVESELESLKLDAAGFLLAAEEKL 255
                                       569********************9999888777766666554 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.8     0.036        17      37      63 ..      87     113 ..      86     122 .. 0.69
   2 ?    5.5   0.4     0.037        18      34      61 ..     215     242 ..     213     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  37 aLekeNksLkseleelkkevekLkskv 63 
                                       aLe+e ++ + +++el +e+++L++++
  gi|313127577|ref|YP_004037847.1|  87 ALEEELEEIRTQVNELDDERQELRQNL 113
                                       577777777777777777777777664 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  34 rvkaLekeNksLkseleelkkevekLks 61 
                                        v +Le e ++ +s l++ + e e+Lk 
  gi|313127577|ref|YP_004037847.1| 215 YVRELEHEQQQIRSDLDSVESELESLKL 242
                                       4778888888888888888888888885 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.7     0.011       5.3       9      44 ..      88     123 ..      86     125 .. 0.86
   2 ?    0.1   0.0         2   9.7e+02      21      45 ..     217     241 ..     211     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                              XhlA   9 ietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                       +e++l+++ ++v++l++   e ++++  +ee+++ +
  gi|313127577|ref|YP_004037847.1|  88 LEEELEEIRTQVNELDDERQELRQNLRDIEERIDTI 123
                                       688899999999999999999999999999999877 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2
                              XhlA  21 dkleekaaeaeekiknleedlkkle 45 
                                        +le  +   ++ ++++e +l++l+
  gi|313127577|ref|YP_004037847.1| 217 RELEHEQQQIRSDLDSVESELESLK 241
                                       5666666666666666666666665 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.43   2.1e+02      73     124 ..      91     116 ..      64     129 .. 0.64
   2 ?    7.5   0.7    0.0078       3.8      47      95 ..     218     266 ..     213     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.43
                           DUF1640  73 efaalrseteklqreleklkqkLreeidklkadirldlnleKgrireelakl 124
                                       e +++r++ ++l  e ++l+q+Lr+                          +
  gi|313127577|ref|YP_004037847.1|  91 ELEEIRTQVNELDDERQELRQNLRD--------------------------I 116
                                       3344444444444444444444443..........................3 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0078
                           DUF1640  47 elekseylqkaalselrkevqisersefaalrseteklqreleklkqkL 95 
                                       ele ++++++++l+++ +e+++++   +  l +  ekl ++++k +  L
  gi|313127577|ref|YP_004037847.1| 218 ELEHEQQQIRSDLDSVESELESLKLDAAGFLLAAEEKLSIDVQKTEAPL 266
                                       789999************************************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (742 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); expected 358.6 (0.02)
Passed Vit filter:                       216  (0.0120475); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.94u 0.32s 00:00:01.26 Elapsed: 00:00:00.52
# Mc/sec: 4263.34
//
Query:       gi|313127578|ref|YP_004037848.1|  [L=110]
Description: ATP synthase, h subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0086   16.2  27.9     0.0095   16.0  19.1    2.2  2  ATP-synt_B       ATP synthase B/B' CF(0)
  ------ inclusion threshold ------
      0.014   15.8  25.5      0.074   13.5  25.5    1.8  1  V-ATPase_G_2     Vacuolar (H+)-ATPase G subunit
      0.019   15.0  18.2       0.77    9.8  11.6    2.1  2  DivIVA           DivIVA protein
      0.025   15.1  23.7       0.16   12.5  22.4    2.1  1  V-ATPase_G       Vacuolar (H+)-ATPase G subunit
       0.03   14.9  15.8       0.56   10.8   3.1    2.1  2  DUF883           Bacterial protein of unknown function (DUF88
      0.037   13.2   9.5      0.045   13.0   9.5    1.0  1  DLP_helical      Dynamin-like helical domain
      0.042   13.7   9.2       0.07   13.0   9.2    1.4  1  HrpE             HrpE/YscL/FliH and V-type ATPase subunit E
       0.12   12.3   3.9       0.11   12.4   3.1    1.4  1  UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
       0.36   10.2  26.7       0.34   10.3  12.2    2.5  2  DUF3552          Domain of unknown function (DUF3552)
       0.73   10.0  12.6        1.3    9.2   7.6    2.1  2  Caudo_TAP        Caudovirales tail fibre assembly protein, la
       0.84   10.2  11.8        1.4    9.5   0.8    2.4  2  YtxH             YtxH-like protein
       0.95    8.3   8.0          1    8.2   8.0    1.0  1  DUF3435          Protein of unknown function (DUF3435)
        1.9    8.4   4.8        3.9    7.5   0.2    2.4  2  Trm5_N           tRNA methyltransferase 5 N-terminal domain
        2.3    8.2  22.9        3.4    7.6  22.9    1.2  1  Merozoite_SPAM   Merozoite surface protein (SPAM)
        6.8    6.4   9.1        7.7    6.2   9.1    1.1  1  AAA_11           AAA domain
        9.5    6.7   9.0         17    5.9   2.7    2.5  2  Arm-DNA-bind_3   Arm DNA-binding domain


Domain annotation for each model (and alignments):
>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  19.1   8.5e-06    0.0095      34      98 ..       5      70 ..       3      75 .. 0.85
   2 !    8.3   8.3    0.0021       2.3      71     122 ..      58     109 ..      55     110 .] 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.5e-06
                        ATP-synt_B 34 kIadeiaeAeerrkea.aallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlke 98
                                      ++ + i+ Ae  +++  a ++ ++e++ ++Ar++A+ei+++A++ea++   e+ aea++e+e  +e
  gi|313127578|ref|YP_004037848.1|  5 EVLERIKTAESDADDIvADAETDREERIADARRKAEEIRQQAEEEAKEYESERLAEARKEIEAERE 70
                                      577889999999888537799999999999999999999999999999999999999999997665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0021
                        ATP-synt_B  71 iknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvval 122
                                        ++A+ke+e ++e i +e e+  +rl+ +A+++ e + + a+++ +e v a+
  gi|313127578|ref|YP_004037848.1|  58 LAEARKEIEAERETILNEGEETRKRLIRDAEENTEEAVEYAIDQFEEAVHAQ 109
                                       6789999999999999999999999999999999999999999999998876 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  25.5   6.6e-05     0.074       6     100 ..       6     100 ..       3     103 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-05
                                       HTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2   6 llkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqa 82 
                                       +l+ ++  E++ d  + +A  + e++++ A+  A+ i ++Ae++ak+ ++e  +e ++e++++re + +++e+  ++
  gi|313127578|ref|YP_004037848.1|   6 VLERIKTAESDADDIVADAETDREERIADARRKAEEIRQQAEEEAKEYESERLAEARKEIEAERETILNEGEETRKR 82 
                                       89999999********************************************************************* PP

                                       HHHHHHCSHHHHHHHHHH CS
                      V-ATPase_G_2  83 vrkraearlqqAvelilk 100
                                       + + ae+  ++Ave  ++
  gi|313127578|ref|YP_004037848.1|  83 LIRDAEENTEEAVEYAID 100
                                       **************9876 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  11.6   0.00069      0.77      71     122 ..      12      64 ..       5      69 .. 0.75
   2 ?    8.8   2.8    0.0015       1.7      78     114 ..      60      96 ..      57     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00069
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXX CS
                            DivIVA  71 vaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaee.ieelkrq 122
                                       +a++ a+++ a a++  e  i++A+ kae+i ++aeeeak+ ++e ++e +++
  gi|313127578|ref|YP_004037848.1|  12 TAESDADDIVADAETDREERIADARRKAEEIRQQAEEEAKEYESErLAEARKE 64 
                                       68888899999999999999999999999999999999888876524455555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  78 evkanakkeaeliikeAekkaekiveeaeeeakkiae 114
                                       e++++ ++e e+i++e e++ ++++++aee+++++ e
  gi|313127578|ref|YP_004037848.1|  60 EARKEIEAERETILNEGEETRKRLIRDAEENTEEAVE 96 
                                       66788899*********************99988754 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5  22.4   0.00015      0.16      11      94 ..      12      95 ..       5     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSH....HHHHHHHHHHHSSHHHHHHHHH CS
                        V-ATPase_G 11 qAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgs....eeelekkieketeekikelkes 85
                                      +AE +A++iv++A +++++r+ +A+ +Ae    e r++ e+e ke+e+e l++     e+  ++i +e ee+ k+l ++
  gi|313127578|ref|YP_004037848.1| 12 TAESDADDIVADAETDREERIADARRKAE----EIRQQAEEEAKEYESERLAEarkeIEAERETILNEGEETRKRLIRD 86
                                      7*************************995....5677888888888887775522223444455556666666666666 PP

                                      HHHHHHHHH CS
                        V-ATPase_G 86 vkknkeavv 94
                                      +++n e+ v
  gi|313127578|ref|YP_004037848.1| 87 AEENTEEAV 95
                                      666666665 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   7.9    0.0023       2.6       7      55 ..      10      58 ..       5      66 .. 0.67
   2 ?   10.8   3.1    0.0005      0.56      23      72 ..      59     109 ..      54     110 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0023
                            DUF883  7 leslladleellkeaadeageeaeelRerleerlerarerlrdaeeava 55
                                      ++++ +d+++++ +a+ + +e ++++R+++ee  ++a e++++ e +  
  gi|313127578|ref|YP_004037848.1| 10 IKTAESDADDIVADAETDREERIADARRKAEEIRQQAEEEAKEYESERL 58
                                      6777777777777777777777777777777777777777776665543 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0005
                            DUF883  23 deageeaeelRerleerlerarerl.rdaeeavaerakeaaeaaddyVren 72 
                                       +ea++e+e+ Re + ++ e++r+rl rdaee+ +e ++ a+++ +++V+++
  gi|313127578|ref|YP_004037848.1|  59 AEARKEIEAERETILNEGEETRKRLiRDAEENTEEAVEYAIDQFEEAVHAQ 109
                                       68999****************99974899999****************975 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   9.5     4e-05     0.045      60     142 ..      13      96 ..       6     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4e-05
                       DLP_helical  60 ieetkksvirdvlerqlpeaeerleelekevekleesakrie.kelaelkkeieearielreelkayfsdLilqvkg 135
                                        e+ +++++ d  + + + + ++ +++e+ ++++ee+ak+ e ++lae++keie  r+++ +e ++ +++Li++++ 
  gi|313127578|ref|YP_004037848.1|  13 AESDADDIVADAETDREERIADARRKAEEIRQQAEEEAKEYEsERLAEARKEIEAERETILNEGEETRKRLIRDAEE 89 
                                       5677899*****999999999999999999999999999976256******************************99 PP

                       DLP_helical 136 lsletie 142
                                        + e +e
  gi|313127578|ref|YP_004037848.1|  90 NTEEAVE 96 
                                       8888776 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   9.2   6.3e-05      0.07      33     106 ..      29     102 ..       5     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                              HrpE  33 rellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLrglqqeRealeeqlltaveqLLsdalarl 106
                                       +e +a+Ar +Ae++ +qa+e a+e+      +A ++   + + +L++  + R++l +++  + e+ ++ a+ ++
  gi|313127578|ref|YP_004037848.1|  29 EERIADARRKAEEIRQQAEEEAKEYESERLAEARKEIEAERETILNEGEETRKRLIRDAEENTEEAVEYAIDQF 102
                                       355799********************999999**9**9999*************99999998888888887776 PP

>> UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.1    0.0001      0.11      11      81 ..      35     105 ..      29     110 .] 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                   UBA_e1_thiolCys  11 ArdkFeglFekkpeevnkflkd.kekfleelekekeeekletlekvlkllvkerpktfedCvkwArekfekl 81 
                                       Ar k e++ +++ ee++++ ++  +++ +e+e+e e+  l+  e+++k l+++ +++ e++v++A+++fe+ 
  gi|313127578|ref|YP_004037848.1|  35 ARRKAEEIRQQAEEEAKEYESErLAEARKEIEAERETI-LNEGEETRKRLIRDAEENTEEAVEYAIDQFEEA 105
                                       67777777788888888888440333333333333332.56689999999*******************986 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  12.2   0.00031      0.34      27      78 ..       8      55 ..       3      56 .. 0.90
   2 ?    7.4  21.2    0.0024       2.7      25      82 ..      28      85 ..      25     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                           DUF3552 27 kkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelkerrn 78
                                      ++i++Ae++A++i+++A    e+ ++e + +a+ ++ ++r+++e+e ke ++
  gi|313127578|ref|YP_004037848.1|  8 ERIKTAESDADDIVADA----ETDREERIADARRKAEEIRQQAEEEAKEYES 55
                                      6899**********985....78999*********************99776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0024
                           DUF3552 25 aekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelkerrnelqr 82
                                       e++ia+A+++A++i ++A+ eA+++  e l ea+ ei   re + +e +e r+ l r
  gi|313127578|ref|YP_004037848.1| 28 REERIADARRKAEEIRQQAEEEAKEYESERLAEARKEIEAERETILNEGEETRKRLIR 85
                                      6899****************************************99999888877644 PP

>> Caudo_TAP  Caudovirales tail fibre assembly protein, lambda gpK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   7.6    0.0011       1.3      52     107 ..       7      63 ..       4      65 .. 0.86
   2 ?    4.1   0.4     0.043        49      58      85 ..      67      94 ..      60     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                         Caudo_TAP  52 lpawvedk..keeqiqqAeqekqqllaqAseqiaplqdavdlgiatdeEkaaLlawkk 107
                                       l+++++++  +++ +++Ae+ +++++a+A+ + ++++++++ ++a + E ++L++ +k
  gi|313127578|ref|YP_004037848.1|   7 LERIKTAEsdADDIVADAETDREERIADARRKAEEIRQQAE-EEAKEYESERLAEARK 63 
                                       555666666799*************************9987.789********99876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.043
                         Caudo_TAP 58 dkkeeqiqqAeqekqqllaqAseqiapl 85
                                      +++e   ++ e+++++l+++A+e +++ 
  gi|313127578|ref|YP_004037848.1| 67 AERETILNEGEETRKRLIRDAEENTEEA 94
                                      346777889999*********9998764 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   6.0     0.059        66      52      71 ..      28      54 ..       3      75 .. 0.62
   2 ?    9.5   0.8    0.0013       1.4      22      47 ..      75     100 ..      60     110 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.059
                              YtxH 52 a.......kekaedlkekvkekadelk 71
                                              ++kae+++++++e+a+e  
  gi|313127578|ref|YP_004037848.1| 28 ReeriadaRRKAEEIRQQAEEEAKEYE 54
                                      234445557777777777777777765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                              YtxH  22 sGketRkdlkekaddlkekakellee 47 
                                        G+etRk+l + a++  e a e++ +
  gi|313127578|ref|YP_004037848.1|  75 EGEETRKRLIRDAEENTEEAVEYAID 100
                                       699*****999999999999888643 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   8.0   0.00089         1     282     348 ..      24      90 ..       4     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00089
                           DUF3435 282 asveedpelqelkrkreelkkeleakygqvakakgtelyeelekakrelrnerqrlrrelkkkiree 348
                                       a+ +++ +++ ++rk ee +++ e++++++++++++e+ +e+e  ++++ ne  + r++l++++ e+
  gi|313127578|ref|YP_004037848.1|  24 AETDREERIADARRKAEEIRQQAEEEAKEYESERLAEARKEIEAERETILNEGEETRKRLIRDAEEN 90 
                                       56778899999*************************************************9999886 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.7      0.13   1.5e+02       6      18 ..      36      48 ..      35      50 .. 0.83
   2 ?    7.5   0.2    0.0035       3.9       7      18 ..      74      85 ..      73      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.13
                                      GGGHHHHHHHHHH CS
                            Trm5_N  6 kkegEkvRkkLle 18
                                      ++++E++R+   e
  gi|313127578|ref|YP_004037848.1| 36 RRKAEEIRQQAEE 48
                                      79******98665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0035
                                      GGHHHHHHHHHH CS
                            Trm5_N  7 kegEkvRkkLle 18
                                      +egE++Rk+L++
  gi|313127578|ref|YP_004037848.1| 74 NEGEETRKRLIR 85
                                      79********96 PP

>> Merozoite_SPAM  Merozoite surface protein (SPAM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  22.9     0.003       3.4      22     111 ..       6      96 ..       3     109 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.003
                    Merozoite_SPAM  22 lLeevkitsedkediakEnedvveeeeeedleekedeeeEtee..eeteekn....eeeieeetedeedEeeveEee 92 
                                       +Le++k +++d +di+ + e   ee   + + + e++ +  ee  +e e++      +eie e e   +E      e
  gi|313127578|ref|YP_004037848.1|   6 VLERIKTAESDADDIVADAETDREERIADARRKAEEIRQQAEEeaKEYESERlaeaRKEIEAERETILNE-----GE 77 
                                       8***************998877788888887777777666665223444433000034444444444444.....34 PP

                    Merozoite_SPAM  93 ekeeeedkkkekeeeqsne 111
                                       e +   +++ e+++e+  e
  gi|313127578|ref|YP_004037848.1|  78 ETRKRLIRDAEENTEEAVE 96 
                                       4444444444444444333 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   9.1    0.0069       7.7     125     192 ..      20      87 ..       4     101 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0069
                            AAA_11 125 lakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkkerkelskeleeaeesleeev 192
                                       ++ + +  +e+  +++r ++ee+++++++++ke+++++l + r+++++er+++ +e ee++++l ++ 
  gi|313127578|ref|YP_004037848.1|  20 IVADAETDREERIADARRKAEEIRQQAEEEAKEYESERLAEARKEIEAERETILNEGEETRKRLIRDA 87 
                                       44444555555555566666666677777777788888888888888888888777777777766443 PP

>> Arm-DNA-bind_3  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.7     0.015        17      46      63 ..      31      48 ..       9      51 .. 0.91
   2 ?    4.5   0.5     0.042        47      42      63 ..      53      74 ..      50      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                    Arm-DNA-bind_3 46 slaeARkkarelraliaq 63
                                       +a+AR+ka+e+r+++++
  gi|313127578|ref|YP_004037848.1| 31 RIADARRKAEEIRQQAEE 48
                                      589***********9876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.042
                    Arm-DNA-bind_3 42 ypavslaeARkkarelraliaq 63
                                      y +  laeARk+ ++ r+ i +
  gi|313127578|ref|YP_004037848.1| 53 YESERLAEARKEIEAERETILN 74
                                      666689*******999988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2426  (0.135312); expected 358.6 (0.02)
Passed bias filter:                      685  (0.0382063); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 605.03
//
Query:       gi|313127579|ref|YP_004037849.1|  [L=220]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-22   78.8   0.0    5.4e-22   78.3   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    2.4e-20   73.0   0.0    5.1e-20   72.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      8e-16   58.2   0.0      1e-15   57.9   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    8.2e-15   55.0   0.0    1.2e-14   54.4   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.4e-14   54.0   0.0    7.7e-12   45.0   0.0    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.1e-12   46.4   0.0    7.8e-12   45.8   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    7.2e-06   25.3   0.0    8.6e-06   25.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    1.4e-05   24.9   0.0    3.8e-05   23.5   0.0    1.8  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.1e-05   23.3   0.0    5.9e-05   22.8   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00063   19.1   0.0    0.00088   18.6   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0035   16.9   0.0     0.0055   16.3   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.017   14.7   0.0    1.3  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
      0.015   14.2   0.0      0.024   13.6   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.015   13.8   0.0       0.02   13.5   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.037   13.7   0.0      0.048   13.3   0.0    1.1  1  NodS             Nodulation protein S (NodS)
        0.1   11.9   0.0        1.9    7.8   0.0    2.0  2  ADPrib_exo_Tox   ADP-ribosyltransferase exoenzyme
       0.16   11.4   0.0       0.24   10.8   0.0    1.2  1  Corona_6B_7B     Coronavirus 6B/7B protein


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   5.1e-25   5.4e-22       1      93 [.      50     141 ..      50     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 5.1e-25
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       LdvGcGtG  +e l ++  +v ++D s  +++ a  k  ++++ v+f ++dae+lpf+dnsfD+++ss +++++++p
  gi|313127579|ref|YP_004037849.1|  50 LDVGCGTGFATEGLLRYSDDVHALDQSIHQMQKAFGKFGKNDE-VRFYRGDAERLPFADNSFDVIWSSGSIEYWPNP 125
                                       8**************999********99888777666666553.9******************************** PP

                                       HHHHHHHHHHEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGl 93 
                                        +al+e++Rv+kpg +
  gi|313127579|ref|YP_004037849.1| 126 VDALEEFRRVVKPGRR 141
                                       *************955 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   4.9e-23   5.1e-20       1      96 [.      49     139 ..      49     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 4.9e-23
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd+GcGtG  t+ l++     +v+++D s  ++++a  ++ +++ +v+f++gdae+lpf+d+sfD+++ssg+++++
  gi|313127579|ref|YP_004037849.1|  49 VLDVGCGTGFATEGLLRYS--DDVHALDQSIHQMQKAFGKFGKND-EVRFYRGDAERLPFADNSFDVIWSSGSIEYW 122
                                       9***************994..********************7765.************************999***8 PP

                                       SHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpg 96 
                                       ++    +al+e++rv+kpg
  gi|313127579|ref|YP_004037849.1| 123 PN--PVDALEEFRRVVKPG 139
                                       75..569***********8 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   9.6e-19     1e-15       3     152 .]      45     179 ..      43     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 9.6e-19
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                        + rvlD+GCGtG+ t  l +      +v+ +D s +  ++A  +    + d+v+F +gd+e l+  ++d++fD+i 
  gi|313127579|ref|YP_004037849.1|  45 PDDRVLDVGCGTGFATEGLLRY---SDDVHALDQSIHQMQKAFGKFG--KNDEVRFYRGDAERLP--FADNSFDVIW 114
                                       6789*************99944...4579*************99765..4569************..********** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedprllaelp..akveeeskayevvegak.igtqkdelyelleeag 152
                                       s + + + ++p ++lee  rv+kpg ++l+  p+    +p  + +++  +       a+  +++++e+++++eeag
  gi|313127579|ref|YP_004037849.1| 115 SSGSIEYWPNPVDALEEFRRVVKPGRRVLVVGPD----YPesGLFQRVAD-------AImLFYDEHEAQRMFEEAG 179
                                       ******************************9999....443333333333.......1214456666666666665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   1.2e-17   1.2e-14       7     164 ..      31     184 ..      21     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.2e-17
                   Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae....kakkaqkdqfdeq...ea 76 
                                       ee++d  ++ll+  +++ rvLd+GcGtG  +e l ++  +v + D+s ++ ++a     k   +  + f++      
  gi|313127579|ref|YP_004037849.1|  31 EEMRDDALELLG-IQPDDRVLDVGCGTGFATEGLLRYSDDVHALDQSIHQMQKAFgkfgK---NDEVRFYRGdaeRL 103
                                       678877777777.99*************99999989999********9999988784442...44444443311155 PP

                   Methyltransf_23  77 aepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslke 153
                                       ++ +++fd+I ++ ++e  p+p  +l  +++ +kpg ++l+  p+   +e  l     +++ a+  + f+++++  +
  gi|313127579|ref|YP_004037849.1| 104 PFADNSFDVIWSSGSIEYWPNPVDALEEFRRVVKPGRRVLVVGPDY--PESGL-----FQRVADAIMLFYDEHEAQR 173
                                       56999***************************************54..44444.....5667777889********* PP

                   Methyltransf_23 154 lleeaGlevve 164
                                       ++eeaG+ ++e
  gi|313127579|ref|YP_004037849.1| 174 MFEEAGFVDIE 184
                                       *******9886 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   7.3e-15   7.7e-12      13     153 ..      14     146 ..       2     157 .. 0.80
   2 !    7.4   0.0    0.0023       2.5     188     219 ..     155     186 ..     149     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 7.3e-15
                                       XX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHH CS
                   Ubie_methyltran  13 fesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvge 89 
                                       ++ +++ yD++n  +     +  ++   +l + ++  +vlDv +Gtg  +  l++    + +v+ lD + + ++ + 
  gi|313127579|ref|YP_004037849.1|  14 YKYLSKVYDQINPYIW---NEEMRDDALELLGIQPDDRVLDVGCGTGFATEGLLR---YSDDVHALDQSIHQMQKAF 84 
                                       4556777888887664...455678888899999999**********88888876...5667899997765554444 PP

                                       HHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran  90 kklkeegki.nieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                           + gk  +++f  ++ae+Lpf d+sfDv+  s  +   ++   aL+e +rv+kpG r++v+ 
  gi|313127579|ref|YP_004037849.1|  85 ---GKFGKNdEVRFYRGDAERLPFADNSFDVIWSSGSIEYWPNPVDALEEFRRVVKPGRRVLVVG 146
                                       ...44455549**************************************************9985 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHS--HHHHHHHHHHTTEEEEEEE CS
                   Ubie_methyltran 188 yryLvesirafPdqetlkeliedaGfksveye 219
                                       ++ ++++i  f d+++ + ++e+aGf  +e++
  gi|313127579|ref|YP_004037849.1| 155 FQRVADAIMLFYDEHEAQRMFEEAGFVDIEHH 186
                                       56678999******************999876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   7.4e-15   7.8e-12       1      96 [.      50     139 ..      50     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 7.4e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       L++GcGtG  ++ ll++    +++++D s +++++a  k+ k+++     v++   d++ l+   +sfD++++s+ +
  gi|313127579|ref|YP_004037849.1|  50 LDVGCGTGFATEGLLRY--SDDVHALDQSIHQMQKAFGKFGKNDE-----VRFYRGDAERLPFAdNSFDVIWSSGSI 119
                                       8****************..**************666666666664.....5555555444433356*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpg 96 
                                       ++++++ ++l+++r+++kpg
  gi|313127579|ref|YP_004037849.1| 120 EYWPNPVDALEEFRRVVKPG 139
                                       *******************8 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   8.1e-09   8.6e-06      12      84 ..      27      99 ..      20     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 8.1e-09
                                      EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S- CS
                            RrnaAD 12 flknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqD 84
                                      +++n+ + +++l+ l +++++ vl++g G+G+ Te L+ +++ v +l +  + ++    k+ k+  +  +  D
  gi|313127579|ref|YP_004037849.1| 27 YIWNEEMRDDALELLGIQPDDRVLDVGCGTGFATEGLLRYSDDVHALDQSIHQMQKAFGKFGKNDEVRFYRGD 99
                                      99***************************************99999865544444443444466666655555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   3.6e-08   3.8e-05      53      94 ..      25      66 ..       8     140 .. 0.80
   2 ?   -1.9   0.0       2.1   2.2e+03      20      52 ..     157     189 ..     152     202 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.6e-08
                                      TEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHH CS
                              PCMT 53 natiSaphmvalalellelkkgarvLevGsGsGyltavlarl 94
                                      n +i +  m   alell +++ +rvL+vG+G+G+ t  l r+
  gi|313127579|ref|YP_004037849.1| 25 NPYIWNEEMRDDALELLGIQPDDRVLDVGCGTGFATEGLLRY 66
                                      567778889999**********************99766655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                                       HHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEET CS
                              PCMT  20 kvaealeevdReefvpesfkekaYedaplsigy 52 
                                       +va+a+     e+ +++ f+e+ ++d+  +i++
  gi|313127579|ref|YP_004037849.1| 157 RVADAIMLFYDEHEAQRMFEEAGFVDIEHHIQQ 189
                                       677777666677777777888888888777765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   5.6e-08   5.9e-05      11     112 ..      43     149 ..      34     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.6e-08
                              MetW  11 ikpgsrvldlGcGdGelle.llkeekqvdg..rGleldeegvaec.vakGlsviqgdldkdlenfedksfdyvvlsq 83 
                                       i+p  rvld+GcG G   e ll+ + +v++  + + + +++  +   +  +   +gd+++    f+d+sfd++  s 
  gi|313127579|ref|YP_004037849.1|  43 IQPDDRVLDVGCGTGFATEgLLRYSDDVHAldQSIHQMQKAFGKFgKNDEVRFYRGDAER--LPFADNSFDVIWSSG 117
                                       8999***********876537777777766224454444444443123356667777665..68************* PP

                              MetW  84 tlqatrnpkevldellri...grraivsfPnf 112
                                       ++    np   l+e  r+   grr++v  P++
  gi|313127579|ref|YP_004037849.1| 118 SIEYWPNPVDALEEFRRVvkpGRRVLVVGPDY 149
                                       ***************99966678888877765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   8.4e-07   0.00088      51     138 ..      34     120 ..      30     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.4e-07
                                       HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---. CS
                              CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde. 126
                                       +d +le l+++p +++Ld+GcG G   ++   ry  +v +l  S  q+   +k++ + + +++v+ +  d e l+  
  gi|313127579|ref|YP_004037849.1|  34 RDDALELLGIQPDDRVLDVGCGTGFA-TEGLLRYSDDVHALDQSIHQM---QKAFGKFGKNDEVRFYRGDAERLPFa 106
                                       57899*****************9965.667788999999998887776...55666666666777666666665322 PP

                                       ..--SEEEEES-GG CS
                              CMAS 127 ..kvdrvvsvgafe 138
                                          +d + s g +e
  gi|313127579|ref|YP_004037849.1| 107 dnSFDVIWSSGSIE 120
                                       24888888887777 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.2e-06    0.0055      30     101 ..      44     113 ..      36     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.2e-06
                                       CTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEE CS
                               MTS  30 elsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdli 101
                                       + +++vlD+GcG+G+ +  l++ s++  v+++d++ + ++ a   + +n+ ev+++  d+    +++++fd+i
  gi|313127579|ref|YP_004037849.1|  44 QPDDRVLDVGCGTGFATEGLLRYSDD--VHALDQSIHQMQKAFGKFGKND-EVRFYRGDAERlPFADNSFDVI 113
                                       46789****************99999..9********9999999999998.7999999987624558888887 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.6e-05     0.017      55     206 ..      45     192 ..      33     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                   Methyltransf_PK  55 evkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelae.ekkkvgkvyvvglqeftPeegrYdliWiqW 130
                                         +++ld+G+G G  t+ lL  +    D v ++++ ++++++ +++ +k+   ++y    +    +++++d+iW   
  gi|313127579|ref|YP_004037849.1|  45 PDDRVLDVGCGTGFATEGLLR-YS---DDVHALDQSIHQMQKAFGKfGKNDEVRFYRGDAERLPFADNSFDVIWSSG 117
                                       56789*************984.44...566777888999999999977788888998888888889********999 PP

                   Methyltransf_PK 131 cvghLtDedlvaflkrckkalkpn.GlivvkenvakeekdelDkeDssvt..rseaklkklfkkagLklvaeelqkg 204
                                        +   ++   v+ l+   + +kp+  ++vv  +  +++   +    +++    +e++ +++f++ag+  ++++ q+ 
  gi|313127579|ref|YP_004037849.1| 118 SIEYWPNP--VDALEEFRRVVKPGrRVLVVGPDYPESGL--FQRVADAIMlfYDEHEAQRMFEEAGFVDIEHHIQQA 190
                                       88887753..55555555566665246677777777765..555544443125677778888888877777777777 PP

                   Methyltransf_PK 205 lP 206
                                       +P
  gi|313127579|ref|YP_004037849.1| 191 YP 192
                                       76 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.3e-05     0.024     116     213 ..      46     140 ..      29     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                       T-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES- CS
                    Methyltransf_9 116 grtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmGv 191
                                       + ++ldvGcg+G+    ++   ++ v  +d s  + +q +a  k+  +d+  +      e+lp   ++fd+++s G 
  gi|313127579|ref|YP_004037849.1|  46 DDRVLDVGCGTGFATEGLLRY-SDDVHALDQSI-HQMQ-KAFGKFGKNDEVRFY-RGDAERLPFaDNSFDVIWSSGS 118
                                       5689*********98877755.55667777654.3333.788887766665555.4789****8678********** PP

                                       GGG-S-HHHHHHHHHCTEEEEE CS
                    Methyltransf_9 192 lyhrrsPldhllqlkdqlvkgG 213
                                       + +   P+d l +++  ++ g 
  gi|313127579|ref|YP_004037849.1| 119 IEYWPNPVDALEEFRRVVKPGR 140
                                       ************9998776654 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.9e-05      0.02     120     214 ..      48     141 ..      31     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                   Methyltransf_29 120 tvlDvGCgvasfgayll..srdvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdlihCsrCridw 194
                                        vlDvGCg    +  ll  s dv +l  + +   +a  +f  +  v+ + +   ++rlp+  +sfd+i  s   i++
  gi|313127579|ref|YP_004037849.1|  48 RVLDVGCGTGFATEGLLrySDDVHALDQSIHQMQKAFGKFGKNDEVRFYRG--DAERLPFADNSFDVIWSS-GSIEY 121
                                       59*****976554445422789*****999999999999999999999988..589************866.67999 PP

                   Methyltransf_29 195 teedgilllevdRvlRpgGy 214
                                         +    l e  Rv++pg  
  gi|313127579|ref|YP_004037849.1| 122 WPNPVDALEEFRRVVKPGRR 141
                                       999999***********965 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.048      46     118 ..      48     121 ..      28     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                              NodS  46 dalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfs.tdekfdlivvaevlyy 118
                                        +l+vGc +G  te l  y++ +  +d   + +++a  +  +  ++ +   d +++  +d+ fd+i  +  + y
  gi|313127579|ref|YP_004037849.1|  48 RVLDVGCGTGFATEGLLRYSDDVHALDQSIHQMQKAFGKFGKNDEVRFYRGDAERLPfADNSFDVIWSSGSIEY 121
                                       68**************************9999***********************9736889**9977655544 PP

>> ADPrib_exo_Tox  ADP-ribosyltransferase exoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1       0.1   1.1e+02      21      43 ..      10      32 ..       4      47 .. 0.78
   2 ?    7.8   0.0    0.0018       1.9      41      82 ..      66     101 ..      60     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.1
                                      HHHHHHHCCTTHHHHHHHHHCTT CS
                    ADPrib_exo_Tox 21 keaireYtgsgysdINnyLrqnk 43
                                       + +++Y+ + y++IN y  +++
  gi|313127579|ref|YP_004037849.1| 10 ARLFYKYLSKVYDQINPYIWNEE 32
                                      566899***********995544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0018
                                       CTTTSGGGS-SCHHHHHHHHHHHHCCT-B-SS-EEEEEEE-G CS
                    ADPrib_exo_Tox  41 qnkgerndldkselekkiknldsaleksripeniivYRrvde 82 
                                       +++    d+  + l+++i+++ +a+ k   ++++  YR++ e
  gi|313127579|ref|YP_004037849.1|  66 YSD----DV--HALDQSIHQMQKAFGKFGKNDEVRFYRGDAE 101
                                       444....22..799************************9744 PP

>> Corona_6B_7B  Coronavirus 6B/7B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023      0.24      95     134 ..      23      61 ..       7      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                      Corona_6B_7B  95 fvdnfyivsegnqrinlrlvgavpkqkrlnvgchtsfavd 134
                                        + n yi +e  +   l l+g  p ++ l+vgc t fa +
  gi|313127579|ref|YP_004037849.1|  23 QI-NPYIWNEEMRDDALELLGIQPDDRVLDVGCGTGFATE 61 
                                       33.679999999999**********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1440.68
//
Query:       gi|313127580|ref|YP_004037850.1|  [L=166]
Description: flagellin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-07   30.9   1.7    5.2e-07   30.5   1.0    1.6  2  Pilin_N         Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
       0.18   12.0   7.4         16    5.7   7.4    2.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   1.0   5.8e-11   5.2e-07       1      76 [.       4      82 ..       4      87 .. 0.75
   2 ?   -2.9   0.0       1.5   1.3e+04      26      45 ..     128     146 ..     126     155 .. 0.56

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 5.8e-11
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievk...idssastgknavslehkgGdsidtkdlkivl 76
                                      +A SpV+G + +v +++++a v+aa  + +as+ +    as+      +  s + ++n+v ++h+ G +i+ +dl+i +
  gi|313127580|ref|YP_004037850.1|  4 RALSPVVGTLVLVGLVLVAATVVAAASGTVASEFSPRDTASLPSAadpVAFSLTVTGNQVAVTHERGPPIQVADLRIHI 82
                                      699**********************9999966555555566633322433333333455****************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                           Pilin_N  26 fvlglasneekapqasievk 45 
                                       ++ g+ ++++ +p  +++v+
  gi|313127580|ref|YP_004037850.1| 128 VIAGT-NDPQPEPGGTVTVQ 146
                                       55555.56666665555444 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   7.4    0.0017        16      32     152 ..      37     147 ..       8     155 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSE....EEEEEE--TTS--EEGGG-EEEEEESS--EE--E.. CS
                    Arch_flagellin  32 lqqkaqstgeesteqvssgleitgdvgdsatngtine....itiyvklnaGsspidlnkttisvtddgqetlltade 104
                                        + + ++   ++ + v+ +l++tg  ++ +++         + i +   aG +p+ ++  + +++  g         
  gi|313127580|ref|YP_004037850.1|  37 FSPRDTASLPSAADPVAFSLTVTGNQVAVTHERGPPIqvadLRIHIL-VAG-DPLAFQPPVPFFSARG--------- 102
                                       55555555555555555555555555522222221112233333333.223.5555555555555555......... PP

                                       .................T-EE-TT-EEEEEEE--TTT---TT-EEEEEE CS
                    Arch_flagellin 105 fgivvisdtdgsltng.devlekgekvelevnvneddgitagdevsvev 152
                                          +   + +g + +g d v++ ge++ ++++ ++d ++ +g++v+v++
  gi|313127580|ref|YP_004037850.1| 103 ---FR-PGPTGPFNVGsDGVWSAGETGSVVIAGTNDPQPEPGGTVTVQI 147
                                       ...22.3333333333599*************999999*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1057.94
//
Query:       gi|313127581|ref|YP_004037851.1|  [L=445]
Description: hypothetical protein Hbor_28650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2899.77
//
Query:       gi|313127582|ref|YP_004037852.1|  [L=394]
Description: hypothetical protein Hbor_28660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.006   16.4   0.0      0.012   15.4   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.8e-07     0.012      11      48 ..     336     373 ..     335     376 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.8e-07
                                       T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                       +l+e +++++ + + ++tg++ ++v+ lL+++  +G v
  gi|313127582|ref|YP_004037852.1| 336 LLEESGGRMKQANIVKETGWSDAKVSQLLSSMADEGRV 373
                                       689999***************************99966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2640.51
//
Query:       gi|313127583|ref|YP_004037853.1|  [L=268]
Description: electron transfer flavoprotein subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-35  122.4   1.7      3e-35  121.8   1.7    1.3  1  ETF       Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   1.7   1.7e-39     3e-35       7     181 ..      28     216 ..      22     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 1.7e-39
                                       EC.CCCE-HHHHHHHHHHHHHHHH..HT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS-...-CCHHH CS
                               ETF   7 hgvdgklnpvdlealeaArrlkek..aggevtavvvGppeaeealrealaamGadkvilvddpalagy...daeata 78 
                                       +  ++ ln++d++a+e A++l+e+  ++ ev+  ++Gp+++ee++r ala +G+d+++ v+d++ +++   d +  +
  gi|313127583|ref|YP_004037853.1|  28 RYLEYDLNEWDEYAVETAVQLAEAsdEDVEVVSATIGPERSEETIRMALA-KGVDRAVRVWDDDVEAAeflDVDSKV 103
                                       567889******************9655999999****************.****************988999999* PP

                                       HHHHHHHHHC--SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCC.....EEEEEECCCCTEEEEEE- CS
                               ETF  79 kalaalikkedpdlvlagatai.g..kqvaprlAalLgvplitdvteleveggk.....ltvtRpieggnglaevve 147
                                       ++l a++++edpd+vl+g +a  +  + ++  lA   +  + + v +l+ e g      ++v+R++eg  g++e +e
  gi|313127583|ref|YP_004037853.1| 104 RLLEAVVEEEDPDIVLTGVQAHdTgfGATGVALADAIDFEWGAVVNDLDTE-GVledgvARVHRELEG--GVEELTE 177
                                       **********************658*************************9.6789999*********..******* PP

                                       TSSSEEEEE-TTSS--.....--S-TT---EEEE--HHH CS
                               ETF 148 adlpavltvrpgafep.....aaimaakkkeveevevad 181
                                        dlpavlt+++g++ep     ++i++a++ke+   +++d
  gi|313127583|ref|YP_004037853.1| 178 IDLPAVLTIQTGINEPryaslRGIRQAQSKEIAPKTLSD 216
                                       *********************9*********98777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2059.26
//
Query:       gi|313127584|ref|YP_004037854.1|  [L=317]
Description: electron transfer flavoprotein subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-37  126.2   0.3      8e-37  125.1   0.3    1.6  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
    1.7e-30  106.3   0.1    2.7e-30  105.6   0.1    1.3  1  ETF        Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   0.3   8.9e-41     8e-37       1      84 []     196     279 ..     196     279 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 8.9e-41
                                       .-TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHH CS
                         ETF_alpha   1 vdLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqh 77 
                                       vd++ea+v+vs+GrG++++en+el+e+la+alga+++ sR++vd+gw+p++rqvGq+Gk+v+P++yiavGisGa+qh
  gi|313127584|ref|YP_004037854.1| 196 VDITEADVLVSVGRGIEEEENIELVERLADALGATLSSSRPIVDNGWLPKNRQVGQSGKVVTPDVYIAVGISGAVQH 272
                                       699************************************************************************** PP

                                       HGGGTT- CS
                         ETF_alpha  78 laGmkes 84 
                                       +aGmk s
  gi|313127584|ref|YP_004037854.1| 273 VAGMKGS 279
                                       ****987 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.1     3e-34   2.7e-30       2     178 ..       5     173 ..       4     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 3e-34
                                       EEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHH CS
                               ETF   2 lvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeata 78 
                                       l +aeh+ +g l++v+ e+++a+r+l+e++gg++++ ++     +++ +  l   G+d+++ v+  +  +++++ ++
  gi|313127584|ref|YP_004037854.1|   5 LAVAEHR-RGDLRDVSYELVTAGRELAEATGGDLHLAIISG--DVDTFASHLNLDGVDTIHTVEYGE--EFNHDVYT 76 
                                       789***8.*********************999*99888877..46779***************9876..569999** PP

                                       HHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEE CS
                               ETF  79 kalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavlt 155
                                       +a  al +++dp+ vl++++  g ++ap +A +Lg+p+++d+++   + g+ltvtR+++g ++ ++++  +  av+t
  gi|313127584|ref|YP_004037854.1|  77 QAACALTEELDPQYVLTPNSVNGLDYAPAVANRLGLPVVSDAIGMAFD-GGLTVTREMYGSKVETTIEVDSERAVVT 152
                                       ************************************************.66*************999999******* PP

                                       E-TTSS----S-TT---EEEE-- CS
                               ETF 156 vrpgafepaaimaakkkeveeve 178
                                       +r g +ep   +a + ++v +++
  gi|313127584|ref|YP_004037854.1| 153 IRGGEWEPT--EADGDADVAVFD 173
                                       ********5..555566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2251.82
//
Query:       gi|313127585|ref|YP_004037855.1|  [L=280]
Description: farnesyl-diphosphate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-53  180.0   0.0    5.1e-53  179.8   0.0    1.0  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.8   0.0   2.8e-57   5.1e-53       4     232 ..      27     242 ..      24     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 2.8e-57
                                       HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCH CS
                   polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGn 80 
                                       l++ l ++  agGKr+Rp++++l++ea++    + + a + a+++el+h+asLv+DDi+D s++RRG p+a +++G 
  gi|313127585|ref|YP_004037855.1|  27 LSDELAHVALAGGKRVRPAVTILSCEACGG---DADAAVDFAVAIELVHNASLVIDDIIDRSDIRRGTPSAWAEYGY 100
                                       5555667777*******************3...4589**************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHH CS
                   polyprenyl_synt  81 klAindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfal 157
                                         +i ++d ll+ af ll+       +++++++e ++++ eG++ +l ++    ++   ++ey+e  ++KT++lf++
  gi|313127585|ref|YP_004037855.1| 101 GPSIIASDGLLGEAFALLSVD----DHAMQIVAESMVELGEGEATELVAR---PTN---EAEYMELARRKTGALFRA 167
                                       ******************975....47********************655...455...889*************** PP

                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHH CS
                   polyprenyl_synt 158 pvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqr 232
                                       +++l+a++a+a++ ++ea+ ++++++G+aFQi+DD+lD ++d+++lgKp+g+D q  + +++ ++ l+  +++qr
  gi|313127585|ref|YP_004037855.1| 168 AAELGAVAADADPFTVEAFGEYAERVGVAFQIRDDVLDATADADELGKPTGQDEQMDRPSVVQVTDLTPVEANQR 242
                                       ***********9999**************************************************9994444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1817.26
//
Query:       gi|313127586|ref|YP_004037856.1|  [L=380]
Description: hypothetical protein Hbor_28700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.9e-115  383.9   6.5   9.4e-115  383.6   6.5    1.0  1  DUF373    Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.6   6.5  5.3e-119  9.4e-115       2     334 ..       2     357 ..       1     358 [. 0.93

  Alignments for each domain:
  == domain 1  score: 383.6 bits;  conditional E-value: 5.3e-119
                            DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkae...gedvevavvtGde 75 
                                       +Lvlc+D+DdDlgrk+ ++tPvvGr+ v+ aav+la+adPeDSD+N+lf++i+ +d+L a+   +e+veva+vtG++
  gi|313127586|ref|YP_004037856.1|   2 LLVLCIDLDDDLGRKTRFDTPVVGRDSVEAAAVALATADPEDSDSNVLFQGIHEHDSLVADaevDEQVEVAAVTGTQ 78 
                                       79*********************************************************9534588*********** PP

                            DUF373  76 kvgveadrkiaeqldevlsklea..d.saivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalk 149
                                        ++v+a+r+i e++d+vl+ l++  + saiv++DGa+Desvlp+i+srv++dsv+rVvV+q++++Es+yy++k++l+
  gi|313127586|ref|YP_004037856.1|  79 GSDVKANRAIGEEIDRVLAGLSTgeNvSAIVITDGAQDESVLPVIRSRVPIDSVRRVVVRQAQDLESIYYTMKQVLA 155
                                       *********************9987479************************************************* PP

                            DUF373 150 dpelrktiLvplGlllliyallll...lglpe.lalaiillllGlylllrGfgldelleelleklkesleegritfv 222
                                       dpe+r tiLvplG+llliy++l++   +++p+  +l+++++llGly l+rG+gl++++++++++ +++l+egr+t++
  gi|313127586|ref|YP_004037856.1| 156 DPETRGTILVPLGILLLIYPFLTIanrFNVPGaAVLGLVSALLGLYTLFRGLGLETVVDDAVSRGRDILYEGRVTLI 232
                                       ************************99999998688999*************************************** PP

                            DUF373 223 tyvvallllligiisgyislesvss.asvssglltlilafiygavewlalailtaslgkiideylkreekdiarlll 298
                                       tyv+al+l+++g + g++ le++++  +++++    ++a+++gav+w+a+a++t+slg+i+deyl+++  + +r+l+
  gi|313127586|ref|YP_004037856.1| 233 TYVAALALMAVGGFRGVALLEAIQAtVATDPTPPLILAALVHGAVQWFAAAGVTSSLGQITDEYLADR--FKWRYLN 307
                                       ***********************995333344444445589************************655..******* PP

                            DUF373 299 lpflvlaiglvlygasaylls..............lsilalslvvgivva 334
                                       +pf+v ai++vly +s+++l+              l+ la+ l+vg++++
  gi|313127586|ref|YP_004037856.1| 308 APFYVAAIAIVLYVVSGFFLNvngvagvpgvqpfsLTDLAVGLTVGTLLG 357
                                       *******************9999999999998888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2702.75
//
Query:       gi|313127587|ref|YP_004037857.1|  [L=331]
Description: pyruvate formate-lyase-activating protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00024   21.5   0.7      0.004   17.5   0.1    2.4  2  Radical_SAM  Radical SAM superfamily
     0.0022   18.1   0.0     0.0039   17.3   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.075   12.9   0.3       0.39   10.6   0.6    2.1  2  PASTA        PASTA domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   6.7e-07     0.004       6     106 ..      22     124 ..      18     128 .. 0.89
   2 ?    2.0   0.0      0.04   2.4e+02      66     100 ..     142     174 ..     133     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.7e-07
                                       EESS-.-TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTE CS
                                       xxxxx.xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                       Radical_SAM   6 gCnlr.CsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vpgi 78 
                                        C +r C +C+ +e     + +++ ++ ve+  + + e+ +++++ +  ++ggep    d++  ++ l k +  ++ 
  gi|313127587|ref|YP_004037857.1|  22 YCDQRdCFYCPLGENrkNVTDVYANERLVESDDDVISEA-KRMDALGTSITGGEPQEALDKTCHYLSLLKDEfGEDH 97 
                                       588888**********98899999999999999999999.6999*************************99988899 PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvs 106
                                       ++++ t  t   +e ++rl e+g+d + 
  gi|313127587|ref|YP_004037857.1|  98 HTHLYTGITGG-RENMRRLSEAGLDEIR 124
                                       99998888887.***********99875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.04
                                       HHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  66 llerlaklavpgiritvetngtlpdeeklerllel 100
                                       +++ +a++  +g++ ++e++g++ + e+l+ l+e 
  gi|313127587|ref|YP_004037857.1| 142 EILYIARE--EGLTPAFEIPGIRAEQEFLDFLDEG 174
                                       34444444..5888888888888877777777663 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.5e-07    0.0039      11      90 ..      27     106 ..       8     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.5e-07
                           Fer4_14  11 sCkgCd...nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey.pekki 83 
                                        C  C    n+++  + + ++   e  ++++   +++++++ g ++tGGeP   e  ++ ++ ++ lk+e+ ++++ 
  gi|313127587|ref|YP_004037857.1|  27 DCFYCPlgeNRKNVTDVYANERLVESDDDVI--SEAKRMDALGTSITGGEPQ--EALDKTCHYLSLLKDEFgEDHHT 99 
                                       5666665556666666666666666667777..7788888899*********..78999************888*** PP

                           Fer4_14  84 wletngt 90 
                                       +l+t+ t
  gi|313127587|ref|YP_004037857.1| 100 HLYTGIT 106
                                       ****976 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       0.7   4.2e+03       5      23 ..     134     152 ..     134     168 .. 0.81
   2 ?   10.6   0.6   6.5e-05      0.39      31      53 ..     304     326 ..     264     330 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.7
                                       TTTTSBHHHHHHHHHHTT- CS
                             PASTA   5 dvtGmsvdeAkatLkalGl 23 
                                       d+ G  ++e   ++++ Gl
  gi|313127587|ref|YP_004037857.1| 134 DMHGTEWEEILYIAREEGL 152
                                       6789999999999999999 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.5e-05
                                       ECTCCGTTBEEEECS-TTSEECT CS
                             PASTA  31 tsddvpeGtVisQsPeaGtevsk 53 
                                       +  dvpeG +++Q+P  + +v +
  gi|313127587|ref|YP_004037857.1| 304 EEGDVPEGEIVEQYPTVNGTVVE 326
                                       5679*************888855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2272.23
//
Query:       gi|313127588|ref|YP_004037858.1|  [L=148]
Description: hypothetical protein Hbor_28720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-22   80.4  22.4    1.4e-22   80.0  22.4    1.2  1  DUF5518   Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0  22.4     8e-27   1.4e-22       1     116 [.      14     128 ..      14     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 8e-27
                           DUF5518   1 wraaliGavvaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlllglva 77 
                                       w +al+Ga v+++l++l+++ ++s +sl ++l+gGl+aGy+++++++d   +G+++Gl+g++pvl++++ +l+ +++
  gi|313127588|ref|YP_004037858.1|  14 WIYALLGASVSVPLTTLGYWQTGSELSLSPVLLGGLIAGYFSKRNTGDRSGVGVRTGLLGVVPVLWMVADILA-ATS 89 
                                       99**********************************************************************6.777 PP

                           DUF5518  78 aigglagfvallvalllvvllllvvllvilgaiGGaiGg 116
                                       a++g+++f +++val++ + l lv+++++lga +GaiG+
  gi|313127588|ref|YP_004037858.1|  90 ALTGPVWFRVAGVALVIGLSLTLVTVTAGLGAAAGAIGA 128
                                       777777777777777766666666666666655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1218.08
//
Query:       gi|313127589|ref|YP_004037859.1|  [L=170]
Description: methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-10   39.6   0.0      1e-09   38.9   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    2.7e-07   31.2   0.0    5.2e-07   30.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    4.7e-07   29.7   0.0    6.5e-07   29.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      9e-07   28.9   0.4    1.3e-06   28.3   0.3    1.3  1  Methyltransf_23  Methyltransferase domain
      1e-06   29.3   0.0    1.7e-06   28.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.1e-05   25.1   0.0    1.5e-05   24.7   0.0    1.1  1  MTS              Methyltransferase small domain
     0.0014   17.7   0.0     0.0018   17.4   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0035   17.3   0.0     0.0049   16.9   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0039   16.6   0.0     0.0051   16.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.035   13.4   0.0      0.046   13.0   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
       0.04   13.3   0.0      0.052   12.9   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.067   12.8   0.0      0.092   12.3   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.076   12.8   0.0      0.092   12.5   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   7.6e-13     1e-09       1      62 [.      55     110 ..      55     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 7.6e-13
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfed 62 
                                       vL++GcGtG l+ ++ +++  ++v+gvD +e+mle ar++++e    ++++++d+++++ +d
  gi|313127589|ref|YP_004037859.1|  55 VLEFGCGTGPLLTRIEDEY--EEVLGVDADERMLESARKHVSE----ADVLEADFTEWSAAD 110
                                       9*****************8..9*******************75....567777777766555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   3.8e-10   5.2e-07       1      59 [.      56     112 ..      56     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.8e-10
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdll 59 
                                       Le+GcGtG ll +++++    e++gvD +++++e a+++ ++ + + +++ e+ a d++
  gi|313127589|ref|YP_004037859.1|  56 LEFGCGTGPLLTRIEDE--YEEVLGVDADERMLESARKHVSEADVLEADFTEWSAADDI 112
                                       8****************..******************************9999999876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   4.7e-10   6.5e-07       2      56 ..      50     101 ..      49     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.7e-10
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnv 56 
                                       d+++rvl+ GCGtG l+ ++ +e     ev G+D +e+++e+Ar++ ++  + ++
  gi|313127589|ref|YP_004037859.1|  50 DDANRVLEFGCGTGPLLTRIEDEY---EEVLGVDADERMLESARKHVSEADVLEA 101
                                       7899*****************874...47****************8765544444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.3   9.8e-10   1.3e-06      18      62 ..      45     102 ..      27     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.8e-10
                   Methyltransf_23  18 pk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...........k 62 
                                       ++   +  +rvL++GcGtG ll  ++++  +v gvD+++++ e a+            
  gi|313127589|ref|YP_004037859.1|  45 ERyqPDDANRVLEFGCGTGPLLTRIEDEYEEVLGVDADERMLESARkhvseadvleaD 102
                                       232357778*******************99***********99987555554444440 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.2e-09   1.7e-06       1      55 [.      56     106 ..      56     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.2e-09
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl 55 
                                       L++GcGtG l+  +++ +++v+gvD +++ml+ a++++se+++    ++ad+++ 
  gi|313127589|ref|YP_004037859.1|  56 LEFGCGTGPLLTRIEDEYEEVLGVDADERMLESARKHVSEADV----LEADFTEW 106
                                       899************************************9885....77777664 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.1e-08   1.5e-05      16      92 ..      35     111 ..      23     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                                       --HHHHH.HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STT CS
                               MTS  16 lDkGskl.LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvl 90 
                                       lD   ++ Lle  + + +++vl +GcG+G+l + + +e++e  v  vd+d r lesa++ +++ ++  +++++ ++ 
  gi|313127589|ref|YP_004037859.1|  35 LDRDRQVnLLERYQPDDANRVLEFGCGTGPLLTRIEDEYEE--VLGVDADERMLESARKHVSEADVLeADFTEWSAA 109
                                       55555544788888889999*****************9999..9***************998766544776666555 PP

                                       TT CS
                               MTS  91 ee 92 
                                       ++
  gi|313127589|ref|YP_004037859.1| 110 DD 111
                                       55 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-06    0.0018      24      94 ..      45     112 ..      36     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                       HHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHH CS
                            RrnaAD  24 dklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpeev 94 
                                       +  ++ +   vle g G+G l +++ +  ++v  +  der++++ +k++s      v+++Df +++   ++
  gi|313127589|ref|YP_004037859.1|  45 ERYQPDDANRVLEFGCGTGPLLTRIEDEYEEVLGVDADERMLESARKHVS---EADVLEADFTEWSAADDI 112
                                       4556668899*************************************999...889*********998866 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.6e-06    0.0049      21      92 ..      47     111 ..      39     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.6e-06
                   Methyltransf_32  21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieea 92 
                                        + ++a++v+++G+G g L  ++++   e   +v+g+da e++ e+a+k  ++    +  +  f+e s +++
  gi|313127589|ref|YP_004037859.1|  47 YQPDDANRVLEFGCGTGPLLTRIED---E-YEEVLGVDADERMLESARKHVSEAD-VL--EADFTEWSAADD 111
                                       4667899******************...5.459***************9988877.33..334444333333 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.7e-06    0.0051      44     106 ..      48     107 ..      30     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.7e-06
                                       -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE-- CS
                   Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan 106
                                        +  +++vl+  +Gtg l  ++ d+ +   +v ++D +e mL+ ++k++ e  + + +f   +
  gi|313127589|ref|YP_004037859.1|  48 QPDDANRVLEFGCGTGPLLTRIEDEYE---EVLGVDADERMLESARKHVSEADVLEADFTEWS 107
                                       5566789**********9888887665...799******************999998887655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.4e-05     0.046      54     112 ..      43     100 ..      35     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                                       HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS CS
                              CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldler 112
                                       +le+ + ++ +++L+ GcG G l++r  ++y+ +v+g+   +   + a+k+v e+d+ +
  gi|313127589|ref|YP_004037859.1|  43 LLERYQPDDANRVLEFGCGTGPLLTRIEDEYE-EVLGVDADERMLESARKHVSEADVLE 100
                                       56777778889*******************98.8*******************999755 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.7e-05     0.052     153     208 ..      42      97 ..      39     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                              PrmA 153 ealeklvkege.evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNk 208
                                       ++le+++  ++ +vl +G+G+G L +     + ++v++vD De  +++a++ ++  +
  gi|313127589|ref|YP_004037859.1|  42 NLLERYQPDDAnRVLEFGCGTGPL-LTRIEDEYEEVLGVDADERMLESARKHVSEAD 97 
                                       6788887776559*********99.66778899****************99876655 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-05     0.092      13      50 ..      51      87 ..      40     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                              MetW 13 pgsrvldlGcGdGellellkeekqvdgrGleldeegva 50
                                      +  rvl+ GcG G ll+ +++e + +  G++ de+ + 
  gi|313127589|ref|YP_004037859.1| 51 DANRVLEFGCGTGPLLTRIEDEYE-EVLGVDADERMLE 87
                                      5689**************988644.5566777666544 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.7e-05     0.092      68     123 ..      43      98 ..      12     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-05
                                       HTT...--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTT CS
                              PCMT  68 lle...lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldl 123
                                       lle    ++ +rvLe G+G+G    +l+r+  e   v++++  +++ e+a++++ + d+
  gi|313127589|ref|YP_004037859.1|  43 LLEryqPDDANRVLEFGCGTGP---LLTRIEDEYEEVLGVDADERMLESARKHVSEADV 98 
                                       44443356789**********6...5788888889999***************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1239.86
//
Query:       gi|313127590|ref|YP_004037860.1|  [L=225]
Description: hypothetical protein Hbor_28740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        8.8    6.2  10.2       0.58   10.0   0.8    2.7  3  EptA_B_N  Phosphoethanolamine transferase EptA/EptB


Domain annotation for each model (and alignments):
>> EptA_B_N  Phosphoethanolamine transferase EptA/EptB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.8   3.2e-05      0.58       3      45 ..      12      54 ..      10      56 .. 0.90
   2 ?    0.8   0.2     0.023     4e+02      71     113 ..      97     139 ..      86     142 .. 0.59
   3 ?   -0.2   1.9     0.045   8.2e+02      16      23 ..     144     151 ..     115     204 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHHHH--TTTHHHHHHHHHHHHHHHHHHHHHS----SH CS
                          EptA_B_N  3 aalllllsllslryllkpllilllllsaaasYfmdtYgvvidk 45
                                      + +++ ls l +  ++++ l+ +++++a+ +Y + ++g + d+
  gi|313127590|ref|YP_004037860.1| 12 IGVFFGLSALVFGLVFQWSLFAIVVVAAVGTYPFVAFGLLRDD 54
                                      5678999******************************998776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.023
                                       HHHHTHHHHHHHHH-EE----HHHHHHHHHHHHHHHHHHHHHH CS
                          EptA_B_N  71 llllgvlPallllrvkikrksllkellkrlalllvallvivlv 113
                                        l+l++ Pa++ +r     ++l  +    l+l+++a l++v++
  gi|313127590|ref|YP_004037860.1|  97 GLALVLPPAAYAVRHDADVNPLSATQTLALGLIAAASLLLVGL 139
                                       3556667777777777766666666556664444444444433 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.045
                                       TTHHHHHH CS
                          EptA_B_N  16 yllkplli 23 
                                        +l ++ +
  gi|313127590|ref|YP_004037860.1| 144 PILAVIDA 151
                                       22211111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1609.30
//
Query:       gi|313127591|ref|YP_004037861.1|  [L=155]
Description: tRNA(uracil-5)-methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-08   33.0   0.6    6.4e-08   32.5   0.6    1.2  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.6   3.6e-12   6.4e-08       9      61 ..      56     105 ..      49     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.6e-12
                                       EEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM   9 eVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61 
                                        V+v + +   g g+Grt++g++v+v+g lp    ++ V+I++vk++ +r++ 
  gi|313127591|ref|YP_004037861.1|  56 VVTVDDIH-ESGAGVGRTEDGFIVLVDGLLP--EARAVVRIDQVKSNHARSKK 105
                                       599****9.**********************..***************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1161.12
//
Query:       gi|313127592|ref|YP_004037862.1|  [L=170]
Description: DNA-binding protein, tfx family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-31  106.7   0.1    6.4e-31  106.2   0.1    1.2  1  TFX_C         DNA_binding protein, TFX, C-term
    3.4e-06   26.5   1.0    7.2e-06   25.4   1.0    1.6  1  Sigma70_r4    Sigma-70, region 4
    0.00053   20.3   2.7    0.00089   19.6   1.6    1.9  2  HTH_31        Helix-turn-helix domain
    0.00094   18.7   0.4     0.0016   18.0   0.4    1.4  1  GerE          Bacterial regulatory proteins, luxR family
     0.0058   16.7   0.3      0.012   15.6   0.3    1.5  1  HTH_3         Helix-turn-helix
     0.0089   15.8   0.2      0.018   14.8   0.2    1.5  1  HTH_23        Homeodomain-like domain
     0.0097   15.9   0.1      0.023   14.7   0.1    1.8  1  HTH_19        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.023   14.8   0.0    1.5  1  HTH_7         Helix-turn-helix domain of resolvase
      0.019   14.9   0.6       0.21   11.5   0.5    2.3  2  MarR_2        MarR family
      0.044   13.7   0.1      0.071   13.1   0.1    1.4  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.076   12.7   0.3       0.16   11.6   0.1    1.7  2  Sigma70_r4_2  Sigma-70, region 4
       0.08   12.9   0.0       0.13   12.3   0.0    1.4  1  HTH_37        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.1   4.3e-34   6.4e-31       1      83 []      80     162 ..      80     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 4.3e-34
                                       SS-HHHHHHHH---EEEEE--GGGHHHHHHHHHHHHHHHS-S----HHHHHHHHHHH-SSS-----SSS-EEEEESS CS
                             TFX_C   1 AreTlaflealdapvlvtieeGtdlfdipkiiyaeadkagikvkydtieLikllreeapeaikgrvvkedlevyite 77 
                                       AreT+af+eal+apv+v +e+Gtdl+++pk++y+++d+ag+kv+y++++L+k++ + a++a++gr+v e+l v +t+
  gi|313127592|ref|YP_004037862.1|  80 ARETIAFAEALTAPVQVGVEAGTDLYEVPKLVYDACDEAGVKVNYTAPDLMKIIADDAGDAVHGREVIESLLVGVTS 156
                                       9**************************************************************************** PP

                                       SSSEEE CS
                             TFX_C  78 dGeirv 83 
                                       +G++rv
  gi|313127592|ref|YP_004037862.1| 157 TGDVRV 162
                                       ****98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.0   4.8e-09   7.2e-06       4      50 .]      34      79 ..      33      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.8e-09
                                      HS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                        Sigma70_r4  4 sLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLRk 50
                                      +L+ r+ evl lr ++g  ++ I++ lg Sr  V++ie+ A+++++k
  gi|313127592|ref|YP_004037862.1| 34 VLTRRQAEVLALR-ERGIRQSTIADLLGTSRANVSSIESSARQNVKK 79
                                      79**********9.788889***********************9986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.6   5.9e-07   0.00089       9      58 ..      45      94 ..      35     100 .. 0.82
   2 ?   -1.9   0.0       3.1   4.6e+03      37      53 ..     138     153 ..     116     163 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.9e-07
                            HTH_31  9 lReraGLsqeevAerlgvsestlsrlEqGrrgrp.spavlealaralgldp 58
                                      lR ++G++q   A++lg s++ +s +E+ +r+++ + +   a+a+al +++
  gi|313127592|ref|YP_004037862.1| 45 LR-ERGIRQSTIADLLGTSRANVSSIESSARQNVkKARETIAFAEALTAPV 94
                                      44.569**********************77776746669999999999986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                            HTH_31  37 Grrgrpspavlealara 53 
                                       G   +  ++v+e+l+ +
  gi|313127592|ref|YP_004037862.1| 138 GDA-VHGREVIESLLVG 153
                                       444.4567777777655 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.4   1.1e-06    0.0016       2      41 ..      34      73 ..      33      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                      SS-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH CS
                              GerE  2 sLskRErevLrllaeGksnkeIAeelniSekTVkvhksni 41
                                      +L++R++evL+l   G     IA+ l+ S  +V++  s++
  gi|313127592|ref|YP_004037862.1| 34 VLTRRQAEVLALRERGIRQSTIADLLGTSRANVSSIESSA 73
                                      8********************************9866655 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   8.1e-06     0.012       5      32 ..      45      72 ..      42      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.1e-06
                                      HHHTTHHHHHHHHHHTSSHHHHHHHHTT CS
                             HTH_3  5 RkqlglsqeeLAeklGvsrstisriEnG 32
                                      + ++g+ q  +A++lG sr+ +s iE+ 
  gi|313127592|ref|YP_004037862.1| 45 LRERGIRQSTIADLLGTSRANVSSIESS 72
                                      446***********************98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   1.2e-05     0.018       5      32 ..      37      64 ..      33      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                            HTH_23  5 reRlrillllaeGlsvreIAreLgvsrr 32
                                      r+ +++l l  +G+++++IA++Lg sr 
  gi|313127592|ref|YP_004037862.1| 37 RRQAEVLALRERGIRQSTIADLLGTSRA 64
                                      566778888889**************96 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.5e-05     0.023       7      52 ..      44      90 ..      43     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                            HTH_19  7 aReelgltqeelaerlgisrskisaiEng.kkdvpsaelllkiaeal 52
                                      a +e+g+ q  +a+ lg+sr+  s iE+  + +v +a++  ++aeal
  gi|313127592|ref|YP_004037862.1| 44 ALRERGIRQSTIADLLGTSRANVSSIESSaRQNVKKARETIAFAEAL 90
                                      5789***********************99754477788888888877 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-05     0.023      10      36 ..      38      64 ..      30      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                      HHGGGGSSTTTT--STTTSSSS---SS CS
                             HTH_7 10 dinrvvkLleeGisiskIAkevnisRs 36
                                      ++++v++L+e Gi  s+IA+ +++sR+
  gi|313127592|ref|YP_004037862.1| 38 RQAEVLALRERGIRQSTIADLLGTSRA 64
                                      689***********************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.21   3.2e+02      16      35 ..      11      30 ..      10      41 .. 0.81
   2 ?   11.5   0.5   0.00014      0.21       4      41 ..      36      69 ..      21      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.21
                                      CTTTSEEEHHHHHHHHTSSH CS
                            MarR_2 16 rrpgrdltvgelarrlglsk 35
                                      r++g+d+ v+ + +++g ++
  gi|313127592|ref|YP_004037862.1| 11 RGDGGDIDVARILAETGFDP 30
                                      56788899999999999998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsri 41
                                      t+ qa vL aL+ r+   ++++ +a+ lg s+++vs i
  gi|313127592|ref|YP_004037862.1| 36 TRRQAEVL-ALRERG---IRQSTIADLLGTSRANVSSI 69
                                      66666666.466666...9****************976 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.8e-05     0.071      19      41 ..      47      69 ..      19      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                                      EEEHHHHHHHHHTTSSHHHHHHH CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsri 41
                                      e  + q  +A++lG++r  vs i
  gi|313127592|ref|YP_004037862.1| 47 ERGIRQSTIADLLGTSRANVSSI 69
                                      45689***************976 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00011      0.16      11      45 ..      35      68 ..      33      77 .. 0.92
   2 ?   -1.7   0.0       1.6   2.5e+03      40      53 ..      70      83 ..      68      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                      S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHH CS
                      Sigma70_r4_2 11 LperqreifllryleglsykEIAellgisegtVks 45
                                      L+ rq e++ l ++ g  +  IA llg+s ++V s
  gi|313127592|ref|YP_004037862.1| 35 LTRRQAEVLAL-RERGIRQSTIADLLGTSRANVSS 68
                                      899********.69******************976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHHHH CS
                      Sigma70_r4_2 40 egtVksrlsRArkk 53
                                      e++ ++++++Ar+ 
  gi|313127592|ref|YP_004037862.1| 70 ESSARQNVKKARET 83
                                      57889999999975 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.6e-05      0.13      27      58 ..      45      76 ..      23      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.6e-05
                                      HHHCT--HHHHHHHHT--HHHHHHHHTT--TT CS
                            HTH_37 27 iekrelsqseaaqllgiaqPkvsrllrgklsr 58
                                      +++r+++qs +a llg+++++vs+++    ++
  gi|313127592|ref|YP_004037862.1| 45 LRERGIRQSTIADLLGTSRANVSSIESSARQN 76
                                      5789********************99765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1264.46
//
Query:       gi|313127593|ref|YP_004037863.1|  [L=152]
Description: chemotaxis protein CheY [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-20   72.4   0.0    3.7e-20   72.2   0.0    1.1  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0     2e-24   3.7e-20       1     107 [.      11     127 ..      11     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2e-24
                                       EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHHHHHH.......ESEEEEESSCSSSEHHHHHHHHHHCT CS
                      Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealellkeek.......vdlillDinmpgmdGlellkeireed 69 
                                       +l+v+D+p  ++l+++ l++ ++ ++ +++ +g eale l++e+       +dlillD++mp+m G e+l+ei++++
  gi|313127593|ref|YP_004037863.1|  11 ILLVEDNPGDVRLTEKGLQKGNVtNNLHVVPNGIEALEFLRQENeyadaprPDLILLDLDMPKMGGKEVLREIKTDS 87 
                                       89*****************654438999************99888999999**********************9999 PP

                                       ..TTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHH CS
                      Response_reg  70 ..pelpviiltahseeedavealkagaddflsKpfdpeeL 107
                                         + lpv++l++ ++eed+ + +++ a+ +l+Kp+d e  
  gi|313127593|ref|YP_004037863.1|  88 dlKRLPVVVLSSSDAEEDIAKSYDLHANAYLTKPVDFEGF 127
                                       8999*******************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1068.51
//
Query:       gi|313127594|ref|YP_004037864.1|  [L=327]
Description: response regulator with chey-like receiver, aaa-type ATPase, and DNA-binding domains [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-17   62.1   0.0    1.3e-16   60.7   0.0    1.8  1  Response_reg  Response regulator receiver domain
    2.6e-14   53.7   0.4    4.1e-14   53.1   0.4    1.3  1  GAF_2         GAF domain
    2.6e-06   27.8   0.1    4.7e-06   27.0   0.1    1.5  1  GAF_3         GAF domain
    3.3e-05   24.5   0.0    5.3e-05   23.9   0.0    1.4  1  GAF           GAF domain
  ------ inclusion threshold ------
      0.067   12.8   1.0       0.99    9.0   0.1    2.8  3  PP2C_2        Protein phosphatase 2C
        1.8    8.9   6.2        4.2    7.8   0.1    2.9  4  DIMCO_N       Dinitrogenase iron-molybdenum cofactor, N-termi


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   4.4e-20   1.3e-16       2     108 ..      10     123 ..       9     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 4.4e-20
                                       EEESSSHHHHHHHHHHHH.......HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTT CS
                      Response_reg   2 livdDdplvrellrqlle.......eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpe 71 
                                       l+v+D+   ++l++++le        +++ e + +e+ ++ le+l+++++d +llD+ +p+ +Gle+l+++  ++pe
  gi|313127594|ref|YP_004037864.1|  10 LLVEDNLGDARLITRYLEesslpseASEL-ELTHVETLTAGLEHLEKNTYDFVLLDLGLPESTGLETLDRVLSHSPE 85 
                                       78999999999999999954443212233.666899***************************************** PP

                                       SEEEEEESSTSHHHHHHHHHCTESEEEESS.G-HHHHH CS
                      Response_reg  72 lpviiltahseeedavealkagaddflsKp.fdpeeLl 108
                                       lpv++lt+ ++ e avea+  ga+d+l K+ +d ++Ll
  gi|313127594|ref|YP_004037864.1|  86 LPVVVLTGLNNREIAVEAIMRGAQDYLPKDdIDSAQLL 123
                                       *****************************724666665 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.4   1.4e-17   4.1e-14       2     137 ..     160     302 ..     159     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.4e-17
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TT.S-EEEEEEEES-TTSTT-S-B--....-TTHHHHHHHHTS-EEES CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvddd.gglrlaawgeaeeefgaaldrpl....geglvgealrtgrpviln 72 
                                       ++  e+ ++v+++ + ++  +++ +++   d ++++ ++w   ++++ + +   +    g+ l++ea+rt++  +++
  gi|313127594|ref|YP_004037864.1| 160 TSRAEIEQAVCERFIATDpYQFALVGEFSSDfEEFTKRYWESVDKRDLETVLEVKgqllGHQLAAEAVRTREVQVIQ 236
                                       678899999*****999889999999976332334444777776666655544223447999********9999999 PP

                                       -GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  73 dleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                        ++e + +  +    +++ +++ +a+Pl+ e  v+Gvl++ya++p+afde+++e+L el+++i+ ai
  gi|313127594|ref|YP_004037864.1| 237 TVAEGALSEEQKdeIAEHEVKAVAAIPLVFE-TVHGVLVVYADHPYAFDEQEREVLGELGQTIGYAI 302
                                       98884444444445788888888*******8.5*********************************9 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   1.6e-09   4.7e-06      49     127 ..     226     302 ..     202     304 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.6e-09
                             GAF_3  49 sld.edsalarralssgevvsepsfaeedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqia 124
                                       +++ ++ ++++++++  +++se + +e   ++  a+ a+PLv  ++v Gvl+++ ++p afd++++e l +l++ i+
  gi|313127594|ref|YP_004037864.1| 226 AVRtREVQVIQTVAE--GALSEEQKDEIAEHEVKAVAAIPLVF-ETVHGVLVVYADHPYAFDEQEREVLGELGQTIG 299
                                       444233344444422..456667767777788888899*****.********************************* PP

                             GAF_3 125 tai 127
                                        ai
  gi|313127594|ref|YP_004037864.1| 300 YAI 302
                                       999 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.8e-08   5.3e-05      48     133 .]     219     302 ..     180     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.8e-08
                                       TSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHH CS
                               GAF  48 grgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellq 123
                                       g+ +++++++t+++ vi+ + +++  ++ +++d ++++++++++++Plv +  + G+lv++  +p  f+++e+e+l 
  gi|313127594|ref|YP_004037864.1| 219 GHQLAAEAVRTREVQVIQTV-AEGALSE-EQKDEIAEHEVKAVAAIPLVFE-TVHGVLVVYADHPyAFDEQEREVLG 292
                                       44455588999999999944.6666666.68999***************96.89********99999********** PP

                                       HHHHHHHHHH CS
                               GAF 124 vladqvaval 133
                                       +l++ ++ a+
  gi|313127594|ref|YP_004037864.1| 293 ELGQTIGYAI 302
                                       ****999886 PP

>> PP2C_2  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00033      0.99      44      87 ..      98     140 ..      97     176 .. 0.75
   2 ?    0.8   0.0      0.11   3.2e+02     170     205 ..     174     211 ..     161     217 .. 0.73
   3 ?   -0.8   0.0      0.33   9.9e+02      18      44 ..     226     253 ..     216     264 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00033
                            PP2C_2  44 riaveavvealaelleseeeeeeallraleaailadvlkeeaea 87 
                                       +iavea+++  +++l ++++++++llr+l+ ai+++  +ee+ +
  gi|313127594|ref|YP_004037864.1|  98 EIAVEAIMRGAQDYLPKDDIDSAQLLRSLRYAIERKK-REEKLE 140
                                       69*******************************9775.333333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                            PP2C_2 170 lmTDGlanslrdee..rfaelleellrvleeegvseqL 205
                                       ++TD ++ +l+ e   +f+e+++++++++++ ++++ L
  gi|313127594|ref|YP_004037864.1| 174 IATDPYQFALVGEFssDFEEFTKRYWESVDKRDLETVL 211
                                       66777775553222339************999855544 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.33
                            PP2C_2  18 vwtdsggsll.aVaDGaGSakrSerGar 44 
                                       ++++++++++  Va Ga S ++ ++ a+
  gi|313127594|ref|YP_004037864.1| 226 AVRTREVQVIqTVAEGALSEEQKDEIAE 253
                                       5677788888889998888776555454 PP

>> DIMCO_N  Dinitrogenase iron-molybdenum cofactor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.5   7.4e+03      30      57 ..      27      54 ..      15      59 .. 0.62
   2 ?    7.8   0.1    0.0014       4.2      17      45 ..     115     143 ..     108     172 .. 0.72
   3 ?    3.4   0.3     0.032        95      19      72 ..     205     256 ..     196     264 .. 0.70
   4 ?   -3.3   0.0         4   1.2e+04      28      40 ..     294     306 ..     288     325 .. 0.48

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.5
                           DIMCO_N 30 erlgeplteekLakltvtdLktalasad 57
                                      e   +p ++ +L+   v+ L  +l++++
  gi|313127594|ref|YP_004037864.1| 27 EESSLPSEASELELTHVETLTAGLEHLE 54
                                      4444566666777777777777766554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0014
                           DIMCO_N  17 pgvdvaqLlevLqerlgeplteekLaklt 45 
                                       +++d aqLl+ L  +++ +  eekL++l 
  gi|313127594|ref|YP_004037864.1| 115 DDIDSAQLLRSLRYAIERKKREEKLETLN 143
                                       47999*********************984 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.032
                           DIMCO_N  19 vdvaqLlevLqerlgeplteekLakltvtdLktalasadgeeeeldigveseaL 72 
                                        d++  lev  + lg++l +e+ ++  v+ ++t+ + +  +ee+ d ++++++ 
  gi|313127594|ref|YP_004037864.1| 205 RDLETVLEVKGQLLGHQLAAEAVRTREVQVIQTVAE-GALSEEQKD-EIAEHEV 256
                                       4666778888899************99999999764.333343334.3444444 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 4
                           DIMCO_N  28 Lqerlgeplteek 40 
                                       L +++g  +t  +
  gi|313127594|ref|YP_004037864.1| 294 LGQTIGYAITSLE 306
                                       5556666555322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 2551.33
//
Query:       gi|313127595|ref|YP_004037865.1|  [L=342]
Description: mannose-1-phosphate guanylyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-36  124.5   0.0    7.6e-36  124.0   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    1.6e-08   35.1   0.2    1.6e-08   35.1   0.2    2.2  3  NTP_transf_3     MobA-like NTP transferase domain
    3.7e-05   23.7   0.1    7.3e-05   22.7   0.1    1.5  1  MannoseP_isomer  Mannose-6-phosphate isomerase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   0.0   1.3e-39   7.6e-36       2     239 ..      12     266 ..      11     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 1.3e-39
                                       EEEE--S--GGGTTCCTTSSGGGSEETTET.ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgke.rliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       a++LaGG+G+RL+P +r+  +k+++ l ++ +l+  t+sr+   g+ + ++v+t   ++ ++++++e +    + ++
  gi|313127595|ref|YP_004037865.1|  12 ALVLAGGTGSRLYPASRADRPKQFLSLLGDdSLLSRTVSRAR--GVADDVFVST---RPAFADEISEHA---PDAEV 80 
                                       89***********************999999*********99..4555588888...666777777665...35789 PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHH.HHTHSSTT.SEEEEEEESS-CTTSEEEE CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkk.aiekaakg.tvtfgivpveeateyGvie 152
                                       ++ep  k+t +A++ a   ++++  d +v+ L++Dh ++d + +++++ a+ +++ g +vtfg++p+++ t+yG+ie
  gi|313127595|ref|YP_004037865.1|  81 VVEPAAKDTGPALVYATHRIRETVGDCVVVALPSDHTVGDSFAAVMRRgARVADETGsLVTFGVEPTRPDTGYGYIE 157
                                       9***********************9999**************9999882444555579******************* PP

                                       ECTTS....BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTT CS
                   NTP_transferase 153 adeeg....rverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkd 225
                                       ++e++     v  f EKP++++a e++++G  ++n +++    +     + +++ ++d++  +++ ++++ af+  +
  gi|313127595|ref|YP_004037865.1| 158 PGESRgdyaPVSAFHEKPDAETAHEYVEAG-HYWNAGIFAWTPDA-LLAAARDSPLSDLVTDLTDGTDPERAFDGVA 232
                                       **66667789*************9999999.67999999999653.3344566678999999999999999987777 PP

                                       EE....................-EEEXSSHHHHH CS
                   NTP_transferase 226 ae....................yWsDvGtldsll 239
                                       +                      W+D+G++d++ 
  gi|313127595|ref|YP_004037865.1| 233 EVsidygvmertedavvvpapfEWDDLGSWDAFD 266
                                       4499999999*********************985 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.2   2.6e-12   1.6e-08       1      73 [.      12      92 ..      12     154 .. 0.77
   2 ?   -2.4   0.0      0.91   5.4e+03      85     109 ..     198     220 ..     163     235 .. 0.72
   3 ?   -1.7   0.1      0.56   3.3e+03      39      66 ..     306     335 ..     285     341 .. 0.53

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.6e-12
                                      EEEEEESS-TTT......TTTHHHHCC.CCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCTS-EEE-TTS. CS
                      NTP_transf_3  1 aviLAGGrSsRm......ggdKallpl.ggkpllervldalraagvdevvvvggd...eevlaalarlgvrvvededp. 68
                                      a++LAGG +sR+       ++K++l l g+ +ll r++ ++r + +d+v+v++++   +e+ ++   ++++vv+++ + 
  gi|313127595|ref|YP_004037865.1| 12 ALVLAGGTGSRLypasraDRPKQFLSLlGDDSLLSRTVSRARGV-ADDVFVSTRPafaDEISEH--APDAEVVVEPAAk 87
                                      79**********77766557*******9999*************.9*******99555566655..3568888887653 PP

                                      S-SHH CS
                      NTP_transf_3 69 gkgpl 73
                                      ++gp+
  gi|313127595|ref|YP_004037865.1| 88 DTGPA 92
                                      45654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.91
                                       SSSCEEEEETT-TT--HHHHHHHHH CS
                      NTP_transf_3  85 dadavlvlacDmPlltpelverlla 109
                                         da+l +a D Pl  ++lv  l++
  gi|313127595|ref|YP_004037865.1| 198 TPDALLAAARDSPL--SDLVTDLTD 220
                                       45677777777777..556665555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.56
                                       -CEEEEECSHCHHHH..HHTTCTS-EEE-T CS
                      NTP_transf_3  39 vdevvvvggdeevla..alarlgvrvvede 66 
                                       v+++ vv+ d+ vl     + ++vr+++de
  gi|313127595|ref|YP_004037865.1| 306 VSDLAVVTWDDRVLVvpKERAQDVRTLVDE 335
                                       444444444433221001122345555555 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.2e-08   7.3e-05       1      37 [.     304     340 ..     304     342 .] 0.95

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.2e-08
                   MannoseP_isomer   1 vGvedlvvvetkdavlvadkdkvqdvkkvveelkaeg 37 
                                       vGv+dl+vv  +d vlv+ k+++qdv+ +v+elk++g
  gi|313127595|ref|YP_004037865.1| 304 VGVSDLAVVTWDDRVLVVPKERAQDVRTLVDELKQRG 340
                                       79*******************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2611.38
//
Query:       gi|313127596|ref|YP_004037866.1|  [L=92]
Description: hypothetical protein Hbor_28800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 738.95
//
Query:       gi|313127597|ref|YP_004037867.1|  [L=319]
Description: ob-fold nucleic acid binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.04   14.4   0.5      0.065   13.7   0.5    1.3  1  Notch            LNR domain
      0.062   13.3   0.0       0.41   10.7   0.0    2.4  2  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> Notch  LNR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   7.2e-06     0.065       2      26 ..     197     220 ..     196     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-06
                             Notch   2 eqCsaeeyCaekfgdgvCDeeCnne 26 
                                       ++C++e +C +  ++g+C+e+ n e
  gi|313127597|ref|YP_004037867.1| 197 KRCPEE-GCTRVLQNGRCNEHGNVE 220
                                       69**88.************987654 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.5e-05      0.41      13      72 ..     106     162 ..      92     169 .. 0.81
   2 ?   -1.8   0.0      0.36   3.2e+03      14      30 ..     287     303 ..     279     304 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.5e-05
                                       EEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon  13 rsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72 
                                       rs++  +   l D++gr++ v f    t+ + +l+eG v+r    v+  ++g +++k ++
  gi|313127597|ref|YP_004037867.1| 106 RSESISQVGLLGDESGRMKFVSFT---TSELPELEEGAVYRLGNVVTDEYQGNFSVKLNR 162
                                       555555556699************...***************99999888888*999886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.36
                                       EETTEEEEEEEETTEEE CS
                   tRNA_anti-codon  14 sggkvifidlrDgtgri 30 
                                       sg  +  ++l D+t+r+
  gi|313127597|ref|YP_004037867.1| 287 SGPELGRYVLADETDRL 303
                                       55566677888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2374.13
//
Query:       gi|313127598|ref|YP_004037868.1|  [L=212]
Description: hypothetical protein Hbor_28820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1383.27
//
Query:       gi|313127599|ref|YP_004037869.1|  [L=142]
Description: ribbon-helix-helix protein, copg family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-05   23.0   1.4    8.8e-05   22.3   0.2    2.0  2  RHH_1           Ribbon-helix-helix protein, copG family
     0.0026   18.2   0.0     0.0077   16.7   0.0    1.8  2  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys
     0.0037   16.8   0.1     0.0077   15.8   0.1    1.5  1  DUF3562         Protein of unknown function (DUF3562)
     0.0096   16.1   0.7      0.014   15.6   0.7    1.3  1  DUF4047         Domain of unknown function (DUF4047)
  ------ inclusion threshold ------
      0.011   15.7   2.2      0.023   14.7   2.2    1.5  1  Sec2p           GDP/GTP exchange factor Sec2p
      0.049   13.2   0.6          1    9.0   0.0    2.3  2  Sigma70_r4      Sigma-70, region 4


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2     3e-08   8.8e-05       2      37 ..      15      50 ..      14      51 .. 0.94
   2 ?   -2.9   0.1       2.6   7.8e+03      12      16 ..     101     105 ..      97     108 .. 0.47

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3e-08
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                      +s+r+ e+  e+L+e+a++r+ S S+++R+++  ++
  gi|313127599|ref|YP_004037869.1| 15 ISFRVNEDAFETLREIAEERDISLSAVFRDYVDTLV 50
                                      89****************************997765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                                       HHHHH CS
                             RHH_1  12 erLde 16 
                                       e+L+e
  gi|313127599|ref|YP_004037869.1| 101 EQLEE 105
                                       33444 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.6e-06    0.0077      39      75 ..       9      45 ..       2      48 .. 0.88
   2 ?   -2.5   0.1       2.6   7.7e+03      10      10 ..     119     119 ..     103     134 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-06
                    CopG_antitoxin 39 kkktksislrlpedlLealkekAnkrdvpyqslikel 75
                                        k+k+is+r++ed  e+l+e A++rd++ +   +++
  gi|313127599|ref|YP_004037869.1|  9 GNKNKTISFRVNEDAFETLREIAEERDISLSAVFRDY 45
                                      5799*************************99888776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.6
                    CopG_antitoxin  10 e 10 
                                       +
  gi|313127599|ref|YP_004037869.1| 119 D 119
                                       2 PP

>> DUF3562  Protein of unknown function (DUF3562)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.6e-06    0.0077       2      32 ..      21      51 ..      20      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                           DUF3562  2 ddvdeiiqaiAeetdaPeelVsrlyedavaa 32
                                      +d +e +++iAee+d+   +V r y d++ a
  gi|313127599|ref|YP_004037869.1| 21 EDAFETLREIAEERDISLSAVFRDYVDTLVA 51
                                      6889***********************9865 PP

>> DUF4047  Domain of unknown function (DUF4047)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.7   4.7e-06     0.014      13     109 ..      30     125 ..      18     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.7e-06
                           DUF4047  13 tkveatistaiifPktvdtlveqakqhkelilheyeemksklkvdsveeieqalsvwkqgrekikaerealqkvyte 89 
                                          e  is + +f   vdtlv +  q + + +he e+m+++ + +   +++   s  + ++e++  e + l++  +e
  gi|313127599|ref|YP_004037869.1|  30 IAEERDISLSAVFRDYVDTLVAHDGQVQVVPEHELEQMNGNDEESFPPKVKVPKSFIR-EHERLELEADHLREQLEE 105
                                       4556789*********************************988777777776665555.679999999999999999 PP

                           DUF4047  90 ieepynqvqeelkvnksess 109
                                          + n  +e+l  +++e +
  gi|313127599|ref|YP_004037869.1| 106 HKRYVNYLREQLEDEEEEVI 125
                                       99999999999988887765 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.2   7.6e-06     0.023      43      85 ..      87     129 ..      79     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-06
                                       HHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXX CS
                             Sec2p  43 kekealekkneklkeqLkeketlleslqeqLkeLkevlekmee 85 
                                       +e+e+le + ++l+eqL+e +  ++ l eqL++  e + ++e+
  gi|313127599|ref|YP_004037869.1|  87 REHERLELEADHLREQLEEHKRYVNYLREQLEDEEEEVIQLED 129
                                       899****************************997776666665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00034         1      22      37 ..      26      41 ..      15      43 .. 0.91
   2 ?    2.1   0.2     0.047   1.4e+02       4      15 ..     116     127 ..     115     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00034
                                      -HHHHHHHHTS-HHHH CS
                        Sigma70_r4 22 TleEIgerlgiSrerV 37
                                      Tl EI+e+ +iS+++V
  gi|313127599|ref|YP_004037869.1| 26 TLREIAEERDISLSAV 41
                                      9************988 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.047
                                       HS-HHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlel 15 
                                       +L+++e ev++l
  gi|313127599|ref|YP_004037869.1| 116 QLEDEEEEVIQL 127
                                       89********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1382  (0.0770818); expected 358.6 (0.02)
Passed bias filter:                      789  (0.0440069); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1012.24
//
Query:       gi|313127600|ref|YP_004037870.1|  [L=151]
Description: hypothetical protein Hbor_28840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1052.30
//
Query:       gi|313127601|ref|YP_004037871.1|  [L=174]
Description: peroxiredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-26   91.4   0.0    5.4e-26   90.9   0.0    1.2  1  AhpC-TSA  AhpC/TSA family
    3.1e-12   46.4   0.0    3.6e-12   46.2   0.0    1.1  1  Redoxin   Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.0     6e-30   5.4e-26       2     123 ..       5     135 ..       4     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 6e-30
                                       TSB----EEE...STTCEEEECHHH..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHH CS
                          AhpC-TSA   2 gdkapdfelk...nadgetvslsdy..kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspesh 73 
                                       g++ap f+l+     d ++ +ls+y  +g  v+l+fyp+d+ p C  +++ l+++       +  v+g+  ds+++h
  gi|313127601|ref|YP_004037871.1|   5 GQQAPAFSLPgaaGDDMDEHTLSEYveRGWSVILVFYPFDFHPACISQWCTLRDADWLTLLDDTVVLGIGGDSVYAH 81 
                                       9*********665445699*******99999*************************999999*************** PP

                                       HHHHHH-H.SSEEEE-TTSHHHHHTT-EETT....TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  74 kkfiekeslnfpllsDeegkvakaygvlkee....kglalratfvidkegkiry 123
                                       ++f+++++++fpll D++g va+aygv  ++     +++  a fvid++ +i++
  gi|313127601|ref|YP_004037871.1|  82 QEFARTYNIEFPLLTDSDGRVAEAYGVRESDfeghRNVPGMALFVIDPDRTIQF 135
                                       ****************************999****9****************96 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0     4e-16   3.6e-12       2     136 ..       4     142 ..       3     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 4e-16
                                       TTSBB---ECCEET.TCEEEEEHHH..HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH CS
                           Redoxin   2 agdkaPdftlplaa.tdgnsvslse..fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf 75 
                                        g++aP+f+lp+aa +d  +++lse   +g +v+++f+p  f P C  + + l++ + l    +  v+++  d+   
  gi|313127601|ref|YP_004037871.1|   4 LGQQAPAFSLPGAAgDDMDEHTLSEyvERGWSVILVFYPFDFHPACISQWCTLRDADWLTLLDDTVVLGIGGDSVYA 80 
                                       699******99877256689*****8888999***************************666555555555555555 PP

                                       HHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG...EEE-EEEEEEETTEEEEEEESSSC CS
                           Redoxin  76 vkefwgkeglkfpvlsDgsaaftkalGlrleedaseg...lrtpryavidedgkvvylevepep 136
                                        +ef+  +++ fp+l+D ++ +++a+G+r  e   eg   +   +++vid d  +    +++  
  gi|313127601|ref|YP_004037871.1|  81 HQEFARTYNIEFPLLTDSDGRVAEAYGVR--ESDFEGhrnVPGMALFVIDPDRTIQFAWRGDAA 142
                                       9999999********************77..444444668778889999999988877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1316.37
//
Query:       gi|313127602|ref|YP_004037872.1|  [L=52]
Description: hypothetical protein Hbor_28870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 386.70
//
Query:       gi|313127603|ref|YP_004037873.1|  [L=70]
Description: hypothetical protein Hbor_28880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 510.30
//
Query:       gi|313127604|ref|YP_004037874.1|  [L=249]
Description: nuleotide-utilizing enzyme, moea [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-30  106.2   0.2    1.6e-30  105.6   0.2    1.2  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.2   9.2e-35   1.6e-30       1     138 [.       4     165 ..       4     169 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 9.2e-35
                                       EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHH CS
                     MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpea 77 
                                       a++tvG+ell+g+ie+tn+ +la++l+e+gv+v+++ ++pD+e+ i+e++ ++  + d++++tGG+G tpdD+t   
  gi|313127604|ref|YP_004037874.1|   4 AIVTVGNELLAGDIENTNATWLARELTERGVKVARVITIPDEETTIAETVGEWSMSFDAVVVTGGLGGTPDDLTMPG 80 
                                       79************************************************8887888******************** PP

                                       HHHHHSEE-HHHHHHHHHHHHHHCC.............................TTSHGGGGGGE.EETTEEEEE-S CS
                     MoCF_biosynth  78 laklfekelegfeeafrrvslkpgk.............................pvgvapgailsravgktiigLPG 125
                                       +a+ +++el  +++a   v++  ++                             p g+apg++ +     ++++LPG
  gi|313127604|ref|YP_004037874.1|  81 VAAGLDRELAVDPVAAADVEATIDRilerkpdiefdlkvewyasmpagatpipnPEGLAPGCVAE-----NVYVLPG 152
                                       ***********************99********************99999999999999997665.....6****** PP

                                       SHHHHHHHHHHHH CS
                     MoCF_biosynth 126 spkavkealeeil 138
                                        p +++++++++ 
  gi|313127604|ref|YP_004037874.1| 153 IPEEMRAVFDNVA 165
                                       *********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1750.53
//
Query:       gi|313127605|ref|YP_004037875.1|  [L=391]
Description: zn-dependent protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-24   84.6   5.1    2.6e-14   53.4   0.1    2.8  3  CBS             CBS domain
      7e-15   55.0  10.8    5.2e-09   35.7   0.2    2.9  3  Peptidase_M50   Peptidase family M50
    5.3e-05   22.9   4.7    5.3e-05   22.9   4.7    2.2  2  Peptidase_M50B  Peptidase M50B-like


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.65   3.9e+03      36      55 ..     142     166 ..     135     168 .. 0.67
   2 !   32.3   0.5   1.6e-11   9.7e-08       1      51 [.     249     300 ..     249     305 .. 0.82
   3 !   53.4   0.1   4.4e-18   2.6e-14       1      55 [.     313     367 ..     313     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.65
                                       E..ETTT..B.EEEEEEHHHHHHHH CS
                               CBS  36 V..dedg..k.lvGivtlrDllral 55 
                                       V    +g  k ++G++ l+ +l a+
  gi|313127605|ref|YP_004037875.1| 142 VlpATQGsvKfVLGYLALTNILLAV 166
                                       4453445334467***999999886 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 1.6e-11
                                       HHHHSBSSCE..EEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   1 Vgdimtrdvv..tvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDl 51 
                                       V+d+mt++    +v+  t+++e+l++ +  ++++++PVV  +g+lvG+vtl D 
  gi|313127605|ref|YP_004037875.1| 249 VRDVMTPREKldVVDIRTSISELLDRmFY-ERHTGYPVV-QNGRLVGMVTLNDA 300
                                       899*9995544599999*********453.3378*****.7**********996 PP

  == domain 3  score: 53.4 bits;  conditional E-value: 4.4e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+d+m+ ++ t++p+++  +a+ +m ++gv+rlPVVd++g+lvG+++++Dl+ al
  gi|313127605|ref|YP_004037875.1| 313 VKDVMSGELTTISPSADAMDAITTMQQNGVGRLPVVDDEGELVGLISRSDLVTAL 367
                                       89***********************8888**********************9987 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   5.4   2.8e-08   0.00017       2     107 ..      68     138 ..      67     145 .. 0.92
   2 !   35.7   0.2   8.7e-13   5.2e-09     187     250 .]     149     209 ..     140     209 .. 0.88
   3 ?   -3.0   0.0      0.58   3.4e+03      96     109 ..     215     240 ..     211     331 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.8e-08
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka 78 
                                       +++ l+++v++HE+GH lvA   g+++++                    i+l+ +GG+ ++a++ ++          
  gi|313127605|ref|YP_004037875.1|  68 AAIGLFLCVLFHEFGHSLVAMHYGYEIDS--------------------ITLWLFGGVASFAEMPEDW--------- 115
                                       57899**********************99....................999***********99554......... PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  79 flkkspwqrllivlAGplanfilailvfv 107
                                              q+l+i++AGp++ + l+++ fv
  gi|313127605|ref|YP_004037875.1| 116 ------RQELVIAVAGPIVSVALGVISFV 138
                                       ......5*****************99986 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 8.7e-13
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 187 glssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglalllll 250
                                       +++ +l +lal ++ L+++N+lP +++DGg++l+all + r   + +r++++a  vg ++ +ll
  gi|313127605|ref|YP_004037875.1| 149 SVKFVLGYLALTNILLAVFNMLPGFPMDGGRVLRALLARRR---SHARATKLAAEVGKMFAFLL 209
                                       4557899*****************************99777...999*********99998875 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.58
                                       XXXXXXXXXXXXX............- CS
                                       xxxxxxxxxxxxx............x RF
                     Peptidase_M50  96 lanfilailvfvv............p 109
                                       + n+ l  l+f++            +
  gi|313127605|ref|YP_004037875.1| 215 FYNLFLVALAFFIymgasseaqqtvM 240
                                       55655555555554444333333330 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   4.7   8.9e-09   5.3e-05      23     111 ..      74     166 ..      62     175 .. 0.72
   2 ?    0.4   0.5     0.072   4.3e+02     107     143 ..     204     240 ..     177     297 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8.9e-09
                    Peptidase_M50B  23 lvvffHElGHalaalLtGgrvkgielhsdesGvtvtrg..pgglgqiltllaGYlgpallGlllil...lsasgkar 94 
                                       l v+fHE+GH l+a+  G+++++i+l    +Gv+  +   + + +  ++++aG++ +  lG++ ++   ++ +++ +
  gi|313127605|ref|YP_004037875.1|  74 LCVLFHEFGHSLVAMHYGYEIDSITLWLF-GGVASFAEmpEDWRQELVIAVAGPIVSVALGVISFVgfvVLPATQGS 149
                                       679***********************986.6777777777778888999********99887644311133333444 PP

                    Peptidase_M50B  95 lllvllvllllvllllv 111
                                       +  vl+ l+l  +ll v
  gi|313127605|ref|YP_004037875.1| 150 VKFVLGYLALTNILLAV 166
                                       44444444444444444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.072
                    Peptidase_M50B 107 llllvrnlfglvlllllgallllvlllaedellefll 143
                                       ++ +   +fgl+  l+l+al +++ + a++e++++++
  gi|313127605|ref|YP_004037875.1| 204 MFAFLLGIFGLFYNLFLVALAFFIYMGASSEAQQTVM 240
                                       4444445566666666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2806.45
//
Query:       gi|313127606|ref|YP_004037876.1|  [L=125]
Description: cupin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-16   60.1   0.2      2e-16   59.4   0.2    1.3  1  Cupin_2          Cupin domain
    4.4e-07   29.6   0.0    6.8e-07   29.0   0.0    1.3  1  Cupin_1          Cupin
    9.8e-06   25.5   0.0    1.2e-05   25.2   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    1.3e-05   25.2   0.0    1.6e-05   24.8   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
     0.0024   17.5   0.1     0.0045   16.7   0.1    1.5  1  Cupin_3          Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.042   14.1   0.0    1.2  1  CENP-C_C         Mif2/CENP-C like
        0.1   12.8   0.1       0.14   12.3   0.1    1.2  1  ARD              ARD/ARD' family


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.2   7.8e-20     2e-16       3      70 ..      45     111 ..      43     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 7.8e-20
                                       EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       ++l+pG++ p h+ + e +  yVl+G+ ++ +d+ee+e+ aGds+++p g+ H++rN++d +  +l+ 
  gi|313127606|ref|YP_004037876.1|  45 FVLEPGATVPKHTNDVE-HEQYVLSGKYTVGIDDEEYEVAAGDSLFIPGGVIHWYRNDSDVEGTFLCA 111
                                       789**************.******************************************99999985 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.7e-10   6.8e-07      36     113 ..      43     112 ..      36     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.7e-10
                                       EEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEE CS
                           Cupin_1  36 arvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaivv 112
                                        r++lepg+ ++ h++   +  +yvl G+ +vg+  ++        ++ +Gd + +P g++h+  n+ d ++  + +
  gi|313127606|ref|YP_004037876.1|  43 RRFVLEPGATVPKHTN-DVEHEQYVLSGKYTVGIDDEE-------YEVAAGDSLFIPGGVIHWYRNDSDVEGTFLCA 111
                                       56778***********.99999*********9886666.......59********************9888776555 PP

                                       E CS
                           Cupin_1 113 f 113
                                       +
  gi|313127606|ref|YP_004037876.1| 112 V 112
                                       4 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   4.7e-09   1.2e-05      60     128 ..      37     104 ..      28     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.7e-09
                   MannoseP_isomer  60 geryqvkritvkPgeklslqkhhhraeh.WvvvkGtakvtvddevlllkenestyiplgaihrlenpGki 128
                                       + ++ ++r +++Pg++  + kh    eh   v++G   v +dde++++ + +s +ip g+ih   n   +
  gi|313127606|ref|YP_004037876.1|  37 APNFAIRRFVLEPGAT--VPKHTNDVEHeQYVLSGKYTVGIDDEEYEVAAGDSLFIPGGVIHWYRNDSDV 104
                                       5689**********97..578888888844689*****************************99997665 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   6.2e-09   1.6e-05      14      67 ..      51     104 ..      42     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.2e-09
                                       -SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTS CS
                      AraC_binding  14 hsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsed 67 
                                         +p+h+ d  + +yv++G+ ++ +++++y++ +Gd +++p g++H y+ ds+ 
  gi|313127606|ref|YP_004037876.1|  51 ATVPKHTNDVEHEQYVLSGKYTVGIDDEEYEVAAGDSLFIPGGVIHWYRNDSDV 104
                                       56678888877779************************************9964 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.7e-06    0.0045      30      60 ..      65      94 ..      44     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.7e-06
                                      EEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 30 yileGevkvtpeggetvelraGDlvvlpkgl 60
                                      y+l+G+ +v   + e++e+ aGD++++p g 
  gi|313127606|ref|YP_004037876.1| 65 YVLSGKYTVGI-DDEEYEVAAGDSLFIPGGV 94
                                      9**********.999*************886 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.6e-05     0.042      27      78 ..      54     105 ..      37     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                       EEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS- CS
                          CENP-C_C  27 kknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnke 78 
                                       +k+ ++     yV+ G+  v + ++++ ++ g++  +P g     +N+++ e
  gi|313127606|ref|YP_004037876.1|  54 PKHTNDVEHEQYVLSGKYTVGIDDEEYEVAAGDSLFIPGGVIHWYRNDSDVE 105
                                       56777777788****************************9999999988766 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.6e-05      0.14      95     140 ..      63     103 ..      53     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
                               ARD  95 irliveGtgyFdvrskdeawirvlvekGDLivlPagiyhrFtlted 140
                                         ++++G   + v   de++    v +GD +++P g+ h++  ++d
  gi|313127606|ref|YP_004037876.1|  63 EQYVLSG--KYTVGIDDEEYE---VAAGDSLFIPGGVIHWYRNDSD 103
                                       5566665..59999******9...9***************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 906.74
//
Query:       gi|313127607|ref|YP_004037877.1|  [L=686]
Description: DNA/RNA helicase, superfamily ii [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.6e-22   78.3   0.0    1.1e-21   77.4   0.0    1.5  1  DEAD        DEAD/DEAH box helicase
    3.9e-13   49.7   0.0    9.5e-13   48.5   0.0    1.7  1  Helicase_C  Helicase conserved C-terminal domain
    1.9e-11   44.3   0.0    3.5e-11   43.4   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.18   11.7   0.0       0.41   10.6   0.0    1.5  1  DUF4428     Domain of unknown function (DUF4428)


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   2.5e-25   1.1e-21       2     170 ..     226     395 ..     225     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 2.5e-25
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       ++Q+ a+++ l +++d lv  +T++GKTl+  ++ +++ +    +   k+l+++P+ +La+q +++++++    +l+
  gi|313127607|ref|YP_004037877.1| 226 PVQSLAVENGLfDERDQLVVSATATGKTLVGELAGVNRAL----NGDGKMLFLVPLVALANQKHEDFEERYGD-HLN 297
                                       789999999997889*********************9996....57779******************999985.578 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       v   +g ++ +d+ +++d ++di+vgt + +d+ l+tgk +l ++ ++V+DE+++l + +++  ++ ++++l++ ++
  gi|313127607|ref|YP_004037877.1| 298 VTIRVGASRINDDGNRFDPNADIIVGTYEGIDHALRTGK-DLGDIATVVIDEVHTLKEGERGHRLDGMISRLKHYCE 373
                                       88889*********************************9.********************************87777 PP

                                       TSTTT......SEEEEEESSBS CS
                                       xxxxx......xxxxxxxxxxx RF
                              DEAD 155 dgklq......rqvivlSATlp 170
                                       + ++q       q + lSAT+ 
  gi|313127607|ref|YP_004037877.1| 374 TREKQrnsydgAQWVYLSATVG 395
                                       7668877777777*******86 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   2.1e-16   9.5e-13       4     109 ..     432     545 ..     429     547 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.1e-16
                                       HHHHHHH.......HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEES CS
                        Helicase_C   4 eallell.......kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiat 73 
                                       +++ +l+       +++  +g++++f+n+++r++  ++  +k ++ +a++h+ l    r+++ + f +++   +++t
  gi|313127607|ref|YP_004037877.1| 432 DIINKLVrrefdtkSSKGYRGQTIVFTNSRRRCH--EIA-RKLEYDAAPYHAGLDYGRRKKVERMFGNQDLAAVVTT 505
                                       55555555666666677889*************5..554.5558**********************99999****** PP

                                       GGGTSSSTSTTESEEEESSSS....SSHHHHHHHHTTSSS CS
                        Helicase_C  74 dvaerGidipkvnlVinfdlp....rnvtsyiqriGRtgR 109
                                        +++ G+d+p  ++V++  +      +v+++ q+ GR+gR
  gi|313127607|ref|YP_004037877.1| 506 AALAAGVDFPASQVVFDTLAMgiewLSVQEFEQMLGRAGR 545
                                       ****************88877777677************* PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   7.9e-15   3.5e-11      11     169 ..     231     394 ..     210     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 7.9e-15
                                       HHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG...... CS
                            ResIII  11 aienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke.. 84 
                                       a+en l      +++  l++ aT tGKTlv  ++ + r l+  +  k+lflvp  +l +q  e+f++ + ++ +   
  gi|313127607|ref|YP_004037877.1| 231 AVENGL-----FDERDQLVVSATATGKTLVGeLAGVNRALNGDG--KMLFLVPLVALANQKHEDFEERYGDHLNVti 300
                                       443333.....5788899*************9999999999655..*************************987644 PP

                                       ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T........... CS
                            ResIII  85 ..igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk........... 148
                                             +++d+++    ++ n++i+v t++ +d ++      ++ ++ + +  ++iDE+H l++ +           
  gi|313127607|ref|YP_004037877.1| 301 rvGASRINDDGNR----FDPNADIIVGTYEGIDHAL------RTGKDLGDIATVVIDEVHTLKEGErghrldgmisr 367
                                       4322235555555....599****************......7788888899************9444444453333 PP

                                       ..TTHHHHHT---..........SEEEEEESS- CS
                            ResIII 149 ..swreilekfke..........avllglTATp 169
                                         ++ e                 a +++l+AT 
  gi|313127607|ref|YP_004037877.1| 368 lkHYCE------TrekqrnsydgAQWVYLSATV 394
                                       333322......122223344559999999996 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.2e-05      0.41      13      29 ..     123     139 ..     118     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.2e-05
                           DUF4428  13 krlkleDgyvCkdClkK 29 
                                       +++k +++y+C+dC+k+
  gi|313127607|ref|YP_004037877.1| 123 TAIKADNEYICPDCAKR 139
                                       66889999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4735.55
//
Query:       gi|313127608|ref|YP_004037878.1|  [L=626]
Description: di-/tricarboxylate transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-60  204.9   0.7    2.6e-60  204.2   0.2    1.6  2  CitMHS         Citrate transporter
    1.8e-22   80.1  34.1    1.7e-13   50.5  15.1    3.2  3  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    2.2e-19   69.0   4.1    8.8e-12   44.7   0.3    2.5  2  TrkA_C         TrkA-C domain


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.2   0.2   4.3e-64   2.6e-60       1     299 [.      24     566 ..      24     570 .. 0.90
   2 ?    1.8   0.1     0.018   1.1e+02     115     166 ..     561     612 ..     553     622 .. 0.63

  Alignments for each domain:
  == domain 1  score: 204.2 bits;  conditional E-value: 4.3e-64
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll.vltiee......................alsgiaspiillllgamiigaaleet 54 
                                       lv++++e ++ d++al v+v+l ++++ +                      alsg+as+++l++l+++i+++++++t
  gi|313127608|ref|YP_004037878.1|  24 LVFFATEPVPVDITALGVMVTLmLVQPASewlvsanllaepimlfdpyprqALSGFASTATLTVLAMFILSEGVQRT 100
                                       589*****************99955555567777777888888999999**************************** PP

                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                            CitMHS  55 Glfdrlaakllrlaggkrd.llvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaanigga 129
                                       G+++ l+ak+ +++g+++   l +++ ++a +s+f++n+++v+i++p+v +la+r ++++p+ ll+pl++a++ gg+
  gi|313127608|ref|YP_004037878.1| 101 GVVQLLGAKISSFTGNSESrQLGATIGVVAPISGFINNTAAVAILLPMVSDLAER-GGTSPSkLLLPLSYASMFGGT 176
                                       ******************************************************9.9999999************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 130 ltpiGtpttraaarpglslpnlll.....................lalllvgllplvllfmfgvalalpvnapkvkk 185
                                       lt+iGt+            +n+l+                     l++ +vg ++l++++                 
  gi|313127608|ref|YP_004037878.1| 177 LTLIGTS------------TNILAsdlsgrlinrpftmfeftelgLIVSVVGTVYLLTVG----------------- 224
                                       *******............9999999999999999999999999999999999******9................. PP

                                       xxxxxxxxxxxxxxx.............................................................. RF
                            CitMHS 186 qkaiieaiarsllpv.............................................................. 200
                                                r+l p                                                               
  gi|313127608|ref|YP_004037878.1| 225 ---------RWLTPErikprrdlteefemsdyltevtvrsdspligqrvqralvetefdvdliqlirdgqvfleplg 292
                                       .........88887788888888888888888888888899999999999999999999999999999999999999 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|313127608|ref|YP_004037878.1| 293 pkeiqagdvfalrtdrdtlvelldvegldivpnvtvdeaeleageagqnlveivvapgssligeslasasfrqryna 369
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       .........................................................................xxxx RF
                            CitMHS 201 .........................................................................atil 204
                                                                                                                    
  gi|313127608|ref|YP_004037878.1| 370 tvlalrrgeelirrrmdnislrvgdtlliqgatdsierldnnrdfivaqeierhdyreekipvalgivllvvaL--- 443
                                       99999999999999999999999999999999999999999999999999999999999999998876555550... PP

                                       xxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.x..xxx RF
                            CitMHS 205 lla.............................ykkveWsvlllfaGvfllvgaleqtGilealadll.ga.g..gpl 248
                                         a                             y++v+W+v++l+aGv++l+ a+e++  + +la+++  + +   ++
  gi|313127608|ref|YP_004037878.1| 444 --AalnivpivvsalagalamvvtkclrppelYDAVQWDVIFLLAGVIPLGIAMENSAAAALLAEFVvMTgDflSLV 518
                                       ..15555555556666666677999***************************************9994446245777 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 249 valalvlgliallsafisnvavaalmapialgmapalgllspsplalalav 299
                                        +la++++++all+++isn+a ++lm+p+a+ +a +lg   ++ +a++lav
  gi|313127608|ref|YP_004037878.1| 519 GVLAVFYLVTALLTNVISNNASVVLMIPVAVDTAETLG---ANTFAFILAV 566
                                       777999*****************************999...8888888887 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.018
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxx RF
                            CitMHS 115 llliplalaaniggaltpiGtpttraaarpglslpnlll.............lalllvgllplvl 166
                                       ++++++ +aa++   +tp+G              +nl +             +++ l +l++ v+
  gi|313127608|ref|YP_004037878.1| 561 AFILAVTFAASTAF-MTPVGYQ------------TNLFVygpggyrftdylrVGAPLQLLFAAVT 612
                                       47788888888888.*****99............7777766666666666663333333333333 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   3.5   1.1e-08   6.9e-05      30     106 ..      13     104 ..       7     130 .. 0.80
   2 !   17.9   1.2   2.2e-07    0.0013     377     464 ..     134     226 ..     124     229 .. 0.84
   3 !   50.5  15.1   2.8e-17   1.7e-13     301     466 ..     459     620 ..     426     623 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-08
                     Na_sulph_symp  30 awrllaifiaaivglileplplavialialsllavligvla...............akalsevlsgfssdttlLvfa 91 
                                         +++ai+++a v++ +ep+p+ ++al  +  l+++    +                    ++lsgf s++tl v+a
  gi|313127608|ref|YP_004037878.1|  13 IVVVFAIILLALVFFATEPVPVDITALGVMVTLMLVQPASEwlvsanllaepimlfDPYPRQALSGFASTATLTVLA 89 
                                       5689*********************9965555545554444888*******9998877789**************** PP

                     Na_sulph_symp  92 alliaaavektgLgk 106
                                        ++++ +v+ tg  +
  gi|313127608|ref|YP_004037878.1|  90 MFILSEGVQRTGVVQ 104
                                       ***********9655 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.2e-07
                     Na_sulph_symp 377 lfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfga......gylkvkdywrlG 447
                                        f  +tA +a+llp++  +a+   g  p  + l+l  a+ ++g+l+ ++t+ n ++           + + ++  lG
  gi|313127608|ref|YP_004037878.1| 134 GFINNTAAVAILLPMVSDLAERG-GTSPSKLLLPLSYASMFGGTLTLIGTSTNILASDLsgrlinRPFTMFEFTELG 209
                                       6889*****************99.999**************************998543111111345678999*** PP

                     Na_sulph_symp 448 filsiigllillllgal 464
                                       +i+s++g + ll++g +
  gi|313127608|ref|YP_004037878.1| 210 LIVSVVGTVYLLTVGRW 226
                                       *********99999965 PP

  == domain 3  score: 50.5 bits;  conditional E-value: 2.8e-17
                     Na_sulph_symp 301 lvillllrvldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhyl 377
                                          +++++ l     + +   W++++ll+g+i l   +e+s     l+++++ + + +   v +++++ l+ ++ + 
  gi|313127608|ref|YP_004037878.1| 459 ALAMVVTKCLRPP-ELYDAVQWDVIFLLAGVIPLGIAMENSAAAALLAEFVVMTGD-FLSLVGVLAVFYLVTALLTN 533
                                       3345555566555.4666789****************************9987766.999999999999999***** PP

                     Na_sulph_symp 378 faSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiig 454
                                         S+ A ++ ++p+ +  a+++ ga++  ++l++++a s a f++p++   n  v+g g     dy r+G++l++++
  gi|313127608|ref|YP_004037878.1| 534 VISNNASVVLMIPVAVDTAETL-GANTFAFILAVTFAASTA-FMTPVGYQTNLFVYGPGGYRFTDYLRVGAPLQLLF 608
                                       **********************.******************.**********************************9 PP

                     Na_sulph_symp 455 llillllgalww 466
                                        ++  + +a+ w
  gi|313127608|ref|YP_004037878.1| 609 AAVTTVGIAALW 620
                                       998766555444 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.4   1.8e-09   1.1e-05       1      62 [.     248     311 ..     248     317 .. 0.92
   2 !   44.7   0.3   1.5e-15   8.8e-12       1      66 [.     342     409 ..     342     411 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.8e-09
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdl 62 
                                       l+evtv+++spl+G++++ + ++++ +v ++ + R+ ++++ p g  ++++GDv  + +++++l
  gi|313127608|ref|YP_004037878.1| 248 LTEVTVRSDSPLIGQRVQRALVETEfDVDLIQLIRDgQVFLEPLGPKEIQAGDVFALRTDRDTL 311
                                       689****************999999********8888********************9999986 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 1.5e-15
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       lve++v++gs l+G +l+ + +r+r +++v+a+rRg + +   +++  L+ GD+ll+ g  +++++l 
  gi|313127608|ref|YP_004037878.1| 342 LVEIVVAPGSSLIGESLASASFRQRyNATVLALRRGeELIRRRMDNISLRVGDTLLIQGATDSIERLD 409
                                       79**********************************888888888*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 3949.14
//
Query:       gi|313127609|ref|YP_004037879.1|  [L=158]
Description: hypothetical protein Hbor_28950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1057.93
//
Query:       gi|313127610|ref|YP_004037880.1|  [L=186]
Description: hypothetical protein Hbor_28960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1182.39
//
Query:       gi|313127611|ref|YP_004037881.1|  [L=711]
Description: hypothetical protein Hbor_28970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-05   22.9   0.1    0.00039   20.2   0.0    2.3  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    0.00017   21.1   0.1    0.00042   19.8   0.0    1.7  2  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.24   11.4   0.0    1.4  1  HTH_11         HTH domain
       0.13   12.1   0.0       0.42   10.5   0.0    1.8  1  HTH_30         PucR C-terminal helix-turn-helix domain
       0.14   12.0   0.0        0.4   10.6   0.0    1.7  1  TrmB           Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.4   1.4e+03       3      13 ..     454     464 ..     454     464 .. 0.93
   2 !   20.2   0.0   1.1e-07   0.00039       1      41 [.     519     560 ..     519     560 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.4
                     HTH_AsnC-type   3 eiDrkILeaLq 13 
                                       e+D  +L++Lq
  gi|313127611|ref|YP_004037881.1| 454 ELDEGLLNLLQ 464
                                       79********9 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.1e-07
                     HTH_AsnC-type   1 LDeiDrkILeaLqed.aRisyaeLAervGlSestvlrRvrrL 41 
                                       L e+D  ++++L  d + is a+LAer+G+  +t+ + ++rL
  gi|313127611|ref|YP_004037881.1| 519 LTETDVNLVDELLTDgGHISPADLAERIGVHINTCYKSLKRL 560
                                       679************************************998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.9     1e+04       3      13 ..     454     464 ..     453     465 .. 0.82
   2 !   19.8   0.0   1.2e-07   0.00042       2      41 ..     520     560 ..     519     562 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.9
                            HTH_24   3 etdrkILelLq 13 
                                       e+d  +L+lLq
  gi|313127611|ref|YP_004037881.1| 454 ELDEGLLNLLQ 464
                                       678899***99 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.2e-07
                            HTH_24   2 detdrkILelLqknpr.isqreLAerlglSpstvnrrlkrL 41 
                                        etd ++  +L  +++ is ++LAer+g+ ++t+ + lkrL
  gi|313127611|ref|YP_004037881.1| 520 TETDVNLVDELLTDGGhISPADLAERIGVHINTCYKSLKRL 560
                                       68888888667776666***********************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.6e-05      0.24       7      39 ..     528     560 ..     525     564 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
                            HTH_11   7 elLleargpisgeeLAeeLnvSrrtvrrdIkaL 39 
                                         Ll   g+is ++LAe+++v   t ++ +k+L
  gi|313127611|ref|YP_004037881.1| 528 DELLTDGGHISPADLAERIGVHINTCYKSLKRL 560
                                       567789999*********************998 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.42      15      46 ..     539     570 ..     534     577 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                                       HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTS CS
                            HTH_30  15 isatAkaLhvHrnTlryRLrrieellgldldd 46 
                                        ++ A++ +vH nT ++ L+r+  + ++d  +
  gi|313127611|ref|YP_004037881.1| 539 PADLAERIGVHINTCYKSLKRLGNIVQHDYGS 570
                                       5788**********************999876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011       0.4       6      47 ..     519     561 ..     516     565 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                       HHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHH CS
                              TrmB   6 LseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLe 47 
                                       L+e+++     Ll   g  +  ++ae++gv  +++Y++L++L 
  gi|313127611|ref|YP_004037881.1| 519 LTETDVNLVDELLtDGGHISPADLAERIGVHINTCYKSLKRLG 561
                                       7778888888888556778999*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 4379.69
//
Query:       gi|313127612|ref|YP_004037882.1|  [L=140]
Description: hypothetical protein Hbor_28980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 910.81
//
Query:       gi|313127613|ref|YP_004037883.1|  [L=459]
Description: hypothetical protein Hbor_28990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-31  107.3   0.9    8.3e-31  106.1   0.9    1.7  1  DUF4157        Domain of unknown function (DUF4157)
  ------ inclusion threshold ------
      0.022   15.1   0.6       0.05   13.9   0.6    1.7  1  Peptidase_M91  Effector protein
       0.37   10.9   2.1         33    4.7   0.0    3.5  3  Ntox34         Bacterial toxin 34


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.9   1.4e-34   8.3e-31       2      78 ..      98     174 ..      97     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 1.4e-34
                           DUF4157   2 lpeavraemerafgadlsdVrvhtgsaaaraaralgAqAfTlgndivfaageyqpesaagrellaHELtHvvqqreg 78 
                                       l++++++ me ++g++l+dVr+htg++aa+a+++++A+AfT+gn+i+f++gey+p+sa+g+++laHEL+Hv qq++g
  gi|313127613|ref|YP_004037883.1|  98 LDTSIQRAMEDRMGDNLGDVRIHTGPSAAKACEDINARAFTVGNHIAFNHGEYDPSSAEGQHILAHELAHVRQQTGG 174
                                       899***********************************************************************986 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   8.3e-06      0.05      66     135 ..     133     197 ..      68     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.3e-06
                     Peptidase_M91  66 kekgegtdaeinynpafsseeegkegrPsavLyHElaHaydalngtlddgeydgkdeedssgvpneErqA 135
                                       + + ++ +++i +n         +  + +++L+HElaH+++++ g +   +++g+ e d +   + Er+A
  gi|313127613|ref|YP_004037883.1| 133 NARAFTVGNHIAFNHGEYDP---SSAEGQHILAHELAHVRQQTGGAVSMLPQAGELEIDPDP--RLEREA 197
                                       44555666667776663333...5566669**************999888777776666644..555554 PP

>> Ntox34  Bacterial toxin 34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.037   2.2e+02      57      77 ..      55      74 ..      34      77 .. 0.89
   2 ?    4.7   0.0    0.0055        33       9      33 ..      90     114 ..      84     136 .. 0.83
   3 ?    1.3   0.0     0.064   3.8e+02      22      51 ..     398     427 ..     388     435 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.037
                            Ntox34 57 GdiskkdrikktqkaknCrhs 77
                                       di +++ +k+ q++++  h 
  gi|313127613|ref|YP_004037883.1| 55 KDIERRN-AKSVQRSRGAHHE 74
                                      59999*9.*********9995 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0055
                            Ntox34   9 liarrGnvadtGiteevedlindrf 33 
                                       +i+++G + dt i   +ed + d +
  gi|313127613|ref|YP_004037883.1|  90 VISSPGQQLDTSIQRAMEDRMGDNL 114
                                       799***********99999998754 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.064
                            Ntox34  22 teevedlindrfwsdGkkadiCdvldelie 51 
                                       +++++d ind   +d  +a+ C ++ + ++
  gi|313127613|ref|YP_004037883.1| 398 IDRLNDCINDLSEEDFGNAEACTIVPKGMD 427
                                       699************9999***99888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2941.55
//
Query:       gi|313127614|ref|YP_004037884.1|  [L=127]
Description: hypothetical protein Hbor_29000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.61   10.4   6.0        9.5    6.6   3.1    2.1  2  DUF3267   Putative zincin peptidase


Domain annotation for each model (and alignments):
>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0018        32       1      17 [.      23      39 ..      23      47 .. 0.85
   2 ?    6.6   3.1   0.00053       9.5      50     100 ..      81     126 ..      59     127 .] 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0018
                           DUF3267  1 llvlvilHEllHglffk 17
                                      +++ v+ HEl H+ + +
  gi|313127614|ref|YP_004037884.1| 23 MFPAVLAHELTHAAVAW 39
                                      588999******99875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00053
                           DUF3267  50 fiiillaPfvllgilllllalllpsstlllllllalnaagsagDllialll 100
                                       ++ +ll Pfv+    +++ +l +p  t +++   al + +sa Dl ++++l
  gi|313127614|ref|YP_004037884.1|  81 MVGALLTPFVV----PWAFGLEVPLMT-YVFGAWALYTWPSADDLAVLSAL 126
                                       33344444444....555556555443.999999***********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 891.75
//
Query:       gi|313127615|ref|YP_004037885.1|  [L=119]
Description: hypothetical protein Hbor_29010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.6   1.6        0.2   11.7   0.3    2.1  2  Melittin  Melittin
       0.27   11.5   5.1       0.14   12.4   0.4    2.1  2  TrbC      TrbC/VIRB2 family


Domain annotation for each model (and alignments):
>> Melittin  Melittin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   2.2e-05       0.2       1      18 [.      56      76 ..      56      79 .. 0.92
   2 ?   -1.0   0.1      0.24   2.2e+03       2      16 ..      93     107 ..      92     111 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                                      -HHHHHHHHHTH...HHHHHH CS
                          Melittin  1 GiGAvLKvLttG...LPALis 18
                                      GiG +L +Lt G   LPA+is
  gi|313127615|ref|YP_004037885.1| 56 GIGTILYILTEGradLPAVIS 76
                                      9*********998889****9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                                       HHHHHHHHHTHHHHH CS
                          Melittin   2 iGAvLKvLttGLPAL 16 
                                       iGA + +L     AL
  gi|313127615|ref|YP_004037885.1|  93 IGAFMSILFGAALAL 107
                                       899888886555555 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   1.5e-05      0.14      35      88 ..      25      83 ..       1      86 [. 0.77
   2 ?    1.3   0.5     0.043   3.9e+02      80      93 ..      91     104 ..      86     110 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                              TrbC 35 g......dpvetvlqnivdfltgplakviatiaiivaGimlafgrlswrtlvmvviGivi 88
                                             d + ++++ ++d l gp+a+++  i+i  + + l  gr+++++++ ++iG+++
  gi|313127615|ref|YP_004037885.1| 25 DdpwkegDAWAGFVKPFMDLL-GPVAPAMLGIGIGTILYILTEGRADLPAVISILIGGFL 83
                                      256666788999999998865.88*********************************998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.043
                              TrbC  80 vmvviGiviifgAs 93 
                                       + + ++++i+fgA+
  gi|313127615|ref|YP_004037885.1|  91 AKIGAFMSILFGAA 104
                                       55667777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 855.49
//
Query:       gi|313127616|ref|YP_004037886.1|  [L=126]
Description: hypothetical protein Hbor_29020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 955.20
//
Query:       gi|313127617|ref|YP_004037887.1|  [L=1031]
Description: hypothetical protein Hbor_29030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.9   5.1      0.017   15.9   5.1    7.3  8  Big_7            Bacterial Ig domain
      0.065   13.2   5.5       0.19   11.8   0.1    3.9  4  CE2_N            Carbohydrate esterase 2 N-terminal
       0.12   12.3   7.9       0.18   11.8   0.6    4.0  4  Y_Y_Y            Y_Y_Y domain
       0.12   11.4   4.7       0.12   11.4   0.1    2.4  2  ABC2_membrane_3  ABC-2 family transporter protein
       0.18   12.1   0.1       0.18   12.1   0.1    6.0  6  Big_6            Bacterial Ig domain
       0.27   12.0   6.5       0.31   11.8   0.3    3.8  3  DUF3992          Protein of unknown function (DUF3992)
        1.6    8.3   6.7        2.6    7.6   0.3    3.2  3  DUF4998          Domain of unknown function


Domain annotation for each model (and alignments):
>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.5       4.8   1.2e+04      18      43 ..      59      91 ..      43     108 .. 0.53
   2 ?   -2.5   0.2       3.5     9e+03      14      32 ..     217     237 ..     213     238 .. 0.73
   3 ?   -0.6   3.9      0.94   2.4e+03      14      65 ..     286     344 ..     282     346 .. 0.73
   4 ?   10.4   6.1   0.00035      0.89       7      69 ..     368     436 ..     365     437 .. 0.83
   5 ?   -1.9   0.2       2.3   5.9e+03      47      58 ..     447     458 ..     441     475 .. 0.66
   6 ?    4.5   0.9     0.023        59      14      68 ..     475     535 ..     463     537 .. 0.63
   7 ?   15.9   5.1   6.5e-06     0.017       6      68 ..     568     635 ..     561     637 .. 0.84
   8 ?    2.2   0.7      0.12     3e+02      35      60 ..     913     937 ..     890     954 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.8
                                      EEEEEEEEE-SS-E.......EEEEEEETTEE.. CS
                             Big_7 18 tvtisasAsddggv.......skVefyvdgtl.g 43
                                      +v++++s + + +v       ++V+ + dg l +
  gi|313127617|ref|YP_004037887.1| 59 NVSVEGSGTSA-SValegqlnQTVDGFEDGDLsE 91
                                      34444444443.2222444445555555555544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.5
                                       EB.TSEEEEEEEEE-S.S-EE CS
                             Big_7  14 vs.ggtvtisasAsdd.ggvs 32 
                                       ++ +g+v  s sA+d+  +v+
  gi|313127617|ref|YP_004037887.1| 217 YDeAGNVVASLSATDSnETVK 237
                                       556789999999999966665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.94
                                       EBTSEEEEEEEEE-S..S-EEEEEEEETTEE......EEEE-SSSEEEEEE--...SEE CS
                             Big_7  14 vsggtvtisasAsdd..ggvskVefyvdgtl.g....lgtdtsapysltwtttaltagt 65 
                                       +++ + t++ +A d+  ++ + Ve + + ++ +    lg+++   +++++  ++ +agt
  gi|313127617|ref|YP_004037887.1| 286 LQNASATVTIQAYDSstSSWTDVESSTYSSTgNytldLGNTSYEMWRTKVVFDDEPAGT 344
                                       55677888888888877666777776666653355789999999999999998888887 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00035
                                       E--TT--EBTSEEEEEEEEE-S..S-E....EEEEEEETTEE.EEEE-S.SSEEEEEE--...SEEEEEE CS
                             Big_7   7 sPangatvsggtvtisasAsdd..ggv....skVefyvdgtlglgtdts.apysltwtttaltagthtlt 69 
                                       +P+ g+  ++++vt+s+  sd+  ++      +V++y+dg+  ++t t  ++ +++ t t l++g+ht  
  gi|313127617|ref|YP_004037887.1| 368 APSGGSDTNNEDVTLSVPISDSdfSTPqgdsVTVDVYLDGEI-VDTQTItSNQTVSTTVTELEDGNHTWH 436
                                       8999**9999************98555665589999*****9.888875367777888888******965 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2.3
                                       E-SSSEEEEEE- CS
                             Big_7  47 dtsapysltwtt 58 
                                       +ts+++++t++ 
  gi|313127617|ref|YP_004037887.1| 447 TTSSTWNFTVNH 458
                                       567888888876 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.023
                                       EBTSEEEEEEEEE-S..S-E....EEEEEEETTEE..EEEE.-SSSEEEEEE--...SEEEEE CS
                             Big_7  14 vsggtvtisasAsdd..ggv....skVefyvdgtl.glgtd.tsapysltwtttaltagthtl 68 
                                           + tis ++sd    +      kV++ +dg + g  +   + + ++t++   l++g+ht 
  gi|313127617|ref|YP_004037887.1| 475 SRYANETISIDVSDRdfAEPsgdeVKVDLVLDGAVaG--SKnVTKNGTVTFDVGPLEDGNHTW 535
                                       3335667777777775533344448999999999944..33134566677777669*****96 PP

  == domain 7  score: 15.9 bits;  conditional E-value: 6.5e-06
                                       EE--TT--EBTSEEEEEEEEE-S.....S-EEEEEEEETTEE.EEEE-S.SSEEEEEE--...SEEEEE CS
                             Big_7   6 tsPangatvsggtvtisasAsdd.....ggvskVefyvdgtlglgtdts.apysltwtttaltagthtl 68 
                                       +sP++ga++++++vt+s+++sd      g   + ef vd ++ +gtdt  a+ +++ t+t++ +g+h+ 
  gi|313127617|ref|YP_004037887.1| 568 MSPEDGAKLTSKDVTLSVNVSDRdfqldGDTVTAEFVVDSEV-VGTDTLsANGTASTTITDVGGGNHSW 635
                                       69*********************966555556669*******.****6439999999*********985 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.12
                                       EEEETTEE.EEEE-SSSEEEEEE--. CS
                             Big_7  35 efyvdgtlglgtdtsapysltwttta 60 
                                       +f+++ t+ +g+ t++ +++tw + +
  gi|313127617|ref|YP_004037887.1| 913 TFSLNKTV-SGNLTETDWEVTWYAYN 937
                                       68999999.9999*********9853 PP

>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.55   1.4e+03      20      52 ..      58      83 ..      57     108 .. 0.71
   2 ?   11.8   0.1   7.2e-05      0.19      40      86 ..     395     441 ..     380     457 .. 0.82
   3 ?   -0.8   0.0       0.6   1.5e+03      31      79 ..     482     534 ..     472     544 .. 0.74
   4 ?   -0.4   0.1      0.43   1.1e+03      31      79 ..     583     634 ..     574     647 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.55
                                      -EEEEEEEEEEEEEEEEE..SSS-EEEEEEETT CS
                             CE2_N 20 tsvefrftGtslsvrlkdkedkgknrlaviiDg 52
                                      t+v++  +Gts+sv+l++       +l+  +Dg
  gi|313127617|ref|YP_004037887.1| 58 TNVSVEGSGTSASVALEG-------QLNQTVDG 83
                                      677888899999999999.......44444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.2e-05
                                       SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEEE-S CS
                             CE2_N  40 dkgknrlaviiDgkrvkdlkldgeektytlaeglepgehtvrlvkrt 86 
                                       + ++  ++v++Dg+ v ++++++++++ t++++le+g+ht  +    
  gi|313127617|ref|YP_004037887.1| 395 QGDSVTVDVYLDGEIVDTQTITSNQTVSTTVTELEDGNHTWHVETTD 441
                                       5567789*********99999******************97766555 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.6
                                       EEEEEEE......SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEE CS
                             CE2_N  31 lsvrlkd....kedkgknrlaviiDgkrvkdlkldgeektytlaeglepgeht 79 
                                       +s+ ++d    + + ++ ++++++Dg+ + + ++++++++   +  le+g+ht
  gi|313127617|ref|YP_004037887.1| 482 ISIDVSDrdfaEPSGDEVKVDLVLDGAVAGSKNVTKNGTVTFDVGPLEDGNHT 534
                                       55666665666666778899999****98888887777766666899999998 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.43
                                       EEEEEEE.....SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEE CS
                             CE2_N  31 lsvrlkd...kedkgknrlaviiDgkrvkdlkldgeektytlaeglepgeht 79 
                                       lsv+++d   + d ++   ++++D + v + +l++++++ t++++   g+h+
  gi|313127617|ref|YP_004037887.1| 583 LSVNVSDrdfQLDGDTVTAEFVVDSEVVGTDTLSANGTASTTITDVGGGNHS 634
                                       4555555666667788899999*****9999999999999999999999996 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.6   6.7e+03      34      43 ..     312     321 ..     295     323 .. 0.62
   2 ?   11.8   0.6     7e-05      0.18      18      65 ..     406     456 ..     402     457 .. 0.80
   3 ?    2.5   0.0     0.055   1.4e+02      23      63 ..     514     556 ..     505     557 .. 0.84
   4 ?   -2.8   0.1       2.5   6.4e+03      30      56 ..     622     648 ..     614     650 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                                       ES--SEEEEE CS
                             Y_Y_Y  34 tnlppGdYtl 43 
                                       t  + G+Ytl
  gi|313127617|ref|YP_004037887.1| 312 TYSSTGNYTL 321
                                       4456788887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7e-05
                                       ESSEEEESSTS.....EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  18 dkeWveasdysq....easytnlppGdYtlkVkakdndgqwnyditslsfti 65 
                                       d+e v+++  ++    + + t+l+ G+ t +V+++d++g+      +++ft+
  gi|313127617|ref|YP_004037887.1| 406 DGEIVDTQTITSnqtvSTTVTELEDGNHTWHVETTDEYGEATTS-STWNFTV 456
                                       5555544444444457*************************999.99**998 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.055
                                       EESSTS..EEEEES--SEEEEEEEEEEETTS-B-SS-.EEEEE CS
                             Y_Y_Y  23 easdysq.easytnlppGdYtlkVkakdndgqwnydi.tslsf 63 
                                       + +++++ ++   +l+ G+ t +V+ +d++g  ++ +  ++++
  gi|313127617|ref|YP_004037887.1| 514 NVTKNGTvTFDVGPLEDGNHTWHVEMTDEYGLTSESDsFTWEI 556
                                       5566776788889******************999988777765 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2.5
                                       EEEEES--SEEEEEEEEEEETTS-B-S CS
                             Y_Y_Y  30 easytnlppGdYtlkVkakdndgqwny 56 
                                       + ++t    G+   +V++ d++g+ n+
  gi|313127617|ref|YP_004037887.1| 622 STTITDVGGGNHSWYVRVYDEYGSGNS 648
                                       5666666677777899****9998875 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.5     0.099   2.5e+02      54     147 ..     288     456 ..     208     479 .. 0.72
   2 ?   11.4   0.1   4.8e-05      0.12      94     230 ..     871    1026 ..     731    1028 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.099
                   ABC2_membrane_3  54 a.spsvelvyevdseeeakkalkngdidgilvipkgfskdll................................... 94 
                                       + s +v+ ++ +ds ++   ++++ +++  +  + +  ++ +                                   
  gi|313127617|ref|YP_004037887.1| 288 NaSATVT-IQAYDSSTSSWTDVESSTYSSTGNYTLDLGNTSYemwrtkvvfddepagtvaeihdegvwfqprapsid 363
                                       3255565.888999999999999988888776666666555588999999999999999999999999999999999 PP

                   ABC2_membrane_3  95 ...............................kgesatvtvlinssnlnsskailna.lns.llqqlnasalv..... 133
                                                                      +g s tv v+++++ + ++++  n+ +++ +++ + +   +     
  gi|313127617|ref|YP_004037887.1| 364 gaeaapsggsdtnnedvtlsvpisdsdfstpQGDSVTVDVYLDGEIVDTQTITSNQtVSTtVTELEDG---Nhtwhv 437
                                       99999999998888888888888888888888888888888888888877777776455444444333...134466 PP

                   ABC2_membrane_3 134 .....lqseatstsaninv 147
                                            + + +ts++ n++v
  gi|313127617|ref|YP_004037887.1| 438 ettdeYGEATTSSTWNFTV 456
                                       6444444444444444444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.8e-05
                   ABC2_membrane_3   94 l..........kgesatvtvlinssnlnsskailnalns.llqqlnasalv..lqseatstsaninvestql... 152 
                                        +          +++++++ v+i ++n +s+ +++++++  +  ++  +++v  +      t++  +v+ +++   
  gi|313127617|ref|YP_004037887.1|  871 NgvvhfqyhdpTQNTSKLRVIIHAANNSSNEIMNSTYTEgYG-TFSLNKTVsgN-----LTETDWEVTWYAYnss 939 
                                        133444444446688888888888887777777777665333.33333333332.....3333333333333111 PP

                   ABC2_membrane_3  153 ...eeelsnvasf............lvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilg 212 
                                            e++++ a+             + ++il +l++++++ +       + s i  l  v+gv +   wl+++++
  gi|313127617|ref|YP_004037887.1|  940 ntvIESSNDLADGkryvienpigpkWTPVILTCLFLFVGMLFGG-----RLSSIGSL-AVTGVAAVMWWLGWYTA 1008
                                        11433333333336668899988887776666666666554444.....78878876.79*************** PP

                   ABC2_membrane_3  213 dflvyllqlllilllafg 230 
                                        ++ v ++  l+++++a+g
  gi|313127617|ref|YP_004037887.1| 1009 SGGVVVFAGLVAVAMAVG 1026
                                        *************99876 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.9     1e+04      33      55 ..      96     117 ..      93     121 .. 0.73
   2 ?   -1.6   0.0       1.3   3.4e+03      61      76 ..     211     226 ..     206     232 .. 0.71
   3 ?    1.7   0.1      0.12   3.1e+02      23      68 ..     289     339 ..     287     347 .. 0.69
   4 ?    2.7   1.5     0.061   1.6e+02      26      78 ..     398     453 ..     392     458 .. 0.79
   5 ?   12.1   0.1   7.2e-05      0.18      25      80 ..     497     553 ..     492     555 .. 0.88
   6 ?    0.3   1.7      0.33   8.5e+02      14      77 ..     591     652 ..     581     657 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                             Big_6  33 dgtvlgtgtadadGeFsvtlepa 55 
                                        g +++++ +  +G ++v+++p+
  gi|313127617|ref|YP_004037887.1|  96 TGDTVQSSMV-WSGDYAVEMDPS 117
                                       5666777777.789999999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                             Big_6  61 tlsvvatDaagntSda 76 
                                       +l+ ++ D+agn+ + 
  gi|313127617|ref|YP_004037887.1| 211 ELNYTVYDEAGNVVAS 226
                                       6788889999997544 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.12
                             Big_6  23 agatVtvkdadgtvl.....gtgtadadGeFsvtlepaqangetlsvvatD 68 
                                       a atVt++  d ++       ++t +++G+++++l +   +  + +vv  D
  gi|313127617|ref|YP_004037887.1| 289 ASATVTIQAYDSSTSswtdvESSTYSSTGNYTLDLGNTSYEMWRTKVVFDD 339
                                       678888876655543222226678899*******98887777677776666 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.061
                             Big_6  26 tVtv.kdadgtvlgtgtadadGeFsvtlepaqangetlsvvatDaagnt..Sdaat 78 
                                       +Vtv    dg+++ t t++++ + s t+++ +  + t +v  tD+ g++  S + +
  gi|313127617|ref|YP_004037887.1| 398 SVTVdVYLDGEIVDTQTITSNQTVSTTVTELEDGNHTWHVETTDEYGEAttSSTWN 453
                                       56663335999*******************999************99872344444 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 7.2e-05
                             Big_6  25 atVtvkda.dgtvlgtgtadadGeFsvtlepaqangetlsvvatDaagntSdaatvt 80 
                                        +V+v    dg+v g+  ++++G+ ++++ p +  + t +v  tD+ g tS+  ++t
  gi|313127617|ref|YP_004037887.1| 497 DEVKVDLVlDGAVAGSKNVTKNGTVTFDVGPLEDGNHTWHVEMTDEYGLTSESDSFT 553
                                       5677754449*****************************************998877 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.33
                             Big_6  14 gttltGkaeagatVtvkdadgtvlgtgtadadGeFsvtlepaqangetlsvvatDa..agntSdaa 77 
                                       + +l G++ +   V     d +v+gt t +a+G+ s t++     + +  v + D+  +gn S++ 
  gi|313127617|ref|YP_004037887.1| 591 DFQLDGDTVTAEFV----VDSEVVGTDTLSANGTASTTITDVGGGNHSWYVRVYDEygSGNSSNPD 652
                                       55555555444444....477899***************999999999999999973356778775 PP

>> DUF3992  Protein of unknown function (DUF3992)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1         1   2.7e+03      62      80 ..     168     184 ..     166     193 .. 0.78
   2 ?   11.8   0.3   0.00012      0.31      35      70 ..     395     430 ..     386     441 .. 0.91
   3 ?   -0.0   0.2      0.59   1.5e+03      40      66 ..     600     626 ..     586     629 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                           DUF3992  62 sltlarldsiqvvetaGts 80 
                                       + t++++++i+vv+   ts
  gi|313127617|ref|YP_004037887.1| 168 GYTVQDIRIIKVVNG--TS 184
                                       78999*******743..33 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                           DUF3992  35 vgvgpivvvalngavvddqtlapGeSrsltlarlds 70 
                                       +g + +v+v l+g++vd+qt+   +  s t+++l++
  gi|313127617|ref|YP_004037887.1| 395 QGDSVTVDVYLDGEIVDTQTITSNQTVSTTVTELED 430
                                       677889************************999976 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.59
                           DUF3992  40 ivvvalngavvddqtlapGeSrsltla 66 
                                       + +  ++++vv + tl      s t++
  gi|313127617|ref|YP_004037887.1| 600 TAEFVVDSEVVGTDTLSANGTASTTIT 626
                                       3445689****9999976555555554 PP

>> DUF4998  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3     0.001       2.6      65     109 ..     412     456 ..     393     490 .. 0.77
   2 ?    3.1   0.1     0.025        63      70     143 ..     517     591 ..     499     654 .. 0.75
   3 ?   -2.1   0.2      0.95   2.4e+03     103     141 ..     900     937 ..     849     946 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.001
                           DUF4998  65 verkegvdtveviidnLeEgsytFsivtydkkgnsSlksevtgev 109
                                        +    ++tv++++ +Le+g +t ++ t+d+ g+   +s+   +v
  gi|313127617|ref|YP_004037887.1| 412 TQTITSNQTVSTTVTELEDGNHTWHVETTDEYGEATTSSTWNFTV 456
                                       44555689***********************99766655544333 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.025
                           DUF4998  70 gvdtveviidnLeEgsytFsivtydkkgnsSlksevtgevYGdsYqasltnrslksvele...kkeltinwskveqe 143
                                       ++ tv++ +  Le+g +t ++ ++d+ g +S + ++t e+  d+Y+ ++   s++  +     +k++t++ + ++++
  gi|313127617|ref|YP_004037887.1| 517 KNGTVTFDVGPLEDGNHTWHVEMTDEYGLTSESDSFTWEI--DHYEPTVNSSSMSPEDGAkltSKDVTLSVNVSDRD 591
                                       56799999***********************999999888..88887776666654333233377777766666554 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.95
                           DUF4998 103 sevtgevYGdsYqasltnrslksvelekkeltinwskve 141
                                       +e+  ++Y + Y     n++++  +l++++  ++w+  +
  gi|313127617|ref|YP_004037887.1| 900 NEIMNSTYTEGYGTFSLNKTVSG-NLTETDWEVTWYAYN 937
                                       45555556666655555555543.344555555565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1031 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.43
# Mc/sec: 7225.95
//
Query:       gi|313127618|ref|YP_004037888.1|  [L=97]
Description: hypothetical protein Hbor_29040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0051   16.6   1.2      0.006   16.3   1.2    1.1  1  Yip1            Yip1 domain
     0.0064   16.1   0.3     0.0072   16.0   0.3    1.0  1  Virul_fac_BrkB  Virulence factor BrkB
  ------ inclusion threshold ------
      0.033   14.1   0.0       0.47   10.4   0.0    2.0  2  DUF3377         Domain of unknown function (DUF3377)
        2.9    7.6   8.3         29    4.4   8.3    2.1  1  DUF3098         Protein of unknown function (DUF3098)


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.2   1.3e-06     0.006      19      98 ..       6      92 ..       1      94 [. 0.68

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
                              Yip1 19 lrapdlallllalltlllgllas...lnlgqtlasg..........eevqgltlssllgaiiggylglllgllllalll 84
                                      + +++ a+++++ll +l g+++        ++ + +           e++gl     ++  +g+++   ++ +l+ +++
  gi|313127618|ref|YP_004037888.1|  6 RGSYLSAFVIVVLLLFLGGIFVVvgiP---TIDGTAdavkkadngaIEEEGLDDNLSFTLDVGLVI---APTFLMIGIV 78
                                      346888889999999999988885553...333333444777777766666666666666666666...7888888888 PP

                              Yip1 85 hliakllggkgsfk 98
                                       ++  +  gkgsf+
  gi|313127618|ref|YP_004037888.1| 79 AWLYAVVAGKGSFR 92
                                      88888899999997 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.6e-06    0.0072     107     184 ..       8      87 ..       1      92 [. 0.62

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-06
                    Virul_fac_BrkB 107 sflrkrllsllllllllvllllslvlsvflqslllasa..pllglglelsell.llqllrwlvallllvlafallYr 180
                                       s+l+ +++ +lll+l+++++++ + ++  +  ++++    ++ + gl+  +l+ +l ++ ++++++l++ ++a+lY 
  gi|313127618|ref|YP_004037888.1|   8 SYLSAFVIVVLLLFLGGIFVVVGIPTIDGTADAVKKADngAIEEEGLDD-NLSfTLDVGLVIAPTFLMIGIVAWLYA 83 
                                       3666666666666666666666666555555544443365444444333.333588888889999999********9 PP

                    Virul_fac_BrkB 181 vlpn 184
                                       v+  
  gi|313127618|ref|YP_004037888.1|  84 VVAG 87 
                                       9865 PP

>> DUF3377  Domain of unknown function (DUF3377)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.051   2.3e+02      31      40 ..      13      22 ..       3      34 .. 0.53
   2 ?   10.4   0.0    0.0001      0.47      16      51 ..      51      86 ..      35      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.051
                           DUF3377 31 aVvvPlvLll 40
                                       V+v l+L l
  gi|313127618|ref|YP_004037888.1| 13 FVIVVLLLFL 22
                                      3444444443 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0001
                           DUF3377 16 vvkiddeesgtvnaiaVvvPlvLllciLvliyailq 51
                                       + +dd+ s t  +  V+ P +L++ i++ +ya++ 
  gi|313127618|ref|YP_004037888.1| 51 EEGLDDNLSFTLDVGLVIAPTFLMIGIVAWLYAVVA 86
                                      4557999999999********************985 PP

>> DUF3098  Protein of unknown function (DUF3098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   8.3    0.0064        29      45      64 ..      66      85 ..      12      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0064
                           DUF3098 45 irlAPivvliGfvieiyaIl 64
                                      +++AP++++iG+v  +ya++
  gi|313127618|ref|YP_004037888.1| 66 LVIAPTFLMIGIVAWLYAVV 85
                                      68****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 735.34
//
Query:       gi|313127619|ref|YP_004037889.1|  [L=98]
Description: hypothetical protein Hbor_29050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 633.96
//
Query:       gi|313127620|ref|YP_004037890.1|  [L=902]
Description: hypothetical protein Hbor_29060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.021   14.2   0.1      0.057   12.8   0.1    1.7  2  SF-assemblin     SF-assemblin/beta giardin
      0.033   14.1   0.1        3.2    7.6   0.0    3.2  4  Apolipoprotein   Apolipoprotein A1/A4/E domain
       0.09   12.6   0.0       0.16   11.7   0.0    1.3  1  REF              Rubber elongation factor protein (REF)
       0.43   11.2   2.2         16    6.2   0.0    3.7  4  DUF883           Bacterial protein of unknown function (DUF88


Domain annotation for each model (and alignments):
>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.063   2.8e+02      68     133 ..       5      70 ..       3      74 .. 0.77
   2 ?   12.8   0.1   1.3e-05     0.057      62     161 ..      65     170 ..      34     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.063
                      SF-assemblin  68 fkkeikklqekikeevddlalelkkaveelnekinnveanvenekakrrdaieklakelvkelnel 133
                                       ++  i+ +  +  ++v+ +   + + v+ + ++  +v   v n   + +d+    a+++v ++ + 
  gi|313127620|ref|YP_004037890.1|   5 VDDGIDSVTDTASDVVNGVGDSVGEGVDTVTDTASDVTNDVGNSVDSGIDSATDTATDVVSDVGNS 70 
                                       666778888888888888888888888888888888888888888888888888888888877655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.3e-05
                      SF-assemblin  62 kdiqeefkkeikklqekikeevddlalelkkaveelnekinnve..anvenekakr....rdaieklakelvkelne 132
                                        d+ + +++ ++++ e+  ++ + +   ++++ e+ +e +nn e  +n+ ++  k      ++ e++ ++++k++n+
  gi|313127620|ref|YP_004037890.1|  65 SDVGNSVSGGVDTVGETASNVGNAVEESVENSAENTGEAVNNAEfnTNISDDLTKSggllSEDQEQQVRSVAKDIND 141
                                       688899***********************************9643399*9*998863333678899999******** PP

                      SF-assemblin 133 leaaideEkaerkkkedqlnkkveEdlkk 161
                                        + +i++++ +  + ++ + +++ E+ +k
  gi|313127620|ref|YP_004037890.1| 142 YKKTIETDEGGVPDSQEGVPEQLLEGAAK 170
                                       ********999999999999999888776 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00072       3.2      91     184 ..      10     103 ..       3     108 .. 0.76
   2 ?   -0.2   0.1      0.17   7.8e+02      26      65 ..     108     147 ..      97     153 .. 0.59
   3 ?    1.0   0.2     0.072   3.2e+02     100     150 ..     351     403 ..     336     422 .. 0.77
   4 ?   -2.1   0.0      0.67     3e+03     130     144 ..     853     867 ..     836     893 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00072
                                       HCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS-TTS CS
                    Apolipoprotein  91 eelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrveelrekleeqa 167
                                       + + ++ + + +++ +++ ++v+++ ++ +  + ++ +++++ ++   +++++ +  v++ +s  v+ + e+++   
  gi|313127620|ref|YP_004037890.1|  10 DSVTDTASDVVNGVGDSVGEGVDTVTDTASDVTNDVGNSVDSGIDSATDTATDVVSDVGNSVSGGVDTVGETASNVG 86 
                                       55666777777788888888888888888888888888888888888888888888888888888888888888888 PP

                                       HHHHHS--XXXXXXXXX CS
                    Apolipoprotein 168 eelrerleanleelkaq 184
                                       ++++e++e  +e+  + 
  gi|313127620|ref|YP_004037890.1|  87 NAVEESVENSAENTGEA 103
                                       88888888777766554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCC CS
                    Apolipoprotein  26 elrdrlskeleelrarlraeleevrarlepyrdevqeqlg 65 
                                       e+ +++s++l +    l+++ e+++ +++ ++++ +++++
  gi|313127620|ref|YP_004037890.1| 108 EFNTNISDDLTKSGGLLSEDQEQQVRSVAKDINDYKKTIE 147
                                       5555556666666666666666666666666555555554 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.072
                                       HCHHHHHHHHHH..HHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..---- CS
                    Apolipoprotein 100 yaeelrerlerh..vealkarlapyveelrqklaerleelkeslaphaeevee 150
                                        ++e+ erl ++  ++a+ +r++  ++ + +k  ++++++ +++ap++ e   
  gi|313127620|ref|YP_004037890.1| 351 AGREIAERLGDRsrTDAVVDRVSGGTDTTAEKGIRNAQQIPDEAAPEVTEWLK 403
                                       46788888887777999999999999999999999999998888888776554 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.67
                                       HHHHHHHHHH----- CS
                    Apolipoprotein 130 laerleelkeslaph 144
                                       +a+  e+l  +la +
  gi|313127620|ref|YP_004037890.1| 853 VASATEALDATLASA 867
                                       333333333333322 PP

>> REF  Rubber elongation factor protein (REF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.6e-05      0.16      61     182 ..      13     136 ..       8     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                               REF  61 kdvPlelLkfvDrKvdesvtkldkrvpsvvKevssqalavaqkapeaarevasevqr..aGvveaaepvakelytky 135
                                        d   ++++ v   v+e v+++  ++  v  +v + + + + +a+++a +v+s+v +  +G v+++  +a+++ +  
  gi|313127620|ref|YP_004037890.1|  13 TDTASDVVNGVGDSVGEGVDTVTDTASDVTNDVGNSVDSGIDSATDTATDVVSDVGNsvSGGVDTVGETASNVGNAV 89 
                                       566667777788899****************************************763369999999********** PP

                               REF 136 epvaeelavsawrklnrlplvpqvaqvvvptaaylsekYNkvvkaaa 182
                                       e  +e+ a ++ +++n+  +  ++++ + ++   lse   + v+++a
  gi|313127620|ref|YP_004037890.1|  90 EESVENSAENTGEAVNNAEFNTNISDDLTKSGGLLSEDQEQQVRSVA 136
                                       ****************9999999998888888888888888877766 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.028   1.3e+02       8      70 ..      10      65 ..       4      79 .. 0.50
   2 ?    6.2   0.0    0.0035        16       8      70 ..      43     105 ..      35     111 .. 0.88
   3 ?   -3.2   0.0         3   1.4e+04      25      65 ..     125     139 ..     114     149 .. 0.51
   4 ?    1.8   0.2     0.084   3.8e+02      53      89 ..     210     245 ..     190     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.028
                            DUF883  8 eslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVr 70
                                      +s+++++ ++++  +d+ ge ++++ + +++        ++d+ ++v   +++a ++a d+V 
  gi|313127620|ref|YP_004037890.1| 10 DSVTDTASDVVNGVGDSVGEGVDTVTDTASDV-------TNDVGNSVDSGIDSATDTATDVVS 65
                                      44444444444444444444444444444444.......444444444444445555544444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0035
                            DUF883   8 eslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVr 70 
                                       +++ +++++ +++a d+a + ++++ + ++  ++++ e+++++ +av+e++++ ae++ ++V 
  gi|313127620|ref|YP_004037890.1|  43 NDVGNSVDSGIDSATDTATDVVSDVGNSVSGGVDTVGETASNVGNAVEESVENSAENTGEAVN 105
                                       667778888899999*******************************************99997 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3
                            DUF883  25 ageeaeelRerleerlerarerlrdaeeavaerakeaaeaa 65 
                                       ++++ +++R                          ++a++ 
  gi|313127620|ref|YP_004037890.1| 125 SEDQEQQVR--------------------------SVAKDI 139
                                       444444444..........................333333 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.084
                            DUF883  53 avaerakeaaeaaddyVrenPwqavGiAagvGlllGl 89 
                                       +v +  +ea ea  + +r +P++ vG +ag+Gll G+
  gi|313127620|ref|YP_004037890.1| 210 TVTAFGREAGEAMVNEARSSPVEFVG-GAGLGLLTGF 245
                                       555666888888888899********.78*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (902 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 5940.47
//
Query:       gi|313127621|ref|YP_004037891.1|  [L=109]
Description: hypothetical protein Hbor_29070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 805.64
//
Query:       gi|313127622|ref|YP_004037892.1|  [L=334]
Description: hypothetical protein Hbor_29080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.082   13.4   0.1          1    9.9   0.1    2.5  2  YtxH      YtxH-like protein


Domain annotation for each model (and alignments):
>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.056     1e+03      23      66 ..     136     174 ..     123     183 .. 0.52
   2 ?    9.9   0.1   5.7e-05         1      22      53 ..     189     244 ..     187     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.056
                              YtxH  23 GketRkdlkekaddlkekakelleeakekakekaedlkekvkek 66 
                                       G++ R +++++a+dl     ++++ a  ka+e + +l  ++  +
  gi|313127622|ref|YP_004037892.1| 136 GRQARIKMQHYAEDL-----STIDYATWKAQEDGPELIAAAGTQ 174
                                       344555555666666.....334445555555555555555444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 5.7e-05
                              YtxH  22 sGketRkdlkekaddlkekakelleeakeka........................k 53 
                                        G+  R++l e++  +++++ + ++ a++++                        +
  gi|313127622|ref|YP_004037892.1| 189 EGRRARDKLGESVGSARDRLGDGVDAARDRVgddeddpltdggktvidewetmlpT 244
                                       79***************************998887777766665555555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2425.60
//
Query:       gi|313127623|ref|YP_004037893.1|  [L=186]
Description: hypothetical protein Hbor_29090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1363.12
//
Query:       gi|313127624|ref|YP_004037894.1|  [L=81]
Description: hypothetical protein Hbor_29100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.26   11.2   4.6       0.63    9.9   3.3    1.9  2  DUF4605   Domain of unknown function (DUF4605)


Domain annotation for each model (and alignments):
>> DUF4605  Domain of unknown function (DUF4605)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.041   7.4e+02      17      28 ..       6      17 ..       2      20 .. 0.79
   2 ?    9.9   3.3   3.5e-05      0.63      39      56 ..      25      42 ..      23      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.041
                           DUF4605 17 rwnlgekvvePv 28
                                       +++ ++ veP+
  gi|313127624|ref|YP_004037894.1|  6 AFSISSFAVEPL 17
                                      678889999997 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 3.5e-05
                           DUF4605 39 flGlrGlllvgllcfviq 56
                                      +lG+++l+l+gll+++ +
  gi|313127624|ref|YP_004037894.1| 25 MLGMFALGLGGLLFMLAM 42
                                      9*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 591.14
//
Query:       gi|313127625|ref|YP_004037895.1|  [L=158]
Description: hypothetical protein Hbor_29110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.22   12.0   0.1       0.22   12.0   0.1    1.5  2  SecD-TM1         SecD export protein N-terminal TM region
       0.57   11.1   7.6        6.3    7.8   0.9    2.3  2  Pilin_N          Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> SecD-TM1  SecD export protein N-terminal TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.5e-05      0.22      10      58 ..       8      57 ..       4      75 .. 0.74
   2 ?   -4.6   1.0         2   1.8e+04      14      19 ..     135     140 ..     131     145 .. 0.41

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                          SecD-TM1 10 llilvvlligllyalPnlygedpavqisaaka.tlkvdeatlskveqaLk 58
                                      ++ ++v+li+ +y++++++g  pa   s+  + ++++d +  ++v ++  
  gi|313127625|ref|YP_004037895.1|  8 MVTVAVMLIVGIYVVSSIFGTMPAMATSSVANeSITIDVGNATSVDKTYG 57
                                      688999*******************9977655155666666666666655 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 2
                          SecD-TM1  14 vvllig 19 
                                       +vl+ +
  gi|313127625|ref|YP_004037895.1| 135 IVLVAA 140
                                       222222 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9   0.00071       6.3       7      68 ..      11      75 ..       7      81 .. 0.51
   2 ?    6.8   1.0    0.0015        13      13      30 ..     132     149 ..     127     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00071
                           Pilin_N  7 iGviLmvaitvIlaAviaafvlglasneekapqasievk....idssastgkna...vslehkgGdsid 68
                                      + v+L+v i v+  + i + +  +a  + +  +++i+v     +d++++++       ++++++G  ++
  gi|313127625|ref|YP_004037895.1| 11 VAVMLIVGIYVV--SSIFGTMPAMATSSVANESITIDVGnatsVDKTYGEK--YyenETITNSSGTNLT 75
                                      456666666554..5555555555444444444444333332233333332..2345888888887665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0015
                           Pilin_N  13 vaitvIlaAviaafvlgl 30 
                                       va++v++aA+i + v+g+
  gi|313127625|ref|YP_004037895.1| 132 VAVIVLVAALILGLVGGF 149
                                       89***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1066.79
//
Query:       gi|313127626|ref|YP_004037896.1|  [L=192]
Description: hypothetical protein Hbor_29120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0023   18.2   1.0     0.0039   17.4   1.0    1.4  1  DUF4064      Protein of unknown function (DUF4064)
     0.0073   16.1   0.6     0.0097   15.7   0.6    1.1  1  Claudin_2    PMP-22/EMP/MP20/Claudin tight junction
  ------ inclusion threshold ------
        0.2   11.3   0.9       0.36   10.5   0.9    1.3  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.0   6.5e-07    0.0039      17      80 ..     121     184 ..     113     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.5e-07
                           DUF4064  17 illglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgal 80 
                                       +  +l++++++f ++s+ + +    e a+s++ ++++ +  +tl+ v++++++ + +lg+vg +
  gi|313127626|ref|YP_004037896.1| 121 AAVTLIVGIYVFAQISSTMPTPSNPELANSTNTVKSTTGNAFTLGSVAIIVLVASVILGLVGGF 184
                                       34455555555555555555555555899********************************987 PP

>> Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.6   1.6e-06    0.0097     119     190 ..     108     178 ..     100     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-06
                         Claudin_2 119 vlllkaagilfllagvlgllavvvfiesvkkvfeesfqqwmqelqnnvrisfgWSfalAvagvvlsllAglL 190
                                       + ++ a+++ ++ a+v + +++ vf++ +  + + s +++  + +n+v+   g +f+l+ +++ +++ + +L
  gi|313127626|ref|YP_004037896.1| 108 YAAIEATFTRMVSAAVTLIVGIYVFAQISSTMPTPSNPEL-ANSTNTVKSTTGNAFTLGSVAIIVLVASVIL 178
                                       57899************************99888886666.889999***************9887666555 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.9   6.1e-05      0.36      13      71 ..     118     186 ..     108     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.1e-05
                                       XXXXXXXXXXXXXXXX..........XXX.....................XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  13 wligivllavGvwlrl..........khaeaalacllsesaedpailaillivvGvllfllgflGciga 71 
                                       ++ ++v l+vG+++            + ++a+ +++ ++++ ++ +l  + i+v v+ ++lg++G +g 
  gi|313127626|ref|YP_004037896.1| 118 MVSAAVTLIVGIYVFAqisstmptpsNPELANSTNTVKSTTGNAFTLGSVAIIVLVASVILGLVGGFGG 186
                                       78999******9998899*******98888888888899999999999999999999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1305.76
//
Query:       gi|313127627|ref|YP_004037897.1|  [L=90]
Description: hypothetical protein Hbor_29130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.055   13.4   0.0       0.11   12.4   0.0    1.5  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.4e-06      0.11      19      40 ..      63      84 ..      57      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.4e-06
                                      CCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin 19 lgireGdevelevdgdkiilrp 40
                                      +gi++G  +e+ev +++i+++p
  gi|313127627|ref|YP_004037897.1| 63 HGIEKGQLLEVEVREGGILIKP 84
                                      49*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 630.84
//
Query:       gi|313127628|ref|YP_004037898.1|  [L=207]
Description: hypothetical protein Hbor_29140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.038   14.2   0.0    1.6  1  YozE_SAM_like  YozE SAM-like fold


Domain annotation for each model (and alignments):
>> YozE_SAM_like  YozE SAM-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.1e-06     0.038       6      46 ..      98     138 ..      98     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-06
                                       HHTT--S--SHHHHHHHHHHT-TTS-TT---HHHHHHHHHT CS
                     YozE_SAM_like   6 lmtfrnpsedpvgelAenafkDksFPkqstdydeisdYLel 46 
                                       lm f n + +   +  e++++D+sFP +++d ++i++ L++
  gi|313127628|ref|YP_004037898.1|  98 LMDFYNVDAETALNCLEWMEEDPSFPIEARDDEQIMHGLRS 138
                                       68888885555555569******************986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1480.57
//
Query:       gi|313127629|ref|YP_004037899.1|  [L=299]
Description: zonular occludens toxin (zot) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0046   16.6   0.2      0.023   14.4   0.0    1.9  2  Zot       Zonular occludens toxin (Zot)
     0.0049   17.2   0.1       0.02   15.2   0.1    2.0  1  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.011   16.2   0.0       0.05   14.0   0.0    2.0  1  AAA       ATPase family associated with various cellular acti
      0.064   13.2   0.1       0.97    9.4   0.1    3.0  2  AAA_5     AAA domain (dynein-related subfamily)
      0.075   13.1   0.1       0.29   11.2   0.0    1.9  3  DUF87     Helicase HerA, central domain
       0.17   11.9   0.0       0.46   10.5   0.0    1.7  1  ResIII    Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.24   7.2e+02       5      19 ..      43      57 ..      40      74 .. 0.86
   2 !   14.4   0.0   7.5e-06     0.023      79     137 ..      85     145 ..      65     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.24
                               Zot  5 vtGapGsgKtsgavk 19
                                      v G+ G gK++ a+ 
  gi|313127629|ref|YP_004037899.1| 43 VVGETGKGKSYAALR 57
                                      679********9986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.5e-06
                               Zot  79 d..kgallviDEcqeifpvrakegrkdpevinaftehRhlgwDivlltqdiskihkevral 137
                                       d  +g+++v+DE++   + r + +   +     +++ Rh +  ++l+ +++ k++  +r +
  gi|313127629|ref|YP_004037899.1|  85 DqpEGSVIVLDEAGVGASHRDWYDDAHQHLNYVLQTWRHQNRIAILTLPELDKLDPVARSR 145
                                       3349******************87766666699*********************9888865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   6.7e-06      0.02       7     105 ..      40     143 ..      35     169 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.7e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee...erpevv.....fvtlpsst.sskdllrellralglelkaerls 74 
                                       ++vv+Ge+G GK++ + rl+e l  + + ++        +     +v+  +++ s   l ++ + a +++  +   +
  gi|313127629|ref|YP_004037899.1|  40 MGVVVGETGKGKSYAALRLAEALYPDFDVDNvafT----LeeffgLVEEDQPEgSVIVLDEAGVGASHRDWYD---D 109
                                       79********************9555444445541....2333346666666633333444444444444444...7 PP

                            AAA_22  75 seellealeqalraravielliiDEaqhlr...s 105
                                        ++ l+++ q +r++ +i++l + E ++l+   +
  gi|313127629|ref|YP_004037899.1| 110 AHQHLNYVLQTWRHQNRIAILTLPELDKLDpvaR 143
                                       8888888888888888888888888888865541 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-05      0.05       3     125 ..      43     147 ..      42     154 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCC CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgse 78 
                                       ++G  G GK+++a  +a+ l  + + ++   ++          ++e+f  ++e + + s++++DE+   a++r    
  gi|313127629|ref|YP_004037899.1|  43 VVGETGKGKSYAALRLAEALYPD-FDVDNVAFT----------LEEFFGLVEEDQpEGSVIVLDEAGVGASHR---- 104
                                       67889999999999999987533.333333333..........566666666666444777777777777777.... PP

                                       CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSS CS
                               AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfd 125
                                        +  +++ ++L  +l+  +++  + i i++  + dkldp  + +R+ 
  gi|313127629|ref|YP_004037899.1| 105 -DWYDDAHQHLNYVLQTWRHQ--NRIAILTLPELDKLDPVAR-SRLH 147
                                       .45555555555555555553..3467777777777777777.6665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00033      0.97       4      24 ..      43      65 ..      41     224 .. 0.90
   2 ?   -1.5   0.0      0.76   2.3e+03      29      60 ..     194     223 ..     184     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00033
                                      EE--SSSSHHHHHHHGGGGB..S CS
                             AAA_5  4 LvGppGtgKselaerlaaal..n 24
                                      +vG++G gKs  a rla+al   
  gi|313127629|ref|YP_004037899.1| 43 VVGETGKGKSYAALRLAEALypD 65
                                      79*****************9654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.76
                                       EEE--TT--HHHHH--B--.........---- CS
                             AAA_5  29 yvqltrdtteedlkgrreikngttslvdsplv 60 
                                       y+ lt ++++ dl+g +e  +++++++ds  +
  gi|313127629|ref|YP_004037899.1| 194 YKGLTFGLPSVDLIGAYE--ERKEKFTDSLNK 223
                                       666667778888888888..788888887544 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.6e-05      0.29      28      59 ..      43      95 ..      41      98 .. 0.74
   2 ?   -3.3   0.0       2.7     8e+03     119     210 ..     112     134 ..     101     140 .. 0.52
   3 ?   -2.1   0.1       1.1   3.3e+03     118     149 ..     218     251 ..     204     293 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                             DUF87 28 ilgsTGsGKSntvavLleelle.....................kkgatililD 59
                                      ++g+TG GKS+ +  L e l+                      ++ +++++lD
  gi|313127629|ref|YP_004037899.1| 43 VVGETGKGKSYAALRLAEALYPdfdvdnvaftleeffglveedQPEGSVIVLD 95
                                      89****************99976666666666666666666666666666666 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.7
                             DUF87 119 svleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallle 195
                                       + l+++l+++++                                                                 
  gi|313127629|ref|YP_004037899.1| 112 QHLNYVLQTWRH----------------------------------------------------------------- 123
                                       444555555544................................................................. PP

                             DUF87 196 klekegkitiidlsg 210
                                           +++i+i+ l +
  gi|313127629|ref|YP_004037899.1| 124 ----QNRIAILTLPE 134
                                       ....44444444444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.1
                             DUF87 118 rsvleealdqaka..keekeklssdepvekllee 149
                                       ++ l+++ ++a+a  + ++e++s +e v ++++ 
  gi|313127629|ref|YP_004037899.1| 218 TDSLNKTAKEAVApdDDDEEEYSPREAVDEIESR 251
                                       4444445555554554444445555544444443 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.46      22      59 ..      36      73 ..       9      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                      .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEE CS
                            ResIII 22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflf 59
                                      +++  g+++ +TG GK++ a++l+e+l+  ++ +++ f
  gi|313127629|ref|YP_004037899.1| 36 NQNFMGVVVGETGKGKSYAALRLAEALYPDFDVDNVAF 73
                                      7888999********************99988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1892.67
//
Query:       gi|313127630|ref|YP_004037900.1|  [L=392]
Description: ATPase AAA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-16   60.7   0.0    2.7e-16   59.8   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    2.8e-06   27.8   0.0      7e-06   26.5   0.0    1.7  1  AAA              ATPase family associated with various cellul
    4.1e-06   27.3   0.2    0.00046   20.6   0.0    2.4  2  AAA_16           AAA ATPase domain
    0.00013   22.1   0.1    0.00028   21.1   0.1    1.5  1  CbbQ_C           CbbQ/NirQ/NorQ C-terminal
    0.00025   20.9   0.0     0.0017   18.2   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
    0.00031   20.5   0.0      0.035   13.9   0.0    2.3  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00079   19.4   0.0     0.0015   18.4   0.0    1.4  1  Rad17            Rad17 P-loop domain
     0.0016   18.7   0.1     0.0049   17.1   0.0    1.9  2  AAA_28           AAA domain
     0.0067   17.0   0.0       0.02   15.4   0.0    1.9  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.015   15.2   0.0       0.37   10.7   0.0    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
      0.017   15.2   0.0      0.042   13.9   0.0    1.6  1  AAA_14           AAA domain
      0.019   15.4   0.0      0.033   14.6   0.0    1.4  1  RNA_helicase     RNA helicase
      0.023   14.9   0.0      0.061   13.5   0.0    1.7  2  AAA_33           AAA domain
      0.025   14.8   0.1       0.11   12.8   0.0    1.9  2  AAA_22           AAA domain
      0.027   14.0   0.0      0.051   13.1   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.032   13.6   0.0      0.071   12.5   0.0    1.5  1  IPT              Isopentenyl transferase
      0.037   14.5   0.0      0.095   13.2   0.0    1.6  1  ABC_tran         ABC transporter
      0.049   14.1   0.0        0.1   13.1   0.0    1.5  1  AAA_23           AAA domain
      0.078   12.7   0.0       0.31   10.7   0.0    1.9  1  Sigma54_activat  Sigma-54 interaction domain
      0.091   12.2   0.0       0.18   11.2   0.0    1.4  1  TniB             Bacterial TniB protein
       0.11   11.7   0.0       0.61    9.2   0.0    1.9  2  NB-ARC           NB-ARC domain
       0.18   11.7   0.1       0.58   10.1   0.1    1.8  1  NACHT            NACHT domain


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   3.3e-19   2.7e-16       5     137 ..     130     265 ..     127     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 3.3e-19
                                       E--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------....G-SEEEEESGGG- CS
                             AAA_5   5 vGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar....egeilvlDEvera 77 
                                        Gp+G+gK++lae+laa  ++++ ++q++  ++ ++l+g  +i +g+  +vd+pl+ra      +  ++++DEv+ra
  gi|313127630|ref|YP_004037900.1| 130 SGPTGCGKTTLAEYLAADRGAPMITIQCNYALRGAELLGTPQIVGGDVMWVDGPLTRALLasreREVLVLIDEVTRA 206
                                       6*********************************************************9999955556778****** PP

                                       -HHHHHHHHHHHHSSEEE....-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT CS
                             AAA_5  78 esevlnsLlslleerrll.l.eeggelvkaknddllerfrviatanpld.rslnelspalrsR 137
                                            ++L + l++r    + + g+el++  ++d    +  +at+n+ + ++ +el++a  +R
  gi|313127630|ref|YP_004037900.1| 207 TARSKGTLFPALDHRAEVkIkPRGNELISGVAED----MITVATMNEGQdYETEELDAAEERR 265
                                       **************96541315677777766666....**********99*******998777 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   8.6e-09     7e-06       3      87 ..     129     212 ..     127     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 8.6e-09
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS........STTHHHHHHHHHHHHHHHTS..TSEEEEEETGGG CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgsellsk........yvgesekkirelfkeakeka..kpsilfiDEida 69 
                                       ++Gp G+GKT+la+ +a + g+++++i++   l          +vg   + + + +++a   +  + + ++iDE+ +
  gi|313127630|ref|YP_004037900.1| 129 ISGPTGCGKTTLAEYLAADRGAPMITIQCNYALRGaellgtpqIVGGDVMWVDGPLTRALLASreREVLVLIDEVTR 205
                                       68**************************99999446899999*6776666666666666333332359*******99 PP

                                       HHHHHTTCCCHHHHHHHH CS
                               AAA  70 laksrsgseseeeervvn 87 
                                        + ++             
  gi|313127630|ref|YP_004037900.1| 206 ATARS-----------KG 212
                                       97766...........33 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.7e-07   0.00046       6      51 ..     105     151 ..     100     176 .. 0.81
   2 ?    4.1   0.0     0.066        54     125     163 ..     186     223 ..     180     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.7e-07
                            AAA_16   6 eeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd 51 
                                       e+el++++++l+ r ++g+ +   +sG+ G+GK++l++ l+    + 
  gi|313127630|ref|YP_004037900.1| 105 ERELDEIKAVLKaRGATGQLPRFQISGPTGCGKTTLAEYLAADRGAP 151
                                       7899********99999999*****************9998644333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.066
                            AAA_16 125 rllallsrderplvlvlDdlqwadeaslql.laaLlrlle 163
                                       r+l l+sr er +++++D++ +a + s    ++aL +++e
  gi|313127630|ref|YP_004037900.1| 186 RAL-LASR-EREVLVLIDEVTRATARSKGTlFPALDHRAE 223
                                       444.4555.888*************988775777776655 PP

>> CbbQ_C  CbbQ/NirQ/NorQ C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   3.4e-07   0.00028       1      72 [.     283     364 ..     283     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.4e-07
                                       HHHHHHHHHT--HHHHHHHHHHHHHHHTTBTTT....BSS---HHHHHHHHHHHTTT--HH......HHHHHHTTCC CS
                            CbbQ_C   1 EaeivaresgldeevakkLVklAneiRnlkegg....LeegvSTRlLvyaAkLiasglpar......eacraalvep 67 
                                       Eae+va+++ ++++ a+ LV++An +R   e +    ++ gv T  ++ +A+   ++ +        +a++ a+v+p
  gi|313127630|ref|YP_004037900.1| 283 EAELVATKTPMPSTDARVLVDAANVVRDAAEDEsepaITRGVPTPAVISWAQTAYAFAERGlndpvgRAMQSAVVKP 359
                                       89*************************9999877899***************9999887777777889********* PP

                                       C---H CS
                            CbbQ_C  68 ltddp 72 
                                       + d+ 
  gi|313127630|ref|YP_004037900.1| 360 VYDEV 364
                                       99985 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.1e-06    0.0017       5     124 ..     130     261 ..     127     267 .. 0.71
   2 ?   -1.4   0.0       2.4   1.9e+03      18      42 ..     367     391 ..     362     392 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-06
                             AAA_3   5 egvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfan.........llladein 72 
                                        g  G +kt+l++ la   ++ +  iq+   l  +++lGt  +     ++    Gp+            l+l de+ 
  gi|313127630|ref|YP_004037900.1| 130 SGPTGCGKTTLAEYLAADRGAPMITIQCNYALRGAELLGTPQIVG--GDVMWVDGPLTRAllasrerevLVLIDEVT 204
                                       67789*************************999999999965443..4445555665432111122223789***** PP

                             AAA_3  73 rappktqsalleameer.qvtvegethkl....pepflvlatqnPieqeGtyplpea 124
                                       ra+++++ +l+ a++ r +v ++ +  +l     e ++ +at n  +   t +l  a
  gi|313127630|ref|YP_004037900.1| 205 RATARSKGTLFPALDHRaEVKIKPRGNELisgvAEDMITVATMNEGQDYETEELDAA 261
                                       ***********9998653577766555542222678888999887776666666555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                             AAA_3  18 alakaldlefkriqftpdllPsdil 42 
                                        +a +++  +kr    pdl P +++
  gi|313127630|ref|YP_004037900.1| 367 DVAGKIHSALKRADHEPDLGPEEVT 391
                                       5788899999999******999886 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.3e-05     0.035      27      77 ..     118     168 ..     100     232 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                            RuvB_N  27 kkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaa 77 
                                       +  + +l    ++Gp G Gkttla+ +a++ g+ + +       + ++l +
  gi|313127630|ref|YP_004037900.1| 118 RGATGQLPRFQISGPTGCGKTTLAEYLAADRGAPMITIQCNYALRGAELLG 168
                                       4445567778899***************99887654433333333333322 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06    0.0015       9      73 ..      88     152 ..      81     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                             Rad17   9 WfekykPekaeelavhk...kkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgikl 73 
                                       W +++ P++ e++ v++   + ++e+k  lka     +  r   isGP+GCgk+t  + L+   g  +
  gi|313127630|ref|YP_004037900.1|  88 W-DRFVPDT-EDVPVYRqaeRELDEIKAVLKARGATGQLPR-FQISGPTGCGKTTLAEYLAADRGAPM 152
                                       4.8999987.68888863336899********999888555.689************99998887655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.1e-06    0.0049       2      27 ..     127     153 ..     126     159 .. 0.86
   2 ?   -2.6   0.0       6.8   5.5e+03      26      54 ..     233     260 ..     186     270 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.1e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv 27 
                                       + i+G+ ++GKTtl+e Laa+ g p++
  gi|313127630|ref|YP_004037900.1| 127 FQISGPTGCGKTTLAEYLAADrGAPMI 153
                                       569****************86588765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.8
                            AAA_28  26 vvpEaareileeklakgedalpwvedlla 54 
                                        +  +a ++++  + +++++ +  e+l a
  gi|313127630|ref|YP_004037900.1| 233 LISGVAEDMITVATMNEGQDYET-EELDA 260
                                       33334444444444444443333.24444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.5e-05      0.02       3      22 ..     129     148 ..     128     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrl 22 
                                       ++G+ G+GKttla++L+   
  gi|313127630|ref|YP_004037900.1| 129 ISGPTGCGKTTLAEYLAADR 148
                                       79**************7654 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00045      0.37       6      42 ..     109     146 ..     104     155 .. 0.69
   2 ?    2.0   0.0      0.21   1.7e+02     112     131 ..     188     207 ..     183     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                          ATPase_2   6 kelkeleeilerepneiyf.iYGpegsGKtaLlkeiie 42 
                                        e+k +++    + + + f i Gp g+GKt+L   ++ 
  gi|313127630|ref|YP_004037900.1| 109 DEIKAVLKARGATGQLPRFqISGPTGCGKTTLAEYLAA 146
                                       245555555455566666669***********987765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.21
                          ATPase_2 112 kikkkgkkiiiiiDelqkli 131
                                        +  + +++ ++iDe+ ++ 
  gi|313127630|ref|YP_004037900.1| 188 LLASREREVLVLIDEVTRAT 207
                                       56778899********9987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.2e-05     0.042       7      76 ..     129     206 ..     126     236 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                            AAA_14   7 itGaRrvGKTtllkqlikellvkkesilyinldderdkkla..dpe...........kllelileklkeekktylfl 70 
                                       i+G+  +GKTtl++ l+ ++      ++ i+++     ++   +p+            l +++l++  +e++ ++++
  gi|313127630|ref|YP_004037900.1| 129 ISGPTGCGKTTLAEYLAADRG---APMITIQCNYALRGAELlgTPQivggdvmwvdgPLTRALLAS--REREVLVLI 200
                                       89***************9999...899999999876633322233344443433222233444443..268999999 PP

                            AAA_14  71 DEiqev 76 
                                       DE+ ++
  gi|313127630|ref|YP_004037900.1| 201 DEVTRA 206
                                       999987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.1e-05     0.033       3      23 ..     129     149 ..     127     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.1e-05
                      RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                       ++Gp+g+GK+tla++La++  
  gi|313127630|ref|YP_004037900.1| 129 ISGPTGCGKTTLAEYLAADRG 149
                                       89**************99865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.5e-05     0.061       5      35 ..     130     162 ..     128     224 .. 0.84
   2 ?   -2.3   0.0       5.7   4.6e+03      66      87 ..     293     314 ..     239     335 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-05
                            AAA_33   5 vGlpGsGKstlaerllkklg..avllssdtlrr 35 
                                        G+ G+GK+tlae l++ +g  ++++  ++++r
  gi|313127630|ref|YP_004037900.1| 130 SGPTGCGKTTLAEYLAADRGapMITIQCNYALR 162
                                       59**************99998888777776555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.7
                            AAA_33  66 alsagrnvildatnlsrrerar 87 
                                       + s  + v++da n+ r++ ++
  gi|313127630|ref|YP_004037900.1| 293 MPSTDARVLVDAANVVRDAAED 314
                                       4445555666666666655544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013      0.11      10      47 ..     129     157 ..     127     166 .. 0.83
   2 ?   -1.4   0.0       3.2   2.6e+03      89     103 ..     191     206 ..     184     224 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtl 47 
                                       + G++G+GKTtl++ l+            +++ +++++
  gi|313127630|ref|YP_004037900.1| 129 ISGPTGCGKTTLAEYLAADR---------GAPMITIQC 157
                                       78*************99876.........666666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.2
                            AAA_22  89 rav.ielliiDEaqhl 103
                                        +   +l++iDE+ + 
  gi|313127630|ref|YP_004037900.1| 191 SRErEVLVLIDEVTRA 206
                                       3333579999998765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.2e-05     0.051      14      39 ..      15      40 ..      13      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.2e-05
                            HTH_24 14 knprisqreLAerlglSpstvnrrlk 39
                                      +n+  + +e+Ae +g Sps++nr lk
  gi|313127630|ref|YP_004037900.1| 15 ENGARTKNEIAEVVGKSPSNTNRKLK 40
                                      6778899****************988 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.7e-05     0.071       6      37 ..     129     157 ..     126     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.7e-05
                               IPT   6 ifGatttGKtaeaiklaketgapvivlDRvqc 37 
                                       i G+t+ GKt  a  la ++gap+i+   +qc
  gi|313127630|ref|YP_004037900.1| 129 ISGPTGCGKTTLAEYLAADRGAPMIT---IQC 157
                                       89***********************7...566 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.095      14      33 ..     127     146 ..     122     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                                       EEEEESTTSSHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllag 33 
                                        +i G++G+GK+tL++ la 
  gi|313127630|ref|YP_004037900.1| 127 FQISGPTGCGKTTLAEYLAA 146
                                       6899***********99986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00012       0.1      24      39 ..     129     144 ..     125     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                            AAA_23  24 ItGpNGaGKTTildAi 39 
                                       I+Gp+G+GKTT+ + +
  gi|313127630|ref|YP_004037900.1| 129 ISGPTGCGKTTLAEYL 144
                                       9***********9865 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00038      0.31      24      66 ..     126     167 ..     102     256 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETT.TS.-TTCH CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavnca.ai.peell 66 
                                       +  i G +G+GK++la+ + +    + +p+++++c  a+  +ell
  gi|313127630|ref|YP_004037900.1| 126 RFQISGPTGCGKTTLAEYLAA---DRGAPMITIQCNyALrGAELL 167
                                       45699************9865...456899999997332333343 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.18      13      58 ..     101     147 ..      94     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                              TniB  13 yprakeilerLeeLleypk.rkrmpnlllvGdsnnGKtmivekFarl 58 
                                       y +a++ l++++++l++     + p   + G++ +GKt+++e  a++
  gi|313127630|ref|YP_004037900.1| 101 YRQAERELDEIKAVLKARGaTGQLPRFQISGPTGCGKTTLAEYLAAD 147
                                       999**********99997736788****************9987765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00075      0.61       5      39 ..     108     143 ..     104     150 .. 0.68
   2 ?   -0.1   0.0      0.54   4.4e+02     100     148 ..     189     238 ..     181     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00075
                                       HHHHHHHHHCTTTS.CSEEEEEEESTTSSHHHHHHH CS
                            NB-ARC   5 vekviekLlekdel.qslvvalvGmgGvGKttlakq 39 
                                       +++++  L   +   q+    ++G  G+GKttla+ 
  gi|313127630|ref|YP_004037900.1| 108 LDEIKAVLKARGATgQLPRFQISGPTGCGKTTLAEY 143
                                       5666666665433303345789***********986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.54
                                       CCCT.TE.EEEEEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS- CS
                            NB-ARC 100 Lltk.rf.llvlDDVweeedwdkigvvlparenrlrvllTTRdeevanavs 148
                                       L ++ r  l+++D V    + ++ g  +pa ++r +v +  R +e+ + v+
  gi|313127630|ref|YP_004037900.1| 189 LASReREvLVLIDEVT-RATARSKGTLFPALDHRAEVKIKPRGNELISGVA 238
                                       4444555055555555.5577788999999999999998888888754444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00071      0.58       5      22 ..     129     146 ..     126     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00071
                                       EEC-TTTCHHHHHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlqklal 22 
                                       + G+ G+GKTtL++ la 
  gi|313127630|ref|YP_004037900.1| 129 ISGPTGCGKTTLAEYLAA 146
                                       78***********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:01.38
# Mc/sec: 862.48
//
Query:       gi|313127631|ref|YP_004037901.1|  [L=61]
Description: hypothetical protein Hbor_29170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.023   14.7   0.3      0.029   14.4   0.3    1.2  1  DZR          Double zinc ribbon
      0.037   14.2   0.1      0.037   14.2   0.1    1.1  1  IBR          IBR domain, a half RING-finger domain
       0.26   10.8   3.1        3.5    7.2   0.1    2.2  2  zf-ribbon_3  zinc-ribbon domain
       0.41   10.3   1.9         16    5.2   0.1    2.2  2  zf_UBZ       Ubiquitin-Binding Zinc Finger
        1.6    9.0   7.4       0.39   10.9   1.5    2.1  2  zf-CCHC      Zinc knuckle


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3     8e-06     0.029      14      38 ..      31      59 ..      23      61 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-06
                               DZR 14 fCseCgtklkavaa....edrCpsCgekv 38
                                       C++Cg +++++++       C++Cg+ +
  gi|313127631|ref|YP_004037901.1| 31 ECYNCGGTIEPPERpsmvLVECSECGRRN 59
                                      6********98777999999*****9875 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     1e-05     0.037      15      46 ..      26      57 ..       8      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                               IBR 15 dpnlkwCprpdCeaiieksegcks..vtCskCgf 46
                                       p +  C   +C++ ie+ e  ++  v+Cs+Cg 
  gi|313127631|ref|YP_004037901.1| 26 LPAWDECY--NCGGTIEPPERPSMvlVECSECGR 57
                                      567899*9..***********7666788****96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8    0.0094        34      19      24 ..      32      37 ..      31      39 .. 0.86
   2 ?    7.2   0.1   0.00097       3.5       3      11 ..      50      59 ..      48      61 .] 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0094
                       zf-ribbon_3 19 CpyCGt 24
                                      C++CG+
  gi|313127631|ref|YP_004037901.1| 32 CYNCGG 37
                                      99**97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00097
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      v+C++CG  +
  gi|313127631|ref|YP_004037901.1| 50 VECSECGRrN 59
                                      79*****666 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0045        16       4      19 ..      31      46 ..      28      46 .. 0.89
   2 ?    4.6   0.2    0.0066        24       4      10 ..      51      57 ..      49      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0045
                            zf_UBZ  4 lCerCgkeipeselqE 19
                                       C  Cg +i+++e+++
  gi|313127631|ref|YP_004037901.1| 31 ECYNCGGTIEPPERPS 46
                                      5999*********985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0066
                            zf_UBZ  4 lCerCgk 10
                                       C++Cg+
  gi|313127631|ref|YP_004037901.1| 51 ECSECGR 57
                                      7****97 PP

>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.5   0.00011      0.39       2       8 ..      31      37 ..      30      38 .. 0.84
   2 ?    1.7   0.4     0.089   3.2e+02       2       8 ..      51      57 ..      50      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                      CTSSSSS CS
                           zf-CCHC  2 kCynCGe 8 
                                       CynCG+
  gi|313127631|ref|YP_004037901.1| 31 ECYNCGG 37
                                      7*****7 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.089
                                      CTSSSSS CS
                           zf-CCHC  2 kCynCGe 8 
                                       C  CG+
  gi|313127631|ref|YP_004037901.1| 51 ECSECGR 57
                                      6999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 406.74
//
Query:       gi|313127632|ref|YP_004037902.1|  [L=402]
Description: von Willebrand factor A [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-05   25.0   0.0    9.6e-05   22.7   0.0    1.9  2  VWA       von Willebrand factor type A domain
    3.7e-05   24.3   0.0    8.5e-05   23.2   0.0    1.6  1  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.14   1.3e+03       4      15 ..     231     242 ..     229     264 .. 0.79
   2 !   22.7   0.0   1.1e-08   9.6e-05      96     160 ..     310     376 ..     289     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.14
                                       EEEE-STTSCHH CS
                               VWA   4 fvlDgSgsmgee 15 
                                       ++lD Sgsmg+ 
  gi|313127632|ref|YP_004037902.1| 231 IALDMSGSMGNA 242
                                       79*******654 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.1e-08
                                       HGTSST..TSEEEEEEEESS--CS.SHTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHSSSSCHHCE CS
                               VWA  96 sagaRe..nakkviilltdGksnd.gdpkeaaneakeqgikvfavGvgnadekelLnkiasepgeghv 160
                                       ++ +R+  + ++v+  +tdG+++  + + e ++ ++ +g  v+ +G+g ++e + L+++ +  g +hv
  gi|313127632|ref|YP_004037902.1| 310 TRLMRPlkGRERVLFAITDGRPSRaDRVAELVEDLRTYGTAVVGFGFGRVNEST-LEELFGRDGYRHV 376
                                       44456666799***********8866****************************.****999886665 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   9.4e-09   8.5e-05       3     106 ..     231     329 ..     229     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 9.4e-09
                             VWA_2   3 fvlDtSgSmrngdygptrleaakdaveallksl.p.gdrvglvtfsdgpevlipltkdkakilna.lrnleakgggt 76 
                                       + lD+SgSm+n        + ak+av al  +  + +d v + +f  g ++ + +t  +++ +   l+++e+ gggt
  gi|313127632|ref|YP_004037902.1| 231 IALDMSGSMGNA------EHDAKAAVGALALAAsAvDDDVVITAFPQGKRKSALVTGPYESWRWQhLDATEP-GGGT 300
                                       789********8......79999999887774436699**********999999999888887641555555.8*** PP

                             VWA_2  77 nlaaaLqlarkalkkrrkgekrvivlitDg 106
                                        +  aL+ ++ +++   kg++rv++ itDg
  gi|313127632|ref|YP_004037902.1| 301 PMLPALRDVTRLMRPL-KGRERVLFAITDG 329
                                       ************9955.69**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2664.16
//
Query:       gi|313127633|ref|YP_004037903.1|  [L=109]
Description: hypothetical protein Hbor_29190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.014   15.7   0.0    1.2  1  GGDEF_2    GGDEF-like domain
       0.16   12.2   0.0       0.22   11.8   0.0    1.2  1  Pro-NT_NN  Neurotensin/neuromedin N precursor


Domain annotation for each model (and alignments):
>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   1.5e-06     0.014      35      81 ..      26      86 ..       7     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-06
                           GGDEF_2 35 erllraleealralgpdalvavrgdrlvlllpaedeedae..............allerla 81
                                       ++l+ +e++ r+++++ ++av+++++vl+l+++ +e+ e              +++er++
  gi|313127633|ref|YP_004037903.1| 26 GEVLEVWEREHRNSDRTHVIAVDSGEIVLVLASDVDEHGEplaaelvstcyttdEAQERAH 86
                                      3489999*************************99998888555555555555555555555 PP

>> Pro-NT_NN  Neurotensin/neuromedin N precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.5e-05      0.22      14      46 ..      54      86 ..      45      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                         Pro-NT_NN 14 lslcsDvdeekkaleeelltslytskvkqnkqs 46
                                      l+l+sDvde+ + l++el++  yt+   q++++
  gi|313127633|ref|YP_004037903.1| 54 LVLASDVDEHGEPLAAELVSTCYTTDEAQERAH 86
                                      579**********************98666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 765.25
//
Query:       gi|313127634|ref|YP_004037904.1|  [L=77]
Description: hypothetical protein Hbor_29200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 579.94
//
Query:       gi|313127635|ref|YP_004037905.1|  [L=133]
Description: hypothetical protein Hbor_29210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.37   10.4   3.0        5.2    6.7   0.0    2.1  2  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
          1    9.5  10.7          6    7.0   6.6    2.1  2  DUF3180    Protein of unknown function (DUF3180)


Domain annotation for each model (and alignments):
>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0   0.00058       5.2     145     173 ..      11      39 ..       7      59 .. 0.78
   2 ?    3.5   1.5    0.0055        49     140     170 ..      76     107 ..      69     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00058
                         CPP1-like 145 vlltlvgLvvGlllGsllasllqvdvals 173
                                       vl++  gL++G++++ ll++  ++   l+
  gi|313127635|ref|YP_004037905.1|  11 VLIATFGLSLGWVVSRLLSGAREPREFLA 39 
                                       799***************99877764444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0055
                         CPP1-like 140 klgravlltlvgLvvGlllGsllasllqvd.v 170
                                        l  a l+++++L+v+ + ++++ +l+ +  v
  gi|313127635|ref|YP_004037905.1|  76 GLAAAGLMAVLALIVASMTANAFTPLVVTGcV 107
                                       56778899999999999999999998865553 PP

>> DUF3180  Protein of unknown function (DUF3180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0032        29      31      56 ..       7      33 ..       2      58 .. 0.63
   2 ?    7.0   6.6   0.00067         6       3      49 ..      78     124 ..      77     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0032
                           DUF3180 31 avvllvlavvelvlAlqvrrrirgr.p 56
                                      +v+ +++a   l l++ v r + g  +
  gi|313127635|ref|YP_004037905.1|  7 PVAYVLIATFGLSLGWVVSRLLSGArE 33
                                      677888888888888888888876631 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00067
                           DUF3180   3 aaavvaavagwllvrvsygslpplpwlaavvllvlavvelvlAlqvr 49 
                                       aaa ++av+++++++++ + ++pl ++  vv+++l + e+++A+ v 
  gi|313127635|ref|YP_004037905.1|  78 AAAGLMAVLALIVASMTANAFTPLVVTGCVVVVLLELGEVLVAYGVS 124
                                       6788999*********999999***************9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 937.06
//
Query:       gi|313127636|ref|YP_004037906.1|  [L=77]
Description: hypothetical protein Hbor_29220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 540.75
//
Query:       gi|313127637|ref|YP_004037907.1|  [L=201]
Description: phage integrase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-09   36.2   0.0      2e-08   34.3   0.0    1.8  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   1.1e-12     2e-08       4     168 ..      17     184 ..      14     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.1e-12
                                       HHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGE....ECTTTEEEEE...EEECSSSSEEEEECT CS
                   Phage_integrase   4 tedeverllaaleeslkirdklllellyetGlRisEllsLrvkdl....dlengvilvh...eregKgskeravpls 73 
                                       t  e+++l   + +    rd+l+++l  + GlR+ E+ ++  k++    d e+ +++v+    + g g+k r   l+
  gi|313127637|ref|YP_004037907.1|  17 TDSELKQLERVAAN---QRDYLIIRLGGRVGLRAFEIPQICPKHVkrtdDGEHYRLRVPegkDTTGNGGKPRDAYLP 90 
                                       55566666655555...666666666666777766666665555311112233344444554455555666666666 PP

                                       HHHHHHHHHHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S..SC--TTHHHHHHHHHHH.HHCTS CS
                   Phage_integrase  74 eealellkellskaleeaeksellfaskrgkplsrqtvrkafkraveeagie..kpltpHtlRhsfataLl.eagvd 147
                                       + +   +++  + +   + +++  ++   +++  r+ v+++  ra+ee+g e   ++++H+lR+ fa +Ll  ++++
  gi|313127637|ref|YP_004037907.1|  91 KDVEGDIHRFQNAE---DIGRNQPLVDL-TERGVRNVVKRTATRAAEETGDEdfRHVSSHDLRRRFAQRLLvDRQMN 163
                                       66666666655555...22222222222.34566777888888888888888****************976379*** PP

                                       HHHHHHHHT-SSCCHHHHHHC CS
                   Phage_integrase 148 lrvvqkllGHssisttqiYth 168
                                       +rvv+ ++G+ s + ++ Y +
  gi|313127637|ref|YP_004037907.1| 164 PRVVMAVGGWDSFQAIEPYLN 184
                                       **************9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1457.68
//
Query:       gi|313127638|ref|YP_004037908.1|  [L=44]
Description: hypothetical protein Hbor_29240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 292.50
//
Query:       gi|313127639|ref|YP_004037909.1|  [L=66]
Description: hypothetical protein Hbor_29250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 460.73
//
Query:       gi|313127640|ref|YP_004037910.1|  [L=66]
Description: hypothetical protein Hbor_29260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-13   49.8   1.0    3.1e-13   49.7   1.0    1.0  1  DUF2188   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2188  Uncharacterized protein conserved in bacteria (DUF2188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   1.0   1.7e-17   3.1e-13       1      62 []       4      64 ..       4      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.7e-17
                           DUF2188  1 yhVvP.kddgg..WavkreGgsrasktfdTqeeAieaArelAkeqggselvihgrdGqirernsy 62
                                      y ++P ++++   W+v+ +   r+++ ++Tq+ A++aAr++A+   g e+ ihg+ G++r+++++
  gi|313127640|ref|YP_004037910.1|  4 YNIMPtARGEPydWKVEAN--GRKTSSHRTQQNAVDAARRRAAP--GDEINIHGTGGRVRDSWTV 64
                                      6788866666577888886..566******************99..9***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 434.57
//
Query:       gi|313127641|ref|YP_004037911.1|  [L=350]
Description: dual-action metallo-peptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-10   38.9   0.6    0.00083   19.2   0.1    2.5  2  Peptidase_M10  Matrixin
    0.00088   19.8   0.1     0.0062   17.0   0.0    2.1  2  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
    0.00094   19.2   0.1     0.0016   18.5   0.1    1.3  1  Peptidase_M54  Peptidase family M54
     0.0016   18.1   0.5     0.0024   17.5   0.1    1.5  2  Peptidase_M57  Dual-action HEIGH metallo-peptidase
  ------ inclusion threshold ------
      0.012   15.8   2.7      0.027   14.6   0.3    2.2  2  Reprolysin_5   Metallo-peptidase family M12
      0.018   15.0   0.2      0.043   13.7   0.2    1.6  1  Peptidase_M43  Pregnancy-associated plasma protein-A
      0.076   12.9   0.3       0.13   12.2   0.3    1.4  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like


Domain annotation for each model (and alignments):
>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   3.2e-07   0.00083     105     135 ..     153     183 ..      56     196 .. 0.70
   2 !   17.8   0.1   8.9e-07    0.0023       2      73 ..     207     286 ..     206     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.2e-07
                                       SSEEHHHHHHHHHHHHTTBESXSSTTSTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 105 qgvslflVaaHEiGHalGLeHssdkdalmyp 135
                                       +   +    +HE+GH+lG++H ++++ +m  
  gi|313127641|ref|YP_004037911.1| 153 NYRTVKNTIIHEFGHILGITHCEKPHWVMSY 183
                                       3334556689***************999964 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 8.9e-07
                                       TSSSEEEEEESSSX.TTSXHHHHHHHHHHH...HHHHHTTS...SSEEEEE.SSSCESEEEEEESSSSSSSSSXBSS CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxx...xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10   2 wekknltyrilnet.pdleeeevrkairrA...fkvwsevt...plkFtev.kkgeadikieFgrgehgdgypfdgk 70 
                                       w+++nl+  ++ ++ ++ + +e+++++++A   f+ w+++    +++Ft+v + ++adi i+F++++ + +y++ g 
  gi|313127641|ref|YP_004037911.1| 207 WRSTNLSVYVDYSNvSKNSLTETKSQVNHAvtyFEEWKAKEvpsDVSFTRVqDPWKADIVITFAQDRCEGEYTVCGD 283
                                       766666666655552334444455555554333889987766557******889**********9999999988887 PP

                                       SSE CS
                                       xxx RF
                     Peptidase_M10  71 ggv 73 
                                       gg+
  gi|313127641|ref|YP_004037911.1| 284 GGT 286
                                       775 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.4e-06    0.0062      65     123 ..     110     173 ..      75     174 .. 0.78
   2 ?    0.2   0.0      0.39   9.9e+02      45      83 ..     246     285 ..     203     319 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                      Reprolysin_3  65 Dlvhlftarde..sgvgGlAyv...gsvcnsskkagvnsgssvlgkvgadtvaHEiGHnfganH 123
                                       D+ +  +++ +  +g  G+A     ++  ++ +++++ +++s +  + ++t++HE GH +g  H
  gi|313127641|ref|YP_004037911.1| 110 DIIVWYNNTINcpQGASGCAHRlnrTTSARPPENVQILYNKSNNYRTVKNTIIHEFGHILGITH 173
                                       5555555544467888899888666555555556788888877777899************999 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                      Reprolysin_3  45 ealdelaevtaeaergqagyDlvhlftarde...sgvgGlAy 83 
                                       + + + +++t+ +  +  ++D+v  f ++     ++v+G  +
  gi|313127641|ref|YP_004037911.1| 246 KEVPSDVSFTRVQ--DPWKADIVITFAQDRCegeYTVCGDGG 285
                                       2223333333333..677889999998866677777777554 PP

>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   6.1e-07    0.0016     144     170 ..     155     183 ..     144     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.1e-07
                                       HHHH.HHHHHHHHHTT----S-.TSTTS- CS
                     Peptidase_M54 144 rvvk.evlhelGhlyGLshCke.dCvmnf 170
                                       r vk  ++he Gh++G++hC++   vm++
  gi|313127641|ref|YP_004037911.1| 155 RTVKnTIIHEFGHILGITHCEKpHWVMSY 183
                                       44551689**************999**97 PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   9.3e-07    0.0024      74     151 ..      97     175 ..      39     194 .. 0.68
   2 ?   -3.6   0.0       2.8   7.1e+03      47      70 ..     219     242 ..     205     254 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.3e-07
                     Peptidase_M57  74 sltfrltrgtntqasdmvvaditaktasgaggsaGfP...sgGlPykviqigtglesysvdvnehvithelGhtvGl 147
                                       s++f   r ++ +  ++v +++t++ + ga+g a      +  +P + +qi +  +s +  ++   i he+Gh +G+
  gi|313127641|ref|YP_004037911.1|  97 SVDFV-LRPDAENPDIIVWYNNTINCPQGASGCAHRLnrtTSARPPENVQILY-NKSNNYRTVKNTIIHEFGHILGI 171
                                       44453.33444455678889*****9999888886432227899*******55.56778889999999********* PP

                     Peptidase_M57 148 RhsD 151
                                        h +
  gi|313127641|ref|YP_004037911.1| 172 THCE 175
                                       **75 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
                     Peptidase_M57  47 tgsafsstsklrtgLdlaianyna 70 
                                       +  +++s +++++ ++ a+  + +
  gi|313127641|ref|YP_004037911.1| 219 SNVSKNSLTETKSQVNHAVTYFEE 242
                                       333456666667777777776655 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   1.1e-05     0.027      90     159 ..     106     174 ..      41     207 .. 0.68
   2 ?    1.1   0.1      0.14   3.7e+02      43     108 ..     209     279 ..     199     319 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                      Reprolysin_5  90 qqnddlailflmt.nfsgg.vGlAwlgqlcnsgsagsvstrveksnsvvvstatevqvvaHElGHnfGavHD 159
                                       ++n d+ +++ +t n+++g  G+A+  + ++s       ++v+  +++  + +t  +++ HE+GH +G  H 
  gi|313127641|ref|YP_004037911.1| 106 AENPDIIVWYNNTiNCPQGaSGCAHRLNRTTSAR---PPENVQILYNKSNNYRTVKNTIIHEFGHILGITHC 174
                                       4555788888776588888788888877766433...2233333366667788999*************994 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.14
                      Reprolysin_5  43 esnislglanvtildeedpstase......asstgdaselLnefqsassalrgqqnddlailflmtnfsgg.v 108
                                       ++n+s+ +    +++++ ++t+s+      + ++++a+e+ +++  +++  ++ +++d++i f    ++g+  
  gi|313127641|ref|YP_004037911.1| 209 STNLSVYVDYSNVSKNSLTETKSQvnhavtYFEEWKAKEVPSDV--SFTRVQDPWKADIVITFAQDRCEGEyT 279
                                       45666666655566666665555555666677777777777777..788888889999999999999988742 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.7e-05     0.043      58      87 ..     146     176 ..     123     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                     Peptidase_M43  58 ylaa.dststnksstLthelGhfLgLihtfe 87 
                                        l++ ++ +   + t+ he+Gh Lg+ h  +
  gi|313127641|ref|YP_004037911.1| 146 ILYNkSNNYRTVKNTIIHEFGHILGITHCEK 176
                                       344435667778899*************765 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3     5e-05      0.13     116     191 ..     148     229 ..     117     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-05
                      Reprolysin_2 116 sgsaveetkeidvvaHEvGHaFGatHdndgs......sasegveenaatsvedaggkfiMa.pasksnndlFSpcsi 185
                                       ++++++  + ++ + HE GH+ G tH  + +      s s+g+++     + + +++++ +  ++ s  +++S+ s+
  gi|313127641|ref|YP_004037911.1| 148 YNKSNNYRTVKNTIIHEFGHILGITHCEKPHwvmsywSGSHGCKNPTFD-APSVENQSLAWrSTNLSVYVDYSNVSK 223
                                       556666678888999***********99888888876444444433333.678899999994556699999999999 PP

                      Reprolysin_2 186 slisdv 191
                                       +++++ 
  gi|313127641|ref|YP_004037911.1| 224 NSLTET 229
                                       998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2316.62
//
Query:       gi|313127642|ref|YP_004037912.1|  [L=94]
Description: hypothetical protein Hbor_29280 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0019   18.1   0.1     0.0025   17.7   0.1    1.2  1  Cdc6_C     CDC6, C terminal winged helix domain
     0.0028   18.1   0.1     0.0045   17.5   0.1    1.3  1  HTH_27     Winged helix DNA-binding domain
     0.0056   16.2   0.0       0.17   11.5   0.0    2.4  2  HTH_24     Winged helix-turn-helix DNA-binding
     0.0081   16.1   0.2      0.013   15.5   0.2    1.3  1  HTH_45     Winged helix-turn-helix
  ------ inclusion threshold ------
      0.011   15.6   0.9      0.034   14.1   0.7    1.8  2  PadR       Transcriptional regulator PadR-like family
      0.029   14.5   0.1      0.035   14.2   0.1    1.4  1  Mrr_N      Mrr N-terminal domain
       0.12   12.2   0.1       0.18   11.6   0.1    1.2  1  DUF4364    Domain of unknown function (DUF4364)
       0.15   12.1   0.2       0.18   11.8   0.2    1.3  1  HTH_Crp_2  Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.1e-06    0.0025      24      70 ..      30      74 ..      28      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEE CS
                            Cdc6_C 24 vYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtr 70
                                      v+++++e +g++  +++++s+ + +Le+ g+lel+ + k  r+ r +
  gi|313127642|ref|YP_004037912.1| 30 VHHNIAEVRGYSEKSRSTFSRRIGDLEKIGLLELTDETK--RYYRIT 74
                                      7899*******************************9833..455544 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1     2e-06    0.0045      20      68 .]      33      77 ..      27      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                            HTH_27 20 kladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                       +a+++g+   + s++s  +  L++ GL+e     +d   + +r+T+kG
  gi|313127642|ref|YP_004037912.1| 33 NIAEVRGYSEKSRSTFSRRIGDLEKIGLLEL----TDETKRYYRITEKG 77
                                      5799*************************33....4456899******9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.056   1.3e+02      25      39 ..      21      35 ..      20      37 .. 0.87
   2 !   11.5   0.0   7.6e-05      0.17      30      47 ..      44      61 ..      41      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.056
                            HTH_24 25 erlglSpstvnrrlk 39
                                      er+ l p+tv+  + 
  gi|313127642|ref|YP_004037912.1| 21 ERVELQPGTVHHNIA 35
                                      899********9875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.6e-05
                            HTH_24 30 SpstvnrrlkrLeeeGlI 47
                                      S+st +rr+  Le+ Gl+
  gi|313127642|ref|YP_004037912.1| 44 SRSTFSRRIGDLEKIGLL 61
                                      99**************97 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   5.8e-06     0.013      35      67 ..      47      82 ..      44      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.8e-06
                            HTH_45 35 llnkYLdmLvekgli...kkskekYvlTekGlelle 67
                                      ++++ +  L + gl+   +++k  Y++TekGl +le
  gi|313127642|ref|YP_004037912.1| 47 TFSRRIGDLEKIGLLeltDETKRYYRITEKGLAYLE 82
                                      677778899999998777789999*********998 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.4     9e+02      16      37 ..      12      33 ..       8      39 .. 0.77
   2 ?   14.1   0.7   1.5e-05     0.034      25      74 ..      39      82 ..      29      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.4
                                      HHHHHCCSTT-CCTTHHHHHHH CS
                              PadR 16 ikeleelsegllelseGslYpa 37
                                       +e+e  s++ +el++G++  +
  gi|313127642|ref|YP_004037912.1| 12 FREMESISGERVELQPGTVHHN 33
                                      5688888888899999998665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.5e-05
                                      T-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR 25 gllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      g+ e s ++  +   +Lek gl+e + e+      ++yYr+T++G ++l+
  gi|313127642|ref|YP_004037912.1| 39 GYSEKSRSTFSRRIGDLEKIGLLELTDET------KRYYRITEKGLAYLE 82
                                      66666667777777899999999999886......7*********99886 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.6e-05     0.035      59      86 ..      53      82 ..       3      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                             Mrr_N 59 tyLkkagllespk..rgvwkiTekGrevlk 86
                                       +L k glle ++  + +++iTekG ++l+
  gi|313127642|ref|YP_004037912.1| 53 GDLEKIGLLELTDetKRYYRITEKGLAYLE 82
                                      4899******99988999********9985 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.9e-05      0.18      36      71 ..      48      82 ..      46      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.9e-05
                           DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketle 71
                                      ++  + +L++ gl+e  ++e+k +y+iTekG   le
  gi|313127642|ref|YP_004037912.1| 48 FSRRIGDLEKIGLLEL-TDETKRYYRITEKGLAYLE 82
                                      6677899********9.5699**********88775 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   7.8e-05      0.18      34      60 ..      44      74 ..      11      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.8e-05
                                      SHHHHHHHHHHHHHTTSEE.E.T.EE.EEES CS
                         HTH_Crp_2 34 tretvsrilseLkreglis.r.g.rr.iril 60
                                      +r+t+sr +++L++ gl++ + + +r  ri+
  gi|313127642|ref|YP_004037912.1| 44 SRSTFSRRIGDLEKIGLLElTdEtKRyYRIT 74
                                      8******************743334455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 720.47
//
Query:       gi|313127643|ref|YP_004037913.1|  [L=88]
Description: hypothetical protein Hbor_29290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0061   16.5   0.2      0.022   14.8   0.0    1.9  2  ADK_lid    Adenylate kinase, active site lid
  ------ inclusion threshold ------
       0.25   10.4   0.0       0.31   10.1   0.0    1.1  1  RE_HaeIII  HaeIII restriction endonuclease


Domain annotation for each model (and alignments):
>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3      0.21   1.9e+03       1       6 [.      18      23 ..      18      27 .. 0.83
   2 !   14.8   0.0   2.4e-06     0.022       4      32 ..      37      65 ..      35      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.21
                                      EEE-TT CS
                           ADK_lid  1 RrvCpk 6 
                                      R vCp 
  gi|313127643|ref|YP_004037913.1| 18 RYVCPR 23
                                      99**95 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.4e-06
                                      -TTT--EEETTTB--SSTTB-TTT--.-B CS
                           ADK_lid  4 CpkCGrsYhvvfnpPkveglCDkCGepLv 32
                                      C +C r+Yh    p  +e  +  +GepL 
  gi|313127643|ref|YP_004037913.1| 37 CAACARTYHDDIDPEFQELRDRRDGEPLS 65
                                      *********55455569*********995 PP

>> RE_HaeIII  HaeIII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   3.4e-05      0.31     128     156 ..      34      62 ..      30      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.4e-05
                         RE_HaeIII 128 eWfgipcseeywnevepifdelkeekekk 156
                                       +++  +c+++y+++++p f+el+ +++ +
  gi|313127643|ref|YP_004037913.1|  34 HFWCAACARTYHDDIDPEFQELRDRRDGE 62 
                                       566789*****************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 637.36
//
Query:       gi|313127644|ref|YP_004037914.1|  [L=36]
Description: hypothetical protein Hbor_29300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       126  (0.00702772); expected 358.6 (0.02)
Passed bias filter:                      109  (0.00607954); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.27s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 280.12
//
Query:       gi|313127645|ref|YP_004037915.1|  [L=202]
Description: dnaj-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00043   20.4   0.0    0.00084   19.4   0.0    1.5  1  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.7e-08   0.00084       2      52 ..     154     200 ..     153     202 .] 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.7e-08
                                       HHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHH CS
                              DnaJ   2 yYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyev 52 
                                       ++eiLgv++da e+ +k+a r+  ++ HPD+         +Fk++ +A e 
  gi|313127645|ref|YP_004037915.1| 154 PHEILGVASDAPESVVKAAARTRKKETHPDNG----GDVSEFKRVVNAEEE 200
                                       689***************************99....556789988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1452.19
//
Query:       gi|313127646|ref|YP_004037916.1|  [L=342]
Description: site-specific recombinase xerd [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-07   31.5   0.0    2.9e-07   30.4   0.0    1.6  1  Phage_integrase  Phage integrase family
     0.0038   17.5   0.0     0.0084   16.4   0.0    1.7  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
     0.0098   16.2   0.0      0.026   14.8   0.0    1.7  1  Phage_int_SAM_5  Phage integrase SAM-like domain
  ------ inclusion threshold ------
      0.075   12.9   0.5       0.28   11.0   0.1    2.2  3  NT5C             5' nucleotidase, deoxy (Pyrimidine), cytosol


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   6.5e-11   2.9e-07       3     121 ..     120     251 ..     118     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.5e-11
                                       HHHHHHHHHHHCCGC...HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEE.EEE....EEECSSSSE..EE CS
                   Phage_integrase   3 ltedeverllaalee...slkirdklllellyetGlRisEllsLrvkdldlengvi.lvh....eregKgske..ra 69 
                                       l+++++e l+ + ++      +r  ++lel++ tG+R + l+++++ d + +++ + +vh    ++ +K++++  r 
  gi|313127646|ref|YP_004037916.1| 120 LRPEDAEDLIRYYRThdnVYGTRFHAALELAFHTGARLGALRGIDLRDYHSDEQFVeFVHrpetNTPLKNQRSgeRS 196
                                       889999999999999766677788888*********************766666553899999977778777777** PP

                                       EECTHHHHHHHHHHHHHH...CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHH CS
                   Phage_integrase  70 vplseealellkellska...leeaeksellfaskrgkplsrqtvrkafkravee 121
                                       v l +e++ ++ e ++++      + +++ lf+  +++++s++++r+++ ra + 
  gi|313127646|ref|YP_004037916.1| 197 VSLLSEVCDAIDEFIAHNrpsGHDEFGRSPLFLTYHENRVSKNAFRAWIYRATQP 251
                                       ******************998777888999*******************999765 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.9e-06    0.0084      10      45 ..      20      55 ..      13      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
                                      HTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT-- CS
                   Phage_int_SAM_1 10 kerglspnTlraYrrdLrrflkflaergkesleqlt 45
                                        ++ls+ ++r+Yr++L+ ++++ +++++e +e lt
  gi|313127646|ref|YP_004037916.1| 20 RSTELSESSVRTYRYRLKLWVEWCEDENIERVEDLT 55
                                      45799*********************8888888776 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.9e-06     0.026       6      82 ..      13      89 ..      10     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.9e-06
                                      HHHHTHHHHTTS-HHHHHHHHHHHHHTTTS-..S-.--TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5  6 fkeyiekkkkkgskgtlrnykstlkhlkkFlkkkd.itfeeidkefleeFedYLkkkkglsentiskyfkklkavlnk 82
                                      ++ y+++++ + s++++r+y+  lk   +++++++  ++e+++    e+Fe++  +++g++  t +  +++lk  + +
  gi|313127646|ref|YP_004037916.1| 13 VRRYLDRRSTELSESSVRTYRYRLKLWVEWCEDENiERVEDLTGWTFEQFEAFR-SGQGIASPTLHGEMETLKGHIEY 89
                                      578899999999*******************7767468****************.9*****************88775 PP

>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.2e-05      0.28      13      81 ..      29      95 ..      21     107 .. 0.83
   2 ?   -2.7   0.0         1   4.6e+03      42      58 ..     117     133 ..     101     140 .. 0.74
   3 ?   -2.1   0.0      0.68     3e+03      10      35 ..     302     327 ..     301     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.2e-05
                              NT5C 13 adlygkmlevankrfeat..llpeevsswdleefvkPeqreslyrfltepglFadlepipgarevLeelad 81
                                        +y+  l+++ ++ e++  ++ e++++w +e+f   e   +  + +  p l  ++e+++g  e+Le++ +
  gi|313127646|ref|YP_004037916.1| 29 VRTYRYRLKLWVEWCEDEniERVEDLTGWTFEQF---EA-FRSGQGIASPTLHGEMETLKGHIEYLERIEA 95
                                      56788888999999999888999***********...33.333466899*******************975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1
                              NT5C  42 eefvkPeqreslyrflt 58 
                                       +++ +Pe  e l r++ 
  gi|313127646|ref|YP_004037916.1| 117 DTMLRPEDAEDLIRYYR 133
                                       56788999999999975 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.68
                              NT5C  10 gvladlygkmlevankrfeatllpee 35 
                                       +v a+ +++  ev++k+++++ ++e 
  gi|313127646|ref|YP_004037916.1| 302 EVTAERVNASQEVIEKHYDKASQRER 327
                                       68888899999999999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2531.06
//
Query:       gi|313127647|ref|YP_004037917.1|  [L=294]
Description: hypothetical protein Hbor_29330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0026   17.6  36.8      0.013   15.3  16.7    3.1  3  DUF4013        Protein of unknown function (DUF4013)
  ------ inclusion threshold ------
      0.038   14.1   0.3      0.038   14.1   0.3    4.2  5  Col_cuticle_N  Nematode cuticle collagen N-terminal domain
       0.23   11.4   0.1       0.48   10.3   0.1    1.5  1  TMEM154        TMEM154 protein family


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   9.6   5.8e-05      0.35      92     167 ..      30     117 ..       2     119 .. 0.70
   2 !   15.3  16.7   2.2e-06     0.013      54     165 ..     106     213 ..     103     219 .. 0.74
   3 !    3.7   0.8    0.0084        50      70     111 ..     235     272 ..     221     284 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.8e-05
                           DUF4013  92 l..............glllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllv 154
                                       +              ++++  +++++++l ++ +++ ++  +a++  l    nf++ +++ k+ ++ ++ a++lll 
  gi|313127647|ref|YP_004037917.1|  30 FqlplqfvplaapstTIIASAVSLVATVL-VLPFIFGGIFGMADEA-LDGTTNFGTFVEMGKRHYTSMLGAYLLLLG 104
                                       12233333333334355555555555555.8899999999999998.**************9999999999999999 PP

                           DUF4013 155 igivlsllaillv 167
                                        +iv++ +a+++v
  gi|313127647|ref|YP_004037917.1| 105 GSIVFGTIAWVVV 117
                                       9999999998875 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.2e-06
                           DUF4013  54 slvYlliplii.alltllvalaslaagdsaagallvlallglllalllvllllllfglllpvalarfartgslsaaf 129
                                       s+v++ i +++ +l+tl++++  +++ ++++  ll+++++g +l+lll+l+ ++++ ++    ++ f ++g +s++f
  gi|313127647|ref|YP_004037917.1| 106 SIVFGTIAWVVvGLGTLVAIIPVFDSPQALFPVLLLIMVVGSVLFLLLFLIPFIFIQFY--GQAIVFDDEGAFSSFF 180
                                       79999888888566666666666677677777777777777777777666666644444..3566666777****** PP

                           DUF4013 130 nfkeilklikkkigkyiialilllvigivlsllail 165
                                       +   i++   ++++ ++ + ++++ i++v++++++l
  gi|313127647|ref|YP_004037917.1| 181 RSVSIVR---QNFWPVVGYSVVVFGISLVFGFFGSL 213
                                       *******...88999999999999999999998876 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0084
                           DUF4013  70 lvalaslaagdsaagallvlallglllalllvllllllfgll 111
                                       l+ +  +++ +saa++l++++l+gl + ll   l++  ++++
  gi|313127647|ref|YP_004037917.1| 235 LSGVPQISIVASAALTLFATILMGLSAGLL---LTFS-VAFY 272
                                       455566666777777777777777777777...4444.3333 PP

>> Col_cuticle_N  Nematode cuticle collagen N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.26   1.6e+03       5      20 ..      19      34 ..      19      36 .. 0.84
   2 ?   14.1   0.3   6.3e-06     0.038       3      39 ..      45      81 ..      43      84 .. 0.91
   3 ?   -1.7   2.4      0.52   3.1e+03       8      22 ..     146     160 ..     141     163 .. 0.81
   4 ?   -3.3   0.4       1.7     1e+04       2      13 ..     197     208 ..     195     214 .. 0.56
   5 ?   -3.5   3.2         2   1.2e+04       2      14 ..     245     257 ..     241     267 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.26
                     Col_cuticle_N  5 alStvailsslitlps 20
                                      +++++++l +l+ lp+
  gi|313127647|ref|YP_004037917.1| 19 VIAGITVLLALFQLPL 34
                                      57899******98887 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.3e-06
                     Col_cuticle_N  3 avalStvailsslitlpsiyndiqsfqsevldemdef 39
                                       +++S+v++++++++lp+i+  i  + +e ld+  +f
  gi|313127647|ref|YP_004037917.1| 45 TIIASAVSLVATVLVLPFIFGGIFGMADEALDGTTNF 81
                                      5899**********************99999988766 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.52
                     Col_cuticle_N   8 tvailsslitlpsiy 22 
                                       + +++ +l+ +p+i+
  gi|313127647|ref|YP_004037917.1| 146 GSVLFLLLFLIPFIF 160
                                       567899999999998 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.7
                     Col_cuticle_N   2 vavalStvails 13 
                                       ++v++ +  +++
  gi|313127647|ref|YP_004037917.1| 197 SVVVFGISLVFG 208
                                       555555555555 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 2
                     Col_cuticle_N   2 vavalStvailss 14 
                                       +++al ++a++ +
  gi|313127647|ref|YP_004037917.1| 245 ASAALTLFATILM 257
                                       2334444444433 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   8.1e-05      0.48      58      86 ..     139     167 ..     130     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.1e-05
                           TMEM154  58 lvlmiiiPlvllillllvviiliqkkkrk 86 
                                       l+l++++ +vl++ll+l+  i+iq + + 
  gi|313127647|ref|YP_004037917.1| 139 LLLIMVVGSVLFLLLFLIPFIFIQFYGQA 167
                                       47999******************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1851.93
//
Query:       gi|313127648|ref|YP_004037918.1|  [L=228]
Description: ferredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-12   45.2   0.0    1.3e-11   44.3   0.0    1.5  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
    1.7e-09   37.7   0.0    3.4e-09   36.7   0.0    1.5  1  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   1.4e-15   1.3e-11      10      74 ..     129     191 ..     123     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.4e-15
                                       EEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTTSSSSTHHHHHTTEEEEGGG CS
                              Fer2  10 vevadgettlldaaeenggidipysCggggCgtClvevlegev.qsdetelegeeldegklrlaCq 74 
                                       + v+++et ll+aae+  g++ py+C+gg+C+ C+v v ege   ++   l   +ld+ + rl+C+
  gi|313127648|ref|YP_004037918.1| 129 FLVQENET-LLEAAENR-GYAWPYACRGGACANCAVAVFEGEMdTPGDHILPSTMLDS-DIRLSCM 191
                                       55889999.*****976.************************9755567777777655.579***7 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   3.8e-13   3.4e-09       2      54 ..       4      52 ..       3      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 3.8e-13
                                      HHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHT CS
                              DnaJ  2 yYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLs 54
                                      ++eiLg+++da+++e+ +a+r+ ++++HPD+      ++ +F+++  Aye+ +
  gi|313127648|ref|YP_004037918.1|  4 PFEILGIEPDADDAEVDRAFRRRVIEVHPDQG----GSAAEFNRVRSAYEMIK 52
                                      689****************************9....77789*********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1467.83
//
Query:       gi|313127649|ref|YP_004037919.1|  [L=292]
Description: adaptin n terminal region protein, partial [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.4e-07   29.2   0.0    1.5e-06   28.4   0.0    1.4  1  Cnd1       non-SMC mitotic condensation complex subunit 1
    3.8e-05   24.0   7.0    0.00036   20.9   0.7    3.6  4  HEAT_2     HEAT repeats
    4.1e-05   22.3   0.0    7.8e-05   21.4   0.0    1.4  1  Adaptin_N  Adaptin N terminal region
  ------ inclusion threshold ------
       0.15   12.0   0.1        0.4   10.6   0.1    1.8  1  DUF1869    Domain of unknown function (DUF1869)


Domain annotation for each model (and alignments):
>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   3.3e-10   1.5e-06      14     128 ..     172     288 ..     158     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.3e-10
                              Cnd1  14 rvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisekse 90 
                                        +p+ v ++  ++ ++++D ++ VR   +++  kL+ ++  +    +s+l + l+D++++V + a+aal    ++ +
  gi|313127649|ref|YP_004037919.1| 172 AFPEAVTQTDRQIMTAMRDANSSVRLAGVMTAGKLLGAEPNQFPRTVSTLPETLDDDDEEVWEYAHAALIHFVREHP 248
                                       68899999999***************************************************************986 PP

                              Cnd1  91 naiynllpdiisklsdalne...csewgqitilefLlsyip 128
                                       +++   ++++i +l +  +e   + e + +  +++Llsy p
  gi|313127649|ref|YP_004037919.1| 249 SQVP-EKRHVIERLATVSDEelgVREGATKDAMTTLLSYEP 288
                                       6655.447777777764444566999999999999999987 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.02        91      33      56 ..      70      93 ..      55     104 .. 0.59
   2 !    8.7   0.6   0.00049       2.2      16      63 ..     124     176 ..     109     183 .. 0.75
   3 !   20.9   0.7   7.9e-08   0.00036       1      87 [.     144     240 ..     144     241 .. 0.80
   4 ?   -0.3   0.0      0.31   1.4e+03       4      31 ..     240     268 ..     237     285 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.02
                            HEAT_2 33 lpaLvellededpavRraaaeaLg 56
                                      +  L+ +++d d++ R aa eaL 
  gi|313127649|ref|YP_004037919.1| 70 IGDLLAIVRDCDEDARVAAEEALD 93
                                      444444444444444544444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00049
                            HEAT_2  16 vrraairaLgrignp...ealpaLvellededpavRraaaeaLgaigd..pea 63 
                                       v  +a+ +L   ++      l+a ++ l+ ++  +Rraa+   g++g+  pea
  gi|313127649|ref|YP_004037919.1| 124 VGLRALAQLSAVRPAvakNGLDAAISRLQAQHVPTRRAAIAVVGEVGEafPEA 176
                                       556666666666655333569*************************9866665 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 7.9e-08
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignp......ealpaLvellededpavRraaaeaLgai.gd.....pealp 65 
                                       lda +++l +  +  +rraai + g+ g+       ++ + +  +++d+++ vR a ++++g++ g      p++++
  gi|313127649|ref|YP_004037919.1| 144 LDAAISRL-QAQHVPTRRAAIAVVGEVGEAfpeavtQTDRQIMTAMRDANSSVRLAGVMTAGKLlGAepnqfPRTVS 219
                                       57889999.89999***********999866665556678899999****************987433456799*** PP

                            HEAT_2  66 aLkellddddddvvReaAaeaL 87 
                                        L e ldddd++ v e A  aL
  gi|313127649|ref|YP_004037919.1| 220 TLPETLDDDDEE-VWEYAHAAL 240
                                       ****99776655.556666665 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.31
                            HEAT_2   4 Llqalendpdpe.vrraairaLgrignpe 31 
                                       L+ +++++p++   +r++i+ L++  ++e
  gi|313127649|ref|YP_004037919.1| 240 LIHFVREHPSQVpEKRHVIERLATVSDEE 268
                                       66666666665424666666666555543 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.8e-08   7.8e-05      46     183 ..     109     248 ..     102     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-08
                                       HHHCCCCSS-CHHHHHHHHHHHHHCTTSCCHHCCCCHHHHHHCCSSSHHHHHHHHHHHCCC-..-CCCHHHHHHHHH CS
                         Adaptin_N  46 evvklvaskdfelKrlvYlylellaeesedlalLvtnslqkDlkdpnqlirglALrvLssir..vpelaedlapaik 120
                                       ++v + + ++ el +++  +l +l+  ++ +a+   ++    l+ +    r  A+ v++ ++   pe + +  ++i+
  gi|313127649|ref|YP_004037919.1| 109 DIVQFASADRDELSFVGLRALAQLSAVRPAVAKNGLDAAISRLQAQHVPTRRAAIAVVGEVGeaFPEAVTQTDRQIM 185
                                       577777788888888888888888888888888888888888999999999**********96669*********** PP

                                       HHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHH.HCCC CS
                         Adaptin_N 121 kllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleei.kknd 183
                                       ++++d +++vr + ++++ kl+ ++p++++++ v+ + e l+d+d  v   A a+l +  + ++
  gi|313127649|ref|YP_004037919.1| 186 TAMRDANSSVRLAGVMTAGKLLGAEPNQFPRT-VSTLPETLDDDDEEVWEYAHAALIHFvREHP 248
                                       *******************************9.***************9999888877743333 PP

>> DUF1869  Domain of unknown function (DUF1869)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   8.9e-05       0.4      22      54 ..      56      84 ..      51     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.9e-05
                                      E--SCGGC-HHHHHHHHHHHHHHHHHTTSSSSS CS
                           DUF1869 22 feslaeLkdpevaaevvKdLiNivRgYdsdeet 54
                                      +e  ++L +p  a +++ dL+ ivR  d d  +
  gi|313127649|ref|YP_004037919.1| 56 VE--TALTNPVAAGDAIGDLLAIVRDCDED--A 84
                                      44..6799*****************66554..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1981.30
//
Query:       gi|313127650|ref|YP_004037920.1|  [L=222]
Description: hypothetical protein Hbor_29360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00025   21.2   0.0     0.0052   16.9   0.0    2.1  2  Cas_Cas4  Domain of unknown function DUF83


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.01   1.8e+02       8      21 ..      14      27 ..       8      42 .. 0.79
   2 !   16.9   0.0   2.9e-07    0.0052      95     160 ..     146     209 ..     130     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.01
                          Cas_Cas4  8 yliCkrklwlishe 21
                                       ++C+r+l++ +++
  gi|313127650|ref|YP_004037920.1| 14 AAYCPRQLYYAEQR 27
                                      689******98764 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.9e-07
                          Cas_Cas4  95 kkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCayaelC 160
                                       ++  ei ++ +eyp     ++v+lt +++ + ++++  ++++     p +v ++++C +C+y+  C
  gi|313127650|ref|YP_004037920.1| 146 EREREIPRALVEYPAHGVVRTVRLTTRNTGAYRRTLWTVRQMEG--VPSRVRDSSKCAACEYQTSC 209
                                       678899999******************************99744..5999**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1722.16
//
Query:       gi|313127651|ref|YP_004037921.1|  [L=208]
Description: translation factor sua5 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-49  165.9   0.0    7.5e-49  165.7   0.0    1.0  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.7   0.0   4.2e-53   7.5e-49       2     179 .]      14     186 ..      13     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 4.2e-53
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSC CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpi 78 
                                       a+++G+ v++ptetvYgL++d t+++aver++e+Kgr++dkpl++ v++++ ++++++  ++      +++f+PGp+
  gi|313127651|ref|YP_004037921.1|  14 AVKAGAAVVYPTETVYGLGADGTDADAVERVFELKGRSRDKPLSIGVPDVDAAREYTR--LTSFDADFMAEFLPGPV 88 
                                       6799*****************************************************9..6666667788******* PP

                                       EEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS- CS
                    Sua5_yciO_yrdC  79 tlllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildgg 155
                                       t++++r ++ lp+++++g ++vGvr+Pd+++a++++++++ p++aTSan+sg ps+t++++++  l+++v +++d+g
  gi|313127651|ref|YP_004037921.1|  89 TVVVERGSQ-LPDVLTAGGDRVGVRVPDHEVALDFFRRADCPVTATSANRSGAPSVTHPDQLDATLKDSVGAVIDAG 164
                                       *****9666.******************************************************************* PP

                                       --SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 156 eiavgvdstVvdltegkpkilRrG 179
                                       e   g+ stVvd +     i RrG
  gi|313127651|ref|YP_004037921.1| 165 EAPGGTGSTVVDPSR--NVIHRRG 186
                                       ************985..5677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1520.36
//
Query:       gi|313127652|ref|YP_004037922.1|  [L=169]
Description: peroxiredoxin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-18   65.4   0.0    5.5e-18   65.1   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    1.7e-06   27.8   0.0    5.4e-06   26.2   0.0    1.7  1  Redoxin     Redoxin
  ------ inclusion threshold ------
      0.036   14.2   0.0       0.51   10.5   0.0    2.0  2  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   9.1e-22   5.5e-18       2     123 ..      18     145 ..      17     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 9.1e-22
                                       TSB----EEE...STTCEEEECHHH..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHH CS
                          AhpC-TSA   2 gdkapdfelk...nadgetvslsdy..kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspesh 73 
                                       gd apdf+ +   ++  e+v ls++  +g pv+l+f+p+d ++++t  + a +++   ++   ++ +gvs+ sp++h
  gi|313127652|ref|YP_004037922.1|  18 GDVAPDFTRPlvnDEYWEDVALSELtdEG-PVLLLFHPMDGSFPATYLWDAVRDHD--LT-DQIQTVGVSISSPYEH 90 
                                       99********9988889********7555.*********************99965..55.4699************ PP

                                       HHHHHH-H.SSEEEE-TTSHHHHHTT-EETT.....TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  74 kkfiekeslnfpllsDeegkvakaygvlkee.....kglalratfvidkegkiry 123
                                       k+f e+ +   +l+sD+  +va++y++ ++       +   +a+f++d++ +++y
  gi|313127652|ref|YP_004037922.1|  91 KAFLEEREADARLFSDPGAAVATEYDIENPLdgmagITEHRPAVFLVDENRTVQY 145
                                       ****************************9999*9998999**************9 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   9.1e-10   5.4e-06       2     145 ..      17     160 ..      16     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9.1e-10
                                       TTSBB---ECCEET.TCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHH CS
                           Redoxin   2 agdkaPdftlplaa.tdgnsvslse.fkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndaf 75 
                                       +gd aPdft pl++ +  ++v lse   +++v++ f p  +     + +  ++++      +  ++ v+v++++   
  gi|313127652|ref|YP_004037922.1|  17 PGDVAPDFTRPLVNdEYWEDVALSElTDEGPVLLLFHPM-DGSFPATYLWdAVRDH---DLTDQIQTVGVSISSPYE 89 
                                       689999999655541567999999977788888888888.4444444443244444...346889********9999 PP

                                       HHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG..EEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                           Redoxin  76 vkefwgkeglkfpvlsDgsaaftkalGlrleedaseg..lrtpryavidedgkvvylevepepeteesnaea 145
                                        k+f+++ + + +++sD++aa++ +++++   d  +g     p+++++de+  v y  v  e  +++++a++
  gi|313127652|ref|YP_004037922.1|  90 HKAFLEEREADARLFSDPGAAVATEYDIENPLDGMAGitEHRPAVFLVDENRTVQYAWVASEW-PDFPDADD 160
                                       *******999*****************886666666699999**************9988876.45777775 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.5e-05      0.51      12      47 ..      75     111 ..      64     123 .. 0.87
   2 ?    1.9   0.0     0.039   2.3e+02      92     110 ..     130     148 ..     115     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.5e-05
                        AhpC-TSA_2  12 agvklvaigigdp.sakkFvkltgfpfelyvDpsakl 47 
                                         ++ v+++i +p + k+F ++ + ++ l+ Dp a++
  gi|313127652|ref|YP_004037922.1|  75 DQIQTVGVSISSPyEHKAFLEEREADARLFSDPGAAV 111
                                       46899********99******************8876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.039
                        AhpC-TSA_2  92 qrGGtflfdkqgelvyehr 110
                                        r ++fl+d+   ++y++ 
  gi|313127652|ref|YP_004037922.1| 130 HRPAVFLVDENRTVQYAWV 148
                                       6889*****999****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1252.14
//
Query:       gi|313127653|ref|YP_004037923.1|  [L=93]
Description: glutaredoxin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-15   55.9   0.0    5.1e-15   55.7   0.0    1.1  1  GST_N_3        Glutathione S-transferase, N-terminal domain
    4.2e-13   49.3   0.2    5.6e-13   48.9   0.2    1.2  1  Glutaredoxin   Glutaredoxin
    1.4e-12   47.7   0.0    1.7e-12   47.5   0.0    1.1  1  GST_N_2        Glutathione S-transferase, N-terminal domain
    0.00013   22.3   0.0    0.00016   22.0   0.0    1.1  1  GST_N          Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.12   12.7   0.0    1.2  1  Tom37          Outer mitochondrial membrane transport complex
       0.17   12.3   0.0       0.19   12.2   0.0    1.2  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   1.7e-18   5.1e-15       2      73 ..      11      85 ..      10      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.7e-18
                                      ES-TTSHHHHHHHHHHHHHT--EEEE---TTTT.HHHHHHH-TT--SSEEETT..S-EEESHHHHHHHHHHHH-G CS
                           GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevtpgeh.deellaknplgkvPvLedd..gealtdSlaIidyLeelypg 73
                                      y   a+py+ rv  +L+e+++p++ + v+p ++ ++ +++++++++vP+++dd  g  + +S+ I++yL ++y++
  gi|313127653|ref|YP_004037923.1| 11 YRLQACPYCERVIRVLQELDVPYQSRFVEPMHSdRNVVKRISGKRTVPAIVDDetGVTMSESANIVKYLQRTYGD 85
                                      77899************************999956677*************997777**************9985 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.2   1.9e-16   5.6e-13       1      54 [.       8      61 ..       8      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.9e-16
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvf 54
                                      ++++  + CpyC +++r+L+el v+++ + v+ +++ r  +k++sg rtvP ++
  gi|313127653|ref|YP_004037923.1|  8 ITVYRLQACPYCERVIRVLQELDVPYQSRFVEPMHSDRNVVKRISGKRTVPAIV 61
                                      799*************************************************98 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   5.6e-16   1.7e-12       1      69 [.      15      81 ..      15      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 5.6e-16
                                      S-HHHHHHHHHHHHCT--EEEEEEH...-TTSHHHHHHHHCTTTSSSEEE-C.TTEEEESHHHHHHHHHH CS
                           GST_N_2  1 aCPwahRvlialalkglediisvvvlepkgfekseefprlnprgtVPvLwdk.dgqvineSseIlrylet 69
                                      aCP++ Rv  +l+++ ++++  +v +++ + +    ++r++++ tVP+++d+ +g    eS+ I+ yl++
  gi|313127653|ref|YP_004037923.1| 15 ACPYCERVIRVLQELDVPYQSRFVEPMHSDRN---VVKRISGKRTVPAIVDDeTGVTMSESANIVKYLQR 81
                                      7***********************55555544...69**************94555666*********86 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   5.2e-08   0.00016       3      76 .]       8      81 ..       6      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.2e-08
                                      EEEESSSTSHTHHHHHHHHHHTT-EEEEEEECSTTTCGGC.HHHHHHCTTS-SSEEEET..TEEEESHHHHHHHHHH CS
                             GST_N  3 ltlysirgsprahrirlllaakgveyevvpldfeageeks.pellklnplgkvPaLedn..gkkltESraIleYiar 76
                                      +t+y    +p+ +r+  +l++++v+y+  ++++    + +    +++  +  vPa +d+  g +  ES  I++Y+ r
  gi|313127653|ref|YP_004037923.1|  8 ITVYRLQACPYCERVIRVLQELDVPYQSRFVEP---MHSDrNVVKRISGKRTVPAIVDDetGVTMSESANIVKYLQR 81
                                      79999999************************8...4444356666666699**********************975 PP

>> Tom37  Outer mitochondrial membrane transport complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.9e-05      0.12      25      57 ..      50      83 ..      19      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.9e-05
                             Tom37 25 slsptgeLPaLkdge.gtwisgfdnIveylrkks 57
                                       +s ++ +Pa+ d+e g ++s+  nIv+yl++++
  gi|313127653|ref|YP_004037923.1| 50 RISGKRTVPAIVDDEtGVTMSESANIVKYLQRTY 83
                                      4577889******9966666**********9885 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.5e-05      0.19       7      59 ..       6      57 ..       2      84 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.5e-05
                     Thioredoxin_2  7 pvlvvftdpdCpyCkklkkelkel.ddvtvrvllfp.lkpsfepkavaiwcakek 59
                                      p ++v+    CpyC++  ++l+el   +++r  ++  ++++   ++ +i++++ +
  gi|313127653|ref|YP_004037923.1|  6 PAITVYRLQACPYCERVIRVLQELdVPYQSR--FVEpMHSD-RNVVKRISGKRTV 57
                                      788899999***********99993223333..33346666.5555556555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 690.80
//
Query:       gi|313127654|ref|YP_004037924.1|  [L=453]
Description: cbs domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-49  167.5   0.8    3.2e-49  167.0   0.8    1.2  1  DUF21      Cyclin M transmembrane N-terminal domain
    5.5e-19   68.0   2.0    5.5e-19   68.0   2.0    1.9  2  CorC_HlyC  Transporter associated domain
    1.7e-12   47.6   3.1    4.6e-07   30.2   0.1    2.7  2  CBS        CBS domain
  ------ inclusion threshold ------
      0.057   13.4   0.2        6.4    6.8   0.1    2.7  2  Rrp44_S1   S1 domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   0.8   7.1e-53   3.2e-49       2     176 .]      29     209 ..      28     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 7.1e-53
                             DUF21   2 iivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvel 78 
                                       +i++l++lsaffs++E+A++sl ++r+++l+e+g ++a+++++l ++p+rlL+t+l+gn++vni++s+l t l+v +
  gi|313127654|ref|YP_004037924.1|  29 AIIILIGLSAFFSSSEIAMFSLAKHRVDSLVEEGVPGAETVQSLKNDPHRLLITILVGNNIVNIAMSSLSTGLLVYI 105
                                       789**********************************************************************9999 PP

                             DUF21  79 laegalavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil......ese 149
                                          ++ av+iat+ +t l+l+fgE +Pks+a+++ e+++l++a+pl++  ++l Plv+++++l++++       ++ 
  gi|313127654|ref|YP_004037924.1| 106 GFGQGEAVAIATFGITALVLLFGESAPKSYAVENTESWSLRIARPLKISEYVLLPLVVIFDRLTRIVNritggrSAI 182
                                       988999*****************************************************999999988999**9999 PP

                             DUF21 150 sepavseeelkklveeseeegvieeee 176
                                       ++++v+++e++ l++ +e+egviee+e
  gi|313127654|ref|YP_004037924.1| 183 ETSYVTRDEIQDLIQTGEREGVIEEDE 209
                                       *************************98 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2         3   1.3e+04      12      48 ..     332     349 ..     326     354 .. 0.50
   2 !   68.0   2.0   1.2e-22   5.5e-19       4      80 ..     360     435 ..     357     436 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3
                                       TT-BHHHHHHHHTSTTHHCT-SBHHHHHHHHH-S--- CS
                         CorC_HlyC  12 GslpldeleeelglelpeedyeTlgGlllellgriPk 48 
                                       G ++l+++ e                   e  g+i +
  gi|313127654|ref|YP_004037924.1| 332 GLITLEDMVE-------------------EIVGDILE 349
                                       4444444444...................44444443 PP

  == domain 2  score: 68.0 bits;  conditional E-value: 1.2e-22
                                       CTTEEEEETT-BHHHHHHHHTSTTHH.CT-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEEEEEE CS
                         CorC_HlyC   4 degsylvdGslpldeleeelglelpe.edyeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkkvrvek 79 
                                       +e++ lv G++++de++e l+l+lpe e++eTl+G+++++ gr+ +ege++e+d  ++ + ++++d+ rI k r+++
  gi|313127654|ref|YP_004037924.1| 360 NERETLVRGEVNIDEVNEVLELDLPEgEEFETLAGFIFNRAGRLVEEGEEIEYD--SVMIRIEQVDNTRIMKARITV 434
                                       68999*********************889********************55555..*******************97 PP

                                       - CS
                         CorC_HlyC  80 l 80 
                                       +
  gi|313127654|ref|YP_004037924.1| 435 D 435
                                       5 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1     1e-10   4.6e-07       1      55 [.     224     281 ..     224     283 .. 0.85
   2 !   17.1   0.5   1.3e-06    0.0057      10      56 ..     298     344 ..     289     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1e-10
                                       HHHHSBS..SCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTT.BEEEEEEHHHHHHHH CS
                               CBS   1 Vgdimtr..dvvtvppdttleealel.mrekgvsrlPVVdedg.klvGivtlrDllral 55 
                                       ++++mt+  d+  vp d+tl ea+e+ + ++++ r+PV d++  +++Giv  rDl+r  
  gi|313127654|ref|YP_004037924.1| 224 AKEVMTPrlDMTAVPKDATLDEAIETcI-QSDHERVPVYDGNLdNVIGIVNIRDLVREQ 281
                                       579999977779**************88.88899*****433367**********9975 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.3e-06
                                       EEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHHH CS
                               CBS  10 vtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllrall 56 
                                       + vp++ ++ e+l ++ ++++ ++ +V de g   G++tl+D ++ ++
  gi|313127654|ref|YP_004037924.1| 298 LHVPESKNVDELLTEIQDNRL-QMVIViDEFGTTEGLITLEDMVEEIV 344
                                       5899************88776.442236***************99886 PP

>> Rrp44_S1  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.016        70      11      69 ..     107     167 ..     101     176 .. 0.67
   2 ?    6.8   0.1    0.0014       6.4      15      38 ..     320     344 ..     313     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.016
                                       ESSEEEEEETTTTEEEEEEHHHCBS-GGG..-EEETTTTEEEEBBTTSSS-....EEEETTSE CS
                          Rrp44_S1  11 fsNGvvvlvprfGiEglirledlaeeeeskeaefdeeeykleveekkkekk....vtvelFdk 69 
                                       f  G +v ++ fGi +l+ l   +++++   a  + e+++l++ +  k ++      v +Fd+
  gi|313127654|ref|YP_004037924.1| 107 FGQGEAVAIATFGITALVLLFGESAPKSY--AVENTESWSLRIARPLKISEyvllPLVVIFDR 167
                                       667889************99855444333..44566777777776655444444444555555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0014
                                       EEEEETTTT.EEEEEEHHHCBS-GG CS
                          Rrp44_S1  15 vvvlvprfG.iEglirledlaeeee 38 
                                       +v+++  fG  Egli+led++ee  
  gi|313127654|ref|YP_004037924.1| 320 MVIVIDEFGtTEGLITLEDMVEEIV 344
                                       68999****55*********97754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2834.93
//
Query:       gi|313127655|ref|YP_004037925.1|  [L=400]
Description: phosphate/sulfate permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-48  165.8  27.1    1.3e-48  165.8  27.1    1.4  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.8  27.1     7e-53   1.3e-48       7     337 .]      31     387 ..      24     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 7e-53
                              PHO4   7 anafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwlllatvl 83 
                                       +  fa++vg++a+++++A ++++++ ++Ga+l+G++V+++++++++    + p   ++++++all aa +++l ++ 
  gi|313127655|ref|YP_004037925.1|  31 STPFAPAVGANAISVMRAGFIVGLLGLSGAFLQGENVTQAVGTELI----VGPVLTATAATVALLVAAGLVALGVFA 103
                                       678*****************************************99....57888889******************* PP

                              PHO4  84 glPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvl 160
                                       g+P+ t+++++Ga++G++la+  g    w+k  +i+  wvl+P++gg +a+ ++ l+++  +      +++ a+p+l
  gi|313127655|ref|YP_004037925.1| 104 GYPIATAFTVTGAVVGVGLAN--GGLPAWGKYQQILSLWVLTPFVGGGAAYGTARLLRHESV------SERVAVPIL 172
                                       ********************5..45779********************************55......355556666 PP

                              PHO4 161 ...vlvtiailalsilfkge.......................................sk..kddeeteklfkflq 193
                                          v +++a + +++l +g                                        ++    +++  +  + ++
  gi|313127655|ref|YP_004037925.1| 173 ggvVGAIVANIDFAVLATGDanagsisrfvadslppvelfgvslgaalvtlavvllsggAVaqAMHRDEARGQRRFL 249
                                       33255555555666666644444444444445555555555555555555555554444223344444445568889 PP

                              PHO4 194 vvsaalvsfahGanDvanaiGpllaalisiykask.evplw.vlllgglaialGlllgGkrviktvGekitkkltps 268
                                       +v ++lv+f+ G+++v  aiGpl+ +l +       +vpl  +l+ ggl++++G ++g++r+ik+++++++ +l p 
  gi|313127655|ref|YP_004037925.1| 250 LVLGGLVAFSAGGSQVGLAIGPLVPLL-D-----AvAVPLPaLLAGGGLGLLVGSWTGAPRMIKALAQDYS-SLGPR 319
                                       9999*******************6655.4.....3367875489999************************.6**** PP

                              PHO4 269 rGfaaelaaaltvllasklglPvStThvlvgavvGvGlakkresavnwklvrnivlaWvlTlpvsalls 337
                                       r++aa + + ++  +a +lg+PvS+++++v+a+vG G a  + ++v+ + ++++vlaW+ +l +++++s
  gi|313127655|ref|YP_004037925.1| 320 RSIAAMIPSFAIAQTAVALGIPVSFNEIIVSAIVGSGYAA-GGAGVSKEKMGKTVLAWIGSLSLAFAVS 387
                                       ***77766666666**************************.57**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2578.25
//
Query:       gi|313127656|ref|YP_004037926.1|  [L=59]
Description: hypothetical protein Hbor_29420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.3   1.8       0.15   12.1   1.8    1.0  1  TMEM119   TMEM119 family
        1.5    8.8   5.4          2    8.4   5.4    1.2  1  DUF4083   Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> TMEM119  TMEM119 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.8   1.6e-05      0.15      60      96 ..       6      43 ..       2      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                           TMEM119 60 ldGivdffrqyvlliav.vGslaflllfivcaalitrq 96
                                      l G++d f ++vl   v vG l++lllf+  a l +r+
  gi|313127656|ref|YP_004037926.1|  6 LQGLLDDFVEFVLSEPVfVGFLVLLLLFVFFAYLFVRR 43
                                      7899*********987769*************999986 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.4   0.00023         2      12      30 ..      27      45 ..      22      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00023
                           DUF4083 12 ivLilllvfsftlfiRrvv 30
                                      +vL+ll+vf  +lf+Rr++
  gi|313127656|ref|YP_004037926.1| 27 LVLLLLFVFFAYLFVRRTL 45
                                      79***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 439.58
//
Query:       gi|313127657|ref|YP_004037927.1|  [L=300]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-15   55.1   0.1    1.1e-14   54.2   0.1    1.5  1  HTH_20          Helix-turn-helix domain
    4.3e-06   26.5   0.0    9.2e-06   25.5   0.0    1.6  1  MarR_2          MarR family
      1e-05   25.3   0.0    1.8e-05   24.5   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    4.7e-05   22.8   0.0    8.2e-05   22.1   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.023   14.6   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.016   15.1   0.0      0.033   14.1   0.0    1.5  1  MarR            MarR family
      0.018   15.1   0.0      0.029   14.3   0.0    1.3  1  HTH_45          Winged helix-turn-helix
      0.019   15.0   3.7      0.053   13.6   1.8    2.8  2  DprA_WH         DprA winged helix domain
      0.022   14.7   0.0      0.059   13.4   0.0    1.7  2  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.03   14.6   0.0      0.059   13.7   0.0    1.6  1  DUF2513         Hypothetical protein (DUF2513)
       0.12   12.0   0.0       0.17   11.5   0.0    1.2  1  ArsR            ArsR transcriptional regulator
          7    5.8   9.6         12    5.0   9.6    1.4  1  Med13_C         Mediator complex subunit 13 C-terminal domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.1   7.7e-18   1.1e-14       2      55 ..      31      83 ..      30      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 7.7e-18
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++++A+++++ r il+aL  +e++t+sela++ d+s +++ yHL +Le+agL+e
  gi|313127657|ref|YP_004037927.1| 31 ELLSAISSETARTILSAL-HEEPATPSELADTADTSIQNAQYHLGKLEDAGLIE 83
                                      6899**************.**********************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   6.2e-09   9.2e-06       6      52 ..      40      83 ..      34      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 6.2e-09
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      + + +L aL+ +p    t++ela++ + s ++++++l +L++aGL+e
  gi|313127657|ref|YP_004037927.1| 40 TARTILSALHEEP---ATPSELADTADTSIQNAQYHLGKLEDAGLIE 83
                                      5678999999999...6*****************************8 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.2e-08   1.8e-05       2      46 ..      39      83 ..      38      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.2e-08
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +t + IL++L e++++ +ela+  + s  +  +HL kL++aGL+e
  gi|313127657|ref|YP_004037927.1| 39 ETARTILSALHEEPATPSELADTADTSIQNAQYHLGKLEDAGLIE 83
                                      68889**************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.5e-08   8.2e-05       3      48 .]      39      83 ..      37      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.5e-08
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      et r IL++L +    + +eLA+  + S+++  ++l +Le++GlI+
  gi|313127657|ref|YP_004037927.1| 39 ETARTILSALHE-EPATPSELADTADTSIQNAQYHLGKLEDAGLIE 83
                                      678889999999.669*****************************7 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.6e-05     0.023      18      54 ..      48      84 ..      36     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      l ++pat +e+a  ++ + ++++  L +Led+Gl+e 
  gi|313127657|ref|YP_004037927.1| 48 LHEEPATPSELADTADTSIQNAQYHLGKLEDAGLIEP 84
                                      6899*******************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.2e-05     0.033       9      48 ..      45      83 ..      37      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                                      HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      L  l+ ++p++ seLa+   +s+ ++   l +Le++Glie
  gi|313127657|ref|YP_004037927.1| 45 LSALH-EEPATPSELADTADTSIQNAQYHLGKLEDAGLIE 83
                                      44444.56789****************************7 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     2e-05     0.029      10      64 ..      43      95 ..      37      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGle 64
                                       IL+a++e+ a+++++   a+ s ++++  L +L + gli+  ++ Y+  ekG+e
  gi|313127657|ref|YP_004037927.1| 43 TILSALHEEPATPSELADTADTSIQNAQYHLGKLEDAGLIEPGGTAYS--EKGRE 95
                                      69****************************************999996..77776 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.8   3.6e-05     0.053       8      56 ..      35      83 ..       6      86 .. 0.91
   2 ?   -2.4   0.0       3.6   5.4e+03       9      21 ..     114     126 ..     110     130 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                           DprA_WH  8 pplddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                      + +++++r++L+aL  eP +  +L+  +  +++  + +L  LE aGl+e
  gi|313127657|ref|YP_004037927.1| 35 AISSETARTILSALHEEPATPSELADTADTSIQNAQYHLGKLEDAGLIE 83
                                      45699*****************************************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                           DprA_WH   9 plddlerrvLaaL 21 
                                       ++++  ++vL++L
  gi|313127657|ref|YP_004037927.1| 114 DDTSGLQTVLTQL 126
                                       4555556666544 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   2.4e+03      26      48 ..      28      51 ..      17      53 .. 0.75
   2 ?   13.4   0.0     4e-05     0.059      21      54 ..      52      85 ..      29      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                                      HHHHHTT.SSHHHHHHHHHHHHHT CS
                         HTH_Crp_2 26 elAsmlG.ltretvsrilseLkre 48
                                      e +++l  ++ et   ils+L +e
  gi|313127657|ref|YP_004037927.1| 28 EVSELLSaISSETARTILSALHEE 51
                                      556666658889999999988775 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg 54
                                      p t  elA+   ++ +     l++L+++gli+ g
  gi|313127657|ref|YP_004037927.1| 52 PATPSELADTADTSIQNAQYHLGKLEDAGLIEPG 85
                                      88999**************************954 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     4e-05     0.059       5      66 ..      39      96 ..      24     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                           DUF2513  5 dlvRdiLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakss...i 66
                                      +  R iL +l e ++++++l d        +++s ++  yhl +l++agLie   + ++++   +
  gi|313127657|ref|YP_004037927.1| 39 ETARTILSALHEEPATPSELAD-------TADTSIQNAQYHLGKLEDAGLIEPGGTAYSEKgreM 96
                                      4556666666666666666655.......467778899**************9988888774442 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.17       6      58 ..      28      83 ..      24      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                              ArsR  6 eLvpllqvfdsetkkkvyeelskeWlteeeleeklgeeveea...lklLkkikliE 58
                                      e+  ll +++set ++++++l +e  t +el+++++++ ++a   l  L+ ++liE
  gi|313127657|ref|YP_004037927.1| 28 EVSELLSAISSETARTILSALHEEPATPSELADTADTSIQNAqyhLGKLEDAGLIE 83
                                      66679******************************998555422277788888888 PP

>> Med13_C  Mediator complex subunit 13 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   9.6    0.0081        12     161     204 ..     207     253 ..     179     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0081
                           Med13_C 161 sss..stplstPqdsscthilv.fptsattqstpttfasedanaedt 204
                                       s +  +++ +tP d+++thi + + tsat+++t+++ ++ ++++++ 
  gi|313127657|ref|YP_004037927.1| 207 SEVttTASSHTPGDATTTHIQTaTETSATGTPTQAPVPEPTTTTDSV 253
                                       33333777889*********872568888899999999888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2027.47
//
Query:       gi|313127658|ref|YP_004037928.1|  [L=173]
Description: phosphoesterase, mj0936 family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-24   87.4   0.2    1.4e-24   87.1   0.2    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    8.4e-05   23.2   0.0       0.24   11.9   0.0    2.1  2  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.2   1.6e-28   1.4e-24       4     154 ..       3     138 ..       1     147 [. 0.91

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.6e-28
                     Metallophos_2   4 aiiSDlH..snldaleavlealkevgvdaiihaGDleeeepevleellela.pvlaVrGNnDeevveedvlreaael 77 
                                        ++SD+H  ++ ++  + lea++e+  ++++h+GD+     +vl+++++   ++  V+GNnD            a++
  gi|313127658|ref|YP_004037928.1|   3 TVVSDTHstDSHRLSGRTLEAVREA--ELVVHLGDF--MRESVLDAFESESsQLFGVYGNND-----------DAGI 64 
                                       69*****999999999*********..********9..77779999999889**********...........99** PP

                     Metallophos_2  78 gtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdp 154
                                       +++lp+++++++ag +++ +H    g++ al+   +e   g+dvv++GH+H+p+ + +g+v+++nPGs ++pr +++
  gi|313127658|ref|YP_004037928.1|  65 RDRLPDTRTFTFAGLTFAATHTR-RGGSTALSMFGRE--RGADVVLFGHSHRPTFDGTGEVTLLNPGSHAQPRGHRT 138
                                       **********************9.4777777777777..9999*****************************98876 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   2.7e-05      0.24       4      75 ..       3      60 ..       2      83 .. 0.77
   2 !   10.0   0.0    0.0001      0.91     162     204 .]      79     114 ..      60     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                      EEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS CS
                       Metallophos  4 lvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe 75
                                      +v++D+H      +++   ++l+ +++     lv+++GD+  ++     +l+ ++   +   +++ + GN +
  gi|313127658|ref|YP_004037928.1|  3 TVVSDTH---STDSHRLSGRTLEAVREA---ELVVHLGDFMRES-----VLDAFESESS---QLFGVYGNND 60
                                      69*****...899999999999999777...*********9999.....6666777777...7888889988 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0001
                                       EEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 162 wvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHvy 204
                                        +++ +H           g+ al  + ++ g+d+v++GH+H++
  gi|313127658|ref|YP_004037928.1|  79 LTFAATHTRRG-------GSTALSMFGRERGADVVLFGHSHRP 114
                                       55566666666.......788888999999***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1269.48
//
Query:       gi|313127659|ref|YP_004037929.1|  [L=313]
Description: cation diffusion facilitator family transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-27   95.4   7.8    5.4e-27   94.8   7.8    1.3  1  Cation_efflux    Cation efflux family
    8.8e-08   32.2   0.3    1.6e-07   31.4   0.3    1.4  1  ZT_dimer         Dimerisation domain of Zinc Transporter


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   7.8     6e-31   5.4e-27       2     199 .]       9     231 ..       8     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 6e-31
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                       i++l+an ++a+ ++ + l+t S ++l++ +hs+sd+ ++++ll+++++s k+ ++++pfGyg++++++++ +++ll
  gi|313127659|ref|YP_004037929.1|   9 IAALIANGAIAVLKFLGFLVTQSPSMLSETYHSISDTGNQVFLLIGIRYSGKEESRTHPFGYGKAQFFYSFLVSVLL 85 
                                       89*************************************************************************99 PP

                     Cation_efflux  79 lglav.fllleaiqklikegereihaglalvvalvslvvnlalllilrragrkl....................... 131
                                       +g+a   +l ++++ ++++g+++     ++++++ +  vn+++l   ++   +                        
  gi|313127659|ref|YP_004037929.1|  86 FGIAGwESLKHGYDAIMHGGHALGGMVTLAGYTFPGWYVNVVVLVGAIGF--ESyafkkaaaelrrqireyewdgiv 160
                                       99998458888888888444444444444455544444444444433321..122334445555779********** PP

                     Cation_efflux 132 ......rsaalkaaalhvlgDaltslgvlvsalvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                             ++ +  +a+ +   D+++ lg+ +++++++l + +++ ++D+++++ ig++++  ++ l++e+ + Ll
  gi|313127659|ref|YP_004037929.1| 161 dafrktSDVTTLTAFTE---DTIALLGAGIALVGVILSEITGNAVYDAIGAVCIGVLLMSFSVALAWENKRLLL 231
                                       ***99888888888888...*********************99**************************99886 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.3   1.7e-11   1.6e-07       1      78 [.     235     311 ..     235     312 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.7e-11
                                       ....HHHHHHHHHTT-SS-EEEEEEEEE-S-.---EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEE CS
                          ZT_dimer   1 ldeeeeeeireiiksvpgvkgvhdlrtrksG.skifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHv 76 
                                       l+e++e+ +++i++++pgv +v+d+rt ++G +k++v  ++ ++  l  ++    ++e+e+++k+e ++v+  ++ +
  gi|313127659|ref|YP_004037929.1| 235 LPEQVEKSLQSIVRNHPGVAHVDDFRTVHVGpEKVLVTADVSFNSGLETNDIDTDITEIEDKLKAEDKRVK--FVYL 309
                                       689999*************************66*******************************9997764..6777 PP

                                       EE CS
                          ZT_dimer  77 eP 78 
                                       eP
  gi|313127659|ref|YP_004037929.1| 310 EP 311
                                       77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1908.92
//
Query:       gi|313127660|ref|YP_004037930.1|  [L=349]
Description: l-threonine aldolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-90  304.0   0.5    1.2e-90  303.8   0.5    1.0  1  Beta_elim_lyase  Beta-eliminating lyase
    7.2e-11   41.9   0.0    9.3e-11   41.5   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
     0.0002   20.8   0.0      0.023   14.0   0.0    2.4  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.058   11.9   0.1       0.12   10.8   0.1    1.6  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.092   11.4   0.0       0.17   10.5   0.0    1.5  1  Aminotran_3      Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.8   0.5   3.3e-94   1.2e-90       1     289 [.       4     285 ..       4     289 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.8 bits;  conditional E-value: 3.3e-94
                                       E-S-GGG----HHHHHHHHCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEE CS
                   Beta_elim_lyase   1 DLlSDsvtkgteamsdaqaaamlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivt 77 
                                       DL+SD+vt+++eam++a   a +Gd++Yg+d+tvn+Le+a+ael+g+eaal+vp+Gt++n+i+ ++++ rg+e++v+
  gi|313127660|ref|YP_004037930.1|   4 DLRSDTVTRPSEAMREAARDAPVGDDVYGDDPTVNELEAAAAELVGMEAALYVPTGTMGNQIAARVHTDRGQEILVD 80 
                                       9**************************************************************************** PP

                                       TT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHH CS
                   Beta_elim_lyase  78 epahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelreva 154
                                       e+ahi+ +e g++a+l+g ++r++   +a   +++++++   e++ he+ ++l+ +++T+n+ gG +vs+e ++++a
  gi|313127660|ref|YP_004037930.1|  81 EQAHIYKWELGGLAQLSGLQVRTVAAGDAAVPTPQQIQDGYVEQSLHEAGTGLVAVENTHNARGGVAVSPETIDAAA 157
                                       ***************************************8888566******************************* PP

                                       HHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH....HHHHHHHHHHHHT- CS
                   Beta_elim_lyase 155 aiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddeledylaerveqrkylgg 231
                                       + a++ g+p+hlDgAR++na+++l++++++m++ vDsv+++l+K+l+a+vG++la++ +    y+++++++rk  gg
  gi|313127660|ref|YP_004037930.1| 158 DAAHELGVPVHLDGARLFNACVALDVDPARMTRAVDSVMFCLSKGLGAPVGSILAGSSE----YVERARRVRKLFGG 230
                                       ***********************************************************....************** PP

                                       --SSTHHHHH..HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT--EEECCGTTCCEEE CS
                   Beta_elim_lyase 232 glrqagvlaaleagiraleeglaslerdhktaeqlaeklelvrlaiprrvytqehldy 289
                                       g+rqag++aa  +g+ral++  ++l++dh++a++la++l+++++  + +++t+ + ++
  gi|313127660|ref|YP_004037930.1| 231 GMRQAGIIAA--PGLRALDNV-ERLADDHENAARLAAGLDDIDGLSAPEPDTNIVQVF 285
                                       **********..******987.9***********************999999988776 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   2.6e-14   9.3e-11      19     362 ..      13     334 ..       4     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.6e-14
                                       HHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-E CS
                     Aminotran_1_2  19 tlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgde 95 
                                       ++++ ++a+++   a  +   yg+     ele a a+++g         eaa+ v +G+  ++ a+   ++  +g+e
  gi|313127660|ref|YP_004037930.1|  13 PSEAMREAARD---APVGDDVYGDDPTVNELEAAAAELVG--------MEAALYVPTGTMGNQIAARVHTD--RGQE 76 
                                       44555555544...88888899*9999*************........**99999***9999888888886..**** PP

                                       EEEEESS-T...HHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-.-B--HH CS
                     Aminotran_1_2  96 ilvpdptya...syknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtG.tvatle 168
                                       ilv+++ +    +    ++lsg++v++++    +    + +++++ + e++ +++ t +++ve+ hN  G ++ ++e
  gi|313127660|ref|YP_004037930.1|  77 ILVDEQAHIykwELGGLAQLSGLQVRTVAAG--DAAVPTPQQIQDGYVEQSLHEAGTGLVAVENTHNARGgVAVSPE 151
                                       ********633367889************55..8888999999999999999999*************9725679** PP

                                       HHHHHHHHHHHTTEEEEEEET..TTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEE.EHHHHHH CS
                     Aminotran_1_2 169 eleklldlakkynlllfvDea..YagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilg.naavvsq 242
                                       ++ + +d a++ ++ + +D a  + + v  + d     a + ++++  ++  lsK +G++    G il+ ++++v+ 
  gi|313127660|ref|YP_004037930.1| 152 TIDAAADAAHELGVPVHLDGArlFNACVALDVD----PARMTRAVD-SVMFCLSKGLGAPV---GSILAgSSEYVER 220
                                       *******************87446666665444....788999888.9999*********9...***999******* PP

                                       HHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH.. CS
                     Aminotran_1_2 243 lrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae.. 315
                                       +r++   f     ++  ++a  l++ +     + e+ +  ++++ +l ++L+++ gl+  +++++++ +  +s e  
  gi|313127660|ref|YP_004037930.1| 221 ARRVRKLFGGgMRQAGIIAAPGLRALD-----NVERLADDHENAARLAAGLDDIdGLSAPEPDTNIVQV--FSDEag 290
                                       ******988888888888888887755.....3455555678899999999999999999999998754..333323 PP

                                       .CHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEEC.TTS-HHHHHHHHHH CS
                     Aminotran_1_2 316 .takelskkLleevgvyvtpgtsftvpgrlRitv.Aglteeeleelvea 362
                                        +a+++ + + +  gv+  +    +     R++    +++++++ +ve+
  gi|313127660|ref|YP_004037930.1| 291 lSATSFVERCEDA-GVLGGA----HGDHLTRFCThLDVSRADVDDAVER 334
                                       4666666666555.555555....3345556666555566666666665 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   6.4e-06     0.023      18      68 ..      30      79 ..      13      85 .. 0.79
   2 !    4.4   0.0    0.0054        19     208     269 ..     221     278 ..     210     341 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-06
                                      -SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEE CS
                   DegT_DnrJ_EryC1 18 wltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIv 68
                                       +  +p+v+e+E+a a+ +g++ a+ v +Gt ++++a r+   ++g+e++v
  gi|313127660|ref|YP_004037930.1| 30 VYGDDPTVNELEAAAAELVGMEAALYVPTGTMGNQIAARVH-TDRGQEILV 79
                                      55669*******************************98874.345677766 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0054
                                       SSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTT CS
                   DegT_DnrJ_EryC1 208 kryvgevelGynyrlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpke 269
                                        r v ++ +G  +r   i AA gl+ L+++++l +  +e+a+++  +L +++g + ++   +
  gi|313127660|ref|YP_004037930.1| 221 ARRVRKL-FGGGMRQAGIIAAPGLRALDNVERLADD-HENAARLAAGLDDIDGLSAPEP--D 278
                                       4455556.799999999*************998766.6788999********9644332..2 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   3.4e-05      0.12      51     101 ..      34      84 ..      31     273 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.4e-05
                                       -HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSS CS
                   Cys_Met_Meta_PP  51 nptrsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlY 101
                                        pt++ le++ a+L g eaal v++G+   + a +     G+ei+v+++++
  gi|313127660|ref|YP_004037930.1|  34 DPTVNELEAAAAELVGMEAALYVPTGTMGNQIAARVHTDRGQEILVDEQAH 84 
                                       69****************************9999999999*****988653 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.9e-05      0.17     361     406 .]     294     339 ..     230     339 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 361 keilkkakekGvlilsaGdnvirllppliitdeeidelleilkkal 406
                                       ++++++ +++Gvl +  Gd++ r+   l ++ +++d+++e++++a+
  gi|313127660|ref|YP_004037930.1| 294 TSFVERCEDAGVLGGAHGDHLTRFCTHLDVSRADVDDAVERIEAAI 339
                                       689***************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2321.17
//
Query:       gi|313127661|ref|YP_004037931.1|  [L=180]
Description: doxx protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-06   27.4   9.3    3.7e-06   27.4   9.3    2.1  2  DoxX      DoxX
    3.1e-05   24.0   4.3    4.4e-05   23.4   4.3    1.3  1  DoxD      TQO small subunit DoxD


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   9.3   4.1e-10   3.7e-06       2      79 ..      30     124 ..      29     128 .. 0.75
   2 ?   -1.4   0.2       0.4   3.6e+03      70      81 ..     141     152 ..     140     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.1e-10
                              DoxX   2 llllRlllgvlfiahGlqkltg........fgleg..........taasla...alglpp..pellaylaalvElvg 55 
                                       l ++Rl+ g+ f+++G++k+          +   g            +++a   a+   p   e++ +++ ++E++ 
  gi|313127661|ref|YP_004037931.1|  30 LVAVRLITGYWFLHAGWNKFAFvsgesfdaA---GyllngttaspLHGFFAwaaAT---PwlMEFTNFMIPTGEFLI 100
                                       5789*****************7676664440...2444444444344444433122...244899************ PP

                              DoxX  56 glllllGlltRlaAlalavtllva 79 
                                       gl+l++G l+Rla+++ av++++ 
  gi|313127661|ref|YP_004037931.1| 101 GLGLIVGGLVRLASFFGAVLMVFF 124
                                       *********************985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.4
                              DoxX  70 lalavtllvatl 81 
                                       ++l++++ vat+
  gi|313127661|ref|YP_004037931.1| 141 MGLVLFVTVATF 152
                                       567777777776 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   4.3   4.9e-09   4.4e-05       1     148 [.      29     167 ..      29     180 .] 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.9e-09
                              DoxD   1 fllilRlalgliflsagirkkvlkpakLdPnsssyvGgkliefLpqasiikdlleivvlnrsllvtalvlftlvEii 77 
                                       +l+ +Rl+ g  fl+ag+ k    ++    ++++y+        + as++++++   + ++ l   +  ++   E +
  gi|313127661|ref|YP_004037931.1|  29 WLVAVRLITGYWFLHAGWNKFAFVSGE-SFDAAGYLLNG-----TTASPLHGFFAWAAATPWLMEFTNFMIPTGEFL 99 
                                       7899**************998877754.34555554333.....579************999988887888889*** PP

                              DoxD  78 vGlllliGlltRlssl.vafalalgialsayWlgstcedEyqiglllvaaelvliltgsgkl.slDylllkkl 148
                                       +Gl l++G l Rl+s+ +a+ + + ++  a W     ++   +gl+l    +++   g+g++ +lD++l k +
  gi|313127661|ref|YP_004037931.1| 100 IGLGLIVGGLVRLASFfGAVLMVFFYLGNADWAHGL-VNGDLMGLVL---FVTVATFGAGRIlGLDAYLEK-F 167
                                       *************9963788888888889***9983.3332333333...3344445777766****9976.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 1134.24
//
Query:       gi|313127662|ref|YP_004037932.1|  [L=361]
Description: leucyl aminopeptidase (aminopeptidase t) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-72  242.1   0.3    1.1e-71  241.8   0.3    1.0  1  Peptidase_M29  Thermophilic metalloprotease (M29)


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.8   0.3   6.1e-76   1.1e-71       2     404 ..       2     352 ..       1     355 [. 0.88

  Alignments for each domain:
  == domain 1  score: 241.8 bits;  conditional E-value: 6.1e-76
                                       HHHHHHHHHHHHHTTT---TT-EEEEEEETT-HHHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHHHS-TT-TT--- CS
                     Peptidase_M29   2 eeklekyAellvkvglnlqkgqevvinaevealelarlvaeeaykagakkvvvewsdeeltkerlknaseeqleevp 78 
                                       ++++++ A+++ ++++ +  g++vvina+++a el+ +++ee+ ++ga++v++  ++++ ++++l+n ++ ++e+ p
  gi|313127662|ref|YP_004037932.1|   2 DPRIREHAQIIADHSADISDGDNVVINAPAAAEELVVALHEECAERGANPVYM-NNSSRASRAFLRN-HDGEFET-P 75 
                                       67899***********************************************9.5666667777666.5677855.5 PP

                                       HHHHHHHHHHHHTT-EEEEEE--.-GGGSTTS-HHHHHHHHHHHHHHHHHHHHHHHTTSS-B-BEE---TTTHHHH- CS
                     Peptidase_M29  79 eweaekleelveegaarlsilae.dpkllkgvdpekiaaaqkarskalkeyreriasgklrWcvvavPteawAkkvf 154
                                       +       +++ee +a++++ ++ + +  ++vdpe  aa ++a +++l+e      s+  +Wc++++Pt+  A+   
  gi|313127662|ref|YP_004037932.1|  76 DHL----LAMYEEMDAYIAVRGDvNASETADVDPETNAAHRRAMQPVLEE----RLSK--KWCLTQFPTAGNAQ--- 139
                                       555....6***************************999888777776554....3334..5*************... PP

                                       --S-HHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS CS
                     Peptidase_M29 155 pdleaeealeklwdaifkavrldeedpvaaWeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWigga 231
                                           a++++e +++++ +av ld       W+e+ + +++ +++L++   +e+h+ +  +td t+++a +++    +
  gi|313127662|ref|YP_004037932.1| 140 ---LAGMSTEGYENFVWDAVNLD-------WDEQYEFQQQMVEILDD--ADEVHIVAGDETDVTMSVAGNSTLNDKG 204
                                       ...89*****************8.......*****************..******************6666655555 PP

                                       ---SSS----SBSS---EEE-EEEEEEEEEEE-SS-EEETTEEEBS-EEEEETTEEEEEE-SB-HHHHHHHTTSSSG CS
                     Peptidase_M29 232 ektkkgiefvaNiPteevftaPdkrgvnGvvratkPlsysGnliegirltFedGkvveakAekGeevLkklletDeg 308
                                       ek         N+P +evftaP k++vnG v++++Pl+++G++i+g+r++FedG+v +++Ae++eevL+ ++etDeg
  gi|313127662|ref|YP_004037932.1| 205 EK---------NLPGGEVFTAPVKDSVNGEVHFDMPLYRQGREISGVRVRFEDGRVESYSAERNEEVLDGVFETDEG 272
                                       55.........9***************************************************************** PP

                                       GGSEEEEE---TTSHHHHHT-----HHHHHT..TS-EEEEE---GGGB--..-----SHHHHT----S-EEEEE--- CS
                     Peptidase_M29 309 arrLGEvALvpndspisqsgilfyntLfDen..ascHlAlGaaypecleggeelteeelkaaglNdSlihvDfmigs 383
                                       ar+LGE+ ++ n+  i+q   ++yn+LfDe+   ++H+A+G+aype++ +          +++ N+S+ hvD mi +
  gi|313127662|ref|YP_004037932.1| 273 ARYLGELGIGMNR-AIDQ---FTYNMLFDEKmgDTVHMAVGSAYPETVGE----------ENEENESAEHVD-MILD 334
                                       *************.9***...***********99*************644..........6789********.9988 PP

                                       TT-EEEEE.-TTS-EEEEEETT CS
                     Peptidase_M29 384 edldidgi.tedgkevpifrnG 404
                                       +    d i + dg+  ++ rnG
  gi|313127662|ref|YP_004037932.1| 335 MSE--DSIiEVDGE--VVQRNG 352
                                       776..332022333..455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 2055.02
//
Query:       gi|313127663|ref|YP_004037933.1|  [L=36]
Description: hypothetical protein Hbor_29490 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.015   15.2   0.1    1.1  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.049   13.6   0.4      0.057   13.3   0.3    1.3  1  PyrI_C          Aspartate carbamoyltransferase regulatory cha
       0.06   13.1   0.1      0.064   13.0   0.1    1.1  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.073   13.4   0.1        0.1   12.9   0.1    1.3  1  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi


Domain annotation for each model (and alignments):
>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   3.3e-06     0.015      36      50 .]      17      31 ..       6      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-06
                                      TT-B-TTT--B--EE CS
                        zf-C3HC4_3 36 rkkkCpiCrrpiekv 50
                                       + +Cp+Cr++ie+v
  gi|313127663|ref|YP_004037933.1| 17 TRYRCPYCRTDIEDV 31
                                      6789********986 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   1.3e-05     0.057      27      44 ..      12      29 ..       2      32 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                      EETTTTEEEETTT--EEE CS
                            PyrI_C 27 edkekvklkCkYCekeis 44
                                       d  +++++C YC + i+
  gi|313127663|ref|YP_004037933.1| 12 RDGFDTRYRCPYCRTDIE 29
                                      567789*******99887 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.4e-05     0.064      37      52 ..      11      26 ..       5      28 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                    zinc_ribbon_10 37 keeleevkyrCpkCga 52
                                      +++  +++yrCp+C++
  gi|313127663|ref|YP_004037933.1| 11 QRDGFDTRYRCPYCRT 26
                                      6778899*******96 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.3e-05       0.1       2      15 ..      18      31 ..      17      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                           zf-Di19  2 sftCPyCgkeltvk 15
                                       + CPyC+ +++++
  gi|313127663|ref|YP_004037933.1| 18 RYRCPYCRTDIEDV 31
                                      689*****998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 260.65
//
Query:       gi|313127664|ref|YP_004037934.1|  [L=152]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-12   46.7   0.0      4e-12   45.9   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    3.9e-12   45.5   0.1    7.3e-12   44.7   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.7e-08   34.2   0.1    4.2e-08   32.9   0.1    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
    2.5e-08   33.6   0.3    4.4e-08   32.8   0.3    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    5.4e-07   29.5   0.1    3.1e-06   27.0   0.0    2.1  2  HTH_11          HTH domain
    5.7e-07   29.5   0.7    1.9e-06   27.8   0.1    2.1  2  HTH_20          Helix-turn-helix domain
    6.2e-05   22.7   0.1    0.00044   19.9   0.0    2.1  2  HTH_DeoR        DeoR-like helix-turn-helix domain
    6.4e-05   22.8   0.0    0.00016   21.5   0.0    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
    6.6e-05   22.5   0.2    0.00017   21.1   0.0    1.8  2  GntR            Bacterial regulatory proteins, gntR family
    7.2e-05   22.8   0.0    0.00021   21.3   0.0    1.7  2  HTH_28          Helix-turn-helix domain
    0.00016   21.6   0.0    0.00029   20.8   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00017   21.3   0.0    0.00044   20.0   0.0    1.7  1  HTH_10          HTH DNA binding domain
    0.00022   21.1   0.1    0.00091   19.1   0.0    2.0  3  MarR            MarR family
    0.00049   19.9   0.1     0.0011   18.9   0.0    1.6  1  MarR_2          MarR family
     0.0015   18.3   0.1     0.0026   17.5   0.1    1.4  1  HTH_IclR        IclR helix-turn-helix domain
     0.0033   17.6   0.0     0.0086   16.3   0.0    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0042   17.7   0.0      0.025   15.1   0.0    2.2  2  Mga             Mga helix-turn-helix domain
     0.0051   16.4   0.0      0.012   15.2   0.0    1.6  1  HTH_50          Helix-turn-helix domain
      0.006   16.3   0.1      0.016   14.9   0.0    1.7  2  HTH_38          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.8   0.2      0.073   13.6   0.0    2.2  2  HTH_27          Winged helix DNA-binding domain
      0.015   15.1   0.0      0.032   14.0   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.017   14.7   0.1       0.04   13.5   0.1    1.6  1  HTH_47          winged helix-turn-helix
      0.026   15.0   0.0      0.059   13.8   0.0    1.6  1  HTH_40          Helix-turn-helix domain
      0.032   13.7   0.0      0.069   12.6   0.0    1.5  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.041   13.9   0.0      0.064   13.3   0.0    1.3  1  HTH_29          Winged helix-turn helix
      0.047   13.4   0.0       0.12   12.1   0.0    1.6  1  HTH_41          Helix-turn-helix domain
      0.053   13.9   0.0       0.16   12.3   0.0    1.8  1  Rrf2            Transcriptional regulator
       0.07   13.8   0.0        1.1   10.0   0.0    2.2  2  RPA_C           Replication protein A C terminal
      0.072   13.1   0.0       0.12   12.4   0.0    1.3  1  HTH_36          Helix-turn-helix domain
      0.073   13.0   0.1       0.18   11.8   0.0    1.7  1  HTH_1           Bacterial regulatory helix-turn-helix protein
        0.1   12.1   0.3       0.23   11.0   0.0    1.7  1  HTH_CodY        CodY helix-turn-helix domain
       0.11   12.5   0.0       0.25   11.4   0.0    1.6  1  Cdc6_C          CDC6, C terminal winged helix domain
       0.13   11.9   0.1       0.29   10.7   0.0    1.6  2  GerE            Bacterial regulatory proteins, luxR family
       0.13   12.5   0.0       0.28   11.4   0.0    1.5  1  HTH_34          Winged helix DNA-binding domain
       0.16   12.1   0.0       0.44   10.7   0.0    1.7  1  HTH_7           Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   7.8e-15     4e-12       1      74 [.      69     138 ..      69     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 7.8e-15
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       +++++e+++   l e+ e+l+e ++ +++y vtGdyd++++ ++ d++ ++  +++ l +  ++++++ts+vl+
  gi|313127664|ref|YP_004037934.1|  69 IQLKVEGSA---LPEITERLREQKQMISVYEVTGDYDIIAIGKFTDTDGMNSQIKQ-LLTDADIRESNTSVVLN 138
                                       688999888...********************************************.999999*********97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.1   1.4e-14   7.3e-12       5      48 .]       7      50 ..       4      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.4e-14
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d k++++L  ++r s r LAe+l++S++tv+ +l+ Le+eG+I+
  gi|313127664|ref|YP_004037934.1|  7 DAKLINALLGDGRASLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      6799***************************************7 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   8.3e-11   4.2e-08       6      46 ..       9      50 ..       8      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 8.3e-11
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      k++++L   g ++   laeel++s  tvS HL+ L+++G++e
  gi|313127664|ref|YP_004037934.1|  9 KLINALLGdGRASLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      67889998899****************************996 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.3   8.7e-11   4.4e-08       4      42 .]       6      44 ..       4      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 8.7e-11
                     HTH_AsnC-type  4 iDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +D k+++aL  d+R+s + LAe++ +S +tv + +r Le
  gi|313127664|ref|YP_004037934.1|  6 LDAKLINALLGDGRASLRSLAEELDVSVTTVSNHLRDLE 44
                                      8******************************99888776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0     6e-09   3.1e-06      12      44 ..      16      48 ..       8      55 .. 0.84
   2 ?   -0.7   0.0       2.7   1.4e+03       5      20 ..      81      96 ..      79      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6e-09
                            HTH_11 12 argpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                       +g  s   LAeeL+vS +tv +++++Le+ gv
  gi|313127664|ref|YP_004037934.1| 16 GDGRASLRSLAEELDVSVTTVSNHLRDLEDEGV 48
                                      566689999**********************94 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.7
                            HTH_11  5 ilelLleargpisgee 20
                                      i e+L+e+++ is  e
  gi|313127664|ref|YP_004037934.1| 81 ITERLREQKQMISVYE 96
                                      6789999998899865 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   3.8e-09   1.9e-06      18      60 ..      13      55 ..       7      56 .. 0.90
   2 ?   -1.7   0.0       6.3   3.2e+03      28      42 ..     117     134 ..     117     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.8e-09
                                      HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 18 aLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      aL +++ +++  lae+ld+s +t+s+HLr Le+ g +e+ +++
  gi|313127664|ref|YP_004037934.1| 13 ALLGDGRASLRSLAEELDVSVTTVSNHLRDLEDEGVIEGYTPR 55
                                      55589999******************************98875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.3
                                       HHHHHHH...TS-HHHHH CS
                            HTH_20  28 selaerl...dlskntls 42 
                                       s+++++l   d++ ++ s
  gi|313127664|ref|YP_004037934.1| 117 SQIKQLLtdaDIRESNTS 134
                                       578888876678888876 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.7e-07   0.00044       3      44 ..       8      49 ..       7      52 .. 0.94
   2 ?    0.2   0.0       1.3   6.5e+02       4      25 ..      80     102 ..      78     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.7e-07
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                      ++++  l  +g  s+  l+e+l+vS +T+ + L+ Le +g++
  gi|313127664|ref|YP_004037934.1|  8 AKLINALLGDGRASLRSLAEELDVSVTTVSNHLRDLEDEGVI 49
                                      68999999********************************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                          HTH_DeoR   4 qilellk.qqgklsveelvellg 25 
                                       +i+e l+ q++ +sv e++  ++
  gi|313127664|ref|YP_004037934.1|  80 EITERLReQKQMISVYEVTGDYD 102
                                       67788862556789998887776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.1e-07   0.00016       9      53 ..       6      50 ..       4      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.1e-07
                                      HCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB  9 yEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                       +ak   aLl  g+a+ + +aeel+v+ ++v + Lr Led G++e
  gi|313127664|ref|YP_004037934.1|  6 LDAKLINALLGDGRASLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      57888889***********************************98 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.4e-07   0.00017       6      55 ..       3      50 ..       1      52 [. 0.83
   2 ?   -2.4   0.0       7.7     4e+03      21      25 ..      75      79 ..      67      88 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.4e-07
                                      HHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR  6 yerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      ye L++++++  l  G +  s r+La+e++Vs ttv   Lr Le eg++e
  gi|313127664|ref|YP_004037934.1|  3 YENLDAKLINALLGDGRA--SLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      667777777766666655..68*************************996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.7
                                      TSB-- CS
                              GntR 21 GdkLP 25
                                      G++LP
  gi|313127664|ref|YP_004037934.1| 75 GSALP 79
                                      34444 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.2e-07   0.00021       4      47 ..       9      55 ..       8      56 .. 0.92
   2 ?   -1.7   0.0       6.4   3.3e+03       5      22 ..      68      85 ..      67      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.2e-07
                            HTH_28  4 eiiklla.aGh.svreaArelgisrrtvyrWikryeegG.iagLvpr 47
                                      + i +l+ +G+ s r +A+el +s +tv+  ++ +e +G i+g  pr
  gi|313127664|ref|YP_004037934.1|  9 KLINALLgDGRaSLRSLAEELDVSVTTVSNHLRDLEDEGvIEGYTPR 55
                                      678899989******************************77999997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.4
                            HTH_28  5 iikllaaGhsvreaArel 22
                                      ii+l  +G + +e+ ++l
  gi|313127664|ref|YP_004037934.1| 68 IIQLKVEGSALPEITERL 85
                                      889999999999998876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   5.6e-07   0.00029      23      53 ..      21      52 ..       8      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.6e-07
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis.r 53
                                      + + lA+ l ++  tvs  l++L++eg+i+  
  gi|313127664|ref|YP_004037934.1| 21 SLRSLAEELDVSVTTVSNHLRDLEDEGVIEgY 52
                                      5678*************************942 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   8.6e-07   0.00044      23      48 ..      19      44 ..      17      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.6e-07
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkae 48
                                      r++l++LA+el++s +t+s+hLr  e
  gi|313127664|ref|YP_004037934.1| 19 RASLRSLAEELDVSVTTVSNHLRDLE 44
                                      799********************765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.8e-06   0.00091      16      48 ..      18      50 ..      14      54 .. 0.92
   2 ?   -2.1   0.0       7.4   3.8e+03      36      50 ..      80      95 ..      70     100 .. 0.57
   3 ?   -2.3   0.0       8.3   4.3e+03      20      39 ..     119     138 ..     114     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-06
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlie 48
                                      g +s+  La+ l vs +tv++ l+ Le++G ie
  gi|313127664|ref|YP_004037934.1| 18 GRASLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      5678899***********************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.4
                                      HHHHHH.HHTTSEEEE CS
                              MarR 36 rvldrL.ekkGlieRs 50
                                      +++ rL e+k +i+ +
  gi|313127664|ref|YP_004037934.1| 80 EITERLrEQKQMISVY 95
                                      5555554677777665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.3
                                       HHHHHHHHTS-HHHHHHHHH CS
                              MarR  20 vseLakklgvskstvtrvld 39 
                                       +++L     +  s+++ vl 
  gi|313127664|ref|YP_004037934.1| 119 IKQLLTDADIRESNTSVVLN 138
                                       45677777777788887776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.1e-06    0.0011      10      52 ..      10      50 ..       4      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +++aL   ++   + + la++l++s  +vs++l++L++ G +e
  gi|313127664|ref|YP_004037934.1| 10 LINALLGDGR--ASLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      5566666665..8999************************998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.2e-06    0.0026       8      49 ..      10      50 ..       8      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.2e-06
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +++al   +++ +l+ lA++++++ +tv+++L+ L+ +G +e
  gi|313127664|ref|YP_004037934.1| 10 LINALLGDGRA-SLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      67777777776.9**************************886 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.7e-05    0.0086      23      52 ..      20      49 ..      12      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-05
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyv 52
                                      ++   lae+L+vs  +Vs  l+ Le++G +
  gi|313127664|ref|YP_004037934.1| 20 ASLRSLAEELDVSVTTVSNHLRDLEDEGVI 49
                                      66678**********************976 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.9e-05     0.025      15      55 ..       4      44 ..       1      46 [. 0.92
   2 ?   -0.8   0.0       4.8   2.4e+03      12      31 ..     127     146 ..     115     149 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.9e-05
                                      HSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                               Mga 15 eslkyqllkflfeeeevsieelaqelyiSestlkrkikeln 55
                                      e+l+ +l+  l+ + + s+ +la+el +S +t+ +++++l+
  gi|313127664|ref|YP_004037934.1|  4 ENLDAKLINALLGDGRASLRSLAEELDVSVTTVSNHLRDLE 44
                                      678899*******************************9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.8
                                       HHHHSHHHHHHHHHHHHSEE CS
                               Mga  12 llkeslkyqllkflfeeeev 31 
                                        ++es++  +l  ++e+e++
  gi|313127664|ref|YP_004037934.1| 127 DIRESNTSVVLNAVVENEQF 146
                                       34556666666666666665 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.3e-05     0.012      10      45 ..       5      41 ..       2      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                            HTH_50 10 efErelikkayek.YpStRklAkrLGvShtaianklr 45
                                      + +++li++++     S R lA+ L vS t++ n lr
  gi|313127664|ref|YP_004037934.1|  5 NLDAKLINALLGDgRASLRSLAEELDVSVTTVSNHLR 41
                                      5677888888855257******************998 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.2e-05     0.016      13      42 ..      11      41 ..       9      42 .. 0.89
   2 ?   -2.6   0.0       9.8     5e+03      15      30 ..      70      85 ..      64      92 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-05
                            HTH_38 13 IerllaeG.lslreIArrLgrspsTIsRElk 42
                                      I +ll  G  slr  A +L++s +T+s++l+
  gi|313127664|ref|YP_004037934.1| 11 INALLGDGrASLRSLAEELDVSVTTVSNHLR 41
                                      6677777889******************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.8
                            HTH_38 15 rllaeGlslreIArrL 30
                                      +l  eG  l eI  rL
  gi|313127664|ref|YP_004037934.1| 70 QLKVEGSALPEITERL 85
                                      5555666666665555 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00014     0.073       8      49 ..      10      50 ..       4      55 .. 0.86
   2 ?   -1.8   0.0       9.2   4.7e+03      19      35 ..      76      92 ..      68      98 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00014
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                      +++ +   ++r++l+ l++ l+v+ +++s+ l+ L+  G++e
  gi|313127664|ref|YP_004037934.1| 10 LINALL-GDGRASLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      566666.799*****************************995 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 9.2
                            HTH_27 19 kkladlcgrlnvedshi 35
                                      ++l ++ +rl  +++ i
  gi|313127664|ref|YP_004037934.1| 76 SALPEITERLREQKQMI 92
                                      44556666666666555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.3e-05     0.032      16      46 ..      17      49 ..       8      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.3e-05
                            HTH_23 16 e.GlsvreIAreLgvsrrTvyrwlkryreeG.l 46
                                      + ++s r  A+eL+vs  Tv++ l+  + eG +
  gi|313127664|ref|YP_004037934.1| 17 DgRASLRSLAEELDVSVTTVSNHLRDLEDEGvI 49
                                      35789999*****************99669955 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   7.7e-05      0.04      42      77 ..      15      50 ..       2      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                                      H-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 42 laDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      l DG+ sL  +Ae++++++ +v + +r L+++g+++
  gi|313127664|ref|YP_004037934.1| 15 LGDGRASLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      89********************************96 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   0.00011     0.059      14      79 ..      21      88 ..      13      97 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                            HTH_40 14 sieeIAkerglkesTIegHLaelieeg......eeidlerlvseeeekeIeeaiekvgseklkpikealpee 79
                                      s+   A+e  ++++T+ +HL +l  eg       +++++ l   +    I+  +e    + l +i e+l e+
  gi|313127664|ref|YP_004037934.1| 21 SLRSLAEELDVSVTTVSNHLRDLEDEGviegytPRVNYDAL-GYDVTAIIQLKVEG---SALPEITERLREQ 88
                                      78999******************999855555544666444.44444444444444...5588888888765 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.069      23      48 ..      14      40 ..       6      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                      HTH_Tnp_ISL3 23 llles.rsvkavArqlgvSwtTVwril 48
                                      ll ++ +s ++ A++l+vS tTV + l
  gi|313127664|ref|YP_004037934.1| 14 LLGDGrASLRSLAEELDVSVTTVSNHL 40
                                      7778899****************8755 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00012     0.064       6      41 ..      13      48 ..       9      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                            HTH_29  6 lllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      +ll +G  + + +A+ l++s +tv ++l++ e +G+
  gi|313127664|ref|YP_004037934.1| 13 ALLGDGRASLRSLAEELDVSVTTVSNHLRDLEDEGV 48
                                      5677888899*************************3 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00023      0.12       8      36 ..      21      49 ..      15      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                            HTH_41  8 tIeelakeleLSvGlvQkALklLeddkai 36
                                      +  +la+el++Sv +v   L  Led+++i
  gi|313127664|ref|YP_004037934.1| 21 SLRSLAEELDVSVTTVSNHLRDLEDEGVI 49
                                      5679************************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00032      0.16      22      56 ..      17      50 ..       8      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00032
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      + + +s++++ae+ ++s + ++  l+ L+ +g+++
  gi|313127664|ref|YP_004037934.1| 17 D-GRASLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      3.4499***************************98 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0021       1.1      70      97 ..      22      49 ..      15      53 .. 0.93
   2 ?    1.8   0.0      0.76   3.9e+02      29      60 ..     110     142 ..      74     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0021
                                      HHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 70 vdeiaqklrlsvndvkqavdeLsneGii 97
                                      ++ +a++l +sv +v + +++L++eG+i
  gi|313127664|ref|YP_004037934.1| 22 LRSLAEELDVSVTTVSNHLRDLEDEGVI 49
                                      6789**********************98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.76
                                       XXXXXXXXXXXXXXXX..XSXHHHHHHHHHHHH CS
                             RPA_C  29 mgtdgalsgnqaklan.kgltalaqqvlnlikq 60 
                                        +tdg++s+ ++ l+  + ++ ++++vln++ +
  gi|313127664|ref|YP_004037934.1| 110 TDTDGMNSQIKQLLTDaDIRESNTSVVLNAVVE 142
                                       455666666666665566688899999998755 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00023      0.12      26      54 ..      20      48 ..      16      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                            HTH_36 26 psqetlakrlglsknTvsraikeLeqlGy 54
                                      +s + la+ l +s+ Tvs++++ Le+ G 
  gi|313127664|ref|YP_004037934.1| 20 ASLRSLAEELDVSVTTVSNHLRDLEDEGV 48
                                      68899********************9885 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00036      0.18      20      40 ..      26      46 ..      17      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00036
                                      HHHHTS-HHHHHHHHHHHHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEee 40
                                      AeeL +s  +vs ++++LE+e
  gi|313127664|ref|YP_004037934.1| 26 AEELDVSVTTVSNHLRDLEDE 46
                                      9******************86 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00045      0.23       3      36 ..      18      51 ..      16      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00045
                          HTH_CodY  3 GrLtaskiaDriGitrsvivnaLrkLesaGiies 36
                                      Gr    ++a+++ +    + n Lr Le  G+ie 
  gi|313127664|ref|YP_004037934.1| 18 GRASLRSLAEELDVSVTTVSNHLRDLEDEGVIEG 51
                                      66667789999999999***************95 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00048      0.25      37      77 ..      31      74 ..      15      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00048
                                      --HHHHHHHHHHHHHTTSEEEE...EEE-CC.C-EEEEEEESSS CS
                            Cdc6_C 37 ltqrevsdllseLemlgilele...ksskGrregrtrkisLnvd 77
                                      ++ ++vs++l++Le+ g++e     ++    +++ t  i+L+v+
  gi|313127664|ref|YP_004037934.1| 31 VSVTTVSNHLRDLEDEGVIEGYtprVNYDALGYDVTAIIQLKVE 74
                                      4889****************985545555667788888888876 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00057      0.29      23      40 ..      25      42 ..      20      44 .. 0.87
   2 ?   -2.9   0.0        10   5.1e+03      12      27 ..      70      85 ..      67      95 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00057
                                      HHHHHTS-HHHHHHHHHH CS
                              GerE 23 IAeelniSekTVkvhksn 40
                                       Aeel++S +TV++h++ 
  gi|313127664|ref|YP_004037934.1| 25 LAEELDVSVTTVSNHLRD 42
                                      69*************986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 10
                                      HHHCTTS-HHHHHHHH CS
                              GerE 12 rllaeGksnkeIAeel 27
                                      +l +eG    eI e+l
  gi|313127664|ref|YP_004037934.1| 70 QLKVEGSALPEITERL 85
                                      6667777777777776 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00055      0.28       5      45 ..      10      50 ..       7      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00055
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      ++  L+ + +a+ ++l e+l ++    s hl+ Le+ g ie
  gi|313127664|ref|YP_004037934.1| 10 LINALLGDGRASLRSLAEELDVSVTTVSNHLRDLEDEGVIE 50
                                      7889999*****************************99886 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00086      0.44      10      38 ..       7      36 ..       3      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00086
                                      HHGGGGSSTTTT.--STTTSSSS---SSSS CS
                             HTH_7 10 dinrvvkLleeG.isiskIAkevnisRsTv 38
                                      d   + +Ll +G  s + +A+e+++s++Tv
  gi|313127664|ref|YP_004037934.1|  7 DAKLINALLGDGrASLRSLAEELDVSVTTV 36
                                      6677889**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 983.50
//
Query:       gi|313127665|ref|YP_004037935.1|  [L=458]
Description: L-glutamine synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.2e-140  468.4   0.1   1.6e-140  468.0   0.1    1.1  1  Gln-synt_C    Glutamine synthetase, catalytic domain
      1e-31  108.5   0.0    2.3e-31  107.3   0.0    1.7  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
     0.0012   18.7   0.0     0.0099   15.7   0.0    2.3  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.0   0.1  2.6e-144  1.6e-140       2     345 .]     119     454 ..     118     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 468.0 bits;  conditional E-value: 2.6e-144
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR+vlk+a++r++e+G++++++pE+EFflf+++e+++            +++++++ggyf++ap+d a+d+rr+i
  gi|313127665|ref|YP_004037935.1| 119 GDPRYVLKQAIKRANEMGYKINAAPEPEFFLFEEDEEGR-----------ATTKTNDAGGYFDLAPKDLASDVRRDI 184
                                       79*********************************9987...........5678899******************** PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                       +  le++g+e+eashhEva+gQ+Ein++++dal++aDnv tf++vv+++A++h+l+atFmpKp++  nGsgmH+hlS
  gi|313127665|ref|YP_004037935.1| 185 IYGLESMGFEIEASHHEVAEGQHEINFEYDDALTTADNVGTFRTVVRAIAAQHDLHATFMPKPIARINGSGMHTHLS 261
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-. CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa. 231
                                       l+++dg+n+f+dedde +lse+a++f +G+l+ha+a+ta+ +ptvnSYkRlvpgyeaPv++aw+ rNRsal+R pa 
  gi|313127665|ref|YP_004037935.1| 262 LFTEDGENAFHDEDDEFNLSETAKQFTAGILEHAPAITAVSNPTVNSYKRLVPGYEAPVYVAWSDRNRSALIRKPAa 338
                                       ****************************************************************************8 PP

                                       TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHC CS
                        Gln-synt_C 232 skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealee 306
                                         + a+r+E R+pd+s+NPYLa+Aal+ Agl+Gie++le+ +pv++++ye ++++r   gie+lPa+l eA++al+e
  gi|313127665|ref|YP_004037935.1| 339 RVPAASRIEARFPDPSCNPYLAFAALIHAGLNGIERGLECDDPVRENIYEFDEAKReeYGIETLPANLGEAIDALQE 415
                                       89**************************************************9999889****************** PP

                                       SHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 307 dellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       de+++++lge+++e+++++k++E++e++  vs+wel++y
  gi|313127665|ref|YP_004037935.1| 416 DEVVQDALGEHIYEKFVEAKSQEYDEFRVDVSQWELDKY 454
                                       ************************************998 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   0.0   3.9e-35   2.3e-31       2      82 ..      32     110 ..      31     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 3.9e-35
                                       --EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-.EEEEEE CS
                        Gln-synt_N   2 vkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreekktarvic 78 
                                       v f++lqFtDi g++k+v++pa++  e+a++eg+ FDGSsiegf++i+eSDm LkPd++t++i+P+r+    ar+ic
  gi|313127665|ref|YP_004037935.1|  32 VDFLRLQFTDILGTVKNVAVPATQA-EKAFTEGIYFDGSSIEGFVRIQESDMRLKPDPETFAILPWRDGR-SARLIC 106
                                       89***********************.*****************************************999.****** PP

                                       EEE- CS
                        Gln-synt_N  79 dvyd 82 
                                       dv++
  gi|313127665|ref|YP_004037935.1| 107 DVIN 110
                                       **97 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-06    0.0099       4     103 ..      21     112 ..      18     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                                       .......------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS--EEEEE-G CS
                      Gln-synt_N_2   4 eavveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvGelrLvpdP 80 
                                       +avv+++eek+v+++++ ++d  G ++  a+p ++ e+ +++Gi +    ++++    i+e+       ++rL pdP
  gi|313127665|ref|YP_004037935.1|  21 QAVVDEIEEKEVDFLRLQFTDILGTVKNVAVPATQAEKAFTEGIYFD--GSSIEGFVRIQES-------DMRLKPDP 88 
                                       79*****************************************9876..4677777888886.......89****** PP

                                       GG-EEE---SSTTS.EEEEEE-TT CS
                      Gln-synt_N_2  81 asavalpyaPdaaa.llgdlvevd 103
                                        ++  lp   + +a l+ d+ ++ 
  gi|313127665|ref|YP_004037935.1|  89 ETFAILPWRDGRSArLICDVINTS 112
                                       *******98876555999998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3452.78
//
Query:       gi|313127666|ref|YP_004037936.1|  [L=307]
Description: pap2 superfamily protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-14   51.4  14.1    2.9e-13   49.7   8.7    3.3  2  PAP2      PAP2 superfamily
      1e-08   35.1   4.8      1e-08   35.1   4.8    1.8  2  PAP2_3    PAP2 superfamily


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   8.7   3.3e-17   2.9e-13      49     133 ..     104     188 ..      78     191 .. 0.81
   2 ?   -0.2   0.2     0.088   7.9e+02      77      77 ..     244     244 ..     190     298 .. 0.53

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.3e-17
                              PAP2  49 s....keakesfPSgHs..afafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlli 119
                                       +    +e++++fPSgH+  a++f + ++la+ ++r+r +      + ++++++v va+sR+++gvH+l Dv+aG+ +
  gi|313127666|ref|YP_004037936.1| 104 RppgaAEPGYGFPSGHTlgATVFWGGTALAANVGRRRLR------LGVAAAAVVAVAASRVIIGVHYLADVIAGVTV 174
                                       2444578899*******7778888888888888888888......6778888899********************** PP

                              PAP2 120 Gialaalayrlvqk 133
                                       G+a++a++++  + 
  gi|313127666|ref|YP_004037936.1| 175 GVAFLAIVFAAGPG 188
                                       *******9987665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.088
                              PAP2  77 r 77 
                                        
  gi|313127666|ref|YP_004037936.1| 244 A 244
                                       0 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   4.8   1.1e-12     1e-08     116     189 ..     104     180 ..      42     181 .. 0.82
   2 ?   -2.2   0.3      0.32   2.8e+03      42      63 ..     265     287 ..     251     302 .. 0.48

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.1e-12
                            PAP2_3 116 lrgtienglaafPSlHvawallv...alalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalvaia 189
                                        + +  ++ + fPS H+  a+++   +++++ + r+rl   +a++ +v+++++ v  g HYl+DviaGv+++++ +a
  gi|313127666|ref|YP_004037936.1| 104 RPPGAAEPGYGFPSGHTLGATVFwggTALAANVGRRRLRLGVAAAAVVAVAASRVIIGVHYLADVIAGVTVGVAFLA 180
                                       55555667778********998855434457788888888899999*************************998776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.32
                            PAP2_3  42 qvtllvlvllf.lrrrerlrefl 63 
                                       +++l+v++ ++ l+  + +  ++
  gi|313127666|ref|YP_004037936.1| 265 PLPLVVMAAVAeLSMGSLAFVAA 287
                                       44444444433333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2220.71
//
Query:       gi|313127667|ref|YP_004037937.1|  [L=428]
Description: hypothetical protein Hbor_29530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-39  135.2  28.1    3.1e-39  135.2  28.1    2.0  2  Virul_fac_BrkB  Virulence factor BrkB
  ------ inclusion threshold ------
       0.19   12.0   0.2        0.3   11.4   0.2    1.3  1  ABC_tran_CTD    ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.2  28.1   3.4e-43   3.1e-39       2     256 ..      21     256 ..      20     258 .. 0.89
   2 ?   -0.1   0.9     0.063   5.6e+02     127     240 ..     370     400 ..     344     415 .. 0.43

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 3.4e-43
                    Virul_fac_BrkB   2 eddlsllAaalayytllSlfPlllvllavlgllglddelqeqlldllaev.lpegaaevvedilqrllnqaslgllg 77 
                                       e++++ lAa+++yytl Sl+Pll++ l v++++g +++l++ +ldl++++ lp+ + e+v + l++ + q++l++++
  gi|313127667|ref|YP_004037937.1|  21 EREVTFLAASISYYTLVSLVPLLTLGLVVASFVG-GEALRAYVLDLAQQYlLPA-GSEIVASALEDPTGQGALSVVS 95 
                                       678999*************************977.78*************6665.88********9999******** PP

                    Virul_fac_BrkB  78 lavllwsasggvsalrralnkiygveesrsflrkrllsllllllllvllllslvlsvflqslllasapllglglels 154
                                       lav+lw a++++++l+ a+ +iyg e++   ++ +l++ l+ l+ l +  + ++l + + +       +l ++    
  gi|313127667|ref|YP_004037937.1|  96 LAVTLWGALKLFRGLDIAFSRIYGSETG--GIVDQLRDGLIALGSLGAGTIGVALATTVVA-------ILDIP---- 159
                                       *************************995..6777777777777655555555555555555.......34433.... PP

                    Virul_fac_BrkB 155 ellllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYGslgali 231
                                          ++ +l+ l++++ll++af+  Y+++p++  ++r+alpG+l+aa++w ++  +f++y s ++   ++ G+lga++
  gi|313127667|ref|YP_004037937.1| 160 ---FVGVLSPLLLFGLLIAAFFPFYYIFPDAGLTVREALPGTLFAAVGWAVLGAVFGIYASTAG--ASVAGALGAIL 231
                                       ...478888889999**********************************************988..8999******* PP

                    Virul_fac_BrkB 232 illlWlylsalilLlGaelnaelqe 256
                                       +l+ W+y+s++++L Ga++na+l+e
  gi|313127667|ref|YP_004037937.1| 232 LLVTWFYFSGILILTGAVINAVLAE 256
                                       **********************997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.063
                    Virul_fac_BrkB 127 llslvlsvflqslllasapllglglelsellllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallw 203
                                       +++++++ ++q  lla+              ++ l+++                                       
  gi|313127667|ref|YP_004037937.1| 370 AVTIAAFYLIQDDLLAV--------------IAMLITY--------------------------------------- 393
                                       33333333333321111..............1222222....................................... PP

                    Virul_fac_BrkB 204 llvkilfslylsnfasynaiYGslgaliilllWlyls 240
                                                                     l  l l 
  gi|313127667|ref|YP_004037937.1| 394 ------------------------------LSTLGLY 400
                                       ..............................1111111 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   3.3e-05       0.3      16      62 ..     307     348 ..     305     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                      ABC_tran_CTD  16 eIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62 
                                       +Ie+LE + ael a l + e       ++e + e  ++e+eL++   
  gi|313127667|ref|YP_004037937.1| 307 DIEELEDRVAELRADLDAFE-----SDVQERTVERPDVESELKRYVR 348
                                       7****************888.....5579999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1213  (0.0676558); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 2898.26
//
Query:       gi|313127668|ref|YP_004037938.1|  [L=374]
Description: n(2),n(2)-dimethylguanosine tRNA methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-95  318.8   0.0      6e-95  318.6   0.0    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    4.4e-05   23.1   0.0    7.3e-05   22.4   0.0    1.3  1  MTS              Methyltransferase small domain
      9e-05   22.0   0.1    0.00013   21.5   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00075   20.2   0.1     0.0018   18.9   0.1    1.7  1  Methyltransf_25  Methyltransferase domain
    0.00079   19.5   1.4     0.0019   18.2   1.4    1.7  1  Zn-ribbon_8      Zinc ribbon domain
      0.006   16.2   0.0       0.01   15.5   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.072   12.8   0.0       0.15   11.7   0.0    1.5  1  UPF0020          Putative RNA methylase family UPF0020
      0.095   12.5   0.1       0.15   11.9   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
       0.21   11.6   1.4       0.89    9.6   0.1    2.2  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.6   0.0     3e-98     6e-95      18     373 ..      25     367 ..       8     370 .. 0.92

  Alignments for each domain:
  == domain 1  score: 318.6 bits;  conditional E-value: 3e-98
                                       --SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHH CS
                               TRM  18 eeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNv 94 
                                       ++VFYNP qe nRD++v++   l +++++  +  ++lda++asG+R++R a E      v   D+ e Avel ++N 
  gi|313127668|ref|YP_004037938.1|  25 DDVFYNPTQELNRDVTVAT---LRAYRERDDRAESYLDAMAASGIRGVRAAAE---GFDVTCADLDESAVELARRNL 95 
                                       78*****************...5555566566679******************...6678889************** PP

                                       HHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHH CS
                               TRM  95 klneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrkY 171
                                       + ne +   ++ + +An+l+   ++ fd++DlDPfG+p pf d+a +  ++  l++vTaTDta+L+Ga++++++rkY
  gi|313127668|ref|YP_004037938.1|  96 ERNELDG--EAVHRNANALM--YDSVFDIVDLDPFGTPIPFADAAFANTRD--LVCVTATDTAPLCGAHQKSGIRKY 166
                                       *****96..3444479****..6789*******************987766..************************ PP

                                       SSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT--E CS
                               TRM 172 gavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgClse 248
                                       ++ + ++++  E++lR+ll+a+ r+aa+Y+ka +p+ls+++ +Y r +++++  a+k+++++e+lg+v+hC  Cl++
  gi|313127668|ref|YP_004037938.1| 167 STLPQNTDYHPEMGLRVLLSAMIRTAARYDKAAVPILSHVTRHYARTYLELDGRATKADELVEQLGYVYHCEDCLER 243
                                       ***************************************************************************** PP

                                       EEE--GGG--.SB-TTT-SB.EEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-EE CS
                               TRM 249 ekvkglakfk.aecehcgak.lhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldaplyyd 323
                                       +++ gl      +c+ cg++ + +aGPl+lgp+ d +f+ +v +++ +  e   kkr + +L+++  E ld p+ yd
  gi|313127668|ref|YP_004037938.1| 244 DHEFGLIAHPpDDCPACGSSrTLVAGPLYLGPVCDPDFTRRVRDHITE--EMGEKKRARSMLETVAGE-LDRPTHYD 317
                                       9999988866699****97615679********************999..566699************.******** PP

                                       HHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHH CS
                               TRM 324 lsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavve 373
                                        ++l+++ + s+ +++++ ++l+++g+e++++H++++a+kTna++e++  
  gi|313127668|ref|YP_004037938.1| 318 QHRLCKMWSRSATSMDDFLAELRDAGYEATQAHYSGTAFKTNATIEEMRA 367
                                       *********************************************99865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   3.6e-08   7.3e-05      32     101 ..      54     121 ..      38     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.6e-08
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdli 101
                                       +++ lD  +  G+ g+ +a+e  +  vt+ d d  A+e+a++nle+n+l++e+v++++ + + +  fd++
  gi|313127668|ref|YP_004037938.1|  54 AESYLDAMAASGIRGVRAAAEGFD--VTCADLDESAVELARRNLERNELDGEAVHRNANALMYDSVFDIV 121
                                       556778888888888888887666..9*******************************999999999987 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   6.4e-08   0.00013     148     230 ..      40     121 ..      36     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.4e-08
                              PrmA 148 TklclealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell.k 223
                                       T   l+a+ +   + e+ lD  + SGi  + aa  g  +v+  D+De Av+ a++N+e+N+++ +  v+ ++++l  
  gi|313127668|ref|YP_004037938.1|  40 TVATLRAYRERDDRAESYLDAMAASGIRGVRAAAEGF-DVTCADLDESAVELARRNLERNELDGEA-VHRNANALmY 114
                                       88899999999999*****************999886.68889*******************9988.6654444414 PP

                              PrmA 224 eekadvi 230
                                       ++ +d++
  gi|313127668|ref|YP_004037938.1| 115 DSVFDIV 121
                                       5667765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   9.1e-07    0.0018       2      68 ..      58     121 ..      58     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.1e-07
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEE CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlv 68 
                                       Ld+ + +G    ++a+++   +vt+ D++e+++e ar+++e+++l+ e v+ +a++l +++  fD+v
  gi|313127668|ref|YP_004037938.1|  58 LDAMAASGIRGVRAAAEG--FDVTCADLDESAVELARRNLERNELDGEAVHRNANALMYDS-VFDIV 121
                                       566777787778888884..9***********************************98765.89887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.4   9.7e-07    0.0019       4      35 ..     233     264 ..     232     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.7e-07
                       Zn-ribbon_8   4 YeYrCeeCghefevlqsisdapltaCPeCgs.e 35 
                                       Y Y+Ce+C ++  ++  i+  p+ +CP+Cgs +
  gi|313127668|ref|YP_004037938.1| 233 YVYHCEDCLERDHEFGLIAH-PPDDCPACGSsR 264
                                       99******977777776665.4466*****954 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.2e-06      0.01      41     126 ..      53     135 ..      29     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.2e-06
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       + +++LD  a sG  g+ A+  g   +++ + d++av++ ++nle+ +l++   e ++ +++al       ++fdiv
  gi|313127668|ref|YP_004037938.1|  53 RAESYLDAMAASGIRGVRAAAEG-FDVTCADLDESAVELARRNLERNELDG---EAVHRNANALMYD----SVFDIV 121
                                       56679******************.5799********************997...4444444455444....57**** PP

                                       EE--.....SSSTT CS
                     Cons_hypoth95 118 flDP.....Pyake 126
                                        lDP     P+a+ 
  gi|313127668|ref|YP_004037938.1| 122 DLDPfgtpiPFADA 135
                                       ***96666666665 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.5e-05      0.15      77     115 ..      76     114 ..      40     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.5e-05
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG- CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakL 115
                                         + ++Dld+++v+ ar+N+e+ +++++   ++a+a + 
  gi|313127668|ref|YP_004037938.1|  76 FDVTCADLDESAVELARRNLERNELDGEAVHRNANALMY 114
                                       4499***********************999998887644 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.4e-05      0.15       3      78 ..      53     121 ..      51     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.4e-05
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       ++ ++lD+ +++G  + ++a e   + +v+  D +e a+elAr n+++++ld  e  + ++++l   + d+ fD++
  gi|313127668|ref|YP_004037938.1|  53 RAESYLDAMAASGIRGVRAAAE---GFDVTCADLDESAVELARRNLERNELD-GEAVHRNANALM--Y-DSVFDIV 121
                                       6677888888999888899955...45699*********************9.677777777766..3.3778876 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.43   8.6e+02      19      25 ..     234     240 ..     224     242 .. 0.79
   2 ?    9.6   0.1   0.00044      0.89       5      25 ..     257     277 ..     253     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.43
                    PhnA_Zn_Ribbon  19 llvCpeC 25 
                                       ++ C++C
  gi|313127668|ref|YP_004037938.1| 234 VYHCEDC 240
                                       5668888 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00044
                    PhnA_Zn_Ribbon   5 CplCaSeytYedgallvCpeC 25 
                                       Cp C+S+ t++ g l++ p C
  gi|313127668|ref|YP_004037938.1| 257 CPACGSSRTLVAGPLYLGPVC 277
                                       ***********9999987777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2728.43
//
Query:       gi|313127669|ref|YP_004037939.1|  [L=150]
Description: hypothetical protein Hbor_29550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00022   20.8   0.1    0.00034   20.2   0.1    1.3  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.9e-08   0.00034       5      36 ..      90     128 ..      75     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.9e-08
                              SWIM   5 ldder.vrlnkatCsCpefqk......ngipCkHalAvl 36 
                                       ++  + + +++  C+C++ ++      +g  C+H+lA++
  gi|313127669|ref|YP_004037939.1|  90 VGHAAeYVVEDGGCTCKDSSYnldpedDGQRCWHVLAAA 128
                                       4444468888999************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 954.57
//
Query:       gi|313127670|ref|YP_004037940.1|  [L=269]
Description: hypothetical protein Hbor_29560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1894.04
//
Query:       gi|313127671|ref|YP_004037941.1|  [L=287]
Description: ribose-phosphate pyrophosphokinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-20   72.1   0.0    2.1e-19   69.6   0.0    2.1  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    7.9e-13   48.2   2.7    2.5e-12   46.6   0.7    2.5  2  Pribosyltran    Phosphoribosyl transferase domain
    5.3e-08   33.1   0.9    5.3e-08   33.1   0.9    1.8  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    5.8e-05   22.6   0.1    9.1e-05   22.0   0.1    1.4  1  UPRTase         Uracil phosphoribosyltransferase
    0.00099   18.6   0.1     0.0055   16.2   0.3    2.0  2  PRTase_2        Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   5.7e-23   2.1e-19       2     112 ..       1     109 [.       1     112 [. 0.91
   2 ?   -0.3   0.0      0.27   9.6e+02      11      57 ..     165     213 ..     161     235 .. 0.65

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 5.7e-23
                    Pribosyltran_N   2 kifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrras 78 
                                       +i++g ss++La+++a+ ++ +l+ ++  rf+dgE+   + +   ++d  ii+ ++++ nd+ +ell + da+r+a 
  gi|313127671|ref|YP_004037941.1|   1 MIVPGASSQALAAALARAIDEPLAAVEYDRFPDGETLAAVPDF--DDDRAIIVATTDS-NDAWVELLQLQDAVREAG 74 
                                       599**********************************999984..5556666666666.9***************** PP

                    Pribosyltran_N  79 akritaViPylgysrqdrk.ksrepisaklvaklL 112
                                       a +++ ViPy+gy+rqd++ +  +p+sa+  a+  
  gi|313127671|ref|YP_004037941.1|  75 ATEVVTVIPYMGYARQDKAfEDGHPVSARATAQAV 109
                                       *******************999********99976 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.27
                    Pribosyltran_N  11 eLaekiakrlgvelgk.akvsrfadgEikveiee.svrgkdvfiiqsls 57 
                                       +Lae++++ +g   ++  +  r +  +++++ ++ +  ++dv+i+ ++ 
  gi|313127671|ref|YP_004037941.1| 165 DLAESVCDAYGRGDVDyFEKVRHSGTDVEITPSDaDATDRDVVIVDDII 213
                                       5778888877665554234444455555555544467788888888776 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.083     3e+02     106     123 ..      66      83 ..       4     106 .. 0.51
   2 !   46.6   0.7   6.9e-16   2.5e-12      14     141 ..     139     260 ..     125     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.083
                                       HHHHHHCC-BSEEEEEEE CS
                      Pribosyltran 106 alelLkekgpeevriavl 123
                                         ++++e+g++ev ++ +
  gi|313127671|ref|YP_004037941.1|  66 LQDAVREAGATEVVTVIP 83 
                                       234555555555555555 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 6.9e-16
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TTSE CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpagkk 89 
                                       a+a la  + +  +   ++++ ++ g++ +a  + d+   + ++y +kv++++ + e ++          +d  ++ 
  gi|313127671|ref|YP_004037941.1| 139 AAANLADPLPD--DLDDPLFLSPDAGAIDLAESVCDAYgRGDVDYFEKVRHSGTDVEITP--------SDADATDRD 205
                                       33344444444..488899*******************5455889999988888888887........678****** PP

                                       EEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE...E-HHHHHHHHHH-TTS. CS
                      Pribosyltran  90 VliVDDildtGgTllaalelLkekgpeevriavlv...dkpateeevdknakrvf 141
                                       V+iVDDi++tG+T+  a+++L + g+  v +a+++    ++a+++ ++++   ++
  gi|313127671|ref|YP_004037941.1| 206 VVIVDDIIATGSTVSQAVNHLNSDGARNVFAACVHpllVRNARTKLERAGIEQIV 260
                                       **********************************999999999999888776655 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.44   1.6e+03      78     118 ..      40      82 ..      33     133 .. 0.72
   2 !   33.1   0.9   1.5e-11   5.3e-08      80     151 ..     200     271 ..     196     280 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.44
                                       ES--TTSEEEEEE..EEE-S-HHHHHHHHHHHHTT--EEEEEE CS
                    Pribosyl_synth  78 vGdvgGriaiivd..dliddvesfvaaaevlkerGaykiyvla 118
                                       v d     aiiv   d  d    +++  + ++e Ga  ++ ++
  gi|313127671|ref|YP_004037941.1|  40 VPDFDDDRAIIVAttDSNDAWVELLQLQDAVREAGATEVVTVI 82 
                                       5555555666664225556666677777888888888876654 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 1.5e-11
                                       --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHH CS
                    Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqk 151
                                       d + r  +ivdd+i   +++ +a + l+  Ga  +++ + h ll  +a  +le + i+++v t+t+ +++  
  gi|313127671|ref|YP_004037941.1| 200 DATDRDVVIVDDIIATGSTVSQAVNHLNSDGARNVFAACVHPLLVRNARTKLERAGIEQIVGTDTVERDVSI 271
                                       66778899**********************************************************999865 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   2.5e-08   9.1e-05     118     158 ..     200     238 ..     180     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-08
                           UPRTase 118 kiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvls 158
                                       + ++r v+++D +iaTG+++ +a+++L + g+  ++++ ++
  gi|313127671|ref|YP_004037941.1| 200 DATDRDVVIVDDIIATGSTVSQAVNHLNSDGA--RNVFAAC 238
                                       348899***********************886..4665555 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.15   5.3e+02      37      91 ..     141     191 ..     133     197 .. 0.71
   2 !   16.2   0.3   1.5e-06    0.0055     118     153 ..     200     235 ..     179     274 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.15
                          PRTase_2  37 aaLaellaeakkeelpepvlvigfAEtAtaLghgvadal.eeealylhtTRekvag 91 
                                       a+La+ l+    ++l+ + l+++    A+ L+++v da+ ++++ y++  R++ ++
  gi|313127671|ref|YP_004037941.1| 141 ANLADPLP----DDLD-DPLFLSPDAGAIDLAESVCDAYgRGDVDYFEKVRHSGTD 191
                                       55555555....2333.3456666677999*********8889***9999998765 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.5e-06
                          PRTase_2 118 laaakelvLvDDEistGktalnliralqeklprkry 153
                                        a+++ +v+vDD i+tG+t+ + +++l+++  r+ +
  gi|313127671|ref|YP_004037941.1| 200 DATDRDVVIVDDIIATGSTVSQAVNHLNSDGARNVF 235
                                       357899*********************998776443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1929.98
//
Query:       gi|313127672|ref|YP_004037942.1|  [L=74]
Description: hypothetical protein Hbor_29580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 556.84
//
Query:       gi|313127673|ref|YP_004037943.1|  [L=220]
Description: uracil-DNA glycosylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-26   90.9   0.0    9.5e-26   90.6   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.0   5.3e-30   9.5e-26       1     150 [.      48     214 ..      48     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 5.3e-30
                                       HHC-CTT-SEEEEESSTCHHH.........HHHSSSS.-.STT--HHHHHHHCCCCCCCHHGCTEEEEESSS..... CS
                               UDG   1 pgegppdakvvivGeaPgaee.........datglpFsg.ragnllrkllneaglkrdleseqgvyitnvvkcrpp. 66 
                                       +g+g  da v++vGeaPga +         + tg++++  ++g+++rkl+++ag +         y+tn+vkc p  
  gi|313127673|ref|YP_004037943.1|  48 WGNGSSDASVMVVGEAPGAGDpdaeqwqggNHTGMAYTTrHSGRRIRKLIAAAGHAD-------AYYTNAVKCVPCd 117
                                       6899****************99***************999************99865.......9*********955 PP

                                       ..S.ECGCTTCCCCTCCHHHHHHHHHHHHSSEEEEESHHHHHH.....HHHHSCESCCCSCT.......SEEEEES- CS
                               UDG  67 ..g.nrdtptsaeikacaplleeeiellkprlivllGktaakall...geklgklrgklleak......irvlplph 131
                                         g nr +pt+ e ++c+  l+ e+++++p+++v +Gk+a  ++l   g++l+++ +++l++       + +lpl+h
  gi|313127673|ref|YP_004037943.1| 118 gdGsNR-EPTATERANCRTHLDTELDAIEPEVVVSTGKHATATMLafdGRELDGFLDTVLDPVeldafdVMLLPLLH 193
                                       554499.************************************9889999************5577889******** PP

                                       SSTTTTT..TTTSHHHHHHHH CS
                               UDG 132 Psplnrn..ffksnpelkaea 150
                                       Ps++ ++    ++++++ +ea
  gi|313127673|ref|YP_004037943.1| 194 PSYQDVWlsRLGYTESEYREA 214
                                       ****99977444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1472.39
//
Query:       gi|313127674|ref|YP_004037944.1|  [L=100]
Description: hypothetical protein Hbor_29600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-08   33.8   1.3    2.4e-08   33.8   1.3    2.6  3  PLDc_N    Phospholipase_D-nuclease N-terminal
  ------ inclusion threshold ------
        3.1    7.0   4.9        1.9    7.7   0.1    2.1  2  MSP1a     Major surface protein 1a (MSP1a)
        4.8    7.3   9.2        1.2    9.3   5.3    1.8  2  DUF1634   Protein of unknown function (DUF1634)


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.7      0.17   9.9e+02      23      32 ..      14      23 ..       4      29 .. 0.80
   2 ?   -1.0   0.2      0.29   1.8e+03      32      39 ..      35      42 ..      35      43 .. 0.82
   3 !   33.8   1.3     4e-12   2.4e-08       5      40 ..      45      89 ..      41      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.17
                            PLDc_N 23 llvilflPvl 32
                                      l+++ f+P++
  gi|313127674|ref|YP_004037944.1| 14 LVLVAFIPLV 23
                                      6778888876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.29
                            PLDc_N 32 lGailYll 39
                                      lG +lY+ 
  gi|313127674|ref|YP_004037944.1| 35 LGYLLYFA 42
                                      7999**96 PP

  == domain 3  score: 33.8 bits;  conditional E-value: 4e-12
                            PLDc_N  5 ialidiir.d......rnpss..klaWllvilflPvlGailYllf 40
                                      +++i+i++ +      r+++s  klaW+ + +f+P++Ga++Y+l+
  gi|313127674|ref|YP_004037944.1| 45 FVVIHILLpSrvyihaRDHGSnaKLAWTALAFFIPLVGALVYFLV 89
                                      7888999985699989999999*********************96 PP

>> MSP1a  Major surface protein 1a (MSP1a)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   2.1     0.044   2.6e+02     116     134 ..      10      28 ..       2      50 .. 0.64
   2 ?    7.7   0.1   0.00032       1.9      46      79 ..      61      92 ..      39     100 .] 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.044
                             MSP1a 116 aLaalsvlaliaaivaCic 134
                                       +La+l  +a+i  +v  ++
  gi|313127674|ref|YP_004037944.1|  10 VLAGLVLVAFIPLVVMWVT 28 
                                       4555555555554444333 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00032
                             MSP1a 46 alaGasgtLiWgCLalvvLLpLlgaaaviavade 79
                                      +  G+   L W+ La+   +pL+ga ++  v+  
  gi|313127674|ref|YP_004037944.1| 61 RDHGSNAKLAWTALAFF--IPLVGALVYFLVNMA 92
                                      5569999*****99985..799***999988765 PP

>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.3    0.0002       1.2      54     100 ..       8      54 ..       1      56 [. 0.90
   2 ?   -0.4   0.1       0.2   1.2e+03      10      27 ..      73      90 ..      69      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                           DUF1634  54 aiiqlGllvLiatPvlrVvlsliaFlkekdilyviitliVLliLlls 100
                                         ++ Gl++  ++P++   ++++ +      ly +i ++V+ iLl s
  gi|313127674|ref|YP_004037944.1|   8 LAVLAGLVLVAFIPLVVMWVTVMGWDNLGYLLYFAIYFVVIHILLPS 54 
                                       56899***************************************866 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.2
                           DUF1634 10 llsaavvllGlilllvkh 27
                                      +l+ ++ l+G +++++ +
  gi|313127674|ref|YP_004037944.1| 73 ALAFFIPLVGALVYFLVN 90
                                      577888889998888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 704.42
//
Query:       gi|313127675|ref|YP_004037945.1|  [L=139]
Description: hypothetical protein Hbor_29610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0093   16.2   1.2     0.0093   16.2   1.2    1.8  2  DUF5379   Family of unknown function (DUF5379)


Domain annotation for each model (and alignments):
>> DUF5379  Family of unknown function (DUF5379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.2   5.2e-07    0.0093      16      43 ..       7      34 ..       3      41 .. 0.91
   2 ?   -1.2   0.0      0.14   2.5e+03      10      28 ..      57      74 ..      51      81 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-07
                           DUF5379 16 iifgylanyvytlglgllsglatllflf 43
                                      ++f ++ + v+  glg++sglatl f+f
  gi|313127675|ref|YP_004037945.1|  7 LVFQFIFDVVFGSGLGMVSGLATLPFVF 34
                                      6899999******************998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.14
                           DUF5379 10 lhaiggiifgylanyvytl 28
                                      l a+gg++f  l  + ++l
  gi|313127675|ref|YP_004037945.1| 57 LTALGGMLFAALR-FAFSL 74
                                      6788888888763.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 915.59
//
Query:       gi|313127676|ref|YP_004037946.1|  [L=659]
Description: hypothetical protein Hbor_29620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-50  168.4   0.5    3.2e-49  166.2   0.2    2.2  2  DUF460           Protein of unknown function (DUF460)
    2.4e-05   24.6   0.4    2.4e-05   24.6   0.4    3.3  2  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac
     0.0048   16.5   3.0     0.0048   16.5   3.0    1.8  1  Exonuc_VII_L     Exonuclease VII, large subunit
     0.0058   16.0   6.8     0.0058   16.0   6.8    1.5  1  FAM76            FAM76 protein
     0.0083   16.4   0.1       0.87    9.8   0.0    2.9  3  BtrH_N           Butirosin biosynthesis protein H, N-terminal
  ------ inclusion threshold ------
      0.011   16.1  10.1      0.079   13.4   1.1    2.8  2  FlaC_arch        Flagella accessory protein C (FlaC)
      0.019   15.0   8.1       0.07   13.2   8.1    2.0  1  Laminin_II       Laminin Domain II
      0.048   13.7  26.4      0.025   14.6  17.4    2.8  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
      0.087   10.7   9.4       0.14   10.0   9.4    1.3  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.13   12.2   8.3          2    8.4   3.3    2.6  2  Prefoldin        Prefoldin subunit
       0.15   12.7  12.5    3.3e+02    2.0  12.5    3.3  1  SlyX             SlyX
       0.27   11.5   7.0        1.6    9.1   0.7    2.7  2  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.29   10.6  20.4       0.51    9.8  20.4    1.3  1  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.31   10.8  17.5      0.055   13.2   4.1    3.2  2  DivIC            Septum formation initiator
       0.32   10.9   6.9        0.8    9.6   6.9    1.6  1  STAT_alpha       STAT protein, all-alpha domain
       0.41   10.4  22.7      0.048   13.5  16.0    2.3  2  TACC_C           Transforming acidic coiled-coil-containing p
       0.59   10.2   3.1        1.4    9.0   2.0    2.1  2  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
       0.68    8.5   9.7        1.3    7.6   9.7    1.4  1  FapA             Flagellar Assembly Protein A
        1.5    8.9   5.9         11    6.1   5.0    2.4  2  DUF1664          Protein of unknown function (DUF1664)
        2.3    7.5  21.4          1    8.7  12.9    2.2  2  GAS              Growth-arrest specific micro-tubule binding
        2.9    8.0  11.1        8.7    6.4   2.4    3.1  3  MCC-bdg_PDZ      PDZ domain of MCC-2 bdg protein for Usher sy
          3    8.0  22.9        2.1    8.5   2.8    2.7  2  bZIP_1           bZIP transcription factor
        3.3    6.5  22.2        2.7    6.8  17.9    2.1  1  Spc7             Spc7 kinetochore protein
        3.5    7.7  22.7        1.1    9.4  13.6    2.6  2  ADIP             Afadin- and alpha -actinin-Binding
        3.8    7.0  20.1        9.2    5.8  18.6    2.1  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
        4.1    6.9  26.9         19    4.7  12.9    2.3  2  TMCO5            TMCO5 family
        5.2    5.3   6.6        7.8    4.7   6.6    1.2  1  WDCP             WD repeat and coiled-coil-containing protein
        6.6    6.7  17.6        4.5    7.3   6.5    2.7  2  Prefoldin_2      Prefoldin subunit
        7.9    6.8  17.2         13    6.1   4.9    2.7  2  Spc24            Spc24 subunit of Ndc80
          8    6.3  26.6       0.52   10.2  21.3    1.8  1  DASH_Spc19       Spc19


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.9   1.7e+03      45      84 ..      30      65 ..       7      68 .. 0.71
   2 !  166.2   0.2   5.4e-52   3.2e-49       3     141 .]     219     350 ..     217     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.9
                            DUF460 45 avldldgevlalkssreldreevieliselGkpvivAtDv 84
                                      av+ +dge ++    r++ +++ ++ ++e  +p+i+AtD 
  gi|313127676|ref|YP_004037946.1| 30 AVVAFDGENID----RDVVSHRKLRRLVEREQPAILATDN 65
                                      66666666554....4444555566677888999999995 PP

  == domain 2  score: 166.2 bits;  conditional E-value: 5.4e-52
                            DUF460   3 kskdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpvi 79 
                                       +s d +ve+e++++d iefepl  kr++++ivGiDPG+tt+ av+dldg+ l+++s+r++d+++vie++ e G+pvi
  gi|313127676|ref|YP_004037946.1| 219 RSGDTRVEIERERRDGIEFEPL-VKRRDHVIVGIDPGTTTAAAVVDLDGNKLDVHSTRTADTADVIEWLIERGRPVI 294
                                       689*******************.9***************************************************** PP

                            DUF460  80 vAtDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                       vA+Dv+p+petv+k++rs++a++++Pe+dl v+eK + +++      v y++dHeRDalaAA
  gi|313127676|ref|YP_004037946.1| 295 VAADVEPMPETVEKFRRSFDAAAWIPETDLPVDEKLHRTRD------VGYENDHERDALAAA 350
                                       *****************************************......99************9 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.4     4e-08   2.4e-05      29      69 ..     149     184 ..     123     225 .. 0.79
   2 ?   -1.1   0.4       3.7   2.2e+03      67     127 ..     567     634 ..     556     646 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4e-08
                           acVLRF1  29 gtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarl 69 
                                       g      +t +GGwSq R+ Rr+ +++++  +++a+++++ 
  gi|313127676|ref|YP_004037946.1| 149 G-----RSTGKGGWSQDRYTRRIHGSVKRRSREIADRLKQA 184
                                       3.....4699*************************999865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.7
                           acVLRF1  67 arllaeesae..vvlgGdrslvaevledar..lap...latlareell.dvpdprravLedavrrarav 127
                                       +rl  e  ++  + +gG   +++e+l + +   +p   ++ +  +el+ + + +++a++ed+ rra++ 
  gi|313127676|ref|YP_004037946.1| 567 ERLA-ETNPRavIRTGGLSDAADEILFEHEipVGPaenVTMQEIDELAvARESDVSALIEDWERRAEER 634
                                       4443.4444455667777777777766644333332223333333555455556777778887777664 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.0     8e-06    0.0048     175     258 ..     411     506 ..     345     590 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8e-06
                      Exonuc_VII_L 175 asrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k............ekleekkerlkklker 238
                                       +++l++ e++++r ++r+++le++ e+ l+ ++++k e++ee+k++l +            +++++ +++ ++l+++
  gi|313127676|ref|YP_004037946.1| 411 ERELTDEEKKIRRLERRVERLESHTES-LEATIAEKDETIEEYKTELsEakreerrearerREVQRLERDNNRLERK 486
                                       233333333333333333333333333.3333333333333333333222222212211111122222222222333 PP

                      Exonuc_VII_L 239 lelleekkerleeleeklea 258
                                       le+l+e++e+l+  +e+l+ 
  gi|313127676|ref|YP_004037946.1| 487 LESLREENEELTGKIERLKR 506
                                       33444444444444444433 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   6.8   9.7e-06    0.0058     200     296 ..     400     498 ..     332     506 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.7e-06
                             FAM76 200 kesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkele..kea 274
                                       ++ +++++++ + + +d+  ++ +L+ ++++l+ + e+ + ++ ekd +i e k+el e ++e r+  +e++  +  
  gi|313127676|ref|YP_004037946.1| 400 ESDEDDESTHEERELTDEEKKIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEAKREERREARERRevQRL 476
                                       33334444577778888888999999999999999999999999999999999998888877776666555411445 PP

                             FAM76 275 kekieklekkirellkevaels 296
                                       ++  ++le+k ++l+ e+ el+
  gi|313127676|ref|YP_004037946.1| 477 ERDNNRLERKLESLREENEELT 498
                                       6666778888888877776654 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.2   1.2e+02      75     100 ..      42      67 ..      11      70 .. 0.84
   2 ?   -2.5   0.0       9.2   5.5e+03      54      80 ..      99     124 ..      75     129 .. 0.65
   3 !    9.8   0.0    0.0015      0.87      60     102 ..     262     303 ..     239     314 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                            BtrH_N  75 peeawkalkeeLdaGrpvivqvdvyy 100
                                           +++l++ +++ +p+i+++d+ y
  gi|313127676|ref|YP_004037946.1|  42 DVVSHRKLRRLVEREQPAILATDNMY 67 
                                       5567899****************876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.2
                            BtrH_N  54 dlekrlakrlglkvevketkdpeeawk 80 
                                       +   r+a r+g+ +  k  k++e+a +
  gi|313127676|ref|YP_004037946.1|  99 EPLSRVASRHGVPYGKKPMKEAEAA-A 124
                                       6788999999999996555555544.4 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0015
                            BtrH_N  60 akrlglkvevketkdpeeawkalkeeLdaGrpvivqvdvyyLp 102
                                       ++  g k++v++t+++++  + ++  +++Grpviv++dv  +p
  gi|313127676|ref|YP_004037946.1| 262 VDLDGNKLDVHSTRTADT-ADVIEWLIERGRPVIVAADVEPMP 303
                                       555566777777777764.46677789************8776 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.3     0.021        13       1      34 [.     420     453 ..     418     459 .. 0.79
   2 ?   13.4   1.1   0.00013     0.079       2      34 ..     473     505 ..     472     508 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelk 34 
                                       +i  lE ++++l++  e++++++ e  +++ee k
  gi|313127676|ref|YP_004037946.1| 420 KIRRLERRVERLESHTESLEATIAEKDETIEEYK 453
                                       6778888888888888888888888888888765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00013
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelk 34 
                                       ++ lE + ++l+ +le++++eneel  ++e+lk
  gi|313127676|ref|YP_004037946.1| 473 VQRLERDNNRLERKLESLREENEELTGKIERLK 505
                                       6789***************************98 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   8.1   0.00012      0.07       9      98 ..     418     507 ..     407     510 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX..XXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvk.dankairdA..rrsvkkLeklapqLldklkelkqle 82 
                                       ++++   ++ ++ l+  +e +++ + e ++++ee + +++ ++ +  r+A  rr+v+ Le+  ++L+ kl++l++ +
  gi|313127676|ref|YP_004037946.1| 418 EKKIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSeAKREERREAreRREVQRLERDNNRLERKLESLREEN 494
                                       5667777888888999999999999999999999888888344455556633589**************99999999 PP

                                       HH...HHHHHHHHHHH CS
                        Laminin_II  83 eassslsdniseikel 98 
                                       e+   l  +i+++k l
  gi|313127676|ref|YP_004037946.1| 495 EE---LTGKIERLKRL 507
                                       99...*********87 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.7     0.037        22      41      68 ..     413     440 ..     399     441 .. 0.83
   2 ?   14.6  17.4   4.1e-05     0.025       2      69 ..     437     507 ..     436     510 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.037
                        TMF_DNA_bd  41 knkelekeikelkkkleklekeleelee 68 
                                       ++ + ek+i++l++++e+le+  e+le+
  gi|313127676|ref|YP_004037946.1| 413 ELTDEEKKIRRLERRVERLESHTESLEA 440
                                       5667789999999999999999999885 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.1e-05
                        TMF_DNA_bd   2 slekklkeKDeqIaqLmeEGekLskk...elklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                       sle++++eKDe+I++ ++E+ + + +   e +++  + +L  +n+ le ++++l +++e+l+ ++e+l+++
  gi|313127676|ref|YP_004037946.1| 437 SLEATIAEKDETIEEYKTELSEAKREerrEARERREVQRLERDNNRLERKLESLREENEELTGKIERLKRL 507
                                       899*************9999887665111667899*********************************986 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   9.4   0.00024      0.14      15     103 ..     404     505 ..     351     544 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                        V_ATPase_I  15 nedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeea.............eesleapeekeldeleeel 78 
                                       +++ ++ +r+ ++e +++  +er+++ le++ e+le ++++++e+             ee++ea+e++e+++le++ 
  gi|313127676|ref|YP_004037946.1| 404 DDESTHEERELTDEEKKIRRLERRVERLESHTESLEATIAEKDETieeyktelseakrEERREARERREVQRLERDN 480
                                       33334444444444444444444444444444444444433333344444455555555555555555566666666 PP

                        V_ATPase_I  79 ekleeelkelnenleklkkelnelv 103
                                       ++le++l++l+e++e+l+ + ++l+
  gi|313127676|ref|YP_004037946.1| 481 NRLERKLESLREENEELTGKIERLK 505
                                       6666666666666665555555444 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.3    0.0033         2      79     117 ..     421     459 ..     416     462 .. 0.92
   2 ?    5.9   0.2     0.019        11       7      30 ..     482     505 ..     473     529 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaql 117
                                       i+ l++++e le+  e+le+ ++++ ++i+++  +l++ 
  gi|313127676|ref|YP_004037946.1| 421 IRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEA 459
                                       6789****************************9999875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin   7 slqaelaqlkeaieelektletlk 30 
                                       +l+++l++l+e+ eel+  +e+lk
  gi|313127676|ref|YP_004037946.1| 482 RLERKLESLREENEELTGKIERLK 505
                                       333333333333333333333333 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0  12.5      0.56   3.3e+02       4      49 ..     420     465 ..     417     503 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XX CS
                              SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlke 49 
                                       ++ +LE ++  +e   e+L +++ae +++i++ +++l + +++ + 
  gi|313127676|ref|YP_004037946.1| 420 KIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEAKREERR 465
                                       5666666666666666666666666666666666666655554422 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.7    0.0026       1.6      64      95 ..     411     442 ..     386     444 .. 0.79
   2 ?    5.1   0.5     0.048        29      21      55 ..     472     506 ..     466     518 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0026
                           BLOC1_2  64 lqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                        +++ + ek++++Le  v++L++ + +LEa +
  gi|313127676|ref|YP_004037946.1| 411 ERELTDEEKKIRRLERRVERLESHTESLEATI 442
                                       45666778888899999999999998888765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.048
                           BLOC1_2  21 dyklLeklNeaasekykklkdvaaslekkleklne 55 
                                       +++ Le+ N++ ++k ++l+++ ++l+ k+e+l++
  gi|313127676|ref|YP_004037946.1| 472 EVQRLERDNNRLERKLESLREENEELTGKIERLKR 506
                                       55666666777777777777777777766666665 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  20.4   0.00086      0.51     217     323 ..     402     510 ..     386     521 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00086
                            HMMR_N 217 kekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekcklle 293
                                       +e  e   e ++l+++ ++++ + +++e+ +   ++le +++ek++ ie+ k++L+e + e  ++++++  +++ le
  gi|313127676|ref|YP_004037946.1| 402 DEDDESTHEERELTDEEKKIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEAKREERREARERR-EVQRLE 477
                                       344455566689***********************************************97666666665.589999 PP

                            HMMR_N 294 ...kekeelvreeeekeqtlsaEleelkeklkl 323
                                          + +e +++  +e +++l+  +e lk   kl
  gi|313127676|ref|YP_004037946.1| 478 rdnNRLERKLESLREENEELTGKIERLKRLWKL 510
                                       555666777778888888888888888876555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   7.7       1.2   6.9e+02      18      55 ..     427     463 ..     408     474 .. 0.61
   2 ?   13.2   4.1   9.3e-05     0.055      17      51 ..     471     505 ..     467     507 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksded 55 
                                       ++ +l++  + l+a++a++ +++ee + e+++  + e+
  gi|313127676|ref|YP_004037946.1| 427 RVERLESHTESLEATIAEKDETIEEYKTELSEA-KREE 463
                                       344555556666666666666666666666666.3555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.3e-05
                                       XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  17 laykqlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                       + +++l+++ ++l+++l++l++eneeL+ ++++Lk
  gi|313127676|ref|YP_004037946.1| 471 REVQRLERDNNRLERKLESLREENEELTGKIERLK 505
                                       56899*****************************6 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   6.9    0.0013       0.8       3      82 ..     423     504 ..     421     514 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl..eqeraesekkelkkqkellqqmlnaLdqkRkelvd 77 
                                       ++e+r+e l+s+++ +e +i +  ++ ee++ + +e +++   ++r ++e ++l++ ++ l++ l++L ++ +el  
  gi|313127676|ref|YP_004037946.1| 423 RLERRVERLESHTESLEATIAEKDETIEEYKTELSEAKREerREARERREVQRLERDNNRLERKLESLREENEELTG 499
                                       6899*********************************9995544455555555666666666666667666666666 PP

                        STAT_alpha  78 klkel 82 
                                       k+++l
  gi|313127676|ref|YP_004037946.1| 500 KIERL 504
                                       66554 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  16.0     8e-05     0.048       4     103 ..     401     506 ..     399     522 .. 0.73
   2 ?    0.1   0.5      0.97   5.8e+02      23     125 ..     623     645 ..     603     655 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8e-05
                            TACC_C   4 kdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqk......elakkeiqkvl 74 
                                        d d   ++ ++e +++e++i+ l+++ve l+ + + ++ ++ae ++ti++  +e  + k        +++e+q++ 
  gi|313127676|ref|YP_004037946.1| 401 SDEDDESTHEERELTDEEKKIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEAKreerreARERREVQRLE 477
                                       56677777788899999999999999999999999999999999999999887765444400000045566677777 PP

                            TACC_C  75 eekeqlladlnsveksfsdlfkryekqke 103
                                        +++ l  +l+s+  + ++l  ++e++k 
  gi|313127676|ref|YP_004037946.1| 478 RDNNRLERKLESLREENEELTGKIERLKR 506
                                       77777777777777777777777777775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.97
                            TACC_C  23 eiqelkkkveelkkenq.emkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkry 98 
                                        i++++++ ee +ke+q +m                                                         
  gi|313127676|ref|YP_004037946.1| 623 LIEDWERRAEERRKEQQsQM--------------------------------------------------------- 642
                                       44555555555554444333......................................................... PP

                            TACC_C  99 ekqkevlegykkneeslkkcaeeylar 125
                                                               ++r
  gi|313127676|ref|YP_004037946.1| 643 ------------------------VDR 645
                                       ........................333 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.0    0.0023       1.4      65     133 ..     399     463 ..     395     490 .. 0.79
   2 ?   -2.0   0.0       5.3   3.2e+03      22      37 ..     558     583 ..     544     646 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
                                       TBTTTTCHCBHHHHHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS...T CS
                   Semialdhyde_dhC  65 keedkgepetreelkavaetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaa...p 133
                                       +e d++   t ee+   +e+kki   +        rV  l +h+e++ + +++kd+++ee +++l++a   +
  gi|313127676|ref|YP_004037946.1| 399 DESDEDDESTHEERELTDEEKKIRRLER-------RVERLESHTESLEATIAEKDETIEEYKTELSEAkreE 463
                                       5556666688888888888888887776.......******************************9994442 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.3
                                       GGGCHHHHHHHHHHH..........H CS
                   Semialdhyde_dhC  22 vSGaGkkgvreLlkq..........v 37 
                                       +SGaG +  + L++            
  gi|313127676|ref|YP_004037946.1| 558 ASGAGHSTAERLAETnpravirtggL 583
                                       79999987777776655555544440 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   9.7    0.0021       1.3     335     412 ..     431     509 ..     403     546 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0021
                              FapA 335 lkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                       l + ++ le  + e  e +e++k ++++    k e++ e++ + ++++l+++ ++l+++le+l+ee +el  ++e+ 
  gi|313127676|ref|YP_004037946.1| 431 LESHTESLEATIAEKDETIEEYKTELSEA---KREERREARERREVQRLERDNNRLERKLESLREENEELTGKIERL 504
                                       33334455555555555555555554444...457777899999999999999*****************9999998 PP

                              FapA 412 ....k 412
                                           k
  gi|313127676|ref|YP_004037946.1| 505 krlwK 509
                                       44440 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.0     0.019        11      49     121 ..     430     505 ..     413     509 .. 0.66
   2 ?    5.1   0.3     0.036        21      48      82 ..     481     517 ..     470     540 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkei...skeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +le+  esl+at  +  + i++  ++l e k+     +  ++ev+++++d +++++++es++e  e+l +k+er++
  gi|313127676|ref|YP_004037946.1| 430 RLESHTESLEATIAEKDETIEEYKTELSEAKREerrEARERREVQRLERDNNRLERKLESLREENEELTGKIERLK 505
                                       4555555555555555566666666665554331113345678888888888888888888888888888888875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.036
                           DUF1664  48 kqleqvseslaatkrhLssridrvd..kkldeqkeis 82 
                                       ++le+  esl++  ++L+ +i+r+   +kld+++ + 
  gi|313127676|ref|YP_004037946.1| 481 NRLERKLESLREENEELTGKIERLKrlWKLDHSNFAD 517
                                       4555556666666666666666665334555555555 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  20.9     0.019        11      33     120 ..     419     506 ..     406     519 .. 0.85
   2 ?    8.7  12.9    0.0017         1      26      81 ..     447     505 ..     441     544 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.019
                               GAS  33 eeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehe 109
                                       ++i +l+++ er e + + +++   +  e++++ + e+ e +++ ++  +++ + ++l++ +++le++l++l++e+e
  gi|313127676|ref|YP_004037946.1| 419 KKIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEAKREERREARERREVQRLERDNNRLERKLESLREENE 495
                                       56788888888888888899999999999999999999999999999999999999999999999999999999999 PP

                               GAS 110 vleqrfekvek 120
                                        l  ++e++++
  gi|313127676|ref|YP_004037946.1| 496 ELTGKIERLKR 506
                                       99999998876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0017
                               GAS  26 elIkslKeeieelkk...keernekelseisqenkrlkepLkkaeeeveeLrkqlknye 81 
                                       e+I+++K e+ e k+   +e+r ++e++ ++ +n+rl+ +L+ ++ee+eeL  ++++ +
  gi|313127676|ref|YP_004037946.1| 447 ETIEEYKTELSEAKReerREARERREVQRLERDNNRLERKLESLREENEELTGKIERLK 505
                                       57888999998888611145567788888999999999999999999999998887655 PP

>> MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3      0.02        12       1      25 [.     423     447 ..     423     459 .. 0.88
   2 ?    6.4   2.4     0.015       8.7       4      32 ..     471     499 ..     468     506 .. 0.72
   3 ?   -1.2   0.0       3.6   2.1e+03      37      61 ..     616     642 ..     613     644 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.02
                       MCC-bdg_PDZ   1 rLksrIeeLkaqnelLsltleerkq 25 
                                       rL +r+e+L++  e L++t+ e  +
  gi|313127676|ref|YP_004037946.1| 423 RLERRVERLESHTESLEATIAEKDE 447
                                       8******************998765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                       MCC-bdg_PDZ   4 srIeeLkaqnelLsltleerkqqseeLsl 32 
                                       + +++L+ +n++L++ le  ++++eeL+ 
  gi|313127676|ref|YP_004037946.1| 471 REVQRLERDNNRLERKLESLREENEELTG 499
                                       66788888888888888888888888764 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.6
                       MCC-bdg_PDZ  37 aEsnatALvlALe..yserlkeayevl 61 
                                       +Es+++AL    e    er ke  +++
  gi|313127676|ref|YP_004037946.1| 616 RESDVSALIEDWErrAEERRKEQQSQM 642
                                       799999999888876667777777776 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.8    0.0035       2.1      26      63 ..     419     456 ..     417     457 .. 0.92
   2 ?    4.3  12.2     0.074        44      20      61 ..     467     506 ..     458     509 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       ++i +Lerrv+ Le+  +sL  ++ e  +++e+ k+++
  gi|313127676|ref|YP_004037946.1| 419 KKIRRLERRVERLESHTESLEATIAEKDETIEEYKTEL 456
                                       7899****************************999875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  20 sRqRKqaeieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                        R+  + e+++Ler    Le + +sL++e+eel+ ++e Lk 
  gi|313127676|ref|YP_004037946.1| 467 ARE--RREVQRLERDNNRLERKLESLREENEELTGKIERLKR 506
                                       333..3467777777777777777777777777777777764 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  17.9    0.0046       2.7     204     281 ..     410     486 ..     376     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0046
                              Spc7 204 lreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkalee 280
                                         +el++ +++i+++++++++l++  e+le++i+e +e ++e+++e++ea+r  e+++  ++ ev+rl+   ++le+
  gi|313127676|ref|YP_004037946.1| 410 EERELTDEEKKIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEAKRE-ERREARERREVQRLERDNNRLER 485
                                       456899******************************************99885.557778999*********99998 PP

                              Spc7 281 l 281
                                       +
  gi|313127676|ref|YP_004037946.1| 486 K 486
                                       7 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2  10.2      0.15        88      61     117 ..     408     462 ..     386     467 .. 0.58
   2 ?    9.4  13.6    0.0018       1.1      54     123 ..     434     506 ..     433     516 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                              ADIP  61 tirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekee 117
                                       t++  e e++  ++ki+rl++++e+le+ +++++a+ ++   ++++ ++ l + k+e
  gi|313127676|ref|YP_004037946.1| 408 THE--ERELTDEEKKIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEAKRE 462
                                       333..3333444466666666666666666666666666666666666666555555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                              ADIP  54 qreslnetirkleaeierlqski...erlktqleqlerelalvqakerqlekklktleqklknekeelqrlkn 123
                                       + esl++ti +++ +ie  +++    +r +++ ++ +re++ ++++ + le+kl++l + + +++ +++rlk+
  gi|313127676|ref|YP_004037946.1| 434 HTESLEATIAEKDETIEEYKTELseaKREERREARERREVQRLERDNNRLERKLESLREENEELTGKIERLKR 506
                                       6799************9999776111567788899999********************************997 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   2.6      0.17     1e+02      46      93 ..     385     434 ..     383     437 .. 0.71
   2 ?    5.8  18.6     0.015       9.2      44     132 ..     409     504 ..     402     537 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                      HAUS-augmin3  46 geaLeeaLktiepsdlkqedvellev..ileeeeesleaLeqelqeLqke 93 
                                       +e +e +L++i   d++ ed e++++  +l +ee++++ Le+ ++ L++ 
  gi|313127676|ref|YP_004037946.1| 385 EESVEAVLREITGDDESDEDDESTHEerELTDEEKKIRRLERRVERLESH 434
                                       688999******445555555555541145667889999***99999876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.015
                      HAUS-augmin3  44 LegeaLeeaLktie..psdlkq..edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelr 116
                                        e+++L +  k+i   +++ +   +++e+le++++e++e++e++++el+e+++e+++  +++ + q +  ++++ +r
  gi|313127676|ref|YP_004037946.1| 409 HEERELTDEEKKIRrlERRVERleSHTESLEATIAEKDETIEEYKTELSEAKREERREARERREVQRLERDNNRLER 485
                                       57788888888888663333334567899999***********************9999999888888777766666 PP

                      HAUS-augmin3 117 klee...eekeakkklkea 132
                                       kle+   e++e ++k++++
  gi|313127676|ref|YP_004037946.1| 486 KLESlreENEELTGKIERL 504
                                       6665000555555555554 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  13.0     0.034        21      24      99 ..     379     454 ..     373     463 .. 0.82
   2 ?    4.7  12.9     0.032        19      26     122 ..     442     533 ..     441     549 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.034
                             TMCO5  24 rkiqekeetiqslereitkldsllereedeeenfsenekedalkeLeletaklekkneiLlkevveLqkkisrkes 99 
                                        ++ + ee+++  +reit  d+  e+ e  +e+   +++e++ + Le    +le + e L   ++e  + i++ ++
  gi|313127676|ref|YP_004037946.1| 379 ARVVAGEESVEAVLREITGDDESDEDDESTHEERELTDEEKKIRRLERRVERLESHTESLEATIAEKDETIEEYKT 454
                                       5677889************888888888888888999999999999999999999999999999998888887664 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.032
                             TMCO5  26 iqekeetiqslereitkldsllereedeeenfsenekedalkeLeletaklekkneiLlkevveLqkkisrkeskqd 102
                                       i ek+eti++ + e+ + ++ ++re          ++ ++ + Le +  +le+k e L +e  eL +ki+r+++   
  gi|313127676|ref|YP_004037946.1| 442 IAEKDETIEEYKTELSEAKREERRE---------ARERREVQRLERDNNRLERKLESLREENEELTGKIERLKR-LW 508
                                       6778888888888887733333333.........3334445555555555555555555555555555555552.22 PP

                             TMCO5 103 dlek.....etlkqkleelkvklqk 122
                                       +l++      +++++l  +kv  q 
  gi|313127676|ref|YP_004037946.1| 509 KLDHsnfadVNTNKNLVPVKVVEQF 533
                                       3333111112334555555554444 PP

>> WDCP  WD repeat and coiled-coil-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   6.6     0.013       7.8     487     588 ..     406     506 ..     370     531 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.013
                              WDCP 487 qseksgrkLieeiksleqsplssvvdlseka.ssessvaletldaepvnrsaalasasstsdessrpespkvekkkn 562
                                       +s+++ r+L +e k++ ++ + +v +l+ ++ s e+++a +    e+ +++ + a+ +++ + ++r e +++e+ +n
  gi|313127676|ref|YP_004037946.1| 406 ESTHEERELTDEEKKI-RRLERRVERLESHTeSLEATIAEKDETIEEYKTELSEAKREERREARERREVQRLER-DN 480
                                       4555566666665521.122222222222223555555555555566666666666666666666666666653.33 PP

                              WDCP 563 lekekeaeqlskelerlsekltevqq 588
                                        + e+++e+l +e e+l+ k++++++
  gi|313127676|ref|YP_004037946.1| 481 NRLERKLESLREENEELTGKIERLKR 506
                                       45677777777777777777777665 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.5    0.0074       4.5      58     102 ..     415     459 ..     413     463 .. 0.89
   2 ?    3.7   3.9     0.099        59      68     104 ..     463     499 ..     459     501 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0074
                                       E-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                       Prefoldin_2  58 qdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkk 102
                                       +d e+ + +Le r e+le + ++le  + ++ +++ee k+el ++
  gi|313127676|ref|YP_004037946.1| 415 TDEEKKIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEA 459
                                       577888899********************************9875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.099
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  68 eerketlekeiktlekqleklekeleelkeelqkklq 104
                                       e r+++   e+++le+   +le++le l+ee+ ++ +
  gi|313127676|ref|YP_004037946.1| 463 ERREARERREVQRLERDNNRLERKLESLREENEELTG 499
                                       5677788899********************9998765 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   6.3      0.09        54       9      44 ..     417     455 ..     404     470 .. 0.54
   2 ?    6.1   4.9     0.022        13      11      53 ..     471     523 ..     461     544 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.09
                             Spc24   9 iakelsdleselesleselaelkeeleeleeesee...k 44 
                                         k+++ le+ +e+les+ ++l+++++e +e  ee   +
  gi|313127676|ref|YP_004037946.1| 417 EEKKIRRLERRVERLESHTESLEATIAEKDETIEEyktE 455
                                       445555555555555555555555555555555553220 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                             Spc24  11 kelsdleselesleselaelkeeleeleeesee.......keser..ve.det 53 
                                        e++ le++ ++le +l++l+ee eel  + e+       ++s+   v+ +++
  gi|313127676|ref|YP_004037946.1| 471 REVQRLERDNNRLERKLESLREENEELTGKIERlkrlwklDHSNFadVNtNKN 523
                                       67888888888888888888888888888887754444332222234333444 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  21.3   0.00086      0.52      73     157 .]     418     504 ..     404     504 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00086
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXX...XXXXXXXXXXXXXXX CS
                        DASH_Spc19  73 ekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkk...ltkeelerlkkLkqk 146
                                       ek++ +lerr e L++  e +e  + +++++ +e +++ +++++ee++e++e+++ + +    +++ +++l+ L+++
  gi|313127676|ref|YP_004037946.1| 418 EKKIRRLERRVERLESHTESLEATIAEKDETIEEYKTELSEAKREERREARERREVQ-RlerDNNRLERKLESLREE 493
                                       677788888888888888888888877777766666666555555554444443333.23535566669******** PP

                                       XXXXXXXXXXX CS
                        DASH_Spc19 147 KerLkytlerL 157
                                        e+L  ++erL
  gi|313127676|ref|YP_004037946.1| 494 NEELTGKIERL 504
                                       *********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2234  (0.124603); expected 358.6 (0.02)
Passed bias filter:                      880  (0.0490825); expected 358.6 (0.02)
Passed Vit filter:                       202  (0.0112667); expected 17.9 (0.001)
Passed Fwd filter:                        69  (0.00384851); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 1.16u 0.34s 00:00:01.50 Elapsed: 00:00:00.53
# Mc/sec: 3754.75
//
Query:       gi|313127677|ref|YP_004037947.1|  [L=329]
Description: membrane protease subunit, stomatin/prohibitin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-30  107.1   4.5      1e-30  107.1   4.5    1.5  2  Band_7        SPFH domain / Band 7 family
     0.0025   17.6   0.1     0.0046   16.7   0.1    1.4  1  Band_7_1      SPFH domain-Band 7 family
  ------ inclusion threshold ------
      0.033   13.5   0.4      0.065   12.5   0.0    1.6  2  RE_NgoFVII    NgoFVII restriction endonuclease
       0.15   12.5  12.3        2.8    8.4   8.2    2.4  2  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   4.5   2.3e-34     1e-30       3     174 ..      42     229 ..      41     255 .. 0.89
   2 ?   -3.8   0.0       2.5   1.1e+04      37      49 ..     298     310 ..     277     322 .. 0.62

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 2.3e-34
                            Band_7   3 ieegevgvvvrfGklsr.vlepGlhfilPfgrsvtvvsvrvqtldvsv............sltvptkDglpvtidvt 66 
                                       +eeg+v vv   G+  + v epG hfi+P+ +s++  svr q++++s             ++tv+t Dgl+ +idvt
  gi|313127677|ref|YP_004037947.1|  42 VEEGNVKVVKKWGATTGeVFEPGAHFINPISQSTASLSVRPQSYTMSSqqgegeqaqrddAITVLTEDGLRTDIDVT 118
                                       789999999888888889*********************************************************** PP

                            Band_7  67 viyrv.pddapklvaaveresanldnlirrvlesalrevi....semtleellsn..reelaeelknelneqlrkyG 136
                                       v+yrv +++   +++++    + l++  +r++++++r+v+    +++ + e++ +  + +l++ ++++l +++++ G
  gi|313127677|ref|YP_004037947.1| 119 VRYRVdASKSVSFYRSY----RTLETAEKRLIRPSIRSVLrteaGRLPVTEIYTGegQTQLKKAAEKQLSKDFAEAG 191
                                       *****544444455555....77666666666666666666666*********88779******************* PP

                            Band_7 137 vevldvritdidpppevaqalaakqaaeaeaqaeiara 174
                                       + ++ v+i+++++p+++aqa+++k   e+++q+++ + 
  gi|313127677|ref|YP_004037947.1| 192 LILEAVQIRNVELPKQYAQAVEEKEITEQRRQQKQDEL 229
                                       *******************************8887764 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.5
                            Band_7  37 vvsvrvqtldvsv 49 
                                         +++++t+d+s+
  gi|313127677|ref|YP_004037947.1| 298 AGDTSNITVDTSK 310
                                       4566666666666 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     1e-06    0.0046     141     206 ..     146     215 ..     134     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-06
                          Band_7_1 141 ivtrlsdvlaes..kipvldlaa..kseelaeklkealkeelaeyGlelekleienislpeevekaldkr 206
                                       i  ++ +vl ++  ++pv ++ +   +++l +  +++l++++ae Gl le+++i+n++lp++  +a++++
  gi|313127677|ref|YP_004037947.1| 146 IRPSIRSVLRTEagRLPVTEIYTgeGQTQLKKAAEKQLSKDFAEAGLILEAVQIRNVELPKQYAQAVEEK 215
                                       5555555554432257777765411478999*******************************99999876 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05     0.065     190     266 ..      45     118 ..      32     144 .. 0.69
   2 ?   -2.2   0.1      0.44     2e+03     137     143 ..     214     220 ..     170     275 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                                       GGGGGS--.................EE-TTS-EE---TT---EE--HHHTSTT--TT-E....EEEEETTSEEEEEE CS
                        RE_NgoFVII 190 vnaksglnWG..qrshvapgdayirlpakiikskprffpevelevkeitrlegkpkkkrekdefevitDDGtsfkak 264
                                        n k  ++WG    + ++pg  +i+  ++   s  +  p   + + ++ +++g++++ ++ d ++v+t DG      
  gi|313127677|ref|YP_004037947.1|  45 GNVKVVKKWGatTGEVFEPGAHFINPISQSTASL-SVRP---QSY-TMSSQQGEGEQAQRDDAITVLTEDGLRTDID 116
                                       5666778999644477899999997444443331.2223...233.589**********************876555 PP

                                       EE CS
                        RE_NgoFVII 265 ve 266
                                       v+
  gi|313127677|ref|YP_004037947.1| 117 VT 118
                                       54 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.44
                                       HH.HXEE CS
                        RE_NgoFVII 137 sksiskn 143
                                       +k+i+++
  gi|313127677|ref|YP_004037947.1| 214 EKEITEQ 220
                                       2222222 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.2   0.00063       2.8      24      81 ..     175     232 ..     170     241 .. 0.77
   2 ?    5.5   2.3    0.0051        23      20      61 ..     233     270 ..     222     277 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00063
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  24 ArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaq 81 
                                        +k+ae+++++  aeA  il++ + +  +l ++y+q+++e+   ++ + +++ e  ++
  gi|313127677|ref|YP_004037947.1| 175 LKKAAEKQLSKDFAEAGLILEAVQIRNVELPKQYAQAVEEKEITEQRRQQKQDELAVE 232
                                       5899********************************9988655555554444444444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  20 rlEaArkeaereveaAeaeAarilreAeakakalqaeyeqel 61 
                                       +lEa   + +r  ++ ea+A+ril++   + + l+++y ++l
  gi|313127677|ref|YP_004037947.1| 233 KLEA---DRKRIAAQGEADANRILSQSL-DQRILTQKYIDKL 270
                                       2222...223444556777777777654.3456666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1372  (0.0765241); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2141.65
//
Query:       gi|313127678|ref|YP_004037948.1|  [L=113]
Description: hypothetical protein Hbor_29640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.52
# Mc/sec: 656.50
//
Query:       gi|313127679|ref|YP_004037949.1|  [L=290]
Description: epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-64  216.9   0.0    4.1e-64  216.8   0.0    1.0  1  PhzC-PhzF  Phenazine biosynthesis-like protein


Domain annotation for each model (and alignments):
>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.8   0.0   2.3e-68   4.1e-64       1     283 []       9     287 ..       9     287 .. 0.94

  Alignments for each domain:
  == domain 1  score: 216.8 bits;  conditional E-value: 2.3e-68
                                       EEET-SSTTSSEEEEEEESTTCS-HHHHHHHHHHHTSSEEEEEE--SSTTSSEEEEEE-SSSEES--HHHHHHHHHH CS
                         PhzC-PhzF   1 vdaFtespfkGNpaaVvldadelddeelqsiAaelnlseTaFllkpsdekarfrlRyFTPvaEvdlcGHatlasaha 77 
                                       vd+F+e    GN++aV+ da  l+dee+q+iA+e+n+seT+F+  + ++++   +R+FTP aEv+++GH+tl++a +
  gi|313127679|ref|YP_004037949.1|   9 VDVFAERRYAGNQLAVIEDAASLTDEEMQAIAQEMNYSETTFIEGD-AADGAWPVRIFTPNAEVPFAGHPTLGTAAV 84 
                                       8******************************************997.88**************************** PP

                                       HHHHCT-S-SCEEEEEETTEEEEE.EEEEETCEECCEEEEE-SEEEEEE-HHHHHHHHHHCCTSGG-TTS-BEEEES CS
                         PhzC-PhzF  78 laekglvasaetveletkaGilpvkslkekddgeellielkfPvikteevssedlallakllklaaqkalpiavkst 154
                                       l e+    ++++++l+  +G++pv ++ +  d+++  + ++ P +   e++ e+la++++l++++ +++ p++v st
  gi|313127679|ref|YP_004037949.1|  85 LRERFD--AGDEIVLDLAVGEIPV-EVRGTGDDQTYWMTQNPPEFGA-ELDHERLAQVLGLKEDDLDREWPVQVVST 157
                                       ***997..5***************.6999999999999999999985.79*************************** PP

                                       SSEEEEEEBSTCCHHHH----H...HHHHHHCT-EEEEEEEETTTSSCCEEEEEEEEGGGTEEEESS-HHHHHHHHH CS
                         PhzC-PhzF 155 glekvivplsseeavaelspdl...aeeikkcpkkgvivtaaaeagskkdfhsRmFaPklGivEDpvtGsAsgaLaa 228
                                       gl  +++pls++ a+ ++  dl   ++ + ++  + ++++ a ++++++++++RmF+P +++ EDp+tGsA+g La+
  gi|313127679|ref|YP_004037949.1| 158 GLPAIMIPLSNRDALGRAAVDLpayDALLDDVGVENLFPFCADPREDDHHLAARMFSPGYNVPEDPATGSANGCLAG 234
                                       **********************998999999********************************************** PP

                                       HHHHCC-S.SSEEEEEEEE-GGGT--EEEEEEEE.E-TTCEEEEEEEE-EEEEEEE CS
                         PhzC-PhzF 229 ylseklnl.eesakikieqgqalgrsgtlevevevkvdkekervkvtGkAvtvmeg 283
                                       yl++++ + +++ ++ +eqg ++gr++ l++e+e        +v+v G+   v+eg
  gi|313127679|ref|YP_004037949.1| 235 YLARYRYFgDDKVSVSVEQGYEMGRPSVLHLEAEDG---VAVSVRVGGEVEFVAEG 287
                                       ******99667889****************999833...35799999987777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1971.49
//
Query:       gi|313127680|ref|YP_004037950.1|  [L=311]
Description: rnase z [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-24   85.2   0.9    1.7e-21   76.6   0.9    2.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    3.4e-16   59.8   7.6    1.5e-14   54.4   7.6    2.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00037   20.1   0.0    0.00064   19.3   0.0    1.3  1  Lactamase_B_4  tRNase Z endonuclease


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.9   2.9e-25   1.7e-21       2     201 .]      32     270 ..      31     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 2.9e-25
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHHHCCTT CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyapkgvlavlean 73 
                                       r+L+D+g ++  q++r         +   +  +++th H DH+ g++ l +   + +++  + ++ap+g  ++l++ 
  gi|313127680|ref|YP_004037950.1|  32 RLLFDCGEGTQRQMMRFG-------TGFTVSHLFVTHLHGDHVLGIPGLIQtwdFNDREepIAIHAPPGSKRHLQSL 101
                                       89*******888878776.......4458999*******************9985555567999************* PP

                                       CGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C.................................. CS
                     Lactamase_B_2  74 fvylaleeepavnvheldwgesfelgdggleitatparhksgr.................................. 116
                                         +    + ++vn+he+++g+    gd   e+++++  h   r                                  
  gi|313127680|ref|YP_004037950.1| 102 VNAGGYRPSFPVNIHEVKPGNVALSGD-SYEVRTFETDHRNVRsmgfalveddrpgrfnrekaealgvpvgpdfgrl 177
                                       999999999**********99766676.68********************999999555555555555444444444 PP

                                       TCCE-TTTSEEEEEE........CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSH CS
                     Lactamase_B_2 117 rldrnagdtlGlrie........gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeea 184
                                       ++++  ++  G +i         ++g+r++y+gDt  +++ ++  ++ +dll++d+t+ ed+  ++ + gH+t +ea
  gi|313127680|ref|YP_004037950.1| 178 HEGESVELEDGTVIHpeqvvgdpRPGRRLVYTGDTRPVDATVD-VVDEPDLLIHDATFAEDRAERAhGTGHSTGREA 253
                                       3333444445555555555555556666***********9987.*****************997779********** PP

                                       HHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 185 veaaadlgakrlvliHi 201
                                       +e+a+++ga+rl l+Hi
  gi|313127680|ref|YP_004037950.1| 254 AEIANRAGARRLALTHI 270
                                       ****************8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   7.6   2.6e-18   1.5e-14       2     165 ..      17     237 ..      16     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.6e-18
                                       CCCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B   2 gpdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                       ++++ +++l+  dg+ +L+D+G +t+++++      +   +  v+++++THlH DH+ g +gl++++d++ ++++++
  gi|313127680|ref|YP_004037950.1|  17 TERGPSAFLVNRDGERLLFDCGEGTQRQMM------RFGTGFTVSHLFVTHLHGDHVLGIPGLIQTWDFNDREEPIA 87 
                                       567889************************......79*************************************** PP

                                       HHCCHCHHHHHHHHHCCHH...................................................TTCHCGC CS
                       Lactamase_B  79 apalfmeeaddaasrkgll...................................................lagvsad 104
                                        +a+++  +  ++    +                                                      ++ a 
  gi|313127680|ref|YP_004037950.1|  88 IHAPPGSKRHLQSLVNAGGyrpsfpvnihevkpgnvalsgdsyevrtfetdhrnvrsmgfalveddrpgrFNREKAE 164
                                       ******999777776666699*********************************************99995555566 PP

                                       CEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCCEEEECTTTSSHHCCCCCC............TT CS
                       Lactamase_B 105 kpdvdeeeldgnaggrralyvtggpghghghgvvey.gggkvlftGDallagetgridl...........tlr 165
                                       + +v+  ++ g + ++++++   g + ++ ++v +  +g+++++tGD+ ++  t+++               +
  gi|313127680|ref|YP_004037950.1| 165 ALGVPVGPDFGRLHEGESVELEDGTVIHPEQVVGDPrPGRRLVYTGDTRPVDATVDVVDepdllihdatfAED 237
                                       6666666666666666666666666666666666666666666666666666666666533333333333222 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-07   0.00064      12      59 ..      19      65 ..      11      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-07
                     Lactamase_B_4 12 g.PlllLqlds.krYlfGkvgEgtQRavneqkvrlsklesiFLtgkvsws 59
                                      + P+ +L +++ +r lf ++gEgtQR ++  ++ ++ +++ F+t+ +  +
  gi|313127680|ref|YP_004037950.1| 19 RgPSAFLVNRDgERLLF-DCGEGTQRQMMRFGTGFT-VSHLFVTHLH-GD 65
                                      346666777766*****.************999997.8899999988.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2323.94
//
Query:       gi|313127681|ref|YP_004037951.1|  [L=163]
Description: NADH:ubiquinone oxidoreductase subunit N [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-08   34.3   1.0    4.7e-08   32.5   0.6    2.0  2  SHOCT            Short C-terminal domain
     0.0069   16.1   0.6     0.0092   15.7   0.6    1.1  1  SBF              Sodium Bile acid symporter family
  ------ inclusion threshold ------
      0.012   15.6   0.2      0.025   14.6   0.2    1.5  1  DUF1707          Domain of unknown function (DUF1707)
      0.013   15.6   0.2      0.024   14.8   0.0    1.5  2  DUF4719          Domain of unknown function (DUF4719)
      0.034   14.2   0.8      0.053   13.5   0.8    1.3  1  GvpG             Gas vesicle protein G
      0.068   13.3   4.4      0.098   12.8   4.4    1.1  1  SPC12            Microsomal signal peptidase 12 kDa subunit (
      0.068   13.2   2.0        0.1   12.6   2.0    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.48   1.2e+03       9      15 ..      59      65 ..      58      65 .. 0.91
   2 !   32.5   0.6   1.8e-11   4.7e-08       1      28 []     110     137 ..     110     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.48
                             SHOCT  9 LyarGeI 15
                                      L+a+G+I
  gi|313127681|ref|YP_004037951.1| 59 LFAAGLI 65
                                      9****99 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 1.8e-11
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakLL 28 
                                       d L +L+++yarG +++E Fe+k + LL
  gi|313127681|ref|YP_004037951.1| 110 DSLNRLRDRYARGDLSDEQFERKLEVLL 137
                                       6799*********************998 PP

>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.6   3.6e-06    0.0092      31      76 ..      33      74 ..      27      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                               SBF 31 llglvlqwvikPllmfilakillrdlklepelavGlilvglapgga 76
                                         lvl + i+Pll+f+l   ll +l   + +a+Glil++++ g++
  gi|313127681|ref|YP_004037951.1| 33 TSILVLSLGIGPLLGFVLGS-LLVTL---TLFAAGLILLAIVLGSQ 74
                                      55699***************.44444...799*******9987765 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   9.8e-06     0.025      12      41 ..     112     141 ..     109     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-06
                           DUF1707  12 velLrealaeGrLtldEfdeRleaalaArt 41 
                                       +++Lr+ +a+G L+ + f++ le  l  +t
  gi|313127681|ref|YP_004037951.1| 112 LNRLRDRYARGDLSDEQFERKLEVLLDTQT 141
                                       789********************9998887 PP

>> DUF4719  Domain of unknown function (DUF4719)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.2   5.6e+03      79      96 ..      11      28 ..       4      35 .. 0.56
   2 ?   14.8   0.0   9.2e-06     0.024      37     106 ..      50     121 ..      42     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.2
                           DUF4719 79 ggagplggarrpddddds 96
                                      ++ +p+g a   d+ dd+
  gi|313127681|ref|YP_004037951.1| 11 SSQSPAGDASGGDNRDDN 28
                                      444555555555555555 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 9.2e-06
                           DUF4719  37 lsgllillvlfaigyflqriicpsprrynrrqarpgqrpgppggagplg.garrpd.ddddspallrdeaaa 106
                                       l  ll+ l lfa g +l  i+  s  + +  ++  ++ p  p g +p    + +p+   +ds   lrd  a 
  gi|313127681|ref|YP_004037951.1|  50 LGSLLVTLTLFAAGLILLAIVLGSQSKEPNTKTETTRVPPEPEGRSPGVkRTAEPEhSVSDSLNRLRDRYAR 121
                                       6789****************************9999999999888885413445541457888888887665 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8   2.1e-05     0.053      27      64 ..     102     139 ..      97     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                              GvpG  27 lddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdr 64 
                                       ++ ++ +   L +L  +  +G+ ++e+F+r+ e lLd 
  gi|313127681|ref|YP_004037951.1| 102 AEPEHSVSDSLNRLRDRYARGDLSDEQFERKLEVLLDT 139
                                       5566789999***********************99986 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.4   3.8e-05     0.098      13      51 ..      32      70 ..      27      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
                             SPC12 13 lqvilvlsaviafivGyitqdlkltlyillagvvltllv 51
                                      ++ ilvls  i+ ++G+++ +l +tl +++ag++l ++v
  gi|313127681|ref|YP_004037951.1| 32 ITSILVLSLGIGPLLGFVLGSLLVTLTLFAAGLILLAIV 70
                                      567999*****************************9998 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.0     4e-05       0.1      48     101 ..      32      84 ..      28      87 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                   Phage_holin_3_6  48 llalllllval..alalaalwlaalivaavllvlagvlalvglkklkkakplpert 101
                                       ++++l+l++++  +l++    l+ l+v++ l++++++l+++ l   +k++ + ++t
  gi|313127681|ref|YP_004037951.1|  32 ITSILVLSLGIgpLLGF---VLGSLLVTLTLFAAGLILLAIVLGSQSKEPNTKTET 84 
                                       55667777777555666...889999999999999999888888777766633333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1292.38
//
Query:       gi|313116828|ref|YP_004037952.1|  [L=262]
Description: hypothetical protein Hbor_32860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1996.41
//
Query:       gi|313116829|ref|YP_004037953.1|  [L=584]
Description: DNA modification methylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.8e-38  130.3   0.1    4.1e-28   98.6   0.1    2.7  2  N6_N4_Mtase  DNA methylase
  ------ inclusion threshold ------
       0.04   13.6   0.0        5.4    6.7   0.0    2.3  2  UPF0020      Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.1   4.6e-32   4.1e-28       1     190 [.     237     408 ..     237     415 .. 0.88
   2 !   28.6   0.0   1.2e-10     1e-06     195     226 ..     546     577 ..     541     582 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 4.6e-32
                                       EEEEEE--SSSSSCS.......GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT....HHHHHHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy..endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk....elkalade 71 
                                       vdli+t+pPY+ +++y  e de++++e++ eey+e l+ +l+++++ Lk++gs+f+ni+d +  k       ++a++
  gi|313116829|ref|YP_004037953.1| 237 VDLIITSPPYWRKREYldEDDEEFGQESDPEEYVENLVTILDQWKKFLKPTGSVFLNIGDTYRYKslqgIPGLFAEK 313
                                       89*************************************************************99999977888888 PP

                                       HTT.-EEEEEEEEEEESSSTTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHHCHHHCC-B- CS
                       N6_N4_Mtase  72 ifg.gffllnvivwkkpnsmpesnkdrltsthEyilvfsknkkyllkfnldaikvpyeekdklekrgaytskkkgkk 147
                                         + ++ ++n+i+w+k+n++p++++drl ++hE+i++++ +++  ++++ +a    y++ +               +
  gi|313116829|ref|YP_004037953.1| 314 ARKgDWTVRNDIIWTKENGVPSPVDDRLAPRHEHIFHLVLDRDD-YYYDREAYIDLYQTGA---------------N 374
                                       88889************************************999.6666666666665555...............3 PP

                                       -BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS- CS
                       N6_N4_Mtase 148 iediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstk 190
                                         d+W    +++ ++ ++      H a++P++l++r++ l ++
  gi|313116829|ref|YP_004037953.1| 375 PIDVW---SMSHDRNTRN------HLAPFPEDLARRALTLACP 408
                                       4469*...6666666654......*************987664 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.2e-10
                                       EEETT-TTTHHHHHHHHTT-EEEEEESSHHHH CS
                       N6_N4_Mtase 195 vlDpFaGSGtTavaakelgrkfiGieieeeyv 226
                                       vlDpFaGSGtT+++a +lg ++ G++ + +++
  gi|313116829|ref|YP_004037953.1| 546 VLDPFAGSGTTLKVASKLGYHAHGVDLDTSHA 577
                                       9*************************998776 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0006       5.4     113     132 ..     228     247 ..     203     255 .. 0.83
   2 ?    4.4   0.0     0.003        27      31      43 ..     545     557 ..     538     568 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0006
                                       GG--STTS---EEEE----- CS
                           UPF0020 113 akLrlkegevdvivtnpPYG 132
                                        +++ ke++vd+i+t pPY 
  gi|313116829|ref|YP_004037953.1| 228 SEIPVKEESVDLIITSPPYW 247
                                       56777889***********5 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.003
                                       -EEETT-TTSHHH CS
                           UPF0020  31 pllDPmCGsGtil 43 
                                       + lDP+ GsGt l
  gi|313116829|ref|YP_004037953.1| 545 RVLDPFAGSGTTL 557
                                       578*******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3929.32
//
Query:       gi|313116830|ref|YP_004037954.1|  [L=754]
Description: hypothetical protein Hbor_32880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-05   24.8   0.0    3.1e-05   23.8   0.0    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


Domain annotation for each model (and alignments):
>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.7e-09   3.1e-05       4      87 ..      59     174 ..      56     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.7e-09
                       HATPase_c_3   4 ekAlaelvdNsldAdaen................................vkievnknrgktgeivieDdGkGmsee 48 
                                         Al+el+ Ns+dA   +                                +++++  +++ + +++  D+G G +++
  gi|313116830|ref|YP_004037954.1|  59 MAALTELIVNSIDAIILKqfhqtygddfrgdefknlheavegvvdldtaeINLTATGEQNGPLSLSLYDNGCGQPRD 135
                                       579*************999*****************************99999999999999*************** PP

                       HATPase_c_3  49 elkn.alrlatsskeakrkstslGkkGiGlklAslslgkk 87 
                                        +++ +l++ t+ + ++      Gk+G+G  + +l ++ +
  gi|313116830|ref|YP_004037954.1| 136 RFEKtFLNVLTPGEIKQDYDFLQGKYGMG-STGVLPFCGE 174
                                       ***98889*99999987777889******.8888877744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (754 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 5128.95
//
Query:       gi|313116831|ref|YP_004037955.1|  [L=538]
Description: hypothetical protein Hbor_32890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-10   39.9  17.4     0.0056   16.9   0.3    4.6  4  CARDB     CARDB
     0.0035   17.6   8.1       0.23   11.7   0.1    4.4  4  DUF4352   Domain of unknown function (DUF4352)
  ------ inclusion threshold ------
      0.039   13.5   0.0       0.18   11.3   0.0    2.1  2  DUF1833   Domain of unknown function (DUF1833)
      0.061   13.4   2.4        2.8    8.0   0.0    4.0  4  BsuPI     Intracellular proteinase inhibitor


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   1.0   0.00079       3.5       9      85 ..     127     211 ..     123     215 .. 0.77
   2 !   13.8   0.1   1.2e-05     0.052       2      84 ..     224     308 ..     223     313 .. 0.71
   3 !   16.9   0.3   1.3e-06    0.0056      20      69 ..     342     391 ..     327     426 .. 0.87
   4 !   10.7   0.7   0.00011      0.48      12      93 ..     446     529 ..     437     532 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00079
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S.-S-........C CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte.ate........g 76 
                                       t+++++ + ++  +++vtv+N+G+   + +++ + + +++ ++++   + +ge+++ s+t  +    +        g
  gi|313116831|ref|YP_004037955.1| 127 TTTEAAWSGNTLQRVNVTVNNNGDFPVKISEAVVNARDSEMQSSPYVWVMPGETESFSITPSYGkV-SihsagevhG 202
                                       45556666677788**************99999999999998888889999999999999888741.1344656667 PP

                                       EEEEEEEES CS
                             CARDB  77 evtltvvvD 85 
                                       +vt+t ++D
  gi|313116831|ref|YP_004037955.1| 203 SVTVTTSAD 211
                                       777777766 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.2e-05
                                       --EEE.EEEC-SEEET.TSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S..... CS
                             CARDB   2 pDLtvtntlnpseafv.geentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte..... 72 
                                       pDL +   +n++++++ g+  + +vtv+NqG+ ++ a+       +e+ ++++ +s+++g+s++ ++t+        
  gi|313116831|ref|YP_004037955.1| 224 PDLAI---TNVEPVWEgGSLESTRVTVENQGDLTASAWAGIQR-GDEVLASTYNESISPGQSVQYEITHYSGtiyep 296
                                       89999...34444444044445689************976555.5555588999***********999876544445 PP

                                       -S-CEEEEEEEE CS
                             CARDB  73 ategevtltvvv 84 
                                        t+ge++l++ +
  gi|313116831|ref|YP_004037955.1| 297 ETSGEIQLQAIA 308
                                       566777777665 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 1.3e-06
                                       EEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEESEE-CTEEEEEEEEE CS
                             CARDB  20 entitvtvkNqGtaasgatkvalyldgelv.gtvtvpsLaagesttvsftw 69 
                                         + t+t++N+G+  +++++++l+++g +v +++t++sLa ge+++ ++ +
  gi|313116831|ref|YP_004037955.1| 342 LTSATFTLSNNGDV-ATDFSASLIVNGHEVkESQTIQSLAGGETEEYEIVD 391
                                       4567899****975.789************9999**********9988765 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00011
                                       -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE...SEE-CTEEEEEEEEEE-S-S-CEEEEEEEES CS
                             CARDB  12 pseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv...psLaagesttvsftwtteategevtltvvvD 85 
                                        ++  + e + +t+ v+N+G+      +v++ +dg + +t ++   +++++g+stt+ ++   + t+g+ +lt++  
  gi|313116831|ref|YP_004037955.1| 446 NDNSDTPELSDLTLDVQNTGDSVLVYDSVRYEIDGVS-STESLsfeSQIKPGASTTEYLHPDLTVTSGDRQLTIKFI 521
                                       556667788999*************************.67777789***********99988888999999888887 PP

                                       TT-SS--S CS
                             CARDB  86 pdnevaEs 93 
                                        d+ev ++
  gi|313116831|ref|YP_004037955.1| 522 RDGEVVDT 529
                                       77777765 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   5.1e-05      0.23      17      70 ..     116     169 ..     107     224 .. 0.84
   2 ?   -1.3   0.0      0.58   2.6e+03      43      52 ..     244     253 ..     236     257 .. 0.86
   3 ?    3.3   0.2     0.021        92      31     117 ..     334     416 ..     312     427 .. 0.76
   4 ?    4.1   0.4     0.012        52      43      96 ..     458     510 ..     433     513 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.1e-05
                                       EEE.EEEEEETTS-CEETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE CS
                           DUF4352  17 nsv.eytksvgkneylqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgke 70 
                                       +++ e++++   ++++++ +g++   v+vtv+N+g+ +++++++    +d++ ++
  gi|313116831|ref|YP_004037955.1| 116 TASyEGASPTI-TTTEAAWSGNTLQRVNVTVNNNGDFPVKISEAVVNARDSEMQS 169
                                       44436666666.88888999*********************99888887777665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.58
                                       EEEEEE-SSS CS
                           DUF4352  43 dvtvkNkgke 52 
                                       +vtv+N+g+ 
  gi|313116831|ref|YP_004037955.1| 244 RVTVENQGDL 253
                                       69*****985 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.021
                                       EETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB.--EEEE-TT-EEEEEEEEEESTT CS
                           DUF4352  31 lqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskadd.lflgtlnpGkkvtGklvFdvpkg 106
                                       +   + g+   ++ t+ N+g+ a+++++   +L+  +g e++ + +++s a       ++  ++   G+  F  + g
  gi|313116831|ref|YP_004037955.1| 334 TPVWENGRLTSATFTLSNNGDVATDFSA---SLI-VNGHEVKESQTIQSLAGGeTEEYEIVDDSWGAGSALFISNGG 406
                                       55555666677888999*******9954...566.677788888888877776678889999999999999999999 PP

                                       -CGEEEEE.HB CS
                           DUF4352 107 kkkleLeyqts 117
                                       +++++Le+ ts
  gi|313116831|ref|YP_004037955.1| 407 EETVKLEL-TS 416
                                       99988888.33 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.012
                                       EEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB--EEEE-TT-EEE CS
                           DUF4352  43 dvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskaddlflgtlnpGkkvt 96 
                                       ++ v+N+g++ l ++s   ++ dg + + + +++ + k      + l p+ +vt
  gi|313116831|ref|YP_004037955.1| 458 TLDVQNTGDSVLVYDSVRYEI-DGVSSTESLSFESQIKPGASTTEYLHPDLTVT 510
                                       789**************9999.56666666666666666667777888887776 PP

>> DUF1833  Domain of unknown function (DUF1833)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.63   2.8e+03      64      96 ..     236     268 ..     205     277 .. 0.63
   2 ?   11.3   0.0     4e-05      0.18      47      88 ..     321     362 ..     299     378 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.63
                           DUF1833  64 dedkvpeltlildNvgsvitdavegaavservi 96 
                                       + + ++  +++++N g   + a  g ++ ++v+
  gi|313116831|ref|YP_004037955.1| 236 EGGSLESTRVTVENQGDLTASAWAGIQRGDEVL 268
                                       444455555555555555555555555555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4e-05
                           DUF1833  47 kvvvftalaldlalPaededkvpeltlildNvgsvitdaveg 88 
                                       + +  ++l++d   P  +++++  +t++l+N g v+td+  +
  gi|313116831|ref|YP_004037955.1| 321 REISSASLSIDSFTPVWENGRLTSATFTLSNNGDVATDFSAS 362
                                       6788899*******************************9655 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00062       2.8      61      92 ..      75     104 ..      74     110 .. 0.89
   2 ?   -0.5   0.1      0.29   1.3e+03       7      30 ..     132     155 ..     126     166 .. 0.75
   3 ?    1.6   0.0     0.063   2.8e+02      65      94 ..     273     307 ..     268     312 .. 0.79
   4 ?   -3.6   0.0       2.6   1.2e+04      14      26 ..     455     467 ..     448     471 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00062
                                       ---EEEEE-TT-EEEEEEEE.S---SEEEEEE CS
                             BsuPI  61 qalssetlepgesatyeetwdedlepGeYtle 92 
                                       q+++++tlep+++++    +  d++pG+Yt+ 
  gi|313116831|ref|YP_004037955.1|  75 QVIQKTTLEPDQEVAAFSLV--DPRPGNYTII 104
                                       99***********9988888..8******985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
                                       EEE-SS-EEEEEEEEE-SSS-EEE CS
                             BsuPI   7 aeasgeavelaltvtNesdeavtl 30 
                                       a + +   ++++tv+N++d +v++
  gi|313116831|ref|YP_004037955.1| 132 AWSGNTLQRVNVTVNNNGDFPVKI 155
                                       555566678899999999888765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.063
                                       EEEE-TT-EEEEEEEE......S---SEEEEEEEE CS
                             BsuPI  65 setlepgesatyeetwd.....edlepGeYtleae 94 
                                       +e+++pg+s+ ye t +     e+ ++Ge +l+a+
  gi|313116831|ref|YP_004037955.1| 273 NESISPGQSVQYEITHYsgtiyEPETSGEIQLQAI 307
                                       7899*********9998877766777888777776 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 2.6
                                       EEEEEEEEE-SSS CS
                             BsuPI  14 velaltvtNesde 26 
                                        +l+l v+N++d+
  gi|313116831|ref|YP_004037955.1| 455 SDLTLDVQNTGDS 467
                                       5789999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3959.02
//
Query:       gi|313116832|ref|YP_004037956.1|  [L=54]
Description: hypothetical protein Hbor_32900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       125  (0.00697194); expected 358.6 (0.02)
Passed bias filter:                      117  (0.00652574); expected 358.6 (0.02)
Passed Vit filter:                         1  (5.57756e-05); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.50
# Mc/sec: 321.84
//
Query:       gi|313116833|ref|YP_004037957.1|  [L=77]
Description: hypothetical protein Hbor_32910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 568.51
//
Query:       gi|313116834|ref|YP_004037958.1|  [L=678]
Description: HEAT repeat protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-34  116.0  47.4    3.4e-11   43.4   3.2    8.0  8  HEAT_2          HEAT repeats
    1.5e-22   79.9   0.0    1.4e-05   23.9   0.0    5.3  6  Adaptin_N       Adaptin N terminal region
    1.9e-22   80.0   0.3    2.6e-05   24.3   0.1    5.4  5  Cnd1            non-SMC mitotic condensation complex subunit 
    1.3e-21   74.8  17.7    0.00037   20.5   0.1    9.7 10  HEAT            HEAT repeat
    2.7e-21   75.7  41.0    2.7e-06   27.7   2.3   11.3 14  HEAT_EZ         HEAT-like repeat
    1.2e-08   34.9  48.8      0.012   16.2   0.7   11.0  9  HEAT_PBS        PBS lyase HEAT-like repeat
    3.9e-07   30.0   0.7       0.22   11.2   0.0    4.2  4  DNA_alkylation  DNA alkylation repair enzyme
    3.3e-05   24.0   0.1        1.7    8.9   0.0    5.0  4  RTP1_C1         Required for nuclear transport of RNA pol II 
    5.7e-05   23.6   0.0        6.4    7.4   0.0    4.4  5  Vac14_Fab1_bd   Vacuolar 14 Fab1-binding region
      0.001   17.8   0.0         11    4.5   0.0    4.2  4  Ecm29           Proteasome stabiliser
     0.0045   17.0   9.0       0.54   10.4   0.0    6.9  7  Arm             Armadillo/beta-catenin-like repeat
     0.0074   15.2   4.0        9.2    5.0   0.1    4.1  4  API5            Apoptosis inhibitory protein 5 (API5)
     0.0076   16.2   0.1          5    7.0   0.0    4.2  3  DUF3385         Domain of unknown function (DUF3385)
     0.0088   16.3   1.1         36    4.7   0.0    5.3  6  dsDNA_bind      Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.014   14.9   0.0        4.5    6.6   0.0    3.2  3  DUF5578         Family of unknown function (DUF5578)
      0.018   14.6   0.1        1.2    8.6   0.0    2.9  3  CLASP_N         CLASP N terminal
      0.026   15.4   0.0      0.082   13.8   0.0    1.8  1  CDC37_N         Cdc37 N terminal kinase binding
      0.029   13.5   1.0        3.8    6.5   0.2    3.0  3  MMS19_C         RNAPII transcription regulator C-terminal
      0.045   13.5   0.3         13    5.5   0.0    3.2  3  TIP120          TATA-binding protein interacting (TIP20)
      0.048   13.4   2.6         12    5.5   0.0    3.8  4  DUF4042         Domain of unknown function (DUF4042)
       0.46   10.8  10.4         18    5.7   0.1    5.4  5  Cohesin_HEAT    HEAT repeat associated with sister chromatid 
       0.46   10.6   2.6         64    3.7   0.1    4.2  4  DUF3560         Domain of unknown function (DUF3560)
        5.1    6.9   7.7        1.9    8.3   1.0    3.0  3  FdhE            Protein involved in formate dehydrogenase for


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   6.9e-06    0.0054       3      87 ..      35     126 ..      33     127 .. 0.70
   2 !   21.8   1.9   2.4e-07   0.00019       5      87 ..      71     161 ..      66     162 .. 0.77
   3 ?    6.8   2.5     0.011       8.7       8      86 ..     148     230 ..     141     232 .. 0.73
   4 !   24.5   0.2   3.4e-08   2.7e-05       2      64 ..     251     325 ..     250     330 .. 0.84
   5 !    9.8   0.3    0.0013         1      32      77 ..     328     379 ..     323     387 .. 0.81
   6 !   24.6   1.5   3.1e-08   2.4e-05       9      88 .]     407     495 ..     403     495 .. 0.81
   7 !   25.5   2.8   1.7e-08   1.3e-05       5      61 ..     476     537 ..     472     549 .. 0.73
   8 !   43.4   3.2   4.3e-14   3.4e-11       5      87 ..     549     644 ..     545     645 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.9e-06
                            HEAT_2   3 aLlqalendpdpevrraairaLgrign..pealpaLvellededpavRraaaeaLgaig......dpealpaLkell 71 
                                       aL+++l        ++aa+  + +  n  +++  aL ++l +e +++R +a + L +i+      ++ ++++L+e l
  gi|313116834|ref|YP_004037958.1|  35 ALCALLDGRHGRSDAHAALSKISSHPNctRRVAVALQPYLVHETRRTRDEALDMLTWIArtdpnaLDTTIEWLLEHL 111
                                       66666633333456677777777554322689999***********************744332246689******* PP

                            HEAT_2  72 ddddddvvReaAaeaL 87 
                                       d++d+   R  ++ +L
  gi|313116834|ref|YP_004037958.1| 112 DTEDEHM-RDTSVTSL 126
                                       8776665.66667666 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.4e-07
                            HEAT_2   5 lqalendpdpevrraairaLgrignp......ealpaLvellededpavRraaaeaLgaigdpe......alpaLke 69 
                                         +l  ++   +r +a++ L +i+ +      +++++L+e l++ed++ R + +++L ++++ e       ++aL  
  gi|313116834|ref|YP_004037958.1|  71 QPYL-VHETRRTRDEALDMLTWIARTdpnaldTTIEWLLEHLDTEDEHMRDTSVTSLRKLAEAEpvllrpHVDALIG 146
                                       5567.5888999*********9988755666666**************************97664443334555555 PP

                            HEAT_2  70 llddddddvvReaAaeaL 87 
                                       +l   ddd vR+ A++ L
  gi|313116834|ref|YP_004037958.1| 147 SL---DDDAVRANAISLL 161
                                       55...5678899988765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.011
                            HEAT_2   8 lendpdpevrraairaLgrign..pealpaLve.ll.ededpavRraaa.eaLgaig..dpealpaLkelldddddd 77 
                                       l    d++vr++ai  L +i +  pea++  ++ l+  ++d+ + + a+   Lg ++  +p+ ++   e+l++d  +
  gi|313116834|ref|YP_004037958.1| 148 L---DDDAVRANAISLLSTISHayPEAIAPARDeLIaLSADETIDASAIpSPLGTVAlvRPDIIDPVVEMLREDLAA 221
                                       4...6889**********77552378887777756656789999999994457766633699999999999999888 PP

                            HEAT_2  78 vvReaAaea 86 
                                         R +A ++
  gi|313116834|ref|YP_004037958.1| 222 AERDQARIG 230
                                       888888765 PP

  == domain 4  score: 24.5 bits;  conditional E-value: 3.4e-08
                            HEAT_2   2 daLlqalendpdpe....vrraairaLg..rignpea....lpaLvellededpavRraaaeaLgaigd..peal 64 
                                       + Ll+++e+dpd+      r  ++  Lg    ++pe+    l+ L+ ll+d++++vR  a+e+Lg i++  p+a+
  gi|313116834|ref|YP_004037958.1| 251 EELLSLAETDPDDRspdiDRSVVLSFLGgiGVAHPETvvpeLDRLRALLDDDNRMVRSSAVETLGNIATvrPAAV 325
                                       78999999988887777789999999**5555799999999**************************96446655 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.0013
                            HEAT_2  32 alpaLvellededpavRraaaeaLgaig......dpealpaLkelldddddd 77 
                                       a++ +v   +d++++ +  +++aLg+i+       p++++ L +++ dd+ +
  gi|313116834|ref|YP_004037958.1| 328 AIDDIVARFDDTSEDLQFDVVTALGKIAaadpeiAPRVVAKLHDWFEDDTAE 379
                                       5777888889*****************7554444488999999999988764 PP

  == domain 6  score: 24.6 bits;  conditional E-value: 3.1e-08
                            HEAT_2   9 endpdpevrraairaLgri..gnpealpaLvelled..edpavRraaaeaLgaig..dpe....alpaLkelldddd 75 
                                       ++d +++++  +ira gri  ++p+al+ + + ++   +d++  ++aa aLg+ig  +pe    a++ L+ell++ +
  gi|313116834|ref|YP_004037958.1| 407 HDDFEWQLQEDIIRAYGRIgaATPDALDPVMDEIRAclADENLSAEAAAALGEIGgvRPEtvapAVEDLQELLAEGP 483
                                       579999***********8833578998888887743359999************95534466679************ PP

                            HEAT_2  76 ddvvReaAaeaLa 88 
                                        + +R aAa+aL+
  gi|313116834|ref|YP_004037958.1| 484 YWNRR-AAASALG 495
                                       ***66.6788885 PP

  == domain 7  score: 25.5 bits;  conditional E-value: 1.7e-08
                            HEAT_2   5 lqalendpdpevrraairaLgrignpea......lpaLvellededpavRraaaeaLgaigdp 61 
                                        ++l     +  rraa+ aLg+ig          ++ L   l d++ +vR+aaaeaLg i++ 
  gi|313116834|ref|YP_004037958.1| 476 QELL-AEGPYWNRRAAASALGTIGAAAPemaelvVDDLQHRLADSNYRVRAAAAEALGTIATT 537
                                       4444.6667778999999999877653333566799999999999999999999999988753 PP

  == domain 8  score: 43.4 bits;  conditional E-value: 4.3e-14
                            HEAT_2   5 lqalendpdpevrraairaLgrignp......ealpaLvellededpavRraaaeaLgaig......dpealpaLke 69 
                                       +q+l +d +++vr+aa++aLg++g        ++++ L   l+d+d++vR  aa+aL+aig      +  a++aL+ 
  gi|313116834|ref|YP_004037958.1| 549 VQLLLDDDEWKVRAAALEALGQMGAAdrdtaeRVVEDLQTGLRDTDSDVRPSAANALAAIGvsqpvlTATAVEALES 625
                                       58899****************9876555666688***************************666665577******* PP

                            HEAT_2  70 llddddd.dvvReaAaeaL 87 
                                       ++  d++  +vR ++ae+L
  gi|313116834|ref|YP_004037958.1| 626 RFECDEEyLFVRSSIAEGL 644
                                       **98887369999999988 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   9.4e-06    0.0073     343     445 ..      69     167 ..      51     189 .. 0.82
   2 ?    1.9   0.0     0.084        65     329     388 ..     200     259 ..     149     265 .. 0.67
   3 !   23.9   0.0   1.8e-08   1.4e-05      93     240 ..     267     444 ..     238     452 .. 0.74
   4 ?    3.6   0.0     0.025        19     108     165 ..     429     483 ..     414     497 .. 0.83
   5 !   20.6   0.1   1.8e-07   0.00014      99     177 ..     490     569 ..     485     571 .. 0.91
   6 !   17.6   0.0   1.5e-06    0.0012      92     170 ..     557     637 ..     553     660 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.4e-06
                                       HHHHHTTSSXXHHHHHHHHHHHHHHHHHSCCHHHHHHHHHHHHHTTXXHHHHHHHHHHHHHHHHHSTTTSTTCHHHH CS
                         Adaptin_N 343 eLkkyvkevadedfksklvkaIgrlaekfatdaewvldvllellslsgesvkdeivevirdliqkvpelheeiiekL 419
                                        L+ y+  + ++  ++++++ +  +a + ++  ++ +++lle+l +++e+++d +v ++r+l +  p l +  +  L
  gi|313116834|ref|YP_004037958.1|  69 ALQPYL-VHETRRTRDEALDMLTWIARTDPNALDTTIEWLLEHLDTEDEHMRDTSVTSLRKLAEAEPVLLRPHVDAL 144
                                       578888.44456699****************************************************9988888877 PP

                                       CCTCCGXXSHHHHHHHHHHHHHTTTT CS
                         Adaptin_N 420 aellekieseearaaaiWllGeygel 445
                                       +  l++    ++ra+ai ll  ++  
  gi|313116834|ref|YP_004037958.1| 145 IGSLDD---DAVRANAISLLSTISHA 167
                                       777765...56666666666666655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.084
                                       CCCXXTTTHHHHHHHHHHHTTSSXXHH.HHHHHHHHHHHHHHHSCCHHHHHHHHHHHHHTT CS
                         Adaptin_N 329 lklvdesNvkeivkeLkkyvkevaded.fksklvkaIgrlaekfatdaewvldvllellsl 388
                                       ++lv  + ++ +v+ L + ++ + ++d  ++ + +a+gr+a++++++a  v++ ll l ++
  gi|313116834|ref|YP_004037958.1| 200 VALVRPDIIDPVVEMLREDLAAA-ERDqARIGIGSALGRIAVAYPESAPMVVEELLSLAET 259
                                       46777778888999999999555.5554999999**************9999999999875 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 1.8e-08
                                       HHHHHHHHHHHCCC-..-CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHH CS
                         Adaptin_N  93 qlirglALrvLssir..vpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpg 167
                                       ++ r++ L++L+ i+   pe++   ++ +++ll d++ +vr++A+ ++  +  + p ++r+  +++i+  ++d++  
  gi|313116834|ref|YP_004037958.1| 267 DIDRSVVLSFLGGIGvaHPETVVPELDRLRALLDDDNRMVRSSAVETLGNIATVRPAAVRPA-IDDIVARFDDTSED 342
                                       56789999****99977799999999***********************************9.************** PP

                                       HHHHHHHHHHHHHCCCCCCCHHHHHHHCCHHHHH.................................HCS-HH.HHH CS
                         Adaptin_N 168 vvlaAvalleeikkndrlllkllpklvrrLcnll.................................teldpw.lqv 210
                                       ++  +v++l +i    +   +++p  v +L + +                                 ++  +w lq 
  gi|313116834|ref|YP_004037958.1| 343 LQFDVVTALGKI-AAADP--EIAPRVVAKLHDWFeddtaedeavgsdateyglfdltgsvedenaatHDDFEWqLQE 416
                                       ************.66666..688888888877766666666666666666666666666666666554444443455 PP

                                       HHHHHHCC---SSHHHH..HHHHHHHCGGC CS
                         Adaptin_N 211 kiiklltrlarqepeerskkellesllnll 240
                                        ii+   r  + +p++   + +++++ ++l
  gi|313116834|ref|YP_004037958.1| 417 DIIRAYGRIGAATPDAL--DPVMDEIRACL 444
                                       55555555555555555..45555555555 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.025
                                       -CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SS CS
                         Adaptin_N 108 vpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkd 165
                                       +p+ ++ ++++i+++l d++  ++ +Aa a+  +  + p+ + +  ve+++ell++  
  gi|313116834|ref|YP_004037958.1| 429 TPDALDPVMDEIRACLADEN--LSAEAAAALGEIGGVRPETVAPA-VEDLQELLAEGP 483
                                       7888999**********986..899*******************8.********9865 PP

  == domain 5  score: 20.6 bits;  conditional E-value: 1.8e-07
                                       HHHHHCCC-..-CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHH CS
                         Adaptin_N  99 ALrvLssir..vpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAv 173
                                       A ++L++i+   pe+ae ++++++  l d++  vr +Aa a+ ++   d+d   + + ee++ ll+d++ +v +aA+
  gi|313116834|ref|YP_004037958.1| 490 AASALGTIGaaAPEMAELVVDDLQHRLADSNYRVRAAAAEALGTIATTDSDVAAR-VSEEVQLLLDDDEWKVRAAAL 565
                                       667888888779****************************************988.6******************** PP

                                       HHHH CS
                         Adaptin_N 174 alle 177
                                        +l 
  gi|313116834|ref|YP_004037958.1| 566 EALG 569
                                       9985 PP

  == domain 6  score: 17.6 bits;  conditional E-value: 1.5e-06
                                       SHHHHHHHHHHHCCC-..-CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCT.T-SS CS
                         Adaptin_N  92 nqlirglALrvLssir..vpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikell.sdkd 165
                                       +  +r+ AL +L++++  ++++ae +++++++ l+d+++ vr +Aa a++++  ++p l     ve +++ +  d++
  gi|313116834|ref|YP_004037958.1| 557 EWKVRAAALEALGQMGaaDRDTAERVVEDLQTGLRDTDSDVRPSAANALAAIGVSQPVLTATA-VEALESRFeCDEE 632
                                       55789***********9999********************************99999998777.9999888855666 PP

                                       HHHHH CS
                         Adaptin_N 166 pgvvl 170
                                       ++ v+
  gi|313116834|ref|YP_004037958.1| 633 YLFVR 637
                                       65555 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.4e-06    0.0073      16      95 ..      97     174 ..      82     191 .. 0.88
   2 !   18.3   0.0   2.3e-06    0.0018      60     145 ..     292     373 ..     270     383 .. 0.82
   3 ?    3.1   0.0      0.11        89      14      36 ..     428     450 ..     417     476 .. 0.81
   4 !   24.3   0.1   3.4e-08   2.6e-05       8      86 ..     492     572 ..     487     579 .. 0.87
   5 !   10.7   0.0    0.0005      0.39      18      55 ..     578     615 ..     575     655 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.4e-06
                              Cnd1  16 pnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseksena 92 
                                       pn ++ ++e L + L  ed++ R t +  + kL +++ v  + +++ l   l+D+   V+ana+++l+ is+  ++a
  gi|313116834|ref|YP_004037958.1|  97 PNALDTTIEWLLEHLDTEDEHMRDTSVTSLRKLAEAEPVLLRPHVDALIGSLDDD--AVRANAISLLSTISHAYPEA 171
                                       789999**********************************************986..7*************997777 PP

                              Cnd1  93 iyn 95 
                                       i  
  gi|313116834|ref|YP_004037958.1| 172 IAP 174
                                       755 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.3e-06
                              Cnd1  60 lselaklleDenprVvanalaalteiseksenaiynllpdiisklsdalnecsewgqitilefLlsyipkdkqeaes 136
                                       l++l+ ll+D+n++V+++a+  l +i++  + a+     di+ ++     + se+ q  ++++L +  + d + a  
  gi|313116834|ref|YP_004037958.1| 292 LDRLRALLDDDNRMVRSSAVETLGNIATVRPAAVRPAIDDIVARFD----DTSEDLQFDVVTALGKIAAADPEIAPR 364
                                       6889999999999999999999999999999999999999999998....679999999999999999998887777 PP

                              Cnd1 137 lveklcprl 145
                                       +v kl + +
  gi|313116834|ref|YP_004037958.1| 365 VVAKLHDWF 373
                                       777777665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.11
                              Cnd1  14 rvpnlveylvepLrkrLkDedpy 36 
                                         p+ ++++++++r++L De+  
  gi|313116834|ref|YP_004037958.1| 428 ATPDALDPVMDEIRACLADENLS 450
                                       56889999***********9976 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 3.4e-08
                              Cnd1   8 rtlg..cirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaal 82 
                                        +lg      p++ e +v++L++rL D++  VR  aa ++  + + d      + +e++ ll+D++ +V+a al al
  gi|313116834|ref|YP_004037958.1| 492 SALGtiGAAAPEMAELVVDDLQHRLADSNYRVRAAAAEALGTIATTDSDVAARVSEEVQLLLDDDEWKVRAAALEAL 568
                                       555544446799*******************************9999999999**********************99 PP

                              Cnd1  83 teis 86 
                                        ++ 
  gi|313116834|ref|YP_004037958.1| 569 GQMG 572
                                       8775 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.0005
                              Cnd1  18 lveylvepLrkrLkDedpyVRktaaivvakLilndmvk 55 
                                       + e +ve+L+++L+D+d+ VR  aa ++a +   + v 
  gi|313116834|ref|YP_004037958.1| 578 TAERVVEDLQTGLRDTDSDVRPSAANALAAIGVSQPVL 615
                                       57899********************9999884444444 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.6   4.6e+02       6      29 ..     108     131 ..     107     132 .. 0.80
   2 ?    3.2   0.0      0.18   1.4e+02       7      28 ..     143     165 ..     137     167 .. 0.75
   3 !   17.0   0.1   6.5e-06     0.005       3      29 ..     293     319 ..     292     321 .. 0.89
   4 ?   -2.3   0.0       9.9   7.7e+03      10      28 ..     337     355 ..     332     356 .. 0.75
   5 ?   -2.1   0.1       8.5   6.6e+03      19      27 ..     452     460 ..     437     462 .. 0.73
   6 ?    5.2   0.0     0.038        30       7      27 ..     477     497 ..     473     500 .. 0.77
   7 !   20.5   0.1   4.7e-07   0.00037       5      28 ..     512     535 ..     508     537 .. 0.91
   8 !   20.3   0.1   5.6e-07   0.00044       7      27 ..     551     571 ..     548     573 .. 0.87
   9 !    8.5   0.0    0.0034       2.7       5      27 ..     586     608 ..     582     610 .. 0.91
  10 ?    0.6   0.0       1.2   9.5e+02      10      27 ..     629     647 ..     620     649 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.6
                                       HHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   6 lkllsDpspeVReaAakaLgalae 29 
                                       l+ l  ++ + R++++ +L +lae
  gi|313116834|ref|YP_004037958.1| 108 LEHLDTEDEHMRDTSVTSLRKLAE 131
                                       66775577778**********997 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                                       HHHT-.SSHHHHHHHHHHHHHHH CS
                              HEAT   7 kllsD.pspeVReaAakaLgala 28 
                                        l+ + ++  VR++A+  L +++
  gi|313116834|ref|YP_004037958.1| 143 ALIGSlDDDAVRANAISLLSTIS 165
                                       5555557889*********9985 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 6.5e-06
                                       HHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgalae 29 
                                       + l  ll D++  VR++A+++Lg++a 
  gi|313116834|ref|YP_004037958.1| 293 DRLRALLDDDNRMVRSSAVETLGNIAT 319
                                       5678899******************97 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 9.9
                                       T-SSHHHHHHHHHHHHHHH CS
                              HEAT  10 sDpspeVReaAakaLgala 28 
                                        D+s +    ++ aLg++a
  gi|313116834|ref|YP_004037958.1| 337 DDTSEDLQFDVVTALGKIA 355
                                       67777777778999**998 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 8.5
                                       HHHHHHHHH CS
                              HEAT  19 aAakaLgal 27 
                                        Aa aLg++
  gi|313116834|ref|YP_004037958.1| 452 EAAAALGEI 460
                                       478888887 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.038
                                       HHH.T-SSHHHHHHHHHHHHHH CS
                              HEAT   7 kll.sDpspeVReaAakaLgal 27 
                                       +ll + p ++ R+aAa aLg++
  gi|313116834|ref|YP_004037958.1| 477 ELLaEGPYWN-RRAAASALGTI 497
                                       5554447788.*********99 PP

  == domain 7  score: 20.5 bits;  conditional E-value: 4.7e-07
                                       HHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgala 28 
                                       l++ l D++ +VR+aAa+aLg++a
  gi|313116834|ref|YP_004037958.1| 512 LQHRLADSNYRVRAAAAEALGTIA 535
                                       7889*******************8 PP

  == domain 8  score: 20.3 bits;  conditional E-value: 5.6e-07
                                       HHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   7 kllsDpspeVReaAakaLgal 27 
                                        ll D++++VR+aA++aLg++
  gi|313116834|ref|YP_004037958.1| 551 LLLDDDEWKVRAAALEALGQM 571
                                       467****************98 PP

  == domain 9  score: 8.5 bits;  conditional E-value: 0.0034
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       l++ l+D++++VR +Aa+aL+a+
  gi|313116834|ref|YP_004037958.1| 586 LQTGLRDTDSDVRPSAANALAAI 608
                                       7889*****************98 PP

  == domain 10  score: 0.6 bits;  conditional E-value: 1.2
                                       T-SSHH.HHHHHHHHHHHH CS
                              HEAT  10 sDpspe.VReaAakaLgal 27 
                                       +D++   VR++ a+ L al
  gi|313116834|ref|YP_004037958.1| 629 CDEEYLfVRSSIAEGLQAL 647
                                       6755554*******99987 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.24   1.9e+02       3      55 .]      81     129 ..      80     129 .. 0.87
   2 !   12.0   0.1    0.0003      0.23      10      55 .]     125     164 ..     118     164 .. 0.83
   3 ?    5.6   0.1     0.031        24       1      31 [.     151     181 ..     151     185 .. 0.92
   4 ?   -2.2   0.0       8.4   6.6e+03      11      27 ..     197     213 ..     197     218 .. 0.60
   5 ?    2.9   0.0      0.21   1.7e+02      10      41 ..     234     261 ..     224     264 .. 0.76
   6 !   16.6   0.1   1.1e-05    0.0086      26      55 .]     289     317 ..     273     317 .. 0.81
   7 !   14.3   0.0   5.6e-05     0.043       3      42 ..     306     340 ..     305     354 .. 0.86
   8 ?    2.3   0.1      0.33   2.6e+02       3      34 ..     320     352 ..     318     368 .. 0.55
   9 ?    6.1   0.3      0.02        16       1      49 [.     412     455 ..     412     455 .. 0.89
  10 !    9.3   0.5    0.0021       1.6       6      34 ..     452     480 ..     451     483 .. 0.92
  11 !   27.7   2.3   3.5e-09   2.7e-06       3      55 .]     486     534 ..     485     534 .. 0.95
  12 !   13.9   0.2   7.6e-05     0.059      34      55 .]     549     571 ..     537     571 .. 0.78
  13 !   17.7   0.9   4.9e-06    0.0038       1      55 []     558     608 ..     558     608 .. 0.89
  14 ?    5.0   0.2     0.048        37       3      33 ..     597     627 ..     595     633 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.24
                           HEAT_EZ   3 vRraAawaLGr.laggepellqplvpeilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                        R  A+  L + +a   p++l + ++++l  L       +d + R +++  L++l
  gi|313116834|ref|YP_004037958.1|  81 TRDEALDML-TwIARTDPNALDTTIEWLLEHLD-----TEDeHMRDTSVTSLRKL 129
                                       577788888.7888889999*************.....999899*****999886 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0003
                           HEAT_EZ  10 aLGr.laggepellqplvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                        L r la+ ep ll+p+v++++  L       +d+VRa+A+  L+ +
  gi|313116834|ref|YP_004037958.1| 125 SL-RkLAEAEPVLLRPHVDALIGSLD------DDAVRANAISLLSTI 164
                                       56.34999***********8888887......9********999865 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.031
                           HEAT_EZ   1 wrvRraAawaLGrlaggepellqplvpeilp 31 
                                       ++vR++A++ L+++    pe+++p+ +e+++
  gi|313116834|ref|YP_004037958.1| 151 DAVRANAISLLSTISHAYPEAIAPARDELIA 181
                                       589*************************997 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 8.4
                           HEAT_EZ  11 LGrlaggepellqplvp 27 
                                       LG++a ++p+ + p+v+
  gi|313116834|ref|YP_004037958.1| 197 LGTVALVRPDIIDPVVE 213
                                       56666666666666553 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.21
                           HEAT_EZ  10 aLGrlaggepellqplvpeilpaLlalLndds 41 
                                       aLGr+a+  pe  +     ++ +Ll+l ++d+
  gi|313116834|ref|YP_004037958.1| 234 ALGRIAVAYPESAP----MVVEELLSLAETDP 261
                                       99999999999999....56666666665554 PP

  == domain 6  score: 16.6 bits;  conditional E-value: 1.1e-05
                           HEAT_EZ  26 vpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       vp  l+ L alL dd+ +VR  A+ +Lgn+
  gi|313116834|ref|YP_004037958.1| 289 VP-ELDRLRALLDDDNRMVRSSAVETLGNI 317
                                       33.678899*******************98 PP

  == domain 7  score: 14.3 bits;  conditional E-value: 5.6e-05
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsd 42 
                                       vR +A+ +LG++a ++p +++p++++i++ +      d +
  gi|313116834|ref|YP_004037958.1| 306 VRSSAVETLGNIATVRPAAVRPAIDDIVARFD-----DTS 340
                                       899***************************99.....655 PP

  == domain 8  score: 2.3 bits;  conditional E-value: 0.33
                           HEAT_EZ   3 vRraAaw.aLGrlaggepellqplvpeilpaLl 34 
                                       vR aA++ a+  + +  +++ ++l+ +++ aL+
  gi|313116834|ref|YP_004037958.1| 320 VRPAAVRpAIDDIVARFDDTSEDLQFDVVTALG 352
                                       444555555544444444445555555555554 PP

  == domain 9  score: 6.1 bits;  conditional E-value: 0.02
                           HEAT_EZ   1 wrvRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAa 49 
                                       w++++  ++a Gr+ +  p++l p+ +ei ++L+     d+ +  +aAa
  gi|313116834|ref|YP_004037958.1| 412 WQLQEDIIRAYGRIGAATPDALDPVMDEIRACLA-----DENLSAEAAA 455
                                       9999*********8888****************9.....9987766665 PP

  == domain 10  score: 9.3 bits;  conditional E-value: 0.0021
                           HEAT_EZ   6 aAawaLGrlaggepellqplvpeilpaLl 34 
                                        Aa+aLG++ g++pe+++p+v+++  +L+
  gi|313116834|ref|YP_004037958.1| 452 EAAAALGEIGGVRPETVAPAVEDLQELLA 480
                                       69*********************998887 PP

  == domain 11  score: 27.7 bits;  conditional E-value: 3.5e-09
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       +RraAa+aLG++ + +pe  +++v+++   L+     ds  +VRaaAa aLg +
  gi|313116834|ref|YP_004037958.1| 486 NRRAAASALGTIGAAAPEMAELVVDDLQHRLA-----DSNyRVRAAAAEALGTI 534
                                       7**********8888*****************.....**************976 PP

  == domain 12  score: 13.9 bits;  conditional E-value: 7.6e-05
                           HEAT_EZ  34 lalLnddsd.eVRaaAagaLgnl 55 
                                       ++lL dd+  +VRaaA+ aLg++
  gi|313116834|ref|YP_004037958.1| 549 VQLLLDDDEwKVRAAALEALGQM 571
                                       566777777************97 PP

  == domain 13  score: 17.7 bits;  conditional E-value: 4.9e-06
                           HEAT_EZ   1 wrvRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       w vR+aA+ aLG + +  +++ + +v+++   L      d d +VR  Aa aL+++
  gi|313116834|ref|YP_004037958.1| 558 WKVRAAALEALGQMGAADRDTAERVVEDLQTGLR-----DTDsDVRPSAANALAAI 608
                                       99**********9777799999988888888888.....8888**********986 PP

  == domain 14  score: 5.0 bits;  conditional E-value: 0.048
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaL 33 
                                       vR +Aa+aL+++ +  p l +++v+++   +
  gi|313116834|ref|YP_004037958.1| 597 VRPSAANALAAIGVSQPVLTATAVEALESRF 627
                                       8999999999999999999999998876665 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.83   6.5e+02       1      16 [.     153     174 ..     153     185 .. 0.74
   2 ?    7.4   0.0     0.011       8.4       1      23 [.     306     334 ..     306     338 .. 0.79
   3 ?    0.8   0.0       1.5   1.2e+03       5      19 ..     347     367 ..     343     371 .. 0.68
   4 !   10.8   0.6   0.00088      0.69       4      26 ..     452     480 ..     451     481 .. 0.94
   5 !   11.8   0.6   0.00041      0.32       2      21 ..     487     512 ..     487     518 .. 0.72
   6 !   10.7   0.2    0.0009       0.7       1      14 [.     523     536 ..     523     553 .. 0.85
   7 !   16.2   0.7   1.6e-05     0.012       1      27 []     560     592 ..     560     592 .. 0.96
   8 ?    4.3   0.1      0.11        84       4      21 ..     600     623 ..     597     628 .. 0.82
   9 ?    0.5   0.0       1.8   1.4e+03       1      14 [.     636     649 ..     636     667 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHCTS......GG CS
                          HEAT_PBS   1 vRraAakaLgqlgd......ee 16 
                                       vR++A+  L ++ +        
  gi|313116834|ref|YP_004037958.1| 153 VRANAISLLSTISHaypeaiAP 174
                                       89************99544444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHCTS......GGGHHHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgd......eeaipaLle 23 
                                       vR +A++ Lg++ +        ai+ +++
  gi|313116834|ref|YP_004037958.1| 306 VRSSAVETLGNIATvrpaavRPAIDDIVA 334
                                       9*************997777666666655 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.5
                                       HHHHHHHCTS......GGGHH CS
                          HEAT_PBS   5 AakaLgqlgd......eeaip 19 
                                        + aLg++ +      +++++
  gi|313116834|ref|YP_004037958.1| 347 VVTALGKIAAadpeiaPRVVA 367
                                       578******999444444444 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00088
                                       HHHHHHHHCTS......GGGHHHHHHHCT CS
                          HEAT_PBS   4 aAakaLgqlgd......eeaipaLleaLq 26 
                                       +Aa aLg++g         a++ L+e+L+
  gi|313116834|ref|YP_004037958.1| 452 EAAAALGEIGGvrpetvAPAVEDLQELLA 480
                                       8*************************996 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00041
                                       HHHHHHHHHHCTS......GGGHHHH CS
                          HEAT_PBS   2 RraAakaLgqlgd......eeaipaL 21 
                                       RraAa aLg++g+      e +++ L
  gi|313116834|ref|YP_004037958.1| 487 RRAAASALGTIGAaapemaELVVDDL 512
                                       9***********96655555555555 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.0009
                                       HHHHHHHHHHHCTS CS
                          HEAT_PBS   1 vRraAakaLgqlgd 14 
                                       vR+aAa+aLg++ +
  gi|313116834|ref|YP_004037958.1| 523 VRAAAAEALGTIAT 536
                                       9***********98 PP

  == domain 7  score: 16.2 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHCTS......GGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgd......eeaipaLleaLqd 27 
                                       vR+aA++aLgq+g+      e++++ L+  L d
  gi|313116834|ref|YP_004037958.1| 560 VRAAALEALGQMGAadrdtaERVVEDLQTGLRD 592
                                       9***************************99876 PP

  == domain 8  score: 4.3 bits;  conditional E-value: 0.11
                                       HHHHHHHHCTS......GGGHHHH CS
                          HEAT_PBS   4 aAakaLgqlgd......eeaipaL 21 
                                       +Aa aL+++g         a++aL
  gi|313116834|ref|YP_004037958.1| 600 SAANALAAIGVsqpvltATAVEAL 623
                                       8*********98888888888887 PP

  == domain 9  score: 0.5 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHCTS CS
                          HEAT_PBS   1 vRraAakaLgqlgd 14 
                                       vR + a++L +l++
  gi|313116834|ref|YP_004037958.1| 636 VRSSIAEGLQALNT 649
                                       89********9998 PP

>> DNA_alkylation  DNA alkylation repair enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.04        31     140     196 ..      85     143 ..      17     162 .. 0.84
   2 ?    0.8   0.0      0.45   3.5e+02     161     201 ..     296     336 ..     287     341 .. 0.84
   3 !   11.2   0.0   0.00029      0.22     123     188 ..     473     540 ..     466     547 .. 0.88
   4 !    8.3   0.0    0.0021       1.7     128     196 ..     551     622 ..     543     642 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.04
                    DNA_alkylation 140 Aivatlklikk..tdlellleiaeelladkedfiqkAiGwaLrelsktdpdlveeFlek 196
                                       A+ ++++ ++   + l++++e++ e+l+ +++ ++      Lr+l++  p l++  +++
  gi|313116834|ref|YP_004037958.1|  85 ALDMLTWIARTdpNALDTTIEWLLEHLDTEDEHMRDTSVTSLRKLAEAEPVLLRPHVDA 143
                                       55555555555899999****************************99999888877765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.45
                    DNA_alkylation 161 eelladkedfiqkAiGwaLrelsktdpdlveeFlekhakrm 201
                                        +ll+d + +++ +   +L +++   p++v+ +++   +r+
  gi|313116834|ref|YP_004037958.1| 296 RALLDDDNRMVRSSAVETLGNIATVRPAAVRPAIDDIVARF 336
                                       67999999999999999999999999999999998866665 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00029
                    DNA_alkylation 123 dllkeWaksenlWerRaAivatlklikk..tdlellleiaeelladkedfiqkAiGwaLrelsktdpd 188
                                       + l+e+ +    W rRaA++a+ +   +  + +el+++ ++  lad++ +++ A + aL  ++ td d
  gi|313116834|ref|YP_004037958.1| 473 EDLQELLAEGPYWNRRAAASALGTIGAAapEMAELVVDDLQHRLADSNYRVRAAAAEALGTIATTDSD 540
                                       56889999999*******988655555566***********************************987 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0021
                    DNA_alkylation 128 WaksenlWerRaAivatlklikk...tdlellleiaeelladkedfiqkAiGwaLrelsktdpdlveeFlek 196
                                       +  ++++W+ RaA++  l    +   + +e+++e +++ l d +  ++ + ++aL +++  +p l   ++e+
  gi|313116834|ref|YP_004037958.1| 551 LLLDDDEWKVRAAALEALGQMGAadrDTAERVVEDLQTGLRDTDSDVRPSAANALAAIGVSQPVLTATAVEA 622
                                       567899999999986555544442227777777777788999999999999999999999999888888876 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.12        90      16      72 ..      82     134 ..      73     144 .. 0.82
   2 ?    3.8   0.0     0.083        65       6      77 ..     109     174 ..     105     191 .. 0.77
   3 ?    3.2   0.0      0.13        99      46      96 ..     296     349 ..     283     357 .. 0.74
   4 !    8.9   0.0    0.0022       1.7       4      72 ..     549     613 ..     509     658 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                           RTP1_C1  16 rahglvlLrkliekkskeavldiekilkllleaLkdedsYvYLnaikgLvaLadvfp 72 
                                       r ++l +L+ ++++        ++++++ lle+L  ed+ +   ++  L +La++ p
  gi|313116834|ref|YP_004037958.1|  82 RDEALDMLTWIARTD----PNALDTTIEWLLEHLDTEDEHMRDTSVTSLRKLAEAEP 134
                                       667777777766665....5788999*************999999999999998865 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.083
                           RTP1_C1   6 kdlqdpllpvrahglvlLrkliekkskeavldiekilkllleaLkdedsYvYLnaikgLvaLadvfpeevlk 77 
                                       ++l  +  ++r   +++Lrkl+e++   +vl  ++ ++ l+ +L d+   v  nai++L+++ +++pe + +
  gi|313116834|ref|YP_004037958.1| 109 EHLDTEDEHMRDTSVTSLRKLAEAE---PVLLRPH-VDALIGSLDDD--AVRANAISLLSTISHAYPEAIAP 174
                                       5566666778888888888888888...4555555.46667777544..58999999999999999998876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.13
                           RTP1_C1  46 leaLkdedsYvYLnaikgLvaLadvfpeev...lklLleeyeeenekeslderl 96 
                                          L d++  v  +a+++L ++a+v p+ v   ++ +++++ +++e+ + d   
  gi|313116834|ref|YP_004037958.1| 296 RALLDDDNRMVRSSAVETLGNIATVRPAAVrpaIDDIVARFDDTSEDLQFDVVT 349
                                       55678888899999***********99988222445666667777777777655 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0022
                           RTP1_C1   4 alkdlqdpllpvrahglvlLrkliekkskeavldiekilkllleaLkdedsYvYLnaikgLvaLadvfp 72 
                                       +   l d++  vra +l  L ++  + +     ++e++++ l++ L+d+ds v  +a ++L+a++   p
  gi|313116834|ref|YP_004037958.1| 549 VQLLLDDDEWKVRAAALEALGQMGAADR----DTAERVVEDLQTGLRDTDSDVRPSAANALAAIGVSQP 613
                                       5556889999999999999999988776....7889999999999999999999999999999876554 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       9.5   7.4e+03      23      53 ..      98     128 ..      92     136 .. 0.81
   2 !    7.4   0.0    0.0083       6.4      35      84 ..     298     347 ..     285     355 .. 0.81
   3 !    7.3   0.0    0.0089       6.9      16      60 ..     496     540 ..     488     565 .. 0.75
   4 ?    3.3   0.0      0.16   1.3e+02      35      84 ..     552     601 ..     539     610 .. 0.61
   5 ?    1.8   0.0      0.49   3.8e+02      21      54 ..     575     608 ..     560     631 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.5
                     Vac14_Fab1_bd  23 eyleeivkpvlkcfsDkdsrvRyyacEslyn 53 
                                       + l++ ++ +l+ ++ +d+++R +++ sl  
  gi|313116834|ref|YP_004037958.1|  98 NALDTTIEWLLEHLDTEDEHMRDTSVTSLRK 128
                                       5688899999999999999999888877755 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0083
                     Vac14_Fab1_bd  35 cfsDkdsrvRyyacEslyniakvakgevlkllneifdalvklvaDsdesv 84 
                                        ++D+++ vR  a+E+l nia v   +v   + +i   +   + D + +v
  gi|313116834|ref|YP_004037958.1| 298 LLDDDNRMVRSSAVETLGNIATVRPAAVRPAIDDIVARFDDTSEDLQFDV 347
                                       456666779***************99999999999888777777777666 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0089
                     Vac14_Fab1_bd  16 alekkikeyleeivkpvlkcfsDkdsrvRyyacEslyniakvakg 60 
                                       ++++++ e+ e +v+ + + + D++ rvR  a+E+l  ia +  +
  gi|313116834|ref|YP_004037958.1| 496 TIGAAAPEMAELVVDDLQHRLADSNYRVRAAAAEALGTIATTDSD 540
                                       35666889999999**********************998876554 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.16
                     Vac14_Fab1_bd  35 cfsDkdsrvRyyacEslyniakvakgevlkllneifdalvklvaDsdesv 84 
                                        ++D++ +vR  a E+l  +  + ++++ ++++++ ++l    +D+ +s 
  gi|313116834|ref|YP_004037958.1| 552 LLDDDEWKVRAAALEALGQMGAADRDTAERVVEDLQTGLRDTDSDVRPSA 601
                                       56677777777777777777777776666666666555554444443333 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.49
                     Vac14_Fab1_bd  21 ikeyleeivkpvlkcfsDkdsrvRyyacEslyni 54 
                                        ++  e++v+ + + ++D+ds vR  a+ +l  i
  gi|313116834|ref|YP_004037958.1| 575 DRDTAERVVEDLQTGLRDTDSDVRPSAANALAAI 608
                                       55677889999999999******99999888655 PP

>> Ecm29  Proteasome stabiliser
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.055        43     380     440 ..      77     134 ..      68     176 .. 0.82
   2 ?   -0.0   0.0      0.34   2.7e+02     409     454 ..     211     256 ..     196     275 .. 0.74
   3 ?    4.3   0.0     0.016        13     380     437 ..     302     356 ..     290     385 .. 0.79
   4 ?    4.5   0.0     0.014        11     359     435 ..     546     608 ..     496     670 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.055
                             Ecm29 380 aseelrslaYealGlLakrapslvredlsliefLFdsLeeeesevrvsIqeALssllsafk 440
                                       +++ +r  a   l  +a+ +p+  ++    ie+L+++L +e++ +r +   +L+ l++a +
  gi|313116834|ref|YP_004037958.1|  77 ETRRTRDEALDMLTWIARTDPNALDT---TIEWLLEHLDTEDEHMRDTSVTSLRKLAEAEP 134
                                       56678888899999999999999854...79***********9999888888888888755 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.34
                             Ecm29 409 liefLFdsLeeee.sevrvsIqeALssllsafkeleseaskekLeel 454
                                       ++e+L + L+ +e ++ r+ I +AL  ++ a++e+    + e+L +l
  gi|313116834|ref|YP_004037958.1| 211 VVEMLREDLAAAErDQARIGIGSALGRIAVAYPES-APMVVEELLSL 256
                                       5677778888888689****************998.44455555554 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.016
                             Ecm29 380 aseelrslaYealGlLakrapslvredlsliefLFdsLeeeesevrvsIqeALsslls 437
                                       +++ +rs+a e+lG++a   p+ vr  ++ i   Fd  +e+    ++ +  AL  +++
  gi|313116834|ref|YP_004037958.1| 302 DNRMVRSSAVETLGNIATVRPAAVRPAIDDIVARFDDTSEDL---QFDVVTALGKIAA 356
                                       56789*************************999998777665...5555556666555 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.014
                             Ecm29 359 lsglrklidsqgwpepeknssaseelrslaYealGlLakrapslvredlsliefLFdsLeeeesevrvsIqeALssl 435
                                        ++ + l+d+++            ++r+ a ealG++  +++++ +    ++e L + L+  +s+vr s  +AL  +
  gi|313116834|ref|YP_004037958.1| 546 SEEVQLLLDDDE-----------WKVRAAALEALGQMGAADRDTAE---RVVEDLQTGLRDTDSDVRPSAANALAAI 608
                                       444444444433...........44678889999999998888874...4888888888888888888888888766 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.7   3.7e+03      14      22 ..      33      41 ..      32      48 .. 0.76
   2 ?   -0.5   0.0       1.9   1.5e+03      17      40 ..     107     130 ..     105     131 .. 0.89
   3 ?    0.1   0.0       1.2   9.6e+02       5      22 ..     199     216 ..     195     222 .. 0.84
   4 !   10.4   0.0    0.0007      0.54      14      40 ..     292     318 ..     288     319 .. 0.94
   5 ?    2.6   0.0       0.2   1.6e+02      23      41 .]     338     356 ..     333     356 .. 0.89
   6 ?   -1.4   0.1       3.7   2.9e+03      25      39 ..     446     460 ..     445     460 .. 0.82
   7 ?    0.6   0.1      0.83   6.4e+02      21      40 ..     516     535 ..     514     536 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.7
                                      HHHHHHHTT CS
                               Arm 14 vppLvrLLs 22
                                      +++L++LL+
  gi|313116834|ref|YP_004037958.1| 33 IEALCALLD 41
                                      789999998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.9
                                       HHHHTTTSSHHHHHHHHHHHHHHT CS
                               Arm  17 LvrLLssedeevqeeAawALsNLa 40 
                                       L++ L++ede ++  +++ L+ La
  gi|313116834|ref|YP_004037958.1| 107 LLEHLDTEDEHMRDTSVTSLRKLA 130
                                       778899*********999999887 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                                       HHHHHHTTHHHHHHHHTT CS
                               Arm   5 kdavieaGavppLvrLLs 22 
                                       + a+++  +++p v++L+
  gi|313116834|ref|YP_004037958.1| 199 TVALVRPDIIDPVVEMLR 216
                                       679999**********98 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0007
                                       HHHHHHHTTTSSHHHHHHHHHHHHHHT CS
                               Arm  14 vppLvrLLssedeevqeeAawALsNLa 40 
                                       +++L +LL++++ +v+  A+ +L+N+a
  gi|313116834|ref|YP_004037958.1| 292 LDRLRALLDDDNRMVRSSAVETLGNIA 318
                                       689***********************9 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.2
                                       TSSHHHHHHHHHHHHHHTT CS
                               Arm  23 sedeevqeeAawALsNLaa 41 
                                       +++e++q+++++AL+ +aa
  gi|313116834|ref|YP_004037958.1| 338 DTSEDLQFDVVTALGKIAA 356
                                       6899***********9986 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 3.7
                                       SHHHHHHHHHHHHHH CS
                               Arm  25 deevqeeAawALsNL 39 
                                       de++  eAa+AL+ +
  gi|313116834|ref|YP_004037958.1| 446 DENLSAEAAAALGEI 460
                                       6778889*****976 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 0.83
                                       TTTSSHHHHHHHHHHHHHHT CS
                               Arm  21 LssedeevqeeAawALsNLa 40 
                                       L + + +v+ +Aa AL+ +a
  gi|313116834|ref|YP_004037958.1| 516 LADSNYRVRAAAAEALGTIA 535
                                       5678999*********9887 PP

>> API5  Apoptosis inhibitory protein 5 (API5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.043        34      89     155 ..      58     127 ..      44     143 .. 0.81
   2 ?   -0.2   0.0      0.44   3.4e+02      68     122 ..     148     199 ..     126     208 .. 0.80
   3 ?    4.6   0.1     0.015        12      54     116 ..     285     348 ..     283     362 .. 0.79
   4 ?    5.0   0.1     0.012       9.2      67     111 ..     552     596 ..     539     622 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.043
                              API5  89 dtkeyvskiadiLaQlLitedaveldavhkallsllkldaka...sltalfkqieteeetvRekvlkfir 155
                                       + ++ ++++a +L   L+ e    +d     l  + + d++a   +++ l++++ te+e++R+  +  +r
  gi|313116834|ref|YP_004037958.1|  58 SHPNCTRRVAVALQPYLVHETRRTRDEALDMLTWIARTDPNAldtTIEWLLEHLDTEDEHMRDTSVTSLR 127
                                       4577899999999999999999999999999********97544389999************99887775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.44
                              API5  68 iedddlgirkqAikdLpslckdtkeyvskiadiLaQlLitedaveldavhkalls 122
                                       +  dd ++r  Ai  L ++ +  +e+++   d L   L ++++++ +a+ + l +
  gi|313116834|ref|YP_004037958.1| 148 L--DDDAVRANAISLLSTISHAYPEAIAPARDELIA-LSADETIDASAIPSPLGT 199
                                       4..45589*******************999999985.688999988888776655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.015
                              API5  54 PslaekaidaqlDLiedddlgirkqAikdLpslckdtkeyv.skiadiLaQlLitedaveldav 116
                                       P++    +d++  L++dd+ ++r +A+  L ++++  + +v + i di a    t + +  d v
  gi|313116834|ref|YP_004037958.1| 285 PETVVPELDRLRALLDDDNRMVRSSAVETLGNIATVRPAAVrPAIDDIVARFDDTSEDLQFDVV 348
                                       5556667888899**********************99999735788898887777777766655 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.012
                              API5  67 LiedddlgirkqAikdLpslckdtkeyvskiadiLaQlLitedav 111
                                       L++dd+ ++r +A+ +L ++    +++ +++++ L   L   d+ 
  gi|313116834|ref|YP_004037958.1| 552 LLDDDEWKVRAAALEALGQMGAADRDTAERVVEDLQTGLRDTDSD 596
                                       889****************************98886666555554 PP

>> DUF3385  Domain of unknown function (DUF3385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.4   1.9e+03      22      53 ..     338     369 ..     329     402 .. 0.71
   2 ?    2.6   0.0      0.14   1.1e+02      24      46 ..     411     433 ..     403     548 .. 0.64
   3 !    7.0   0.0    0.0064         5      19      56 ..     552     589 ..     547     651 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
                           DUF3385  22 eqsqsirrevikllGilGALDPykhkqveera 53 
                                       ++s++++ +v+  lG + A DP    +v  + 
  gi|313116834|ref|YP_004037958.1| 338 DTSEDLQFDVVTALGKIAAADPEIAPRVVAKL 369
                                       4688999999999******9998876666553 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                           DUF3385  24 sqsirrevikllGilGALDPykh 46 
                                       ++++++++i+  G +GA  P   
  gi|313116834|ref|YP_004037958.1| 411 EWQLQEDIIRAYGRIGAATPDAL 433
                                       56666666666666666555443 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0064
                           DUF3385  19 lkteqsqsirrevikllGilGALDPykhkqveeraedk 56 
                                       l  ++++++r  ++  lG +GA D  +  +v e  ++ 
  gi|313116834|ref|YP_004037958.1| 552 LLDDDEWKVRAAALEALGQMGAADRDTAERVVEDLQTG 589
                                       566789******************99987777663332 PP

>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.3   3.4e+03      54      72 ..     197     215 ..     194     228 .. 0.86
   2 ?    4.7   0.0     0.046        36      54      78 ..     235     259 ..     232     261 .. 0.93
   3 ?    0.5   0.0      0.94   7.3e+02      45      65 ..     305     325 ..     299     336 .. 0.84
   4 ?    3.3   0.0      0.13        99      41      71 ..     444     474 ..     394     483 .. 0.78
   5 ?   -1.1   0.0       2.9   2.3e+03      49      72 ..     489     512 ..     487     522 .. 0.84
   6 ?   -1.3   0.0       3.4   2.6e+03      48      71 ..     525     548 ..     520     554 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.3
                                       HHHHTTT-HHHHHHHHHHH CS
                        dsDNA_bind  54 LsrirlvkperaeavenrL 72 
                                       L++++lv+p+  + v ++L
  gi|313116834|ref|YP_004037958.1| 197 LGTVALVRPDIIDPVVEML 215
                                       899******9999888887 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.046
                                       HHHHTTT-HHHHHHHHHHHHHHHH- CS
                        dsDNA_bind  54 LsrirlvkperaeavenrLiqlaqs 78 
                                       L+ri+++ pe a +v + L+ la++
  gi|313116834|ref|YP_004037958.1| 235 LGRIAVAYPESAPMVVEELLSLAET 259
                                       99********************987 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.94
                                       S--HHHHHHHHHHTTT-HHHH CS
                        dsDNA_bind  45 iLepeAreRLsrirlvkpera 65 
                                       ++ ++A e L++i+ v+p  +
  gi|313116834|ref|YP_004037958.1| 305 MVRSSAVETLGNIATVRPAAV 325
                                       67889************9866 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.13
                                       HHTTS--HHHHHHHHHHTTT-HHHHHHHHHH CS
                        dsDNA_bind  41 iLsqiLepeAreRLsrirlvkperaeavenr 71 
                                       +  + L+ eA++ L++i  v+pe ++   + 
  gi|313116834|ref|YP_004037958.1| 444 LADENLSAEAAAALGEIGGVRPETVAPAVED 474
                                       4457899****************86544444 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 2.9
                                       HHHHHHHHHTTT-HHHHHHHHHHH CS
                        dsDNA_bind  49 eAreRLsrirlvkperaeavenrL 72 
                                        A++ L++i  + pe ae v + L
  gi|313116834|ref|YP_004037958.1| 489 AAASALGTIGAAAPEMAELVVDDL 512
                                       69999*************998877 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHTTT-HHHHHHHHHH CS
                        dsDNA_bind  48 peAreRLsrirlvkperaeavenr 71 
                                         A+e L++i+ +  + a++v + 
  gi|313116834|ref|YP_004037958.1| 525 AAAAEALGTIATTDSDVAARVSEE 548
                                       5799************99999765 PP

>> DUF5578  Family of unknown function (DUF5578)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0058       4.5     161     252 ..      78     167 ..      63     185 .. 0.86
   2 ?    0.4   0.0      0.46   3.6e+02     170     252 ..     275     357 ..     252     371 .. 0.79
   3 ?    3.1   0.0     0.068        53     167     250 ..     489     572 ..     462     598 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0058
                           DUF5578 161 seetqeeaqklleslaegnPkyqkqvykgliallacsspkaqqlalqtlrvvqeivkeakpsivepllelLkslhle 237
                                       + +t++ea ++l+ +a+ +P+  +   + l+  l ++  + +  ++ +lr + e+ +   +  v++l+ +L      
  gi|313116834|ref|YP_004037958.1|  78 TRRTRDEALDMLTWIARTDPNALDTTIEWLLEHLDTEDEHMRDTSVTSLRKLAEAEPVLLRPHVDALIGSLDD--DA 152
                                       56799999999999*******999999********999************99999999999999999999985..57 PP

                           DUF5578 238 vqyeaielikelmst 252
                                       v+++ai+l++++ + 
  gi|313116834|ref|YP_004037958.1| 153 VRANAISLLSTISHA 167
                                       899999999998765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.46
                           DUF5578 170 klleslaegnPkyqkqvykgliallacsspkaqqlalqtlrvvqeivkeakpsivepllelLkslhlevqyeaieli 246
                                       ++l  ++ + P+      + l all  +    +  a++tl  + ++ ++a +  ++ +++    +  ++q++++  +
  gi|313116834|ref|YP_004037958.1| 275 SFLGGIGVAHPETVVPELDRLRALLDDDNRMVRSSAVETLGNIATVRPAAVRPAIDDIVARFDDTSEDLQFDVVTAL 351
                                       56666666666666677778888888888888999999**********************************99999 PP

                           DUF5578 247 kelmst 252
                                        ++++ 
  gi|313116834|ref|YP_004037958.1| 352 GKIAAA 357
                                       888765 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.068
                           DUF5578 167 eaqklleslaegnPkyqkqvykgliallacsspkaqqlalqtlrvvqeivkeakpsivepllelLkslhlevqyeai 243
                                       +a + l +++ + P+  + v + l+  la s  + +  a+++l ++ ++ +++   + e +  lL   + +v+++a+
  gi|313116834|ref|YP_004037958.1| 489 AAASALGTIGAAAPEMAELVVDDLQHRLADSNYRVRAAAAEALGTIATTDSDVAARVSEEVQLLLDDDEWKVRAAAL 565
                                       45556677788888888888888888888888888888888888888888888888888888888888888888888 PP

                           DUF5578 244 elikelm 250
                                       e + ++ 
  gi|313116834|ref|YP_004037958.1| 566 EALGQMG 572
                                       8877765 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.5   1.9e+03       4      70 ..     103     165 ..      98     170 .. 0.59
   2 ?    2.2   0.1      0.14   1.1e+02     181     210 ..     295     324 ..     286     338 .. 0.90
   3 ?    8.6   0.0    0.0016       1.2      88     196 ..     501     601 ..     491     613 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.5
                           CLASP_N   4 kaeellaafegketelnwdaReknilklrslikgn..vpedaveelleclkqlleailkalssLrttls 70 
                                       ++e ll+++   +te +  +R +++++lr+l + +    + +v++l+ +l    +a+  ++ sL +t+s
  gi|313116834|ref|YP_004037958.1| 103 TIEWLLEHL---DTEDE-HMRDTSVTSLRKLAEAEpvLLRPHVDALIGSLD--DDAVRANAISLLSTIS 165
                                       555555555...44444.578888888888877775333445555555555..5555555666666555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                           CLASP_N 181 lkkgleDanptVRetaRstfweffkvwPsr 210
                                       l+++l D n  VR++a +t+ +++ v+P+ 
  gi|313116834|ref|YP_004037958.1| 295 LRALLDDDNRMVRSSAVETLGNIATVRPAA 324
                                       8999****************9999999975 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0016
                           CLASP_N  88 ldpmveillptLlkllgdtKkiisqnanqalaallsnas.fsprilqvlsvalqdKnvqpReysaiwLkilltrfes 163
                                         +m+e +++ L  +l+d   +++++a+ al ++ +  s +  r+   ++++l d   + R+ +++ L ++      
  gi|313116834|ref|YP_004037958.1| 501 APEMAELVVDDLQHRLADSNYRVRAAAAEALGTIATTDSdVAARVSEEVQLLLDDDEWKVRAAALEALGQMGAADR- 576
                                       5679999***************************87655499***************************9998888. PP

                           CLASP_N 164 hkskleasllldliekslkkgleDanptVReta 196
                                                  + +++ l+ gl D ++ VR +a
  gi|313116834|ref|YP_004037958.1| 577 --------DTAERVVEDLQTGLRDTDSDVRPSA 601
                                       ........444788999*************887 PP

>> CDC37_N  Cdc37 N terminal kinase binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0    0.0001     0.082      16      93 ..      54     131 ..      53     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                           CDC37_N  16 sDievHPNVDkrsfirwKqrdihekreqrkaeikklklerein.dkllkridkllealkekeveeeevvfkalnesl 91 
                                       s i  HPN  +r  +  +   +he r  r + ++ l++  +++ ++l + i+ lle+l++++++ +++++++l++ +
  gi|313116834|ref|YP_004037958.1|  54 SKISSHPNCTRRVAVALQPYLVHETRRTRDEALDMLTWIARTDpNALDTTIEWLLEHLDTEDEHMRDTSVTSLRKLA 130
                                       67899********************************99888725678899*********99999888888888877 PP

                           CDC37_N  92 ee 93 
                                        e
  gi|313116834|ref|YP_004037958.1| 131 -E 131
                                       .3 PP

>> MMS19_C  RNAPII transcription regulator C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2    0.0048       3.8     379     420 ..     107     148 ..      98     149 .. 0.92
   2 ?    4.2   0.0     0.024        19     365     419 ..     285     335 ..     248     336 .. 0.76
   3 ?   -3.5   0.0       5.5   4.3e+03     294     313 ..     523     541 ..     508     558 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0048
                           MMS19_C 379 LlqaLdlpdaevkastLetlksileespslvsehlssLvprL 420
                                       Ll+ Ld++d++++  + + l+ ++e +p l+ +h+++L+ +L
  gi|313116834|ref|YP_004037958.1| 107 LLEHLDTEDEHMRDTSVTSLRKLAEAEPVLLRPHVDALIGSL 148
                                       9999*********************99***********9776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.024
                           MMS19_C 365 kslllpeLptLlPlLlqaLdlpdaevkastLetlksileespslvsehlssLvpr 419
                                       +++++peL  L  l    Ld +++ v++s+ etl +i++  p++v + ++++v r
  gi|313116834|ref|YP_004037958.1| 285 PETVVPELDRLRAL----LDDDNRMVRSSAVETLGNIATVRPAAVRPAIDDIVAR 335
                                       55566666665544....3889999**************99***********987 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.5
                           MMS19_C 294 lgqlvakafgvlvsddevvl 313
                                       ++ ++a+a+g+++++d + +
  gi|313116834|ref|YP_004037958.1| 523 VRAAAAEALGTIATTDSD-V 541
                                       555566666666665554.2 PP

>> TIP120  TATA-binding protein interacting (TIP20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.5   1.2e+03      78     110 ..     116     148 ..      77     181 .. 0.64
   2 ?    4.2   0.0     0.042        33      69     113 ..     294     339 ..     287     374 .. 0.78
   3 ?    5.5   0.0     0.017        13      37     107 ..     555     624 ..     524     646 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.5
                            TIP120  78 hdikllcnlmlsklvalapeevlerldelveal 110
                                       ++ + ++ + l kl++ +p  +  ++d+l+ +l
  gi|313116834|ref|YP_004037958.1| 116 EHMRDTSVTSLRKLAEAEPVLLRPHVDALIGSL 148
                                       556666666677777777666666666666544 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.042
                            TIP120  69 rvlaGlsDe.hdikllcnlmlsklvalapeevlerldelvealrkt 113
                                       r+ a l+D+   ++  +  +l ++++++p++v   +d++v+ +  t
  gi|313116834|ref|YP_004037958.1| 294 RLRALLDDDnRMVRSSAVETLGNIATVRPAAVRPAIDDIVARFDDT 339
                                       5666677776778888888888888888888888888888877655 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.017
                            TIP120  37 DdGLelRKaaYetlytlletaldrldlselldrvlaGlsDe.hdikllcnlmlsklvalapeevlerldelv 107
                                       Dd   +R aa e l ++  +  dr   + +++ + +Gl+D+  d++  +   l+ + + +p  +++ +++l 
  gi|313116834|ref|YP_004037958.1| 555 DDEWKVRAAALEALGQMGAA--DRDTAERVVEDLQTGLRDTdSDVRPSAANALAAIGVSQPVLTATAVEALE 624
                                       77888999999999988777..8889999************9****99999999999999988888877765 PP

>> DUF4042  Domain of unknown function (DUF4042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.3   5.7e+03       2      16 ..     153     167 ..     152     171 .. 0.76
   2 ?    4.5   0.1     0.033        26      49      76 ..     516     543 ..     512     550 .. 0.79
   3 ?    5.5   0.0     0.016        12      46      67 ..     550     571 ..     537     584 .. 0.89
   4 ?    0.7   0.0      0.47   3.6e+02      45      67 ..     586     608 ..     572     628 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.3
                           DUF4042   2 vRiaalqllqalvka 16 
                                       vR  a++ll+++  a
  gi|313116834|ref|YP_004037958.1| 153 VRANAISLLSTISHA 167
                                       788888888888765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.033
                           DUF4042  49 lkDpspkvRaaalqvlaalLdgsksfLs 76 
                                       l D++ +vRaaa+++l ++    + + +
  gi|313116834|ref|YP_004037958.1| 516 LADSNYRVRAAAAEALGTIATTDSDVAA 543
                                       78**************998776666655 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.016
                           DUF4042  46 tillkDpspkvRaaalqvlaal 67 
                                       ++ll D + kvRaaal++l ++
  gi|313116834|ref|YP_004037958.1| 550 QLLLDDDEWKVRAAALEALGQM 571
                                       57899**************998 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.47
                           DUF4042  45 ltillkDpspkvRaaalqvlaal 67 
                                       l+++l+D+ + vR  a+++laa+
  gi|313116834|ref|YP_004037958.1| 586 LQTGLRDTDSDVRPSAANALAAI 608
                                       56678888888888888888876 PP

>> Cohesin_HEAT  HEAT repeat associated with sister chromatid cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2         1   7.9e+02      33      42 .]     305     314 ..     299     314 .. 0.85
   2 ?    3.0   0.0      0.17   1.3e+02       8      33 ..     427     450 ..     420     455 .. 0.79
   3 ?    5.7   0.1     0.024        18      23      38 ..     512     527 ..     494     531 .. 0.87
   4 ?    3.6   0.3       0.1        82       3      42 .]     531     568 ..     530     568 .. 0.81
   5 ?    0.1   0.1       1.3     1e+03       2      35 ..     567     598 ..     567     601 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1
                                       HHHHHHHHHH CS
                      Cohesin_HEAT  33 sVRdAaLell 42 
                                       +VR +a+e+l
  gi|313116834|ref|YP_004037958.1| 305 MVRSSAVETL 314
                                       9*******97 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.17
                                       HH-GGGGGSHHHHHHHHHHHHSS-HH CS
                      Cohesin_HEAT   8 ekdpsiLsapevldtiarrltDssps 33 
                                        + p+ L+  +v+d i ++l D+  s
  gi|313116834|ref|YP_004037958.1| 427 AATPDALD--PVMDEIRACLADENLS 450
                                       56666666..************9877 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.024
                                       HHHHHHSS-HHHHHHH CS
                      Cohesin_HEAT  23 iarrltDsspsVRdAa 38 
                                       +++rl Ds   VR+Aa
  gi|313116834|ref|YP_004037958.1| 512 LQHRLADSNYRVRAAA 527
                                       899************9 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.1
                                       HHHHHHH-GGGGGSHHHHHHHHHHHHSS-HHHHHHHHHHH CS
                      Cohesin_HEAT   3 lsslvekdpsiLsapevldtiarrltDsspsVRdAaLell 42 
                                       l+ +++ d+++ +   v + ++  l D +  VR+AaLe l
  gi|313116834|ref|YP_004037958.1| 531 LGTIATTDSDVAA--RVSEEVQLLLDDDEWKVRAAALEAL 568
                                       7777888888855..8888888889999999******986 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.3
                                       HHHHHHHH-GGGGGSHHHHHHHHHHHHSS-HHHH CS
                      Cohesin_HEAT   2 alsslvekdpsiLsapevldtiarrltDsspsVR 35 
                                       al++++ +d    +a+ v + ++  l+D+++ VR
  gi|313116834|ref|YP_004037958.1| 567 ALGQMGAAD--RDTAERVVEDLQTGLRDTDSDVR 598
                                       689999999..899999999999999**999999 PP

>> DUF3560  Domain of unknown function (DUF3560)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.57   4.4e+02      82     118 ..      83     120 ..      76     124 .. 0.69
   2 ?   -1.4   0.0       3.2   2.5e+03      76     108 ..     483     514 ..     477     520 .. 0.76
   3 ?    3.7   0.1     0.082        64      77     109 ..     520     552 ..     514     557 .. 0.88
   4 ?    2.1   0.0      0.26     2e+02      76     114 ..     556     594 ..     549     602 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.57
                           DUF3560  82 aeaaesnasissddpdaierliekleae.krkqermka 118
                                        ea +  + i+++dp+a++  ie+l +   +++e m++
  gi|313116834|ref|YP_004037958.1|  83 DEALDMLTWIARTDPNALDTTIEWLLEHlDTEDEHMRD 120
                                       45555555599************986550555555554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.2
                           DUF3560  76 eyyesraeaaesnasissddpdaierlieklea 108
                                        y+++ra+a +  + i    p++ e   + l+ 
  gi|313116834|ref|YP_004037958.1| 483 PYWNRRAAASALGT-IGAAAPEMAELVVDDLQH 514
                                       59999999999888.788888887777766665 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.082
                           DUF3560  77 yyesraeaaesnasissddpdaierliekleae 109
                                        y+ ra+aae   +i+ +d d+ +r  e+++ +
  gi|313116834|ref|YP_004037958.1| 520 NYRVRAAAAEALGTIATTDSDVAARVSEEVQLL 552
                                       6999***********************999865 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.26
                           DUF3560  76 eyyesraeaaesnasissddpdaierliekleaekrkqe 114
                                       ++++ ra+a e   ++   d d+ er  e l++  r ++
  gi|313116834|ref|YP_004037958.1| 556 DEWKVRAAALEALGQMGAADRDTAERVVEDLQTGLRDTD 594
                                       689****************************99887665 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.34   2.6e+02      32     125 ..      30     126 ..      11     189 .. 0.59
   2 ?   -1.6   0.0       2.6     2e+03      88     144 ..     295     350 ..     287     370 .. 0.70
   3 ?    8.3   1.0    0.0025       1.9      57     144 ..     518     604 ..     498     629 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHHHCS---.....--HHHHHHHHHTT--TT-HHHHHHH-TTHHHHHHHHHT--S-SSHHHHH CS
                              FdhE  32 adYLrflaalaeaqqkvlaaekpla...ldaeaieraqehgmpplaakalerdeawqelLqallealkeelpealre 105
                                       +d ++ l al + ++   +a+++l+    +++ ++r + + +p l +++ +  ++  ++L+ +  +  ++l  +++ 
  gi|313116834|ref|YP_004037958.1|  30 DDEIEALCALLDGRHGRSDAHAALSkisSHPNCTRRVAVALQPYLVHETRRTRDEALDMLTWIARTDPNALDTTIEW 106
                                       55555555555555555443333333312222222333333344444444444444455555544555555555555 PP

                                       HHHHHHH--HHHHHHHHHHH CS
                              FdhE 106 alerlrkadaeelealadal 125
                                       +le+l + d++ +++ +++l
  gi|313116834|ref|YP_004037958.1| 107 LLEHLDTEDEHMRDTSVTSL 126
                                       55555555555555555544 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
                                       HHHHHHT--S-SSHHHHHHHHHHHH--HHHHHHHHHHHHTT-GGGS-GGGHHHHHHH CS
                              FdhE  88 LqallealkeelpealrealerlrkadaeelealadallageleavdaakavfvaaA 144
                                       L+all++ +  +  ++ e+l ++ +  +++ +  +d+++a  ++ ++++ ++ v+ A
  gi|313116834|ref|YP_004037958.1| 295 LRALLDDDNRMVRSSAVETLGNIATVRPAAVRPAIDDIVAR-FDDTSEDLQFDVVTA 350
                                       77888888888888888888888888888888777777763.455555555444444 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0025
                                       --HHHHHHHHHTT--TT-HHHHHHH-TTHHHHHHHHHT--S-SSHHHHHHHHHHHH--HHHHHHHHHHHHTT-GGGS CS
                              FdhE  57 ldaeaieraqehgmpplaakalerdeawqelLqallealkeelpealrealerlrkadaeelealadallageleav 133
                                        ++ ++++a++++   +a+++ + ++++ e +q ll++ + ++ +a+ eal ++ +ad+++ e+++++l +g  + +
  gi|313116834|ref|YP_004037958.1| 518 DSNYRVRAAAAEALGTIATTDSDVAARVSEEVQLLLDDDEWKVRAAALEALGQMGAADRDTAERVVEDLQTGL-RDT 593
                                       4555677788889999999999999****************************************99987664.344 PP

                                       -GGGHHHHHHH CS
                              FdhE 134 daakavfvaaA 144
                                       d++  +  a A
  gi|313116834|ref|YP_004037958.1| 594 DSDVRPSAANA 604
                                       44444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.91u 0.33s 00:00:01.24 Elapsed: 00:00:00.51
# Mc/sec: 4009.37
//
Query:       gi|313116835|ref|YP_004037959.1|  [L=52]
Description: hypothetical protein Hbor_32930, partial [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00031   21.2   0.0    0.00033   21.1   0.0    1.1  1  DUF2262   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2262  Uncharacterized protein conserved in bacteria (DUF2262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.8e-08   0.00033     103     130 ..       2      29 ..       1      39 [. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.8e-08
                           DUF2262 103 dsisieeegeftlyfddgdlFaghsiiv 130
                                       ++++i+++geft+++ d+d  +gh+i++
  gi|313116835|ref|YP_004037959.1|   2 NTVTIHPDGEFTFWHGDDDPLFGHAILL 29 
                                       799***************7777***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 368.98
//
Query:       gi|313116836|ref|YP_004037960.1|  [L=82]
Description: phage integrase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00016   21.6   0.2    0.00016   21.5   0.2    1.1  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   8.9e-09   0.00016     126     169 ..      34      79 ..       6      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.9e-09
                                       SC--TTHHHHHHHHHHH.HHCTSHHHHHHHHT-SSCCHH.HHHHCC CS
                   Phage_integrase 126 kpltpHtlRhsfataLl.eagvdlrvvqkllGHssistt.qiYthv 169
                                       +++tpH+lRhs+  +++ ++   +   +k l H+ ++tt qiY h 
  gi|313116836|ref|YP_004037960.1|  34 DDVTPHSLRHSVVYRMMtYEDKHIYDMKKRLRHAPLQTTdQIYSHF 79 
                                       79**********99976267889999*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 583.35
//
Query:       gi|313116837|ref|YP_004037961.1|  [L=601]
Description: DNA/RNA helicase, superfamily I [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   34.7   0.1    2.2e-08   33.8   0.1    1.5  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    7.5e-05   22.3   0.0    0.00011   21.7   0.0    1.2  1  UvrD_C           UvrD-like helicase C-terminal domain
    0.00026   21.3   0.0    0.00091   19.6   0.0    1.8  2  AAA_19           AAA domain
    0.00043   20.1   0.0       0.16   11.7   0.0    2.9  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
      0.014   14.8   0.0          4    6.8   0.0    2.3  2  PhoH             PhoH-like protein
       0.12   11.6   0.0       0.27   10.4   0.0    1.5  1  DUF2075          Uncharacterized conserved protein (DUF2075)
        0.2   11.1   0.0         19    4.6   0.0    2.3  2  UvrD-helicase    UvrD/REP helicase N-terminal domain


Domain annotation for each model (and alignments):
>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   8.6e-12   2.2e-08       2      51 ..     490     542 ..     489     543 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 8.6e-12
                          UvrD_C_2   2 ayaltihkaQGsefpaVivfdpd..laaarmgel..rrrlLYtavTRAreklil 51 
                                       ++++tih a+G+e+  V+v+  +   ++++++ l   r+ +++a+TR+r+++++
  gi|313116837|ref|YP_004037961.1| 490 VTISTIHLAKGNEAASVYVVGLNnaITNPYRE-LvqARNEVFVAITRSRAWCTI 542
                                       6899***************9988646666644.369***************987 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.2e-08   0.00011     283     345 ..     486     543 ..     454     547 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.2e-08
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 283 kkekipiiTiHqAKGlEFdvVflagleegtfPsyrskkekrleEEkRlfYVaiTRAkkrLfis 345
                                       +  +++i+TiH AKG E   V+++gl++ ++  yr+  +      ++  +VaiTR +   +i+
  gi|313116837|ref|YP_004037961.1| 486 RPGEVTISTIHLAKGNEAASVYVVGLNNAITNPYRELVQ-----ARNEVFVAITRSRAWCTIT 543
                                       3379************************99877886665.....7899*******99877776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.5e-07   0.00091       8     141 ..     124     296 ..     117     301 .. 0.77
   2 ?   -1.6   0.0       1.2     3e+03      37      77 ..     438     499 ..     427     565 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.5e-07
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrA.akelrerlaalgae.............at 70 
                                       ++ ++  + + +G+GKT +l ++ a +   ++   +  ++++f  ++  + +++ ++ + ++             ++
  gi|313116837|ref|YP_004037961.1| 124 IPPGPQQIRGIAGSGKTVLLAMKAAKMAVDHK---DWTIALTFQTKSlYDHITDLTERFYRRfsngqslaesdssIE 197
                                       56677788999**********99999888874...567788887776257788877666666777778888888877 PP

                            AAA_19  71 TiHrlal...............................ldfddlltealelleeaeeekklqeee.llivDEfqdvd 115
                                        iH+ +                                 d+d+++  a+ell       ++ + + +++vDE+qd  
  gi|313116837|ref|YP_004037961.1| 198 IIHGWGGhttgegiykriaeatpnatfrsvtdaraefgSDTDPQEAVAAELLAT----GDIPDLFdAILVDEAQDFG 270
                                       77777669999999999999999999999999**99998888888888888774....45556667*********** PP

                            AAA_19 116 elqyrLlkallgekkklllvGDpdQl 141
                                       +  +++  a l+++++l+   D+ Q+
  gi|313116837|ref|YP_004037961.1| 271 PHFFNMCLAALDSSNRLIWGYDEAQN 296
                                       88888777777677778876677775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                            AAA_19  37 lggvkpeeillvaftgrAakelrerlaalgae.......................atTiHrlal 77 
                                       ++g++pe+il+v +   A ++ ++   +l+++                       ++TiH la 
  gi|313116837|ref|YP_004037961.1| 438 EEGLPPERILVVPLGLDAKDRGQQLQ-SLLRAhdlgatcawegdrtefsrpgevtISTIH-LAK 499
                                       44466777777766666665554433.333333555666666666666667777777777.333 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0093        24       3      36 ..     131     162 ..     130     193 .. 0.67
   2 ?   -0.8   0.0      0.42   1.1e+03      62     106 ..     257     302 ..     222     312 .. 0.73
   3 !   11.7   0.0   6.1e-05      0.16     183     232 ..     481     542 ..     456     544 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0093
                   Viral_helicase1   3 vhGvpGcGKStlirkllrtsliltvnrptaellt 36 
                                       + G++G+GK+ l+   + +    + ++  +++lt
  gi|313116837|ref|YP_004037961.1| 131 IRGIAGSGKTVLLAMKAAK--MAVDHKDWTIALT 162
                                       68********998766655..3344444444444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.42
                   Viral_helicase1  62 kgkililDEylllhaGyilllaalskaklvilfG.DplQipfhsrn 106
                                        ++ +++DE++   +  +++++a   +++ +++G D++Q  ++ r+
  gi|313116837|ref|YP_004037961.1| 257 LFDAILVDEAQDFGPHFFNMCLAALDSSNRLIWGyDEAQNLHSLRA 302
                                       478899****999999999955555555555555588886555444 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 6.1e-05
                   Viral_helicase1 183 r.........evttvhevqGltfdkVtlvllketdlelis...esrenllvAlTRhrkslvi 232
                                       r          ++t h + G ++ +V +v l++   + ++   + r+ ++vA+TR+r  ++i
  gi|313116837|ref|YP_004037961.1| 481 RtefsrpgevTISTIHLAKGNEAASVYVVGLNNAITNPYRelvQARNEVFVAITRSRAWCTI 542
                                       2445555555699******************99887777788867***********987776 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0041        11      25      47 ..     132     154 ..     128     167 .. 0.76
   2 ?    6.8   0.0    0.0016         4     123     158 ..     261     296 ..     257     308 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0041
                                       E--TTSSTTHHHHHHHHHHHHTT CS
                              PhoH  25 iGpaGtGKtylavalavealkkk 47 
                                        G aG+GKt l  + a+++  ++
  gi|313116837|ref|YP_004037961.1| 132 RGIAGSGKTVLLAMKAAKMAVDH 154
                                       689******98777777766554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0016
                                       EEE-SGGG--HHHHHHHHTTB-TT-EEEEEE----- CS
                              PhoH 123 vilDEAQnttkeqmkmfltRlGenskvvvtGdvtqi 158
                                       +++DEAQ++ ++  +m+l  l+++ +++   d +q 
  gi|313116837|ref|YP_004037961.1| 261 ILVDEAQDFGPHFFNMCLAALDSSNRLIWGYDEAQN 296
                                       89************************9988888776 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0001      0.27       6      98 ..     131     267 ..     130     308 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                           DUF2075   6 VtGvaGtGKtvvllnllael.......................................eddeeertavylsvNhpl 43 
                                       ++G aG+GKtv+l   +a++                                        ++++  + ++  + h  
  gi|313116837|ref|YP_004037961.1| 131 IRGIAGSGKTVLLAMKAAKMavdhkdwtialtfqtkslydhitdlterfyrrfsngqslAESDSSIEIIHGWGGHTT 207
                                       89**********99888888666666666666655555555555555555555555444444466666666777777 PP

                           DUF2075  44 vlvlrealakkeekkkkkeafeklssfinnlsef.....kkaeekkeepkedvvivDEAh 98 
                                        + +++++a+ + + +++++    ++f  +++       +  +  +  + +d ++vDEA+
  gi|313116837|ref|YP_004037961.1| 208 GEGIYKRIAEATPNATFRSVTDARAEFGSDTDPQeavaaELLATGDIPDLFDAILVDEAQ 267
                                       777777777777777777777777777777776666664444444455567777777777 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.011        27      17      53 ..     130     163 ..     116     207 .. 0.78
   2 ?    4.6   0.0    0.0075        19     255     275 ..     256     276 ..     242     309 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.011
                                       EEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEES CS
                     UvrD-helicase  17 lveAsAGsGKTfvlaerilrlikeeeiepdrilvvTF 53 
                                        +   AGsGKT  la + +++   +    d  +++TF
  gi|313116837|ref|YP_004037961.1| 130 QIRGIAGSGKTVLLAMKAAKMAVDH---KDWTIALTF 163
                                       56667********999987654443...444556666 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0075
                                       HHSSEEEESSGGG-BHHHHHH CS
                     UvrD-helicase 255 erykeiliDEyQDTnkiQyri 275
                                         ++ il+DE+QD  +  +++
  gi|313116837|ref|YP_004037961.1| 256 DLFDAILVDEAQDFGPHFFNM 276
                                       5699*********77665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3744.02
//
Query:       gi|313116838|ref|YP_004037962.1|  [L=66]
Description: hypothetical protein Hbor_33000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0049   17.0   0.6     0.0054   16.9   0.6    1.0  1  DUF5366   Family of unknown function (DUF5366)


Domain annotation for each model (and alignments):
>> DUF5366  Family of unknown function (DUF5366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6     3e-07    0.0054      70     123 ..       6      59 ..       3      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3e-07
                           DUF5366  70 kkvrsgsviyllgslvsllslqsllllvilfvlatliyfiyfvykiseslslag 123
                                        + r+  ++ l+++++ +++++++l l+ lf   t+++fi +v  i++ + + +
  gi|313116838|ref|YP_004037962.1|   6 PETRAERMLQLIAGVLVVVAVADFLELIDLFSYWTYVFFISTVSIIYDIIGTRK 59 
                                       577899999**********************************99999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 485.96
//
Query:       gi|313116839|ref|YP_004037963.1|  [L=86]
Description: hypothetical protein Hbor_33010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 628.14
//
Query:       gi|313116840|ref|YP_004037964.1|  [L=77]
Description: hypothetical protein Hbor_33020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 494.08
//
Query:       gi|313116841|ref|YP_004037965.1|  [L=225]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-32  111.5   0.0    6.6e-32  110.7   0.0    1.4  1  DDE_Tnp_IS240  DDE domain
    4.1e-07   29.7   0.3    8.8e-07   28.6   0.3    1.6  1  rve_3          Integrase core domain
  ------ inclusion threshold ------
      0.031   14.5   0.1       0.06   13.5   0.1    1.7  1  rve            Integrase core domain
      0.037   13.8   0.0        1.5    8.6   0.0    2.2  2  DDE_3          DDE superfamily endonuclease
       0.05   13.1   0.1       0.11   12.0   0.1    1.5  1  DDE_Tnp_IS66   Transposase IS66 family


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.0   1.8e-35   6.6e-32       2     140 .]      80     212 ..      79     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.8e-35
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkel 77 
                                       k+++vDET+vki+G+w++ly+a+D e++ ild+ ++ r +t++a+afl+++ +k++l+++++++D+++ y++al++l
  gi|313116841|ref|YP_004037965.1|  80 KRVAVDETAVKINGEWSWLYAAIDIETKlILDVELFGRHGTDPAAAFLHRLSEKHDLSDAVFLVDGYG-YQTALSRL 155
                                       789*****************************************************************.******** PP

                     DDE_Tnp_IS240  78 kregelfdevshvqvkylnnriEsdhrtlKkrl..rptrgfkslksaaktlagfeavknlrkghk 140
                                       + +g+ +d+       +++n iE+++ tlK+r+  ++++++ s  s++++  +f+ ++n++++h+
  gi|313116841|ref|YP_004037965.1| 156 GLSGR-LDY-------VERNLIEKWFHTLKMRVdrFHNSWVGSHGSVREWFIQFAQYYNFQRPHQ 212
                                       **887.455.......789**************9889**************************95 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.3   2.5e-10   8.8e-07      34      67 .]     186     219 ..     165     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.5e-10
                             rve_3  34 elfrslaearekleawredYNteRPHssLgykTP 67 
                                       ++  s   +re+  ++ ++YN +RPH+sL+++TP
  gi|313116841|ref|YP_004037965.1| 186 SWVGSHGSVREWFIQFAQYYNFQRPHQSLNGRTP 219
                                       336677889************************9 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.7e-05      0.06       6      73 ..      80     144 ..      75     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                               rve   6 elwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsD 73 
                                       +++ vD t v+i   g++++l++++d  ++lil + l  ++ ++ ++a+l+r  ++   +   ++l D
  gi|313116841|ref|YP_004037965.1|  80 KRVAVDETAVKIN--GEWSWLYAAIDIETKLILDVELFGRHGTDPAAAFLHRLSEKHDLS-DAVFLVD 144
                                       6788999*99955..447*********************************999887776.4666666 PP

>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00041       1.5      29      91 ..      87     149 ..      70     153 .. 0.87
   2 ?    2.8   0.2     0.026        92     120     135 ..     167     182 ..     165     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00041
                             DDE_3  29 leeygrrgrvnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDnasiH 91 
                                        + +++++  +l++a+d +++l++ v   ++  ++  a+fl rl e+++ +   v+++D+ ++ 
  gi|313116841|ref|YP_004037965.1|  87 TAVKINGEWSWLYAAIDIETKLILdVELFGRHGTDPAAAFLHRLSEKHDLS-DAVFLVDGYGYQ 149
                                       5667888999**************9999999999999*************8.999999988775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.026
                             DDE_3 120 NpiEivwsklkrellk 135
                                       N iE++++ lk ++ +
  gi|313116841|ref|YP_004037965.1| 167 NLIEKWFHTLKMRVDR 182
                                       9**********98876 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     3e-05      0.11      13     135 ..      31     148 ..      27     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                      DDE_Tnp_IS66  13 lvlkyadhlPlyRqeeilarlGvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkgkk 89 
                                       +v+ +a +++l+  +eil+ lGve s +++ +wv+r a+   +  ea        +++++DET ++       +g+ 
  gi|313116841|ref|YP_004037965.1|  31 AVQLHATGCSLRETKEILRILGVERSHQAVWQWVHRLADSGHNPPEATP------KRVAVDETAVK------INGEW 95 
                                       57789999*******************************9877777755......56789******......78888 PP

                      DDE_Tnp_IS66  90 sylWvyvtdkrkpavlfeysp.sRg.gevaealLag.......fkGvlvsDgyag 135
                                       s+l++++  ++    +++++  +R  ++ a a+L            v  +Dgy+ 
  gi|313116841|ref|YP_004037965.1|  96 SWLYAAIDIET--KLILDVELfGRHgTDPAAAFLHRlsekhdlSDAVFLVDGYGY 148
                                       88888887774..222233222333133445554444445655446777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1571.99
//
Query:       gi|313116842|ref|YP_004037966.1|  [L=134]
Description: hypothetical protein Hbor_33040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   14.5   0.0        0.1   13.8   0.0    1.3  1  EthD      EthD domain


Domain annotation for each model (and alignments):
>> EthD  EthD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.7e-06       0.1      50      88 ..      46      85 ..      40      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-06
                                      TTC--SEEEEEEEEE.SSHHHHHHHHCSHHHHH.HHHHHH CS
                              EthD 50 pgsdadyDgiaelwf.dsleaflaafadpeyaavlaaDee 88
                                       ++d  + g++ ++f ++++af+a+ +d+ ++++l+aD e
  gi|313116842|ref|YP_004037966.1| 46 VNEDLWFEGWTKVYFqPTIDAFEAICSDELGREALQADLE 85
                                      66778899*******99********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 951.34
//
Query:       gi|313116843|ref|YP_004037967.1|  [L=527]
Description: hypothetical protein Hbor_33050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.2   0.2        6.3    6.3   0.1    2.6  2  DUF533    Protein of unknown function (DUF533)


Domain annotation for each model (and alignments):
>> DUF533  Protein of unknown function (DUF533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1   0.00035       6.3      66      89 ..     194     216 ..     115     222 .. 0.85
   2 ?    4.3   0.0    0.0015        27      84     141 ..     357     415 ..     355     425 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00035
                            DUF533  66 eeeekaelllrAmiaAAkADGhid 89 
                                        ++e+a++l++Ami A kA G++d
  gi|313116843|ref|YP_004037967.1| 194 VRQEFAQALVNAMIDAGKA-GRLD 216
                                       56899*************9.5555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0015
                            DUF533  84 ADGhideeErqrIlqeleelgldaeekalledeLrkPld.lqelaaavknpelaaevYl 141
                                       ADG+ d++ +qr+ +++ + gl + + a l d L++ ld l++l+a+ ++  l   v++
  gi|313116843|ref|YP_004037967.1| 357 ADGNSDTDWQQRLAETIVSTGLGPVDSARLGDSLEALLDsLDSLVADHPDDDLLRLVFA 415
                                       9***********************************99747889998877776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3437.46
//
Query:       gi|313116844|ref|YP_004037968.1|  [L=760]
Description: hypothetical protein Hbor_33060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-07   31.7  36.9      0.021   15.3   0.3    8.9 10  BTAD             Bacterial transcriptional activator domain
      6e-05   23.5  34.0       0.02   15.4   0.1   10.3 12  TPR_19           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.061   13.8  20.6        9.5    6.7   0.1    7.8  8  Phage_TAC_6      Phage tail assembly chaperone protein, TAC
        0.1   13.0   0.1         69    4.2   0.0    4.3  5  TPR_17           Tetratricopeptide repeat
       0.13   12.6   2.4         20    5.5   0.0    3.8  3  Sulfotransfer_3  Sulfotransferase family
       0.18   12.5  15.0         17    6.3   0.3    8.3 11  TPR_6            Tetratricopeptide repeat
        1.7    9.7  52.0         19    6.4   3.5   13.3 14  TPR_14           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.27   6.8e+02      79     107 ..       3      31 ..       1      38 [. 0.90
   2 ?   -1.0   0.8      0.84   2.1e+03      32      35 ..      76      79 ..      11     124 .. 0.59
   3 ?    0.7   2.1      0.25   6.3e+02      53     108 ..     114     169 ..      54     173 .. 0.67
   4 !   10.0   0.0   0.00035      0.89      65     106 ..     222     263 ..     201     274 .. 0.83
   5 !   15.3   0.3     8e-06     0.021      72     128 ..     278     334 ..     267     341 .. 0.89
   6 ?    1.4   0.0      0.15   3.9e+02      78     107 ..     328     357 ..     324     361 .. 0.86
   7 ?    3.1   0.1     0.046   1.2e+02      75     107 ..     415     447 ..     399     467 .. 0.81
   8 ?    2.1   0.7     0.093   2.4e+02      50      90 ..     469     509 ..     455     554 .. 0.61
   9 !    9.1   3.4   0.00067       1.7      53     116 ..     567     633 ..     538     647 .. 0.79
  10 !    6.5   0.0    0.0041        11      55      99 ..     702     746 ..     686     755 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHSTT-HHHHHHHHHHHH CS
                              BTAD  79 eealaelealvaehPlrErlhrqlmrAla 107
                                       e++l++l++l++ hP + +   q  rAla
  gi|313116844|ref|YP_004037968.1|   3 EACLDRLDRLTDDHPEDTEIQLQFARALA 31 
                                       78999**************9999999998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.84
                                      HHTT CS
                              BTAD 32 Alal 35
                                      A al
  gi|313116844|ref|YP_004037968.1| 76 ASAL 79
                                      2222 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHH CS
                              BTAD  53 ererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlar 108
                                        ++r+ ++ l+  + +  +  +++r e  l++le l+  hP  ++   +l  Ala 
  gi|313116844|ref|YP_004037968.1| 114 DVQRMLAKTLSLATFHDSEAGQFERVETHLDRLETLAFDHPAGDACQSELASALAN 169
                                       44445555555555555555566688888999999999999999999999888876 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00035
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHH CS
                              BTAD  65 lealaeaelrlGraeealaelealvaehPlrErlhrqlmrAl 106
                                       + +  + +l++  +++ l++le+l+ e+P++E+ hr l + l
  gi|313116844|ref|YP_004037968.1| 222 YMDGSDRRLEYDTIQRYLDRLEGLAGEYPTDEEIHRRLAEGL 263
                                       5555667899999************************98877 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 8e-06
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLae 128
                                       +++  ++e+ l++l++l++e P+++   +ql +A +r+ r a   +++e+ +r+L++
  gi|313116844|ref|YP_004037968.1| 278 RIESDEHERYLDRLSELATEFPTDDGITAQLATAHRRVARDAGGVGTFETQQRHLDR 334
                                       456779*******************************************99999975 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHH CS
                              BTAD  78 aeealaelealvaehPlrErlhrqlmrAla 107
                                        ++ l++l++l++ hP++++   +l +Al 
  gi|313116844|ref|YP_004037968.1| 328 QQRHLDRLHELAYDHPHNDDVLFELAQALE 357
                                       5677899***************99999986 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.046
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAla 107
                                       + + ++++++le++v+e+Pl+ + + ql  A +
  gi|313116844|ref|YP_004037968.1| 415 FSELRACIDQLEEMVTEYPLQSEIRIQLAVAHF 447
                                       4467799***************99999988865 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.093
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  50 leaererleelrlealealaeaelrlGraeealaelealva 90 
                                       le+ ++++ + r e++e+l++a++  ++++  +++ +al++
  gi|313116844|ref|YP_004037968.1| 469 LETLAAEYPDTRREVHERLIKALFNTAKYQGQADRFDALTD 509
                                       33333334444444444444444444444444444444444 PP

  == domain 9  score: 9.1 bits;  conditional E-value: 0.00067
                                       HHHHHHHHHHHHHHHHHHHHHHTT...-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHH CS
                              BTAD  53 ererleelrlealealaeaelrlG...raeealaelealvaehPlrErlhrqlmrAlarsGrqaeAL 116
                                       ++ ++++++ +al  +++a+++     +a++ +++l++++a+ P +E+l +   rAl    r+a A 
  gi|313116844|ref|YP_004037968.1| 567 HVPEIRRRFAKALHGMMDALWSADrvdEARATMDRLRSAAAAFPADEELQCVSARALVNHSRNAGAA 633
                                       44556666667777777777766633377788999************************99999885 PP

  == domain 10  score: 6.5 bits;  conditional E-value: 0.0041
                                       HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHH CS
                              BTAD  55 erleelrlealealaeaelrlGraeealaelealvaehPlrErlh 99 
                                        +l ++ l+++ + + ++ r + ae++l++ eal+a+hP +E   
  gi|313116844|ref|YP_004037968.1| 702 PYLYAKTLSIVSKYLGENGRSETAEQCLGRIEALAAAHPADEVIQ 746
                                       5677888999999999999**********************9765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0099        25      11      35 ..       6      30 ..       3      33 .. 0.89
   2 ?   -1.2   0.5       1.2     3e+03      12      37 ..      56      81 ..      55      83 .. 0.82
   3 !    5.9   0.6     0.007        18       8      34 ..      96     122 ..      85     127 .. 0.73
   4 ?   -3.1   0.0       4.6   1.2e+04      38      59 ..     133     154 ..     130     170 .. 0.67
   5 ?   -4.2   0.0         7   1.8e+04      42      63 ..     162     182 ..     157     185 .. 0.61
   6 ?    2.1   0.0      0.11   2.9e+02      11      33 ..     239     261 ..     231     264 .. 0.86
   7 ?   -0.9   0.0      0.92   2.4e+03      12      35 ..     289     312 ..     283     314 .. 0.89
   8 ?    3.2   0.1     0.052   1.3e+02      13      35 ..     334     356 ..     329     359 .. 0.81
   9 !    6.1   0.0    0.0061        16      11      37 ..     422     448 ..     417     451 .. 0.89
  10 ?    1.0   0.1      0.25   6.4e+02       4      38 ..     456     494 ..     455     533 .. 0.57
  11 !   15.4   0.1   7.7e-06      0.02      12      56 ..     556     607 ..     538     622 .. 0.81
  12 ?   -2.7   0.1       3.6   9.1e+03      38      55 ..     719     736 ..     718     742 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0099
                            TPR_19 11 lalleqalqedpknaearllLAeal 35
                                      l++l ++ ++ p++ e++l+ A+al
  gi|313116844|ref|YP_004037968.1|  6 LDRLDRLTDDHPEDTEIQLQFARAL 30
                                      67999999***************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                            TPR_19 12 alleqalqedpknaearllLAealla 37
                                      ++l ++ + +p+  +++  LA al++
  gi|313116844|ref|YP_004037968.1| 56 DRLDALAARYPDATWIQSELASALYN 81
                                      57788888999999999999999876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.007
                            TPR_19   8 aeAlalleqalqedpknaearllLAea 34 
                                        +A+a+l ++ +++p+ ++++  LA+ 
  gi|313116844|ref|YP_004037968.1|  96 RSAQARLDALATDYPDTDDVQRMLAKT 122
                                       467777777777777777777777766 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 4.6
                            TPR_19  38 lgqldeAealLdalpeedpdda 59 
                                       +gq++  e  Ld+l   + d++
  gi|313116844|ref|YP_004037968.1| 133 AGQFERVETHLDRLETLAFDHP 154
                                       6777777777777766555544 PP

  == domain 5  score: -4.2 bits;  conditional E-value: 7
                            TPR_19  42 deAealLdalpeedpddaryas 63 
                                       + A al + +p + +d  ++ +
  gi|313116844|ref|YP_004037968.1| 162 ELASALANVAPYQRRD-GYVDD 182
                                       4466666666666666.66655 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.11
                            TPR_19  11 lalleqalqedpknaearllLAe 33 
                                       l++le +  e+p ++e+  +LAe
  gi|313116844|ref|YP_004037968.1| 239 LDRLEGLAGEYPTDEEIHRRLAE 261
                                       5678889999***********97 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 0.92
                            TPR_19  12 alleqalqedpknaearllLAeal 35 
                                       ++l+++ +e p ++ + ++LA a+
  gi|313116844|ref|YP_004037968.1| 289 DRLSELATEFPTDDGITAQLATAH 312
                                       6899999*************9875 PP

  == domain 8  score: 3.2 bits;  conditional E-value: 0.052
                            TPR_19  13 lleqalqedpknaearllLAeal 35 
                                       +l ++  + p+n++++  LA+al
  gi|313116844|ref|YP_004037968.1| 334 RLHELAYDHPHNDDVLFELAQAL 356
                                       556655579************98 PP

  == domain 9  score: 6.1 bits;  conditional E-value: 0.0061
                            TPR_19  11 lalleqalqedpknaearllLAealla 37 
                                       ++ le++ +e+p ++e+r++LA a+++
  gi|313116844|ref|YP_004037968.1| 422 IDQLEEMVTEYPLQSEIRIQLAVAHFN 448
                                       5679*******************9986 PP

  == domain 10  score: 1.0 bits;  conditional E-value: 0.25
                            TPR_19   4 egdyaeAlalleq...alqedpk.....naearllLAeallal 38 
                                       +g++++ +++l +   + +e+p+     ++    +L++al+++
  gi|313116844|ref|YP_004037968.1| 456 AGRFDQVHSHLDRletLAAEYPDtrrevHE----RLIKALFNT 494
                                       567777755555522144555555332222....444444444 PP

  == domain 11  score: 15.4 bits;  conditional E-value: 7.7e-06
                            TPR_19  12 alleqalqedpk.......naearllLAeallalgqldeAealLdalpeedp 56 
                                       ++l  + +++p+        a a+ ++++al+++ ++deA+a++d+l  +++
  gi|313116844|ref|YP_004037968.1| 556 DRLDDLVTDYPHvpeirrrFAKALHGMMDALWSADRVDEARATMDRLRSAAA 607
                                       567777788888444444445555589*******************988765 PP

  == domain 12  score: -2.7 bits;  conditional E-value: 3.6
                            TPR_19  38 lgqldeAealLdalpeed 55 
                                       +g+ + Ae++L ++ + +
  gi|313116844|ref|YP_004037968.1| 719 NGRSETAEQCLGRIEALA 736
                                       678888999998887655 PP

>> Phage_TAC_6  Phage tail assembly chaperone protein, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       2.3   5.9e+03      46      56 ..       7      17 ..       6      19 .. 0.88
   2 ?    6.7   0.1    0.0037       9.5      46      57 ..      56      67 ..      47      68 .. 0.89
   3 ?    6.6   0.2     0.004        10      44      58 .]      98     112 ..      80     112 .. 0.79
   4 ?   -1.6   0.0       1.5   3.7e+03      46      56 ..     289     299 ..     286     301 .. 0.91
   5 ?   -2.4   0.0       2.6   6.8e+03      46      56 ..     423     433 ..     422     433 .. 0.91
   6 ?    3.1   0.0     0.051   1.3e+02      46      58 .]     467     479 ..     457     479 .. 0.89
   7 ?    0.7   0.0      0.28   7.2e+02      45      56 ..     555     566 ..     536     567 .. 0.83
   8 ?    4.2   0.3     0.023        58      46      57 ..     687     698 ..     675     699 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
                       Phage_TAC_6 46 adLdaLmarfP 56
                                      ++Ld+L +++P
  gi|313116844|ref|YP_004037968.1|  7 DRLDRLTDDHP 17
                                      69********9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0037
                       Phage_TAC_6 46 adLdaLmarfPD 57
                                      ++LdaL+ar+PD
  gi|313116844|ref|YP_004037968.1| 56 DRLDALAARYPD 67
                                      79********** PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.004
                       Phage_TAC_6  44 sRadLdaLmarfPDk 58 
                                         a+LdaL++++PD+
  gi|313116844|ref|YP_004037968.1|  98 AQARLDALATDYPDT 112
                                       569***********5 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.5
                       Phage_TAC_6  46 adLdaLmarfP 56 
                                       ++L++L+++fP
  gi|313116844|ref|YP_004037968.1| 289 DRLSELATEFP 299
                                       68********9 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 2.6
                       Phage_TAC_6  46 adLdaLmarfP 56 
                                       ++L+++++++P
  gi|313116844|ref|YP_004037968.1| 423 DQLEEMVTEYP 433
                                       58********9 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.051
                       Phage_TAC_6  46 adLdaLmarfPDk 58 
                                       ++L+ L+a++PD+
  gi|313116844|ref|YP_004037968.1| 467 DRLETLAAEYPDT 479
                                       68**********5 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 0.28
                       Phage_TAC_6  45 RadLdaLmarfP 56 
                                        ++Ld+L++++P
  gi|313116844|ref|YP_004037968.1| 555 IDRLDDLVTDYP 566
                                       589********9 PP

  == domain 8  score: 4.2 bits;  conditional E-value: 0.023
                       Phage_TAC_6  46 adLdaLmarfPD 57 
                                       ++Ld+L+a++PD
  gi|313116844|ref|YP_004037968.1| 687 DRLDDLAAKYPD 698
                                       69********** PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         7   1.8e+04       9      25 ..      16      32 ..      11      33 .. 0.78
   2 ?   -2.5   0.0       3.6   9.2e+03      17      29 ..     117     136 ..     105     138 .. 0.70
   3 ?    4.2   0.0     0.027        69       9      24 ..     342     357 ..     337     368 .. 0.80
   4 ?   -3.5   0.0         7   1.8e+04       4      18 ..     383     397 ..     382     398 .. 0.78
   5 ?    3.1   0.0     0.057   1.5e+02      17      34 .]     703     727 ..     698     727 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7
                            TPR_17  9 dPnnadaynnLAelllk 25
                                      +P + +   + A++l++
  gi|313116844|ref|YP_004037968.1| 16 HPEDTEIQLQFARALAN 32
                                      78888888899999887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.6
                            TPR_17  17 nnLAelll.......knGdl 29 
                                        +LA++l+       ++G++
  gi|313116844|ref|YP_004037968.1| 117 RMLAKTLSlatfhdsEAGQF 136
                                       67888888666666677766 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.027
                            TPR_17   9 dPnnadaynnLAelll 24 
                                       +P n d++++LA++l+
  gi|313116844|ref|YP_004037968.1| 342 HPHNDDVLFELAQALE 357
                                       699***********97 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 7
                            TPR_17   4 kaleldPnnadaynn 18 
                                        a+  +P +++++++
  gi|313116844|ref|YP_004037968.1| 383 AAALAYPADVNVLFQ 397
                                       566779999999986 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.057
                            TPR_17  17 nnLAelll.......knGdlmtArq 34 
                                       +++A++l+       +nG+++tA+q
  gi|313116844|ref|YP_004037968.1| 703 YLYAKTLSivskylgENGRSETAEQ 727
                                       789999999999999********98 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0079        20      85     129 ..      28      71 ..       5      74 .. 0.64
   2 ?    3.5   0.2     0.032        82      89     127 ..     444     480 ..     414     564 .. 0.69
   3 ?    0.3   0.1       0.3   7.8e+02      36     124 ..     566     654 ..     557     701 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0079
                                       TT-BHHHHHHHHHHHTTTSEEEE.EESSGGG-HHHHHHHBSSEEEE CS
                   Sulfotransfer_3  85 aalasvilealarvpsyarwlvd.KsPshlfrldlllelfPdAkfi 129
                                       +ala++++   a+  +  ++l +    +hl rld+l++ +PdA+ i
  gi|313116844|ref|YP_004037968.1|  28 RALANRVCA--APFADDGSHLGEtSVRFHLDRLDALAARYPDATWI 71 
                                       344444332..34444455555534569***************987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHTTTSEEEEEESSGGG-HHHHHHHBSSEE CS
                   Sulfotransfer_3  89 svilealarvpsyarwlvdKsPshlfrldlllelfPdAk 127
                                        ++++a+a++++  r  +d   shl rl++l++ +Pd +
  gi|313116844|ref|YP_004037968.1| 444 VAHFNATAPAGKAGR--FDQVHSHLDRLETLAAEYPDTR 480
                                       444555555555444..4666677777777777777654 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.3
                                       T.-SBHHHHHHHHTT-S...TTTHHHHHHHHHH.T--HHHHHHHHHHHHHTT-BHHHHHHHHHHHTTTSEEEE..EE CS
                   Sulfotransfer_3  36 prllalleawskdgrelrrlldagltqeeaelp.hledaeepeedlqllraalasvilealarvpsyarwlvd..Ks 109
                                       p++++ +++++k    l  ++da ++  + +     +d    + + + ++++l+ v+ +al+++ ++a   +     
  gi|313116844|ref|YP_004037968.1| 566 PHVPEIRRRFAKA---LHGMMDALWSADRVDEArATMDRLRSAAAAFPADEELQCVSARALVNHSRNAGAACHldLL 639
                                       5555555533332...3333344333333333337777888888888888888888888888888777554432255 PP

                                       SSGGG-HHHHHHHBS CS
                   Sulfotransfer_3 110 PshlfrldlllelfP 124
                                         hl +l +l+e +P
  gi|313116844|ref|YP_004037968.1| 640 SDHLDQLVTLYESYP 654
                                       666666666666666 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         3   7.6e+03      18      32 ..       4      18 ..       2      19 .. 0.82
   2 ?   -1.3   0.0       1.7   4.4e+03      22      32 ..      57      67 ..      55      68 .. 0.82
   3 ?    6.3   0.3    0.0067        17       2      33 .]      78     112 ..      77     112 .. 0.92
   4 ?   -2.4   0.0       3.8   9.8e+03      15      32 ..     283     300 ..     278     301 .. 0.82
   5 ?   -2.3   0.0       3.7   9.4e+03       1      11 [.     347     357 ..     347     367 .. 0.79
   6 ?   -2.9   0.0       5.7   1.5e+04      18      31 ..     420     433 ..     417     433 .. 0.82
   7 ?    0.7   0.0      0.41   1.1e+03      22      33 .]     468     479 ..     466     479 .. 0.86
   8 ?    0.4   0.1      0.52   1.3e+03       2      33 .]     490     524 ..     489     524 .. 0.64
   9 ?   -1.9   0.0       2.7   6.9e+03      22      31 ..     557     566 ..     538     567 .. 0.77
  10 ?    4.0   0.1     0.035        90       2      27 ..     578     603 ..     577     606 .. 0.90
  11 ?    1.5   0.0      0.22   5.7e+02      15      32 ..     678     698 ..     659     699 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3
                                      HHHHHHHHHHHH-TT CS
                             TPR_6 18 kAlealerlikeYPd 32
                                      + l+ l+rl +++P+
  gi|313116844|ref|YP_004037968.1|  4 ACLDRLDRLTDDHPE 18
                                      5678899******96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                                      HHHHHHHH-TT CS
                             TPR_6 22 alerlikeYPd 32
                                       l+ l  +YPd
  gi|313116844|ref|YP_004037968.1| 57 RLDALAARYPD 67
                                      578999****9 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0067
                                       HHHHHHHHHHHH...HHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   2 Alyklalsyrkl...gdtdkAlealerlikeYPdS 33 
                                       Aly++a +   +    d + A + l+ l ++YPd+
  gi|313116844|ref|YP_004037968.1|  78 ALYNAAVAAADGdhvADRRSAQARLDALATDYPDT 112
                                       9999999999998888999**************96 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHHH-TT CS
                             TPR_6  15 dtdkAlealerlikeYPd 32 
                                       ++++ l+ l +l +e+P+
  gi|313116844|ref|YP_004037968.1| 283 EHERYLDRLSELATEFPT 300
                                       5677888999999***96 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyr 11 
                                       d+l+ la++++
  gi|313116844|ref|YP_004037968.1| 347 DVLFELAQALE 357
                                       68999999987 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 5.7
                                       HHHHHHHHHHHH-T CS
                             TPR_6  18 kAlealerlikeYP 31 
                                       + ++ le+ ++eYP
  gi|313116844|ref|YP_004037968.1| 420 ACIDQLEEMVTEYP 433
                                       5678899999***9 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 0.41
                                       HHHHHHHH-TT- CS
                             TPR_6  22 alerlikeYPdS 33 
                                        le l  eYPd+
  gi|313116844|ref|YP_004037968.1| 468 RLETLAAEYPDT 479
                                       6999******96 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHHHH...HHHHHHHHHHHH-TT- CS
                             TPR_6   2 Alyklalsyrklgdtd...kAlealerlikeYPdS 33 
                                       Al++ a+ + ++++ d   + ++  e+l   YP S
  gi|313116844|ref|YP_004037968.1| 490 ALFNTAKYQGQADRFDaltDTIDRAEELAATYPSS 524
                                       66666766665523333336667999999999987 PP

  == domain 9  score: -1.9 bits;  conditional E-value: 2.7
                                       HHHHHHHH-T CS
                             TPR_6  22 alerlikeYP 31 
                                        l++l+++YP
  gi|313116844|ref|YP_004037968.1| 557 RLDDLVTDYP 566
                                       6889999999 PP

  == domain 10  score: 4.0 bits;  conditional E-value: 0.035
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerli 27 
                                       Al  +  ++ ++++ d+A+++++rl+
  gi|313116844|ref|YP_004037968.1| 578 ALHGMMDALWSADRVDEARATMDRLR 603
                                       8889999999999***********97 PP

  == domain 11  score: 1.5 bits;  conditional E-value: 0.22
                                       HHH...HHHHHHHHHHHH-TT CS
                             TPR_6  15 dtd...kAlealerlikeYPd 32 
                                       + d   ++l+ l++l  +YPd
  gi|313116844|ref|YP_004037968.1| 678 QFDdlfRSLDRLDDLAAKYPD 698
                                       44444489999*********8 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.11   2.7e+02      19      43 ..       4      28 ..       1      29 [. 0.85
   2 ?    0.0   1.4      0.85   2.2e+03      19      43 ..      75      99 ..      60     102 .. 0.84
   3 ?    2.6   1.9      0.12   3.2e+02      17      43 ..      95     121 ..      78     123 .. 0.76
   4 ?    0.7   0.0       0.5   1.3e+03       7      28 ..     125     147 ..     122     164 .. 0.79
   5 ?    3.4   0.1      0.07   1.8e+02      17      43 ..     232     261 ..     227     262 .. 0.76
   6 ?    1.1   0.1      0.36   9.3e+02      17      42 ..     281     309 ..     268     311 .. 0.66
   7 ?    2.5   0.2      0.13   3.4e+02      17      43 ..     325     354 ..     303     355 .. 0.69
   8 ?    4.8   0.0     0.024        62      16      43 ..     417     444 ..     402     445 .. 0.83
   9 ?   -0.8   0.0       1.5   3.9e+03      14      41 ..     456     487 ..     455     490 .. 0.57
  10 ?    1.3   0.2      0.32   8.1e+02      15      42 ..     502     532 ..     485     534 .. 0.66
  11 ?    2.1   0.2      0.18   4.6e+02       6      43 ..     537     577 ..     532     579 .. 0.75
  12 ?    6.4   3.5    0.0074        19       3      43 ..     578     621 ..     576     622 .. 0.80
  13 ?    2.2   0.1      0.17   4.4e+02      13      33 ..     675     695 ..     657     708 .. 0.73
  14 ?    3.6   0.0     0.058   1.5e+02      13      42 ..     718     750 ..     710     752 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.11
                            TPR_14 19 eAiallrralalaPddaeawlllaq 43
                                      + ++ l+r+ +++P+d e++l+ a+
  gi|313116844|ref|YP_004037968.1|  4 ACLDRLDRLTDDHPEDTEIQLQFAR 28
                                      5677899999**********99887 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.85
                            TPR_14 19 eAiallrralalaPddaeawlllaq 43
                                       A al+++a+a+a +d +a ++ aq
  gi|313116844|ref|YP_004037968.1| 75 LASALYNAAVAAADGDHVADRRSAQ 99
                                      5889999999999999998888777 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.12
                            TPR_14  17 pdeAiallrralalaPddaeawlllaq 43 
                                        + A a l+++  ++Pd ++++++la+
  gi|313116844|ref|YP_004037968.1|  95 RRSAQARLDALATDYPDTDDVQRMLAK 121
                                       445778888888899**********97 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.5
                            TPR_14   7 laeal.lalGdpdeAiallrral 28 
                                       la ++  ++G++++ +++l+r+ 
  gi|313116844|ref|YP_004037968.1| 125 LATFHdSEAGQFERVETHLDRLE 147
                                       666664689**********9985 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.07
                            TPR_14  17 pdeAiallrrala...laPddaeawlllaq 43 
                                       +d+  ++l+r+      +P+d+e++++la+
  gi|313116844|ref|YP_004037968.1| 232 YDTIQRYLDRLEGlagEYPTDEEIHRRLAE 261
                                       666777777764433578**********96 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.36
                            TPR_14  17 pdeAiallrrala...laPddaeawllla 42 
                                        de +++l+r+ +    +P+d+ +  +la
  gi|313116844|ref|YP_004037968.1| 281 SDEHERYLDRLSElatEFPTDDGITAQLA 309
                                       56677788887663336899999999988 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.13
                            TPR_14  17 pdeAiallrrala...laPddaeawlllaq 43 
                                       +++  ++l+r+ +   ++P +++++++laq
  gi|313116844|ref|YP_004037968.1| 325 FETQQRHLDRLHElayDHPHNDDVLFELAQ 354
                                       555567777777755668**********99 PP

  == domain 8  score: 4.8 bits;  conditional E-value: 0.024
                            TPR_14  16 dpdeAiallrralalaPddaeawlllaq 43 
                                       ++++ i+ l++++  +P + e++++la 
  gi|313116844|ref|YP_004037968.1| 417 ELRACIDQLEEMVTEYPLQSEIRIQLAV 444
                                       46679999999999************96 PP

  == domain 9  score: -0.8 bits;  conditional E-value: 1.5
                            TPR_14  14 lGdpdeAiallrrala...laPdda.eawlll 41 
                                       +G++d+   +l+r+      +Pd + e++ +l
  gi|313116844|ref|YP_004037968.1| 456 AGRFDQVHSHLDRLETlaaEYPDTRrEVHERL 487
                                       67788877777776551114565432566666 PP

  == domain 10  score: 1.3 bits;  conditional E-value: 0.32
                            TPR_14  15 GdpdeAiallrrala...laPddaeawllla 42 
                                       +++d+  +  +ra +   ++P+++e+++ +a
  gi|313116844|ref|YP_004037968.1| 502 DRFDALTDTIDRAEElaaTYPSSDEVQRTYA 532
                                       4555555555555443338899999998777 PP

  == domain 11  score: 2.1 bits;  conditional E-value: 0.18
                            TPR_14   6 alaeallalGdpdeAiallrrala...laPddaeawlllaq 43 
                                        +a a +++++++e + + +r+ +   ++P  +e++++ a+
  gi|313116844|ref|YP_004037968.1| 537 TAATAARRADRFEECRIHIDRLDDlvtDYPHVPEIRRRFAK 577
                                       56888999999999777777764433378999999998776 PP

  == domain 12  score: 6.4 bits;  conditional E-value: 0.0074
                            TPR_14   3 allalaeallalGdpdeAiallrr...alalaPddaeawlllaq 43 
                                       al  + +al+ +++ deA+a  +r   a a++P+d+e++   a+
  gi|313116844|ref|YP_004037968.1| 578 ALHGMMDALWSADRVDEARATMDRlrsAAAAFPADEELQCVSAR 621
                                       6677889*****************44445589***999987776 PP

  == domain 13  score: 2.2 bits;  conditional E-value: 0.17
                            TPR_14  13 alGdpdeAiallrralalaPd 33 
                                       ++G++d+  + l+r+ +la +
  gi|313116844|ref|YP_004037968.1| 675 EAGQFDDLFRSLDRLDDLAAK 695
                                       589****99999998665443 PP

  == domain 14  score: 3.6 bits;  conditional E-value: 0.058
                            TPR_14  13 alGdpdeAiallrrala...laPddaeawllla 42 
                                       ++G+ ++A+++l r+ a   ++P+d++++ +l 
  gi|313116844|ref|YP_004037968.1| 718 ENGRSETAEQCLGRIEAlaaAHPADEVIQSRLS 750
                                       679999999999997663346899999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (760 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 4418.03
//
Query:       gi|313116845|ref|YP_004037969.1|  [L=1410]
Description: hypothetical protein Hbor_33070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-05   24.2   5.1        1.6    9.1   2.3    5.1  3  AAA_16    AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.8   1.3       0.96    9.6   0.2    3.8  3  AAA_33    AAA domain


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00046       4.1      21      49 ..      18      45 ..       5      78 .. 0.79
   2 !    9.1   2.3   0.00018       1.6      24      52 ..     413     456 ..     404     596 .. 0.56
   3 ?    2.1   0.0     0.025   2.3e+02      78     136 ..    1224    1309 ..    1194    1316 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00046
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellrale 49
                                      s++ e++l+ G++ vGKs  +r++  ++e
  gi|313116845|ref|YP_004037969.1| 18 SPG-EVTLVLGAPSVGKSHHLRQVGPSVE 45
                                      333.89**************999875544 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00018
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd...............g 52 
                                       +++v+lsG++++GK +l+  ++++l++                +
  gi|313116845|ref|YP_004037969.1| 413 GGVVVLSGPKASGKRRLAANVATELTTWgatvrlsdlsrpdyiR 456
                                       479***********************994444444444444440 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.025
                            AAA_16   78 reellrqlldeaesaeleawrekleeala............................avpelagaeasrllellk 124 
                                        ++ l     ++++ a++e w +  +e+++                            av +++   ++rl ++l+
  gi|313116845|ref|YP_004037969.1| 1224 ARALAVVGRTNSDHANVETWLDVVTERIEatatravpedpaefvasvytrayvdtveAVEDDTTTWRRRLDNELR 1298
                                        3333333333344444555555555555555555444444444444445555653335555555555******** PP

                            AAA_16  125 rllallsrderp 136 
                                        +++a +s  ++p
  gi|313116845|ref|YP_004037969.1| 1299 AFAASASV-DDP 1309
                                        ***99998.443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.019   1.7e+02       1      25 [.      22      50 ..      22     111 .. 0.79
   2 ?    9.6   0.2   0.00011      0.96       1      35 [.     415     451 ..     415     536 .. 0.59
   3 ?   -2.9   0.1      0.76   6.8e+03      73      93 ..    1228    1248 ..    1215    1301 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.019
                            AAA_33  1 lvllvGlpGsGKstlaerl...lkklg.a 25
                                      ++l+ G+p +GKs+ ++++   +++l+ a
  gi|313116845|ref|YP_004037969.1| 22 VTLVLGAPSVGKSHHLRQVgpsVERLAaA 50
                                      67899***********9986665555543 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00011
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg..avllssdtlrr 35 
                                       +v+l G+++sGK  la +++ +l+  + +++  +l+r
  gi|313116845|ref|YP_004037969.1| 415 VVVLSGPKASGKRRLAANVATELTtwGATVRLSDLSR 451
                                       899*********************9966666666655 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.76
                            AAA_33   73 vildatnlsrrerarflklar 93  
                                        +++  tn ++++ + +l ++ 
  gi|313116845|ref|YP_004037969.1| 1228 AVVGRTNSDHANVETWLDVVT 1248
                                        555566666666655555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.82u 0.28s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 8772.93
//
Query:       gi|313116846|ref|YP_004037970.1|  [L=240]
Description: ribonuclease HI [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-08   35.5   0.0    9.4e-08   32.4   0.0    2.0  2  RNase_H   RNase H
      1e-05   25.4   0.0    1.5e-05   24.8   0.0    1.2  1  RVT_3     Reverse transcriptase-like


Domain annotation for each model (and alignments):
>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0     1e-11   9.4e-08       3      75 ..      80     158 ..      78     164 .. 0.78
   2 ?    0.8   0.0     0.055     5e+02      60      79 ..     179     198 ..     168     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1e-11
                                       SEEEEEEEEEECTTTCEEEEEEECTT...E..EEEEEECCCCHHHHHHHHHHHHHHH.TT.SC..SEEEEEES-HHH CS
                           RNase_H   3 avvvYtDGsclgnpgeggagavlykeg.ar..nisapleeaqtnnraELsAvieaLk.alksd..ekvniytDSkYv 73 
                                       + ++Y+DGs++gnpg++gagav+   + ++   + +p++ ++ nn+aE  A+   +   l +   ++++++ DS  v
  gi|313116846|ref|YP_004037970.1|  80 SFILYVDGSSRGNPGPAGAGAVIMDATeTElaRLGRPVSSRTGNNTAEYVALQLGIAgLLARYelQTLEVRIDSMTV 156
                                       679******************664443233457779999*************88887433333449999****9877 PP

                                       HH CS
                           RNase_H  74 vk 75 
                                       + 
  gi|313116846|ref|YP_004037970.1| 157 IR 158
                                       65 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.055
                                       SCSEEEEEES-HHHHHHHHC CS
                           RNase_H  60 sdekvniytDSkYvvkgitq 79 
                                       s   v++y+DS ++ + i +
  gi|313116846|ref|YP_004037970.1| 179 SRRLVTLYSDSWWTSGKISS 198
                                       456789*****999887776 PP

>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.7e-09   1.5e-05       2      76 ..      85     160 ..      84     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-09
                             RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLq.lalklgirrlvvegDsktvvqll 76 
                                       +dg+ + + g +gag+vi d++   l+   +++++++ + +AE+ AL  G+  l ++++++ l+v +Ds+tv++ +
  gi|313116846|ref|YP_004037970.1|  85 VDGSSRGNPGPAGAGAVIMDATETELARLGRPVSSRTGNNTAEYVALQLGIAgLLARYELQTLEVRIDSMTVIRDV 160
                                       799999************************9********************84667889*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1581.19
//
Query:       gi|313116847|ref|YP_004037971.1|  [L=344]
Description: hypothetical protein Hbor_33100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2643.54
//
Query:       gi|313116848|ref|YP_004037972.1|  [L=34]
Description: hypothetical protein Hbor_33110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       170  (0.00948185); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 252.00
//
Query:       gi|313116849|ref|YP_004037973.1|  [L=397]
Description: ferrichrome-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-14   52.5   0.0    6.6e-14   52.0   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   3.7e-18   6.6e-14      26     237 ..     101     344 ..      83     345 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 3.7e-18
                                       GGG--GGGGGGT.........TS-BSBESSSB-H..HHHHHH--SEEEE-GGG.........GGGHHHHHHHS-EEE CS
                      Peripla_BP_2  26 tttsdpldadklee.......aivevgadgeidv..EklaalkPDlvilskgl......gltdedeellksgiptvi 87 
                                       ++++ pl++++++        a+ ++g + e  +  E   +++ D+ ++++++       + ++ ee++++  p + 
  gi|313116849|ref|YP_004037973.1| 101 AFDRLPLKYYDALPgvdfdadAVRTLGESAESKYdkEVFYDVDADVHLMDSRMlkkysgWDDEDLEEIESNVGPILG 177
                                       55555555555555555555544445555555554466667777777777777666665455666666666667777 PP

                                       ----TTS......HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.....-EEEEEEEETTE..EEEE CS
                      Peripla_BP_2  88 vessntg......eslkeqiralgellgledeaeklvaeidsklaaaksaidse....kpkpvlvfggadeggyvva 154
                                          ++ +      + l+e ++  ++++++++++e++v+  +s +a+++s+++         +++ fg+++e+g+++a
  gi|313116849|ref|YP_004037973.1| 178 SLIRFPFggrdpyYTLYEAFEKAAQIFQRQAQYEAWVTLKESFYADIESRVPVSggdePTVAAFNFGFDPESGKFFA 254
                                       7777777899999***************************************9998433334455667777888888 PP

                                       -TTSTT...THHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH....HHHT-S--HHHHT-SHHHHTSH CS
                      Peripla_BP_2 155 gsnsyi...gdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr....aeadnktgleflkenpllaelp 224
                                       ++       +  ++ lg++n+++ +    +++++ E +l  dpd+i + g     ++++ ++++e  + +++l++l 
  gi|313116849|ref|YP_004037973.1| 255 ANIDAPrndTRSFRMLGVNNAFQGEEYVPFKPVGIEKLLDVDPDYIGMIGYlsyiDDSQLQKVVETAQDHDVLSQLR 331
                                       877655222568999******99988999********************99************************** PP

                                       HHHTT-EEEE-HH CS
                      Peripla_BP_2 225 AvkngrVyaldss 237
                                       Av+ng++++++ +
  gi|313116849|ref|YP_004037973.1| 332 AVENGNFVRTGGQ 344
                                       ********99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2747.36
//
Query:       gi|313116850|ref|YP_004037974.1|  [L=311]
Description: thioredoxin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-10   39.5   0.3    2.2e-07   30.4   0.0    2.3  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.7e-06   27.5   1.6    0.00069   18.9   0.2    2.8  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    3.1e-06   26.5   1.4    0.00027   20.1   0.4    2.3  2  Lycopene_cycl  Lycopene cyclase protein
    1.7e-05   24.2   0.5    6.4e-05   22.4   0.2    2.1  2  FAD_binding_3  FAD binding domain
    3.9e-05   23.8   0.3    0.00011   22.4   0.3    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    8.8e-05   21.4   0.1     0.0011   17.7   0.1    2.3  2  HI0933_like    HI0933-like protein
    0.00047   19.4   0.9    0.00047   19.4   0.9    3.3  2  FAD_binding_2  FAD binding domain
    0.00051   20.6   3.7     0.0075   16.8   0.1    2.9  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00067   19.0   0.6     0.0027   17.0   0.1    2.0  2  Thi4           Thi4 family
     0.0015   17.9   1.7     0.0015   17.9   1.7    2.2  2  FAD_oxidored   FAD dependent oxidoreductase
     0.0023   17.1   0.9     0.0023   17.1   0.9    2.1  2  GIDA           Glucose inhibited division protein A
     0.0045   16.6   3.7     0.0045   16.6   3.7    3.9  4  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
       0.11   12.4   9.4       0.94    9.5   0.1    3.0  3  NAD_binding_9  FAD-NAD(P)-binding
        1.2    8.9   2.9          1    9.2   0.1    2.0  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
        1.4    8.5   3.7       0.41   10.3   0.2    1.9  2  ApbA           Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.9e-10   2.2e-07       2     107 ..       7     111 ..       6     143 .. 0.80
   2 !    7.0   0.1    0.0025         3     260     294 .]     146     177 ..     136     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.9e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielllg 72 
                                       dvv++GgGpAG+a+   +a++g++v+++ ++g+  +++c   + +lg+++  +i++      ++   +++g +l+ +
  gi|313116850|ref|YP_004037974.1|   7 DVVIVGGGPAGCAVGVCIARYGLDVVIF-DRGNSSLRRCAFLENYLGFPAGIDIETfyklmhDH--AVEAGCDLVSD 80 
                                       8***************************.************99999999999999999998733..55666666666 PP

                                       CTCEEEEESCEEEEETEEECTCEEEEEESEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAt 107
                                         v ++++  +++ ++   +++e+++   ++v At
  gi|313116850|ref|YP_004037974.1|  81 -MVESVERTDGNFRVR---TQEERSVLVPRVVAAT 111
                                       .666666666777773...3445666666666665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0025
                                       --TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 260 vdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                        d  +rt+++g+y++G  a   g  e++ +A  +G
  gi|313116850|ref|YP_004037974.1| 146 ADADGRTSIDGLYVAGGLA---GHGEQVLVAAGHG 177
                                       58999**************...8888988888776 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   5.8e-07   0.00069       1      32 [.       9      39 ..       9      47 .. 0.94
   2 !    5.8   0.0    0.0058       6.9     102     132 ..      80     111 ..      77     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.8e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni 32
                                      +I+G+GPaG a+++ + + gl d++i ++gn 
  gi|313116850|ref|YP_004037974.1|  9 VIVGGGPAGCAVGVCIARYGL-DVVIFDRGNS 39
                                      7********************.8******985 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0058
                       Pyr_redox_3 102 eeVesvkkedegfevetske.tyeAkkviiAt 132
                                        +Vesv+++d++f+v+t++e ++  ++v+ At
  gi|313116850|ref|YP_004037974.1|  80 DMVESVERTDGNFRVRTQEErSVLVPRVVAAT 111
                                       589**************998688888888887 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.4   2.3e-07   0.00027       1      38 [.       7      42 ..       7      47 .. 0.94
   2 !    5.0   0.0    0.0088        11      87     140 ..      60     112 ..      54     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.3e-07
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllf 38
                                      Dvv++G+GpAg+++   +  a++gl vv+ + ++s+l+
  gi|313116850|ref|YP_004037974.1|  7 DVVIVGGGPAGCAVGVCI--ARYGLDVVIFDRGNSSLR 42
                                      9**************999..***********9999876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0088
                     Lycopene_cycl  87 krlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarg 140
                                       + + + ++ + ve+g  l++  vesve  +  + +v ++++r +  + vv a+ 
  gi|313116850|ref|YP_004037974.1|  60 ETFYKLMHDHAVEAGCDLVSDMVESVERTDG-NFRVRTQEERSVLVPRVVAATT 112
                                       678889999*****************99887.************9999999875 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   5.4e-08   6.4e-05       3      36 ..       7      40 ..       5      44 .. 0.92
   2 ?   -1.9   0.0       1.3   1.5e+03     107     139 ..      62      93 ..      54     109 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.4e-08
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                      dV+IVG+GpaG   +   +++G +vv+ ++ ++ 
  gi|313116850|ref|YP_004037974.1|  7 DVVIVGGGPAGCAVGVCIARYGLDVVIFDRGNSS 40
                                      8****************************98765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHTEEETCSEEEECCEECCCCCC CS
                     FAD_binding_3 107 leriLvehaeerglqvrfktevesleqdeegvt 139
                                       + +++ +ha+e+g+++     ves+e+++ + +
  gi|313116850|ref|YP_004037974.1|  62 FYKLMHDHAVEAGCDLVS-DMVESVERTDGNFR 93 
                                       567888999999988753.34666666655544 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.3   9.2e-08   0.00011       1      30 [.      10      39 ..      10      44 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.2e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                      IvG+G +G++    +a++g+dv++++++++
  gi|313116850|ref|YP_004037974.1| 10 IVGGGPAGCAVGVCIARYGLDVVIFDRGNS 39
                                      9**************************985 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   9.3e-07    0.0011       2      38 ..       7      43 ..       6      46 .. 0.92
   2 ?    1.0   0.0      0.11   1.3e+02     129     162 ..      79     111 ..      53     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.3e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      dv+++GgG+AG    + +a+ g +V++++++++ +r+
  gi|313116850|ref|YP_004037974.1|  7 DVVIVGGGPAGCAVGVCIARYGLDVVIFDRGNSSLRR 43
                                      8**********9999999*************998875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.11
                                       S--EEEEECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 129 etevksvekeedgkfrvktkseeeleadklvlAt 162
                                       +  v+sve++ dg+frv+t++e+++   ++v At
  gi|313116850|ref|YP_004037974.1|  79 SDMVESVERT-DGNFRVRTQEERSVLVPRVVAAT 111
                                       5679999775.555*****999999999999886 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.9   3.9e-07   0.00047       1      33 [.       7      39 ..       7      45 .. 0.94
   2 ?    1.6   0.3     0.094   1.1e+02     379     405 ..     147     167 ..     133     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.9e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      Dv+++G+G AG+a ++ +a+ Gl+v++ + +++
  gi|313116850|ref|YP_004037974.1|  7 DVVIVGGGPAGCAVGVCIARYGLDVVIFDRGNS 39
                                      9**************************998875 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.094
                                       ETTSBESTTEEESSBTEEE-STCEESS CS
                     FAD_binding_2 379 dengrvldadgqpipGLYAaGevaagg 405
                                       d++gr+       i+GLY aG  a+ g
  gi|313116850|ref|YP_004037974.1| 147 DADGRT------SIDGLYVAGGLAGHG 167
                                       666666......9********999554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   6.2e-06    0.0075       2      35 ..       8      41 ..       7      50 .. 0.93
   2 ?    3.8   0.1      0.07        83      39      69 ..     233     263 ..     226     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.2e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      vv+vGgG  g+ ++  +a++g +V +++r++  l
  gi|313116850|ref|YP_004037974.1|  8 VVIVGGGPAGCAVGVCIARYGLDVVIFDRGNSSL 41
                                      8****************************99877 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.07
                                       SHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox  39 Deeaskilqeklekngievllntkveeiegs 69 
                                       D++++++  ++++++ ie++ +t + + e +
  gi|313116850|ref|YP_004037974.1| 233 DHDIEQERLQRIRQREIEFVKSTHLDRSEID 263
                                       899********************99887754 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.3e-06    0.0027      17      49 ..       5      36 ..       1      40 [. 0.91
   2 ?   -0.2   0.0      0.41   4.9e+02     161     178 ..     106     123 ..      84     175 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.3e-06
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                      + DvvivG+G++G + +  +a+  +l v+i++r
  gi|313116850|ref|YP_004037974.1|  5 NRDVVIVGGGPAGCAVGVCIARY-GLDVVIFDR 36
                                      68*********************.******987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.41
                                       EEEE--GSSSTTTTHHHH CS
                              Thi4 161 vvvdatGhdgeivavvvk 178
                                        vv at hdge    +  
  gi|313116850|ref|YP_004037974.1| 106 RVVAATTHDGEYLRGLDS 123
                                       477788888876554433 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.7   1.3e-06    0.0015       1      31 [.       7      37 ..       7      39 .. 0.95
   2 ?    0.7   1.4      0.23   2.7e+02     208     284 ..     203     277 ..     165     303 .. 0.46

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      Dvv+vGGgpaG+a  +  ar G  v++ ++ 
  gi|313116850|ref|YP_004037974.1|  7 DVVIVGGGPAGCAVGVCIARYGLDVVIFDRG 37
                                      9**************************9986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.23
                      FAD_oxidored 208 pfekkpegydparyelarvfeaklskgklpgektdvnwpr......vstdlienldlpeaeyegreqireeareltq 278
                                       ++ ++++++d ++ +  + +++++  ++ +++  d+  +r       +      +++ ++++ +r +i ++ ++  +
  gi|313116850|ref|YP_004037974.1| 203 DWLRRRAALDYDWDDE-ETWHRRFADHRVADD-HDIEQERlqrirqRE------IEFVKSTHLDRSEIDNRRERAHR 271
                                       3333333333333333.122222333344433.344444332222223......33334444444444433333333 PP

                      FAD_oxidored 279 gllkyl 284
                                        l+ +l
  gi|313116850|ref|YP_004037974.1| 272 RLATHL 277
                                       333333 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.9   1.9e-06    0.0023       1      29 [.       7      38 ..       7      75 .. 0.85
   2 ?   -0.6   0.3      0.46   5.5e+02     354     386 ..     153     186 ..     150     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.9e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE...E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi...t 29
                                      dv+++GgG AGc+  + +ar G++v+++    
  gi|313116850|ref|YP_004037974.1|  7 DVVIVGGGPAGCAVGVCIARYGLDVVIFdrgN 38
                                      79************************994443 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.46
                                       SSBTEEE-CGGGTB.-SHHHHHHHHHHHHHHHHH CS
                              GIDA 354 kvkgLflAGqinGt.eGYeEaaaqGllAGinaar 386
                                       +++gL++AG + G  e  + aa+ G+  G+ + +
  gi|313116850|ref|YP_004037974.1| 153 SIDGLYVAGGLAGHgEQVLVAAGHGMTVGRELLA 186
                                       5899*****9999865566778899998887665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.7   3.8e-06    0.0045       1      30 [.       7      38 ..       7      45 .. 0.94
   2 ?    2.5   0.0     0.073        88     146     200 ..      60     111 ..      45     137 .. 0.75
   3 ?    3.5   0.5     0.037        45     320     349 ..     150     178 ..     119     180 .. 0.82
   4 ?    0.5   1.6      0.31   3.7e+02      70     125 ..     193     248 ..     181     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.8e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                      dvvi+GGG +G+++    ar g  V+++++g+
  gi|313116850|ref|YP_004037974.1|  7 DVVIVGGGPAGCAVGVCIARYGldVVIFDRGN 38
                                      9*****************************94 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.073
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE-- CS
                               DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaa 200
                                       + + + + + a ++G++++    v+++e++dg   +v   t++e+ + +  vV a+
  gi|313116850|ref|YP_004037974.1|  60 ETFYKLMHDHAVEAGCDLVSD-MVESVERTDGN-FRV--RTQEERsVLVPRVVAAT 111
                                       5566778899**********9.9****998877.888..55544323235577776 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.037
                                       EEEETEEEEEEEEECTTTHHHHHHHHHHHH CS
                               DAO 320 getpgvkglylatGhsghGltlapatGkll 349
                                       g+t+  +gly+a G  ghG +   a+G+ +
  gi|313116850|ref|YP_004037974.1| 150 GRTS-IDGLYVAGGLAGHGEQVLVAAGHGM 178
                                       4443.68**************999999876 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.31
                                       HHHHHHSSTTS.EEEEEEEEEESSHHHHHHHHHHHHHH...HHTTTTEEEEEHHHHHHHS CS
                               DAO  70 eleeelgidid.yrrtGllslaadeeelealdkllall...leagldaelldaeevrele 125
                                        + ee +++ d +rr+  l + +d+  +e + +++a+     +++++ e l +  +r++e
  gi|313116850|ref|YP_004037974.1| 193 GYWEEAAPHYDwLRRRAALDYDWDD--EETWHRRFADHrvaDDHDIEQERLQR--IRQRE 248
                                       5667788888856667777776664..77777777765555445555555555..33333 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0016       1.9       1      37 [.       9      41 ..       9      49 .. 0.83
   2 ?    9.5   0.1   0.00078      0.94     114     155 ..      72     113 ..      60     114 .. 0.84
   3 ?   -2.6   0.7       4.1   4.9e+03      71      93 ..     203     223 ..     196     278 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepg 37
                                      +ivG+Gp+G av   +++       l++ +fd+ +++ 
  gi|313116850|ref|YP_004037974.1|  9 VIVGGGPAGCAVGVCIARY-----GLDVVIFDRgNSSL 41
                                      7************999998.....5999***9966656 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00078
                     NAD_binding_9 114 gvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       +   +++++ v+++e+++++++v++++++s+ + +Vv A+ h
  gi|313116850|ref|YP_004037974.1|  72 EAGCDLVSDMVESVERTDGNFRVRTQEERSVLVPRVVAATTH 113
                                       4457789999******************************99 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.1
                     NAD_binding_9  71 eWlrergaleeaeeldpddfvpR 93 
                                       +Wlr+r+al++  ++d+++   R
  gi|313116850|ref|YP_004037974.1| 203 DWLRRRAALDY--DWDDEETWHR 223
                                       67777776333..2222222222 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00085         1       2      38 ..       8      44 ..       7      48 .. 0.93
   2 ?   -0.8   0.6         1   1.2e+03      32      89 ..     238     298 ..     228     302 .. 0.42

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00085
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                                      v ++G G  G  +   +a+ gl+Vv++d+ +++l+++
  gi|313116850|ref|YP_004037974.1|  8 VVIVGGGPAGCAVGVCIARYGLDVVIFDRGNSSLRRC 44
                                      89***************************99998875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHHCCTTTTSS-....HHHHCCCHHCEEEES-...HHHHHC-SEEEE-S-SS CS
                           3HCDH_N  32 eealekalekieksleklvekgklk....eeeveaalarisfttd...leeavdadlviEavvEn 89 
                                       +e+l    ++i+++  ++v++ +l+    ++ +e+a  r+ ++ d   l e++d d  +E v+E+
  gi|313116850|ref|YP_004037974.1| 238 QERL----QRIRQREIEFVKSTHLDrseiDNRRERAHRRLATHLDeelLLEVIDDDRLQEYVAEQ 298
                                       3333....444444444444444441111233333333333333311122333556666666665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00035      0.41       1      33 [.       8      41 ..       8      48 .. 0.90
   2 ?   -3.7   0.4       6.8   8.2e+03      10      26 ..     156     172 ..     156     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rl 33
                                      ++i+G G  G+ +++++a+ g dv++ +r++  l
  gi|313116850|ref|YP_004037974.1|  8 VVIVGGGPAGCAVGVCIARYGLDVVIFDRGNsSL 41
                                      68***************************99555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.8
                                       HHHHHHHHHHHTHCEEE CS
                              ApbA  10 GsllaakLakagadvtl 26 
                                       G ++a+ La +g++v +
  gi|313116850|ref|YP_004037974.1| 156 GLYVAGGLAGHGEQVLV 172
                                       88999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2173.38
//
Query:       gi|313116851|ref|YP_004037975.1|  [L=80]
Description: hypothetical protein Hbor_33140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.31s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 539.47
//
Query:       gi|313116852|ref|YP_004037976.1|  [L=409]
Description: sugar phosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-20   72.2   0.0    2.2e-19   69.4   0.0    2.3  3  Hydrolase_6     Haloacid dehalogenase-like hydrolase
    1.2e-19   70.6   0.1    2.3e-19   69.7   0.1    1.4  1  NUDIX           NUDIX domain
    1.2e-15   57.3   0.1    3.7e-15   55.7   0.1    1.9  1  Hydrolase_like  HAD-hyrolase-like
    8.9e-06   26.1   1.3    6.6e-05   23.3   1.3    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
    3.9e-05   23.8   0.0    0.00014   22.0   0.0    1.9  2  HAD_2           Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   6.2e-23   2.2e-19       1     100 [.       9     107 ..       9     108 .. 0.98
   2 ?   -0.6   0.0      0.42   1.5e+03       4      29 ..     147     172 ..     144     180 .. 0.84
   3 ?   -3.5   0.0       3.2   1.2e+04      74      95 ..     192     213 ..     188     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 6.2e-23
                                       EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkr 77 
                                       fl+ +dGvL  gd+++ +a+ ++n+l ++ k++ +lTN  + ++++++++l+++g+++te +++tsa a+a++l + 
  gi|313116852|ref|YP_004037976.1|   9 FLIGLDGVLSSGDEVLSNAVTTVNRLYDQDKQIRFLTNDPRPTRDTIVTRLRDFGIEVTETEIITSAWATAAFLDQ- 84 
                                       67889**********************************************************************9. PP

                                       SXXXEEEEESXHHHHHHHHHTTX CS
                       Hydrolase_6  78 kadkkvlvigeeglreelkeagf 100
                                       ++ ++  v+g+eglr+el++ag+
  gi|313116852|ref|YP_004037976.1|  85 QDISTTAVVGSEGLRSELRDAGI 107
                                       9********************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.42
                                       ESTTTSEETTEE-TTHHHHHHHHHHT CS
                       Hydrolase_6   4 DidGvLwrgdkaipgaaealnalraa 29 
                                         dG +   d + pga  +++a++a+
  gi|313116852|ref|YP_004037976.1| 147 NSDGAFSTPDGPAPGAGAIVRAVEAT 172
                                       5699999999*********9999875 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.2
                                       HHHHSXXXEEEEESXHHHHHHH CS
                       Hydrolase_6  74 lkkrkadkkvlvigeeglreel 95 
                                       l ++ ad++ +v+g +++ ++l
  gi|313116852|ref|YP_004037976.1| 192 LDEIAADQQAVVVGDNPATDIL 213
                                       6677788899999988877766 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.1   6.5e-23   2.3e-19       3     119 ..     271     387 ..     269     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 6.5e-23
                                       EEEEEEEEEETTSEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHS..EEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   3 rravgvvllnekgevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtG..leaellellgrlhylapydgp 77 
                                       r++vg+v+ ne +evLlvrr+  +   W+lP G+ve gE++ eA +RE++EEtG  +++e+l+ + + ++ + +  p
  gi|313116852|ref|YP_004037976.1| 271 RPGVGAVVVNETDEVLLVRRA--DNERWALPTGTVERGEAVDEAIIREMREETGlqISVEQLTGVYSRPHQQVFSYP 345
                                       799******************..6666***************************44444544444444444444444 PP

                                       EEE.EEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHH CS
                             NUDIX  78 ygd.eheilyvfl.eevegelepndenevsevrwvpleellkek 119
                                        g+  h+i+ +fl   + g+le++ ++ev e+ +++ ++l +++
  gi|313116852|ref|YP_004037976.1| 346 SGRaVHFITNCFLcTIDAGTLEVD-TDEVLEINFFESDDL-PAD 387
                                       444899999999977888888888.**************9.333 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.1     1e-18   3.7e-15       1      74 [.     179     250 ..     179     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1e-18
                                       E.STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   1 vlgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                       v+gKPep m+++al ++ +d ++ +++GD++atDi+gA++aG+ +vLV+   +++   + +  +p++ + +lae
  gi|313116852|ref|YP_004037976.1| 179 VIGKPEPLMFEMALDEIAAD-QQAVVVGDNPATDILGAHRAGLPGVLVADEQHTAPSDS-DFRQPDATIGTLAE 250
                                       68***************776.699**************************999997756.44799998888877 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   1.3   1.9e-08   6.6e-05       4     210 .]       9     219 ..       6     219 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.9e-08
                                       EEEESBTTTBCHHHHHHHHHHHH....CHHHHHHHHHH..HHCHHHHHHHHHHHHHHHHHHHHHHETTTE..HHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                         Hydrolase   4 vvfDkdGTLttgepsvedvivsa....alalaaaletg..sehpigkalvaaakarsgaltgfatfigrg..ayaig 72 
                                       +++ +dG+L  g  ++  ++  +    + + +  +      ++p    +v    + ++++t+ + ++     a+   
  gi|313116852|ref|YP_004037976.1|   9 FLIGLDGVLSSGDEVLSNAVTTVnrlyDQDKQIRF--LtnDPRPTRDTIVTRLRDFGIEVTETEIITSAWatAAFLD 83 
                                       55667888888885555544444222233333333..2558888888888888888777755555433333333333 PP

                                       HHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEH..HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                         Hydrolase  73 kpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnp..et 147
                                       +++  t        +   +++ ++g +    ++    v+  ad+ + + ++  a +++  +g   +++t+++   +t
  gi|313116852|ref|YP_004037976.1|  84 QQDISTTA--VVGSEGLRSELRDAGIDIT--EDAPEVVVVGADEQTTYLDIQRAARHID-QGA-QFVATNSDGafST 154
                                       33333333..2222233333344444444..448999999999999******9999988.566.4555555542267 PP

                                       HHHHHHHTT..GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 148 aeraanqlG..ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                       ++  a  +G   ++++a++++  ++++kp+p +++ a++e+ +  ++ ++VGD++  D+ ++ +Ag
  gi|313116852|ref|YP_004037976.1| 155 PDGPAPGAGaiVRAVEATVETVPTVIGKPEPLMFEMALDEI-AADQQAVVVGDNPAtDILGAHRAG 219
                                       7778888884333334444444444****************.66669***************9998 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.86   3.1e+03      82     129 ..      25      75 ..      21      79 .. 0.71
   2 !   22.0   0.0   3.9e-08   0.00014     133     174 ..     180     221 ..     165     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.86
                             HAD_2  82 dgvkelLeeLkeagyklgivTsk...sreaveekleqlgiesyFdvivtse 129
                                       +++  +++ L +++ ++   T+    +r+++   l+ +gie   + i+ts 
  gi|313116852|ref|YP_004037976.1|  25 SNAVTTVNRLYDQDKQIRFLTNDprpTRDTIVTRLRDFGIEVTETEIITSA 75 
                                       566778888888888888888875455667777777788887777777765 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 3.9e-08
                             HAD_2 133 kkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagik 174
                                         KP+p ++e al++  +++ ++++vGD+p tDi +a++ag+ 
  gi|313116852|ref|YP_004037976.1| 180 IGKPEPLMFEMALDEIAADQ-QAVVVGDNPaTDILGAHRAGLP 221
                                       459*************9876.5678****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2749.11
//
Query:       gi|313116853|ref|YP_004037977.1|  [L=395]
Description: MFS transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.1e-16   58.1  30.0    7.1e-16   58.1  30.0    2.1  2  MFS_1       Major Facilitator Superfamily
    6.4e-06   25.3   7.9     0.0026   16.7   0.2    2.3  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
        2.4    8.5   5.6        3.6    7.9   0.2    3.0  3  UPF0444     Transmembrane protein C12orf23, UPF0444
        2.5    8.1  10.0      0.095   12.7   2.8    2.2  2  HAP         Hydrophobic abundant protein (HAP)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1  30.0   1.6e-19   7.1e-16      13     351 ..      18     348 ..      12     349 .. 0.79
   2 !    6.6   8.5   0.00069       3.1      34      79 ..     335     380 ..     331     389 .. 0.64

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.6e-19
                             MFS_1  13 silgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfass...lw 86 
                                       ++++p+   +l ++ g+s seig+l +ly ++ + a +p+G+++dr+G rr l+l++l++a+g+  l+++++   + 
  gi|313116853|ref|YP_004037977.1|  18 GLIAPVWV-LLLQARGLSYSEIGFLGALYWAVLVSAEIPTGYIGDRLGYRRSLFLSALVTAVGVGGLALSHTivpFA 93 
                                       56777777.888999************************************************33333554422133 PP

                             MFS_1  87 lllvlrvlqGlga.galfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                       l l  +++   +  g++ +  ++++a   + +  + + g  +a   ++++ +++lg++++ s + +a+f++ a+++ 
  gi|313116853|ref|YP_004037977.1|  94 LALGTWAIGRTFRsGTADAWLYSALANSGAVDAYTTVHGRGQAIKLAATAATAILGSIVY-SQSLTAPFLLTALLLG 169
                                       445555555555546667777777777777788888888888989999999999999999.55799*********** PP

                             MFS_1 163 lafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsglltllplylqevl 238
                                         + ++l +  + + +r+ +++ ++     ++   + +k+++++p +  ++ +++llf+++  + ++  p+ + ++ 
  gi|313116853|ref|YP_004037977.1| 170 GNAAIVLSFPSTANMKRPFPAESTR----LETTRQE-LKQVFTQPGVRgFVSYTVLLFGLVEVTRTFIQPIVVGDQV 241
                                       **88755555444444444444444....5555566.********7755788888888888888888888889**** PP

                             MFS_1 239 glsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl..iGfg 313
                                       gl+ ++ +g+l+a + +v+a+++ ++ r+ + +g +r   +a +ll++++++l +l+v        +v  +  +   
  gi|313116853|ref|YP_004037977.1| 242 GLP-VIAVGVLYASFNIVAAGASAVTDRIERIIGLHRWFRIAPILLAASFVLLPILSVL-------AVPSFisMEAI 310
                                       ***.**************************99999888888888888888888888888.......44444025555 PP

                             MFS_1 314 lgfvfpsllalasdlappeeagtasglfntagslggal 351
                                       + + ++    +++d +  ++++t+++++++ag++++++
  gi|313116853|ref|YP_004037977.1| 311 WRVSQTFQSGVINDRTRDHRRATILSVVSMAGGVAAIV 348
                                       5556888888999999999****************997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00069
                             MFS_1  34 igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       ++ +  + +++a+v+ +++G+l+d fG+  +l + +l+f++g+ +l
  gi|313116853|ref|YP_004037977.1| 335 LSVVSMAGGVAAIVFRIVGGVLADLFGPLIMLAALALAFIIGGRVL 380
                                       4555666677777777777777777777777777777777773333 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   5.8e-07    0.0026      16      75 ..      18      77 ..       7      93 .. 0.87
   2 !   11.0   3.1     3e-05      0.14     166     379 ..     149     362 ..     136     368 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.8e-07
                        MFS_1_like 16 gsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilsllls 75
                                      g + P + + l+ +gl++seig++ ++  ++ + ++  +g + Dr+g r  + + +l+ +
  gi|313116853|ref|YP_004037977.1| 18 GLIAPVWVLLLQARGLSYSEIGFLGALYWAVLVSAEIPTGYIGDRLGYRRSLFLSALVTA 77
                                      7789*********************************************99876666554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3e-05
                        MFS_1_like 166 Gilidhysvnllp....ysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilg 238
                                       G ++   s         + all+   a +v+s+ + + ++    ++++ + +++q+l++++ +p v +f+  +++l 
  gi|313116853|ref|YP_004037977.1| 149 GSIVYSQSL---TapflLTALLLGGNAAIVLSFPSTANMKRPFPAESTRLETTRQELKQVFTQPGVRGFVSYTVLLF 222
                                       444333333...223665666666777788888888888888888888888889*********************** PP

                        MFS_1_like 239 mswgiienFlflYL..kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiiena 313
                                        ++ +  +F++     +++g + + +G+l a   +       +  ++ +++G+ +   ia ++ ++ f+l+ i++++
  gi|313116853|ref|YP_004037977.1| 223 GLVEVTRTFIQPIVvgDQVGLPVIAVGVLYASFNIVAAGASAVTDRIERIIGLHRWFRIAPILLAASFVLLPILSVL 299
                                       *********9977779***************9999999*********************************999766 PP

                        MFS_1_like 314 wlvlpievLhgisfgllwaaaveyvski....apksleatgqgllsglyfglGralGsliGGllwdlksa 379
                                        +  +i      s+ ++w +  ++ s +    + ++ +at+ +++s++  g+   +  ++GG+l dl+++
  gi|313116853|ref|YP_004037977.1| 300 AVPSFI------SMEAIWRVSQTFQSGVindrTRDHRRATILSVVSMA-GGVAAIVFRIVGGVLADLFGP 362
                                       554443......444444444444444300004444556666666655.566677777778777777765 PP

>> UPF0444  Transmembrane protein C12orf23, UPF0444
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.3   5.9e+03      34      46 ..      76      88 ..      67     105 .. 0.58
   2 ?    7.9   0.2   0.00079       3.6      51      78 ..     243     270 ..     218     276 .. 0.85
   3 ?    1.8   0.1     0.063   2.8e+02      62      79 ..     336     353 ..     325     358 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                           UPF0444 34 awvGgksLeltks 46
                                      + vG   L+l+++
  gi|313116853|ref|YP_004037977.1| 76 TAVGVGGLALSHT 88
                                      3333333444444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00079
                           UPF0444  51 vpevGvglvkgsvsavagGvsavgsava 78 
                                        p + vg+  +s+++va+G sav+ ++ 
  gi|313116853|ref|YP_004037977.1| 243 LPVIAVGVLYASFNIVAAGASAVTDRIE 270
                                       788999******************9875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.063
                           UPF0444  62 svsavagGvsavgsavas 79 
                                       sv  +agGv+a+  ++++
  gi|313116853|ref|YP_004037977.1| 336 SVVSMAGGVAAIVFRIVG 353
                                       788999999999888776 PP

>> HAP  Hydrophobic abundant protein (HAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.7      0.61   2.7e+03      59      78 ..     223     243 ..     205     277 .. 0.53
   2 ?   12.7   2.8   2.1e-05     0.095      24      81 ..     326     384 ..     316     388 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.61
                               HAP  59 glv.vtlsgvleivvgvvlll 78 
                                       glv vt + +  ivvg  ++l
  gi|313116853|ref|YP_004037977.1| 223 GLVeVTRTFIQPIVVGDQVGL 243
                                       444334444444555544444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.1e-05
                               HAP  24 kkasekvarltvrglldcvvallaqivsgllrviiglvvtlsgv.leivvgvvlllvdv 81 
                                       ++   + + l+v  + + v a++ +iv+g+l  + g ++ l+ + l  ++g  +llv++
  gi|313116853|ref|YP_004037977.1| 326 TRDHRRATILSVVSMAGGVAAIVFRIVGGVLADLFGPLIMLAALaLAFIIGGRVLLVAT 384
                                       55667778899*************************99999875499**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2997.45
//
Query:       gi|313116854|ref|YP_004037978.1|  [L=750]
Description: allosteric NADP-dependent malic enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-94  316.2   0.0    3.5e-94  315.7   0.0    1.2  1  PTA_PTB   Phosphate acetyl/butaryl transferase
    3.1e-28   98.8   0.3    6.8e-26   91.2   0.3    2.6  1  malic     Malic enzyme, N-terminal domain
    1.4e-21   76.9   0.2    3.8e-21   75.5   0.2    1.7  1  Malic_M   Malic enzyme, NAD binding domain
  ------ inclusion threshold ------
       0.03   14.2   0.1       0.11   12.3   0.0    2.0  2  DUF2732   Protein of unknown function (DUF2732)


Domain annotation for each model (and alignments):
>> PTA_PTB  Phosphate acetyl/butaryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.7   0.0   7.8e-98   3.5e-94       3     318 ..     430     744 ..     428     745 .. 0.97

  Alignments for each domain:
  == domain 1  score: 315.7 bits;  conditional E-value: 7.8e-98
                                       HHHHHHHHCTS--EEEES-TTSHHHHHHHHHHHHTTSSEEEEES-HHHHHHHHHHCTB--TT-EEE-TTT-CCHHHH CS
                           PTA_PTB   3 lerivekakkekkrivlpegedervlkAakelleegiadviLigdeaeikakaleldldlsgieivdpetsekleey 79 
                                       ++ +++ka++++kr++l+ege+e++++Aa++l+e gia+++Lig + +i +k++el+ld + + +v+p++ e  ++y
  gi|313116854|ref|YP_004037978.1| 430 MRVVMNKAQSDPKRVALAEGENEKTIRAASQLVEDGIAEPVLIGRRDHILQKTEELGLDFDPV-VVNPREGE-WTHY 504
                                       6789****************************************9999999999999999986.78999888.99** PP

                                       HHHHHHHCCCC.S-HCCHHHHTT.SHHHHHHHHHHTTSSSEEEE-TTS-HHHHHHHHHHCT-B-TT----EEEEEEE CS
                           PTA_PTB  80 adelyelrkrkgvtieearevvr.datyfaamlvklgeaDglvsGavnttadtlrpalqiiktkpgvklvSsvfiml 155
                                       +d lye r+rkg t +ea+e +r d +yfa  +v+ g+aD++++G++n +  +lrp lq+i+t++ ++ +++v ++ 
  gi|313116854|ref|YP_004037978.1| 505 VDYLYEHRQRKGLTRTEANELIRqDSNYFASVMVEMGDADAMLTGLTNHYPSALRPPLQVIGTAENANYAAGVYMLT 581
                                       ***************************************************************************** PP

                                       ETTEEEEEESSSS-SS--HHHHHHHHHHHHHHHHHCCSS--EEEEE-SSSTTSS-SHHHHHHHHHHHHHHH.H-TTS CS
                           PTA_PTB 156 ledrlllfaDcavnvnPtaeelaeialesaktakalgeeeprvAlLSyStkgsakgesvekvrealkivke.kapdl 231
                                        ++r+++ aD+ vn +P+ e lae++  +a+ ak+++  epr+AlLSyS++gs + e v k r+a++i++    +d+
  gi|313116854|ref|YP_004037978.1| 582 FRNRVVFCADTTVNLDPDEEVLAEVTKHTAELAKRFN-VEPRAALLSYSDFGSVETEGVRKPRNAVNILHDdPDVDF 657
                                       *************************************.*****************************9865157899 PP

                                       EEEEEE-HHHHH-HHHHHHH-TTSTTTT--SEEE-SSHHHHHHHHHHHHHCCTEEEEEEEEESBSS-EEE--TT--H CS
                           PTA_PTB 232 vvdGelqlDaAlseevaekkapesevaGkAnvlvfPdLeagnigykivqrlakaeaiGPilqGlakPvndlSrgasv 308
                                        vdGe+q+D Al+ee+  + +   e+ G AnvlvfP+Leagnigyk++qrl++aeaiGP+l+G++kPv +l rg++v
  gi|313116854|ref|YP_004037978.1| 658 PVDGEMQADTALVEEMLTETYEFAELDGPANVLVFPNLEAGNIGYKVLQRLGGAEAIGPMLVGMDKPVYVLQRGDEV 734
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                           PTA_PTB 309 edivnvaait 318
                                       +divn+a ++
  gi|313116854|ref|YP_004037978.1| 735 KDIVNLASVA 744
                                       *****99877 PP

>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.3   1.5e-29   6.8e-26       2     180 ..      17     147 ..      16     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 1.5e-29
                                       TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSB CS
                             malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeri 78 
                                       +k e+ ++k+++++  ++l+++Y+P+v+++c++++e++++a+   + +++                 v vv++g+++
  gi|313116854|ref|YP_004037978.1|  17 GKVEIATTKPTNTQ--RDLSLAYSPGVATPCRDIAENPEQAY-RNTVKGNL----------------VGVVSNGSAV 74 
                                       57889999999999..**************************.88888888................9********* PP

                                       TTTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHH CS
                             malic  79 LGlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveav 154
                                       LGlGd+G  a++++m+GK +L++++a+id   v++++ld                             + d f +av
  gi|313116854|ref|YP_004037978.1|  75 LGLGDIGaQASKPVMEGKGVLFKRFADID---VFDIELDLD---------------------------DPDTFTQAV 121
                                       *******9999******************...*********...........................99******* PP

                                       HHHHGCTSEEEE-S--CCHHHHHHHH CS
                             malic 155 kelfppkaliqfEDfkaknafeiler 180
                                       ++++p++++i++ED+ka+++fei++ 
  gi|313116854|ref|YP_004037978.1| 122 AAMEPTFGGINLEDIKAPECFEIESD 147
                                       ***********************975 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.2   8.4e-25   3.8e-21       3     229 ..     163     359 ..     161     364 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 8.4e-25
                                       HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S-.. CS
                           Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrek.. 77 
                                       gTa+++ a+l +a+ i gk+ls+ ++ ++GaG+a++  a    + +v+ G+ +    ++i + D +G+l e r++  
  gi|313116854|ref|YP_004037978.1| 163 GTAIISGAALQNAADIVGKNLSDLHVTFAGAGAAATATA----RFYVSLGIPR----ENITMCDIDGILSEARAEag 231
                                       9*********************************98665....5667778775....5799**********995434 PP

                                       .--TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS- CS
                           Malic_M  78 .leeekkpfakkkeelkeakdkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEat 153
                                        l+e+ +pfa  +++ +       Le++++   ++v +Gls v+g+ ++e+vr+ma+    Pii+++ NP+   E t
  gi|313116854|ref|YP_004037978.1| 232 dLNEFTEPFACGEDDGE-------LEDAMEG--ADVFVGLS-VGGIVSQEMVRTMAD---DPIIFAMANPDP--EIT 293
                                       48999999999888876.......9999996..69*****8.89***********85...7*********86..89* PP

                                       HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHH CS
                           Malic_M 154 aedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseee 229
                                        ed+ +  d+++++a+G          +  +++Q NN++ fP +  g++ +ra++i++em laaa+ala+l++e+ 
  gi|313116854|ref|YP_004037978.1| 294 YEDAKDARDDTVIMATG----------RSDYPNQVNNVLGFPFIFRGALDVRATEINEEMKLAAADALADLAREDV 359
                                       ****************8..........56789**************************************999876 PP

>> DUF2732  Protein of unknown function (DUF2732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.9   1.3e+04      14      29 ..     428     443 ..     424     444 .. 0.79
   2 ?   12.3   0.0   2.5e-05      0.11      40      67 ..     506     533 ..     503     539 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.9
                           DUF2732  14 ealavlLnkArseerk 29 
                                       e + v +nkA+s+ ++
  gi|313116854|ref|YP_004037978.1| 428 EMMRVVMNKAQSDPKR 443
                                       5678899999999876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.5e-05
                           DUF2732  40 naLaihiqqkelsavEaaeLLrkEaerf 67 
                                       + L +h q+k+l+++Ea eL+r+ +  f
  gi|313116854|ref|YP_004037978.1| 506 DYLYEHRQRKGLTRTEANELIRQDSNYF 533
                                       56889******************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 5345.62
//
Query:       gi|313116855|ref|YP_004037979.1|  [L=89]
Description: hypothetical protein Hbor_33180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   13.9   2.7      0.046   13.5   2.7    1.3  1  DUF4118   Domain of unknown function (DUF4118)


Domain annotation for each model (and alignments):
>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.7   2.6e-06     0.046      54      89 ..      34      69 ..      21      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-06
                           DUF4118 54 svllfnyfftpPyftltiadpeylltlvvflvvall 89
                                        +lf y+ + P+ +l++     l+tl++ +vv+++
  gi|313116855|ref|YP_004037979.1| 34 VGILFSYLYIRPVISLNMGPFPKLITLLLTIVVGIC 69
                                      3479******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 577.77
//
Query:       gi|313116856|ref|YP_004037980.1|  [L=122]
Description: hypothetical protein Hbor_33190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 853.68
//
Query:       gi|313116857|ref|YP_004037981.1|  [L=216]
Description: hypothetical protein Hbor_33200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-11   44.5   0.0      2e-11   43.8   0.0    1.4  1  HTH_20    Helix-turn-helix domain
      3e-05   23.5   0.0    9.1e-05   21.9   0.0    1.8  1  HTH_24    Winged helix-turn-helix DNA-binding
    0.00047   20.0   0.0    0.00081   19.2   0.0    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.042   13.8   0.0    1.8  2  MarR_2    MarR family
      0.037   14.3   0.0      0.058   13.7   0.0    1.3  1  DUF2513   Hypothetical protein (DUF2513)
      0.046   14.2   0.0       0.12   12.9   0.0    1.8  1  HTH_27    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   6.7e-15     2e-11       2      57 ..      33      87 ..      32      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 6.7e-15
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +++e L++++ +ri+r L  +e+  + ela +ld + ++++yHL++Leea+L+  v
  gi|313116857|ref|YP_004037981.1| 33 ELFETLGSETTYRIYRQL-HEEPKVPRELATALDSTIQNIHYHLNKLEEADLIQPV 87
                                      689***************.*********************************9765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0     3e-08   9.1e-05       3      48 .]      41      85 ..      40      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3e-08
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      et+++I++ L ++p+ + reLA +l+ ++++++++l++Lee+ lI+
  gi|313116857|ref|YP_004037981.1| 41 ETTYRIYRQLHEEPKVP-RELATALDSTIQNIHYHLNKLEEADLIQ 85
                                      78999999999999986.9************************995 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.7e-07   0.00081       6      45 ..      45      84 ..      40      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.7e-07
                                      HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +I ++L e+++   ela +l+ +  ++ +HL+kL+ea+L+
  gi|313116857|ref|YP_004037981.1| 45 RIYRQLHEEPKVPRELATALDSTIQNIHYHLNKLEEADLI 84
                                      6778999********************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.8   8.2e+03      11      20 ..       5      14 ..       5      23 .. 0.66
   2 ?   13.8   0.0   1.4e-05     0.042      23      52 ..      56      85 ..      40      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.8
                                      HHHHHCTTTS CS
                            MarR_2 11 LaaLgrrpgr 20
                                      L+++ +r+++
  gi|313116857|ref|YP_004037981.1|  5 LHEILHRERP 14
                                      7888888876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.4e-05
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLve 52
                                       ++ela +l+ + ++++++l++L++a L++
  gi|313116857|ref|YP_004037981.1| 56 VPRELATALDSTIQNIHYHLNKLEEADLIQ 85
                                      689*************************97 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.9e-05     0.058      34      68 ..      63      97 ..      34     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                           DUF2513 34 idgyskeeiiyhlkllaeagLieaekkkakssiis 68
                                      + + + ++i yhl +l+ea+Li+ ++++++++ ++
  gi|313116857|ref|YP_004037981.1| 63 ALDSTIQNIHYHLNKLEEADLIQPVDTWHSENGVE 97
                                      44456678*****************9999887444 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.1e-05      0.12      17      49 ..      52      85 ..      16      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                            HTH_27 17 rrkkl.adlcgrlnvedshisyslkkLtekGLve 49
                                      ++ k  ++l+ +l+ + ++i+y l+kL+e++L++
  gi|313116857|ref|YP_004037981.1| 52 EEPKVpRELATALDSTIQNIHYHLNKLEEADLIQ 85
                                      4444469*************************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1597.40
//
Query:       gi|313116858|ref|YP_004037982.1|  [L=224]
Description: hypothetical protein Hbor_33210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.15   11.8   0.0    1.2  1  MdcG      Phosphoribosyl-dephospho-CoA transferase MdcG


Domain annotation for each model (and alignments):
>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.5e-06      0.15     125     175 ..     109     158 ..      69     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.5e-06
                              MdcG 125 ylhesSDLDLlirvasalqlarlldllaaleaaavrlDgeielpsggaval 175
                                       +lh++SD  L +++ s++ +++ +  +++l+ ++  +Dg + l sg+  ++
  gi|313116858|ref|YP_004037982.1| 109 TLHNQSDTELTFNPYSWTIRRHSQSEWQQLQLQP-TADGTLTLSSGESQSW 158
                                       79****************************8888.9*********998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1598.12
//
Query:       gi|313116859|ref|YP_004037983.1|  [L=258]
Description: hypothetical protein Hbor_33220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.11   12.6   2.8       0.16   12.1   2.8    1.2  1  Involucrin2  Involucrin


Domain annotation for each model (and alignments):
>> Involucrin2  Involucrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.8   8.9e-06      0.16      11      25 ..       3      15 ..       1      17 [. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-06
                       Involucrin2 11 qqQkqqepqepELhL 25
                                      qq  q+++qe+E h+
  gi|313116859|ref|YP_004037983.1|  3 QQ--QEKSQEQEIHV 15
                                      33..36666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2092.34
//
Query:       gi|313116860|ref|YP_004037984.1|  [L=260]
Description: hypothetical protein Hbor_33230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1988.90
//
Query:       gi|313116861|ref|YP_004037985.1|  [L=263]
Description: hypothetical protein Hbor_33240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00017   21.4   0.0    0.00051   19.9   0.0    1.8  2  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0012   18.7   0.0     0.0033   17.3   0.0    1.7  2  MarR_2    MarR family
     0.0016   18.9   0.0     0.0038   17.7   0.0    1.5  1  HTH_27    Winged helix DNA-binding domain
  ------ inclusion threshold ------
       0.01   15.9   0.1      0.033   14.3   0.1    2.0  1  HTH_20    Helix-turn-helix domain
       0.02   14.8   0.0      0.093   12.7   0.0    2.0  2  MarR      MarR family
      0.025   14.9   0.0      0.052   13.9   0.0    1.5  1  Rrf2      Transcriptional regulator
       0.15   12.0   0.0        0.3   11.1   0.0    1.5  1  HTH_45    Winged helix-turn-helix
       0.17   12.0   0.0       0.36   10.9   0.0    1.6  1  HemN_C    HemN C-terminal domain
       0.19   11.6   0.0       0.39   10.6   0.0    1.5  1  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.6e-07   0.00051      22      58 ..      27      63 ..      23      82 .. 0.86
   2 ?   -3.7   0.0       5.8   1.2e+04      42      53 ..     128     139 ..     127     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.6e-07
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      p + +++   l++prs+  +++r+Le+kGlV  ++g+
  gi|313116861|ref|YP_004037985.1| 27 PQEKRTLTDSLDIPRSTLDDIVRELEEKGLVSYRDGE 63
                                      677889999**********************988776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.8
                                       HHHHHHHCTSEE CS
                              TrmB  42 vLrsLedkGlVe 53 
                                       +L++Le++  ++
  gi|313116861|ref|YP_004037985.1| 128 ILERLEKANDIR 139
                                       689999887665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06    0.0033       9      56 ..      18      62 ..      12      65 .. 0.83
   2 ?   -3.4   0.0       4.9   9.7e+03      41      48 ..     128     135 ..     126     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      + L  + + p      + l++ l++++s++  i+++L+++GLv +r+g
  gi|313116861|ref|YP_004037985.1| 18 DCLRTINDDPQ---EKRTLTDSLDIPRSTLDDIVRELEEKGLVSYRDG 62
                                      55666666663...6678999**********************99987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.9
                                       HHHHHHHT CS
                            MarR_2  41 ilkrLvaa 48 
                                       il+rL++a
  gi|313116861|ref|YP_004037985.1| 128 ILERLEKA 135
                                       89999988 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.9e-06    0.0038       9      48 ..      20      57 ..      13      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                      L++i+  +++++++ l + l++  s+   ++++L+ekGLv
  gi|313116861|ref|YP_004037985.1| 20 LRTIN--DDPQEKRTLTDSLDIPRSTLDDIVRELEEKGLV 57
                                      89999..********************************* PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.6e-05     0.033      16      59 ..      20      62 ..       2      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                      HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      lr +  ++++    l + ld++++tl++ +r+Lee gLv  ++ 
  gi|313116861|ref|YP_004037985.1| 20 LRTI-NDDPQEKRTLTDSLDIPRSTLDDIVRELEEKGLVSYRDG 62
                                      4444.555555556777889*******************98875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.6e-05     0.093       6      48 ..      17      58 ..      14      61 .. 0.81
   2 ?   -1.5   0.0       1.2   2.5e+03      36      45 ..     127     136 ..     123     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +++Lr++ + +p+    L + l + +st+  ++++Le+kGl++
  gi|313116861|ref|YP_004037985.1| 17 LDCLRTIND-DPQEKRTLTDSLDIPRSTLDDIVRELEEKGLVS 58
                                      556666644.4566679************************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHTT CS
                              MarR  36 rvldrLekkG 45 
                                       ++l rLek++
  gi|313116861|ref|YP_004037985.1| 127 TILERLEKAN 136
                                       6888999986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.6e-05     0.052      24      60 ..      26      62 ..      12      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvrG 60
                                       p + +++ ++ +i++s l  i+++L+++glv  + G
  gi|313116861|ref|YP_004037985.1| 26 DPQEKRTLTDSLDIPRSTLDDIVRELEEKGLVSYRDG 62
                                      44566899************************99988 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015       0.3       9      65 ..      17      73 ..      12      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlel 65
                                      +d L+ i+++ ++k  +  + ++  ++l+  +  L ekgl++ +++++ +T  G+  
  gi|313116861|ref|YP_004037985.1| 17 LDCLRTINDDPQEKRTLTDSLDIPRSTLDDIVRELEEKGLVSYRDGEWHTTPWGQLA 73
                                      6889999999999999***********************************999865 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018      0.36      35      65 ..      41      71 ..      11      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                            HemN_C 35 eellaaaleklqeqGLLeldggrlrltprGr 65
                                      + +l +++++l+e+GL++ ++g +++tp G 
  gi|313116861|ref|YP_004037985.1| 41 RSTLDDIVRELEEKGLVSYRDGEWHTTPWGQ 71
                                      5567899********************9886 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.39       9      50 ..      20      59 ..      17      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      L+ ++  pqe   + l + +++p+St   +++ L+e G+v +
  gi|313116861|ref|YP_004037985.1| 20 LRTINDDPQE--KRTLTDSLDIPRSTLDDIVRELEEKGLVSY 59
                                      6666666666..6788999*********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2015.60
//
Query:       gi|313116862|ref|YP_004037986.1|  [L=38]
Description: hypothetical protein Hbor_33250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 267.83
//
Query:       gi|313116863|ref|YP_004037987.1|  [L=214]
Description: hypothetical protein Hbor_33260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1620.91
//
Query:       gi|313116864|ref|YP_004037988.1|  [L=394]
Description: hypothetical protein Hbor_33270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-29  101.8  18.6    2.6e-14   53.4   4.4    3.1  3  PQQ_2            PQQ-like domain
    6.6e-13   48.7  34.8      0.033   14.7   0.7    8.3  8  PQQ_3            PQQ-like domain
    8.3e-07   28.7   3.7        1.7    8.7   0.2    6.6  7  PQQ              PQQ enzyme repeat
  ------ inclusion threshold ------
       0.19   11.7   0.0       0.38   10.7   0.0    1.4  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   4.4   5.8e-18   2.6e-14      98     236 ..      69     205 ..      52     206 .. 0.90
   2 !   46.2   1.9   9.4e-16   4.2e-12       5     114 ..     192     291 ..     190     318 .. 0.79
   3 !   22.0   0.5   2.2e-08   9.9e-05      17      91 ..     322     391 ..     309     394 .] 0.82

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 5.8e-18
                             PQQ_2  98 rlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtselsrvgdisgrpvvaeg 174
                                        +W  + ++++ +++ +++ p+v+ d+ vv +++  +v l+++dG + W r+l+ ++  s +  +g   ++pv+++g
  gi|313116864|ref|YP_004037988.1|  69 IQWKAHVSTSSVTDADVDTGPVVVADETVVLTTPESVVSLSLSDGTEQWRRSLTPATVPSVV-GIGEAPASPVLSNG 144
                                       689977777677778899999999999999999********************766767766.6************* PP

                             PQQ_2 175 tVyassgqgrllaldlatgrrlwskeissinglpildgdllyvvsagelialdratGavlWk 236
                                       + + ++ +g ++al++  g ++w ++ s+ +g p+++ d l+v +a+++++++  tG+++W+
  gi|313116864|ref|YP_004037988.1| 145 RAFLATANG-VVALEIDDGTVVWRNTDSTGTGVPVVTRDALFVPTADGITRFESDTGERQWT 205
                                       9999999**.8*********99*9999999*******************************8 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 9.4e-16
                             PQQ_2   5 vsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvv 81 
                                       +++++ +tG++ W+ d      +g+  av ++g +++  +  + valdaat +v+W++   +++ g p va+g v+v
  gi|313116864|ref|YP_004037988.1| 192 ITRFESDTGERQWTADA-----NGTRLAV-ANGSVVA--TDEQTVALDAATSEVRWRQP--EETSGYPVVADGTVYV 258
                                       8999***********86.....4554599.7777777..5899999************9..667899********99 PP

                             PQQ_2  82 vasdgqlialdaedGkrlWstqqrse.epaelrs 114
                                         + g+l++ + +dG+++W++++ ++ e+  + +
  gi|313116864|ref|YP_004037988.1| 259 T-ESGELLGRSLADGTEQWRIDRGRSfEMPVVTP 291
                                       8.799***************88777533333333 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 2.2e-08
                             PQQ_2  17 WrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlial 91 
                                       W ++   +lgg v +a   ++t+f+ +  + l+a+ +  G+ +W++++e + vg+  v +g +v v++dg+++a+
  gi|313116864|ref|YP_004037988.1| 322 WCSET--SLGGAV-TAA-TDDTVFTSQMDDGLTAFTTRFGEAVWRYSAEPE-VGSLAVLDGGIVSVSPDGTVVAI 391
                                       44433..456666.555.9*****************************999.5556**************99987 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.2    0.0059        27       9      36 ..      81     108 ..      68     112 .. 0.72
   2 !   13.2   0.3   2.2e-05     0.097       1      38 [.     113     159 ..     113     161 .. 0.67
   3 !    7.4   0.5    0.0015       6.6       1      31 [.     162     191 ..     162     197 .. 0.88
   4 !    7.0   0.5    0.0019       8.4       1      40 []     200     234 ..     200     234 .. 0.83
   5 !   13.6   0.1   1.6e-05     0.072       2      27 ..     236     259 ..     236     266 .. 0.78
   6 ?   -0.2   0.1      0.35   1.6e+03       1      10 [.     272     281 ..     272     311 .. 0.73
   7 !    7.8   0.1    0.0011       4.9       4      36 ..     321     352 ..     319     355 .. 0.74
   8 !   14.7   0.7   7.4e-06     0.033       1      36 [.     357     391 ..     357     394 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0059
                             PQQ_3   9 lpgpvnssp.avdgglvyvgtgdGtlyAl 36 
                                       ++++v ++p +v++ +v+ +t+  ++++l
  gi|313116864|ref|YP_004037988.1|  81 TDADVDTGPvVVADETVVLTTP-ESVVSL 108
                                       4568888887889******998.666655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.2e-05
                             PQQ_3   1 GevlWsv...........qlpgpvnsspavdgglvyvgtgdGtlyAlDa 38 
                                       G+++W++           +++ ++ +sp++++g+ + +t  ++++Al+ 
  gi|313116864|ref|YP_004037988.1| 113 GTEQWRRsltpatvpsvvGIG-EAPASPVLSNGRAFLATA-NGVVALEI 159
                                       899999965555444333333.334566***********9.77777765 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0015
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdG 31 
                                       G+v+W+ +    +++ p+v  + ++v t dG
  gi|313116864|ref|YP_004037988.1| 162 GTVVWRNTDS-TGTGVPVVTRDALFVPTADG 191
                                       99****9876.455889************98 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0019
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       Ge++W+ +  g     +av++g v++++     +AlDa+t
  gi|313116864|ref|YP_004037988.1| 200 GERQWTADANGT---RLAVANGSVVATD--EQTVALDAAT 234
                                       899999998873...38*******9987..5999999987 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 1.6e-05
                             PQQ_3   2 evlWsvqlpgpvnsspavdgglvyvg 27 
                                       ev+W+++    ++  p+v++g+vyv+
  gi|313116864|ref|YP_004037988.1| 236 EVRWRQPEETSGY--PVVADGTVYVT 259
                                       79****8666555..**********6 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 0.35
                             PQQ_3   1 GevlWsvqlp 10 
                                       G+++W+ + +
  gi|313116864|ref|YP_004037988.1| 272 GTEQWRIDRG 281
                                       8999999766 PP

  == domain 7  score: 7.8 bits;  conditional E-value: 0.0011
                             PQQ_3   4 lWsvql..pgpvnsspavdgglvyvgtgdGtlyAl 36 
                                       +W  ++  +g+v   +a+ +++v+++ +d +l+A+
  gi|313116864|ref|YP_004037988.1| 321 RWCSETslGGAV---TAATDDTVFTSQMDDGLTAF 352
                                       555544115555...6999***************9 PP

  == domain 8  score: 14.7 bits;  conditional E-value: 7.4e-06
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                       Ge +W+++   +v +s+av +g ++ +++dGt++A+
  gi|313116864|ref|YP_004037988.1| 357 GEAVWRYSAEPEV-GSLAVLDGGIVSVSPDGTVVAI 391
                                       7889****99888.77877666666779*******8 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.32   1.4e+03      11      32 ..     104     125 ..      96     130 .. 0.74
   2 !    8.7   0.2   0.00039       1.7       4      25 ..     147     167 ..     144     169 .. 0.82
   3 ?    0.2   0.0      0.19   8.6e+02      17      31 ..     197     211 ..     183     215 .. 0.83
   4 !    7.7   0.0    0.0008       3.6       3      29 ..     220     244 ..     218     246 .. 0.82
   5 ?   -3.0   0.0         2   8.8e+03       2      24 ..     255     276 ..     254     277 .. 0.58
   6 ?    3.7   0.0     0.014        64      20      37 ..     357     374 ..     338     375 .. 0.84
   7 ?    1.1   0.0     0.098   4.4e+02       1      15 [.     377     391 ..     377     394 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                                       EEEEEETTTCCEEEEEESSSCG CS
                               PQQ  11 ylyAlDadTGkvlWrfktggpv 32 
                                        ++ l +++G++ Wr  + ++ 
  gi|313116864|ref|YP_004037988.1| 104 SVVSLSLSDGTEQWRRSLTPAT 125
                                       667788999***9998887766 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00039
                                       EEEETTSEEEEEETTTCCEEEE CS
                               PQQ   4 ylgsadGylyAlDadTGkvlWr 25 
                                       +l++a+  ++Al +d+G+v+Wr
  gi|313116864|ref|YP_004037988.1| 147 FLATAN-GVVALEIDDGTVVWR 167
                                       666666.799***********7 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.19
                                       TTTCCEEEEEESSSC CS
                               PQQ  17 adTGkvlWrfktggp 31 
                                        dTG+  W+ +++g 
  gi|313116864|ref|YP_004037988.1| 197 SDTGERQWTADANGT 211
                                       689*****9999886 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0008
                                       EEEEETTSEEEEEETTTCCEEEEEESS CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWrfktg 29 
                                       v+++  d + +AlDa+T +v+Wr +++
  gi|313116864|ref|YP_004037988.1| 220 VVAT--DEQTVALDAATSEVRWRQPEE 244
                                       5555..7899*************9875 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 2
                                       EEEEEETTSEEEEEETTTCCEEE CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlW 24 
                                       +vy++   G l+   +++G++ W
  gi|313116864|ref|YP_004037988.1| 255 TVYVT-ESGELLGRSLADGTEQW 276
                                       56665.55566666667777666 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.014
                                       CCEEEEEESSSCGSSESE CS
                               PQQ  20 GkvlWrfktggpvlslpi 37 
                                       G+ +Wr+ ++++v sl +
  gi|313116864|ref|YP_004037988.1| 357 GEAVWRYSAEPEVGSLAV 374
                                       8889*********99876 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 0.098
                                       TEEEEEETTSEEEEE CS
                               PQQ   1 gvvylgsadGylyAl 15 
                                       g+++  s+dG+++A+
  gi|313116864|ref|YP_004037988.1| 377 GGIVSVSPDGTVVAI 391
                                       567888*******98 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.6e-05      0.38      38     108 ..      77     149 ..      68     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.6e-05
                   Methyltransf_18  38 akkviasDinegplekakeniekagledkievrlsdGleklkee.e.vdtvviaGmGgelileILeeakeklk 108
                                       +++v+ +D+ +gp+  a+e++  +  e+ +++ lsdG e+ +++   +++  + G+G    + +L++++  l+
  gi|313116864|ref|YP_004037988.1|  77 TSSVTDADVDTGPVVVADETVVLTTPESVVSLSLSDGTEQWRRSlTpATVPSVVGIGEAPASPVLSNGRAFLA 149
                                       5788999**********************************9663467888999***9999999999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2457.97
//
Query:       gi|313116865|ref|YP_004037989.1|  [L=101]
Description: hypothetical protein Hbor_33290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 790.54
//
Query:       gi|313116866|ref|YP_004037990.1|  [L=317]
Description: hypothetical protein Hbor_33300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-06   25.4   0.0    1.9e-05   24.3   0.0    1.6  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.1e-09   1.9e-05      31     227 ..      41     255 ..      15     294 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.1e-09
                                       GHHHHHHHHS..TS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBSSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Ribonuc_red_sm  31 lskDlkdwke..kLsedekefikkvlaflalldtivnenlverllsevqipearafygfqaamEniHaesYslllet 105
                                       l++D  ++ +   L e++ +++ + +a++ + +  v+e l+  l+  ++  +a++f++ q+++E+ H++ +  +   
  gi|313116866|ref|YP_004037990.1|  41 LKEDRTNLLTtdDLDEQQFDLLRSQIALFGAGEEAVTEDLA-PLALVLDDIDAQMFVASQIYEEAKHTQFFDRYWRE 116
                                       556655554445799999999999***************99.677899999************************** PP

                                       HT...........-HHHHHHHHCHHHH-HHHHHHHHHHHHHHCTTTSCHHHHHHHHHHH.HHHHC....CCHHHHHH CS
                    Ribonuc_red_sm 106 lvk..........dekekdelfnaieenpalqkkaewikkwyeskkdeekfaerlvafa.llegi....lfysgFaa 167
                                       +++          ++ + ++     +++ +l ++ e ++k + +++++e+ a++   +  ++e++     +y gF+a
  gi|313116866|ref|YP_004037990.1| 117 VIRpvteergyepTSPTDER--YFSDQYIELFDRTETAMKRLVTDDTPENRAKAFCHYHlVIESVlaqtAYY-GFTA 190
                                       **866666666642222233..33466677788888887777766666555555555544555553332333.3555 PP

                                       HHHHHHTTS.........SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHH CS
                    Ribonuc_red_sm 168 ilwlkkrgl.........lpglaeiielilrDeglHtdfagllfkelkeenelenkeleeeveelikea 227
                                        ++ ++ ++         lpgl e i++i  Deg H+ f++  +++l +e         + v+e+++ +
  gi|313116866|ref|YP_004037990.1| 191 RYSESRSEIhnttdamphLPGLLEGISYIRADEGRHVGFGMHSVRTLIHED----GVDDAVVRETLQSL 255
                                       44444332111122223499***************************9994....44444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2299.48
//
Query:       gi|313116867|ref|YP_004037991.1|  [L=260]
Description: hypothetical protein Hbor_33310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1671.67
//
Query:       gi|313116868|ref|YP_004037992.1|  [L=1039]
Description: ABC transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-21   75.4   0.1    6.5e-06   25.8   0.0    3.2  3  ABC_transp_aux  ABC-type uncharacterized transport system
    1.1e-11   45.0   5.1     0.0016   18.9   0.0    4.7  4  DUF4350         Domain of unknown function (DUF4350)
    3.2e-10   40.4   0.0    1.6e-08   34.9   0.0    2.4  2  SNase           Staphylococcal nuclease homologue
    2.1e-07   29.7   0.0    0.00033   19.1   0.0    3.0  3  DUF2194         Uncharacterised protein conserved in bacteria
    1.1e-06   29.0   0.4     0.0011   19.2   0.0    3.2  3  ThuA            Trehalose utilisation
    0.00069   20.0   0.0        4.3    7.8   0.0    3.6  3  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.066   12.0   0.1          2    7.2   0.0    2.7  3  DDOST_48kD      Oligosaccharyltransferase 48 kDa subunit beta


Domain annotation for each model (and alignments):
>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.5e-09   6.5e-06     155     261 ..      35     130 ..      25     137 .. 0.78
   2 !   21.5   0.0   5.3e-08   0.00013     166     235 ..     351     419 ..     300     443 .. 0.82
   3 !   24.1   0.0   8.3e-09   2.1e-05     135     258 ..     660     776 ..     658     782 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.5e-09
                    ABC_transp_aux 155 ghgelslsspse.adfleelee.nYnveevdldsedilpedidvlviakptkdlseeelykldqflmnGgkllvfld 229
                                       ghg+  +   ++ ++f +  e+ +Y+v++++  + d   ++ +++vi  p++++s+ el +l+ f+ +Gg +++  +
  gi|313116868|ref|YP_004037992.1|  35 GHGQYYNL--ARfSAFETYAESnGYDVQATSDLTADL--SGASAVVITSPSDAFSDAELSALSSFVAEGGAVFLHHQ 107
                                       66653332..4556799999999*******9998887..7******************************9876544 PP

                    ABC_transp_aux 230 pvaeeqdslsepsaaprtsnLedllaeyGvri 261
                                                    ++++t nL+ + +e+G+++
  gi|313116868|ref|YP_004037992.1| 108 SDFD---------DFDETDNLNTIASELGLSF 130
                                       4332.........3456777777777777655 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5.3e-08
                    ABC_transp_aux 166 e.adfleelee.nYnveevdldsedilpedidvlviakptkdlseeelykldqflmnGgkllvfldpvaeeq 235
                                       + ++f+++ e+ +Y+v +vd  + d   ++id++v   ++++ s++el +l  f++ Gg + ++ +   e++
  gi|313116868|ref|YP_004037992.1| 351 SfSNFVSNAESaGYTVSTVDSLDADL--SGIDLVVCS-QPQQPSDTELSALTTFVEDGGAVYAMGKSDYEDY 419
                                       224599999999**********8887..7****9999.99999******************99987766665 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 8.3e-09
                    ABC_transp_aux 135 ltsairkltdkkkpkvgfltghgelsls.s.p.se.adfleelee.nYnveevdldsedilpedidvlviakptkdl 206
                                       l+++i +l+dk+  +v +  ghg+       + +  a +++ le  + + e+v+++ +++l +d +++++  p +++
  gi|313116868|ref|YP_004037992.1| 660 LSNLIDSLSDKN-GDVLIDGGHGQFGAGyAlSsEDaAYYQRYLEGvGLTLEQVNTAYSERL-DDARAIIVTTPVSEF 734
                                       567899999988.99999999998877544336334557799999999************9.89************* PP

                    ABC_transp_aux 207 seeelykldqflmnGgkllvfldpvaeeqdslsepsaaprtsnLedllaeyG 258
                                       + +e+ +l++f  n+g ++++ ++ a          + ++t nLe+l +e+G
  gi|313116868|ref|YP_004037992.1| 735 TADEVAALSDFAANDGAVVLLGSAAA----------PGSTTANLERLASELG 776
                                       *********************99999..........3446888888888877 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.1e-07    0.0016       8      67 ..      46     104 ..      45     105 .. 0.84
   2 ?   -1.4   0.0       1.3   3.4e+03      34      56 ..     248     270 ..     225     272 .. 0.64
   3 !    9.7   0.0   0.00045       1.1      10      63 ..     355     406 ..     351     408 .. 0.83
   4 !   14.8   0.2   1.1e-05     0.029      13      68 ..     700     755 ..     696     756 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.1e-07
                           DUF4350   8 ralaelLeaqGvevrrvrkpfdalegedgtllvvapdlrlteeelaallewvarGntlvl 67 
                                       +a+ +++e+ G++v+++ ++  +l g+   +++++p   ++++el al  +va G+ ++l
  gi|313116868|ref|YP_004037992.1|  46 SAFETYAESNGYDVQATSDLTADLSGAS-AVVITSPSDAFSDAELSALSSFVAEGGAVFL 104
                                       79*************7666666666555.7788888868*****************9997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                           DUF4350  34 edgtllvvapdlrlteeelaall 56 
                                         +t l+ a++  +t+ e+ a+l
  gi|313116868|ref|YP_004037992.1| 248 YSATTLLAADGSPYTDGETTAVL 270
                                       45677777777688888887776 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00045
                           DUF4350  10 laelLeaqGvevrrvrkpfdalegedgtllvvapdlrlteeelaallewvarGn 63 
                                       +++ +e++G++v++v++++ +l g d  l+v ++    ++ el al  +v+ G+
  gi|313116868|ref|YP_004037992.1| 355 FVSNAESAGYTVSTVDSLDADLSGID--LVVCSQPQQPSDTELSALTTFVEDGG 406
                                       66667899**************9999..666666656777*************9 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 1.1e-05
                           DUF4350  13 lLeaqGvevrrvrkpfdalegedgtllvvapdlrlteeelaallewvarGntlvla 68 
                                       +Le  G ++++v + +++  +  + ++v++p   +t +e+aal +++a+ + +vl+
  gi|313116868|ref|YP_004037992.1| 700 YLEGVGLTLEQVNTAYSERLDDARAIIVTTPVSEFTADEVAALSDFAANDGAVVLL 755
                                       56666899999***99966666669*******99**************98888886 PP

>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.06   1.5e+02       2      17 ..     205     220 ..     204     238 .. 0.84
   2 !   34.9   0.0   6.4e-12   1.6e-08      18     108 .]     479     575 ..     467     575 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.06
                                       EEETTEE-STSSBTTT CS
                             SNase   2 vrLvgidaPetakpkk 17 
                                       +r +gid+Pe+a    
  gi|313116868|ref|YP_004037992.1| 205 IRVLGIDTPESASASD 220
                                       9**********97655 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 6.4e-12
                                       TTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEET.......TEEHHHHHHHTTSSEE---BTTST CS
                             SNase  18 tvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvyln.......kknineeLvkeGlArvyevyekne 85 
                                       ++ +++++A+ ++++++++k+ ++  +++   +D  +r+lay  ++       ++  n++++++GlAr   vy +  
  gi|313116868|ref|YP_004037992.1| 479 YLVNWANQATSVAEEELSGKTIEIYFDENegVRDPFDRVLAYADYDatgdgnrDTTYNAKMIEDGLAR---VYGSTL 552
                                       56789*************66666655555899*******************9999*************...566666 PP

                                       TTHHHHHHHHHHHHHTT-GGGCT CS
                             SNase  86 ekkkellkaeeeAkkkrkglWse 108
                                        +++e+  +e+ A+ + +glW+e
  gi|313116868|ref|YP_004037992.1| 553 SRHDEFWDLEHTARTEGRGLWNE 575
                                       799******************85 PP

>> DUF2194  Uncharacterised protein conserved in bacteria (DUF2194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.3e-07   0.00033      49     152 ..      58     157 ..      33     205 .. 0.79
   2 !    3.6   0.0    0.0066        17      71     132 ..     384     447 ..     356     454 .. 0.74
   3 !    3.1   0.0    0.0095        24      46     129 ..     707     787 ..     695     819 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-07
                           DUF2194  49 dveklnfskidlekYetVivtyyseeldklkeyLkqlvefvengGklffannlga..stdsselnsilnklGisyks 123
                                       dv+ + + + dl+   +V++t  s+ +++   +L++l++fv +gG +f+ ++      +++ +ln+i  +lG s+++
  gi|313116868|ref|YP_004037992.1|  58 DVQATSDLTADLSGASAVVITSPSDAFSD--AELSALSSFVAEGGAVFLHHQSDFddFDETDNLNTIASELGLSFRF 132
                                       66666778888888889999985555555..458***************9876551145566*************** PP

                           DUF2194 124 gykklevsgieiekeylikapstvkkpve 152
                                          ++++ + ++  +y+     t+++  +
  gi|313116868|ref|YP_004037992.1| 133 NDAQVTDATNNTGVNYVP----TTSQFND 157
                                       ****99999888888876....4444444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0066
                           DUF2194  71 yseeldklkeyLkqlvefvengGklffannlgast..dsselnsilnklGisyksgykklevsg 132
                                        s+  +  +++L++l++fve+gG +  + +  +++  ++ + n il   G  +++   ++ +s+
  gi|313116868|ref|YP_004037992.1| 384 CSQPQQPSDTELSALTTFVEDGGAVYAMGKSDYEDydNTTASNDILDAAGAPFRFNDAQVVDSE 447
                                       35666777889*************9988776665411555788888888888888777776666 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.0095
                           DUF2194  46 elkdveklnfskidlekYetVivtyyseeldklkeyLkqlvefvengGklffannlgastd.sselnsilnklGisy 121
                                        l++v++   +   l++ +++ivt   +  +  ++++ +l++f+ n G ++++    a  + + +l+++  +lG + 
  gi|313116868|ref|YP_004037992.1| 707 TLEQVNT--AYSERLDDARAIIVTT--PVSEFTADEVAALSDFAANDGAVVLLGSAAAPGStTANLERLASELGTDL 779
                                       5566666..4555566778888888..5666677889***********99987766554430469*********998 PP

                           DUF2194 122 ksgykkle 129
                                       + g+  + 
  gi|313116868|ref|YP_004037992.1| 780 RLGSAVTD 787
                                       88876654 PP

>> ThuA  Trehalose utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.4e-07    0.0011      19     143 ..      44     162 ..      29     181 .. 0.70
   2 !    5.1   0.0    0.0093        24      27      85 ..     359     411 ..     336     494 .. 0.80
   3 ?    0.6   0.0      0.21   5.4e+02      44      90 ..     715     760 ..     689     813 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.4e-07
                                       ..HHHHHH-HHHT-EEEEETTS.G--HHHHHT-SEEEEE-G..GS-HHHHHH.HHHHHHTT-EEEEEGGG.GS.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                              ThuA  19 aieaieklgkengfevdatedaavfteenLaqydvvvflstegevldaaqeaalqryveaGgGfvglhsA.adaeer 94 
                                          a+e  +++ng++v+at+d   +t++ L+  ++vv  s + + +++a+ +al ++v +Gg +   h+  +d +++
  gi|313116868|ref|YP_004037992.1|  44 RFSAFETYAESNGYDVQATSD---LTAD-LSGASAVVITSPS-DAFSDAELSALSSFVAEGGAVFLHHQSdFD-DFD 114
                                       4679999*************9...4666.***********96.7788888888***********999999887.443 PP

                                       .H.....HHH.HH-SEEEEET.............TSGGGTT--.SEEEEEEEEE- CS
                                       xx.....xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                              ThuA  95 sk.....wfsgLiGarfvghppvqeatvkvedr.shpateglpeewertdewYnf 143
                                        +       s+L G  f+ +      + +v+d  ++  ++ +p++ + +de+ +f
  gi|313116868|ref|YP_004037992.1| 115 ETdnlntIASEL-GLSFRFN------DAQVTDAtNNTGVNYVPTTSQFNDEFPYF 162
                                       222334433333.5555544......23344443555555555555555555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0093
                                       -HHHT-EEEEETTS.G--HHHHHT-SEEEEE-G..GS-HHHHHH.HHHHHHTT-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThuA  27 gkengfevdatedaavfteenLaqydvvvflstegevldaaqeaalqryveaGgGfvgl 85 
                                       ++++g++v+ t d+    ++ L+ +d+vv  +   +  ++ + +al ++ve+Gg + ++
  gi|313116868|ref|YP_004037992.1| 359 AESAGYTVS-TVDS---LDADLSGIDLVVCSQP--QQPSDTELSALTTFVEDGGAVYAM 411
                                       455555662.2333...4677********9887..4566666677*********98766 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.21
                                       -HHHHHT-SEEEEE-G..GS-HHHHHH.HHHHHHTT-EEEEEGGGGS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThuA  44 teenLaqydvvvflstegevldaaqeaalqryveaGgGfvglhsAad 90 
                                        +e L++ +++++ +    +++a++ aal ++  + g +v l sAa 
  gi|313116868|ref|YP_004037992.1| 715 YSERLDDARAIIVTTP-VSEFTADEVAALSDFAANDGAVVLLGSAAA 760
                                       34789*******9997.47899999999*****99999999988854 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0017       4.3      51      91 ..      56      96 ..      39     105 .. 0.81
   2 ?    0.3   0.0      0.37   9.4e+02      50      75 ..     356     387 ..     321     405 .. 0.71
   3 !    6.7   0.0    0.0037       9.5      54      89 ..     708     744 ..     687     756 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                                      BTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCC CS
                    UDPG_MGDP_dh_C 51 ekgvevvdsleealkgadaiviltehdefkeldlaklkelm 91
                                       ++v+ +++l+  l+ga+a+vi+ + d f + +l+ l + +
  gi|313116868|ref|YP_004037992.1| 56 GYDVQATSDLTADLSGASAVVITSPSDAFSDAELSALSSFV 96
                                      5789999************************9988887766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
                                       G......BTCCEEES-CHHHHTT-SEEEE-S- CS
                    UDPG_MGDP_dh_C  50 e......ekgvevvdsleealkgadaivilte 75 
                                               ++v++vdsl+  l+g+d++v   +
  gi|313116868|ref|YP_004037992.1| 356 VsnaesaGYTVSTVDSLDADLSGIDLVVCSQP 387
                                       1334444689999************9997665 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0037
                                       CEEES-C.HHHHTT-SEEEE-S--GGGGGS-HHHHHH CS
                    UDPG_MGDP_dh_C  54 vevvdsl.eealkgadaiviltehdefkeldlaklke 89 
                                       +e v+++ +e+l++a ai+++t+ +ef+  ++a l +
  gi|313116868|ref|YP_004037992.1| 708 LEQVNTAySERLDDARAIIVTTPVSEFTADEVAALSD 744
                                       5556666699******************976666655 PP

>> DDOST_48kD  Oligosaccharyltransferase 48 kDa subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00079         2      60     118 ..      83     144 ..      46     171 .. 0.86
   2 ?   -1.7   0.0      0.37   9.5e+02      63      88 ..     391     416 ..     342     455 .. 0.62
   3 ?    1.2   0.0     0.051   1.3e+02      52     105 ..     725     780 ..     716     803 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00079
                        DDOST_48kD  60 elgksltpkallefvnkggniLvalsssk....lpesirsllselgielsergskvvDhfnyd 118
                                       +++ + + +al  fv +gg +++  +s+      ++++++++selg+++  ++++v+D  n+ 
  gi|313116868|ref|YP_004037992.1|  83 AFSDA-ELSALSSFVAEGGAVFLHHQSDFddfdETDNLNTIASELGLSFRFNDAQVTDATNNT 144
                                       44444.77899*************888767788899**********************99986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.37
                        DDOST_48kD  63 ksltpkallefvnkggniLvalsssk 88 
                                       ++ + +al+ fv++gg + ++++s+ 
  gi|313116868|ref|YP_004037992.1| 391 SDTELSALTTFVEDGGAVYAMGKSDY 416
                                       33455677777777777777766655 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.051
                        DDOST_48kD  52 illapkvkelgksltpkallefvnkggniLvalsssk...lpesirsllselgiels 105
                                       i+ ++ v+e++ + +++al +f  ++g +++ +s      ++ ++++l+selg +l 
  gi|313116868|ref|YP_004037992.1| 725 IIVTTPVSEFTAD-EVAALSDFAANDGAVVLLGSAAApgsTTANLERLASELGTDLR 780
                                       6777778888888.999************999888878888999999****998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1039 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 6856.72
//
Query:       gi|313116869|ref|YP_004037993.1|  [L=112]
Description: hypothetical protein Hbor_33330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 909.00
//
Query:       gi|313116870|ref|YP_004037994.1|  [L=193]
Description: hypothetical protein Hbor_33340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.23   11.2   2.5       0.36   10.6   2.5    1.3  1  Iron_permease  Low affinity iron permease
        0.5   10.3  10.2      0.093   12.6   3.5    2.6  2  YrhK           YrhK-like protein
        6.1    7.2  18.0         17    5.8  18.0    1.9  1  DUF4199        Protein of unknown function (DUF4199)


Domain annotation for each model (and alignments):
>> Iron_permease  Low affinity iron permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.5   6.1e-05      0.36      14      62 ..      30      78 ..      20      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.1e-05
                     Iron_permease 14 seiafvlallvivvwavsgplfkysdtwQLviNtgttiitFlmvfliqn 62
                                      + +++++++l  + + +++++f +  t QL+  tg+ +++ l v+ i +
  gi|313116870|ref|YP_004037994.1| 30 TFATVITGVLSAIWFLAGSAWFFHESTVQLLTWTGAGVVALLGVLYIIS 78
                                      45677778777777777777788889****************9988765 PP

>> YrhK  YrhK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.5   1.6e-05     0.093       6      40 ..      32      68 ..      29      89 .. 0.84
   2 ?    0.8   0.5     0.074   4.4e+02       9      26 ..     150     166 ..     139     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                              YrhK  6 islandiigsllFlvGSilflpnsefw..kwqiagvw 40
                                      + ++++++ +++Fl GS  f+ +s+ +   w+ agv+
  gi|313116870|ref|YP_004037994.1| 32 ATVITGVLSAIWFLAGSAWFFHESTVQllTWTGAGVV 68
                                      5678999**************8887667788888875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.074
                              YrhK   9 andiigsllFlvGSilfl 26 
                                       +++ i++++F ++ +  +
  gi|313116870|ref|YP_004037994.1| 150 LLYKITAGWFSIALL-SF 166
                                       5688999***99744.44 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  18.0    0.0029        17       4      92 ..      34     127 ..      32     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0029
                           DUF4199   4 lilglvwilifll.ilyllglh.qi.lstg.....pllgllallllllvpflvylalkkyrkknlgGfisfgqafgf 72 
                                       +i+g++++++fl+  + +++++  + l+       +llg+l+++++++  + +y++ + +  +   ++ s+ ++ ++
  gi|313116870|ref|YP_004037994.1|  34 VITGVLSAIWFLAgSAWFFHEStVQlLTWTgagvvALLGVLYIISVASASVSAYILWRLFASE---HNWSYLRGGSV 107
                                       688999999999887777777655544333555556666666666666688888888888555...589******** PP

                           DUF4199  73 gflislvagllsavfqyiyf 92 
                                       g+++ ++  ++++  ++i +
  gi|313116870|ref|YP_004037994.1| 108 GLAMGVLWHVITGFGWFIVL 127
                                       *****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1423.48
//
Query:       gi|313116871|ref|YP_004037995.1|  [L=292]
Description: hypothetical protein Hbor_33350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-05   25.1   0.0    2.8e-05   24.1   0.0    1.5  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.4   1.4        2.6    8.1   0.2    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.021   14.7   0.0      0.068   13.0   0.0    1.8  1  HTH_5           Bacterial regulatory protein, arsR family
      0.044   13.5   0.1          3    7.6   0.0    2.5  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.17   11.6   0.0       0.32   10.7   0.0    1.4  1  AMP_N           Aminopeptidase P, N-terminal domain
       0.19   12.0   4.6          2    8.7   0.1    2.6  2  zinc_ribbon_9   zinc-ribbon
       0.24   11.4   3.2        7.1    6.7   0.1    2.6  3  zinc-ribbons_6  zinc-ribbons
        1.8    8.5   6.2        1.3    9.0   0.2    3.1  3  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.2e-08   2.8e-05       5      51 ..      14      67 ..      10      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.2e-08
                                      HHHS-HHHHHHHHHH.......STCTTB-HHHHHHHHTS-HHH.HHHHHHHHHHC CS
                            HTH_20  5 eALahPvRrrilraL.......araegltaselaerldlsknt.lsyHLrvLeea 51
                                       AL++++R  il aL       ++ + l++s+l er+++++++  syHL++L+  
  gi|313116871|ref|YP_004037995.1| 14 AALTDETRVQILFALadqydeaWSSGWLSFSQLRERVGVADTSrFSYHLDALQ-D 67
                                      59**************************************************5.4 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0056        12      20      31 ..     110     121 ..     103     128 .. 0.72
   2 ?    8.1   0.2    0.0012       2.6       7      26 ..     161     180 ..     157     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0056
                     Zn_Tnp_IS1595  20 vCPhCgsrkayr 31 
                                        CPhC+ + +++
  gi|313116871|ref|YP_004037995.1| 110 QCPHCEQSLVIT 121
                                       699999775555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0012
                     Zn_Tnp_IS1595   7 ralLealrWpngfvCPhCgs 26 
                                       r++ +++r  +  vCPhC s
  gi|313116871|ref|YP_004037995.1| 161 RKHACDVRLLQDGVCPHCWS 180
                                       6788899999999*****76 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.1e-05     0.068       1      41 [.      18      67 ..      18      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                                      SHHHHHHHHHHTT........SSEEHHHHHHHHTS-H.HHHHHHHHHHHH CS
                             HTH_5  1 dptRlkILklLae........gelcvcelaeelglsq.stvShHLkkLre 41
                                      d+tR++IL++La+        g l++++l e +g+   s  S+HL +L +
  gi|313116871|ref|YP_004037995.1| 18 DETRVQILFALADqydeawssGWLSFSQLRERVGVADtSRFSYHLDALQD 67
                                      89***********9999998777999999999999764899999999976 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0014         3      37      52 ..     101     116 ..      92     118 .. 0.81
   2 ?    3.2   0.0     0.033        75      24      40 ..     174     190 ..     172     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                    zinc_ribbon_10  37 keeleevkyrCpkCga 52 
                                       + + ++++y+Cp+C +
  gi|313116871|ref|YP_004037995.1| 101 TVDRRQTEYQCPHCEQ 116
                                       5677899*******85 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.033
                    zinc_ribbon_10  24 ICskChshnGlapkeel 40 
                                       +C++C s+ Gl  ++e+
  gi|313116871|ref|YP_004037995.1| 174 VCPHCWSTAGLSFPRES 190
                                       79999999999876665 PP

>> AMP_N  Aminopeptidase P, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014      0.32      47     114 ..       6      72 ..       4      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                       ----SS-EEEEEESSEEEE...EEEE----HHHHHHH----HHHHHHHHHT-SEE....EEGGGHHHHHHHH CS
                             AMP_N  47 GfnepdavlvlekeedkkehkstLfvprkdpekelWdGarlgleeakelfgvdea....epidelesalakl 114
                                       G    d +++l    + ++   +Lf+   d+++e W+   l++++++e++gv ++    +++d l++ l + 
  gi|313116871|ref|YP_004037995.1|   6 GSSYDDTYAAL----TDETRVQILFAL-ADQYDEAWSSGWLSFSQLRERVGVADTsrfsYHLDALQDELVRK 72 
                                       66678999999....446667888877.79999*******************98866666666666666554 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0009         2      11      29 ..      99     116 ..      97     119 .. 0.85
   2 ?    4.0   1.0     0.027        61       6      27 ..     163     178 ..     163     181 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0009
                     zinc_ribbon_9  11 fVsvspdedsdvlCPhCgg 29 
                                       +V+v +++++   CPhC++
  gi|313116871|ref|YP_004037995.1|  99 TVTVDRRQTEYQ-CPHCEQ 116
                                       799999999999.****86 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.027
                     zinc_ribbon_9   6 hqCdrfVsvspdedsdvlCPhC 27 
                                       h Cd  V++    ++ v CPhC
  gi|313116871|ref|YP_004037995.1| 163 HACD--VRL---LQDGV-CPHC 178
                                       5666..665...35668.**** PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0032       7.1      13      26 ..     105     118 ..      97     140 .. 0.65
   2 ?    4.7   0.0     0.013        29      20      37 ..     163     180 ..     149     184 .. 0.88
   3 ?   -3.1   0.1       3.6   8.2e+03      30      35 ..     205     210 ..     202     212 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0032
                                       -SSEEE-TTT--EE CS
                    zinc-ribbons_6  13 rgeqyhCeaCqedl 26 
                                       r+++y+C +C+++l
  gi|313116871|ref|YP_004037995.1| 105 RQTEYQCPHCEQSL 118
                                       55666666666632 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.013
                                       TTT--EEEEEEE-SSS-S CS
                    zinc-ribbons_6  20 eaCqedlkkealCpeCeq 37 
                                       +aC+ +l +  +Cp+C +
  gi|313116871|ref|YP_004037995.1| 163 HACDVRLLQDGVCPHCWS 180
                                       68**************65 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.6
                                       EE-SSS CS
                    zinc-ribbons_6  30 alCpeC 35 
                                       a C++C
  gi|313116871|ref|YP_004037995.1| 205 AACDTC 210
                                       445555 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.17   3.7e+02      28      31 ..     111     114 ..     108     118 .. 0.77
   2 ?    9.0   0.2   0.00058       1.3      27      34 ..     174     181 ..     170     184 .. 0.87
   3 ?   -2.1   0.1       1.6   3.7e+03      23      32 ..     202     211 ..     202     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.17
                           DUF35_N  28 CphC 31 
                                       CphC
  gi|313116871|ref|YP_004037995.1| 111 CPHC 114
                                       8998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00058
                           DUF35_N  27 vCphCgsd 34 
                                       vCphC+s+
  gi|313116871|ref|YP_004037995.1| 174 VCPHCWST 181
                                       8******8 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.6
                           DUF35_N  23 PPravCphCg 32 
                                       +++a+C  C+
  gi|313116871|ref|YP_004037995.1| 202 YATAACDTCW 211
                                       5678898887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2381.64
//
Query:       gi|313116872|ref|YP_004037996.1|  [L=252]
Description: CAAX amino terminal protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-18   65.6   5.7      4e-18   65.6   5.7    2.3  2  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
      0.064   12.7   0.5      0.064   12.7   0.5    2.4  2  DUF1129   Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   3.4       0.9     8e+03      64      64 ..      49      49 ..      16     118 .. 0.59
   2 !   65.6   5.7   4.5e-22     4e-18       5      92 .]     146     244 ..     142     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.9
                                      H CS
                              CPBP 64 l 64
                                      +
  gi|313116872|ref|YP_004037996.1| 49 V 49
                                      2 PP

  == domain 2  score: 65.6 bits;  conditional E-value: 4.5e-22
                                       HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.........HHHH....HHHHHHHHH CS
                              CPBP   5 llvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.........gpsv....llaalaGlv 68 
                                       ++ ++l + l + +EE++fRg+++ +l+e +s++ a+ i++++F+l+H+++         +  +    ++++l+G++
  gi|313116872|ref|YP_004037996.1| 146 AFGAILSFTLIGPTEEFFFRGVMQGRLREAFSPVSAVGIAGAAFALFHVYPvlllspplaT--IahmaAYYTLMGMI 220
                                       5667778888899*****************999******************8877776662..04444********* PP

                                       HHHHHHHTT-HHHHHHHHHHHHHH CS
                              CPBP  69 lgylylktgsllaaillHallnll 92 
                                       +g++y++t +l++++l+H+++n++
  gi|313116872|ref|YP_004037996.1| 221 FGWVYYRTDNLVVPALVHGIFNAV 244
                                       **********************85 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   7.2e-06     0.064     139     193 ..      15      69 ..       5      80 .. 0.90
   2 ?    0.3   0.2     0.045     4e+02     116     135 ..     214     233 ..     162     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.2e-06
                           DUF1129 139 kkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLpplvliiigviafvv 193
                                         ++r+++++++++l++++v+ lv++++++l +avi  +L + +++++g++ + +
  gi|313116872|ref|YP_004037996.1|  15 GATDRTGTVRTATVLAGIIVAALVATVAATLATAVIGSRLGETATFVVGIVGIEL 69 
                                       56789********************************************997765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.045
                           DUF1129 116 lllvalvgGlamvlvyrllt 135
                                       ++l+++++G++++ + +l+ 
  gi|313116872|ref|YP_004037996.1| 214 YTLMGMIFGWVYYRTDNLVV 233
                                       56778888888887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1759.46
//
Query:       gi|313116873|ref|YP_004037997.1|  [L=75]
Description: hypothetical protein Hbor_33370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          1    9.9   3.7        3.1    8.3   3.7    1.8  1  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.7   0.00017       3.1      20      59 ..      30      70 ..       3      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00017
                            DUF202 20 lialglallrffl.tgepsalgkilglilivlgiltllvgl 59
                                       +a+g++ l f + + e  +l k++g++l+++++l+  + +
  gi|313116873|ref|YP_004037997.1| 30 VAAVGVLYLSFVRdEMETGPLMKVAGFLLLGMALLAYYWPM 70
                                      34455555556556556666789999999999999877755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 551.89
//
Query:       gi|313116874|ref|YP_004037998.1|  [L=298]
Description: sugar ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-21   77.2  17.6    1.3e-21   77.2  17.6    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   5.3      0.71   1.3e+04      19      36 ..      37      54 ..      24     111 .. 0.44
   2 !   77.2  17.6   7.3e-26   1.3e-21       3     176 ..     114     284 ..     112     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 0.71
                      BPD_transp_1 19 llrpliivllslPsfvla 36
                                      +++ ++ ++  +P+++ +
  gi|313116874|ref|YP_004037998.1| 37 AILLFMSAVAVFPFVWAF 54
                                      444444444444444411 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 7.3e-26
                      BPD_transp_1   3 llGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrsl 79 
                                       l+G+ +a +  +k++ ++++l+i +l +P+ v++++l+     ++ l +++++++i++l+ a p+ ++++r+++  +
  gi|313116874|ref|YP_004037998.1| 114 LAGYALA-KGDFKGKSIIYTLVIGTLVIPPQVVLVPLY---LEMTMLNWSNTYWAIMVLYIANPFGTFMMRQFFLGV 186
                                       5678888.8999**************************...59********************************** PP

                      BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydyseisn 155
                                       p++l+eaar++G+s++qi+ +++lP+a+p + ++ +++f++++g ++++++++++ + + +++   +l   ys+   
  gi|313116874|ref|YP_004037998.1| 187 PDSLIEAARMDGCSTFQIYTRIMLPLAKPALSSLGVFTFIFVWGSFLWPLIILNDAAmFPLQVGIGLLTGRYSSQWG 263
                                       *******************************************************9885566666666666666663 PP

                      BPD_transp_1 156 ggvlalviavlllnlvadilq 176
                                        +++a++ia l++++++ + q
  gi|313116874|ref|YP_004037998.1| 264 QLLAAVIIAALPVMVAYLLAQ 284
                                       344555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1913.59
//
Query:       gi|313116875|ref|YP_004037999.1|  [L=312]
Description: sugar ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-16   60.7  19.4    1.5e-16   60.7  19.4    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.5     0.041   7.4e+02     116     154 ..      35      69 ..      30     107 .. 0.61
   2 !   60.7  19.4   8.5e-21   1.5e-16       3     175 ..     106     301 ..     104     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.041
                      BPD_transp_1 116 lafggllggavlleflgswpGlgtllleailgydyseis 154
                                       ++f+ ++  a++l++ +    +g + ++  ++ ++++  
  gi|313116875|ref|YP_004037999.1|  35 IVFPKVFLFAAVLLIPF----VGAFYISLHQWEPLAASH 69 
                                       67777777777777777....777777777777766554 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 8.5e-21
                      BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf...................vilsilghlilpvii 58 
                                       ++++ +a  ln+n +++k+ +  i+++  +  +v+ ++++++                     +l++ +++  +++i
  gi|313116875|ref|YP_004037999.1| 106 PIALGLAllLNMNLRGTKFYSAAIFLPVVTSWVVVSLIWTWLYnpqygfinaalgmiglpqlDWLQSSKTALASIAI 182
                                       6666667779999999************9999999999997779999999999999999888999999999999*** PP

                      BPD_transp_1  59 llllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswp 135
                                       ++++  ++++++i+ a+l+ +p+d++eaa ++Ga+rwq++r+++lP+++p+++  + ++++ ++  +v +  ++ ++
  gi|313116875|ref|YP_004037999.1| 183 MSIWKHIGFNMVIFLAGLKGIPDDFYEAAIVDGANRWQRLRHITLPLLKPTTFFVVTVTLIMSFRLYVQVFVMTRGG 259
                                       **********************************************************************9999666 PP

                      BPD_transp_1 136 G..lgtllleailgydyseisnggvlalviavlllnlvadil 175
                                       +   ++ ++   ++  ++e ++g++ a++++++++++ + il
  gi|313116875|ref|YP_004037999.1| 260 ParSTYSIVYYFWQTGFQEFQMGYASAIAVVLFIIVFGLSIL 301
                                       666445555555555555555455555554444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1891.14
//
Query:       gi|313116876|ref|YP_004038000.1|  [L=443]
Description: sugar ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-26   92.8   1.6    4.4e-26   92.3   1.6    1.2  1  SBP_bac_8  Bacterial extracellular solute-binding protein
    2.7e-20   73.6   3.3    4.3e-20   72.9   3.3    1.3  1  SBP_bac_1  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   1.6   4.9e-30   4.4e-26       6     277 ..      86     382 ..      82     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 4.9e-30
                                       HHHH-TE.EEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGS.TTHHH-.HHHHHTT- CS
                         SBP_bac_8   6 fekktgv.kvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdl.dnlddl.tdalaavg 79 
                                       f+   +v  v  ++++ + + +k+++a++ag+apd+ +++    +++++  +g+ +dl+    n+dd+ ++a + ++
  gi|313116876|ref|YP_004038000.1|  86 FKNNFDVgGVDWQYYPFENYLSKATSAIPAGNAPDS-LALS-VLWVSRFGSKGAAVDLEANgFNADDYvPAARNNAS 160
                                       555556524888999999****************95.5666.57***************77799999736688888* PP

                                       -TS.----EEEEEEE-EEEEEHHHHHHS.....--...-BHHHHHHHHHHH..HHH-SEGG--.-GGGGGGTHHETT CS
                         SBP_bac_8  80 ydgklygvPyasetpyvliynkdlleka....edp...ktwdellaaakkl..kgkfglpdpa.sgwlqaallakdg 146
                                       ydgkl +vP+ + +  +l+ n +++++a     dp    +wde+ +++ +l  +  +++++pa +g+  + l   + 
  gi|313116876|ref|YP_004038000.1| 161 YDGKLWAVPWYADC-RLLCINRSMFKEAglevPDPtyrPSWDEWETWVTELskTHGTAYSMPAgEGFDSFVLSN-GS 235
                                       *************9.8***********9997755566679****999999954466688999855655555555.33 PP

                                       EE---H.......HHH.HHHHHHHHH.HHHTT-EE...-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE. CS
                         SBP_bac_8 147 ksldddg.....gkdglkealellkk.lkdngkty...dtgadavsefanGevaftingswdiaaaqkagkklgai. 213
                                        +l++dg     ++d+  ea+++l+  ++++  ++   + g++av++f  Ge+ ++++gsw +  ++k g ++++  
  gi|313116876|ref|YP_004038000.1| 236 GYLSEDGteariNSDAALEAANFLQPkIVEDDSILarnPGGTSAVEDFLAGEAPMFYAGSWHFPRLRKSGLDWQYNp 312
                                       333666556555565556666666642333333447878999**********************************4 PP

                                       --....S--EEEEEEE..EEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHHHHH- CS
                         SBP_bac_8 214 vp....kqgsfaggkg..lavpknaknedlaAldFlkwltspenqaalaektgyipvnksaalspevkkd 277
                                        p     + s ++++g  + vp+  +++++  l++l+++ s e q++  +++g +p +k+a+++++++++
  gi|313116876|ref|YP_004038000.1| 313 HPsgpnVDVSHTWSAGvfYSVPSRGGASKELGLKWLEYIDSMEVQKNVTKAMGGFPGRKDAYETDAFQQY 382
                                       45543334588888876466888766666669*******************************9999965 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   3.3   4.8e-24   4.3e-20      25     314 ..      93     357 ..      72     358 .. 0.79

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 4.8e-24
                                       EEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHHHHTHHH CS
                         SBP_bac_1  25 ikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkdaadklsssvlpki 101
                                         V +++ ++ ++  k t ai aG++p D  a +  w++r+ ++g++ +l +   +   +++   a++++ s+++k 
  gi|313116876|ref|YP_004038000.1|  93 GGVDWQYYPFENYLSKATSAIPAGNAP-DSLALSVLWVSRFGSKGAAVDLEANGFNADDYVP---AARNNASYDGKL 165
                                       5688*********************88.999999****************999999866664...556667777777 PP

                                       HCEEEESEEEEE.EEEEEEETTTHHCTTGGG.....SHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHHHHH CS
                         SBP_bac_1 102 ldskvlyvPlya.argliYNkdlfekagldp.....pwtWdelveaakklkekgkkpiggarggsasgtayyfalal 172
                                       ++     vP+ya  r+l +N + f++agl++      ++Wde+  +  +l +  ++      ++  +g+++     +
  gi|313116876|ref|YP_004038000.1| 166 WA-----VPWYAdCRLLCINRSMFKEAGLEVpdptyRPSWDEWETWVTELSKTHGTA-----YSMPAGEGFD---SF 229
                                       77.....****88***************************************99999.....2222222222...34 PP

                                       HHHHTGGGEECCCT..HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHH CS
                         SBP_bac_1 173 akslggkvfdkdgg..gldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaala 247
                                        +s+g+ + ++dg   +++      ++++l+++++ + +  e     a n +g++a+ +f aGea+m+++g+w    
  gi|313116876|ref|YP_004038000.1| 230 VLSNGSGYLSEDGTeaRIN------SDAALEAANFLQPKIVEDDSILARNPGGTSAVEDFLAGEAPMFYAGSWH--- 297
                                       5778888999997655444......5555555555555557889******************************... PP

                                       HHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE..EEEEEEEEBTTCST.....HHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 248 amkvapkvafaadkekpkeelgvaplPagkggkpgi..lgayglaipkgskn.....peaAkkFldfllspeaq 314
                                                  +  +k + ++ + p P g++   +         +++++ +      +e   k+l+++ s e q
  gi|313116876|ref|YP_004038000.1| 298 ----------FPRLRKSGLDWQYNPHPSGPNVDVSHtwS----AGVFYSVPSrggasKELGLKWLEYIDSMEVQ 357
                                       ..........**********************9995553....4444444443333466699999998777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3023.32
//
Query:       gi|313116877|ref|YP_004038001.1|  [L=378]
Description: sugar ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-33  114.0   0.0    1.1e-32  113.4   0.0    1.3  1  ABC_tran         ABC transporter
    2.7e-10   40.3   0.2    7.7e-10   38.8   0.2    1.8  1  TOBE_2           TOBE domain
    9.4e-09   36.0   0.0    3.5e-08   34.1   0.0    2.1  1  OB_MalK          MalK OB fold domain
    2.6e-08   34.1   0.1     0.0047   16.8   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    3.6e-06   27.2   0.1    7.4e-06   26.2   0.1    1.6  1  TOBE             TOBE domain
    0.00025   20.6   0.0    0.00063   19.2   0.0    1.6  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00027   21.5   0.0    0.00047   20.7   0.0    1.7  1  AAA_23           AAA domain
     0.0027   17.6   0.0     0.0061   16.5   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
     0.0029   18.0   0.0     0.0052   17.2   0.0    1.5  1  AAA_16           AAA ATPase domain
     0.0044   17.0   0.0     0.0068   16.3   0.0    1.3  1  Rad17            Rad17 P-loop domain
     0.0079   16.7   0.0      0.024   15.2   0.0    1.9  1  CysA_C_terminal  CysA C-terminal regulatory domain
     0.0091   15.7   0.0      0.018   14.8   0.0    1.5  2  AAA_15           AAA ATPase domain
  ------ inclusion threshold ------
      0.013   15.8   0.2      0.026   14.8   0.2    1.7  1  AAA_22           AAA domain
      0.015   15.7   0.2      0.087   13.2   0.2    2.1  1  AAA              ATPase family associated with various cellul
      0.029   14.1   0.0      0.056   13.2   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.044   13.3   0.1       0.77    9.3   0.0    2.6  3  AAA_25           AAA domain
      0.049   13.0   0.0       0.11   11.9   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.088   13.0   0.3       0.15   12.2   0.3    1.6  1  AAA_33           AAA domain
        0.1   12.3   0.0       0.47   10.1   0.0    1.9  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.0   1.2e-35   1.1e-32       2     136 ..      24     166 ..      23     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 1.2e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++++++++ ge + +vG++G+GKSt l+++agl++ t+G+i ld++d+++  ++ +++ i++++q+  l p++t+r+
  gi|313116877|ref|YP_004038001.1|  24 DDLNIDIEDGEFLIFVGPSGCGKSTTLRCIAGLESATSGQIILDDTDITN--KPPTDRDIAMVFQNYALYPHMTARD 98 
                                       899**********************************************9..9999********************* PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              e +e++e+ ++ +g+++l d++      +LSgGq+qrval ra++++p+++l+DEp 
  gi|313116877|ref|YP_004038001.1|  99 NigfglkmstdmekdEIRERVEQTAEMMGIEDLLDKKP----GELSGGQQQRVALGRAIVREPSVFLMDEPL 166
                                       ********999876666666888888888888777776....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.2   8.1e-13   7.7e-10       1      76 []     282     353 ..     282     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 8.1e-13
                            TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       l++RPE ++la+ag+ n+++  V+ +e +G++t ++v+++++q  +v +   +    ++pG+t+++ ++ d+++++
  gi|313116877|ref|YP_004038001.1| 282 LGVRPESIELASAGDTNAIEVPVVVTEPMGETTYVYVDIGDQQY-TVTVGGDR---IVEPGSTLHVVFPEDKMHLF 353
                                       79********6555457*************************99.77777777...9*****************98 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   3.7e-11   3.5e-08       1      53 []     240     289 ..     240     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3.7e-11
                           OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       GSP+MNf+++++  dg  +  + ++ +l++e   ++ + ++ +++lG+RPE i
  gi|313116877|ref|YP_004038001.1| 240 GSPSMNFFEVEYA-DG-SLIHETFRYDLSRET-SEELSVREGPLTLGVRPESI 289
                                       9************.66.699999*******99.555666889*********87 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.4e-05     0.013       2      52 ..      36      74 ..      35      89 .. 0.69
   2 !   16.8   0.0   4.9e-06    0.0047     234     298 ..     136     198 ..      93     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldly 52
                                       +++Gp g+GKS+ L+++ +l +              +g+i+ ++  ++++
  gi|313116877|ref|YP_004038001.1| 36 LIFVGPSGCGKSTTLRCIAGLES------------ATSGQIILDDTDITNK 74
                                      689*****************944............3444444444444333 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.9e-06
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       + elS G+++  al  a+ r +   s++l DEp ++L+ kl ++  + l +l++  g+  i +TH+
  gi|313116877|ref|YP_004038001.1| 136 PGELSGGQQQRVALGRAIVREP---SVFLMDEPLSNLDAKLRTTMRTELQDLQQqLGITTIYVTHD 198
                                       5688999999999999999999...************************777777**********8 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   7.9e-09   7.4e-06       4      64 .]     297     352 ..     294     352 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.9e-09
                              TOBE   4 rNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                        N++++ Vvv ep g +++V+vd+g+++  t++v +++ +e    pG+++++++   k+hl
  gi|313116877|ref|YP_004038001.1| 297 TNAIEVPVVVTEPMGETTYVYVDIGDQQ-YTVTVGGDRIVE----PGSTLHVVFPEDKMHL 352
                                       699*************************.************....*********9999986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   6.7e-07   0.00063      25     206 ..      34     204 ..      24     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.7e-07
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkk.lkiekeevs 98 
                                       +f + vGp G+GKs  l  i    G      l s++  ++i      +++  +  +++++f+n       + ++++ 
  gi|313116877|ref|YP_004038001.1|  34 EFLIFVGPSGCGKSTTLRCI---AG------LESATSGQIILDdtDITNKPPTDRDIAMVFQNYALYpHMTARDNIG 101
                                       57889************999...45......5666777777776666788888999999999998874445556666 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                          +++++ e + +i ++  + +e++ +    + ++ +LSgG+++ val    Ai  v+  +++l+De  ++LD+k 
  gi|313116877|ref|YP_004038001.1| 102 FGLKMSTDME-KDEIRERVEQTAEMMGIEDLLDKKPGELSGGQQQRVALG--RAI--VREPSVFLMDEPLSNLDAKL 173
                                       6666665555.445655555555555555555557899******977664..444..6778899************* PP

                                       HHHHHHHHHHHCTTSEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkeksknaQfivislreemlekad 206
                                       ++ + + l+  +++  +  i ++++++e + 
  gi|313116877|ref|YP_004038001.1| 174 RTTMRTELQDLQQQLGITTIYVTHDQTEAMT 204
                                       *********9998876666666666655554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     5e-07   0.00047       2      40 ..       4      54 ..       3     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5e-07
                            AAA_23  2 Lkienfrsf...........rdqeidFskgltlI.tGpNGaGKTTildAik 40
                                      L i+n+r+            +d +id ++g +lI +Gp G+GK+T l++i 
  gi|313116877|ref|YP_004038001.1|  4 LDIRNLRKVfeddggsivavDDLNIDIEDGEFLIfVGPSGCGKSTTLRCIA 54
                                      66677777667766666777999****888776527*************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.5e-06    0.0061      89     129 ..      22      63 ..       7      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.5e-06
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                       ++++l+  ++d ++ ++vG+SG GKSt +  +++ +++  g+
  gi|313116877|ref|YP_004038001.1|  22 AVDDLNIDIEDgEFLIFVGPSGCGKSTTLRCIAGLESATSGQ 63 
                                       5678888888889****************9999876665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.5e-06    0.0052      23      58 ..      32      67 ..      22     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd.ggiflrg 58
                                      ++e ++++G+sG+GKs+ +r+++  le +  g  +  
  gi|313116877|ref|YP_004038001.1| 32 DGEFLIFVGPSGCGKSTTLRCIAG-LESAtSGQIILD 67
                                      44899*****************94.444412444433 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.3e-06    0.0068      46      67 ..      34      55 ..      22      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.3e-06
                             Rad17 46 riLLisGPsGCgkstvvkvLsk 67
                                      + L+  GPsGCgkst+++ ++ 
  gi|313116877|ref|YP_004038001.1| 34 EFLIFVGPSGCGKSTTLRCIAG 55
                                      57999************99875 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-05     0.024       1      43 []     245     291 ..     245     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                   CysA_C_terminal   1 NlFhGrvedGklriGglalpvP....elagadgqevvayVRPhDlei 43 
                                       N+F+    dG l    ++ ++     e+  +++++ +++VRP+ +e+
  gi|313116877|ref|YP_004038001.1| 245 NFFEVEYADGSLIHETFRYDLSretsEELSVREGPLTLGVRPESIEL 291
                                       9*********************877633333677***********97 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.9e-05     0.018      15      74 ..      24      80 ..      22     146 .. 0.65
   2 ?   -2.3   0.0         3   2.8e+03     323     365 ..     156     198 ..     144     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenises 74
                                      +d  id+++  + +++G+ ++GKS+ l+ +  + + +    +  i +++ d+ ++  ++++
  gi|313116877|ref|YP_004038001.1| 24 DDLNIDIEDGeFLIFVGPSGCGKSTTLRCIAGLESAT----SGQIILDDTDITNKPPTDRD 80
                                      57789999988*****************998777755....34455555555544444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++ ++l++EP  +L  ++ + +   l++l ++    +i+ TH 
  gi|313116877|ref|YP_004038001.1| 156 EPSVFLMDEPLSNLDAKLRTTMRTELQDLQQQLGITTIYVTHD 198
                                       5678889999999999999999999999999988889999996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   2.8e-05     0.026       4      28 ..      32      56 ..      29     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      +  +l+ +G+sG+GK+t+lr ++  
  gi|313116877|ref|YP_004038001.1| 32 DGEFLIFVGPSGCGKSTTLRCIAGL 56
                                      56799**************987755 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   9.2e-05     0.087       1      37 [.      36      74 ..      36     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.2e-05
                                      EEEESSTTSSHHHHHHHHHHH..HTHEEEEEETTTCSSS CS
                               AAA  1 vllyGppGtGKTllakavake..lgvefleisgsellsk 37
                                      ++++Gp G+GK+++ + +a    + +  + ++ +++++k
  gi|313116877|ref|YP_004038001.1| 36 LIFVGPSGCGKSTTLRCIAGLesATSGQIILDDTDITNK 74
                                      589***************986223344556666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.9e-05     0.056      15      39 ..      26      50 ..      21      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                        i+i+  ++ +++GpsG GKST l
  gi|313116877|ref|YP_004038001.1| 26 LNIDIEDGEFLIFVGPSGCGKSTTL 50
                                      5567774449999**********76 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00081      0.77      30      50 ..      30      50 ..      10      64 .. 0.88
   2 ?    0.1   0.0      0.54   5.1e+02      78      98 ..     107     134 ..     103     181 .. 0.69
   3 ?   -1.7   0.0       1.9   1.8e+03     166     188 ..     175     197 ..     164     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00081
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +  ge+ +++G++g+GK+t +
  gi|313116877|ref|YP_004038001.1| 30 IEDGEFLIFVGPSGCGKSTTL 50
                                      4689**************976 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.54
                            AAA_25  78 saEdsedelrrRlravgeal.......r 98 
                                       s+++  de+r+R++++ e +       +
  gi|313116877|ref|YP_004038001.1| 107 STDMEKDEIRERVEQTAEMMgiedlldK 134
                                       78899999******99999966654442 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.9
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       + + + l+++++++g++++ v H
  gi|313116877|ref|YP_004038001.1| 175 TTMRTELQDLQQQLGITTIYVTH 197
                                       56667899999*******99999 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.11      15      73 ..      26      84 ..      13     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                      Mg_chelatase 15 leiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekll 73
                                      l+i +  g  l++vGp+G+GK+   +++++l ++ s + +l+ + i+    ++++ +++
  gi|313116877|ref|YP_004038001.1| 26 LNIDIEDGEFLIFVGPSGCGKSTTLRCIAGLESATSGQIILDDTDITNKPPTDRDIAMV 84
                                      56666667789********************9999999999988887655555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   0.00016      0.15       2      20 ..      36      54 ..      35     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                      +++vG++G+GKst ++ ++
  gi|313116877|ref|YP_004038001.1| 36 LIFVGPSGCGKSTTLRCIA 54
                                      69***********998764 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0005      0.47      20      50 ..      35      65 ..      29      67 .. 0.82
   2 ?   -1.3   0.0       1.6   1.5e+03      32      68 ..     175     211 ..     174     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0005
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvi 50
                                      + + +Gp G GK+t+l+ ++ +  a  g++i
  gi|313116877|ref|YP_004038001.1| 35 FLIFVGPSGCGKSTTLRCIAGLESATSGQII 65
                                      7899**************9998888766665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                            AAA_30  32 ttalkalreaweaaggrviglAptgkaAkvLaeelgi 68 
                                       tt+ ++l+++ ++ g + i +++ ++ A ++++ + i
  gi|313116877|ref|YP_004038001.1| 175 TTMRTELQDLQQQLGITTIYVTHDQTEAMTMGDRIAI 211
                                       6777788888888899999999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2474.20
//
Query:       gi|313116878|ref|YP_004038002.1|  [L=320]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-20   74.0   0.0    2.7e-20   73.4   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    4.1e-08   33.2   0.1    1.2e-07   31.7   0.1    1.8  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    3.8e-06   26.6   0.1      2e-05   24.3   0.0    2.1  2  ox_reductase_C  Putative oxidoreductase C terminal domain
  ------ inclusion threshold ------
      0.064   14.0   0.0       0.14   12.9   0.0    1.5  2  CoA_binding     CoA binding domain
       0.13   12.2   0.0       0.44   10.5   0.0    1.8  2  53-BP1_Tudor    Tumour suppressor p53-binding protein-1 Tudor
       0.16   12.6   0.3       0.38   11.3   0.1    1.8  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.0   8.9e-24   2.7e-20       3     120 .]       5     123 ..       3     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 8.9e-24
                                       EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCT..TESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladp..eidavivatpngthee 77 
                                       v+++GaG i+  hl +l +  +++ +va+ d+d era+ava+  g+ ay+d  el a++    da++va+p+  he 
  gi|313116878|ref|YP_004038002.1|   5 VGFVGAGGIAAVHLDSLDQY-DGATLVAVADIDGERARAVADPRGATAYTDGHELIAEEseSLDALVVAIPPFAHEG 80 
                                       89************777777.******************************99999888778*************** PP

                                       HHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  78 lakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       ++++a+ ag+++++EKP+ ++ e + +  + +e++g++ +vgy
  gi|313116878|ref|YP_004038002.1|  81 YEREAADAGIDLFVEKPVGLDSEVVAATRRELESSGVVTQVGY 123
                                       ****************************************998 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1     4e-11   1.2e-07      23     109 ..     151     232 ..     135     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4e-11
                                       EEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSCSEEEEEEEEEEETTEEEE CS
                    GFO_IDH_MocA_C  23 ragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaededaavmsvlnlekgsgevi 99 
                                       + + +++++w+ r ++sgG+l++ ++H +D+ ++L+G++ +v  + +    +  ++ d+++a     +l+++sg+v+
  gi|313116878|ref|YP_004038002.1| 151 WVSVPDTSWWSSR-AHSGGQLVEQSTHVFDVHRYLLGEVETVRGDGT--DGLLADGLDFQDA--TSTTLSHESGAVS 222
                                       5555666666655.6***********************976655444..5666666666666..49*********** PP

                                       EEEECCTSSS CS
                    GFO_IDH_MocA_C 100 tlesgvskgl 109
                                       +++s +++++
  gi|313116878|ref|YP_004038002.1| 223 HISSTCASPE 232
                                       ******9876 PP

>> ox_reductase_C  Putative oxidoreductase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   6.6e-09     2e-05      33      69 ..     153     190 ..     126     208 .. 0.74
   2 ?   -0.8   0.0      0.36   1.1e+03     105     131 ..     209     235 ..     197     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.6e-09
                    ox_reductase_C  33 haakkawwe.ksisaGpvveqathfcdlsryfgGdvdl 69 
                                           + ww+ ++ s+G +veq+th+ d+ ry+ G+v++
  gi|313116878|ref|YP_004038002.1| 153 SVPDTSWWSsRAHSGGQLVEQSTHVFDVHRYLLGEVET 190
                                       3446789963688999*******************985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.36
                    ox_reductase_C 105 ltsaswkyksGavGslehavalqGtky 131
                                       +ts++  ++sGav +++ + a    ++
  gi|313116878|ref|YP_004038002.1| 209 ATSTTLSHESGAVSHISSTCASPESRF 235
                                       68999999*****99987776555555 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.6e-05      0.14       3      91 ..       2      94 ..       1      95 [. 0.83
   2 ?   -4.2   0.0         6   1.8e+04      30      42 ..     174     186 ..     171     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-05
                                      TEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTT..CEETTEEEESCHHHHHHHC.T.TTEEEEES-HHHHHH CS
                       CoA_binding  3 dtkviviGagglgiaglyhfkeklkygikavfgvnprkvg..tevlglpvyksvdeleekt.e.vdvavitvPaesaqe 77
                                      +t v+ +Gagg +   l + ++  +  ++av++++++ +    + +g ++y++ +el+++  e  d+ v+++P+ + + 
  gi|313116878|ref|YP_004038002.1|  2 TTTVGFVGAGGIAAVHLDSLDQYDGATLVAVADIDGERARavADPRGATAYTDGHELIAEEsEsLDALVVAIPPFAHEG 80
                                      589*********55555888888888899******99554226677*************98657999999999988888 PP

                                      HHHHHHHTT-SEEE CS
                       CoA_binding 78 avdelveagikgiv 91
                                         e+++agi + v
  gi|313116878|ref|YP_004038002.1| 81 YEREAADAGIDLFV 94
                                      8899999*999876 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 6
                                       EEEEEEC-TTTTT CS
                       CoA_binding  30 ikavfgvnprkvg 42 
                                        ++vf+v    +g
  gi|313116878|ref|YP_004038002.1| 174 STHVFDVHRYLLG 186
                                       6899999876655 PP

>> 53-BP1_Tudor  Tumour suppressor p53-binding protein-1 Tudor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.44      39      77 ..      79     119 ..      75     127 .. 0.86
   2 ?   -2.5   0.0       1.6   4.7e+03      92     101 ..     266     275 ..     243     295 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                       TS-EEEE..EGGGEESSSS--TT-EEEEEBTTBSSEEEEEE CS
                      53-BP1_Tudor  39 dgyecev..lgkdillcdpipletevtalledeyfsigvvk 77 
                                       +gye e   +g d+++  p+ l++ev a +  e  s gvv 
  gi|313116878|ref|YP_004038002.1|  79 EGYEREAadAGIDLFVEKPVGLDSEVVAATRRELESSGVVT 119
                                       78987762268999999**********************96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                       ETTEEEEEEG CS
                      53-BP1_Tudor  92 kegqrkwykr 101
                                        +g+  wy+r
  gi|313116878|ref|YP_004038002.1| 266 FQGDGSWYQR 275
                                       3455556655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00013      0.38       1      81 [.       4      85 ..       4      94 .. 0.83
   2 ?   -3.1   0.0         4   1.2e+04      56      68 ..     296     308 ..     287     318 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH...H-SEEEE-S-HHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae...eadvvvlavkpedvee 76
                                      ++g++GaG +++  +  l + +  ++ + va + + e+a++ a+  g+++ +  +e  ae   + d +v+a++p ++e 
  gi|313116878|ref|YP_004038002.1|  4 TVGFVGAGGIAAVHLDSLDQYD-GATLVAVA-DIDGERARAVADPRGATAYTDGHELIAEeseSLDALVVAIPPFAHEG 80
                                      58**************999998.66667766.***************999997777777744455899******99987 PP

                                      HHHHC CS
                     F420_oxidored 77 vlsel 81
                                        +e+
  gi|313116878|ref|YP_004038002.1| 81 YEREA 85
                                      66655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4
                                       HHHHHH-SEEEE- CS
                     F420_oxidored  56 eeaaeeadvvvla 68 
                                       ++aa+  +v + a
  gi|313116878|ref|YP_004038002.1| 296 ADAARTFEVTLAA 308
                                       4444433333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2315.74
//
Query:       gi|313116879|ref|YP_004038003.1|  [L=267]
Description: sugar phosphate isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-28   99.6   0.5    2.1e-28   99.2   0.5    1.2  1  AP_endonuc_2    Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.022   14.5   0.4       0.38   10.5   0.1    3.0  3  AP_endonuc_2_N  AP endonuclease family 2 C terminus


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.5   2.3e-32   2.1e-28       2     193 ..      20     206 ..      19     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 2.3e-32
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraie 77 
                                       +++a+aG+dg+E ++  + p ++  d++++++   +  l l+++++s++ ++   + +  +a+ re+ +da +r+i 
  gi|313116879|ref|YP_004038003.1|  20 EQLASAGYDGIEPNLTADGPLWD--DDAVAAFGDCISTLELEVPAVSTTLHWKQQLSS-PDAEtREAGIDAGERMIH 93 
                                       689*******************5..9****************************7764.444489999********* PP

                                       HHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTT CS
                      AP_endonuc_2  78 laaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeelarlldavdsp 154
                                       +a +L+a  + + p      ++ ++++a++r+ es++ la+ a++++v++++E+ ++++  +   e+a+++d+ +  
  gi|313116879|ref|YP_004038003.1|  94 IADELNAGAILVVPA--IVDEETPYDAAYDRALESVRTLAETAAEYDVTVCIENVWNDFLLSP-LEFAQFVDEASEA 167
                                       ***************..99****************************************9888.***********99 PP

                                       T.EEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESS CS
                      AP_endonuc_2 155 n.vgvclDtgHlliaeedvddalraladrikhvHikDakg 193
                                         vg ++D+g+     +++++++r l+dri  vH+kD++ 
  gi|313116879|ref|YP_004038003.1| 168 GpVGAYFDVGNVRRF-GRPEQWIRILGDRIERVHVKDYDA 206
                                       9**********9988.*********************998 PP

>> AP_endonuc_2_N  AP endonuclease family 2 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.12   1.1e+03       8      16 ..      21      29 ..      19      30 .. 0.87
   2 ?   -1.0   0.0      0.17   1.5e+03      11      30 ..     134     155 ..     125     159 .. 0.73
   3 ?   10.5   0.1   4.3e-05      0.38       1      21 [.     223     243 ..     223     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                    AP_endonuc_2_N  8 aLrqiGYdg 16
                                      +L+++GYdg
  gi|313116879|ref|YP_004038003.1| 21 QLASAGYDG 29
                                      6999****9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.17
                    AP_endonuc_2_N  11 qiGYdgplSiE..wEDslmsre 30 
                                       ++ Yd  + iE  w D l s++
  gi|313116879|ref|YP_004038003.1| 134 AAEYDVTVCIEnvWNDFLLSPL 155
                                       5789999999966777766665 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 4.3e-05
                    AP_endonuc_2_N   1 dwkdifsaLrqiGYdgplSiE 21 
                                       dw ++  aL++iGYdg+l  E
  gi|313116879|ref|YP_004038003.1| 223 DWYAVRDALADIGYDGWLTAE 243
                                       7889999**********9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2099.06
//
Query:       gi|313116880|ref|YP_004038004.1|  [L=385]
Description: Major Facilitator Superfamily transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-39  133.4  17.5      2e-38  132.3  17.5    1.5  1  MFS_1_like     MFS_1 like family
    5.4e-17   61.8  61.5    2.4e-15   56.3  40.8    2.1  2  MFS_1          Major Facilitator Superfamily
    1.4e-11   43.8   5.1    1.4e-11   43.8   5.1    1.9  2  LacY_symp      LacY proton/sugar symporter
    8.7e-07   28.3  22.7    1.2e-06   27.8  22.7    1.1  1  Nuc_H_symport  Nucleoside H+ symporter
  ------ inclusion threshold ------
      0.027   13.1  30.6      0.033   12.7   2.6    2.8  2  MFS_2          MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3  17.5   5.5e-42     2e-38       2     383 ..       5     351 ..       4     352 .. 0.94

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 5.5e-42
                        MFS_1_like   2 islkilyFfffaalgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavl 78 
                                       ++l+ +yF+ff + +++l +  +y++s gl+ s+ g++ ++l ++ i+++p+wg l+Dr+g++k vv+++l +s +l
  gi|313116880|ref|YP_004038004.1|   5 TRLQSFYFVFFLSSSGILAFRNVYFRSVGLSGSDMGLVGAALLVVGIVAQPVWGLLSDRLGAQKRVVLIALAVSGAL 81 
                                       6899**********************************************************************999 PP

                        MFS_1_like  79 flsllfippskerqeesklevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGs 155
                                        l   f p                    a+  + +l+ l + + +f++++ +++++++l +       yG +r fGs
  gi|313116880|ref|YP_004038004.1|  82 SL--AFPP-------------------AARVGVLALVGLTIAFAAFQSPVRPVANSLVLSA----GYGYGTVRAFGS 133
                                       88..4435...................37899**************************975....788********* PP

                        MFS_1_like 156 vGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifll 232
                                       + +++ + + G+++  +  +     +l+yv+a+   ++++vvl  + +   + ++v    + + ++l+n++ +++l+
  gi|313116880|ref|YP_004038004.1| 134 IAFGVGTLAYGLVLARTDPS-----VLFYVYAVGAALAFFVVLRTPVGDGDPLDGVG---RRVPALLRNRSFAGLLA 202
                                       ***************99995.....489***************************99...7899************* PP

                        MFS_1_like 233 valilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyai 309
                                       +++++g++ ++ ++++  + + +g  n++ G++ a+++ ae + f+   +     + + l +++ la+++ f++y +
  gi|313116880|ref|YP_004038004.1| 203 ATFVVGIVLSANNSYFVFFVNAVGGGNETTGAAFAVKTTAEAIAFLAFVR--AAPSRRLLFVAGGLAHAAVFSMYVL 277
                                       *****************************************999987544..4456666777889************ PP

                        MFS_1_like 310 ienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                          +  v+ ++ L g+ ++++  ++ve + ++ p++l at q  l++l +glG+a G+l++G+l d  + + lF
  gi|313116880|ref|YP_004038004.1| 278 GGTTAAVIAVQPLLGVGYAAVMTSVVELADELSPDELGATAQTALTALGIGLGGATGELLSGALLDVLGIFRLF 351
                                       *****************************************************************999999888 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3  40.8   6.8e-19   2.4e-15       5     340 ..      11     321 ..       9     325 .. 0.80
   2 !   19.2  12.8   1.3e-07   0.00048      62     174 ..     258     369 ..     257     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 6.8e-19
                             MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll 80 
                                       +f+ +l++s ++++    + ++ g+s+s +gl+ ++  ++ +va++++G lsdr+G+ + v+l++l+++++   l++
  gi|313116880|ref|YP_004038004.1|  11 YFVFFLSSSGILAFRN-VYFRSVGLSGSDMGLVGAALLVVGIVAQPVWGLLSDRLGAQKrVVLIALAVSGAL-SLAF 85 
                                       7888999999888888.78899**********************************5555777777777777.2333 PP

                             MFS_1  81 .fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                         a+ +  +l+l  l+ ++a++  p+  ++ + + +    g ++g + a+ s+++ +g l+ gl+++    +++fy+
  gi|313116880|ref|YP_004038004.1|  86 pPAARVG-VLALVGLTIAFAAFQSPVRPVANSLVLSA---GYGYGTVRAFGSIAFGVGTLAYGLVLARTDPSVLFYV 158
                                       1134444.33333344444456666666666666666...999***************99999999*********** PP

                             MFS_1 157 laivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply 233
                                        a+ ++laf    ++l+++  +  +  ++ +              all+++ +  ll+a +++++++s+  +++ ++
  gi|313116880|ref|YP_004038004.1| 159 YAVGAALAFF---VVLRTPVGDGDPLDGVGR-----------RVPALLRNRSFAGLLAATFVVGIVLSANNSYFVFF 221
                                       ********66...666666666666666666...........35678888988789999999999****99999999 PP

                             MFS_1 234 lqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvli 310
                                       ++ v g +   ++g+++a+   + ai++l + r +   ++rr l++a++l+ +a++++++l+ t  ++++++v  l+
  gi|313116880|ref|YP_004038004.1| 222 VNAVGGGN--ETTGAAFAVKTTAEAIAFLAFVRAA---PSRRLLFVAGGLAHAAVFSMYVLGGT--TAAVIAVQPLL 291
                                       77777777..9999999999999977755555544...55899999999999999999999999..66666778889 PP

                             MFS_1 311 Gfglgfvfpsllalasdlappeeagtasgl 340
                                       G+g++ v++s+  la++l p e  +ta+ +
  gi|313116880|ref|YP_004038004.1| 292 GVGYAAVMTSVVELADELSPDELGATAQTA 321
                                       *******************98888887765 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.3e-07
                             MFS_1  62 rrvlllglllfalglllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsa.gfslGail 136
                                       r ++++g l+ a+ + + ++  + + +++++  l G+g++a++++++ l+ +++p+e  + a   l+a g++lG + 
  gi|313116880|ref|YP_004038004.1| 258 RLLFVAGGLAHAAVFSMYVL-GGTTaAVIAVQPLLGVGYAAVMTSVVELADELSPDELGATAQTALTAlGIGLGGAT 333
                                       44666666666666233334.666669*****************************9888888666666******** PP

                             MFS_1 137 gpllggllasslgWravfyilaivsllafvlfllllpe 174
                                       g ll+g+l++ lg   +f   a+v+++++v+  +l ++
  gi|313116880|ref|YP_004038004.1| 334 GELLSGALLDVLGIFRLFGGYAVVAVVSVVV--FLATV 369
                                       *************777888888888888664..33333 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   5.1     4e-15   1.4e-11      13     184 ..       8     170 ..       2     180 .. 0.82
   2 ?   -1.8   0.2      0.28     1e+03     170     170 ..     220     220 ..     189     299 .. 0.60

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4e-15
                         LacY_symp  13 alffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfap 89 
                                       ++f+f++f+  s + ++  v+++  +gls++++G+v +++ ++ i+ qp++Gl+sd+lG +k+++     + + ++ 
  gi|313116880|ref|YP_004038004.1|   8 QSFYFVFFLSSSGILAFRNVYFRS-VGLSGSDMGLVGAALLVVGIVAQPVWGLLSDRLGAQKRVVL----IALAVSG 79 
                                       55666666668999*******986.69***********************************9763....3334455 PP

                         LacY_symp  90 fliyvfepllqlnilvGalvGgvflGlvysagagaieayiekvsraskfeyGkarvfGclGyalcaslaGilf.sid 165
                                        l   f p  ++ +l  alvG   l + ++a  + +    + +  ++ + yG++r+fG++ + +++   G+++   d
  gi|313116880|ref|YP_004038004.1|  80 ALSLAFPPAARVGVL--ALVG---LTIAFAAFQSPVRPVANSLVLSAGYGYGTVRAFGSIAFGVGTLAYGLVLaRTD 151
                                       567789999887665..5666...789999999999999***************************9999765169* PP

                         LacY_symp 166 pslvfwlasgfalilllll 184
                                       ps+ f++ +  a++  +++
  gi|313116880|ref|YP_004038004.1| 152 PSVLFYVYAVGAALAFFVV 170
                                       ******9887766544443 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.28
                         LacY_symp 170 f 170
                                       f
  gi|313116880|ref|YP_004038004.1| 220 F 220
                                       1 PP

>> Nuc_H_symport  Nucleoside H+ symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8  22.7   3.2e-10   1.2e-06       4     393 ..       4     364 ..       1     371 [. 0.77

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.2e-10
                     Nuc_H_symport   4 slrLkvlsflqyfiWGaWlvklfsylsktlfaaaeiglvysslgiaailspilvgiiaDkflsaervlavlhli.ga 79 
                                       s rL+ + f+ ++     l+    y+   + ++ ++glv+++l +  i++  + g ++D+    +rv+ ++  + ga
  gi|313116880|ref|YP_004038004.1|   4 STRLQSFYFVFFLSSSGILAFRNVYFRSVGLSGSDMGLVGAALLVVGIVAQPVWGLLSDRLGAQKRVVLIALAVsGA 80 
                                       566666666644444444555567999999******************************98888887776655256 PP

                     Nuc_H_symport  80 vvl.flaaqvtefealflvlLvyslaymPtlaltnsiafanlrDvvtdfprirvlGtvGfilaslaflllvvsladl 155
                                       + l f  a      al  + ++++    P   ++ns+  +       +++++r +G + f + +la+ l    la  
  gi|313116880|ref|YP_004038004.1|  81 LSLaFPPAARVGVLALVGLTIAFAAFQSPVRPVANSLVLS----AGYGYGTVRAFGSIAFGVGTLAYGL---VLART 150
                                       6662445777777888888888888888999999988665....6789************999777643...34455 PP

                     Nuc_H_symport 156 elsrlqlliaagvslllavyaltLPkiPakkkakqslkkllgldafvLlknkrllvfflvslllavvlqiyyvfana 232
                                       ++s + +++ a+ ++ la +   + ++P    ++ +    +g++  +Ll+n+ ++ +   ++++++vl   + +   
  gi|313116880|ref|YP_004038004.1| 151 DPS-VLFYVYAVGAA-LAFFV--VLRTP---VGDGDPLDGVGRRVPALLRNRSFAGLLAATFVVGIVLSANNSYFVF 220
                                       554.55777765544.44443..34788...7788888899**************************9998888777 PP

                     Nuc_H_symport 233 fLtevakivvklasillslsqvaeilfiLtlpfflkrfGikkvlllslvaaalrfalfaygaddepvgvvlllLsli 309
                                       f++ v+    + +   +++   ae + +L+  f+ +    +  ++ + +a+a+ f++++ g     v+ v  lL   
  gi|313116880|ref|YP_004038004.1| 221 FVNAVG-GGNETTGAAFAVKTTAEAIAFLA--FVRAAPSRRLLFVAGGLAHAAVFSMYVLGGTTAAVIAVQPLL--- 291
                                       777777.344556678999999**988775..666777778888999**************6666666555555... PP

                     Nuc_H_symport 310 vyGvaydffyitayvfvdkevpkdirasaqGlflllvnGvGallgsilsgalvemftvdgvvdwqtlwlvfaamalv 386
                                         Gv y+    ++    d+  p ++ a+aq  ++ l  G+G   g +lsgal +++         +++ +f ++a+v
  gi|313116880|ref|YP_004038004.1| 292 --GVGYAAVMTSVVELADELSPDELGATAQTALTALGIGLGGATGELLSGALLDVL---------GIFRLFGGYAVV 357
                                       ..*************************************************99877.........344444444444 PP

                     Nuc_H_symport 387 lavlfll 393
                                       ++v +++
  gi|313116880|ref|YP_004038004.1| 358 AVVSVVV 364
                                       4444333 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.6   9.3e-06     0.033     250     327 ..      28     105 ..       3     118 .. 0.69
   2 ?    5.0  20.1    0.0021       7.4     215     386 ..     186     347 ..     124     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.3e-06
                             MFS_2 250 yltyvlgngsaasvfllvvtisallgiplwqplakrlg.kkntyllgalltivllvlvlllqpsnlllflvllviag 325
                                       y++ v  +gs++ ++ +++ + ++++ p+w  l  rlg  k+++l+++++  +l++ +  + ++  +l+lv l+ia+
  gi|313116880|ref|YP_004038004.1|  28 YFRSVGLSGSDMGLVGAALLVVGIVAQPVWGLLSDRLGaQKRVVLIALAVSGALSLAFPPA-ARVGVLALVGLTIAF 103
                                       5566555*******************************54566666666666665555555.455555555555544 PP

                             MFS_2 326 fg 327
                                        +
  gi|313116880|ref|YP_004038004.1| 104 AA 105
                                       44 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0021
                             MFS_2 215 eqlkevfrnraflillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkn 290
                                       + + +++rnr f  ll++ +++   l  +n+ ++++++ v g n++  ++f++ +t+ a+++++++ ++      ++
  gi|313116880|ref|YP_004038004.1| 186 RRVPALLRNRSFAGLLAATFVVGIVLSANNSYFVFFVNAVGGgNETTGAAFAVKTTAEAIAFLAFVRAAP----SRR 258
                                       667789************************************7777777777766777777776665555....569 PP

                             MFS_2 291 tyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregv.ffavlsfis 366
                                       + +++  l+ +  + +++l  + ++++++++ + g+g+++        ++ vv+     +++    +  +a++++  
  gi|313116880|ref|YP_004038004.1| 259 LLFVAGGLAHAAVFSMYVL-GGTTAAVIAVQPLLGVGYAA-------VMTSVVELADELSPDELGATaQTALTALGI 327
                                       99999999999999*****.*****************554.......455566666666666666655788888888 PP

                             MFS_2 367 klatgiglgvsgllLsafgy 386
                                        l+++ g ++sg+lL+  g+
  gi|313116880|ref|YP_004038004.1| 328 GLGGATGELLSGALLDVLGI 347
                                       88888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2390.58
//
Query:       gi|313116881|ref|YP_004038005.1|  [L=125]
Description: endoribonuclease L-PSP [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-40  137.1   0.0    3.1e-40  136.9   0.0    1.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   0.0   1.7e-44   3.1e-40       2     120 ..       7     123 ..       6     124 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 1.7e-44
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFladied 78 
                                       ++ap +++p+sq+++ g+ +yvsGq p+dp++g++v +d+++qt+q+l+n++avL++ag sl+dvVk+tvF++d++d
  gi|313116881|ref|YP_004038005.1|   7 DEAPPSIGPFSQGIRDGDRIYVSGQGPIDPDSGDIVGEDATAQTEQTLDNVEAVLESAGQSLDDVVKATVFVTDMDD 83 
                                       67999************************************************************************ PP

                                       HHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  79 faevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       + +vnevy++ +++++  ParsaveV +Lp +++vEIe+ia 
  gi|313116881|ref|YP_004038005.1|  84 YDAVNEVYGDRMSQPY--PARSAVEVVELPVDIRVEIEVIAS 123
                                       ***************7..**********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 800.08
//
Query:       gi|313116882|ref|YP_004038006.1|  [L=246]
Description: hypothetical protein Hbor_33460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-71  241.1   0.0    1.3e-71  240.9   0.0    1.0  1  GATase1_like  Putative glutamine amidotransferase
  ------ inclusion threshold ------
      0.099   13.3   0.0        0.2   12.3   0.0    1.4  1  PGM_PMM_II    Phosphoglucomutase/phosphomannomutase, alpha/be


Domain annotation for each model (and alignments):
>> GATase1_like  Putative glutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.9   0.0   1.5e-75   1.3e-71       1     246 [.       3     243 ..       3     244 .. 0.98

  Alignments for each domain:
  == domain 1  score: 240.9 bits;  conditional E-value: 1.5e-75
                      GATase1_like   1 kvllvGeswvssathikGfdqftsvkyeegaklllealkdseyevtympaheaaekfPatleglaaydaiilsdiGs 77 
                                       +vll+Gesw++ +  +kG + ++ + y ++ ++l++al+     v++++  e+ ++fP t e+l++yd ++lsd+G+
  gi|313116882|ref|YP_004038006.1|   3 RVLLAGESWTTVTFEVKGRNVLVDADYGTAEEHLVAALEVNGAAVDFLTCEETLTSFPGTREELDSYDLVLLSDVGA 79 
                                       59*************************************************************************** PP

                      GATase1_like  78 ntlllspatflesksvPnrlkllkdyvaeGggllmvGGylsfqGidgkarykktpvedvlPvtcldvddrvevPeGl 154
                                       ++l l+pa+    ++  +r +ll++yv +Gg+l m+GGy+sf G  g ary +tp++dvlPv++ d ddrve P+G+
  gi|313116882|ref|YP_004038006.1|  80 DSLQLTPAVT-AGDTDTDRCRLLAEYVRDGGALGMIGGYMSFAGKGGAARYGRTPIADVLPVEIRDGDDRVETPAGA 155
                                       *******985.578899************************************************************ PP

                      GATase1_like 155 aaevvasehpvlkglssewPkllGyneveakdnaevlatvsedshPllvvGeygkGrtaaftsdisphwlspefldw 231
                                       ++ +      v + l+++wP +lGyn+++akd+a+v atv++ + P++vvGe g Grt af++d++phw ++e+l+w
  gi|313116882|ref|YP_004038006.1| 156 IPMNRG----VPADLPETWPAVLGYNHLQAKDDADVWATVGDRADPFVVVGEAGAGRTFAFATDCAPHWAPMELLEW 228
                                       998765....899**************************************************************** PP

                      GATase1_like 232 egyarlwknvldwlt 246
                                       +g   lw  +ldw+t
  gi|313116882|ref|YP_004038006.1| 229 DGLPVLWGALLDWAT 243
                                       *************97 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.2e-05       0.2      19      97 ..      19      99 ..      10     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                                      HT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT.-TTSS----TT-TTTTHHHHGGGG.G-.SEEEEE-TTS- CS
                        PGM_PMM_II 19 sglkvvidplhGaggeilkellkelgvdvvelnaepdpd.fptkapnpeekealkllielvkke.ga.dlglafDgDaD 94
                                      +g  v++d+ +G+++e l  +l+  g+ v  l +e   + fp++  +  ++ +l ll+++  ++ +   ++ a D D D
  gi|313116882|ref|YP_004038006.1| 19 KGRNVLVDADYGTAEEHLVAALEVNGAAVDFLTCEETLTsFPGT-REELDSYDLVLLSDVGADSlQLtPAVTAGDTDTD 96
                                      45589**********************99998888775516654.4555548898888886655355688899999999 PP

                                      BEE CS
                        PGM_PMM_II 95 Rlg 97
                                      R+ 
  gi|313116882|ref|YP_004038006.1| 97 RCR 99
                                      985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1807.88
//
Query:       gi|313116883|ref|YP_004038007.1|  [L=356]
Description: theronine dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-31  107.0   0.3      8e-31  106.2   0.3    1.4  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    5.5e-23   81.4   0.3    8.2e-23   80.8   0.3    1.2  1  ADH_zinc_N    Zinc-binding dehydrogenase
    7.8e-13   48.4   0.4    1.3e-12   47.7   0.4    1.4  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    0.00071   20.6   0.1     0.0012   19.9   0.1    1.3  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.019   14.6   0.1      0.033   13.8   0.1    1.5  1  ApbA          Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.3   2.2e-34     8e-31       1     108 [.      41     148 ..      41     149 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 2.2e-34
                                       TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT- CS
                             ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkege 77 
                                       pge+l++v+a+giCgsD+ +++g+  + + +pl++GHE++ ev+e+g++v++l+vGdrV+++ ++ cg+C aC+eg+
  gi|313116883|ref|YP_004038007.1|  41 PGEALVRVSAVGICGSDIGLMEGEGPPWTDYPLVPGHEVCAEVVELGEGVEDLNVGDRVALHGFVYCGTCTACREGR 117
                                       589************************************************************************** PP

                                       GGG-TTBEETTTSS-SSSBSEEEECGGGEEE CS
                             ADH_N  78 enlCeeakllgvsldGgfaeyvvvpekklvk 108
                                       +  C++ k +g+++dGg+ ey  +p+ +l +
  gi|313116883|ref|YP_004038007.1| 118 YYQCDDLKEVGFTIDGGYREYAALPAYTLTP 148
                                       ************************9988776 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   0.3   2.3e-26   8.2e-23       2     128 ..     190     315 ..     189     317 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 2.3e-26
                                       HHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   2 vGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       +Gl++vql++a G+  vi +   ee+le+ +  Ga  +in +e+d+veri e t+g+g+d+ +e++G+g++++++lk
  gi|313116883|ref|YP_004038007.1| 190 LGLYGVQLLRAQGVkDVILTGTREERLEIGEHHGASLTINVREEDPVERILEYTDGKGADICVEAAGAGDVVNTCLK 266
                                       7****************************************555********************************* PP

                                       CEEEEEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  78 llkpgGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkealdll 128
                                       +++++G +v+ G+++g +e+d+++++ ke++++G + +s  +++ +++dl+
  gi|313116883|ref|YP_004038007.1| 267 ATRKRGNVVLTGVFGGMKEIDPNDIVSKELQVVGGVTAS--HTVDQVIDLF 315
                                       *************666666***************99999..9999998885 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.4   3.5e-16   1.3e-12      32     210 ..     180     354 ..     148     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.5e-16
                       Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatY..vdsretpvdeipeas..eemdlv 104
                                       ++ +vlG GslGL  + ll+a  +g+++v  +g+r++   ++++ e+ Ga       +e+pv++i e +  +  d+ 
  gi|313116883|ref|YP_004038007.1| 180 DTGVVLGPGSLGLYGVQLLRA--QGVKDVILTGTREE---RLEIGEHHGASLtiNVREEDPVERILEYTdgKGADIC 251
                                       5789*************9997..89****99998876...78889999996521345689*****876522679*** PP

                       Glu_dehyd_C 105 vEaTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpesl 181
                                       vEa G+  ++   ++a +  G ++L+Gv  +   e+d +    ++v +   +vG v a+  h    v +L +  +  
  gi|313116883|ref|YP_004038007.1| 252 VEAAGAGDVVNTCLKATRKRGNVVLTGVFGGM-KEIDPN----DIVSKELQVVGGVTAS--HTVDQVIDLFRRGDLS 321
                                       *****************************998.899975....67888999*****986..5556677777888888 PP

                       Glu_dehyd_C 182 ldelvtkvvdldeleeAfe....dddetiKtvv 210
                                       +d +vt++ dl+e+e+A e    + d  +K+v+
  gi|313116883|ref|YP_004038007.1| 322 IDGIVTHEFDLAEYETAIEtvreRRDGVVKAVL 354
                                       9****************9855556677777775 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   3.4e-07    0.0012       2     126 ..     223     346 ..     222     348 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.4e-07
                                       T-SEEEETT.STTHH...HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EE CS
                      ADH_zinc_N_2   2 GAdevidyr.tedfe...aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsv 73 
                                       GA   i+ r ++ +e   + t+g+g D+ ++++g  + +  +lk+ +++G +v  g      +++ ++     ++ +
  gi|313116883|ref|YP_004038007.1| 223 GASLTINVReEDPVErilEYTDGKGADICVEAAGAGDVVNTCLKATRKRGNVVLTGvFG-GMKEIDPND--IVSKEL 296
                                       89999999*777777*******************66666*******888**98877431.222222222..233444 PP

                                       EE--GGG...-.-HHHHHHHHHHHHHHH--..--EEEEEEGGGHHHHHHHHHSS- CS
                      ADH_zinc_N_2  74 kyeflfsmkasaqadileelaalieeGklr..pvvdrvfpleeaaeAhrylesgr 126
                                       +++  +  +as   ++ +++ +l+  G l     v+++f+l+e  +A++ ++++r
  gi|313116883|ref|YP_004038007.1| 297 QVVGGV--TAS---HTVDQVIDLFRRGDLSidGIVTHEFDLAEYETAIETVRERR 346
                                       445554..343...4499**********7622689999***********999877 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   9.3e-06     0.033       2      50 ..     183     234 ..     183     310 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.3e-06
                                       EEES-SHHHHHHHHHHHHHTHC.EEEE-SCH.HHHHHHHHCEEEEETT.CEE CS
                              ApbA   2 ailGaGaiGsllaakLakagad.vtlilrsr.rlealkknGlrltseg.gee 50 
                                       ++lG+G++G +    L ++g + v+l + ++ rle  +++G +lt++  +e 
  gi|313116883|ref|YP_004038007.1| 183 VVLGPGSLGLYGVQLLRAQGVKdVILTGTREeRLEIGEHHGASLTINVrEED 234
                                       59*******88777776655544****99999**************993332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2587.04
//
Query:       gi|313116884|ref|YP_004038008.1|  [L=233]
Description: LmbE-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-31  108.8   0.7    4.7e-31  108.1   0.7    1.3  1  PIG-L           GlcNAc-PI de-N-acetylase
      0.003   17.6   0.0     0.0045   17.0   0.0    1.3  1  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.7   5.2e-35   4.7e-31       2     130 ..       5     124 ..       4     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 5.2e-35
                                       EEESSTTHHHHHHHHHHHHHHHTT-EEEEEECE--TT---STTTTHH-HHHHHHHHHHHHHHHHCTE..EEEEECCC CS
                             PIG-L   2 lvlAHpDDellfaggtiaklvaagvevkivcltaGdagsplatleekeelaeiRekEaraaakhlgvadedvffldf 78 
                                       +++AHpDD+ +f+ggt++k++++g +v iv++t+G++g  + t    ee+ae+Re Ea+aaa++l +   ++ fldf
  gi|313116884|ref|YP_004038008.1|   5 AIVAHPDDADIFCGGTLKKHAERGDDVTIVYMTRGEYGGFDTTE---EEVAETRESEAEAAAEALDA---EARFLDF 75 
                                       69************************************444443...49******************...9****** PP

                                       BTT-STTS-CHHHHHHHHHHHHHH--SEEEEE-TTTTH-HHHHHHHHHHHHH CS
                             PIG-L  79 pDgslesydedellddlaklieryrPdvvltldpegddhpDHtavasaavaa 130
                                       +Dg+  +    e + +l+++i+++rPd++lt+ +++  hpDH+++++++++a
  gi|313116884|ref|YP_004038008.1|  76 RDGRITY--SMENRLELVDVIRELRPDIILTHFRDDM-HPDHRVTSRLVTDA 124
                                       *******..8888889*********************.**********9987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.1e-07    0.0045      14     108 ..      23     141 ..      18     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.1e-07
                    Glyco_transf_4  14 aLarrGheVtvv..tpgddgpleeev...............elvvrvprvplpllkrllrslaflrrlrrllkrekp 73 
                                         a+rG +Vt+v  t+g  g ++  +               e + +  r+  + ++r  +s+ +++ l  ++++ +p
  gi|313116884|ref|YP_004038008.1|  23 KHAERGDDVTIVymTRGEYGGFDTTEeevaetreseaeaaaEALDAEARFLDFRDGRITYSMENRLELVDVIRELRP 99 
                                       5689********996665554444445567777888998887888888888899999999***************** PP

                    Glyco_transf_4  74 DvvHahspaalgaallalrr.......rlgiplVltvHglye 108
                                       D++ +h+   +   ++   r          +pl  t H  +e
  gi|313116884|ref|YP_004038008.1| 100 DIILTHFRDDMHPDHRVTSRlvtdayyMASLPLAQTDHEEWE 141
                                       ***888776666555555555668888899999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1560.81
//
Query:       gi|313116885|ref|YP_004038009.1|  [L=426]
Description: ORC complex protein Cdc6/Orc1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-19   69.1   0.3    1.2e-17   63.6   0.1    2.5  2  Cdc6_C           CDC6, C terminal winged helix domain
    4.1e-13   49.8   0.0    1.6e-12   47.9   0.0    1.9  2  AAA_22           AAA domain
    2.6e-06   27.9   5.9    4.7e-05   23.8   5.9    2.6  1  AAA_16           AAA ATPase domain
     0.0011   18.2   0.0     0.0023   17.2   0.0    1.6  2  NB-ARC           NB-ARC domain
     0.0013   18.2   0.0     0.0038   16.7   0.0    1.7  2  TniB             Bacterial TniB protein
     0.0014   18.6   0.4      0.024   14.6   0.4    2.5  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0015   18.0   0.4       0.51    9.8   0.0    2.4  2  PhoH             PhoH-like protein
     0.0031   17.6   0.0      0.012   15.7   0.0    1.9  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0033   16.6   0.0     0.0077   15.4   0.0    1.6  2  DUF815           Protein of unknown function (DUF815)
     0.0063   16.9   1.3      0.083   13.3   1.3    2.5  1  AAA              ATPase family associated with various cellul
     0.0096   15.6   0.1      0.025   14.3   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.027   14.6   0.0    1.6  1  TIP49_C          TIP49 AAA-lid domain
      0.012   15.3   0.4      0.033   13.9   0.2    1.9  2  AAA_24           AAA domain
      0.037   13.8   2.2        5.6    6.7   0.2    2.5  2  DEAD             DEAD/DEAH box helicase
      0.083   11.7   0.6        5.1    5.7   0.3    2.2  2  AAA_32           AAA domain
      0.085   12.8   0.0       0.32   10.9   0.0    2.0  2  NACHT            NACHT domain
       0.14   12.5   0.0       0.44   11.0   0.0    1.9  1  RNA_helicase     RNA helicase
       0.15   11.6   0.1       0.48    9.9   0.1    1.7  1  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0       0.1     1e+02      29      80 ..     107     153 ..     105     156 .. 0.86
   2 !   63.6   0.1   1.2e-20   1.2e-17       1      82 [.     319     400 ..     319     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.1
                                       HHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHH CS
                            Cdc6_C  29 CesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpdd 80 
                                       C++e+ +++  r + + l++ e   i+  e++      gr+r+++L +d  d
  gi|313116885|ref|YP_004038009.1| 107 CSQEDTETRAVRCIARELNDPEETDIVIPETG-----LGRSRYYTLLWDVLD 153
                                       88889999999999999999999999999987.....69*********9877 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 1.2e-20
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+++vll+ ++++++++t e+y  Y+++C ++g+++l+ r+v+dll+e e+l +l++ + + Gr++g + ++ L  d
  gi|313116885|ref|YP_004038009.1| 319 LLSVVLLALSEKTRTFKTPEIYTAYEEICADTGLEVLSKRRVHDLLREWEFLEVLDIVRTGDGRARGSYLEHHLVED 395
                                       8999999999******************************************************************* PP

                                       CHHHH CS
                            Cdc6_C  78 pddvl 82 
                                       p+ ++
  gi|313116885|ref|YP_004038009.1| 396 PSVIR 400
                                       *9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   1.6e-15   1.6e-12       7     126 ..      67     195 ..      62     207 .. 0.86
   2 ?   -1.3   0.0       2.4   2.4e+03      39      69 ..     316     348 ..     277     368 .. 0.50

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.6e-15
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlssee 77 
                                        ++++G +GtGK+++++  +++ +e+a  ++  ++ v v+++++ + +   r ++r+l+++ ++       +l +++
  gi|313116885|ref|YP_004038009.1|  67 NVFLYGKTGTGKSLCAKYATKRTVEAAVENDITVGRVVVDCSQEDTETRAVRCIARELNDPEETdivipeTGLGRSR 143
                                       6789*****************9975444333555556********************************9999**** PP

                            AAA_22  78 llealeqalraravielliiDEaqhlrseealeeLrsllnl...srkgvqli 126
                                       ++++l++ l++r++++++++DE++hl ++++l +L++ ++    sr+ + +i
  gi|313116885|ref|YP_004038009.1| 144 YYTLLWDVLDSRFDVAFIVLDEIDHLETDDILMQLSRAAESekiSRCALGII 195
                                       **************************55*******88888666666666555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                            AAA_22  39 rpevvfvtlpsst.sskdl.lrellralglelk 69 
                                       ++++++v l +++ + +++   e+  a+++ + 
  gi|313116885|ref|YP_004038009.1| 316 KATLLSVVLLALSeKTRTFkTPEIYTAYEEICA 348
                                       333332222222223333333333333333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   5.9   4.7e-08   4.7e-05       2      82 ..      42     125 ..      41     325 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.7e-08
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd........ggiflrgkcdqlesaipy 69 
                                        vGR ee+++L+  l+++  g++ ++v+l+G  G+GKs  ++ + ++  ++        g   +  +c q ++++  
  gi|313116885|ref|YP_004038009.1|  42 IVGRNEEIRRLAGSLSPATVGDSpNNVFLYGKTGTGKSLCAKYATKRTVEAavenditvGR--VVVDCSQEDTET-- 114
                                       69**************66666655*****************87777555544444443321..333333321121.. PP

                            AAA_16  70 salaqalareell 82 
                                          ++++ar el 
  gi|313116885|ref|YP_004038009.1| 115 -RAVRCIAR-ELN 125
                                       .14444433.443 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.3e-06    0.0023       6     112 ..      50     166 ..      45     192 .. 0.66
   2 ?   -4.1   0.1         7     7e+03      92     110 ..     356     374 ..     346     377 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHC...TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEE..ESXXHHHHHHHXXHHHH CS
                            NB-ARC   6 ekviekLle...kdelqslvvalvGmgGvGKttlakqilnksdevegrFd.svawvvv..sktdkseeiletilkeL 76 
                                       +++++ L+     d+++   v+l+G+ G GK+  ak + +   e   + d  v  vvv  s++d++ + ++ i++eL
  gi|313116885|ref|YP_004038009.1|  50 RRLAGSLSPatvGDSPN--NVFLYGKTGTGKSLCAKYATKRTVEAAVENDiTVGRVVVdcSQEDTETRAVRCIAREL 124
                                       55666665432234555..89********************8888888884333444444***************** PP

                                       HCCCT.TSSSS-STTS...HHHHHHHHCCCT..TEEEEEEEE CS
                            NB-ARC  77 slsed.dleekeeves...lkrklvrlLltk..rfllvlDDV 112
                                       ++ e+ d+ + e++       + l  +L ++     +vlD +
  gi|313116885|ref|YP_004038009.1| 125 NDPEEtDIVIPETGLGrsrYYTLLWDVLDSRfdVAFIVLDEI 166
                                       876441444444444344445556666666665556666666 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 7
                                       HHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  92 lkrklvrlLltkrfllvlD 110
                                        kr+++ lL++  fl vlD
  gi|313116885|ref|YP_004038009.1| 356 SKRRVHDLLREWEFLEVLD 374
                                       5788999999999999998 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.8e-06    0.0038      33     133 ..      63     171 ..      45     214 .. 0.74
   2 ?   -2.6   0.0       3.2   3.2e+03     126     145 ..     302     321 ..     302     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-06
                              TniB  33 krmpnlllvGdsnnGKtmivekFarlhppekd.edaekvpvlvvqappkpdekrlyaaiLealgaplkara...... 102
                                       + ++n+ l+G++ +GK+  + k+a +++ e   e++ +v  +vv++ ++ +e r  + i ++l+ p +++       
  gi|313116885|ref|YP_004038009.1|  63 DSPNNVFLYGKTGTGKSL-CAKYATKRTVEAAvENDITVGRVVVDCSQEDTETRAVRCIARELNDPEETDIvipetg 138
                                       556899**********95.667776666665426667889999***********************76654555333 PP

                              TniB 103 .rvskleqqvlrll.relkvrvLiiDEihnlla 133
                                          s+ +     +l ++++v  +++DEi++l++
  gi|313116885|ref|YP_004038009.1| 139 lGRSRYYTLLWDVLdSRFDVAFIVLDEIDHLET 171
                                       3334445555556644799***********985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                              TniB 126 DEihnllagsarkqreflna 145
                                       D + +llag  ++q+++l +
  gi|313116885|ref|YP_004038009.1| 302 DRFRELLAGATDQQKATLLS 321
                                       56788999999999988755 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.4   2.5e-05     0.024       1      97 [.      67     190 ..      67     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------............. CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar............. 64 
                                       +v+L G++GtgKs  a++  +++    ++ +   d+t   ++   + +++t+ +   ++ r+ +             
  gi|313116885|ref|YP_004038009.1|  67 NVFLYGKTGTGKSLCAKYATKRT----VEAAVENDITVGRVVVDCS-QEDTETRAVRCIARELNdpeetdivipetg 138
                                       69***********9999887766....4445555566666665555.355555555555555556666666667777 PP

                                       ..................G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE.. CS
                             AAA_5  65 ..................egeilvlDEverae.sevlnsLlslleerrllle 97 
                                                           + +vlDE++++e +++l+ L +  e ++++ +
  gi|313116885|ref|YP_004038009.1| 139 lgrsryytllwdvldsrfDVAFIVLDEIDHLEtDDILMQLSRAAESEKISRC 190
                                       788889********999999999*********999****9999998888765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00051      0.51      21      62 ..      67     108 ..      48     116 .. 0.84
   2 !    6.1   0.1    0.0067       6.6     118     149 ..     156     187 ..     154     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00051
                                       EEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT CS
                              PhoH  21 ivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveag 62 
                                        vf  G++GtGK++ a  +  + +++   + i + r +v++ 
  gi|313116885|ref|YP_004038009.1|  67 NVFLYGKTGTGKSLCAKYATKRTVEAAVENDITVGRVVVDCS 108
                                       5899**********9988888888888778888888888774 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0067
                                       B-SEEEEE-SGGG--HHHHHHHHTTB-TT-EE CS
                              PhoH 118 lndafvilDEAQnttkeqmkmfltRlGenskv 149
                                       ++ af++lDE   +++  + m l+R  e+ k+
  gi|313116885|ref|YP_004038009.1| 156 FDVAFIVLDEIDHLETDDILMQLSRAAESEKI 187
                                       6789*********************9887765 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05     0.012       1      42 [.      43      86 ..      43     100 .. 0.83
   2 ?   -1.2   0.0       2.1   2.1e+03      60     101 ..     147     190 ..     117     200 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                      X---HHHHHHHHHHHHHH..T-SS-EEEEEETT--HHHHHHCC- CS
                   Sigma54_activ_2  1 lgasaaiqelkerLeqaa..qsklpvfltGekGsgkelvArlLh 42
                                      +g+ + i +l+  L  a    s  +vfl G  G+gk+l+A++  
  gi|313116885|ref|YP_004038009.1| 43 VGRNEEIRRLAGSLSPATvgDSPNNVFLYGKTGTGKSLCAKYAT 86
                                      6788888899999987775578889****************965 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                                       -HHHHHHH.TTTSEEEEEE-TT--HHH.HHHHHHHHHHHTTTT- CS
                   Sigma54_activ_2  60 lpldlleq.akggtLylkdiadlskae.qkeLlellakaekssl 101
                                       l  d+l++  + + ++l +i++l+ ++ +++L  + ++++ s++
  gi|313116885|ref|YP_004038009.1| 147 LLWDVLDSrFDVAFIVLDEIDHLETDDiLMQLSRAAESEKISRC 190
                                       45667776346677889999999876526777766666655555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.7e-06    0.0077      28      79 ..      40      91 ..      17     112 .. 0.87
   2 ?   -3.1   0.0       3.6   3.5e+03     175     220 ..     206     250 ..     198     268 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.7e-06
                            DUF815 28 ddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyae 79
                                      d++vg +++ ++l    +    g + nnv+L+G+ GtGKS + k +++++ e
  gi|313116885|ref|YP_004038009.1| 40 DRIVGRNEEIRRLAGSLSPATVGDSPNNVFLYGKTGTGKSLCAKYATKRTVE 91
                                      567888888888888888889999****************999988887665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.6
                            DUF815 175 aveekl..sLsdRFGlwlgFykldqeeYleiveklakklglelekeel 220
                                        ++e++  sL +R    + F +  +++  ei+++ a+ +++++ ++e+
  gi|313116885|ref|YP_004038009.1| 206 RLQERVksSLQER---EIVFAPYGRDKLREILRSRADAFQTDTLSNEV 250
                                       5555443355555...56777777777777777777777665544333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.3   8.3e-05     0.083       1     114 [.      68     206 ..      68     223 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.3e-05
                                       EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS......................STTHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel.........gvefleisgsellsk......................yvgesekki 46 
                                       v lyG  GtGK+l+ak   k +          v  + +++s+   +                        g + ++ 
  gi|313116885|ref|YP_004038009.1|  68 VFLYGKTGTGKSLCAKYATKRTveaavendiTVGRVVVDCSQEDTEtravrciarelndpeetdivipETGLGRSRY 144
                                       679**************999964433333321222333333333223466666666666777888877555555555 PP

                                       HHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGG CS
                               AAA  47 relfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdk 114
                                         l+ ++  ++ +   +++DEid l +++          ++ qL ++ + +k ++  + +ig++n+    d+
  gi|313116885|ref|YP_004038009.1| 145 YTLLWDVLDSRfDVAFIVLDEIDHLETDD----------ILMQLSRAAESEKISRCALGIIGISNKigyRDR 206
                                       55555544444556899999999996666..........999999999999998888889999998444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.5e-05     0.025       2      45 ..      43      88 ..      42     114 .. 0.74
   2 ?   -2.9   0.0       4.8   4.8e+03      96     108 ..     160     172 ..     155     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-05
                                      ---SHHHHHHHHHHHHHC..TSSS-EEEECSTTSSHHHHHHHHHHH CS
                   Sigma54_activat  2 igesealkelleqikkva..ktdlsvlitGesGtGKellaraihea 45
                                      +g++e++++l  +++ ++  +++ +v++ G++GtGK+l+a+   ++
  gi|313116885|ref|YP_004038009.1| 43 VGRNEEIRRLAGSLSPATvgDSPNNVFLYGKTGTGKSLCAKYATKR 88
                                      666777777776665444227779****************987664 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.8
                                       EEEEETGGGS-HH CS
                   Sigma54_activat  96 tlfLDeigelple 108
                                        + LDei +l+++
  gi|313116885|ref|YP_004038009.1| 160 FIVLDEIDHLETD 172
                                       6889999999764 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.7e-05     0.027      31      63 ..     266     298 ..     251     299 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                           TIP49_C  31 RYaiqLltpasilakkrkkkevevedveeveeL 63 
                                       R ai Ll  a  +a+ ++++ v v++v+e++eL
  gi|313116885|ref|YP_004038009.1| 266 RKAIDLLRHAGEVARSNGETAVGVDHVREANEL 298
                                       669****************************98 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.3e-05     0.033       3      33 ..      66      96 ..      64     189 .. 0.57
   2 ?   -2.9   0.0       4.6   4.6e+03     110     142 ..     303     340 ..     300     349 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakelgpkplfidtek 33
                                      +++++yG+ g+GK+ +ak ++++++   +e+
  gi|313116885|ref|YP_004038009.1| 66 NNVFLYGKTGTGKSLCAKYATKRTVEAAVEN 96
                                      6899****************99999997776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                            AAA_24 110 efrrllkklqelrk.....nvifiahektrkdedpege 142
                                       +fr+ll   ++ +k      v +   ektr++++pe  
  gi|313116885|ref|YP_004038009.1| 303 RFRELLAGATDQQKatllsVVLLALSEKTRTFKTPEIY 340
                                       56666666666666666634444557788888888444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2    0.0079       7.9      15      39 ..      66      90 ..      54     117 .. 0.77
   2 ?    6.7   0.2    0.0056       5.6     121     146 ..     157     182 ..     121     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0079
                                      CEEEEEESTTSSHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTlaflipvlqiv 39
                                      ++v++ ++TG+GK+l++  +  ++v
  gi|313116885|ref|YP_004038009.1| 66 NNVFLYGKTGTGKSLCAKYATKRTV 90
                                      699*************977765555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0056
                                       TEEEEEEETHHHHHHTTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 121 qvrflVlDEadrlldqgfsdfinril 146
                                       +v f+VlDE+d l  ++   +++r +
  gi|313116885|ref|YP_004038009.1| 157 DVAFIVLDEIDHLETDDILMQLSRAA 182
                                       799**********9997777777655 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.018        18      31      63 ..      66      97 ..      46      99 .. 0.79
   2 ?    5.7   0.3    0.0052       5.1     477     509 ..     265     297 ..     242     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.018
                            AAA_32 31 YNifvlGesgtGrttlvkrlleeiakkeptpdD 63
                                       N+f+ G++gtG++ ++k + ++ + ++++ +D
  gi|313116885|ref|YP_004038009.1| 66 NNVFLYGKTGTGKSLCAKYATKR-TVEAAVEND 97
                                      5************9877766555.445555555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0052
                            AAA_32 477 fseiadllrEAdywakkegaevveaehVekAle 509
                                        ++ +dllr A  +a+++g+++v  +hV++A e
  gi|313116885|ref|YP_004038009.1| 265 ARKAIDLLRHAGEVARSNGETAVGVDHVREANE 297
                                       57889*************************976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00032      0.32       3      99 ..      68     175 ..      66     255 .. 0.76
   2 ?   -1.2   0.0       1.6   1.6e+03     124     161 ..     326     366 ..     288     389 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C....... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgnarsladllfsqlpepaapvse....... 71 
                                       v+l G+ G GK+  ++       e   +++  +  v + +++e+++  ++r++a+ l ++    +  +++       
  gi|313116885|ref|YP_004038009.1|  68 VFLYGKTGTGKSLCAKYATKRTVEAAVENDItVGRVVVDCSQEDTETRAVRCIARELNDPEETDIVIPETglgrsry 144
                                       7999********99887766666666666543444555555555555555677776666666666666669****** PP

                                       ...CHHHHCCSCCCEEEEEE-STT-SS-TCH CS
                             NACHT  72 ...vwavllelperlLlilDglDelvtdlgq 99 
                                           w vl ++++ + ++lD +D l+td+  
  gi|313116885|ref|YP_004038009.1| 145 ytlLWDVLDSRFDVAFIVLDEIDHLETDDIL 175
                                       **************************98755 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                       EEEEECCCHHHHCTTSSCE............EEEE--TCCHHHHHHHH CS
                             NACHT 124 lltvrpralrdleeqleea..........ivlevegfsesrrkqlvrk 161
                                        l+       +  ++++++          + + +e +s+ r+  l+r+
  gi|313116885|ref|YP_004038009.1| 326 ALS-------EKTRTFKTPeiytayeeicADTGLEVLSKRRVHDLLRE 366
                                       222.......22222222221111222233344444555555555544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00044      0.44       1      22 [.      68      89 ..      68     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakal 22
                                      ++lyG++g+GKS++ak+ +k+ 
  gi|313116885|ref|YP_004038009.1| 68 VFLYGKTGTGKSLCAKYATKRT 89
                                      689*************954444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00048      0.48      34      56 ..      66      88 ..      59     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00048
                             AAA_7 34 kpvllvGptGtGKtviikdllkk 56
                                      ++v+l+G+tGtGK++++k  +k+
  gi|313116885|ref|YP_004038009.1| 66 NNVFLYGKTGTGKSLCAKYATKR 88
                                      789*************9986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2736.92
//
Query:       gi|313116886|ref|YP_004038010.1|  [L=332]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-24   85.4   0.2    7.6e-24   84.8   0.2    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    2.7e-11   43.5   0.0    5.7e-11   42.4   0.0    1.5  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    0.00045   20.6   0.1      0.001   19.5   0.1    1.5  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
     0.0037   17.4   0.0     0.0066   16.6   0.0    1.4  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
     0.0087   16.7   0.1      0.016   15.9   0.1    1.4  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
  ------ inclusion threshold ------
      0.022   15.3   0.0      0.069   13.7   0.0    1.8  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.2   2.5e-27   7.6e-24       2     120 .]       3     121 ..       2     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 2.5e-27
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHH.TTHEEESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaes.fgveaysdleelladpeidavivatpngthee 77 
                                       rv+++G+G +++ h+++++e  +++evva+ + +++r e +ae+  g+++y d ee+++d ++ ++  +tp+ th+ 
  gi|313116886|ref|YP_004038010.1|   3 RVGLVGSGLMATTHANSYQEV-DDAEVVAVASHGENRDEFAAEHaPGADVYYDPEEMMDDADVTVIDACTPTPTHRP 78 
                                       89*************999999.*****************9966516888**************************** PP

                                       HHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  78 lakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       l++aa+ +g +v+ EKP+a tve+a+++v+++e++g +++ g+
  gi|313116886|ref|YP_004038010.1|  79 LIEAAADRGLDVFSEKPMARTVEDAEAVVNAVEESGITFMTGH 121
                                       ************************************9998876 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.9e-14   5.7e-11       1      96 [.     133     222 ..     133     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.9e-14
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCT CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaea 77 
                                       K  I++g++G++ +     +  +++++ + +w  +k++sgGvl d++iHd+D+l+w +G + +v++ +   ++++++
  gi|313116886|ref|YP_004038010.1| 133 KRRIDDGEIGTPGTLR-AERLSSPPRYGTENWFSDKAQSGGVLLDMAIHDFDFLRWVAGDVERVFTRT---AEWDND 205
                                       7889***********9.999999******************************************999...577655 PP

                                       CCSCSEEEEEEEEEEETTE CS
                    GFO_IDH_MocA_C  78 aededaavmsvlnlekgsg 96 
                                         +  aav  +l++e+g++
  gi|313116886|ref|YP_004038010.1| 206 HLHQHAAV--HLRFEDGTV 222
                                       55555553..666666654 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   3.4e-07     0.001       1     115 [.       3     112 ..       3     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.4e-07
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpag 77 
                                       +v++vG +G + +  ++  +e  ++e+v+++s+ ++  +  ae+++    g+d+ +++ ++ + ++v ++  ++p  
  gi|313116886|ref|YP_004038010.1|   3 RVGLVG-SGLMATTHANSYQEVDDAEVVAVASHGENRDEFAAEHAP----GADVYYDPEEMMDDADVTVIDACTPTP 74 
                                       699999.999999999999999999999999988877777777766....99999999666666777777789**** PP

                                       HHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHG CS
                    Semialdhyde_dh  78 vskelapklaeagvkviDlssdfRlkddavyvlpevnr 115
                                       ++++l +++a++g+ v++  +  R  +da  v+  v +
  gi|313116886|ref|YP_004038010.1|  75 THRPLIEAAADRGLDVFSEKPMARTVEDAEAVVNAVEE 112
                                       ****************************9999998876 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.2e-06    0.0066       2      82 ..       3      77 ..       2      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SE.EEE-S-HHH CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadv.liDFTtpea 79
                                      +v++vG  G m ++ ++  +e +d+e+va+ ++ e      +  e++  +  g  v+ d ee++++adv +iD  tp+ 
  gi|313116886|ref|YP_004038010.1|  3 RVGLVGS-GLMATTHANSYQEVDDAEVVAVASHGE------NRDEFAAEHAPGADVYYDPEEMMDDADVtVIDACTPTP 74
                                      7999**7.**********************99976......788999999******************8579**99998 PP

                                      HHH CS
                            DapB_N 80 vle 82
                                      +  
  gi|313116886|ref|YP_004038010.1| 75 THR 77
                                      765 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   5.2e-06     0.016       2     110 ..       4     113 ..       4     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.2e-06
                                       -SHHHHHHHHHHHH---S..SEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTH CS
                     NAD_binding_3   2 lGaiGsavleqlkrqqse..ielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelv 76 
                                       +G +Gs++++   ++  +   ++e+vava +    ++ +++ ++ ++++ d +++++++d+ v+  c++    + l+
  gi|313116886|ref|YP_004038010.1|   4 VGLVGSGLMATTHANSYQevDDAEVVAVASHGENRDEFAAEHAPGADVYYDPEEMMDDADVTVIDACTPTPTHRPLI 80 
                                       6999999999888776666689**********4444449999***************6666655556********** PP

                                       HHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS CS
                     NAD_binding_3  77 lkaLkagkdvvtankgaladealyeeLreaaean 110
                                       ++a  +g dv      a +  +  e+ ++a e++
  gi|313116886|ref|YP_004038010.1|  81 EAAADRGLDVFSEKPMART-VEDAEAVVNAVEES 113
                                       *********9765554444.55555555555555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-05     0.069       1      72 [.       3      74 ..       3      89 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..-EEECECHHHHHHH-SEEEE..-S-HH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..vkvtavdneeaaeeadvvvl..avkpe 72
                                      ++g++G+G m+ + a+  ++ +  + e+v a  ++ e ++e+a+e    ++v   d ee++++adv v+  + ++ 
  gi|313116886|ref|YP_004038010.1|  3 RVGLVGSGLMATTHANSYQEVD--DAEVV-AVASHGENRDEFAAEHApgADVYY-DPEEMMDDADVTVIdaCTPTP 74
                                      699****************999..88888.557777777777766663466666.99********98874344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2392.04
//
Query:       gi|313116887|ref|YP_004038011.1|  [L=345]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-17   63.6   0.5    5.7e-17   62.6   0.2    1.7  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    3.4e-08   33.5   0.1    8.3e-08   32.3   0.1    1.7  1  GFO_IDH_MocA_C   Oxidoreductase family, C-terminal alpha/beta
  ------ inclusion threshold ------
      0.013   15.2   0.0       0.02   14.6   0.0    1.2  1  Oxidoreduct_C    Putative oxidoreductase C terminal domain
      0.029   14.6   0.7        1.8    8.9   0.5    3.0  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.2   1.3e-20   5.7e-17      23     119 ..      24     119 ..       3     120 .. 0.80
   2 ?   -3.5   0.0         4   1.8e+04      25      42 ..     186     203 ..     166     210 .. 0.58

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.3e-20
                                       TTTEEEEEEECSSHHHHHHH...HHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEEEESSS- CS
                      GFO_IDH_MocA  23 qrleevvalldpdaeraeav...aesfgveaysdleelladpeidavivatpngtheelakaaleagkhvllEKPla 96 
                                       ++++e v++ + d  + +++   a+++gv++y + +ell+  ++d v+v++ n  h++ +++a+ ag+++l+EKPla
  gi|313116887|ref|YP_004038011.1|  24 ESDAEFVGVTEHDDRA-DDAqakAAEYGVDFY-EPDELLE--RVDGVVVCSTNAAHRDWVEHAADAGVDILCEKPLA 96 
                                       2567889988776633.333344888888855.6899999..9********************************** PP

                                       SSHHHHHHHHHHHHHHTS-EEEE CS
                      GFO_IDH_MocA  97 ttveeakelvelaekkgklvsvg 119
                                        ++e+a+++ve++++++++++v+
  gi|313116887|ref|YP_004038011.1|  97 PSIEDAEQMVETCREADVHLGVA 119
                                       *******************9986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4
                                       TEEEEEEECSSHHHHHHH CS
                      GFO_IDH_MocA  25 leevvalldpdaeraeav 42 
                                       +eev+ ++ +   r +++
  gi|313116887|ref|YP_004038011.1| 186 GEEVAEVYAETGTRFHDI 203
                                       346666666666666665 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   1.8e-11   8.3e-08       3      85 ..     134     210 ..     132     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.8e-11
                                       HHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCC CS
                    GFO_IDH_MocA_C   3 lIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaae 79 
                                       ++e+++lGe +  +++ +++++g +    ++     +gG+++d+++H  D ++w +G++ ++v+a +++    ++ +
  gi|313116887|ref|YP_004038011.1| 134 ALEDDALGELRFLSGTNRGQMPGGWFADPEQ----AGGGAVTDHSVHLVDAVRWMTGEEVAEVYAETGT--RFHDIA 204
                                       6777777777777766666666666555555....8******************************955..555577 PP

                                       SCSEEE CS
                    GFO_IDH_MocA_C  80 dedaav 85 
                                       +ed +v
  gi|313116887|ref|YP_004038011.1| 205 VEDVNV 210
                                       777664 PP

>> Oxidoreduct_C  Putative oxidoreductase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.5e-06      0.02      46      75 ..     157     187 ..     146     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-06
                     Oxidoreduct_C  46 aWffDveqqGeG.ivDvtthLvDlvqweafp 75 
                                        Wf D eq G G ++D ++hLvD v+w +  
  gi|313116887|ref|YP_004038011.1| 157 GWFADPEQAGGGaVTDHSVHLVDAVRWMTGE 187
                                       5********998567************8755 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.5   0.00039       1.8      49     101 ..      44      99 ..       5     117 .. 0.72
   2 ?    1.8   0.0     0.058   2.6e+02      73     101 ..     177     205 ..     164     230 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00039
                                       EEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGHHHHHHHHHHHT-EEEE.....SS- CS
                   Sacchrp_dh_NADP  49 feaialdaenyeavLaallkegdlvvnlsppissldvlkaCietgvhyvd.....tsi 101
                                       ++a++  ++ ye   ++ll+  d vv +s++  ++d ++ ++++gv+ ++     +si
  gi|313116887|ref|YP_004038011.1|  44 AKAAEYGVDFYEP--DELLERVDGVVVCSTNAAHRDWVEHAADAGVDILCekplaPSI 99 
                                       3444444444444..6799999*************************99866655555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.058
                                       EEE-SSGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  73 vvnlsppissldvlkaCietgvhyvdtsi 101
                                       +v+++  + +++v++  +etg+++ d+++
  gi|313116887|ref|YP_004038011.1| 177 LVDAVRWMTGEEVAEVYAETGTRFHDIAV 205
                                       45555555666777777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2717.78
//
Query:       gi|313116888|ref|YP_004038012.1|  [L=331]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-13   50.6   0.0    5.7e-13   49.7   0.0    1.5  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    9.1e-05   22.4   0.0    0.00017   21.6   0.0    1.5  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   6.4e-17   5.7e-13      14     116 ..      17     115 ..       3     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 6.4e-17
                                       HHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEE CS
                      GFO_IDH_MocA  14 khlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaaleagkhvl 90 
                                        ++ +l  + ++ e+v++ d++ er ++ a + g +a+s  e + +   ++ v++++p+  h el   al + ++vl
  gi|313116888|ref|YP_004038012.1|  17 VYA-ALLSKLSDVELVGISDENVERGRRRASAVGTKAMSRSELMRS---VEGVVICSPTAIHGELFDLALVHDVAVL 89 
                                       344.666777888***************999999998887665555...9*************************** PP

                                       EESSS-SSHHHHHHHHHHHHHHTS-E CS
                      GFO_IDH_MocA  91 lEKPlattveeakelvelaekkgklv 116
                                        EKPlat+++eak+l ++++++g + 
  gi|313116888|ref|YP_004038012.1|  90 TEKPLATSLSEAKRLRDRCDESGIVA 115
                                       *******************9998665 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.9e-08   0.00017       5      74 ..     135     200 ..     131     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.9e-08
                                       HTTTTSSEEEEEEEEECBEEECHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEE CS
                    GFO_IDH_MocA_C   5 engklGevvsvdvwtldtragaeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqn 74 
                                       e+g lG+vv+v++  ++ ++g     +w  ++   +gG+++d+  H+iD+++w+++++ + v+a   +r++
  gi|313116888|ref|YP_004038012.1| 135 EDGTLGDVVAVSGVNRGRMPG-----GWFTNPeLAGGGAVMDHTDHIIDVVRWITNEEVEDVYAELDTRFY 200
                                       789999999997444444444.....444445569**********************99999987555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2591.40
//
Query:       gi|313116889|ref|YP_004038013.1|  [L=323]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-06   29.0   0.0    2.4e-06   28.4   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00022   21.2   0.0    0.00045   20.2   0.0    1.5  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.7e-10   2.4e-06      46     109 ..      41     104 ..       2     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.7e-10
                                       TTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHH CS
                      GFO_IDH_MocA  46 fgveaysdleelladpeidavivatpngtheelakaaleagkhvllEKPlattveeakelvela 109
                                       + ++ ++++++ ++++e+dav v+ p + h + ++aal   + v ++ P+a++ + ++++ ela
  gi|313116889|ref|YP_004038013.1|  41 TAIPTFESVSDAVTETEADAVDVCGPGSAHVQSVEAALDEEIPVRCDPPVALDTQTVERVEELA 104
                                       45899*********9*************************************888888877776 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.1e-08   0.00045       4      68 ..     130     196 ..     128     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.1e-08
                                       HHTTTTSSEEEEEEEEECBEEECHHHHCCGGSH......HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEE CS
                    GFO_IDH_MocA_C   4 IengklGevvsvdvwtldtragaeakkrwkrrk......kksgGvlgdlgiHdiDllqwLfGqppsvvaal 68 
                                       +e+g +G+  +     + +r +++++++w++++        +  +l d  +Hd D l+w fG++ +v+a +
  gi|313116889|ref|YP_004038013.1| 130 VESGDIGTLGVA----RVKRTAPFDRVGWNDSYlgidraSSPEDALCDVVSHDVDTLHWTFGPVERVFARR 196
                                       577777777777....68999999******99999998888999*********************999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2124.69
//
Query:       gi|313116890|ref|YP_004038014.1|  [L=403]
Description: selenocysteine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-10   38.4   0.0    1.2e-09   37.6   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    1.3e-09   37.6   0.6    4.8e-08   32.4   0.3    3.2  2  SelA             L-seryl-tRNA selenium transferase
    1.4e-07   31.2   3.4    9.1e-07   28.5   2.9    2.0  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.7e-05   23.5   0.1    0.00065   18.3   0.0    2.1  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0022   17.3   0.6     0.0042   16.4   0.1    2.0  2  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.034   14.8   0.1       0.18   12.5   0.0    2.1  2  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   4.1e-13   1.2e-09     127     221 ..     146     240 ..     119     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 4.1e-13
                                       BEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS-..--HHHHTESEEEEETTT CS
                       Aminotran_5 127 ldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghip..idvkklgvDflafsghK 201
                                       +++ e+e++++e+t+++a+ + + +t    p+ +++++a+++++ vlvDaa+ v+ +     + + gvD+++fsg K
  gi|313116890|ref|YP_004038014.1| 146 IEPWEIETAITEDTAAIAYLQKEYTT---PPLSKVVEIAHRHDIPVLVDAAAEVPPKAnlTRFIDAGVDLVVFSGGK 219
                                       667899***************99865...8999999999***************865512456789*********** PP

                                       .TTSSTT-EEEEEEHHHHHTS CS
                       Aminotran_5 202 .llgPtGiGvlyvrkellekl 221
                                        + gP+ +G+l +r +l+e++
  gi|313116890|ref|YP_004038014.1| 220 aIRGPQSTGILAGRADLIESA 240
                                       *****************9986 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.3   1.6e-11   4.8e-08       2     234 ..      17     241 ..      16     249 .. 0.76
   2 ?    0.3   0.0     0.091   2.7e+02     236     265 ..     272     301 ..     266     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.6e-11
                                       EEESS-SS-TTTTSS---HHHHHHHHHHHHSEBSTTEETTTTEE--STHHHHHHHHHHHT-SEEEEES-HHHHHHHH CS
                              SelA   2 inltGvvlhtnLGrallaeeaveavleaarkysnleydleegkrgsrdalveellkeltgaedalvvnnnaaavllv 78 
                                       +n++G+  +t +G +l+  eavea+++aa+  + +         ++ +a  +el++  tgae+  v    aaa+ l 
  gi|313116890|ref|YP_004038014.1|  17 VNAAGT--KTRIGGSLIRPEAVEAMSRAAEGFARI---------SDLQARASELITDCTGAEAGYVASGAAAAMTLG 82 
                                       566665..677777777777777777777766555.........33345567999999*******999999999999 PP

                                       HHHHHBTSEEEE........ETTSGTEETTTEEH..HHHHHHHTBEEEEESBSSB--HHHHHHT--T...TEEEEEE CS
                              SelA  79 Lntlaagkevii........srGeLveiGGsfri..PdvmkkaGvkLvevGttnkthlkDyekaine...ntalllk 142
                                        ++  ag +v           r + v +  + r    + +++aG+++v+vGt n  hl   ++ai++   +ta+   
  gi|313116890|ref|YP_004038014.1|  83 TAACIAGDDVAAmdrlpdteGRPDEVIMPRTHRTgyDHAIRAAGATIVDVGT-NDPHLGTGSAAIEPweiETAITED 158
                                       8888888777542222222245566667778886325799***********6.888999999999865457888877 PP

                                       E---SEEEEES-B---HHHHHHHHHHHT--EEEEEES-B-S-GGGGT-----BHHHHHHTT-SEEEEETTSTT-SSS CS
                              SelA 143 vhtsnyrieGftkevelaeLvelgkekglpvleDlGsGllvdlseyglskePtvqealaeGvdlvsfsGDkllGgpq 219
                                       +    y  + +t + +l+++ve+++++++pvl D+ +          ++   ++   + +Gvdlv fsG k + gpq
  gi|313116890|ref|YP_004038014.1| 159 TAAIAYLQKEYT-TPPLSKVVEIAHRHDIPVLVDAAA---------EVPPKANLTRFIDAGVDLVVFSGGKAIRGPQ 225
                                       777788777766.578999************999764.........578889999*********************9 PP

                                       -.EEEEE-HHHHHHHH CS
                              SelA 220 a.GiivGkkelieklk 234
                                       + Gi+ G+ +lie   
  gi|313116890|ref|YP_004038014.1| 226 StGILAGRADLIESAA 241
                                       559*********9765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.091
                                       STHHHHTB--HHHHHHHHHHHHHHH..TT- CS
                              SelA 236 nplkraLrvDkltlaaleatlrlyldpekl 265
                                       + + r L+v k  l +l  +l+l+l+++++
  gi|313116890|ref|YP_004038014.1| 272 QGIGRTLKVGKEELVGLIRALELFLEEDQD 301
                                       56889********************98875 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   2.9   3.1e-10   9.1e-07      35     147 ..      70     194 ..      60     216 .. 0.81
   2 ?    0.8   0.0     0.079   2.4e+02     238     301 ..     301     364 ..     297     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.1e-10
                                       HHT-SEEEEESSHHHHHHHHHHHTTTT.......TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TT.....TSSB CS
                   DegT_DnrJ_EryC1  35 ylgvkhaiavssGtaAlhlaLralgvg.......pgdeVIvpsltFvatanavlelgakpvfvDvdpd.....tyni 99 
                                       y+ +  a a++ GtaA   +  +  ++       + deVI+p +  ++  +a++ +ga+ v v  +       +  i
  gi|313116890|ref|YP_004038014.1|  70 YVASGAAAAMTLGTAACIAGDDVAAMDrlpdtegRPDEVIMPRTHRTGYDHAIRAAGATIVDVGTNDPhlgtgSAAI 146
                                       666667777777777776654443333333443488************************9998765422222568* PP

                                       -GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT CS
                   DegT_DnrJ_EryC1 100 dpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAh 147
                                       +p +ie aite t+aI           ++++ +ia++h+++v+ DaA 
  gi|313116890|ref|YP_004038014.1| 147 EPWEIETAITEDTAAIAYLQKEYTTPPLSKVVEIAHRHDIPVLVDAAA 194
                                       *********************9999*********************97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.079
                                       HHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHH.HCHHHHHHHHHHCC CS
                   DegT_DnrJ_EryC1 238 delvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeae.vkrdelvealkeeg 301
                                       delva+ ++ ++l++ eL +++  + ++t    k  +   + v+v+e+a  ++ +elv al++e+
  gi|313116890|ref|YP_004038014.1| 301 DELVAEWTDRTALLDAELTDVDT-LSCETVGGGKVDVAPALHVTVDEDAAgMTAAELVLALRREN 364
                                       67888888999999999999996.56666666666788888899999988899999999999873 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.2   0.1    0.0089        27      65      99 ..      64      97 ..      46     113 .. 0.82
   2 !   18.3   0.0   2.2e-07   0.00065     151     209 ..     169     228 ..     144     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0089
                                      HT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEEST CS
                   Cys_Met_Meta_PP 65 eggeaalavssGmaAiaaailallkaGdeivvsdd 99
                                        g++a  v+sG aA ++  +a + aGd++ ++d 
  gi|313116890|ref|YP_004038014.1| 64 T-GAEAGYVASGAAAAMTLGTAACIAGDDVAAMDR 97
                                      3.455666899*****99999999*****998886 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.2e-07
                                       T----HHHHHHHHHHTT-EEEEEGTTTHT...TTS-GGGGT-SEEEEETTTTTTCSSS--EE CS
                   Cys_Met_Meta_PP 151 lkvvDiekiaklakkagvlvvvDntfasp...llqrplklgaDivvhSaTKylgGhsdvvaG 209
                                       + ++ + k++++a+ ++++v+vD++   p    l+r ++ g+D+vv S+ K + G + +  G
  gi|313116890|ref|YP_004038014.1| 169 YTTPPLSKVVEIAHRHDIPVLVDAAAEVPpkaNLTRFIDAGVDLVVFSGGKAIRGPQST--G 228
                                       56677899*****************99987767899******************97653..4 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.5   4.4e+03     130     157 ..      16      43 ..      14      45 .. 0.79
   2 !   16.4   0.1   1.4e-06    0.0042     149     223 ..     173     241 ..      58     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.5
                                       EEEEESSBTTTTTB---HHHHHHHHHHH CS
                   Beta_elim_lyase 130 lisltvTnntagGqvvsleelrevaaia 157
                                       ++  + T   +gG  + +e +++++  a
  gi|313116890|ref|YP_004038014.1|  16 VVNAAGTKTRIGGSLIRPEAVEAMSRAA 43 
                                       6666778889999999999999988776 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHH.TTSSEEEEESSSTT--SS-.EEEEE-HH....HHHHHH CS
                   Beta_elim_lyase 149 elrevaaiakkygiplhlDgARfanaakslgeivkemf.syvDsvtmslkKdllanvG.gvlafrddeledylaerv 223
                                        l +v +ia++++ip+++D+A    a +  ++ + + + ++vD v++s+ K +  +   g+la+r d     ++++ 
  gi|313116890|ref|YP_004038014.1| 173 PLSKVVEIAHRHDIPVLVDAA----AEVPPKANLTRFIdAGVDLVVFSGGKAIRGPQStGILAGRAD----LIESAA 241
                                       5789****************9....6678888888888789**************9988*******9....555554 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.1   3.4e+03      49      71 ..      47      68 ..      29      94 .. 0.69
   2 ?   12.5   0.0   5.9e-05      0.18      44      91 ..     167     217 ..     151     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                                      --HHHHHHHHS.-EEEEE-S--HH CS
                     NAD_binding_3 49 ldlddliahld.pdvvVEcassea 71
                                      +++ dl a  +   ++ +c++ ea
  gi|313116890|ref|YP_004038014.1| 47 ARISDLQA--RaSELITDCTGAEA 68
                                      45555555..44789999988875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.9e-05
                                       --CB---HHHHHHHH...S-EEEEE-S--HHHHTTHHHHHHTTEEEE-S-- CS
                     NAD_binding_3  44 sealtldlddliahl...dpdvvVEcasseavaelvlkaLkagkdvvtank 91 
                                       +e +t +l ++++ +   d++v+V++a+    +  +++++ ag+d+v+ + 
  gi|313116890|ref|YP_004038014.1| 167 KEYTTPPLSKVVEIAhrhDIPVLVDAAAEVPPKANLTRFIDAGVDLVVFSG 217
                                       4444445555554334449*****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2790.83
//
Query:       gi|313116891|ref|YP_004038015.1|  [L=245]
Description: sugar phosphate isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-23   82.8   0.3    1.7e-21   76.7   0.1    2.1  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
     0.0026   16.6   0.0     0.0035   16.2   0.0    1.2  1  UxuA          D-mannonate dehydratase (UxuA)
  ------ inclusion threshold ------
      0.042   13.5   0.0       0.06   13.0   0.0    1.2  1  DUF2334       Uncharacterized protein conserved in bacteria (
      0.048   14.1   0.0        3.5    8.1   0.0    2.6  2  NYN           NYN domain


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.1   3.7e-25   1.7e-21       1     209 [.      15     197 ..      15     198 .. 0.91
   2 !    4.6   0.0    0.0042        19      72     117 ..     200     240 ..     197     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 3.7e-25
                                       HHHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHH CS
                      AP_endonuc_2   1 laaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraie 77 
                                       l+++a+ G+dgvE+++r   +         +++r+al e++l  +s + +++          ++       +++ +e
  gi|313116891|ref|YP_004038015.1|  15 LRRVADEGYDGVEFAYRVRESPP-------EDVRQALTENDLSAVSAHVPYDELE-------SD-------FESVVE 70 
                                       57899************999996.......9************666655555555.......44.......99**** PP

                                       HHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC.HHHHHHHHHHTT CS
                      AP_endonuc_2  78 laaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd.eelarlldavds 153
                                       +  +LG+ +lv+++    + +  +  ea++  a +l  l+d + ++g  l++++++ ++    +   ++rl++++++
  gi|313116891|ref|YP_004038015.1|  71 MYGELGCSTLVIPAL---DDSHFESTEAVAETATKLSSLGDRLSDRGFDLLYHNHTHEFGDIDGdLAFERLIRETSD 144
                                       *************88...88888888*********************************8776688999******96 PP

                                       TTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSS CS
                      AP_endonuc_2 154 pnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGe 209
                                         vg+ lD+g +   ++d+ ++lr++adri +vH+ D+ +   + + +hv++g+G+
  gi|313116891|ref|YP_004038015.1| 145 -SVGFELDVGLATKGGADPVALLRTYADRIPLVHVTDTLV--DDPDRDHVELGDGD 197
                                       .6**************************************..899**********7 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0042
                                       HHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  72 lkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslnela 117
                                       l++a+e a++LG++  v+      +g++   +e+++r  e+l+ l+
  gi|313116891|ref|YP_004038015.1| 200 LESAVEVARDLGIEWFVFE-----HGQSTAQAETLQRGGERLQSLL 240
                                       7899***************.....5688888888888888877665 PP

>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.9e-07    0.0035     248     328 ..     155     232 ..     134     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.9e-07
                                       TTSTT--HHHHHHHHGGGEEEEE--EEEE-SSTT-EEEE-TTSSSS-HHHHHHHHHHHHHHH-EE-----B-GGGG- CS
                              UxuA 248 garadndlvemikefadriyFahlRnikreedeksFveaahleGsvdlaevvkalleeeyrrylRpDhgrlllddkk 324
                                       +++   d v++++++adri+ +h+ ++ + + +++ ve    +G++dl + v+   + + ++++  +hg+  ++ + 
  gi|313116891|ref|YP_004038015.1| 155 ATKGGADPVALLRTYADRIPLVHVTDTLVDDPDRDHVE--LGDGDTDLESAVEVARDLGIEWFV-FEHGQSTAQAET 228
                                       4444567899********************98888777..678******************988.578887766554 PP

                                       -STT CS
                              UxuA 325 lrPG 328
                                       l+ G
  gi|313116891|ref|YP_004038015.1| 229 LQRG 232
                                       5555 PP

>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05      0.06      33     134 ..      78     230 ..      56     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                           DUF2334  33 svavIPrykdpktgskvnlsen.pefvevLkylqakGgeialHGYtHqygtvk..........sevsgegfef.... 94 
                                       s +vIP   d +  s++  +e  +++ ++ ++l ++G  ++ H  tH++g  +          ++   +gfe     
  gi|313116891|ref|YP_004038015.1|  78 STLVIPALDDSHFESTEAVAETaTKLSSLGDRLSDRGFDLLYHNHTHEFGDIDgdlaferlirETSDSVGFELdvgl 154
                                       6789*****9955555555555055555558888****************9889999999998777788888899** PP

                           DUF2334  95 ....................................lseseakeriekGieilkklgikpkgFeaPhyaaseetyk 134
                                                                            +       +e++ e++++lgi+  +Fe  + +a++et++
  gi|313116891|ref|YP_004038015.1| 155 atkggadpvallrtyadriplvhvtdtlvddpdrdhVELGDGDTDLESAVEVARDLGIEWFVFEHGQSTAQAETLQ 230
                                       *****************************99999996667788999999999999999999999888888888876 PP

>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.046   2.1e+02     106     128 ..      63      87 ..      58     112 .. 0.76
   2 ?    8.1   0.0   0.00078       3.5      91     133 ..     182     224 ..     175     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.046
                               NYN 106 gDFaplveklrergkrVevlla..e 128
                                       +DF+++ve   e+g+ + v+ a   
  gi|313116891|ref|YP_004038015.1|  63 SDFESVVEMYGELGCSTLVIPAldD 87 
                                       8**************9988876541 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00078
                               NYN  91 aydnky.dtivLvsgDgDFaplveklrergkrVevlla.eeasts 133
                                       ++d++  d++ L  gD D++++ve +r +g+  e + + + +st+
  gi|313116891|ref|YP_004038015.1| 182 LVDDPDrDHVELGDGDTDLESAVEVARDLGI--EWFVFeHGQSTA 224
                                       445544699**********************..666654334554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1896.63
//
Query:       gi|313116892|ref|YP_004038016.1|  [L=400]
Description: N-acyl-D-glucosamine 2-epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-95  319.7   8.3    3.2e-95  319.3   8.3    1.0  1  GlcNAc_2-epim    N-acylglucosamine 2-epimerase (GlcNAc 2-epim
    5.3e-06   26.2   4.5    0.00028   20.5   3.0    2.3  2  Glyco_hydro_76   Glycosyl hydrolase family 76
     0.0008   19.0   0.2       0.81    9.2   0.0    2.6  2  C5-epim_C        D-glucuronyl C5-epimerase C-terminus
      0.006   15.1   0.6       0.47    8.9   0.1    2.2  2  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
  ------ inclusion threshold ------
       0.11   11.4   0.0        9.5    5.0   0.0    2.1  2  Glyco_hydro_47   Glycosyl hydrolase family 47


Domain annotation for each model (and alignments):
>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.3   8.3     9e-99   3.2e-95       1     346 []      35     389 ..      35     389 .. 0.96

  Alignments for each domain:
  == domain 1  score: 319.3 bits;  conditional E-value: 9e-99
                                       E.E--.B-TTS-B-GGG-EEHHHHHHHHHHHHHHHHTT-TTHHH.HHHHHHHHTTTTTB-TTTSSB-SEEETTEEEE CS
                     GlcNAc_2-epim   1 Gffee.ldadGkvldkdkreivlqaRqvycfavaaqlgrpgwld.lvehGlkflekvlrdaehggyfsalrdggvld 75 
                                       G++++  d+dG+++d++++++v +aR+v++f+++a l+ p w + ++ehGl++l++v+ d+ehggy ++ + ++v d
  gi|313116892|ref|YP_004038016.1|  35 GYITQvSDRDGAIYDSRTKHLVPTARFVFAFSIGALLDGPVWCEpAAEHGLSYLRNVAYDEEHGGYSWLFEGRNVTD 111
                                       77777679*****************************99998887******************************** PP

                                       --EEHHHHHHHHHHHHHHHTTT-TTHHHHHHHHHHHHHHHTEETTTTEE--EE-TTSS-B....EEHHHHHHHHHHH CS
                     GlcNAc_2-epim  76 askdaYdhaFvllalasalaageeeakdlldetlavlekhlweekaglvkeesdkefskl....rgsnpnMhlleAm 148
                                       +++  Y+haFvlla+a+a  ag  + +d ++et+++l++++wee++g+++ + + e+ +     rg+n+nMh +eA+
  gi|313116892|ref|YP_004038016.1| 112 ETRSTYGHAFVLLAYATATRAGIGDVEDDIRETFDILDERFWEEEHGAFASNRTAEWDPAepdyRGQNANMHSCEAL 188
                                       *********************************************************99999*************** PP

                                       HHHHHTT-BTHHHHHHHHHHHHHTTTTGGGGTT----EE-TT--B-TTTTTT...-STT-SSB-HHHHHHHHHHHHH CS
                     GlcNAc_2-epim 149 LalaeatgdkeyleraeeiaelvisefadaesglvrEhfdedWnvapdynge...dlfrpygvePGHqiEwawLlld 222
                                       La++eatg+++yl ra ++ae++ ++  d+ +gl+ Ehf++dW+++++yn++   dlfrp+g++PGH++Ewa+Ll++
  gi|313116892|ref|YP_004038016.1| 189 LAAYEATGEERYLSRAVTVAETIARDKPDEADGLLCEHFTSDWEIDWEYNRDqkaDLFRPWGYQPGHMLEWAKLLVR 265
                                       ***************************************************************************** PP

                                       HHHHTT----THHHHHHHHHHHHHHHHBS-SSSSB-S-B-TTS-BSS--EEHHHHHHHHHHHHHHHHHH--CHHHHH CS
                     GlcNAc_2-epim 223 lallkreraakllekArkLfetalakgwdkdrgglvytldaagkpvddakllWpqtEalkaaaalaeltgearylew 299
                                       l+  + +  + +l+ A++ f++++++gwd +rgg++yt+d++g p +dak+ W   E l aaa+l ++t ++ry+ew
  gi|313116892|ref|YP_004038016.1| 266 LH--HHHDGNWYLDRAKRFFDASVTDGWDDERGGFYYTIDRDGAPIVDAKYTWALEEGLGAAARLGAVTNDDRYWEW 340
                                       **..566666677**************************************************************** PP

                                       HHHHHHHHHHHTB-TTTSSB-SEE-TTS-...B-----------TTTHHH CS
                     GlcNAc_2-epim 300 yarvaeylerhlidpekGlWfdkldadge...vaekvpaGksdfYHilga 346
                                       ++r+++yl+++  ++  G  +++l++dge     ++ p  ks  YH + a
  gi|313116892|ref|YP_004038016.1| 341 FDRIHAYLHENATNHSLGIRYERLTPDGEihpTIDETPKVKSG-YHHVNA 389
                                       *****************************77545666777888.998876 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.1    0.0042        15      95     128 ..     187     215 ..     153     242 .. 0.66
   2 !   20.5   3.0   7.9e-08   0.00028     106     188 ..     268     350 ..     225     372 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0042
                                       HHHHHHHH.....H--HHHHHHHHHHHHHHHHCB CS
                    Glyco_hydro_76  95 aamtaaernfpeptdepswLalAqavfntqasrw 128
                                       a ++a+e+     t+e+++L++A  v +t+a+  
  gi|313116892|ref|YP_004038016.1| 187 ALLAAYEA-----TGEERYLSRAVTVAETIARDK 215
                                       34444444.....677777777777777766653 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 7.9e-08
                                       ..H--HHHHHHHHHHHHHHHHC.B-SCSCCS-BBSEC...ESS--SEEEHHHHHHHHHHHHHHHHHH--CHHHHHHH CS
                    Glyco_hydro_76 106 eptdepswLalAqavfntqasr.wdeetcgGGlrWqi.ftwnsgydyknsisngplfqlaarLarytgnetYlewAe 180
                                       +  d + +L++A+ +f+  ++  wd+e+  GG ++ i  +  +  d k +++  + + +aarL  +t+++ Y ew +
  gi|313116892|ref|YP_004038016.1| 268 HHHDGNWYLDRAKRFFDASVTDgWDDER--GGFYYTIdRDGAPIVDAKYTWALEEGLGAAARLGAVTNDDRYWEWFD 342
                                       3467888**********988877****7..*******55555999*******************************9 PP

                                       HHHHHHHH CS
                    Glyco_hydro_76 181 kvwdWved 188
                                       ++ +++ +
  gi|313116892|ref|YP_004038016.1| 343 RIHAYLHE 350
                                       99999887 PP

>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00023      0.81      32      60 ..     182     210 ..     161     223 .. 0.85
   2 !    7.2   0.1    0.0009       3.2       5      61 ..     229     286 ..     224     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00023
                         C5-epim_C  32 gqaisvllrAYeltgdekYlkaakkalks 60 
                                        +   +ll+AYe+tg+e+Yl+ a  + + 
  gi|313116892|ref|YP_004038016.1| 182 MHSCEALLAAYEATGEERYLSRAVTVAET 210
                                       5677899**************99877665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0009
                         C5-epim_C   5 ggwrinveyklyegkklspGWlsamaqgqa...isvllrAYeltgdekYlkaakkalksf 61 
                                        +w+i++ey+  ++ +l ++W    + g++   +++l+r  ++ + + Yl+ ak+  +++
  gi|313116892|ref|YP_004038016.1| 229 SDWEIDWEYNRDQKADLFRPWG--YQPGHMlewAKLLVRLHHHHDGNWYLDRAKRFFDAS 286
                                       57*********88888*****5..444544111689******************987665 PP

>> Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00013      0.47     163     209 ..     167     213 ..     157     245 .. 0.74
   2 !    4.8   0.1    0.0023       8.1     182     266 ..     261     348 ..     229     356 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00013
                                       CS-CCHHHHHTTTHHCTHHHHHHHHHHHHT-CHHHHHHHHCCHHCCH CS
                   Glyco_hydro_127 163 klgdeqlqkalvpehggieealvklyelTgdkrYldlAkrfidergl 209
                                       + ++++   ++ +     +eal+  ye+Tg++rYl  A    ++ + 
  gi|313116892|ref|YP_004038016.1| 167 EWDPAEPDYRGQNANMHSCEALLAAYEATGEERYLSRAVTVAETIAR 213
                                       55555555556666666789***************999777666555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHT-CHHHHHHHHCCHHCCHCC.......T-HCTTT-SSTCGCHHCHHCCHHHHHHHHHHHHHHHHHCT CS
                   Glyco_hydro_127 182 ealvklyelTgdkrYldlAkrfidergldp.......eklaykqdelpvrhqntaigkavRatylysgladvyeetg 251
                                       + lv+l+ +   + Yld Akrf d+ ++d          ++  +d  p ++++   +           +a++ ++t+
  gi|313116892|ref|YP_004038016.1| 261 KLLVRLHHHHDGNWYLDRAKRFFDASVTDGwdderggFYYTIDRDGAPIVDAKYTWALEE----GLGAAARLGAVTN 333
                                       5689999999999***********999887444333211444444444444333332222....1235678899999 PP

                                       THCCHHHHHHHHHHH CS
                   Glyco_hydro_127 252 ddkllkaaerlwdnv 266
                                       dd++++  +r++  +
  gi|313116892|ref|YP_004038016.1| 334 DDRYWEWFDRIHAYL 348
                                       999999988888765 PP

>> Glyco_hydro_47  Glycosyl hydrolase family 47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0044        16     367     393 ..     185     211 ..     115     219 .. 0.70
   2 ?    5.0   0.0    0.0026       9.5     158     186 ..     327     355 ..     325     370 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHHH--THHHHHHHHHHHHH CS
                    Glyco_hydro_47 367 iESlfylYritgdekyrevgwemfeal 393
                                        E l  +Y +tg+e+y+  + ++ e +
  gi|313116892|ref|YP_004038016.1| 185 CEALLAAYEATGEERYLSRAVTVAETI 211
                                       555555555555555555555555544 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0026
                                       HHHHHHT-CHHHHHHHCCHHHHHCHCC.H CS
                    Glyco_hydro_47 158 rLsqlTgdkkYedlaervtkaleelqekt 186
                                       rL  +T+d++Y++  +r+  +l+e+ +++
  gi|313116892|ref|YP_004038016.1| 327 RLGAVTNDDRYWEWFDRIHAYLHENATNH 355
                                       8999********************76433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2656.07
//
Query:       gi|313116893|ref|YP_004038017.1|  [L=472]
Description: 3-hydroxy-3-methylglutaryl-CoA synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-07   28.7   3.0    1.6e-06   27.8   3.0    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    4.6e-05   23.3   2.9    0.00012   22.0   1.7    2.4  2  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
     0.0014   18.8   0.2      0.004   17.3   0.2    1.7  1  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
     0.0027   17.1   0.1     0.0055   16.1   0.1    1.5  1  Thiolase_N     Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   3.0   3.6e-10   1.6e-06       4      33 ..     342     371 ..     339     373 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.6e-10
                           DUF35_N   4 aaegrLvgqrCpdCGtvqfPPravCphCgs 33 
                                        +++rLv+++C+ C ++ fPP+ +C+ Cg 
  gi|313116893|ref|YP_004038017.1| 342 PQRHRLVAGQCAECESLAFPPEGACSSCGT 371
                                       79**************************94 PP

>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.64   2.9e+03      44      59 ..      37      52 ..      31      55 .. 0.85
   2 !   22.0   1.7   2.6e-08   0.00012       2      63 ..     378     448 ..     377     450 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.64
                                      E-EEEEEEES..TT-B CS
                     OB_aCoA_assoc 44 arlvgvdpdevriGmr 59
                                      + ++g+d+d++  G++
  gi|313116893|ref|YP_004038017.1| 37 TSVTGADEDTLTMGYE 52
                                      6799******999985 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.6e-08
                                       EEE-GG-EEEEEEEEEE-T......TS-EEEEEEEEEEEE-TT.....-EE-EEEEEEES...TT-B-EEE CS
                     OB_aCoA_assoc   2 velsgrGtvysftvvhrap......pgfaeeaPyvvgvVeLde..gvrimarlvgvdpde.vriGmrVrav 63 
                                       v+l+g+Gtv+++tv+ +        + +a +  yv +vV Ld   g+++ a ++ vd de   iG+ ++a+
  gi|313116893|ref|YP_004038017.1| 378 VALPGTGTVEAATVIGQGGappefvEQQARDGSYVSAVVALDApdGGTVSAPMQVVDTDEkPAIGDALTAT 448
                                       89*************99888889999999999**********98877766666666655543499999886 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2     9e-07     0.004      30      88 ..     236     292 ..     229     293 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9e-07
                                       HHT--GG..GB--THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTTEEEEEEE CS
                     ACP_syn_III_C  30 klglpee..kvvvnldeyGntsaasiplaLdeaveegklkpgdlvllvgfGaGltwgaall 88 
                                       +lg+++e  ++  +++e+G t+aa  +l L +a+++g     d++l+vg G G   +aa++
  gi|313116893|ref|YP_004038017.1| 236 ELGVDAEtiQAGATVHELGDTGAAMPLLGLTKALDNG----ADRILVVGYGSGSEATAAVI 292
                                       57888887788899*********************77....9***************9997 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.2e-06    0.0055      20      95 ..      43     118 ..      32     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-06
                                       TS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHH CS
                        Thiolase_N  20 dlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavala 95 
                                       d  +  ++ ea++++l+ a +d+e+v+ +i+G+    +e++  +  +a  +g+ ++v+++ ++     g+++++l+
  gi|313116893|ref|YP_004038017.1|  43 DEDTLTMGYEAATRALSAADIDAEAVTTLIFGTTTPPNEEESATARLASFLGLTDDVATTQLTGSANAGVNGLTLG 118
                                       55667899*****************************88888777788889**99999887777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 3056.41
//
Query:       gi|313116894|ref|YP_004038018.1|  [L=390]
Description: acetyl-CoA acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-27   95.4   0.3    1.8e-26   93.1   0.3    2.0  1  Thiolase_N     Thiolase, N-terminal domain
    1.3e-09   37.7   0.2      5e-09   35.9   0.0    2.1  2  Thiolase_C     Thiolase, C-terminal domain
    9.4e-07   28.7   2.3    1.9e-06   27.7   1.0    2.0  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
    0.00019   21.2   0.9      0.059   13.2   0.1    2.6  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.3     4e-30   1.8e-26       2     258 ..       5     223 ..       4     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 4e-30
                                       EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHT..S-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHTTS-TT CS
                        Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekag..vdpeevdevivGnvlqagegqn.iarqaalkagipee 75 
                                       +iv+a  tp+g     + + s++ L +ea +a+++++   +++e++de +vG+   +g      a +++ ++g+ ++
  gi|313116894|ref|YP_004038018.1|   5 YIVGAGQTPFGA----FPSESYRTLFTEAFEAAVASVDgsLNAEDIDEAVVGTLGVGGRQLGlSAPAVTEHVGL-HN 76 
                                       79*********9....99*****************99889**************99988877688889999***.** PP

                                       SEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTT CS
                        Thiolase_N  76 vpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafne 152
                                       +p+++++++c+ g  av +a+q+i +g advv+agGvE m++ + +++ +   g++  +++ + l+ ++        
  gi|313116894|ref|YP_004038018.1|  77 IPCSRIENACAAGGFAVRQAVQAIESGMADVVLAGGVEVMTDMSGDTT-KYWLGVSG-ETEWERLTGTT------FS 145
                                       *******************************************99997.54444433.23333333222......22 PP

                                       SEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS CS
                        Thiolase_N 153 ehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLakl 229
                                          +  a+ ++++y+++ e++ ++Avk+h+++a+++ka+ +                 ++ ++a +++++a++L+ +
  gi|313116894|ref|YP_004038018.1| 146 GVYAQMADAYLDQYDATPEDLSRVAVKNHANGAKNPKAH-LGF--------------SCSLEDATNAPTVADPLNLY 207
                                       3567889*******************************9.322..............478999************** PP

                                       -BSSSTTSS-BTTSB--BEEEEEEEEEEE CS
                        Thiolase_N 230 kpaFkkeGtvtAgnasqisDGaaavllms 258
                                                     +++ sDGaaavll+s
  gi|313116894|ref|YP_004038018.1| 208 -------------HCCPTSDGAAAVLLAS 223
                                       .............9*************98 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.4   6.3e+03     108     119 ..      84      95 ..      65     107 .. 0.69
   2 !   35.9   0.0   1.1e-12     5e-09      26     102 ..     263     357 ..     247     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.4
                                       EEEETTTEEEEE CS
                        Thiolase_C 108 alCigggqgval 119
                                        +C++gg +v  
  gi|313116894|ref|YP_004038018.1|  84 NACAAGGFAVRQ 95 
                                       456666655544 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 1.1e-12
                                       HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTT CS
                        Thiolase_C  26 yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGa 84 
                                        a k + + ag++ +d+d+ E+++ Fa   L + ++l++ +                    vN  GG  + GHP+Ga
  gi|313116894|ref|YP_004038018.1| 263 EAGKTAYEMAGIEPDDLDFAEVHDCFAIAELLAYEDLGFCApgeaatllregvtdpdgdLPVNTSGGLKSKGHPIGA 339
                                       67788999*******************************999***************9889**************** PP

                                       HHHHHHHHHHHHHHHCTT CS
                        Thiolase_C  85 sGaRivvtllselkkegg 102
                                       +G+ ++v +  +l+ + g
  gi|313116894|ref|YP_004038018.1| 340 TGTGQMVEAFDQLTGSAG 357
                                       *******99999976543 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   1.0   4.1e-10   1.9e-06     171     207 ..      82     118 ..      63     122 .. 0.89
   2 ?   -2.5   0.0      0.66     3e+03      94     114 ..     263     283 ..     257     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 4.1e-10
                                       EESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                     ketoacyl-synt 171 vdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                       ++ AC+++  av +avq++ sg adv+laGGve+++ 
  gi|313116894|ref|YP_004038018.1|  82 IENACAAGGFAVRQAVQAIESGMADVVLAGGVEVMTD 118
                                       677******************************9975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.66
                                       HHHHHHHHHHTS-HHTCTTGG CS
                     ketoacyl-synt  94 eaawealedagltpeeldgsr 114
                                       ea + a e ag++p++ld  +
  gi|313116894|ref|YP_004038018.1| 263 EAGKTAYEMAGIEPDDLDFAE 283
                                       678889999999999987555 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   1.3e-05     0.059       3      39 ..      82     118 ..      81     129 .. 0.89
   2 !    5.8   0.1    0.0027        12      41      64 ..     201     224 ..     194     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlsk 39 
                                       +++aC++  +a+ +A ++iesg+a  vL  g e++++
  gi|313116894|ref|YP_004038018.1|  82 IENACAAGGFAVRQAVQAIESGMADVVLAGGVEVMTD 118
                                       679*************************999999876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0027
                                       S-TTTHHHHTTB-EEEEEEEEEEE CS
                       ACP_syn_III  41 lDwkdrstavlfGDGAgAvvleas 64 
                                        D+ +   +   +DGA+Av+l  +
  gi|313116894|ref|YP_004038018.1| 201 ADPLNLYHCCPTSDGAAAVLLASG 224
                                       566666667778899999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2766.47
//
Query:       gi|313116895|ref|YP_004038019.1|  [L=396]
Description: Fe3+-hydroxamate ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-18   65.3   0.2    8.2e-18   64.8   0.2    1.2  1  Peripla_BP_2     Periplasmic binding protein
    0.00031   20.5   3.3    0.00053   19.7   3.3    1.3  1  TAT_signal       TAT (twin-arginine translocation) pathway si
  ------ inclusion threshold ------
       0.11   12.2   0.0        0.2   11.4   0.0    1.3  1  PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.2   1.4e-21   8.2e-18       3     234 ..      91     351 ..      90     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.4e-21
                                       E-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-H.......HHHHHH--SEEEE-GGG... CS
                      Peripla_BP_2   3 slspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidv.......EklaalkPDlvilskgl... 69 
                                       s++ +++++ +alG+ d + +++  +++ +  ++++ + v+v++ +   +       E   +l+ D+ + ++++   
  gi|313116895|ref|YP_004038019.1|  91 SYTADYADMGVALGQGDGLSAIGVRARFGTHLYEEL-SGVSVDKADLTQLwqdgtgkEVFYELDADVHLIDPNFmvn 166
                                       68899****************************999.99999999999999999999**********8888888566 PP

                                       ...GGGHHHHHHHS-EEE----TTS................HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHH CS
                      Peripla_BP_2  70 gltdedeellksgiptvivessntg................eslkeqiralgellgledeaeklvaeidsklaaaks 130
                                        l+ ++e++++ +      +  +++                + l+e ++ ++ +++ +d++e++ + +++ +a+++s
  gi|313116895|ref|YP_004038019.1| 167 RLQWSQEDIDEID-----SNVAPFFgntiftraydwhdyadYTLYEAFEKVADVFQAQDRFEAFETYHNEVIADVQS 238
                                       3333334444333.....33333333334577********************************************* PP

                                       TS-TT.-EEEEEEEETTE....EEEE-TTSTTTHHHHTS--EESTTT--...STT-EEE-HHHHHHH--SEEEEEEH CS
                      Peripla_BP_2 131 aidsekpkpvlvfggade..ggyvvagsnsyigdlldalgieniaaesk...kseyeeisaEqilasdpdvifvsgr 202
                                       +++ e+p++++++  + +  ++y +   ++  ++  ++l + +++a++     +++++i+ E++l+ dpd++ ++ +
  gi|313116895|ref|YP_004038019.1| 239 RLPDETPDIAILYPADVPpeSFYPYLVGSGSQSKHWNDLHVGDALANQDitdAQAGGTIDYETLLEIDPDALAIRLQ 315
                                       *****99999999876556699999999999999999999999999999999************************* PP

                                       ....HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 203 ....aeadnktgleflkenpllaelpAvkngrVyal 234
                                           +e +   ++++lk+++++++l Av+n rV++ 
  gi|313116895|ref|YP_004038019.1| 316 geitPEYFEENIVSHLKNHDVASQLRAVQNDRVVYG 351
                                       *********************************987 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   3.3   8.9e-08   0.00053       3      25 ..      10      32 ..       9      33 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.9e-08
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      SRR FL+++A+ a  +al+gca+
  gi|313116895|ref|YP_004038019.1| 10 SRRRFLRTGAGIAVSGALAGCAG 32
                                      9********************97 PP

>> PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.3e-05       0.2      12      45 ..     183     216 ..     169     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                   PhoLip_ATPase_N  12 kkyasNkIsTsKYtlltFlpknLfeqFrrvaNlY 45 
                                         +  N I T  Y +  +    L+e F++va ++
  gi|313116895|ref|YP_004038019.1| 183 APFFGNTIFTRAYDWHDYADYTLYEAFEKVADVF 216
                                       4899***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2808.99
//
Query:       gi|313116896|ref|YP_004038020.1|  [L=309]
Description: hypothetical protein Hbor_33600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2034.38
//
Query:       gi|313116897|ref|YP_004038021.1|  [L=739]
Description: beta-glucosidase-like glycosyl hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-73  248.1   0.0    1.8e-73  247.7   0.0    1.2  1  Glyco_hydro_3    Glycosyl hydrolase family 3 N terminal domai
      2e-50  171.6   0.0      3e-50  171.0   0.0    1.3  1  Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domai
    4.3e-11   42.7   1.2    6.2e-11   42.3   0.2    1.8  2  Fn3-like         Fibronectin type III-like domain
      3e-06   27.4   1.9    8.3e-06   26.0   1.9    1.7  1  DUF11            Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.016   15.5   0.1       0.03   14.6   0.1    1.4  1  CARDB            CARDB


Domain annotation for each model (and alignments):
>> Glyco_hydro_3  Glycosyl hydrolase family 3 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.7   0.0   5.1e-77   1.8e-73       1     319 []      27     352 ..      27     352 .. 0.94

  Alignments for each domain:
  == domain 1  score: 247.7 bits;  conditional E-value: 5.1e-77
                                       -HHHHHHHTEE-B-SE...-S--HHHHHHHHHH--SEEE--GG..GTS..SHHHHHHHHHHHHHH-SS....S--EE CS
                     Glyco_hydro_3   1 tldekigqLlvvevse...ekkseeaaellkkyqvGgiilfae..nle..dtkqleelieaarqaseksrlgiPlll 70 
                                       tl+ek+gqL+   v++   ek+ e+a +++ + +vG++  f+   +++  ++ ++e++++ +r+a+e+++ giP+ +
  gi|313116897|ref|YP_004038021.1|  27 TLEEKVGQLVGTYVGHmgaEKTLEDAISEIVDDHVGSVSPFGIgiSTRddPKLAAETANRLQRVAIEETQHGIPIHI 103
                                       79********988877889999999999************99877554114667789999***************** PP

                                       EE---BTTB---SSS---S-HHHHHHHT-HHHHHHHHHHHHHHHHHHT--EE---B-----STTSSSGGGSS-SSHH CS
                     Glyco_hydro_3  71 avDqegGlvqrlgegtlfPsalalaatssldlikelgriiakelralgididfaPvvdvnrdprngigvrsFsedpe 147
                                        +D+++G     g+ t+fP++l++aa ++++l++  g+++++e++a+g +++++P+ dv+rd r+g+ +++++e+p+
  gi|313116897|ref|YP_004038021.1| 104 PIDAVHGHAYLNGT-TVFPHNLGMAAVRDPELVERSGEVTGREAAATGATVNYGPTCDVARDQRWGRVFETYGESPY 179
                                       *********66665.************************************************************** PP

                                       HHHHHHHHHHHHHHHT....T-EEEEEEETTGTT-SSETTTSEEB----HHHHHHTTHHHHHHHHHTT-SEEEE--- CS
                     Glyco_hydro_3 148 lvaalaaamvkGlqga....gvaatvKHFpghGdgavdshkelptvdhseeelrevdlvpfqaaieagvdsVMtaHv 220
                                       l + laaa+++Gl+g      +aat+KHFp++  g+   + +  +v++se  +r + l pf+  +eagvd+VM+   
  gi|313116897|ref|YP_004038021.1| 180 LCGELAAAEARGLRGSadnpTIAATAKHFPAY--GQPTRGEDASVVEISESTFRRDFLPPFERVLEAGVDVVMPC-- 252
                                       ***************99***************..8888999**********************************.. PP

                                       B-TTT---BGGG-HHHHIIIIIIIS---SEEEES-TTSHHHHCCS-....HHHHHHHHHHHT-SBEES-S---SGHH CS
                     Glyco_hydro_3 221 qfpaldgtpatgskklltdvLRkelGFdGvvvsDalamkeiadrgg....keeavvlaLkAGvDilLvpeertseik 293
                                        ++++dg+pa+gsk  lt +LR+elGFdGvv sD+ +++++ ++++     ++a+ +a  AG+D+  v    +   +
  gi|313116897|ref|YP_004038021.1| 253 -YNSIDGEPAHGSKRFLTSLLRDELGFDGVVTSDWDGVEHLHQYHRtadsRRTAAWQAFSAGLDLVSVGGPSY--AE 326
                                       .*******************************************998877788999********988777665..8* PP

                                       HHHHHHHTTSS-HHHHHHHHHHHHHH CS
                     Glyco_hydro_3 294 alkkavkeGeltearidesvrrvlrl 319
                                       ++ ++v++ el+e+rid+svrrvl+l
  gi|313116897|ref|YP_004038021.1| 327 EVCELVRAEELSEKRIDRSVRRVLKL 352
                                       ***********************985 PP

>> Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.0   0.0   8.3e-54     3e-50       1     204 []     390     624 ..     390     624 .. 0.89

  Alignments for each domain:
  == domain 1  score: 171.0 bits;  conditional E-value: 8.3e-54
                                       -EEEEEGSS--S-S-STEEEEEESGGGS.SS-SS-BSSS--..--S---HHHHHHHHHHH...............-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx.............xxx RF
                   Glyco_hydro_3_C   1 iVLLkNennlLPLkkklkkiaviGpnad.etlklGggsgtv..tvsylvsplegirerles.............eeg 61 
                                       ++LLkN+ ++LPL+++l  ++v+Gpnad    + Gg+s        + v++ egi++ +++             +e+
  gi|313116897|ref|YP_004038021.1| 390 MTLLKND-GVLPLSESLDDVLVTGPNADdLHHQFGGWSVMDdaD-LTGVTVREGIEAIVGEesvtyepgsgiteTED 464
                                       79*****.********************6667778888766431.244799********999***********9889 PP

                                       HHHHHHHHHHTSEEEEEEEES..............SB-TTSCSGHHSSTTHHHHHHHHHHTTSSEEEEEEESSGG-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Glyco_hydro_3_C  62 ideaveaakeaDvavvvvgedpei...........egEgvDrtdlalpeaqdelikavaaanknvvvvlqsggpvav 127
                                        ++a++aa++aD+avvv+ged ++           +gE   rt+l lp+aq+el++av+ +++++v+vl+sg+p+ +
  gi|313116897|ref|YP_004038021.1| 465 VAAATDAAEDADAAVVVLGEDWYLhefgpqqmnraTGEFPTRTQLGLPDAQRELLEAVQTTGTPTVLVLVSGRPLSI 541
                                       9********************887*********9999999************************************* PP

                                       TTTGTTTEEEEEE-S--GCCHHHHHHHHHTTSS---B--SS-EESSSGGG.....................S----- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.xx.......xxxxxxx RF
                   Glyco_hydro_3_C 128 epwkeenvkAilaawlpGqegGtaiadvLfGdvnPsGkLpvtfpksledlpd..dyyeek.dt.......ykfegtp 194
                                       +++ +e+v++il+a++pG +gGta+a+ LfG+ nPsG+Lp+++p+s+++lp+  +   +  ++          + +p
  gi|313116897|ref|YP_004038021.1| 542 AWA-DEHVPGILMAYYPGMDGGTAVAETLFGRHNPSGRLPISVPRSVGHLPTryN---YLrHPtpigadeHPDSYDP 614
                                       887.99********************************************99433...3321134566633477889 PP

                                       SETTTT-BCH CS
                                       xxxxxxxxxx RF
                   Glyco_hydro_3_C 195 lYpeGlglsY 204
                                       lY +G+glsY
  gi|313116897|ref|YP_004038021.1| 615 LYAFGHGLSY 624
                                       9********9 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.8   9.9e+03      31      40 ..     641     650 ..     627     653 .. 0.61
   2 !   42.3   0.2   1.7e-14   6.2e-11       2      68 ..     662     726 ..     661     729 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                                       TT-EEEEEEE CS
                          Fn3-like  31 pGesktvtft 40 
                                       p  + tv++t
  gi|313116897|ref|YP_004038021.1| 641 PAGTVTVEVT 650
                                       3344444444 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 1.7e-14
                                       EEEEEEEESS-STTSBS-EEEEEEEEEE-TT-EEEEEEEEECGGG-EEETTTTEEE--SCEEEEEEE CS
                          Fn3-like   2 vvqlYvsdpessverpvkeLkgFekveLapGesktvtftldrkdlsvwdeekqkwvvepGeytvlvg 68 
                                        v l+v+d  ss  +pv+e +gFek+++++Ges+t+++++++++l+v  ++ +  +vepGe+ ++  
  gi|313116897|ref|YP_004038021.1| 662 AVDLFVEDVVSSRVTPVREHVGFEKTTVEAGESATLSMSVPVERLAVHGRDYE--RVEPGEFVFHCE 726
                                       588************************************************64..7******99975 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   1.9   2.3e-09   8.3e-06       5      83 ..     634     708 ..     631     716 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.3e-09
                             DUF11   5 vdksevrpGdtvtytltvtNtgpas...angvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrv 78 
                                        ++s+v p +tvt+ +tv Ntg ++   a ++ v+D++ + ++ v+   +       +  +++eagesatls++v v
  gi|313116897|ref|YP_004038021.1| 634 LSSSTVGPAGTVTVEVTVENTGDRDgtkAVDLFVEDVVSSRVTPVREHVG-------FEKTTVEAGESATLSMSVPV 703
                                       5678999***************76511167888***************99.......444899************99 PP

                             DUF11  79 trtaa 83 
                                        r a 
  gi|313116897|ref|YP_004038021.1| 704 ERLAV 708
                                       98665 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   8.2e-06      0.03       3      72 ..     626     704 ..     624     717 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.2e-06
                                       -EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE........SEE-CTEEEEEEEEEE CS
                             CARDB   3 DLtv.tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv........psLaagesttvsftwt 70 
                                       D++v + +l+ s++ +  ++t++vtv+N+G+ + ++    ++ d  +   ++v        + ++ages+t s++++
  gi|313116897|ref|YP_004038021.1| 626 DFEVtDLSLSSSTVGPAGTVTVEVTVENTGDRDGTKAVDLFVEDVVSSRVTPVrehvgfekTTVEAGESATLSMSVP 702
                                       777766677888888999*************99777655555555555778889999******************99 PP

                                       -S CS
                             CARDB  71 te 72 
                                       +e
  gi|313116897|ref|YP_004038021.1| 703 VE 704
                                       88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.88
# Mc/sec: 2535.97
//
Query:       gi|313116898|ref|YP_004038022.1|  [L=247]
Description: transcriptional regulator, AsnC family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-11   44.2   0.3    2.2e-11   43.4   0.3    1.4  1  TrkA_C         TrkA-C domain
    8.8e-09   34.8   0.0    1.9e-08   33.7   0.0    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
    1.1e-08   34.8   0.1    2.7e-08   33.5   0.1    1.8  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    0.00017   21.4   0.0     0.0004   20.3   0.0    1.6  1  HTH_11         HTH domain
      0.005   16.7   0.1      0.021   14.7   0.1    2.0  2  MarR_2         MarR family
     0.0055   16.4   0.0      0.015   15.1   0.0    1.7  1  HTH_DeoR       DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.031   14.3   0.0    1.8  1  HTH_20         Helix-turn-helix domain
      0.033   13.8   0.0      0.091   12.4   0.0    1.8  2  HrcA_DNA-bdg   Winged helix-turn-helix transcription represso
      0.041   14.0   0.0      0.092   12.9   0.0    1.6  1  HTH_28         Helix-turn-helix domain
      0.071   12.8   0.0        0.2   11.4   0.0    1.7  2  HTH_41         Helix-turn-helix domain
       0.15   12.0   0.1       0.49   10.4   0.1    1.9  2  HTH_1          Bacterial regulatory helix-turn-helix protein,
       0.17   12.1   0.0        0.4   11.0   0.0    1.6  1  HTH_Tnp_Tc3_2  Transposase


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.3   1.5e-14   2.2e-11       1      58 [.     173     233 ..     173     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.5e-14
                                       CEEEEEE--GGGTTSBHHHHT....HHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEE CS
                            TrkA_C   1 lvevtvpagsplvGktlkeln....lrargvlvvairRggeliipsgdtvLeeGDvllvvgs 58 
                                       +vev v++g+ ++G+tl+e+n    ++   vlvv++ R++e++ p+gdt+++++D++++++ 
  gi|313116898|ref|YP_004038022.1| 173 VVEVSVTPGAEVDGMTLSEANeqglVEP-EVLVVSVERDEEILTPRGDTEIRADDLVTLFAR 233
                                       79*****************776664444.*****************************9975 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   1.3e-11   1.9e-08       1      48 []       5      53 ..       5      53 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.3e-11
                            HTH_24  1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      lde d++IL  L +++r +s   +Ae+ ++S +t++ r+k+Le +G+I+
  gi|313116898|ref|YP_004038022.1|  5 LDEVDKRILYHLVQDARnTSAPMVAEEAHVSAGTIRNRIKQLEADGVIR 53
                                      79***************999999*************************7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   1.8e-11   2.7e-08       1      42 []       5      47 ..       5      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.8e-11
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaR.isyaeLAervGlSestvlrRvrrLe 42
                                      LDe+D++IL +L +daR +s   +Ae+ ++S+ t+++R+++Le
  gi|313116898|ref|YP_004038022.1|  5 LDEVDKRILYHLVQDARnTSAPMVAEEAHVSAGTIRNRIKQLE 47
                                      8**************98578889*******************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.7e-07    0.0004       4      44 ..      11      51 ..       9      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.7e-07
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                       il  L +   + s+   Aee +vS  t+r++Ik+Le+ gv
  gi|313116898|ref|YP_004038022.1| 11 RILYHLVQDARNTSAPMVAEEAHVSAGTIRNRIKQLEADGV 51
                                      5788888888889**************************95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.4e-05     0.021       9      52 ..      11      53 ..       8      69 .. 0.89
   2 ?   -2.1   0.0       2.4   3.6e+03      42      52 ..     189     199 ..     187     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      r+L++L    ++  ++  +a++ ++s +++ +++k L+a G ++
  gi|313116898|ref|YP_004038022.1| 11 RILYHLVQDARN-TSAPMVAEEAHVSAGTIRNRIKQLEADGVIR 53
                                      789999888865.7***************************996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                                       HHHHHHTTSEE CS
                            MarR_2  42 lkrLvaaGLve 52 
                                       l ++ ++GLve
  gi|313116898|ref|YP_004038022.1| 189 LSEANEQGLVE 199
                                       5677899**98 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.9e-06     0.015       5      47 ..      13      55 ..      10      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.9e-06
                          HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      + +l+++ +  s   ++e+  vS  TiR+ +++Le++g+++  
  gi|313116898|ref|YP_004038022.1| 13 LYHLVQDARNTSAPMVAEEAHVSAGTIRNRIKQLEADGVIRGY 55
                                      678999999999999************************7655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.1e-05     0.031       9      56 ..       6      54 ..       5      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                      -HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  9 hPvRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ++v  ril +L  +a+  +a+ +ae+  +s  t+++++++Le  g +++
  gi|313116898|ref|YP_004038022.1|  6 DEVDKRILYHLvQDARNTSAPMVAEEAHVSAGTIRNRIKQLEADGVIRG 54
                                      567789999999999**************************99999975 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.1e-05     0.091       2      55 ..       5      54 ..       4      57 .. 0.83
   2 ?   -3.1   0.0       4.2   6.3e+03      34      44 ..      62      72 ..      60      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.1e-05
                      HrcA_DNA-bdg  2 LtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLveg 55
                                      L +v k il  L++  r+ ++++    +Ae  +   Gt+RN ++ L a g++ g
  gi|313116898|ref|YP_004038022.1|  5 LDEVDKRILYHLVQDARNTSAPM----VAEEAHVSAGTIRNRIKQLEADGVIRG 54
                                      66788999999998877777665....78888999************9998877 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.2
                      HrcA_DNA-bdg 34 krneGtvRNql 44
                                      +r eG +RN +
  gi|313116898|ref|YP_004038022.1| 62 ERAEGRLRNLV 72
                                      6889****975 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.2e-05     0.092      12      41 ..      22      51 ..      12      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-05
                            HTH_28 12 GhsvreaArelgisrrtvyrWikryeegGi 41
                                        s++ +A+e ++s  t++  ik++e+ G+
  gi|313116898|ref|YP_004038022.1| 22 NTSAPMVAEEAHVSAGTIRNRIKQLEADGV 51
                                      458999*********************994 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013       0.2      12      36 ..      28      52 ..      20      54 .. 0.90
   2 ?   -3.5   0.0       6.1   9.1e+03      31      42 ..     223     234 ..     222     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                            HTH_41 12 lakeleLSvGlvQkALklLeddkai 36
                                       a+e  +S G++   +k Le+d++i
  gi|313116898|ref|YP_004038022.1| 28 VAEEAHVSAGTIRNRIKQLEADGVI 52
                                      68999*******************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.1
                            HTH_41  31 eddkaislerrG 42 
                                        +d  ++l +rG
  gi|313116898|ref|YP_004038022.1| 223 RADDLVTLFARG 234
                                       678899999999 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00033      0.49       7      39 ..      16      48 ..      11      49 .. 0.85
   2 ?   -3.1   0.0       5.5   8.2e+03      10      26 ..     161     177 ..     160     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                                      HHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1  7 fvavaeegsftrAAeeLglsqpavsrqikrLEe 39
                                      +v+ a++ s    Aee ++s  ++  +ik+LE+
  gi|313116898|ref|YP_004038022.1| 16 LVQDARNTSAPMVAEEAHVSAGTIRNRIKQLEA 48
                                      6666788888889*******************7 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.5
                                       HHHHSSHHHHHHHHTS- CS
                             HTH_1  10 vaeegsftrAAeeLgls 26 
                                       +a+  s+++ Ae + +s
  gi|313116898|ref|YP_004038022.1| 161 IADFMSLSGGAEVVEVS 177
                                       67778999999998887 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027       0.4       1      41 [.      10      45 ..      10      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                     HTH_Tnp_Tc3_2  1 krrIvrlvrkdPritlreLanelkeeGksvsreTirrrLrk 41
                                      kr ++ lv+  + +++ ++a+e      +vs+ Tir+r+++
  gi|313116898|ref|YP_004038022.1| 10 KRILYHLVQDARNTSAPMVAEEA-----HVSAGTIRNRIKQ 45
                                      577899*****************.....**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1622.80
//
Query:       gi|313116899|ref|YP_004038023.1|  [L=236]
Description: K+ transport system, NAD-binding component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-26   90.5   1.1    1.5e-25   89.7   1.1    1.4  1  TrkA_N           TrkA-N domain
    2.1e-12   46.7   0.7    8.6e-12   44.7   0.1    2.1  2  TrkA_C           TrkA-C domain
      8e-05   22.6   0.1     0.0018   18.3   0.3    2.1  2  ADH_zinc_N       Zinc-binding dehydrogenase
    0.00044   20.7   0.1    0.00065   20.2   0.1    1.3  1  XdhC_C           XdhC Rossmann domain
     0.0021   18.3   0.1     0.0031   17.8   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0024   17.5   0.7     0.0036   16.9   0.6    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0035   17.3   2.0      0.012   15.5   0.8    2.1  2  NAD_binding_10   NAD(P)H-binding
     0.0052   17.1   1.3      0.013   15.8   0.1    2.0  2  Peripla_BP_3     Periplasmic binding protein-like domain
     0.0054   16.6   0.3     0.0083   16.0   0.3    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0063   16.9   0.3      0.014   15.9   0.3    1.5  1  NAD_binding_7    Putative NAD(P)-binding
     0.0096   16.5   1.0      0.033   14.8   0.6    2.0  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
      0.012   14.9   0.8      0.018   14.3   0.8    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
       0.02   14.3   0.2      0.031   13.7   0.2    1.3  1  adh_short        short chain dehydrogenase
      0.029   14.6   0.1      0.071   13.3   0.1    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.029   15.0   0.1      0.051   14.2   0.1    1.5  1  PglD_N           PglD N-terminal domain
      0.053   14.1   1.4      0.096   13.2   1.4    1.5  1  ATPgrasp_N       ATP-grasp N-terminal domain
       0.13   11.8   0.2        0.2   11.2   0.2    1.2  1  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   1.1   1.4e-28   1.5e-25       2     116 .]       4     118 ..       3     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 1.4e-28
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddean 76 
                                       i++G+G +G  l++  ++ g+ +vvv+++d+e++e +++e  + v++ dat +e+L eag+ +ada+i +t++d++n
  gi|313116899|ref|YP_004038023.1|   4 IVVGAGGIGIPLVDIATRsGH-EVVVVETDDEKAEYVAAEYdCLVLNDDATVKETLLEAGARRADAIISTTDEDATN 79 
                                       9*****************666.6***************999999********************************* PP

                                       HHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  77 ilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       ++++lla el   + +++ +++p+h  l++++ga+++ +p
  gi|313116899|ref|YP_004038023.1|  80 VMVCLLATELAV-PSVVSVVHNPHHRPLFERIGANTIENP 118
                                       *******99888.89********************99776 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0         1   1.1e+03       5      31 ..       5      30 ..       1      41 [. 0.64
   2 !   44.7   0.1   8.2e-15   8.6e-12       1      70 []     147     221 ..     147     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                                      EEE--GGGTTSBHHHHTHHHH.S-EEEE CS
                            TrkA_C  5 tvpagsplvGktlkelnlrar.gvlvva 31
                                      +v+ag   +G +l ++  r    v vv 
  gi|313116899|ref|YP_004038023.1|  5 VVGAGG--IGIPLVDIATRSGhEVVVVE 30
                                      555555..89999996666655555554 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 8.2e-15
                                       CEEEEEE--GGGTTSBHHHHT....HHHHS-EEEEEE-T..-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkeln....lrargvlvvairRg..geliipsgdtvLeeGDvllvvgspsdlaelrellg 70 
                                       ++e++v++++p+vG++l+++     l++ +vlvva+ R+    +i p g+t  ++GD+l+v++ + ++ ++++++g
  gi|313116899|ref|YP_004038023.1| 147 VFEIRVSESAPIVGMRLDDAAgdglLPD-DVLVVAVERNdeSNPITPHGSTAVRSGDLLTVYSAKGATPDVTDVFG 221
                                       79*****************888******.*******9999999***************************999986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   1.7e-06    0.0018       1      72 [.      10      78 ..      10      88 .. 0.80
   2 ?    2.6   0.0      0.11   1.2e+02       5      41 ..      81     118 ..      77     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                                      HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHH CS
                        ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakk.lGadevinykeadlverikeltggegvdvvfecvGsgatl 72
                                      g+G+ +v +A  +G ev++v  ++ek+e+++  + + ++ +    +++e + e+   + +d+++ ++  +++ 
  gi|313116899|ref|YP_004038023.1| 10 GIGIPLVDIATRSGHEVVVVETDDEKAEYVAAeYDCLVLNDD-A-TVKETLLEAG-ARRADAIISTTD-EDAT 78
                                      89***************************9875775555544.4.7999999999.789999998887.5444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEET CS
                        ADH_zinc_N   5 aavqlAkalGa.eviavdsseeklelakklGadeviny 41 
                                       +++ lA  l +  v+ v+++++ + l +++Ga+ + n+
  gi|313116899|ref|YP_004038023.1|  81 MVCLLATELAVpSVVSVVHNPHHRPLFERIGANTIENP 118
                                       66677777777899******************988777 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   6.1e-07   0.00065       1      66 [.       3      88 ..       3     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.1e-07
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG.......-GGG-TT-SE.....................-EEEE-- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefa.......tkerfpeade.....................tavvvlt 51
                                      l+++Gag ++ +l+++a + g +v+vv++++e a       +                              +a++  t
  gi|313116899|ref|YP_004038023.1|  3 LIVVGAGGIGIPLVDIATRSGHEVVVVETDDEKAeyvaaeyD--------ClvlnddatvketlleagarraDAIISTT 73
                                      79****************************985545454440........14444455555556666778888888888 PP

                                      S-HHHHHHHHHHHSS CS
                            XdhC_C 52 hdhklDaealeaalr 66
                                       + ++  +++  a +
  gi|313116899|ref|YP_004038023.1| 74 DEDATNVMVCLLATE 88
                                      888888888887774 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.9e-06    0.0031       2      75 ..       4      71 ..       3     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvn 75
                                      +++GaG++G ++++   r+++   e++v++ ++ek+e +aa+    ++     da  +e +L+a  + +d++++
  gi|313116899|ref|YP_004038023.1|  4 IVVGAGGIGIPLVDIATRSGH---EVVVVETDDEKAEYVAAE---YDCLVLNDDATVKETLLEAGARRADAIIS 71
                                      89*****************98...6**********9999854...55555555555555556666666666665 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   3.4e-06    0.0036       3      68 ..       3      68 ..       1      88 [. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.4e-06
                                      EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES CS
                    UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsftt 68
                                      + v+G+G +G++   +  + ghev++v  d+ek + + ++   ++ ++ +++ ++ +e+g  ++  
  gi|313116899|ref|YP_004038023.1|  3 LIVVGAGGIGIPLVDIATRSGHEVVVVETDDEKAEYVAAEYDCLVLNDDATVKETLLEAGARRADA 68
                                      679******************************998877655555555555555555555555555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.8   1.1e-05     0.012       3      73 ..       8      78 ..       7     149 .. 0.86
   2 ?    0.5   0.0      0.46   4.8e+02      17      65 ..     174     220 ..     168     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHH.TT-SEEEES---TCC CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaeal.kgadaVvsalggggk 73
                                       G++G  lv+ + ++ ghev+++  + ek++ ++ae  + v+  d+t +e+l ea  + ada++s++  +++
  gi|313116899|ref|YP_004038023.1|  8 AGGIGIPLVDIATRS-GHEVVVVETDDEKAEYVAAEYDCLVLNDDATVKETLLEAGaRRADAIISTTDEDAT 78
                                      79************9.5****************99999999******9999777752689******976665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.46
                                       C-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEE CS
                    NAD_binding_10  17 rgghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVv 65 
                                       + ++ v+a+ Rn e+ + +  +  + v +gd+++v + + a  ++  V+
  gi|313116899|ref|YP_004038023.1| 174 D-DVLVVAVERNDESNP-ITPHGSTAVRSGDLLTVYSAKGATPDVTDVF 220
                                       5.467899999999999.6668888999999999888887777766665 PP

>> Peripla_BP_3  Periplasmic binding protein-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.3e-05     0.013      51     107 ..      32      98 ..      16     129 .. 0.74
   2 ?   -0.0   0.1      0.94   9.9e+02     100     124 ..     172     196 ..     163     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                                       -SS-SSHHHHH.............HHH.HHCC.-SEEEEESSCCHHHHHHHHHCCTT--TTTTEEEE CS
                      Peripla_BP_3  51 addpaaaaaaraalll........qal.klaa.lPtAviaasDelAlgvlqalreaglrvPedlsvi 107
                                       +d++a++ aa++++l+        + l +++a +++A+i ++De A  v+ +l + +l+vP  +sv+
  gi|313116899|ref|YP_004038023.1|  32 DDEKAEYVAAEYDCLVlnddatvkETLlEAGArRADAIISTTDEDATNVMVCLLATELAVPSVVSVV 98 
                                       23333344444444233443334444464444699******************************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.94
                                       TTTTEEEEBSS--SCCCSSSS--EE CS
                      Peripla_BP_3 100 vPedlsvigfddselaalssPplTt 124
                                        P+d+ v++++  ++++  +P  +t
  gi|313116899|ref|YP_004038023.1| 172 LPDDVLVVAVERNDESNPITPHGST 196
                                       5********9977887888887766 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   7.9e-06    0.0083       4      69 ..       5      72 ..       3      99 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.9e-06
                                      EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH.HHHC.CTTTTSS-HHHHCCCHHCEEE CS
                           3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseealekalekiek.slek.lvekgklkeeeveaalarisf 69
                                      v+GaG +G  +  ++ ++g+eVv+v++++e++e ++++     l+  +  k+ l e+ +++a a is+
  gi|313116899|ref|YP_004038023.1|  5 VVGAGGIGIPLVDIATRSGHEVVVVETDDEKAEYVAAEYDClVLNDdATVKETLLEAGARRADAIIST 72
                                      9*******************************999988776422220222222333444444444443 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   1.3e-05     0.014      11      94 ..       4     100 ..       2     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                     NAD_binding_7  11 lvvGgGevAarkvrklleagakvtvvapevkeele............elvklaeeelekdlegadlviaatddreln 75 
                                       +vvG+G ++   v    ++g +v+vv  +  e++e            +  +++e+ le+   +ad +i +td+++ n
  gi|313116899|ref|YP_004038023.1|   4 IVVGAGGIGIPLVDIATRSGHEVVVVETD-DEKAEyvaaeydclvlnDDATVKETLLEAGARRADAIISTTDEDATN 79 
                                       79*************************99.333334555454333333333444445777999************** PP

                     NAD_binding_7  76 eriaeaakarri..lvnvadk 94 
                                         ++ +a +  +  +v v+ +
  gi|313116899|ref|YP_004038023.1|  80 VMVCLLATELAVpsVVSVVHN 100
                                       ****99998877333555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.6   3.1e-05     0.033       2      33 ..       3      34 ..       2      42 .. 0.93
   2 ?   -1.7   0.0       4.3   4.5e+03      30      50 ..      65      85 ..      64      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                      ++vvG+G ig+ l  ++++ g++V vve  d+
  gi|313116899|ref|YP_004038023.1|  3 LIVVGAGGIGIPLVDIATRSGHEVVVVETDDE 34
                                      68**************************9886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
                                      SSSSSSTTSSHHHHHHHHHHH CS
                         Pyr_redox 30 rsdkllrllDeeaskilqekl 50
                                      r+d + +  De+a +++   l
  gi|313116899|ref|YP_004038023.1| 65 RADAIISTTDEDATNVMVCLL 85
                                      678888899999999998766 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.8   1.7e-05     0.018      32      98 ..       4      72 ..       2      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                      EEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE.HCHHHHHHHHHHHH-SEEEE- CS
                       AlaDh_PNT_C 32 lviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev.lksqeellaeavkeadvvigt 98
                                      +v+G+G  G+  + +a++ g +V+v++++ +++e++ + +   +++   + +e ll+  +++ad +i+t
  gi|313116899|ref|YP_004038023.1|  4 IVVGAGGIGIPLVDIATRSGHEVVVVETDDEKAEYVAAeYDCLVLNDdATVKETLLEAGARRADAIIST 72
                                      79**********************************997555444334677888999999*******99 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     3e-05     0.031       4      58 ..       4      59 ..       1      84 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                                      EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TT CS
                         adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDv 58
                                      +v+Ga +GIG  +++   ++G +vvvv+  +ek+e va+e   +  +++a++ ++ +
  gi|313116899|ref|YP_004038023.1|  4 IVVGA-GGIGIPLVDIATRSGHEVVVVETDDEKAEYVAAEYDCLvlNDDATVKETLL 59
                                      55665.5*******************************9988655555555555544 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.7e-05     0.071       4      62 ..       5      72 ..       3     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-05
                                      EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........EEE-SSHHHH.HHHCSEEEE- CS
                     NAD_binding_2  4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........akaaesieel.vasldvvitm 62
                                      ++G G +G +++   +++g++v+v++ + ek+e ++ae         a++ e++ e+ ++++d++i  
  gi|313116899|ref|YP_004038023.1|  5 VVGAGGIGIPLVDIATRSGHEVVVVETDDEKAEYVAAEYdclvlnddATVKETLLEAgARRADAIIST 72
                                      79*******************************99999777776666444444433313333555443 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.8e-05     0.051       2      49 ..       3      53 ..       2      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.8e-05
                            PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflDdnkkteveg...ypvlgkaie 49
                                      ++++GaGG g    di+ ++g   +++ +Dd+k++ v     + vl ++ +
  gi|313116899|ref|YP_004038023.1|  3 LIVVGAGGIGIPLVDIATRSGHEVVVVETDDEKAEYVAAeydCLVLNDDAT 53
                                      79*******************777788999999875543322556655544 PP

>> ATPgrasp_N  ATP-grasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.4   9.1e-05     0.096       4      81 ..      19      92 ..      16      93 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.1e-05
                                      HHHTT-EEEEEEETTS----S-TT.EEEEEEE-TTT-HHHHHHHHHHHHHHS--SEEE---G..GGHHHHHHHHHHTT- CS
                        ATPgrasp_N  4 AkaLGikvvlvdeedewapeelaelvekfipldlaqdpdaaleavralsrerpvdGivtftd..lavplvArlaeaLgL 80
                                      A + G++vv+v+ +de a+  +ae  + ++  d       + e++ + + +r+ d+i+++td  ++ ++v  la +L  
  gi|313116899|ref|YP_004038023.1| 19 ATRSGHEVVVVETDDEKAEYVAAE-YDCLVLNDD----ATVKETLLE-AGARRADAIISTTDedATNVMVCLLATELAV 91
                                      8899*************9998888.444443333....445555555.3456789998887522567889999988877 PP

                                      S CS
                        ATPgrasp_N 81 P 81
                                      P
  gi|313116899|ref|YP_004038023.1| 92 P 92
                                      6 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00019       0.2       3      74 ..       4      75 ..       3      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                      ESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHH.HTT-SEEEE---G CS
                              NmrA  3 viGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelv.kgdlddkeslvea.lkgvdvvfsvtgf 74
                                      ++ ++G +G  +v++++++gh+v   v +t+ e+a+ ++++   lv ++d+  ke l ea  + +d+++s+t  
  gi|313116899|ref|YP_004038023.1|  4 IVVGAGGIGIPLVDIATRSGHEVV--VVETDDEKAEYVAAEYDCLVlNDDATVKETLLEAgARRADAIISTTDE 75
                                      4556688**************996..558999999999999999998999887776655538999*99999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1507.99
//
Query:       gi|313116900|ref|YP_004038024.1|  [L=140]
Description: hypothetical protein Hbor_33640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.15   11.6   1.7       0.18   11.3   1.7    1.1  1  HGTP_anticodon2  Anticodon binding domain of tRNAs


Domain annotation for each model (and alignments):
>> HGTP_anticodon2  Anticodon binding domain of tRNAs
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.7     1e-05      0.18      92     131 ..      29      66 ..      20      93 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1e-05
                   HGTP_anticodon2  92 ldelvswlkqeirerekereesaksskssaessqkedeas 131
                                       l+e+v + +q+irer+ +re+++ +++  +e+s+++++ s
  gi|313116900|ref|YP_004038024.1|  29 LREVVRYAQQQIRERQGKREHQQRQEQ--HEPSERQESVS 66 
                                       689************955554444443..34444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1534  (0.0855597); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1001.63
//
Query:       gi|313116901|ref|YP_004038025.1|  [L=602]
Description: di-/tricarboxylate transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-65  218.9   1.3      1e-64  218.6   0.1    1.6  2  CitMHS         Citrate transporter
    3.6e-21   75.8  37.7    3.2e-14   52.9  17.8    3.2  3  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    6.1e-19   67.6   2.5      1e-11   44.5   0.3    2.5  2  TrkA_C         TrkA-C domain


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.6   0.1   1.7e-68     1e-64       1     299 [.      12     544 ..      12     547 .. 0.84
   2 ?    2.4   0.5     0.012        73     116     168 ..     540     592 ..     535     599 .. 0.74

  Alignments for each domain:
  == domain 1  score: 218.6 bits;  conditional E-value: 1.7e-68
                                       xxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll.......vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlagg 70 
                                       lvl+++e+ ++dv+a+lv+vll        +++ e +sg+a+p+++++l++ i++ ++++tG+++ +++k++ +ag+
  gi|313116901|ref|YP_004038025.1|  12 LVLFATERFPIDVTAILVMVLLmvlepwtQISPREGISGFANPATITVLAMLILSTGVNRTGIVQLIGRKMAAFAGT 88 
                                       69************************999999999****************************************** PP

                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  71 krd.llvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpg 145
                                        r+  l+++v +t+ +s+f++n++vv+i++p++ +la++ ++++p+ ll+pl++a+++gg+lt+iGt+         
  gi|313116901|ref|YP_004038025.1|  89 DRRkQLAATVGVTGPVSGFINNTPVVAILVPVIADLAHE-GRTSPSkLLMPLSFASMLGGTLTLIGTS--------- 155
                                       **************************************8.9999999*********************......... PP

                                       xxxxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                            CitMHS 146 lslpnlll............................lalllvgllplvllfmfgvalalpvnap............. 181
                                          +n+l+                            +++++vg l+l++++    +  lp  +p             
  gi|313116901|ref|YP_004038025.1| 156 ---TNILAsdiaaqlgaespglglhafgmfeftklgVVVFAVGSLYLMTIG----VRLLPKRIPadedlveeyalqe 225
                                       ...9999999999999999999999999999999999999999********....3333333333334444444444 PP

                                       .......xxxxxxxxxxxxxxxxxxx................................................... RF
                            CitMHS 182 .......kvkkqkaiieaiarsllpv................................................... 200
                                                                +                                                   
  gi|313116901|ref|YP_004038025.1| 226 yladvvvP-----------------Ansqligqtvgealgddnldidvlqlirygerfdeplarkeihendtlrlrt 285
                                       44444440.................2555566666666666666666666666666666666666666666666677 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|313116901|ref|YP_004038025.1| 286 nretleyimdaegltlsggprteddlhpeeeepvlvevvipsgsflvgetlasssfrqrydanvlafrtrgdvvrdr 362
                                       77777777777777888888888888888888888888888888888888888888888888888888888888888 PP

                                       ........................................................................xxxxx RF
                            CitMHS 201 ........................................................................atill 205
                                                                                                               a++++
  gi|313116901|ref|YP_004038025.1| 363 fedirirvgdtllvqappdsltrlvenedfivahefdevtyrsdkipfavgiiagvvalpalnilpivvsalAGVVA 439
                                       88888888888999999999999999999999999999999999999999999888888888888877777744444 PP

                                       xx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 206 la..........ykkveWsvlllfaGvfllvgaleqtGilealadllga...g.gplvalalvlgliallsafisnv 268
                                       ++          y +veW+v++l+aGv++l+ al+qt  + +l+d++ a     +p+ +l++++++++ll+++isn+
  gi|313116901|ref|YP_004038025.1| 440 MIftgvlkptelYSSVEWNVIFLLAGVIPLGIALQQTEAAALLGDAVAAtslFlPPIGVLWVFYLATGLLTSVISNN 516
                                       447889****************************************95567626999999***************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 269 avaalmapialgmapalgllspsplalalav 299
                                       a ++lm+p+a+++a+++g   ++++a++lav
  gi|313116901|ref|YP_004038025.1| 517 ASVVLMIPVAANAAQSIG---ANAFAFVLAV 544
                                       ***************999...9999999998 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.012
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxx RF
                            CitMHS 116 lliplalaaniggaltpiGtpttraaarpglslpnlll.............lalllvgllplvllf 168
                                       +++++ +aa++   +tp+G              +nl +             +++ l +ll +v+++
  gi|313116901|ref|YP_004038025.1| 540 FVLAVTFAASTAF-MTPVGYQ------------TNLFVygpggytfsdfirVGAPLQFLLSIVTVL 592
                                       6788999999999.*******............888887777777777777666666666666665 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   4.3   1.1e-08   6.4e-05      32     118 ..       3      88 ..       1     101 [. 0.89
   2 !   11.8   0.9   1.5e-05      0.09     378     431 ..     107     159 ..     103     169 .. 0.91
   3 !   52.9  17.8   5.3e-18   3.2e-14     296     467 ..     432     599 ..     412     601 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-08
                     Na_sulph_symp  32 rllaifiaaivglileplplavialialsllavligvlaakalsevlsgfssdttlLvfaalliaaavektgLgkRi 108
                                       +++a +++a v + +e +p  v+a++ + ll+vl  +++  +  e +sgf + +t+ v+a l+++++v  tg+ + i
  gi|313116901|ref|YP_004038025.1|   3 VVFALILLALVLFATERFPIDVTAILVMVLLMVLEPWTQ-ISPREGISGFANPATITVLAMLILSTGVNRTGIVQLI 78 
                                       5799999******************************99.9999****************************98877 PP

                     Na_sulph_symp 109 AlvlvkivGk 118
                                          +  + G+
  gi|313116901|ref|YP_004038025.1|  79 GRKMAAFAGT 88 
                                       7666666665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.5e-05
                     Na_sulph_symp 378 faSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpi 431
                                       f  +t  +a+l+p+++ +a+      p  + ++l +a+ l+g+l+ ++t+ n +
  gi|313116901|ref|YP_004038025.1| 107 FINNTPVVAILVPVIADLAHEG-RTSPSKLLMPLSFASMLGGTLTLIGTSTNIL 159
                                       7789999*************99.77799999******************99976 PP

  == domain 3  score: 52.9 bits;  conditional E-value: 5.3e-18
                     Na_sulph_symp 296 vaivvlvillllrvldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfv 372
                                        a+ ++v ++ + vl+    + +   Wn+++ll+g+i l   l+++     lg++++ ++  + p + ++ ++ l  
  gi|313116901|ref|YP_004038025.1| 432 SALAGVVAMIFTGVLKPT-ELYSSVEWNVIFLLAGVIPLGIALQQTEAAALLGDAVAATSL-FLPPIGVLWVFYLAT 506
                                       4778889999999*9999.6777899******************************99888.999999999999999 PP

                     Na_sulph_symp 373 lvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfi 449
                                        + +   S+ A ++ ++p+ + +aq+i ga+   ++l++++a s a f++p++   n  v+g g     d+ r+G++
  gi|313116901|ref|YP_004038025.1| 507 GLLTSVISNNASVVLMIPVAANAAQSI-GANAFAFVLAVTFAASTA-FMTPVGYQTNLFVYGPGGYTFSDFIRVGAP 581
                                       999************************.******************.****************************** PP

                     Na_sulph_symp 450 lsiigllillllgalwwk 467
                                       l+++  ++ +l +a +w 
  gi|313116901|ref|YP_004038025.1| 582 LQFLLSIVTVLGIAFFWG 599
                                       ****99999999999995 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   9.9e-09   5.9e-05       2      65 ..     228     293 ..     227     297 .. 0.90
   2 !   44.5   0.3   1.7e-15     1e-11       1      65 [.     320     386 ..     320     390 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.9e-09
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlael 65 
                                       + v+vpa+s+l+G+t++e+   ++ ++ v+ + R  +++  p    +++e+D+l + +++++l+ +
  gi|313116901|ref|YP_004038025.1| 228 ADVVVPANSQLIGQTVGEALGDDNlDIDVLQLIRYgERFDEPLARKEIHENDTLRLRTNRETLEYI 293
                                       689***************555556********9999*************************99876 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 1.7e-15
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T-EEES--T.T-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRggeliipsg.dtvLeeGDvllvvgspsdlael 65 
                                       lvev++p+gs lvG tl+ + +r+r +++v+a r +g+++  +  d +++ GD+llv ++p++l +l
  gi|313116901|ref|YP_004038025.1| 320 LVEVVIPSGSFLVGETLASSSFRQRyDANVLAFRTRGDVVRDRFeDIRIRVGDTLLVQAPPDSLTRL 386
                                       79*******************************755455555555*****************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3782.61
//
Query:       gi|313116902|ref|YP_004038026.1|  [L=118]
Description: hypothetical protein Hbor_33660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 744.15
//
Query:       gi|313116903|ref|YP_004038027.1|  [L=110]
Description: hypothetical protein Hbor_33670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   13.2   1.5       0.59   10.8   0.0    2.2  2  DUF883    Bacterial protein of unknown function (DUF883)


Domain annotation for each model (and alignments):
>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3     0.021   3.7e+02      23      39 ..      18      34 ..      10      67 .. 0.80
   2 ?   10.8   0.0   3.3e-05      0.59      10      41 ..      78     109 ..      69     110 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.021
                            DUF883 23 deageeaeelRerleer 39
                                      ++ +++ e++R+r++e 
  gi|313116903|ref|YP_004038027.1| 18 QQPDRKQEKVRDRAHED 34
                                      56677778888888875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.3e-05
                            DUF883  10 lladleellkeaadeageeaeelRerleerle 41 
                                        +++lee+l ++++++ ++a+++R+r+   ++
  gi|313116903|ref|YP_004038027.1|  78 GTESLEEVLASTKNQTYDSADDVRSRILGLIH 109
                                       5789**********************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 752.22
//
Query:       gi|313116904|ref|YP_004038028.1|  [L=46]
Description: hypothetical protein Hbor_33680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 316.53
//
Query:       gi|313116905|ref|YP_004038029.1|  [L=392]
Description: Zn-dependent protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-24   86.4   0.7    4.7e-14   52.6   0.0    2.4  2  CBS             CBS domain
    4.7e-13   49.0   9.3    9.1e-09   35.0   0.2    3.3  3  Peptidase_M50   Peptidase family M50
    5.4e-06   26.2   2.7    5.4e-06   26.2   2.7    2.3  3  Peptidase_M50B  Peptidase M50B-like
  ------ inclusion threshold ------
      0.035   14.1   0.1      0.074   13.1   0.1    1.5  1  SpoVT_C         Stage V sporulation protein T C-terminal, tra
       0.11   12.0   0.0       0.18   11.3   0.0    1.3  1  Peptidase_M64   IgA Peptidase M64


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.3     4e-11   1.4e-07       1      50 [.     249     299 ..     249     300 .. 0.91
   2 !   52.6   0.0   1.3e-17   4.7e-14       1      54 [.     313     366 ..     313     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4e-11
                                       HHHHSBS..SCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHH CS
                               CBS   1 Vgdimtr..dvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrD 50 
                                       V+d+mt+  ++ tv+++tt++++l + ++e+++ ++PV+  +g lvG+vtl D
  gi|313116905|ref|YP_004038029.1| 249 VSDVMTSeeNLETVSEETTISDLLARmFTERHI-GYPVM-RNGDLVGMVTLDD 299
                                       89*****88889************995677779.*****.7999*******99 PP

  == domain 2  score: 52.6 bits;  conditional E-value: 1.3e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+d+m+++++t +pd++   a+++m ++gv+rlPVV++ g lvGi++++D +ra
  gi|313116905|ref|YP_004038029.1| 313 VEDVMSTEPHTTSPDADAMTAFQQMQQNGVGRLPVVNDAGDLVGIISRTDMMRA 366
                                       89***********************8888***********************98 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.6   1.6e-06    0.0058       3     107 ..      69     138 ..      67     152 .. 0.83
   2 !   35.0   0.2   2.5e-12   9.1e-09     191     247 ..     153     206 ..     147     212 .. 0.80
   3 ?   -2.0   0.0      0.49   1.8e+03      98     109 ..     217     253 ..     209     338 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaf 79 
                                       +l l+  v++HE+GH lvA + g+++++                    i+l+ LGG+ ++ +               
  gi|313116905|ref|YP_004038029.1|  69 ALGLFTGVLLHEFGHSLVALRYGYEIDS--------------------ITLWLLGGVASFTEFP------------- 112
                                       5778899*******************99....................8888899977777766............. PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  80 lkkspwqrllivlAGplanfilailvfv 107
                                         ++  ++l+i++AGp++ ++l++  +v
  gi|313116905|ref|YP_004038029.1| 113 --ENWRHELVIAIAGPVVSVLLGVGSYV 138
                                       ..34568899999999999988887776 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 2.5e-12
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 191 flqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglall 247
                                       ++ +la++++ L+ +NLlP +++DGg++l+all +++     +++++ a  vg ++ 
  gi|313116905|ref|YP_004038029.1| 153 VFGYLAILNIVLAAFNLLPGFPMDGGRILRALLARTQ---PHAKATQQAAAVGKVFA 206
                                       6889*****************************9888...44455555555555554 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.49
                                       XXXXXXXXXXX.........................- CS
                                       xxxxxxxxxxx.........................x RF
                     Peptidase_M50  98 nfilailvfvv.........................p 109
                                       n  l +l+f++                         +
  gi|313116905|ref|YP_004038029.1| 217 NWFLIVLAFFIyiaasgeaqqttikaafeditvsdvM 253
                                       5444444444433343333332222222222222220 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   1.0       1.8   6.5e+03     120     144 ..      20      44 ..      12      50 .. 0.48
   2 !   26.2   2.7   1.5e-09   5.4e-06      24      98 ..      75     150 ..      59     173 .. 0.73
   3 ?   -0.8   1.0      0.27   9.7e+02      94     126 ..     198     230 ..     180     249 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
                    Peptidase_M50B 120 llllgallllvlllaedelleflll 144
                                        l+++ l+++++ ++  el+ ++ +
  gi|313116905|ref|YP_004038029.1|  20 FLIVLPLFAVFIAWDIAELVVVINQ 44 
                                       3333334444444444455555444 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.5e-09
                    Peptidase_M50B  24 vvffHElGHalaalLtGgrvkgielhsdesGvtvtrg..pgglgqiltllaGYlgpallGlllillsasgkarlllv 98 
                                        v++HE+GH l+al  G+++++i+l    +Gv+  +   +++    ++++aG++ + llG++  ++  s  +++ +v
  gi|313116905|ref|YP_004038029.1|  75 GVLLHEFGHSLVALRYGYEIDSITLWLL-GGVASFTEfpENWRHELVIAIAGPVVSVLLGVGSYVAFISLPPSVDAV 150
                                       489**********************986.566666666777778899*************99888776544443333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.27
                    Peptidase_M50B  94 rlllvllvllllvllllvrnlfglvlllllgal 126
                                       +++++ ++++ l ll l  n+f++vl +++ ++
  gi|313116905|ref|YP_004038029.1| 198 AAAVGKVFAFGLGLLGLFTNWFLIVLAFFIYIA 230
                                       445555566666666666777777666665544 PP

>> SpoVT_C  Stage V sporulation protein T C-terminal, transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.1e-05     0.074      29      98 ..     228     298 ..     227     316 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                           SpoVT_C  29 iiavagaskkellekeiske.leklmeerktvlakkeekklvveeekeeysa.qviaPIiaeGdviGaVill 98 
                                       +ia++g +++  ++   ++  + ++m +++++ + +ee+++  +   + +++  + +P++ +Gd +G+V l 
  gi|313116905|ref|YP_004038029.1| 228 YIAASGEAQQTTIKAAFEDItVSDVMTSEENLETVSEETTIS-DLLARMFTErHIGYPVMRNGDLVGMVTLD 298
                                       599999999999999998866999******965554544444.3334455555999*************985 PP

>> Peptidase_M64  IgA Peptidase M64
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     5e-05      0.18     141     167 ..      72      98 ..      50     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                                       THHHHHHHHHHHHTT------EES--- CS
                     Peptidase_M64 141 yatyilvHElgHslagLadEYeytsdv 167
                                        +t +l+HE+gHsl++L   Ye +s +
  gi|313116905|ref|YP_004038029.1|  72 LFTGVLLHEFGHSLVALRYGYEIDSIT 98 
                                       6889*************9999988866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2603.19
//
Query:       gi|313116906|ref|YP_004038030.1|  [L=157]
Description: hypothetical protein Hbor_33700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1114.72
//
Query:       gi|313116907|ref|YP_004038031.1|  [L=73]
Description: hypothetical protein Hbor_33710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 553.63
//
Query:       gi|313116908|ref|YP_004038032.1|  [L=272]
Description: hypothetical protein Hbor_33730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-10   38.7   0.9    2.5e-09   37.5   0.9    1.7  1  CBS           CBS domain
  ------ inclusion threshold ------
      0.098   12.6   1.0        2.4    8.1   0.1    2.4  2  17kDa_Anti_2  17 kDa outer membrane surface antigen


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.9   2.7e-13   2.5e-09       1      55 [.      90     145 ..      90     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.7e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllral 55 
                                       V+ +m++ v tv  +++l e++e+m e+++s+l VV  d+ +++ Givt++D+++al
  gi|313116908|ref|YP_004038032.1|  90 VRNLMSDAVATVERSAPLDEVVETMFEREISSL-VVtaDDTDEPNGIVTKTDVIEAL 145
                                       7889********************64777****.666999999***********997 PP

>> 17kDa_Anti_2  17 kDa outer membrane surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1   0.00026       2.4      14      69 ..       3      55 ..       2      63 .. 0.89
   2 ?    2.8   0.1     0.012   1.1e+02      11      47 ..      64     100 ..      57     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00026
                      17kDa_Anti_2 14 svvtGsvaesaeedsdkesDaaavrnavssvdlkklkdssvPWanattGsaGvits 69
                                      sv+ G+++   e+++d+  +++a+ na   + + +++d   P   + tGs+G +++
  gi|313116908|ref|YP_004038032.1|  3 SVCRGTIS---EQEEDGAPEESAADNAGRRIYVAREQDGVAPVRKTRTGSNGGLDP 55
                                      67889995...55679999999******************************9876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.012
                      17kDa_Anti_2  11 vdrsvvtGsvaesaeedsdkesDaaavrnavssvdlk 47 
                                       + +s++  +va + +++++ ++ ++ vrn++s++  +
  gi|313116908|ref|YP_004038032.1|  64 PSASNASDTVALTMNKNEGANALNIPVRNLMSDAVAT 100
                                       668899999*999999****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2228.55
//
Query:       gi|313116909|ref|YP_004038033.1|  [L=466]
Description: hypothetical protein Hbor_33740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        8.4    6.5   9.0        1.2    9.2   0.6    3.3  3  DUF4267   Domain of unknown function (DUF4267)


Domain annotation for each model (and alignments):
>> DUF4267  Domain of unknown function (DUF4267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6   6.9e-05       1.2      58     110 ..      94     142 ..      92     146 .. 0.75
   2 ?   -1.2   0.1      0.11     2e+03       2      11 ..     297     306 ..     263     328 .. 0.64
   3 ?    0.9   0.2     0.026   4.7e+02      11      42 ..     384     414 ..     374     463 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 6.9e-05
                           DUF4267  58 slqgnrralgvvlllgavvglgDalivwrqggaektaalghlvtalvilalgl 110
                                       +++   +alg++l+ g++++l+ ++i +r +        + l t++ +++lgl
  gi|313116909|ref|YP_004038033.1|  94 YVRNVPHALGILLITGGISALIGGYIALRLSIDV----SVVLSTSVAVGVLGL 142
                                       677889*********************9997733....345555555555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.11
                           DUF4267   2 laltalGlla 11 
                                       +++++lG +a
  gi|313116909|ref|YP_004038033.1| 297 VGIVILGSIA 306
                                       2333333333 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.026
                           DUF4267  11 allrPeeaaasFGlppdssvkdsaaanalial 42 
                                        +++ e+a ++F lp+++++ + +a+++++a+
  gi|313116909|ref|YP_004038033.1| 384 PVSDLETAVEMFALPVTEPS-RPEANHTVLAI 414
                                       56666788899999987444.44444444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3371.88
//
Query:       gi|313116910|ref|YP_004038034.1|  [L=134]
Description: hypothetical protein Hbor_33750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-07   31.1   0.3    3.2e-07   30.5   0.3    1.4  1  DUF2178   Predicted membrane protein (DUF2178)


Domain annotation for each model (and alignments):
>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.3   1.8e-11   3.2e-07      10      75 ..      25      90 ..      17     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.8e-11
                           DUF2178 10 lvglgiwaaignvllaviavaaGvllaillkkkveevveDERlariaekAsrktlqillfliallg 75
                                       ++lg+++aig  l++v ++aa  + +i++ ++ ++ + DER+  ++  As++tl i+ ++ a++ 
  gi|313116910|ref|YP_004038034.1| 25 GIALGVFIAIGYPLVGVGLFAACAAGSIVVVRRYDGPLFDERDWTVQAAASKRTLGIMGIVSAIGF 90
                                      4555556699***********************************************999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 932.26
//
Query:       gi|313116911|ref|YP_004038035.1|  [L=65]
Description: XRE family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-15   57.5   0.0    1.1e-15   57.4   0.0    1.0  1  HTH_3          Helix-turn-helix
    1.7e-09   37.9   0.2    1.8e-09   37.8   0.2    1.0  1  HTH_31         Helix-turn-helix domain
      4e-09   36.4   0.0      4e-09   36.4   0.0    1.0  1  HTH_19         Helix-turn-helix domain
    4.4e-06   27.0   0.0    4.6e-06   27.0   0.0    1.0  1  HTH_26         Cro/C1-type HTH DNA-binding domain
     0.0009   19.1   0.3     0.0012   18.6   0.3    1.2  1  HTH_25         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.026   14.5   0.1      0.035   14.1   0.1    1.2  1  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.031   14.1   0.1      0.047   13.6   0.1    1.2  1  MarR_2         MarR family
      0.065   12.8   0.1      0.089   12.3   0.1    1.2  1  Sigma70_r4     Sigma-70, region 4
      0.069   12.7   0.0       0.11   12.0   0.0    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.07   13.1   0.0       0.07   13.1   0.0    1.1  1  HTH_37         Helix-turn-helix domain
       0.12   12.5   0.0       0.35   11.0   0.1    1.7  2  HTH_7          Helix-turn-helix domain of resolvase
       0.13   12.4   0.0       0.16   12.1   0.0    1.1  1  Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix do


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   7.6e-19   1.1e-15       1      55 []       5      59 ..       5      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 7.6e-19
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55
                                      ++e+Rk++ ++q +LA++++v+r++i++iE+G+ nPsle ++kla  +++  ++l
  gi|313116911|ref|YP_004038035.1|  5 VRERRKAREMTQGDLADAVDVTRQSINAIERGRYNPSLELALKLAVEFDCAVEDL 59
                                      69***********************************************988775 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.2   1.2e-12   1.8e-09       6      58 ..       5      56 ..       4      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.2e-12
                            HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldp 58
                                      +r++R+++ ++q ++A+++ v++  ++ +E+Gr  +ps++   +la  ++  +
  gi|313116911|ref|YP_004038035.1|  5 VRERRKAREMTQGDLADAVDVTRQSINAIERGRY-NPSLELALKLAVEFDCAV 56
                                      69********************************.6*****999997766655 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   2.7e-12     4e-09       4      60 ..       5      60 ..       3      65 .] 0.92

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.7e-12
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                      ++e R+ + +tq +la+ ++++r +i+aiE g++ +ps el lk+a +++  +e l+
  gi|313116911|ref|YP_004038035.1|  5 VRERRKAREMTQGDLADAVDVTRQSINAIERGRY-NPSLELALKLAVEFDCAVEDLF 60
                                      7899*****************************9.***********99988777766 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   3.1e-09   4.6e-06       3      61 ..       6      63 ..       4      65 .] 0.93

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.1e-09
                            HTH_26  3 relmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleye 61
                                      re  ++r++t+ +La ++++++++++ +  g+  ++sl+   k++  ++c ++DL+ +e
  gi|313116911|ref|YP_004038035.1|  6 RERRKAREMTQGDLADAVDVTRQSINAIERGR-YNPSLELALKLAVEFDCAVEDLFWLE 63
                                      677899**************************.6*********************9666 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   8.1e-07    0.0012       3      36 ..       6      39 ..       5      45 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.1e-07
                                      HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  3 raaRearglsleevaketkIrkdylealEeddfd 36
                                      r++R+ar ++  ++a+   +  + + a+E+++++
  gi|313116911|ref|YP_004038035.1|  6 RERRKAREMTQGDLADAVDVTRQSINAIERGRYN 39
                                      89*****************************997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.4e-05     0.035      21      40 ..      13      32 ..       3      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                                      EHHHHHHHHHTTSSHHHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsr 40
                                       +tq +lA+ + +tr++++ 
  gi|313116911|ref|YP_004038035.1| 13 EMTQGDLADAVDVTRQSINA 32
                                      69****************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.1e-05     0.047      16      41 ..       8      33 ..       6      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                                      CTTTSEEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2 16 rrpgrdltvgelarrlglsksavsri 41
                                      rr  r++t+g+la++ ++++++++ i
  gi|313116911|ref|YP_004038035.1|  8 RRKAREMTQGDLADAVDVTRQSINAI 33
                                      5566789***************9876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.9e-05     0.089      15      42 ..       8      35 ..       2      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                                      HHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 15 lrfgeglTleEIgerlgiSrerVrqiek 42
                                       r  +++T+ ++++  +++r  +  ie+
  gi|313116911|ref|YP_004038035.1|  8 RRKAREMTQGDLADAVDVTRQSINAIER 35
                                      45589*******************9997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.6e-05      0.11      15      36 ..      10      32 ..       8      33 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                            HTH_24 15 npr.isqreLAerlglSpstvnr 36
                                      ++r ++q +LA++++++++ +n+
  gi|313116911|ref|YP_004038035.1| 10 KAReMTQGDLADAVDVTRQSINA 32
                                      5555***************9996 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.7e-05      0.07      23      57 ..       5      39 ..       1      57 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                                      HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--T CS
                            HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllrgkls 57
                                      ++e +++re +q ++a +  +++ ++++++rg+ +
  gi|313116911|ref|YP_004038035.1|  5 VRERRKAREMTQGDLADAVDVTRQSINAIERGRYN 39
                                      78999**************************9975 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00024      0.35      12      38 ..       3      30 ..       1      31 [. 0.93
   2 ?   -1.2   0.0       1.5   2.3e+03      26      35 ..      47      56 ..      44      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                      GGGGSSTTTT.--STTTSSSS---SSSS CS
                             HTH_7 12 nrvvkLleeG.isiskIAkevnisRsTv 38
                                      n+v++++++  ++  ++A++v+++R+++
  gi|313116911|ref|YP_004038035.1|  3 NSVRERRKAReMTQGDLADAVDVTRQSI 30
                                      78999999999***************87 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                      TTSSSS---S CS
                             HTH_7 26 kIAkevnisR 35
                                      k+A e+++++
  gi|313116911|ref|YP_004038035.1| 47 KLAVEFDCAV 56
                                      7899999987 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.16      14      57 ..      15      59 ..      10      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                      SCHHHHCCTT--HHHHHHHHHSSS--.HHHHHHHHHHH---HHHH CS
                     Phage_CI_repr 14 mqkeLAdlLgiakssvstwvrRdffP.gdvvvtcaletdtsLewL 57
                                      +q +LAd  ++ ++s+    r  ++P  ++ +++a+e d   e+L
  gi|313116911|ref|YP_004038035.1| 15 TQGDLADAVDVTRQSINAIERGRYNPsLELALKLAVEFDCAVEDL 59
                                      578*************988888888889***********999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 474.78
//
Query:       gi|313116912|ref|YP_004038036.1|  [L=330]
Description: hypothetical protein Hbor_33770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-05   23.8   0.0    6.6e-05   22.9   0.0    1.5  1  HTH_20        Helix-turn-helix domain
  ------ inclusion threshold ------
          2    9.0   5.8        2.4    8.8   0.8    2.2  2  Secretin_N_2  Secretin N-terminal domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   7.4e-09   6.6e-05       2      48 ..      30      83 ..      29      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.4e-09
                                      HHHHHHS-HHHHHHHHHH......STCTTB-HHHHHHHHTS-HHH.HHHHHHHH CS
                            HTH_20  2 qiaeALahPvRrrilraL......araegltaselaerldlsknt.lsyHLrvL 48
                                       ++ A+++P+R +ilr+L      +++e + +++l +r ++ ++   +yHL++L
  gi|313116912|ref|YP_004038036.1| 30 AAFAAVSDPTRIAILRELgshareTGEETVGFAALRKRAGVEDSGrFRYHLNTL 83
                                      6899************************************************99 PP

>> Secretin_N_2  Secretin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4     0.021   1.9e+02      24      44 ..       6      23 ..       1      46 [. 0.46
   2 ?    8.8   0.8   0.00027       2.4      14      51 ..     196     232 ..     189     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.021
                      Secretin_N_2 24 Gsvsssgsssssssssssssg 44
                                      +s+ss  +s+++s+++s   +
  gi|313116912|ref|YP_004038036.1|  6 SSDSSKAESGDTSETDS---D 23
                                      12222222222222211...1 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00027
                      Secretin_N_2  14 sGlsntsvtsGsvsssgsssssssssssssgsssssss 51 
                                        G+++t++tsG+  + gs+  +++s+++s g+ ++s +
  gi|313116912|ref|YP_004038036.1| 196 YGTMTTRITSGKRDEDGSNRRDEGSEDGSGGD-GDSDT 232
                                       6899***************9999998855222.22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2224.44
//
Query:       gi|313116913|ref|YP_004038037.1|  [L=169]
Description: hypothetical protein Hbor_33780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 1139.38
//
Query:       gi|313116914|ref|YP_004038038.1|  [L=107]
Description: hypothetical protein Hbor_33790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 826.55
//
Query:       gi|313116915|ref|YP_004038039.1|  [L=307]
Description: hypothetical protein Hbor_33800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-15   56.9   1.7    5.1e-09   35.9   0.9    2.6  2  MarR_2           MarR family
    1.3e-09   37.8   0.2    0.00047   20.0   0.0    2.5  2  TrmB             Sugar-specific transcriptional regulator Trm
    5.8e-09   35.4   0.1     0.0032   17.0   0.0    2.5  2  HTH_24           Winged helix-turn-helix DNA-binding
    1.7e-08   34.2   0.0    0.00098   19.0   0.1    2.5  2  MarR             MarR family
      2e-08   34.5   0.0     0.0072   16.6   0.0    2.4  2  Rrf2             Transcriptional regulator
    2.7e-07   31.0   0.9    2.4e-06   28.0   0.4    2.3  2  HTH_27           Winged helix DNA-binding domain
      4e-07   29.7   0.2      0.018   14.9   0.1    2.8  2  HTH_IclR         IclR helix-turn-helix domain
    4.2e-07   29.9   0.5      0.031   14.3   0.3    2.6  2  HTH_20           Helix-turn-helix domain
    7.7e-07   28.7   0.1      0.014   15.2   0.0    2.8  2  HTH_23           Homeodomain-like domain
    1.2e-06   28.4   0.0     0.0012   18.8   0.0    2.5  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    7.6e-06   25.9   0.3       0.15   12.1   0.0    2.7  2  HTH_29           Winged helix-turn helix
    7.7e-05   22.7   0.1      0.082   13.1   0.0    2.9  2  HTH_28           Helix-turn-helix domain
    0.00012   21.8   0.0       0.31   10.9   0.0    2.5  2  HTH_5            Bacterial regulatory protein, arsR family
    0.00036   20.1   0.1        1.1    9.0   0.0    2.7  3  GntR             Bacterial regulatory proteins, gntR family
     0.0013   18.5   0.0     0.0037   17.1   0.0    1.8  1  DUF746           Domain of Unknown Function (DUF746)
     0.0026   18.1   0.0        2.4    8.5   0.0    2.4  2  Penicillinase_R  Penicillinase repressor
     0.0048   16.5   0.7      0.026   14.2   0.3    2.2  2  Crp              Bacterial regulatory proteins, crp family
  ------ inclusion threshold ------
      0.037   13.8   1.4        2.9    7.7   0.0    2.7  3  HTH_38           Helix-turn-helix domain
      0.038   14.5   0.1      0.097   13.2   0.0    1.7  1  LZ_Tnp_IS481     leucine-zipper of insertion element IS481
      0.077   13.0   0.1        5.3    7.1   0.0    2.5  2  HTH_11           HTH domain
        0.1   12.2   0.1        2.2    7.9   0.0    2.4  2  Sigma70_r4       Sigma-70, region 4
       0.11   13.2   0.0       0.24   12.1   0.0    1.6  1  RPA_C            Replication protein A C terminal
       0.14   11.8   0.0       0.45   10.2   0.0    1.8  2  HTH_41           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.9   6.6e-12   5.1e-09       7      59 ..       6      54 ..       2      57 .. 0.87
   2 !   19.1   0.0   1.2e-06    0.0009      11      51 ..      89     128 ..      82     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 6.6e-12
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59
                                      ++ vLa + r++    t++ela +l++s s++sr++++Lv++GLv ++++ + 
  gi|313116915|ref|YP_004038039.1|  6 ELEVLATVDRGD----TISELATKLDHSESYLSRAVADLVEKGLVYTERDGRR 54
                                      667888888887....********************************97554 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.2e-06
                                       HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51 
                                       L +L+  + ++ tv+e+a+r +  + +v+r+lkr+ ++GLv
  gi|313116915|ref|YP_004038039.1|  89 LEVLYYLDQPR-TVSEIADRSDNYRNTVNRVLKRFRDRGLV 128
                                       44555555554.****************************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.8e-05     0.014      23      66 ..      17      61 ..       6      63 .. 0.86
   2 !   20.0   0.0     6e-07   0.00047      21      56 ..      97     132 ..      87     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE-- CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravd 66
                                       t++e+a +l+ ++s   +++  L++kGlV++e+ gr+k+ ++ d
  gi|313116915|ref|YP_004038039.1| 17 DTISELATKLDHSESYLSRAVADLVEKGLVYTERdGRRKRVVPSD 61
                                      5899****************************9955577777665 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6e-07
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                       +p t++eia +++  r++v++vL++  d+GlV   +
  gi|313116915|ref|YP_004038039.1|  97 QPRTVSEIADRSDNYRNTVNRVLKRFRDRGLVGSAD 132
                                       789*****************************7665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     4e-06    0.0032      19      47 ..      18      46 ..       2      47 .. 0.92
   2 !   16.0   0.0   8.4e-06    0.0066      17      47 ..      98     128 ..      85     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4e-06
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +++eLA +l+ S s ++r +  L+e+Gl+
  gi|313116915|ref|YP_004038039.1| 18 TISELATKLDHSESYLSRAVADLVEKGLV 46
                                      789************************98 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.4e-06
                            HTH_24  17 risqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                         + +e+A+r++  ++tvnr lkr+ + Gl+
  gi|313116915|ref|YP_004038039.1|  98 PRTVSEIADRSDNYRNTVNRVLKRFRDRGLV 128
                                       56899************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.3e-06   0.00098      19      58 ..      18      57 ..       6      58 .. 0.89
   2 !   12.7   0.0   0.00012     0.094       8      47 ..      88     128 ..      85     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR 19 svseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      ++seLa kl  s s+++r++  L++kGl++ +++ + +R+
  gi|313116915|ref|YP_004038039.1| 18 TISELATKLDHSESYLSRAVADLVEKGLVYTERDGRRKRV 57
                                      789**************************99998766665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                                       HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR   8 iLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGli 47 
                                       +L+ ly+ ++  +vse+a+++   + tv rvl+r  ++Gl+
  gi|313116915|ref|YP_004038039.1|  88 ALEVLYYLDQpRTVSEIADRSDNYRNTVNRVLKRFRDRGLV 128
                                       577777777746889************************98 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.3e-06    0.0072      17      59 ..      10      50 ..       7      54 .. 0.87
   2 !   15.1   0.0   2.7e-05     0.021      23      61 ..      96     134 ..      86     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.3e-06
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      La+ +++   +++e+a++ + s+syl++ +a L ++glv ++r
  gi|313116915|ref|YP_004038039.1| 10 LATVDRGD--TISELATKLDHSESYLSRAVADLVEKGLVYTER 50
                                      55555555..99***************************9986 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.7e-05
                                       CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2  23 eepvsseeiaerqnispsylekilakLrkaglvksvrGk 61 
                                       ++p +++eia+r +  ++ + ++l++ r  glv s  G+
  gi|313116915|ref|YP_004038039.1|  96 DQPRTVSEIADRSDNYRNTVNRVLKRFRDRGLVGSADGH 134
                                       4567899*****************************997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.4     3e-09   2.4e-06       3      66 ..       4      61 ..       2      62 .. 0.85
   2 ?    0.9   0.0      0.85   6.6e+02      10      53 ..      90     130 ..      87     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3e-09
                            HTH_27  3 rqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66
                                      r +  vL ++    r++++++l+ +l+++ s  s ++  L+ekGLv     e+d+r+krv  +d
  gi|313116915|ref|YP_004038039.1|  4 RIELEVLATVD---RGDTISELATKLDHSESYLSRAVADLVEKGLV---YTERDGRRKRVVPSD 61
                                      55666777776...********************************...556899*99997766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.85
                            HTH_27  10 hlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgd 53 
                                       ++++  + + + +++++r +    ++  +lk+   +GLv   g+
  gi|313116915|ref|YP_004038039.1|  90 EVLYYLDQPRTVSEIADRSDNYRNTVNRVLKRFRDRGLV---GS 130
                                       5556334445558888888877778889**********9...44 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.3e-05     0.018       9      50 ..       7      48 ..       7      50 .. 0.94
   2 !   11.8   0.0    0.0002      0.15      15      48 ..      95     128 ..      86     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      L+ la+ +++ t+selA +++ + S  +R ++ Lve G+v +
  gi|313116915|ref|YP_004038039.1|  7 LEVLATVDRGDTISELATKLDHSESYLSRAVADLVEKGLVYT 48
                                      78999999999*****************************86 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0002
                                       TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  15 apqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                        +q+ t+se+A+r++  + tv R L+ +  +G+v
  gi|313116915|ref|YP_004038039.1|  95 LDQPRTVSEIADRSDNYRNTVNRVLKRFRDRGLV 128
                                       456668**************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3     4e-05     0.031      15      61 .]       9      53 ..       1      53 [. 0.86
   2 !   13.1   0.0   9.6e-05     0.075      13      54 ..      89     128 ..      83     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4e-05
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      +l+  + ++g t sela  ld s + ls+ ++ L+e gLv ++r gr
  gi|313116915|ref|YP_004038039.1|  9 VLA--TVDRGDTISELATKLDHSESYLSRAVADLVEKGLVYTERDGR 53
                                      334..5599***********************************997 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.6e-05
                                       HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20  13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54 
                                       +++l +L  ++++t+se+a+r d  +nt+++ L+  ++ gLv
  gi|313116915|ref|YP_004038039.1|  89 LEVLYYL--DQPRTVSEIADRSDNYRNTVNRVLKRFRDRGLV 128
                                       5677788..*******************************98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00043      0.33       7      46 ..       6      45 ..       1      47 [. 0.89
   2 !   15.2   0.0   1.8e-05     0.014      10      48 ..      91     129 ..      87     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                            HTH_23  7 RlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                       l++l  +++G++++e A++L+ s++ ++r +   +e+Gl
  gi|313116915|ref|YP_004038039.1|  6 ELEVLATVDRGDTISELATKLDHSESYLSRAVADLVEKGL 45
                                      4669999999**********************99999997 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.8e-05
                            HTH_23  10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeGleg 48 
                                       +l+ l++  +v+eIA++ +  r+Tv r+lkr+r  Gl g
  gi|313116915|ref|YP_004038039.1|  91 VLYYLDQPRTVSEIADRSDNYRNTVNRVLKRFRDRGLVG 129
                                       66666665599*********************9999977 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0065         5      25      55 ..      20      53 ..      12      68 .. 0.79
   2 !   18.8   0.0   1.5e-06    0.0012      21      52 ..      98     129 ..      83     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0065
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TE CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis..r.gr 55
                                       elA  l  + + +sr+ ++L ++gl+   r gr
  gi|313116915|ref|YP_004038039.1| 20 SELATKLDHSESYLSRAVADLVEKGLVYteRdGR 53
                                      689999999999***************9643333 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.5e-06
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis 52 
                                       p t  e+A++    r tv+r+l++++++gl+ 
  gi|313116915|ref|YP_004038039.1|  98 PRTVSEIADRSDNYRNTVNRVLKRFRDRGLVG 129
                                       66889*************************97 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00038       0.3       3      55 ..       8      56 ..       7      74 .. 0.83
   2 !   12.1   0.0   0.00019      0.15      14      47 ..     100     134 ..      90     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                            HTH_29  3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn 55
                                      ++l+ +++G  t+s++A  l+ s+++  r++ + +e+Gl  + +    gr ++
  gi|313116915|ref|YP_004038039.1|  8 EVLATVDRGD-TISELATKLDHSESYLSRAVADLVEKGLVYTER---DGRRKR 56
                                      6788899999.9**************************754444...444443 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00019
                            HTH_29  14 tvsqiAkllglsrrtvyrwlkrfeegGlaalld.r 47 
                                       tvs+iA + +  r tv+r+lkrf+  Gl +  d +
  gi|313116915|ref|YP_004038039.1| 100 TVSEIADRSDNYRNTVNRVLKRFRDRGLVGSADgH 134
                                       899999999999***************98877745 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.012         9       3      41 ..       7      45 ..       7      56 .. 0.80
   2 !   13.1   0.0    0.0001     0.082       6      42 ..      91     128 ..      89     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                            HTH_28  3 leiikllaaGhsvreaArelgisrrtvyrWikryeegGi 41
                                      le++  + +G++++e+A +l  s++ ++r +  + e G+
  gi|313116915|ref|YP_004038039.1|  7 LEVLATVDRGDTISELATKLDHSESYLSRAVADLVEKGL 45
                                      68889999*********************9999988776 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0001
                            HTH_28   6 ikllaaG.hsvreaArelgisrrtvyrWikryeegGia 42 
                                       +++++++ ++v+e+A +   +r tv r +kr++  G+ 
  gi|313116915|ref|YP_004038039.1|  91 VLYYLDQpRTVSEIADRSDNYRNTVNRVLKRFRDRGLV 128
                                       678888857************************99975 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0004      0.31      17      46 ..      18      47 ..       7      48 .. 0.92
   2 !    8.5   0.0    0.0023       1.8       5      45 ..      89     128 ..      85     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +++ela +l+ s+s +S+  + L e GLV+
  gi|313116915|ref|YP_004038039.1| 18 TISELATKLDHSESYLSRAVADLVEKGLVY 47
                                      89***************************7 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0023
                                       HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       l++L++L +++++v+e+a+  +  + tv + Lk+ r+ GLV
  gi|313116915|ref|YP_004038039.1|  89 LEVLYYL-DQPRTVSEIADRSDNYRNTVNRVLKRFRDRGLV 128
                                       7888887.79**********999999999999999999999 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0014       1.1      27      57 ..      19      49 ..      10      55 .. 0.89
   2 !    8.1   0.0    0.0027       2.1      26      59 ..     100     133 ..      98     134 .. 0.91
   3 ?   -3.3   0.0       9.5   7.4e+03      28      36 ..     296     304 ..     287     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverr 57
                                       +eLa++++ s + + +A   L+++glv  +
  gi|313116915|ref|YP_004038039.1| 19 ISELATKLDHSESYLSRAVADLVEKGLVYTE 49
                                      48*************************9765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0027
                                       -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR  26 sereLaaefgVsrttvReALrrLeaeglverrqg 59 
                                       +++e+a++ +  r+tv+++L+r   +glv + +g
  gi|313116915|ref|YP_004038039.1| 100 TVSEIADRSDNYRNTVNRVLKRFRDRGLVGSADG 133
                                       578999999999*****************98876 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9.5
                                       HHHHHHHTS CS
                              GntR  28 reLaaefgV 36 
                                       +eLaa ++V
  gi|313116915|ref|YP_004038039.1| 296 QELAADYEV 304
                                       789999987 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.8e-06    0.0037       4      50 ..      90     136 ..      87     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.8e-06
                            DUF746   4 elIrlLsqplslaeaadllgtdegiiakwvreFrewllqLDPSGqle 50 
                                       e+  +L qp+ + e+ad+ +   +++++ +++Fr++ l   + G++e
  gi|313116915|ref|YP_004038039.1|  90 EVLYYLDQPRTVSEIADRSDNYRNTVNRVLKRFRDRGLVGSADGHYE 136
                                       67889*******************************99999999998 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0031       2.4      22      61 ..      17      56 ..       9      85 .. 0.80
   2 !    7.2   0.0    0.0079       6.1      18      55 ..      99     132 ..      86     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
                                      HHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEE CS
                   Penicillinase_R 22 evveeleeekelaysTVktllrrLvkKgllsrekegrafi 61
                                      + ++el+ + + ++s     +  Lv+Kgl+ +e++gr+ +
  gi|313116915|ref|YP_004038039.1| 17 DTISELATKLDHSESYLSRAVADLVEKGLVYTERDGRRKR 56
                                      5577888888888888889999***************974 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0079
                                       EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEE CS
                   Penicillinase_R  18 atvkevveeleeekelaysTVktllrrLvkKgllsrek 55 
                                        tv+e+ ++ ++     ++TV  +l+r  ++gl+ +  
  gi|313116915|ref|YP_004038039.1|  99 RTVSEIADRSDNY----RNTVNRVLKRFRDRGLVGSAD 132
                                       6666666665555....****************98754 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   8.9e+02      20      31 ..      34      45 ..      33      46 .. 0.90
   2 !   14.2   0.3   3.3e-05     0.026      16      31 ..     112     127 ..     112     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                                      HHHHHHHHHTTS CS
                               Crp 20 SRlLtrLrekGL 31
                                      SR + +L ekGL
  gi|313116915|ref|YP_004038039.1| 34 SRAVADLVEKGL 45
                                      89999******9 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHHHHHHTTS CS
                               Crp  16 rETVSRlLtrLrekGL 31 
                                       r TV+R+L+r+r +GL
  gi|313116915|ref|YP_004038039.1| 112 RNTVNRVLKRFRDRGL 127
                                       56*************9 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.045        35      13      41 ..       7      37 ..       3      38 .. 0.79
   2 ?    7.7   0.0    0.0037       2.9      16      43 ..      94     121 ..      89     121 .. 0.87
   3 ?   -2.4   0.1       5.3   4.2e+03      24      33 ..     149     158 ..     148     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.045
                            HTH_38 13 Ierl..laeGlslreIArrLgrspsTIsREl 41
                                      +e l   ++G +++e A +L+ s s  sR +
  gi|313116915|ref|YP_004038039.1|  7 LEVLatVDRGDTISELATKLDHSESYLSRAV 37
                                      555532479***************9999976 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0037
                            HTH_38  16 llaeGlslreIArrLgrspsTIsRElkR 43 
                                        l++  +++eIA r +  ++T++R lkR
  gi|313116915|ref|YP_004038039.1|  94 YLDQPRTVSEIADRSDNYRNTVNRVLKR 121
                                       45667899*******************9 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.3
                            HTH_38  24 reIArrLgrs 33 
                                       re A +L+r 
  gi|313116915|ref|YP_004038039.1| 149 RELAHHLHRQ 158
                                       7888888886 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.097      12      59 ..      85     132 ..      72     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                      LZ_Tnp_IS481  12 lGrvllvrrvvedrrtvaqvarelGvslrtaykwlarfraeGldGlld 59 
                                        G++l v   +++ rtv ++a      ++t  + l rfr  Gl G  d
  gi|313116915|ref|YP_004038039.1|  85 TGKALEVLYYLDQPRTVSEIADRSDNYRNTVNRVLKRFRDRGLVGSAD 132
                                       6999***************************************99877 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0068       5.3      17      43 ..      18      44 ..       7      52 .. 0.87
   2 ?    3.2   0.0      0.11        85       6      43 ..      89     126 ..      86     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0068
                            HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      +++eLA +L+ S++   r +++L e+g
  gi|313116915|ref|YP_004038039.1| 18 TISELATKLDHSESYLSRAVADLVEKG 44
                                      899********************9998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
                            HTH_11   6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                       le L+  ++p + +e+A++ +  r tv r +k+ ++ g
  gi|313116915|ref|YP_004038039.1|  89 LEVLYYLDQPRTVSEIADRSDNYRNTVNRVLKRFRDRG 126
                                       77888889999********9999999999999876655 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.23   1.8e+02      18      39 ..      14      35 ..       2      43 .. 0.77
   2 ?    7.9   0.0    0.0028       2.2      15      43 ..      92     121 ..      88     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.23
                                      TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 18 geglTleEIgerlgiSrerVrq 39
                                      ++g T +E++ +l+ S++  ++
  gi|313116915|ref|YP_004038039.1| 14 DRGDTISELATKLDHSESYLSR 35
                                      56679*********99987665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0028
                                       HHH.TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  15 lrf.geglTleEIgerlgiSrerVrqiekr 43 
                                       l++ ++++T +EI++r +  r +V + +kr
  gi|313116915|ref|YP_004038039.1|  92 LYYlDQPRTVSEIADRSDNYRNTVNRVLKR 121
                                       7889***********998888888887777 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00031      0.24      67     102 ..      16      51 ..       9      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00031
                                       TEEHHHHHHHSTSXHHHHHHHHHHHHHTTSEEESSS CS
                             RPA_C  67 GvhvdeiaqklrlsvndvkqavdeLsneGiiYsTiD 102
                                       G  ++e+a kl  s++ + +av +L+++G++Y+  D
  gi|313116915|ref|YP_004038039.1|  16 GDTISELATKLDHSESYLSRAVADLVEKGLVYTERD 51 
                                       55789***************************9766 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00058      0.45       4      43 ..      14      53 ..      13      54 .. 0.96
   2 ?   -2.8   0.0       7.1   5.5e+03       8      36 ..     100     128 ..      99     131 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
                            HTH_41  4 dRlktIeelakeleLSvGlvQkALklLeddkaislerrGr 43
                                      dR +tI+ela +l+ S      A+  L++++ +++er Gr
  gi|313116915|ref|YP_004038039.1| 14 DRGDTISELATKLDHSESYLSRAVADLVEKGLVYTERDGR 53
                                      6779***********************************8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.1
                            HTH_41   8 tIeelakeleLSvGlvQkALklLeddkai 36 
                                       t++e+a  ++  + +v   Lk   d + +
  gi|313116915|ref|YP_004038039.1| 100 TVSEIADRSDNYRNTVNRVLKRFRDRGLV 128
                                       56666665555566666677777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2183.91
//
Query:       gi|313116916|ref|YP_004038040.1|  [L=267]
Description: hypothetical protein Hbor_33810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0097   15.9   0.2      0.025   14.6   0.2    1.6  1  HTH_20         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.029   14.0   0.2       0.28   10.8   0.0    2.1  2  DUF2204        Nucleotidyl transferase of unknown function (D
      0.046   13.5   0.0       0.13   12.1   0.0    1.8  1  IF2_N          Translation initiation factor IF-2, N-terminal
      0.054   13.3   0.0       0.11   12.4   0.0    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.056   13.5   0.1       0.11   12.6   0.1    1.5  1  Sigma70_r3     Sigma-70 region 3
        0.1   12.3   0.0       0.21   11.3   0.0    1.5  2  DUF4423        Domain of unknown function (DUF4423)
       0.16   11.5   0.0       0.26   10.9   0.0    1.2  1  DDRGK          DDRGK domain
       0.19   11.2   0.0       0.35   10.3   0.0    1.4  1  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
       0.79    9.9   4.8       0.16   12.1   0.5    2.1  2  DprA_WH        DprA winged helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   1.3e-05     0.025      14      48 ..     218     250 ..     217     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                                       HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHH CS
                            HTH_20  14 rilraLaraegltaselaerldlskntlsyHLrvL 48 
                                       ++l+aL  +e +t+ ela++l+l+  +++++L+ L
  gi|313116916|ref|YP_004038040.1| 218 EVLQAL--DESMTVDELAAELELDTDEVHDRLAYL 250
                                       79****..***********************9877 PP

>> DUF2204  Nucleotidyl transferase of unknown function (DUF2204)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.14   2.9e+02      18      43 ..      26      50 ..      12      56 .. 0.78
   2 ?   10.8   0.0   0.00014      0.28     113     156 ..     124     165 ..     107     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.14
                           DUF2204 18 kfvviGgtvvelalgrkrlekDvDlF 43
                                        ++iGg+ + l    k  +kD+Dl 
  gi|313116916|ref|YP_004038040.1| 26 TVYLIGGGAMSLR-DLKGATKDIDLV 50
                                      5799999987765.57889*****96 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00014
                           DUF2204 113 ggvevkvislEdyivlKaraareeaeeeldeiarlikelklkld 156
                                       +  +v+ +s Ed ++ Ka a+r++++e ++ + +   +    + 
  gi|313116916|ref|YP_004038040.1| 124 DRLTVRLVSNEDIFLFKAIAGRDDDIEDMNMLVQAGLD--YDVV 165
                                       77899***********************9999865433..3344 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.8e-05      0.13       3      27 ..     226     249 ..     224     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.8e-05
                             IF2_N   3 kirVyeLAkeLgvkskevikkLfke 27 
                                        ++V eLA eL ++  ev ++L ++
  gi|313116916|ref|YP_004038040.1| 226 SMTVDELAAELELDTDEVHDRL-AY 249
                                       69****************9999.76 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.4e-05      0.11      15      41 ..     224     250 ..     217     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.4e-05
                     HTH_AsnC-type  15 daRisyaeLAervGlSestvlrRvrrL 41 
                                       d ++++ eLA+++ l++++v+ R++ L
  gi|313116916|ref|YP_004038040.1| 224 DESMTVDELAAELELDTDEVHDRLAYL 250
                                       6899*******************9876 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.6e-05      0.11      12      39 ..     218     245 ..     208     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.6e-05
                                       HHHHHHSSXXXHHHHHHHHTXXHHHHHH CS
                        Sigma70_r3  12 eLeqelgrePtpeEiAeeLglseekVre 39 
                                       e  q l+ + t++E+A+eL+l+ ++V++
  gi|313116916|ref|YP_004038040.1| 218 EVLQALDESMTVDELAAELELDTDEVHD 245
                                       56799999******************97 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.4   8.8e+03       5      20 ..     171     186 ..     169     190 .. 0.76
   2 ?   11.3   0.0   0.00011      0.21      28      77 ..     218     264 ..     209     267 .] 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.4
                           DUF4423   5 nkirkLdeeefeyfss 20 
                                       ++i+ L++++f+ f +
  gi|313116916|ref|YP_004038040.1| 171 AQIKRLGDDQFATFAN 186
                                       6788999999997765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                           DUF4423  28 ellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyr 77 
                                       e+l++ d++ +++ela  l   ++++ev++ l +L   + +++d+d ++r
  gi|313116916|ref|YP_004038040.1| 218 EVLQALDESMTVDELAAELE--LDTDEVHDRLAYLSTFDRVRRDGD-TVR 264
                                       567777788***********..***********************9.666 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.26     114     142 ..     227     255 ..     219     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                       E-HHHHHHHH-S-HHHHHHHHHHHHHHSS CS
                             DDRGK 114 vlleelavkfklktqevierikeLeeqgs 142
                                       ++++ela++++l+t+ev +r+  L + ++
  gi|313116916|ref|YP_004038040.1| 227 MTVDELAAELELDTDEVHDRLAYLSTFDR 255
                                       689******************99987665 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00018      0.35      20      50 ..     219     249 ..     218     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                      HTH_Tnp_ISL3  20 ilelllesrsvkavArqlgvSwtTVwrildr 50 
                                       +l++l es++v + A++l ++++ V+++l +
  gi|313116916|ref|YP_004038040.1| 219 VLQALDESMTVDELAAELELDTDEVHDRLAY 249
                                       78999999*******************9976 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3       4.4   8.8e+03      43      50 ..     186     193 ..     185     193 .. 0.84
   2 ?   12.1   0.5   8.2e-05      0.16      17      56 ..     219     257 ..     217     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                           DprA_WH  43 saaLleLE 50 
                                       + aL+eLE
  gi|313116916|ref|YP_004038040.1| 186 NEALVELE 193
                                       579****9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.2e-05
                           DprA_WH  17 vLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56 
                                       vL+aL  e+++vD+L++++ l+++ev   L  L    +v+
  gi|313116916|ref|YP_004038040.1| 219 VLQALD-ESMTVDELAAELELDTDEVHDRLAYLSTFDRVR 257
                                       788887.779****************99988776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1815.77
//
Query:       gi|313116917|ref|YP_004038041.1|  [L=212]
Description: SWIM zinc finger-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.3   0.7      0.032   13.9   0.7    1.8  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.7   1.8e-06     0.032       1      32 [.     164     190 ..     154     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-06
                              SWIM   1 yrVtlddervrlnkatCsCpefqk..ngipCkHa 32 
                                       y V++        + +C+Cp++q       CkH+
  gi|313116917|ref|YP_004038041.1| 164 YEVDVI-------DESCTCPDWQQrsPEGGCKHL 190
                                       444444.......88********86655668886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1418.91
//
Query:       gi|313116918|ref|YP_004038042.1|  [L=53]
Description: hypothetical protein Hbor_33830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.11   12.5   0.0    1.0  1  DUF1326   Protein of unknown function (DUF1326)


Domain annotation for each model (and alignments):
>> DUF1326  Protein of unknown function (DUF1326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.2e-06      0.11      48      87 ..       9      48 ..       5      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-06
                           DUF1326 48 lveapgnllegnwkavlliDerAddeqreALeaifsGeag 87
                                      +++  ++++e + +++  iD++A +  r A+ +i++G+a 
  gi|313116918|ref|YP_004038042.1|  9 VLREAEHVAEQHEQVARTIDNQAHEYLRYAVLRILEGQAD 48
                                      56667889999***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 386.35
//
Query:       gi|313116919|ref|YP_004038043.1|  [L=286]
Description: hypothetical protein Hbor_33840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-10   39.6  14.9    1.5e-09   37.6  14.9    1.8  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
        3.2    5.9  11.1        3.6    5.8  11.1    1.1  1  DUF2070          Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6  14.9   1.7e-13   1.5e-09       2     288 .]      12     285 ..      11     285 .. 0.67

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.7e-13
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllpli.......dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtd 71 
                                        +++ Efr+++rsr ++++   l+l+        + + +++ ++s+   ++ ++++                + d  
  gi|313116919|ref|YP_004038043.1|  12 SVIRLEFRRHRRSRGTVGTLTGLALFcsfwslhNLSISAYPPDASLVNDGVFSVVAPGQD----------LLLLDV- 77 
                                       578999999999999999999999995555555555555554444444444444332222..........222221. PP

                   ABC2_membrane_2  72 qdlkvvstimavlipvi...aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvlla 145
                                              +   +++p++   ++l+g+  ++  + +gTl+   + P+ R+++ lg + +++a+     va++++vl+ 
  gi|313116919|ref|YP_004038043.1|  78 -------ATSVFVGPLLlctGVLLGVGTVTTPRVEGTLRTVQTFPYGRRSVFLGLVFSRIAV-----VAVVIAVLMI 142
                                       .......2445556666666******************************************.....6666666666 PP

                   ABC2_membrane_2 146 laiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellag 222
                                         +++a+   ++l+ ++++ +a +l+l +   +a+g++lS++  +  +  +l ++  v l+++ ++++++    +++
  gi|313116919|ref|YP_004038043.1| 143 CTVVVASLSGVRLSPMVVFGFAGLLTLHVAGGVAVGAMLSTLRSQPIVVYLLGVVAAVGLLVFGGLLSSQ----FLP 215
                                       6666677777788888888888887766446789999999875544443333333333343333333333....222 PP

                   ABC2_membrane_2 223 pavp.qeindflsllsptsayntllneilagsdlna......lgstatnllilllllavllvlgyvlFkrkDl 288
                                       + v  +     + l   + + ++l+++ la +   +       gsta+ +l+l+++ +v++vlg+v+++r Dl
  gi|313116919|ref|YP_004038043.1| 216 AGVVaPRTAFHVALAGLHENWTALFQQALADT---TgdirplFGSTAAGILVLCAWVLVPTVLGAVSYERGDL 285
                                       22210223333455666666666666666655...1457889****************************997 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  11.1    0.0004       3.6      42     149 ..      88     209 ..      60     273 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0004
                           DUF2070  42 llfglpalvaflltlpvlrilggr...ltykrslflalltelivviisllaillsallqalvllalvlslalvfalr 115
                                       l+ g+ + v ++ t +v  +l++    ++ +rs+fl l++  i+v+ +++a+l+   +   +l  + ls ++vf++ 
  gi|313116919|ref|YP_004038043.1|  88 LCTGVLLGVGTVTTPRVEGTLRTVqtfPYGRRSVFLGLVFSRIAVVAVVIAVLMICTVVVASLSGVRLSPMVVFGFA 164
                                       344444444444444444444444773555677*******************9997774445555566655555554 PP

                           DUF2070 116 .llvlvavsdesllkavlpaliqpllailllvly..........f 149
                                        ll l + ++  ++ ++     qp++++ll v+           +
  gi|313116919|ref|YP_004038043.1| 165 gLLTLHVAGGVAVGAMLSTLRSQPIVVYLLGVVAavgllvfgglL 209
                                       166667777788888888888999999999988854444444431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1964.74
//
Query:       gi|313116920|ref|YP_004038044.1|  [L=310]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.9e-26   91.9   0.0    1.4e-25   90.4   0.0    1.7  2  ABC_tran     ABC transporter
    1.4e-15   58.0   0.0    2.3e-09   37.5   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    8.2e-06   25.4   0.0        0.1   12.0   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    3.6e-05   24.4   0.0    6.8e-05   23.5   0.0    1.5  1  DUF4162      Domain of unknown function (DUF4162)
    3.6e-05   23.6   1.8    0.00011   21.9   0.7    2.2  2  AAA_30       AAA domain
    6.1e-05   22.7   0.1    0.00011   21.8   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0035   17.9   0.0     0.0053   17.3   0.0    1.2  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.021   14.4   0.0    1.3  1  AAA_27       AAA domain
      0.019   15.0   0.2        1.1    9.3   0.0    2.6  2  MMR_HSR1     50S ribosome-binding GTPase
      0.069   13.1   0.1       0.13   12.1   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
       0.16   12.2   0.6        2.9    8.1   0.3    2.5  2  AAA_22       AAA domain
        0.2   11.4   0.0       0.32   10.8   0.0    1.3  1  ATP_bind_1   Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   9.1e-29   1.4e-25       2     136 ..      28     165 ..      27     166 .. 0.95
   2 ?   -1.6   0.0       2.4   3.6e+03      80      98 ..     195     213 ..     174     249 .. 0.57

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 9.1e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       k++ +++ +g++++++G+nGaGKSt + +l gl++ teG++++ g d+++ +  + r++ g+lp   +  ++lt re
  gi|313116920|ref|YP_004038044.1|  28 KELRMTVPAGSVYGLLGPNGAGKSTTIDALVGLVHATEGTVRVLGLDIRT-SPVEIRRRTGILPDGFTPYERLTGRE 103
                                       7899**********************************************.66778999****************** PP

                                       H........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +          +++ ++al+++gl + +d+++      +S G+ qr+ la+al+ +p+ll+lDEp 
  gi|313116920|ref|YP_004038044.1| 104 HldaaacanGVTVDTDEALARVGLADAADRTA----GGYSRGMSQRLGLAMALVGAPDLLVLDEPA 165
                                       *9999988777888*************99999....*****************************7 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                                       HHHTCHHHHHHHSTTGGTT CS
                                       xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 esdeeiekalsklglkelk 98 
                                       ++ +++e++ +++g++++ 
  gi|313116920|ref|YP_004038044.1| 195 HQLAQVEAVCDTVGIIDDG 213
                                       4555666666666666633 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.7e-07    0.0014       2      22 ..      40      60 ..      39      96 .. 0.83
   2 !   37.5   0.0   1.6e-12   2.3e-09     231     298 ..     132     196 ..     123     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.7e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +l GpNg+GKS+ +dal +l
  gi|313116920|ref|YP_004038044.1| 40 YGLLGPNGAGKSTTIDALVGL 60
                                      5799**************988 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.6e-12
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +++a   S G+ + l+l+ al  a+   +ll++DEp +gL+P+ ++ l ++++e++++ga v+l+TH+
  gi|313116920|ref|YP_004038044.1| 132 DRTAGGYSRGMSQRLGLAMALVGAP---DLLVLDEPAAGLDPHGIKLLRRIIREEHARGATVLLSTHQ 196
                                       567778899**9999**********...9*************9999999999***************8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   6.9e-05       0.1      26      44 ..      39      57 ..      22      70 .. 0.84
   2 !   11.3   0.0   0.00011      0.17     148     213 ..     145     211 ..     129     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                      +  ++GpNG+GKs  +dA+
  gi|313116920|ref|YP_004038044.1| 39 VYGLLGPNGAGKSTTIDAL 57
                                      56789*************9 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                                       HHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 148 aLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvtk 213
                                        L +A+  v    l +lDe +a LD + +k + ++++e++ + a ++  +++  ++e +  +vg+  
  gi|313116920|ref|YP_004038044.1| 145 RLGLAMALVGAPDLLVLDEPAAGLDPHGIKLLRRIIREEHARgATVLLSTHQLAQVEAVCDTVGIID 211
                                       566777778888899**********************76655599*******999999998888865 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.5e-08   6.8e-05       6      77 ..     224     303 ..     220     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.5e-08
                                       HHTTS.-SSEEEEE.....-------...---EEEE-TTS-EEEEE-------------.----EEEEEEEE---HH CS
                           DUF4162   6 iKrsy.gknrieve.....adaeell.eepgveeveeeggelelkledeeaanellkal.tsgveirsFeeeePsLn 74 
                                       ++r    +++++++     + a++ll +++gv  v+ egg l+++++ e++   ++++l +s+v+++s+e   P L+
  gi|313116920|ref|YP_004038044.1| 224 LRRTVgTETTLRIRlagslDRASDLLhDLDGVAGVTAEGGALIVRCDAEQDTAGVIAELeRSDVTLESYEKSHPGLE 300
                                       6666633445557777775335555515577****************************77**************** PP

                                       HHH CS
                           DUF4162  75 dIF 77 
                                        +F
  gi|313116920|ref|YP_004038044.1| 301 QVF 303
                                       *** PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.7   7.6e-08   0.00011      20     133 ..      39     202 ..      26     209 .. 0.79
   2 ?    0.3   0.1      0.32   4.7e+02      84     123 ..     200     240 ..     191     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7.6e-08
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgi........eastiakllkrlk...... 81 
                                       v  l Gp G+GK+t++ al+ +++a +g+v +l    + + v +++ +gi        e     +l+ r        
  gi|313116920|ref|YP_004038044.1|  39 VYGLLGPNGAGKSTTIDALVGLVHATEGTVRVLGLDIRTSPVeIRRRTGIlpdgftpyE-----RLTGREHldaaac 110
                                       77799*********************99**********999889988887664333221.....2222222444556 PP

                            AAA_30  82 ......................................grarlepgtllivDEagmv....dtkqlaallkaaekag 116
                                                                             ++a + + +ll+ DE +      ++k l++++++ +++g
  gi|313116920|ref|YP_004038044.1| 111 angvtvdtdealarvgladaadrtaggysrgmsqrlglAMALVGAPDLLVLDEPAAGldphGIKLLRRIIREEHARG 187
                                       6666666678888888999*****************9976778888*******66655677999999999999999* PP

                            AAA_30 117 akvilvGDerQlasVea 133
                                       a+v+l   ++Qla Vea
  gi|313116920|ref|YP_004038044.1| 188 ATVLLS--THQLAQVEA 202
                                       ***996..778888775 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.32
                            AAA_30  84 arlepgtllivDEagmvdtkqlaallkaaek.agakvilvG 123
                                       ++   +t+ i+D   +v+ ++++al + + + +  +++l+G
  gi|313116920|ref|YP_004038044.1| 200 VEAVCDTVGIIDDGQLVAEDSAEALRRTVGTeTTLRIRLAG 240
                                       44455689999999999999999999999883458998888 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   7.6e-08   0.00011      22      48 ..      36      63 ..      25      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.6e-08
                            AAA_29 22 kg.atlltGpsGsGKSTllDAiqalLvp 48
                                      +g ++ l Gp+G+GKST +DA+  l  +
  gi|313116920|ref|YP_004038044.1| 36 AGsVYGLLGPNGAGKSTTIDALVGLVHA 63
                                      4557889**************9887765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.5e-06    0.0053      22      39 ..      40      57 ..      29      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.5e-06
                            AAA_23 22 tlItGpNGaGKTTildAi 39
                                      + + GpNGaGK+T +dA+
  gi|313116920|ref|YP_004038044.1| 40 YGLLGPNGAGKSTTIDAL 57
                                      5689*************8 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-05     0.021       9      51 ..      19      62 ..      18      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                            AAA_27  9 eryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdllf 51
                                      +r+G++t  ++l++   + ++  ++GpN AGKst+++A+  l++
  gi|313116920|ref|YP_004038044.1| 19 KRFGSVTAvKELRMTVPAGSVYGLLGPNGAGKSTTIDALVGLVH 62
                                      578888763578888888889999**************998876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00075       1.1       3      22 ..      41      60 ..      39      92 .. 0.78
   2 ?    3.2   0.0     0.059        88      26      59 ..     182     216 ..     173     305 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00075
                                      EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                      +++G   +GKSt i al+g 
  gi|313116920|ref|YP_004038044.1| 41 GLLGPNGAGKSTTIDALVGL 60
                                      789**************995 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.059
                                       ESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS....H CS
                          MMR_HSR1  26 vsdkpgtTrdinegrvklkgkeielvDtpGlie....g 59 
                                        ++  g+T    +++++   +   ++Dt+G+i+     
  gi|313116920|ref|YP_004038044.1| 182 EEHARGATVLLSTHQLA---QVEAVCDTVGIIDdgqlV 216
                                       45666777777777666...234799****87522221 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.8e-05      0.13      90     130 ..      27      68 ..      14      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.8e-05
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++el+  +   ++  l+G+ G+GKSt i+al++  ++  g v
  gi|313116920|ref|YP_004038044.1|  27 VKELRMTVPAgSVYGLLGPNGAGKSTTIDALVGLVHATEGTV 68 
                                       666766665558999****************99766655555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3     0.002       2.9      10      31 ..      42      63 ..      36     200 .. 0.65
   2 ?    2.1   0.1      0.15   2.2e+02      77     129 ..     191     240 ..     173     249 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.002
                            AAA_22 10 vtGesGtGKTtllrrlleqlde 31
                                      + G+ G+GK+t++  l+   ++
  gi|313116920|ref|YP_004038044.1| 42 LLGPNGAGKSTTIDALVGLVHA 63
                                      67************99988754 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.15
                            AAA_22  77 ell.ealeqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvG 129
                                        l  ++l+q    +++  + iiD+ q +  e+  e Lr+ +   ++ +++ L+G
  gi|313116920|ref|YP_004038044.1| 191 LLStHQLAQVEAVCDT--VGIIDDGQLV-AEDSAEALRRTVG-TETTLRIRLAG 240
                                       3333555555555555..99********.8999999987776.56666666666 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.32       2      33 ..      43      74 ..      42      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                      +Gp G+GK+t + al+ ++++++ +v+v+ LD
  gi|313116920|ref|YP_004038044.1| 43 LGPNGAGKSTTIDALVGLVHATEGTVRVLGLD 74
                                      7****************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1924.51
//
Query:       gi|313116921|ref|YP_004038045.1|  [L=287]
Description: copper ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-17   61.3  14.7    2.9e-16   59.6  14.7    1.9  1  ABC2_membrane_2  ABC-2 family transporter protein
    7.8e-07   29.2   0.6    1.5e-06   28.3   0.6    1.5  1  ABC2_membrane_4  ABC-2 family transporter protein
    0.00014   21.1   1.0    0.00018   20.7   1.0    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
     0.0069   16.0   0.1      0.011   15.2   0.1    1.3  1  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.35   10.2   8.7       0.58    9.5   8.7    1.5  1  ABC2_membrane    ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6  14.7   8.1e-20   2.9e-16      78     288 .]      82     287 .]      16     287 .] 0.77

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 8.1e-20
                   ABC2_membrane_2  78 stimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgi 154
                                          +++++p++a++++a a+ag+ e+g l+ l + PvsR++++ gK+++++a+   +   + +++ ++ +++     
  gi|313116921|ref|YP_004038045.1|  82 ARVLTLFLPLVAVVLAAGALAGDAESGRLRTLQTFPVSRRAVVGGKLLARSAV---VGSVVAVGLAAGALVSWFRFG 155
                                       457899***********************************************...777777776676666666666 PP

                   ABC2_membrane_2 155 vlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailv..pivlygvaellagpavpqei 229
                                        ++  ++ l++++sv l l   ++++++++S+++  +++a+al+lg ++  a++   p+v  +v+   +        
  gi|313116921|ref|YP_004038045.1| 156 TVDPVSYGLFLLVSVGLSL--SLTGITVAVSTLTTARSRAIALSLGPLLGCAFFGvdPGVP-TVLRTGLLV------ 223
                                       6666777777777777777..569**********************998766553114555.333333333...... PP

                   ABC2_membrane_2 230 ndflsllsptsayntllneilagsdlna.....lgstatnllilllllavllvlgyvlFkrkDl 288
                                       ++  +l+  t++  +++  + ++s  ++      +s++ +l +l+++++vll +++ +++r+Dl
  gi|313116921|ref|YP_004038045.1| 224 QPYQLLVAGTHSQLVAIPRVVSTSFPRTqldglALSDGISLWALCAWPVVLLRISAGRYRRRDL 287
                                       3344666777777777788888886555899999****************************97 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.6   4.2e-10   1.5e-06      42     161 ..      72     186 ..      18     207 .. 0.57

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4.2e-10
                   ABC2_membrane_4  42 dpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitv 118
                                       +++ ++++ ++   l+l+lpl+ +++a+  +    +++ l+ L t Pvsr++++ +Kl++   ++  ++ v +++ +
  gi|313116921|ref|YP_004038045.1|  72 STTAVVLF-TLARVLTLFLPLVAVVLAAGALAGDAESGRLRTLQTFPVSRRAVVGGKLLARSAVVGSVVAVGLAAGA 147
                                       22333333.23345669******************************************987665555556555555 PP

                   ABC2_membrane_4 119 lfallsgfvgfsvklvlellkkclelgllvffavlpiialvll 161
                                       l+++   f   +v++v + l+ ++ +gl + ++ +  +a+++l
  gi|313116921|ref|YP_004038045.1| 148 LVSW---FRFGTVDPVSYGLFLLVSVGLSLSLTGIT-VAVSTL 186
                                       5555...44445666666555555555443332221.223222 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.0   5.1e-08   0.00018     160     285 ..      77     208 ..      51     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.1e-08
                   ABC2_membrane_3 160 asflvg..liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...l..af 229
                                       + f ++  l l++++  +++ +a +++ + es+ +  + + +vs+ + + +k+l+  +v   ++++ l+   l  +f
  gi|313116921|ref|YP_004038045.1|  77 VLFTLArvLTLFLPLVAVVL-AAGALAGDAESGRLRTLQTFPVSRRAVVGGKLLARSAVVGSVVAVGLAagaLvsWF 152
                                       34444464566666655555.6778999999966666669*************997777666665555434435655 PP

                   ABC2_membrane_3 230 gl.gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffg 285
                                        +  ++  ++gl+ll+++  +l+++ ++ ++s+l++  + a++l +  +l  ++ffg
  gi|313116921|ref|YP_004038045.1| 153 RFgTVDPVSYGLFLLVSVGLSLSLTGITVAVSTLTTARSRAIALSLGPLL-GCAFFG 208
                                       5346666699****************************999986444333.444443 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   3.2e-06     0.011      39     138 ..      84     184 ..      71     216 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-06
                   ABC2_membrane_5  39 ifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlik.gnvtis 114
                                       +++++ ++++++l+  +l+ D  s+  + l t+Pv+r+ +V  K l    ++ +++ ++l+++++++ ++ g+v+  
  gi|313116921|ref|YP_004038045.1|  84 VLTLFLPLVAVVLAAGALAGDAESGRLRTLQTFPVSRRAVVGGKLLARSAVVGSVVAVGLAAGALVSWFRfGTVDPV 160
                                       44555555666667789999********************************9999999999987666551556544 PP

                   ABC2_membrane_5 115 evllsiliglvialiflaivlPly 138
                                       +  l++l++++++l ++ i+  + 
  gi|313116921|ref|YP_004038045.1| 161 SYGLFLLVSVGLSLSLTGITVAVS 184
                                       444445555555555555555444 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   8.7   0.00016      0.58      53     170 ..      82     202 ..      13     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00016
                     ABC2_membrane  53 pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlve.lpvsllqalifllivyf.lvgldl 127
                                       + +l  ++  +a+++++++ +  + e g l  + ++p+ s+ a+v +k+l+  ++v+ ++a+ + + +++ ++ +  
  gi|313116921|ref|YP_004038045.1|  82 ARVLTLFLPLVAVVLAAGA-LAGDAESGRLRTLQTFPV-SRRAVVGGKLLARsAVVGSVVAVGLAAGALVsWFRFGT 156
                                       4555566666665555555.999***************.************98788888888777744442444433 PP

                     ABC2_membrane 128 s...rfflflllllltalaasslgllisalapsfedasqlaslvll 170
                                           + +lfll+ + ++l ++++ +++s+l++    a+ l+   ll
  gi|313116921|ref|YP_004038045.1| 157 VdpvSYGLFLLVSVGLSLSLTGITVAVSTLTTARSRAIALSLGPLL 202
                                       345567************************9988888877765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1755.76
//
Query:       gi|313116922|ref|YP_004038046.1|  [L=169]
Description: hypothetical protein Hbor_33870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1196.51
//
Query:       gi|313116923|ref|YP_004038047.1|  [L=198]
Description: Sugar-specific transcriptional regulator TrmB [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-09   37.7   0.3    3.7e-09   36.4   0.1    1.7  2  TrmB             Sugar-specific transcriptional regulator Trm
    6.9e-05   22.8   0.1    0.00021   21.3   0.0    1.9  2  HTH_20           Helix-turn-helix domain
    0.00016   21.2   0.0     0.0015   18.0   0.0    2.3  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0011   18.8   0.3     0.0039   17.1   0.0    2.0  2  MarR_2           MarR family
     0.0019   18.0   0.0     0.0048   16.7   0.0    1.7  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0083   15.9   0.2      0.052   13.4   0.0    2.3  2  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.035   13.8   0.0    1.4  1  RP-C             Replication protein C N-terminal domain
      0.052   13.7   0.0         11    6.1   0.0    2.2  2  F-112            F-112 protein
      0.052   13.9   0.0       0.11   12.9   0.0    1.5  1  Penicillinase_R  Penicillinase repressor
      0.061   13.8   0.2        0.2   12.2   0.0    2.0  2  HTH_27           Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1     2e-12   3.7e-09      11      64 ..      29      83 ..      28      87 .. 0.93
   2 ?   -2.2   0.0       2.2   3.9e+03      20      46 ..     142     168 ..     135     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2e-12
                                      CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE CS
                              TrmB 11 akvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYra 64
                                      a+ Y++L ++g+at++ +  +l++ + ++Y+++++L+d+G+V++ + + p++Y a
  gi|313116923|ref|YP_004038047.1| 29 AQLYAYLAREGEATVQNVMDDLKLAQGTAYSYVNRLVDAGVVDVTDDEqPRRYAA 83
                                      689******************************************9666****98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
                                       HCCCHHCHHCCCTTSSCHCHHHHHHHH CS
                              TrmB  20 lgpatadeiaeelgvprskvYevLrsL 46 
                                       +g+ t +  ae+l+++   +  +L+ L
  gi|313116923|ref|YP_004038047.1| 142 RGEVTHRLMAEDLDISPLAAEMILQAL 168
                                       577778888888888877777777766 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.2e-07   0.00021       3      59 ..      19      75 ..      17      77 .. 0.93
   2 ?   -2.8   0.0         4   7.1e+03      15      21 ..     164     169 ..     163     189 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +a++L +P  + ++++Lar++++t+  +++ l l++ t++  ++ L++ag v+v++ 
  gi|313116923|ref|YP_004038047.1| 19 VADLLEEPQLAQLYAYLAREGEATVQNVMDDLKLAQGTAYSYVNRLVDAGVVDVTDD 75
                                      788899999999******************************************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4
                                       HHHHHST CS
                            HTH_20  15 ilraLar 21 
                                       il+aL r
  gi|313116923|ref|YP_004038047.1| 164 ILQAL-R 169
                                       77777.2 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.6e-07    0.0015       9      47 ..      32      70 ..      30      71 .. 0.94
   2 ?   -0.0   0.0      0.37   6.6e+02      16      31 ..     143     158 ..     137     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.6e-07
                            HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + +L +++  + + + + l l ++t   +++rL+++G++
  gi|313116923|ref|YP_004038047.1| 32 YAYLAREGEATVQNVMDDLKLAQGTAYSYVNRLVDAGVV 70
                                      6799*********************************98 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.37
                            HTH_24  16 prisqreLAerlglSp 31 
                                       +  + r  Ae l++Sp
  gi|313116923|ref|YP_004038047.1| 143 GEVTHRLMAEDLDISP 158
                                       568999999*999998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.1e-06    0.0039      12      61 ..      33      80 ..      15      80 .. 0.89
   2 ?   -1.9   0.0       1.8   3.2e+03      21      41 ..     144     164 ..     131     168 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                                      HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      a+L+r+++   tv+ + + l+l ++++   ++rLv+aG v  ++++  +R
  gi|313116923|ref|YP_004038047.1| 33 AYLAREGE--ATVQNVMDDLKLAQGTAYSYVNRLVDAGVVDVTDDEQPRR 80
                                      67999999..9******************************999887776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                                       EEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2  21 dltvgelarrlglsksavsri 41 
                                       ++t +  a+ l++s+ a+  i
  gi|313116923|ref|YP_004038047.1| 144 EVTHRLMAEDLDISPLAAEMI 164
                                       356666666677776555555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.7e-06    0.0048      11      46 ..      35      71 ..      30      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-06
                                      HTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 11 Lae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      La+ ge++v   +++l+l q+t   + ++L +aG+V+
  gi|313116923|ref|YP_004038047.1| 35 LAReGEATVQNVMDDLKLAQGTAYSYVNRLVDAGVVD 71
                                      6666*******************************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.9e-05     0.052      10      49 ..      33      71 ..      28      74 .. 0.90
   2 ?   -0.7   0.1      0.69   1.2e+03      12      42 ..     138     168 ..     137     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                                      CT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 10 dalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                       +la+++++ t++ + + + l+  t++ +++ Lv  G v 
  gi|313116923|ref|YP_004038047.1| 33 AYLAREGEA-TVQNVMDDLKLAQGTAYSYVNRLVDAGVVD 71
                                      589999997.**************************9985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.69
                                       -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHH CS
                          HTH_IclR  12 laeapqeltlselArrtglpkStvhRlLqtL 42 
                                       +a+ ++e+t + +A+ +++++ ++  +Lq L
  gi|313116923|ref|YP_004038047.1| 138 VARDRGEVTHRLMAEDLDISPLAAEMILQAL 168
                                       6788888888888888888776666666665 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05     0.035      78     125 ..      47      94 ..      42      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                              RP-C  78 sralglsestlrrhlaaLveaGliirrDspngkRyarrdreGeieeAf 125
                                       +  l+l++ t    + +Lv+aG++   D    +Rya r+ +  +++A 
  gi|313116923|ref|YP_004038047.1|  47 MDDLKLAQGTAYSYVNRLVDAGVVDVTDDEQPRRYAAREIDLTVTTAA 94 
                                       567889999999**************************9887777665 PP

>> F-112  F-112 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0098        18      11      43 ..      30      62 ..      23      88 .. 0.85
   2 ?    6.1   0.0    0.0063        11      12      54 ..     135     177 ..     128     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0098
                                      HHHHHHHHHSEE-HHHHHHHH---HHHHHHHHH CS
                             F-112 11 ilykilekkkeltledilaqfeisvssayaiqr 43
                                      +ly  l + +e t+++++   +++  +ay+  +
  gi|313116923|ref|YP_004038047.1| 30 QLYAYLAREGEATVQNVMDDLKLAQGTAYSYVN 62
                                      79***************************8654 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0063
                                       HHHHHHHHSEE-HHHHHHHH---HHHHHHHHHHHHHHHHH-TT CS
                             F-112  12 lykilekkkeltledilaqfeisvssayaiqralkaicerhqd 54 
                                        y + ++++e+t   +    +is+ +a  i +al+ + ++h +
  gi|313116923|ref|YP_004038047.1| 135 TYAVARDRGEVTHRLMAEDLDISPLAAEMILQALRPVVHEHYE 177
                                       589999*******999999****************99999965 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.1e-05      0.11       7      64 ..      30      83 ..      26      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-05
                                      HHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE- CS
                   Penicillinase_R  7 evmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsp 64
                                      + + +l ++geatv++v++ l+     a+ T  + ++rLv+ g+++   +++  +Y++
  gi|313116923|ref|YP_004038047.1| 30 QLYAYLAREGEATVQNVMDDLKL----AQGTAYSYVNRLVDAGVVDVTDDEQPRRYAA 83
                                      66778889999******999875....588888899****************999998 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011       0.2      14      59 ..      36      81 ..      23     103 .. 0.88
   2 ?   -1.8   0.0       2.5   4.5e+03      55      64 ..     140     149 ..     137     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                       r+++++   +++ l++ + ++ + +++L+ +G+v  t de++rr+
  gi|313116923|ref|YP_004038047.1| 36 AREGEATVQNVMDDLKLAQGTAYSYVNRLVDAGVVDVTDDEQPRRY 81
                                      5789999999***********************************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.5
                            HTH_27  55 adrrekrvrl 64 
                                       +dr+e+++rl
  gi|313116923|ref|YP_004038047.1| 140 RDRGEVTHRL 149
                                       7999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1539.53
//
Query:       gi|313116924|ref|YP_004038048.1|  [L=108]
Description: hypothetical protein Hbor_33890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 776.59
//
Query:       gi|313116925|ref|YP_004038049.1|  [L=196]
Description: hypothetical protein Hbor_33900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0038   17.4   0.1     0.0051   17.0   0.1    1.2  1  FUR            Ferric uptake regulator family
     0.0059   16.7   0.0     0.0082   16.2   0.0    1.2  1  Replic_Relax   Replication-relaxation
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.027   14.8   0.0    1.3  1  HTH_WhiA       WhiA C-terminal HTH domain
      0.018   15.3   0.1      0.033   14.4   0.1    1.4  1  HTH_Tnp_Tc3_2  Transposase
      0.024   14.6   0.1      0.046   13.7   0.1    1.4  1  HTH_11         HTH domain
      0.034   14.8   0.3       0.09   13.4   0.1    1.9  2  HTH_32         Homeodomain-like domain
       0.15   11.4   0.0       0.21   11.0   0.0    1.2  1  TatD_DNase     TatD related DNase


Domain annotation for each model (and alignments):
>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     2e-06    0.0051       5      74 ..      17      84 ..      13      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                                      CHHHHHHHHHHHHHHHSS.SBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS CS
                               FUR  5 klTkqRekilevleksee.hlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelak 74
                                        T + e++++++ +s+  ++s  +++ ++k   pe+s aTV + L+ l+ +++v + ++ d+ + y++++
  gi|313116925|ref|YP_004038049.1| 17 DNTLSQEHVVKTMIESDRpFFSLRQLHARIK---PEVSRATVRNRLQELQTIDVVATETYPDSITLYYINH 84
                                      56888999*******************9996...78*********************99999999999986 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.2e-06    0.0082       9      75 ..      36     107 ..      29     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.2e-06
                      Replic_Relax   9 vlTtrqiarllfashra.tarrrLarLrelgllsr.lrkr.vggarggsepyvYaLtpkGarllaaqra..e 75 
                                       + + rq+++ + +++++ t+r+rL++L+  +++++ +++  ++       +  + L p G+r+l+++ +  +
  gi|313116925|ref|YP_004038049.1|  36 FFSLRQLHARIKPEVSRaTVRNRLQELQTIDVVATeTYPDsITLYYINHPESDWPLSPEGKRALHTDTPldR 107
                                       56779*****************************9966650555555667788***********66654331 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     1e-05     0.027      47      83 ..      29      65 ..       8      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                                      HHHHH-TTS-HHHHHHTT..T--HHHHHHHHHHHHHH CS
                          HTH_WhiA 47 elRlenpdaSLkeLgelleppisKSgvnhrlrklkel 83
                                       +  + p +SL++L   ++p++s+ +v +rl+ l+++
  gi|313116925|ref|YP_004038049.1| 29 MIESDRPFFSLRQLHARIKPEVSRATVRNRLQELQTI 65
                                      55668899*************************9986 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.3e-05     0.033      10      42 ..      33      62 ..      27      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                     HTH_Tnp_Tc3_2 10 kdPritlreLanelkeeGksvsreTirrrLrka 42
                                       +P+ +lr+L +++     +vsr+T+r+rL++ 
  gi|313116925|ref|YP_004038049.1| 33 DRPFFSLRQLHARI---KPEVSRATVRNRLQEL 62
                                      57999*********...*************985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.8e-05     0.046       5      41 ..      25      64 ..      22      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                            HTH_11  5 ilelLleargp.isgeeLAeeL..nvSrrtvrrdIkaLee 41
                                      +++  +e++ p +s  +L  ++  +vSr+tvr+++++L++
  gi|313116925|ref|YP_004038049.1| 25 VVKTMIESDRPfFSLRQLHARIkpEVSRATVRNRLQELQT 64
                                      5555566666668888888887557*************97 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.5e-05      0.09      33      73 .]      22      59 ..       8      59 .. 0.82
   2 ?   -2.2   0.0       2.6   6.6e+03      50      59 ..     177     186 ..     170     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                            HTH_32 33 vrariiallre.eprWsprqlaarlaeregvkvShstvyriL 73
                                      +++ ++ ++++ +p +s+rql+ar+ + e   vS+ tv++ L
  gi|313116925|ref|YP_004038049.1| 22 QEHVVKTMIESdRPFFSLRQLHARI-KPE---VSRATVRNRL 59
                                      56667777765468***********.666...******9866 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                            HTH_32  50 rqlaarlaer 59 
                                       ++la+++++r
  gi|313116925|ref|YP_004038049.1| 177 ERLARWVRDR 186
                                       3455555333 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     8e-05      0.21     176     236 ..       4      64 ..       1      80 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8e-05
                                       E-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHH.HHHHHT CS
                        TatD_DNase 176 lsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvvek.laelka 236
                                       l+ ++  + +++l++++ + +  + +iE+D P+++  +  ++r +p+  +++v+  l el  
  gi|313116925|ref|YP_004038049.1|   4 LPSWIDERIDRNLDNTLSQEHVVKTMIESDRPFFSL-RQLHARIKPEVSRATVRNrLQELQT 64 
                                       5667777778999***********************.6667999999888887641444544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1596.13
//
Query:       gi|313116926|ref|YP_004038050.1|  [L=279]
Description: hypothetical protein Hbor_33910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-07   31.7   3.9    1.3e-07   31.7   3.9    2.8  2  DUF4870    Domain of unknown function (DUF4870)
  ------ inclusion threshold ------
      0.065   13.3   0.1         16    5.6   0.0    2.3  2  TetR_C_29  Tetracyclin repressor-like, C-terminal domain
       0.66   10.2   4.9        4.5    7.5   4.4    2.4  1  DUF4293    Domain of unknown function (DUF4293)


Domain annotation for each model (and alignments):
>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   3.9   2.2e-11   1.3e-07       7     109 ..      24     142 ..      19     143 .. 0.81
   2 ?   -4.6   7.3         3   1.8e+04      82      88 ..     191     197 ..     156     274 .. 0.55

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.2e-11
                           DUF4870   7 lihlsalsklliplgniilPlviwllkkdksefvdeqgkealNFqislliysiilivlsllvli............. 70 
                                       l+hl+++     p  +++++ +++l+  ++  f ++++++al +++ +l ++++ +  ++++               
  gi|313116926|ref|YP_004038050.1|  24 LVHLLSI-----PT-GVVGAGIVYLVATNE--FTKRNARNALDWHLAVLALTVLTFSSVFTF-Aeltgqgitngitl 91 
                                       4555555.....65.9**************..****************99887777763333.3589********** PP

                           DUF4870  71 ..........gfll....lllllllllnlvlviiaaikanegeeyrypltirf 109
                                                    +    l+++++  + + +  ia+ ka  g  +ryplt  +
  gi|313116926|ref|YP_004038050.1|  92 sepiaaggsfV--IsalfLVWMIITTCTFLVGFIATGKAIFGDAWRYPLTPAL 142
                                       **999987441..233348889999999999******************9765 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 3
                           DUF4870  82 llnlvlv 88 
                                       l+ l+lv
  gi|313116926|ref|YP_004038050.1| 191 LFGLILV 197
                                       2222222 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0027        16      71     103 ..      54      86 ..      44      93 .. 0.88
   2 ?    5.5   0.0    0.0029        18      71     101 ..     103     133 ..      97     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0027
                                       --HHHHHHHHHHHHHHHHHTHHHHHHHH---TT CS
                         TetR_C_29  71 vdaldlyllisslcffrvsnrhtlsalfgrdls 103
                                        +ald +l++ +l++  +s   t+ +l g+ ++
  gi|313116926|ref|YP_004038050.1|  54 RNALDWHLAVLALTVLTFSSVFTFAELTGQGIT 86 
                                       5799**********************9998766 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0029
                                       --HHHHHHHHHHHHHHHHHTHHHHHHHH--- CS
                         TetR_C_29  71 vdaldlyllisslcffrvsnrhtlsalfgrd 101
                                       ++al l+++i+  c+f v   +t +a+fg  
  gi|313116926|ref|YP_004038050.1| 103 ISALFLVWMIITTCTFLVGFIATGKAIFGDA 133
                                       78999***********************975 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.4   0.00074       4.5      45     114 ..     179     251 ..      59     274 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00074
                           DUF4293  45 eaetsvnvsvwvlvilllliailaliaIflyknRklQlrlcl.inllllvllyvllal..lllvnkanaaaes 114
                                       +++  ++ +v++l+ l l+ + l+ +a+ l+ +R  Q    +   +   ++  vl+a+  ++l  + + + ++
  gi|313116926|ref|YP_004038050.1| 179 HEGAAFFATVFGLFGLILVLTPLTGVAMYLHAKRASQTDTAWePHTAAYIGAPVLVAVlaYALSGAFTDSINP 251
                                       66677899999**************************998851333344444444333234444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1927.24
//
Query:       gi|313116927|ref|YP_004038051.1|  [L=105]
Description: hypothetical protein Hbor_33930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 823.66
//
Query:       gi|313116928|ref|YP_004038052.1|  [L=888]
Description: copper/silver-translocating P-type ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-49  166.9   1.1    6.9e-49  165.8   1.1    1.6  1  E1-E2_ATPase   E1-E2 ATPase
    1.1e-48  166.3   5.1    2.8e-48  165.0   5.1    1.6  1  Hydrolase      haloacid dehalogenase-like hydrolase
    4.1e-29  100.8   1.1    1.4e-13   51.1   0.0    3.3  3  HMA            Heavy-metal-associated domain
    7.7e-07   29.1   2.4     0.0016   18.2   0.6    3.0  3  Hydrolase_3    haloacid dehalogenase-like hydrolase
     0.0007   19.7   0.6      0.012   15.8   0.0    3.2  5  Hydrolase_6    Haloacid dehalogenase-like hydrolase
     0.0011   19.4   0.5     0.0033   17.8   0.2    2.0  2  HAD            haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.095   12.8   0.4         30    4.8   0.0    3.2  3  Thioredoxin_3  Thioredoxin domain
       0.13   12.5   0.1       0.33   11.2   0.1    1.6  1  Yippee-Mis18   Yippee zinc-binding/DNA-binding /Mis18, centro
       0.26   11.7   1.9          2    8.8   0.1    2.9  3  Fer2_BFD       BFD-like [2Fe-2S] binding domain
       0.69   10.0   3.1       0.49   10.5   0.6    1.9  2  4_1_CTD        4.1 protein C-terminal domain (CTD)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.8   1.1   3.9e-52   6.9e-49       2     179 ..     299     500 ..     298     502 .. 0.94

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 3.9e-52
                                       SS--EEEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEE CS
                      E1-E2_ATPase   2 llpptakvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvv 77 
                                       ++++ta+++  dgte+e++++++++GD  ++++g+++p+Dg++v+g++ vdes++TGEs+pvek++gd+v + t++ 
  gi|313116928|ref|YP_004038052.1| 299 MEADTATLVaDDGTEREVPIEDVEVGDWMKVRPGEQIPTDGVVVDGQSAVDESMVTGESVPVEKTEGDEVVGATINE 375
                                       677889999899***************************************************************** PP

                                       E-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT......... CS
                      E1-E2_ATPase  78 sgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla......... 145
                                       +g +++++t++gedt l++i++ v+ea+s+++++q+ +d++++++vp+v+l al+  +++++   +la         
  gi|313116928|ref|YP_004038052.1| 376 NGVLVVEATNVGEDTALQQIVQTVKEAQSRQPDIQNLADRISAYFVPAVILNALFWGVVWYFFPVTLAefvgslplw 452
                                       **************************************************************666666777777778 PP

                                       ..............HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 146 ..............eallralallvaaiPcaLplavplalalgarrla 179
                                                     +a++ + + +++a+PcaL+la+p a+++g++  a
  gi|313116928|ref|YP_004038052.1| 453 glvgggpaalsafeFAVVVFASSVLIACPCALGLATPAATMVGTTIGA 500
                                       888888889*999999999999999******************98766 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.0   5.1   1.6e-51   2.8e-48       1     209 [.     518     782 ..     518     782 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.0 bits;  conditional E-value: 1.6e-51
                                       SSEEEEESBTTTBCHHHHHHHHHHHH..................................CHHHHHHHHHHHHCHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..................................xxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa..................................alalaaaletgsehpig 43 
                                       ++tvvfDk+GTLt+ge+s++dv++                                     l laaa e gsehp++
  gi|313116928|ref|YP_004038052.1| 518 VDTVVFDKTGTLTKGEMSLTDVVAFGdsgtaltdggshspsdlasdggaitarerpredeVLRLAAAAESGSEHPLA 594
                                       68*************************************************************************** PP

                                       HHHHHHHHHHHHHH...HHHHHETTTE........HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH..... CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxx........xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..... RF
                         Hydrolase  44 kalvaaakarsgal...tgfatfigrg........ayaigkpewltal.dippdlgaaigsaqsqgrtvall..... 103
                                       +a+v+ a++r+ a+   t+f+ ++g+g         +++g++++l++    p+   ++++ ++s+g+t++l+     
  gi|313116928|ref|YP_004038052.1| 595 RAIVEGAQERGLAVpdaTSFENVPGQGvratvegtDVLVGNRKLLRDAgIDPEPAAETMERLESEGKTAMLVarvrg 671
                                       **********7777777*******************************98899999********************* PP

                                       ...............TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEE CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 104 ...............qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdavia 165
                                                       +++l+v++ ad+  vk+ a++av +L+++g ev ++tgdn++ta+++a+q+G         
  gi|313116928|ref|YP_004038052.1| 672 sersanrdasaetprAGELLGVVADADT--VKESAKDAVSTLRDRGAEVMMITGDNSRTARAVAEQVG--------- 737
                                       *********99999999***********..**************************************......... PP

                                       HHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 166 sdiet...vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                         i+     a+++pe+k  a++ +q+++++ +mVGDgvnDa+ala A
  gi|313116928|ref|YP_004038052.1| 738 --IDPenvRAEVLPEDKSDAVEDIQADGRKAMMVGDGVNDAPALAVA 782
                                       ..444469************************************987 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   7.7e-17   1.4e-13       2      61 ..       8      67 ..       7      68 .. 0.97
   2 !   47.1   0.0   1.4e-15   2.5e-12       4      61 ..      78     135 ..      75     136 .. 0.93
   3 ?   -2.9   0.2       5.4   9.6e+03      34      59 ..     375     402 ..     371     403 .. 0.72

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 7.7e-17
                               HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61
                                      ++++gm Ca+C+++v +++++++gV++++v++at++ tVe+d+e+++l ++  ai++agy
  gi|313116928|ref|YP_004038052.1|  8 IDIQGMSCANCSQTVADAVESVDGVSEANVNFATDEGTVEYDPEQVSLGAVYDAIDDAGY 67
                                      789********************************************************9 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 1.4e-15
                               HMA   4 vsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                       + +m Ca+C+ +v+++L++ pgV s++v++at++++V++++++++  ++  aie+agy
  gi|313116928|ref|YP_004038052.1|  78 ITDMSCANCSETVQEALESTPGVVSADVNFATDEAQVTYNPAEASRPDFYSAIEDAGY 135
                                       679************************************999977788*********9 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.4
                               HMA  34 atktvtVeg..daestklrkiieaieka 59 
                                       +++ ++Ve   + e+t l +i++++++a
  gi|313116928|ref|YP_004038052.1| 375 ENGVLVVEAtnVGEDTALQQIVQTVKEA 402
                                       5677888888655556678899999875 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.3   2.4e+03     201     212 ..     534     545 ..     529     546 .. 0.86
   2 !    9.0   0.0    0.0006       1.1      12      55 ..     696     739 ..     692     746 .. 0.91
   3 !   18.2   0.6   9.2e-07    0.0016     197     242 ..     757     802 ..     751     813 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                                       --GGGEEEEESS CS
                       Hydrolase_3 201 isleeviafGDg 212
                                       +sl +v+afGD+
  gi|313116928|ref|YP_004038052.1| 534 MSLTDVVAFGDS 545
                                       7899*******7 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0006
                                       TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  12 sdkkisektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       +  +++e++k+a+  l+++g +v+  TG + r+++ v+e++g+d
  gi|313116928|ref|YP_004038052.1| 696 DADTVKESAKDAVSTLRDRGAEVMMITGDNSRTARAVAEQVGID 739
                                       567899************************************98 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 9.2e-07
                                       HHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEE CS
                       Hydrolase_3 197 kelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyv 242
                                       + ++ +  + + +GDg ND + L +a +g+A+g++++ +++aAd +
  gi|313116928|ref|YP_004038052.1| 757 EDIQADGRKAMMVGDGVNDAPALAVAYVGCAIGSGTDVAIEAADVT 802
                                       56778999***********************************986 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.3   9.5e+03       6      17 ..     338     349 ..     337     351 .. 0.86
   2 ?   -1.4   0.0       1.5   2.7e+03       6      21 ..     502     517 ..     501     521 .. 0.90
   3 ?   -2.1   0.0       2.4   4.4e+03       1      19 [.     521     539 ..     521     542 .. 0.83
   4 ?   -3.4   0.0       6.2   1.1e+04      19      36 ..     649     666 ..     647     668 .. 0.87
   5 !   15.8   0.0   6.5e-06     0.012       7      51 ..     692     736 ..     689     745 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.3
                                       TTTSEETTEE-T CS
                       Hydrolase_6   6 dGvLwrgdkaip 17 
                                       dGv+++g++a++
  gi|313116928|ref|YP_004038052.1| 338 DGVVVDGQSAVD 349
                                       9******99987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                                       TTTSEETTEE-TTHHH CS
                       Hydrolase_6   6 dGvLwrgdkaipgaae 21 
                                        GvL +g+++++ a++
  gi|313116928|ref|YP_004038052.1| 502 NGVLFKGGDVLERAKD 517
                                       6***********9997 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.4
                                       EEEESTTTSEETTEE-TTH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipga 19 
                                       ++fD  G+L +g+  +  +
  gi|313116928|ref|YP_004038052.1| 521 VVFDKTGTLTKGEMSLTDV 539
                                       69*********99877666 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHTT-EEEEE CS
                       Hydrolase_6  19 aaealnalraagkpvvll 36 
                                       aae++++l+++gk+ +l+
  gi|313116928|ref|YP_004038052.1| 649 AAETMERLESEGKTAMLV 666
                                       89999******9998886 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 6.5e-06
                                       TTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                       Hydrolase_6   7 GvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                       Gv+ + d++ + a++a+ +lr++g +v+++T  +s++ +++a+++
  gi|313116928|ref|YP_004038052.1| 692 GVVADADTVKESAKDAVSTLRDRGAEVMMITGDNSRTARAVAEQV 736
                                       9****************************************9986 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.6   4.7e+03     174     180 ..     539     545 ..     521     601 .. 0.61
   2 !   17.8   0.2   1.9e-06    0.0033      78     187 ..     695     779 ..     630     780 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                               HAD 174 vvayGDs 180
                                       vva+GDs
  gi|313116928|ref|YP_004038052.1| 539 VVAFGDS 545
                                       3333333 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.9e-06
                               HAD  78 aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegk 154
                                       a++    + ++ a+++++  r++G +v +++g +++ ++++++++g    ++ e      + +e       v  e+k
  gi|313116928|ref|YP_004038052.1| 695 ADAD---TVKESAKDAVSTLRDRGAEVMMITGDNSRTARAVAEQVG----IDPE-----NVRAE-------VLPEDK 752
                                       2222...467899*****999*************************....8885.....66666.......666667 PP

                               HAD 155 vaalrewlaaegegidleevvayGDspsDlpll 187
                                        +a+++        +d  + + +GD+++D p+l
  gi|313116928|ref|YP_004038052.1| 753 SDAVED------IQADGRKAMMVGDGVNDAPAL 779
                                       777777......555667799**********98 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.017        30       2      22 ..       7      28 ..       6      49 .. 0.77
   2 ?    4.3   0.1     0.022        40       3      39 ..      76     111 ..      74     117 .. 0.69
   3 ?   -2.4   0.0       2.8   4.9e+03      38      56 ..     408     427 ..     397     434 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.017
                                      EEEEESSSSTTCH.HHHHHHHH CS
                     Thioredoxin_3  2 eikvlgpgCakCp.klekavke 22
                                      +i + g +Ca+C  +++ av++
  gi|313116928|ref|YP_004038052.1|  7 RIDIQGMSCANCSqTVADAVES 28
                                      588999*******555556654 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.022
                                       EEEESSSSTTCHHHHHHHHHHCHCC.T.CECEEECCTTH CS
                     Thioredoxin_3   3 ikvlgpgCakCpklekavkeaaaek.g.ikaevekvtdf 39 
                                       i + + +Ca+C    + v+ea+++  g ++a+v  +td 
  gi|313116928|ref|YP_004038052.1|  76 IGITDMSCANCS---ETVQEALESTpGvVSADVNFATDE 111
                                       566778999999...666777776666677777766665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.8
                                       THHHH.HHCT-SSSSEEECT CS
                     Thioredoxin_3  38 dfeei.ekygVmsvPalvid 56 
                                       d++++ ++   + vPa++++
  gi|313116928|ref|YP_004038052.1| 408 DIQNLaDRISAYFVPAVILN 427
                                       6777778888899****998 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018      0.33       4      73 ..      14      98 ..      12     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                      EETTTS-EEEECCCEEE..EECC...............CEEEES---CCCEEEECEEEETTSTTEEEEEEEETTT--EE CS
                      Yippee-Mis18  4 qCkkCktilgdslqlvs..egra...............lnivvlkkvtrnvvvgkelvtdeegkctystlsCkgCnsvl 65
                                      +C++C++ ++d+++ v+  +  +               ++ v l +v +++     + + e+++  ++ +sC++C++++
  gi|313116928|ref|YP_004038052.1| 14 SCANCSQTVADAVESVDgvS--EanvnfatdegtveydPEQVSLGAVYDAIDDAGYSPVAETTTIGITDMSCANCSETV 90
                                      7****************651..44567777778888889999999999999998888888777899***********99 PP

                                      EEEEEECS CS
                      Yippee-Mis18 66 GwkYkste 73
                                         ++st+
  gi|313116928|ref|YP_004038052.1| 91 QEALESTP 98
                                      88887776 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.35   6.3e+02      35      49 ..      12      26 ..      10      28 .. 0.85
   2 ?    8.8   0.1    0.0011         2       7      50 ..      52      95 ..      51      96 .. 0.93
   3 ?   -2.7   0.0       4.5   8.1e+03      12      30 ..     810     827 ..     810     831 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.35
                          Fer2_BFD 35 gtgCggCrpaieeiL 49
                                      g+ C+ C + +++ +
  gi|313116928|ref|YP_004038052.1| 12 GMSCANCSQTVADAV 26
                                      899******998765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                          Fer2_BFD  7 gvtegeIrdairraglttveevkrrtkagtgCggCrpaieeiLa 50
                                      +v+ g + dai  ag + v+e +    + + C+ C + ++e L+
  gi|313116928|ref|YP_004038052.1| 52 QVSLGAVYDAIDDAGYSPVAETTTIGITDMSCANCSETVQEALE 95
                                      79999******9999**************************997 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.5
                          Fer2_BFD  12 eIrdairraglttveevkr 30 
                                       +I++ai r    t++ +k+
  gi|313116928|ref|YP_004038052.1| 810 DIVKAI-RISEGTLAKIKQ 827
                                       699999.633477777775 PP

>> 4_1_CTD  4.1 protein C-terminal domain (CTD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.5   4.6e+03      45      64 ..      73      92 ..      68      94 .. 0.79
   2 ?   10.5   0.6   0.00027      0.49      27      96 ..     337     410 ..     328     413 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.5
                           4_1_CTD 45 tTtThitKtvkggisETriE 64
                                      tTt  it +   ++sET  E
  gi|313116928|ref|YP_004038052.1| 73 TTTIGITDMSCANCSETVQE 92
                                      566679*9999999*99765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00027
                           4_1_CTD  27 dpgvlvsaqtitsetesttTtThitKtvkggisETri.EkrivitgdadiDhdka...LaqaikeakeqnPdls 96 
                                       ++gv+v  q+   e+  t     + Kt+ ++++   i E  + + + +++  d a   + q++kea+  +Pd++
  gi|313116928|ref|YP_004038052.1| 337 TDGVVVDGQSAVDESMVTGESVPVEKTEGDEVVGATInENGVLVVEATNVGEDTAlqqIVQTVKEAQSRQPDIQ 410
                                       579999***********999999********998777366787888888999998333456889999999*985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (888 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 5989.58
//
Query:       gi|313116929|ref|YP_004038053.1|  [L=396]
Description: amidohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-17   64.2   0.1    1.2e-15   57.7   0.1    2.4  1  Amidohydro_1  Amidohydrolase family
    6.8e-17   62.1   8.7      4e-12   46.4   0.1    3.0  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.1   1.3e-19   1.2e-15       2     342 ..      51     378 ..      51     380 .. 0.64

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.3e-19
                                       EEE-EEEEEEECETTECSSSGHHHHH.........................STTHHHHHHHHHHHHHH.HHTTEEEE CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwl.........................vppetaaealesgikta.lksGtttv 52 
                                       v+PGl+DaH H+ + +        w                            +e++++a+++g++t   + G + v
  gi|313116929|ref|YP_004038053.1|  51 VTPGLVDAHSHAGMAE--------WGepedgdinegtdpvtphvnaldgfhPRDEELKYAFQNGVTTVsARMGSGNV 119
                                       79**********8774........44555555556668888888888888866666677777776665245565555 PP

                                       EEEEHSSTH....HHHHHHHHHHTSSSEEEEEEESSEGGS.......GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE CS
                      Amidohydro_1  53 admgattst....giealleaaeelplglrilggkvsldr.......gsaetskasreklkagaaetikgkadgvvk 118
                                        +  +        g+ a +  ++e   g+ +  g  +++r       +++ t++ ++ +l++  ++++   a+    
  gi|313116929|ref|YP_004038053.1| 120 VGGVIC--SmktyGDVADRMLVRED--GMKAAMG-ENPKRfhgeqkdRQPATRPGVAATLRQALMDAEDYVAKREKA 191
                                       555443..23355666666666665..5555555.455557877777777777777777777776666544444444 PP

                                       EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEH CS
                      Amidohydro_1 119 valapheapafsdeelkealkeakkrdlpvaiHa..letkgevedaeaafgetiehgthlevaeslglldeiklila 193
                                       v+ +++++  ++ e l+ ++    + dlp+ +Ha  +++  +v+ + ++fg + ++    e a +++      li++
  gi|313116929|ref|YP_004038053.1| 192 VEDGEPFDRDLGLENLARVV----EGDLPLRVHAhrADDIMTVFRIAEEFGIDNIS---IEHATEGH------LIAE 255
                                       66666666666666666666....45777777775588888888888888855444...33333333......4444 PP

                                       CTCEEE.HHHHHHHHHHHHHHCEE...HHHHHHHHSEHHHHHHHHHHHH.TSCEEEEEECT....TSSCCGGHHHHH CS
                      Amidohydro_1 194 hgvhlt.pteaellkerlkeagva...hcpfsnsilrsgrealrkalde.GvkvglgtDga....asgnslnlleel 261
                                         v  + p+             v+   ++  +   lr  ++     l+e Gv+v++ tD       + +++     +
  gi|313116929|ref|YP_004038053.1| 256 EFVERDiPA-------------VCgpsLYSGAKYELRNITFETPGILHEaGVNVAIQTDAPvlpqRHLDVC-----V 314
                                       433333322.............2222233333334788888888999999*********436444333444.....6 PP

                                       HHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEE CS
                      Amidohydro_1 262 rlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvi 338
                                        la+           + gl+ + al+++T n+A++lg++d+vG++++G dAD+vv+d+       +   d + ++v+
  gi|313116929|ref|YP_004038053.1| 315 GLAV-----------REGLPEAAALDVVTRNPAEILGIEDRVGTLAEGTDADIVVWDGP------FYQFDTSAQHVF 374
                                       7777...........999**************************************873......334455566666 PP

                                       ETTE CS
                      Amidohydro_1 339 vkGk 342
                                       v+G+
  gi|313116929|ref|YP_004038053.1| 375 VDGE 378
                                       6665 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   4.8   1.4e-06     0.012       2     209 ..      43     222 ..      42     238 .. 0.62
   2 !   46.4   0.1   4.5e-16     4e-12     364     473 .]     290     381 ..     275     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-06
                      Amidohydro_3   2 viDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfpy 78 
                                       +iD +G+ v+PG+vD+H+H   +g    ++ +++++  ++++ ++ v  +++                    +r+  
  gi|313116929|ref|YP_004038053.1|  43 EIDVDGAPVTPGLVDAHSH---AG----MAEWGEPEDGDINEGTDPVTPHVNA--------------LDGFHPRD-- 96 
                                       79*****************...44....5566666667776666665555543..............23333333.. PP

                      Amidohydro_3  79 alaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlaplar 155
                                          el+ +++++   ++a+ + + v+  ++  +    ++  d a + ++r++  + a+g    +++   +d +p++r
  gi|313116929|ref|YP_004038053.1|  97 --EELKYAFQNGVTTVSARMGSGNVVGGVICSM----KTYGDVADRMLVREDGMKAAMGENPKRFHGEQKDRQPATR 167
                                       ..4677777777777777777777777777777....2222222233333332222555555444444455567777 PP

                      Amidohydro_3 156 eaeaaavaaalaalasyGitsv..eagggnvsslddleplfeltaeeklplrviik 209
                                          aa +++al +++ y+ ++   + +g++ + +  le l+++ + + lplrv+ +
  gi|313116929|ref|YP_004038053.1| 168 PGVAATLRQALMDAEDYVAKREkaVEDGEPFDRDLGLENLARVVEGD-LPLRVHAH 222
                                       77777777777777777777777766666666666777777777776.77777744 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 4.5e-16
                      Amidohydro_3 364 lnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadA 440
                                        +agv+va  +D   +p+ p  ++  +v +  r         e l+  +al+ +Tr+pA++lg edr GtL++G dA
  gi|313116929|ref|YP_004038053.1| 290 HEAGVNVAIQTD---APVLPQRHLDVCVGLAVR---------EGLPEAAALDVVTRNPAEILGIEDRVGTLAEGTDA 354
                                       678999999999...888888888888887774.........67999****************************** PP

                      Amidohydro_3 441 DlvvldadpldvdppelaearvrltvvdGrvvy 473
                                       D+vv+d    ++d++      + ++ vdG+ v+
  gi|313116929|ref|YP_004038053.1| 355 DIVVWDGPFYQFDTS------AQHVFVDGEHVF 381
                                       **************9......9*******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2719.20
//
Query:       gi|313116930|ref|YP_004038054.1|  [L=232]
Description: outer membrane lipoprotein-sorting protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-05   22.7   0.1    0.00011   21.9   0.1    1.4  1  MucB_RseB  MucB/RseB N-terminal domain
    0.00022   21.1   0.6    0.00041   20.1   0.0    1.7  2  LolA_like  Outer membrane lipoprotein-sorting protein


Domain annotation for each model (and alignments):
>> MucB_RseB  MucB/RseB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.2e-08   0.00011      17     172 ..      52     216 ..      44     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-08
                         MucB_RseB  17 nYegtfvyqrggeleslrivHavddgg.eyerlesLdGpprevirrndevscfepeskavsvesrkikdslpallpa 92 
                                        Ye t++   + + ++++++  v  ++ e +r+e+ +Gp+  ++ + d  s  +p++ + s++ + ++d+      a
  gi|313116930|ref|YP_004038054.1|  52 RYEATVTKTVQTTSDTSSVRATVSVDTaESARIEYHTGPRAGTVANIDL-SSASPARPSLSTSVQSATDGQVPTYGA 127
                                       5999999999999999999999976666***********9999987765.556999999999999999999999999 PP

                         MucB_RseB  93 dlealeehYefrllGreRvAgreaqvvrilPkDqlRYg......yrlwiDeetgLlLksdll..dedge.vLEqfaf 160
                                         ++l ++ +++++  +   gr++ vv ++P+ +   g       r+w+D+e  ++L+++++  +e+ge v E ++ 
  gi|313116930|ref|YP_004038054.1| 128 LASELVRSNNVTVERTTVLDGRQTAVVSLVPNADETNGtavsveRRVWVDTERLIPLRIETTwtGESGEtVTETVRY 204
                                       999**9**9**997778889***********977655422222279**************998855555489***** PP

                         MucB_RseB 161 tslelgeeleka 172
                                       t+++l+ee e++
  gi|313116930|ref|YP_004038054.1| 205 TNVTLSEERENT 216
                                       *****9965544 PP

>> LolA_like  Outer membrane lipoprotein-sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.25   2.2e+03     141     164 ..      50      73 ..      33      86 .. 0.53
   2 !   20.1   0.0   4.6e-08   0.00041      54     120 ..     120     189 ..     107     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.25
                                       EEEEEEEEEEETTT--EEEEEEEE CS
                         LolA_like 141 rwtptkmtmedlkkghkTvleise 164
                                       + + + ++++ +++ + T  +   
  gi|313116930|ref|YP_004038054.1|  50 IDRYEATVTKTVQTTSDTSSVRAT 73 
                                       333333333334444444333333 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 4.6e-08
                                       TTC.EHHHHC--SCCCEEEEEEEEEEETTEEEEEEEEEESS....TTSSECEEEEEEETTT--EEEEEEE CS
                         LolA_like  54 GsdfsyeDlssrevedythellgeeevggkdcyvleltpkd...aadvsYskivlwvdketylplkvefy 120
                                       G+  +y+ l+s+ v+  ++++++++ ++g+++ v+ l+p+    +  +   ++++wvd+e+++pl++e  
  gi|313116930|ref|YP_004038054.1| 120 GQVPTYGALASELVRSNNVTVERTTVLDGRQTAVVSLVPNAdetNGTAVSVERRVWVDTERLIPLRIETT 189
                                       667789999999****************************96654455677999*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1558.18
//
Query:       gi|313116931|ref|YP_004038055.1|  [L=304]
Description: ClpP class periplasmic serine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-21   75.4   1.0    4.3e-12   46.2   1.0    2.4  2  Peptidase_S49  Peptidase family S49
    1.6e-08   34.6   0.2    5.6e-08   32.9   0.2    2.0  1  CLP_protease   Clp protease
    2.5e-05   23.4   0.1    3.6e-05   22.9   0.1    1.2  1  SDH_sah        Serine dehydrogenase proteinase
    0.00024   20.5   0.4       0.12   11.7   0.4    2.3  1  ECH_1          Enoyl-CoA hydratase/isomerase
     0.0041   16.9   0.1      0.014   15.2   0.1    1.9  2  Ligase_CoA     CoA-ligase
  ------ inclusion threshold ------
        0.1   12.9   0.0       0.19   12.0   0.0    1.4  1  OKR_DC_1_N     Orn/Lys/Arg decarboxylase, N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   1.0   1.4e-15   4.3e-12       2      46 ..      98     142 ..      97     146 .. 0.94
   2 !   26.6   0.0   1.6e-09   4.7e-06      86     153 ..     167     235 ..     156     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.4e-15
                                       HHHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEE CS
                     Peptidase_S49   2 akkakkPvvasaenvaaSggYylasaadkivanpstivgsiGvit 46 
                                       + ++++Pvv+s+ ++aaSggYy+ + ad+++++p++ vgs+Gv +
  gi|313116931|ref|YP_004038055.1|  98 RTQQEMPVVVSVTGMAASGGYYMTAPADEVYVTPASTVGSVGVRA 142
                                       5789***************************************76 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1.6e-09
                                       HHHHHHHHHHHHHHHHHHHHHHTS-HHHH.HCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCHC CS
                     Peptidase_S49  86 eilqrlldetyqqFvqtVaknRnlsveqv.dkiAegrvltgqqAlklgLvdelgtvddavaeleelakv 153
                                       + ++r++++++  Fv +V ++R+ s + + +++  ++v++g+ ++klgL+d++g++d+a++ +++ a++
  gi|313116931|ref|YP_004038055.1| 167 AEVRRRVEALRRAFVGSVMEERSESLKLTeEELSYAKVYSGARGVKLGLADSIGGIDTAIQGAADRAGL 235
                                       668999****************86555442568888**************************9998876 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.2   1.9e-11   5.6e-08      19     107 ..      45     133 ..      41     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.9e-11
                                       EEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS..SS-EEEEEEEEEETHHHHHH CS
                      CLP_protease  19 iflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi..kpdvsticlGlaaSmgslll 93 
                                       + + + i+ ++a+++i +L  + ++d+++ ++l inspGG  +a+  +y +++    + +v++ ++G+aaS g  + 
  gi|313116931|ref|YP_004038055.1|  45 VEMHGTITGDSATEVIDNLREARQNDSIRAVVLDINSPGGAASASEQLYLAVKRTqqEMPVVVSVTGMAASGGYYMT 121
                                       677889999*******************************************99844567888899*******9999 PP

                                       HTS-TTGEEEETTE CS
                      CLP_protease  94 aagekgkRfalpna 107
                                       a +++   +++p +
  gi|313116931|ref|YP_004038055.1| 122 APADEV--YVTPAS 133
                                       988877..666665 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   1.2e-08   3.6e-05      73     156 ..      51     139 ..      42     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.2e-08
                           SDH_sah  73 itiedseevlrairltpkd...kpidliihtpGGlvlaatqiakalkehkaktrviv..phyamsGGtlialaadei 144
                                       it + + ev+  +r + ++   + + l i +pGG + a++q+  a+k  + ++ v+v     a sGG  ++  ade+
  gi|313116931|ref|YP_004038055.1|  51 ITGDSATEVIDNLREARQNdsiRAVVLDINSPGGAASASEQLYLAVKRTQQEMPVVVsvTGMAASGGYYMTAPADEV 127
                                       555666677766666665511145567799****************9988887777611567889************ PP

                           SDH_sah 145 ildenavlGpvd 156
                                        + + + +G v 
  gi|313116931|ref|YP_004038055.1| 128 YVTPASTVGSVG 139
                                       ***999999886 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.4     4e-05      0.12      78     116 ..      92     130 ..      40     142 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4e-05
                                       HHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEE CS
                             ECH_1  78 lelwtklytvpkpviaavnGaaigGGlelalacDiviaa 116
                                       l l  k ++ ++pv+  v G a+ GG  +   +D v++ 
  gi|313116931|ref|YP_004038055.1|  92 LYLAVKRTQQEMPVVVSVTGMAASGGYYMTAPADEVYVT 130
                                       223334467789999999999999999999999988875 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   4.7e-06     0.014      59     121 ..      57     115 ..      40     124 .. 0.90
   2 ?   -2.1   0.0      0.99     3e+03      71      94 ..     279     302 ..     268     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH CS
                        Ligase_CoA  59 tkriealkklaadpevkvilldivlGygahedpaaellkaikeakaegrelpvvarvaGtead 121
                                       t++i+ l++  +++++++++ldi    g ++   ++l  a+k+++   +e+pvv++v+G  a 
  gi|313116931|ref|YP_004038055.1|  57 TEVIDNLREARQNDSIRAVVLDINSP-GGAASASEQLYLAVKRTQ---QEMPVVVSVTGMAAS 115
                                       7899*******************998.88999999*********9...***********9887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.99
                                       -TT-SEEEEEEEESSSEHHHHHHH CS
                        Ligase_CoA  71 dpevkvilldivlGygahedpaae 94 
                                        ++v+ ++l + +G  ++e +a+e
  gi|313116931|ref|YP_004038055.1| 279 VDTVQYLMLHGSIGAPSQEVKANE 302
                                       57899999******9999998876 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.3e-05      0.19      27      70 ..      60     109 ..      51     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                        OKR_DC_1_N  27 dDllsvieqnsriaavvlsvd......deaaelldeirernedlPvFlla 70 
                                        D l  ++qn +i avvl+++       ++++l  +++++++++Pv + +
  gi|313116931|ref|YP_004038055.1|  60 IDNLREARQNDSIRAVVLDINspggaaSASEQLYLAVKRTQQEMPVVVSV 109
                                       56667789*******************999****************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1965.35
//
Query:       gi|313116932|ref|YP_004038056.1|  [L=351]
Description: hypothetical protein Hbor_33980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-05   22.7   0.0    7.4e-05   22.3   0.0    1.2  1  ABC_transp_aux  ABC-type uncharacterized transport system
     0.0011   19.3   0.2      0.011   16.1   0.0    2.5  2  DUF4350         Domain of unknown function (DUF4350)


Domain annotation for each model (and alignments):
>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   8.2e-09   7.4e-05     190     261 ..     128     205 ..      61     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.2e-09
                    ABC_transp_aux 190 lpedidvlviakptkdlseeelykldqflmnGgkllvfldpvaeeqdsls.......epsaaprtsnLedllaeyGv 259
                                       l  + d+ ++a+p ++++++e+  +++f ++Gg++l+++d  +++  s++       ++ + + t + +++  ++G+
  gi|313116932|ref|YP_004038056.1| 128 L-RNADAFIVANPASSYNNKEVNGIEAFADAGGRVLILADTATQASSSSPsiipgisSGGSISATGQPTNVAGRFGI 203
                                       5.799**************************************8884444455554444444445555555555555 PP

                    ABC_transp_aux 260 ri 261
                                       ++
  gi|313116932|ref|YP_004038056.1| 204 TF 205
                                       55 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-06     0.011      34      69 .]     130     165 ..      79     165 .. 0.84
   2 ?    0.2   0.0      0.12   1.1e+03      14      49 ..     258     294 ..     234     308 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                           DUF4350  34 edgtllvvapdlrlteeelaallewvarGntlvlaa 69 
                                         + ++v +p+ +++++e++ +++++++G++++++a
  gi|313116932|ref|YP_004038056.1| 130 NADAFIVANPASSYNNKEVNGIEAFADAGGRVLILA 165
                                       56789****************************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.12
                           DUF4350  14 LeaqGvevrrvrkpfd.alegedgtllvvapdlrlte 49 
                                       L + +v+++ +rk  + a++ +dg +l v+++  l++
  gi|313116932|ref|YP_004038056.1| 258 LTSEDVRLSSTRKGGNyAVAVRDGSVLAVGDTWFLSP 294
                                       3344445555555444344556677777776655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2317.64
//
Query:       gi|313116933|ref|YP_004038057.1|  [L=549]
Description: PAS domain S-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-53  182.2  15.5    1.7e-53  181.9  15.5    1.1  1  HisKA_7TM    N-terminal 7TM region of histidine kinase
      2e-15   57.3   0.0    3.8e-15   56.4   0.0    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    6.7e-09   36.0   0.6    5.2e-08   33.1   0.1    2.6  2  PAS_4        PAS fold
    4.6e-08   33.2   0.5    4.6e-07   30.1   0.1    2.7  2  PAS_9        PAS domain
    1.6e-06   28.1   0.0    3.2e-06   27.1   0.0    1.4  1  HATPase_c_2  Histidine kinase-like ATPase domain
    1.3e-05   25.1   0.4    7.9e-05   22.6   0.1    2.4  2  PAS_8        PAS domain
    0.00018   21.5   0.1     0.0012   18.8   0.1    2.4  2  PAS          PAS fold
     0.0024   18.0   0.9       0.75   10.0   0.0    3.1  4  PAS_7        PAS fold
      0.009   15.9   0.0      0.017   15.0   0.0    1.3  1  HATPase_c_5  GHKL domain


Domain annotation for each model (and alignments):
>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9  15.5   8.8e-57   1.7e-53       2     220 .]       2     224 ..       1     224 [. 0.94

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 8.8e-57
                         HisKA_7TM   2 llisallslvlaiyawrrrskpgaraflllllavalwslgyalellattleakllwaklqylgivfipvlwllfale 78 
                                       l++s+ +  + ai+awr+r +pga+++++lll+ ++ws++ +++l a+t++ kllwa+l ++g+v+ipv+wllf+le
  gi|313116933|ref|YP_004038057.1|   2 LFVSVAVGTAAAILAWRQRPEPGATPLVALLLGQSWWSACLIFRLRAPTVSSKLLWADLAWVGVVTIPVAWLLFSLE 78 
                                       899***************9********************************************************** PP

                         HisKA_7TM  79 ytgkrrwltrrrlallllvpvltlilvltnplhhlfy....vsagsfvvlefehGplfwvhlaysyllliagvvlli 151
                                       ytg+++++  r +++l++vp++t++lv+t ++h+l+y        + v+++ + G+++ v+++y+yll  +g++ ++
  gi|313116933|ref|YP_004038057.1|  79 YTGHDEYIHLRSVIALSAVPLVTILLVVTAQYHNLLYvrpgGVGPDGVMIVHHGGVWYRVITGYTYLLGGTGMLAVL 155
                                       ************************************987763333445555589999988***************** PP

                         HisKA_7TM 152 ralirssglyrrqalllligllvPwlanllyllglsplpgidltplafaltglllaiaifryrlldivP 220
                                       + l ++  ++r q ++ll+gll+Pwl+n+l+l++++   gid+tp++f+++g++++ ai ryrl+ + P
  gi|313116933|ref|YP_004038057.1| 156 ELLTSDAATFRSQGVALLVGLLAPWLTNALFLTDFFMPTGIDPTPISFSISGVAYLSAISRYRLFGTNP 224
                                       99999999************************8766656**************************9988 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   1.9e-18   3.8e-15       6     109 ..     441     540 ..     436     543 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.9e-18
                                       HHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                       Lr ++sn+v+Nav+++t ++++++v+++  +++++isv DnG+Gi+  +l+ + e     +s++  + g+GlGl i+
  gi|313116933|ref|YP_004038057.1| 441 LRTVLSNVVENAVEHNTsDDPHVWVRVREADQRVHISVVDNGPGIDTYELN-VLED----GSETALKHGSGLGLWIA 512
                                       99*************666999*******7558*******************.5552....33446678********* PP

                                       HHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  82 kklvelmgGeiwvesepgrGttftftlp 109
                                       k  +e  gG+i+++++   G+ +t+ +p
  gi|313116933|ref|YP_004038057.1| 513 KWGTEIAGGNISFSENNPTGSVVTVDVP 540
                                       **9999*******99999******9877 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   2.6e-11   5.2e-08       1     107 [.     235     331 ..     235     334 .. 0.87
   2 ?   -2.2   0.0       2.4   4.8e+03      48      84 ..     402     440 ..     376     450 .. 0.61

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.6e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +d+++++ +v+d++ +++++N + +++fg++ +++lG +  e++p  d+     + + +l+g+ +i +++      +
  gi|313116933|ref|YP_004038057.1| 235 FDRMQAGAIVVDTNDHIVDTNDSCEDIFGMDEQDILGAPADEIVPGYDRL----PCEGALSGHLTINDET------G 301
                                       7899***************************************9973333....3345667766666655......9 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTe 107
                                       e++y+++++P+ + +G+ ig +++++Di++
  gi|313116933|ref|YP_004038057.1| 302 EHPYDVTVTPISNVRGKSIGRVITFHDISR 331
                                       ****************************85 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.4
                             PAS_4  48 daarleralrrvlegeepiefleelll..pgeerhyelr 84 
                                       d ++l++ l+++l++ ++ + + +      g+++++ ++
  gi|313116933|ref|YP_004038057.1| 402 DSRPLSALLQQCLDSARREHPEVTFEYdpLGDDVTVAWS 440
                                       667777777777777666554444333434444444444 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   2.3e-10   4.6e-07       3     103 ..     242     330 ..     240     331 .. 0.81
   2 ?   -1.3   0.0       1.3   2.5e+03      66      66 ..     390     390 ..     344     468 .. 0.59

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.3e-10
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                       +i++d++d+ i++ N++ ++++G++++++lg + ++++  + +++   + al  +         ++ +++g + +++
  gi|313116933|ref|YP_004038057.1| 242 AIVVDTNDH-IVDTNDSCEDIFGMDEQDILGAPADEIV--PGYDRLPCEGALSGHL--------TINDETG-EHPYD 306
                                       466665666.****************************..6666666655555555........5555555.77899 PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDit 103
                                       +t++p+ +  g+ +g +++++Di+
  gi|313116933|ref|YP_004038057.1| 307 VTVTPISNVRGKSIGRVITFHDIS 330
                                       ******999**************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                             PAS_9  66 v 66 
                                        
  gi|313116933|ref|YP_004038057.1| 390 A 390
                                       1 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.6e-09   3.2e-06      30     104 ..     439     511 ..     415     515 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.6e-09
                       HATPase_c_2  30 deirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlal 104
                                       + +r +++ ++ Naveh++ ++p  +v vr++ ++++++++v D+Gpg d+ +l+  +  + ++ +  +G+Gl +
  gi|313116933|ref|YP_004038057.1| 439 WSLRTVLSNVVENAVEHNTSDDP--HVWVRVREADQRVHISVVDNGPGIDTYELNVLEDGSETALKHGSGLGLWI 511
                                       567778888899*********99..6777777****************666666666666667888999999987 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.3   2.7e+03      11      22 ..     123     137 ..     123     140 .. 0.71
   2 !   22.6   0.1     4e-08   7.9e-05       4      55 ..     231     284 ..     229     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                             PAS_8  11 pdgiavvdlgd...r 22 
                                       pdg+++v  g+   r
  gi|313116933|ref|YP_004038057.1| 123 PDGVMIVHHGGvwyR 137
                                       8*****986654555 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 4e-08
                             PAS_8   4 ra.lfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       r+ +f+ ++ g +vvd ++  ivd N++ ++++G + +d++g++ ++++p+ + l
  gi|313116933|ref|YP_004038057.1| 231 RQlIFDRMQAGAIVVDtNDH-IVDTNDSCEDIFGMDeQDILGAPADEIVPGYDRL 284
                                       5526************5555.*************445555555555777666555 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   6.3e-07    0.0012       3      57 ..     231     287 ..     229     338 .. 0.72
   2 ?   -3.1   0.0       3.8   7.5e+03      60      81 ..     407     428 ..     399     440 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.3e-07
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH..H CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda..e 57 
                                       ++ i++ + ++ +vvD +  i+ +N++ e+++G +++++lg +  + ++  d+   e
  gi|313116933|ref|YP_004038057.1| 231 RQLIFDRMQAGAIVVDTNDHIVDTNDSCEDIFGMDEQDILGAPADEIVPGYDRLpcE 287
                                       5789999**********************************9877666666655663 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.8
                                       HHHHHHHHHTT-ECCCCEEEEC CS
                               PAS  60 elleqlleqgeesrageisfkl 81 
                                       ++l+q+++++ ++++ e++f++
  gi|313116933|ref|YP_004038057.1| 407 SALLQQCLDSARREHPEVTFEY 428
                                       6788888889999999999987 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00038      0.75       2      45 ..     236     278 ..     235     287 .. 0.93
   2 ?    4.9   0.1     0.014        28      90     115 .]     312     337 ..     295     337 .. 0.79
   3 ?   -3.0   0.0       4.1   8.1e+03      47      76 ..     394     423 ..     380     430 .. 0.67
   4 ?   -2.0   0.0         2     4e+03      62      89 ..     448     475 ..     443     479 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00038
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleell 45 
                                       + m+ G +v+D ++ +v  N+ + +++++ e+ +  g+p +e++
  gi|313116933|ref|YP_004038057.1| 236 DRMQAGAIVVDTNDHIVDTNDSCEDIFGMDEQDI-LGAPADEIV 278
                                       78*****************************999.999999986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                             PAS_7  90 vrgnplpdgGfVttytDiTerrraee 115
                                       + + +    G V+t++Di+++ r+++
  gi|313116933|ref|YP_004038057.1| 312 ISNVRGKSIGRVITFHDISRHLRQQQ 337
                                       5555566789**********999875 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.1
                             PAS_7  47 ynaergefgagdveaeverrlaaaragkph 76 
                                       +n  r+ ++++  +a ++++l++ar+++p+
  gi|313116933|ref|YP_004038057.1| 394 FNGGREGHDSRPLSALLQQCLDSARREHPE 423
                                       444455555566788899999999988776 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2
                             PAS_7  62 everrlaaaragkphsfererpdgrvie 89 
                                        ve+ +++ ++++ph   r r++ + ++
  gi|313116933|ref|YP_004038057.1| 448 VVENAVEHNTSDDPHVWVRVREADQRVH 475
                                       6889999999999999999998877665 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.3e-06     0.017       6      90 ..     441     528 ..     438     537 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.3e-06
                       HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkkle..sskskkeehGiGlksire 76 
                                       l ++l+n+ +NA+e  +  ++ ++ + + vre ++ + is+  +  g    e + le  s++  k+  G+Gl   + 
  gi|313116933|ref|YP_004038057.1| 441 LRTVLSNVVENAVEHNT--SD-DPHVWVRVREADQRVHISVVDNGPGidtyELNVLEdgSETALKHGSGLGLWIAKW 514
                                       6789**********755..44.8***********9999988766555444455666633445555666666666555 PP

                       HATPase_c_5  77 ivkkykgnlsieae 90 
                                        ++  +gn+s++ +
  gi|313116933|ref|YP_004038057.1| 515 GTEIAGGNISFSEN 528
                                       56666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3671.88
//
Query:       gi|313116934|ref|YP_004038058.1|  [L=306]
Description: 4-hydroxybenzoate polyprenyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-16   60.1  22.8    1.9e-16   60.1  22.8    1.9  2  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.1    0.0018        32     187     235 ..      27      76 ..      13      82 .. 0.51
   2 !   60.1  22.8   1.1e-20   1.9e-16      27     232 ..      60     272 ..      36     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0018
                              UbiA 187 aarillalllavllla..llllllalllllylllalllaalallraarlvr 235
                                       +a++ + ++++v++++  ++++++al l++ ++ +++ ++ + ++   +++
  gi|313116934|ref|YP_004038058.1|  27 DALV-YSSIYLVFIAMveVATAMFALSLPPSPAPFVVGLVTFSVYVGDRIA 76 
                                       3333.2333333333345666666666666666666655555555444444 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 1.1e-20
                              UbiA  27 lgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllallly 103
                                       + + l+++++++ ++++Dr++D     tp+     Gr     + ++ +v++ l+++++ ++ +pl+++++ll  ++ 
  gi|313116934|ref|YP_004038058.1|  60 FVVGLVTFSVYVGDRIADRDSDEM--TTPEQSAFVGRHA-SILSVLTAVSYGLAVAIA-ITGGPLALAITLLPGAFW 132
                                       334478899999************..9999977777766.677778888999999999.****************** PP

                              UbiA 104 vvYt.........g.lrlKrrtllgtvvggiafglppllgwaa.vtgslsllalllalavflltwaialan.dlrdr 168
                                       v+Y          +  rlK++ +++  +++ a++++++l  +a +   l+++++++++  f++ + + +   ++rdr
  gi|313116934|ref|YP_004038058.1| 133 VLYAsdwlpsvggQfKRLKDILVVNSAIVAGAWAIAVVLLPVAfADAALTPTTAVVFIY-FFVDTFVNTEIpNVRDR 208
                                       ***9999999998788***************************6666668888888887.444444444447***** PP

                              UbiA 169 egDrkagiktlpvvlGrkaaril..lalllavlllallllllalllllylllalllaalallraar 232
                                       +gD+++g+ tlpvv+G +++r++  +  l ++l+ +l++++la+ll+++l +++l+++   l+ a 
  gi|313116934|ref|YP_004038058.1| 209 KGDAEIGVSTLPVVFGVRRTRQIlyA--LDLCLIGFLVTAFLAGLLSIALTVGILVGLGYALILAA 272
                                       **********************7433..33333333556777777777777766666555444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1934.21
//
Query:       gi|313116935|ref|YP_004038059.1|  [L=220]
Description: DNA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-18   66.1   0.1    2.8e-18   65.5   0.1    1.3  1  HTH_10          HTH DNA binding domain
    0.00027   20.8   0.1     0.0059   16.5   0.0    2.3  2  HTH_11          HTH domain
     0.0013   18.2   0.0     0.0026   17.3   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0066   15.9   0.1      0.013   15.0   0.1    1.5  1  Sigma70_r4      Sigma-70, region 4
      0.008   16.0   0.1       0.02   14.8   0.1    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.026   14.1   0.1       0.12   11.9   0.1    1.8  2  GerE            Bacterial regulatory proteins, luxR family
      0.061   13.0   0.3       0.17   11.5   0.0    1.9  3  Sigma70_r4_2    Sigma-70, region 4
      0.063   13.2   0.0       0.12   12.4   0.0    1.4  1  MarR            MarR family
      0.065   13.4   0.0       0.15   12.3   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
        0.1   12.4   0.1       0.48   10.2   0.1    2.0  1  LexA_DNA_bind   LexA DNA binding domain
       0.11   12.5   0.0       0.25   11.4   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.12   12.1   0.0       0.29   10.9   0.0    1.6  1  HTH_Tnp_4       Helix-turn-helix of DDE superfamily endonucle


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.1   1.8e-21   2.8e-18       1      53 []     162     214 ..     162     214 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.8e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LTd+qle+  lA++ GY++ PR++t ++LA +l++s  t+sehL+++esk+++
  gi|313116935|ref|YP_004038059.1| 162 LTDRQLEIFDLAVREGYYEIPRQTTHQDLATKLDVSTGTVSEHLQRIESKIVT 214
                                       9**************************************************85 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.18   2.6e+02      33      54 ..      51      80 ..      50      81 .. 0.88
   2 !   16.5   0.0   3.9e-06    0.0059      16      43 ..     185     212 ..     180     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.18
                            HTH_11 33 rrdIkaLeelg........vpIesepgrGY 54
                                      r dI++ eel+        ++I+++ grG 
  gi|313116935|ref|YP_004038059.1| 51 RGDIERAEELLddspdaleYDITGTEGRGV 80
                                      6799999999999999999********995 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.9e-06
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                        + ++LA +L+vS+ tv  +++++e++ 
  gi|313116935|ref|YP_004038059.1| 185 TTHQDLATKLDVSTGTVSEHLQRIESKI 212
                                       5789********************9976 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06    0.0026      18      40 ..     185     207 ..     182     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                       ++ ++LA +l++S +tv+++l+r
  gi|313116935|ref|YP_004038059.1| 185 TTHQDLATKLDVSTGTVSEHLQR 207
                                       799******************99 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   8.4e-06     0.013       5      43 ..     162     207 ..     160     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.4e-06
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekr 43 
                                       L++r+ e++ l          +  T+++++ +l++S ++V+ ++ r
  gi|313116935|ref|YP_004038059.1| 162 LTDRQLEIFDLAVregyyeiPRQTTHQDLATKLDVSTGTVSEHLQR 207
                                       899999999999999988887889*****************98877 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.3e-05      0.02      17      39 ..     186     208 ..     181     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                       EHHHHHHHHTS-HHHHHHHHHHH CS
                             HTH_5  17 cvcelaeelglsqstvShHLkkL 39 
                                       +  +la +l++s +tvS+HL + 
  gi|313116935|ref|YP_004038059.1| 186 THQDLATKLDVSTGTVSEHLQRI 208
                                       5679****************865 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.78   1.2e+03       3      14 ..     162     173 ..     161     178 .. 0.85
   2 ?   11.9   0.1     8e-05      0.12      21      45 ..     188     212 ..     183     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.78
                                       S-HHHHHHHHHH CS
                              GerE   3 LskRErevLrll 14 
                                       L++R++e++ l 
  gi|313116935|ref|YP_004038059.1| 162 LTDRQLEIFDLA 173
                                       9******99875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8e-05
                                       HHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  21 keIAeelniSekTVkvhksnimkKL 45 
                                       ++ A +l++S+ TV+ h+++i +K+
  gi|313116935|ref|YP_004038059.1| 188 QDLATKLDVSTGTVSEHLQRIESKI 212
                                       6789*****************9997 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.4   6.6e+03       3      13 ..     129     139 ..     128     140 .. 0.84
   2 ?   -3.3   0.0       4.9   7.4e+03      11      26 ..     162     177 ..     161     178 .. 0.77
   3 ?   11.5   0.0   0.00012      0.17      28      52 ..     186     210 ..     184     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                                       HHHHHHTTS-H CS
                      Sigma70_r4_2   3 alrealaeLpe 13 
                                       a+++a+a Lp+
  gi|313116935|ref|YP_004038059.1| 129 AIQDAVADLPT 139
                                       79999999995 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.9
                                       S-HHHHHHHHHHHTS- CS
                      Sigma70_r4_2  11 Lperqreifllryleg 26 
                                       L+ rq eif l   eg
  gi|313116935|ref|YP_004038059.1| 162 LTDRQLEIFDLAVREG 177
                                       7788989998887776 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00012
                                       -HHHHHHHHT--HHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArk 52 
                                       ++++ A +l++s gtV  +l+R   
  gi|313116935|ref|YP_004038059.1| 186 THQDLATKLDVSTGTVSEHLQRIES 210
                                       89********************765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.8e-05      0.12      16      44 ..     182     211 ..     178     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                                       TTEEHH.HHHHHHTS-HHHHHHHHHHHHHT CS
                              MarR  16 gplsvs.eLakklgvskstvtrvldrLekk 44 
                                       + ++ + +La kl vs++tv++ l r e k
  gi|313116935|ref|YP_004038059.1| 182 PRQTTHqDLATKLDVSTGTVSEHLQRIESK 211
                                       5545445*****************998865 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.15      25      48 ..     187     210 ..     183     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                       HHHHHHHHTS-HHHHHHHHHHHHH CS
                    Fe_dep_repress  25 tkdlaerLnvspssVsemlkkLek 48 
                                        +dla  L+vs  +Vse l++ e+
  gi|313116935|ref|YP_004038059.1| 187 HQDLATKLDVSTGTVSEHLQRIES 210
                                       679******************986 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00032      0.48       4      53 ..     162     211 ..     159     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                                       --HHHHHHHHH.HHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind   4 LTerQrevldl.ikasieetgypPsireiaralglkSpsaveehLkaLerK 53 
                                       LT+rQ e++dl +++   e     +  ++a +l ++ + +v ehL++ e K
  gi|313116935|ref|YP_004038059.1| 162 LTDRQLEIFDLaVREGYYEIPRQTTHQDLATKLDVS-TGTVSEHLQRIESK 211
                                       9*********93445556666667999999999986.9*********9988 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.25      11      46 ..     173     209 ..     157     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                       HCTTTC..EEEEEHHHHHHHHHTTSSHHHHHHHHHHHH CS
                         HTH_Crp_2  11 aeragg..eielpltqeelAsmlGltretvsrilseLk 46 
                                       a r+ g  ei  + t+++lA  l ++  tvs  l++ +
  gi|313116935|ref|YP_004038059.1| 173 AVRE-GyyEIPRQTTHQDLATKLDVSTGTVSEHLQRIE 209
                                       4443.336788899********************9876 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.29      21      44 ..     186     209 ..     184     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                         HTH_Tnp_4  21 tyqdLayrFgvsestvsrifhkwv 44 
                                       t+qdLa   +vs++tvs   ++++
  gi|313116935|ref|YP_004038059.1| 186 THQDLATKLDVSTGTVSEHLQRIE 209
                                       9****************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1423.57
//
Query:       gi|313116936|ref|YP_004038060.1|  [L=449]
Description: cytochrome P450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-96  322.2   0.0    5.9e-96  322.0   0.0    1.0  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.0   0.0  3.3e-100   5.9e-96       1     444 [.      14     429 ..      14     446 .. 0.90

  Alignments for each domain:
  == domain 1  score: 322.0 bits;  conditional E-value: 3.3e-100
                                       --SESEHHCCHCHHHHTTTCCHHHHHHHHHHHH-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHH CS
                              p450   1 Ppgptplplvgnllqlgrkeelhevlrklqkkygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallat 77 
                                       Ppgp+ lp+vgn + +   +e++e++++++++yg+i+++   + pv  l++p+++++vl++++++ ++      +++
  gi|313116936|ref|YP_004038060.1|  14 PPGPDGLPVVGNYPSYI--REPFEFMTRNAREYGDIVGWEERNGPVYQLNHPDHIEQVLVQNNQNYVK---GDAFQS 85 
                                       9****************..89*****************************************966666...344555 PP

                                       HHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHH CS
                              p450  78 srkpfkgkgvlfangekwkklRrfltptltsfgklsleelveeeaedlveklrkkagesselditellskaaldvig 154
                                         +p  g g+l+++g+ w+++R+++ p+++ + ++++ e+++ ++e+++e++ +  +      i+e++  ++l +++
  gi|313116936|ref|YP_004038060.1|  86 TLGPITGSGILNSEGAIWRRNRHLIQPAFHPNRIEEYSEMMTGYTEEMLETWSDGETRE----IHEDMMTVTLKIVS 158
                                       578*****************************888*****************9988877....************** PP

                                       HHHHSSHHHTTTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCH CS
                              p450 155 silFgarfdlledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerretl 231
                                       + lFg+ +d   +    ++ +a e  ++    s   ++l+      +pt+ +++++ a+++l+d++ +lie+rr++ 
  gi|313116936|ref|YP_004038060.1| 159 RALFGVDIDDHVE----DIGEALESFMEAS-ESLSHYVLPEE----IPTPSRKQIQGAREQLDDVVYELIEDRRANP 226
                                       ******9773333....4555555553333.33334555555....8*****************************9 PP

                                       CHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCC CS
                              p450 232 dsakksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlg 308
                                        ++     d ++ ll+ + + +g+ +ls e+++ +v +ll+aG++Tt+  ls++ y La++Pe+++kl eE+devl 
  gi|313116936|ref|YP_004038060.1| 227 GEQ-----DVISMLLDVT-DDDGN-TLSTEQIRDEVVTLLLAGHETTALSLSFTAYALARHPEAEAKLVEELDEVLD 296
                                       999.....9********7.77776.9**************************************************7 PP

                                       TTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--G CS
                              p450 309 dkreptyddlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdp 385
                                       + r+pt++dl++l+y+++v+kE++Rl+p+vp ++ Re  k+  i+gy ip+G +v +  + +hrd+  +++P  F p
  gi|313116936|ref|YP_004038060.1| 297 G-RTPTMSDLSELTYTEQVVKESMRLYPPVP-GIVREPVKPDIIGGYEIPAGATVRMHQWVVHRDERWYDDPLAFEP 371
                                       7.58***************************.********************************************* PP

                                       GGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSGG CS
                              p450 386 eRFldekgnskrksfaflPFGaGpRnCiGerlArmelklflatlLqnFevelqpetdpp 444
                                       eR+ d+ ++ + ++ a++PF aGpR CiG r+A++e +l+lat+ q++ +el p+t+  
  gi|313116936|ref|YP_004038060.1| 372 ERWTDDLEQ-SIPKLAYFPFAAGPRRCIGDRFAMLEARLLLATIYQKYHLELTPGTELD 429
                                       ******995.5*****************************************9976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3228.04
//
Query:       gi|313116937|ref|YP_004038061.1|  [L=75]
Description: hypothetical protein Hbor_34030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   11.7   1.6        1.4    9.0   0.9    2.1  2  Hol_Tox   Putative Holin-like Toxin (Hol-Tox)


Domain annotation for each model (and alignments):
>> Hol_Tox  Putative Holin-like Toxin (Hol-Tox)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.018   3.2e+02      24      36 ..      14      26 ..       7      39 .. 0.74
   2 ?    9.0   0.9   8.1e-05       1.4      30      51 ..      46      68 ..      40      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.018
                           Hol_Tox 24 rallsvsealQli 36
                                      ra l  + a+Q+i
  gi|313116937|ref|YP_004038061.1| 14 RAALFFFHAVQMI 26
                                      6777889999976 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 8.1e-05
                           Hol_Tox 30 sealQ.liLaFGtFilallalVV 51
                                      ++++    L FG F l +lalVV
  gi|313116937|ref|YP_004038061.1| 46 FDTVHeTALLFGLFGLNILALVV 68
                                      5665325689************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 542.31
//
Query:       gi|313116938|ref|YP_004038062.1|  [L=587]
Description: subtilisin-like serine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-49  167.7   9.1    3.5e-49  167.7   9.1    1.5  2  Peptidase_S8     Subtilase family
  ------ inclusion threshold ------
      0.017   15.7   0.3       0.22   12.1   0.0    2.5  2  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.7   9.1   3.9e-53   3.5e-49       1     284 [.     124     357 ..     124     387 .. 0.89
   2 ?   -3.8   0.0      0.65   5.8e+03      42      68 ..     439     461 ..     415     472 .. 0.64

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 3.9e-53
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g+g  va+lDtG+d++hpdls+++ +             g++  ds+ +++ w++d n     HGth+AGia a  +
  gi|313116938|ref|YP_004038062.1| 124 GSGAHVAILDTGIDSEHPDLSQNLGE-------------GYAVVDSDRGDVPWNDDHN-----HGTHCAGIANAV-N 181
                                       78999****************76544.............577789999******9998.....************.* PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnkk 154
                                       +++++ gv + a++ svkvl+++gg +   ++++++i++aa ++ dvi+mslg +ts ++  ++    a+++a  ++
  gi|313116938|ref|YP_004038062.1| 182 NDQGILGVSTRATLHSVKVLSGDGGGSA--SGVAEGIKWAADQGHDVISMSLG-ATSGSSIIKD----AVEYAY-ER 250
                                       ************************9986..8**********************.7777777766....9*****.99 PP

                                       T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 155 gvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrq 231
                                       g+l+v +aGN+g      +++  v++p+ + +vi+vg++++e+++++fSs+G+++      +ivapG++i st+   
  gi|313116938|ref|YP_004038062.1| 251 GSLLVGAAGNEG------PCSDCVHYPGAYPEVIAVGSVNDEDELSEFSSTGSEV------EIVAPGTEIRSTV-IG 314
                                       ************......9999*******************************98......8*******55444.44 PP

                                       CHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 232 snnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdl 284
                                       +        yq  sGTSmA+P++agaaA+l+s    +++e+ r+ l  +A+d+
  gi|313116938|ref|YP_004038062.1| 315 G--------YQVYSGTSMATPHVAGAAAILMS--TGISNEEARKRLTEAAEDI 357
                                       4........79********************7..3467888888888888877 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.65
                                       GEETT-SS-TT-SC-SSS....HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  42 ngadsettstnwarddngnsieHGthv 68 
                                        g++s t+s+n +++d    +eHGt  
  gi|313116938|ref|YP_004038062.1| 439 SGHQSSTGSFNADVSD----LEHGTTY 461
                                       4455555555655555....3499875 PP

>> Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.4e-05      0.22      44      84 ..     430     470 ..     389     483 .. 0.82
   2 ?    0.7   0.0     0.086   7.7e+02      61      82 ..     548     570 ..     511     584 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                   Pur_ac_phosph_N  44 aeatsstyettnyksgyshkatltgLepgttYyYrvgddeg 84 
                                        + ts+++e+  + s  s++a +++Le gttY++   ++++
  gi|313116938|ref|YP_004038062.1| 430 RDETSERVESGHQSSTGSFNADVSDLEHGTTYVFEAFAETD 470
                                       45566777888999999*****************9877754 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.086
                   Pur_ac_phosph_N  61 shkatltgLepgttYy.Yrvgdd 82 
                                        +  +l  Le +ttY+   v+ d
  gi|313116938|ref|YP_004038062.1| 548 DTFDELVHLESDTTYVaVAVCID 570
                                       55557889*******75555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3683.02
//
Query:       gi|313116939|ref|YP_004038063.1|  [L=94]
Description: transcriptional regulator, PadR family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-15   54.8   0.8    8.2e-15   54.5   0.8    1.1  1  PadR      Transcriptional regulator PadR-like family
    0.00013   22.4   0.0    0.00016   22.1   0.0    1.2  1  HTH_27    Winged helix DNA-binding domain
    0.00025   21.1   0.0    0.00034   20.7   0.0    1.2  1  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.037   13.8   0.0    1.2  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
      0.032   14.0   0.0      0.042   13.6   0.0    1.1  1  DUF4364   Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.8   2.3e-18   8.2e-15       2      73 ..      12      78 ..      11      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2.3e-18
                                      HHHH.CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                              PadR  2 Lall.eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                      L+l+ + ++ +G+ i++ele++++  + + +G+lYp+L+ L ++g++++ +++    +++++Y+lT+ Gr+++
  gi|313116939|ref|YP_004038063.1| 12 LYLVaGLEKPHGLGIKRELEQYYG--ESITQGRLYPNLDALVEDGYIKKGEKD----RRTNFYELTASGRQAI 78
                                      6666344666************95..59**********************998....7************975 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   4.4e-08   0.00016      16      68 .]      22      74 ..       4      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.4e-08
                            HTH_27 16 rrrkkladlcgrlnvedshis..yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ++  ++++l +++  + +++    +l++L+e G++  ++ e+drr+ +++lT++G
  gi|313116939|ref|YP_004038063.1| 22 HGLGIKRELEQYYGESITQGRlyPNLDALVEDGYI--KKGEKDRRTNFYELTASG 74
                                      5555667777777777777666358**********..77789***********98 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.5e-08   0.00034      26      71 ..      38      80 ..      28      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.5e-08
                            HTH_34 26 atdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71
                                      +t+g+L+ +l++L + gYi+  k+ k++ +   +++T  Gr+a  +
  gi|313116939|ref|YP_004038063.1| 38 ITQGRLYPNLDALVEDGYIK--KGEKDR-RTNFYELTASGRQAILD 80
                                      89****************95..777777.8899*********9876 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     1e-05     0.037      51      85 ..      42      76 ..      26      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1e-05
                           DUF1495 51 krynsessLielGLveeeeeseglklYklteeGie 85
                                        y + ++L+e G +++ e+++ +++Y+lt +G++
  gi|313116939|ref|YP_004038063.1| 42 RLYPNLDALVEDGYIKKGEKDRRTNFYELTASGRQ 76
                                      5678889**************************97 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.042      40      70 ..      47      78 ..      37      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                           DUF4364 40 lseLvesglieee.ekenktlykiTekGketl 70
                                      l+ Lve+g+i++  +++ +++y++T +G++++
  gi|313116939|ref|YP_004038063.1| 47 LDALVEDGYIKKGeKDRRTNFYELTASGRQAI 78
                                      899*********9677999**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 730.55
//
Query:       gi|313116940|ref|YP_004038064.1|  [L=56]
Description: hypothetical protein Hbor_34060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.13   11.5   0.0       0.13   11.5   0.0    1.0  1  USP7_ICP0_bdg  ICP0-binding domain of Ubiquitin-specific prot


Domain annotation for each model (and alignments):
>> USP7_ICP0_bdg  ICP0-binding domain of Ubiquitin-specific protease 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.4e-06      0.13     125     150 ..      17      42 ..       8      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.4e-06
                     USP7_ICP0_bdg 125 klkqtlkkaelqdGdIicfqkelsee 150
                                       ++ +++++ +l dG+Ii+f+++++e 
  gi|313116940|ref|YP_004038064.1|  17 DVYEPFAAIDLGDGNIIVFDRDVQEA 42 
                                       56689999*************99983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 422.45
//
Query:       gi|313116941|ref|YP_004038065.1|  [L=247]
Description: hypothetical protein Hbor_34070 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1805.00
//
Query:       gi|313116942|ref|YP_004038066.1|  [L=122]
Description: HxlR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-27   94.6   0.0    3.1e-27   94.3   0.0    1.1  1  HxlR      HxlR-like helix-turn-helix
     0.0016   18.3   0.0     0.0025   17.7   0.0    1.3  1  PadR      Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.0   3.4e-31   3.1e-27       1      89 [.      26     115 ..      26     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 3.4e-31
                                       HHHSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                              HxlR   1 liggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76 
                                       l++ kWk +i+  llk g+  fsel++ +++is k L+++L+eLe+d++++r+v++e P +veY lt++Gr+lep++
  gi|313116942|ref|YP_004038066.1|  26 LLSRKWKPVIVDRLLKsGPCGFSELQNLIGNISGKALSNNLKELEADRIVNRSVISERPYRVEYALTDRGRDLEPLI 102
                                       5889*******999988************************************************************ PP

                                       HHHHHHHHHHHHC CS
                              HxlR  77 qelkkwgeeylee 89 
                                        ++ +wg+++ e+
  gi|313116942|ref|YP_004038066.1| 103 VAMREWGSKHFEP 115
                                       *********9987 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.8e-07    0.0025      33      71 ..      61      97 ..      47      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-07
                                      HHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR 33 slYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                       l  +Lk+Le++++v+++     e+p r  Y+lTd+Gr+
  gi|313116942|ref|YP_004038066.1| 61 ALSNNLKELEADRIVNRSVIS--ERPYRVEYALTDRGRD 97
                                      56679***********99775..69************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 929.30
//
Query:       gi|313116943|ref|YP_004038067.1|  [L=67]
Description: hypothetical protein Hbor_34090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       149  (0.00831056); expected 358.6 (0.02)
Passed bias filter:                      125  (0.00697194); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 507.91
//
Query:       gi|313116944|ref|YP_004038068.1|  [L=972]
Description: PAS domain S-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-44  150.9   4.8    2.5e-44  150.9   4.8    2.5  3  BAT           GAF and HTH_10 associated domain
    8.3e-39  132.0   0.0    4.5e-15   55.8   0.0    4.0  3  PAS_9         PAS domain
    3.1e-33  114.1   0.0    1.1e-09   38.3   0.0    4.0  3  PAS           PAS fold
    1.2e-23   82.6   0.0    1.2e-07   31.5   0.0    3.9  3  PAS_8         PAS domain
    8.2e-23   81.2   1.4    2.2e-10   41.0   0.0    2.9  2  GAF_2         GAF domain
      7e-22   77.0   0.0      2e-21   75.5   0.0    1.9  1  HTH_10        HTH DNA binding domain
      1e-20   74.0   1.1    2.7e-06   27.6   0.0    4.3  3  PAS_4         PAS fold
    1.4e-18   66.9   0.0      1e-05   25.7   0.0    4.8  4  PAS_3         PAS fold
    1.8e-15   57.4   0.3    1.2e-06   28.9   0.1    2.6  2  GAF_3         GAF domain
    5.4e-08   33.5   0.1      0.023   15.4   0.0    2.8  2  GAF           GAF domain
     0.0033   17.1   0.0     0.0098   15.5   0.0    1.9  1  Sigma70_r4_2  Sigma-70, region 4
     0.0068   16.5   0.0        3.1    8.0   0.0    3.4  3  PAS_11        PAS domain
  ------ inclusion threshold ------
      0.043   13.3   0.0       0.12   11.9   0.0    1.9  1  Sigma70_r4    Sigma-70, region 4
       0.06   12.9   0.0       0.17   11.5   0.0    1.7  1  GerE          Bacterial regulatory proteins, luxR family
       0.06   13.9   0.0        0.2   12.3   0.0    1.8  1  DUF134        Protein of unknown function  DUF134
      0.063   14.0   0.0       0.44   11.2   0.0    2.6  1  PAS_2         PAS fold
      0.066   12.9   0.0         12    5.5   0.0    3.1  3  PAS_12        UPF0242 C-terminal PAS-like domain
      0.084   12.5   0.0       0.22   11.1   0.0    1.8  1  HTH_24        Winged helix-turn-helix DNA-binding
       0.11   12.1   1.4        0.3   10.7   1.4    1.6  1  LUC7          LUC7 N_terminus
       0.13   12.8   0.6          9    6.9   0.0    3.0  2  ATP-cone      ATP cone domain
       0.27   11.1   2.0         18    5.3   0.8    2.8  2  DUF5315       Disordered region of unknown function (DUF5315)


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3       5.1   4.4e+03     107     132 ..      92     117 ..      78     138 .. 0.56
   2 ?   -3.2   0.1       7.8   6.6e+03       8      42 ..     464     498 ..     463     499 .. 0.87
   3 !  150.9   4.8     3e-47   2.5e-44       1     156 []     750     904 ..     750     904 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.1
                               BAT 107 dgrarlvvevPpgadvRsvvealeer 132
                                       d ++++++  ++g +v   + a +++
  gi|313116944|ref|YP_004038068.1|  92 DATTDITLVHADGHAVSVALTAESTE 117
                                       44444444444444444444444444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.8
                               BAT   8 leirdeddvlvalaaeldcrveleglvprsdgevl 42 
                                       ++++d+++ l +  +++d +++l g   rs+++v+
  gi|313116944|ref|YP_004038068.1| 464 VAVTDAAQKLLDSRSAFDLEISLAGRAYRSGETVV 498
                                       68999999999999999999999999999998875 PP

  == domain 3  score: 150.9 bits;  conditional E-value: 3e-47
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D++veLe++++d+++++v  +++l+cr++leg++p++dg +l+++++++ +++++ +aae++++++d+r+v+e+d++
  gi|313116944|ref|YP_004038068.1| 750 DEIVELEFAVSDTESIPVYFSKHLECRCRLEGTTPTEDGNYLCYLRIEDKSVADALEAAERMESIADARLVKEYDEE 826
                                       899************************************************************************** PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                       +lle+   ++s    + + G+++rsa+a+ g++++v+evP+++d+R+vvea++  yp+ eLva+re++r+vrt++ef
  gi|313116944|ref|YP_004038068.1| 827 CLLEVIK-TESAPGEMIDVGASIRSASANCGEGTVVLEVPQTVDIREVVEAFQHLYPNSELVAKREVDRSVRTAAEF 902
                                       *****95.8889999************************************************************** PP

                               BAT 155 ra 156
                                       r+
  gi|313116944|ref|YP_004038068.1| 903 RD 904
                                       95 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   3.4e-11   2.9e-08       2      82 ..      30     113 ..      29     128 .. 0.85
   2 !   55.8   0.0   5.2e-18   4.5e-15       2     104 .]     161     260 ..     160     260 .. 0.96
   3 !   37.7   0.0   2.3e-12   1.9e-09       2     104 .]     280     405 ..     279     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.4e-11
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.....kerevevvlirkng 73 
                                       +gil  ++dg++++a++  ++llGy+p+e++g s+  lf  +p++++ l+ + ++ ++        + +++l++ +g
  gi|313116944|ref|YP_004038068.1|  30 EGILSLDEDGTVVFASQPIEQLLGYDPDELVGESVGRLF--SPDHERPLETVRREAEReptevGDATTDITLVHADG 104
                                       7999888********************************..*********999999988887777777777777777 PP

                             PAS_9  74 etfwvllta 82 
                                         + v lta
  gi|313116944|ref|YP_004038068.1| 105 HAVSVALTA 113
                                       666666655 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 5.2e-18
                             PAS_9   2 dgili.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       ++i++ d+++ +i+ +N+ a++ lGys+ee+l  s +d+++t++    ++++++e g+   +++e+ ++  +getf+
  gi|313116944|ref|YP_004038068.1| 161 EAIFVfDTDNDEIIECNPRACERLGYSREELLSVSPSDIYATEEAFVGFIKEVFEHGT--SWTDELSCRAADGETFP 235
                                       567766888889**********************************************..***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       ++++a+ ++ d++  v+  v+ rDi+e
  gi|313116944|ref|YP_004038068.1| 236 IEASATLLYVDGKPHVL--VFGRDISE 260
                                       ************99999..******98 PP

  == domain 3  score: 37.7 bits;  conditional E-value: 2.3e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf.......................vtdpeanerlraale 55 
                                       +g++  ++++r + aNe+ ++l+Gy+++e++g s+t ++                       v++++a++  +++l+
  gi|313116944|ref|YP_004038068.1| 280 EGVFAADDKFRFTVANEGTAKLTGYTKDELIGSSLTRFLageddrvdrseyeelqtserrtvVDAESAESARKELLK 356
                                       6888888********************************98888888888888888888887777777777777777 PP

                             PAS_9  56 qgrkkerevevvlirkngetfwvlltaspvkdd.dgelvgiivilrDite 104
                                       + r  +  ve  + +k++e ++v++++s +  + d+ ++g+ ++l+D++e
  gi|313116944|ref|YP_004038068.1| 357 SER-DVMKVEAPICTKDDEIVPVEVRFSELPTEsDDDFRGMTGVLIDVSE 405
                                       777.99************************9999**************98 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0     3e-11   2.5e-08       3      92 ..      21     105 ..      19     122 .. 0.78
   2 !   38.3   0.0   1.3e-12   1.1e-09       5     113 .]     154     258 ..     150     258 .. 0.94
   3 !   37.3   0.0   2.6e-12   2.2e-09       1      74 [.     269     340 ..     269     403 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3e-11
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       +r+++ ++ ++i+ +Dedg ++++++ +e+llG++++e++g+s+ +l++++    + + le++++++e++ ++  + 
  gi|313116944|ref|YP_004038068.1|  21 FREVVFDTEEGILSLDEDGTVVFASQPIEQLLGYDPDELVGESVGRLFSPD----HERPLETVRREAEREPTEVGDA 93 
                                       6667777889***************************************99....7777777777766655543333 PP

                                       ECTTSSEEEEEEE CS
                               PAS  80 klrdgrpihlevr 92 
                                       ++ d + +h++ +
  gi|313116944|ref|YP_004038068.1|  94 TT-DITLVHADGH 105
                                       33.5555555544 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 1.3e-12
                                       HHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   5 aileslpdpifvvD.edgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                        ++e + ++ifv D  + +i+++N+ a+e lG+sree+l+ s +d + +e+   ++  ++++ e+g++++++  ++ 
  gi|313116944|ref|YP_004038068.1| 154 KVFEYSNEAIFVFDtDNDEIIECNPRACERLGYSREELLSVSPSDIYATEEA--FVGFIKEVFEHGTSWTDELSCRA 228
                                       56677889******999******************************99976..*****************999999 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         dg+++++e  a+ ++  g+   ++l+++rdi
  gi|313116944|ref|YP_004038068.1| 229 A-DGETFPIEASATLLYVDGKP--HVLVFGRDI 258
                                       9.*************9999877..********8 PP

  == domain 3  score: 37.3 bits;  conditional E-value: 2.6e-12
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECC CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesra 74 
                                       e++r+i+e+  +++f+ D + r++ +N+ +++l+G++ +e++g+sl +++  edd  ++++ e  ++q++e+r+
  gi|313116944|ref|YP_004038068.1| 269 ERYRTIVEAVGEGVFAADDKFRFTVANEGTAKLTGYTKDELIGSSLTRFLAGEDD--RVDRSEYEELQTSERRT 340
                                       68****************************************************9..66666666666666555 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06    0.0016      11      63 ..      29      83 ..      19      87 .. 0.80
   2 !   31.5   0.0   1.5e-10   1.2e-07       4      41 ..     153     192 ..     153     216 .. 0.78
   3 !   27.9   0.0     2e-09   1.7e-06       1      58 [.     269     329 ..     269     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                             PAS_8 11 pdgiavvd.lgdrivdvNqaalellGys.adlkgellg.qllpvlrplledaeqll 63
                                       +gi+ +d +g+ +v++ q  ++llGy+ ++l ge +g  + p+++ +le+ ++++
  gi|313116944|ref|YP_004038068.1| 29 EEGILSLDeDGT-VVFASQPIEQLLGYDpDELVGESVGrLFSPDHERPLETVRREA 83
                                      689999995555.************************9777777777777777665 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 1.5e-10
                             PAS_8   4 ralfesspdgiavvd..lgdrivdvNqaalellGys.adlk 41 
                                       + +fe s+++i+v+d  ++  i+++N++a+e lGys ++l+
  gi|313116944|ref|YP_004038068.1| 153 QKVFEYSNEAIFVFDtdND-EIIECNPRACERLGYSrEELL 192
                                       579**********996455.5*************9944443 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 2e-09
                             PAS_8   1 erlralfesspdgiavvdlgd..rivdvNqaalellGys.adlkgellgqllpvlrplle..d 58 
                                       er+r+++e++ +g++ +d  d  r++ +N+ +++l+Gy+ ++l+g+ l ++l + ++  +  +
  gi|313116944|ref|YP_004038068.1| 269 ERYRTIVEAVGEGVFAAD--DkfRFTVANEGTAKLTGYTkDELIGSSLTRFLAGEDDRVDrsE 329
                                       7**************999..5568999******************999755555555444334 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.3   1.9e-12   1.7e-09       1     137 [.     426     553 ..     426     554 .. 0.80
   2 !   41.0   0.0   2.5e-13   2.2e-10       5     137 ..     600     738 ..     599     739 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.9e-12
                                       HHHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-.EEEEEEEES-TTS.TT-S-B---TTHHHHHHHHTS-EEES-G CS
                             GAF_2   1 aadleelldlvldelvel.gaalgyillvdddgg.lrlaawgeaeeef.gaaldrplgeglvgealrtgrpvilndl 74 
                                       a+d + +++ +ld+++++ g+++g++ + d + + l+++a + a  ++ +++   +l+ +l+g+a+r+g+ v+ n++
  gi|313116944|ref|YP_004038068.1| 426 AMDRDAIARDTLDAVERIlGFDVGCVRMFDSESNtLETVAVTDAAQKLlDSRSAFDLEISLAGRAYRSGETVV-NQP 501
                                       57999************66*****999999554436655444444444144443377999*********9888.554 PP

                                       GG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       ++        +g  g  ++l++Pl   g  +G l+++++  ++f+e+d++++e la+++ + +
  gi|313116944|ref|YP_004038068.1| 502 AA-------GEGVTGDEASLHLPL---G-KHGTLSMFTESADEFTETDIQFIEVLAATVTTHL 553
                                       44.......5688888899*****...9.9******999999***************998776 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 2.5e-13
                                       HHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--....-TTHHHHHHHHTS-EEES-GG CS
                             GAF_2   5 eelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrpl....geglvgealrtgrpvilndle 75 
                                       e++ ++v+++l+      +++i+ v+  g+  ++ + ++ e+ + +ald +     g+g v +a++tg+  ++ ++ 
  gi|313116944|ref|YP_004038068.1| 600 ETIEERVCQQLAASSlYKYAWIAAVEVTGKnATIKTGAGVEKDHLDALDNMSisqlGNGTVKQAIETGEISVVRQYL 676
                                       567789999998855577********666645566888888888888877334556***9*********99999999 PP

                                       G-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  76 edpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                        +   k +++++ +l  ++a+Pl +++rv+Gvl++ + +++a++e+ ++ Le l+++i++ i
  gi|313116944|ref|YP_004038068.1| 677 VEGKDKDEREDEDKLEVTAAIPLQYGNRVYGVLVVNSVREDALSEQAQAGLEVLGDTIGFTI 738
                                       98899999999999*99******9999********************************988 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   2.4e-24     2e-21       1      53 []     910     962 ..     910     962 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.4e-24
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LTdkq +++k Ay +GYFd+PR  t++++A+ +GIs +t+++hLrkae+kl++
  gi|313116944|ref|YP_004038068.1| 910 LTDKQQMAAKSAYYAGYFDWPRGSTAEDVAESMGISSATFHQHLRKAEQKLMA 962
                                       9**************************************************95 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.9e-07   0.00016       6      59 ..      30      83 ..      26     109 .. 0.86
   2 !   27.6   0.0   3.2e-09   2.7e-06       2     109 ..     157     262 ..     156     263 .. 0.93
   3 !   20.0   0.3     7e-07    0.0006       2     110 .]     276     408 ..     275     408 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-07
                             PAS_4  6 dalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrv 59
                                      ++++ ld+dg+v++a++ +++l+g++p+el+G+++  l+++++ ++le+  r++
  gi|313116944|ref|YP_004038068.1| 30 EGILSLDEDGTVVFASQPIEQLLGYDPDELVGESVGRLFSPDHERPLETVRREA 83
                                      68999************************************7777776655555 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 3.2e-09
                             PAS_4   2 dslpdalavldpdg.rvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       + +++a++v+d+d   ++ +N++a+e +g+++eell  ++ +++ +   +++   +++v e +++++++   +  +g
  gi|313116944|ref|YP_004038068.1| 157 EYSNEAIFVFDTDNdEIIECNPRACERLGYSREELLSVSPSDIYAT--EEAFVGFIKEVFEHGTSWTDELSCRAaDG 231
                                       66899*****887537**************************9995..8*********************99999** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       e+ ++e +++ l   +G+  +vlv++rDi+e+r
  gi|313116944|ref|YP_004038068.1| 232 ETFPIEASATLLY-VDGK-PHVLVFGRDISEQR 262
                                       ************6.9***.9***********98 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 7e-07
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.....................daarleralr 57 
                                       +++ +++++ d+ +r++ aN+  a+l g++ +el+G++l  +l  e                     da+  e+a +
  gi|313116944|ref|YP_004038068.1| 276 EAVGEGVFAADDKFRFTVANEGTAKLTGYTKDELIGSSLTRFLAGEddrvdrseyeelqtserrtvvDAESAESARK 352
                                       78899************************************999999******999999999999999999999999 PP

                             PAS_4  58 rvlegeepiefleelll..pgeerhyelrllPlrdesGe.vigvlvisrDiTerrr 110
                                       ++l++e+ +  +e + +  ++e +++e+r++ l  es +  +g  ++++D++er++
  gi|313116944|ref|YP_004038068.1| 353 ELLKSERDVMKVEAPICtkDDEIVPVEVRFSELPTESDDdFRGMTGVLIDVSERKE 408
                                       999999999999988889999999******66666666669************985 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.3e-06    0.0011       2      78 ..      42     120 ..      41     125 .. 0.89
   2 !   25.7   0.0   1.2e-08     1e-05       1      83 [.     173     250 ..     173     254 .. 0.89
   3 !   10.1   0.0   0.00091      0.78       3      45 ..     293     333 ..     291     343 .. 0.82
   4 ?    6.1   0.0     0.016        13      34      77 ..     343     388 ..     336     400 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD...rervrealqealkkgepyegeyRirrkdGeyrwveararvi 75 
                                       +++s+ +e++lGy+p+el g   s+  l  p+    +e vr++ ++  ++ ++ ++++ ++++dG+ + v  +a+ +
  gi|313116944|ref|YP_004038068.1|  42 VFASQPIEQLLGYDPDELVGE--SVGRLFSPDHerpLETVRREAEREPTEVGDATTDITLVHADGHAVSVALTAEST 116
                                       899******************..9999999999877899999999999999999**************999999988 PP

                             PAS_3  76 .rde 78 
                                        +de
  gi|313116944|ref|YP_004038068.1| 117 eYDE 120
                                       4444 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.2e-08
                             PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvird 77 
                                       ii +++r +e lGys+eell+   s  d+   e+   +   ++e+++ g++++ e  +r +dGe++ +ea+a+ + +
  gi|313116944|ref|YP_004038068.1| 173 IIECNPRACERLGYSREELLSV--SPSDIYATEE--AFVGFIKEVFEHGTSWTDELSCRAADGETFPIEASATLL-Y 244
                                       589*******************..8888888877..66666778889****************************.9 PP

                             PAS_3  78 engkpv 83 
                                        +gkp 
  gi|313116944|ref|YP_004038068.1| 245 VDGKPH 250
                                       999997 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00091
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqea 45 
                                        ++e   +++Gy+++el+g+  s+  ++  eD    r++++e+
  gi|313116944|ref|YP_004038068.1| 293 VANEGTAKLTGYTKDELIGS--SLTRFLAGEDDRVDRSEYEEL 333
                                       579999**************..**********66666666655 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.016
                             PAS_3  34 Drervrealqealkkge.pyegeyRirrkdGeyrwveararvi.rd 77 
                                       D e +++a +e+lk+ + ++++e  i++kd e++ ve r + +   
  gi|313116944|ref|YP_004038068.1| 343 DAESAESARKELLKSERdVMKVEAPICTKDDEIVPVEVRFSELpTE 388
                                       88999999*****9999788*****************998766444 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.1   1.4e-09   1.2e-06       3     129 .]     430     555 ..     428     555 .. 0.93
   2 !   26.2   0.0   9.4e-09   8.1e-06      20     127 ..     619     738 ..     604     740 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.4e-09
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse...sldedsalarralssgevvsepsfaeed 76 
                                       d ++ ++l+++ ++lg++vg + ++d + n+l ++a +d++++l     ++d + +la ra+ sge v+ + +a+e 
  gi|313116944|ref|YP_004038068.1| 430 DAIARDTLDAVERILGFDVGCVRMFDSESNTLETVAVTDAAQKLLDsrsAFDLEISLAGRAYRSGETVVNQPAAGEG 506
                                       678899********************************8888885567799999*************999999**** PP

                             GAF_3  77 glpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                        + d+a l +PL       G+l + + +  +f+++d +++e lA+ + t+++r
  gi|313116944|ref|YP_004038068.1| 507 VTGDEASLHLPLGK----HGTLSMFTESADEFTETDIQFIEVLAATVTTHLDR 555
                                       ************99....899*999999999*******************997 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 9.4e-09
                             GAF_3  20 evgalllldedgnklqvaagw.dgkpalse..sld.edsalarralssgevvsepsf........aeedglpdraal 84 
                                        ++a +++++   ++++ ag  + + +     s+   ++   + a+++ge+ +++++        ++ed   ++   
  gi|313116944|ref|YP_004038068.1| 619 AWIAAVEVTGKNATIKTGAGVeKDHLDALDnmSISqLGNGTVKQAIETGEISVVRQYlvegkdkdEREDEDKLEVTA 695
                                       4455558887777888888886444444342244454555555999****999966655555444667888899999 PP

                             GAF_3  85 avPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       a+PL+ g++v+Gvl+++s ++ a++++ ++ le l++ i+  i
  gi|313116944|ref|YP_004038068.1| 696 AIPLQYGNRVYGVLVVNSVREDALSEQAQAGLEVLGDTIGFTI 738
                                       9************************************999877 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.6e-05     0.023       1     131 [.     428     551 ..     428     553 .. 0.73
   2 !   15.2   0.0   2.9e-05     0.025      36     131 ..     643     736 ..     599     738 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-05
                                       SHHHHHHHHHHHHHHHHTESEEEEEE..EEETTEEE.CEEEEECCEEEET.....TSHHHHHHHHHSSSEEESTGGT CS
                               GAF   1 dleelldtvveelrellgadrvalyl..pdydGlhy.dipqasrwlfmkn.....grgicgqvlatgqplvipdstp 69 
                                       d++ +++ +++ ++++lg d +++ +  ++++ l++  +++a++ l ++        +++g+++++g+++v + ++ 
  gi|313116944|ref|YP_004038068.1| 428 DRDAIARDTLDAVERILGFDVGCVRMfdSESNTLETvAVTDAAQKLLDSRsafdlEISLAGRAYRSGETVVNQPAAG 504
                                       7899********************5544444444445566666663333323333344578999*999999995333 PP

                                       STTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHH CS
                               GAF  70 dprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvav 131
                                       ++             +g  +sl +Pl  +    G+l+   +s+ +ft+ ++++++vla+ v  
  gi|313116944|ref|YP_004038068.1| 505 EGV------------TGDEASLHLPLGKH----GTLSMFTESAdEFTETDIQFIEVLAATVTT 551
                                       333............4557********86....889999977779*************99875 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.9e-05
                                       EEEEECC.EEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE.S CS
                               GAF  36 ipqasrw.lfmkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn.p 110
                                         +a++  +  + g g + q+++tg++ v+  +  ++   +  +r+  +  ++   +++Pl  +++++G+lv+ + +
  gi|313116944|ref|YP_004038068.1| 643 HLDALDNmSISQLGNGTVKQAIETGEISVVRQYLVEGKDKD--EREDEDKLEVT--AAIPLQYGNRVYGVLVVNSvR 715
                                       3333333244444777778************8777777666..55555666665..89*****************64 PP

                                       SS.CSHHHHHHHHHHHHHHHHH CS
                               GAF 111 sp.pftreelellqvladqvav 131
                                        +   ++++ + l+vl+d ++ 
  gi|313116944|ref|YP_004038068.1| 716 -EdALSEQAQAGLEVLGDTIGF 736
                                       .4479************99986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-05    0.0098      26      54 .]     932     960 ..     931     960 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                                       ---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  26 glsykEIAellgisegtVksrlsRArkkL 54 
                                       g++ +++Ae +gis++t  ++l++A +kL
  gi|313116944|ref|YP_004038068.1| 932 GSTAEDVAESMGISSATFHQHLRKAEQKL 960
                                       7899*********************9998 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0036       3.1       3      60 ..      30      84 ..      28     123 .. 0.77
   2 ?    0.9   0.0      0.57   4.8e+02      13      46 ..     172     202 ..     161     222 .. 0.85
   3 ?    2.9   0.0      0.13   1.2e+02      28      64 ..     302     337 ..     291     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0036
                            PAS_11  3 qfttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevi 60
                                      + ++ ld dg ++   +    ++  lg+  +elvg s+ +L++p++ + l++  re  
  gi|313116944|ref|YP_004038068.1| 30 EGILSLDEDGTVVFASQ---PIEQLLGYDPDELVGESVGRLFSPDHERPLETVRREAE 84
                                      55678999*******99...99************************999888877766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.57
                            PAS_11  13 kIisvDtsaLrasfslglekeelvgrsiydLchp 46 
                                        Ii++++   ra  +lg+++eel+ +s  d+   
  gi|313116944|ref|YP_004038068.1| 172 EIIECNP---RACERLGYSREELLSVSPSDIYAT 202
                                       69*****...***************999988765 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.13
                            PAS_11  28 lglekeelvgrsiydLchpqdlstlkshlrevissng 64 
                                       +g++k+el+g s+ +++  +d +  +s ++e + +++
  gi|313116944|ref|YP_004038068.1| 302 TGYTKDELIGSSLTRFLAGEDDRVDRSEYEELQ-TSE 337
                                       69*******************998888888888.433 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.12       5      48 ..     910     960 ..     908     962 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L++++++  +  +        +g T e+++e +giS  + +q++++A +kL
  gi|313116944|ref|YP_004038068.1| 910 LTDKQQMAAKSAYyagyfdwPRGSTAEDVAESMGISSATFHQHLRKAEQKL 960
                                       555555555555556555666789***********************9998 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.17      17      46 ..     932     961 ..     929     963 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                       TS-HHHHHHHHTS-HHHHHHHHHHHHHHHT CS
                              GerE  17 GksnkeIAeelniSekTVkvhksnimkKLn 46 
                                       G + +++Ae+++iS  T + h++ + +KL 
  gi|313116944|ref|YP_004038068.1| 932 GSTAEDVAESMGISSATFHQHLRKAEQKLM 961
                                       8999************************96 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00023       0.2      52      83 ..     934     965 ..     923     969 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                            DUF134  52 kqeeaaklmGiskatlwrlltearkkiakalv 83 
                                       + e+ a+ mGis at+++ l +a +k+ ++ +
  gi|313116944|ref|YP_004038068.1| 934 TAEDVAESMGISSATFHQHLRKAEQKLMASFF 965
                                       67999*******************99987665 PP

>> PAS_2  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00052      0.44      22      86 ..      36      97 ..      31     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00052
                                      ETTTTEEEEEETTHHHHCSS-CCCCTTTCCCCCSECTTHHHHCCHS-CCCHCCCCCEEEE.EEECC CS
                             PAS_2 22 dekslrvlqvSeNaaemLglteekllgtdlralltassaalLekalsareisllnpilih.srtsg 86
                                      de + +v+ +S+  +++Lg  +++l+g+ +  l+++ +   Le + +++e +   p++++ ++t+ 
  gi|313116944|ref|YP_004038068.1| 36 DE-DGTVVFASQPIEQLLGYDPDELVGESVGRLFSPDHERPLETVRREAERE---PTEVGdATTDI 97
                                      44.5678889********************************9988777766...66666444455 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.014        12      67      89 ..      39      61 ..      32      66 .. 0.87
   2 ?    2.9   0.0     0.091        78      56      89 ..     160     193 ..     147     206 .. 0.87
   3 ?   -0.7   0.0       1.2     1e+03      66      88 ..     288     310 ..     276     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                            PAS_12 67 nkllfaNaqirallGwssdkflq 89
                                        ++fa + i++llG+ +d+++ 
  gi|313116944|ref|YP_004038068.1| 39 GTVVFASQPIEQLLGYDPDELVG 61
                                      5799***************9985 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.091
                            PAS_12  56 lgailvysqkenkllfaNaqirallGwssdkflq 89 
                                       + ai+v+   ++ ++  N +  + lG+s +++l+
  gi|313116944|ref|YP_004038068.1| 160 NEAIFVFDTDNDEIIECNPRACERLGYSREELLS 193
                                       678***************************9986 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.2
                            PAS_12  66 enkllfaNaqirallGwssdkfl 88 
                                       + +   aN+ + +l+G+ +d+++
  gi|313116944|ref|YP_004038068.1| 288 KFRFTVANEGTAKLTGYTKDELI 310
                                       4467789*************987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.22      18      44 ..     933     959 ..     930     959 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                            HTH_24  18 isqreLAerlglSpstvnrrlkrLeee 44 
                                        +  ++Ae  g+S++t +++l++ e++
  gi|313116944|ref|YP_004038068.1| 933 STAEDVAESMGISSATFHQHLRKAEQK 959
                                       57789******************9975 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4   0.00035       0.3      80     153 ..     533     604 ..     524     617 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              LUC7  80 gyeeeflrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelgeeGkVde 153
                                       ++ e  ++f+e+l ++v    +++++   l+++eke  ++  +++ + l++++e i++l+ e  e+g++  ++e
  gi|313116944|ref|YP_004038068.1| 533 EFTETDIQFIEVLAATVTTHLDRTERERMLQKSEKEYRNQ--RDQLNTLNRINELIQELIGELVEAGMRETIEE 604
                                       5666667888888888888888876655555555543333..3689************************9997 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.22   1.8e+02      19      74 ..     559     619 ..     550     624 .. 0.61
   2 ?    6.9   0.0     0.011         9      50      79 ..     648     677 ..     637     684 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.22
                                       HHHHHHHHHH.........-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHHH CS
                          ATP-cone  19 kraiekAceg.........seeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyava 74 
                                       +r+++k+ ++         ++++i+e++    +e+  +l++    e I + v ++l+++  y++a
  gi|313116944|ref|YP_004038068.1| 559 ERMLQKSEKEyrnqrdqlnTLNRINELI----QELIGELVEAGMRETIEERVCQQLAASSLYKYA 619
                                       5666666444555555333333344444....444555555555688999999999988888876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                                       IT-BHHHHHHHHHHHHHHSS-HHHHHHHHH CS
                          ATP-cone  50 dgisteeIqdlvektliehpdyavaaayil 79 
                                       d++s++++++  +k++ie ++ +v++ y++
  gi|313116944|ref|YP_004038068.1| 648 DNMSISQLGNGTVKQAIETGEISVVRQYLV 677
                                       78**************************97 PP

>> DUF5315  Disordered region of unknown function (DUF5315)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.062        53      35      52 ..      64      81 ..      58      84 .. 0.84
   2 ?    5.3   0.8     0.021        18      41      64 ..     407     430 ..     406     442 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.062
                           DUF5315 35 kthvFgeehekaLeelRe 52
                                       ++ F+++he+ Le +R+
  gi|313116944|ref|YP_004038068.1| 64 VGRLFSPDHERPLETVRR 81
                                      4889************97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.021
                           DUF5315  41 eehekaLeelReaqikLaqawrrs 64 
                                       +ehe++L  l ea  kL qa+ r 
  gi|313116944|ref|YP_004038068.1| 407 KEHERRLRALSEASRKLTQAMDRD 430
                                       58*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (972 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.82u 0.33s 00:00:01.14 Elapsed: 00:00:00.50
# Mc/sec: 5836.56
//
Query:       gi|313116945|ref|YP_004038069.1|  [L=307]
Description: acyl dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-21   75.1   0.4    3.7e-09   36.9   0.0    2.6  2  CBS              CBS domain
    1.2e-19   70.1   0.0    2.3e-19   69.1   0.0    1.5  1  MaoC_dehydratas  MaoC like domain
      1e-07   32.1   0.0    2.6e-07   30.8   0.0    1.7  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.29   11.5   0.0    1.7  1  4HBT             Thioesterase superfamily


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   8.3e-13   3.7e-09       1      56 [.       7      61 ..       7      62 .. 0.90
   2 !   35.9   0.1   1.7e-12   7.7e-09       1      51 [.      71     120 ..      71     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 8.3e-13
                                      HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      V+++mt+ v t +p+tt +ea+ + + ek+v++l V   +g +vGi+t+ Dl ++l+
  gi|313116945|ref|YP_004038069.1|  7 VSEVMTDSVETTTPETTAREAAVKlF-EKEVGSLVVC-RNGSPVGIITEYDLTKLLA 61
                                      89***************999997758.999****666.699***********99986 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 1.7e-12
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                       V+++m+++++t+  d++++ea++++r k + +lPV+d+d+ lvG++   Dl
  gi|313116945|ref|YP_004038069.1|  71 VSEFMSDPLITIEHDADISEAAKMLRAKQIEHLPVTDGDE-LVGVLAAVDL 120
                                       89***********************8888*******8777.****977666 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   5.2e-23   2.3e-19      15     103 ..     176     261 ..     168     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 5.2e-23
                                       EEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--BT CS
                   MaoC_dehydratas  15 eitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVlp 91 
                                       + t++e+d++++a+ sgD+n +H+++e+Ak+++fg++IahG l+++++++++++  g    + + ++++ F +pV +
  gi|313116945|ref|YP_004038069.1| 176 SKTISEEDVERFAASSGDTNRLHLSDEYAKQTRFGKRIAHGTLVAGLISAALARLPGL---TIYLSQELTFHAPVEI 249
                                       789*******************************************************...77************** PP

                                       TCEEEEEEEEEE CS
                   MaoC_dehydratas  92 gdtlkvelevvg 103
                                       g+++++  ev +
  gi|313116945|ref|YP_004038069.1| 250 GSRVTAVCEVIE 261
                                       *****9998876 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   5.9e-11   2.6e-07       8     100 ..     173     259 ..     168     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 5.9e-11
                   MaoC_dehydrat_N   8 epvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhgeqefey 84 
                                       ++ + ++++e+v +fa + g+tn ++l++e+a+++++++ ia  t++  l  +a  l +  g+    ++ ++qe+++
  gi|313116945|ref|YP_004038069.1| 173 AEFSKTISEEDVERFAASSGDTNRLHLSDEYAKQTRFGKRIAHGTLVAGLISAA--LARLPGL----TIYLSQELTF 243
                                       567889*********************************************999..6665555....5799****** PP

                   MaoC_dehydrat_N  85 hepiraGDelttesri 100
                                       h+p+  G ++t ++++
  gi|313116945|ref|YP_004038069.1| 244 HAPVEIGSRVTAVCEV 259
                                       ***********99986 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.6e-05      0.29      34      58 ..     237     261 ..     218     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.6e-05
                                       EEEEEEESS-BBTTCEEEEEEEEEE CS
                              4HBT  34 velsidflrpvrlgdeltvearvlr 58 
                                       ++ +++f++pv +g+++t+ ++v++
  gi|313116945|ref|YP_004038069.1| 237 LSQELTFHAPVEIGSRVTAVCEVIE 261
                                       56789*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1961.25
//
Query:       gi|313116946|ref|YP_004038070.1|  [L=360]
Description: hypothetical protein Hbor_34120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2522.23
//
Query:       gi|313116947|ref|YP_004038071.1|  [L=177]
Description: Copper binding protein, plastocyanin/azurin family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-08   34.6   0.1    2.6e-08   34.2   0.1    1.2  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    2.7e-07   30.6   0.0    1.2e-06   28.5   0.0    1.8  1  Cupredoxin_1  Cupredoxin-like domain
    2.5e-05   24.3   0.2    4.2e-05   23.5   0.2    1.4  1  Cu-oxidase_3  Multicopper oxidase
    0.00054   19.7   0.2     0.0021   17.8   0.2    2.0  1  Cu-oxidase_2  Multicopper oxidase
     0.0043   16.6   0.0      0.014   14.9   0.0    1.9  1  SoxE          Sulfocyanin (SoxE) domain
  ------ inclusion threshold ------
      0.046   13.6   0.4      0.093   12.6   0.4    1.6  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
        0.1   12.4   0.0       0.18   11.5   0.0    1.4  1  DUF3553       Protein of unknown function (DUF3553)
        1.8    6.1   9.2        2.4    5.7   9.2    1.1  1  TALPID3       Hedgehog signalling target
        5.7    6.9  16.8          1    9.3  12.3    2.0  2  DUF3558       Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   1.3e-11   2.6e-08      20      98 ..      90     175 ..      70     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.3e-11
                                       EEETTEEEEEEEESSSSBEEEEET...TSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEET.T.TTT CS
                       Copper-bind  20 tvkkgekvtfvnlavmgHNvvldk...dgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffCs.P.Haa 89 
                                       tv +  ++ f n   ++HN+ + +   d+     ++++ +   +t  i +G+++svtf+   +gt+ + C+   H+ 
  gi|313116947|ref|YP_004038071.1|  90 TVGQELTIHFENVGEVAHNLTVGEfpaDERTVADQDEEGSFIVKTDTIQPGKTTSVTFTptSTGTFPYWCDvAgHRE 166
                                       34444578899999******999866644333333333333348999************878888******867*** PP

                                       TTSEEEEEE CS
                       Copper-bind  90 agMkgkvtv 98 
                                       agM+g++tv
  gi|313116947|ref|YP_004038071.1| 167 AGMVGEMTV 175
                                       ******998 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   6.1e-10   1.2e-06      14      97 ..      64     164 ..      57     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6.1e-10
                      Cupredoxin_1  14 kaaaaaektveitvkdggfePskievkagekvklkiknkdktpeefesed.................lgeekvlapg 73 
                                       ++ +a + ++++t ++    P+  ++  g++++++++n ++ ++++++ +                 + +  +++pg
  gi|313116947|ref|YP_004038071.1|  64 PTPNALDGEITVTGSEWVLAPDAFQATVGQELTIHFENVGEVAHNLTVGEfpadertvadqdeegsfIVKTDTIQPG 140
                                       5556778899999999**************************9888888888888999999*****977779***** PP

                      Cupredoxin_1  74 ktttitiaplkpGeYeftcdmhmd 97 
                                       ktt++t++p + G++++ cd    
  gi|313116947|ref|YP_004038071.1| 141 KTTSVTFTPTSTGTFPYWCDVAGH 164
                                       ********************7653 PP

>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   2.1e-08   4.2e-05      28     114 ..      86     175 ..      65     177 .] 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.1e-08
                                       EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.........GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE-- CS
                      Cu-oxidase_3  28 tievregdtvvvnvtNkldentsihwhGlqqrktswmD....GvpgvtqcpiqpgesftyrftvkqqagtlwYhshl 100
                                       +++++ g++++++++N  +    +++  +  ++ +++D    G   v ++ iqpg++ + +ft +   gt+ Y+  +
  gi|313116947|ref|YP_004038071.1|  86 AFQATVGQELTIHFENVGEVAHNLTVGEFPADERTVADqdeeGSFIVKTDTIQPGKTTSVTFTPTS-TGTFPYWCDV 161
                                       5678888888888888776666666666666666665555669999********************.********** PP

                                       TTHHHTT-EEEEEE CS
                      Cu-oxidase_3 101 slqqaaGlaGaiii 114
                                       ++++ aG++G +++
  gi|313116947|ref|YP_004038071.1| 162 AGHREAGMVGEMTV 175
                                       **********9987 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   1.1e-06    0.0021      92     133 ..     134     175 ..      43     177 .] 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                       EEEE-TTEEEEEEEES.S-EEEEEEESSHHHHHTT-EEEEEE CS
                      Cu-oxidase_2  92 tvqvppggwvairfkadnpGvwllHCHilwHldqGmalqfvv 133
                                       t +++pg+++ + f+++ +G + + C ++ H ++Gm+++++v
  gi|313116947|ref|YP_004038071.1| 134 TDTIQPGKTTSVTFTPTSTGTFPYWCDVAGHREAGMVGEMTV 175
                                       446779********************************9987 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.1e-06     0.014      96     138 ..     133     175 ..      60     177 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.1e-06
                              SoxE  96 avsGissGqsasGlledlsaGtywlacgilGhaesGmWvdliv 138
                                       +++ i  G+++s  + + s+Gt+   c ++Gh e+Gm  ++ v
  gi|313116947|ref|YP_004038071.1| 133 KTDTIQPGKTTSVTFTPTSTGTFPYWCDVAGHREAGMVGEMTV 175
                                       5678999******************************877665 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   4.7e-05     0.093       1      25 [.       2      24 ..       2      25 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.7e-05
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalggcaa 25
                                      +lSRR+ L   + + A+++l+gc+a
  gi|313116947|ref|YP_004038071.1|  2 QLSRRNVLG--LSGVALGVLAGCTA 24
                                      58*******..888889******97 PP

>> DUF3553  Protein of unknown function (DUF3553)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.1e-05      0.18      21      39 ..      88     106 ..      73     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.1e-05
                           DUF3553  21 qSaiagrvtvnFenaGkkv 39 
                                       q  +++ +t++Fen+G++ 
  gi|313116947|ref|YP_004038071.1|  88 QATVGQELTIHFENVGEVA 106
                                       8899************986 PP

>> TALPID3  Hedgehog signalling target
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.2    0.0012       2.4     941     992 ..      23      75 ..      14      92 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0012
                           TALPID3 941 dvskketllptPvptPqptppqsPpssek.elspvktPdsSpseseadgavss 992
                                       +++++et+  +P  tP  +p  +P++++   +sp +tP++ p++ + dg++++
  gi|313116947|ref|YP_004038071.1|  23 TAPSEETPGESPTDTPTSSPTATPSPTTDaTPSPTQTPTATPTPNALDGEITV 75 
                                       45666776667777777777776665544146777888888877777777665 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  12.3   0.00051         1       2      36 ..      18      60 ..      17      77 .. 0.64
   2 ?   -0.5   0.1      0.54   1.1e+03     120     120 ..     144     144 ..      86     176 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00051
                           DUF3558  2 llaGCssttdGt.......apaasssassssttsssaapav.p 36
                                      +laGC+++++ t       +p++s++a++s+tt ++++p++ p
  gi|313116947|ref|YP_004038071.1| 18 VLAGCTAPSEETpgesptdTPTSSPTATPSPTTDATPSPTQtP 60
                                      79****7777774546666555555555555555555555542 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.54
                           DUF3558 120 a 120
                                        
  gi|313116947|ref|YP_004038071.1| 144 S 144
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1206.56
//
Query:       gi|313116948|ref|YP_004038072.1|  [L=514]
Description: hypothetical protein Hbor_34140 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   16.2   1.7          2    9.1   0.0    4.3  4  FecR      FecR protein
      0.054   13.3   5.1         28    4.6   0.0    5.3  6  DUF3868   Domain of unknown function, B. Theta Gene descripti


Domain annotation for each model (and alignments):
>> FecR  FecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00022         2      42      93 ..      45      98 ..      20      99 .. 0.80
   2 ?    1.3   0.0     0.061   5.4e+02      59      95 ..     186     227 ..     162     228 .. 0.72
   3 ?    1.4   0.0     0.054   4.9e+02      53      82 ..     220     248 ..     209     284 .. 0.64
   4 ?   -0.7   0.0      0.26   2.4e+03      61      82 ..     414     435 ..     378     458 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00022
                              FecR 42 vsllkGe..vlfdvakdkkrpfevktpsatigvrgtefrvrksdkqtevavleG 93
                                      + l +G+  v  + ++d+ r+ ev+t++++i+  g +++v+++++ +  +  eG
  gi|313116948|ref|YP_004038072.1| 45 IGLASGHdmVVNSHESDASRDVEVETEDGEIEQHGDDVEVEDDEEDLDFESNEG 98
                                      667777754445555666688*******************99999888777777 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.061
                              FecR  59 rpfevktpsatigvrgtef.....rvrksdkqtevavleGeV 95 
                                       +  ev+t +++ +  g +f     +++ +++ + v+  +GeV
  gi|313116948|ref|YP_004038072.1| 186 ESVEVETDEVEYERGGNKFeddasDLEFENDDVDVERDHGEV 227
                                       238999999999999999966554445666666677777777 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.054
                              FecR  53 vakdkkrpfevktpsatigvrgtefrvrks 82 
                                       v++d+  + e++t + +i+  g + +v+k 
  gi|313116948|ref|YP_004038072.1| 220 VERDHG-EVEIETDEHEIEHDGKKLEVEKA 248
                                       444443.36666666666666666555443 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.26
                              FecR  61 fevktpsatigvrgtefrvrks 82 
                                        e +t + +i+ rg +++v+++
  gi|313116948|ref|YP_004038072.1| 414 VEFETDEHEIEQRGDAVEVETH 435
                                       5556666666666666666444 PP

>> DUF3868  Domain of unknown function, B. Theta Gene description (DUF3868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0031        28      15      47 ..      53      85 ..      45      98 .. 0.86
   2 ?    1.8   0.0     0.022     2e+02      29      49 ..     173     193 ..     169     196 .. 0.88
   3 ?    1.7   0.0     0.025   2.3e+02      27      48 ..     226     247 ..     213     280 .. 0.85
   4 ?   -3.8   0.0       1.2   1.1e+04      30      47 ..     330     347 ..     322     357 .. 0.75
   5 ?   -3.0   0.0      0.71   6.4e+03      31      47 ..     347     363 ..     339     364 .. 0.84
   6 ?    2.2   0.0     0.017   1.5e+02      27      48 ..     413     434 ..     405     450 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0031
                           DUF3868 15 lnigeaeaqrsyegkisvkpvqleqkGdslhid 47
                                      +++++ e + s +++++ ++ ++eq+Gd + ++
  gi|313116948|ref|YP_004038072.1| 53 MVVNSHESDASRDVEVETEDGEIEQHGDDVEVE 85
                                      77889999999*******************997 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.022
                           DUF3868  29 kisvkpvqleqkGdslhidid 49 
                                       ++++++ ++eq+G+s+ ++ d
  gi|313116948|ref|YP_004038072.1| 173 DVEFEDNEIEQRGESVEVETD 193
                                       6789999**********9976 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.025
                           DUF3868  27 egkisvkpvqleqkGdslhidi 48 
                                       e++i+  ++++e++G++l ++ 
  gi|313116948|ref|YP_004038072.1| 226 EVEIETDEHEIEHDGKKLEVEK 247
                                       7889999**********99974 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 1.2
                           DUF3868  30 isvkpvqleqkGdslhid 47 
                                       +++ ++  e++G+ l  +
  gi|313116948|ref|YP_004038072.1| 330 VEIDDIDFENDGNRLEFE 347
                                       667788888888887655 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 0.71
                           DUF3868  31 svkpvqleqkGdslhid 47 
                                       + +++ +eq+ ds+ ++
  gi|313116948|ref|YP_004038072.1| 347 ETEDHDIEQDDDSVDVE 363
                                       568999******99885 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.017
                           DUF3868  27 egkisvkpvqleqkGdslhidi 48 
                                       e++ +  ++++eq+Gd + ++ 
  gi|313116948|ref|YP_004038072.1| 413 EVEFETDEHEIEQRGDAVEVET 434
                                       556678899999***9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.15u 0.37s 00:00:01.52 Elapsed: 00:00:00.52
# Mc/sec: 2978.95
//
Query:       gi|313116949|ref|YP_004038073.1|  [L=472]
Description: hypothetical protein Hbor_34150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00073   20.1   0.2         75    4.1   0.0    5.6  6  FecR          FecR protein
  ------ inclusion threshold ------
       0.11   12.2   6.5         34    4.3   0.0    5.6  7  DUF3868       Domain of unknown function, B. Theta Gene descr


Domain annotation for each model (and alignments):
>> FecR  FecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.018   1.6e+02      49      86 ..      31      68 ..      25      74 .. 0.76
   2 ?    0.3   0.0      0.12   1.1e+03      56      85 ..     110     139 ..     103     144 .. 0.77
   3 !    4.1   0.0    0.0084        75      54      84 ..     143     174 ..     123     181 .. 0.74
   4 ?    3.8   0.0      0.01        90      57      86 ..     234     262 ..     211     266 .. 0.80
   5 ?   -1.1   0.0      0.33     3e+03      62      84 ..     280     302 ..     272     328 .. 0.67
   6 ?   -1.3   0.0      0.38   3.4e+03      53      82 ..     364     392 ..     334     395 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.018
                              FecR 49 vlfdvakdkkrpfevktpsatigvrgtefrvrksdkqt 86
                                      ++  +a +++++  ++t++++i+  g e +++++d+ +
  gi|313116949|ref|YP_004038073.1| 31 AMPVAADHQDNEVDIDTEDGEIEHSGDEAEIEDDDDDL 68
                                      4444444555569***************9998888765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                              FecR  56 dkkrpfevktpsatigvrgtefrvrksdkq 85 
                                       d+ ++  v+t + +i+ r  e++v+++++ 
  gi|313116949|ref|YP_004038073.1| 110 DGGDDVDVETDDHEIEQRDDEVEVEDEEND 139
                                       444569999*******99999999877665 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0084
                              FecR  54 akdkkrp.fevktpsatigvrgtefrvrksdk 84 
                                       ++d + +   v+t++a+i+  g + +v+++ +
  gi|313116949|ref|YP_004038073.1| 143 EADDDGDrVDVETGEAEIEQDGDRLEVEDDTD 174
                                       444443349999******99999999976654 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.01
                              FecR  57 kkrpfevktpsatigvrgtefrvrksdkqt 86 
                                       + +++ v+t + +i+ rg + +v+++d+ +
  gi|313116949|ref|YP_004038073.1| 234 G-DDIDVETDEREIEQRGDDLEVEDDDNDL 262
                                       3.3599*****************9998876 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.33
                              FecR  62 evktpsatigvrgtefrvrksdk 84 
                                        ++ + + + v g ef+ +++++
  gi|313116949|ref|YP_004038073.1| 280 DIEHRGGDADVEGEEFEFENDRN 302
                                       56666777777777775544443 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 0.38
                              FecR  53 vakdkkrpfevktpsatigvrgtefrvrks 82 
                                       +++d++ + e++t +  i+  g   +v+k+
  gi|313116949|ref|YP_004038073.1| 364 FENDGD-ETELETDDHDIEHSGDNLDVEKD 392
                                       333333.46667777777777766666555 PP

>> DUF3868  Domain of unknown function, B. Theta Gene description (DUF3868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0    0.0085        76       7      47 ..      18      62 ..      12      71 .. 0.69
   2 ?    4.3   0.0    0.0038        34      26      47 ..      77      98 ..      68     107 .. 0.85
   3 ?   -1.0   0.0      0.16   1.5e+03      28      47 ..     115     134 ..     111     143 .. 0.86
   4 ?    1.4   0.0      0.03   2.7e+02      28      54 ..     151     177 ..     139     184 .. 0.79
   5 ?   -3.9   0.0       1.4   1.2e+04      33      48 ..     192     207 ..     187     213 .. 0.76
   6 ?   -1.2   0.1      0.19   1.7e+03      31      47 ..     240     256 ..     228     265 .. 0.76
   7 ?    0.3   0.0     0.067     6e+02      27      49 ..     370     392 ..     363     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0085
                           DUF3868  7 vlllvvlslnigeae...aq.rsyegkisvkpvqleqkGdslhid 47
                                      +l+l+v  +  g+a+   a+ +  e++i+ ++ ++e++Gd+  i+
  gi|313116949|ref|YP_004038073.1| 18 ILFLMVGMITAGAAMpvaADhQDNEVDIDTEDGEIEHSGDEAEIE 62
                                      45555555555554322144477889999***********98886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0038
                           DUF3868 26 yegkisvkpvqleqkGdslhid 47
                                       e +++++++ leq+Gd l ++
  gi|313116949|ref|YP_004038073.1| 77 DEADVEFEDLDLEQDGDDLEVE 98
                                      578899*************997 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.16
                           DUF3868  28 gkisvkpvqleqkGdslhid 47 
                                       ++++  ++++eq+ d++ ++
  gi|313116949|ref|YP_004038073.1| 115 VDVETDDHEIEQRDDEVEVE 134
                                       5678899*********9986 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.03
                           DUF3868  28 gkisvkpvqleqkGdslhidididlen 54 
                                       ++++  + ++eq+Gd l ++ d d ++
  gi|313116949|ref|YP_004038073.1| 151 VDVETGEAEIEQDGDRLEVEDDTDGHD 177
                                       567788899**********98877555 PP

  == domain 5  score: -3.9 bits;  conditional E-value: 1.4
                           DUF3868  33 kpvqleqkGdslhidi 48 
                                        + ++e++Gd+  +++
  gi|313116949|ref|YP_004038073.1| 192 DETEIEKRGDEADVEL 207
                                       5678999999988775 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 0.19
                           DUF3868  31 svkpvqleqkGdslhid 47 
                                       +  + ++eq+Gd l ++
  gi|313116949|ref|YP_004038073.1| 240 ETDEREIEQRGDDLEVE 256
                                       45567889999999886 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 0.067
                           DUF3868  27 egkisvkpvqleqkGdslhidid 49 
                                       e +++  ++ +e++Gd+l ++ d
  gi|313116949|ref|YP_004038073.1| 370 ETELETDDHDIEHSGDNLDVEKD 392
                                       5678899***********99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.25u 0.35s 00:00:01.60 Elapsed: 00:00:00.52
# Mc/sec: 2726.19
//
Query:       gi|313116950|ref|YP_004038074.1|  [L=109]
Description: hypothetical protein Hbor_34160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.047   14.0   0.7      0.095   13.0   0.6    1.6  1  zf-Di19     Drought induced 19 protein (Di19), zinc-binding
       0.14   12.6   0.8       0.31   11.5   0.1    1.9  2  Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
        1.4    9.5   3.7         41    4.8   0.7    2.6  3  zf-H2C2_2   Zinc-finger double domain


Domain annotation for each model (and alignments):
>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6   1.6e-05     0.095       4      29 ..       6      36 ..       4      41 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                           zf-Di19  4 tCPyCgkel.....tvkeLveHvedeHrves 29
                                      +CPyC + +     +++ Lv+H+ + H+v++
  gi|313116950|ref|YP_004038074.1|  6 ACPYCDEVFqigseEDNPLVDHIREFHTVTE 36
                                      6*****976223224577*********9986 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.2e-05      0.31       1      16 [.       5      20 ..       5      30 .. 0.79
   2 ?   -1.4   0.1      0.58   3.5e+03      14      21 ..      43      50 ..      41      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.2e-05
                        Zn-C2H2_12  1 KeCPlCseqFpknvdq 16
                                      + CP C+e+F+ +++ 
  gi|313116950|ref|YP_004038074.1|  5 RACPYCDEVFQIGSEE 20
                                      78********988765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.58
                        Zn-C2H2_12 14 vdqdeFee 21
                                       +qde+++
  gi|313116950|ref|YP_004038074.1| 43 FSQDELQR 50
                                      58999986 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.7    0.0068        41      17      24 ..       7      14 ..       4      14 .. 0.89
   2 ?    4.7   0.0    0.0077        46       2      11 ..      24      34 ..      24      40 .. 0.85
   3 ?   -2.6   0.0       1.6   9.4e+03       2       6 ..      70      74 ..      70      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0068
                         zf-H2C2_2 17 CplCdkaF 24
                                      Cp+Cd +F
  gi|313116950|ref|YP_004038074.1|  7 CPYCDEVF 14
                                      *****988 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0077
                         zf-H2C2_2  2 LrrHirk.Htg 11
                                      L+ Hir+ Ht+
  gi|313116950|ref|YP_004038074.1| 24 LVDHIREfHTV 34
                                      788***77*96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.6
                         zf-H2C2_2  2 LrrHi 6 
                                      ++rHi
  gi|313116950|ref|YP_004038074.1| 70 YKRHI 74
                                      57896 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 761.28
//
Query:       gi|313116951|ref|YP_004038075.1|  [L=264]
Description: Sugar-specific transcriptional regulator TrmB [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-06   25.5   0.0    1.7e-05   24.6   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00015   21.5   0.0    0.00029   20.6   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00028   20.8   0.1    0.00058   19.7   0.1    1.6  1  HTH_11          HTH domain
    0.00083   19.1   0.0     0.0016   18.2   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
     0.0016   18.0   0.0     0.0027   17.2   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0023   17.8   0.0     0.0069   16.3   0.0    1.7  2  HTH_36          Helix-turn-helix domain
     0.0026   17.5   0.1      0.007   16.1   0.1    1.7  1  HTH_23          Homeodomain-like domain
     0.0026   17.7   0.0     0.0045   16.9   0.0    1.4  1  HTH_45          Winged helix-turn-helix
     0.0048   16.9   0.0      0.014   15.5   0.0    1.8  1  HTH_20          Helix-turn-helix domain
     0.0051   16.4   0.0      0.012   15.2   0.0    1.6  1  GntR            Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.018   15.1   0.2      0.046   13.9   0.2    1.7  1  HTH_28          Helix-turn-helix domain
      0.022   14.7   0.1       0.05   13.6   0.1    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.054   13.4   0.0       0.11   12.5   0.0    1.4  1  MarR            MarR family
      0.073   13.3   0.0       0.14   12.3   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.077   12.9   0.1       0.34   10.8   0.1    2.1  2  MarR_2          MarR family
      0.078   13.5   0.0       0.18   12.3   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
      0.082   13.0   0.0       0.14   12.3   0.0    1.3  1  Trp_repressor   Trp repressor protein
      0.092   12.9   1.3       0.16   12.1   0.1    2.2  2  DUF1724         Domain of unknown function (DUF1724)


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.7e-08   1.7e-05      20      57 ..      28      65 ..      20      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.7e-08
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                       gp   ++i e +gv+rs++Y+++++Le++Gl +r  +
  gi|313116951|ref|YP_004038075.1| 28 DGPQYNRDIRESVGVSRSTAYKAISELEEMGLARRGSE 65
                                      6778889*************************998765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.9e-07   0.00029       3      45 ..      18      60 ..      17      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.9e-07
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                       R +I++ L +g+++  ++ e +g+s+st     + L+e+GL 
  gi|313116951|ref|YP_004038075.1| 18 RRAEIMQRLLDGPQYNRDIRESVGVSRSTAYKAISELEEMGLA 60
                                      799**************************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   5.8e-07   0.00058      18      54 ..      33      67 ..      18      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.8e-07
                            HTH_11 18 geeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr.GY 54
                                        ++ e  +vSr+t ++ I +Lee+g    +++g+ GY
  gi|313116951|ref|YP_004038075.1| 33 NRDIRESVGVSRSTAYKAISELEEMG---LARRGSeGY 67
                                      56788999******************...666666666 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-06    0.0016       1      50 [.      15      62 ..      15      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                                      HHHHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  1 sldRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +++R ++i++ l  +pq   ++++ +  g+++St++  ++ L+e+G+ ++
  gi|313116951|ref|YP_004038075.1| 15 AVSRRAEIMQRLLDGPQY--NRDIRESVGVSRSTAYKAISELEEMGLARR 62
                                      688889999999999997..9**************************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.7e-06    0.0027      20      46 ..      33      59 ..      21      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.7e-06
                            HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGl 46
                                      +r++ e +g+S+st  + + +Lee+Gl
  gi|313116951|ref|YP_004038075.1| 33 NRDIRESVGVSRSTAYKAISELEEMGL 59
                                      89************************7 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     7e-06    0.0069      28      54 ..      33      59 ..      25      60 .. 0.93
   2 ?   -2.0   0.0       3.6   3.6e+03       2      26 ..      68      93 ..      67      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7e-06
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGy 54
                                      ++++ +  g+s++T+++ai eLe+ G+
  gi|313116951|ref|YP_004038075.1| 33 NRDIRESVGVSRSTAYKAISELEEMGL 59
                                      689999******************997 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                            HTH_36  2 rLspsaklllgslasfankngg.cfp 26
                                      +L+ + +ll+ + ++f n  +  c p
  gi|313116951|ref|YP_004038075.1| 68 ELTATGRLLFEEYRRFRNRVEAvCHP 93
                                      79999999999988888888888877 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1     7e-06     0.007       5      47 ..      17      60 ..      14      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7e-06
                            HTH_23  5 reRlrillllae.GlsvreIAreLgvsrrTvyrwlkryreeGle 47
                                       +R++i++ l++  +  r+I +  gvsr+T y+ ++  +e Gl+
  gi|313116951|ref|YP_004038075.1| 17 SRRAEIMQRLLDgPQYNRDIRESVGVSRSTAYKAISELEEMGLA 60
                                      69999999999988899********************9999987 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.5e-06    0.0045      11      74 ..      22      85 ..      18      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-06
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkelee 74
                                      I++ + +g +    i  ++  s +++ k ++ L e gl +  +e Y+lT+ G+ l e+++++++
  gi|313116951|ref|YP_004038075.1| 22 IMQRLLDGPQYNRDIRESVGVSRSTAYKAISELEEMGLARRGSEGYELTATGRLLFEEYRRFRN 85
                                      5555555666777777888889999999*********************************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05     0.014      12      58 ..      19      64 ..      11      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      R++i++ L  ++++   ++ e +++s++t+++ + +Lee gL ++  
  gi|313116951|ref|YP_004038075.1| 19 RAEIMQRL-LDGPQYNRDIRESVGVSRSTAYKAISELEEMGLARRGS 64
                                      999*****.*********************************87755 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.012      28      56 ..      34      62 ..      32      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglver 56
                                      r++++  gVsr+t  +A+++Le+ gl+ r
  gi|313116951|ref|YP_004038075.1| 34 RDIRESVGVSRSTAYKAISELEEMGLARR 62
                                      7899*********************9987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   4.6e-05     0.046       1      41 [.      18      59 ..      18      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                            HTH_28  1 qRleiikllaaGh.svreaArelgisrrtvyrWikryeegGi 41
                                      +R+ei+++l++G    r++ + +g+sr+t y+ i+ +ee G+
  gi|313116951|ref|YP_004038075.1| 18 RRAEIMQRLLDGPqYNRDIRESVGVSRSTAYKAISELEEMGL 59
                                      69**********736666******************999776 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     5e-05      0.05      24      60 ..      33      70 ..      15      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                                      HHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EEES CS
                         HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglisrgrr.iril 60
                                      ++++ + +G++r+t  +++seL++ gl +rg +  +++
  gi|313116951|ref|YP_004038075.1| 33 NRDIRESVGVSRSTAYKAISELEEMGLARRGSEgYELT 70
                                      5677789*********************9863336555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.11      16      49 ..      29      62 ..      28      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      gp+++ ++ + +gvs+st+ +++ +Le+ Gl +R
  gi|313116951|ref|YP_004038075.1| 29 GPQYNRDIRESVGVSRSTAYKAISELEEMGLARR 62
                                      789999************************9777 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.14      26      51 ..      34      59 ..      29      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                      HHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGy 51
                                       d+ e  +vs s++ + +++Le++G+
  gi|313116951|ref|YP_004038075.1| 34 RDIRESVGVSRSTAYKAISELEEMGL 59
                                      6788999******************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00034      0.34      25      54 ..      34      63 ..      15      66 .. 0.92
   2 ?   -2.2   0.0       3.9   3.9e+03      22      37 ..     160     175 ..     152     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                                      HHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 25 gelarrlglsksavsrilkrLvaaGLverr 54
                                      +++ +  g+s+s++ +++ +L++ GL +r 
  gi|313116951|ref|YP_004038075.1| 34 RDIRESVGVSRSTAYKAISELEEMGLARRG 63
                                      699************************985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                                       EEHHHHHHHHTSSHHH CS
                            MarR_2  22 ltvgelarrlglsksa 37 
                                       + +gel+++l  +++a
  gi|313116951|ref|YP_004038075.1| 160 FVAGELEAELVFERAA 175
                                       5689999999888775 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.18      17      65 ..      29      70 ..      19      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                            HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlT 65
                                      +++  +d+++ + v+ s++ +++++L+e+GL  r g+e       ++lT
  gi|313116951|ref|YP_004038075.1| 29 GPQYNRDIRESVGVSRSTAYKAISELEEMGLA-RRGSE------GYELT 70
                                      555569*************************8.44444......45555 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.14      32      65 ..      13      46 ..       9      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                     Trp_repressor 32 realaqRlqvvkeLLkeelsqreIaeelgvSiAt 65
                                      ++a++ R +++++LL++ +  r+I e +gvS  t
  gi|313116951|ref|YP_004038075.1| 13 VDAVSRRAEIMQRLLDGPQYNRDIRESVGVSRST 46
                                      689***************************9877 PP

>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.9   3.9e+03      49      57 ..      73      81 ..      73      82 .. 0.84
   2 ?   12.1   0.1   0.00016      0.16      36      61 ..     231     257 ..     196     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.9
                           DUF1724 49 GeeLFeyYl 57
                                      G+ LFe Y+
  gi|313116951|ref|YP_004038075.1| 73 GRLLFEEYR 81
                                      778*****8 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00016
                           DUF1724  36 k.dlisfdesAlkWGeeLFeyYlkrSe 61 
                                       + +++ ++e A++WGe+  e Y++ + 
  gi|313116951|ref|YP_004038075.1| 231 RgFILNDSENAVEWGEKKWERYREAAA 257
                                       448999****************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1820.75
//
Query:       gi|313116952|ref|YP_004038076.1|  [L=300]
Description: hypothetical protein Hbor_34180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.073   13.2   0.0       0.18   12.0   0.0    1.6  1  GM_CSF    Granulocyte-macrophage colony-stimulating factor


Domain annotation for each model (and alignments):
>> GM_CSF  Granulocyte-macrophage colony-stimulating factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     1e-05      0.18      19      67 ..      13      63 ..       8      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                                      HHHHHHH.HHH----HHHHTSEEEEESS--BSSS.--SHHHHHHHHHHT-S CS
                            GM_CSF 19 ikealsl.lnessdlaavlneevevvseefdlqe.ptclqtrlklykqGlr 67
                                       +ea ++ l+ +++++a  n+ ve v + fd+     clq  l+l++ G +
  gi|313116952|ref|YP_004038076.1| 13 TQEAYDVyLDLAQEVTAHENDVVETVPDFFDIGSvHECLQFPLNLWESGRK 63
                                      567776438999*******************987257**********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2199.80
//
Query:       gi|313116953|ref|YP_004038077.1|  [L=258]
Description: hypothetical protein Hbor_34190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0034   17.2   0.1       0.65    9.8   0.0    2.8  4  DUF3540          Protein of unknown function (DUF3540)
     0.0095   15.8   0.0          8    6.3   0.0    3.2  3  DUF2345          Uncharacterized protein conserved in bacteri
  ------ inclusion threshold ------
      0.017   15.7   0.1         12    6.5   0.0    3.5  3  FecR             FecR protein
        1.5    9.4  13.0         27    5.4   2.1    3.7  3  Cadherin-like    Cadherin-like beta sandwich domain


Domain annotation for each model (and alignments):
>> DUF3540  Protein of unknown function (DUF3540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.16   7.1e+02      69      91 ..      81     103 ..      71     132 .. 0.65
   2 ?    3.4   0.0     0.013        58      62     114 ..     106     158 ..      99     164 .. 0.84
   3 ?    2.1   0.0     0.032   1.5e+02      69     107 ..     145     184 ..     133     191 .. 0.80
   4 !    9.8   0.0   0.00014      0.65      62     106 ..     203     248 ..     197     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                           DUF3540  69 dleleaeaGrlsleaakavalaa 91 
                                       d+++  +++++++ a ++++l+ 
  gi|313116953|ref|YP_004038077.1|  81 DVHVDHDDDEIEVGADDGLELDH 103
                                       47777777777777777777753 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.013
                           DUF3540  62 aklsveGdleleaeaGrlsleaakaval.aaaeeldlaaerlkvsaekaevave 114
                                        +++v+ d ++e +++ l+ e+   +++ +++ e+d+a ++++v+ ++ e++v+
  gi|313116953|ref|YP_004038077.1| 106 DEIEVDDDAHVEHDEDDLEAEGD-DIHVdHGDDEIDAAGDDAHVEHDEDELEVG 158
                                       579999*************8888.6666368899**********9999998876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.032
                           DUF3540  69 dleleaeaGrlsleaakavala.aaeeldlaaerlkvsae 107
                                       d ++e ++++l++ + ++v+++ ++ e++++ ++++v+ +
  gi|313116953|ref|YP_004038077.1| 145 DAHVEHDEDELEVGSDDGVEVDhGDDEIEAEGDDAHVEHD 184
                                       689999**************96267889999888888765 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00014
                           DUF3540  62 aklsveGdleleaeaGrlsleaakavala.aaeeldlaaerlkvsa 106
                                        +++v+Gd e+e +++ l++e+  +v+l+ ++ e+d++ ++++++ 
  gi|313116953|ref|YP_004038077.1| 203 DEIEVDGDAEVEFDDDDLEVEGDGEVELDhGDDEIDVEGDDIEIDH 248
                                       6899************************637789999999998865 PP

>> DUF2345  Uncharacterized protein conserved in bacteria (DUF2345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.014        64      95     127 ..      80     112 ..      65     133 .. 0.74
   2 ?    2.5   0.0     0.027   1.2e+02      75     117 ..     141     175 ..     122     201 .. 0.52
   3 !    6.3   0.0    0.0018         8      83     136 ..     199     250 ..     190     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.014
                           DUF2345  95 kdvtvtStegkieisAkkeillaaggayirleg 127
                                       +dv+v   +++ie+ A++ ++l  g+  i++++
  gi|313116953|ref|YP_004038077.1|  80 DDVHVDHDDDEIEVGADDGLELDHGDDEIEVDD 112
                                       467777777888888888888888777777764 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.027
                           DUF2345  75 AakgkveiqAqsdalellAkkdvtvtStegkieisAkkeilla 117
                                       Aa ++  ++  +d+le+ +++ v+v   +++ie+        +
  gi|313116953|ref|YP_004038077.1| 141 AAGDDAHVEHDEDELEVGSDDGVEVDHGDDEIEA--------E 175
                                       3333333344444444444444444444444333........3 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0018
                           DUF2345  83 qAqsdalellAkkdvtvtStegkieisAkkeillaaggayirleggnIelgtpG 136
                                          +d++e+  + +v++    +++e++ + e++l  g+  i +eg +Ie+   G
  gi|313116953|ref|YP_004038077.1| 199 DHGDDEIEVDGDAEVEFDD--DDLEVEGDGEVELDHGDDEIDVEGDDIEIDHDG 250
                                       5556777777777777765..8999************************98766 PP

>> FecR  FecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.017        75      54      93 ..      59      98 ..      53      99 .. 0.81
   2 ?    6.5   0.0    0.0028        12      19      87 ..     106     189 ..      89     204 .. 0.67
   3 ?    1.4   0.0      0.12   5.2e+02      21      56 ..     205     242 ..     196     255 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                              FecR 54 akdkkrpfevktpsatigvrgtefrvrksdkqtevavleG 93
                                        d +++ e++ ++  +++ g ++ v+++d+++ev   +G
  gi|313116953|ref|YP_004038077.1| 59 DDDDDEEVELDFGDDHVEAEGDDVHVDHDDDEIEVGADDG 98
                                      4455556899999999******************988776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0028
                              FecR  19 svvrlnenssl.ekaadsskrrrevsllkGevlfdvakdkk.............rp.fevktpsatigvrgtefrvr 80 
                                         +++++++++ +   d +++  ++ +++G   +d+a+d +             ++  ev+ ++ +i++ g +  v+
  gi|313116953|ref|YP_004038077.1| 106 DEIEVDDDAHVeHDEDDLEAEGDDIHVDHGDDEIDAAGDDAhvehdedelevgsDDgVEVDHGDDEIEAEGDDAHVE 182
                                       56888888999744444555555699999998888888887777777777777633588888888888888888888 PP

                              FecR  81 ksdkqte 87 
                                       ++++ +e
  gi|313116953|ref|YP_004038077.1| 183 HDGDDFE 189
                                       8888777 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.12
                              FecR  21 vrlnenssl..ekaadsskrrrevsllkGevlfdvakd 56 
                                       ++++ ++++  + +  + + + ev+l++G   +dv++d
  gi|313116953|ref|YP_004038077.1| 205 IEVDGDAEVefDDDDLEVEGDGEVELDHGDDEIDVEGD 242
                                       44555555544333333344445666666666665554 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.24   1.1e+03      53      71 ..      60      78 ..      31      93 .. 0.56
   2 ?    4.8   4.8    0.0093        42      18      70 ..      80     141 ..      44     175 .. 0.86
   3 ?    5.4   2.1     0.006        27      36      75 ..     175     212 ..     159     256 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.24
                     Cadherin-like 53 stetkdvsLneGrnkieik 71
                                      ++   +v+L+ G++ +e +
  gi|313116953|ref|YP_004038077.1| 60 DDDDEEVELDFGDDHVEAE 78
                                      3444445554444444433 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0093
                     Cadherin-like  18 YtvdVdedvdsvtitatae............dsvatvtvngvaveegstetkdvsLneGrnkiei 70 
                                        +v Vd+d d++ + a               d++a+v+ ++++ e    e +d+ ++ G+++i+ 
  gi|313116953|ref|YP_004038077.1|  80 DDVHVDHDDDEIEVGADDGleldhgddeievDDDAHVEHDEDDLE---AEGDDIHVDHGDDEIDA 141
                                       679999999999999999899999988888888899999999998...68999999999998876 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.006
                     Cadherin-like  36 edsvatvtvngvaveegstetkdvsLneGrnkieikvtae 75 
                                       e ++a+v+ +g++ e   ++ + v+++ G+++ie+   ae
  gi|313116953|ref|YP_004038077.1| 175 EGDDAHVEHDGDDFEA--EGDDGVEVDHGDDEIEVDGDAE 212
                                       5566666666666665..5566666666666666554333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.84u 0.30s 00:00:01.13 Elapsed: 00:00:00.44
# Mc/sec: 1755.28
//
Query:       gi|313116954|ref|YP_004038078.1|  [L=83]
Description: hypothetical protein Hbor_34200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 566.13
//
Query:       gi|313116955|ref|YP_004038079.1|  [L=461]
Description: hypothetical protein Hbor_34210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.24u 0.36s 00:00:01.60 Elapsed: 00:00:00.54
# Mc/sec: 2558.17
//
Query:       gi|313116956|ref|YP_004038080.1|  [L=461]
Description: hypothetical protein Hbor_34220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.021   15.4   1.1         41    4.9   0.0    4.5  5  FecR          FecR protein
       0.56   10.7  19.6        0.4   11.1   1.8    4.1  4  HtaA          Htaa


Domain annotation for each model (and alignments):
>> FecR  FecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0047        42      50      90 ..      25      65 ..      14      69 .. 0.76
   2 ?    4.9   0.0    0.0045        41      54      84 ..     138     167 ..     113     210 .. 0.82
   3 ?   -0.9   0.0      0.29   2.6e+03      55      85 ..     228     255 ..     193     259 .. 0.72
   4 ?   -1.0   0.0      0.31   2.8e+03      61      84 ..     273     296 ..     265     322 .. 0.67
   5 ?   -2.8   0.0       1.2   1.1e+04      68      88 ..     338     358 ..     326     366 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0047
                              FecR 50 lfdvakdkkrpfevktpsatigvrgtefrvrksdkqtevav 90
                                       + ++++++++  v+t++++i+  g + +v+++++ +  ++
  gi|313116956|ref|YP_004038080.1| 25 PVAASHGGNDKVDVDTEDGEIEHDGDDAEVEDDENDLDAET 65
                                      45556666677*******************99998877665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0045
                              FecR  54 akdkkrpfevktpsatigvrgtefrvrksdk 84 
                                       ++d  ++  v+t++a+i+  g + +v+++ +
  gi|313116956|ref|YP_004038080.1| 138 EEDD-DEVDVETGEAEIEQSGNRLEVEDDTD 167
                                       3333.34889999999999999998866554 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.29
                              FecR  55 kdkkrpfevktpsatigvrgtefrvrksdkq 85 
                                       +   ++  ++t + +i+  g + +v++++++
  gi|313116956|ref|YP_004038080.1| 228 N---DDVDIDTDDQEIEQDGDDLEVENERNN 255
                                       3...347899999999999999988777665 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.31
                              FecR  61 fevktpsatigvrgtefrvrksdk 84 
                                        e++   + + v g ef+ +++++
  gi|313116956|ref|YP_004038080.1| 273 HEIEHTGSDADVEGEEFEFENDRN 296
                                       566667777777777775544443 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 1.2
                              FecR  68 atigvrgtefrvrksdkqtev 88 
                                         i+ rg +++v+++++ +e 
  gi|313116956|ref|YP_004038080.1| 338 HDIEQRGDDVDVENHEDDVEF 358
                                       467778888888777777665 PP

>> HtaA  Htaa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.058   5.2e+02      69     125 ..      33      86 ..      24     106 .. 0.65
   2 ?   11.1   1.8   4.5e-05       0.4      26     140 ..     118     244 ..     107     261 .. 0.74
   3 ?    5.8   0.8     0.002        18      25      72 ..     275     331 ..     270     350 .. 0.68
   4 ?    3.1   0.2     0.013   1.2e+02      28      77 ..     353     403 ..     349     446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.058
                              HtaA  69 ngaLdltlsnpkievsgetgtLladvsskdkeggekvtkedvalatldlsgakv..kdg 125
                                       n+  d++ ++ +ie +g+ +++  d +       +++t+ed++ a+++ +g+++  +++
  gi|313116956|ref|YP_004038080.1|  33 NDKVDVDTEDGEIEHDGDDAEVEDDEN-----DLDAETNEDEDTADIESDGNEIeqDND 86 
                                       555666666777777776666655533.....245567888888888887766643333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.5e-05
                              HtaA  26 elsggakan..kggafqFpv..asgsvdkdtkkgeirfkGs.vhftgh...........ngaLdltlsnpkievsge 86 
                                       e  +g+++   ++++++F++  +   vd +t+++ei+ +G+ ++++             ++ Ld++  + +ie +g+
  gi|313116956|ref|YP_004038080.1| 118 EKHDGVAEVedDENDLDFEAeeDDDEVDVETGEAEIEQSGNrLEVEDDtdghdldyeaeDDDLDVEHDEAEIEKHGD 194
                                       5555555543566*******765578899999999999999998887788779999999999999999999999999 PP

                              HtaA  87 tgtLladvsskdkeggekvtkedvalatldlsgakvkdgsvslsgapatltaeG 140
                                        +++  d +++ ++ +   ++e ++  ++d++    +++ v++   ++ + ++G
  gi|313116956|ref|YP_004038080.1| 195 DAEVESDNVEY-ENENGDLDFESEDAGDIDIDL---DNDDVDIDTDDQEIEQDG 244
                                       99999997754.333445666666666666643...445555555555555555 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.002
                              HtaA  25 welsggakankggafqFpvas.........gsvdkdtkkgeirfkGsvhftghngaL 72 
                                       +e +g++++ +g++f+F+ ++           v+++++++e+++++ v f++ n   
  gi|313116956|ref|YP_004038080.1| 275 IEHTGSDADVEGEEFEFENDRngidfrndaTDVEQEDDELEVDTDDGVDFESDNEET 331
                                       67777777778888888883334555543245556666************9986655 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.013
                              HtaA  28 sggakan.kggafqFpvasgsvdkdtkkgeirfkGsvhftghngaLdltls 77 
                                       ++ ++++ ++++++F+ +   +++ +++++++ +G v  ++ + + dl+ s
  gi|313116956|ref|YP_004038080.1| 353 EDDVEFEnDENELEFENDDHDIEQSGDRLDVEKDGGVDLESDGETVDLERS 403
                                       56777776889******9988989999**********99999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.16u 0.33s 00:00:01.49 Elapsed: 00:00:00.48
# Mc/sec: 2906.30
//
Query:       gi|313116957|ref|YP_004038081.1|  [L=130]
Description: HxlR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-20   72.3   0.0    3.3e-20   71.7   0.0    1.3  1  HxlR      HxlR-like helix-turn-helix


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   1.9e-24   3.3e-20       1      79 [.      39     118 ..      39     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 1.9e-24
                                       HHHSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                              HxlR   1 liggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76 
                                       lig kW+l+i+ +ll+ g++ fsel++++ +is+k+La +L+ Le   +++re+++e P +veYslt++G + e ++
  gi|313116957|ref|YP_004038081.1|  39 LIGRKWNLVIVAKLLHgGPMGFSELEAEIDGISNKVLAVSLQTLEDYDVVDREIVSERPFRVEYSLTQQGLAFESII 115
                                       69*************989********************************************************999 PP

                                       HHH CS
                              HxlR  77 qel 79 
                                         +
  gi|313116957|ref|YP_004038081.1| 116 RRV 118
                                       876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 925.43
//
Query:       gi|313116958|ref|YP_004038082.1|  [L=106]
Description: hypothetical protein Hbor_34240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 770.61
//
Query:       gi|313116959|ref|YP_004038083.1|  [L=130]
Description: HxlR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-25   88.3   0.0    2.8e-25   88.0   0.0    1.1  1  HxlR      HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.074   12.9   0.0      0.097   12.6   0.0    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
       0.11   12.5   0.0       0.16   12.0   0.0    1.3  1  PadR      Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0   4.6e-29   2.8e-25       1      89 [.      32     121 ..      32     123 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 4.6e-29
                                       HHHSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                              HxlR   1 liggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76 
                                       lig+kW+ +i++ ll+ g+  f+elk+ + +is k+L+ +L  Le++++++re+++e P +v+Yslt++G sl+p++
  gi|313116959|ref|YP_004038083.1|  32 LIGKKWHPVIIHRLLEhGPSGFNELKEDVDGISSKVLSDSLEDLEEKQIVNREIISERPFRVQYSLTHHGDSLSPII 108
                                       79***********9988************************************************************ PP

                                       HHHHHHHHHHHHC CS
                              HxlR  77 qelkkwgeeylee 89 
                                        ++ +wg e+l+e
  gi|313116959|ref|YP_004038083.1| 109 YAMRDWGLEHLSE 121
                                       *******998865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05     0.097      17      58 ..      45      87 ..      43     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                                      HHHHCCCHHCHHCCCT.TSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 17 Llklgpatadeiaeel.gvprskvYevLrsLedkGlVerekgr 58
                                      Ll++gp+  +e+ e++ g++     ++L+ Le+k +V+re  +
  gi|313116959|ref|YP_004038083.1| 45 LLEHGPSGFNELKEDVdGISSKVLSDSLEDLEEKQIVNREIIS 87
                                      9**************9446666669************998644 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.6e-05      0.16      30      70 ..      64     102 ..      41     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                                       THHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCC CS
                              PadR  30 seGslYpaLkrLekeglveseweesgegpprkyYrlTdaGr 70 
                                       s   l + L++Le++++v++e     e+p r  Y lT  G+
  gi|313116959|ref|YP_004038083.1|  64 SSKVLSDSLEDLEEKQIVNREIIS--ERPFRVQYSLTHHGD 102
                                       555566789************986..69**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 756.08
//
Query:       gi|313116960|ref|YP_004038084.1|  [L=225]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-32  110.7   0.0    1.1e-31  109.9   0.0    1.4  1  DDE_Tnp_IS240  DDE domain
    1.1e-06   28.3   0.3    2.3e-06   27.3   0.3    1.6  1  rve_3          Integrase core domain
  ------ inclusion threshold ------
       0.03   14.5   0.1      0.059   13.6   0.1    1.7  1  rve            Integrase core domain
      0.037   13.8   0.0        1.5    8.6   0.0    2.2  2  DDE_3          DDE superfamily endonuclease
       0.05   13.1   0.1       0.11   12.0   0.1    1.5  1  DDE_Tnp_IS66   Transposase IS66 family


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.0   3.2e-35   1.1e-31       2     140 .]      80     212 ..      79     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 3.2e-35
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkel 77 
                                       k+++vDET+vki+G+w++ly+a+D e++ ild+ ++ r +t++a+afl+++ +k++l+++++++D+++ y++al++l
  gi|313116960|ref|YP_004038084.1|  80 KRVAVDETAVKINGEWSWLYAAIDIETKlILDVELFGRHGTDPAAAFLHRLSEKHDLSDAVFLVDGYG-YQTALSRL 155
                                       789*****************************************************************.******** PP

                     DDE_Tnp_IS240  78 kregelfdevshvqvkylnnriEsdhrtlKkrl..rptrgfkslksaaktlagfeavknlrkghk 140
                                       + +g+ +d+       +++n iE+++ tlK+r+  ++++++ s  s++++  +f+ ++n++++h+
  gi|313116960|ref|YP_004038084.1| 156 GLSGR-LDY-------VERNLIEKWFHTLKMRVdrFHNSWVGSHGSIREWFIQFAQYYNFQRPHQ 212
                                       **887.455.......789**************9889**************************95 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.3   6.5e-10   2.3e-06      35      67 .]     187     219 ..     165     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.5e-10
                             rve_3  35 lfrslaearekleawredYNteRPHssLgykTP 67 
                                       +  s    re+  ++ ++YN +RPH+sL+++TP
  gi|313116960|ref|YP_004038084.1| 187 WVGSHGSIREWFIQFAQYYNFQRPHQSLNGRTP 219
                                       355777789999********************9 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.6e-05     0.059       6      73 ..      80     144 ..      75     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                               rve   6 elwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsD 73 
                                       +++ vD t v+i   g++++l++++d  ++lil + l  ++ ++ ++a+l+r  ++   +   ++l D
  gi|313116960|ref|YP_004038084.1|  80 KRVAVDETAVKIN--GEWSWLYAAIDIETKLILDVELFGRHGTDPAAAFLHRLSEKHDLS-DAVFLVD 144
                                       6788999*99955..447*********************************999888776.4666666 PP

>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00041       1.5      29      91 ..      87     149 ..      70     153 .. 0.87
   2 ?    2.8   0.2     0.026        92     120     135 ..     167     182 ..     165     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00041
                             DDE_3  29 leeygrrgrvnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDnasiH 91 
                                        + +++++  +l++a+d +++l++ v   ++  ++  a+fl rl e+++ +   v+++D+ ++ 
  gi|313116960|ref|YP_004038084.1|  87 TAVKINGEWSWLYAAIDIETKLILdVELFGRHGTDPAAAFLHRLSEKHDLS-DAVFLVDGYGYQ 149
                                       5667888999**************9999999999999*************8.999999988775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.026
                             DDE_3 120 NpiEivwsklkrellk 135
                                       N iE++++ lk ++ +
  gi|313116960|ref|YP_004038084.1| 167 NLIEKWFHTLKMRVDR 182
                                       9**********98876 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     3e-05      0.11      13     135 ..      31     148 ..      27     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                      DDE_Tnp_IS66  13 lvlkyadhlPlyRqeeilarlGvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkgkk 89 
                                       +v+ +a +++l+  +eil+ lGve s +++ +wv+r a+   +  ea        +++++DET ++       +g+ 
  gi|313116960|ref|YP_004038084.1|  31 AVQLHATGCSLRETKEILRILGVERSHQAVWQWVHRLADSGHNPPEATP------KRVAVDETAVK------INGEW 95 
                                       57789999*******************************9877777755......56789******......78888 PP

                      DDE_Tnp_IS66  90 sylWvyvtdkrkpavlfeysp.sRg.gevaealLag.......fkGvlvsDgyag 135
                                       s+l++++  ++    +++++  +R  ++ a a+L            v  +Dgy+ 
  gi|313116960|ref|YP_004038084.1|  96 SWLYAAIDIET--KLILDVELfGRHgTDPAAAFLHRlsekhdlSDAVFLVDGYGY 148
                                       88888887774..222233222333133445554444445655446777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1472.28
//
Query:       gi|313116961|ref|YP_004038085.1|  [L=377]
Description: citrate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   3.6e-105  352.0   0.0   4.1e-105  351.8   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain
  ------ inclusion threshold ------
       0.11   12.6   0.2         14    5.8   0.0    2.6  2  TetR_C_27     Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.8   0.0  4.6e-109  4.1e-105       1     361 []       9     360 ..       9     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 351.8 bits;  conditional E-value: 4.6e-109
                                       GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHH CS
                      Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlea 77 
                                       gl++v ++et++s++dge gel+  G++++eLa  ++++ee ++lLl+ +lP++eel++f+++la++r + ++v   
  gi|313116961|ref|YP_004038085.1|   9 GLEDVSVAETRLSQIDGEVGELTIGGFPVDELA-VNATYEESVFLLLHDRLPSSEELDDFRSDLAARRGIGDEVHAV 84 
                                       7999*****************************.7****************************************** PP

                                       HHCSS.TTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHH CS
                      Citrate_synt  78 lealp.kdahpmavlraavsalsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyae 153
                                       l+++  ++   m++lr++ +a          +e+ +e++ r    ++A +pti+a+++r+ ++++p+ep+ + s+a+
  gi|313116961|ref|YP_004038085.1|  85 LQRAAdEQKPAMDALRMGAAAATLGT----GDEDVDEDIRR----IVAVFPTIVATYWRYLQDEDPVEPRAEFSHAK 153
                                       **666588899******999955543....45666777777....******************99*****99***** PP

                                       HHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHH CS
                      Citrate_synt 154 nflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmlee 230
                                       n+lyml+g +p+++e++ l+++l  + DH+lnaSTf arvv St +d+ sa++a++g+lkGplhgga   vl+ml+ 
  gi|313116961|ref|YP_004038085.1| 154 NYLYMLNGVEPTDDEVRGLETYLNTVIDHGLNASTFSARVVVSTESDVVSAVTAAVGTLKGPLHGGAPGPVLDMLQT 230
                                       ***************************************************************************** PP

                                       HSSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHH. CS
                      Citrate_synt 231 igsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklaeeleevapevlkeke. 306
                                       ++++  + eey++++la++ erl+GfGHrvy++ DpRa++l e+ae+ +e  ++d+ +++++ +e+va ++l+e++ 
  gi|313116961|ref|YP_004038085.1| 231 VHESG-NPEEYVRETLAAG-ERLMGFGHRVYRVRDPRAAVLSEAAERFYEASDDDEFFQTVTSFEDVAVDILEEHKp 305
                                       *6665.***********86.*******************************************************9* PP

                                       GCT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------E CS
                      Citrate_synt 307 eknlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileqladnkiiRPr 361
                                       ++ l +Nv+fy+++l++ +g+p+elft+ f+isRv Gw+Ah +eql+dn++iRPr
  gi|313116961|ref|YP_004038085.1| 306 DRRLQTNVEFYTAALLHGVGVPKELFTATFGISRVGGWTAHCREQLEDNRLIRPR 360
                                       ******************************************************8 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0016        14      46      81 ..     170     205 ..     162     218 .. 0.79
   2 ?    4.0   0.1    0.0055        49      18      44 ..     277     303 ..     265     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHCT-STT--HHHHHHHHHHHS CS
                         TetR_C_27  46 eeleeqlaeIireGvaaGeFkaadpeaaaravfdat 81 
                                       + le +l ++i++G +a +F+a+ + ++ + v+ a+
  gi|313116961|ref|YP_004038085.1| 170 RGLETYLNTVIDHGLNASTFSARVVVSTESDVVSAV 205
                                       56899****************998887766555544 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0055
                                       HHHHH-HHHHHHHHHHHHH-HHHHHHH CS
                         TetR_C_27  18 rkarddpelFatyvvlieeelevvekh 44 
                                        +a dd e+F+t+++  + ++++ e+h
  gi|313116961|ref|YP_004038085.1| 277 YEASDDDEFFQTVTSFEDVAVDILEEH 303
                                       5799***********999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2803.68
//
Query:       gi|313116962|ref|YP_004038086.1|  [L=370]
Description: dissimilatory nitrite reductase (NO-forming), copper type apoprotein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-10   39.8   0.1    7.6e-10   38.8   0.1    1.5  1  Cu-oxidase_3  Multicopper oxidase
    2.4e-06   27.9   0.4    2.1e-05   24.9   0.1    2.6  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    3.2e-06   26.9   1.2    0.00011   22.0   0.4    2.8  2  Cu-oxidase_2  Multicopper oxidase
     0.0054   16.8   0.0      0.011   15.8   0.0    1.6  1  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.1   1.7e-13   7.6e-10       3     118 ..      80     192 ..      78     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.7e-13
                                       EEEEEECTTEESEEEEEECTSSBS-EEEEETT-EEEEEEEE-S..SS-B-EEEET--S-GG.....GSCSGGG-B-T CS
                      Cu-oxidase_3   3 tektvsplggterevitvNgqfpgptievregdtvvvnvtNkl..dentsihwhGlqqrktswmDGvpgvtqcpiqp 77 
                                       +e t++++ g++ + +t++gq+pgp i+vr+gdtv  +++N    d +  + +h +   +        g      +p
  gi|313116962|ref|YP_004038086.1|  80 KEVTAEIEPGVTFNYMTFDGQIPGPMIRVRQGDTVSFTLKNLPenDMPHNVDMHAIYGTGG-------GSVATTAAP 149
                                       66788888889999***************************88445567788888887777.......56678889* PP

                                       T-EEEEEEE--S-SEEEEEEE--TT...HHH.TT-EEEEEEE-HH CS
                      Cu-oxidase_3  78 gesftyrftvkqqagtlwYhshlsl...qqa.aGlaGaiiiedke 118
                                       ge+ + +f++    g + Yh  + +   +   aG++G+i++e+ke
  gi|313116962|ref|YP_004038086.1| 150 GEENSEQFKAMY-PGAYIYHCAVPNldyH-IsAGMFGIILVEPKE 192
                                       ************.*******999888745.45**********986 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   4.8e-09   2.1e-05      17      99 .]     104     189 ..      84     189 .. 0.77
   2 ?   -0.8   0.0      0.48   2.2e+03      37      72 ..     206     244 ..     203     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.8e-09
                                       SEEEEETTEEEEEEEE....SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEET.T CS
                       Copper-bind  17 keitvkkgekvtfvnl....avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffCs.P 86 
                                         i+v +g++v f+ +    ++m+HNv +++     g  + +++a       ++Ge+ s +f+   +g+Y ++C+ P
  gi|313116962|ref|YP_004038086.1| 104 PMIRVRQGDTVSFTLKnlpeNDMPHNVDMHAIY-GTGGGSVATTA-------APGEENSEQFKamYPGAYIYHCAvP 172
                                       479*******9887666899*******998744.23444444444.......79*********888999*******9 PP

                                       ....TTTTTSEEEEEEE CS
                       Copper-bind  87 ....HaaagMkgkvtve 99 
                                           H +agM g + ve
  gi|313116962|ref|YP_004038086.1| 173 nldyHISAGMFGIILVE 189
                                       9999********99885 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.48
                                       BEEEEET...TSSTTTGGGTTSCTTCEEEEBSTTEEEEE CS
                       Copper-bind  37 HNvvldk...dgvpagvdkdkvkaedetkliggGekdsv 72 
                                       H + +dk    + ++g+d +++  ed t++  +Gek+  
  gi|313116962|ref|YP_004038086.1| 206 HELYTDKeagTKGHHGFDFEAMAREDPTYVLLNGEKYAY 244
                                       555555533323356788888888889999999999875 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.4   2.4e-08   0.00011       2     136 ..      65     191 ..      64     192 .. 0.76
   2 ?   -1.7   0.0       0.5   2.3e+03      60      74 ..     220     240 ..     219     277 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.4e-08
                                       XS-SCCCCCCCEEEEEEEEEEE.......ETCCTT..TSSEEEEEETTEEEEEEEEE..-SSS-EEEEESS-EEEEE CS
                      Cu-oxidase_2   2 vppklptllqltsgneeaseit.......ngeefs..entnvitlpkgevveiviqn..ntklpHPfHlHGhdfqvl 67 
                                       v++++p+++++t  ++e +          n ++f+     ++i++++g++v ++++n  ++++pH + +H     + 
  gi|313116962|ref|YP_004038086.1|  65 VDWSEPKHHDVTLETKEVTA-EiepgvtfNYMTFDgqIPGPMIRVRQGDTVSFTLKNlpENDMPHNVDMHA----IY 136
                                       67888888888855444443.24888888777666667889999999999999999954444477776664....47 PP

                                       EEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEES.S-EEEEEEESSH...HHHHTT-EEEEEEECH CS
                      Cu-oxidase_2  68 grgpgndpeedpksynlenpvrrdtvqvppggwvairfkadnpGvwllHCHil...wHldqGmalqfvvrpd 136
                                       g+g+g+                  t++  pg++   +fka +pG++++HC +    +H ++Gm + ++v+p+
  gi|313116962|ref|YP_004038086.1| 137 GTGGGS----------------VATTAA-PGEENSEQFKAMYPGAYIYHCAVPnldYHISAGMFGIILVEPK 191
                                       888888................456665.67888889*************876667**********999986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.5
                                       SS-EEEEEEEEECC......C CS
                      Cu-oxidase_2  60 HGhdfqvlgrgpgn......d 74 
                                       HG+df+ ++r+  +      +
  gi|313116962|ref|YP_004038086.1| 220 HGFDFEAMAREDPTyvllngE 240
                                       888998888777664443330 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.5e-06     0.011      36      94 ..     105     171 ..      71     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-06
                      Cupredoxin_1  36 kievkagekvklkiknkdkt..peefesed......lgeekvlapgktttitiaplkpGeYeftcdm 94 
                                        i v +g  v++++kn  +   p+++ ++        ++ ++ apg++++ ++++ +pG Y ++c  
  gi|313116962|ref|YP_004038086.1| 105 MIRVRQGDTVSFTLKNLPENdmPHNVDMHAiygtggGSVATTAAPGEENSEQFKAMYPGAYIYHCAV 171
                                       699*************9888446999999999999999***************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2324.01
//
Query:       gi|313116963|ref|YP_004038087.1|  [L=766]
Description: nitric oxide reductase, NorZ apoprotein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-58  198.7  52.9    1.5e-58  198.7  52.9    1.6  2  COX1      Cytochrome C and Quinol oxidase polypeptide I
    8.2e-05   22.9   1.4    8.2e-05   22.9   1.4    2.2  2  DUF2871   Protein of unknown function (DUF2871)


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2      0.22     2e+03     156     252 ..     225     241 ..     187     249 .. 0.62
   2 !  198.7  52.9   1.7e-62   1.5e-58       2     431 ..     274     722 ..     273     723 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSCE-HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHTSC CS
                              COX1 156 vwavlatailillalpvlalalllllldrslgkffspgdplldqhlfWffgHpeVyililpalgivyyilpkfagrp 232
                                       +w+v+++++l++ +                                                               
  gi|313116963|ref|YP_004038087.1| 225 TWSVISMVLLVAAV--------------------------------------------------------------- 238
                                       22222222222222............................................................... PP

                                       CCTHHHHHHHHHHHHHHCCC CS
                              COX1 233 lfsyklsvlafililflsfl 252
                                                        ++ 
  gi|313116963|ref|YP_004038087.1| 239 -----------------GIG 241
                                       .................222 PP

  == domain 2  score: 198.7 bits;  conditional E-value: 1.7e-62
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT...............-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHH CS
                              COX1   2 igllylilalvlllvggllgllirlqlafp...............dletynqlrtlHgnlmiflfatpfilgfgnyl 63 
                                       +++ ++ la +l+++++llg l++++++                 + + ++ + t H+ l+i+++a  + lg+g++l
  gi|313116963|ref|YP_004038087.1| 274 AATRFIPLAGALFALQVLLGGLLAHYYVERhaffgieklfgveliSVLPFSLAKTFHLDLAILWIASLW-LGAGLFL 349
                                       57789999*******************6333333344444444445588********************.******* PP

                                       HHHHHCTSS-S-HHHHHHHHHHHHHHHHH.HHHHHHCS............S-STTTTTTTC.SHHHHHHHHHHHHHH CS
                              COX1  64 vplllgardlafprlnalsfwlvvlgvvl.lllsllga............attgwteYaplsevdlwllglllvvvs 127
                                        pll++ ++  ++    +++ ++++++v+ l+  ++ga            +++g  eY++   ++lw++gll++   
  gi|313116963|ref|YP_004038087.1| 350 PPLLTNYEPPRQKTYIHVLLGALIVAAVGgLAGIWFGAqgyidgalwwilGNEGL-EYLE--VGRLWQVGLLVG--- 420
                                       *****9999999988888888666666664777777444568888****9****5.***9..**********99... PP

                                       HHHHHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSCE-HHHHHHHHHH CS
                              COX1 128 sllgainfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslgkffspgdplldqhlfWf 204
                                       ++l+ + +++ + +  +++      +l+   v+a   ++ll+++++ ++  +++              ++ ++++W+
  gi|313116963|ref|YP_004038087.1| 421 FVLWTALVWRGFRPLIKRESRYGLAHLI---VYAGGSIGLLFTAGMLYTPQTNI--------------VMTEFWRWW 480
                                       4446777777777744444444444555...88888899999999999998987..............9******** PP

                                       HHTHHH.HHHHHHHHHHHHHHHHHHHT..SCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHT CS
                              COX1 205 fgHpeV.yililpalgivyyilpkfag..rplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslli 278
                                       ++H++V + ++++++ iv   l+ + g  ++  ++k+++++++ ++  ++++ aHH++++g p+++  lgsvfs+l+
  gi|313116963|ref|YP_004038087.1| 481 VVHMWVeGAFEFFIVSIVGLTLVSM-GllKKRSAEKAVAFQALFVMGSGVIGAAHHYWWVGQPDVWVPLGSVFSTLE 556
                                       *************************.779************************************************ PP

                                       HHHHHHCCCHHHHCC.....TTS-CHCHHHHHHHHHHHHHH.HHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTT CS
                              COX1 279 avPsglkvfnwlatl.....wrgsirfktpmlfflgfavlf.iigGltGvllalpsvnyvvhntywvvaHfHlvllg 349
                                        +P++l +f  ++         + + ++ p++f++++++++ +++G+ G++++lp +ny+ h+ty++v+H+H++++g
  gi|313116963|ref|YP_004038087.1| 557 LIPLILILFEAMGQYralatSDDGFPYTLPFMFIIASGFWNfVGAGVLGFFINLPLINYYEHGTYLTVGHAHAAMFG 633
                                       ******666655555554422444556************************************************** PP

                                       HHHHHHHHHHHHHHHHHH.SB.--HHHHHHHHHHHHHHHHHHHHH.HHHHHHHTTHB.........SSSST--SCCC CS
                              COX1 350 avvfllfaaiyyllpklt.gr.mlserlaklhfwllfiGlvlmfl.pmhilGllgmp.........rraadyksfle 414
                                       a++fl++++ +y+l ++  +  ++  +  +++fwl++iGl++m++ + +++G+l +          +r+     +++
  gi|313116963|ref|YP_004038087.1| 634 AFGFLALGMATYML-RISaKPaQWTGKRLRWAFWLWNIGLAVMVFvSVLPVGFLQLEtaftqsyaaARSL----AFY 705
                                       **************.66633337788888************99999********6664554433332222....233 PP

                                       CHHHCHHHHHHHHHHHH CS
                              COX1 415 tvpelqplnvlrtiggv 431
                                       + + +q l ++r  g++
  gi|313116963|ref|YP_004038087.1| 706 NGELVQLLFWARLPGDT 722
                                       45677888888888876 PP

>> DUF2871  Protein of unknown function (DUF2871)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1      0.91   8.2e+03      75      87 ..     448     463 ..     412     472 .. 0.49
   2 !   22.9   1.4   9.1e-09   8.2e-05      21     101 ..     606     693 ..     589     707 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.91
                           DUF2871  75 ivY...niglvltvvm 87 
                                       ivY    igl++t++m
  gi|313116963|ref|YP_004038087.1| 448 IVYaggSIGLLFTAGM 463
                                       2221112344444444 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 9.1e-09
                           DUF2871  21 fyReftklneftgktqLsvvHtHllvLGfvvfLlvllleklfkls......eekkfkkffivYniglvltvvm.mlv 90 
                                       f+ ++  +n +++ t L+v H+H  ++G + fL + + + ++++s      + k++++ f+++nigl+++v + +l 
  gi|313116963|ref|YP_004038087.1| 606 FFINLPLINYYEHGTYLTVGHAHAAMFGAFGFLALGMATYMLRISakpaqwTGKRLRWAFWLWNIGLAVMVFVsVLP 682
                                       55677778899999*******************99888888888843333345899************998651556 PP

                           DUF2871  91 rGilqvlgael 101
                                        G+lq+  a +
  gi|313116963|ref|YP_004038087.1| 683 VGFLQLETAFT 693
                                       79999877433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4874.16
//
Query:       gi|313116964|ref|YP_004038088.1|  [L=92]
Description: hypothetical protein Hbor_34310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00028   20.6   1.2    0.00034   20.3   1.2    1.1  1  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
  ------ inclusion threshold ------
      0.034   14.3   1.0       0.12   12.5   0.5    1.9  2  YtpI       YtpI-like protein
      0.043   13.7   3.0      0.051   13.5   3.0    1.1  1  DUF4345    Domain of unknown function (DUF4345)
      0.059   13.5   0.0       0.11   12.6   0.0    1.5  1  DUF2534    Protein of unknown function (DUF2534)


Domain annotation for each model (and alignments):
>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.2   7.7e-08   0.00034     119     186 ..      15      82 ..       3      90 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.7e-08
                         CPP1-like 119 palllalglgasiyflnrKek.klgravlltlvgLvvGlllGsllasllqvdvalsglsseellvslvt 186
                                       +alll  ++    +  +r+ +   +ra+++++++  +G+++G+++ +ll+ d++l+ l+ e+l++++  
  gi|313116964|ref|YP_004038088.1|  15 LALLLGGSITYHAFKAYRRTRsPALRALAIGFGVVTLGAIFGGVVDQLLPLDPNLA-LVVESLFTTVGF 82 
                                       5566666666666666677663689************************9988888.444554555433 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0048        21      57      83 ..       8      34 ..       4      38 .. 0.84
   2 ?   12.5   0.5   2.7e-05      0.12      15      75 ..      27      87 ..      15      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0048
                              YtpI 57 valvvgavflvlGlanlfaGiraykhy 83
                                        +v  ++ l+lG   ++++++ay++ 
  gi|313116964|ref|YP_004038088.1|  8 ALVVLKTLALLLGGSITYHAFKAYRRT 34
                                      557889999***************975 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.7e-05
                              YtpI 15 kvka.frtkdplekkllsakasialGlflilfgin.qllllestvalvvgavflvlGlanlfa 75
                                       +ka +rt++p+ ++l  +   ++lG++  + g++ qll l+  +alvv+ +f  +G++ +++
  gi|313116964|ref|YP_004038088.1| 27 AFKAyRRTRSPALRALAIGFGVVTLGAI--FGGVVdQLLPLDPNLALVVESLFTTVGFGIILY 87
                                      44443999******************85..568889*********************998876 PP

>> DUF4345  Domain of unknown function (DUF4345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.0   1.1e-05     0.051      38     114 ..       2      80 ..       1      85 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                           DUF4345  38 natldselRflaglllglGllllwaipri..ekrraalrllalviflgglgRliSlaldglpsaflivalvvElvla 112
                                       ++++ + l  l  l l lG ++ + ++++  ++r+ alr+la+ ++++ lg + + ++d l +    +alvvE ++ 
  gi|313116964|ref|YP_004038088.1|   2 TPNVATALVVLKTLALLLGGSITYHAFKAyrRTRSPALRALAIGFGVVTLGAIFGGVVDQLLPLDPNLALVVESLFT 78 
                                       56777778888889999***********97778899************************88877788999999887 PP

                           DUF4345 113 pl 114
                                        +
  gi|313116964|ref|YP_004038088.1|  79 TV 80 
                                       66 PP

>> DUF2534  Protein of unknown function (DUF2534)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.5e-05      0.11      15      62 ..      39      89 ..      29      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                           DUF2534 15 llivfivalsvvsratigGvidqYnlPl....seWttsmfliqgamvavYsl 62
                                      l +++i  + v   a++gGv+dq  lPl    +    s+f + g+ +++Ysl
  gi|313116964|ref|YP_004038088.1| 39 LRALAIGFGVVTLGAIFGGVVDQL-LPLdpnlALVVESLFTTVGFGIILYSL 89
                                      445555556666689********6.565111156678*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 588.57
//
Query:       gi|313116965|ref|YP_004038089.1|  [L=124]
Description: IclR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-11   44.7   0.2    1.5e-11   44.1   0.2    1.3  1  HTH_20    Helix-turn-helix domain
    0.00013   21.7   0.0    0.00029   20.6   0.0    1.6  1  HTH_IclR  IclR helix-turn-helix domain
    0.00051   19.9   0.0    0.00074   19.4   0.0    1.3  1  MarR_2    MarR family
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.023   14.6   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.078   13.1   0.0       0.16   12.1   0.0    1.5  1  HTH_7     Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.2   4.3e-15   1.5e-11       1      59 [.      14      70 ..      14      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 4.3e-15
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +++++AL++P  r i  ++  ++++ta+++a+++d++ +t ++ L+ L+ea L+e + e
  gi|313116965|ref|YP_004038089.1| 14 QDVLDALDDPDCRTIIEHI--DGAMTANDIADACDVPLSTTYRKLDLLSEASLLEEQVE 70
                                      689****************..*********************************98755 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   8.2e-08   0.00029      15      50 ..      32      67 ..      15      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.2e-08
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       ++++t  ++A+++++p St++R L  L e  ++e 
  gi|313116965|ref|YP_004038089.1| 32 IDGAMTANDIADACDVPLSTTYRKLDLLSEASLLEE 67
                                      4788************************99999985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.1e-07   0.00074      20      61 ..      26      76 ..      11      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.1e-07
                                      S........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS.SSS CS
                            MarR_2 20 r........dltvgelarrlglsksavsrilkrLvaaGLverrpgpe.DkR 61
                                      r         +t++++a++++++ s++ r l+ L++a L+e++  ++ D+R
  gi|313116965|ref|YP_004038089.1| 26 RtiiehidgAMTANDIADACDVPLSTTYRKLDLLSEASLLEEQVELRtDGR 76
                                      45555555569*****************************99944444888 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.3e-06     0.023      21      55 ..      34      68 ..      31      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.3e-06
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      g +ta++ia + +vp s+ Y+ L  L+++ l e +
  gi|313116965|ref|YP_004038089.1| 34 GAMTANDIADACDVPLSTTYRKLDLLSEASLLEEQ 68
                                      889***********************999888876 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.4e-05      0.16      20      42 ..      33      56 ..      20      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                                      TT.--STTTSSSS---SSSS--SS CS
                             HTH_7 20 eG.isiskIAkevnisRsTvYRyl 42
                                      +G +++++IA++ ++  sT YR+l
  gi|313116965|ref|YP_004038089.1| 33 DGaMTANDIADACDVPLSTTYRKL 56
                                      466*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 832.64
//
Query:       gi|313116966|ref|YP_004038090.1|  [L=218]
Description: DNA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-18   66.4   0.1    2.4e-18   65.6   0.1    1.4  1  HTH_10    HTH DNA binding domain
     0.0021   17.8   1.7        0.1   12.4   0.0    2.7  3  HTH_IclR  IclR helix-turn-helix domain
     0.0038   17.1   0.2     0.0075   16.2   0.2    1.5  1  BAT       GAF and HTH_10 associated domain
     0.0068   16.3   0.0      0.012   15.5   0.0    1.4  1  PuR_N     Bacterial purine repressor, N-terminal
  ------ inclusion threshold ------
      0.012   15.5   0.2      0.051   13.5   0.1    2.2  3  MarR_2    MarR family
       0.03   14.4   0.0      0.053   13.6   0.0    1.3  1  HTH_35    Winged helix-turn-helix DNA-binding
      0.047   13.3   0.0       0.16   11.5   0.0    1.9  2  HTH_24    Winged helix-turn-helix DNA-binding
      0.072   13.1   0.1       0.14   12.2   0.1    1.5  1  NYD-SP28  Sperm tail
      0.076   13.1   0.7       0.92    9.6   0.4    2.6  3  HTH_20    Helix-turn-helix domain
       0.14   12.4   0.0        0.3   11.3   0.0    1.5  1  UPF0122   Putative helix-turn-helix protein, YlxM / p13 like


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.1   1.4e-21   2.4e-18       1      53 []     150     202 ..     150     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.4e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT++ql+ + +A+e GY+d+PR+++l +LA++l ++kst se L +ae+k+++
  gi|313116966|ref|YP_004038090.1| 150 LTERQLRLVSAAVERGYYDTPRECSLTDLAETLELAKSTCSETLHRAEEKIVK 202
                                       9**************************************************85 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.024        44       6      24 ..      28      46 ..      25      48 .. 0.91
   2 ?   -3.1   0.0       3.9     7e+03      16      28 ..     117     128 ..     115     129 .. 0.66
   3 !   12.4   0.0   5.8e-05       0.1      15      39 ..     169     193 ..     168     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.024
                                      HHHHCT-CTTBSS-BHHHH CS
                          HTH_IclR  6 laiLdalaeapqeltlsel 24
                                      ++iL al+    +++l+e+
  gi|313116966|ref|YP_004038090.1| 28 VRILSALTGDEAGVGLAEI 46
                                      79****************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                                       BSS-BHHHHHHHH CS
                          HTH_IclR  16 pqeltlselArrt 28 
                                       pq  +lsel  ++
  gi|313116966|ref|YP_004038090.1| 117 PQ-HRLSELGTQL 128
                                       44.5899987665 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 5.8e-05
                                       TBSS-BHHHHHHHHTS-HHHHHHHH CS
                          HTH_IclR  15 apqeltlselArrtglpkStvhRlL 39 
                                       +p+e +l++lA+ + l+kSt +  L
  gi|313116966|ref|YP_004038090.1| 169 TPRECSLTDLAETLELAKSTCSETL 193
                                       68999***************76655 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   4.2e-06    0.0075      24     118 ..      24     118 ..       5     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-06
                               BAT  24 ldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpslastlaehGgtv 100
                                        d++v++ ++ + +d+  + +++++  d ++v++  +d d+v ++++++++ d+ l++++++ p l+  + + G+ +
  gi|313116966|ref|YP_004038090.1|  24 PDATVRILSALT-GDEAGVGLAEITAPDLQDVVSDIQDSDSVVELEILQQYQDTVLVQFETTMPLLLFPVQDSGVPL 99 
                                       567777776666.455556899999999999*********************************9999******976 PP

                               BAT 101 r.saeaedgrarlvvevPp 118
                                          ++++dg+a+  +  P+
  gi|313116966|ref|YP_004038090.1| 100 TmPFTIQDGQAEWELTAPQ 118
                                       5158999999988887776 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.7e-06     0.012      15      56 ..     168     213 ..     152     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.7e-06
                             PuR_N  15 enPnklisltyfaerfeaAKSsiSeDl.....aiikealekeglGkl 56 
                                       ++P++ +slt++ae +e AKS+ Se l     +i+k+ le+ +  ++
  gi|313116966|ref|YP_004038090.1| 168 DTPRE-CSLTDLAETLELAKSTCSETLhraeeKIVKQFLEDLDGTTI 213
                                       55554.69*****************9944333467777776666665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.4   7.9e+03       8      19 ..      28      39 ..      24      52 .. 0.53
   2 ?   -2.5   0.0       2.7   4.9e+03      21      29 ..     134     142 ..     119     144 .. 0.67
   3 ?   13.5   0.1   2.9e-05     0.051      19      48 ..     170     199 ..     153     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                                      HHHHHHHHCTTT CS
                            MarR_2  8 arvLaaLgrrpg 19
                                       r+L aL   + 
  gi|313116966|ref|YP_004038090.1| 28 VRILSALTGDEA 39
                                      566666554443 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.7
                                       EEEHHHHHH CS
                            MarR_2  21 dltvgelar 29 
                                       ++tv+e+ +
  gi|313116966|ref|YP_004038090.1| 134 PFTVNEIRQ 142
                                       589999976 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 2.9e-05
                                       TSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  19 grdltvgelarrlglsksavsrilkrLvaa 48 
                                       +r+++ ++la++l l ks+ s +l r++++
  gi|313116966|ref|YP_004038090.1| 170 PRECSLTDLAETLELAKSTCSETLHRAEEK 199
                                       347899********************9985 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     3e-05     0.053      14      41 ..     171     198 ..     169     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                            HTH_35  14 rgttLaalsreaglssstlsnaltrpwp 41 
                                       r+ +L++l+++++l++st+s++l+r   
  gi|313116966|ref|YP_004038090.1| 171 RECSLTDLAETLELAKSTCSETLHRAEE 198
                                       889*********************9753 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5   4.4e+03       7      14 ..      29      36 ..      24      38 .. 0.74
   2 ?   11.5   0.0     9e-05      0.16      15      43 ..     169     198 ..     166     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                            HTH_24  7 kILelLqk 14
                                      +IL++L  
  gi|313116966|ref|YP_004038090.1| 29 RILSALTG 36
                                      89999875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9e-05
                            HTH_24  15 npr.isqreLAerlglSpstvnrrlkrLee 43 
                                        pr +s ++LAe l l +st+++ l r ee
  gi|313116966|ref|YP_004038090.1| 169 TPReCSLTDLAETLELAKSTCSETLHRAEE 198
                                       57779*****************98877666 PP

>> NYD-SP28  Sperm tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.9e-05      0.14      34      84 ..     158     209 ..     137     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                          NYD-SP28  34 kfeeinekWreilrknkpqeLrkeleeqkqaceelideK.dklikelqeeLk 84 
                                        ++++++ +  + r++   +L + le  k++c+e +++  +k++k++ e+L+
  gi|313116966|ref|YP_004038090.1| 158 VSAAVERGYYDTPRECSLTDLAETLELAKSTCSETLHRAeEKIVKQFLEDLD 209
                                       567777888889999**********************98688999***9997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.37   6.6e+02      13      20 ..      28      41 ..      22      70 .. 0.69
   2 ?   -1.7   0.0       1.7   3.1e+03      29      45 ..     123     144 ..     114     151 .. 0.67
   3 ?    9.6   0.4   0.00051      0.92      21      46 ..     169     194 ..     147     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.37
                                      HHHHHHH......S CS
                            HTH_20 13 rrilraL......a 20
                                       ril+aL       
  gi|313116966|ref|YP_004038090.1| 28 VRILSALtgdeagV 41
                                      68999996444444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                                       HHHHHHT.....S-HHHHHHHH CS
                            HTH_20  29 elaerld.....lskntlsyHL 45 
                                       el  +ld      + n++++H+
  gi|313116966|ref|YP_004038090.1| 123 ELGTQLDefgipFTVNEIRQHI 144
                                       5555554444555667777776 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00051
                                       TCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  21 raegltaselaerldlskntlsyHLr 46 
                                       ++++ ++++lae+l+l+k+t+s  L+
  gi|313116966|ref|YP_004038090.1| 169 TPRECSLTDLAETLELAKSTCSETLH 194
                                       57889*****************9985 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017       0.3      16      65 ..     148     205 ..     145     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                           UPF0122  16 sLLTekqanylel.....yyad..DlSlsEiAeefnvsrqavydnikrte.kllekyE 65 
                                       +LLTe+q + ++      yy+   + Sl+++Ae+ ++ +++ +++++r+e k+++++ 
  gi|313116966|ref|YP_004038090.1| 148 QLLTERQLRLVSAavergYYDTprECSLTDLAETLELAKSTCSETLHRAEeKIVKQFL 205
                                       799****9887543333488743389*********************98625666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1601.45
//
Query:       gi|313116967|ref|YP_004038091.1|  [L=74]
Description: hypothetical protein Hbor_34340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-21   75.7   0.1    2.1e-21   75.6   0.1    1.0  1  DUF2249   Uncharacterized conserved protein (DUF2249)


Domain annotation for each model (and alignments):
>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.1   1.2e-25   2.1e-21       1      70 []       8      73 ..       8      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1.2e-25
                           DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearrpgffsweylergpgewrvlitk 70
                                      +lDvRe+ ++e++  I +a+++L + etl+lvn+++P+pL+++Le+r  gf +++++++g +ew+v+it+
  gi|313116967|ref|YP_004038091.1|  8 ELDVREI-EGEPFGEIVAALDTLCEHETLVLVNSFEPVPLYDVLEQR--GF-TYKTSQEGSEEWHVRITH 73
                                      69****9.99*************************************..**.****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 512.95
//
Query:       gi|313116968|ref|YP_004038092.1|  [L=89]
Description: hypothetical protein Hbor_34350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-15   55.1   0.8    5.9e-15   54.9   0.8    1.1  1  DUF2249   Uncharacterized conserved protein (DUF2249)
    0.00041   20.1   0.0    0.00051   19.8   0.0    1.1  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.057   13.5   0.0       0.07   13.2   0.0    1.1  1  Y2_Tnp    Putative transposase


Domain annotation for each model (and alignments):
>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.8   9.9e-19   5.9e-15       1      64 [.      21      82 ..      21      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 9.9e-19
                           DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearrpgffsweylergpge.w 64
                                      tlD Relppp+++++++e++++L++  +l+ +nd+ P++L++ L +r  g+ ++e++e+++ +  
  gi|313116968|ref|YP_004038092.1| 21 TLDTRELPPPKPLRNTLERVTELDDETVLLQMNDRAPQHLYPKLTDR--GY-DFETVEADEFVaT 82
                                      79*********************************************..**.******9987644 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.5e-08   0.00051       1      65 [.      20      80 ..      20      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.5e-08
                                      EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EE CS
                              TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyr 65
                                      ++lD+r l+ P Pl  +++ + +l+++ vl + ++d+a+ +++   +  +g++++ v  e +e++
  gi|313116968|ref|YP_004038092.1| 20 ETLDTRELPPPKPLRNTLERVTELDDETVL-LQMNDRAP-QHLYPKLTDRGYDFETV--EADEFV 80
                                      58**********************999888.89999965.8999999******9988..555554 PP

>> Y2_Tnp  Putative transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05      0.07     122     164 ..      38      89 .]      35      89 .] 0.96

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                            Y2_Tnp 122 kRlvstdeekvtfrlkdkr.........rkktktvtlepeefirrllahVpp 164
                                       +R++++d+e+v ++++d+          +++++  t+e++ef++ +++h pp
  gi|313116968|ref|YP_004038092.1|  38 ERVTELDDETVLLQMNDRApqhlypkltDRGYDFETVEADEFVATVIWHTPP 89 
                                       799***************99*******9999******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 641.12
//
Query:       gi|313116969|ref|YP_004038093.1|  [L=370]
Description: Fe-S oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-19   69.2   0.0    7.2e-19   68.8   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    3.8e-06   27.2   0.0    5.9e-06   26.6   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    4.4e-05   23.6   0.0    9.1e-05   22.6   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
    0.00047   20.6   0.0     0.0011   19.5   0.0    1.6  1  SPASM        Iron-sulfur cluster-binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.0   1.6e-22   7.2e-19       3     166 ..      19     176 ..      17     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 1.6e-22
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgi 78 
                                        t++C l+C++C    +  +++++ +l++ e  ++++e++   g +  v+l+gg+pl++ d +el+        +g+
  gi|313116969|ref|YP_004038093.1|  19 LTQACELACKHCRADAK--PNRHPDELTTAEGQQLLDEAA-QFGdGQLVVLSGGDPLAREDAAELVQYGTD---AGL 89 
                                       689************96..********************6.5555*************8888666665555...5** PP

                                       EEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpd.eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                       r+t++ +gt    ++ +++l+++g+ rv+l+++ ++ e  ++ ++  +++f+++++a e++++ag++    + + ++
  gi|313116969|ref|YP_004038093.1|  90 RMTLTPSGTASLtRDSIDELADAGLQRVALSIDGGSAE-AHDAFRkENGSFDQTVAAAEAAKSAGLP--LQVNTTVC 163
                                       **********559*************************.888888899*******************..55556666 PP

                                       TTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 154 Gendeeleellel 166
                                        e+ +el ++++l
  gi|313116969|ref|YP_004038093.1| 164 AETVDELPKIRQL 176
                                       6999999888876 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.3e-09   5.9e-06       9      84 ..      15      89 ..       9     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.3e-09
                           Fer4_12  9 slf..vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi.egltllGGEPllpenaeallelvkevkeekp 84
                                      +++  ++ C+l+Ck C   +++  ++ +e t++  +++++++++  + + ++l+GG+Pl+   +e+ +elv++   +++
  gi|313116969|ref|YP_004038093.1| 15 LVWelTQACELACKHCR-ADAKPNRHPDELTTAEGQQLLDEAAQFGDgQLVVLSGGDPLA---REDAAELVQYGTDAGL 89
                                      4555589********98.7888888899999999999999998854459***********...7777777777666655 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     2e-08   9.1e-05       5      95 ..      20     103 ..      16     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2e-08
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       +  C+l+Ck C   ++ + +  +  t e   q l d  ++  + q +vl+GG+PL     ++  +lv++  + +  +
  gi|313116969|ref|YP_004038093.1|  20 TQACELACKHCRADAKPNRHPDELTTAEGQ-QLL-DEAAQFGDGQLVVLSGGDPLAR---EDAAELVQYGTDAG--L 89 
                                       568*********999777777777666654.555.66677777888*********54...77777887777777..6 PP

                           Fer4_14  82 kiwletngtleiel 95 
                                       + +l  +gt+ +  
  gi|313116969|ref|YP_004038093.1|  90 RMTLTPSGTASLTR 103
                                       66666666666554 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.4e-07    0.0011       6      67 ..     264     318 ..     260     319 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.4e-07
                             SPASM   6 rslfInsdGdVvpCcvdkktyveelklGnireesleeIw.nseeyqefrkskkfplielCrnC 67 
                                         +f+++ G+V+p  +       + + Gn+re+s+ +I+ ns+ ++ +r+   ++l   C  C
  gi|313116969|ref|YP_004038093.1| 264 GFAFVSHIGKVYPSGFL------PQSAGNVREQSVVDIYrNSDLFRSLRD--PDALRGKCGAC 318
                                       6689**********333......58**************5666******4..66666679988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2469.89
//
Query:       gi|313116970|ref|YP_004038094.1|  [L=104]
Description: glutamyl-tRNAGlu reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-09   36.3   1.1      7e-09   36.0   1.1    1.1  1  GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
  ------ inclusion threshold ------
      0.051   13.7   0.0      0.055   13.6   0.0    1.1  1  EcoEI_R_C    EcoEI R protein C-terminal
      0.065   13.6   0.3      0.092   13.1   0.3    1.3  1  DUF2564      Protein of unknown function (DUF2564)


Domain annotation for each model (and alignments):
>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   1.1   1.2e-12     7e-09      22      96 ..      24     101 ..      19     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.2e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHS-S......--------TTHHHHHHHHHHHHHHHHHHSS-TTTTHHHHHHHHH CS
                       GlutR_dimer  22 vvptIkalrekaeeireeeleralkkla....ldgedreelekltrslvnkllheptarLkeaedeeeellealrrl 94 
                                       ++ +   +r++ e+i+++elera++ l+    l++e+r+ +e+++  +v+ +l +p + L  + ++++++++++ +l
  gi|313116970|ref|YP_004038094.1|  24 IETAQETIRASGESIKRDELERAFATLEsegeLTTEQRRIVERMATEIVDEILAAPESMLETD-KSADRTAQTVVEL 99 
                                       555667899*****************************************************9.77779******** PP

                                       .. CS
                       GlutR_dimer  95 Fn 96 
                                       F 
  gi|313116970|ref|YP_004038094.1| 100 FS 101
                                       95 PP

>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.2e-06     0.055      91     151 ..      41     100 ..      16     104 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-06
                         EcoEI_R_C  91 erverafkrwikekkfteeqrewLelildhiaangvielddldeapefkqkgglgkayklF 151
                                       +  eraf+ +  e ++t eqr+++e+++  i++++   ++ + e++  ++  + +++++lF
  gi|313116970|ref|YP_004038094.1|  41 DELERAFATLESEGELTTEQRRIVERMATEIVDEILAAPESMLETD-KSADRTAQTVVELF 100
                                       44566666666566*************************9999999.55556999999999 PP

>> DUF2564  Protein of unknown function (DUF2564)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   1.5e-05     0.092       8      58 ..      20      74 ..      15      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                           DUF2564  8 velavetAqkmvGqATmsmdpdqlesAtqAied....Areqlssaeehatgvdee 58
                                       el +etAq ++ +   s  +d le A + +e       eq +  e+ at++ +e
  gi|313116970|ref|YP_004038094.1| 20 TELDIETAQETIRASGESIKRDELERAFATLESegelTTEQRRIVERMATEIVDE 74
                                      599*************************999872222334444555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 705.80
//
Query:       gi|313116971|ref|YP_004038095.1|  [L=180]
Description: halocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-15   55.6   1.2    2.7e-14   53.4   1.2    2.0  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
      5e-05   23.3   0.1    7.1e-05   22.9   0.1    1.2  1  Cupredoxin_1  Cupredoxin-like domain
    0.00056   19.6   2.4      0.001   18.8   2.4    1.4  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   1.2   4.4e-18   2.7e-14       3      99 .]      95     180 .]      91     180 .] 0.84

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 4.4e-18
                                       EEEEETTETSEEESSEEEEETTEEEEEEEE.SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSE CS
                       Copper-bind   3 vklgvesgdlqFetkeitvkkgekvtfvnl.avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeag 78 
                                       v +++++g+ +F + +i+v++g++v++ ++ ++  HNv  + ++     ++++        ++ +G +++ tf+e+g
  gi|313116971|ref|YP_004038095.1|  95 VGAKGNGGAYAFAPPAIRVSSGTTVVWEWTgKGSFHNVAAKDGSF----KSEQ--------VNKKGHTFEHTFKESG 159
                                       445566777********************989999**98877664....3344........44469*********** PP

                                       EEEEEETTTTTTTSEEEEEEE CS
                       Copper-bind  79 tYkffCsPHaaagMkgkvtve 99 
                                       t k+ C+PH  +gMkg v+ve
  gi|313116971|ref|YP_004038095.1| 160 THKYACTPHEPMGMKGVVVVE 180
                                       ******************996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   1.2e-08   7.1e-05      15     104 .]      83     179 ..      75     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.2e-08
                      Cupredoxin_1  15 aaaaaektveitvkdg......gfePskievkagekvklkiknkdktp.eefesed..lgeekvlapgktttitiap 82 
                                       ++a ++++v+++v  +      +f P  i v +g+  ++ ++ ++k + +++ ++d  ++ e+v ++g t++ t+  
  gi|313116971|ref|YP_004038095.1|  83 TDATGKDKVTVKVGAKgnggayAFAPPAIRVSSGT--TVVWEWTGKGSfHNVAAKDgsFKSEQVNKKGHTFEHTF-- 155
                                       55677777888877667899999***********9..7888888888889*****988888899999*******9.. PP

                      Cupredoxin_1  83 lkpGeYeftcdmhm.d.akGkliV 104
                                       ++ G+++++c  h+   +kG+++V
  gi|313116971|ref|YP_004038095.1| 156 KESGTHKYACTPHEpMgMKGVVVV 179
                                       99*********8886789****98 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.4   1.7e-07     0.001       2      25 ..       8      31 ..       7      32 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR+ L++++A   ++al+gc++
  gi|313116971|ref|YP_004038095.1|  8 VNRRTILRATGASVVGVALAGCTG 31
                                      89********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1284.27
//
Query:       gi|313116972|ref|YP_004038096.1|  [L=163]
Description: hypothetical protein Hbor_34390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1216.79
//
Query:       gi|313116973|ref|YP_004038097.1|  [L=388]
Description: hypothetical protein Hbor_34400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2813.48
//
Query:       gi|313116974|ref|YP_004038098.1|  [L=48]
Description: hypothetical protein Hbor_34410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.095   12.6   0.0      0.095   12.6   0.0    1.1  1  ACCA       Acetyl co-enzyme A carboxylase carboxyltransferase
       0.17   11.8   0.0       0.27   11.2   0.0    1.4  1  Ectatomin  Ectatomin


Domain annotation for each model (and alignments):
>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05     0.095      61      86 ..      20      45 ..       5      48 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                              ACCA 61 RhpeRpktldyiealfedfvelhGDr 86
                                      ++++Rp+t  yi+++++ f +l G +
  gi|313116974|ref|YP_004038098.1| 20 KNEQRPETARYIKRVTNVFAPLFGRQ 45
                                      5789******************9965 PP

>> Ectatomin  Ectatomin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05      0.27       9      30 ..      10      33 ..       4      35 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                         Ectatomin  9 vCPTlksmAKKCeG..dIATyIKk 30
                                      vCP  +s AKK e   + A yIK+
  gi|313116974|ref|YP_004038098.1| 10 VCPEHESGAKKNEQrpETARYIKR 33
                                      9**********9853378889998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 382.90
//
Query:       gi|313116975|ref|YP_004038099.1|  [L=383]
Description: copper oxidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-30  103.4  13.3    2.1e-18   66.4   4.2    3.0  2  Cu-oxidase_2  Multicopper oxidase
    2.5e-22   79.1   5.6    1.1e-18   67.4   0.5    2.6  2  Cu-oxidase_3  Multicopper oxidase
    5.3e-12   46.1   0.2    2.3e-11   44.1   0.0    1.9  2  Cu-oxidase    Multicopper oxidase
    3.5e-06   27.1   0.0      0.026   14.6   0.0    2.6  2  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.081   12.8   2.2       0.13   12.1   2.2    1.4  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   1.6   7.8e-14   2.8e-10      24     136 ..     107     206 ..      87     207 .. 0.85
   2 !   66.4   4.2     6e-22   2.1e-18       7     126 ..     244     350 ..     235     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 7.8e-14
                                       ETCCTTTSSEEEEEETTEEEEEEEEE-SSS.-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTE CS
                      Cu-oxidase_2  24 ngeefsentnvitlpkgevveiviqnntkl.pHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppgg 99 
                                       ++++ s   ++i++ +ge +e++++n++   pH++H+HG + +  + g  +                   ++v pg+
  gi|313116975|ref|YP_004038099.1| 107 DDRDPSVPGPIIRTTEGEEMEVTLDNTDGKrPHTVHFHGARKAWKDDGVPT----------------TTGITVSPGE 167
                                       555667788999**************99999*********77776444443................5678999999 PP

                                       EEEEEEES.S-EEEEEEESSH..HHHHTT-EEEEEEECH CS
                      Cu-oxidase_2 100 wvairfkadnpGvwllHCHil..wHldqGmalqfvvrpd 136
                                       + ++ + a+ pG  l+HCH++   H d+Gm++ f v+p+
  gi|313116975|ref|YP_004038099.1| 168 KHTYTIPANVPGTHLYHCHFQthRHIDMGMYGIFRVDPK 206
                                       9999999**************9999**********9986 PP

  == domain 2  score: 66.4 bits;  conditional E-value: 6e-22
                                       CCCCCCEEEEEEEEEEEETC.CTTTSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSS CS
                      Cu-oxidase_2   7 ptllqltsgneeaseitnge.efsentnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksy 82 
                                       p+++++  g+        ++  ++e+ +++++++g+ v++ + n + + HP+H+H h+fq +++++g+        +
  gi|313116975|ref|YP_004038099.1| 244 PDVFTVN-GKV------APRtLHPEDGSPLVVEHGDSVRVHFVNGGYMSHPLHIHNHRFQRVEKDGGT--------V 305
                                       4444444.222......23327789******************************************9........3 PP

                                       GCCGSSCBSEEEE-TTEEEEEEEES..S-EEEEEEESSHHHHHTT CS
                      Cu-oxidase_2  83 nlenpvrrdtvqvppggwvairfkad.npGvwllHCHilwHldqG 126
                                          +  + d+++v p ++ +++f+ad +pG +l+HCH  +H+ +G
  gi|313116975|ref|YP_004038099.1| 306 PEAARHEMDVTNVAPAERHTVEFTADaDPGIYLMHCHKVEHVMNG 350
                                       33455566*****************98***************998 PP

>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.5     3e-22   1.1e-18      23     117 ..     112     206 ..     108     207 .. 0.95
   2 !   13.5   0.5   1.6e-05     0.056      26     107 ..     263     350 ..     233     358 .. 0.67

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 3e-22
                                       SSBS-EEEEETT-EEEEEEEE-S.SS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE CS
                      Cu-oxidase_3  23 qfpgptievregdtvvvnvtNkl.dentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhs 98 
                                       ++pgp i+ +eg++++v++ N   +++ ++h+hG +  ++   DGvp  t   ++pge+ ty+++++   gt++Yh 
  gi|313116975|ref|YP_004038099.1| 112 SVPGPIIRTTEGEEMEVTLDNTDgKRPHTVHFHGARKAWK--DDGVPTTTGITVSPGEKHTYTIPANV-PGTHLYHC 185
                                       68********************99****************..**************************.******** PP

                                       --TT.HHH.TT-EEEEEEE-H CS
                      Cu-oxidase_3  99 hlsl.qqa.aGlaGaiiiedk 117
                                       h+++ ++  +G++G++ +++k
  gi|313116975|ref|YP_004038099.1| 186 HFQThRHIdMGMYGIFRVDPK 206
                                       ****65558*********986 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.6e-05
                                       S-EEEEETT-EEEEEEEE-S..SS-B-EEEET--S-GG............GSCSGGG-B-TT-EEEEEEE--S-SEE CS
                      Cu-oxidase_3  26 gptievregdtvvvnvtNkl..dentsihwhGlqqrktswmDG.......vpgvtqcpiqpgesftyrftvkqqagt 93 
                                       g  + v+ gd+v+v+++N    ++++ ih h +q  ++   DG          +    ++p e+ t +ft++   g 
  gi|313116975|ref|YP_004038099.1| 263 GSPLVVEHGDSVRVHFVNGGymSHPLHIHNHRFQRVEK---DGgtvpeaaRHEMDVTNVAPAERHTVEFTADADPGI 336
                                       456889************87446666666666666655...88452221112234457999************9*** PP

                                       EEEEE--TTHHHTT CS
                      Cu-oxidase_3  94 lwYhshlslqqaaG 107
                                       ++ h h   + ++G
  gi|313116975|ref|YP_004038099.1| 337 YLMHCHKVEHVMNG 350
                                       99999987766666 PP

>> Cu-oxidase  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.32   1.1e+03      36      77 ..     138     177 ..     120     193 .. 0.58
   2 !   44.1   0.0   6.5e-15   2.3e-11      32     145 ..     235     352 ..     213     366 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.32
                                       -SEEEETTBSS.......CTTTTSGGGEEEEETTEEEEEE.EE CS
                        Cu-oxidase  36 pdavlingkggfnatladkdgaslatltvepgktyrlrii.nv 77 
                                       p +v + g ++  +   d++   ++ +tv pg+++   i  nv
  gi|313116975|ref|YP_004038099.1| 138 PHTVHFHGARKAWK---DDGVPTTTGITVSPGEKHTYTIPaNV 177
                                       55666666333222...22333567788888888877665455 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 6.5e-15
                                       H.....TT--SEEEETTBSS.......CTTTTSGGGEEEEETTEEEEEEEESSS-BEEEEETSB-EEEEEETCETTS CS
                        Cu-oxidase  32 t.....ppvpdavlingkggfnatladkdgaslatltvepgktyrlriinvsaddslnfsIeGHkltVvevDgvyve 103
                                       +       +pd +++ngk  +  tl +    +   l ve+g+ +r++++n++ + s+++ I++H+++ ve Dg  v 
  gi|313116975|ref|YP_004038099.1| 235 VsysprNRTPDVFTVNGKVAPR-TLHP---EDGSPLVVEHGDSVRVHFVNGGYM-SHPLHIHNHRFQRVEKDGGTVP 306
                                       123344668********55544.5444...5689999**************998.69******************99 PP

                                       ...EEEESCEEE-TTEEEEEEEEE-SSSEEEEEEEE.GSSSCHHHH CS
                        Cu-oxidase 104 ...pvevdsldIavGqrysvlvtanqapgnYwivas.grsnlieaf 145
                                            e+d  ++a+++r +v +ta+++pg Y ++++ ++++ + +f
  gi|313116975|ref|YP_004038099.1| 307 eaaRHEMDVTNVAPAERHTVEFTADADPGIYLMHCHkVEHVMNGNF 352
                                       88889******************************66555555555 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   7.3e-06     0.026      39      96 ..     120     189 ..     115     194 .. 0.85
   2 !    9.7   0.0   0.00024      0.87      19     100 ..     270     350 ..     251     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.3e-06
                      Cupredoxin_1  39 vkagekvklkiknkdkt.peefesed...........lgeekvlapgktttitiaplkpGeYeftcdmhm 96 
                                         +ge+++++++n+d + p+++ ++              +  ++ pg+++t ti++  pG++ ++c ++ 
  gi|313116975|ref|YP_004038099.1| 120 TTEGEEMEVTLDNTDGKrPHTVHFHGarkawkddgvpTTTGITVSPGEKHTYTIPANVPGTHLYHCHFQT 189
                                       56899999999999976369999998889999999775555699***********************986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00024
                      Cupredoxin_1  19 aektveitvkdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiap.lkpGeYeftcdm 94 
                                       + ++v++ + +gg+    ++++  +    ++++++ t+ e   +++++ +++ap + +t+++++  +pG Y ++c  
  gi|313116975|ref|YP_004038099.1| 270 HGDSVRVHFVNGGYMSHPLHIHNHR--FQRVEKDGGTVPEAARHEMDV-TNVAPAERHTVEFTAdADPGIYLMHCHK 343
                                       5567899999999999999999887..336788888889999999999.99******9999976258********96 PP

                      Cupredoxin_1  95 hmd.akG 100
                                        +  + G
  gi|313116975|ref|YP_004038099.1| 344 VEHvMNG 350
                                       6655655 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.2   3.7e-05      0.13       2      23 ..      12      33 ..      11      36 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggc 23
                                      lSRR FL ++ +++ Aa++g  
  gi|313116975|ref|YP_004038099.1| 12 LSRREFLAATSGLGTAALAGCQ 33
                                      8*******99888877766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2734.94
//
Query:       gi|313116976|ref|YP_004038100.1|  [L=363]
Description: halocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-29  101.9   8.5    3.7e-14   52.9   0.8    3.3  2  Copper-bind  Copper binding proteins, plastocyanin/azurin fam
  ------ inclusion threshold ------
      0.039   14.3   0.4        6.1    7.2   0.1    2.2  2  DUF2924      Protein of unknown function (DUF2924)
      0.099   12.9   0.1         21    5.4   0.0    2.3  2  DUF272       Protein of unknown function (DUF272)
        7.7    5.2   6.5         13    4.4   6.5    1.3  1  Herpes_LMP2  Gammaherpesvirus latent membrane protein (LMP2) 


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.8   8.3e-18   3.7e-14       4      98 ..      70     153 ..      67     154 .. 0.86
   2 !   50.9   1.5   3.6e-17   1.6e-13       3      98 ..     225     309 ..     222     310 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 8.3e-18
                                       EEEETTETSEEESSEEEEETTEEEEEEEE.SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEE CS
                       Copper-bind   4 klgvesgdlqFetkeitvkkgekvtfvnl.avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagt 79 
                                        +++++g+++F +++++v++g++v+++++ ++ +HNvv + ++        k+++     +  +G ++++tf+++g 
  gi|313116976|ref|YP_004038100.1|  70 GATGNGGNFAFGPAAVRVDPGTTVVWKWNgKGGSHNVVAKDGSF-------KSEM-----VGETGHTFEQTFEKEGI 134
                                       56778899*******************998999****9887775.......3333.....2335************* PP

                                       EEEEETTTTTTTSEEEEEE CS
                       Copper-bind  80 YkffCsPHaaagMkgkvtv 98 
                                        k+ C+PH  +gMkg+v+v
  gi|313116976|ref|YP_004038100.1| 135 VKYACTPHEPMGMKGAVVV 153
                                       *****************98 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 3.6e-17
                                       EEEEETTETSEEESSEEEEETTEEEEEEEE.SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSE CS
                       Copper-bind   3 vklgvesgdlqFetkeitvkkgekvtfvnl.avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeag 78 
                                       v +++++g+++F +++++v++g++v++ ++ ++  HNv  ++++     +++ v +        +G +++ tf+++g
  gi|313116976|ref|YP_004038100.1| 225 VGATGNGGNFAFGPAAVRVDPGTTVVWEWNgKGGTHNVAAKEGSF----ESEMVGE--------TGHTFEHTFEKSG 289
                                       556778889*******************9989999***9999986....4444444........49*********** PP

                                       EEEEEETTTTTTTSEEEEEE CS
                       Copper-bind  79 tYkffCsPHaaagMkgkvtv 98 
                                          ++C+PH+++gMkg+v+v
  gi|313116976|ref|YP_004038100.1| 290 VHRYVCAPHKTMGMKGAVVV 309
                                       ******************98 PP

>> DUF2924  Protein of unknown function (DUF2924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0058        26      76     104 ..      83     113 ..      50     119 .. 0.77
   2 ?    7.2   0.1    0.0014       6.1      76     105 ..     239     270 ..     210     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0058
                           DUF2924  76 kkeelkpGtrLvRewkgr..ehevtvledgf 104
                                       ++ ++ pGt++v +w+g+  +h+v++ +  f
  gi|313116976|ref|YP_004038100.1|  83 AAVRVDPGTTVVWKWNGKggSHNVVAKDGSF 113
                                       556788*********9873256665555445 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
                           DUF2924  76 kkeelkpGtrLvRewkgr..ehevtvledgfe 105
                                       ++ ++ pGt++v ew+g+  +h+v + e  fe
  gi|313116976|ref|YP_004038100.1| 239 AAVRVDPGTTVVWEWNGKggTHNVAAKEGSFE 270
                                       567789*********98644788888887786 PP

>> DUF272  Protein of unknown function (DUF272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0052        23      12      43 ..     112     142 ..     107     155 .. 0.78
   2 ?    5.4   0.0    0.0047        21      10      45 ..     266     300 ..     262     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0052
                            DUF272  12 ilkskkkkLelghfFegtFeekengkweckkY 43 
                                        +ks+    e gh Fe tFe++   k+ c+ +
  gi|313116976|ref|YP_004038100.1| 112 SFKSE-MVGETGHTFEQTFEKEGIVKYACTPH 142
                                       55555.34489***********999****977 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0047
                            DUF272  10 egilkskkkkLelghfFegtFeekengkweckkYvk 45 
                                       eg + s+    e gh Fe tFe++  +++ c  +++
  gi|313116976|ref|YP_004038100.1| 266 EGSFESE-MVGETGHTFEHTFEKSGVHRYVCAPHKT 300
                                       6666666.44589***********999***998854 PP

>> Herpes_LMP2  Gammaherpesvirus latent membrane protein (LMP2) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   6.5    0.0029        13       8     123 ..     144     262 ..     141     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0029
                                       XXXX.XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXSXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP2   8 pmga.gppspggdpd.gydggnnsqypsasgssgntptppndeeresneepp.ppyedpywgngdrhsdyqplgtqd 81 
                                       pmg  g    g   d g dg + s      g sgn+    nd +  s e+   p y d +    +     +  g ++
  gi|313116976|ref|YP_004038100.1| 144 PMGMkGAVVVGSAGDgGNDGSESSGDDRNDGDSGNSGDSENDGDGASAEQASePEYGDWFTDVSNFDGTVDRTGQNE 220
                                       55542444445555516788888999999****************99998652779998888788788888888888 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP2  82 qslylglqhdgndglppppysprddssqhiyeeagrgsmnpv 123
                                        ++ +g   +g +    p     d  +  ++e  g+g    v
  gi|313116976|ref|YP_004038100.1| 221 ITVTVGATGNGGNFAFGPAAVRVDPGTTVVWEWNGKGGTHNV 262
                                       888888887776665566666667777888888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2675.11
//
Query:       gi|313116977|ref|YP_004038101.1|  [L=412]
Description: ferrichrome-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-15   55.7   0.0    7.1e-15   55.2   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
        1.5    8.2   4.1         29    4.1   0.0    2.5  2  UCR_Fe-S_N    Ubiquitinol-cytochrome C reductase Fe-S subunit


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   7.9e-19   7.1e-15      40     236 ..     135     354 ..      96     356 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 7.9e-19
                                       TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS.....................H CS
                      Peripla_BP_2  40 aivevgadgeidvEklaalkPDlvilskglgltdedeellksgiptvivessntg.....................e 95 
                                       + + + +++e++ Ekl +l+ D+ ++++ +  +++ +   + +++ +  +  +++                     +
  gi|313116977|ref|YP_004038101.1| 135 DWKGLYSSWEPSKEKLYELDSDVHLADPAG--VSALDSWNADDVEAIGENIAPWFgnyysdrhatppeawtddyqyY 209
                                       55778899**********************..8888888888888888888888888888889************** PP

                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTHHH...HTS-- CS
                      Peripla_BP_2  96 slkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigdll...dalgi 169
                                       +l e+++ +++++ +e+++e+l++ + + ++ +++ ++   ++p++v++g  + ++++a+     g l+   +a+g+
  gi|313116977|ref|YP_004038101.1| 210 DLWEMFERVAQVFREEARYEALAEIHRRLVETVQEELPPVEARPTAVLIGPSDLEKIYAYKLDTPGFLTahtRAAGA 286
                                       ****************************************9999999999999777777766666666511144666 PP

                                       EESTTT--STT-EEE-HHHHHHH--SEEEEEEH..HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 170 eniaaeskkseyeeisaEqilasdpdvifvsgr..aeadnktgleflkenpllaelpAvkngrVyalds 236
                                         ++ +   +++++++aE++l ++pdvif  g   ++ +   + ++l  n +  e+ Avkn rVya ++
  gi|313116977|ref|YP_004038101.1| 287 VGAFGDD-VQSGSTVDAETLLDANPDVIFALGGmhPKTSMADIRDGLGGNNVTREVAAVKNDRVYAQGA 354
                                       6666666.***********************998999999999**********************8766 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0032        29       3      24 ..       5      26 ..       3      32 .. 0.83
   2 ?    2.9   2.7    0.0078        70      14      27 ..     276     289 ..     275     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0032
                        UCR_Fe-S_N  3 eaesdeptRRDFLyiATgavga 24
                                      ++e d ptRR++  ++++ +g+
  gi|313116977|ref|YP_004038101.1|  5 ANETDAPTRREYVKYGAVLTGG 26
                                      578899*******999998887 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0078
                        UCR_Fe-S_N  14 FLyiATgavgaVGa 27 
                                       FL + T a+gaVGa
  gi|313116977|ref|YP_004038101.1| 276 FLTAHTRAAGAVGA 289
                                       99999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2678.98
//
Query:       gi|313116978|ref|YP_004038102.1|  [L=543]
Description: cysteine desulfurase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.6e-147  489.1   0.0   9.1e-147  488.8   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    1.1e-14   54.7   0.0      2e-14   53.8   0.0    1.4  1  NifU_N           NifU-like N terminal domain
    1.6e-10   40.8   0.3    2.9e-10   40.0   0.3    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.8e-06   27.4   0.0    2.4e-06   27.0   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
      7e-05   21.5   0.1    0.00015   20.4   0.0    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0074   15.0   0.0      0.026   13.3   0.1    1.7  2  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
  ------ inclusion threshold ------
      0.056   12.4   0.0       0.24   10.3   0.0    1.8  1  SelA             L-seryl-tRNA selenium transferase
       0.22   11.2   0.0       0.33   10.6   0.0    1.2  1  Cloacin          Colicin-like bacteriocin tRNase domain


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.8   0.0  4.1e-150  9.1e-147       1     371 []      25     397 ..      25     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 488.8 bits;  conditional E-value: 4.1e-150
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-ST.GGGEEEESSHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaes.eeeiiftsGtteainl 76 
                                       +yld+aAttq+p++V d  +e+y  ynanvhr++h+l++ea+ a+eea++++ae+i+a+  +ee+ift++tte+inl
  gi|313116978|ref|YP_004038102.1|  25 VYLDNAATTQTPEQVYDVFEEFYAGYNANVHRGIHTLSHEASVAYEEAHDRLAEFIGASGgREELIFTKNTTESINL 101
                                       7*********************************************************953799************* PP

                                       HHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTT CS
                       Aminotran_5  77 valslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvt 152
                                       va++++ + l pgd++v+te+ehha lv+wq++akrtga+v++i++d++g+ldl+++++l++++t+l++i hvsnv+
  gi|313116978|ref|YP_004038102.1| 102 VAYGVGLNeLGPGDNVVTTEMEHHASLVTWQQVAKRTGADVRFIRVDDDGKLDLEHAAELIDNDTQLMSIVHVSNVL 178
                                       ******99********************************************************************* PP

                                       TEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STT CS
                       Aminotran_5 153 GtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllgge 229
                                       Gt++pvee+++la++++alv++D+aqav+ +++dv+++++Df+afsghK+ gPtG+G ly++++lle++ep+l+gge
  gi|313116978|ref|YP_004038102.1| 179 GTVNPVEELTELAHEQDALVFIDGAQAVPNRRVDVEEIDADFYAFSGHKMAGPTGVGCLYGKHHLLESMEPFLYGGE 255
                                       ***************************************************************************** PP

                                       SEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-C CS
                       Aminotran_5 230 mveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkae 306
                                       m+++v++e++t++ +p+kfeaGTp++a+ i+l+aa++yl+++g++ +e++e+ela+y+lerl + ++v++ygp   e
  gi|313116978|ref|YP_004038102.1| 256 MIRHVTYEDSTWNRPPWKFEAGTPPIAEGIALAAAADYLDDVGMDFVEERENELAQYALERLTERDDVEVYGPPLGE 332
                                       ***************************************************************************** PP

                                       TCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 307 rrasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       +r+++v+fn++gvh +d+  lLde+gIavr+G hc+qpl++rl+++g+vRaS+y+ynt +e+d+l
  gi|313116978|ref|YP_004038102.1| 333 ARSGLVAFNLDGVHGHDLSALLDERGIAVRAGDHCTQPLHDRLDIPGSVRASFYVYNTTDEIDQL 397
                                       ***************************************************************97 PP

>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   9.1e-18     2e-14       1     119 [.     416     530 ..     416     536 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 9.1e-18
                                       CSCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHH CS
                            NifU_N   1 aysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelv 77 
                                       +y+d v +hy+nP+n G l++      + +     cGD   +++ v e+ + ie++ F+++ C+ + A++s+l e +
  gi|313116978|ref|YP_004038102.1| 416 QYHDLVYEHYRNPQNTGGLSNPTF---TKHSEETSCGDDGEFHVDVAED-GTIENIAFESESCAVSSAVASMLSERL 488
                                       69*****************99994...8999999**************7.9************************** PP

                                       TTSBHHHHCCCCHHHHHHHHTC.SCSSSCHCSCHHHHHHHHHH CS
                            NifU_N  78 kgktleealkitnkeiaeelgg.lpkeklhcsvlaedalkaav 119
                                       +g++lee++++    + e l g  p+ +++c v  e+++ +a+
  gi|313116978|ref|YP_004038102.1| 489 EGMSLEEVAELDG-FVDEVLDGtYPDIRRDCVVGPEEVICEAA 530
                                       ********88764.35555555789999999999999998876 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.3   1.3e-13   2.9e-10      27     150 ..      75     207 ..      57     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.3e-13
                                       HHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTT...TT-EEEEESSS-THHH....HHHHHTT-EEEEE-B-TTT CS
                   DegT_DnrJ_EryC1  27 eFEkafaaylgvkhaiavssGtaAlhlaLralgvg...pgdeVIvpsltFvata....navlelgakpvfvDvdpdt 96 
                                       ++++ + a  g +  i + + t+++ l+   +g++   pgd V+++ +   a+     +++ ++ga++ f+ vd d+
  gi|313116978|ref|YP_004038102.1|  75 RLAEFIGASGGREELIFTKNTTESINLVAYGVGLNelgPGDNVVTTEMEHHASLvtwqQVAKRTGADVRFIRVD-DD 150
                                       44555555556789999999999987765554444666*********9999985333378999***********.99 PP

                                       SSB-GGGCGGG--TTEEEEEEB-...GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1  97 ynidpaaieaaitertkaIlpVh...lyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                         +d ++++++i + t+   +Vh   ++G v+ +++l+++a++++  v+ D A+A+ 
  gi|313116978|ref|YP_004038102.1| 151 GKLDLEHAAELIDNDTQLMSIVHvsnVLGTVNPVEELTELAHEQDALVFIDGAQAVP 207
                                       ****************766666622368***************************86 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.1e-09   2.4e-06      28     224 ..      67     307 ..      19     364 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.1e-09
                                       CT--HHHHHHHHHHHHHTT-SEEEEES-HHHH.HHHHH....HHH--TTEEEEEETT.-HHHHSSTTHHHHCC--EE CS
                   Beta_elim_lyase  28 YgedktvnrLedavaelfgkeaalfvpqGtaA.nsill....killqrgeevivtep.ahihfdetgaiaelagvkl 98 
                                        + ++   rL++ + +  g e  +f+ + t + n +++    +  l +g++v+ te   h    + +++a   g+ +
  gi|313116978|ref|YP_004038102.1|  67 VAYEEAHDRLAEFIGASGGREELIFTKNTTESiNLVAYgvglNE-LGPGDNVVTTEMeHHASLVTWQQVAKRTGADV 142
                                       44555555666666667778888999998877577777554233.359999999988577778888*********** PP

                                       EEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH CS
                   Beta_elim_lyase  99 rdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa 175
                                       r ++ +++Gk+dle  +++i++  +    ++l s+    n+  G+v ++ee   ++++a++++  +++DgA  + + 
  gi|313116978|ref|YP_004038102.1| 143 RFIRVDDDGKLDLEHAAELIDN--D----TQLMSIVHVSNV-LGTVNPVEE---LTELAHEQDALVFIDGAQAVPNR 209
                                       **********************..3....345544444443.488888766...56799************888777 PP

                                       HHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH...................................... CS
                   Beta_elim_lyase 176 kslgeivkemfsyvDsvtmslkKdllanvG.gvlafrddel.................................... 215
                                          +++v+e+   +D   +s+ K    + G g l +++  l                                    
  gi|313116978|ref|YP_004038102.1| 210 ---RVDVEEI--DADFYAFSGHKM-AGPTGvGCLYGKHHLLesmepflyggemirhvtyedstwnrppwkfeagtpp 280
                                       ...8899998..689999999996.4568878888888866777777777777777777777777777777777777 PP

                                       ....................HHHHHHH CS
                   Beta_elim_lyase 216 ..................edylaerve 224
                                                          d+++er +
  gi|313116978|ref|YP_004038102.1| 281 iaegialaaaadylddvgMDFVEEREN 307
                                       777777777777777777677766654 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.4   3.2e+03     242     268 ..      54      81 ..      52      90 .. 0.80
   2 !   20.4   0.0   6.8e-08   0.00015      88     179 ..     111     207 ..     103     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.4
                                       HHHHHTTHHHHHHHHHHHHH.HHHHHHH CS
                   Cys_Met_Meta_PP 242 llrGlkTLslRlerhqenAl.kvAefLe 268
                                       ++rG++TLs   + + e A  ++Aef+ 
  gi|313116978|ref|YP_004038102.1|  54 VHRGIHTLSHEASVAYEEAHdRLAEFIG 81 
                                       6899***999999888888636888875 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 6.8e-08
                                       S-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHH CS
                   Cys_Met_Meta_PP  88 lkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaikentklvylEtptnpllkvvDieki 159
                                       l  Gd++v+++  +  +    ++v+k++g +v+f+ +      dle+ ++ i++ t+l+ +  ++n l  v  +e++
  gi|313116978|ref|YP_004038102.1| 111 LGPGDNVVTTEMEHHASLVTWQQVAKRTGADVRFIRVdddgkLDLEHAAELIDNDTQLMSIVHVSNVLGTVNPVEEL 187
                                       567******************************99873233345677788999************************ PP

                                       HHHHHHTT-EEEEEGTTTHT CS
                   Cys_Met_Meta_PP 160 aklakkagvlvvvDntfasp 179
                                       ++la+++++lv++D + a p
  gi|313116978|ref|YP_004038102.1| 188 TELAHEQDALVFIDGAQAVP 207
                                       **************987766 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   1.2e-05     0.026     156     277 ..     129     237 ..     114     248 .. 0.84
   2 ?   -1.4   0.0      0.34   7.6e+02     339     374 ..     303     342 ..     296     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEE CS
                     Pyridoxal_deC 156 ssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlH 232
                                       + ++++a+ +g  +r+i++d++gkl  ++  ++i +d +  + ++ v   lGt +      ++el ++ ++ d  + 
  gi|313116978|ref|YP_004038102.1| 129 VTWQQVAKRTGADVRFIRVDDDGKLDLEHAAELIDNDTQL-MSIVHVSNVLGTVN-----PVEELTELAHEQDALVF 199
                                       5689*********************************999.66669999999975.....799************** PP

                                       EE-TTGGGGGGSGGGGGGGTTGGGESEEEEECCCCTS--SS-EEE CS
                     Pyridoxal_deC 233 vDAAyaGsaficpeirhllkgieradSitvnphKlllvlldcsal 277
                                       +D A a      p+ r  ++ i+ ad  ++++hK+ + + ++++l
  gi|313116978|ref|YP_004038102.1| 200 IDGAQAV-----PNRRVDVEEID-ADFYAFSGHKMAG-PTGVGCL 237
                                       ****998.....99888888887.8999999999765.4555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHTTTTEEECS....TTBSSEEEEEE CS
                     Pyridoxal_deC 339 irksvelakyleklirkderfeiva....evelglVcFrl 374
                                        ++  ela+y  +++ ++ + e+      e   glV+F l
  gi|313116978|ref|YP_004038102.1| 303 EERENELAQYALERLTERDDVEVYGpplgEARSGLVAFNL 342
                                       577889**************99988888999999999986 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011      0.24     117     234 ..     146     248 ..     131     251 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                                       EESBSSB--HHHHHHT--TTEEEEEEE---SEEEEES-B---HHHHHHHHHHHT--EEEEEES-B-S-GGGGT---- CS
                              SelA 117 evGttnkthlkDyekainentalllkvhtsnyrieGftkevelaeLvelgkekglpvleDlGsGllvdlseyglske 193
                                        v    k  l+   + i+++t l+  vh sn  + G ++ v  +eL+el++e++  v+ D  +           +  
  gi|313116978|ref|YP_004038102.1| 146 RVDDDGKLDLEHAAELIDNDTQLMSIVHVSN--VLGTVNPV--EELTELAHEQDALVFIDG-A-----------QAV 206
                                       4555556666777778999***********9..78888765..69*********9999883.2...........222 PP

                                       -BHHHHHHT.T-SEEEEETTSTT-SSS-EEEEE-HHHHHHHH CS
                              SelA 194 Ptvqealae.GvdlvsfsGDkllGgpqaGiivGkkelieklk 234
                                       P+ +  ++e  +d  +fsG k+ G    G + Gk++l+e ++
  gi|313116978|ref|YP_004038102.1| 207 PNRRVDVEEiDADFYAFSGHKMAGPTGVGCLYGKHHLLESME 248
                                       333333322146999********************9999885 PP

>> Cloacin  Colicin-like bacteriocin tRNase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.33      96     166 ..     103     174 ..      85     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                                       -EEEEEEEE-HHHHH.HH-TT---EEEEEEEGGGT--S-GGGS-TT--EEEES-EEEEEEETTEEEEEEEES CS
                           Cloacin  96 ivgiaiaklkPasia.kdkevrtskivstlpveqvtdvpvsklplakktVavtkrvtdivkderqfiavvtg 166
                                       + g+++ +l P++   + ++  +  +v++++v + t  +v+ ++++++        ++++++++q +++v  
  gi|313116978|ref|YP_004038102.1| 103 AYGVGLNELGPGDNVvTTEMEHHASLVTWQQVAKRTGADVRFIRVDDDGKLDLEHAAELIDNDTQLMSIVHV 174
                                       679*********8751666777899**********************9999999999999********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3783.16
//
Query:       gi|313116979|ref|YP_004038103.1|  [L=139]
Description: lactoylglutathione lyase-like lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-16   60.9   0.0    1.6e-16   60.7   0.0    1.1  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    9.9e-12   45.1   0.0    1.2e-11   44.8   0.0    1.2  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
      2e-06   27.7   0.0    1.2e-05   25.2   0.0    1.9  1  Glyoxalase_2  Glyoxalase-like domain
    0.00016   21.9   0.0    0.00025   21.2   0.0    1.3  1  Glyoxalase_3  Glyoxalase-like domain
    0.00035   21.3   0.0    0.00049   20.9   0.0    1.3  1  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   4.4e-20   1.6e-16       2     128 .]       6     136 ..       5     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 4.4e-20
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE.........EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCC CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdn.........teeteglriaffhaggghielvlneapsgaakhvkk 69 
                                        +hv + v+dle +++FY++ L+++l++++              + +  +a + a+g ++el+ +e+++ ++     
  gi|313116979|ref|YP_004038103.1|   6 AHHVGITVSDLENAVEFYQETLDLTLLDRFTVsgenfstavGVDGATGQFAHLEADGVRVELIEYEPEGASRGEA-- 80 
                                       7************************************988544448889999***************99999999.. PP

                                       BSC.TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  70 iee.tvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                         + +  ++a++ l+ved++ +++ l    v+ v  p+++ +g+++ f +rDp G+l+e+
  gi|313116979|ref|YP_004038103.1|  81 --SiNRPGTAHLGLTVEDIDSFYESLPNS-VESVSRPQTTDTGSRILF-VRDPEGNLIEL 136
                                       ..5579*******************9765.6999999********988.*********96 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   3.4e-15   1.2e-11       1      89 [.       7     107 ..       7     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 3.4e-15
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETT.........TTEEEEEEEETTEEEEEEEESSTT-THHH...T CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqe.........vdlafallgsgsvqieLieplegpeflae...h 65 
                                       +++gi V Dle av++++++l+++  +r+++  ++         ++ +fa+l    v++eLie  ++  +  e   +
  gi|313116979|ref|YP_004038103.1|   7 HHVGITVSDLENAVEFYQETLDLTLLDRFTVSGENfstavgvdgATGQFAHLEADGVRVELIEYEPEGASRGEasiN 83 
                                       8****************************999886333333223577888888766******98887633333477* PP

                                       S-EEEEEEEEES-HHHHHHHHCTT CS
                      Glyoxalase_4  66 geglhhlaywvddldaavarleeq 89 
                                       ++g  hl++ v+d+d   ++l + 
  gi|313116979|ref|YP_004038103.1|  84 RPGTAHLGLTVEDIDSFYESLPNS 107
                                       ****************99998775 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.4e-09   1.2e-05       6     115 ..      11     138 ..       7     139 .] 0.71

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.4e-09
                                       -EES-HHHHHHHHHHTT---EEEE-...SSEEEETTS-EE..........EEH..HHHHH----...---S....-- CS
                      Glyoxalase_2   6 lvvkdieeskkFYedvlelkikldf...Genvsfetgfal..........ked..lkelinlde...siae....qs 60 
                                       ++v d+e++ +FY++ l+l +   f   Gen  f+t + +          + d    eli+++    s  e    + 
  gi|313116979|ref|YP_004038103.1|  11 ITVSDLENAVEFYQETLDLTLLDRFtvsGEN--FSTAVGVdgatgqfahlEADgvRVELIEYEPegaSRGEasinRP 85 
                                       6899***************998877433454..44444443344444444333434577755321122222001144 PP

                                       SS-EEEEEES-HHHHHHHH..GGGS-EEEEEEE-TTS-EEEEEE-TT--EEEEEE CS
                      Glyoxalase_2  61 nnfeLyFevedvdaflqklkeaeniellhelkekpWgqrvirfyDpDkhiiEige 115
                                          +L+  ved+d+f + l   +++e + +++    g r++ + Dp++++iE+ e
  gi|313116979|ref|YP_004038103.1|  86 GTAHLGLTVEDIDSFYESL--PNSVESVSRPQTTDTGSRILFVRDPEGNLIELLE 138
                                       5689***************..7789***************************865 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.8e-08   0.00025       2     123 ..       7     128 ..       6     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.8e-08
                      Glyoxalase_3   2 DHvvlavpdleeaaarfarrlGftvtpggehpgl.........gtaNalvmf.gdg.YlEllavdpeapaperprlf 67 
                                       +Hv++ v+dle+a++ ++++l +t+ ++   +g          g+  + +++ +dg  +El++++pe ++++++   
  gi|313116979|ref|YP_004038103.1|   7 HHVGITVSDLENAVEFYQETLDLTLLDRFTVSGEnfstavgvdGATGQFAHLeADGvRVELIEYEPEGASRGEAS-- 81 
                                       7*************************7777776666777777788888899987899************954332.. PP

                      Glyoxalase_3  68 gldrlakgeglhtlalrtddidataarlraaGvdeagrrv.rpdggdlrwrllflad 123
                                        +    +++g  +l l+++did  ++ l +       + v rp+ +d   r+lf++d
  gi|313116979|ref|YP_004038103.1|  82 -I----NRPGTAHLGLTVEDIDSFYESLPNSV-----ESVsRPQTTDTGSRILFVRD 128
                                       .2....35********************9876.....33336666666666666666 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.4e-07   0.00049       4     106 ..      11     136 ..       8     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                      Glyoxalase_6   4 ldaadpaalaaFwaaalgweveree..........aaledpegvgpaaedaatllfqrvpe................ 54 
                                       + ++d + +++F+++ l++++ ++           +           + d+at  f + +                 
  gi|313116979|ref|YP_004038103.1|  11 ITVSDLENAVEFYQETLDLTLLDRFtvsgenfstaV-----------GVDGATGQFAHLEAdgvrvelieyepegas 76 
                                       5678999*************9999966665555541...........333333333333333344455555667999 PP

                      Glyoxalase_6  55 ......paknrvHldlavedldaevarlvalGArvlreprdgthgr..vlaDPeGneFcv 106
                                                   Hl l+ved+d   + l +   +v r++  +t+ r   ++DPeGn   +
  gi|313116979|ref|YP_004038103.1|  77 rgeasiNRPGTAHLGLTVEDIDSFYESLPNSVESVSRPQTTDTGSRilFVRDPEGNLIEL 136
                                       99876633345***********999999999999999999999999**********8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1013.40
//
Query:       gi|313116980|ref|YP_004038104.1|  [L=419]
Description: ORC complex protein Cdc6/Orc1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-16   59.7   0.1    9.1e-16   57.6   0.0    2.2  1  Cdc6_C           CDC6, C terminal winged helix domain
    4.6e-13   49.9   0.3    1.8e-12   48.0   0.3    2.1  1  AAA_16           AAA ATPase domain
    7.1e-12   45.8   0.1    2.3e-11   44.1   0.0    1.8  2  AAA_22           AAA domain
    3.9e-06   26.2   0.0    9.7e-06   24.9   0.0    1.7  1  DUF815           Protein of unknown function (DUF815)
    2.9e-05   24.1   0.0    7.1e-05   22.8   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
    3.9e-05   24.1   0.2    0.00013   22.4   0.2    1.9  1  AAA              ATPase family associated with various cellul
    4.9e-05   23.1   0.0    9.4e-05   22.2   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
    0.00022   20.5   0.0    0.00031   20.0   0.0    1.3  1  NB-ARC           NB-ARC domain
    0.00031   20.9   0.0      0.028   14.5   0.0    2.2  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00053   19.8   0.6      0.011   15.5   0.3    2.3  2  IstB_IS21        IstB-like ATP binding protein
    0.00074   20.0   0.0     0.0021   18.6   0.0    1.8  2  ABC_tran         ABC transporter
    0.00084   19.3   0.0     0.0015   18.5   0.0    1.4  1  NACHT            NACHT domain
    0.00091   18.1   0.1       0.21   10.3   0.1    2.1  2  AAA_32           AAA domain
      0.001   18.0   0.0     0.0061   15.4   0.0    2.0  2  DUF2791          P-loop Domain of unknown function (DUF2791)
     0.0016   18.8   0.1     0.0056   17.1   0.1    2.1  1  RNA_helicase     RNA helicase
     0.0036   17.1   0.2       0.01   15.6   0.2    1.8  1  AAA_30           AAA domain
     0.0048   16.4   0.1      0.015   14.8   0.1    1.8  2  AAA_7            P-loop containing dynein motor region
      0.006   16.0   0.0      0.011   15.1   0.0    1.4  1  TniB             Bacterial TniB protein
      0.009   15.6   0.7       0.17   11.5   0.0    2.9  2  AAA_25           AAA domain
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.017   14.3   0.0    1.3  1  KAP_NTPase       KAP family P-loop domain
      0.015   14.7   0.1        1.5    8.2   0.0    2.3  2  PhoH             PhoH-like protein
      0.017   15.1   0.0      0.033   14.1   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
      0.047   13.0   0.0      0.073   12.4   0.0    1.2  1  DnaB_C           DnaB-like helicase C terminal domain
      0.049   13.4   1.2        5.3    6.8   0.1    2.5  2  DEAD             DEAD/DEAH box helicase
      0.049   13.6   0.0      0.096   12.7   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.058   12.6   0.0      0.097   11.8   0.0    1.3  1  DAP3             Mitochondrial ribosomal death-associated pro
      0.063   13.4   0.1       0.11   12.6   0.1    1.3  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.066   12.4   0.1       0.34   10.0   0.1    2.1  2  PIF1             PIF1-like helicase
      0.075   12.9   0.0       0.16   11.8   0.0    1.6  1  AAA_lid_3        AAA+ lid domain
       0.08   12.8   0.9       0.44   10.5   0.0    2.6  2  Phage-MuB_C      Mu B transposition protein, C terminal
      0.083   12.2   0.1       0.16   11.2   0.1    1.4  1  Zeta_toxin       Zeta toxin


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   1.6e-18   9.1e-16       1      79 [.     312     390 ..     312     396 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.6e-18
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L a+++l++ ++++e+++ ++ e+Y++lCe +g ++++ r+v+d +++L++l ilel+k++ Gr++g t + +L+ d
  gi|313116980|ref|YP_004038104.1| 312 LSAVTALHKGTDDDEFSMAQIIETYTKLCEATGTSTRSDRRVRDFVRRLAFLDILELRKQNLGRAGGITIYARLQPD 388
                                       7799*******************************************************************999876 PP

                                       CH CS
                            Cdc6_C  78 pd 79 
                                        d
  gi|313116980|ref|YP_004038104.1| 389 HD 390
                                       54 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.3   3.1e-15   1.8e-12       2     145 ..      38     161 ..      37     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 3.1e-15
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysala 73 
                                        vGR++e+++L + l+++  g++ e+v+l+Ge G+GKs +++++++a++ +    ++ +++ +c         ++ +
  gi|313116980|ref|YP_004038104.1|  38 IVGRDDEIRALSTELRSAVNGDSpENVILYGETGTGKSLVAKHVAKAAKSNagdvRIGTVYVDCSTD------DTET 108
                                       69*********9999955555555*********************9999998887555566666666......2246 PP

                            AAA_16  74 qalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                       qa+   ++ r l+de+e++ + +     ++ ++           + +  l  +l++l   +  ++++lD+++
  gi|313116980|ref|YP_004038104.1| 109 QAI-S-TIARTLNDESETDIRVPE----TGLAK----------AAYYTRLYTILDKLY--DV-VIIILDEAD 161
                                       677.4.677777777555222222....22222..........233444444442222..23.666666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0     4e-14   2.3e-11       7     118 ..      63     178 ..      58     193 .. 0.84
   2 ?   -1.9   0.0       6.5   3.8e+03      49      88 ..     319     359 ..     271     366 .. 0.62

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 4e-14
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlssee 77 
                                        ++++Ge+GtGK+++++ +++ ++  ++a + r ++v+v+++ + + ++  + ++r l++e ++       +l + +
  gi|313116980|ref|YP_004038104.1|  63 NVILYGETGTGKSLVAKHVAKAAK--SNAGDVRIGTVYVDCSTDDTETQAISTIARTLNDESETdirvpeTGLAKAA 137
                                       5799******************84..555669****************************9999*****77777777 PP

                            AAA_22  78 llealeqalraravielliiDEaqhlrs.eealeeLrsllnl 118
                                       ++++l+  l++ ++++++i+DEa+   + +++l  L++ ++ 
  gi|313116980|ref|YP_004038104.1| 138 YYTRLYTILDKLYDVVIIILDEADMH-PdDQILMSLSRAVET 178
                                       77************9*********86.547777777666665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.5
                            AAA_22  49 sst.sskdl.lrellralglelkaerlsseellealeqalra 88 
                                       +++ + +++ + ++ + ++  ++a +++s +  +++++ +r+
  gi|313116980|ref|YP_004038104.1| 319 HKGtDDDEFsMAQIIETYTKLCEA-TGTSTRSDRRVRDFVRR 359
                                       333355555566666666666666.55555555555555554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.7e-08   9.7e-06      21      82 ..      29      92 ..      12     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-08
                            DUF815 21 evdevklddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..L 82
                                        +  + +++vg d++ +al +  +  ++g + +nv+L+G+ GtGKS + k + ++++++   +
  gi|313116980|ref|YP_004038104.1| 29 VEHVPSPERIVGRDDEIRALSTELRSAVNGDSPENVILYGETGTGKSLVAKHVAKAAKSNAgdV 92
                                      4444567899***************************************999999887765454 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.2e-07   7.1e-05       1      92 [.      63     179 ..      63     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-07
                                       EEEEE--SSSSHHHHHHHGGGGB.......S--EEEEE--TT--HHHHH--B--..............--------. CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.......nreveyvqltrdtteedlkgrreik.....ngttslvdsplvraar. 64 
                                       +v+L G++GtgKs +a+++a+a        +  ++yv ++ d te++ +  +  +     + + +  +  l +aa  
  gi|313116980|ref|YP_004038104.1|  63 NVILYGETGTGKSLVAKHVAKAAksnagdvRIGTVYVDCSTDDTETQAISTIARTlndesETDIRVPETGLAKAAYy 139
                                       69*********************998887777889999988877777766666555676433344444556655559 PP

                                       ...........G-SEEEEESGGG--.HHHHHHHHHHHHSS CS
                             AAA_5  65 ...........egeilvlDEverae.sevlnsLlslleer 92 
                                                     i++lDE ++ + +++l+sL +  e+ 
  gi|313116980|ref|YP_004038104.1| 140 trlytildklyDVVIIILDEADMHPdDQILMSLSRAVETG 179
                                       999*****999999********999999999999888776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   2.2e-07   0.00013       1      70 [.      64     163 ..      64     209 .. 0.57

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.2e-07
                                       EEEESSTTSSHHHHHHHHHHHHTHE.......EEEEETTTCSSS..........STTHHHHHHHHHHHHHHHTS... CS
                               AAA   1 vllyGppGtGKTllakavakelgve.......fleisgsellsk..........yvgesekkirelfkeakeka... 57 
                                       v+lyG  GtGK+l+ak vak ++++        + +++s+   +          +  ese +ir   + + + a   
  gi|313116980|ref|YP_004038104.1|  64 VILYGETGTGKSLVAKHVAKAAKSNagdvrigTVYVDCSTDDTEtqaistiartLNDESETDIRVPETGLAKAAyyt 140
                                       79*******************98774444444222222222211445666666644444444443333332222344 PP

                                       ..........TSEEEEEETGGGH CS
                               AAA  58 ..........kpsilfiDEidal 70 
                                                 + +i+++DE+d  
  gi|313116980|ref|YP_004038104.1| 141 rlytildklyDVVIIILDEADMH 163
                                       44444455555688888888865 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.6e-07   9.4e-05       1      51 [.      38      90 ..      38     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.6e-07
                                      ----SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                   Sigma54_activat  1 ligesealkelleqikkvaktd..lsvlitGesGtGKellaraiheaskrkek 51
                                      ++g+++++++l ++++++++ d   +v++ Ge+GtGK+l+a+++ +a k +++
  gi|313116980|ref|YP_004038104.1| 38 IVGRDDEIRALSTELRSAVNGDspENVILYGETGTGKSLVAKHVAKAAKSNAG 90
                                      67899999999999999997665589*****************9997766544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   5.3e-07   0.00031      15     110 ..      58     158 ..      41     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.3e-07
                                       TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STT CS
                            NB-ARC  15 kdelqslvvalvGmgGvGKttlakqilnksdevegrFd.svawvvvsktdkseeiletilkeLslseddleekeeve 90 
                                        d+++   v l+G  G GK+ +ak++ +  ++  g    + ++v  s  d++ + + ti++ L+++++ +   +e  
  gi|313116980|ref|YP_004038104.1|  58 GDSPE--NVILYGETGTGKSLVAKHVAKAAKSNAGDVRiGTVYVDCSTDDTETQAISTIARTLNDESETDIRVPETG 132
                                       45556..789*******************999999888799**********************99876555555443 PP

                                       S....HHHHHHHHCCCT..TEEEEEE CS
                            NB-ARC  91 s....lkrklvrlLltk..rfllvlD 110
                                              ++l+ +L +    ++++lD
  gi|313116980|ref|YP_004038104.1| 133 LakaaYYTRLYTILDKLydVVIIILD 158
                                       33555556666666665544455555 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.8e-05     0.028       1      46 [.      39      86 ..      39      99 .. 0.84
   2 ?    4.1   0.0     0.082        47      35     109 ..     112     193 ..     108     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-05
                                      X---HHHHHHHHHHHHHH..T-SS-EEEEEETT--HHHHHHCC--TTS CS
                   Sigma54_activ_2  1 lgasaaiqelkerLeqaa..qsklpvfltGekGsgkelvArlLhknsg 46
                                      +g+   i +l ++L +a+   s  +v l Ge G+gk+lvA+  +k + 
  gi|313116980|ref|YP_004038104.1| 39 VGRDDEIRALSTELRSAVngDSPENVILYGETGTGKSLVAKHVAKAAK 86
                                      67888999*********94455667****************9887655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.082
                                       HHHHHCC--TTS-EE--SSTTHHHH-H.....HHHHHHTTTSEEEEEE-TT--HHHH..HHHHHHHHHHT.TTT-EE CS
                   Sigma54_activ_2  35 elvArlLhknsgpwleifvverlaklp.....ldlleqakggtLylkdiadlskaeq..keLlellakae.ksslrl 103
                                       +++Ar+L ++s++++ + +   lak+        +l+++ ++++++ d ad+ +++q  + L  +++ ++ ++++ l
  gi|313116980|ref|YP_004038104.1| 112 STIARTLNDESETDIRVPET-GLAKAAyytrlYTILDKLYDVVIIILDEADMHPDDQilMSLSRAVETGKtGCRIGL 187
                                       57899999999987766544.33332233444999******************999855688889999877888888 PP

                                       EEEEEE CS
                   Sigma54_activ_2 104 Vstssk 109
                                       +++s k
  gi|313116980|ref|YP_004038104.1| 188 IAISNK 193
                                       998865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   1.9e-05     0.011      37      83 ..      51      97 ..      39     157 .. 0.63
   2 ?    3.0   0.1      0.12        72      90     124 ..     133     167 ..     128     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                         IstB_IS21 37 eLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrv 83
                                      eL++    ++ en++l G +G+GKs +a  ++++a  +   v+  +v
  gi|313116980|ref|YP_004038104.1| 51 ELRSAVNGDSPENVILYGETGTGKSLVAKHVAKAAKSNAGDVRIGTV 97
                                      56666666788********************9999887777765444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                         IstB_IS21  90 lkrarrdgklaralkrllkvdllilDdlgllpldq 124
                                       l++a    +l ++l++l  v ++ilD+  ++p dq
  gi|313116980|ref|YP_004038104.1| 133 LAKAAYYTRLYTILDKLYDVVIIILDEADMHPDDQ 167
                                       5666777899999**************99998776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.7e-06    0.0021      12      90 ..      62     147 ..      56     212 .. 0.76
   2 ?   -2.2   0.0       9.8   5.7e+03      80      95 ..     289     304 ..     252     366 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.7e-06
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.......HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.......es 81 
                                       e v + Ge+G+GKS ++k +a+  k ++G++++    ++  +     + i+++  + +  +e+ +r         ++
  gi|313116980|ref|YP_004038104.1|  62 ENVILYGETGTGKSLVAKHVAKAAKSNAGDVRIGTVYVDCSTDDTETQAISTIARTLNDESETDIRVPetglakaAY 138
                                       7899***************************9998888887788888888888888666555554443446666633 PP

                                       HTCHHHHHH CS
                                       xxxxxxxxx RF
                          ABC_tran  82 deeiekals 90 
                                         +++++l+
  gi|313116980|ref|YP_004038104.1| 139 YTRLYTILD 147
                                       333444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.8
                                       HHHTCHHHHHHHSTTG CS
                                       xxxxxxxxxxxxxxxx RF
                          ABC_tran  80 esdeeiekalsklglk 95 
                                       ++++e +++++ +g  
  gi|313116980|ref|YP_004038104.1| 289 KMEAEKDRFRDLIGGL 304
                                       3333333333332222 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.6e-06    0.0015       3      95 ..      64     165 ..      62     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.6e-06
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C....... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse....... 71 
                                       vil Ge G GK+  ++++a a++++  +      v+ + ++++ ++++a  ++a++l ++    ++ +++       
  gi|313116980|ref|YP_004038104.1|  64 VILYGETGTGKSLVAKHVAKAAKSNAGDVR-IGTVY-VDCSTDDTETQAiSTIARTLNDESETDIRVPETglakaay 138
                                       89******************9999997774.55555.5555555555443777777777777666666669999998 PP

                                       ...CHHHHCCSCCCEEEEEE-STT-SS CS
                             NACHT  72 ...vwavllelperlLlilDglDelvt 95 
                                            ++l +l + + +ilD +D  ++
  gi|313116980|ref|YP_004038104.1| 139 ytrLYTILDKLYDVVIIILDEADMHPD 165
                                       887777788888888899999997765 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0088       5.1       6      78 ..      34     110 ..      29     116 .. 0.70
   2 !   10.3   0.1   0.00036      0.21     478     511 ..     259     292 ..     255     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0088
                            AAA_32   6 pleeiigqeRAvealefglkikkkg...YNifvlGesgtGrttlvkrlleeiakkeptp.dDwcYvnnfdnpeePka 78 
                                       + e+i+g++  ++al++ l+   +g    N+ + Ge+gtG++ ++k++ +++++++       +Yv   ++ +e +a
  gi|313116980|ref|YP_004038104.1|  34 SPERIVGRDDEIRALSTELRSAVNGdspENVILYGETGTGKSLVAKHVAKAAKSNAGDVrIGTVYVDCSTDDTETQA 110
                                       55677888888888877776655543347****************99998877665433146777766666666555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00036
                            AAA_32 478 seiadllrEAdywakkegaevveaehVekAleek 511
                                       ++ +d+lr A ++a+++g+++v+++hVe+A  e 
  gi|313116980|ref|YP_004038104.1| 259 RQAIDVLRNAGMLAQRDGSDTVTRDHVEDAKMEA 292
                                       6789*************************96554 PP

>> DUF2791  P-loop Domain of unknown function (DUF2791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05    0.0061      28      76 ..      39      88 ..      34     131 .. 0.80
   2 ?   -0.2   0.0      0.58   3.4e+02     182     213 ..     322     353 ..     272     377 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                           DUF2791 28 VGrereiealledlervaeggaafrf.irGeYGsGKtFllqllreraler 76
                                      VGr++ei+al+++l++  +g +   + + Ge G+GK+ +++ +++ a+++
  gi|313116980|ref|YP_004038104.1| 39 VGRDDEIRALSTELRSAVNGDSPENViLYGETGTGKSLVAKHVAKAAKSN 88
                                      9**************99999887665168***********9999988764 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.58
                           DUF2791 182 keegdeelksaalrWLrGeyktktearkelgv 213
                                       +++++ ++++ +  + +   +t t++r++  v
  gi|313116980|ref|YP_004038104.1| 322 TDDDEFSMAQIIETYTKLCEATGTSTRSDRRV 353
                                       33333333333333333333333333333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   9.6e-06    0.0056       1      42 [.      64     105 ..      64     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.6e-06
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpedd 42 
                                       ++lyG++g+GKS++ak++aka  ++ ++ + ++vy+  ++dd
  gi|313116980|ref|YP_004038104.1|  64 VILYGETGTGKSLVAKHVAKAAKSNAGDVRIGTVYVDCSTDD 105
                                       689******************999999999999999666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.8e-05      0.01      20     114 ..      63     177 ..      50     188 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk............... 81 
                                        ++l G  GtGK+ + k++++a++++ g+v + +     + + +e    + stia+ l+                  
  gi|313116980|ref|YP_004038104.1|  63 NVILYGETGTGKSLVAKHVAKAAKSNAGDVRIGTVYVDCSTDDTET--QAISTIARTLNDESetdirvpetglakaa 137
                                       57999*******************9965665555444444332221..13344444443333444555555555566 PP

                            AAA_30  82 .........grarlepgtllivDEagmvdtkqlaallkaaek 114
                                                +  +l +  ++i DEa m   +q+   l++a +
  gi|313116980|ref|YP_004038104.1| 138 yytrlytilD--KLYDVVIIILDEADMHPDDQILMSLSRAVE 177
                                       6666876542..455667888899999966665554444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.6e-05     0.015      34      80 ..      62     110 ..      50     132 .. 0.72
   2 ?   -0.5   0.0       1.3   7.4e+02      17      66 ..     106     154 ..      96     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld..kekylsltinfsaqtsanqlqd 80 
                                        +v+l+G+tGtGK++++k++ k+ +    ++ + t+ +  +t+ +++q 
  gi|313116980|ref|YP_004038104.1|  62 ENVILYGETGTGKSLVAKHVAKAAKsnAGDVRIGTVYVDCSTDDTETQA 110
                                       689****************877666113445555555555555555554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                             AAA_7  17 vdtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylslt 66 
                                       ++t  +s++ ++l +++   + v +tG +K ++ ++l + ld + y +++
  gi|313116980|ref|YP_004038104.1| 106 TETQAISTIARTLNDESETDIRVPETGLAKAAYYTRLYTILD-KLYDVVI 154
                                       5778888889999999999999999*******9999988888.5555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-05     0.011      25     128 ..      51     160 ..      37     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkar 101
                                       eL ++ + + ++n++l+G++ +GK+ ++++ a+  ++  ++ + ++  ++v++ +  +e +  + i ++l+ + +++
  gi|313116980|ref|YP_004038104.1|  51 ELRSAVNGDSPENVILYGETGTGKSLVAKHVAKAAKS--NAGDVRIGTVYVDCSTDDTETQAISTIARTLNDESETD 125
                                       566666778889*****************99887654..557789999******************99999886555 PP

                              TniB 102 a.......rvskleqqvlrllrel.kvrvLiiDEi 128
                                                 ++ + + +++l++l +v ++i+DE 
  gi|313116980|ref|YP_004038104.1| 126 IrvpetglAKAAYYTRLYTILDKLyDVVIIILDEA 160
                                       43333333444556677777776437888888886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00029      0.17      11      57 ..      41      85 ..      33     161 .. 0.77
   2 ?    1.5   0.1      0.34     2e+02     146     180 ..     310     344 ..     219     347 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                            AAA_25 11 svadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalav 57
                                      ++++++a  +++r  v g  p  e ++l+G +gtGK+ +a ++a a 
  gi|313116980|ref|YP_004038104.1| 41 RDDEIRALSTELRSAVNGDSP--ENVILYGETGTGKSLVAKHVAKAA 85
                                      567788889999999999988..779*************98887655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.34
                            AAA_25 146 vviDplsralggdensnsdvgalvealeriarrtg 180
                                       +v+  +++++ g  +++  +++++e   +++++tg
  gi|313116980|ref|YP_004038104.1| 310 LVLSAVTALHKGTDDDEFSMAQIIETYTKLCEATG 344
                                       45555666666666666667777777777777776 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     3e-05     0.017      23      99 ..      64     140 ..      46     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                        KAP_NTPase  23 vgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaLadaleeeygqlatkllrakklk 99 
                                       v Lyg+ G+GKs + + + ++ k++a  vr+  ++++    +++ +a+ ++ ++L d+ e++  + +t+l +a  ++
  gi|313116980|ref|YP_004038104.1|  64 VILYGETGTGKSLVAKHVAKAAKSNAGDVRIGTVYVDCSTDDTETQAISTIARTLNDESETDIRVPETGLAKAAYYT 140
                                       78******************************************************************999885544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0026       1.5      20      43 ..      62      85 ..      45      94 .. 0.79
   2 ?    4.1   0.0     0.047        27     121     145 ..     153     177 ..     147     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0026
                                      SEEEEE--TTSSTTHHHHHHHHHH CS
                              PhoH 20 divfaiGpaGtGKtylavalavea 43
                                      + v+  G++GtGK+++a  +a +a
  gi|313116980|ref|YP_004038104.1| 62 ENVILYGETGTGKSLVAKHVAKAA 85
                                      568999***********8887554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.047
                                       EEEEE-SGGG--HHHHHHHHTTB-T CS
                              PhoH 121 afvilDEAQnttkeqmkmfltRlGe 145
                                        ++ilDEA      q+ m l+R  e
  gi|313116980|ref|YP_004038104.1| 153 VIIILDEADMHPDDQILMSLSRAVE 177
                                       579******************9755 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.7e-05     0.033      10     128 ..      51     161 ..      39     172 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                          ATPase_2  10 eleeilerepneiyfiYGpegsGKtaLlkeiienledkdk....yviyyialreesiskldefieeeeekkklekal 82 
                                       el++ ++ ++ e + +YG  g GK+ + k++++  ++         +y++   ++ ++++ ++i+ + +++     +
  gi|313116980|ref|YP_004038104.1|  51 ELRSAVNGDSPENVILYGETGTGKSLVAKHVAKAAKSNAGdvriGTVYVDCSTDDTETQAISTIARTLNDE---SET 124
                                       567778888889999****************9988554333565889998776666666666655333333...233 PP

                          ATPase_2  83 giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelq 128
                                        i+vp++ l        ++  ++ ++l+  + k    +iii+De+ 
  gi|313116980|ref|YP_004038104.1| 125 DIRVPETGL--------AK-AAYYTRLYTILDKLYDVVIIILDEAD 161
                                       456777777........33.35666677777777777888888875 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.073      21     121 ..      63     172 ..      47     192 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                       EEEEEEXTTSSHHHHHHHHHHHHHHCST.SE.......EEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTSXHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  21 liiiAarpsmGktalalniaenaavkek.lp.......vavfslemsaeqlvqRllsseaeidskklrtgklkeedw 89 
                                        +i+ +  ++Gk+ +a ++a++a  ++  ++       +     e +a + ++R l  e+e d +  +tg  k + +
  gi|313116980|ref|YP_004038104.1|  63 NVILYGETGTGKSLVAKHVAKAAKSNAGdVRigtvyvdCSTDDTETQAISTIARTLNDESETDIRVPETGLAKAAYY 139
                                       3678899*************987763331222232111333345666777799**********9999***99999** PP

                                       HHHHHHHHHHHHSEEEEEEXSSXCHHH.HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                            DnaB_C  90 eklteaieelseaklfiddtpaltvse.irska 121
                                       ++l + +++l ++ ++i d++++++ + i + +
  gi|313116980|ref|YP_004038104.1| 140 TRLYTILDKLYDVVIIILDEADMHPDDqILMSL 172
                                       ********************9998754244443 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0092       5.3      15      32 ..      62      79 ..      47     109 .. 0.84
   2 ?    4.9   0.2     0.034        20     118     146 ..     148     176 ..     103     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0092
                                      CEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTlafl 32
                                      ++v++ +eTG+GK+l++ 
  gi|313116980|ref|YP_004038104.1| 62 ENVILYGETGTGKSLVAK 79
                                      79************9974 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.034
                                       HCTTEEEEEEETHHHHHHTTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 118 nlsqvrflVlDEadrlldqgfsdfinril 146
                                       +l +v +++lDEad+  d++    ++r +
  gi|313116980|ref|YP_004038104.1| 148 KLYDVVIIILDEADMHPDDQILMSLSRAV 176
                                       288999********998887666666655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017     0.096       5      46 ..      43      88 ..      39      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  5 eetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgve 46
                                      +e++al ++l +a+     + ++L+G+ G+GK+  ++++aka + +
  gi|313116980|ref|YP_004038104.1| 43 DEIRALSTELRSAVngdsPENVILYGETGTGKSLVAKHVAKAAKSN 88
                                      678889999988777544456*******************998764 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017     0.097      12      48 ..      50      86 ..      44      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                      HHHTTS-SSS---EEEEE-SSSSSTTTTHHHHHHHGG CS
                              DAP3 12 kklkkadkkkkvkrlvltGekgsGKSvlLlqalayAl 48
                                      ++l +a +    + ++l+Ge+g+GKS++  ++   A 
  gi|313116980|ref|YP_004038104.1| 50 TELRSAVNGDSPENVILYGETGTGKSLVAKHVAKAAK 86
                                      56667767778899*************9999887775 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00018      0.11       5      78 ..      63     161 ..      59     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                       -EEEE--TTSSHHHHHHHHHHHTT-.......-EEEEEGGG---.----THHHHHHHHHTTT-HHHHTTS....... CS
                             AAA_2   5 silllgptgvGktelakalaellfv...kkekkliradaselle.eeevehlvsrligappgyvgaeegG....... 70 
                                       +++l g+tg+Gk+++ak +a+  +    + +   + +d+s+  +  ++++++   l  +++ ++++ e G       
  gi|313116980|ref|YP_004038104.1|  63 NVILYGETGTGKSLVAKHVAKAAKSnagDVRIGTVYVDCSTDDTeTQAISTIARTLNDESETDIRVPETGlakaayy 139
                                       78899****************999877777778889999876552666677777788899***************** PP

                                       ..............EEEEETGG CS
                             AAA_2  71 ..............ivllDEid 78 
                                                     i+ lDE d
  gi|313116980|ref|YP_004038104.1| 140 trlytildklydvvIIILDEAD 161
                                       ********************88 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00058      0.34      11      52 ..      50      91 ..      42     177 .. 0.65
   2 ?   -1.4   0.0       1.7     1e+03     277     300 ..     197     220 ..     186     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00058
                                      HHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCC CS
                              PIF1 11 daiieavlnekgklfFvtGsgGtgKtflwkallkklrsegki 52
                                       +   av+ ++++++ ++G  GtgK+ + k++ k+ +s+   
  gi|313116980|ref|YP_004038104.1| 50 TELRSAVNGDSPENVILYGETGTGKSLVAKHVAKAAKSNAGD 91
                                      5566788889***********************999995433 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                                       HHHHHHHHHCCSSS--EEEE-EEE CS
                              PIF1 277 vdeiNnyvlsklpgeekeylssDs 300
                                        +++N++v s l+  e ++ s+D 
  gi|313116980|ref|YP_004038104.1| 197 AEDLNDRVKSSLQPRELNFHSYDA 220
                                       6789******************97 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028      0.16      22      45 .]     264     287 ..     263     287 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                         AAA_lid_3  22 lcreAallAlrrgikeitmedfee 45 
                                       + r+A++lA r+g +++t ++ e+
  gi|313116980|ref|YP_004038104.1| 264 VLRNAGMLAQRDGSDTVTRDHVED 287
                                       679******************986 PP

>> Phage-MuB_C  Mu B transposition protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       4.3   2.5e+03       4      40 ..      78     116 ..      75     118 .. 0.60
   2 ?   10.5   0.0   0.00076      0.44      39      75 ..     252     289 ..     237     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.3
                                       --TT-.-SS-SGGGTTHHHHSSSS.SSSHHHHHHHTTSS CS
                       Phage-MuB_C   4 gkrvs.ikktkkeDvkaiaaAwgl.tdeelmkllqeiae 40 
                                       +k+v+  +k++++Dv+  +      td+ ++++++ ia+
  gi|313116980|ref|YP_004038104.1|  78 AKHVAkAAKSNAGDVRIGTVYVDCsTDDTETQAISTIAR 116
                                       555541356666777655555555677777777777776 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00076
                                       SSS-S-HHHHHHHHGGGT-TT-TTS--S.SHHHHHHHH CS
                       Phage-MuB_C  39 aekpGaLRaltktLrlAamfAkgegeel.tadliraAw 75 
                                       a+  G  R+    Lr A+m A+ +g+   t+d++ +A+
  gi|313116980|ref|YP_004038104.1| 252 AQDHGDARQAIDVLRNAGMLAQRDGSDTvTRDHVEDAK 289
                                       4556777999999*********9998766*******96 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00028      0.16      10      49 ..      55      94 ..      46      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                        Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdelerqgnvvrl 49
                                       +++++P  ++l G +G GKs +a+ ++++ +++ + vr+
  gi|313116980|ref|YP_004038104.1| 55 AVNGDSPENVILYGETGTGKSLVAKHVAKAAKSNAGDVRI 94
                                      456799***********************99888777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 2987.49
//
Query:       gi|313116981|ref|YP_004038105.1|  [L=513]
Description: ATPase AAA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-39  133.4   0.0    1.9e-38  131.9   0.0    1.8  1  AAA              ATPase family associated with various cellul
    1.2e-08   34.6   0.2    3.7e-08   33.1   0.2    1.9  1  AAA_lid_3        AAA+ lid domain
    1.4e-06   28.4   0.6    9.9e-06   25.6   0.6    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
    2.9e-05   24.2   0.1    0.00014   22.1   0.0    2.2  1  AAA_33           AAA domain
    3.5e-05   23.6   0.0    0.00013   21.7   0.0    1.9  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.6e-05   23.3   0.0    0.00015   22.3   0.0    1.5  1  AAA_18           AAA domain
    0.00016   22.0   1.3     0.0017   18.6   0.3    2.8  2  AAA_22           AAA domain
     0.0026   18.1   0.1     0.0026   18.1   0.1    3.5  3  AAA_16           AAA ATPase domain
     0.0048   16.6   0.0      0.015   15.1   0.0    1.8  1  AAA_30           AAA domain
     0.0054   16.3   0.0      0.015   14.9   0.0    1.7  1  AAA_25           AAA domain
      0.007   15.6   0.4       0.29   10.3   0.0    2.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0082   15.4   0.0      0.015   14.6   0.0    1.5  1  TIP49            TIP49 P-loop domain
     0.0085   16.1   0.0      0.019   15.0   0.0    1.5  1  AAA_14           AAA domain
     0.0085   15.3   0.0       0.15   11.2   0.0    2.2  1  DUF815           Protein of unknown function (DUF815)
     0.0094   15.7   0.0      0.025   14.3   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.021   14.9   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.016   15.0   0.0       0.03   14.2   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
      0.029   14.3   0.3        9.8    6.1   0.0    2.5  2  NACHT            NACHT domain
      0.033   14.6   0.0      0.067   13.6   0.0    1.6  1  RNA_helicase     RNA helicase
      0.054   13.7   6.6       0.25   11.6   0.0    3.6  3  AAA_28           AAA domain
      0.056   13.6   0.1       0.84    9.7   0.0    2.3  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.063   13.1   0.1       0.19   11.5   0.1    1.7  1  AAA_11           AAA domain
      0.071   13.2   0.0       0.16   12.1   0.0    1.5  1  Torsin           Torsin
      0.082   13.2   0.2       0.26   11.6   0.2    1.9  1  AAA_19           AAA domain
      0.084   13.0   0.0       0.31   11.1   0.0    2.0  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.089   12.2   0.0        0.2   11.1   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
        0.1   12.3   0.0       0.18   11.5   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   12.3   0.0       0.27   11.3   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.16   11.5   0.0       0.37   10.3   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
       0.44   11.3   1.4       0.66   10.7   0.1    1.9  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.9   0.0   3.1e-41   1.9e-38       1     131 [.     272     401 ..     272     402 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 3.1e-41
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       +ll+GppGtGKT++ +a+a elg++fl+i  ++++sk+vg+s+++++++f+ a++++ psi+fiDE+dal+++r  +
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELGRPFLRITPANVTSKFVGKSADNVAKVFEVARKHQ-PSIVFIDELDALGTDRsAT 347
                                       69******************************************************9.****************777 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       +++++e++++nqLl el +++ +  +v+vigatn+ d+ld+al r gRfd+ i ++
  gi|313116981|ref|YP_004038105.1| 348 HNTQSERQMQNQLLMELAELEAD--DVVVIGATNKLDELDEALTRtGRFDEWIAVP 401
                                       79999*****************5..8************************999887 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.2   6.1e-11   3.7e-08       3      40 ..     427     464 ..     422     474 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 6.1e-11
                         AAA_lid_3   3 dlkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                                       dl e A +T+G+S  D++++ +eAa++A++++ ++ t 
  gi|313116981|ref|YP_004038105.1| 427 DLGEFATLTDGFSASDIESIANEAARRAIEETYDTGTR 464
                                       79999**************************9886554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.6   1.7e-08   9.9e-06       2     135 ..     272     389 ..     271     393 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.7e-08
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK+ +++ la  l+r+++ +  +++ t++ +  + +        v ++  + ar  +++i+++DE++ 
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELGRPFLRIT-PANVTSKFVGKSAD-------NVAKV-FEVARkhQPSIVFIDELDA 339
                                       89***********************98764.55565555555555.......23333.333444699*********8 PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                       + ++   + ++  +er+++   + el   ++dd    + vi+++n+ld    el++al 
  gi|313116981|ref|YP_004038105.1| 340 LGTDRS-ATHNTQSERQMQNQLLMELAELEADD----VVVIGATNKLD----ELDEALT 389
                                       887765.567889******99999999999998....***********....7777775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.3e-07   0.00014       2      72 ..     272     370 ..     272     413 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.3e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt..........................dytr 50 
                                       +ll+G+pG+GK+++++ l+ +lg  + +++  ++ ++ +g+  ++                              t+
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELGrpFLRITPANVTSKFVGKSADNVAkvfevarkhqpsivfideldalgtdrSATH 348
                                       689*********************99999999966666664333333233333333444445555555555444455 PP

                            AAA_33  51 vldrlyqilnelarkalsagrn 72 
                                        +++ +q++n+l+ + ++ +++
  gi|313116981|ref|YP_004038105.1| 349 NTQSERQMQNQLLMELAELEAD 370
                                       6666666666666666665555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.2e-07   0.00013      33      97 ..     269     341 ..     265     394 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.2e-07
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvk.lkitsgPv....lekagdlaalltnleek...dvlfideihrls 97 
                                       ++ +ll+GpPG Gkt +++ +a elg   l+it + v    + k++d +a + ++ +k    ++fide+  l 
  gi|313116981|ref|YP_004038105.1| 269 INGILLHGPPGTGKTYVSRALAGELGRPfLRITPANVtskfVGKSADNVAKVFEVARKhqpSIVFIDELDALG 341
                                       5679*********************9863577766551111456666666655554331227******98775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.6e-07   0.00015       1      78 [.     272     374 ..     272     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.6e-07
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.........ald 47 
                                       Ill G+pG+GKt ++++L+ +lg                      + ++ +va+++++++ + +e         a++
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELGRpflritpanvtskfvgksadnVAKVFEVARKHQPSIVFIDEldalgtdrsATH 348
                                       89****************99987788999999999999******99999**********999999998876554333 PP

                            AAA_18  48 eskrldedkldklldaleenssaleegknlv 78 
                                       +++ +++++ ++ll +l e    le  +++v
  gi|313116981|ref|YP_004038105.1| 349 NTQSERQMQ-NQLLMELAE----LEADDVVV 374
                                       333333333.333333333....23344444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.2   3.7e+03      24      65 ..      70     113 ..      65     128 .. 0.72
   2 !   18.6   0.3   2.8e-06    0.0017       8      83 ..     272     361 ..     268     388 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.2
                            AAA_22  24 rlleqldeeakaee..erpevvfvtlpsstsskdllrellralg 65 
                                       r+l + ++e++ae    r+e ++ ++++++s++ l+ + + a++
  gi|313116981|ref|YP_004038105.1|  70 RVLGTEQIEEFAEAceTRAEEITSEAAAQCSPARLRAHAADAVE 113
                                       55556666666666777888888899999999999888877776 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.8e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.....sskdllrellralglelka......... 70 
                                       ++++G++GtGKT++ r l+ +l         +++++++t+++ t     +s   + ++++ +++ +k+         
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGEL---------GRPFLRITPANVTskfvgKS---ADNVAKVFEVARKHqpsivfide 336
                                       79********************.........66666666666553222111...22222222222222222333333 PP

                            AAA_22  71 ............erlsseelleale 83 
                                                   +++s++++ ++l 
  gi|313116981|ref|YP_004038105.1| 337 ldalgtdrsathNTQSERQMQNQLL 361
                                       3333333333655555555554444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.0       3.8   2.3e+03     117     122 ..     109     114 ..      34     178 .. 0.50
   2 !   18.1   0.1   4.4e-06    0.0026      20      51 ..     265     296 ..     258     315 .. 0.80
   3 ?    3.5   0.3      0.14        84     123     149 ..     317     342 ..     303     375 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.8
                            AAA_16 117 srllel 122
                                        +  e 
  gi|313116981|ref|YP_004038105.1| 109 ADAVEF 114
                                       222222 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 4.4e-06
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd 51 
                                         g+ + +ll+G++G+GK+ + r+l+ +l + 
  gi|313116981|ref|YP_004038105.1| 265 GLGTINGILLHGPPGTGKTYVSRALAGELGRP 296
                                       5577799******************9988877 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.14
                            AAA_16 123 lkrllallsrderplvlvlDdlqwade 149
                                       +++ ++ +++ ++p ++++D+l+ + +
  gi|313116981|ref|YP_004038105.1| 317 VAKVFEVARK-HQPSIVFIDELDALGT 342
                                       5566677888.888*********5544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-05     0.015      22     106 ..     273     346 ..     268     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                            AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEag 98 
                                       +l+Gp+GtGKt++ +al+    + g++ + ++p +  +k ++++    a+++ak+ +  ++    ++ +++ +DE  
  gi|313116981|ref|YP_004038105.1| 273 LLHGPPGTGKTYVSRALA---GELGRPFLRITPANVTSKFVGKS----ADNVAKVFEVARK----HQPSIVFIDELD 338
                                       689*********987765...456899999***99999998877....8999999954443....56699*****99 PP

                            AAA_30  99 mvdtkqla 106
                                        ++t+  a
  gi|313116981|ref|YP_004038105.1| 339 ALGTDRSA 346
                                       99887654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.5e-05     0.015      36     159 ..     272     386 ..     267     393 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagv. 111
                                       +ll G+pgtGKt +   la +  +G+p+l  + p +++  +v    s+d++++ ++ +++++  ++ +++  l+   
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGE--LGRPFLR-ITPANVTSKFVG--KSADNVAKVFEVARKHQ--PSIVFIDELDALg 341
                                       689*********987666655..699**99.667788888888..88888***********9..5666666665555 PP

                            AAA_25 112 eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggde 159
                                       +++  +++++ + +     ++l  ++ e e  ++vvi   +++ + de
  gi|313116981|ref|YP_004038105.1| 342 TDRSATHNTQSERQ---MQNQLLMELAELEADDVVVIGATNKLDELDE 386
                                       55544443333333...3356777777778899999988888777766 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.079        47     136     218 ..      66     169 ..      60     243 .. 0.79
   2 !   10.3   0.0   0.00048      0.29       4      55 ..     272     328 ..     270     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.079
                           DUF2075 136 lntgeigteeelkklakkleveleekv.....................hLksqfRvaaseaviewvdalldgkkeka 191
                                       l+ + + ++e+++++a+ +e  +ee +                       ++  R aa+ ++ +w +a +  +++++
  gi|313116981|ref|YP_004038105.1|  66 LHFERVLGTEQIEEFAEACETRAEEITseaaaqcsparlrahaadaveFVNNAARGAAEHRYWDWDRAQTPIGRNGR 142
                                       67777888888999888888888877788899988888999999988888999999999999999999999999999 PP

                           DUF2075 192 kplssqenfdirvfddleelkkalkek 218
                                         +s  ++f+i++ d l++ +++  + 
  gi|313116981|ref|YP_004038105.1| 143 FVQSLPDGFHIELRDALKAEFDWASHA 169
                                       999999999999999888777776555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00048
                           DUF2075   4 vlVtGvaGtGKtvvllnllael.....eddeeertavylsvNhplvlvlrealakke 55 
                                       +l +G +GtGKt+v  +l+ el     + +  + t++++ ++ + v+++ e  +k++
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELgrpflRITPANVTSKFVGKSADNVAKVFEVARKHQ 328
                                       6789******************99998888899999999999988888877666555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.5e-05     0.015      52      96 ..     271     313 ..     264     395 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt 96 
                                       ++Ll Gp+gtGkt ++ a++ elg   pf  ++ ++v s  v k+
  gi|313116981|ref|YP_004038105.1| 271 GILLHGPPGTGKTYVSRALAGELG--RPFLRITPANVTSKFVGKS 313
                                       79**********************..69*****999999888775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.2e-05     0.019       5     126 ..     272     403 ..     270     407 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.2e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT++ + l+ el    + +l i+  + + k   +++++   ++e +++++ +++f+DE   +     
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELG---RPFLRITPANVTSKFVGKSADNVAKVFEVARKHQPSIVFIDELDALgtdrs 345
                                       6899***************9999...777777766666644444444455555544456899**********99999 PP

                            AAA_14  77 ........pewekalkslvdegknldvivtGSnskllskeiatslagrvaeielypls 126
                                               +++++ l   + e +  dv+v G  +kl   + a + +gr +e    pl 
  gi|313116981|ref|YP_004038105.1| 346 athntqseRQMQNQLLMELAELEADDVVVIGATNKLDELDEALTRTGRFDEWIAVPLP 403
                                       9999988844444444444444466999999999999888888888888887777775 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00026      0.15      54     117 ..     270     338 ..     263     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvel...lrerperfilfvDDLs 117
                                       n +LL G  GtGK  + +al  e+ +  Lr+   +v+ + + +  + v++   ++++++  i+f+D L 
  gi|313116981|ref|YP_004038105.1| 270 NGILLHGPPGTGKTYVSRALAGELGRPFLRITpaNVTSKFVGKSADNVAKvfeVARKHQPSIVFIDELD 338
                                       789***************************963367766665544444330114456677899*99884 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.2e-05     0.025      48      77 ..     270     299 ..     242     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavragls 77 
                                       ++i+l Gp+G+GK++++ al+ e  r  l+
  gi|313116981|ref|YP_004038105.1| 270 NGILLHGPPGTGKTYVSRALAGELGRPFLR 299
                                       6899****************9876655554 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.6e-05     0.021       6     100 ..     272     361 ..     268     370 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                       ill gp g+Gkt++++ala  l     +++ r+   +++  + v ++ ++     +   ++ +  iv++DE+d    
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELG----RPFLRITPANVTS-KFVGKSADNVAKVFE-VARKHQPSIVFIDELDALGT 342
                                       8999******************9....7999998888888.344444444333333.33456777********9999 PP

                                       -.---------HHHHHHHH CS
                             AAA_2  83 k.essgadvSregVqrdLL 100
                                         + + +  S+   q+ LL
  gi|313116981|ref|YP_004038105.1| 343 DrSATHNTQSERQMQNQLL 361
                                       9555566678889999887 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     5e-05      0.03       2      71 ..     272     337 ..     271     406 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladei 71 
                                       +ll+g PG++kt + +ala  l+  f ri  tp  + s  +G++  + + k fe+ +     ++++ de+
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELGRPFLRI--TPANVTSKFVGKSADNVA-KVFEVARKH-QPSIVFIDEL 337
                                       79************************997..888888888887754443.334433321.2244444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.016       9.8       3      25 ..     272     294 ..     270     300 .. 0.86
   2 ?    5.9   0.1     0.018        11      64     113 ..     312     365 ..     298     419 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                                       EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                       ++l+G++G GKT+  + la ++ 
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELG 294
                                       789**********9999987765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.018
                                       S--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..............HHHHH CS
                             NACHT  64 epaapvsevwavllelperlLlilDglDelvtdlgq.....kekqpvrtlLseli 113
                                       ++a++v +v++v  +++ ++++i D lD l td ++     +e+q  ++lL el 
  gi|313116981|ref|YP_004038105.1| 312 KSADNVAKVFEVARKHQPSIVFI-DELDALGTDRSAthntqSERQMQNQLLMELA 365
                                       56778888999988999999885.9999999988888888677777777776653 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00011     0.067       1      36 [.     272     307 ..     272     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       i+l+Gp+g+GK+++++ La +l + +  ++  +v s
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELGRPFLRITPANVTS 307
                                       689******************998885555555543 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.5      0.99   5.9e+02      28      71 ..      38      85 ..      23     125 .. 0.79
   2 ?   11.6   0.0   0.00042      0.25       2      25 ..     272     296 ..     271     328 .. 0.84
   3 ?    2.5   0.1      0.25   1.5e+02      14      52 ..     433     471 ..     432     501 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.99
                            AAA_28 28 pEaareileekl..akgedalpwv.edllafaervleeqleeeaaa.a 71
                                       E +re++++ +   +++++ ++  +  l+f++ +  eq+ee a+a +
  gi|313116981|ref|YP_004038105.1| 38 DEQVREYVTSAGflVRDGQMVAANvAATLHFERVLGTEQIEEFAEAcE 85
                                      577888888887675666666666688888888888888888887742 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00042
                            AAA_28   2 ivitGgestGKTtlleaLaar.gyp 25 
                                       i + G+++tGKT +++aLa + g p
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGElGRP 296
                                       7899***************554766 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.25
                            AAA_28  14 tlleaLaargypvv.pEaareileeklakgedalpwvedl 52 
                                       tl+  ++a +++ +  Eaar+ +ee +++g+++  ++ + 
  gi|313116981|ref|YP_004038105.1| 433 TLTDGFSASDIESIaNEAARRAIEETYDTGTRQPIAA-RH 471
                                       788888888888777************9998754432.33 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.71   4.3e+02      12      52 ..      55      98 ..      53     133 .. 0.74
   2 ?    9.7   0.0    0.0014      0.84       8     102 ..     278     376 ..     272     381 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.71
                   Cytidylate_kin2 12 GetigeaLAekLglp.fydreiieevakelglseeev..eevde 52
                                      G+ ++ ++A  L+++ ++  e iee a+  +   ee+  e++ +
  gi|313116981|ref|YP_004038105.1| 55 GQMVAANVAATLHFErVLGTEQIEEFAEACETRAEEItsEAAAQ 98
                                      88899********962667899***9999999999885333333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde....rsrlssflskllaarvagdtl..dekld 78 
                                        G+g++++ +aLA +Lg pf+     + ++k  g s + v++v e    ++++  f+++l a     ++   +++++
  gi|313116981|ref|YP_004038105.1| 278 PGTGKTYVSRALAGELGRPFLRITPANVTSKFVGKSADNVAKVFEvarkHQPSIVFIDELDALG---TDRsaTHNTQ 351
                                       79***************99998766666666667777777666554323444444444443332...2224355555 PP

                   Cytidylate_kin2  79 delfeaqervirela..aeesvVivG 102
                                       +e +++q +++ ela  + ++vV++G
  gi|313116981|ref|YP_004038105.1| 352 SE-RQMQNQLLMELAelEADDVVVIG 376
                                       44.99**********88788999988 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00033      0.19      20      41 ..     272     293 ..     263     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                        l++GPPGtgKT +  +l  +l
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGEL 293
                                       599*********8887777666 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00026      0.16      57      79 ..     273     295 ..     268     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00026
                                       EEEE-TTSSHHHHHHHHHHHHST CS
                            Torsin  57 sfhGwtGtGknfvaeiiaenlyr 79 
                                        +hG +GtGk +v++ +a +l r
  gi|313116981|ref|YP_004038105.1| 273 LLHGPPGTGKTYVSRALAGELGR 295
                                       58**************9988755 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00043      0.26      13      90 ..     272     360 ..     268     394 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
                            AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae...........atTiHrlall 78 
                                       +l+ ++pGtGKT+v ++   +l +   +     +   f g++a+++++  +++ ++           a    r a+ 
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELGRPFLRITPANVTSKFVGKSADNVAKVFEVARKHqpsivfideldALGTDRSATH 348
                                       7899**********999998888766443344445567777888887777544444667555444442222222223 PP

                            AAA_19  79 dfddlltealel 90 
                                       +++++ +++ +l
  gi|313116981|ref|YP_004038105.1| 349 NTQSERQMQNQL 360
                                       333333333333 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00052      0.31      24      82 ..     272     341 ..     268     396 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                                       EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..............HHHHHHTTTSEEEEEE-TT-- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp..............ldlleqakggtLylkdiadls 82 
                                       ++l G++G+gk++v+r+L+ + g+   +f  +++a+ +               ++  + ++ + ++ +++ l+
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELGR---PFLRITPANVTskfvgksadnvakvFEVARKHQPSIVFIDELDALG 341
                                       799***************987766...5555555554422333343334222333333477777777777665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033       0.2       4      80 ..     272     379 ..     271     383 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                                       EEEE--TTSSHHHHHHHHHHHHHH...............................TT--EEEE-.THHHH.TTSSS- CS
                             KTI12   4 vvltGlPssGKstrakeLakalee...............................ekrsvvvid.deslgiekdsyk 48 
                                       ++l G P +GK+ +++ La +l                                 ++ s+v id  ++lg++++  +
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELGRpflritpanvtskfvgksadnvakvfevarkHQPSIVFIDeLDALGTDRSATH 348
                                       7899*************************************************987777888874578889999999 PP

                                       -GGGHHHHHHHHHHHHHHHHTT.SEEEE-S-- CS
                             KTI12  49 dsakekalRsslrsavkrdLskekvVIvDsln 80 
                                       ++++e++++++l  + + +L+ ++vV++ ++n
  gi|313116981|ref|YP_004038105.1| 349 NTQSERQMQNQLLMELA-ELEADDVVVIGATN 379
                                       ************99987.69999999998888 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.18       1      71 [.     272     337 ..     272     351 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                   Viral_helicase1   1 ivvhGvpGcGKStlirkllrtsliltvnrptaelltegk...pklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       i+ hG pG GK+ + r l+ +      +rp +  +t++    ++++++  + ++ f+ a++ +    i+++DE 
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGE-----LGRP-FLRITPANvtsKFVGKSADNVAKVFEVARKHQ--PSIVFIDEL 337
                                       678****************99.....4555.33333333355677777777778888887765..78*****96 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00045      0.27       7      45 ..     240     295 ..     234     307 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHCH......TEE............EEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE   7 tealgkklakal......gdv............ilLeGdLGaGKTtlvrglakalgv 45 
                                       ++++  +l++++                     ilL+G+ G+GKT  +r+la +lg 
  gi|313116981|ref|YP_004038105.1| 240 MHEVKDRLQQTVlnplrdP-DlfeeyglgtingILLHGPPGTGKTYVSRALAGELGR 295
                                       5555555555444333331.0344445555677*******************99975 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00061      0.37      36     115 ..     272     343 ..     266     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00061
                             AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDlnmp 112
                                       +ll Gp GtGKt + + l  +l           f   t an + +++ ++ +  +k   ++ +++  +vF+D+l+  
  gi|313116981|ref|YP_004038105.1| 272 ILLHGPPGTGKTYVSRALAGELG--------RPFLRITPANVTSKFVGKSADNVAKVFEVARKHQPSIVFIDELDAL 340
                                       89*************99999998........5677788889999999999999988888888899999999998876 PP

                             AAA_7 113 ake 115
                                         +
  gi|313116981|ref|YP_004038105.1| 341 GTD 343
                                       665 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0011      0.66      33      98 ..     314     377 ..     300     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                                       SSTHHHHHHHHHHHT-SEEEESSHHHHHHHHHHHHHTTSSSEEEESHHHHHHHHCHTT-SEEEE-- CS
                   DXP_reductoisom  33 gsnvellaeqakefkpklvavadeeaaeelkealkekelktevlvGeealkelaeeeeadvvvaai 98 
                                        +nv++++e+a++++p++v + + +a  + ++a++  +++ e  + ++ l elae e  dvvv + 
  gi|313116981|ref|YP_004038105.1| 314 ADNVAKVFEVARKHQPSIVFIDELDALGTDRSATH--NTQSERQMQNQLLMELAELEADDVVVIGA 377
                                       5799*****************99999999888885..6778888999**********999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 2857.19
//
Query:       gi|313116982|ref|YP_004038106.1|  [L=225]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-32  111.5   0.0    6.6e-32  110.7   0.0    1.4  1  DDE_Tnp_IS240  DDE domain
    4.1e-07   29.7   0.3    8.8e-07   28.6   0.3    1.6  1  rve_3          Integrase core domain
  ------ inclusion threshold ------
      0.031   14.5   0.1       0.06   13.5   0.1    1.7  1  rve            Integrase core domain
      0.037   13.8   0.0        1.5    8.6   0.0    2.2  2  DDE_3          DDE superfamily endonuclease
       0.05   13.1   0.1       0.11   12.0   0.1    1.5  1  DDE_Tnp_IS66   Transposase IS66 family


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.0   1.8e-35   6.6e-32       2     140 .]      80     212 ..      79     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.8e-35
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkel 77 
                                       k+++vDET+vki+G+w++ly+a+D e++ ild+ ++ r +t++a+afl+++ +k++l+++++++D+++ y++al++l
  gi|313116982|ref|YP_004038106.1|  80 KRVAVDETAVKINGEWSWLYAAIDIETKlILDVELFGRHGTDPAAAFLHRLSEKHDLSDAVFLVDGYG-YQTALSRL 155
                                       789*****************************************************************.******** PP

                     DDE_Tnp_IS240  78 kregelfdevshvqvkylnnriEsdhrtlKkrl..rptrgfkslksaaktlagfeavknlrkghk 140
                                       + +g+ +d+       +++n iE+++ tlK+r+  ++++++ s  s++++  +f+ ++n++++h+
  gi|313116982|ref|YP_004038106.1| 156 GLSGR-LDY-------VERNLIEKWFHTLKMRVdrFHNSWVGSHGSVREWFIQFAQYYNFQRPHQ 212
                                       **887.455.......789**************9889**************************95 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.3   2.5e-10   8.8e-07      34      67 .]     186     219 ..     165     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.5e-10
                             rve_3  34 elfrslaearekleawredYNteRPHssLgykTP 67 
                                       ++  s   +re+  ++ ++YN +RPH+sL+++TP
  gi|313116982|ref|YP_004038106.1| 186 SWVGSHGSVREWFIQFAQYYNFQRPHQSLNGRTP 219
                                       336677889************************9 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.7e-05      0.06       6      73 ..      80     144 ..      75     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                               rve   6 elwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsD 73 
                                       +++ vD t v+i   g++++l++++d  ++lil + l  ++ ++ ++a+l+r  ++   +   ++l D
  gi|313116982|ref|YP_004038106.1|  80 KRVAVDETAVKIN--GEWSWLYAAIDIETKLILDVELFGRHGTDPAAAFLHRLSEKHDLS-DAVFLVD 144
                                       6788999*99955..447*********************************999887776.4666666 PP

>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00041       1.5      29      91 ..      87     149 ..      70     153 .. 0.87
   2 ?    2.8   0.2     0.026        92     120     135 ..     167     182 ..     165     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00041
                             DDE_3  29 leeygrrgrvnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDnasiH 91 
                                        + +++++  +l++a+d +++l++ v   ++  ++  a+fl rl e+++ +   v+++D+ ++ 
  gi|313116982|ref|YP_004038106.1|  87 TAVKINGEWSWLYAAIDIETKLILdVELFGRHGTDPAAAFLHRLSEKHDLS-DAVFLVDGYGYQ 149
                                       5667888999**************9999999999999*************8.999999988775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.026
                             DDE_3 120 NpiEivwsklkrellk 135
                                       N iE++++ lk ++ +
  gi|313116982|ref|YP_004038106.1| 167 NLIEKWFHTLKMRVDR 182
                                       9**********98876 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     3e-05      0.11      13     135 ..      31     148 ..      27     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                      DDE_Tnp_IS66  13 lvlkyadhlPlyRqeeilarlGvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkgkk 89 
                                       +v+ +a +++l+  +eil+ lGve s +++ +wv+r a+   +  ea        +++++DET ++       +g+ 
  gi|313116982|ref|YP_004038106.1|  31 AVQLHATGCSLRETKEILRILGVERSHQAVWQWVHRLADSGHNPPEATP------KRVAVDETAVK------INGEW 95 
                                       57789999*******************************9877777755......56789******......78888 PP

                      DDE_Tnp_IS66  90 sylWvyvtdkrkpavlfeysp.sRg.gevaealLag.......fkGvlvsDgyag 135
                                       s+l++++  ++    +++++  +R  ++ a a+L            v  +Dgy+ 
  gi|313116982|ref|YP_004038106.1|  96 SWLYAAIDIET--KLILDVELfGRHgTDPAAAFLHRlsekhdlSDAVFLVDGYGY 148
                                       88888887774..222233222333133445554444445655446777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1425.20
//
Query:       gi|313116983|ref|YP_004038107.1|  [L=156]
Description: hypothetical protein Hbor_34500 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.078   13.1   1.0       0.15   12.2   0.1    1.9  2  Cylicin_N        Cylicin N-terminus
       0.17   10.6   7.7       0.18   10.5   7.7    1.0  1  Presenilin       Presenilin
       0.29    9.6  10.0       0.33    9.4  10.0    1.0  1  Borrelia_P83     Borrelia P83/100 protein
        0.4   10.6  13.2       0.49   10.3  13.2    1.2  1  Spore_coat_CotO  Spore coat protein CotO
        1.1    9.2   8.3        1.4    8.9   8.3    1.1  1  Mucin            Mucin-like glycoprotein
        1.1    8.6  12.3        1.4    8.2  12.3    1.1  1  DUF4746          Domain of unknown function (DUF4746)
        1.7    7.3  12.7        1.8    7.3  12.7    1.0  1  NPR3             Nitrogen Permease regulator of amino acid tr
          3    7.3   8.9        3.3    7.2   8.9    1.2  1  Sec62            Translocation protein Sec62
          7    4.6   9.8        7.7    4.5   9.8    1.0  1  Hid1             High-temperature-induced dauer-formation pro
        7.3    5.2  13.0        8.5    5.0  13.0    1.0  1  SAPS             SIT4 phosphatase-associated protein
        7.4    4.7  16.0        8.2    4.6  16.0    1.1  1  CDC45            CDC45-like protein
        9.1    5.2   8.6         10    5.0   8.6    1.1  1  SLC12            Solute carrier family 12


Domain annotation for each model (and alignments):
>> Cylicin_N  Cylicin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.4   2.1e+03      41      58 ..      20      40 ..      11      52 .. 0.45
   2 ?   12.2   0.1    0.0001      0.15      53      87 ..      78     112 ..      52     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.4
                         Cylicin_N 41 rskpselqetv...prhdkrk 58
                                      r ++ e++et    + ++ +k
  gi|313116983|ref|YP_004038107.1| 20 RARTDESNETEetdKSEETDK 40
                                      333333333321013333444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0001
                         Cylicin_N  53 rhdkrklkedqkpahiWirrslrkiserpsvylaa 87 
                                        + k+ +k++qkp+ +++ +s+r+ + r    l a
  gi|313116983|ref|YP_004038107.1|  78 DEPKESVKDVQKPTYMYLPHSVRRDLDRAYSMLKA 112
                                       456899*******************9998777665 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.7   0.00012      0.18     236     308 ..      12      84 ..       2     137 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                        Presenilin 236 eeeeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessesseeeeee 308
                                       +++++a++++++++++++ee++++e+++k+++s+++ e +e+++ ++++++ee++e+ke+e+++e++e +e+ 
  gi|313116983|ref|YP_004038107.1|  12 RRRQRARDRARTDESNETEETDKSEETDKTGESAKTAEAAETAKLDETAKTEETAEKKETEATDETDEPKESV 84 
                                       2333333333333333333444444444444444444444444444444444444443333333333322222 PP

>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  10.0   0.00022      0.33     257     357 ..      14     123 ..       3     147 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00022
                      Borrelia_P83 257 aknlpepadvsskkedkkvaeekkreiekaqkeikkkdeeakkakdakaedlkke..skaeekeaedkeleakkere 331
                                        +++ ++a++ +++e ++    k  e +k   e  k +e a+ ak +  e +k e  + ++e ea d + e k+  +
  gi|313116983|ref|YP_004038107.1|  14 RQRARDRARTDESNETEETD--KSEETDK-TGESAKTAEAAETAKLD--ETAKTEetAEKKETEATDETDEPKESVK 85 
                                       34444444444444444333..3333333.33334444444433333..2222221122333344444444455555 PP

                      Borrelia_P83 332 evae............Dlqkikeevkakktseaedaid 357
                                       +v +            Dl +     ka+   e ++  +
  gi|313116983|ref|YP_004038107.1|  86 DVQKptymylphsvrrDLDRAYSMLKAEYEYEYQEGFE 123
                                       55446666666666666666666666666666665555 PP

>> Spore_coat_CotO  Spore coat protein CotO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  13.2   0.00033      0.49      36     115 ..      17      90 ..       6     127 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
                   Spore_coat_CotO  36 kkqaaakekkdeaeekkpekaveeeveqekkkeaaePaeqeeeekaeeeekkeeeeqkeeeeekqetveaekPeqea 112
                                         + a  ++++e+ee  ++++ ++  e  k +eaae a+ +e +k ee+ +k+e e + e +e++e v      ++ 
  gi|313116983|ref|YP_004038107.1|  17 ARDRARTDESNETEETDKSEETDKTGESAKTAEAAETAKLDETAKTEETAEKKETEATDETDEPKESV------KDV 87 
                                       22333444444444444455555555555555666666666666666666666666666665555555......444 PP

                   Spore_coat_CotO 113 rkP 115
                                       +kP
  gi|313116983|ref|YP_004038107.1|  88 QKP 90 
                                       444 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   8.3   0.00094       1.4      37     104 ..      25      92 ..      13     108 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00094
                             Mucin  37 eaaegqskltttttttkppttttttttasttittkttkattt.tttttttttateaPsdavttaeaPtt 104
                                       e++e+++  ++  t  k+  +++t+++a t++  +t+k+  t   ++t +t  t+ P ++v   + Pt 
  gi|313116983|ref|YP_004038107.1|  25 ESNETEETDKSEETD-KTGESAKTAEAAETAKLDETAKTEETaEKKETEATDETDEPKESVKDVQKPTY 92 
                                       333333333333333.3333334444455666666666655505678889999********99999985 PP

>> DUF4746  Domain of unknown function (DUF4746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  12.3   0.00097       1.4      76     150 ..      24      91 ..       5     109 .. 0.40

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00097
                           DUF4746  76 evsseeetlekqekekektkakeaeltadepaeeeeaeeeeeeeaveeeeeeeeeeeeeeedkeltktktvkiPp 150
                                       ++s+e+   e+++k++e+ k+ e+ +ta+++++++ +e ++ ee+ e++    e e  +e+d+++ ++k v+ P 
  gi|313116983|ref|YP_004038107.1|  24 DESNET---EETDKSEETDKTGESAKTAEAAETAKLDETAKTEETAEKK----ETEATDETDEPKESVKDVQKPT 91 
                                       111111...2222222222222222222222222222233333333333....2222333344444445555543 PP

>> NPR3  Nitrogen Permease regulator of amino acid transport activity 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  12.7    0.0012       1.8      43     117 ..       9      81 ..       2     125 .. 0.45

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                              NPR3  43 kwrkskkkkkkskrkrssrskekkskesskksesssksesseekksskeseeseekesneeeeeeededdeesek 117
                                       + r+++++ +   r  +s+++e+++k+++++++++s+++++++++++ ++++++e++ +++e+e++de+de   k
  gi|313116983|ref|YP_004038107.1|   9 RLRRRRQRARDRARTDESNETEETDKSEETDKTGESAKTAEAAETAKLDETAKTEETAEKKETEATDETDE--PK 81 
                                       33444333333333333333333333333333333333332222222222222222222222222222222..11 PP

>> Sec62  Translocation protein Sec62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   8.9    0.0022       3.3      10      76 ..      19      83 ..       5     124 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0022
                             Sec62 10 kvvralksekekkkskkkkeklkevkkkekaekvfkelkksqlalrvekl...kekekkkkkeekkkkkk 76
                                         r+ +s     +++++++k++e++k+ +++k+ ++ ++++l  +++++   ++ke+++++e+++ k++
  gi|313116983|ref|YP_004038107.1| 19 DRARTDES-----NETEETDKSEETDKTGESAKTAEAAETAKLDETAKTEetaEKKETEATDETDEPKES 83
                                      22222222.....222222222222222222222222222222222222200022222222222222222 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   9.8    0.0052       7.7     612     695 ..      16      90 ..       2     123 .. 0.44

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0052
                              Hid1 612 srsesrspslsevpelksslaitddeskaereksatessssqavsqlremsekarakesaesteesrqesatskksp 688
                                       + ++  +  +s++ e+++++++td++ ++ +  +a e+         ++++e+a+ +e ae++e ++++++ ++k+ 
  gi|313116983|ref|YP_004038107.1|  16 RARDRARTDESNETEETDKSEETDKTGESAKTAEAAET---------AKLDETAKTEETAEKKETEATDETDEPKES 83 
                                       12222222222333333333333333222222222222.........333444444444444444444444444433 PP

                              Hid1 689 sgmsqsa 695
                                        +++q+ 
  gi|313116983|ref|YP_004038107.1|  84 VKDVQKP 90 
                                       3333333 PP

>> SAPS  SIT4 phosphatase-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  13.0    0.0057       8.5     246     324 ..      14      85 ..       2     110 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0057
                              SAPS 246 ivkerDevrerlleeltseeealedvsdeaskeesaesedltdkdedvsleesksakdenkesdesesdtaeessee 322
                                        +++rD  r+  +       ++ e+++++++++++ es++++++ e  +l+e++++++++++++++++d+++e +e+
  gi|313116983|ref|YP_004038107.1|  14 RQRARDRARTDES-------NETEETDKSEETDKTGESAKTAEAAETAKLDETAKTEETAEKKETEATDETDEPKES 83 
                                       2333444444433.......333444433333333333444444444444444444443333333333333333333 PP

                              SAPS 323 de 324
                                        +
  gi|313116983|ref|YP_004038107.1|  84 VK 85 
                                       22 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  16.0    0.0055       8.2     114     220 ..       8     114 ..       2     143 .. 0.38

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0055
                             CDC45 114 eeleeereayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeee.sddddersr 189
                                       ++l++ r+      + +es+e + e++++++ d+  e+ ++ +  ++ + +e++k ++ ++++e+e+ +++d+ +++
  gi|313116983|ref|YP_004038107.1|   8 DRLRRRRQRARDRARTDESNETE-ETDKSEETDKTGESAKTAEAAETAKLDETAKTEETAEKKETEAtDETDEPKES 83 
                                       45555555444444444443222.22222222222222222222222222222222222222222222444444444 PP

                             CDC45 190 krrrsepsakklrrq.lkkerrkyeavlekyy 220
                                        ++ ++p+   l ++ ++++ r y + l++ y
  gi|313116983|ref|YP_004038107.1|  84 VKDVQKPTYMYLPHSvRRDLDRAY-SMLKAEY 114
                                       444444333333333222222222.2233333 PP

>> SLC12  Solute carrier family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   8.6    0.0068        10     153     209 ..      23      79 ..       2     120 .. 0.36

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0068
                             SLC12 153 eekkkakkkklleekskekeekekleekdsnlslseekkeeekekkkekkkkkekke 209
                                       ++++++++++ ++e++ ++ e+ k+ e+ ++++l+e++k+ee+ +kke+++++e++e
  gi|313116983|ref|YP_004038107.1|  23 TDESNETEETDKSEETDKTGESAKTAEAAETAKLDETAKTEETAEKKETEATDETDE 79 
                                       111111111111111111111112222222222222222111111111111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2427  (0.135367); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); expected 358.6 (0.02)
Passed Vit filter:                       181  (0.0100954); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 993.57
//
Query:       gi|313116984|ref|YP_004038108.1|  [L=272]
Description: ATPase involved in chromosome partitioning [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-44  150.0   0.0    9.4e-44  149.4   0.0    1.2  1  AAA_31        AAA domain
    9.2e-21   74.2   0.0    1.2e-20   73.8   0.0    1.1  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    1.5e-12   47.4   2.2    1.1e-05   24.9   0.1    2.1  2  MipZ          ATPase MipZ
    7.6e-10   38.7   0.0    2.8e-09   36.8   0.0    1.8  1  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
    2.4e-09   37.0   0.2    2.1e-08   33.9   0.2    2.3  2  ParA          NUBPL iron-transfer P-loop NTPase
    2.4e-08   33.8   0.0    0.00016   21.3   0.0    2.2  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    6.3e-07   28.9   1.9    7.3e-06   25.4   0.6    3.2  3  ArsA_ATPase   Anion-transporting ATPase
     0.0072   16.1   3.8       0.67    9.7   3.3    3.1  2  ATP_bind_1    Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.027   14.0   0.0    1.4  2  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
      0.045   13.5   0.0       0.21   11.3   0.0    1.9  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
       0.11   12.3   0.0       0.26   11.0   0.0    1.5  1  AAA_24        AAA domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.4   0.0   5.8e-47   9.4e-44       4     171 ..      13     183 ..      11     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 5.8e-47
                            AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne..iektlyevli...eeknikeaiik 75 
                                       ++i+nqKGGvGKTT ++n+a a+ ++g+ vL vDlDpQ+nat +lg+ +       tl+++l+    ++++ e++  
  gi|313116984|ref|YP_004038108.1|  13 LCISNQKGGVGKTTIAINVAGAINERGHDVLFVDLDPQGNATENLGLMEAYddEPPTLFDCLTdpeMRESVTEIVR- 88 
                                       589*******************************************95443125679****953113344444444. PP

                            AAA_31  76 tkvenldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeay 152
                                        ++e++d+ips+id+ +ae el+  +++ e+l+ +l++++d+YDy+i+DcpP+Lg l++naL+a + v+ip  ae  
  gi|313116984|ref|YP_004038108.1|  89 -EHEEMDVIPSNIDMTAAEPELTLSRRSGEQLSLVLRELEDDYDYVIVDCPPNLGNLMDNALFATQNVLIPALAEST 164
                                       .68899*********************************************************************** PP

                            AAA_31 153 aleGleqllktieevkkkl 171
                                       + + +e l+++++ ++ ++
  gi|313116984|ref|YP_004038108.1| 165 SKRAFELLFDHVDALEYDY 183
                                       ***********99988765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   7.5e-24   1.2e-20       1     125 [.      13     236 ..      13     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 7.5e-24
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ++i ++kGGvGKTt+a+n a a+++rg++Vl vD+Dpq+n+++ l   e + ++                       
  gi|313116984|ref|YP_004038108.1|  13 LCISNQKGGVGKTTIAINVAGAINERGHDVLFVDLDPQGNATENLGLMEAYDDEpptlfdcltdpemresvteivre 89 
                                       5899***************************************666666666669********************** PP

                                       ..........................................................................CCH CS
                                       ..........................................................................xxx RF
                              CbiA  55 ..........................................................................dlk 57 
                                                                                                                 + k
  gi|313116984|ref|YP_004038108.1|  90 heemdvipsnidmtaaepeltlsrrsgeqlslvlreleddydyvivdcppnlgnlmdnalfatqnvlipalaesTSK 166
                                       **************************************************************************555 PP

                                       CCCHHH....HHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EEEEEE--CCHCCCCHHT CS
                                       xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  58 rllell....ealgkkkalllkiagvvlnrvdgeneetllkealeelkqry.gvpvlgviprdeavaeaparg 125
                                       r  ell     al   ++ ++k  gvv+nr+d +  +++ +e+++ +++++  vpv   i+++ +v +a   g
  gi|313116984|ref|YP_004038108.1| 167 RAFELLfdhvDALEYDYEIEIKDRGVVINRIDVR--KKQAREMVDWINAAFdDVPVW-QIRERADVQKALDAG 236
                                       55555533227777777777**************..9999*******999999***9.6*******9998776 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   6.8e-09   1.1e-05       4      40 ..      14      50 ..      11      61 .. 0.91
   2 !   22.5   0.4   3.6e-08   5.9e-05      69     199 ..     101     234 ..      78     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.8e-09
                                      EE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                              MipZ  4 vlgnekGGsGksttavhvavaLlkkGarvaaidldlr 40
                                       ++n+kGG Gk+t+a+ va a+ ++G+ v  +dld +
  gi|313116984|ref|YP_004038108.1| 14 CISNQKGGVGKTTIAINVAGAINERGHDVLFVDLDPQ 50
                                      689********************************75 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.6e-08
                                       -SSS-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SE.EEEEEESSHH..HHCCC.EE CS
                              MipZ  69 alseaeeaeveeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladt.lvtPlndsfv..dfdll.gk 141
                                        ++ ae +      + e  +l+ ++++le ++d++++d+P +  +l+  a       l+  l +s     f+ll  +
  gi|313116984|ref|YP_004038108.1| 101 DMTAAEPELTLSRRSGE--QLSLVLRELEDDYDYVIVDCPPNLGNLMDNALFATQNvLIPALAESTSkrAFELLfDH 175
                                       44444444444444444..99*************************9999876665055568887642279987478 PP

                                       E-SSS--EEEE-HHHHHHHHHHHTTTTT-SS--EEEEE.EESB-S--HHHHHHHHHHHH CS
                              MipZ 142 vdpetlkvkrpslyaelvwearkkrakaerkevdWvvl.rnrlsalearnkkkveeale 199
                                       vd+  ++ + +     +v +    r+k++r++vdW+    + + + + r + +v++al+
  gi|313116984|ref|YP_004038108.1| 176 VDALEYDYEIEIKDRGVVINRIDVRKKQAREMVDWINAaFDDVPVWQIRERADVQKALD 234
                                       *******999999999****99**************75157889999999999999986 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   1.7e-12   2.8e-09       4     224 ..      13     250 ..      11     258 .. 0.67

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.7e-12
                          CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspd....nlLrlhFnvdieqregwaraeldgapwrqa...al 73 
                                       l+++  +GGvG+t+++   a a++e g+ vl +Dl p+    + L l    d ++  ++   ++d  ++r++   ++
  gi|313116984|ref|YP_004038108.1|  13 LCISNQKGGVGKTTIAINVAGAINERGHDVLFVDLDPQgnatENLGLMEAYD-DEPPTLFDCLTD-PEMRESvteIV 87 
                                       5667779****************************88632224456655555.566677777666.55665501156 PP

                          CBP_BcsQ  74 eyapgldllPfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdan 150
                                       +  +++d++P     ++ + +l+ ++++ e+l   l+el+ +y+++++D+p +  +l+ ++l  ++ vl  + +++ 
  gi|313116984|ref|YP_004038108.1|  88 REHEEMDVIPSNIDMTAAEPELTLSRRSGEQLSLVLRELEDDYDYVIVDCPPNLGNLMDNALFATQNVLIPALAEST 164
                                       66789*****88777777777888999999*******************************9977777766666666 PP

                          CBP_BcsQ 151 ch....vrL.hqqalp.......aaellLiNqfeaasqlqqDllqlWlqslrrllPl.vihrDealaEalaakqPlg 214
                                       ++    ++  h  al+       + + + iN+ ++  + +++++  W++ + + +P+  i++ + ++ al a   l 
  gi|313116984|ref|YP_004038108.1| 165 SKrafeLLFdHVDALEydyeieiKDRGVVINRIDVRKKQAREMV-DWINAAFDDVPVwQIRERADVQKALDAGVSLL 240
                                       54111122222223321111111233456666666666655553.56666666666644555555666666666666 PP

                          CBP_BcsQ 215 eyrpdslaae 224
                                       e+ p++ ++e
  gi|313116984|ref|YP_004038108.1| 241 EFNPECDMCE 250
                                       6666666666 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.2   1.3e-11   2.1e-08       5     125 ..      12     143 ..      10     165 .. 0.73
   2 ?   -1.0   0.0      0.59   9.6e+02     212     243 ..     226     257 ..     199     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.3e-11
                              ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee............ekpeqsekkliPve 69 
                                       +++++  KGGVGK+t+a+n+A a++++g++v  +D+D  G    +l  +e             ++pe++e+    v+
  gi|313116984|ref|YP_004038108.1|  12 KLCISNQKGGVGKTTIAINVAGAINERGHDVLFVDLDPQGNATENLGLMEAyddepptlfdclTDPEMRESVTEIVR 88 
                                       5678899*********************************9988876555567889988888866666665554444 PP

                              ParA  70 a.kgikvmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgD 125
                                         +++ v+  ++ ++   e+ +  +    + ++ +l++ e ++ Dy+i+D+PP  g 
  gi|313116984|ref|YP_004038108.1|  89 EhEEMDVIPSNIDMT-AAEPELTLSRRSGEQLSLVLRELE-DDYDYVIVDCPPNLGN 143
                                       447788886655554.334444444445555555666655.679*********9883 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.59
                              ParA 212 dpeireasdegkplvlkepeseaakaleeiae 243
                                       + ++++a d+g +l++ +pe ++ +++++ia+
  gi|313116984|ref|YP_004038108.1| 226 RADVQKALDAGVSLLEFNPECDMCEVFRDIAA 257
                                       56889999*******999**999999999986 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   9.5e-08   0.00016       7      69 ..      18      84 ..      12      98 .. 0.80
   2 !   10.4   0.0    0.0002      0.33     172     247 ..     185     262 ..     175     268 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.5e-08
                         Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrll..lggk..aqetvldtlrekgavedvk 69
                                       kGG+Gk+t + n++ a+ e+g+ vl v  DP+ ++t  l  +++     +t++d l++ ++ e v+
  gi|313116984|ref|YP_004038108.1| 18 QKGGVGKTTIAINVAGAINERGHDVLFVDLDPQGNATENLglMEAYddEPPTLFDCLTDPEMRESVT 84
                                      59*********************************99753225544113468888888888877764 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0002
                         Fer4_NifH 172 ggvrlgGliinsrkvddereliekfaeelgtkv....levvPrdeivrkaelrkktvieyapeseqakeyrelarki 244
                                        +++  G++in r +d +++ ++++++ ++       +  +    +v+ka  +   + e++pe+++++ +r++a  +
  gi|313116984|ref|YP_004038108.1| 185 IEIKDRGVVIN-R-IDVRKKQAREMVDWINAAFddvpVWQIRERADVQKALDAGVSLLEFNPECDMCEVFRDIAAGL 259
                                       56677899**9.4.5666666666666666543111144455566667776677789*****************988 PP

                         Fer4_NifH 245 len 247
                                        e+
  gi|313116984|ref|YP_004038108.1| 260 DEQ 262
                                       776 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.6   4.5e-09   7.3e-06       8     134 ..      18     139 ..      11     146 .. 0.67
   2 ?   -1.7   0.0      0.76   1.2e+03      92     127 ..     145     183 ..     139     189 .. 0.73
   3 ?   -0.7   0.0      0.39   6.3e+02     256     283 ..     196     223 ..     187     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.5e-09
                                       ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS..--BSS-EEETSSEEEEE--HHHHHHHHHCCHHG CS
                       ArsA_ATPase   8 GKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdq..klgkeptkvkeNLsavEidpeveleeakqevqk 82 
                                        KGGVGKtt++  +a  + e g++vl + +DP  +    +        ep  + + L+  E+  +v +   ++e ++
  gi|313116984|ref|YP_004038108.1|  18 QKGGVGKTTIAINVAGAINERGHDVLFVDLDPQGNATENLGLmeAYDDEPPTLFDCLTDPEMRESVTEIVREHEEMD 94 
                                       5********************************99999887633456667777777777777666433333444444 PP

                                       GGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBS CS
                       ArsA_ATPase  83 eeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaP 134
                                        + + + ++  e  l     s     e ls+  +l+++ e++yd+v++D +P
  gi|313116984|ref|YP_004038108.1|  95 VIPSNIDMTAAEPELTLSRRS----GEQLSL--VLREL-EDDYDYVIVDCPP 139
                                       444444444444444444444....344443..44444.5788888888887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.76
                                       HHHHHHHHHHTSSTTHHHHHH...HHHHHHHHHCSSSSE CS
                       ArsA_ATPase  92 eledvlaeelaslPGideils...feellkyvkeeeydv 127
                                       + + ++a +   +P + e +s   fe l ++v++ eyd+
  gi|313116984|ref|YP_004038108.1| 145 MDNALFATQNVLIPALAESTSkraFELLFDHVDALEYDY 183
                                       555666777777888888875333888899999999997 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHHHHHHTTTSEEEEE CS
                       ArsA_ATPase 256 flearkkiqkkylkeieelfedlevvkl 283
                                       +++ rkk  +++++ i+  f+d++v ++
  gi|313116984|ref|YP_004038108.1| 196 RIDVRKKQAREMVDWINAAFDDVPVWQI 223
                                       56779999999************99876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   3.3   0.00041      0.67       6      39 ..      21      57 ..      19     226 .. 0.70
   2 ?   -2.7   0.0       2.6   4.2e+03      32      51 ..     233     252 ..     222     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00041
                        ATP_bind_1  6 GsGKttfvgalseilelrgrsvavvNLDP...Aaeel 39
                                      G+GKtt+  +++  +++rg +v  v LDP   A e+l
  gi|313116984|ref|YP_004038108.1| 21 GVGKTTIAINVAGAINERGHDVLFVDLDPqgnATENL 57
                                      9****************************54444444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                        ATP_bind_1  32 LDPAaeelpYeaavdireli 51 
                                       LD +++ l+++++ d+ e++
  gi|313116984|ref|YP_004038108.1| 233 LDAGVSLLEFNPECDMCEVF 252
                                       89999999999999998875 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.6e-05     0.027       4      86 ..      25     107 ..      21     122 .. 0.85
   2 ?   -3.5   0.1       3.9   6.3e+03      48      68 ..     197     216 ..     186     234 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnnag 78 
                                         I+  +A a++e+G +v+++dl+ ++ + +   l e+++ e     D   + ++++ v e+v++++++D++  n+ 
  gi|313116984|ref|YP_004038108.1|  25 TTIAINVAGAINERGHDVLFVDLDPQGnATENLGLMEAYDDEpPTLFDCLTDPEMRESVTEIVREHEEMDVIPSNID 101
                                       679************************77777778899998845****************************99998 PP

                                       --EGCSS- CS
                      adh_short_C2  79 iapklkgp 86 
                                       ++ +  +p
  gi|313116984|ref|YP_004038108.1| 102 MTAA--EP 107
                                       8777..44 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.9
                                       --TTSHHHHHHHHHHHHHHHS CS
                      adh_short_C2  48 cDVtdeeqvealveevvekfg 68 
                                       +DV++ +q +++v+ + + f+
  gi|313116984|ref|YP_004038108.1| 197 IDVRK-KQAREMVDWINAAFD 216
                                       44433.233444444444443 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.21       4      33 ..      21      50 ..      19      55 .. 0.92
   2 ?   -0.7   0.0      0.67   1.1e+03      81     110 ..     166     196 ..     153     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                       +GK+T+a + +  + ++g+ +++vDlD+ 
  gi|313116984|ref|YP_004038108.1| 21 GVGKTTIAINVAGAINERGHDVLFVDLDPQ 50
                                      59**************************95 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.67
                            CLP1_P  81 lalvkelareveek.leenkkakasgliInt 110
                                       +++++ l+++v+   ++ + + k+ g++In 
  gi|313116984|ref|YP_004038108.1| 166 KRAFELLFDHVDALeYDYEIEIKDRGVVINR 196
                                       5566777777774335566677899999995 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00016      0.26      11      77 ..      20     141 ..      11     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                            AAA_24  11 sgiGKTtlakel.......gpkplfi.......dtek.Glksldadkfpdie...swedfldevvel.......... 59 
                                        g+GKTt+a +        g ++lf+        te+ Gl + ++d+ p++    + +++++ v+e+          
  gi|313116984|ref|YP_004038108.1|  20 GGVGKTTIAINVagainerGHDVLFVdldpqgnATENlGLMEAYDDEPPTLFdclTDPEMRESVTEIvreheemdvi 96 
                                       69************************444444445555555555555554449996666777777777777777999 PP

                            AAA_24  60 ...........................aaeladyktlviDtidel 77 
                                                                  ++ ++dy+ +++D    l
  gi|313116984|ref|YP_004038108.1|  97 psnidmtaaepeltlsrrsgeqlslvlRELEDDYDYVIVDCPPNL 141
                                       999999999999999999999999999999999999999965555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1952.84
//
Query:       gi|313116985|ref|YP_004038109.1|  [L=146]
Description: flavin-nucleotide-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-17   64.2   0.0    1.3e-17   64.1   0.0    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    0.00055   20.1   0.0     0.0007   19.7   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.046   13.7   0.0      0.063   13.2   0.0    1.3  1  FB_lectin       Fungal fruit body lectin


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   2.3e-21   1.3e-17       2     141 .]      14     143 ..      13     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 2.3e-21
                                       HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEE.EET.TSHCCHCCCT--.ECEEEEEEEEEEE-SEGG CS
                      Pyridox_ox_2   2 reeilalLdegevgrlafvddgepvilPvnyvvdgdslyfh.gak.gsrlaaalrgap.vcvvvtevdglvlarsfn 75 
                                       +eei++ L+++  g+l+++d+g+ + +Pv++ +dg+sl+f+ g + +s++++  + ++ +c+v++ vdg   + s  
  gi|313116985|ref|YP_004038109.1|  14 DEEIEKRLQTETAGVLSLADEGRAYGVPVSHHYDGESLFFRlGDDdHSKKLEFVETTKeACFVLFGVDG---DDS-- 85 
                                       69***************************************666699999999996666**********...777.. PP

                                       EEEEEEEEEEEEEEEE--HHHHHHHCCCHHHHHST.TT.GGCSB---CCCCCTEEEEEEEEEEEEEEE CS
                      Pyridox_ox_2  76 slnyrSVvvrGraeevtdeeekaealellvekivp.gr.wenlrpptrkelkatsvlrlkieevsgrr 141
                                          + S++v+G+++e+ + +e++e + + ++ +    r ++    +  +e++  ++++++i +v+gr+
  gi|313116985|ref|YP_004038109.1|  86 ---W-SILVTGTLSEL-SGDERKEFDAATINDWFGsFRvFD----EAIDEIEL-TLFEMEISSVTGRK 143
                                       ...*.***********.999999999999999944022333....33344444.77999999999995 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.2e-07    0.0007       2      87 ..      14     100 ..      12     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT..GSEEEE CS
                    Putative_PNPOx   2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde..lgrgvr 76 
                                       dee+++ l+++ a+vl+ +  +Gr +++pv+  ++ +   + +  + +s+kl+ +e+   ++++++  +  + +++ 
  gi|313116985|ref|YP_004038109.1|  14 DEEIEKRLQTETAGVLSLA-DEGRAYGVPVSHHYDGESLFFRLGDDDHSKKLEFVETTKEACFVLFGVDgdDSWSIL 89 
                                       679**************99.999***************99999999999*********9977655555548899999 PP

                                       EEEEEEEESCH CS
                    Putative_PNPOx  77 ieGtaelvsdg 87 
                                       + Gt   +s +
  gi|313116985|ref|YP_004038109.1|  90 VTGTLSELSGD 100
                                       99998888776 PP

>> FB_lectin  Fungal fruit body lectin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.063      40      84 ..      50      94 ..      20     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                         FB_lectin 40 elvltmggSGtsGllRfesdsgesfvvalGvHnykpWcDivtklk 84
                                      +l +++g+   s  l f ++++e+++v +Gv   + W   vt++ 
  gi|313116985|ref|YP_004038109.1| 50 SLFFRLGDDDHSKKLEFVETTKEACFVLFGVDGDDSWSILVTGTL 94
                                      5678899999999************************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 995.10
//
Query:       gi|313116986|ref|YP_004038110.1|  [L=915]
Description: phosphoenolpyruvate synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-81  272.6   0.0    6.7e-81  272.1   0.0    1.1  1  PPDK_N         Pyruvate phosphate dikinase, PEP/pyruvate bind
    3.3e-21   74.8   0.2    7.4e-21   73.7   0.2    1.6  1  PEP-utilizers  PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
       0.13   12.2   0.0        0.3   11.0   0.0    1.6  1  PDEase_I_N     3'5'-cyclic nucleotide phosphodiesterase N-ter


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.1   0.0   1.1e-84   6.7e-81       2     311 ..      20     313 ..      19     325 .. 0.95

  Alignments for each domain:
  == domain 1  score: 272.1 bits;  conditional E-value: 1.1e-84
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelP 78 
                                       +lvGGKganLa+l  +ag+++Pp  +it++++r + +++  ++++ e+l++ld ++++e ++ ++e+r+ + + ++ 
  gi|313116986|ref|YP_004038110.1|  20 ALVGGKGANLARL-VDAGVSTPPALCITTETYRVLSSDK-TSKTLFERLDSLDKKEMEEATDLAAELRNHLRDRPIA 94 
                                       58***********.77****************9775555.89*********************************** PP

                            PPDK_N  79 eeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYr 155
                                       + ++++++e ++e         +p a+RSSataEDlp asfaGq d+yLnv g ++v+ea++ ++aSlf++rA++Yr
  gi|313116986|ref|YP_004038110.1|  95 DVIRDKLTETLDEE--------TPYAIRSSATAEDLPHASFAGQHDSYLNVCGIDAVIEAVRDCMASLFTDRAVSYR 163
                                       *******9999886........79***************************************************** PP

                            PPDK_N 156 kekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilek 232
                                       +++g++h  va avvvq+mv++d  a+GV f++dp +G++ +++i+a +GlGe+VVaG v+pd ++v+++t +i + 
  gi|313116986|ref|YP_004038110.1| 164 TKNGISHRTVANAVVVQEMVDAD--AAGVLFTADPDSGNRTVAVIEANFGLGESVVAGDVEPDAVRVDRPTTEIRSY 238
                                       ***********************..**************************************************** PP

                            PPDK_N 233 kigekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpe 309
                                       ++g+k++ i   +++ gt+ ve+++ ++++ +L+ ++v++L  ++ ++e  +++p+diE+a+   +g++++lQaRp+
  gi|313116986|ref|YP_004038110.1| 239 RVGTKAVSIRPHDDG-GTEAVELDT-DSNARVLRTAQVKTLVALGDRVETLFDRPQDIEWALV--DGEFVVLQARPI 311
                                       ********9977776.89*****77.556666******************************9..***********9 PP

                            PPDK_N 310 tr 311
                                       + 
  gi|313116986|ref|YP_004038110.1| 312 SS 313
                                       76 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.2   1.2e-24   7.4e-21       2      73 .]     835     906 ..     834     906 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.2e-24
                                       --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       +e g+ILva++ +p +++ + +aaG+v+e GG+ SH A+vAre+g+PaVv v eat ++++g+++ +Dg++G
  gi|313116986|ref|YP_004038110.1| 835 VERGEILVAPSSDPGWTPLFLNAAGMVVEVGGRISHGALVAREYGLPAVVSVAEATDRIQTGQRVRIDGTRG 906
                                       5789******************************************************************99 PP

>> PDEase_I_N  3'5'-cyclic nucleotide phosphodiesterase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.9e-05       0.3       9      53 ..     135     177 ..     130     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.9e-05
                        PDEase_I_N   9 LsevesdaVPseVrdWLastFtrqqeakkrrseekpkfrsvanai 53 
                                       L+ +  daV + Vrd +as Ft + ++++r +++  + r+vana+
  gi|313116986|ref|YP_004038110.1| 135 LNVCGIDAVIEAVRDCMASLFTDR-AVSYR-TKNGISHRTVANAV 177
                                       777889****************94.77775.5578899*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (915 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 5808.82
//
Query:       gi|313116987|ref|YP_004038111.1|  [L=634]
Description: penicillin-binding protein, beta-lactamase class C [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-51  175.9   1.4    2.2e-51  175.1   1.4    1.3  1  Beta-lactamase   Beta-lactamase
  ------ inclusion threshold ------
      0.044   13.7   0.1       0.27   11.2   0.0    2.3  2  TMEM65           Transmembrane protein 65


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.1   1.4   2.4e-55   2.2e-51       6     313 ..      53     358 ..      47     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 2.4e-55
                                       HHHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEEST.TSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGG CS
                    Beta-lactamase   6 relmaqggipGvavavvrdgkvvldkggGvadleggrpvta.dtlfriaSvtKtftaaavlqlveeGkldLddpVsk 81 
                                       r+l  ++++ G+ vavv+dg+v l+ g+G+a      pv++ +tlfr++Sv+K+ t++a++qlv+++k++ d+pV +
  gi|313116987|ref|YP_004038111.1|  53 RAL-SNYDAGGLTVAVVKDGEVALTEGYGHAYQSESVPVKPdETLFRVGSVSKVATWTAAMQLVDRDKVEVDAPVND 128
                                       333.348889*******************************779********************************* PP

                                       TST..TCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSS..TTSCEE-SHHHHHHHHH CS
                    Beta-lactamase  82 ylP..efagpgkgkiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkya..pGtkwgYsntgygllge 154
                                        l   e ++  +++iTl++L+tHt G+      +++ + +++ + l + ++t  p +   pG+ ++Y n+++ l+g+
  gi|313116987|ref|YP_004038111.1| 129 SLDavEIPQTYDEPITLEHLATHTPGFELR-GWGDTVNKPQYVRPLAESVSTNVPGRVrpPGELCQYTNYAAALAGQ 204
                                       ***************************555.888888888888*********99987677***************** PP

                                       HHHHHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC..TTTBEEEEHHHHH CS
                    Beta-lactamase 155 llekvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeae..gagglistardla 229
                                       l++ v+g++++ ++++++++pLgm++ ++ p++s+    a+g       a  +++ + +  +  +a gl +t +d+a
  gi|313116987|ref|YP_004038111.1| 205 LVADVSGQQFGSYVTKHVFEPLGMTNSTFRPAPSK-LVPASGK------AVKDTVSFYS--DvaPASGLHTTGNDMA 272
                                       *******************************9999.4444444......2333334444..25599*********** PP

                                       HHHHHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEEC.ECSSEEEEECCHTEEEEEEE..STEEEEEEEECGGTE CS
                    Beta-lactamase 230 rflglalegglllsaetlaqltaklssgttrpagiragl.glGwvladktgapgtfghtG..ggygtyvfvdpeanl 303
                                       r+l+ +l++g + ++++l++ + + +  ++ ++  r     +G++ + +++  +++gh+G    +   + ++pe + 
  gi|313116987|ref|YP_004038111.1| 273 RLLQAHLNDGVVDGERILSADAVEEMHKQWYTPHERFDGmAFGLFEESRGD-TRLVGHSGavMDFACEFSLIPEDGT 348
                                       ***9999*********99999999998888888887764366665555555.8************************ PP

                                       EEEEEESBCS CS
                    Beta-lactamase 304 vvavltnrdp 313
                                       +++v+++++ 
  gi|313116987|ref|YP_004038111.1| 349 GLFVVAHGTE 358
                                       *****99987 PP

>> TMEM65  Transmembrane protein 65
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     3e-05      0.27      35      72 ..     195     233 ..     189     249 .. 0.77
   2 ?   -1.6   0.1      0.29   2.6e+03      38      58 ..     537     557 ..     534     570 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                            TMEM65  35 stlaaAalGnlvsdvaGvvlggvveala.erlglkkpkl 72 
                                       +  aaA  G+lv+dv+G ++g++v + + e lg++++++
  gi|313116987|ref|YP_004038111.1| 195 TNYAAALAGQLVADVSGQQFGSYVTKHVfEPLGMTNSTF 233
                                       66799999***************9875415577766655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.29
                            TMEM65  38 aaAalGnlvsdvaGvvlggvv 58 
                                       aaA++G lv  va ++ +++v
  gi|313116987|ref|YP_004038111.1| 537 AAAGIGGLVLFVAALAASSIV 557
                                       899999999888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4263.42
//
Query:       gi|313116988|ref|YP_004038112.1|  [L=283]
Description: hypothetical protein Hbor_34550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   14.3   0.0        1.9    9.0   0.0    2.8  3  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0     0.098   1.8e+03       4      17 ..      53      66 ..      52      81 .. 0.86
   2 ?    1.4   0.0     0.023     4e+02       6      49 ..     145     188 ..     142     197 .. 0.80
   3 ?    9.0   0.0   0.00011       1.9      95     141 .]     218     262 ..     203     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.098
                                      EEEEEE-SSHHHHH CS
                               Usp  4 rIlVavDgseeskk 17
                                      r +V+vD+++++++
  gi|313116988|ref|YP_004038112.1| 53 RFVVPVDNTTAAQA 66
                                      789***99888875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.023
                                       EEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCC CS
                               Usp   6 lVavDgseeskkAlewAlelakargaelillhvidprasgavsd 49 
                                       lV+v   ++ +  l  A    ++++a +   hv+d ++s ++ d
  gi|313116988|ref|YP_004038112.1| 145 LVPVARGPHLDTTLNIARVIGETHDAWIDFFHVVDNDESRSETD 188
                                       677777777777777777788999***********998877665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00011
                                       HHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  95 ilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       i++   +  +d  V+++ ++s+l++++ GS++e v   ++  V+ Vr
  gi|313116988|ref|YP_004038112.1| 218 IVDQ--SSYYDATVIAAPQKSRLREFVDGSTTEVVQSLCENTVVTVR 262
                                       4444..444677788888889**************999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1967.47
//
Query:       gi|313116989|ref|YP_004038113.1|  [L=68]
Description: hypothetical protein Hbor_34560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 489.29
//
Query:       gi|313116990|ref|YP_004038114.1|  [L=317]
Description: Inosine-uridine nucleoside N-ribohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-79  265.1   0.8    1.1e-78  264.9   0.8    1.0  1  IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase


Domain annotation for each model (and alignments):
>> IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.9   0.8   6.2e-83   1.1e-78       1     303 [.       3     300 ..       3     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 264.9 bits;  conditional E-value: 6.2e-83
                                       EEEEEEE--SHHHHHHHHHHHCTHTTEEEEEEEE-SSSS-HHHHHHHHHHHHHHHCTTT.S-EEEE-SS-SSSS.S- CS
                      IU_nuc_hydro   1 rkvilDtDpGiDDalAlllalaespeiellgittvaGnvsleqatrnalrvlealggrddipvyaGaekpllre.ka 76 
                                       r+vi+DtD+  DD +A+l+a+ + ++i++ ++t+vaGnv+ +  ++na ++l ++++++dipvy+Ga+kpl+++ ++
  gi|313116990|ref|YP_004038114.1|   3 RRVIIDTDTAGDDSMAILMAALA-DSIDVEALTIVAGNVEFDYEVENAKYTL-EVADATDIPVYEGARKPLVKDhEH 77 
                                       68***************888554.78**************************.8889999**************555 PP

                                       SHHHHTTTSSTSS-.--SSHCSCSSHHHHHHHHHHHHCHHTTTTEEEEECS-SHHHHHHHHHTCCHHHHEEEEEEE- CS
                      IU_nuc_hydro  77 aaeihGedGlgdvllpeperkaesesavdalidaveaareypgevtlvatGplTNiAlalrldpelakkvkrlviMG 153
                                       a+++hGe Glg+ l pe+  + ++++ ++a+++ v   re pge+tlv++GplTNiAlalrl+p+l ++v ++++MG
  gi|313116990|ref|YP_004038114.1|  78 ADQVHGEGGLGGNLFPETGIPSADQHGANAIVERV---RESPGEITLVCIGPLTNIALALRLEPNLNELVDEVWVMG 151
                                       555**********99*999999999***9999999...999999********************************* PP

                                       --SSS--SSSSSS-HHHHHSHHHHHHHHHTS-E.EEEE-HHHHTTSCHEECHHHHHHHHCSTCBHHHHHHHHHHHHH CS
                      IU_nuc_hydro 154 GaftarGNvtpvaEfNifvDPeAAkiVlesapvkitlvpldvthkvqalltseeveelaalekglgafladllefyi 230
                                       Ga++  GN tp+aEfN++vDPeAA++V+++   ++tlv +d++ ++  +++ e ++e++a+e++   f++++ e   
  gi|313116990|ref|YP_004038114.1| 152 GAVNTLGNDTPSAEFNFWVDPEAASVVVDEL--DVTLVDWDLSLRQ-GRFDAEMLAEIEAAETKYADFFTTISERAR 225
                                       ****************************655..55********944.499999999988876555559999999999 PP

                                       HHHHHHHHSSEEE-HHHHHHHHHH-GGGEEE.EEEEEEEESSSSTTTTEEEEETSTT.TTS--EEEEEEE-HHHH CS
                      IU_nuc_hydro 231 kaykeaegsdgaplhDplavavaldpelvtt.krlavdveleggltrGrtvvdlrrl.kkaknvkvatevdverf 303
                                       ++++e+ g+  +   D la+a++l+pel+t+ ++++vdv+ ++g trG ++vd r+  ++++n+++++++d+e f
  gi|313116990|ref|YP_004038114.1| 226 EFAREQYGEVSTTQPDSLAMACVLEPELITEsNEYYVDVDEREGMTRGYSLVDERGVtDNEPNANIVETIDEEVF 300
                                       999999999999999**************9999**********************999**************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2180.73
//
Query:       gi|313116991|ref|YP_004038115.1|  [L=257]
Description: short-chain alcohol dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-68  231.2   0.1    1.5e-68  230.8   0.1    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    6.9e-55  185.5   0.1    8.9e-55  185.2   0.1    1.1  1  adh_short        short chain dehydrogenase
    1.1e-15   58.0   0.0    1.9e-15   57.3   0.0    1.4  1  KR               KR domain
    0.00043   20.2   0.1     0.0006   19.7   0.1    1.2  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00075   19.0   0.1     0.0013   18.3   0.1    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.002   17.2   0.1     0.0025   16.9   0.1    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0061   16.8   0.1      0.012   15.9   0.1    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0089   15.4   0.8      0.013   14.8   0.0    1.7  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.025   14.6   0.1    1.4  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
      0.034   14.0   0.0       0.18   11.6   0.0    1.9  2  DFP              DNA / pantothenate metabolism flavoprotein


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.8   0.1   8.5e-72   1.5e-68       3     232 ..      15     252 ..      13     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 230.8 bits;  conditional E-value: 8.5e-72
                                       TTSHHHHHHHHHHHTT-EEEEEESSGGH...HHHHHHHHHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea...kkrveelaeelgae.v.lecDVtdeeqvealveevvekfgklDilv 74 
                                         gIGr+iA+++a++Ga+vv++d++ee       ++el +e gae + +ecDV+d +++ a+ve++ ++fg++D++v
  gi|313116991|ref|YP_004038115.1|  15 SGGIGRGIARTFADHGASVVVADISEEPregGTPTHELLQEEGAEsMyVECDVSDYDDCVAAVEAA-DEFGGIDVMV 90 
                                       579**********************99853345678888888877546***************985.68******** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaervvpnynaygaaKaal 148
                                       nnagi+ + + p+++++ e++++ +++nl ++++ +kaa+  ++++g  gsivn+ssv++  ++ + + y+aaK+++
  gi|313116991|ref|YP_004038115.1|  91 NNAGIVGP-QDPLVDIDLEDYRNLISINLDGVVHGSKAAALaMLEQGvhGSIVNMSSVAGITGFGGITPYSAAKGGV 166
                                       ********.******************************99455566****************************** PP

                                       HHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT..HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT-- CS
                      adh_short_C2 149 ealtrylAvelgpkgiRvNavspgpikTlaasgikg..fdelleelearaplgrlgtpeevaeaalfLasdeasyit 223
                                        ++t +lA elgp+giRvNav+pg+i+T+++++ +     e +e++   +pl+r+g+pe+va ++ fLasd+asy+t
  gi|313116991|ref|YP_004038115.1| 167 RSFTYALASELGPDGIRVNAVHPGIIETTMTTEDSPfvGTEQEEKMLPTIPLRRVGQPEDVAGVVTFLASDLASYVT 243
                                       ******************************7776663456799999******************************* PP

                                       SEEEEESTT CS
                      adh_short_C2 224 GqtlvvDgG 232
                                        + ++vDgG
  gi|313116991|ref|YP_004038115.1| 244 AESVIVDGG 252
                                       ********9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.2   0.1     5e-58   8.9e-55       1     190 [.       7     200 ..       7     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 185.2 bits;  conditional E-value: 5e-58
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHH...HHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHH CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekle...evakelkeegakalaiqvDvtdreevealvekavkk 74 
                                       k++++tG s+GIGr ia+++a  Ga+vvv+d+see+ e    +++ l+eega+ +++++Dv+d++++ a+ve+a ++
  gi|313116991|ref|YP_004038115.1|   7 KTAVITGSSGGIGRGIARTFADHGASVVVADISEEPREggtPTHELLQEEGAESMYVECDVSDYDDCVAAVEAA-DE 82 
                                       79*******************************99876331356666667*********************999.99 PP

                                       HSSESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHH CS
                         adh_short  75 lgkldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaY 149
                                       +g++dv+vnNAGi   + p  +++ e+++++i++Nl gv++ ++a++ aml ++  G+Ivn+sSvag  ++ g ++Y
  gi|313116991|ref|YP_004038115.1|  83 FGGIDVMVNNAGIvGPQDPLVDIDLEDYRNLISINLDGVVHGSKAAALAMLeQGVHGSIVNMSSVAGITGFGGITPY 159
                                       *************888899***************************9999977889********************* PP

                                       HHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 150 sAsKaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                       sA+K++v+++t +la el p+girvnav+PG+++T m++e 
  gi|313116991|ref|YP_004038115.1| 160 SAAKGGVRSFTYALASELGPDGIRVNAVHPGIIETTMTTED 200
                                       *************************************9886 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0     1e-18   1.9e-15       3     154 ..       9     164 ..       7     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1e-18
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        +itG  Gg+G+ +ar+ a++ga+ +v    + +++e  + + + l++ gae ++v++Dvsd d+  a++e+++ e+
  gi|313116991|ref|YP_004038115.1|   9 AVITGSSGGIGRGIARTFADHGASVVVADISE-EPREGGTPTHELLQEEGAESMYVECDVSDYDDCVAAVEAAD-EF 83 
                                       68********************9988875444.5888888899999**************************98.88 PP

                                       S---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--TT-HHHH CS
                                KR  80 ppikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsagqanYa 150
                                       + i   ++ Ag++  +++l + + ed++++++  ++G+ +  ++ +           +v +SS+ag++g  g + Y+
  gi|313116991|ref|YP_004038115.1|  84 GGIDVMVNNAGIVGpQDPLVDIDLEDYRNLISINLDGVVHGSKAAALamleqGVHGSIVNMSSVAGITGFGGITPYS 160
                                       9**********9986889************99999988887776555222225566899****************** PP

                                       HHHH CS
                                KR 151 aaNa 154
                                       aa  
  gi|313116991|ref|YP_004038115.1| 161 AAKG 164
                                       *974 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.4e-07    0.0006       6      68 ..      13      75 ..       7      93 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.4e-07
                                      --.SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEE CS
                           3HCDH_N  6 Ga.GtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalaris 68
                                      G+ G +G+gia  fa +g +Vv+ disee  e ++ + e   e+ +e+  ++  +v+++ + + 
  gi|313116991|ref|YP_004038115.1| 13 GSsGGIGRGIARTFADHGASVVVADISEEPREGGTPTHELLQEEGAESMYVE-CDVSDYDDCVA 75
                                      54599************************99998888876555555544444.44444444444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1     7e-07    0.0013       2      78 ..      10      99 ..       9     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7e-07
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.........EEEE--TT-HH...HHHHHHHHH.T-SE CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.........elveldltdrs...alerlfkee.qpda 67
                                      ++tG +G iG+ +++ ++++g  v++ d  ++ ++ +   +            ve+d+ d +   a  ++ +e+ ++d+
  gi|313116991|ref|YP_004038115.1| 10 VITGSSGGIGRGIARTFADHGASVVVADISEEPREGGTPTHEllqeegaesMYVECDVSDYDdcvAAVEAADEFgGIDV 88
                                      79*********************999999977777777777789******99999999999955555566677789999 PP

                                      EEE--S---HH CS
                         Epimerase 68 vihlAavggva 78
                                       ++ A++ g++
  gi|313116991|ref|YP_004038115.1| 89 MVNNAGIVGPQ 99
                                      99999965555 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.4e-06    0.0025       1      70 [.      10      83 ..      10     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-06
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespe.....lleelskvnvkk.viegDvtdkdkleealegvdvv 70
                                      v+tG++G +Gr + +++ + +    v v+D+ e+p+     ++e l++ + ++ ++e+Dv d d+  +a+e +d  
  gi|313116991|ref|YP_004038115.1| 10 VITGSSGGIGRGIARTFADHG--ASVVVADISEEPReggtpTHELLQEEGAESmYVECDVSDYDDCVAAVEAADEF 83
                                      79*****************99..59*****988765222215666666676669***************9987754 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   6.6e-06     0.012       2      75 ..      10      91 ..       9     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.6e-06
                                      EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.....TTTCEEEEE--TTTHHHHHHHHHTTS.... CS
                   Sacchrp_dh_NADP  2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka.....lgvrfeaialdaenyeavLaallkeg.... 70
                                      +i G+ G++G+++a+  a+h+     ++vad s+e  e    +       g +   +++d+++y++  +a+++ +    
  gi|313116991|ref|YP_004038115.1| 10 VITGSsGGIGRGIARTFADHGAS---VVVADISEEPREGGTPTHellqeEGAESMYVECDVSDYDD-CVAAVEAAdefg 84
                                      678999**************986...********9966443333556669999999**********.777777664455 PP

                                      ..SEEEE CS
                   Sacchrp_dh_NADP 71 ..dlvvn 75
                                        d+ vn
  gi|313116991|ref|YP_004038115.1| 85 giDVMVN 91
                                      5555555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   7.5e-06     0.013      34      93 ..       4      66 ..       1      70 [. 0.78
   2 ?   -2.6   0.2       1.6   2.9e+03      37      47 ..     146     156 ..     134     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.5e-06
                                      GTTSEEEEES-.SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTCEECSHHHHHHH-S CS
                      2-Hacid_dh_C 34 lsgktvGiiGl.GrIGqavakrlkafgmkviaydrskkkee..eeeelgvelvsleellaesD 93
                                      l+gkt  i G  G IG+ +a++++  g+ v++ d s++++e  +  ++ ++ +  e ++ e+D
  gi|313116991|ref|YP_004038115.1|  4 LEGKTAVITGSsGGIGRGIARTFADHGASVVVADISEEPREggTPTHELLQEEGAESMYVECD 66
                                      899******9549***********************998886444444445556666666666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                                       SEEEEES-SHH CS
                      2-Hacid_dh_C  37 ktvGiiGlGrI 47 
                                       +  Gi G+G I
  gi|313116991|ref|YP_004038115.1| 146 SVAGITGFGGI 156
                                       5689****998 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.4e-05     0.025      20      54 ..       3      38 ..       1      42 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                      --TTSEEEEE--.SHHHHHHHHHHHHCT-EEEEE-S CS
                     AdoHcyase_NAD 20 llaGkvavvaGy.GdvGkGcaaslkglGarvivtev 54
                                      ll Gk+av++G  G +G+G a+++  +Ga v+v+++
  gi|313116991|ref|YP_004038115.1|  3 LLEGKTAVITGSsGGIGRGIARTFADHGASVVVADI 38
                                      789*******95499******************998 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.18      26      86 ..      13      76 ..       9      83 .. 0.70
   2 ?   -0.4   0.0      0.47   8.4e+02      33      72 ..     171     212 ..     168     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                      ----HHHHHHHHHHHHTT-EEEEEE-S-SS--..-TT-EEEE--SHHHHHHHHH.HHHTT-SEE CS
                               DFP 26 rSSGkmGyalAeaaaarGaeVtlvsgpvslet..pegvevvkvesaeemleave.ealkeadiv 86
                                       SSG  G  +A+ +a+ Ga+V +   + + ++   ++ e+++ e ae+m+ +++ + ++++ ++
  gi|313116991|ref|YP_004038115.1| 13 GSSGGIGRGIARTFADHGASVVVADISEEPREggTPTHELLQEEGAESMYVECDvSDYDDCVAA 76
                                      59*******************9875553322222447789999999999988873333333333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.47
                                       HHHHHHHHHTT-EEEEEE-S.-SS-.--TT-EEEE--SHHHH CS
                               DFP  33 yalAeaaaarGaeVtlvsgp.vsle.tpegvevvkvesaeem 72 
                                       yalA+++   G +V+ v+    +++ t e   +v  e+ e+m
  gi|313116991|ref|YP_004038115.1| 171 YALASELGPDGIRVNAVHPGiIETTmTTEDSPFVGTEQEEKM 212
                                       89**************99552333313334445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1977.52
//
Query:       gi|313116992|ref|YP_004038116.1|  [L=310]
Description: sugar kinase, ribokinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-42  144.3   5.9    1.3e-41  142.8   5.9    1.8  1  PfkB          pfkB family carbohydrate kinase
    5.4e-06   26.0   0.0    0.00035   20.0   0.0    2.6  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    0.00033   20.2   0.6     0.0018   17.8   0.6    2.0  1  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
      0.016   15.2   0.9      0.048   13.7   0.9    1.8  1  PepSY_2       Peptidase propeptide and YPEB domain
      0.051   14.1   0.0       0.18   12.3   0.0    1.9  2  XdhC_C        XdhC Rossmann domain


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.8   5.9   3.8e-45   1.3e-41      22     301 ..      45     301 ..       1     302 [. 0.89

  Alignments for each domain:
  == domain 1  score: 142.8 bits;  conditional E-value: 3.8e-45
                                       TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSEEEEEEEEET CS
                              PfkB  22 egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkidedtrtglalivvd 98 
                                       ++++  ++  e++ GG+gaN+Ava+a  gad++++g+vG D+   +++++l+k+gvd+  v+ ++d +tg a++ vd
  gi|313116992|ref|YP_004038116.1|  45 FPDSLAQAYDERYLGGKGANQAVAAAAAGADTSLLGMVGEDESEYEVRTTLSKRGVDVTEVE-STDGPTGAAYVAVD 120
                                       4555667777999*********************************************9999.8888********** PP

                                       TTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTEEEEEECESSSHHHHH CS
                              PfkB  99 edgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggtfdpnlldplgaqfke 175
                                       e+ge+ i +  ga+   +++ +e ++  l +ad l +      elp ++++++ +   + ++   +++dp++a  ++
  gi|313116992|ref|YP_004038116.1| 121 ETGENYIAILAGANGRVDDAYVERHVGSLTSADCLLVQN----ELPAETVRAALDHLAERDNRPTVVYDPAPA--AD 191
                                       *******************99999999999999999999....9999999999888888888899*******6..44 PP

                                       HHHHHH.CTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS- CS
                              PfkB 176 allell.aladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkv 251
                                       a   l   ++d+++pn+ E e l +         ++a           vv t+G+eG++v  +++ + vp+ p+v++
  gi|313116992|ref|YP_004038116.1| 192 ATTILThDCVDVVTPNRGEYETLRDD--------IEAFDG-------IVVRTRGAEGVVVE-GEDRFTVPS-PSVEP 251
                                       44444369*************55544........466544.......7*********9887.*********.***** PP

                                       SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSCC CS
                              PfkB 252 vDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslpt 301
                                       +DttGAGD f+g + a l++g +le+a+r+a+ ++a++++++g++a++p+
  gi|313116992|ref|YP_004038116.1| 252 IDTTGAGDVFAGFLGAELAAGSDLEQAVRLATVAGAVSTEREGVQAAVPS 301
                                       *********************************************99885 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.7e-08   0.00035     175     225 ..     233     283 ..     161     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.7e-08
                                       EEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHH CS
                      Phos_pyr_kin 175 dvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAk 225
                                        v+++ge+ ++++++ +e  +t G+G++++  + aela g +le+Av+ A+
  gi|313116992|ref|YP_004038116.1| 233 GVVVEGEDRFTVPSPSVEPIDTTGAGDVFAGFLGAELAAGSDLEQAVRLAT 283
                                       5788999999*************************************9986 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6   5.2e-07    0.0018     117     222 ..     199     290 ..     126     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.2e-07
                                       TSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHH CS
                       Carb_kinase 117 kaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkgekdvivspegevlinstgssalakGGsGDvL 193
                                        +  + TP+ +E++ L ++i               +  + vv  +g++ v+v+ e+  +  s +     + G GDv 
  gi|313116992|ref|YP_004038116.1| 199 DCVDVVTPNRGEYETLRDDIE--------------AFDGIVVRTRGAEGVVVEGEDRFTVPSPSVEPIDTTGAGDVF 261
                                       466677888888888877777..............55566666788889999978777777778888999******* PP

                                       HHHHHHHHHCTSSHHHHHHHHHHHHHHHH CS
                       Carb_kinase 194 aGligalLaqneasyeaaiaaawlhgaas 222
                                       aG +ga La   +  +a+  a+++ + + 
  gi|313116992|ref|YP_004038116.1| 262 AGFLGAELAAGSDLEQAVRLATVAGAVST 290
                                       ************99999988877665554 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.9   1.3e-05     0.048       9      79 ..      66     136 ..      63     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                           PepSY_2   9 allaaaAlAgrrdtdspkadwlpreklvakleaqGykvkkievddggcyEve.gldkdGkkveikldpatge 79 
                                       a++aaaA A ++     + ++ ++ ++++ l ++G +v+++e +dg    ++ ++d+ G+ + + l +a+g 
  gi|313116992|ref|YP_004038116.1|  66 AVAAAAAGA-DTSLLGMVGEDESEYEVRTTLSKRGVDVTEVESTDGPTGAAYvAVDETGENYIAILAGANGR 136
                                       456666666.8888889999999************************9****999**999988777777776 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.1e-05      0.18      58     109 ..      65     117 ..      16     132 .. 0.83
   2 ?   -1.3   0.0      0.83     3e+03      10      52 ..     167     198 ..     161     229 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHSSS--SEEEESS-HHHHHHHCTTS.--.......TTEESS-S--.S CS
                            XdhC_C  58 aealeaalrkkaayigllGSrkkaarrlerlraaglseeelarlhaPiGld.i 109
                                       +++ +aa   +++ +g++G  +   ++++ l+++g++ +e++    P G + +
  gi|313116992|ref|YP_004038116.1|  65 QAVAAAAAGADTSLLGMVGEDESEYEVRTTLSKRGVDVTEVESTDGPTGAAyV 117
                                       4445555557799************************************8843 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE-EEEE--S CS
                            XdhC_C  10 aqalarlaaalgfrvtvvdpreefatkerfpeadetavvvlth 52 
                                        +al +la++ +  ++v+dp +++           +a  +lth
  gi|313116992|ref|YP_004038116.1| 167 RAALDHLAERDNRPTVVYDPAPAA-----------DATTILTH 198
                                       455555555555566666666642...........33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2047.35
//
Query:       gi|313116993|ref|YP_004038117.1|  [L=210]
Description: hypothetical protein Hbor_34600 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.4   2.2     0.0051   17.0   0.2    2.2  2  DUF4232   Protein of unknown function (DUF4232)
  ------ inclusion threshold ------
      0.017   15.1   0.0       0.29   11.2   0.0    2.2  1  BsuPI     Intracellular proteinase inhibitor


Domain annotation for each model (and alignments):
>> DUF4232  Protein of unknown function (DUF4232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.5     0.014   1.2e+02      75     124 ..      55     102 ..      24     107 .. 0.60
   2 !   17.0   0.2   5.6e-07    0.0051      23      96 ..      91     182 ..      74     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.014
                           DUF4232  75 aglrwtnaggdgdgectaaglrvtppdgtksvtvpdlgatgtdvdvgklt 124
                                         l+++++++ +d++  + +++vt+ ++t+s++   l at t+ ++ +lt
  gi|313116993|ref|YP_004038117.1|  55 PELSIVSTDELPDAPVRP-AIEVTQKTATESQPPG-LKATVTNESDRTLT 102
                                       556666666666665554.6777766666666444.55555555555544 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.6e-07
                           DUF4232  23 ltltNtgsrtCtl.dGyPgVsll..dadgqqvgaaaeregpaavp................vtLapGesAyaglrwt 80 
                                        t+tN ++rt tl +G + V +   d +++ + ++a ++ p +++                vtL+pGesA+  l++ 
  gi|313116993|ref|YP_004038117.1|  91 ATVTNESDRTLTLgEGRAIVFAYrnDTANNLMLLPAGSDYPVEAGcwrltegiaiteeyrmVTLEPGESASQVLELY 167
                                       58999999999994455544433577777888888888888777799999*************************** PP

                           DUF4232  81 naggdgdgectaaglr 96 
                                        a++++++ +t  ++r
  gi|313116993|ref|YP_004038117.1| 168 GAPDTDACLPTG-TFR 182
                                       **9999988875.555 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.3e-05      0.29       2      90 ..      75     182 ..      74     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.3e-05
                                       EEEEEEEE-SS-EEEEEEEEE-SSS-EEE........EESSS--EEEEEE.....-TT--EEEETTTT-------EE CS
                             BsuPI   2 elaleaeasgeavelaltvtNesdeavtl........qFssgqkydlvvk.....deegeevwrysegrmFtqalss 65 
                                       e+++++++++++  l+ tvtNesd++ tl        ++++    +l++         +   wr +eg + t+ ++ 
  gi|313116993|ref|YP_004038117.1|  75 EVTQKTATESQPPGLKATVTNESDRTLTLgegraivfAYRNDTANNLMLLpagsdYPVEAGCWRLTEGIAITEEYRM 151
                                       67778888888999999999999977665222222224555555555555887766667789*************** PP

                                       EEE-TT-EEEEEEEE.......S---SEEEE CS
                             BsuPI  66 etlepgesatyeetwd......edlepGeYt 90 
                                       +tlepgesa+   +++        l+ G+++
  gi|313116993|ref|YP_004038117.1| 152 VTLEPGESASQVLELYgapdtdACLPTGTFR 182
                                       *******998777766555443355555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 1396.75
//
Query:       gi|313116994|ref|YP_004038118.1|  [L=300]
Description: thioredoxin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-12   44.8   0.5    2.9e-07   30.0   0.2    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.3e-08   33.7   0.0      0.004   16.4   0.0    2.4  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.4e-07   30.7   4.9    2.3e-05   24.2   0.6    2.9  4  DAO            FAD dependent oxidoreductase
      1e-06   28.1   0.5      3e-06   26.6   0.5    1.7  1  GIDA           Glucose inhibited division protein A
    1.5e-06   27.5   3.7    3.4e-06   26.4   0.1    2.7  4  FAD_binding_2  FAD binding domain
    2.5e-06   27.1   0.7    2.5e-06   27.1   0.7    2.3  2  FAD_oxidored   FAD dependent oxidoreductase
    4.1e-06   25.7   0.1    0.00011   21.1   0.0    2.3  3  HI0933_like    HI0933-like protein
    4.5e-06   26.8   0.3    1.1e-05   25.5   0.3    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    9.8e-06   25.0   0.0    1.9e-05   24.1   0.0    1.5  1  FAD_binding_3  FAD binding domain
    2.1e-05   23.8   0.1     0.0082   15.2   0.0    2.7  3  Lycopene_cycl  Lycopene cyclase protein
    0.00048   19.5   0.0    0.00072   18.9   0.0    1.2  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0013   19.2   0.1     0.0045   17.5   0.1    1.9  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0021   17.3   0.1     0.0073   15.6   0.0    1.8  2  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.084   12.9   3.7       0.93    9.5   0.1    2.7  3  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.2   2.3e-10   2.9e-07       1      42 [.      13      53 ..      13      67 .. 0.84
   2 !   13.1   0.0   3.2e-05      0.04     188     293 ..      72     178 ..      65     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.3e-10
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll 42
                                      +dvvv+GgGpAG++aa ++a++g++++++ ++g   +++c +
  gi|313116994|ref|YP_004038118.1| 13 HDVVVVGGGPAGCSAAVFAARYGFDTVVF-DRGRSSLRHCGY 53
                                      59***************************.777777777765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 188 aleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdef 263
                                        +++++e+ G +++  + v  ++++g++ + +++dg+++ a  vv a+ + ++    + ++  l+ d +gg++ d++
  gi|313116994|ref|YP_004038118.1|  72 LMHDHVEAAGCTIV-PELVSSVEREGDEFRIETQDGTVVRAPRVVAATKYDADYLD-GlDEELLQPDGHGGMELDPS 146
                                       67888999999999.77888*******999******************88888533.47888888899****99988 PP

                                       S.....BESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                       x.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 264 l.....rtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                              t v+g+y++G +    ++ ++a  A  +
  gi|313116994|ref|YP_004038118.1| 147 FsdadgSTPVDGLYVAGPIS---DVEDQAIIAAGH 178
                                       867666799********998...666666666665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05     0.015       1      31 [.      16      45 ..      16      56 .. 0.90
   2 !   16.4   0.0   3.1e-06     0.004     235     305 .]      89     163 ..      83     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      +++G+GPaG +aa+ + + g+ d ++ ++g+
  gi|313116994|ref|YP_004038118.1| 16 VVVGGGPAGCSAAVFAARYGF-DTVVFDRGR 45
                                      79*******************.689*99996 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.1e-06
                       Pyr_redox_3 235 vkeikekeeeykvktedgkkvevkddvvlatGykpd.lsflkkslfeldedg....rpvlteeteetnvpglflaG 305
                                       v +++++  e++++t+dg+ v++  +vv+at y+ d l+ l+++l++ d  g     p + +++ +t v+gl++aG
  gi|313116994|ref|YP_004038118.1|  89 VSSVEREGDEFRIETQDGTVVRA-PRVVAATKYDADyLDGLDEELLQPDGHGgmelDPSFSDADGSTPVDGLYVAG 163
                                       778999999********988876.889********9447799999998877644447999999***********99 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.6   1.8e-08   2.3e-05       1      30 [.      14      45 ..      14      53 .. 0.93
   2 !    7.2   0.1    0.0026       3.3     144     209 ..      65     128 ..      48     209 .. 0.78
   3 ?   -0.7   0.1      0.63   8.1e+02     194     207 ..     170     183 ..     148     238 .. 0.58
   4 ?   -1.1   0.1      0.84   1.1e+03     106     126 ..     207     228 ..     173     280 .. 0.55

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.8e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                      dvv++GGG +G+s+A ++ar g  ++++++g+
  gi|313116994|ref|YP_004038118.1| 14 DVVVVGGGPAGCSAAVFAARYGfdTVVFDRGR 45
                                      9*****************************95 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0026
                                       EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHH.HT CS
                               DAO 144 dpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdll.gl 209
                                       d  ++   + + +ea+G++i+ +  v ++e+e g+  ++  +t+ g++  ++a  vV a+   +d l gl
  gi|313116994|ref|YP_004038118.1|  65 DIDAFYTLMHDHVEAAGCTIVPE-LVSSVERE-GDEFRI--ETQdGTV--VRAprVVAATKYDADYLdGL 128
                                       667788889999**********9.99999775.666889..8888998..44455****98888866333 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.63
                                       EEEEE--GGGHHHH CS
                               DAO 194 davVnaaGawsdll 207
                                       d+ ++aaG++++  
  gi|313116994|ref|YP_004038118.1| 170 DQAIIAAGHGARVG 183
                                       55666666665533 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.84
                                       H.HHTTTTEEEEEHHHHHHHST CS
                               DAO 106 l.leagldaelldaeevrelep 126
                                       + +e  l +e+ d+++ rel+ 
  gi|313116994|ref|YP_004038118.1| 207 VrKESTLTEEWRDRDRWRELFD 228
                                       2222233334555554444442 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.5   2.3e-09     3e-06       1      39 [.      14      52 ..      14     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.3e-09
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--S CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaels 39
                                      dv+V+GgG AGc AA+ aar G++++ +    +++ +++
  gi|313116994|ref|YP_004038118.1| 14 DVVVVGGGPAGCSAAVFAARYGFDTVVFDRGRSSLRHCG 52
                                      79************************9955544444444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   2.6e-09   3.4e-06       1      32 [.      14      45 ..      14      51 .. 0.93
   2 ?   -3.5   0.0       3.1     4e+03     182     198 ..      87     110 ..      72     118 .. 0.59
   3 ?    1.2   0.0      0.12   1.6e+02     374     400 ..     139     164 ..     132     181 .. 0.87
   4 ?   -1.6   0.0      0.82     1e+03     319     344 ..     192     262 ..     165     275 .. 0.57

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.6e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      Dv+V+G+G AG++AA+ aa+ G +++v + + 
  gi|313116994|ref|YP_004038118.1| 14 DVVVVGGGPAGCSAAVFAARYGFDTVVFDRGR 45
                                      9**************************99876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.1
                                       T......TTTCEEEEEES.EEEE- CS
                     FAD_binding_2 182 p......esgrevrirak.avvla 198
                                       +      ++g e+ri+ + ++v+ 
  gi|313116994|ref|YP_004038118.1|  87 ElvssveREGDEFRIETQdGTVVR 110
                                       344444566777777777766654 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.12
                                       -EEEBETTSBESTTEEESSBTEEE-ST CS
                     FAD_binding_2 374 gGvetdengrvldadgqpipGLYAaGe 400
                                       gG+e d+++    ++ +p++GLY aG 
  gi|313116994|ref|YP_004038118.1| 139 GGMELDPSFSD-ADGSTPVDGLYVAGP 164
                                       88999999886.88999*******995 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.82
                                       T..............................................SSHHHHHHHSHHHHHHHHHCCT.. CS
                     FAD_binding_2 319 h.............................................gldaegleatleaineeaangldkd 344
                                                                                     ++d++++e+ +e++++e + ++ +d
  gi|313116994|ref|YP_004038118.1| 192 RndgywdavaayydwvrkestlteewrdrdrwrelfdehfapddggQYDPSHIERVREEYIDERKAKYATD 262
                                       24444444444444444444444444444555555555555555557888888888888888877777655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.7   1.9e-09   2.5e-06       1      31 [.      14      44 ..      14      47 .. 0.94
   2 ?    0.9   0.5      0.18   2.3e+02     201     270 ..     197     266 ..      60     285 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.9e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      DvvVvGGgpaG+ AA+ Aar G  +++ ++ 
  gi|313116994|ref|YP_004038118.1| 14 DVVVVGGGPAGCSAAVFAARYGFDTVVFDRG 44
                                      9*************************99876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                      FAD_oxidored 201 skp.enrvpfekkpegydparyelarvfeaklskgklpgektdvnwpr...vstdlienldlpeaeyegreqir 270
                                       ++  +  +++ +k+  +++++++  + ++  ++++  p++  +++  +   v+ ++i   d  +a+y++ e+i+
  gi|313116994|ref|YP_004038118.1| 197 WDAvAAYYDWVRKESTLTEEWRDR-DRWRELFDEHFAPDDGGQYDPSHierVREEYI---DERKAKYATDEEIA 266
                                       333344444444444444444444.22222244444444433333332333333333...44444444444444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.2e-08   0.00011       1      37 [.      13      49 ..      13      51 .. 0.93
   2 ?    2.0   0.0     0.052        66     121     162 ..      79     118 ..      68     119 .. 0.79
   3 ?   -4.0   0.0       3.5   4.5e+03     374     388 ..     155     169 ..     151     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.2e-08
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                      +dv+v+GgG+AG  aA+ aa+ g ++++++++++ +r
  gi|313116994|ref|YP_004038118.1| 13 HDVVVVGGGPAGCSAAVFAARYGFDTVVFDRGRSSLR 49
                                      59*****************************988665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.052
                                       HHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 121 eagvklrletevksvekeedgkfrvktkseeeleadklvlAt 162
                                       +ag+++   + v+sve+e d+ fr++t++++ ++a ++v At
  gi|313116994|ref|YP_004038118.1|  79 AAGCTIV-PELVSSVEREGDE-FRIETQDGTVVRAPRVVAAT 118
                                       5555554.356999*999998.*****99*********9986 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 3.5
                                       TSTTEEE-GGGBSEE CS
                       HI0933_like 374 kvpgLffaGEvlDve 388
                                        v gL++aG + Dve
  gi|313116994|ref|YP_004038118.1| 155 PVDGLYVAGPISDVE 169
                                       689******999986 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.3   8.8e-09   1.1e-05       1      29 [.      17      45 ..      17      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 8.8e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      +vG+G +G++aA ++a++gfd +++++++
  gi|313116994|ref|YP_004038118.1| 17 VVGGGPAGCSAAVFAARYGFDTVVFDRGR 45
                                      8*************************986 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.5e-08   1.9e-05       3      37 ..      14      48 ..      12      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.5e-08
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37
                                      dV++VG+GpaG ++a + +++G ++v+ ++ ++  
  gi|313116994|ref|YP_004038118.1| 14 DVVVVGGGPAGCSAAVFAARYGFDTVVFDRGRSSL 48
                                      8****************************988765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   6.4e-06    0.0082       1      38 [.      14      49 ..      14      57 .. 0.87
   2 !    5.2   0.0    0.0071       9.1      89     139 ..      69     118 ..      62     131 .. 0.87
   3 ?   -0.9   0.0      0.51   6.5e+02      85     132 ..     219     267 ..     196     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.4e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllf 38
                                      Dvvv+G+GpAg+s A     a++g   v+ + + s+l+
  gi|313116994|ref|YP_004038118.1| 14 DVVVVGGGPAGCSAAVFA--ARYGFDTVVFDRGRSSLR 49
                                      9************99877..999999999998888776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0071
                     Lycopene_cycl  89 lkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdar 139
                                       +   ++ ++  +g + +   v sve e + e ++ +++g  +ra+ vv a+
  gi|313116994|ref|YP_004038118.1|  69 FYTLMHDHVEAAGCTIVPELVSSVEREGD-EFRIETQDGTVVRAPRVVAAT 118
                                       66677777778899999999******999.******************987 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.51
                     Lycopene_cycl  85 sskrlkeellerlv.engvklleakvesveeeeageslvvleggrkira 132
                                        ++r +e   e+++ ++g ++  + +e+v+ee   e+ +  + +++i  
  gi|313116994|ref|YP_004038118.1| 219 DRDRWRELFDEHFApDDGGQYDPSHIERVREEYIDERKAKYATDEEIAR 267
                                       5778888888999989999999999999999999888888888888765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.6e-07   0.00072      27      68 ..      11      52 ..       2      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.6e-07
                                      ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       AlaDh_PNT_C 27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparleqle 68
                                      ++  v+v+GgG aG +A+  a++ g +++v+D   + l++  
  gi|313116994|ref|YP_004038118.1| 11 DAHDVVVVGGGPAGCSAAVFAARYGFDTVVFDRGRSSLRHCG 52
                                      4567****************************9988888765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.5e-06    0.0045       2      36 ..      15      49 ..      14      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSST CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllr 36
                                      vvvvGgG  g+ +A ++a++g ++ v++r+   lr
  gi|313116994|ref|YP_004038118.1| 15 VVVVGGGPAGCSAAVFAARYGFDTVVFDRGRSSLR 49
                                      8**************************99987765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.7e-06    0.0073      18      49 ..      13      43 ..       8      48 .. 0.89
   2 ?   -1.9   0.0       1.3   1.6e+03     152     171 ..     104     123 ..      77     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.7e-06
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       Dvv+vG+G++G +aa   a+  ++ +++++r
  gi|313116994|ref|YP_004038118.1| 13 HDVVVVGGGPAGCSAAVFAARY-GFDTVVFDR 43
                                      6***************999998.999999987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                       -B-EEEEEEEEEE--GSSST CS
                              Thi4 152 vDPlvirakvvvdatGhdge 171
                                        D  v+ra  vv at +d++
  gi|313116994|ref|YP_004038118.1| 104 QDGTVVRAPRVVAATKYDAD 123
                                       57889999999999999987 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.044        56       1      14 [.      16      29 ..      16      50 .. 0.80
   2 ?    9.5   0.1   0.00073      0.93     111     153 ..      76     118 ..      67     119 .. 0.84
   3 ?   -1.9   0.1       2.2   2.9e+03      69      90 ..     203     231 ..     185     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.044
                     NAD_binding_9  1 aivGaGprGlavle 14
                                      ++vG+Gp+G +++ 
  gi|313116994|ref|YP_004038118.1| 16 VVVGGGPAGCSAAV 29
                                      69********9986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00073
                     NAD_binding_9 111 lpegvtvevhraevvdleeradgqavlladgaslaadaVvLAl 153
                                         e    +++ + v ++e+++d++++ ++dg+ ++a +Vv A+
  gi|313116994|ref|YP_004038118.1|  76 HVEAAGCTIVPELVSSVEREGDEFRIETQDGTVVRAPRVVAAT 118
                                       4455677899999***************************997 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.2
                     NAD_binding_9  69 faeWlrerga.....lee...aeeldpddf 90 
                                       +++W+r+++        +    +el +++f
  gi|313116994|ref|YP_004038118.1| 203 YYDWVRKESTlteewR-DrdrWRELFDEHF 231
                                       6667766665433321.0223334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 1911.55
//
Query:       gi|313116995|ref|YP_004038119.1|  [L=214]
Description: thiamine-phosphate diphosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-60  203.6   3.4    2.2e-60  203.1   3.4    1.2  1  TMP-TENI      Thiamine monophosphate synthase
    2.4e-06   27.1   3.9    2.4e-06   27.1   3.9    2.1  3  ThiG          Thiazole biosynthesis protein ThiG
      3e-05   23.4   2.6      3e-05   23.4   2.6    1.7  2  DHO_dh        Dihydroorotate dehydrogenase
    6.7e-05   22.4   7.2    9.1e-05   22.0   7.2    1.2  1  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.024   13.8   0.5      0.065   12.4   0.5    1.7  1  DUF561        Protein of unknown function (DUF561)
      0.027   14.0   3.7      0.062   12.8   1.4    2.0  2  His_biosynth  Histidine biosynthesis protein
        0.1   11.7   0.9       0.14   11.3   0.5    1.5  2  Dus           Dihydrouridine synthase (Dus)
       0.13   11.7   0.1         15    4.9   0.0    2.1  2  TniB          Bacterial TniB protein


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.1   3.4   9.7e-64   2.2e-60       2     181 .]       8     190 ..       7     190 .. 0.97

  Alignments for each domain:
  == domain 1  score: 203.1 bits;  conditional E-value: 9.7e-64
                          TMP-TENI   2 ylvtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgvH 78 
                                       ylvt+  + +++   ++v++a++ggv++vq+Rek+ +are++el ++l+al+r++++p+++ndrvd+a av+adgvH
  gi|313116995|ref|YP_004038119.1|   8 YLVTQGDRSRGRGTGSIVRAAIEGGVDIVQMREKHTSARERYELGKELRALTREADIPFVVNDRVDIAAAVDADGVH 84 
                                       99**999999999**************************************************************** PP

                          TMP-TENI  79 lgqddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkda...eplgleglkelaealeiP 152
                                       lg ddlpv+ ar  lg+++iiG Sv+++e a eae++gadY+gvG++f+TdtK+ +   + +g e+++e+ae++ iP
  gi|313116995|ref|YP_004038119.1|  85 LGDDDLPVSVARDHLGEEAIIGRSVSTPEAASEAERAGADYLGVGAVFATDTKDVNegeAEIGTETIAEIAETVDIP 161
                                       *****************************************************86655689**************** PP

                          TMP-TENI 153 vvaiGGitlenvaevleagadgvavvsai 181
                                       +v iGGi+++n+ ev++aga+gvavv+ i
  gi|313116995|ref|YP_004038119.1| 162 IVGIGGINADNATEVVNAGAAGVAVVTTI 190
                                       **************************987 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.99   2.2e+03     185     211 ..      20      46 ..      18      60 .. 0.62
   2 ?   -0.0   0.1       0.2   4.4e+02     166     189 ..      54      77 ..      46     122 .. 0.76
   3 !   27.1   3.9   1.1e-09   2.4e-06     164     229 ..     148     212 ..     126     214 .] 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.99
                                       -SHHHHHHHHHTT-SEEEESHHHHTSS CS
                              ThiG 185 gspsdaaqamelGadavllntavaeak 211
                                       g+ s + +a+e G+d v +    ++a+
  gi|313116995|ref|YP_004038119.1|  20 GTGSIVRAAIEGGVDIVQMREKHTSAR 46 
                                       555666666666666666655555544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.2
                                       HHHHHHHH-SS-BEEES---SHHH CS
                              ThiG 166 alkiiieeakvPvivDAGigspsd 189
                                        l+ +++ea++P +v+  +  +  
  gi|313116995|ref|YP_004038119.1|  54 ELRALTREADIPFVVNDRVDIAAA 77 
                                       688999999999999877665544 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 1.1e-09
                                       HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHH CS
                              ThiG 164 kealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklaveaGrl 229
                                       +e++  i e++++P++   Gi ++ +a+++++ Ga +v + t+++ a+dp+a  + +++ave Gr+
  gi|313116995|ref|YP_004038119.1| 148 TETIAEIAETVDIPIVGIGGI-NADNATEVVNAGAAGVAVVTTITDADDPAAATQQLRQAVENGRT 212
                                       5789999*******9876666.6899**************************************97 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.36   8.1e+02     253     277 ..     109     133 ..     100     142 .. 0.79
   2 !   23.4   2.6   1.3e-08     3e-05     228     278 ..     145     192 ..     141     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.36
                                       --SHHHHHHHHHHTECEEEESHHHH CS
                            DHO_dh 253 iesgeDalekieaGAslvqvytalv 277
                                       +++ e a e  +aGA  + v++ + 
  gi|313116995|ref|YP_004038119.1| 109 VSTPEAASEAERAGADYLGVGAVFA 133
                                       7888889999999999999998764 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHH CS
                            DHO_dh 228 dialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvf 278
                                       +i++++i e++++++  ipi+g+GGi+ ++ a e ++aGA+ v+v t ++ 
  gi|313116995|ref|YP_004038119.1| 145 EIGTETIAEIAETVD--IPIVGIGGIN-ADNATEVVNAGAAGVAVVTTITD 192
                                       689************..*********7.799*************9998754 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   7.2   4.1e-08   9.1e-05      86     236 ..      50     201 ..      25     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.1e-08
                               NMO  86 eleeaalelnieegvr..fyrkvevvldekvevvsfgfglpteevvarlkeagvvliptissvkearkvearGaDal 160
                                       el+++   l  e  ++     +v++ + + ++ v +g ++ +  v       ++++  ++s+ ++a ++e++GaD l
  gi|313116995|ref|YP_004038119.1|  50 ELGKELRALTREADIPfvVNDRVDIAAAVDADGVHLGDDDLPVSVARDHLGEEAIIGRSVSTPEAASEAERAGADYL 126
                                       34433333333333343334899999999999999998888666655555666777789****************** PP

                               NMO 161 ivqGpeaGGhqGtpevgd.kglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakda 236
                                        v    a   +  ++ g+ +  ++ ++++++ vdiP++  GGi+  +    +  +GA+gv++ t    +++  a   
  gi|313116995|ref|YP_004038119.1| 127 GVGAVFATDTKD-VNEGEaEIGTETIAEIAETVDIPIVGIGGINADNA-TEVVNAGAAGVAVVTTITDADDPAAATQ 201
                                       997777776666.55555466688899****************97665.56889**********9877766555443 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   2.9e-05     0.065     172     228 ..     148     201 ..     113     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                            DUF561 172 lstlastyeiskkvslPvicasGlsdvtvplalslgasGiGigsavsklndeeemva 228
                                       ++t+a   ei+++v++P++   G++   +   +++ga+G+ +  +++  +d  +  +
  gi|313116995|ref|YP_004038119.1| 148 TETIA---EIAETVDIPIVGIGGINADNATEVVNAGAAGVAVVTTITDADDPAAATQ 201
                                       44444...89******************9999**********999998887665555 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.016        37      69     124 ..      96     151 ..      69     152 .. 0.79
   2 ?   12.8   1.4   2.8e-05     0.062      59     107 ..     145     192 ..     138     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.016
                                       HHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGE CS
                      His_biosynth  69 aeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqki 124
                                       ++++  +  +G  +++ e++ e+ +agad++ +g + +++ + ++e   ++g + i
  gi|313116995|ref|YP_004038119.1|  96 RDHLGEEAIIGRSVSTPEAASEAERAGADYLGVGAVFATDTKDVNEGEAEIGTETI 151
                                       455566777888899999******************99999999999999998766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                      His_biosynth  59 eanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                       e+ ++ ++eiae+v+ip+   GGI+  + ++e+++aga  v + t   +
  gi|313116995|ref|YP_004038119.1| 145 EIGTETIAEIAETVDIPIVGIGGINADN-ATEVVNAGAAGVAVVTTITD 192
                                       556799************999***9887.9*******998887776543 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.1   2.5e+03     177     189 ..      57      69 ..      27      85 .. 0.55
   2 ?   11.3   0.5     6e-05      0.14     139     213 ..     110     187 ..      89     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                                       HHHHH-SS-EEEE CS
                               Dus 177 evkqavsipviaN 189
                                       ++ ++  ip+++N
  gi|313116995|ref|YP_004038119.1|  57 ALTREADIPFVVN 69 
                                       2222333344333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6e-05
                                       .HHHHHHHHHHCT-SEEEEESS....ECCCTT-C.G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEE CS
                               Dus 139 nalelakiveaaGaqaltvHgR....traqnyeg.tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgv 210
                                        + e+a  +e+aGa+ l v +     t+  n  + ++  e+I+e+ + v ip+++ G+I  a++a ++++  Ga gv
  gi|313116995|ref|YP_004038119.1| 110 STPEAASEAERAGADYLGVGAVfatdTKDVNEGEaEIGTETIAEIAETVDIPIVGIGGIN-ADNATEVVNA-GAAGV 184
                                       57899999*********99888885544443333577889*******************7.5677777777.88888 PP

                                       EES CS
                               Dus 211 mig 213
                                        ++
  gi|313116995|ref|YP_004038119.1| 185 AVV 187
                                       765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0085        19     134     172 ..      43      81 ..      38      84 .. 0.87
   2 ?    4.9   0.0    0.0068        15     144     169 ..     149     174 ..     138     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0085
                              TniB 134 gsarkqreflnalksLgnelkipivlvGteealralrtD 172
                                        sar++ e+   l+ L++e +ip+v+    ++ +a+++D
  gi|313116995|ref|YP_004038119.1|  43 TSARERYELGKELRALTREADIPFVVNDRVDIAAAVDAD 81 
                                       5789999999***************98888888887776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0068
                              TniB 144 nalksLgnelkipivlvGteealral 169
                                       +++  + ++++ipiv++G  +a +a 
  gi|313116995|ref|YP_004038119.1| 149 ETIAEIAETVDIPIVGIGGINADNAT 174
                                       57788999**********99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1704.44
//
Query:       gi|313116996|ref|YP_004038120.1|  [L=275]
Description: hydroxyethylthiazole kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-64  215.1   4.9    1.2e-63  214.8   4.9    1.0  1  HK            Hydroxyethylthiazole kinase family
    1.6e-05   24.4   0.5    2.1e-05   24.0   0.5    1.1  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.13   11.7   8.3      0.076   12.5   5.1    1.8  2  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.8   4.9     2e-67   1.2e-63       1     242 [.      11     256 ..      11     258 .. 0.98

  Alignments for each domain:
  == domain 1  score: 214.8 bits;  conditional E-value: 2e-67
                                       HHHHHHH--EEEEE--TTTHHHHHHHHHHHT-EEEE--STTTHHHHHHTSSEEEEE-TT--HHHHHHHHHHHHHHHH CS
                                HK   1 lkklreksPlvhhiTNkVaqnfsANvllAlgaSPimseaeeEvselakianaLllNiGtleekaiealkaAvksake 77 
                                       l+++r+++Plv+++TN+V+  ++A v+l  g+ P+ms++e Ev ++++ a+a llN+Gt++e    a+ aA++sa++
  gi|313116996|ref|YP_004038120.1|  11 LSAIRSTKPLVNSVTNNVTVGDVADVTLYWGGLPVMSDDEREVGDMVAGAQACLLNMGTVSEGGEAAMVAAGRSAND 87 
                                       6899************************************************************************* PP

                                       TT--EEEE-TTBTTBHHHHHHHHHHHHHS--SEEEEEHHHHHHHHTSSCCSCSSSSSS-SHHHHHHHHHHHHHHTSE CS
                                HK  78 vnrPvvlDPVgvgAtelRrelalellkevklavikGNasEilslaglelkvkGvDskeaataavaavqkvAqklrvv 154
                                       +++P+v+DPVgvgAt +R+++a  l++e  ++v+ GN +Ei +l+g++ +v+Gv+s  + +++ +++ + A+++++v
  gi|313116996|ref|YP_004038120.1|  88 HGVPLVVDPVGVGATPTRNRVADRLVTELDVDVLNGNYGEISALVGEDAEVRGVESVGEYAEIAETAVACARQTGAV 164
                                       *********************************************************999999999*********** PP

                                       EEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHHHHTT.. CS
                                HK 155 vvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaarsegs.. 229
                                       vv++Ge+Dvv+ + + ++++ G+e++g+++++GC+lg ++a+f++v +   +aa++++l++ +Ag++aa ++ g+  
  gi|313116996|ref|YP_004038120.1| 165 VVASGETDVVATADEAFEVHAGHEMMGNVVGTGCMLGVTLATFAGVMDSVRDAALAGTLAFGLAGEAAADEQFGTya 241
                                       *********************************************************************99999999 PP

                                       ..HHHHHHHHHHHHH CS
                                HK 230 ..gsFqvelldalsq 242
                                         +s++v++lda+s 
  gi|313116996|ref|YP_004038120.1| 242 gpASYKVTFLDAVSG 256
                                       999********9975 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.5   3.5e-09   2.1e-05      74     221 ..      75     218 ..      55     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.5e-09
                                       HHHHHHHHH..HHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT..---S...SHHH CS
                      Phos_pyr_kin  74 iievvaekl..kkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlg..ekik...teed 143
                                        +++va+    + ++vp+V+DPV v   g++ +++++ + l +eL   ++v+  N  E++aL+g   +++   ++ +
  gi|313116996|ref|YP_004038120.1|  75 EAAMVAAGRsaNDHGVPLVVDPVGV---GATPTRNRVADRLVTEL--DVDVLNGNYGEISALVGedAEVRgveSVGE 146
                                       4555555443255788*******87...45555555666666555..589**************6644443224444 PP

                                       HHHHHHHHHH..TT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHH CS
                      Phos_pyr_kin 144 mkeaakkllk..lgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesle 218
                                         e a++ ++   ++ aV++  g+        tdv+ + +e +e++a +    n  GtGC l   +a+     +s++
  gi|313116996|ref|YP_004038120.1| 147 YAEIAETAVAcaRQTGAVVVASGE--------TDVVATADEAFEVHAGHEMMGNVVGTGCMLGVTLATFAGVMDSVR 215
                                       444454444432345566666665........39999777777777777777****************999999999 PP

                                       HHH CS
                      Phos_pyr_kin 219 eAv 221
                                       +A 
  gi|313116996|ref|YP_004038120.1| 216 DAA 218
                                       886 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2     0.067     4e+02     190     218 ..      54      81 ..      47     105 .. 0.77
   2 ?   12.5   5.1   1.3e-05     0.076     139     230 ..     146     237 ..      73     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.067
                                       HHHHHHHHHHHHHCTSSHHHHHHHHHHHH CS
                       Carb_kinase 190 GDvLaGligalLaqneasyeaaiaaawlh 218
                                       GD  aG+ ++lL +     e + aa ++ 
  gi|313116996|ref|YP_004038120.1|  54 GDMVAGAQACLLNMGT-VSEGGEAAMVAA 81 
                                       9***********9988.333333444444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.3e-05
                                       HCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG.-STTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                       Carb_kinase 139 keddrlelarelaqklnavvllkgekdvivspegevlinstgssal.akGGsGDvLaGligalLaqneasyeaaiaa 214
                                       +  + +e+a + a++ +avv+  ge dv+++ ++e + +++g  ++  + G+G  L   ++ +  +  +  +aa+a+
  gi|313116996|ref|YP_004038120.1| 146 EYAEIAETAVACARQTGAVVVASGETDVVAT-ADEAFEVHAGHEMMgNVVGTGCMLGVTLATFAGVMDSVRDAALAG 221
                                       555678899999*******************.677777777766552789***999999999999999********* PP

                                       HHHHHHHHHHHCCCT- CS
                       Carb_kinase 215 awlhgaasdeaaekkg 230
                                       + + g a+++aa+++ 
  gi|313116996|ref|YP_004038120.1| 222 TLAFGLAGEAAADEQF 237
                                       **********998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2037.46
//
Query:       gi|313116997|ref|YP_004038121.1|  [L=243]
Description: short-chain alcohol dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-48  165.6   0.3    1.6e-48  165.3   0.3    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      1e-42  145.9   0.2    1.4e-42  145.4   0.2    1.1  1  adh_short        short chain dehydrogenase
    5.1e-19   68.9   0.2    6.7e-19   68.5   0.2    1.1  1  KR               KR domain
    1.4e-07   31.2   0.3      3e-07   30.2   0.3    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00024   20.3   0.0    0.00027   20.2   0.0    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0041   17.0   3.0      0.006   16.5   2.9    1.4  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.019   14.0   0.1      0.025   13.6   0.1    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      0.029   14.6   0.6      0.064   13.5   0.6    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.043   12.9   0.1       0.06   12.4   0.1    1.3  1  RmlD_sub_bind    RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   0.3   8.1e-52   1.6e-48       4     234 .]      10     241 ..       7     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 8.1e-52
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea..kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnna 77 
                                        gIGra++++  e   +vv+++ ++e+   + v++  +e+ ++ +l++DVtd ++vea++ee++++++++D++v+ +
  gi|313116997|ref|YP_004038121.1|  10 GGIGRAVVERKRE--SDVVFSYHRDEDgaSELVADTDAETATTqALQLDVTDADSVEAFAEEATATLDTVDGVVHTV 84 
                                       5999999998655..689999999998766777777777775558******************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg.gsivnlssvgaervvpnynaygaaKaalealtr 153
                                       gi+++  + +++ +++++ r++++nl + +++a+a+lp+++e+ gs+v lssvg++ + +  + y+a+K +l++l+r
  gi|313116997|ref|YP_004038121.1|  85 GIVEP--ELLEQSTDDQWSRVIETNLIGSARVARAFLPALRESsGSLVFLSSVGGTAG-TVDTSYAASKSGLHGLVR 158
                                       *****..888889*************************777777*********98555.55689************* PP

                                       HHHHHHGGGTEEEEEEEE--BHCTGGGGSTT...HHHHHHHHHHHSTTSS.-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikg...fdelleelearaplgr.lgtpeevaeaalfLasdeasyitGqt 226
                                       +lA+e+gp+g+RvNa +pgp++T ++  i +   + ++l + +  + l   +  peeva+ + +L+   +s++ G++
  gi|313116997|ref|YP_004038121.1| 159 ALAREVGPDGVRVNALAPGPVETSMNGTIVDyleSTAFLGHENVDTHLPTyACAPEEVAQSVTYLLD--SSFTHGEI 233
                                       *************************9999885444445555555555666256*************7..89****** PP

                                       EEESTTGG CS
                      adh_short_C2 227 lvvDgGlt 234
                                       l v+gG++
  gi|313116997|ref|YP_004038121.1| 234 LNVNGGMH 241
                                       *******8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.2     7e-46   1.4e-42       4     190 ..       4     187 ..       2     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 7e-46
                                       EEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                         adh_short   4 lvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkld 79 
                                       +vtG+++GIGra++++  ++  +vv+ + r e+ + e+++   +e a+  a+q+Dvtd+++vea+ e+a + l+++d
  gi|313116997|ref|YP_004038121.1|   4 VVTGGTGGIGRAVVERKRES--DVVFsYHRDEDGASELVADTDAETATTQALQLDVTDADSVEAFAEEATATLDTVD 78 
                                       8**************97666..455559************************************************* PP

                                       EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHH CS
                         adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaav 156
                                        +v+ +Gi +++  ++ ++++w rvie+Nl g   ++ra+lpa l++ssG+ v+ sSv g  +  + ++Y+AsK ++
  gi|313116997|ref|YP_004038121.1|  79 GVVHTVGIVEPELLEQSTDDQWSRVIETNLIGSARVARAFLPA-LRESSGSLVFLSSVGGT-AGTVDTSYAASKSGL 153
                                       ********9999999999999**********************.67************995.5667889******** PP

                                       HHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 157 agltrslakelaptgirvnavaPGlvdTdmakel 190
                                       +gl+r+la+e+ p+g+rvna+aPG+v+T m+ ++
  gi|313116997|ref|YP_004038121.1| 154 HGLVRALAREVGPDGVRVNALAPGPVETSMNGTI 187
                                       ******************************9876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.2   3.3e-22   6.7e-19       4     166 ..       4     163 ..       2     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 3.3e-22
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tGG+Gg+G+++++    + +++ v++s + + ++ +++l+a   a  a+ +++++Dv+d+d+vea  ee++a+ +
  gi|313116997|ref|YP_004038121.1|   4 VVTGGTGGIGRAVVE----RKRESDVVFSYH-RDEDGASELVADTDAETATTQALQLDVTDADSVEAFAEEATATLD 75 
                                       79********99865....555555666666.46777788************************************* PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esldffvlfSSiagllgsagqanYaaaNa 154
                                       ++ Gv+h+ g+++ +lle+ t++++ +v++  + G+  + +++ +   es   +v++SS++g+ g+   ++Yaa  +
  gi|313116997|ref|YP_004038121.1|  76 TVDGVVHTVGIVEPELLEQSTDDQWSRVIETNLIGSARVARAFLPalrESSGSLVFLSSVGGTAGTV-DTSYAASKS 151
                                       *******************************************988889999**********99986.578****99 PP

                                       HHHHHHHHHHHH CS
                                KR 155 flDalaeyrrsq 166
                                        l++l++  +++
  gi|313116997|ref|YP_004038121.1| 152 GLHGLVRALARE 163
                                       999999877665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.3   1.5e-10     3e-07       2     116 ..       4     135 ..       3     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.5e-10
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHHHT.....-S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfkeeq.....pd 66 
                                       +VtG+tG iG+a+v++  e   +v+   ++ +++++++ +d+       +  +ld+td++++e++ +e       +d
  gi|313116997|ref|YP_004038121.1|   4 VVTGGTGGIGRAVVERKRES--DVVFSYHRDEDGASELVADTdaetattQALQLDVTDADSVEAFAEEATatldtVD 78 
                                       7**************98875..6999999999999999999899******************999988532222279 PP

                                       EEEE--S..---HHHHHHSH..HHHHHHHTHHHHHHHHHHH...HHTCTEEEEEEEG CS
                         Epimerase  67 avihlAa..vggvaassedp..adfieknlqgtlnlleaar...kagvkrllflsSs 116
                                        v+h  +  +    ++s+d   +++ie+nl+g+ +++ a     +     l+flsS+
  gi|313116997|ref|YP_004038121.1|  79 GVVHTVGivEPELLEQSTDDqwSRVIETNLIGSARVARAFLpalRESSGSLVFLSSV 135
                                       9****8743334434443332267999*********99988444445559*****93 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.3e-07   0.00027       2     127 ..       4     133 ..       3     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.... CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel.. 76 
                                       +vtG++G iG+++v++  k++   ++ + rdE    e+  ++++e+++++      ++  dv+d++++e   ee   
  gi|313116997|ref|YP_004038121.1|   4 VVTGGTGGIGRAVVER--KRESDVVFSYHRDEDGASELVADTDAETATTQ------ALQLDVTDADSVEAFAEEAta 72 
                                       79************98..556677999*********99999765554433......344688888888877765422 PP

                                       ...T-SEEEE------HHHHHH....SHHHHHHHHHHHHHHHHHH...HHHTT-SEEEEEE CS
                   Polysacc_synt_2  77 ...kvdvvfhaAAlKhVPlvee....npleaiktNvlgtenviea...aieagvkkvvliS 127
                                          +vd v+h+  + +  l+e+    ++  +i+tN +g+  v++a   a++    ++v++S
  gi|313116997|ref|YP_004038121.1|  73 tldTVDGVVHTVGIVEPELLEQstddQWSRVIETNLIGSARVARAflpALRESSGSLVFLS 133
                                       22368999******99999987333357899***********9984444555555666666 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.9     3e-06     0.006       1      64 [.       7      73 ..       7     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3e-06
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH.....CTTTCEEEE--TT-CCHHHHHHTT-SEE CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaele.....aeeglevvegdvtdvedlaealkgadaV 64
                                      G+tG++Gr++v++  ++ +  v  + R+++ ++el      +++ ++++++dvtd++++++  + a a 
  gi|313116997|ref|YP_004038121.1|  7 GGTGGIGRAVVERKRES-D-VVFSYHRDEDGASELVadtdaETATTQALQLDVTDADSVEAFAEEATAT 73
                                      9***********88887.3.7899*****99997753443344677899*********99988866654 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.2e-05     0.025       1      78 [.       4      88 ..       4     141 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk....viegDvtdkdklee.......alegvd 68
                                      vvtGg+G +Gra+v++  + +    v     r+++  +e +  ++ ++     ++ Dvtd+d++e+        l+ vd
  gi|313116997|ref|YP_004038121.1|  4 VVTGGTGGIGRAVVERKRESD----VVFSYHRDEDGASELVADTDAETattqALQLDVTDADSVEAfaeeataTLDTVD 78
                                      8***********998754444....3333333333333333333333222349**********9871111111344555 PP

                         3Beta_HSD 69 vvihlaslvd 78
                                       v+h+ ++v+
  gi|313116997|ref|YP_004038121.1| 79 GVVHTVGIVE 88
                                      6666666664 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   3.2e-05     0.064       2      79 ..       4      79 ..       3      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                      EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP  2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkegdlvvnls 77
                                      ++ G+ G++G+av+e   r++dv   +   +r+++++ +l+a++     + +a +ld+ + ++ ++a  +e+++ ++ +
  gi|313116997|ref|YP_004038121.1|  4 VVTGGtGGIGRAVVERK-RESDV---VFSYHRDEDGASELVADTdaETATTQALQLDVTDADS-VEAFAEEATATLDTV 77
                                      566777********985.55677...899*************998889999999*********.999999998888876 PP

                                      SG CS
                   Sacchrp_dh_NADP 78 pp 79
                                        
  gi|313116997|ref|YP_004038121.1| 78 DG 79
                                      55 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     3e-05      0.06       1      52 [.       1      72 [.       1     134 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3e-05
                                      EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.....................T--TTSHHHHHHHHHHH-- CS
                     RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre.....................eldltdaeavaellkeakp 52
                                      m ++vtG++G +G++++++ +e++  v + +r+                     +ld+tda++v+++ +ea  
  gi|313116997|ref|YP_004038121.1|  1 MGLVVTGGTGGIGRAVVERKRESD-VVFSYHRDedgaselvadtdaetattqalQLDVTDADSVEAFAEEATA 72
                                      6689*****************999.6777777779******************************99988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1608.11
//
Query:       gi|313116998|ref|YP_004038122.1|  [L=276]
Description: phosphomethylpyrimidine kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-84  281.0   0.2    8.7e-84  280.7   0.2    1.0  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    7.9e-08   32.0   0.9    1.8e-07   30.8   0.9    1.5  1  PfkB          pfkB family carbohydrate kinase
     0.0084   15.6   0.0      0.011   15.2   0.0    1.2  1  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
      0.032   13.6   0.7       0.19   11.1   0.7    2.0  1  HK            Hydroxyethylthiazole kinase family


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.7   0.2   1.9e-87   8.7e-84       1     241 [.      19     258 ..      19     262 .. 0.98

  Alignments for each domain:
  == domain 1  score: 280.7 bits;  conditional E-value: 1.9e-87
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds+GGAGiqADlkt++ lgvyg svi  +t qnt+gv++ h lp+e ++aq++av +d+++ avK+Gmla+a+++++
  gi|313116998|ref|YP_004038122.1|  19 DSGGGAGIQADLKTMTRLGVYGGSVIVGVTSQNTRGVRSTHVLPSEEIRAQFDAVHDDFDIGAVKLGMLATADAVRT 95 
                                       9**************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHT CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllkl 154
                                       v ++l+ y+  vV+DPVmva sg++lle +a++a+++ L+ +at++tPN +E+e+L+ge  ++ +  ++aa+++ + 
  gi|313116998|ref|YP_004038122.1|  96 VDDCLDAYDGAVVIDPVMVAASGDRLLELDAIDAYTD-LFAQATLVTPNADETEELTGEWPDSDDARDAAASQFFEW 171
                                       ************************************9.********************9999999999********* PP

                                       T-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 155 gakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvtea 231
                                       ga+aVl kGgh+ ++ ++++d+l+++++ +++ ++ri+t++thG+GCtlssaiaa+la+g++l +Av+++ ++v++a
  gi|313116998|ref|YP_004038122.1| 172 GADAVLFKGGHVAENGDEIRDILVTQDGSQTFASPRIDTETTHGSGCTLSSAIAARLARGDDLSTAVERGISFVRAA 248
                                       ***************************************************************************** PP

                                       HHCG-BSTSS CS
                      Phos_pyr_kin 232 ikealelgkg 241
                                       i++  ++g++
  gi|313116998|ref|YP_004038122.1| 249 IERPAAVGEN 258
                                       **99999953 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.9   4.1e-11   1.8e-07     150     291 ..      98     250 ..      77     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 4.1e-11
                                       HHHHHHHHTTEEEEEECESSSHH.....HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSS CS
                              PfkB 150 elaeaaknggtfdpnlldplgaq.....fkeallellaladllkpneeElealtgekledieealaalhklkakgak 221
                                          +a   +   dp++++++g+      + +a+ +l+a+a+l++pn++E e+ltge  ++ +   aa+ ++ + ga+
  gi|313116998|ref|YP_004038122.1|  98 DCLDAYDGAVVIDPVMVAASGDRlleldAIDAYTDLFAQATLVTPNADETEELTGEWPDSDDARDAAASQFFEWGAD 174
                                       4455555555589999999998899999*****************************9888888888999999999* PP

                                       EEEEEEG...GGEEEEEE....TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHT CS
                              PfkB 222 tvvvtlG...keGalvve....kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvq 291
                                        v+++ G   ++G  + +    +dg++ + + p ++   t G G +  ++++a l++g +l +a++++  +  ++++
  gi|313116998|ref|YP_004038122.1| 175 AVLFKGGhvaENGDEIRDilvtQDGSQTFAS-PRIDTETTHGSGCTLSSAIAARLARGDDLSTAVERGISFVRAAIE 250
                                       ****998443344333335554778878888.8899999****************************9766666655 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-06     0.011     104     217 ..     121     244 ..      47     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-06
                                       GGSGGGG.....TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEESTT.........SEEEE CS
                       Carb_kinase 104 Lnllaqkne..lserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkgek.........dvivs 169
                                       L  l+   +  +  + +++  TP++ E + L++    ++d r  +a+++ +     vl kg +         d++v+
  gi|313116998|ref|YP_004038122.1| 121 LLELDAI-DayTDLFAQATLVTPNADETEELTGEWPDSDDARDAAASQFFEWGADAVLFKGGHvaengdeirDILVT 196
                                       3333332.2457788999******************999**************99****998655555555589999 PP

                                       CTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHH CS
                       Carb_kinase 170 pegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawl 217
                                       ++g  +  s      ++ GsG +L+ +i+a La   +   a+  + + 
  gi|313116998|ref|YP_004038122.1| 197 QDGSQTFASPRIDTETTHGSGCTLSSAIAARLARGDDLSTAVERGISF 244
                                       999999999999999999***********9999998777776555554 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   4.2e-05      0.19     183     225 ..     213     254 ..      77     270 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.2e-05
                                       STTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHH CS
                                HK 183 itasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaar 225
                                         +sGC+l+s++aa la   d+l +ave  +++  A+ e  a 
  gi|313116998|ref|YP_004038122.1| 213 THGSGCTLSSAIAARLAR-GDDLSTAVERGISFVRAAIERPAA 254
                                       459*************96.556666666555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2020.03
//
Query:       gi|313116999|ref|YP_004038123.1|  [L=195]
Description: hypothetical protein Hbor_34660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-52  176.5   0.1      4e-52  176.2   0.1    1.1  1  DrsE_2    DsrE/DsrF/DrsH-like family
    3.1e-08   34.0   0.0    1.2e-07   32.1   0.0    1.8  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.2   0.1   4.4e-56     4e-52       4     153 .]      46     194 ..      44     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 176.2 bits;  conditional E-value: 4.4e-56
                                       EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG---TT--HHHHHHHHHS-SS--SSS-GGG CS
                            DrsE_2   4 klaiifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkeekkkvkkkslekmamkmvtrksklskmnmag 80 
                                       k++ii++kgtld+a+++lilAs+Aaa+g+evt+F+tFwGL il++e++k++k +s+++++m+m+++    + + m++
  gi|313116999|ref|YP_004038123.1|  46 KMSIIATKGTLDMAYPPLILASTAAAFGYEVTVFHTFWGLDILHEERSKDLKLSSVGNPNMPMPNAL--GALPGMDR 120
                                       89************************************************************98764..466899** PP

                                       HHHHHHHHHHHHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC-SEEEE CS
                            DrsE_2  81 igtkmmkkvmkekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeeadvnLf 153
                                       ++t+mmkk ++++++as+eeL++++ + gv+++aCqmt+dlmg+++++++ gv + +gaat ++++++adv+L+
  gi|313116999|ref|YP_004038123.1| 121 LTTEMMKKRIRDNDTASIEELIQTSLDLGVEFQACQMTIDLMGYDEDDFFSGVtTGVGAATAIQDMADADVQLM 194
                                       *****************************************************999****************96 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.3e-11   1.2e-07       5     109 ..      49     188 ..      46     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.3e-11
                                       EEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS................................. CS
                              DrsE   5 ilvtggpygseaarealelalaaaalghevsvffygdGvllllk................................. 48 
                                       i+ t+g  + ++a+ +l la  aaa+g+ev vf++  G  +l++                                 
  gi|313116999|ref|YP_004038123.1|  49 IIATKG--TLDMAYPPLILASTAAAFGYEVTVFHTFWGLDILHEerskdlklssvgnpnmpmpnalgalpgmdrltt 123
                                       666755..78899**************************************************************** PP

                                       ...---TGGGTS---GGGGGGCGGGT-EEEEEHHHHHHTT--GGGE-.T--EEEE-HHHHHHHHH CS
                              DrsE  49 ...gqtanpadeknlaellkalkeygvklyvCgqaakargldededl.gvgvevsglgelaelqn 109
                                          ++   ++d  ++ el+++  + gv++ +C+++ + +g+ded+ + gv+  v++++++ ++++
  gi|313116999|ref|YP_004038123.1| 124 emmKKRIRDNDTASIEELIQTSLDLGVEFQACQMTIDLMGYDEDDFFsGVTTGVGAATAIQDMAD 188
                                       *99888889999999***************************99877888888888887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1234.07
//
Query:       gi|313117000|ref|YP_004038124.1|  [L=80]
Description: disulfide bond formation regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-21   73.8   0.0      8e-21   73.7   0.0    1.0  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.25   11.3   0.0    1.3  1  DUF2249   Uncharacterized conserved protein (DUF2249)


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   8.9e-25     8e-21       2      70 .]       9      78 ..       8      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 8.9e-25
                                      EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTE.EEEEEE-GCC-EEEEEEE CS
                              TusA  2 elDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklgh.elveveeedgeyrivirk 70
                                      +lD++G+ CP+P++k+k+ +++l +g+vlev+a+d +++ di  +a+ +   el++++e dg+y+ +++k
  gi|313117000|ref|YP_004038124.1|  9 TLDVKGENCPMPVVKTKQGIDELTAGDVLEVVATDSGSMSDIAGWADTTDGvELLDQSEGDGVYTHYVQK 78
                                      89********************************************987655****************98 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.7e-05      0.25       1      33 [.       9      41 ..       9      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.7e-05
                           DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvn 33
                                      tlDv +   p +  ++ + +++L +G++le+v+
  gi|313117000|ref|YP_004038124.1|  9 TLDVKGENCPMPVVKTKQGIDELTAGDVLEVVA 41
                                      79*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 548.03
//
Query:       gi|313117001|ref|YP_004038125.1|  [L=392]
Description: Zn-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-20   72.3   4.8    7.4e-20   71.8   4.8    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.9e-09   37.4   0.0    5.6e-09   36.5   0.0    1.5  1  Rhodanese      Rhodanese-like domain
    0.00011   21.8   0.8    0.00031   20.3   0.9    1.7  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.069   13.0   0.0       0.12   12.3   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   4.8   1.7e-23   7.4e-20       5     197 .]     139     306 ..     135     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1.7e-23
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       ++ +yl+  dg++ +iD++     +   +    ++  + d+++ + TH H+DHi+g + l e+td+  +  a + + 
  gi|313117001|ref|YP_004038125.1| 139 GCLAYLVASDGEAAVIDPLRAFTDEYVQD----ARALGTDLTYALDTHVHADHISGIRTLSEQTDATAVLPAPAVAR 211
                                       6889**********************975....******************************************** PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                       + +  +                    ++e + dg++++++ + + +++++gh++g   y+ g+vlftGD l++++ +
  gi|313117001|ref|YP_004038125.1| 212 GVEYDV--------------------PFEQVADGDTLSVGNVDIEVIHTPGHTSGMTAYKVGDVLFTGDGLFTESVA 268
                                       ******....................*************************************************** PP

                                       CCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                       Lactamase_B 159 ridltlrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                       r dl   ++e+  ++  + y++  +k+  l++e++v+ +H
  gi|313117001|ref|YP_004038125.1| 269 RPDL--EDPEAATDAARTLYTSLTEKVLPLPDETVVApAH 306
                                       ****..8888888888888888888888********9888 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   1.2e-12   5.6e-09       1     105 [.      16     114 ..      16     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.2e-12
                         Rhodanese   1 sakelkellekgkva.llDvRppeeYekghI..pgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycd 74 
                                       ++++l + +++g+ a +lDvR+++ ++++hI  p+  ++    +++     + l+ +p++ll++ + +++t+ v+c+
  gi|313117001|ref|YP_004038125.1|  16 TPEQLNAQISDGDGAfILDVRSADNFDEWHIegPNVESL---NYPY----FELLDGIPDDLLAQ-LPEDRTITVLCA 84 
                                       6899999998888778***************44333333...2233....33333344444443.6679******** PP

                         Rhodanese  75 gggraaaaaallkklGyknvsvldGGfkawk 105
                                       +gg+++  a  +++ G  +v +l+ G+k+w+
  gi|313117001|ref|YP_004038125.1|  85 KGGSSEMIAESIQEEG-FDVNHLERGMKGWA 114
                                       ****7777888888**.7************7 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.39   1.7e+03      58     135 ..      79     150 ..      67     177 .. 0.64
   2 !   20.3   0.9   6.8e-08   0.00031      22     110 ..     168     242 ..     151     277 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.39
                                       EEEE.EEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECT CS
                     Lactamase_B_2  58 lply.apkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegg 133
                                       ++++ a+ g ++ ++++++ + ++++ ++++    w    e ++ ++++ at a+   +       + +l+++++++
  gi|313117001|ref|YP_004038125.1|  79 ITVLcAKGGSSEMIAESIQEEGFDVN-HLERGMKGWARIYEYDELDVDVAATVAQYRRPS------SGCLAYLVASD 148
                                       55553444455555555555555555.555555557777777777777888877777777......77777777755 PP

                                       TE CS
                     Lactamase_B_2 134 gk 135
                                       g+
  gi|313117001|ref|YP_004038125.1| 149 GE 150
                                       54 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 6.8e-08
                                       -SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEE CS
                     Lactamase_B_2  22 velrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfel 98 
                                       ++++ +  ++   l th H+DH+ g+ tl e ++    ++  + v++ +e             v++++++ g+++++
  gi|313117001|ref|YP_004038125.1| 168 ARALGT--DLTYALDTHVHADHISGIRTLSEQTD-ATAVLPAPAVARGVEYD-----------VPFEQVADGDTLSV 230
                                       234455..8999999****************332.23344445566555555...........45566777777777 PP

                                       CSTTEEEEEEEE CS
                     Lactamase_B_2  99 gdggleitatpa 110
                                       g++++e+  tp 
  gi|313117001|ref|YP_004038125.1| 231 GNVDIEVIHTPG 242
                                       755544444443 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.7e-05      0.12       9      86 ..     142     243 ..     138     261 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                     Lactamase_B_3   9 sflletagarilvDPfka.nlgyeppaeeaDlvlisqaledHahletlkql........................ae 60 
                                       ++l+ ++g   ++DP +a + +y ++a +a    ++ al++H h++ + ++                        + 
  gi|313117001|ref|YP_004038125.1| 142 AYLVASDGEAAVIDPLRAfTDEYVQDA-RALGTDLTYALDTHVHADHISGIrtlseqtdatavlpapavargveyDV 217
                                       5789999*********99555555554.3334457889999999999999888888877777777777777666655 PP

                     Lactamase_B_3  61 nvkvleegeslevggleiravatshd 86 
                                        ++ +++g++l vg+++i+ ++t   
  gi|313117001|ref|YP_004038125.1| 218 PFEQVADGDTLSVGNVDIEVIHTPGH 243
                                       55556669999999999999998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2906.93
//
Query:       gi|313117002|ref|YP_004038126.1|  [L=164]
Description: transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-12   47.9  11.8    1.6e-12   47.6  11.8    1.1  1  Sulf_transp  Sulphur transport
  ------ inclusion threshold ------
      0.079   12.5   0.0       0.15   11.6   0.0    1.4  1  GXGXG        GXGXG motif


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6  11.8   1.8e-16   1.6e-12     172     306 ..      14     148 ..       6     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.8e-16
                       Sulf_transp 172 lfrkpwslvlgavllgllavlawllsak.tgrsfglgft.vpgakilqylvlgtskflnwgvvlvlGiilGaflaal 246
                                       + r+ w+++lg++l+gl a  ++l ++  +g s+ l  t + ++++ ++   +  +   w vv+  Gi+ Ga++  l
  gi|313117002|ref|YP_004038126.1|  14 FPRGIWPYLLGGLLVGLGASGIYLSTGLiAGASTFLESTlSYVSDVPRFNRSKYVQSRRWRVVFTAGIVSGAAVYGL 90 
                                       45789***********88877777654423444333333033445555555555556679***************** PP

                       Sulf_transp 247 lsgefkleapkarellaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvflll 306
                                       +     ++     + ++ l GG+l+G+G+rl+ GC++G+g+ g+ sls ++++ ++++l+
  gi|313117002|ref|YP_004038126.1|  91 VLDPGLWT--TDVQWWRLLGGGFLVGVGTRLGKGCTSGHGVCGLGSLSNTSVVNVLTFLA 148
                                       97777774..799**************************************996665554 PP

>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.7e-05      0.15     123     167 ..       8      53 ..       3      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                                       EEESEB.-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE-SSS CS
                             GXGXG 123 avvegv.gdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvldede 167
                                       +vv++     +  Y+ GG +v Lg  g ++++G+  G+  +l+++ 
  gi|313117002|ref|YP_004038126.1|   8 VVVGDLfPRGIWPYLLGGLLVGLGASGIYLSTGLIAGASTFLESTL 53 
                                       6666665556678************************988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1414.08
//
Query:       gi|313117003|ref|YP_004038127.1|  [L=154]
Description: transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-08   32.7  18.1    8.2e-08   32.2   7.4    2.0  2  Sulf_transp  Sulphur transport
  ------ inclusion threshold ------
       0.44    9.3   7.8       0.02   13.7   0.8    1.8  2  DUF2207      Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   4.6    0.0014        13      55      72 ..      12      29 ..       2      31 .. 0.84
   2 !   32.2   7.4   9.1e-12   8.2e-08       9     108 ..      35     139 ..      28     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0014
                       Sulf_transp 55 vglivGGllFGvGMalaG 72
                                       ++ +GGl+FG+G+a++G
  gi|313117003|ref|YP_004038127.1| 12 AAVYLGGLVFGFGLAISG 29
                                      5789************99 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 9.1e-12
                       Sulf_transp   9 airdivvekdgrllralllaiavaavgfqlla.aaglidlpks.......afpvvglivGGllFGvGMalaGgCasg 77 
                                        + d++ ++d+ l+ ++  a +v+av+f++ + +++ ++++         +f    ++vGG +FGvG  l+G C++ 
  gi|313117003|ref|YP_004038127.1|  35 VVLDFLQFNDFGLIFVMGGAAVVTAVVFAVATrYFDRAPITAReytrrvkEFD-RNVVVGGAIFGVGWGLSGICPGA 110
                                       56677778887777666656666665555444377777764431111111444.889******************** PP

                       Sulf_transp  78 tlyrvGeGslralitllffilgavalltgil 108
                                       +++  G G+   l++++++ lga+a  +g++
  gi|313117003|ref|YP_004038127.1| 111 AYASFGVGNYPILWAIAGMFLGAYA--QGLV 139
                                       ***********************98..4444 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.8   2.3e-06      0.02     380     452 ..       8      87 ..       2      89 .. 0.87
   2 ?    0.3   0.6     0.025   2.2e+02     389     436 ..      95     141 ..      84     151 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-06
                           DUF2207 380 lkklsalglgliilglilillallllvll.......lvfllilllillliaiivlllfsrllgrrteeGaellakwk 449
                                       l+ l a++lg++++g+ l++ +++   ++        ++l +++ + +++ ++v+++++r+++r     +e+ +++k
  gi|313117003|ref|YP_004038127.1|   8 LTFLAAVYLGGLVFGFGLAISGMARPEVVldflqfnDFGLIFVMGGAAVVTAVVFAVATRYFDRAPITAREYTRRVK 84 
                                       55678889999999999999888887777******9999999**********************9999999999999 PP

                           DUF2207 450 gFk 452
                                        F 
  gi|313117003|ref|YP_004038127.1|  85 EFD 87 
                                       885 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.025
                           DUF2207 389 gliilglilillallllvlllvfllilllillliaiivlllfsrllgr 436
                                       +++ +g+ l+ +  +++++ +++ + + ++++++++++ +++++l++ 
  gi|313117003|ref|YP_004038127.1|  95 AIFGVGWGLSGICPGAAYA-SFGVGNYPILWAIAGMFLGAYAQGLVRT 141
                                       3333333333222223333.7777777777777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1223.12
//
Query:       gi|313117004|ref|YP_004038128.1|  [L=53]
Description: hypothetical protein Hbor_34710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 393.80
//
Query:       gi|313117005|ref|YP_004038129.1|  [L=330]
Description: ribonucleotide reductase, beta subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-79  267.9   0.0    1.4e-79  267.5   0.0    1.1  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.5   0.0   7.8e-84   1.4e-79       2     279 .]      13     298 ..      12     298 .. 0.98

  Alignments for each domain:
  == domain 1  score: 267.5 bits;  conditional E-value: 7.8e-84
                                       T-TTS-SSHHHHHHHHHHHCT---GGGS-GHHHHHHHHS.TS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBS CS
                    Ribonuc_red_sm   2 fvlfpikypeiwelykkleanfWtpeevdlskDlkdwke.kLsedekefikkvlaflalldtivnenlverllsevq 77 
                                       +++ pi+y+++ ++y+  +an W+pee+++++D+++w+   Ls+ ek++++ +l+f+++++++ ++n+v++l+++v+
  gi|313117005|ref|YP_004038129.1|  13 NKILPIDYDWARQYYRDGVANNWVPEEIPMQEDIAQWNGdALSDSEKQLVEWNLGFFSTAESLTANNIVLALYEYVT 89 
                                       5789*********************************989************************************* PP

                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.-HHHHHHHHCHHHH-HHHHHHHHHHHHHHCTTTSC..........H CS
                    Ribonuc_red_sm  78 ipearafygfqaamEniHaesYsllletlvkdekekdelfnaieenpalqkkaewikkwyeskkde..........e 144
                                       +pe+r+++ +qa++E+iH++++ +++++l+ d++    ++ +++ +p++++k e++ +++++ +d+          +
  gi|313117005|ref|YP_004038129.1|  90 APECRQYLLRQAYEEAIHTDTFIYCCDSLGFDPE---YMYGMYDRVPSIKEKDEFVVDLTRNLDDPdftvedtadvR 163
                                       ******************************6665...7***********************999889*********9 PP

                                       HHHHHHHHHH.HHHHCCCHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS.HHHHHHHHHH CS
                    Ribonuc_red_sm 145 kfaerlvafa.llegilfysgFaailwlkkrgllpglaeiielilrDeglHtdfagllfkelkeen.elenkeleee 219
                                       ++++ lv f+ ++eg++fy+gFa++l lk+++++ g+++++e+i+rDe+lH+ f+++l++++++en + +++e+ +e
  gi|313117005|ref|YP_004038129.1| 164 DLLRDLVGFYvVMEGVFFYAGFAMMLALKRQNKMVGIGQQFEYIMRDESLHVGFGVDLINQIRAENpDAWTDEFGAE 240
                                       99********9****************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHTTT.BTTCHHHHHHHHHHHHHHHHHHCTT---SS-TT---C CS
                    Ribonuc_red_sm 220 veelikeavelEkefitdalpvellglnkedvkqYieyvadrllmnlgyeklYnveeenP 279
                                       v++li++av+lE+ ++++a+p ++lg++ +++ +Y+e+vadr+l +l++++ Y++  +nP
  gi|313117005|ref|YP_004038129.1| 241 VRDLIEKAVDLEQIYAREACPDDVLGMSPDQFAEYVEHVADRRLGQLDLDASYGT--DNP 298
                                       ******************************************************9..888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2430.83
//
Query:       gi|313117006|ref|YP_004038130.1|  [L=845]
Description: ribonucleoside-diphosphate reductase, alpha subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-182  608.1   0.0   1.5e-182  607.8   0.0    1.1  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    2.7e-21   75.4   0.0    2.1e-20   72.5   0.0    2.4  2  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
  ------ inclusion threshold ------
      0.077   13.5   0.2        5.1    7.7   0.0    2.7  2  TipAS            TipAS antibiotic-recognition domain
       0.16   12.5   0.2       0.61   10.7   0.2    2.0  1  ATP-cone         ATP cone domain


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.8   0.0  3.4e-186  1.5e-182       1     523 [.     224     758 ..     224     759 .. 0.97

  Alignments for each domain:
  == domain 1  score: 607.8 bits;  conditional E-value: 3.4e-186
                                       EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRr 77 
                                       ssC++++ved+le+I++++k+ a+lsk++gG+G ++++lRa+g+l+++t+ +++G v+f+k+ ++v+ +++  GkRr
  gi|313117006|ref|YP_004038130.1| 224 SSCYLTTVEDDLEHIFDSYKHHAQLSKWSGGLGNDWTNLRAEGALIESTGVESTGTVPFLKISNDVTAAINRSGKRR 300
                                       8**************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  78 GAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeee 154
                                       GAa++yle+wH+D+  f+d++ +ntg+e++r++++n++ +vpdlFme+v++d++wtLfsP++v++l+++ygeef e 
  gi|313117006|ref|YP_004038130.1| 301 GAACGYLEAWHMDFPAFLDLR-RNTGDERRRTHDMNTAAWVPDLFMERVENDETWTLFSPDEVPELHETYGEEFAEL 376
                                       *********************.99***************************************************** PP

                                       .................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                                       xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                   Ribonuc_red_lgC 155 yeeleekakik....kkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyes. 226
                                       y+e+eeka+ +     ++v+a +L++++++  +etg+P+++fkD +N r+++   ++g+++++NlC+Ei+l+++ + 
  gi|313117006|ref|YP_004038130.1| 377 YREYEEKAEAGelrqYETVDAADLWRTMLTRLFETGHPWITFKDPCNVRSPQ--DHVGTVHSSNLCTEITLNTSAEe 451
                                       *******8877787778***********************************..999***************99887 PP

                                       ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 227 vavCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladala 303
                                       +avCnL+s+nL+++v      + e d + l+++i++++r+Ldnv+d+ +yp+ e+e++++++R++GlGvmg++dal+
  gi|313117006|ref|YP_004038130.1| 452 HAVCNLGSVNLSNHV-----ADSELDREALADTIETATRMLDNVVDLCFYPTDEAEYSNMRHRPVGLGVMGFHDALM 523
                                       9**************.....4579***************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....X............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxx.......... RF
                   Ribonuc_red_lgC 304 klgipydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdef.....eeke.......... 365
                                       + g    seea++ a++  e+++y+++  S++lAkerg++++fe+sk+ +gilp d++     e  +          
  gi|313117006|ref|YP_004038130.1| 524 QVGTSMASEEAVEAANRWQEFVSYHTILNSSRLAKERGAYETFEGSKWDRGILPHDTVdrleaE--Rgreiptdrse 598
                                       **********************************************************665550..15566666677 PP

                                       ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 366 kedweeLreeikkyGlrnamvtalaPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwsee 442
                                       ++dw+++r++i+++G+rn++++a+aPT++iS i+gt+ +iePi++++y+ks+++g+f+++n++++++Lk++glw++e
  gi|313117006|ref|YP_004038130.1| 599 TMDWDRVRDHIAEHGMRNSNTMAIAPTATISTINGTTPSIEPIYSNLYVKSNMSGDFTVINEQLVDDLKAEGLWDDE 675
                                       ***************************************************************************** PP

                                       XXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 443 llkki...lesvqgleeipeeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwkl 516
                                       + ++i    +s+q++  ipee+++++++a++id+++ +++ a + +widqsiS+++++  + + + + ++y +Aw+l
  gi|313117006|ref|YP_004038130.1| 676 MVDQIkffDGSIQEVSAIPEEMRELYRSAFEIDPRHQLRLTAHRGQWIDQSISHNVFF-PSTDGSLLDDVYKTAWRL 751
                                       *****999999***********************************************.67799************* PP

                                       XXXXXXX CS
                                       xxxxxxx RF
                   Ribonuc_red_lgC 517 GlKgvty 523
                                       G+K+++y
  gi|313117006|ref|YP_004038130.1| 752 GVKTTYY 758
                                       *****99 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.33   1.5e+03       3      28 ..      70      95 ..      69      97 .. 0.82
   2 !   72.5   0.0   4.7e-24   2.1e-20       2      82 ..     145     220 ..     144     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.33
                   Ribonuc_red_lgN  3 ltynalkvledrYllkdengeivEsp 28
                                      ++y a+ + ++rY+++   +++ E+ 
  gi|313117006|ref|YP_004038130.1| 70 YKYVAADIHRRRYFRRVTGEQLSETA 95
                                      6799999********99966787775 PP

  == domain 2  score: 72.5 bits;  conditional E-value: 4.7e-24
                   Ribonuc_red_lgN   2 kltynalkvledrYllkde.ngeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmn 77 
                                       k++y+a+ +l +rY++k+e +g+++E pq ++mRvA++lai+e      ++ +++a efyd++s++ f+p++Ptl+ 
  gi|313117006|ref|YP_004038130.1| 145 KFDYIAMSTLTQRYFIKTEvDGDPLELPQAFWMRVAMGLAIEE------DDPQARALEFYDVLSRLLFTPSTPTLFH 215
                                       79*****************888*******************77......59************************** PP

                   Ribonuc_red_lgN  78 aGtel 82 
                                       +Gt +
  gi|313117006|ref|YP_004038130.1| 216 SGTTH 220
                                       **976 PP

>> TipAS  TipAS antibiotic-recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.038   1.7e+02      33      75 ..     369     410 ..     349     422 .. 0.70
   2 ?    7.7   0.0    0.0011       5.1      46      73 ..     521     548 ..     517     564 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.038
                                       XXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TipAS  33 lkaelkelfaklaaalaagkdpdseeaqelaeehralieefwg 75 
                                       + +e++el+++  +  +ag+   + e  ++a+ +r+++++ ++
  gi|313117006|ref|YP_004038130.1| 369 YGEEFAELYREYEEKAEAGE-LRQYETVDAADLWRTMLTRLFE 410
                                       44567777777777766666.7777777778888888777665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
                                       XX..XXXXXXXXXXXXXXXXXXXXXXXX CS
                             TipAS  46 aalaagkdpdseeaqelaeehralieef 73 
                                       a+++ g++ +seea e+a +++++++++
  gi|313117006|ref|YP_004038130.1| 521 ALMQVGTSMASEEAVEAANRWQEFVSYH 548
                                       78899********************965 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00014      0.61      28      81 ..      22      80 ..       4      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                      H.-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHH....HSS-HHHHHHHHHHH CS
                          ATP-cone 28 g.seeeideiaeeveaevrkrlrdgisteeIqdlvektli....ehpdyavaaayilyr 81
                                      g ++   de+ ++++ e +++l+dg s++e+ + +e +      + p y+++aa i  r
  gi|313117006|ref|YP_004038130.1| 22 GyEDVLTDEVMDRLVTETERNLYDGASIDEVYEALEGVTTarieRDPAYKYVAADIHRR 80
                                      35566689999999**********************98888899999*****9988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (845 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 5165.02
//
Query:       gi|313117007|ref|YP_004038131.1|  [L=169]
Description: transcriptional regulator NrdR [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-15   56.9   0.1    3.3e-15   56.4   0.1    1.2  1  ATP-cone       ATP cone domain
     0.0017   18.3   1.5     0.0026   17.7   1.5    1.3  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.6   3.2      0.019   14.8   3.2    1.4  1  TFIIS_C        Transcription factor S-II (TFIIS)
      0.089   12.3   3.4       0.12   11.9   0.6    2.4  2  TF_Zn_Ribbon   TFIIB zinc-binding
      0.092   12.8   0.4       0.16   12.1   0.1    1.6  2  Elf1           Transcription elongation factor Elf1 like
       0.23   11.3   0.6        1.4    8.8   0.1    2.0  2  zf-ZPR1        ZPR1 zinc-finger domain


Domain annotation for each model (and alignments):
>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.1   1.1e-18   3.3e-15       2      84 ..      50     135 ..      49     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.1e-18
                                       EEE-TTS-EEE--HHHHHHHHHHHHHH...-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHHHH CS
                          ATP-cone   2 kViKRdGtvepfdvekIkraiekAceg...seeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyavaa 75 
                                       +V+KRdG++epfd+ek++  ie+A+e+   +++ ++ ++e ve e+  r  + +s++ +++l  + l+e + +a+++
  gi|313117007|ref|YP_004038131.1|  50 QVKKRDGRIEPFDREKLRGGIERAVEKrpvDDDAVESLIEDVERELAGRETRIVSSSLVGELASERLRELDSVAYIR 126
                                       8****************************99999******************************************* PP

                                       HHHHHHHHH CS
                          ATP-cone  76 ayilyrnlr 84 
                                       + ++y+ + 
  gi|313117007|ref|YP_004038131.1| 127 FVSVYKAFS 135
                                       *****9875 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.5   8.8e-07    0.0026      21      45 ..       3      36 ..       1      37 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.8e-07
                     Zn_Tnp_IS1595 21 CPhCgsr..kayrikt.......rglfqCkeCrk 45
                                      CP Cg++  ++  ++t       r++ +Ck+C+ 
  gi|313117007|ref|YP_004038131.1|  3 CPDCGHDrtSVVDTRTgedgttvRRRRECKRCSF 36
                                      *******555555555****************85 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.2   6.2e-06     0.019       2      39 .]       2      39 ..       1      39 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.2e-06
                           TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvf..ykCtkCghrWr 39
                                       Cp Cg+++++ +   tR ++ ++tv    +C+ C +r++
  gi|313117007|ref|YP_004038131.1|  2 DCPDCGHDRTSVV--DTRTGEDGTTVRrrRECKRCSFRFT 39
                                      6**********87..9********9862268******996 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   4.1e-05      0.12       2      19 ..       2      20 ..       1      20 [. 0.88
   2 ?    0.1   0.1      0.19   5.7e+02       3      13 ..      31      41 ..      29      49 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                                      EETTTTCEE.CHEETSTTC CS
                      TF_Zn_Ribbon  2 kCPnCgstn.lveDperge 19
                                       CP+Cg+++  v+D+ +ge
  gi|313117007|ref|YP_004038131.1|  2 DCPDCGHDRtSVVDTRTGE 20
                                      5******8856******98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.19
                                      ETTTTCEECHE CS
                      TF_Zn_Ribbon  3 CPnCgstnlve 13
                                      C+ C+ +++++
  gi|313117007|ref|YP_004038131.1| 31 CKRCSFRFTTY 41
                                      88888777333 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.3e-05      0.16      23      58 ..       2      41 ..       1      51 [. 0.82
   2 ?   -3.8   0.0       4.8   1.4e+04      66      74 ..     128     136 ..     126     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
                              Elf1 23 dCpfCnheksvevkldkkek....iaevsCkvCgesfetk 58
                                      dCp C+h+++  v+  + e+    + + +Ck C+ +f+t 
  gi|313117007|ref|YP_004038131.1|  2 DCPDCGHDRTSVVDTRTGEDgttvRRRRECKRCSFRFTTY 41
                                      8***************9999555555668*****999975 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.8
                              Elf1  66 vDvYskwiD 74 
                                       v vY+ + D
  gi|313117007|ref|YP_004038131.1| 128 VSVYKAFSD 136
                                       779999988 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00047       1.4       2      41 ..       2      39 ..       1      55 [. 0.90
   2 ?    1.0   0.0      0.12   3.5e+02      99     152 ..      84     151 ..      76     156 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00047
                           zf-ZPR1  2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknn 41
                                      +Cp Cg+   +t ++ t+    +  +    eC++C ++ +
  gi|313117007|ref|YP_004038131.1|  2 DCPDCGH--DRTSVVDTRTGEDGTTVRRRRECKRCSFRFT 39
                                      7****84..599*************************976 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                           zf-ZPR1  99 vEGlLeqikeele..ke.........egdqaer...edeekekieeflekleeliegee...pftlildDp 152
                                       vE l+e++++el   ++         e   +er      +  ++ +f++  +++ + ee   ++  ildD 
  gi|313117007|ref|YP_004038131.1|  84 VESLIEDVERELAgrETrivssslvgE-LASERlreL--DSVAYIRFVSVYKAFSDPEEfldELDTILDDR 151
                                       899999999999765113444444421.222222111..22222333333333333332333666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1305.63
//
Query:       gi|313117008|ref|YP_004038132.1|  [L=336]
Description: Ca2+/Na+ antiporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-40  138.3  34.4    9.7e-22   77.6  13.2    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6  13.2   5.4e-26   9.7e-22       3     150 ..       9     162 ..       7     163 .. 0.83
   2 !   67.0  13.2   9.7e-23   1.7e-18       3     150 ..     182     323 ..     181     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 5.4e-26
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       +++++l++++i++++ +l +s + ++++ g++  v G ++ A g+s+pEl+s +++al+g+  l++g+++Gs+ifn+
  gi|313117008|ref|YP_004038132.1|   9 VGIILLATVGIYIGSGWLEQSSDTLSSYYGLPLVVQGAIVAAVGSSFPELASVVFSALSGSFGLGVGAIVGSAIFNI 85 
                                       6799************************************************************************* PP

                                       HTHHHHHHHHHHBTTSSCE.CCHHHHHHHHHHHHHHHHHHHTCHHHHH......HTEEHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdses.lkldlgllllvallllllvlllllplfv......pgrltvleglvllllYalylvls 149
                                       l++ +l+++++   ++s+  l ++   + ++a+ ++++++++ ++  +      +gr+t+  +++ l+lY+ly++++
  gi|313117008|ref|YP_004038132.1|  86 LVIPALSGIVTHDDIESSRtLVYKEAQFYMIAVSVVVITFAMAVIY-FpngaplTGRVTRPLAVMPLALYGLYIFIQ 161
                                       **********994444444122222333444444444444433333.35788************************9 PP

                                       H CS
                          Na_Ca_ex 150 l 150
                                       +
  gi|313117008|ref|YP_004038132.1| 162 Y 162
                                       7 PP

  == domain 2  score: 67.0 bits;  conditional E-value: 9.7e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       +++++++l++i v+ + lv ++  ++++ g ++ + G+t+lA+++slp++++s+ aa+ g +  +++nvlGsn+f+l
  gi|313117008|ref|YP_004038132.1| 182 WGTLVAGLIVILVSVEQLVHAVKFVGNVYGAPDFLWGITVLAAATSLPDTLVSVRAAKDGRGVTSLANVLGSNTFDL 258
                                       6799************************************************************************* PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       l+ i++ +li +       +++ + +  ++ +l l++vll +++l+++  lt  e+  ll++Y+ ++++++
  gi|313117008|ref|YP_004038132.1| 259 LVAIPIGVLIVG----AAPINFAI-AVPTMGFLTLATVLL-FTVLRTDLSLTDGEAYGLLVAYIGFVLWMI 323
                                       **********44....22333333.334444444443444.5566789*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2092.85
//
Query:       gi|313117009|ref|YP_004038133.1|  [L=121]
Description: hypothetical protein Hbor_34770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 861.29
//
Query:       gi|313117010|ref|YP_004038134.1|  [L=320]
Description: fructosamine-3-kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-19   69.8   4.3    5.7e-19   69.0   4.3    1.5  1  APH              Phosphotransferase enzyme family
    2.2e-07   30.4   0.0    2.2e-06   27.1   0.0    2.4  1  Fructosamin_kin  Fructosamine kinase
      0.006   16.6   0.0      0.012   15.7   0.0    1.4  1  DUF4128          Bacteriophage related domain of unknown func
  ------ inclusion threshold ------
      0.095   12.9   0.4       0.27   11.5   0.4    1.7  1  HD               HD domain


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   4.3   1.3e-22   5.7e-19       6     210 ..      27     241 ..      24     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 1.3e-22
                                       --.SSCEEEEEEETT.--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE----E CS
                               APH   6 sggasnrtylvttpa.gryvlrrnpparaaeeirrevallrlLakagv.pvPevlagdtddeeigllfalieyvpgr 80 
                                       s +a nrt+ v  ++ +r++l+++  +    +i+re a+  ++ ++ + +vP v+a++t + + +l  + ++++p +
  gi|313117010|ref|YP_004038134.1|  27 SWNAQNRTVAVDFGDgQRVFLKVAVNG-DRSRIERERAVISYVGANCAvSVPNVIATETTGPVPYLATEPVSGQPLT 102
                                       56789**********67**********.9***************77777*******877777777777777777777 PP

                                       E-SSHHHHHHHHHHHHHHHHHHCCHHCH..........-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCC.HHHH CS
                               APH  81 sllrklsaaqlpellealgeflaalhqv.........dpaalpladflaqdlellrqlesatarllaselld.llee 147
                                       +ll   +  ++ +l+ ++g++la++h++         +++a++l+ ++ ++ ++l    s+++   +++ +d   e 
  gi|313117010|ref|YP_004038134.1| 103 TLLADATRTERAALAHDVGSALARVHDCrfeehghvvGGDADHLELDTGTWTDVLVETISEMREMAPCDRFDqHFEM 179
                                       7777888999******************5555544443445555555556677777777777777777777722223 PP

                                       HHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH....H CS
                               APH 148 leeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll....r 210
                                       + ++v + +++l +   +++llHgD+  +N   +  ++ v G++D+e++++g+p+ D   +l    +
  gi|313117010|ref|YP_004038134.1| 180 VSDAVERNRDRLDR--ASATLLHGDPACPNCFRT--GDGV-GFLDWELSHVGDPVRDRSRTLdqqfD 241
                                       33335555555555..8*****************..7888.9***************9999933322 PP

>> Fructosamin_kin  Fructosamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   4.9e-10   2.2e-06      31     282 ..      32     303 ..       1     309 [. 0.68

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.9e-10
                   Fructosamin_kin  31 neaylls.eeeqrfFvklnekealemFeaEaesLealaetqtirvPkvlavGelkdasfLvleyLelk......... 97 
                                       n+++ ++  + qr+F+k+  +  ++  e E + ++ + +  ++ vP+v+a+ ++    +L++e +  +         
  gi|313117010|ref|YP_004038134.1|  32 NRTVAVDfGDGQRVFLKVAVNGDRSRIERERAVISYVGANCAVSVPNVIATETTGPVPYLATEPVSGQplttllada 108
                                       344444467899**********************************************9999976433210111001 PP

                   Fructosamin_kin  98 ..lekkesaaelgqqLaklHraseqkefGfdvdntigktpqpNewqssWaeFfaeqRlgvqlel.akekglefakie 171
                                         +e++  a+++g++La++H      +f  +   + g+       +  W++   e   ++   + + + + +f+ ++
  gi|313117010|ref|YP_004038134.1| 109 trTERAALAHDVGSALARVHD----CRFEEHGHVVGGDADHLELDTGTWTDVLVETISEMREMApCDRFDQHFEMVS 181
                                       012233345667788888887....3444444556678888888889999998887555543331344444588888 PP

                   Fructosamin_kin 172 elvervaellskhqpkpsllHGdLWsgNaaltkdge.......pvifdPaayygdrEvdlamtelf....ggfpsef 237
                                       + ver +++l     +++llHGd    N+ +t dg          + dP      r +d  + +l     +g  s+f
  gi|313117010|ref|YP_004038134.1| 182 DAVERNRDRLDR--ASATLLHGDPACPNCFRTGDGVgfldwelSHVGDPVRD-RSRTLDQQFDSLRegspEGVVSAF 255
                                       888888888865..5678****************977777777666666432.23444555555541111567789* PP

                   Fructosamin_kin 238 yegYqsiv.pldegyeeRkelYqLYhlLnhlnlF..gggylsqaqkli 282
                                       y+gY+s    l +g+eeR+++Y++  lL  +  F   ++y++++++ +
  gi|313117010|ref|YP_004038134.1| 256 YDGYRSQAgGLPSGFEERRPIYEVIRLLSVSGYFerTADYRDESRSDL 303
                                       ****98652799*****************9999944467877776655 PP

>> DUF4128  Bacteriophage related domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.6e-06     0.012      17      63 ..      70     116 ..      58     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-06
                           DUF4128  17 palpvawpnvkftpptge.pYLrvsvvpadtepltlggdddrrrtGlf 63 
                                       ++++v +pnv +t++tg  pYL+ + v++++ ++ l+ d++r++++ +
  gi|313117010|ref|YP_004038134.1|  70 ANCAVSVPNVIATETTGPvPYLATEPVSGQPLTTLLA-DATRTERAAL 116
                                       68****************9******************.8888777654 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4     6e-05      0.27      24      93 ..     107     169 ..      98     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                                       HHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHH CS
                                HD  24 drellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldledvaklirehheswe 93 
                                       d  +++ aaL HD+G  + +        +  +f++H  v    + ++e++ g+ ++ ++++i+e++e+ +
  gi|313117010|ref|YP_004038134.1| 107 DATRTERAALAHDVGSALARV-------HDCRFEEHGHVVGGDADHLELDTGTWTDVLVETISEMREMAP 169
                                       5667999***********554.......334555666666666999999998889999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2324.93
//
Query:       gi|313117011|ref|YP_004038135.1|  [L=342]
Description: subtilisin-like serine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.6e-27   94.0   2.2    1.9e-26   93.0   2.2    1.4  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   2.2   1.1e-30   1.9e-26       1     266 [.      41     260 ..      41     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 1.1e-30
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g+g +vav+D+Gvd +h  +         +          ++++ + t  +++  dd g    HGt vAG++a    
  gi|313117011|ref|YP_004038135.1|  41 GRGLTVAVMDSGVDETHEVFD-------GI----------TVEHHNFTDAPDEPLDDVG----HGTAVAGLIAQL-- 94 
                                       89*****************66.......33..........4555555555555555555....**********99.. PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHH..CT-SEEEE-EESCETTCHHCHHHHHHHHHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaae..dkvdvinmslgestslpktgrsiealainravn 152
                                           + g+    ki ++++++tsg     ++ + +a e+a    d+ d in+s+g+ ++ ++ +r ++     +++ 
  gi|313117011|ref|YP_004038135.1|  95 ----SPGIE---KIVDLRIFGTSGRGT--SKPIFDAYEWAQThaDELDTINLSWGARSQSSEIDREHS-----KLM- 156
                                       ....55555...899*****9999765..3899999999877456777*******8888888888765.....666. PP

                                       CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-.CCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                      Peptidase_S8 153 kkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgn.ivstw 228
                                       + gv  v+SaGN g         ++ g+p t++ + ++ga+t+e+++  fSs+ p +    +pd+va G +  ++ +
  gi|313117011|ref|YP_004038135.1| 157 NAGVQDVVSAGNTG---------ETSGSPVTANDAYGIGAITEEKELTRFSSYNPGI--VENPDVVALGKDvRLPRA 222
                                       677889********.........88999999999*********************98..59**********777888 PP

                                       CCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 229 srqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalp 266
                                       s+ s  +    +y + sGTS+++P a++a+ l ++  +
  gi|313117011|ref|YP_004038135.1| 223 SNTSMGTVLNDDYVKASGTSFSAPIATAAMNLFIEQRE 260
                                       888877777777****************9988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 2104.50
//
Query:       gi|313117012|ref|YP_004038136.1|  [L=199]
Description: hypothetical protein Hbor_34800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-18   65.4  19.6    5.3e-18   65.4  19.6    1.7  2  Rhomboid  Rhomboid family
  ------ inclusion threshold ------
        0.2   12.2   0.1        0.2   12.2   0.1    2.5  3  DUF1751   Eukaryotic integral membrane protein (DUF1751)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.14   1.2e+03      33      54 ..      16      38 ..      11      55 .. 0.43
   2 !   65.4  19.6   5.9e-22   5.3e-18       7     144 ..      56     196 ..      50     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.14
                                      HHHHHHHHH.HHHHHHHHHHHHH CS
                          Rhomboid 33 fGsplerrl.Gslrflllyllsg 54
                                      fG+p++++l   l + +l+ ++ 
  gi|313117012|ref|YP_004038136.1| 16 FGNPVAETLlAMLFVSVLTWTVS 38
                                      44444444311111112222222 PP

  == domain 2  score: 65.4 bits;  conditional E-value: 5.9e-22
                                       TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S.....-EESSHHHHHH CS
                          Rhomboid   7 lwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses..plvGaSGaifg 81 
                                        w+l+ts+  H+g  Hll N++++l+ G+ + +   +lrf ++++ +g +++l+++++    +    ++G SGa f+
  gi|313117012|ref|YP_004038136.1|  56 PWTLVTSVYAHVGPGHLLSNAVIVLLAGTLVSMSTTRLRFHAFFVGTGALAGLAHVWLAGLFGVpsAVLGSSGAAFA 132
                                       6*********************************************************9999887799********* PP

                                       HHHHHHHHHHCCCCGS----HC....CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHH CS
                          Rhomboid  82 llgallvlvprnrkllrkliia.llllllfillnlvlgllpraggvsnlAHlgGllaGlllgll 144
                                       l+g++l+  p +   l++l +    ++++++++ lvl +l +a+g + +AH++G+++Gl++g+l
  gi|313117012|ref|YP_004038136.1| 133 LVGYVLAANPASSAILDRLRLSsRAVIAIVAIVALVLTVLFSAPGSALIAHFTGAVMGLIAGRL 196
                                       *****************9999974555555555555555555578**************99876 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.69   6.2e+03      15      23 ..      28      36 ..      19      47 .. 0.46
   2 ?   12.2   0.1   2.3e-05       0.2       7      64 ..      55     112 ..      50     139 .. 0.86
   3 ?    1.0   0.2      0.07   6.3e+02      59      86 ..     160     187 ..     150     196 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.69
                           DUF1751 15 sfveqnvwk 23
                                       fv +  w+
  gi|313117012|ref|YP_004038136.1| 28 LFVSVLTWT 36
                                      222222222 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.3e-05
                           DUF1751   7 ypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvl 64 
                                        pwtl+t+ +  +   ++l +++++ll+g+++  +  +  +  F++ ++ +++l  v 
  gi|313117012|ref|YP_004038136.1|  55 PPWTLVTSVYAHVGPGHLLSNAVIVLLAGTLVSMSTTRLRFHAFFVGTGALAGLAHVW 112
                                       59*****************************999888888888888877777776655 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.07
                           DUF1751  59 nllvvlltlllylvtkseelllvpisGl 86 
                                       +++++++ +l++l+++  ++l +++ G+
  gi|313117012|ref|YP_004038136.1| 160 AIVAIVALVLTVLFSAPGSALIAHFTGA 187
                                       4555555555555555555565666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1318.39
//
Query:       gi|313117013|ref|YP_004038137.1|  [L=80]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-08   31.9   0.0    1.1e-07   31.3   0.0    1.3  1  HTH_24       Winged helix-turn-helix DNA-binding
    6.8e-07   29.1   0.1    8.1e-07   28.8   0.1    1.1  1  MarR_2       MarR family
    1.1e-06   28.5   0.0    1.3e-06   28.2   0.0    1.2  1  HTH_11       HTH domain
    2.5e-05   23.8   0.1    3.6e-05   23.3   0.1    1.2  1  GntR         Bacterial regulatory proteins, gntR family
     0.0003   20.5   0.2    0.00044   20.0   0.2    1.2  1  HTH_DeoR     DeoR-like helix-turn-helix domain
    0.00078   18.9   0.0      0.001   18.6   0.0    1.2  1  HTH_CodY     CodY helix-turn-helix domain
     0.0011   18.8   0.1     0.0018   18.1   0.1    1.4  1  HTH_5        Bacterial regulatory protein, arsR family
     0.0016   18.3   0.1     0.0025   17.7   0.1    1.2  1  MarR         MarR family
     0.0018   18.2   0.0     0.0034   17.3   0.0    1.6  1  HTH_36       Helix-turn-helix domain
      0.002   18.0   0.0     0.0023   17.9   0.0    1.2  1  HTH_Crp_2    Crp-like helix-turn-helix domain
     0.0021   17.9   0.1     0.0025   17.6   0.1    1.1  1  HxlR         HxlR-like helix-turn-helix
     0.0021   18.1   0.1     0.0029   17.6   0.1    1.2  1  HTH_20       Helix-turn-helix domain
     0.0041   17.6   0.1     0.0051   17.3   0.1    1.2  1  HTH_27       Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.013   15.4   0.0    1.1  1  TFIIE_alpha  TFIIE alpha subunit
      0.013   15.3   0.0      0.017   15.0   0.0    1.2  1  TrmB         Sugar-specific transcriptional regulator TrmB
      0.016   15.3   0.0      0.022   14.9   0.0    1.3  1  HTH_28       Helix-turn-helix domain
      0.026   14.9   0.0      0.037   14.4   0.0    1.2  1  Rrf2         Transcriptional regulator
      0.064   13.3   0.0       0.08   13.0   0.0    1.2  1  HTH_54       ParA helix turn helix domain
      0.071   12.5   0.0      0.085   12.3   0.0    1.1  1  RepL         Firmicute plasmid replication protein (RepL)
       0.14   12.1   0.0       0.17   11.8   0.0    1.1  1  HTH_43       Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   1.2e-10   1.1e-07      11      47 ..      24      60 ..      21      61 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.2e-10
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +L+++++++q eL +r+ lS  tv+  l++Le +G++
  gi|313117013|ref|YP_004038137.1| 24 VLKQESHLTQGELTDRTQLSTRTVRDALRKLEAAGIV 60
                                      7999*******************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   9.1e-10   8.1e-07      12      61 ..      23      70 ..      12      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 9.1e-10
                                      HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      ++L  +    lt+gel++r++ls  +v  +l++L+aaG v +  +++D+R
  gi|313117013|ref|YP_004038137.1| 23 FVLKQESH--LTQGELTDRTQLSTRTVRDALRKLEAAGIVHEDVCLRDAR 70
                                      45556666..9*****************************9999999999 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.5e-09   1.3e-06       5      44 ..      20      59 ..      17      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.5e-09
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                       ++++l+++++++  eL +++ +S+rtvr  +++Le++g+
  gi|313117013|ref|YP_004038137.1| 20 FVHFVLKQESHLTQGELTDRTQLSTRTVRDALRKLEAAGI 59
                                      678888********************************94 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1     4e-08   3.6e-05      18      55 ..      25      61 ..      21      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4e-08
                                      S-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 18 lrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      l+ ++ L ++ eL ++   s+ tvR ALr+Lea+g+v+
  gi|313117013|ref|YP_004038137.1| 25 LKQESHL-TQGELTDRTQLSTRTVRDALRKLEAAGIVH 61
                                      6778999.****************************96 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   4.9e-07   0.00044       8      45 ..      24      61 ..      19      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.9e-07
                          HTH_DeoR  8 llkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                       lkq+ +l+  el+++ + S+ T+R  L++Le++g+++
  gi|313117013|ref|YP_004038137.1| 24 VLKQESHLTQGELTDRTQLSTRTVRDALRKLEAAGIVH 61
                                      589********************************975 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06     0.001       2      35 ..      28      61 ..      27      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                          HTH_CodY  2 eGrLtaskiaDriGitrsvivnaLrkLesaGiie 35
                                      e  Lt  ++ Dr  +    + +aLrkLe+aGi+ 
  gi|313117013|ref|YP_004038137.1| 28 ESHLTQGELTDRTQLSTRTVRDALRKLEAAGIVH 61
                                      78899999*****99888889***********85 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     2e-06    0.0018      13      46 ..      28      61 ..      21      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                                      TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 13 egelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      e+ l+ +el++ ++ls  tv+  L+kL+ aG+V+
  gi|313117013|ref|YP_004038137.1| 28 ESHLTQGELTDRTQLSTRTVRDALRKLEAAGIVH 61
                                      355999***************************6 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.8e-06    0.0025      12      57 ..      25      70 ..      23      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-06
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                      l+++  l++ eL ++ ++s+ tv  +l++Le +G ++   + +D R
  gi|313117013|ref|YP_004038137.1| 25 LKQESHLTQGELTDRTQLSTRTVRDALRKLEAAGIVHEDVCLRDAR 70
                                      7888889****************************98777666666 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.8e-06    0.0034      27      55 .]      32      60 ..      12      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.8e-06
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      +q  l  r+ ls +Tv+ a+++Le +G++
  gi|313117013|ref|YP_004038137.1| 32 TQGELTDRTQLSTRTVRDALRKLEAAGIV 60
                                      6788999********************85 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.5e-06    0.0023      20      59 ..      29      66 ..       9      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrgrriri 59
                                       +ltq el ++  l+  tv  +l++L+ +g++     + +
  gi|313117013|ref|YP_004038137.1| 29 SHLTQGELTDRTQLSTRTVRDALRKLEAAGIVHED--VCL 66
                                      589****************************9843..444 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.8e-06    0.0025      22      66 ..      34      77 ..      19      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.8e-06
                                      HHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE- CS
                              HxlR 22 selkralpkisqkmLaqrLreLeqdglierevypevPpkveYslt 66
                                      +el+++  ++s+++    Lr+Le+ g+++ +v  +   k  Ysl 
  gi|313117013|ref|YP_004038137.1| 34 GELTDRT-QLSTRTVRDALRKLEAAGIVHEDVCLRDARKRVYSLE 77
                                      5777776.99********************************995 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   3.2e-06    0.0029      22      55 ..      28      61 ..      20      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.2e-06
                                      CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 22 aegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +  lt +el +r +ls  t+++ Lr+Le ag+v+
  gi|313117013|ref|YP_004038137.1| 28 ESHLTQGELTDRTQLSTRTVRDALRKLEAAGIVH 61
                                      5567889*************************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   5.7e-06    0.0051      11      64 ..      23      76 ..      15      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.7e-06
                            HTH_27 11 lirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64
                                       +  ++   ++ +l +r++++  ++  +l+kL+++G v++  + +d r + ++l
  gi|313117013|ref|YP_004038137.1| 23 FVLKQESHLTQGELTDRTQLSTRTVRDALRKLEAAGIVHEDVCLRDARKRVYSL 76
                                      5555666778899*********************************99999886 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.4e-05     0.013      16      58 ..      19      61 ..      15      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                      + v +vL +++ +t  +l   +++    +r +L +L  a++v 
  gi|313117013|ref|YP_004038137.1| 19 KFVHFVLKQESHLTQGELTDRTQLSTRTVRDALRKLEAAGIVH 61
                                      567789*********************************9996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.8e-05     0.017      17      54 ..      25      62 ..      19      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      L ++  +t  e+  ++ ++  +v ++Lr+Le +G+V+ 
  gi|313117013|ref|YP_004038137.1| 25 LKQESHLTQGELTDRTQLSTRTVRDALRKLEAAGIVHE 62
                                      4467789999**************************86 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.4e-05     0.022      13      41 ..      30      59 ..      20      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                            HTH_28 13 h.svreaArelgisrrtvyrWikryeegGi 41
                                      h ++ e+  + ++s rtv++ ++++e+ Gi
  gi|313117013|ref|YP_004038137.1| 30 HlTQGELTDRTQLSTRTVRDALRKLEAAGI 59
                                      568999999999*****************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.1e-05     0.037      22      56 ..      27      61 ..      20      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.1e-05
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +e++++  e+ +r+++s + ++  l+kL+ ag+v+
  gi|313117013|ref|YP_004038137.1| 27 QESHLTQGELTDRTQLSTRTVRDALRKLEAAGIVH 61
                                      4455999**************************97 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.9e-05      0.08      28      59 ..      31      62 ..      26      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-05
                            HTH_54 28 yskaalaklpklsrrkvdkavsemeaeGyefe 59
                                       ++++l+ +++ls r+v +a+ ++ea+G++ e
  gi|313117013|ref|YP_004038137.1| 31 LTQGELTDRTQLSTRTVRDALRKLEAAGIVHE 62
                                      68899***********************9866 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.5e-05     0.085      76     106 ..      31      61 ..      19      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.5e-05
                              RepL  76 atnRelaeetgislktvsetlkileeanilk 106
                                        t+ el ++t +s++tv+  l+ le a+i+ 
  gi|313117013|ref|YP_004038137.1|  31 LTQGELTDRTQLSTRTVRDALRKLEAAGIVH 61 
                                       58999***********************986 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.17      11      51 ..      20      61 ..      18      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                      HHHHHHHHS-B.-HHHHHHHH---HHHHHHHHHGGGGGT-EE CS
                            HTH_43 11 ylaylideeea.nvpklieltgmPRRtlqDtlkalaeldiel 51
                                      ++ +++++e++ +  +l++ t++  Rt+ D+l+ l+  +i  
  gi|313117013|ref|YP_004038137.1| 20 FVHFVLKQESHlTQGELTDRTQLSTRTVRDALRKLEAAGIVH 61
                                      577889999998999********************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 596.29
//
Query:       gi|313117014|ref|YP_004038138.1|  [L=192]
Description: thioredoxin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-17   62.6   3.2    4.4e-08   32.7   1.4    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    9.1e-11   41.9   0.3    0.00027   20.6   0.0    2.1  2  DAO             FAD dependent oxidoreductase
    9.2e-11   41.5   0.0    0.00029   20.2   0.0    2.4  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    6.6e-10   38.2   0.0    3.3e-06   26.0   0.0    2.1  2  HI0933_like     HI0933-like protein
      8e-09   35.7   0.1    1.1e-05   25.5   0.0    2.3  2  NAD_binding_9   FAD-NAD(P)-binding
    3.3e-07   29.8   0.6    4.8e-05   22.6   0.1    2.4  2  GIDA            Glucose inhibited division protein A
    4.9e-07   29.2   0.2    1.2e-06   27.9   0.0    1.7  2  FAD_binding_2   FAD binding domain
    1.2e-06   28.0   0.1      8e-05   22.0   0.0    2.1  2  FAD_binding_3   FAD binding domain
    9.6e-06   25.7   0.0    2.8e-05   24.3   0.0    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.1e-05   24.5   1.8     0.0024   16.8   0.5    2.1  2  Trp_halogenase  Tryptophan halogenase
      4e-05   23.1   0.0    6.7e-05   22.4   0.0    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
    6.8e-05   22.3   0.0     0.0001   21.7   0.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00017   20.8   0.3      0.057   12.5   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein
     0.0014   17.9   0.0     0.0027   17.0   0.0    1.4  1  Thi4            Thi4 family
     0.0067   17.0   0.0      0.014   15.9   0.0    1.5  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.016   14.5   0.1      0.059   12.7   0.0    1.8  2  Amino_oxidase   Flavin containing amine oxidoreductase
       0.09   13.3   0.0       0.14   12.7   0.0    1.4  1  XdhC_C          XdhC Rossmann domain
       0.13   12.7   0.0       0.17   12.3   0.0    1.5  1  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   3.4e-10   3.4e-07       2      37 ..       3      38 ..       2      49 .. 0.89
   2 !   32.7   1.4   4.4e-11   4.4e-08     187     290 ..      58     154 ..      46     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.4e-10
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtcln 37
                                      +v+v+GgGpAGl+aal+++++g+++t+++ ++t+l+
  gi|313117014|ref|YP_004038138.1|  3 NVIVVGGGPAGLSAALFAQKNGLETTVFDTDQTWLH 38
                                      79**************************97777765 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 4.4e-11
                                       HHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 187 aaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvde 262
                                       ++l+++ e  Gve +  ++v ++ + ge    +v+ dge +d d+vv+a+G    ++l+ ++lg+e  +++ + vd 
  gi|313117014|ref|YP_004038138.1|  58 ETLRRQAEGFGVERV-DAEVSDVSESGE--GfTVTADGEDYDGDYVVLATGAN--RDLA-DTLGCEF-DGDIVDVDV 127
                                       566677777788866.999999999998..348*****************965..5578.9******.666669*** PP

                                       TSBESSTTEEE-GGGCTECCSS--HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 263 flrtnvpgiyaiGDvaggkggpelaqaA 290
                                       +++t+++g ya G+++ + + ++ +  A
  gi|313117014|ref|YP_004038138.1| 128 TMETSIEGAYATGAMV-RAEEWQAVISA 154
                                       **************99.44444444444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.3e-07   0.00062       2      29 ..       4      33 ..       3      40 .. 0.92
   2 !   20.6   0.0   2.7e-07   0.00027     135     207 ..      42     111 ..      33     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.3e-07
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      v+++GGG +Gls+A+++++ g  +t+++ +
  gi|313117014|ref|YP_004038138.1|  4 VIVVGGGPAGLSAALFAQKNGleTTVFDTD 33
                                      9****************9999*****9987 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.7e-07
                                       EE.ETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHH CS
                               DAO 135 lf.ypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdll 207
                                       lf yp+ g  d  +++  l+r+ae  Gve +   ev +++e +g + +v  t++ge  d  d+vV+a+Ga  dl+
  gi|313117014|ref|YP_004038138.1|  42 LFnYPGIGSQDGTAFLETLRRQAEGFGVERVDA-EVSDVSE-SGEGFTV--TADGEDyDG-DYVVLATGANRDLA 111
                                       5557777888999*******************8.*****76.5677999..666888566.99******997666 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.9e-07   0.00029       1      30 [.       5      33 ..       5      47 .. 0.84
   2 !   18.8   0.0   7.6e-07   0.00076      87     134 ..      60     106 ..      50     117 .. 0.83
   3 ?   -2.0   0.0       1.7   1.7e+03     291     305 .]     126     140 ..     108     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      i++G+GPaGl+aa+ ++k+gle  ++ + +
  gi|313117014|ref|YP_004038138.1|  5 IVVGGGPAGLSAALFAQKNGLE-TTVFDTD 33
                                      89*******************6.5677655 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 7.6e-07
                       Pyr_redox_3  87 lrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                       lr+ a+ f ++ + + eV +v++++egf+v+++ e+y  ++v++AtG 
  gi|313117014|ref|YP_004038138.1|  60 LRRQAEGFGVE-RVDAEVSDVSESGEGFTVTADGEDYDGDYVVLATGA 106
                                       55555555553.67899******************************6 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.7
                       Pyr_redox_3 291 eeteetnvpglflaG 305
                                       + t+et ++g +  G
  gi|313117014|ref|YP_004038138.1| 126 DVTMETSIEGAYATG 140
                                       5699******99887 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   3.4e-09   3.3e-06       2      38 ..       3      39 ..       2      50 .. 0.93
   2 !   10.6   0.0   0.00016      0.16     111     164 ..      56     106 ..      49     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.4e-09
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      +viv+GgG+AGl aA+ a+k+g ++++++  ++ ++K
  gi|313117014|ref|YP_004038138.1|  3 NVIVVGGGPAGLSAALFAQKNGLETTVFDTDQTWLHK 39
                                      79****************************9999888 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 111 ivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                        +++l ++++  gv+ r++ ev++v+++ +g f+v++ ++e +  d++vlAtG 
  gi|313117014|ref|YP_004038138.1|  56 FLETLRRQAEGFGVE-RVDAEVSDVSESGEG-FTVTA-DGEDYDGDYVVLATGA 106
                                       577888888888887.7899*****888887.*****.9*************97 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0025       2.5       2      37 ..       6      36 ..       5      44 .. 0.79
   2 !   25.5   0.0   1.1e-08   1.1e-05     103     155 ..      56     106 ..      53     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      +vG+Gp+Gl+++  L a+   k+ le t+fd ++++
  gi|313117014|ref|YP_004038138.1|  6 VVGGGPAGLSAA--LFAQ---KNGLETTVFDTDQTW 36
                                      8********987..6666...578999999887765 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 1.1e-08
                     NAD_binding_9 103 lfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       ++e+l +++ eg+ ve + aev d++e+++g++v +adg+ ++ d+VvLA+G 
  gi|313117014|ref|YP_004038138.1|  56 FLETLRRQA-EGFGVERVDAEVSDVSESGEGFTV-TADGEDYDGDYVVLATGA 106
                                       556666565.79*******************977.9****************5 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   4.8e-08   4.8e-05       1      29 [.       3      36 ..       3      74 .. 0.80
   2 !    5.6   0.0     0.007         7     115     150 ..      73     106 ..      50     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.8e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE.....E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.....t 29
                                      +viV+GgG AG+ AAl a + G++++ +      
  gi|313117014|ref|YP_004038138.1|  3 NVIVVGGGPAGLSAALFAQKNGLETTVFdtdqtW 36
                                      59************************99654442 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.007
                                       ES-EEEEEECTTEEEE.EEETTS-EEEECEEEE--TT CS
                              GIDA 115 eeeveeliveekkvkg.vvtedgetikakavviatGt 150
                                        +ev++++    + +g  vt+dge +  + vv+atG+
  gi|313117014|ref|YP_004038138.1|  73 DAEVSDVSE---SGEGfTVTADGEDYDGDYVVLATGA 106
                                       556666633...556657899***************8 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.2e-09   1.2e-06       2      32 ..       4      34 ..       3      41 .. 0.92
   2 ?   -3.4   0.0       3.9   3.9e+03     377     402 ..     124     143 ..     118     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.2e-09
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      viV+G+G AGL+AAl a+++Gl+++v +  q
  gi|313117014|ref|YP_004038138.1|  4 VIVVGGGPAGLSAALFAQKNGLETTVFDTDQ 34
                                      9************************998766 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.9
                                       EBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 377 etdengrvldadgqpipGLYAaGeva 402
                                        +d ++++       i+G YA G++ 
  gi|313117014|ref|YP_004038138.1| 124 DVDVTMET------SIEGAYATGAMV 143
                                       56777777......899999999765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.1e-08     8e-05       3      35 ..       3      35 ..       1      46 [. 0.87
   2 ?    4.5   0.2     0.018        18     137     190 ..      71     127 ..      50     184 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.1e-08
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      +V++VG+GpaGl++al+ ++ G ++++ +  +t
  gi|313117014|ref|YP_004038138.1|  3 NVIVVGGGPAGLSAALFAQKNGLETTVFDTDQT 35
                                      79************************9987655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.018
                                       CCCCEEE.ECCTTEEEEEEE.......EEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEE CS
                     FAD_binding_3 137 gvtaevr.dketgeeetvra.......kYlvGaDGgrStvrktlgiefegeetvyeagvldv 190
                                        v+aev   +e+ge  tv+a       +Y+v a G++   ++tlg ef g   ++     dv
  gi|313117014|ref|YP_004038138.1|  71 RVDAEVSdVSESGEGFTVTAdgedydgDYVVLATGANRDLADTLGCEFDGDIVDV-----DV 127
                                       4566666334555555555522222227*******************99987553.....33 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   2.8e-08   2.8e-05       1      28 [.       6      33 ..       6      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.8e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vG+G +Gl+aA +++k+g++ +++++ 
  gi|313117014|ref|YP_004038138.1|  6 VVGGGPAGLSAALFAQKNGLETTVFDTD 33
                                      8*************************86 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0018       1.8       1      22 [.       3      24 ..       3      39 .. 0.79
   2 !   16.8   0.5   2.4e-06    0.0024     153     215 ..      53     112 ..      50     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0018
                                      EEEEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                      ++++vGGG+aG  aA   +k +
  gi|313117014|ref|YP_004038138.1|  3 NVIVVGGGPAGLSAALFAQKNG 24
                                      599********99998777665 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIII CS
                    Trp_halogenase 153 aalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllie 215
                                          + + Lrr ae  Gv+rv+++v +v    +g+     ++dg+ +++d ++ ++G ++ l +
  gi|313117014|ref|YP_004038138.1|  53 GTAFLETLRRQAEGFGVERVDAEVSDVSESGEGFT---VTADGEDYDGDYVVLATGANRDLAD 112
                                       5678899********************99999984...5679**************9998765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   6.7e-08   6.7e-05       2      31 ..       4      33 ..       3      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.7e-08
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      v+VvGGgpaG+ AA+ A ++G ++ + +++
  gi|313117014|ref|YP_004038138.1|  4 VIVVGGGPAGLSAALFAQKNGLETTVFDTD 33
                                      9***********************988765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     1e-07    0.0001      29      68 ..       2      41 ..       1      75 [. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1e-07
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqle 68
                                      a+v+v+GgG aGl+A+  a++ g ++tv+D++++ l++ +
  gi|313117014|ref|YP_004038138.1|  2 ANVIVVGGGPAGLSAALFAQKNGLETTVFDTDQTWLHKAH 41
                                      89******************************99887765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   5.7e-05     0.057       2      34 ..       4      34 ..       3      45 .. 0.84
   2 !    6.7   0.0    0.0031       3.1      93     160 ..      60     123 ..      44     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasp 34
                                      v+v+G+GpAgls A     +k gl+ ++ ++ +
  gi|313117014|ref|YP_004038138.1|  4 VIVVGGGPAGLSAALFA--QKNGLETTVFDTDQ 34
                                      9***********99877..99999988887655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0031
                     Lycopene_cycl  93 llerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslkkarrlglQtfyGvev 160
                                       l ++    gv++++a v  v e+ +     v+++g+  ++  vv a+g a+++ a +lg   f G  v
  gi|313117014|ref|YP_004038138.1|  60 LRRQAEGFGVERVDAEVSDVSESGE--GFTVTADGEDYDGDYVVLATG-ANRDLADTLGC-EFDGDIV 123
                                       4444446699**********98765..8999*****************.66655555543.4555555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.7e-06    0.0027      18      49 ..       2      32 ..       1      36 [. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.7e-06
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                      ++v++vG+G++GL+aa    k+ +l++++++ 
  gi|313117014|ref|YP_004038138.1|  2 ANVIVVGGGPAGLSAALFAQKN-GLETTVFDT 32
                                      579*************988888.**9999875 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.4e-05     0.014       1      33 [.       3      35 ..       3      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdk 33
                                      +v+vvGgG  gl +A ++++ g ++tv++   +
  gi|313117014|ref|YP_004038138.1|  3 NVIVVGGGPAGLSAALFAQKNGLETTVFDTDQT 35
                                      599************************987665 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.81   8.1e+02       2      21 ..      12      31 ..      11      34 .. 0.90
   2 ?   12.7   0.0   5.9e-05     0.059     226     261 ..      71     105 ..      54     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.81
                                      HHHHHHHHHHHTTEEEEEEE CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlE 21
                                      aGL+aA   + +G+++tv+ 
  gi|313117014|ref|YP_004038138.1| 12 AGLSAALFAQKNGLETTVFD 31
                                      9***************9985 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.9e-05
                                       ETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S- CS
                     Amino_oxidase 226 rlntrVkeikregdgvtvtledgevveaDaVvvTvp 261
                                       r++++V++++ +g+g tvt  dge++++D+Vv+++ 
  gi|313117014|ref|YP_004038138.1|  71 RVDAEVSDVSESGEGFTVT-ADGEDYDGDYVVLATG 105
                                       78899*************5.7************986 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014      0.14       1      39 [.       4      42 ..       4     115 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerf 39
                                      ++++G+g+ + + a +a++ g+++tv+d++++  +k+++
  gi|313117014|ref|YP_004038138.1|  4 VIVVGGGPAGLSAALFAQKNGLETTVFDTDQTWLHKAHL 42
                                      689***************************966633333 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.17       9      54 ..       3      78 ..       1     187 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele..............................elvklaeee 54
                                      +v+vvGgG+ +++ +    ++g + tv + + +  ++                              e+v+++ ++
  gi|313117014|ref|YP_004038138.1|  3 NVIVVGGGPAGLSAALFAQKNGLETTVFDTDQTWLHKahlfnypgigsqdgtafletlrrqaegfgvERVDAEVSD 78
                                      79***************************99866666666677777777766666555555555555444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1253.56
//
Query:       gi|313117015|ref|YP_004038139.1|  [L=333]
Description: hypothetical protein Hbor_34830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.7  38.4    1.6e-15   57.5  38.4    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
          3    8.3   7.2         16    6.0   0.4    3.0  2  DUF3917          Protein of unknown function (DUF3917)


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5  38.4   1.7e-19   1.6e-15       2     298 ..       8     318 ..       7     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.7e-19
                   LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvl...lralrWrlllrslgarislrrllrayl 75 
                                       l+g++l+++ +a  l+ ++++++a  + +l p   ++ +l++        ++a+  ++ +++lg+ +s r++++  +
  gi|313117015|ref|YP_004038139.1|   8 LIGVVLGGGAFAGYLSYIGVGNVAGRVTELAPEAAVFVVLFVV---AeglADAIGVWASVNPLGRGLSKRQSVQFAM 81 
                                       789999966666667888*************976666666333...35559999878999***************** PP

                   LPG_synthase_TM  76 iglfvnnvtPgalg.Gevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa.vlllla 150
                                       +g f+ ++ P++ +  e++ a+++  ++  ++s+ala+  v + +   a++ll  +++l+++    + ++ vl++l+
  gi|313117015|ref|YP_004038139.1|  82 AGDFFDTLSPAGPVsSEPIMARFIGVTTETTYSDALAVRGVAKYVKSGAQLLLSTVLALAITVGG-SSPRfVLITLG 157
                                       ****************************************************9988887766543.33335666666 PP

                   LPG_synthase_TM 151 lallllavlallll.lllrrrlarlarvlkrlarllarfarklasakr................klvlasprrllla 210
                                       +a+++lav +++ll +++ + ++ + +v + +ar ++ + r                        l++ +p+ ++l+
  gi|313117015|ref|YP_004038139.1| 158 GAVVALAVAGVVLLrFRVAASQVVVVAVTPIVARVSS-LYRDDP---YdrtvveaaverfwsrvLLFRDRPGLVALI 230
                                       6666655555544404444444555544444444444.443333...14458************9************ PP

                   LPG_synthase_TM 211 fllslliwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllall.Gvsaaealaaa 286
                                           ++  ++ a++l+ +l++ g++v l+ + +++++l  ++ ++p+Pg lG++++ l  +la + G  +a ++aa+
  gi|313117015|ref|YP_004038139.1| 231 ACGGVIEQVFVAAALWTALAGTGATVGLLPI-IAIVPLPQASSIVPIPGSLGAYDVFLGGALAVVtGAAPASTAAAV 306
                                       *******************************.77778888899999************99999999*********** PP

                   LPG_synthase_TM 287 llyrlitlylll 298
                                       l++r +tl + l
  gi|313117015|ref|YP_004038139.1| 307 LVVRTVTLPFGL 318
                                       *******96665 PP

>> DUF3917  Protein of unknown function (DUF3917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4    0.0018        16       8      39 ..       4      35 ..       2      55 .. 0.80
   2 ?    4.4   1.6    0.0057        51      43      65 ..     150     171 ..     129     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0018
                           DUF3917  8 lkrfvpGsilaGialityvasifvesvsvevs 39
                                      l rf+ G +l G a+  y++ i v +v+  v+
  gi|313117015|ref|YP_004038139.1|  4 LARFLIGVVLGGGAFAGYLSYIGVGNVAGRVT 35
                                      78*********************999987664 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0057
                           DUF3917  43 vfvaitlfaGsimvlmvaGivlf 65 
                                        fv itl  G+++ l vaG+vl+
  gi|313117015|ref|YP_004038139.1| 150 RFVLITL-GGAVVALAVAGVVLL 171
                                       5888887.799**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2168.85
//
Query:       gi|313117016|ref|YP_004038140.1|  [L=838]
Description: PAS domain S-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-39  135.0  12.9    9.1e-13   48.4   0.2    4.5  4  PAS_4         PAS fold
    4.5e-28   97.5   0.4    2.6e-12   46.7   0.0    5.3  4  PAS           PAS fold
    2.6e-24   85.5   0.0    2.3e-11   43.8   0.0    4.6  4  PAS_9         PAS domain
    4.1e-22   78.5   0.0    1.2e-21   77.0   0.0    1.7  1  Response_reg  Response regulator receiver domain
      5e-20   71.1   3.7    9.3e-07   28.7   0.1    4.9  4  PAS_8         PAS domain
    2.9e-15   56.8   0.0    6.7e-15   55.6   0.0    1.6  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    4.4e-11   42.7   1.5    4.4e-11   42.7   1.5    3.5  4  HisKA         His Kinase A (phospho-acceptor) domain
    6.2e-10   39.2   0.0    6.8e-06   26.3   0.0    3.8  3  PAS_3         PAS fold
    1.9e-07   31.3   0.4      0.019   15.1   0.0    5.1  5  PAS_7         PAS fold
     0.0007   19.8   0.1      0.018   15.3   0.0    3.0  3  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain
  ------ inclusion threshold ------
      0.046   13.7   0.0       0.16   11.9   0.0    2.0  1  HATPase_c_2   Histidine kinase-like ATPase domain
      0.075   13.6   0.0        1.8    9.2   0.0    2.9  2  PrmC_N        PrmC N-terminal domain


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.4   2.7e-15     4e-12       4     109 ..     144     247 ..     141     248 .. 0.95
   2 !   48.4   0.2   6.1e-16   9.1e-13       2     109 ..     265     370 ..     264     371 .. 0.97
   3 !   17.4   0.1   2.6e-06    0.0039       2     109 ..     388     498 ..     387     499 .. 0.87
   4 !   29.5   0.3   4.5e-10   6.7e-07       1     110 []     511     623 ..     511     623 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.7e-15
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerh 80 
                                         da+++ d+d r++++N+a  el g+++eell ++  +l+ ++d ++++++ +r l+ge + +++e+l+ +g+ ++
  gi|313117016|ref|YP_004038140.1| 144 CRDAIFISDSDARFVDVNEATVELTGYDREELLSMRIPDLHEDDDLDAYREYHERILSGEPATTMAEILRADGSKVP 220
                                       5799********************************************************99999999999****** PP

                             PAS_4  81 yelrllPlrdesGevigvlvisrDiTerr 109
                                       +e++ ++l d +G+      ++rD+Ter 
  gi|313117016|ref|YP_004038140.1| 221 VEFSNRRL-DVEGD-TYMHTVARDLTERT 247
                                       ********.9****.888899******96 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 6.1e-16
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       d++pd+++v d+dgr++ +    ++l      +l G+tl++ ++ ++a+ +++a+++ +e++++++ +  l  +g +
  gi|313117016|ref|YP_004038140.1| 265 DAIPDMVVVYDTDGRFRSVLSGPEDLPVDGLGSLEGETLEDAFNSDAADCIQAAIDETVESGAVQTVEYALMSNGNR 341
                                       89********************999**************************************************** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                       r++e ++  l  + G+++ +++++rDiTer+
  gi|313117016|ref|YP_004038140.1| 342 RWFEAHVASL--DTGDTDRAVLVARDITERK 370
                                       **********..4699**************8 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 2.6e-06
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgapp..eellGktlaellpee.....daarleralrrvlegeepieflee 71 
                                        +lp++++v d+   vl +N+a +e++ +p+  ++l+G+ ++  + +      d +++ + +++ ++++ p++ +  
  gi|313117016|ref|YP_004038140.1| 388 ANLPVGVLVEDAKRDVLMTNEALCEILDLPGttDDLIGRNCEKAAADLkdlfaDPDGFVTGIKERIDQRVPVSNEV- 463
                                       689*******************9998777653389*******7777767888999999999999999999999988. PP

                             PAS_4  72 lllpgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       l+l  ++r++e  ++P + ++Ge  + l++ rD+T+r+
  gi|313117016|ref|YP_004038140.1| 464 LDL-ADGRTLERDYVPYDLPDGE--ANLWLYRDVTDRV 498
                                       444.69*****************..***********97 PP

  == domain 4  score: 29.5 bits;  conditional E-value: 4.5e-10
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla....ellpeedaarleralrrvlegeepiefleell 73 
                                       ++++ da+ + dpdg+ +++N   a+ +g++pe+++Gk       +++ +e  a + + ++r l+g++   +le +l
  gi|313117016|ref|YP_004038140.1| 511 VEHVGDAVWIHDPDGTLRFVNDPPAAALGLSPEDIVGKQAMavlaSVADPEKLATFTQEVQRILAGKTDTARLELPL 587
                                       68999******************9999***********9885665677777***********************999 PP

                             PAS_4  74 l.pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         + e+rh+++r++     +G+ +++++++r i e++r
  gi|313117016|ref|YP_004038140.1| 588 YlETETRHLDVRVTAA-TINGT-RHAVGLARNIDEQKR 623
                                       9**************9.67888.888999999988875 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.8e-15   2.6e-12       4      93 ..     138     225 ..     136     239 .. 0.93
   2 ?    5.3   0.0     0.012        19       2     113 .]     259     366 ..     258     366 .. 0.68
   3 !   14.1   0.0   2.4e-05     0.035       5      45 ..     385     427 ..     383     452 .. 0.94
   4 !   24.0   0.0     2e-08     3e-05       2      52 ..     506     556 ..     505     618 .. 0.70

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.8e-15
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                        ai+e  +d+if+ D d r++ vN+a+ el+G++ree+l+  +  ++he+dd + ++++++++++ge+++++   ++
  gi|313117016|ref|YP_004038140.1| 138 NAIFEGCRDAIFISDSDARFVDVNEATVELTGYDREELLSMRIP-DLHEDDDLDAYREYHERILSGEPATTMAEILR 213
                                       58999***************************************.78899999************************ PP

                                       CTTSSEEEEEEEE CS
                               PAS  81 lrdgrpihlevra 93 
                                         dg+++++e  +
  gi|313117016|ref|YP_004038140.1| 214 A-DGSKVPVEFSN 225
                                       *.*****998665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +++ai +++pd+++v D dgr+  v +  e+l       + g++l d ++ +     a++++ ++ ++ es a+++ 
  gi|313117016|ref|YP_004038140.1| 259 RMHAITDAIPDMVVVYDTDGRFRSVLSGPEDLPVDGLGSLEGETLEDAFNSD----AADCIQAAIDETVESGAVQTV 331
                                       6889999999999999999998777666666666666666666777666665....677777777777777777665 PP

                                       EEC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fkl..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +     +g  +++e +++++  ++     +++v+rdi
  gi|313117016|ref|YP_004038140.1| 332 EYAlmSNGNRRWFEAHVASLDTGDTD--RAVLVARDI 366
                                       55577777777777777777777666..666666665 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 2.4e-05
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTH..HHCTTSB CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsr..eevlgks 45 
                                       +i+ +lp++++v D++ ++l +N+a +e+l l+   ++++g++
  gi|313117016|ref|YP_004038140.1| 385 TIVANLPVGVLVEDAKRDVLMTNEALCEILDLPGttDDLIGRN 427
                                       5899*****************************9999999998 PP

  == domain 4  score: 24.0 bits;  conditional E-value: 2e-08
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBST CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldlihe 52 
                                       ++++i+e+  d++++ D dg   +vN+  +  lGls+e+++gk  + ++  
  gi|313117016|ref|YP_004038140.1| 506 QFERIVEHVGDAVWIHDPDGTLRFVNDPPAAALGLSPEDIVGKQAMAVLAS 556
                                       79*****************************************99888754 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   1.6e-14   2.3e-11       2     104 .]     146     245 ..     145     245 .. 0.93
   2 !   12.1   0.0   0.00012      0.17      32     104 .]     299     368 ..     281     368 .. 0.77
   3 !    8.0   0.0    0.0022       3.3       1      40 [.     391     432 ..     391     479 .. 0.74
   4 !   15.9   0.0     8e-06     0.012       2      71 ..     516     592 ..     515     620 .. 0.66

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.6e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       d+i+i ++d r +++Nea  +l+Gy++ee+l  +i dl  ++d +a ++ ++ + +g+  + +   ++ r +g++++
  gi|313117016|ref|YP_004038140.1| 146 DAIFISDSDARFVDVNEATVELTGYDREELLSMRIPDLHeDDDLDAYREYHERILSGE--PATTMAEILRADGSKVP 220
                                       799**99********************************7777777777777777777..***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       v+++ +++  +++++++   + rD+te
  gi|313117016|ref|YP_004038140.1| 221 VEFSNRRLDVEGDTYMH--TVARDLTE 245
                                       *****************..*******8 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00012
                             PAS_9  32 lgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                        g  ++d f  + ++  +  +++ +e+g   +++ve+ l+ + g++ w++++++ +  d g   +++++ rDite
  gi|313117016|ref|YP_004038140.1| 299 EGETLEDAFnsDAADCIQAAIDETVESGA--VQTVEYALMSN-GNRRWFEAHVASL--DTGDTDRAVLVARDITE 368
                                       56677777755555556666666667777..99999988877.99***********..445556678*******8 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0022
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllG..yspeevlgksitdlf 40 
                                       p+g+l+ + +  +l  Nea++++l    + ++++g++++   
  gi|313117016|ref|YP_004038140.1| 391 PVGVLVEDAKRDVLMTNEALCEILDlpGTTDDLIGRNCEKAA 432
                                       678999556666************97777********87554 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 8e-06
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk........kerevevvlir 70 
                                       d+++i +pdg++ ++N+  +  lG spe+++gk+   ++  +  + e+l+ + ++ ++           e ++ l +
  gi|313117016|ref|YP_004038140.1| 516 DAVWIHDPDGTLRFVNDPPAAALGLSPEDIVGKQAMAVL-ASVADPEKLATFTQEVQRilagktdtARLELPLYLET 591
                                       7899*88***888*********************99999.5555555555555555554446555544444444444 PP

                             PAS_9  71 k 71 
                                       +
  gi|313117016|ref|YP_004038140.1| 592 E 592
                                       4 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   7.7e-25   1.2e-21       1     101 [.       7     108 ..       7     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 7.7e-25
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl vdDdp++++  + lle  ++ + +v++a++++eal+ l  e++d+i+ D +mp+ +G+ellk++re++p+lp i
  gi|313117016|ref|YP_004038140.1|   7 VLHVDDDPDFADMAAHLLEreDDRF-SVTVATSASEALDRLADEAFDCIVSDYDMPRQNGVELLKTVREDNPDLPFI 82 
                                       789****************866777.*************************************************** PP

                                       EEESSTSHHHHHHHHHCTESEEEESS CS
                      Response_reg  76 iltahseeedavealkagaddflsKp 101
                                       ++t++++ee+a +a++ag+ d+l+K 
  gi|313117016|ref|YP_004038140.1|  83 LFTGKGSEEVASDAISAGVTDYLQKG 108
                                       ************************96 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   6.2e-10   9.3e-07       5      54 ..     139     188 ..     126     200 .. 0.76
   2 ?    4.7   0.1     0.021        32       3      25 ..     260     282 ..     258     283 .. 0.81
   3 !   17.7   0.0   1.8e-06    0.0026       5      63 ..     385     446 ..     383     450 .. 0.88
   4 !   17.0   0.0   2.9e-06    0.0043       1      56 [.     505     562 ..     505     574 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.2e-10
                             PAS_8   5 alfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrp 54 
                                       a+fe  +d+i++ d + r+vdvN+a+ el+Gy+ ++l+ + + ++l++ ++
  gi|313117016|ref|YP_004038140.1| 139 AIFEGCRDAIFISDSDARFVDVNEATVELTGYDrEELLSMRI-PDLHEDDD 188
                                       59**********997779*************99666666555.44444444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                             PAS_8   3 lralfesspdgiavvdlgdrivd 25 
                                         a+ +++pd ++v+d+++r++ 
  gi|313117016|ref|YP_004038140.1| 260 MHAITDAIPDMVVVYDTDGRFRS 282
                                       57899***********7777765 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 1.8e-06
                             PAS_8   5 alfesspdgiavvd.lgdrivdvNqaalellGys...adlkgellgqllpvlrplledaeqll 63 
                                       +++ ++p+g++v d   d +++ N+a +e+l ++   +dl+g  + +   +l++l++d + ++
  gi|313117016|ref|YP_004038140.1| 385 TIVANLPVGVLVEDaKRD-VLMTNEALCEILDLPgttDDLIGRNCEKAAADLKDLFADPDGFV 446
                                       6899*******8787778.*************99999******99999999999999777665 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 2.9e-06
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg.qllpvlrpll 56 
                                       ++++ ++e++ d++++ d +g+ +++vN+  +  lG+s +d+ g+    +l  v +p++
  gi|313117016|ref|YP_004038140.1| 505 QQFERIVEHVGDAVWIHDpDGT-LRFVNDPPAAALGLSpEDIVGKQAMaVLASVADPEK 562
                                       6899**************6666.*******99999999888888776546666666655 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   4.5e-18   6.7e-15       2     107 ..     733     831 ..     732     834 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4.5e-18
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlG 77 
                                       d +rL+q++ nl  Na+++   a++ ++ + +  d+  + v D+G+Gip++ ++++f   +s+         gtG+G
  gi|313117016|ref|YP_004038140.1| 733 DTDRLQQLFENLFRNAIEH--GAEDATICVGPLADRRGFYVVDDGPGIPEATRDEVFNfGYST------FEDGTGFG 801
                                       789***************9..567777777754689**********************99999......447***** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftft 107
                                       l+ivk++v+ +g +i++++  ++G +f +t
  gi|313117016|ref|YP_004038140.1| 802 LAIVKEVVDAHGWNITLTDGADGGARFEIT 831
                                       **************************9875 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.39   5.9e+02      22      54 ..      19      46 ..      16      53 .. 0.68
   2 ?   -2.8   0.1       4.5   6.7e+03      33      56 ..     243     265 ..     234     269 .. 0.65
   3 !   42.7   1.5   2.9e-14   4.4e-11       2      65 ..     635     693 ..     634     695 .. 0.95
   4 ?   -3.1   0.0       5.5   8.2e+03      48      58 ..     734     744 ..     730     748 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.39
                                      HHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHH CS
                             HisKA 22 gnaeaLkregklteelkeyletiesearrldhl 54
                                      ++a++L+r     e+ +  + ++ s ++ ld+l
  gi|313117016|ref|YP_004038140.1| 19 MAAHLLER-----EDDRFSVTVATSASEALDRL 46
                                      689***99.....66666666666666666655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                                       -HSSCHHHHHHHHHHHHHHHHHHH CS
                             HisKA  33 lteelkeyletiesearrldhlve 56 
                                       lte+ ++  +t+e+  +r+ ++ +
  gi|313117016|ref|YP_004038140.1| 243 LTERTER-KRTLERDQNRMHAITD 265
                                       4444444.6788888888888876 PP

  == domain 3  score: 42.7 bits;  conditional E-value: 2.9e-14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l +f++ v+H+Lr+PL++  g +++  +     e   e l ++++  +r+ +l++dlL+l+r +
  gi|313117016|ref|YP_004038140.1| 635 LDEFASVVSHDLRNPLNVAHGRVSLALE-----EHDSEHLSVAQNALDRMGALIDDLLTLARQG 693
                                       689**********************988.....9***************************976 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5.5
                                       HHHHHHHHHHH CS
                             HisKA  48 arrldhlvedl 58 
                                       ++rl++l e+l
  gi|313117016|ref|YP_004038140.1| 734 TDRLQQLFENL 744
                                       67888888887 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   4.5e-09   6.8e-06       2      69 ..     158     222 ..     157     237 .. 0.90
   2 ?    3.1   0.0     0.076   1.1e+02      25      75 ..     302     351 ..     295     363 .. 0.78
   3 ?    4.9   0.0     0.021        31       4      50 ..     530     578 ..     527     585 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.5e-09
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwve 69 
                                       + v+e+  e++Gy++eell+   ++ dl   +D++ +re ++++l +gep +++  i+r+dG+ + ve
  gi|313117016|ref|YP_004038140.1| 158 VDVNEATVELTGYDREELLSM--RIPDLHEDDDLDAYREYHERIL-SGEPATTMAEILRADGSKVPVE 222
                                       789******************..9999999999999999999999.999*************988887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.076
                             PAS_3  25 swldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvi 75 
                                       ++ d+   +  + +++a++e +++g++ ++ey +   +G  rw+ea++  +
  gi|313117016|ref|YP_004038140.1| 302 TLEDAFNSDAADCIQAAIDETVESGAVQTVEYAL-MSNGNRRWFEAHVASL 351
                                       6666667777778899999999****99****55.579*******998776 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.021
                             PAS_3   4 vserveeilGyspeellgk..veswldlvhpeDrervrealqealkkge 50 
                                       v++     lG+spe++ gk  +  ++++  pe ++ + +++q++l++++
  gi|313117016|ref|YP_004038140.1| 530 VNDPPAAALGLSPEDIVGKqaMAVLASVADPEKLATFTQEVQRILAGKT 578
                                       555566789**********98788888888999*********9998776 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.049        73       5      42 ..     145     181 ..     141     277 .. 0.79
   2 ?   -0.8   0.0       1.1   1.6e+03      59     112 ..     315     371 ..     300     373 .. 0.69
   3 !   15.1   0.0   1.3e-05     0.019       2     114 ..     388     501 ..     387     502 .. 0.75
   4 !    6.0   0.0    0.0089        13       1      79 [.     511     590 ..     511     626 .. 0.81
   5 ?   -2.5   0.0       3.8   5.7e+03      42      99 ..     626     680 ..     602     683 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.049
                             PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelvqvgvple 42 
                                       +++i + D+d r v +N+  +el ++ +e +   +++ 
  gi|313117016|ref|YP_004038140.1| 145 RDAIFISDSDARFVDVNEATVELTGYDREEL-LSMRIP 181
                                       6789999****************99987755.444444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                             PAS_7  59 veaeverrlaaaragkphsfererpdgrvievrgnplpdg...GfVttytDiTerrr 112
                                       ++a++++++++ + ++ ++   +  + r+ e +   l+ g     V +  DiTer++
  gi|313117016|ref|YP_004038140.1| 315 IQAAIDETVESGAVQTVEYALMSNGNRRWFEAHVASLDTGdtdRAVLVARDITERKA 371
                                       556666666666666666677777777777777777766522246999999999986 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.3e-05
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelv.qvgvpleellrynaergefgagdveaeverrlaaaragkphs 77 
                                        n++ G++v Da+  +++ N+  +e+ldlp +    +g++ e+  + +   +++  +d++ +v+ + +++ ++ p s
  gi|313117016|ref|YP_004038140.1| 388 ANLPVGVLVEDAKRDVLMTNEALCEILDLPGTTDdLIGRNCEKAAADL---KDLF-ADPDGFVTGIKERIDQRVPVS 460
                                       68999*************************876523566666544433...3333.467777777777777777777 PP

                             PAS_7  78 fer.erpdgrvievrgnpl...pdgGfVttytDiTerrrae 114
                                        e+   +dgr++e    p    ++   +  y D+T+r+  e
  gi|313117016|ref|YP_004038140.1| 461 NEVlDLADGRTLERDYVPYdlpDGEANLWLYRDVTDRVDRE 501
                                       76525799****999998655344689999*****999877 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0089
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg..agdveaeverrlaaaragkp 75 
                                       +e++ +++ + D d+ L+++N+     l+l++e + vg++  ++l+  a+ ++++  +++v+  ++  ++ ar + p
  gi|313117016|ref|YP_004038140.1| 511 VEHVGDAVWIHDPDGTLRFVNDPPAAALGLSPEDI-VGKQAMAVLASVADPEKLAtfTQEVQRILAGKTDTARLELP 586
                                       6899999**************************99.9*********9999999984445555555555555555555 PP

                             PAS_7  76 hsfe 79 
                                        ++e
  gi|313117016|ref|YP_004038140.1| 587 LYLE 590
                                       5555 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 3.8
                             PAS_7  42 eellrynaergefgagdveaeverrlaaaragkphsfererpdgrvievrgnplpdgG 99 
                                       +el r n++  ef+ + v++ +++ l+ a+ +   s+  e++d + ++v +n+l+  G
  gi|313117016|ref|YP_004038140.1| 626 QELQRQNKRLDEFA-SVVSHDLRNPLNVAHGR--VSLALEEHDSEHLSVAQNALDRMG 680
                                       45555555555555.44444455555433332..333333445555666666666555 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-05     0.018      16      92 ..      29     107 ..      17     128 .. 0.75
   2 ?    0.1   0.0      0.65   9.8e+02      62     109 ..     388     433 ..     358     434 .. 0.71
   3 ?   -1.1   0.0       1.5   2.2e+03      51      76 ..     572     598 ..     548     618 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                        OKR_DC_1_N  16 egfevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlreidgf 89 
                                       + f+v+ +ts +++l  +    + +++v ++d   ++  ell+ +re n+dlP  l++ + ++e ++  + + ++ +
  gi|313117016|ref|YP_004038140.1|  29 DRFSVTVATSASEALDRLAD-EAFDCIVSDYDmprQNGVELLKTVREDNPDLPFILFTGKGSEEVASDAISAGVTDY 104
                                       56778888888888877765.899*****************************999998666666666666666666 PP

                        OKR_DC_1_N  90 iel 92 
                                       ++ 
  gi|313117016|ref|YP_004038140.1| 105 LQK 107
                                       665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.65
                        OKR_DC_1_N  62 edlPvFllaetr.tsedvpadvlreidgfielledtpefiarqieaaak 109
                                       ++lPv +l+e+  ++  +++++l    ++++l  +t + i+r+ e+aa+
  gi|313117016|ref|YP_004038140.1| 388 ANLPVGVLVEDAkRDVLMTNEALC---EILDLPGTTDDLIGRNCEKAAA 433
                                       688998888844333344444443...5669999999999999999986 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.5
                        OKR_DC_1_N  51 aelldeirernedlPvFllaetr.tse 76 
                                       + l  + +    +lP++l +etr  + 
  gi|313117016|ref|YP_004038140.1| 572 RILAGKTDTARLELPLYLETETRhLDV 598
                                       444455666678999999999663333 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.16      29     112 ..     734     812 ..     698     826 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                       HATPase_c_2  29 ldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlali 105
                                       +d+++   e ++ Na+eh+ ++a+     +++   +++  + v D+Gpg + +t+++    ++++ ++  G+Gla++
  gi|313117016|ref|YP_004038140.1| 734 TDRLQQLFENLFRNAIEHGAEDAT-----ICVGPLADRRGFYVVDDGPGIPEATRDEVFNFGYSTFEDGTGFGLAIV 805
                                       456666677789999999997555.....67777788888999******99999999988899************** PP

                       HATPase_c_2 106 kglvDev 112
                                       k++vD  
  gi|313117016|ref|YP_004038140.1| 806 KEVVDAH 812
                                       *****86 PP

>> PrmC_N  PrmC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0012       1.8      28      65 ..     166     204 ..     164     206 .. 0.86
   2 ?    0.2   0.0      0.78   1.2e+03      29      63 ..     537     576 ..     535     577 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                            PrmC_N  28 hvlglsrsdll.lrgerelteeqlerfeelierRaareP 65 
                                       +++g++r +ll +r  +  ++++l++++e+ er +++eP
  gi|313117016|ref|YP_004038140.1| 166 ELTGYDREELLsMRIPDLHEDDDLDAYREYHERILSGEP 204
                                       5799*******556666668899**************** PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.78
                            PrmC_N  29 vlglsrsdll.....lrgerelteeqlerfeelierRaar 63 
                                       +lgls+ d++     +      ++e+l++f++ ++r +a+
  gi|313117016|ref|YP_004038140.1| 537 ALGLSPEDIVgkqamAVLASVADPEKLATFTQEVQRILAG 576
                                       66666665554444456667789*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 5481.52
//
Query:       gi|313117017|ref|YP_004038141.1|  [L=418]
Description: transposase, IS605 OrfB family, central region [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-24   84.3   2.3    8.8e-24   83.2   2.3    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    3.2e-21   75.7   0.0    6.9e-21   74.7   0.0    1.6  1  OrfB_IS605       Probable transposase
     0.0058   16.9   1.9      0.016   15.5   1.9    1.7  1  C1_2             C1 domain
  ------ inclusion threshold ------
      0.083   12.9   3.8       0.23   11.5   3.8    1.8  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.13   12.4   2.9      0.096   12.8   0.7    1.9  2  Ribosomal_L37ae  Ribosomal L37ae protein family


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   2.3   2.4e-27   8.8e-24       1      69 []     309     378 ..     309     378 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.4e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++++ leyka+eyGi v  v++++TSktCs+Cg++ +  ++++ +++C++C +++++Dvn+a+Ni ++
  gi|313117017|ref|YP_004038141.1| 309 FNRFTNLLEYKAEEYGILVDRVDEENTSKTCSCCGKIRDSnRVERGLYVCSSCETTMNADVNGAVNIRRK 378
                                       89*************************************9999************************985 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   1.9e-24   6.9e-21       3     119 ..     176     285 ..     156     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.9e-24
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       +++ e + + ++gn++agiDlGi+n ++   edg+++ly g+ lk+d+ y+++e  + +            s++ ++
  gi|313117017|ref|YP_004038141.1| 176 VCKKEIPVEDAPGNNTAGIDLGISNYLAIDYEDGESELYPGNVLKEDKHYFTREEYQTEGENGP-------SKRARK 245
                                       56666678899******************************************99888777544.......567888 PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                         +k+srr +h+lh l++h+++++ e+gve++ vg+++di
  gi|313117017|ref|YP_004038141.1| 246 ARQKLSRRKDHFLHTLSKHIVERCVEEGVEKIAVGDLSDI 285
                                       88999********************************987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.9   4.4e-06     0.016      14      42 ..     332     365 ..     319     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-06
                              C1_2  14 dssesfnCsaCgrk..idgff.....YsCseCdfsl 42 
                                       +++ s++Cs+Cg+   +  ++     Y Cs C+ ++
  gi|313117017|ref|YP_004038141.1| 332 EENTSKTCSCCGKIrdS--NRverglYVCSSCETTM 365
                                       56778*********554..4455999******9876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.8   6.4e-05      0.23      19      45 ..     337     363 ..     333     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                        +C  Cg+   + r+++ gl+ C++C +
  gi|313117017|ref|YP_004038141.1| 337 KTCSCCGKIrDSNRVER-GLYVCSSCET 363
                                       57*****9999999997.********86 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.1   7.7e+03      31      50 ..     261     280 ..     245     280 .. 0.75
   2 ?   12.8   0.7   2.7e-05     0.096      31      62 ..     334     366 ..     326     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.1
                                       HS-BEESSSSSSEEEEEETT CS
                   Ribosomal_L37ae  31 hakytCpfcgktkvkRkavg 50 
                                        +k+  ++c ++ v++ avg
  gi|313117017|ref|YP_004038141.1| 261 LSKHIVERCVEEGVEKIAVG 280
                                       56788888888888888886 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.7e-05
                                       HS-BEESSSSSS.EEEEEETTEEEETTTTEEEE CS
                   Ribosomal_L37ae  31 hakytCpfcgkt.kvkRkavgiwkCkkcgktva 62 
                                       +++ tC+ cgk  + +R+  g++ C++c+ t+ 
  gi|313117017|ref|YP_004038141.1| 334 NTSKTCSCCGKIrDSNRVERGLYVCSSCETTMN 366
                                       44569******9899**************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3066.76
//
Query:       gi|313117018|ref|YP_004038142.1|  [L=91]
Description: hypothetical protein Hbor_34860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-17   63.2   0.0    2.5e-17   62.9   0.0    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.0   1.4e-21   2.5e-17       3      72 ..      20      85 ..      18      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.4e-21
                            HalOD1  3 espstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeie 72
                                      e++  ++v+++a+++g++p +l+pLy ++D++A+++L+++    +++ + ++sF+yeg +VtV+sdg i+
  gi|313117018|ref|YP_004038142.1| 20 EEMALKIVSVIADAKGCKPLDLKPLYWVVDTEAIEQLVEQ----SSTVSFEISFDYEGGQVTVTSDGNIT 85
                                      677889**********************************....67788******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 618.74
//
Query:       gi|313117019|ref|YP_004038143.1|  [L=68]
Description: hypothetical protein Hbor_34870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.001   18.9   0.9     0.0014   18.5   0.9    1.2  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
     0.0063   16.5   0.7     0.0089   16.0   0.7    1.2  1  zinc-ribbons_6   zinc-ribbons
     0.0068   16.4   1.1      0.099   12.7   0.1    2.0  2  Zn_Tnp_IS91      Transposase zinc-binding domain
     0.0096   15.6   0.2       0.01   15.5   0.2    1.1  1  DpnI             Dam-replacing family
  ------ inclusion threshold ------
      0.019   15.3   0.6      0.025   15.0   0.6    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.028   14.5   1.2        3.4    7.8   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
      0.034   14.0   0.5      0.047   13.6   0.5    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
       0.16   11.7   3.6          4    7.3   0.4    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.55   10.0   5.5       0.92    9.3   0.6    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.9     7e-07    0.0014       4      30 ..      14      42 ..      12      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7e-07
                                      ESTTTSBEEEEECSCCCE..EEESSSS-E CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegkn..feCrqCgYe 30
                                      Cp+Cg+ +l  + ++  +  f C +C Y 
  gi|313117019|ref|YP_004038143.1| 14 CPDCGDEMLFSGTQSAGYaqFFCENCRYR 42
                                      ******9999999999899*********6 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.7   4.4e-06    0.0089      31      56 ..      13      40 ..       8      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.4e-06
                                      E-SSS-S--..-EEEETTEEEE--TTTT CS
                    zinc-ribbons_6 31 lCpeCeqel..evlkaCgavdyfCnkcn 56
                                       Cp+C++e+  +  +  g +++fC++c+
  gi|313117019|ref|YP_004038143.1| 13 WCPDCGDEMlfSGTQSAGYAQFFCENCR 40
                                      6999999973345789999999999996 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.024        48      35      49 ..       7      21 ..       3      24 .. 0.79
   2 !   12.7   0.1     5e-05     0.099      26      52 ..      20      46 ..      19      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.024
                       Zn_Tnp_IS91 35 lGfaryeCeeCghek 49
                                      +G++   C++Cg+e 
  gi|313117019|ref|YP_004038143.1|  7 QGVHPEWCPDCGDEM 21
                                      588999999999865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5e-05
                       Zn_Tnp_IS91 26 kilrCrtaalGfaryeCeeCghekivy 52
                                      ++l  +t++ G+a++ Ce+C+ ++ vy
  gi|313117019|ref|YP_004038143.1| 20 EMLFSGTQSAGYAQFFCENCRYRHDVY 46
                                      577789**************9888776 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   5.1e-06      0.01      33      64 ..      13      44 ..       9      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.1e-06
                                      --TTT--SS-EE--------EEE-TTT--EEE CS
                              DpnI 33 yCpkCgskklsefennkpvaDfyCesckeefe 64
                                      +Cp Cg+++l + +     a f+Ce+c+ +++
  gi|313117019|ref|YP_004038143.1| 13 WCPDCGDEMLFSGTQSAGYAQFFCENCRYRHD 44
                                      8*********99999************97665 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.6   1.3e-05     0.025       6      42 ..      14      46 ..      12      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCgastpwfk 42
                                      CP Cg +     +q+  +    +++C++C +  ++++
  gi|313117019|ref|YP_004038143.1| 14 CPDCGDEMLFSGTQSAGYA---QFFCENCRY-RHDVY 46
                                      ********99999999998...*********.33332 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0017       3.4      26      34 ..      10      19 ..       1      22 [. 0.70
   2 ?    6.0   0.1    0.0065        13       6      19 ..      34      47 ..      33      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                       Zn-ribbon_8 26 lta.CPeCgs 34
                                       ++ CP+Cg 
  gi|313117019|ref|YP_004038143.1| 10 HPEwCPDCGD 19
                                      5677****97 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0065
                       Zn-ribbon_8  6 YrCeeCghefevlq 19
                                      + Ce+C  +++v +
  gi|313117019|ref|YP_004038143.1| 34 FFCENCRYRHDVYV 47
                                      88*****9999765 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   2.4e-05     0.047      10      37 ..      10      42 ..       4      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                                      S--B-TTT-SB-....-S.SSS-EEEETTT--E CS
                              C1_1 10 qptfCkhCgefl....wg.kekqglkCswCkll 37
                                      +p +C  Cg+ +     +  ++  + C++C+++
  gi|313117019|ref|YP_004038143.1| 10 HPEWCPDCGDEMlfsgTQsAGYAQFFCENCRYR 42
                                      799*******9999885558888999****996 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2    0.0083        16       2       8 ..      14      20 ..      14      21 .. 0.73
   2 ?    7.3   0.4     0.002         4      15      21 ..      35      41 ..      25      42 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0083
                     zinc_ribbon_2  2 CpnCGae 8 
                                      Cp CG e
  gi|313117019|ref|YP_004038143.1| 14 CPDCGDE 20
                                      8888855 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                     zinc_ribbon_2 15 FCpyCGt 21
                                      FC++C++
  gi|313117019|ref|YP_004038143.1| 35 FCENCRY 41
                                      5999987 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.4     0.039        78      17      21 ..      14      18 ..      13      19 .. 0.86
   2 ?    9.3   0.6   0.00046      0.92       1      16 [.      34      49 ..      34      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.039
                      Rubredoxin_2 17 CpsCg 21
                                      Cp+Cg
  gi|313117019|ref|YP_004038143.1| 14 CPDCG 18
                                      9***8 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00046
                      Rubredoxin_2  1 YvCsqCGfesakwfGr 16
                                      + C++C +++  ++Gr
  gi|313117019|ref|YP_004038143.1| 34 FFCENCRYRHDVYVGR 49
                                      78********999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 462.08
//
Query:       gi|313117020|ref|YP_004038144.1|  [L=296]
Description: universal stress protein UspA-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-64  215.8   6.0    9.4e-35  120.2   0.7    2.0  2  Usp       Universal stress protein family
    0.00047   19.9   0.1        1.3    8.9   0.1    2.8  2  DUF5615   Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
       0.06   13.3   0.1        0.2   11.6   0.0    1.8  2  FR47      FR47-like protein


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.5   6.5e-32   3.9e-28       1     141 []       1     141 [.       1     141 [. 0.95
   2 !  120.2   0.7   1.6e-38   9.4e-35       2     141 .]     151     290 ..     150     290 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 6.5e-32
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+ Il+ +Dg+e+s +A++++l++a+a++a++++++vi  +a g   da   +++  + le + ++   + a ++a
  gi|313117020|ref|YP_004038144.1|   1 MYDEILLTTDGTECSVQAAKHGLAFAEAFDAAVRIITVINVQAAGGLFDAGGVTADYVESLESRGQKMIDEIADLAA 77 
                                       9******************************************999999998888888877777777777899**** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                          +v+++v+ g p+++ile+ae+e+ dl+V+G++gr+g++r+l GSv+e v+rha++p l Vr
  gi|313117020|ref|YP_004038144.1|  78 PTTTVRTEVLKGIPSDSILEYAEKESFDLVVLGTHGRTGVQRVLTGSVAEHVIRHADVPILTVR 141
                                       *************************************************************998 PP

  == domain 2  score: 120.2 bits;  conditional E-value: 1.6e-38
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       ++rIlV++Dgse++++A+e++l  a+a++a++++l+v+d+   +++ +   ++   ++ ++e + + +a + +a+  
  gi|313117020|ref|YP_004038144.1| 151 FERILVPTDGSEYAQQAVEHGLSVAEAFDATVHALYVVDTGIIAPRLEDHIPETVRAALETEGKTAIEAVESQARRT 227
                                       78******************************************9999988888877777777777777899***** PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        v++++ ++eg p +eil +a+e+d+dli +Gs+gr+gl+r+llGS++e+vlr+ap pVl Vr
  gi|313117020|ref|YP_004038144.1| 228 SVETVTSLTEGVPEREILAYADEHDIDLITMGSHGRTGLDRFLLGSTTERVLREAPSPVLSVR 290
                                       ************************************************************987 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00036       2.1      16      51 ..      71     106 ..      62     109 .. 0.83
   2 !    8.9   0.1   0.00021       1.3      22      53 ..     227     257 ..     215     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00036
                           DUF5615  16 llreaghdvlhvrelglegasDeeileyAkeedrii 51 
                                       +++++   +++vr + l+g++ + ileyA++e + +
  gi|313117020|ref|YP_004038144.1|  71 EIADLAAPTTTVRTEVLKGIPSDSILEYAEKESFDL 106
                                       56666667899********************98755 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00021
                           DUF5615  22 hdvlhvrelglegasDeeileyAkeedriivT 53 
                                         v +v++l  eg++ +eil+yA+e+d  ++T
  gi|313117020|ref|YP_004038144.1| 227 TSVETVTSLT-EGVPEREILAYADEHDIDLIT 257
                                       4566775554.78**************99999 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.4e-05       0.2      27      75 ..     106     154 ..      95     156 .. 0.93
   2 ?   -2.8   0.0       1.1   6.3e+03      30      61 ..     258     289 ..     255     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                                       EEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHH CS
                              FR47  27 lqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyekl 75 
                                       l vl +h r G  ++l+ ++a+++++  + ++l v++ +++ +  +e++
  gi|313117020|ref|YP_004038144.1| 106 LVVLGTHGRTGVQRVLTGSVAEHVIRHADVPILTVRERDERVEPSFERI 154
                                       78999**********************************9998888886 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                                       -GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEE CS
                              FR47  30 lpehrrrGlgsrlvkalakeiaergktvllvv 61 
                                         +h r Gl + l  + ++++ ++   ++l v
  gi|313117020|ref|YP_004038144.1| 258 MGSHGRTGLDRFLLGSTTERVLREAPSPVLSV 289
                                       56788999999999999998888777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1653.53
//
Query:       gi|313117021|ref|YP_004038145.1|  [L=135]
Description: hypothetical protein Hbor_34890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-08   32.3   0.2    7.7e-08   31.8   0.2    1.3  1  SHOCT            Short C-terminal domain
      3e-05   24.0   0.5    5.5e-05   23.2   0.5    1.4  1  DUF1707          Domain of unknown function (DUF1707)
  ------ inclusion threshold ------
      0.023   14.8   3.7      0.031   14.3   3.7    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.027   14.3   0.3        1.4    8.8   0.1    2.4  2  DUF2970          Protein of unknown function (DUF2970)
      0.053   13.5   0.3      0.075   13.0   0.3    1.2  1  GvpG             Gas vesicle protein G
      0.058   13.0   0.1      0.067   12.8   0.1    1.1  1  DUF4131          Domain of unknown function (DUF4131)
      0.078   12.7   0.2        0.1   12.3   0.2    1.1  1  YihI             Der GTPase activator (YihI)
       0.14   12.2   0.2       0.27   11.3   0.0    1.5  2  TAFH             NHR1 homology to TAF


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.2   3.5e-11   7.7e-08       2      28 .]      92     118 ..      91     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.5e-11
                             SHOCT   2 aLekLkeLyarGeIteEEFeakKakLL 28 
                                       + e+L+++ya+G +++EEF+++ ++LL
  gi|313117021|ref|YP_004038145.1|  92 PVETLRQRYAEGKLSDEEFQRRLDQLL 118
                                       6799**********************8 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.5   2.4e-08   5.5e-05      12      39 ..      93     120 ..      90     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.4e-08
                           DUF1707  12 velLrealaeGrLtldEfdeRleaalaA 39 
                                       ve Lr+ +aeG L+ +Ef++Rl++ l+ 
  gi|313117021|ref|YP_004038145.1|  93 VETLRQRYAEGKLSDEEFQRRLDQLLET 120
                                       789*********************9876 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.7   1.4e-05     0.031      38     100 ..      15      77 ..      12      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                   Phage_holin_3_6  38 gllgaagvlallalllllvalalala.a..lwlaalivaavllvlagvlalvglkklkkakplper 100
                                       g  ++a +  l+++++l+++l+ + + a    + +l+  ++ll++a+ + l  ++++ +a+    +
  gi|313117021|ref|YP_004038145.1|  15 GRTAVAIIASLIGVPALVLGLIGITGnAvaNGFLFLLASLALLAVAWCMTLGVVRQANAAPD---A 77 
                                       56788889999999999999974443333567777777899999999999999998887543...3 PP

>> DUF2970  Protein of unknown function (DUF2970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00064       1.4      24      52 ..      11      39 ..       6      43 .. 0.80
   2 ?    3.4   0.0     0.032        71       6      27 ..      57      79 ..      53      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00064
                           DUF2970 24 DfaqlsplhviivGlilaalfvllLillV 52
                                      D   ++    ii+ li++ ++vl+Li++ 
  gi|313117021|ref|YP_004038145.1| 11 DSPAGRTAVAIIASLIGVPALVLGLIGIT 39
                                      55666677789***************985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.032
                           DUF2970  6 kaVlaaf.fGVrkgknrerDfaq 27
                                       aV++ + +GV +++n + D++ 
  gi|313117021|ref|YP_004038145.1| 57 LAVAWCMtLGVVRQANAAPDATP 79
                                      689999879*********99985 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   3.4e-05     0.075      33      67 ..      89     123 ..      69     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                              GvpG  33 lrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLea 67 
                                        ++   +L q+  +G+ ++eeF+rr ++lL+  ea
  gi|313117021|ref|YP_004038145.1|  89 TQTPVETLRQRYAEGKLSDEEFQRRLDQLLETEEA 123
                                       5667789***********************87665 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     3e-05     0.067       8      95 ..      24     117 ..      15     134 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                           DUF4131   8 vllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlles...gqeviveGvvaslpel 81 
                                        l+++ +l+l l+++  + +  + +l+ll+ l+lla++++      ++an  ++++++   ++e + +  v++l ++
  gi|313117021|ref|YP_004038145.1|  24 SLIGVPALVLGLIGITGN-AVANGFLFLLASLALLAVAWCMTLGVVRQANAAPDATPLtnpQTEDVTQTPVETLRQR 99 
                                       344444455555544444.8888899999999999999999999999999999999888663333334455555555 PP

                           DUF4131  82 tgsgt....rfvleverv 95 
                                       +++g+     f+ + +++
  gi|313117021|ref|YP_004038145.1| 100 YAEGKlsdeEFQRRLDQL 117
                                       555554444444444444 PP

>> YihI  Der GTPase activator (YihI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   4.5e-05       0.1      75     122 ..      87     134 ..      67     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                              YihI  75 kkkkaekekekklspeqeLakLEnderLnaLLdrLeegekLskedqky 122
                                        +++++ e+ ++  +e +L   E   rL++LL+  e+g++++++++ +
  gi|313117021|ref|YP_004038145.1|  87 DVTQTPVETLRQRYAEGKLSDEEFQRRLDQLLETEEAGRTVNETERVF 134
                                       222222245556778889*************************99865 PP

>> TAFH  NHR1 homology to TAF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.5   1.2e+04      63      72 ..      49      58 ..      49      71 .. 0.73
   2 ?   11.3   0.0   0.00012      0.27      17      53 ..      82     119 ..      78     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.5
                              TAFH 63 FLkksLpaLr 72
                                      FL +sL++L 
  gi|313117021|ref|YP_004038145.1| 49 FLLASLALLA 58
                                      7778887775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00012
                              TAFH  17 gkqspe.vaenvkeLvqelldgkiepeeftsklqeeln 53 
                                       ++q ++ +++ v++L q+  +gk++ eef+++l + l+
  gi|313117021|ref|YP_004038145.1|  82 NPQTEDvTQTPVETLRQRYAEGKLSDEEFQRRLDQLLE 119
                                       55555514567**********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 881.10
//
Query:       gi|313117022|ref|YP_004038146.1|  [L=469]
Description: hypothetical protein Hbor_34900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-09   35.1  45.6    0.00025   20.0  16.8    3.8  3  COX1           Cytochrome C and Quinol oxidase polypeptide I
  ------ inclusion threshold ------
        7.1    6.9  14.1        3.9    7.7   0.1    4.6  4  DUF2964        Protein of unknown function (DUF2964)


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0  16.8   2.8e-08   0.00025       6     144 ..      37     156 ..      32     162 .. 0.77
   2 !   13.1  13.9   3.5e-06     0.032       5     178 ..     162     325 ..     158     338 .. 0.67
   3 !   12.1   0.2   7.2e-06     0.065     345     392 ..     340     404 ..     335     411 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.8e-08
                                       HHHHHHHHHHHHHHHHHHHHHHCTCT-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S-HHHHHHH CS
                              COX1   6 ylilalvlllvggllgllirlqlafpdletynqlrtlHgnlmiflfatpfilgfgnylvplllgardlafprlnals 82 
                                       +++++l++ll ggl+gll+ +          +q++ +H+ l++ +++   i+g++  +vp  +g++  +++rl+al+
  gi|313117022|ref|YP_004038146.1|  37 HFVVGLAFLLGGGLVGLLAPFGAL------PGQAMLVHLHLLLAGWVCITIMGAMTQFVPVWSGTTL-HSERLSALQ 106
                                       789999999999999999999966......5999999999999999999999999999999986665.555599999 PP

                                       HHHHHHHHHHHHHHHHCSS-STTTTTTTC.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              COX1  83 fwlvvlgvvllllsllgaattgwteYaplsevdlwllglllvvvssllgainfivtilkrra 144
                                       +wlv++g+++++ sl      g +e +p+ +      g +l+  +++++++n+ +t+l  r 
  gi|313117022|ref|YP_004038146.1| 107 LWLVTAGLFGFATSL----LLGLYELLPVFG------GTMLA--GFWMFVYNVGRTLLGSRP 156
                                       999999999999999....456667777333......34444..456667888888877665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.5e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHCTCT....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S..- CS
                              COX1   5 lylilalvlllvggllgllirlqlafp....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardla..f 75 
                                        ++++al + lv +++gll++l ++ p     +     lrt+H++l++f+ +++ ++g+ + l  + + ++dl   +
  gi|313117022|ref|YP_004038146.1| 162 RHFAVALGFVLVLTVFGLLLALGYTHPilarLPFDRTDLRTAHATLAVFGAVLTTVFGALYQLGTMFT-QSDLRgiD 237
                                       6899********************988774433555679****************8888887777766.44443013 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCSS-STTTTTTTC.SHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHTT-CCG CS
                              COX1  76 prlnalsfwlvvlgvvllllsllgaattgwteYaplsevdlwllglllvvvssllgainfivtilk.rrapgmtvak 151
                                         l+ +  + +++gvv+l+        tg+  +     ++++++g llvv++ ++++i++++ +   + ++++ + +
  gi|313117022|ref|YP_004038146.1| 238 MPLKRVEEIGYPVGVVVLA--------TGR-LFE---SSTMAHIGALLVVAGLFAFGIILARRLTGaTVEWNPMLRR 302
                                       3356666668888888877........453.344...6788999999998888877777777776633333444444 PP

                                       S-HHHHHHHHHHHHHHHHCHHHHHHHH CS
                              COX1 152 lplfvwavlatailillalpvlalall 178
                                        +++    +a +i+++ +++ + +a +
  gi|313117022|ref|YP_004038146.1| 303 YAVV----AASMIAWASLTVPVWIADP 325
                                       4444....4444444444444444444 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 7.2e-06
                                       HHHTTHHHHHHHHHHHHHHHHHH.SB--HHHHH................HHHHHHHHHHHHHHHH CS
                              COX1 345 lvllgavvfllfaaiyyllpklt.grmlserla................klhfwllfiGlvlmfl 392
                                       l l+g+++f++++ +y+++p +   + +s  l+                 + f+ l++G++l+++
  gi|313117022|ref|YP_004038146.1| 340 LLLFGVIGFVVLGTLYHIVPFIIwVHRYSDMLGladvpmiddlyddrlaTVDFVALLLGFALLVV 404
                                       689*****************9996767777777677777777777777799********999887 PP

>> DUF2964  Protein of unknown function (DUF2964)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00044       3.9       3      33 ..     197     224 ..     196     231 .. 0.81
   2 ?    3.3   1.4     0.011        97      23      55 ..     253     285 ..     250     288 .. 0.86
   3 ?    1.1   0.2     0.051   4.6e+02      41      54 ..     338     351 ..     331     355 .. 0.82
   4 ?   -1.0   0.1      0.23   2.1e+03      30      53 ..     382     404 ..     381     408 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00044
                           DUF2964   3 rselRvvlAtiavFiaLagiaaaihGlLfde 33 
                                       r++lR++ At+avF   + ++ ++ G L+  
  gi|313117022|ref|YP_004038146.1| 197 RTDLRTAHATLAVF---GAVLTTVFGALYQL 224
                                       889***********...67788888888865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.011
                           DUF2964  23 aaaihGlLfdedavlrygvialliGiaafVvlL 55 
                                       ++   G Lf+ +   + g+++++ G  af ++L
  gi|313117022|ref|YP_004038146.1| 253 VVLATGRLFESSTMAHIGALLVVAGLFAFGIIL 285
                                       5566799*********************98887 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.051
                           DUF2964  41 vialliGiaafVvl 54 
                                         +ll+G++ fVvl
  gi|313117022|ref|YP_004038146.1| 338 MYLLLFGVIGFVVL 351
                                       56799*******98 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.23
                           DUF2964  30 LfdedavlrygvialliGiaafVv 53 
                                       L+d  +      +all+G a +Vv
  gi|313117022|ref|YP_004038146.1| 382 LYDD-RLATVDFVALLLGFALLVV 404
                                       6666.667777899999*999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3073.29
//
Query:       gi|313117023|ref|YP_004038147.1|  [L=182]
Description: sulfite oxidase-like oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-14   52.7   0.0      7e-14   51.8   0.0    1.4  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   3.9e-18     7e-14      52     163 ..      31     134 ..       2     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 3.9e-18
                                       HHC.HH--SS----TTSEEEEEEEEEEHHHHHHHTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEE CS
                    Oxidored_molyb  52 eln.kkkvkglqwgagavsnaeWtGvrlrdvLekagvkkpearhvvfegadeeleeskygasiplekaleddvlLAy 127
                                       e+  ++k   ++  +g   +a+W+Gv + dvLe a    pe++h+vfe+       s+y+a++pl++al    l+A+
  gi|313117023|ref|YP_004038147.1|  31 EMAwTTKHVCVECASGERYDATWSGVAVGDVLELASAA-PETTHLVFESD------SGYAACVPLRDAL--GGLIAV 98 
                                       33323345555666777889*****************7.**********4......48***********..79**** PP

                                       EETTEE--CCCTTT-EEE-TTB-GGGSBTTEEEEEE CS
                    Oxidored_molyb 128 emngepLppdhGyPlRlvvpglvgarsvKwlkriev 163
                                       e +ge+L  ++ y  R+v p + gar vK ++ri+ 
  gi|313117023|ref|YP_004038147.1|  99 ERDGERLGDSEPYATRFVAPDVDGARFVKGVSRIRA 134
                                       **********************************84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1294.31
//
Query:       gi|313117024|ref|YP_004038148.1|  [L=139]
Description: hypothetical protein Hbor_34920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-06   27.1   0.1    3.8e-06   26.5   0.1    1.2  1  Cupin_2       Cupin domain
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.021   14.7   0.0    1.1  1  AraC_binding  AraC-like ligand binding domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   4.2e-10   3.8e-06       5      70 ..      35      99 ..      33     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.2e-10
                                      EETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2  5 lppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70
                                      ++pG+ +p h  p++d ++ V +G g+++ ++ e+++  Gd+v ++agt  ++r + d+ ++ l v
  gi|313117024|ref|YP_004038148.1| 35 FDPGQFIPVHA-PDSDVVISVRSGAGVVREGDIEHDVASGDVVAVEAGTSRGIRAADDTRLEALLV 99
                                      67999999999.8999*******************************************9999876 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.4e-06     0.021      12      76 ..      37     101 ..      29     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-06
                                       TT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE CS
                      AraC_binding  12 pdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyf 76 
                                       p++  p h +d  v++ v +G+g +r ++ ++d+ +Gd++ +  g+   ++++++ ++e   ++ 
  gi|313117024|ref|YP_004038148.1|  37 PGQFIPVHAPDSDVVISVRSGAGVVREGDIEHDVASGDVVAVEAGTSRGIRAADDTRLEALLVTA 101
                                       6777899**************************************99999999887777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1056.55
//
Query:       gi|313117025|ref|YP_004038149.1|  [L=102]
Description: cupin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-08   33.6   0.5    4.3e-08   32.7   0.2    1.6  2  Cupin_2         Cupin domain
    0.00025   21.2   0.0    0.00033   20.8   0.0    1.1  1  Pirin_C_2       Quercetinase C-terminal cupin domain
     0.0086   15.8   0.1      0.011   15.4   0.1    1.1  1  AraC_binding_2  AraC-binding-like domain
     0.0094   15.9   0.0      0.011   15.8   0.0    1.1  1  HutD            HutD
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.016   15.1   0.0    1.2  1  AraC_binding    AraC-like ligand binding domain
      0.098   13.0   0.0       0.11   12.9   0.0    1.1  1  Pirin_C         Pirin C-terminal cupin domain
       0.11   12.2   0.0       0.15   11.8   0.0    1.2  1  Cupin_3         Protein of unknown function (DUF861)
       0.12   12.3   0.0       0.14   12.1   0.0    1.2  1  Cupin_7         ChrR Cupin-like domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.62   1.4e+03      52      64 ..      12      24 ..       5      31 .. 0.80
   2 !   32.7   0.2   1.9e-11   4.3e-08       3      51 ..      29      77 ..      27      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.62
                                      T-EEEEEE-SSS- CS
                           Cupin_2 52 gtpHrfrNtgdep 64
                                      gtpH+ + +++ep
  gi|313117025|ref|YP_004038149.1| 12 GTPHANVFPESEP 24
                                      7999988888886 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1.9e-11
                                      EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-T CS
                           Cupin_2  3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpa 51
                                       +l+  e + +h Hpg   +++Vl+G +el++++e++ le+Gd++ f+ 
  gi|313117025|ref|YP_004038149.1| 29 LTLEADERIAPHDHPGRSIVLHVLDGALELELGDETHALERGDVARFDG 77
                                      57888899999**********************************9986 PP

>> Pirin_C_2  Quercetinase C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.5e-07   0.00033      22      83 ..      28      93 ..      23      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.5e-07
                         Pirin_C_2 22 aakldegesleyelaagrkaYlqvieGevev....ngeslaagDGlaiedesslsltaeedaevLl 83
                                      +++l+++e++  + ++gr++ l+v++G++e+    +++ l++gD + +++++++s  a+e++ +Ll
  gi|313117025|ref|YP_004038149.1| 28 RLTLEADERIAPHDHPGRSIVLHVLDGALELelgdETHALERGDVARFDGDQDISPLATEPSTALL 93
                                      67899999999999****************95444479999**********************998 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     5e-06     0.011      38     105 ..      28      95 ..      25     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5e-06
                    AraC_binding_2  38 rlrygaavsirpselddfylvqlplsGraeveqggrevvlgpgdavvldpgrpyrlrwsadceqlvlr 105
                                       rl+  a+ +i+p +  +   v+  l G  e+e g+++  l++gd++ +d +++ +   ++++  l++ 
  gi|313117025|ref|YP_004038149.1|  28 RLTLEADERIAPHDHPGRSIVLHVLDGALELELGDETHALERGDVARFDGDQDISPLATEPSTALLVL 95 
                                       788888899988888778899999*****************************995555555555554 PP

>> HutD  HutD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.7e-06     0.011      55      92 ..      48      82 ..      24      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.7e-06
                                      EEEEEESS-EEEEETE..E---B-BT--EEEETTS-EE CS
                              HutD 55 vlvlLeGegltLevaggeeekllepleplaFsGdaavs 92
                                      vl +L+G+ l+Le ++  e++ le+ ++++F+Gd+++s
  gi|313117025|ref|YP_004038149.1| 48 VLHVLDGA-LELELGD--ETHALERGDVARFDGDQDIS 82
                                      67888888.7787775..77888889999999998885 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   7.3e-06     0.016      13      50 ..      34      72 ..      27      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.3e-06
                                      T-SEEEETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-E CS
                      AraC_binding 13 dhsfpphvhd.eyvihyvteGtgrlrlngrtydlgpGdl 50
                                      d++ +ph h+   ++  v++G+  l+l+++t+ l+ Gd+
  gi|313117025|ref|YP_004038149.1| 34 DERIAPHDHPgRSIVLHVLDGALELELGDETHALERGDV 72
                                      67889*****9999999*********************8 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.9e-05      0.11       2      69 ..      27      96 ..      26     102 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.9e-05
                                      EEEEE-TT-EEEEE--TT-EEEEEEEES-E..EESSTTEEE-TTEEEEE-SSSEEEEE--SS-EEEEEEE CS
                           Pirin_C  2 ldltleagaelelplpegleaavyvleGel..evggerseieeeqlavlgdgdslvvkaeekgarvlLla 69
                                      + ltlea+++++    +g   ++ vl+G l  e+g+e++++e +++a ++  +++   a+e ++ +l+la
  gi|313117025|ref|YP_004038149.1| 27 VRLTLEADERIAPHDHPGRSIVLHVLDGALelELGDETHALERGDVARFDGDQDISPLATEPSTALLVLA 96
                                      6789********9999************97336677779***********99999999996666677776 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.5e-05      0.15      29      56 ..      43      75 ..      18      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-05
                                      E......EEEECEEEEEETTTEEEEEETTEEEEE CS
                           Cupin_3 29 c......yileGevkvtpeggetvelraGDlvvl 56
                                             ++l G  +++  g et++l+ GD++++
  gi|313117025|ref|YP_004038149.1| 43 PgrsivlHVLDGALELEL-GDETHALERGDVARF 75
                                      0444556***********.************998 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.2e-05      0.14      24      84 ..      24      89 ..      11      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                                      EEEEEEEE-TTEE---EE-TT-EEEE.EEEEEEE....ETTEEEETTEEEEE-TT-EE--EESS-E CS
                           Cupin_7 24 ratslvryapgsafsahkHpggeeil.VLeGvfs....deegdypaGsylrnppgsshapvseeGc 84
                                        t  + ++++++ ++h+Hpg   +l VL+G+++    de++  ++G+  r + ++  +p++ e  
  gi|313117025|ref|YP_004038149.1| 24 PKTVRLTLEADERIAPHDHPGRSIVLhVLDGALElelgDETHALERGDVARFDGDQDISPLATEPS 89
                                      455567799***********9887655****87633337777778888888888888888866554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 708.08
//
Query:       gi|313117026|ref|YP_004038150.1|  [L=114]
Description: phenylacetic acid degradation protein B [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-08   34.8   0.1      2e-08   34.4   0.1    1.2  1  PaaB      Phenylacetic acid degradation B


Domain annotation for each model (and alignments):
>> PaaB  Phenylacetic acid degradation B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1   1.1e-12     2e-08       4      63 ..      36      93 ..      34     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.1e-12
                              PaaB  4 lfEVfkrdkeglshqhvgSvhAadaemALlvArdvfvRReeavslwvvkseailastpee 63
                                      ++EVf+r++++ + +hvgSv A+ a++A ++A ++f     a ++wv +++a+++ +   
  gi|313117026|ref|YP_004038150.1| 36 EWEVFVREDDDDALRHVGSVSAPSADIAYEQATKLFGW--YANDIWVCPADAVCRYSTHT 93
                                      7***********************************85..7889*******998876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 850.63
//
Query:       gi|313117027|ref|YP_004038151.1|  [L=403]
Description: Fe-S oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-25   89.0   0.0    1.4e-24   87.4   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
    7.8e-11   42.4   0.0    1.6e-10   41.4   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    4.9e-07   29.9   0.0    2.6e-06   27.5   0.0    2.0  2  Fer4_14      4Fe-4S single cluster domain
    6.4e-05   23.4   0.0    0.00014   22.3   0.0    1.6  1  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
        0.1   12.9   0.0        0.2   11.9   0.0    1.5  1  Hydrolase    haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   3.9e-28   1.4e-24       2     166 ..      44     199 ..      43     200 .. 0.94
   2 ?   -1.0   0.0      0.57     2e+03      31      91 ..     236     296 ..     207     312 .. 0.49

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 3.9e-28
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       + t+ Cnl C +C+   +  +e  + +ls+ e +++++ l a+ gv +v+++ggepl+++d vel+e +a +   gi
  gi|313117027|ref|YP_004038151.1|  44 NLTKRCNLYCAHCYAAAD--TETAPGELSTAEGKRLLDDL-ADYGVPVVLFSGGEPLVRDDVVELVEYAADR---GI 114
                                       5799*************8..********************.8*****************************8...** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                       r +++tngtl+++ek+++l+++g+ +  ++++ + ++   +  +  + f++ +++++++ +ag+k +  r+++ + +
  gi|313117027|ref|YP_004038151.1| 115 RPVLSTNGTLITPEKARALRDAGLQYAGVSVDGLPER-NDEFRGAEGAFDAAVRGIRACLDAGLK-TGLRYTITE-Q 188
                                       ************************************9.99999999*******************.899998877.8 PP

                                       SHHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 156 ndeeleellel 166
                                       n e+l  +++l
  gi|313117027|ref|YP_004038151.1| 189 NAEDLPGVVDL 199
                                       88888766665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTEEEEEEECSSCHGH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                       Radical_SAM  31 veeileevkelkaekgvkevilgggepllypdfvellerlakla.vpgiritvetngtlpde 91 
                                       v ++ ++ +e+ +e+g++  +l+ g+  + + +ve+++r   ++  + i   +  ng+ p+ 
  gi|313117027|ref|YP_004038151.1| 236 VKRVCDLTREY-HEQGAEIETLLVGNYADAAYLVEYARRHLGEQtAERIYEYLRRNGGDPTG 296
                                       44455555666.45554444444443333333333333333332444455555555555554 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   4.4e-14   1.6e-10       8     122 ..      40     152 ..      31     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 4.4e-14
                           Fer4_12   8 lslf..vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkee 82 
                                       ++++  +++Cnl C+ C++ +  +   g+  t e  +++++dl+++ ++ + ++GGEPl+   +++++elv++   +
  gi|313117027|ref|YP_004038151.1|  40 VVVWnlTKRCNLYCAHCYAAADTETAPGELSTAE-GKRLLDDLADYGVPVVLFSGGEPLV---RDDVVELVEYAADR 112
                                       45666699**********9999999999888855.689**********************...99************ PP

                           Fer4_12  83 kpekdiwlytgytleelskk.ekeellkeidvlvdGkfees 122
                                       ++   +++++g+ +   +++  ++  l++  v vdG  e +
  gi|313117027|ref|YP_004038151.1| 113 GIR-PVLSTNGTLITPEKARaLRDAGLQYAGVSVDGLPERN 152
                                       **5.699999*999888777567778999999999987765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   7.4e-10   2.6e-06       4      92 ..      45     125 ..      42     147 .. 0.83
   2 ?   -0.7   0.0      0.41   1.5e+03      65      92 ..     237     264 ..     233     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 7.4e-10
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80 
                                        + +Cnl C  C+  ++ +   g+ +t e   + l+dl ++ +    + ++GGePL     +++++lv++  +++  
  gi|313117027|ref|YP_004038151.1|  45 LTKRCNLYCAHCYAAADTETAPGELSTAEGK-RLLDDLADYGV--PVVLFSGGEPLVR---DDVVELVEYAADRG-- 113
                                       5789************999999999999887.89988888888..5599*******44...8999******9999.. PP

                           Fer4_14  81 kkiwletngtle 92 
                                       ++  l tngtl 
  gi|313117027|ref|YP_004038151.1| 114 IRPVLSTNGTLI 125
                                       888899999875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.41
                           Fer4_14  65 kellklvkrlkeeypekkiwletngtle 92 
                                       k +++l ++++e++ e++  l  n+  +
  gi|313117027|ref|YP_004038151.1| 237 KRVCDLTREYHEQGAEIETLLVGNYADA 264
                                       67999999****9999999998888766 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0     4e-08   0.00014       6      67 ..     298     356 ..     294     357 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4e-08
                             SPASM   6 rslfInsdGdVvpCcvdkktyveelklGnireesleeIw...nseeyqefrkskkfplielCrnC 67 
                                       r + ++++G+V++     + ++  ++lGn+r+ s+  Iw   +++ ++++r ++ + l   C++C
  gi|313117027|ref|YP_004038151.1| 298 RIADVDYQGNVHLT----QFWQG-YSLGNVRDRSFGAIWddeTNPLLRRLR-ERPEHLTGRCADC 356
                                       55679999******....67744.***************666666788888.5566677889999 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.5e-05       0.2     108     160 ..      88     141 ..      20     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH..HHHHHTTGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                         Hydrolase 108 lavftiadplkvkpeaaeavasLkaagievvlltgdnpetae..raanqlGddyf 160
                                       + +f   +p  v+++++e+v++  ++gi+ vl t++   t+e  ra++ +G +y 
  gi|313117027|ref|YP_004038151.1|  88 VVLFSGGEP-LVRDDVVELVEYAADRGIRPVLSTNGTLITPEkaRALRDAGLQYA 141
                                       334444455.8**************************998887444444884444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2519.15
//
Query:       gi|313117028|ref|YP_004038152.1|  [L=77]
Description: hypothetical protein Hbor_34960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-26   92.1   0.8    1.6e-26   92.0   0.8    1.0  1  DUF2249   Uncharacterized conserved protein (DUF2249)
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.049   13.4   0.0    1.6  2  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.8   1.7e-30   1.6e-26       1      69 [.       5      75 ..       5      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 1.7e-30
                           DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearr..pgffsweylergpgewrvlit 69
                                      tlD+R++ppperh++I++afe+L++Ge+lelvndhdPkpL+y+++a++  +++  +e+++rgp e+++++ 
  gi|313117028|ref|YP_004038152.1|  5 TLDLRDVPPPERHPKIHDAFESLESGEALELVNDHDPKPLFYEMQAEVdsFDAEGYEVEQRGPTEFVARLP 75
                                      79**********************************************9967779***********99876 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.5e-06     0.049       2      36 ..       5      39 ..       4      45 .. 0.93
   2 ?   -1.3   0.0      0.22     2e+03      48      57 ..      56      64 ..      47      74 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-06
                                      EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESS CS
                              TusA  2 elDlrGlvCPePllklkkalekleegevlevladd 36
                                      +lDlr+ + Pe   k++ a e+le+ge le++ d+
  gi|313117028|ref|YP_004038152.1|  5 TLDLRDVPPPERHPKIHDAFESLESGEALELVNDH 39
                                      8*****************************99887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.22
                                      HHHTEEEEEE CS
                              TusA 48 kklghelvev 57
                                      + +g+e ve+
  gi|313117028|ref|YP_004038152.1| 56 DAEGYE-VEQ 64
                                      567888.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 541.42
//
Query:       gi|313117029|ref|YP_004038153.1|  [L=199]
Description: hypothetical protein Hbor_34970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1490.97
//
Query:       gi|313117030|ref|YP_004038154.1|  [L=52]
Description: hypothetical protein Hbor_34980 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.5   0.5      0.032   14.3   0.5    1.1  1  Elf1      Transcription elongation factor Elf1 like
       0.19   11.8   3.2       0.48   10.6   0.2    2.2  2  UPF0547   Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   3.6e-06     0.032      21      56 ..       6      39 ..       2      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-06
                              Elf1 21 kFdCpfCnheksvevkldkkekiaevsCkvCgesfe 56
                                       FdCp C+    v+v  + +++i e  C  C++ ++
  gi|313117030|ref|YP_004038154.1|  6 IFDCPECDTV--VTVGTEIRTEILEHGCVLCETAVS 39
                                      6*******99..666666667799999999988765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   5.3e-05      0.48       3      12 ..       9      18 ..       8      22 .. 0.82
   2 ?    2.1   0.3     0.023   2.1e+02       6      14 ..      34      42 ..      31      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.3e-05
                           UPF0547  3 CPeCeakvPv 12
                                      CPeC++ v v
  gi|313117030|ref|YP_004038154.1|  9 CPECDTVVTV 18
                                      *****98865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.023
                           UPF0547  6 CeakvPvaa 14
                                      Ce+ v+++a
  gi|313117030|ref|YP_004038154.1| 34 CETAVSADA 42
                                      ******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 357.36
//
Query:       gi|313117031|ref|YP_004038155.1|  [L=213]
Description: DNA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-18   65.0   0.0    6.4e-18   64.3   0.0    1.3  1  HTH_10         HTH DNA binding domain
    0.00022   21.1   0.6     0.0004   20.3   0.6    1.4  1  BAT            GAF and HTH_10 associated domain
  ------ inclusion threshold ------
      0.016   16.0   0.1      0.032   15.0   0.1    1.4  1  GnHR_trans     Gonadotropin hormone receptor transmembrane re
      0.054   12.9   0.8      0.094   12.2   0.3    1.6  2  DUF3587        Protein of unknown function (DUF3587)
      0.059   12.9   0.0       0.14   11.7   0.0    1.7  1  Sigma70_r4     Sigma-70, region 4
       0.06   13.5   0.2       0.17   12.1   0.1    1.8  2  Pcc1           Transcription factor Pcc1
      0.089   12.6   0.1       0.27   11.1   0.1    1.8  1  LexA_DNA_bind  LexA DNA binding domain
       0.15   11.6   0.1         20    4.8   0.0    2.5  2  GerE           Bacterial regulatory proteins, luxR family


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   2.8e-21   6.4e-18       1      52 [.     156     207 ..     156     208 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.8e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++q evl +A+emGYF  P+++++ e+A++l+I +st+ ehL++a+skl+
  gi|313117031|ref|YP_004038155.1| 156 LTERQQEVLETAHEMGYFGHPKDANATEVANALDINRSTFAEHLSAAQSKLL 207
                                       9*************************************************98 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.6   1.8e-07    0.0004      60     148 ..      51     143 ..      24     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.8e-07
                               BAT  60 edldavedvrvvseeddg..tllelt..vsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeer 132
                                       e+     + + v ++dd+   ++e++  ++ +++ + + ++G  vrs+++++    +     + +++R++v +l+e+
  gi|313117031|ref|YP_004038155.1|  51 ESGTEFNSTEEVFHYDDKtvHRFECKtgTTPSCPCEFVESRGCPVRSFRTTENALVVQFVARDIRNLREIVVGLREQ 127
                                       444444444555555555335677764455778888****************999999999999************* PP

                               BAT 133 ypdveLvarrererpv 148
                                       +pdv+L++    ++p+
  gi|313117031|ref|YP_004038155.1| 128 FPDVSLRRLTRSQEPE 143
                                       ******9988777775 PP

>> GnHR_trans  Gonadotropin hormone receptor transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.4e-05     0.032      11      55 ..      18      66 ..       7      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                        GnHR_trans 11 Cnkssarqdlddltgerth....drsleedlissyskeedigeveFdYD 55
                                      C   +++q+ +++++ +      ++s+  d+ +++++e++ +e  F+YD
  gi|313117031|ref|YP_004038155.1| 18 CRIGNMPQKTEEISSISRStmpsEDSVTVDFTAESGTEFNSTEEVFHYD 66
                                      666666666666655332211458999*********************7 PP

>> DUF3587  Protein of unknown function (DUF3587)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   4.2e-05     0.094     102     149 ..      46      93 ..      29     104 .. 0.85
   2 ?   -2.3   0.0       1.1   2.5e+03      86      98 ..     145     157 ..     139     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                           DUF3587 102 ggivppaveeFtsiselenfvkehvhlnkCsdyryasCpChllnkeee 149
                                        +++++   eF+s +e+ ++ +++vh  +C+ ++  sCpC+  +++  
  gi|313117031|ref|YP_004038155.1|  46 VDFTAESGTEFNSTEEVFHYDDKTVHRFECKTGTTPSCPCEFVESRGC 93 
                                       5666777789******************************98887764 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                           DUF3587  86 eeerilinvdsLl 98 
                                       +++ +lin d+L+
  gi|313117031|ref|YP_004038155.1| 145 NNNLVLINRDTLT 157
                                       6789999999996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.2e-05      0.14       3      36 ..     154     194 ..     154     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                                       HHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHH CS
                        Sigma70_r4   3 asLpererevlelrf.......geglTleEIgerlgiSrer 36 
                                       ++L+er++evle           ++ +  E+++ l+i r++
  gi|313117031|ref|YP_004038155.1| 154 DTLTERQQEVLETAHemgyfghPKDANATEVANALDINRST 194
                                       69************99999988888999*********9987 PP

>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.3   1.2e+04      40      49 ..      41      50 ..      28      53 .. 0.51
   2 ?   12.1   0.1   7.5e-05      0.17      34      61 ..      96     123 ..      89     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.3
                                      TTEEEEEEEE CS
                              Pcc1 40 gnvLqveykA 49
                                      +  ++v+++A
  gi|313117031|ref|YP_004038155.1| 41 EDSVTVDFTA 50
                                      3345555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.5e-05
                                       EEEEEETTEEEEEEEESSHHHHHHHHHH CS
                              Pcc1  34 rslslegnvLqveykAttnrmLRvavng 61 
                                       rs+++++n L+v++ A + r LR  v g
  gi|313117031|ref|YP_004038155.1|  96 RSFRTTENALVVQFVARDIRNLREIVVG 123
                                       89*********************77655 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00012      0.27       3      53 ..     155     205 ..     153     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       ---HHHHHHHHHHHHHHHHHSS--..-HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind   3 kLTerQrevldlikasieetgypP..sireiaralglkSpsaveehLkaLerK 53 
                                        LTerQ+evl+   +++   g+p      e+a+al ++  s+ +ehL a + K
  gi|313117031|ref|YP_004038155.1| 155 TLTERQQEVLETA-HEMGYFGHPKdaNATEVANALDIN-RSTFAEHLSAAQSK 205
                                       6**********85.578999999622567999999999.88899999886655 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.015        33       2      13 ..     155     166 ..     154     172 .. 0.88
   2 ?    4.8   0.0    0.0088        20      21      45 ..     182     206 ..     175     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                                       SS-HHHHHHHHH CS
                              GerE   2 sLskRErevLrl 13 
                                       +L++R++evL+ 
  gi|313117031|ref|YP_004038155.1| 155 TLTERQQEVLET 166
                                       8*********86 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0088
                                       HHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  21 keIAeelniSekTVkvhksnimkKL 45 
                                       +e+A +l+i   T   h+s +++KL
  gi|313117031|ref|YP_004038155.1| 182 TEVANALDINRSTFAEHLSAAQSKL 206
                                       79**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1517.63
//
Query:       gi|313117032|ref|YP_004038156.1|  [L=194]
Description: hypothetical protein Hbor_35000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.96    9.5  10.3          6    6.9   0.9    3.9  4  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0034        61      22      36 ..       6      20 ..       5      42 .. 0.78
   2 ?    0.3   0.0     0.039   7.1e+02      23      32 ..      66      75 ..      59      96 .. 0.66
   3 ?    6.9   0.9   0.00033         6      15      36 ..     131     152 ..     130     160 .. 0.77
   4 ?    1.6   0.3     0.016   2.9e+02      19      39 ..     166     185 ..     164     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0034
                            OppC_N 22 illlllliaifaPli 36
                                      ++++llli+++ P++
  gi|313117032|ref|YP_004038156.1|  6 VVVVLLLIVVLLPMW 20
                                      677888888888887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.039
                            OppC_N 23 lllllliaif 32
                                      ++l+ l+a++
  gi|313117032|ref|YP_004038156.1| 66 VALFGLVAVL 75
                                      3333333333 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00033
                            OppC_N  15 lAvvglvilllllliaifaPli 36 
                                       lA+ gl il++ +++ + ++++
  gi|313117032|ref|YP_004038156.1| 131 LAMGGLTILAIAFAALFTGEYL 152
                                       79********666555558998 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.016
                            OppC_N  19 glvilllllliaifaPliaPy 39 
                                       g+++ l+ll +a +a ++ P+
  gi|313117032|ref|YP_004038156.1| 166 GMFVSLALLTVAYYA-WFLPH 185
                                       899999999999998.44464 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1363.84
//
Query:       gi|313117033|ref|YP_004038157.1|  [L=219]
Description: Rieske Fe-S protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-13   48.0   0.0    1.3e-12   47.5   0.0    1.3  1  Rieske    Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
        0.1   11.2   0.2       0.14   10.8   0.2    1.2  1  HCV_NS1   Hepatitis C virus non-structural protein E2/NS1


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.5e-16   1.3e-12      37      89 .]     130     195 ..      93     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.5e-16
                                       E..............EEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE..TTSBEEE-TTHHHEEEET CS
                            Rieske  37 y..............AlsdvCtHrgaplsegkidekgvleCpcHgwayd..adGkvikgPaprplatyp 89 
                                       y              A+s+vCtH+g+ +s++++   ++l+CpcH +++d  a +kv++gP+prpl+++p
  gi|313117033|ref|YP_004038157.1| 130 YsggtkleytvagyaAYSKVCTHAGCMVSNEEG---ETLVCPCHFGKFDptAGAKVVGGPPPRPLPQLP 195
                                       334555555555555************998655...58***********98889***********9976 PP

>> HCV_NS1  Hepatitis C virus non-structural protein E2/NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   1.6e-05      0.14     168     216 ..     139     186 ..     117     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.6e-05
                                       EEEBTTSXEEEEEXXGGGGSXTTTTXSSSXSXXXXXXXXXXXXXXXSSX CS
                           HCV_NS1 168 twmnstgftktcgappcriggdgnatllcptdcfrkhpeatylkcgsgp 216
                                       t    + ++k+c    c ++++  +tl+cp   f k+  ++ +k+  gp
  gi|313117033|ref|YP_004038157.1| 139 TVAGYAAYSKVCTHAGCMVSNEEGETLVCPCH-FGKFDPTAGAKVVGGP 186
                                       444556799*********************86.6777666667766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1560.72
//
Query:       gi|313117034|ref|YP_004038158.1|  [L=474]
Description: menaquinol-cytochrome c reductase cytochrome b subunit precursor [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-44  151.0   0.8    2.9e-44  151.0   0.8    3.0  3  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    2.6e-30  105.7  15.1      1e-29  103.8   9.7    2.6  2  Cytochrome_B     Cytochrome b/b6/petB
    5.7e-05   23.3   1.2    5.7e-05   23.3   1.2    2.5  4  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD
    0.00045   20.7   6.6    0.00045   20.7   6.6    3.8  4  DUF4405          Domain of unknown function (DUF4405)
  ------ inclusion threshold ------
      0.069   12.9   0.0       0.28   11.0   0.0    2.0  1  SP_C-Propep      Surfactant protein C, N terminal propeptide


Domain annotation for each model (and alignments):
>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       0.2   7.3e+02      23      48 ..      40      65 ..      31      77 .. 0.80
   2 !  151.0   0.8   8.1e-48   2.9e-44       2     166 ..     120     317 ..     119     323 .. 0.82
   3 ?   -1.5   0.1      0.61   2.2e+03      37      68 ..     417     444 ..     403     469 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.2
                   Cytochrom_B_N_2 23 pRelnWiiGvllllltllegflGysL 48
                                      p e ++++G + l++ ++ +++G  L
  gi|313117034|ref|YP_004038158.1| 40 PAEDSFLLGEVALFCFVMLALTGMFL 65
                                      66788999999999999999999877 PP

  == domain 2  score: 151.0 bits;  conditional E-value: 8.1e-48
                   Cytochrom_B_N_2   2 imiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvel 78 
                                       +++++i +HmlrvfftGaY++pRe nW++G  l  l+++++++Gy Lp+d  ++ta+ +g+++++s+P+vg+++ ++
  gi|313117034|ref|YP_004038158.1| 120 LFVASIGLHMLRVFFTGAYRNPREPNWVVGTGLAGLAMGAAYTGYALPFDEFAATATGIGYNLATSIPFVGSVVGKV 196
                                       79*************************************************************************** PP

                   Cytochrom_B_N_2  79 lfGgelpgeallsrlyalHilllpalllalivahlllvekkgqtp..............................sr 125
                                       +fGge+p++a+++rly +H+l++p+ ++ l+++h++++ ++++t+                                
  gi|313117034|ref|YP_004038158.1| 197 VFGGEFPSSATIPRLYFFHVLVIPVAIAILLAIHMAILVRQKHTEaprnddvrgaeppqstrtpdagavsdggteT- 272
                                       ************************************9755555552355555555555555555554444444441. PP

                   Cytochrom_B_N_2 126 rkeknvvg...........eplvpvnavkmlllflvlvallialalinPvpl 166
                                              +            p +p++a+ + ++f++++a l+al  ++Pv +
  gi|313117034|ref|YP_004038158.1| 273 -------AvakeddtvvvgLPAFPNQAAVSAVVFFLTLATLAALGGFFPVHN 317
                                       .......044444444444*******99999999988888888887877765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.61
                   Cytochrom_B_N_2  37 ltllegflGysLpddllsvtalrvgagiissv 68 
                                       ++++++++G     + l + al+vg+++++ +
  gi|313117034|ref|YP_004038158.1| 417 FIMIASIAGM----NNLLGRALDVGTEVVNPI 444
                                       4444444442....333344444444444432 PP

>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   9.7   2.8e-33     1e-29      14     187 ..      45     236 ..      40     238 .. 0.89
   2 ?   -3.5   0.2       2.1   7.6e+03     137     153 ..     356     372 ..     340     380 .. 0.69

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 2.8e-33
                      Cytochrome_B  14 ynlGsllllvlvlqiltGvalafyytptvt.................laflsvqyilrdvnfGwlirsvhangasll 73 
                                       + lG ++l+++v+  ltG++l +++ p+++                 +af+sv +i +d+ fG +ir +h ++a l+
  gi|313117034|ref|YP_004038158.1|  45 FLLGEVALFCFVMLALTGMFLGMFFEPSTSaveyegsvaafqgeevpEAFASVLHITYDIPFGMFIRRIHHWAAHLF 121
                                       779*********************9885432222222222223333379**************************** PP

                      Cytochrome_B  74 flllylhifrglllgglkktrelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPviGstlvellw 150
                                       +  + lh+ r++++g++ ++re  Wv+G  l+ l +  a++Gy+Lp+d  +  a+ +  nl+ +iP++Gs++ + ++
  gi|313117034|ref|YP_004038158.1| 122 VASIGLHMLRVFFTGAYRNPREPNWVVGTGLAGLAMGAAYTGYALPFDEFAATATGIGYNLATSIPFVGSVVGKVVF 198
                                       ***************************************************************************** PP

                      Cytochrome_B 151 gsvsvddatLtrffslh.fllPflllillllhllllhk 187
                                       g+++ ++at+ r++ +h +++P  ++ill +h+ +l +
  gi|313117034|ref|YP_004038158.1| 199 GGEFPSSATIPRLYFFHvLVIPVAIAILLAIHMAILVR 236
                                       *****************8889************99865 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.1
                      Cytochrome_B 137 aiPviGstlvellwgsv 153
                                       +iPv+G  + +   g+v
  gi|313117034|ref|YP_004038158.1| 356 TIPVVGVHVSTEFVGGV 372
                                       67777777666655554 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       3.8   1.4e+04      75      84 ..      54      63 ..      47      79 .. 0.55
   2 ?   -3.1   0.1       2.7   9.8e+03      34      47 ..     216     229 ..     210     241 .. 0.57
   3 ?   -3.6   0.1       3.9   1.4e+04      69      82 ..     296     309 ..     290     316 .. 0.56
   4 !   23.3   1.2   1.6e-08   5.7e-05       1      82 [.     323     423 ..     323     448 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.8
                                      HHHHHHHHHT CS
                     Cytochrom_B_C 75 sfvvLgylGv 84
                                      +fv+L++ G+
  gi|313117034|ref|YP_004038158.1| 54 CFVMLALTGM 63
                                      3333333332 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                                       HHHHHHHHHGGGCH CS
                     Cytochrom_B_C  34 vvamgaaivilfll 47 
                                       v+++ +ai+il+++
  gi|313117034|ref|YP_004038158.1| 216 VLVIPVAIAILLAI 229
                                       55555555555443 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHHH CS
                     Cytochrom_B_C  69 lallvvsfvvLgyl 82 
                                       ++++++++++L+ l
  gi|313117034|ref|YP_004038158.1| 296 AVVFFLTLATLAAL 309
                                       34444455555544 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 1.6e-08
                                       B--TTC--TT----GGGHHHHHHHHCSS................SHHHHHHHHHHHHHGGGCHHHH---SSSSSTT- CS
                     Cytochrom_B_C   1 panplktPahIaPeWYflpfYaiLraip................akllGvvamgaaivilfllpwldrskvksiryr 61 
                                       p np  tP+ I P W+++++Y  L+ +p                + ++Gv++ ++ +  +++ p++d +++      
  gi|313117034|ref|YP_004038158.1| 323 PNNPAGTPELIMPDWFLMWVYGFLKLLPswmsftipvvgvhvstEFVGGVLLPTVVFGAIAVWPFIDYRENPVHFTA 399
                                       5799**********************866777777777888876778889888888889999999987766544444 PP

                                       .HHHHH...HHHHHHHHHHHHHHH CS
                     Cytochrom_B_C  62 kplakv...llallvvsfvvLgyl 82 
                                       +pl +    ++ + +++f++++ +
  gi|313117034|ref|YP_004038158.1| 400 SPLDRPwqtAVGVAAIQFIMIASI 423
                                       444433111345555566555443 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   6.6   1.3e-07   0.00045       6      62 ..      51     129 ..      47     132 .. 0.83
   2 ?   -1.9   0.2       1.4     5e+03       3      25 ..     149     171 ..     147     192 .. 0.70
   3 ?   -4.1   0.9         5   1.8e+04      53      63 ..     222     232 ..     219     233 .. 0.73
   4 ?    1.3   0.0      0.14   5.1e+02       5      23 ..     445     463 ..     440     470 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                           DUF4405   6 lllsflvlaiSGillsfavlpsgrgaywa..................flgl.....skhqwrdiHeilgllflilvv 59 
                                       +l++f++la++G+ l    ++++  a ++                   l++       +++r iH+++++lf++ ++
  gi|313117034|ref|YP_004038158.1|  51 ALFCFVMLALTGMFLGMF-FEPSTSAVEYegsvaafqgeevpeafasVLHItydipFGMFIRRIHHWAAHLFVASIG 126
                                       799***********9988.555555555568****************5555444466899***************** PP

                           DUF4405  60 lHl 62 
                                       lH+
  gi|313117034|ref|YP_004038158.1| 127 LHM 129
                                       **7 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                           DUF4405   3 dlllllsflvlaiSGillsfavl 25 
                                        ++l+ + +++a++G  l f  +
  gi|313117034|ref|YP_004038158.1| 149 GTGLAGLAMGAAYTGYALPFDEF 171
                                       56777788899999988876644 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 5
                           DUF4405  53 lflilvvlHlg 63 
                                       +  il+++H++
  gi|313117034|ref|YP_004038158.1| 222 AIAILLAIHMA 232
                                       56788888875 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.14
                           DUF4405   5 llllsflvlaiSGillsfa 23 
                                       l++ +f+v  +SG+l ++ 
  gi|313117034|ref|YP_004038158.1| 445 LTVALFVVPGVSGLLTYRL 463
                                       5667889999****99975 PP

>> SP_C-Propep  Surfactant protein C, N terminal propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.7e-05      0.28      35      70 ..     207     242 ..     201     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.7e-05
                       SP_C-Propep  35 nlkrllivvvvvvlvvvvvlgallmglhmsqkhtem 70 
                                        + rl    v+v+ v + +l a+ m + + qkhte 
  gi|313117034|ref|YP_004038158.1| 207 TIPRLYFFHVLVIPVAIAILLAIHMAILVRQKHTEA 242
                                       578999999*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 3273.66
//
Query:       gi|313117035|ref|YP_004038159.1|  [L=70]
Description: hypothetical protein Hbor_35030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 485.77
//
Query:       gi|313117036|ref|YP_004038160.1|  [L=996]
Description: respiratory nitrate reductase alpha subunit apoprotein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-93  311.8   0.0    1.2e-92  311.2   0.0    1.3  1  Molybdopterin    Molybdopterin oxidoreductase
    2.4e-20   72.6   0.0    5.2e-20   71.5   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
      0.038   14.0   0.4      0.094   12.7   0.4    1.6  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
      0.061   13.9   0.0       0.21   12.2   0.0    1.9  2  HHH_5            Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.2   0.0   2.7e-96   1.2e-92       1     432 []     180     704 ..     180     704 .. 0.86

  Alignments for each domain:
  == domain 1  score: 311.2 bits;  conditional E-value: 2.7e-96
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       R+k+P++R+++rgeGk++r++WdeAl++ia+ ++  ++    d++ gf ++p+ms +s+as+++l++llgg   sfy
  gi|313117036|ref|YP_004038160.1| 180 RIKHPLKRVGERGEGKWKRITWDEALTEIAEHVVDEVEAGRYDAISGFTPIPAMSPVSFASGSRLINLLGGVSHSFY 256
                                       9**************************************************************************** PP

                                       ECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HC CS
                     Molybdopterin  78 dwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryael 154
                                       dwy dlpp+++    ++++++n es     d++n+d+ii+wGsN+  +r ++  +++ +  ++ +k + i ++y+++
  gi|313117036|ref|YP_004038160.1| 257 DWYSDLPPGQP--ITWGTQTDNAESA----DWYNADYIIAWGSNINVTRIPDAKYFLESGYNG-TKRVGIFTDYSQT 326
                                       ***********..8899999999999....**********************66666655554.6666666677778 PP

                                       GGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCS................... CS
                     Molybdopterin 155 lkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleee................... 212
                                       + + dewl+++pg+d alal+m+ +i++e+++d+         ke+tdmpllv ++                     
  gi|313117036|ref|YP_004038160.1| 327 AIHTDEWLSPDPGSDTALALGMAQTIVSEGLYDE------AHLKEQTDMPLLVRQDTGkflrasdvpsvnssadrpe 397
                                       88********************************......99************99889****************** PP

                                       .........................................................................HHHH CS
                     Molybdopterin 213 .........................................................................tgkk 216
                                                                                                                + k 
  gi|313117036|ref|YP_004038160.1| 398 wmllmldsngqlreapgslgerdgqkdysksidldfdprldaettvqtddgsvqvrsvwaelrdelaqydpetVTKM 474
                                       ************************************************************************98888 PP

                                       HHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESS............ CS
                     Molybdopterin 217 kevvariarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnG............ 281
                                       ++v  ++ +++ar++a+ +  + ii G+g+n++++ d   ra+  L+ l+gn g++g+g+ h++G            
  gi|313117036|ref|YP_004038160.1| 475 TGVGTETYQRVAREFADVER-AKIIHGKGVNDWYHNDLGNRAIQLLVTLTGNLGRQGTGVDHYVGqekiwtfhgwkt 550
                                       88889999999999999998.66777***************************************777666666555 PP

                                       ..............CTTHHHCHHHHTCCTTCCCCCCCTT..........HHHHHCCCTTTCSTSS--ECGGCHHHHH CS
                     Molybdopterin 282 ..............qlilagaaekvgalpvllsvkslke..........ekikfaaeqpgnlgnfprnlfversnll 334
                                                                             +              +aa+ ++ + +       e  +  
  gi|313117036|ref|YP_004038160.1| 551 lsfptgkvrgvpttL-----------------------WtyyhagildnTDADTAAKIRESIDKGWMPVYPEEREDG 604
                                       555555555555550.......................344444455552233333333333332222233333333 PP

                                       HTTSSSEEEEESH.HHHHSTTSCCCHCHHH.CSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEE.E CS
                     Molybdopterin 335 kssgkkvlyllgnnpevdhadenevekale.kldlvvvldgrltstalyaDiiLPaatwyEkedlytndegrfqh.l 409
                                       ++ ++  +++ + n +++++ ++ ve++l  kldlvv + +r++staly+Di+LP+a+ yEk+dl+++d++   h +
  gi|313117036|ref|YP_004038160.1| 605 SRPDPTTMFVWRGNYFNQAKGNVAVEEELWpKLDLVVDINFRMDSTALYSDIVLPTASHYEKHDLSMTDMHTYVHpF 681
                                       3344445555555666666666666655555********************************************** PP

                                       EESSS-STT-BEHHHHHHHHHHH CS
                     Molybdopterin 410 kqavsppgeaksdwkIlkaLakk 432
                                        +av+p ge+k+dw+I+k+La+k
  gi|313117036|ref|YP_004038160.1| 682 TPAVEPLGESKTDWQIFKDLAEK 704
                                       *********************96 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   1.2e-23   5.2e-20       3     101 ..     856     955 ..     854     959 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.2e-23
                                       EEEE-BTTBSTTTT.TCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEES CS
                   Molydop_binding   3 Litgrsldqlhsqt.rtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpf 78 
                                       ++t++ ++ +hs+  ++ ++lrl++ ep  v+inp+dAa++Gi+dGd+Vev+++ G+vev+ak+ ++  +G++   f
  gi|313117036|ref|YP_004038160.1| 856 YNTPHGRWAIHSTWrDSEKMLRLQRGEP-IVYINPDDAAERGIEDGDTVEVFNDLGAVEVQAKIYPSSERGTLRHFF 931
                                       6899********998999*********9.************************************************ PP

                                       SHCC......S-GHCTS--SCSTT CS
                   Molydop_binding  79 gwwe.agekggnaNaltddatdpl 101
                                        w++ ++ ++ n N+l++ +++p+
  gi|313117036|ref|YP_004038160.1| 932 SWEKfQYASRNNFNTLVPMYMKPT 955
                                       *****************9888886 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   2.1e-05     0.094      10      54 ..     125     176 ..     117     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                       SBTT--EEEEEEETTEEE.......EEEE-TTSTTTTT---HHHHTCHHCCC CS
                    Molybdop_Fe4S4  10 yCgvgCglevhvkdgkiv.......kvegdpdhpvnegrlCvKGrtllervy 54 
                                       +C+ +C+ +v+vk+g++        + + d++ p+ + r C KG+   ++v+
  gi|313117036|ref|YP_004038160.1| 125 NCTGSCSWNVYVKNGQVWreeqsgdYPRFDESLPDPNPRGCQKGACYTDYVN 176
                                       8****************98888888888888889999********9999998 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.5   1.1e+04       4      14 ..      67      77 ..      62      87 .. 0.59
   2 ?   12.2   0.0   4.6e-05      0.21      27      55 ..     461     489 ..     452     491 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.5
                                      HHTSTT--HHH CS
                             HHH_5  4 LlsvsGiGpkt 14
                                      L sv GiG + 
  gi|313117036|ref|YP_004038160.1| 67 LASVLGIGSAS 77
                                      34444555443 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.6e-05
                                       HHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5  27 edlaaadveeLakipGiGkktAeriilel 55 
                                       ++la+ d+e+++k++G+G +t +r+  e 
  gi|313117036|ref|YP_004038160.1| 461 DELAQYDPETVTKMTGVGTETYQRVAREF 489
                                       79**********************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (996 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.41
# Mc/sec: 7319.53
//
Query:       gi|313117037|ref|YP_004038161.1|  [L=353]
Description: respiratory nitrate reductase beta subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-29  101.1   6.3      3e-29  101.1   6.3    1.8  2  Fer4_11   4Fe-4S dicluster domain
    3.9e-11   42.9  18.1      2e-05   24.6   7.8    3.3  3  Fer4_10   4Fe-4S dicluster domain
    1.1e-10   41.9  15.7    5.6e-05   23.7   7.3    3.5  3  Fer4_7    4Fe-4S dicluster domain
    6.6e-08   32.6  18.5     0.0034   17.5   7.0    3.4  4  Fer4_9    4Fe-4S dicluster domain
    0.00013   22.6   5.1       0.24   12.2   0.1    3.7  3  Fer4_15   4Fe-4S single cluster domain
    0.00022   21.2  29.5     0.0021   18.1   2.3    4.0  3  Fer4_2    4Fe-4S binding domain
    0.00034   21.1  19.6       0.11   13.1   0.1    3.9  3  Fer4_17   4Fe-4S dicluster domain
    0.00056   20.0  18.4       0.03   14.5   1.7    3.0  3  Fer4_21   4Fe-4S dicluster domain
    0.00076   19.2  29.8      0.014   15.2   2.7    5.4  5  Fer4      4Fe-4S binding domain
    0.00086   19.3  26.4      0.011   15.8   0.9    4.2  5  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.016   15.7   1.3      0.016   15.7   1.3    4.1  4  Fer4_4    4Fe-4S binding domain
       0.18   12.4  14.0       0.21   12.2   0.1    3.7  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.69   11.0  35.2       0.11   13.4   5.8    4.2  4  Fer4_3    4Fe-4S binding domain
        2.4    9.2  27.1        5.8    7.9   1.0    4.0  2  Fer4_16   4Fe-4S double cluster binding domain
        4.6    7.8  23.8    2.5e+02    2.2   1.1    4.0  3  Fer4_8    4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.9       4.7   5.6e+03      68      75 ..      29      36 ..      18      44 .. 0.59
   2 !  101.1   6.3   2.5e-32     3e-29       3      98 ..     144     244 ..     142     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.7
                           Fer4_11 68 vekCdmcl 75
                                      ++kC +c 
  gi|313117037|ref|YP_004038161.1| 29 LNKCIGCQ 36
                                      45555554 PP

  == domain 2  score: 101.1 bits;  conditional E-value: 2.5e-32
                           Fer4_11   3 wlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrve 79 
                                       +++lp++C+hC++p+Cv+++p++ai+k+ee+G+Vl+d+++++ ++r +ve+cPyk+v++n++++++ekC +c++r e
  gi|313117037|ref|YP_004038161.1| 144 YFYLPRICNHCTHPSCVEACPRKAIYKREEDGIVLIDQERCR-GYRYCVEGCPYKKVYYNAAKKTSEKCIFCYPRLE 219
                                       79***************************************9.********************************98 PP

                           Fer4_11  80 ......aGllpacvescptgalnfg 98 
                                             +  +pac e cp +++ +g
  gi|313117037|ref|YP_004038161.1| 220 gegpegETFAPACAEDCPPQLRLVG 244
                                       43332233579******99887665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.2e-06     0.005       2      19 ..      25      42 ..      24      91 .. 0.78
   2 !   24.6   7.8   1.6e-08     2e-05       6      56 .]     148     195 ..     144     195 .. 0.96
   3 !   20.8   3.9   2.6e-07   0.00031       2      56 .]     177     237 ..     176     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.2e-06
                           Fer4_10  2 vvidddtCirCgkCvkaC 19
                                      +v d ++Ci+C++C+ aC
  gi|313117037|ref|YP_004038161.1| 25 MVMDLNKCIGCQTCTVAC 42
                                      7899************** PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.6e-08
                           Fer4_10   6 ddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +  C +C+   Cv+aCP      +a+++++e++ v ++ e+C g  +Cve CP
  gi|313117037|ref|YP_004038161.1| 148 PRICNHCThpSCVEACPR-----KAIYKREEDGIVLIDQERCRGYRYCVEGCP 195
                                       678*****99********.....*****************************9 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 2.6e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc............g...aCveaCP 56 
                                       v id+++C + + Cv+ CP+         ++ + +a +k +ekC++c            +   aC+e CP
  gi|313117037|ref|YP_004038161.1| 177 VLIDQERCRGYRYCVEGCPY---------KKVYYNAAKKTSEKCIFCyprlegegpegeTfapACAEDCP 237
                                       689*****************.........7788888888899*****8888888777651567******9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.9e-06     0.011       1      18 [.      31      48 ..      14     108 .. 0.81
   2 !   23.7   7.3   4.7e-08   5.6e-05       2      50 ..     151     196 ..     150     198 .. 0.91
   3 !   13.3   6.2   8.1e-05     0.097       1      49 [.     183     237 ..     183     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.9e-06
                            Fer4_7  1 rCigCgaCvaaCpvkaie 18
                                      +CigC+ C++aC++ + e
  gi|313117037|ref|YP_004038161.1| 31 KCIGCQTCTVACKSLWTE 48
                                      688888888888655544 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 4.7e-08
                            Fer4_7   2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       C +C    Cv+aCp kai+ +ee   +    v id+e+C g + Cv+ CP+
  gi|313117037|ref|YP_004038161.1| 151 CNHCThpSCVEACPRKAIYKREE---D--GIVLIDQERCRGYRYCVEGCPY 196
                                       9***888*************987...3..5899*****************8 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 8.1e-05
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgC...............gaCvavCP 49 
                                       rC g ++Cv+ Cp+k ++++ +         +  +ekC++C                aC++ CP
  gi|313117037|ref|YP_004038161.1| 183 RCRGYRYCVEGCPYKKVYYNAA---------KKTSEKCIFCyprlegegpegetfaPACAEDCP 237
                                       799999*************987.........345789999955555555555444459*****9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   1.1e-05     0.013      34      47 ..      30      43 ..       5      55 .. 0.71
   2 !   10.8   2.4   0.00035      0.42      34      51 .]     149     168 ..     123     168 .. 0.74
   3 !   17.5   7.0   2.9e-06    0.0034       2      49 ..     151     197 ..     150     199 .. 0.90
   4 !   11.7   4.5   0.00019      0.23       2      49 ..     184     239 ..     183     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                            Fer4_9 34 eaCigCgaCveaCp 47
                                      ++CigC++C+ aC+
  gi|313117037|ref|YP_004038161.1| 30 NKCIGCQTCTVACK 43
                                      56777777777776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00035
                            Fer4_9  34 eaCigCga..CveaCpkgai 51 
                                         C +C    CveaCp++ai
  gi|313117037|ref|YP_004038161.1| 149 RICNHCTHpsCVEACPRKAI 168
                                       4599999899******9987 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 2.9e-06
                            Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C+ C+   CveaCp +++ +++  +++ ++++   +C g + Cve Cp +
  gi|313117037|ref|YP_004038161.1| 151 CNHCTHpsCVEACPRKAIYKREEDGIVLIDQE---RCRGYRYCVEGCPYK 197
                                       ****8666******************999774...8**99********85 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00019
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga...............CveaCpkg 49 
                                       C g ++Cve Cp++ v + aa+++ +       +Ci+C                 C+e Cp +
  gi|313117037|ref|YP_004038161.1| 184 CRGYRYCVEGCPYKKVYYNAAKKTSE-------KCIFCYPrlegegpegetfapaCAEDCPPQ 239
                                       677789**********9999999988.......5*****9999*****************976 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1    0.0002      0.24       2      38 ..      26      61 ..      25      74 .. 0.77
   2 ?    1.5   0.4      0.44   5.2e+02      56      64 ..     160     168 ..     157     170 .. 0.87
   3 !    8.9   0.1     0.002       2.4       1      19 [.     177     195 ..     177     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                           Fer4_15  2 vvDrdaCigcglCvaeapevfeldedglasvllddge 38
                                      v D ++Cigc  C  +++ + ++   g +++  ++ e
  gi|313117037|ref|YP_004038161.1| 26 VMDLNKCIGCQTCTVACKSLWTEG-GGRDYMYWNNVE 61
                                      57999************9888776.566666655555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.44
                           Fer4_15  56 araCPvdAI 64 
                                       ++aCP +AI
  gi|313117037|ref|YP_004038161.1| 160 VEACPRKAI 168
                                       589*****9 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.002
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       V +D+++C g   Cv+ +p
  gi|313117037|ref|YP_004038161.1| 177 VLIDQERCRGYRYCVEGCP 195
                                       78**************997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.3   1.7e-06    0.0021       3      20 ..      25      42 ..      23      44 .. 0.90
   2 !   14.7   2.8   2.1e-05     0.025       3      21 ..     144     164 ..     142     165 .. 0.90
   3 !    7.7   0.2    0.0035       4.1       3      22 .]     177     196 ..     175     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      +v d ++CigC +C+ aC
  gi|313117037|ref|YP_004038161.1| 25 MVMDLNKCIGCQTCTVAC 42
                                      67899************* PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.1e-05
                            Fer4_2   3 vvvdtdrCigCg..aCvsaCP 21 
                                       +++ +++C++C   +Cv aCP
  gi|313117037|ref|YP_004038161.1| 144 YFYLPRICNHCThpSCVEACP 164
                                       7899*******889******* PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0035
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       v +d +rC g + Cv  CP+
  gi|313117037|ref|YP_004038161.1| 177 VLIDQERCRGYRYCVEGCPY 196
                                       78999***9988*******5 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   8.9e-05      0.11      44      57 ..      30      43 ..       9      84 .. 0.75
   2 !   10.2   0.9   0.00071      0.85       2      24 ..     151     175 ..     150     179 .. 0.88
   3 ?    3.2   8.3      0.11   1.3e+02       1      31 [.     183     213 ..     183     241 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-05
                           Fer4_17 44 slCieCgeCerkCP 57
                                      ++Ci+C+ C+ +C 
  gi|313117037|ref|YP_004038161.1| 30 NKCIGCQTCTVACK 43
                                      55666666665553 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00071
                           Fer4_17   2 CiqCgy..ClpeCpsyeaydnepkk 24 
                                       C++C +  C+++Cp+ ++y+ e++ 
  gi|313117037|ref|YP_004038161.1| 151 CNHCTHpsCVEACPRKAIYKREEDG 175
                                       *****888**********9998875 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.11
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraakl 31 
                                       rC++ +yC++ Cp+ + y n  kk+ ++  +
  gi|313117037|ref|YP_004038161.1| 183 RCRGYRYCVEGCPYKKVYYNAAKKTSEKCIF 213
                                       79***************99999999888655 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.7   2.5e-05      0.03       3      19 ..      27      43 ..      24      48 .. 0.88
   2 !   13.0   5.4   7.1e-05     0.085       8      53 ..     151     196 ..     148     200 .. 0.77
   3 ?   -1.7   0.1       2.8   3.3e+03       5      11 ..     208     214 ..     202     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                           Fer4_21  3 idedkCigCgkCliaCe 19
                                      +d +kCigC+ C++aC+
  gi|313117037|ref|YP_004038161.1| 27 MDLNKCIGCQTCTVACK 43
                                      6789************8 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.1e-05
                           Fer4_21   8 CigCg..kCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPv 53 
                                       C +C+  +C+ aC+    +ai + ++  + ++ +++C G   C++ CP 
  gi|313117037|ref|YP_004038161.1| 151 CNHCThpSCVEACP---RKAIYKREEDGIVLIdQERCRGYRYCVEGCPY 196
                                       77887445999999...699977766655554399*************6 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.8
                           Fer4_21   5 edkCigC 11 
                                       ++kCi C
  gi|313117037|ref|YP_004038161.1| 208 SEKCIFC 214
                                       4566665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.7   1.2e-05     0.014       2      18 ..      26      42 ..      25      44 .. 0.90
   2 !   11.5   0.5   0.00018      0.21      14      24 .]     159     169 ..     158     169 .. 0.92
   3 !    6.7   0.5    0.0056       6.7       2      20 ..     178     196 ..     177     197 .. 0.89
   4 ?    3.8   0.2     0.046        54       5      11 ..     208     214 ..     204     215 .. 0.83
   5 ?   -1.0   1.6       1.5   1.8e+03      13      19 ..     231     237 ..     231     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                      EEETTTSSS-THHHHHS CS
                              Fer4  2 videekCigCGaCvevC 18
                                      v d +kCigC +C  +C
  gi|313117037|ref|YP_004038161.1| 26 VMDLNKCIGCQTCTVAC 42
                                      56999************ PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00018
                                       HHHHSTTTEEE CS
                              Fer4  14 CvevCPvgAIt 24 
                                       Cve+CP  AI+
  gi|313117037|ref|YP_004038161.1| 159 CVEACPRKAIY 169
                                       *********96 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0056
                                       EEETTTSSS-THHHHHSTT CS
                              Fer4   2 videekCigCGaCvevCPv 20 
                                        id+e+C g  +Cve CP+
  gi|313117037|ref|YP_004038161.1| 178 LIDQERCRGYRYCVEGCPY 196
                                       5999999999********8 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.046
                                       TTTSSS- CS
                              Fer4   5 eekCigC 11 
                                        ekCi+C
  gi|313117037|ref|YP_004038161.1| 208 SEKCIFC 214
                                       69***** PP

  == domain 5  score: -1.0 bits;  conditional E-value: 1.5
                                       HHHHHST CS
                              Fer4  13 aCvevCP 19 
                                       aC+e CP
  gi|313117037|ref|YP_004038161.1| 231 ACAEDCP 237
                                       7*****9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.9   9.3e-06     0.011       3      20 ..      26      43 ..      24      48 .. 0.91
   2 !   11.1   3.0   0.00028      0.33       8      24 .]     150     168 ..     146     168 .. 0.91
   3 !    9.2   0.2    0.0011       1.3       1      21 [.     176     196 ..     176     203 .. 0.89
   4 ?   -2.6   0.1       5.9   7.1e+03       7      13 ..     209     215 ..     208     216 .. 0.74
   5 ?   -2.0   0.5       3.8   4.5e+03      14      20 ..     231     237 ..     231     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.3e-06
                            Fer4_6  3 eidpdkCigCgdCvrvCP 20
                                      + d +kCigC  C+++C 
  gi|313117037|ref|YP_004038161.1| 26 VMDLNKCIGCQTCTVACK 43
                                      7899*************5 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00028
                            Fer4_6   8 kCigCgd..CvrvCPegai 24 
                                        C++C    Cv +CP +ai
  gi|313117037|ref|YP_004038161.1| 150 ICNHCTHpsCVEACPRKAI 168
                                       7**************9987 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0011
                            Fer4_6   1 vveidpdkCigCgdCvrvCPe 21 
                                       +v id+++C g + Cv  CP+
  gi|313117037|ref|YP_004038161.1| 176 IVLIDQERCRGYRYCVEGCPY 196
                                       5889****************8 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 5.9
                            Fer4_6   7 dkCigCg 13 
                                       +kCi C+
  gi|313117037|ref|YP_004038161.1| 209 EKCIFCY 215
                                       7999776 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 3.8
                            Fer4_6  14 dCvrvCP 20 
                                       +C+  CP
  gi|313117037|ref|YP_004038161.1| 231 ACAEDCP 237
                                       5999999 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   1.3   1.3e-05     0.016       2      15 ..      30      43 ..      29      53 .. 0.92
   2 ?    8.5   1.3    0.0027       3.2       4      16 ..     151     165 ..     142     170 .. 0.92
   3 ?    5.1   1.4     0.033        39       1      16 [.     181     196 ..     181     199 .. 0.89
   4 ?   -2.5   0.4         9   1.1e+04       9      15 ..     231     237 ..     230     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++CigC  C+ aC+
  gi|313117037|ref|YP_004038161.1| 30 NKCIGCQTCTVACK 43
                                      89***********8 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0027
                            Fer4_4   4 CigCg..sCvaaCPq 16 
                                       C++C   sCv aCP 
  gi|313117037|ref|YP_004038161.1| 151 CNHCThpSCVEACPR 165
                                       9***9889******5 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.033
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       qerC g + Cv  CP+
  gi|313117037|ref|YP_004038161.1| 181 QERCRGYRYCVEGCPY 196
                                       789999999******8 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 9
                            Fer4_4   9 sCvaaCP 15 
                                       +C   CP
  gi|313117037|ref|YP_004038161.1| 231 ACAEDCP 237
                                       6887888 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00017      0.21       2      27 ..      28      53 ..      26      71 .. 0.80
   2 ?    2.8   0.6      0.14   1.7e+02      10      26 ..     157     175 ..     150     178 .. 0.68
   3 ?    3.6   2.7     0.082        98       1      17 [.     179     195 ..     179     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                           Fer4_13  2 DrdtCiacgaCvelaPdvFeeddegg 27
                                      D ++Ci+c++C  ++  +  e     
  gi|313117037|ref|YP_004038161.1| 28 DLNKCIGCQTCTVACKSLWTEGGGRD 53
                                      789************98887766555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                           Fer4_13  10 gaCvelaPd..vFeeddeg 26 
                                        +Cve++P   +++++++g
  gi|313117037|ref|YP_004038161.1| 157 PSCVEACPRkaIYKREEDG 175
                                       3799999953378877775 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.082
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D+++C +   Cve +P
  gi|313117037|ref|YP_004038161.1| 179 IDQERCRGYRYCVEGCP 195
                                       8***************9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.4     0.012        14       1      11 [.      32      42 ..      32      44 .. 0.94
   2 ?   13.4   5.8   9.6e-05      0.11       1      15 []     151     167 ..     151     167 .. 0.90
   3 ?    5.9   0.8     0.024        28       3      14 ..     186     197 ..     183     198 .. 0.71
   4 ?    1.2   1.3      0.77   9.2e+02       1      12 [.     211     237 ..     211     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gC++C ++C
  gi|313117037|ref|YP_004038161.1| 32 CIGCQTCTVAC 42
                                      *********** PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.6e-05
                            Fer4_3   1 CtgCg..aCvevCPvgA 15 
                                       C++C    Cve+CP +A
  gi|313117037|ref|YP_004038161.1| 151 CNHCThpSCVEACPRKA 167
                                       ****8667******998 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.024
                            Fer4_3   3 gCgaCvevCPvg 14 
                                       g + Cve CP++
  gi|313117037|ref|YP_004038161.1| 186 GYRYCVEGCPYK 197
                                       3347******86 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.77
                            Fer4_3   1 CtgCg...............aCvevCP 12 
                                       C+ C+               aC e CP
  gi|313117037|ref|YP_004038161.1| 211 CIFCYprlegegpegetfapACAEDCP 237
                                       999*98888899999999888999888 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.0    0.0049       5.8      49      64 ..      27      42 ..       3      44 .. 0.66
   2 ?   -0.5  19.2       2.1   2.6e+03       2      57 ..     151     214 ..     150     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0049
                           Fer4_16 49 kkqeaitgCdiCqdvC 64
                                      +  ++++gC++C+ +C
  gi|313117037|ref|YP_004038161.1| 27 MDLNKCIGCQTCTVAC 42
                                      4457778888887777 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.1
                           Fer4_16   2 CgtCgk..CaevCPtnaikekkekei...earecisy....ntaekkdlaedeekckkqeaitgC 57 
                                       C  C+   C+e+CP +ai +++e  i   ++++c  y    +    k+++ +++k++  e++++C
  gi|313117037|ref|YP_004038161.1| 151 CNHCTHpsCVEACPRKAIYKREEDGIvliDQERCRGYrycvEGCPYKKVYYNAAKKT-SEKCIFC 214
                                       99999888***********99666543448888888887774444455555555554.4666666 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4  19.3      0.36   4.3e+02       2      64 ..      29     166 ..      28     199 .. 0.62
   2 ?    2.2   1.1      0.21   2.5e+02       4      63 ..     183     196 ..     180     212 .. 0.61
   3 ?    0.1   0.0      0.98   1.2e+03      56      62 ..     231     237 ..     227     263 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.36
                            Fer4_8   2 lekCieCgaCqsaCpvlrr.....................................tkkhlldargeaae....... 34 
                                       l+kCi+C+ C+ aC +l +                                                  e       
  gi|313117037|ref|YP_004038161.1|  29 LNKCIGCQTCTVACKSLWTegggrdymywnnvetkpgegyprdwensgggwkssehN------------Erqpgqip 93 
                                       79************7444434444444444444444444444444444443322221............02222222 PP

                            Fer4_8  35 ....dvqeeqvlee........................................eealwsCttcga..CtevCpvg 64 
                                           + ++++ +++                                         +    C++c +  C+e+Cp +
  gi|313117037|ref|YP_004038161.1|  94 sqedYGESWEFNHQeimydgsdqplrpqsdpewgpnwdedqgdgeypnsyyfylPR---ICNHCTHpsCVEACPRK 166
                                       23443333333333666666666666777777777777777788999988744444...455555455*****986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.21
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       +                                              C + + C+e Cp 
  gi|313117037|ref|YP_004038161.1| 183 R----------------------------------------------CRGYRYCVEGCPY 196
                                       4..............................................5555555555554 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.98
                            Fer4_8  56 aCtevCp 62 
                                       aC+e Cp
  gi|313117037|ref|YP_004038161.1| 231 ACAEDCP 237
                                       4666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2590.21
//
Query:       gi|313117038|ref|YP_004038162.1|  [L=274]
Description: DMSO reductase type II enzyme, heme b subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-29  101.3   5.7    2.8e-14   53.7   0.1    2.1  2  EB_dh     Ethylbenzene dehydrogenase
  ------ inclusion threshold ------
      0.079   12.2   1.6       0.15   11.3   1.6    1.4  1  MSP1a     Major surface protein 1a (MSP1a)


Domain annotation for each model (and alignments):
>> EB_dh  Ethylbenzene dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.1   3.1e-18   2.8e-14       3     135 ..      58     163 ..      56     172 .. 0.93
   2 !   50.0   1.9   4.1e-17   3.7e-13     191     248 ..     167     229 ..     162     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 3.1e-18
                                       HHHTS-EEEEE-EE--GGGG--S-----EEEEEEEE-SSEEEEEEEEE----.......-S--STT----EEEEEEE CS
                             EB_dh   3 dWskappveislsgqklvipvpgkeevkpvtVkAaydgeniyfrleWkdptksalpsevgegkeddeyedkvAvmfd 79 
                                       +W+k+ppve++l++++   p + ++ v++v+V++a ++ + y+r++W+d+t+      + ++ + +e++d+ Av+++
  gi|313117038|ref|YP_004038162.1|  58 AWDKVPPVEVPLTSAPSGLPNASDTSVETVRVQSARTDGRFYLRMSWHDGTA------DRNASDPREFADAAAVQVP 128
                                       8***************************************************......8999*************** PP

                                       S............STT--GGG..........T-BTTB-EEEEEEETT-SS-EEEEE CS
                             EB_dh  80 ddqaGcwgtchegarglpgapakeeatgskymgtagsfvdlwqWkagrseplglvd 135
                                       +           ++   p++           mg++ ++v++w+W a  ++++ l+ 
  gi|313117038|ref|YP_004038162.1| 129 V-----------NTSVRPPIS----------MGSTRNLVNVWYWHADGETEELLAG 163
                                       *...........99999**99..........****************999777665 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 4.1e-17
                                       .......---EEEEEEETTEEEEEEEEES---TTS..---TTEEEEEEEEEE-GGGT--TT-S CS
                             EB_dh 191 dt.....advkaeakykdGkWtVelvRpLkagnpldvalepgkvydvafAvwdgkagershhk 248
                                       +t     ++vk+ + y dG+WtV+++R+++++ +++++++ ++++dv+fAvw+g+++ers+ k
  gi|313117038|ref|YP_004038162.1| 167 TTtefesSSVKTATNYDDGRWTVVVSRAITTDTANQTSFAVDHDVDVSFAVWNGSNMERSGTK 229
                                       444556699***************************************************987 PP

>> MSP1a  Major surface protein 1a (MSP1a)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.6   1.7e-05      0.15     150     236 ..      11      99 ..       7     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.7e-05
                             MSP1a 150 aalvLfaisaavvva..trdessaltvsavPasdqqpdvreavasgGsqedsaqvpttsvP..aaess.avaPdtiv 221
                                       aa +L a+  +v +a  ++   +a+ ++++P+   + + ++  +s    e   +vp  +vP  +a s+  +a dt+v
  gi|313117038|ref|YP_004038162.1|  11 AAWALVAACFVVLTAvlGPATVAARPANQIPVESVSAEENPQQPS---SEAWDKVPPVEVPltSAPSGlPNASDTSV 84 
                                       7788887777776542267777889999***99999966666555...5666889999999876777734789**** PP

                             MSP1a 222 vsvspdsvatlGagv 236
                                        +v  +s  t G + 
  gi|313117038|ref|YP_004038162.1|  85 ETVRVQSARTDGRFY 99 
                                       **********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1773.46
//
Query:       gi|313117039|ref|YP_004038163.1|  [L=257]
Description: DMSO reductase type II enzyme chaperone [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-10   39.2   0.1    1.7e-09   37.8   0.1    1.9  1  Nitrate_red_del  Nitrate reductase delta subunit


Domain annotation for each model (and alignments):
>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.1   9.7e-14   1.7e-09      32     128 ..     119     210 ..      69     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 9.7e-14
                   Nitrate_red_del  32 eYtrLFlg...pgrrsasPyesvYlsekkgllfgestlevrefyrqaglevaeefneppDHlaveLeflahLaerea 105
                                       eYt+  +g   ++++++s+y+s Y+       +++  l+++++y  +gl+v+++ ++  D+l+  Lef ++La+rea
  gi|313117039|ref|YP_004038163.1| 119 EYTDRTDGslhSDGPPVSLYGSSYRP---DASWNDVNLDLARAYDYFGLTVDQSARDNHDYLPYQLEFAGYLARREA 192
                                       34443344775699************...579********************************************9 PP

                   Nitrate_red_del 106 eaeeaeeaealleaqkafleehl 128
                                       +     ++ ++ +a  +f ++hl
  gi|313117039|ref|YP_004038163.1| 193 D-----SSPDAGRARLDFHDRHL 210
                                       7.....56777788888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1702.11
//
Query:       gi|313117040|ref|YP_004038164.1|  [L=297]
Description: hypothetical protein Hbor_35080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0097   15.6   1.1     0.0097   15.6   1.1    4.3  7  FixS      Cytochrome oxidase maturation protein cbb3-type


Domain annotation for each model (and alignments):
>> FixS  Cytochrome oxidase maturation protein cbb3-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   1.9      0.47   8.5e+03      13      20 ..      99     106 ..      94     109 .. 0.47
   2 ?   -3.3   0.2      0.44   7.8e+03      11      18 ..     120     127 ..     118     134 .. 0.65
   3 ?   -3.1   1.1      0.37   6.7e+03      12      16 ..     153     157 ..     148     166 .. 0.43
   4 ?   -3.7   0.6      0.58     1e+04      11      19 ..     198     206 ..     196     211 .. 0.44
   5 ?   -1.8   0.1      0.15   2.7e+03      10      20 ..     221     231 ..     217     236 .. 0.69
   6 !   15.6   1.1   5.4e-07    0.0097       7      31 ..     234     258 ..     229     265 .. 0.82
   7 ?   -2.3   0.1      0.22   3.9e+03      12      14 ..     281     283 ..     267     289 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.47
                              FixS  13 lgllalaa 20 
                                       +g+++l+a
  gi|313117040|ref|YP_004038164.1|  99 VGGFGLIA 106
                                       33344443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.44
                              FixS  11 lllgllal 18 
                                       +++g+l++
  gi|313117040|ref|YP_004038164.1| 120 VVFGGLFV 127
                                       45666665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.37
                              FixS  12 llgll 16 
                                       l++++
  gi|313117040|ref|YP_004038164.1| 153 LVVAV 157
                                       22222 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 0.58
                              FixS  11 lllgllala 19 
                                       l  g++a a
  gi|313117040|ref|YP_004038164.1| 198 LAAGVVAGA 206
                                       333444333 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 0.15
                              FixS  10 Slllgllalaa 20 
                                       ++ll+++++++
  gi|313117040|ref|YP_004038164.1| 221 AVLLVGGGVVG 231
                                       67777777764 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 5.4e-07
                              FixS   7 iplSlllgllalaaFlWavksGQFD 31 
                                       i l ++ +++++a+++ a+++GQFD
  gi|313117040|ref|YP_004038164.1| 234 IALVVFAVGGGVAGLIAALRRGQFD 258
                                       445566678899************9 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 0.22
                              FixS  12 llg 14 
                                       +++
  gi|313117040|ref|YP_004038164.1| 281 VFV 283
                                       122 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1948.28
//
Query:       gi|313117041|ref|YP_004038165.1|  [L=277]
Description: HEAT repeat protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-22   78.6  22.8    1.8e-12   47.5   6.4    3.2  3  HEAT_2         HEAT repeats
    7.9e-10   38.1  11.8      0.001   19.1   0.0    6.0  6  HEAT           HEAT repeat
    0.00033   20.7   0.1        3.5    7.6   0.0    3.9  4  Cnd1           non-SMC mitotic condensation complex subunit 1
     0.0037   17.8  16.6        1.2   10.0   0.1    5.6  6  HEAT_PBS       PBS lyase HEAT-like repeat
     0.0078   16.7  15.6       0.14   12.7   0.1    4.7  5  HEAT_EZ        HEAT-like repeat
  ------ inclusion threshold ------
      0.025   14.5   0.3      0.066   13.2   0.3    1.7  1  DUF2019        Domain of unknown function (DUF2019)
       0.06   13.9   0.0        7.9    7.2   0.0    2.7  2  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   1.3    0.0028       7.3      30      60 ..      60      90 ..      35     104 .. 0.68
   2 !   44.1   5.0     8e-15   2.1e-11       3      85 ..      97     179 ..      95     182 .. 0.94
   3 !   47.5   6.4     7e-16   1.8e-12       7      86 ..     164     242 ..     160     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0028
                            HEAT_2 30 pealpaLvellededpavRraaaeaLgaigd 60
                                       +a++ L++ l+ +d   Rr aa aL++  +
  gi|313117041|ref|YP_004038165.1| 60 SDAVADLLSSLSGDDVVERRRAALALSERER 90
                                      3778888888888888888888888887764 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 8e-15
                            HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvv 79 
                                        L  a+++d+d +vr+ a+++L+++g p a ++   l++dedp+vR++a+ +L ++++ + ++  + +ldd +++ +
  gi|313117041|ref|YP_004038165.1|  97 GLAHAATTDADADVRQFAVESLAKLGGPVAAETASVLVDDEDPWVRAEAVVSLDRLDRGAHADRIEGALDDAHHAAR 173
                                       57788999********************************************************************* PP

                            HEAT_2  80 ReaAae 85 
                                       R+aA++
  gi|313117041|ref|YP_004038165.1| 174 RNAAIS 179
                                       *99875 PP

  == domain 3  score: 47.5 bits;  conditional E-value: 7e-16
                            HEAT_2   7 alendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaA 83 
                                       al +d++++ rr+a+++L + + ++alp L++l++d++++vR+ aa+ Lg i+d++a + L++l+ +d+ +vvRe A
  gi|313117041|ref|YP_004038165.1| 164 AL-DDAHHAARRNAAISLFKHRGEDALPELLDLADDPSERVREWAAHLLGGIADDRAHETLERLAEEDERSVVRETA 239
                                       35.9************************************************************************* PP

                            HEAT_2  84 aea 86 
                                       ++a
  gi|313117041|ref|YP_004038165.1| 240 VRA 242
                                       986 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.22   5.5e+02       5      21 ..      67      83 ..      63      87 .. 0.66
   2 !    9.4   0.0   0.00052       1.3       6      27 ..      99     121 ..      94     122 .. 0.81
   3 ?    5.3   0.1     0.011        28       9      26 ..     134     151 ..     131     155 .. 0.84
   4 ?    0.1   0.0      0.53   1.4e+03       5      24 ..     161     180 ..     159     181 .. 0.79
   5 !   19.1   0.0   4.1e-07     0.001       2      29 ..     189     216 ..     188     217 .. 0.94
   6 ?    5.3   0.1     0.011        29       5      23 ..     223     242 ..     221     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.22
                                      HHHHHT-SSHHHHHHHH CS
                              HEAT  5 llkllsDpspeVReaAa 21
                                      l +l  D+  e R+aA+
  gi|313117041|ref|YP_004038165.1| 67 LSSLSGDDVVERRRAAL 83
                                      44455888888777765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00052
                                       HHHH.T-SSHHHHHHHHHHHHHH CS
                              HEAT   6 lkll.sDpspeVReaAakaLgal 27 
                                        ++  +D +++VR+ A+++L++l
  gi|313117041|ref|YP_004038165.1|  99 AHAAtTDADADVRQFAVESLAKL 121
                                       556559**************987 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.011
                                       HT-SSHHHHHHHHHHHHH CS
                              HEAT   9 lsDpspeVReaAakaLga 26 
                                         D++p VR+ A+ +L +
  gi|313117041|ref|YP_004038165.1| 134 VDDEDPWVRAEAVVSLDR 151
                                       58**********988866 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.53
                                       HHHHHT-SSHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaL 24 
                                       +  +l D +   R++Aa +L
  gi|313117041|ref|YP_004038165.1| 161 IEGALDDAHHAARRNAAISL 180
                                       56779999999999999776 PP

  == domain 5  score: 19.1 bits;  conditional E-value: 4.1e-07
                                       HHHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgalae 29 
                                       lP ll l  Dps +VRe Aa  Lg +a 
  gi|313117041|ref|YP_004038165.1| 189 LPELLDLADDPSERVREWAAHLLGGIAD 216
                                       899*********************9985 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.011
                                       HHHHH.T-SSHHHHHHHHHH CS
                              HEAT   5 llkll.sDpspeVReaAaka 23 
                                       l +l  +D+ + VRe+A++a
  gi|313117041|ref|YP_004038165.1| 223 LERLAeEDERSVVRETAVRA 242
                                       5566668**********987 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0029       7.5      20      82 ..      92     149 ..      79     154 .. 0.67
   2 ?    3.8   0.0     0.021        54      30      48 ..     134     152 ..     128     162 .. 0.77
   3 !    7.6   0.0    0.0014       3.5      25      94 ..     160     223 ..     155     230 .. 0.78
   4 ?   -1.1   0.0      0.65   1.7e+03      31      42 ..     229     240 ..     221     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0029
                              Cnd1  20 eylvepLrk.rLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaal 82 
                                       +++v+ L + + +D d+ VR+ a+  +akL  +   +          l++De+p V+a a+ +l
  gi|313117041|ref|YP_004038165.1|  92 DPIVQGLAHaATTDADADVRQFAVESLAKLGGPVAAETAS------VLVDDEDPWVRAEAVVSL 149
                                       6666666541467999999999999999996655554444......445677777777776666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.021
                              Cnd1  30 LkDedpyVRktaaivvakL 48 
                                       + Dedp VR  a++ + +L
  gi|313117041|ref|YP_004038165.1| 134 VDDEDPWVRAEAVVSLDRL 152
                                       5799999999999988777 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0014
                              Cnd1  25 pLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseksenaiy 94 
                                       +++ +L D +   R++aai + k       + ++ l el++l +D+++rV++ a ++l  i++    +++
  gi|313117041|ref|YP_004038165.1| 160 RIEGALDDAHHAARRNAAISLFK------HRGEDALPELLDLADDPSERVREWAAHLLGGIADDRAHETL 223
                                       56677888888888888887766......344558999********************999988655554 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.65
                              Cnd1  31 kDedpyVRktaa 42 
                                       +De + VR+ta+
  gi|313117041|ref|YP_004038165.1| 229 EDERSVVRETAV 240
                                       699999999998 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.1     8e+03       9      23 ..      47      68 ..      42      71 .. 0.62
   2 ?    1.8   0.3       0.2   5.2e+02       2      11 ..      78      87 ..      77     102 .. 0.86
   3 !    6.0   0.0    0.0094        24       1      19 [.     110     128 ..     110     132 .. 0.90
   4 ?   -1.4   0.1       2.3   5.9e+03       1      11 [.     141     151 ..     141     154 .. 0.83
   5 !   10.0   0.1   0.00046       1.2       1      27 []     172     198 ..     172     198 .. 0.95
   6 !    8.0   0.3    0.0021       5.4       1      25 [.     203     227 ..     203     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.1
                                      HHHCTS.......GGGHHHHHH CS
                          HEAT_PBS  9 Lgqlgd.......eeaipaLle 23
                                      L++l +        +a++ Ll 
  gi|313117041|ref|YP_004038165.1| 47 LAELAAsdtepveSDAVADLLS 68
                                      5566556666666567777665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.2
                                      HHHHHHHHHH CS
                          HEAT_PBS  2 RraAakaLgq 11
                                      Rr+Aa aL +
  gi|313117041|ref|YP_004038165.1| 78 RRRAALALSE 87
                                      99*****975 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0094
                                       HHHHHHHHHHHCTSGGGHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaip 19 
                                       vR  A+++L++lg + a++
  gi|313117041|ref|YP_004038165.1| 110 VRQFAVESLAKLGGPVAAE 128
                                       8999*********988876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHH CS
                          HEAT_PBS   1 vRraAakaLgq 11 
                                       vR++A+ +L +
  gi|313117041|ref|YP_004038165.1| 141 VRAEAVVSLDR 151
                                       899**998865 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.00046
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       +Rr+Aa +L + + e+a+p Ll + +d
  gi|313117041|ref|YP_004038165.1| 172 ARRNAAISLFKHRGEDALPELLDLADD 198
                                       5*********************99887 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       vR +Aa  Lg + d++a ++L ++ 
  gi|313117041|ref|YP_004038165.1| 203 VREWAAHLLGGIADDRAHETLERLA 227
                                       8********************9876 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.6    0.0048        12      14      53 ..      47      86 ..      41      87 .. 0.86
   2 !    5.7   0.6    0.0085        22       3      55 .]      77     121 ..      76     121 .. 0.77
   3 ?   -1.9   0.2         2   5.2e+03      37      51 ..     165     179 ..     139     180 .. 0.58
   4 !   12.7   0.1   5.4e-05      0.14      28      53 ..     187     212 ..     186     212 .. 0.95
   5 ?    3.9   0.0     0.031        79      32      51 ..     222     242 ..     217     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0048
                           HEAT_EZ 14 laggepellqplvpeilpaLlalLnddsdeV..RaaAagaLg 53
                                      la+ ++ + +p+ +++++ Ll+ L  + d+V  R  Aa aL+
  gi|313117041|ref|YP_004038165.1| 47 LAELAASDTEPVESDAVADLLSSL--SGDDVveRRRAALALS 86
                                      778889999999999999999999..999999******9998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0085
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLl.alLnddsdeVRaaAagaLgnl 55 
                                       +Rr Aa+aL    +++ ++++     i+  L+ a+ +d +++VR+ A+  L++l
  gi|313117041|ref|YP_004038165.1|  77 ERRRAALAL----SERERTDP-----IVQGLAhAATTDADADVRQFAVESLAKL 121
                                       5999*****....77778888.....8888884444555559999999998875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2
                           HEAT_EZ  37 LnddsdeVRaaAaga 51 
                                       L d + + R +Aa+ 
  gi|313117041|ref|YP_004038165.1| 165 LDDAHHAARRNAAIS 179
                                       222222447777665 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 5.4e-05
                           HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLg 53 
                                       ++lp+Ll l  d+s +VR+ Aa+ Lg
  gi|313117041|ref|YP_004038165.1| 187 DALPELLDLADDPSERVREWAAHLLG 212
                                       789*********************98 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.031
                           HEAT_EZ  32 aLlalLnddsdeV.RaaAaga 51 
                                        L +l + d+ +V R++A++a
  gi|313117041|ref|YP_004038165.1| 222 TLERLAEEDERSVvRETAVRA 242
                                       68888888888888*****98 PP

>> DUF2019  Domain of unknown function (DUF2019)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   2.6e-05     0.066      40      92 ..     181     233 ..     168     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                                       HHHSTT-GGGGGGGGGGSS-HHHHHHHHHTTTTT-HHHHHHHHHHHHHHT-TT CS
                           DUF2019  40 LkrrdGDqRraLlsLyehpnvqvRlkAAkatLAvapaeArkqleaiasskelp 92 
                                        k+r  D    Ll L + p  +vR  AA+ +  +a  +A ++le +a+  e +
  gi|313117041|ref|YP_004038165.1| 181 FKHRGEDALPELLDLADDPSERVREWAAHLLGGIADDRAHETLERLAEEDERS 233
                                       57777888889***********************************9988766 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0031       7.9      24      52 ..      90     119 ..      79     152 .. 0.81
   2 ?    4.0   0.0     0.029        74      26      65 ..     186     225 ..     171     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0031
                     Vac14_Fab1_bd  24 yleeivkpvlk.cfsDkdsrvRyyacEsly 52 
                                        ++ iv+ + + + +D+d+ vR +a+Esl 
  gi|313117041|ref|YP_004038165.1|  90 RTDPIVQGLAHaATTDADADVRQFAVESLA 119
                                       556666666541578*************95 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.029
                     Vac14_Fab1_bd  26 eeivkpvlkcfsDkdsrvRyyacEslyniakvakgevlkl 65 
                                       e+ ++ +l+  +D ++rvR +a+  l  ia    +e l+ 
  gi|313117041|ref|YP_004038165.1| 186 EDALPELLDLADDPSERVREWAAHLLGGIADDRAHETLER 225
                                       67788999************99998888777666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1955.76
//
Query:       gi|313117042|ref|YP_004038166.1|  [L=433]
Description: ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-63  211.9   0.0    1.3e-62  211.4   0.0    1.1  1  ParA            NUBPL iron-transfer P-loop NTPase
    7.3e-17   61.0   0.1    1.9e-16   59.7   0.1    1.8  1  DUF2249         Uncharacterized conserved protein (DUF2249)
    1.5e-11   44.3   8.3    3.5e-11   43.1   4.3    2.6  2  FeS_assembly_P  Iron-sulfur cluster assembly protein
    1.3e-10   41.4   0.0    3.1e-10   40.2   0.0    1.6  2  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    2.1e-05   24.4   0.2     0.0053   16.6   0.0    2.4  2  AAA_26          AAA domain
    5.9e-05   23.1   0.2    0.00025   21.0   0.1    1.9  2  AAA_31          AAA domain
    0.00037   19.8   1.7       0.26   10.5   1.6    2.6  2  ArsA_ATPase     Anion-transporting ATPase
     0.0056   16.0   0.1       0.01   15.2   0.1    1.3  1  VirC1           VirC1 protein
      0.006   16.2   6.0      0.099   12.2   0.4    2.4  2  AAA_25          AAA domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.4   0.0   6.7e-66   1.3e-62       4     228 ..     114     336 ..     111     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 211.4 bits;  conditional E-value: 6.7e-66
                              ParA   4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea....kgikvm 76 
                                       +viav+S+KGGVGKStva+ lA+ La+ + ++gl+DaDi+Gp++p+ll++++   ++++ + +P  a     ++ vm
  gi|313117042|ref|YP_004038166.1| 114 TVIAVASAKGGVGKSTVATGLACGLAA-DRETGLFDADIHGPNVPTLLDIDGPIRSADDGSPLPAVAsgqnADLDVM 189
                                       79***********************75.789*********************755555656677766676678**** PP

                              ParA  77 SigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladv 153
                                       S+g++ +   +++ wrG+m++ a+++l++d++w+  D L++DlPPGtgD+ lt +q++p++g+v+Vttp  ++l+d+
  gi|313117042|ref|YP_004038166.1| 190 SVGLMET--GAPLAWRGAMAHDALTELYEDTAWHADDTLVLDLPPGTGDVVLTTLQEVPVDGVVVVTTPFPASLKDT 264
                                       ***9877..******************************************************************** PP

                              ParA 154 kkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlk 228
                                        +++e+f++  v+vlGvv Nm  f cp+cg+++ +f +g+     e+l++pll+e+p++p+++e+ + g+p+   
  gi|313117042|ref|YP_004038166.1| 265 ARSVELFRDNGVPVLGVVVNMGSFDCPSCGDSHPLFPEGSP---GETLSAPLLAELPFSPALQETPEPGTPHDSM 336
                                       ************************************99875...467889*******************985433 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.1   9.5e-20   1.9e-16       2      69 ..     360     431 ..     359     432 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 9.5e-20
                           DUF2249   2 lDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearr....pgffsweylergpgewrvlit 69 
                                       lD+R+ +p++r++++ e+f++L++G +++lv+d+dP+p++++L+       ++  + ++++++p++w++ +t
  gi|313117042|ref|YP_004038166.1| 360 LDLRGDTPEKRKERVSERFTSLESGAQFTLVSDRDPTPVREFLATLSdcrpDELADLQVERQTPNDWVLSVT 431
                                       9**********************************************9**99999*************9887 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   4.3   1.8e-14   3.5e-11       1      72 [.      24      95 ..      24      96 .. 0.93
   2 ?    2.3   0.1     0.099     2e+02      41      67 ..     328     353 ..     326     357 .. 0.75

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.8e-14
                                      HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEE CS
                    FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeairadaeaalralpgvevveV 72
                                      +++v+aaLr V+DP  +v++ ++glv++i+ie++ V+v  ++t    + a  + ++  +alr +pgve++ V
  gi|313117042|ref|YP_004038166.1| 24 EDRVEAALRAVRDPDADVNVFEAGLVESITIEDDAVTVEAAVTEFDDANAQVVMRAMLQALRDVPGVESAHV 95
                                      589*********************************************9999999999********666655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.099
                                       --SSTT-TTHHHHHHHHHHHHC.STT- CS
                    FeS_assembly_P  41 tltypacslaeairadaeaalralpgv 67 
                                       ++++p+ s ++++++++ +a+++ + v
  gi|313117042|ref|YP_004038166.1| 328 EPGTPHDS-MAELADAVADAAETAWDV 353
                                       68999999.667788888888876664 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.6e-13   3.1e-10       1      83 [.     116     285 ..     116     291 .. 0.85
   2 ?   -2.9   0.0       3.4   6.7e+03     105     125 ..     310     330 ..     304     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.6e-13
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ia+as kGGvGK+t+a++La+ la   +++ l+DaD  ++n  +l    + i+                        
  gi|313117042|ref|YP_004038166.1| 116 IAVASAKGGVGKSTVATGLACGLAA-DRETGLFDADIHGPNVPTLLDIDGPIRSaddgsplpavasgqnadldvmsv 191
                                       89***********************.*****************8666666666677799999999999999999999 PP

                                       ....................................................................CCHCCCHHH CS
                                       ....................................................................xxxxxxxxx RF
                              CbiA  55 ....................................................................dlkrllell 63 
                                                                                                           +lk   +++
  gi|313117042|ref|YP_004038166.1| 192 glmetgaplawrgamahdaltelyedtawhaddtlvldlppgtgdvvlttlqevpvdgvvvvttpfpaSLKDTARSV 268
                                       99999999999999999999999999999999999999999999999999999999999999999998444444444 PP

                                       HHHCHCHHHH..EEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              CbiA  64 ealgkkkalllkiagvvlnr 83 
                                       e ++ +    + ++gvv+n+
  gi|313117042|ref|YP_004038166.1| 269 ELFRDN---GVPVLGVVVNM 285
                                       444433...26689999986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.4
                                       TS-EEEEEE--CCHCCCCHHT CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA 105 gvpvlgviprdeavaeaparg 125
                                         p+l+++p++ a+ e p+ g
  gi|313117042|ref|YP_004038166.1| 310 SAPLLAELPFSPALQETPEPG 330
                                       679999*****9999988765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.3    0.0088        18       3      25 ..     116     138 ..     114     147 .. 0.86
   2 !   16.6   0.0   2.7e-06    0.0053     131     195 ..     250     324 ..     236     326 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0088
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvral 25 
                                       i v++   gvGK++v++gL+  l
  gi|313117042|ref|YP_004038166.1| 116 IAVASAKGGVGKSTVATGLACGL 138
                                       77999**************9777 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.7e-06
                            AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNkvrnp.....e.....nvetlekksgipvlGvvPylpdle 195
                                       v++V+++   ++++++ ++e++r+++v+vlGv++N    +     +     +  +  ++ + p+l+++P +p l+
  gi|313117042|ref|YP_004038166.1| 250 VVVVTTPFPASLKDTARSVELFRDNGVPVLGVVVNMGSFDcpscgDshplfPEGSPGETLSAPLLAELPFSPALQ 324
                                       7888888999*************************8322233333233333333344444479999999998886 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   1.3e-07   0.00025       2      29 ..     114     141 ..     113     155 .. 0.86
   2 ?   -0.8   0.0       0.6   1.2e+03     119     155 ..     224     262 ..     184     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalakl 29 
                                        vIa+a  KGGvGK+T ++ la+ la  
  gi|313117042|ref|YP_004038166.1| 114 TVIAVASAKGGVGKSTVATGLACGLAAD 141
                                       59***********************964 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.6
                            AAA_31 119 DyiiiDcpPsLglltenaL..vasdsviipvqaeayale 155
                                       D  ++D pP  g ++ + L  v  d v++++ + + +l+
  gi|313117042|ref|YP_004038166.1| 224 DTLVLDLPPGTGDVVLTTLqeVPVDGVVVVTTPFPASLK 262
                                       88999****999888877733456888888877666665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   1.6   0.00013      0.26       6      30 ..     119     143 ..     114     147 .. 0.84
   2 !    6.6   0.0    0.0019       3.8     207     244 ..     248     285 ..     236     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                       EEESTTSSHHHHHHHHHHHHHHTTS CS
                       ArsA_ATPase   6 vgGKGGVGKttvsaatavklsekgk 30 
                                        + KGGVGK+tv++ +a+ l+  ++
  gi|313117042|ref|YP_004038166.1| 119 ASAKGGVGKSTVATGLACGLAADRE 143
                                       578****************998876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0019
                                       EEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 207 tsfrlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                         +++V++p   slk+t R+++ +   g+ v  v+vN 
  gi|313117042|ref|YP_004038166.1| 248 DGVVVVTTPFPASLKDTARSVELFRDNGVPVLGVVVNM 285
                                       56899********************************6 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.1e-06      0.01       3      41 ..     115     152 ..     114     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
                             VirC1   3 litfcslkGGaGkttalmglcsalasdgkrvalfeaden 41 
                                       +i+++s kGG Gk+t   gl + la+d+   +lf+ad  
  gi|313117042|ref|YP_004038166.1| 115 VIAVASAKGGVGKSTVATGLACGLAADR-ETGLFDADIH 152
                                       6899****************99999985.56*****965 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.9    0.0034       6.8      79     132 ..      16      67 ..      13      86 .. 0.69
   2 !   12.2   0.4     5e-05     0.099      34      62 ..     115     143 ..     105     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0034
                            AAA_25  79 aEdsedelrrRlravgealrddarllvldlagv.eslpLfakdrggtlltadvda 132
                                        E + d+l+ R++a+++a+rd++    +  ag  es+++   +++  +++a+v +
  gi|313117042|ref|YP_004038166.1|  16 VETDSDTLEDRVEAALRAVRDPDADVNVFEAGLvESITI---EDDAVTVEAAVTE 67 
                                       69999**************77665555556787788876...2333334444433 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5e-05
                            AAA_25  34 elallaGapgtGKttlaldlalavatGkp 62 
                                        +a+  + +g+GK+t+a+ la+ +a +++
  gi|313117042|ref|YP_004038166.1| 115 VIAVASAKGGVGKSTVATGLACGLAADRE 143
                                       5677889*****************95543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2919.56
//
Query:       gi|313117043|ref|YP_004038167.1|  [L=429]
Description: sugar phosphate permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-38  133.1  50.3    1.1e-35  123.3  34.2    2.0  2  MFS_1       Major Facilitator Superfamily
    2.6e-08   33.1  16.8    4.9e-06   25.7  15.9    2.6  2  MFS_1_like  MFS_1 like family
    2.9e-05   23.0  10.0    0.00023   20.1   2.9    2.2  2  LacY_symp   LacY proton/sugar symporter
  ------ inclusion threshold ------
      0.035   12.5  22.1      0.099   11.0  15.1    2.3  2  MFS_3       Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.3  34.2   2.4e-39   1.1e-35       6     309 ..      29     339 ..      21     346 .. 0.83
   2 !   14.7  11.9   2.4e-06     0.011      93     180 ..     337     424 ..     329     429 .] 0.90

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 2.4e-39
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                       fl+ + r+++ p++  a + ++g+s++++gl++t+ + ++a++++p G +sdrfG+  v+ +g ++ alg+l l+f 
  gi|313117043|ref|YP_004038167.1|  29 FLAKFVRYAFPPLFE-AFQASYGLSVATVGLVYTGLMTVYALLQFPSGMISDRFGSVQVITAGSIVAALGSLTLVFD 104
                                       677788888999999.99****************************************************7777786 PP

                             MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslg......... 149
                                       ++ +l++v+ vl G+g+ga  ++++ ++++++p  + gr++g++ +  s G + + +++  +l+             
  gi|313117043|ref|YP_004038167.1| 105 APAPLFVVAAVLVGAGTGAHKTVSIRVLSRVYPS-RTGRVLGIFDTIGSYGGVGAsAVVTLFLV-VPPiarplisrl 179
                                       7778*****************************9.***********888777555166666666.333669999999 PP

                             MFS_1 150 ....Wravfyilaivsllafvlfllllpeepperkrkspkeee...kgtgpaplvpawkallkdpvlwillialllf 219
                                           Wr+vf++++++++l++  f++l+p    +   ++ +++      t+   l++ ++ l+ +     ++++ ++f
  gi|313117043|ref|YP_004038167.1| 180 pgepWRGVFLLAGLFGILLAAAFAWLVPSQLAATDDPNATQDDdgrDPTVFDYLRQ-FSDLRFSA----FILVTIFF 251
                                       9********************99999977777777777777742222333333344.66666666....66666666 PP

                             MFS_1 220 ffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallav 296
                                       +f+++g++++lplyl e+ +++   +a +l+++l++++ i+++++g +sdr+gr ++l+++l+++++a+++l+++a 
  gi|313117043|ref|YP_004038167.1| 252 SFAYNGAVAFLPLYLSETADFT-TTTANILYSVLFALS-IVQIVTGDISDRTGRLPILVVTLVVAAAALVALVVFAS 326
                                       67********************.788888899999998.668*********************************** PP

                             MFS_1 297 tssavllllvlvl 309
                                       +   vl+ +v++l
  gi|313117043|ref|YP_004038167.1| 327 AGPLVLGSAVVAL 339
                                       *555444444444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.4e-06
                             MFS_1  93 vlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfl 169
                                       v  ++g+ ++ p+ +++++++ p+   + ++g++ +    + ++ p++ g++a+ +++r +f++la+ ++ a+ l++
  gi|313117043|ref|YP_004038167.1| 337 VALAVGSHGFRPVRGVYLVEILPEWIAAGGLGVVRTLLMGAGAVSPAIIGYVADVFNFRIAFVVLAASMAGAAALAA 413
                                       677889999***************************************************************99888 PP

                             MFS_1 170 lllpeepperk 180
                                        ll+ e+ ++ 
  gi|313117043|ref|YP_004038167.1| 414 GLLLSERDTST 424
                                       88877766655 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7  15.9   1.1e-09   4.9e-06      18     384 ..      38     399 ..      25     400 .. 0.81
   2 !    7.4   0.2   0.00039       1.7      37      86 ..     368     418 ..     362     424 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.1e-09
                        MFS_1_like  18 llPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqee 94 
                                       + P +  +  s gl+++ +g++++ l+ +  l +   g+++Drfg   +v+ ++++++a+  l l+f          
  gi|313117043|ref|YP_004038167.1|  38 FPPLFEAFQASYGLSVATVGLVYTGLMTVYALLQFPSGMISDRFGSV-QVITAGSIVAALGSLTLVFDA-------- 105
                                       66788888899*********************************986.688889999999888888755........ PP

                        MFS_1_like  95 sklevsvaqdvdaektfwilfllvvlasfflaailvll.daatlkelgedrkdyGrqrlfGsvGyaifa..fitGil 168
                                                   +   f++ ++lv  ++   +++ + +   +    +g   + +  +  +G vG   ++  f++   
  gi|313117043|ref|YP_004038167.1| 106 ------------PAPLFVVAAVLVGAGTGAHKTVSIRVlSRVYPSRTGRVLGIFDTIGSYGGVGASAVVtlFLVVPP 170
                                       ............78899999999999999998876655055555778999999**********97555401444444 PP

                        MFS_1_like 169 idhysvnllp......ysallyvlaallvisllvvlilnetekesklkvtksl.......qvllnilknpeviifll 232
                                       i    ++ lp      +  ll+ l ++l+++ +  l++ +  + ++ + t+ +        + l+ +++ +  +f+l
  gi|313117043|ref|YP_004038167.1| 171 IARPLISRLPgepwrgV-FLLAGLFGILLAAAFAWLVPSQLAATDDPNATQDDdgrdptvFDYLRQFSDLRFSAFIL 246
                                       55555555558996542.33344455566666666888888888888888766899988867889999********* PP

                        MFS_1_like 233 valilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllya 308
                                       v+++  ++++ + +Fl lYL +  ++++t++ +l  +  +++i+   +   + +++G   +l+++l++ ++ ++ + 
  gi|313117043|ref|YP_004038167.1| 247 VTIFFSFAYNGAVAFLPLYLsETADFTTTTANILYSVLFALSIVQI-VTGDISDRTGRLPILVVTLVVAAAALVALV 322
                                       ********************99999*****9999999999999875.5678************************** PP

                        MFS_1_like 309 iienawlvlpievLhgisfgllwa..aaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                       ++ +a  +++  +  ++++g      +   y  +i p+ ++a g g++ +l +g+G  + ++iG ++ d ++ +++F
  gi|313117043|ref|YP_004038167.1| 323 VFASAGPLVLGSAVVALAVGSHGFrpVRGVYLVEILPEWIAAGGLGVVRTLLMGAGAVSPAIIG-YVADVFNFRIAF 398
                                       **77777777777777777654330144458888*****************************9.888999999988 PP

                        MFS_1_like 384 r 384
                                        
  gi|313117043|ref|YP_004038167.1| 399 V 399
                                       6 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00039
                        MFS_1_like  37 giitlilpltsilsppiwgvlaDrfgkrkk..vvilslllsavlflsllfip 86 
                                       g++ ++l+    +sp i+g +aD f+ r +  v+++s+  +a+l ++ll ++
  gi|313117043|ref|YP_004038167.1| 368 GVVRTLLMGAGAVSPAIIGYVADVFNFRIAfvVLAASMAGAAALAAGLL-LS 418
                                       888899999999***********99988885355555666666666666.44 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.7   0.00036       1.6      13      99 ..      25     116 ..      13     143 .. 0.73
   2 !   20.1   2.9     5e-08   0.00023       7      96 ..     239     325 ..     233     418 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00036
                         LacY_symp  13 alffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkel.....lwvi.sll 83 
                                       a  +f+  f+  a+ plf  + +   gls + +G+v++ +  +  l+q   G+isd++G  + +     + ++ sl 
  gi|313117043|ref|YP_004038167.1|  25 AAIWFLAKFVRYAFPPLFEAF-QASYGLSVATVGLVYTGLMTVYALLQFPSGMISDRFGSVQVItagsiVAALgSLT 100
                                       556777778877888888876.56789**********99988888889999********765431111133333455 PP

                         LacY_symp  84 lvlfapfliyvfepll 99 
                                       lv+ ap  ++v + +l
  gi|313117043|ref|YP_004038167.1| 101 LVFDAPAPLFVVAAVL 116
                                       7777777777766554 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5e-08
                         LacY_symp   7 tnfylfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvisll 83 
                                         f  f l+  f+ f +    +++p++l+e  +++ t   i++sv+  +si+ q + G isd+ G    l+  ++l+
  gi|313117043|ref|YP_004038167.1| 239 LRFSAFILVTIFFSFAYNGAVAFLPLYLSETADFTTTTANILYSVLFALSIV-QIVTGDISDRTGRLPILV--VTLV 312
                                       467788888888888899999************************8777765.899********9655444..4444 PP

                         LacY_symp  84 lvlfapfliyvfe 96 
                                       +   a   + vf+
  gi|313117043|ref|YP_004038167.1| 313 VAAAALVALVVFA 325
                                       4444444455553 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.6   0.00091       4.1      43     107 ..      52     116 ..      42     159 .. 0.84
   2 ?   11.0  15.1   2.2e-05     0.099     227     400 ..     247     422 ..     231     427 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00091
                             MFS_3  43 splmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlll 107
                                       s ++v lv         ll  ++G ++D f   +v+ a+ ++ al+s++l+  a   l+ + ++l
  gi|313117043|ref|YP_004038167.1|  52 SVATVGLVYTGLMTVYALLQFPSGMISDRFGSVQVITAGSIVAALGSLTLVFDAPAPLFVVAAVL 116
                                       66677777776666678999999********9999999999999999999988877777666655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.2e-05
                             MFS_3 227 aalFglsa.savlaLLPlvardqld....gdalvyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvl 298
                                        ++F+ +a    +a LPl   ++ d    +  + y +l++   v  ++g ++  + R  +   +lv  aa+ +Alv+
  gi|313117043|ref|YP_004038167.1| 247 VTIFFSFAyNGAVAFLPLYLSETADftttTANILYSVLFALSIVQIVTGDISDRTGRLPILVVTLVVAAAALVALVV 323
                                       3455555416789*****88776542221556778888887777888888999999999****************** PP

                             MFS_3 299 lslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaealsvtla 375
                                       ++ a    l  av++l++g  ++  +   + v    ++P+W+ + +l v  t+l+G+ a   ++ G va+  + ++a
  gi|313117043|ref|YP_004038167.1| 324 FASAGPLVLGSAVVALAVGSHGFRPVRGVYLV---EILPEWIAAGGLGVVRTLLMGAGAVSPAIIGYVADVFNFRIA 397
                                       *9999999999999999999999887776655...579*************************************99 PP

                             MFS_3 376 Llaaaaalllaaaillllklpelea 400
                                         + aa++  aaa+   l l e+++
  gi|313117043|ref|YP_004038167.1| 398 FVVLAASMAGAAALAAGLLLSERDT 422
                                       9999999988888877777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2929.04
//
Query:       gi|313117044|ref|YP_004038168.1|  [L=328]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-21   75.4   0.0      1e-20   74.7   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
  ------ inclusion threshold ------
      0.095   12.7   0.0       0.17   11.9   0.0    1.4  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   1.2e-24     1e-20       1     117 [.       1     117 [.       1     120 [. 0.95

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.2e-24
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHH CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngthe 76 
                                       +r++i  + +ig+kh+ p  ++  ++ev a+ +++++ra++va++fg++ +++++e+l+a ++ida++   pn++h+
  gi|313117044|ref|YP_004038168.1|   1 MRFGILSTANIGTKHFLPAIKQ-TDHEVSAIASRNSSRAQTVADEFGIPeVCDSYEALVAREDIDAIYNPLPNSLHA 76 
                                       578888899******9999888.899***********************88888*********************** PP

                                       HHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EE CS
                      GFO_IDH_MocA  77 elakaaleagkhvllEKPlattveeakelvelaekkgklvs 117
                                         +k+a+e+  hvl+EKP + + +ea++l +++e ++ +v+
  gi|313117044|ref|YP_004038168.1|  77 TWTKRAIENDLHVLCEKPSTVDADEARKLRATVEASDSVVM 117
                                       ***********************************999887 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.9e-05      0.17       5     114 ..     135     235 ..     132     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                                       HTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSC CS
                    GFO_IDH_MocA_C   5 engklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaede 81 
                                         +++ e++sv+  +    + +++ +r +++   +gG+ +d g +  Dl++  +G+p +v+  l      ++ + d+
  gi|313117044|ref|YP_004038168.1| 135 IRNQFSEIRSVTARFAFLLQDRPDDIRLQDE--LDGGSMMDVGYYPVDLTRSVLGTPETVYGSL---LDPRDSGTDT 206
                                       5577888999977888888888888888876..7*************************99877...4445444444 PP

                                       SEEEEEEEEEEETTEEEEEEEECCTSSSEEEEE CS
                    GFO_IDH_MocA_C  82 daavmsvlnlekgsgevitlesgvskglsiryv 114
                                         +    + +e+ sg++++ +sg+ ++ls  y+
  gi|313117044|ref|YP_004038168.1| 207 VMN----ALFEYPSGATANVSSGFESTLSQFYR 235
                                       444....89999999999999999998887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1917.75
//
Query:       gi|313117045|ref|YP_004038169.1|  [L=295]
Description: peptide ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-31  109.1   7.1      2e-31  109.1   7.1    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0013   18.7   1.1     0.0013   18.7   1.1    2.2  2  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.08   7.1e+02     155     175 ..      34      54 ..      10     104 .. 0.74
   2 !  109.1   7.1   2.3e-35     2e-31       1     181 [.     112     292 ..     112     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.08
                      BPD_transp_1 155 nggvlalviavlllnlvadil 175
                                         +++++++ +l+++++a +l
  gi|313117045|ref|YP_004038169.1|  34 GLLSVVILAPILVFSFAAPVL 54 
                                       456666666666666666555 PP

  == domain 2  score: 109.1 bits;  conditional E-value: 2.3e-35
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g++lGi+++ + ++++d+++++l+++l+s+Ps++la+l+v      ++lg++    +++++++++++++r++r++ l
  gi|313117045|ref|YP_004038169.1| 112 GVPLGIFSG-YLGGRFDEVVMRLMDTLFSFPSLLLALLVV------TGLGSGLVNtILAIGVVFTPGIARITRSSTL 181
                                       89*******.******************************......*********9********************* PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       ++++++++ aa+a+G s ++i ++ +lPn+ + i+  + +++g+ +   + l+flg    lgt+   + +gy++s+ 
  gi|313117045|ref|YP_004038169.1| 182 SVINEEYITAAEARGESLFRIAFREILPNVSSAILVEASIRIGFGILIGTSLSFLG----LGTQPPFPDWGYMISSS 254
                                       ********************************************************....***************88 PP

                      BPD_transp_1 154 s..........nggvlalviavlllnlvadilqrlldp 181
                                                   ++ lal++ ++ +nl+ d+l +++dp
  gi|313117045|ref|YP_004038169.1| 255 RshlhdsiwfmLWPGLALGLTIMGFNLLGDALRDVIDP 292
                                       8************************************8 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.1   1.4e-07    0.0013      16      51 .]      34      71 ..      26      71 .. 0.83
   2 ?   -1.3   0.2      0.25   2.3e+03      24      37 ..     160     173 ..     143     185 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-07
                            OppC_N 16 AvvglvilllllliaifaPliaPydp..qdliqnllpP 51
                                       +++ vil+ +l++++ aP++aPydp  ++ i+++++P
  gi|313117045|ref|YP_004038169.1| 34 GLLSVVILAPILVFSFAAPVLAPYDPtaTHIIDKFAAP 71
                                      57899*********************876555557777 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.25
                            OppC_N  24 llllliaifaPlia 37 
                                        +l++ ++f P ia
  gi|313117045|ref|YP_004038169.1| 160 TILAIGVVFTPGIA 173
                                       34444567788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1661.57
//
Query:       gi|313117046|ref|YP_004038170.1|  [L=320]
Description: peptide ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-40  137.5   7.3    4.1e-40  137.5   7.3    2.2  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2      0.14   2.5e+03     164     175 ..      18      29 ..       5      51 .. 0.61
   2 ?   -0.0   0.3     0.035   6.2e+02     137     172 ..      77     115 ..      68     117 .. 0.73
   3 !  137.5   7.3   2.3e-44   4.1e-40       1     184 [.     116     316 ..     116     317 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.14
                      BPD_transp_1 164 avlllnlvadil 175
                                        ++l++l+++ +
  gi|313117046|ref|YP_004038170.1|  18 TLILISLIVFGV 29 
                                       333333333333 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.035
                      BPD_transp_1 137 lgtllleailgydyseis...nggvlalviavlllnlva 172
                                        g++ +++ +++++++i+    + ++ l+i++l l++v+
  gi|313117046|ref|YP_004038170.1|  77 TGNWGTSFANQQPVTAIIfprLVRSAQLAIVTLTLVTVT 115
                                       688888888888888888888778888888888888776 PP

  == domain 3  score: 137.5 bits;  conditional E-value: 2.3e-44
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..................vilsilghlilpviil 59 
                                       +i+lG+laa+++ +++d l ++  +v+ slP fv++ l++ +f                   i ++++h+ilp ++l
  gi|313117046|ref|YP_004038170.1| 116 AIPLGVLAAVKQDSIWDLLASVGGYVGVSLPEFVIGTLFITLFagpvfqilpfggyeplsaGIVTWAKHMILPSVTL 192
                                       69*************************************************************************** PP

                      BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                       +++ +a ++rl+r++++++l +d+v+ ar++G+s+ +++ k++l+n l p+it+l+l++g+llg  v++e +++ pG
  gi|313117046|ref|YP_004038170.1| 193 SIILTAHVMRLTRSEIVEVLREDYVRSARLKGLSELKVLTKHTLRNGLLPTITLLALNIGYLLGSIVIVEEVFTFPG 269
                                       ***************************************************************************** PP

                      BPD_transp_1 137 lgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       lg+ll+++i+ ++++  + ++v  ++i++ + nl+adi++++ldpr++
  gi|313117046|ref|YP_004038170.1| 270 LGRLLVRSIQTRNLPVLQ-ASVMLIAIVYTVTNLAADIMYTYLDPRIE 316
                                       ******************.***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2100.05
//
Query:       gi|313117047|ref|YP_004038171.1|  [L=693]
Description: peptide ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-64  215.4   0.0    1.1e-30  107.0   0.0    2.5  2  ABC_tran         ABC transporter
    8.5e-36  122.3   0.6    8.6e-17   61.4   0.1    2.5  2  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
      1e-17   64.9   8.3    5.2e-09   36.3   0.2    4.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      5e-17   62.1   0.2    8.3e-08   31.9   0.0    2.8  2  SMC_N            RecF/RecN/SMC N terminal domain
    5.4e-09   36.7   0.1     0.0012   19.2   0.0    2.5  2  AAA_16           AAA ATPase domain
    3.8e-07   29.8   0.7      0.021   14.5   0.1    2.3  2  AAA_29           P-loop containing region of AAA domain
      5e-06   26.5   1.0       0.55   10.1   0.1    3.5  3  NACHT            NACHT domain
    6.3e-06   26.2   0.6      0.027   14.4   0.1    2.4  2  RsgA_GTPase      RsgA GTPase
      1e-05   25.4   1.2       0.96    9.2   0.0    3.8  4  IstB_IS21        IstB-like ATP binding protein
    1.2e-05   25.6   5.3        0.1   12.9   0.2    3.9  2  AAA_22           AAA domain
    1.4e-05   25.2   0.1        1.1    9.6   0.0    3.9  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
    4.2e-05   23.2   0.2       0.21   11.1   0.0    3.6  4  AAA_25           AAA domain
      6e-05   23.2   0.9       0.26   11.4   0.2    2.6  2  DUF87            Helicase HerA, central domain
     0.0002   21.1   0.0      0.038   13.7   0.0    2.2  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    0.00066   19.5   0.1       0.19   11.4   0.0    2.4  2  PRK              Phosphoribulokinase / Uridine kinase family
     0.0012   18.3   0.2        1.2    8.5   0.0    3.4  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0019   17.4   1.0        1.3    8.1   0.1    2.7  2  NB-ARC           NB-ARC domain
     0.0026   17.5   2.1        4.2    7.0   0.0    3.6  4  Sigma54_activat  Sigma-54 interaction domain
     0.0044   17.4   0.3        4.5    7.7   0.0    2.4  2  RNA_helicase     RNA helicase
     0.0051   16.8   1.8        3.4    7.7   0.0    3.5  3  AAA_5            AAA domain (dynein-related subfamily)
     0.0066   16.6   0.1        1.5    9.0   0.0    2.7  2  AAA_33           AAA domain
     0.0069   16.8   0.1        6.2    7.3   0.0    2.9  2  AAA              ATPase family associated with various cellul
     0.0078   16.3   0.3       0.24   11.4   0.2    2.5  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0099   16.0   1.0        2.9    8.0   0.1    2.6  2  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.01   16.4   0.0        7.8    7.1   0.0    2.7  2  AAA_18           AAA domain
      0.011   16.2   0.0        2.5    8.5   0.0    2.3  2  AAA_23           AAA domain
      0.011   14.4   1.0        1.6    7.3   0.0    3.3  4  AAA_13           AAA domain
      0.012   14.9   0.4        2.5    7.3   0.1    2.7  3  Zeta_toxin       Zeta toxin
      0.012   15.3   0.2        2.1    8.0   0.1    2.4  2  AAA_24           AAA domain
      0.016   15.1   1.7       0.31   10.9   0.1    2.6  2  NTPase_1         NTPase
      0.018   14.4   0.2        6.6    6.0   0.0    2.4  2  ATPase           KaiC
      0.026   14.4   0.3        2.7    7.9   0.0    2.3  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.035   13.4   0.2        1.9    7.7   0.0    2.3  2  Septin           Septin
      0.039   13.4   0.4        5.6    6.3   0.0    3.5  4  TniB             Bacterial TniB protein
      0.041   13.6   1.1        8.8    5.9   0.1    2.9  3  AAA_15           AAA ATPase domain
      0.047   13.6   0.8       0.58   10.0   0.1    2.5  2  APS_kinase       Adenylylsulphate kinase
      0.062   12.8   0.1        5.4    6.5   0.0    2.4  2  AAA_7            P-loop containing dynein motor region
      0.071   13.2   0.0        4.4    7.4   0.0    2.4  2  tRNA_lig_kinase  tRNA ligase kinase domain
      0.082   12.1   0.1       0.17   11.1   0.1    1.4  1  TIP49            TIP49 P-loop domain
       0.12   12.4   0.0       0.29   11.1   0.0    1.6  1  Methyltransf_32  Methyltransferase domain
       0.14   11.7   0.1          3    7.3   0.0    2.2  2  GTP_EFTU         Elongation factor Tu GTP binding domain
       0.19   11.7   0.2        1.6    8.7   0.1    2.2  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.21   11.1   0.8         16    5.0   0.1    2.4  2  Hpr_kinase_C     HPr Serine kinase C-terminal domain
       0.25   11.6   0.3         13    6.1   0.1    2.4  2  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.48   10.2   2.4         16    5.2   0.2    2.4  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.0   5.4e-33   2.1e-30       2     136 ..      37     194 ..      36     195 .. 0.92
   2 !  107.0   0.0   2.7e-33   1.1e-30       2     136 ..     387     537 ..     386     538 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 5.4e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..x RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....qeleslrkeigvlpqe..p 68 
                                       ++vsl++++ge+++i Ge+G+GKStL+  +++ l      t+G+i++ g+++ +    + +    +ei+ +pq+  +
  gi|313117047|ref|YP_004038171.1|  37 RDVSLHINAGETLGIAGESGSGKSTLALSILRYLGEngriTSGNIEYHGASILDlsskELRALRGNEIAHVPQDpnT 113
                                       79************************99999888766777999999999999999995555666789*******989 PP

                                       -S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEE CS
                                       xxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpklll 131
                                       +l+p ++v+++              e+ e+ +++l+++++++ +++++k+ p++LSgGq+qrv la al+++p+ll+
  gi|313117047|ref|YP_004038171.1| 114 SLNPSMRVGDQiaevlrthrdisraEAMEQTYDVLREVNIPD-PERNAKQYPHELSGGQQQRVLLAIALACQPQLLI 189
                                       9********************999999999************.99999***************************** PP

                                       EESTT CS
                                       xxxxx RF
                          ABC_tran 132 lDEpt 136
                                       lDEpt
  gi|313117047|ref|YP_004038171.1| 190 LDEPT 194
                                       ****9 PP

  == domain 2  score: 107.0 bits;  conditional E-value: 2.7e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + vs++++ +e++a+vGe+G+GKStL ++l+ l + t G++ ++g+d+ e   q ++++r+e ++++q+  ++l+p+
  gi|313117047|ref|YP_004038171.1| 387 DGVSFDIHDSETLAVVGESGCGKSTLGSVLLDLQSRTDGSVSYKGTDVGEmnsQAMKEFRSECQIVFQNphSSLNPK 463
                                       78**********************************************99999****************9899**** PP

                                       SBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +tv+e               +++e+++++l+++g   l+ + +k+ p+ LSgG+kqrva+ara+  +p++++lDEp 
  gi|313117047|ref|YP_004038171.1| 464 HTVGEAikrplemftdlsdaAQRERVAELLTQVG---LQPDYAKRYPRDLSGGEKQRVAIARAFSVNPSFVVLDEPV 537
                                       *****************55555555555555555...555777778******************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   1.4e-18   5.5e-16       1      65 []     246     308 ..     246     308 .. 0.97
   2 !   61.4   0.1   2.2e-19   8.6e-17       2      63 ..     590     652 ..     589     655 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.4e-18
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E+g+++k+f++p++PYT++Ll+s+p+ d+++   + i+g+  +l++ ++GC Fa+RC+fa ++C
  gi|313117047|ref|YP_004038171.1| 246 LEYGSTEKIFESPANPYTQGLLASLPQGDNQRL--KPIPGQIGDLTAVSDGCTFANRCEFAEPAC 308
                                       69**************************99888..****************************** PP

  == domain 2  score: 61.4 bits;  conditional E-value: 2.2e-19
                         oligo_HPY   2 ErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfale 63 
                                       E+g+++++f+ p+HPYT+aLl+s+p+ d+  +     ++g++ps+++ ++GCpF++RCp++  
  gi|313117047|ref|YP_004038171.1| 590 EIGTTEEIFEPPYHPYTRALLSSIPSTDPTVEtDRIYLDGDVPSARDPPSGCPFHTRCPQKIG 652
                                       99***************************999767789**********************875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4      0.28   1.1e+02       4      22 ..      51      70 ..      49      96 .. 0.66
   2 !   36.3   0.2   1.3e-11   5.2e-09     225     302 ..     155     230 ..     100     231 .. 0.77
   3 ?    5.8   0.0     0.026        11       3      25 ..     400     422 ..     399     454 .. 0.75
   4 !   22.4   0.0   2.3e-07   9.3e-05     227     302 ..     500     573 ..     460     574 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.28
                            AAA_21  4 liGpNgsGKSnL.Ldaldll 22
                                      + G  gsGKS+L L +l++l
  gi|313117047|ref|YP_004038171.1| 51 IAGESGSGKSTLaLSILRYL 70
                                      8899*******933333333 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 1.3e-11
                            AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                       ++++  +  ++elS G+++   l+ al+ ++    ll++DEp +gL+   ++++l+l++el + +++ v+l TH+  
  gi|313117047|ref|YP_004038171.1| 155 DPERNAKQYPHELSGGQQQRVLLAIALACQP---QLLILDEPTTGLDVTTQAKILDLINELIEeRNTSVLLITHNLG 228
                                       55666777899********977777777777...9***********************6666669**********98 PP

                            AAA_21 301 ll 302
                                       ++
  gi|313117047|ref|YP_004038171.1| 229 VI 230
                                       87 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.026
                            AAA_21   3 vliGpNgsGKSnLLdaldllarl 25 
                                       +++G  g+GKS+L   l  l++ 
  gi|313117047|ref|YP_004038171.1| 400 AVVGESGCGKSTLGSVLLDLQSR 422
                                       689**************999864 PP

  == domain 4  score: 22.4 bits;  conditional E-value: 2.3e-07
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       +d+ ++ +r+lS G k+  a++ a+   +   s++++DEp + L+ ++++++l ll el++  g+  +l +H+ +++
  gi|313117047|ref|YP_004038171.1| 500 PDYAKRYPRDLSGGEKQRVAIARAFSVNP---SFVVLDEPVSALDVSVQASILNLLTELREaYGTSYLLISHDLSVV 573
                                       67888999**********77777777777...9***********************99988899*********8876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.2     9e-09   3.6e-06      27     213 ..      49     241 ..      32     246 .. 0.73
   2 !   31.9   0.0   2.1e-10   8.3e-08      25     207 ..     397     578 ..     385     588 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9e-09
                                       EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCC...CCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrsekls...dlihk..skekasvkkaeveitfdnedkklkiekeevs 98 
                                         i G+ GSGKs l  +il +LGe+    + s +++   + i    ske +++   e++ + ++++ +    ++++ 
  gi|313117047|ref|YP_004038171.1|  49 LGIAGESGSGKSTLALSILRYLGENG--RITSGNIEyhgASILDlsSKELRALRGNEIAHVPQDPNTS---LNPSMR 120
                                       4699*******************753..3444444311122222346677777778888877777776...667777 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                       +  ++ +  +++  i + e+ ++ + ++l++++i            +LSgG+++ v la+ +A q   p  l +lDe
  gi|313117047|ref|YP_004038171.1| 121 VGDQIAEVLRTHRDISRAEAMEQTY-DVLREVNIPDPernakqyphELSGGQQQRVLLAIALACQ---P-QLLILDE 192
                                       7777777777777777777665544.56666666444466666666********99999998865...4.4899*** PP

                                       TTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 167 idaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvtk 213
                                           LD +  +k+ +l++e  ++  + ++ i+++ +++++    vg++ 
  gi|313117047|ref|YP_004038171.1| 193 PTTGLDVTTQAKILDLINELIEErnTSVLLITHNLGVISRIADRVGIMY 241
                                       ******************865433399********99999988888765 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 2.1e-10
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       +  a+vG+ G+GKs l   +   L  r+  +  s k +d+   +++  +  + e +i+f+n+ ++    +++ ++  
  gi|313117047|ref|YP_004038171.1| 397 ETLAVVGESGCGKSTLGSVL-LDLQSRTDGS-VSYKGTDVGEMNSQAMKEFRSECQIVFQNPHSS---LNPKHTVGE 468
                                       4569**********998777.4444444433.34555566555566677778889999****999...788999999 PP

                                       EEETTSEEEEEETTE.EE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingk.evtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                        +kr  e  ++ + +  ++++ v+ell ++g++++        LSgGek+ va+a  f+++     ++++lDe  +a
  gi|313117047|ref|YP_004038171.1| 469 AIKRPLE--MFTDLSdAAQRERVAELLTQVGLQPDyakryprDLSGGEKQRVAIARAFSVN----PSFVVLDEPVSA 539
                                       9999888..4444440456699*************9999999***************9986....47********** PP

                                       S-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkekskn..aQfivislreemlekadk 207
                                       LD +  + + +ll e ++   + ++ is++  +++  + 
  gi|313117047|ref|YP_004038171.1| 540 LDVSVQASILNLLTELREAygTSYLLISHDLSVVRYISD 578
                                       **************9998766788999988877776654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     3e-06    0.0012      21     106 ..      45     130 ..      32     219 .. 0.67
   2 !   15.0   0.0   6.2e-05     0.025      23      66 ..     395     438 ..     376     565 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3e-06
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde......... 88 
                                       +g  e + + GesG+GKs+l+ ++lr+l ++ g  ++g+ + ++++     ++++ ++ el +  ++e         
  gi|313117047|ref|YP_004038171.1|  45 AG--ETLGIAGESGSGKSTLALSILRYLGEN-GRITSGNIEYHGAS-----ILDLSSK-ELRALRGNEiahvpqdpn 112
                                       33..67889****************999988.88899998888222.....3333322.333333333222222233 PP

                            AAA_16  89 aesaeleawrekleeala 106
                                       ++ +   +  +++ e+l+
  gi|313117047|ref|YP_004038171.1| 113 TSLNPSMRVGDQIAEVLR 130
                                       222233333333444433 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.2e-05
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesa 66 
                                       ++e + ++GesG+GKs+l   ll+  ++++g + +  +d  e++
  gi|313117047|ref|YP_004038171.1| 395 DSETLAVVGESGCGKSTLGSVLLDLQSRTDGSVSYKGTDVGEMN 438
                                       558899*************9999766666677777777776555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.4e-05     0.021      15      38 ..      39      62 ..      34      70 .. 0.79
   2 !   13.4   0.1   0.00012     0.049      13      38 ..     387     412 ..     384     418 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.4e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTl 38
                                       +++i+  ++  ++G+sGsGKSTl
  gi|313117047|ref|YP_004038171.1| 39 VSLHINAGETLGIAGESGSGKSTL 62
                                      566777555777***********9 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00012
                            AAA_29  13 dghtieidlkgatlltGpsGsGKSTl 38 
                                       dg +++i+ +++  ++G+sG GKSTl
  gi|313117047|ref|YP_004038171.1| 387 DGVSFDIHDSETLAVVGESGCGKSTL 412
                                       77889999888999***********8 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1    0.0014      0.55       2      26 ..      48      72 ..      47      78 .. 0.84
   2 ?    4.4   0.1     0.078        31      70     129 ..     173     226 ..     129     242 .. 0.68
   3 !    8.7   0.0    0.0037       1.5       2      18 ..     398     414 ..     397     465 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      ++ + Ge+GsGK+tL+ ++ + + e
  gi|313117047|ref|YP_004038171.1| 48 TLGIAGESGSGKSTLALSILRYLGE 72
                                      56699***********999887765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.078
                                       -CCHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEEC CS
                             NACHT  70 sevwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrp 129
                                       ++v   ++   +  LlilD   e  t l+  +++++ +l++eli++   +++s+ll++++
  gi|313117047|ref|YP_004038171.1| 173 QRVLLAIALACQPQLLILD---EPTTGLDVTTQAKILDLINELIEE---RNTSVLLITHN 226
                                       2244444444455557776...6666666666799***********...66666666654 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0037
                                       CEEEEC-TTTCHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlq 18 
                                       ++++ Ge+G+GK+tL  
  gi|313117047|ref|YP_004038171.1| 398 TLAVVGESGCGKSTLGS 414
                                       789***********844 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0018      0.73      88     119 ..      34      66 ..      14      81 .. 0.76
   2 !   14.4   0.1   6.8e-05     0.027      93     132 ..     389     429 ..     374     443 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinal 119
                                       +++++++ +++  +t  ++G+SG GKStL  ++
  gi|313117047|ref|YP_004038171.1|  34 KAVRDVSLHINAgETLGIAGESGSGKSTLALSI 66 
                                       46666776776669999************7655 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.8e-05
                                       HHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinallpelelktgevse 132
                                       ++  ++d +t ++vG+SG GKStL  +ll  ++   g+vs 
  gi|313117047|ref|YP_004038171.1| 389 VSFDIHDsETLAVVGESGCGKSTLGSVLLDLQSRTDGSVSY 429
                                       56667776999*************99999877766677765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0094       3.8      43      67 ..      42      66 ..      23      78 .. 0.81
   2 ?    4.8   0.1     0.051        20      98     149 ..     174     227 ..     166     233 .. 0.70
   3 !    9.2   0.0    0.0024      0.96      39      81 ..     387     430 ..     376     448 .. 0.83
   4 ?   -1.9   0.0       5.8   2.3e+03     107     154 ..     526     575 ..     514     578 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0094
                         IstB_IS21 43 fiekkenivllGpsGvGKshlaial 67
                                      +i++ e + + G sG GKs la ++
  gi|313117047|ref|YP_004038171.1| 42 HINAGETLGIAGESGSGKSTLALSI 66
                                      689999****************987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.051
                         IstB_IS21  98 klaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsi...iitsnl 149
                                       ++  a++   +++llilD+   + ld   +++++++i++  e r +   +it nl
  gi|313117047|ref|YP_004038171.1| 174 RVLLAIALACQPQLLILDEPT-TGLDVTTQAKILDLINELIEERNTsvlLITHNL 227
                                       555566777899*******64.567888888888888888877654212566665 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0024
                         IstB_IS21  39 atlsf.iekkenivllGpsGvGKshlaialgveavraglsvlfv 81 
                                        + sf i+++e ++++G sG GKs l   l     r++ sv++ 
  gi|313117047|ref|YP_004038171.1| 387 DGVSFdIHDSETLAVVGESGCGKSTLGSVLLDLQSRTDGSVSYK 430
                                       5566668999****************999988888888888885 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.8
                         IstB_IS21 107 lkvdllilDd.lgllpld.qaeaellfeviekryerrsiiitsnlpfaew 154
                                       ++++ ++lD+ ++ l+++ qa+  +l+  + ++y+++ ++i+ +l++ ++
  gi|313117047|ref|YP_004038171.1| 526 VNPSFVVLDEpVSALDVSvQASILNLLTELREAYGTSYLLISHDLSVVRY 575
                                       55678889985566666624445568888899999999999999888665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   1.0    0.0026       1.1      10      38 ..      51      84 ..      46     232 .. 0.52
   2 !   12.9   0.2   0.00026       0.1       8      38 ..     399     446 ..     393     574 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0026
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaee.....e 38
                                      + GesG+GK+tl+  +l+ l e   ++      +
  gi|313117047|ref|YP_004038171.1| 51 IAGESGSGKSTLALSILRYLGENGRITSgnieyH 84
                                      78***********999999876655555444331 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00026
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.....................e 38 
                                       l+v+GesG+GK+tl   ll+   +     +                     +
  gi|313117047|ref|YP_004038171.1| 399 LAVVGESGCGKSTLGSVLLDLQSRT----DgsvsykgtdvgemnsqamkefR 446
                                       89************99999987431....12333433333333333333330 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0027       1.1      24      89 ..     158     210 ..     136     211 .. 0.71
   2 !    9.5   0.0    0.0029       1.2      32      89 ..     509     553 ..     487     554 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0027
                           SbcCD_C  24 kelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       ++ ++   +lSGG++q +  la+a  la   +       +++l++LDE   +lD +++a++l+l++
  gi|313117047|ref|YP_004038171.1| 158 RNAKQYPHELSGGQQQRV-LLAIA--LA---C-------QPQLLILDEPTTGLDVTTQAKILDLIN 210
                                       455666678888888433.33333..22...2.......26799***************9999976 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0029
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                        lSGGekq         a+a ++s       ++++v+LDE  s lD   +a++l+ll+
  gi|313117047|ref|YP_004038171.1| 509 DLSGGEKQR-------VAIARAFSV------NPSFVVLDEPVSALDVSVQASILNLLT 553
                                       677777743.......344455555......5899*******************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00054      0.21      29      53 ..      42      66 ..      35      75 .. 0.90
   2 ?   -2.4   0.0       7.5     3e+03     136     150 ..     179     192 ..     136     225 .. 0.56
   3 ?    5.6   0.0     0.026        11      32      53 ..     395     416 ..     370     419 .. 0.84
   4 ?    1.7   0.0      0.42   1.7e+02     143     188 ..     528     568 ..     472     569 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00054
                            AAA_25 29 llpagelallaGapgtGKttlaldl 53
                                      ++ age+  +aG +g+GK+tlal++
  gi|313117047|ref|YP_004038171.1| 42 HINAGETLGIAGESGSGKSTLALSI 66
                                      7899*******************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.5
                            AAA_25 136 aieevegvrlvviDp 150
                                        + + ++++l+++D 
  gi|313117047|ref|YP_004038171.1| 179 IALA-CQPQLLILDE 192
                                       3444.5677777774 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.026
                            AAA_25  32 agelallaGapgtGKttlaldl 53 
                                         e+ +++G +g+GK+tl + l
  gi|313117047|ref|YP_004038171.1| 395 DSETLAVVGESGCGKSTLGSVL 416
                                       568889***********98765 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.42
                            AAA_25 143 vrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                       + +vv+D   +al+ + +     +++++ l ++++++g   ll+ H
  gi|313117047|ref|YP_004038171.1| 528 PSFVVLDEPVSALDVSVQ-----ASILNLLTELREAYGTSYLLISH 568
                                       788888888888888777.....789999***************99 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.2   0.00065      0.26      14      48 ..      39      71 ..      29      81 .. 0.80
   2 !    9.5   0.0    0.0023      0.94      23      45 ..     396     418 ..     382     427 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00065
                             DUF87 14 vyldlnklvtrHlAilgsTGsGKSntvavLleell 48
                                      v+l++n    + l+i g++GsGKS+++ ++l+ l 
  gi|313117047|ref|YP_004038171.1| 39 VSLHINA--GETLGIAGESGSGKSTLALSILRYLG 71
                                      5666633..4679*****************99775 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0023
                             DUF87  23 trHlAilgsTGsGKSntvavLle 45 
                                       ++ lA++g++G GKS++ +vLl+
  gi|313117047|ref|YP_004038171.1| 396 SETLAVVGESGCGKSTLGSVLLD 418
                                       4679*****************97 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   9.4e-05     0.038       6      89 ..      38     161 ..      34     164 .. 0.89
   2 ?    5.1   0.0      0.04        16       9      44 ..     391     426 ..     383     497 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-05
                                       HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                       ATP-synt_ab   6 DalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg.................................. 48 
                                       D+ + i  G++++i g++g Gk++++ s++++  ++   i  g                                  
  gi|313117047|ref|YP_004038171.1|  38 DVSLHINAGETLGIAGESGSGKSTLALSILRYLGEN-GRITSGnieyhgasildlsskelralrgneiahvpqdpnt 113
                                       66677889************************9777.777777788888999999********************** PP

                                       .......ESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS-HHHHHHH CS
                                       .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  49 .......iGergnevaevleefpegtimkrtvlvantsnepvaareas 89 
                                              +G +  ev +  +++ ++++m++t  v+ + n p  +r a 
  gi|313117047|ref|YP_004038171.1| 114 slnpsmrVGDQIAEVLRTHRDISRAEAMEQTYDVLREVNIPDPERNAK 161
                                       ***99999999999999999999999****999999999999888776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.04
                                       S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   9 fpivqGqrtlipgafgvGktvisqslskqsnsddai 44 
                                       f i   ++++++g++g+Gk+++ + l+  ++ +d +
  gi|313117047|ref|YP_004038171.1| 391 FDIHDSETLAVVGESGCGKSTLGSVLLDLQSRTDGS 426
                                       667788999*************98887765444433 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00048      0.19       2      34 ..      49      82 ..      48     116 .. 0.75
   2 ?    5.7   0.0     0.027        11       3      22 ..     400     419 ..     398     463 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00048
                               PRK  2 IgvagsSGaGkttvarklekifgrek.vkaaeie 34
                                      +g+ag+SG+Gk+t+a  +   +g+++ +++ +ie
  gi|313117047|ref|YP_004038171.1| 49 LGIAGESGSGKSTLALSILRYLGENGrITSGNIE 82
                                      59****************9999966413444444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.027
                               PRK   3 gvagsSGaGkttvarkleki 22 
                                       +v g+SG+Gk+t+   l ++
  gi|313117047|ref|YP_004038171.1| 400 AVVGESGCGKSTLGSVLLDL 419
                                       899*********87766655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.12        49      19      46 ..      43      70 ..      30      89 .. 0.78
   2 ?    2.2   0.0      0.25     1e+02       4      49 ..     166     212 ..     164     232 .. 0.76
   3 !    8.5   0.0     0.003       1.2      25      93 ..     399     468 ..     389     475 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                      Mg_chelatase 19 aaGgHnlllvGppGsGKtmlakrlpsll 46
                                      +  g  l ++G +GsGK+ la  +   l
  gi|313117047|ref|YP_004038171.1| 43 INAGETLGIAGESGSGKSTLALSILRYL 70
                                      4555678899***********8776655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                      Mg_chelatase   4 dvkGqeeakraleiaaaGgHnlllvGppGsGKtmlak.rlpsllppl 49 
                                       ++ G ++++  l ia a + +ll++  p +G  +  + ++  l+ +l
  gi|313117047|ref|YP_004038171.1| 166 ELSGGQQQRVLLAIALACQPQLLILDEPTTGLDVTTQaKILDLINEL 212
                                       67899999********************9997655431344455544 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.003
                      Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeee.kllkrrpfraphhsaskaalvGg 93 
                                       l +vG +G+GK+ l + l  l ++ + + + + + +  ++++  +e +   +  f++ph s      vG 
  gi|313117047|ref|YP_004038171.1| 399 LAVVGESGCGKSTLGSVLLDLQSRTDGSVSYKGTDVGEMNSQAMKEfRSECQIVFQNPHSSLNPKHTVGE 468
                                       7789**********************9999999999988885444414555678******9998888875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0034       1.3      22      42 ..      48      68 ..      32      76 .. 0.85
   2 !    7.0   0.0    0.0074         3      20      38 ..     396     414 ..     383     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0034
                                      EEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 22 vvalvGmgGvGKttlakqiln 42
                                       +++ G  G+GK+tla +il+
  gi|313117047|ref|YP_004038171.1| 48 TLGIAGESGSGKSTLALSILR 68
                                      689*************99987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0074
                                       SEEEEEEESTTSSHHHHHH CS
                            NB-ARC  20 slvvalvGmgGvGKttlak 38 
                                       s  +a+vG  G+GK+tl +
  gi|313117047|ref|YP_004038171.1| 396 SETLAVVGESGCGKSTLGS 414
                                       4489************976 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.011       4.2      11      44 ..      35      68 ..      27      85 .. 0.78
   2 ?   -1.1   0.1       3.4   1.4e+03      96     119 ..     187     211 ..     175     230 .. 0.83
   3 ?    6.7   0.0     0.013       5.4      23      52 ..     397     426 ..     384     444 .. 0.78
   4 ?   -0.3   0.0         2   7.8e+02      95     119 ..     529     554 ..     516     559 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                                      HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellaraihe 44
                                      +++ ++  ++   ++ i GesG+GK++la +i +
  gi|313117047|ref|YP_004038171.1| 35 AVRDVSLHINAGETLGIAGESGSGKSTLALSILR 68
                                      4555666666777888*************88865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.4
                                       EEEEET.GGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  96 tlfLDe.igelplelQekLlrvlqe 119
                                        l LDe  + l++++Q+k+l +++e
  gi|313117047|ref|YP_004038171.1| 187 LLILDEpTTGLDVTTQAKILDLINE 211
                                       6788984457999*******99987 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.013
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekp 52 
                                        ++ ++GesG+GK++l + + + ++r++++
  gi|313117047|ref|YP_004038171.1| 397 ETLAVVGESGCGKSTLGSVLLDLQSRTDGS 426
                                       466799*************99988888764 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2
                                       SEEEEET.GGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  95 GtlfLDe.igelplelQekLlrvlqe 119
                                       + + LDe ++ l++++Q+ +l++l e
  gi|313117047|ref|YP_004038171.1| 529 SFVVLDEpVSALDVSVQASILNLLTE 554
                                       5678999899************9976 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.014       5.5       3      25 ..      51      73 ..      49      89 .. 0.80
   2 ?    7.7   0.0     0.011       4.5       3      19 ..     401     417 ..     399     455 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.014
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkk 25
                                      + G+sg GKStla ++ + l ++
  gi|313117047|ref|YP_004038171.1| 51 IAGESGSGKSTLALSILRYLGEN 73
                                      68***********9998888754 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.011
                      RNA_helicase   3 lyGpsgeGKStlakeLa 19 
                                       ++G+sg+GKStl   L 
  gi|313117047|ref|YP_004038171.1| 401 VVGESGCGKSTLGSVLL 417
                                       89*********988754 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0085       3.4       5      28 ..      52      75 ..      49      88 .. 0.84
   2 ?    5.3   0.0     0.045        18       4      22 ..     401     419 ..     398     430 .. 0.82
   3 ?    0.4   0.0       1.5   5.8e+02      59      94 ..     520     557 ..     502     598 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0085
                                      E--SSSSHHHHHHHGGGGBS--EE CS
                             AAA_5  5 vGppGtgKselaerlaaalnreve 28
                                       G++G+gKs+la ++++ l+ +  
  gi|313117047|ref|YP_004038171.1| 52 AGESGSGKSTLALSILRYLGENGR 75
                                      6****************9966554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.045
                                       EE--SSSSHHHHHHHGGGG CS
                             AAA_5   4 LvGppGtgKselaerlaaa 22 
                                       +vG++G+gKs+l   l+ +
  gi|313117047|ref|YP_004038171.1| 401 VVGESGCGKSTLGSVLLDL 419
                                       79*********98877665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.5
                                       ------.G-SEEEEES.GGG--HHHHHHHHHHHHSSEE CS
                             AAA_5  59 lvraar.egeilvlDE.veraesevlnsLlslleerrl 94 
                                       + ra+  +++ +vlDE v  ++ +v++s l+ll e r 
  gi|313117047|ref|YP_004038171.1| 520 IARAFSvNPSFVVLDEpVSALDVSVQASILNLLTELRE 557
                                       444555677778888835555699**999999987654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0038       1.5       5      59 ..      52     129 ..      50     145 .. 0.64
   2 ?    4.6   0.0     0.081        32       4      19 ..     401     416 ..     399     424 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0038
                            AAA_33   5 vGlpGsGKstlaerllkklg.avllssdt..............lrrrlfg........tdqqsktdytrvldrlyqi 58 
                                        G +GsGKstla ++l+ lg   +++s +              ++r+l+g        + ++s++ + rv d++ + 
  gi|313117047|ref|YP_004038171.1|  52 AGESGSGKSTLALSILRYLGeNGRITSGNieyhgasildlsskELRALRGneiahvpqDPNTSLNPSMRVGDQIAEV 128
                                       589************99999877777766677777777776674445554333333223333444555555555555 PP

                            AAA_33  59 l 59 
                                       l
  gi|313117047|ref|YP_004038171.1| 129 L 129
                                       4 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.081
                            AAA_33   4 lvGlpGsGKstlaerl 19 
                                       +vG +G+GKstl   l
  gi|313117047|ref|YP_004038171.1| 401 VVGESGCGKSTLGSVL 416
                                       79*********97665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.016       6.2       3      35 ..      51      97 ..      49     232 .. 0.81
   2 ?    6.7   0.0     0.023       9.3       3      52 ..     401     455 ..     399     487 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.016
                                      EESSTTSSHHHHHHHHHHHH..............THEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakel..............gvefleisgsell 35
                                      + G  G GK++la ++ + l              g+++l +s +el+
  gi|313117047|ref|YP_004038171.1| 51 IAGESGSGKSTLALSILRYLgengritsgnieyhGASILDLSSKELR 97
                                      5799***************9443333333222222335555555554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.023
                                       EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfke 52 
                                       ++G  G+GK++l + +         +v++  +++ e+ s+ ++e  ++ + +f++
  gi|313117047|ref|YP_004038171.1| 401 VVGESGCGKSTLGSVLLDLQsrtdgSVSYKGTDVGEMNSQAMKEFRSECQIVFQN 455
                                       79***********999998733333366777777777777888888888888776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.2   0.00061      0.24       5      27 ..      52      74 ..      49      78 .. 0.89
   2 ?    2.0   0.0      0.49     2e+02       6      43 ..     403     440 ..     399     582 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00061
                                      ESSTTSSHHHHHHHHHHHHHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  5 stkGGvGKTtlaanLaralarrg 27
                                      ++ +G+GK+tla++++r+l ++g
  gi|313117047|ref|YP_004038171.1| 52 AGESGSGKSTLALSILRYLGENG 74
                                      689****************9976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.49
                                       SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannla 43 
                                       + +G GK+tl   L+ + +r    V    +D+   n+ 
  gi|313117047|ref|YP_004038171.1| 403 GESGCGKSTLGSVLLDLQSRTDGSVSYKGTDVGEMNSQ 440
                                       789******98888777666544444444666666665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1      0.03        12       2      21 ..      49      68 ..      48      85 .. 0.80
   2 !    8.0   0.1    0.0073       2.9       2      24 ..     399     421 ..     398     443 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.03
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                       +i+G + +GKStL  ++++
  gi|313117047|ref|YP_004038171.1| 49 LGIAGESGSGKSTLALSILR 68
                                      689***********888765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0073
                                       EEEEESTTSSHHHHHHHHHTSTE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgeka 24 
                                        a+vG +  GKStL + l++ ++
  gi|313117047|ref|YP_004038171.1| 399 LAVVGESGCGKSTLGSVLLDLQS 421
                                       69************999987444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0      0.02       7.8       2      22 ..      50      70 ..      49     187 .. 0.82
   2 ?    6.6   0.0     0.027        11       3      22 ..     401     420 ..     399     461 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.02
                            AAA_18  2 lltGtpGvGKttlakeLskrl 22
                                      +++G +G+GK+tla  + + l
  gi|313117047|ref|YP_004038171.1| 50 GIAGESGSGKSTLALSILRYL 70
                                      599**********97765544 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.027
                            AAA_18   3 ltGtpGvGKttlakeLskrl 22 
                                       + G +G+GK+tl+  L ++ 
  gi|313117047|ref|YP_004038171.1| 401 VVGESGCGKSTLGSVLLDLQ 420
                                       7899**********995443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0064       2.5      23      45 ..      50      72 ..      33     175 .. 0.82
   2 ?    5.3   0.0     0.064        25      16      35 ..     392     412 ..     382     414 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0064
                            AAA_23 23 lItGpNGaGKTTildAiklaLyg 45
                                       I G+ G+GK+T+   i   L++
  gi|313117047|ref|YP_004038171.1| 50 GIAGESGSGKSTLALSILRYLGE 72
                                      59***********8777666665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.064
                            AAA_23  16 dF.skgltlItGpNGaGKTTi 35 
                                       d  ++   +++G+ G+GK+T+
  gi|313117047|ref|YP_004038171.1| 392 DIhDSETLAVVGESGCGKSTL 412
                                       4455566789**********8 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.7   6.8e+02      23      56 ..      53      84 ..      51      93 .. 0.67
   2 ?    2.9   0.0     0.084        34     528     577 ..     186     233 ..     180     242 .. 0.87
   3 ?   -0.8   0.0       1.1   4.3e+02      23      44 ..     403     424 ..     400     451 .. 0.82
   4 ?    7.3   0.0    0.0041       1.6     526     580 ..     527     579 ..     506     590 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                            AAA_13 23 GwNGaGKTtLSrllrslelgetepkfangsieit 56
                                      G  G+GK+tL+  +    lge + + ++g+ie++
  gi|313117047|ref|YP_004038171.1| 53 GESGSGKSTLALSILRY-LGE-NGRITSGNIEYH 84
                                      788*******9655443.344.456777777665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.084
                            AAA_13 528 kivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkev 577
                                       +  ++D P   LD + +  +  li++ +  ++    +++ THnl     +
  gi|313117047|ref|YP_004038171.1| 186 QLLILDEPTTGLDVTTQAKILDLINELI--EERNTSVLLITHNLGVISRI 233
                                       56799**********************9..7778889999***9876655 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                            AAA_13  23 GwNGaGKTtLSrllrslelget 44 
                                       G  G GK+tL ++l +l+++  
  gi|313117047|ref|YP_004038171.1| 403 GESGCGKSTLGSVLLDLQSRTD 424
                                       7889**********99988654 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0041
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                       +   vv+D PvS LD  ++ ++ +l+ +   ++   + l+i+ H l+  ++++++
  gi|313117047|ref|YP_004038171.1| 527 NPSFVVLDEPVSALDVSVQASILNLLTELR-EAYGTSYLLIS-HDLSVVRYISDR 579
                                       6778**********************9985.66666666665.888888888765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0063       2.5      21      45 ..      51      75 ..      47      78 .. 0.88
   2 ?   -2.4   0.0         6   2.4e+03      88     113 ..     137     162 ..     114     186 .. 0.74
   3 ?    4.6   0.0     0.044        18      21      57 ..     401     437 ..     396     472 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0063
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgn 45
                                      ++G +G+GKs+la  + ++l+++g+
  gi|313117047|ref|YP_004038171.1| 51 IAGESGSGKSTLALSILRYLGENGR 75
                                      79**************999987776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6
                        Zeta_toxin  88 lqeaiengyniivegtlrspdvvkkl 113
                                       ++ea+e+ y+++ e  + +p+  +k+
  gi|313117047|ref|YP_004038171.1| 137 RAEAMEQTYDVLREVNIPDPERNAKQ 162
                                       57889999999888877777766664 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.044
                        Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57 
                                       ++G +G+GKs+l + l d   r+++ v  +++d+ e+
  gi|313117047|ref|YP_004038171.1| 401 VVGESGCGKSTLGSVLLDLQSRTDGSVSYKGTDVGEM 437
                                       78**********9999998888888888777776655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0054       2.1       5      22 ..      49      66 ..      45      78 .. 0.85
   2 ?    4.9   0.0     0.049        19       5      22 ..     399     416 ..     396     466 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0054
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      + i G+sg+GK+tla+++
  gi|313117047|ref|YP_004038171.1| 49 LGIAGESGSGKSTLALSI 66
                                      679************987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.049
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       ++++G+sg GK+tl + l
  gi|313117047|ref|YP_004038171.1| 399 LAVVGESGCGKSTLGSVL 416
                                       789**********97765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00077      0.31       3      32 ..      50      79 ..      48      85 .. 0.90
   2 ?    2.9   0.0      0.24        94       2      26 ..     399     423 ..     398     448 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00077
                                      EEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgG 32
                                       i G++G+GK+Tl   +l+ l ++g   +G
  gi|313117047|ref|YP_004038171.1| 50 GIAGESGSGKSTLALSILRYLGENGRITSG 79
                                      699******************999988887 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.24
                                       EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss 26 
                                       +++ G++G GK+Tl + +l+l ++ 
  gi|313117047|ref|YP_004038171.1| 399 LAVVGESGCGKSTLGSVLLDLQSRT 423
                                       5789*********988777655444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.016       6.6      18      37 ..      45      64 ..      40      73 .. 0.87
   2 ?    5.7   0.0      0.02       8.1      17      37 ..     394     414 ..     386     428 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                            ATPase 18 egrvvlitGepGtGKtifal 37
                                       g++  i+Ge+G+GK+++al
  gi|313117047|ref|YP_004038171.1| 45 AGETLGIAGESGSGKSTLAL 64
                                      678899************97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                            ATPase  17 pegrvvlitGepGtGKtifal 37 
                                        + ++  ++Ge+G+GK++++ 
  gi|313117047|ref|YP_004038171.1| 394 HDSETLAVVGESGCGKSTLGS 414
                                       5678899***********996 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0068       2.7       2      27 ..      49      74 ..      48      88 .. 0.89
   2 ?    4.4   0.0     0.082        33       2      29 ..     399     426 ..     398     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0068
                              MobB  2 lgivgksgsGKTtLleklipelkarg 27
                                      lgi+g sgsGK tL   +++ l ++g
  gi|313117047|ref|YP_004038171.1| 49 LGIAGESGSGKSTLALSILRYLGENG 74
                                      89*****************9999887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.082
                              MobB   2 lgivgksgsGKTtLleklipelkarglr 29 
                                       l++vg sg+GK tL + l+   ++ + +
  gi|313117047|ref|YP_004038171.1| 399 LAVVGESGCGKSTLGSVLLDLQSRTDGS 426
                                       789***********99988876666555 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.11        43       6      25 ..      48      67 ..      45      86 .. 0.86
   2 ?    7.7   0.0    0.0047       1.9       6      32 ..     398     424 ..     395     461 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.11
                                      EEEEEEBTTSSCCCCCCTTS CS
                            Septin  6 tlmvvGesglGkttlintlf 25
                                      tl ++Gesg Gk+tl  +++
  gi|313117047|ref|YP_004038171.1| 48 TLGIAGESGSGKSTLALSIL 67
                                      67799**********88776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                                       EEEEEEBTTSSCCCCCCTTSSSS---- CS
                            Septin   6 tlmvvGesglGkttlintlfetdliee 32 
                                       tl vvGesg Gk+tl   l+  +  ++
  gi|313117047|ref|YP_004038171.1| 398 TLAVVGESGCGKSTLGSVLLDLQSRTD 424
                                       799************999987776666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.2   1.7e+03      38      52 ..      49      63 ..      46      72 .. 0.85
   2 ?    6.3   0.0     0.014       5.6     106     159 ..     171     222 ..     157     228 .. 0.83
   3 ?    2.0   0.0      0.31   1.2e+02      36      52 ..     397     413 ..     392     430 .. 0.81
   4 ?   -0.8   0.0       2.1   8.4e+02     107     155 ..     515     561 ..     461     570 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.2
                              TniB 38 lllvGdsnnGKtmiv 52
                                      l ++G+s  GK++++
  gi|313117047|ref|YP_004038171.1| 49 LGIAGESGSGKSTLA 63
                                      5699********986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                              TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       ++++  l++  ++++++Li+DE    l   +++q ++l ++  L +e + ++ l
  gi|313117047|ref|YP_004038171.1| 171 QQQRVLLAIALACQPQLLILDEPTTGL--DVTTQAKILDLINELIEERNTSVLL 222
                                       556666777889************999..889999*********9999888866 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.31
                              TniB  36 pnlllvGdsnnGKtmiv 52 
                                       + l +vG+s +GK+++ 
  gi|313117047|ref|YP_004038171.1| 397 ETLAVVGESGCGKSTLG 413
                                       6799**********985 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.1
                              TniB 107 leqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelki 155
                                       +++ +++   ++++  +++DE  ++l   ++ q  +ln+l  L + +  
  gi|313117047|ref|YP_004038171.1| 515 KQRVAIARAFSVNPSFVVLDEPVSAL--DVSVQASILNLLTELREAYGT 561
                                       33444444445666788888888887..666678888888888777665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.78   3.1e+02      15      43 ..      37      66 ..      34     105 .. 0.76
   2 ?    5.9   0.1     0.022       8.8     288     368 ..     158     229 ..     110     230 .. 0.80
   3 ?    4.0   0.0     0.086        34      22      43 ..     396     416 ..     385     461 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.78
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileal 43
                                      +dv+++++   +  + G+ +sGKS+++  +
  gi|313117047|ref|YP_004038171.1| 37 RDVSLHINAGeTLGIAGESGSGKSTLALSI 66
                                      5655555555366799*********97555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.022
                            AAA_15 288 ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                        + +++ ++ + G+q+ +ll++ ++   +         +l+++EP + L    q  + +l+ el+++ +t v++ TH
  gi|313117047|ref|YP_004038171.1| 158 RNAKQYPHELSGGQQQRVLLAIALACQPQ---------LLILDEPTTGLDVTTQAKILDLINELIEERNTSVLLITH 225
                                       56666777778888888888877665444.........6************************************** PP

                            AAA_15 365 Sphi 368
                                       +  +
  gi|313117047|ref|YP_004038171.1| 226 NLGV 229
                                       9766 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.086
                            AAA_15  22 seeltvliGkNnsGKSsileal 43 
                                       se +  ++G+ ++GKS++  +l
  gi|313117047|ref|YP_004038171.1| 396 SE-TLAVVGESGCGKSTLGSVL 416
                                       33.889***********97766 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0015      0.58       3      32 ..      47      76 ..      45      89 .. 0.88
   2 ?    1.2   0.1      0.74     3e+02       4      23 ..     398     417 ..     395     435 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT-- CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgis 32
                                       ++ ++G sgsGKst+a  + ++L e+g+ 
  gi|313117047|ref|YP_004038171.1| 47 ETLGIAGESGSGKSTLALSILRYLGENGRI 76
                                      577899******************999864 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.74
                                       EEEEESSTTSSHHHHHHHHH CS
                        APS_kinase   4 vvwltGlsgsGKstianale 23 
                                       ++ + G sg GKst+   l 
  gi|313117047|ref|YP_004038171.1| 398 TLAVVGESGCGKSTLGSVLL 417
                                       67789**********87664 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.014       5.4      26      59 ..      39      72 ..      23      84 .. 0.84
   2 ?    3.6   0.0       0.1        41      34      54 ..     397     417 ..     391     428 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.014
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkldk 59
                                      ++l+++++  + + G++G+GK++++ ++l+ l +
  gi|313117047|ref|YP_004038171.1| 39 VSLHINAGETLGIAGESGSGKSTLALSILRYLGE 72
                                      567899999999*************999998874 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                             AAA_7  34 kpvllvGptGtGKtviikdll 54 
                                         + +vG++G+GK+++ + ll
  gi|313117047|ref|YP_004038171.1| 397 ETLAVVGESGCGKSTLGSVLL 417
                                       56779*********9876555 PP

>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.011       4.4       9      66 ..      56     115 ..      49     144 .. 0.79
   2 ?    3.3   0.0       0.2        78       7      58 ..     404     452 ..     398     480 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                                       TSSHHHHHHHHHHH-TTSEEEEGGGS-TT..-SS-HHHHHHHTTSSTT--EEEEES---S CS
                   tRNA_lig_kinase   9 GCGkttvaltlenlfgeWghvqnDnitgk..dkkklvkealellkkdeskvvlvDrnnhq 66 
                                       G Gk+t al + +  ge g + + ni+ +  +  +l ++ l++l+ +e+  v  D n + 
  gi|313117047|ref|YP_004038171.1|  56 GSGKSTLALSILRYLGENGRITSGNIEYHgaSILDLSSKELRALRGNEIAHVPQDPNTSL 115
                                       89************************766437789999**************99999653 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.2
                                       -TTSSHHHHHHHHHHH-TT.SEEEEGGGS-TT-SS-HHHHHHHTTSSTT--EE CS
                   tRNA_lig_kinase   7 tiGCGkttvaltlenlfge.WghvqnDnitgkdkkklvkealellkkdeskvv 58 
                                         GCGk+t   +l +l     g v     +g+d  ++ ++a++++ ++e ++v
  gi|313117047|ref|YP_004038171.1| 404 ESGCGKSTLGSVLLDLQSRtDGSV---SYKGTDVGEMNSQAMKEF-RSECQIV 452
                                       459**********99987322222...234445555555555555.4444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00042      0.17      49      77 ..      45      73 ..      30      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 49 aGravLlaGpsgtGktalaiaiskelged 77
                                      aG ++ +aG+sg+Gk+ la++i + lge+
  gi|313117047|ref|YP_004038171.1| 45 AGETLGIAGESGSGKSTLALSILRYLGEN 73
                                      799999*******************9986 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00072      0.29      20      87 ..     393     462 ..     382     498 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00072
                   Methyltransf_32  20 lakesgaltvvDvGaGkgYLsfvlal..kekeyklkvvgidakeelvekaekraeklgkkfnkrlsfael 87 
                                       ++++++   v + G+Gk+ L++vl +  ++++ +++  g d+ e ++++ ++ +++++  f++ +s  + 
  gi|313117047|ref|YP_004038171.1| 393 IHDSETLAVVGESGCGKSTLGSVLLDlqSRTDGSVSYKGTDVGEMNSQAMKEFRSECQIVFQNPHSSLNP 462
                                       4555556666789*************8444458999******************9999888666665554 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0076         3       6      45 ..      49      91 ..      46     107 .. 0.78
   2 ?    2.0   0.0      0.33   1.3e+02       5      32 ..     398     425 ..     394     449 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0076
                                      EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHSTHCH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskkgeka...eeervlDt 45
                                      +gi+g   +GK+TL  ++l ++g+  + ++ +    ++++lD 
  gi|313117047|ref|YP_004038171.1| 49 LGIAGESGSGKSTLALSILRYLGENGRITSGNieyHGASILDL 91
                                      799*******************998887765554333555555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.33
                                       EEEEEESTTSSHHHHHHHHHHHTTSSCH CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaisk 32 
                                       +++++g    GK+TL   Ll   ++++ 
  gi|313117047|ref|YP_004038171.1| 398 TLAVVGESGCGKSTLGSVLLDLQSRTDG 425
                                       6789***********9999966665554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0041       1.6      19      50 ..      46      78 ..      28      81 .. 0.81
   2 ?    0.0   0.0         2     8e+02      19      39 ..     396     416 ..     384     426 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0041
                                      TEEEEEEESTTSSHHHHHHHHHHHTT--.---- CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglakalgve.evkS 50
                                      g+++ + G+ G+GK+tl+ ++++ lg + +++S
  gi|313117047|ref|YP_004038171.1| 46 GETLGIAGESGSGKSTLALSILRYLGENgRITS 78
                                      778999********************9999998 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2
                                       TEEEEEEESTTSSHHHHHHHH CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrgl 39 
                                       +++++  G+ G+GK+tl   l
  gi|313117047|ref|YP_004038171.1| 396 SETLAVVGESGCGKSTLGSVL 416
                                       4568999*********97655 PP

>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.074        29      23      39 ..      51      67 ..      32      70 .. 0.86
   2 ?    5.0   0.1      0.04        16       7      38 ..     384     416 ..     381     445 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.074
                                      EEESTCHHHHHHHHHHH CS
                      Hpr_kinase_C 23 itGesgvGKselaleLi 39
                                      i Gesg GKs lal ++
  gi|313117047|ref|YP_004038171.1| 51 IAGESGSGKSTLALSIL 67
                                      89***********9876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.04
                                       EEEESEEEEETTEEEE.EEESTCHHHHHHHHHH CS
                      Hpr_kinase_C   7 tsvhGvlvdvygvGvL.itGesgvGKselaleL 38 
                                       ++v Gv  d+++   L ++Gesg GKs l+  L
  gi|313117047|ref|YP_004038171.1| 384 KAVDGVSFDIHDSETLaVVGESGCGKSTLGSVL 416
                                       6788999999998766489********887544 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.24        94       4      20 ..      51      67 ..      48      99 .. 0.80
   2 ?    6.1   0.1     0.032        13       2      40 ..     399     438 ..     398     454 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.24
                                      EESSTTSSHHHHHHCHC CS
                               Roc  4 lvGdsgvGKtsllkrfv 20
                                      + G+sg+GK++l+ +++
  gi|313117047|ref|YP_004038171.1| 51 IAGESGSGKSTLALSIL 67
                                      68**********98766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.032
                                       EEEESSTTSSHHHHHHCHCT-CC.C-EEETTTTEEEEEEE CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkf.sekekstigvdfltke 40 
                                       + +vG+sg GK++l + +++ +  ++ + s  g d+ + +
  gi|313117047|ref|YP_004038171.1| 399 LAVVGESGCGKSTLGSVLLDLQSrTDGSVSYKGTDVGEMN 438
                                       579***********99998855414445566666665554 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.065        26       1      23 [.      53      75 ..      53      79 .. 0.89
   2 ?    5.2   0.2     0.041        16       1      34 [.     403     436 ..     403     440 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.065
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgr 23
                                      G++ sGKSTla  +l y+ ++gr
  gi|313117047|ref|YP_004038171.1| 53 GESGSGKSTLALSILRYLGENGR 75
                                      8899************9988876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.041
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34 
                                       G++ +GKSTl  +Ll+   r   ++ y  +DvG 
  gi|313117047|ref|YP_004038171.1| 403 GESGCGKSTLGSVLLDLQSRTDGSVSYKGTDVGE 436
                                       78899***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 4431.02
//
Query:       gi|313117048|ref|YP_004038172.1|  [L=540]
Description: peptide ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-75  252.8   0.3      7e-75  252.3   0.3    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.047   13.7   0.2        7.2    6.7   0.0    2.4  2  DUF3320    Protein of unknown function (DUF3320)


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.3   0.3   7.8e-79     7e-75       1     373 [.      89     451 ..      89     455 .. 0.89

  Alignments for each domain:
  == domain 1  score: 252.3 bits;  conditional E-value: 7.8e-79
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddyt 77 
                                       ev+++LAe+ w+ +d   ++tf+LR+ ++F+DG  +tA+Dv+++fe + d d +s+ + ++     i++veavd++t
  gi|313117048|ref|YP_004038172.1|  89 EVYGDLAED-WSSNDASDEWTFTLRE-ATFHDGGTVTASDVKATFETVYDDDVGSPGKGTMG---AIERVEAVDEKT 160
                                       6899*****.799*************.**********************************6...************ PP

                                       EEEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTST.....TTSC CS
                         SBP_bac_5  78 vrftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYw.....gggk 149
                                       vrftl+ +n++f  l+a+ + si+ ++ + + ++      +  g+G+++l++f+pg+k++ +r +dY+     g  +
  gi|313117048|ref|YP_004038172.1| 161 VRFTLENANSDFHKLVAKGWGSIVPEEIVTDPKRRQALGSEEHGSGAFTLESFSPGDKLTGVRYDDYYrtgddGEPL 237
                                       ************************87777777777777777789**********************999**877788 PP

                                       SSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHH CS
                         SBP_bac_5 150 pkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqA 226
                                       p++d+i+  +ip+++++++al++G++d++++p  +++ +l+  ++ +  +++pgg++  +++  + +p +dkrvRqA
  gi|313117048|ref|YP_004038172.1| 238 PYIDKITQITIPEKSNQVNALRTGDVDIIWQPGYGQWGTLQGLSDANT-HRTPGGEIANFVMDVNTEPWSDKRVRQA 313
                                       9***********************************************.**************************** PP

                                       HHHHS-HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEE CS
                         SBP_bac_5 227 lsyAiDreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltll 302
                                       +++AiDre+i++ v  g++t+++   l+p + ++ +       + d+ekAk+lL++aGy+dg +       +++ l+
  gi|313117048|ref|YP_004038172.1| 314 VMHAIDREAIIEGVQDGLGTVGQDSlLSPAYEYYADVGAR---EQDLEKAKQLLADAGYPDGINLT-----EEFGLT 382
                                       *********************9999788887777776665...679****************8654.....567777 PP

                                       EETTSHHHH.HHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTT CS
                         SBP_bac_5 303 lasgspaek.aiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsss 373
                                       l + s ++   +a ++q+ql++iGi++++++++   ++ ++   ++ +++++++g   +++ nf+  +l+s 
  gi|313117048|ref|YP_004038172.1| 383 LETASIPHMeGTAVMMQEQLQQIGIEFDIQVMSY-DNF-SADVWTKSPFYVGAYGM-RISGANFMKLLLHSE 451
                                       7777777766**********************88.455.45556666666655544.466666766666665 PP

>> DUF3320  Protein of unknown function (DUF3320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1    0.0037        33       5      24 ..     303     322 ..     302     325 .. 0.91
   2 ?    6.7   0.0   0.00081       7.2       5      25 ..     477     497 ..     476     497 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0037
                           DUF3320   5 epeykptLaeliakIVevEG 24 
                                       ep++++++++++++ ++ E+
  gi|313117048|ref|YP_004038172.1| 303 EPWSDKRVRQAVMHAIDREA 322
                                       799****************8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00081
                           DUF3320   5 epeykptLaeliakIVevEGP 25 
                                       +p++k++L + +++IV+ EGP
  gi|313117048|ref|YP_004038172.1| 477 DPDRKQKLMKKAQQIVRDEGP 497
                                       688999**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3765.18
//
Query:       gi|313117049|ref|YP_004038173.1|  [L=259]
Description: IclR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-30  106.1   0.0    1.6e-30  105.6   0.0    1.2  1  IclR            Bacterial transcriptional regulator
    9.1e-09   35.0   0.0    2.6e-08   33.5   0.0    1.8  2  HTH_IclR        IclR helix-turn-helix domain
    9.4e-08   31.8   0.0    3.3e-07   30.1   0.0    2.0  2  HTH_5           Bacterial regulatory protein, arsR family
    8.3e-07   29.0   0.0      2e-06   27.7   0.0    1.7  2  HTH_20          Helix-turn-helix domain
    4.7e-06   26.1   0.0      2e-05   24.0   0.0    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
    9.6e-06   25.4   0.0      2e-05   24.4   0.0    1.5  1  MarR_2          MarR family
    1.3e-05   25.0   0.0    9.5e-05   22.2   0.0    2.2  2  TrmB            Sugar-specific transcriptional regulator TrmB
    4.4e-05   23.3   0.0     0.0001   22.2   0.0    1.6  1  MarR            MarR family
    6.8e-05   22.7   0.0    0.00027   20.8   0.0    2.1  1  HTH_11          HTH domain
      0.009   16.2   0.0      0.024   14.8   0.0    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.052   13.4   0.0    1.8  1  TetR_N          Bacterial regulatory proteins, tetR family
      0.017   15.3   0.0       0.21   11.8   0.0    2.4  2  HTH_17          Helix-turn-helix domain
      0.028   14.5   0.0      0.077   13.1   0.0    1.9  1  HTH_22          HTH domain
      0.059   13.2   0.1        0.2   11.5   0.0    1.8  2  HTH_10          HTH DNA binding domain
      0.077   13.5   0.0       0.21   12.0   0.0    1.8  1  HTH_40          Helix-turn-helix domain
       0.14   12.2   0.0        0.3   11.1   0.0    1.6  1  HTH_29          Winged helix-turn helix
       0.19   11.6   0.0        0.6   10.0   0.0    1.9  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.0   1.5e-33   1.6e-30      15     128 ..     139     251 ..     130     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 1.5e-33
                                       GGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEEEE-TTS CS
                              IclR  15 lyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciAapifdasg 91 
                                       l+ ++ GKa+La+l++ee+++++e+++l ++ e+Titd++eL+ee +++R+qGya++++Ee +g+r+i+api +  +
  gi|313117049|ref|YP_004038173.1| 139 LHWSSSGKAYLAHLPPEEARTIVEEQGLPSMNENTITDQAELFEEFETIRKQGYAINDQEEILGTRAIGAPIQN-DN 214
                                       8*************************************************************************.55 PP

                                       SEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  92 evvaAvsvsgptarlteeelkeellalvreaArkisr 128
                                          +A+s+sgp++r++ e+l++el ++v+eaA+ is 
  gi|313117049|ref|YP_004038173.1| 215 GLYGAISISGPKSRFSFEKLHNELSEKVIEAANIISV 251
                                       679*******************************996 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   2.5e-11   2.6e-08       2      50 ..      12      59 ..      11      61 .. 0.93
   2 ?   -2.6   0.0       4.6   4.9e+03      22      29 ..      92      99 ..      91     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.5e-11
                                      HHHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  2 ldRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++++ +++d l+e +++ t++elA+++gl+k+ v+++L+tL ++ +v +
  gi|313117049|ref|YP_004038173.1| 12 VENTCRVIDTLEEMDGA-TVTELADALGLSKPGVYNHLATLKKMEFVVK 59
                                      88999***********8.*************************999976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.6
                                      HHHHHHHT CS
                          HTH_IclR 22 selArrtg 29
                                      +elA++tg
  gi|313117049|ref|YP_004038173.1| 92 KELAEETG 99
                                      699**998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   3.1e-10   3.3e-07       6      45 ..      17      57 ..      13      59 .. 0.89
   2 ?   -2.2   0.0       3.9   4.1e+03      14      26 ..      87      99 ..      81      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.1e-10
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +++  L+e   ++v+ela++lgls++ v  HL+ L+++ +V
  gi|313117049|ref|YP_004038173.1| 17 RVIDTLEEmDGATVTELADALGLSKPGVYNHLATLKKMEFV 57
                                      677788886669***************************99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                                      SSEEHHHHHHHHT CS
                             HTH_5 14 gelcvcelaeelg 26
                                      ge    elaee+g
  gi|313117049|ref|YP_004038173.1| 87 GENVTKELAEETG 99
                                      7778899**9986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.9e-09     2e-06      12      54 ..      15      57 ..       7      65 .. 0.88
   2 ?   -3.2   0.0       8.6   9.1e+03      16      27 ..     149     160 ..     149     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.9e-09
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                       +r+ + L + +g+t++ela++l+lsk  +++HL++L + ++v
  gi|313117049|ref|YP_004038173.1| 15 TCRVIDTLEEMDGATVTELADALGLSKPGVYNHLATLKKMEFV 57
                                      6999999*999***************************99995 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.6
                                       HHHHSTCTTB-H CS
                            HTH_20  16 lraLaraeglta 27 
                                       l++L+++e++t 
  gi|313117049|ref|YP_004038173.1| 149 LAHLPPEEARTI 160
                                       689999999985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.9e-08     2e-05       4      47 ..      14      57 ..      13      58 .. 0.93
   2 ?   -1.5   0.0       1.9     2e+03      21      28 ..      92      99 ..      91      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.9e-08
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++ +++ +L++  + + +eLA++lglS++ v  +l  L++++++
  gi|313117049|ref|YP_004038173.1| 14 NTCRVIDTLEEMDGATVTELADALGLSKPGVYNHLATLKKMEFV 57
                                      567899999999*****************************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                            HTH_24 21 reLAerlg 28
                                      +eLAe++g
  gi|313117049|ref|YP_004038173.1| 92 KELAEETG 99
                                      89***998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.9e-08     2e-05       8      56 ..      16      62 ..      14      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.9e-08
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                       rv+  L   +g   tv+ela++lglsk+ v ++l+ L +  +v++++g
  gi|313117049|ref|YP_004038173.1| 16 CRVIDTLEEMDG--ATVTELADALGLSKPGVYNHLATLKKMEFVVKSDG 62
                                      68999*******..9*****************************99987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     9e-08   9.5e-05      19      60 ..      24      65 ..      13      72 .. 0.91
   2 ?   -0.4   0.0       1.1   1.1e+03      17      35 ..     149     167 ..     146     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9e-08
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      + + at++e+a +lg++++ vY+ L  L+++ +V +++g+++
  gi|313117049|ref|YP_004038173.1| 24 EMDGATVTELADALGLSKPGVYNHLATLKKMEFVVKSDGEYR 65
                                      67899********************************99976 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                       HHHHCCCHHCHHCCCTTSS CS
                              TrmB  17 Llklgpatadeiaeelgvp 35 
                                       L  l p +a++i ee g+p
  gi|313117049|ref|YP_004038173.1| 149 LAHLPPEEARTIVEEQGLP 167
                                       56778999******99998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   9.5e-08    0.0001       7      50 ..      17      60 ..      13      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.5e-08
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      +++ +l+e+++++v+eLa++lg+sk+ v + l +L k +++ +s
  gi|313117049|ref|YP_004038173.1| 17 RVIDTLEEMDGATVTELADALGLSKPGVYNHLATLKKMEFVVKS 60
                                      6889************************************9876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.5e-07   0.00027      14      49 ..      26      61 ..      17      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-07
                            HTH_11 14 gpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIese 49
                                      +  +  eLA+ L++S+  v++++++L+++ + + s+
  gi|313117049|ref|YP_004038173.1| 26 DGATVTELADALGLSKPGVYNHLATLKKMEFVVKSD 61
                                      44799************************9988886 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.3e-05     0.024       7      53 ..      13      58 ..       8      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                                      HHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  7 EdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      E+  ++I tl+ e + +++++la +L+ s++ V   l  L+k+++v+
  gi|313117049|ref|YP_004038173.1| 13 ENTCRVIDTLE-EMDGATVTELADALGLSKPGVYNHLATLKKMEFVV 58
                                      55566676666.7888999**************************97 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.9e-05     0.052      14      36 ..      25      47 ..      23      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.9e-05
                                      TTT--HHHHHHHHTSSHHHHHHH CS
                            TetR_N 14 ydattvreIAkrAGvskgalYry 36
                                      +d++tv e+A+++G+sk+ +Y +
  gi|313117049|ref|YP_004038173.1| 25 MDGATVTELADALGLSKPGVYNH 47
                                      6899*****************99 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.21       3      37 ..      29      65 ..      29      72 .. 0.76
   2 ?    0.7   0.0       0.6   6.4e+02       4      20 ..     242     258 ..     241     259 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                            HTH_17  3 tveEaAelLgvsrstvyrli...rrgelpaakiGrrwr 37
                                      tv E+A+ Lg+s+  vy+ +   ++ e+ ++k  + +r
  gi|313117049|ref|YP_004038173.1| 29 TVTELADALGLSKPGVYNHLatlKKMEF-VVKSDGEYR 65
                                      89***************96645556666.667545466 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.6
                            HTH_17   4 veEaAelLgvsrstvyr 20 
                                       v EaA++  v  st+++
  gi|313117049|ref|YP_004038173.1| 242 VIEAANIISVNISTLQN 258
                                       67************987 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.3e-05     0.077      43      62 ..      29      48 ..       6      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-05
                            HTH_22 43 avekvAekLgiSraTvYryL 62
                                      +v ++A++Lg S++ vY++L
  gi|313117049|ref|YP_004038173.1| 29 TVTELADALGLSKPGVYNHL 48
                                      58899**************9 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019       0.2      24      45 ..      28      49 ..      25      53 .. 0.91
   2 ?   -2.8   0.0       5.4   5.7e+03      27      34 ..      92      99 ..      91      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                            HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                                      +t+ eLA++lG+sk+ +++hL 
  gi|313117049|ref|YP_004038173.1| 28 ATVTELADALGLSKPGVYNHLA 49
                                      7899****************95 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.4
                            HTH_10 27 keLAkelG 34
                                      keLA+e G
  gi|313117049|ref|YP_004038173.1| 92 KELAEETG 99
                                      89***987 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.21      11      41 ..      26      56 ..      18      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                            HTH_40 11 eglsieeIAkerglkesTIegHLaelieege 41
                                      +g ++ e A+  gl++  +++HLa l + + 
  gi|313117049|ref|YP_004038173.1| 26 DGATVTELADALGLSKPGVYNHLATLKKMEF 56
                                      799***********************99965 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028       0.3      13      34 ..      26      49 ..      16      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                            HTH_29 13 s..tvsqiAkllglsrrtvyrwlk 34
                                      +  tv ++A +lgls++ vy++l 
  gi|313117049|ref|YP_004038173.1| 26 DgaTVTELADALGLSKPGVYNHLA 49
                                      3359*****************985 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00057       0.6      18      35 ..      28      45 ..      17      52 .. 0.84
   2 ?   -1.9   0.0         3   3.1e+03      20      28 ..      91      99 ..      81      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00057
                     HTH_AsnC-type 18 isyaeLAervGlSestvl 35
                                      ++++eLA+++GlS + v 
  gi|313117049|ref|YP_004038173.1| 28 ATVTELADALGLSKPGVY 45
                                      789**********99876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3
                     HTH_AsnC-type 20 yaeLAervG 28
                                       +eLAe++G
  gi|313117049|ref|YP_004038173.1| 91 TKELAEETG 99
                                      589**9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2034.87
//
Query:       gi|313117050|ref|YP_004038174.1|  [L=382]
Description: glycine/D-amino acid oxidase, deaminating [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-46  158.6   0.1    3.4e-46  158.4   0.1    1.0  1  DAO            FAD dependent oxidoreductase
     0.0035   16.1   0.0       0.14   10.8   0.0    2.1  2  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
       0.02   14.1   0.3        0.8    8.9   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.029   13.6   0.5       0.39    9.9   0.5    2.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
       0.47   10.4   5.1       0.63   10.0   1.1    2.8  3  NAD_binding_9  FAD-NAD(P)-binding
        2.7    8.3   4.3        2.1    8.6   0.2    2.9  4  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.4   0.1   1.2e-49   3.4e-46       1     352 []       9     364 ..       9     364 .. 0.85

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 1.2e-49
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgllhsglrylpeaselarlslealeelreleee 74 
                                       dv+++G G iG+++ y+L++rg  V+ l++ +i+ s g+S++ s+l++   ++ p   e+++ +++++++++ leee
  gi|313117050|ref|YP_004038174.1|   9 DVIVVGVGGIGSAAVYHLSQRGldVLGLDQYSIPNSvGSSHGDSRLIRLTNYEDP---EYVPHVRRSIDLWESLEEE 82 
                                       8**********************************99************876566...789**************** PP

                                       HSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..ST.TTSEEEEETTEEEEEHHHH CS
                               DAO  75 lgididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa..lp.gllgalfypdtgqvdpakl 148
                                       +g ++ +r tG++  +   e  e ++  + +++e++l++e l+a+e+ e +p+  lp +   a++ pd+g ++p + 
  gi|313117050|ref|YP_004038174.1|  83 YGEQLLFR-TGTVDAGP--EGSETVEGAITACEEYDLPYEHLSAAELSEQFPGfrLPsD-FEAVHQPDGGFIHPTRC 155
                                       **988766.******84..357888888899999******************9765434.478************** PP

                                       HHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTTCTTTSEEEEEEEE CS
                               DAO 149 taalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gllkeldlpispvrgq 223
                                       ++a  + a ++G+e + +++v++ + +d ++++v  +t+  +  +ad++V++aGaw d + +++     +++p r  
  gi|313117050|ref|YP_004038174.1| 156 VQAHVAGAHDNGAETHAHETVVEWDTTD-DGVRV--QTDlTT-YEADQLVLTAGAWKDVFpERV---AEKLTPWRVI 225
                                       ***********************97764.44666..554343.357**********88664444...44669***** PP

                                       EEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTS..EEEEEESSE.....EETTCSSTSCSHHHHHH....HH CS
                               DAO 224 vlvlkplseklvspaailpvpetdddgrgvyvtprkdg..rvlvGgtad.....eesgdddpevdeedide....ll 289
                                       v  ++p s +   p   lpv+ +++++ g+y  p + g  ++++G  +      ++s++d+ +++e++ ++    l+
  gi|313117050|ref|YP_004038174.1| 226 VGGFQPESPEKFTP-DALPVFSINEGDQGYYGAPAA-GtsGFKFGLVDNledvaDPSDFDP-RPTEKEKERlrtvLY 299
                                       *99*9988866555.7888888************74.312499999988988865666666.8888888888899** PP

                                       HHHHHHSGG.GCGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 290 ealrklfPq.lgdvlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                       +++r++fP+  ++ +r  +++ + +pd +++++  p  + + + +G+sg G++++ ++G+lla+l
  gi|313117050|ref|YP_004038174.1| 300 DKAREYFPEgARSTKRLKTCMVThTPDQDFIVDSLPDRPQVKVGAGFSGKGFKFSGLMGELLADL 364
                                       *********53445566667777568********98899************************97 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.011        32       1      33 [.       8      40 ..       8      88 .. 0.81
   2 !   10.8   0.0   4.6e-05      0.14     112     164 ..     156     206 ..     150     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.011
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +dviv+G G  G  a  ++++rg +Vl l++ +
  gi|313117050|ref|YP_004038174.1|  8 YDVIVVGVGGIGSAAVYHLSQRGLDVLGLDQYS 40
                                      59************************9999865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 112 vdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       v+a ++ ++++g + + +++v ++++++dg +rv+t + +++ead+lvl+ G 
  gi|313117050|ref|YP_004038174.1| 156 VQAHVAGAHDNGAETHAHETVVEWDTTDDG-VRVQT-DLTTYEADQLVLTAGA 206
                                       6777788899**************999999.*****.9************995 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.014        42       1      36 [.      11      45 ..      11      58 .. 0.89
   2 ?    8.9   0.0   0.00027       0.8      97     135 ..     169     207 ..     160     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.014
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnignsi 36
                                      i++G G +G aa ++l + gl d+l l++ +i ns+
  gi|313117050|ref|YP_004038174.1| 11 IVVGVGGIGSAAVYHLSQRGL-DVLGLDQYSIPNSV 45
                                      89*******************.79999988887775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00027
                       Pyr_redox_3  97 piklfeeVesvkkedegfevetsketyeAkkviiAtGef 135
                                       + +++e+V + + +d+g +v+t+  tyeA+++++ +G +
  gi|313117050|ref|YP_004038174.1| 169 ETHAHETVVEWDTTDDGVRVQTDLTTYEADQLVLTAGAW 207
                                       678999999***************************986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5   0.00013      0.39       1     114 [.       8     211 ..       8     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE..........TTHCHHHCSHHHHCHHHHHHHHHHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve..........legtclnggcllskallgvaedaeias.......... 57 
                                       +dv+v+G G  G aa  +l+q g++v+ ++          + g   + +   ++  + v++ ++ +           
  gi|313117050|ref|YP_004038174.1|   8 YDVIVVGVGGIGSAAVYHLSQRGLDVLGLDqysipnsvgsSHGDSRLIRLTNYEDPEYVPHVRRSIDlwesleeeyg 84 
                                       68999999999999999999999999999555554444443333333333334444444444433336777777777 PP

                                       ..........................................................................HHH CS
                                       ..........................................................................xxx RF
                       Pyr_redox_2  58 ..........................................................................evv 60 
                                                                                                                  v 
  gi|313117050|ref|YP_004038174.1|  85 eqllfrtgtvdagpegsetvegaitaceeydlpyehlsaaelseqfpgfrlpsdfeavhqpdggfihptrcvqaHVA 161
                                       78888888888999999999999999999999999999999999999999999999999999999988888886333 PP

                                       HCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  61 kklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl 114
                                           +g e+ + e+vv+ d+    v ++     d +++++d+lvl  G++   +
  gi|313117050|ref|YP_004038174.1| 162 GAHDNGAETHAHETVVEWDTTDDGVRVQ----TDLTTYEADQLVLTAGAWKDVF 211
                                       4445668888887799999888788884....4567999999999999987666 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.33   9.8e+02       2      20 ..      12      30 ..      11      61 .. 0.86
   2 ?   10.0   1.1   0.00021      0.63     104     154 ..     156     205 ..     153     206 .. 0.85
   3 ?   -0.9   0.0      0.48   1.4e+03       3      32 ..     342     378 ..     341     382 .] 0.59

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.33
                     NAD_binding_9  2 ivGaGprGlavlerLlara 20
                                      +vG G  G a++ +L +r 
  gi|313117050|ref|YP_004038174.1| 12 VVGVGGIGSAAVYHLSQRG 30
                                      8**************9984 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00021
                     NAD_binding_9 104 feellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       +++ +a ++++   ++ +++vv+ ++++dg++v ++d ++++ad++vL+ G
  gi|313117050|ref|YP_004038174.1| 156 VQAHVAGAHDNGAETHAHETVVEWDTTDDGVRV-QTDLTTYEADQLVLTAG 205
                                       5666777777777788899***********977.99*************99 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.48
                     NAD_binding_9   3 vGaGprG.....lavlerLlara..kkkspleitlfd 32 
                                       vGaG++G       ++ +Lla    +++s++++ +f+
  gi|313117050|ref|YP_004038174.1| 342 VGAGFSGkgfkfSGLMGELLADLvtEEASKVDLEIFE 378
                                       6777777222223455566666666667778888877 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0007       2.1       1      27 [.      12      38 ..      12      48 .. 0.92
   2 ?   -3.6   0.0       4.6   1.4e+04      18      29 ..     292     303 ..     290     321 .. 0.77
   3 ?   -1.9   0.2       1.4   4.2e+03       2       8 ..     342     348 ..     342     349 .. 0.94
   4 ?   -1.4   0.0      0.99     3e+03       4      27 ..     354     379 ..     354     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0007
                                      EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                      +vG G  G++a y+L+++g+dvl l++
  gi|313117050|ref|YP_004038174.1| 12 VVGVGGIGSAAVYHLSQRGLDVLGLDQ 38
                                      899999****************98886 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.6
                                       CTEEEEEE-SSS CS
                     NAD_binding_8  18 agfdvlllekrd 29 
                                       ++++ +l++k++
  gi|313117050|ref|YP_004038174.1| 292 ERLRTVLYDKAR 303
                                       567888888875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.4
                                       E--SHHH CS
                     NAD_binding_8   2 vGaGlsG 8  
                                       vGaG+sG
  gi|313117050|ref|YP_004038174.1| 342 VGAGFSG 348
                                       9*****9 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.99
                                       -SHHHHHHHHHHHCC..TEEEEEE-S CS
                     NAD_binding_8   4 aGlsGlvaAylLaka..gfdvlllek 27 
                                       +Gl G ++A l +++  ++d +++e+
  gi|313117050|ref|YP_004038174.1| 354 SGLMGELLADLVTEEasKVDLEIFEM 379
                                       68888889999988767999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2994.58
//
Query:       gi|313117051|ref|YP_004038175.1|  [L=562]
Description: thiamine pyrophosphate-dependent enzyme, possible carboligase or decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-34  118.6   0.6    2.9e-34  117.8   0.0    1.8  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    1.5e-32  112.5   1.4    2.7e-32  111.7   0.9    1.7  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    2.2e-29  102.3   0.0    6.7e-28   97.4   0.0    2.3  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
  ------ inclusion threshold ------
       0.25   11.1   0.0       0.45   10.3   0.0    1.3  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha


Domain annotation for each model (and alignments):
>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.0   6.4e-38   2.9e-34       3     137 .]     204     340 ..     202     340 .. 0.93
   2 ?   -3.8   0.1       2.2   9.7e+03      63      85 ..     425     448 ..     422     455 .. 0.59

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 6.4e-38
                                       HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-S CS
                      TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaD 79 
                                        a ++l+ a rpvi++G+gv+ s++ +el e+ae++++ v+t++ gk++ipe+h++ +g++g +g++ an+a+ eaD
  gi|313117051|ref|YP_004038175.1| 204 TASKILSDADRPVIIAGNGVHVSQCYDELLEVAEAYDAVVTTSYLGKSTIPETHDRAAGVIGSFGHEGANQAVSEAD 280
                                       67899************************************************************************ PP

                                       EEEEES-SSSTCCCTTTTT.TTTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  80 lvlalGarfddirttgsep.efapea.kiihididpaeigknyqvdlaivgdvketleaL 137
                                        +l++G+r++ + t  +    + p++  iih di+  ++g +y++d++++gd++++l+aL
  gi|313117051|ref|YP_004038175.1| 281 ALLVVGCRMNPMDTNWQAAsFIRPDEqAIIHADIETRNAGWVYPADVGLIGDAGQSLSAL 340
                                       ***********88877666344455579*****************************997 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.2
                                       SGGGSCHHHHHHH.HH-SEEEEES CS
                      TPP_enzyme_M  63 lglhgskaaneal.eeaDlvlalG 85 
                                       +g +g + +++a+  + D+v + G
  gi|313117051|ref|YP_004038175.1| 425 MGWAGPAGVSAAItTDKDVVAVAG 448
                                       555555555555545566666655 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.4   6.5e+03      98     125 ..     200     226 ..     189     246 .. 0.47
   2 !  111.7   0.9   5.9e-36   2.7e-32       1     153 []     396     537 ..     396     537 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.4
                                       CTTTTSBB.BS----HHHHHHHTTSEEE CS
                      TPP_enzyme_C  98 krksgpagkdlkpvdfaklaealGakga 125
                                       ++ s+ + k+l + d   ++++ G+++ 
  gi|313117051|ref|YP_004038175.1| 200 ETVSTAS-KILSDADRPVIIAGNGVHVS 226
                                       4444433.34455555555555555533 PP

  == domain 2  score: 111.7 bits;  conditional E-value: 5.9e-36
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitv 77 
                                       d G++ +w+ ++l+    r+y+ sgg g mG++ pa++ a++   d++vva++GDGgf m+++ ++tav++++  t+
  gi|313117051|ref|YP_004038175.1| 396 DSGNNRFWLLNYLQTPAIRTYFGSGGVGGMGWAGPAGVSAAIT-TDKDVVAVAGDGGFTMTMTCVETAVEYGVAPTF 471
                                       78*************99*************************6.588****************************** PP

                                       EEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  78 vvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       vvln+ ++gm+++  ++  g     ++   ++++df+++ae++Ga+g+rv+++  e l++ lkea + + p++++v
  gi|313117051|ref|YP_004038175.1| 472 VVLNDTSLGMVRQMDDSIPG-----VE---FHDTDFVAVAEGFGAEGMRVTEP--ENLAARLKEAKAADVPTVVDV 537
                                       *************8666654.....33...8899***************9999..*******************98 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.0   1.5e-31   6.7e-28       7     170 ..       8     177 ..       3     179 .. 0.91
   2 ?    2.4   0.1     0.024   1.1e+02      66     143 ..     442     526 ..     404     540 .. 0.75

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 1.5e-31
                                       HHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-C.HHHHHHCHHH CS
                      TPP_enzyme_N   7 lvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvts.gpGatnalta 82 
                                       +vr+L+ lgve++fg+pG+r  +ll++l++++ i+vv+ r+E+ a ++A+ y r ++ pgv+  +  ++G + a+++
  gi|313117051|ref|YP_004038175.1|   8 IVRVLEHLGVEYLFGYPGGRAIELLESLADSD-IQVVRPRDEREASVMAEMYGRYHQSPGVLTGQGpWIGSIGAIGQ 83 
                                       89*****************************6.*********************************9********** PP

                                       HHHHHHHT--EEEEEEE--CCCHH..S..TC--T..-CCHH.....HCCCSSEEEE-SSGGGHHHHHHHHHHHHHSS CS
                      TPP_enzyme_N  83 laeAkvdriPllvlsgdrptslrg..qgvlqqel..dqlal.....frpvtkyaervtspeelpealrrAirtalsg 150
                                       + eA++ ++P+++l+  +++ + +     + q+   d  ++     +  +tk+ ++++s++e+ + ++ A+++++ +
  gi|313117051|ref|YP_004038175.1|  84 M-EAQLGSSPMVALTEASERGDYStlA--PYQQArgDYGGFslpkiLDGITKEWWFPRSANETIRSVQLAFKHSTAN 157
                                       9.**********************553..44444464444444444******************************* PP

                                       S--EEEEEEEHHHCC-EEEH CS
                      TPP_enzyme_N 151 rpgPvylelpkdvlleevde 170
                                       rpgP+++ l  d +++ev+e
  gi|313117051|ref|YP_004038175.1| 158 RPGPTAVILDGDAVTAEVPE 177
                                       *****************987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.024
                                       EEEEE-CHHHHHHCHHHHHHHHHHT-.-EEEEEEE--CCCHH......S..TC--T-CCHHHCCCSSEEEE-SSGGG CS
                      TPP_enzyme_N  66 gvvlvtsgpGatnaltalaeAkvdri.Pllvlsgdrptslrg......qgvlqqeldqlalfrpvtkyaervtspee 135
                                        vv+v    G+t ++t + +A   ++ P +v+  d++  +++       gv  + +d +a+++ +  +  rvt+pe+
  gi|313117051|ref|YP_004038175.1| 442 DVVAVAGDGGFTMTMTCVETAVEYGVaPTFVVLNDTSLGMVRqmddsiPGVEFHDTDFVAVAEGFGAEGMRVTEPEN 518
                                       56666666688888888888877754377777778888777777766633333366888888888888889999998 PP

                                       HHHHHHHH CS
                      TPP_enzyme_N 136 lpealrrA 143
                                       l+  l++A
  gi|313117051|ref|YP_004038175.1| 519 LAARLKEA 526
                                       88888776 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0001      0.45       8      47 ..     185     224 ..     174     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                                       XXXXXXXXXX--EEE--SHHHHHHHHHSSSEEEEE-S--. CS
                             CO_dh   8 fdeaaianskkatleealkvvakmikkakrPllivGpqvl 47 
                                       + ea+  n   a  ee + ++ k+++ a+rP++i G+ v 
  gi|313117051|ref|YP_004038175.1| 185 SPEAQTRNWDSAPTEETVSTASKILSDADRPVIIAGNGVH 224
                                       446777888899999999******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3796.88
//
Query:       gi|313117052|ref|YP_004038176.1|  [L=333]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-41  142.4   0.3      2e-41  142.0   0.3    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.7e-40  139.4   0.2    5.7e-39  134.4   0.2    2.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    9.9e-22   77.2   0.0    1.3e-21   76.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.3e-16   58.5   1.4    7.1e-16   58.1   1.4    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.9e-12   47.0   0.0    9.1e-11   41.4   0.1    2.2  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.6e-10   41.1   0.2    2.6e-10   40.5   0.2    1.3  1  NAD_binding_10   NAD(P)H-binding
    3.1e-08   33.1   1.1    1.1e-05   24.8   1.1    2.3  1  NAD_binding_4    Male sterility protein
    2.1e-07   31.0   0.2    5.2e-07   29.7   0.2    1.7  1  KR               KR domain
    3.3e-07   30.0   0.6    3.3e-07   30.0   0.6    1.7  2  adh_short        short chain dehydrogenase
    8.3e-05   22.3   0.3    0.00017   21.3   0.3    1.5  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    0.00017   21.2   0.4     0.0003   20.4   0.4    1.5  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.054   12.9   0.1        0.1   11.9   0.1    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.18   11.1   0.1       0.31   10.3   0.1    1.3  1  CCB2_CCB4        Cofactor assembly of complex C subunit B, CC


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.0   0.3   1.5e-44     2e-41       1     240 [.      16     259 ..      16     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 1.5e-44
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE--S. CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihlAa. 73 
                                       +lVtG+tGfiGs++ k++le+g++vi+ d  ++++  ++l  +   e+ ++d+ d++++  +++e++ ++++hlAa 
  gi|313117052|ref|YP_004038176.1|  16 VLVTGGTGFIGSYVSKQFLEHGHDVIAYDLSTDTRILEKLGIAadvEVRRGDVSDATDVVSAVSETGTTHIVHLAAl 92 
                                       79****************************9887766555444777******************************5 PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHH..TCTEEEEEEEGGGGTSCSS.SS..BSTCSTTS--.--SSHHHH CS
                         Epimerase  74 vggvaassedpadfieknlqgtlnlleaarka..gvkrllflsSsevYGkdae.qp..keettltgpl.kpnspYaa 144
                                         + a+  ++p + ++ n++gt n++eaar+   +v+r+  +sS++vY ++++     +  +t ++ l +p + Y+a
  gi|313117052|ref|YP_004038176.1|  93 LTNTAE--SNPRAAMQVNIEGTSNVFEAARTLddQVERVAWASSAAVYAPPHNyDDggDWWVT-EDDLvYPDTLYGA 166
                                       555555..5666789***************8877999************99995334333344.33445******** PP

                                       HHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHH CS
                         Epimerase 145 aKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaea 221
                                       +K + e++++ y+++y+++ +++r++  yGp+  e+  s +++ +i+k + g+ ++ +   g++  d+ +veD+a++
  gi|313117052|ref|YP_004038176.1| 167 TKEYNEHQARVYHEEYDVSHVAIRPTVAYGPY-RETGGSAFLANIIEKPAVGE-SFSV-EYGDQEIDWQHVEDIAQG 240
                                       ********************************.77779**************9.5555.89**************** PP

                                       HHHHHHHHTT-STTEEEEE CS
                         Epimerase 222 illvlehvdagdkgeiyni 240
                                       + l++  +d+  +++iyn+
  gi|313117052|ref|YP_004038176.1| 241 FRLAAFTPDEELSQRIYNV 259
                                       ******************8 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4   0.2   4.1e-42   5.7e-39       1     331 [.      17     319 ..      17     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 4.1e-42
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG++GfiGsy+ +++le g++v+    ++ s++t+ +e+l          ++++ +gD++D++ + ++++e+  +
  gi|313117052|ref|YP_004038176.1|  17 LVTGGTGFIGSYVSKQFLEHGHDVIA---YDLSTDTRILEKLGI------AADVEVRRGDVSDATDVVSAVSETGTT 84 
                                       9**********************965...677888899999874......457899********************* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S......SSSB-TTS--- CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq......evpqtEttpfy 148
                                        +++LAA    ++  ++P + ++vn+ Gt +++ea+r+l   +  r+  aS++ vY  +       +  +tE+  +y
  gi|313117052|ref|YP_004038176.1|  85 HIVHLAALLT-NTAESNPRAAMQVNIEGTSNVFEAARTLDD-QVERVAWASSAAVYAPPHnyddggDWWVTEDDLVY 159
                                       *******965.555678**********************74.678***********99863332224568******* PP

                                       --SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEE CS
                     GDP_Man_Dehyd 149 PrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwgh 225
                                       P   Y+a+K y ++ ++ y+e+y++  v  +    ++p+r et     + +++ + a+g+   +++G+     dw+h
  gi|313117052|ref|YP_004038176.1| 160 PDTLYGATKEYNEHQARVYHEEYDVSHVAIRPTVAYGPYR-ETGGSAFLANIIEKPAVGESFSVEYGDQ--EIDWQH 233
                                       ***************************************8.8899999************988888876..68**** PP

                                       HHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS- CS
                     GDP_Man_Dehyd 226 vkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpge 302
                                       v+D++++++l+     p++    +++ ++vr+ +  ++ e+ +t+e                     +d     +ge
  gi|313117052|ref|YP_004038176.1| 234 VEDIAQGFRLAAFT--PDEE--LSQRIYNVRGELA-TVREAAETVEGI--------------IPDADID--VSDDGE 289
                                       ********996643..3332..3555666665443.233333333221..............1122233..223344 PP

                                       -.SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 303 v.dlllgdaskakeeLgWkpkvsfeelvre 331
                                          +   d++ka+e+Lg+ p++++e++ r+
  gi|313117052|ref|YP_004038176.1| 290 LpWTQRLDMTKAQEDLGYDPQYDLESGFRD 319
                                       4145589******************99886 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   9.6e-25   1.3e-21       1     229 [.      17     245 ..      17     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 9.6e-25
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleeale..gvdvvihlas 75 
                                       +vtGg+GF+G+++ k++++ +  ++v ++Dl +++++le+l      +v  gDv d+ ++  a+   g   ++hla+
  gi|313117052|ref|YP_004038176.1|  17 LVTGGTGFIGSYVSKQFLEHG--HDVIAYDLSTDTRILEKLGIAADVEVRRGDVSDATDVVSAVSetGTTHIVHLAA 91 
                                       69*******************..5**************9999888888***************972256889***** PP

                         3Beta_HSD  76 lvdvagkltedeimkvnvkGTrnvleacv..kagvrvlvYtSsaevvgpnslgeeilngdEeleyesl...hqdayp 147
                                       l   + + +    m+vn++GT nv ea++  + +v+++ + Ssa v  p    ++  +g + +  e     +   y 
  gi|313117052|ref|YP_004038176.1|  92 LLTNTAESNPRAAMQVNIEGTSNVFEAARtlDDQVERVAWASSAAVYAP---PHNYDDGGDWWVTEDDlvyPDTLYG 165
                                       ***************************9722568***************...7777788887777665444667788 PP

                         3Beta_HSD 148 esKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk.....llvpllkqlaklglalfkigdeevlsdrvYvg 219
                                        +K+  E+       r+ ++  ++  +a+Rp++ yG++ +     +l + +++ a  +   +++gd+e+  d+  v+
  gi|313117052|ref|YP_004038176.1| 166 ATKEYNEHQA-----RVYHEEYDVSHVAIRPTVAYGPYREtggsaFLANIIEKPAVGESFSVEYGDQEI--DWQHVE 235
                                       8888888754.....445556699*************76511111444555555544555566666665..999999 PP

                         3Beta_HSD 220 NvawahilAa 229
                                        +a+   lAa
  gi|313117052|ref|YP_004038176.1| 236 DIAQGFRLAA 245
                                       9998888877 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   1.4   5.2e-19   7.1e-16       2     214 ..      15     261 ..      14     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 5.2e-19
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE--- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaAA 60 
                                       ++lvtG++G +Gs + kq+ e+g++v+a + +                  + d++da+ v ++++e+    +v++AA
  gi|313117052|ref|YP_004038176.1|  15 TVLVTGGTGFIGSYVSKQFLEHGHDVIAYDLStdtrileklgiaadvevrRGDVSDATDVVSAVSETGTTHIVHLAA 91 
                                       68***************************88889******************************************* PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E...EEEEEEGGGS-S-.....TTS-B.-TTS----SSHHHHH CS
                     RmlD_sub_bind  61 ytavDkaEseeeaayavnaeavealAeaaaavgal...LihvStDyVFdGe.....kkrpY.eeddetsPlnvYGrt 128
                                             aEs+++aa++vn e++ ++ eaa+  + +   +   S+  V+          + + +edd + P ++YG+t
  gi|313117052|ref|YP_004038176.1|  92 LL-TNTAESNPRAAMQVNIEGTSNVFEAARTLDDQverVAWASSAAVYAPPhnyddGGDWWvTEDDLVYPDTLYGAT 167
                                       86.579************************998651226889*****987666664333343789999********* PP

                                       HHHHHHHHHH....H-SSEEEEEE-SEESS....SSS-HHHHHHHHHHH-SEEEEES.S-EE--EEHHHHHHHHHHH CS
                     RmlD_sub_bind 129 KlaGEqavla....agkkalivRtswvyge....kgknfvktmlrlakereelkvva.DqlgsPTsardlAevllql 196
                                       K   E+  +     +   ++ +R ++ yg      g  f+++++++ +  e+ +v   Dq     +++d+A+    +
  gi|313117052|ref|YP_004038176.1| 168 KEYNEHQARVyheeYDVSHVAIRPTVAYGPyretGGSAFLANIIEKPAVGESFSVEYgDQEIDWQHVEDIAQGFRLA 244
                                       *****9988722324457899*******9866667899**************9996449999999999999987666 PP

                                       HHHCHH.GGG-EEEE--- CS
                     RmlD_sub_bind 197 lekaaeekelagvyHlan 214
                                       + +  e +  +++y + +
  gi|313117052|ref|YP_004038176.1| 245 AFTPDE-ELSQRIYNVRG 261
                                       655554.33366665555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   6.6e-14   9.1e-11       1     128 [.      16     134 ..      16     144 .. 0.78
   2 ?    3.3   0.0     0.028        38     128     158 ..     154     184 ..     151     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 6.6e-14
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG++G iGs + +q+l++    +i ++ +     +i ++l   + + +++v+     gdv d++ + +a++e++
  gi|313117052|ref|YP_004038176.1|  16 VLVTGGTGFIGSYVSKQFLEHGHD-VIAYDLST--DTRILEKLG--I-AADVEVR----RGDVSDATDVVSAVSETG 82 
                                       8******************98765.55565543..334445542..1.2234444....7***************** PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHH..TT-SEEEEEEE CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaie..agvkkvvliSt 128
                                          ++h AAl    ++e+np  a++ N+ gt+nv eaa +   +v++v   S+
  gi|313117052|ref|YP_004038176.1|  83 TTHIVHLAALL-TNTAESNPRAAMQVNIEGTSNVFEAARTldDQVERVAWASS 134
                                       *********96.589**********************9751157888777665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.028
                                       EGGGSS--SHHHHHHHHHHHHHHHGGG--SS CS
                   Polysacc_synt_2 128 tDKAvnPtnvmGatKrlaekllqalakesee 158
                                        D  v+P  ++GatK + e  +  +++e   
  gi|313117052|ref|YP_004038176.1| 154 EDDLVYPDTLYGATKEYNEHQARVYHEEYDV 184
                                       58889**************998888877644 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.2   1.9e-13   2.6e-10       1     144 [.      20     192 ..      20     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.9e-13
                                       TTTSHHHHHHHHHHHHC-T-EEEEE..ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT..T-S.EEEES-.... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtal..vRnpeklaeleaeeglevvegdvtdvedlaealk..gad.aVvsal.... 68 
                                       G+tG +G+++ k+ l++ gh+v a+    ++  l++l  ++ +ev  gdv+d+ d+ +a++  g+  +V  a+    
  gi|313117052|ref|YP_004038176.1|  20 GGTGFIGSYVSKQFLEH-GHDVIAYdlSTDTRILEKLGIAADVEVRRGDVSDATDVVSAVSetGTThIVHLAAlltn 95 
                                       9****************.5*****7535666677889888********************84443337766666775 PP

                                       ...--TCC.HHHH........HHHHHHHHHH..CT--EEEEEEETTTTSGCGCH....HHHHHHH.......CCHHH CS
                    NAD_binding_10  69 ...ggggk.deeg........aknivdaake..agvkRfvlvsaigvgdevpge....fgewnke.......llkay 120
                                          +   + +  +        + n+ +aa++   +v+R+ + s++ v+   p++     ++w++e       +l  +
  gi|313117052|ref|YP_004038176.1|  96 taeS---NpR--AamqvniegTSNVFEAARTldDQVERVAWASSAAVYAP-PHNyddgGDWWVTEddlvypdTLYGA 166
                                       4331...131..133445666*********85578*************63.32211213455543333322244444 PP

                                       HHH..HHHHHHHHHHSSSEEEEEEE- CS
                    NAD_binding_10 121 laa..kraaeellrasgldwTivrpg 144
                                        ++   ++a  + ++ ++  + +rp+
  gi|313117052|ref|YP_004038176.1| 167 TKEynEHQARVYHEEYDVSHVAIRPT 192
                                       45411334444556667777777776 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   1.1     8e-09   1.1e-05       1     208 [.      18     196 ..      18     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8e-09
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+TGF+G+++ ++ L+   +  +++     +  s   R+   lek ++           ++v  GD+s+    +s
  gi|313117052|ref|YP_004038176.1|  18 VTGGTGFIGSYVSKQFLEHGHD--VIAY----DL-STDTRI---LEKLGIAA--------DVEVRRGDVSDATDVVS 76 
                                       6899999999999999988885..3332....22.445677...55556654........45788999998874444 PP

                                       HHHHHHHHHH--EEEE--SS-S.ST..TSSEEHHHHHHHHHHHHHHHTSSS--..-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfde..pykellrvNveGtrevlelakklkkl.kvllhvSTayvngeregeveekv 151
                                       + +       +++i+h aA ++ ++  + + +++vN+eGt +v+e a++l  + + +   S+a+v+   ++      
  gi|313117052|ref|YP_004038176.1|  77 AVS----ETGTTHIVHLAALLTNTAesNPRAAMQVNIEGTSNVFEAARTLDDQvERVAWASSAAVYAPPHNY----- 144
                                       333....345799******876554225567*****************987766899999996666666633..... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                            ++  +   ++++l    + Y  +K   E+  r ++++ ++  v +Rp++ +g
  gi|313117052|ref|YP_004038176.1| 145 -----DDGGDWWVTEDDLVYPDTLYGATKEYNEHQARVYHEEYDVSHVAIRPTVAYG 196
                                       .....3556777888888888889****************************98877 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.2   3.8e-10   5.2e-07       1     138 [.      14     136 ..      14     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3.8e-10
                                       SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                                KR   1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77 
                                       +t+l+tGG+G +G  ++++ +e+g   +++   +      +++ +++l    a+vev++ Dvsd+++v ++++e  +
  gi|313117052|ref|YP_004038176.1|  14 ATVLVTGGTGFIGSYVSKQFLEHGHDVIAYDLST------DTRILEKL-GIAADVEVRRGDVSDATDVVSAVSETGT 83 
                                       689*********************9999873333......22234444.4578********************9985 PP

                                       HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT..S--SEEEEEEEHH CS
                                KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled..esldffvlfSSia 138
                                       +      ++h A +l     +++ +++ +++++  ++G+ n+ e+ +   ++++ +   SS+a
  gi|313117052|ref|YP_004038176.1|  84 T-----HIVHLAALL-----TNTAESNPRAAMQVNIEGTSNVFEAARTldDQVERVAWASSAA 136
                                       5.....5****9765.....566788889999999******9999887668888888888877 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.6   2.4e-10   3.3e-07       2     105 ..      15     116 ..      14     136 .. 0.82
   2 ?   -2.7   0.0       2.5   3.5e+03     148     174 ..     163     189 ..     161     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.4e-10
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHH.SS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkkl.gk 77 
                                       +vlvtG+++ IG  ++k++++ G +v+++d s ++   ++++l+  +a++ + ++Dv+d+++v  +v++    +  +
  gi|313117052|ref|YP_004038176.1|  15 TVLVTGGTGFIGSYVSKQFLEHGHDVIAYDLSTDTR--ILEKLGI-AADVEVRRGDVSDATDVVSAVSETGTTHiVH 88 
                                       79******************************9977..9999996.689*********9999999888886655499 PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervi 105
                                       l +L +N++ ++++++ +++ e + +v+
  gi|313117052|ref|YP_004038176.1|  89 LAALLTNTAESNPRAAMQVNIEGTSNVF 116
                                       9999999888655555555554444444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHHHHHHGGGTEEE CS
                         adh_short 148 aYsAsKaavagltrslakelaptgirv 174
                                        Y+A+K   ++ +r  ++e+  + + +
  gi|313117052|ref|YP_004038176.1| 163 LYGATKEYNEHQARVYHEEYDVSHVAI 189
                                       688888888888888888877776655 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3   1.2e-07   0.00017       6     114 ..      25     120 ..      22     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG CS
                      adh_short_C2   6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapk 82 
                                       IG  + k++ e+G +v++ dl+ +  + +e+l  + + ev + DV+d ++v ++v+e+  ++     +v+ a+  ++
  gi|313117052|ref|YP_004038176.1|  25 IGSYVSKQFLEHGHDVIAYDLSTDT-RILEKLGIAADVEVRRGDVSDATDVVSAVSETGTTH-----IVHLAALLTN 95 
                                       89999*******************9.8999999999999****************9998876.....5666666555 PP

                                       CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHH CS
                      adh_short_C2  83 lkgpfletsreefdraldvnlyslfllakaal 114
                                              t +++ + a++vn+ ++ ++ +aa+
  gi|313117052|ref|YP_004038176.1|  96 -------TAESNPRAAMQVNIEGTSNVFEAAR 120
                                       .......5555556666666666666666554 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   2.2e-07    0.0003       1      69 [.      16      85 ..      16     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SEEE CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelv.kgdlddkeslvealkgvdvvf 69
                                      +lv+G+TG +G++v + +l++gh+v a    t++  +++l  a  + v  gd+ d   +v+a+++  +  
  gi|313117052|ref|YP_004038176.1| 16 VLVTGGTGFIGSYVSKQFLEHGHDVIAYDLSTDTRILEKLGIAADVEVrRGDVSDATDVVSAVSETGTTH 85
                                      79**************************************866655555*************99876554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.5e-05       0.1      33      96 ..      10      76 ..       3      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                                      -GTTSEEEEE.S-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC...SHHHHHHH-SEEE CS
                      2-Hacid_dh_C 33 elsgktvGii.GlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv...sleellaesDivs 96
                                        ++ tv +  G+G IG+ v k + + g +viayd s +++   e+lg+  +      ++   +D+vs
  gi|313117052|ref|YP_004038176.1| 10 MAENATVLVTgGTGFIGSYVSKQFLEHGHDVIAYDLSTDTRI-LEKLGIAADvevRRGDVSDATDVVS 76
                                      566777777637*************************88555.7777763322123345555555555 PP

>> CCB2_CCB4  Cofactor assembly of complex C subunit B, CCB2/CCB4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00022      0.31      43      88 ..      89     135 ..      67     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                         CCB2_CCB4  43 lvgllwkrlk..pkppeavelegaeevfelaedlsdalkeeLaWasea 88 
                                       l +ll + ++  p+++ +v++eg+++vfe a++l+d + e +aWas a
  gi|313117052|ref|YP_004038176.1|  89 LAALLTNTAEsnPRAAMQVNIEGTSNVFEAARTLDD-QVERVAWASSA 135
                                       555555555436999*******************66.55779***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2313.37
//
Query:       gi|313117053|ref|YP_004038177.1|  [L=203]
Description: hypothetical protein Hbor_35210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-10   39.2   0.3    1.2e-09   38.5   0.3    1.3  1  HD        HD domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.019   15.1   0.0    1.3  1  HD_6      HD domain
       0.16   11.7   0.1       0.38   10.5   0.1    1.6  2  HD_2      HD containing hydrolase-like enzyme


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.3   1.9e-13   1.2e-09       3     116 ..      65     174 ..      63     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.9e-13
                                       HHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHTTTTHHHHTS..HHH.......HHH..CTCCHHHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlge....eedrellllaaLlHDiGkgpfgdafekk.......eee..fekflaHekvgaei 66 
                                       eH ++V k+a + ae        + d +++++a+LlHD+Gk++++     +         e  ++++  H++ g+ +
  gi|313117053|ref|YP_004038177.1|  65 EHVRGVTKIALQSAEVQRDfhgaDPDIDVIVAACLLHDVGKCYEYVDHVDAelldgtdR-EhyANEEIPHSISGYAL 140
                                       9*********9999866669***********************8864444477777642.26899999********* PP

                                       HHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHH CS
                                HD  67 lrevekrlgldledvaklirehheswegkkrprglaerqlslearivkla 116
                                       ++ev+ +l     dv+++i + ++  +             +lea +vk a
  gi|313117053|ref|YP_004038177.1| 141 AHEVGCPL-----DVQRAIPHFLGEVP-----------TRTLEAELVKSA 174
                                       ********.....**********9999...........557777777655 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.2e-06     0.019      39     107 ..      81     149 ..      58     192 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.2e-06
                                       HHHC.TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHH......H CS
                              HD_6  39 arllrgleeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalle......e 107
                                       +r++     +   +++++ + lHD+GK+ +   +  +el++  +++++    ++e+++H+  g+al +      +
  gi|313117053|ref|YP_004038177.1|  81 QRDF--HGADPDIDVIVAACLLHDVGKCYEYVDHVDAELLDGTDREHY----ANEEIPHSISGYALAHevgcplD 149
                                       4444..34455568899999********98666666666665554433....3489*********9554444441 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   6.3e-05      0.38      22      66 ..      59     103 ..      47     108 .. 0.88
   2 ?   -2.7   0.0      0.72   4.3e+03     113     134 ..     155     176 ..     146     201 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.3e-05
                              HD_2  22 reenvaeHslevaliahalalienkkfggkldaerlallalyHDa 66 
                                       ++ +  eH   v+ ia   a ++++ +g + d++ ++++ l+HD+
  gi|313117053|ref|YP_004038177.1|  59 HDVTNVEHVRGVTKIALQSAEVQRDFHGADPDIDVIVAACLLHDV 103
                                       5556689******************9999***************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.72
                              HD_2 113 eelladeeaeeeekklvkaaDk 134
                                        ++l++  +++ e +lvk a +
  gi|313117053|ref|YP_004038177.1| 155 PHFLGEVPTRTLEAELVKSANS 176
                                       4455444444556666666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1156.65
//
Query:       gi|313117054|ref|YP_004038178.1|  [L=231]
Description: hypothetical protein Hbor_35220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-24   84.9  11.0      2e-12   48.1   0.7    3.9  2  EthD      EthD domain
    1.8e-23   83.2   5.5    1.8e-12   47.7   0.6    3.8  2  MmlI      Methylmuconolactone methyl-isomerase
     0.0097   16.0   0.6       0.42   10.8   0.0    2.4  2  DUF4543   Domain of unknown function (DUF4543)
  ------ inclusion threshold ------
      0.022   15.4   0.3        9.4    6.9   0.1    2.6  2  FOXP-CC   FOXP coiled-coil domain
      0.049   13.8   0.4         13    6.0   0.1    2.9  3  ABM       Antibiotic biosynthesis monooxygenase


Domain annotation for each model (and alignments):
>> EthD  EthD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   3.7   7.6e-13   2.7e-09       3      92 ..       1      85 [.       1      87 [. 0.77
   2 !   48.1   0.7   5.5e-16     2e-12       1      90 [.     121     205 ..     121     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 7.6e-13
                                      S-HHHHHHHHHHTHHHHHCTSTT............--EEEEEEEEEBTTC--SEEEEEEEEESSHHHHHHHHCSHHHHH CS
                              EthD  3 lspeeFrdyweevHaplvkdllggirryvlratktrpateagvalagpgsdadyDgiaelwfdsleaflaafadpeyaa 81
                                      +s+eeF ++w+++H+p +kd+ g ++ry               +l+ +++ a++Dg ael+f++l+++  a+ ++   +
  gi|313117054|ref|YP_004038178.1|  1 MSHEEFVEHWQHTHTPIAKDIEG-VVRYQ-------------QVLPTEPEHAEFDGLAELYFETLDELHEALGSEG-SR 64
                                      89*********************.55555.............458899999***************9999998742.22 PP

                                      ...........HHHHHHHHCG CS
                              EthD 82 v..........laaDeenFaD 92
                                                  + D++nF+D
  gi|313117054|ref|YP_004038178.1| 65 DydptkeiaakARQDVDNFLD 85
                                      223333333337778888877 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 5.5e-16
                                       --S-HHHHHHHHHHTHHHHHCTSTT............--EEEEEEEEEBTTC--SEEEEEEEEESSHHHHHHHHCSH CS
                              EthD   1 pglspeeFrdyweevHaplvkdllggirryvlratktrpateagvalagpgsdadyDgiaelwfdsleaflaafadp 77 
                                       +g+++eeF d+w+++H+p +k++ g ++ry++               +  ++ a++Dgiael+fd++e ++ a+ ++
  gi|313117054|ref|YP_004038178.1| 121 EGMTHEEFLDHWQNTHTPIAKEIEG-VVRYCQV-------------VPTDPDNAEFDGIAELYFDDIEKLYDALGSE 183
                                       69***********************.9999955.............67788899**************999999764 PP

                                       ...HHHH.......HHHHHHHH CS
                              EthD  78 ...eyaav......laaDeenF 90 
                                          +y+a+       ++D++nF
  gi|313117054|ref|YP_004038178.1| 184 gsrDYEATggkaaeAREDVDNF 205
                                       1114555466666666666666 PP

>> MmlI  Methylmuconolactone methyl-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.4     3e-11   1.1e-07      14      85 ..       1      61 [.       1      67 [. 0.86
   2 !   47.7   0.6   5.1e-16   1.8e-12       6      94 ..     115     192 ..     110     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3e-11
                              MmlI 14 lsheqflahwrevhaplvhavtGlrryqqnrvvderftqfvPvveydgypvdgivelWfedlasleksfasp 85
                                      +she+f++hw++ h p++ ++ G+ ryqq           +P  e +  ++dg++el+fe l++l++++ s+
  gi|313117054|ref|YP_004038178.1|  1 MSHEEFVEHWQHTHTPIAKDIEGVVRYQQV----------LPT-EPEHAEFDGLAELYFETLDELHEALGSE 61
                                      8**************************975..........455.4455678999******999999988776 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 5.1e-16
                              MmlI   6 gllsrredlsheqflahwrevhaplvhavtGlrryqqnrvvderftqfvPvveydgypvdgivelWfedlasleksf 82 
                                       + l+r+e+++he+fl hw++ h p++ ++ G+ ry q           vP  + d  ++dgi+el+f+d+++l  ++
  gi|313117054|ref|YP_004038178.1| 115 AFLVRKEGMTHEEFLDHWQNTHTPIAKEIEGVVRYCQ----------VVPT-DPDNAEFDGIAELYFDDIEKLYDAL 180
                                       6799*******************************75..........5787.789999**************99999 PP

                              MmlI  83 aspaakllaahG 94 
                                        s+  + + a G
  gi|313117054|ref|YP_004038178.1| 181 GSEGSRDYEATG 192
                                       988776666655 PP

>> DUF4543  Domain of unknown function (DUF4543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.03   1.1e+02      49      62 ..       2      15 ..       1      21 [. 0.86
   2 !   10.8   0.0   0.00012      0.42      36      62 ..     111     137 ..      95     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.03
                           DUF4543 49 aeeqflehWlnPhc 62
                                      ++e+f+ehW   h 
  gi|313117054|ref|YP_004038178.1|  2 SHEEFVEHWQHTHT 15
                                      689******99885 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                           DUF4543  36 reyllylqrleqraeeqflehWlnPhc 62 
                                         +  +l r e  ++e+fl+hW n h 
  gi|313117054|ref|YP_004038178.1| 111 YKHSAFLVRKEGMTHEEFLDHWQNTHT 137
                                       56888999*****************95 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0026       9.4      18      39 ..       2      23 ..       1      34 [. 0.78
   2 ?    5.9   0.0    0.0058        21      19      39 ..     125     145 ..     120     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0026
                           FOXP-CC 18 dveeflkhlnseHalddkstaq 39
                                      ++eef++h++++H++  k ++ 
  gi|313117054|ref|YP_004038178.1|  2 SHEEFVEHWQHTHTPIAKDIEG 23
                                      5789**********98887765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0058
                           FOXP-CC  19 veeflkhlnseHalddkstaq 39 
                                       +eefl h++++H++  k ++ 
  gi|313117054|ref|YP_004038178.1| 125 HEEFLDHWQNTHTPIAKEIEG 145
                                       789**********98887765 PP

>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0037        13      15      48 ..       3      36 ..       2      67 .. 0.90
   2 ?   -2.6   0.0       1.7   6.1e+03      20      42 ..      49      69 ..      40      78 .. 0.61
   3 ?    5.2   0.0    0.0066        24      15      42 ..     125     152 ..     115     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0037
                                      HHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETST CS
                               ABM 15 aeafldafaeavesllaeepGclgyellrstedp 48
                                      +e+f++ +++ + ++ ++ +G  +y+ +++te +
  gi|313117054|ref|YP_004038178.1|  3 HEEFVEHWQHTHTPIAKDIEGVVRYQQVLPTEPE 36
                                      89************************99966654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                      HHHHHHHHHHHHTSTTEEEEEEE CS
                               ABM 20 dafaeavesllaeepGclgyell 42
                                      + + e++e+l    +G ++y++ 
  gi|313117054|ref|YP_004038178.1| 49 ETLDELHEAL--GSEGSRDYDPT 69
                                      4455555533..56666666655 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0066
                                       HHHHHHHHHHHHHHHHHTSTTEEEEEEE CS
                               ABM  15 aeafldafaeavesllaeepGclgyell 42 
                                       +e+fld +++ + ++ +e +G  +y  +
  gi|313117054|ref|YP_004038178.1| 125 HEEFLDHWQNTHTPIAKEIEGVVRYCQV 152
                                       59*******************9999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1400.07
//
Query:       gi|313117055|ref|YP_004038179.1|  [L=422]
Description: Xaa-Pro aminopeptidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-29  102.8   0.1    2.8e-29  102.3   0.1    1.3  1  Peptidase_M24  Metallopeptidase family M24
    0.00034   21.3   0.0    0.00066   20.3   0.0    1.6  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.1   3.1e-33   2.8e-29       1     209 []     190     403 ..     190     403 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 3.1e-33
                                       HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTT.BCSSSB--TTEE CS
                     Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhy.tpndrvlkegdl 76 
                                       e++r++a+i++a +++++e  +pgv+e e+   + ++ l rhga  ++  + v sg+n+   h  + +dr++++gd+
  gi|313117055|ref|YP_004038179.1| 190 ECLRQVAAICEAGFQKIKETARPGVKESEVWGHASKE-LWRHGAMVQG--GYVTSGPNTWPKHQaNTTDRQIRPGDI 263
                                       689********************************99.8999988885..77********99996667********* PP

                                       EEEEEE.EEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHT........T CS
                     Peptidase_M24  77 vlidag.aeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesa........g 144
                                       v  d+  + y gy s   rT++ G++t++q+++ye++++ ++ +++ ++pG+t++ei +   +   ++         
  gi|313117055|ref|YP_004038179.1| 264 VYADFYnIGYLGYRSCYYRTFSMGEPTKAQKDAYETARDNLYDVLERIEPGATTDEICKGFPDMEGEHadwydatdH 340
                                       ****8725677**********************************************99999988886554455544 PP

                                       BCCGBSSCSEEEESSSSSEEEEEESS..STTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                     Peptidase_M24 145 lakffphglGHgvGlevhdegpsvsr..esndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                       + +  +++  Hg+Gl++ ++ p ++r   +++  ++eeGm++++E++  ++ + +gvr+e++v+v+e
  gi|313117055|ref|YP_004038179.1| 341 W-QMTTNHWAHGLGLQLYEV-PLIWRglSPDHPIEIEEGMTMAVETM--EPADRQGVRVEEMVVVRE 403
                                       5.88899***********98.****9876668999***********6..344566**********86 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   7.3e-08   0.00066       1      57 [.      31      88 ..      31     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.3e-08
                                      HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS.....-SSSEEEEEEESSCEEEEEECTT CS
                      Creatinase_N  1 RlerlralmeekgldallvtspenlrYltGfa..tetgsrglalvvtadgalllvdalr 57
                                      R e++ +++++ +l ++l+ s+ n+rY+tG a    +g  ++ l +t++g++   d+ +
  gi|313117055|ref|YP_004038179.1| 31 RYEKALERLQDSDLGSMLLVSDPNIRYVTGLAmtGGSGADHYTL-LTEEGDIVHWDTAD 88
                                      789****************************9443444566777.78888844444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 2313.94
//
Query:       gi|313117056|ref|YP_004038180.1|  [L=333]
Description: flavin-dependent oxidoreductase, F420-dependent methylene-tetrahydromethanopterin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-53  182.5   0.0    1.5e-53  182.2   0.0    1.1  1  Bac_luciferase   Luciferase-like monooxygenase
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.23   11.2   0.1    1.5  1  Trehalase_Ca-bi  Neutral trehalase Ca2+ binding domain


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.2   0.0   1.7e-57   1.5e-53       6     313 ..       8     300 ..       1     301 [. 0.88

  Alignments for each domain:
  == domain 1  score: 182.2 bits;  conditional E-value: 1.7e-57
                    Bac_luciferase   6 flptrqggalgaasaslrylvelaraaEelGfdavwvaehhggpgga.ldaftllaalaaaTerirlgtavtplytr 81 
                                       f+  +++++++++++  ++++el r+++e+G+d+ wv+ehh+ +++  + ++  l+ala++T++i++gt++  ++++
  gi|313117056|ref|YP_004038180.1|   8 FTCQQRPDDDRSMTEIHDEMLELGRTIDEAGLDSTWVSEHHFSDDSYlSGTMPALGALASVTDNIEIGTCIALAPLY 84 
                                       4444444455555577899***********************99999999999************************ PP

                    Bac_luciferase  82 hPavlAqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsv.kgal 157
                                       + ++lA++aat+d ls+GR+ lgl  g++++e+++fGv+++er++rl + v++lr++w++++ d++ ef+ v  +++
  gi|313117056|ref|YP_004038180.1|  85 DGVRLAEDAATVDLLSDGRLTLGLSIGSNPNEFEQFGVPREERVERLSDQVNLLRGAWSDGPLDYDAEFHDVsPDVT 161
                                       **********************************************************99999******999***** PP

                    Bac_luciferase 158 llprpgqgpiPvyvaaaspaglelaarhadglllag.eppeeaaelierlragaaeagrdpadirvgisltvivadt 233
                                       ++p+p++g +P+++++a   +++ aar+ad++   +  +   +++++e++r   +  + d ++++++i  +  v+d+
  gi|313117056|ref|YP_004038180.1| 162 VTPKPKDG-VPIMLGGAAKPAVRRAARTADAWCAPSkLSITGLQRRVEDIRNVRETEDID-GEFQIYILQHGWVGDS 236
                                       *****999.*************************999**************988888885.58************** PP

                    Bac_luciferase 234 eeeAraearaliagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaea 310
                                       +e+A++ +++ ++             +   +++  e + ++  ++  +  ++  +++ a+ Gtp+qv+++l +y+ea
  gi|313117056|ref|YP_004038180.1| 237 REDAWETMKDGYL-------------YI--QRRYAEIFGGEPVDELPAE-RKQELKEQAIFGTPDQVVDELNEYREA 297
                                       ********88882.............22..2333444444444444444.3667889999**************999 PP

                    Bac_luciferase 311 gvd 313
                                        +d
  gi|313117056|ref|YP_004038180.1| 298 LGD 300
                                       876 PP

>> Trehalase_Ca-bi  Neutral trehalase Ca2+ binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.5e-05      0.23       1      16 [.     210     225 ..     210     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.5e-05
                   Trehalase_Ca-bi   1 LeqLLeqEDTDgnfQI 16 
                                       ++++ e ED Dg fQI
  gi|313117056|ref|YP_004038180.1| 210 IRNVRETEDIDGEFQI 225
                                       67899*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 2193.73
//
Query:       gi|313117057|ref|YP_004038181.1|  [L=338]
Description: pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase component beta subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-48  164.0   0.0    4.1e-48  163.4   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.3e-34  118.7   0.0    2.3e-34  117.9   0.0    1.4  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.055   13.8   0.0      0.096   13.0   0.0    1.4  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.0   6.8e-52   4.1e-48       6     176 ..      19     190 ..      14     191 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 6.8e-52
                                       HHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEE CS
                      Transket_pyr   6 rkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaq 80 
                                        +a+ + l +++ + ++vv++g+Dv+  gg+f +++gl +++ge+rvid++++E++++g a+G+al+g l++++e+q
  gi|313117057|ref|YP_004038181.1|  19 VEAICDGLYTEMSQSDDVVVMGEDVGknGGVFRATNGLYEEFGEERVIDTPLAEAGIVGSAIGLALSG-LRPVAEMQ 94 
                                       577888899***********************************************************.9******* PP

                                       EHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHH CS
                      Transket_pyr  81 FgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllr 155
                                       F+ F+ +A  qi+ ++a  + +++g++ v++v+r+p+g g ++peh+s + eaf+ + pglkvv+Ps+p ++k+ll 
  gi|313117057|ref|YP_004038181.1|  95 FMGFIYPAfdQIVSHAARLRSRSHGQYSVPMVVRAPYGGGIRAPEHHSESKEAFFVHEPGLKVVTPSTPHDAKGLLI 171
                                       ***************************************************************************** PP

                                       HHHHSSS.SEEEEEE-SSEEC CS
                      Transket_pyr 156 rairredrkPvvlrlpksllr 176
                                       + +r  d++Pv++++pk  +r
  gi|313117057|ref|YP_004038181.1| 172 ASLR--DPDPVIFLEPKLIYR 190
                                       ****..899********9997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.9   0.0   3.9e-38   2.3e-34       2     124 .]     207     328 ..     206     328 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 3.9e-38
                                       EEEEEETTSSEEEEEETTHHHHHHHHHHHHHTT.TTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   2 kaeilregkdvtlvayGsmveealeAaeeLeke.gisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       +a i+reg+d+ + ++G+m + al Aa++L++e g+++eVvdlrt++plD+eti es kktgr  vv+ea k+gG+g
  gi|313117057|ref|YP_004038181.1| 207 EASIRREGSDISVYTWGAMTRPALIAADNLADErGVDVEVVDLRTLSPLDTETIVESFKKTGRAAVVHEAPKTGGLG 283
                                       6899****************************9******************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                       +e++++++eea+ + +ap+kr++g+d+++p     +e++++++a +i
  gi|313117057|ref|YP_004038181.1| 284 AEISSTIQEEALLHQEAPIKRITGFDAPVPLH--GVEDYYLPQAVRI 328
                                       ***************************66665..89******99776 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.6e-05     0.096       2      81 ..     216     293 ..     215     312 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                       SEEEEE-STHHHHHHHHHHHHH.HTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   2 evvivamGsvagtaksavdelR.eegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       ++ + + G++ + a  a+d+l  e+g++v ++ lrtl P  +e + e  kk+ + +v+  +     +G l+ e+++ 
  gi|313117057|ref|YP_004038181.1| 216 DISVYTWGAMTRPALIAADNLAdERGVDVEVVDLRTLSPLDTETIVESFKKTGRAAVVHEAP---KTGGLGAEISST 289
                                       6778889999999999999876378************************9999999998888...358899999999 PP

                                       TGGG CS
                           PFOR_II  78 lkks 81 
                                       ++++
  gi|313117057|ref|YP_004038181.1| 290 IQEE 293
                                       8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2243.72
//
Query:       gi|313117058|ref|YP_004038182.1|  [L=382]
Description: pyruvate dehydrogenase E1 component, alpha subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-82  277.4   0.0    1.4e-82  277.0   0.0    1.1  1  E1_dh            Dehydrogenase E1 component
    8.9e-07   28.4   0.0    1.5e-06   27.6   0.0    1.4  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    4.1e-05   23.4   0.3    0.00023   21.0   0.3    2.1  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    0.00014   20.9   0.1    0.00025   20.1   0.1    1.5  1  Transketolase_N  Transketolase, thiamine diphosphate binding 


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.0   0.0   3.1e-86   1.4e-82       6     295 ..      55     340 ..      50     344 .. 0.94

  Alignments for each domain:
  == domain 1  score: 277.0 bits;  conditional E-value: 3.1e-86
                                       HHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TTTSSG CS
                             E1_dh   6 lrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvkgkgg 82 
                                       l+r +d+++++++r++r+ +y+++ gqe ++v+   al+++D+++++YRe+  + ++g++l ++l+ l+g +     
  gi|313117058|ref|YP_004038182.1|  55 LARRFDQRAISFQRQGRLATYAPMTGQEGAQVATSYALDDQDWLFPTYREHAAKHVHGVDLASLLKPLRGLR----- 126
                                       67889*****************************************************************99..... PP

                                       TT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EE.EEEEGGGTT-HHHHHHHHHHHHTT--EEEEE CS
                             E1_dh  83 srhelmyaekesrilggngivgaqvplvaGialaakiegkkevai.lliGDgAanqGdvyealnlaalwklpvifvv 158
                                          e++  +  +++++  +++++qvp++ G+a  +k++gk+  a+ +  GDgA+++Gd++e+ln+a ++++p++fv+
  gi|313117058|ref|YP_004038182.1| 127 ---EGYAVPDDVNVMPEYIPIATQVPQAMGMAWGHKMQGKTDQAVlCHLGDGATSEGDFHEGLNFAGVFDVPTVFVC 200
                                       ...689999999************************9998766651567**************************** PP

                                       EEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT-....-EEEEEEE--SS-SS CS
                             E1_dh 159 eNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkg....pllielvtYRyggHs 231
                                       +NN+++is+++e+++as+++a++a+++gi g+rVdg Dplavy+++k+A + a++  g    p+lie+v YRyg H+
  gi|313117058|ref|YP_004038182.1| 201 NNNQWAISVPRERQTASETIAQKAQAYGIDGVRVDGLDPLAVYQVTKEALNKAKSPTGdelrPTLIEAVQYRYGAHT 277
                                       *****************************************************9855433338************** PP

                                       TTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS- CS
                             E1_dh 232 esDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskk 295
                                       + Ddps yr ++e +e+++k dp+ rl+++L ++g+++e  + ei++++++++ +a+++aes++
  gi|313117058|ref|YP_004038182.1| 278 TADDPSVYREADEADEWKEK-DPVDRLQKYLYNEGLLDEGIEAEIDDRIEAKISDAIAEAESAE 340
                                       *********88888877666.****************************************985 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   3.4e-10   1.5e-06     115     177 ..     146     209 ..     144     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.4e-10
                    DXP_synthase_N 115 tsisaalGlavardlkg.ekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk 177
                                       t + +a+G+a  ++++g +++ v++ +GDga + G  +e+ln +g  +   + + N+N+++is 
  gi|313117058|ref|YP_004038182.1| 146 TQVPQAMGMAWGHKMQGkTDQAVLCHLGDGATSEGDFHEGLNFAGVFDVPTVFVCNNNQWAISV 209
                                       77889***********9557889999**********************************9985 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.3   5.2e-08   0.00023      32     147 ..     150     255 ..     134     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.2e-08
                                       THHHHHHHHHH.HSTTSEEEEEEEHHHHHHT.GGGHHHHHHT.T-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB CS
                      TPP_enzyme_C  32 yglpaAiGakl.akpdrevvaivGDGgflmi.lqelatavrr.nlpitvvvlnNegygmtggqqepfggkrksgpag 105
                                        ++++A G k+  k d+ v +  GDG++    ++e  +++   ++p ++v+ nN++   + ++ +++     s    
  gi|313117058|ref|YP_004038182.1| 150 QAMGMAWGHKMqGKTDQAVLCHLGDGATSEGdFHEGLNFAGVfDVPTVFVCNNNQWAISVPRE-RQTA----S---- 217
                                       46778888888547799**********999997776666665155655555555554333332.2221....1.... PP

                                       .BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH.CSSS CS
                      TPP_enzyme_C 106 kdlkpvdfaklaealGakgarvekadveeleealkeal.ekkg 147
                                           +  +a+ a+a+G++g+rv+  d+  + ++ keal + k 
  gi|313117058|ref|YP_004038182.1| 218 ----E-TIAQKAQAYGIDGVRVDGLDPLAVYQVTKEALnKAKS 255
                                       ....1.48889*******************9*99999963333 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   5.6e-08   0.00025     142     269 ..     163     295 ..     144     370 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.6e-08
                                       S----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEG.GGT--S-HHHHHHHTT-EEEEETTTT CS
                   Transketolase_N 142 ivdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGet.eisftedvakrfeaygWhvievedge 217
                                        +d+ + + lgDg   eG  +e  ++ag+  +  + v  ++n+ +i      ++ +e +a++ +ayg + ++v++ +
  gi|313117058|ref|YP_004038182.1| 163 KTDQAVLCHLGDGATSEGDFHEGLNFAGVFDVPTVFV-CNNNQWAISVPReRQTASETIAQKAQAYGIDGVRVDGLD 238
                                       5789999************************998655.5677766665440456789999*********99974443 PP

                                       ..-HHHH.HHHHHHHHH-TT...S-EEEEEE--TTTTSTTTTTSGGGTSS---HHHHH CS
                   Transketolase_N 218 ..dveai.kaaieeakaekd...kPsliklrtviGygspakagtedvhGapLgedeva 269
                                         +v ++ k+a+++ak+ +    +P+li+      yg+ ++a+  +v+  + ++de +
  gi|313117058|ref|YP_004038182.1| 239 plAVYQVtKEALNKAKSPTGdelRPTLIEAVQ-YRYGAHTTADDPSVYREADEADEWK 295
                                       113444436899999986543449***98643.5677777777777766665555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2627.79
//
Query:       gi|313117059|ref|YP_004038183.1|  [L=475]
Description: SNF family Na+-dependent transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-49  167.7  27.4    4.9e-25   88.2   9.0    2.3  2  SNF           Sodium:neurotransmitter symporter family
  ------ inclusion threshold ------
          3    8.2   6.8       0.66   10.3   0.2    2.9  3  DUF2919       Protein of unknown function (DUF2919)


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   9.0   5.5e-29   4.9e-25       1     115 [.       3     119 ..       3     128 .. 0.93
   2 !   86.7   8.9   1.5e-28   1.4e-24     181     393 ..     143     349 ..     127     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 5.5e-29
                               SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrki. 76 
                                       R+tw +++ fil++vG+avgLgn+WRFP+++ +nGG afl+ Yl++++ +G+P +   l +G++++   +++++ + 
  gi|313117059|ref|YP_004038183.1|   3 RDTWASRIGFILAAVGSAVGLGNIWRFPWMTAQNGGSAFLVTYLFIVIGVGVPGLLATLVIGRRSNLNPVGAFKSLk 79 
                                       89*****************************************************************9999999873 PP

                               SNF  77 .cPllkgiGyasivvalyvglyYnvilawalfYlfssftt 115
                                        +  +  +G   ++ ++++  +Y v+ +w l Y+++sft 
  gi|313117059|ref|YP_004038183.1|  80 gSRSWVLLGGICVLTSIVLISFYSVVGGWVLRYFIESFTG 119
                                       355677789888999999999*****************96 PP

  == domain 2  score: 86.7 bits;  conditional E-value: 1.5e-28
                               SNF 181 tlcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdlekllep..kvWidaa 255
                                       ++ l+++ ++v++++  G+++++kv++       ++l+ + + +   p a++g +fyl  d + l++    v   aa
  gi|313117059|ref|YP_004038183.1| 143 VVFLIITALIVMIGVREGIETTTKVMMPGIA---ILLTAMAIWAFRQPNAAQGYQFYLAFDGQYLSKNflPVLSSAA 216
                                       356778889999****************999...9******************************997446999*** PP

                               SNF 256 tqiffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgekisevaeeGpgLaFi 332
                                        q +f+l+ig G+++++asY + +  + +da  ++++n  + vlaglvvF +l   a           + Gpg +F+
  gi|313117059|ref|YP_004038183.1| 217 GQALFTLSIGGGTMLTYASYIEEDRSLPFDASSIAILNLGIGVLAGLVVFPLLFSYADG-------PTSGGPGALFV 286
                                       ***************************************************99655543.......3578******* PP

                               SNF 333 aypealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllr..rrelltliva 393
                                         + a ++lp++++++  FFl+++l++++s+++++e  ++ +vDef       +r +l l+va
  gi|313117059|ref|YP_004038183.1| 287 SIAGAFANLPAGKFLGATFFLVVLLAAITSSISMLEIPVAFLVDEFGFERSkvTRGMLLLVVA 349
                                       *********************************************998444345666655554 PP

>> DUF2919  Protein of unknown function (DUF2919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   7.4e-05      0.66      55     110 ..      45     102 ..      43     117 .. 0.75
   2 ?   -1.8   0.1       0.4   3.6e+03      70     100 ..     152     178 ..     137     195 .. 0.46
   3 ?    0.0   0.2      0.11   9.6e+02      87     133 ..     411     461 ..     360     470 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.4e-05
                           DUF2919  55 sfylgLalgvpalllllligrrkkssew..leklwragrplllllllvdlllqlyrla 110
                                       ++++ + +gvp+ll+ l+igrr++ +++  ++ l  +  ++ll  + v +++ l++++
  gi|313117059|ref|YP_004038183.1|  45 YLFIVIGVGVPGLLATLVIGRRSNLNPVgaFKSLKGSRSWVLLGGICVLTSIVLISFY 102
                                       689999****************875543226677777778888777666666555554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.4
                           DUF2919  70 llligrrkkssewleklwragrplllllllv 100
                                       +++ig r+     +e+ ++ + p + +ll +
  gi|313117059|ref|YP_004038183.1| 152 IVMIGVREG----IETTTKVMMPGIAILLTA 178
                                       344444433....222222222222222222 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.11
                           DUF2919  87 wragr....plllllllvdlllqlyrlalsheafswltaltlllllwvlly 133
                                       wr+      p+ ll  + + +l l  +  + +++ ++t+lt++  ++++ +
  gi|313117059|ref|YP_004038183.1| 411 WRYAIgsvfPIFLLFSFYTDSLSLAGVSVNSMEVLVITLLTAVPFIIFIHW 461
                                       444434333222222233333333334444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3018.63
//
Query:       gi|313117060|ref|YP_004038184.1|  [L=372]
Description: aspartate/tyrosine/aromatic aminotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-59  199.5   0.0    9.8e-59  199.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.8e-13   50.5   0.0    2.7e-13   50.0   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    7.6e-08   31.7   0.0    1.2e-07   31.1   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    5.9e-06   25.8   0.0    1.1e-05   24.9   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00036   19.2   0.0    0.00052   18.7   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.3   0.0   2.7e-62   9.8e-59       2     361 ..      26     363 ..      25     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 199.3 bits;  conditional E-value: 2.7e-62
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d inLg++++++     t+++++ a+   a + g + +y+ ++g   l+e + + + r+ +l+++++ +++ +sGa+
  gi|313117060|ref|YP_004038184.1|  26 DDINLGIGQPDFP----TPEHIRDAALS-AVEDGVVDSYTGNKGILGLREGISEKYERDSGLSVDPD-NIIATSGAS 96 
                                       679*********9....**********9.**************************************.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       +++ ++i +  +  g e+++pdp +  y++ + l+gg+  +++l+  +d +ld   +e+a++e       t +++v+
  gi|313117060|ref|YP_004038184.1|  97 EALHIAIEAH-VRNGGEVIIPDPGFVAYEQLAVLAGGTPKPVELR--DDLTLDPATVEDAITE------DTDLFIVN 164
                                       ***9999999.89999***************************99..****************......899***** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       sp NPtG+v t+ + ++ +++a++y ++ ++De+Y++ vf+ + + +  +++++ +n++ v+ +sK+++++G+R+G+
  gi|313117060|ref|YP_004038184.1| 165 SPANPTGAVQTESDMREFARIADEYDVVCLLDEVYEHIVFEGE-HRS-PMEFATTDNVVQVNACSKSYSMTGWRLGW 239
                                       *****************************************65.233.99999************************ PP

                                       EEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmf 307
                                       ++++++ ++ + ++++ +    s+++q+a+ aal+ +++    +eem++ +++rr++l d+L+++gl+   ++++++
  gi|313117060|ref|YP_004038184.1| 240 VTASDDRIERMLRVHQYVQAcaSAPAQYAAEAALKGPQE---PVEEMVSAFETRRDVLLDGLDDIGLETPRPEGAFY 313
                                       ***9999999999998776667****************7...8********************************** PP

                                       EEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                     Aminotran_1_2 308 lltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                        +  +++      + + l++ gv+v+pg  f+    g  Ri++ +++ e+l+e++e
  gi|313117060|ref|YP_004038184.1| 314 AMPSVPEG----WASEVLDN-GVIVVPGDVFGErgAGYARISY-ATNVETLKEALE 363
                                       ******99....55558999.9***********9999******.**********98 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   7.6e-17   2.7e-13      27     144 ..      75     196 ..      54     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 7.6e-17
                                       HHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGG CS
                   DegT_DnrJ_EryC1  27 eFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaa 103
                                       ++E++    +  ++ ia+s +++Alh+a++a  v +g eVI+p  +Fva  + ++ +g +p +v+   d++++dpa+
  gi|313117060|ref|YP_004038184.1|  75 KYERDSGLSVDPDNIIATSGASEALHIAIEAH-VRNGGEVIIPDPGFVAYEQLAVLAGGTPKPVELR-DDLTLDPAT 149
                                       566666666777889***************95.777******************************9.99******* PP

                                       CGGG--TTE.EEEE..EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 104 ieaaitert.kaIl..pVhlyGqva...dmdalkaiaakhglkvieD 144
                                       +e aite t   I+  p++  G+v    dm +  +ia++++++ + D
  gi|313117060|ref|YP_004038184.1| 150 VEDAITEDTdLFIVnsPANPTGAVQtesDMREFARIADEYDVVCLLD 196
                                       *********6455455677788774455*************998877 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   3.3e-11   1.2e-07      61     177 ..      86     198 ..      82     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.3e-11
                                       GGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-- CS
                       Aminotran_5  61 eeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln 137
                                        ++ii tsG++ea+ +++ +    +++g e+++ + +  a     ++la   g + k ++l ++ +ld+ ++e++++
  gi|313117060|ref|YP_004038184.1|  86 PDNIIATSGASEALHIAIEAH---VRNGGEVIIPDPGFVA----YEQLAVLAGGTPKPVELRDDLTLDPATVEDAIT 155
                                       489*************99999...9**********99655....55999999************************* PP

                                       TTEEEEEEESBETTTTEB-...-HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 138 ektklvaithvsnvtGtiq...pveeigklakkkgalvlvDaa 177
                                       e+t+l +++   n tG +q   ++ e++++a +++++ l+D +
  gi|313117060|ref|YP_004038184.1| 156 EDTDLFIVNSPANPTGAVQtesDMREFARIADEYDVVCLLDEV 198
                                       ****************987344677788888889999999976 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0     3e-09   1.1e-05      14     167 ..      43     196 ..      36     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3e-09
                                       HHHHH.HCS----.CCCT--HHHHHHHHHHHHHTT-SEEEE.......ES-H.HHHHHHHHHHH--TTEEEEEETT- CS
                   Beta_elim_lyase  14 msdaq.aaamlGd.esYgedktvnrLedavaelfgkeaalf.......vpqG.taAnsillkillqrgeevivtepa 80 
                                       ++da  +a++ G  +sY ++k++  L + + e ++ + +l        +++G   A +i+++++++ g evi+ +p+
  gi|313117060|ref|YP_004038184.1|  43 IRDAAlSAVEDGVvDSYTGNKGILGLREGISEKYERDSGLSvdpdniiATSGaSEALHIAIEAHVRNGGEVIIPDPG 119
                                       5566667777776679****************99999999778899976666256888999***************9 PP

                                       HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHH CS
                   Beta_elim_lyase  81 hihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaia 157
                                        +  +e  ++a+lag ++++++ +++ ++d++ +e+ai+e+ +      +i+   +n t  G v +   +re a ia
  gi|313117060|ref|YP_004038184.1| 120 FVA-YE--QLAVLAGGTPKPVELRDDLTLDPATVEDAITEDTD-----LFIVNSPANPT--GAVQTESDMREFARIA 186
                                       664.44..567799999********9**************444.....77777777777..**************** PP

                                       HHCT-EEEEE CS
                   Beta_elim_lyase 158 kkygiplhlD 167
                                       ++y++  +lD
  gi|313117060|ref|YP_004038184.1| 187 DEYDVVCLLD 196
                                       ****999988 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.4e-07   0.00052      71     176 ..      90     199 ..      83     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-07
                                       EEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH..TTCEEEEESTTSHHHHHHHCCTTEEEEEEES CS
                   Cys_Met_Meta_PP  71 lavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk..lgievkfvdtsdleelekaikentklvylEt 145
                                       +a+s    A++ ai a +++G e+++ d  +   ++l   ++      +e +   t d++ +e ai+e t+l+ + +
  gi|313117060|ref|YP_004038184.1|  90 IATSGASEALHIAIEAHVRNGGEVIIPDPGFVAYEQL-AVLAGGtpKPVELRDDLTLDPATVEDAITEDTDLFIVNS 165
                                       4444445599999999999999999999988654444.34333311446666666789******************* PP

                                       S-TTTT--...--HHHHHHHHHHTT-EEEEEGTT CS
                   Cys_Met_Meta_PP 146 ptnpllkv...vDiekiaklakkagvlvvvDntf 176
                                       p+np+  v    D+++ a++a + +v+ ++D ++
  gi|313117060|ref|YP_004038184.1| 166 PANPTGAVqteSDMREFARIADEYDVVCLLDEVY 199
                                       ****97763337*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2399.82
//
Query:       gi|313117061|ref|YP_004038185.1|  [L=84]
Description: hypothetical protein Hbor_35290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-05   24.1   0.0    2.9e-05   23.5   0.0    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
    9.9e-05   22.2   0.0    0.00014   21.7   0.0    1.2  1  MarR_2          MarR family
     0.0019   17.9   0.0     0.0026   17.5   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
     0.0027   18.2   0.1      0.004   17.6   0.1    1.2  1  HTH_27          Winged helix DNA-binding domain
     0.0066   16.3   0.3      0.013   15.3   0.3    1.5  1  TFIIE_alpha     TFIIE alpha subunit
     0.0091   15.9   0.0      0.012   15.5   0.0    1.2  1  MarR            MarR family
  ------ inclusion threshold ------
      0.057   13.5   0.0      0.071   13.2   0.0    1.1  1  HTH_54          ParA helix turn helix domain
      0.067   12.9   0.0       0.11   12.2   0.0    1.4  1  GntR            Bacterial regulatory proteins, gntR family
      0.068   13.3   0.0      0.077   13.2   0.0    1.1  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.07   13.0   0.1      0.097   12.6   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.6e-08   2.9e-05      16      48 .]       6      38 ..       2      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.6e-08
                            HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + ++q++L e++ l+  tv++ ++ Le++G+++
  gi|313117061|ref|YP_004038185.1|  6 GELTQSDLVEETLLPARTVRYAVNTLEDDGYLE 38
                                      789****************************85 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.9e-08   0.00014      19      54 ..       7      40 ..       2      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.9e-08
                                      TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +  lt+++l++++ l+  +v ++++ L++ G++e r
  gi|313117061|ref|YP_004038185.1|  7 E--LTQSDLVEETLLPARTVRYAVNTLEDDGYLESR 40
                                      3..9*****************************988 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.5e-06    0.0026      17      50 ..       6      39 ..       3      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +elt s+l ++t lp  tv+  ++tL+  Gy+e 
  gi|313117061|ref|YP_004038185.1|  6 GELTQSDLVEETLLPARTVRYAVNTLEDDGYLES 39
                                      789*****************************96 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.2e-06     0.004      17      64 ..       6      53 ..       3      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-06
                            HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64
                                      ++ +++dl++ + + + ++ y+++ L+  G++e+ ++ +d r ++++l
  gi|313117061|ref|YP_004038185.1|  6 GELTQSDLVEETLLPARTVRYAVNTLEDDGYLESRHYWKDARKRLYSL 53
                                      677899**************************************9986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   7.3e-06     0.013      22      71 ..       2      52 ..       1      75 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.3e-06
                                      HHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE.EEEEETTTEEEE CS
                       TFIIE_alpha 22 LlekgevteedlakelkidlnelrklLnrLyearlvky.krrrdeekswyk 71
                                      L +kge+t  dl +e+ +    +r ++n L +++  +  + ++d  k  y+
  gi|313117061|ref|YP_004038185.1|  2 LEIKGELTQSDLVEETLLPARTVRYAVNTLEDDGYLESrHYWKDARKRLYS 52
                                      6789*****************************977651568996666554 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.8e-06     0.012      15      57 ..       5      47 ..       1      48 [. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.8e-06
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                      +g+l++s+L +   +   tv  ++ +Le++G++e+++  +D R
  gi|313117061|ref|YP_004038185.1|  5 KGELTQSDLVEETLLPARTVRYAVNTLEDDGYLESRHYWKDAR 47
                                      689*********************************9999988 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     4e-05     0.071      29      76 ..       9      58 ..       6      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                            HTH_54 29 skaalaklpklsrrkvdkavsemeaeGyefekkeagstek..Yaltiqnv 76
                                      +++ l +++ l  r+v +av+ +e++Gy  +++  + ++k  Y+l +  v
  gi|313117061|ref|YP_004038185.1|  9 TQSDLVEETLLPARTVRYAVNTLEDDGYLESRHYWKDARKrlYSLEVAAV 58
                                      677888999999****************9999988888764477776665 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.1e-05      0.11      24      58 ..       8      41 ..       2      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.1e-05
                                      ---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR 24 LPsereLaaefgVsrttvReALrrLeaeglverrq 58
                                      L ++++L++e    + tvR A ++Le +g++e+r+
  gi|313117061|ref|YP_004038185.1|  8 L-TQSDLVEETLLPARTVRYAVNTLEDDGYLESRH 41
                                      6.77888888888899****************986 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.077      19      55 ..       8      49 ..       5      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                    B-block_TFIIIC 19 itqsdLakeskqdprslfyrlksLekkgLIvkqsii.....d 55
                                      +tqsdL+ e+   +r + y +++Le+ g+ + + +      +
  gi|313117061|ref|YP_004038185.1|  8 LTQSDLVEETLLPARTVRYAVNTLEDDGYLESRHYWkdarkR 49
                                      59****************************999986554440 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.4e-05     0.097      20      56 ..       5      41 ..       1      59 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      +g++t +++ ee+ +p  +v  +++ Led G+ e ++
  gi|313117061|ref|YP_004038185.1|  5 KGELTQSDLVEETLLPARTVRYAVNTLEDDGYLESRH 41
                                      89******************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 600.39
//
Query:       gi|313117062|ref|YP_004038186.1|  [L=453]
Description: NAD-dependent aldehyde dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.3e-138  461.6   0.0   2.6e-138  461.4   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.4   0.0  1.5e-142  2.6e-138       9     462 .]       1     450 [.       1     450 [. 0.99

  Alignments for each domain:
  == domain 1  score: 461.4 bits;  conditional E-value: 1.5e-142
                                       EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHH CS
                            Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplae 85 
                                       ++++nPatge ia+++a + + v++ + +A+++f++w++ p++eR+++L+ a d+l+e++e  a+l+t+e+Gkp+a+
  gi|313117062|ref|YP_004038186.1|   1 MDSVNPATGERIATYEADSDDIVESKLGTAANTFDEWRDRPLREREKLLASAGDVLRENEETYATLMTREMGKPIAQ 77 
                                       5899************************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHH.HSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE CS
                            Aldedh  86 araeveeaidvlryyaelaek.legevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKP 161
                                       araev++++  ++ yae+a++ le e+ ps +g++  +++ePlG v+a++PWN+P+  +++ +ap + aGN+ +lK 
  gi|313117062|ref|YP_004038186.1|  78 ARAEVQKCAWACDHYAEYASTyLESEHHPSPPGTTVKTVHEPLGPVLAVMPWNYPFWQVIRFAAPYITAGNVGLLKH 154
                                       *********************8888*****99********************************************* PP

                                       -TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE-- CS
                            Aldedh 162 aeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGG 238
                                       a+++p +a +l e+f+eag P+gv++ ++  gs+  + ++e+++v++v++tGs + gr +a++a++nlk+++lElGG
  gi|313117062|ref|YP_004038186.1| 155 ASNVPGCAQALEEIFREAGYPEGVFQTLMI-GSSKVDGVIEDDRVRAVTLTGSGPAGRAVAETAGRNLKQTVLELGG 230
                                       ****************************99.8999999*************************************** PP

                                       -EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHH CS
                            Aldedh 239 knplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPlisea 315
                                        +p+ivl+daDld+ave  v +   n+GQ Ciaa+r++v+e iy+e+v++lv a+++ ++gdp+de+td+GP+++++
  gi|313117062|ref|YP_004038186.1| 231 SDPFIVLDDADLDAAVETGVLARNQNNGQSCIAAKRFIVHEAIYEEYVDRLVSAFADQTIGDPMDETTDIGPQADPD 307
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHS CS
                            Aldedh 316 qlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNd 392
                                        ++ ++++v    e+ga++ +Gg   e+ +++g+++ Ptvl++v++  +  +eE+FGPV++v+k++d eeai++aNd
  gi|313117062|ref|YP_004038186.1| 308 LMAALHEQVTASAEAGATVRTGG---EPLDRTGAYYPPTVLTDVPEGCPADTEELFGPVAAVYKVSDAEEAIDVAND 381
                                       ***********************...889************************************************ PP

                                       SSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                            Aldedh 393 teyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                       t++GL+a+++t+d er er+a+r++aG vy+N+ t++++   pfgG+++Sg+Gre +  g++e+++ ktv
  gi|313117062|ref|YP_004038186.1| 382 TRFGLGASIWTADRERGERLANRINAGCVYVNQLTKSDPRV-PFGGIGDSGYGRELSGPGIREFVNRKTV 450
                                       *****************************************.*************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 3569.63
//
Query:       gi|313117063|ref|YP_004038187.1|  [L=259]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-33  113.8   0.1    9.8e-33  112.7   0.0    1.6  2  IclR           Bacterial transcriptional regulator
    1.4e-08   34.4   0.2    3.6e-08   33.1   0.2    1.7  1  HTH_IclR       IclR helix-turn-helix domain
    2.8e-08   33.2   0.5    1.5e-07   30.9   0.4    2.3  3  HTH_24         Winged helix-turn-helix DNA-binding
    1.3e-06   28.1   0.2    3.1e-06   27.0   0.2    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
      7e-06   25.9   0.5    4.1e-05   23.4   0.4    2.3  2  HTH_11         HTH domain
    1.2e-05   25.3   0.2    1.2e-05   25.3   0.2    2.1  3  HTH_20         Helix-turn-helix domain
    6.8e-05   22.7   0.0    0.00025   20.9   0.0    1.9  1  MarR_2         MarR family
    9.8e-05   22.2   0.1    0.00021   21.2   0.1    1.6  1  MarR           MarR family
     0.0032   17.2   0.1     0.0078   15.9   0.1    1.7  1  HTH_DeoR       DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.4   0.6      0.067   13.0   0.2    2.3  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.051   13.5   0.0       0.12   12.2   0.0    1.6  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.054   13.6   0.3      0.054   13.6   0.3    2.4  3  DprA_WH        DprA winged helix domain
       0.06   14.0   1.9      0.077   13.6   0.2    2.1  2  HTH_32         Homeodomain-like domain
      0.069   13.0   0.0       0.54   10.1   0.0    2.2  2  HTH_10         HTH DNA binding domain


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.1   5.3e+03      43      64 ..      22      43 ..      12      45 .. 0.68
   2 !  112.7   0.0   7.7e-36   9.8e-33       7     126 ..     130     249 ..     126     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.1
                                      --SSTTS--SHHHHHHHHHHHH CS
                              IclR 43 krlterTitdpeeLleeLakvR 64
                                      ++l ++   + +eL eeL+  R
  gi|313117063|ref|YP_004038187.1| 22 EQLKDNPGRTLDELTEELDLAR 43
                                      4555666666778888887766 PP

  == domain 2  score: 112.7 bits;  conditional E-value: 7.7e-36
                                       TSTT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEE CS
                              IclR   7 saiGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciA 83 
                                        ++G+r  l+  a+GKa+La+l++ee   ++ r++l + t++Titd+e+LleeL+++Re+Gya++ +E+ eg+++++
  gi|313117063|ref|YP_004038187.1| 130 ARVGQRRHLHQLAAGKAILAYLPDEESHGIIDRQGLIEATDQTITDREALLEELDEIRERGYAFNLGESIEGLNAVG 206
                                       469************************************************************************** PP

                                       EEEE-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHH CS
                              IclR  84 apifdasgevvaAvsvsgptarlteeelkeellalvreaArki 126
                                       api+d++g++v+++s+sgp++r++ + l++el  ++ ++ ++i
  gi|313117063|ref|YP_004038187.1| 207 APIRDEEGTPVGGISISGPANRVKGSLLRDELPDKLLATIDEI 249
                                       ********************************99999998877 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.2   2.8e-11   3.6e-08       6      48 ..      18      59 ..      15      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.8e-11
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      ++iL++l   p++ tl el ++++l++St hR+L tL+   ++
  gi|313117063|ref|YP_004038187.1| 18 IQILEQLKDNPGR-TLDELTEELDLARSTIHRHLLTLEDNDLL 59
                                      79***********.***********************987776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.4   1.2e-10   1.5e-07       4      46 ..      16      58 ..      14      59 .. 0.93
   2 ?   -3.2   0.0       5.2   6.6e+03      16      26 ..      81      91 ..      78      92 .. 0.84
   3 ?   -2.4   0.0       2.8   3.6e+03      12      28 ..     117     133 ..     116     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.2e-10
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                        ++ILe L++np+ +  eL e+l+l +st++r+l  Le++ l
  gi|313117063|ref|YP_004038187.1| 16 SSIQILEQLKDNPGRTLDELTEELDLARSTIHRHLLTLEDNDL 58
                                      5689***********************************9876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.2
                            HTH_24 16 prisqreLAer 26
                                       ris  ++A+r
  gi|313117063|ref|YP_004038187.1| 81 DRISFFDVARR 91
                                      59999999987 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.8
                            HTH_24  12 LqknprisqreLAerlg 28 
                                       L+k ++ s  e + r+g
  gi|313117063|ref|YP_004038187.1| 117 LYKASGASPLETSARVG 133
                                       77889999999999998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   2.4e-09   3.1e-06       5      44 ..      18      58 ..      15      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.4e-09
                                      HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                             HTH_5  5 lkILklLaege.lcvcelaeelglsqstvShHLkkLreaGL 44
                                      ++IL +L +++ ++  el+eel+l +st+ +HL  L++ +L
  gi|313117063|ref|YP_004038187.1| 18 IQILEQLKDNPgRTLDELTEELDLARSTIHRHLLTLEDNDL 58
                                      69************************************998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.4   3.2e-08   4.1e-05       4      41 ..      19      55 ..      17      59 .. 0.91
   2 ?   -1.9   0.0       2.6   3.3e+03      36      49 ..     199     212 ..     198     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.2e-08
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLee 41
                                      qile+L+++ g  + +eL eeL++ r+t++r++ +Le+
  gi|313117063|ref|YP_004038187.1| 19 QILEQLKDNPG-RTLDELTEELDLARSTIHRHLLTLED 55
                                      9*****77777.8********************99986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                            HTH_11  36 IkaLeelgvpIese 49 
                                       I+ L++ g+pI  e
  gi|313117063|ref|YP_004038187.1| 199 IEGLNAVGAPIRDE 212
                                       7889******9755 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   9.1e-09   1.2e-05      13      54 ..      18      59 ..      11      63 .. 0.92
   2 ?   -2.5   0.1       4.3   5.5e+03      42      51 ..     135     144 ..     132     149 .. 0.78
   3 ?   -2.2   0.0       3.6   4.7e+03      30      30 ..     160     160 ..     143     185 .. 0.58

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.1e-09
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                        il  L+++ g+t+ el e+ldl+++t+++HL +Le+ +L+
  gi|313117063|ref|YP_004038187.1| 18 IQILEQLKDNPGRTLDELTEELDLARSTIHRHLLTLEDNDLL 59
                                      679************************************997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                                       HHHHHHHHHC CS
                            HTH_20  42 syHLrvLeea 51 
                                       ++HL++L+  
  gi|313117063|ref|YP_004038187.1| 135 RRHLHQLAAG 144
                                       6899999755 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.6
                                       H CS
                            HTH_20  30 l 30 
                                       +
  gi|313117063|ref|YP_004038187.1| 160 I 160
                                       1 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.9e-07   0.00025       8      54 ..      18      62 ..      13      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       ++L  L ++pg   t  el+++l+l +s+++r+l  L++  L+ r+
  gi|313117063|ref|YP_004038187.1| 18 IQILEQLKDNPG--RTLDELTEELDLARSTIHRHLLTLEDNDLLFRE 62
                                      689*********..6***********************999998777 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.6e-07   0.00021       2      49 ..      14      61 ..      13      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      t++ + iL++l+++++ ++ eL + l + +st+ r l +Le+++l+ R
  gi|313117063|ref|YP_004038187.1| 14 TESSIQILEQLKDNPGRTLDELTEELDLARSTIHRHLLTLEDNDLLFR 61
                                      788999**************************************9977 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   6.1e-06    0.0078       4      49 ..      19      64 ..      17      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.1e-06
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthG 49
                                      qile lk+    +++el+e+l+ +  Ti R L +Le  +ll R  G
  gi|313117063|ref|YP_004038187.1| 19 QILEQLKDNPGRTLDELTEELDLARSTIHRHLLTLEDNDLLFRENG 64
                                      89**************************************999766 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   5.2e-05     0.067       6      36 ..      18      48 ..      15      54 .. 0.92
   2 ?   -0.6   0.0      0.92   1.2e+03      16      28 ..      89     101 ..      81     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlr 36
                                      ++ILe L  ++ ++  eL e++ l++st++r
  gi|313117063|ref|YP_004038187.1| 18 IQILEQLKDNPGRTLDELTEELDLARSTIHR 48
                                      69****************************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.92
                     HTH_AsnC-type  16 aRisyaeLAervG 28 
                                       aR+ + +LAe++G
  gi|313117063|ref|YP_004038187.1|  89 ARRQVDRLAEETG 101
                                       6777788888776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.6e-05      0.12      11      58 ..      18      65 ..      13      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.6e-05
                                      CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 11 akvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      +++   L  +   t de+ eel++ rs++ + L  Led +l  re g+
  gi|313117063|ref|YP_004038187.1| 18 IQILEQLKDNPGRTLDELTEELDLARSTIHRHLLTLEDNDLLFRENGQ 65
                                      5666677778899***************************99999875 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   4.2e-05     0.054       4      50 ..       7      54 ..       2      64 .. 0.86
   2 ?   -1.1   0.0       1.7   2.1e+03      26      36 ..      91     101 ..      87     108 .. 0.83
   3 ?   -2.9   0.1       6.1   7.9e+03      11      22 ..     173     184 ..     167     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                           DprA_WH  4 ppaepplddlerrvLaaLgpeP.vhvDqLvrrtglpaaevsaaLleLE 50
                                      +  + ++++   ++L++L   P +++D+L +++ l  +++ ++Ll LE
  gi|313117063|ref|YP_004038187.1|  7 SNRPVTTTESSIQILEQLKDNPgRTLDELTEELDLARSTIHRHLLTLE 54
                                      344556789999******998737***********************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                           DprA_WH  26 vhvDqLvrrtg 36 
                                       ++vD L+++tg
  gi|313117063|ref|YP_004038187.1|  91 RQVDRLAEETG 101
                                       689*****999 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.1
                           DprA_WH  11 ddlerrvLaaLg 22 
                                         +++++L+ L 
  gi|313117063|ref|YP_004038187.1| 173 ITDREALLEELD 184
                                       568888888875 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2     6e-05     0.077      19      73 .]       3      50 ..       1      50 [. 0.83
   2 ?   -1.5   0.1       3.1     4e+03       6       6 ..     115     115 ..      87     161 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                            HTH_32 19 drprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73
                                      ++pr+ rp ++++   + + +l  ++p  ++++l ++l      ++++st++r L
  gi|313117063|ref|YP_004038187.1|  3 EQPRSNRPVTTTESSIQILEQLK-DNPGRTLDELTEEL------DLARSTIHRHL 50
                                      57889999966666666666666.99999*********......8********87 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.1
                            HTH_32   6 l 6  
                                       +
  gi|313117063|ref|YP_004038187.1| 115 V 115
                                       1 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00042      0.54      25      45 ..      31      51 ..      28      56 .. 0.89
   2 ?   -0.5   0.0      0.88   1.1e+03      17      34 ..      85     101 ..      85     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                            HTH_10 25 tlkeLAkelGIskstlsehLr 45
                                      tl+eL +el++++st++ hL 
  gi|313117063|ref|YP_004038187.1| 31 TLDELTEELDLARSTIHRHLL 51
                                      89*****************96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.88
                            HTH_10  17 YFdyPRrvtlkeLAkelG 34 
                                       +Fd+ Rr +++ LA+e G
  gi|313117063|ref|YP_004038187.1|  85 FFDVARR-QVDRLAEETG 101
                                       7888887.7899999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2001.32
//
Query:       gi|313117064|ref|YP_004038188.1|  [L=220]
Description: reduced coenzyme F420:NADP oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-17   63.3   0.5    5.2e-17   62.2   0.3    1.6  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00027   21.0   0.1    0.00072   19.6   0.1    1.6  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00067   19.3   0.0    0.00099   18.8   0.0    1.2  1  ApbA            Ketopantoate reductase PanE/ApbA
    0.00074   18.6   0.0    0.00091   18.3   0.0    1.2  1  PDH             Prephenate dehydrogenase
     0.0056   17.1   0.1       0.01   16.2   0.1    1.5  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
      0.051   13.6   0.0      0.088   12.9   0.0    1.5  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
       0.11   12.3   0.1       0.29   11.0   0.0    1.8  2  KR              KR domain


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.3     2e-20   5.2e-17       1      97 []       2     103 ..       2     103 .. 0.94
   2 ?   -2.6   0.0       3.2   8.3e+03      28      47 ..     159     179 ..     144     187 .. 0.57

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 2e-20
                                       EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........vkvtavdneeaaeeadvvvla 68 
                                       +i+i+ G+G++ge++a +l  +   +he+v++ sr+ eka e+a ++g         ++ + +n+ aa+ a++v+la
  gi|313117064|ref|YP_004038188.1|   2 RIAIVgGTGDFGEGIAVRLGVHT--DHEVVIG-SRTAEKAVEAAVSYGnniddesaERIHGASNSRAASTAEIVILA 75 
                                       79**************9986654..7****88.**********************999999**************** PP

                                       S-HHHHHHHHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  69 vkpedveevlselakdalkgklvisvlag 97 
                                       v+p +v +++++l +++l+++++++ ++g
  gi|313117064|ref|YP_004038188.1|  76 VPPFHVRDTVRDL-SEQLEETTLVTPAVG 103
                                       *************.999999999998875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                                       EEEEEESSC.CCHHHHHHHHC CS
                     F420_oxidored  28 ivvansrnp.ekaeelaeelg 47 
                                       +vv+n+++  e + elaee++
  gi|313117064|ref|YP_004038188.1| 159 LVVGNDPDArEMIVELAEEIN 179
                                       455555543134556666654 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.8e-07   0.00072       2     106 ..       3     104 ..       2     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.8e-07
                                       EEEE.--SHHHHHHHHHHHTTT.--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE- CS
                    NAD_Gly3P_dh_N   2 iavl.GaGswGtalAkvlaeng.hevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlv 76 
                                       ia++ G+G +G  +A  l+ ++ hev++ +r +e + e   +  n+   +  +  e ++  ++  +a++ a+i++l+
  gi|313117064|ref|YP_004038188.1|   3 IAIVgGTGDFGEGIAVRLGVHTdHEVVIGSRTAEKAVEAAVSYGNNI--D-DESAERIHGASNS-RAASTAEIVILA 75 
                                       6777257************9998999999999877666655555553..3.4667888888876.56677******* PP

                                       --HHHHHHHHHHHCCC--TT-EEEE---SE CS
                    NAD_Gly3P_dh_N  77 vPsqalrevlkklkgllkkkailvsliKGi 106
                                       vP  ++r+++++l++ l++ ++lv  + G+
  gi|313117064|ref|YP_004038188.1|  76 VPPFHVRDTVRDLSEQLEE-TTLVTPAVGL 104
                                       ***************9955.5555555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.9e-07   0.00099       3      98 ..       6      98 ..       3     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.9e-07
                                      EES-SHHHHHHHHHHHH.HTHCEEEE-SCH..HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                              ApbA  3 ilGaGaiGsllaakLak.agadvtlilrsr..rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKa 78
                                      + G+G  G  +a++L   + ++v++  r++   +ea ++ G ++++e+ e+i   +++ +a      + +++vi++v+ 
  gi|313117064|ref|YP_004038188.1|  6 VGGTGDFGEGIAVRLGVhTDHEVVIGSRTAekAVEAAVSYGNNIDDESAERIHGASNSRAA------STAEIVILAVPP 78
                                      3479***********88899***99999998667889999999999995555544444444......48********** PP

                                      GGHHHHHHHHGGGECTCEEE CS
                              ApbA 79 yqteealeeikplldpntvv 98
                                      +++ + ++++ + l+++t v
  gi|313117064|ref|YP_004038188.1| 79 FHVRDTVRDLSEQLEETTLV 98
                                      ****************9877 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.6e-07   0.00091      36      77 ..      60     100 ..      17     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.6e-07
                                       EES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE CS
                               PDH  36 atddieavkeadivvlavPvevilevlkelaphlkedalitD 77 
                                       a +  +a+++a+iv+lavP+  +++++++l+++l+e+ l+t 
  gi|313117064|ref|YP_004038188.1|  60 ASN-SRAASTAEIVILAVPPFHVRDTVRDLSEQLEETTLVTP 100
                                       334.478999****************************9984 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.1e-06      0.01       1      86 [.       2      88 ..       2      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.1e-06
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG...GGTTTECEBEEE.GGGGGCTT-SEEEE-SC CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk...aleegkdlkved.vdeeelkevdivflalp 75
                                      ++aivG+tG  G+ ++ +L  h + e+v   +s+  a k++++av+   ++++++  +++   ++ + + ++iv+la+p
  gi|313117064|ref|YP_004038188.1|  2 RIAIVGGTGDFGEGIAVRLGVHTDHEVVI--GSRT-AEKAVEAAVSygnNIDDESAERIHGaSNSRAASTAEIVILAVP 77
                                      69********************9999887..6666.778888777755544444444444446777779*********9 PP

                                      HHHHHHHHHHH CS
                    Semialdhyde_dh 76 agvskelapkl 86
                                          ++ +++l
  gi|313117064|ref|YP_004038188.1| 78 PFHVRDTVRDL 88
                                      88777777766 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.4e-05     0.088      16      82 ..       4      75 ..       1     100 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                                      EEE.S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHH.....HHHHT-SEEEE- CS
                      Shikimate_DH 16 lli.GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelk.....ellaeadvvisa 82
                                       ++ G+G  +e +a  L  ++ ++vv+  Rt e+a e a +++++ i   + e ++     ++ + a++vi a
  gi|313117064|ref|YP_004038188.1|  4 AIVgGTGDFGEGIAVRLGVHTDHEVVIGSRTAEKAVEAAVSYGNN-IDDESAERIHgasnsRAASTAEIVILA 75
                                      444279********************************9999444.555554444311111455666666666 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.29       4      36 ..       4      42 ..       2     100 .. 0.79
   2 ?   -1.6   0.0      0.84   2.2e+03      74      88 ..     127     141 ..     117     192 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                      EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS........ CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvllsRsa......a 36
                                       i+GG+G +G  +a  l  +  +++v+ sR+a      a
  gi|313117064|ref|YP_004038188.1|  4 AIVGGTGDFGEGIAVRLGVHTDHEVVIGSRTAekaveaA 42
                                      59*****************************63333330 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.84
                                       HHHHHSS---EEEE- CS
                                KR  74 eikaeeppikGviha 88 
                                       ++  ++ p+ G +h 
  gi|313117064|ref|YP_004038188.1| 127 DAAPDGTPVVGAFHN 141
                                       555555555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1311.82
//
Query:       gi|313117065|ref|YP_004038189.1|  [L=91]
Description: hypothetical protein Hbor_35330 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.13   12.2   7.2       0.32   11.0   7.2    1.7  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
          3    8.3   9.3         24    5.4   9.3    2.3  1  Arc_trans_TRASH  Archaeal TRASH domain


Domain annotation for each model (and alignments):
>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   7.2   3.6e-05      0.32       2      40 ..      44      86 ..      43      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                            zf-FCS  2 vkkrCwfCkkyikgkpef....tyvlend....gvvgqFCStsClds 40
                                      ++ rC++C++ i  k+      t    +d     + + FC+++C +s
  gi|313117065|ref|YP_004038189.1| 44 SDHRCDYCGEVIGEKT-QyrnvT---VRDsngeICDYAFCTEECSTS 86
                                      5779********7777.334533...33345699**********886 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   9.3    0.0026        24       1      12 [.      48      59 ..      48      87 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0026
                   Arc_trans_TRASH  1 CDYCGkeivgeP 12
                                      CDYCG++i ++ 
  gi|313117065|ref|YP_004038189.1| 48 CDYCGEVIGEKT 59
                                      ******997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 619.86
//
Query:       gi|313117066|ref|YP_004038190.1|  [L=91]
Description: hypothetical protein Hbor_35340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 662.56
//
Query:       gi|313117067|ref|YP_004038191.1|  [L=369]
Description: inosine-5'-monophosphate dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.4e-120  402.5   3.4   1.6e-120  402.2   3.4    1.1  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    4.3e-08   32.9   0.7    5.4e-05   22.8   0.1    2.2  2  His_biosynth  Histidine biosynthesis protein
    1.6e-06   27.4  11.2    4.9e-06   25.8  11.2    1.8  1  FMN_dh        FMN-dependent dehydrogenase
    9.3e-05   22.0  12.5      0.016   14.6   8.5    2.5  3  NMO           Nitronate monooxygenase
     0.0006   19.0   4.3     0.0019   17.4   4.0    2.0  2  Glu_synthase  Conserved region in glutamate synthase
     0.0048   16.2   2.5      0.017   14.5   1.9    2.0  2  TMP-TENI      Thiamine monophosphate synthase
     0.0059   15.9   1.0      0.012   14.8   1.0    1.5  1  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
       0.05   13.9   0.5       0.22   11.9   0.4    2.1  2  DUF1269       Protein of unknown function (DUF1269)
      0.073   12.2   0.2       0.19   10.8   0.1    1.5  2  Dus           Dihydrouridine synthase (Dus)
      0.089   12.2   3.1       0.12   11.8   0.7    2.0  2  Aldolase      KDPG and KHG aldolase
       0.42    9.9   6.0      0.067   12.5   1.0    1.9  2  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.2   3.4    1e-123  1.6e-120       1     345 []       7     339 ..       7     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 402.2 bits;  conditional E-value: 1e-123
                                       E--GGGEEEE---B-S-GG.GSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH   1 gltfddvllvpaksevlpk.evdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeev 76 
                                       gl++ dvllvp++s v ++ +vdl+t+lt +i+ln+Plvsaamdtvte+em i+l+reGg gvih+ l++eeqa++v
  gi|313117067|ref|YP_004038191.1|   7 GLSYGDVLLVPKRSPVDSRdDVDLSTNLTPSIELNTPLVSAAMDTVTEDEMGIELSREGGFGVIHRFLDPEEQAAQV 83 
                                       699***************989******************************************************** PP

                                       HHHHTSTTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  77 kkvkrspnaakdekgrllvgaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnv 153
                                       ++v  +            vgaavg++ed  er +alveagvd+lvvd+ahgh e++l+av+++ ++++e  +iaGnv
  gi|313117067|ref|YP_004038191.1|  84 RAVTTA---------GQSVGAAVGINEDFVERSTALVEAGVDALVVDVAHGHLERTLTAVETLADEFPETPLIAGNV 151
                                       ***933.........346*********************************************************** PP

                                       -SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 154 ataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGa 230
                                       at +g+++L++agad+vkvGiGpGs Cttr vag+GvpqltA+ ++a++a++ gv+++aDGGi++sgd vkAl aGa
  gi|313117067|ref|YP_004038191.1| 152 ATPAGVEDLAAAGADCVKVGIGPGSHCTTRKVAGAGVPQLTAIDDCASVADELGVTICADGGIRTSGDAVKALMAGA 228
                                       ***************************************************************************** PP

                                       SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH-SS-TTS-..--SS-SBEEEEEE--B-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 231 davmlGsllagteEspgeviliegrkyKeyrGmgslgamkkgskdryfqkkeklvpeGvegrvpykgsvkevveqlv 307
                                       d+vmlGs++agt E+pge++ i+g++yK  rGm++++a + +++d+    ++    eGve+ +pykgs+++vve+++
  gi|313117067|ref|YP_004038191.1| 229 DTVMLGSIFAGTAEAPGEIVEIDGHQYKRSRGMATTAAAE-DRDDKH---NNVDADEGVEALTPYKGSLRAVVEEFC 301
                                       ************************************9993.444444...45789********************** PP

                                       HHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 308 gglrsgmgylGaktieelkekakfvritaaglkeshvH 345
                                       +g+rsg++y+G  ti + +e+a+f+r+++++ +  + H
  gi|313117067|ref|YP_004038191.1| 302 AGIRSGLSYCGGYTIPQARENAEFMRVAQSAKEREGFH 339
                                       *****************************998776665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1   0.00079       1.3      27     102 ..      99     171 ..      82     175 .. 0.89
   2 !   22.8   0.1   3.3e-08   5.4e-05      61     110 ..     193     242 ..     183     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00079
                                       ETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEES CS
                      His_biosynth  27 yagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviig 102
                                       +++d ve  +++ e+g+d l+ vD+  a+ + e+ l++ve++a+e+  +  + G + +   ve+l  agad v +g
  gi|313117067|ref|YP_004038191.1|  99 INEDFVERSTALVEAGVDALV-VDV--AHGHLERTLTAVETLADEFPETPLIAGNVATPAGVEDLAAAGADCVKVG 171
                                       68899999**********985.799..89999***************************************87765 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.3e-08
                                       HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-TH CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpe 110
                                        +d  + +a+e+ ++++ +GGIr+  d+ ++l agad v++g+  +   e
  gi|313117067|ref|YP_004038191.1| 193 AIDDCASVADELGVTICADGGIRTSGDAVKALMAGADTVMLGSIFAGTAE 242
                                       566667899**********************************9765555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8  11.2     3e-09   4.9e-06     204     307 ..     130     241 ..      27     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3e-09
                                       -HHHHHHHHHHHS.SEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT---HHHCHHHH...HHHH... CS
                            FMN_dh 204 twddikwlreqtk.lplvvKGvltaedakraveaGvdgivvSNHGG.....RqldgapatidvLpei...veavgg. 270
                                       t + +++l ++ +  pl+   v t++ ++ +++aG+d + v    G     R++ ga   +  L +i   +  +++ 
  gi|313117067|ref|YP_004038191.1| 130 TLTAVETLADEFPeTPLIAGNVATPAGVEDLAAAGADCVKVGIGPGshcttRKVAGA--GVPQLTAIddcASVADEl 204
                                       555678888777657999999999999999999999999996555544444666554..333444442213333333 PP

                                       SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHH CS
                            FMN_dh 271 rievlvDgGirrGsDvlkAlalGAdavllGRpflygl 307
                                        +++ +DgGir+  D++kAl  GAd v+lG  f+  +
  gi|313117067|ref|YP_004038191.1| 205 GVTICADGGIRTSGDAVKALMAGADTVMLGSIFAGTA 241
                                       4*****************************9886555 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00087       1.4       4      58 ..      34      87 ..      31     100 .. 0.82
   2 ?    0.7   0.9      0.16   2.7e+02     147     222 ..     105     171 ..      88     172 .. 0.75
   3 !   14.6   8.5     1e-05     0.016     147     232 ..     155     244 ..     143     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00087
                               NMO  4 ltellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvk 58
                                      lt  ++ + p+v + m  ++++++    s +Gg Gv+    l + + a+++r+v 
  gi|313117067|ref|YP_004038191.1| 34 LTPSIELNTPLVSAAMDTVTEDEMGIELSREGGFGVIH-RFLDPEEQAAQVRAVT 87
                                      556677889****************************9.7788866666666554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                               NMO 147 kearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqig 222
                                       +   ++ ++G Dal+v+   a Gh        + l+a++  + +  + P+iA G + +  gv+   a+GA  v++g
  gi|313117067|ref|YP_004038191.1| 105 ERSTALVEAGVDALVVDV--AHGHLE------RTLTAVETLADEFPETPLIA-GNVATPAGVEDLAAAGADCVKVG 171
                                       556677888888888874..456665......23667777777777899995.99999999999999999999988 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1e-05
                               NMO 147 kearkvearGaDalivqGpeaGGhqGtpevgd..kglfaLvpqvldavd...iPviAaGGiidrrgvaaaLalGAsg 218
                                         +  ++a+GaD + v G   G h  t++v++  + +++ ++  +++ d   + + A GGi +  +   aL +GA  
  gi|313117067|ref|YP_004038191.1| 155 AGVEDLAAAGADCVKV-GIGPGSHCTTRKVAGagVPQLTAIDDCASVADelgVTICADGGIRTSGDAVKALMAGADT 230
                                       556778999***8655.9999*****99999955444555666666666777**************999******** PP

                               NMO 219 vqigtrfLltkesd 232
                                       v +g+ f +t e++
  gi|313117067|ref|YP_004038191.1| 231 VMLGSIFAGTAEAP 244
                                       ***********987 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   4.0   1.2e-06    0.0019     223     305 ..     160     236 ..     145     266 .. 0.81
   2 ?   -2.7   0.0       1.5   2.4e+03     140     154 ..     326     340 ..     320     359 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
                                       HHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SE CS
                      Glu_synthase 223 vakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAda 299
                                       +a a+ad++++ G+  G   +    +  aG+P ++a+     +  e g    v++ adGg++t+ d vkal+ GAd+
  gi|313117067|ref|YP_004038191.1| 160 LAAAGADCVKV-GIGPGSHCTTR-KVAGAGVPQLTAIDDCASVADELG----VTICADGGIRTSGDAVKALMAGADT 230
                                       46677777777.55444444333.345689999999998887766555....89*********************** PP

                                       EE-SHH CS
                      Glu_synthase 300 vgigta 305
                                       v +g++
  gi|313117067|ref|YP_004038191.1| 231 VMLGSI 236
                                       **9975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                                       EE---TTSTTS--EE CS
                      Glu_synthase 140 ikiaQGakpgeGgql 154
                                       +++aQ ak +eG + 
  gi|313117067|ref|YP_004038191.1| 326 MRVAQSAKEREGFHA 340
                                       689*******99875 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.9     1e-05     0.017      37     177 ..      74     233 ..      63     237 .. 0.79
   2 ?    3.0   0.0     0.033        54     108     132 ..     219     243 ..     215     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                          TMP-TENI  37 ldarellelaeklaalcrkygvpliindrvdlala...........vgadgvHlgqddlpvaearellgpdliiGlS 102
                                       ld++e +++++++  + +  g+++ in+++                v++   Hl  +  +v++++  +++  +i   
  gi|313117067|ref|YP_004038191.1|  74 LDPEEQAAQVRAVTTAGQSVGAAVGINEDFVERSTalveagvdalvVDVAHGHLERTLTAVETLADEFPETPLIAGN 150
                                       5788889999999999999999999998653222224455877777888999************************* PP

                          TMP-TENI 103 vhsleeaeeaealgadYigvGpifpTdtKkda.eplgleglkelaeale......iPvvaiGGitle.nvaevleag 171
                                       v +++ +e ++a+gad + vG    +++ + + + +g+ +l+++ + ++      + ++a GGi+++ ++ ++l ag
  gi|313117067|ref|YP_004038191.1| 151 VATPAGVEDLAAAGADCVKVGIGPGSHCTTRKvAGAGVPQLTAIDDCASvadelgVTICADGGIRTSgDAVKALMAG 227
                                       ****************9866655555555555567777777777777666667779********8753788888899 PP

                          TMP-TENI 172 adgvav 177
                                       ad v +
  gi|313117067|ref|YP_004038191.1| 228 ADTVML 233
                                       988865 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.033
                          TMP-TENI 108 eaeeaealgadYigvGpifpTdtKk 132
                                       +a +a ++gad +++G+if+ +   
  gi|313117067|ref|YP_004038191.1| 219 DAVKALMAGADTVMLGSIFAGTAEA 243
                                       688999*************987655 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.0   7.6e-06     0.012     233     276 ..     196     237 ..     179     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.6e-06
                                       HHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 233 virelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                          +++++l   + i + GGi ++ Da+  ++aGA  v +++ +
  gi|313117067|ref|YP_004038191.1| 196 DCASVADELG--VTICADGGIRTSGDAVKALMAGADTVMLGSIF 237
                                       5555666666..999************************99865 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.8e+03      47      93 ..      33      80 ..      26      88 .. 0.75
   2 ?   11.9   0.4   0.00013      0.22      29      81 ..      88     140 ..      67     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                           DUF1269 47 elgeklkpgtsalfllvekatvdkvlealaklgg.kvlrtslskeeee 93
                                      +l  +++ +t  + + ++ +t+d++  +l++ gg  v+++ l+ ee++
  gi|313117067|ref|YP_004038191.1| 33 NLTPSIELNTPLVSAAMDTVTEDEMGIELSREGGfGVIHRFLDPEEQA 80
                                      566666777777778888899999999998888668999999887765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                           DUF1269  29 GAlvgalsdvgidddflkelgeklkpgtsalfllvekatvdkvlealaklggk 81 
                                        A ++  + vgi++df+++  + +++g  al++ v + + ++ l+a+++l  +
  gi|313117067|ref|YP_004038191.1|  88 TAGQSVGAAVGINEDFVERSTALVEAGVDALVVDVAHGHLERTLTAVETLADE 140
                                       3334445578*******************************999999887655 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.86   1.4e+03     169     213 ..     128     171 ..      91     177 .. 0.64
   2 ?   10.8   0.1   0.00012      0.19     158     213 ..     177     234 ..     153     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.86
                                       G--CHHHHHHHHH-S.S-EEEESS--SHHHHHHHHHHH--SEEEES CS
                               Dus 169 tadweaIkevkqavs.ipviaNGdIkdaedaqaileetGadgvmig 213
                                       +  + a++ + ++++ +p+ia G++ ++  +++  +  Gad v +g
  gi|313117067|ref|YP_004038191.1| 128 ERTLTAVETLADEFPeTPLIA-GNVATPAGVEDLAAA-GADCVKVG 171
                                       444566777777777777766.777777777776555.77776665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                                       ESSECCCTT-C...G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
                               Dus 158 HgRtraqnyeg...tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                                       H+ tr+    g      +++ ++v +++ +++ a G+I++  da ++l   Gad vm g
  gi|313117067|ref|YP_004038191.1| 177 HCTTRKVAGAGvpqLTAIDDCASVADELGVTICADGGIRTSGDAVKALMA-GADTVMLG 234
                                       7878887777765456788889999*******************999999.******98 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   7.5e-05      0.12      19      84 ..     100     168 ..      92     194 .. 0.83
   2 ?   -0.3   0.1      0.37     6e+02      44      79 ..     208     243 ..     194     252 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.5e-05
                                       GGGHHHHHHHHHHTT--EEEEETTS...TTHHHHHHHHHHH-TTSEEEEES--SHHHHHHHHHCT-SEE CS
                          Aldolase  19 kedalplaeaLvagGlrvlevtlrt...eaaldairvlrkerpdllvgaGtvlnaeqlaeakeaGaqfv 84 
                                       +ed ++   aLv+ G+ +l v +     e +l a++ l+ e p+  + aG v ++  +++ ++aGa+ v
  gi|313117067|ref|YP_004038191.1| 100 NEDFVERSTALVEAGVDALVVDVAHghlERTLTAVETLADEFPETPLIAGNVATPAGVEDLAAAGADCV 168
                                       578889999*******9887766542237899**********************************976 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.37
                                       TTHHHHHHHHHHH-TTSEEEEES--SHHHHHHHHHC CS
                          Aldolase  44 eaaldairvlrkerpdllvgaGtvlnaeqlaeakea 79 
                                        +a   ir +   ++ l+ ga tv+  + +a  +ea
  gi|313117067|ref|YP_004038191.1| 208 ICADGGIRTSGDAVKALMAGADTVMLGSIFAGTAEA 243
                                       455555666666666677777777666666655555 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.4      0.48   7.7e+02     147     199 ..      85     139 ..      77     189 .. 0.55
   2 ?   12.5   1.0   4.1e-05     0.067     169     211 ..     199     241 ..     184     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.48
                                       EBEEBSSSTTS----S-HHH..HHHHHHH-SS-BEEES---SHHHHHHHHHTT-S CS
                              ThiG 147 avmPlaapiGsglGllnkea..lkiiieeakvPvivDAGigspsdaaqamelGad 199
                                       av   +  +G++ G+++  +   + ++e     ++vD   g+ +   +a+e  ad
  gi|313117067|ref|YP_004038191.1|  85 AVTTAGQSVGAAVGINEDFVerSTALVEAGVDALVVDVAHGHLERTLTAVETLAD 139
                                       5555555666666665443200223333333345556555555555555555444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.1e-05
                                       HHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSS CS
                              ThiG 169 iiieeakvPvivDAGigspsdaaqamelGadavllntavaeak 211
                                        + +e+ v +  D Gi+++ da++a+  Gad+v+l +  a ++
  gi|313117067|ref|YP_004038191.1| 199 SVADELGVTICADGGIRTSGDAVKALMAGADTVMLGSIFAGTA 241
                                       6788999****************************99887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2486.37
//
Query:       gi|313117068|ref|YP_004038192.1|  [L=400]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-66  224.5   0.1    3.5e-66  224.2   0.1    1.1  1  DAO            FAD dependent oxidoreductase
    3.9e-08   32.9   0.0     0.0069   15.6   0.0    2.5  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    7.6e-08   32.0   0.7    0.00034   20.0   0.2    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    3.3e-07   29.3   0.2     0.0011   17.8   0.0    2.5  3  HI0933_like    HI0933-like protein
    9.4e-06   25.7   0.7     0.0025   17.8   0.0    2.5  2  NAD_binding_9  FAD-NAD(P)-binding
    3.7e-05   23.9   0.0    0.00011   22.4   0.0    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    4.1e-05   22.3   0.0       0.16   10.5   0.0    2.2  2  Mqo            Malate:quinone oxidoreductase (Mqo)
     0.0004   20.9   0.1       0.29   11.7   0.0    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00042   19.6   0.0     0.0011   18.2   0.0    1.7  1  Thi4           Thi4 family
     0.0019   17.4   0.3      0.082   12.0   0.0    2.5  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0043   17.5   0.0      0.012   16.0   0.0    1.8  2  NAD_binding_7  Putative NAD(P)-binding
     0.0067   15.5   0.5        0.4    9.7   0.0    2.2  2  Lycopene_cycl  Lycopene cyclase protein
     0.0073   15.4   0.7      0.027   13.6   0.7    1.8  1  FAD_binding_2  FAD binding domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.2   0.1   2.5e-69   3.5e-66       1     351 [.       5     394 ..       5     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 224.2 bits;  conditional E-value: 2.5e-69
                                       EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleee 74 
                                       dv+iiGGG +GlstA +L++     ++++ek++ +++++Sgrnsg+lh+g+ y+p+ s++a+++ e+ +++++++++
  gi|313117068|ref|YP_004038192.1|   5 DVAIIGGGCVGLSTAKHLTELTdldIAVFEKEHHLAEHQSGRNSGVLHPGFNYPPN-SKKAQFATEGTRRMKQYCAD 80 
                                       8*****************9875589**************************96665.599***************** PP

                                       HSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEH.HHHHHHSTT.STTTSEEEEETTEEEEEHHHHH CS
                               DAO  75 lgididyrrtGllslaadeeelealdkllallleagldaellda.eevrelepa.lpgllgalfypdtgqvdpaklt 149
                                       ++  i+ ++ G+l++a +++e+e ld l+ +++++g+++e ld+ +e++e ep+ + g ++al+ p+++ vd ++++
  gi|313117068|ref|YP_004038192.1|  81 HN--IPCEEFGVLVVAKTDHEEEHLDVLASQAEANGVEYERLDScAEIQEHEPHaV-G-QAALYAPEAASVDSQQYV 153
                                       99..677899*******9999****999999999*****99***99*******533.2.699*************** PP

                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTT.CTTTSEEEEEEEE CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgll.keldlpispvrgq 223
                                        alar+++++ v +++g+ v++++++   ++++  tt+  e+da +++VnaaG+++d l++++    d ++ p+rg+
  gi|313117068|ref|YP_004038192.1| 154 YALAREIQQNDVSLYTGHAVERVRKK-TSGYRL--TTSnSEIDA-THLVNAAGLHADtLAQQVgVGEDYQMIPFRGE 226
                                       ***********************664.234555..555343233.66**********66677765568999****** PP

                                       EEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE............EETTCSSTSCSHH..... CS
                               DAO 224 vlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtad............eesgdddpevdee..... 283
                                       ++ + p +++ v++  i+p+p++  ++ gv++t+r dg+v+vG++a+                        +     
  gi|313117068|ref|YP_004038192.1| 227 YYEVTP-DRSDVCQTMIYPTPDPELPFLGVHYTRRTDGKVIVGPNAVlafgreayqntdA-----------Dlselk 291
                                       ****77.56688999*******************************98776655444330...........233455 PP

                                       .............................HHHHHHHHHHHHSGGG..CGEEEEEEEEEE.E..TTS....SEEEEEE CS
                               DAO 284 .............................didellealrklfPql..gdvlrkwaGlrp.l..pdg....lpliget 322
                                                                    +  ++ ea+++l+P++   d+ ++++G+r+ l   dg    +pl    
  gi|313117068|ref|YP_004038192.1| 292 divaydgfqkllssktmlavawselnksyRKSKFTEAAQRLVPGIrsNDLNKSYSGIRAqLvsADGdlvkDPLTI-- 366
                                       666666777777777777777777777778888***********6558899********7444699444455544.. PP

                                       ETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                               DAO 323 pgvkglylatGhsghGltlapatGkllae 351
                                        ++++ +++ ++ ++Glt+++  G+++a+
  gi|313117068|ref|YP_004038192.1| 367 -ETDDAVHVLNAVSPGLTSSLPFGEHIAK 394
                                       .469***********************96 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   8.3e-06     0.011       1      37 [.       4      41 ..       4     131 .. 0.81
   2 !   15.6   0.0     5e-06    0.0069     188     250 ..     155     214 ..     140     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.3e-06
                                      CSEEEE--SHHHHHHHHHHHH.HTS-EEEEETTHCHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq.agakvtlvelegtcln 37
                                      +dv++iGgG  Gl++a++l +   ++++++e+e ++  
  gi|313117068|ref|YP_004038192.1|  4 HDVAIIGGGCVGLSTAKHLTElTDLDIAVFEKEHHLAE 41
                                      59*******************77*******75555544 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5e-06
                                       HHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 188 aleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklgl 250
                                       al++++++++v +++g+ v++++++++ ++  +++++eida  +v a+G+ ++t    +++g+
  gi|313117068|ref|YP_004038192.1| 155 ALAREIQQNDVSLYTGHAVERVRKKTSGYR-LTTSNSEIDATHLVNAAGLHADTLA--QQVGV 214
                                       678999*****************9999666.7778888***************955..67776 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00021      0.29       2      32 ..       8      38 ..       7      43 .. 0.92
   2 !   20.0   0.2   2.5e-07   0.00034      75     136 ..     144     205 ..     123     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgni 32
                                      IiG+G  Gl++a +l ++   d+ + Ek+++
  gi|313117068|ref|YP_004038192.1|  8 IIGGGCVGLSTAKHLTELTDLDIAVFEKEHH 38
                                      9*****************999*******965 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2.5e-07
                       Pyr_redox_3  75 eeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefd 136
                                          +  +++++ l++  ++++++  + + Ve+v k+ +g++++ts++++ A++++ A+G   
  gi|313117068|ref|YP_004038192.1| 144 AASVDSQQYVYALAREIQQNDVSLYTGHAVERVRKKTSGYRLTTSNSEIDATHLVNAAGLHA 205
                                       55677899999999999******************************************755 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00038      0.53       1      36 [.       4      40 ..       4      46 .. 0.88
   2 ?   -2.5   0.0       1.1   1.5e+03     106     140 ..      97     131 ..      74     138 .. 0.81
   3 !   17.8   0.0   7.7e-07    0.0011     106     163 ..     147     202 ..     139     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00038
                                      -SEEEE--SHHHHHHHHHH.HHTT--EEEE-SSSSS- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisa.akrgkrVlllekakklg 36
                                      +dv++iGgG  Gl +A ++ + ++ +++++ek+++l+
  gi|313117068|ref|YP_004038192.1|  4 HDVAIIGGGCVGLSTAKHLtELTDLDIAVFEKEHHLA 40
                                      59****************9566899******998876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                       .-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETT CS
                       HI0933_like 106 dkaedivdallkelkeagvklrletevksvekeed 140
                                       d+ e+ +d+l ++++++gv+++   + ++++++e 
  gi|313117068|ref|YP_004038192.1|  97 DHEEEHLDVLASQAEANGVEYERLDSCAEIQEHEP 131
                                       55667789999999999999999999888876654 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 7.7e-07
                                       .-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 106 dkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                        ++++ v al +e+++++v+l++ ++v++v+k+++g +r++t s++e+ a++lv A G
  gi|313117068|ref|YP_004038192.1| 147 VDSQQYVYALAREIQQNDVSLYTGHAVERVRKKTSG-YRLTT-SNSEIDATHLVNAAG 202
                                       578999************************998888.*****.9**********9988 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.8e-06    0.0025       1      37 [.       7      39 ..       7      57 .. 0.88
   2 !    6.0   0.1    0.0076        11     102     154 ..     151     202 ..      84     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      ai+G+G+ Gl+++++L +     ++l+i +f+++++ 
  gi|313117068|ref|YP_004038192.1|  7 AIIGGGCVGLSTAKHLTEL----TDLDIAVFEKEHHL 39
                                      8******************....6*********7664 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0076
                     NAD_binding_9 102 dlfeellarlpegvtvevhra.evvdleeradgqavlladgaslaadaVvLAlG 154
                                       +++ +l+++ +++ +v+++++  v++++++ +g+++ ++++++++a ++v A G
  gi|313117068|ref|YP_004038192.1| 151 QYVYALAREIQQN-DVSLYTGhAVERVRKKTSGYRL-TTSNSEIDATHLVNAAG 202
                                       3444455555444.6777766266678888888766.88999999999998887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.7e-08   0.00011       1      32 [.       8      40 ..       8      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.7e-08
                                      EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka.gfdvlllekrdrlG 32
                                      I+G+G  Gl++A +L++  ++d+ ++ek ++l 
  gi|313117068|ref|YP_004038192.1|  8 IIGGGCVGLSTAKHLTELtDLDIAVFEKEHHLA 40
                                      9****************77***********994 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00012      0.16       2      68 ..       3      63 ..       2      77 .. 0.84
   2 !    9.8   0.0   0.00018      0.25     167     398 ..     137     355 ..     124     387 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                               Mqo  2 kvdvvliGaGimsatlgvllkelepelsievlerldkvaeessnawnnaGtGHsalcElnYtpeked 68
                                      ++dv +iG+G +  + +  l+el+ +l+i+v+e+ ++ ae  s    n+G  H ++   nY p++++
  gi|313117068|ref|YP_004038192.1|  3 HHDVAIIGGGCVGLSTAKHLTELT-DLDIAVFEKEHHLAEHQSG--RNSGVLHPGF---NYPPNSKK 63
                                      68*********************6.89************99876..6889888775...77776665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00018
                               Mqo 167 aatrieeGtdvnfgaltrqllkalekkkgvelklkhevkdlkreedgkWkvkvkdlktgekkkvkakfvfiGaGGga 243
                                       aa ++ e + v+  +   +l++++++ ++v+l ++h v++++++++g +++++++      ++++a+++   aG +a
  gi|313117068|ref|YP_004038192.1| 137 AALYAPEAASVDSQQYVYALAREIQQ-NDVSLYTGHAVERVRKKTSG-YRLTTSN------SEIDATHLVNAAGLHA 205
                                       55666777888999999999999965.9*************998885.7887775......5677777777899999 PP

                               Mqo 244 lklLqksgipeakgyggfPvsGqflvcknpevveqheakvYgkaavgaPPmsvpHlDtRvidgkksllfGPfa..gf 318
                                        +l q+ g+ e  +y   P  G++   + p+  +  ++ +Y   +   P + v +  tR  dgk  ++ GP a  +f
  gi|313117068|ref|YP_004038192.1| 206 DTLAQQVGVGE--DYQMIPFRGEYYEVT-PDRSDVCQTMIYPTPDPELPFLGVHY--TRRTDGK--VIVGPNAvlAF 275
                                       99999999976..68889999*999876.56677788899999999999999865..6777776..45577662223 PP

                               Mqo 319 stkflk..egslldllksvklsnllpllavglknldLvkYlieqvlkskedrlealreflpeakkedWelvvaGqRv 393
                                            +  +++l +l   v  + +++ll+  +     v +   +    k++ +ea ++ +p  +++d +   +G R 
  gi|313117068|ref|YP_004038192.1| 276 GREAYQntDADLSELKDIVAYDGFQKLLSSKTMLA--VAWSELNKSYRKSKFTEAAQRLVPGIRSNDLNKSYSGIRA 350
                                       32222200233445555555555555554432222..2222222222334445666777777777777777777777 PP

                               Mqo 394 qvikk 398
                                       q++  
  gi|313117068|ref|YP_004038192.1| 351 QLVSA 355
                                       77766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00021      0.29       2      34 ..       6      39 ..       5      47 .. 0.84
   2 !    6.5   0.0    0.0087        12      46      74 ..     156     183 ..     150     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                      EEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvversdkl 34
                                      v+++GgG +gl  A+ l+el   ++ v+e + +l
  gi|313117068|ref|YP_004038192.1|  6 VAIIGGGCVGLSTAKHLTELTdLDIAVFEKEHHL 39
                                      89*****************884588888887766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0087
                                       HHHHHHHTTEEEECSEEEEEEEEETTSEE CS
                         Pyr_redox  46 lqeklekngievllntkveeiegsedgve 74 
                                       l++++++n + +++++ ve+++++++g +
  gi|313117068|ref|YP_004038192.1| 156 LAREIQQNDVSLYTGHAVERVRKKTSG-Y 183
                                       78999*****************99998.3 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.3e-07    0.0011      18      50 ..       4      36 ..       1      45 [. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.3e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailers 50
                                       Dv+i+G+G  GL++a+ l++  dl +a++e++
  gi|313117068|ref|YP_004038192.1|  4 HDVAIIGGGCVGLSTAKHLTELTDLDIAVFEKE 36
                                      7*****************************985 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0     6e-05     0.082       2      42 ..       3      42 ..       2      47 .. 0.93
   2 ?    2.8   0.0     0.039        53     291     328 ..     161     197 ..     137     207 .. 0.78
   3 ?   -3.0   0.0       2.2     3e+03     250     291 ..     314     355 ..     308     379 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                       K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalflerqpefaWh 42
                                      ++D+++iG G   Ls a +l e   +l++ ++e++++ a h
  gi|313117068|ref|YP_004038192.1|  3 HHDVAIIGGGCVGLSTAKHLTELT-DLDIAVFEKEHHLAEH 42
                                      79**********************.**********998766 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.039
                       K_oxygenase 291 geerlrllpnrevesaeaegkgeveltlrneesgeeet 328
                                       ++++++l++ ++ve+++++++ +++lt++n+e ++++ 
  gi|313117068|ref|YP_004038192.1| 161 QQNDVSLYTGHAVERVRKKTS-GYRLTTSNSEIDATHL 197
                                       57789**************96.******9987766554 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.2
                       K_oxygenase 250 yslpeekreallkeqkatnykgvdaelieelyeelyeqkvkg 291
                                        +l+++ r++  +e  +++  g++++ +++ y  +++q v+ 
  gi|313117068|ref|YP_004038192.1| 314 SELNKSYRKSKFTEAAQRLVPGIRSNDLNKSYSGIRAQLVSA 355
                                       567788888888888888888999988888888888887765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.9e-06     0.012       6      93 ..       2     121 ..       1     131 [. 0.66
   2 ?   -2.9   0.0         7   9.6e+03      55      68 ..     183     201 ..     141     205 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.9e-06
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklle.agakvtvvapevkeele............................elvklaee 53 
                                       k   v ++GgG v+++ +++l e ++ ++ v  +e    +e                            ++ ++++ 
  gi|313117068|ref|YP_004038192.1|   2 KHHDVAIIGGGCVGLSTAKHLTElTDLDIAVFEKEH-HLAEhqsgrnsgvlhpgfnyppnskkaqfateGTRRMKQY 77 
                                       567899*****************778******9996.2223457778888888887777774444443333333333 PP

                     NAD_binding_7  54 elekd..legad.lviaatddrelner.iaeaakarrilvnvad 93 
                                       +++++  +e++  lv+a td++e+    +a +a+a+++   + d
  gi|313117068|ref|YP_004038192.1|  78 CADHNipCEEFGvLVVAKTDHEEEHLDvLASQAEANGVEYERLD 121
                                       33333556666657777777777665534556677776655555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7
                     NAD_binding_7  55 l.....ekdlegadlviaa 68 
                                       +     +++++ ++lv aa
  gi|313117068|ref|YP_004038192.1| 183 YrlttsNSEIDATHLVNAA 201
                                       2222224556666666665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00029       0.4       1      30 [.       5      33 ..       5      43 .. 0.80
   2 ?    4.1   0.1     0.014        19      82     152 ..     145     214 ..     112     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvli 30
                                      Dv++iG+G  gls A++lt + ++l + + 
  gi|313117068|ref|YP_004038192.1|  5 DVAIIGGGCVGLSTAKHLT-ELTDLDIAVF 33
                                      9*****************5.5566666555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.014
                     Lycopene_cycl  82 grvsskrlkeellerlvengvklleak.vesveeeeageslvvleggrkirarlvvdarglaslkkarrlgl 152
                                       ++v s++    l++++ +n v+l+ +  ve+v++++    +  +  + +i+a   v a gl + + a+++g+
  gi|313117068|ref|YP_004038192.1| 145 ASVDSQQYVYALAREIQQNDVSLYTGHaVERVRKKTS--GYRLTTSNSEIDATHLVNAAGLHADTLAQQVGV 214
                                       5799999999999999999999888752778888777..566777899************888876666654 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.7   1.9e-05     0.027       1     167 [.       5     176 ..       5     206 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                       SEEEE--SHHHHHHHHHHHH.TTT-EEEEESSSGGGS.GGGG--S-EE.-TT..SSGGSTC.CHHHHHHHHHHHHTT CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaae.aGlkvavvekeqefgg.atawsqGgid.avlspeqkkagikdspelhrtdtlkald 74 
                                       Dv +iG+G  GL+ A  ++e   l++av eke+     ++   +G +    ++p++ k+    +     t  +k+  
  gi|313117068|ref|YP_004038192.1|   5 DVAIIGGGCVGLSTAKHLTElTDLDIAVFEKEHHLAEhQSGRNSGVLHpGFNYPPNSKK---AQFATEGTRRMKQYC 78 
                                       9*******************7777********997665555555555412222332111...112333333333333 PP

                                       T-S-HHHHHHHH......HTHHHHHHHHHHT....T----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHH CS
                     FAD_binding_2  75 eladqplveafv......eaapeavdeLeel....gvpfsrtedgpvdvrelGglsatartlhdaadarretlvtgh 141
                                        +++ p  e++v      ++ +e +d L+++    gv + r        +e  ++ ++  ++  a+ a++ + v+ +
  gi|313117068|ref|YP_004038192.1|  79 ADHNIPCEEFGVlvvaktDHEEEHLDVLASQaeanGVEYER----LDSCAEIQEHEPH-AVGQAALYAPEAASVDSQ 150
                                       33333344444400000034444444444445555555555....4455666666666.444434444447777888 PP

                                       HHHHHHHHHHHTCTEEEEESEEEEEE CS
                     FAD_binding_2 142 allarlvesarkagvdfqerteadeL 167
                                       + +++l++++++++v +++ ++++++
  gi|313117068|ref|YP_004038192.1| 151 QYVYALAREIQQNDVSLYTGHAVERV 176
                                       88888888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2977.44
//
Query:       gi|313117069|ref|YP_004038193.1|  [L=387]
Description: acyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-30  106.5   1.5    2.1e-30  105.9   1.5    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.6e-26   92.0   0.0    8.5e-26   90.8   0.0    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
      2e-24   85.6   0.0    3.7e-24   84.7   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      5e-11   43.0   1.0    7.6e-11   42.4   1.0    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   1.5   4.6e-34   2.1e-30       2     148 ..     233     379 ..     232     381 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 4.6e-34
                                       BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                     Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaeal 78 
                                       kG++  ++ l++ R ++a++a+g+a+ a++ea +ya +r++fg+p++ +ql +++laema++++ a ll+ r+ae+ 
  gi|313117069|ref|YP_004038193.1| 233 KGMKGPLSCLTQARYGIAWGAIGAAKDAFREAQDYATDREQFGQPIGGFQLQQQNLAEMATQITLAELLAHRLAELK 309
                                       6999999********************************************************************** PP

                                       ------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                     Acyl-CoA_dh_1  79 dagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                       ++g+ ++  +smaK    ++a++ ++ a ++lGg+G++++y+  r++ ++ +   +eGt +i+ +++++ 
  gi|313117069|ref|YP_004038193.1| 310 EQGNLRPEHVSMAKRNNVRMARNQTRVAREMLGGNGITTDYSPMRHMANMETVYTYEGTHDIHTLVLGKD 379
                                       ***************************************************************9998875 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   1.9e-29   8.5e-26       2     113 .]      13     123 ..      12     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1.9e-29
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                        e++++rd+vref+++e++p +a+++ eg+fp el+ +++elGl++ ++ e yg  +++  ++ ++++el+++d+gl
  gi|313117069|ref|YP_004038193.1|  13 SEERMIRDSVREFVQNEVKPDIADHYVEGTFPTELITEFGELGLYAPNL-EGYGLPNVSERAYGLIMQELEAGDSGL 88 
                                       79*******************************************9999.9**9999******************** PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                       +++ +v+ +lv+++i +fG+e+qk+++Lpkl sge
  gi|313117069|ref|YP_004038193.1|  89 RSMASVQGALVMYPIHAFGSEAQKDEWLPKLGSGE 123
                                       ********************************998 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   8.3e-28   3.7e-24       1      97 []     127     221 ..     127     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 8.3e-28
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrr 77 
                                       +f+lTEp++Gs+  +++t  aerdg+eyvlnG+K+witn++i+++a+v+ar  + + +  ++ flv++d+ gv+ ++
  gi|313117069|ref|YP_004038193.1| 127 CFGLTEPEHGSNPSAMET-YAERDGDEYVLNGSKTWITNSPISDVAVVWARDRSSE-DTPVRGFLVETDRDGVTTNK 201
                                       9*****************.9*******************************44445.999***************** PP

                                       ---BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                       i++kl lr   tge+ +++v
  gi|313117069|ref|YP_004038193.1| 202 IDDKLSLRASITGEIALQNV 221
                                       ***************99987 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   1.0   1.7e-14   7.6e-11       2     131 ..     248     367 ..     247     370 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.7e-14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       gia  a+GaA+ a+ e++++a++r +  +g+++  ++  q+ lae+a+++  A++l +r a+      ++g+   +e
  gi|313117069|ref|YP_004038193.1| 248 GIAWGAIGAAKDAFREAQDYATDREQ--FGQPIGGFQLQQQNLAEMATQITLAELLAHRLAEL----KEQGNL-RPE 317
                                       678889********************..***********************************....555555.677 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGG CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaa 131
                                       ++  a+r+ ++ +++ +++   + e+ Gg+++++++   R++ +++++ ++++
  gi|313117069|ref|YP_004038193.1| 318 HVSMAKRNNVRMARNQTRV---AREMLGGNGITTDYSPMRHMANMETVYTYEG 367
                                       7777777776555555555...5566799999999888888888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2738.07
//
Query:       gi|313117070|ref|YP_004038194.1|  [L=478]
Description: acetyl-CoA hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-39  134.7   0.0    3.5e-39  134.2   0.0    1.2  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    3.3e-10   40.3   0.0      7e-10   39.2   0.0    1.5  1  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
    8.5e-05   21.6   0.3     0.0002   20.4   0.3    1.6  1  CitF             Citrate lyase, alpha subunit (CitF)
    0.00051   19.5   0.1     0.0012   18.3   0.0    1.6  2  CoA_trans        Coenzyme A transferase
  ------ inclusion threshold ------
      0.048   13.3   0.1       0.26   10.9   0.1    2.0  2  DUF2204          Nucleotidyl transferase of unknown function 


Domain annotation for each model (and alignments):
>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   0.0   9.7e-43   3.5e-39       1     153 [.     308     454 ..     308     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 9.7e-43
                                       S-HHHHHHHTT.-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSEC.TTCCTCGGTTHHHHHHHHHH CS
                   AcetylCoA_hyd_C   1 Gskklydflde.npkielrpveyvndpeviaqnkkvvsinsalevdltGqvnsesl.ggrvvsGvGgqldFvrgaal 75 
                                       G+++l++ +++  ++i+lrp ++ n+p  i q   vv +nsa+e+d++G+vns+++ g+r+v+G+Gg+ d+ r+a l
  gi|313117070|ref|YP_004038194.1| 308 GQRRLFEDIERyAEDIVLRPADVANHPGLIDQ-FGVVGVNSAIEFDIYGNVNSTHIrGKRMVNGIGGSADYNRNALL 383
                                       899*******999*******************.9******************************************* PP

                                       STT-EEEEE--SEETTTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHT.TS-HHHHHHHH CS
                   AcetylCoA_hyd_C  76 skggksiialpStakkgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealik.iAhpdfreeLl 151
                                            si alpS+ ++ge+Sr+vp+     hv++t+hd+d++vTE+G+ad+rg s+ erae++i+ +Ahp+f+ +L+
  gi|313117070|ref|YP_004038194.1| 384 -----SICALPSALDDGETSRVVPMTF---HVDHTEHDIDVFVTEQGVADVRGCSPVERAERIIEhCAHPSFKSDLQ 452
                                       .....**********************...*********************************************98 PP

                                       HH CS
                   AcetylCoA_hyd_C 152 ee 153
                                       ++
  gi|313117070|ref|YP_004038194.1| 453 SY 454
                                       76 PP

>> AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   1.9e-13     7e-10      11     198 .]       9     205 ..       6     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.9e-13
                   AcetylCoA_hydro  11 epeeaaelvkngshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevleekdavlyrpa 87 
                                       ++e aa  + +   +  sgf +vg +kaip +la   +   +++  l     vg+ + ++     l e+ a++ r  
  gi|313117070|ref|YP_004038194.1|   9 DAETAAARIASDATVLTSGFGSVGYPKAIPLALA---NSDRDLRLTLVSSGNVGDEIDVD-----LVESGAISRR-F 76 
                                       57889999999999********************...44455555555555555544444.....5566666666.* PP

                   AcetylCoA_hydro  88 pkqvgellrkainqglvsfvdkhlsevpqklekgfvp.iDvalieataldedGylnlGvgvrakKviiEv....... 156
                                       ++q+++  r a n   + f d  +s +++++++g +   Dva++ea a+  +G++++  +v  + + +E        
  gi|313117070|ref|YP_004038194.1|  77 SYQSSSVARRATNRRDIAFSDRNASSIGDEVQYGGMVdPDVAIVEAVAVG-EGWFVPSTSVGQVPAFVEAadelfie 152
                                       *********************************866559********996.6******9988888888888888888 PP

                   AcetylCoA_hydro 157 .........aelvvivvkknpPrvngydelialdkv..dyivvdpekvvavve 198
                                                  +++i  +  pP + +++      ++   y++  pek v vve
  gi|313117070|ref|YP_004038194.1| 153 lnhqhplglQSVHDIYRPDSPPNRTPIPLTDPGGRIgtSYVQFAPEKLVGVVE 205
                                       8999999999999*************999999999999999999999999987 PP

>> CitF  Citrate lyase, alpha subunit (CitF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   5.6e-08    0.0002     271     403 ..     279     424 ..     209     440 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.6e-08
                              CitF 271 dlleeglveklldvqsfdsvaaeslarnknhl...eisaney........anpsskGasvdrldvv.ilsaleidtk 335
                                       +l ++gl++ +ld   + s++a+s+a  ++ +     + ++y        a+ ++    +d++ vv + sa+e d  
  gi|313117070|ref|YP_004038194.1| 279 ELIQDGLLD-MLDSGRLASASATSMALTADGQrrlFEDIERYaedivlrpADVANHPGLIDQFGVVgVNSAIEFDIY 354
                                       455666665.5677788888888887765432111234444511112222678899999****998688******** PP

                              CitF 336 fnvnvltGsdGvirGasGGhcdtaaaaklsiivap..lvrGriptvveevttvitpGesvdvlvtdvGia 403
                                        nvn        +   +GG +d    a lsi   p  l  G  + vv+    v    + +dv+vt++G+a
  gi|313117070|ref|YP_004038194.1| 355 GNVNSTHIRGKRMVNGIGGSADYNRNALLSICALPsaLDDGETSRVVPMTFHVDHTEHDIDVFVTEQGVA 424
                                       ****9877776777789**************986644789*****************************8 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.2e-07    0.0012       4      69 ..      10      76 ..       7     136 .. 0.69
   2 ?   -3.5   0.0       1.5   5.4e+03     111     139 ..     351     374 ..     347     381 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.2e-07
                                      HHHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHT.TTSEEEEESTTTE..ECCHHHHHTTTEEEEE CS
                         CoA_trans  4 aaeavakeikdGmtvavGGFgligiPealiaalarsg.vkdltviiseagv..lglgplllngsvkkvi 69
                                      a+ a+a +i +++tv+ +GFg++g P+a+  ala+s+   +lt ++s + +  +++++ + +g + + +
  gi|313117070|ref|YP_004038194.1| 10 AETAAA-RIASDATVLTSGFGSVGYPKAIPLALANSDrDLRLTLVSSGNVGdeIDVDL-VESGAISRRF 76
                                      677777.*******************88888999998556788888888773545443.3344444444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.5
                                       EETTEEEESTTTTSHGGTTESEEEEETTE CS
                         CoA_trans 111 lpelgfltntgigtlvapklkkvpgfgGa 139
                                        + +g++++t+i     +k  +v g+gG 
  gi|313117070|ref|YP_004038194.1| 351 FDIYGNVNSTHIR----GK-RMVNGIGGS 374
                                       5667889998888....88.699999986 PP

>> DUF2204  Nucleotidyl transferase of unknown function (DUF2204)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.28     1e+03      57      89 ..     121     152 ..     114     172 .. 0.78
   2 ?   10.9   0.1   7.4e-05      0.26      25      47 ..     399     421 ..     396     425 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.28
                           DUF2204  57 reiaeeedwdvgstelgtvkliakvekeevevd 89 
                                       + +a  e+w v st++g+v   +++ +e + ++
  gi|313117070|ref|YP_004038194.1| 121 EAVAVGEGWFVPSTSVGQVPAFVEAADE-LFIE 152
                                       6788899************999999876.4444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.4e-05
                           DUF2204  25 tvvelalgrkrlekDvDlFitek 47 
                                        vv++ + ++++e+D+D+F+te+
  gi|313117070|ref|YP_004038194.1| 399 RVVPMTFHVDHTEHDIDVFVTEQ 421
                                       69*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2952.17
//
Query:       gi|313117071|ref|YP_004038195.1|  [L=71]
Description: hypothetical protein Hbor_35390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 509.79
//
Query:       gi|313117072|ref|YP_004038196.1|  [L=664]
Description: TRAP transporter, 4TM/12TM fusion protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-53  179.9  46.6      7e-53  179.9  46.6    1.9  2  DctM      Tripartite ATP-independent periplasmic transporter,


Domain annotation for each model (and alignments):
>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.6     0.031   5.6e+02     218     280 ..      21      81 ..       2     127 .. 0.55
   2 !  179.9  46.6   3.9e-57     7e-53       5     416 .]     124     572 ..     119     572 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.031
                              DctM 218 palllpliiligillgiftpteagavavvyalviallvyrrltleevaaallstakttaavlf 280
                                        ++ +  i++  i+lg++   e + v  +++++++ +      l ++++al+++ ++ aavl+
  gi|313117072|ref|YP_004038196.1|  21 VSVTMSAIVFWLIVLGWAYTQEMSRVK-YGVIFVGGI-MSVYALDQTRQALEDGNRIDAAVLL 81 
                                       455566666666777776555555443.233333333.3446677777777777777777764 PP

  == domain 2  score: 179.9 bits;  conditional E-value: 3.9e-57
                              DctM   5 lvllalgvpvaislalasl.lllallgelllgv.......pleqilaqrvve......glssfallaipfFvlaGiv 67 
                                       ++ l  +   + +l+l++  +++ ++g+ ++g+       + +++l+  v +      +l++ +   i  F+l + +
  gi|313117072|ref|YP_004038196.1| 124 ILYLTWREFGNLFLGLVGGaIVYGMYGNYAPGIlnhggmtE-LTLLQSLVTDlygfygSLTQLTAAWIAPFLLYAGL 199
                                       45556667778889999888999999999999999999852.3355544444666887899999999999******* PP

                              DctM  68 lersGlakrlidlaaalvGrvrGGlakvsvvgsalfgaiSGsavAnvaavGsitipamkrsGykrefaaaviaasst 144
                                       l   G+ + ++++a++    ++ G+a+++v++sa++g+i Gs  An+a +Gs+tip mk+sG+  ++aa++++ +st
  gi|313117072|ref|YP_004038196.1| 200 LFGYGAFDLILRVAIQSGKYIESGVAQTAVLASAVIGSINGSYTANAAMTGSFTIPTMKDSGMSSHRAAGIESVAST 276
                                       ****************99999******************************************************** PP

                              DctM 145 lgqiiPPslglivfama.vlgvsigdlfaaaiipglllavglllavaiaakkenlrs......ktkaelkrlgqalk 214
                                        gq++PP++g+ +f+ma +l vs+ d+++a++ip+++l+  + +av++ a  ++ ++        ++el  +++a+ 
  gi|313117072|ref|YP_004038196.1| 277 SGQVLPPVMGASAFVMAsYLQVSYLDIVTAGLIPAAILVACIGIAVHYVAISDASSQgmdfeeFFDDELTTRQKAFE 353
                                       *************************************7777777777666644444444444366677777776665 PP

                              DctM 215 eaipalllpliiligillgi..ftpteagavavvyalviallv................yrrltleevaaallstak 273
                                       +    + +p+ +li  llgi  ft + a+ + +v + v ++ +                +   +l+++ +++  +a 
  gi|313117072|ref|YP_004038196.1| 354 SVR--FGIPFCVLI-YLLGIlqFTVMTAALWTIVSMVVCGVTIpvvqrlvdntstspgtEIVQQLRNTVHGFRRGAI 427
                                       554..999999999.67777788888899999998888888888889999998888776666677888888999999 PP

                              DctM 274 ttaavlfilaaagifaglltltgvplklselllslsggk.llfLilvnllvlvlGmfldttaaiiilvpilaPaa.a 348
                                       + a +++il a++ +  ++++tgvp k++ ll+ lsgg  ll ++l++l+++++G++++t+aa++i+++++aP +  
  gi|313117072|ref|YP_004038196.1| 428 ILAPIAIILVAVNGVIDIFSVTGVPNKIALLLMDLSGGMlLLAVLLAMLVSILMGVGMPTVAAYVIVAILIAPTLvT 504
                                       99************************************988899999**************************7616 PP

                              DctM 349 klgidpihfgvvivlnlsiglitPPvGlalfvassiakvsveeivkalvPflvvlvvalvlitlvpel 416
                                        +gi +i+++  +++++ ++ itPPv++a+ v+++ia++ + ++  a+++ + +l+++ + + ++p++
  gi|313117072|ref|YP_004038196.1| 505 DFGIPKIAAHYTVFYAAILAGITPPVATAAVVTAGIAEANFWRVCGAAIKIAAPLFILPIAFVYNPAM 572
                                       7*********************************************************9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.41
# Mc/sec: 4883.26
//
Query:       gi|313117073|ref|YP_004038197.1|  [L=367]
Description: TRAP transporter solute receptor, TAXI family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      5e-21   75.4   0.3    6.5e-21   75.0   0.3    1.1  1  NMT1_3      NMT1-like family
     0.0026   17.8   0.0     0.0079   16.2   0.0    1.7  2  NMT1        NMT1/THI5 like
  ------ inclusion threshold ------
       0.28   10.6   0.1       0.28   10.6   0.1    2.0  2  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.3   1.1e-24   6.5e-21      13     288 ..      73     356 ..      63     356 .. 0.81

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.1e-24
                            NMT1_3  13 vGvaiatliseklakdqkvkasaqssaGsveNiqllkkgeadlailqsdvayeAyeGegefegkkplknlraitml. 88 
                                       vG a+ + +s++   ++k+   + +s G v  i  + + ++  +i+ +   ++A + +g+f++ k ++++ + + + 
  gi|313117073|ref|YP_004038197.1|  73 VGLAVERTVSQH---SDKLDYATVESPGYVGTIYRMAQDQFSGGITDNNSLTKALTDRGSFSD-KSVDEIPYYGFYa 145
                                       577777777655...4678888889*************************************9.7999999988773 PP

                            NMT1_3  89 yaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealgls..ekdlklleelgygesadalkdgqldg 163
                                        +  ++l++++  +i++++dl gk+v + ++g +t+++++++ +   ++  +++++ ++++g+g++  a+ +g++d+
  gi|313117073|ref|YP_004038197.1| 146 FPYSIYLIARDGTDIETFDDLAGKNVYPAEPGYSTRATTLDVWSQDPTKeiYEQMN-IQNMGVGDAPGAMEEGRIDA 221
                                       567799999**********************************9988774345665.599****************9 PP

                            NMT1_3 164 aalvaGvPv...savtqlaasedikliplddeqldkllkeypvftkyvipagty..p...qdedikTiavpnflvvr 232
                                       a   + +++   + vt+  a+ d+++++ +d+  +++   y+   + +i  +    +   ++ ++ T         +
  gi|313117073|ref|YP_004038197.1| 222 AIAYGTPGAgytGWVTEYDARLDVHYVEPTDALKESVAT-YSGAGSSTISMSDWsmQqdiGTDEVFTWDLEVNYTFT 297
                                       876655554223779*************99997777765.6666666666554413212235678888888889999 PP

                            NMT1_3 233 adldeelvYeitkaifenldelnsihkaakeislekalaglp...vplHpGAerYYkEq 288
                                        + +++ vYe+++ + e++d +n++++++++++    + g+    +p+HpGA++YYkE+
  gi|313117073|ref|YP_004038197.1| 298 PEANADAVYELCRVVDEHNDVVNEAEAQFNDFESTADMLGSArekIPVHPGAAKYYKEN 356
                                       9*****************************988875554333345************95 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-06    0.0079      77     148 ..     152     225 ..     147     232 .. 0.86
   2 ?   -2.3   0.0      0.59   3.5e+03      18      35 ..     240     257 ..     230     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-06
                                       EEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT-..-GGG-EEEE-.TT-HHHHHHCTSSSEEECEE CS
                              NMT1  77 livlkdsgikspkDLkGkrigyvg.spfekallkallakdgg..dpsdvtlvnvggtslakalltgkvDaaiggy 148
                                       li++++++i+++ DL+Gk +   + +  ++a+  +++++d     +++++++n+g+ ++  a+ +g++Daai +y
  gi|313117073|ref|YP_004038197.1| 152 LIARDGTDIETFDDLAGKNVYPAEpGYSTRATTLDVWSQDPTkeIYEQMNIQNMGVGDAPGAMEEGRIDAAI-AY 225
                                       68899999***********98666467799**********9944469*******8888877**********9.44 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.59
                                       HTTEEEEEE--SSTTHHH CS
                              NMT1  18 eeGldVeivepadpsdat 35 
                                       ++ ldV +vep+d  +  
  gi|313117073|ref|YP_004038197.1| 240 DARLDVHYVEPTDALKES 257
                                       567999999999965443 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   4.7e-05      0.28       8      26 ..       5      22 ..       2      26 .. 0.75
   2 ?   -3.9   1.6       1.5   9.1e+03      18      32 ..     221     235 ..     221     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.7e-05
                        UCR_Fe-S_N  8 eptRRDFLyiATgavgaVG 26
                                        +RR+FLy AT a g VG
  gi|313117073|ref|YP_004038197.1|  5 TLQRREFLYGATTA-GIVG 22
                                      568*****999976.6666 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.5
                        UCR_Fe-S_N  18 ATgavgaVGaaaaaw 32 
                                       A+ a g+ Ga+++ w
  gi|313117073|ref|YP_004038197.1| 221 AAIAYGTPGAGYTGW 235
                                       788999999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2741.89
//
Query:       gi|313117074|ref|YP_004038198.1|  [L=258]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-32  112.3   0.0    3.8e-32  110.8   0.0    1.7  2  IclR            Bacterial transcriptional regulator
    8.6e-11   41.5   0.1      3e-10   39.7   0.0    1.9  2  HTH_IclR        IclR helix-turn-helix domain
    9.8e-08   31.4   0.0    2.2e-07   30.3   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    4.1e-07   29.7   0.1    9.7e-07   28.6   0.1    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
    9.7e-07   28.8   0.0    2.8e-06   27.3   0.0    1.8  1  HTH_20          Helix-turn-helix domain
    0.00025   20.9   0.0    0.00052   19.8   0.0    1.5  1  MarR_2          MarR family
    0.00036   20.4   0.0    0.00086   19.2   0.0    1.7  1  HTH_11          HTH domain
    0.00066   19.6   0.0     0.0012   18.7   0.0    1.4  1  MarR            MarR family
     0.0018   18.1   0.1     0.0055   16.6   0.0    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0039   16.9   0.1      0.016   15.0   0.0    2.1  3  HTH_23          Homeodomain-like domain
     0.0093   16.1   0.0      0.056   13.7   0.0    2.1  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.041   13.6   0.0    1.7  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.068   13.0   0.0       0.17   11.7   0.0    1.6  1  HTH_38          Helix-turn-helix domain
      0.086   12.4   0.0       0.18   11.4   0.0    1.5  1  GerE            Bacterial regulatory proteins, luxR family
       0.11   12.6   0.0       0.41   10.8   0.0    2.0  2  EF1_GNE         EF-1 guanine nucleotide exchange domain
       0.13   12.3   0.0       0.37   10.8   0.0    1.8  1  HTH_29          Winged helix-turn helix
       0.14   12.6   0.1        1.1    9.7   0.0    2.3  3  HTH_40          Helix-turn-helix domain
       0.19   11.4   0.2       0.42   10.2   0.2    1.5  1  Syntaxin        Syntaxin


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.4   2.4e+03      47      66 ..      10      29 ..       9      40 .. 0.81
   2 !  110.8   0.0   3.8e-35   3.8e-32       9     127 ..     134     252 ..     127     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.4
                                      TTS--SHHHHHHHHHHHHHH CS
                              IclR 47 erTitdpeeLleeLakvReq 66
                                      + T+ +  +L++ L+ v+e+
  gi|313117074|ref|YP_004038198.1| 10 PDTVQSARTLFDVLQCVKED 29
                                      57999999999999999975 PP

  == domain 2  score: 110.8 bits;  conditional E-value: 3.8e-35
                                       TT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEE CS
                              IclR   9 iGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciAap 85 
                                       +G+r+plya ++GKa+La l+e+el++++e++e+++lte+Titdp+ L++eLa++Re+Gy ++r+E+  g++++++ 
  gi|313117074|ref|YP_004038198.1| 134 LGSRIPLYAASAGKAILAELPEQELSEYIEQVEFEQLTENTITDPAVLRDELAEIRERGYGFNRQETVRGTHAVGVA 210
                                       7**************************************************************************** PP

                                       EE-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  86 ifdasgevvaAvsvsgptarlteeelkeellalvreaArkis 127
                                       +   +g  ++++sv+gp+ rl+ +++++ l +l+  aA++++
  gi|313117074|ref|YP_004038198.1| 211 VTAPEGGAIGGLSVTGPSHRLKGDQFENVLPNLLLGAANELE 252
                                       ****************************99999999999986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0     3e-13     3e-10       6      48 ..      20      61 ..      16      65 .. 0.96
   2 ?   -1.8   0.0       2.8   2.8e+03      20      29 ..      94     103 ..      92     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 3e-13
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      +++L+++ e ++  t+se+++ +  ++StvhR+L+tL+ lGy+
  gi|313117074|ref|YP_004038198.1| 20 FDVLQCVKEDQGK-TVSEVSDDLEYARSTVHRHLRTLEDLGYL 61
                                      89**********9.****************************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.8
                                       BHHHHHHHHT CS
                          HTH_IclR  20 tlselArrtg 29 
                                       ++ e+A+ tg
  gi|313117074|ref|YP_004038198.1|  94 KVEEIAETTG 103
                                       688****998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.3e-10   2.2e-07       3      47 ..      17      61 ..      16      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.3e-10
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +t +++L++++++ + + +e+++ l   +stv+r+l+ Le+ G++
  gi|313117074|ref|YP_004038198.1| 17 RTLFDVLQCVKEDQGKTVSEVSDDLEYARSTVHRHLRTLEDLGYL 61
                                      57899**************************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   9.7e-10   9.7e-07      12      45 ..      27      61 ..      21      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.7e-10
                                      TT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5 12 ae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                       e + ++v+e +++l+  +stv +HL+ L+++G++
  gi|313117074|ref|YP_004038198.1| 27 KEdQGKTVSEVSDDLEYARSTVHRHLRTLEDLGYL 61
                                      563559***************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.8e-09   2.8e-06      13      58 ..      20      65 ..      15      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.8e-09
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                       ++l+  ++++g t+se+ + l+ +++t+++HLr+Le+ g++  + 
  gi|313117074|ref|YP_004038198.1| 20 FDVLQCVKEDQGKTVSEVSDDLEYARSTVHRHLRTLEDLGYLIHRP 65
                                      5788899*******************************99986665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.2e-07   0.00052      14      56 ..      26      66 ..      12      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.2e-07
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +    g + tv+e+ + l + +s+v+r+l+ L++ G++  rp+
  gi|313117074|ref|YP_004038198.1| 26 VKEDQG-K-TVSEVSDDLEYARSTVHRHLRTLEDLGYLIHRPD 66
                                      333444.3.*****************************99987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.6e-07   0.00086       2      46 ..      19      62 ..      18      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.6e-07
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      l+++l++++e +g  + +e ++ L+  r+tv+r++++Le+lg+ I
  gi|313117074|ref|YP_004038198.1| 19 LFDVLQCVKEDQG-KTVSEVSDDLEYARSTVHRHLRTLEDLGYLI 62
                                      6799****88888.5***************************877 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.2e-06    0.0012       4      47 ..      18      61 ..      16      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      t f++L +++e ++ +vse  + l+  +stv r l++Le+ G++
  gi|313117074|ref|YP_004038198.1| 18 TLFDVLQCVKEDQGKTVSEVSDDLEYARSTVHRHLRTLEDLGYL 61
                                      789***************************************87 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.5e-06    0.0055      19      59 ..      28      68 ..      16      71 .. 0.86
   2 ?   -3.3   0.1       8.9   8.8e+03       8      28 ..     155     175 ..     152     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.5e-06
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                      + + +t++e++ +l+  rs+v + Lr Led G+   ++  +
  gi|313117074|ref|YP_004038198.1| 28 EDQGKTVSEVSDDLEYARSTVHRHLRTLEDLGYLIHRPDGY 68
                                      56789***************************988776655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.9
                                       HHCCCHCHHHHHHCCCHHCHH CS
                              TrmB   8 eyEakvYlaLlklgpatadei 28 
                                       e E + Y+  ++ +++t ++i
  gi|313117074|ref|YP_004038198.1| 155 EQELSEYIEQVEFEQLTENTI 175
                                       677777887788888887776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.6e-05     0.016      10      41 ..      22      55 ..      14      60 .. 0.84
   2 ?   -3.1   0.0       7.8   7.7e+03      19      27 ..      94     102 ..      90     103 .. 0.75
   3 ?   -2.6   0.0       5.6   5.5e+03       5      16 ..     111     122 ..     110     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrwlkry 41
                                      +l+ ++e  G++v+e+++ L   r+Tv r l++ 
  gi|313117074|ref|YP_004038198.1| 22 VLQCVKEdqGKTVSEVSDDLEYARSTVHRHLRTL 55
                                      677777677********************99984 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.8
                            HTH_23  19 svreIAreL 27 
                                        v+eIA+  
  gi|313117074|ref|YP_004038198.1|  94 KVEEIAETT 102
                                       689999975 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.6
                            HTH_23   5 reRlrillllae 16 
                                       +e++++++l++ 
  gi|313117074|ref|YP_004038198.1| 111 EEHAEAVYLARS 122
                                       689999999986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.6e-05     0.056      24      57 ..      33      66 ..      20      68 .. 0.89
   2 ?   -0.8   0.0       1.9   1.9e+03      10      54 ..     114     161 ..     110     164 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                      ++++++  L+ + s+V   l+ Le+ Gy+++ ++
  gi|313117074|ref|YP_004038198.1| 33 TVSEVSDDLEYARSTVHRHLRTLEDLGYLIHRPD 66
                                      6899***************************997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                                       HHHHHHHHH..HHSSB-HHHHHHHHTS-HHHHHHH.HHHHHHTTSEEE CS
                    Fe_dep_repress  10 LetIYtlse..ekkvvktkdlaerLnvspssVsem.lkkLekdGyvey 54 
                                        e++Y +    e++v +   l +r+   ++s+ +  l +L ++++ ey
  gi|313117074|ref|YP_004038198.1| 114 AEAVYLARSvgEHAVQTDPGLGSRIPLYAASAGKAiLAELPEQELSEY 161
                                       577777766545555555667777777788887752577777777766 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.1e-05     0.041       6      46 ..      23      64 ..      21      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                          HTH_DeoR  6 lellkqqgklsveelvellgvSeaTiRRDLneLeeqgl.ltR 46
                                      l+ +k+++  +v e+++ l+++  T+ R L++Le  g  ++R
  gi|313117074|ref|YP_004038198.1| 23 LQCVKEDQGKTVSEVSDDLEYARSTVHRHLRTLEDLGYlIHR 64
                                      7899999999**************************994554 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.17      19      42 ..      30      53 ..      28      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            HTH_38 19 eGlslreIArrLgrspsTIsRElk 42
                                      +G++++e+   L +++sT++R+l+
  gi|313117074|ref|YP_004038198.1| 30 QGKTVSEVSDDLEYARSTVHRHLR 53
                                      8*********************98 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.18      16      40 ..      30      54 ..      20      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                      TTS-HHHHHHHHTS-HHHHHHHHHH CS
                              GerE 16 eGksnkeIAeelniSekTVkvhksn 40
                                      +Gk++ e++++l+ +  TV+ h++ 
  gi|313117074|ref|YP_004038198.1| 30 QGKTVSEVSDDLEYARSTVHRHLRT 54
                                      7*********************985 PP

>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         5     5e+03      50      69 ..      23      42 ..      22      50 .. 0.79
   2 ?   10.8   0.0   0.00042      0.41      43      86 ..      70     169 ..      48     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5
                                      EEEEESSS-GGGGHHHHHHT CS
                           EF1_GNE 50 iscvieddkvstdeleekie 69
                                      ++cv ed+   + e+ + +e
  gi|313117074|ref|YP_004038198.1| 23 LQCVKEDQGKTVSEVSDDLE 42
                                      57899998888888888776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00042
                                       SS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.............................................. CS
                           EF1_GNE  43 fGlkkLqiscvieddkvstdeleekieeieg.............................................. 73 
                                        Glk L + +   d+ v+ d + ek+eei +                                              
  gi|313117074|ref|YP_004038198.1|  70 VGLKFLDLGVSARDNYVGYDLIREKVEEIAEttgercqffveehaeavylarsvgehavqtdpglgsriplyaasag 146
                                       59**************************9998888888888888888888888888888888888888888888888 PP

                                       ...............SEEEEEEE CS
                           EF1_GNE  74 ..........eledlVqsveivs 86 
                                                 el++++++ve ++
  gi|313117074|ref|YP_004038198.1| 147 kailaelpeqELSEYIEQVEFEQ 169
                                       88888888755888888887665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00037      0.37       9      40 ..      29      59 ..      22      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                            HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegG 40
                                      ++G  tvs++   l + r+tv r+l+  e  G
  gi|313117074|ref|YP_004038198.1| 29 DQGK-TVSEVSDDLEYARSTVHRHLRTLEDLG 59
                                      5565.9*******************9988877 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0011       1.1      11      37 ..      30      56 ..      24      78 .. 0.90
   2 ?   -2.8   0.0       8.9   8.9e+03      14      20 ..      94     100 ..      79     109 .. 0.67
   3 ?   -0.4   0.0       1.6   1.6e+03      57      69 ..     158     170 ..     143     193 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                            HTH_40 11 eglsieeIAkerglkesTIegHLaeli 37
                                      +g+++ e+++  + ++sT+ +HL  l 
  gi|313117074|ref|YP_004038198.1| 30 QGKTVSEVSDDLEYARSTVHRHLRTLE 56
                                      8**********************7765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.9
                            HTH_40  14 sieeIAk 20 
                                       ++eeIA+
  gi|313117074|ref|YP_004038198.1|  94 KVEEIAE 100
                                       3445554 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.6
                            HTH_40  57 Ieeaiekvgsekl 69 
                                       + e+ie+v+ e+l
  gi|313117074|ref|YP_004038198.1| 158 LSEYIEQVEFEQL 170
                                       3333333332221 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00042      0.42     133     171 ..     153     191 ..     148     200 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                          Syntaxin 133 vseeeieelietgesevflqkllqeqrgarealseieeR 171
                                         e+e+ e ie+ e e+++++ +++  + r+ l+ei+eR
  gi|313117074|ref|YP_004038198.1| 153 LPEQELSEYIEQVEFEQLTENTITDPAVLRDELAEIRER 191
                                       568999********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2040.63
//
Query:       gi|313117075|ref|YP_004038199.1|  [L=410]
Description: hypothetical protein Hbor_35430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-12   47.0   0.1    3.8e-12   46.1   0.1    1.5  1  HTH_20    Helix-turn-helix domain
    2.2e-05   24.2   0.0    4.7e-05   23.2   0.0    1.6  1  MarR_2    MarR family
    0.00084   18.8   0.0     0.0016   18.0   0.0    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.03   14.2   0.0      0.051   13.4   0.0    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
      0.063   13.5   0.2      0.063   13.5   0.2    1.9  2  UPF0444   Transmembrane protein C12orf23, UPF0444


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.1   1.1e-15   3.8e-12       1      59 [.      24      81 ..      24      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.1e-15
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      d +++AL++++ r+il++L  + + t++ela++ ++s +++ yHL++Lee +L +vv++
  gi|313117075|ref|YP_004038199.1| 24 DAVFDALSSKTTRMILAEL-HRSPSTPTELADQTETSIQNAMYHLEKLEETDLARVVDT 81
                                      679****************.**********************************99976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.3e-08   4.7e-05       6      56 ..      34      81 ..      29      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.3e-08
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      + +++La+L+r+p    t++ela+ +  s +++ ++l++L++  L + ++ 
  gi|313117075|ref|YP_004038199.1| 34 TTRMILAELHRSPS---TPTELADQTETSIQNAMYHLEKLEETDLARVVDT 81
                                      6789*********6...****************************998865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.3e-07    0.0016       3      44 ..      33      73 ..      31      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-07
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeee 44
                                      +t+r IL +L + +  + +eLA+++  S+++  ++l++Lee 
  gi|313117075|ref|YP_004038199.1| 33 KTTRMILAELHR-SPSTPTELADQTETSIQNAMYHLEKLEET 73
                                      899*********.889************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.051       3      45 ..      34      76 ..      32      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      t + IL  L +++ + +ela++++ s  +  +HL kL+e +L 
  gi|313117075|ref|YP_004038199.1| 34 TTRMILAELHRSPSTPTELADQTETSIQNAMYHLEKLEETDLA 76
                                      5578999999*****************************9886 PP

>> UPF0444  Transmembrane protein C12orf23, UPF0444
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.8e-05     0.063      16      82 ..     111     179 ..     101     188 .. 0.73
   2 ?   -2.7   0.1       2.1   7.7e+03      48      65 ..     234     254 ..     206     271 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                           UPF0444  16 gGlfsvtkGavGatvgGvawvGgksLeltksavta...vpevGvglvkgsvsavagGvsa.vgsavaskvp 82 
                                        Glfs+ k  +Ga +g v+ + g+ L++t+s   a   +pe  v+   +s+ a ag +++ v s v++   
  gi|313117075|ref|YP_004038199.1| 111 DGLFSMFKRFLGA-IG-VIALIGVVLQATTSVLEAvqqIPEGQVASSPNSLVAFAGAITTlVVSYVSNDDS 179
                                       69*********98.56.66666788*****98888222455555555668999999998845666666554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                           UPF0444  48 vta..vpevGvglvkg.svsa 65 
                                        t+   +++Gv  v + +v +
  gi|313117075|ref|YP_004038199.1| 234 ETTgsEANAGVPDVSDeTVHV 254
                                       344334556665555434443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2856.87
//
Query:       gi|313117076|ref|YP_004038200.1|  [L=243]
Description: hypothetical protein Hbor_35440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1897.55
//
Query:       gi|313117077|ref|YP_004038201.1|  [L=192]
Description: MarR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-08   32.7   0.0    8.2e-08   32.1   0.0    1.3  1  MarR             MarR family
    1.7e-07   31.0   0.2    3.5e-07   30.0   0.2    1.5  1  MarR_2           MarR family
    7.4e-07   29.0   0.3    1.2e-06   28.3   0.3    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
      3e-06   26.9   0.2    4.9e-06   26.2   0.2    1.3  1  HTH_IclR         IclR helix-turn-helix domain
      2e-05   24.5   1.0      4e-05   23.5   1.1    1.5  1  Trp_oprn_chp     Tryptophan-associated transmembrane protein 
    2.9e-05   23.5   0.0    5.1e-05   22.7   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0004   20.4   0.2    0.00069   19.6   0.2    1.4  1  HTH_20           Helix-turn-helix domain
     0.0012   19.3   0.2     0.0032   17.9   0.2    1.6  1  HTH_27           Winged helix DNA-binding domain
     0.0014   18.8   0.1     0.0023   18.1   0.1    1.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0015   18.4   0.0     0.0027   17.5   0.0    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0029   17.2   0.3     0.0049   16.5   0.3    1.3  1  GntR             Bacterial regulatory proteins, gntR family
     0.0036   17.0   0.5     0.0074   16.0   0.1    1.7  2  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0078   16.2   0.2      0.013   15.5   0.2    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0095   15.4   1.1      0.016   14.6   1.1    1.3  1  SfLAP            Sap, sulfolipid-1-addressing protein
  ------ inclusion threshold ------
      0.011   15.6   0.2      0.028   14.4   0.1    1.6  2  HTH_11           HTH domain
      0.011   15.1   0.0      0.019   14.4   0.0    1.3  1  RepL             Firmicute plasmid replication protein (RepL)
      0.026   14.4   0.1      0.054   13.3   0.1    1.6  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.043   13.9   0.0      0.069   13.3   0.0    1.3  1  Trp_repressor    Trp repressor protein
      0.069   13.8   0.2       0.11   13.1   0.2    1.3  1  DUF2809          Protein of unknown function (DUF2809)
      0.075   13.4   0.3       0.19   12.1   0.3    1.7  1  Penicillinase_R  Penicillinase repressor
       0.16   12.0   2.5        4.1    7.5   0.0    2.9  3  DDE_Tnp_1_assoc  DDE_Tnp_1-associated


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   9.6e-11   8.2e-08      11      51 ..     142     182 ..     133     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.6e-11
                                       HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       +++  g+l + +L +   +sk+tv+r+ld+Le+++l+eR++
  gi|313117077|ref|YP_004038201.1| 142 LIEADGELPQRKLVEETDLSKATVSRTLDKLEHRELVERER 182
                                       6788899********************************87 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.2   4.1e-10   3.5e-07      14      55 ..     142     182 ..     137     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.1e-10
                                       HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       L  ++g+ l ++ l+++++lsk++vsr+l++L+ + Lver++
  gi|313117077|ref|YP_004038201.1| 142 LIEADGE-LPQRKLVEETDLSKATVSRTLDKLEHRELVERER 182
                                       5556664.9*******************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.3   1.4e-09   1.2e-06       6      56 ..     131     182 ..     130     189 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.4e-09
                                       HHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB   6 LseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                       L+ +E  vY+aL+ + g++  +++ ee+++++++v ++L +Le + lVere+
  gi|313117077|ref|YP_004038201.1| 131 LQNNEEVVYTALIeADGELPQRKLVEETDLSKATVSRTLDKLEHRELVERER 182
                                       6789999******999**********************************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   5.8e-09   4.9e-06      11      51 ..     141     181 ..     140     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.8e-09
                                       T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       al ea++el  + l ++t+l+k+tv+R L  L+++ +ve++
  gi|313117077|ref|YP_004038201.1| 141 ALIEADGELPQRKLVEETDLSKATVSRTLDKLEHRELVERE 181
                                       6889***********************************96 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   1.1   4.6e-08     4e-05      69     165 ..      11     119 ..       8     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.6e-08
                      Trp_oprn_chp  69 vvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaaveltawpvlalaggvllllagvllllrarswpa 145
                                       +v+++l +a++  +v a++l+t ++  +   +++a+++ +  +  ++ + ++++++++vl+ + g  l+l+ r+++ 
  gi|313117077|ref|YP_004038201.1|  11 LVAAVLFVASV--LVLAMQLITPSPIMVSMGDSSAQAT-QLGEYFTY-SDVAVVVVAAVLCGASGTYLVLHDRAQQL 83 
                                       46666666554..5667888888887777777553332.22223334.4567778999******************* PP

                      Trp_oprn_chp 146 mssrYerpaarraeaeae................ds 165
                                        + +++rp+ar++ a +                 +s
  gi|313117077|ref|YP_004038201.1|  84 VQPKHDRPDARSQPAVNGgvepsngvsdsdsgtwES 119
                                       ***********9988766899999988554444444 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     6e-08   5.1e-05      11      47 ..     142     178 ..     140     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6e-08
                            HTH_24  11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       l+++++ ++qr L e+++lS++tv+r l++Le  +l+
  gi|313117077|ref|YP_004038201.1| 142 LIEADGELPQRKLVEETDLSKATVSRTLDKLEHRELV 178
                                       6899***************************977776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   8.1e-07   0.00069      30      60 ..     154     184 ..     138     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.1e-07
                                       HHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  30 laerldlskntlsyHLrvLeeagLvevvreg 60 
                                       l e+ dlsk+t+s+ L++Le  +Lve++r+g
  gi|313117077|ref|YP_004038201.1| 154 LVEETDLSKATVSRTLDKLEHRELVERERVG 184
                                       456679***********************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   3.8e-06    0.0032       4      52 ..     135     182 ..     133     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.8e-06
                            HTH_27   4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52 
                                        ++++  li+  +++  ++ l++ ++++++++s  l+kL+ ++Lver++
  gi|313117077|ref|YP_004038201.1| 135 EEVVYTALIE-ADGELPQRKLVEETDLSKATVSRTLDKLEHRELVERER 182
                                       6777788888.999999****************************9875 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.7e-06    0.0023      11      55 ..     136     181 ..     127     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                                       HHHHHHH.HHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress  11 etIYtls.eekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55 
                                       e++Yt+  e  +   + +l e+ + s+++Vs +l kLe  ++ve e
  gi|313117077|ref|YP_004038201.1| 136 EVVYTALiEADGELPQRKLVEETDLSKATVSRTLDKLEHRELVERE 181
                                       67888641566666677899***********************965 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.2e-06    0.0027      14      46 ..     147     179 ..     140     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.2e-06
                                       SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  14 gelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       gel    l+ee++ls++tvS+ L kL+   LVe
  gi|313117077|ref|YP_004038201.1| 147 GELPQRKLVEETDLSKATVSRTLDKLEHRELVE 179
                                       7777788*********************99997 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   5.7e-06    0.0049      19      58 ..     144     182 ..     135     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.7e-06
                                       -TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR  19 rpGdkLPsereLaaefgVsrttvReALrrLeaeglverrq 58 
                                       ++   L ++r+L++e + s+ tv + L++Le + lver++
  gi|313117077|ref|YP_004038201.1| 144 EADGEL-PQRKLVEETDLSKATVSRTLDKLEHRELVERER 182
                                       667789.99****************************975 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.8   5.8e+03      18      29 ..      46      57 ..      42      59 .. 0.77
   2 !   16.0   0.1   8.7e-06    0.0074       8      48 ..     142     182 ..     140     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.8
                          HTH_DeoR 18 eelvellgvSea 29
                                      ++l e++ +S+ 
  gi|313117077|ref|YP_004038201.1| 46 TQLGEYFTYSDV 57
                                      688899999986 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.7e-06
                          HTH_DeoR   8 llkqqgklsveelvellgvSeaTiRRDLneLeeqglltRth 48 
                                       l++ +g l   +lve+ + S+aT+ R L++Le+  l++R +
  gi|313117077|ref|YP_004038201.1| 142 LIEADGELPQRKLVEETDLSKATVSRTLDKLEHRELVERER 182
                                       677788888899*************************9976 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.5e-05     0.013      23      65 ..     150     191 ..     128     192 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHH CS
                         HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkreglisrgrririldleaL 65 
                                        q+ l +   l+  tvsr+l +L+ + l++r+r + i +  +L
  gi|313117077|ref|YP_004038201.1| 150 PQRKLVEETDLSKATVSRTLDKLEHRELVERER-VGIGNTVRL 191
                                       5666667778999*****************987.877666555 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.1   1.9e-05     0.016     111     195 ..      12      97 ..       3     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                             SfLAP 111 eggalwvAlvlgllsakplllylaalaaigasgasvgtqvvalvvFvvvalavveiplla....ylvapertqavle 183
                                        +++l vA vl+l++   l+    +++ +g s a+ +tq++  + ++ va+ vv++ l +    ylv ++r+q++++
  gi|313117077|ref|YP_004038201.1|  12 VAAVLFVASVLVLAM--QLITPSPIMVSMGDSSAQ-ATQLGEYFTYSDVAVVVVAAVLCGasgtYLVLHDRAQQLVQ 85 
                                       344555666665555..344444566777777777.99********999999988888643444************* PP

                             SfLAP 184 rlkdwlrsnrrl 195
                                       + +d  +++++ 
  gi|313117077|ref|YP_004038201.1|  86 PKHDRPDARSQP 97 
                                       ***998888876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.6   6.5e+03      17      32 ..      44      59 ..      40      60 .. 0.80
   2 ?   14.4   0.1   3.2e-05     0.028       6      40 ..     139     173 ..     134     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.6
                            HTH_11 17 sgeeLAeeLnvSrrtv 32
                                       + +L e++  S  +v
  gi|313117077|ref|YP_004038201.1| 44 QATQLGEYFTYSDVAV 59
                                      5789999998888887 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.2e-05
                            HTH_11   6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLe 40 
                                       ++ L+ea+g ++  +L ee+++S++tv r +++Le
  gi|313117077|ref|YP_004038201.1| 139 YTALIEADGELPQRKLVEETDLSKATVSRTLDKLE 173
                                       56799****************************97 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.3e-05     0.019      78     111 ..     151     184 ..     143     187 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                              RepL  78 nRelaeetgislktvsetlkileeanilkkkanG 111
                                       +R+l eet++s +tvs+tl  le+ +++ ++  G
  gi|313117077|ref|YP_004038201.1| 151 QRKLVEETDLSKATVSRTLDKLEHRELVERERVG 184
                                       8**************************9998877 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.3e-05     0.054      11      42 .]     142     173 ..     141     173 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                     HTH_AsnC-type  11 aLqedaRisyaeLAervGlSestvlrRvrrLe 42 
                                       ++++d+ ++ ++L e++ lS +tv r +++Le
  gi|313117077|ref|YP_004038201.1| 142 LIEADGELPQRKLVEETDLSKATVSRTLDKLE 173
                                       6789***************************8 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.1e-05     0.069      47      76 ..     146     175 ..     122     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.1e-05
                     Trp_repressor  47 keelsqreIaeelgvSiAtItRvsrsLktg 76 
                                       ++el+qr++ ee++ S At++R   +L+++
  gi|313117077|ref|YP_004038201.1| 146 DGELPQRKLVEETDLSKATVSRTLDKLEHR 175
                                       589********************9999876 PP

>> DUF2809  Protein of unknown function (DUF2809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   0.00013      0.11      31      80 ..       8      58 ..       2      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                           DUF2809 31 splllalavllfavliEllQltql.pallglrattlgrlvLGstfdwsDll 80
                                      +++l+a++ ++++vl+ ++Ql+ + p + +++++++ ++ LG+ f+ sD++
  gi|313117077|ref|YP_004038201.1|  8 NTHLVAAVLFVASVLVLAMQLITPsPIMVSMGDSSAQATQLGEYFTYSDVA 58
                                      567789**************987538899********************97 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00022      0.19      25      57 ..     152     184 ..     133     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                       HT--GGG---HHHHHHHHHHHHHTTS-EEEEET CS
                   Penicillinase_R  25 eeleeekelaysTVktllrrLvkKgllsrekeg 57 
                                        +l ee++l+++TV  +l +L+ ++l++re+ g
  gi|313117077|ref|YP_004038201.1| 152 RKLVEETDLSKATVSRTLDKLEHRELVERERVG 184
                                       4688899***********************986 PP

>> DDE_Tnp_1_assoc  DDE_Tnp_1-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       3.9   3.3e+03      16      33 ..       8      25 ..       4      27 .. 0.78
   2 ?    7.5   0.0    0.0048       4.1      19      39 ..      53      73 ..      46      86 .. 0.85
   3 ?    3.6   0.0      0.08        69      34      75 ..     120     172 ..     117     180 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.9
                   DDE_Tnp_1_assoc 16 krhpladiLlialcavia 33
                                       +h +a +L++a + v+a
  gi|313117077|ref|YP_004038201.1|  8 NTHLVAAVLFVASVLVLA 25
                                      578899999999888876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0048
                   DDE_Tnp_1_assoc 19 pladiLlialcaviagadswe 39
                                        +d+ +++++av++ga++ +
  gi|313117077|ref|YP_004038201.1| 53 TYSDVAVVVVAAVLCGASGTY 73
                                      5689*************9865 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.08
                   DDE_Tnp_1_assoc  34 gadsweeieefakekeewlrefleleng...........iPshdtirrvlsri 75 
                                        +++we+ +e  +++ee + + l   +g             s++t++r l ++
  gi|313117077|ref|YP_004038201.1| 120 HHERWEATAERLQNNEEVVYTALIEADGelpqrklveetDLSKATVSRTLDKL 172
                                       57899999999999999999999444444334444444445555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1442.95
//
Query:       gi|313117078|ref|YP_004038202.1|  [L=210]
Description: hypothetical protein Hbor_35460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1705.46
//
Query:       gi|313117079|ref|YP_004038203.1|  [L=654]
Description: 3-hydroxyacyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-62  209.6   0.0    5.6e-62  208.8   0.0    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
    1.2e-54  185.2   0.0    1.8e-54  184.7   0.0    1.2  1  ECH_1          Enoyl-CoA hydratase/isomerase
    9.4e-45  151.2   0.4    8.7e-22   77.6   0.0    2.9  3  3HCDH          3-hydroxyacyl-CoA dehydrogenase, C-terminal do
    6.7e-31  108.0   0.0      5e-27   95.3   0.0    2.5  3  ECH_2          Enoyl-CoA hydratase/isomerase
     0.0061   16.8   0.1      0.017   15.3   0.1    1.7  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
       0.15   11.3   0.3       0.24   10.7   0.3    1.3  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.8   0.0   1.9e-65   5.6e-62       1     179 [.       8     187 ..       8     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.8 bits;  conditional E-value: 1.9e-65
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77 
                                       +v v+GaG mG+gi++v+a ag++V++ d++e+ ++++ e i+ slekl+ek +l+ e+v+++l ri ++ +le av
  gi|313117079|ref|YP_004038203.1|   8 QVSVLGAGNMGHGITEVAAIAGYDVTMRDVEEDLVADGYEDIKWSLEKLAEKDHLD-ESVDEVLGRIDTAVELEPAV 83 
                                       699****************************************************9.9******************* PP

                                       .C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-T CS
                           3HCDH_N  78 .dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrge 153
                                        dadlviEa++E+++lK+++f +l++ a++da+lasnTSslsi+e+a+a++rpe v+g+HFfnPp +m+LvEv+ ge
  gi|313117079|ref|YP_004038203.1|  84 aDADLVIEAAPERMDLKKDIFGDLDAFAPDDALLASNTSSLSITEMATATSRPEDVVGMHFFNPPVKMNLVEVIYGE 160
                                       ***************************************************************************** PP

                                       T--HHHHHHHHHHHHHTT-EEEEE.CS CS
                           3HCDH_N 154 kTseetvatvvelakkigktpvvv.kd 179
                                       +Ts+et ++++e++++++ktp+ v kd
  gi|313117079|ref|YP_004038203.1| 161 ETSDETAEAAYEFVESLDKTPIYVrKD 187
                                       ************************777 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.7   0.0   6.2e-58   1.8e-54       3     250 ..     410     653 ..     409     654 .] 0.96

  Alignments for each domain:
  == domain 1  score: 184.7 bits;  conditional E-value: 6.2e-58
                                       ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHCHHHHHHHCCHH CS
                             ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeekakqallkeevl 78 
                                       e+g++++ l+rPe +Nals  ll E+ + l  ++ d  vr v  +G gd+aF+aGad+   a   + +       v 
  gi|313117079|ref|YP_004038203.1| 410 ENGLLEVELDRPERMNALSMSLLGEIDALLSSVNSD-DVRCVTFEGaGDRAFSAGADIGGFADLTPTD----AMDVT 481
                                       6899*********************99999999999.**************************85443....45677 PP

                                       HHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHH CS
                             ECH_1  79 elwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilll 155
                                         ++ + + + p+ia + G+++g+GlelalacD+++a  na+fg +e+ lGlipg ggtq+l r +G+ +A+e++  
  gi|313117079|ref|YP_004038203.1| 482 PAFETVNDFERPTIAKIDGYCLGAGLELALACDLRVATANAKFGSPEIGLGLIPGGGGTQRLLRVLGETRAKELVFR 558
                                       88899************************************************************************ PP

                                       T-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHH CS
                             ECH_1 156 gkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskdd 232
                                       g++i a+ a+++Gl++++vp++++ ++    +  ++e +p  l+ +k+ ln+ ++  l+++l++e++ f  ++ ++d
  gi|313117079|ref|YP_004038203.1| 559 GNRIDAERAEEWGLINRAVPAKEFDDTVSDFVDDIVEGPPIGLKVAKKVLNQGADASLEAALTMESQGFGLLMGTED 635
                                       ***************************************************************************** PP

                                       HHHHHHHHHTCSH----- CS
                             ECH_1 233 ikeGlqaflEkrkpefed 250
                                       ++eG +af   r+pef++
  gi|313117079|ref|YP_004038203.1| 636 VREGTTAFRDDRDPEFRG 653
                                       ***************986 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.1   9.4e+03      41      85 ..      19      61 ..      11      67 .. 0.54
   2 !   77.6   0.0   2.9e-25   8.7e-22       1      97 []     190     279 ..     190     279 .. 0.94
   3 !   70.7   0.0   3.9e-23   1.2e-19       5      97 .]     298     390 ..     295     390 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                                      SCHHHHHHHHHHHHH.HHHHH.HHHHHTTTHGGHH-HHHHHHHHTT- CS
                             3HCDH 41 mGpfelldlvgldva.kkile.vlaeelgerayapsplleklveagr 85
                                       G+ e++  +g dv  +++ e  +a+++++ ++     lekl+e+++
  gi|313117079|ref|YP_004038203.1| 19 HGITEVAAIAGYDVTmRDVEEdLVADGYEDIKWS----LEKLAEKDH 61
                                      5777777777777640334442233333333333....555555555 PP

  == domain 2  score: 77.6 bits;  conditional E-value: 2.9e-25
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GFvvn vl+p+++e  ++v ++ a++++ Daam  + G+pmGpfel+dl g+dv+++++     e g +    +p++
  gi|313117079|ref|YP_004038203.1| 190 GFVVNTVLGPFIDEPAWMVSNEEATIREADAAMVHRRGYPMGPFELVDLSGIDVGYHVRT----EAGRP---IPPIM 259
                                       9**********************************************************5....33344...358** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       ++ vea++lgrktg+g+y+y
  gi|313117079|ref|YP_004038203.1| 260 KEKVEADELGRKTGRGYYDY 279
                                       ******************98 PP

  == domain 3  score: 70.7 bits;  conditional E-value: 3.9e-23
                                       HHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHH CS
                             3HCDH   5 nRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklv 81 
                                        Rv a+++nea rlv + va+pe+iD+ +rlglG+p G+ +  d++gldv+++ l+ l+e++++++++p + l +lv
  gi|313117079|ref|YP_004038203.1| 298 LRVEARMVNEAARLVGDDVATPEEIDTGVRLGLGFPEGICRRGDEIGLDVVLDKLRSLHEKTEQDRFEPDDYLVELV 374
                                       6999************************************************************************* PP

                                       HTT--BGGGTBSSSBC CS
                             3HCDH  82 eagrlgrktgkgfyky 97 
                                       e+gr g+ +g+gf +y
  gi|313117079|ref|YP_004038203.1| 375 EQGRTGEDAGAGFHDY 390
                                       *************998 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.6   4.8e+03     179     207 ..      48      78 ..      18     122 .. 0.59
   2 !   95.3   0.0   1.7e-30     5e-27       4     182 ..     416     587 ..     413     593 .. 0.91
   3 !   11.0   0.0   7.4e-05      0.22     251     312 ..     588     648 ..     583     653 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.6
                                       HHHHHHHTT..........--------.... CS
                             ECH_2 179 aleeaLaelessd..eeaveevleelaeeae 207
                                       +++ +L++l ++d  +e+v+evl ++ +++e
  gi|313117079|ref|YP_004038203.1|  48 DIKWSLEKLAEKDhlDESVDEVLGRIDTAVE 78 
                                       3333333333333345566666666554444 PP

  == domain 2  score: 95.3 bits;  conditional E-value: 1.7e-30
                                       EEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHH CS
                             ECH_2   4 itLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYkln 80 
                                       ++L+rp+ +NaLs++++ ++++ l++++ +d+v++v+ +gag++af+AG D+  +++   +++ +    ++      
  gi|313117079|ref|YP_004038203.1| 416 VELDRPERMNALSMSLLGEIDALLSSVN-SDDVRCVTFEGAGDRAFSAGADIGGFADLTPTDAMD----VTPA---F 484
                                       79***********************985.667**************************9998766....3333...3 PP

                                       HHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTH.HHHHHHH--- CS
                             ECH_2  81 yliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgel.GlylalTGar 156
                                        +++++++p++a +dG+++G G+ l++ + +rv+t +++f  PE+++Gl+P  Gg+  L r+ ge+ ++ l   G+r
  gi|313117079|ref|YP_004038203.1| 485 ETVNDFERPTIAKIDGYCLGAGLELALACDLRVATANAKFGSPEIGLGLIPGGGGTQRLLRVLGETrAKELVFRGNR 561
                                       57899********************************************************97755499******** PP

                                       B-HHHHHHTTS--EE--GGGHHHHHH CS
                             ECH_2 157 lkgadalaaglathyvpseklealee 182
                                       ++++ a + gl +  vp++++++  +
  gi|313117079|ref|YP_004038203.1| 562 IDAERAEEWGLINRAVPAKEFDDTVS 587
                                       *******************9998765 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-- CS
                             ECH_2 251 ktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkd 312
                                       + ++ + +  P+ lkv+ + l++g+++s l+ +l+mE +    l+ ++D+ eG +a   d+d
  gi|313117079|ref|YP_004038203.1| 588 DFVDDIVEGPPIGLKVAKKVLNQGADAS-LEAALTMESQGFGLLMGTEDVREGTTAFRDDRD 648
                                       5667788899*****************5.************************999754443 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   5.7e-06     0.017       2     103 ..       9     133 ..       8     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.7e-06
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......................EEE-SSHHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......................akaaesieelvas 55 
                                       + ++G G+MG+ + +  + agy+v++ +++++ v +  ++                        +++a ++e +va+
  gi|313117079|ref|YP_004038203.1|   9 VSVLGAGNMGHGITEVAAIAGYDVTMRDVEEDLVADGYEDIkwsleklaekdhldesvdevlgrIDTAVELEPAVAD 85 
                                       789***************************87777766665678888888889999999999999999999999999 PP

                                       CSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHHH CS
                     NAD_binding_2  56 ldvvitmvkagkavdeviegllealkkgdilidgstsspedtrelake 103
                                       +d+vi   ++  + ++ i+g l+a++++d l+ + tss + t+  ++ 
  gi|313117079|ref|YP_004038203.1|  86 ADLVIEAAPERMDLKKDIFGDLDAFAPDDALLASNTSSLSITEMATAT 133
                                       9****9999999999999999999999999999999888877665554 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3     8e-05      0.24      27      99 ..       5      93 ..       1      94 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8e-05
                                      ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH.HHHTTTCECEE................HCHHHHHHHHH CS
                       AlaDh_PNT_C 27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparleq.leslgakfvev................lksqeellaea 88
                                      + ++v v+G+G  G    ++a+  g +Vt+ Dv+++      e+++ + +e                 +  ++ +l+ a
  gi|313117079|ref|YP_004038203.1|  5 NIGQVSVLGAGNMGHGITEVAAIAGYDVTMRDVEEDLVADgYEDIKWS-LEKlaekdhldesvdevlgRIDTAVELEPA 82
                                      5689******************************99765515556665.444577899999999999999999999999 PP

                                      HHH-SEEEE-- CS
                       AlaDh_PNT_C 89 vkeadvvigtv 99
                                      v++ad+vi ++
  gi|313117079|ref|YP_004038203.1| 83 VADADLVIEAA 93
                                      99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3920.93
//
Query:       gi|313117080|ref|YP_004038204.1|  [L=143]
Description: sterol carrier protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-07   32.3   0.0    1.2e-07   32.1   0.0    1.2  1  SCP2      SCP-2 sterol transfer family
  ------ inclusion threshold ------
       0.86   10.1   5.2        4.2    7.9   0.2    2.4  2  CBM_10    Cellulose or protein binding domain


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.4e-11   1.2e-07      24      99 ..      41     126 ..      16     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.4e-11
                                       EEEEECTC.T......EEEEEETTSTEEE....SSCTTBS-SEEEEEEHHHHHHHHCTSS-HHHHHHTTSSEEEC-H CS
                              SCP2  24 lrfdltdlkg......sltldlkegqldv....aakdegkadvtlslsledllelaegklnpqkafmqgkLkieGDi 90 
                                       + f+l++ ++      ++++ l +g ++      ++d+++  +  ++ +ed+++l++g ++p + +m+g  +++GD+
  gi|313117080|ref|YP_004038204.1|  41 FLFELQPDETyegdpiHFFVGLEDGDCTEsyvvDDPDKEDWGFAYRGEYEDWKQLMQGDIDPVEGMMDGTFDLDGDM 117
                                       667777776677776677777776544335653455548888*********************************** PP

                                       HHHHHHHHH CS
                              SCP2  91 elaqkleal 99 
                                       +++++++++
  gi|313117080|ref|YP_004038204.1| 118 QKVMQYSQA 126
                                       ******986 PP

>> CBM_10  Cellulose or protein binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2   0.00047       4.2      17      28 ..      24      35 ..      12      40 .. 0.89
   2 ?    4.0   0.8    0.0079        71      12      28 ..      67      83 ..      66      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00047
                                      .SEEETTEEEEE CS
                            CBM_10 17 vvytDddggWGv 28
                                       +y+D++ gWGv
  gi|313117080|ref|YP_004038204.1| 24 KEYSDTGEGWGV 35
                                      58*********9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0079
                                      -STS..SEEETTEEEEE CS
                            CBM_10 12 CsnckvvytDddggWGv 28
                                      C+   vv ++d  +WG+
  gi|313117080|ref|YP_004038204.1| 67 CTESYVVDDPDKEDWGF 83
                                      88888999********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1087.31
//
Query:       gi|313117081|ref|YP_004038205.1|  [L=355]
Description: Zn-dependent alcohol dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-25   89.1   0.1    3.5e-25   88.0   0.1    1.6  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    1.2e-24   86.7   0.0    1.8e-24   86.1   0.0    1.3  1  ADH_zinc_N       Zinc-binding dehydrogenase
    9.5e-05   23.5   0.0    0.00022   22.3   0.0    1.6  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
     0.0001   21.7   0.6    0.00015   21.1   0.6    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0011   18.5   0.5     0.0017   17.9   0.5    1.2  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
  ------ inclusion threshold ------
       0.02   15.1   0.3      0.033   14.4   0.3    1.3  1  TrkA_N           TrkA-N domain
      0.054   13.1   0.2      0.083   12.5   0.2    1.2  1  Urocanase        Urocanase Rossmann-like domain
      0.091   12.1   0.1       0.14   11.5   0.1    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.13   13.0   0.1       0.24   12.1   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
       0.14   12.2   0.0       0.23   11.4   0.0    1.2  1  SIS_2            SIS domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.1     2e-28   3.5e-25       2     108 ..      26     139 ..      25     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 2e-28
                                       TEEEEEEEEEEE-HHHHHHHTTS...TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHT CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkgg...kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCke 75 
                                       + v+++++a+giC+sD h ++g+     +  +++li+GHE vG ++evg++v++++ G++V+ +++ s+g+C++C+ 
  gi|313117081|ref|YP_004038205.1|  26 NGVVVETEACGICRSDWHAWQGDwewLGIIPQPGLIFGHEPVGRIVEVGENVTRFSEGEMVTNPFNLSDGTCPYCRA 102
                                       679*******************954323345556******************************************* PP

                                       T-GGG-TTBEETTTS..S-SSSBSEEEEC..GGGEEE CS
                             ADH_N  76 geenlCeeakllgvs..ldGgfaeyvvvp..ekklvk 108
                                       g+ n+Ce+   +g+   ++G+fae + v+  +++l+k
  gi|313117081|ref|YP_004038205.1| 103 GRGNICESSIPMGFVhfQKGAFAEEYSVRnaDQNLIK 139
                                       ********9999999999******9999866666666 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.0     1e-27   1.8e-24       1     128 [.     182     314 ..     182     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 1e-27
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTT.TSSEEEEEESSCSHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltg.gegvdvvfecvGsgatleaa 75 
                                       gvGl av  A alG +via+d+ eekle+a++lGa e+in++e  d+ +++k++t+ g+gv v++e++G+ +t++++
  gi|313117081|ref|YP_004038205.1| 182 GVGLSAVHTATALGGNVIAIDIVEEKLEFARDLGAVETINSTEVdDIPQAVKSITDgGRGVSVSVEALGISQTIKDS 258
                                       9******************************************************77******************** PP

                                       HHCEEEEEEEEECSC...TSSEEE....EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  76 lkllkpgGrlvvvGg...gkgeee....fdlrnlllkeksilGsllgslreefkealdll 128
                                       +++l+pgG+   vG+       e     +++  ++  e+ ++G+ +   ++e+ + ++++
  gi|313117081|ref|YP_004038205.1| 259 VNCLAPGGQHLQVGLttsE---EGgevsLPIDFMVQDEREFYGTYGMP-PHEYDDIFRMM 314
                                       ***************7642...2234579999999*********9999.99998877765 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.2e-07   0.00022       1     124 [.     214     343 ..     214     348 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-07
                                       TT-SEEEETT.STTHH.....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT CS
                      ADH_zinc_N_2   1 lGAdevidyr.tedfe.....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkg 70 
                                       lGA e i+++  +d+         gg+gv+v ++++g  +++++s+++l++gG+ +++g  +         +++ ++
  gi|313117081|ref|YP_004038205.1| 214 LGAVETINSTeVDDIPqavksITDGGRGVSVSVEALGISQTIKDSVNCLAPGGQHLQVGlTT---------SEEGGE 281
                                       799999999955555588875333469**********66677*******888***9999332.........221233 PP

                                       -EEEE--GGG...-.........-HHHHHHHHHHHHHHH---..-EEEEEEGGGHHHHHHHHHS CS
                      ADH_zinc_N_2  71 rsvkyeflfsmkas........aqadileelaalieeGklrp..vvdrvfpleeaaeAhryles 124
                                        s+ + f+++  ++         +++  +++++++++Gk+ p   v+++ +l +++  +++l +
  gi|313117081|ref|YP_004038205.1| 282 VSLPIDFMVQ-DERefygtygmPPHE-YDDIFRMMSSGKIDPgkIVSETCSLGDIPSVMERLGE 343
                                       4444444442.222455555644666.9************985568888888888888777765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.6   8.5e-08   0.00015      31      82 ..     175     224 ..     157     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.5e-08
                                       EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHH CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqe 82 
                                       v v G G +Gl+A++ta++lg +V ++D+ +++le  ++lga   e+++s+e
  gi|313117081|ref|YP_004038205.1| 175 VAVHGCGGVGLSAVHTATALGGNVIAIDIVEEKLEFARDLGAV--ETINSTE 224
                                       8899***********************************9986..5555443 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.5   9.3e-07    0.0017      34     136 ..     175     277 ..     159     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.3e-07
                       Glu_dehyd_C  34 alvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdlvvEaTGs 110
                                       + v G G +GL a+ + +a   ++  + +++ + +  + +  ve + +t vd   + v++i++  + + + vEa G 
  gi|313117081|ref|YP_004038205.1| 175 VAVHGCGGVGLSAVHTATALGGNVIAIDIVEEKLEFARDLGAVETINSTEVDDIPQAVKSITDGGRGVSVSVEALGI 251
                                       6899*******999888877777778889999999999999999999*****999********************** PP

                       Glu_dehyd_C 111 akhafeaiealapnGvaaLlGvpeds 136
                                       ++ + ++++ lap G    +G+++++
  gi|313117081|ref|YP_004038205.1| 252 SQTIKDSVNCLAPGGQHLQVGLTTSE 277
                                       ***************99999998765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   1.9e-05     0.033       1      46 [.     175     221 ..     175     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.SEEEE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.levvv 46 
                                       +++ G+G vG s +++ ++ gg +v++id  ee++e +r+ g +e+++
  gi|313117081|ref|YP_004038205.1| 175 VAVHGCGGVGLSAVHTATAlGG-NVIAIDIVEEKLEFARDLGaVETIN 221
                                       6899***************999.5***************999666665 PP

>> Urocanase  Urocanase Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   4.6e-05     0.083      26     101 ..     170     246 ..     154     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.6e-05
                                       -TT-EEEEE--STTGGGHHHHHHHTT-EEEEEES-HHHHHHHHHTTS-SEE.ES-HHHHHHHHHHHHHCT--EEEEE CS
                         Urocanase  26 lkgklvvtaGlGgMsgaQplAatiagavalvvevdesriekrleqgyvdev.addldealalikeakkekealsigl 101
                                        +g +v   G+Gg + +    at  g+ ++++++ e+++e   + g v+++  +++d++ + +k+ ++ ++ +s+++
  gi|313117081|ref|YP_004038205.1| 170 KAGDWVAVHGCGGVGLSAVHTATALGGNVIAIDIVEEKLEFARDLGAVETInSTEVDDIPQAVKSITDGGRGVSVSV 246
                                       4699********************************************99725689*************99999987 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.8e-05      0.14      36      76 ..     172     212 ..     162     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.8e-05
                                       TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHH CS
                      2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeee 76 
                                       g  v++ G+G +G ++ ++++a+g +via+d  ++k e ++
  gi|313117081|ref|YP_004038205.1| 172 GDWVAVHGCGGVGLSAVHTATALGGNVIAIDIVEEKLEFAR 212
                                       56699***************************988665344 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00013      0.24       5      45 ..     179     219 ..     175     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                       T-T.TSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTT CS
                   Methyltransf_25   5 GcG.tGrltlalakrlgkakvtgvDiseemleaareraeeeg 45 
                                       GcG  G  + + a++lg ++v+++Di ee le ar   + e 
  gi|313117081|ref|YP_004038205.1| 179 GCGgVGLSAVHTATALG-GNVIAIDIVEEKLEFARDLGAVET 219
                                       66516999999999998.*****************9875443 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.23      32      96 ..     169     236 ..     167     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                       HHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE--GGGSSSSST.....THHHHHTT-TTHHHHHH CS
                             SIS_2  32 lenggkvlvfGsGhSaalaeelaaragglaeferialpalalhtda...eatkssalerdegyakqil 96 
                                       +++g +v v G+G+  + a ++a+ +gg +    i++++l +  d    e+ +s++++ +++ +k+i 
  gi|313117081|ref|YP_004038205.1| 169 IKAGDWVAVHGCGGVGLSAVHTATALGGNVIAIDIVEEKLEFARDLgavETINSTEVDDIPQAVKSIT 236
                                       799***************************************99844589999999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 2144.39
//
Query:       gi|313117082|ref|YP_004038206.1|  [L=522]
Description: NAD-dependent aldehyde dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   6.3e-158  526.1   0.0   7.2e-158  525.9   0.0    1.0  1  Aldedh      Aldehyde dehydrogenase family
    0.00014   21.4   0.0     0.0051   16.3   0.0    2.2  2  DUF1487     Protein of unknown function (DUF1487)
     0.0028   17.9   1.8     0.0067   16.7   1.8    1.6  1  Invasin_D3  Invasin, domain 3
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.31   11.4   0.0    1.6  1  DUF5063     Domain of unknown function (DUF5063)
       0.14   12.5   1.8       0.27   11.5   1.8    1.5  1  DUF349      Domain of Unknown Function (DUF349)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.9   0.0    2e-161  7.2e-158       1     462 []      41     511 ..      41     511 .. 0.97

  Alignments for each domain:
  == domain 1  score: 525.9 bits;  conditional E-value: 2e-161
                                       EET-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH.HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHH CS
                            Aldedh   1 wveses.etievinPatgeviakvpaataedvdaavaaAkeafk.awaklpaeeRaeiLrkaadlleerkeelaele 75 
                                       wv+se+ ++   i+P+tge +a+++ +t++dvd+av+aA++af+ aw + ++++R+e L ++ad lee+k ela++e
  gi|313117082|ref|YP_004038206.1|  41 WVDSEGgGEGVAIDPTTGESLATFQVGTTADVDRAVKAARDAFEeAWGQHSPRQRGEKLDEIADRLEEKKAELAKIE 117
                                       899999777999********************************88******************************* PP

                                       HHHH---HHHHHH.HHHHHHHHHHHHHHHHHH.HSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHH CS
                            Aldedh  76 tletGkplaeara.eveeaidvlryyaelaek.legevlpssegklalvrrePlGvvgaItPWNfPlllaawklapa 150
                                       tle+Gkp  ++r  ++e  ++ +r +a+ a++  +g+v+p++++k+ +++reP+GvvgaI++WNfP++ ++wkl pa
  gi|313117082|ref|YP_004038206.1| 118 TLEAGKPNLHSRFvDIEILVEQFRHFAAVARTaDTGRVVPTDDEKHVVTKREPYGVVGAISAWNFPAMFVSWKLGPA 194
                                       ********************************6677*****99********************************** PP

                                       HHTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHC CS
                            Aldedh 151 laaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaak 227
                                       laaGN+vv+KP+++++l +l +a +++   lP g +nvvtgsgs vg+a+ +h+++dkv++tGs + g   ++ aa+
  gi|313117082|ref|YP_004038206.1| 195 LAAGNSVVFKPSSKAVLATLEIADICDT-VLPTGTVNVVTGSGSVVGDAISQHDGIDKVTLTGSKAAGVATLEGAAD 270
                                       ***************************9.7*********************************************** PP

                                       TTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTST CS
                            Aldedh 228 nlkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplde 304
                                       ++++v+lElGGk+p+iv++daDl++a+e+++ ++f+n+GQ C+a+srl+++e+i def+++l e++ +l vgdpl +
  gi|313117082|ref|YP_004038206.1| 271 TITPVSLELGGKSPNIVFPDADLEQAIEGTIVSIFFNSGQQCTAGSRLFLHEDIRDEFLDRLRERIDELVVGDPLSP 347
                                       ***************************************************************************** PP

                                       T-SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT......E.SB-SSST.TEE--EEEES-TTTSHHHHS---SSE CS
                            Aldedh 305 dtdvGPliseaqlekvekyveeakeegaklllGge......reeaglekg.yfvePtvlanvtpdmriaqeEiFGPV 374
                                       +td+GP+i+++++++v++y+++a+e+ga+ l+G +       e a++  g  fv+Ptvl++v++++++a++E+FGPV
  gi|313117082|ref|YP_004038206.1| 348 QTDIGPMIDHEHAREVKGYISRAIEDGARSLVGDDsdetdaGEPASETAGaPFVQPTVLTDVDDSAEVACDEVFGPV 424
                                       ********************************99877665534455566657************************* PP

                                       EEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHH CS
                            Aldedh 375 lsvikfkdeeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggke 451
                                       l+v++ ++ ee+++ aNdt++GLaagv+t+dle+a++va++leaG+v++N++ +    a p+gG+k+SglGre  +e
  gi|313117082|ref|YP_004038206.1| 425 LTVFEWSEREEVVKRANDTRFGLAAGVWTQDLETAHTVADELEAGTVWVNTYDDLLDPA-PHGGFKESGLGRELAEE 500
                                       ****************************************************8888888.***************** PP

                                       HHHHTEEEEEE CS
                            Aldedh 452 gleeytevktv 462
                                       +l++y++vk+v
  gi|313117082|ref|YP_004038206.1| 501 ALDDYSRVKSV 511
                                       *********97 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.4e-06    0.0051       9      60 ..     286     339 ..     282     346 .. 0.83
   2 ?    2.7   0.0     0.021        74     116     175 ..     424     482 ..     403     488 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                           DUF1487   9 vifedgDlnsalealvesl..kePfaegavatvlveesirdefvervrsklkpl 60 
                                       ++f d+Dl++a+e  + s+  +   ++ a   ++++e irdef++r+r+++ +l
  gi|313117082|ref|YP_004038206.1| 286 IVFPDADLEQAIEGTIVSIffNSGQQCTAGSRLFLHEDIRDEFLDRLRERIDEL 339
                                       89**********96555542245677888899*****************99876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.021
                           DUF1487 116 vvTlhtFrnakEvvkllakeslkfasvsvwneklaavyelvarlnvdvftiNCakvslkp 175
                                       v+T+  +++ +Evvk ++  +  + +  vw + l +++ ++ +l+  ++ +N ++  l+p
  gi|313117082|ref|YP_004038206.1| 424 VLTVFEWSEREEVVKRANDTRFGL-AAGVWTQDLETAHTVADELEAGTVWVNTYDDLLDP 482
                                       677777777888877655555544.4579***********************99988877 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.8   1.9e-06    0.0067      22      80 ..     210     269 ..     195     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-06
                        Invasin_D3  22 stltvtlkDangnpvsgltvtfsttsag.tlsavtdngdGtytatLta.ttagtatitptv 80 
                                        + t+ + D  +  +   tv++ t  +g +++++ +++dG+ ++tLt+ ++ag+at++   
  gi|313117082|ref|YP_004038206.1| 210 VLATLEIADICDTVLPTGTVNVVTG-SGsVVGDAISQHDGIDKVTLTGsKAAGVATLEGAA 269
                                       45699999***************88.776999999*************888*****98765 PP

>> DUF5063  Domain of unknown function (DUF5063)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.6e-05      0.31     118     151 ..      57      90 ..      51      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.6e-05
                           DUF5063 118 lknglavyregneeemeeAlwawqesFesyWGqh 151
                                       +++ la+++ g++  ++ A+ a +++Fe+ WGqh
  gi|313117082|ref|YP_004038206.1|  57 TGESLATFQVGTTADVDRAVKAARDAFEEAWGQH 90 
                                       56789****************************9 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.8   7.6e-05      0.27       5      73 ..      75     147 ..      71     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.6e-05
                            DUF349   5 rFraacdafferrkahfeeqdaer....eenlekKealieeaealaksttdwksatkrlkelqeeWkeiGpVp 73 
                                         +aa+daf+e+  +h   q+ e+    ++ le+K+a ++++e+l++ + ++ s +  ++ l e++++   V 
  gi|313117082|ref|YP_004038206.1|  75 AVKAARDAFEEAWGQHSPRQRGEKldeiADRLEEKKAELAKIETLEAGKPNLHSRFVDIEILVEQFRHFAAVA 147
                                       579*********************9999*****************8876678888888888888887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3454.07
//
Query:       gi|313117083|ref|YP_004038207.1|  [L=424]
Description: sugar phosphate permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-38  130.3  63.1    4.6e-30  104.7  38.9    2.0  2  MFS_1     Major Facilitator Superfamily
    8.2e-06   24.9   7.9    8.2e-06   24.9   7.9    2.1  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7  38.9   5.1e-34   4.6e-30       5     317 ..      22     335 ..      17     345 .. 0.78
   2 !   39.5  16.2   3.6e-14   3.2e-10      39     170 ..     271     404 ..     267     419 .. 0.85

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 5.1e-34
                             MFS_1   5 aflsalarsi....lgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.l 76 
                                       +++++++ ++    l+p+    +a dlg+  + i  ++++ ++g ++++lp+G+l+d+++ r  + lg++l++++ +
  gi|313117083|ref|YP_004038207.1|  22 FLVHMTSVTLvwqaLSPLKK-QMAVDLGVPWQDIAVVYAAISFGLVFTQLPGGALGDKYSVRYAVGLGAVLTGVAtA 97 
                                       44444444443333666666.688899999999******************************************33 PP

                             MFS_1  77 llllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllgglla.sslgWr 151
                                       + ++f ++l+  +++ +l+ +g g+++p+ + ++++wfp ++ g++ g+l++g+ lG+ l+  l +g+l+ + ++W+
  gi|313117083|ref|YP_004038207.1|  98 VRFAF-PTLTGQIAVSLLATVGIGIVNPNLIKVVTEWFPSSQLGLGQGVLMTGNTLGIGLAlSLSAGFLLtTIGSWQ 173
                                       33336.898899**********************************************88856667777767777** PP

                             MFS_1 152 avfyilaivsllafvlfllllpeepperkrkspkeee...kgtgpaplvpawkallkdpvl.w.illialllfffgf 223
                                        vf + ++++++++++ +ll++++p++ +r++ +e +    + ++ p+++ + a+l++p   w i ++al+++   +
  gi|313117083|ref|YP_004038207.1| 174 NVFALYGGITAVVGIF-WLLFVRSPRKDERPTNVETGlpfTSSEGVPFRDSLPAVLRSPSTpWaISFAALAYW--SV 247
                                       ***************5.66666777777777777776677666666666677899999988785555555555..89 PP

                             MFS_1 224 sglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssa 300
                                       +g l+ lp y  + + ++ + + +  l+++ ++g ++all+  lsdr+ rr  l+l++++l++   g++l++v+ s 
  gi|313117083|ref|YP_004038207.1| 248 FGSLAVLPEY-ADAHAFA-VPEYV--LGVSPFAGTAGALLLPLLSDRYTRRLGLNLGIVGLAA---GIILTGVAPSF 317
                                       99********.*******.88888..89999999999**********6665555555555555...55555555555 PP

                             MFS_1 301 vllllvlvliGf.glgfv 317
                                       ++++l++++ G  g+g++
  gi|313117083|ref|YP_004038207.1| 318 PVFILAMLVSGSsGGGLA 335
                                       777777777777555554 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 3.6e-14
                             MFS_1  39 tlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpagaaliadwf 114
                                       ++  ++  +++l+l  lsdr+ rr  l lg++++a+g ++l+ +a+s+++++++ +++G  +g+l+++ ++l  +++
  gi|313117083|ref|YP_004038207.1| 271 GVSPFAGTAGALLLPLLSDRYTRRLGLNLGIVGLAAG-IILTgVAPSFPVFILAMLVSGSSGGGLAAMFYILPGELA 346
                                       55667788999**********8888************.666656688889999999999999999999999988887 PP

                             MFS_1 115 pk..eergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                           ++ g + g+l + ++lGa++g ++g+  +ss+g +++ +++a+ +ll+++++  
  gi|313117083|ref|YP_004038207.1| 347 DIdpNHVGTMSGVLLSLAQLGAVVGSIIGAQALSSYGVEVSVIVVAGPCLLGLLMIPR 404
                                       64336***********************************************886544 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8  13.3    0.0023        21      46     196 ..      52     198 ..       6     198 .. 0.82
   2 !   24.9   7.9   9.1e-10   8.2e-06      55     166 ..     273     384 ..     264     407 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0023
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                        ++ ++ ++ ++G ++++l +g lgd+++ +++   +avl+ +++++ +a +   ++   i+  +l+ +g+G+++  
  gi|313117083|ref|YP_004038207.1|  52 QDIAVVYAAISFGLVFTQLPGGALGDKYSVRYAVGLGAVLTGVATAVRFAFP---TLTGQIAVSLLATVGIGIVNPN 125
                                       5678999*************************************99999999...7777788889************ PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCC.HHHHHHHHHHGGGS---HH CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglq.lvpallllilllflPESPr 196
                                           + E  p +  g   ++  ++ t+Gi +a  + +g+  t+    w+  ++l   + a++ +++llf++ SPr
  gi|313117083|ref|YP_004038207.1| 126 LIKVVTEWFPSSQLGLGQGVLMTGNTLGIGLALSLSAGFLLTTI-GSWQNVFALYgGITAVVGIFWLLFVR-SPR 198
                                       *****************9**************999999955555.56999999851678888899999999.998 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 9.1e-10
                                       HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS CS
                          Sugar_tr  55 flvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiA 131
                                         + +++G+l++ ll+dr+ R+ +l  ++v + +g++l+++a+   s+ v+i++ +++G + G+  ++  ++ +E+A
  gi|313117083|ref|YP_004038207.1| 273 SPFAGTAGALLLPLLSDRYTRRLGLNLGIVGLAAGIILTGVAP---SFPVFILAMLVSGSSGGGLAAMFYILPGELA 346
                                       5577899************************************...******************************* PP

                                       ..-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS- CS
                          Sugar_tr 132 ..pkklRgalvslyqlaitfGilvaaifglgl.nktsn 166
                                          +++ g++ ++  +  ++G +v++i+g+   + ++ 
  gi|313117083|ref|YP_004038207.1| 347 diDPNHVGTMSGVLLSLAQLGAVVGSIIGAQAlSSYGV 384
                                       99889999999999999999999999999876444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2613.51
//
Query:       gi|313117084|ref|YP_004038208.1|  [L=420]
Description: alkyl sulfatase-like hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-25   90.0   0.1    3.2e-25   89.2   0.1    1.4  1  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    1.2e-21   77.6   2.4    1.2e-21   77.6   2.4    1.8  2  Lactamase_B      Metallo-beta-lactamase superfamily
    6.5e-06   25.8   0.1    1.6e-05   24.6   0.1    1.6  1  Lactamase_B_2    Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.16   11.8   0.1       0.68    9.7   0.0    1.9  2  DUF3708          Phosphate ATP-binding cassette transporter


Domain annotation for each model (and alignments):
>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.1     7e-29   3.2e-25       4     136 ..     283     413 ..     281     416 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 7e-29
                                       CHHHC----HHHHTSGGGSSSSS-HHHHHHHHHHHHH-S--S-GGGTS---HHHHHHHHHHHTTSHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr   4 eiaekvklPeslanepylreyYGtvehnvraiyqrylGWfdgnPanLnplppeekakrlvelmGgaekvlekakeal 80 
                                       +i++++ lP+   +e +l+  Y+  e+ +r++ + y GW+ g+P++L+p+ + + a+++++l+G+ae+++e+a++ +
  gi|313117084|ref|YP_004038208.1| 283 DIVREIDLPDP--EESWLQSEYDCGEFIARNVIRYYGGWWTGRPSELKPAGRGAVAEEIADLAGDAETLAERAEALI 357
                                       89999***998..789************************************************************* PP

                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYlsgakel 136
                                       +egd r+a++l++++++adpen++ +++ a+++e++++++e +++ ni+ s+ k  
  gi|313117084|ref|YP_004038208.1| 358 DEGDERLACHLADYALEADPENEAVQTAVANVYEARAEATEDMMSANIFASSVKYA 413
                                       *************************************************9998765 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   2.4   2.8e-25   1.2e-21       6     197 .]      37     241 ..      34     241 .. 0.90
   2 ?   -2.7   0.0       1.1   4.9e+03      64      98 ..     298     335 ..     297     364 .. 0.62

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 2.8e-25
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       +n++  ++ +g++L+DtG+s   +++a   a+++  + +v++ i+TH+H+DH++gl+++  + + p+ + a+ea a+
  gi|313117084|ref|YP_004038208.1|  37 ANVTAFDTAKGLVLVDTGLSKLSQQLAT--ALREHTDSPVHTAIYTHGHTDHAFGLDEFLIEGQEPPNVIAHEAMAG 111
                                       7999999*******************95..*********************************************** PP

                                       HCHHHHHHHHHCCHH.....................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEE CS
                       Lactamase_B  83 fmeeaddaasrkgll.....................lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvv 138
                                       + +   + +++ +++                         +  +p ++  ++ +++ g+ ++++++  g + +h  +
  gi|313117084|ref|YP_004038208.1| 112 RFDRYARTEEYNKIIngrqlsadpaaaeyhslweddMFCWPNYPPTTWYSDDITITVGDTTFEIHHARGETDDHTWL 188
                                       ***********************************744444556778888888999********************* PP

                                       EETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 139 eygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       ++++++vl +GD++ a+    + +       r+p+d+++   +l+++a+l+a +l+pgH
  gi|313117084|ref|YP_004038208.1| 189 YCPDRDVLCSGDLVTAAAPNAGNP---QKVQRYPWDWAD---ALREMAALNAGTLLPGH 241
                                       ***************888888888...344455555555...559************** PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                       CTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH...T CS
                       Lactamase_B  64 lveatdvpvgavaeeapalfmeeaddaasrkgll...l 98 
                                       l +++d+  ++ + + +++ +++ ++ ++ k++     
  gi|313117084|ref|YP_004038208.1| 298 LQSEYDCGEFIARNVIRYYGGWWTGRPSELKPAGrgaV 335
                                       66777777777778888888888777776665433330 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   3.5e-09   1.6e-05       3      72 ..      49     115 ..      48     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.5e-09
                                       EEES--TT.HHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCT CS
                     Lactamase_B_2   3 iLiDagpd.lrqqalralqPve.lrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavlea 72 
                                       +L+D+g++ l qq++ al   +   d+  p++  ++th+H DH  gl+ +   +++   +++a++ ++   ++
  gi|313117084|ref|YP_004038208.1|  49 VLVDTGLSkLSQQLATAL---ReHTDS--PVHTAIYTHGHTDHAFGLDEFLIeGQEP-PNVIAHEAMAGRFDR 115
                                       79******6666633333...213555..*******************998854332.568898877766555 PP

>> DUF3708  Phosphate ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.28   1.3e+03      88     144 ..      11      68 ..       2      73 .. 0.72
   2 ?    9.7   0.0   0.00015      0.68      81     162 ..     329     410 ..     293     413 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.28
                           DUF3708  88 ledvrniaegldaLsaaeaealkatadeirallaavgvalgtevtpavva.aaahlra 144
                                       + d++n  +g+d  + ae+ +  ++ ++++a+ +a+g++l+ ++ + + +  a++lr+
  gi|313117084|ref|YP_004038208.1|  11 IFDIKNFDSGIDITEVAEDTYQCTSFANVTAFDTAKGLVLVDTGLSKLSQqLATALRE 68 
                                       5688899999999555555555568999999999999999987776666557777665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00015
                           DUF3708  81 egqrqllledvrniaegldaLsaaeaealkatadeirallaavgvalgtevtpavva..aaahlrarqrvervlrta 155
                                        + r ++ e++  +a  ++ L ++ ++ ++++ ++++  la+   al ++++++ v+  +a+ ++ar + ++ +++a
  gi|313117084|ref|YP_004038208.1| 329 PAGRGAVAEEIADLAGDAETLAERAEALIDEGDERLACHLADY--ALEADPENEAVQtaVANVYEARAEATEDMMSA 403
                                       4567889999999999999999999999998888888888888..99999999999999****************** PP

                           DUF3708 156 vvlalav 162
                                        ++a++v
  gi|313117084|ref|YP_004038208.1| 404 NIFASSV 410
                                       9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2921.68
//
Query:       gi|313117085|ref|YP_004038209.1|  [L=200]
Description: DNA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-16   58.2   0.0    7.7e-16   57.6   0.0    1.3  1  HTH_10        HTH DNA binding domain
    1.2e-05   24.7   0.3      2e-05   24.0   0.3    1.4  1  Sigma70_r4    Sigma-70, region 4
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.045   13.5   0.0    1.4  1  HTH_Tnp_4     Helix-turn-helix of DDE superfamily endonucleas
      0.026   14.2   0.5       0.46   10.2   0.2    2.7  2  Sigma70_r4_2  Sigma-70, region 4
      0.032   14.4   0.0      0.059   13.6   0.0    1.4  1  SgrR_N        Sugar transport-related sRNA regulator N-term


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   2.1e-19   7.7e-16       1      52 [.     129     180 ..     129     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 2.1e-19
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       L+d+q+evl+ Aye+GY+ +PR++tl+++A e+  s+++++e+L+++e++li
  gi|313117085|ref|YP_004038209.1| 129 LSDRQREVLRRAYELGYYRRPREATLDDVAAEFECSQANVQEILQRIENNLI 180
                                       89************************************************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.3   5.7e-09     2e-05       2      43 ..     126     174 ..     125     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.7e-09
                                       HHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4   2 LasLpererevlelrf.......geglTleEIgerlgiSrerVrqiekr 43 
                                       L++L++r+revl+  +        ++ Tl ++++++  S+  V  i+ r
  gi|313117085|ref|YP_004038209.1| 126 LSKLSDRQREVLRRAYelgyyrrPREATLDDVAAEFECSQANVQEILQR 174
                                       89******************99999******************999887 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.2e-05     0.045      21      49 ..     153     181 ..     151     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                         HTH_Tnp_4  21 tyqdLayrFgvsestvsrifhkwvdlLae 49 
                                       t +d+a+ F++s+ +v+ i +++++ L  
  gi|313117085|ref|YP_004038209.1| 153 TLDDVAAEFECSQANVQEILQRIENNLIS 181
                                       899*********************99875 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.66   2.4e+03       7      15 ..      62      70 ..      60      74 .. 0.77
   2 ?   10.2   0.2   0.00013      0.46       8      49 ..     126     174 ..     123     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.66
                                      HHTTS-HHH CS
                      Sigma70_r4_2  7 alaeLperq 15
                                       l +Lpe++
  gi|313117085|ref|YP_004038209.1| 62 RLLQLPEEY 70
                                      6889**998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00013
                                       HTTS-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2   8 laeLperqreifllrylegl.......sykEIAellgisegtVksrlsR 49 
                                       l++L+ rqre++   y+ g+       + +++A+++++s ++V+  l+R
  gi|313117085|ref|YP_004038209.1| 126 LSKLSDRQREVLRRAYELGYyrrpreaTLDDVAAEFECSQANVQEILQR 174
                                       89****************9866666666777777777777777666655 PP

>> SgrR_N  Sugar transport-related sRNA regulator N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.059      15      45 ..     147     177 ..     132     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                            SgrR_N  15 gkevevtLqelAdvlfCsrRhartlLkkmqe 45 
                                       + + e+tL+++A+ + Cs+ +++ +L+++++
  gi|313117085|ref|YP_004038209.1| 147 RRPREATLDDVAAEFECSQANVQEILQRIEN 177
                                       78999**********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1350.97
//
Query:       gi|313117086|ref|YP_004038210.1|  [L=145]
Description: hypothetical protein Hbor_35540 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-20   72.6  10.7    3.6e-20   72.3  10.7    1.1  1  GtrA      GtrA-like protein


Domain annotation for each model (and alignments):
>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3  10.7     2e-24   3.6e-20       1     117 []      20     139 ..      20     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 2e-24
                              GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakl...lkqflkFvlvsllg 74 
                                       rFl vG+lg+++d ++l++l+e+  l++++  +ia +++i++ F+ln+rwtF  ++ ++    l++f+   lv+++g
  gi|313117086|ref|YP_004038210.1|  20 RFLSVGALGAVIDNVTLAALVEFGLLGPVMGAVIAKEASITTMFLLNERWTFSGATAGRWwsiLRRFICSNLVRAVG 96 
                                       8*******************************************************9998888999999999***** PP

                              GtrA  75 lllnllilwllveklgleallaklvgiivalvlnyvlsklfvF 117
                                       + + +++l++l++ +gl +l+a+++gi+v++v+ny++++l+++
  gi|313117086|ref|YP_004038210.1|  97 ASVGIAVLAVLTQEFGLWYLFANVAGIGVGFVFNYIFESLLTW 139
                                       ****************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1098.54
//
Query:       gi|313117087|ref|YP_004038211.1|  [L=645]
Description: mannosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-12   45.9   8.4    2.6e-11   44.0   8.4    1.9  1  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
    1.5e-06   28.0   8.5    2.7e-06   27.2   8.5    1.3  1  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   8.4   2.9e-15   2.6e-11       7     132 ..      67     196 ..      61     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.9e-15
                             PMT_2   7 awllalftklf...gfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvl 80 
                                       ++++++  ++f   g s++++rlv al+g +  ++  l  r l ++++ ++a lll++ p+++++s+ ++ d pl +
  gi|313117087|ref|YP_004038211.1|  67 PFFIRVNSAIFgaiGVSDFSARLVVALLGGILPIAALLFRRHLRDSTVLAFA-LLLTANPILLYYSRFMRYDLPLAA 142
                                       5666666666644478***************999987777776665555555.55555699**************** PP

                             PMT_2  81 lwalalylllraleknklkywllagvlfGlgflsKytaallliaall..yllis 132
                                       + +++l +++ra ++++ +y ++a+v  +l+f +K  ++l+l + l    ll++
  gi|313117087|ref|YP_004038211.1| 143 FSLFTLGFIVRAYDTGQRRYAYAAAVTGALAFTTKESVLLYLASWLGaaVLLLD 196
                                       *****************99***********************998886444444 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   8.5     3e-10   2.7e-06      77     233 ..      80     242 ..      64     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3e-10
                               PMT  77 penvpyvslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvk 153
                                       ++ v+ +s+Rl  allg  +++ + l+  + + +  t+l +all++  ++l+  sr++  d pL++f l ++ + v+
  gi|313117087|ref|YP_004038211.1|  80 IG-VSDFSARLVVALLGGILPIAA-LLF-RRHLRDSTVLAFALLLTANPILLYYSRFMRYDLPLAAFSLFTLGFIVR 153
                                       55.899***********7666554.444.445567999*************************************** PP

                               PMT 154 ferkapfsrswwlwllltgvalglavsvK.wvglftvllvgllliwelwqllg.............dkslllksivk 216
                                       ++       +++  ++++ v+ +la ++K +v+l++ +++g  ++    + l               ++ +l++++ 
  gi|313117087|ref|YP_004038211.1| 154 AY-----DTGQRRYAYAAAVTGALAFTTKeSVLLYLASWLGAAVLLLDYRFLRardigsdwrgviqSQWQTLQNSIR 225
                                       *8.....5689999***************999999999988655432222221344554444443333333333377 PP

                               PMT 217 hllaralaliviPvtly 233
                                       h+ + ++   ++ ++++
  gi|313117087|ref|YP_004038211.1| 226 HWGVHLIGAGALWLAVF 242
                                       77766666555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 4603.26
//
Query:       gi|313117088|ref|YP_004038212.1|  [L=540]
Description: chitinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-83  278.6   8.8    1.4e-82  278.0   8.8    1.3  1  Glyco_hydro_18  Glycosyl hydrolases family 18
    6.5e-16   57.9   3.6    1.9e-15   56.5   3.6    1.8  1  PKD             PKD domain
      2e-05   24.9   1.9    8.5e-05   22.9   1.9    2.2  1  CBM_5_12        Carbohydrate binding domain
     0.0022   18.2   0.0      0.028   14.6   0.1    2.4  2  ig              Immunoglobulin domain
  ------ inclusion threshold ------
      0.042   13.9   0.0      0.093   12.8   0.0    1.6  1  I-set           Immunoglobulin I-set domain
      0.059   12.1   0.0      0.096   11.5   0.0    1.2  1  REJ             REJ domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_18  Glycosyl hydrolases family 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.0   8.8   4.5e-86   1.4e-82       1     312 []     172     527 ..     172     527 .. 0.93

  Alignments for each domain:
  == domain 1  score: 278.0 bits;  conditional E-value: 4.5e-86
                                       EEEEEEEGGGGGSSGC....SHTTTESEEEEEEEEEEETTTEEEESS.TTHH........HHHHHHHHHHHHTSTT- CS
                                       xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx........xxxxxxxxxxxxxxxxx RF
                    Glyco_hydro_18   1 rvvgYysswesygnny....lpsaklthiiyaFakidgengkvvvsd.wedl........gnfeqlkklkkkknpgv 64 
                                       rvvgYy +w++ +++y    +p++k+th++yaF+ +++ +g+v   + ++++        +  + +++l+  ++p +
  gi|313117088|ref|YP_004038212.1| 172 RVVGYYMQWAQWDREYtpgdIPLDKVTHVNYAFLTVKQ-DGSVAYINeNAAMrvlkpeswHDHKGFNELV--DDPTT 245
                                       79*********98865578899**************77.9899988877777888886666666777777..99*** PP

                                       EEEEEEEETTTTTHHHHHHTSHHHHHHHHHHHHHHHHHCT-SEEEEEES-TTTS........TCHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxx RF
                    Glyco_hydro_18  65 kvllsiGGwtdssgfslaastdasrkkfadsvvsllrkygfDGiDidweypggn........pedkenytallkelr 133
                                       k+l+siGGw+ds+ fs+aa+t+asr++fa+++v+++r+++fDG+Didweypgg         + dk+ y++ll+++r
  gi|313117088|ref|YP_004038212.1| 246 KFLFSIGGWNDSKYFSNAAETEASRQRFAKTAVEIMREHNFDGLDIDWEYPGGGgksgnivrDGDKKRYSDLLAAVR 322
                                       ***************************************************9999*****99999************ PP

                                       HHHHHHHHHTSTTCEEEEEEESSHHHHHHHCHHHHHHHHTSEEEEETTTSSSTTSSBE--SS-SSB......T...C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......x...x RF
                    Glyco_hydro_18 134 ealdkakategkkllLsaavpasasdlskgydlpkiakylDyvnvmtYDfhgswdnvtghhaplyd......a...s 201
                                       ++ld+a++++g+++lL+ a++a +++ + g d +    +lD+vnvmtYDfhg++d++t+h++ply            
  gi|313117088|ref|YP_004038212.1| 323 AELDAAEEEDGQEYLLTTALSADPKKNE-GLDHQRNTGLLDFVNVMTYDFHGAFDDYTNHQSPLYFkendpsPraeD 398
                                       ****9999******************65.54777768889**************************9876651567* PP

                                       SSHHHHHHHHHHTT--GGGEEEEEESEEEEEEESSSSSS...............TSTTTEEEHHHHHHHH.TEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxx.xxxxxx RF
                    Glyco_hydro_18 202 lnvdeavkeylkagvpakklvlGvpfygrawalvsgadn...............tkeegvlsykelkell.kkakak 262
                                       +nvd+a+ ++++   ++++l +G+pfygr++ +v  +dn                +++g++++ ++ ++l  +++++
  gi|313117088|ref|YP_004038212.1| 399 FNVDAAMTYWANTAFDSSQLSMGLPFYGRSFGNVASSDNgglyqsfegspdgtwGQDNGIMEFWDINQNLePSSEYE 475
                                       ************************************999*************998999************87889** PP

                                       EEEETTTTEEEEEETT..EEEEE-SHHHHHHHHHHHHHTTESEEEEETGGGS CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Glyco_hydro_18 263 rkydskakapyvydge..efvsyDdpksikakadyvkakglgGvmiWsldqD 312
                                       +++d++ak+p++y+++  ++vsyD+pksi  k dy+ ++ +gG+m+W++++D
  gi|313117088|ref|YP_004038212.1| 476 YYWDDTAKVPWIYSDSsdVLVSYDNPKSIGLKTDYAVDNDIGGMMFWAFSGD 527
                                       ***************9*********************************998 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   3.6   6.2e-19   1.9e-15       4      68 ..      91     152 ..      86     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 6.2e-19
                                       --S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-E CS
                               PKD   4 sptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgs 68 
                                       s  v+ pg+tv+f a+   ++ + + Wdfgd   ++++s+  v+htY+s+GeY+Vt+t++++ g+
  gi|313117088|ref|YP_004038212.1|  91 SDLVINPGETVEFDASGSGDTATQFDWDFGD---GTTGSGEVVSHTYESAGEYTVTLTVTDDSGA 152
                                       578999***********8899999*******...***************************9886 PP

>> CBM_5_12  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.9   2.8e-08   8.5e-05       1      25 []      48      71 ..      48      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.8e-08
                          CBM_5_12  1 ynGkaYqAkwwtqggqPattangpW 25
                                      ++G +++Akwwt+g +P t a  +W
  gi|313117088|ref|YP_004038212.1| 48 HDGYIWEAKWWTRGTEPTTDAS-VW 71
                                      9******************996.88 PP

>> ig  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   9.4e-06     0.028       5      50 ..      92     135 ..      89     165 .. 0.77
   2 ?    0.2   0.0       0.3   8.9e+02      26      70 ..     288     336 ..     284     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.4e-06
                                       EEEEETTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETT CS
                                ig   5 lvlvleGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnr 50 
                                       ++++++Ge++++  s s +++ t++ W + ++t  +++  v +++ 
  gi|313117088|ref|YP_004038212.1|  92 DLVINPGETVEFDASGS-GDTATQFDWDFGDGTTGSGEV-VSHTYE 135
                                       6789*************.***************999988.333332 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.3
                                       TSEEEEEESSSSCSEEEEEEEEETTCEEEE.....EEEECSSTGGGTEEE CS
                                ig  26 ptdvtWkkegqtkiesqkvvkegnrrkgss.....slliskvteedaGtY 70 
                                       ++d+ W+  g+  +++   v +g+++++s      +  ++ + eed+++Y
  gi|313117088|ref|YP_004038212.1| 288 GLDIDWEYPGGGGKSGNI-VRDGDKKRYSDllaavRAELDAAEEEDGQEY 336
                                       578999999999999988.8888888888878888888899999999888 PP

>> I-set  Immunoglobulin I-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.1e-05     0.093       4      61 ..      87     145 ..      84     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                                       EES-CEEEEETTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEET.TEEEEEES CS
                             I-set   4 tqklkdvevseGesvelectveGepepsvsWakdgselkssqrvkvtvee.aeytLtIs 61 
                                       + +++d++++ Ge+ve++++ +G+   ++ W  ++  + s + v+ t+e+ +eyt t++
  gi|313117088|ref|YP_004038212.1|  87 SFTVSDLVINPGETVEFDASGSGDTATQFDWDFGDGTTGSGEVVSHTYESaGEYTVTLT 145
                                       567899*********************************99999999998855555543 PP

>> REJ  REJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.2e-05     0.096     148     203 ..     113     168 ..      95     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                               REJ 148 ealsgtllssstssltfpaselvanltynftltvskrsrksasteqtilvvdgepp 203
                                       ++++  + + +t+s ++ +++ ++  +y++tltv+++s  + st+++++  dg  p
  gi|313117088|ref|YP_004038212.1| 113 TQFDWDFGDGTTGSGEVVSHTYESAGEYTVTLTVTDDSGATGSTTKVVTASDGGMP 168
                                       55556677889999999999999999************99*********9999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3590.41
//
Query:       gi|313117089|ref|YP_004038213.1|  [L=570]
Description: chitinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-70  238.7   0.9    1.3e-70  238.7   0.9    1.6  2  Glyco_hydro_18  Glycosyl hydrolases family 18
    1.5e-19   69.6   4.6    4.4e-19   68.1   4.6    1.8  1  PKD             PKD domain
    4.9e-06   26.8   1.8    2.5e-05   24.6   1.8    2.3  1  CBM_5_12        Carbohydrate binding domain
  ------ inclusion threshold ------
        3.5    8.3   5.1       0.73   10.5   0.3    2.4  3  Ig_3            Immunoglobulin domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_18  Glycosyl hydrolases family 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       0.4   1.8e+03     265     289 ..      44      68 ..      20      83 .. 0.77
   2 !  238.7   0.9   2.8e-74   1.3e-70       2     312 .]     172     555 ..     171     555 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.4
                                       EETTTTEEEEEETTEEEEE-SHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Glyco_hydro_18 265 ydskakapyvydgeefvsyDdpksi 289
                                        d ++  +y+++++ ++  D p + 
  gi|313117089|ref|YP_004038213.1|  44 GDRVTHDGYIWEAKWWTKGDEPTTD 68 
                                       47788889**999999999977664 PP

  == domain 2  score: 238.7 bits;  conditional E-value: 2.8e-74
                                       EEEEEEGGGGGSS.GC....SHTTTESEEEEEEEEEEETTTEEEESS.TTHH.HHHHHHHHHHHHTSTT-EEEEEEE CS
                                       xxxxxxxxxxxxx.xx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                    Glyco_hydro_18   2 vvgYysswesygn.ny....lpsaklthiiyaFakidgengkvvvsd.wedl.gnfeqlkklkkkknpgvkvllsiG 71 
                                       vvgYy sw+ ++  +y    +p +k+t ++yaF+++++ +g+vv+ d + d  g ++ +++lk+  + ++ + lsiG
  gi|313117089|ref|YP_004038213.1| 172 VVGYYPSWKGNEDyQYypedIPFDKVTDVLYAFLNVKS-DGSVVIPDsNVDHeGLLQSFADLKQGPASDTTLKLSIG 247
                                       89******98877675688899**************99.*******98777789999******88888********* PP

                                       ETTTTTHHHHHHTSHHHHHHHHHHHHHHHHHCT-SEEEEEES-TTTS........TCHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxx RF
                    Glyco_hydro_18  72 GwtdssgfslaastdasrkkfadsvvsllrkygfDGiDidweypggn........pedkenytallkelrealdkak 140
                                       Gw+ s gf++aa+t+++r++fa+++v+l++ky+fDGiDidwe pg n        ++  ++ ++llk++r +ld+ +
  gi|313117089|ref|YP_004038213.1| 248 GWALSPGFEDAAATEENRTRFAETAVALMQKYDFDGIDIDWEHPGPNrgicecgsQKGPAHHVKLLKAVRDKLDAVE 324
                                       ********************************************9999*****998889***************999 PP

                                       HHTSTTCEEEEEEESSHHHHHHHCHHHHHHHHTSEEEEETTTSSSTTSSBE--SS-SSB........T...CSSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........x...xxxxxx RF
                    Glyco_hydro_18 141 ategkkllLsaavpasasdlskgydlpkiakylDyvnvmtYDfhgswdnvtghhaplyd........a...slnvde 206
                                       +++g++++Ls+a  +s ++     + +++ +++D + +m+YDf+g w++++g +ap+y+            +++v++
  gi|313117089|ref|YP_004038213.1| 325 EEDGRTYYLSVANGGSDWNAA-LVKHREVERVVDEIYMMAYDFTGVWHQTAGLNAPIYGtpkdyppdGdaqQYTVET 400
                                       9*****************943.3488999******************************998777651567****** PP

                                       HHHHHHHTT...............--GGGEEEEEESEEEEEEESSS...............SSS............. CS
                                       xxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxx...............xxx............. RF
                    Glyco_hydro_18 207 avkeylkag...............vpakklvlGvpfygrawalvsg...............adn............. 240
                                       +++ + ++g                +++ lvlG+pfygr+ +  +g               + +             
  gi|313117089|ref|YP_004038213.1| 401 TLEIWKEQGywvdwmqwedygepvEDPASLVLGLPFYGRGCKVENGiwdtfslaewqqgdpK-Hqnevippgtwnhl 476
                                       **99999999*************55599***********77776665555555555444431.15677777888888 PP

                                       ....TSTTTEEEHHHHHHHH.TEEEEEEEEETTTTEEEEEETT..EEEEE-SHHHHHHHHHHHHHTTESEEEEETGG CS
                                       ....xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Glyco_hydro_18 241 ....tkeegvlsykelkell.kkakakrkydskakapyvydge..efvsyDdpksikakadyvkakglgGvmiWsld 310
                                           + ++g ++y +l+e++ ++++++++++++ ++p+++++e  +f+syDdp+si +k+++++++glgGvm+W+l+
  gi|313117089|ref|YP_004038213.1| 477 lgpdQANTGAFDYGDLEENYeGADGWEKNVNEQGQVPWLWNEEkgIFISYDDPASIEEKVKLAQSEGLGGVMFWELS 553
                                       88888999************9999***************************************************** PP

                                       GS CS
                                       xx RF
                    Glyco_hydro_18 311 qD 312
                                       qD
  gi|313117089|ref|YP_004038213.1| 554 QD 555
                                       *9 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   4.6   9.9e-23   4.4e-19       4      71 .]      91     155 ..      86     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 9.9e-23
                                       --S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEEE CS
                               PKD   4 sptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsata 71 
                                       s ++++pg +vaf a+  +g++++y+Wdfgd   ++++s++t++htY+s+ eY+Vt+t++n++gs t+
  gi|313117089|ref|YP_004038213.1|  91 SDSYVEPGVEVAFDASGSSGSPTSYQWDFGD---GTTGSGKTTSHTYESEQEYTVTLTVENEDGSDTT 155
                                       5789***************************...******************************9885 PP

>> CBM_5_12  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   1.8   5.7e-09   2.5e-05       1      25 []      49      72 ..      49      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.7e-09
                          CBM_5_12  1 ynGkaYqAkwwtqggqPattangpW 25
                                      ++G +++Akwwt g++P t an  W
  gi|313117089|ref|YP_004038213.1| 49 HDGYIWEAKWWTKGDEPTTDAN-MW 72
                                      9******************998.77 PP

>> Ig_3  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   0.4         4   1.8e+04      34      42 ..      58      66 ..      58      77 .. 0.72
   2 ?   10.5   0.3   0.00016      0.73      11      68 ..      93     152 ..      85     170 .. 0.70
   3 ?   -1.9   0.0       1.2   5.3e+03      62      79 .]     320     337 ..     299     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 4
                                      EEEETTS.. CS
                              Ig_3 34 tWykngekl 42
                                      +W+k++e++
  gi|313117089|ref|YP_004038213.1| 58 WWTKGDEPT 66
                                      799999952 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                                       EEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEE..SSEECCCTEEEESS--GG CS
                              Ig_3  11 tvvtegesvtLtCeaegnppptitWykngeklssnstsss..issegssssLtisnvtks 68 
                                       + v++g +v +  + ++++p +++W ++++++ s++t+s+  +s+++++ +Lt++n + s
  gi|313117089|ref|YP_004038213.1|  93 SYVEPGVEVAFDASGSSGSPTSYQWDFGDGTTGSGKTTSHtyESEQEYTVTLTVENEDGS 152
                                       4468999999999997777779*****999855555555567677777777777774433 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                                       ESS--GGG-EEEEEEEEE CS
                              Ig_3  62 isnvtksdsGtYtCvAsN 79 
                                       ++ v+++d  tY+ ++ N
  gi|313117089|ref|YP_004038213.1| 320 LDAVEEEDGRTYYLSVAN 337
                                       567999999999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3552.75
//
Query:       gi|313117090|ref|YP_004038214.1|  [L=479]
Description: hypothetical protein Hbor_35580 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-15   55.4   2.3    8.9e-15   54.3   2.3    1.6  1  PKD       PKD domain
    0.00024   21.5   0.9    0.00085   19.8   0.9    2.0  1  CBM_5_12  Carbohydrate binding domain
  ------ inclusion threshold ------
      0.015   15.4   1.3      0.039   14.1   1.3    1.8  1  DUF5011   Domain of unknown function (DUF5011)


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   2.3   1.5e-18   8.9e-15       4      70 ..      94     157 ..      90     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.5e-18
                                       --S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                               PKD   4 sptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                       s+t++ pg++++  a+  +g+  +y+Wdfgd   +++++e t++htY ++GeY++++t+++a+g+++
  gi|313117090|ref|YP_004038214.1|  94 SATFVQPGTEITCDASASTGDLSSYEWDFGD---GTTKTELTTSHTYDTTGEYTISLTVTDADGNTA 157
                                       4569***************************...******************************975 PP

>> CBM_5_12  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.9   1.4e-07   0.00085       4      25 .]      54      74 ..      51      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-07
                          CBM_5_12  4 kaYqAkwwtqggqPattangpW 25
                                      ++++Akwwt g++P + an  W
  gi|313117090|ref|YP_004038214.1| 54 HIWEAKWWTKGDEPTADAN-MW 74
                                      78**************998.55 PP

>> DUF5011  Domain of unknown function (DUF5011)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.3   6.5e-06     0.039      29      71 .]     123     165 ..     101     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.5e-06
                                       EE-GGG-EEES---TTS-EEEEEEEEEE-TTSEEEEEEEEEEE CS
                           DUF5011  29 gditskvkvtgsVdtskvGtYtitYtvtdssgneatvtRtVkV 71 
                                       gd t+k + t s  + ++G+Yti  tvtd++gn+a +t + +V
  gi|313117090|ref|YP_004038214.1| 123 GDGTTKTELTTSHTYDTTGEYTISLTVTDADGNTADATQKLTV 165
                                       677777777777788899*****************99977766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 3233.49
//
Query:       gi|313117091|ref|YP_004038215.1|  [L=473]
Description: hypothetical protein Hbor_35590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-11   43.2   4.3    7.4e-11   41.7   4.3    1.8  1  PKD       PKD domain


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   4.3   4.1e-15   7.4e-11       4      69 ..      95     157 ..      92     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 4.1e-15
                                       --S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EE CS
                               PKD   4 sptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsa 69 
                                       s + + pg++v f a+  +g++ +y W f d   +++ +++tv+h+++s+G+Y V++t+  a+g +
  gi|313117091|ref|YP_004038215.1|  95 SDSTVTPGTSVSFDASESTGTIESYDWSFSD---GASATGKTVSHSFASTGSYMVKLTVAGADGGT 157
                                       567899*************************...**************************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2910.94
//
Query:       gi|313117092|ref|YP_004038216.1|  [L=247]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-21   75.1   0.1    6.5e-20   71.3   0.0    2.4  3  IclR      Bacterial transcriptional regulator
    7.2e-12   44.9   0.5    3.1e-11   42.9   0.0    2.3  3  HTH_IclR  IclR helix-turn-helix domain
    6.1e-07   29.2   0.0    1.5e-06   27.9   0.0    1.7  1  HTH_5     Bacterial regulatory protein, arsR family
    8.4e-06   25.8   0.1    2.7e-05   24.1   0.0    1.9  2  HTH_20    Helix-turn-helix domain
    5.9e-05   22.9   0.0    0.00019   21.3   0.0    1.9  2  HTH_11    HTH domain
    0.00016   21.5   0.0    0.00048   20.0   0.0    1.8  1  MarR_2    MarR family
     0.0016   18.3   0.0     0.0044   16.9   0.0    1.7  2  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0096   15.5   0.0      0.022   14.3   0.0    1.7  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.035   14.4   0.0      0.087   13.2   0.0    1.6  1  Rrf2      Transcriptional regulator


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.21   4.2e+02      45      70 ..      41      66 ..      32      69 .. 0.71
   2 ?   -2.2   0.0       1.7   3.4e+03       9      20 ..      79      90 ..      75     103 .. 0.77
   3 !   71.3   0.0   3.3e-23   6.5e-20      14     122 ..     133     239 ..     123     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.21
                                      SSTTS--SHHHHHHHHHHHHHHTSEE CS
                              IclR 45 lterTitdpeeLleeLakvReqGyav 70
                                      +t+ T  +  + l+eL +vR+ G+ +
  gi|313117092|ref|YP_004038216.1| 41 FTRSTTYKHLATLRELGYVRKVGVEY 66
                                      56666665666677899999999866 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                                      TT-EEEGGGSHH CS
                              IclR  9 iGtrlplyatai 20
                                      i  r ply t++
  gi|313117092|ref|YP_004038216.1| 79 IRGRSPLYRTSN 90
                                      556788888875 PP

  == domain 3  score: 71.3 bits;  conditional E-value: 3.3e-23
                                       EGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEEEE-TT CS
                              IclR  14 plyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciAapifdas 90 
                                        l++ta GKa+La+l++e++e +l + +l + t++Titd + L  +L+++Re+G+a++r+E+  + + +A+  f++ 
  gi|313117092|ref|YP_004038216.1| 133 HLHCTAPGKAILAHLSDEQVEDVLDAAGLPARTDNTITDADVLAGDLSNIRERGIAIERGEQRTDQNGVAV-AFEHD 208
                                       69*****************************************************************8886.47755 PP

                                       SSEEEEEEEEEETTTSHHHHHHHHHHHHHHHH CS
                              IclR  91 gevvaAvsvsgptarlteeelkeellalvrea 122
                                          vaAv v+g++ rl++++l+e++  +v  +
  gi|313117092|ref|YP_004038216.1| 209 -GEVAAVYVVGHADRLSNKRLEENIPGMVLGT 239
                                       .56799*****************988888665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.6e-14   3.1e-11       4      51 ..      15      62 ..      12      63 .. 0.96
   2 ?   -1.3   0.0      0.98   1.9e+03       8      18 ..      92     102 ..      91     106 .. 0.81
   3 ?   -2.5   0.0       2.4   4.8e+03      13      31 ..     145     162 ..     142     163 .. 0.64

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.6e-14
                                      HHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  4 RalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +++a+++a a +++++++s lA++++ ++St++ +L+tL elGyv++ 
  gi|313117092|ref|YP_004038216.1| 15 KTFALIEAMADRDGPVGVSALADELDFTRSTTYKHLATLRELGYVRKV 62
                                      89********************************************86 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.98
                                       HHCT-CTTBSS CS
                          HTH_IclR   8 iLdalaeapqe 18 
                                       ++d+lae++ e
  gi|313117092|ref|YP_004038216.1|  92 LIDQLAETTNE 102
                                       78999999987 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.4
                                       CTTBSS-BHHHHHHHHTS- CS
                          HTH_IclR  13 aeapqeltlselArrtglp 31 
                                       a+   e  + ++ +++glp
  gi|313117092|ref|YP_004038216.1| 145 AHLSDE-QVEDVLDAAGLP 162
                                       444454.577888888888 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   7.7e-10   1.5e-06       9      47 .]      21      61 ..      18      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 7.7e-10
                                      HHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  9 klLae..gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                       ++a+  g+  v+ la+el+ ++st+  HL+ Lre+G+V+k
  gi|313117092|ref|YP_004038216.1| 21 EAMADrdGPVGVSALADELDFTRSTTYKHLATLRELGYVRK 61
                                      56666679999****************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.3e-08   2.7e-05      20      59 ..      25      64 ..      16      66 .. 0.89
   2 ?   -2.3   0.0       2.4   4.8e+03      14      23 ..     142     150 ..     141     165 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.3e-08
                                      STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 20 araegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                       r++++ +s+la++ld +++t ++HL++L+e g+v+ v++
  gi|313117092|ref|YP_004038216.1| 25 DRDGPVGVSALADELDFTRSTTYKHLATLRELGYVRKVGV 64
                                      67899999****************************9986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                                       HHHHHHSTCT CS
                            HTH_20  14 rilraLarae 23 
                                       +il++L ++e
  gi|313117092|ref|YP_004038216.1| 142 AILAHL-SDE 150
                                       688888.332 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   9.3e-08   0.00019       5      44 ..      19      58 ..      15      65 .. 0.85
   2 ?   -3.4   0.0       4.8   9.6e+03      35      47 ..     178     190 ..     177     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.3e-08
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      ++e   + +gp+  + LA+eL+ +r+t ++++++L+elg+
  gi|313117092|ref|YP_004038216.1| 19 LIEAMADRDGPVGVSALADELDFTRSTTYKHLATLRELGY 58
                                      56666667788999*************************5 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.8
                            HTH_11  35 dIkaLeelgvpIe 47 
                                       d+  ++e g+ Ie
  gi|313117092|ref|YP_004038216.1| 178 DLSNIRERGIAIE 190
                                       7889999999987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.4e-07   0.00048       8      54 ..      17      62 ..      15      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + ++ a ++r+g+ + v++la++l+ ++s++ ++l+ L + G+v+++
  gi|313117092|ref|YP_004038216.1| 17 FALIEAMADRDGP-VGVSALADELDFTRSTTYKHLATLRELGYVRKV 62
                                      567889999**98.9*****************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.2e-06    0.0044      20      60 ..      27      67 ..      21      75 .. 0.86
   2 ?   -3.3   0.0       4.4   8.7e+03      21      36 ..     148     163 ..     143     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                       gp  ++ +a el+  rs+ Y+ L  L + G+V+++  ++ 
  gi|313117092|ref|YP_004038216.1| 27 DGPVGVSALADELDFTRSTTYKHLATLRELGYVRKVGVEYS 67
                                      588999****************************9987754 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.4
                                       CCCHHCHHCCCTTSSC CS
                              TrmB  21 gpatadeiaeelgvpr 36 
                                          +++++  ++g+p 
  gi|313117092|ref|YP_004038216.1| 148 SDEQVEDVLDAAGLPA 163
                                       5567888888888885 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.1e-05     0.022       9      48 .]      20      60 ..      14      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                            HTH_24  9 LelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +e++ + ++    + LA++l+ ++st+ ++l  L e G+++
  gi|313117092|ref|YP_004038216.1| 20 IEAMADrDGPVGVSALADELDFTRSTTYKHLATLRELGYVR 60
                                      555555577788899************************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.4e-05     0.087      18      57 ..      22      61 ..      16      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      a+ ++++pv ++++a++ +  +s   k la+Lr+ g+v+ 
  gi|313117092|ref|YP_004038216.1| 22 AMADRDGPVGVSALADELDFTRSTTYKHLATLRELGYVRK 61
                                      56677889******************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1830.70
//
Query:       gi|313117093|ref|YP_004038217.1|  [L=222]
Description: fructose-2,6-bisphosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-31  109.9   0.1    1.5e-31  109.6   0.1    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.1   8.4e-36   1.5e-31       1     182 [.      19     203 ..      19     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 8.4e-36
                                       EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTT.S---EEEE-SSHHHHHHHHHHHH.CTT--EEE-G CS
                        His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlag.epidaiysSplkRarqTaeliae.alglpvelde 75 
                                       ++L+RHG+tew +++rl g+  vpLte+G+  + a+++rla+  ++d++y+ +   ar+Ta+l+    lg +++ ++
  gi|313117093|ref|YP_004038217.1|  19 IVLLRHGQTEWDRQNRLHGHVPVPLTETGYDSVTAIGRRLASqYDFDRMYAADTMAARETAALVRLtGLGPRPQFEA 95 
                                       79***************************************99********************9751566******* PP

                                       GGS----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSE.EEEEE-HHHH CS
                        His_Phos_1  76 gLrEidfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarheget.vlvVsHggvi 151
                                       ++r +d G+++gl ++e+ + + ++l++  +  + + p ggE l+d +aRv + +e+l++r + ++ vlvV+H  ++
  gi|313117093|ref|YP_004038217.1|  96 AWRPRDAGVFQGLAYDELGDGMTDDLDTDVDVLQ-PLPRGGEPLADGRARVLDRWERLCERSNADEqVLVVTHDFPM 171
                                       ***************************9999988.67888*********************999989********** PP

                                       HHHHHHHH.T--GGGGGGB---TT-EEEEEE- CS
                        His_Phos_1 152 rallarll.glpleelrrleldnaslsvlefd 182
                                        ++la++    ++++l r++   +s++ ++ +
  gi|313117093|ref|YP_004038217.1| 172 ATILADIDdAGSVADLGRYAPGKCSMTTVRRT 203
                                       ********888999999**********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1498.89
//
Query:       gi|313117094|ref|YP_004038218.1|  [L=275]
Description: hypothetical protein Hbor_35620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-83  279.0   0.0    3.4e-83  278.8   0.0    1.0  1  ComA      (2R)-phospho-3-sulfolactate synthase (ComA)


Domain annotation for each model (and alignments):
>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.8   0.0   1.9e-87   3.4e-83       1     242 [.      12     260 ..      12     261 .. 0.98

  Alignments for each domain:
  == domain 1  score: 278.8 bits;  conditional E-value: 1.9e-87
                                       XXXX-SS-SSS-EEEEESS.....--HHHHHHHHHHHGGG-SEEEE-TTGGGGSTCHHHHHHHHHHHCTT-EEEE-H CS
                              ComA   1 eereekPrktGlTeviDkG.....lglreledlletageyiDglKlgggtsallpeeilrekielahehgvyvstGg 72 
                                       ++r++kPr++G+Te+  +G     +g+rel+d+let+g y+D++K++gg++al++++++ e+i+++he++v+vstGg
  gi|313117094|ref|YP_004038218.1|  12 NDRPPKPRTKGITEI--RGpyydpMGPRELRDILETMGRYVDIYKFSGGSFALMDQSTVTELIDICHEYDVDVSTGG 86 
                                       68*************..************************************************************ PP

                                       HHHHHHHHTT..-HHHHHHHHHHCT-SEEEE--SSS---HHHHHHHHHHHCCTTSEEEEEES-SSH..........H CS
                              ComA  73 tlfEaalaqg..kvdeyleeckelgfdviEvsdgtlelpeeeklrliekakkeglkvlpevgkkdg..........e 137
                                        ++E +l+++  kv++y++e+++lgfd++E+s+g+l +++++ ++l+e +++ +lk +pe+ +++g          e
  gi|313117094|ref|YP_004038218.1|  87 -FIENVLVRDndKVEAYVAEAEKLGFDIVEISSGFLAIDTDDLVSLTELVADYNLKPKPEINVQFGaggasdpdelE 162
                                       .******99999*************************************************************9777 PP

                                       HHTT--CCHHHHHHHHHHHHTECEEEE--TTT--SSTTB-TTS-B-HHHHHHHHTTS-GGGEEEE--SHHHHHHHHH CS
                              ComA 138 lesesdveklieeakrdleaGaekviiEaresGitegvydekgevrtdvvekiierlgleklifEApekkqqewfik 214
                                       +e ++d++  i+e++r leaGa+ +++Ea+  Gite+v     e+rtdvv +++++lg+e+l+fEAp ++ +ew+ik
  gi|313117094|ref|YP_004038218.1| 163 REGQQDPSMAIREGQRHLEAGADLLMVEAE--GITEEV----HEWRTDVVYELANELGMENLVFEAPGPEMFEWYIK 233
                                       7777**************************..******....*********************************** PP

                                       HH-TT--EEEEEGGGHHHHHHHHCT-SG CS
                              ComA 215 efGpnVnLgnvdpsevlaLealRlglrg 242
                                       +fGpnVnL +vd s++++Le++R+gl+g
  gi|313117094|ref|YP_004038218.1| 234 NFGPNVNL-FVDNSQIVELECMRSGLWG 260
                                       ********.******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1856.99
//
Query:       gi|313117095|ref|YP_004038219.1|  [L=450]
Description: propionate catabolism protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.4e-128  427.5   0.6   5.5e-128  427.2   0.6    1.0  1  MmgE_PrpD        MmgE/PrpD family
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.054   13.1   0.0    1.6  1  MMS19_N          Dos2-interacting transcription regulator of 
      0.065   13.2   0.4        1.1    9.3   0.1    2.5  2  Rib              Rib/alpha-like repeat
       0.27   11.3   1.6       0.37   10.8   0.1    2.0  2  PheRS_DBD2       PheRS DNA binding domain 2
          1    9.2   3.1          2    8.3   1.6    2.2  2  Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal do


Domain annotation for each model (and alignments):
>> MmgE_PrpD  MmgE/PrpD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.2   0.6  1.5e-131  5.5e-128       1     438 [.       4     438 ..       4     439 .. 0.97

  Alignments for each domain:
  == domain 1  score: 427.2 bits;  conditional E-value: 1.5e-131
                                       HHHHHHHHHH-----H..HHHHHHHHHHHHHHHHHHHHTT-HHHHTT-SSSTT-B-TT-EE-TTSS-EE-HHHHHHH CS
                         MmgE_PrpD   1 teqlaefvaelryddlpeevverakrlilDtlGvalaglrepavkkaleavkgtggpggatvigtgerlspvkAAfv 77 
                                       t+++aefv++++yd+ +e+vve+ k+++lD++G+++++l +++v+ + e v+g   +g++t++g++  +s+++AA+ 
  gi|313117095|ref|YP_004038219.1|   4 TQSIAEFVEAANYDNFDEKVVEELKKRVLDSVGIGIGALGAEPVEVVFETVSGVDESGSCTLWGRDASASAPQAAMH 80 
                                       789************************************************************************** PP

                                       HHHHHHCTS-S-BEES.SSEE-GGGGHHHHHHHHHHHHHHBHHHHHHHHHHHHHHHHHCCC--SCCCT.B-THHHHH CS
                         MmgE_PrpD  78 nGaaihalDfdDthla.aelhhpsdvlpaalAvAealgasgkdlLtAivvGyEvqgrlglalsfnhygfhdtvtlgt 153
                                       n a++++lD+ D +la  e+ hpsd+++ ++A+ e++gasgkdl++A+ v+yE qg l+  + +++ g +d+vt++ 
  gi|313117095|ref|YP_004038219.1|  81 NTALTRYLDYMDSFLApGETPHPSDNIGSIIACGEQTGASGKDLIEAVGVAYELQGELAWNAPVRDKG-WDHVTHTV 156
                                       **************9846**************************************************.******** PP

                                       HHHHHHHHHHTT--HHHHHHHHHHHHCT-B-BSGGGSTTT--CHHCHHHHHHHHHHHHHHHHHTT---TTTTT-TTT CS
                         MmgE_PrpD 154 fgaaaaaakLlgLdaeqianAlgiaatqaaglrqyrhagtkskklwaaGdAarnGveaallAkrGftGpsdilegew 230
                                       ++aaa+a+++lgL+ eq++nA+gia+t + +lr +r++g++ +k +a+++Aarn+v+++llA++G++Gp++++eg++
  gi|313117095|ref|YP_004038219.1| 157 LSAAAGAGSILGLNHEQLRNAVGIAGTAHNALRVTRTGGINEWKGIASANAARNAVYSCLLAANGMEGPKNLFEGQK 233
                                       ***************************************************************************** PP

                                       SHHHHHSTT-----S.S-SS...SHHHHC-B---SSS-CCCHHHHHHHHHHHHHHCCTCCCEEEEEEEE-HHHHHHC CS
                         MmgE_PrpD 231 GflavlsggkdlelevkplgegesweienvlfKpypaerhthaaidaalklraelklkpddIesieirtseaalrii 307
                                       G+ +++sg+ d+el+ ++ +     ++ ++++K+y ae ++++a++ +++l ++ k++++++e+i+++t++ a  ii
  gi|313117095|ref|YP_004038219.1| 234 GWKQIISGDFDVELD-PNCE-----RVFDTMTKRYVAETYAQSAVEGLIELAEREKIEAEQVEEIHLDTFHGAKLII 304
                                       ************999.7766.....9*************************************************** PP

                                       ---S....---SHHHHCT-CCHHHHHHHHCS---CCCCSCCCCTSCHHCCHHCCEEEEE-HHHHHHH.TTT---EEE CS
                         MmgE_PrpD 308 gkkg....ppenradadhSlqyvvAvalldgrvtledfederladpevqaLrekvevvedpeltady.pekrsivvv 379
                                       g ++    + e++a+adhSl+y++A+al+d+++t + +++er+++++vq+L++ v+v+edp+lt+++   ++++  +
  gi|313117095|ref|YP_004038219.1| 305 GGGEgsryEVETKAQADHSLPYMLAAALIDREMTNDAYDPERIQRDDVQSLLRTVTVEEDPKLTERFeSGEMPANIT 381
                                       **999**************************************************************8777777777 PP

                                       EETTS-B---EEESS-TTSGGHHHHHHHHHHHHHHHHHCCS-HHHHHHHHHHHHHHSHH CS
                         MmgE_PrpD 380 vlkdggrtleerveypkGhprnplsreeleeKfrrlaegvlseeeaereeileevlele 438
                                       v++d+g+t+e++ + + Ghp+np+++e++eeKf+++++g+++  +++r+ei++ v +le
  gi|313117095|ref|YP_004038219.1| 382 VTLDDGTTHEVQKDDFQGHPNNPMDWEQVEEKFETMTSGRYD--QQRRDEIVHTVKHLE 438
                                       778999************************************..999999988877765 PP

>> MMS19_N  Dos2-interacting transcription regulator of RNA-Pol-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.5e-05     0.054      47     139 ..     258     366 ..     248     372 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                           MMS19_N  47 flsrledfavlkealkgllaLlrlkkfsaeeavevlralf............eevhvqslaqadRklvyelldalle 111
                                       +++r   ++  ++a++gl +L++++k++ae+++e+    f            + ++v+++aqad +l y l  al++
  gi|313117095|ref|YP_004038219.1| 258 MTKRYVAETYAQSAVEGLIELAEREKIEAEQVEEIHLDTFhgakliigggegSRYEVETKAQADHSLPYMLAAALID 334
                                       666777788899**********************99998889999999*999************************7 PP

                           MMS19_N 112 k..hrealk..elgedflegfvelvdgEkDPr 139
                                       +  +++a +  ++++d ++ ++  v+ E DP+
  gi|313117095|ref|YP_004038219.1| 335 RemTNDAYDpeRIQRDDVQSLLRTVTVEEDPK 366
                                       73234444433566699**************7 PP

>> Rib  Rib/alpha-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.11     4e+02       5      20 ..      97     112 ..      95     128 .. 0.74
   2 ?    9.3   0.1    0.0003       1.1      36      58 ..     371     393 ..     358     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                               Rib   5 vGevpdatdgikNksd 20 
                                       +Ge+p + d+i+    
  gi|313117095|ref|YP_004038219.1|  97 PGETPHPSDNIGSIIA 112
                                       8*********987655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0003
                               Rib  36 tksGekeavvvVtYPDGskdevp 58 
                                        +sGe +a + Vt  DG++ ev+
  gi|313117095|ref|YP_004038219.1| 371 FESGEMPANITVTLDDGTTHEVQ 393
                                       479******************97 PP

>> PheRS_DBD2  PheRS DNA binding domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0001      0.37      12      29 ..      13      30 ..       9      32 .. 0.88
   2 ?   -2.4   0.2       1.4   5.1e+03       1      10 [.     350     359 ..     350     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                        PheRS_DBD2 12 eGkadelddkeknELKKR 29
                                      + ++d+ d+k++ ELKKR
  gi|313117095|ref|YP_004038219.1| 13 AANYDNFDEKVVEELKKR 30
                                      6689999*********** PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                        PheRS_DBD2   1 DeVqekLkli 10 
                                       D Vq+ L+ +
  gi|313117095|ref|YP_004038219.1| 350 DDVQSLLRTV 359
                                       99***99976 PP

>> Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.6   0.00056         2      58     116 ..     161     219 ..     156     221 .. 0.93
   2 ?   -2.0   0.0      0.85     3e+03     101     114 ..     263     277 ..     254     283 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00056
                   Peptidase_M17_N  58 VGLGkeeeltaealrkaagaaaralkgakvttiavalplegknsdekaeaaaegallgl 116
                                        G G+   l+ e+lr a+g a  a ++++vt+++    ++g +s+++a++a+ ++ll++
  gi|313117095|ref|YP_004038219.1| 161 AGAGSILGLNHEQLRNAVGIAGTAHNALRVTRTGGINEWKGIASANAARNAVYSCLLAA 219
                                       678888889*******************************************9999985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.85
                   Peptidase_M17_N 101 sd.ekaeaaaegall 114
                                        + ++a++a+eg+ +
  gi|313117095|ref|YP_004038219.1| 263 VAeTYAQSAVEGLIE 277
                                       445899999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.56
# Mc/sec: 2411.16
//
Query:       gi|313117096|ref|YP_004038220.1|  [L=423]
Description: Fe3+-hydroxamate ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-14   53.3   0.0    4.6e-14   52.5   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein
     0.0012   18.6   0.6     0.0024   17.6   0.6    1.4  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
  ------ inclusion threshold ------
          1    9.3   6.6        1.7    8.6   6.6    1.3  1  DUF3558       Protein of unknown function (DUF3558)


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   7.7e-18   4.6e-14      10     232 ..      89     366 ..      80     370 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 7.7e-18
                                       HHHHHTT-GGGEEEB-GGG--GGGGGGT..........TS.-BSBESSSB-HHHHHHH--SEEEE-GGG........ CS
                      Peripla_BP_2  10 eillalGatdkvvgvdtttsdpldadklee........ai.vevgadgeidvEklaalkPDlvilskgl......gl 71 
                                       ++l alG++d++vg +    + +  ++l+         ai  +v+++ +++ E l +l+PDl+  +++       ++
  gi|313117096|ref|YP_004038220.1|  89 DVLMALGQADRIVGMSRPGFWFQGFYELLPgvsmrdttAIpNTVSKGYSLNEELLYELDPDLLATDPNRfiawygSD 165
                                       7899***********************9998988888755256788889999**************999999***** PP

                                       .GGGHHHHHHHS-EEE----TTS...............HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS- CS
                      Peripla_BP_2  72 tdedeellksgiptvivessntg...............eslkeqiralgellgledeaeklvaeidsklaaaksaid 133
                                       t+  e l + ++p++  es++                 + + e ++ +g++++++++a ++v  ++ +l+++ s+++
  gi|313117096|ref|YP_004038220.1| 166 TATVESLVDDIAPFFGNESRSKRpsgwpnwptgedydyYAIPEFVERYGQVFQEQKRATAMVDLYETTLDDITSRLP 242
                                       ********************999************9999999*********************************** PP

                                       TT.-EEEEEEEETTE............EEEE-TTSTTTHHHHTS--EESTTT--....STT-EEE-HHHHHHH--SE CS
                      Peripla_BP_2 134 sekpkpvlvfggade..........ggyvvagsnsyigdlldalgieniaaesk....kseyeeisaEqilasdpdv 196
                                        ++++p++ + +a            + ++ a + +   +   +lg+ +++ae+     +++  ++++E +la dpdv
  gi|313117096|ref|YP_004038220.1| 243 PLDERPTVGVLSAFTnpensghfgvSNPIPALDATHELKHYGDLGVVDAFAEQYgeerGHYDLTVGFEGLLAVDPDV 319
                                       **77777777766666889988888666666666666666677******777666**999999************** PP

                                       EEEEEH...........HHHT-S--HHHHT-SHHHHTSHHHHTT-EE CS
                      Peripla_BP_2 197 ifvsgr...........aeadnktgleflkenpllaelpAvkngrVy 232
                                       ++++              ++     le l ++++ ++l+Av+n r y
  gi|313117096|ref|YP_004038220.1| 320 LIFDEAvnalggqtvygNTKAYERTLELLRTDDIGQRLTAVQNDRLY 366
                                       *****************9***************************99 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.6     4e-07    0.0024       3      25 ..       9      31 ..       8      32 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4e-07
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      +RRd LKg+ A+   + l+gc++
  gi|313117096|ref|YP_004038220.1|  9 TRRDVLKGGSALIGSGFLAGCTS 31
                                      7********************97 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.6   0.00028       1.7       3      46 ..      26      67 ..      24      82 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00028
                           DUF3558  3 laGCssttdGtapaasssassssttsssaapavpldtsgvlfdp 46
                                      laGC+s+ + t p ++s++s+ss+ +s+ + ++ ++ + v+ dp
  gi|313117096|ref|YP_004038220.1| 26 LAGCTSSGQST-PPSDSTSSDSSRGTSTDTATT-EQSYSVSLDP 67
                                      8****666666.555555555555544444444.4778888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2787.82
//
Query:       gi|313117097|ref|YP_004038221.1|  [L=185]
Description: hypothetical protein Hbor_35650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-12   46.2   0.4    2.3e-10   40.4   0.1    2.2  2  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.1   1.3e-14   2.3e-10       1      63 [.      38      97 ..      38     101 .. 0.95
   2 !    4.0   0.0     0.003        53      35      67 ..     104     135 ..     101     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.3e-14
                                      HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHH CS
                               CMD  1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaev 63
                                      pe+l+a+ ++ + l+  +  L  + +eL++l+v++a+g  y+++ H+ +A+++Gvt ee +++
  gi|313117097|ref|YP_004038221.1| 38 PEVLEATLEYLNTLY--DQ-LGERRKELVILTVARARGARYEWHQHVDIARDKGVTVEEMQAI 97
                                      899*********997..78.***************************************9975 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.003
                                       HHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHH CS
                               CMD  35 aangceyCvdaHtraAleaGvteeeiaevlaqa 67 
                                       ++ + ey v   +++A+e G   ++i e+l+  
  gi|313117097|ref|YP_004038221.1| 104 VFDDTEY-VLLQYARAVESGTVTDQIHEALTRQ 135
                                       5556677.88899****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1062.19
//
Query:       gi|313117098|ref|YP_004038222.1|  [L=70]
Description: hypothetical protein Hbor_35660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 394.27
//
Query:       gi|313117099|ref|YP_004038223.1|  [L=211]
Description: hypothetical protein Hbor_35670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1265.39
//
Query:       gi|313117100|ref|YP_004038224.1|  [L=71]
Description: hypothetical protein Hbor_35680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 404.76
//
Query:       gi|313117101|ref|YP_004038225.1|  [L=529]
Description: transposase protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-08   33.6   0.0    4.4e-08   33.0   0.0    1.3  1  DDE_Tnp_1    Transposase DDE domain
     0.0037   15.6   0.3      0.016   13.5   0.3    1.9  1  DDE_Tnp_1_4  Transposase DDE domain group 1
  ------ inclusion threshold ------
       0.04   13.9   0.0       0.15   12.1   0.0    2.0  1  DUF772       Transposase domain (DUF772)


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   7.3e-12   4.4e-08      67     205 ..     338     481 ..     325     490 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 7.3e-12
                         DDE_Tnp_1  67 qlldelrpr.kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrk...gaeskrrgrlrkhdrnkiltksqk 139
                                        l++++++     +vl Da ++ + +++tl   gv+y+++        r+   ++ + +r+ + ++d     t+++ 
  gi|313117101|ref|YP_004038225.1| 338 RLVRRAQELvPIETVLCDAEFDAKLVYQTLSNLGVNYLVPK-------RSfnaERAAIKRMSEDGQDVAVESTTVHT 407
                                       355555555899***************************75.......33555566778899999999999999999 PP

                         DDE_Tnp_1 140 rrnk.........skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaql 205
                                        ++          s+k++g+ +++tn+    ++ae + + y++RwqiE+  k++k++f   ++++++++    ++
  gi|313117101|ref|YP_004038225.1| 408 DQGShamrflyvpSTKGDGTAVFATNLRVGPAEAEAYCQRYSRRWQIENEYKSIKYDFL-AKTSSKDYRVRLFYF 481
                                       8888****************************************************887.455555554444444 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.3   2.7e-06     0.016     198     374 ..     332     492 ..     318     500 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-06
                       DDE_Tnp_1_4 198 aveaLarlvkrirerwpetkilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkeke 274
                                       +  +++rlv+r +e  p  +  v +D+ f  + +++++ + gv+Y++  ++ ++ +a+i++++e+ ++         
  gi|313117101|ref|YP_004038225.1| 332 IHRVVRRLVRRAQELVPIET--VLCDAEFDAKLVYQTLSNLGVNYLVPKRSFNAERAAIKRMSEDGQD--------- 397
                                       56788999999888888886..5589999999999999999999999877777777777766666654......... PP

                       DDE_Tnp_1_4 275 reyrefayqaesWskerrVvakaerpaeglnlrfvvTsla.klspeelyeqlYcaRGemEnrIKeakldlaadrtss 350
                                       + +++++ +++  s+ +r ++  + +++g  +  + T+l+   ++ e y q Y +R ++En  K+ k d+ + +tss
  gi|313117101|ref|YP_004038225.1| 398 VAVESTTVHTDQGSHAMRFLY--VPSTKGDGTAVFATNLRvGPAEAEAYCQRYSRRWQIENEYKSIKYDF-LAKTSS 471
                                       455556666777788899886..4556666667789****8777788899*****************887.567888 PP

                       DDE_Tnp_1_4 351 hsfaaNqlrlllsalAynLlaalr 374
                                       ++    ++rl+  ++A  L+++ r
  gi|313117101|ref|YP_004038225.1| 472 KDY---RVRLFYFVFAALLHNIWR 492
                                       876...578888888888877666 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.5e-05      0.15       4      67 ..      53     110 ..      51     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
                            DUF772   4 ayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRk.rlee.le 67 
                                       +yp + m+kl+++ ++ g S r l ++ +  + f    gl    +++pd+s+lsr+ + r+ +  +
  gi|313117101|ref|YP_004038225.1|  53 SYPFRGMVKLFYYREITGESYRSLTRQQELAVLF----GL----KKIPDESVLSRTWHnRFDDaGR 110
                                       89******************99999887666655....98....89*********99988876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 2967.03
//
Query:       gi|313117102|ref|YP_004038226.1|  [L=68]
Description: hypothetical protein Hbor_35700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.7   3.3      0.032   14.4   3.3    1.0  1  RDD       RDD family
      0.049   13.9   2.3      0.049   13.9   2.3    1.9  2  TadE      TadE-like protein
      0.098   12.8   2.1       0.11   12.6   2.1    1.1  1  YrhC      YrhC-like protein
        6.3    6.8   6.9        2.2    8.3   1.4    2.1  2  FixQ      Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   3.3   7.1e-06     0.032      13      71 ..      11      63 ..       9      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.1e-06
                               RDD 13 iDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkg 71
                                      +D++llli+++++ +l+  ++      ++ ++ + ll+ +++++++ ++++l+ +sk++
  gi|313117102|ref|YP_004038226.1| 11 FDIFLLLILGIIFLGLFLRVM------QDVTTVQDLLIKGAIFTVAIAIFFLYAVSKWQ 63
                                      69*****************77......99999999999999999999999999999975 PP

>> TadE  TadE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.3   1.1e-05     0.049      13      36 ..      13      36 ..      13      39 .. 0.87
   2 ?   -0.3   0.2      0.29   1.3e+03       7      15 ..      47      55 ..      40      61 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                              TadE 13 lllllllgiiefgrylyarqtlnn 36
                                      ++lll+lgii +g++l + q +++
  gi|313117102|ref|YP_004038226.1| 13 IFLLLILGIIFLGLFLRVMQDVTT 36
                                      69**************88887765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.29
                              TadE  7 FALvlPlll 15
                                      F++++ +++
  gi|313117102|ref|YP_004038226.1| 47 FTVAIAIFF 55
                                      334444444 PP

>> YrhC  YrhC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.1   2.5e-05      0.11       6      66 ..       4      64 ..       1      65 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                              YrhC  6 kveDYkrFafvLLalsaFLyiGlviPseaketlkksillgaivvfLllaflflrrskkyqk 66
                                      k++   rF + LL + + +++Gl +   +  t+ + +l+ + + ++++a++fl  + k q+
  gi|313117102|ref|YP_004038226.1|  4 KIRSIGRFDIFLLLILGIIFLGLFLRVMQDVTTVQDLLIKGAIFTVAIAIFFLYAVSKWQD 64
                                      555566899999999999********999999999999999999********999998886 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.4   0.00048       2.2      11      29 ..      12      30 ..       9      32 .. 0.88
   2 ?    1.7   0.4     0.059   2.6e+02      13      25 ..      46      58 ..      42      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00048
                              FixQ 11 dswgllflvllfygvviya 29
                                      d+++ll+l ++f+g+ + +
  gi|313117102|ref|YP_004038226.1| 12 DIFLLLILGIIFLGLFLRV 30
                                      89************98765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.059
                              FixQ 13 wgllflvllfygv 25
                                      +++++ +++f+ +
  gi|313117102|ref|YP_004038226.1| 46 IFTVAIAIFFLYA 58
                                      5788888888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 422.66
//
Query:       gi|313117103|ref|YP_004038227.1|  [L=51]
Description: hypothetical protein Hbor_35710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       139  (0.0077528); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 381.79
//
Query:       gi|313117104|ref|YP_004038228.1|  [L=94]
Description: hypothetical protein Hbor_35720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.051   13.5   0.0      0.059   13.3   0.0    1.1  1  H_kinase_N  Signal transduction histidine kinase


Domain annotation for each model (and alignments):
>> H_kinase_N  Signal transduction histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.3e-06     0.059      77     136 ..      26      83 ..       6      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-06
                                       SHHHHHHHH-------------------EEEEEE.EETEEEEEEEEE--GGGS----HHH CS
                        H_kinase_N  77 eplvdraleegrivrekdpdwsggvpvreeaiPVrrrgkviAVltretnlssartpsrle 136
                                        +++d++++e+     ++    + +  + + +P   r+++iA l++e+n+ + rt s  e
  gi|313117104|ref|YP_004038228.1|  26 LTEIDNTWQERGFNSRSE--FVRYTLRDATEFPTFDRDELIALLQAEENIREGRTMSTDE 83 
                                       567888888887766666..444556668889**999******************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 664.45
//
Query:       gi|313117105|ref|YP_004038229.1|  [L=34]
Description: hypothetical protein Hbor_35730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 257.33
//
Query:       gi|313117106|ref|YP_004038230.1|  [L=1180]
Description: DNA/RNA helicase, superfamily I [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-47  162.0   2.6    2.4e-47  162.0   2.6    2.8  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    1.2e-27   97.0   0.0    1.2e-26   93.8   0.0    2.5  1  AAA_19           AAA domain
    4.7e-14   52.5   0.0    5.2e-10   39.2   0.0    5.0  4  UvrD_C           UvrD-like helicase C-terminal domain
    1.9e-07   31.0   0.0    7.3e-05   22.6   0.0    2.5  2  AAA_30           AAA domain
      2e-07   30.7   0.2    0.00032   20.5   0.0    2.6  2  UvrD_C_2         UvrD-like helicase C-terminal domain
  ------ inclusion threshold ------
      0.021   14.6   0.0       0.15   11.9   0.0    2.4  2  CAMSAP_CC1       Spectrin-binding region of Ca2+-Calmodulin
      0.026   14.3   0.1         14    5.3   0.0    3.7  4  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.75    8.8  10.9      0.042   12.9   0.6    3.0  3  Clusterin        Clusterin
        2.4    8.7  24.2        2.8    8.5   4.5    5.3  4  Spectrin         Spectrin repeat
        4.8    6.7   6.3        1.2    8.6   0.2    3.0  4  Peripla_BP_2     Periplasmic binding protein
        6.5    6.8   6.7        5.7    7.0   0.7    3.7  3  PilJ             Type IV pili methyl-accepting chemotaxis tra
        9.5    6.6  16.8        1.7    9.0   2.0    5.2  4  DUF4164          Domain of unknown function (DUF4164)


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   2.6   1.6e-50   2.4e-47       1     314 [.     432     874 ..     432     875 .. 0.83

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 1.6e-50
                                       SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCT CS
                     UvrD-helicase   1 lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqess 77 
                                       ln+eq+ a+     ++ v+A+AG+GKTf l  r+ +l++e+ ++ d+il++TFT+kAa E+  R+ e++        
  gi|313117106|ref|YP_004038230.1| 432 LNAEQELAVYRNDIHNQVIAGAGTGKTFSLSCRVKYLVEEG-VSEDDILAMTFTRKAATEMSDRLDEMFD------- 500
                                       689999999999999**************************.*************************998....... PP

                                       T-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT..................................SHTTTEE CS
                     UvrD-helicase  78 dderlrlalqnlseanisTlHsfcqkilkkeanrig..................................ldpnfri 120
                                                  +s ++ sTlHsf+++ l++    +                                   l ++ ++
  gi|313117106|ref|YP_004038230.1| 501 -----------ISGVETSTLHSFGNRALNEIDPTLVqiedqsrlrevgrlirslyqadqefrkhydefleLYKEANL 566
                                       ...........789999***********9976665558888887776664444444333333333333332222222 PP

                                       ECHHHHH........HCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHHHCCCCCH..................... CS
                     UvrD-helicase 121 ldeedee........dlkqqellkelleksaddslnldkkkleklikelsksrnik..................... 168
                                       +d+++e         +                                       k                     
  gi|313117106|ref|YP_004038230.1| 567 KDDDKERrdflnslrY---------------------------------------Ksdttlrgeevqsrfneekdah 604
                                       2222211222222220.......................................1222233555555555555566 PP

                                       ............................................................................. CS
                     UvrD-helicase 169 ............................................................................. 168
                                                                                                                    
  gi|313117106|ref|YP_004038230.1| 605 tsvadllfkhdisyhyrkyaawagnpkdqayipdfslpehnivieylpseptrqrkrwynqkrsrdevekifegtdq 681
                                       66677778888888888888899****************************************************** PP

                                       ...........................................HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHS CS
                     UvrD-helicase 169 ...........................................keelslskskaeelrelvskakekqlspkelkka 202
                                                                                   e++  ++ +   ++e+v+kak + ++p+++ ++
  gi|313117106|ref|YP_004038230.1| 682 tllivsgdqtdpsrvetvvktqleklgvtfesplrgkalrdetYEHNICWRDVESTFAEFVKKAKTNRINPEDQLDN 758
                                       *****************************************9888888899999********************998 PP

                                       S.....TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHH CS
                     UvrD-helicase 203 f.....ekasdlqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyr 274
                                             e+   +++++  +l+eyq+  +++na Df d+++ ++ + +++e    +   +++++++DE+QD+n +Q++
  gi|313117106|ref|YP_004038230.1| 759 LsesedEELYHFSHAATRLLQEYQSVYDRYNAYDFVDMIVMATDAIKSGEI---DNIAQFRHVMVDEFQDLNLVQIE 832
                                       8876555555667888999****************************9543...34479****************** PP

                                       HHHHHHTTTTT..EEEEE-GGG--GGGGTB-THHHHHHHHHS CS
                     UvrD-helicase 275 ilkllasghee..lfmvGDpkQsIYgFRgAdielflkkkkdf 314
                                       +++ l s+h+   lf vGD+ QsIYgF+gA+++ f  + ++f
  gi|313117106|ref|YP_004038230.1| 833 FVQALLSRHDDarLFAVGDDWQSIYGFKGARPDYFIDFADHF 874
                                       *********999***********************9998877 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0   7.9e-30   1.2e-26       2     146 .]     437     860 ..     436     860 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 7.9e-30
                            AAA_19   2 reavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae....atTiHr 74 
                                       + av + ++ +  v+aG+GtGKT  l ++v++lve+g v+ ++il+++ft++Aa e+++rl+++       ++T+H+
  gi|313117106|ref|YP_004038230.1| 437 ELAV-YRNDIHNQVIAGAGTGKTFSLSCRVKYLVEEG-VSEDDILAMTFTRKAATEMSDRLDEMFDIsgveTSTLHS 511
                                       5666.666777789**********************9.667********************8885545555****** PP

                            AAA_19  75 lal.......................................................................... 77 
                                       +++                                                                          
  gi|313117106|ref|YP_004038230.1| 512 FGNralneidptlvqiedqsrlrevgrlirslyqadqefrkhydeflelykeanlkdddkerrdflnslryksdttl 588
                                       *99************************************************************************** PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|313117106|ref|YP_004038230.1| 589 rgeevqsrfneekdahtsvadllfkhdisyhyrkyaawagnpkdqayipdfslpehnivieylpseptrqrkrwynq 665
                                       ***************************************************************************** PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|313117106|ref|YP_004038230.1| 666 krsrdevekifegtdqtllivsgdqtdpsrvetvvktqleklgvtfesplrgkalrdetyehnicwrdvestfaefv 742
                                       ***************************************************************************** PP

                            AAA_19  78 ................................................ldfddlltealelleeaeeekklqeee.l 105
                                                                                        df d + +a  ++++  e +++ +++ +
  gi|313117106|ref|YP_004038230.1| 743 kkaktnrinpedqldnlsesedeelyhfshaatrllqeyqsvydrynaYDFVDMIVMATDAIKS-GEIDNI-AQFrH 817
                                       **********************************************999999999999999886.444556.4666* PP

                            AAA_19 106 livDEfqdvdelqyrLlkallgek..kklllvGDpdQliyvfr 146
                                       ++vDEfqd++ +q ++++all ++  ++l++vGD+ Q+iy f+
  gi|313117106|ref|YP_004038230.1| 818 VMVDEFQDLNLVQIEFVQALLSRHddARLFAVGDDWQSIYGFK 860
                                       ********************98774456************995 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   4.7       1.5   2.3e+03     175     233 ..      10     117 ..       1     216 [. 0.67
   2 ?   -4.3   8.8         6     9e+03     189     281 ..     385     574 ..     198     581 .. 0.60
   3 !   20.6   0.0   1.6e-07   0.00023       2      99 ..     881     987 ..     880     990 .. 0.77
   4 !   39.2   0.0   3.5e-13   5.2e-10     286     344 ..     992    1063 ..     988    1066 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                                       xxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                            UvrD_C 175 eeFieliraleeknl................elllkkiektaeerqalvskyadlfkelaeklaelkekseskr... 232
                                       +e+    r+le+k++                  l+ +ie++ ++rq++ ++y  l k ++e   +++e     r   
  gi|313117106|ref|YP_004038230.1|  10 DEYQ---RELEQKQNktlfnilpgglqrllyGSLVAEIESADQRRQEIEKEYHSLNKSAREITSTVEEMIRGPRrrg 83 
                                       6666...4444444444588888888888884477889999999999999999999999888888888888888667 PP

                                       .................................x RF
                            UvrD_C 233 .................................k 233
                                                                        +
  gi|313117106|ref|YP_004038230.1|  84 eplpseaqeslrtleeiradlsgllqdnkqflrT 117
                                       7776655544444444333332222222222220 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 6
                                       x............................................................................ RF
                            UvrD_C 189 l............................................................................ 189
                                                                                                                    
  gi|313117106|ref|YP_004038230.1| 385 Drsrfesiaseianirgqlegynqklieqqrdkyeetfsgfgdddlslnaeqelavyrndihnqviagagtgktfsl 461
                                       03333333333333333333333333333333333333333333336666666666666666666666666666666 PP

                                       ....xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxx RF
                            UvrD_C 190 ....elllkk.iektaeerqalvskyadlfkelaeklaelkekseskr.....................kkeeklen 240
                                           ++l+++ + +    ++++ +k a + +    ++ ++                             +++++l++
  gi|313117106|ref|YP_004038230.1| 462 scrvKYLVEEgVSEDDILAMTFTRKAATEMSDRLDEMFDISGVE---TstlhsfgnralneidptlvqiEDQSRLRE 535
                                       65555555555554444444444444443333333333333332...244578888888888888887655669999 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 241 lreLysllkelekkeeeeeveeklneileiatLseselees 281
                                       + +L++ l ++++ e  +++ e + e+ ++a L+++++e+ 
  gi|313117106|ref|YP_004038230.1| 536 VGRLIRSLYQADQ-EFRKHYDE-FLELYKEANLKDDDKERR 574
                                       9999999999999.44446554.999999999999988765 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 1.6e-07
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                            UvrD_C   2 vLekNyRStksLlkaankflenilnrrale.kekktvekgekivvl....eaeteeeEaekiaatikall.eknekl 72 
                                       +Le+NyR ++s++ka n++++n+  ++ ++ + +k+ e + ++++     +++ +++  +ki++++k+ + e + k 
  gi|313117106|ref|YP_004038230.1| 881 RLETNYRCPPSVVKAGNDLIKNNEAKTDKTvTAHKSLETTPRVHLVpgsdDFQYRRNGIKKIVQLVKSSVrESDRKP 957
                                       69******************9999994444455555555555554421117777788888888888888899999** PP

                                       xxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                            UvrD_C  73 ediavLvRsnkd...adkiskaLkkegipf 99 
                                       +d+ vL R+++    +++isk L+  +ip+
  gi|313117106|ref|YP_004038230.1| 958 NDVMVLARNQSGspfIREISKRLRDADIPV 987
                                       ********98753337999****9999986 PP

  == domain 4  score: 39.2 bits;  conditional E-value: 3.5e-13
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  286 kipiiTiHqAKGlEFdvVflagleegt...fPsyrskk..........ekrleEEkRlfYVaiTRAkkrLfi 344 
                                         ++++  HqAKG E   V++a+++ g    fP  +  +            +++EE+RlfYVa+TRA +rL i
  gi|313117106|ref|YP_004038230.1|  992 GVEVTKAHQAKGKEAGHVIIANAAGGMsdgFPPTERDRsltqlveidtGSHMDEERRLFYVALTRAEERLDI 1063
                                        5888889**************987553223774443335888889889779*****************9966 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.9e-08   7.3e-05       2      80 ..     432     516 ..     431     540 .. 0.75
   2 !    5.8   0.0    0.0066       9.8      81     127 ..     802     854 ..     764     919 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.9e-08
                            AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaag...grviglAptgkaAkvLa.......eelgi 68 
                                       lnaeQ+ av      +d    + ++AGtGKt++l+  ++ + ++g    ++++++ t kaA +++       + +g+
  gi|313117106|ref|YP_004038230.1| 432 LNAEQELAVY----RNDIHNQVIAGAGTGKTFSLSCRVKYLVEEGvseDDILAMTFTRKAATEMSdrldemfDISGV 504
                                       6677766663....33445668999***********99999999888899***************333333335568 PP

                            AAA_30  69 eastiakllkrl 80 
                                       e+st++++ +r 
  gi|313117106|ref|YP_004038230.1| 505 ETSTLHSFGNRA 516
                                       ******998654 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0066
                            AAA_30  81 k.....grarlepgtllivDEagmvdtkqlaallkaaekag.akvilvGDerQ 127
                                       +     +  ++++ + ++vDE   ++  q++ + + +++++ a++  vGD+ Q
  gi|313117106|ref|YP_004038230.1| 802 DaiksgEIDNIAQFRHVMVDEFQDLNLVQIEFVQALLSRHDdARLFAVGDDWQ 854
                                       1555654445666699*******9999999999988888544*********99 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0022       3.3       6      22 ..     997    1013 ..     993    1021 .. 0.82
   2 !   20.5   0.0   2.1e-07   0.00032      19      49 ..    1033    1061 ..    1029    1063 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                          UvrD_C_2    6 tihkaQGsefpaVivfd 22  
                                          h+a+G e+ +Vi+++
  gi|313117106|ref|YP_004038230.1|  997 KAHQAKGKEAGHVIIAN 1013
                                        56*************65 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.1e-07
                          UvrD_C_2   19 ivfdpdlaaarmgelrrrlLYtavTRArekl 49  
                                        +++++d+ +++  ++ rrl+Y+a+TRA e+l
  gi|313117106|ref|YP_004038230.1| 1033 QLVEIDTGSHM--DEERRLFYVALTRAEERL 1061
                                        67777777776..457************998 PP

>> CAMSAP_CC1  Spectrin-binding region of Ca2+-Calmodulin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.9e-05      0.15       5      41 ..     385     422 ..     382     424 .. 0.86
   2 ?   -1.7   0.0       1.9   2.8e+03      36      49 ..     695     708 ..     692     711 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.9e-05
                        CAMSAP_CC1   5 dssdsselaselselrlkLEE.KRRaIEaqKrkiEaal 41 
                                       d+s+ +  ase+ ++r +LE    + IE+q+ k E+++
  gi|313117106|ref|YP_004038230.1| 385 DRSRFESIASEIANIRGQLEGyNQKLIEQQRDKYEETF 422
                                       56677789************84689**********988 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                        CAMSAP_CC1  36 kiEaalarqRqklG 49 
                                       ++E++++ q +klG
  gi|313117106|ref|YP_004038230.1| 695 RVETVVKTQLEKLG 708
                                       89**********99 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.6   3.9e+03       6      21 ..     452     467 ..     442     509 .. 0.77
   2 ?    4.1   0.0     0.021        32      61     141 ..     813     899 ..     792     931 .. 0.64
   3 ?   -2.1   0.0       1.7   2.6e+03     183     201 ..     990    1011 ..     940    1013 .. 0.78
   4 ?    5.3   0.0    0.0095        14     213     232 ..    1044    1063 ..    1029    1065 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.6
                   Viral_helicase1   6 vpGcGKStlirkllrt 21 
                                        +G GK+ ++   ++ 
  gi|313117106|ref|YP_004038230.1| 452 GAGTGKTFSLSCRVKY 467
                                       5899999988777654 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                   Viral_helicase1  61 tkgkililDEylllhaGyilllaalskak...lvilfGDplQipfhsrnasfllahlpssl.shrvgrr.....tty 128
                                        +++ + +DE++ l+  +i++++al + +    ++++GD  Q+ +  +     +++++  + +h+++       t y
  gi|313117106|ref|YP_004038230.1| 813 AQFRHVMVDEFQDLNLVQIEFVQALLSRHddaRLFAVGDDWQSIYGFK---GARPDYFIDFaDHFSPAVetrleTNY 886
                                       3588999**********99998776543322278999*****988863...36888888886555544411111446 PP

                   Viral_helicase1 129 llpsdvaeilsak 141
                                       ++p  v+++ ++ 
  gi|313117106|ref|YP_004038230.1| 887 RCPPSVVKAGNDL 899
                                       6666655555555 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                   Viral_helicase1  183 r...evttvhevqGltfdkVtl 201 
                                        +   evt  h++ G+++ +V++
  gi|313117106|ref|YP_004038230.1|  990 EngvEVTKAHQAKGKEAGHVII 1011
                                        145559999*******999987 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0095
                   Viral_helicase1  213 sesrenllvAlTRhrkslvi 232 
                                         e+r  ++vAlTR+ ++l i
  gi|313117106|ref|YP_004038230.1| 1044 DEERRLFYVALTRAEERLDI 1063
                                        35699*********999866 PP

>> Clusterin  Clusterin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.5     0.066        98     112     198 ..     112     199 ..     101     273 .. 0.71
   2 ?   12.9   0.6   2.8e-05     0.042     138     241 ..     318     422 ..     282     452 .. 0.78
   3 ?   -2.2   0.2       1.1   1.6e+03     141     185 ..     519     564 ..     485     606 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.066
                         Clusterin 112 eeflnkispfsfwlneeridsllv.seedeeedaeleqledsfsqlssdvdslfnrslkvfkqmqqefdqafqsafl 187
                                       ++fl+ + + +    ++++++l++  + ++e+dae+++++ + + l+s++++  +    + +++++e+ + +++a  
  gi|313117106|ref|YP_004038230.1| 112 KQFLRTSEQTTAESLRSDVKELESyLKAKREQDAEISEIQGAIEALESEIQAECSAEGLLSEETESELRERVSKAEG 188
                                       6899999999998888888888864588899*****************99998888888888888888777777655 PP

                         Clusterin 188 sdldlteeefl 198
                                         ++++e  ++
  gi|313117106|ref|YP_004038230.1| 189 WITSAKEDIET 199
                                       54444444433 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.8e-05
                         Clusterin 138 edeeedaeleqledsfsqlssdvdslfnrslkvfkqmqqefdqafqsaflsdldlteeeflpalskarksrllrsl. 213
                                        +   d+++e le+   +l+s+v+++fn++ +++++ q+ +++ f +a+++ ++++e+  l  l+++ +sr+     
  gi|313117106|ref|YP_004038230.1| 318 AKSAFDNQIEVLEEWADELKSTVEDIFNERSYLATPEQRCYEKRFDEAQSRVVKTEENIDLNLLANSDRSRFESIAs 394
                                       5567799****************************************999999998887877777777777655446 PP

                         Clusterin 214 glenlfqpffdfsrsvfesvsevvtetl 241
                                       ++ n+   +   +++++e+ +++ +et+
  gi|313117106|ref|YP_004038230.1| 395 EIANIRGQLEGYNQKLIEQQRDKYEETF 422
                                       6667766666666666666666666665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                         Clusterin 141 eedaeleqleds..fsqlssdvdslfnrslkvfkqmqqefdqafqsa 185
                                       e d  l+q+ed+   +++ + ++sl++   ++ k+ ++ f +  ++a
  gi|313117106|ref|YP_004038230.1| 519 EIDPTLVQIEDQsrLREVGRLIRSLYQADQEFRKHYDE-FLELYKEA 564
                                       44555555554311334444444444444444444443.22223333 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.5     0.012        17      29     103 ..      37     115 ..      32     117 .. 0.87
   2 ?    8.5   4.5    0.0019       2.8      21      81 ..     118     182 ..     107     186 .. 0.80
   3 ?    6.5   0.4    0.0075        11       7      55 ..     180     229 ..     177     260 .. 0.81
   4 ?    1.1   0.1      0.38   5.7e+02      27      70 ..     303     346 ..     289     360 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                                       CSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT....HTTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  29 lgkdleevqallkkhkaleaelaaqqervkalnelaeklldeg....hsaseeieerleelnerWeeLkelaaerkq 101
                                       +g+ ++e+++  ++ +++e+e  +  +  ++++ + e+++       ++ + e +e+l  l+e  ++L+ l+++ kq
  gi|313117106|ref|YP_004038230.1|  37 YGSLVAEIESADQRRQEIEKEYHSLNKSAREITSTVEEMIRGPrrrgEPLPSEAQESLRTLEEIRADLSGLLQDNKQ 113
                                       78999**********************************88766666888899999999999999999999998888 PP

                                       HH CS
                          Spectrin 102 kL 103
                                        L
  gi|313117106|ref|YP_004038230.1| 114 FL 115
                                       66 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                                       HHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHTT...HTTHHHHHHH CS
                          Spectrin  21 eellssedlgkdleevqallkkhkaleaelaaqqervkaln.elaeklldeg...hsaseeieer 81 
                                        e+ + e l +d+ e+++ lk+ ++  ae+++ q+ ++al+ e++ ++ +eg   ++++ e++er
  gi|313117106|ref|YP_004038230.1| 118 SEQTTAESLRSDVKELESYLKAKREQDAEISEIQGAIEALEsEIQAECSAEGllsEETESELRER 182
                                       4566689999*******************************999999988875544444555555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0075
                                       HHHHHHHHHHHHHHHHHHCCSSC.SSSHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin   7 aqdadeleeWieekeellssedl.gkdleevqallkkhkaleaelaaqqe 55 
                                        ++++  e Wi+ ++e++++++l + dle   +l ++  +l++ ++ + e
  gi|313117106|ref|YP_004038230.1| 180 RERVSKAEGWITSAKEDIETRQLsETDLERFDELFERTSGLRQRVTIYNE 229
                                       5678999***********999999*************9999999888655 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.38
                                       SSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          Spectrin  27 edlgkdleevqallkkhkaleaelaaqqervkalnelaekllde 70 
                                       +++g+ l+ +++ +++  a+ ++++  +e+ ++l+ + e++++e
  gi|313117106|ref|YP_004038230.1| 303 RQYGSILQRTRKFVNAKSAFDNQIEVLEEWADELKSTVEDIFNE 346
                                       45566666666666666677777777777777777777666444 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.5      0.62   9.3e+02      89     135 ..     118     164 ..      98     171 .. 0.82
   2 ?   -3.6   0.0       4.4   6.6e+03     110     138 ..     232     260 ..     231     264 .. 0.84
   3 ?    8.6   0.2   0.00083       1.2      78     135 ..     278     336 ..     271     374 .. 0.91
   4 ?   -3.3   0.0       3.6   5.3e+03     113     152 ..     589     636 ..     585     697 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.62
                                       ---TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT CS
                      Peripla_BP_2  89 essntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse 135
                                        ++ t+esl   +++l   l  ++e ++ ++ei+++++a++s i+ e
  gi|313117106|ref|YP_004038230.1| 118 SEQTTAESLRSDVKELESYLKAKREQDAEISEIQGAIEALESEIQAE 164
                                       444455999999999999999*********************99876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.4
                                       -HHHHHHHHHHHHHHHHHHHHTS-TT.-E CS
                      Peripla_BP_2 110 ledeaeklvaeidsklaaaksaidsekpk 138
                                       +ed ++ l+ +++s++ ++k  +++  ++
  gi|313117106|ref|YP_004038230.1| 232 TEDTYKSLIGRLESEVPELKHEVEQSREE 260
                                       7999999*************999998554 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00083
                                       HHHHHS-EEE----TTS.HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT CS
                      Peripla_BP_2  78 llksgiptvivessntg.eslkeqiralgellgledeaeklvaeidsklaaaksaidse 135
                                       ll+s+++++  +s++ + ++ ++++r++g +l++++++  + + +d+ ++ +++ +d++
  gi|313117106|ref|YP_004038230.1| 278 LLESIADFLSSRSTEYIsAKQEDELRQYGSILQRTRKFVNAKSAFDNQIEVLEEWADEL 336
                                       7899**********9999********************************999999988 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHHHHHHHTS-TT.........-EEEEEEEETTE..EE CS
                      Peripla_BP_2 113 eaeklvaeidsklaaaksaidse........kpkpvlvfggadeggyv 152
                                       ++e+++++++++ +a  s +d +         +k +++ g+  +++y+
  gi|313117106|ref|YP_004038230.1| 589 RGEEVQSRFNEEKDAHTSVADLLfkhdisyhYRKYAAWAGNPKDQAYI 636
                                       778888888888888777777665444444333444444444444444 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.7    0.0038       5.7      37      98 ..      46     121 ..      31     130 .. 0.75
   2 ?    1.7   0.3      0.17   2.6e+02      40      89 ..     119     162 ..     113     186 .. 0.78
   3 ?   -2.7   0.0       3.9   5.8e+03      76     104 ..     391     415 ..     360     425 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0038
                              PilJ  37 a.....ydaaearaqlretiaqfdrtlaalrlgdpapgllvpae.........avraqleaveqlWqelkkpaeaa 98 
                                       +     ++++++  +l+++++++  t++++ +g   +g + p+e         ++ra+l+++ q+ +++++  e+ 
  gi|313117106|ref|YP_004038230.1|  46 SadqrrQEIEKEYHSLNKSAREITSTVEEMIRGPRRRGEPLPSEaqeslrtleEIRADLSGLLQDNKQFLRTSEQT 121
                                       34445589999999*****************************999777777777777777777777777766544 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.17
                              PilJ  40 aaearaqlretiaqfdrtlaalrlgdpapgllvpaeavraqleaveqlWq 89 
                                        ++  ++lr+ +++++  l+a r++d++      + +++ ++ea+e++ q
  gi|313117106|ref|YP_004038230.1| 119 EQTTAESLRSDVKELESYLKAKREQDAEI-----S-EIQGAIEALESEIQ 162
                                       4778899*****************99996.....2.67777777666654 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.9
                              PilJ  76 avraqleaveqlWqelkkpaeaalaqqdd 104
                                       ++ +++++++ + + + + +     +q++
  gi|313117106|ref|YP_004038230.1| 391 SIASEIANIRGQLEGYNQKL----IEQQR 415
                                       44455555555555554444....33333 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.0      0.81   1.2e+03       3      69 ..      51     122 ..      49     124 .. 0.77
   2 ?    9.0   2.0    0.0011       1.7       8      47 ..     121     160 ..     115     163 .. 0.90
   3 ?    3.4   0.1     0.063        94      30      87 ..     229     286 ..     204     288 .. 0.88
   4 ?    0.1   0.1      0.68     1e+03      23      53 ..     321     352 ..     304     377 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.81
                           DUF4164   3 tkeleaaltrLeaaldsLEkavdrrleaerkr.....deleaeiealgedrsRLaeeLdqaearaarleevn 69 
                                       ++e+e+  + L+++  ++++ v+++++  r r     +e+++ ++ l+e r+ L   L + +  +++ e+++
  gi|313117106|ref|YP_004038230.1|  51 RQEIEKEYHSLNKSAREITSTVEEMIRGPRRRgeplpSEAQESLRTLEEIRADLSGLLQDNKQFLRTSEQTT 122
                                       578888889999999999999999999988888888888888899998888888777766666555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                           DUF4164   8 aaltrLeaaldsLEkavdrrleaerkrdeleaeiealged 47 
                                         ++ L+  +++LE+ +++++e++++ +e++  ieal+++
  gi|313117106|ref|YP_004038230.1| 121 TTAESLRSDVKELESYLKAKREQDAEISEIQGAIEALESE 160
                                       55778999*****************************986 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.063
                           DUF4164  30 aerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietiravL 87 
                                       + +++d +++ i +l+++   L +e  q++ +   l +  +E+  +L+ + e+i + L
  gi|313117106|ref|YP_004038230.1| 229 ESQTEDTYKSLIGRLESEVPELKHEVEQSREEGVPLPREHDEIVCELDPLLESIADFL 286
                                       345568899999*****************************************99877 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.68
                           DUF4164  23 avdrrleaerkr.deleaeiealgedrsRLae 53 
                                       a d+++e  ++  del++++e + ++rs La 
  gi|313117106|ref|YP_004038230.1| 321 AFDNQIEVLEEWaDELKSTVEDIFNERSYLAT 352
                                       55666666555459999999999999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1292  (0.072062); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.96u 0.30s 00:00:01.26 Elapsed: 00:00:00.51
# Mc/sec: 7017.08
//
Query:       gi|313117107|ref|YP_004038231.1|  [L=287]
Description: hypothetical protein Hbor_35750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.31   11.0   4.0       0.46   10.5   4.0    1.2  1  MSA-2c    Merozoite surface antigen 2c


Domain annotation for each model (and alignments):
>> MSA-2c  Merozoite surface antigen 2c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.0   2.6e-05      0.46     133     195 ..     184     243 ..     133     247 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.6e-05
                            MSA-2c 133 tdiaalkdvteeLlkelqekkPsrt.ssaetPaPsdaesaaaqPPeskpaqaPaPtspsqsees 195
                                       t  +   d+t  +  +++  +Ps++ +s+ +P+P+ +    a PP ++p  +P+P +p  + +s
  gi|313117107|ref|YP_004038231.1| 184 TSQSGDADTTRTVTNTEPATTPSPSvQSTSIPSPTPT----AVPPTAQPIVSPTPITPDVTTDS 243
                                       6666677888888889999999988356669999887....789*99***********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1923.40
//
Query:       gi|313117108|ref|YP_004038232.1|  [L=177]
Description: hypothetical protein Hbor_35760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-10   38.8   0.9    1.2e-09   38.2   0.9    1.4  1  bPH_2     Bacterial PH domain
  ------ inclusion threshold ------
      0.022   13.8   0.1      0.029   13.4   0.1    1.1  1  PalH      PalH/RIM21
       0.12   12.5   0.0       0.22   11.7   0.0    1.3  1  S1FA      DNA binding protein S1FA


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.9   2.1e-13   1.2e-09       4      79 ..     100     174 ..      95     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.1e-13
                             bPH_2   4 ttytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeelael 79 
                                       t+y +t +rvv ++ +l+ ++ ++p +++q ++ +++l++r+l +g+++ie+ag+++   ++ +r++ d+ +l + 
  gi|313117108|ref|YP_004038232.1| 100 TKYYVTTDRVVETYQLLSVTQKTMPQRQVQGIEKRKTLIERLLSVGHVRIESAGDTG-TSRIIARNIRDPTQLVNA 174
                                       56******************************************************7.89999***9999998775 PP

>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.9e-06     0.029      68     146 ..      70     143 ..      66     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.9e-06
                              PalH  68 iipilfslsaicVitwmLvlllfllprknhkrplllklavllvaivltialakttkevfeeqyskgyqdaselekei 144
                                       ++p+++ +++++V+ w+ +l l  l r     + l+k +v +  +v+t++l ++t++++ + + +g+ + + l +++
  gi|313117108|ref|YP_004038232.1|  70 SLPLAYPVCVSVVGVWFYTLGLTRLWR-----NSLTKYYVTTDRVVETYQLLSVTQKTMPQRQVQGIEKRKTLIERL 141
                                       689****************87777666.....47*************************999999999999988877 PP

                              PalH 145 vs 146
                                       +s
  gi|313117108|ref|YP_004038232.1| 142 LS 143
                                       66 PP

>> S1FA  DNA binding protein S1FA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.6e-05      0.22      26      57 ..     110     141 ..     106     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                              S1FA  26 vgnyvlyvyaqktlPprkkkPvskkkmkrekl 57 
                                       v  y l   +qkt+P+r+ + + k+k   e+l
  gi|313117108|ref|YP_004038232.1| 110 VETYQLLSVTQKTMPQRQVQGIEKRKTLIERL 141
                                       778999999*****************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1206.34
//
Query:       gi|313117109|ref|YP_004038233.1|  [L=323]
Description: hypothetical protein Hbor_35770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.037   14.0   3.6       0.47   10.4   0.8    2.5  2  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
       0.17   11.9   5.2       0.11   12.4   1.4    2.2  2  DUF2116         Uncharacterized protein containing a Zn-ribbo
       0.56   10.3   5.5        9.8    6.3   1.0    2.5  2  DZR             Double zinc ribbon


Domain annotation for each model (and alignments):
>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.8   7.9e-05      0.47       6      20 ..      45      59 ..      40      64 .. 0.83
   2 ?    3.5   0.1     0.012        70       4      12 ..     234     242 ..     230     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.9e-05
                      zf-dskA_traR  6 CeeCGEpIpeaRlra 20
                                      Ce+CG  Ip+ R r 
  gi|313117109|ref|YP_004038233.1| 45 CEVCGGSIPPTRARC 59
                                      ************885 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.012
                      zf-dskA_traR   4 gsCeeCGEp 12 
                                       +sC  CGE 
  gi|313117109|ref|YP_004038233.1| 234 RSCPNCGEA 242
                                       46*****95 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.4   1.9e-05      0.11       5      22 ..      44      61 ..      41      66 .. 0.89
   2 ?    0.3   0.1      0.12   7.1e+02       4      12 ..     234     242 ..     232     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                           DUF2116  5 HCivCGkaIpldesfCse 22
                                      HC vCG +Ip++   C +
  gi|313117109|ref|YP_004038233.1| 44 HCEVCGGSIPPTRARCVD 61
                                      ************999976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                           DUF2116   4 kHCivCGka 12 
                                       + C++CG+a
  gi|313117109|ref|YP_004038233.1| 234 RSCPNCGEA 242
                                       56*****98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2    0.0026        15       7      31 ..      37      59 ..      25      70 .. 0.68
   2 ?    6.3   1.0    0.0016       9.8      11      34 ..     232     270 ..     205     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0026
                               DZR  7 elppdarfCseCgtklkavaaedrC 31
                                      +++++   C+ Cg +++  ++  rC
  gi|313117109|ref|YP_004038233.1| 37 DVEASPAHCEVCGGSIP--PTRARC 59
                                      45555566666666665..334444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0016
                               DZR  11 darfCseCgtklkavaa...............edrCpsC 34 
                                       ++r C++Cg++ +   +                 +C  C
  gi|313117109|ref|YP_004038233.1| 232 RNRSCPNCGEATQHIFDgydgghpsvhvdgvaLWTCLTC 270
                                       566677777666533335555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2481.12
//
Query:       gi|313117110|ref|YP_004038234.1|  [L=1090]
Description: DEAD_2 domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-29  100.8   0.0    1.8e-28   99.8   0.0    1.5  1  Helicase_C_2  Helicase C-terminal domain
    4.8e-11   42.6   0.0    4.4e-10   39.5   0.0    2.1  2  DEAD_2        DEAD_2
  ------ inclusion threshold ------
      0.017   14.6   0.1      0.037   13.5   0.1    1.5  1  PhoH          PhoH-like protein
      0.022   14.8   0.0      0.077   13.0   0.0    1.9  2  ResIII        Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.0   4.1e-32   1.8e-28       9     158 ..     767     915 ..     759     930 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 4.1e-32
                      Helicase_C_2   9 pggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidfsddll 85 
                                       +g++lv +p+y+  e ++++lk++++sk++++ +++++ +++++le++ +     a+++ + rG++ EG+d+ +++l
  gi|313117110|ref|YP_004038234.1| 767 RGNILVAMPNYREAEWAYNYLKKQGSSKRFHLDQSSSALETDETLESFFA--DGDAVIFTSSRGTITEGVDYDGEKL 841
                                       689****************************99998999***********..************************* PP

                      Helicase_C_2  86 raviivglPfpnpkdpeveakreyldekgk.knsgkewylpealravnQaiGRliRhkdDygaivllDeRfake 158
                                         ++ vg+P+ ++++ +++a  e +de+ + k++++++ + +a+r+v+Qa+GR+iR +d+ g  +l+DeR+ + 
  gi|313117110|ref|YP_004038234.1| 842 HGCVAVGIPLLPTNSKRIDAVIEAYDERIGvKSGFETALMIPAVRKVRQAFGRVIRGSDEAGFRLLVDERYGST 915
                                       ***************************9987788*************************************874 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.092   4.1e+02       7      39 ..     144     177 ..     141     179 .. 0.84
   2 !   39.5   0.0   9.8e-14   4.4e-10      89     172 ..     337     423 ..     325     427 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHHHHHHHCHH.HS---EEEE--CCC CS
                            DEAD_2   7 sqleqvvkelkklesykkk.kekvkvviLgSRkn 39 
                                       +ql+q+v+e+k +++   + k+ v +v++ +R +
  gi|313117110|ref|YP_004038234.1| 144 QQLHQFVREMKGINASLPEaKAPVSTVVIRGRTD 177
                                       79**********9876665689999999999976 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 9.8e-14
                                       HHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTCCCHHHH CS
                            DEAD_2  89 llleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslk...gislknsivilDEAhNiedv 162
                                       ++ ++v+d e+l ++  + ++CP+ ++  l+  a++++  Y  L+d+++r  ++   g+  +++iv +DE+h ie+ 
  gi|313117110|ref|YP_004038234.1| 337 HADHHVFDQETLFQTAASRGICPHEAMAMLAGRAEVVLGNYYHLFDPQTRLLTDdkiGLLDSETIVAVDEGHQIEER 413
                                       567899********************************************99998676778999************* PP

                                       HHHCC-EEEE CS
                            DEAD_2 163 ceeaasveis 172
                                       +++++s++++
  gi|313117110|ref|YP_004038234.1| 414 VRDMLSMSLD 423
                                       *******986 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.2e-06     0.037      11      48 ..      80     117 ..      73     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.2e-06
                                       HHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS CS
                              PhoH  11 eylealkkndivfaiGpaGtGKtylavalavealkkkk 48 
                                       ++le l++n   +  G  GtGKt+ av+ +++a+++++
  gi|313117110|ref|YP_004038234.1|  80 TFLELLSENGYYVFEGACGTGKTLAAVTGGIHAIRDQS 117
                                       567889999999*********************99865 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05     0.077       5      53 ..      71     118 ..      68     178 .. 0.73
   2 ?   -2.4   0.0      0.95   4.2e+03     106     146 ..     372     412 ..     366     428 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S... CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgk 53 
                                       ++ Q++a++ +le l+  ++  ++++ a+GtGKTl a +  i +++ +  
  gi|313117110|ref|YP_004038234.1|  71 YQDQIDAVDTFLELLS--ENGYYVFEGACGTGKTLAAvTGGIHAIRDQST 118
                                       6789**********96..888999**********9986556666655544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.95
                                       EEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS CS
                            ResIII 106 ilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlga 146
                                       +++ ++  l  ++++   +++  l d++ ++ +DE H + +
  gi|313117110|ref|YP_004038234.1| 372 VVLGNYYHLFDPQTRLLTDDKIGLLDSETIVAVDEGHQIEE 412
                                       55555555555553334444455566777999*****9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1090 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 6932.58
//
Query:       gi|313117111|ref|YP_004038235.1|  [L=493]
Description: ATPase AAA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-31  107.0   0.0    1.6e-30  106.3   0.0    1.4  1  AAA              ATPase family associated with various cellul
    1.7e-08   34.1   0.1    4.4e-08   32.8   0.1    1.6  1  AAA_lid_3        AAA+ lid domain
    2.5e-06   27.6   0.0    5.6e-06   26.4   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    7.9e-05   22.8   0.0     0.0002   21.5   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    0.00012   22.5   1.1    0.00054   20.4   0.1    2.3  2  AAA_16           AAA ATPase domain
    0.00044   19.6   0.0     0.0028   16.9   0.0    1.9  2  TIP49            TIP49 P-loop domain
     0.0011   18.3   0.2       0.14   11.3   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0014   18.8   0.0     0.0025   18.0   0.0    1.6  1  AAA_33           AAA domain
     0.0014   18.4   0.0     0.0026   17.5   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0015   18.8   0.0      0.058   13.7   0.0    2.4  1  AAA_22           AAA domain
     0.0087   15.8   0.0      0.038   13.7   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.028   13.6   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
      0.019   14.3   0.0       0.04   13.3   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.023   13.8   0.0      0.047   12.8   0.0    1.4  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.025   14.4   2.6      0.042   13.6   0.0    2.3  3  AAA_11           AAA domain
      0.028   14.9   0.8       0.72   10.3   0.1    2.4  2  AAA_23           AAA domain
      0.029   14.9   0.1      0.083   13.4   0.0    1.7  1  ABC_tran         ABC transporter
       0.04   14.0   0.0      0.082   12.9   0.0    1.5  1  AAA_14           AAA domain
      0.042   13.8   0.0      0.097   12.6   0.0    1.6  2  NACHT            NACHT domain
      0.058   13.1   0.0       0.11   12.2   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.058   13.6   0.0        4.8    7.4   0.0    2.6  2  AAA_28           AAA domain
      0.059   13.8   0.0       0.13   12.7   0.0    1.6  1  RNA_helicase     RNA helicase
      0.065   13.2   0.0       0.14   12.2   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.11   12.6   0.0       0.23   11.6   0.0    1.4  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.13   12.3   0.0       0.28   11.3   0.0    1.6  1  SKI              Shikimate kinase
       0.17   11.4   0.0       0.29   10.6   0.0    1.3  1  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0   2.3e-33   1.6e-30       1     131 [.     285     413 ..     285     414 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 2.3e-33
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       +l+ GppGtGKTl+a+a+a+ l+++f+e+  ++l+ +y+ +s++ i+ lf+ea++     ++fiDE+++l ++r   
  gi|313117111|ref|YP_004038235.1| 285 LLFQGPPGTGKTLFARAIANALDRPFVELTQADLTHEYINKSPQLIKRLFEEAQHLG--GVVFIDEAEQLLSDRtrG 359
                                       6999*************************************************9998..***************988 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++++ e+++v n +l++l ++++   ++i++++tn+ d +d+a+lr gR+d ++ei+
  gi|313117111|ref|YP_004038235.1| 360 ENAHAEDQKVTNMFLSALTKEEQ---DFILLLTTNQRDGMDEAILRpGRIDCEFEIG 413
                                       88999*****************9...6**************************9997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.1   6.3e-11   4.4e-08       4      43 ..     440     479 ..     438     481 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6.3e-11
                         AAA_lid_3   4 lkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                       +k+LAe T+G+SGADl+al + A l A +++ k+++ +++
  gi|313117111|ref|YP_004038235.1| 440 VKRLAEHTDGWSGADLEALANQAKLKAAEQDAKHLEWRHI 479
                                       689****************************999988887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   8.2e-09   5.6e-06       2     131 ..     285     397 ..     284     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 8.2e-09
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                       +l +GppGtgK+ +a+ +a al r++++ + ++d+t e +  + +       l +  + +a   g ++++DE e++ 
  gi|313117111|ref|YP_004038235.1| 285 LLFQGPPGTGKTLFARAIANALDRPFVE-LTQADLTHEYINKSPQ-------LIKRLFEEAQHLGGVVFIDEAEQLL 353
                                       899********************99876.4455666666665555.......566666666669**********999 PP

                                       HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TT CS
                             AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnels 131
                                       s+ +   +   e++++  + +  l+k+++d     f ++ t+n++d     ++
  gi|313117111|ref|YP_004038235.1| 354 SDRTRGENAHAEDQKVTNMFLSALTKEEQD-----FILLLTTNQRD----GMD 397
                                       999999999999999998888888888886.....99999999999....333 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.9e-07    0.0002       6     100 ..     285     374 ..     280     379 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.9e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                       +l+ gp g+Gkt+ a+a+a+ l+ +   +l+ ad +     +++ +l++rl  +++       gG+v++DE +   +
  gi|313117111|ref|YP_004038235.1| 285 LLFQGPPGTGKTLFARAIANALD-RPFVELTQADLTHEYI-NKSPQLIKRLFEEAQ-----HLGGVVFIDEAEQLLS 354
                                       699********************.7777777777665444.466666666665554.....5589*********999 PP

                                       -..---------HHHHHHHH CS
                             AAA_2  83 k..essgadvSregVqrdLL 100
                                          + ++a    + V +++L
  gi|313117111|ref|YP_004038235.1| 355 DrtRGENAHAEDQKVTNMFL 374
                                       86666666677777888887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       1.6   1.1e+03      76     117 ..     190     232 ..     187     272 .. 0.76
   2 !   20.4   0.1   7.8e-07   0.00054      24     139 ..     281     386 ..     267     399 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.6
                            AAA_16  76 lareellrqlldeaesaeleawrekleealaavpelagaea.s 117
                                       +++e+l++ + ++ae+a+ e++++  ee l +++e++ +   +
  gi|313117111|ref|YP_004038235.1| 190 IDKEKLVKIVQQNAEEALTEEDADSTEEYLDEGDEDDEDTGiE 232
                                       5678999999999999999999999999888666655554443 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 7.8e-07
                            AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde..........a 89 
                                       p + +l+ G++G+GK+  +r++++al +    f++ +  +l+   +   +++     +l++ l +e          +
  gi|313117111|ref|YP_004038235.1| 281 PsRGLLFQGPPGTGKTLFARAIANALDRP---FVELTQADLT--HE---YINKS-P-QLIKRLFEEaqhlggvvfiD 347
                                       4589*******************999999...4443333331..12...55555.4.66666666633333334444 PP

                            AAA_16  90 esaeleawrekleealaavpelagaeasrllellkrll.allsrderplvl 139
                                       e+ +l  +r++ e a            ++  +++++++ + l+++e+ ++l
  gi|313117111|ref|YP_004038235.1| 348 EAEQLLSDRTRGENA------------HAEDQKVTNMFlSALTKEEQDFIL 386
                                       444444444444444............444444444444333333333444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.1e-06    0.0028      51     102 ..     283     332 ..     280     339 .. 0.90
   2 ?    1.3   0.0      0.22   1.5e+02     266     289 ..     330     351 ..     315     355 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqa 102
                                       r++L++Gp+gtGkt  a ai+++l    pfv l+ +++    ++k+  l++ 
  gi|313117111|ref|YP_004038235.1| 283 RGLLFQGPPGTGKTLFARAIANALD--RPFVELTQADLTHEYINKSPQLIKR 332
                                       89*********************97..7*********999999998877765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.22
                                       XXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 266 vakyveegkaeivpGvlfiDevhm 289
                                       +++  e  +a+ + Gv+fiDe+  
  gi|313117111|ref|YP_004038235.1| 330 IKRLFE--EAQHLGGVVFIDEAEQ 351
                                       555555..48999********975 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00021      0.14       5      47 ..     286     333 ..     282     341 .. 0.85
   2 !    6.3   0.2     0.007       4.8      73     133 ..     325     391 ..     314     399 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                           DUF2075   5 lVtGvaGtGKtvvllnllael.....eddeeertavylsvNhplvlvl 47 
                                       l +G +GtGKt+ + +++++l     e ++ + t+ y+ ++ +l++ l
  gi|313117111|ref|YP_004038235.1| 286 LFQGPPGTGKTLFARAIANALdrpfvELTQADLTHEYINKSPQLIKRL 333
                                       679******************988888888999999999988888766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.007
                           DUF2075  73 nlsefkkaeekkeepkedvvivDEAhrllt.....ksdqaekqseenqlkelmkr.akvvvalvDeg 133
                                       +  +  k+  ++++    vv +DEA  ll+     ++ +ae+q+ +n++ + + + ++  ++l+  +
  gi|313117111|ref|YP_004038235.1| 325 KSPQLIKRLFEEAQHLGGVVFIDEAEQLLSdrtrgENAHAEDQKVTNMFLSALTKeEQDFILLLTTN 391
                                       4443334444666667789******999996766644445555555555554444355555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.7e-06    0.0025       3      42 ..     286     338 ..     285     463 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.7e-06
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdt...........lrrrlfgtdq 42 
                                       l+ G+pG+GK+ +a+ ++++l+  +v l++ +           l++rlf++ q
  gi|313117111|ref|YP_004038235.1| 286 LFQGPPGTGKTLFARAIANALDrpFVELTQADltheyinkspqLIKRLFEEAQ 338
                                       799******************99988899888677777777775555554222 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.8e-06    0.0026      35      96 ..     284     352 ..     243     372 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvkl.kitsg....Pvlekagdlaalltnlee..kdvlfideihrl 96 
                                        +l++GpPG Gkt +a+ ia+ l+  + + t +      ++k+ +l+  l +  +  + v+fide  +l
  gi|313117111|ref|YP_004038235.1| 284 GLLFQGPPGTGKTLFARAIANALDRPFvELTQAdlthEYINKSPQLIKRLFEEAQhlGGVVFIDEAEQL 352
                                       479********************9764144443111146788888877665443312689999998776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   8.4e-05     0.058       9      49 ..     286     317 ..     280     388 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.4e-05
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49 
                                       +  G++GtGKT+ +r +++ l         ++++v+ t + 
  gi|313117111|ref|YP_004038235.1| 286 LFQGPPGTGKTLFARAIANAL---------DRPFVELTQAD 317
                                       556999999999999999999.........45555333332 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.4e-05     0.038      25      66 ..     285     323 ..     266     331 .. 0.85
   2 ?   -1.1   0.0       1.9   1.3e+03      89     105 ..     334     352 ..     326     356 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                                       EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCH CS
                   Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfvavncaaipeell 66 
                                       +l +G  GtGK+l+arai +a +   +pfv++  a++++e +
  gi|313117111|ref|YP_004038235.1| 285 LLFQGPPGTGKTLFARAIANALD---RPFVELTQADLTHEYI 323
                                       799***************98766...7999999999888766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                                       HHHTT..TSEEEEETGGGS CS
                   Sigma54_activat  89 fekad..gGtlfLDeigel 105
                                       fe+a+  gG++f+De ++l
  gi|313117111|ref|YP_004038235.1| 334 FEEAQhlGGVVFIDEAEQL 352
                                       67776448*******9887 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.1e-05     0.028      21     157 ..     240     398 ..     228     403 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                            DUF815  21 evdevklddLvgidkqkealventeqfleg..........lpannvLLwGarGtGKSslvkallneyaeeg..Lrli 85 
                                       e+ ev+++d+ g+++ ke+l + + + l+           +p++ +L+ G  GtGK    +a+ n++ +    L   
  gi|313117111|ref|YP_004038235.1| 240 EPPEVRFEDIGGYNDVKEELSSQVINPLQSdsesydrfdvEPSRGLLFQGPPGTGKTLFARAIANALDRPFveLTQA 316
                                       5566666667777666666655443333221111111111688999***********************99334445 PP

                            DUF815  86 evekedlkelpklvellrerperf..ilfvDD....LsFeeeeeey....ksLksvLeGsleakpenvliyaTsNrR 152
                                       ++++e +++ p+l++ l e+++++  ++f+D     Ls  ++ e++    +++  ++  +l+++ ++ ++  T+N+R
  gi|313117111|ref|YP_004038235.1| 317 DLTHEYINKSPQLIKRLFEEAQHLggVVFIDEaeqlLSDRTRGENAhaedQKVTNMFLSALTKEEQDFILLLTTNQR 393
                                       68899************9988876669***97444344322221112333566666667788888888888888888 PP

                            DUF815 153 hLlpe 157
                                       + + e
  gi|313117111|ref|YP_004038235.1| 394 DGMDE 398
                                       76655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.9e-05      0.04      25      46 ..     285     306 ..     281     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlpsll 46 
                                       ll+ GppG+GKt+ a+++++ l
  gi|313117111|ref|YP_004038235.1| 285 LLFQGPPGTGKTLFARAIANAL 306
                                       89**************998766 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.8e-05     0.047      83     139 ..     253     307 ..     242     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-05
                         Parvo_NS1  83 nriykllslngynpvevgqvllawlskqlgkrntvwfyGpantGktnlaeaIakavp 139
                                       n++ ++ls +  np++  ++++  ++ +  +   ++f Gp+ tGkt  a+aIa+a++
  gi|313117111|ref|YP_004038235.1| 253 NDVKEELSSQVINPLQSDSESYDRFDVE--PSRGLLFQGPPGTGKTLFARAIANALD 307
                                       7788888888889999998888888887..777899******************987 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.4       2.6   1.8e+03     121     173 ..     176     198 ..     127     232 .. 0.39
   2 ?   13.6   0.0   6.1e-05     0.042      20      41 ..     285     306 ..     268     340 .. 0.79
   3 ?   -2.5   0.0       4.9   3.4e+03     210     228 ..     333     351 ..     328     357 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.6
                            AAA_11 121 e............kaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkke 173
                                       +            +                                           +++kl k 
  gi|313117111|ref|YP_004038235.1| 176 NhsinpaesdpepD------------------------------------------IDKEKLVKI 198
                                       01111111111111..........................................111111111 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.1e-05
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                        l+qGPPGtgKT +  ++ ++l
  gi|313117111|ref|YP_004038235.1| 285 LLFQGPPGTGKTLFARAIANAL 306
                                       699*********9999999988 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.9
                            AAA_11 210 lleklakkfdvviIDEAaq 228
                                       l+e++++   vv IDEA q
  gi|313117111|ref|YP_004038235.1| 333 LFEEAQHLGGVVFIDEAEQ 351
                                       677777777899*****87 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.19   1.3e+02      70     162 ..     123     222 ..      86     260 .. 0.66
   2 ?   10.3   0.1     0.001      0.72       9      84 ..     273     339 ..     270     481 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.19
                            AAA_23  70 kvkayveltfenkdgrytrsiererelskkkgkttkkaklellei.....deleqfisellgskki......ilnli 135
                                       +  + ++ +fe+k+++     +++   +++ g+t +++  ++ ++     ++ + + +++++  ++        + +
  gi|313117111|ref|YP_004038235.1| 123 HPYGTYSPEFESKNRE----TQWQTDSTSTVGETGSDTPASQPTEsndksEAEQSNHNHSINPAESdpepdiDKEKL 195
                                       4444466678777774....778888888888888777555555522222444444444555554477777766666 PP

                            AAA_23 136 lflgqerfeefelkdkkerleelekel 162
                                       + + q+++ee +++++ +  ee+ +e 
  gi|313117111|ref|YP_004038235.1| 196 VKIVQQNAEEALTEEDADSTEEYLDEG 222
                                       666677766667776666666665554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.001
                            AAA_23   9 sfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdg 84 
                                       s+++++++ s+gl l+ Gp G+GKT + +Ai  aL   + +l          +d + e  +k ++ +++ fe  + 
  gi|313117111|ref|YP_004038235.1| 273 SYDRFDVEPSRGL-LFQGPPGTGKTLFARAIANALDRPFVELTQ--------ADLTHEYINKSPQLIKRLFEEAQH 339
                                       89999********.******************999764443333........222222233444446666655444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012     0.083       6      80 ..     277     365 ..     275     407 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.. RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren.. 79 
                                       +++++++ + + G+ G+GK+ +++++a+ l+     ++l ++dl+++ ++++ + i+ l++e+q+  ++  + e   
  gi|313117111|ref|YP_004038235.1| 277 FDVEPSRGLLFQGPPGTGKTLFARAIANALDR--PFVELTQADLTHEYINKSPQLIKRLFEEAQHLGGVVfIDEAeq 351
                                       8899999999******************9975..6677788888887777777777777777666655542333355 PP

                                       .............H CS
                                       .............x RF
                          ABC_tran  80 .............e 80 
                                                    e
  gi|313117111|ref|YP_004038235.1| 352 llsdrtrgenahaE 365
                                       54444444436532 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.082       5      76 ..     285     352 ..     282     396 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       l+ +G+  +GKT +++ +++ l    + +++++  d + + ++++ +l++ ++e++++    ++f+DE+ ++
  gi|313117111|ref|YP_004038235.1| 285 LLFQGPPGTGKTLFARAIANALD---RPFVELTQADLTHEYINKSPQLIKRLFEEAQH-LGGVVFIDEAEQL 352
                                       5678999*******999997777...88888887777776666544566666666555.6789*****9877 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014     0.097       3      26 ..     285     308 ..     283     322 .. 0.87
   2 ?   -2.8   0.0       7.6   5.3e+03      88     117 ..     347     381 ..     324     400 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       EEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                       ++ qG++G GKT +++ +a a+ +
  gi|313117111|ref|YP_004038235.1| 285 LLFQGPPGTGKTLFARAIANALDR 308
                                       689****************99976 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.6
                                       E-STT-SS-TCH..............HHHHHCTTT CS
                             NACHT  88 DglDelvtdlgq.....kekqpvrtlLselirkkl 117
                                       D +++l +d        +e q+v +++ + ++k+ 
  gi|313117111|ref|YP_004038235.1| 347 DEAEQLLSDRTRgenahAEDQKVTNMFLSALTKEE 381
                                       44444444433355666666666666666666633 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.11      47      70 ..     282     305 ..     268     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                         IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                       + ++++ Gp+G+GK+ +a a++ +
  gi|313117111|ref|YP_004038235.1| 282 SRGLLFQGPPGTGKTLFARAIANA 305
                                       5678999**************976 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.007       4.8       4      27 ..     287     311 ..     285     325 .. 0.80
   2 ?    3.7   0.0     0.098        67      94     155 ..     324     387 ..     313     393 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.007
                            AAA_28   4 itGgestGKTtlleaLaar.gypvv 27 
                                       + G+++tGKT  ++a+a+  + p v
  gi|313117111|ref|YP_004038235.1| 287 FQGPPGTGKTLFARAIANAlDRPFV 311
                                       67***************76565555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.098
                            AAA_28  94 geaeaelea..aarekrydlvfllppapeidddgeRre.dleereaiderlrealrelgipviiv 155
                                       ++ +++l +   +++++   v++ ++a+ + +d +R e   +e +++++++++al++   ++i +
  gi|313117111|ref|YP_004038235.1| 324 NK-SPQLIKrlFEEAQHLGGVVFIDEAEQLLSDRTRGEnAHAEDQKVTNMFLSALTKEEQDFILL 387
                                       33.5555553334455566699999999889*****87366889***********9998888876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00019      0.13       2      26 ..     286     310 ..     285     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl 26 
                                       +++Gp+g+GK+++a+ +a+al + +
  gi|313117111|ref|YP_004038235.1| 286 LFQGPPGTGKTLFARAIANALDRPF 310
                                       789****************998766 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002      0.14      21      45 ..     284     308 ..     254     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                                       EEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgv 45 
                                        +l++G+ G+GKT ++r++a+al+ 
  gi|313117111|ref|YP_004038235.1| 284 GLLFQGPPGTGKTLFARAIANALDR 308
                                       389******************9964 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00034      0.23      24      82 ..     285     353 ..     280     359 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                                       EEEEEETT--HHHHHHCC--T.TS-EE--SSTTHHHH-H........HHHHHHT..TTSEEEEEE-TT-- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhkn.sgpwleifvverlaklp........ldlleqa..kggtLylkdiadls 82 
                                       ++  G++G+gk+l+Ar++++  + p +e+++ +  ++          ++l+e+a   gg+ ++ + ++l 
  gi|313117111|ref|YP_004038235.1| 285 LLFQGPPGTGKTLFARAIANAlDRPFVELTQADLTHE-YinkspqliKRLFEEAqhLGGVVFIDEAEQLL 353
                                       6778**************9862556666665544432.13344466688888876679999999988875 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00041      0.28       1      24 [.     291     314 ..     291     360 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                                       TTSSHHHHHHHHHHHHTSEEEEHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlD 24 
                                       +G+GK+ +++++A++l+++f++l 
  gi|313117111|ref|YP_004038235.1| 291 PGTGKTLFARAIANALDRPFVELT 314
                                       69*******************973 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00042      0.29      34      59 ..     283     308 ..     277     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldk 59 
                                       + +l+ Gp GtGKt+ ++ + ++ld+
  gi|313117111|ref|YP_004038235.1| 283 RGLLFQGPPGTGKTLFARAIANALDR 308
                                       678*****************999994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1213  (0.0676558); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 2973.92
//
Query:       gi|313117112|ref|YP_004038236.1|  [L=442]
Description: ADP-ribosylglycohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-66  224.6   2.3    3.7e-66  223.8   2.3    1.3  1  ADP_ribosyl_GH   ADP-ribosylglycohydrolase
  ------ inclusion threshold ------
       0.11   12.3   0.3       0.21   11.3   0.3    1.5  1  SurE             Survival protein SurE


Domain annotation for each model (and alignments):
>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.8   2.3   4.1e-70   3.7e-66       1     286 [.     107     374 ..     107     376 .. 0.94

  Alignments for each domain:
  == domain 1  score: 223.8 bits;  conditional E-value: 4.1e-70
                                       HHHHHHHHHHHHHGGGTT--HHHHHHHTSS--S-----STTTTTS-TT---HHHHHHHHHHHTEET.TEE-HHHHHH CS
                    ADP_ribosyl_GH   1 GallGaavGDAlGlpvefwsydeirrrygelgetpdktgfghfglkpgewtddtqmalllleslleaggldpedlar 77 
                                       G +lG+a+GDAlG pvef+s +ei++++g      ++ g g +++++g++tddt++al l+  ll++g+++++ +a+
  gi|313117112|ref|YP_004038236.1| 107 GIILGLACGDALGRPVEFMSSSEIEAEHGTVT---KFFGDGSHNQPAGTVTDDTNLALYLVANLLAHGEFNAARYAE 180
                                       789**************************987...9999************************************** PP

                                       HHHH.HHT....T--SS--HHHHHHHHHTTTT-...-S-B.........---BTTTGGG-HHHHHHTSS-HHHHHHH CS
                    ADP_ribosyl_GH  78 rflaeWleepgdteprgignttrealrnlksgepppeagana......ngsagngalmRaaplgllyagdpeeaael 148
                                       ++++ W+e    + p+++g tt ++++ l++g p+ eag++       n++agng++mR+apl+++y++d++ + e+
  gi|313117112|ref|YP_004038236.1| 181 QLVE-WFE----SDPFDVGVTTISSITWLQNGVPASEAGHKTlesrgaNNAAGNGSVMRCAPLAIAYPDDQQMLQEM 252
                                       *888.***....99**************************99*********************************** PP

                                       HHHHHHTTB--HHHHHHHHHHHHHHHHHHTT--STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH........ CS
                    ADP_ribosyl_GH 149 aeeaarlTHnhpeavagaaayaaliaaalrgksleealdaaeeelavapaeeelaaalrkalaladsdkdvdvdaee 225
                                       +++++ +TH++p++ +g+a++++++aa+l+g+++  +++     +  ++a+ el ++l+++ +              
  gi|313117112|ref|YP_004038236.1| 253 SRKSSEITHADPRCTHGCAVLNLTLAAILNGSEEPLQVALT---ALSDDAPAELVERLERVPDE------------V 314
                                       ********************************998888888...55666666666666666553............3 PP

                                       HHHHH--SSBHHHHHHHHHHHHHH.-SSHHHHHHHHHTS-SSHHHHHHHHHHHHHHHH-GG CS
                    ADP_ribosyl_GH 226 avdelgsggyavealaaalyallhaaddfeeallaavnlGgDtdttgaiaGallGalyGle 286
                                       + d+l ++g+++++l++aly  l+ ad+ e+a+  avn GgD+dt+ga+aG ++Ga++G++
  gi|313117112|ref|YP_004038236.1| 315 SEDDLENSGFVLDTLETALYYGLT-ADSAEDAIVSAVNNGGDADTIGAVAGTIVGARFGAG 374
                                       466799******************.99********************************86 PP

>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   2.3e-05      0.21      60     117 ..     315     373 ..     247     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
                                       TTCEEEESS-HHHHHHHHHHTTTTTS..SSEEEEEEEES---GGGGGG-HHHHHHHHHH CS
                              SurE  60 eeeeyavsGtPadcvklaleellkek.kpdlVvSGiNhGaNlgtdvlySGTvgAaleaa 117
                                       +e+  + sG   d+ ++al   l ++ ++d +vS +N+G  + t     GT+ +a+ +a
  gi|313117112|ref|YP_004038236.1| 315 SEDDLENSGFVLDTLETALYYGLTADsAEDAIVSAVNNGGDADTIGAVAGTIVGARFGA 373
                                       44555667888899999998888766577*************9999******9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2979.50
//
Query:       gi|313117113|ref|YP_004038237.1|  [L=61]
Description: hypothetical protein Hbor_35810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-05   23.6   0.0    6.8e-05   23.1   0.0    1.3  1  DUF4177   Domain of unknown function (DUF4177)


Domain annotation for each model (and alignments):
>> DUF4177  Domain of unknown function (DUF4177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.8e-09   6.8e-05       1      51 [.       4      50 ..       4      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.8e-09
                           DUF4177  1 YEYkvvevkegglg...ngkieeeeleeyqeilnelAkeGWrlvsiipvkesrg 51
                                      YEY +vev ++      +g+++ + + +    lnel+++GW +v+  p++++rg
  gi|313117113|ref|YP_004038237.1|  4 YEYRTVEVDSSVMVaglGGNVD-PPVGR----LNELGADGWDVVA--PITDKRG 50
                                      9*******99988888878888.44444....7************..8877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 436.76
//
Query:       gi|313117114|ref|YP_004038238.1|  [L=218]
Description: ribonuclease HI [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-09   35.6   0.0    8.8e-09   35.2   0.0    1.1  1  RVT_3     Reverse transcriptase-like
    2.6e-07   30.9   0.0    3.2e-07   30.6   0.0    1.3  1  RNase_H   RNase H


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   9.8e-13   8.8e-09       2     122 ..      85     206 ..      84     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 9.8e-13
                             RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLqlal.klgirrlvvegDsktvvqlln 77 
                                       +dg  + + g +gag+vi d++   l+   +++++++ + +AE+ AL  GL   l ++  r l+v +Ds+tv++   
  gi|313117114|ref|YP_004038238.1|  85 VDGGSRGNPGPAGAGAVIMDATETELARLGRPVGSRTGNNTAEYVALQLGLSELLaRYDPRSLEVRIDSMTVIRDAW 161
                                       6899999***********************9********************76651567888***********9999 PP

                             RVT_3  78 grekvksselanlldeirkllksfesvsvehipReqNrvAdalAk 122
                                       ++ +++++ ++ + + i + l s  + + +h   +   +AdalA+
  gi|313117114|ref|YP_004038238.1| 162 DDDDPTEPGVETYSEAIATALLSVPEHRYTHLADSDPNPADALAT 206
                                       99999**************************************97 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   3.5e-11   3.2e-07       3      75 ..      80     158 ..      78     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.5e-11
                                       SEEEEEEEEEECTTTCEEEEEEECTT...E..EEEEEECCCCHHHHHHHHHHHHHHHTT....SCSEEEEEES-HHH CS
                           RNase_H   3 avvvYtDGsclgnpgeggagavlykeg.ar..nisapleeaqtnnraELsAvieaLkal...ksdekvniytDSkYv 73 
                                       + ++Y+DG ++gnpg++gagav+   + ++   + +p+  ++ nn+aE  A+   L++l   + + +++++ DS  v
  gi|313117114|ref|YP_004038238.1|  80 SFILYVDGGSRGNPGPAGAGAVIMDATeTElaRLGRPVGSRTGNNTAEYVALQLGLSELlarYDPRSLEVRIDSMTV 156
                                       6799*****************6644432334567788889*****************774445559999**9*9877 PP

                                       HH CS
                           RNase_H  74 vk 75 
                                       + 
  gi|313117114|ref|YP_004038238.1| 157 IR 158
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1503.17
//
Query:       gi|313117115|ref|YP_004038239.1|  [L=243]
Description: sugar fermentation stimulation protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-38  130.1   0.0    7.9e-38  129.5   0.0    1.3  1  SfsA       Sugar fermentation stimulation protein RE domain
    6.1e-15   55.1   0.0    1.3e-14   54.1   0.0    1.6  1  SfsA_N     SfsA N-terminal OB domain
  ------ inclusion threshold ------
      0.034   13.9   0.0        1.3    8.8   0.0    2.2  2  ChuX_HutX  Haem utilisation ChuX/HutX


Domain annotation for each model (and alignments):
>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   0.0   1.3e-41   7.9e-38       2     136 ..      92     228 ..      91     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 1.3e-41
                                       HHHHHHHHHHEE...........EEES-EE.TTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHH CS
                              SfsA   2 lpnklveealesgli.elagyeeikrevky.gnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhl 76 
                                       l+n+l+e+al ++ i +++gy+  kre ++ ++ r Df le+++++ + vE+Ks+t +e+ ia fPd  teRg++hl
  gi|313117115|ref|YP_004038239.1|  92 LANDLFERALGRNAIpAFDGYTCRKREPALpDHGRTDFRLETPSGNTASVEIKSCTHVEDRIAKFPDRQTERGRRHL 168
                                       79********9988889******************************************99**************** PP

                                       HHHHHHHHTT-EEEEEEEE-SSS--EEEE-TTT-HHHHHHHHHHHHHT-EEEEEEEEE-T CS
                              SfsA  77 eeLaelvkegyravvlfvvqredarefkpnkeidpefaealreaaeaGVevlaydckvtp 136
                                       + L +l ++g+++ v+fvvqr+d+++f+p++++dpefae+l +++e GV v+a++++++p
  gi|313117115|ref|YP_004038239.1| 169 RSLEALCEDGHETHVVFVVQRPDVERFRPYRDVDPEFAELLSQVQETGVGVHAITTSFKP 228
                                       *****************************************************9988765 PP

>> SfsA_N  SfsA N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   2.2e-18   1.3e-14       1      63 []      23      88 ..      23      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.2e-18
                                      EEEEETTEEEEEEE.....EE----S--TTT--TT-EEEEE....ESSS-SEEEEEEEETTEEEE- CS
                            SfsA_N  1 lrRpnRFladveldg...tvHvpntGrlkelllpGarvllsksdnpkrKtkytleavekegtwvgi 63
                                      + RpnRF+++v++++   +v++ ++G+l++ ++pG ++l+ ++d+p+r t+y+ +av++++++v++
  gi|313117115|ref|YP_004038239.1| 23 VDRPNRFVVRVRFEDepeRVFLGDPGALEGTIEPGHEILCAPVDDPERATDYDAIAVHVDTVYVSV 88
                                      68**********9964556******************************************99986 PP

>> ChuX_HutX  Haem utilisation ChuX/HutX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00022       1.3      94     132 ..     159     196 ..     150     198 .. 0.80
   2 ?    3.0   0.0     0.014        82      23      46 ..     201     224 ..     196     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00022
                                       EEE.TT..EEEEEEEEETTSSEEEEEEEBSTSSHHHHHHHH CS
                         ChuX_HutX  94 eptkrg..esrslqffdadGeavhkvyvrdeeseeqvaafe 132
                                       ++t+rg  + rsl+ + +dG+  h v+ + ++   +v++f+
  gi|313117115|ref|YP_004038239.1| 159 RQTERGrrHLRSLEALCEDGHETHVVF-VVQRP--DVERFR 196
                                       5566555599*****************.66666..677775 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.014
                                       EEGGGHHHHHHHHTTS-E.EEEEEE CS
                         ChuX_HutX  23 ldgedfeallealeelge.vmalvr 46 
                                       +d+ +f++ll +++e g  v a++ 
  gi|313117115|ref|YP_004038239.1| 201 VDP-EFAELLSQVQETGVgVHAITT 224
                                       788.9*************9**9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1898.92
//
Query:       gi|313117116|ref|YP_004038240.1|  [L=110]
Description: hypothetical protein Hbor_35840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 920.12
//
Query:       gi|313117117|ref|YP_004038241.1|  [L=132]
Description: nucleotidyltransferase protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-10   38.9   0.0    9.2e-10   38.5   0.0    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    3.2e-06   27.3   0.1    4.1e-06   27.0   0.1    1.3  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0     1e-13   9.2e-10      16      85 ..       2      76 ..       1      80 [. 0.89

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1e-13
                                      TTEEEEEE-S------EEEEEEEESS-.....--HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS-E CS
                           Polbeta 16 aylFGSrakgkareeSDiDlavllkek.....ldleeelelaaelediklgkkvDlvdlneapplllyeilkegk 85
                                      + lFGS a+g++++ SD D+av l+++        +  + l+a+l+d+   ++v lvd+++ +p +++++++ g 
  gi|313117117|ref|YP_004038241.1|  2 CTLFGSHATGTTHPTSDTDIAVELETTdredpAYNDAFFGLSADLSDALGTDDVYLVDIHTLSPSVAASVFEAGV 76
                                      78************************98877433444889********999*********999******999886 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   4.6e-10   4.1e-06      18      48 ..       3      37 ..       2      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.6e-10
                                      EEEHHHHCTTSCTTSSEEEEEEESTTCHHH....H CS
                      NTP_transf_2 18 vlfGSyarGtalkgSDiDllvvlpeevsre....k 48
                                      +lfGS a+Gt++++SD D++v l+    ++    +
  gi|313117117|ref|YP_004038241.1|  3 TLFGSHATGTTHPTSDTDIAVELETTDREDpaynD 37
                                      59**********************99654455441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1070.25
//
Query:       gi|313117118|ref|YP_004038242.1|  [L=90]
Description: hypothetical protein Hbor_35860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.39   10.3   3.8        0.1   12.2   0.4    1.6  2  Pox_P21   Poxvirus P21 membrane protein
       0.91    9.4   0.0       0.91    9.4   0.0    2.8  3  Imm17     Immunity protein 17


Domain annotation for each model (and alignments):
>> Pox_P21  Poxvirus P21 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   1.1e-05       0.1     118     155 ..      14      51 ..       9      66 .. 0.91
   2 ?   -1.1   0.2      0.13   1.2e+03      65      75 ..      71      81 ..      63      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                           Pox_P21 118 ntvgmsivcvllsivtivvnsvsvsktlktisyivLav 155
                                       +++g+++ c+l s++++++ +  +s+++ ti+ i L+ 
  gi|313117118|ref|YP_004038242.1|  14 SDIGVAVFCLLGSVFILFMSHALASAGILTIAGIALLR 51 
                                       689****************************9999875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.13
                           Pox_P21 65 irsLlglilfv 75
                                      i  L+gl+++v
  gi|313117118|ref|YP_004038242.1| 71 ILVLIGLVMLV 81
                                      45678888876 PP

>> Imm17  Immunity protein 17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.5     0.049   4.4e+02       5      16 ..      17      28 ..      16      31 .. 0.84
   2 ?   -0.5   0.7      0.13   1.2e+03      47      56 ..      40      49 ..      36      52 .. 0.53
   3 ?    9.4   0.0    0.0001      0.91      34      58 ..      57      81 ..      55      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.049
                             Imm17  5 llgllsllgail 16
                                      ++ +++llg+++
  gi|313117118|ref|YP_004038242.1| 17 GVAVFCLLGSVF 28
                                      688999999987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.13
                             Imm17 47 gilgliliil 56
                                      gil++++i+l
  gi|313117118|ref|YP_004038242.1| 40 GILTIAGIAL 49
                                      3444444443 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0001
                             Imm17 34 venfGrkgaRifygilgliliilgl 58
                                      v+ + ++  R+f+ il+li++++ +
  gi|313117118|ref|YP_004038242.1| 57 VRDWTDEHTRLFQLILVLIGLVMLV 81
                                      577889999***********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 670.37
//
Query:       gi|313117119|ref|YP_004038243.1|  [L=42]
Description: hypothetical protein Hbor_35870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      108  (0.00602376); expected 358.6 (0.02)
Passed Vit filter:                         1  (5.57756e-05); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.36
# Mc/sec: 345.82
//
Query:       gi|313117120|ref|YP_004038244.1|  [L=195]
Description: hypothetical protein Hbor_35880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1462.81
//
Query:       gi|313117121|ref|YP_004038245.1|  [L=261]
Description: hypothetical protein Hbor_35890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-07   29.4   0.1    1.6e-06   28.0   0.0    1.7  2  HTH_45         Winged helix-turn-helix
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.017   15.0   0.0    1.3  1  MarR_2         MarR family
      0.042   14.0   0.2       0.15   12.2   0.0    1.9  2  Trp_repressor  Trp repressor protein
      0.095   12.8   0.1       0.19   11.8   0.1    1.4  1  HTH_20         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   3.5e-10   1.6e-06       9      75 ..      15      81 ..       9      83 .. 0.96
   2 ?   -3.1   0.0       1.8   8.1e+03      21      29 ..     124     132 ..     120     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.5e-10
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleel 75
                                      +dILe + +++++k  ++ + +Ls +++++ ++ L+e + i+ ++++Y+ Te G+  +++++++ ++
  gi|313117121|ref|YP_004038245.1| 15 HDILEELVDSSQSKPDLVSQMDLSRSTIDRGVNELLEHDCITRTGSTYEATETGRLAIREYERYLRF 81
                                      69************************************************************99876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.8
                            HTH_45  21 kkTkimyka 29 
                                       k T++m++a
  gi|313117121|ref|YP_004038245.1| 124 KSTELMKNA 132
                                       679999988 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.7e-06     0.017       7      54 ..      14      58 ..       8      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-06
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       +++L +L ++     +  +l+  ++ls+s++ r +++L ++  ++r+
  gi|313117121|ref|YP_004038245.1| 14 RHDILEELVDSS---QSKPDLVSQMDLSRSTIDRGVNELLEHDCITRT 58
                                      6899*******9...5*****************************997 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.3e-05      0.15      34      74 ..      10      50 ..       2      55 .. 0.91
   2 ?   -1.9   0.0      0.87   3.9e+03      55      65 ..     172     182 ..     160     193 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.3e-05
                     Trp_repressor 34 alaqRlqvvkeLLkeelsqreIaeelgvSiAtItRvsrsLk 74
                                      ++ +R  +++eL + ++s  ++ ++++ S  tI R+ ++L 
  gi|313117121|ref|YP_004038245.1| 10 TIRKRHDILEELVDSSQSKPDLVSQMDLSRSTIDRGVNELL 50
                                      6889**********************************985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.87
                     Trp_repressor  55 IaeelgvSiAt 65 
                                       ++ee++  iAt
  gi|313117121|ref|YP_004038245.1| 172 LSEEMQEMIAT 182
                                       44444444444 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.3e-05      0.19      12      58 ..      14      59 ..      12      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.3e-05
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      R +il +L  +  ++ ++l  ++dls++t+++ +++L e++ +++++
  gi|313117121|ref|YP_004038245.1| 14 RHDILEEL-VDSSQSKPDLVSQMDLSRSTIDRGVNELLEHDCITRTG 59
                                      779*****.********************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1880.81
//
Query:       gi|313117122|ref|YP_004038246.1|  [L=163]
Description: hypothetical protein Hbor_35900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1155.60
//
Query:       gi|313117123|ref|YP_004038247.1|  [L=236]
Description: hypothetical protein Hbor_35910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   13.7   0.1       0.06   13.1   0.1    1.3  1  TgMIC1    Toxoplasma gondii micronemal protein 1 TgMIC1


Domain annotation for each model (and alignments):
>> TgMIC1  Toxoplasma gondii micronemal protein 1 TgMIC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.3e-06      0.06      67     135 ..      59     129 ..      41     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-06
                            TgMIC1  67 GsavltiGlGskGrlavvldyarlnaalrsvay..vvedsGcksieevllqGlnsGaklvvttlGesstav 135
                                        +a l+i l +k + a+vl  a+l+ +l+++ay     d   + i e  + G++ Ga+ vv ++ +  t+ 
  gi|313117123|ref|YP_004038247.1|  59 SAAGLAITLAEKTQAALVLSGAQLANSLGQIAYdkKTPDDSASFIWEGGYSGIERGAHQVVFSVANYLTSS 129
                                       45789****************************442457778899999**********9998887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1726.57
//
Query:       gi|313117124|ref|YP_004038248.1|  [L=185]
Description: hypothetical protein Hbor_35940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   15.1   1.0      0.091   13.5   0.3    1.9  2  DUF2203   Uncharacterized conserved protein (DUF2203)
      0.037   13.2   0.0       0.05   12.7   0.0    1.1  1  APG17     Autophagy protein Apg17
      0.037   14.4   0.0      0.068   13.6   0.0    1.3  1  ZapB      Cell division protein ZapB
      0.076   13.6   0.1       0.11   13.1   0.1    1.2  1  ArdA      Antirestriction protein (ArdA)
       0.11   12.8   0.1       0.26   11.6   0.1    1.5  1  BLOC1_2   Biogenesis of lysosome-related organelles complex-1
       0.17   12.5   0.1       0.25   12.0   0.1    1.2  1  YabA      Initiation control protein YabA


Domain annotation for each model (and alignments):
>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3     3e-05     0.091      23      88 ..      52     121 ..      27     128 .. 0.70
   2 ?   -0.0   0.0      0.46   1.4e+03      67      89 ..     142     166 ..     124     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                           DUF2203  23 ralrkeleeleeeleeakaeaekse.....aaeleaeleeleaeieelveeieelGvevkdleaglvDFpa 88 
                                        a+ +++++leee e+ +++ +k +     ++++e++++++ + + +   e  ++ v+ k + +gl+DF  
  gi|313117124|ref|YP_004038248.1|  52 SAVVERFQSLEEESEQLRDRLDKLGdigerKTSKEEKIAAIVTFAARKKGEKPAITVKPKTI-KGLIDFSR 121
                                       333333333333444444433333356666899999**************************.6*****65 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.46
                           DUF2203  67 eeieelGvevkdlea..glvDFpak 89 
                                       +++++ G+  kd ++  +l+DF + 
  gi|313117124|ref|YP_004038248.1| 142 TQVDQYGMLEKDTSQkgILIDFDGV 166
                                       5788888888885433379999654 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05      0.05     250     331 ..      43     124 ..      38     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHH CS
                             APG17 250 rleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekleeleeLref 326
                                       +++ + +a +++ e+ +++e+ +++l++ l++l ++g++  +  + ++a+ +f +r++ ek  i  k ++++ L++f
  gi|313117124|ref|YP_004038248.1|  43 EYDHVAEAASAVVERFQSLEEESEQLRDRLDKLGDIGERKTSKEEKIAAIVTFAARKKGEKPAITVKPKTIKGLIDF 119
                                       678888899999999*********************888888888899****************************9 PP

                                       HHHHH CS
                             APG17 327 YegFl 331
                                        ++++
  gi|313117124|ref|YP_004038248.1| 120 SRRYA 124
                                       88885 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.3e-05     0.068      20      65 ..      27      75 ..      23      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                              ZapB 20 itlLqmeieeL...keeneelkeenreleeeneqlkeereawqerlkkL 65
                                      it+L++ +++L    +e    +e + ++ e  + l+ee e++++rl+kL
  gi|313117124|ref|YP_004038248.1| 27 ITALRKLVYRLapaDREYDHVAEAASAVVERFQSLEEESEQLRDRLDKL 75
                                      55666666655111567777788888888******************98 PP

>> ArdA  Antirestriction protein (ArdA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.6e-05      0.11      75     137 ..      43     147 ..      11     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                              ArdA  75 eleeh.geafaawvehfgdleeledafee..eylgeydsle.................................... 112
                                       e  +h  ea  a+ve f++lee ++++ +  + lg + + +                                    
  gi|313117124|ref|YP_004038248.1|  43 EY-DHvAEAASAVVERFQSLEEESEQLRDrlDKLGDIGERKtskeekiaaivtfaarkkgekpaitvkpktikglid 118
                                       22.23688889999999977777777777566666666555777788899999999999999999999999999999 PP

                              ArdA 113 ...dyAeelveelgllk..e.eeipeslenY 137
                                           yA++lv++++  +  e ++ p+++ +Y
  gi|313117124|ref|YP_004038248.1| 119 fsrRYAYDLVDDMH--DeyEwAHDPTQVDQY 147
                                       999**********9..335778889988888 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   8.7e-05      0.26      33      75 ..      41      83 ..      38      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.7e-05
                           BLOC1_2 33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvt 75
                                       ++y+ ++++a+ + + ++ l+e++e+l+  l+++ +i ++ t
  gi|313117124|ref|YP_004038248.1| 41 DREYDHVAEAASAVVERFQSLEEESEQLRDRLDKLGDIGERKT 83
                                      579**********************************988655 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.4e-05      0.25       9      56 ..      29      83 ..      24     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.4e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH........XXXX CS
                              YabA  9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerl........eeee 56
                                      +l++l  +l+   +e +++ e+ ++++e+ ++Le e e+lr+rl        + ++
  gi|313117124|ref|YP_004038248.1| 29 ALRKLVYRLAPADREYDHVAEAASAVVERFQSLEEESEQLRDRLdklgdigeR-KT 83
                                      56677777888889999999************************666655321.11 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1187.81
//
Query:       gi|313117125|ref|YP_004038249.1|  [L=76]
Description: hypothetical protein Hbor_35950 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 570.63
//
Query:       gi|313117126|ref|YP_004038250.1|  [L=159]
Description: hypothetical protein Hbor_35960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1288.69
//
Query:       gi|313117127|ref|YP_004038251.1|  [L=40]
Description: hypothetical protein Hbor_35970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 299.53
//
Query:       gi|313117128|ref|YP_004038252.1|  [L=402]
Description: ferrichrome-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-23   81.8   0.0    1.1e-22   80.8   0.0    1.5  1  Peripla_BP_2  Periplasmic binding protein
     0.0013   18.5   0.2     0.0023   17.7   0.2    1.4  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   0.0   1.2e-26   1.1e-22       4     234 ..      87     353 ..      85     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 1.2e-26
                                       -SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..............TS-BSBESSSB-H.......HHHHHH--S CS
                      Peripla_BP_2   4 lspsvteillalGatdkvvgvdtttsdpldadklee............aivevgadgeidv.......EklaalkPD 61 
                                       ++ +++++ +alG++d++ g++   ++ +  ++++             +           +       E   +++ D
  gi|313117128|ref|YP_004038252.1|  87 YGGDYADMGVALGHADSMIGIGQPGEYYTYVYEELPgvsvdkdrieknD-----------LveagmskELFYEMDSD 152
                                       6789****************************99977666443333333...........34445666777779*** PP

                                       EEEE-GGG........GGGHHHHHHHS-EEE----TTS................HHHHHHHHHHHHHTT-HHHHHHH CS
                      Peripla_BP_2  62 lvilskgl.....gltdedeellksgiptvivessntg................eslkeqiralgellgledeaekl 117
                                       + i ++g+     +        ++++i  +  + ++++                + l+e ++ ++el+++ d++e++
  gi|313117128|ref|YP_004038252.1| 153 VHIIDTGMlrnwfD-------WRDEDIAEISEQVGPFLgnmifrrsdswhdyrfYTLYEAFEKVAELFQERDRYEAF 222
                                       ********554441.......44444444444444444444566666678*************************** PP

                                       HHHHHHHHHHHHHTS-TT...-EEEEEEEETTE.....EEEE-TTSTTTHHHHTS--EESTTT--.....STT-EEE CS
                      Peripla_BP_2 118 vaeidsklaaaksaidse..kpkpvlvfggade...ggyvvagsnsyigdlldalgieniaaesk.....kseyeei 184
                                        + +d+ + +++s+ +     p  +l+f g +e    +++  ++++  ++  ++lg+++++a        +++++e+
  gi|313117128|ref|YP_004038252.1| 223 KQYHDEFITEIQSRMPPSgeRPNVMLTFEGTNEpdtFSPYRLTDKGTSKKQWNDLGVADALAGTDienlsTDNRGEL 299
                                       ******************877888888888888888455555566666666777******999999*********** PP

                                       -HHHHHHH--SEEEEEEH....HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 185 saEqilasdpdvifvsgr....aeadnktgleflkenpllaelpAvkngrVyal 234
                                       + E++l+ dpdv++++g+    a+++++t+l+ +k +p+ +el+Av+n+rVy+ 
  gi|313117128|ref|YP_004038252.1| 300 DYENLLEVDPDVLLIRGHeqksASEFRDTVLAYMKDHPVGSELTAVQNNRVYRG 353
                                       ****************************************************86 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   2.5e-07    0.0023       3      25 ..      12      34 ..      10      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.5e-07
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      +RRd +K ++A+    al+gca+
  gi|313117128|ref|YP_004038252.1| 12 TRRDYMKYGGAVIGSSALAGCAG 34
                                      8********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2643.93
//
Query:       gi|313117129|ref|YP_004038253.1|  [L=77]
Description: hypothetical protein Hbor_35990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 588.47
//
Query:       gi|313117130|ref|YP_004038254.1|  [L=367]
Description: hypothetical protein Hbor_36000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2876.77
//
Query:       gi|313117131|ref|YP_004038255.1|  [L=94]
Description: hypothetical protein Hbor_36010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.062   13.5   0.4      0.062   13.5   0.4    1.6  2  DUF423           Protein of unknown function (DUF423)
        5.2    7.7   6.4        1.1    9.9   0.5    2.1  2  Renin_r          Renin receptor-like protein
        9.8    6.7  13.5    1.1e+03    0.1  13.5    2.4  1  DUF202           Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF423  Protein of unknown function (DUF423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.34     2e+03      60      75 ..       7      22 ..       5      31 .. 0.58
   2 ?   13.5   0.4     1e-05     0.062      16      71 ..      33      88 ..      17      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.34
                            DUF423 60 aGivlFSgslyllalt 75
                                      +Gi +F + l ++a++
  gi|313117131|ref|YP_004038255.1|  7 TGIGFFVFGLAVTAYS 22
                                      5666666666555553 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1e-05
                            DUF423 16 kalesfetavqYqlyhalallavallaskaaasrllklagllflaGivlFSgslyl 71
                                      ++++ +++++   ++ ++ l +++++++ + + r    + + +++G++lF   + +
  gi|313117131|ref|YP_004038255.1| 33 HTVNLWSVGALIIMISGVCLSLIGIYSTISPEGRFAVNTRYPLIFGTILFISAILI 88
                                      67889*********************98888999999999**********766655 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.8     0.097   5.8e+02      56      78 ..      34      56 ..      17      64 .. 0.80
   2 ?    9.9   0.5   0.00019       1.1      46      68 ..      68      90 ..      60      94 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.097
                           Renin_r 56 niiLwlvvvlvlaliaivvalas 78
                                       + Lw v +l++ +  ++++l+ 
  gi|313117131|ref|YP_004038255.1| 34 TVNLWSVGALIIMISGVCLSLIG 56
                                      57799999999999999888765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00019
                           Renin_r 46 kyssdYpaiFniiLwlvvvlvla 68
                                      ++++ Yp iF  iL+++ +l+l 
  gi|313117131|ref|YP_004038255.1| 68 AVNTRYPLIFGTILFISAILILL 90
                                      5899*************999875 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1  13.5      0.18   1.1e+03      16      62 ..       7      60 ..       5      91 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.18
                            DUF202 16 tslalialglallrffl.......tgepsalgkilglilivlgiltllvglvry 62
                                      t+++++++gla+++           ++  +l ++ +li+++ g+++ l+g+++ 
  gi|313117131|ref|YP_004038255.1|  7 TGIGFFVFGLAVTAYSYvtaipflVSHTVNLWSVGALIIMISGVCLSLIGIYST 60
                                      8999*********84335566555333333335556777777777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 655.21
//
Query:       gi|313117132|ref|YP_004038256.1|  [L=147]
Description: hypothetical protein Hbor_36020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.3   4.6       0.28   11.5   0.1    2.2  2  DUF3040   Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   1.6e-05      0.28      35      72 ..      30      73 ..      18      83 .. 0.67
   2 ?    2.3   1.0     0.012   2.1e+02      48      65 ..     119     136 ..      86     143 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.6e-05
                           DUF3040 35 rarrrslrrlavlavllfvaGllllvlG.vaaaa......vvlgv 72
                                      r+r+  +rr  ++ +l +v+Gl ++ l  v+ +       ++  +
  gi|313117132|ref|YP_004038256.1| 30 RRRHTGMRR-SIRYALSAVVGLGVMALTaVVDNGntglmaMIPLI 73
                                      355556777.99999999*********955544355554444444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.012
                           DUF3040  48 avllfvaGllllvlGvaa 65 
                                       ++++ +aG  l+v+G+a+
  gi|313117132|ref|YP_004038256.1| 119 SLAAGIAGYGLFVFGMAL 136
                                       334444455555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 959.56
//
Query:       gi|313122370|ref|YP_004038257.1|  [L=370]
Description: hypothetical protein Hbor_36040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-29  102.8   0.0    2.4e-29  102.5   0.0    1.1  1  DUF354    Protein of unknown function (DUF354)


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.0   1.3e-33   2.4e-29       1     309 [.      24     335 ..      24     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 1.3e-33
                            DUF354   1 ldvwidltnaphvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhGvtlkekliesakrvinlsk 77 
                                       +dvw+dl+   h  +f+ l   + +  ++  +t+r+  +   l +  +++f+++Gk     + + +    r+ +l+ 
  gi|313122370|ref|YP_004038257.1|  24 IDVWVDLASPSHPFFFKALTDSLTN--VKTTVTVREKTETVPLARQVGYEFQTLGKDYENPHLRKLGIPLRTAQLA- 97 
                                       59***************99999876..67889************************98776666667777888876. PP

                            DUF354  78 liaevkpdvalakhsvelprvafGlnipvvyvldneha.....eaankltlpl...adeiikpividendlkktGad 146
                                        +   k dval+         a   ++p+++  dn+       + a+ l   l   a + + p++ +   l + Gad
  gi|313122370|ref|YP_004038257.1|  98 -VKAPKADVALSSRNAMCVLAAKARGMPSIHFTDNDICayvdgLKAEELYHRLeaqATHNVVPEAFQSEVLTERGAD 173
                                       .6778999***999999999999999********9965121223444554444222556789*************** PP

                            DUF354 147 pnrirryeGtsevinvqsyeideeilkdlnlkledektilmrpepslasyldadchkdvltkive.klkdridilvi 222
                                       p+ ++ y G  e + v +++ d   l++l    + e+ i++rpe   a+y+da    +++++i+   ++  ++++ +
  gi|313122370|ref|YP_004038257.1| 174 PDSVHTYSGYKEDVYVAAFDPDPTFLDELP--FDSEEFIVVRPEALSATYVDA--NGSLVPDILAgAVERGVNVVYL 246
                                       ****************************99..9*******************9..789999998625667799**** PP

                            DUF354 223 prdeeqkeiyeev..dnviviketvdalsllkrsdlviGaGGtmnreaallGipvvscypqkllsvdkyliekdlmi 297
                                       pr+e+++   +++  + + ++ +++  l l  ++  v+   Gtm reaa + +p+vs +p   +svd+ li+ + ++
  gi|313122370|ref|YP_004038257.1| 247 PREENDRSFADGLpaERIYIPDNPLSGLELSWHARCVLTGSGTMAREAARMETPAVSFFPSTRISVDRALIDAGEIF 323
                                       *******9999863367899********************************************************* PP

                            DUF354 298 rstdvdeivnta 309
                                       +s d ++i++ +
  gi|313122370|ref|YP_004038257.1| 324 HSRDAEDILDYV 335
                                       ********9832 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2609.58
//
Query:       gi|313122371|ref|YP_004038258.1|  [L=264]
Description: hypothetical protein Hbor_36050 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.073   13.2   0.9         14    5.9   0.1    2.3  2  Vwaint    VWA / Hh  protein intein-like


Domain annotation for each model (and alignments):
>> Vwaint  VWA / Hh  protein intein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0   0.00092        17      33      48 ..      55      70 ..      43      77 .. 0.85
   2 ?    5.9   0.1   0.00077        14      38      56 ..      84     102 ..      83     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00092
                            Vwaint 33 llSllsaHarQrcnsf 48
                                      + +l+saH  Q++ns 
  gi|313122371|ref|YP_004038258.1| 55 AIALVSAHHTQTANSS 70
                                      6799**********96 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.00077
                            Vwaint  38 saHarQrcnsfkdpgpqaY 56 
                                        +HarQ+++++   +  +Y
  gi|313122371|ref|YP_004038258.1|  84 GSHARQVRTTRHGTDNNRY 102
                                       59*********98777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1994.71
//
Query:       gi|313122372|ref|YP_004038259.1|  [L=407]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-23   84.0   0.0    2.4e-23   83.2   0.0    1.4  1  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
  ------ inclusion threshold ------
      0.028   14.9   0.1      0.056   13.9   0.1    1.5  1  CoA_binding_2  CoA binding domain
      0.036   14.6   0.0        0.1   13.2   0.0    1.8  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.0     4e-27   2.4e-23       1     120 []       3     133 ..       3     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 4e-27
                                       EEEEEETTSHH.HHHHHHHHHHTTTTE.....EEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHTCTTESEEEE CS
                      GFO_IDH_MocA   1 lrvaiiGaGki.gskhlrplnesqrle.....evvalldpdaeraeavaesfgve...aysdleelladpeidaviv 68 
                                       +r++++G+G   g+ ++ +++++   e     e va  d+ +e+a a+a++++++   +y+++ee+l+++e+d+v+v
  gi|313122372|ref|YP_004038259.1|   3 FRIGFVGTGDPdGDGFAMAYRHAAGYErlddcEPVACADIVPENAAAFAAAYDIDdanVYEKYEEMLSETEPDVVSV 79 
                                       79999999988855555555555444455555***********************999******************* PP

                                       -S-GGGHHHHHHHHHHTT-..EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  69 atpngtheelakaaleagk..hvllEKPlattveeakelvelaekkgklvsvgy 120
                                       ++p++th++++ ++++ g+  ++ +EKPla+t+ +ak++ve +e +g+ +++++
  gi|313122372|ref|YP_004038259.1|  80 CVPPDTHADIVVDIAQSGVveAIHCEKPLALTWGDAKRMVEECEAEGVALTINH 133
                                       ************************************************999876 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   9.3e-06     0.056      40      82 ..      56     100 ..      39     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.3e-06
                                       ETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH--SE CS
                     CoA_binding_2  40 ilgekvyaslae.d.pepvdlvdvftppeatpeivkealalgaka 82 
                                       i+ ++vy++ +e   ++++d+v+v++pp++ ++iv ++++ g+  
  gi|313122372|ref|YP_004038259.1|  56 IDDANVYEKYEEmLsETEPDVVSVCVPPDTHADIVVDIAQSGVVE 100
                                       66777888888753699*********************9998544 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05       0.1       1      82 [.       4      94 ..       4     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                      EEEEETTSHH...HHHHHHHHHHTTS...-GGCEEEEEESSCCCHHHHHHHHC...-EEECECHHHHHH..H-SEEEE- CS
                     F420_oxidored  1 kigiiGaGnm...gealasgllaaga...qpheivvansrnpekaeelaeelg...vkvtavdneeaae..eadvvvla 68
                                      +ig++G+G+    g+a+a + +a  +   + + +  a +  pe a+++a+++    ++v + ++ee+++  e dvv ++
  gi|313122372|ref|YP_004038259.1|  4 RIGFVGTGDPdgdGFAMAYRHAAGYErldDCEPVACA-DIVPENAAAFAAAYDiddANVYE-KYEEMLSetEPDVVSVC 80
                                      6899999985544888888766544477566667755.899************99899999.88888886889****** PP

                                      S-HHHHHHHHHHCG CS
                     F420_oxidored 69 vkpedveevlsela 82
                                      v+p  +++++ ++a
  gi|313122372|ref|YP_004038259.1| 81 VPPDTHADIVVDIA 94
                                      ********998883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3123.90
//
Query:       gi|313122373|ref|YP_004038260.1|  [L=317]
Description: sugar phosphate isomerase/epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-13   51.2   0.2    9.5e-07   28.5   0.0    2.2  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.045   12.6   0.0      0.068   12.0   0.0    1.2  1  UxuA          D-mannonate dehydratase (UxuA)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.1e-10   9.5e-07       2     133 ..      26     136 ..      25     160 .. 0.89
   2 !   21.0   0.0   2.1e-08   0.00019     144     210 .]     189     255 ..     162     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.1e-10
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraie 77 
                                       +++++aGf+gvE++ r             ++++ al+e+g+             p+  + +    ee+v+ + + +e
  gi|313122373|ref|YP_004038260.1|  26 RRVSNAGFEGVEFANRFFEEDP-------EAVADALAETGVV------------PVAAHADLSaVEEAVEGANDLLE 83 
                                       67999************99996.......9************............66654444467899********* PP

                                       HHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--T CS
                      AP_endonuc_2  78 laaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtla 133
                                       + + +G++ ++++     ++   + + a++ l  +l ++a +++++gv+l+++t+ 
  gi|313122373|ref|YP_004038260.1|  84 RLETVGCDRVIVPHI---SPRHFQTRWAVRSLSYRLTDVAHELDAHGVRLGYHTMR 136
                                       ************944...8888899999999***********************96 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.1e-08
                                       HHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 144 larlldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGei 210
                                       +++ll ++ ++ v +  D+g   +a++d+++a++  a ri  +H+ D+  +++ g  + + +geG++
  gi|313122373|ref|YP_004038260.1| 189 FWNLLARTTPEDVCFEVDVGEVTAAGFDPAAAVELAAGRIPCIHVRDVAATGRFGTYDNADPGEGDV 255
                                       799999**9999*****************************************************96 PP

>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.6e-06     0.068     261     312 ..     223     274 ..     201     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-06
                                       HHGGGEEEEE--EEEE-SSTT-EEEE-TTSSSS-HHHHHHHHHHHHHHH-EE CS
                              UxuA 261 efadriyFahlRnikreedeksFveaahleGsvdlaevvkalleeeyrrylR 312
                                         a+ri+  h+R++  +    ++ +a   eG+vd+ +v +a  + + ++ + 
  gi|313122373|ref|YP_004038260.1| 223 LAAGRIPCIHVRDVAATGRFGTYDNADPGEGDVDFDAVAHAARKSGTEWLVY 274
                                       4578*************9999*************************999663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2145.77
//
Query:       gi|313122374|ref|YP_004038261.1|  [L=379]
Description: hypothetical protein Hbor_36080 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-25   90.0  22.3    1.1e-10   41.9   0.7    5.9  6  VCBS             Repeat domain in Vibrio, Colwellia, Bradyrhi
    2.5e-17   62.7  28.0      0.018   15.2   0.0    7.2  7  FG-GAP           FG-GAP repeat
    1.9e-05   24.1   8.1        5.3    6.4   0.0    6.3  7  TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal reg
  ------ inclusion threshold ------
      0.017   15.1   0.8        7.1    6.7   0.0    4.0  5  BBS2_Mid         Ciliary BBSome complex subunit 2, middle reg
      0.044   12.8   5.1        3.4    6.6   0.4    3.7  5  Itfg2            Integrin-alpha FG-GAP repeat-containing prot
      0.073   12.6  16.6        1.5    8.4   0.6    5.4  5  EF-hand_5        EF hand
       0.11   12.2   9.3         14    5.5   0.1    4.8  5  PliI             Periplasmic lysozyme inhibitor of I-type lys
        4.8    7.0  18.2        6.8    6.5   0.4    5.5  6  EF-hand_1        EF hand
        8.1    6.7  14.2         74    3.7   0.1    5.5  6  Dockerin_1       Dockerin type I domain


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0082        16       1      13 [.      24      36 ..      17      86 .. 0.82
   2 !   21.6   2.2   1.3e-07   0.00025       1      60 [.      99     161 ..      99     162 .. 0.71
   3 !   13.9   0.4     3e-05      0.06      39      60 ..     194     215 ..     179     216 .. 0.81
   4 !   17.3   0.5   2.7e-06    0.0055      19      61 .]     219     258 ..     216     258 .. 0.84
   5 !   14.3   0.1   2.4e-05     0.047      35      61 .]     284     311 ..     270     311 .. 0.80
   6 !   41.9   0.7   5.6e-14   1.1e-10       1      60 [.     300     363 ..     300     364 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0082
                              VCBS  1 DldgDGrlDlvva 13
                                      Dl g+Gr+D++v+
  gi|313122374|ref|YP_004038261.1| 24 DLTGNGRPDVLVG 36
                                      6777777777776 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.3e-07
                              VCBS   1 DldgDGrlDlvvand.gglrvyrnngdGtftdvtktslgg..sgggtgvavgDlDgDGdlDll 60 
                                       D+ g G  Dlv++++ ++  +y+ ++  + +++++  l +     ++ vav+D+DgDG  +++
  gi|313122374|ref|YP_004038261.1|  99 DITGTGTVDLVAGQNlNQYDLYWFEQPDDPRESWTRRLVTddFEKYHDVAVADVDGDGESEVI 161
                                       99***********65566666665554444555444333334777889**********88876 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 3e-05
                              VCBS  39 gsgggtgvavgDlDgDGdlDll 60 
                                       ++ +  gv vgD+DgDG  ++l
  gi|313122374|ref|YP_004038261.1| 194 DNINVEGVQVGDIDGDGTVEIL 215
                                       4556679************998 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 2.7e-06
                              VCBS  19 rvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDllv 61 
                                       +v++ + dG++t      +++++++t v+++D+DgDG  +++v
  gi|313122374|ref|YP_004038261.1| 219 NVFHREDDGSWTR---ERIATGWDWTRVVAADVDGDGESEVIV 258
                                       6777777888764...67999****************999987 PP

  == domain 5  score: 14.3 bits;  conditional E-value: 2.4e-05
                              VCBS  35 tslgg.sgggtgvavgDlDgDGdlDllv 61 
                                       t+l++   +++++ ++DlDg+G +D++v
  gi|313122374|ref|YP_004038261.1| 284 TILHDdLSNPHSLQLADLDGNGSPDVYV 311
                                       4455567899****************98 PP

  == domain 6  score: 41.9 bits;  conditional E-value: 5.6e-14
                              VCBS   1 DldgDGrlDlvva......n.dgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       Dldg+G +D++va      + + +  v++n+gdGtf++       ++   + + ++DlDgDG+lD++
  gi|313122374|ref|YP_004038261.1| 300 DLDGNGSPDVYVAemglesGhNPRQFVFWNRGDGTFEEEVI---VEGVPTHEAKLVDLDGDGRLDIV 363
                                       9************99998744677999*********98543...333345689************97 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     9e-06     0.018       7      26 ..      22      42 ..      18      46 .. 0.78
   2 ?   -0.3   0.8      0.63   1.3e+03       6      21 ..      96     111 ..      93     117 .. 0.81
   3 !   12.2   0.4   7.6e-05      0.15       4      19 ..     146     161 ..     144     162 .. 0.86
   4 !   13.6   1.0   2.9e-05     0.057       4      23 ..     200     218 ..     197     228 .. 0.84
   5 !   13.9   0.3   2.3e-05     0.046       4      21 ..     242     259 ..     240     268 .. 0.85
   6 !   11.8   0.0   9.9e-05       0.2       4      30 ..     295     318 ..     292     322 .. 0.83
   7 !   11.0   0.1   0.00018      0.35       7      19 ..     351     363 ..     348     372 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9e-06
                                      EESTSSSSS-EEEEEE..TT-E CS
                            FG-GAP  7 vgDvNGDGyaDLavGA..pesk 26
                                      ++D+ G G +D++vGA  +e  
  gi|313122374|ref|YP_004038261.1| 22 TTDLTGNGRPDVLVGAlgGE-Y 42
                                      45*************98544.3 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.63
                                       EEESTSSSSS-EEEEE CS
                            FG-GAP   6 avgDvNGDGyaDLavG 21 
                                       a+gD+ G G  DL+ G
  gi|313122374|ref|YP_004038261.1|  96 ALGDITGTGTVDLVAG 111
                                       8999999999999999 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 7.6e-05
                                       SEEEESTSSSSS-EEE CS
                            FG-GAP   4 slavgDvNGDGyaDLa 19 
                                        +av+Dv+GDG  +++
  gi|313122374|ref|YP_004038261.1| 146 DVAVADVDGDGESEVI 161
                                       59*********88876 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 2.9e-05
                                       SEEEESTSSSSS-EEEEEET CS
                            FG-GAP   4 slavgDvNGDGyaDLavGAp 23 
                                       ++ vgD++GDG  +++ G p
  gi|313122374|ref|YP_004038261.1| 200 GVQVGDIDGDGTVEILAG-P 218
                                       689*************99.3 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 2.3e-05
                                       SEEEESTSSSSS-EEEEE CS
                            FG-GAP   4 slavgDvNGDGyaDLavG 21 
                                        + ++Dv+GDG  +++v+
  gi|313122374|ref|YP_004038261.1| 242 RVVAADVDGDGESEVIVT 259
                                       58899***********98 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 9.9e-05
                                       SEEEESTSSSSS-EEEEEETT-ETCST CS
                            FG-GAP   4 slavgDvNGDGyaDLavGApeskggay 30 
                                       sl ++D++G G +D+ v+  e  g++ 
  gi|313122374|ref|YP_004038261.1| 295 SLQLADLDGNGSPDVYVA--E-MGLES 318
                                       899**************9..6.56665 PP

  == domain 7  score: 11.0 bits;  conditional E-value: 0.00018
                                       EESTSSSSS-EEE CS
                            FG-GAP   7 vgDvNGDGyaDLa 19 
                                       ++D++GDG  D++
  gi|313122374|ref|YP_004038261.1| 351 LVDLDGDGRLDIV 363
                                       68*********98 PP

>> TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.93   1.8e+03      25      46 ..      16      35 ..      11      44 .. 0.79
   2 ?    0.5   0.1      0.17   3.5e+02      33      46 ..      97     110 ..      87     121 .. 0.81
   3 !    6.4   0.0    0.0027       5.3      30      56 ..     146     175 ..     137     183 .. 0.82
   4 ?    3.5   0.1      0.02        40      31      47 ..     201     216 ..     177     223 .. 0.78
   5 ?    3.8   0.0     0.016        33      28      48 ..     240     260 ..     228     275 .. 0.79
   6 ?    2.5   0.0     0.042        83      30      45 ..     295     310 ..     281     323 .. 0.81
   7 !    5.4   0.0    0.0055        11      30      46 ..     348     364 ..     335     374 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.93
                   TcdB_toxin_midN 25 svedtnlslaDldGdGladlvl 46
                                      +++++     Dl G+G +d+++
  gi|313122374|ref|YP_004038261.1| 16 RMSFC--LTTDLTGNGRPDVLV 35
                                      56677..568*********764 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                   TcdB_toxin_midN  33 laDldGdGladlvl 46 
                                       l+D+ G+G+ dlv 
  gi|313122374|ref|YP_004038261.1|  97 LGDITGTGTVDLVA 110
                                       78*********875 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0027
                   TcdB_toxin_midN  30 nlslaDldGdGladlvltipsag...tgav 56 
                                       ++ +aD+dGdG ++++ ++ +++   +++v
  gi|313122374|ref|YP_004038261.1| 146 DVAVADVDGDGESEVIALSQESEvifYYDV 175
                                       4689**********8888777778888887 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.02
                   TcdB_toxin_midN  31 lslaDldGdGladlvlt 47 
                                       ++++D+dGdG+ +++ +
  gi|313122374|ref|YP_004038261.1| 201 VQVGDIDGDGTVEIL-A 216
                                       589********9954.4 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.016
                   TcdB_toxin_midN  28 dtnlslaDldGdGladlvlti 48 
                                        t + +aD+dGdG +++++t 
  gi|313122374|ref|YP_004038261.1| 240 WTRVVAADVDGDGESEVIVTE 260
                                       577899*********988765 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.042
                   TcdB_toxin_midN  30 nlslaDldGdGladlv 45 
                                        l+laDldG+G +d+ 
  gi|313122374|ref|YP_004038261.1| 295 SLQLADLDGNGSPDVY 310
                                       4899**********65 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.0055
                   TcdB_toxin_midN  30 nlslaDldGdGladlvl 46 
                                       + +l+DldGdG +d+v 
  gi|313122374|ref|YP_004038261.1| 348 EAKLVDLDGDGRLDIVG 364
                                       5689**********985 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       7.1   1.4e+04      86     100 ..      23      37 ..      20      41 .. 0.54
   2 ?   -2.4   0.0       2.4   4.7e+03       5      20 ..      98     113 ..      96     122 .. 0.63
   3 ?    6.7   0.0    0.0036       7.1       2      27 ..     147     172 ..     146     177 .. 0.89
   4 ?    0.0   0.0      0.44   8.7e+02       3      19 ..     202     218 ..     200     222 .. 0.81
   5 ?    2.8   0.0     0.059   1.2e+02       3      21 ..     244     262 ..     233     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.1
                          BBS2_Mid  86 ydingdgtkelivgw 100
                                        d++g+g  +++vg 
  gi|313122374|ref|YP_004038261.1|  23 TDLTGNGRPDVLVGA 37 
                                       455555555555554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                          BBS2_Mid   5 advdgdgeneLvvgsd 20 
                                        d++g g+ +Lv+g +
  gi|313122374|ref|YP_004038261.1|  98 GDITGTGTVDLVAGQN 113
                                       5666666666666654 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0036
                          BBS2_Mid   2 laladvdgdgeneLvvgsddfeirvf 27 
                                       +a+advdgdge+e+++ s++ e+  +
  gi|313122374|ref|YP_004038261.1| 147 VAVADVDGDGESEVIALSQESEVIFY 172
                                       589*****************999776 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.44
                          BBS2_Mid   3 aladvdgdgeneLvvgs 19 
                                        + d+dgdg+ e+++g 
  gi|313122374|ref|YP_004038261.1| 202 QVGDIDGDGTVEILAGP 218
                                       57799999999999986 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.059
                          BBS2_Mid   3 aladvdgdgeneLvvgsdd 21 
                                       + advdgdge+e++v   d
  gi|313122374|ref|YP_004038261.1| 244 VAADVDGDGESEVIVTEGD 262
                                       4578889999988887655 PP

>> Itfg2  Integrin-alpha FG-GAP repeat-containing protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.95   1.9e+03      85     124 ..      98     137 ..      97     141 .. 0.84
   2 ?    3.6   0.1     0.014        27      81     104 ..     146     169 ..     122     182 .. 0.77
   3 ?    6.6   0.4    0.0017       3.4      37      98 ..     153     217 ..     147     220 .. 0.57
   4 ?    3.9   0.0     0.012        23      82     101 ..     243     262 ..     234     266 .. 0.87
   5 ?   -3.1   0.0       1.5     3e+03      84      96 ..     351     363 ..     345     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.95
                             Itfg2  85 aDidgDgkvElvvgytDrvvrayrWeeseeeeeslskklv 124
                                        Di g g+v+lv+g        y +e++++ +es +++lv
  gi|313122374|ref|YP_004038261.1|  98 GDITGTGTVDLVAGQNLNQYDLYWFEQPDDPRESWTRRLV 137
                                       599999999***9999998888888888888888888887 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                             Itfg2  81 vvliaDidgDgkvElvvgytDrvv 104
                                        v +aD+dgDg+ E+++   +  v
  gi|313122374|ref|YP_004038261.1| 146 DVAVADVDGDGESEVIALSQESEV 169
                                       57799*********9876555554 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0017
                             Itfg2  37 saeGwchlfdlakkadaseevskelekkeelkpvfsqhlpa...ntkvvliaDidgDgkvElvvg 98 
                                        ++G  ++ +l+++++     +     ++e  pv + h++a   n + v + DidgDg+vE+++g
  gi|313122374|ref|YP_004038261.1| 153 DGDGESEVIALSQESEVIFYYDVPADPRREPWPVANRHVVAdniNVEGVQVGDIDGDGTVEILAG 217
                                       34444444444444444333333444455556666667666433566789999999999999876 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.012
                             Itfg2  82 vliaDidgDgkvElvvgytD 101
                                       v+ aD+dgDg+ E++v+  D
  gi|313122374|ref|YP_004038261.1| 243 VVAADVDGDGESEVIVTEGD 262
                                       7789***********98766 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 1.5
                             Itfg2  84 iaDidgDgkvElv 96 
                                       + D+dgDg++++v
  gi|313122374|ref|YP_004038261.1| 351 LVDLDGDGRLDIV 363
                                       5699999999987 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.04        79       8      14 ..     150     156 ..     148     157 .. 0.87
   2 ?    3.3   0.3     0.032        64       9      17 ..     205     213 ..     202     214 .. 0.82
   3 ?    3.7   0.2     0.024        47       7      14 ..     245     252 ..     244     253 .. 0.89
   4 ?    2.2   0.0     0.073   1.5e+02       5      14 ..     296     305 ..     294     306 .. 0.86
   5 ?    8.4   0.6   0.00076       1.5       7      17 ..     351     361 ..     350     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.04
                                       H-SS-SS CS
                         EF-hand_5   8 iDlNgDG 14 
                                       +D++gDG
  gi|313122374|ref|YP_004038261.1| 150 ADVDGDG 156
                                       8****** PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.032
                                       -SS-SSCE- CS
                         EF-hand_5   9 DlNgDGkIs 17 
                                       D +gDG++ 
  gi|313122374|ref|YP_004038261.1| 205 DIDGDGTVE 213
                                       99****985 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.024
                                       HH-SS-SS CS
                         EF-hand_5   7 aiDlNgDG 14 
                                       a+D++gDG
  gi|313122374|ref|YP_004038261.1| 245 AADVDGDG 252
                                       79****** PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.073
                                       HHHH-SS-SS CS
                         EF-hand_5   5 FqaiDlNgDG 14 
                                       +q +Dl+g G
  gi|313122374|ref|YP_004038261.1| 296 LQLADLDGNG 305
                                       6899****99 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.00076
                                       HH-SS-SSCE- CS
                         EF-hand_5   7 aiDlNgDGkIs 17 
                                        +Dl+gDG+++
  gi|313122374|ref|YP_004038261.1| 351 LVDLDGDGRLD 361
                                       58*******99 PP

>> PliI  Periplasmic lysozyme inhibitor of I-type lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0068        14      41      80 ..     126     165 ..     112     178 .. 0.72
   2 ?    1.3   0.1      0.14   2.8e+02      51      76 ..     190     215 ..     167     220 .. 0.79
   3 ?    4.3   0.1     0.016        32      62      78 ..     243     259 ..     226     262 .. 0.87
   4 ?    1.1   0.0      0.15     3e+02      61      85 ..     295     319 ..     285     327 .. 0.86
   5 ?    1.4   0.1      0.13   2.6e+02      60      76 ..     347     363 ..     326     368 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0068
                                       TSTTSSEEEEEEEEESSEEEEEEEE-SSSSSS-EEEEEEE CS
                              PliI  41 dtdldefvaGlvlsRdGsveevkladvngdkkkelvvlkr 80 
                                       d++ +++   lv+      ++v +adv+gd++ e++ l +
  gi|313122374|ref|YP_004038261.1| 126 DDPRESWTRRLVTDDFEKYHDVAVADVDGDGESEVIALSQ 165
                                       555555555555555556678**************98765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                                       EEEEESSEEEEEEEE-SSSSSS-EEE CS
                              PliI  51 lvlsRdGsveevkladvngdkkkelv 76 
                                       +v++ +  ve v++ d++gd++ e++
  gi|313122374|ref|YP_004038261.1| 190 HVVADNINVEGVQVGDIDGDGTVEIL 215
                                       67788888999**********99985 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.016
                                       EEEE-SSSSSS-EEEEE CS
                              PliI  62 vkladvngdkkkelvvl 78 
                                       v  adv+gd++ e++v+
  gi|313122374|ref|YP_004038261.1| 243 VVAADVDGDGESEVIVT 259
                                       7789************8 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.15
                                       EEEEE-SSSSSS-EEEEEEE-SSTT CS
                              PliI  61 evkladvngdkkkelvvlkrsaGsG 85 
                                       +++lad++g++++++ v +    sG
  gi|313122374|ref|YP_004038261.1| 295 SLQLADLDGNGSPDVYVAEMGLESG 319
                                       589************9988766666 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.13
                                       EEEEEE-SSSSSS-EEE CS
                              PliI  60 eevkladvngdkkkelv 76 
                                       +e+kl+d++gd++ ++v
  gi|313122374|ref|YP_004038261.1| 347 HEAKLVDLDGDGRLDIV 363
                                       359**********9998 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2       4.9   9.8e+03      10      18 ..      99     107 ..      98     108 .. 0.84
   2 ?    2.3   0.1     0.075   1.5e+02       8      15 ..     149     156 ..     148     157 .. 0.85
   3 ?    3.5   0.2      0.03        61      10      18 ..     205     213 ..     201     214 .. 0.84
   4 ?    1.8   0.1      0.11   2.1e+02       9      15 ..     246     252 ..     244     253 .. 0.87
   5 ?    2.0   0.0     0.096   1.9e+02       7      15 ..     297     305 ..     295     306 .. 0.87
   6 ?    6.5   0.4    0.0034       6.8       7      18 ..     350     361 ..     350     362 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.9
                                       TTTSSSEEE CS
                         EF-hand_1  10 DkDgdGkId 18 
                                       D  g+G++d
  gi|313122374|ref|YP_004038261.1|  99 DITGTGTVD 107
                                       78899*998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.075
                                       HHTTTSSS CS
                         EF-hand_1   8 efDkDgdG 15 
                                       ++D+DgdG
  gi|313122374|ref|YP_004038261.1| 149 VADVDGDG 156
                                       68****** PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.03
                                       TTTSSSEEE CS
                         EF-hand_1  10 DkDgdGkId 18 
                                       D DgdG+++
  gi|313122374|ref|YP_004038261.1| 205 DIDGDGTVE 213
                                       9*****996 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.11
                                       HTTTSSS CS
                         EF-hand_1   9 fDkDgdG 15 
                                       +D+DgdG
  gi|313122374|ref|YP_004038261.1| 246 ADVDGDG 252
                                       7*****9 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.096
                                       HHHTTTSSS CS
                         EF-hand_1   7 refDkDgdG 15 
                                       +++D Dg+G
  gi|313122374|ref|YP_004038261.1| 297 QLADLDGNG 305
                                       789*****9 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.0034
                                       HHHTTTSSSEEE CS
                         EF-hand_1   7 refDkDgdGkId 18 
                                       +++D DgdG++d
  gi|313122374|ref|YP_004038261.1| 350 KLVDLDGDGRLD 361
                                       689*******98 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         7   1.4e+04       2      11 ..      98     107 ..      97     108 .. 0.80
   2 ?    3.7   0.1     0.037        74      32      44 ..     145     157 ..     133     161 .. 0.79
   3 ?    2.6   0.6     0.078   1.5e+02       2      11 ..     204     213 ..     193     215 .. 0.74
   4 ?    3.3   0.1     0.049        98      35      44 ..     244     253 ..     235     256 .. 0.82
   5 ?    0.1   0.0      0.48   9.5e+02      26      44 ..     288     306 ..     284     309 .. 0.81
   6 ?    1.3   0.0       0.2     4e+02      34      46 ..     349     361 ..     341     363 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7
                                       TETTSSSC-S CS
                        Dockerin_1   2 gDVNgDgkVn 11 
                                       gD++g g+V+
  gi|313122374|ref|YP_004038261.1|  98 GDITGTGTVD 107
                                       8999988887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.037
                                       CCHGGGSTT-SSC CS
                        Dockerin_1  32 sngkaaDvNgDGr 44 
                                        + + aDv+gDG+
  gi|313122374|ref|YP_004038261.1| 145 HDVAVADVDGDGE 157
                                       5678899999996 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.078
                                       TETTSSSC-S CS
                        Dockerin_1   2 gDVNgDgkVn 11 
                                       gD++gDg+V 
  gi|313122374|ref|YP_004038261.1| 204 GDIDGDGTVE 213
                                       6777777775 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.049
                                       GGGSTT-SSC CS
                        Dockerin_1  35 kaaDvNgDGr 44 
                                        aaDv+gDG+
  gi|313122374|ref|YP_004038261.1| 244 VAADVDGDGE 253
                                       5899999996 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 0.48
                                       EBTTSCCCHGGGSTT-SSC CS
                        Dockerin_1  26 egqssssngkaaDvNgDGr 44 
                                       ++ s++   + aD++g+G+
  gi|313122374|ref|YP_004038261.1| 288 DDLSNPHSLQLADLDGNGS 306
                                       56678889999*****996 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.2
                                       HGGGSTT-SSCES CS
                        Dockerin_1  34 gkaaDvNgDGrvn 46 
                                        k  D++gDGr +
  gi|313122374|ref|YP_004038261.1| 349 AKLVDLDGDGRLD 361
                                       5678999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2452.62
//
Query:       gi|313122375|ref|YP_004038262.1|  [L=288]
Description: methyltransferase, FkbM family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-17   63.3   0.0    3.7e-17   62.9   0.0    1.2  1  Methyltransf_21  Methyltransferase FkbM domain
    2.7e-07   30.2   0.0    1.9e-06   27.4   0.0    1.9  2  V_cholerae_RfbT  Vibrio cholerae RfbT protein
    1.3e-06   28.3   0.0      2e-06   27.7   0.0    1.2  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.035   13.7   0.0      0.057   13.0   0.0    1.2  1  MTS              Methyltransferase small domain
      0.039   13.9   0.0      0.078   12.9   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
      0.066   13.9   0.0       0.18   12.5   0.0    1.7  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.0   1.2e-20   3.7e-17       1     168 [.     111     265 ..     111     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.2e-20
                   Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksggkyfpfavgd 77 
                                       dvGa++gv++  a    +   + g+v+aiEP+p+   ++e+lr+n   l  +  ++++  +++  + ++ +   v++
  gi|313122375|ref|YP_004038262.1| 111 DVGAHVGVFSVLA----AGQVPAGTVIAIEPLPE---NAEQLREN---LKRNGRDATVR-QLALDDESRRAELGVNS 176
                                       9******544444....45678999*********...********...66554544444.55555557788888888 PP

                   Methyltransf_21  78 tngfstssvlggedaryievpvvtld...sfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkf 151
                                       ++g++    l  +  + ++ ++v+ d   s+  ++  + +++lk+Dv+GaEl+vL+G q+ l  c++  + v   + 
  gi|313122375|ref|YP_004038262.1| 177 PSGAGAFGTL--NGLSSRRRTTVQTDcgdSLVTDG-VPAPTVLKVDVQGAELNVLRGLQRSLLGCRIVCVNV--YEK 248
                                       8888888877..66666666666666663666666.9*************************9*****9543..333 PP

                   Methyltransf_21 152 kefetelfdeirqflre 168
                                       +++++++ +eir++l++
  gi|313122375|ref|YP_004038262.1| 249 HFTRGDEGEEIRDILES 265
                                       34456888999999876 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   6.4e-10   1.9e-06      43     126 ..      70     152 ..      59     162 .. 0.80
   2 ?    0.4   0.0      0.11   3.3e+02     193     209 ..     214     230 ..     204     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 6.4e-10
                   V_cholerae_RfbT  43 efglhcfprvqlnhalsyknpnfdlgmrhwivnhckhdttyidiganvgtfcgiaarhitqgkiiaiepltemensi 119
                                       e+ ++   r + +    y+     l ++h+ v   + d    d+ga vg f  +aa ++  g +iaiepl e  + +
  gi|313122375|ref|YP_004038262.1|  70 EWRFRISTRFEYESLSKYRTDPDRLVLQHF-VRSLRDDDVVWDVGAHVGVFSVLAAGQVPAGTVIAIEPLPENAEQL 145
                                       556666666666666667766667778887.56678888899*********************************** PP

                   V_cholerae_RfbT 120 rmnvqln 126
                                       r n++ n
  gi|313122375|ref|YP_004038262.1| 146 RENLKRN 152
                                       *999877 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                   V_cholerae_RfbT 193 vvikidaegaeieilnq 209
                                        v+k+d +gae+++l  
  gi|313122375|ref|YP_004038262.1| 214 TVLKVDVQGAELNVLRG 230
                                       589**********9975 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   6.6e-10     2e-06      94     160 ..      99     165 ..      86     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6.6e-10
                                       HHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-G CS
                            Met_10  94 laklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDg 160
                                        ++  ++++vV dv A +G f++ +a    a +v+ai+  Pe  + l+en+k+N  + +v+ +  D 
  gi|313122375|ref|YP_004038262.1|  99 FVRSLRDDDVVWDVGAHVGVFSVLAAGQVPAGTVIAIEPLPENAEQLRENLKRNGRDATVRQLALDD 165
                                       56778999******************99********************************9988876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.9e-05     0.057      21      92 ..      93     166 ..      85     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                                       HHHHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTT CS
                               MTS  21 klLletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvlee 92 
                                       +l l+++  +   ++ v D+G+ +Gv ++ +a + p  +v +++   +  e  +enl++n+ +++v++  + +e
  gi|313122375|ref|YP_004038262.1|  93 RLVLQHFVRSlrDDDVVWDVGAHVGVFSVLAAGQVPAGTVIAIEPLPENAEQLRENLKRNGRDATVRQLALDDE 166
                                       677888888764555699*******************************************9999888766655 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.6e-05     0.078       5      67 ..      96     158 ..      93     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                   Methyltransf_18   5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledki 67 
                                       L++ ++ ++++++v+D+G+  g+ ++ ++ +  a +via++  ++  e+ +en++++g +  +
  gi|313122375|ref|YP_004038262.1|  96 LQHFVRSLRDDDVVWDVGAHVGVFSVLAAGQVPAGTVIAIEPLPENAEQLRENLKRNGRDATV 158
                                       677778889999*******************************************99877655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.1e-05      0.18       1      55 [.     109     163 ..     109     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.1e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda 55 
                                       v d+G+  G ++  +a ++++++v+++++ +e  e+ re+++++g +++++q  +
  gi|313122375|ref|YP_004038262.1| 109 VWDVGAHVGVFSVLAAGQVPAGTVIAIEPLPENAEQLRENLKRNGRDATVRQLAL 163
                                       67****************999********************99998777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2118.91
//
Query:       gi|313122376|ref|YP_004038263.1|  [L=285]
Description: xylanase/chitin deacetylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-28   98.4   0.0    4.9e-28   97.5   0.0    1.4  1  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
       0.13   11.4   0.0       0.19   10.9   0.0    1.1  1  DUF693           Protein of unknown function (DUF693)


Domain annotation for each model (and alignments):
>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.0   5.5e-32   4.9e-28       5     118 ..      82     233 ..      79     237 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 5.5e-32
                                       TSTEEEEEEEESSCSCHHHHHHHHHHCT--EEEEE-HHHHCH-.................................. CS
                   Polysacc_deac_1   5 gkksvalTfDdgprdntteilpvLkkykvkatffvigglvedy.................................. 47 
                                       g+k valTfDd++ d+++++lp+L++y+v+at+fv  + v+                                    
  gi|313122376|ref|YP_004038263.1|  82 GGKRVALTFDDAYDDFYENVLPLLREYNVPATLFVPVEFVGGCpddyayrfarspidhesfndpslfdgetvrgpsm 158
                                       789*******************************9777755555556****************************** PP

                                       ..HHHHHHHHHTT.EEEEE--SS--EGGGS.HHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHHHHH CS
                   Polysacc_deac_1  48 ..pdevremaasG.veignHtinhsnlkrl.seeevrreierakdalrkalgreprlfryPygsasatvlevare 118
                                         +d+++e+aa++ v++g Ht +h++l r   +e+++ ei  a+d+l++ lg ++  f+yPyg++s +++ v++e
  gi|313122376|ref|YP_004038263.1| 159 msWDRLNEVAADPlVTVGTHTRTHPDLGRIhDRETLEYEIVGARDVLEERLGVDVDRFCYPYGRYSGEAVSVVEE 233
                                       ***************************66515669*********************************9998876 PP

>> DUF693  Protein of unknown function (DUF693)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.1e-05      0.19      21      70 ..     224     273 ..     213     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.1e-05
                            DUF693  21 ssdgislieeipkiiintqdgihidisisnvysnintvkskrakvvlwnl 70 
                                       s + +s++ee  ++ + +q+g+ idi  ++ y   ++   k+ + v w+l
  gi|313122376|ref|YP_004038263.1| 224 SGEAVSVVEESHRLAVTSQHGVLIDIEAADRYRLPRVRAHKEEQYVRWDL 273
                                       667899**************************999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2193.83
//
Query:       gi|313122377|ref|YP_004038264.1|  [L=337]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-14   52.1   0.3    1.2e-13   51.3   0.3    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
      3e-09   37.1   0.9    4.9e-08   33.1   0.9    2.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.6e-08   34.4   0.1    0.00036   20.1   0.0    2.1  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.033   13.8   0.0      0.065   12.9   0.0    1.5  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase
      0.037   13.6   0.0       0.13   11.9   0.0    1.8  2  ThiP_synth       Thiamine-phosphate synthase
       0.13   12.1   0.6        2.4    8.0   0.6    2.2  1  Glyco_trans_2_3  Glycosyl transferase family group 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.3   3.9e-17   1.2e-13       1     147 [.      59     197 ..      59     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3.9e-17
                                       EEEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       svv++t++   +    +l+++ aq +++ fe++vv++g     ++i  +l++ d +  ++ + +n G   a+n g++
  gi|313122377|ref|YP_004038264.1|  59 SVVVVTFQTsRNAFDSVLTAIEAQ-TDDAFELVVVNNGV---DWDIESRLHDLDCGTAYVELIRNCGVTIARNLGAE 131
                                       89******9999999999999999.*************9...89999999999************************ PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCC CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrsl 147
                                        a +d++lflD+D +p+++++     a ++   dvv++  + +++++++++r +r   ++ l  ++    l
  gi|313122377|ref|YP_004038264.1| 132 LALSDLLLFLDDDAVPEENFVAAHRCAHDD--SDVVAVRGRIFPQSKTFYNRLQR---WYDLGDRTLPYLL 197
                                       *******************99877555555..78899999999999999999987...4444444443333 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.9   1.6e-11   4.9e-08       1     224 [.      56     268 ..      56     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.6e-11
                   Glyco_tranf_2_3   1 prdlavlVptfneed.vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgks 76 
                                       p  ++v+V+tf+ ++    +vl+++ aq+ +++e+vvv ++ d +  +++  l  +++++ v ++   rn g+t ++
  gi|313122377|ref|YP_004038264.1|  56 PA-ISVVVVTFQTSRnAFDSVLTAIEAQTDDAFELVVVNNGVDWDIESRLHDL--DCGTAYVELI---RNCGVTIAR 126
                                       56.9*********9967778999999**99*************9999999887..9999999988...666876664 PP

                   Glyco_tranf_2_3  77 ralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfl.lnrstlvsalgalefaerhlrflaar 152
                                          n + + + sdl+l++DdD+v e +++++  + + +++ ++v ++ +   + +t+ ++l++     ++    + +
  gi|313122377|ref|YP_004038264.1| 127 ---NLGAELALSDLLLFLDDDAVPEENFVAA-HRCA-HDDSDVVAVRGRIfPQSKTFYNRLQR-----WYD---LGD 190
                                       ...58999999****************9554.5555.66666666443331455566554444.....443...556 PP

                   Glyco_tranf_2_3 153 ralg.vltlnGsgslirrevlkelegldp..lfllt.dDyelglrlrragf...rtayvpgaavrevfpsslkayik 222
                                       r+l   l + G++  i+re ++   g+d+  ++  + ++++l++rl r+g+   +++y+p+a++++   +sl+ yi+
  gi|313122377|ref|YP_004038264.1| 191 RTLPyLLNIEGNT-SIDREAYRSVSGFDEklGGRAGhEGIDLTYRLIRTGYdrdQIVYCPDAVIYHDYATSLSGYIR 266
                                       6666346666765.59*************97555668***********999333477*******************9 PP

                   Glyco_tranf_2_3 223 qr 224
                                        r
  gi|313122377|ref|YP_004038264.1| 267 KR 268
                                       87 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.2e-07   0.00036       2      92 ..      61     145 ..      59     159 .. 0.75
   2 !   12.7   0.0   2.2e-05     0.067     140     225 ..     165     264 ..     145     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-07
                   Glyco_tranf_2_2   2 vviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGas 78 
                                       vv+ +++s++       +  +  + d+ +el+vv++g   ++ + +  +      v l     +  + + arN+Ga+
  gi|313122377|ref|YP_004038264.1|  61 VVVTFQTSRNA--FDSVLTAIEAQTDDAFELVVVNNGVDWDIESRLHDLDCGTAYVELI----RNCGVTIARNLGAE 131
                                       45556666555..455557788899*************999777777765555555332....346*********** PP

                   Glyco_tranf_2_2  79 kaesdlvlFlDaDc 92 
                                        a sdl+lFlD D 
  gi|313122377|ref|YP_004038264.1| 132 LALSDLLLFLDDDA 145
                                       ***********886 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.2e-05
                   Glyco_tranf_2_2 140 ltassrvledllaakstlvk..........ffapssssilinrraflevGGyDErfrGh.gaEDfdlllRlaka... 202
                                       + +++r+  +  ++++ l +          ++++   +  i r+a+  v G+DE++ G  g E  dl  Rl +    
  gi|313122377|ref|YP_004038264.1| 165 VAVRGRIFPQSKTFYNRLQRwydlgdrtlpYLLNIEGNTSIDREAYRSVSGFDEKLGGRaGHEGIDLTYRLIRTgyd 241
                                       5566777777777777777777777777777788888999****************99637899***9888654111 PP

                   Glyco_tranf_2_2 203 ikslekmpvellykarakslsny 225
                                         ++   p  + y++ a sls y
  gi|313122377|ref|YP_004038264.1| 242 RDQIVYCPDAVIYHDYATSLSGY 264
                                       45666788888899988888855 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.2e-05     0.065      14      62 ..     193     242 ..     186     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                   Glyco_transf_7C  14 lpyekyfgGvlalrkedfekiNGfsntfwgW.GgEDdelyaRlakkglei 62 
                                       lpy   + G++++++e ++++ Gf++++ g  G E  +l  Rl++ g++ 
  gi|313122377|ref|YP_004038264.1| 193 LPYLLNIEGNTSIDREAYRSVSGFDEKLGGRaGHEGIDLTYRLIRTGYDR 242
                                       56666678*******************99854999999999999999874 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.99     3e+03      59     100 ..      63     107 ..      52     115 .. 0.56
   2 ?   11.9   0.0   4.2e-05      0.13      24      47 ..     149     172 ..     143     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.99
                                       EEETS-CHHHHHHHHHHCC-TT...--EEEEEE--HHHHHHHCCT CS
                        ThiP_synth  59 pefgasshvarvllaamkfdpe...vraainirydekilealeel 100
                                       ++f  s++    +l+a +++ +     +++n   d +i+++l++l
  gi|313122377|ref|YP_004038264.1|  63 VTFQTSRNAFDSVLTAIEAQTDdafELVVVNNGVDWDIESRLHDL 107
                                       566666666666666666554421122345555555555555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.2e-05
                                       B-EEEE-ST--SGGGEEEETT-EE CS
                        ThiP_synth  24 sNiayalpdAksieDvaavpGRIv 47 
                                        N+++a + A + +Dv+av+GRI+
  gi|313122377|ref|YP_004038264.1| 149 ENFVAAHRCAHDDSDVVAVRGRIF 172
                                       59*********************7 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.6   0.00082       2.4       3     137 ..     139     268 ..     137     292 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00082
                   Glyco_trans_2_3   3 lllDaDtvlppdclreiaaelaspevaivqgpvlvm..nvanwleelaalffaedhgkdilvrealgrvvpsvGsga 77 
                                       l+lD+D v+ +++++  +   ++ +v +v g ++++     n l+++++l        d+         +     ++
  gi|313122377|ref|YP_004038264.1| 139 LFLDDDAVPEENFVAAHRCAHDDSDVVAVRGRIFPQskTFYNRLQRWYDL-------GDRTL-----PYLLNIEGNT 203
                                       56777777777777766555556677777777777621113333333332.......11111.....1222335689 PP

                   Glyco_trans_2_3  78 flrrsalqevggwdgdes....svsEDfdmglrlqrkGyrv...rfvpeslvkekspltlraalrQr 137
                                       +++r+a ++v+g+d  e+    +  E  d+  rl r Gy+    +++p+++++     +l  ++r r
  gi|313122377|ref|YP_004038264.1| 204 SIDREAYRSVSGFD--EKlggrAGHEGIDLTYRLIRTGYDRdqiVYCPDAVIYHDYATSLSGYIRKR 268
                                       99999999999999..444455888999999999999975333389999999999888888777743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2667.72
//
Query:       gi|313122378|ref|YP_004038265.1|  [L=110]
Description: hypothetical protein Hbor_36120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   13.4   0.0      0.018   13.3   0.0    1.0  1  COG6      Conserved oligomeric complex COG6


Domain annotation for each model (and alignments):
>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     1e-06     0.018     375     427 ..      20      70 ..      16      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-06
                              COG6 375 klakkkffsllkdklakllpelppsdLspPewlsealskllelletyesslas 427
                                       + +++++f++  +++++l++ +p++ LspP   ++als++++ +++ +   ++
  gi|313122378|ref|YP_004038265.1|  20 NGTMEVIFTTGDSHVRTLREYPPTDSLSPPTPAIDALSTATPAIDSLSL--TT 70 
                                       567899************85555566****************9987655..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 916.95
//
Query:       gi|313122379|ref|YP_004038266.1|  [L=623]
Description: hypothetical protein Hbor_36130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4309.98
//
Query:       gi|313122380|ref|YP_004038267.1|  [L=351]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-25   88.1   0.0      7e-25   87.5   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-24   87.3   0.0    2.4e-24   86.3   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
    9.7e-16   58.2   1.1    1.9e-15   57.3   1.1    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.6e-14   54.7   3.4    3.3e-14   53.6   3.4    1.6  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    9.8e-10   38.7   0.0    4.1e-08   33.5   0.0    2.4  2  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00052   20.1   0.0    0.00082   19.4   0.0    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   2.3e-28     7e-25      15     172 .]     176     328 ..     168     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 2.3e-28
                                       -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                   Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                       ++ ++++++  ++Kg++ l++a+++l ++ ++n++++i G+g+  +      + +e  ++v + g+vs+e++ e+l+
  gi|313122380|ref|YP_004038267.1| 176 PPHLVFISNHIERKGIKELVEAVDTLMRN-DENCRVTIGGSGPLSHLAA---DIAERHERVSYEGYVSEERKREILN 248
                                       5667888999999*************999.**********988854444...44555567***************** PP

                                       CESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHH CS
                   Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgen 168
                                        +++fvlp + E ++i+llEAma g   +++ +g ++ +++d   G+lv+p+na ala+ + +l++d+e+ e++ + 
  gi|313122380|ref|YP_004038267.1| 249 DSSMFVLPTYAENLPIALLEAMAGGNVLVSTTVGAIPSLINDDN-GVLVEPGNATALAATLSDLVHDPERVEQMAQT 324
                                       ****************************************9998.******************************99 PP

                                       HHHH CS
                   Glycos_transf_1 169 arkr 172
                                       +r+r
  gi|313122380|ref|YP_004038267.1| 325 SRER 328
                                       9876 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0     8e-28   2.4e-24       2     134 .]     177     314 ..     176     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 8e-28
                                       EEEEEES---GG.GTHHHHHHHH.HHHH.HH.EEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleav.pllrkkd.vrlvivGdgprpeeleelaagleerveftGfv..edlaellaaad 74 
                                       p+++f+++   ++kg++ l+eav  l+r+++ +r++i G+gp + +l + +a+ +erv++ G+v  e ++e+l++++
  gi|313122380|ref|YP_004038267.1| 177 PHLVFISNHI-ERKGIKELVEAVdTLMRNDEnCRVTIGGSGPLS-HLAADIAERHERVSYEGYVseERKREILNDSS 251
                                       789****995.56**********777776635*********965.777666544589*******8555********* PP

                                       EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrLled 134
                                       +fv+P+  e ++++llEama g   V+t+vg+i+ ++  +ng+lv+pg++ ala+ + +L++d
  gi|313122380|ref|YP_004038267.1| 252 MFVLPTyaENLPIALLEAMAGGNVLVSTTVGAIPSLInDDNGVLVEPGNATALAATLSDLVHD 314
                                       ********9*********************99*****99*******************99986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   1.1   6.4e-19   1.9e-15      58     170 .]      57     167 ..      15     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 6.4e-19
                    Glyco_transf_4  58 laflrrlrrllkrekpDvvHahs..paalgaallalrr...rlgiplVltvHglyekrllkarlkplsrllralerr 129
                                       laf+ ++ r   r +pDvvH+hs  + +++ ++l+ ++    +++p+Vl++Hg+       ++ + +s+ +r +   
  gi|313122380|ref|YP_004038267.1|  57 LAFV-QILRFPFRRRPDVVHVHSshWNSFYQSGLYVLLastIWRVPVVLHIHGSS----FDSFMQTESKPVRLFQSV 128
                                       3333.344444455*****99962233343333333334446*************....577788888899999999 PP

                    Glyco_transf_4 130 llrradrviavSeatadelrerygvppekitVipnGvDler 170
                                       +++++drvi+ S++ +d +    + ++ekitV+pn+vD+++
  gi|313122380|ref|YP_004038267.1| 129 VFSQCDRVIVLSDYWRDIVGV--RAAEEKITVLPNAVDPDE 167
                                       9******************99..6678***********985 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   3.4   1.1e-17   3.3e-14      35     159 ..      30     161 ..       2     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.1e-17
                   Glyco_trans_4_4  35 leedgvrvhrlpvprrps.pladlaalralrrll.rqrrerpdvvhahspt......aglaarlarrrrgiplvvtl 103
                                        +   +r++ + vp + s +   +a l a+ ++l    r+rpdvvh+hs++      +gl+++la+  +++p+v+++
  gi|313122380|ref|YP_004038267.1|  30 PRSVSARTYDVSVPTSDSiRAFAVAILLAFVQILrFPFRRRPDVVHVHSSHwnsfyqSGLYVLLASTIWRVPVVLHI 106
                                       33446777777788777633334566677777774336**********9766789999********99********* PP

                   Glyco_trans_4_4 104 hglllrrgsgavrrlyralerrllrradavlvvseaeaeelralgvpadrvvvvpn 159
                                       hg  +++ +  +   +r +++ +++++d+v+v+s+++++ +  + +  ++++v+pn
  gi|313122380|ref|YP_004038267.1| 107 HGSSFDSFMQTESKPVRLFQSVVFSQCDRVIVLSDYWRDIVGVRAAE-EKITVLPN 161
                                       **99998888888888999********************99999887.9******9 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.059   1.8e+02      49      67 ..     191     209 ..     179     214 .. 0.89
   2 !   33.5   0.0   1.4e-11   4.1e-08       8      90 ..     259     342 ..     246     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.059
                   Glyco_trans_1_2  49 leelaekiryllanpeerr 67 
                                        +el+e+++ l++n+e +r
  gi|313122380|ref|YP_004038267.1| 191 IKELVEAVDTLMRNDENCR 209
                                       689************9876 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 1.4e-11
                   Glyco_trans_1_2   8 sespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaeht 82 
                                       +e +   l+Ea+a G +++++   +++ l++++  ++l+e  +   la+ +  l+ +pe+ +++a+  rerv+++++
  gi|313122380|ref|YP_004038267.1| 259 AENLPIALLEAMAGGNVLVSTTVGAIPSLINDD-NGVLVEpgNATALAATLSDLVHDPERVEQMAQTSRERVEQNYS 334
                                       466667799************99******9998.6666666************************************ PP

                   Glyco_trans_1_2  83 ydhraeql 90 
                                       ++ + e+l
  gi|313122380|ref|YP_004038267.1| 335 WAVATERL 342
                                       *9988876 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.8e-07   0.00082      50     115 ..      40     118 ..      26     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.8e-07
                   Glyco_trans_4_2  50 lkvd.....rkgpleylkaf.klkklikkikPDvvhahya.....kpygllgslaarlsgvipvvlsvwGldv...l 112
                                       + v+     r++++  l af ++ +  +++ PDvvh+h        + gl+  la+ + + +pvvl ++G+++   +
  gi|313122380|ref|YP_004038267.1|  40 VSVPtsdsiRAFAVAILLAFvQILRFPFRRRPDVVHVHSShwnsfYQSGLYVLLASTIWR-VPVVLHIHGSSFdsfM 115
                                       5444222324445555556669999999**********9876544333888878888888.***********96532 PP

                   Glyco_trans_4_2 113 kfp 115
                                       +++
  gi|313122380|ref|YP_004038267.1| 116 QTE 118
                                       222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2554.97
//
Query:       gi|313122381|ref|YP_004038268.1|  [L=531]
Description: hypothetical protein Hbor_36150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-47  161.7   0.0    5.7e-46  157.7   0.0    2.2  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.7   0.0   3.2e-50   5.7e-46       2     344 ..      12     422 ..      11     436 .. 0.81

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 3.2e-50
                                       EEEEETT-BTTHHHHHG.S.TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEE CS
                      Phosphodiest   2 lvislDGlradlldrla.e.llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgey 76 
                                        v++lDG+++ ll+rl  + +lpn+++L++eg s+p lr+++P+ T+ ++ s++TG+ P++HG + +  ++ ++++ 
  gi|313122381|ref|YP_004038268.1|  12 FVLGLDGVPWGLLERLVdDgELPNFERLLNEGASGP-LRSTVPANTPVAWPSIATGTWPDKHGLYEFMKLNAAYKQS 87 
                                       599**************879****************.*****************************77776666664 PP

                                       EEEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC...........TBHHSBTCT.CSTTS. CS
                      Phosphodiest  77 vvfvtededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs..........etppryleddfnakv. 142
                                        +++ +d       +++p+w+ +     ++   + +p+s++  ++   +vs           + p+ l+ +f+  + 
  gi|313122381|ref|YP_004038268.1|  88 -PYSSADI------DQPPLWELVSPS-VVANVPMTYPTSDPGEDSG--IVSgmmtpqidgaAVNPDSLRSEFDRRLp 154
                                       .6666655......578888888888.4433344458888888732..44467778888887777777665555556 PP

                                       .........CHHHHHHHHHHHHHHHCHTHSHHHHHCT.......SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHH CS
                      Phosphodiest 143 .........pledkvdkavlqtwldaafakvvlekel.......ekpdlllvyleetDtvgHkfGpdspevedalrr 203
                                                ++ +++++ +l+++ +  + ++     l       e ++l+++++ ++D+ +H + +d++++++ + +
  gi|313122381|ref|YP_004038268.1| 155 dyeidikwrDYAGRKAE-FLRDLENVLDGRRQ----LmemlmenEAWRLFFFVYVAPDRLQHLI-WDEETLREHYGK 225
                                       66666655533333333.44444333332222....13334666********************.************ PP

                                       HHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGH........................... CS
                      Phosphodiest 204 vDkaigdLlealderglsaetniilvSDHGmadvsddkvielndlleekg........................... 253
                                       +D+ +gd +++ +er    + n+ +vSDHG+a++  +kvi +n++l+++g                           
  gi|313122381|ref|YP_004038268.1| 226 LDEILGDVMAYCEER----DSNLYVVSDHGFAPI--EKVISVNRILADEGlltvkdsdgtrgalssiglnkarvqsa 296
                                       ***************....***************..***************************************** PP

                                       ..................................GEEEEECBHHS.SSE......EEEEESTEE.E.CCCTTHHHHH CS
                      Phosphodiest 254 ..................................llhlkdegkggakal......iainpkare.lnrvaeaeaeev 289
                                                                         + + +++      a+      ++in  +r   ++v++ ++e+ 
  gi|313122381|ref|YP_004038268.1| 297 lksvgitdeklvrslpksvvdffaeripgshglyDVEFDRTD-----AFlhglgsVYINDTERFeQGTVPPTAVERT 368
                                       *******99999999999999988888888885544444444.....3345567899999999999*********** PP

                                       HHHHHTCHHCCHST.HTT.TEEEEEGG.GS-GGGCHSTTS-SEEEEE-TTEEEESSTT CS
                      Phosphodiest 290 yaelkakleelrkk.ege.alavylke.aipkrlhykkrapdlvlvadpgwsitskdk 344
                                         e+   le+ +++ +g+  l+v++ +  +p++    + apd+v+ a++g+++  k +
  gi|313122381|ref|YP_004038268.1| 369 KCEVIGVLEAATDPeTGDsLLTVHDGDeLFPND----PEAPDIVVEAKDGYHVEPKLG 422
                                       **********99999999999******779*95....89************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3634.46
//
Query:       gi|313122382|ref|YP_004038269.1|  [L=532]
Description: hypothetical protein Hbor_36160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-06   26.2   9.6     0.0034   17.2   2.4    3.3  3  Beta_helix       Right handed beta helix region
     0.0023   17.8   1.8       0.17   11.7   0.2    3.4  3  Pectate_lyase_3  Pectate lyase superfamily protein


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.6   6.6e-06      0.06     106     149 ..     251     294 ..     145     304 .. 0.58
   2 !   17.2   2.4   3.8e-07    0.0034      11     114 ..     248     373 ..     234     388 .. 0.62
   3 !   14.0   1.2   3.7e-06     0.033       8     101 ..     359     466 ..     353     479 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-06
                                       ES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS CS
                        Beta_helix 106 enNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss 149
                                       +n +i+n +++Gi+ + ++ nv+v++  ++nn g G+ ++g +s
  gi|313122382|ref|YP_004038269.1| 251 RNLHIENGGEHGIYASKGQGNVRVEGGLFKNNLGDGVRIAGEGS 294
                                       44455555555555555555555555555555555555554444 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.8e-07
                                       .EEESEEEES-SS-SEEE-SSS-..EEES-EEES-SS-SEEE-TT-S-EEES-EE...........E---..SEEE- CS
                        Beta_helix  11 vtiknntisnsggyGiylrgssn.vvienneiannsgsGiyilgssnntisnnti...........sdnn..gggia 73 
                                       v  +n +i+n g +Giy+  +++ v++e+  + nn g+G++i g +++++++ t+           ++n+  + gi+
  gi|313122382|ref|YP_004038269.1| 248 VYYRNLHIENGGEHGIYASKGQGnVRVEGGLFKNNLGDGVRIAG-EGSWVKGATVvidmddrtpgnRGNWhqARGIH 323
                                       56677788888888888776655477778888888888888877.77777777777777666655422225555666 PP

                                       TT--....S--EEES-EEES-....SS-SEE-T.T-S--EEES-EEESTT CS
                        Beta_helix  74 lfga....snnlienneitdn....ggsGiyln.yssnntienNiidnna 114
                                       l+ +     + l+e+++++       ++ + ++ ++   t++n+++ nn+
  gi|313122382|ref|YP_004038269.1| 324 LQSGeygyTGGLVEDCTVIAHasprTEALLKIEhSQGAATVRNCRFFNNT 373
                                       55441111456777777777744433335555534445777777777776 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.7e-06
                                       S-E.EEESEEEES-SS-SEEE-SSS-............EEES-EEES..-SS-SEEE-TT-S-EEES-EEE---..S CS
                        Beta_helix   8 ssnvtiknntisnsggyGiylrgssn...........vvienneian..nsgsGiyilgssnntisnntisdnn..g 69 
                                       ++ +t++n+ + n+ +y   + +              v++en ei++  +++  + ++  ++++isn ti       
  gi|313122382|ref|YP_004038269.1| 359 QGAATVRNCRFFNNTDYRTIVVDKPAtgpqqpkkpweVTFENIEISGraSNTVAMLLEDRPGSKISNVTIDLPSvgV 435
                                       34479*********55544444444449*******************9888889999999**********8777778 PP

                                       EEE-TT--S--EEES-EEES-SS-SEE-TT-S CS
                        Beta_helix  70 ggialfgasnnlienneitdnggsGiylnyss 101
                                       +gi l++  +++i+n ++   g   ++++++s
  gi|313122382|ref|YP_004038269.1| 436 DGIVLNNCEGTVIDNMNVVTGGY-PLRVSSNS 466
                                       9**************99988844.55555444 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   1.9e-05      0.17      20     175 ..      84     267 ..      79     296 .. 0.62
   2 ?    2.7   0.1     0.011        99     106     188 ..     301     408 ..     294     448 .. 0.46
   3 ?   -0.4   0.0     0.095   8.5e+02     129     167 ..     422     456 ..     397     473 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                                       HHHHHH......HTSS-EEE-SEEEEESS-E..EE-SSEEEEES-TTTEEEEE-TT-..........SS--SEEES- CS
                   Pectate_lyase_3  20 aiqkaiscasatttgavVYfPaGtYlvsspi..ilksgvqLvGdgngrpvlkaaaaf..........vgaglidgdp 84 
                                       ai + +  +++ ++g ++ +P+GtY+v++       s   +vG g++r  ++ ++                   g++
  gi|313122382|ref|YP_004038269.1|  84 AIDDSL--DQTLREGTLIEVPPGTYRVKRRHdvEGVSRWGIVGIGTNRRAVQFTPPTgrsfrwlmvdG------GSD 152
                                       566666..99999**************99864477788889****99999999987754222222221......222 PP

                                       TT.T-..-EEEEEEEEEEEGGGG-SS---S..............SEEE.....ES-EEEEEEEEEEES-SSEEE-SS CS
                   Pectate_lyase_3  85 yv.sggsealiatnnfyrqirnlkiditav..............apga.....tgihwqtaqatslenvefemseas 141
                                       +  ++    + +   f+r+i    +  +++              +  +     +gi +q+ + + +  v++ ++++ 
  gi|313122382|ref|YP_004038269.1| 153 ILiKN--FTMQQGRKFDRSIGMGFLVDDGLklynvekagsnpreN--SgsgaeNGIVVQVTKPDGVAVVDTFVRKGP 225
                                       22222..22333334444433322222222334443333343332..145777889999999999888888777776 PP

                                       S....---TT---SS--E..EEE..ES-EEES-SS-SEEES- CS
                   Pectate_lyase_3 142 g....tkhqgifiengsg..gfl..ndlvfsglgdigiavgn 175
                                       +    + ++ i++  g g  g++  ++l +++ g++gi  ++
  gi|313122382|ref|YP_004038269.1| 226 QdfahYPGNAITVFTGRGhlGTVyyRNLHIENGGEHGIYASK 267
                                       666675666555555555445555699999999999998753 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.011
                                       G-SS---SSEEE.......ES-EEE....EEEEEEEES-SSEEE-SSS---TT---SS--E.EEEES-EEES-SS-S CS
                   Pectate_lyase_3 106 lkiditavapga.......tgihwq....taqatslenvefemseasgtkhqgifiengsg.gflndlvfsglgdig 170
                                       ++id+++ +pg+       +gih q      ++  +e+++  + +as  ++  + ie+++g  ++++++f ++ d+ 
  gi|313122382|ref|YP_004038269.1| 301 VVIDMDDRTPGNrgnwhqaRGIHLQsgeyGYTGGLVEDCT-VIAHASPRTEALLKIEHSQGaATVRNCRFFNNTDYR 376
                                       6677777766662333333334443222111112233332.222222233333345555554444555554433333 PP

                                       EEE.S...........-EEEEEES-EEE-..S CS
                   Pectate_lyase_3 171 iav.g...........nqqftvrnitfnn..a 188
                                         v             + ++t++ni +++  +
  gi|313122382|ref|YP_004038269.1| 377 TIVvDkpatgpqqpkkPWEVTFENIEISGraS 408
                                       33312455555555555555666666665553 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.095
                                       EEES-SSEEE-SSS---TT---SS--EEEEES-EEES-S CS
                   Pectate_lyase_3 129 slenvefemseasgtkhqgifiengsggflndlvfsglg 167
                                       +++nv++++++      +gi+++n +g +++++ +   g
  gi|313122382|ref|YP_004038269.1| 422 KISNVTIDLPSVG---VDGIVLNNCEGTVIDNMNVVT-G 456
                                       4556666666555...356666666665555554444.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3833.10
//
Query:       gi|313122383|ref|YP_004038270.1|  [L=862]
Description: hypothetical protein Hbor_36170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00059   19.7  28.8     0.0045   16.8   6.2    4.3  5  Beta_helix  Right handed beta helix region
  ------ inclusion threshold ------
      0.019   15.1   0.1        6.3    7.1   0.0    3.8  3  DUF4115     Domain of unknown function (DUF4115)
        3.1    7.8  14.3         10    6.2  14.3    1.9  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.2   1.2e+03       3      43 ..     142     181 ..     140     209 .. 0.66
   2 !   16.8   6.2   7.5e-07    0.0045       9     124 ..     237     384 ..     229     391 .. 0.78
   3 !   13.6   4.2   7.7e-06     0.046      18      72 ..     402     458 ..     393     476 .. 0.62
   4 ?    0.7   0.0     0.068   4.1e+02      34      52 ..     540     560 ..     513     626 .. 0.61
   5 ?   -2.4   0.1      0.62   3.7e+03      48      48 ..     735     735 ..     656     800 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                                       EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.....EEES-EEES CS
                        Beta_helix   3 isingssnvtiknntisnsggyGiylrgssn....vvienneian 43 
                                       i++ ++ ++ +kn+ti++  +y  +++ ++n          ++ n
  gi|313122383|ref|YP_004038270.1| 142 INFGNVAGAVLKNFTIDRLDDYDTTVGMGGNikrnF-----VLKN 181
                                       567777778888888888888888777777733333.....3333 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 7.5e-07
                                       -E.EEESEEEES-SS-SEEE-SSS-..EEES-EEES-SS-SEEE-TT-S-EEES-EE.................E-- CS
                        Beta_helix   9 snvtiknntisnsggyGiylrgssn.vvienneiannsgsGiyilgssnntisnnti.................sdn 67 
                                       ++  ++n +i+n + +Giy + +++  +ie+ ++ n  ++ ++  g  ++t++n+ti                 +  
  gi|313122383|ref|YP_004038270.1| 237 GHMVLRNIEIHNGSESGIYTGKGNGtYLIEDGYFKNVVHTAVRAAG-RDSTVRNCTIvmdtedwdprnekvestY-- 310
                                       34789***************99999899********9999****98.**********888888777666655552.. PP

                                       -...........SEEE-TT--S--EEES-EEES-SS-.....SEE-T.T-S--EEES-EEESTT--SEE---TT CS
                        Beta_helix  68 n...........gggialfgasnnlienneitdnggs.....Giyln.yssnntienNiidnnagsGividdss 124
                                                       + ++ s+ +ie+++i+  +++     Giy+n ++   +i+n +i   +g+ i i+ +s
  gi|313122383|ref|YP_004038270.1| 311 DdgepiqlnraiWAQTNDKQFSGPVIEDCDIIIKNTTstalaGIYVNfDTGGAKIRNTRIQCDSGHVIPIYGQS 384
                                       055677774455455555566788899998776633346666******************98888888888877 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 7.7e-06
                                       EES-..SS-SEEE-SSS-.EEES-EEES.-SS-SEEE-TT-S-EEES-EEE---SEEE CS
                        Beta_helix  18 isns..ggyGiylrgssnvvienneian.nsgsGiyilgssnntisnntisdnngggi 72 
                                       +++s   +++ y+++  n vi+n+ i++ n+ +G+ + +++++t++n +i+ ++  + 
  gi|313122383|ref|YP_004038270.1| 402 VTGSawDKAAMYFEDRPNSVIRNCCIQSsNNNDGVLLDNCDGSTVENTNINVGG-RAT 458
                                       444444667777777777777777777777777777777777777777777555.222 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.068
                                       .EEES-EEES..-SS-SEEE- CS
                        Beta_helix  34 vvienneian..nsgsGiyil 52 
                                        v+enn++++    +sG++ +
  gi|313122383|ref|YP_004038270.1| 540 GVVENNTVSDrvGPESGVDSY 560
                                       355555555555444444444 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 0.62
                                       S CS
                        Beta_helix  48 G 48 
                                       G
  gi|313122383|ref|YP_004038270.1| 735 G 735
                                       2 PP

>> DUF4115  Domain of unknown function (DUF4115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.028   1.7e+02      12      30 ..     198     216 ..     197     229 .. 0.91
   2 ?    7.1   0.0     0.001       6.3      43      67 ..     661     685 ..     654     691 .. 0.82
   3 ?   -0.5   0.0      0.24   1.5e+03      49      63 ..     758     772 ..     734     777 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.028
                           DUF4115  12 eVrdadGkvlfegtlkaGe 30 
                                       +V+d+dG+ +++g+ + G 
  gi|313122383|ref|YP_004038270.1| 198 NVTDSDGTAVVDGLYRTGP 216
                                       69************99985 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.001
                           DUF4115  43 tiGnagavevsvnGkpvdllgyarg 67 
                                       t+  a+ ++v+vnGk++d+++y  g
  gi|313122383|ref|YP_004038270.1| 661 TFDGAEYATVTVNGKEIDPNQYGEG 685
                                       555678899***********99665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.24
                           DUF4115  49 avevsvnGkpvdllg 63 
                                        ++v vnG++vd++ 
  gi|313122383|ref|YP_004038270.1| 758 DAKVFVNGNEVDPAT 772
                                       567889999999975 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  14.3    0.0017        10       4      25 ..      29      50 ..      27      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0017
                        TAT_signal  4 RRdFLKgsAAaaAAaalggcaa 25
                                      RRd LK +AA+aA aa +g+a+
  gi|313122383|ref|YP_004038270.1| 29 RRDALKLGAATAAVAAGAGAAT 50
                                      ****************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (862 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.41
# Mc/sec: 6277.57
//
Query:       gi|313122384|ref|YP_004038271.1|  [L=81]
Description: hypothetical protein Hbor_36180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.061   13.7   0.2      0.091   13.2   0.2    1.4  1  MKRN1_C   E3 ubiquitin-protein ligase makorin-1, C-terminal


Domain annotation for each model (and alignments):
>> MKRN1_C  E3 ubiquitin-protein ligase makorin-1, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   5.1e-06     0.091      13      61 ..      16      62 ..       5      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-06
                           MKRN1_C 13 rnqrrthlweileeresespfdnddeelvtfeLselLlmllaagaddEl 61
                                       ++   h+++ +e r  +s fd   +e v + L+e+L ++  a+ ddE 
  gi|313122384|ref|YP_004038271.1| 16 EVSLPVHILDRIEGRLPRSNFDT-SDEYVAYVLEEVLARVEDAS-DDEY 62
                                      555567999*************9.789*************9999.6664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 634.62
//
Query:       gi|313122385|ref|YP_004038272.1|  [L=408]
Description: arylsulfatase A family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-43  148.1   0.2    4.6e-43  147.8   0.2    1.1  1  Sulfatase      Sulfatase
  ------ inclusion threshold ------
      0.088   12.2   0.2       0.17   11.2   0.2    1.4  1  Metalloenzyme  Metalloenzyme superfamily


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   0.2   5.1e-47   4.6e-43       2     280 ..       3     296 ..       2     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 5.1e-47
                                       EEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHHC CS
                         Sulfatase   2 nvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevggggl 78 
                                       +vvl+++d+++ +  g+ g     tp++drla+ gl+f n+++ a+++s s ++++tgryp++ + a+  ++   + 
  gi|313122385|ref|YP_004038272.1|   3 DVVLVTIDSFRTDRCGFLGSDDGLTPAMDRLAADGLVFENAVAPAGATSGSSSTFFTGRYPIERSTAEDRKAVMRQN 79 
                                       79*************************************************************88666666666999 PP

                                       TTTS-HHHHHHHHTT-EEEEEE..ES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCC......T CS
                         Sulfatase  79 pqteatLpellkeaGYntaaig..kwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrv......p 147
                                        +   tLp+ +k+ GY+ta +   +w+  ++  ++++  + f++f+++  +s+++++ ++++++ + +++       
  gi|313122385|ref|YP_004038272.1|  80 LKAGRTLPQQFKDMGYRTAGFTanPWTSRFFGYDAGF--DHFEDFMDGDLTSDTIEKGDRGGTFSDLTSQllnwwqG 154
                                       9999**************6443225666666666643..4488899999999999999988888877777******* PP

                                       TTTCSHHHHHHHHHHHHH.HCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH.............. CS
                         Sulfatase 148 peggysddrlldealefl.larn.dkpfflylatlapHappeapdeyakkyatffddgseaar.............. 208
                                       +++++s d+++d++l++l  ar+ d+pffl++ +  +H p+  p++y  ++++  +    a++              
  gi|313122385|ref|YP_004038272.1| 155 QDMYMSWDAYYDQILDWLdEAREgDEPFFLWIFLVDVHMPYLPPKGYRSQSSAAAY---AANAwlfggakqntplsg 228
                                       *******************88888**************988888888777544443...333357788889999999 PP

                                       ....HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEE CS
                         Sulfatase 209 ....qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvw 280
                                           +ll+ay+++v+ +D++++r+  a+     +d+t +++ +Dhg+s +e   + + g g + ye+ +rvPl+v+
  gi|313122385|ref|YP_004038272.1| 229 llhdRLLRAYDDTVRFTDEFVDRIARAV-----DDDTALCVHADHGESFGE--RDGHYGHG-SLYEETVRVPLFVA 296
                                       ****************************.....****************66..67777777.99**********97 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   1.9e-05      0.17     147     187 ..     231     270 ..     227     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.9e-05
                                       HTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 147 HtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgn 187
                                       H++ l a+ + +   De v +i  a++++   l v ADHg 
  gi|313122385|ref|YP_004038272.1| 231 HDRLLRAYDDTVRFTDEFVDRIARAVDDDT-ALCVHADHGE 270
                                       899999999****************98887.********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3230.05
//
Query:       gi|313122386|ref|YP_004038273.1|  [L=332]
Description: glycosyl transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-33  115.3   0.1    3.8e-33  114.7   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.1e-20   74.5   0.5      2e-20   73.7   0.5    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    8.4e-11   41.9   0.0    6.6e-10   38.9   0.0    1.9  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.064   13.9   1.3       0.16   12.7   1.3    1.7  1  TPR_16           Tetratricopeptide repeat
      0.081   12.7   0.0       0.14   11.9   0.0    1.3  1  UPF0167          Uncharacterised protein family (UPF0167)
      0.084   13.0   0.0       0.24   11.6   0.0    1.8  1  TPR_2            Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   0.1   1.3e-36   3.8e-33       1     169 [.      11     175 ..      11     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 1.3e-36
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnaglr 76 
                                       svv+p+y ++++l +++es+ +q +y  +e++vvDD+S+D  + i+ ++   + +rv+v+r+e n+G  +a+n+g++
  gi|313122386|ref|YP_004038273.1|  11 SVVVPAYGRPEYLDAAVESVNDQ-TYAPIELVVVDDCSPDPIEPIVADAETdSLHRVHVVRHEVNRGANAARNTGIE 86 
                                       8**********************.*************************99************************** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCC..HCCCCCCS CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfker..krslkgnl 151
                                       a++g++++flD+Dd++ p ++ek v+a+e+  +   +g ++  + +      ++    n+r++++++   ++l++++
  gi|313122386|ref|YP_004038273.1|  87 ASRGEFVAFLDDDDYWRPRKVEKQVRAFENASD--EVGFVYTGQENVADDGTTT----NYRVPETRGwvTHELFRGA 157
                                       ******************************666..8888888888888888775....4666666662257889999 PP

                                       TTCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 152 sfeigsaallrrealeel 169
                                       + + +s  ++rr++++e+
  gi|313122386|ref|YP_004038273.1| 158 PLCPFSSVMVRRSVIDEV 175
                                       **************9997 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.5   6.6e-24     2e-20       4     199 ..      10     200 ..       8     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 6.6e-24
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v+Vp+++++++l + +es+  q+y ++e+vvv+d s +   + +  ++ ++ + rv+vv+ + n   +g+  a n
  gi|313122386|ref|YP_004038273.1|  10 VSVVVPAYGRPEYLDAAVESVNDQTYAPIELVVVDDCSPDPIEPIVADAETDSLH-RVHVVRHEVN---RGANAARN 82 
                                       79*****************************************998886777767.9**9966554...57778889 PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff..ltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarral 155
                                        +++a ++++v+++DdD+ + P+ +++++++f  ++++vg+v+t +++  ++ +++ +   e+  +     ++++ +
  gi|313122386|ref|YP_004038273.1|  83 TGIEASRGEFVAFLDDDDYWRPRKVEKQVRAFenASDEVGFVYTGQENVADDGTTTNYRVPETRGW-----VTHELF 154
                                       ********************************98899******88877766655553333254455.....457888 PP

                   Glyco_tranf_2_3 156 gvltlnG.sgslirrevlkelegldplflltdDyelglrlrr.agf 199
                                       + ++l + s +++rr+v +e ++ld +f  + D e  lr+ +   f
  gi|313122386|ref|YP_004038273.1| 155 RGAPLCPfSSVMVRRSVIDEVGLLDTRFPSWQDREWYLRVSEvCAF 200
                                       888888889************************9998888765555 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.2e-13   6.6e-10      14     205 ..      22     200 ..      11     226 .. 0.70

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.2e-13
                   Glyco_tranf_2_2  14 yieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDa 90 
                                       y+   v   + +    iel+vvdd S++++   v       l+       +   +  aarN G++ + +++v FlD 
  gi|313122386|ref|YP_004038273.1|  22 YLDAAVESVNDQTYAPIELVVVDDCSPDPIEPIVADAETDSLHRVHVVRHEVNRGANAARNTGIEASRGEFVAFLDD 98 
                                       45555533333333689************7777766554444433223334678999******************** PP

                   Glyco_tranf_2_2  91 DcfissDkfekilklitikklrenida.avvlpvvdlnkedsevlkdvedltassrvledllaakstlvkffapsss 166
                                       D+++ + k+ek+++     ++++  d    v++  + n +d     ++    +++ v ++l+   ++    + p  s
  gi|313122386|ref|YP_004038273.1|  99 DDYWRPRKVEKQVR-----AFENASDEvGFVYTG-QENVADDGTTTNYRVPETRGWVTHELFR-GAP----LCPF-S 163
                                       ************99.....444443330344443.3455666666777777788888888887.344....4444.4 PP

                   Glyco_tranf_2_2 167 silinrraflevGGyDErfrGhgaEDfdlllRlakaiks 205
                                       s++++r  + evG  D rf  ++  D + +lR+   + +
  gi|313122386|ref|YP_004038273.1| 164 SVMVRRSVIDEVGLLDTRF--PSWQDREWYLRVSEVCAF 200
                                       5778999999999999999..999999999999888866 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   5.2e-05      0.16       3      41 ..     260     295 ..     258     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllg 41 
                                       la+aal +g+y+dA++ l + +++d   P  ae+  +l+
  gi|313122386|ref|YP_004038273.1| 260 LAHAALVNGQYRDAVRFLLRSIRYD---PSQAESFPALA 295
                                       8************************...76666655555 PP

>> UPF0167  Uncharacterised protein family (UPF0167)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.7e-05      0.14      77     149 ..     168     242 ..     154     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                           UPF0167  77 deelleellkrtpgyiswqqeqWlahCddacaflgevgaeelealkiklekeelaaikddle.s.kieellelle 149
                                        +++++e+      + swq+ +W+    ++caf   ++   +++++ + + ++ +++k+d++ +  +e+++ l +
  gi|313122386|ref|YP_004038273.1| 168 RRSVIDEVGLLDTRFPSWQDREWYLRVSEVCAFETVTEPLAVRRVDSHGQISDNYEQKRDVSyPlFLEKHRPLAR 242
                                       5677777776666789*****************999999999999999999999999999984466676665555 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.1e-05      0.24       7      33 ..     260     286 ..     257     287 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.1e-05
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPn 33 
                                       l+ a++ +g+y +A++++ +++++dP 
  gi|313122386|ref|YP_004038273.1| 260 LAHAALVNGQYRDAVRFLLRSIRYDPS 286
                                       8999*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2268.82
//
Query:       gi|313122387|ref|YP_004038274.1|  [L=504]
Description: membrane protein involved in the export of O-antigen and teichoic acid [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-75  252.7   5.9    4.2e-75  252.7   5.9    1.7  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
      1e-35  123.5  10.0      1e-35  123.5  10.0    2.2  2  Polysacc_synt    Polysaccharide biosynthesis protein
    5.7e-16   58.9  14.0    5.7e-16   58.9  14.0    3.0  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
      0.061   13.4   0.5      0.061   13.4   0.5    3.4  4  DUF2613          Protein of unknown function (DUF2613)
      0.075   12.7   9.1       0.13   12.0   0.1    4.1  4  Kinocilin        Kinocilin protein


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.7   5.9   1.2e-78   4.2e-75       1     292 [.      45     340 ..      45     341 .. 0.98
   2 ?   -1.9   0.4      0.43   1.6e+03      63      75 ..     444     456 ..     387     493 .. 0.60

  Alignments for each domain:
  == domain 1  score: 252.7 bits;  conditional E-value: 1.2e-78
                   Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssaliqke.dlteedlstvftfnlvlgllialvlfllapliasfy 76 
                                       vLARL+ p   G+v++al+ +s ++ f+++Gl+ al+q e ++ +e+l+tv+ ++++ g++i+ +l+l+ap+ia+++
  gi|313122387|ref|YP_004038274.1|  45 VLARLIGPTQIGLVGVALLALSGIKKFTNVGLDAALVQDEnEDVDEHLNTVWILEIARGAIISGLLVLAAPFIAQIL 121
                                       8***************************************889999******************************* PP

                   Polysacc_synt_3  77 nqpel...vtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllss 150
                                       ++ ++    t+++v+al+++l g+ +    +++++l+F k f++++ + vv+vivai+ Al+  ++ +Lv g ++++
  gi|313122387|ref|YP_004038274.1| 122 GDGNIqstTTLIQVIALSPLLLGFKNPGMVYFQKNLDFHKRFVYRVSGDVVQVIVAIAWALVSPTAMSLVAGYVAAD 198
                                       876541117899***************************************************************** PP

                   Polysacc_synt_3 151 llslvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvae 227
                                       +l+lvl++l +++rp+l+fs++s++el+++g+++++s++l +l+++ d+ ++G ++++a L++Y+ a+r++++p +e
  gi|313122387|ref|YP_004038274.1| 199 FLRLVLSYLLHDFRPNLSFSRESANELINYGKWITGSSILYFLYSEGDDAFVGAFIGAAPLAFYQYAYRFSNAPATE 275
                                       ***************************************************************************** PP

                   Polysacc_synt_3 228 itsviakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWleav 292
                                       +tsvi++V+fPa+S+lqdd ++lr++++k+lr+ a+i+ P+a+g+avva  +v v lG++W  +v
  gi|313122387|ref|YP_004038274.1| 276 LTSVISSVMFPAFSKLQDDTEQLRNTFKKTLRVNAFISAPVAFGIAVVAPDFVMVALGEEWMTMV 340
                                       *************************************************************9997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.43
                   Polysacc_synt_3  63 lvlfllapliasf 75 
                                       ++++ + ++i s+
  gi|313122387|ref|YP_004038274.1| 444 AIMAGVVWYINSI 456
                                       2222222333322 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5  10.0   2.8e-39     1e-35       1     274 []      21     292 ..      21     292 .. 0.96
   2 ?   -0.9   8.5      0.23   8.4e+02     101     239 ..     331     466 ..     295     484 .. 0.61

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 2.8e-39
                     Polysacc_synt   1 llkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvsli 77 
                                       ++k +i+ +  + + + l++  lv+lar++gp++ Glv +al  ++ +  +t+ Gl+aalv+  ++  ++ +l +++
  gi|313122387|ref|YP_004038274.1|  21 VVKSAIWAMGQNAFGRVLQLAMLVVLARLIGPTQIGLVGVALLALSGIKKFTNVGLDAALVQDENEDVDE-HLNTVW 96 
                                       57999***************************************************************95.****** PP

                     Polysacc_synt  78 llnvllvllvlvllfllllliaaflgl...pelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqls 151
                                       +l++  + +++ ll+l++++ia++lg+   +  ++l++++al+ lll + +   + +++ l + k ++ +++  ++ 
  gi|313122387|ref|YP_004038274.1|  97 ILEIARGAIISGLLVLAAPFIAQILGDgniQSTTTLIQVIALSPLLLGFKNPGMVYFQKNLDFHKRFVYRVSGDVVQ 173
                                       ***********************886522277899****************************************** PP

                     Polysacc_synt 152 rvilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyid 228
                                       ++++++ a+  +   +++v+g+v+a ++++++s+++    frp+ +++ ++   el+ ++ ++t+ss++  ly   d
  gi|313122387|ref|YP_004038274.1| 174 VIVAIAWALVSPT-AMSLVAGYVAADFLRLVLSYLLHD--FRPNLSFS-RESANELINYGKWITGSSILYFLYSEGD 246
                                       **99999999999.9**************999999999..********.**************************** PP

                     Polysacc_synt 229 sillglllgaeavGiYnaayqllvaisgllapivtaalfPvfselq 274
                                         + g+++ga  +++Y+ ay++++a+   l++ +++++fP+fs+lq
  gi|313122387|ref|YP_004038274.1| 247 DAFVGAFIGAAPLAFYQYAYRFSNAPATELTSVISSVMFPAFSKLQ 292
                                       *******************************************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.23
                     Polysacc_synt 101 flglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavla 176
                                        lg++  ++++++ +l+++ +l +  ++++ + ++l r   ++   +++++ ++ ++  ++ +++    ++++   a
  gi|313122387|ref|YP_004038274.1| 331 ALGEEWMTMVLPMQILAIYgFLRALGQTFGPIWKALGRPDLLTKLGTLRVILIALTIYPVTVTWG----YGIAG-TA 402
                                       45555555555444555554555555566666666666666555555555555555555555555....44444.45 PP

                     Polysacc_synt 177 alvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsi.llglllgae 239
                                       a+v++i+ + ++ +  + + + l+ + +      ++p+ +s ++  + +yi+si  l ++++ +
  gi|313122387|ref|YP_004038274.1| 403 AVVTAIYVFPMMPIDIYLTAKMLEIHPFETVREIGFPVLASAIMAGVVWYINSIvQLPAIAELV 466
                                       5555566666666665544555558999999999*******************95566665554 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.4      0.83     3e+03     125     125 ..      98      98 ..      33     147 .. 0.58
   2 ?   -0.7   0.8      0.38   1.4e+03      53      80 ..     180     208 ..     132     238 .. 0.62
   3 !   58.9  14.0   1.6e-19   5.7e-16       2     141 ..     343     483 ..     342     485 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.83
                   Polysacc_synt_C 125 l 125
                                       l
  gi|313122387|ref|YP_004038274.1|  98 L 98 
                                       1 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.38
                   Polysacc_synt_C  53 fgivG.aaiatvlallvvavlnlyalrrl 80 
                                       + +v   a++ v++++++ +l l++ + l
  gi|313122387|ref|YP_004038274.1| 180 WALVSpTAMSLVAGYVAADFLRLVLSYLL 208
                                       22222245555555555555555544444 PP

  == domain 3  score: 58.9 bits;  conditional E-value: 1.6e-19
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf..givG.aaiatvlallvvavlnly 75 
                                       ++ila++ ++ +l ++++ i  +lgr+++++k   + +++  +  ++ +  +  gi G aa+ t++  + ++ + +y
  gi|313122387|ref|YP_004038274.1| 343 MQILAIYGFLRALGQTFGPIWKALGRPDLLTKLGTLRVILIALTIYPVTVTWgyGIAGtAAVVTAIYVFPMMPIDIY 419
                                       8************************************************6663379********************* PP

                   Polysacc_synt_C  76 alrrllgikl.ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllll 141
                                       +  + l i++ e +r +  p+la+++m++vv+++++++      a  +l+++++vga+ Y+ ++ ll
  gi|313122387|ref|YP_004038274.1| 420 LTAKMLEIHPfETVREIGFPVLASAIMAGVVWYINSIVQLPAI-A--ELVIGIVVGAATYFMVVALL 483
                                       ***********88*****************9988888765443.3..9*************999876 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.22     8e+02       4      17 ..     184     197 ..     182     228 .. 0.80
   2 ?   -3.9   0.2       4.5   1.6e+04      10      19 ..     248     257 ..     248     259 .. 0.76
   3 ?   -4.3   0.5         5   1.8e+04      17      23 ..     400     406 ..     398     409 .. 0.59
   4 ?   13.4   0.5   1.7e-05     0.061       4      30 ..     459     485 ..     457     488 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.22
                           DUF2613   4 gPaaaSaVaGivlG 17 
                                        P a S VaG v +
  gi|313122387|ref|YP_004038274.1| 184 SPTAMSLVAGYVAA 197
                                       599*******9876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.5
                           DUF2613  10 aVaGivlGvv 19 
                                       a++G+ +G++
  gi|313122387|ref|YP_004038274.1| 248 AFVGAFIGAA 257
                                       5788888876 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 5
                           DUF2613  17 Gvvavfg 23 
                                       G++av++
  gi|313122387|ref|YP_004038274.1| 400 GTAAVVT 406
                                       6666664 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 1.7e-05
                           DUF2613   4 gPaaaSaVaGivlGvvavfgvtavvqq 30 
                                       +Pa+a  V+Giv+G+++ f v+a +++
  gi|313122387|ref|YP_004038274.1| 459 LPAIAELVIGIVVGAATYFMVVALLER 485
                                       69*******************998765 PP

>> Kinocilin  Kinocilin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.11   3.8e+02      45      65 ..     102     122 ..      95     136 .. 0.77
   2 ?   12.0   0.1   3.5e-05      0.13      23      63 ..     232     272 ..     228     293 .. 0.86
   3 ?   -1.7   0.2       0.6   2.1e+03      12      45 ..     377     410 ..     373     425 .. 0.75
   4 ?    2.5   0.2     0.031   1.1e+02      18      53 ..     441     479 ..     426     490 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
                         Kinocilin  45 igaaglgllllaypflkarfn 65 
                                        ga   gll+la pf+   + 
  gi|313122387|ref|YP_004038274.1| 102 RGAIISGLLVLAAPFIAQILG 122
                                       588889*********987665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.5e-05
                         Kinocilin  23 lagsiiigvsvskaaaavggifigaaglgllllaypflkar 63 
                                       ++gs i+    s+   a  g figaa l ++ +ay f +a 
  gi|313122387|ref|YP_004038274.1| 232 ITGSSILYFLYSEGDDAFVGAFIGAAPLAFYQYAYRFSNAP 272
                                       68999999999**************************9874 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.6
                         Kinocilin  12 clqlacvalsllagsiiigvsvskaaaavggifi 45 
                                        l++  +al++   ++  g  ++ +aa v  i++
  gi|313122387|ref|YP_004038274.1| 377 TLRVILIALTIYPVTVTWGYGIAGTAAVVTAIYV 410
                                       5666677777777777788888888888887775 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.031
                         Kinocilin  18 valsllagsiiig...vsvskaaaavggifigaaglgll 53 
                                        a +++ag +  +   v +   a  v gi +gaa+  ++
  gi|313122387|ref|YP_004038274.1| 441 LASAIMAGVVWYInsiVQLPAIAELVIGIVVGAATYFMV 479
                                       455667777655500044555677799******987554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3845.89
//
Query:       gi|313122388|ref|YP_004038275.1|  [L=464]
Description: arylsulfatase A family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-34  119.0   0.6    3.4e-34  118.6   0.6    1.2  1  Sulfatase      Sulfatase
    0.00038   20.1   0.1       0.12   11.9   0.0    2.4  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
  ------ inclusion threshold ------
      0.077   12.4   0.7       0.13   11.6   0.7    1.3  1  Metalloenzyme  Metalloenzyme superfamily


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.6   5.7e-38   3.4e-34       2     308 ..       4     334 ..       3     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 5.7e-38
                                       EEEEEEESSE-TTGSGGGTTTSCSSHHHHHHH..HTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTH CS
                         Sulfatase   2 nvvliladdlgagdlglyggktattpnldrla..eeglrftnfysaaplcspsraalltgryphnsgvasntevggg 76 
                                       ++v+i++++++ ++ +l g+ + ttp+l++la    g +f+  +s    +  s a++ltg+ + +++ ++++    +
  gi|313122388|ref|YP_004038275.1|   4 DIVWITLESVRQDHTSLDGYRRDTTPFLQSLAdrSDGATFKHCFSHDVWTRASSASILTGLASSSHRTWTQE----N 76 
                                       79******************************999********************************99888....9 PP

                                       HCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC..CTTTSE..EEETSSSCHHTCCCCCCCCCECTCCC... CS
                         Sulfatase  77 glpqteatLpellkeaGYntaaigkwhlgwssrqsvyk..nrgfdr..flgfptgsaalkdpekseyngevlrv... 146
                                        l  +++t+pe l++  Y+ta++ +         s ++  +rgfd+  +lg  t+ +        +y +    +   
  gi|313122388|ref|YP_004038275.1|  77 RLSSDVPTIPEALQRTDYRTACVSPNPQL-----SEVTglARGFDHfhYLGKDTLLDEAGVLTVLGYLT----Klnq 144
                                       ********************998755544.....43334699***933344333333333333333333....2445 PP

                                       ..........TTTTCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH..... CS
                         Sulfatase 147 ..........ppeggysddrlldealefllarndkpfflylatlapHappeapdeyakkyatffddgseaar..... 208
                                                 + + gy +d+++ + ++  +a++d++ fly+++  +H+p++ p++y++ +a++f++   +       
  gi|313122388|ref|YP_004038275.1| 145 hsagyttdtaKHSVGYVSDAIARRHIRE-AAQADEDLFLYVHLGDSHHPYYPPKPYQDLFADGFEMSVGESLdlvle 220
                                       6999999999999999999999999999.8999****************************9998765554478888 PP

                                       .....................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCT CS
                         Sulfatase 209 .....................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggk 264
                                                             l + y+++++yvDd + ++++ +  ++ l++ +vv+tSDhg+  +e      +  
  gi|313122388|ref|YP_004038275.1| 221 mssnlhgyiargvpftndewnALQAMYDATIRYVDDTVRSIVECA--ENRLNDPIVVVTSDHGELFGE---QEMLAH 292
                                       88999999999999999***999999*******************..9****************9966...333333 PP

                                       TCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 265 ganayeggtrvPllvwwpgekaprvseelvshiDlfptildlag 308
                                        + a +   +vPl+v + +  ++   +++v h D + t+l  +g
  gi|313122388|ref|YP_004038275.1| 293 MVVADDAVSHVPLVVCGIEAVES--HNGVVQHADAMKTVLNEVG 334
                                       336899999******98887777..99***********997655 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0015       8.7      13      62 ..      19      70 ..       5      81 .. 0.78
   2 !   11.9   0.0     2e-05      0.12     197     233 ..     247     281 ..     149     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0015
                                      HHHHHG.STSHHHHHHHHHSEEESE.EE-SSS-SHHHHHHHHHHSS-HHHHS CS
                      Phosphodiest 13 lldrla.ellpnlaaLakegvsapn.lrpvfPtlTfpnhaslvTGlyPgeHG 62
                                       ld ++ +++p+l++La+++  a+  +  +    T ++ as++TGl  ++H 
  gi|313122388|ref|YP_004038275.1| 19 SLDGYRrDTTPFLQSLADRSDGATFkHCFSHDVWTRASSASILTGLASSSHR 70
                                      56666767**********6666665477777888999**********99996 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 197 vedalrrvDkaigdLlealderglsaetniilvSDHG 233
                                         +++r+vD+++  ++e ++ r   ++  ++++SDHG
  gi|313122388|ref|YP_004038275.1| 247 YDATIRYVDDTVRSIVECAENR--LNDPIVVVTSDHG 281
                                       56899***************99..56666*******9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   2.1e-05      0.13     156     218 ..     249     314 ..     242     337 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHHHTTS-T..TTEEEEEE-SSB-...-TTTSS........-----EEEEEESTT--- CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 156 aaieaaDeavkeildaieq..vdgilvvtADHgn...aedmvkrdkqplTsHtlepVPilivgkglap 218
                                       a i ++D  v  i++  e+  +d i+vvt+DHg     ++m    +  + +  + +VP+++ g +  +
  gi|313122388|ref|YP_004038275.1| 249 ATIRYVDDTVRSIVECAENrlNDPIVVVTSDHGElfgEQEMLA--HMVVADDAVSHVPLVVCGIEAVE 314
                                       67999*********9887633799*********6332455555..68899999999999999877443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3428.13
//
Query:       gi|313122389|ref|YP_004038276.1|  [L=213]
Description: haloacid dehalogenase superfamily enzyme, subfamily IA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-19   69.3   0.0    6.4e-19   68.7   0.0    1.3  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.9e-09   38.1   2.0    7.4e-08   32.9   0.6    2.6  2  Hydrolase       haloacid dehalogenase-like hydrolase
    1.6e-08   35.2   0.2    2.5e-08   34.6   0.2    1.2  1  HAD             haloacid dehalogenase-like hydrolase
    2.8e-08   33.7   0.1    6.8e-08   32.5   0.1    1.7  1  Hydrolase_like  HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0   1.4e-22   6.4e-19       3     177 ..       7     185 ..       5     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.4e-22
                             HAD_2   3 FDlDgTlldteeliiqafnelleey.......glselseeelrkliglslrellrklgeseeeeekieellrkynee 72 
                                       FDlDgTlld e+   + f++++  +        +++     l+++   +++ +++ + +++  + + e l  ++++ 
  gi|313122389|ref|YP_004038276.1|   7 FDLDGTLLDYETPFDTWFERTVPVEataaiteTFGSNLTASLDSFEPDPYERAFEVVCNEYGIDADPEALATTFVDT 83 
                                       ************99999999997775555555555555566666666666666666666666666************ PP

                             HAD_2  73 kkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklk 149
                                       +    +++ + v+ l+ ++ +++++ gi T++++ ++++k+e +g++++ d iv+se+v+ +KPd+ ++e+a e+l 
  gi|313122389|ref|YP_004038276.1|  84 EVA-ATRVAPSVRRLVASV-AERHQSGILTNGNETVQRRKVETHGLDELVDEIVVSEEVGARKPDAGIFETAKERLP 158
                                       ***.***************.99*************************************************999875 PP

                             HAD_2 150 lkkeeviyvGDsp.tDieaakkagikvia 177
                                         ++  ++vGDs  tDi  a++ g +++ 
  gi|313122389|ref|YP_004038276.1| 159 --ADAFVFVGDSYeTDIVPAQEHGFETVY 185
                                       ..6789******************99986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.6   1.6e-11   7.4e-08       2     208 ..       3     178 ..       2     180 .. 0.81
   2 ?   -0.9   0.0      0.37   1.6e+03     190     208 ..     180     199 ..     176     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.6e-11
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHH.HHHHHHHHHHH.HHHHHETTTEHHHHTHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkal.vaaakarsgal.tgfatfigrgayaigkpew 76 
                                       +tv fD+dGTL++ e    + +++                    + v+a  a+++   ++ ++      +   +p+ 
  gi|313122389|ref|YP_004038276.1|   3 TTVYFDLDGTLLDYETPFDTWFERT-------------------VpVEATAAITETFgSNLTA-----SLDSFEPDP 55 
                                       6999***********8888888888...................3367777775555566666.....666666666 PP

                                       HHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  77 ltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraan 153
                                        ++      ++    ++  ++  +al       + ++a + +v p ++ +vas  ++    ++lt++n++ ++r  +
  gi|313122389|ref|YP_004038276.1|  56 YERA-----FEVVCNEYGIDADPEALA--TTFVDTEVAAT-RVAPSVRRLVASVAERHQ-SGILTNGNETVQRRKVE 123
                                       6666.....566666678888888888..66667777755.6***********998855.9**************** PP

                                       HTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHH CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                         Hydrolase 154 qlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.Daaalaa 208
                                         G d+ +d ++ s++++  kp+  +++ a ++L ++    ++VGD+   D+  +++
  gi|313122389|ref|YP_004038276.1| 124 THGlDELVDEIVVSEEVGARKPDAGIFETAKERLPADA--FVFVGDSYEtDIVPAQE 178
                                       ***88888**************************8888..********999876665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.37
                                       GGGEEEEESSHH.HHHHHHH CS
                                       xxxxxxxxxxxx.xxxxxxx RF
                         Hydrolase 190 peevamVGDgvn.Daaalaa 208
                                       + e++ VGD    Da  +aa
  gi|313122389|ref|YP_004038276.1| 180 GFETVYVGDDHRpDATVAAA 199
                                       45678888888777777765 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.2   5.5e-12   2.5e-08       2     181 ..       6     169 ..       5     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5.5e-12
                               HAD   2 lfDfDgTLldgdsle.lllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                        fD+DgTLld ++ +  +++   r+ + ++ +a+ e++   l ++l +++ + +++++e     +  +++ + l+  
  gi|313122389|ref|YP_004038276.1|   6 YFDLDGTLLDYETPFdTWFE---RTVPVEATAAITETFGSNLTASLDSFEPDPYERAFEVVCNEYGiDADPEALATT 79 
                                       6**********777736666...5555677999*****************************999887666666666 PP

                               HAD  77 v..aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrg 151
                                       +   ev++++   p +++l+a + a+ ++  ++++g++ + +++ + +g de++++       +  e  +  kp +g
  gi|313122389|ref|YP_004038276.1|  80 FvdTEVAATR-VAPSVRRLVASV-AERHQSGILTNGNETVQRRKVETHGLDELVDE------IVVSEEVGARKPDAG 148
                                       6576666666.66********66.7779*********************9999999......888888888899988 PP

                               HAD 152 egkvaalrewlaaegegidleevvayGDsp 181
                                             + e  a+e  ++d    v++GDs+
  gi|313122389|ref|YP_004038276.1| 149 ------IFE-TAKERLPADA--FVFVGDSY 169
                                       ......333.1234444444..68889997 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1   1.5e-11   6.8e-08       3      55 ..     143     193 ..     141     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.5e-11
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-T CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrp 55 
                                       +KP +++++ a e+l  + ++ +++GD+++tDi  A+++G ++v V      +
  gi|313122389|ref|YP_004038276.1| 143 RKPDAGIFETAKERL--PADAFVFVGDSYETDIVPAQEHGFETVYVGDDHRPD 193
                                       8*************7..7789************************98766444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1623.51
//
Query:       gi|313122390|ref|YP_004038277.1|  [L=347]
Description: glycosyl transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-23   83.8   0.0    2.6e-23   82.7   0.0    1.5  2  Glycos_transf_2  Glycosyl transferase family 2
    8.4e-08   32.4   0.2    1.8e-07   31.3   0.2    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.076   13.5   0.0       0.15   12.6   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.0   4.3e-27   2.6e-23       2     168 ..       9     190 ..       8     191 .. 0.97
   2 ?   -3.2   0.0       1.1   6.3e+03      99     149 ..     205     265 ..     198     282 .. 0.50

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 4.3e-27
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.................C-TTEEEEEE CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.................edprvrvirr 61 
                                       vv+p+yNee  + +t+es+ +      ++++ vDDgStD+t++ ++e a+                 e+p+v  ir+
  gi|313122390|ref|YP_004038277.1|   9 VVVPAYNEERFVGRTIESVPSY----VDRVYAVDDGSTDDTWQEIRETARrlnddraepvapdgghhEGPHVVPIRH 81 
                                       9********************9....*************************************************** PP

                                       SSS-HHHHHHHHHHHH--SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEE CS
                   Glycos_transf_2  62 eenvGkagalnaglraatgd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgen 135
                                       e n G ++++ +g  +a  d   ++++++ D ++dp  l+ +++++ +++ad + g r  ++ + +e++  +  + n
  gi|313122390|ref|YP_004038277.1|  82 ETNSGVGAGIKTGYYRAMADemdVVAVMNGDAQMDPAVLPHFLDPIVEGRADYAKGDRISRRENVGEMSSWRL-FGN 157
                                       ********************************************************************97655.699 PP

                                       ECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHH CS
                   Glycos_transf_2 136 erlyfkerkrslkgnlsfeigsaallrrealee 168
                                         l + ++  s ++++ +   +++++++e+le+
  gi|313122390|ref|YP_004038277.1| 158 KLLTRLTNLSSGYWKTIDSQNGYTAISVEVLER 190
                                       99999*************************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                                       HHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS..........EEEECCHCCCCHCCCCC CS
                   Glycos_transf_2  99 klvealekdgadvvlgqrprifgetdeiernkrv..........generlyfkerkrslkg 149
                                       +++  l+ ++a vv + + +  g++      +++          ++  rl ++  +rs+++
  gi|313122390|ref|YP_004038277.1| 205 DMLTTLNLHDARVVNVPHQAVYGDEESGIVYRTFvpslsgllfqNFLRRLGHRASDRSYQP 265
                                       5555555555555544444444333333333333355555555555555555555555555 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.2     3e-11   1.8e-07       3     112 ..       6     127 ..       4     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3e-11
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvna..rnlgstgksr 77 
                                       ++av+Vp++nee+ +g+++es+ ++    ++v+ v+d+s+++t ++++e+a++l d r   v ++  +  g+ +   
  gi|313122390|ref|YP_004038277.1|   6 RVAVVVPAYNEERFVGRTIESVPSY---VDRVYAVDDGSTDDTWQEIRETARRLNDDRAEPVAPDggHHEGPHV--V 77 
                                       59*********************96...999************************9999988774333234433..3 PP

                   Glyco_tranf_2_3  78 alnealra..........vk.....sdlvllvDdDtvvePdtlkrllqff 112
                                        + ++ +           ++      d+v+++++D+  +P +l+ +l  +
  gi|313122390|ref|YP_004038277.1|  78 PIRHETNSgvgagiktgyYRamadeMDVVAVMNGDAQMDPAVLPHFLDPI 127
                                       333444434444644444114456788***************99988777 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.5e-05      0.15       1      40 [.      14      52 ..      14      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkel 40
                                      +ne+ + +++++   ++ +dr++ +d++stD+t++ ++e 
  gi|313122390|ref|YP_004038277.1| 14 YNEERFVGRTIESVPSY-VDRVYAVDDGSTDDTWQEIRET 52
                                      69999999999999999.***************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2321.80
//
Query:       gi|313122391|ref|YP_004038278.1|  [L=291]
Description: TIM-barrel fold metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-51  173.5   1.1    1.2e-50  172.9   1.1    1.3  1  Amidohydro_2  Amidohydrolase
     0.0006   19.3   0.0     0.0052   16.2   0.0    2.1  1  TatD_DNase    TatD related DNase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.9   1.1   1.4e-54   1.2e-50       1     291 []      13     290 ..      13     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 172.9 bits;  conditional E-value: 1.4e-54
                                       EEEEEEE..SHHHCCCCCCGGCTSCCCHHHHHCHHTSS....ECCCEHCHHHHHHHHTSHHCH......HHHHHHHH CS
                      Amidohydro_2   1 iDvHaHllppeaairddgepngfdpeerlafmkragvd....pqlaspeallvlnaaagiara......vivaalcr 67 
                                       iD+HaH            +  +f  + + ++m++a  +     +  + ea++++++ +gi++a      + +     
  gi|313122391|ref|YP_004038278.1|  13 IDTHAH-----------QPTAEFLEDAGGEMMQDAARKfgteTETWDYEAMREEYHEQGISKAillgwdAETNTGNP 78 
                                       899999...........333334444444444433333111133444566666666666666644443322222222 PP

                                       HHHHHHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-E CS
                      Amidohydro_2  68 gannrvlaeaakrpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglp 144
                                          n+++ae+++ +++f+ g+ +v++  +d+++e++r+ve+l + G++++   +g d++++++  ++f  +e+lg+p
  gi|313122391|ref|YP_004038278.1|  79 PVPNDYVAEICDDYPDFFVGFGSVDPLKDDCVEEAIRCVEDLDLSGFKFQQIAQGFDPSDEAHA-ELFDTIEDLGVP 154
                                       344667777777777777777888889999**********************************.************ PP

                                       EEEE......CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHH CS
                      Amidohydro_2 145 vdihtGps..pewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglyte 219
                                       v +h G s  +++++gg++ ++ + +p+l+++va+++P  +i +aH ++p  + r+ l+++ +  nvy++lsg    
  gi|313122391|ref|YP_004038278.1| 155 VVFHGGNStlGAGSPGGRGLRIKYGNPMLIDDVAAEHPQMPILIAHPAFP--WEREQLAICQQKGNVYMDLSG---- 225
                                       ****5555******************************************..*********************.... PP

                                       SSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHHCTB CS
                      Amidohydro_2 220 llyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNAarlygl 291
                                           + p+++ + +++  ++v +d+++fG+DyP++ +e++ e ++++++    s+e ++kil++NA++++gl
  gi|313122391|ref|YP_004038278.1| 226 ----WLPKYIDEQVVHYAKTVLQDKVMFGTDYPMIRPEQWFESFDEVFD---ASEEIQRKILWENAEEFLGL 290
                                       ....7899*************************************9988...4*****************97 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.8e-07    0.0052     134     212 ..     140     259 ..      13     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.8e-07
                                       -HHHHHHHHHHCGGCCSEEEETT...........................................--S-HHHHHHH CS
                        TatD_DNase 134 aeedlleilkeaaeakakvvlHs...........................................fsgsaeeakkf 167
                                       a+++l + +++++   + vv+H                                            f  + e+++ +
  gi|313122391|ref|YP_004038278.1| 140 AHAELFDTIEDLG---VPVVFHGgnstlgagspggrglrikygnpmliddvaaehpqmpiliahpaFPWEREQLAIC 213
                                       4555555555542...3466666666666666666666666666666666666666666666666677777777777 PP

                                       H.HTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEEC CS
                        TatD_DNase 168 l.klgyyislsglltfknakelrelvkavpldrlLiETDaPyltpk 212
                                         k+++y+ lsg+l++  ++++   +k+v  d+++ +TD+P ++p+
  gi|313122391|ref|YP_004038278.1| 214 QqKGNVYMDLSGWLPKYIDEQVVHYAKTVLQDKVMFGTDYPMIRPE 259
                                       7688************99*************************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1692.67
//
Query:       gi|313122392|ref|YP_004038279.1|  [L=254]
Description: enoyl-CoA hydratase/carnithine racemase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-59  200.0   0.3    4.3e-59  199.8   0.3    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    4.6e-30  105.3   0.2    6.3e-30  104.8   0.2    1.2  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.8   0.3   4.8e-63   4.3e-59       3     248 ..       6     253 ..       4     254 .] 0.97

  Alignments for each domain:
  == domain 1  score: 199.8 bits;  conditional E-value: 4.8e-63
                                       ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC...HHHHHHHCC CS
                             ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek...akqallkee 76 
                                        +gv  i+++rP+++Na++ae+  El++al +l  + +  a+vLtG + aF+aG+d+++mae+ +   + ++ ++ +
  gi|313122392|ref|YP_004038279.1|   6 DDGVRRITFDRPQVKNAFTAEVARELADALDELTAE-THDAAVLTGEGDAFSAGGDIQAMAERDEtarEAYQRVRDT 81 
                                       67999******************************9.9************************988766778888999 PP

                                       HHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHH CS
                             ECH_1  77 vlelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeil 153
                                       +    + ++t p+pvia vnG a+g+Gl ++ acD+++aa++a+f+++++++Gl+p+aggt +l+  vG ++A+e++
  gi|313122392|ref|YP_004038279.1|  82 LGRVAESVLTAPVPVIARVNGDAAGAGLSVVAACDFAYAAEDARFAASFVNVGLVPDAGGTVTLPHLVGLRAAKELA 158
                                       999999*********************************************************************** PP

                                       HHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                             ECH_1 154 llgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfsk 230
                                        +g+ isa+ a++  lv+ vvp+++l  +  e+++kl++++ ++++ +kea++a+l +    +le ea+ ++   ++
  gi|313122392|ref|YP_004038279.1| 159 FTGDLISAERANELDLVNDVVPADELDATVAEMVAKLVSQPTESIALAKEAIHANLGRSWHDGLEREAQAQTMAYDT 235
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHTCSH--- CS
                             ECH_1 231 ddikeGlqaflEkrkpef 248
                                       d  keG+ afl  r pef
  gi|313122392|ref|YP_004038279.1| 236 DAHKEGVSAFLDGRSPEF 253
                                       ***************999 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.2   7.1e-34   6.3e-30       1     203 [.       9     211 ..       9     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 7.1e-34
                                       .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHH CS
                             ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeY 77 
                                       v++it++rp+  Na + e++r+l++al+e  ++ + ++ vl+g+g  af+AGgD++a++e  ++ +++ +++  +  
  gi|313122392|ref|YP_004038279.1|   9 VRRITFDRPQVKNAFTAEVARELADALDELTAE-THDAAVLTGEG-DAFSAGGDIQAMAERDETAREAYQRVRDTLG 83 
                                       589**************************9665.56777889988.8*************99998877689999999 PP

                                       HHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH CS
                             ECH_2  78 klnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalT 153
                                       ++   + t p pv+a ++G + G G+++ + + f  + e+++fA   +++Gl+PD Gg+  L++l g + ++ la T
  gi|313122392|ref|YP_004038279.1|  84 RVAESVLTAPVPVIARVNGDAAGAGLSVVAACDFAYAAEDARFAASFVNVGLVPDAGGTVTLPHLVGlRAAKELAFT 160
                                       *****************************************************************9889******** PP

                                       ---B-HHHHHHTTS--EE--GGGHHHHHHHHHTT.........-------- CS
                             ECH_2 154 GarlkgadalaaglathyvpseklealeeaLaelessd.eeaveevleela 203
                                       G+ ++++ a +++l + +vp+++l+a  +++ +   s+ +e+++ + e+++
  gi|313122392|ref|YP_004038279.1| 161 GDLISAERANELDLVNDVVPADELDATVAEMVAKLVSQpTESIALAKEAIH 211
                                       ************************988777766544443444433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1432.24
//
Query:       gi|313122393|ref|YP_004038280.1|  [L=212]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-19   67.9   0.0    8.5e-19   67.1   0.0    1.4  1  HTH_10         HTH DNA binding domain
    1.4e-09   38.0   0.9    1.9e-09   37.6   0.3    1.5  1  BAT            GAF and HTH_10 associated domain
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.041   13.4   0.0    1.8  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.035   13.7   0.0       0.31   10.7   0.0    2.2  2  HTH_50         Helix-turn-helix domain
      0.058   13.2   0.5       0.24   11.2   0.1    2.2  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   2.4e-22   8.5e-19       1      52 [.     156     207 ..     156     208 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.4e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++q e +++A+emGYF+ PR+vt+ e+A+elGIsk++++e+Lr+a+  l+
  gi|313122393|ref|YP_004038280.1| 156 LTPAQEESIRVAVEMGYFELPRTVTAVEVADELGISKTAFLERLRRAQGSLF 207
                                       9***********************************************9987 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.3   5.2e-13   1.9e-09       7     132 ..       9     131 ..       3     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 5.2e-13
                               BAT   7 eleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllelt 83 
                                       e++i+ +d +l++++a++d++++ +    r dg vl  f+++    +e+ +++++ d v  + +vs++d+++ +++ 
  gi|313122393|ref|YP_004038280.1|   9 EFRIEGDDCPLATATANADAAIDARPPQLRADGNVLIQFSAQPS--DELSETLDADDRV-RYLHVSHTDGRSNYRCL 82 
                                       9*****************************************94..6************.88899999999****** PP

                               BAT  84 vsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeer 132
                                        + p+++  l++ G  v+s++ e+g+a+++  v     +R v+ea  ++
  gi|313122393|ref|YP_004038280.1|  83 SKHPCVVHELVNAGFLVESMRYENGGATMRGAVVGYDVLRGVMEAAGRT 131
                                       *****************************99998888888888887665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05     0.041      18      40 ..     179     201 ..     176     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                        +  e+A++lg+S+++ ++rl+r
  gi|313122393|ref|YP_004038280.1| 179 VTAVEVADELGISKTAFLERLRR 201
                                       6889******************9 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.16   5.7e+02      32      38 ..      67      73 ..      65      74 .. 0.87
   2 ?   10.7   0.0   8.6e-05      0.31      29      46 ..     184     201 ..     182     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.16
                            HTH_50 32 rLGvSht 38
                                       L+vSht
  gi|313122393|ref|YP_004038280.1| 67 YLHVSHT 73
                                      59****9 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.6e-05
                            HTH_50  29 lAkrLGvShtaianklrk 46 
                                       +A  LG+S+ta + +lr+
  gi|313122393|ref|YP_004038280.1| 184 VADELGISKTAFLERLRR 201
                                       899*************98 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.53   1.9e+03      23      34 ..     128     139 ..     125     140 .. 0.78
   2 ?   11.2   0.1   6.8e-05      0.24      20      40 ..     181     201 ..     178     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.53
                     HTH_AsnC-type  23 LAervGlSestv 34 
                                        ++ vG+S ++v
  gi|313122393|ref|YP_004038280.1| 128 AGRTVGVSLQRV 139
                                       5899***97776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.8e-05
                     HTH_AsnC-type  20 yaeLAervGlSestvlrRvrr 40 
                                         e+A+++G+S ++ l+R+rr
  gi|313122393|ref|YP_004038280.1| 181 AVEVADELGISKTAFLERLRR 201
                                       679*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1233.55
//
Query:       gi|313122394|ref|YP_004038281.1|  [L=318]
Description: hypothetical protein Hbor_36280 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-76  256.4   0.4    2.8e-76  256.1   0.4    1.1  1  PaaA_PaaC  Phenylacetic acid catabolic protein


Domain annotation for each model (and alignments):
>> PaaA_PaaC  Phenylacetic acid catabolic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.1   0.4   1.6e-80   2.8e-76       3     261 .]      20     297 ..       2     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 256.1 bits;  conditional E-value: 1.6e-80
                                       ...........HHHHHHHHHHHHHHHHHHHHHHTTTTTSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS.-HH CS
                         PaaA_PaaC   3 eakdwmpeeyrkalirlllqlAdselilaqresewigrAPsLeediallnivlDelGharllysaaeelegkgkded 79 
                                       ++kd+mpeeyrka++r++  +A+se+++a+ e  +i +APsLe+++a++++v+DelGh++lly+aae+l    k+++
  gi|313122394|ref|YP_004038281.1|  20 SPKDDMPEEYRKAATRMIQFHANSEIMGAYLERPFIRKAPSLERKLAFSAKVQDELGHGQLLYRAAESL--GIKTRE 94 
                                       689******************************************************************..4689** PP

                                       HHHHC--CCC----CGGGS---SHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         PaaA_PaaC  80 dlaflrdegefknsllvelpngdwadtivrqflvdaaaiilleaLkrssygplaaiaakvlkEesyHlrhgeewvlr 156
                                       +++++++eg+ k+++++++p ++w +t +++f+vd+aa+ ++++Lk+ss++p+a++++kv+ Ee +H++hge+++++
  gi|313122394|ref|YP_004038281.1|  95 EMLDELAEGKGKFLNCFHYPMESWIETPMIGFFVDGAAMRRQATLKSSSWEPYAHAMDKVCFEEGFHVKHGESILRE 171
                                       ***************************************************************************** PP

                                       HHTSSHHHHHHHHHHHHHHGGGGGGGG---HHH.....HHHHHTTSS--GGGGHHHHHHHHHHHHHHTT-----S-- CS
                         PaaA_PaaC 157 LgdGteeskrrvqeAlnrlwpyvlelfgpddae.....ealaekgkavdndeLrqkfeakvvpvleeagltlPdepa 228
                                       L +Gt+++++++qeA++ +wp + ++fgp+d++      a++ + k+ +ndeLr++f +++ p++e++gl+lP+ p+
  gi|313122394|ref|YP_004038281.1| 172 LSQGTKKQQEQLQEAFEMWWPRIIQFFGPTDDKsthhdFAAEVGLKQNTNDELRKAFLNMYLPKVEKYGLELPEYPR 248
                                       *********************************99999999999********************************* PP

                                       ----GGGT---TTHHHH................HHHHHHHHHHSTT--- CS
                         PaaA_PaaC 229 lkeggkqGehsehlgel................laelqalqrahpeaaW 261
                                       +++++++Ge++ + ++l                + ++++++r+++  aW
  gi|313122394|ref|YP_004038281.1| 249 IEYDEDTGEYTVNEDDLdwdeffqiakneyepgVGQIDSRKRTQEAVAW 297
                                       ************9999999999999999999999999999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2044.83
//
Query:       gi|313122395|ref|YP_004038282.1|  [L=104]
Description: uncharacterized enzyme of phenylacetate metabolism [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-21   75.0   0.1    5.2e-21   74.7   0.1    1.1  1  PaaB      Phenylacetic acid degradation B


Domain annotation for each model (and alignments):
>> PaaB  Phenylacetic acid degradation B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.1   2.9e-25   5.2e-21       4      83 ..       2      79 ..       1      85 [. 0.94

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 2.9e-25
                              PaaB  4 lfEVfkrdkeglshqhvgSvhAadaemALlvArdvfvRReeavslwvvkseailastpeekeslfapakektYrhqtyY 82
                                      ++EVf ++k+g  hqh+g vhA+d emALl+A+ ++ RR+++ slwvv++++i +++ e   + f  +++k+Yr +  +
  gi|313122395|ref|YP_004038282.1|  2 IWEVFRQEKKGDYHQHCGNVHAPDREMALLFAQVQHARRKPTNSLWVVPKDEIGEVDAEH--AKFGGTTDKSYRWAMTF 78
                                      6*******************************************************9998..569*********88766 PP

                              PaaB 83 g 83
                                      +
  gi|313122395|ref|YP_004038282.1| 79 N 79
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 713.09
//
Query:       gi|313122396|ref|YP_004038283.1|  [L=289]
Description: phenylacetate-CoA oxygenase, PaaI subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-57  193.2   0.7    6.1e-57  192.8   0.7    1.1  1  PaaA_PaaC     Phenylacetic acid catabolic protein
    0.00011   22.0   0.2    0.00024   20.9   0.2    1.6  1  MiaE_2        tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like
     0.0054   17.1   0.6      0.055   13.9   0.2    2.7  2  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.015   15.7   0.3       0.69   10.3   0.1    2.8  2  HEAT_2        HEAT repeats
      0.035   14.1   1.0      0.059   13.3   0.1    1.8  2  SAM_LFY       Floricaula / Leafy protein SAM domain
      0.091   13.0   0.6       0.46   10.8   0.3    2.3  3  PerC          PerC transcriptional activator


Domain annotation for each model (and alignments):
>> PaaA_PaaC  Phenylacetic acid catabolic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.8   0.7     2e-60   6.1e-57       9     254 ..      13     272 ..       7     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 192.8 bits;  conditional E-value: 2e-60
                                       .....HHHHHHHHHHHHHHHHHHHHHHTTTTTSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS.-HHHHHHC- CS
                         PaaA_PaaC   9 peeyrkalirlllqlAdselilaqresewigrAPsLeediallnivlDelGharllysaaeelegkgkdeddlaflr 85 
                                       ++++++a   ll ++Ad+e++la r  ew  rAP++e di ++ni++DelGharl+y ++e+    g +e dl+ +r
  gi|313122396|ref|YP_004038283.1|  13 TDKEQEAIELLLRRMADDEFVLAERYTEWQVRAPTIESDISIANIAQDELGHARLWYDLLEDF---GYTEPDLLWER 86 
                                       55566666666778*************************************************...9********** PP

                                       -CCC----CGGGS---..SHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                         PaaA_PaaC  86 degefknsllvelpng..dwadtivrqflvdaaaiilleaLkrssygplaaiaakvlkEesyHlrhgeewvlrLgdG 160
                                       d + f++s+lvelp +  dwad ivr++++d a++++++aL++ssy+++   ++kvl Ee yH++h+ +w++rL + 
  gi|313122396|ref|YP_004038283.1|  87 DPETFRHSTLVELPFEegDWADCIVRSYFYDEAEHLRMTALEKSSYPRIRDRVEKVLGEEGYHREHSMNWLRRLVS- 162
                                       ************996555*******************************************************886. PP

                                       SHHHHHHHHHHHHHHGGGGGGGG---HHH....HHHHHTTS.S--GGGGHHHHHHHHHHHHHHTT-----....... CS
                         PaaA_PaaC 161 teeskrrvqeAlnrlwpyvlelfgpddae....ealaekgk.avdndeLrqkfeakvvpvleeagltlPd....... 225
                                       ++e +rrvq+A +rl+py+l +f+p +++    +a+ e g+ + + +++r+++ ++v++++ e+g++l +       
  gi|313122396|ref|YP_004038283.1| 163 SDEGRRRVQAATDRLFPYALTFFEPAADApeaeAAIDELGVrTRTLADMREEWLETVTETMTEIGIDLRTpeiddeg 239
                                       6889*********************9998777677777665156789****************99776543377777 PP

                                       ...S------.GGGT---TTHHHHHHHHHHHHH CS
                         PaaA_PaaC 226 ...epalkeg.gkqGehsehlgellaelqalqr 254
                                          + al e  g++G h+ h + l+++ ++ +r
  gi|313122396|ref|YP_004038283.1| 240 nvsADALPEHlGRDGDHTDHWQVLFDDFTEAYR 272
                                       776566666678999999988888777665555 PP

>> MiaE_2  tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   7.9e-08   0.00024       4     146 ..      17     164 ..      14     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.9e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCC-SSSTTHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHGGGHHHHHHH CS
                            MiaE_2   4 deavvdllgalayGelsaferlaedarlaPtladraalaklaaaefrhyelledrlaeiGveaeeamePfvaavddf 80 
                                       +ea+  ll  +a  e+   er++e    aPt++    +a++a  e++h +l  d l++ G    + +       + f
  gi|313122396|ref|YP_004038283.1|  17 QEAIELLLRRMADDEFVLAERYTEWQVRAPTIESDISIANIAQDELGHARLWYDLLEDFGYTEPDLLW--ERDPETF 91 
                                       5667778999**************************************************99888764..4445566 PP

                                       HHTT......--SSHHHHHHHHHHHHHHHHHHHHHHCCCS-HHHHHHHHHHS--HH.HHHHHHHHHHHHHHH- CS
                            MiaE_2  81 hkrt......aPadwleslvkayvgdsvaadfyrevaeyldadtrelvlavlddtg.haevaeekvraaladd 146
                                       +++t      +  dw + +v++y  d        ++ +   +  r+ v++vl ++g h e   + +r  +++d
  gi|313122396|ref|YP_004038283.1|  92 RHSTlvelpfEEGDWADCIVRSYFYDEAEHLRMTALEKSSYPRIRDRVEKVLGEEGyHREHSMNWLRRLVSSD 164
                                       66653332225679************97777777788888999999999999887634555555555555544 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.27   8.1e+02      26      44 ..      15      33 ..      10      44 .. 0.70
   2 !   13.9   0.2   1.8e-05     0.055      15     131 ..      36     151 ..      23     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.27
                                      TT-HHHHHHHHHHHHHHHH CS
                      Rubrerythrin 26 egypqiaelFeelAeeEre 44
                                      ++ + i+ l++++A++E  
  gi|313122396|ref|YP_004038283.1| 15 KEQEAIELLLRRMADDEFV 33
                                      4457788888899998875 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHH...HH CS
                      Rubrerythrin  15 rlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLe...ea 88 
                                       ++Y+e + +a     ++   +  +A++E  Ha++ ++lle++ +++  + + +  +++++  + ++ +       ++
  gi|313122396|ref|YP_004038283.1|  36 ERYTEWQVRAP--TIESDISIANIAQDELGHARLWYDLLEDFGYTEP-DLLWERDPETFRHSTLVELPFEEGdwaDC 109
                                       56777777777..6667777889******************999998.67777777777777776666655544344 PP

                                       HHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  89 iegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHee 131
                                       i +  + + e++     ++ek  +++++++++k+  +E +H e
  gi|313122396|ref|YP_004038283.1| 110 IVR-SYFYDEAEHLRMTALEKSSYPRIRDRVEKVLGEEGYHRE 151
                                       433.4557777777778889999****************9987 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.055   1.6e+02      60      75 ..      16      31 ..       1      44 [. 0.72
   2 ?   10.3   0.1   0.00023      0.69       6      52 ..     125     173 ..     120     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.055
                            HEAT_2 60 dpealpaLkelldddd 75
                                      ++ea+++L+++++dd+
  gi|313122396|ref|YP_004038283.1| 16 EQEAIELLLRRMADDE 31
                                      4778888888888764 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00023
                            HEAT_2   6 qalendpdpevrraairaLg..rignpealpaLvellededpavRraaa 52 
                                        ale+++ p +r ++ ++Lg   ++ + ++++L++l+++++ + R +aa
  gi|313122396|ref|YP_004038283.1| 125 TALEKSSYPRIRDRVEKVLGeeGYHREHSMNWLRRLVSSDEGRRRVQAA 173
                                       5788888888999999999987788888999999999655544333333 PP

>> SAM_LFY  Floricaula / Leafy protein SAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       3.5     1e+04      40      62 ..      16      38 ..      11      42 .. 0.56
   2 ?   13.3   0.1     2e-05     0.059      21      51 ..     196     226 ..     192     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.5
                           SAM_LFY 40 elddmmkslseifrlellvGery 62
                                      e + +   l  +   e+++ ery
  gi|313122396|ref|YP_004038283.1| 16 EQEAIELLLRRMADDEFVLAERY 38
                                      44444444444555566677777 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2e-05
                           SAM_LFY  21 akiaelGftvstlvnmkeeelddmmkslsei 51 
                                       a i elG    tl +m+ee l+ + ++++ei
  gi|313122396|ref|YP_004038283.1| 196 AAIDELGVRTRTLADMREEWLETVTETMTEI 226
                                       7899************************987 PP

>> PerC  PerC transcriptional activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00015      0.46       2      45 ..     135     178 ..     134     205 .. 0.87
   2 ?   -2.4   0.0         2     6e+03      65      80 ..     217     232 ..     202     235 .. 0.71
   3 ?   -1.7   0.0       1.2   3.6e+03      69      78 ..     269     278 ..     260     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                              PerC   2 vrdkvaekLeakGlyRRaadRWaevmvlletdaeRklvalkRae 45 
                                       +rd+v + L ++G++R  +  W++ +v  ++ ++R ++a  R++
  gi|313122396|ref|YP_004038283.1| 135 IRDRVEKVLGEEGYHREHSMNWLRRLVSSDEGRRRVQAATDRLF 178
                                       79**********************99998888999999998877 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                              PerC  65 kavdrtykelGlatvs 80 
                                       ++v +t+ e+G++   
  gi|313122396|ref|YP_004038283.1| 217 ETVTETMTEIGIDLRT 232
                                       5688888999998665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.2
                              PerC  69 rtykelGlat 78 
                                       ++y+e+Gl  
  gi|313122396|ref|YP_004038283.1| 269 EAYREMGLHE 278
                                       6899***954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1967.44
//
Query:       gi|313122397|ref|YP_004038284.1|  [L=140]
Description: metal-sulfur cluster biosynthetic enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-20   72.6   0.2      3e-20   72.1   0.2    1.2  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
       0.18   12.2   0.1        2.1    8.9   0.0    2.1  2  HMA             Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.2   3.4e-24     3e-20       1      70 [.      39     110 ..      39     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 3.4e-24
                                       HHHHHHHHTT-B-TTTSSBCCCCT---E..EEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EE CS
                    FeS_assembly_P   1 keavlaaLrtVtDPelgvdlvslglvre..idieggkVsvditltypacslaeairadaeaalralpgvevv 70 
                                       ++av++aL +V DPe+++++v+lgl+++  +d+e g++++d+tlty +c++ +++++d+++a+ a++g+++v
  gi|313122397|ref|YP_004038284.1|  39 ERAVWDALYSVEDPEMPISIVDLGLIYAvgVDVEAGEARIDMTLTYTGCPARDMLEDDIREAVLAVEGIKDV 110
                                       579*************************7778888*********************************7765 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.084   7.5e+02      26      42 ..      64      80 ..      61      84 .. 0.87
   2 ?    8.9   0.0   0.00023       2.1      14      34 ..      95     115 ..      94     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.084
                               HMA 26 VesvkvdlatktvtVeg 42
                                      +++v vd++++++ ++ 
  gi|313122397|ref|YP_004038284.1| 64 IYAVGVDVEAGEARIDM 80
                                      7999*******999975 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00023
                               HMA  14 akvekvLselpgVesvkvdla 34 
                                        ++++++++++g+++v ++l+
  gi|313122397|ref|YP_004038284.1|  95 DDIREAVLAVEGIKDVMLNLV 115
                                       68****************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1036.61
//
Query:       gi|313122398|ref|YP_004038285.1|  [L=55]
Description: hypothetical protein Hbor_36320 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00024   21.2   3.0      0.031   14.4   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
     0.0016   18.7   4.4     0.0019   18.5   4.4    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.025   14.5   1.4      0.025   14.5   1.4    1.5  2  Toxin_16         Janus-atracotoxin
      0.025   14.1   6.0       0.25   10.9   6.0    2.1  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.13   12.9   2.7       0.17   12.5   2.7    1.2  1  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.34   11.2   0.2       0.34   11.2   0.2    2.2  2  zinc_ribbon_9    zinc-ribbon


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1     1e-05     0.031      22      38 ..      11      29 ..       3      30 .. 0.77
   2 !    7.4   0.5    0.0016       4.7       8      18 ..      44      54 ..      41      55 .] 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                       Zn-ribbon_8 22 sdaplta.CPeCgs.evrr 38
                                      s +++ta CP Cg+ +++r
  gi|313122398|ref|YP_004038285.1| 11 SGKDETAeCPYCGGtNTER 29
                                      43457777******99998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                       Zn-ribbon_8  8 CeeCghefevl 18
                                      C++C + fe++
  gi|313122398|ref|YP_004038285.1| 44 CNDCEEPFEKF 54
                                      *********86 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   4.4   6.4e-07    0.0019       3      36 ..      16      49 ..      14      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.4e-07
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga 36
                                         CP Cgg ++  +++++++    + yC dC+ 
  gi|313122398|ref|YP_004038285.1| 16 TAECPYCGGTNTEREHPKGPSLCRSMHYCNDCEE 49
                                      578******************9888*******85 PP

>> Toxin_16  Janus-atracotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.4   8.3e-06     0.025      12      34 ..      17      39 ..      10      41 .. 0.92
   2 ?   -3.7   0.5       3.9   1.2e+04      32      34 ..      43      45 ..      42      47 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.3e-06
                          Toxin_16 12 ACCPCCPGtsCkapesnGvsYCR 34
                                      A CP C Gt  +   + G s CR
  gi|313122398|ref|YP_004038285.1| 17 AECPYCGGTNTEREHPKGPSLCR 39
                                      78***********99*******9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.9
                          Toxin_16 32 YCR 34
                                      YC 
  gi|313122398|ref|YP_004038285.1| 43 YCN 45
                                      553 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.0   8.4e-05      0.25       3      22 ..      19      38 ..      17      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.4e-05
                                      ETTTTCEECHEETSTTCEEE CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvC 22
                                      CP+Cg+tn+++++  g  +C
  gi|313122398|ref|YP_004038285.1| 19 CPYCGGTNTEREHPKGPSLC 38
                                      ************99998887 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.7   5.8e-05      0.17       3      30 ..      17      45 ..      15      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-05
                           zf-ISL3  3 hrCPnCgsk.tvvkhgkkerrvrhlpigg 30
                                        CP+Cg + t + h k ++ +r   +++
  gi|313122398|ref|YP_004038285.1| 17 AECPYCGGTnTEREHPKGPSLCRSMHYCN 45
                                      57*******888999999*****999987 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00011      0.34      11      29 ..       7      24 ..       5      30 .. 0.71
   2 ?    2.3   1.7     0.067     2e+02      23      31 ..      43      51 ..      29      51 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                     zinc_ribbon_9 11 fVsvspdedsdvlCPhCgg 29
                                      +V+ s +++ +  CP+Cgg
  gi|313122398|ref|YP_004038285.1|  7 SVNTSGKDETAE-CPYCGG 24
                                      566665555556.*****9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.067
                     zinc_ribbon_9 23 lCPhCgggF 31
                                      +C++C+  F
  gi|313122398|ref|YP_004038285.1| 43 YCNDCEEPF 51
                                      588887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 406.97
//
Query:       gi|313122399|ref|YP_004038286.1|  [L=483]
Description: aldehyde dehydrogenase (acceptor) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.2e-177  590.2   0.0   2.5e-177  590.0   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.06   13.8   0.0       0.23   11.9   0.0    2.0  1  YCII      YCII-related domain


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.0   0.0  2.8e-181  2.5e-177       1     462 []      15     478 ..      15     478 .. 0.99

  Alignments for each domain:
  == domain 1  score: 590.0 bits;  conditional E-value: 2.8e-181
                                       EET-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH...HHTTS-HHHHHHHHHHHHHHHHHTHHHHHH CS
                            Aldedh   1 wveses.etievinPatgeviakvpaataedvdaavaaAkeafk...awaklpaeeRaeiLrkaadlleerkeelae 73 
                                       w+++ s et+++++Pat+++ a+v+ a++edv++av+aA +a +   +w +l+++eR++ Lr++ad++eerk+e++ 
  gi|313122399|ref|YP_004038286.1|  15 WTDAVSgETLQTFDPATETEYATVALAGEEDVRRAVDAASRAAErgsEWTELDPAERGAALRRMADAIEERKDEITL 91 
                                       888888788********************************9998889***************************** PP

                                       HHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHH CS
                            Aldedh  74 letletGkplaearaeveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapa 150
                                       +e+ ++Gk+  ea  ev+ +id++ry+a++ +kl+ge+ p+  ++l++++rePlGv+g I+PWN+P+ la ++lapa
  gi|313122399|ref|YP_004038286.1|  92 VESHDNGKTPFEAGMEVQMVIDTFRYFAGWTDKLTGEHNPVPGDRLNYTTREPLGVTGHIVPWNYPFQLAGRSLAPA 168
                                       *****************************************99********************************** PP

                                       HHTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHC CS
                            Aldedh 151 laaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaak 227
                                       la+GNt v+KP+++tplsal+   ++eeaglP+gv+nv++gsgse+g+al+eh++v++v+ftGste+g+++++ aa+
  gi|313122399|ref|YP_004038286.1| 169 LACGNTAVVKPSSQTPLSALYYGLAAEEAGLPDGVVNVIPGSGSEAGAALAEHDDVAHVAFTGSTEIGKRVMADAAQ 245
                                       ***************************************************************************** PP

                                       TTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTST CS
                            Aldedh 228 nlkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplde 304
                                       n++ vtlElGGk p++v+++aDl +a+++i  g+f+naGQ C+a+srllv+e+++d++ve++ve a++  +g++ d+
  gi|313122399|ref|YP_004038286.1| 246 NVTGVTLELGGKGPHLVFPEADLGAAAKGIHYGIFMNAGQMCWAGSRLLVHEDVADDLVERVVEGAESTPLGSGIDD 322
                                       ***************************************************************************** PP

                                       T-SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEES CS
                            Aldedh 305 dtdvGPliseaqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfk 381
                                       d  +GP++se+q+e++ +y++++++ega++ +Gg    +++e+gyfvePtvl++vt+dm++a+eEiFGPVlsvi+f+
  gi|313122399|ref|YP_004038286.1| 323 DGRMGPVVSEDQREQILDYIQTGVDEGATVACGG-GVPEDKESGYFVEPTVLTDVTNDMTVAREEIFGPVLSVIEFS 398
                                       ********************************99.458999************************************ PP

                                       SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEE CS
                            Aldedh 382 deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeyte 458
                                       deeeaie+aNd++yGL +g++t++l+ra+rva++l++G+v +N++ +  +++ pfgG k+Sg+Gre+g e+++eyt+
  gi|313122399|ref|YP_004038286.1| 399 DEEEAIELANDSPYGLLSGIWTEQLSRAHRVADALDYGMVSVNEYPVTFPQT-PFGGTKESGNGREQGLEAVREYTQ 474
                                       *********************************************9999999.************************ PP

                                       EEEE CS
                            Aldedh 459 vktv 462
                                       +k+v
  gi|313122399|ref|YP_004038286.1| 475 TKNV 478
                                       **97 PP

>> YCII  YCII-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.6e-05      0.23      19      85 ..     333     418 ..     329     423 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHHHHHHHHTTGEEEE.......................EEEECSCSSSSCGGCEEE.EEEEEEESSHHHH CS
                              YCII  19 allaahlayleelkkeGvllaa.......................GpklvidGpfaetkeqlg.Gfyiveaadldea 71 
                                       + +++ l+y +   +eG  +a+                       ++++v++       e++g  + ++e+ d++ea
  gi|313122399|ref|YP_004038286.1| 333 DQREQILDYIQTGVDEGATVACgggvpedkesgyfveptvltdvtNDMTVAR------EEIFGpVLSVIEFSDEEEA 403
                                       5678888888888888888888888888888888888877666666666665......355552567********** PP

                                       HHHHHT-HHHHT.TE CS
                              YCII  72 ieiaardPfvea.Gl 85 
                                       ie+a + P+    G+
  gi|313122399|ref|YP_004038286.1| 404 IELANDSPYGLLsGI 418
                                       ********9876455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 3094.68
//
Query:       gi|313122400|ref|YP_004038287.1|  [L=128]
Description: hypothetical protein Hbor_36340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-14   53.4   0.3    3.8e-14   52.8   0.3    1.3  1  4HBT      Thioesterase superfamily
    5.1e-07   29.9   0.0    6.5e-07   29.6   0.0    1.1  1  DUF4442   Domain of unknown function (DUF4442)
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.018   15.3   0.0    1.1  1  4HBT_3    Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.3   6.4e-18   3.8e-14       4      77 ..      47     116 ..      46     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 6.4e-18
                                       B-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT   4 vhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                        hgGv ++l+D+++gaal s  +  + v++++++id+l +++ +  l++ea v+r+g+ + +v+v+v++ d+ +
  gi|313122400|ref|YP_004038287.1|  47 AHGGVAFTLADTVGGAALVSEVD--QPVPTIDMRIDYLNAGTGD--LYAEADVVRVGGDVGTVDVDVYATDDDT 116
                                       6*********************9..9*****************9..***********************99976 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.1e-10   6.5e-07      12     126 ..       9     121 ..       3     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.1e-10
                                       HSGGGGGG--EEEEEETTEEEEEE---GGGB.-TTS.SB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S CS
                           DUF4442  12 kaPYfgtvgprieelepgraevrlkkrrrvr.Nhig.tvHAiAicnlaElamGllaeatlpdthrwipkgmevdYla 86 
                                        +P+ + +g+ ++e++ g+ae r++ r ++  N  +   H++ +++la+++ G+ +   + +    i+  m++dYl+
  gi|313122400|ref|YP_004038287.1|   9 SMPFAQLLGVEVTEVADGHAEGRIEMREELSwNSDRvMAHGGVAFTLADTVGGAALVSEVDQPVPTID--MRIDYLN 83 
                                       68999999************9999999877624333146*******************9999888885..9****** PP

                                       ---S-EEEEEE-TTS-TT--EEEEEEEEEEETTE.EEEEE CS
                           DUF4442  87 katgdltavaelepedvgekeelvvevevrdekgeevvra 126
                                        +tgdl a+a++ +    + +++ v+v+++d++   v++a
  gi|313122400|ref|YP_004038287.1|  84 AGTGDLYAEADVVRVGG-DVGTVDVDVYATDDDT-LVAQA 121
                                       **********9988543.3579999999999987.67665 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.1e-06     0.018       4      81 ..      39     121 ..      37     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-06
                                       GGECTTC..-HHHHHHHHHHHHHHT.......-S.SSEEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEEEETT CS
                            4HBT_3   4 pwtpgga.gyGGyvlAlalraaqrtv......pdprlhslhvyFlrpgdagpviyhvervrdGrsfstrtvelsqgg 73 
                                       +w+ +++ ++GG++  la  +  +++      p p++  + +++l++g    +  ++++vr G  + t+ v ++  +
  gi|313122400|ref|YP_004038287.1|  39 SWNSDRVmAHGGVAFTLADTVGGAALvsevdqPVPTI-DMRIDYLNAGTG-DLYAEADVVRVGGDVGTVDVDVYATD 113
                                       5999999559999999998888877557775433345.999999999976.89999999999999999999999987 PP

                                       EEEEEEEE CS
                            4HBT_3  74 rpiftata 81 
                                        + ++a+a
  gi|313122400|ref|YP_004038287.1| 114 DDTLVAQA 121
                                       77777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 946.89
//
Query:       gi|313122401|ref|YP_004038288.1|  [L=429]
Description: phenylacetate-CoA ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-23   82.3   0.0    4.9e-23   81.3   0.0    1.6  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
      6e-16   58.1   1.0    1.4e-15   56.9   1.0    1.6  1  AMP-binding      AMP-binding enzyme
  ------ inclusion threshold ------
      0.021   13.7   0.0      0.043   12.7   0.0    1.4  1  GH3              GH3 auxin-responsive promoter


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   8.2e-27   4.9e-23       1      96 []     335     429 .]     335     429 .] 0.96

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 8.2e-27
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--.EEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsv.kvel 76 
                                       Gvnv+Ps+ie+v+ e+++v+p+Y+i ++reg++D+le++vE++e+f d+  +++al+k++ ++l ++l++++ k++l
  gi|313122401|ref|YP_004038288.1| 335 GVNVYPSEIESVVLEFDGVAPHYRIDLSREGTMDRLELTVELAEEF-DG--DRSALRKSLLDRLSNVLSLEPdKLDL 408
                                       9********************************************9.43..89******************878*** PP

                                       E-TT-S-----.----EEE-S CS
                   AMP-binding_C_2  77 vepgtlprseg.KakrviDkR 96 
                                       v+pg ++r+e  K +rv+D+R
  gi|313122401|ref|YP_004038288.1| 409 VAPGAIERTEVgKVQRVYDRR 429
                                       *********966*******99 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   1.0   2.3e-19   1.4e-15     139     370 ..      63     286 ..      20     334 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.3e-19
                                       HCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS-TTS CS
                       AMP-binding 139 eeeeseekaekpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr..fklkeddvvlsilplah 213
                                       ++++++  ++ p++  +++ + l+ i  +SGTTGkPK V ++ + l+   +++ ++     +l+ +d++     +  
  gi|313122401|ref|YP_004038288.1|  63 FTTKEDFRDNYPTDLFAVDMEALVRIHASSGTTGKPKIVGYTENDLARW-QEVMCRGFeaAGLDTSDTLQNAYGYGL 138
                                       22222222212445557899999********************998765.444333222244555888877777776 PP

                                       CHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEE CS
                       AMP-binding 214 ifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlv 288
                                        +g   +  +a + G++vv + + ++ ++    +el+++l++t i+++P+ + +l+e + +    ++  +l+ +++v
  gi|313122401|ref|YP_004038288.1| 139 FTGGLGFHDGATAMGMAVVPVGGGQTqRQ----VELLSDLEATAICLTPSYALYLAEtAAEMG--YDPAELP-VETV 208
                                       6666699999999******9999988444....8*********************99554444..4433444.**** PP

                                       EEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTS CS
                       AMP-binding 289 llggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdge 363
                                       l g+ep+ + +  ++++++g + +e YGl+E  g  + +   e+   +  +G  ++      +++D++tg pv++ge
  gi|313122401|ref|YP_004038288.1| 209 LYGAEPCTEPMRAEIEDRLGATAVENYGLSEIIGPGV-AA--EC---RAQTGMHIWedQFYPEVIDPQTGDPVGEGE 279
                                       *********************99999*********99.44..33...2346888873356678************** PP

                                       EEEEEEE CS
                       AMP-binding 364 eGellvr 370
                                       eGel++ 
  gi|313122401|ref|YP_004038288.1| 280 EGELVLT 286
                                       ****975 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.3e-06     0.043      76     108 ..      85     116 ..      81     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-06
                                       -SEEEEECCEETTEEEEEEESHHHHHHHHHH.H CS
                               GH3  76 iklfalsSGTtsgksKliPvteeslkelallvl 108
                                       ++++  sSGTt gk+K++ +te+ l +++ +++
  gi|313122401|ref|YP_004038288.1|  85 LVRIHASSGTT-GKPKIVGYTENDLARWQEVMC 116
                                       567889*****.***************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3097.80
//
Query:       gi|313122402|ref|YP_004038289.1|  [L=241]
Description: amino acid/amide ABC transporter ATP-binding protein 2, HAAT family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.4e-34  117.4   0.0    8.9e-34  116.9   0.0    1.2  1  ABC_tran    ABC transporter
    3.8e-09   36.8   0.4     0.0011   18.9   0.1    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
  ------ inclusion threshold ------
      0.012   15.8   0.6       0.12   12.7   0.1    2.1  2  AAA_22      AAA domain
      0.015   15.6   0.5      0.024   15.0   0.5    1.6  1  AAA_16      AAA ATPase domain
      0.017   14.8   0.1      0.033   13.9   0.0    1.4  2  AAA_15      AAA ATPase domain
      0.023   13.9   0.0      0.039   13.2   0.0    1.3  1  Zeta_toxin  Zeta toxin
      0.027   13.9   0.1        4.2    6.7   0.0    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
      0.034   13.3   0.1      0.051   12.8   0.1    1.5  1  NB-ARC      NB-ARC domain
      0.044   13.3   0.2      0.071   12.7   0.1    1.7  1  AAA_25      AAA domain
      0.059   13.9   0.0       0.11   12.9   0.0    1.4  1  AAA_23      AAA domain
      0.069   12.9   0.1       0.15   11.8   0.1    1.6  1  AAA_29      P-loop containing region of AAA domain
       0.12   12.5   0.2       0.32   11.1   0.0    1.7  3  MMR_HSR1    50S ribosome-binding GTPase
       0.12   12.0   0.3       0.21   11.2   0.3    1.4  1  SRP54       SRP54-type protein, GTPase domain
       0.14   12.1   0.5       0.31   10.9   0.1    1.7  2  NACHT       NACHT domain
       0.15   11.8   0.0       0.24   11.1   0.0    1.4  1  AAA_24      AAA domain
       0.15   11.8   1.0       0.19   11.4   1.0    1.5  1  AAA_30      AAA domain
       0.17   12.3   0.1       0.49   10.8   0.1    2.0  1  AAA         ATPase family associated with various cellular ac
       0.19   12.0   0.3        1.4    9.2   0.3    2.1  1  SbcCD_C     Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.9   0.0   8.9e-37   8.9e-34       1     136 [.      21     165 ..      21     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 8.9e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l+ v++++  g++v ++G+nG GK+t l+++ g + pteG++ +dg+d+++  +++ +r+ i+ +p++ ++fp+ltv
  gi|313122402|ref|YP_004038289.1|  21 LQGVDIDVPSGSVVTLIGRNGVGKTTTLRTIHGSVAPTEGSVMFDGTDITDySPEQTAREGIALVPEDRRVFPGLTV 97 
                                       68899*********************************************99999********************** PP

                                       HHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ren           + +  +e+++s++++     ++ +s++s LSgG++q++a+aral+++p+ll+lDEpt
  gi|313122402|ref|YP_004038289.1|  98 RENveigriggrrdTTKPAVEEIISEFENLR---RHRESNGSALSGGEQQMLAIARALVSAPDLLMLDEPT 165
                                       ********999765555559******99777...4445689*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.6e-06    0.0026       2      97 ..      34     131 ..      33     134 .. 0.75
   2 !   18.9   0.1   1.1e-06    0.0011     186     279 ..     122     181 ..     109     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarl...drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryg 75 
                                         liG+Ng+GK++ L+++ +   +    ++v +++++ +++++++  +  + l  ++ ++  +++ + ++    r g
  gi|313122402|ref|YP_004038289.1|  34 VTLIGRNGVGKTTTLRTIHGS--VaptEGSVMFDGTDITDYSPEQTAREGIALVPEDRRVFPGLT-VRENVEIGRIG 107
                                       579***************543..356888888888888888888888888888888888877777.77777777777 PP

                            AAA_21  76 lrlersqv..eeklssvetllesg 97 
                                        r +      ee +s++e+l++++
  gi|313122402|ref|YP_004038289.1| 108 GRRDTTKPavEEIISEFENLRRHR 131
                                       777777777777777777777765 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.1e-06
                            AAA_21 186 qrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgslll 262
                                       +++++ ++ +e++ s+l                                   S G +++la++ al +a+   +ll 
  gi|313122402|ref|YP_004038289.1| 122 SEFENLRRHRESNGSAL-----------------------------------SGGEQQMLAIARALVSAP---DLLM 160
                                       44444444444444444...................................***************999...9*** PP

                            AAA_21 263 iDEpEngLHP....kllrrll 279
                                       +DEp  gL P    +++r+++
  gi|313122402|ref|YP_004038289.1| 161 LDEPTEGLAPsivqQVQRKIA 181
                                       **********55555556665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00012      0.12       6      26 ..      32      52 ..      29      82 .. 0.91
   2 ?    1.3   0.1      0.39   3.8e+02      59     127 ..     119     192 ..     107     201 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                            AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                      ++++++G  G+GKTt+lr+++
  gi|313122402|ref|YP_004038289.1| 32 SVVTLIGRNGVGKTTTLRTIH 52
                                      6889**************976 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.39
                            AAA_22  59 ellralglelkaerlsseellealeqalrarav.....ielliiDEaqh.lrseealeeL.rsllnlsrkgvqliL 127
                                       e+ +++++ + + r s+   l+  eq++ a a+     + ll++DE    l  + +++++ r+++ l++ gv+++L
  gi|313122402|ref|YP_004038289.1| 119 EIISEFENLRRH-RESNGSALSGGEQQMLAIARalvsaPDLLMLDEPTEgL-APSIVQQVqRKIASLNDEGVTILL 192
                                       555555554444.44444444444444444444455567799999966656.444444443333333355555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.5   2.4e-05     0.024      23      58 ..      30      65 ..      18     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrg 58
                                      ++++v l+G  GvGK++ +r+++ ++  ++g ++  
  gi|313122402|ref|YP_004038289.1| 30 SGSVVTLIGRNGVGKTTTLRTIHGSVAPTEGSVMFD 65
                                      33899******************9998886555333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.3e-05     0.033      14      43 ..      21      51 ..      19      53 .. 0.80
   2 ?   -3.8   0.0       7.8   7.8e+03     324     354 ..     156     186 ..     153     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileal 43
                                      l+ v+id+ +  + +liG+N++GK++ l+ +
  gi|313122402|ref|YP_004038289.1| 21 LQGVDIDVPSGsVVTLIGRNGVGKTTTLRTI 51
                                      56666776666799*************9877 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.8
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkeland 354
                                       +++l+++EP   L p+  +++ +++++l ++
  gi|313122402|ref|YP_004038289.1| 156 PDLLMLDEPTEGLAPSIVQQVQRKIASLNDE 186
                                       5788888887777777777777777776555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.9e-05     0.039      18      60 ..      33      75 ..      26      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                      ++ l G  G GK+++++ +  +++++++ v +d++d+  + Pe
  gi|313122402|ref|YP_004038289.1| 33 VVTLIGRNGVGKTTTLRTIHGSVAPTEGSVMFDGTDITDYSPE 75
                                      5778899********************************9998 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0      0.01        10      25      44 ..      32      51 ..      19      57 .. 0.81
   2 ?    6.7   0.0    0.0042       4.2     125     184 ..     126     181 ..      75     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.01
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      s+  ++G+NG GK+  l  i
  gi|313122402|ref|YP_004038289.1| 32 SVVTLIGRNGVGKTTTLRTI 51
                                      57789*********887766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0042
                                       HHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 125 ellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                       +l ++ + + ++LSgGe++++a+a  +    v+   l +lDe    L  + v++v + + 
  gi|313122402|ref|YP_004038289.1| 126 NLRRHRESNGSALSGGEQQMLAIARAL----VSAPDLLMLDEPTEGLAPSIVQQVQRKIA 181
                                       344444455669********9997442....33344666666666666666666665555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   5.1e-05     0.051      21      52 ..      32      65 ..      19     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.1e-05
                                      EEEEEEESTTSSHHHHHHHHCCSHCCCCC..CBT CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnksdeveg..rFd 52
                                       vv+l G+ GvGKtt ++ i+ + + +eg   Fd
  gi|313122402|ref|YP_004038289.1| 32 SVVTLIGRNGVGKTTTLRTIHGSVAPTEGsvMFD 65
                                      69******************99887777755566 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.1e-05     0.071      30      66 ..      28      71 ..      19     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava..tGkpwlg.....p 66
                                      +p g+++ l+G+ g+GKtt +  +  +va  +G+  ++     +
  gi|313122402|ref|YP_004038289.1| 28 VPSGSVVTLIGRNGVGKTTTLRTIHGSVAptEGSVMFDgtditD 71
                                      599****************9998888888877766666666663 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011      0.11      10      39 ..      18      51 ..      12      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            AAA_23 10 f...rdqeidF.skgltlItGpNGaGKTTildAi 39
                                          ++++id  s  ++ ++G NG GKTT l+ i
  gi|313122402|ref|YP_004038289.1| 18 TrvlQGVDIDVpSGSVVTLIGRNGVGKTTTLRTI 51
                                      44448888999777899999*********99877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00015      0.15      14      39 ..      23      48 ..      19      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                            AAA_29 14 ghtieidlkg.atlltGpsGsGKSTll 39
                                      g +i++  +g ++ l+G++G+GK+T l
  gi|313122402|ref|YP_004038289.1| 23 GVDIDVP-SGsVVTLIGRNGVGKTTTL 48
                                      5667776.555999***********76 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032      0.32       2      26 ..      34      58 ..      33      87 .. 0.82
   2 ?   -1.2   0.0       2.1   2.1e+03      65      82 ..     175     192 ..      92     212 .. 0.66
   3 ?   -2.2   0.0       4.3   4.3e+03      28      42 ..     184     198 ..     167     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                                      EEEEESTTSSHHHHHHHHHTSTEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaiv 26
                                      v ++Gr  vGK+t ++++ g++a +
  gi|313122402|ref|YP_004038289.1| 34 VTLIGRNGVGKTTTLRTIHGSVAPT 58
                                      789****************997755 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHCTSEEEEE CS
                          MMR_HSR1  65 glgkaflaleeadlillv 82 
                                       ++++++++l++  + +l+
  gi|313122402|ref|YP_004038289.1| 175 QVQRKIASLNDEGVTILL 192
                                       333333333333333333 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.3
                                       SSTTSSSSEEEEEEE CS
                          MMR_HSR1  28 dkpgtTrdinegrvk 42 
                                       +  g+T+  +e +v+
  gi|313122402|ref|YP_004038289.1| 184 NDEGVTILLVEQNVQ 198
                                       333444444333333 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00021      0.21       2      33 ..      32      63 ..      31      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvl 33
                                      +v+ l+G +G+GKTttl  +   +   + +v+
  gi|313122402|ref|YP_004038289.1| 32 SVVTLIGRNGVGKTTTLRTIHGSVAPTEGSVM 63
                                      5899************9877666555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00032      0.31       2      22 ..      33      53 ..      32      61 .. 0.87
   2 ?   -2.0   0.0         3   2.9e+03      53      91 ..     167     205 ..     159     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                                      CEEEEC-TTTCHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                      +v l G++G+GKTt l+ ++ 
  gi|313122402|ref|YP_004038289.1| 33 VVTLIGRNGVGKTTTLRTIHG 53
                                      799**************9975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                                       -HCHHHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-ST CS
                             NACHT  53 sladllfsqlpepaapvsevwavllelperlLlilDglD 91 
                                       +la  +++q + ++a  +   + +l +++ +   lD +D
  gi|313122402|ref|YP_004038289.1| 167 GLAPSIVQQVQRKIASLNDEGVTILLVEQNVQVALDTAD 205
                                       666667777776666666644445555555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024      0.24       4      27 ..      33      54 ..      30      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkpl 27
                                       + ++G +g+GKTt+++++  +  
  gi|313122402|ref|YP_004038289.1| 33 VVTLIGRNGVGKTTTLRTI--HGS 54
                                      6899*************99..333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   0.00019      0.19      19      45 ..      32      58 ..      27     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa 45
                                       v++l G+ G GKtt+l+++   ++  
  gi|313122402|ref|YP_004038289.1| 32 SVVTLIGRNGVGKTTTLRTIHGSVAPT 58
                                      4899***************97655554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00049      0.49       2      35 ..      35      70 ..      34     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
                                      EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                               AAA  2 llyGppGtGKTllakavakelg..vefleisgsell 35
                                       l+G  G+GKT++ + +  ++      + ++g++++
  gi|313122402|ref|YP_004038289.1| 35 TLIGRNGVGKTTTLRTIHGSVAptEGSVMFDGTDIT 70
                                      699*************99887422334666666666 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0014       1.4      26      50 ..     131     155 ..     114     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaal 50 
                                        +++ ++lSGGe+q+la    + ++
  gi|313122402|ref|YP_004038289.1| 131 RESNGSALSGGEQQMLAIARALVSA 155
                                       5677899******877654444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1629.14
//
Query:       gi|313122403|ref|YP_004038290.1|  [L=254]
Description: amino acid/amide ABC transporter ATP-binding protein 1, HAAT family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-28   99.8   0.0    2.3e-28   99.4   0.0    1.1  1  ABC_tran      ABC transporter
    3.9e-08   33.0   0.0    8.9e-08   31.9   0.0    1.6  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    0.00016   21.6   0.1      0.025   14.4   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00019   21.2   0.1     0.0003   20.6   0.0    1.4  1  AAA_30        AAA domain
    0.00057   19.2   0.0    0.00086   18.6   0.0    1.3  1  Zeta_toxin    Zeta toxin
    0.00094   19.7   0.0     0.0011   19.6   0.0    1.2  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.023   14.4   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.098   12.7   0.4       0.19   11.8   0.4    1.8  1  MMR_HSR1      50S ribosome-binding GTPase
       0.14   11.6   0.2       0.29   10.5   0.2    1.7  1  SMC_N         RecF/RecN/SMC N terminal domain
       0.14   11.8   0.1       0.32   10.6   0.0    1.7  2  SRP54         SRP54-type protein, GTPase domain
       0.16   11.9   0.0       0.31   10.9   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
       0.31   10.7   0.0       0.36   10.5   0.0    1.1  1  AAA_15        AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.0   1.5e-31   2.3e-28       2     137 .]      22     181 ..      21     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 1.5e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++v+l++++ge   ++G+nGaGK+t ++ll+g ++p +G++++dg+d+++  +++++r+ ++  +q +++f++ltvr
  gi|313122403|ref|YP_004038290.1|  22 DDVNLDIERGEFRSLIGPNGAGKTTTFNLLTGAMRPSNGSVRFDGEDVTTlAPHQRVRRGLARSFQITNVFNGLTVR 98 
                                       89************************************************9************************** PP

                                       HH...........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTS CS
                                       xx...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkp 127
                                       en                           + +e+ e++l++ gl +   + +      L +G k+r+++a +l+++p
  gi|313122403|ref|YP_004038290.1|  99 ENvrlaaqaarddgftpseeylndaqafdDVNEHTERVLDRSGLLGRGGEMA----DVLAYGDKRRLEIAIVLATDP 171
                                       *********9999999999988555544444444666666666666555554....9******************** PP

                                       SEEEEESTTT CS
                                       xxxxxxxxxx RF
                          ABC_tran 128 kllllDEpta 137
                                       +++llDEpta
  gi|313122403|ref|YP_004038290.1| 172 EMVLLDEPTA 181
                                       ********97 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0     6e-11   8.9e-08       2      23 .]     229     250 ..     228     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 6e-11
                      BCA_ABC_TP_C   2 vIAeGtPaEvrndPrVieAYLG 23 
                                       ++AeG+P+E+  + +V+eAY G
  gi|313122403|ref|YP_004038290.1| 229 ILAEGSPDEIADNDDVREAYFG 250
                                       89******************98 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.7e-05     0.025       4      23 ..      36      55 ..      35      89 .. 0.81
   2 !    5.5   0.0    0.0084        13     247     284 ..     163     197 ..     106     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                            AAA_21  4 liGpNgsGKSnLLdaldlla 23
                                      liGpNg+GK++ + +l ++ 
  gi|313122403|ref|YP_004038290.1| 36 LIGPNGAGKTTTFNLLTGAM 55
                                      8************9998773 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0084
                            AAA_21 247 lltallralkkgsllliDEpEngLHPkllrrllellke 284
                                       ++  l+ ++     +l+DEp +g+  + +r  ++l+++
  gi|313122403|ref|YP_004038290.1| 163 IAIVLATDP---EMVLLDEPTAGMSAEETRATMDLIDD 197
                                       444444444...9************9999999999843 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     2e-07    0.0003      20      74 ..      33      98 ..      28     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2e-07
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkvLaeelgi....eastia 74
                                      +  l Gp G+GKtt+ + l+ a++ + g      ++v  lAp +++ + La++++i    ++ t+ 
  gi|313122403|ref|YP_004038290.1| 33 FRSLIGPNGAGKTTTFNLLTGAMRPSnGsvrfdgEDVTTLAPHQRVRRGLARSFQItnvfNGLTVR 98
                                      67799*******************9966*****9*****************999874444444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.8e-07   0.00086      23      62 ..      38      77 ..      29     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.8e-07
                        Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldpDdlRelhPeye 62
                                      G  GAGK+++ +ll+ ++++ ++ vr+d+ d+ +l P+ +
  gi|313122403|ref|YP_004038290.1| 38 GPNGAGKTTTFNLLTGAMRPSNGSVRFDGEDVTTLAPHQR 77
                                      789**********************************954 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.1e-07    0.0011       6      43 ..      14      55 ..      12     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.1e-07
                            AAA_23  6 nfrsf...rdqeidFskglt.lItGpNGaGKTTildAiklaL 43
                                       f+s+   +d+++d ++g +  ++GpNGaGKTT ++ ++ a+
  gi|313122403|ref|YP_004038290.1| 14 KFGSLvavDDVNLDIERGEFrSLIGPNGAGKTTTFNLLTGAM 55
                                      57888887888888877655489**************99887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.5e-05     0.023      13      53 ..      22      63 ..      19      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvr 53
                                      d+  ++i++ ++  l+Gp+G+GK+T +  ++  + p++ +vr
  gi|313122403|ref|YP_004038290.1| 22 DDVNLDIERGEFRSLIGPNGAGKTTTFNLLTGAMRPSNgSVR 63
                                      55678888666999***********99777777777665555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00013      0.19       4      39 ..      36      77 ..      34     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                      EEESTTSSHHHHHHHHHTS......TEEESSSTTSSSSEEEE CS
                          MMR_HSR1  4 ivGrpNvGKStLinaltge......kaivsdkpgtTrdineg 39
                                      ++G   +GK+t +n ltg+       ++   +  tT+ + ++
  gi|313122403|ref|YP_004038290.1| 36 LIGPNGAGKTTTFNLLTGAmrpsngSVRFDGEDVTTLAPHQR 77
                                      79***************9542222345666666777766554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2    0.0002      0.29      25      43 ..      32      50 ..      12     228 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                                      SEEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldA 43
                                      +f +++GpNG+GK+  ++ 
  gi|313122403|ref|YP_004038290.1| 32 EFRSLIGPNGAGKTTTFNL 50
                                      699**********987665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.32       6      33 ..      36      63 ..      33     106 .. 0.85
   2 ?   -3.1   0.1       3.3   4.9e+03      85     109 ..     172     196 ..     163     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvl 33
                                      l+G++GaGKTtt   L   ++ ++ +v 
  gi|313122403|ref|YP_004038290.1| 36 LIGPNGAGKTTTFNLLTGAMRPSNGSVR 63
                                      89**********9999887777666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                                       SEEEEE..E--SSTTHHHHHHHHHHHH CS
                             SRP54  85 dvvlvD..TaGrlqndkelmeelkkik 109
                                       ++vl+D  TaG ++++++   +l  i 
  gi|313122403|ref|YP_004038290.1| 172 EMVLLDepTAGMSAEETRATMDL--ID 196
                                       67777777888777776655444..44 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.31      99     131 ..      30      63 ..      11      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                       T.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                         ++  l+G+ G+GK+t  n l++ ++ + g+v+
  gi|313122403|ref|YP_004038290.1|  30 RgEFRSLIGPNGAGKTTTFNLLTGAMRPSNGSVR 63 
                                       447889*****************99877766665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00024      0.36      16      43 ..      23      51 ..      20     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsileal 43
                                      dv +d++   +  liG+N++GK++  ++l
  gi|313122403|ref|YP_004038290.1| 23 DVNLDIERGeFRSLIGPNGAGKTTTFNLL 51
                                      5556666556999***********98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1791.32
//
Query:       gi|313122404|ref|YP_004038291.1|  [L=656]
Description: branched-chain amino acid ABC-type transport system, permease component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-84  282.3  86.8    4.6e-48  163.7  40.5    2.1  2  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7  40.5   2.6e-52   4.6e-48       2     268 .]      11     279 ..      10     279 .. 0.93
   2 !  124.7  38.4     2e-40   3.6e-36       3     267 ..     340     616 ..     338     618 .. 0.89

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 2.6e-52
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllal.llsllllallvallvgaavglllgllv 77 
                                       +ln+lt++++++++A Gl+++fg++ vin++hg+++alGay a+ ++a  +++ +++al++a l+ a+vg+ +++l 
  gi|313122404|ref|YP_004038291.1|  11 VLNGLTVGMVYVLLAAGLSIIFGVMDVINFAHGELFALGAYFAFAIAAPlGGAGFWVALVAAPLLVAVVGMGIERLA 87 
                                       689************************************887776666505566**********************9 PP

                      BPD_transp_2  78 lrlkvde.liitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv....llalllvlavllll 149
                                       +r  + + ++  +ll++ lv++++ l t  +++ + +  ++++l+ + +ll f  + ++    ++ + l++  +lll
  gi|313122404|ref|YP_004038291.1|  88 VRRLYGRdPLYHILLTFGLVLIINDLITAVWGKAAKPFPIPAALDQPVTLLGFTYSLYNygivIFGAMLAIGTWLLL 164
                                       998875438899999999999999999999999999999999999999999999888889999************** PP

                      BPD_transp_2 150 rrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGgag 226
                                       +rt+fG+++ra  +++e++r+lGinv+ + +ltf +++alAg+aG++l ++++++p  +g   ++ a+++vvlGg+g
  gi|313122404|ref|YP_004038291.1| 165 NRTKFGMIIRAGSQDREMVRNLGINVDTYYTLTFGFGAALAGVAGIVLGAFQNVSP-TMGNSVIIPAFVIVVLGGLG 240
                                       ***************************************************88888.******************** PP

                      BPD_transp_2 227 sllgtviGaliigvvksllltllgiptelarvllgallilvl 268
                                       s +g+v+G+l +gvv++l++t++++   l+ +++++l+i+vl
  gi|313122404|ref|YP_004038291.1| 241 SFRGAVVGGLFVGVVQTLARTYTPF---LEGLIVFLLMIAVL 279
                                       ***********************77...************97 PP

  == domain 2  score: 124.7 bits;  conditional E-value: 2e-40
                      BPD_transp_2   3 lnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlr 79 
                                       + ll   +i+a++Al+l lv g+aG+++lgh+ f+++Gay+a l l  + +++++al+va++v+aa++ ++g+l++r
  gi|313122404|ref|YP_004038291.1| 340 VTLLEDMLIWALFALSLDLVLGYAGLVSLGHALFYGVGAYAAVLSLMHVTPSVFVALAVAIIVCAAIAWVIGYLSIR 416
                                       56788899********************************************************************* PP

                      BPD_transp_2  80 lkvdeliitllllsvlvg..ltlllltgitsgvkgqssvkellgfagallsflsaviv.............llalll 141
                                       +    +++ +l++  l++  ++ + +tg++ g +g++++ +l+g+  +l+ f  a+               +l+++ 
  gi|313122404|ref|YP_004038291.1| 417 VSGVFFAMITLAFAQLFYnaVFKFKWTGGSDGLFGVDTFYGLAGVGIDLSAFELAFGPvildgglvryyflVLVVVG 493
                                       ****99999987766665115566677788888888888888888888877777766699*******9765555555 PP

                      BPD_transp_2 142 vlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnai 217
                                        +++  +l r +fG+ l a++e+ee a ++G++v+ +k  +fv+sg+lAglaG l+a+  g + p +  +  + ++i
  gi|313122404|ref|YP_004038291.1| 494 GYLLARRLIRAPFGTVLQAIRESEERASFVGYDVTAYKRRAFVVSGGLAGLAGGLFAANNGYVAPsFLHWIHSGEVI 570
                                       6788888999*******************************************************88999999**** PP

                      BPD_transp_2 218 aavvlGgagsllgtviGaliigvvksllltllgiptelarvllgallilv 267
                                       ++ vlGg+g+l+g+++Ga ++++ ++ l++++ +    +++++g l++l+
  gi|313122404|ref|YP_004038291.1| 571 VMTVLGGMGTLYGPMLGAGVFVAFEDILSSYIDQ----WQLVIGTLFVLF 616
                                       ********************************66....777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 4097.37
//
Query:       gi|313122405|ref|YP_004038292.1|  [L=422]
Description: amino acid/amide ABC transporter substrate-binding protein, HAAT family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-70  237.9   4.5    2.8e-70  237.7   4.5    1.0  1  Peripla_BP_6     Periplasmic binding protein
    9.2e-34  117.0   0.2    1.1e-33  116.7   0.2    1.0  1  Peripla_BP_5     Periplasmic binding protein domain
    3.8e-15   55.9   0.0    5.2e-15   55.4   0.0    1.1  1  ANF_receptor     Receptor family ligand binding region
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.051   13.5   0.0    1.4  1  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.7   4.5   6.4e-74   2.8e-70       2     335 ..      51     383 ..      50     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 237.7 bits;  conditional E-value: 6.4e-74
                                       EEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BS CS
                      Peripla_BP_6   2 ikiGlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgpls 78 
                                       ++ G+++p++Gpy+ + +++++ga++a++++N++   ++++ie v +D++ dp+++ ++a+ lv+qdg+  l+g+ s
  gi|313122405|ref|YP_004038292.1|  51 VTYGVVSPMTGPYGGLAEGQRNGAKLAIRHVNESDD-LDVEIEGVYEDTEADPSTGSRKAQSLVEQDGASFLMGAIS 126
                                       5669*****************************854.8*************************************** PP

                                       HHHHHHHHHHHHHHT-EEEE...SS-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHH CS
                      Peripla_BP_6  79 savaaavaevlakdgvpvig...pagltgekcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregi 152
                                       s++a+a+ e++ ++ v++     ++  tg +c+++vf++  +++++a+a+ ++ a++lg +kv +  adya+g +++
  gi|313122405|ref|YP_004038292.1| 127 SSTALALNEFAKEQEVIYNPggaAVPITGSNCNEWVFRAETNTAQMAEAVSDFTAENLG-TKVWFHIADYAYGESVM 202
                                       ******************99653337889***************************999.66777778********* PP

                                       HHHHHHHHCC.TEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-C CS
                      Peripla_BP_6 153 aalkaaakaa.GgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillvswsgs 228
                                       + +++ +k+   ++vvg  + ++g+++f +++ qi+++ a++v+l++tg+dl++++k+aa++Gl+  ++ l+s++++
  gi|313122405|ref|YP_004038292.1| 203 NRVEKRMKQGrSIDVVGRSRSKFGSSNFNSYISQIANSDAEVVVLGMTGGDLINFVKQAASQGLKD-NVNLMSPTMT 278
                                       ********984456***************************************************6.7********* PP

                                       HHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHHHH CS
                      Peripla_BP_6 229 eedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaagsltreavr 305
                                        + ++ + g+aa g+++ + y+p+ld+ +++ fv+ay++ y+   pp+ fa  +y+++++ ++++ +ags +++av+
  gi|313122405|ref|YP_004038292.1| 279 FSVVRNALGKAAYGTYGGVRYVPELDTGTNQSFVEAYQNEYDT--PPDNFARVAYLSIRMTAKGIAEAGSSDPAAVK 353
                                       ******************************************8..6******************************* PP

                                       HHHHHS-BECCCTCCBEECTTSBEE--EEE CS
                      Peripla_BP_6 306 aaleslgfdgllgplkftaedhqasrpvyv 335
                                       +al +l++++++g+++f+++dhqa++pv+ 
  gi|313122405|ref|YP_004038292.1| 354 DALPGLEMETIMGTNQFRDCDHQAMNPVWP 383
                                       ***************************985 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.2   2.5e-37   1.1e-33       4     335 ..      54     384 ..      51     398 .. 0.91

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 2.5e-37
                      Peripla_BP_5   4 GvLhSlsGtmaisekslkdaallaieeinaagGvlgrkieavvvdpasdwelfaekaeklieedkvevvfGcwtSas 80 
                                       Gv+  ++G ++   + + ++a+lai ++n+++  l  +ie v +d ++d+++ ++ka++l+e+d+ ++++G++ S++
  gi|313122405|ref|YP_004038292.1|  54 GVVSPMTGPYGGLAEGQRNGAKLAIRHVNESDD-LDVEIEGVYEDTEADPSTGSRKAQSLVEQDGASFLMGAISSST 129
                                       788889**************************7.6789*********************************986655 PP

                      Peripla_BP_5  81 RkavlpvveelnalLfYp....vqYEGeEssknviYtGaapnqqaipavdyllselgakrvflvGsdyvypre.tnr 152
                                           l+ + +++++++ p    v   G  + + v+ +     q a  + d+ +++lg ++v +  +dy y  + +nr
  gi|313122405|ref|YP_004038292.1| 130 -ALALNEFAKEQEVIYNPggaaVPITGSNCNEWVFRAETNTAQMAEAVSDFTAENLG-TKVWFHIADYAYGESvMNR 204
                                       .566777888889999875555899********************************.55555559****9862688 PP

                      Peripla_BP_5 153 ilkallkakggevvgeeYlplgssdvqkivakikkakpdvvlstinGdsnvafykelkeagikaekipvvslsvaee 229
                                       + k + + + ++vvg +  ++gss++++ +++i++  ++vv+  + G   ++f k+ +++g+k +++  +s +++ +
  gi|313122405|ref|YP_004038292.1| 205 VEKRMKQGRSIDVVGRSRSKFGSSNFNSYISQIANSDAEVVVLGMTGGDLINFVKQAASQGLK-DNVNLMSPTMTFS 280
                                       88888888899***************************************************8.5788999999999 PP

                      Peripla_BP_5 230 elaaidaealvGhlaawnYfqsvdtpenkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekvrea 306
                                        +++   +a+ G +  + Y   +dt +n++fv+++++++++    ++ +  ay+++++ a+ +++ags+d+++v++a
  gi|313122405|ref|YP_004038292.1| 281 VVRNALGKAAYGTYGGVRYVPELDTGTNQSFVEAYQNEYDT--PPDNFARVAYLSIRMTAKGIAEAGSSDPAAVKDA 355
                                       99999999*****************************9965..78999***************************** PP

                      Peripla_BP_5 307 llgqelkapeGevkidpenhhlsktvrig 335
                                       l g e+++  G+ +++   h ++ +v  g
  gi|313122405|ref|YP_004038292.1| 356 LPGLEMETIMGTNQFRDCDHQAMNPVWPG 384
                                       ************99999888887777655 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   1.2e-18   5.2e-15       4     301 ..      72     371 ..      70     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.2e-18
                                       HHHHHHHHHHHT-TTSSTTEEEEEEEEE-TT-HHHHHHHHHHHCCCC.EEEEEE-SSHHHHHHHHHHHCCTT-EEEE CS
                      ANF_receptor   4 eAmklAveeinsdpnllpgiklgyeiidtccdfslaleaaldflkgk.vvaviGpssssvsdavaslanlfkiPvis 79 
                                       + +klA++++n++ +l  +++++   +dt+ d+s++ ++a+++++++ +  + G+ sss++ a+ ++a++ +++   
  gi|313122405|ref|YP_004038292.1|  72 NGAKLAIRHVNESDDL--DVEIEGVYEDTEADPSTGSRKAQSLVEQDgASFLMGAISSSTALALNEFAKEQEVIYNP 146
                                       5789*******99543..36777777*******************97699999********************9997 PP

                                       SS---GG.GG-TTTTTTEEESS--CHHHHHHHHHHHH.HTT--EEEEEEESSHHHHHHHHHHHHHHHHTT.-EEEEE CS
                      ANF_receptor  80 ygstspe.lsdknryptflrtvpsdtsqaqAivdilk.hfgWkkvaliysdddygesglqaleeeleerg.icvalk 153
                                        g+  p   s+ n++   +r   +++++a+A++d    ++g k    i++   yges+++ +e+++++ + i v+ +
  gi|313122405|ref|YP_004038292.1| 147 GGAAVPItGSNCNEWV--FRAETNTAQMAEAVSDFTAeNLGTKVWFHIADYA-YGESVMNRVEKRMKQGRsIDVVGR 220
                                       7776666588888877..***************9766499999889999999.***********6665444999988 PP

                                       EEEST.CHHHCHHHHHHHHHHTTT--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHH CS
                      ANF_receptor 154 ekipe.ssnddevvrkllkeikskarvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgle 229
                                        + +  ssn+++ ++++    +s+a v+vl + + d+ +++k+a ++gl ++  + + s ++t s v +   + g  
  gi|313122405|ref|YP_004038292.1| 221 SRSKFgSSNFNSYISQIA---NSDAEVVVLGMTGGDLINFVKQAASQGLKDN-VNLM-SPTMTFSVVRN---ALGKA 289
                                       886646777778888886...78****************************5.6666.55544444444...34899 PP

                                       HHTT-EEEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHH......... CS
                      ANF_receptor 230 aaegvlgfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkk......... 297
                                       a++   g+r+++   +++ + +          + y+ne  ++++ +a   Y ++ + a+++ ++++++         
  gi|313122405|ref|YP_004038292.1| 290 AYGTYGGVRYVPELDTGTNQSF---------VEAYQNEYDTPPDNFARVAYLSIRMTAKGIAEAGSSDpaavkdalp 357
                                       9****************99999.........7889999999999999999***************888666666666 PP

                                       ..........SSSH CS
                      ANF_receptor 298 ..........kpgr 301
                                                 +++r
  gi|313122405|ref|YP_004038292.1| 358 glemetimgtNQFR 371
                                       55555555443333 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.051      31     106 ..     171     251 ..     146     279 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                   Glyco_tran_WecB  31 dlieelleraeee.glrvfllGgkpevlekaaerlrekyp...glriagthdgy.keeeeeaiieainaskpdlllv 102
                                       +++e++ +  +e+ g +v++  ++  + e++ +r++++++    ++++g++  +  +++ +++i++i++s+++++++
  gi|313122405|ref|YP_004038292.1| 171 QMAEAVSDFTAENlGTKVWFHIADYAYGESVMNRVEKRMKqgrSIDVVGRSRSKfGSSNFNSYISQIANSDAEVVVL 247
                                       55555555555555677777666655555555555555433339*****999977689******************* PP

                   Glyco_tran_WecB 103 glGa 106
                                       g++ 
  gi|313122405|ref|YP_004038292.1| 248 GMTG 251
                                       **86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2742.04
//
Query:       gi|313122406|ref|YP_004038293.1|  [L=155]
Description: acyl dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-19   69.0   0.1    3.2e-19   68.7   0.1    1.1  1  MaoC_dehydratas  MaoC like domain
     0.0044   17.2   0.3      0.014   15.6   0.3    1.7  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.1   3.5e-23   3.2e-19       7     108 ..      16     118 ..      12     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 3.5e-23
                                       TSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTT..EGGGEEEE CS
                   MaoC_dehydratas   7 gekvetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdn..vvarvgei 81 
                                       g+++e    +tvtead ++  ++sgD+  +H+++e+A+ ++fg++IahG +t+  +++ v++ +  +   +a++g++
  gi|313122406|ref|YP_004038293.1|  16 GKEFES-VGRTVTEADFMMHSALSGDWTELHTNKEYAEDTQFGQRIAHGPMTFVQSTGFVYRSGIVErtAIAFLGMN 91 
                                       666666.89*****************************************************999999999****** PP

                                       EEEE-S--BTTCEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  82 kvrFtkpVlpgdtlkvelevvgkrdvr 108
                                        +  ++pV++gdtl  +++v++ +dv 
  gi|313122406|ref|YP_004038293.1|  92 YMDLPNPVFIGDTLSQTMVVSERKDVG 118
                                       *********************977765 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.5e-06     0.014       4     130 ..      16     141 ..      15     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
                   MaoC_dehydrat_N   4 Gaefepvkaevereavrefakavgetnpayldeeaaraagyrslia..Pptflivlatkap.ellealgidlsrllh 77 
                                       G+efe v  +v++ +   +    g+  ++++++e+a+++ +++ ia  P+tf+  +++    ++ e   i       
  gi|313122406|ref|YP_004038293.1|  16 GKEFESVGRTVTEADFMMHSALSGDWTELHTNKEYAEDTQFGQRIAhgPMTFVQSTGFVYRsGIVERTAIA----FL 88 
                                       89999999*******************************88777775599999888884411344444443....34 PP

                   MaoC_dehydrat_N  78 geqefeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepva 130
                                       g + + + +p+  GD+l+ +  + + +d  + + + ++v + ++t q+G +v 
  gi|313122406|ref|YP_004038293.1|  89 GMNYMDLPNPVFIGDTLSQTMVVSERKDVGSRDDAGLVVLDVEMTKQDGTVVL 141
                                       5699999*********************966999999*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1047.24
//
Query:       gi|313122407|ref|YP_004038294.1|  [L=135]
Description: hypothetical protein Hbor_36410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-13   49.0   1.5    1.1e-12   48.1   1.5    1.5  1  4HBT      Thioesterase superfamily
      1e-07   32.2   0.0    1.3e-07   31.8   0.0    1.1  1  DUF4442   Domain of unknown function (DUF4442)
     0.0044   17.3   0.6     0.0056   17.0   0.6    1.1  1  4HBT_3    Thioesterase-like superfamily
     0.0097   15.2   0.1      0.016   14.5   0.1    1.3  1  PS-DH     Polyketide synthase dehydratase


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   1.5   2.5e-16   1.1e-12       1      77 [.      50     123 ..      50     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.5e-16
                                       TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                       +G+ hgG++++l+D a +aa +s+g+   +++++e +i +l +v +g++l++ a+ ++ g+++a +ev v+d++g  
  gi|313122407|ref|YP_004038294.1|  50 HGTPHGGAVYTLADAAFAAASNSHGD---AAFALETNISYLDAVEVGETLRAVAEETHRGGRTAAYEVVVTDGGGDR 123
                                       6889*********************9...7******************************************99876 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0     3e-11   1.3e-07      14     103 ..      19     105 ..      13     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3e-11
                                       GGGGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S---S CS
                           DUF4442  14 PYfgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlakatg 90 
                                       P+ gtvg+  ++++ g+ae +l+   ++ N  gt H++A+++la++a+ +    + +d +       +++Yl   + 
  gi|313122407|ref|YP_004038294.1|  19 PFCGTVGVELADVSGGYAETTLTVGDEHLNFHGTPHGGAVYTLADAAFAAA-SNSHGDAAFA--LETNISYLDAVEV 92 
                                       9*********************************************99654.3444444444..4556788877554 PP

                                       -EEEEEE-TTS-T CS
                           DUF4442  91 dltavaelepedv 103
                                       + t +a++e+  +
  gi|313122407|ref|YP_004038294.1|  93 GETLRAVAEETHR 105
                                       4444444444333 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.6   1.3e-06    0.0056       8      77 ..      50     125 ..      44     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
                                       TTC.-HHHHHHHHHHHHHHT....-S.SS.EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEET.TEEEE CS
                            4HBT_3   8 ggagyGGyvlAlalraaqrtv...pdprl.hslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqg.grpif 77 
                                        g+++GG+v  la +a  ++     d+ +     +++l ++++g  ++  +e++ +G +++ ++v ++ g g  i+
  gi|313122407|ref|YP_004038294.1|  50 HGTPHGGAVYTLADAAFAAASnshGDAAFaLETNISYLDAVEVGeTLRAVAEETHRGGRTAAYEVVVTDGgGDRIA 125
                                       5668****99998777666655555555788************************************997344444 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.5e-06     0.016     209     285 ..      62     129 ..      56     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-06
                                       HHHHHHHG..GG----------EEEEEEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEES CS
                             PS-DH 209 lDaalQllaaalsaeaekadaaylPvaierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeieg 285
                                        Daa+ +      ++++++ a++l + i+ l+      + ge+l+++a+ + +g+r+++++++++d  G  +a+++g
  gi|313122407|ref|YP_004038294.1|  62 ADAAFAAA-----SNSHGDAAFALETNISYLDAV----EVGETLRAVAEETHRGGRTAAYEVVVTDGGGDRIATFRG 129
                                       56666655.....566777777788888888887....4899*******************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 801.18
//
Query:       gi|313122408|ref|YP_004038295.1|  [L=429]
Description: phenylacetate-CoA ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-22   79.5   0.0    4.3e-22   78.2   0.0    1.7  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
      5e-18   64.9   0.2    1.5e-17   63.4   0.2    1.7  1  AMP-binding      AMP-binding enzyme
     0.0025   16.9   0.0        0.1   11.6   0.0    2.1  2  LuxE             Acyl-protein synthetase, LuxE


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   7.3e-26   4.3e-22       1      96 []     333     427 ..     333     427 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 7.3e-26
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--.EEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsv.kvel 76 
                                       Gvnv+Ps+ie+v+ e++ev+p+Y+i ++r+++lD+le++vE++egf     +++++++ki ++l ++l++++ +++l
  gi|313122408|ref|YP_004038295.1| 333 GVNVYPSEIESVVLEFDEVAPHYRIDLRRDDNLDTLELTVELEEGFDG---STDDVREKILNRLSNVLSFTPdELTL 406
                                       9********************************************944...699*****************868*** PP

                                       E-TT-S-----.----EEE-S CS
                   AMP-binding_C_2  77 vepgtlprseg.KakrviDkR 96 
                                       ve g ++r+e  K +rv+D+R
  gi|313122408|ref|YP_004038295.1| 407 VESGGIARTEVgKVQRVYDHR 427
                                       *********966*******99 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.2   2.4e-21   1.5e-17     129     370 ..      57     284 ..      15     332 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.4e-21
                                       CS-HCCHCCCHCCCCSCTT.S-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHH.HHHHHHHH.HHHCSCCTTT CS
                       AMP-binding 129 dellkeeelkeeeeseeka.ekpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnl.vanvaslk.letrfklked 202
                                       ++l+++      ++++  + + p+e  +++ dd++ i  +SGTTGkPK V ++++ l v++  +++ +    +l++d
  gi|313122408|ref|YP_004038295.1|  57 QKLPFT------TKEDFRDnY-PTEMFAVDMDDVVRIHASSGTTGKPKIVSYTQDDLdVWS-DAIArCLVAAGLDSD 125
                                       222222......222222212.3345579*************************9998665.66655555577889* PP

                                       -EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHH CS
                       AMP-binding 203 dvvlsilplahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaak 277
                                       dvv     +   +g      ++   Gatv+ + + ++ ++    +e++++l+   +a++P+ + +l+e + +    +
  gi|313122408|ref|YP_004038295.1| 126 DVVQNAYGYGLFTGGLGLHQGVEELGATVIPIGGGQTqRQ----VEMLADLESDALACTPSYALYLAEtAAEMG--V 196
                                       ***9998888888875666677788999999998888444....89********************99554444..5 PP

                                       HHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE- CS
                       AMP-binding 278 kakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplp..gvevkivD 352
                                       + +dl+ lrlv++g+ep+ + + +++++++g + +++YGl+E  g  + +++ e+       G  ++      ++vD
  gi|313122408|ref|YP_004038295.1| 197 DIRDLP-LRLVIFGAEPCTEPMREEIEERLGVTGVDIYGLSEIVGPGVSIECLEQ------DGLHVWedRFYPEVVD 266
                                       666888.*************************************99984443333......2666662255678*** PP

                                       TTTSCBEETTSEEEEEEE CS
                       AMP-binding 353 eetgepvpdgeeGellvr 370
                                       ++tgepv++geeGel++ 
  gi|313122408|ref|YP_004038295.1| 267 PQTGEPVEEGEEGELVLT 284
                                       ***************975 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.0   0.0     0.007        42      20     107 ..      10     100 ..       4     121 .. 0.81
   2 !   11.6   0.0   1.7e-05       0.1     267     359 ..     230     326 ..     224     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.007
                              LuxE  20 seeekeklrkkflldelvnhykhneeyrkycqknkvddlvtegevddiPviPvsv...fk.aigtkllsvsedeika 92 
                                       s ee   l  + l ++++n y+    yr+      + +  +e  +dd+  +P      f+    t + +v+ d++  
  gi|313122408|ref|YP_004038295.1|  10 SREELRTLQTERLQEAVRNAYESVPFYREKLEEMGLKPGDIE-RIDDVQKLPFTTkedFRdNYPTEMFAVDMDDVVR 85 
                                       778888899999999*****************9999999999.8999999997652225424578999999999999 PP

                              LuxE  93 klqssatsGlkstvl 107
                                          ss+t+G +  v 
  gi|313122408|ref|YP_004038295.1|  86 IHASSGTTGKPKIVS 100
                                       999999999887765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.7e-05
                              LuxE 267 vdiygfteqvelntpdfkdelkrkrvysdviir...deetlkvvgdGkvGlleyvdalstsyPafvvltddlGviee 340
                                       vdiyg++e v+   +    e    +v  d +     d++t ++v +G  G l     +  + P     t dl  ++ 
  gi|313122408|ref|YP_004038295.1| 230 VDIYGLSEIVGPGVSIECLEQDGLHVWEDRFYPevvDPQTGEPVEEGEEGELVLTTLSKDALPVLRYRTGDLTTLNY 306
                                       799999999987654433344444444443322233***************************************** PP

                              LuxE 341 slcegqkaGklvk.vlrrvk 359
                                         c+++++ ++++ + +r++
  gi|313122408|ref|YP_004038295.1| 307 DTCDCGRTAVRMDnITGRAD 326
                                       **********9963667876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2684.38
//
Query:       gi|313122409|ref|YP_004038296.1|  [L=294]
Description: 3-hydroxyacyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-64  215.5   2.3    7.4e-64  214.9   2.3    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    3.2e-32  111.0   0.3    1.1e-31  109.3   0.1    2.0  2  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
    4.7e-06   26.7   0.1    8.5e-06   25.8   0.1    1.4  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    3.7e-05   23.4   0.2    5.9e-05   22.7   0.2    1.3  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00013   22.2   3.6    0.00033   20.8   3.6    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00068   20.2   2.2      0.034   14.7   2.2    2.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.02   14.9   1.1      0.028   14.4   0.4    1.6  2  HisG             ATP phosphoribosyltransferase
      0.029   13.6   0.5       0.11   11.8   1.2    1.6  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
       0.13   12.5   1.1        0.2   11.9   0.2    1.7  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.21   11.9   1.5         19    5.6   0.0    2.6  2  DUF3618          Protein of unknown function (DUF3618)


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.9   2.3   4.1e-67   7.4e-64       1     179 [.       2     181 ..       2     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.9 bits;  conditional E-value: 4.1e-67
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77 
                                       +vav+GaGtmG+gia+v a ag++V++ di++e ++++l++ie++l+  ve+ k++e+e++a+l+r++ tt+l +av
  gi|313122409|ref|YP_004038296.1|   2 HVAVLGAGTMGHGIAQVSAMAGHDVTMRDIESEYVQNGLDAIEENLRGGVERDKVTEAEMAATLDRLTGTTSLGDAV 78 
                                       69*************************************************************************** PP

                                       .C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-T CS
                           3HCDH_N  78 .dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrge 153
                                        dadlv+Eav+E++elK+++++e+e  a++da+la+nTSsls++e+ +al++per ig+HFfnP+++m LvEvv +e
  gi|313122409|ref|YP_004038296.1|  79 aDADLVVEAVPEDMELKQETMREVEGFADDDAVLATNTSSLSVTEILSALEHPERGIGMHFFNPVHIMALVEVVVAE 155
                                       ***************************************************************************** PP

                                       T--HHHHHHHHHHHHHTT-EEEEECS CS
                           3HCDH_N 154 kTseetvatvvelakkigktpvvvkd 179
                                       +T++ t++ ++e++ +i+kt+v+v+d
  gi|313122409|ref|YP_004038296.1| 156 QTDDGTLDLAHEFVDDIDKTAVEVRD 181
                                       ************************98 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.9   3.4e+03      41      59 ..      13      31 ..       4      66 .. 0.69
   2 !  109.3   0.1   6.3e-35   1.1e-31       1      97 []     184     279 ..     184     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.9
                                      SCHHHHHHHHHHHHHHHHH CS
                             3HCDH 41 mGpfelldlvgldvakkil 59
                                       G+ +++ ++g+dv  + +
  gi|313122409|ref|YP_004038296.1| 13 HGIAQVSAMAGHDVTMRDI 31
                                      5777777777777754433 PP

  == domain 2  score: 109.3 bits;  conditional E-value: 6.3e-35
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+ +R+ ++l  ea+r+v+egvasped+Daam+lg+++pmGp el d+vgldv + ile+l+eelger ++p+++l
  gi|313122409|ref|YP_004038296.1| 184 GFASSRLGVALGVEAMRMVQEGVASPEDVDAAMELGYNHPMGPVELGDVVGLDVRLGILEYLREELGER-FRPPQIL 259
                                       9*******************************************************************9.999**** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       ++ v+ag+lg+ktg+gfy +
  gi|313122409|ref|YP_004038296.1| 260 KRKVRAGKLGKKTGEGFYVW 279
                                       ******************75 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   4.7e-09   8.5e-06       2      99 ..       3     112 ..       2     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.7e-09
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-H....HHHHHHHHH......SSBTTTBTT----TTEEEES-HHHHHT CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree....elieeinee......henvkyLpgiklpenlvattdlaealk 68 
                                       +avlGaG  G  +A+v a +gh+v++   e+    + +++i+e+      +  v+  +  +  + l+ tt l +a++
  gi|313122409|ref|YP_004038296.1|   3 VAVLGAGTMGHGIAQVSAMAGHDVTMRDIESeyvqNGLDAIEENlrggveRDKVTEAEMAATLDRLTGTTSLGDAVA 79 
                                       9**************************99998888444555544111111444555555666677899********* PP

                                       T--EEEE---HHH..HHHHHHHHCCC--TT-EE CS
                    NAD_Gly3P_dh_N  69 gadiivlvvPsqa..lrevlkklkgllkkkail 99 
                                       +ad++v +vP  +   +e++++++g+ +++a+l
  gi|313122409|ref|YP_004038296.1|  80 DADLVVEAVPEDMelKQETMREVEGFADDDAVL 112
                                       **********86421566777777776666655 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   3.3e-08   5.9e-05       1      90 [.       1      94 [.       1     118 [. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.3e-08
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHH....HHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekv....dklnsgkipiyepgLeelvkkavesgrlsfttdvekave 75
                                      m+++v+G+G +G   a v a +gh+v++ Di++e v    d+++++    +e++  +  + a++ +rl++tt++  av+
  gi|313122409|ref|YP_004038296.1|  1 MHVAVLGAGTMGHGIAQVSAMAGHDVTMRDIESEYVqnglDAIEENLRGGVERDKVTEAEMAATLDRLTGTTSLGDAVA 79
                                      789*****************************9998222234666666667776666666666679************* PP

                                      C-SEEEE-----B-T CS
                    UDPG_MGDP_dh_N 76 eadvifiaVgTPskk 90
                                      +ad+++ aV+  ++ 
  gi|313122409|ref|YP_004038296.1| 80 DADLVVEAVPEDMEL 94
                                      ******999865555 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   3.6   1.9e-07   0.00033       2     100 ..       3     125 ..       2     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.9e-07
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelva 54 
                                       ++++G G+MG+ +a+  + ag++v++ + ++e v++ +++                         +++++s+ ++va
  gi|313122409|ref|YP_004038296.1|   3 VAVLGAGTMGHGIAQVSAMAGHDVTMRDIESEYVQNGLDAIeenlrggverdkvteaemaatldrLTGTTSLGDAVA 79 
                                       89*****************************99998888755679999***************************** PP

                                       HCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHH CS
                     NAD_binding_2  55 sldvvitmvkagkavdeviegllealkkgdilidgstsspedtrel 100
                                       ++d+v+  v+++ + ++ + + +e ++ +d ++ + tss + t+ l
  gi|313122409|ref|YP_004038296.1|  80 DADLVVEAVPEDMELKQETMREVEGFADDDAVLATNTSSLSVTEIL 125
                                       **************99888887888888888888888887777654 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.2   1.9e-05     0.034       2      70 ..       3      89 ..       2     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......................-EEECECHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......................vkvtavdnee 57
                                      ++++GaG mg+++a+  + ag   h+++   + + e ++   ++++                        + t+ +  +
  gi|313122409|ref|YP_004038296.1|  3 VAVLGAGTMGHGIAQVSAMAG---HDVT-MRDIESEYVQNGLDAIEenlrggverdkvteaemaatldrLTGTT-SLGD 76
                                      89*******************...9999.435555555555555555555777777777777777776433333.6777 PP

                                      HHHH-SEEEE-S- CS
                     F420_oxidored 58 aaeeadvvvlavk 70
                                      a+++ad vv av+
  gi|313122409|ref|YP_004038296.1| 77 AVADADLVVEAVP 89
                                      7777777777776 PP

>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   1.6e-05     0.028      85     156 ..      46     126 ..       9     130 .. 0.78
   2 ?   -3.2   0.0         4   7.1e+03      22      41 ..     200     220 ..     191     222 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                       T.............T-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHSH CS
                              HisG  85 k.............glkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkkk 148
                                       +             ++ +++ +l+G + +  a+  aD++v+ v     L+++ ++++e   +  avL +n++sl+  
  gi|313122409|ref|YP_004038296.1|  46 NlrggverdkvteaEMAATLDRLTGTTSLGDAVADADLVVEAVPEDMELKQETMREVEGFADDDAVLATNTSSLS-- 120
                                       455555555555558899999***********************************************9999887.. PP

                                       HHHHHHHH CS
                              HisG 149 ekieelle 156
                                         ++e+l+
  gi|313122409|ref|YP_004038296.1| 121 --VTEILS 126
                                       ..444444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4
                                       HHHHH.CT...TEEEEEEESE CS
                              HisG  22 DvveE.skeeeeveelldLgf 41 
                                        +v+E   + e+v+  ++Lg+
  gi|313122409|ref|YP_004038296.1| 200 RMVQEgVASPEDVDAAMELGY 220
                                       567775245668888888887 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.2     6e-05      0.11      30      98 ..       2      87 ..       1      91 [. 0.75
   2 ?   -3.6   0.0         3   5.4e+03      53      73 ..     231     252 ..     229     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE.................HCHHHHHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev.................lksqeellaeavk 90
                                      +v v+G+G+ G   +++++  g +Vt+ D++++  ++  + ++++ ++                  +     +l +av+
  gi|313122409|ref|YP_004038296.1|  2 HVAVLGAGTMGHGIAQVSAMAGHDVTMRDIESEYVQNGLDaIEEN-LRGgverdkvteaemaatldRLTGTTSLGDAVA 79
                                      699****************************99877654425554.555566677777777777665566666777777 PP

                                      H-SEEEE- CS
                       AlaDh_PNT_C 91 eadvvigt 98
                                      +ad+v+ +
  gi|313122409|ref|YP_004038296.1| 80 DADLVVEA 87
                                      77777766 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3
                                       EEEEEESSHHHHHHHHH.TTTC CS
                       AlaDh_PNT_C  53 kVtvlDvrparleqles.lgak 73 
                                       +V+ lDvr   le+l++ lg++
  gi|313122409|ref|YP_004038296.1| 231 DVVGLDVRLGILEYLREeLGER 252
                                       68899***99999999878877 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00011       0.2       1      71 [.       3      76 ..       3      93 .. 0.79
   2 ?   -3.0   0.0       4.5     8e+03      26      43 ..     150     167 ..     145     183 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHHTTS...S CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaallkeg...d 71
                                      v ++GaG +G+++a++ a  ++    +t  d + e +++ ++++   l+  +e  +++ ++ +a+L++l   +   d
  gi|313122409|ref|YP_004038296.1|  3 VAVLGAGTMGHGIAQVSAMAGHD---VTMRDIESEYVQNGLDAIeenLRGGVERDKVTEAEMAATLDRLTGTTslgD 76
                                      679****************9985...88888877777777666666689999***********99999876655553 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                                       EEEEEESSHHHHHHHHCH CS
                   Sacchrp_dh_NADP  26 eitvadrskeklealaak 43 
                                       e++va++++++   la++
  gi|313122409|ref|YP_004038296.1| 150 EVVVAEQTDDGTLDLAHE 167
                                       788888888886665543 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.4      0.02        36      16      28 ..      59      71 ..      56      81 .. 0.85
   2 ?    5.6   0.0     0.011        19      23      40 ..     247     264 ..     246     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.02
                           DUF3618 16 aeLaeTvdeLaar 28
                                      ae+a+T+d L+  
  gi|313122409|ref|YP_004038296.1| 59 AEMAATLDRLTGT 71
                                      89********975 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                           DUF3618  23 deLaaradPkrladraka 40 
                                       +eL++r +P+++ +r++ 
  gi|313122409|ref|YP_004038296.1| 247 EELGERFRPPQILKRKVR 264
                                       79*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2040.57
//
Query:       gi|313122410|ref|YP_004038297.1|  [L=267]
Description: short chain enoyl-CoA hydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-65  219.2   0.1    6.2e-65  219.0   0.1    1.0  1  ECH_1         Enoyl-CoA hydratase/isomerase
    4.3e-36  125.1   0.1    1.8e-30  106.6   0.0    2.0  2  ECH_2         Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.062   12.9   0.3       0.43   10.1   0.1    2.0  2  NTP_transf_5  Uncharacterised nucleotidyltransferase
       0.12   11.7   0.1       0.16   11.3   0.1    1.1  1  PrgH          Type III secretion system protein PrgH-EprH (Pr


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   0.1   1.4e-68   6.2e-65       4     249 ..      20     265 ..      17     267 .] 0.94

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 1.4e-68
                                       TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE..BTSEEEEEB-HHHHHHHHCHHHHHHHCCHH CS
                             ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtG..gdkaFaaGadlkemaeeekakqallkeevl 78 
                                       +gv  +++ rP+a Nal+a+l++El  +l  +e++  +r+vvLtG    kaF aGad++e+ e+ +  ++   ++  
  gi|313122410|ref|YP_004038297.1|  20 EGVTTVTMTRPDARNALNAQLRAELKRVLDAVEES-DARVVVLTGadEAKAFVAGADVTELRERDM-LAQREASKRP 94 
                                       79********************************9.9********544579************986.3333444455 PP

                                       HHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHH CS
                             ECH_1  79 elwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilll 155
                                         ++ + ++  pvia +nG+a+gGG+ela acD++ia + a+ g++e++lG++pg ggtq+lar vG+ +A++++l 
  gi|313122410|ref|YP_004038297.1|  95 RVYEYVDDLRQPVIARLNGHALGGGCELAQACDVRIAHERAKLGQPEINLGIMPGGGGTQRLARLVGEGQAMRLVLS 171
                                       67778888999****************************************************************** PP

                                       T-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHH CS
                             ECH_1 156 gkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskdd 232
                                       g+ isa+ea ++Glvd+v  +e++ e   ela  +aeks  al+ +k+a++a++++ l++++e ea+lf ++f++ d
  gi|313122410|ref|YP_004038297.1| 172 GELISAEEAYDIGLVDEVHDDETFDERVYELAGSMAEKSGVALEYAKKAVKAASRMDLEQGIEYEAELFAQLFATGD 248
                                       ***************************************************************************** PP

                                       HHHHHHHHHTCSH---- CS
                             ECH_1 233 ikeGlqaflEkrkpefe 249
                                         eG++af E r+pe+ 
  gi|313122410|ref|YP_004038297.1| 249 KDEGIDAFFEDRDPEWP 265
                                       99**************5 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0     4e-34   1.8e-30       2     183 ..      23     201 ..      22     205 .. 0.91
   2 !   18.0   0.0   3.5e-07    0.0016     250     317 ..     200     264 ..     192     267 .] 0.90

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 4e-34
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk 78 
                                       +++t+ rp+a NaL+ ++  +lk+ l+++e++d+  +v+  +++ kaf AG Dv +l+e     ++e     ++  +
  gi|313122410|ref|YP_004038297.1|  23 TTVTMTRPDARNALNAQLRAELKRVLDAVEESDARVVVLTGADEAKAFVAGADVTELRERDMLAQRE----ASKRPR 95 
                                       689**************************98886655555556789************998887766....478889 PP

                                       HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH- CS
                             ECH_2  79 lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTG 154
                                       +  ++ ++++pv+a ++G ++GgG+ l++ + +r++ er+++  PE+++G++P  Gg+  L+rl g   ++ l l+G
  gi|313122410|ref|YP_004038297.1|  96 VYEYVDDLRQPVIARLNGHALGGGCELAQACDVRIAHERAKLGQPEINLGIMPGGGGTQRLARLVGeGQAMRLVLSG 172
                                       9999***********************************************************9775789******* PP

                                       --B-HHHHHHTTS--EE--GGGHHHHHHH CS
                             ECH_2 155 arlkgadalaaglathyvpseklealeea 183
                                       + +++++a+ +gl + + ++e +++   +
  gi|313122410|ref|YP_004038297.1| 173 ELISAEEAYDIGLVDEVHDDETFDERVYE 201
                                       *****************999998876555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.5e-07
                                       HHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------- CS
                             ECH_2 250 kktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkW 317
                                        + + +++++s ++l+ + ++++ ++++ +l++ ++ E +l ++l+a++D  eG+ a + d+d  P+W
  gi|313122410|ref|YP_004038297.1| 200 YELAGSMAEKSGVALEYAKKAVKAASRM-DLEQGIEYEAELFAQLFATGDKDEGIDAFFEDRD--PEW 264
                                       5677899*********************.5****************************98876..988 PP

>> NTP_transf_5  Uncharacterised nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   9.6e-05      0.43      52     104 ..      36      89 ..      29      96 .. 0.82
   2 ?    0.3   0.0     0.099   4.4e+02     189     215 ..     108     134 ..     101     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.6e-05
                      NTP_transf_5  52 rnllllaeleellalleeegipvllLKGpalaq.lYpdpalRemgDiDllvkre 104
                                        n++l+ael+++l++ ee + +v++L G+  a+ +   +   e +  D+l +re
  gi|313122410|ref|YP_004038297.1|  36 LNAQLRAELKRVLDAVEESDARVVVLTGADEAKaFVAGADVTELRERDMLAQRE 89 
                                       5899*************************9997577777777777777777666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.099
                      NTP_transf_5 189 alHlakhfwnrglgLrwlvDiaallrk 215
                                       +++l  h++ +g+ L + +D++   ++
  gi|313122410|ref|YP_004038297.1| 108 IARLNGHALGGGCELAQACDVRIAHER 134
                                       577888999************987666 PP

>> PrgH  Type III secretion system protein PrgH-EprH (PrgH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   3.5e-05      0.16     155     230 ..      38     114 ..      19     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
                                       XXXXXXHHHHHHHSGGGTTTEEEEEXTTSX.EEEEESSHHHHHHHHHHHHHTTCTTTEEEEE.HHHHHHHHHHHHHH CS
                              PrgH 155 asakeevaelaavldddkarvelLpgrdgk.lYvlAktqrdaewarqallraelakevevvs.lddererveqwLde 229
                                       a+ ++e++ + ++++++ arv++L+g d+   +v+ ++  ++  +r +l+++e+ k+++v + +dd r+ v ++L+ 
  gi|313122410|ref|YP_004038297.1|  38 AQLRAELKRVLDAVEESDARVVVLTGADEAkAFVAGADVTELR-ERDMLAQREASKRPRVYEyVDDLRQPVIARLNG 113
                                       34478999999999**************985777777777765.788888888888888875379999999999886 PP

                                       H CS
                              PrgH 230 e 230
                                       +
  gi|313122410|ref|YP_004038297.1| 114 H 114
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1794.83
//
Query:       gi|313122411|ref|YP_004038298.1|  [L=71]
Description: hypothetical protein Hbor_36450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       150  (0.00836633); expected 358.6 (0.02)
Passed bias filter:                      109  (0.00607954); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 539.00
//
Query:       gi|313122412|ref|YP_004038299.1|  [L=103]
Description: hypothetical protein Hbor_36460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-16   59.0   0.5    7.9e-15   55.3   0.5    2.0  1  MmlI         Methylmuconolactone methyl-isomerase
    8.5e-14   52.5   1.9    2.1e-13   51.2   1.9    1.6  1  EthD         EthD domain
  ------ inclusion threshold ------
      0.027   15.1   0.1      0.038   14.6   0.1    1.3  1  Dabb         Stress responsive A/B Barrel Domain
       0.11   12.2   0.1       0.14   11.9   0.1    1.2  1  Ald_deCOase  Long-chain fatty aldehyde decarbonylase


Domain annotation for each model (and alignments):
>> MmlI  Methylmuconolactone methyl-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.5   1.8e-18   7.9e-15       6      99 ..       3      85 ..       1     102 [. 0.87

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.8e-18
                              MmlI  6 gllsrredlsheqflahwrevhaplvhavtGlrryqqnrvvderftqfvPvveydgypvdgivelWfedlasleksfas 84
                                      + l+r++d +he+f+++w+  h +++ +++Gl++y           + vP  + +  ++dgi el+fed+a+l ++f s
  gi|313122412|ref|YP_004038299.1|  3 NHLVRKDDYTHEEFVERWLGEHTDIAKEMPGLKKYT----------TSVPT-DPERAEYDGIIELYFEDMAALSAAFES 70
                                      5689******************************96..........56777.566789********************* PP

                              MmlI 85 paakllaahGktfia 99
                                      +a +++ a+ + fi 
  gi|313122412|ref|YP_004038299.1| 71 EAGERTNADAAEFID 85
                                      *************96 PP

>> EthD  EthD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   1.9   4.7e-17   2.1e-13       2      93 ..      10      86 ..       9      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 4.7e-17
                                      -S-HHHHHHHHHHTHHHHHCTSTT............--EEEEEEEEEBTTC--SEEEEEEEEESSHHHHHHHHCSHHHH CS
                              EthD  2 glspeeFrdyweevHaplvkdllggirryvlratktrpateagvalagpgsdadyDgiaelwfdsleaflaafadpeya 80
                                      + ++eeF ++w ++H+  +k+ +g  ++y+                +  ++ a+yDgi el+f++++a+ aaf++++++
  gi|313122412|ref|YP_004038299.1| 10 DYTHEEFVERWLGEHTDIAKEMPG-LKKYT-------------TSVPTDPERAEYDGIIELYFEDMAALSAAFESEAGE 74
                                      569*********************.44444.............446789999*************************** PP

                                      H.HHHHHHHHCGG CS
                              EthD 81 avlaaDeenFaDk 93
                                      +  +aD ++F+D+
  gi|313122412|ref|YP_004038299.1| 75 R-TNADAAEFIDM 86
                                      9.8*********7 PP

>> Dabb  Stress responsive A/B Barrel Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   8.4e-06     0.038      11      75 ..      10      72 ..       3      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-06
                                      STTTHHHHHHHHHHHHHHHHGSTTTSEEEEEEESSSSSTSTT-SEEEEEEESSHHHHHHHHTSHH CS
                              Dabb 11 devteeekaevlealeaLkdkipgiksievgrnvspeklakgydvvliseFeseedlkaYlehpa 75
                                      d ++ee +++ l + + + +++pg+k+ +++    pe+    yd +++ +Fe++++l a  e  a
  gi|313122412|ref|YP_004038299.1| 10 DYTHEEFVERWLGEHTDIAKEMPGLKKYTTSVPTDPER--AEYDGIIELYFEDMAALSAAFESEA 72
                                      4455555677788889999******************9..99**************977555555 PP

>> Ald_deCOase  Long-chain fatty aldehyde decarbonylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.1e-05      0.14     129     154 ..       5      30 ..       1      40 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHHHHHHHHHHTHHHHHH CS
                       Ald_deCOase 129 gvvkdeylhlnfGeeWlkenfeevke 154
                                        v kd+y+h +f e+Wl e+ + +ke
  gi|313122412|ref|YP_004038299.1|   5 LVRKDDYTHEEFVERWLGEHTDIAKE 30 
                                       5789***************9887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 664.28
//
Query:       gi|313122413|ref|YP_004038300.1|  [L=62]
Description: hypothetical protein Hbor_36470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 459.45
//
Query:       gi|313122414|ref|YP_004038301.1|  [L=200]
Description: hypothetical protein Hbor_36480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-09   37.1   0.0    4.9e-09   36.5   0.0    1.3  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   2.7e-13   4.9e-09       3     116 ..      64     172 ..      62     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.7e-13
                                       HHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHTTTTHHHHTS..HHH.......HHHCTCCHHHHHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlge....eedrellllaaLlHDiGkgpfgdafekk.......eeefekflaHekvgaeilr 68 
                                       eH ++V ++a + ae+       + d +++++a+LlHD+Gk++++  f  +       +e ++ ++ H+  g+ +++
  gi|313122414|ref|YP_004038301.1|  64 EHVRGVTRIAVQSAEEQRDfhgaDPDFDVIRAACLLHDVGKCYEYVDFVDDdvlstpdPEYATAEVPHSLSGYALAH 140
                                       9*************998889***********************99999999888776544499999*********** PP

                                       HHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHH CS
                                HD  69 evekrlgldledvaklirehheswegkkrprglaerqlslearivkla 116
                                       ev+ +l     +v+++i +  + ++             +lea +vk a
  gi|313122414|ref|YP_004038301.1| 141 EVGCPL-----AVQRAIPHFIGEIP-----------TRTLEAELVKSA 172
                                       ******.....********999999...........557777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1384.06
//
Query:       gi|313122415|ref|YP_004038302.1|  [L=34]
Description: hypothetical protein Hbor_36490 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.083   13.4   0.0      0.091   13.2   0.0    1.0  1  MmlI      Methylmuconolactone methyl-isomerase


Domain annotation for each model (and alignments):
>> MmlI  Methylmuconolactone methyl-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.1e-06     0.091       1      32 [.       1      32 [.       1      33 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-06
                              MmlI  1 mikrlgllsrredlsheqflahwrevhaplvh 32
                                      m k+++ll+r++++++e f +++ e    +v 
  gi|313122415|ref|YP_004038302.1|  1 MYKHVALLVRKDGVADEGFAERFAERRTRVVM 32
                                      7899******************9998887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       151  (0.00842211); expected 358.6 (0.02)
Passed bias filter:                      124  (0.00691617); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.44
# Mc/sec: 232.78
//
Query:       gi|313122416|ref|YP_004038303.1|  [L=74]
Description: hypothetical protein Hbor_36500 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0052   16.7   0.4     0.0082   16.1   0.4    1.3  1  zinc-ribbons_6  zinc-ribbons
  ------ inclusion threshold ------
      0.016   14.6   1.5          3    7.4   0.4    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.033   14.2   2.2       0.13   12.3   2.2    1.9  1  DZR             Double zinc ribbon
      0.051   13.1   2.5        4.3    6.9   0.2    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.052   13.6   1.5          2    8.6   0.1    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.076   12.8   4.4        2.8    7.8   0.5    2.1  2  PADR1           PADR1 (NUC008) domain
       0.13   12.4   4.8        3.7    7.7   0.1    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.14   12.3   1.0       0.14   12.3   1.0    2.4  2  UPF0547         Uncharacterised protein family UPF0547
       0.16   11.8   4.1        1.4    8.8   0.1    2.2  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.61   10.0   2.9        5.6    6.9   0.1    2.3  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   4.6e-06    0.0082       3      41 ..      29      66 ..      27      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                                      -SSS-S--EE-S.SEEE-TTT--EEEEEEE-SSS-S---E CS
                    zinc-ribbons_6  3 CpeCqqelekrg.eqyhCeaCqedlkkealCpeCeqelev 41
                                      Cp+C   l + g ++yhC+       ++  CpeCe+ l+v
  gi|313122416|ref|YP_004038303.1| 29 CPSCGLLLGQGGdASYHCDVYG--AARVERCPECEETLSV 66
                                      *****99996554899999866..578999*******987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0017         3      19      24 ..      29      34 ..      23      37 .. 0.71
   2 ?    6.1   0.0    0.0041       7.3       4      13 ..      56      65 ..      53      70 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0017
                       zf-ribbon_3 19 CpyCGt 24
                                      Cp+CG 
  gi|313122416|ref|YP_004038303.1| 29 CPSCGL 34
                                      666665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0041
                       zf-ribbon_3  4 rCPnCGa.pls 13
                                      rCP+C + + s
  gi|313122416|ref|YP_004038303.1| 56 RCPECEEtL-S 65
                                      899997744.5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2   7.2e-05      0.13      10      39 ..      24      65 ..       4      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.2e-05
                               DZR 10 pdarfCseCgtklkavaa............edrCpsCgekvd 39
                                      ++ + C+ Cg  l +  +             +rCp+C+e ++
  gi|313122416|ref|YP_004038303.1| 24 SGPEPCPSCGLLLGQGGDasyhcdvygaarVERCPECEETLS 65
                                      5666788888888644447888888888889******99876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.004       7.2      22      30 ..      29      37 ..      22      40 .. 0.90
   2 ?    6.9   0.2    0.0024       4.3      21      36 ..      56      71 ..      53      73 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.004
                                      ESSSSBEEE CS
                      TF_Zn_Ribbon 22 CtdCGlVle 30
                                      C++CGl+l 
  gi|313122416|ref|YP_004038303.1| 29 CPSCGLLLG 37
                                      *****9986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0024
                                      EESSSSBEEEECCCCC CS
                      TF_Zn_Ribbon 21 vCtdCGlVlednside 36
                                      +C++C++ l  +si++
  gi|313122416|ref|YP_004038303.1| 56 RCPECEETLSVRSIVP 71
                                      4777777777777665 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.025        44       4       8 ..      29      33 ..      29      36 .. 0.84
   2 ?    8.6   0.1    0.0011         2       3      12 ..      56      65 ..      56      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.025
                            zf-ACC  4 CpsCg 8 
                                      CpsCg
  gi|313122416|ref|YP_004038303.1| 29 CPSCG 33
                                      99998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                            zf-ACC  3 KCpsCgemly 12
                                      +Cp+C+e+l 
  gi|313122416|ref|YP_004038303.1| 56 RCPECEETLS 65
                                      6******986 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.5    0.0016       2.8      13      34 ..      26      47 ..      25      52 .. 0.73
   2 ?    6.4   1.4    0.0043       7.7      12      21 ..      53      62 ..      46      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                             PADR1 13 lekCpeCkegqlvfdss..gYkCt 34
                                      +e+Cp+C+   l    +   Y+C 
  gi|313122416|ref|YP_004038303.1| 26 PEPCPSCG-LLLGQG-GdaSYHCD 47
                                      58******.555544.35899996 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0043
                             PADR1 12 alekCpeCke 21
                                      ++e+CpeC+e
  gi|313122416|ref|YP_004038303.1| 53 RVERCPECEE 62
                                      479*****95 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0021       3.7      23      33 ..      23      33 ..      10      36 .. 0.76
   2 ?    5.5   1.8      0.01        19      27      35 ..      54      63 ..      43      69 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                       Zn-ribbon_8 23 dapltaCPeCg 33
                                      d+ +++CP+Cg
  gi|313122416|ref|YP_004038303.1| 23 DSGPEPCPSCG 33
                                      444556****9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.01
                       Zn-ribbon_8 27 ta.CPeCgse 35
                                      ++ CPeC ++
  gi|313122416|ref|YP_004038303.1| 54 VErCPECEET 63
                                      444****884 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.5      0.14   2.5e+02      17      21 ..      29      33 ..      27      34 .. 0.66
   2 ?   12.3   1.0   7.6e-05      0.14       2      12 ..      56      66 ..      56      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.14
                           UPF0547 17 CphCG 21
                                      Cp CG
  gi|313122416|ref|YP_004038303.1| 29 CPSCG 33
                                      55555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.6e-05
                           UPF0547  2 vCPeCeakvPv 12
                                      +CPeCe++++v
  gi|313122416|ref|YP_004038303.1| 56 RCPECEETLSV 66
                                      6*******997 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.7     0.019        35       3      10 ..      28      35 ..      26      38 .. 0.78
   2 ?    8.8   0.1   0.00075       1.4       1      14 [.      54      67 ..      54      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.019
                                      E-SSS--E CS
                    zf-C4_Topoisom  3 kCPkCggd 10
                                       CP+Cg  
  gi|313122416|ref|YP_004038303.1| 28 PCPSCGLL 35
                                      6****955 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00075
                                      -EE-SSS--EEEEE CS
                    zf-C4_Topoisom  1 vekCPkCggdLvlk 14
                                      ve CP+C + L ++
  gi|313122416|ref|YP_004038303.1| 54 VERCPECEETLSVR 67
                                      589*****999887 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0031       5.6       6      22 ..      19      35 ..      18      48 .. 0.84
   2 ?    3.5   0.4     0.034        62      14      20 ..      55      61 ..      47      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0031
                         zf-C2H2_3  6 lgqksfgasqCkeCgMv 22
                                      lg  + g + C+ Cg++
  gi|313122416|ref|YP_004038303.1| 19 LGTADSGPEPCPSCGLL 35
                                      5777888877*****85 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.034
                         zf-C2H2_3 14 sqCkeCg 20
                                      ++C+eC+
  gi|313122416|ref|YP_004038303.1| 55 ERCPECE 61
                                      56****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 526.63
//
Query:       gi|313122417|ref|YP_004038304.1|  [L=75]
Description: hypothetical protein Hbor_36510 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 503.16
//
Query:       gi|313122418|ref|YP_004038305.1|  [L=396]
Description: Nucleoside-diphosphate-sugar pyrophosphorylase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-42  144.0   0.0    8.9e-42  143.4   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase
    2.2e-15   57.4   0.8      4e-15   56.5   0.8    1.4  1  NTP_transf_3     MobA-like NTP transferase domain
    3.8e-11   42.2  14.3       0.01   15.6   0.2    4.9  5  Hexapep          Bacterial transferase hexapeptide (six repea
    3.7e-07   30.1   0.1    6.8e-07   29.2   0.1    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.011   16.0   0.5      0.031   14.6   0.5    1.7  1  Bactofilin       Polymer-forming cytoskeletal
      0.026   14.5   0.0      0.039   13.9   0.0    1.2  1  CTP_transf_3     Cytidylyltransferase
       0.28   10.1   0.0       0.62    8.9   0.0    1.5  1  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.0   3.5e-45   8.9e-42       2     243 ..       3     224 ..       2     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 3.5e-45
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       +v+La G G+R+wPLt +++k+++pv+gk +l+ +t+ +++++g +ei++v+  +++  v++ +++++ +gv v++a
  gi|313122418|ref|YP_004038305.1|   3 TVVLAAGVGSRMWPLTASRPKPMLPVAGK-PLVAHTVDAAVEAGATEIVLVVG-YEADDVRSFFGTEY-AGVPVEYA 76 
                                       69***************************.*****************666665.88999******999.8******* PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                       ++ e+ gtAdAv+ a+e+led +    + vL+gD l++      +++  +       ++g  +ve++t+yGv ++d+
  gi|313122418|ref|YP_004038305.1|  77 VQAEQLGTADAVRSALEVLEDGS----FAVLNGDALYDV---PSLTNLYDG----GPAVGSFEVEDPTSYGVLKTDG 142
                                       ********************999....8**********4...333333333....447999**************** PP

                                       TSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEX CS
                   NTP_transferase 156 egrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDv 232
                                       +g v   vEKP++++ s+l+++G Yvf + ++  l++ +e ++rge e+td+l++ +e  +v   + f+    W Dv
  gi|313122418|ref|YP_004038305.1| 143 SGYVAGVVEKPSNPP-SNLINAGAYVFPEAAHGWLLD-VEASERGELELTDVLSRSCETYDVR-TVAFDR---WLDV 213
                                       ***************.*******************87.*********************8776.456666...**** PP

                                       SSHHHHHHHHH CS
                   NTP_transferase 233 Gtldslleane 243
                                       G +  lleane
  gi|313122418|ref|YP_004038305.1| 214 GRPWELLEANE 224
                                       *********97 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.8   1.6e-18     4e-15       2      98 ..       4     109 ..       3     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.6e-18
                                       EEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC..HHHH....HHTTCTS-EEE-TT CS
                      NTP_transf_3   2 viLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggde..evla....alarlgvrvveded 67 
                                       v+LA+G +sRm      ++K++lp++gkpl+++++da+ +ag+ e+v+v+g+e  +v++    ++a+ +v++++++ 
  gi|313122418|ref|YP_004038305.1|   4 VVLAAGVGSRMwpltaSRPKPMLPVAGKPLVAHTVDAAVEAGATEIVLVVGYEadDVRSffgtEYAGVPVEYAVQA- 79 
                                       9**********8877446**********************************622454455445677788888887. PP

                                       SS-SHHHHHHHHHHHH.SSSCEEEEETT-TT CS
                      NTP_transf_3  68 pgkgplaslaaalraaadadavlvlacDmPl 98 
                                       ++ g++ ++++al+ + ++  ++vl +D  +
  gi|313122418|ref|YP_004038305.1|  80 EQLGTADAVRSALEVL-EDGSFAVLNGDALY 109
                                       589***********99.89999****99855 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.2   1.1e+04      11      19 ..      98     106 ..      98     107 .. 0.73
   2 !   11.2   0.3   9.4e-05      0.24      14      36 .]     242     264 ..     233     264 .. 0.90
   3 !   14.2   0.1     1e-05     0.027       3      35 ..     267     299 ..     265     300 .. 0.89
   4 !   15.6   0.2   3.9e-06      0.01       2      35 ..     301     333 ..     300     334 .. 0.87
   5 !    9.1   0.2   0.00042       1.1       1      22 [.     359     380 ..     359     389 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.2
                                       -TTEEEETT CS
                           Hexapep  11 gpfaviggn 19 
                                       g+fav+ g+
  gi|313122418|ref|YP_004038305.1|  98 GSFAVLNGD 106
                                       678898876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.4e-05
                                       EEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  14 aviggnVkIGdnvkIgagvvigg 36 
                                       a + g+V++ +++k+ +gvvi g
  gi|313122418|ref|YP_004038305.1| 242 AELNGPVVVEEGAKVRSGVVIDG 264
                                       7799*****************75 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1e-05
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                        I s++ +gp+a+++g + I +++k+g+ v ++
  gi|313122418|ref|YP_004038305.1| 267 LIQSGASVGPNAYVRGATLICEDAKVGHAVEVK 299
                                       6999***********************977775 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 3.9e-06
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +v+ +++++g+ a++ g+ ++G+nv  gag+ ++
  gi|313122418|ref|YP_004038305.1| 301 SVLMEDATVGHLAYV-GDSVLGRNVNFGAGTNVA 333
                                       68899**********.5555**********9886 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.00042
                                       TEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkI 22 
                                       ++vIG++++ g ++ + ++V++
  gi|313122418|ref|YP_004038305.1| 359 GVVIGDGAKTGINSSLNAGVVL 380
                                       689****************986 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   2.7e-10   6.8e-07       2      99 ..       2     106 ..       1     111 [. 0.71

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.7e-10
                                       EEEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG......CCEE CS
                              IspD   2 vvvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld......ksiq 69 
                                         v+ AAG+G+Rm    a +pK  l ++g++l++htvda+ + +a + ++vv  e d   ++++ +        +  
  gi|313122418|ref|YP_004038305.1|   2 QTVVLAAGVGSRMwplTASRPKPMLPVAGKPLVAHTVDAAVEAGATEIVLVVGYEAD--DVRSFFGTeyagvpVEYA 76 
                                       579*********9665799***********************999999988876655..333333332435331122 PP

                                       EEE--SSHHHHHHHHHHTTSSTTSEEEE-- CS
                              IspD  70 lvaGGdeRaesVlnglkalegeakfVLvHD 99 
                                       + a     a++V  +l++le+    VL  D
  gi|313122418|ref|YP_004038305.1|  77 VQAEQLGTADAVRSALEVLEDGSFAVLNGD 106
                                       222233457888888888888777777655 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   1.2e-05     0.031      18      93 ..     231     309 ..     224     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                        Bactofilin  18 dlridGkveGdieakgklvvgeggkvegnikaee..vvvaGtvkG.nveaeekvelkktakveGdikaksleieega 91 
                                       + ridG+v+ d e +g +vv+eg+kv+  +  +   ++ +G   G n ++++   + ++akv   +++k+ ++ e+a
  gi|313122418|ref|YP_004038305.1| 231 ETRIDGDVSEDAELNGPVVVEEGAKVRSGVVIDGpaLIQSGASVGpNAYVRGATLICEDAKVGHAVEVKNSVLMEDA 307
                                       67999999999999*************9977744326666*977779********************9999988888 PP

                        Bactofilin  92 vf 93 
                                       ++
  gi|313122418|ref|YP_004038305.1| 308 TV 309
                                       76 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.5e-05     0.039      16      45 ..      23      52 ..      21      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                      GGGSEETTEEHHHHHHHHHHHTTTTSEEEE CS
                      CTP_transf_3 16 Knlldlggkpliayvleaalkskafekviv 45
                                      K++l+ +gkpl+a++++aa++++a e v v
  gi|313122418|ref|YP_004038305.1| 23 KPMLPVAGKPLVAHTVDAAVEAGATEIVLV 52
                                      9**********************9887665 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00024      0.62     271     326 ..     293     348 ..     277     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00024
                        Fucokinase 271 kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpd 326
                                        + + v nSvl ++++vg  +++ +s l+ nv+ g+++ v +l+ +  + +l+++d
  gi|313122418|ref|YP_004038305.1| 293 GHAVEVKNSVLMEDATVGHLAYVGDSVLGRNVNFGAGTNVANLRHDGANVKLTVKD 348
                                       5567799************************************9998755555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2627.02
//
Query:       gi|313122419|ref|YP_004038306.1|  [L=147]
Description: HTH domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-09   35.7   0.1    1.1e-08   34.9   0.1    1.4  1  HTH_20          Helix-turn-helix domain
    1.2e-08   34.8   0.0    2.1e-08   34.0   0.0    1.5  1  HTH_11          HTH domain
    3.9e-07   29.8   0.0    7.1e-07   29.0   0.0    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
    5.7e-07   29.3   0.1    8.8e-07   28.7   0.1    1.3  1  MarR_2          MarR family
    9.7e-06   25.3   0.0    1.7e-05   24.6   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    2.3e-05   24.1   0.0    3.4e-05   23.6   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
    4.4e-05   23.0   0.0    7.3e-05   22.3   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    5.5e-05   22.8   0.0    9.6e-05   22.0   0.0    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    0.00012   21.9   0.0    0.00022   21.1   0.0    1.3  1  MarR            MarR family
    0.00019   21.2   0.3    0.00044   20.0   0.3    1.7  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00057   19.8   0.0    0.00096   19.1   0.0    1.3  1  HTH_29          Winged helix-turn helix
    0.00082   19.3   0.0     0.0013   18.6   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0017   18.0   0.0     0.0027   17.3   0.0    1.3  1  GntR            Bacterial regulatory proteins, gntR family
      0.002   17.9   0.0     0.0035   17.1   0.0    1.4  1  HTH_23          Homeodomain-like domain
     0.0037   17.6   0.0     0.0073   16.6   0.0    1.5  1  Rrf2            Transcriptional regulator
     0.0047   17.1   0.0     0.0078   16.4   0.0    1.3  1  FUR             Ferric uptake regulator family
     0.0062   17.0   0.0      0.012   16.1   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
     0.0098   15.8   0.0      0.017   15.1   0.0    1.3  1  PadR            Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.013   15.6   0.0    1.1  1  Replic_Relax    Replication-relaxation
      0.011   15.9   0.0      0.029   14.6   0.0    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.019   15.1   0.0      0.034   14.3   0.0    1.4  1  HTH_28          Helix-turn-helix domain
       0.02   14.7   0.0      0.039   13.8   0.0    1.5  1  TetR_N          Bacterial regulatory proteins, tetR family
      0.023   14.7   0.0      0.039   13.9   0.0    1.4  1  HTH_36          Helix-turn-helix domain
      0.025   14.3   0.0      0.035   13.8   0.0    1.2  1  DUF4423         Domain of unknown function (DUF4423)
      0.025   15.0   0.0      0.047   14.1   0.0    1.4  1  DUF4140         N-terminal domain of unknown function (DUF414
      0.042   14.4   0.0       0.11   13.2   0.0    1.6  1  Mga             Mga helix-turn-helix domain
      0.074   12.5   0.0       0.12   11.8   0.0    1.3  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
       0.11   12.3   0.0       0.22   11.4   0.0    1.4  1  HTH_10          HTH DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.8e-11   1.1e-08       1      56 [.       7      61 ..       7      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.8e-11
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      d++++AL++ v r+il a    +++ta+ela+ +d+s +t++++L+ L e gLve+
  gi|313122419|ref|YP_004038306.1|  7 DDLLDALGDDVARKILVAG-KQGPVTAEELADSCDVSESTIYRRLDRLNELGLVER 61
                                      6899**************9.***********************************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   3.3e-11   2.1e-08      12      50 ..      26      69 ..      19      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 3.3e-11
                            HTH_11 12 argpisgeeLAeeLnvSrrtvrrdIkaLeelg.....vpIesep 50
                                      ++gp+++eeLA+  +vS++t++r++++L+elg      p+ s++
  gi|313122419|ref|YP_004038306.1| 26 KQGPVTAEELADSCDVSESTIYRRLDRLNELGlvercNPLLSTS 69
                                      5778****************************776666666665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.1e-09   7.1e-07      17      54 ..      22      61 ..      20      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.1e-09
                                      HH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 17 Ll..klgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      L+  k+gp ta+e+a   +v++s++Y+ L +L + GlVer
  gi|313122419|ref|YP_004038306.1| 22 LVagKQGPVTAEELADSCDVSESTIYRRLDRLNELGLVER 61
                                      667799********************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   1.4e-09   8.8e-07      20      54 ..      19      62 ..       8      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.4e-09
                                      S.........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 20 r.........dltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      r         ++t+ ela+ +++s s++ r+l+rL + GLver+
  gi|313122419|ref|YP_004038306.1| 19 RkilvagkqgPVTAEELADSCDVSESTIYRRLDRLNELGLVERC 62
                                      444444444459******************************98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.6e-08   1.7e-05      12      50 ..      23      61 ..       8      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.6e-08
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +a  ++++t  elA+ ++++ St +R L  L elG+ve+
  gi|313122419|ref|YP_004038306.1| 23 VAGKQGPVTAEELADSCDVSESTIYRRLDRLNELGLVER 61
                                      5777888******************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.4e-08   3.4e-05       5      46 ..      19      60 ..      15      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.4e-08
                                      HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +kIL +  +g+ ++ ela+  ++s+st+ + L +L e+GLVe
  gi|313122419|ref|YP_004038306.1| 19 RKILVAGKQGPVTAEELADSCDVSESTIYRRLDRLNELGLVE 60
                                      677777778********************************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.1e-07   7.3e-05      14      48 .]      26      60 ..      15      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.1e-07
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      k++  +  eLA+ +++S st+ rrl+rL e Gl++
  gi|313122419|ref|YP_004038306.1| 26 KQGPVTAEELADSCDVSESTIYRRLDRLNELGLVE 60
                                      56778999*************************96 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.5e-07   9.6e-05      11      46 ..      26      61 ..      22      63 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.5e-07
                          HTH_DeoR 11 qqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +qg ++ eel++ ++vSe Ti R L+ L e gl++R
  gi|313122419|ref|YP_004038306.1| 26 KQGPVTAEELADSCDVSESTIYRRLDRLNELGLVER 61
                                      7999******************************99 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.5e-07   0.00022      14      49 ..      26      61 ..      22      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.5e-07
                                      HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 14 eqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                       qgp +  eLa+   vs st+ r ldrL + Gl+eR
  gi|313122419|ref|YP_004038306.1| 26 KQGPVTAEELADSCDVSESTIYRRLDRLNELGLVER 61
                                      689********************************9 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   6.8e-07   0.00044      15      41 ..      27      53 ..       8      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.8e-07
                     HTH_AsnC-type 15 daRisyaeLAervGlSestvlrRvrrL 41
                                      ++  + +eLA+ + +Sest+ rR++rL
  gi|313122419|ref|YP_004038306.1| 27 QGPVTAEELADSCDVSESTIYRRLDRL 53
                                      488899********************9 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.5e-06   0.00096      13      57 ..      28      77 ..      20      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-06
                            HTH_29 13 s..tvsqiAkllglsrrtvyrwlkrfeegGlaa....lld.rrrsgrprnrl 57
                                      +  t  ++A  +++s++t+yr l+r +e Gl      ll+ ++  g + +r+
  gi|313122419|ref|YP_004038306.1| 28 GpvTAEELADSCDVSESTIYRRLDRLNELGLVErcnpLLStSK--GSYQTRI 77
                                      3458899***********************6555676666444..5555555 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.1e-06    0.0013      20      53 ..      28      61 ..       9      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisr 53
                                       p+t eelA+ + ++ +t+ r l +L + gl++r
  gi|313122419|ref|YP_004038306.1| 28 GPVTAEELADSCDVSESTIYRRLDRLNELGLVER 61
                                      499*****************************96 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.2e-06    0.0027       6      56 ..      10      61 ..       5      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.2e-06
                                      HHHHHHHHHTTSS-TTSB--.-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR  6 yerLredIlsgelrpGdkLP.sereLaaefgVsrttvReALrrLeaeglver 56
                                       ++L +d+ ++ l +G + P + +eLa+  +Vs +t+ + L+rL + glver
  gi|313122419|ref|YP_004038306.1| 10 LDALGDDVARKILVAGKQGPvTAEELADSCDVSESTIYRRLDRLNELGLVER 61
                                      577888888888888887664789**************************98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.5e-06    0.0035      19      46 ..      31      58 ..      21      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-06
                            HTH_23 19 svreIAreLgvsrrTvyrwlkryreeGl 46
                                      + +e A+ ++vs++T+yr l r +e Gl
  gi|313122419|ref|YP_004038306.1| 31 TAEELADSCDVSESTIYRRLDRLNELGL 58
                                      66899******************99886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0073      21      56 ..      25      60 ..      19      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                       +++pv++ee+a++ ++s+s + + l +L++ glv+
  gi|313122419|ref|YP_004038306.1| 25 GKQGPVTAEELADSCDVSESTIYRRLDRLNELGLVE 60
                                      46779******************************7 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0078      35      62 ..      36      63 ..      28      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                                      HTTTT--HHHHHHHHHHHHHTTSEEEEE CS
                               FUR 35 eedpeislaTVYrtLklleeaglvkele 62
                                       ++ ++s +T+Yr L+ l+e+glv++ +
  gi|313122419|ref|YP_004038306.1| 36 ADSCDVSESTIYRRLDRLNELGLVERCN 63
                                      56789********************987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.9e-05     0.012      12      50 ..      23      61 ..      19      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-05
                            HTH_27 12 irhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                      +++ ++++++++l++  +v+ s+i   l++L e GLver
  gi|313122419|ref|YP_004038306.1| 23 VAGKQGPVTAEELADSCDVSESTIYRRLDRLNELGLVER 61
                                      667899*******************************76 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.6e-05     0.017      22      49 ..      35      61 ..      30      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-05
                                      CSTT-CCTTHHHHHHHHHHHHHTTSEEE CS
                              PadR 22 lsegllelseGslYpaLkrLekeglves 49
                                      l     ++se+++Y+ L+rL + glve+
  gi|313122419|ref|YP_004038306.1| 35 LA-DSCDVSESTIYRRLDRLNELGLVER 61
                                      43.3479*******************86 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   2.1e-05     0.013       7      54 ..      27      73 ..      23      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                      Replic_Relax  7 hrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggs 54
                                       ++ T++ +a  +  s+++ ++rrL rL+elgl++r ++   + +g +
  gi|313122419|ref|YP_004038306.1| 27 QGPVTAEELADSCDVSEST-IYRRLDRLNELGLVERCNPLLSTSKGSY 73
                                      5678888999998888888.*****************99876666644 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.6e-05     0.029      19      53 ..      26      60 ..      15      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-05
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      ++++v+  +la   +vs s++   l +L++ G+ve
  gi|313122419|ref|YP_004038306.1| 26 KQGPVTAEELADSCDVSESTIYRRLDRLNELGLVE 60
                                      7999*****************************97 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.2e-05     0.034      13      41 ..      30      58 ..      20      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.2e-05
                            HTH_28 13 hsvreaArelgisrrtvyrWikryeegGi 41
                                      +++ e+A    +s++t+yr + r++e G+
  gi|313122419|ref|YP_004038306.1| 30 VTAEELADSCDVSESTIYRRLDRLNELGL 58
                                      4778899999****************996 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     6e-05     0.039      16      36 ..      29      49 ..      16      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-05
                                      T--HHHHHHHHTSSHHHHHHH CS
                            TetR_N 16 attvreIAkrAGvskgalYry 36
                                       +t +e+A+++ vs++++Yr+
  gi|313122419|ref|YP_004038306.1| 29 PVTAEELADSCDVSESTIYRR 49
                                      5899***************95 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.1e-05     0.039      28      55 .]      32      59 ..      25      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-05
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                       e la  + +s++T++r ++ L +lG++
  gi|313122419|ref|YP_004038306.1| 32 AEELADSCDVSESTIYRRLDRLNELGLV 59
                                      689***********************85 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.4e-05     0.035      30      94 ..      23      84 ..      17      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-05
                           DUF4423 30 lplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevkseav 94
                                      ++ k++  + eela+ +   +s++ + + l++L +lgl+++ +   +  ++ s +t  +  s+av
  gi|313122419|ref|YP_004038306.1| 23 VAGKQGPVTAEELADSCD--VSESTIYRRLDRLNELGLVERCNP-LLSTSKGSYQTRIDGLSLAV 84
                                      5556667799********..*********************998.66666666667777777766 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.3e-05     0.047      17      57 ..      67     108 ..      57     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.3e-05
                           DUF4140  17 elkaGtnevtiegLpptldedSlrVe.gagaatildvqverv 57 
                                       ++++G+ + +i+gL+ ++de+ +r+e g+ + ti  +++  +
  gi|313122419|ref|YP_004038306.1|  67 STSKGSYQTRIDGLSLAVDEEGIRIEqGPSDSTIDAMETILD 108
                                       6789**********************8777788888876554 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00016      0.11      31      57 ..      30      56 ..      20      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                                      EEHHHHHHHCT--HHHHHHHHHHHHHH CS
                               Mga 31 vsieelaqelyiSestlkrkikelnkl 57
                                      v+ eela++  +Sest++r +++ln+l
  gi|313122419|ref|YP_004038306.1| 30 VTAEELADSCDVSESTIYRRLDRLNEL 56
                                      7899*********************86 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.12      27      51 ..      28      53 ..      16      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                      HTH_Tnp_ISL3 27 s.rsvkavArqlgvSwtTVwrildry 51
                                      +  +  + A+ ++vS++T+ r+ldr+
  gi|313122419|ref|YP_004038306.1| 28 GpVTAEELADSCDVSESTIYRRLDRL 53
                                      55566789999*************97 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00034      0.22      24      46 ..      30      52 ..      29      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                            HTH_10 24 vtlkeLAkelGIskstlsehLrk 46
                                      vt++eLA+  ++s+st++ +L +
  gi|313122419|ref|YP_004038306.1| 30 VTAEELADSCDVSESTIYRRLDR 52
                                      799***************99977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1124.65
//
Query:       gi|313122420|ref|YP_004038307.1|  [L=605]
Description: glutamine--fructose-6-phosphate transaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      4e-55  185.2   0.5    3.7e-28   98.0   0.0    2.3  2  SIS        SIS domain
    2.3e-20   73.1   0.0    5.8e-20   71.9   0.0    1.7  1  GATase_6   Glutamine amidotransferase domain
    8.5e-17   61.2   0.0    3.7e-16   59.2   0.0    2.0  2  GATase_7   Glutamine amidotransferase domain
    0.00023   20.2   0.0    0.00039   19.4   0.0    1.3  1  GATase_4   Glutamine amidotransferases class-II
    0.00042   20.3   0.9      0.087   12.8   0.1    2.8  3  SIS_2      SIS domain
  ------ inclusion threshold ------
      0.045   14.0   0.1       0.56   10.5   0.1    2.3  2  Hydrolase  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.1   9.4e-28   2.8e-24       3     128 ..     290     413 ..     288     416 .. 0.92
   2 !   98.0   0.0   1.2e-31   3.7e-28       2     128 ..     459     585 ..     458     587 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 9.4e-28
                                       CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHT CS
                               SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelaker 79 
                                       ++ +++ ++G+Gtsy++a++++  l + g++++++ +a+e    v++++++++lvi++++sget+d+++a++ ak+ 
  gi|313122420|ref|YP_004038307.1| 290 TDVDQVQFVGMGTSYHAAMYASSMLSSRGVPAYAF-QAGE-YGLVCPPVTDGTLVIAVTQSGETADTLDAIRRAKSA 364
                                       677899*******************6666665555.5666.5999******************************** PP

                                       TSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                               SIS  80 gakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldal 128
                                       ga ++a+T+  gs++ re+  +l i+a+pe++va+tk++ +q +al++l
  gi|313122420|ref|YP_004038307.1| 365 GADTVAVTNTVGSSITRECEDTLLIRAGPEIGVAATKTFCSQVTALSLL 413
                                       *********************************************9987 PP

  == domain 2  score: 98.0 bits;  conditional E-value: 1.2e-31
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelake 78 
                                       + ++++ +++G+G   ++a+e+alk++ei++ ++e+ +aselkhg+lal++++++v++i +  e   ++ + +++++
  gi|313122420|ref|YP_004038307.1| 459 IEDSESYFFIGRGIAHSAALEGALKFKEITYEHAEGFAASELKHGPLALVTPNTPVFAIFTGFEDEATLSSMKEVQA 535
                                       6788999********************************************************************** PP

                                       TTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                               SIS  79 rgakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldal 128
                                       rga++iaIT++++s +a++ad++l i++     +++  s+++ql+a++a+
  gi|313122420|ref|YP_004038307.1| 536 RGAPVIAITSKTDSEIAEFADYVLSIPETHPDVAGIPVSVQLQLVAYHAA 585
                                       ****************************9999999************996 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   1.9e-23   5.8e-20      13     103 ..      61     165 ..      49     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.9e-23
                          GATase_6  13 e.....valaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall... 81 
                                       +     ++++H+R+a++g  ++e a+P + e+gr+++vhNG i ny++l++el++  g+ f+s++Dtev+ +l+   
  gi|313122420|ref|YP_004038307.1|  61 DpmsgsLGIGHTRWATHGGVTDENAHPHTDESGRIAVVHNGIIGNYQSLKKELES-NGHVFASDTDTEVVPHLIeae 136
                                       3344449************977777******************************.******************977 PP

                          GATase_6  82 eelG.......eevlerlrGmfafaiwdk 103
                                        ++G         +++rl G +a+a++  
  gi|313122420|ref|YP_004038307.1| 137 LNTGateeeafRSAIARLSGTYAIAAIIG 165
                                       3334666444566777****999998765 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   1.2e-19   3.7e-16       9     121 ..      81     197 ..      71     199 .. 0.91
   2 ?   -1.4   0.0      0.71   2.1e+03      34      64 ..     428     458 ..     424     476 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.2e-19
                          GATase_7   9 seagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnG 76 
                                       ++++a P + +e+gr+++v+nG i Ny++l++eLe++gh f++++Dtev+ +l+ea         e  ++a+ rl G
  gi|313122420|ref|YP_004038307.1|  81 TDENAHPHT-DESGRIAVVHNGIIGNYQSLKKELESNGHVFASDTDTEVVPHLIEAelntgateeEAFRSAIARLSG 156
                                       577888999.69****************************************************999********** PP

                          GATase_7  77 mfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                        +A+a +   ++ +++ R      PL +g  +g ++++aS + a+
  gi|313122420|ref|YP_004038307.1| 157 TYAIAAIIGGDEAIYATRS---GSPLCLGIGPG-QYFLASDVPAF 197
                                       ******9999999***999...58999999986.89999988876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.71
                          GATase_7  34 NykelreeLeakghrfrtksDtevllallea 64 
                                       + +el e L++   ++++  Dt+v  al ++
  gi|313122420|ref|YP_004038307.1| 428 DGRELVEALSRLPGHVQEILDTSVAPALAQE 458
                                       5679999999999999999*****9888765 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.3e-07   0.00039      57     133 ..      51     129 ..      36     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-07
                          GATase_4  57 esplaelvreypiksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTD 129
                                        s+l   v + p+  ++ + H R at+G v++en+hp + e ++  +   HnG + +y+       ++ +    +TD
  gi|313122420|ref|YP_004038307.1|  51 VSELVAAVESDPMSGSLGIGHTRWATHGGVTDENAHPHTDESGR--IAVVHNGIIGNYQSLKkeleSNGHVFASDTD 125
                                       4555555667789999***********************99654..5567**9998766544333544455567888 PP

                          GATase_4 130 sEla 133
                                       +E++
  gi|313122420|ref|YP_004038307.1| 126 TEVV 129
                                       8876 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   2.9e-05     0.087     103     137 ..     338     372 ..     332     373 .. 0.90
   2 ?   -2.8   0.0         2     6e+03      24      55 ..     451     482 ..     442     492 .. 0.77
   3 !    4.8   0.0    0.0089        26     119     138 .]     526     545 ..     519     545 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                                       TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2 103 pgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                        g + + + +sG+ a  ++a++ ak+ g+ ++A+t
  gi|313122420|ref|YP_004038307.1| 338 DGTLVIAVTQSGETADTLDAIRRAKSAGADTVAVT 372
                                       566788999*************************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                                       HHHHHHHHHHTT--EEEEESGGGHHHHHHTSS CS
                             SIS_2  24 aaeliadslenggkvlvfGsGhSaalaeelaa 55 
                                       +a ++a+ +e+ +  +  G G ++ +a e a 
  gi|313122420|ref|YP_004038307.1| 451 VAPALAQEIEDSESYFFIGRGIAHSAALEGAL 482
                                       67788888999999999999877777776655 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0089
                                       HHHHHHHHHHHT-EEEEEE- CS
                             SIS_2 119 vveaaeaakergmkviAlts 138
                                        +  ++++++rg++viA+ts
  gi|313122420|ref|YP_004038307.1| 526 TLSSMKEVQARGAPVIAITS 545
                                       5667899************8 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.18   5.4e+02     121     143 ..     352     374 ..     203     386 .. 0.86
   2 ?   10.5   0.1   0.00019      0.56       5     153 ..     418     556 ..     416     571 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.18
                                       TTHHHHHHHHHHTTEEEEEEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 121 peaaeavasLkaagievvlltgd 143
                                        ++ +a+++ k+ag ++v +t+ 
  gi|313122420|ref|YP_004038307.1| 352 ADTLDAIRRAKSAGADTVAVTNT 374
                                       44557888899999999999986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00019
                                       EEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE....HHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                         Hydrolase   5 vfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrg....ayaigkpewl 77 
                                       v D++GT tt  +++++++ ++    +++l t+         va a a +++ ++   figrg    a+++g  ++ 
  gi|313122420|ref|YP_004038307.1| 418 VEDITGTRTTDGRELVEALSRLPGHVQEILDTS---------VAPALAQEIEDSESYFFIGRGiahsAALEGALKFK 485
                                       569******999999999999967777777777.........8888888888899999*********9999999999 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHH.HHHHHHHHTTEEEEEEESSEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaa.eavasLkaagievvlltgdnpetaeraan 153
                                       +    +++ +    s+ ++g  + +       vf+i       +ea    +++ +a+g +v+ +t+   +   + a+
  gi|313122420|ref|YP_004038307.1| 486 EIT--YEHAEGFAASELKHGPLALVT--PNTPVFAIFTG--FEDEATlSSMKEVQARGAPVIAITSKTDSEIAEFAD 556
                                       999..99999999999999*******..99999999999..999***9***********988888666554444554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4056.67
//
Query:       gi|313122421|ref|YP_004038308.1|  [L=390]
Description: Nucleoside-diphosphate-sugar pyrophosphorylase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-34  118.1   0.0    5.9e-34  117.7   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    3.2e-18   66.6   0.1    5.5e-18   65.8   0.1    1.5  1  NTP_transf_3     MobA-like NTP transferase domain
    1.3e-13   50.1  18.0    3.1e-05   23.5   0.8    4.8  4  Hexapep          Bacterial transferase hexapeptide (six repea
    9.7e-11   41.2  17.4    1.3e-07   31.2   1.4    4.2  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    1.3e-05   25.1   0.1    2.6e-05   24.1   0.1    1.5  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
       0.05   12.6   0.8       0.22   10.4   0.1    2.4  3  Fucokinase       L-fucokinase
       0.15   11.9   0.0       0.33   10.8   0.0    1.5  1  CTP_transf_3     Cytidylyltransferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.0   2.3e-37   5.9e-34       2     237 ..       7     224 ..       6     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 2.3e-37
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       av+La G+G RL+PLt+ l+k+++pv++  ++i+++l +l++sgie+ +vv+  ++  +++++l++++k   +++++
  gi|313122421|ref|YP_004038308.1|   7 AVVLAAGEGRRLRPLTKYLPKPMLPVANR-PVIDYVLDALVESGIER-VVVVVGYRGDRIQTHLTAEYKG-ANIEFV 80 
                                       89***************************.*****************.78888899************75.5***** PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++p++ g+ +A+++a  +++ e+     lv++gD +i+   ++ ++++  +++    +t+++ + + ++eyGv+ ++
  gi|313122421|ref|YP_004038308.1|  81 QQPSRLGSGHALLQATGMVNGEF-----LVVNGDSIINAaIVTSTLERYDSTDC--AATVAVAHSDTPEEYGVVITN 150
                                       ********************888.....9*********9556677777766666..99****************988 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                         g + ++ E P e +  +++++G+Yvf+++v+  l  d +e ++ge  +td+++ +  +g +  ++l ++  +W D
  gi|313122421|ref|YP_004038308.1| 151 R-GLIADIDEHPVERE-GYVVNAGVYVFDESVFAAL--DRTEPWQGEIRLTDAIEHL--DG-PVTSILVNG--GWLD 218
                                       7.89************.*******************..579*************998..54.444667777..6888 PP

                                       XSSHHH CS
                   NTP_transferase 232 vGtlds 237
                                         t+  
  gi|313122421|ref|YP_004038308.1| 219 PSTPWQ 224
                                       655555 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.1   2.1e-21   5.5e-18       1     128 [.       7     166 ..       7     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.1e-21
                                       EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC......HHHHHHTTCTS-EEE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggde......evlaalarlgvrvvede 66 
                                       av+LA+G+++R+       +K++lp++++p++++vldal ++g+++vvvv+g++      +++a++++ ++++v+++
  gi|313122421|ref|YP_004038308.1|   7 AVVLAAGEGRRLRPltkylPKPMLPVANRPVIDYVLDALVESGIERVVVVVGYRgdriqtHLTAEYKGANIEFVQQP 83 
                                       79**********8444579********************************9965566667788889999******8 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS.SEE............... CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptye.ger............... 127
                                        +  g +++l+ a   +  +  +lv+ +D + +++++v   l+++++++++++v+++  +++               
  gi|313122421|ref|YP_004038308.1|  84 -SRLGSGHALLQATGMV--NGEFLVVNGDSI-INAAIVTSTLERYDSTDCAATVAVAHsDTPeeygvvitnrgliad 156
                                       .6899999999999987..79*********5.6***************99886665540444666666666666666 PP

                                       .........E CS
                      NTP_transf_3 128 .........g 128
                                                g
  gi|313122421|ref|YP_004038308.1| 157 idehpvereG 166
                                       6655555552 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.8   1.2e-08   3.1e-05       3      35 ..     242     274 ..     238     275 .. 0.88
   2 !   18.5   0.9   4.6e-07    0.0012       4      30 ..     267     293 ..     267     294 .. 0.67
   3 !    8.6   0.1   0.00063       1.6       2      26 ..     300     323 ..     299     324 .. 0.85
   4 !   18.4   1.6   5.1e-07    0.0013       2      35 ..     346     379 ..     345     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.2e-08
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                        + + + ++  av+ g+V+IG+++ +g+g+vi+
  gi|313122421|ref|YP_004038308.1| 242 YVADSARVHESAVVEGPVVIGKDCDVGPGAVIR 274
                                       55677888889*********************7 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.6e-07
                                       EETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIga 30 
                                       +G +++I+p++ + +nV++G n+++++
  gi|313122421|ref|YP_004038308.1| 267 VGPGAVIRPGTCLQDNVHVGANAVVER 293
                                       466777777777777777777777765 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00063
                                       EEEETTEEE-TTEEEETTEEE-TTE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnv 26 
                                       +++G ++l++  +v+g+++ IGd v
  gi|313122421|ref|YP_004038308.1| 300 AHVGAHTLLR-DSVVGSGARIGDCV 323
                                       7889999999.99999999999965 PP

  == domain 4  score: 18.4 bits;  conditional E-value: 5.1e-07
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++ + +++g++a+++++  +G  +++gagvv+ 
  gi|313122421|ref|YP_004038308.1| 346 SIVADRATVGANATLAAGSSVGAEATVGAGVVVD 379
                                       5677899*************************96 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.22   5.7e+02      25      32 ..     168     175 ..     164     176 .. 0.84
   2 !   31.2   1.4   5.1e-11   1.3e-07       1      33 [.     258     292 ..     258     293 .. 0.97
   3 ?   -1.9   0.0       1.2     3e+03      24      30 ..     311     317 ..     309     321 .. 0.46
   4 !   17.9   1.6   7.5e-07    0.0019       6      33 ..     350     379 ..     347     379 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                                       EE-TT-EE CS
                         Hexapep_2  25 vvgaGvvi 32 
                                       vv aGv++
  gi|313122421|ref|YP_004038308.1| 168 VVNAGVYV 175
                                       99*****8 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 5.1e-11
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                       pv IG++C +G+ a+i  G+ l dn++vga+ v+ 
  gi|313122421|ref|YP_004038308.1| 258 PVVIGKDCDVGPGAVIrpGTCLQDNVHVGANAVVE 292
                                       8********************************96 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                                       -EE-TT- CS
                         Hexapep_2  24 cvvgaGv 30 
                                       +vvg+G 
  gi|313122421|ref|YP_004038308.1| 311 SVVGSGA 317
                                       4444443 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 7.5e-07
                                       TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                         Hexapep_2   6 dnCliGanagi..GvslGdncvvgaGvvit 33 
                                       d+  +Gana+   G s+G +++vgaGvv++
  gi|313122421|ref|YP_004038308.1| 350 DRATVGANATLaaGSSVGAEATVGAGVVVD 379
                                       7899******557***************96 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1     1e-08   2.6e-05       3     133 ..       7     140 ..       5     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1e-08
                                       EEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEEE CS
                              IspD   3 vvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlva 72 
                                       +v+ AAG+G+R++   + lpK  l +++++++   +dal + + ++++vvvv     +++++ l++     +i+ v+
  gi|313122421|ref|YP_004038308.1|   7 AVVLAAGEGRRLRpltKYLPKPMLPVANRPVIDYVLDALVE-SGIERVVVVVGYRG-DRIQTHLTAeykgANIEFVQ 81 
                                       79*********85332789*********************9.67899988887666.56665555558787899998 PP

                                       --SSHHHHHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSE CS
                              IspD  73 GGdeRaesVlnglkalegeakfVLvHDaARpllkaadiaellaaaeqstqgailalpvkDt 133
                                           R  s  + l+a    +   Lv ++   +++aa + + l+  + +  +a +a++ +Dt
  gi|313122421|ref|YP_004038308.1|  82 QP-SRLGSGHALLQATGMVNGEFLVVNGDS-IINAAIVTSTLERYDSTDCAATVAVAHSDT 140
                                       75.588888888888777776677777766.899999999999999888888889998888 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.21   5.5e+02      48      96 ..      98     150 ..      91     185 .. 0.60
   2 ?   10.4   0.1   8.4e-05      0.22     279     317 ..     277     315 ..     231     325 .. 0.78
   3 ?   -3.3   0.0       1.3   3.3e+03     278     312 ..     345     380 ..     344     386 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.21
                        Fucokinase  48 m.kpGvlvtssDvlllf...dseeisfdka...gvtalavpstldigtnHGVfvld 96 
                                       m ++ +lv+++D ++     +s   + d++     +a+a+    d+ ++ GV++++
  gi|313122421|ref|YP_004038308.1|  98 MvNGEFLVVNGDSIINAaivTSTLERYDSTdcaATVAVAHS---DTPEEYGVVITN 150
                                       54788888888888844332222222222222233444443...344555555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.4e-05
                        Fucokinase 279 Svlessvsvgegsviehsslkgnvsigsnsivsgleles 317
                                       + l+ +v+vg+++v+e s l+ + ++g+++++ +  + s
  gi|313122421|ref|YP_004038308.1| 277 TCLQDNVHVGANAVVERSILSTDAHVGAHTLLRDSVVGS 315
                                       568888999999999999999999999988887776655 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.3
                        Fucokinase 278 nSvlessvsvgegsvie.hsslkgnvsigsnsivsg 312
                                        S+++ +++vg+++ +   ss++++ ++g++ +v g
  gi|313122421|ref|YP_004038308.1| 345 GSIVADRATVGANATLAaGSSVGAEATVGAGVVVDG 380
                                       588888999997776653688889999999888865 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.33      16      45 ..      27      55 ..      25      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                      GGGSEETTEEHHHHHHHHHHHTTTTSEEEE CS
                      CTP_transf_3 16 Knlldlggkpliayvleaalkskafekviv 45
                                      K++l+ +++p i+yvl+a+++s+  e+v+v
  gi|313122421|ref|YP_004038308.1| 27 KPMLPVANRPVIDYVLDALVESGI-ERVVV 55
                                      9*********************99.77665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2587.15
//
Query:       gi|313122422|ref|YP_004038309.1|  [L=202]
Description: hypothetical protein Hbor_36560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.007   16.2   0.0     0.0077   16.1   0.0    1.1  1  FA_desaturase  Fatty acid desaturase
  ------ inclusion threshold ------
      0.027   14.6   1.4       0.05   13.8   1.4    1.5  1  GreA_GreB_N    Transcription elongation factor, N-terminal
      0.036   14.4   0.1      0.058   13.7   0.1    1.3  1  YwiC           YwiC-like protein


Domain annotation for each model (and alignments):
>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-06    0.0077     140     185 ..     150     198 ..      76     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                     FA_desaturase 140 wlllllawlglwlalllllglall...lwlvplllllfllalvlnyveH 185
                                       ++++ ++++g++++ll+++g+al+   +w+v+ +++l++l+ +++y +H
  gi|313122422|ref|YP_004038309.1| 150 AAVAGVVGIGVAAGLLGAPGFALVpdaAWAVVSTTALVVLTAMETYHQH 198
                                       333344459999999999999999************************* PP

>> GreA_GreB_N  Transcription elongation factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.4   8.4e-06      0.05      16      55 ..      41      80 ..      27      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-06
                                      HHHHHXHHHHHHHHHHHHHHHSSSTSSHHHHHHHHHHHHH CS
                       GreA_GreB_N 16 eelktverpeiaeaikeareeGDlsENaeYdaAkeeqaei 55
                                      e lk+++r ++++ +ke   e+ l + aeY aAke   ei
  gi|313122422|ref|YP_004038309.1| 41 ELLKNQRRRDAIRYLKENDGEAKLGDMAEYIAAKENDIEI 80
                                      669********************************87766 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   9.7e-06     0.058      52     103 ..     146     197 ..     134     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.7e-06
                              YwiC  52 rrrarylkplliYgavallllllalllqpallwwallflplvavavyeakrk 103
                                       ++r+++++ ++  g++a+ll+++ ++l p   w+++   +lv++ ++e++++
  gi|313122422|ref|YP_004038309.1| 146 SKRNAAVAGVVGIGVAAGLLGAPGFALVPDAAWAVVSTTALVVLTAMETYHQ 197
                                       578889999999*************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1436.73
//
Query:       gi|313122423|ref|YP_004038310.1|  [L=178]
Description: hypothetical protein Hbor_36570 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00045   20.2   0.0       0.43   10.7   0.0    2.3  2  HTH_20         Helix-turn-helix domain
    0.00071   19.4   0.0        1.2    9.0   0.0    2.3  2  HTH_5          Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
       0.17   11.7   2.0       0.23   11.2   2.0    1.2  1  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   7.3e-05      0.43       1      34 [.       7      41 ..       7      62 .. 0.87
   2 !    7.5   0.0   0.00069       4.1      43      61 .]      68      86 ..      63      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.3e-05
                                      HHHHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHH CS
                            HTH_20  1 dqiaeALahPvRrrilraL.araegltaselaerl 34
                                      d+++++L++  Rr i  +L   ++++++++la+r+
  gi|313122423|ref|YP_004038310.1|  7 DELFRILSNSRRRYIIYYLhEAGDEMSLKQLAARI 41
                                      689****************9999**********98 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00069
                                      HHHHHHHHCTTEEEECTEE CS
                            HTH_20 43 yHLrvLeeagLvevvregr 61
                                       HL +Leeag+v   +e+r
  gi|313122423|ref|YP_004038310.1| 68 THLPKLEEAGIVSYDDEER 86
                                      59**********9988875 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00037       2.2       2      23 ..      16      39 ..      15      42 .. 0.90
   2 !    9.0   0.0    0.0002       1.2      34      47 .]      68      81 ..      67      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00037
                                      HHHHHHHHHHTT..SSEEHHHHHH CS
                             HTH_5  2 ptRlkILklLae..gelcvcelae 23
                                      + R+ I+++L e   e++  +la+
  gi|313122423|ref|YP_004038310.1| 16 SRRRYIIYYLHEagDEMSLKQLAA 39
                                      78***********999******98 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0002
                                      HHHHHHHHTTSEEE CS
                             HTH_5 34 hHLkkLreaGLVek 47
                                       HL kL+eaG+V++
  gi|313122423|ref|YP_004038310.1| 68 THLPKLEEAGIVSY 81
                                      6***********86 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.0   3.9e-05      0.23     127     180 ..     103     157 ..      87     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.9e-05
                     FA_desaturase 127 psksrrrkwrllawlllllawlglwlalllllglall.lwlvplllllfllalvl 180
                                       ++++ +r+w  +++ l +++wl++++ +++l+ +a+l ++++++++  ++l+lv 
  gi|313122423|ref|YP_004038310.1| 103 RTEDEPRPWATYYAILGVVGWLAILARIIGLPLFAALpWVAIAVFVSTAILVLVG 157
                                       4566778899999999999999999999999999999777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1371.83
//
Query:       gi|313122424|ref|YP_004038311.1|  [L=92]
Description: transcriptional regulator, PadR family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-13   50.2   0.2    2.2e-13   50.0   0.2    1.1  1  PadR      Transcriptional regulator PadR-like family
    0.00025   20.8   0.0     0.0003   20.5   0.0    1.3  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
     0.0063   16.3   0.0     0.0069   16.2   0.0    1.1  1  DUF4364   Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.025   14.7   0.0    1.2  1  HTH_34    Winged helix DNA-binding domain
      0.046   13.9   0.0      0.051   13.7   0.0    1.1  1  FUR       Ferric uptake regulator family
      0.059   13.4   0.0      0.076   13.0   0.0    1.2  1  HTH_45    Winged helix-turn-helix
      0.065   13.7   0.0      0.086   13.3   0.0    1.4  1  HTH_27    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.2   8.5e-17   2.2e-13       2      74 ..      12      78 ..      11      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 8.5e-17
                                      HHHH..CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  2 Lall..eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      L+++  +e+p  G ei++++ + + g  e+++G+lYp+L+ L +eglv++ +++    ++++yY++ + Gr++++
  gi|313122424|ref|YP_004038311.1| 12 LYVIagSERP-SGQEIKEKIGKDV-G--EVNHGRLYPNLDALVEEGLVDKGQQD----RRTNYYTISESGRQAIR 78
                                      7777534455.8**********96.5..8**********************998....7*************987 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.2e-07    0.0003      50      86 ..      40      76 ..      10      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                           DUF1495 50 gkrynsessLielGLveeeeeseglklYklteeGiei 86
                                      g  y + ++L+e GLv + ++++ +++Y+++e+G++ 
  gi|313122424|ref|YP_004038311.1| 40 GRLYPNLDALVEEGLVDKGQQDRRTNYYTISESGRQA 76
                                      55688889**************************975 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.7e-06    0.0069      29      71 ..      35      78 ..      11      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-06
                           DUF4364 29 eytnYfdlqqalseLvesglieee.ekenktlykiTekGketle 71
                                      + +n   l   l+ Lve+gl+++  +++ +++y+i+e+G+++++
  gi|313122424|ref|YP_004038311.1| 35 GEVNHGRLYPNLDALVEEGLVDKGqQDRRTNYYTISESGRQAIR 78
                                      5566666777799**********9777999**********9986 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   9.8e-06     0.025      22      75 ..      33      83 ..      11      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.8e-06
                            HTH_34 22 ealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvka 75
                                      +  e++ g+L+ +l++L + g   vdk+ +++ +   ++i + Gr+a  k  ++
  gi|313122424|ref|YP_004038311.1| 33 DVGEVNHGRLYPNLDALVEEGL--VDKGQQDR-RTNYYTISESGRQAIRKRREW 83
                                      344799***************7..58999999.8899**********9998777 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05     0.051      23      74 ..      20      71 ..       4      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                      SBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS CS
                               FUR 23 hlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelak 74
                                       +s +e+ +++ ++  e+    +Y +L+ l e+glv++ + +  +++y +++
  gi|313122424|ref|YP_004038311.1| 20 RPSGQEIKEKIGKDVGEVNHGRLYPNLDALVEEGLVDKGQQDRRTNYYTISE 71
                                      47899************************************99999988875 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     3e-05     0.076      31      73 ..      37      84 ..      19      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                            HTH_45 31 LsykllnkYLdmLvekgli.....kkskekYvlTekGlelleklkele 73
                                       +  +l   Ld Lve+gl+     + +++ Y++ e G++ ++k +e e
  gi|313122424|ref|YP_004038311.1| 37 VNHGRLYPNLDALVEEGLVdkgqqDRRTNYYTISESGRQAIRKRREWE 84
                                      5666777889*********999755588999********999988876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.4e-05     0.086      38      68 .]      45      73 ..       4      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                            HTH_27 38 slkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +l++L+e GLv   +  +drr+  ++++++G
  gi|313122424|ref|YP_004038311.1| 45 NLDALVEEGLV--DKGQQDRRTNYYTISESG 73
                                      699********..666689*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 633.71
//
Query:       gi|313122425|ref|YP_004038312.1|  [L=26]
Description: hypothetical protein Hbor_36590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (26 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       151  (0.00842211); expected 358.6 (0.02)
Passed bias filter:                       78  (0.00435049); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 187.92
//
Query:       gi|313122426|ref|YP_004038313.1|  [L=375]
Description: UDP-N-acetylglucosamine 2-epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.9e-110  368.0   0.0   4.6e-110  367.7   0.0    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.088   12.8   0.0    1.9  1  Glyco_transf_4   Glycosyltransferase Family 4
       0.17   11.9   0.0       0.27   11.2   0.0    1.2  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.7   0.0  7.8e-114  4.6e-110       3     346 ..      31     362 ..      29     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: 367.7 bits;  conditional E-value: 7.8e-114
                                       HTTS-..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHH CS
                       Epimerase_2   3 lkaeselelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtne 79 
                                       ++++  +++ l++tGqH+++++++++f++le+++pdy+l+++s s++++tgr+l+g+e++le+  pD+vlv+GDtn+
  gi|313122426|ref|YP_004038313.1|  31 CDRR-GVDCLLIHTGQHYSEDLDQVFFDQLELPTPDYNLEVGSRSHGEQTGRMLEGIENLLEAHTPDIVLVQGDTNS 106
                                       5555.789********************************************************************* PP

                                       HHHHHHHHHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHH CS
                       Epimerase_2  80 tlagalaAfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviD 156
                                       +lagala++k +i+v+HveAGlRsfd++  mpeE+nR+++d++sd++faptee ++ L +e + + +i+v+Gnt++D
  gi|313122426|ref|YP_004038313.1| 107 VLAGALAGAKSNIDVGHVEAGLRSFDRE--MPEETNRVVTDHVSDYLFAPTEETKRYLERESV-PGEIVVTGNTIVD 180
                                       ****************************..********************************9.668********** PP

                                       HHHHHHHHHH...T-HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHH CS
                       Epimerase_2 157 alllskeeieeklkaseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkr 231
                                       +l+++++ ++ek    ++l+e  ++e++++l+t+Hr+en+d  +++ ++le +++ a+++d evv+p+h  pr ++r
  gi|313122426|ref|YP_004038313.1| 181 SLYEYRDLAAEKS---DVLNElnVAEDDFYLLTAHRAENVDTRDSFDRLLEGVSRFAAQTDREVVYPIH--PRAQSR 252
                                       *********9655...99999999*********************************************..****** PP

                                       HHHHHHH-.TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HH CS
                       Epimerase_2 232 lleeleel.envtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgtdke 307
                                       l e   ++ e+++ iepl++ldfl+l ++a lv tdSgG+qeE+++lg+p+v+lR +teRpe+   g+n+l+g d++
  gi|313122426|ref|YP_004038313.1| 253 LDEFGLAVpEEIRTIEPLDFLDFLRLESAAALVFTDSGGVQEETCILGTPCVTLRYSTERPETAYVGANCLAGLDPD 329
                                       *887777767******************************************************************* PP

                                       HHHHHHHHHCT-..--......--TT-SS-HHHHHHHHH CS
                       Epimerase_2 308 eIvaaleklledkkelekmanaknpYgdGkaseriveil 346
                                       +Iv+a + +l +      +a++  p+gdG+a+eri+++l
  gi|313122426|ref|YP_004038313.1| 330 DIVEAGTMMLGK------CADWDVPFGDGRAAERILDVL 362
                                       **********65......677777*************98 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.5e-05     0.088      11     165 ..      27     177 ..      25     181 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                    Glyco_transf_4  11 LaraLarrGheVtvv.tpgddgpleeev.....elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs. 80 
                                       L++a  rrG+++ ++ t ++  +  ++v     el +        ++    ++ ++l  + +ll+++ pD+v +++ 
  gi|313122426|ref|YP_004038313.1|  27 LIKACDRRGVDCLLIhTGQHYSEDLDQVffdqlELPTPDYNLEVGSRSHGEQTGRMLEGIENLLEAHTPDIVLVQGd 103
                                       678899999999999533333333333366654333333333445566677888899999************99972 PP

                    Glyco_transf_4  81 paalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl.lrradrviavSeatadelrerygvpp 156
                                         +++a++la ++ ++i + +   gl          ++ + + ++  r +  + +d ++a++e+t+++l++   vp 
  gi|313122426|ref|YP_004038313.1| 104 TNSVLAGALAGAK-SNIDVGHVEAGLR---------SFDREMPEETNRVVtDHVSDYLFAPTEETKRYLER-ESVP- 168
                                       4555666666665.9988888877777.........33333333333333344599***************.8899. PP

                    Glyco_transf_4 157 ekitVipnG 165
                                         i+V  n 
  gi|313122426|ref|YP_004038313.1| 169 GEIVVTGNT 177
                                       688887775 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.6e-05      0.27      13      97 ..      24     117 ..      11     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.6e-05
                   Glyco_trans_4_2  13 tlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd.......rkgpleylk.af.klkklikkikPDvvha 80 
                                       +  l+k+   rg+++ +i  +++++++l +  +   +l+ +       +++  e    ++  + +l+++  PD+v +
  gi|313122426|ref|YP_004038313.1|  24 CAPLIKACDRRGVDCLLIHTGQHYSEDLDQVFFDQLELPTPdynlevgSRSHGEQTGrMLeGIENLLEAHTPDIVLV 100
                                       4557888899999999999999999999999999999955566666657776666644776**************** PP

                   Glyco_trans_4_2  81 hyakpygllgslaarls 97 
                                       +  +  +l+g+la  +s
  gi|313122426|ref|YP_004038313.1| 101 QGDTNSVLAGALAGAKS 117
                                       **999999999986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2953.01
//
Query:       gi|313122427|ref|YP_004038314.1|  [L=433]
Description: nucleotide sugar dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-51  172.2   0.0    1.6e-50  171.3   0.0    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    1.3e-22   79.8   0.0    2.2e-22   79.1   0.0    1.4  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    4.3e-20   72.1   0.9    1.3e-18   67.3   0.1    3.2  3  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    7.8e-07   29.6   0.3       0.46   11.1   0.0    3.8  4  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      2e-05   24.8   0.0    4.9e-05   23.6   0.0    1.7  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    6.3e-05   22.4   0.0      0.021   14.2   0.0    2.9  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00019   21.5   0.0     0.0032   17.5   0.0    2.4  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00037   20.7   0.3     0.0078   16.5   0.0    2.9  3  TrkA_N          TrkA-N domain
    0.00053   19.9   0.0    0.00098   19.1   0.0    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    0.00071   19.2   0.0     0.0013   18.4   0.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.3   0.0   8.7e-54   1.6e-50       1     183 [.       1     178 [.       1     181 [. 0.96

  Alignments for each domain:
  == domain 1  score: 171.3 bits;  conditional E-value: 8.7e-54
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77 
                                       mki+v G GY+Gl taa++a+ gh+v+g D +e+ v++l++g+   +e +L+e+v +a+         + +++v ea
  gi|313122427|ref|YP_004038314.1|   1 MKICVHGIGYIGLATAALFANNGHDVVGYDPNEKLVEELRAGNPRTTEDDLREYVLDAL-----DEDFEPSNEVVEA 72 
                                       8*********************************************************9.....344556777899* PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE--- CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPE 154
                                       d ++i+V+TP +++ k aDl+yve a +++ae+l++g++v+++STvp+gt+ee++ +il+ a+ + g+df++ ++PE
  gi|313122427|ref|YP_004038314.1|  73 DCHIICVPTPYEEESKRADLSYVEMAGQTVAEHLREGDMVILESTVPPGTTEEVLAPILAAAELTPGRDFSLSHCPE 149
                                       ****************************************************************99*********** PP

                                       ---TTSHHHHHHS-S-EEEEESSCHHHHH CS
                    UDPG_MGDP_dh_N 155 flregsavkdllnpdrvviGveekkaeaa 183
                                        +++g++ ++l+++dr+++G +++++ ++
  gi|313122427|ref|YP_004038314.1| 150 TVLPGNIAHELVHNDRIIGGIDDESTDKT 178
                                       ***********************998854 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   1.2e-25   2.2e-22       2      93 ..     198     283 ..     197     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.2e-25
                      UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeel 78 
                                       tAE++Kl +Na+++++I+f+Nela+++  +gi  ++ i+ ++ +pr    +l+pg+GvGG+clp D+++L + +++ 
  gi|313122427|ref|YP_004038314.1| 198 TAEFVKLSQNAYRDVNIAFANELARVAADYGISSRDAIDLANVHPR--VDILNPGPGVGGHCLPIDPWFLGQFSDS- 271
                                       9*********************************************..59************************99. PP

                      UDPG_MGDP_dh  79 gleaelleavrevNe 93 
                                          ++l+e++r+vN+
  gi|313122427|ref|YP_004038314.1| 272 ---LNLIESARRVND 283
                                       ...599*******97 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.29   5.3e+02      24      51 ..      17      56 ..      13     101 .. 0.60
   2 ?   -0.8   0.0       1.2   2.1e+03      30      63 ..     176     208 ..     166     226 .. 0.67
   3 !   67.3   0.1   7.4e-22   1.3e-18       1     104 [.     306     419 ..     306     420 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.29
                                      HHHHHCTSEEEEE-SSTHHCCCCHHGG............B CS
                    UDPG_MGDP_dh_C 24 eeLleegaevkiyDPkvkeeaveaele............e 51
                                      +  +++g +v+ yDP+ k  ++ + ++            +
  gi|313122427|ref|YP_004038314.1| 17 ALFANNGHDVVGYDPNEKLVEELRAGNprtteddlreyvL 56
                                      5667889999999997665555444444556655554442 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       TSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHH CS
                    UDPG_MGDP_dh_C  30 gaevkiyDPkvkeeaveaeleekgvevvdsleea 63 
                                       ++ +  yDP v+    +a ++++++e+v+  ++a
  gi|313122427|ref|YP_004038314.1| 176 DKTIALYDPLVEGTIHRA-PDATTAEFVKLSQNA 208
                                       567899999998866655.444444444433444 PP

  == domain 3  score: 67.3 bits;  conditional E-value: 7.4e-22
                                       EEE-SSSSTT-S--TT-HHHHHHHHHHHCTS.................EEEEE-SSTHHCCCCHHGGBTCCEEES-C CS
                    UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleega.................evkiyDPkvkeeaveaeleekgvevvdsl 60 
                                       a+lG+a+K ++dD R+Sp l+++e+L+ ++                   v+++DP+v++++++       + +v +l
  gi|313122427|ref|YP_004038314.1| 306 AVLGVAYKGNVDDARHSPGLRLVERLTTMEPrevgaaaadggqtracgSVRVHDPHVESDESSD------IDIV-DL 375
                                       89************************9996667777***********************99875......8888.7* PP

                                       HHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS-EEEESSS-CC CS
                    UDPG_MGDP_dh_C  61 eealkgadaiviltehdefkeldlaklkelmkpavvfDgrnvld 104
                                       e+al+gada+v++  hd f +++ a++++lm  +v++D   +ld
  gi|313122427|ref|YP_004038314.1| 376 ETALDGADAVVVCAGHDAFCDINPAEAADLMDGRVIVDSFSILD 419
                                       ***************************************99998 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00025      0.46       1      52 [.       2      48 ..       2      83 .. 0.78
   2 !    7.2   0.0    0.0043       7.7      27      82 ..      75     131 ..      58     137 .. 0.75
   3 ?   -2.6   0.0         5   8.9e+03      57      71 ..     298     312 ..     289     315 .. 0.78
   4 !    7.2   0.1    0.0042       7.5      49      93 ..     369     413 ..     348     416 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEEC CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvta 52
                                      ki++ G G +g a a  ++++g   h++v + ++n++ +eel++   +++t+
  gi|313122427|ref|YP_004038314.1|  2 KICVHGIGYIGLATAALFANNG---HDVV-GYDPNEKLVEELRAGN-PRTTE 48
                                      67888*****************...****.*9****9999997654.34444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0043
                                       CEEEEEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SEEEE..-S-HHHHHHHHHHCG CS
                     F420_oxidored  27 eivvansrnpekaeelaeelg.vkvtavdneeaaeeadvvvl..avkpedveevlsela 82 
                                       +i+  + ++p + e+ +++l+ v++ + + +e ++e d+v+l  +v+p  +eevl+ + 
  gi|313122427|ref|YP_004038314.1|  75 HII--CVPTPYEEESKRADLSyVEMAGQTVAEHLREGDMVILesTVPPGTTEEVLAPIL 131
                                       444..455555555555555448999999************9888**********9984 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5
                                       HHHHH-SEEEE-S-H CS
                     F420_oxidored  57 eaaeeadvvvlavkp 71 
                                         +e+ad+ vl v +
  gi|313122427|ref|YP_004038314.1| 298 SSLENADIAVLGVAY 312
                                       567899999999865 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0042
                                       EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                     F420_oxidored  49 kvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                       ++  vd e+a++ ad vv++    ++ ++  + a+d+  g+++++
  gi|313122427|ref|YP_004038314.1| 369 DIDIVDLETALDGADAVVVCAGHDAFCDINPAEAADLMDGRVIVD 413
                                       6677889**************************9*********99 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.7e-08   4.9e-05       1     101 [.       2     127 ..       2     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.7e-08
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...............EEE-SSHHHHHHHCSEEEE- CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...............akaaesieelvasldvvitm 62 
                                       ki + G+G +G   a  ++++g++v++y+ +++ veel a +               ++   ++++ v ++d+ i++
  gi|313122427|ref|YP_004038314.1|   2 KICVHGIGYIGLATAALFANNGHDVVGYDPNEKLVEELRAGNprtteddlreyvldaLDEDFEPSNEVVEADCHIIC 78 
                                       68899**********************************99898888888888866544555556666666999*** PP

                                       SSSHHHHHHHHHS..........HCCC--TT-EEEE-S---HHHHHHHH CS
                     NAD_binding_2  63 vkagkavdevieg..........llealkkgdilidgstsspedtrela 101
                                       v+   + ++   +          ++e+l++gd++i  st+ p +t+e+ 
  gi|313122427|ref|YP_004038314.1|  79 VPTPYEEESKRADlsyvemagqtVAEHLREGDMVILESTVPPGTTEEVL 127
                                       *9876666655555666789999**********************9986 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.2e-05     0.021      38      75 ..       2      39 ..       1      58 [. 0.81
   2 ?   -1.0   0.0      0.53   9.4e+02      80     106 ..      97     123 ..      68     150 .. 0.58
   3 ?    4.5   0.0     0.011        19      48      99 ..     340     389 ..     338     395 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeee 75
                                      ++++ G+G IG a+a +++  g +v++yd+++k  ee 
  gi|313122427|ref|YP_004038314.1|  2 KICVHGIGYIGLATAALFANNGHDVVGYDPNEKLVEEL 39
                                      7899***************************9866633 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.53
                                       CEECSHHHHHHH-SEEEE-S--STTTT CS
                      2-Hacid_dh_C  80 velvsleellaesDivslhlpltpetr 106
                                       +  +++ e l+e D+v+l   + p t+
  gi|313122427|ref|YP_004038314.1|  97 MAGQTVAEHLREGDMVILESTVPPGTT 123
                                       333466666777777666655555544 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHTT-.EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  48 Gqavakrlkafgm.kviaydrskkkeeeeeelgvelvsleellaesDivslhl 99 
                                       G a+a+  +   +  v ++d++ +++   e+  ++ v+le++l  +D v++++
  gi|313122427|ref|YP_004038314.1| 340 GAAAADGGQTRACgSVRVHDPHVESD---ESSDIDIVDLETALDGADAVVVCA 389
                                       55555555555555789999997744...4667899*************9975 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.8e-06    0.0032       1      79 [.       2      81 ..       2      94 .. 0.80
   2 ?   -3.5   0.0         5     9e+03      60      77 ..     293     310 ..     279     313 .. 0.66
   3 ?    0.9   0.0      0.23   4.1e+02      61      83 ..     373     395 ..     368     412 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH..SSBTTTBTT----TTEEEES-HHHHHTT--EEEE-- CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeinee..henvkyLpgiklpenlvattdlaealkgadiivlvv 77
                                      ki+v G G  G a A+++a+ngh+v+ +  +e+l+ee+++   ++ ++ L+++ l+ +l    +  + + +ad+ ++ v
  gi|313122427|ref|YP_004038314.1|  2 KICVHGIGYIGLATAALFANNGHDVVGYDPNEKLVEELRAGnpRTTEDDLREYVLD-ALDEDFEPSNEVVEADCHIICV 79
                                      79************************************864115666777777665.4666666666666777777777 PP

                                      -H CS
                    NAD_Gly3P_dh_N 78 Ps 79
                                      P+
  gi|313122427|ref|YP_004038314.1| 80 PT 81
                                      76 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5
                                       ES-HHHHHTT--EEEE-- CS
                    NAD_Gly3P_dh_N  60 ttdlaealkgadiivlvv 77 
                                        +d  ++l++adi vl v
  gi|313122427|ref|YP_004038314.1| 293 LEDELSSLENADIAVLGV 310
                                       455556777777777776 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.23
                                       S-HHHHHTT--EEEE---HHHHH CS
                    NAD_Gly3P_dh_N  61 tdlaealkgadiivlvvPsqalr 83 
                                        dl++al+gad +v+   + a+ 
  gi|313122427|ref|YP_004038314.1| 373 VDLETALDGADAVVVCAGHDAFC 395
                                       69************998888775 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.4e-06    0.0078       1      73 [.       3      82 ..       3     103 .. 0.82
   2 ?   -0.9   0.0       1.1   1.9e+03       9      27 ..      98     114 ..      93     118 .. 0.79
   3 ?    0.2   0.0       0.5     9e+02      58      75 ..     377     394 ..     350     428 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.4e-06
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSE.......EEES-TTSHHHHHHTTGGGESEEEE-SSS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreegle.......vvvgdatdeevLeeagiekadaviaatgd 72
                                      i + G G +G + a  + ++g+dvv+ d +e+ veelr+ + +        +v da de++  + ++ +ad+ i++++ 
  gi|313122427|ref|YP_004038314.1|  3 ICVHGIGYIGLATAALFANNGHDVVGYDPNEKLVEELRAGNPRtteddlrEYVLDALDEDFEPSNEVVEADCHIICVPT 81
                                      6799***************6669**************887733233444488999999999999999999998888875 PP

                                      H CS
                            TrkA_N 73 d 73
                                       
  gi|313122427|ref|YP_004038314.1| 82 P 82
                                      4 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHTTEEEEEE CS
                            TrkA_N   9 vGrslaeeLseggkdvvvi 27 
                                        G+++ae L+eg   +v+ 
  gi|313122427|ref|YP_004038314.1|  98 AGQTVAEHLREGD--MVIL 114
                                       599******9977..4554 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.5
                                       TTGGGESEEEE-SSSHHH CS
                            TrkA_N  58 agiekadaviaatgddea 75 
                                         ++ adav++++g+d++
  gi|313122427|ref|YP_004038314.1| 377 TALDGADAVVVCAGHDAF 394
                                       568899******999964 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   5.4e-07   0.00098       1      42 [.       2      43 ..       2      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.4e-07
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42
                                      k+ v G G +G   aa+fa++g++Vv +d +e+ +e+ ++  
  gi|313122427|ref|YP_004038314.1|  2 KICVHGIGYIGLATAALFANNGHDVVGYDPNEKLVEELRAGN 43
                                      58899*****************************99988765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   7.2e-07    0.0013       1      82 [.       3      85 ..       3     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.2e-07
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKa 78
                                      i++ G+G iG   aa  a++g+dv+ ++ ++  +e+l+  + r t+++  e++++    ++e++ e  ++d  i++v++
  gi|313122427|ref|YP_004038314.1|  3 ICVHGIGYIGLATAALFANNGHDVVGYDPNEkLVEELRAGNPRTTEDDLREYVLDALDEDFEPSNEVVEADCHIICVPT 81
                                      89*****************************9****************8889998888888888999**********98 PP

                                      GGHH CS
                              ApbA 79 yqte 82
                                         e
  gi|313122427|ref|YP_004038314.1| 82 PYEE 85
                                      7655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3013.85
//
Query:       gi|313122428|ref|YP_004038315.1|  [L=121]
Description: hypothetical protein Hbor_36620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 808.70
//
Query:       gi|313122429|ref|YP_004038316.1|  [L=265]
Description: dTDP-glucose pyrophosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-40  137.4   0.0    7.3e-40  137.1   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    2.4e-17   63.8   0.0      3e-17   63.4   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    8.9e-08   32.1   0.0    3.3e-07   30.3   0.0    1.8  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.1   0.0   1.2e-43   7.3e-40       1     237 [.       2     226 ..       2     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 137.1 bits;  conditional E-value: 1.2e-43
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kav+La G+GtRL PLt++ +k lv v g  ++++++l +l++ + +e i+v+ +++++++++   e  +  + +++
  gi|313122429|ref|YP_004038316.1|   2 KAVVLAAGKGTRLQPLTNDKPKALVEVDGR-PILEHCLDTLSELDADEFILVVGHRKEQIIARFGDEYRN--IPITY 75 
                                       79*************************999.*****************9999999999988886666655..56*** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       a+++e  g+A+Av+ a+e ++d++    +l+Lg D +++ ++ e+v++  ++ a+   ++  vp++ea++yGv  ++
  gi|313122429|ref|YP_004038316.1|  76 AHQREALGLAHAVLTAEEHVDDDF----MLMLG-DNIFEANLDEVVARQHDDHADAAFLVEEVPWDEASRYGVCVTN 147
                                       *********************999....67775.567788******999999998999999**************** PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE. CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs. 230
                                       ++g++ + vEKP++++ s+l+ +G Y+f + +++   + +++++rge e+ d++  ++++g+   a+  ++   W+ 
  gi|313122429|ref|YP_004038316.1| 148 DDGDIVEVVEKPDNPE-SNLVMTGFYTFSPAIFHAC-NLVQPSDRGEYELPDAIDLLIRSGRTISAIPCDG---WRv 219
                                       ****************.*****************99.88**********************9998877777...644 PP

                                       EXSSHHH CS
                   NTP_transferase 231 DvGtlds 237
                                       DvG +++
  gi|313122429|ref|YP_004038316.1| 220 DVGYPED 226
                                       9998876 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   5.1e-21     3e-17       1     125 [.       3     133 ..       3     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 5.1e-21
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC....TS-EEE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarl....gvrvvede 66 
                                       av+LA+G+++R++     ++Kal++++g+p+le++ld+l+++ +de ++v+g+  e++ a++ +     ++++++++
  gi|313122429|ref|YP_004038316.1|   3 AVVLAAGKGTRLQpltndKPKALVEVDGRPILEHCLDTLSELDADEFILVVGHrkEQIIARFGDEyrniPITYAHQR 79 
                                       79**********7443335***************************9999999444455444322332245555554 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSS CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeg 125
                                        +  g ++++++a +++  +d ++++++D ++  ++ +++++a+ ++++ad+++++ e 
  gi|313122429|ref|YP_004038316.1|  80 -EALGLAHAVLTAEEHV--DDDFMLMLGDNIF--EANLDEVVARQHDDHADAAFLVEEV 133
                                       .4689999999999997..799********99..8889999999999999999887765 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   5.5e-11   3.3e-07       2      55 ..       2      58 ..       1      74 [. 0.87
   2 ?   -1.1   0.0      0.22   1.3e+03     158     219 ..     176     234 ..     142     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 5.5e-11
                                      EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGG CS
                              IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvsedd 55
                                       +v+ AAG+G+R++   +++pK+++e++g+++leh +d+l +  a + i+vv ++++
  gi|313122429|ref|YP_004038316.1|  2 KAVVLAAGKGTRLQpltNDKPKALVEVDGRPILEHCLDTLSELDADEFILVVGHRKE 58
                                      69**********8755479***********************999999999988876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.22
                                       EEEEEHHHHHHHHHHHHHCT---SSHHHHHHHTT--EEEEE--TTG----SHHHHHHHHHHH CS
                              IspD 158 PqgFrvdlllaahakgeqegaeitDdaslvekiGlsvkvVeGeednlKittpeDlalAeail 219
                                       P  F+   l +  ++g    +e  D ++l+ + G ++  ++ +   + + +peD  +Ae ++
  gi|313122429|ref|YP_004038316.1| 176 PAIFHACNLVQPSDRG---EYELPDAIDLLIRSGRTISAIPCDGWRVDVGYPEDRDRAERLI 234
                                       3334443444444444...4678889999999999999999999999999999998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1929.46
//
Query:       gi|313122430|ref|YP_004038317.1|  [L=441]
Description: phosphomannomutase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-32  109.8   0.0    1.4e-31  109.0   0.0    1.4  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.6e-20   73.4   0.0      3e-20   72.5   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.2e-17   61.7   0.2    2.8e-16   60.0   0.2    1.9  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    6.5e-15   55.1   1.1    1.1e-14   54.4   0.1    1.9  2  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
  ------ inclusion threshold ------
      0.012   15.8   1.5      0.092   12.9   0.2    2.4  2  CinA_KH      Damage-inducible protein CinA KH domain


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.0   3.9e-35   1.4e-31       4     136 ..       2     127 ..       1     129 [. 0.96

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 3.9e-35
                                       BBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HH CS
                         PGM_PMM_I   4 fgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptP 80 
                                       fgtsG+Rg vg +++t++l++ +gqa+a  ++a     + vvGrD+Rv+++ la+al  gl + G +vi++g++ tP
  gi|313122430|ref|YP_004038317.1|   2 FGTSGIRGPVG-ETVTADLALHIGQAVA--VEA----DRAVVGRDARVTGDVLADALSVGLRECGTDVIRVGVAATP 71 
                                       9**********.779************9..555....579************************************* PP

                                       HHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT-E CS
                         PGM_PMM_I  81 avsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekeee 136
                                        ++ +++ ++ad g+ itaSHnp+ +ngiK+ +++G  +sp + e+Ie+++++ ++
  gi|313122430|ref|YP_004038317.1|  72 TIARSVEWFGADVGVAITASHNPAADNGIKLWNESGQAFSPTQNERIERRLDNDDS 127
                                       **************************************************999876 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   8.4e-24     3e-20       1     110 [.     246     350 ..     246     355 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 8.4e-24
                                       HHHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEET CS
                       PGM_PMM_III   1 dgdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifl 77 
                                       +gd llal+a+++ +   + g  v+ +v tsl++ +v++++g+++v t+vGd y++e++ ++g+v+GgE Sg +i +
  gi|313122430|ref|YP_004038317.1| 246 PGDVLLALFARDAVS---P-GDSVAVPVDTSLLVADVVASAGGTVVYTPVGDVYIAEAVSQSGFVFGGEPSGAWIWP 318
                                       69*********9966...4.556****************************************************** PP

                                       TTBSS--HHHHHHHHHHHHHHHTS-HHHHHHHH CS
                       PGM_PMM_III  78 deattkDGilaallvleilaetgkslselleel 110
                                       d++   D+ +aal+++ +++++g +lse ++++
  gi|313122430|ref|YP_004038317.1| 319 DQTLAPDANYAALRLADLIRREG-PLSEQVADI 350
                                       *******************9987.888888664 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.2   7.7e-20   2.8e-16       4     102 ..     149     241 ..     145     242 .. 0.87
   2 ?   -2.7   0.0       2.5     9e+03      17      34 ..     280     294 ..     273     337 .. 0.70

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 7.7e-20
                                       HHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGG CS
                        PGM_PMM_II   4 iealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkk 80 
                                       + a+++ +d    + +gl  v+d ++G+g+ ++ ++l elg+ v +l a+pd++fp + ++p++ e+l  l+++v +
  gi|313122430|ref|YP_004038317.1| 149 VSAITDEFD----SMTGLNAVVDLGNGTGRVTV-DALYELGATVNTLDAQPDGTFPARKSEPNA-ETLTTLQRTVPA 219
                                       445555555....6789999********98655.678899************************.************ PP

                                       GG-SEEEEE-TTS-BEEEEETT CS
                        PGM_PMM_II  81 egadlglafDgDaDRlgvvder 102
                                        +ad+g+a+DgD DR+++v + 
  gi|313122430|ref|YP_004038317.1| 220 LDADFGIAHDGDSDRMVAVSDT 241
                                       ******************9665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                       HHHT-EEEEE-TT-TTHH CS
                        PGM_PMM_II  17 kksglkvvidplhGagge 34 
                                       +++g +vv++p +     
  gi|313122430|ref|YP_004038317.1| 280 ASAGGTVVYTPVGD---V 294
                                       45566777777543...3 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.5   9.1e+03      25      46 ..      39      60 ..      17      70 .. 0.58
   2 !   54.4   0.1     3e-18   1.1e-14       5      73 ..     363     434 ..     360     435 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                                      CCCCCCCCGCCEEEE.EEEETT CS
                        PGM_PMM_IV 25 ikeglkilledGrrlavRpSGT 46
                                       + +   +l+d++++ +R  GT
  gi|313122430|ref|YP_004038317.1| 39 DARVTGDVLADALSVGLRECGT 60
                                      4444444455555555666665 PP

  == domain 2  score: 54.4 bits;  conditional E-value: 3e-18
                                       CHCC-TT..EECCCCCTTH....HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHHH CS
                        PGM_PMM_IV   5 rveekakvvaalaallkva....sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevaell 73 
                                       +v++ka +++a+++ll ++    ++ +g+++++ dG+ l vR+SGTepl+rv +Ea+ +++++ l eev+ l+
  gi|313122430|ref|YP_004038317.1| 363 PVDDKASAMRAIDGLLSAKyddiDTTDGVRVDTDDGWLL-VRASGTEPLVRVTAEARQESKADALLEEVTSLI 434
                                       688887799********99********************.****************************99887 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.12   4.3e+02      16      57 ..     331     375 ..     328     380 .. 0.81
   2 ?   12.9   0.2   2.6e-05     0.092      33      64 ..     404     435 ..     400     437 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                                       HHHGGGS-BSSS...EEEEEEETTEEEEEEE...EEHHHHHHHHH CS
                           CinA_KH  16 ekladlidrenp...tlAiyakegevtvRltakaaneeeaealia 57 
                                        +ladli+re p   ++A  a    +t Rl+   ++++ a + i+
  gi|313122430|ref|YP_004038317.1| 331 LRLADLIRREGPlseQVADIAASRYTTRRLSLPVDDKASAMRAID 375
                                       5899*****887767899999999899999988888888888876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.6e-05
                                       EETTEEEEEEE...EEHHHHHHHHH....HHH CS
                           CinA_KH  33 akegevtvRltakaaneeeaealiapveeeir 64 
                                       a+  e  vR+ta+a++e +a+al+++v+  i+
  gi|313122430|ref|YP_004038317.1| 404 ASGTEPLVRVTAEARQESKADALLEEVTSLIE 435
                                       6677889*******************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 3104.52
//
Query:       gi|313122431|ref|YP_004038318.1|  [L=106]
Description: hypothetical protein Hbor_36650 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-23   82.6   0.2    2.2e-23   82.3   0.2    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.2   1.2e-27   2.2e-23       2      75 .]      29      96 ..      28      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 1.2e-27
                            HalOD1  2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                      +e +st +v ++aa+e+++ptel+pL  +iDpdALd+Lf++      +++g+v+F+y gye+t+++dg  e+ p
  gi|313122431|ref|YP_004038318.1| 29 SELISTNIVLTIAAIEETEPTELPPLATTIDPDALDNLFTE------DSSGHVTFSYTGYEITIHNDGSLEIVP 96
                                      6789*************************************......788*******************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 787.64
//
Query:       gi|313122432|ref|YP_004038319.1|  [L=192]
Description: metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-08   32.9   5.7    6.2e-08   32.1   5.7    1.4  1  YdjM         LexA-binding, inner membrane-associated putative
  ------ inclusion threshold ------
      0.034   14.2   2.9      0.034   14.2   2.9    1.9  2  PsbX         Photosystem II reaction centre X protein (PsbX)
      0.036   13.5   0.0      0.041   13.3   0.0    1.2  1  DUF1616      Protein of unknown function (DUF1616)
      0.058   13.4   0.0      0.081   12.9   0.0    1.3  1  Zn_dep_PLPC  Zinc dependent phospholipase C


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   5.7   1.4e-11   6.2e-08       6     127 ..      13     130 ..       8     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.4e-11
                              YdjM   6 HallGaalglalaallgaake.avllavavlgAllPD.iDhpsstlgrklgllskklaklvgHRgftHSllflalla 80 
                                       H++++ +l   +  l  + +  +  +a+++lg+ +PD iD     l+ +l ll +        R+f HSl+  a+++
  gi|313122432|ref|YP_004038319.1|  13 HLAFAYVLYSSFFRLRYRLPPtWPGVALLALGSQAPDlID---KPLAWTLSLLPS-------GRSFAHSLVLGAVIV 79 
                                       55555555444433333322247899**************...566666666667.......9*********99999 PP

                              YdjM  81 lvlllllrlfgrsalrlglllllgvlsHlllDlltk.......yGvpllwPfsk 127
                                       +v+ +++r+++        ++++g+ sHl++D+  +           llwPf +
  gi|313122432|ref|YP_004038319.1|  80 VVAVAIIRRLDLP---GEKAFVIGYYSHLVGDSYRSvltgkfhELAFLLWPFAP 130
                                       9999999999976...6788************9988665444322356888864 PP

>> PsbX  Photosystem II reaction centre X protein (PsbX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.9   7.5e-06     0.034       3      25 ..      63      85 ..      62      86 .. 0.91
   2 ?   -2.9   1.0       1.6   7.3e+03      14      20 ..     160     166 ..     158     169 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.5e-06
                                      HHHHHHHHHHHHHH.HHHHHHHH CS
                              PsbX  3 PSLaNfllSLvaGalvVvipiaa 25
                                      PS  +f  SLv Ga++Vv+++a+
  gi|313122432|ref|YP_004038319.1| 63 PSGRSFAHSLVLGAVIVVVAVAI 85
                                      899999********999999986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.6
                                       HHH.HHH CS
                              PsbX  14 aGalvVv 20 
                                       ++++vV+
  gi|313122432|ref|YP_004038319.1| 160 FAGVVVL 166
                                       5674665 PP

>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.1e-06     0.041      90     121 ..      73     104 ..      56     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.1e-06
                           DUF1616  90 lslftlllalvAivrRsrlpeeerfsvplral 121
                                       + + ++++++vAi+rR+ lp e+ f + + + 
  gi|313122432|ref|YP_004038319.1|  73 VLGAVIVVVAVAIIRRLDLPGEKAFVIGYYSH 104
                                       456789999*****************966544 PP

>> Zn_dep_PLPC  Zinc dependent phospholipase C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05     0.081      28     106 ..      40     110 ..      37     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHGGGG.....-TT-GGG--BTTTTB-HHHHS-HHHHHHHHHHHHHHHHHC.....T-HHHHHHHHHHHHHH CS
                       Zn_dep_PLPC  28 alllGsvaPDl...eylfnasshsykthtkagllgedhhweetgkfllllikklrelyksegslklaafllGvlsHy 101
                                        l lGs aPDl   +        ++ +  +++   + h +   +  +  ++  +r+l        + af +G+ sH+
  gi|313122432|ref|YP_004038319.1|  40 LLALGSQAPDLidkP-------LAWTLSLLPSGRSFAHSLVLGAVIVVVAVAIIRRL----DLPGEKAFVIGYYSHL 105
                                       688999999994421.......34444444444667788888999999999999884....68889*********** PP

                                       HHHHT CS
                       Zn_dep_PLPC 102 vaDvf 106
                                       v D+ 
  gi|313122432|ref|YP_004038319.1| 106 VGDSY 110
                                       ***85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1382.42
//
Query:       gi|313122433|ref|YP_004038320.1|  [L=428]
Description: arylsulfatase A family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.5e-22   78.1   0.3      1e-21   77.7   0.3    1.2  1  Sulfatase  Sulfatase
  ------ inclusion threshold ------
      0.094   12.1   0.0       0.19   11.1   0.0    1.5  1  DUF560     Protein of unknown function (DUF560)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.3   1.1e-25     1e-21       2     309 .]       2     321 ..       1     321 [. 0.83

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 1.1e-25
                                       EEEEEEESSE-TTGSGGGTTTSCS.SHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHH CS
                         Sulfatase   2 nvvliladdlgagdlglyggktat.tpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggg 77 
                                       +vvl++a  ++ +++++ +g ++   p+l+rla+  ++f+++y+++p    ++ a+ltg  p+++            
  gi|313122433|ref|YP_004038320.1|   2 HVVLVTASAVRHDHVHAGNGQIHSsLPTLSRLADDATVFSRAYTSSPDHESTLRAILTGTHPTRDL----------- 67 
                                       699*******************999***************************************55........... PP

                                       CTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCC........ CS
                         Sulfatase  78 lpqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrv........ 146
                                           ++tL++   e G +t+++++ + g+       +++gf+   ++ t s++ + ++  +       +        
  gi|313122433|ref|YP_004038320.1|  68 --GVVPTLVDTIAESGWETGLFHGDSDGPL------TSWGFEVPDESTTHSTTEQFRQMLGQ------Kitaettlg 130
                                       ..5799*************77776666666......67788744443333333332222222......122334578 PP

                                       ..................TTTTCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSST.....CTCGGHTCCGSTTT CS
                         Sulfatase 147 ..................ppeggysddrlldealefllarndkpfflylatlapHapp.....eapdeyakkyatff 200
                                                           ++ +  ++++++al + l ++++p+fl++++    ap+     +++d++ k++at+ 
  gi|313122433|ref|YP_004038320.1| 131 gllergdrllgsslgirlTSSPTHAGEAVTERALSW-LTETTEPQFLWVHYDDAAAPHvpregTVSDDIDKRTATKL 206
                                       88888888999*******99****************.5888**********85554444459999999999999888 PP

                                       TCCCCCCH.........HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSS CS
                         Sulfatase 201 ddgseaar.........qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkgana 268
                                         + e+a           l + y + +e  D+++g++++ ++    +++t+  f +  g  l+e ++++  +   + 
  gi|313122433|ref|YP_004038320.1| 207 AYATENAPetltddeqeTLNTLYRGELEHLDQCLGQLFDGIQSRLDANETVTAFAGTSGCPLGEHGTWYETTS--DF 281
                                       7777773366777777688888999*************************************88444444444..69 PP

                                       SHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTTE CS
                         Sulfatase 269 yeggtrvPllvwwpgekaprvseelvshiDlfptildlagi 309
                                       +++++rvPl++++p+  a+ ++e  +s++D++pt+l+++g+
  gi|313122433|ref|YP_004038320.1| 282 HDESVRVPLFIHGPEFDAE-TVEFAASSVDILPTLLAAVGV 321
                                       **************99999.******************996 PP

>> DUF560  Protein of unknown function (DUF560)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.1e-05      0.19      85     148 ..     317     379 ..     312     419 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.1e-05
                            DUF560  85 aslglgyknakqdvsllpFvekrfygnkryskasGvrlslsywlsekwqlstsleyekeryter 148
                                       a +g++y++++   +l++F+ +r+ + + + +asG +ls     +++w+l+ +l+  +e+ +++
  gi|313122433|ref|YP_004038320.1| 317 AAVGVKYDQQRGGSDLRTFMGRRVTERQVF-AASGNALSEAMVCNSRWKLARALREGRETLFDH 379
                                       6789*******************8766655.689***********************9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3056.72
//
Query:       gi|313122434|ref|YP_004038321.1|  [L=418]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-26   93.3   0.2    4.2e-26   92.0   0.0    1.8  2  Glyco_trans_1_4  Glycosyl transferases group 1
    7.1e-25   87.5   0.0    1.2e-24   86.7   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.2e-18   67.7   1.6    2.3e-18   66.7   1.6    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.2e-16   61.6   6.4    1.2e-16   61.6   6.4    1.9  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.7e-08   34.8   0.0    4.8e-08   33.3   0.0    1.8  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.036   14.5   0.0    1.7  1  DUF1697          Protein of unknown function (DUF1697)


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3     4e+03      88     103 ..      91     107 ..      56     131 .. 0.63
   2 !   92.0   0.0   1.4e-29   4.2e-26       3     134 .]     220     367 ..     218     367 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                                       HHHH.HTT-EEEE-TGG CS
                   Glyco_trans_1_4  88 lEam.aaglpvVatdvg 103
                                       +Ea+ a+ lp+V t+++
  gi|313122434|ref|YP_004038321.1|  91 IEALhAHDLPMVHTALA 107
                                       44442566777777663 PP

  == domain 2  score: 92.0 bits;  conditional E-value: 1.4e-29
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaa 72 
                                       vi +vG l  ++ g+d +++ +p++ ++ + ++lvivG+g+  +++le+ +   g+ ++v+ftG+v  ed++++++a
  gi|313122434|ref|YP_004038321.1| 220 VISYVGTLGGPHRGLDAVVRSMPAVVERvPsAHLVIVGNGQeYRSHLESIVTdlGIGDHVTFTGRVpfEDVPSYIDA 296
                                       799*****5577**************99757********998667999877569999******************** PP

                                       -SEEEE--......-.--SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs......e.gfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       +dv+++P       e +++ kl ++ma+ +pvV+tdv+ +++vv   ++g++v ++dp+ +a a ++L +d
  gi|313122434|ref|YP_004038321.1| 297 SDVCLVPHqstghtEtTVPHKLFQYMAMSRPVVVTDVEPLRRVVedADAGVVVRADDPAGFALAFVELATD 367
                                       ********9877763589*******************989**99877899*****************9887 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   4.1e-28   1.2e-24       9     171 ..     213     380 ..     206     381 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 4.1e-28
                                       TTTTTT-EEEEEESS-T.TTTTHHHHHHHHHCCCCCHCSCEEEEEES..STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                   Glycos_transf_1   9 lgknekkkiilsvgrle.keKgvdllikafallkkqlnpnvklviaG.ngeeekelkklaeelelsdnviflgevsr 83 
                                        g+ e++ +i +vg l  ++ g+d ++++++ + ++  p ++lvi+G ++e++  l++ +  l+++d+v+f+g+v+ 
  gi|313122434|ref|YP_004038321.1| 213 VGF-EDDFVISYVGTLGgPHRGLDAVVRSMPAVVER-VPSAHLVIVGnGQEYRSHLESIVTDLGIGDHVTFTGRVPF 287
                                       555.8999*******95489**************99.**********9999************************** PP

                                       SSHHHHHHCESEEEEEESS.....BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHH CS
                   Glycos_transf_1  84 edleellknadifvlpsis.....EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkl 155
                                       ed+++++ ++d+ ++p +s        ++ l  +ma   pv+++++++++ vv+d++ G++v + +++ +a a+ +l
  gi|313122434|ref|YP_004038321.1| 288 EDVPSYIDASDVCLVPHQStghteTTVPHKLFQYMAMSRPVVVTDVEPLRRVVEDADAGVVVRADDPAGFALAFVEL 364
                                       ***********************7789************************************************** PP

                                       HHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 156 ledeelrerlgenark 171
                                        +d e+++rlgen+r+
  gi|313122434|ref|YP_004038321.1| 365 ATDHERARRLGENGRR 380
                                       **************96 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   1.6   7.8e-22   2.3e-18      12     169 ..      17     203 ..      12     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 7.8e-22
                    Glyco_transf_4  12 araLarrGheVtvvtpgddgpleeev....elvvrvprvplpllkrllrslaflr.............rlrrllkre 71 
                                       ++ La++Gh V++++ +d++ +++e+         v+r+p+   +  l  +a+               +l  ++  e
  gi|313122434|ref|YP_004038321.1|  17 VESLAADGHTVYILSEADEDLPDREEvgsaT----VIRRPFQAAYAGLDGVAAGTrtlvtnvveswvhALDDIVPTE 89 
                                       578***************9999999844441....444444333333332222111111122222222666777777 PP

                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglye.................krllkarlkplsrllralerrll 131
                                       ++  +Hah+ + +  al+a   ++++p+V+ +H  ++                  r++ +rl +   +++++er ++
  gi|313122434|ref|YP_004038321.1|  90 GIEALHAHDLPMVHTALAAGE-KHDLPVVADLHENWPeavkqyrrgdsldsftnFRYVARRLTRPVLRWKRIERDAV 165
                                       *********999877765555.5*****************************773344444444344456689999* PP

                    Glyco_transf_4 132 rradrviavSeatadelrerygvppekitVipnGvDle 169
                                       +radrviav+e++a+++++ +g++++k+ ++ n v le
  gi|313122434|ref|YP_004038321.1| 166 QRADRVIAVTEEAAAHYVRDCGIDASKVDIVSNYVSLE 203
                                       *********************************99886 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   6.4     4e-20   1.2e-16      11     159 ..      17     198 ..      11     199 .. 0.72
   2 ?   -1.7   0.1       1.1   3.4e+03     124     136 ..     337     349 ..     301     387 .. 0.59

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 4e-20
                   Glyco_trans_4_4  11 araLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaal.............ralrrllrqrrerp 74 
                                       +++Laa+Gh V +l  a+   ++++e + ++v+r p+ ++ ++l  +aa              +al +++    e++
  gi|313122434|ref|YP_004038321.1|  17 VESLAADGHTVYILSEADEDLPDREEVGSATVIRRPFQAAYAGLDGVAAGtrtlvtnvveswvHALDDIV--PTEGI 91 
                                       799************99988888899999*******8877644444332112234444444447788888..9**** PP

                   Glyco_trans_4_4  75 dvvhahsptaglaarlarrrrgiplvvtlh....................glllr...rgsgavrrlyralerrllr 128
                                         +hah+++    a++a  ++++p+v +lh                    +  +r   r+ ++    ++++er +++
  gi|313122434|ref|YP_004038321.1|  92 EALHAHDLPMVHTALAAGEKHDLPVVADLHenwpeavkqyrrgdsldsftN--FRyvaRRLTRPVLRWKRIERDAVQ 166
                                       *******88877888888899*********555555444444433322210..221112222222345889****** PP

                   Glyco_trans_4_4 129 radavlvvseaeaeelra.lgvpadrvvvvpn 159
                                       rad+v++v+e+ a+++++ +g++a++v++v n
  gi|313122434|ref|YP_004038321.1| 167 RADRVIAVTEEAAAHYVRdCGIDASKVDIVSN 198
                                       *************999999**********988 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                   Glyco_trans_4_4 124 rrllrradavlvv 136
                                       rr++  ada +vv
  gi|313122434|ref|YP_004038321.1| 337 RRVVEDADAGVVV 349
                                       3333334333333 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.6e-11   4.8e-08       3      90 ..     301     395 ..     299     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.6e-11
                   Glyco_trans_1_2   3 Lnpsrs.....espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaea 72 
                                       L p++s      ++  +lf ++a+ ++++++d e l++ +++ + +++++  d++ +a ++ +l ++ e++r+++e+
  gi|313122434|ref|YP_004038321.1| 301 LVPHQStghteTTVPHKLFQYMAMSRPVVVTDVEPLRRVVEDADAGVVVRadDPAGFALAFVELATDHERARRLGEN 377
                                       5566663333334556************************************************************* PP

                   Glyco_trans_1_2  73 arervlaehtydhraeql 90 
                                       +r+ v++++ +d + e l
  gi|313122434|ref|YP_004038321.1| 378 GRRAVETRYCWDTAGESL 395
                                       ***********9887766 PP

>> DUF1697  Protein of unknown function (DUF1697)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.036      31     121 ..     285     377 ..     277     386 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                           DUF1697  31 lGfedVkTyiqSGNvvfeseedaaeleakiekaleeefgfevpvlvrtaeeleaivaanPfeee..eeeekklyvif 105
                                       + fedV +yi   +v + +++++   e+++ + l + + ++ pv+v + e l+++v+++ +     +++++   ++f
  gi|313122434|ref|YP_004038321.1| 285 VPFEDVPSYIDASDVCLVPHQSTGHTETTVPHKLFQYMAMSRPVVVTDVEPLRRVVEDADAGVVvrADDPAGFALAF 361
                                       5699*****************************************************99888778899999999999 PP

                           DUF1697 106 lkeepsaealeeleal 121
                                       ++ ++++e++++l + 
  gi|313122434|ref|YP_004038321.1| 362 VELATDHERARRLGEN 377
                                       9999999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2685.33
//
Query:       gi|313122435|ref|YP_004038322.1|  [L=612]
Description: methyltransferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-07   29.5   0.0    1.9e-06   28.4   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    3.5e-05   24.4   0.0    9.4e-05   23.1   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.023   13.8   1.2        1.3    8.0   0.3    2.6  3  Glyco_hydro_88   Glycosyl Hydrolase Family 88


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   3.2e-10   1.9e-06      19      96 .]      71     149 ..      56     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.2e-10
                                       SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-.CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  19 arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv.edpekalkeiaRvLkpgGll 94 
                                        +vv +D+s+ + ++a+e+  ++  + e+ + +a +lpf+dn fD  v+    ++   d++ + +e++Rv   +Gl 
  gi|313122435|ref|YP_004038322.1|  71 DEVVRLDFSADASETAREELGDRVDTYEVTEPEAPRLPFPDNHFDGAVCIGPYDWKfLDVAGLTDEVHRVTTADGLY 147
                                       689*******************98777788888889***************9999889*****************99 PP

                                       EE CS
                   Methyltransf_11  95 vi 96 
                                       v+
  gi|313122435|ref|YP_004038322.1| 148 VF 149
                                       86 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.6e-08   9.4e-05      21      97 .]      70     145 ..      54     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.6e-08
                                       SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  21 kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                       + +v+ +D+s+++ e+are++ ++    e+ + +a +lpf+d++fD  v++g + + +  d++ + +e++rv++ +G
  gi|313122435|ref|YP_004038322.1|  70 ADEVVRLDFSADASETAREELGDRVDTYEVTEPEAPRLPFPDNHFDGAVCIGPYDW-KFLDVAGLTDEVHRVTTADG 145
                                       689******************87655999*********************877776.445889999*****998887 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.55   3.3e+03     218     244 ..     242     268 ..     239     273 .. 0.82
   2 ?    3.1   0.0    0.0069        41      46     118 ..     404     485 ..     375     494 .. 0.79
   3 ?    8.0   0.3   0.00022       1.3      28     104 ..     514     589 ..     493     603 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.55
                                       HHHHHHHHHHHHHCTS-TTSSEBSBTT CS
                    Glyco_hydro_88 218 linllrdlvkalaklqdeeglWhqild 244
                                        + +l+  v++l +   e+g+W+ + d
  gi|313122435|ref|YP_004038322.1| 242 FKSYLQRGVESLFRPTGENGFWDEVTD 268
                                       567788888999999999999999887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0069
                                       --HHHHHHHHHHHHHCCCTTS-..........CTTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B.T CS
                    Glyco_hydro_88  46 gdkeyldyakawadslideggk..........telelDdidigllllllyeltkderykeaaeeladyvlakpprts 112
                                        d+++++++k+  ++  d+ ++          t+++ +++     l++  e t+++ y   +e + dy +++  r +
  gi|313122435|ref|YP_004038322.1| 404 TDERVRAFVKRGLSEISDRRATeglfhfdnatTRRHQNQMYTCWALARAIEVTGQTGYLTDVESALDYTIEHRMR-K 479
                                       4677888888877777777777888888888889999999999999999******************99988877.8 PP

                                       TS.B.S CS
                    Glyco_hydro_88 113 eGgfwh 118
                                       +G f+ 
  gi|313122435|ref|YP_004038322.1| 480 DGAFIW 485
                                       999975 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00022
                                       .HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-CTTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHH CS
                    Glyco_hydro_88  28 ewtnGvflsglleayeatgdkeyldyakawadslideggktelelDdidigllllllyeltkderykeaaeeladyv 104
                                       e ++ +f+++++++y+a g+++y++++ + + + ++++g+ +  +D   ig + +++    ++ + ++ +  ++d +
  gi|313122435|ref|YP_004038322.1| 514 ECHQTFFVNAVAHYYDAGGENDYTQAVRRAMAWIFETNGTGRDLVDVSGIG-VPMRQVTVDGRMDNRQFTSGWRDQQ 589
                                       458999*********************************955556655555.4466666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4385.03
//
Query:       gi|313122436|ref|YP_004038323.1|  [L=479]
Description: arylsulfatase A family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-38  130.5   3.1      1e-37  130.2   0.4    1.9  2  Sulfatase      Sulfatase
    0.00034   20.3   1.6      0.023   14.3   1.6    2.3  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
  ------ inclusion threshold ------
      0.022   14.1   0.1      0.038   13.4   0.1    1.3  1  Metalloenzyme  Metalloenzyme superfamily


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.2   0.4   1.7e-41     1e-37       1     308 [.       8     349 ..       8     350 .. 0.86
   2 ?    0.7   0.1     0.048   2.8e+02     193     236 ..     413     454 ..     394     460 .. 0.72

  Alignments for each domain:
  == domain 1  score: 130.2 bits;  conditional E-value: 1.7e-41
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHH..HTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrla..eeglrftnfysaaplcspsraalltgryphnsgvasntevgg 75 
                                       pn+++i +++++a++ ++ g+++ ttpnl r+a  + g  f   ++ a  +  +  ++ltg y +++gv++ +   +
  gi|313122436|ref|YP_004038323.1|   8 PNIIWISLESVRADHTSVGGYHRDTTPNLRRIAdlRDGRSFDECFAHARWTPAVSTSILTGTYLTTHGVGHANTRDV 84 
                                       9*******************************************************************987776666 PP

                                       HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC.CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC..... CS
                         Sulfatase  76 gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk.nrgfdrflgfptgsaalkdpekseyngevlrv..... 146
                                        +lp +  t pellk+ GY t  +g  ++ w+s        rgfdrf ++p+ ++++  p  +   +++lr      
  gi|313122436|ref|YP_004038323.1|  85 RQLPGDLKTAPELLKSEGYTT--AGFSSNPWISDVI--GlDRGFDRFKANPN-RDDFLSPRGVRAGCNYLREfttmg 156
                                       *********************..6666777775555..35789999999555.777777777777788888899999 PP

                                       ...............TTTTCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH CS
                         Sulfatase 147 ...............ppeggysddrlldealefllarndkpfflylatlapHappeapdeyakkyatffddgseaar 208
                                                      p   +y  + l + + ++   ++d+p fly + +++H+p++ p    k++ ++fd ++++a 
  gi|313122436|ref|YP_004038323.1| 157 agfetepiyhaqclpP---YYQYQSLCEWVDDL--SNEDRPYFLYTHMNSSHHPYNPPLSLLKRFLGEFDGTPKEAI 228
                                       9999999888875433...33333444444444..455***************999999999999999999888866 PP

                                       ..........................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTT CS
                         Sulfatase 209 ..........................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngp 259
                                                                  l ++y++ ++  D+++g++++ + +++ +++t++v+t+Dhg+  +e +g+
  gi|313122436|ref|YP_004038323.1| 229 etakeltnniwrevahgcdftaqqraALKAVYDAEIAFSDHFVGKLFEHV-RANTDQKTVFVITGDHGELFGE-QGV 303
                                       77888999999999999999999999999*********************.******************9966.333 PP

                                       SSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 260 lrggkganayeggtrvPllvwwpgekaprvseelvshiDlfptildlag 308
                                         g++  + ++g t+vP++ ++ +  ++ v e++v h+D++ t+ +++g
  gi|313122436|ref|YP_004038323.1| 304 -LGHNL-TLHDGLTKVPMVTYGMNFSES-VTENVVQHMDVMQTLVSAVG 349
                                       .33443.79*************999999.***************99986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.048
                                       TCCGSTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         Sulfatase 193 akkyatffddgseaarqlleaylnsveyvDdligrvlaaLeeng 236
                                        ++++ f+ +++e  ++++++y ++ +++D ++++ l +++ + 
  gi|313122436|ref|YP_004038323.1| 413 DDRTELFKLPDEE--TNVVDKYPDAAAEMDAALDEMLPEAQFDD 454
                                       4444455444333..399***************99887775555 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.6   3.8e-06     0.023       3     233 ..      12     295 ..      10     323 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-06
                                       EEEETT-BTTHHHHHG.S..TSHHHHHHHH..HSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEE.ETTT CS
                      Phosphodiest   3 vislDGlradlldrla.e..llpnlaaLak..egvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfy.drkt 73 
                                        isl ++rad  +    +  ++pnl+++a+   g s++++ +++   T++  +s++TG+y   HG+ + + +  r++
  gi|313122436|ref|YP_004038323.1|  12 WISLESVRADHTSVGGyHrdTTPNLRRIADlrDGRSFDECFAHA-RWTPAVSTSILTGTYLTTHGVGHANTRdVRQL 87 
                                       57777777666554333345999999999988999999766665.57999999************988555522333 PP

                                       TEEEEEETTTTGG............GGGCTTS-HHHHHHHTH..............TTCEEEESE.....TTTTSEB CS
                      Phosphodiest  74 geyvvfvtededa............prwwqgepiwdtaakar..............glkaaalfw.....pgsevdy 119
                                         +++  +e                ++ w ++ i  +  ++r              g++a++ +      +g+++++
  gi|313122436|ref|YP_004038323.1|  88 PGDLKTAPE---LlksegyttagfsSNPWISDVIGLDRGFDRfkanpnrddflsprGVRAGCNYLrefttMGAGFET 161
                                       332222222...13335555555554444443333333333355555666688888999998888888665555555 PP

                                       TTCT.SC.TBHHSBTCT.....CSTTS..................CHHHHHHHHHHHHHHHCHTHSHHHHHCTSSES CS
                      Phosphodiest 120 styyylvsetppryled....dfnakv..................pledkvdkavlqtwldaafakvvlekelekpd 174
                                          y    ++ p+y++     ++ +++                  p++  +                          
  gi|313122436|ref|YP_004038323.1| 162 EPIYHA--QCLPPYYQYqslcEWVDDLsnedrpyflythmnsshhPYNPPL-------------------------S 211
                                       544433..5666665223444444444333344444444444444222222.........................3 PP

                                       EEEEEECCCHHHHHHH-TTSHH..............................HHHHHHHHHHHHHHHHHHHHHTTGT CS
                      Phosphodiest 175 lllvyleetDtvgHkfGpdspe..............................vedalrrvDkaigdLlealdergls 221
                                       ll   l e D   ++  +   e                                ++++  D+++g+L+e ++ +  +
  gi|313122436|ref|YP_004038323.1| 212 LLKRFLGEFDGTPKEA-I---EtakeltnniwrevahgcdftaqqraalkavYDAEIAFSDHFVGKLFEHVRAN-TD 283
                                       3333333333333333.2...012224444444444444444455555555589999***************87.99 PP

                                       TTEEEEEEES-- CS
                      Phosphodiest 222 aetniilvSDHG 233
                                       ++t +++++DHG
  gi|313122436|ref|YP_004038323.1| 284 QKTVFVITGDHG 295
                                       9**********9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.3e-06     0.038     158     224 ..     264     333 ..     246     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-06
                                       HHHHHHHHHHHHTTS-T...TTEEEEEE-SSB--TTTSS........-.----EEEEEESTT----S--SS CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 158 ieaaDeavkeildaieq...vdgilvvtADHgnaedmvkrdkqplTsH.tlepVPilivgkglapdkvkeg 224
                                       i   D+ v+++++++++   +++++v+t+DHg     ++   + lT H  l +VP++ +g ++ + +v+e+
  gi|313122436|ref|YP_004038323.1| 264 IAFSDHFVGKLFEHVRAntdQKTVFVITGDHGELFGEQGVLGHNLTLHdGLTKVPMVTYGMNFSE-SVTEN 333
                                       555699999999999751115679********8655555446999*9945899********9997.44443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3205.14
//
Query:       gi|313122437|ref|YP_004038324.1|  [L=1486]
Description: glucose/sorbosone dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-48  164.9   0.0    4.9e-48  164.1   0.0    1.3  1  GSDH        Glucose / Sorbosone dehydrogenase
    9.4e-29  100.0  57.1    4.4e-16   59.4  16.3   10.2  9  Big_9       Bacterial Ig domain
    2.6e-15   56.8  42.4    2.4e-10   40.9  11.2    9.8  9  Cadherin_4  Bacterial cadherin-like domain
    1.9e-12   46.8   3.2    1.9e-12   46.8   3.2    5.6  5  PKD         PKD domain
    2.9e-10   40.0  19.8    6.9e-07   29.2   7.9    6.9  8  Cadherin_5  Cadherin-like domain
    0.00026   20.9   5.2       0.85    9.6   0.1    4.4  3  Cadherin_3  Cadherin-like
  ------ inclusion threshold ------
      0.046   13.7   2.9       0.12   12.4   2.9    1.8  1  PGF-CTERM   PGF-CTERM motif
       0.17   12.2   0.1       0.17   12.2   0.1    5.7  5  DUF5122     Domain of unknown function (DUF5122) beta-propell
        3.5    7.9   6.4          1    9.6   0.4    3.2  4  ASH         Abnormal spindle-like microcephaly-assoc'd, ASPM-


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.1   0.0   2.5e-51   4.9e-48       1     320 [.      69     411 ..      69     419 .. 0.82

  Alignments for each domain:
  == domain 1  score: 164.1 bits;  conditional E-value: 2.5e-51
                                       -S-EEEEEE-TTS-EEEEETTTEEEEEE...TTEE...EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE- CS
                              GSDH   1 lehPwslaflpdgrlLvtersGrlrlvk..adgkl..kepiagvpevvakgqgGlldvalhpdfaenrlvYltyaea 73 
                                       l+ P +  flpdgr+L+ ++ G++ + +  ++g      +i++v+++  + + Gll++a++pdf++++ +Y++y++ 
  gi|313122437|ref|YP_004038324.1|  69 LDRPTETVFLPDGRILIIQQGGKILIDDptTKGGAetYLNINQVDSLESNRERGLLGIAIAPDFEQSGDFYVYYTRL 145
                                       5789999******************9774333333135678899999****************************77 PP

                                       .........TTSSEEEEEEEEE-SS........-EEEEEEEEEEE---TT...-------EEE-TTS-EEEE---TT CS
                              GSDH  74 ......eeekggagtavararlsed......eaaledlevifrqepkves...gahfGsrlafgpdgtLfvtvGdrs 135
                                             +e++ + ++++a ++ +e+      +a  ++ + ++r+e ++ +     hfG+ l +gpdg++++t+G+++
  gi|313122437|ref|YP_004038324.1| 146 dnpgaeDEADTEPENVLAAFTHRENsggttsRADPNSKQILWRNEIRTGKsivCCHFGGGLDIGPDGKIYITTGEEF 222
                                       88887544555667889999998888887665666788999**988755424467********************** PP

                                       -GGGGG-TT-SSSEEEEE-TTSSB-TT-TTTT-T..TS-TTEEEE--SCE---EE-TTT--EEEEEE--SSS..... CS
                              GSDH 136 kreeaqdlsselGkilrlnkdGsvpadnpfvgka..gakpeiwsyGhRnpqGlaldpdtgeLwesEhGprgg..... 205
                                       +  ++qdls + Gk++rln+dGs+p+dnpfv++   +   e+w+yG Rnp+ + + p+ g+L+  E G++++     
  gi|313122437|ref|YP_004038324.1| 223 QGWRSQDLSVPDGKVIRLNQDGSIPQDNPFVDDGdpETLGEVWAYGLRNPYRAKFAPN-GNLYIGEVGSNREeepss 298
                                       *******************************765126667******************.*********998867777 PP

                                       .EEEEEE-TT-B--TTT-S......S-.....-S-TTS---SEEET.......T---EEEEEEE.........TTEE CS
                              GSDH 206 .DelnlieaGknYGWplvsygeeYsgkkigesetreglekpvlvwt.......psiapsglafytgdafp.ewkgdl 273
                                         +++l  +G+nYGWp  +  +           +++ +++p+++++       p+ a+    +ytgd++p e+++ l
  gi|313122437|ref|YP_004038324.1| 299 qEDIHLGAKGANYGWPNCEGNC-----------DDPAYDDPIYTYShidsgdpPGAAVTVGPVYTGDMYPaEYDNVL 364
                                       788**************99433...........334444444433311100014577777779******857***** PP

                                       EEEETTTTEEEEEEEEEEEEEEEEEEEEESS-.-EEEEEE-TTS-EE CS
                              GSDH 274 lvggLksqsllrleldegekvveeerlleelgeriRdVeqgpdGaly 320
                                       + +  +   + +l+l++++++v ++  ++     + +++ gpdGaly
  gi|313122437|ref|YP_004038324.1| 365 FYSDYNDGWVKYLTLNDDGTTVGQSYNFDADAGPLVSLTMGPDGALY 411
                                       ***************9888888888888555559************9 PP

>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.56   1.1e+03      53      88 ..     194     235 ..     146     237 .. 0.66
   2 ?   -3.7   0.1         9   1.8e+04      59      67 ..     377     390 ..     345     409 .. 0.64
   3 ?  -10.8  24.1         9   1.8e+04       9      62 ..     430     488 ..     424     654 .. 0.85
   4 ?   -2.3   0.1         4   7.9e+03      54      54 ..     723     723 ..     653     776 .. 0.61
   5 ?   -2.9   0.0       5.9   1.2e+04      29      68 ..     792     831 ..     749     834 .. 0.55
   6 !   40.3  14.2     2e-13     4e-10       9      90 .]     935    1017 ..     932    1017 .. 0.91
   7 !   59.4  16.3   2.2e-19   4.4e-16       2      90 .]    1025    1115 ..    1022    1115 .. 0.91
   8 !   31.6  10.6     1e-10     2e-07       2      90 .]    1121    1210 ..    1120    1210 .. 0.86
   9 ?  -17.3  25.6         9   1.8e+04       5      70 ..    1310    1393 ..    1293    1455 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.56
                             Big_9  53 a......panGtvtinadgtltytpnagfsgtdsftYtvsDg 88 
                                       +        +G + i +dg++  t  + f+g  s + +v Dg
  gi|313122437|ref|YP_004038324.1| 194 GksivccHFGGGLDIGPDGKIYITTGEEFQGWRSQDLSVPDG 235
                                       155555556799999***************999998888887 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9
                             Big_9  59 vtinadgt.....l 67 
                                       +t+n+dgt     +
  gi|313122437|ref|YP_004038324.1| 377 LTLNDDGTtvgqsY 390
                                       44555554333222 PP

  == domain 3  score: -10.8 bits;  conditional E-value: 9
                             Big_9   9 tpvndaPvavddsvtvtedsv......landtdpdgdaltvtsltvtlvtapanGtvtin 62 
                                       + +n aP + ++sv+ +++         a+++dp+gd+lt+t + + + t++ + +vt +
  gi|313122437|ref|YP_004038324.1| 430 EDTNSAPSIDSTSVSPESGAIplevtfEASASDPNGDDLTYT-WHFGDGTTTRGASVTHT 488
                                       56899999999998888555555544477**********987.66777777555555443 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4
                             Big_9  54 p 54 
                                        
  gi|313122437|ref|YP_004038324.1| 723 E 723
                                       1 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 5.9
                             Big_9  29 v...landtdpdgdaltvtsltvtlvtapanGtvtinadgtlt 68 
                                       +   +an td +g       + +    + +   +++++ g+lt
  gi|313122437|ref|YP_004038324.1| 792 SmflVANYTDNNGGFGG---VAYGRGGNNKAFGLVVDDKGRLT 831
                                       25556777777776654...34444455444445555555555 PP

  == domain 6  score: 40.3 bits;  conditional E-value: 2e-13
                             Big_9    9 tpvndaPvavddsvtvt....edsvlandtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtd 79  
                                        t  nd+P   d svt t    + +v+a ++dpdgd +     +v +v +p+ Gtvt n+dgt+ty  ++  + +d
  gi|313122437|ref|YP_004038324.1|  935 TEPNDPPELGDISVTYTggekSINVTAAASDPDGDVDP---SSVRIVEQPTSGTVTNNGDGTVTYATSDESATSD 1006
                                        568**********999977666666**********986...46899***************************** PP

                             Big_9   80 sftYtvsDgsg 90  
                                        sft+ +sD++g
  gi|313122437|ref|YP_004038324.1| 1007 SFTVAISDTDG 1017
                                        ********997 PP

  == domain 7  score: 59.4 bits;  conditional E-value: 2.2e-19
                             Big_9    2 atvtvtvtpvndaPvavddsvtvtedsv.....landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytp 71  
                                          +t +++ +n +P+a+dd+++vt +++     l nd d dg+ +t    +vt+v++p+ G+vti++dg +tyt 
  gi|313122437|ref|YP_004038324.1| 1025 VDLTYQISETNAPPTANDDAANVTVGQSvkipvLGNDGDSDGSLDT---SSVTIVAQPSTGSVTIDGDGAITYTH 1096
                                        456777888***************99988999999*******9887...36789********************* PP

                             Big_9   72 nagfsgtdsftYtvsDgsg 90  
                                        + + + tdsftY vsD++g
  gi|313122437|ref|YP_004038324.1| 1097 TGDSATTDSFTYEVSDDDG 1115
                                        ****************997 PP

  == domain 8  score: 31.6 bits;  conditional E-value: 1e-10
                             Big_9    2 atvtvtvtp...vndaPvavddsvtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpna 73  
                                        atv++tv+    ++  P  +dd+ tv+++++++  + + +d+ +v++ t+ ++  +++Gt+t+  +g+l+y+ + 
  gi|313122437|ref|YP_004038324.1| 1121 ATVEITVAEpdpADGVPETNDDHGTVESGETVTLSVLA-NDSASVDASTLRIDGDADHGTATVE-NGQLVYQHSG 1193
                                        8*******9999999***********988885544433.34445666689999***********.9********* PP

                             Big_9   74 gfsgtdsftYtvsDgsg 90  
                                        + + +d ++Ytv D++g
  gi|313122437|ref|YP_004038324.1| 1194 DSATDDMIEYTVADANG 1210
                                        **************997 PP

  == domain 9  score: -17.3 bits;  conditional E-value: 9
                             Big_9    5 tvtvtp.vndaPvavdds...vtvtedsvlandtdpdgdaltvtsltvtlvta..................panG 57  
                                        +vtv   vn   v+ ++     ++t d ++ ndt +d  +ltv +   ++                     ++ G
  gi|313122437|ref|YP_004038324.1| 1310 NVTVGEtVNASAVVDNTGnaaGSTTVDLAVGNDT-VDARSLTVGAGANVT--VafsytfdqsgayelrlgnQSLG 1381
                                        5666664666666666554445555555577887.777888766432222..13466666666666666666666 PP

                             Big_9   58 tvtinadgtltyt 70  
                                        tvt++ + t t  
  gi|313122437|ref|YP_004038324.1| 1382 TVTVS-NATQTDE 1393
                                        66666.3354444 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.7   7.3e+03      62      69 ..     377     384 ..     327     409 .. 0.67
   2 ?    0.2   7.9       0.6   1.2e+03      11      70 ..     433     495 ..     427     517 .. 0.61
   3 ?   -9.0  13.9         9   1.8e+04      30      55 ..     516     575 ..     496     634 .. 0.65
   4 ?   -2.9   0.9       5.8   1.1e+04      43      54 ..     724     736 ..     682     774 .. 0.48
   5 !   27.4   7.7     2e-09   3.9e-06       8      72 .]     935     996 ..     933     996 .. 0.88
   6 !   40.9  11.2   1.2e-13   2.4e-10       3      72 .]    1027    1094 ..    1023    1094 .. 0.89
   7 !   19.8   7.5   4.7e-07   0.00093       1      72 []    1121    1189 ..    1121    1194 .. 0.81
   8 ?  -10.8  17.3         9   1.8e+04       4      65 ..    1310    1386 ..    1307    1416 .. 0.74
   9 ?   -5.3   4.3         9   1.8e+04      30      30 ..    1416    1416 ..    1382    1465 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.7
                        Cadherin_4  62 ltlnadGs 69 
                                       ltln+dG+
  gi|313122437|ref|YP_004038324.1| 377 LTLNDDGT 384
                                       56666665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.6
                        Cadherin_4  11 ndaPvavddsatvted.tpltitagnvlandtDvdgddltvtav.....tvagtyGtltlnadGsf 70 
                                       n aP +   s++ + +  pl +   +  a ++D++gddlt+t       t+ g+  t t+++ Gs+
  gi|313122437|ref|YP_004038324.1| 433 NSAPSIDSTSVSPESGaIPLEV---TFEASASDPNGDDLTYTWHfgdgtTTRGASVTHTYSEAGSY 495
                                       4444444444443332122333...34499*********998653322222333336667777776 PP

  == domain 3  score: -9.0 bits;  conditional E-value: 9
                        Cadherin_4  30 t....................itagnvlandtDvdgddltvtavt..............v 55 
                                       t                    +++ +v a+ tD+++++l+  +v               +
  gi|313122437|ref|YP_004038324.1| 516 TageppqvdittpangslfraGDSIDVAADVTDPEDGQLSGDSVEwsaflthndhihpdT 575
                                       144444444444444555565445688899999999999988886444444444444431 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 5.8
                        Cadherin_4  43 vdgdd.ltvtavt 54 
                                       +d++  + +++vt
  gi|313122437|ref|YP_004038324.1| 724 ADSGVqMNASGVT 736
                                       3333323333332 PP

  == domain 5  score: 27.4 bits;  conditional E-value: 2e-09
                        Cadherin_4   8 tgvndaPvavddsatvtedtpltitagnvlandtDvdgdd..ltvtavtvagtyGtltlnadGsftY 72 
                                       t  nd+P   d s+t t ++       nv+a ++D+dgd    +v +v  ++t Gt+t n+dG++tY
  gi|313122437|ref|YP_004038324.1| 935 TEPNDPPELGDISVTYTGGEKSI----NVTAAASDPDGDVdpSSVRIVE-QPTSGTVTNNGDGTVTY 996
                                       678*********99998876654....58999****9998889999999.****************9 PP

  == domain 6  score: 40.9 bits;  conditional E-value: 1.2e-13
                        Cadherin_4    3 vtitvtgvndaPvavddsatvtedtpltitagnvlandtDvdgdd..ltvtavtvagtyGtltlnadGsftY 72  
                                        +t ++  +n +P+a+dd+a+vt ++++ i+   vl+nd D dg     +vt+v+ +++ G++t+++dG +tY
  gi|313122437|ref|YP_004038324.1| 1027 LTYQISETNAPPTANDDAANVTVGQSVKIP---VLGNDGDSDGSLdtSSVTIVA-QPSTGSVTIDGDGAITY 1094
                                        5778999**********************6...*******99744438888888.****************9 PP

  == domain 7  score: 19.8 bits;  conditional E-value: 4.7e-07
                        Cadherin_4    1 atvtitvt...gvndaPvavddsatvtedtpltitagnvlandtD.vdgddltvtavtvagtyGtltlnadGsft 71  
                                        atv itv+   +++  P ++dd +tv+ ++++t    +vland+  vd  +l++ +   ++++Gt t+++ G+  
  gi|313122437|ref|YP_004038324.1| 1121 ATVEITVAepdPADGVPETNDDHGTVESGETVTL---SVLANDSAsVDASTLRIDG---DADHGTATVEN-GQLV 1188
                                        8******833356778******************...8*****9659999999985...56888888864.5554 PP

                        Cadherin_4   72 Y 72  
                                        Y
  gi|313122437|ref|YP_004038324.1| 1189 Y 1189
                                        4 PP

  == domain 8  score: -10.8 bits;  conditional E-value: 9
                        Cadherin_4    4 titvtgvndaPvavddsatvtedtpltitagnvlandtDvdgddltvtavt...........vagty........ 59  
                                        ++tv  + +a  +vd++++++  t++        +ndt vd  +ltv a +                        
  gi|313122437|ref|YP_004038324.1| 1310 NVTVGETVNASAVVDNTGNAAGSTTVDL----AVGNDT-VDARSLTVGAGAnvtvafsytfdQ---Sgayelrlg 1376
                                        7899999999999999999999999999....369999.999999995544233333343331...033355555 PP

                        Cadherin_4   60 ....Gtltln 65  
                                            Gt+t++
  gi|313122437|ref|YP_004038324.1| 1377 nqslGTVTVS 1386
                                        5555888875 PP

  == domain 9  score: -5.3 bits;  conditional E-value: 9
                        Cadherin_4   30 t 30  
                                         
  gi|313122437|ref|YP_004038324.1| 1416 D 1416
                                        1 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   3.2   9.7e-16   1.9e-12       4      65 ..     444     504 ..     441     509 .. 0.91
   2 ?    1.7   0.3      0.12   2.3e+02      54      70 ..     597     613 ..     529     614 .. 0.65
   3 ?    2.7   0.5     0.059   1.2e+02       2      56 ..     663     710 ..     662     711 .. 0.86
   4 ?   -2.5   0.1       2.5   4.9e+03       6      20 ..    1144    1158 ..    1137    1165 .. 0.57
   5 ?    0.5   2.1      0.27   5.4e+02       8      60 ..    1311    1375 ..    1304    1389 .. 0.61

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 9.7e-16
                                       --S--BSSEEEEEEEES...-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-S CS
                               PKD   4 sptvlvpgatvaftaav..pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasna 65 
                                       sp + ++  +v+f+a+   p g+++ty+W fgd   ++++++ +vthtY+++G+Y   v +s+ 
  gi|313122437|ref|YP_004038324.1| 444 SPESGAIPLEVTFEASAsdPNGDDLTYTWHFGD---GTTTRGASVTHTYSEAGSYDTYVEVSDG 504
                                       5667788899******99899************...*************************997 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                                       EEEEEEEEEE-SS-EEE CS
                               PKD  54 GeYeVtvtasnavgsat 70 
                                         Y ++vta++++g+ t
  gi|313122437|ref|YP_004038324.1| 597 VGYRLSVTATDSDGLQT 613
                                       36***********9977 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.059
                                       E---S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEE CS
                               PKD   2 sasptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeY 56 
                                       sa ++v+ +g+t++ft+ ++d ++   ++++         s  t t  Y s+G++
  gi|313122437|ref|YP_004038324.1| 663 SAPESVCRQGTTYEFTGWSDDNTERVRTFTVPE-------SDTTLTAQYQSAGSC 710
                                       6778999************99999999999999.......888888888888887 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.5
                                        S--BSSEEEEEEEES CS
                               PKD    6 tvlvpgatvaftaav 20  
                                        + ++ g+tv+++   
  gi|313122437|ref|YP_004038324.1| 1144 GTVESGETVTLSVLA 1158
                                        445556666665555 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.27
                                        -BSSEEEEEEEES.....-SS-SEEEEE--SS........--EEEEETTEEEEEE-SSEEEEEEE CS
                               PKD    8 lvpgatvaftaav....pdganvtysWdfgdg........svvqvlseptvthtYlspGeYeVtv 60  
                                        + +g+tv+ +a+v      + ++t    +g++          ++  +   +++t+ + G Ye+++
  gi|313122437|ref|YP_004038324.1| 1311 VTVGETVNASAVVdntgNAAGSTTVDLAVGNDtvdarsltVGAGANVTVAFSYTFDQSGAYELRL 1375
                                        66677777777774332224444555666666666654432233334445678888899999876 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.2   4.5e+03      59      85 ..     210     236 ..     201     245 .. 0.84
   2 ?    2.8   2.7      0.06   1.2e+02      31      95 ..     458     515 ..     432     517 .. 0.74
   3 ?   -3.3   0.4       4.7   9.5e+03      32      49 ..     545     562 ..     540     619 .. 0.44
   4 !   26.4   4.0   2.6e-09   5.1e-06      22      96 ..     957    1028 ..     937    1030 .. 0.76
   5 !   29.2   7.9   3.4e-10   6.9e-07       2      97 ..    1035    1127 ..    1033    1128 .. 0.81
   6 !   14.3   3.1   1.4e-05     0.029      15      90 ..    1145    1214 ..    1133    1222 .. 0.76
   7 ?   -1.6   2.3       1.4   2.7e+03      40      85 ..    1298    1343 ..    1292    1366 .. 0.74
   8 ?   -5.8   3.2         9   1.8e+04      41      91 ..    1383    1432 ..    1380    1437 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.2
                        Cadherin_5  59 gdGtftftpeanynGevtlsYtvsDge 85 
                                        dG++ +t  ++++G  + + +v Dg+
  gi|313122437|ref|YP_004038324.1| 210 PDGKIYITTGEEFQGWRSQDLSVPDGK 236
                                       799999*********999999999997 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.06
                        Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggtttatasl 95 
                                       a asD++gd+L+ +      ++Gt+++ +  t t+  +  y+  v    +vsDg++++ + t+++
  gi|313122437|ref|YP_004038324.1| 458 ASASDPNGDDLTYTWH---FGDGTTTRGASVTHTYSEAGSYDTYV----EVSDGNTTVESGTTTI 515
                                       789********99876...3569****999999999999999877....5899997766666665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.7
                        Cadherin_5  32 nasDvdgdtLsvssltad 49 
                                       +++D+++ +Ls +s++ +
  gi|313122437|ref|YP_004038324.1| 545 DVTDPEDGQLSGDSVEWS 562
                                       556666666665555431 PP

  == domain 4  score: 26.4 bits;  conditional E-value: 2.6e-09
                        Cadherin_5   22 ltitaaqLLanasDvdgdt..LsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgegg.tttata 93  
                                        + +      a asD+dgd    sv  ++ + ++Gtv++ngdGt+t+    +   + +++  +sD+ g+ +++at+
  gi|313122437|ref|YP_004038324.1|  957 INV-----TAAASDPDGDVdpSSVRIVE-QPTSGTVTNNGDGTVTYATSDESATSDSFTVAISDTDGAeSAPATV 1025
                                        444.....47889999876658888886.5569********************************9875667777 PP

                        Cadherin_5   94 slt 96  
                                        +lt
  gi|313122437|ref|YP_004038324.1| 1026 DLT 1028
                                        665 PP

  == domain 5  score: 29.2 bits;  conditional E-value: 3.4e-10
                        Cadherin_5    2 ndaPvvssevtlaagseDtaltitaaqLLanasDvdg..dtLsvssltadaenGtvvdngdGtftftpeanynGe 74  
                                        n  P+++++  +a+++ ++++ i    +L n+ D dg  dt sv+ ++ + ++G+v+ +gdG +t+t + +   +
  gi|313122437|ref|YP_004038324.1| 1035 NAPPTANDD--AANVTVGQSVKIP---VLGNDGDSDGslDTSSVTIVA-QPSTGSVTIDGDGAITYTHTGDSATT 1103
                                        555666654..5567777777777...9********756788888884.6669********************** PP

                        Cadherin_5   75 vtlsYtvsDgegg.tttatasltv 97  
                                         +++Y+vsD+ g  +  at+++tv
  gi|313122437|ref|YP_004038324.1| 1104 DSFTYEVSDDDGDiSNVATVEITV 1127
                                        ***********9955667888877 PP

  == domain 6  score: 14.3 bits;  conditional E-value: 1.4e-05
                        Cadherin_5   15 agseDtaltitaaqLLana.sDvdgdtLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggt 88  
                                        +++ ++++t++   +Lan+   vd  tL +++    a++Gt +  ++G+ +++   +   +  ++Ytv D++g+ 
  gi|313122437|ref|YP_004038324.1| 1145 TVESGETVTLS---VLANDsASVDASTLRIDGD---ADHGTATV-ENGQLVYQHSGDSATDDMIEYTVADANGNR 1212
                                        34444455555...566651689*******995...55699887.89*************************986 PP

                        Cadherin_5   89 tt 90  
                                        ++
  gi|313122437|ref|YP_004038324.1| 1213 SA 1214
                                        54 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 1.4
                        Cadherin_5   40 tLsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDge 85  
                                        + +vs+++++++n tv +  + + +++ + n  G++t++  v  ++
  gi|313122437|ref|YP_004038324.1| 1298 SFEVSNVALSSTNVTVGETVNASAVVDNTGNAAGSTTVDLAVGNDT 1343
                                        5789999999999999999999999999999999999988885332 PP

  == domain 8  score: -5.8 bits;  conditional E-value: 9
                        Cadherin_5   41 LsvssltadaenGtvvdngdGtftftpeanynGevtlsYtvsDgeggttta 91  
                                        ++vs+ t+++ + +  d gdG+ t +  ++ +G+ + + +v+ g+ ++t++
  gi|313122437|ref|YP_004038324.1| 1383 VTVSNATQTD-ESNNDDTGDGDSTSEAVTEGTGTDERNERVENGNRSSTET 1432
                                        6777776544.6777788888888888888888888888888887655554 PP

>> Cadherin_3  Cadherin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.12   2.3e+02      62     110 ..     981    1014 ..     949    1015 .. 0.62
   2 !    8.2   0.6    0.0012       2.4      87     110 ..    1089    1112 ..    1019    1113 .. 0.72
   3 !    9.6   0.1   0.00043      0.85      82     110 ..    1179    1207 ..    1141    1208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
                        Cadherin_3   62 psnGrlelkgapgekvtsFtqadidaglvvyvhdgseslsdsfsfqvtD 110 
                                        p+ G ++++g+               g v y  ++++++sdsf++ ++D
  gi|313122437|ref|YP_004038324.1|  981 PTSGTVTNNGD---------------GTVTYATSDESATSDSFTVAISD 1014
                                        44444444444...............55666666666666666666665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                        Cadherin_3   87 aglvvyvhdgseslsdsfsfqvtD 110 
                                        +g + y+h+g+++++dsf+++v+D
  gi|313122437|ref|YP_004038324.1| 1089 DGAITYTHTGDSATTDSFTYEVSD 1112
                                        489********************9 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00043
                        Cadherin_3   82 qadidaglvvyvhdgseslsdsfsfqvtD 110 
                                         a +++g++vy+h+g+++++d ++++v D
  gi|313122437|ref|YP_004038324.1| 1179 TATVENGQLVYQHSGDSATDDMIEYTVAD 1207
                                        5789***********9**********998 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.9   6.1e-05      0.12       1      23 []    1461    1484 ..    1461    1484 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.1e-05
                         PGF-CTERM    1 tPGFGavlAlaGLLaaa.lLaRRr 23  
                                        tPGFG  +A+   L a+  L RRr
  gi|313122437|ref|YP_004038324.1| 1461 TPGFGPFVAVLSVLLAVvMLGRRR 1484
                                        9***********988888*****8 PP

>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.96   1.9e+03       2       8 ..      79      85 ..      78      86 .. 0.86
   2 ?   12.2   0.1   8.4e-05      0.17       2      32 ..     210     246 ..     209     246 .. 0.76
   3 ?   -3.1   0.1       5.2     1e+04       9      18 ..     861     871 ..     861     873 .. 0.77
   4 ?   -1.4   1.0       1.5   3.1e+03      27      35 ..     965     973 ..     965     973 .. 0.91
   5 ?    0.8   1.7      0.31   6.2e+02      27      35 ..    1063    1071 ..    1063    1071 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.96
                           DUF5122  2 pDGKIlV 8 
                                      pDG+Il+
  gi|313122437|ref|YP_004038324.1| 79 PDGRILI 85
                                      9****98 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.4e-05
                           DUF5122   2 pDGKI.lVaGsftsy.....ngssdfalvRLnaDGsl 32 
                                       pDGKI +  G+  +       +++d  ++RLn+DGs+
  gi|313122437|ref|YP_004038324.1| 210 PDGKIyITTGEEFQGwrsqdLSVPDGKVIRLNQDGSI 246
                                       78888555555553466666***************96 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.2
                           DUF5122   9 aGsftsy.ngs 18 
                                       +G ft+y ng+
  gi|313122437|ref|YP_004038324.1| 861 GGQFTQYaNGQ 871
                                       89***885666 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.5
                           DUF5122  27 naDGslDts 35 
                                       ++DG++D+s
  gi|313122437|ref|YP_004038324.1| 965 DPDGDVDPS 973
                                       69******8 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.31
                           DUF5122   27 naDGslDts 35  
                                        ++DGslDts
  gi|313122437|ref|YP_004038324.1| 1063 DSDGSLDTS 1071
                                        58******8 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       8.3   1.7e+04      50      73 ..     503     526 ..     484     526 .. 0.77
   2 ?   -2.8   0.1       3.9   7.8e+03      30      60 ..     985    1015 ..     985    1030 .. 0.74
   3 ?   -0.8   0.0      0.91   1.8e+03      55      72 ..    1139    1156 ..    1118    1175 .. 0.70
   4 ?    9.6   0.4   0.00052         1      17      76 ..    1309    1365 ..    1297    1387 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8.3
                                       XXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  50 ekgfsveetelevqpgesvtltvt 73 
                                       + + +ve  ++++++ge+ ++++t
  gi|313122437|ref|YP_004038324.1| 503 DGNTTVESGTTTITAGEPPQVDIT 526
                                       567788888999999998888775 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.9
                                        EEESS-SS--EEEEEEEE--XXXXXXXXXXX CS
                               ASH   30 tveNpseepaevkvskvpaaekgfsveetel 60  
                                        tv+N+++ +++ ++s+ +a++  f+v  + +
  gi|313122437|ref|YP_004038324.1|  985 TVTNNGDGTVTYATSDESATSDSFTVAISDT 1015
                                        6899999998888888888999999976655 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.91
                                        XXXXXXXXXXXXXXXXXX CS
                               ASH   55 veetelevqpgesvtltv 72  
                                         + ++ +v+ ge+vtl+v
  gi|313122437|ref|YP_004038324.1| 1139 TNDDHGTVESGETVTLSV 1156
                                        4455699*********98 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00052
                                        -----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH   17 gdvkvGssaerlLtveNpseepaevkvskvpaaekgfsveetelevqpgesvtltvtwtP 76  
                                         +v+vG++  ++ +v+N+++++ +++v+ ++    + +v++++l+v +g +vt+ +++t 
  gi|313122437|ref|YP_004038324.1| 1309 TNVTVGETVNASAVVDNTGNAAGSTTVDLAV---GNDTVDARSLTVGAGANVTVAFSYTF 1365
                                        689*******************999999999...7779****************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.94u 0.25s 00:00:01.19 Elapsed: 00:00:00.44
# Mc/sec: 10133.87
//
Query:       gi|313122438|ref|YP_004038325.1|  [L=312]
Description: hypothetical protein Hbor_36720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   13.9   1.0       0.39   10.8   0.0    2.5  2  DUF3244   Domain of unknown function (DUF3244)


Domain annotation for each model (and alignments):
>> DUF3244  Domain of unknown function (DUF3244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.2e-05      0.39      31      92 ..      67     126 ..      47     129 .. 0.79
   2 ?    0.6   0.4     0.034     6e+02      39      66 ..     225     250 ..     207     256 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.2e-05
                                       TTEEEEEESS--SEE.EEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS- CS
                           DUF3244  31 gnilsiefesplsdv.titikdeetgevvyestivnasgstisidlsgeesgeYkleltskgg 92 
                                       g+ + ++   p +++  +t+  +  g+v +++++++  g+++ +d s +++g+Y l l+++g+
  gi|313122438|ref|YP_004038325.1|  67 GEEVLVNVAAPADELaVVTVRTA-DGTVRQKDSVTT--GESVLVDSSEYDPGTYYLVLSTDGQ 126
                                       55667777888888835566666.788888888885..5*******************98876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.034
                                       SS--SEEEEEEEETTT--EEEEEEE-GG CS
                           DUF3244  39 esplsdvtitikdeetgevvyestivna 66 
                                       +s+++  t+t+ + +tge v   +++++
  gi|313122438|ref|YP_004038325.1| 225 TSQVR--TVTVGSTDTGESVAVASDTTE 250
                                       44444..555566666776666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1762.10
//
Query:       gi|313122439|ref|YP_004038326.1|  [L=292]
Description: hypothetical protein Hbor_36730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-05   21.9   0.0    0.00016   21.1   0.0    1.3  1  GIDE      E3 Ubiquitin ligase
  ------ inclusion threshold ------
       0.15   10.8   0.0        0.8    8.4   0.0    1.9  2  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> GIDE  E3 Ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.7e-08   0.00016      63     154 ..     192     281 ..     178     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-08
                              GIDE  63 asrvtlllgffsldlek.tlGyryeEkvLpvgkrvtvvGeaqsdedgtleiqkpeekgqpffisekseeeLieslas 138
                                        ++++++lg++  +l++    ++ +E v++ g ++tvvG ++ ++d  ++++  +      +i++ s +eL+++ + 
  gi|313122439|ref|YP_004038326.1| 192 EHQSQGVLGRLLSKLRTpAGTVQFQEAVMRAGEPLTVVGRVVGSRDKRVKLEENDAV--DPIITRLSPSELRSKHR- 265
                                       4788899999999996656779********************999999999997776..889**********9988. PP

                              GIDE 139 sarllfygsialgvva 154
                                       +a ++ + ++ l+++a
  gi|313122439|ref|YP_004038326.1| 266 RAYVTQLYAVPLVLIA 281
                                       7788887777777666 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.026   2.3e+02     210     250 ..       7      43 ..       2      77 .. 0.62
   2 ?    8.4   0.0     9e-05       0.8     111     227 ..     175     290 ..     169     292 .] 0.71

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.026
                           DUF2207 210 illilllilllllllllliklllwkkygrepkvkevdpeYe 250
                                       +++++   ll++++l+l+ + +l++ +  + k+     eY+
  gi|313122439|ref|YP_004038326.1|   7 VVNAVGSGLLVFAVLMLFASPILYRGWQNRVKYH----EYA 43 
                                       4444555555555555555545444444444443....343 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 9e-05
                           DUF2207 111 wdvpienvtitvtlPseaksggdlrawlHgldgsttvkkddgsvtftarnlppgeglevrvlfptnnarktsgnkld 187
                                       w  ++en+ ++v +    +++ +++  l  l    + ++  g+v+f+    ++ge+l+v+  +         g++ +
  gi|313122439|ref|YP_004038326.1| 175 WPQEYENLGARVGVQ---SDEHQSQGVLGRL--LSKLRTPAGTVQFQEAVMRAGEPLTVVGRVV--------GSRDK 238
                                       777777777777443...3333333333331..245677899*********************4........55667 PP

                           DUF2207 188 eilkeeqk............ntreraarlslallillilllillllllllll 227
                                        ++ ee++            + r++++r +++ l ++ l+li+++ l  +++
  gi|313122439|ref|YP_004038326.1| 239 RVKLEENDavdpiitrlspsELRSKHRRAYVTQLYAVPLVLIAFASLTGYAV 290
                                       7777777788999999998888888888888888888888888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1704.49
//
Query:       gi|313122440|ref|YP_004038327.1|  [L=417]
Description: ORC complex protein Cdc6/Orc1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-19   67.8   0.1    1.4e-18   66.6   0.1    1.7  1  Cdc6_C           CDC6, C terminal winged helix domain
    6.5e-12   45.9   0.0    1.9e-11   44.4   0.0    1.7  1  AAA_22           AAA domain
      2e-11   44.5   1.8    4.4e-11   43.5   0.2    2.3  2  AAA_16           AAA ATPase domain
    3.1e-05   24.0   0.0    5.2e-05   23.2   0.0    1.3  1  NACHT            NACHT domain
    9.8e-05   21.6   0.0    0.00023   20.4   0.0    1.6  2  DUF815           Protein of unknown function (DUF815)
    0.00035   19.9   0.0     0.0006   19.1   0.0    1.3  1  NB-ARC           NB-ARC domain
    0.00037   20.9   0.0    0.00097   19.6   0.0    1.8  1  AAA              ATPase family associated with various cellul
     0.0025   17.4   0.0     0.0041   16.7   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.019   14.9   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
      0.011   15.5   0.0        0.5   10.1   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
      0.011   15.1   0.0      0.018   14.5   0.0    1.2  1  TniB             Bacterial TniB protein
      0.014   15.1   0.0      0.029   14.1   0.0    1.5  2  AAA_30           AAA domain
      0.021   15.2   0.1      0.046   14.1   0.1    1.8  1  RNA_helicase     RNA helicase
      0.025   14.6   0.2       0.19   11.7   0.2    2.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.026   13.4   0.1       0.39    9.4   0.0    2.0  2  AAA_32           AAA domain
      0.027   15.0   0.0       0.12   13.0   0.0    2.1  2  AAA_18           AAA domain
       0.11   12.5   0.0       0.22   11.5   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.11   11.7   0.1        5.2    6.2   0.0    2.1  2  KAP_NTPase       KAP family P-loop domain
       0.12   11.6   0.0       0.18   10.9   0.0    1.2  1  PIF1             PIF1-like helicase
       0.12   12.0   0.0       0.21   11.2   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
       0.16   11.7   0.0       0.27   10.9   0.0    1.4  1  AAA_24           AAA domain
       0.17   11.7   0.0       0.34   10.7   0.0    1.5  1  Bac_DnaA         Bacterial dnaA  protein
       0.18   10.6   0.0       0.29   10.0   0.0    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.1   1.8e-21   1.4e-18       1      83 [.     302     383 ..     302     384 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.8e-21
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+al+ l   ++++++++++v  +Y++ +e  + dpl  r+++d+lseL+mlgi++++++++Grr+g +r++ L++d
  gi|313122440|ref|YP_004038327.1| 302 LYALLTLDL-EDETPIRSRDVRPRYTRFAELANRDPLVPRRMRDHLSELAMLGIVSVTERNEGRRGGTYREYALDMD 377
                                       89***9999.******************************************************************* PP

                                       CHHHHH CS
                            Cdc6_C  78 pddvle 83 
                                        + +l 
  gi|313122440|ref|YP_004038327.1| 378 VELILS 383
                                       998875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   2.4e-14   1.9e-11       6     118 ..      50     167 ..      45     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.4e-14
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka...erlsseel 78 
                                       + ++++G +G+GKT   + ll+ l e+a++ +  + +v f ++ ++tss +++++l++ l +e +     +  +  +
  gi|313122440|ref|YP_004038327.1|  50 NNVFLYGKTGVGKTAATKYLLSHLREDAAQYDdIDLSVTFLNCDGLTSSYQIATRLVNSLRSESNQistTGYPLASV 126
                                       56799******************9766555557788888***********************9999*9999999999 PP

                            AAA_22  79 lealeqalraravielliiDEaqhlrseealeeL.rsllnl 118
                                       +e+l++ l++ra ++l+++DE++h++ + +l +L r ++n 
  gi|313122440|ref|YP_004038327.1| 127 YEMLWEELDDRAGTVLVVLDEIDHVNDDSILYQLpRARANG 167
                                       *************************6688888887777774 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.2   5.6e-14   4.4e-11       1     151 [.      25     155 ..      25     172 .. 0.69
   2 ?   -1.6   0.1       3.9     3e+03     118     118 ..     277     277 ..     195     352 .. 0.58

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 5.6e-14
                            AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqa 75 
                                       +lvGR+eel++ ++al++v  g+  ++v+l+G  GvGK++  + ll +l++d     ++++d+      +s+ ++++
  gi|313122440|ref|YP_004038327.1|  25 QLVGRDEELRTYQAALQPVINGEQpNNVFLYGKTGVGKTAATKYLLSHLRED-----AAQYDDI----DLSVtFLNC 92 
                                       79*****************999999***************************.....4444444....233335555 PP

                            AAA_16  76 lareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwadeas 151
                                           +   q+++++ ++++++  +  ++ +              l+ + ++l + l  ++ ++++vlD+++ + ++s
  gi|313122440|ref|YP_004038327.1|  93 D-GLTSSYQIATRLVNSLRSESNQISTTGYP-------------LASVYEMLwEELDDRAGTVLVVLDEIDHVNDDS 155
                                       5.33666666666555555555554445444.............333333333444444445888888888777754 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.9
                            AAA_16 118 r 118
                                       r
  gi|313122440|ref|YP_004038327.1| 277 R 277
                                       0 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   6.6e-08   5.2e-05       3      96 ..      52     154 ..      50     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.6e-08
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C....... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgnarsladllfsqlpepaapvse....... 71 
                                       v+l G+ G+GKT+  + l + ++e+  + +     v fl++  l+ s     +a+ l+  l  ++ ++s+       
  gi|313122440|ref|YP_004038327.1|  52 VFLYGKTGVGKTAATKYLLSHLREDAAQYDDiDLSVTFLNCDGLTSSY---QIATRLVNSLRSESNQISTtgyplas 125
                                       899**********99999999999988877756668899999999985...55666666666666666666666888 PP

                                       ....CHHHHCCSCCCEEEEEE-STT-SS- CS
                             NACHT  72 ....vwavllelperlLlilDglDelvtd 96 
                                            w++l  ++  +L +lD +D + +d
  gi|313122440|ref|YP_004038327.1| 126 vyemLWEELDDRAGTVLVVLDEIDHVNDD 154
                                       88889*******************98875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.9e-07   0.00023      25      80 ..      21      76 ..      15     104 .. 0.91
   2 ?   -3.6   0.0       6.2   4.8e+03     148     164 ..     331     347 ..     322     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.9e-07
                            DUF815 25 vklddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaee 80
                                       + ++Lvg d++ ++ ++  +  ++g++ nnv+L+G+ G+GK +  k ll++++e+
  gi|313122440|ref|YP_004038327.1| 21 YQPEQLVGRDEELRTYQAALQPVINGEQPNNVFLYGKTGVGKTAATKYLLSHLRED 76
                                      56789*********************************************999876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.2
                            DUF815 148 TsNrRhLlpeklsdnee 164
                                        +Nr  L+p++++d+ +
  gi|313122440|ref|YP_004038327.1| 331 LANRDPLVPRRMRDHLS 347
                                       589999******99865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   7.7e-07    0.0006      17     115 ..      48     151 ..      35     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.7e-07
                                       TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT....EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-ST CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksdevegrFd....svawvvvsktdkseeiletilkeLslseddleekeev 89 
                                       +++   v+l+G+ GvGKt   k  l+++ e   ++d    sv ++      +s++i  ++++ L  ++++++    +
  gi|313122440|ref|YP_004038327.1|  48 QPN--NVFLYGKTGVGKTAATKYLLSHLREDAAQYDdidlSVTFLNCDGLTSSYQIATRLVNSLRSESNQISTT--G 120
                                       444..79****************************9655556777888889999**********7776665554..4 PP

                                       TS...HHHHHHHHCCCT..TEEEEEEEE-SH CS
                            NB-ARC  90 es...lkrklvrlLltk..rfllvlDDVwee 115
                                       ++     ++l + L ++   +l+vlD + + 
  gi|313122440|ref|YP_004038327.1| 121 YPlasVYEMLWEELDDRagTVLVVLDEIDHV 151
                                       44446899********998999999988544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-06   0.00097       1     131 [.      52     205 ..      52     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                                       EEEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS...................STTHHHHHH.H CS
                               AAA   1 vllyGppGtGKTllakavakel..........gvefleisgsellsk...................yvgesekki.r 47 
                                       v lyG  G+GKT++ k + ++l          + ++  +++  l+s+                   + g   +++ +
  gi|313122440|ref|YP_004038327.1|  52 VFLYGKTGVGKTAATKYLLSHLredaaqyddiDLSVTFLNCDGLTSSyqiatrlvnslrsesnqisTTGYPLASVyE 128
                                       679******************85554444433355666666667766678888888888888866633333333303 PP

                                       HHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHHS CS
                               AAA  48 elfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpallr 121
                                       +l++e+   a+++ +++DEid ++ ++          ++ qL ++  + + + +k+ +ig++n+    d+l+p++ +
  gi|313122440|ref|YP_004038327.1| 129 MLWEELDDRAGTVLVVLDEIDHVNDDS----------ILYQLPRARANGNLEVAKIGLIGISNDfsfRDDLSPKVKS 195
                                       333444444467999********8877..........9999999999888889999999999998888888888887 PP

                                       TTSSEEEETT CS
                               AAA 122 gRfdrkieie 131
                                       + ++++i+++
  gi|313122440|ref|YP_004038327.1| 196 SLCEQEIHFP 205
                                       7888877765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.2e-06    0.0041      32      71 ..      48      87 ..      26     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.2e-06
                             AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsa 71
                                      + ++v+l+G+tG+GKt+ +k ll++l ++  ++  i +s 
  gi|313122440|ref|YP_004038327.1| 48 QPNNVFLYGKTGVGKTAATKYLLSHLREDAAQYDDIDLSV 87
                                      45789**********************9999888887775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.4e-05     0.019      10      47 ..      39      76 ..      26     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                          ATPase_2 10 eleeilerepneiyfiYGpegsGKtaLlkeiienledk 47
                                       l+ +++ e+ + +f+YG  g+GKta  k +++ l++ 
  gi|313122440|ref|YP_004038327.1| 39 ALQPVINGEQPNNVFLYGKTGVGKTAATKYLLSHLRED 76
                                      4777889999999*****************99999663 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00064       0.5       3      31 ..      36      66 ..      34      83 .. 0.79
   2 ?    3.2   0.0     0.085        66     123     138 ..     141     156 ..     100     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00064
                                      HHHHHHHHHHTT..CEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                              DEAD  3 iQaeaiplilgg..gdvlvaaeTGsGKTlaf 31
                                      +Qa+  p i g+  ++v++ ++TG GKT+a 
  gi|313122440|ref|YP_004038327.1| 36 YQAALQPVINGEqpNNVFLYGKTGVGKTAAT 66
                                      688888888844337*************995 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.085
                                       EEEEEETHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD 123 rflVlDEadrlldqgf 138
                                        ++VlDE+d + d++ 
  gi|313122440|ref|YP_004038327.1| 141 VLVVLDEIDHVNDDSI 156
                                       589********99865 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.3e-05     0.018      32     132 ..      46     152 ..      30     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                              TniB  32 rkrmpnlllvGdsnnGKtmivekFarlhppekd..edaekvpvlvvqappkpdekrlyaaiLealgaplkararvsk 106
                                        ++++n+ l+G++ +GKt+  + +  +h +e+    d+  + v  +++    +  ++ ++++++l+ + ++  ++  
  gi|313122440|ref|YP_004038327.1|  46 GEQPNNVFLYGKTGVGKTAATK-YLLSHLREDAaqYDDIDLSVTFLNCDGLTSSYQIATRLVNSLRSESNQISTTGY 121
                                       567899************9765.5555655544114455779*************************9888776665 PP

                              TniB 107 leqqvlrll.....relkvrvLiiDEihnll 132
                                         + v+++l     ++ ++ ++++DEi+++ 
  gi|313122440|ref|YP_004038327.1| 122 PLASVYEMLweeldDRAGTVLVVLDEIDHVN 152
                                       555555555322234567778899***9985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.7e-05     0.029       7     115 ..      38     166 ..      32     178 .. 0.72
   2 ?   -3.0   0.0       6.7   5.2e+03     160     186 ..     273     299 ..     258     301 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-05
                            AAA_30   7 aaavealltsgdrvavltGpAGtGKttalkalreaweaag............grviglAptgkaAkvLaeelgieas 71 
                                       aa+   + +++   ++l G  G GKt a k l  +++++              +  gl+++ + A +L ++l  e++
  gi|313122440|ref|YP_004038327.1|  38 AALQPVINGEQPNNVFLYGKTGVGKTAATKYLLSHLREDAaqyddidlsvtfLNCDGLTSSYQIATRLVNSLRSESN 114
                                       555545555555678899*********99999777766644788888888777777899999999998888888888 PP

                            AAA_30  72 tiakllkrlk........grarlepg.tllivDEagmvdtkqlaallkaaeka 115
                                        i    + l+        +  + ++g  l++ DE+  v+ +++   l +a+++
  gi|313122440|ref|YP_004038327.1| 115 QISTTGYPLAsvyemlweE-LDDRAGtVLVVLDEIDHVNDDSILYQLPRARAN 166
                                       8888888888999999852.344455467888**9999877776666666654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.7
                            AAA_30 160 seeraaalalregdaeealealadrgr 186
                                       ++ r+  +al++g+++e ++ l ++g+
  gi|313122440|ref|YP_004038327.1| 273 DHVRRGRRALERGRIKEGINGLTEHGH 299
                                       444555567777777777777777776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.9e-05     0.046       1      26 [.      52      77 ..      52     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      ++lyG++g+GK+ ++k+L ++l ++ 
  gi|313122440|ref|YP_004038327.1| 52 VFLYGKTGVGKTAATKYLLSHLREDA 77
                                      689**************999998654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00024      0.19       1      24 [.      51      80 ..      51     175 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                      EEEEE--SSSSHHHHHHHGGGGB......S CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal......n 24
                                      +v+L G++G+gK+  +++l++ l       
  gi|313122440|ref|YP_004038327.1| 51 NVFLYGKTGVGKTAATKYLLSHLredaaqY 80
                                      69******************9997553330 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0005      0.39      31      64 ..      50      83 ..      22      91 .. 0.85
   2 ?    1.6   0.0      0.12        93     478     507 ..     249     278 ..     243     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0005
                            AAA_32 31 YNifvlGesgtGrttlvkrlleeiakkeptpdDw 64
                                       N+f+ G++g+G+t ++k ll++  +++++ dD+
  gi|313122440|ref|YP_004038327.1| 50 NNVFLYGKTGVGKTAATKYLLSHLREDAAQYDDI 83
                                      59**********************9999999986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                            AAA_32 478 seiadllrEAdywakkegaevveaehVekA 507
                                       ++ +dll+ A  +a++e+ e++e++hV++ 
  gi|313122440|ref|YP_004038327.1| 249 RQSIDLLMKAGDLARDEDTETIEEDHVRRG 278
                                       56789**********************975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00015      0.12       1      39 [.      52      85 ..      52     153 .. 0.69
   2 ?   -1.6   0.0       4.6   3.6e+03      29      79 ..     259     302 ..     244     315 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglll 39
                                      ++l G+ GvGKt  +k+L ++l       d a+ +++ l
  gi|313122440|ref|YP_004038327.1| 52 VFLYGKTGVGKTAATKYLLSHL-----REDAAQYDDIDL 85
                                      799***************8876.....445555444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.6
                            AAA_18  29 rdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvi 79 
                                       +d+a+++++++ ++++ +++ +r+ e    ++ ++++     l+e+++lv+
  gi|313122440|ref|YP_004038327.1| 259 GDLARDEDTETIEEDH-VRRGRRALERG--RIKEGIN----GLTEHGHLVL 302
                                       3444444444444444.44444444444..2222222....2556677666 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.22      10      44 ..      36      74 ..      28      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                                      HHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE 10 lgkklakal....gdvilLeGdLGaGKTtlvrglakalg 44
                                        ++l+ ++     + ++L+G+ G+GKT+ ++ l+++l 
  gi|313122440|ref|YP_004038327.1| 36 YQAALQPVIngeqPNNVFLYGKTGVGKTAATKYLLSHLR 74
                                      4555555445333345******************99885 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.024        19      19      61 ..      48      95 ..      34     118 .. 0.69
   2 ?    6.2   0.0    0.0067       5.2     140     191 ..     104     157 ..      78     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.024
                        KAP_NTPase 19 tpivvgLygkWGsGKssllnkledelkefa.....kpvrflfaefnaw 61
                                      +p  v Lygk G+GK++  + l + l+e a        +++f + + +
  gi|313122440|ref|YP_004038327.1| 48 QPNNVFLYGKTGVGKTAATKYLLSHLREDAaqyddIDLSVTFLNCDGL 95
                                      466789***********9999999999988666663334444444444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0067
                        KAP_NTPase 140 raaklkeeaplkkl..qteveelladmektLdalqkrlVvviDdLDrceteevl 191
                                       r+++++ +++++ +  +   +++++++ ++Ld+   +++vv+D++D + ++ +l
  gi|313122440|ref|YP_004038327.1| 104 RLVNSLRSESNQISttGYPLASVYEMLWEELDDRAGTVLVVLDEIDHVNDDSIL 157
                                       55555544444433004455668999999*******************999875 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00024      0.18       8      49 ..      34      76 ..      29      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                      HHHHHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                              PIF1  8 kvfdaiieavln.ekgklfFvtGsgGtgKtflwkallkklrse 49
                                      + ++a+++ v+n e+++++F++G  G gKt   k ll+ lr+ 
  gi|313122440|ref|YP_004038327.1| 34 RTYQAALQPVINgEQPNNVFLYGKTGVGKTAATKYLLSHLRED 76
                                      56778888888879*****************999999999975 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.21       2      53 ..      27      80 ..      26      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                                      ---SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
                   Sigma54_activat  2 igesealkelleqikkvaktd..lsvlitGesGtGKellaraiheaskrkekpf 53
                                      +g++e+l++  + ++ v++ +   +v++ G++G+GK+   + + ++ +++++++
  gi|313122440|ref|YP_004038327.1| 27 VGRDEELRTYQAALQPVINGEqpNNVFLYGKTGVGKTAATKYLLSHLREDAAQY 80
                                      6788888888888888886554499*************9999987666665555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00034      0.27       3      79 ..      50     153 ..      48     168 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                            AAA_24   3 lkiliyGpsgiGKTtlakel..............gpkplfidtekGlksldadkfpdieswedfldevvel...... 59 
                                       +++++yG+ g+GKT   k l                ++ f+++++ l s + +    ++          +l      
  gi|313122440|ref|YP_004038327.1|  50 NNVFLYGKTGVGKTAATKYLlshlredaaqyddiDLSVTFLNCDG-LTSSYQIATRLVN----------SLrsesnq 115
                                       6899**********9999998888866665555555555556655.3333333333332..........22222222 PP

                            AAA_24  60 ..................aaeladyktlviDtidelee 79 
                                                          ++ a+   +v+D id++ +
  gi|313122440|ref|YP_004038327.1| 116 isttgyplasvyemlweeLDDRAGTVLVVLDEIDHVND 153
                                       23335555555555555467777777778888887765 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00043      0.34      30      74 ..      45      94 ..      17     117 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                                      TTT.S--EEEE-SSSSSHH....HHHHHHHHHHHH.HSSSS-EEEEEHHH CS
                          Bac_DnaA 30 pgkkynPlfiygevGlGkt....HLlkaignevle.napelrvvYltaee 74
                                       g++ n +f+yg++G+Gkt    +Ll  +   + + +  +l v++l+ + 
  gi|313122440|ref|YP_004038327.1| 45 NGEQPNNVFLYGKTGVGKTaatkYLLSHLREDAAQyDDIDLSVTFLNCDG 94
                                      4567899***********94444456555554433145566777766554 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00037      0.29       9      43 ..      43      77 ..      35      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                     TrwB_AAD_bind  9 lpkeretqhilivGttGsGKtqalekllrairarg 43
                                      + + +  + +++ G tG GKt a++ ll ++r+ +
  gi|313122440|ref|YP_004038327.1| 43 VINGEQPNNVFLYGKTGVGKTAATKYLLSHLREDA 77
                                      55556667899********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 2517.50
//
Query:       gi|313122441|ref|YP_004038328.1|  [L=140]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-15   56.3   0.7      6e-15   55.6   0.7    1.4  1  HTH_32        Homeodomain-like domain
    5.6e-11   42.4   0.0    2.8e-10   40.2   0.0    1.9  2  HTH_28        Helix-turn-helix domain
    1.4e-10   41.0   0.0    4.5e-10   39.4   0.0    1.8  2  HTH_29        Winged helix-turn helix
    7.9e-09   35.1   0.0    1.6e-08   34.1   0.0    1.5  1  HTH_23        Homeodomain-like domain
    1.1e-06   28.2   0.2    6.2e-06   25.8   0.1    2.2  2  HTH_33        Winged helix-turn helix
    0.00026   21.2   0.0    0.00078   19.7   0.0    1.8  2  HTH_Tnp_1     Transposase
     0.0016   18.5   0.1        1.7    8.8   0.0    2.4  2  HTH_7         Helix-turn-helix domain of resolvase
     0.0022   17.7   0.0     0.0049   16.6   0.0    1.7  1  HTH_psq       helix-turn-helix, Psq domain
     0.0037   17.7   0.0      0.007   16.9   0.0    1.5  1  LZ_Tnp_IS481  leucine-zipper of insertion element IS481
  ------ inclusion threshold ------
      0.034   14.3   0.0       0.05   13.8   0.0    1.3  1  HTH_Tnp_1_2   Helix-turn-helix of insertion element transposa
      0.042   13.4   0.0       0.31   10.6   0.0    2.3  2  Sigma70_r4    Sigma-70, region 4
      0.045   13.9   0.1       0.14   12.3   0.1    1.8  2  MerR_1        MerR HTH family regulatory protein
       0.13   11.9   0.0       0.27   10.9   0.0    1.4  1  CENP-B_N      CENP-B N-terminal DNA-binding domain
       0.15   12.4   3.8       0.36   11.2   0.9    2.5  2  HBS1_N        HBS1 N-terminus
        0.6   10.4   0.2        0.6   10.4   0.2    3.0  3  zf-HC2        Putative zinc-finger


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.7     5e-18     6e-15       1      73 []      53     134 ..      53     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 5e-18
                            HTH_32   1 TvsrwlkRyneeGle.gLkdrprrgrprklsdevrariiallreep........rWsprqlaarlaeregvkvShst 68 
                                       T++ wl R+++e +e ++ d+ r+grprkl++e r r++  l + p        +W+p++++++++  +gv++S  +
  gi|313122441|ref|YP_004038328.1|  53 TLYYWLDRFETESIEeAITDEDRPGRPRKLDEEDRNRLRSHLDTTPreynydadEWTPELVREHVEHTFGVTYSVGH 129
                                       89***********999**************************88889******************7777******** PP

                            HTH_32  69 vyriL 73 
                                       ++r+L
  gi|313122441|ref|YP_004038328.1| 130 IRRLL 134
                                       ***98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.3e-13   2.8e-10       1      52 []      26      80 ..      26      80 .. 0.93
   2 ?   -0.5   0.0       1.2   1.4e+03      22      36 ..     121     137 ..     117     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.3e-13
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrrtvyrWikryeegGia.gLvp..rrrrpr 52
                                      +Rl + + +++ ++v+ +A ++gi r+t+y W+ r+e++ i+ +  +  r++rpr
  gi|313122441|ref|YP_004038328.1| 26 KRLVVALDYLDDVPVSVLADRYGIPRSTLYYWLDRFETESIEeAITDedRPGRPR 80
                                      599999**********************************954988888899997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                            HTH_28  22 lgi..srrtvyrWikry 36 
                                       +g+  s  +++r+++ +
  gi|313122441|ref|YP_004038328.1| 121 FGVtySVGHIRRLLRDL 137
                                       56655789999999975 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         3   3.6e+03      19      35 ..       2      18 ..       1      22 [. 0.77
   2 !   39.4   0.0   3.8e-13   4.5e-10       1      62 [.      27      87 ..      27      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3
                            HTH_29 19 Akllglsrrtvyrwlkr 35
                                      +kl +++++  +r+l  
  gi|313122441|ref|YP_004038328.1|  2 VKLDDVDPDELRRTLAE 18
                                      56778999999999875 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 3.8e-13
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprnrlseeqe 62
                                      R+ + l + + v+ vs +A ++g+ r+t y wl+rfe++ ++ ++    r+grpr+ l+ee +
  gi|313122441|ref|YP_004038328.1| 27 RLVVALDYLDDVP-VSVLADRYGIPRSTLYYWLDRFETESIEEAITdEDRPGRPRK-LDEEDR 87
                                      5667788999999.**************************9998888********6.***987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.3e-11   1.6e-08       1      47 [.      21      67 ..      21      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.3e-11
                            HTH_23  1 dasereRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGle 47
                                      +a+e +Rl ++l +++  +v+  A+++g++r+T+y wl r++ e +e
  gi|313122441|ref|YP_004038328.1| 21 SAKEAKRLVVALDYLDDVPVSVLADRYGIPRSTLYYWLDRFETESIE 67
                                      589**************************************778765 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.3e+03      23      33 ..      50      60 ..      41      62 .. 0.75
   2 !   25.8   0.1   5.2e-09   6.2e-06       4      33 ..     107     136 ..     104     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                            HTH_33 23 svsgvyrlLkr 33
                                       +s++y +L+r
  gi|313122441|ref|YP_004038328.1| 50 PRSTLYYWLDR 60
                                      46888999988 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.2e-09
                            HTH_33   4 rWtlarlaqlieerfgvsysvsgvyrlLkr 33 
                                        Wt + +++++e +fgv+ysv +++rlL+ 
  gi|313122441|ref|YP_004038328.1| 107 EWTPELVREHVEHTFGVTYSVGHIRRLLRD 136
                                       5***************************86 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.6e-07   0.00078      10      67 ..      24      88 ..      21      93 .. 0.74
   2 ?   -2.1   0.0       4.2     5e+03       7      24 ..     108     125 ..     106     132 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.6e-07
                         HTH_Tnp_1 10 efKariVreslepgksvsevArrhgvspnqLykWrrqyr....egeeaspae.......feltaleeen 67
                                      e K  +V++ +  +++vs +A r+g+ +++Ly W   ++    e  ea   +       ++ +++e++n
  gi|313122441|ref|YP_004038328.1| 24 EAKRLVVALDYLDDVPVSVLADRYGIPRSTLYYWLDRFEtesiE--EAI--TdedrpgrPRKLDEEDRN 88
                                      778889999999*************************9865331..222..123446556666666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.2
                         HTH_Tnp_1   7 wsdefKariVreslepgk 24 
                                       w++e   + V+ ++   +
  gi|313122441|ref|YP_004038328.1| 108 WTPELVREHVEHTFGVTY 125
                                       888888887777765555 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0014       1.7      23      39 ..      39      55 ..      36      58 .. 0.91
   2 !    7.2   0.2    0.0046       5.5       1      15 [.      77      91 ..      77      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                                      -STTTSSSS---SSSS- CS
                             HTH_7 23 siskIAkevnisRsTvY 39
                                      ++s +A++++i RsT+Y
  gi|313122441|ref|YP_004038328.1| 39 PVSVLADRYGIPRSTLY 55
                                      67889************ PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0046
                                      S---SS-HHHHGGGG CS
                             HTH_7  1 GRpsklskndinrvv 15
                                      GRp+kl+++d nr++
  gi|313122441|ref|YP_004038328.1| 77 GRPRKLDEEDRNRLR 91
                                      9********999875 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.1e-06    0.0049      22      37 ..      43      58 ..      38      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.1e-06
                           HTH_psq 22 AArkYgiPrsTLwrrk 37
                                      +A++YgiPrsTL++ +
  gi|313122441|ref|YP_004038328.1| 43 LADRYGIPRSTLYYWL 58
                                      79**********9765 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.8e-06     0.007      23      66 ..      35      81 ..      21      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.8e-06
                      LZ_Tnp_IS481 23 edrrtvaqvarelGvslrtaykwlarfraeGldGll...drssrPrr 66
                                       d  +v   a   G+ + t y wl+rf +e ++  +   dr  rPr+
  gi|313122441|ref|YP_004038328.1| 35 LDDVPVSVLADRYGIPRSTLYYWLDRFETESIEEAItdeDRPGRPRK 81
                                      57789999999*********************876523356666665 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.2e-05      0.05      13      49 ..      23      60 ..      13      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                                      HHHHHHHHHHHH.--S-HHHHHHHHTS-HHHHHHHHH- CS
                       HTH_Tnp_1_2 13 kkaaellvendy.ekltldeiaeevgvsrsTlykWkkk 49
                                      k a  l+v  dy + + ++ +a+  g+ rsTly W++ 
  gi|313122441|ref|YP_004038328.1| 23 KEAKRLVVALDYlDDVPVSVLADRYGIPRSTLYYWLDR 60
                                      56778999999999999******************964 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00026      0.31       7      36 ..      24      53 ..      23      54 .. 0.93
   2 ?   -0.6   0.0      0.81   9.7e+02      33      42 ..     126     135 ..     124     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                                      HHHHHHHHHHHTTT--HHHHHHHHTS-HHH CS
                        Sigma70_r4  7 ererevlelrfgeglTleEIgerlgiSrer 36
                                      e  r v+ l ++++ + + +++r+gi+r++
  gi|313122441|ref|YP_004038328.1| 24 EAKRLVVALDYLDDVPVSVLADRYGIPRST 53
                                      56799***********************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.81
                                       -HHHHHHHHH CS
                        Sigma70_r4  33 SrerVrqiek 42 
                                       S +++r++++
  gi|313122441|ref|YP_004038328.1| 126 SVGHIRRLLR 135
                                       889****987 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00011      0.14       3      47 ..      40      91 ..      38      93 .. 0.84
   2 ?   -2.1   0.0       3.7   4.4e+03      57      66 ..     125     134 ..     116     136 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      HHHHHHHHTS-HHHHHHHHHHTT...-S-EE...-TTS-.EEEEHHHHHHHH CS
                            MerR_1  3 igevakilgvtthtlrywekegl...lkpkr...teggr.ryYtdedierLk 47
                                      ++ +a + g++ +tl yw +++    +  ++   +  gr r  ++ed +rL+
  gi|313122441|ref|YP_004038328.1| 40 VSVLADRYGIPRSTLYYWLDRFEtesIEEAItdeDRPGRpRKLDEEDRNRLR 91
                                      567999****************987777777888888888888888888887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                                       --GGG---XX CS
                            MerR_1  57 ltlkgikkll 66 
                                       +++ +i++ll
  gi|313122441|ref|YP_004038328.1| 125 YSVGHIRRLL 134
                                       4445555554 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022      0.27      28      44 ..      43      59 ..      39      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                                      HHHHHT--CCHHHHHHH CS
                          CENP-B_N 28 larrfnvpestlsdilk 44
                                      la r+++p+stl+ +l+
  gi|313122441|ref|YP_004038328.1| 43 LADRYGIPRSTLYYWLD 59
                                      789************98 PP

>> HBS1_N  HBS1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.44   5.3e+02      16      34 ..       3      21 ..       3      27 .. 0.88
   2 ?   11.2   0.9    0.0003      0.36       6      31 ..      67      96 ..      58     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.44
                            HBS1_N 16 eLsdedqarLrscldevre 34
                                      +L+d d + Lr  l+ev +
  gi|313122441|ref|YP_004038328.1|  3 KLDDVDPDELRRTLAEVDS 21
                                      59999*******9999975 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0003
                            HBS1_N  6 eddeeeeeee......eLsdedqarLrsclde 31
                                      e+ + +e  +      +L++ed+ rLrs ld 
  gi|313122441|ref|YP_004038328.1| 67 EEAITDE--DrpgrprKLDEEDRNRLRSHLDT 96
                                      3444443..1469999************9986 PP

>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       8.4     1e+04      17      25 ..       5      13 ..       4      14 .. 0.47
   2 ?   10.4   0.2    0.0005       0.6      15      30 ..      81      96 ..      80      96 .. 0.92
   3 ?    1.2   0.4      0.37   4.4e+02      17      29 ..     106     118 ..     104     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.4
                                      SCCCHCCCH CS
                            zf-HC2 17 speerarve 25
                                      ++ + ++++
  gi|313122441|ref|YP_004038328.1|  5 DDVDPDELR 13
                                      455555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0005
                                      T-SCCCHCCCHHHHCH CS
                            zf-HC2 15 eLspeerarveaHLae 30
                                       L++e+r r++ HL++
  gi|313122441|ref|YP_004038328.1| 81 KLDEEDRNRLRSHLDT 96
                                      69************96 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.37
                                       SCCCHCCCHHHHC CS
                            zf-HC2  17 speerarveaHLa 29 
                                       ++++ + v++H++
  gi|313122441|ref|YP_004038328.1| 106 DEWTPELVREHVE 118
                                       7788899****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 786.52
//
Query:       gi|313122442|ref|YP_004038329.1|  [L=221]
Description: hypothetical protein Hbor_36760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.036   14.1   0.1    1.5  1  HypA         Hydrogenase/urease nickel incorporation, metallo
      0.072   13.0   0.1       0.18   11.7   0.1    1.6  1  SCAB-ABD     Actin-binding domain of plant-specific actin-bin
      0.099   13.1   0.5        1.4    9.4   0.1    2.3  2  ZapB         Cell division protein ZapB
       0.24   11.5   3.1        4.6    7.4   3.1    2.1  1  PknG_rubred  Protein kinase G rubredoxin domain


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   8.1e-06     0.036      67     107 ..     180     219 ..     144     221 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.1e-06
                                       E--EEEETTTS-EEECHH.H.HHS-TTTSSS-EEEEESSSEEE CS
                              HypA  67 vpvkvrCreCgkefelee.k.alrCpkCgsadveivsGeellv 107
                                       v+v+v Cr+Cg+++++++   + +C+ Cg+    + +G+e  v
  gi|313122442|ref|YP_004038329.1| 180 VDVRVFCRDCGTQYDVQDlLeEGQCE-CGGDI--VSTGSEADV 219
                                       6899***********98742356776.87754..456777665 PP

>> SCAB-ABD  Actin-binding domain of plant-specific actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     4e-05      0.18      14      33 ..      40      59 ..      33      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4e-05
                          SCAB-ABD 14 dqhkRLSVRDLasKFekgla 33
                                      ++  RLS R+La  F++ l 
  gi|313122442|ref|YP_004038329.1| 40 NREERLSLRELADDFNRRLL 59
                                      5789************9885 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.094   4.2e+02      11      32 ..      15      35 ..      14      59 .. 0.71
   2 ?    9.4   0.1   0.00032       1.4      10      32 ..     137     159 ..     137     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.094
                              ZapB 11 skiqkaidtitlLqmeieeLke 32
                                      sk+q +id+++ L  e e+L+ 
  gi|313122442|ref|YP_004038329.1| 15 SKVQRLIDEYD-LDGEGERLED 35
                                      69999999986.5666666655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00032
                              ZapB  10 EskiqkaidtitlLqmeieeLke 32 
                                       E +iqk +dti++L+ + +++ e
  gi|313122442|ref|YP_004038329.1| 137 EDRIQKGLDTIQRLRSRTAAVSE 159
                                       89**************9998876 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.1     0.001       4.6      12     133 ..      86     202 ..      76     208 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.001
                                       XXXXXXXXXXXXXXXXXXX..XXXXX.XXXXXX.XXXXXXXXXXXXXXXXXXXXETTTTEEEE------TTGGG-CS CS
                       PknG_rubred  12 asaatarpvstqavfRpev..ddded.saslealsteastrsasatrslspvrrlGgGLveiprvveadPleAlltn 85 
                                       + ++ ++++++q+++R  v  dd ++   s +a++t  ++ +++++ +++ + r+  GL  i+r++++   +A +++
  gi|313122442|ref|YP_004038329.1|  86 DVSSGMQTQARQTLEREGVdvDDLQKnFVSHQAIHTYLTKYRGVTQDKQTDEDRIQKGLDTIQRLRSR---TAAVSE 159
                                       5567788889999***998534444335677777777777779999999999*********9999874...555555 PP

                                       S---GGG-B-TTT--.B-S---SS----SEEE-TTT--EEE-S-SS-TT CS
                       PknG_rubred  86 pvvpEskRfCwrCGr.pvGRsekerkgaseGtCpkCgspysFlPqLspG 133
                                        +v++        Gr  vG  + e   +   +C  Cg +y+    L++G
  gi|313122442|ref|YP_004038329.1| 160 NIVENL---V-STGRiHVG--DFEVLVDVRVFCRDCGTQYDVQDLLEEG 202
                                       555542...2.22321455..4455556666777777777777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1274.54
//
Query:       gi|313122443|ref|YP_004038330.1|  [L=647]
Description: Chromosome segregation protein (Spc25, Csm1, Pcs1) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-10   40.8  17.9    3.3e-10   40.8  17.9    4.9  3  AAA_23           AAA domain
    1.4e-05   25.0   1.5     0.0008   19.2   0.0    2.7  2  AAA_15           AAA ATPase domain
    1.7e-05   23.8  62.7      0.051   12.5  21.3    4.4  4  Spc7             Spc7 kinetochore protein
    3.8e-05   23.2  42.9      0.011   15.1   1.6    3.5  3  DUF4407          Domain of unknown function (DUF4407)
    9.9e-05   22.7  64.3     0.0071   16.6  16.2    4.3  3  ATG16            Autophagy protein 16 (ATG16)
    0.00024   21.5  32.5       0.26   11.8   0.2    6.9  6  NPV_P10          Nucleopolyhedrovirus P10 protein
    0.00077   18.3  37.1     0.0025   16.6  12.9    2.5  2  AAA_13           AAA domain
    0.00098   19.2  20.6        1.2    9.1   2.4    5.5  4  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
     0.0025   18.2   8.1     0.0025   18.2   8.1    5.6  2  HrpB7            Bacterial type III secretion protein (HrpB7)
     0.0038   16.4  47.6       0.28   10.2  13.8    4.3  4  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0041   16.5  52.7      0.067   12.5  14.4    4.7  5  GAS              Growth-arrest specific micro-tubule binding
     0.0045   16.3  33.2      0.024   14.0   4.3    4.2  4  HemX             HemX, putative uroporphyrinogen-III C-methyl
     0.0051   16.8  16.9     0.0051   16.8  16.9    5.2  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0058   16.6  35.9        0.2   11.7   1.7    5.0  5  FlxA             FlxA-like protein
     0.0059   16.7  71.3      0.025   14.6   6.3    5.3  4  DHR10            Designed helical repeat protein 10 domain
      0.006   16.0   4.4      0.006   16.0   4.4    4.6  4  Rab5-bind        Rabaptin-like protein
     0.0062   17.0   1.1      0.053   14.0   0.2    2.8  2  HsbA             Hydrophobic surface binding protein A
  ------ inclusion threshold ------
       0.01   14.3  56.4     0.0036   15.7  21.7    2.3  2  MAD              Mitotic checkpoint protein
       0.01   16.2  61.6       0.02   15.3  18.8    5.9  5  DUF4200          Domain of unknown function (DUF4200)
      0.017   15.4   6.7      0.017   15.4   6.7    7.0  5  CCDC-167         Coiled-coil domain-containing protein 167
      0.021   15.1  47.4      0.029   14.7   1.8    6.8  6  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.021   15.3  47.7       0.27   11.8   7.6    5.2  4  Spectrin         Spectrin repeat
      0.026   14.9   1.0      0.026   14.9   1.0    6.3  7  kleA_kleC        Uncharacterized KorC regulated protein A
      0.031   13.8  37.4       0.11   12.1   1.9    6.1  6  Fzo_mitofusin    fzo-like conserved region
       0.04   14.2   0.1       0.04   14.2   0.1    7.4  6  Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
      0.043   13.8  38.3       0.72    9.9   4.3    5.9  7  DUF1664          Protein of unknown function (DUF1664)
      0.048   14.1  55.0       0.13   12.7  22.2    3.9  3  Fez1             Fez1
       0.06   10.9  56.6       0.98    6.9  37.0    2.3  2  DUF3584          Protein of unknown function (DUF3584)
      0.079   13.2  70.9       0.74   10.0   3.2    5.3  5  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
      0.082   12.9  32.2       0.23   11.5   7.2    5.6  5  Laminin_II       Laminin Domain II
      0.093   12.8  60.5        2.1    8.4   4.6    5.7  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.12   12.2  60.6       0.87    9.4  31.7    3.2  2  ERM              Ezrin/radixin/moesin family
       0.14   10.4  48.0      0.068   11.4  19.2    2.5  2  FPP              Filament-like plant protein, long coiled-coi
       0.14   12.9  18.3        3.3    8.5   0.1    6.1  3  FliD_N           Flagellar hook-associated protein 2 N-termin
       0.16   12.0  36.8       0.44   10.6   4.7    6.2  5  COG2             COG (conserved oligomeric Golgi) complex com
       0.19   12.0  56.3       0.64   10.3   5.1    5.6  5  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.34   11.4  85.3       0.73   10.4  15.3    6.2  5  APG6_N           Apg6 coiled-coil region
       0.35   11.1  49.1       0.14   12.5   9.5    7.1  7  DUF5082          Domain of unknown function (DUF5082)
       0.41   10.2  32.8        3.4    7.1  12.3    3.2  2  Exonuc_VII_L     Exonuclease VII, large subunit
        0.5    8.9  42.9       0.31    9.6   1.3    4.2  4  FapA             Flagellar Assembly Protein A
       0.59    8.8  47.4      0.098   11.3  16.6    2.5  2  WEMBL            Weak chloroplast movement under blue light
       0.67    9.1  45.2        1.7    7.8  19.5    2.5  2  Taxilin          Myosin-like coiled-coil protein
       0.87    9.3  19.6        6.2    6.6   1.6    4.6  4  Lectin_N         Hepatic lectin, N-terminal domain
       0.99    9.3  27.2       0.94    9.3   0.4    7.2  6  DASH_Dam1        DASH complex subunit Dam1
        1.1    9.4  66.2        0.4   10.8   8.4    4.2  4  UPF0242          Uncharacterised protein family (UPF0242) N-t
        1.2    9.0  52.6          5    7.0   6.8    5.1  2  DASH_Spc19       Spc19
        1.4    8.7  45.2       0.16   11.7  10.8    4.4  4  TACC_C           Transforming acidic coiled-coil-containing p
        1.9    8.6  49.7       0.58   10.3   4.0    5.3  5  Mod_r            Modifier of rudimentary (Mod(r)) protein
        3.1    8.3  22.7       0.91   10.0   1.1    7.2  8  LPP              Lipoprotein leucine-zipper
        3.1    7.5  54.3      0.013   15.2  18.2    5.2  4  DUF4201          Domain of unknown function (DUF4201)
        3.1    7.0  58.0        1.1    8.5  15.5    5.1  5  DUF3450          Protein of unknown function (DUF3450)
        3.3    7.8  79.9        7.3    6.7  29.9    5.0  4  Tropomyosin_1    Tropomyosin like
        5.2    7.6  70.4      0.068   13.6  12.4    7.8  5  ZapB             Cell division protein ZapB
        5.5    7.3  20.8         15    5.9   0.2    7.1  6  WXG100           Proteins of 100 residues with WXG
        5.8    7.1  36.0        3.1    8.0   2.2    4.7  4  Fib_alpha        Fibrinogen alpha/beta chain family
        6.1    7.2  49.2        9.8    6.5   0.7    5.0  4  OmpH             Outer membrane protein (OmpH-like)
        6.3    7.1  73.8       0.34   11.2   8.7    7.3  5  ABC_tran_CTD     ABC transporter C-terminal domain
        7.5    4.9  23.7       0.77    8.2   7.5    2.9  2  Baculo_F         Baculovirus F protein


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8  17.9   1.1e-12   3.3e-10       2     200 .]      13     227 ..      12     227 .. 0.68
   2 ?    0.2   6.4       2.8   8.8e+02     150     193 ..     218     279 ..     197     286 .. 0.36
   3 ?    1.1   3.8       1.5   4.7e+02     139     198 ..     443     503 ..     433     505 .. 0.67

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.1e-12
                            AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvelt 78 
                                       L++en++ +r++++++++g+t++ G N +  T++l+ i  aL+ + + l+++ ++g+++  v  ++        ++t
  gi|313122443|ref|YP_004038330.1|  13 LHVENIGGIRETTVELGPGVTALAGRNATNRTSLLQSIMAALGSDRASLKGDADEGSVTLTVGDQTY-------TRT 82 
                                       9*******************************************99999998777777766654333.......222 PP

                            AAA_23  79 fenkdgry.................trsier.erelskkkgkttkkaklelleideleqfisellgskkiilnlilf 137
                                       +++ + +                     +e  e   +   g+  ++ + + +++++ +++i+el + k +i n i+ 
  gi|313122443|ref|YP_004038330.1|  83 LKRRGSTVvtegdpyledatladlfAFLLESnEARQAVARGDDLRELIMRPIDTEAIQEEIRELEQEKREIDNEISS 159
                                       32222222233334466666655542222221222222333444444555555566777777633333333344444 PP

                            AAA_23 138 lgqer....feefelkdkkerleelekeleeledekkllekl.eqekekekeleeleeeleeilkele 200
                                       l++ +    + e+++ + ke++ee + elee+e+e+++ +++ eq  + ++ele+  ++l+++ ++le
  gi|313122443|ref|YP_004038330.1| 160 LDSLDgrlpELEQKRTSLKEKIEEKRAELEEKEQEIEEADANvEQTRDDRDELENRLDDLKQARSDLE 227
                                       44444566687888899999999999999999999999999988999999999999999999998886 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.8
                            AAA_23 150 dkke.................rleelekeleeledekkllekl.eqekekekeleeleeele 193
                                       d k+                  +++le+e +el++e++ + ++   + e e+++++l+++++
  gi|313122443|ref|YP_004038330.1| 218 DLKQarsdledvrydidaeaeSIDALETERDELTTEREDIPEEiDGADEIEAQISDLRDQMQ 279
                                       11112221112222111111144444444444444333333332233334445555555554 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.5
                            AAA_23 139 gqerfeefelkdkkerleelekeleeledekkllekle.qekekekeleeleeeleeilke 198
                                        + ++ efe  + +++le+++ e+e  e + +  ++le +++e  +el +l+ ++e i++e
  gi|313122443|ref|YP_004038330.1| 443 REANELEFEIGRLENELESVNSEMESVESRLDDRDDLEaRREEIADELADLRTRIERIESE 503
                                       4555556666666677777777777777777766666525556666888888888888765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.6e-06    0.0008       6     194 ..      13     289 ..      11     298 .. 0.65
   2 ?   -0.1   4.4       1.9   5.9e+02     148     276 ..     395     524 ..     335     565 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.6e-06
                            AAA_15   6 ikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn............................ 54 
                                       ++++N + +++++++l + +t l G+N++  +s+l+ +   l  + + +                            
  gi|313122443|ref|YP_004038330.1|  13 LHVENIGGIRETTVELGPGVTALAGRNATNRTSLLQSIMAALGSD-RASlkgdadegsvtltvgdqtytrtlkrrgs 88 
                                       79************************************7766644.3336799999***********9999999999 PP

                            AAA_15  55 ...............................................kkvikiekedleifeniseskdikIdvef. 83 
                                                                                       +     +e++++ e++++++d +I     
  gi|313122443|ref|YP_004038330.1|  89 tvvtegdpyledatladlfafllesnearqavargddlrelimrpidTE---AIQEEIRELEQEKREIDNEISSLDs 162
                                       9999999999999999998888888888888777777777776655422...3333333333333333333333335 PP

                            AAA_15  84 ...............aekekakeyektlkskekkkadlllkkkesdlkktikd.kklklkknelsdekisvekkksk 144
                                                      +ek ++k  e ++k++e+++ad  ++++++d +++ +   +lk   ++l d +++++ + ++
  gi|313122443|ref|YP_004038330.1| 163 ldgrlpeleqkrtslKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRlDDLKQARSDLEDVRYDIDAEAES 239
                                       55777777666665544455666666666666666666666666554444332123344455666666666666666 PP

                            AAA_15 145 kelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksai 194
                                        +  + ++++l++e e++  + + ++++  +++    + ++l+++ ++++
  gi|313122443|ref|YP_004038330.1| 240 IDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNELQ 289
                                       66666666666666666655544444444444444444444445555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                            AAA_15 148 pkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd.edsekkssllgklke 223
                                        +e+ + + ++ e+lk + edl++  ++le+ +++ e        + ++ ++ +  R++++ e++    ++  +  +
  gi|313122443|ref|YP_004038330.1| 395 IDEELDRRRERRESLKQKREDLTNRVETLESEVEELE--------SRDYGDILERHREANElEFEIGRLENELESVN 463
                                       3444445555566666666666666666666666655........55556666666666664333333333333333 PP

                            AAA_15 224 kileealqekl.........eeelteklkeiqeklkeidkklaeelkkilkkkidkikkfny 276
                                       +  e+ ++++l         +ee+ ++l ++ + ++ i+++  ee + +++  +d +++ n 
  gi|313122443|ref|YP_004038330.1| 464 SEMES-VESRLddrddlearREEIADELADLRTRIERIESEAIEEFNTHMETVLDILDYDNL 524
                                       33332.44444665566667777777777777777777777777777666666666655554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5  21.3   0.00017     0.051     171     280 ..     138     245 ..     134     247 .. 0.74
   2 !   10.8   6.3   0.00053      0.16     171     254 ..     211     296 ..     208     308 .. 0.42
   3 !   10.9  14.3   0.00049      0.15     156     254 ..     341     431 ..     335     435 .. 0.50
   4 !    8.1   4.1    0.0035       1.1     214     288 ..     437     510 ..     432     529 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                              Spc7 171 eleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksele 247
                                       +++ee  ele+e +++ ++  +l+s+   +L el ++ ++lk++ieek++el+e+++++ee ++++e++++ ++ele
  gi|313122443|ref|YP_004038330.1| 138 AIQEEIRELEQEKREIDNEISSLDSL-DGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELE 213
                                       34455555555555555544444444.46788888888899999999999999999999999999999999999999 PP

                              Spc7 248 eeiaeaervleeckgwsesevsrlkeevkalee 280
                                       +++   ++ +   +++ ++++++  e+ +ale 
  gi|313122443|ref|YP_004038330.1| 214 NRLDDLKQARSDLEDV-RYDIDAEAESIDALET 245
                                       9999999988876665.5777777777777775 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00053
                              Spc7 171 eleeekaeleeeleklqeaaeeles..idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkse 245
                                       ele++ ++l++   +l++ + ++++     + Le+ r+el++  ++i e  +  +e ++q+ +l+++++ l+++ +e
  gi|313122443|ref|YP_004038330.1| 211 ELENRLDDLKQARSDLEDVRYDIDAeaESIDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNE 287
                                       33333333333333333322222221122344444444444444444444444444444444444444444444444 PP

                              Spc7 246 leeeiaeae 254
                                       l++ i+  e
  gi|313122443|ref|YP_004038330.1| 288 LQTVIQFNE 296
                                       444444444 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00049
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleel 232
                                       +++e+  + l +l  e   ++++l++++++l++++        +eLe+l+++  +l+  +++  +el++++e++e+l
  gi|313122443|ref|YP_004038330.1| 341 SQIEETVDRLRSLRREKLDQRNDLRDQIDDLESER--------DELEQLHRRRGRLDDRLQSIDEELDRRRERRESL 409
                                       44455555555555555555555555555555555........5555555555555555555555555555555555 PP

                              Spc7 233 eekieelkeqkseleeeiaeae 254
                                       ++k e+l+++ ++le+e++e e
  gi|313122443|ref|YP_004038330.1| 410 KQKREDLTNRVETLESEVEELE 431
                                       5555555555555555555544 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0035
                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivs 288
                                       +i e+ +e +el+ ++ +le+++e+++++++++e+++   ++ le++++  ++e+  l+++ +++e++   ++ +
  gi|313122443|ref|YP_004038330.1| 437 DILERHREANELEFEIGRLENELESVNSEMESVESRLD-DRDDLEARREEIADELADLRTRIERIESEAIEEFNT 510
                                       56678889999999999999999999999999999998.566778888888999999999999998876555555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4  18.2   0.00023     0.072     110     229 ..     136     257 ..     128     262 .. 0.80
   2 !   15.1   1.6   3.5e-05     0.011     122     235 ..     266     384 ..     259     392 .. 0.68
   3 ?    5.8   9.1     0.025       7.8     130     232 ..     394     499 ..     380     517 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                           DUF4407 110 aelaeeqqeeakelkeqlaaa......ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaG 180
                                       +e ++e  +e ++ k++++++      l+ +l ele+++++l+++i++++a+l+++++e + e+d +  ++   ++ 
  gi|313122443|ref|YP_004038330.1| 136 TEAIQEEIRELEQEKREIDNEissldsLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIE-EADANV-EQ---TRD 207
                                       444444444444445555555556678********************************99.666433.22...456 PP

                           DUF4407 181 kgpaakekkaqldaaqaelaelkakld.atarlaalraelaeleaerake 229
                                       + ++ +++ ++l++a+ +l++++ ++d +++ ++al++e++el++er+++
  gi|313122443|ref|YP_004038330.1| 208 DRDELENRLDDLKQARSDLEDVRYDIDaEAESIDALETERDELTTEREDI 257
                                       7899999******************9999999**************9876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.5e-05
                           DUF4407 122 elkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake........... 187
                                       e+++q+  +l++++++l++ +++lq+ i+  e+ l+ + a++++ l    gt    v        +           
  gi|313122443|ref|YP_004038330.1| 266 EIEAQIS-DLRDQMQRLDSSVNELQTVIQFNEDMLEGTSADVAAALRD--GTDSGSVTD------Alvesdtvvcwt 333
                                       3333332.4555555555555555555555555555555555555443..222112333......255556699999 PP

                           DUF4407 188 .....kkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqa 235
                                             ++q+++   +l +l+++  + +++++lr+++++le+er++ ++ +++
  gi|313122443|ref|YP_004038330.1| 334 cgtevETSQIEETVDRLRSLRRE--KLDQRNDLRDQIDDLESERDELEQLHRR 384
                                       **99999****************..********************99887765 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.025
                           DUF4407 130 altaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakl 206
                                       + ++el++ ++++++l+++ + + +r+++l+ e+++  + + g+    +  +  +a e + ++ ++++el+++++++
  gi|313122443|ref|YP_004038330.1| 394 SIDEELDRRRERRESLKQKREDLTNRVETLESEVEELESRDYGD----ILERHREANELEFEIGRLENELESVNSEM 466
                                       36788888888888999999999999999999998555544432....34456666666666666666666666665 PP

                           DUF4407 207 d.......atarlaalraelaeleaerakeraa 232
                                       +        +++l+a+r+e+a+  a++++++++
  gi|313122443|ref|YP_004038330.1| 467 EsvesrldDRDDLEARREEIADELADLRTRIER 499
                                       544443333333333333333333333322222 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7  26.4   0.00035      0.11      27     168 ..     139     286 ..     112     290 .. 0.82
   2 !   16.6  16.2   2.3e-05    0.0071      63     144 ..     351     432 ..     290     437 .. 0.85
   3 ?    3.8   5.7       0.2        61      92     148 ..     440     499 ..     435     515 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00035
                             ATG16  27 Lldrtsaleaenaklekaaasaks.....sksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrg 98 
                                       + + +++le+e++++ ++++s  s     ++   +++ ++++++    ++++a++++ eq++ +  + ++++   r 
  gi|313122443|ref|YP_004038330.1| 139 IQEEIRELEQEKREIDNEISSLDSldgrlPEL--EQKRTSLKEK---IEEKRAELEEKEQEIEEADANVEQTRDDRD 210
                                       678999***************99998643222..2233333333...347899999********************* PP

                             ATG16  99 elaqrllelneelqklee...klkedeerlaeleaeraaletklkdreeelrek...eklvqdlqDElsaLqlqln 168
                                       el++rl +l+++ ++le+    + +++e++++le+er +l+t+++d  ee+ +    e+ + dl+D ++ L   +n
  gi|313122443|ref|YP_004038330.1| 211 ELENRLDDLKQARSDLEDvryDIDAEAESIDALETERDELTTEREDIPEEIDGAdeiEAQISDLRDQMQRLDSSVN 286
                                       *****999998877776655599***************************986611156788*******9987776 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.3e-05
                             ATG16  63 asasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletkl 139
                                       +s + ++ +q++++ ++ + l + r+el++l+++rg l +rl++  eel++++e+ ++ +++ ++l++++++le ++
  gi|313122443|ref|YP_004038330.1| 351 RSLRREKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEV 427
                                       222235668888899999999999***************************************************** PP

                             ATG16 140 kdree 144
                                       +++e 
  gi|313122443|ref|YP_004038330.1| 428 EELES 432
                                       99885 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.2
                             ATG16  92 elyksrgelaqrllelneelqkleeklkedeerla...eleaeraaletklkdreeelre 148
                                       e +++ +el+  + +l++el+  ++++++ e+rl+   +lea+r+++ ++l+d++ +++ 
  gi|313122443|ref|YP_004038330.1| 440 ERHREANELEFEIGRLENELESVNSEMESVESRLDdrdDLEARREEIADELADLRTRIER 499
                                       678888999999999999999999999999999862225777777777777777776654 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.9      0.15        47      22      60 ..     138     176 ..     134     199 .. 0.59
   2 ?    3.8   4.1      0.26        80      13      57 ..     202     246 ..     180     252 .. 0.78
   3 !   11.3   3.2    0.0012      0.37       9      65 ..     229     292 ..     224     306 .. 0.66
   4 ?    5.1   0.4       0.1        32      22      59 ..     363     400 ..     340     404 .. 0.72
   5 ?    6.7   0.3     0.032       9.9      16      63 ..     388     432 ..     386     440 .. 0.89
   6 !   11.8   0.2   0.00084      0.26      13      63 ..     452     502 ..     448     524 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.15
                           NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       a+q+++ +++++ +++++  + Ld++   L ele+k ++
  gi|313122443|ref|YP_004038330.1| 138 AIQEEIRELEQEKREIDNEISSLDSLDGRLPELEQKRTS 176
                                       566666666666666666556666666666666654333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.26
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletk 57 
                                       ++++ d  d l++++dd+++   d++++   +da ++++++let+
  gi|313122443|ref|YP_004038330.1| 202 VEQTRDDRDELENRLDDLKQARSDLEDVRYDIDAEAESIDALETE 246
                                       556666667888888888888888888888888888888888875 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0012
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdv.......telnekLdaqsaqLaeletkvenIqdiL 65 
                                       +r di a  + +dal+++ d+++++ +d+       +e+++++ ++ +q++ l+++v++ q + 
  gi|313122443|ref|YP_004038330.1| 229 VRYDIDAEAESIDALETERDELTTEREDIpeeidgaDEIEAQISDLRDQMQRLDSSVNELQTVI 292
                                       5667777777777777776555555555421111116788888888888888888888887765 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.1
                           NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                        l +q+dd++++  ++++l+ +  ++ + L++++++++
  gi|313122443|ref|YP_004038330.1| 363 DLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELD 400
                                       56777777777777777777777777777777776654 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.032
                           NPV_P10  16 vddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       +dd+++++++++d+ +e  +    l++k +++++ +++le++ve+ ++
  gi|313122443|ref|YP_004038330.1| 388 LDDRLQSIDEELDRRRERRES---LKQKREDLTNRVETLESEVEELES 432
                                       799999999999998887766...99*****************99865 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00084
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       i  +++ ++++++++++v++ l d ++l+++ ++++++La+l t +e I++
  gi|313122443|ref|YP_004038330.1| 452 IGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIES 502
                                       6678889999**************************************986 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  12.9   8.1e-06    0.0025     279     447 ..     137     307 ..     120     319 .. 0.63
   2 !    7.0  16.3    0.0065         2     286     470 ..     341     515 ..     335     539 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.1e-06
                            AAA_13 279 defeekqerLekliekveskkselleklk.avsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfk. 353
                                       ++ +e++++Le+ + ++++++s+l ++l+  + + ++++   +e++ee +ae+e+ e++++++   +e+ r++  + 
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSL-DSLDgRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDEl 212
                                       345667777777777777777543.5544133445667777777777777777777777777777777766554332 PP

                            AAA_13 354 ..sve.lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaiek 427
                                         +++ l+++ +++e +  ++++  e+i +     ++l++e+e++ +++    + e+e++++ + +++++l+ ++++
  gi|313122443|ref|YP_004038330.1| 213 enRLDdLKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDIPEEIDG--ADEIEAQISDLRDQMQRLDSSVNE 287
                                       003322344444445666666666666666666666666666666666655..688888888888888888888888 PP

                            AAA_13 428 lekelkeeeaelkkleeeik 447
                                       l++ ++ +e+ l+   ++++
  gi|313122443|ref|YP_004038330.1| 288 LQTVIQFNEDMLEGTSADVA 307
                                       88888888877777777765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0065
                            AAA_13 286 erLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvka 362
                                       +++e++++++ s ++e l++ ++           ++++++l++e ++le qL   + +l+++ + + +  el++  +
  gi|313122443|ref|YP_004038330.1| 341 SQIEETVDRLRSLRREKLDQRND----------LRDQIDDLESERDELE-QLHRRRGRLDDRLQSIDE--ELDRRRE 404
                                       33444444444443333333333..........4444445555554443.355555555555555544..5666666 PP

                            AAA_13 363 kiesikklvaeineliakhNekvanleeekeeakkklelhl.veeleseldeykkkykklekaieklekel...kee 435
                                       + es+k++ +++ + ++     v++le++  +  + le+h+ ++ele e+ ++++++++++ ++e++e +l   ++ 
  gi|313122443|ref|YP_004038330.1| 405 RRESLKQKREDLTNRVETLESEVEELESR--DYGDILERHReANELEFEIGRLENELESVNSEMESVESRLddrDDL 479
                                       66666666666666666666666666554..3344455544356666666666666666666666666544111678 PP

                            AAA_13 436 eaelkkleeeikeLekqlrdek.paaeeinkeLkaf 470
                                       ea+ +++++e ++L+++++ ++ +a+ee+n+ ++ +
  gi|313122443|ref|YP_004038330.1| 480 EARREEIADELADLRTRIERIEsEAIEEFNTHMETV 515
                                       999999999********9886527899***999876 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.7      0.11        33      37      91 ..     158     220 ..     136     228 .. 0.68
   2 !    9.1   2.4     0.004       1.2      17      84 ..     225     293 ..     210     312 .. 0.57
   3 ?    7.7   3.8     0.011       3.5      36     138 ..     409     519 ..     340     521 .. 0.71
   4 ?   -1.4   0.0       7.2   2.2e+03     111     129 ..     599     617 ..     588     627 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.11
                      Baculo_PEP_C  37 atlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq......dtlrneLtnln 91 
                                       +  ld+++++L +l+++ +sl +++++   +l++  +++++a ++++      d+l+n+L+ l+
  gi|313122443|ref|YP_004038330.1| 158 S-SLDSLDGRLPELEQKRTSLKEKIEEkraELEEKEQEIEEADANVEqtrddrDELENRLDDLK 220
                                       3.46778888888887777776666666667888888888888877766677777777777665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.004
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlr 84 
                                       dL +v  +i +   +i  +l+t  d++ t+ +++ e++     e+++   +l +++++L++++n+lq+ ++
  gi|313122443|ref|YP_004038330.1| 225 DLEDVRYDIDAEAESI-DALETERDELTTEREDIPEEIDG-ADEIEAqisDLRDQMQRLDSSVNELQTVIQ 293
                                       4444444554444555.56666666666666666666665.334444555778888888888888884443 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.011
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq...dtlrneLtnlnsilt...nLlssvtN 103
                                       l++  +++ +++++l++++++l +       + +  +++L+  + +l+   +++++e+++++s l    +L +    
  gi|313122443|ref|YP_004038330.1| 409 LKQKREDLTNRVETLESEVEELESRDYGdilERHREANELEFEIGRLEnelESVNSEMESVESRLDdrdDLEARREE 485
                                       56666677777777777777754322223333344567777777777777778888888888887522257777788 PP

                      Baculo_PEP_C 104 instLnnllqalnnldlgalsqeledaldtveeil 138
                                       i   L+ l + ++ ++++a+++  +  ++tv +il
  gi|313122443|ref|YP_004038330.1| 486 IADELADLRTRIERIESEAIEEFNT-HMETVLDIL 519
                                       8888888888888887777765544.677777776 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 7.2
                      Baculo_PEP_C 111 llqalnnldlgalsqeled 129
                                       ll +l+++d+g ++q  + 
  gi|313122443|ref|YP_004038330.1| 599 LLDSLEAIDSGRIAQLVDY 617
                                       78999*******9998765 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   8.1   7.9e-06    0.0025      15      67 ..     172     224 ..     165     227 .. 0.92
   2 !    9.1   8.0    0.0051       1.6      21     119 ..     209     309 ..     206     317 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.9e-06
                             HrpB7  15 rreerlraeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgss 67 
                                       +++  l++++e++ra+l++ e+++++a a+ve+ rd+ ++ e+rlddl  ++s
  gi|313122443|ref|YP_004038330.1| 172 QKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQARS 224
                                       56778*******************************************99887 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0051
                             HrpB7  21 raeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspf..siadylacrayrdvlegrvraaeael 95 
                                       r+ele++ ++l++a  +l++    ++a+++  +a e + d+ltt ++ +   i+ +   +a ++ l+++++ +++ +
  gi|313122443|ref|YP_004038330.1| 209 RDELENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDIpeEIDGADEIEAQISDLRDQMQRLDSSV 285
                                       56666666666666666666666666666666666666666666665332246666666666666666666666666 PP

                             HrpB7  96 aaarqaldaaedavaatarkiaRn 119
                                         ++  ++  ed ++ t + +a +
  gi|313122443|ref|YP_004038330.1| 286 NELQTVIQFNEDMLEGTSADVAAA 309
                                       666666666666666666655543 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2  13.8   0.00089      0.28      41     130 ..     139     221 ..     117     240 .. 0.52
   2 !    8.5   0.3     0.003      0.91      24     112 ..     219     307 ..     217     328 .. 0.78
   3 ?    4.3  14.1     0.059        18      41     126 ..     343     431 ..     331     434 .. 0.57
   4 !    7.9   7.6    0.0047       1.5      26     122 ..     408     501 ..     405     547 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00089
                             Atg14  41 lkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsd 117
                                       ++++i +++++k+       +i+n+  +l++l  +  +l+++   lk+k+++ ++e+eek +++++ ++++ + r d
  gi|313122443|ref|YP_004038330.1| 139 IQEEIRELEQEKR-------EIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDD 208
                                       4444444444443.......555555555555555555555555555555555555555555555555555544444 PP

                             Atg14 118 leslqneleerrk 130
                                        + l+n+l   ++
  gi|313122443|ref|YP_004038330.1| 209 RDELENRLDDLKQ 221
                                       4444444433222 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                             Atg14  24 lyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieek 100
                                       l + r +l +++ + ++  + i++++++++e ++++++i  + + ++e+ ++i+dlr+++q+l  ++ +l+  i+  
  gi|313122443|ref|YP_004038330.1| 219 LKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNELQTVIQFN 295
                                       55666677777777777777778788888888999999999999999999999999999999999999999999888 PP

                             Atg14 101 kkklaklsdklk 112
                                          l++ s++++
  gi|313122443|ref|YP_004038330.1| 296 EDMLEGTSADVA 307
                                       888888887776 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.059
                             Atg14  41 lkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkk...laklsdklkkR 114
                                       +++ ++++ + ++e+ +++++++ + ++le+ + + ++l++r  +l d+l++ ++e++ ++++   l++++++l  R
  gi|313122443|ref|YP_004038330.1| 343 IEETVDRLRSLRREKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERresLKQKREDLTNR 419
                                       33444444444446666777777777777777777777777777777777777777766555511133344444455 PP

                             Atg14 115 rsdleslqnele 126
                                        ++les  +ele
  gi|313122443|ref|YP_004038330.1| 420 VETLESEVEELE 431
                                       555555555544 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0047
                             Atg14  26 elrerlaklksekeslkkkiekalegke........eaeqledkiknkkakleelksliadlrer...lqelkdkls 91 
                                       +l+++  +l  + e+l++++e+++++ +        ea++le +i ++ + le+  s++++ ++r      l+++++
  gi|313122443|ref|YP_004038330.1| 408 SLKQKREDLTNRVETLESEVEELESRDYgdilerhrEANELEFEIGRLENELESVNSEMESVESRlddRDDLEARRE 484
                                       55666666677777777777777777776544444455566666666666666666666666655222223333333 PP

                             Atg14  92 qlkkeieekkkklaklsdklkkRrsdleslq 122
                                       +  +e+++ + ++++              ++
  gi|313122443|ref|YP_004038330.1| 485 EIADELADLRTRIER--------------IE 501
                                       333333333333333..............33 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.9     0.061        19      65     110 ..     138     183 ..     134     186 .. 0.83
   2 !   12.5  14.4   0.00022     0.067      53     136 ..     178     261 ..     176     287 .. 0.64
   3 ?    1.5   0.1      0.52   1.6e+02      50      81 ..     265     296 ..     260     304 .. 0.81
   4 ?    5.9  20.9     0.023       7.2      51     166 ..     356     474 ..     336     498 .. 0.75
   5 ?    4.1   4.1     0.084        26      33     106 ..     425     495 ..     420     539 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.061
                               GAS  65 kaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehev 110
                                       + +ee+ eL+++ ++ +++ +sl++l  rl ele++ ++lk++ e 
  gi|313122443|ref|YP_004038330.1| 138 AIQEEIRELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEE 183
                                       6789999999999999999999999999999999999998877665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00022
                               GAS  53 sqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkf 129
                                       +++ ++ + +L++ e+e+ee  +++++ + d+ +l+n    lk++ + l+d++++ +   + ++++e erdel+ + 
  gi|313122443|ref|YP_004038330.1| 178 KEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTER 254
                                       45556666677777777777777777777777777777777777777777777777777777777777777777666 PP

                               GAS 130 eaaiqev 136
                                       e+  +e+
  gi|313122443|ref|YP_004038330.1| 255 EDIPEEI 261
                                       6655544 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.52
                               GAS  50 seisqenkrlkepLkkaeeeveeLrkqlknye 81 
                                       +ei+++ ++l++++++++  v+eL+  +++ e
  gi|313122443|ref|YP_004038330.1| 265 DEIEAQISDLRDQMQRLDSSVNELQTVIQFNE 296
                                       67888888999999999999999988777654 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.023
                               GAS  51 eisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelyk 127
                                       e   + ++l++++  +e e++eL++  ++  +   +l+++ ++l +  +  ++lk++ e l  r+e++e+e +el++
  gi|313122443|ref|YP_004038330.1| 356 EKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELES 432
                                       55556778999999999999999999999999999999999999999999999999999999999999999999999 PP

                               GAS 128 kfeaaiqevqqkt...glknllLekklkalqeelEkkeaqle 166
                                       +    i e + ++   +++   Le+ l++++ e+E+ e +l+
  gi|313122443|ref|YP_004038330.1| 433 RDYGDILERHREAnelEFEIGRLENELESVNSEMESVESRLD 474
                                       998888777665411156666667777777777776666654 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.084
                               GAS  33 eeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                       +e+eel+ ++     ++ e   e ++l+ ++ ++e+e+e  + +++  e+   + + l+ar +e  +el dl+ 
  gi|313122443|ref|YP_004038330.1| 425 SEVEELESRD---YGDILERHREANELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRT 495
                                       4444444443...2333334444444444444444444444444444444444444455555555555544443 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   8.1     0.011       3.3      37     100 ..     157     220 ..     132     228 .. 0.56
   2 ?    4.5   1.9     0.057        18      37      96 ..     233     292 ..     211     305 .. 0.63
   3 !   14.0   4.3   7.7e-05     0.024      35     102 ..     359     426 ..     347     437 .. 0.85
   4 ?    4.7   0.3     0.049        15      29      99 ..     444     515 ..     435     544 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                              HemX  37 v...aelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvs 100
                                       +   ++l+ +l +leq+ ++   +ke+ +e  ++l+++++++e++ +++eq+  + +el+++l +++
  gi|313122443|ref|YP_004038330.1| 157 IsslDSLDGRLPELEQKRTS---LKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLK 220
                                       12224455555555555555...55566666666666667777777777777777777777666665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.057
                              HemX  37 vaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqql 96 
                                       +++ ++ + ale++ +++++e+e+  e ++  ++ + ++++l+ +++ l+++++elq+ +
  gi|313122443|ref|YP_004038330.1| 233 IDAEAESIDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNELQTVI 292
                                       355556666666666666666666666666666666666666666666666666666544 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 7.7e-05
                              HemX  35 aevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                        + ++l++q+  le++ +++e+++++  +l +rlq  +e+l++++++ e+l+++ e l++++++++++
  gi|313122443|ref|YP_004038330.1| 359 DQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESE 426
                                       45589999999999999999999999999999999999999999999999999999999999999876 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.049
                              HemX  29 qvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlq.kqleelqqqlskv 99 
                                       +++el+ e+ +l+++l+++++++++ve+   + ++le+r ++ a++l++l++++e  + +++ee ++++++v
  gi|313122443|ref|YP_004038330.1| 444 EANELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIEsEAIEEFNTHMETV 515
                                       555667777889999999999999999999999999999999999999999888875415677777777665 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.3      0.28        86      76     100 ..     137     161 ..     127     164 .. 0.52
   2 ?    5.6  24.6      0.05        15      10     113 ..     165     281 ..     160     306 .. 0.57
   3 !   16.8  16.9   1.7e-05    0.0051      23     107 ..     347     431 ..     339     434 .. 0.95
   4 ?    5.0   9.7     0.073        23      15      81 ..     441     503 ..     431     514 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.28
                    CENP-F_leu_zip  76 valrsekeeLekelqkkqervseLe 100
                                       +a+++e  eLe+e ++  +++s+L+
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSLD 161
                                       3344444444444444444444444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.05
                    CENP-F_leu_zip  10 ekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr....... 79 
                                       ++L e e+k  sLk+k+e+  +ele+ e++ e++  ++E+ +    +l++ ++ l++ +++le    ++        
  gi|313122443|ref|YP_004038330.1| 165 GRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQARSDLEDVRYDIDaeaesid 241
                                       55667777777777777777777777777777777777777777777777777766666655532222221112222 PP

                    CENP-F_leu_zip  80 ...sekeeLekelqkkqerv...seLeslnsslenlleek 113
                                           e++eL+ e ++  e++   +e e+  s+l+ +++++
  gi|313122443|ref|YP_004038330.1| 242 aleTERDELTTEREDIPEEIdgaDEIEAQISDLRDQMQRL 281
                                       2225555555555544444422224444444444444444 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.7e-05
                    CENP-F_leu_zip  23 kdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseL 99 
                                        d+  +L re+ ++ +++ + i + E+++ e+e+l+    +l  +l+ +  +L+  r+ +e+L+++ ++  +rv++L
  gi|313122443|ref|YP_004038330.1| 347 VDRLRSLRREKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETL 423
                                       58999************************************************************************ PP

                    CENP-F_leu_zip 100 eslnssle 107
                                       es  ++le
  gi|313122443|ref|YP_004038330.1| 424 ESEVEELE 431
                                       *9988877 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.073
                    CENP-F_leu_zip  15 serkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrse 81 
                                         r+a+ L+  + +Le ele ++++ e+v    E+       l++  ee+a el +l++ ++ + se
  gi|313122443|ref|YP_004038330.1| 441 RHREANELEFEIGRLENELESVNSEMESV----ESRLDDRDDLEARREEIADELADLRTRIERIESE 503
                                       44555555555555555555555555544....344445566********************99998 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1  12.3         3   9.3e+02      15      84 ..     139     207 ..     135     225 .. 0.75
   2 !   11.7   1.7   0.00063       0.2      16      71 ..     223     284 ..     217     308 .. 0.78
   3 ?    3.8   4.7      0.19        57      25      89 ..     360     424 ..     337     434 .. 0.70
   4 !   10.1   0.2    0.0019       0.6      13      72 ..     407     466 ..     402     472 .. 0.91
   5 !   11.3   0.1   0.00084      0.26      16      75 ..     449     507 ..     440     514 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3
                              FlxA  15 sasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqekqqsek 84 
                                       ++++i++L+++  ++ +++++l + d   +e  ++++  ++++I+  +a+++ ++q+ +e  ++ +q+  
  gi|313122443|ref|YP_004038330.1| 139 IQEEIRELEQEKREIDNEISSLDSLDGRLPE-LEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRD 207
                                       6788999999999999999999999666555.99*****************9998876655554444433 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00063
                              FlxA  16 asqiasLqkQiknlqkqLkelses.deltkeekk.....kqqqliqaQIqqlqaQIaqlqqq 71 
                                        s+++  +  i+   ++++ l ++ delt+e          +++i+aQI++l+ Q+++l + 
  gi|313122443|ref|YP_004038330.1| 223 RSDLEDVRYDIDAEAESIDALETErDELTTEREDipeeiDGADEIEAQISDLRDQMQRLDSS 284
                                       566666777777777888888887788888744477777999****************9875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.19
                              FlxA  25 QiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaql.qqqqaekaqekqqsekeeksk 89 
                                       Q ++l +q+++l ++     e+   ++  +   +q++  ++ +  ++ ++ k+++++ +++ e+ +
  gi|313122443|ref|YP_004038330.1| 360 QRNDLRDQIDDLESE-RDELEQLHRRRGRLDDRLQSIDEELDRRrERRESLKQKREDLTNRVETLE 424
                                       777888888888888.77777888888888888888888886541444555555555555555444 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0019
                              FlxA  13 sgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqq 72 
                                       ++ +++ + L++ +++l+ +++el + d  +  e+   +++++ +I  l+++++ + ++ 
  gi|313122443|ref|YP_004038330.1| 407 ESLKQKREDLTNRVETLESEVEELESRDYGDILERHREANELEFEIGRLENELESVNSEM 466
                                       567888999********************************************9988875 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00084
                              FlxA  16 asqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaek 75 
                                       + +i +L++++++++ +++++ +    + ++ ++++++i  ++ +l+  I+++++++ e+
  gi|313122443|ref|YP_004038330.1| 449 EFEIGRLENELESVNSEMESVESR-LDDRDDLEARREEIADELADLRTRIERIESEAIEE 507
                                       567899***************999.55566677**********************98766 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  20.3      0.17        54       6      85 ..     138     221 ..     135     228 .. 0.84
   2 !   14.6   6.3   8.1e-05     0.025       2      89 ..     214     301 ..     213     313 .. 0.92
   3 ?    4.6  16.8       0.1        32      55     115 ..     357     423 ..     337     425 .. 0.67
   4 !   11.2   5.9   0.00094      0.29      40     101 ..     443     504 ..     436     514 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.17
                             DHR10   6 eekeelaelErkarelqakidalqvvekdl....rsciklleeieaelakleeakkklkelrdaleekeielreler 78 
                                       + +ee+ elE+  re+ + i +l+ ++  l    ++ + l e+ie++ a+lee +++++e+ +++e+ + ++ ele+
  gi|313122443|ref|YP_004038330.1| 138 AIQEEIRELEQEKREIDNEISSLDSLDGRLpeleQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELEN 214
                                       66899999999999999999999999998855556668888889999999999999999999999999999999999 PP

                             DHR10  79 keerlqr 85 
                                       + + l++
  gi|313122443|ref|YP_004038330.1| 215 RLDDLKQ 221
                                       9988875 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 8.1e-05
                             DHR10   2 eslaeekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielreler 78 
                                       ++l++ k++ ++lE    ++ a +++++ +e++  ++++  e+i +e+   +e ++++++lrd+++ +   ++el++
  gi|313122443|ref|YP_004038330.1| 214 NRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNELQT 290
                                       67889999********************************************************************* PP

                             DHR10  79 keerlqrqlen 89 
                                        ++  +  le 
  gi|313122443|ref|YP_004038330.1| 291 VIQFNEDMLEG 301
                                       99987777765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.1
                             DHR10  55 akkklkelrdaleeke...ielrelerkeerlqrqlenaeeklerlreqae...ekreaakarleel 115
                                         ++ ++lrd+++++e    el++l+r++ rl  +l++  e+l+r re++e   +kre+  +r+e l
  gi|313122443|ref|YP_004038330.1| 357 KLDQRNDLRDQIDDLEserDELEQLHRRRGRLDDRLQSIDEELDRRRERREslkQKREDLTNRVETL 423
                                       344555555555555500055666678999***************9988762226777777777776 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00094
                             DHR10  40 klleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqa 101
                                       + ++e+e e+ +le + + +++ ++ +e++  ++ +le+++e +   l+  + ++er + +a
  gi|313122443|ref|YP_004038330.1| 443 REANELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIESEA 504
                                       567899***************************************************99876 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  14.5     0.065        20     189     271 ..     141     222 ..     127     234 .. 0.83
   2 ?    2.5   3.2      0.26        81     205     256 ..     236     290 ..     219     310 .. 0.59
   3 ?   -0.4  11.3       1.9   5.9e+02     201     280 ..     353     428 ..     334     435 .. 0.50
   4 !   16.0   4.4   1.9e-05     0.006     193     257 ..     446     510 ..     437     526 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.065
                         Rab5-bind 189 EnlEetlqleierlkeelasisslkveleeikvekeslekslaektrqldklqtikselEeqlkelekekaaveqlv 265
                                       E++   l++e  ++ +e++s++sl  +l e+   + sl++  +ek ++l++  + ++e ++++++ ++++ ++e+ +
  gi|313122443|ref|YP_004038330.1| 141 EEIR-ELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRL 216
                                       4443.377788888899999999999999999999999999999999999999999999999999999999999998 PP

                         Rab5-bind 266 leeknk 271
                                        + k+ 
  gi|313122443|ref|YP_004038330.1| 217 DDLKQA 222
                                       888775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.26
                         Rab5-bind 205 elasisslkveleeikvekesleksl...aektrqldklqtikselEeqlkelek 256
                                       e +si++l +e +e+  e+e++ +      e  +q+ +l+  ++ l++ ++el+ 
  gi|313122443|ref|YP_004038330.1| 236 EAESIDALETERDELTTEREDIPEEIdgaDEIEAQISDLRDQMQRLDSSVNELQT 290
                                       4455666777777777777775443311145556666666666666666665543 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.9
                         Rab5-bind 201 rlkeelasisslkveleeikvekeslekslaektrqldklqtikselEeqlkelekekaaveqlvleeknkaqrLqt 277
                                         +e+l++ + l+ +++++  e+++le+  + + r  d lq+i    +e+l   ++ + +++q+  +  n+ ++L  
  gi|313122443|ref|YP_004038330.1| 353 LRREKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSI----DEELDRRRERRESLKQKREDLTNRVETLES 425
                                       4455555555555555555555555555544444433333333....333333444455555555555555555555 PP

                         Rab5-bind 278 ELD 280
                                       E++
  gi|313122443|ref|YP_004038330.1| 426 EVE 428
                                       443 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.9e-05
                         Rab5-bind 193 etlqleierlkeelasisslkveleeikvekeslekslaektrqldklqtikselEeqlkeleke 257
                                       + l+ ei rl +el+s++s +  +e  + ++++le+ ++e   +l +l+t+++ +E++  e+ + 
  gi|313122443|ref|YP_004038330.1| 446 NELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIESEAIEEFNT 510
                                       45889***************************************************986665554 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       3.2   9.8e+02      16      93 ..     151     228 ..     137     252 .. 0.61
   2 !   14.0   0.2   0.00017     0.053       2     114 ..     265     378 ..     264     381 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.2
                                       HHHHHHHHH--S.H..HHHHHHHHHHHHHHHHHHHHHHHTS----HHHHHHHHHHHHHCHHHHHHHHHHHHHTHHHH CS
                              HsbA  16 taldtavnafnG.gasalpilsasnalvsaikkattdaqasapltdeealalaqavqtLepdvkaaldaliaKkpaf 91 
                                         +d+ +++ +  ++ + ++ ++ ++l+ +i++ ++  +  ++   eea a ++++ + +++ ++ ld+l+  ++++
  gi|313122443|ref|YP_004038330.1| 151 REIDNEISSLDSlDGRLPELEQKRTSLKEKIEEKRAELEEKEQ-EIEEADANVEQTRDDRDELENRLDDLKQARSDL 226
                                       5555666666554235667777777777777776666665555.555555556666666666666666666666665 PP

                                       HH CS
                              HsbA  92 dk 93 
                                       + 
  gi|313122443|ref|YP_004038330.1| 227 ED 228
                                       54 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHHHHHHHHH--S.H...HHHHHHHHHHHHHHHHHHHHHHHTS----HHHHHHHHHHHHH.CHH CS
                              HsbA   2 atvisdittistavtaldtavnafnG.g.asalpilsasnalvsaikkattdaqasapltdeealalaqavqt.Lep 75 
                                       +++ ++i+++ ++++ ld++vn  +    ++   +  +s+++ +a++++t+  + ++ l ++++    +  ++  + 
  gi|313122443|ref|YP_004038330.1| 265 DEIEAQISDLRDQMQRLDSSVNELQTvIqFNEDMLEGTSADVAAALRDGTDSGSVTDALVESDTVVCWTCGTEvETS 341
                                       78999*******************999457889*************************9999976554443332345 PP

                                       HHHHHHHHHHH.THHHHHHHT-HHHHHHHHHHHHHHHHHH CS
                              HsbA  76 dvkaaldalia.KkpafdkagltslvlssLqdlkaasdaL 114
                                       +++ ++d l + +++++d+   +   +++++dl ++ d+L
  gi|313122443|ref|YP_004038330.1| 342 QIEETVDRLRSlRREKLDQ---RNDLRDQIDDLESERDEL 378
                                       6777777777655555553...445666666666655555 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7  21.7   1.2e-05    0.0036      68     232 ..     136     305 ..     114     312 .. 0.84
   2 ?    4.0  26.6     0.043        13      74     241 ..     337     501 ..     332     519 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                               MAD  68 eealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldll 144
                                        ea +e+i +  + k+  ++  + +   + +l e+++  ++lk++++e + ++e++e+e++e + ++e+ +   d+l
  gi|313122443|ref|YP_004038330.1| 136 TEAIQEEIRELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDEL 212
                                       46677777666667777777777778889999999999*************************************** PP

                               MAD 145 kkklseleqliqqlekkqkelaeaeqrikeLefeiqs....qeddslivknskselaripelekelerlreenkkln 217
                                       +++l +l+q +++le       ++ + i  Le e  +     ed  +++  + +  a+i++l  +++rl +  ++l+
  gi|313122443|ref|YP_004038330.1| 213 ENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDEltteREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNELQ 289
                                       **********************99********998876665666667777776666********************* PP

                               MAD 218 elke.nkelLkEeved 232
                                       ++++ n  +L+   +d
  gi|313122443|ref|YP_004038330.1| 290 TVIQfNEDMLEGTSAD 305
                                       9877366677766665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.043
                               MAD  74 qiElarlkkknlealnkkekekesklaearevisalk...nelaelkrqiekqelelsekeseleelqerldllkkk 147
                                       ++E ++  + + + l ++ +ek ++ +++r+ i+ l+   +el++l+r   + +  l++ ++el + +er + lk+k
  gi|313122443|ref|YP_004038330.1| 337 EVETSQ-IEETVDRLRSLRREKLDQRNDLRDQIDDLEserDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQK 412
                                       455555.5666677777777777777777777766641114566666666667777777777777777777777777 PP

                               MAD 148 lseleqliqqlekkqkelaeae........qrikeLefeiqs....qeddslivknskselaripelekelerlree 212
                                        ++l++++++le++ +el+ ++            eLefei       e+ + ++++++s+l    +le+  e+    
  gi|313122443|ref|YP_004038330.1| 413 REDLTNRVETLESEVEELESRDygdilerhREANELEFEIGRleneLESVNSEMESVESRLDDRDDLEARREEIAD- 488
                                       7777777777777777665443111110003334444444332222223333333333333333333333333333. PP

                               MAD 213 nkklnelkenkelLkEevedlkkkLereE 241
                                                       e++dl++++er E
  gi|313122443|ref|YP_004038330.1| 489 ----------------ELADLRTRIERIE 501
                                       ................3444444444443 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3  18.8   6.5e-05      0.02      27     108 ..     137     221 ..     124     229 .. 0.89
   2 ?    8.5   2.5     0.008       2.5      29     101 ..     219     290 ..     217     297 .. 0.83
   3 ?    6.1   2.3     0.047        14      60     101 ..     339     380 ..     336     384 .. 0.90
   4 ?    6.2   6.3     0.043        13      41      95 ..     379     433 ..     377     436 .. 0.87
   5 ?    4.4   9.8      0.15        46      28     104 ..     401     474 ..     392     478 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.5e-05
                           DUF4200  27 ealkqreeelekkeqeleedllkfdkf...lkendakraralkkaeeerklkkekeaeikklkaeietlkseiekle 100
                                       ea++++ +ele++++e+ +++  +d     l e ++kr+   +k+ee+r + +eke+ei+++ a++e+ + ++++le
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSLDSLdgrLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELE 213
                                       7899999**********9988666553333*********************************************** PP

                           DUF4200 101 ekleeykk 108
                                       ++l+++k+
  gi|313122443|ref|YP_004038330.1| 214 NRLDDLKQ 221
                                       ****9987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.008
                           DUF4200  29 lkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseieklee 101
                                       lkq++ +le+ ++ +  +++  d    e d + +  ++ + ee +  +e ea+i +l++++++l s  ++l+ 
  gi|313122443|ref|YP_004038330.1| 219 LKQARSDLEDVRYDIDAEAESIDALETERD-ELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNELQT 290
                                       789999999999999999988887555555.5566678899999********************999999886 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.047
                           DUF4200  60 kraralkkaeeerklkkekeaeikklkaeietlkseieklee 101
                                       ++++ ++ +++ r l++ek  + ++l+++i++l+se+++le+
  gi|313122443|ref|YP_004038330.1| 339 ETSQIEETVDRLRSLRREKLDQRNDLRDQIDDLESERDELEQ 380
                                       5677888999999***************************97 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.043
                           DUF4200  41 qeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkse 95 
                                       ++l ++  ++d  l+++d++  r +++ e+ ++++++ ++ ++ l++e+e+l+s+
  gi|313122443|ref|YP_004038330.1| 379 EQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELESR 433
                                       5778888899999999999999999999999999999999999999999999886 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.15
                           DUF4200  28 alkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleekle 104
                                       + ++r+e l++k++ l ++++ ++  ++e ++   r    + e +++  e e ei +l++e+e ++se+e  e +l+
  gi|313122443|ref|YP_004038330.1| 401 RRRERRESLKQKREDLTNRVETLESEVEELES---RDYGDILERHREANELEFEIGRLENELESVNSEMESVESRLD 474
                                       45678888888888888888888877777665...556667777788899999999999999999999999998876 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   3.8       3.9   1.2e+03      32      55 ..     138     161 ..     115     178 .. 0.67
   2 ?    3.4   0.2      0.32        98       7      29 ..     265     287 ..     257     301 .. 0.84
   3 ?    0.2   2.7       3.1   9.4e+02      30      66 ..     348     383 ..     333     386 .. 0.56
   4 ?    0.2  14.4       3.2     1e+03       5      61 ..     377     430 ..     367     435 .. 0.83
   5 ?   15.4   6.7   5.6e-05     0.017       5      57 ..     451     503 ..     448     505 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3.9
                          CCDC-167  32 lseeeResleeEeaslkeqleene 55 
                                         +ee ++le+E++++ +++++ +
  gi|313122443|ref|YP_004038330.1| 138 AIQEEIRELEQEKREIDNEISSLD 161
                                       444455667777777777766554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.32
                          CCDC-167   7 dkleeklascrerLeaverrlrk 29 
                                       d++e +++++r++++++++++++
  gi|313122443|ref|YP_004038330.1| 265 DEIEAQISDLRDQMQRLDSSVNE 287
                                       67999*************99876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 3.1
                          CCDC-167  30 eelseeeResleeEeaslkeqleenekeLksLrkeNr 66 
                                       ++l + +Re+l   ++ l+ q+++ e+e  +L + +r
  gi|313122443|ref|YP_004038330.1| 348 DRLRSLRREKLD-QRNDLRDQIDDLESERDELEQLHR 383
                                       345555566665.556666666666665555555554 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 3.2
                          CCDC-167   5 eIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLksL 61 
                                       e+++l  +  ++ +rL++++ +l +++   e+Resl++ ++ l++++e+ e+e ++L
  gi|313122443|ref|YP_004038330.1| 377 ELEQLHRRRGRLDDRLQSIDEELDRRR---ERRESLKQKREDLTNRVETLESEVEEL 430
                                       7788888999999*******9999885...788888888888888888888887776 PP

  == domain 5  score: 15.4 bits;  conditional E-value: 5.6e-05
                          CCDC-167   5 eIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleeneke 57 
                                       eI +le++l+s++ ++e+ve+rl ++   e +Re++ +E+a l++++e+ e+e
  gi|313122443|ref|YP_004038330.1| 451 EIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIESE 503
                                       899*********************************************98875 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.1     0.013       3.9      43      79 ..     136     172 ..     134     179 .. 0.91
   2 ?    2.9   6.0      0.44   1.4e+02      45      92 ..     180     227 ..     173     235 .. 0.52
   3 ?   14.7   1.8   9.5e-05     0.029      40      93 ..     237     290 ..     228     293 .. 0.91
   4 ?    3.5   0.9      0.28        87      56      79 ..     357     380 ..     336     384 .. 0.46
   5 ?    7.3   1.1     0.018       5.7      39      86 ..     388     432 ..     382     442 .. 0.71
   6 ?    4.9   1.1       0.1        32      37      93 ..     446     502 ..     439     505 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.013
                           BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       ++ +++++ +l++++ e+++ ++++d ++ ++ eLe+
  gi|313122443|ref|YP_004038330.1| 136 TEAIQEEIRELEQEKREIDNEISSLDSLDGRLPELEQ 172
                                       578999*****************************98 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.44
                           BLOC1_2  45 slekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       ++e+k  +l+ek++e+++   +++q  ++ +eLe+  + L +  ++LE
  gi|313122443|ref|YP_004038330.1| 180 KIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQARSDLE 227
                                       344444445555555555555555555555555555444444444444 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 9.5e-05
                           BLOC1_2  40 kdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       +++++ le++ ++l  + e + + ++  d+ie+q+++L +  ++LD+ + eL+ 
  gi|313122443|ref|YP_004038330.1| 237 AESIDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNELQT 290
                                       57788999******************************************9985 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.28
                           BLOC1_2  56 kyeelqpylqqidqiekqvteLee 79 
                                       k ++ + + +qid++e + +eLe+
  gi|313122443|ref|YP_004038330.1| 357 KLDQRNDLRDQIDDLESERDELEQ 380
                                       222333445555555555555554 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.018
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                       l+d+++s+ ++l++ +e+ e+l++   + +++ ++v++Le+ v+eL++
  gi|313122443|ref|YP_004038330.1| 388 LDDRLQSIDEELDRRRERRESLKQ---KREDLTNRVETLESEVEELES 432
                                       556666666666666665555554...446777888888888888876 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.1
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       ++l+ ++  le++le +n++ e++++ l+  d++e++ +e+ +  + L + + ++E+
  gi|313122443|ref|YP_004038330.1| 446 NELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIES 502
                                       667777788888999999999999998888888888887777766666666666665 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.0    0.0027      0.83      50     105 .]     136     190 ..     133     190 .. 0.93
   2 ?   11.8   7.6   0.00086      0.27      18      98 ..     203     287 ..     191     293 .. 0.78
   3 ?    3.3   8.7      0.37   1.2e+02      25      94 ..     360     432 ..     341     436 .. 0.67
   4 ?    7.0   3.4     0.026       8.1       7      77 ..     442     511 ..     436     534 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  50 laaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkLee 105
                                        +a qe++++l++ ++++ d++ s+ + +  rl el+++  +Lke+++e++++Lee
  gi|313122443|ref|YP_004038330.1| 136 TEAIQEEIRELEQEKREI-DNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEE 190
                                       6789999****9999999.88899******************************97 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00086
                                       HHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT......HTTHHHHHHHHHHHHHH CS
                          Spectrin  18 eekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeg......hsaseeieerleelner 88 
                                       e+++ +   ++l++ l+++++   ++++++ +++a+ e ++al++  ++l++e        + ++eie+++++l+++
  gi|313122443|ref|YP_004038330.1| 203 EQTRDDR--DELENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTERedipeeIDGADEIEAQISDLRDQ 277
                                       3333333..566999999999999**************************55554776656667************* PP

                                       HHHHHHHHHH CS
                          Spectrin  89 WeeLkelaae 98 
                                        + L + ++e
  gi|313122443|ref|YP_004038330.1| 278 MQRLDSSVNE 287
                                       **99987765 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.37
                                       CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTT..HTTHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  25 ssedlgkdleevqallkkhkaleaelaaqqervkalnelaekl.ldeg..hsaseeieerleelnerWeeLke 94 
                                       + +dl  +++++++  +++++l++     ++r+++++e  ++  + ++  +++ e++++r+e l++  eeL++
  gi|313122443|ref|YP_004038330.1| 360 QRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRrERREslKQKREDLTNRVETLESEVEELES 432
                                       4556677777777777777777777777777777777333333122223366668888888888887777765 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTHTTHHH CS
                          Spectrin   7 aqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaekl.ldeghsasee 77 
                                       +++a+ele  i   e++l  e + +++e+v++ l++ ++lea  ++  +++ +l +  e++  ++ ++ + +
  gi|313122443|ref|YP_004038330.1| 442 HREANELEFEIGRLENEL--ESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIeSEAIEEFNTH 511
                                       789999999999999999..6667799999999997777777777777777777777777733333444444 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   3.8      0.93   2.9e+02      10      58 ..     144     192 ..     136     207 .. 0.85
   2 ?   -1.0   0.3       7.6   2.3e+03      13      39 ..     196     222 ..     193     237 .. 0.57
   3 ?    0.7   0.4       2.2   6.9e+02       9      41 ..     216     248 ..     209     250 .. 0.71
   4 ?   14.9   1.0   8.3e-05     0.026       9      54 ..     240     285 ..     237     301 .. 0.90
   5 ?   -0.5   0.4       5.3   1.6e+03      44      59 ..     354     369 ..     339     387 .. 0.50
   6 ?    4.6   2.9      0.14        42      10      52 ..     390     432 ..     388     443 .. 0.88
   7 ?    4.0   1.4       0.2        63      17      49 ..     477     506 ..     464     515 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.93
                         kleA_kleC  10 DeLpevatdlvarRdkiAaklaeAeeLvrqaeeLRakvyeesaaLedra 58 
                                        eL++ + ++ ++   +  +  +  eL+++   L+ k+ e++a Le++ 
  gi|313122443|ref|YP_004038330.1| 144 RELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKE 192
                                       57888888888888888888889999*******************9975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 7.6
                         kleA_kleC  13 pevatdlvarRdkiAaklaeAeeLvrq 39 
                                       +e++ ++   Rd+  ++ ++ ++L++ 
  gi|313122443|ref|YP_004038330.1| 196 EEADANVEQTRDDRDELENRLDDLKQA 222
                                       556666666666555555555555433 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2.2
                         kleA_kleC   9 iDeLpevatdlvarRdkiAaklaeAeeLvrqae 41 
                                       +D L ++  dl   R +i a  ++ + L+ + +
  gi|313122443|ref|YP_004038330.1| 216 LDDLKQARSDLEDVRYDIDAEAESIDALETERD 248
                                       577777778888888777777777777766554 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 8.3e-05
                         kleA_kleC   9 iDeLpevatdlvarRdkiAaklaeAeeLvrqaeeLRakvyeesaaL 54 
                                       iD L+   ++l+ +R++i + +  A+e++ q+ +LR +  +  ++ 
  gi|313122443|ref|YP_004038330.1| 240 IDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSV 285
                                       899**999****************************9988766665 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 5.3
                         kleA_kleC  44 RakvyeesaaLedrak 59 
                                       R + + ++  L d++ 
  gi|313122443|ref|YP_004038330.1| 354 RREKLDQRNDLRDQID 369
                                       4444444444444432 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.14
                         kleA_kleC  10 DeLpevatdlvarRdkiAaklaeAeeLvrqaeeLRakvyeesa 52 
                                       D L+ ++++l  rR++   + ++ e+L+ ++e L  +v e ++
  gi|313122443|ref|YP_004038330.1| 390 DRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELES 432
                                       88999******************************99987655 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.2
                         kleA_kleC  17 tdlvarRdkiAaklaeAeeLvrqaeeLRakvye 49 
                                       +dl arR++iA+ la   +L  ++e++  ++ e
  gi|313122443|ref|YP_004038330.1| 477 DDLEARREEIADELA---DLRTRIERIESEAIE 506
                                       89*********9875...677777777766655 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.2    0.0095       2.9     110     154 ..     139     183 ..     132     187 .. 0.90
   2 ?    4.0   3.9      0.11        33      98     150 ..     169     221 ..     167     231 .. 0.69
   3 ?    6.1   0.2     0.024       7.3     111     156 ..     244     289 ..     235     294 .. 0.83
   4 ?   12.1   1.9   0.00034      0.11      97     154 ..     341     401 ..     324     406 .. 0.78
   5 ?    3.4   1.0      0.16        50     110     152 ..     409     452 ..     402     461 .. 0.71
   6 ?    6.1   0.7     0.024       7.6      93     133 ..     460     502 ..     454     514 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0095
                     Fzo_mitofusin 110 vdetekeleeeikelekeiekleevqkkakllrnkaslleseLek 154
                                       ++e  +ele+e +e+++ei++l+++  ++  l +k ++l++++e+
  gi|313122443|ref|YP_004038330.1| 139 IQEEIRELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEE 183
                                       567779**********************************99876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.11
                     Fzo_mitofusin  98 elsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslles 150
                                       el++    l+++++e ++elee+ +e+e+  +++e++      l n+   l++
  gi|313122443|ref|YP_004038330.1| 169 ELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQ 221
                                       56667777777777777777777777777777777777777777777666654 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.024
                     Fzo_mitofusin 111 detekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                       ++ ++el++e +++ +ei+  +e++ +   lr++ ++l+s++++ +
  gi|313122443|ref|YP_004038330.1| 244 ETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNELQ 289
                                       5677899999999999999999999999999999999998887765 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00034
                     Fzo_mitofusin  97 qelsstfarlcqqvde...tekeleeeikelekeiekleevqkkakllrnkaslleseLek 154
                                       +++++t++rl++  +e   ++++l+++i++le+e ++le+++++   l ++ +++++eL++
  gi|313122443|ref|YP_004038330.1| 341 SQIEETVDRLRSLRREkldQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDR 401
                                       3566777776654443111789*************************************97 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.16
                     Fzo_mitofusin 110 vdetekeleeeikelekeiekleevqkkakllrnk.aslleseL 152
                                        ++ +++l++++++le+e+e+le+      l r++ a++le e+
  gi|313122443|ref|YP_004038330.1| 409 LKQKREDLTNRVETLESEVEELESRDYGDILERHReANELEFEI 452
                                       56788999999999999999999977655555543256666555 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.024
                     Fzo_mitofusin  93 hqvqqelsstfarlcqq..vdetekeleeeikelekeieklee 133
                                       ++v++e++s+ +rl  +   +  ++e+ +e+++l+++ie++e+
  gi|313122443|ref|YP_004038330.1| 460 ESVNSEMESVESRLDDRddLEARREEIADELADLRTRIERIES 502
                                       57999*********87611567789***************997 PP

>> Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.7       1.4   4.3e+02      43      66 .]     197     220 ..     193     227 .. 0.56
   2 ?   -0.5   0.0       5.1   1.6e+03      43      65 ..     259     281 ..     254     282 .. 0.84
   3 ?    1.8   0.1      0.95   2.9e+02      42      65 ..     372     395 ..     369     396 .. 0.92
   4 ?    0.4   1.0       2.7   8.4e+02      42      65 ..     400     423 ..     396     424 .. 0.87
   5 ?   14.2   0.1   0.00013      0.04       2      27 ..     448     473 ..     447     477 .. 0.92
   6 ?   -1.0   0.8       7.4   2.3e+03       1      24 [.     478     501 ..     478     503 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.4
                   Val_tRNA-synt_C  43 eekaklaeleeqaeklkerLskLk 66 
                                       e  a++++ ++ ++ l++rL++Lk
  gi|313122443|ref|YP_004038330.1| 197 EADANVEQTRDDRDELENRLDDLK 220
                                       555555555555555555555553 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 5.1
                   Val_tRNA-synt_C  43 eekaklaeleeqaeklkerLskL 65 
                                       ee + + e e+q   l++++++L
  gi|313122443|ref|YP_004038330.1| 259 EEIDGADEIEAQISDLRDQMQRL 281
                                       56667789999*********998 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.95
                   Val_tRNA-synt_C  42 eeekaklaeleeqaeklkerLskL 65 
                                       e e++ l++l + + +l +rL+++
  gi|313122443|ref|YP_004038330.1| 372 ESERDELEQLHRRRGRLDDRLQSI 395
                                       889******************986 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 2.7
                   Val_tRNA-synt_C  42 eeekaklaeleeqaeklkerLskL 65 
                                       ++ +++ ++l++++e l++r + L
  gi|313122443|ref|YP_004038330.1| 400 DRRRERRESLKQKREDLTNRVETL 423
                                       567999************998877 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 0.00013
                   Val_tRNA-synt_C   2 vekeraRLeKeLaklekeiervqkKL 27 
                                       +e e+ RLe eL+ +++e+e+v+++L
  gi|313122443|ref|YP_004038330.1| 448 LEFEIGRLENELESVNSEMESVESRL 473
                                       6789*********************9 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 7.4
                   Val_tRNA-synt_C   1 DvekeraRLeKeLaklekeiervq 24 
                                       D+e+ r+    eLa l++ ier++
  gi|313122443|ref|YP_004038330.1| 478 DLEARREEIADELADLRTRIERIE 501
                                       667777777777777777777765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2       0.4   1.2e+02      83     121 ..     137     171 ..     127     174 .. 0.67
   2 ?    7.8   7.2      0.01       3.2      49     115 ..     162     228 ..     149     245 .. 0.81
   3 ?    6.3   1.3     0.031       9.6      55     111 ..     241     293 ..     223     304 .. 0.51
   4 ?    9.9   4.3    0.0023      0.72      46     107 ..     364     431 ..     338     434 .. 0.72
   5 ?    9.2   3.8    0.0038       1.2      40     116 ..     389     472 ..     387     478 .. 0.61
   6 ?    5.1   1.0     0.069        21      62     113 ..     460     512 ..     444     523 .. 0.46
   7 ?    2.0   0.3      0.63   1.9e+02      36      72 ..     483     520 ..     476     557 .. 0.50

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.4
                           DUF1664  83 keikeevtevredlseigedvesvkeaveglesklerie 121
                                       ++i+ee+ e++++ +ei+++++s++    +l+++l ++e
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSLD----SLDGRLPELE 171
                                       5677777777777777777777664....3455555555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.01
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       +l+    +l++ +  L+++i++  ++l+e ++ ++e +++v++ r+d +e+++ ++ +k+a ++le 
  gi|313122443|ref|YP_004038330.1| 162 SLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQARSDLED 228
                                       5677777888999999999999999999999999999999999999999999999999988888875 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.031
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       ++l++ +++L+ + + + +++d       ei+++++++r++++++++ v++++++++
  gi|313122443|ref|YP_004038330.1| 241 DALETERDELTTEREDIPEEIDGAD----EIEAQISDLRDQMQRLDSSVNELQTVIQ 293
                                       3333344444444333333333332....3333444455555555555555554444 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0023
                           DUF1664  46 vskqleqvs......eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                       +  q++++       e+l++ + +L +r++++d++ld   e  +++k++ +++ + +++++++ve+++
  gi|313122443|ref|YP_004038330.1| 364 LRDQIDDLEserdelEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELE 431
                                       33444444333333367778888888888888888888888888888888888888888888888776 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0038
                           DUF1664  40 sdavesvskqleqvs...eslaatkrhLssridrvdkkldeqkeisk....eikeevtevredlseigedvesvkea 109
                                        d ++s+ ++l++     esl++ +++L++r+++++++++e +        e ++e +e++ ++ ++++++esv++ 
  gi|313122443|ref|YP_004038330.1| 389 DDRLQSIDEELDRRRerrESLKQKREDLTNRVETLESEVEELESRDYgdilERHREANELEFEIGRLENELESVNSE 465
                                       56667777777765544489999999999999999999988765432111133445555555555555555555555 PP

                           DUF1664 110 veglesk 116
                                       +e++es+
  gi|313122443|ref|YP_004038330.1| 466 MESVESR 472
                                       5555555 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.069
                           DUF1664  62 rhLssridrvdkklde...qkeiskeikeevtevredlseigedvesvkeavegl 113
                                       +  +s++++v+++ld+    ++  +ei++e++++r  +++i+++  +++e  +++
  gi|313122443|ref|YP_004038330.1| 460 ESVNSEMESVESRLDDrddLEARREEIADELADLRTRIERIESE--AIEEFNTHM 512
                                       22233333333333330003334455666666666666666443..344444444 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.63
                           DUF1664  36 krslsdavesvskqleqvs.eslaatkrhLssridrvd 72 
                                       +  ++d ++++ +++e++  e++++   h++  +d +d
  gi|313122443|ref|YP_004038330.1| 483 REEIADELADLRTRIERIEsEAIEEFNTHMETVLDILD 520
                                       33344444444444444422444444444444444444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  22.2   0.00041      0.13      25     146 ..     145     287 ..     137     300 .. 0.74
   2 ?   12.0  13.9   0.00068      0.21      18     163 ..     204     376 ..     203     380 .. 0.72
   3 ?    1.0  26.4       1.6   4.8e+02      30     115 ..     354     474 ..     337     556 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00041
                              Fez1  25 evtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelre 101
                                       e+ q   ei +  ++l  l  +l e e++ ++l+e++eek +ele+ e+e++++ +++e +r+  ++le+ l +l++
  gi|313122443|ref|YP_004038330.1| 145 ELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQ 221
                                       55666666666667788899999***********************************************9999999 PP

                              Fez1 102 elselsleeeeaa..........lesdeakaqrqe..................aeeleelkreverlraeLke 146
                                       + s+l+  +++            +       +r+e                  + ++++l+ +++rl ++++e
  gi|313122443|ref|YP_004038330.1| 222 ARSDLEDVRYDIDaeaesidaleT-------ERDEltteredipeeidgadeiEAQISDLRDQMQRLDSSVNE 287
                                       888777666665544444443332.......333366666668888888888866777777777777665544 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00068
                              Fez1  18 QLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk...kseaellrekvek 91 
                                       Q +d + e+ ++l+++ + +++l ++r +++++ e+i+ le++++e t+e e + +e++ +   +++ + lr+++++
  gi|313122443|ref|YP_004038330.1| 204 QTRDDRDELENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDIPEEIDGAdeiEAQISDLRDQMQR 280
                                       899******************************************************99886667788889****** PP

                              Fez1  92 leeelkelreelselsleeeeaa.........lesdeakaqrqe.......................aeeleelkre 136
                                       l++ ++el++ ++ ++    e +                                            + e+++ +++
  gi|313122443|ref|YP_004038330.1| 281 LDSSVNELQTVIQFNEDM-LEGTsadvaaalrD----------GtdsgsvtdalvesdtvvcwtcgtEVETSQIEET 346
                                       ********9966553322.22222334444440..........2345556666666667777777776667777777 PP

                              Fez1 137 verlra...eLkeerqkkeeqassFeqERr 163
                                       v+rlr+   e   +r+   +q ++ e+ER 
  gi|313122443|ref|YP_004038330.1| 347 VDRLRSlrrEKLDQRNDLRDQIDDLESERD 376
                                       777765221222333444456666777775 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.6
                              Fez1  30 lseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelsel 106
                                         e +  +++lr+   +le++ +e+++l+ ++   ++ l+ +++el+r++++ e l++k e l + ++ l +e++el
  gi|313122443|ref|YP_004038330.1| 354 RREKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEEL 430
                                       56777888999999999999999999999999999999999999999999999999999999999999998888887 PP

                              Fez1 107 sleeeeaa...................................l 115
                                       +++++  +                                    
  gi|313122443|ref|YP_004038330.1| 431 ESRDYGDIlerhreanelefeigrlenelesvnsemesvesrlD 474
                                       76666655333333334444444444433333322222222221 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  37.0    0.0032      0.98     271     520 ..     139     393 ..     109     401 .. 0.52
   2 ?    2.2  24.5      0.08        25     304     931 ..     344     519 ..     335     550 .. 0.37

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0032
                           DUF3584 271 lkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklk 347
                                       +++++++l++++ e++++  +l  +l+    el++++  l++++++++a+l++ke+e+e+++++ ++  d++ ++l+
  gi|313122443|ref|YP_004038330.1| 139 IQEEIRELEQEKREIDNEISSLD-SLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDR-DELE 213
                                       34444445555555554444443.344444567777777777777777777777777777777777766554.5567 PP

                           DUF3584 348 adldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrl..kaaieeale 422
                                       + ld l + rs+le++  ++da  e++ +++ + d++  +++ +  ee+ + +e +++i++ +d+   +    ++l+
  gi|313122443|ref|YP_004038330.1| 214 NRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTERE-DIPEEIDGADEIEAQISDLRDQMqrLDSSVNELQ 289
                                       777777777777777777777777777777777776666543.4555555555555555555555433333334444 PP

                           DUF3584 423 alesqlrkqleaqkeelneeek......elesrlselklrldsatateEeleqieeadealekaqeelekaeaevea 493
                                        + +  ++ le   ++++ +         ++ +l+e ++ +  +  te e+ qiee +++l+  ++e     +++++
  gi|313122443|ref|YP_004038330.1| 290 TVIQFNEDMLEGTSADVAAALRdgtdsgSVTDALVESDTVVCWTCGTEVETSQIEETVDRLRSLRREKL---DQRND 363
                                       444444444444444444333200001145555555555555555666666666666666666554433...33333 PP

                           DUF3584 494 lqaeeeqlrkkrde...adealqkaerrle 520
                                       l ++   l+++rde    ++++ +  +rl+
  gi|313122443|ref|YP_004038330.1| 364 LRDQIDDLESERDEleqLHRRRGRLDDRLQ 393
                                       333333333333330003333333333333 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.08
                           DUF3584 304 keaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqek 380
                                       +e++d+l++   ++ ++ +  +++++ le+++++ e+    + + d d+l si +el                    
  gi|313122443|ref|YP_004038330.1| 344 EETVDRLRSLRREKLDQRNDLRDQIDDLESERDELEQLHRRRGRLD-DRLQSIDEELDR------------------ 401
                                       3333333333333333333333333333333332222221111111.233333333333.................. PP

                           DUF3584 381 ydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrl 457
                                                                                                                    
  gi|313122443|ref|YP_004038330.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                           DUF3584 458 dsatateEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqaleeleeqls 534
                                                                                                                    
  gi|313122443|ref|YP_004038330.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                           DUF3584 535 PqagsLlefLrkeapdWeesigklispelLeRtDLdPelvessekdtlyGvsLdleridvpdyaaseeeLrerlqal 611
                                                                                                                    
  gi|313122443|ref|YP_004038330.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                           DUF3584 612 eealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaerkqqaeeqlqk 688
                                                                                                                    
  gi|313122443|ref|YP_004038330.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                           DUF3584 689 ldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaartqakarlkeleeaykreLksk 765
                                                                                                                    
  gi|313122443|ref|YP_004038330.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                           DUF3584 766 dvDpetvkelkrkieeLekkieriekrreevreYraflqetwlkvdslaeerpalkeqveelesaaeeleqeltrli 842
                                                                                       +e+r+ lk++ e+l + +e le e ++l+
  gi|313122443|ref|YP_004038330.1| 402 -----------------------------------------------RRERRESLKQKREDLTNRVETLESEVEELE 431
                                       ...............................................333333333333333333333333333333 PP

                           DUF3584 843 edtklerkklekerkalekqldqldenlrklrdllskl.aelkldadaeqaegelaerlaaleelkrkrer.lsedv 917
                                       +    ++ +  +e++ le  + +l+++l  ++++++ + ++l    d e      +e  + l +l+++ er +se++
  gi|313122443|ref|YP_004038330.1| 432 SRDYGDILERHREANELEFEIGRLENELESVNSEMESVeSRLDDRDDLEARR---EEIADELADLRTRIERiESEAI 505
                                       3333333333333333334444444444444444444433433333333333...2223333333333222134445 PP

                           DUF3584 918 kkalerfkgvlkdk 931
                                       ++++ ++++vl   
  gi|313122443|ref|YP_004038330.1| 506 EEFNTHMETVLDIL 519
                                       55555555555444 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  19.4     0.045        14      27     107 ..     135     222 ..     126     229 .. 0.78
   2 ?   10.0   3.2    0.0024      0.74      32     101 ..     237     306 ..     224     309 .. 0.87
   3 ?    5.9  14.7     0.047        15      25     105 ..     337     417 ..     335     423 .. 0.95
   4 ?    2.4   1.1      0.57   1.8e+02      58      79 ..     412     433 ..     410     447 .. 0.78
   5 ?   10.0   6.4    0.0024      0.75      15      87 ..     446     519 ..     442     522 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.045
                       TMF_TATA_bd  27 Elaslkeelerleaerdeareeivklm.......keneelkelkkeleelekeleelqeryetlLellGeksEeveE 96 
                                       + ++++ee+ +le+e++e+ +ei +l        +  ++ ++lk+++ee ++elee +++ e++     +  +  +E
  gi|313122443|ref|YP_004038330.1| 135 DTEAIQEEIRELEQEKREIDNEISSLDsldgrlpELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDE 211
                                       567899*****************9987333333233444455666777777799999999999999999999999** PP

                       TMF_TATA_bd  97 LraDvaDlKem 107
                                       L++ ++DlK+ 
  gi|313122443|ref|YP_004038330.1| 212 LENRLDDLKQA 222
                                       *********86 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0024
                       TMF_TATA_bd  32 keelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDv 101
                                        e++  le+erde++ e  ++ +e +  +e ++++++l+ +++ l++  ++l ++++  ++  e   aDv
  gi|313122443|ref|YP_004038330.1| 237 AESIDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSVNELQTVIQFNEDMLEGTSADV 306
                                       678999****************************************999999988887777777766666 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.047
                       TMF_TATA_bd  25 EgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDv 101
                                       E+E ++++e++ rl + r+e  ++  +l  + ++l+++ +ele+l ++   l++r++++ e l  + E+ e L++  
  gi|313122443|ref|YP_004038330.1| 337 EVETSQIEETVDRLRSLRREKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKR 413
                                       99************************************************************************998 PP

                       TMF_TATA_bd 102 aDlK 105
                                       +Dl 
  gi|313122443|ref|YP_004038330.1| 414 EDLT 417
                                       8885 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.57
                       TMF_TATA_bd  58 elkelkkeleelekeleelqer 79 
                                       + ++l +++e+le+e+eel++r
  gi|313122443|ref|YP_004038330.1| 412 KREDLTNRVETLESEVEELESR 433
                                       5677889999999999999998 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0024
                       TMF_TATA_bd  15 erlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleeleke.leelqeryetlLell 87 
                                       ++l+ ei rlE+El+s+++e+e++e+  d+  +  ++  +  +el++l +++e +e+e +ee +++ et+L +l
  gi|313122443|ref|YP_004038330.1| 446 NELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIESEaIEEFNTHMETVLDIL 519
                                       6788999******************9999999999999999999**********99864899*******99998 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   7.2   0.00075      0.23      18      89 ..     159     230 ..     139     243 .. 0.86
   2 ?    4.3   0.2      0.12        36      19      48 ..     264     293 ..     248     312 .. 0.76
   3 ?   -0.6   0.1         4   1.2e+03      66      94 ..     341     370 ..     320     373 .. 0.75
   4 ?    8.4   2.9    0.0066       2.1      17      74 ..     376     433 ..     361     457 .. 0.76
   5 ?    2.5   0.6      0.45   1.4e+02      20      77 ..     446     499 ..     437     514 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00075
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HH CS
                        Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasssls 89 
                                        l  l+ +l+++++k  ++++++ee  ++++++ + i++A  +v +     ++L+++l  lkq ++  + + 
  gi|313122443|ref|YP_004038330.1| 159 SLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQARSDLEDVR 230
                                       56778999********************************************************99877654 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.12
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  19 laplsqnlentkeklseinrsveetnekvk 48 
                                         +++++++ ++++++++++sv+e + +++
  gi|313122443|ref|YP_004038330.1| 264 ADEIEAQISDLRDQMQRLDSSVNELQTVIQ 293
                                       567888888888888888888888877766 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 4
                                       -TTTTTGGGHHHHHHHHHH....HHHHHHH CS
                        Laminin_II  66 klapqLldklkelkqleeasss.lsdnise 94 
                                        ++++ +d+l++l+  +  + + l d+i+ 
  gi|313122443|ref|YP_004038330.1| 341 SQIEETVDRLRSLRREKLDQRNdLRDQIDD 370
                                       567777888888877666655558888875 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0066
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGG CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldk 74 
                                       + l++l+ +  ++ + l++i++++++  e  +++++  +d  + v +Le ++++L+++
  gi|313122443|ref|YP_004038330.1| 376 DELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELESR 433
                                       6788899999999999999999999999999999999999999999999999999988 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.45
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                        Laminin_II  20 aplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklke 77 
                                       ++l+ ++ +++++l+++n+++e ++  ++      +d +    ++  ++ +L  ++++
  gi|313122443|ref|YP_004038330.1| 446 NELEFEIGRLENELESVNSEMESVESRLD----DRDDLEARREEIADELADLRTRIER 499
                                       45555556666666666666443333333....2233333333333333333333333 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  18.4     0.021       6.4      46     117 ..     147     221 ..     134     228 .. 0.81
   2 ?    5.3   1.5     0.062        19      41      92 ..     253     290 ..     234     312 .. 0.40
   3 ?    6.5  13.0     0.027       8.3      54     117 ..     366     432 ..     340     434 .. 0.72
   4 ?    8.4   4.6    0.0067       2.1      59     115 ..     445     500 ..     438     503 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.021
                        TPR_MLP1_2  46 erelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelek...elselekriedlne 117
                                       e+e  +  +++ +l +l  +l el++++++lk++ e+ +aelee+e+++ee   + e+   + +ele+r++dl++
  gi|313122443|ref|YP_004038330.1| 147 EQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQtrdDRDELENRLDDLKQ 221
                                       5566666778999999999999****************************998877762226789*******997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.062
                        TPR_MLP1_2  41 aqqkYerelvkhaedvkelqalreel.......nelkaeiaelkaeaesakaeleesee 92 
                                         ++                     +       +e++a+i++l+++ +++ ++++e + 
  gi|313122443|ref|YP_004038330.1| 253 ERED---------------------IpeeidgaDEIEAQISDLRDQMQRLDSSVNELQT 290
                                       2222.....................1222222233333333333333333333333333 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.027
                        TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaeaesakaele...eseesweeqkeelekelselekriedlne 117
                                       +++++l++ r+el++l  ++  l ++++s  +el+   e +es+++++e l ++++ le+ +e+l++
  gi|313122443|ref|YP_004038330.1| 366 DQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDrrrERRESLKQKREDLTNRVETLESEVEELES 432
                                       4567777888888888888888888888888887622244567777888888888888888888765 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0067
                        TPR_MLP1_2  59 lqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedl 115
                                        ++l  e+ +l++e++++++e es+++ l+  +  +e ++ee+ +el++l++rie +
  gi|313122443|ref|YP_004038330.1| 445 ANELEFEIGRLENELESVNSEMESVESRLDD-RDDLEARREEIADELADLRTRIERI 500
                                       4455556666777777777777777777765.4568999999999999999999876 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  31.7    0.0028      0.87      32     197 ..     140     374 ..     127     380 .. 0.60
   2 ?    5.2  21.5     0.051        16       1     133 [.     379     515 ..     379     575 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0028
                               ERM  32 eetaelLaekarraeeeaelLeq...kaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeser...ke 102
                                       +e++++L++++r+  +e   L+    +  e+e++ + lke+ e++ +e e+ e++++ea++++++ ++++++   + 
  gi|313122443|ref|YP_004038330.1| 140 QEEIRELEQEKREIDNEISSLDSldgRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDElenRL 216
                                       66677777777777777654443111445556666666666666666666666666666666666664444411144 PP

                               ERM 103 eeaerLkeeleeareaeeeakekllealstpsks.....eseenveeseteeeeensee.................. 156
                                        + ++ +++le +r +   ++ +  +al+t++++     e       +e + ++e   e                  
  gi|313122443|ref|YP_004038330.1| 217 DDLKQARSDLEDVRYDIDAEA-ESIDALETERDEltterE----DIPEEIDGADEI--Eaqisdlrdqmqrldssvn 286
                                       444444446666666664333.444444444333222220....112222222222..0234555566666666666 PP

                               ERM 157 ...............................................esaeletdeveklsleieeeRvtylekskr 186
                                                                                        +e+et ++e+++++    R++ l++ + 
  gi|313122443|ref|YP_004038330.1| 287 elqtviqfnedmlegtsadvaaalrdgtdsgsvtdalvesdtvvcwtCGTEVETSQIEETVDRLRSLRREKLDQRND 363
                                       7777777777777777777777777777777777777777666666544899999999******************* PP

                               ERM 187 lqeqLkeLkse 197
                                       l++q ++L+se
  gi|313122443|ref|YP_004038330.1| 364 LRDQIDDLESE 374
                                       ********998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.051
                               ERM   1 eeaerekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaa....eaeeeiqrlkesaeke 73 
                                       e+  r++ +l +rL+++ ee ++++e  +  +++ e L ++ + +e e e+Le +      e ++e ++l+ +  + 
  gi|313122443|ref|YP_004038330.1| 379 EQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELESRDYgdilERHREANELEFEIGRL 455
                                       678899***********************************************9985333366999999******** PP

                               ERM  74 eeekeklerklreaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstp 133
                                       e+e e+++ +++ +e+++ +  + + r+ee a++L +   ++++ e ea e+  + ++t 
  gi|313122443|ref|YP_004038330.1| 456 ENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIESEAIEEFNTHMETV 515
                                       *******************99999999999999998888888888888888887777765 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  19.2   0.00022     0.068     685     838 ..     141     309 ..     110     312 .. 0.72
   2 ?    3.9  20.7     0.038        12     686     819 ..     365     507 ..     315     517 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                               FPP 685 sk....keenkllkeeleelks...ekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlk 754
                                       ++    ++e++   +e+ +l+s   +  +le +  s +e++e+  a l+e+Eq ++e  +++e++++ +  +e+ l+
  gi|313122443|ref|YP_004038330.1| 141 EEirelEQEKREIDNEISSLDSldgRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLD 217
                                       333333455556666666666511145677888889999************************************** PP

                               FPP 755 cmkesyesletrateleae...lnelkqkieaLeve...Leeekksheeleakckelqeqlervekkevs..kssae 823
                                         k+  ++le    +++ae   +  l+++ ++L+ e   + ee +   e ea++ +l+ q++r  +  +   +  + 
  gi|313122443|ref|YP_004038330.1| 218 DLKQARSDLEDVRYDIDAEaesIDALETERDELTTEredIPEEIDGADEIEAQISDLRDQMQRLDSSVNElqTVIQF 294
                                       *********9988777766224566777777777662225568888999**************98654432145555 PP

                               FPP 824 eedkklkqekeiaAA 838
                                       +ed+   +  ++aAA
  gi|313122443|ref|YP_004038330.1| 295 NEDMLEGTSADVAAA 309
                                       666666677777776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.038
                               FPP 686 k..keenkllkeeleelksekenlevelksate.......nleslkaqlqesEqllaelkseLeslkeskslaetql 753
                                       +   +  ++ ++ele+l+ ++  l+ +l+s  e       + eslk + ++  + ++ l+se+e+l+ s+    + l
  gi|313122443|ref|YP_004038330.1| 365 RdqIDDLESERDELEQLHRRRGRLDDRLQSIDEeldrrreRRESLKQKREDLTNRVETLESEVEELE-SRD-YGDIL 439
                                       1223445555566666666665555555555551111111555555555555555556666655554.222.33457 PP

                               FPP 754 kcmkesyesletrateleaelnelkqkieaLeveLeeekks...heeleakckelqeqlervekkevsk 819
                                       + + e +e le     le+el+++++++e++e+ L+++ +     ee   +  +l+ ++er+e++   +
  gi|313122443|ref|YP_004038330.1| 440 ERHREANE-LEFEIGRLENELESVNSEMESVESRLDDRDDLearREEIADELADLRTRIERIESEAIEE 507
                                       88888877.999999999999999999999999998886541115666677888999999988766543 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.5      0.54   1.7e+02      19      61 ..     142     182 ..     125     242 .. 0.61
   2 ?    8.5   0.1     0.011       3.3      12      76 ..     240     302 ..     230     320 .. 0.66
   3 ?    5.0   0.7      0.13        39       5      52 ..     343     393 ..     340     434 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.54
                                       XXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXXGGGGG CS
                            FliD_N  19 kldkleqkktklewkqsayrelnsklsnlksalsalsksstfs 61 
                                       ++ +leq+k ++++++s + +l   l +l+++ ++l  +++++
  gi|313122443|ref|YP_004038330.1| 142 EIRELEQEKREIDNEISSLDSLDGRLPELEQKRTSL--KEKIE 182
                                       455566666666666666666666666666644333..22222 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.011
                                       XXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXXGGGGGXEEEEEC.STTTEEEE CS
                            FliD_N  12 lmkaerakldkleqkktklewkqsayrelnsklsnlksalsalsksstfsakkatss.desvvtat 76 
                                       + + e ++ d+l+++ +++ ++++   e++ ++s+l+++++ l   s++++ ++  + +e+++  t
  gi|313122443|ref|YP_004038330.1| 240 IDALE-TERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLD--SSVNELQTVIQfNEDMLEGT 302
                                       44444.45699***************************887663..33333333322144555444 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.13
                                       XXXXXXXXXXXXXXXXXX...XXXXXXXXXXXHHHHHHHHHHHHHHHHHHH CS
                            FliD_N   5 tdslvkqlmkaerakldk...leqkktklewkqsayrelnsklsnlksals 52 
                                       +++ v+ l +  r kld+   l  +  +le++++++++l      l + l+
  gi|313122443|ref|YP_004038330.1| 343 IEETVDRLRSLRREKLDQrndLRDQIDDLESERDELEQLHRRRGRLDDRLQ 393
                                       7899999******9999988899**************99998888888663 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.7    0.0014      0.44      63     128 ..     159     225 ..     156     229 .. 0.81
   2 ?    4.9   0.5     0.084        26      68     113 ..     209     254 ..     203     262 .. 0.84
   3 ?    5.8   0.1     0.045        14      62     107 ..     269     314 ..     265     325 .. 0.89
   4 ?    1.5   0.6      0.98     3e+02      77     130 ..     342     396 ..     336     399 .. 0.69
   5 ?    5.8   7.7     0.045        14      23     124 ..     404     495 ..     399     504 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0014
                              COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllkldevvek 128
                                       +L +l+ +l e+e++ +++++k+e+ r++l+e+e+e+e+  ++ ++ ++ r el ++l +l++  + 
  gi|313122443|ref|YP_004038330.1| 159 SLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRdELENRLDDLKQARSD 225
                                       6889999*******************************99999999999985444455555555555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.084
                              COG2  68 qeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       ++ele+   +l++ar+++e+vr  +++  e +++   e+ el+ +r
  gi|313122443|ref|YP_004038330.1| 209 RDELENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTER 254
                                       5677777788999999999999999999999999999999998887 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.045
                              COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeak 107
                                       ++  +l++++++++s+++++++ ++ +++ l+ ++++v + l++ +
  gi|313122443|ref|YP_004038330.1| 269 AQISDLRDQMQRLDSSVNELQTVIQFNEDMLEGTSADVAAALRDGT 314
                                       5678999*******************************99998766 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.98
                              COG2  77 plaaarkkvesvreklsereeeveskleeakeleekr.ellklllkldevvekle 130
                                       ++++++++++s+r++  ++++++++++++ ++ +++  +l ++  +ld+++++++
  gi|313122443|ref|YP_004038330.1| 342 QIEETVDRLRSLRREKLDQRNDLRDQIDDLESERDELeQLHRRRGRLDDRLQSID 396
                                       5677788888888888888888888888877766665355566666776666666 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.045
                              COG2  23 rhgvpLeslrrdLeaylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeev 99 
                                       +++ +L++ r+dL + ++ le+e+ el  +dy d ++   +   l+ e+ ++e +l+++ +++esv++         
  gi|313122443|ref|YP_004038330.1| 404 ERRESLKQKREDLTNRVETLESEVEELESRDYGDILERHREANELEFEIGRLENELESVNSEMESVESR-------- 472
                                       5678999*************************9987766555555555555555555555555555544........ PP

                              COG2 100 eskleeakeleekr.ellklllklde 124
                                          l+++ +le+ r e+ + l +l +
  gi|313122443|ref|YP_004038330.1| 473 ---LDDRDDLEARReEIADELADLRT 495
                                       ...44444444444444444444444 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.1      0.33     1e+02      76      99 ..     136     159 ..     111     164 .. 0.65
   2 ?    3.0  18.9      0.38   1.2e+02      13      99 ..     142     228 ..     134     241 .. 0.64
   3 ?    6.6   5.6     0.029       8.9       8      87 ..     206     289 ..     201     300 .. 0.52
   4 ?    2.6  10.4      0.51   1.6e+02      15      95 ..     355     432 ..     343     433 .. 0.77
   5 ?   10.3   5.1    0.0021      0.64      27      97 ..     434     504 ..     427     510 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.33
                                       CHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  76 vkelkeelkaleaelkeleaelek 99 
                                       +++++ee+ +le+e +e+++e+ +
  gi|313122443|ref|YP_004038330.1| 136 TEAIQEEIRELEQEKREIDNEISS 159
                                       456667777777777777776654 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.38
                                       HHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  13 avkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleae 89 
                                       +++e  ++++e ++++ +l +ld +  el+++  +l+++  e  +e +++ ++ e+a++ ++++++  +el++  ++
  gi|313122443|ref|YP_004038330.1| 142 EIRELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDD 218
                                       44554455556777777777777777777777777777777777777777776666666666666555555555555 PP

                                       HHHHHHHHHH CS
                      Seryl_tRNA_N  90 lkeleaelek 99 
                                       lk+++++le+
  gi|313122443|ref|YP_004038330.1| 219 LKQARSDLED 228
                                       5555555555 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.029
                                       HH-HHHHHHHHCCCTCCCHHHHHHH.HHH...HHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHH CS
                      Seryl_tRNA_N   8 renpeavkeklkkRgedkadvdell.eld...ekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelk 80 
                                       r++ ++++++l   +++ +d++++  ++d   e   +l++e +el +er  + +eI  a + ++++++l+++++ l 
  gi|313122443|ref|YP_004038330.1| 206 RDDRDELENRLDDLKQARSDLEDVRyDIDaeaESIDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLD 282
                                       55555555555555544444444431222000223345566666666666666666666666666666666666665 PP

                                       HHHHHHH CS
                      Seryl_tRNA_N  81 eelkale 87 
                                         +++l+
  gi|313122443|ref|YP_004038330.1| 283 SSVNELQ 289
                                       5555554 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.51
                                       HHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  15 keklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelk 91 
                                       +ekl +R++   ++d+l +  ++ ++l  +   l  +  ++ +e  +     e +e+l+++ ++l +++++le e++
  gi|313122443|ref|YP_004038330.1| 355 REKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRR---ERRESLKQKREDLTNRVETLESEVE 428
                                       6788888877777777777777777777777777777777777766555...6689999999999999999999999 PP

                                       HHHH CS
                      Seryl_tRNA_N  92 elea 95 
                                       ele+
  gi|313122443|ref|YP_004038330.1| 429 ELES 432
                                       9875 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  27 dvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleael 97 
                                       d  ++le  ++  el++e+  l +e  +++ e+++   + +d+++l a+ +e+ +el++l ++ + +e+e 
  gi|313122443|ref|YP_004038330.1| 434 DYGDILERHREANELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIESEA 504
                                       56789999999**************************999***********************99999875 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3  19.5       9.7     3e+03      46      98 ..     140     195 ..     127     198 .. 0.46
   2 ?   -0.3  29.5       4.7   1.5e+03      11     100 ..     160     246 ..     160     312 .. 0.76
   3 ?    5.9   5.4     0.059        18      55      97 ..     339     381 ..     334     387 .. 0.57
   4 ?   10.4  15.3    0.0024      0.73      51     130 ..     387     470 ..     380     473 .. 0.86
   5 ?    7.8   9.8     0.014       4.4      26     107 ..     433     513 ..     431     524 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 9.7
                            APG6_N  46 deeleeleeeleklekeeeel...leeLkelekereeleaelaaleeelealeeee 98 
                                       +ee++ele+e +++++e ++l      L ele++r +l++++++ ++ele++e+e 
  gi|313122443|ref|YP_004038330.1| 140 QEEIRELEQEKREIDNEISSLdslDGRLPELEQKRTSLKEKIEEKRAELEEKEQEI 195
                                       23344444444444443333200023455555555555555555555555555553 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 4.7
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal 87 
                                       l+ ld +l ++e++r +++e  ++ ++e +e+e   +e+ee++  +e+++++++el++ L++l+++r++le+ + ++
  gi|313122443|ref|YP_004038330.1| 160 LDSLDGRLPELEQKRTSLKEKIEEKRAELEEKE---QEIEEADANVEQTRDDRDELENRLDDLKQARSDLEDVRYDI 233
                                       578888999999999999988888888865554...69999999999999999999999999999988888777777 PP

                            APG6_N  88 eeelealeeeeer 100
                                        +e+e +++ e++
  gi|313122443|ref|YP_004038330.1| 234 DAEAESIDALETE 246
                                       6666666665544 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.059
                            APG6_N  55 eleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                       e +++e++ ++l +  +e  ++r +l++++ +le+e ++le+ 
  gi|313122443|ref|YP_004038330.1| 339 ETSQIEETVDRLRSLRREKLDQRNDLRDQIDDLESERDELEQL 381
                                       4555555555555555555566666666666666666666554 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0024
                            APG6_N  51 eleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee....erfwreynelqlelleleeeldsle 123
                                       +l+++l+ +++e ++  e  + l+++re+l + +++le+e e+le        +  re nel+ e  +le+el+s++
  gi|313122443|ref|YP_004038330.1| 387 RLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELESRDygdiLERHREANELEFEIGRLENELESVN 463
                                       688999***************************************9873333566788999**************** PP

                            APG6_N 124 aqyehaq 130
                                       +++e  +
  gi|313122443|ref|YP_004038330.1| 464 SEMESVE 470
                                       *998765 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.014
                            APG6_N  26 daYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeL...kelekereeleaelaaleeelealeeeee 99 
                                       ++Y + l++ ++ ++ e     e+ +le+ele +++e e+ ++ L   ++le+ ree+++ela+l+   e++e e  
  gi|313122443|ref|YP_004038330.1| 433 RDYGDILERHREANELEF----EIGRLENELESVNSEMESVESRLddrDDLEARREEIADELADLRTRIERIESEAI 505
                                       667777887777766665....9***********9999888777622268**********************99988 PP

                            APG6_N 100 rfwreyne 107
                                       ++++ + e
  gi|313122443|ref|YP_004038330.1| 506 EEFNTHME 513
                                       77766655 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   6.4      0.46   1.4e+02      20      63 ..     137     180 ..     134     191 .. 0.61
   2 ?    2.8   1.6      0.45   1.4e+02       2      28 ..     171     197 ..     170     199 .. 0.86
   3 ?   12.5   9.5   0.00045      0.14       3     108 ..     193     289 ..     191     303 .. 0.75
   4 ?    2.2   0.3      0.69   2.1e+02      18      51 ..     339     372 ..     336     377 .. 0.84
   5 ?    4.9  10.6       0.1        31       4     120 ..     360     475 ..     354     477 .. 0.88
   6 ?    4.2   7.0      0.16        49       3     114 ..     404     519 ..     402     520 .. 0.85
   7 ?    1.6   0.3         1   3.2e+02      16      79 ..     487     547 ..     474     558 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.46
                           DUF5082  20 aaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGk 63 
                                       +a++e I++L++ k++++ e +sl++    l + + +  s+k k
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEK 180
                                       55666666666666666666666666666666666666566555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.45
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIer 28 
                                        +k+++l+++i+e+r+e++  e+ Ie+
  gi|313122443|ref|YP_004038330.1| 171 EQKRTSLKEKIEEKRAELEEKEQEIEE 197
                                       689999999999999999999999986 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00045
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirs..nles 77 
                                       ++i+++ a ++++r +++ le  +  Lk+a++ l+d+   ++++ +++   + + ++++ ++e+  ++i    ++e 
  gi|313122443|ref|YP_004038330.1| 193 QEIEEADANVEQTRDDRDELENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDIPEEIDGadEIEA 269
                                       799*************************************************9999998888777666655444444 PP

                           DUF5082  78 syqtyvdkldelidaieeEIerLenqiseaq 108
                                       +++   d+            +rL ++++e+q
  gi|313122443|ref|YP_004038330.1| 270 QISDLRDQ-----------MQRLDSSVNELQ 289
                                       44333333...........333333333333 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.69
                           DUF5082  18 eiaaleekIerLkeaktklsdekeslkqkkkkle 51 
                                       e +++ee + rL++ +++  d+ + l +++ +le
  gi|313122443|ref|YP_004038330.1| 339 ETSQIEETVDRLRSLRREKLDQRNDLRDQIDDLE 372
                                       6789999999999999999999999999888876 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.1
                           DUF5082   4 kisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyq 80 
                                       ++++l+ qi++l+se++ le+  +r  +  ++l++ +e+l+  ++  e    + e ++++ e  +++ ++    +y 
  gi|313122443|ref|YP_004038330.1| 360 QRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELESRDYG 436
                                       78999999999999999999998998999999999999999999999999999999999988877777777778899 PP

                           DUF5082  81 tyvdkldelidaieeEIerLenqiseaqgvldtlqsqlns 120
                                        + ++ +e+  ++e EI rLen++++  + +++ +s l++
  gi|313122443|ref|YP_004038330.1| 437 DILERHREA-NELEFEIGRLENELESVNSEMESVESRLDD 475
                                       999998887.579*************99999999999876 PP

  == domain 6  score: 4.2 bits;  conditional E-value: 0.16
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLk.eaktklsdekeslkqkkkklekplnssesWkGk..eennydgirsnle 76 
                                       +++++l+++ ++l +++++le+ +e+L+ + +  + +   ++ + + ++   +n+ es + +    ++  ++r +le
  gi|313122443|ref|YP_004038330.1| 404 ERRESLKQKREDLTNRVETLESEVEELEsRDYGDILERHREANELEFEIGRLENELESVNSEmeSVESRLDDRDDLE 480
                                       5789999999*****************97889999999999999999999999999998877422344455666999 PP

                           DUF5082  77 ssyqtyvdkldelidaiee.EIerLenqiseaqgvldtl 114
                                          +++ d+l +l  +ie+ E e +e+ ++++++vld l
  gi|313122443|ref|YP_004038330.1| 481 ARREEIADELADLRTRIERiESEAIEEFNTHMETVLDIL 519
                                       999999999999999999779999999999999999876 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 1
                           DUF5082  16 rseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessy 79 
                                         e+a+l   Ier +   ++  +e ++  ++  ++ +++n +  W  ++e+++ + r+++++s+
  gi|313122443|ref|YP_004038330.1| 487 ADELADLRTRIERIE---SEAIEEFNTHMETVLDILDYDNLDRIWIERTEQTVREGRRKVQKSV 547
                                       333333333333332...2222233333334445667777777888888888888888887776 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  12.3     0.011       3.4     147     238 ..     144     246 ..     100     295 .. 0.39
   2 ?    2.3  16.2      0.32     1e+02     145     241 ..     329     441 ..     264     580 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                      Exonuc_VII_L 147 eqleeler....................rlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleral 203
                                       ++le+ +r                    + ++++k+++eek+++le+ +++++++++ +e+ r+  dele+rl+   
  gi|313122443|ref|YP_004038330.1| 144 RELEQEKReidneissldsldgrlpeleQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDD-- 218
                                       233333331111111111111111111111222233333333333333333333333333333333333333333.. PP

                      Exonuc_VII_L 204 kkqlkkkrerleelkerlkekleekkerlkklker 238
                                          lk++r++le ++     ++++++e++++l+++
  gi|313122443|ref|YP_004038330.1| 219 ---LKQARSDLEDVR----YDIDAEAESIDALETE 246
                                       ...222222222222....1122222222111111 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.32
                      Exonuc_VII_L 145 l..........eeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkr 211
                                       +          ++q+ee+ +rl++  +++l++++  l+    +l+s ++ le+ ++r  +l +rl++ ++++l+++r
  gi|313122443|ref|YP_004038330.1| 329 VvcwtcgteveTSQIEETVDRLRSLRREKLDQRN-DLRDQIDDLESERDELEQLHRRRGRLDDRLQS-IDEELDRRR 403
                                       3455555555555666666666666666664333.33333334433333333333333333334433.333333333 PP

                      Exonuc_VII_L 212 erleelkerlk...ekleekkerlkklkerle.....l 241
                                       er e+lk++ +   +++e+ ++++++l++r       +
  gi|313122443|ref|YP_004038330.1| 404 ERRESLKQKREdltNRVETLESEVEELESRDYgdileR 441
                                       33333332221122233333333322222211222210 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  11.8     0.015       4.8     340     407 ..     137     205 ..     112     214 .. 0.67
   2 ?    9.6   1.3     0.001      0.31     332     431 ..     209     306 ..     200     320 .. 0.82
   3 ?    5.7   6.8     0.016       4.9     329     411 ..     352     430 ..     328     441 .. 0.59
   4 ?    2.3   7.8      0.16        51     333     411 ..     407     493 ..     405     522 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                              FapA 340 keleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkee 407
                                       ++++ee++ele+e ++++++i++l++l    ++le+++ +  +k++e++ +l+e+ +e+ee  +++++ 
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSLDSLDGrLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQT 205
                                       566777777777777777777777776665566666666666666666666666666666666655554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.001
                              FapA 332 epelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeel 408
                                       + el ++l++l++   +le+   +++++ +++++l+ e +   + +e++ + +    +++ ++++l++++++l++++
  gi|313122443|ref|YP_004038330.1| 209 RDELENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDIPEEIDGADEIEAQISDLRDQMQRLDSSV 285
                                       45677777777777777777777888888888888888888889999999999999********************* PP

                              FapA 409 eskkeeakikvnkeiypgvkiki 431
                                       ++   ++ i+ n+ +  g+   +
  gi|313122443|ref|YP_004038330.1| 286 NEL--QTVIQFNEDMLEGTSADV 306
                                       *99..779999999999987665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.016
                              FapA 329 gldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelk 405
                                       +l++ +l+++ ++l++++ +le+e ++l++  ++       ++  + + e+l++ +e +e+lk++ e+l+++ ++l+
  gi|313122443|ref|YP_004038330.1| 352 SLRREKLDQR-NDLRDQIDDLESERDELEQLHRRRGR---LDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLE 424
                                       4453444444.77777777776666666655222222...2223344556666666666777777777777777777 PP

                              FapA 406 eelesk 411
                                       +e+e+ 
  gi|313122443|ref|YP_004038330.1| 425 SEVEEL 430
                                       766665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.16
                              FapA 333 pelkeklkeleeeleeleeeleklkkk.....ikklpklka...ekqlesekkeqlkklletkeklkeeleeleeel 401
                                        +lk+k+++l +++e le+e+e+l+++     +++ ++ ++   e    ++ +e++++  e+ e+  ++  +le+++
  gi|313122443|ref|YP_004038330.1| 407 ESLKQKREDLTNRVETLESEVEELESRdygdiLERHREANElefEIGRLENELESVNSEMESVESRLDDRDDLEARR 483
                                       46777778888888888888888888877665333333222100222234444455555555555555555566666 PP

                              FapA 402 kelkeelesk 411
                                       +e+ +el++ 
  gi|313122443|ref|YP_004038330.1| 484 EEIADELADL 493
                                       6666666655 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  16.6   0.00032     0.098     196     370 ..     111     290 ..      90     324 .. 0.67
   2 ?    2.7  22.8      0.13        40     109     318 ..     342     552 ..     336     559 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                             WEMBL 196 LesahaahleaeEkrlgaalareqdklnwekeLkqaeeelqrLneellsakdlkskletasallldLkaeLaayve. 271
                                       Les  a    a    l+  + r  d+ + ++e+++ e+e +++++e++s + l  +l + +++ ++Lk+ +      
  gi|313122443|ref|YP_004038330.1| 111 LESNEARQAVARGDDLRELIMRPIDTEAIQEEIRELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAe 187
                                       66677777777777777788888899999999999999999999999999999999988888888888777643321 PP

                             WEMBL 272 ..sklkeeaeeeeee..........kksetsikealasarkELeevkaniekakdevklLkvaaasLrseLekekae 336
                                         +k +e +e    +          + + ++    l++ar +Le+v+ +i+   + + +L+      r eL  e+++
  gi|313122443|ref|YP_004038330.1| 188 leEKEQEIEE----AdanveqtrddRDELENRLDDLKQARSDLEDVRYDIDAEAESIDALET----ERDELTTERED 256
                                       1022222221....123455565543333334456788899999999999887777777754....46666666666 PP

                             WEMBL 337 LaslrqregmasiavssLeaelsrtkselelvqa 370
                                       + +         + +s L+++++r  s ++ +q+
  gi|313122443|ref|YP_004038330.1| 257 IPEEIDGADEIEAQISDLRDQMQRLDSSVNELQT 290
                                       6544444444444566666666666665555544 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.13
                             WEMBL 109 emeqgiaseesvaakaqlevakerhaaavaeLksvkeeLeslqkeyaslvserdaaikkaeeavsaskevekaveel 185
                                       ++e+ + ++ +   +++l+  ++ +   + +L+s ++eLe+l++++  l +  +   +  +      +  +++ e+l
  gi|313122443|ref|YP_004038330.1| 342 QIEETV-DRLRSLRREKLDQRNDLR-DQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDL 416
                                       566666.667777888898877765.569***************998887666555555555555666667778999 PP

                             WEMBL 186 tielialkesLesahaa..hleaeEkrlgaalareqdklnwekeLkqaeeelqrLneellsakdlkskletasalll 260
                                       t  + +l  ++e   +    +  e +r       e +  ++e+eL+ +++e++ ++++l  ++dl+++ e+  + l+
  gi|313122443|ref|YP_004038330.1| 417 TNRVETLESEVEELESRdyGDILERHREAN--ELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELA 491
                                       999998888887665541034455555444..567889999************************************ PP

                             WEMBL 261 dLkaeLaayvesklkeeaeeeeee....kksetsikealasarkELeevkaniekakdevkl 318
                                       dL++ +   +es+  ee +++ e+        +  +  ++++ + + e + +++k   ++++
  gi|313122443|ref|YP_004038330.1| 492 DLRTRIER-IESEAIEEFNTHMETvldiLDYDNLDRIWIERTEQTVREGRRKVQKSVFDMHI 552
                                       ****9875.55555666655555557764444444555666666666666666666555555 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  17.8     0.012       3.6       6     128 ..     160     287 ..     137     298 .. 0.84
   2 ?    7.8  19.5    0.0055       1.7      61     219 ..     339     498 ..     335     520 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                           Taxilin   6 lkeslsklespeekleaLvkkyaelleerkrlqkqlkklkkkleqlqkekeqlqaelskaalaksKLekLcRelqkq 82 
                                       l ++  +l++ e+k   L++k++e  +e +++++++ +++ ++eq+  ++++l++ l++ ++a+s Le    +++ +
  gi|313122443|ref|YP_004038330.1| 160 LDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQARSDLEDVRYDIDAE 236
                                       55555689999****************************************************************99 PP

                           Taxilin  83 nkklk...eeskqrareeeekrkel..aekfqakLkdiqaqieeksernek 128
                                        + +     e  ++++e e+  +e+  a+  +a+++d+++q+++ +++ ++
  gi|313122443|ref|YP_004038330.1| 237 AESIDaleTERDELTTEREDIPEEIdgADEIEAQISDLRDQMQRLDSSVNE 287
                                       988764336666667777776666633578899999999999886655544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0055
                           Taxilin  61 elskaalaksKLekLcRelqkqnkklkeeskqrareeeekrk..elaekfqakLkdiqaqieekserneklreenae 135
                                       e+s+   + ++L +L Re  +q++ l+++  ++  e +e  +      ++ + L++i++ +++++er+e+l+++ ++
  gi|313122443|ref|YP_004038330.1| 339 ETSQIEETVDRLRSLRREKLDQRNDLRDQIDDLESERDELEQlhRRRGRLDDRLQSIDEELDRRRERRESLKQKRED 415
                                       899999***********************999888877665511456789*************************** PP

                           Taxilin 136 lteKlkslieqyelreehf.......ekllktkel.elqlaeaKlqqadallkeeqekkkrekeyllkeakeltkkv 204
                                       lt++ ++l  ++e  e +        +     +e  el++   +l  +++l + + e +  e  +   + ++l+++ 
  gi|313122443|ref|YP_004038330.1| 416 LTNRVETLESEVEELESRDygdilerH-----REAnELEFEIGRL--ENELESVNSEMESVESRL--DDRDDLEARR 483
                                       ********9988876665444344331.....2221333344444..222223333333333333..5555556666 PP

                           Taxilin 205 kalketekelkeqln 219
                                       +++ ++ ++l+++++
  gi|313122443|ref|YP_004038330.1| 484 EEIADELADLRTRIE 498
                                       666666666666554 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.6      0.02       6.2      71     109 ..     153     194 ..     135     217 .. 0.56
   2 ?    0.9   0.2       1.2   3.6e+02      69     103 ..     265     299 ..     217     311 .. 0.69
   3 ?    5.9   2.2     0.032       9.8      61     125 ..     365     431 ..     349     433 .. 0.81
   4 ?    5.2   0.1     0.053        16      70     117 ..     447     493 ..     440     503 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.02
                          Lectin_N  71 tlaeiqalss...qggslsekvtsleaklekkqqdlkadhse 109
                                       +  ei++l+s   +  +l++k tsl+ k+e+k+++l++   e
  gi|313122443|ref|YP_004038330.1| 153 IDNEISSLDSldgRLPELEQKRTSLKEKIEEKRAELEEKEQE 194
                                       344555555533322244555555555555555555544333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.2
                          Lectin_N  69 sstlaeiqalssqggslsekvtsleaklekkqqdl 103
                                        +++a+i++l+ q ++l+  v+ l++ ++ ++  l
  gi|313122443|ref|YP_004038330.1| 265 DEIEAQISDLRDQMQRLDSSVNELQTVIQFNEDML 299
                                       45566666666666666666666666666555555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.032
                          Lectin_N  61 ketfsnfssstlaeiqalssqggslsekvtsleaklekk...qqdlkadhselllhvkqlvkdLrtLs 125
                                       +++++++  s   e+++l+ + g+l+++++s++ +l+++   +++lk+   +l+ +v +l +++  L+
  gi|313122443|ref|YP_004038330.1| 365 RDQIDDLE-SERDELEQLHRRRGRLDDRLQSIDEELDRRrerRESLKQKREDLTNRVETLESEVEELE 431
                                       55555554.456799********************98751115789***************9998875 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.053
                          Lectin_N  70 stlaeiqalssqggslsekvtsleaklekkqqdlkadhselllhvkql 117
                                       + + ei  l+ + +s++ +++s+e++l+ +  dl+a   e+ + +  l
  gi|313122443|ref|YP_004038330.1| 447 ELEFEIGRLENELESVNSEMESVESRLDDR-DDLEARREEIADELADL 493
                                       66889999******************9876.46777777666666555 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       1.4   4.3e+02       2      30 ..     140     168 ..     139     176 .. 0.86
   2 ?    1.6   0.2      0.78   2.4e+02      12      31 ..     209     228 ..     187     243 .. 0.70
   3 ?    9.3   0.4     0.003      0.94       1      25 [.     267     291 ..     267     298 .. 0.86
   4 ?    4.1   0.9      0.13        41       6      27 ..     362     383 ..     358     405 .. 0.91
   5 ?    1.4   0.1       0.9   2.8e+02       6      23 ..     414     431 ..     409     434 .. 0.82
   6 ?    6.2   0.1     0.029       8.8       6      34 ..     484     510 ..     479     516 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.4
                         DASH_Dam1   2 epafaeLaDsletLdknledLqqihesLs 30 
                                       +++++eL+ + +++d+ ++ L++++ +L 
  gi|313122443|ref|YP_004038330.1| 140 QEEIRELEQEKREIDNEISSLDSLDGRLP 168
                                       688999************99999998875 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.78
                         DASH_Dam1  12 letLdknledLqqihesLsd 31 
                                        ++L+++l+dL+q + +L+d
  gi|313122443|ref|YP_004038330.1| 209 RDELENRLDDLKQARSDLED 228
                                       55566666666665555554 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.003
                         DASH_Dam1   1 lepafaeLaDsletLdknledLqqi 25 
                                       +e ++++L D+++ Ld+ +++Lq +
  gi|313122443|ref|YP_004038330.1| 267 IEAQISDLRDQMQRLDSSVNELQTV 291
                                       5789******************976 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.13
                         DASH_Dam1   6 aeLaDsletLdknledLqqihe 27 
                                       ++L D++++L++  ++L+q+h 
  gi|313122443|ref|YP_004038330.1| 362 NDLRDQIDDLESERDELEQLHR 383
                                       6899***************996 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.9
                         DASH_Dam1   6 aeLaDsletLdknledLq 23 
                                       ++L+  +etL++ +e+L+
  gi|313122443|ref|YP_004038330.1| 414 EDLTNRVETLESEVEELE 431
                                       789999999999999997 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.029
                         DASH_Dam1   6 aeLaDsletLdknledLqqihesLsdfNe 34 
                                       +e+aD+l++L++++e++++  e++++fN 
  gi|313122443|ref|YP_004038330.1| 484 EEIADELADLRTRIERIES--EAIEEFNT 510
                                       79**************995..88999985 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  18.4     0.036        11     105     183 ..     136     220 ..     111     221 .. 0.86
   2 ?   10.8   8.4    0.0013       0.4      81     167 ..     209     294 ..     198     306 .. 0.81
   3 ?    7.0  15.3     0.018       5.6      67     142 ..     340     429 ..     328     435 .. 0.71
   4 ?    2.4   9.4      0.46   1.4e+02      77     165 ..     427     512 ..     418     520 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.036
                           UPF0242 105 ldakeeelerlkeenqqLqekleaiae......dfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieqL 175
                                        +a +ee+++l++e+ ++  + +          + e+ +  l+e+++ek+  l+e +++iee  + +e+  d   +L
  gi|313122443|ref|YP_004038330.1| 136 TEAIQEEIRELEQEKREIDNEISSLDSldgrlpELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDEL 212
                                       6788999999999999999998888779999999999********************************99999*** PP

                           UPF0242 176 eskVrDln 183
                                       e +  Dl+
  gi|313122443|ref|YP_004038330.1| 213 ENRLDDLK 220
                                       *9999985 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0013
                           UPF0242  81 deglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqet 157
                                       +++l++  + l++++++ e+ +  +da  e +  l+ e  +L  + e+i e+++    e+e+q+   + ++q +  +
  gi|313122443|ref|YP_004038330.1| 209 RDELENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDIPEEIDG-ADEIEAQISDLRDQMQRLDSS 284
                                       356777778888888888888888**************************99976.568999999999999999999 PP

                           UPF0242 158 ieeqrsvlek 167
                                       ++e++ v++ 
  gi|313122443|ref|YP_004038330.1| 285 VNELQTVIQF 294
                                       9999999875 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.018
                           UPF0242  67 kskleekeaklteld..............eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleai 129
                                       +s++ee    l +l+              ++l+ ++++le+l  +  +L ++l++ +eel r++e+ ++L++k e+ 
  gi|313122443|ref|YP_004038330.1| 340 TSQIEETVDRLRSLRrekldqrndlrdqiDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDL 416
                                       45555555555555444444444444444678888888888888888888889999999999999999999999999 PP

                           UPF0242 130 aedfeelklelee 142
                                        + +e l  e+ee
  gi|313122443|ref|YP_004038330.1| 417 TNRVETLESEVEE 429
                                       9988888888876 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.46
                           UPF0242  77 lteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqe 153
                                       + el+   +     + e+  e +eL+ e+   e+ele  + e ++++++l +   d e+ + e+ ++La  +++++ 
  gi|313122443|ref|YP_004038330.1| 427 VEELE---SRDYGDILERHREANELEFEIGRLENELESVNSEMESVESRLDD-RDDLEARREEIADELADLRTRIER 499
                                       33333...344448999999999999999999******99999999999999.889999999999999999999887 PP

                           UPF0242 154 yq.etieeqrsvl 165
                                        + e iee    +
  gi|313122443|ref|YP_004038330.1| 500 IEsEAIEEFNTHM 512
                                       6514566665555 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  17.7       0.2        63      59     151 ..     151     227 ..     136     255 .. 0.61
   2 ?    7.0   6.8     0.016         5      49     147 ..     249     357 ..     243     388 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.2
                                       HHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXXXXXX CS
                        DASH_Spc19  59 eeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkkltke 135
                                        ei+ +i++ l+ ++  l +le+++++Lk+k+e ++  l+++e++ +e++++ e+++++++e +             
  gi|313122443|ref|YP_004038330.1| 151 REIDNEISS-LDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELE------------- 213
                                       466666665.578999999999999999999999999999965555555555555444443333............. PP

                                       XXXXXXXXXXXXXXXX CS
                        DASH_Spc19 136 elerlkkLkqkKerLk 151
                                         +rl +Lkq +  L+
  gi|313122443|ref|YP_004038330.1| 214 --NRLDDLKQARSDLE 227
                                       ..44444444444443 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.016
                                       THHHHHHHHHHHTT..THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX CS
                        DASH_Spc19  49 dleaakaslaeeie..PqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenk 123
                                       +l++ ++++ eei+   +ie +++ +++++++l++  ++L++ ++ +e  l+ ++  + +++ ++ +++ + + ++ 
  gi|313122443|ref|YP_004038330.1| 249 ELTTEREDIPEEIDgaDEIEAQISDLRDQMQRLDSSVNELQTVIQFNEDMLEGTS-ADVAAALRDGTDSGSVT-DAL 323
                                       688889999999964479***********************************53.22222222223322222.222 PP

                                       ....XXXX..............XXXXXXXXXXXXXXXX CS
                        DASH_Spc19 124 eeekskkk..............ltkeelerlkkLkqkK 147
                                        e+    +                +e  +rl+ L+++K
  gi|313122443|ref|YP_004038330.1| 324 VES----DtvvcwtcgtevetsQIEETVDRLRSLRREK 357
                                       222....1245788989987753344447888877665 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  13.3     0.059        18      66     167 ..     139     242 ..     130     252 .. 0.73
   2 ?    5.5   0.5     0.042        13      18      52 ..     265     299 ..     244     312 .. 0.77
   3 ?    5.7   8.1     0.036        11      49     132 ..     344     426 ..     336     432 .. 0.80
   4 ?   11.7  10.8   0.00053      0.16       6     119 ..     388     504 ..     383     516 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.059
                            TACC_C  66 akkeiqkvleek...eqlladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkah 139
                                        ++ei ++ +ek   ++ ++ l s++  + +l ++   +ke +e+ ++  e   +++ee  a+v++     ++L + 
  gi|313122443|ref|YP_004038330.1| 139 IQEEIRELEQEKreiDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENR 215
                                       45555555555511144556667777788888888888888888888888888888888888888888888888876 PP

                            TACC_C 140 aeekLekAneeiaqvrskakaetaalqa 167
                                        +  L++A +++++vr   +ae+  + a
  gi|313122443|ref|YP_004038330.1| 216 LD-DLKQARSDLEDVRYDIDAEAESIDA 242
                                       64.6888888888888888888877665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.042
                            TACC_C  18 eekeeeiqelkkkveelkkenqemkkivaefekti 52 
                                       +e e +i++l+++++ l+  ++e++ +++  e ++
  gi|313122443|ref|YP_004038330.1| 265 DEIEAQISDLRDQMQRLDSSVNELQTVIQFNEDML 299
                                       457899*******************9998777665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.036
                            TACC_C  49 ektiaqlieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylar 125
                                       e+t+ +l +   ++k  +++++   + + e    +l+++ +    l  r++   e l+  ++  eslk+++e++ +r
  gi|313122443|ref|YP_004038330.1| 344 EETVDRLRSL-RREKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNR 419
                                       5555555443.467777778888888888888888899999999999999999999********************* PP

                            TACC_C 126 vkkeeqR 132
                                       v++ e  
  gi|313122443|ref|YP_004038330.1| 420 VETLESE 426
                                       **98865 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00053
                            TACC_C   6 ldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlla 82 
                                       ld  l+ ++ee +++ e+ + lk+k e+l+++++ ++  v+e e+  +  i e+++++++ + ei ++ +e e +++
  gi|313122443|ref|YP_004038330.1| 388 LDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELESRDYGDILERHREANELEFEIGRLENELESVNS 464
                                       79999********98888788******************************************************** PP

                            TACC_C  83 dlnsveksfs...dlfkryekqkevlegykkneeslkkca 119
                                       +++sve  ++   dl  r e   + l ++++  e+  ++a
  gi|313122443|ref|YP_004038330.1| 465 EMESVESRLDdrdDLEARREEIADELADLRTRIERIESEA 504
                                       ******9986222688888888888888988888776654 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  13.9     0.065        20       6      84 ..     141     223 ..     124     230 .. 0.70
   2 ?   10.3   4.0    0.0019      0.58      13      96 ..     207     290 ..     202     310 .. 0.76
   3 ?    1.2  11.2       1.2   3.6e+02      36     115 ..     344     431 ..     333     433 .. 0.64
   4 ?    6.6   8.7     0.025       7.6       6      89 ..     376     464 ..     375     468 .. 0.89
   5 ?    5.5   1.4     0.054        17      16      67 ..     457     508 ..     451     521 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.065
                             Mod_r   6 eeLqelledeeklealvktlpe....vkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefe 78 
                                       ee++el +++  +++ +++l++    + +l++++++l +++e+   +  ++e+e+ee  ++++++++  +ele++++
  gi|313122443|ref|YP_004038330.1| 141 EEIRELEQEKREIDNEISSLDSldgrLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLD 217
                                       78888888888888888755443334667777777776666666555555577777777777777777777777777 PP

                             Mod_r  79 ekeqel 84 
                                       +++q  
  gi|313122443|ref|YP_004038330.1| 218 DLKQAR 223
                                       777655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0019
                             Mod_r  13 edeeklealvktlpe.vkqlkeekeellaeneslaeknlsl.epeleelrselqekleelkelekefeekeqeldel 87 
                                       +d + le+++++l++   +l++ + ++ ae es+ +  l+  ++el+ +r+++ e+++ ++e+e++  ++  ++++l
  gi|313122443|ref|YP_004038330.1| 207 DDRDELENRLDDLKQaRSDLEDVRYDIDAEAESI-D-ALETeRDELTTEREDIPEEIDGADEIEAQISDLRDQMQRL 281
                                       6778888888877443666777777776666666.3.3444377******************************999 PP

                             Mod_r  88 lqkfspdal 96 
                                        +++++  +
  gi|313122443|ref|YP_004038330.1| 282 DSSVNELQT 290
                                       888776554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.2
                             Mod_r  36 eellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell........qkfspdallarLqtav 104
                                       ee ++  +sl +++l+++++l+++ ++l+++++el++l+++  ++  +l+++         ++ s++  ++ L + v
  gi|313122443|ref|YP_004038330.1| 344 EETVDRLRSLRREKLDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDeeldrrreRRESLKQKREDLTNRV 420
                                       55556667777888888888888888888888887777777777777776666444563333333334444466666 PP

                             Mod_r 105 aeaeeeSeala 115
                                       +  e e e+l+
  gi|313122443|ref|YP_004038330.1| 421 ETLESEVEELE 431
                                       66666666665 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.025
                             Mod_r   6 eeLqelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrs....elqekleelkelekef 77 
                                       +eL++l      l+ +++++ +e+++ +e++e+l ++ e+l ++   le e+eel s    ++ e++ e++ele e 
  gi|313122443|ref|YP_004038330.1| 376 DELEQLHRRRGRLDDRLQSIdEELDRRRERRESLKQKREDLTNRVETLESEVEELESrdygDILERHREANELEFEI 452
                                       79******************888********************99999**9999987333469999999******** PP

                             Mod_r  78 eekeqeldellq 89 
                                        ++e+el+++ +
  gi|313122443|ref|YP_004038330.1| 453 GRLENELESVNS 464
                                       ******998765 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.054
                             Mod_r  16 eklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekl 67 
                                         le++ +++++v++  +++++l+a  e++a++  +l++++e   se +e++
  gi|313122443|ref|YP_004038330.1| 457 NELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIESEAIEEF 508
                                       3455555556666666666666666666666666666666666666666555 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.0       7.2   2.2e+03      10      36 ..     168     194 ..     136     217 .. 0.71
   2 ?   -1.1   0.3       8.4   2.6e+03      16      32 ..     216     228 ..     195     242 .. 0.53
   3 ?   10.0   1.1    0.0029      0.91       3      30 ..     265     292 ..     264     297 .. 0.91
   4 ?    0.7   0.1       2.4   7.3e+02      10      25 ..     362     377 ..     359     404 .. 0.72
   5 ?    3.0   0.0      0.44   1.4e+02       3      21 ..     414     432 ..     412     442 .. 0.88
   6 ?    2.7   0.1      0.55   1.7e+02       3      32 ..     446     475 ..     444     485 .. 0.76
   7 ?   -0.6   0.1       5.7   1.8e+03      12      37 ..     479     504 ..     474     506 .. 0.64
   8 ?   -0.8   0.0       6.9   2.1e+03       3      23 ..     484     504 ..     482     515 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 7.2
                               LPP  10 sqLkskvdqlssdvnsakaaaqaakeE 36 
                                        +L++k  +l++++++ +a++++  +E
  gi|313122443|ref|YP_004038330.1| 168 PELEQKRTSLKEKIEEKRAELEEKEQE 194
                                       456666666666666666665555444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 8.4
                               LPP  16 vdqlssdvnsakaaaqa 32 
                                        d     +++a++++++
  gi|313122443|ref|YP_004038330.1| 216 LDD----LKQARSDLED 228
                                       222....3333333333 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0029
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaaa 30 
                                       de+ +q+s+L ++++ l s vn++++ +
  gi|313122443|ref|YP_004038330.1| 265 DEIEAQISDLRDQMQRLDSSVNELQTVI 292
                                       8999*******************99866 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 2.4
                               LPP  10 sqLkskvdqlssdvns 25 
                                       ++L +++d l+s+ ++
  gi|313122443|ref|YP_004038330.1| 362 NDLRDQIDDLESERDE 377
                                       5677777777776443 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.44
                               LPP   3 deLssqVsqLkskvdqlss 21 
                                       + L++ V++L+s+v++l+s
  gi|313122443|ref|YP_004038330.1| 414 EDLTNRVETLESEVEELES 432
                                       679999********99987 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.55
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                       +eL  ++ +L+++ ++++s+++s+++ +++
  gi|313122443|ref|YP_004038330.1| 446 NELEFEIGRLENELESVNSEMESVESRLDD 475
                                       577788999999999999999998877765 PP

  == domain 7  score: -0.6 bits;  conditional E-value: 5.7
                               LPP  12 LkskvdqlssdvnsakaaaqaakeEA 37 
                                       L++  ++++++++++++ ++ +  EA
  gi|313122443|ref|YP_004038330.1| 479 LEARREEIADELADLRTRIERIESEA 504
                                       55555666666666666666666666 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 6.9
                               LPP   3 deLssqVsqLkskvdqlssdv 23 
                                       +e+++++ +L + ++ ++s++
  gi|313122443|ref|YP_004038330.1| 484 EEIADELADLRTRIERIESEA 504
                                       577888888888888888873 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2  18.2   4.3e-05     0.013      79     173 ..     167     259 ..     130     263 .. 0.86
   2 ?   -1.0   0.1       3.9   1.2e+03     104     123 ..     268     287 ..     264     301 .. 0.47
   3 ?   -1.3  17.5       4.9   1.5e+03      69     172 ..     361     463 ..     336     468 .. 0.62
   4 ?    2.0   2.7      0.49   1.5e+02      84     131 ..     457     504 ..     437     545 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.3e-05
                           DUF4201  79 lthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekve 155
                                       l +l +k++ l+++ +e++ el+eke+++++ ++++++++ +rd l+++ ++lkq   +   +++ +D d + e ++
  gi|313122443|ref|YP_004038330.1| 167 LPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDLKQARSD--LEDVRYDIDAEAESID 241
                                       5578899*************************************************999..68************** PP

                           DUF4201 156 ekrksvkkLrrkvkilem 173
                                        ++ + ++L ++ +++ +
  gi|313122443|ref|YP_004038330.1| 242 ALETERDELTTEREDIPE 259
                                       *****9999998888765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.9
                           DUF4201 104 eerlaklrkelykvklerdk 123
                                       e+++ +lr++++++    + 
  gi|313122443|ref|YP_004038330.1| 268 EAQISDLRDQMQRLDSSVNE 287
                                       34444444444443333332 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.9
                           DUF4201  69 kkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlk 145
                                       ++   +++  l+ +++ l  l +   +l ++l++++e+l++ r++ +++k++r+ l ++ e l+++ ++l+  +   
  gi|313122443|ref|YP_004038330.1| 361 RNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELESRDY-G 436
                                       334444555566666666666666667777777777777777777777777777777777777777666665554.3 PP

                           DUF4201 146 DYdktkekveekrksvkkLrrkvkile 172
                                       D  ++  + +e++ ++  L+ ++++++
  gi|313122443|ref|YP_004038330.1| 437 DILERHREANELEFEIGRLENELESVN 463
                                       455566666666666666666666665 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.49
                           DUF4201  84 eklhmleselselkkelkekeerlaklrkelykvklerdklrkqnekl 131
                                       + l  ++se++  +++l+++++ +a+ ++   ++   r+++++  ++ 
  gi|313122443|ref|YP_004038330.1| 457 NELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIESEA 504
                                       445566777777777777777777777777777777777776655554 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  10.3     0.016         5      33      99 ..     137     203 ..     135     205 .. 0.91
   2 ?    4.1  11.0      0.08        25      16     133 ..     193     312 ..     192     322 .. 0.63
   3 ?    2.6   4.3      0.23        71      32      75 ..     340     383 ..     335     401 .. 0.71
   4 ?    5.5   7.2     0.029         9      20      86 ..     366     432 ..     362     438 .. 0.85
   5 ?    8.5  15.5    0.0035       1.1      34     161 ..     394     523 ..     386     548 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                           DUF3450  33 aqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelv 99 
                                       +++q++i +l++ek+e+ +e+ +l +   +l   +++ ++l ++ e+++a+lee+ +eiee  ++++
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVE 203
                                       689***********************99999999999999999999999999999999999887776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.08
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       +++++a++  e++ + + + +++ d+l++ +++l++   ++ +e+es+++    le   +++ +e++++ e+i+ ++
  gi|313122443|ref|YP_004038330.1| 193 QEIEEADANVEQTRDDRDELENRLDDLKQARSDLEDVRYDIDAEAESIDA----LETERDELTTEREDIPEEIDGAD 265
                                       56778888999999999999999999999999998877777777776654....44444555666777777777777 PP

                           DUF3450  93 eierelvpl......lekmidrLeqfveldlPflleeRqarlakLke 133
                                       eie++++ l      l++ +++L+++++    +l+ + ++  a L++
  gi|313122443|ref|YP_004038330.1| 266 EIEAQISDLrdqmqrLDSSVNELQTVIQFNEDMLEGTSADVAAALRD 312
                                       77777766511111134445666666665555555555555555555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.23
                           DUF3450  32 aaqsqkkidklddekqellaeyralkeeleslevyneqlerlva 75 
                                        +q+++ +d+l   ++e l++ ++l++++++le ++++le+l +
  gi|313122443|ref|YP_004038330.1| 340 TSQIEETVDRLRSLRREKLDQRNDLRDQIDDLESERDELEQLHR 383
                                       46777888888888888888888888888888888888777654 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.029
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                       + ++  e+  ++ +q +++  +ldd  q++ +e+ + +e+ esl+ ++e l++ v+++e+e+++le 
  gi|313122443|ref|YP_004038330.1| 366 DQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESLKQKREDLTNRVETLESEVEELES 432
                                       5555666667777888999999999999999999999999999999999999999999999999986 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0035
                           DUF3450  34 qsqkkidklddekqellaeyralkeeleslevyneqlerl....vasqeqeiasleeqieeieeierelvpllekmi 106
                                       ++ ++ d+  + +++l+++ ++l++++e le + e+le+     + + ++e ++le +i ++e+  +++   +e++ 
  gi|313122443|ref|YP_004038330.1| 394 SIDEELDRRRERRESLKQKREDLTNRVETLESEVEELESRdygdILERHREANELEFEIGRLENELESVNSEMESVE 470
                                       44455555556666666666666666666666666665543333678899*************************** PP

                           DUF3450 107 drLeqfveldlPflleeRqarlakLkelmdradvslaekyrrvleayqiEaeYgr 161
                                       +rL++  + dl  + ee +++la+L++ ++r + ++ e ++  +e+     +Y++
  gi|313122443|ref|YP_004038330.1| 471 SRLDD--RDDLEARREEIADELADLRTRIERIESEAIEEFNTHMETVLDILDYDN 523
                                       ****9..8*********************************************97 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  29.9     0.024       7.3      17     134 ..     137     257 ..     135     264 .. 0.90
   2 ?    0.9   9.3       1.4   4.5e+02      11     127 ..     259     378 ..     249     379 .. 0.61
   3 ?    3.0  25.6      0.34   1.1e+02      20     138 ..     361     473 ..     342     475 .. 0.75
   4 ?    4.1  11.6      0.16        48      28     118 ..     443     534 ..     437     549 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.024
                     Tropomyosin_1  17 eeleekvKeleqenlekeqeiksLtk...knqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeele 90 
                                       e+++e+++eleqe+ e ++ei+sL     ++ +le++   l+ek++e ++++ee+e++  +++a   + +   +ele
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSLDSldgRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELE 213
                                       7899*****************976533339*********************************9999999999**** PP

                     Tropomyosin_1  91 esdkkLkettekLretdvkaeelERkvkaLeqerdewekkyeel 134
                                       +   +Lk++   L+++    +     + aLe+erde  +  e++
  gi|313122443|ref|YP_004038330.1| 214 NRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDI 257
                                       ***************9999999999**********998877765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.4
                     Tropomyosin_1  11 eaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkea.kekaeesekkktnnealtrkiqlLE 86 
                                       e  + a+e+e+++ +l ++ ++ ++ +++L++ +q  e+ +e +++++  a ++  ++++ +++  e+ t       
  gi|313122443|ref|YP_004038330.1| 259 EEIDGADEIEAQISDLRDQMQRLDSSVNELQTVIQFNEDMLEGTSADVAAAlRDGTDSGSVTDALVESDTVVCWTCG 335
                                       45567899999999999999999999999999999999999988888765513334444444445554444444445 PP

                     Tropomyosin_1  87 eeleesdkkLkettekLretdv....kaeelERkvkaLeqerdew 127
                                        e+e s  +++et+++Lr        + ++l  ++ +Le+erde 
  gi|313122443|ref|YP_004038330.1| 336 TEVETS--QIEETVDRLRSLRRekldQRNDLRDQIDDLESERDEL 378
                                       555544..5777777777542210112233444566666666665 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.34
                     Tropomyosin_1  20 eekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeeleesdkk. 95 
                                       +++++++ ++ +++ +e+++L+++   l++ +  ++e+l   +   e  e++k++ e lt +++ LE e+ee +++ 
  gi|313122443|ref|YP_004038330.1| 361 RNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSIDEELDRRR---ERRESLKQKREDLTNRVETLESEVEELESRd 434
                                       33445555566666789999****************9998765...556678888999***********99988641 PP

                     Tropomyosin_1  96 LkettekLretdvkaeelERkvkaLeqerdewekkyeeleeky 138
                                         + +e+ r    +a+elE ++ +Le+e +  ++ +e +e+++
  gi|313122443|ref|YP_004038330.1| 435 YGDILERHR----EANELEFEIGRLENELESVNSEMESVESRL 473
                                       455555555....577888888888888888888888888775 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.16
                     Tropomyosin_1  28 qenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeel.eesdkkLkettekL 103
                                        e+ e e ei  L++ ++ +++e+e +e++l +  +     e+ + +   l  +i+ +E e+ ee ++++++ ++ L
  gi|313122443|ref|YP_004038330.1| 443 REANELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADELADLRTRIERIESEAiEEFNTHMETVLDIL 519
                                       5677889999999999999999999999999999999888888888888**********775377777777777776 PP

                     Tropomyosin_1 104 retdvkaeelERkvk 118
                                          ++    +ER  +
  gi|313122443|ref|YP_004038330.1| 520 DYDNLDRIWIERTEQ 534
                                       666655555555555 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   3.5      0.12        38      21      46 ..     137     168 ..     130     175 .. 0.77
   2 ?   13.6  12.4   0.00022     0.068       5      65 ..     159     219 ..     155     220 .. 0.94
   3 ?    3.5   1.3      0.31        97      18      64 ..     238     283 ..     232     292 .. 0.59
   4 ?   -1.2  16.2       9.5   2.9e+03       7      34 ..     407     434 ..     376     475 .. 0.47
   5 ?    5.6   1.0     0.071        22       7      43 ..     477     514 ..     477     547 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.12
                              ZapB  21 tlLqmeieeLkeeneelkeenrele......e 46 
                                       ++ q+ei+eL++e++e  +e+  l        
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSLDsldgrlP 168
                                       6789************9999998875554443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00022
                              ZapB   5 lLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                        L+ L  +  ++ ++ t+L+++iee ++e ee ++e++e  + +eq +++r ++++rl+ L
  gi|313122443|ref|YP_004038330.1| 159 SLDSLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVEQTRDDRDELENRLDDL 219
                                       689999999999999*******************************************976 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.31
                              ZapB  18 dtitlLqmeieeLkeeneelkeenrele...eeneqlkeereawqerlkk 64 
                                       + i++L  e +eL  e e   ee++      ++++ l+++ +    rl++
  gi|313122443|ref|YP_004038330.1| 238 ESIDALETERDELTTEREDIPEEIDGADeieAQISDLRDQMQ----RLDS 283
                                       678888888888888888888876655411144444444333....3433 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 9.5
                              ZapB   7 eqLEskiqkaidtitlLqmeieeLkeen 34 
                                       e L +k + + +++++L  e+eeL+ + 
  gi|313122443|ref|YP_004038330.1| 407 ESLKQKREDLTNRVETLESEVEELESRD 434
                                       3344444444444555555555554444 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.071
                              ZapB   7 eqLEskiqkaidtitlLqmeieeLkeen.eelkeenre 43 
                                       + LE++ ++  d+++ L+ +ie+ + e  ee +  ++ 
  gi|313122443|ref|YP_004038330.1| 477 DDLEARREEIADELADLRTRIERIESEAiEEFNTHMET 514
                                       679********************998874444444444 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.81   2.5e+02       4      32 ..     134     162 ..     133     168 .. 0.85
   2 ?    1.2   0.4       1.4   4.4e+02      13      38 ..     195     221 ..     183     228 .. 0.53
   3 ?    5.9   0.2     0.047        15       7      34 ..     265     292 ..     261     310 .. 0.57
   4 ?    1.6   0.2       1.1   3.3e+02       8      39 ..     342     373 ..     336     404 .. 0.66
   5 ?    4.9   0.2       0.1        32      16      85 ..     409     477 ..     394     478 .. 0.76
   6 ?   -0.9   0.0       6.3   1.9e+03      17      38 ..     480     501 ..     476     504 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.81
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   4 vdpeelrqaaarfqkqaeeledelqrlka 32 
                                       +d+e++++ ++++ +++ e+ +e+++l++
  gi|313122443|ref|YP_004038330.1| 134 IDTEAIQEEIRELEQEKREIDNEISSLDS 162
                                       68889999999999999999999998886 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHC.G CS
                            WXG100  13 aarfqkqaeeledelqrlkaevdal.q 38 
                                       + +++++ e+ +d  ++l++ +d+l q
  gi|313122443|ref|YP_004038330.1| 195 IEEADANVEQTRDDRDELENRLDDLkQ 221
                                       444444444444445555544444422 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.047
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaev 34 
                                       +e+++ ++++++q ++l + +++l+  +
  gi|313122443|ref|YP_004038330.1| 265 DEIEAQISDLRDQMQRLDSSVNELQTVI 292
                                       4455555555555555555555555555 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                            WXG100   8 elrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                       +++++  r+++ + e  d+ ++l+ ++d+l+s
  gi|313122443|ref|YP_004038330.1| 342 QIEETVDRLRSLRREKLDQRNDLRDQIDDLES 373
                                       55555555555555555555555555555543 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  16 fqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                       +++++e+l++++++l++ev++l+s   G+  ++ + e +e+  ++ +l ++Le+++++++++ +++ d D
  gi|313122443|ref|YP_004038330.1| 409 LKQKREDLTNRVETLESEVEELESRDYGDILERHR-EANELEFEIGRLENELESVNSEMESVESRLDDRD 477
                                       67889999999999999999996655566555544.4577888888888888888888888887777766 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 6.3
                                       HHHHHHHHHHHHHHHHHHHHCG CS
                            WXG100  17 qkqaeeledelqrlkaevdalq 38 
                                        + +ee+ del++l+  ++ ++
  gi|313122443|ref|YP_004038330.1| 480 EARREEIADELADLRTRIERIE 501
                                       5667888899999888887764 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.2      0.01       3.1      80     130 ..     137     186 ..     132     191 .. 0.90
   2 ?    7.0   4.6      0.02       6.1      35     126 ..     207     293 ..     193     308 .. 0.53
   3 ?    3.9   5.5      0.18        57      29      99 ..     360     429 ..     336     435 .. 0.48
   4 ?    4.4   1.1      0.13        39      37     111 ..     445     519 ..     439     549 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.01
                                       HHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  80 kksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqker 130
                                       + +++e++ e ++ k++id+++s++  L + l ++eqk + L+++i++k++
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIR-ELEQEKREIDNEISSLDSLDGRLPELEQKRTSLKEKIEEKRA 186
                                       56778888.8999999******************************99976 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.02
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                       +d ++len+l+++++  ++ e++  +i+   ++  + +++ d+++++ ++  e ei       d+ e +i  L++ +
  gi|313122443|ref|YP_004038330.1| 207 DDRDELENRLDDLKQARSDLEDVRYDIDAEAESIDALETERDELTTEREDIPE-EID-GA---DEIEAQISDLRDQM 278
                                       44466777777777777777777666666666666666655555544333222.221.11...12223344444444 PP

                                       HHHHHHHHHHHHHHH CS
                         Fib_alpha 112 esneqkiqkLeqdid 126
                                       +++++++++L++ i+
  gi|313122443|ref|YP_004038330.1| 279 QRLDSSVNELQTVIQ 293
                                       444444444444333 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.18
                                       CCCCCCHHHCCCCCC...CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  29 yekdvkkdleklene...leeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketida 99 
                                       +++d+++++++le+e   le+++++    ++  ++i++ l ++ +  +     +k+ +++l +++++l+ ++ +
  gi|313122443|ref|YP_004038330.1| 360 QRNDLRDQIDDLESErdeLEQLHRRRGRLDDRLQSIDEELDRRRERRE----SLKQKREDLTNRVETLESEVEE 429
                                       444555555555433111333333333444444444444433333333....4555555555555555555544 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.13
                                       HCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHHH CS
                         Fib_alpha  37 lekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.snirvLqnvl 111
                                        ++le e+ +++n+ +++++ ++++++ l ++   ++  +++  ++  +l+++i+r++ + ++++ ++++   ++l
  gi|313122443|ref|YP_004038330.1| 445 ANELEFEIGRLENELESVNSEMESVESRLDDRDDLEARREEIADEL-ADLRTRIERIESEAIEEFnTHMETVLDIL 519
                                       5788888889999999999999999999999998888655555555.57888999999888887767776666655 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  17.7      0.17        51      23      74 ..     169     221 ..     110     233 .. 0.57
   2 ?    6.2   2.2     0.041        13      18      84 ..     220     289 ..     216     312 .. 0.44
   3 ?    5.3   7.8     0.073        23      19      94 ..     342     420 ..     338     434 .. 0.61
   4 ?    6.5   0.7     0.032       9.8      20      87 ..     444     512 ..     430     523 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHH CS
                              OmpH  23 qlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqq 74 
                                       +le+k+++l++++e+k++el+++++e++++ ++  ++++++ el+++ ++l+q
  gi|313122443|ref|YP_004038330.1| 169 ELEQKRTSLKEKIEEKRAELEEKEQEIEEADANVeQTRDDRDELENRLDDLKQ 221
                                       33333355555555555555555555554444432344444445555555555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHTTTS.....-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  18 kaaqeqlekkfkklqae......leakekelqklqeelqkkakkle....keekeqelqkkeqelqqkqqqkaqelq 84 
                                       k+a+++le+ + +++ae      le++++el++++e++       e      e e ++ ++++++q+ ++   +elq
  gi|313122443|ref|YP_004038330.1| 220 KQARSDLEDVRYDIDAEaesidaLETERDELTTEREDIP------EeidgADEIEAQISDLRDQMQR-LDSSVNELQ 289
                                       555555555554444440000005555555555555553......3222333334444444444444.222223333 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.073
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS......-HHHHHH....HHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  19 aaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e....keekeqe....lqkkeqelqqkqqqkaqelqkk 86 
                                       +++e +++ ++ ++++l+ ++++l++++++l+ +  +l +    +          lq   +el + ++++++ l++k
  gi|313122443|ref|YP_004038330.1| 342 QIEETVDRLRSLRREKLD-QRNDLRDQIDDLESERDELeQlhrrRG----RlddrLQSIDEELDR-RRERRESLKQK 412
                                       555555555655555555.566666666666655555433333233....223358888888888.77777999999 PP

                                       HHHHHHHH CS
                              OmpH  87 qqellkpi 94 
                                       +++l++++
  gi|313122443|ref|YP_004038330.1| 413 REDLTNRV 420
                                       99999863 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS...-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  20 aqeqlekkfkklqaeleakekelqklqeelqkkakkle..keekeqelqkkeqelqqkqqqkaqelqkkq 87 
                                         ++le ++ +l++ele+ + e+++ + +l+++  +le  +ee + el+++++++++  +++ +e++   
  gi|313122443|ref|YP_004038330.1| 444 EANELEFEIGRLENELESVNSEMESVESRLDDRD-DLEarREEIADELADLRTRIERIESEAIEEFNTHM 512
                                       3345555556666666666666666666664222.21122333333355555555552222225554443 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  11.8    0.0011      0.35      11      66 ..     137     190 ..     134     190 .. 0.92
   2 ?    0.4  12.2       2.5   7.8e+02      11      58 ..     179     227 ..     178     229 .. 0.74
   3 ?   -0.4   5.8       4.6   1.4e+03       9      35 ..     253     282 ..     230     300 .. 0.57
   4 ?    3.0  11.1      0.39   1.2e+02       6      63 ..     374     433 ..     350     433 .. 0.78
   5 ?   11.2   8.7    0.0011      0.34       7      63 ..     442     496 ..     440     514 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0011
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWee 66 
                                       e++ +eI +LE+e+ e+++e+++ +  s + +l el ++ + l++++ee+ ++ ee
  gi|313122443|ref|YP_004038330.1| 137 EAIQEEIRELEQEKREIDNEISSLD--SLDGRLPELEQKRTSLKEKIEEKRAELEE 190
                                       899*******************999..8899*****************99877665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.5
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpelysdp.eklaelsaeleeleaeLe 58 
                                       e++e++ ++LEe+ +e+e++ a+ e + d+ ++l      l++++++Le
  gi|313122443|ref|YP_004038330.1| 179 EKIEEKRAELEEKEQEIEEADANVEQTRDDrDELENRLDDLKQARSDLE 227
                                       6778888888888888888888888776666777777777777777776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 4.6
                      ABC_tran_CTD   9 eleeleaeIe...aLEeeiaeleaeladpe 35 
                                       e e +++eI+   ++E++i++l ++++  +
  gi|313122443|ref|YP_004038330.1| 253 EREDIPEEIDgadEIEAQISDLRDQMQRLD 282
                                       333455555322245555555555555444 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.39
                      ABC_tran_CTD   6 eqreleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelyer 63 
                                       e+ ele+l ++  +L+ +++++++el        +  +k  +l+++ e+le+e eel++r
  gi|313122443|ref|YP_004038330.1| 374 ERDELEQLHRRRGRLDDRLQSIDEELDRRRERRESlkQKREDLTNRVETLESEVEELESR 433
                                       778899999999999999999999888777444445566777777777777777777765 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.0011
                      ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyer 63 
                                        re  ele eI +LE+e+++++ e+++ e  s+ +   +l a+ ee+ +eL+ l  r
  gi|313122443|ref|YP_004038330.1| 442 HREANELEFEIGRLENELESVNSEMESVE--SRLDDRDDLEARREEIADELADLRTR 496
                                       58999*********************999..66666788888888888888776555 PP

>> Baculo_F  Baculovirus F protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   8.3      0.51   1.6e+02      92     240 ..     153     293 ..     134     298 .. 0.51
   2 ?    8.2   7.5    0.0025      0.77      94     231 ..     358     503 ..     336     537 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.51
                          Baculo_F  92 ikkelesi..ikkkienlvekhnsidkklakkseeesleklelekk.vkkrkkRggllnfvGrvdkylfGvmDdkDA 165
                                       i++e++s+  ++ ++++l +k++s+++k+ +k+ e ++++ e+e+   +  + R++  +   r+d+      D +D+
  gi|313122443|ref|YP_004038330.1| 153 IDNEISSLdsLDGRLPELEQKRTSLKEKIEEKRAELEEKEQEIEEAdANVEQTRDDRDELENRLDDLKQARSDLEDV 229
                                       33333332225556666666666666666666555555555555554333333333334444566555555555555 PP

                          Baculo_F 166 elLhklaksenslneqvkqltdeliklseyveskkqeieeqkedkCeyieaklnllkdqldeieslytkldravd 240
                                       +   +     ++  e +  l++e  +l+   e++      ++ d  ++iea+++ l+dq++ ++s  ++l++ ++
  gi|313122443|ref|YP_004038330.1| 230 RY--D----IDAEAESIDALETERDELTTEREDI-----PEEIDGADEIEAQISDLRDQMQRLDSSVNELQTVIQ 293
                                       42..2....2222233333333333333333333.....114566677888888888888888888888888776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                          Baculo_F  94 kelesiikkkienlvekhnsidkklakkseeeslekl...elekk.vkk....rkkRggllnfvGrvdkylfGvmDd 162
                                        +  + + ++i +l +++++++++  ++++ +++ +    el+++   +    ++kR++l n v+++   +  + ++
  gi|313122443|ref|YP_004038330.1| 358 LDQRNDLRDQIDDLESERDELEQLHRRRGRLDDRLQSideELDRRrE-RreslKQKREDLTNRVETLESEVEEL-ES 432
                                       55566688999999999999999999998877444333434444431.1234477777********99998765.55 PP

                          Baculo_F 163 kDAelLhklaksenslneqvkqltdeliklseyveskkqeieeq..kedkCeyieaklnllkdqldeiesl 231
                                       +D     +  ++ n+l+  + +l++el ++ + +es +++++++   e  +e+i+ +l  l++ ++ ies 
  gi|313122443|ref|YP_004038330.1| 433 RDYGDILERHREANELEFEIGRLENELESVNSEMESVESRLDDRddLEARREEIADELADLRTRIERIESE 503
                                       56555559999**************************8888887545567788888888888888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2533  (0.141279); expected 358.6 (0.02)
Passed bias filter:                      992  (0.0553294); expected 358.6 (0.02)
Passed Vit filter:                       285  (0.015896); expected 17.9 (0.001)
Passed Fwd filter:                       205  (0.011434); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              58  [number of targets reported over threshold]
# CPU time: 2.91u 0.45s 00:00:03.36 Elapsed: 00:00:00.81
# Mc/sec: 2421.54
//
Query:       gi|313122444|ref|YP_004038331.1|  [L=776]
Description: hypothetical protein Hbor_36780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.9e-07   29.5   5.1      1e-06   28.5   5.1    1.6  1  PGF-CTERM    PGF-CTERM motif
     0.0005   20.1   3.1     0.0005   20.1   3.1    2.3  3  Trypan_PARP  Procyclic acidic repetitive protein (PARP)
    0.00075   19.6   0.3       0.14   12.3   0.0    3.7  3  bMG6         Bacterial macroglobulin domain 6


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   5.1   1.7e-10     1e-06       1      22 [.     753     774 ..     753     775 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.7e-10
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRR 22 
                                       tPGFG+v+A+++LLaaalL  R
  gi|313122444|ref|YP_004038331.1| 753 TPGFGVVVAIVALLAAALLTIR 774
                                       9****************99655 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.4       1.5   9.2e+03       8      29 ..      12      32 ..       7      45 .. 0.61
   2 ?   -3.0   0.4       1.1   6.8e+03      22      62 ..     134     176 ..     131     177 .. 0.61
   3 !   20.1   3.1   8.3e-08    0.0005      55     130 ..     699     770 ..     677     773 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.5
                       Trypan_PARP  8 llaillfsanlfag.vgfaaaae 29
                                      l a++++s  +fag v fa a+ 
  gi|313122444|ref|YP_004038331.1| 12 LSALMVLS--VFAGtVAFAGASA 32
                                      55555544..7887567776543 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                       Trypan_PARP  22 vgfaaaaegpedkg.ltkggkgkekgtkvsdd.dtngtdpepe 62 
                                       v faa++ gp+ ++   kg     + + v+ d +++gtd e e
  gi|313122444|ref|YP_004038331.1| 134 VAFAATTVGPNGDVnAYKGSIVAVEAASVNTDiEVSGTDDETE 176
                                       7899999888766514466555545555544326677777665 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 8.3e-08
                       Trypan_PARP  55 ngtdpepepepepepepepepepepetepeeepepepepepepepepepepepepepgaatlksvalpfaiaaval 130
                                       n +++    e e e      +e e ete    +e e+e   e e+e e  +e e e g+  +  v   +a+ a+al
  gi|313122444|ref|YP_004038331.1| 699 NVAEVGNMTETETETV----TETETETETTTGTETETETVTETETETETVTETETETGTPGFGVVVAIVALLAAAL 770
                                       3333333333333333....33333334444444455555556666666677777777777777776777777766 PP

>> bMG6  Bacterial macroglobulin domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   2.4e-05      0.14      70     107 ..     266     304 ..     250     308 .. 0.81
   2 ?   -2.9   0.0       1.3   7.6e+03      65      90 ..     328     354 ..     323     375 .. 0.62
   3 ?    2.6   0.0     0.024   1.4e+02      74     101 ..     399     426 ..     388     433 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                              bMG6  70 sgtvdlsaegkaklsl.pvdwGrYrleVedeesgaatsv 107
                                       s t dls +g+ ++sl pv+ G+Y +eV+d +sg++t+ 
  gi|313122444|ref|YP_004038331.1| 266 SVTADLSGQGEYEFSLgPVETGEYTVEVTDLGSGVVTES 304
                                       4456677777888888888**************999975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                              bMG6  65 dkpvasgtvdlsaegkaklslpv.dwG 90 
                                       +  +a+ tv++++ ++a+l++   d G
  gi|313122444|ref|YP_004038331.1| 328 RGDIANITVSIANADEATLTVGSdDVG 354
                                       556677788888888888877654555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.024
                              bMG6  74 dlsaegkaklslpvdwGrYrleVedees 101
                                       + + + + ++s  +d G+Y leV+  ++
  gi|313122444|ref|YP_004038331.1| 399 TSDIDPQNTVSSLLDAGEYDLEVRTGSD 426
                                       44445567888888*********98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (776 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 4736.08
//
Query:       gi|313122445|ref|YP_004038332.1|  [L=146]
Description: hypothetical protein Hbor_36790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1099.57
//
Query:       gi|313122446|ref|YP_004038333.1|  [L=193]
Description: hypothetical protein Hbor_36800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1242.90
//
Query:       gi|313122447|ref|YP_004038334.1|  [L=297]
Description: hydrolase or acyltransferase of alpha/beta superfamily [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-25   89.6   0.3    5.2e-24   85.3   0.3    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
      1e-21   78.6   3.4    1.3e-21   78.3   3.4    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    5.9e-12   45.4   0.0      9e-12   44.8   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
     0.0078   15.7   0.1      0.096   12.1   0.0    2.2  2  Peptidase_S9   Prolyl oligopeptidase family
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.14   12.3   0.0    1.2  1  Thioesterase   Thioesterase domain
       0.16   11.5   0.0        4.4    6.8   0.0    2.6  2  DLH            Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.3   1.7e-27   5.2e-24       1     256 [.      43     285 ..      43     286 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 1.7e-27
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEE CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltl 77 
                                       p++v+lhG p+ ++ w++   +  L ++gf+v+++D+rG+  S+++     d y+t +++dd++ +    g ++ ++
  gi|313122447|ref|YP_004038334.1|  43 PLVVLLHGHPDFWYGWRA--QIISLVEAGFRVVVPDQRGCNLSEAPTGI--DPYRTPNLCDDIRELIHDEGRESAHV 115
                                       78****************..99999999********************9..99***********999999******* PP

                                       EEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHH CS
                     Abhydrolase_1  78 vGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqr 154
                                       vGh++G  +a+++a++ p+ V++l  l+     +++    ++ ++s+    + ++ ++ + p  p +  + +  e  
  gi|313122447|ref|YP_004038334.1| 116 VGHDFGAYVAWNLALRQPSVVNRLGILNV----PHPTVYRDTLRASLRQIVRSWYVWFYQVPKLPEWMLSRNEMENM 188
                                       ************************99999....78888899999999999999999999999998776555554444 PP

                                       HHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC........THHHHSEEEEEEETTCS CS
                     Abhydrolase_1 155 hrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre........lknvlaptlvisgtsDp 223
                                                   + +++  +s++ + +  + + ++  w  t  +++++++r+         + v++ptl+ +g++D 
  gi|313122447|ref|YP_004038334.1| 189 ------------VASLE-VTSNQGTFDEETIHRYRAAWRHTGVGPRINWYRGfrrserpaRNTVTQPTLICWGEDDI 252
                                       ............44444.47789999999*****************************99999************** PP

                                       SSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 224 lvppkaledlaqllpkkrlvvisdagHlafleg 256
                                       +  p +  ++ + + + +l+ ++da H+++ e+
  gi|313122447|ref|YP_004038334.1| 253 ALVPAMAQKSIDYCENGQLRMFPDASHWVHHER 285
                                       *****************************9886 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   3.4   4.3e-25   1.3e-21       1     219 [.      45     290 ..      45     291 .. 0.73

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 4.3e-25
                                       EEEE--...GC.....GCHHHHHHHHCCTCEEEEE--TTS.TS-GGCS--HHHC......HHHHHHHCCTT..TTSE CS
                     Abhydrolase_6   1 vlllHG...agssassWlvapLaallaagvhvlapDlpGh.Grsdpppldledl......adlaalldelaagggpv 67 
                                       v+llHG   +    ++W  a++  l  ag++v++pD +G+    + +p++ +++      +d+++l+++++  +  +
  gi|313122447|ref|YP_004038334.1|  45 VVLLHGhpdF---WYGW-RAQIISLVEAGFRVVVPDQRGCnL--SEAPTGIDPYrtpnlcDDIRELIHDEG--RESA 113
                                       8*****3332...4556.57********************54..666666655333333444488888884..7777 PP

                                       EEEEETCHHHHHHHHHHCC.........EE..EEES-..----TTTS----TTHHHHHHTT-C....CCCHCCH... CS
                     Abhydrolase_6  68 vlvGHSlGGalalaaapla.......lvvg..vlldppptalpagllaaalelllallallrl....lawlsre... 128
                                       ++vGH++G+++a+    la          +  +l  p pt+++++l+a ++++++ ++ ++      ++w+  +   
  gi|313122447|ref|YP_004038334.1| 114 HVVGHDFGAYVAWN---LAlrqpsvvN--RlgILNVPHPTVYRDTLRASLRQIVRSWYVWFYQvpklPEWMLSRnem 185
                                       **************...6666678543..456*******99999999999999997777444444568999444455 PP

                                       ..........S-HSCCCCHHH.CCCCHCHCCCGHHHHCCHHCHTT...CCHHTT-TTGCEEECTT-C..HHHHCHHC CS
                     Abhydrolase_6 129 ..........plprlfladed.adaawrarlarlaallaglgllp...aaawadlpvpllvlggeDp..lvprller 189
                                                 +   + +++e+  +++ ++r++++ +  ++   ++   ++a  +++ p+l+ +geD+  lvp+++++
  gi|313122447|ref|YP_004038334.1| 186 enmvaslevtSNQ-GTFDEETiHRYRAAWRHTGVGPRINWYRGFRrseRPARNTVTQPTLICWGEDDiaLVPAMAQK 261
                                       6677777665222.3333333345888888888888888777443233556666666667768*****999999999 PP

                                       CCH.STTEEETCE...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 190 lla.qagarlpvvlpgaGHlphleepdevae 219
                                            +  +l   +p+a+H++h  e +ev e
  gi|313122447|ref|YP_004038334.1| 262 SIDyCENGQL-RMFPDASHWVHH-EREEVTE 290
                                       9999999999.************.9988876 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0     3e-15     9e-12       6     239 .]      44     286 ..      40     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 3e-15
                       Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrg.hvpsfddyvdDlaafvekvkeehpelplfll 81 
                                       +vvl+HG  +        +  L+++Gf v+  D+rG   se  +g +  ++  ++dD+++++     +++++   ++
  gi|313122447|ref|YP_004038334.1|  44 LVVLLHGHPDFWYGWRAQIISLVEAGFRVVVPDQRGCNLSEAPTGiDPYRTPNLCDDIRELI----HDEGRESAHVV 116
                                       7999****9999888999999********************666648889999******997....4566677899* PP

                       Hydrolase_4  82 GhSmGGliallyllrypdkva.glilsaPalkikakl......kappllklllkllgkllpklqv............ 139
                                       Gh  G+++a +++lr+p+ v+   il  P   +  ++      +   +++            ++v            
  gi|313122447|ref|YP_004038334.1| 117 GHDFGAYVAWNLALRQPSVVNrLGILNVPHPTVYRDTlraslrQ---IVRS-----------WYVwfyqvpklpewm 179
                                       ******************99955588888877776655544431...2222...........222222222233344 PP

                       Hydrolase_4 140 ...........snnlkadslsrdpevvaayeadplv.hgkitvrlllelldamkrleeraakitlPllllhGeaDkv 204
                                                  s ++ +++ + d+e + +y+a     + ++++++++++ +    ++   + +t P+l+  Ge+D  
  gi|313122447|ref|YP_004038334.1| 180 lsrnemenmvaSLEVTSNQGTFDEETIHRYRAAWRHtGVGPRINWYRGFRRSERPAR---NTVTQPTLICWGEDDIA 253
                                       47777777777888899999************9999899*******99988765554...55679************ PP

                       Hydrolase_4 205 vdpeasrelyerlgskdktlklypglyHellnEpd 239
                                         p+ +++ ++ +   + +l+++p + H +++E++
  gi|313122447|ref|YP_004038334.1| 254 LVPAMAQKSIDYCE--NGQLRMFPDASHWVHHERE 286
                                       *************9..7****************85 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.073   2.2e+02       7      25 ..      62      80 ..      55      84 .. 0.78
   2 !   12.1   0.0   3.2e-05     0.096      98     196 ..     194     290 ..     183     297 .] 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.073
                                      HHHHHCCT-EEEEE--TTS CS
                      Peptidase_S9  7 lqlladrGyvvvvanirGs 25
                                      + +l ++G+ vvv++ rG 
  gi|313122447|ref|YP_004038334.1| 62 IISLVEAGFRVVVPDQRGC 80
                                      33445************95 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.2e-05
                                       ---CCCHHCSTTS..THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH-- CS
                      Peptidase_S9  98 vvdvlrydsdtdl..lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkk 172
                                       v+ +  +  ++++  + + + ++g   + +  y+ +   +  ++ ++++p+L++ G+ D   +pa a k ++ +++ 
  gi|313122447|ref|YP_004038334.1| 194 VTSNQGTFDEETIhrYRAAWRHTGVGPRIN-WYRGFRRSERPARNTVTQPTLICWGEDDIALVPAMAQKSIDYCEN- 268
                                       666666666666677777777777764444.4667777766666689***********************999986. PP

                                       S-SEEEEEETTS-SSTTSSHHHH.H CS
                      Peptidase_S9 173 gknvlllifpdegHgvgkprakv.e 196
                                           +l++fpd+ H+v  +r +v e
  gi|313122447|ref|YP_004038334.1| 269 ---GQLRMFPDASHWVHHEREEVtE 290
                                       ...68************88887744 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.7e-05      0.14      51     121 ..      97     160 ..      91     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHCT-SEEEEEEESCCCCCCHHCHHCCCHTTHHT CS
                      Thioesterase  51 laaeyaealrqiqpegPyalfGhSlGgllAfevArqLesqGlavkslflidssapseteaqeasrraedee 121
                                       l++ + e +  +  e   +++Gh +G+++A  +A +   q + v++l++  +++p +   + ++ ra++++
  gi|313122447|ref|YP_004038334.1|  97 LCDDIRELIHDEGRE-SAHVVGHDFGAYVAWNLALR---QPSVVNRLGILNVPHPTV---YRDTLRASLRQ 160
                                       566666666666666.99****************85...8899*********99966...66666666666 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.051   1.5e+02      35      47 ..      64      76 ..      32     141 .. 0.59
   2 ?    6.8   0.0    0.0015       4.4     122     193 ..     218     285 ..     208     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.051
                               DLH 35 rlaeeGYvalaPd 47
                                      +l+e+G+ +++Pd
  gi|313122447|ref|YP_004038334.1| 64 SLVEAGFRVVVPD 76
                                      6677777777776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0015
                               DLH 122 vdaavafYGlspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFands 193
                                       v   + +Y  +  +e  + + + +p l+  ge D       v+ ++++ +++  + +l ++p+a H  + ++
  gi|313122447|ref|YP_004038334.1| 218 VGPRINWYRGFRRSERPARNTVTQPTLICWGEDDIAL----VPAMAQKSIDYCENGQLRMFPDASHWVHHER 285
                                       556678888788888889999***********99654....566899999999*************666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1596.31
//
Query:       gi|313122448|ref|YP_004038335.1|  [L=59]
Description: hypothetical protein Hbor_36820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.47
# Mc/sec: 375.60
//
Query:       gi|313122449|ref|YP_004038336.1|  [L=185]
Description: hypothetical protein Hbor_36830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1299.78
//
Query:       gi|313122450|ref|YP_004038337.1|  [L=134]
Description: hypothetical protein Hbor_36840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 961.53
//
Query:       gi|313122451|ref|YP_004038338.1|  [L=271]
Description: ATPase involved in chromosome partitioning [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-35  121.6   0.0    4.2e-35  121.3   0.0    1.1  1  AAA_31          AAA domain
    1.7e-17   63.7   0.0    2.2e-17   63.3   0.0    1.1  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    3.4e-10   39.8   0.2    5.5e-08   32.6   0.1    2.1  2  ParA            NUBPL iron-transfer P-loop NTPase
    5.1e-07   29.2   1.3    9.2e-05   21.8   0.5    2.6  3  MipZ            ATPase MipZ
    6.9e-06   25.5   0.1    0.00029   20.1   0.1    2.1  2  ArsA_ATPase     Anion-transporting ATPase
    5.7e-05   22.7   0.2      0.001   18.6   0.3    2.1  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
    0.00073   19.1   0.0     0.0022   17.5   0.0    1.7  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
  ------ inclusion threshold ------
      0.013   14.8   0.1      0.024   13.9   0.1    1.3  1  VirC1           VirC1 protein
      0.019   14.8   0.1      0.029   14.2   0.1    1.2  1  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
      0.044   13.8   0.1       0.12   12.4   0.1    1.8  1  Glyco_transf_4  Glycosyltransferase Family 4
      0.075   12.6   0.0       0.16   11.5   0.0    1.6  1  AAA_25          AAA domain
        0.1   12.2   0.1       0.18   11.4   0.1    1.3  1  SRP54           SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.3   0.0   2.8e-38   4.2e-35       2     169 ..       3     175 ..       2     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 2.8e-38
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgie..kneiektlyevli..eeknikeaii 74 
                                       + ++++ qKGGvGKTT ++nla ala +g+ vLlvDlD Q+nat g+g +   ++ e ++ ++l+  + ++++e+i 
  gi|313122451|ref|YP_004038338.1|   3 RAVSVSLQKGGVGKTTVAINLADALAARGNDVLLVDLDQQGNATEGVGRKdlYETEEPHVGDLLTddDPVDVREIIH 79 
                                       6799******************************************9963222336668888887334566677766 PP

                            AAA_31  75 ktkvenldlipssidLaeaeielvelekkeeil.kellekvk.deYDyiiiDcpPsLglltenaLvasdsviipvqa 149
                                         +  + dlip+++dL ++e+++ + +     + ++++e +  +eYDyi+iD pPsLg l + +L+ +  vi+p+ +
  gi|313122451|ref|YP_004038338.1|  80 --DRGEFDLIPAHVDLDDIEDRIRNSTFGVLWVrRRIIEPLLgEEYDYIVIDSPPSLGPLSDASLIGAGNVIVPLLM 154
                                       ..67799****************9999887776588888865277******************************** PP

                            AAA_31 150 eayaleGleqllkt.ieevkk 169
                                       ++ +++G+e+++++ i+ ++k
  gi|313122451|ref|YP_004038338.1| 155 SEPSVSGFERMVEQqIRPIRK 175
                                       **********99742555555 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0   1.5e-20   2.2e-17       5     100 ..       9     205 ..       5     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 1.5e-20
                                       ESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                              CbiA   5 stkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                        +kGGvGKTt+a+nLa ala rg++VllvD+D q+n+++     +++++                            
  gi|313122451|ref|YP_004038338.1|   9 LQKGGVGKTTVAINLADALAARGNDVLLVDLDQQGNATEG----VGRKDLyeteephvgdlltdddpvdvreiihdr 81 
                                       59*************************************3....2222223356789******************** PP

                                       ............................................................................C CS
                                       ............................................................................x RF
                              CbiA  55 ............................................................................d 55 
                                                                                                                   +
  gi|313122451|ref|YP_004038338.1|  82 gefdlipahvdlddiedrirnstfgvlwvrrriiepllgeeydyividsppslgplsdasligagnvivpllmsepS 158
                                       ****************************************************************************9 PP

                                       CHCCCHHHHHHCHCHHHH....EEEEEEEEESS...-TTCHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  56 lkrllellealgkkkall..lkiagvvlnrvdgeneetllkealeel 100
                                       ++ +++++e+  ++ +++  l i+ +v+n   g+nee++++++le  
  gi|313122451|ref|YP_004038338.1| 159 VSGFERMVEQQIRPIRKEvdLGILAIVPNDLSGNNEEKRIIDDLESS 205
                                       99999999998889888899**********************99975 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   3.7e-11   5.5e-08       5      45 ..       4      44 ..       1      61 [. 0.90
   2 !    5.5   0.0    0.0068        10     110     129 ..     121     138 ..     111     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.7e-11
                              ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGp 45
                                       + v+  KGGVGK+tva+nlA aLa++g +v l+D+D  G 
  gi|313122451|ref|YP_004038338.1|  4 AVSVSLQKGGVGKTTVAINLADALAARGNDVLLVDLDQQGN 44
                                      5778889******************************9986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0068
                              ParA 110 gelDyLiiDlPPGtgDeqlt 129
                                       +e Dy++iD PP  g   l+
  gi|313122451|ref|YP_004038338.1| 121 EEYDYIVIDSPPSLG--PLS 138
                                       578*********987..334 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.5   6.2e-08   9.2e-05       3      40 ..       5      42 ..       3      50 .. 0.89
   2 !    5.2   0.0    0.0072        11      96     129 ..     119     152 ..      74     157 .. 0.88
   3 ?   -1.9   0.0         1   1.6e+03     202     233 ..     217     248 ..     213     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.2e-08
                                      EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlr 40
                                      + ++ +kGG Gk+t+a+ +a aL+++G  v  +dld +
  gi|313122451|ref|YP_004038338.1|  5 VSVSLQKGGVGKTTVAINLADALAARGNDVLLVDLDQQ 42
                                      567789******************************86 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0072
                                       HHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEE CS
                              MipZ  96 leaeldfividtPGsdsalsrlahsladtlvtPl 129
                                       l +e+d+ivid+P s  +ls  +   a  ++ Pl
  gi|313122451|ref|YP_004038338.1| 119 LGEEYDYIVIDSPPSLGPLSDASLIGAGNVIVPL 152
                                       5689***************999999999999998 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1
                                       HHHHT-EEE---B--GGGTTTGGGT--GGGSS CS
                              MipZ 202 skrvGfrvasGlserviyrelfpsGltlldlk 233
                                       s r G    +Gl+ r+ +   +  G tl + +
  gi|313122451|ref|YP_004038338.1| 217 SERFGESPGPGLRHRIAFSRAWRDGETLREYD 248
                                       6788888899******9999999999987554 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   1.9e-07   0.00029       9      38 ..      11      40 ..       4      56 .. 0.93
   2 ?    3.2   0.0     0.028        43     121     135 ..     119     133 ..     108     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.9e-07
                                      STTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  9 KGGVGKttvsaatavklsekgkkvllistD 38
                                      KGGVGKttv+  +a  l+  g++vll+ +D
  gi|313122451|ref|YP_004038338.1| 11 KGGVGKTTVAINLADALAARGNDVLLVDLD 40
                                      9**************************998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.028
                                       HCSSSSEEEEESBSC CS
                       ArsA_ATPase 121 keeeydvvvlDtaPT 135
                                        +eeyd++v+D++P 
  gi|313122451|ref|YP_004038338.1| 119 LGEEYDYIVIDSPPS 133
                                       479**********95 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3     7e-07     0.001      10      39 ..      11      40 ..       3      45 .. 0.91
   2 ?    1.8   0.0     0.093   1.4e+02     112     136 ..     119     143 ..      86     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7e-07
                          CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDls 39
                                      +GGvG+t+++  La+al + g+ vl++Dl 
  gi|313122451|ref|YP_004038338.1| 11 KGGVGKTTVAINLADALAARGNDVLLVDLD 40
                                      7***************************85 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.093
                          CBP_BcsQ 112 lkeqyrwillDlpagasaltrella 136
                                       l e+y++i++D p    +l  + l 
  gi|313122451|ref|YP_004038338.1| 119 LGEEYDYIVIDSPPSLGPLSDASLI 143
                                       5699*********999988776655 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.5e-06    0.0022       8      44 ..      11      47 ..       4      80 .. 0.85
   2 ?   -1.9   0.0       1.2   1.8e+03     221     245 ..     241     265 ..     234     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                         Fer4_NifH  8 kGGiGksttsqnlsaalaemgkkvlivGCDPkaDstr 44
                                      kGG+Gk+t + nl+ ala++g+ vl+v  D + ++t 
  gi|313122451|ref|YP_004038338.1| 11 KGGVGKTTVAINLADALAARGNDVLLVDLDQQGNATE 47
                                      9***************************999988885 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                         Fer4_NifH 221 kktvieyapeseqakeyrelarkil 245
                                        +t+ ey+p+s++ +   +la+ + 
  gi|313122451|ref|YP_004038338.1| 241 GETLREYDPNSDMLDRLDKLAQVVE 265
                                       689999******9999999998765 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.6e-05     0.024       6      40 ..       7      41 ..       2      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                             VirC1  6 fcslkGGaGkttalmglcsalasdgkrvalfeade 40
                                      ++  kGG Gktt  + l  ala++g+ v l + d+
  gi|313122451|ref|YP_004038338.1|  7 VSLQKGGVGKTTVAINLADALAARGNDVLLVDLDQ 41
                                      45569*************************99987 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     2e-05     0.029       4      31 ..      13      40 ..      11      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                       +GK+T+a +L++ ++ +g+ +++vDlD
  gi|313122451|ref|YP_004038338.1| 13 GVGKTTVAINLADALAARGNDVLLVDLD 40
                                      59************************** PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.9e-05      0.12       5      76 ..      17      87 ..      12     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                    Glyco_transf_4  5 erhvleLaraLarrGheVtvvtpgddgpleeev..elvvrvprvplpllkrllrslaflrrlrrllkre.kpDvv 76
                                       +++ +La aLa+rG +V +v  +++g + e v  +      +    ++ + l++   + ++r++++   ++D++
  gi|313122451|ref|YP_004038338.1| 17 TTVAINLADALAARGNDVLLVDLDQQGNATEGVgrK----DLYETEEPHVGDLLTDDDPVDVREIIHDRgEFDLI 87
                                      68999****************766666666663321....11111122222233334444555555544455555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.16      41      65 ..      11      36 ..       2      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                            AAA_25 41 apgtGKttlaldlalava.tGkpwlg 65
                                       +g+GKtt+a++la a+a +G  +l 
  gi|313122451|ref|YP_004038338.1| 11 KGGVGKTTVAINLADALAaRGNDVLL 36
                                      58****************88887654 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.18      11      39 ..      13      41 ..       6      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      TSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54 11 GaGKTttlaKLaallkkegkkvllvaaDt 39
                                      G+GKTt +  La+ l ++g++vllv +D 
  gi|313122451|ref|YP_004038338.1| 13 GVGKTTVAINLADALAARGNDVLLVDLDQ 41
                                      9************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1972.78
//
Query:       gi|313122452|ref|YP_004038339.1|  [L=942]
Description: transglutaminase-like enzyme, cysteine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-31  107.0   0.0    1.5e-30  105.9   0.0    1.6  1  Transglut_core   Transglutaminase-like superfamily
    7.3e-05   22.9   0.4    7.3e-05   22.9   0.4    2.7  2  DUF4129          Domain of unknown function (DUF4129)
     0.0019   17.2   0.4     0.0033   16.4   0.4    1.3  1  DUF3488          Domain of unknown function (DUF3488)
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.063   13.2   0.0    2.1  1  Transglut_core3  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.0   3.4e-34   1.5e-30       2     112 .]     233     346 ..     232     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 3.4e-34
                    Transglut_core   2 alaeeltagakdplekakaiyewvrknveysaprrtpgsrdaeavle.tgkGncedfaslfvallRalGipaRvvtg 77 
                                       +l++++ta+a++p+eka+ai++++++n +ys + + +g++ ++++l+    G+ce fas ++++lR   ipaR+v+g
  gi|313122452|ref|YP_004038339.1| 233 SLTADITANASTPYEKAVAIERYLESNKDYSLSASHDGDDPVSSFLFeMDDGYCEYFASSMAVMLRTQDIPARYVVG 309
                                       6899*******************************************8888************************** PP

                    Transglut_core  78 ylsgeeekeq..svasedaHawvevylegygWvplDp 112
                                       y sge ++++  +v++ +aHawvevy+++ gWv++Dp
  gi|313122452|ref|YP_004038339.1| 310 YSSGELTGDNtyTVRNMNAHAWVEVYFPDVGWVRFDP 346
                                       *****99999**************************9 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.1      0.54   2.4e+03      13      35 ..     735     765 ..     732     835 .. 0.61
   2 !   22.9   0.4   1.6e-08   7.3e-05       8      59 ..     854     907 ..     847     919 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.54
                           DUF4129  13 gldrrpgeTprEyarrv.riaps........p 35 
                                       g  +r+g +p  y+ ++   + s         
  gi|313122452|ref|YP_004038339.1| 735 GTAYRRGSSPLAYLSALrS-RASalldtllgV 765
                                       5678899999999998842.222234444440 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.6e-08
                           DUF4129   8 aLaer.gldrrpgeTprEyarrv.riapspaaalaalaelfeearYGgrpasae 59 
                                         + +  +++++++Tp+E+a+++ ++ + pa+++  + + f+++ YGgr ++  
  gi|313122452|ref|YP_004038339.1| 854 EFRGHvTVPKQASRTPGELAAHAvEADGLPAEPVFVIRDGFRDVEYGGRSPTDR 907
                                       5566667999**************999**********************99975 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   7.3e-07    0.0033     216     317 ..      96     195 ..      89     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.3e-07
                           DUF3488 216 fegavppqselYWRglvleefdGrtWaekaraekkaaslets.gepakgkavrYevtlePsqqrwlfaLdvp....a 287
                                       f+ +  +++  YWR+  + ++ G  W    ++++++++++ + +++a+g+++ Y+v l+ s +  l++   p     
  gi|313122452|ref|YP_004038339.1|  96 FTVE--SPESAYWRTGSYATYSGSGW----EQTTDSQPYSGDiSPAARGERMTYRVSLKTSATA-LPTAWRPntvnL 165
                                       4444..78999***************....23333333333346677899********998876.777777744432 PP

                           DUF3488 288 sapeevrlsadlqllsrrpvtqrirYrlrs 317
                                        +++++++++   ++++  +++ + Y+++s
  gi|313122452|ref|YP_004038339.1| 166 DSDTDLAVTEGRAVTASSGLDAGTTYTAES 195
                                       222366666666677777777778888777 PP

>> Transglut_core3  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.063      57      97 ..     285     334 ..     221     336 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                   Transglut_core3  57 kCLpralalalllrrrgipatlviGvrkedd.........pfaaHAWvev 97 
                                        C   a  +a++lr + ipa+ v+G    +          +++aHAWvev
  gi|313122452|ref|YP_004038339.1| 285 YCEYFASSMAVMLRTQDIPARYVVGYSSGELtgdntytvrNMNAHAWVEV 334
                                       677778999****************9887545667788888*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (942 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 6594.42
//
Query:       gi|313122453|ref|YP_004038340.1|  [L=258]
Description: hypothetical protein Hbor_36870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.022   14.7   0.2        7.6    6.6   0.1    2.3  2  HLH         Helix-loop-helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HLH  Helix-loop-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0   0.00073        13      10      28 ..      62      80 ..      61     108 .. 0.85
   2 ?    6.6   0.1   0.00043       7.6      10      36 ..     180     207 ..     175     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00073
                                      HHHHHHHHHHHHHHHHCST CS
                               HLH 10 rrRRdriNsaleeLrellP 28
                                      rrR  +  +++ eLre+ P
  gi|313122453|ref|YP_004038340.1| 62 RRRASSTSDRFTELREMPP 80
                                      99**************988 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00043
                                       HHHHHHHHHHHHHHHHC.STCSTTSS-S CS
                               HLH  10 rrRRdriNsaleeLrel.lPslppskKl 36 
                                       rrR+d   +al+eLre  +P++++s++l
  gi|313122453|ref|YP_004038340.1| 180 RRRVDATLDALFELREGvVPASEDSERL 207
                                       66779999*******9868877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1739.41
//
Query:       gi|313122454|ref|YP_004038341.1|  [L=462]
Description: hypothetical protein Hbor_36880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-16   60.2   1.6    3.4e-16   59.3   0.3    2.2  2  DUF58        Protein of unknown function DUF58
    8.6e-09   35.6   2.5      0.002   18.4   0.0    2.9  2  DUF11        Domain of unknown function DUF11
     0.0009   19.5   2.0      0.051   13.8   0.2    3.0  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
     0.0084   16.4   0.0       0.02   15.2   0.0    1.6  1  CARDB        CARDB
  ------ inclusion threshold ------
      0.015   15.4   0.6        7.5    6.7   0.0    3.1  3  Fn3-like     Fibronectin type III-like domain


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.4   8.8e+03      41      63 ..      74      96 ..      71     104 .. 0.72
   2 !   59.3   0.3   9.5e-20   3.4e-16       1      84 [.     208     293 ..     208     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                             DUF58 41 rtvllvldlspemslgstgdekl 63
                                       tv+l + +s+   ++s++d++ 
  gi|313122454|ref|YP_004038341.1| 74 VTVTLTVENSSATESSSATDDAS 96
                                      57888888888877777766655 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 9.5e-20
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg..dekletavsaaaslar 75 
                                       gl+f+++ReY++gDpl+r+dW+  A+tgel + ef +++a++v +v d+++ m+  + +   ++ e +++aa+   r
  gi|313122454|ref|YP_004038341.1| 208 GLEFHSTREYRSGDPLSRVDWRHLAKTGELTTVEFREQQASRVAVVADAREPMRAVAGPgrPTAAELCAYAALRTHR 284
                                       689**************************************************987665889999999999999999 PP

                             DUF58  76 qlldegdrv 84 
                                       +l + g+ v
  gi|313122454|ref|YP_004038341.1| 285 TLTADGHDV 293
                                       888888877 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.6e-07     0.002       1      30 [.      59      88 ..      59      93 .. 0.89
   2 !   15.7   0.6   3.8e-06     0.014      26      80 ..      99     145 ..      94     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.6e-07
                             DUF11  1 ltKtvdksevrpGdtvtytltvtNtgpasa 30
                                      +++ +d+++++pG+ vt+tltv N++++ +
  gi|313122454|ref|YP_004038341.1| 59 IRREFDPVAPAPGERVTVTLTVENSSATES 88
                                      6899**********************9876 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.8e-06
                             DUF11  26 gpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                       g++++++v+v D +Pa+la  s+s +         + sL++ge+ t+++ v +tr
  gi|313122454|ref|YP_004038341.1|  99 GGRTLTDVRVVDGVPAALAVESGSPR--------ASLSLAPGETETVTYDVVATR 145
                                       899****************9999999........3369*************9987 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.018        64       3      18 ..      70      85 ..      68      91 .. 0.67
   2 !   13.8   0.2   1.4e-05     0.051      12      69 ..      94     151 ..      87     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.018
                       NPCBM_assoc  3 pGetvtltltvtndgt 18
                                      pGe+vt+tltv n+  
  gi|313122454|ref|YP_004038341.1| 70 PGERVTVTLTVENSSA 85
                                      6777777777777653 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.4e-05
                       NPCBM_assoc  12 tvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGd 69 
                                        +++dg++++t+v++   +P+   v++ sp+   slapGet ++t +V +  g +a+d
  gi|313122454|ref|YP_004038341.1|  94 DASDDGGRTLTDVRVVDGVPAALAVESGSPRASLSLAPGETETVTYDVVATRGDFAFD 151
                                       5789********************9999999888**************9999988887 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.5e-06      0.02       4      72 ..      57     144 ..      54     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.5e-06
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEE..................SEE-CTE CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtv..................psLaage 61 
                                       L +  ++ p ++ +ge +t+t+tv+N+   +s + + +   dg  + ++v v                   sLa+ge
  gi|313122454|ref|YP_004038341.1|  57 LGIRREFDPVAPAPGERVTVTLTVENSSATESSSATDDASDDGGRTlTDVRVvdgvpaalavesgsprasLSLAPGE 133
                                       67788899999****************98887777777777666655889989****99999999999998999999 PP

                                       EEEEEEEEE-S CS
                             CARDB  62 sttvsftwtte 72 
                                       ++tv++ ++++
  gi|313122454|ref|YP_004038341.1| 134 TETVTYDVVAT 144
                                       99999988765 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0049        18      23      44 ..      62      83 ..      61     120 .. 0.82
   2 ?    6.7   0.0    0.0021       7.5      28      43 ..     128     143 ..     125     169 .. 0.76
   3 ?   -2.6   0.0       1.7   6.1e+03      31      54 ..     234     258 ..     232     266 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0049
                                      EEEEEEE-TT-EEEEEEEEECG CS
                          Fn3-like 23 gFekveLapGesktvtftldrk 44
                                       F+ v+ apGe  tvt+t++ +
  gi|313122454|ref|YP_004038341.1| 62 EFDPVAPAPGERVTVTLTVENS 83
                                      68888889**********9974 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0021
                                       EE-TT-EEEEEEEEEC CS
                          Fn3-like  28 eLapGesktvtftldr 43 
                                       +LapGe++tvt ++ +
  gi|313122454|ref|YP_004038341.1| 128 SLAPGETETVTYDVVA 143
                                       79*********98754 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.7
                                       TT-EEEEEEEEEC.GGG-EEETTTT CS
                          Fn3-like  31 pGesktvtftldr.kdlsvwdeekq 54 
                                        Ge +tv+f+ ++ ++++v+ + ++
  gi|313122454|ref|YP_004038341.1| 234 TGELTTVEFREQQaSRVAVVADARE 258
                                       5888888887665467777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 3081.66
//
Query:       gi|313122455|ref|YP_004038342.1|  [L=541]
Description: hypothetical protein Hbor_36890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3557.14
//
Query:       gi|313122456|ref|YP_004038343.1|  [L=183]
Description: acetyltransferase, ribosomal protein N-acetylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-22   79.0   0.0    6.4e-22   78.7   0.0    1.1  1  Acetyltransf_3  Acetyltransferase (GNAT) domain
    1.9e-11   44.3   0.0    2.6e-11   43.9   0.0    1.0  1  Acetyltransf_4  Acetyltransferase (GNAT) domain
    4.2e-08   33.4   0.0    5.3e-08   33.1   0.0    1.2  1  Acetyltransf_1  Acetyltransferase (GNAT) family
    1.9e-06   27.6   0.0    4.1e-06   26.5   0.0    1.5  1  Acetyltransf_8  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.038   13.9   0.0      0.089   12.8   0.0    1.7  2  FR47            FR47-like protein
       0.14   12.4   0.0       0.17   12.1   0.0    1.2  1  Lys             C-type lysozyme/alpha-lactalbumin family


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.0   2.1e-25   6.4e-22       4     138 .]      14     150 ..      12     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 2.1e-25
                    Acetyltransf_3   4 LrplteeDlealfelrsdpevmry..lpepltleeaeewlerawaeeseeegygwaivlkdtgv.iGsvglrdleee 77 
                                       L p+ ++Dl+ l    +dp+v++   ++ p++ + a+++l  ++    +ee +g++i+  d+ + +G+v l + +++
  gi|313122456|ref|YP_004038343.1|  14 LCPADQSDLNFLRTHENDPRVRKTrtVRFPTSTDHATTRLGGTMG--RNEETVGLVIR-ADD-EsVGFVYLLREDPN 86 
                                       45666667777755689*****97556669999999999997654..45678899994.444.55****88776666 PP

                    Acetyltransf_3  78 dee...aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                             ael y++a ++w  Gyat a++ +++y f+elgl+r+ a + ++Ne S rvlek+Gfe
  gi|313122456|ref|YP_004038343.1|  87 AIDfryAELAYWIAYEHWDAGYATAAAKTMVKYGFDELGLHRITASTLASNESSKRVLEKVGFE 150
                                       444899*********************************************************7 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   8.7e-15   2.6e-11       5     153 ..      18     168 ..      15     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 8.7e-15
                    Acetyltransf_4   5 teeDakeilaiyaeyvvntaitfeyevssveefekfleal.dsekeyvflvae.sdrivGyaylgqfkkr.akdwka 78 
                                        ++D++ ++   ++++v++  t +    s + + ++l  + +  +e v lv+  +d+ vG  yl   ++       a
  gi|313122456|ref|YP_004038343.1|  18 DQSDLNFLRTHENDPRVRKTRTVRF-PTSTDHATTRLGGTmGRNEETVGLVIRaDDESVGFVYLLREDPNaIDFRYA 93 
                                       6899999999999999999888874.45566677******88888999999999**********988888678899* PP

                    Acetyltransf_4  79 elsvylaerdnnkeglgrelidaleqvl.keqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiDm 153
                                       el +++a     ++g++ +  + ++++   e ++++++a++ ++ne+s+ +++++GFe +g  ++  +  g+w D 
  gi|313122456|ref|YP_004038343.1|  94 ELAYWIA-YEHWDAGYATAAAKTMVKYGfDELGLHRITASTLASNESSKRVLEKVGFEREGVAREEVYTDGEWHDR 168
                                       ******9.679***********9999988*********************************************97 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.8e-11   5.3e-08      31     117 .]      60     149 ..      26     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.8e-11
                                       TTC.EEEEEEETTEEEEEEEEEEEET.TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETT CS
                    Acetyltransf_1  31 eae.gllvaeedgeliGfisllkipd.ekggvayieslaVspeyrgkGlGsaLlealeeraree.gikkivlaveed 104
                                       ++e  +lv++ d+e +Gf+ ll  ++     +++   ++++ e++  G+++a  ++++++ ++e g+++i + + ++
  gi|313122456|ref|YP_004038343.1|  60 NEEtVGLVIRADDESVGFVYLLREDPnAIDFRYAELAYWIAYEHWDAGYATAAAKTMVKYGFDElGLHRITASTLAS 136
                                       333467779999*******88888888555778888***************************************** PP

                                       EHHHHHHHHHTTE CS
                    Acetyltransf_1 105 ndaairlYeklGF 117
                                       n+ + r++ek+GF
  gi|313122456|ref|YP_004038343.1| 137 NESSKRVLEKVGF 149
                                       ************9 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.4e-09   4.1e-06       3     141 ..      19     153 ..      18     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.4e-09
                                       GGGHHHHHHHCTSCCCHHHH-----H.HHHHHHHH..HHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS--- CS
                    Acetyltransf_8   3 eaDlellhrWmnrprvaewweeagtl.eevrella..kldadphsepliglldgepvgyfeiYwakedelaeyydae 76 
                                       ++Dl+ l++  n+prv+++     +  ++++ ++   ++ +++++  l+++ d+e vg++  Y  +ed+    +  +
  gi|313122456|ref|YP_004038343.1|  19 QSDLNFLRTHENDPRVRKTRTVRFPTsTDHATTRLggTMGRNEETVGLVIRADDESVGFV--YLLREDP----NAID 89 
                                       5788888888999999999988886655555544333777899999999999***99996..7788995....5666 PP

                                       TT-EEEEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  77 pgdrGiHlligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                            + ++i+  e+   g++ta  +++v+y f++ +  r+ +   ++Ne + r+lek+Gfe+e+
  gi|313122456|ref|YP_004038343.1|  90 FRYAELAYWIAY-EHWDAGYATAAAKTMVKYGFDELGLHRITASTLASNESSKRVLEKVGFEREG 153
                                       667778899995.55689********************************************987 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   6.1e+03      54      66 ..      61      73 ..      53      83 .. 0.55
   2 ?   12.8   0.0     3e-05     0.089      32      80 ..     102     152 ..      93     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                      -S-EEEEEETT-H CS
                              FR47 54 gktvllvvvasNt 66
                                      ++tv lv++a+++
  gi|313122456|ref|YP_004038343.1| 61 EETVGLVIRADDE 73
                                      4444555555443 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3e-05
                                       GG-SSSHHHHHHHHHHH.HHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  32 ehrrrGlgsrlvkalak.eiaerg.ktvllvvvasNtpsirlyeklGfeki 80 
                                       eh   G+++  +k + k +  e g + +++ + asN+ s r++ek+Gfe  
  gi|313122456|ref|YP_004038343.1| 102 EHWDAGYATAAAKTMVKyGFDELGlHRITASTLASNESSKRVLEKVGFERE 152
                                       566678888888877652566666367999******************975 PP

>> Lys  C-type lysozyme/alpha-lactalbumin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.8e-05      0.17      19      76 ..      89     147 ..      80     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.8e-05
                                       TGGGB-HHHHHHHHHHHHTTBTT-EEEET.TSEEEETTTTEETTTTSBBSSCTTS--TT CS
                               Lys  19 gykgvslaewvClaehesgydtkavvkna.ngstdyGlfqindklwCkdsktpksknaC 76 
                                       +++  +la w+   ++++gy t a ++    g  + Gl +i   +  ++++ ++  ++ 
  gi|313122456|ref|YP_004038343.1|  89 DFRYAELAYWIAYEHWDAGYATAAAKTMVkYGFDELGLHRITASTLASNESSKRVLEKV 147
                                       59999******************99888768999*******999998888877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1200.71
//
Query:       gi|313122457|ref|YP_004038344.1|  [L=232]
Description: hypothetical protein Hbor_36910 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.6e-39  133.2  17.2    7.6e-39  133.2  17.2    1.6  2  DUF4013        Protein of unknown function (DUF4013)
  ------ inclusion threshold ------
          1    9.7  12.8        2.4    8.4   0.0    3.5  3  Adeno_E3B      Adenovirus E3B protein
        1.1    8.2   3.8       0.22   10.6   0.1    1.6  2  Man-6-P_recep  Mannose-6-phosphate receptor


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2  17.2   1.3e-42   7.6e-39       3     167 ..      25     184 ..      23     185 .. 0.88
   2 ?    0.8   0.4     0.065   3.9e+02      47      77 ..     181     211 ..     179     221 .. 0.59

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 1.3e-42
                           DUF4013   3 sllliiaivlslvllGYlvrvlrdtirgddelPefddwgkllvdGlkafvvslvYllipliialltllvalaslaag 79 
                                       +++ +i++v++++l+GYlvrvl++t++g+ e+P fddwgk++vdGlkaf v+lvY+++p+++   ++++++++l++g
  gi|313122457|ref|YP_004038344.1|  25 LIFGFILVVPVFLLYGYLVRVLEATAHGKPEPPAFDDWGKMFVDGLKAFGVTLVYGFVPFAL---MGASLGVGLSGG 98 
                                       68888999999999************************************************...444444444444 PP

                           DUF4013  80 dsaa.gallvlallglllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllvi 155
                                       +s+   a+++l+ +g+l + ++++++++ +++l+p+al+++a ++s++aaf+++++ +++ +   +y++a+i+ +++
  gi|313122457|ref|YP_004038344.1|  99 ASGSdTAAGLLGGIGALGFGVSFFAMFI-IYYLVPAALTNMAVEDSFGAAFDISRLKDVLLSA--DYFVAWIIPFLL 172
                                       444446777778888888888888****.*******************************885..9*********** PP

                           DUF4013 156 givlsllaillv 167
                                       ++v+++l+++lv
  gi|313122457|ref|YP_004038344.1| 173 AFVAYVLTGFLV 184
                                       *********997 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.065
                           DUF4013  47 Glka.fvvslvYllipliialltllvalasla 77 
                                       G+ + + +++  ll+p+i  ++t+++++ ++ 
  gi|313122457|ref|YP_004038344.1| 181 GFLVaITIGIGTLLVPTIQ-FYTNVAVFYMFG 211
                                       5553366666666777777.555555555554 PP

>> Adeno_E3B  Adenovirus E3B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.6      0.07   4.2e+02      13      25 ..      34      46 ..      23      50 .. 0.79
   2 ?    8.4   0.0    0.0004       2.4       5      28 ..      66      89 ..      63      96 .. 0.83
   3 ?    4.1   3.9    0.0095        56      11      47 ..     173     208 ..     160     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.07
                         Adeno_E3B 13 tvyllygfvtlil 25
                                       v+llyg++  +l
  gi|313122457|ref|YP_004038344.1| 34 PVFLLYGYLVRVL 46
                                      5899999987665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0004
                         Adeno_E3B  5 evdcippftvyllygfvtlilics 28
                                       vd +  f v l+ygfv + l+ +
  gi|313122457|ref|YP_004038344.1| 66 FVDGLKAFGVTLVYGFVPFALMGA 89
                                      58999************9988754 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0095
                         Adeno_E3B  11 pftvyllygfvtlilicslvtvviafiqfidwvcvri 47 
                                        f  y+l gf+  i i  + t+++  iqf   v v  
  gi|313122457|ref|YP_004038344.1| 173 AFVAYVLTGFLVAITI-GIGTLLVPTIQFYTNVAVFY 208
                                       5889******999988.588999999***99888865 PP

>> Man-6-P_recep  Mannose-6-phosphate receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   3.7e-05      0.22     162     216 ..      18      69 ..      12      78 .. 0.85
   2 ?   -2.9   0.6      0.47   2.8e+03     178     188 ..     175     185 ..     165     214 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.7e-05
                     Man-6-P_recep 162 klsvGsillivllslvavyligGflyqrlvvgakGleqiPnyafWqdlGnlvadG 216
                                       ++ +Gs+l+  ++ +v v+l+ G+l + l   a G    P +  W   G++  dG
  gi|313122457|ref|YP_004038344.1|  18 RIVIGSLLIFGFILVVPVFLLYGYLVRVLEATAHGKPEPPAFDDW---GKMFVDG 69 
                                       5789*************************9*****9999998777...5555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.47
                     Man-6-P_recep 178 avyligGflyq 188
                                        +y+++Gfl  
  gi|313122457|ref|YP_004038344.1| 175 VAYVLTGFLVA 185
                                       45677777643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1619.90
//
Query:       gi|313122458|ref|YP_004038345.1|  [L=94]
Description: hypothetical protein Hbor_36920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 636.54
//
Query:       gi|313122459|ref|YP_004038346.1|  [L=122]
Description: hypothetical protein Hbor_36930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.086   13.1   0.1       0.29   11.4   0.0    1.8  2  Catalase-rel  Catalase-related immune-responsive


Domain annotation for each model (and alignments):
>> Catalase-rel  Catalase-related immune-responsive
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.6e-05      0.29      13      38 ..      10      35 ..       6      44 .. 0.89
   2 ?   -1.4   0.0      0.16   2.8e+03      25      36 ..      85      96 ..      79     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.6e-05
                                      HHHHHS-HHHHHHHHHHHHHHHTTSS CS
                      Catalase-rel 13 llyrsmseeekerlvnniafelskve 38
                                      +ly+ +seee+e+++++++++l+ v+
  gi|313122459|ref|YP_004038346.1| 10 ELYEQLSEEEREDFFHRLSGDLDWVS 35
                                      79*******************98776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.16
                                      HHHHHHHHHHTT CS
                      Catalase-rel 25 rlvnniafelsk 36
                                      ++ +ni+++  +
  gi|313122459|ref|YP_004038346.1| 85 HITTNIVNHHRG 96
                                      788999998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 848.40
//
Query:       gi|313122460|ref|YP_004038347.1|  [L=53]
Description: hypothetical protein Hbor_36940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.025   14.4   0.0    1.1  1  DUF2017   Domain of unknown function (DUF2017)


Domain annotation for each model (and alignments):
>> DUF2017  Domain of unknown function (DUF2017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-06     0.025     121     150 ..      11      40 ..       4      52 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-06
                           DUF2017 121 wlaaLnDvRlalgtrlgieeeedaeleelp 150
                                       + a+LnD+R a+g++l + e e+++  +  
  gi|313122460|ref|YP_004038347.1|  11 LRATLNDLRQAVGEALVVVEAEESTGLSTR 40 
                                       5689*************9999985532222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 373.94
//
Query:       gi|313122461|ref|YP_004038348.1|  [L=466]
Description: dienelactone hydrolase-like enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-39  135.5   0.0    5.4e-39  134.3   0.0    1.5  1  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin
    4.9e-28   97.7   0.0    7.5e-28   97.1   0.0    1.3  1  Bile_Hydr_Trans  Acyl-CoA thioester hydrolase/BAAT N-terminal
     0.0021   17.7   0.1       0.14   11.7   0.2    2.6  2  DLH              Dienelactone hydrolase family
     0.0063   15.5   0.0      0.011   14.7   0.0    1.3  1  Chlorophyllase2  Chlorophyllase enzyme
  ------ inclusion threshold ------
       0.01   14.9   0.0       0.02   13.9   0.0    1.4  1  Chlorophyllase   Chlorophyllase


Domain annotation for each model (and alignments):
>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   0.0   1.5e-42   5.4e-39       1     204 [.     235     458 ..     235     465 .. 0.84

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 1.5e-42
                                       EECHHHHHHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE......... CS
                            BAAT_C   1 vdleYFeeainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdes........ 69 
                                       v+leY ++++++l+++p v    +gllG+SkG+elall +++++ + av ++++s +v +g  +  + +        
  gi|313122461|ref|YP_004038348.1| 235 VPLEYLQRGYDWLTSRPAVRDGSVGLLGTSKGAELALLAGATFDWVGAVAAYAPSGIVWAGLTYGGEMTsswtldgd 311
                                       89*********************************************************99999888878999***6 PP

                                       .......EE----B-GGG-EE....-TTS-EE-TT-B--TTTGGGCCCB--GGG--SEEEEEEETT-SSS-HHHHHH CS
                            BAAT_C  70 ......kvlpelklsmeklkv....nknglldivdvlallkeklaekalipvekakgpillvvgedDknwpSkesae 136
                                              ++p+  +    +++      + +  +   l++   +  ++a ipve+++gp+ lv+g dD++wpS++  +
  gi|313122461|ref|YP_004038348.1| 312 pvpfvpTAFPPSVIADYVASWplggSVSLRPTYEVGLEQASTERISEATIPVENIDGPVTLVSGGDDRLWPSATFGR 388
                                       6555554444444444444456654333333333344555556668899**************************** PP

                                       HHHHHHHCTT--.--EEEEETTB-S---STT-----..EEEETTTTEEEE--B-HHHHHHHHHHHHHHHH CS
                            BAAT_C 137 kaserLkkagkkvevqlltYpkaGHliepPyfplce..avlaklvgekvlyGGetkahakAqedsWkkil 204
                                       ++++rL+++++++ v+++t + aGH+i +Py+p++   a+++   g+ ++ GG ++  a+A+++sW  +l
  gi|313122461|ref|YP_004038348.1| 389 MVVRRLRNHEHPYPVRHVTTETAGHAISFPYQPTTGltAISSPPPGTTMALGGSPEGLARANKESWPVVL 458
                                       **********************************97224566778888******************8665 PP

>> Bile_Hydr_Trans  Acyl-CoA thioester hydrolase/BAAT N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.0   2.1e-31   7.5e-28       1     119 [.      54     166 ..      54     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 2.1e-31
                   Bile_Hydr_Trans   1 DepvkikvsglppgqkvtlrasltdekgelfeSfAvykadekGevdlsrdaplgGsYtgvepmGLfwsmkpekekkr 77 
                                       Dep+++ vsg++pg+ vt++a++ d +g+++ SfA+++a +kG vd++++ap  G+Y+ v+pmGL+wsm+p+++++ 
  gi|313122461|ref|YP_004038348.1|  54 DEPFTLMVSGIAPGTAVTITARTFDREGRQWASFATFTASSKGVVDIETHAPDAGTYETVSPMGLIWSMRPTDGES- 129
                                       9**************************************************************************9. PP

                   Bile_Hydr_Trans  78 rllkkdvstpfvvtlevlekkekegkelasatveRlfvapgV 119
                                       +++ +  +    +tl+++    ++g+++ ++tv+R+f  ++ 
  gi|313122461|ref|YP_004038348.1| 130 SIY-APPEGGSDLTLTAS----ADGRQIGQQTVTRWFGPKKL 166
                                       455.44445556667777....88************977665 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   3.9e-05      0.14       4     129 ..     178     287 ..     175     297 .. 0.74
   2 ?   -1.8   0.0      0.53   1.9e+03     138     163 ..     361     386 ..     353     417 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                               DLH   4 ylatpkna.kkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvl 79 
                                        l++p    ++p+v+v++   G        +  la  GY+a+aP+  ++            +a+    ++v+ e   
  gi|313122461|ref|YP_004038348.1| 178 TLFRPSGDgPYPGVMVLHGSGGQPAVGS--ALMLAAHGYAAFAPQY-FGPP----------DAVPDQLAEVPLE--- 238
                                       56778877899*******9999886554..7789**********95.5444..........1222222333222... PP

                               DLH  80 ddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafY 129
                                         l+   ++l s+p v ++ vg+ G   G++lall  a  + v a++a+ 
  gi|313122461|ref|YP_004038348.1| 239 -YLQRGYDWLTSRPAVRDGSVGLLGTSKGAELALLAGATFDWVGAVAAYA 287
                                       .2333358999999999999999999999999999999999888888875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.53
                               DLH 138 eeaakikapilalfgeeDefipadev 163
                                       + +++i +p+  + g+ D   p ++ 
  gi|313122461|ref|YP_004038348.1| 361 IPVENIDGPVTLVSGGDDRLWPSATF 386
                                       5578999***********99888764 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.1e-06     0.011       8      75 ..     179     249 ..     172     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-06
                   Chlorophyllase2   8 vvaPteageYpvllflhGylllnslYsqlLkhiashgfivvapqlyk..vaeada.kei..ksaakvlnWlak 75 
                                        + P+  g Yp ++ lhG   ++ + s l+  +a hg+ ++apq      a +d+ +e+  +  ++  +Wl++
  gi|313122461|ref|YP_004038348.1| 179 LFRPSGDGPYPGVMVLHGSGGQPAVGSALM--LAAHGYAAFAPQYFGppDAVPDQlAEVplEYLQRGYDWLTS 249
                                       589*************************98..79**********88765333443344422445555555554 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.5e-06      0.02      26      93 ..     166     235 ..     144     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-06
                    Chlorophyllase  26 rsspapPkpli..ivtPaeaGtypvvlflhGtllsnkfyskllnhiashGfivvaPqlykllp..Psaqdei 93 
                                        +  a+P+ l+  +  P  +G yp v++lhG   +    s l+  +a+hG+   aPq +      P++  e+
  gi|313122461|ref|YP_004038348.1| 166 LHTEASPDGLLgtLFRPSGDGPYPGVMVLHGSGGQPAVGSALM--LAAHGYAAFAPQYFGPPDavPDQLAEV 235
                                       55666777775336789************************98..69**********996433446666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2924.13
//
Query:       gi|313122462|ref|YP_004038349.1|  [L=268]
Description: hypothetical protein Hbor_36960 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.0   0.0       0.37   10.8   0.0    1.6  1  DUF5345   Family of unknown function (DUF5345)


Domain annotation for each model (and alignments):
>> DUF5345  Family of unknown function (DUF5345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     2e-05      0.37      17      58 ..     133     174 ..     127     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2e-05
                           DUF5345  17 PsleeleqllaeekerkrkrlrrElllFlliAllilslllla 58 
                                       P    l++++ ++++++r+r rr  l F +++ ++l++l ++
  gi|313122462|ref|YP_004038349.1| 133 PVVPGLKAFVGSKAAASRRRTRRGALRFGVLSGVVLTFLSVL 174
                                       7778899***********************999999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1444.43
//
Query:       gi|313122463|ref|YP_004038350.1|  [L=135]
Description: ferredoxin subunit of nitrite reductase and ring-hydroxylating dioxygenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-09   38.1   0.1    1.5e-09   37.7   0.1    1.2  1  Rieske           Rieske [2Fe-2S] domain
     0.0042   17.0   0.0     0.0055   16.6   0.0    1.1  1  Rieske_2         Rieske-like [2Fe-2S] domain
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.24   11.2   0.0    1.4  1  GCD14_N          tRNA methyltransferase complex GCD14 subunit
       0.14   12.1   1.4       0.32   10.9   1.4    1.5  1  Antifungal_pept  Antifungal peptide


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   3.3e-13   1.5e-09       6      83 ..       6      91 ..       3     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.3e-13
                                      EEGGGC-TTC.....EEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-B.CGGSEE..ETT.EEE-TTT--EEE.TTSB CS
                            Rieske  6 akesdvpegd.....pltvkvggeplvvlrdedgevyAlsdvCtHrgap.lsegki..dekgvleCpcHgwayd.adGk 75
                                      +  s+++egd     +++ +  +e++v++r+ d+ v+A  ++C+H+  + l++g +    +g+++Cp Hg+ yd ++G 
  gi|313122463|ref|YP_004038350.1|  6 CSLSELDEGDswlftVREADGSEEEVVLVRT-DDCVRAWLNYCQHETDQrLDRGFGaaMRDGEIVCPKHGSMYDaCSGY 83
                                      6778888888665445555666778*****6.*************98774766555226999***************** PP

                                      EEE-TTHH CS
                            Rieske 76 vikgPapr 83
                                      + +g+a +
  gi|313122463|ref|YP_004038350.1| 84 CDNGKAAE 91
                                      *9998875 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-06    0.0055       5     102 ..       5     107 ..       3     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-06
                                       EEECCCS-TTB-.....EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEET CS
                          Rieske_2   5 vckledlvketg.....vaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdL 76 
                                       +c+l++l ++ +       a   +++v+l+r+ ++ v A  n++  ++ + l rG+ ++   +  +++P +++ +d 
  gi|313122463|ref|YP_004038350.1|   5 LCSLSELDEGDSwlftvREADGSEEEVVLVRT-DDCVRAWLNYCQHETDQRLDRGFGAAM-RDGEIVCPKHGSMYDA 79 
                                       78888888888754421122224678888888.9*********************96666.778899********** PP

                                       TT-BBSS..-TTSB-BEE-EEESTSEEE CS
                          Rieske_2  77 ktGecle..deevslkvypvrvedgkve 102
                                        +G c +  ++e +l   +v  +dg v 
  gi|313122463|ref|YP_004038350.1|  80 CSGYCDNgkAAESTLVSVDVETRDGDVV 107
                                       *****87657778888888888888886 PP

>> GCD14_N  tRNA methyltransferase complex GCD14 subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.5e-05      0.24      15      45 ..      99     129 ..      97     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.5e-05
                           GCD14_N  15 aKgrkhtitLepGgefhthrGaieHDdlIGr 45 
                                          r   ++L+++ +++ h Gaie Ddl G+
  gi|313122463|ref|YP_004038350.1|  99 VETRDGDVVLTDDDRTFLHEGAIEADDLPGS 129
                                       55678889*******************9886 PP

>> Antifungal_pept  Antifungal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.4   7.2e-05      0.32       7      23 ..      70      86 ..      68      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.2e-05
                   Antifungal_pept  7 CkkDGsmGvCeSGyClq 23
                                      C k Gsm   +SGyC  
  gi|313122463|ref|YP_004038350.1| 70 CPKHGSMYDACSGYCDN 86
                                      99*************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 936.53
//
Query:       gi|313122464|ref|YP_004038351.1|  [L=200]
Description: SprT-like family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-06   28.4   0.0    1.6e-06   27.9   0.0    1.2  1  SprT-like  SprT-like family
      0.005   17.0   1.4       0.74   10.1   0.1    2.8  3  DUF4157    Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.8e-10   1.6e-06      17     101 ..      52     146 ..      35     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.8e-10
                         SprT-like  17 aaggvkiiwskrlnttaGranlkr............atvrhhasIeLseklldsrsedrllntLaHElcHlalfvis 81 
                                       ++ +v++++s+r ++ a   +  +            a +   +++ L     +  +e++   tL HEl+H+  f+ +
  gi|313122464|ref|YP_004038351.1|  52 DLSRVEWEVSTRAKRRAAAVKRPQisgatvgepkswADGIPACTVSLTWAAFEAFDETEWTATLRHELVHVEQFQRF 128
                                       567888889988887777644444899999999999999999*********************************** PP

                         SprT-like  82 gvrnnpHGaeFkawaakvek 101
                                       g  ++ HG++Fk+ a+ v+ 
  gi|313122464|ref|YP_004038351.1| 129 G--TTNHGPRFKRRAESVDA 146
                                       *..9************9965 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.3   2.7e+03      16      31 ..      21      36 ..      17      46 .. 0.72
   2 !    5.1   0.1     0.003        27      14      36 ..      49      71 ..      36      83 .. 0.84
   3 !   10.1   0.1   8.3e-05      0.74      61      76 ..     111     126 ..     101     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.3
                           DUF4157 16 adlsdVrvhtgsaaar 31
                                      + +++V  h++  a +
  gi|313122464|ref|YP_004038351.1| 21 ETFEAVTTHDDLLAWS 36
                                      5689999999855544 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.003
                           DUF4157 14 fgadlsdVrvhtgsaaaraaral 36
                                      f+ dls+V++ + ++a+r a+a+
  gi|313122464|ref|YP_004038351.1| 49 FDVDLSRVEWEVSTRAKRRAAAV 71
                                      7899*********9999999887 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 8.3e-05
                           DUF4157  61 grellaHELtHvvqqr 76 
                                        +++l HEL+Hv q +
  gi|313122464|ref|YP_004038351.1| 111 WTATLRHELVHVEQFQ 126
                                       5789*********966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:02.09
# Mc/sec: 290.49
//
Query:       gi|313122465|ref|YP_004038352.1|  [L=325]
Description: K+dependent Na+ exchanger related-protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-45  154.7  35.6    6.1e-24   84.7  13.1    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein
  ------ inclusion threshold ------
       0.39   10.7   0.0       0.39   10.7   0.0    3.1  3  FixQ      Cbb3-type cytochrome oxidase component FixQ
        2.2    7.6   5.3        1.3    8.3   0.9    2.3  2  DUF4407   Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7  13.1     1e-27   6.1e-24       3     150 ..      10     149 ..       8     150 .. 0.90
   2 !   76.2  14.5   4.3e-25   2.6e-21       3     139 ..     182     310 ..     181     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       ++++++s+++++++a +lv+s+  +a+ +g+s+ ++Glt++A+g+s pEl+++  aal g +d+a+gnv+Gsni nl
  gi|313122465|ref|YP_004038352.1|  10 VGIVVVSVAGLWIGARLLVDSVVRLARRVGLSELTIGLTVVAAGTSTPELVVTADAALVGLGDIAVGNVVGSNIYNL 86 
                                       67899************************************************************************ PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                        +++G++ l+  ++++++ + +d  + llv+ +l ++++          ++t+ eg+vl++l+++y++++l
  gi|313122465|ref|YP_004038352.1|  87 AFILGVVSLLRVVPIERSLVHRDG-VALLVSTFLGVYAIS-D------SVVTRGEGAVLVGLFVAYIAFLL 149
                                       **********88888888877777.656666655454444.4......9******************9976 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 4.3e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       +vl++++l+++ ++ d++v sa+e+a+  g+s+ v+G t++A+g+s pE+++s++a+++g   +++gnv+Gsn+fnl
  gi|313122465|ref|YP_004038352.1| 182 VVLLVAGLAIVLISGDLMVGSASELARGAGVSEWVIGGTIVAAGTSTPEFAVSLVAMRRGRLGVSVGNVVGSNVFNL 258
                                       68999************************************************************************ PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvll 139
                                       l+++G+ a+i +l+  ++   l+l  +l+++ ++++++l+        +rl++ eg +++
  gi|313122465|ref|YP_004038352.1| 259 LVIMGVGAVIRPLSLSGSI-GLSL-TWLVAVSVAVVAALWTG------RRLSRAEGGLFA 310
                                       **********997666644.8888.55555555556677766......777777777665 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.7       1.2   7.2e+03      15      26 ..     111     122 ..     110     123 .. 0.79
   2 ?   10.7   0.0   6.5e-05      0.39      17      35 ..     136     154 ..     135     164 .. 0.82
   3 ?    0.1   0.1      0.14   8.4e+02      15      34 ..     281     299 ..     277     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                              FixQ  15 llflvllfygvv 26 
                                         +lv +f+gv+
  gi|313122465|ref|YP_004038352.1| 111 VALLVSTFLGVY 122
                                       568999999997 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.5e-05
                              FixQ  17 flvllfygvviyafrpgnr 35 
                                       +lv+lf++++++++r+g +
  gi|313122465|ref|YP_004038352.1| 136 VLVGLFVAYIAFLLRSGIT 154
                                       79**************975 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.14
                              FixQ  15 llflvllfygvviyafrpgn 34 
                                       l +lv++ ++vv+ a++ g+
  gi|313122465|ref|YP_004038352.1| 281 LTWLVAVSVAVVA-ALWTGR 299
                                       6789999999997.666665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.03   1.8e+02      33      66 ..      73     107 ..      59     110 .. 0.84
   2 ?    8.3   0.9   0.00022       1.3      25      71 ..     114     160 ..      94     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.03
                           DUF4407  33 yAlytvlkspll.lallvGllwgllIfnlDRfivs 66 
                                        A+  v++s+++ la + G++  l ++ ++R++v 
  gi|313122465|ref|YP_004038352.1|  73 IAVGNVVGSNIYnLAFILGVVSLLRVVPIERSLVH 107
                                       6888889999889********************95 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00022
                           DUF4407  25 llAalsgayAlytvlksplllallvGllwgllIfnlDRfivssikkr 71 
                                       l+ ++ g yA++  +  +  +a+lvGl+++++ f l   i+  ++ +
  gi|313122465|ref|YP_004038352.1| 114 LVSTFLGVYAISDSVVTRGEGAVLVGLFVAYIAFLLRSGITDEMSAD 160
                                       56789999999999999999***************999998888443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2292.94
//
Query:       gi|313122466|ref|YP_004038353.1|  [L=322]
Description: MoxR-like ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-64  216.0   0.0    1.7e-64  215.5   0.0    1.2  1  AAA_3            ATPase family associated with various cellul
    4.9e-17   61.5   3.3    4.9e-17   61.5   3.3    2.2  2  AAA_lid_2        AAA lid domain
    1.7e-15   57.2   0.0    5.6e-15   55.5   0.0    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
      1e-06   29.2   0.0    6.6e-06   26.6   0.0    2.2  2  AAA              ATPase family associated with various cellul
    4.8e-05   23.1   0.0    0.00025   20.8   0.0    1.9  1  Sigma54_activat  Sigma-54 interaction domain
    0.00082   18.5   0.0     0.0012   18.0   0.0    1.2  1  MCM              MCM P-loop domain
  ------ inclusion threshold ------
      0.022   14.5   0.0       0.45   10.2   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.039   13.3   0.1        2.9    7.2   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5   0.0   7.8e-68   1.7e-64       1     130 [.      40     169 ..      40     170 .. 0.99

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 7.8e-68
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvlle+vPG++ktl+++++a al+l+f riqftpdllP+di+G++v++e++  fef++Gp+fan++ladeinrappk
  gi|313122466|ref|YP_004038353.1|  40 HVLLEDVPGTGKTLTARSIAAALGLSFARIQFTPDLLPADITGSNVYDERQGAFEFQPGPIFANVVLADEINRAPPK 116
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                       tq+alleam e qvtv+g th+lp+pf+v+atqnP+eqeGt+ lpeaq drf+
  gi|313122466|ref|YP_004038353.1| 117 TQAALLEAMGEGQVTVDGVTHDLPNPFFVIATQNPVEQEGTFRLPEAQRDRFI 169
                                       ****************************************************8 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.2   2.7e+03      54      71 ..     192     209 ..     190     211 .. 0.78
   2 !   61.5   3.3   2.2e-20   4.9e-17       1      71 [.     233     304 ..     233     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                         AAA_lid_2  54 Rlrrepeaegetteeive 71 
                                       R+rr+p+a+++ t+e+v+
  gi|313122466|ref|YP_004038353.1| 192 RTRRSPSASRVVTDEQVS 209
                                       999999999988887775 PP

  == domain 2  score: 61.5 bits;  conditional E-value: 2.2e-20
                         AAA_lid_2   1 latrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeive 71 
                                       +atr++ ++ +gvs+r + + l +aArA+A ++grdy +p+Dvk+aap V++HRl+   +++  g++  ++v+
  gi|313122466|ref|YP_004038353.1| 233 RATREDARVDVGVSPR-GIQRLFEAARARAVIRGRDYAVPDDVKAAAPSVFRHRLVltSDARVRGVDPLDVVD 304
                                       589*************.***************************************88888777776666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   2.5e-18   5.6e-15       1     138 []      40     168 ..      40     168 .. 0.95
   2 ?   -1.6   0.0       1.1   2.4e+03      65      93 ..     265     293 ..     245     304 .. 0.72

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.5e-18
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vlL   pGtgK+  a+++aaal+ ++  +q+t d+ ++d++g+  ++  +g  +++++p+      + +++ DE++
  gi|313122466|ref|YP_004038353.1|  40 HVLLEDVPGTGKTLTARSIAAALGLSFARIQFTPDLLPADITGSNVYDerQGAFEFQPGPIF-----ANVVLADEIN 111
                                       6888889****************************************999************.....9********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra+++++++Ll  + e ++   +g +    ++      f viat np++  +  +l +a r+Rf
  gi|313122466|ref|YP_004038353.1| 112 RAPPKTQAALLEAMGEGQVT-VDGVTHDLPNP------FFVIATQNPVEqEGTFRLPEAQRDRF 168
                                       *******************9.67777777777......9**********99999********99 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                                       G-SEEEEESGGG--HHHHHHHHHHHHSSE CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslleerr 93 
                                         + +v D+v+ a ++v+   l l ++ r
  gi|313122466|ref|YP_004038353.1| 265 GRDYAVPDDVKAAAPSVFRHRLVLTSDAR 293
                                       44567889999999999887777766665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.9e-09   6.6e-06       2     129 ..      42     173 ..      41     176 .. 0.73
   2 ?   -0.3   0.0      0.62   1.4e+03      39      57 ..     243     261 ..     208     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.9e-09
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHT CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksrs 75 
                                       ll   pGtGKTl+a+++a  lg +f +i+  ++ll  ++ g +  + r+   e +       +++ DEi +  ++  
  gi|313122466|ref|YP_004038353.1|  42 LLEDVPGTGKTLTARSIAAALGLSFARIQFtPDLLpADITGSNVYDERQGAFEFQPGPiFANVVLADEINRAPPKT- 117
                                       67778********************9999636788555555555444444434333335448**********9999. PP

                                       TCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEE CS
                               AAA  76 gseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkie 129
                                                 +++Ll+++ + +           ++++vi++ n        +l++a + +Rf +k e
  gi|313122466|ref|YP_004038353.1| 118 ----------QAALLEAMGEGQVTvdgvthdlPNPFFVIATQNPveqegTFRLPEAQR-DRFIVKTE 173
                                       ..........999999999999989999999877788888888754444456777777.77766665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.62
                                       TTHHHHHHHHHHHHHHHTS CS
                               AAA  39 vgesekkirelfkeakeka 57 
                                       vg s++ i+ lf++a++ a
  gi|313122466|ref|YP_004038353.1| 243 VGVSPRGIQRLFEAARARA 261
                                       899999******9999876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.1e-07   0.00025      15     145 ..      31     152 ..      20     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.1e-07
                                       HHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHH CS
                   Sigma54_activat  15 ikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfek 91 
                                       + + +  + +vl++   GtGK+l ar+i +a   + +  +++    +p+++  s+++  ++GaF      + G + +
  gi|313122466|ref|YP_004038353.1|  31 VLTGVLARGHVLLEDVPGTGKTLTARSIAAALGLSFA-RIQFTPDLLPADITGSNVYDERQGAFE----FQPGPIFA 102
                                       55556667899*****************987764433.46777778899999*****99999995....56777653 PP

                                       TTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-H CS
                   Sigma54_activat  92 adgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedl 145
                                           +++ Dei++ p+++Q+ Ll+++ eg+v+  G ++  +  + +ia t++ +
  gi|313122466|ref|YP_004038353.1| 103 ---NVVLADEINRAPPKTQAALLEAMGEGQVTVDGVTHDLPNPFFVIA-TQNPV 152
                                       ...47899************************9999999988776665.54444 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.2e-07    0.0012      56     175 ..      37     153 ..       7     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.2e-07
                                       SS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSS...SSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEES CS
                               MCM  56 gdinvllvgdpgtaKsqlLkyveklapravytsgkgs...saagLtaavvrdeetgefvleaGalvladkGvcciDe 129
                                       ++ +vll   pgt+K+   +++++ +    ++ ++ +     a++t + v de++g f ++ G +      v++ De
  gi|313122466|ref|YP_004038353.1|  37 ARGHVLLEDVPGTGKTLTARSIAAAL-GLSFARIQFTpdlLPADITGSNVYDERQGAFEFQPGPIFAN---VVLADE 109
                                       55688888889999998888887544.33444444441115689999****************98754...9***** PP

                                       GGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                               MCM 130 fdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                       +++   +++ al+Eam + ++++   G++  L+    v+a  np++
  gi|313122466|ref|YP_004038353.1| 110 INRAPPKTQAALLEAMGEGQVTVD--GVTHDLPNPFFVIATQNPVE 153
                                       ********************9996..99****************85 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002      0.45      33      61 ..      38      66 ..      23      84 .. 0.85
   2 ?    1.8   0.0     0.082   1.8e+02      86     113 ..     103     130 ..      98     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                            RuvB_N 33 ldhvllyGpPGlGkttlakiiakelgvkl 61
                                        hvll   PG Gkt  a+ ia+ lg ++
  gi|313122466|ref|YP_004038353.1| 38 RGHVLLEDVPGTGKTLTARSIAAALGLSF 66
                                      57*********************999875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.082
                            RuvB_N  86 dvlfideihrlsraveevlysamedfrl 113
                                       +v++ dei r  ++++  l  am + ++
  gi|313122466|ref|YP_004038353.1| 103 NVVLADEINRAPPKTQAALLEAMGEGQV 130
                                       78999******************87766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0013       2.9      23      46 ..      39      62 ..      21      68 .. 0.84
   2 ?    3.9   0.0     0.013        30     109     159 ..     104     152 ..      91     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlpsll 46
                                       ++ll   pG+GKt+ a+ +++ l
  gi|313122466|ref|YP_004038353.1| 39 GHVLLEDVPGTGKTLTARSIAAAL 62
                                      57999*************998765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                       v++ DE+     k+  +L e + +g+vt+   +++   p  f ++a+ Np 
  gi|313122466|ref|YP_004038353.1| 104 VVLADEINRAPPKTQAALLEAMGEGQVTVDGVTHD--LPNPFFVIATQNPV 152
                                       7788*************************988776..588899******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2152.70
//
Query:       gi|313122467|ref|YP_004038354.1|  [L=393]
Description: enolase superfamily enzyme related to L-alanine-DL-glutamate epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-48  162.9   0.4      1e-47  162.5   0.4    1.2  1  MR_MLE_C  Enolase C-terminal domain-like
    9.5e-15   54.8   0.0    3.7e-13   49.7   0.0    2.3  2  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.5   0.4   1.2e-51     1e-47       3     219 ..     172     385 ..     170     387 .. 0.92

  Alignments for each domain:
  == domain 1  score: 162.5 bits;  conditional E-value: 1.2e-51
                                       HHHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGT..ESEE CS
                          MR_MLE_C   3 aeearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeld..llwl 77 
                                       +++a+e + e g+  +K k g+ d++edv+r++a+ ++v  + ++++++D nq+w+ ++Airv+ +l++ +  l+++
  gi|313122467|ref|YP_004038354.1| 172 RQRAAEVLNE-GYSVLKTKAGR-DWTEDVARIEAMHDEV--DGELSFRLDPNQGWTIDQAIRVGSKLADAGiyLQYM 244
                                       5667676666.********777.5***************..6689**********************8866559*** PP

                                       ESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEE CS
                          MR_MLE_C  78 EEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpva 153
                                       E+P++  d  ++la l+ r+ + pi  +E+ y ++ +r+l++aga+d++ +d++ +gGit++r+ aa+a+ +g+p +
  gi|313122467|ref|YP_004038354.1| 245 EQPIRV-DAHDSLAGLK-RQtRQPIGPNEDTYIPHNLRRLVAAGAIDVAVLDLTPAGGITGLRQEAAIAADAGIPAV 319
                                       *****9.77********.55589****************************************************** PP

                                       EBSC.SSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB-HH CS
                          MR_MLE_C 154 pHsg.sgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGveldee 219
                                       +H+  ++g+ +aa lh    ip++    ++ +   +e+++  +p++v dG+++vp+  GlG+e+d++
  gi|313122467|ref|YP_004038354.1| 320 HHCAfDLGIRTAAILHAVHGIPGFSLPPDSVYYG-WEDDVIADPFDVADGTLRVPQDSGLGIEIDRD 385
                                       ***7358***************999998888876.******************************64 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   4.2e-17   3.7e-13      14     117 .]      24     126 ..      13     126 .. 0.92
   2 ?    2.8   0.0     0.014   1.3e+02      90     104 ..     282     296 ..     256     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 4.2e-17
                                       CEEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSSCH CS
                          MR_MLE_N  14 rPvqlavttvqkqslvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlgnm 90 
                                       +P+++  ++  +   vlv++ t+eG+ G+ge      ++ +  ++++d + pl+vg+ + ++++l++ +      + 
  gi|313122467|ref|YP_004038354.1|  24 APYVTNHNSLTDMDRVLVRVDTDEGISGWGEVRVFL-TPAATVSIIEDGIRPLVVGQSPFELEALRRQVFVEYANAD 99 
                                       588999999999999****************99988.77888899********************999998888899 PP

                                       HHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  91 sAkaaidmAlwDlkakalnlpladLlG 117
                                       +  a +++A wD+ +++l+ p+++LlG
  gi|313122467|ref|YP_004038354.1| 100 MFFAPVEVACWDIVGQSLDKPVYELLG 126
                                       999***********************9 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHH CS
                          MR_MLE_N  90 msAkaaidmAlwDlk 104
                                        +A+ aid+A++Dl 
  gi|313122467|ref|YP_004038354.1| 282 LVAAGAIDVAVLDLT 296
                                       679999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2756.16
//
Query:       gi|313122468|ref|YP_004038355.1|  [L=269]
Description: uncharacterized protein, amidase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-63  214.1   0.2    2.4e-63  213.8   0.2    1.0  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.8   0.2   1.3e-67   2.4e-63       9     240 ..      23     259 ..      17     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 213.8 bits;  conditional E-value: 1.3e-67
                      Creatininase   9 eea.lkeddvailPvGstEqHGphlplgtDtliaealaervaeklgak..alvlPtlpyGvseehlgfpGTislspe 82 
                                       +++  ++++v+++PvGs+EqHG hlp++tDtl+ae++a + a+++ a+  +lv+P +  G+s++hl   GT+s + e
  gi|313122468|ref|YP_004038355.1|  23 AAVgGTDGSVLVVPVGSIEQHGAHLPVATDTLLAERVATASAKRIVADvpILVAPSVRPGYSPHHLPVGGTLSAGFE 99 
                                       555556789*******************************8888866667*************************** PP

                      Creatininase  83 tliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaae.aaeese 158
                                       tl+++lrd++e   ++Gf+ +v+vngHggn+++++ a++e+++eh++          e+   +++e +a+ aa ++e
  gi|313122468|ref|YP_004038355.1| 100 TLLDLLRDMAETGLDNGFDALVFVNGHGGNTSLIDAAVSEIGREHPDR---------EILGLTYFELVADlAATVRE 167
                                       *********************************************555.........566668999999999***** PP

                      Creatininase 159 eee.gggHAgelEtSlmlalrpelVrmdraedpeeaklakeg.........vstaedaeelspsGvlGdpskataek 225
                                       ++  g+ H+ge+EtS+ml+l+pelV++d+++++   +  ++g          s++++++e+s+sG++Gdps a++  
  gi|313122468|ref|YP_004038355.1| 168 SDLgGMAHGGEFETSMMLHLFPELVDTDEMPAEYWDEHYEQGgadlvvggpLSVYRSFDEYSESGAIGDPSVADENT 244
                                       *****************************99998887777669********************************** PP

                      Creatininase 226 Gealleaaveelael 240
                                       G++l++ av +l +l
  gi|313122468|ref|YP_004038355.1| 245 GRQLFDGAVTALSDL 259
                                       **********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1818.42
//
Query:       gi|313122469|ref|YP_004038356.1|  [L=122]
Description: hypothetical protein Hbor_37030 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-09   38.4   0.2    1.2e-09   38.1   0.2    1.1  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.2   6.7e-14   1.2e-09       6      77 ..      17      92 ..      12      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 6.7e-14
                                      S---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT..........-EEEEEGG.CEECCCTEEEETTS-G CS
                               PRC  6 asdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi.....gekevliPfdlavkigkdriivdapke 77
                                      a dl G  Vyt dG +lG    v +d ++g+ ++l+v++     +     g+k v iP+  +++ ++d+i+vd+  +
  gi|313122469|ref|YP_004038356.1| 17 APDLSGEAVYTHDGYRLGQAVGVTVDLDQGKATGLLVADIDENRFpnlptGNKGVSIPYP-RIDGIGDVIVVDVLGS 92
                                      679**********************************99887777999************.************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 868.05
//
Query:       gi|313122470|ref|YP_004038357.1|  [L=158]
Description: hypothetical protein Hbor_37040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1120.96
//
Query:       gi|313122471|ref|YP_004038358.1|  [L=902]
Description: PAS domain S-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-26   90.4   0.7    2.4e-13   50.1   0.0    3.9  4  PAS_3         PAS fold
    3.5e-18   65.8   0.2    6.5e-07   29.5   0.0    4.3  3  PAS_9         PAS domain
    5.3e-18   65.1   3.9      3e-08   33.7   0.1    4.7  4  PAS           PAS fold
    1.3e-17   64.4   0.2    5.2e-17   62.4   0.1    2.1  2  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    1.7e-16   60.4   8.5    4.9e-07   30.0   0.1    5.3  4  PAS_4         PAS fold
    2.1e-16   60.1   0.0    9.3e-16   58.0   0.0    2.2  1  Response_reg  Response regulator receiver domain
      2e-12   46.9   5.9    3.1e-12   46.3   1.4    3.5  3  HisKA         His Kinase A (phospho-acceptor) domain
      7e-12   45.8   1.3      2e-11   44.3   0.3    2.4  3  GAF_2         GAF domain
      4e-11   42.7   0.0    4.1e-06   26.7   0.0    3.3  3  PAS_8         PAS domain
    1.7e-07   31.7   0.1    1.6e-06   28.4   0.0    2.6  2  GAF_3         GAF domain
    9.6e-06   25.7   0.0     0.0034   17.5   0.0    2.7  2  PAS_11        PAS domain
     0.0079   16.5   3.0      0.016   15.5   0.0    2.8  2  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain
     0.0082   16.0   0.0      0.024   14.5   0.0    1.8  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
  ------ inclusion threshold ------
      0.015   15.8   1.6      0.015   15.8   1.6    2.6  3  DUF3391       Domain of unknown function (DUF3391)
      0.027   14.4   0.3       0.23   11.4   0.0    2.7  2  HATPase_c_2   Histidine kinase-like ATPase domain
       0.45   10.7   5.0         13    6.0   0.0    4.8  5  PAS_7         PAS fold


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.5   6.2e+03      29      52 ..       7      30 ..       4      33 .. 0.84
   2 !   36.0   0.1   5.8e-12   6.5e-09       3      75 ..     171     243 ..     169     255 .. 0.84
   3 !   50.1   0.0   2.2e-16   2.4e-13       3      74 ..     290     361 ..     288     368 .. 0.92
   4 ?   -3.1   0.0       9.1     1e+04      63      81 ..     475     493 ..     442     497 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.5
                             PAS_3 29 lvhpeDrervrealqealkkgepy 52
                                      ++h +D + + e ++++l++++ +
  gi|313122471|ref|YP_004038358.1|  7 VLHVDDDPAFAELVATHLERQGGF 30
                                      78**********999999887755 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 5.8e-12
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqeal.kkge.pyegeyRirrkdGeyrwveararvi 75 
                                       +v++r +e++Gy++eel ++  ++ +l+hp+D ervr+  ++   ++ e p     Ri++kdG+    + +++ i
  gi|313122471|ref|YP_004038358.1| 171 FVNRRTCELTGYDEEELNET--EIWKLIHPDDKERVRDIAAKRRrEDPEtPSRYTARIVTKDGTAKRCKFSVQGI 243
                                       79******************..****************99977745555577888********988777777777 PP

  == domain 3  score: 50.1 bits;  conditional E-value: 2.2e-16
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.py.egeyRirrkdGeyrwveararv 74 
                                       y s+++e+ilG+spe ++g+  s++ ++hpeDr+++++ l e+ ++++ ++ +  +R r++dG+++w+e+ ar+
  gi|313122471|ref|YP_004038358.1| 290 YQSPSCERILGVSPELVEGQ--SVMTFIHPEDRAEMQNLLTEMYNSDSsRVeTARFRSRHADGSWVWLESIARA 361
                                       789*****************..**********************99998775666**************99875 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 9.1
                             PAS_3  63 Geyrwveararvirdengk 81 
                                       G++ ++e + +++rde+  
  gi|313122471|ref|YP_004038358.1| 475 GDIEYIEVTFSPLRDEHES 493
                                       6666777777788777765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   5.8e-10   6.5e-07      13     102 ..     169     258 ..     158     260 .. 0.83
   2 !   26.7   0.0   4.7e-09   5.2e-06       4     104 .]     279     379 ..     276     379 .. 0.85
   3 ?    4.4   0.0     0.038        43       7      93 ..     404     495 ..     399     517 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.8e-10
                             PAS_9  13 ilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirkngetfwvlltaspv 85 
                                         ++N+  ++l+Gy++ee+  + i+ l+  +p+++er+r++    r+    ++ +++  +++k+g+   +++++  +
  gi|313122471|ref|YP_004038358.1| 169 FQFVNRRTCELTGYDEEELNETEIWKLI--HPDDKERVRDIAAKRRRedpeTPSRYTARIVTKDGTAKRCKFSVQGI 243
                                       459*************************..88888888888888888889*************************** PP

                             PAS_9  86 kdddgelvgiivilrDi 102
                                       + ++++ v+  + +r +
  gi|313122471|ref|YP_004038358.1| 244 QYEGERAVL--GSVREM 258
                                       988766666..666655 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 4.7e-09
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirkngetf 76 
                                       + i+  dg+i y +++ +r+lG spe v g+s+ +++  +pe++ +++++l ++ +     +++     ++ +g+ +
  gi|313122471|ref|YP_004038358.1| 279 VTIIGRDGTIKYQSPSCERILGVSPELVEGQSVMTFI--HPEDRAEMQNLLTEMYNsdssRVETARFRSRHADGSWV 353
                                       567789**888**************************..888888888888888888888***************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w +   ++  d  + + gi+v +rD+t+
  gi|313122471|ref|YP_004038358.1| 354 WLE--SIARADPVESIDGIVVNSRDVTD 379
                                       *55..44444445568888899****96 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.038
                             PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgksitdlf.......vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       + +dg  +++++ a + +   +e + g +++ l        ++ +  +  ++++l+  +   ++ve++   + g   
  gi|313122471|ref|YP_004038358.1| 404 IGTDGCFEFVSPVAGTRMREPEENIRGEHVSVLHetgmidaDGLEAVQTAIDRILDGES-DNERVELEVDIP-GDIE 478
                                       45777777777777777655566688888888888886665566666666666666666.445555555555.6677 PP

                             PAS_9  77 wvlltaspvkdddgelv 93 
                                       ++++t+sp++d+++  +
  gi|313122471|ref|YP_004038358.1| 479 YIEVTFSPLRDEHESAC 495
                                       889*******9986655 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0         1   1.1e+03      49      96 ..       7      67 ..       3      84 .. 0.72
   2 !   26.0   0.1   6.3e-09   7.1e-06       2     111 ..     149     256 ..     148     258 .. 0.81
   3 !   33.7   0.1   2.6e-11     3e-08       1     112 [.     266     376 ..     266     377 .. 0.86
   4 ?    2.5   0.0      0.12   1.4e+02       2     101 ..     389     492 ..     388     500 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                                      GBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC................TTSSEEEEEEEEEEE CS
                               PAS 49 liheeddaelaelleqlleqgeesrageisfkl................rdgrpihlevraspv 96
                                      ++h +d   +++  e ++ + e++ ++e+++++                 dg++ ++e+ +s +
  gi|313122471|ref|YP_004038358.1|  7 VLHVDD---DPAFAELVATHLERQGGFEVCVETdtdsvvthlgdadgavSDGETAQIECVVSDY 67
                                      566666...6666667777788888888888887777888888888888888888888777655 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 6.3e-09
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHH.HTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlle.qgeesragei 77 
                                        +r+ +e ++d+i +      + +vN+ ++el+G+++ee+    +  lih++d + ++++  ++++ + e ++ +  
  gi|313122471|ref|YP_004038358.1| 149 LYRTAVERSHDAIYIY-QGEQFQFVNRRTCELTGYDEEELNETEIWKLIHPDDKERVRDIAAKRRReDPETPSRYTA 224
                                       6899999999999999.888999***************************999886666655554404455666666 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlr 111
                                       ++ ++dg+ + +   +  +  +g++   +lg +r
  gi|313122471|ref|YP_004038358.1| 225 RIVTKDGTAKRCKFSVQGIQYEGER--AVLGSVR 256
                                       6666********9999999999987..7777666 PP

  == domain 3  score: 33.7 bits;  conditional E-value: 2.6e-11
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e+++a++e + d + ++ +dg i y +++ e++lG s+e v g+s++ +ih+ed+ae++ ll++ +++ +++     
  gi|313122471|ref|YP_004038358.1| 266 ERFQALIERSSDLVTIIGRDGTIKYQSPSCERILGVSPELVEGQSVMTFIHPEDRAEMQNLLTEMYNSDSSRVE-TA 341
                                       689***************************************************************99998887.77 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrd 112
                                       +f+ r+    ++ ++   + d+ + i g+++  rd
  gi|313122471|ref|YP_004038358.1| 342 RFRSRHADGSWVWLESIARADPVESIDGIVVNSRD 376
                                       78886666666666666666776666677766666 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH......HHHHHHHHHHHHTT-E CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda......elaelleqlleqgees 72 
                                       ++++++ s++ +  ++  dg++ +v++ a +    ++e + g++++ ++he+ +        ++ ++ + l   +++
  gi|313122471|ref|YP_004038358.1| 389 RYENVVRSTTQGAYIIGTDGCFEFVSPVAGTRMREPEENIRGEHVS-VLHETGMIdadgleAVQTAIDRILDGESDN 464
                                       5788888888888888888888888888888888888888888888.777776667777878888888888888999 PP

                                       CCCCEEEECTTSSEEEEEEEEEEEEETTE CS
                               PAS  73 rageisfklrdgrpihlevraspvrdagg 101
                                       + +e  ++   g + ++ev+ sp+rd+ +
  gi|313122471|ref|YP_004038358.1| 465 ERVELEVDI-PGDIEYIEVTFSPLRDEHE 492
                                       999999999.****************977 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.7   1.1e+04       8      20 ..     124     136 ..     122     159 .. 0.74
   2 !   62.4   0.1   4.6e-20   5.2e-17       3     107 ..     800     897 ..     798     901 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.7
                                       HHHHHHHHHHHHH CS
                         HATPase_c   8 qiisnlvdNavkf 20 
                                       +++ n + Nav++
  gi|313122471|ref|YP_004038358.1| 124 ELLANRINNAVEH 136
                                       7899999999998 PP

  == domain 2  score: 62.4 bits;  conditional E-value: 4.6e-20
                                       HHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHH CS
                         HATPase_c   3 ekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGl 78 
                                       e rL+q++ nl  N++++++++++i+v++      + + veD+G+Gip++d++++fe   s+      + +gtGlGl
  gi|313122471|ref|YP_004038358.1| 800 EGRLKQLFENLFRNSIDHNSPDETITVRVG--RLSNGFFVEDDGRGIPEADRDEVFEpGVST------QPQGTGLGL 868
                                       89****************889999****99..4467888******************55555......679****** PP

                                       HHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  79 sivkklvelmgGeiwvesepgrGttftft 107
                                        iv+ ++  ++ ++++++++++G +f ++
  gi|313122471|ref|YP_004038358.1| 869 GIVRTIAHAHEWTVHITESETGGARFEIR 897
                                       ********9****************9985 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.047        52      16      55 ..     168     207 ..     154     262 .. 0.87
   2 !   30.0   0.1   4.4e-10   4.9e-07       2     110 .]     273     382 ..     272     382 .. 0.90
   3 !   25.5   0.5   1.1e-08   1.2e-05       2     109 ..     395     519 ..     394     520 .. 0.78
   4 ?   -2.5   0.1       5.5   6.2e+03      19      43 ..     661     685 ..     658     701 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.047
                             PAS_4  16 rvlyaNaaaaelfgappeellGktlaellpeedaarlera 55 
                                       +++++N++ +el g++ eel     + l  ++d++r++++
  gi|313122471|ref|YP_004038358.1| 168 QFQFVNRRTCELTGYDEEELNETEIWKLIHPDDKERVRDI 207
                                       6889**********************99999999999876 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 4.4e-10
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll...p 75 
                                       ++++d+++++++dg++ y +++ ++++g++pe + G+++  +  +ed+a+ ++ l+++  ++ +  ++   +    +
  gi|313122471|ref|YP_004038358.1| 273 ERSSDLVTIIGRDGTIKYQSPSCERILGVSPELVEGQSVMTFIHPEDRAEMQNLLTEMYNSDSSRVETARFRSrhaD 349
                                       789*************************************999999*************999887777777777888 PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       g+++++e  ++   d+   ++g++v srD+T++r+
  gi|313122471|ref|YP_004038358.1| 350 GSWVWLESIARA--DPVESIDGIVVNSRDVTDQRE 382
                                       888888877766..888889************985 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 1.1e-08
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.....daarleralrrvlegeepiefleell 73 
                                        s+ ++ +++++dg ++++++ a   ++ p e ++G+++  l+ ++       +++++a++r l+ge   e++e  +
  gi|313122471|ref|YP_004038358.1| 395 RSTTQGAYIIGTDGCFEFVSPVAGTRMREPEENIRGEHVSVLHETGmidadGLEAVQTAIDRILDGESDNERVELEV 471
                                       5778999*********************************44444455554999*************9999999888 PP

                             PAS_4  74 l.pgeerhyelrllPlrdesGe.v..........igvlvisrDiTerr 109
                                       + pg+ +++e++++Plrde+   +          +gv+++++D+Ter+
  gi|313122471|ref|YP_004038358.1| 472 DiPGDIEYIEVTFSPLRDEHESaCevgigdesqqRGVVALTTDVTERK 519
                                       89***************9874311112222222267777777777776 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 5.5
                             PAS_4  19 yaNaaaaelfgappeellGktlael 43 
                                        a++a+a+l ++++e+ll ++ +el
  gi|313122471|ref|YP_004038358.1| 661 LASNASAALERVEREQLLRHHEREL 685
                                       4555567788999999988888875 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   8.3e-19   9.3e-16       1     105 [.       7     121 ..       7     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 8.3e-19
                                       EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHH..........HHHHESEEEEESSCSSSEHHHHHHHHH CS
                      Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealell..........keekvdlillDinmpgmdGlellkeir 66 
                                       vl vdDdp+++el+++ le + g+ ev + +d ++++ +l          ++ ++ +++ D +m + +G++ll+++r
  gi|313122471|ref|YP_004038358.1|   7 VLHVDDDPAFAELVATHLErQGGF-EVCVETDTDSVVTHLgdadgavsdgETAQIECVVSDYEMGETTGIDLLRRVR 82 
                                       789****************66777.77777777777777756666666556666*********************** PP

                                       HCTTTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HH CS
                      Response_reg  67 eedpelpviiltahseeedavealkagaddflsKpfdpe 105
                                       + d+ lp i++t++++ee+a ea++ag+ d+++K  + e
  gi|313122471|ref|YP_004038358.1|  83 DVDERLPFILFTSRGSEEVASEAISAGVTDYIQKRTRVE 121
                                       **********************************97665 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       3.3   3.7e+03      20      55 ..     251     282 ..     249     284 .. 0.64
   2 !   46.3   1.4   2.8e-15   3.1e-12       2      66 ..     692     758 ..     691     759 .. 0.87
   3 ?    0.1   0.0      0.77   8.6e+02      37      59 ..     789     811 ..     772     817 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.3
                                       HHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHH CS
                             HisKA  20 ilgnaeaLkregklteelkeyletiesearrldhlv 55 
                                       +lg +  +++e    e+++e ++ +++ +  l  ++
  gi|313122471|ref|YP_004038358.1| 251 VLGSVREMSDE----ERVEERFQALIERSSDLVTII 282
                                       66777777663....777777776666666666655 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 2.8e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC.....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre...gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++ ++ v+H+Lr+PL+  +g +++L+     g   +  ++ le+ie+  +r+++++ed+L l+r ++
  gi|313122471|ref|YP_004038358.1| 692 LEQVASVVSHDLRNPLNLASGQLQILRANheaG-QYDTIEKRLERIEDAHQRMRQIIEDMLSLARQGQ 758
                                       788999********************8877843.45666668**********************9875 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.77
                                       CHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  37 lkeyletiesearrldhlvedlL 59 
                                       ++++l ti  ++ rl +l e+l 
  gi|313122471|ref|YP_004038358.1| 789 VADNLGTIAAHEGRLKQLFENLF 811
                                       678999**************994 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       9.8   1.1e+04      38      69 ..     335     364 ..     304     376 .. 0.51
   2 !   44.3   0.3   1.8e-14     2e-11       2     138 .]     539     670 ..     538     670 .. 0.84
   3 ?   -3.2   0.0       8.7   9.8e+03      18      55 ..     828     863 ..     823     882 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.8
                                       EEEES-TTSTT-S-B---TTHHHHHHHHTS-E CS
                             GAF_2  38 awgeaeeefgaaldrplgeglvgealrtgrpv 69 
                                       +++ ++++f++++  + g+ ++ e+++   pv
  gi|313122471|ref|YP_004038358.1| 335 SSRVETARFRSRH--ADGSWVWLESIARADPV 364
                                       3334444444444..33555566666665555 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 1.8e-14
                                       HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG CS
                             GAF_2   2 adleelldlvldelvel.gaalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndlee 76 
                                       ++ ee++ +v d+++++ +  l  i ++d+d++ l ++a + a +e  +    p g+g++++++++g+  +++++ +
  gi|313122471|ref|YP_004038358.1| 539 TTYEEVATIVSDAAENIlNYPLNSISFYDEDRDaLLTHAVSDAAKEIVDDEVIPRGHGIAWRVFESGEGEVFENVST 615
                                       6789************66***********99995333344444444444443466*************9999**999 PP

                                       -S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  77 dpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       dp+  +    +  ++s++++P+   g  vGvl  ++ +p++++++ ++l++ la+ ++ a+e
  gi|313122471|ref|YP_004038358.1| 616 DPAVMN---PDTEIQSEVVLPI---G-DVGVLMAGSREPGTLNDSRVSLARILASNASAALE 670
                                       776544...67***********...9.9*****99999999*******************97 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8.7
                                       SS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--.- CS
                             GAF_2  18 lg.aalgyillvdddgglrlaawgeaeeefgaaldrpl.g 55 
                                       +g  + g+++++d++g    +a + +  e g ++  ++ g
  gi|313122471|ref|YP_004038358.1| 828 VGrLSNGFFVEDDGRGI--PEADRDEVFEPGVST--QPqG 863
                                       55566788888776555..444444444444444..3332 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   3.7e-09   4.1e-06       1      57 [.     148     204 ..     148     215 .. 0.81
   2 !   12.2   0.0   0.00012      0.14       1      61 [.     266     324 ..     266     331 .. 0.77
   3 ?   -3.1   0.0       8.1   9.1e+03      27      38 ..     549     567 ..     548     588 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.7e-09
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57 
                                       + +r+++e s+d+i  ++ g+++ +vN++++el+Gy+ ++l + ++++l++  + +++
  gi|313122471|ref|YP_004038358.1| 148 QLYRTAVERSHDAIY-IYQGEQFQFVNRRTCELTGYDeEELNETEIWKLIHPDDKERV 204
                                       68*************.665558***************999999888877776666655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpvlrplledaeq 61 
                                       er++al+e s+d + ++ ++++i +  ++ +++lG+s++l +   + +++ ++p+ +  +q
  gi|313122471|ref|YP_004038358.1| 266 ERFQALIERSSDLVTIIGRDGTIKYQSPSCERILGVSPELVE--GQSVMTFIHPEDRAEMQ 324
                                       7**************9974456*************8866666..55777777777774444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.1
                             PAS_8  27 NqaalellGys.......a 38 
                                        +aa+ +l y+       +
  gi|313122471|ref|YP_004038358.1| 549 SDAAENILNYPlnsisfyD 567
                                       6888899888854333333 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.3   1.5e+03      88     125 ..     499     537 ..     483     538 .. 0.69
   2 !   28.4   0.0   1.5e-09   1.6e-06       2     129 .]     541     671 ..     540     671 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.3
                             GAF_3  88 LvagrqviGvlalastkpra.fdaedlelleslArqiat 125
                                       + +++q +Gv+al ++ ++    +++l+ l s +r + t
  gi|313122471|ref|YP_004038358.1| 499 IGDESQQRGVVALTTDVTERkQYQARLSALHSASRELTT 537
                                       556679*******88865532445666666666666665 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.5e-09
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse..sldedsalarralssgev.vsepsfae. 74 
                                       ++e++ ++ +++ ++l+    ++  +ded++ l + a +d+++ ++   +++++   a+r+++sge  v+e+ + + 
  gi|313122471|ref|YP_004038358.1| 541 YEEVATIVSDAAENILNYPLNSISFYDEDRDALLTHAVSDAAKEIVDdeVIPRGHGIAWRVFESGEGeVFENVSTDp 617
                                       689999999********************99998888888888887776889*************863444333222 PP

                             GAF_3  75 ...edglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                           + ++ ++ +++P+ +    +Gvl+++s++p+ +++++++l + lA+ ++ a+er
  gi|313122471|ref|YP_004038358.1| 618 avmNPDTEIQSEVVLPIGD----VGVLMAGSREPGTLNDSRVSLARILASNASAALER 671
                                       222677999**********....*********************************98 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.021        23      28      54 ..     180     206 ..     172     236 .. 0.83
   2 !   17.5   0.0     3e-06    0.0034      33      84 ..     304     356 ..     293     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.021
                            PAS_11  28 lglekeelvgrsiydLchpqdlstlks 54 
                                       +g+ +eel ++ i++L+hp+d +++++
  gi|313122471|ref|YP_004038358.1| 180 TGYDEEELNETEIWKLIHPDDKERVRD 206
                                       68999****************887765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3e-06
                            PAS_11  33 eelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrl..sqdkfvkvk 84 
                                       e + g s+ +++hp+d+ ++++ l e++ +++ ++  + R+r+  +++ +v++ 
  gi|313122471|ref|YP_004038358.1| 304 ELVEGQSVMTFIHPEDRAEMQNLLTEMY-NSDSSRVETARFRSrhADGSWVWLE 356
                                       45668999********************.7888888888888877999999975 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05     0.016      35     111 .]      56     137 ..      18     137 .. 0.83
   2 ?   -0.1   0.1         1   1.1e+03      10      35 ..     525     550 ..     517     554 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                        OKR_DC_1_N  35 qnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlreidgfiel..ledtpefiarqiea 106
                                       + ++i +vv +++       +ll+ +r+  e+lP  l++++ ++e ++  + + ++ +i+     ++ e +a++i+ 
  gi|313122471|ref|YP_004038358.1|  56 ETAQIECVVSDYEmgeTTGIDLLRRVRDVDERLPFILFTSRGSEEVASEAISAGVTDYIQKrtRVEQYELLANRINN 132
                                       4588999999999*999999*******************98899999999999999999984456788999****** PP

                        OKR_DC_1_N 107 aakkY 111
                                       a+++Y
  gi|313122471|ref|YP_004038358.1| 133 AVEHY 137
                                       **999 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                        OKR_DC_1_N  10 aealekegfevvgvtstdDllsvieq 35 
                                        +al++ ++e++++t+++++ ++++ 
  gi|313122471|ref|YP_004038358.1| 525 LSALHSASRELTTATTYEEVATIVSD 550
                                       57899999**********99999876 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.2e-05     0.024      10      61 ..     810     860 ..     805     888 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                       HATPase_c_3  10 lvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatssk 61 
                                       l +Ns+d ++   +i+v   r  ++ + +eDdG G++e++ +++++++ s++
  gi|313122471|ref|YP_004038358.1| 810 LFRNSIDHNSPDETITVRVGR-LSNGFFVEDDGRGIPEADRDEVFEPGVSTQ 860
                                       678****77665555555544.358********************9987765 PP

>> DUF3391  Domain of unknown function (DUF3391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4       3.2   3.6e+03     102     116 ..     126     155 ..      94     160 .. 0.53
   2 ?   -2.8   0.1       7.8   8.7e+03      86     115 ..     517     545 ..     477     555 .. 0.50
   3 ?   15.8   1.6   1.4e-05     0.015      84     132 ..     679     761 ..     644     765 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.2
                           DUF3391 102 e...............eleraeklyeeakq 116
                                                       +l++ e+ly+ a++
  gi|313122471|ref|YP_004038358.1| 126 LanrinnavehyrterRLRESEQLYRTAVE 155
                                       133444444333334466677777766665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.8
                           DUF3391  86 leeekqerperleaereeleraeklyeeak 115
                                       ++++ q+r ++l++  +el+ a+  yee  
  gi|313122471|ref|YP_004038358.1| 517 ERKQYQARLSALHSASRELTTAT-TYEEVA 545
                                       22223333334444444554443.345544 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.4e-05
                           DUF3391  84 aeleeekqerperleaere..................................eleraeklyeeakqlvrslfsdvr 126
                                       ++ e e +++ e+le+ ++                                  +ler+e ++++++q++++++s +r
  gi|313122471|ref|YP_004038358.1| 679 RHHERELEHQNEQLEQVASvvshdlrnplnlasgqlqilranheagqydtiekRLERIEDAHQRMRQIIEDMLSLAR 755
                                       22222222223333333336667888889999999999999999999****************************** PP

                           DUF3391 127 lgkaid 132
                                       +g++++
  gi|313122471|ref|YP_004038358.1| 756 QGQPVE 761
                                       ***997 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.6     4e+03      17      47 ..     529     559 ..     518     594 .. 0.67
   2 ?   11.4   0.0    0.0002      0.23      40     114 ..     811     880 ..     786     892 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.6
                       HATPase_c_2  17 avlrraglseelldeirlaveEactNaveha 47 
                                         ++r   ++ + +e+   v+ a  N+ ++ 
  gi|313122471|ref|YP_004038358.1| 529 HSASRELTTATTYEEVATIVSDAAENILNYP 559
                                       4457778888888888888888888888775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0002
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDevey 114
                                       + N + h+ +   +++++vr+ + ++ + v  +D+G+g + +++++  e++ +++ +  G+Gl ++++++   e+
  gi|313122471|ref|YP_004038358.1| 811 FRNSIDHNSP---DETITVRVGRLSNGFFV--EDDGRGIPEADRDEVFEPGVSTQPQGTGLGLGIVRTIAHAHEW 880
                                       5666777665...67799998888888776..899888888877777777778999*************999887 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         2   2.2e+03      15      35 ..     167     187 ..     154     198 .. 0.83
   2 ?    1.6   0.0      0.26   2.9e+02      97     114 ..     366     384 ..     298     385 .. 0.71
   3 ?    6.0   0.0     0.012        13      95     114 ..     503     522 ..     490     523 .. 0.88
   4 ?   -2.1   0.1       3.7   4.1e+03      41      63 ..     674     695 ..     654     729 .. 0.60
   5 ?   -0.4   0.8       1.1   1.2e+03      43      77 ..     715     746 ..     680     766 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2
                             PAS_7  15 lrLvawNrrylelldlpeelv 35 
                                       ++  ++Nrr +el ++ ee +
  gi|313122471|ref|YP_004038358.1| 167 EQFQFVNRRTCELTGYDEEEL 187
                                       567899*******99998765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                             PAS_7  97 d.gGfVttytDiTerrrae 114
                                          G+V+   D+T++r+ e
  gi|313122471|ref|YP_004038358.1| 366 SiDGIVVNSRDVTDQRERE 384
                                       34699***********988 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.012
                             PAS_7  95 lpdgGfVttytDiTerrrae 114
                                        +++G+V+  tD+Ter++ +
  gi|313122471|ref|YP_004038358.1| 503 SQQRGVVALTTDVTERKQYQ 522
                                       5789************9976 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.7
                             PAS_7  41 leellrynaergefgagdveaev 63 
                                        e+llr+  ++ e+++++  ++v
  gi|313122471|ref|YP_004038358.1| 674 REQLLRHHERELEHQNEQL-EQV 695
                                       4455555544444442222.222 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.1
                             PAS_7  43 ellrynaergefgagdveaeverrlaaaragkphs 77 
                                       ++lr n+e g+++  ++e+ +e r++ a+++ ++ 
  gi|313122471|ref|YP_004038358.1| 715 QILRANHEAGQYD--TIEKRLE-RIEDAHQRMRQI 746
                                       6777788888877..2222222.222233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (902 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 5526.97
//
Query:       gi|313122472|ref|YP_004038359.1|  [L=247]
Description: sporulation control protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-75  253.1   0.1    2.1e-75  252.9   0.1    1.0  1  Spo0M       SpoOM protein
  ------ inclusion threshold ------
       0.07   13.6   0.0        0.1   13.0   0.0    1.2  1  Arrestin_C  Arrestin (or S-antigen), C-terminal domain


Domain annotation for each model (and alignments):
>> Spo0M  SpoOM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.9   0.1   2.3e-79   2.1e-75       1     210 []       1     207 [.       1     207 [. 0.99

  Alignments for each domain:
  == domain 1  score: 252.9 bits;  conditional E-value: 2.3e-79
                                       XXXXXXXXX----EEEEEES-SEE-TT-EEEEEEEEE--SS-EEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEE CS
                             Spo0M   1 fkklLasvGiGgakVdtvLekeevrpGetlegevevkGGsveqeieeieleLvtrvekeeddkeveetvelarvrva 77 
                                       +kk+LasvGiG+a+VdtvL +++v pGet+++ev+v+GG++eq+i++i+le+ tr+++ee+    ++++++ r+r++
  gi|313122472|ref|YP_004038359.1|   1 MKKILASVGIGNASVDTVLPSTTVSPGETVDAEVRVSGGDAEQSISAIDLEVETRYRTEEG----YRDTTVGRMRLS 73 
                                       79*********************************************************99....899********* PP

                                       --EEE-TT-EEEEEEEEE--TT-----TT--EEEEEEEEESSS--EEEEEEEEE---HHHHHHHHHHHHTTEEEEEE CS
                             Spo0M  78 eaftiepgeereipfelelpletPitlggakvwleTeldiagavDpgDkDplevePlplqeavlealeelGfrlrsa 154
                                       e+f iepgee++++ e+++p+etP+tlg+++vw+eTel+i++avDp+D D+l+v+P+p ++av++a eelGf+lr++
  gi|313122472|ref|YP_004038359.1|  74 ESFDIEPGEETTYDAEITIPWETPLTLGSTEVWVETELEIDMAVDPEDVDYLDVQPTPRMQAVFDAAEELGFSLRTT 150
                                       ***************************************************************************** PP

                                       EEEE-G.GG--.SSSEEEEEEEEE.SHHHHHH-S-EEEEEEEETTEEEEEEEE-TTT CS
                             Spo0M 155 dleegklrgagqelpfvQelefvP.sgeyagrldelEvvflaeeeelevvlevDrra 210
                                       ++e+ ++       +fvQe+ef+P sge++g++de+E+vf++++++l+v++evDrr+
  gi|313122472|ref|YP_004038359.1| 151 ECEADPYGRYVGGRRFVQEFEFRPsSGEFRGDVDEIELVFVPSASSLDVFVEVDRRG 207
                                       ******9888889******************************************96 PP

>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.2e-05       0.1       4      92 ..      12      97 ..      11     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                                      -EEEEEEES-SEEETT--EEEEEEEE.E-SSSEEEEEEEEEEEEEEEESS..SEEEEEEEEEEEEE---B-TTEE.EEE CS
                        Arrestin_C  4 kvsleaslpkkgyvpGetipvtvkid.ndskkkvkkikvslvqhvdvcafnrsnkkeknvvaksdsvkvtsaakdklet 81
                                      + s++ +lp++ + pGet++ +v +   d  +++  i ++++ +++       +  +   ++ s+s +++++++++++ 
  gi|313122472|ref|YP_004038359.1| 12 NASVDTVLPSTTVSPGETVDAEVRVSgGDAEQSISAIDLEVETRYRTEEG--YRDTTVGRMRLSESFDIEPGEETTYD- 87
                                      5678899*******************88**********999776666666..66666666666777777889999999. PP

                                      EEEE.--..--B- CS
                        Arrestin_C 82 evelqiP..eelt 92
                                       +e++iP  +  +
  gi|313122472|ref|YP_004038359.1| 88 -AEITIPweT--P 97
                                      .888889442..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1696.31
//
Query:       gi|313122473|ref|YP_004038360.1|  [L=515]
Description: IclR-like transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-05   23.8   0.0    6.4e-05   22.7   0.0    1.5  1  HTH_IclR     IclR helix-turn-helix domain
    0.00021   21.4  36.0      0.002   18.3   5.0    6.1  5  Binary_toxB  Clostridial binary toxin B/anthrax toxin PA Ca-b
     0.0038   17.1   0.1     0.0075   16.1   0.1    1.4  1  MarR_2       MarR family
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.041   13.8   0.0    1.5  1  TrmB         Sugar-specific transcriptional regulator TrmB
      0.039   13.9   0.1      0.073   13.1   0.1    1.4  1  HTH_Crp_2    Crp-like helix-turn-helix domain
      0.044   13.3   0.0      0.093   12.3   0.0    1.5  1  HTH_24       Winged helix-turn-helix DNA-binding
      0.052   13.5   0.0       0.11   12.4   0.0    1.4  1  MarR         MarR family
       0.11   12.6   0.0       0.23   11.5   0.0    1.4  1  DUF3489      Protein of unknown function (DUF3489)


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.8e-08   6.4e-05       7      49 ..     445     487 ..     440     489 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.8e-08
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       +i+ +l+ea+++l  s +  +tg++k+tv+R L+++  +G v+
  gi|313122473|ref|YP_004038360.1| 445 EIIAILEEAGGRLEQSTIVSETGWSKATVSRVLSSMADEGRVT 487
                                       58999*********************************99776 PP

>> Binary_toxB  Clostridial binary toxin B/anthrax toxin PA Ca-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.018        41       2      17 ..     134     149 ..     133     154 .. 0.91
   2 !    7.1   8.2    0.0028       6.2       2      54 ..     156     208 ..     155     210 .. 0.94
   3 !   18.3   5.0   8.9e-07     0.002       2      61 ..     179     238 ..     178     243 .. 0.82
   4 !    8.5   0.1     0.001       2.2      38      61 ..     238     261 ..     235     270 .. 0.85
   5 ?    4.5   6.4     0.018        41       1      60 [.     270     329 ..     270     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.018
                                       -SSSSSS-HHHHHH-E CS
                       Binary_toxB   2 DsDdDgipdslEvnGY 17 
                                       D DdDg+ ++ EvnG 
  gi|313122473|ref|YP_004038360.1| 134 DIDDDGLSNKEEVNGK 149
                                       99************96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0028
                                       -SSSSSS-HHHHHH-EEEESEEEEE--TTHHHHHT---B---TT-SSTTSSSS CS
                       Binary_toxB   2 DsDdDgipdslEvnGYtldktllvPwvdklaekkgltkyvsdpnksstagDPy 54 
                                       D+DdDg+ d  Evn    d t  +  +d+l +  ++  y ++p++ +t++D  
  gi|313122473|ref|YP_004038360.1| 156 DTDDDGLNDGEEVNTHGTDPTKSDSDNDNLGDSLEVSTYNTNPTDPHTDSDNL 208
                                       9********************************9****************965 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 8.9e-07
                                       -SSSSSS-HHHHHH-EEEESEEEEE--TTHHHHH..T---B---TT-SSTTSSSS-HHHHHH CS
                       Binary_toxB   2 DsDdDgipdslEvnGYtldktllvPwvdklaekk..gltkyvsdpnksstagDPysDlekvs 61 
                                       DsD+D + dslEv  Y  + t  +P +d  + k+  +++ky ++p++  t+ D  sD++++ 
  gi|313122473|ref|YP_004038360.1| 179 DSDNDNLGDSLEVSTYNTNPT--DPHTDSDNLKDgvEVNKYSTSPTNGDTDDDGLSDAAEIR 238
                                       9*************9987665..5665544444434899*******************9986 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.001
                                       --B---TT-SSTTSSSS-HHHHHH CS
                       Binary_toxB  38 tkyvsdpnksstagDPysDlekvs 61 
                                         y ++pnk  t+gD  sD +++ 
  gi|313122473|ref|YP_004038360.1| 238 RTYNTNPNKADTDGDSLSDGAEIN 261
                                       68*****************99887 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.018
                                       --SSSSSS-HHHHHH-EEEESEEEEE--TTHHHHHT---B---TT-SSTTSSSS-HHHHH CS
                       Binary_toxB   1 lDsDdDgipdslEvnGYtldktllvPwvdklaekkgltkyvsdpnksstagDPysDlekv 60 
                                       +D+D+D + d +Ev+    + + ++   d l++  +++ + +dpnk  t+gD  sD  ++
  gi|313122473|ref|YP_004038360.1| 270 PDTDNDNLADAIEVEETNTNPNKADTDSDGLKDGAEVNVHGTDPNKPDTDGDGTSDKVEI 329
                                       69*************999999999999998888889****************99996555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.4e-06    0.0075      13      53 ..     448     488 ..     443     494 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.4e-06
                                       HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                       a+  + g++l ++ ++ ++g sk++vsr+l  + + G v++
  gi|313122473|ref|YP_004038360.1| 448 AILEEAGGRLEQSTIVSETGWSKATVSRVLSSMADEGRVTK 488
                                       444555556*************************9998775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-05     0.041      21      56 ..     455     490 ..     447     499 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                       g+++ ++i +e+g ++++v +vL+s+ d G V+++ 
  gi|313122473|ref|YP_004038360.1| 455 GRLEQSTIVSETGWSKATVSRVLSSMADEGRVTKIS 490
                                       678889**************************9975 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.3e-05     0.073      22      58 ..     457     498 ..     440     502 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TEE..EE CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis.r..grr..ir 58 
                                       l q  + s  G +  tvsr+ls + +eg ++    grr  i+
  gi|313122473|ref|YP_004038360.1| 457 LEQSTIVSETGWSKATVSRVLSSMADEGRVTkIslGRRnlIT 498
                                       667777788999*****************9962345554555 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.1e-05     0.093       7      47 ..     445     486 ..     445     487 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.1e-05
                            HTH_24   7 kILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +I+ +L++ ++ + q+ +  ++g S++tv+r l  + +eG +
  gi|313122473|ref|YP_004038360.1| 445 EIIAILEEAGGrLEQSTIVSETGWSKATVSRVLSSMADEGRV 486
                                       599999995555****************************87 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.9e-05      0.11       8      48 ..     446     487 ..     443     490 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR   8 iLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlie 48 
                                       i++il+e g+ l +s + +  g sk+tv+rvl  + ++G ++
  gi|313122473|ref|YP_004038360.1| 446 IIAILEEAGGrLEQSTIVSETGWSKATVSRVLSSMADEGRVT 487
                                       78899999999**************************99776 PP

>> DUF3489  Protein of unknown function (DUF3489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.23       7      40 ..     441     475 ..     437     490 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                           DUF3489   7 tKqarlialLrrpeGatia.eimeatgWqahtvRg 40 
                                       t+++++ia+L++++G   + +i+++tgW + tv  
  gi|313122473|ref|YP_004038360.1| 441 TREDEIIAILEEAGGRLEQsTIVSETGWSKATVSR 475
                                       7899***********976537***********944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 3512.24
//
Query:       gi|313122474|ref|YP_004038361.1|  [L=281]
Description: oxidoreductase, aryl-alcohol dehydrogenase like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-64  216.3   0.0    8.2e-63  212.3   0.0    1.9  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.3   0.0   4.6e-67   8.2e-63       1     291 [.      19     281 .]      19     281 .] 0.98

  Alignments for each domain:
  == domain 1  score: 212.3 bits;  conditional E-value: 4.6e-67
                                       .EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE... CS
                      Aldo_ket_red   1 elglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv... 70 
                                       +lg+G+++++++    ++ ++e a ++l++a+  G+n++DtA++Yg+g se+l+ eal+      ee+++atK+   
  gi|313122474|ref|YP_004038361.1|  19 RLGFGAMRITGEniigKPDDEENAKRVLQTAVNLGVNLIDTADSYGPGVSERLIREALAP---YPEELVVATKGgll 92 
                                       59************9888888999999*********************************...************** PP

                                       --SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHH CS
                      Aldo_ket_red  71 dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqle 147
                                       ++rd+++ +++ ++ +r++   sl rLg++ +Dl++lHr dp+++  e  + al+el++eG i +iG+Sn+sveqle
  gi|313122474|ref|YP_004038361.1|  93 RNRDGDWLPHGDPDYLRNAHLCSLDRLGVESIDLYQLHRRDPDVD-FEASVTALAELKDEGVIEHIGLSNVSVEQLE 168
                                       *********************************************.******************************* PP

                                       HHHHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HH CS
                      Aldo_ket_red 148 kakkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsk 224
                                        a     v++++vq+++nl  ++e+  +l +c+++++++i++ pl+ G l+                          
  gi|313122474|ref|YP_004038361.1| 169 TA--RDIVDVATVQNKFNLG-HREDDDVLAACEEYDIGFIPWFPLAAGELD-------------------------- 216
                                       99..****************.******************************.......................... PP

                                       HHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 225 nldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                         ++++ l+++a++h+ +  q+ l+++l++++v+ +ipg+s++e+l++n++a  l+l++ee+a+ld+
  gi|313122474|ref|YP_004038361.1| 217 --EKVDVLESVAENHDATEYQVMLAWLLQHSPVTLPIPGTSSVEHLKQNIGATRLELTDEEMARLDK 281
                                       ..7889***********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1997.22
//
Query:       gi|313122475|ref|YP_004038362.1|  [L=831]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-43  150.2   0.1      1e-43  150.2   0.1    2.1  2  SBP_bac_8     Bacterial extracellular solute-binding protein
    4.6e-42  143.7  53.2    7.9e-39  133.2  29.2    3.3  3  MCPsignal     Methyl-accepting chemotaxis protein (MCP) signa
      3e-32  112.8   1.2    6.2e-32  111.8   1.2    1.5  1  SBP_bac_1     Bacterial extracellular solute-binding protein
    1.3e-07   31.9   0.6    1.2e-05   25.6   0.1    3.6  2  HAMP          HAMP domain
    3.1e-05   22.3  19.1     0.0017   16.7   9.7    2.2  2  EzrA          Septation ring formation regulator, EzrA
    0.00017   21.1   0.0       0.28   10.6   0.0    2.5  2  SBP_bac_6     Bacterial extracellular solute-binding protein
     0.0037   16.7   0.7     0.0062   15.9   0.0    1.7  2  Mo25          Mo25-like
     0.0064   16.7  38.9       0.13   12.5   3.8    6.2  4  DUF948        Bacterial protein of unknown function (DUF948)
  ------ inclusion threshold ------
      0.016   14.2  15.5       0.18   10.7   0.7    3.0  2  IFT57         Intra-flagellar transport protein 57
       0.14   12.3  19.7       0.94    9.6   5.6    3.9  4  Mod_r         Modifier of rudimentary (Mod(r)) protein
       0.23   10.3  28.0       0.96    8.3   6.4    2.6  3  Spc7          Spc7 kinetochore protein
       0.38   10.8  27.6        0.6   10.1   1.4    4.5  4  DUF1664       Protein of unknown function (DUF1664)
       0.46   10.6   1.9        5.7    7.0   0.1    3.0  3  TssO          Type VI secretion system, TssO
       0.51   10.4  41.8        0.8    9.7   3.3    5.1  4  Laminin_II    Laminin Domain II
       0.72   10.2  26.7        7.2    7.0   0.6    5.7  5  BLOC1_2       Biogenesis of lysosome-related organelles compl
        1.4    9.0   6.1         13    5.8   0.1    4.3  4  DASH_Dad4     DASH complex subunit Dad4
        2.1    7.4  15.8          1    8.4   2.5    2.6  2  BAR_2         Bin/amphiphysin/Rvs domain for vesicular traffi
        2.1    7.5  15.7       0.41    9.9   0.4    3.1  3  TMPIT         TMPIT-like protein
        2.3    7.2   6.8       0.61    9.1   3.0    1.9  2  DUF2009       Protein of unknown function (DUF2009)
        2.9    7.5  30.3        1.2    8.7   9.8    3.9  3  YkyA          Putative cell-wall binding lipoprotein
        3.3    5.5  14.7       0.63    7.9  10.4    1.8  2  Prominin      Prominin
        3.6    7.9  24.6        8.5    6.7   4.7    4.9  4  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
        4.1    7.9  26.0        1.3    9.5   4.5    5.1  6  FlgN          FlgN protein
        4.3    6.7  15.2        4.3    6.7   4.3    3.4  3  DUF4618       Domain of unknown function (DUF4618)
        4.7    6.7  29.1       0.94    9.0   2.4    2.9  3  Filament      Intermediate filament protein
          5    7.5   7.1        0.9    9.9   0.2    3.1  3  DUF4709       Domain of unknown function (DUF4709)
        5.1    6.8  44.8       0.28   10.9   2.9    4.2  4  DUF745        Protein of unknown function (DUF745)
        5.1    5.5   6.4        1.5    7.3   0.2    2.2  2  Baculo_F      Baculovirus F protein
        5.3    7.2   7.4        9.2    6.4   0.0    3.8  3  Med9          RNA polymerase II transcription mediator comple
        5.4    6.4  17.5        5.6    6.3   2.7    2.5  2  Not3          Not1 N-terminal domain, CCR4-Not complex compon
        7.1    5.0  19.6       0.23    9.9   6.3    2.3  2  FUSC          Fusaric acid resistance protein family
        7.6    6.7   5.6         14    5.9   0.5    3.3  3  GM_CSF        Granulocyte-macrophage colony-stimulating facto


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       5.4     3e+03     169     169 ..     279     279 ..     199     366 .. 0.51
   2 !  150.2   0.1   1.9e-46     1e-43       3     279 ..     447     766 ..     445     769 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.4
                                       H CS
                         SBP_bac_8 169 k 169
                                        
  gi|313122475|ref|YP_004038362.1| 279 A 279
                                       0 PP

  == domain 2  score: 150.2 bits;  conditional E-value: 1.9e-46
                                       HHHHHHH-.TEEEEEEE-.-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGS.TTHHH....-H CS
                         SBP_bac_8   3 akefekkt.gvkvnvvta.asndleqklkaalaagtapdidvvwanedalatlaeeglladlsdl.dnldd....lt 72 
                                       a+ef++++ ++ v  ++  ++ ++ + + aa+ +g+ p++ +++  +   +++ ++g++ +++++ +  ++    ++
  gi|313122475|ref|YP_004038362.1| 447 AEEFNDEHdDIHVHMSPKgNYRGTFDATMAAARSGSPPTVAQLFEIG--TKRALDSGVFTPVESVlPAETStsdlVP 521
                                       89******99*****************************88666654..5778889*******66555555334467 PP

                                       HHHHTT--TS.----EEEEEEE-EEEEEHHHHHHS......---BHHHHHHHHHHH..HHH-....SEGG---GGGG CS
                         SBP_bac_8  73 dalaavgydgklygvPyasetpyvliynkdlleka.....edpktwdellaaakkl..kgkf....glpdpasgwlq 138
                                       + ++++  dg+l ++P++s++p vl+yn+d++e a     ++p+t+d+l++aa+k+   g++    ++++ +++  q
  gi|313122475|ref|YP_004038362.1| 522 SIANYYRDDGTLWSLPFNSSNP-VLYYNADAFERAgldpsNPPETFDDLTQAAEKVveSGAAeygaTWANYSWFIEQ 597
                                       79*******************9.***********999999****************87455555667788888888* PP

                                       GGTHH.......ETTEE---H.....HHH.HHHHHHHHHHHHTT-EE....-S..--SSTTTTTSBSEEEE-TTH.. CS
                         SBP_bac_8 139 aalla.......kdgksldddg...gkdglkealellkklkdngkty....dtgadavsefanGevaftingswd.. 199
                                       ++++a       ++g + ++++   ++d+ + +++++ +l   g  +    +++  a ++f +G++a+ + +s++  
  gi|313122475|ref|YP_004038362.1| 598 WFATAgetlvdaSNGRDGTATTanlSSDTGETIFRWWSDLARTGLLFdpgiEARGRAREAFLDGDAAMLVDSSSNtl 674
                                       *****8888888555555555566688999**************844466699*****************8776633 PP

                                       ..HHHHH-TTTSEEEE.--....S--EEEEEEEEEEBTTS-HHHH.HHHHHHHHHTTSHHHHHHHHHH---BS-S-T CS
                         SBP_bac_8 200 ..iaaaqkagkklgai.vp....kqgsfaggkglavpknaknedl.aAldFlkwltspenqaalaektgyipvnksa 268
                                         +  a++ g++  ++ +p    ++g+++gg++l+v  + +++++ aA +Fl wlt+pe+q+ ++++tgy+pv  +a
  gi|313122475|ref|YP_004038362.1| 675 svVEGADERGFNASVGkFPapgtQEGVVVGGASLWVADDVPAREQeAAGRFLAWLTEPEQQRRWHQQTGYFPVHGDA 751
                                       32555557799999999886677788***********************************************9998 PP

                                       TT....HHHHHH-HH CS
                         SBP_bac_8 269 al....spevkkdpa 279
                                       +     + ++ + p+
  gi|313122475|ref|YP_004038362.1| 752 ERmlrrDGWFEEHPE 766
                                       855555666666655 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   8.3   4.7e-07   0.00026      79     167 ..     102     190 ..      93     194 .. 0.86
   2 !  133.2  29.2   1.4e-41   7.9e-39       3     169 ..     197     367 ..     195     370 .. 0.94
   3 ?    0.6   2.5      0.78   4.4e+02      76     144 ..     365     405 ..     357     424 .. 0.40

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.7e-07
                                       HHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  79 kLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                       +L ++   +  +++   +++ + ++++v+s+e++r+   + s+ v++ +e   + +e+++eva+++++++a++ee +
  gi|313122475|ref|YP_004038362.1| 102 DLFAELHGTMADVDVFAKQVSASTESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSATVEEVA 178
                                       5555555566677778889999******************************************************* PP

                                       HHHHHHHHHHHH CS
                         MCPsignal 156 asieevnqavee 167
                                       +s++e++++ + 
  gi|313122475|ref|YP_004038362.1| 179 SSADEIASSTSD 190
                                       ******999875 PP

  == domain 2  score: 133.2 bits;  conditional E-value: 1.4e-41
                                       HHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHH CS
                         MCPsignal   3 laeeaseeAeeg....gkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAd 75 
                                        a++a eeA +g    +++ + +v+q++++++  ++i+ +++ i eia+QTN+LALNA+iEAARA e+G GFaVVAd
  gi|313122475|ref|YP_004038362.1| 197 QARDAAEEAIDGldaiDEQTQRTVSQVDSLNELIDDITGVVTQISEIAEQTNILALNASIEAARANEAGAGFAVVAD 273
                                       678889999999777777888899999999999******************************************** PP

                                       HHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  76 EVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaase 152
                                       EV++LA+++++a+++iea+i+ei ++++++ve ++e+r+rv++ se++ee+  +l e+ve v+e +++vqei+ a++
  gi|313122475|ref|YP_004038362.1| 274 EVKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMVEDVQETNASVQEISDATD 350
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHH CS
                         MCPsignal 153 eqsasieevnqaveeva 169
                                        q+++++ev    +ev 
  gi|313122475|ref|YP_004038362.1| 351 SQATTAQEVVGQADEVG 367
                                       ********988777765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.78
                                       HHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH CS
                         MCPsignal  76 EVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlv 144
                                       EV ++                             eet  ++ + ++ +++ +++l+e  ++v+ +a++ 
  gi|313122475|ref|YP_004038362.1| 365 EVGAIS----------------------------EETAAQATTVVKSARRQTTSLSEAMTNVNALAEQA 405
                                       333333............................33333333333333333333333333333333222 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   1.2   1.1e-34   6.2e-32       8     314 ..     440     735 ..     436     736 .. 0.82

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 1.1e-34
                                       HHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTS..SSCSEEEECGGHHHHHHHTTSBECCHHHHHHTT CS
                         SBP_bac_1   8 aalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGd..gpaDviavdndwiarlakaglllpldpyvkayl 82 
                                       a+l++ +a++f+ eh +i V   +   g+++  + + +aa +   p+ v++ +   ++r  ++g+++p+ +++ a++
  gi|313122475|ref|YP_004038362.1| 440 AILMESFAEEFNDEHDDIHVHMSPK--GNYRGTFDATMAAARsgSPPTVAQLFEIGTKRALDSGVFTPVESVLPAET 514
                                       578888989******8899988777..99999444444444444677*****999999******************6 PP

                                       ECTTCCTEEEEHHHHTHHHHCE.EE...ES.EEEEE.EEEEEEETTTHHCTTGGG...SHBHHHHHHHHHHHHHHCT CS
                         SBP_bac_1  83 apgvkdaadklsssvlpkilds.kv...ly.vPlya.argliYNkdlfekagldp...pwtWdelveaakklkekgk 150
                                                  +s+ +p+i ++ ++   l+ +P+++ + +l+YN d fe agldp   p+t+d+l+ aa+k++e+g 
  gi|313122475|ref|YP_004038362.1| 515 S----------TSDLVPSIANYyRDdgtLWsLPFNSsNPVLYYNADAFERAGLDPsnpPETFDDLTQAAEKVVESGA 581
                                       4..........55678888887666789*******66**************************************** PP

                                       CTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT........HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEE CS
                         SBP_bac_1 151 kpiggarggsasgtayyfalalakslggkvfdkdgg........gldnpegvtaatylvklyavanltkelkgkgae 219
                                       ++     +g+ + + ++f +++++ +g +++d+ +g        +l++++g+t + ++ +l      t  l+++g e
  gi|313122475|ref|YP_004038362.1| 582 AE-----YGATWANYSWFIEQWFATAGETLVDASNGrdgtattaNLSSDTGETIFRWWSDLA----RTGLLFDPGIE 649
                                       **.....9999***************************999999999999999999999999....34455555555 PP

                                       CSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCS CS
                         SBP_bac_1 220 nkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsk 296
                                         + +a + +f  G+aam++++++ +       + v   ad ++++  +g++p P++  g    +g+  l++  + +
  gi|313122475|ref|YP_004038362.1| 650 ARG-RA-REAFLDGDAAMLVDSSSNT-------LSVVEGADERGFNASVGKFPAPGTQEGVV--VGGASLWVADDVP 715
                                       554.44.59999***********994.......44444444444444555556565555544..69999******** PP

                                       T..HHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 297 n..peaAkkFldfllspeaq 314
                                          +eaA  Fl++l++pe+q
  gi|313122475|ref|YP_004038362.1| 716 AreQEAAGRFLAWLTEPEQQ 735
                                       955666*************9 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   2.1e-08   1.2e-05      13      52 ..      69     108 ..      67     109 .. 0.93
   2 ?    2.0   0.0      0.48   2.7e+02      13      48 ..     142     178 ..     140     186 .. 0.40

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.1e-08
                                       HHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP  13 LaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                        ++a+++  +Gdl++r++v  + E+++La+++N++  +L+
  gi|313122475|ref|YP_004038362.1|  69 FTAAVNQFTDGDLSVRVDVPDDPEMAQLAESLNDLFAELH 108
                                       689********************************99997 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.48
                                       HHHHHHHHTTT........BTSSTCCTTSSSHHHHHHHHHHHHH CS
                              HAMP  13 LaraarriaaG........dldtrlpvsgrDEiGeLarafNaMl 48 
                                       ++++++ ia+G        d       +  +E++ L +++++ +
  gi|313122475|ref|YP_004038362.1| 142 VSDSVDDIAEGatqqsesiD-------EVANEMRNLSATVEEVA 178
                                       55666666666333333220.......23333333333333322 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.9   0.00018     0.099      97     222 ..     119     242 ..      93     251 .. 0.76
   2 !   16.7   9.7   2.9e-06    0.0017      98     221 ..     281     406 ..     272     420 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                       HHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH CS
                              EzrA  97 kkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleni 173
                                       k++ ++ +++ + +++ ++ ++++ + ++++ e  ++++e i+++ ++ r+l+ ++++   s  e++++  +     
  gi|313122475|ref|YP_004038362.1| 119 KQVSASTESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSATVEEVASSADEIASSTSDAATRG 195
                                       55666666777777777788999999999999999999999999999999999999988888777777777777777 PP

                                       ----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTT CS
                              EzrA 174 ekefsefeeltengdyveakeilkkleeeideleevieeiPelleelkk 222
                                       ++  ++ ee+ +  d  + +e+++++ +++d+l+e+i++i  +++++++
  gi|313122475|ref|YP_004038362.1| 196 QQARDAAEEAIDGLD--AIDEQTQRTVSQVDSLNELIDDITGVVTQISE 242
                                       777777777776544..56677777777777777777777777776654 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.9e-06
                                       HTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH- CS
                              EzrA  98 kakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqlenie 174
                                       +++++ +++e+ ++e+++++++  e+++e +e    ++e ie++    +e+ ++++++++s +e+ ++ ++q  + +
  gi|313122475|ref|YP_004038362.1| 281 ETQEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMVEDVQETNASVQEISDATDSQATTAQ 357
                                       678999*********************************************************************** PP

                                       ---------..------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT CS
                              EzrA 175 kefsefeel..tengdyveakeilkkleeeideleevieeiPelleelk 221
                                       +   + +e+   +++   +a  ++k++++++++l+e + ++ +l e+++
  gi|313122475|ref|YP_004038362.1| 358 EVVGQADEVgaISEETAAQATTVVKSARRQTTSLSEAMTNVNALAEQAD 406
                                       ******996326788899999********************99988765 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0005      0.28      17      81 ..     496     570 ..     493     573 .. 0.80
   2 !    7.6   0.0    0.0039       2.2     187     219 ..     713     748 ..     692     768 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                         SBP_bac_6  17 kfieeglfqpld.........panlpnvnkdfaeeglkdpdgkyy..pygvgplvlavnkdrlkgrpv.....PksW 77 
                                       ++ + g+f+p++         ++ +p+++     + ++d dg+ +  p++ +  vl++n+d+++   +     P+++
  gi|313122475|ref|YP_004038362.1| 496 RALDSGVFTPVEsvlpaetstSDLVPSIA-----NYYRD-DGTLWslPFNSSNPVLYYNADAFERAGLdpsnpPETF 566
                                       67789999999988888755555555555.....55666.6777779****************99999989989*** PP

                         SBP_bac_6  78 aDLl 81 
                                       +DL+
  gi|313122475|ref|YP_004038362.1| 567 DDLT 570
                                       ***7 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0039
                         SBP_bac_6 187 g...kkkelakafidfllspevqailakaggvfPvv 219
                                       +   +++e a +f+ +l++pe q+ +  ++g fPv 
  gi|313122475|ref|YP_004038362.1| 713 DvpaREQEAAGRFLAWLTEPEQQRRWHQQTGYFPVH 748
                                       4445599***************************94 PP

>> Mo25  Mo25-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       3.1   1.8e+03      29      49 ..     156     176 ..      95     250 .. 0.59
   2 !   15.9   0.0   1.1e-05    0.0062      21     159 ..     294     446 ..     275     553 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.1
                              Mo25  29 kkkaeeelskqLkslkeillg 49 
                                       +++ ++e+++++++l +++ +
  gi|313122475|ref|YP_004038362.1| 156 QSESIDEVANEMRNLSATVEE 176
                                       222345555555555444433 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.1e-05
                              Mo25  21 skld...........nskkkkka.eeelskqLkslkeillgdpdteps.keqvaqLlqeilkedllyklvknlkkle 84 
                                       ++++           +++++  + +e +++ L sl e++ + ++t++s +e  ++  ++    + +   + ++  ++
  gi|313122475|ref|YP_004038362.1| 294 EEIRaqseetvegitEARERVATeSETIEEALGSLDEMVEDVQETNASvQEISDATDSQATTAQEVVGQADEVGAIS 370
                                       333333344444443444443333677**************999998855555554445555555666677888888 PP

                              Mo25  85 fearkdvaqifsnllrrkt..ksklpaveyletkpeilqlllegyeskeialhagsilrecikyealariiLyseef 159
                                        e+  ++++++ +  r+ t  ++ ++ v+ l ++ ++lq  l+ y+  +  + ag+ + ++ +  +  + iL ++ f
  gi|313122475|ref|YP_004038362.1| 371 EETAAQATTVVKSARRQTTslSEAMTNVNALAEQADVLQETLDEYDLGKAETVAGKTIVQFWHAMSGSKAILMES-F 446
                                       899999999999998886622456669999****************889999*******9999888888888554.2 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   3.8   0.00024      0.13      27      88 ..     117     178 ..      90     179 .. 0.63
   2 ?    3.9   1.3      0.11        64      37      79 ..     204     242 ..     181     251 .. 0.43
   3 !    9.4   8.4    0.0022       1.2      23      88 ..     281     346 ..     225     347 .. 0.76
   4 ?    2.3   4.6      0.36     2e+02      29      84 ..     350     405 ..     344     415 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                        +++++a+ e++ + v+     ++++ + v +++e+ ++++e++d++ +++++l+++v+e+ 
  gi|313122475|ref|YP_004038362.1| 117 FAKQVSASTESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSATVEEVA 178
                                       223333344444444444444444444444447777788*******************9986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                            DUF948  37 elekqvdpilkevedllakvnelledvneklekvdplteavad 79 
                                       e  + +d+i +++++++++v      +ne ++++  +++++ +
  gi|313122475|ref|YP_004038362.1| 204 EAIDGLDAIDEQTQRTVSQVDS----LNELIDDITGVVTQISE 242
                                       2223333333333333333332....22222222222222222 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0022
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       + ++  + ++a+iee++ q +++++ ++++ + v +  e ++e l ++d+++e v+++ +sv+e++
  gi|313122475|ref|YP_004038362.1| 281 ETQEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMVEDVQETNASVQEIS 346
                                       233444445555555555555555555555566666788888899999*************99986 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.36
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       d+ a+t +e+  q+d++   +e++ a++ ++++  ++++ ++ + +++v+ l+e+ 
  gi|313122475|ref|YP_004038362.1| 350 DSQATTAQEVVGQADEVGAISEETAAQATTVVKSARRQTTSLSEAMTNVNALAEQA 405
                                       55666666777666666666777777777777777777777777777777666654 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.7   0.00032      0.18     236     332 ..      96     192 ..      91     202 .. 0.82
   2 ?    8.6   5.9    0.0014       0.8     247     333 ..     275     358 ..     258     413 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                             IFT57 236 ieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeise 312
                                       ++esl+++  +l     d++   +++++  + +  ++e++ +  r+++++++++ e   q se++ e  +e++++s 
  gi|313122475|ref|YP_004038362.1|  96 LAESLNDLFAELHGTMADVDVFAKQVSASTESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSA 172
                                       45566666666777777788888888888888888899999999999999999999999999999999999999999 PP

                             IFT57 313 elekvkqemeergssmtDgs 332
                                        +e+v +  +e  ss +D++
  gi|313122475|ref|YP_004038362.1| 173 TVEEVASSADEIASSTSDAA 192
                                       99999999999999999985 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0014
                             IFT57 247 lkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemee 323
                                       +k l ++ +++ e ie+  + +  q ee+++   ea+e++++ +e ++++ +++ e+ ++ +e++  +++++   ++
  gi|313122475|ref|YP_004038362.1| 275 VKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMVEDVQETNASVQEISDATDS 351
                                       44444444444444444444444444444444444444444444444444444444444333333333333322222 PP

                             IFT57 324 rgssmtDgsp 333
                                       +   +t ++ 
  gi|313122475|ref|YP_004038362.1| 352 Q---ATTAQE 358
                                       2...222222 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3      0.06        34      28      96 ..     125     193 ..      89     196 .. 0.57
   2 ?    9.1   1.2    0.0023       1.3      17     102 ..     173     258 ..     143     264 .. 0.69
   3 ?    9.6   5.6    0.0017      0.94      18      99 ..     275     357 ..     271     379 .. 0.83
   4 ?    2.5   1.1      0.25   1.4e+02       4      77 ..     341     415 ..     340     424 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.06
                             Mod_r  28 vkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspdal 96 
                                       ++++ ++ e+ + + +++ ++  +  +  +++++++ e  +e+++l++++ee  +  de+ +++s++a+
  gi|313122475|ref|YP_004038362.1| 125 TESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSATVEEVASSADEIASSTSDAAT 193
                                       223333333333333333333333344677777777777777888888888888888888888887765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                             Mod_r  17 klealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfsp 93 
                                        +e+++++++e+ + +++     ++ ++ ae+ ++  + ++e+ +++ ++ ++l+el +      ++ +e+ ++++ 
  gi|313122475|ref|YP_004038362.1| 173 TVEEVASSADEIASSTSDAATRGQQARDAAEEAIDGLDAIDEQTQRTVSQVDSLNELIDDITGVVTQISEIAEQTNI 249
                                       23344445577777777777777777788888888888888888888888888888888888888888888888777 PP

                             Mod_r  94 dallarLqt 102
                                        al a  ++
  gi|313122475|ref|YP_004038362.1| 250 LALNASIEA 258
                                       777666555 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0017
                             Mod_r  18 lealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfsp 93 
                                       +++l++++ + +++++++ ee++a+ e++ e   + ++++  +++ ++e+l +l+e+ + ++e ++  +e+++ +++
  gi|313122475|ref|YP_004038362.1| 275 VKSLATETqEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMVEDVQETNASVQEISDATDS 351
                                       66777777577999*****************99999************************************99988 PP

                             Mod_r  94 dallar 99 
                                       +a+ a+
  gi|313122475|ref|YP_004038362.1| 352 QATTAQ 357
                                       876653 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.25
                             Mod_r   4 SkeeLqellede.eklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekef 77 
                                       S++e+ +  +++    +++v +++ev ++ ee     ++ ++ a+++  +  e   + + l+e+ + l+e  +e+
  gi|313122475|ref|YP_004038362.1| 341 SVQEISDATDSQaTTAQEVVGQADEVGAISEETAAQATTVVKSARRQTTSLSEAMTNVNALAEQADVLQETLDEY 415
                                       677777777777667777887888888888888888788888877766665544444444555444444444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.4    0.0017      0.96     151     284 ..     100     236 ..      91     259 .. 0.78
   2 ?    8.2  13.6    0.0018         1     148     292 ..     240     383 ..     228     399 .. 0.82
   3 ?    5.0   4.5     0.017       9.5     146     244 ..     326     420 ..     318     424 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                              Spc7 151 leedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles.id..keeLeelreelaelkaeieekkkelae 224
                                       l++  ++L+  ++ +d + +++++  +++ + +e+ ++a++++++ +d   e   +  e+++e+ +e++++++ ++e
  gi|313122475|ref|YP_004038362.1| 100 LNDLFAELHGTMADVDVFAKQVSASTESVVDSVEDSRSASRNVSDsVDdiAEGATQQSESIDEVANEMRNLSATVEE 176
                                       55555778888999999999999999999999999999888887744446677788889999999999999999999 PP

                              Spc7 225 lqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgw 284
                                       + +  +e++++ ++++++ ++++++ +ea + l++  + ++  vs++ +  + ++++tg+
  gi|313122475|ref|YP_004038362.1| 177 VASSADEIASSTSDAATRGQQARDAAEEAIDGLDAIDEQTQRTVSQVDSLNELIDDITGV 236
                                       999999999999999999999999999998887777777777777777766667776665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0018
                              Spc7 148 legleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelae 224
                                       ++++ e+ + L+ + +   +  +e  + +a + +e+++l ++ +e ++  ++ +ee+r + +e  + i e ++++a+
  gi|313122475|ref|YP_004038362.1| 240 ISEIAEQTNILALNASIEAARANEAGAGFAVVADEVKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERVAT 316
                                       55555566666666665566667777788899999999999999977777999************************ PP

                              Spc7 225 lqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivslsgs 292
                                         e +ee   +++e+ e  +e+++ ++e  + ++  +  +++ev    +ev a+ e+t  + +++ +s
  gi|313122475|ref|YP_004038362.1| 317 ESETIEEALGSLDEMVEDVQETNASVQEISDATD-SQATTAQEVVGQADEVGAISEETAAQATTVVKS 383
                                       ************************9999888877.788999****************99999998855 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.017
                              Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkel 222
                                         l+++ ed ++ +++ +e++++ ++  +  +e+  ++++  + +ee ++   + ++++r++ ++l++ +     ++
  gi|313122475|ref|YP_004038362.1| 326 GSLDEMVEDVQETNASVQEISDATDSQATTAQEVVGQADEVGAISEETAAQATTVVKSARRQTTSLSEAMT----NV 398
                                       45677778888777888888888888888888999999999999999999999999999999888888877....67 PP

                              Spc7 223 aelqeqleeleekieelkeqks 244
                                       + l eq + l+e+++e +  k+
  gi|313122475|ref|YP_004038362.1| 399 NALAEQADVLQETLDEYDLGKA 420
                                       7777777777777766665555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.4    0.0011       0.6      39     120 ..      96     177 ..      91     179 .. 0.86
   2 ?    8.4   2.3    0.0036         2      37     114 ..     168     244 ..     165     257 .. 0.74
   3 ?    7.9   3.7    0.0055       3.1      46     114 ..     271     339 ..     259     349 .. 0.49
   4 ?    1.6   1.2      0.47   2.6e+02      60     112 ..     348     404 ..     339     415 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       l++ ++++  +l   ++++    ++ s+  ++v ++++++  +s+++++ v+++ e+ ++ +e +++v + +++l +
  gi|313122475|ref|YP_004038362.1|  96 LAESLNDLFAELHGTMADVDVFAKQVSASTESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSA 172
                                       66677777788888888888889999999999999999999999999999999999999999999999999999999 PP

                           DUF1664 116 kleri 120
                                       ++e++
  gi|313122475|ref|YP_004038362.1| 173 TVEEV 177
                                       98876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0036
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       r+ls  ve+v+++ +++ +s +++  + ++  d  ++ +d   +i +++++ v++v +   e+ +d++ v + ++++
  gi|313122475|ref|YP_004038362.1| 168 RNLSATVEEVASSADEIASSTSDAATRGQQARDAAEEAIDGLDAIDEQTQRTVSQVDSLN-ELIDDITGVVTQISEI 243
                                       89******************9999999999999999999888888888888877775433.3333333333333333 PP

                           DUF1664 114 e 114
                                       +
  gi|313122475|ref|YP_004038362.1| 244 A 244
                                       3 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0055
                           DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       v+ +++++ ++ +++ +++++ i+++ ++ +e+ e ++e +e v++ +e ++e    ++++ e v++ +
  gi|313122475|ref|YP_004038362.1| 271 VADEVKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMVEDVQETN 339
                                       444444455555555555555555555555555555555555544444444444333333333344444 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.47
                           DUF1664  60 tkrhLssridrvdkkldeqkeiskeikee....vtevredlseigedvesvkeaveg 112
                                       + +  +   ++v  + de+ +is+e++++    v+++r+++++++e +++v+++ e+
  gi|313122475|ref|YP_004038362.1| 348 ATDSQATTAQEVVGQADEVGAISEETAAQattvVKSARRQTTSLSEAMTNVNALAEQ 404
                                       444445555667777777777777776661111444555555555555555555444 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.2   6.8e+02      53      93 ..     149     190 ..     131     196 .. 0.72
   2 ?    7.0   0.1      0.01       5.7      43     146 ..     202     305 ..     192     307 .. 0.83
   3 ?    1.3   0.1       0.6   3.4e+02      50      96 ..     304     350 ..     294     359 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.2
                              TssO  53 feekqkelkkkvdsiykkIdsL.kpevnavfleneIkkdlnd 93 
                                       + e   ++++ +d++ +++ +L   ++  +   +eI  + +d
  gi|313122475|ref|YP_004038362.1| 149 IAEGATQQSESIDEVANEMRNLsATVEEVASSADEIASSTSD 190
                                       555566788899999999999955555555666777776665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.01
                              TssO  43 llkelerkkkfeekqkelkkkvdsiykkIdsLkpevnavfleneIkkdlndikntygknssdeRykmyaqiakfykm 119
                                        ++ ++   +++e+ + + ++vds+ + Id ++ +v ++ +  e ++++  ++ +++    +e    +a++a+  k+
  gi|313122475|ref|YP_004038362.1| 202 AEEAIDGLDAIDEQTQRTVSQVDSLNELIDDITGVVTQISEIAE-QTNILALNASIEAARANEAGAGFAVVADEVKS 277
                                       467788889999************************99998888.889999999999988888899**********9 PP

                              TssO 120 lledKke.lksvseniklfkkqLeecei 146
                                       l +  +e   +++  i++++ q ee  +
  gi|313122475|ref|YP_004038362.1| 278 LATETQEaTEDIEAAIEEIRAQSEETVE 305
                                       9766555056667799999999999765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.6
                              TssO  50 kkkfeekqkelkkkvdsiykkIdsLkpevnavfleneIkkdlndikn 96 
                                        + + e  + ++++ ++i++ + sL+  v +v+++n   ++++d+ +
  gi|313122475|ref|YP_004038362.1| 304 VEGITEARERVATESETIEEALGSLDEMVEDVQETNASVQEISDATD 350
                                       56677778888999999999999999999999999887777777665 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.3    0.0014       0.8       5      69 ..     111     175 ..      90     177 .. 0.74
   2 ?    8.1   7.4    0.0045       2.5       6      98 ..     154     246 ..     145     261 .. 0.71
   3 ?    8.7   4.6     0.003       1.7       4      66 ..     271     333 ..     269     338 .. 0.91
   4 ?    3.1   7.6      0.16        91       9      68 ..     332     395 ..     327     420 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                       +a+++  ak+v + ++ +   +e  ++   ++ +sv+ + e + + ++ i+++ +++++L  +++
  gi|313122475|ref|YP_004038362.1| 111 MADVDVFAKQVSASTESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSATVE 175
                                       45666667777777778888888888888888888888888888888888888888888777665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0045
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       ++ +e++ ev + + +ls+ +e++ +++ ei++s        ++a  a ++A +    ++++ ++ ++++ +l++l 
  gi|313122475|ref|YP_004038362.1| 154 TQQSESIDEVANEMRNLSATVEEVASSADEIASSTSDAATRGQQARDAAEEAIDGLDAIDEQTQRTVSQVDSLNELI 230
                                       44556667777777777777777777777777775555555556666666666667778899999999999999999 PP

                                       HH...HHHHHHHHHHH CS
                        Laminin_II  83 eassslsdniseikel 98 
                                       +    +  +isei e+
  gi|313122475|ref|YP_004038362.1| 231 DDITGVVTQISEIAEQ 246
                                       9977777777777665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.003
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-- CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLek 66 
                                       +a+e+++ a+e++e ++++++ +e+++++ +e  + + e  e v   +++i++A  s  ++ +
  gi|313122475|ref|YP_004038362.1| 271 VADEVKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMVE 333
                                       68999***********************************************99998887765 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.16
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXX--TT CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveet....nekvkdankairdArrsvkkLekla 68 
                                        e ++e+ + ++++s  ++     ++e+ ++++e+    +e + +a++++++Arr+   L + +
  gi|313122475|ref|YP_004038362.1| 332 VEDVQETNASVQEISDATDSQATTAQEVVGQADEVgaisEETAAQATTVVKSARRQTTSLSEAM 395
                                       4555555555555555555555555555555555411113344466666666666666555432 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.6     0.013       7.2      13      89 ..     105     182 ..      94     190 .. 0.70
   2 ?    6.3   0.6     0.021        12      47      88 ..     203     244 ..     190     255 .. 0.60
   3 ?    6.2   3.0     0.023        13      25      86 ..     293     347 ..     269     357 .. 0.55
   4 ?    3.1   0.7      0.21   1.2e+02      41      83 ..     372     414 ..     361     417 .. 0.69
   5 ?    0.8   0.0       1.1     6e+02      23      40 ..     813     830 ..     797     831 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                           BLOC1_2  13 aeleatvedyklLeklNeaasekykkl.kdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                       ael +t +d+++  k   a++e + +  +d+ +  ++ ++ ++   e   ++ ++id++ ++ + L ++v+e+ +  
  gi|313122475|ref|YP_004038362.1| 105 AELHGTMADVDVFAKQVSASTESVVDSvEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSATVEEVASSA 181
                                       67888888888888777777766554404444444444556777777888888888888888888888888876655 PP

                           BLOC1_2  89 k 89 
                                        
  gi|313122475|ref|YP_004038362.1| 182 D 182
                                       5 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.021
                           BLOC1_2  47 ekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                       e+ ++ l++ +e+ q  ++q+d +++ +++++ +v ++ e+ 
  gi|313122475|ref|YP_004038362.1| 203 EEAIDGLDAIDEQTQRTVSQVDSLNELIDDITGVVTQISEIA 244
                                       444555555555666666666666666666666555554443 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.023
                           BLOC1_2  25 LeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                       +e++  ++       ++ ++++++  e++  ++e++++ l ++d++ ++v+e  + v+e+  
  gi|313122475|ref|YP_004038362.1| 293 IEEIRAQS-------EETVEGITEARERVATESETIEEALGSLDEMVEDVQETNASVQEISD 347
                                       33444444.......45555555555555555555555555555555555555555555544 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.21
                           BLOC1_2  41 dvaaslekkleklnekyeelqpylqqidqiekqvteLeeavse 83 
                                       + aa++++ ++  +++  +l++ +++++++ +q + L+e+ +e
  gi|313122475|ref|YP_004038362.1| 372 ETAAQATTVVKSARRQTTSLSEAMTNVNALAEQADVLQETLDE 414
                                       4556666666777777777777777777777777777776554 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.1
                           BLOC1_2  23 klLeklNeaasekykklk 40 
                                       ++Le++Ne+++++  +++
  gi|313122475|ref|YP_004038362.1| 813 RVLEEMNEQVEYRLSEYD 830
                                       789*******99988765 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.4   1.4e+03       8      45 ..     155     192 ..     153     198 .. 0.80
   2 ?    0.9   0.3      0.79   4.4e+02      14      47 ..     217     250 ..     214     256 .. 0.83
   3 ?    5.8   0.1     0.023        13      14      52 ..     312     350 ..     308     357 .. 0.87
   4 ?    0.6   0.0      0.98   5.5e+02       8      38 ..     386     416 ..     383     436 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.4
                         DASH_Dad4   8 qqsalLsRIiknvekLnesvvelnkeleeinkkNknve 45 
                                       qqs  ++ + + + +L+ +v+e+ ++  ei +++++ +
  gi|313122475|ref|YP_004038362.1| 155 QQSESIDEVANEMRNLSATVEEVASSADEIASSTSDAA 192
                                       77777888888899999999999999999988887765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.79
                         DASH_Dad4  14 sRIiknvekLnesvvelnkeleeinkkNknvelv 47 
                                       +R ++ v+ Lne + ++   + +i++  ++++++
  gi|313122475|ref|YP_004038362.1| 217 QRTVSQVDSLNELIDDITGVVTQISEIAEQTNIL 250
                                       79999********999998888888777776665 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.023
                         DASH_Dad4  14 sRIiknvekLnesvvelnkeleeinkkNknvelvsqlwe 52 
                                       +R+ +  e + e++  l++++e++++ N++v+ +s+  +
  gi|313122475|ref|YP_004038362.1| 312 ERVATESETIEEALGSLDEMVEDVQETNASVQEISDATD 350
                                       57778889999*********************9998765 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.98
                         DASH_Dad4   8 qqsalLsRIiknvekLnesvvelnkeleein 38 
                                       +q+  Ls  ++nv+ L e+   l+++l e+ 
  gi|313122475|ref|YP_004038362.1| 386 RQTTSLSEAMTNVNALAEQADVLQETLDEYD 416
                                       7888888899999999999999999998875 PP

>> BAR_2  Bin/amphiphysin/Rvs domain for vesicular trafficking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.5    0.0019         1      77     168 ..      97     188 ..      89     193 .. 0.88
   2 ?    5.5   3.8     0.015       8.2      67     185 ..     224     344 ..     220     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                             BAR_2  77 gaklkelknvssleedeivllgkkkkekskeekesqatsallprtlaqalskaakdsslilqeleekdedlepLikv 153
                                       ++ l++l+     + + +  ++k+ +++++   +s ++s + +r     +  +a++++++ ++++e  +++ +L+  
  gi|313122475|ref|YP_004038362.1|  97 AESLNDLFAELHGTMADVDVFAKQVSASTESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSAT 173
                                       55666666666677777778999999999999999****************************************** PP

                             BAR_2 154 leqvssaykeiaeak 168
                                        e+v+s+  eia++ 
  gi|313122475|ref|YP_004038362.1| 174 VEEVASSADEIASST 188
                                       ***********9875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                             BAR_2  67 esisdwwksigaklkelknvssleedeivllgkkkkekskeekesqatsallprtlaqalskaakdsslilqeleek 143
                                       +s++++ + i+  +++++++++ ++   +  + +++ ++++     a  a   ++la    +a++d +  ++e++++
  gi|313122475|ref|YP_004038362.1| 224 DSLNELIDDITGVVTQISEIAEQTNILALNASIEAARANEAGA-GFAVVADEVKSLATETQEATEDIEAAIEEIRAQ 299
                                       7888888888888888888876665555444444444433333.477788889*********************987 PP

                             BAR_2 144 ded.lepLikvleqvssaykeiaeakleqDsli..vkefnkkLee 185
                                       +e+ +e + ++ e v++  + i+ea    D+++  v+e n+ ++e
  gi|313122475|ref|YP_004038362.1| 300 SEEtVEGITEARERVATESETIEEALGSLDEMVedVQETNASVQE 344
                                       7662688999******************99998555677776665 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.012       6.5       5      86 ..      98     178 ..      95     179 .. 0.87
   2 ?    9.9   0.4   0.00073      0.41       2      92 ..     158     247 ..     157     256 .. 0.89
   3 ?    0.3   8.1      0.58   3.2e+02      16      82 ..     284     356 ..     269     432 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                       e+l++ f el+ t   +    +++s++ ++++ +++  +   +++++s++++ + + ++++e ++e+++e+++ +++
  gi|313122475|ref|YP_004038362.1|  98 ESLNDLFAELHGTMADVDVFAKQVSASTESVVDSVEDSRSASRNVSDSVDDIAEGA-TQQSESIDEVANEMRNLSAT 173
                                       67788888899999999999999999999999999999999999999999999985.79999999999999999998 PP

                             TMPIT  82 lkeve 86 
                                       ++ev+
  gi|313122475|ref|YP_004038362.1| 174 VEEVA 178
                                       88875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00073
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                       e+++e+++e+++l++t +e+ ++ +e++++ s+ +++ ++ +  ++e  + l+ +++++ +++ ++v++l+e ++++
  gi|313122475|ref|YP_004038362.1| 158 ESIDEVANEMRNLSATVEEVASSADEIASSTSDAATRGQQARDAAEEAIDGLDAIDEQT-QRTVSQVDSLNELIDDI 233
                                       67899**************************************************9995.78999999999999999 PP

                             TMPIT  79 kkvlkevesllpkk 92 
                                       + v+ +++++  ++
  gi|313122475|ref|YP_004038362.1| 234 TGVVTQISEIAEQT 247
                                       99999998875554 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.58
                             TMPIT  16 etakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeelkerkkvl 82 
                                       e+ + +++ +ee+ ++ +++++ i++ ++r+   ++++++   s++      +e++  v+e+++ ++++ ++ 
  gi|313122475|ref|YP_004038362.1| 284 EATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDemvedvQETNASVQEISDATDSQATTA 356
                                       2222333333333333333333333333333333333332222221111122334444444444444333333 PP

>> DUF2009  Protein of unknown function (DUF2009)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.9   1.1e+03     169     194 ..     147     172 ..     114     232 .. 0.52
   2 ?    9.1   3.0    0.0011      0.61     141     232 ..     263     354 ..     218     430 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.9
                           DUF2009 169 eeiqkeikekeeaieklakkysskkl 194
                                       ++i + +++++e+i+++a++ ++ ++
  gi|313122475|ref|YP_004038362.1| 147 DDIAEGATQQSESIDEVANEMRNLSA 172
                                       33333344444444444444444333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                           DUF2009 141 eekealelledklielataeisaekksreeiqkeikekeeaieklakkysskklskeeieqvlysiednnafleanr 217
                                       e+    +++ d+  +lat++ +a++   ++i++   + ee++e +++  ++  +++e+ie++l s++++ + ++++ 
  gi|313122475|ref|YP_004038362.1| 263 EAGAGFAVVADEVKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMVEDVQETN 339
                                       445566899999999999999999999999**999****************99*********************999 PP

                           DUF2009 218 epvekllkllekffe 232
                                        +v+++ +  +++ +
  gi|313122475|ref|YP_004038362.1| 340 ASVQEISDATDSQAT 354
                                       999998877665544 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.4     0.015       8.3      54     162 ..     123     233 ..      91     253 .. 0.52
   2 ?    8.7   9.8    0.0022       1.2      13     109 ..     261     348 ..     251     361 .. 0.77
   3 ?    3.3   5.2       0.1        58      11     112 ..     329     414 ..     327     428 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                              YkyA  54 klsdealenveeReellekekesieeakeefekikeeieei..edeelkkeaeelieameeryeaydklykaYkeal 128
                                       +  + ++++ve+ ++   +  +s+++  e  ++ +e+i+e+  e  +l   +ee++++ +e  ++ ++  ++ ++a 
  gi|313122475|ref|YP_004038362.1| 123 ASTESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVanEMRNLSATVEEVASSADEIASSTSDAATRGQQAR 199
                                       44455555555555555555555555555555555555555322234555555555555555555555555555555 PP

                              YkyA 129 eldkeLYemLkkeeltleeleeqiekiNesyeev 162
                                       ++ +e  + L   + + ++   q++++Ne  +++
  gi|313122475|ref|YP_004038362.1| 200 DAAEEAIDGLDAIDEQTQRTVSQVDSLNELIDDI 233
                                       5555555555554444444444555555444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0022
                              YkyA  13 avelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekike 89 
                                       a+e+  +f+  +++ ++l  + qe  e+i e+ ++e   i ++s+e +e + e +e++++e e ieea   ++++ e
  gi|313122475|ref|YP_004038362.1| 261 ANEAGAGFAVVADEVKSLATETQEATEDI-EAAIEE---IRAQSEETVEGITEARERVATESETIEEALGSLDEMVE 333
                                       445557889999999999*******9999.456666...****************************9999999998 PP

                              YkyA  90 eieeiedeelkkeaeeliea 109
                                       +++e++       ++e  +a
  gi|313122475|ref|YP_004038362.1| 334 DVQETNA-----SVQEISDA 348
                                       8888832.....23333333 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.1
                              YkyA  11 eeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefeki 87 
                                       +e+ve+ +e ++  ++++++   +  + +e++               +a e     ee  ++  +++++a+ + +++
  gi|313122475|ref|YP_004038362.1| 329 DEMVEDVQETNASVQEISDATDSQATTAQEVV--------------GQADEVGAISEETAAQATTVVKSARRQTTSL 391
                                       45555555555555555555555555555555..............5555555555555555555555555555555 PP

                              YkyA  88 keeieeiedeelkkeaeelieamee 112
                                       +e + ++  ++l ++a+ l+e+++e
  gi|313122475|ref|YP_004038362.1| 392 SEAMTNV--NALAEQADVLQETLDE 414
                                       5555555..3344555555544443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  10.4    0.0011      0.63     167     416 ..      96     340 ..      93     348 .. 0.80
   2 ?    5.7   2.6    0.0052       2.9     258     379 ..     275     399 ..     259     419 .. 0.45

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                          Prominin 167 ldegleesketvkrgledlrtflkdvpqhidhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaeler 243
                                       l e+l++   +++ ++ d+  f k+v++  ++v++    e    +s +++d  + + +   +++es   ++ +e+++
  gi|313122475|ref|YP_004038362.1|  96 LAESLNDLFAELHGTMADVDVFAKQVSASTESVVDS--VEDSRSASRNVSDSVDDIAEGATQQSESI-DEVANEMRN 169
                                       677778888889999********************9..66666999999999999*99999999997.9999***** PP

                          Prominin 244 llenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcl.dqlpn 319
                                       l   ++e+  +  ++ +++++    g+q rd+ +++ + l+ + ++  ++++ s++ s +e   +d  + +  q+++
  gi|313122475|ref|YP_004038362.1| 170 LSATVEEVASSADEIASSTSDAATRGQQARDAAEEAIDGLDAIDEQ--TQRTVSQVDSLNEL--IDDITGVvTQISE 242
                                       ***********************************99999988777..22344444444433..3333333355555 PP

                          Prominin 320 vdevle..aleevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdl 394
                                       + e+ +  al+  +e+  ++ +  g a + +  + ++++t+e ++d+  a++++r+q +++ + i +ea ++v+ + 
  gi|313122475|ref|YP_004038362.1| 243 IAEQTNilALNASIEAARANEAGAGFAVVADEVKSLATETQEATEDIEAAIEEIRAQSEETVEGI-TEARERVATES 318
                                       544433116777778887777888888887777778899**************************.88888888888 PP

                          Prominin 395 enterssktfddvvekyekyrw 416
                                       e++e+ + + d+ ve ++++  
  gi|313122475|ref|YP_004038362.1| 319 ETIEEALGSLDEMVEDVQETNA 340
                                       8888888888888887776654 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0052
                          Prominin 258 vnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcl.dqlpnvdevlealeevlet 333
                                       v++l +e ++ ++++++++++++ + +++++   +++e   ++s++  e l +  ++ + +++++  ++++ +++++
  gi|313122475|ref|YP_004038362.1| 275 VKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMvEDVQETNASVQEISDATDS 351
                                       55555666666666666666666666666665322222222222222222222222224444444444444444333 PP

                          Prominin 334 nls..sivkeglarlneipekvknqtaevvpdlkkalakgreqikkla 379
                                       + +  + v  + +++ +i+e  + q ++vv++  ++ ++ +e++ ++ 
  gi|313122475|ref|YP_004038362.1| 352 QATtaQEVVGQADEVGAISEETAAQATTVVKSARRQTTSLSEAMTNVN 399
                                       222002222334445555555555555555555544444444433333 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.7     0.027        15      31      95 ..     132     186 ..     108     194 .. 0.47
   2 ?    6.7   4.7     0.015       8.5      14      98 ..     192     290 ..     186     307 .. 0.63
   3 ?    2.4   6.4      0.32   1.8e+02      23      92 ..     284     358 ..     272     370 .. 0.50
   4 ?    0.7   0.2       1.1   5.9e+02      58      93 ..     380     415 ..     371     417 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  31 lleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkelea 95 
                                       + +  ++ r++   ++++ +   + s          e ++e+ +e+++l++ ++++    +e+ +
  gi|313122475|ref|YP_004038362.1| 132 VEDSRSASRNVSDSVDDIAEGATQQS----------ESIDEVANEMRNLSATVEEVASSADEIAS 186
                                       33333333333333333333333333..........44444444444444444444444444443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.015
                                       HHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT..............S-TCCCCCCC CS
                      Seryl_tRNA_N  14 vkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk..............edaeeliaev 76 
                                         + +++R ++++ +d l ++de+ +++ +++++l++    ++  + ++++                + a+e  a  
  gi|313122475|ref|YP_004038362.1| 192 ATRGQQARDAAEEAIDGLDAIDEQTQRTVSQVDSLNELIDDITGVVTQISEIAeqtnilalnasieaARANEAGAGF 268
                                       55677888888889999999999999999999999888888877666655544333555544444333333444444 PP

                                       HHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  77 kelkeelkaleaelkeleaele 98 
                                       + + +e+k l +e +e+++++e
  gi|313122475|ref|YP_004038362.1| 269 AVVADEVKSLATETQEATEDIE 290
                                       4444555555555555544444 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.32
                                       CCCHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  23 edkadvdell.eldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelke 92 
                                       e+++d+++ + e+ ++ +e+   + e++++  + s++I++a  +     ed +e  a+v+e+++ ++   ++ +e
  gi|313122475|ref|YP_004038362.1| 284 EATEDIEAAIeEIRAQSEETVEGITEARERVATESETIEEALGSLdemvEDVQETNASVQEISDATDSQATTAQE 358
                                       333444333302333333333444555555555555555555554444466666666666666655555555555 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.1
                                       HCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  58 eIgkakkkkedaeeliaevkelkeelkaleaelkel 93 
                                        +++a ++    +e +  v++l e+ + l+++l+e 
  gi|313122475|ref|YP_004038362.1| 380 VVKSARRQTTSLSEAMTNVNALAEQADVLQETLDEY 415
                                       567777777888999999999999999999999875 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.7   1.5e+03      84     132 ..      88     136 ..      63     142 .. 0.70
   2 ?    5.5   4.4     0.042        23      38     116 ..     144     222 ..     133     257 .. 0.63
   3 ?    4.7   5.4     0.074        41      36     132 ..     222     311 ..     213     313 .. 0.68
   4 ?    9.5   4.5    0.0023       1.3      45     114 ..     273     346 ..     265     366 .. 0.74
   5 ?    0.3   1.5       1.7   9.3e+02      62     100 ..     367     412 ..     341     417 .. 0.43
   6 ?   -1.6   0.0       6.2   3.5e+03      58      98 ..     733     776 ..     725     778 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.7
                                       TCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHXX CS
                              FlgN  84 eedeelkelwqelkelleelkelnelNgrlieqslefnqrllnllqgaa 132
                                       ++d+e ++l ++l +l +el+ +      + +q  +++++ ++ +  ++
  gi|313122475|ref|YP_004038362.1|  88 PDDPEMAQLAESLNDLFAELHGTMADVDVFAKQVSASTESVVDSVEDSR 136
                                       5788888888888888888888777777777777777777766666555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN  38 eaLeelleekqellekleqleqkrakllaelglsaeeatlsellak..eedeelkelwqelkelleelkelnelNgr 112
                                       ++ ++++e  +++ e +++ ++++++l a ++++    + +e++++  +++++ ++++++ +e+++ l ++ e+ +r
  gi|313122475|ref|YP_004038362.1| 144 DSVDDIAEGATQQSESIDEVANEMRNLSATVEEV--ASSADEIASStsDAATRGQQARDAAEEAIDGLDAIDEQTQR 218
                                       5566666777777777777777777777777777..45666666655566666666666666666666666666666 PP

                                       HHHH CS
                              FlgN 113 lieq 116
                                       ++ q
  gi|313122475|ref|YP_004038362.1| 219 TVSQ 222
                                       6554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN  36 dieaLeelleekqellekleqleqkrakllaelglsaeeatlsellakeedeelkelwqelkelleelkelnelNgr 112
                                       ++++L+el+++++ ++ ++++++++   l  +++ +       ++ a+e+ +  + + +e+k+l+ e +e+ e  + 
  gi|313122475|ref|YP_004038362.1| 222 QVDSLNELIDDITGVVTQISEIAEQTNILALNASIE-------AARANEAGAGFAVVADEVKSLATETQEATEDIEA 291
                                       566777777777777777777777766666666666.......5555577777777777777777777777777777 PP

                                       HHHHCCHHHHHHHHHCCHXX CS
                              FlgN 113 lieqslefnqrllnllqgaa 132
                                       +ie   ++ +++++ +++a+
  gi|313122475|ref|YP_004038362.1| 292 AIEEIRAQSEETVEGITEAR 311
                                       77777777777766666665 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT.....TCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN  45 eekqellekleqleqkrakllaelglsaeeatlsellak.....eedeelkelwqelkelleelkelnelNgrli 114
                                       +e ++l+ + +++ ++++++++e+  + +e+t++ + ++     +e e ++e+  +l+e++e+++e+n + +++ 
  gi|313122475|ref|YP_004038362.1| 273 DEVKSLATETQEATEDIEAAIEEIRAQ-SEETVEGITEArervaTESETIEEALGSLDEMVEDVQETNASVQEIS 346
                                       566677777777777888888888777.44444444444444889***********************9888765 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.7
                                       HHHHHHTT--.........SCHHHHHHHHCTTCCHHHHHHHHHHHHHH CS
                              FlgN  62 akllaelgls.........aeeatlsellakeedeelkelwqelkell 100
                                        ++ +e + +          ++++lse+      ++l+e+ + l+e+l
  gi|313122475|ref|YP_004038362.1| 367 GAISEETAAQattvvksarRQTTSLSEAMT--NVNALAEQADVLQETL 412
                                       333333333311112222333444444443..4444444444444444 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHTT--SCHHHHHHHHCT....TCCHHHHHHHHHHHH CS
                              FlgN  58 eqkrakllaelglsaeeatlsellak....eedeelkelwqelke 98 
                                       eq+ +++ ++ g+ + +   +++l++    ee++e + + ++l e
  gi|313122475|ref|YP_004038362.1| 733 EQQ-RRWHQQTGYFPVHGDAERMLRRdgwfEEHPEFAVAFEQLNE 776
                                       444.455556666679999999999999999****9999999976 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.05        28     187     225 ..     145     183 ..      91     188 .. 0.70
   2 ?    1.4   0.9      0.32   1.8e+02      64     104 ..     274     314 ..     269     320 .. 0.67
   3 ?    6.7   4.3    0.0077       4.3       6      98 ..     323     413 ..     318     417 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.05
                           DUF4618 187 enqvlkkeiekfrefieeleeeipeLkaeveqLqaqaee 225
                                       +  ++++   ++ e i+e  +e+ +L a+ve+ + +a e
  gi|313122475|ref|YP_004038362.1| 145 SVDDIAEGATQQSESIDEVANEMRNLSATVEEVASSADE 183
                                       345667777899999999999999999999998888776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                           DUF4618  64 qleqakaeLqeweekeekklekLeqqleqlnakvqklqeel 104
                                       +++++  e qe +e +e  +e+++ q e+  + +++++e +
  gi|313122475|ref|YP_004038362.1| 274 EVKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERV 314
                                       55666667777777777777777777777777666666655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0077
                           DUF4618   6 ksleelkkheaeLtklnkeLvkeIqdtedstakkvrklLqqyeklktvisileksskkqleqakaeLqeweekeekk 82 
                                       ++l  l +  ++ +++n++ v+eI d  ds a  ++++  q + ++ +++ +  +  + +++a+++  ++ e +  +
  gi|313122475|ref|YP_004038362.1| 323 EALGSLDEMVEDVQETNAS-VQEISDATDSQATTAQEVVGQADEVGAISEETAAQATTVVKSARRQTTSLSEAM-TN 397
                                       5677788888999999988.689*******************************************99998887.58 PP

                           DUF4618  83 lekLeqqleqlnakvq 98 
                                       ++ L++q++ l++++ 
  gi|313122475|ref|YP_004038362.1| 398 VNALAEQADVLQETLD 413
                                       9******999988776 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.4    0.0017      0.94     194     276 ..     136     218 ..      62     233 .. 0.69
   2 ?    8.6  12.4    0.0023       1.3     162     276 ..     284     400 ..     251     416 .. 0.80
   3 ?   -2.0   0.5       3.7   2.1e+03     266     286 ..     810     830 ..     805     831 .] 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                                       XXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 194 kskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleee 270
                                       +s   +++++++   e + +  e i e+  ++ +l++ +e++ ++++ + ++ +++  r +++++ ++e+++ l++ 
  gi|313122475|ref|YP_004038362.1| 136 RSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSATVEEVASSADEIASSTSDAATRGQQARDAAEEAIDGLDAI 212
                                       34456778888888888888889999999999999999999999999999999999999999999999888888764 PP

                                       HHHHHH CS
                          Filament 271 laeire 276
                                        +++++
  gi|313122475|ref|YP_004038362.1| 213 DEQTQR 218
                                       444333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0023
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 162 arkldLteilkeiraqyeelaeknreeaeewy..kskleelqeaaeknsealrsakeeitelrrqiqsleieleslk 236
                                       + + d++++++eiraq ee +e  +e  e++   ++ +ee+  + ++  e++++++  ++e+    +s  +  +++ 
  gi|313122475|ref|YP_004038362.1| 284 EATEDIEAAIEEIRAQSEETVEGITEARERVAteSETIEEALGSLDEMVEDVQETNASVQEISDATDSQATTAQEVV 360
                                       45678****************98777666543114456666666777778888899999999999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 237 kqkasleaqlaeleerleaeleklqeklseleeelaeire 276
                                       +q++ + a  +e+ ++  + +++++++ ++l e+++++ +
  gi|313122475|ref|YP_004038362.1| 361 GQADEVGAISEETAAQATTVVKSARRQTTSLSEAMTNVNA 400
                                       9999999999999999999999999999999999998864 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHHHHHHHHH CS
                          Filament 266 eleeelaeireemarqlreYq 286
                                       e+e+ l+e+ e+++ +l+eY+
  gi|313122475|ref|YP_004038362.1| 810 EVERVLEEMNEQVEYRLSEYD 830
                                       566667777777777777775 PP

>> DUF4709  Domain of unknown function (DUF4709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.9   1.6e+03      27      87 ..      91     153 ..      75     176 .. 0.64
   2 ?    9.9   0.2    0.0016       0.9      10      94 ..     207     289 ..     200     307 .. 0.89
   3 ?   -1.5   0.1       5.2   2.9e+03      10      55 ..     366     410 ..     359     415 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.9
                           DUF4709  27 lelkeltevtqkLvkevkslkrdfeflkqllqakyeeklk..eealelytrlndklkelekly 87 
                                       +e+ +l+e++++L  e++    d+++  + + a+ e+ +   e + +  +++ d ++++ +  
  gi|313122475|ref|YP_004038362.1|  91 PEMAQLAESLNDLFAELHGTMADVDVFAKQVSASTESVVDsvEDSRSASRNVSDSVDDIAEGA 153
                                       567777777777777777777777777776666666655422455555555666666555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0016
                           DUF4709  10 vGffatDhatQTdvsEilelkeltevtqkLvkevkslkrdfeflkqllqakyeeklkeealelytrlndklkelekl 86 
                                        G+ a D+ tQ  vs + +l+el++ +  +v++++++ +++++l  +l+a+ e    +ea + +  + d++k+l + 
  gi|313122475|ref|YP_004038362.1| 207 DGLDAIDEQTQRTVSQVDSLNELIDDITGVVTQISEIAEQTNIL--ALNASIEAARANEAGAGFAVVADEVKSLATE 281
                                       578889*********************************99987..6999999999*****************9999 PP

                           DUF4709  87 ykekvevv 94 
                                       ++e  e +
  gi|313122475|ref|YP_004038362.1| 282 TQEATEDI 289
                                       99887765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 5.2
                           DUF4709  10 vGffatDhatQTdvsEilelkeltevtqkLvkevkslkrdfeflkq 55 
                                       vG +++  a+Q  +  + + ++ t+++++ +++v++l +++++l++
  gi|313122475|ref|YP_004038362.1| 366 VGAISEETAAQATT-VVKSARRQTTSLSEAMTNVNALAEQADVLQE 410
                                       55555555555432.2333344444444444444444444444444 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.9    0.0005      0.28      57     133 ..     107     184 ..     104     190 .. 0.85
   2 ?    2.6   1.0      0.17        98      43      75 ..     192     224 ..     185     247 .. 0.63
   3 ?    1.8  12.6      0.31   1.7e+02      46     132 ..     255     344 ..     241     348 .. 0.67
   4 ?    5.5   9.3     0.022        13      61     127 ..     343     409 ..     340     416 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0005
                            DUF745  57 LaGKqqlveqleqelr.eaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqq 132
                                       L+G  + v+   ++++  +e+vv+++++s ++s +  +++ ++a+ a+qq e++ ++ +++++  +++e+va++a +
  gi|313122475|ref|YP_004038362.1| 107 LHGTMADVDVFAKQVSaSTESVVDSVEDSRSASRNVSDSVDDIAEGATQQSESIDEVANEMRNLSATVEEVASSADE 183
                                       5566666666667765257999***************************************************9976 PP

                            DUF745 133 e 133
                                        
  gi|313122475|ref|YP_004038362.1| 184 I 184
                                       4 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.17
                            DUF745  43 AdkAlqAakAAeAaLaGKqqlveqleqelreae 75 
                                       A +  qA  AAe a++G  ++ eq+++ ++  +
  gi|313122475|ref|YP_004038362.1| 192 ATRGQQARDAAEEAIDGLDAIDEQTQRTVSQVD 224
                                       556667777777777777777777766665543 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.31
                            DUF745  46 AlqAakAAeAaLaGKqql...veqleqelreaeavvqeekksl.qsseanakaaakaakqaqqqlealkallkaake 118
                                        ++Aa+A eA  aG  ++   v++l  e +ea + ++   +++ ++se++++  ++a++ + ++ e+++++l +  e
  gi|313122475|ref|YP_004038362.1| 255 SIEAARANEAG-AGFAVVadeVKSLATETQEATEDIEAAIEEIrAQSEETVEGITEARERVATESETIEEALGSLDE 330
                                       35666665553.44444411155667777777777777666663578888888888888888888888888888888 PP

                            DUF745 119 nlenaeqvaagaqq 132
                                        +e++++++a++q+
  gi|313122475|ref|YP_004038362.1| 331 MVEDVQETNASVQE 344
                                       88888888877764 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.022
                            DUF745  61 qqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqva 127
                                       q + + ++++ + a++vv +  +  + se++a+ a++++k+a++q ++l++++ ++++ +e+a+ ++
  gi|313122475|ref|YP_004038362.1| 343 QEISDATDSQATTAQEVVGQADEVGAISEETAAQATTVVKSARRQTTSLSEAMTNVNALAEQADVLQ 409
                                       678889999***********************************************99999987665 PP

>> Baculo_F  Baculovirus F protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0026       1.5     154     243 ..     105     192 ..      80     199 .. 0.86
   2 ?    0.4   1.7      0.32   1.8e+02     180     244 ..     273     337 ..     212     415 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0026
                          Baculo_F 154 kylfGvmDdkDAelLhklaksenslneqvkqltdeliklseyveskkqeieeqkedkCeyieaklnllkdqldeies 230
                                         l G m d D+ +  ++  s++s+ + v    +   ++s+ v+++ +e  +q++++ +++++++ +l ++++e++s
  gi|313122475|ref|YP_004038362.1| 105 AELHGTMADVDVFAK-QVSASTESVVDSVEDSRSASRNVSDSVDDI-AEGATQQSESIDEVANEMRNLSATVEEVAS 179
                                       567888988888775.8999999999********************.666677799********************* PP

                          Baculo_F 231 lytkldravddAl 243
                                         +++    +dA 
  gi|313122475|ref|YP_004038362.1| 180 SADEIASSTSDAA 192
                                       *999998887775 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.32
                          Baculo_F 180 eqvkqltdeliklseyveskkqeieeqkedkCeyieaklnllkdqldeieslytkldravddAlk 244
                                       + vk+l +e+ + +e +e   +ei+ q+e++ e i++  + + ++ + ie++   ld+ v+d ++
  gi|313122475|ref|YP_004038362.1| 273 DEVKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERVATESETIEEALGSLDEMVEDVQE 337
                                       46777777777777777777777777777777777777777777777777777777766666553 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.016       9.2       5      71 ..     102     172 ..      98     181 .. 0.81
   2 ?    0.3   0.1       1.4   7.7e+02      21      73 ..     181     237 ..     171     243 .. 0.63
   3 ?    1.9   0.4      0.42   2.4e+02      21      74 ..     279     333 ..     270     345 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                              Med9   5 liydilksiekdpnlsskdletktgelrhkLkkarelirelpg....idrsveeqeaeieeleeqlakKre 71 
                                       +++  l+ +  d  + +k+++++t ++ +  +  r++ r++++    i +   +q + i+e  +++++  +
  gi|313122475|ref|YP_004038362.1| 102 DLFAELHGTMADVDVFAKQVSASTESVVDSVEDSRSASRNVSDsvddIAEGATQQSESIDEVANEMRNLSA 172
                                       56666666666667778999999999999999999999999999999999999999999999999887665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                              Med9  21 skdletktgelrhkLkkarelirelpg....idrsveeqeaeieeleeqlakKrelL 73 
                                       + ++ ++t++  ++ ++ar + +e  +    id+ ++    ++++l+e ++    + 
  gi|313122475|ref|YP_004038362.1| 181 ADEIASSTSDAATRGQQARDAAEEAIDgldaIDEQTQRTVSQVDSLNELIDDITGVV 237
                                       555556666666666667665555443344488888888888888877766655555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.42
                              Med9  21 skdletktgelrhkLkkarelire.lpgidrsveeqeaeieeleeqlakKrelLk 74 
                                       +++++ +t ++   ++++r++ +e ++gi +  e    e e+ ee l    e+ +
  gi|313122475|ref|YP_004038362.1| 279 ATETQEATEDIEAAIEEIRAQSEEtVEGITEARERVATESETIEEALGSLDEMVE 333
                                       4555566666666666666666542455666666666666666666555555555 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.7      0.01       5.6     120     207 ..     155     248 ..     130     263 .. 0.63
   2 ?    5.1   7.0     0.023        13     112     214 ..     273     374 ..     253     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.01
                              Not3 120 ekeearewlkdaideLneqvekleaeieklsskk.....kkkkk.skekarveeleklierhkfhieklelllrlle 190
                                       +++e ++ + + +++L+  ve++ +++++++s++     + +++ +++++ ++ l+++ e+++  +++++ l +l++
  gi|313122475|ref|YP_004038362.1| 155 QQSESIDEVANEMRNLSATVEEVASSADEIASSTsdaatRGQQArDAAEEAIDGLDAIDEQTQRTVSQVDSLNELID 231
                                       34444444555555555555555555555555443333222222355556777777777888888888888888888 PP

                              Not3 191 neelepeevekikedie 207
                                       + +   +++ +i e+ +
  gi|313122475|ref|YP_004038362.1| 232 DITGVVTQISEIAEQTN 248
                                       77777788888777765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                              Not3 112 ekldpkekekeearewlkdaideLneqvekleaeieklsskkkkkkkskekarveeleklierhkfhieklelllrl 188
                                       ++++    e +ea+e ++ ai+e++ q e++ + i + +++  ++  +++++ + +l++++e  +   ++++++ ++
  gi|313122475|ref|YP_004038362.1| 273 DEVKSLATETQEATEDIEAAIEEIRAQSEETVEGITEARERVATES-ETIEEALGSLDEMVEDVQETNASVQEISDA 348
                                       4567778889999999999999999999988887777666555544.677789999999999999999999999999 PP

                              Not3 189 leneelepeevekikedieyyvesnq 214
                                        + ++ +++ev    +++  + e++ 
  gi|313122475|ref|YP_004038362.1| 349 TDSQATTAQEVVGQADEVGAISEETA 374
                                       99999999999999999988877655 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   5.1      0.19   1.1e+02     210     321 ..      89     212 ..      49     224 .. 0.41
   2 ?    9.9   6.3   0.00041      0.23     213     334 ..     218     356 ..     214     384 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.19
                              FUSC 210 esprirararalrrllsrmlallallsslarllarlraeeaaavpe.......laallaelaaleaaaaaealeaal 279
                                       ++p++++ a+ l+ l +++   +a ++ +a++  +  ++  ++v++       +++ ++++a+  a++++e +++ +
  gi|313122475|ref|YP_004038362.1|  89 DDPEMAQLAESLNDLFAELHGTMADVDVFAKQVSASTESVVDSVEDsrsasrnVSDSVDDIAE-GATQQSESIDEVA 164
                                       444444444444444444444444444444444444444433333333332333333333333.3333333333333 PP

                              FUSC 280 aalrarlralrrale......adadtaalllarlaellaelaqllasl 321
                                       +++r   + +++ ++       +++ aa   +++++  +e+++ l+++
  gi|313122475|ref|YP_004038362.1| 165 NEMRNLSATVEEVASsadeiaSSTSDAATRGQQARDAAEEAIDGLDAI 212
                                       333333333333333222443333333333333333344444433333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00041
                              FUSC 213 rirararalrrllsrmlallallsslarlla..rlraeeaaavpe.....laallaelaal..eaaaaaealeaala 280
                                       r+  +++ l++l  +++ +++++s++a++ +  +l+a+ +aa++      +a + +e+++l  e ++a+e++eaa++
  gi|313122475|ref|YP_004038362.1| 218 RTVSQVDSLNELIDDITGVVTQISEIAEQTNilALNASIEAARANeagagFAVVADEVKSLatETQEATEDIEAAIE 294
                                       555678899*****************998762255555555555566677777777777766544455555555555 PP

                              FUSC 281 alrarlralrrale...adadtaalllarlaellaelaqllaslraleaaiaa.....arra 334
                                       ++ra+ +++ +      ++ +t+ + +++++  l+e+++  ++ +a+ ++i++     a  a
  gi|313122475|ref|YP_004038362.1| 295 EIRAQSEETVEGITearERVATESETIEEALGSLDEMVEDVQETNASVQEISDatdsqATTA 356
                                       55555555555555999889999999999999999999999999999998888444433333 PP

>> GM_CSF  Granulocyte-macrophage colony-stimulating factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.71     4e+02       7      48 ..     190     231 ..     185     249 .. 0.81
   2 ?    5.9   0.5     0.024        14      14      54 ..     316     356 ..     302     365 .. 0.87
   3 ?   -1.8   0.0       6.1   3.4e+03       9      48 ..     391     413 ..     367     426 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.71
                                       -TTT-TTHHHHHHHHHHHHHHH----HHHHTSEEEEESS--B CS
                            GM_CSF   7 spvtrpwkhvdaikealsllnessdlaavlneevevvseefd 48 
                                        ++tr  +  da +ea++ l+  ++++     +v+ + e  d
  gi|313122475|ref|YP_004038362.1| 190 DAATRGQQARDAAEEAIDGLDAIDEQTQRTVSQVDSLNELID 231
                                       5789999**************999888888888887776654 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHH----HHHHTSEEEEESS--BSSS--S CS
                            GM_CSF  14 khvdaikealsllnessdlaavlneevevvseefdlqeptc 54 
                                          ++i+eal  l+e+ +   + n +v+ +s+  d+q  t 
  gi|313122475|ref|YP_004038362.1| 316 TESETIEEALGSLDEMVEDVQETNASVQEISDATDSQATTA 356
                                       45689************999****************99886 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 6.1
                                       TT-TTHHHHHHHHHHHHHHH----HHHHTSEEEEESS--B CS
                            GM_CSF   9 vtrpwkhvdaikealsllnessdlaavlneevevvseefd 48 
                                        + +   v+a                 l e+ +v++e++d
  gi|313122475|ref|YP_004038362.1| 391 LSEAMTNVNA-----------------LAEQADVLQETLD 413
                                       2222222333.................3334444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (831 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2075  (0.115734); expected 358.6 (0.02)
Passed bias filter:                      843  (0.0470188); expected 358.6 (0.02)
Passed Vit filter:                       165  (0.00920297); expected 17.9 (0.001)
Passed Fwd filter:                        96  (0.00535445); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 1.71u 0.34s 00:00:02.04 Elapsed: 00:00:00.52
# Mc/sec: 4811.13
//
Query:       gi|313122476|ref|YP_004038363.1|  [L=257]
Description: dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-63  213.4   3.5    3.8e-63  213.2   3.5    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    2.1e-59  200.3   2.2    2.8e-59  199.9   2.2    1.1  1  adh_short       short chain dehydrogenase
    3.1e-15   56.6   0.3      4e-15   56.2   0.3    1.1  1  KR              KR domain
    2.7e-05   23.7   0.1    4.4e-05   23.1   0.1    1.5  1  Epimerase       NAD dependent epimerase/dehydratase family
     0.0057   15.8   0.1       0.01   14.9   0.1    1.5  1  RmlD_sub_bind   RmlD substrate binding domain
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.021   14.1   0.0    1.5  1  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
      0.014   14.8   0.1      0.023   14.1   0.1    1.5  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
      0.048   13.6   0.4      0.095   12.6   0.4    1.5  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.2   3.5   1.7e-66   3.8e-63       1     230 [.      17     246 ..      17     247 .. 0.93

  Alignments for each domain:
  == domain 1  score: 213.2 bits;  conditional E-value: 1.7e-66
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilv 74 
                                       Ga sgIG+ iA+++a+eGa+vv++ +++ + +  ++ + e  g ++  +ecDVtd+e+vealve++ve+fg lD+lv
  gi|313122476|ref|YP_004038363.1|  17 GASSGIGKTIAERFAAEGANVVVCSREQGNvNPVADGINEGDGGRAlaVECDVTDREAVEALVEATVEEFGDLDCLV 93 
                                       899************************999555555555555555336***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg.gsivnlssvgaervvpnynaygaaKaalea 150
                                       nnag +    ++f ++s +++++++d+nl++++++++ a +++k+g g ++nl+sv+++ + p  ++ygaaKa++++
  gi|313122476|ref|YP_004038363.1|  94 NNAGASFM--SSFDDISANGWETVVDINLTGTYHCTQVAGEYLKDGgGTVINLASVAGTEGAPFMSHYGAAKAGVVN 168
                                       *******9..*******************************999998****************************** PP

                                       HHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEE CS
                      adh_short_C2 151 ltrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtl 227
                                       lt +lA+e++++++RvN+++pg+++T+ +++        ++++++   +r+gt+ee+a++a fLas+++syi G+t+
  gi|313122476|ref|YP_004038363.1| 169 LTTTLAYEWADENVRVNCIAPGFVATPGVESQM--GVSADNIDREEVKRRIGTAEEIADLAQFLASPASSYIVGETV 243
                                       ***************************988776..456788999999999**************************9 PP

                                       EES CS
                      adh_short_C2 228 vvD 230
                                       v+ 
  gi|313122476|ref|YP_004038363.1| 244 VAQ 246
                                       875 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.9   2.2   1.2e-62   2.8e-59       1     188 [.      11     198 ..      11     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 199.9 bits;  conditional E-value: 1.2e-62
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklg 76 
                                       ++++vtGassGIG+ ia+++a+eGa+vvv++r++ +++ va+ ++e  g +ala+++Dvtdre+vealve+ v+++g
  gi|313122476|ref|YP_004038363.1|  11 QTAIVTGASSGIGKTIAERFAAEGANVVVCSREQGNVNPVADGINEGdGGRALAVECDVTDREAVEALVEATVEEFG 87 
                                       589*******************************************99***************************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                        ld+LvnNAG + +++f ++s++ we v+++Nltg++++t+ + ++ lk  +G+++n +Svag ++ + ++ Y+A+K
  gi|313122476|ref|YP_004038363.1|  88 DLDCLVNNAGASFMSSFDDISANGWETVVDINLTGTYHCTQVAGEY-LKDGGGTVINLASVAGTEGAPFMSHYGAAK 163
                                       ******************************************9999.6699************************** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmak 188
                                       a+v+ lt +la e+a++++rvn++aPG+v+T+ ++
  gi|313122476|ref|YP_004038363.1| 164 AGVVNLTTTLAYEWADENVRVNCIAPGFVATPGVE 198
                                       *******************************9765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.3   1.8e-18     4e-15       2     154 ..      12     164 ..      11     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.8e-18
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78 
                                       t ++tG+  g+G+++a+  a++ga ++v++sR++ + +  ++ i+  e  g +  +v++Dv+d++aveal+e+  +e
  gi|313122476|ref|YP_004038363.1|  12 TAIVTGASSGIGKTIAERFAAEGA-NVVVCSREQGNVNPVADGIN--EGDGGRALAVECDVTDREAVEALVEATVEE 85 
                                       569********************8.68899***766666665666..45699************************* PP

                                       SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esldffvlfSSiagllgsagqanYaaa 152
                                       ++ +   ++ Ag++  + +++ +a+ +e+v+   ++G+ +  ++  +   +    ++ ++S+ag+ g++  ++Y aa
  gi|313122476|ref|YP_004038363.1|  86 FGDLDCLVNNAGASFMSSFDDISANGWETVVDINLTGTYHCTQVAGEylkDGGGTVINLASVAGTEGAPFMSHYGAA 162
                                       ********************************************99866566779*********************9 PP

                                       HH CS
                                KR 153 Na 154
                                        a
  gi|313122476|ref|YP_004038363.1| 163 KA 164
                                       76 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1     2e-08   4.4e-05       2      72 ..      14      96 ..      13     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2e-08
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHH....HH.T-SEE CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfk....ee.qpdav 68
                                      +VtGa+  iG+ ++++++++g +v++ +r++ + n  ++            ve+d+tdr+a+e+l++    e+ + d+ 
  gi|313122476|ref|YP_004038363.1| 14 IVTGASSGIGKTIAERFAAEGANVVVCSREQGNVNPVADGINegdggraLAVECDVTDREAVEALVEatveEFgDLDCL 92
                                      8*****************************77777655444499****999*********8887765111133455555 PP

                                      EE-- CS
                         Epimerase 69 ihlA 72
                                      ++ A
  gi|313122476|ref|YP_004038363.1| 93 VNNA 96
                                      5554 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   4.6e-06      0.01       4      50 ..      14      82 ..      11     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-06
                                      EEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................T--TTSHHHHHHHHHHH CS
                     RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlaltre......................eldltdaeavaellkea 50
                                      +vtGa+  +G+ +a+++a+eg++v+ ++re                      e+d+td+eav++l++++
  gi|313122476|ref|YP_004038363.1| 14 IVTGASSGIGKTIAERFAAEGANVVVCSREqgnvnpvadginegdggralavECDVTDREAVEALVEAT 82
                                      79**************************999*********************************99876 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.6e-06     0.021      32      73 ..       6      47 ..       1      54 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.6e-06
                                      ---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCH CS
                     THF_DHG_CYH_C 32 ielegkkvvvvGrsnivgkplallLleknatVtvchsktkdl 73
                                        ++g++++v G+s+ +gk++a  +++++a V vc ++  ++
  gi|313122476|ref|YP_004038363.1|  6 FGVDGQTAIVTGASSGIGKTIAERFAAEGANVVVCSREQGNV 47
                                      5689*******************************9987665 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     1e-05     0.023       2     111 ..      15     128 ..      14     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.... CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.... 74 
                                       +TG +  iG  +ae++ ++g +v++  r + ++n   ++   +  +e   ++   +++D+tD++++e l++ +    
  gi|313122476|ref|YP_004038363.1|  15 VTGASSGIGKTIAERFAAEGANVVVCSREQGNVN--PVA---DGINEGDGGRALAVECDVTDREAVEALVEATveef 86 
                                       99*9999****************98766555444..443...3333455689999**************99886766 PP

                                       .T-SEEEE--S---H....HHHTTSHHHHHHHHTHHHHHHHH CS
                     GDP_Man_Dehyd  75 .qpdevynLAAqshV....dvsfekPeytaevnvlGtlrLLe 111
                                        + d  +n A+ s+     d s +  e+++++n++Gt++  +
  gi|313122476|ref|YP_004038363.1|  87 gDLDCLVNNAGASFMssfdDISANGWETVVDINLTGTYHCTQ 128
                                       778888888888776222245777778888888888877655 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   4.3e-05     0.095       1      59 [.      17      80 ..      17      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH......CTTTCEEEE--TT-CCHHHHHHT CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaele......aeeglevvegdvtdvedlaealk 59
                                      GA+ ++G+ ++++ +a+g  +v++  R++  ++ ++      +  ++ +ve dvtd e++++ ++
  gi|313122476|ref|YP_004038363.1| 17 GASSGIGKTIAERFAAEG-ANVVVCSREQGNVNPVAdginegDGGRALAVECDVTDREAVEALVE 80
                                      9****************5.9********99998655344444557999************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1873.14
//
Query:       gi|313122477|ref|YP_004038364.1|  [L=81]
Description: hypothetical protein Hbor_37110 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-18   67.4   0.6    1.9e-18   67.0   0.6    1.2  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
      0.093   13.3   3.1      0.089   13.4   1.3    1.7  2  DUF883        Bacterial protein of unknown function (DUF883)


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.6   2.1e-22   1.9e-18       1      69 []       7      69 ..       7      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 2.1e-22
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgilseeeadeiekaskelrkefk 69
                                      +++++++++Y++Lk +K+egeSFsd++ r++++++      ll+l+gils++ead +++a++e +++++
  gi|313122477|ref|YP_004038364.1|  7 RNVRLTEDAYQRLKMRKQEGESFSDTVARIAGERS------LLDLAGILSDDEADAMRDAIREREEQSR 69
                                      5899**************************99777......************************9976 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.18   1.6e+03      34      52 ..      13      31 ..       3      40 .. 0.52
   2 ?   13.4   1.3   9.9e-06     0.089      16      54 ..      41      79 ..      31      81 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.18
                            DUF883 34 erleerlerarerlrdaee 52
                                      e + +rl+  +++ +  ++
  gi|313122477|ref|YP_004038364.1| 13 EDAYQRLKMRKQEGESFSD 31
                                      3444444444444444444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.9e-06
                            DUF883 16 ellkeaadeageeaeelRerleerlerarerlrdaeeav 54
                                      +ll+ a+  +++ea+++R+ ++er e++r+rl+++++++
  gi|313122477|ref|YP_004038364.1| 41 SLLDLAGILSDDEADAMRDAIREREEQSRDRLDRLSDEM 79
                                      788899999*************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 594.84
//
Query:       gi|313122478|ref|YP_004038365.1|  [L=130]
Description: nucleic acid-binding protein, contains PIN domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-11   43.5   0.0    5.4e-11   43.1   0.0    1.2  1  PIN       PIN domain
     0.0013   19.4   0.1     0.0015   19.3   0.1    1.4  1  PIN_3     PIN domain
  ------ inclusion threshold ------
       0.02   15.4   0.0      0.044   14.3   0.0    1.6  2  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   9.1e-15   5.4e-11       1     120 [.       1     123 [.       1     125 [. 0.83

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 9.1e-15
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCH CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpida 75 
                                       +++DT+vli+l+  +e+ ++++r+l +e   l++s+ +l El++ ++r     +  +e+++      ++    p d 
  gi|313122478|ref|YP_004038365.1|   1 MIVDTNVLIRLMqGDEDATRKIRELEDEHVPLALSSMTLFELYHSVER----VDSPDERRRKIASvIDSKPTYPADG 73 
                                       68**********99999999999999999*******************....4444433333333377777778889 PP

                                       HHHHHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTH.HHHHH CS
                               PIN  76 eiaeeaaeialkyg.....llpnDaliaAtAkehgikliatfDed.frrva 120
                                       ++ ++a+++  ++      +++ D +iaAtA+ h  +++ t +   f+r++
  gi|313122478|ref|YP_004038365.1|  74 AVMKKAGRLDGRLTddgrqVGIGDTVIAATALVHEEPVL-TENVAhFERID 123
                                       9999999999998899**********************9.98755477776 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   2.5e-07    0.0015       3      56 ..       2      53 ..       1     117 [. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.5e-07
                             PIN_3  3 vlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypq 56
                                      ++Dtnvl+  +  d+ a rki+++ e++ + l +s ++l+El+  ++r+ + p+
  gi|313122478|ref|YP_004038365.1|  2 IVDTNVLIRLMQGDEDATRKIREL-EDEHVPLALSSMTLFELYHSVERV-DSPD 53
                                      68**********999899998887.******************988777.4443 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.4e-06     0.044       2      52 ..       2      49 ..       1      82 [. 0.81
   2 ?   -1.0   0.0      0.36   2.1e+03     138     150 ..      91     103 ..      50     109 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.4e-06
                            PIN_12  2 fiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekk 52
                                      ++DTn++++ +++ +e+ a +k++el ++ ++ l++++++l E+++ +e++
  gi|313122478|ref|YP_004038365.1|  2 IVDTNVLIR-LMQGDED-ATRKIRELEDE-HVPLALSSMTLFELYHSVERV 49
                                      69******7.7777777.*****887777.6*************9998876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.36
                            PIN_12 138 kkkgfgDaliwes 150
                                        + g+gD++i  +
  gi|313122478|ref|YP_004038365.1|  91 RQVGIGDTVIAAT 103
                                       3445666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 914.74
//
Query:       gi|313122479|ref|YP_004038366.1|  [L=404]
Description: acyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-38  130.6   1.0    7.7e-38  130.0   1.0    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    7.1e-20   71.0   0.0    1.2e-19   70.3   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.3e-19   70.9   0.4    2.9e-19   69.8   0.2    1.8  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.7e-16   60.7   1.4    3.1e-16   59.8   1.4    1.5  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.024   14.3   0.0    1.5  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina
      0.066   13.2   0.1       0.17   11.9   0.1    1.7  1  Subtilosin_A   Bacteriocin subtilosin A


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   1.0   2.6e-41   7.7e-38       1     148 [.     239     386 ..     239     388 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 2.6e-41
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       ++Gf+ a+++l   Rl+++++  g+a rale a +y ++r+af   l ++q+vr+ +ae +++l+a+r +v++aa +
  gi|313122479|ref|YP_004038366.1| 239 NRGFEHAQQRLGPARLTHCMRYTGMATRALEVAKAYTKEREAFDSSLSEKQSVRFTVAEAETRLHAVRTMVRDAAGR 315
                                       79*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                       + ag+++r  +sm K+++++++q+v+d+++ql+Gg+G++++ p++ +y d+r++r+ +G++e+++++iar 
  gi|313122479|ref|YP_004038366.1| 316 IAAGEEARIPVSMSKVYTANVVQDVIDDCLQLCGGNGIAKDLPLADFYEDVRAFRLIDGADEVHKRVIARD 386
                                       *********************************************************************96 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   4.1e-23   1.2e-19       1      97 []     127     227 ..     127     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 4.1e-23
                                       EEE---..SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEE CS
                     Acyl-CoA_dh_M   1 afalTE..pqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvs 74 
                                       +f +TE  p++Gsd + ++++ a+++g+e+v++G+K+w t++ +a++++v+art+ ++  ++g slflvp+da gv+
  gi|313122479|ref|YP_004038366.1| 127 GFSMTEpaPGGGSDPKMIRSE-ARKEGDEWVIDGHKWWTTQGSEADVLIVMARTDPEAhPYEGTSLFLVPADADGVE 202
                                       5899**77789*********5.5556666************************5555589***************** PP

                                       E.-----BSS.-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  75 v.rrieeklG.lrglptgelvfedv 97 
                                       + r+i++  G l g +++e+++e+v
  gi|313122479|ref|YP_004038366.1| 203 IvRDIPHVGGdLLGSSHAEIRYENV 227
                                       *999976544445666777777775 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.2   9.8e-23   2.9e-19       1     113 []       6     123 ..       6     123 .. 0.91
   2 ?   -3.7   0.0         6   1.8e+04       5      26 ..     142     162 ..     140     172 .. 0.65

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 9.8e-23
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHH.H...HHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefpre.l...wkklaelGllgitvpeeygGagldyleaaivaeelar 73 
                                       te+ ++l ++vref++e++ p+++++  +g +p+e +   ++++ e +l++ ++p eygG+gl++ + + ++ee +r
  gi|313122479|ref|YP_004038366.1|   6 TETARELAKRVREFVDERVIPVERDYLGDGPVPDEeIaalREEARERDLYAPQIPAEYGGQGLNFRDVLPAFEEAGR 82 
                                       7899*****************99999999999955335669999********************************* PP

                                       H-HHHHH.HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  74 adaglal.llgvhsslvapailrfGteeqkrryLpklasge 113
                                         +g ++  +++ +  +++++   Gte+qk++yL++l++ge
  gi|313122479|ref|YP_004038366.1|  83 SLLGPSAmRIAAPDEGNMHTLELVGTEAQKEEYLRPLVAGE 123
                                       888655548999***************************98 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6
                                       HHHHHHHHHHHHHHTHHHHHHH CS
                     Acyl-CoA_dh_N   5 ealrdtvrefaeeelaphaaew 26 
                                       +++r ++r+  +e + +  ++w
  gi|313122479|ref|YP_004038366.1| 142 KMIRSEARKEGDEWVID-GHKW 162
                                       68888888877777765.3344 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   1.4     1e-19   3.1e-16       2     126 ..     255     369 ..     254     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       ++++  +G+A +al+ + ++++er    +  +l++++ + +++aea++rl+A r+++++aa r    +aag+e    
  gi|313122479|ref|YP_004038366.1| 255 THCMRYTGMATRALEVAKAYTKEREA--FDSSLSEKQSVRFTVAEAETRLHAVRTMVRDAAGR----IAAGEEA--- 322
                                       6888999*******************..***********************************....8889986... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaa 126
                                        r   +++++++++  ++++d++ +++Gg++++k+ pl  ++ D++a 
  gi|313122479|ref|YP_004038366.1| 323 -RIPVSMSKVYTANVVQDVIDDCLQLCGGNGIAKDLPLADFYEDVRAF 369
                                       .9999*********************************9999999886 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.1e-06     0.024     180     229 ..     156     204 ..     138     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-06
                                       EEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEE CS
                            HpaB_N 180 vVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlkli 229
                                       v+ G k  +T++  ad ++v+    + ++   +    f vp+da+G++++
  gi|313122479|ref|YP_004038366.1| 156 VIDGHKWWTTQGSEADVLIVMARTDP-EAHPYEGTSLFLVPADADGVEIV 204
                                       9**********************888.7778888999**********987 PP

>> Subtilosin_A  Bacteriocin subtilosin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.7e-05      0.17      14      27 ..      32      45 ..      31      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.7e-05
                                      -TTTT---S--S-T CS
                      Subtilosin_A 14 LvdGPiPDFEvAai 27
                                      L dGP+PD E+Aa 
  gi|313122479|ref|YP_004038366.1| 32 LGDGPVPDEEIAAL 45
                                      569*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2939.63
//
Query:       gi|313122480|ref|YP_004038367.1|  [L=361]
Description: aminoglycoside phosphotransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-43  149.0   6.6    2.8e-43  148.6   6.6    1.2  1  APH       Phosphotransferase enzyme family
    8.3e-05   22.0   0.0    0.00013   21.4   0.0    1.2  1  EcKinase  Ecdysteroid kinase
  ------ inclusion threshold ------
       0.03   13.2   0.0      0.046   12.6   0.0    1.1  1  DUF1679   Protein of unknown function (DUF1679)


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   6.6   4.6e-47   2.8e-43       2     221 ..      39     270 ..      38     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 4.6e-47
                                       EEEE--.SSCEEEEEEETT--EEEEEE-TT...S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE CS
                               APH   2 vrelsggasnrtylvttpagryvlrrnppa...raaeeirrevallrlLakagvpvPevlagdtddeeigllfalie 75 
                                       v+++++g sn t ++t++a+++v rr+pp+   ++a ++ re++++++L++++vpvPe +  + d++++g  f++++
  gi|313122480|ref|YP_004038367.1|  39 VERHPAGHSNETLFLTWGARDLVIRRPPPGetaETAHDVLREYRVMDALQQTPVPVPETVLACDDHDVLGSDFYVMS 115
                                       7899**************************66666666669************************************ PP

                                       ----EE-SS.....HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCC.... CS
                               APH  76 yvpgrsllr.....klsaaqlpellealgeflaalhqvdpaalpladflaqdlellrqlesatarllaselld.... 143
                                       +v+g +l++       +++ + +l+++l+++la++h+v+p++ +l+ f++   +  rq+e++ + +la +++     
  gi|313122480|ref|YP_004038367.1| 116 RVEGDVLRDevperFADEESRHQLGYELVDTLADIHEVAPESVGLDEFGHAPGYTGRQVERWGK-QLAWAFERttek 191
                                       *************9999*********************************************65.444444445567 PP

                                       .HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC...TTEEEEE---TT-EEEECCHHHHCCHHHCSCHCCC CS
                               APH 144 .lleeleeqvlaalaallpgelptvllHgDlhpgNllvd.pddgrvtGviDfedaglgpplyDlavllrswtseldp 218
                                         +  l+e v ++la+++p++ p++l+HgD++++N++   + d+ +++v+D+e+++lg+p +Dl+++l +w+++ dp
  gi|313122480|ref|YP_004038367.1| 192 rAVPVLRE-VGDWLAENAPTDHPETLVHGDYKLDNVMYApESDPNLVAVFDWEMSTLGDPRADLGWMLSYWRDAKDP 267
                                       66667777.******************************96666667*********************88**99996 PP

                                       HCH CS
                               APH 219 efl 221
                                        ++
  gi|313122480|ref|YP_004038367.1| 268 DPA 270
                                       554 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.2e-08   0.00013     209     261 ..     208     258 ..     170     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.2e-08
                          EcKinase 209 ekeeefnvlnHGDlwvnNimfkydeegepedvilvDFQlsrygSpalDLlyfl 261
                                        ++++  +l+HGD+ + N+m+   +e++p+ v  +D+ +s +g p  DL  +l
  gi|313122480|ref|YP_004038367.1| 208 APTDHPETLVHGDYKLDNVMYA--PESDPNLVAVFDWEMSTLGDPRADLGWML 258
                                       5667779*************95..5678********************97665 PP

>> DUF1679  Protein of unknown function (DUF1679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.7e-06     0.046     269     314 ..     215     258 ..     210     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-06
                           DUF1679 269 vlvhgDlwsaNiLfseeeegklklkkviDyQlvslgnpaeDlvrll 314
                                        lvhgD    N++++ e++   +l +v D+ + +lg p  Dl+ +l
  gi|313122480|ref|YP_004038367.1| 215 TLVHGDYKLDNVMYAPESD--PNLVAVFDWEMSTLGDPRADLGWML 258
                                       79**************999..56779****************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2576.60
//
Query:       gi|313122481|ref|YP_004038368.1|  [L=264]
Description: ABC-type multidrug transport system, ATPase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-27   97.0   0.0    1.7e-27   96.6   0.0    1.2  1  ABC_tran  ABC transporter
    4.6e-15   56.2   0.0    7.2e-10   39.1   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00052   19.8   0.0       0.27   10.9   0.0    2.1  2  AAA_15    AAA ATPase domain
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.019   15.5   0.0    1.2  1  AAA_23    AAA domain
      0.024   14.4   0.6      0.072   12.8   0.6    1.8  1  AAA_30    AAA domain
      0.039   14.2   0.1       0.24   11.7   0.1    2.1  1  AAA_22    AAA domain
      0.046   14.1   0.0       0.25   11.8   0.0    2.0  1  AAA       ATPase family associated with various cellular acti
      0.052   13.9   0.0       0.09   13.2   0.0    1.4  1  AAA_16    AAA ATPase domain
        0.1   11.2   0.1        1.7    7.2   0.0    2.0  2  AAA_13    AAA domain
        0.1   12.4   0.3        0.2   11.5   0.3    1.5  1  AAA_29    P-loop containing region of AAA domain
       0.18   11.4   0.0       0.32   10.6   0.0    1.4  1  AAA_27    AAA domain
       0.26   10.9   0.7       0.53    9.9   0.7    1.5  1  SRP54     SRP54-type protein, GTPase domain
       0.28   11.4   2.0        1.5    9.1   0.2    2.6  2  AAA_28    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   1.2e-30   1.7e-27       2     137 .]      20     162 ..      19     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 1.2e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + +sl++ +g++++++G+nGaGK+t +++l+gll+pt G+ ++ g+++ +  + +lr +ig+lp+ep l ++ t++e
  gi|313122481|ref|YP_004038368.1|  20 DGLSLDIPQGTVYGFLGPNGAGKTTTMRMLTGLLRPTDGTATVSGASVAD--RDKLRPRIGYLPEEPPLYEQATAYE 94 
                                       789**********************************************9..************************* PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +             + +++ +++ + lgl+    +++    + +S+G++q+va a++++ +p++++lDEpt+
  gi|313122481|ref|YP_004038368.1|  95 QleyvgglrglsadDVRARGDELFDALGLDVGSSDRI----ADFSKGMRQKVAYAQTVMHDPDVVFLDEPTS 162
                                       ***********9666666699*********9999999....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.2e-06     0.013       3      49 ..      33      76 ..      31     109 .. 0.69
   2 !   39.1   0.0   5.2e-13   7.2e-10     234     298 ..     131     192 ..      92     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.2e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll 49
                                      ++ GpNg+GK++ ++ l +l r     +g+ ++++ ++  r+  +  
  gi|313122481|ref|YP_004038368.1| 33 GFLGPNGAGKTTTMRMLTGLLR---PTDGTATVSGASVADRDKLRPR 76
                                      689*****************55...4444444444444444444444 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 5.2e-13
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       ++++S G+++  a +  +  ++   +++++DEp +gL+P++ r+l + + +l++ g+ v+l+TH 
  gi|313122481|ref|YP_004038368.1| 131 IADFSKGMRQKVAYAQTVMHDP---DVVFLDEPTSGLDPRAARTLRDRIQRLADDGTTVFLSTHI 192
                                       6899*******99999999888...9**************************************6 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0032       4.4      28      48 ..      34      54 ..      22      74 .. 0.85
   2 !   10.9   0.0   0.00019      0.27     323     364 ..     151     191 ..     135     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0032
                            AAA_15 28 liGkNnsGKSsilealdlFln 48
                                      + G+N++GK++ +++l  +l 
  gi|313122481|ref|YP_004038368.1| 34 FLGPNGAGKTTTMRMLTGLLR 54
                                      78*************987776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++++++++EP   L p a + l + +++la+d+   v+++TH
  gi|313122481|ref|YP_004038368.1| 151 DPDVVFLDEPTSGLDPRAARTLRDRIQRLADDGT-TVFLSTH 191
                                       7899*****************************7.9****** PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.4e-05     0.019      21      42 ..      31      52 ..      17      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                            AAA_23 21 ltlItGpNGaGKTTildAikla 42
                                      ++ + GpNGaGKTT ++ ++  
  gi|313122481|ref|YP_004038368.1| 31 VYGFLGPNGAGKTTTMRMLTGL 52
                                      67899***********998865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6   5.2e-05     0.072      22      52 ..      33      63 ..      27     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.2e-05
                            AAA_30 22 vltGpAGtGKttalkalreaweaa.ggrvigl 52
                                         Gp G+GKtt+++ l+ +++   g +  + 
  gi|313122481|ref|YP_004038368.1| 33 GFLGPNGAGKTTTMRMLTGLLRPTdG-TATVS 63
                                      5679**************99998844.33322 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00017      0.24      11      46 ..      35      63 ..      28     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_22 11 tGesGtGKTtllrrlleqldeeakaeeerpevvfvt 46
                                       G+ G+GKTt++r+l+  l        + +++++v 
  gi|313122481|ref|YP_004038368.1| 35 LGPNGAGKTTTMRMLTGLLR-------PTDGTATVS 63
                                      59*************98874.......244444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.25       3      67 ..      34     160 ..      32     199 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       + Gp G GKT++++ +   l       ++sg+++ +                                         
  gi|313122481|ref|YP_004038368.1|  34 FLGPNGAGKTTTMRMLTGLLRptDGTATVSGASVADRdklrprigylpeepplyeqatayeqleyvgglrglsaddv 110
                                       78**************9998532334555555555334566666666666666666666666666666666666666 PP

                                       ...................STTHHHHHHHHHHHHHHHTS.TSEEEEEETG CS
                               AAA  38 ...................yvgesekkirelfkeakeka.kpsilfiDEi 67 
                                                           + + +k +r+ ++ a++   +p ++f+DE 
  gi|313122481|ref|YP_004038368.1| 111 rargdelfdalgldvgssdRIADFSKGMRQKVAYAQTVMhDPDVVFLDEP 160
                                       66666666667766666667777777777777777666677888888885 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.5e-05      0.09      29     127 ..      34     180 ..      23     191 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-05
                            AAA_16  29 lsGesGvGKsslvrellralekdggif.lrgkcdqlesa......ipy...sa.laqalareellrqlldeaesael 94 
                                       + G+ G GK++ +r+l   l+ ++g + ++g  +   ++        y    + l +++++ e l+ ++      ++
  gi|313122481|ref|YP_004038368.1|  34 FLGPNGAGKTTTMRMLTGLLRPTDGTAtVSGASVAD-RDklrpriG-YlpeEPpLYEQATAYEQLEYVGGLRG-LSA 107
                                       68***************8777774333244444444.222333320.13332223333333333333333311.122 PP

                            AAA_16  95 eawrekleeala........................................avpelagaeasrllellkrll 127
                                       ++ r++ +e +                                         +++ l++ +a+ l++ ++rl+
  gi|313122481|ref|YP_004038368.1| 108 DDVRARGDELFDalgldvgssdriadfskgmrqkvayaqtvmhdpdvvfldePTSGLDPRAARTLRDRIQRLA 180
                                       3333333333333334444444444444455555555555555555555555555555555555555555554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0013       1.7      23      40 ..      36      53 ..      30      77 .. 0.78
   2 ?    2.1   0.0     0.042        58     522     571 ..     147     193 ..     140     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
                            AAA_13 23 GwNGaGKTtLSrllrsle 40
                                      G NGaGKTt  r+l  l 
  gi|313122481|ref|YP_004038368.1| 36 GPNGAGKTTTMRMLTGLL 53
                                      89***********99884 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.042
                            AAA_13 522 seigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnl 571
                                       + +    +v++D P S LD  +       i+  +   ++   +f++TH l
  gi|313122481|ref|YP_004038368.1| 147 TVMHDPDVVFLDEPTSGLDPRAARTLRDRIQRLA---DDGTTVFLSTHIL 193
                                       4556789*************99888888888887...9999999999966 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00014       0.2      15      50 ..      22      57 ..      15      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                            AAA_29 15 htieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                       +++i  +g ++ + Gp+G+GK+T +  ++ lL p+ 
  gi|313122481|ref|YP_004038368.1| 22 LSLDIP-QGtVYGFLGPNGAGKTTTMRMLTGLLRPTD 57
                                      566675.5558889**********9988888888765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00023      0.32      18      50 ..      23      53 ..       4      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      sld++  +  +   +GpN AGK+t++r ++ ll
  gi|313122481|ref|YP_004038368.1| 23 SLDIP--QGTVYGFLGPNGAGKTTTMRMLTGLL 53
                                      44444..45555668************999887 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.7   0.00038      0.53       3      25 ..      31      53 ..      29      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00038
                                      EEEEEESTTSSHHHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaall 25
                                      v+ ++G++GaGKTtt+  L  ll
  gi|313122481|ref|YP_004038368.1| 31 VYGFLGPNGAGKTTTMRMLTGLL 53
                                      56699**********98887666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0011       1.5       4      27 ..      34      62 ..      32      73 .. 0.77
   2 ?    1.4   0.1      0.24   3.4e+02      52      85 ..     131     166 ..     107     263 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                            AAA_28  4 itGgestGKTtlleaLa.....argypvv 27
                                      ++G+ ++GKTt+++ L+      +g+ +v
  gi|313122481|ref|YP_004038368.1| 34 FLGPNGAGKTTTMRMLTgllrpTDGTATV 62
                                      78*************98554333366665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.24
                            AAA_28  52 llafaervleeqleeeaaaaankvlfcD..rglldt 85 
                                       + +f +++ ++ + +++  ++++v+f+D  ++ ld+
  gi|313122481|ref|YP_004038368.1| 131 IADFSKGMRQKVAYAQTVMHDPDVVFLDepTSGLDP 166
                                       555666655554444444466666666633333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1625.62
//
Query:       gi|313122482|ref|YP_004038369.1|  [L=555]
Description: hypothetical protein Hbor_37160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.062   12.5   0.1       0.12   11.5   0.1    1.4  1  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
       0.63    9.0  10.8        1.2    8.0  10.8    1.4  1  Gaa1           Gaa1-like, GPI transamidase component
        1.9    8.7   6.4       0.17   12.1   0.7    2.2  2  Pox_A9         A9 protein conserved region


Domain annotation for each model (and alignments):
>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.1e-05      0.12      55      90 ..     494     529 ..     491     536 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.1e-05
                     PEP_hydrolase  55 agllpygnaNeivvemakevlpvvketpvlaGvcat 90 
                                       agll+y  a   v+e+ +e+lp+v+ t+v +Gv a 
  gi|313122482|ref|YP_004038369.1| 494 AGLLAYLVASPGVAEFVSEILPIVTPTAVRFGVSAA 529
                                       89*******************************986 PP

>> Gaa1  Gaa1-like, GPI transamidase component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  10.8   0.00021       1.2     302     440 ..      36     183 ..      14     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00021
                              Gaa1 302 lllvlllvlvlhllg.llllllptkltqleenlkteealllalllltvlllllplllslllkrll..ka.keq...k 371
                                       +l++l+  +++ ++g ll+++++t +  +++ l+ + a++++++++ v++ +++++ ++ +++ll  +a + +    
  gi|313122482|ref|YP_004038369.1|  36 ILSTLVPSVMFLFIGlLLVSAISTDTIAISDGLRGTVAMFWSFAVFLVTQRVVSTYPRPEAESLLltTAsTRSvvfG 112
                                       56666667777788856667778888888*******************************99988763323336778 PP

                              Gaa1 372 vellksvsllllgl..llsalallNfSLallvallavPltfiarpkaeslrrllrllasvlllllsPlvvl 440
                                       ++l +++ +l +++  +l++ all +S++ +v +++vPl+++    +  ++ +l     +lll +sP+v  
  gi|313122482|ref|YP_004038369.1| 113 LALAETLRVLAYAIapILVLAALLAYSIGSVVLMAVVPLVVVLLAVTAVVTGSLIGYGIALLLATSPFVAR 183
                                       8888888888777633688999*******************998666666677777777788888888765 PP

>> Pox_A9  A9 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   2.8e-05      0.17      22      50 ..      32      60 ..      25      63 .. 0.87
   2 ?   -3.1   0.6       1.5   9.1e+03      34      44 ..     249     259 ..     245     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                            Pox_A9 22 fafVvlksiisMvmyLvlGvaLlyissnd 50
                                      f f +l +++  vm+L +G+ L++  s d
  gi|313122482|ref|YP_004038369.1| 32 FIFTILSTLVPSVMFLFIGLLLVSAISTD 60
                                      99********************9976655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                            Pox_A9  34 vmyLvlGvaLl 44 
                                       ++ LvlG +Ll
  gi|313122482|ref|YP_004038369.1| 249 ILVLVLGGVLL 259
                                       7889***9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3667.22
//
Query:       gi|313122483|ref|YP_004038370.1|  [L=171]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00024   21.3   0.3    0.00051   20.2   0.3    1.5  1  HTH_Tnp_Tc3_2  Transposase
  ------ inclusion threshold ------
      0.051   13.4   1.2       0.14   12.0   1.2    1.7  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.08   13.6   0.4       0.21   12.3   0.3    1.8  1  HTH_32         Homeodomain-like domain
      0.097   12.3   0.5        2.6    7.7   0.2    2.2  2  HTH_24         Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.3   1.1e-07   0.00051       4      41 ..      17      55 ..      14      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-07
                     HTH_Tnp_Tc3_2  4 IvrlvrkdPritlreLanelkee.GksvsreTirrrLrk 41
                                      I+r+ ++dP++++reL++ l+e+  + vs+ Ti+ ++r+
  gi|313122483|ref|YP_004038370.1| 17 ILRELAADPQRSSRELTQILAEKhDIDVSHVTISETIRR 55
                                      99********************************98875 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.2   3.1e-05      0.14       5      42 .]      14      57 ..      12      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                     HTH_AsnC-type  5 DrkILeaLqedaRisyaeLAe......rvGlSestvlrRvrrLe 42
                                      D  IL++L +d+ +s +eL +       + +S  t+ + +rr++
  gi|313122483|ref|YP_004038370.1| 14 DTVILRELAADPQRSSRELTQilaekhDIDVSHVTISETIRRMR 57
                                      999************99987766668888888888888888886 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   4.6e-05      0.21      36      70 ..      17      50 ..       5      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.6e-05
                            HTH_32 36 riiallreeprWsprqlaarlaeregvkvShstvy 70
                                       +++l+  +p+ s r+l + lae++ ++vSh t+ 
  gi|313122483|ref|YP_004038370.1| 17 ILRELA-ADPQRSSRELTQILAEKHDIDVSHVTIS 50
                                      567777.89999*********9999999***9997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2   0.00058       2.6       5      27 ..      14      36 ..      11      37 .. 0.86
   2 ?    2.6   0.0     0.022        98      33      46 ..      48      61 ..      42      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00058
                            HTH_24  5 drkILelLqknprisqreLAerl 27
                                      d  IL++L ++p  s reL + l
  gi|313122483|ref|YP_004038370.1| 14 DTVILRELAADPQRSSRELTQIL 36
                                      667****************8865 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.022
                            HTH_24 33 tvnrrlkrLeeeGl 46
                                      t+++ ++r+ eeG+
  gi|313122483|ref|YP_004038370.1| 48 TISETIRRMREEGV 61
                                      78999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1303.13
//
Query:       gi|313122484|ref|YP_004038371.1|  [L=379]
Description: acyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-49  166.9   2.9    5.2e-49  166.3   2.9    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.4e-31  109.5   0.2    3.6e-31  108.1   0.2    1.8  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    9.9e-30  102.6   0.1    2.3e-29  101.4   0.1    1.7  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    9.7e-25   87.4   8.7    1.7e-24   86.6   8.7    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    0.00049   19.8   4.7     0.0013   18.5   1.9    2.6  2  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.3   2.9   1.5e-52   5.2e-49       1     150 []     228     379 .]     228     379 .] 0.98

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 1.5e-52
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       ++Gf++ m+ ++ +R +vaa+a+g+ ++a++ a +ya++r++ g+++ ++q+v++klaema+++eaar+l+yraa +
  gi|313122484|ref|YP_004038371.1| 228 DQGFYQLMTFFAGGRTSVAAQAVGVGQAAVDAATDYANEREQGGQKIHEYQAVSHKLAEMATNIEAARSLTYRAATH 304
                                       58*************************************************************************** PP

                                       -------..HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                     Acyl-CoA_dh_1  78 ldagkpd..raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrll 150
                                       +++g+++   + asmaKlfase a++vad+ +q++GgaG+ +++p er+yrdar++ i+eGtseiq+niia+++l
  gi|313122484|ref|YP_004038371.1| 305 VEDGDDQtaAKFASMAKLFASEQAVDVADEGIQVHGGAGFVTDHPAERFYRDARITKIYEGTSEIQKNIIADQIL 379
                                       *******99999***********************************************************9985 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.2     1e-34   3.6e-31       1     113 []       6     117 ..       6     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 1e-34
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       +eeq+ +rd vref e+e++p+a+e+dee+++p+el++k+a+ +l++ ++peeygGag+d+l++a+++eel rad g
  gi|313122484|ref|YP_004038371.1|   6 NEEQRTIRDVVREFGENEIRPVAREHDEERKYPHELVEKAAKYDLVAPSIPEEYGGAGMDMLTTAVITEELWRADPG 82 
                                       69**************************99*********************************************** PP

                                       HHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkrryLpklasge 113
                                       +++++g   + ++ +i +fG e  k+++Lpk+a+g+
  gi|313122484|ref|YP_004038371.1|  83 IGSAIGS-RGFGTTMIEKFGDEWMKEEWLPKVAAGD 117
                                       *998866.567789*******************996 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.1   6.5e-33   2.3e-29       1      97 []     121     216 ..     121     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 6.5e-33
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrr 77 
                                       + +++Ep +Gsdvas++t  ae+dg+eyvlnG+K+witn++ia++a+v+a+t+  +r+rg++ flvp+d  g++ ++
  gi|313122484|ref|YP_004038371.1| 121 CSCISEPAHGSDVASIET-RAEEDGDEYVLNGTKMWITNGTIADVAVVMAKTTPGERHRGITAFLVPTDLDGFETTK 196
                                       88****************.99999999************************444447******************** PP

                                       ---BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                       i +klG+r  + +e+v++dv
  gi|313122484|ref|YP_004038371.1| 197 ISNKLGIRASDLAEVVLDDV 216
                                       ******************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   8.7   4.8e-28   1.7e-24       2     133 ..     244     367 ..     243     368 .. 0.93

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 4.8e-28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       ++aa+a+G+ +aa+++++++a+er +  +g+k+ + +a+ ++lae+a++++AAr l++raa+     +++g+  t+ 
  gi|313122484|ref|YP_004038371.1| 244 SVAAQAVGVGQAAVDAATDYANEREQ--GGQKIHEYQAVSHKLAEMATNIEAARSLTYRAATH----VEDGDDQTA- 313
                                       68************************..***********************************....666666544. PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                         + a++a+++a+e a++++d+ ++++Gg +  +++p +R++RDa++++++++++
  gi|313122484|ref|YP_004038371.1| 314 -AKFASMAKLFASEQAVDVADEGIQVHGGAGFVTDHPAERFYRDARITKIYEGTS 367
                                       .4567899*******************************************9987 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.9   3.6e-07    0.0013     179     271 ..     147     224 ..     126     224 .. 0.78
   2 ?   -1.3   0.1      0.38   1.4e+03      62     107 ..     270     315 ..     253     350 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.6e-07
                                       EEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEEE-------S..-TTT-TTTTT----E CS
                            HpaB_N 179 ivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlklicresfedkleesefdyplssrfdend 255
                                        v +G+k+ +T++ +ad  +v+   ++   e  +   af vp+d +G +    ++             +        
  gi|313122484|ref|YP_004038371.1| 147 YVLNGTKMWITNGTIADVAVVMAKTTP--GERHRGITAFLVPTDLDGFETTKISNKLG----------IR--A-SDL 208
                                       5899*******************9666..57888899**********87643333222..........22..2.245 PP

                                       EEEEEEEEEEEGGGEE CS
                            HpaB_N 256 alvvfDdVfVPwerVf 271
                                       a vv+DdV VP e+V+
  gi|313122484|ref|YP_004038371.1| 209 AEVVLDDVRVPAENVI 224
                                       6799*********995 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.38
                                       TTEEEEGGG----SHHHHHHHHHHHHHHHHHTTT--S--THHHHHH CS
                            HpaB_N  62 tgekvnrffhiprskeDllkkrkairelarktggclgRcpdydaln 107
                                       +g+k++ +  + ++  +++ + +a r l+ + ++ ++   d +a+ 
  gi|313122484|ref|YP_004038371.1| 270 GGQKIHEYQAVSHKLAEMATNIEAARSLTYRAATHVEDGDDQTAAK 315
                                       4555555555555555555555555555544444443333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2757.67
//
Query:       gi|313122485|ref|YP_004038372.1|  [L=523]
Description: acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   8.3e-109  364.0   0.0   9.8e-109  363.7   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.3e-22   80.6   0.6    2.6e-22   79.6   0.6    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.7   0.0  1.1e-112  9.8e-109       3     422 ..       7     421 ..       5     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: 363.7 bits;  conditional E-value: 1.1e-112
                                       HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                       AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                       ++a+  pd +a+ +  +gq ++Y++l+  v+r+AagL+ +Gv++gdrVa++lpn p++v a++++l aG++vvp+np
  gi|313122485|ref|YP_004038372.1|   7 ATAESSPDETAVGF--RGQEWSYEQLWGMVSRFAAGLEDHGVEPGDRVAVYLPNLPQFVTAFQGTLHAGGIVVPMNP 81 
                                       578999******77..9*********************88************************************* PP

                                       TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS- CS
                       AMP-binding  80 tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeel 156
                                       +++ +e++++l ds+a+v++    ++l++ +++++++   ++++ v++ ++ ++    ++ee  +++    +e +e 
  gi|313122485|ref|YP_004038372.1|  82 QYKTREISHLLGDSGATVVV--ALADLVPFVDSVRDE---TDVEHVVSVGGEAEG-AIPFEEFLADEG---TEIVER 149
                                       ********************..333334444444443...233344444444443.566666566553...467799 PP

                                       BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EE CS
                       AMP-binding 157 kpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk..letrfklkeddvvlsilplahifglilelllallsGatv 231
                                       + dd+a+  YTSGTTGkPKGV l+h nl++ +++ +  ++  +++++dd++l +lpl+hi+g+++ ++++l+ G++ 
  gi|313122485|ref|YP_004038372.1| 150 DDDDVAVQPYTSGTTGKPKGVLLTHHNLAWDARATArlMP--DGVRPDDKYLGVLPLFHIYGMTVTMIGTLFEGGSY 224
                                       **********************************765443..67889*****************************9 PP

                                       EE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHH CS
                       AMP-binding 232 vllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralf 307
                                       + lp ++a++    l+lie ++ tv++gvP++++ l++ ++a      ++d ss+r++ +gg++l+ e++r+f++lf
  gi|313122485|ref|YP_004038372.1| 225 YPLPSWDAAE---SLALIESEELTVLHGVPAMFNDLINfEDAD-----EYDTSSIRFANSGGSSLPIEVMRQFESLF 293
                                       9999998844...379********************9955433.....4599************************* PP

                                       TCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE..............TTSEEEEEEE CS
                       AMP-binding 308 geevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvp..............dgeeGellvr 370
                                       g e++egYGlTE ++v++ ++ ++  +++gs+Gkpl g + +ivDe+  e vp              d+ +Gel+++
  gi|313122485|ref|YP_004038372.1| 294 GVELYEGYGLTEGSPVTH-ANYPGT-RRPGSIGKPLDGLDTRIVDEN-FEDVPpvekgpvneaeidlDEITGELVIH 367
                                       *****************8.553333.589*****************9.7777779*****99999988888****** PP

                                       ETTS-SEBTT-HHHHHHHEEE.T.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 371 gpgvmkgYlkkpeataeafds.e.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                       gp+vmkgY++ p+a+++af++ + +rw++TGD+g++ded  ++iv+R k++i++
  gi|313122485|ref|YP_004038372.1| 368 GPNVMKGYHGLPDANEKAFTEaDgKRWYHTGDIGYRDEDDFYYIVDREKHMIVT 421
                                       *******************9752457**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.6   2.9e-26   2.6e-22       1      76 []     430     505 ..     430     505 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 2.9e-26
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                       e+E+ l +hp++a+aaVvG+pde++Ge+++afVv+ ++ e ++e++ka++ ++l++y+ p++v f+delp+t++GK
  gi|313122485|ref|YP_004038372.1| 430 EIEELLFEHPDIADAAVVGIPDERRGETVKAFVVPVPDAEVTPEAVKAYCLENLAEYKHPREVSFIDELPRTTTGK 505
                                       8**********************************65545589********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3835.51
//
Query:       gi|313122486|ref|YP_004038373.1|  [L=315]
Description: ADP-ribosylglycohydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-63  213.8   0.3    5.2e-63  213.5   0.3    1.1  1  ADP_ribosyl_GH   ADP-ribosylglycohydrolase
  ------ inclusion threshold ------
      0.016   15.1   6.3       0.19   11.6   2.2    2.4  2  Rick_17kDa_Anti  Glycine zipper 2TM domain
      0.031   14.0   3.7       0.52   10.1   0.8    2.3  2  Gly-zipper_YMGG  YMGG-like Gly-zipper
       0.29   11.2   3.9        1.2    9.1   0.9    2.3  2  Gly-zipper_Omp   Glycine zipper
        2.2    8.4   5.3        6.3    7.0   1.2    2.5  2  Bacteriocin_IIc  Bacteriocin class II with double-glycine lea


Domain annotation for each model (and alignments):
>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.5   0.3   1.4e-66   5.2e-63       1     290 [.      12     280 ..      12     281 .. 0.94

  Alignments for each domain:
  == domain 1  score: 213.5 bits;  conditional E-value: 1.4e-66
                                       HHHHHHHHHHHHHGGGTT--HHHHHHHTSS--S-----STTTTTS-TT---HHHHHHHHHHHTEET.TEE-HHHHHH CS
                    ADP_ribosyl_GH   1 GallGaavGDAlGlpvefwsydeirrrygelgetpdktgfghfglkpgewtddtqmalllleslleaggldpedlar 77 
                                       G l+G+a+GDA+G pvef s+ ++ +++g ++   ++ ++g+  +++g++tddt+++l +++sl+++ +ldped+ +
  gi|313122486|ref|YP_004038373.1|  12 GVLVGVACGDAIGRPVEFVSQTAVSEQFGTID---GPVDGGRPPRPAGTVTDDTELTLRTARSLVDCHRLDPEDVSA 85 
                                       89****************************98...99**************************************** PP

                                       HHHH.HHT....T--SS--HHHHHHHHHTTTT-...-S-B.........---BTTTGGG-HHHHHHTSS-HHHHHHH CS
                    ADP_ribosyl_GH  78 rflaeWleepgdteprgignttrealrnlksgepppeagana......ngsagngalmRaaplgllyagdpeeaael 148
                                       rf++ Wl     ++p ++g  tr++l+++++g+++  a   a       ++agng+lmR+ p+++++  dp+ ++  
  gi|313122486|ref|YP_004038373.1|  86 RFVD-WLG----SSPLDVGYLTRDVLEKIAAGKDWSLASYEAsmqapdGRDAGNGSLMRCTPIAVAFRADPQSLVSG 157
                                       *999.***....99********************999998889********************************** PP

                                       HHHHHHTTB--HHHHHHHHHHHHHHHHHHTT--STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH........ CS
                    ADP_ribosyl_GH 149 aeeaarlTHnhpeavagaaayaaliaaalrgksleealdaaeeelavapaeeelaaalrkalaladsdkdvdvdaee 225
                                       ++ ++++TH++ ++  ++a++++++a+++rg+++e     +   ++++  ++el++ +  ++a +            
  gi|313122486|ref|YP_004038373.1| 158 SRVISAITHYDTRCQWSCALFNYIVAQLIRGDKPELTPFLQ---EYKHRLPSELQDGVSNWRATE------------ 219
                                       **********************************9988888...666666666666666665533............ PP

                                       HHHHH--SSBHHHHHHHHHHHHHH.-SSHHHHHHHHHTS-SSHHHHHHHHHHHHHHHH-GGGS-H CS
                    ADP_ribosyl_GH 226 avdelgsggyavealaaalyallhaaddfeeallaavnlGgDtdttgaiaGallGalyGleaiPe 290
                                           ++ +gy+  +l aaly  l+ a++++e+++++vn+GgD+dt+ga++GallGa++G++a P 
  gi|313122486|ref|YP_004038373.1| 220 ---PTYDSGYVISTLHAALYHGLT-AESPREGICESVNHGGDADTIGALTGALLGARFGATAFPT 280
                                       ...35559****************.99***********************************995 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0062        22      23      39 ..       9      25 ..       7      28 .. 0.84
   2 ?   11.6   2.2   5.2e-05      0.19      18      40 ..     254     276 ..     250     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0062
                   Rick_17kDa_Anti 23 rvlGavvGAaaGavaGn 39
                                      r++G +vG+a+G ++G+
  gi|313122486|ref|YP_004038373.1|  9 RAAGVLVGVACGDAIGR 25
                                      78999999999988885 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.2e-05
                   Rick_17kDa_Anti  18 gggggrvlGavvGAaaGavaGna 40 
                                       +gg+ +++Ga+ GA++Ga  G++
  gi|313122486|ref|YP_004038373.1| 254 HGGDADTIGALTGALLGARFGAT 276
                                       77899999999999999999986 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.009        32       8      22 ..      10      24 ..       5      35 .. 0.80
   2 ?   10.1   0.8   0.00015      0.52       9      22 ..     261     274 ..     250     284 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.009
                                      XXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  8 aiGAaaGAvvGaliG 22
                                      a+G  +G + G++iG
  gi|313122486|ref|YP_004038373.1| 10 AAGVLVGVACGDAIG 24
                                      788888888888888 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                                       XXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG   9 iGAaaGAvvGaliG 22 
                                       iGA +GA++Ga +G
  gi|313122486|ref|YP_004038373.1| 261 IGALTGALLGARFG 274
                                       55555555555555 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.048   1.7e+02       5      18 ..      11      24 ..       8      32 .. 0.65
   2 ?    9.1   0.9   0.00034       1.2       1      15 [.     261     275 ..     254     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.048
                    Gly-zipper_Omp  5 iGAaaGaliGgavg 18
                                      +G ++G + G+a g
  gi|313122486|ref|YP_004038373.1| 11 AGVLVGVACGDAIG 24
                                      55556666555555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00034
                    Gly-zipper_Omp   1 iGaaiGAaaGaliGg 15 
                                       iGa++GA++Ga +G+
  gi|313122486|ref|YP_004038373.1| 261 IGALTGALLGARFGA 275
                                       688888888887776 PP

>> Bacteriocin_IIc  Bacteriocin class II with double-glycine leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.037   1.3e+02      21      41 ..       6      26 ..       4      49 .. 0.78
   2 ?    7.0   1.2    0.0018       6.3      17      47 ..     255     282 ..     251     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.037
                   Bacteriocin_IIc 21 aqgtvggivggalaGaatGaa 41
                                      +q++++g+++g + G a+G +
  gi|313122486|ref|YP_004038373.1|  6 VQDRAAGVLVGVACGDAIGRP 26
                                      688999999999999999987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0018
                   Bacteriocin_IIc  17 GGkcaqgtvggivggalaGaatGaatlgilg 47 
                                       GG   ++   g+++gal Ga  Ga+++++++
  gi|313122486|ref|YP_004038373.1| 255 GG---DADTIGALTGALLGARFGATAFPTAW 282
                                       55...66667888999999999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2468.08
//
Query:       gi|313122487|ref|YP_004038374.1|  [L=92]
Description: hypothetical protein Hbor_37210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 778.12
//
Query:       gi|313122488|ref|YP_004038375.1|  [L=333]
Description: hypothetical protein Hbor_37220 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2152.70
//
Query:       gi|313122489|ref|YP_004038376.1|  [L=746]
Description: hypothetical protein Hbor_37230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0096   16.1   0.4      0.019   15.1   0.4    1.4  1  NPP1       Necrosis inducing protein (NPP1)
  ------ inclusion threshold ------
        0.5   10.7   2.4        1.3    9.4   2.4    1.7  1  TFIIE-A_C  C-terminal general transcription factor TFIIE alph


Domain annotation for each model (and alignments):
>> NPP1  Necrosis inducing protein (NPP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   2.1e-06     0.019      65     111 ..     122     165 ..     108     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-06
                              NPP1  65 imYayYfpkdqaakssghrHdWenvvVwidndakeeskvlgvsasah 111
                                       + Y +Y   dq +  + h HdWe v V+id++  ++s  l+v+ s++
  gi|313122489|ref|YP_004038376.1| 122 VQYWFYSAFDQFT-TNFHWHDWEVVHVFIDTE--RDSARLHVASSHS 165
                                       5577888888876.89**************99..5555666666654 PP

>> TFIIE-A_C  C-terminal general transcription factor TFIIE alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.4   0.00014       1.3       2      49 ..     467     517 ..     466     530 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00014
                         TFIIE-A_C   2 eSdtsesdedskskkaaatasese...veeeeeeeeeeeaddptvmVaGrp 49 
                                        Sd+ e+++ ++++ +++ta+  +   ++ee+e e+e +++ p v VaG  
  gi|313122489|ref|YP_004038376.1| 467 VSDATENETATNNATETETAAGGTddaTAEETESENEADQTPPGVAVAGVD 517
                                       5888899988888888888777666665566666666667999******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (746 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 5146.62
//
Query:       gi|313122490|ref|YP_004038377.1|  [L=353]
Description: Zn-dependent alcohol dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-26   90.8   0.8      1e-25   89.7   0.8    1.5  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    6.7e-22   77.9   1.4    1.1e-21   77.2   0.4    1.9  2  ADH_zinc_N       Zinc-binding dehydrogenase
    3.3e-05   23.3   0.5    5.5e-05   22.6   0.5    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    0.00058   20.9   0.0     0.0013   19.8   0.0    1.6  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.031   14.0   0.0    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
       0.03   14.6   0.3      0.061   13.6   0.3    1.5  1  TrkA_N           TrkA-N domain
      0.081   13.6   0.3       0.22   12.2   0.3    1.8  1  Methyltransf_25  Methyltransferase domain
       0.09   12.1   0.0       0.16   11.3   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.12   13.1   0.3       0.36   11.5   0.1    1.9  2  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.8   5.1e-29     1e-25       2     104 ..      26     133 ..      25     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 5.1e-29
                                       TEEEEEEEEEEE-HHHHHHHTTS...TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHT CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkgg...kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCke 75 
                                       + v+++++a+giC+sD h ++g+     l+ + ++ilGHE +G v+ vg++v++++ Gd+V+++++  +g+C++C +
  gi|313122490|ref|YP_004038377.1|  26 DGVVVELEACGICRSDWHAWQGDwdwLGLKPPKGQILGHEPAGRVVGVGSDVETVREGDHVAIPFNLGDGTCPQCAN 102
                                       679*******************963333444555******************************************* PP

                                       T-GGG-TTBEETTTS..S-SSSBSEEEECGG CS
                             ADH_N  76 geenlCeeakllgvs..ldGgfaeyvvvpek 104
                                       g+ n Ce+   lg+    +G+fae+v vp++
  gi|313122490|ref|YP_004038377.1| 103 GHGNTCENVVPLGFAevAQGAFAEQVHVPAA 133
                                       ***************99***********965 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         2   4.1e+03      81      90 ..      66      75 ..      64      89 .. 0.76
   2 !   77.2   0.4   5.5e-25   1.1e-21       1     128 [.     182     312 ..     182     314 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2
                                      EEEEEEECSC CS
                        ADH_zinc_N 81 pgGrlvvvGg 90
                                      p Gr+v vG 
  gi|313122490|ref|YP_004038377.1| 66 PAGRVVGVGS 75
                                      7899999995 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 5.5e-25
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaal 76 
                                       gvGl av +A alG +v+avd +++klela++lGa +++n+++a ++  +++++  ++ v v+++++G+++t ++++
  gi|313122490|ref|YP_004038377.1| 182 GVGLSAVHIADALGGNVVAVDLDDQKLELAEELGAAATVNANDAgSVPGAVRAIA-DDHVGVSVDALGIPETCRNSI 257
                                       9******************************************************.88******************* PP

                                       HCEEEEEEEEECSC...TSSEEE....EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGg...gkgeee....fdlrnlllkeksilGsllgslreefkealdll 128
                                       ++l  +G+ v +G+    +        +++  +++ e+ ++Gsl+   + ++ e ++++
  gi|313122490|ref|YP_004038377.1| 258 QSLGARGQHVQIGLtteAE---GgtieLPTDAMVMSEIEFIGSLGMP-PTKYDEIFRMV 312
                                       *************966533...2344799999************998.78877777766 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.5   2.7e-08   5.5e-05      31      82 ..     175     225 ..     152     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.7e-08
                                       EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHH CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqe 82 
                                       v v G G +Gl+A+++a +lg +V+++D++ ++le  e+lga   +v ++++
  gi|313122490|ref|YP_004038377.1| 175 VAVHGCGGVGLSAVHIADALGGNVVAVDLDDQKLELAEELGAA-ATVNANDA 225
                                       8899***********************************9998.66655554 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   6.4e-07    0.0013       1     129 [.     214     346 ..     214     350 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.4e-07
                                       TT-SEEEETT.STTHH...HHH-TT-EEEEEES-HHHHH.HHHHHHE.EEEEEEEE----..S-EEE-CHHHCTTT- CS
                      ADH_zinc_N_2   1 lGAdevidyr.tedfe...aatggegvDvvldtvggealleaslkvl.pggGrlvsiggpp.lsaallkpakkrkgr 71 
                                       lGA   ++   + ++    +a+  ++v v +d++g ++++++s++ l +  G+ v+ig +  +  ++ +++      
  gi|313122490|ref|YP_004038377.1| 214 LGAAATVNANdAGSVPgavRAIADDHVGVSVDALGIPETCRNSIQSLgAR-GQHVQIGLTTeAEGGTIELPT-DAMV 288
                                       6777777555344443667888999**********77777*******666.*******54443333333333.2234 PP

                                       EEEE--GGG...-.-HHHHHHHHHHHHHHH---..-EEEEEEGGGHHHHHHHHHSS--SS CS
                      ADH_zinc_N_2  72 svkyeflfsmkasaqadileelaalieeGklrp..vvdrvfpleeaaeAhrylesgrarG 129
                                          +ef+ s+ +  +++  +e+++++++Gkl p  vv+ +  l+++ e ++++ +  ++G
  gi|313122490|ref|YP_004038377.1| 289 MSEIEFIGSLGMP-PTK-YDEIFRMVASGKLDPsaVVTDRVALDDVSETLAAMTNFETVG 346
                                       4556666654444.777.99***********96447777899***999999987776666 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.6e-05     0.031       8      61 ..     148     201 ..     144     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                       THHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEE CS
                     ELFV_dehydrog   8 eaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvav 61 
                                       ++ glG++++++  +   + d  +g  va+ G G vg  a+ ++  lg +vvav
  gi|313122490|ref|YP_004038377.1| 148 DMAGLGCRFMTSFHALAHRADIEAGDWVAVHGCGGVGLSAVHIADALGGNVVAV 201
                                       799****99987544444666558999**************************8 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3     3e-05     0.061       1      45 [.     175     220 ..     175     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE.EE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegle.vv 45 
                                       +++ G+G vG s ++   + gg +vv++d d++++e ++e g+  +v
  gi|313122490|ref|YP_004038377.1| 175 VAVHGCGGVGLSAVHIADAlGG-NVVAVDLDDQKLELAEELGAAaTV 220
                                       6899***************999.5**************999954144 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   0.00011      0.22       5      47 ..     179     221 ..     175     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                       T-T.TSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTT CS
                   Methyltransf_25   5 GcG.tGrltlalakrlgkakvtgvDiseemleaareraeeegln 47 
                                       GcG  G  + ++a++lg ++v++vD++++ le a+e  +++ +n
  gi|313122490|ref|YP_004038377.1| 179 GCGgVGLSAVHIADALG-GNVVAVDLDDQKLELAEELGAAATVN 221
                                       66516999********8.*****************988665543 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.2e-05      0.16      36      80 ..     172     216 ..     157     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.2e-05
                                       TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                      2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80 
                                       g  v++ G+G +G ++ +++ a+g +v+a+d   +k e +eelg+
  gi|313122490|ref|YP_004038377.1| 172 GDWVAVHGCGGVGLSAVHIADALGGNVVAVDLDDQKLELAEELGA 216
                                       56799**************************99887775555554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.4   1.5e+04      51      67 ..      14      30 ..      12      35 .. 0.82
   2 ?   11.5   0.1   0.00018      0.36       4      42 ..     179     219 ..     177     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.4
                                      ECCCTSS-TT-EEEEEE CS
                   Methyltransf_11 51 daeklpfednsfDlvvs 67
                                      ++e++  +d+  D vv+
  gi|313122490|ref|YP_004038377.1| 14 SIEDVAAPDAAADGVVV 30
                                      57888899999999986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00018
                                       T-T.TSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT CS
                   Methyltransf_11   4 GcG.tGrlaealakrg.arvvgvDlskemlklakekaseeg 42 
                                       GcG  G+ a ++a++  ++vv+vDl+++ l+la+e +  + 
  gi|313122490|ref|YP_004038377.1| 179 GCGgVGLSAVHIADALgGNVVAVDLDDQKLELAEELGAAAT 219
                                       89769999999995555****************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 2249.67
//
Query:       gi|313122491|ref|YP_004038378.1|  [L=85]
Description: hypothetical protein Hbor_37250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   11.8   0.3       0.15   11.5   0.3    1.0  1  Spo7      Spo7-like protein


Domain annotation for each model (and alignments):
>> Spo7  Spo7-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   8.3e-06      0.15      45     105 ..      10      70 ..       5      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.3e-06
                              Spo7  45 flyalflapredgsgvggsvywvvevvek.vlliggvvTlvLfwlsGeyertiviprrflsv 105
                                       f+ a+f+    + +++  sv ++++v++  + ++ +v+ +v+  +  +++r+iv+prr + +
  gi|313122491|ref|YP_004038378.1|  10 FILAVFMDVTLS-VTMPVSVLVFWRVALGpIGIMESVICVVIGLIGYIFARGIVLPRRLFVT 70 
                                       666777744444.44555888899988752778888999999899999**********8864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 658.75
//
Query:       gi|313122492|ref|YP_004038379.1|  [L=49]
Description: hypothetical protein Hbor_37260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0087   16.1   0.5      0.012   15.6   0.5    1.3  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.039   14.1   2.1      0.088   12.9   2.1    1.6  1  Zn-ribbon_8    Zinc ribbon domain
       0.09   12.7   1.8        4.3    7.3   0.1    2.2  2  zinc_ribbon_4  zinc-ribbon domain
       0.11   12.8   4.5       0.62   10.4   4.6    1.9  2  zinc_ribbon_9  zinc-ribbon
       0.11   12.1   0.7       0.11   12.1   0.7    2.1  2  WCCH           WCCH motif


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   3.4e-06     0.012      14      37 ..       3      35 ..       1      40 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.4e-06
                               DZR 14 fCseCgtklkavaa...........edrCpsCgek 37
                                      +C++C t++++  +            ++Cp+C++ 
  gi|313122492|ref|YP_004038379.1|  3 TCDHCSTHVSE--RfvrvfaddsgaVRACPNCSAN 35
                                      8*******984..3569999************986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.1   2.5e-05     0.088       8      35 ..       4      35 ..       2      38 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                       Zn-ribbon_8  8 CeeCg.hefevlqsis.dap.lta.CPeCgse 35
                                      C+ C  h+ e++++++ d++  +  CP+C ++
  gi|313122492|ref|YP_004038379.1|  4 CDHCStHVSERFVRVFaDDSgAVRaCPNCSAN 35
                                      8888625566777777655556667****876 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.006        22       4      10 ..       3       9 ..       1      11 [. 0.66
   2 ?    7.3   0.1    0.0012       4.3       5      15 ..      29      39 ..      26      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.006
                     zinc_ribbon_4  4 tCpsCka 10
                                      tC +C++
  gi|313122492|ref|YP_004038379.1|  3 TCDHCST 9 
                                      6777766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0012
                     zinc_ribbon_4  5 CpsCkakyeid 15
                                      Cp+C+a   i+
  gi|313122492|ref|YP_004038379.1| 29 CPNCSANAGIA 39
                                      ****9976665 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.7       0.3   1.1e+03      23      28 ..       3       8 ..       1      10 [. 0.78
   2 ?   10.4   4.6   0.00017      0.62       9      28 ..      13      33 ..       4      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.3
                     zinc_ribbon_9 23 lCPhCg 28
                                      +C hC 
  gi|313122492|ref|YP_004038379.1|  3 TCDHCS 8 
                                      799996 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00017
                     zinc_ribbon_9  9 drfVsvspdedsdv.lCPhCg 28
                                       rfV+v +d++ +v +CP+C 
  gi|313122492|ref|YP_004038379.1| 13 ERFVRVFADDSGAVrACPNCS 33
                                      69*******999999*****6 PP

>> WCCH  WCCH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   3.2e-05      0.11       7      14 ..       3      10 ..       3      14 .. 0.90
   2 ?    1.0   0.9     0.095   3.4e+02       8      11 ..      29      32 ..      28      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
                              WCCH  7 cCPhCPRH 14
                                      +C+hC++H
  gi|313122492|ref|YP_004038379.1|  3 TCDHCSTH 10
                                      6******* PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.095
                              WCCH  8 CPhC 11
                                      CP+C
  gi|313122492|ref|YP_004038379.1| 29 CPNC 32
                                      **** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 361.56
//
Query:       gi|313122493|ref|YP_004038380.1|  [L=181]
Description: methionine-S-sulfoxide reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-68  229.0   0.5      3e-68  228.8   0.5    1.0  1  PMSR      Peptide methionine sulfoxide reductase
  ------ inclusion threshold ------
      0.053   13.5   1.0        0.1   12.6   0.6    1.7  1  DUF4298   Domain of unknown function (DUF4298)


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.8   0.5   3.4e-72     3e-68       2     152 ..       7     158 ..       6     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 228.8 bits;  conditional E-value: 3.4e-72
                                       EEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-TT CS
                              PMSR   2 avlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDpt 78 
                                       a+l+gGCFW++e+ +++l Gv+s+++GYagG++enptYeevc+g+tghaE+++v++dpe++s++elle+ff ihDpt
  gi|313122493|ref|YP_004038380.1|   7 ATLGGGCFWCLEAPMKELVGVESVTSGYAGGHVENPTYEEVCEGTTGHAEVIQVEFDPEEISFAELLEVFFAIHDPT 83 
                                       89*************************************************************************** PP

                                       -SSEETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH-TTS.-- CS
                              PMSR  79 qlnrqgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYleknpeg.yc 152
                                       +++rqg DvG+qYrsa++y++e+q+e++e++++e++++  ++++ivte++pl++fy+aeeyHq+Y+eknp++ yc
  gi|313122493|ref|YP_004038380.1|  84 TEDRQGPDVGSQYRSAVFYHTEAQRETVESLIDEMNESGVYDDDIVTEVAPLDTFYEAEEYHQDYYEKNPDQpYC 158
                                       ************************************************************************9*9 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   1.1e-05       0.1      12      53 ..     112     153 ..     103     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHHHHHTHHHHHHHHHHHTSHHHHHHHTS--S CS
                           DUF4298  12 sallqqLeealeqwkklqkklakLdeYYqseqwredleasnk 53 
                                       ++l+++++e+     ++ +++a+Ld++Y+ e++ +d+ + n 
  gi|313122493|ref|YP_004038380.1| 112 ESLIDEMNESGVYDDDIVTEVAPLDTFYEAEEYHQDYYEKNP 153
                                       55555555555555678899****************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1385.48
//
Query:       gi|313122494|ref|YP_004038381.1|  [L=173]
Description: hypothetical protein Hbor_37280 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0023   18.0   1.8     0.0027   17.7   0.6    1.6  2  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0     0.071   1.3e+03      52      74 ..      32      55 ..      31      58 .. 0.77
   2 !   17.7   0.6   1.5e-07    0.0027      10     110 ..      57     155 ..      51     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.071
                                      HHHHS.EEEEEEEEEEEEEEEEEE CS
                             NUDIX 52 eEEtG.leaellellgrlhylapy 74
                                      +EEt  +e+ + ell+ l++lap+
  gi|313122494|ref|YP_004038381.1| 32 FEETDtVEEAQFELLDNLDDLAPV 55
                                      799995555999999999888775 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.5e-07
                                       EEETTSEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE.EEEEE CS
                             NUDIX  10 llnekgevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd.eheil 85 
                                       + ne+gevL++r s++ +p   +P   vepgE++++ A+  ++  +G+++ l  + g+++ +   ++  ++ ++ ++
  gi|313122494|ref|YP_004038381.1|  57 VVNEDGEVLVMRVSEDCTPK--IPSAAVEPGEDYAAVAQQWVRQQAGIDVTLDGVEGVWTVTVRLEDEAREaTRNFV 131
                                       679*********99455555..*************************977444444444443333333333445555 PP

                                       EEEEEEECSGCSSTSTTTEEEEEEE CS
                             NUDIX  86 yvfleevegelepndenevsevrwv 110
                                       ++ + +++g+ ++  e++  e+ w+
  gi|313122494|ref|YP_004038381.1| 132 VFAATPETGDAAVH-EGDAFEADWY 155
                                       44447888887777.8888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1338.48
//
Query:       gi|313122495|ref|YP_004038382.1|  [L=416]
Description: arabinose efflux permease family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.6e-41  140.6  67.6    1.2e-28  100.0  33.4    2.0  2  MFS_1       Major Facilitator Superfamily
    1.2e-05   24.1  31.3    0.00043   19.0  30.6    2.9  1  MFS_2       MFS/sugar transport protein
     0.0042   15.4   1.2     0.0042   15.4   1.2    1.9  2  OATP        Organic Anion Transporter Polypeptide (OATP) fami
  ------ inclusion threshold ------
       0.25   10.1  11.3      0.011   14.6   3.8    2.3  3  LacY_symp   LacY proton/sugar symporter
       0.62    8.9  11.3      0.043   12.7   5.8    1.7  2  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0  33.4   3.4e-32   1.2e-28       4     257 ..      51     290 ..      48     290 .. 0.87
   2 !   54.4  26.3   2.6e-18   9.2e-15       2     170 ..     247     413 ..     246     416 .] 0.94

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 3.4e-32
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       + ++  ++r++l+p+lp a+ +dlgi+++++gl l+++  ++a++++p+G  sd++ r  ++l gl+++++g+ll+ 
  gi|313122495|ref|YP_004038382.1|  51 GWAVLQMGRFLLSPLLP-AIISDLGITEATAGLTLAAFQGVYALTQYPGGEYSDNWNRTTLILPGLAILVVGFLLFG 126
                                       5567889**********.999***********************************8888************44444 PP

                             MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                       + +++  +++v+ v+ Glg g+++  + al++d+f+  +rgra+g+++ag+ +G +l+ +++ l ++++ Wr +f+ 
  gi|313122495|ref|YP_004038382.1| 127 V-ATSLaIFVVAAVVVGLGKGLFAIPSRALVSDLFTA-RRGRALGIYAAGTDVGGLLASGIAVLALTYATWRTPFLP 201
                                       5.55555******************************.*************************************** PP

                             MFS_1 157 laivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply 233
                                       +a++++++ vl    ++++++ r  +s+ +         ++++ +++ ++ +    l+a+ lf f++ g+  ++p+y
  gi|313122495|ref|YP_004038382.1| 202 VAVILAVVTVL--YAVWTRETFRVGSSSLDA--------VSTVRRLVASSEQR-GTLLAFSLFYFMVGGFINFFPTY 267
                                       ********999..888888888888888888........22223344444444.49999999999************ PP

                             MFS_1 234 lqevlgls.glllaglllallalvg 257
                                       l   + +s g  +a+  +a+++lvg
  gi|313122495|ref|YP_004038382.1| 268 LARAHEFSdGQASAT--FAVVFLVG 290
                                       ********8756666..88888876 PP

  == domain 2  score: 54.4 bits;  conditional E-value: 2.6e-18
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       lla+ l +++ + ++ ++p +la+++ +s  +++  +++++l+ ++  +++G l+dr++rr++ + glll a++l+ 
  gi|313122495|ref|YP_004038382.1| 247 LLAFSLFYFMVGGFINFFPTYLARAHEFSDGQASATFAVVFLVGLAVKPLAGGLGDRYSRRSIAVGGLLLAAVALAG 323
                                       78999*********************************************************************555 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       l++ ++++  ll++ v++++g+ ++fp++ a+i d +p +  g  +g + a f  + +lgp+  g++++++++ ++f
  gi|313122495|ref|YP_004038382.1| 324 LTL-ATSTvGLLAATVVAAAGYKTGFPLADAIIMDDAPADGMGADLGAARALFLGANALGPAYVGVVVTYASYAYAF 399
                                       667.566668****************************************************************999 PP

                             MFS_1 155 yilaivsllafvlfll 170
                                         l + +l+a++l  l
  gi|313122495|ref|YP_004038382.1| 400 GGLVVCLLVAAML--L 413
                                       9999999999885..3 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0  30.6   1.2e-07   0.00043      70     341 ..     110     357 ..      73     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-07
                             MFS_2  70 wlllsaiilavsiillftppelsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlg 146
                                       ++l ++ il v  +llf +     +++++ ++v+++++ +   lf ip+ +lv+ l      R ++ ++    + +g
  gi|313122495|ref|YP_004038382.1| 110 LILPGLAIL-VVGFLLFGV-----ATSLAIFVVAAVVVGLGKGLFAIPSRALVSDL--FTARRGRALGIYAAGTDVG 178
                                       444444444.444555555.....468999**************************..7778999999999999999 PP

                             MFS_2 147 gvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrn 223
                                       g+la+ +a+l +           ++++  l  a++ ++++++ +  t+e   +         ++l +   ++++  +
  gi|313122495|ref|YP_004038382.1| 179 GLLASGIAVLALTYA--------TWRTPFLPVAVILAVVTVLYAVWTRETFRV-------GSSSLDAVSTVRRLVAS 240
                                       999998888774433........467766666666666666666777888555.......89999999999999999 PP

                             MFS_2 224 raflillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgallt 299
                                          +  ll+f+l+++++g   + +  yl    + ++ +as+ ++vv++ +l++ pl+  l  r++++ +++ g+ll+
  gi|313122495|ref|YP_004038382.1| 241 SEQRGTLLAFSLFYFMVGGFINFFPTYLARAHEfSDGQASATFAVVFLVGLAVKPLAGGLGDRYSRRSIAVGGLLLA 317
                                       9999999999999999999999999999999998******************************************* PP

                             MFS_2 300 ivllvlvlllqpsnlllflvllviagfgvgvaallpwsmlad 341
                                       +v l+++ l+  ++++ +l+++v+a  g+ + + l++++++d
  gi|313122495|ref|YP_004038382.1| 318 AVALAGLTLA--TSTVGLLAATVVAAAGYKTGFPLADAIIMD 357
                                       *****99999..9***************************98 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.17     6e+02     134     144 ..     133     143 ..      47     198 .. 0.66
   2 !   15.4   1.2   1.2e-06    0.0042     283     353 ..     230     300 ..     217     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.17
                                       xxxxxxxxxxx RF
                              OATP 134 lfflaqlllGi 144
                                       +f++a +++G+
  gi|313122495|ref|YP_004038382.1| 133 IFVVAAVVVGL 143
                                       34444444444 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.2e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 283 fpkalkrllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGl 353
                                        +++++rl+ +     ++l+  + +++v Gfi F p yl +  + s  +A+  ++vv+++g a+  l+gGl
  gi|313122495|ref|YP_004038382.1| 230 AVSTVRRLVASSEQRGTLLAFSLFYFMVGGFINFFPTYLARAHEFSDGQASATFAVVFLVGLAVKPLAGGL 300
                                       5667777777777777888999999***************************************9999997 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2      0.49   1.8e+03      83     110 ..     115     142 ..      70     172 .. 0.57
   2 ?   -0.5   0.0      0.11   3.9e+02      19      56 ..     202     239 ..     189     244 .. 0.79
   3 ?   14.6   3.8     3e-06     0.011      14     129 ..     248     355 ..     245     415 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.49
                         LacY_symp  83 llvlfapfliyvfepllqlnilvGalvG 110
                                       l +l+  fl++  +  l + +++ ++vG
  gi|313122495|ref|YP_004038382.1| 115 LAILVVGFLLFGVATSLAIFVVAAVVVG 142
                                       3455566666666665555444444443 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.11
                         LacY_symp  19 yffimsayfplfpvwlkevlglsktetGivfsvislfs 56 
                                          i++++  l++vw +e   +  + +  v +v +l++
  gi|313122495|ref|YP_004038382.1| 202 VAVILAVVTVLYAVWTRETFRVGSSSLDAVSTVRRLVA 239
                                       5578999999********99999999888888877765 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 3e-06
                         LacY_symp  14 lffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfapf 90 
                                       l f++++f+++ + ++fp +l+   ++s+++    f+v+ l+ +  +pl G + d+   +   +  + l  v     
  gi|313122495|ref|YP_004038382.1| 248 LAFSLFYFMVGGFINFFPTYLARAHEFSDGQASATFAVVFLVGLAVKPLAGGLGDRYSRRSIAVGGLLLAAV----- 319
                                       679****************************************************98766533322222111..... PP

                         LacY_symp  91 liyvfepllqlnilvGalvGgvflGlvysagagaieayi 129
                                            + l     +vG+l  +v    +y++g ++ +a i
  gi|313122495|ref|YP_004038382.1| 320 ---ALAGLTLATSTVGLLAATVVAAAGYKTGFPLADAII 355
                                       ...123444444556666666666666666666666665 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3      0.19   6.9e+02     290     330 ..     108     148 ..      54     186 .. 0.71
   2 ?   12.7   5.8   1.2e-05     0.043     183     383 ..     200     399 ..     177     400 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.19
                        MFS_1_like 290 vklliiallayilrfllyaiienawlvlpievLhgisfgll 330
                                       ++l++ +l + ++ fll ++ +++ + +++ v  g+  gl+
  gi|313122495|ref|YP_004038382.1| 108 TTLILPGLAILVVGFLLFGVATSLAIFVVAAVVVGLGKGLF 148
                                       56666666666666666666666666666666666655555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.2e-05
                        MFS_1_like 183 lyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYL.kelgas 258
                                       l v+ +l v+++l ++   et    +  + ++ + + +++   e  + ll+  +  +++g + nF+  YL   +++s
  gi|313122495|ref|YP_004038382.1| 200 LPVAVILAVVTVLYAVWTRETFRVGSSSLDAVST-VRRLVASSEQRGTLLAFSLFYFMVGGFINFFPTYLaRAHEFS 275
                                       3333333333333333333333333333333333.444444555555555555555666666689999999999*** PP

                        MFS_1_like 259 ntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaav 335
                                          ++++ a+  +  + +  +a  l ++++ + + + +ll+ ++ + ++ + ++++ +l + v  ++ + + +  a 
  gi|313122495|ref|YP_004038382.1| 276 DGQASATFAVVFLVGLAVKPLAGGLGDRYSRRSIAVGGLLLAAVALAGLTLATSTVGLLAATVVAAAGYKTGFPLAD 352
                                       ******************************************************************99999999999 PP

                        MFS_1_like 336 eyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                         + + ap    +   g   +l+ g+ +alG  + G++  + s +++F
  gi|313122495|ref|YP_004038382.1| 353 AIIMDDAPADGMGADLGAARALFLGA-NALGPAYVGVVVTYASYAYAF 399
                                       99999999998888888888887775.678877777777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 2775.87
//
Query:       gi|313122496|ref|YP_004038383.1|  [L=265]
Description: dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-45  153.2   0.0    1.2e-44  152.6   0.0    1.2  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.2e-38  132.5   0.0    1.5e-38  132.3   0.0    1.0  1  adh_short     short chain dehydrogenase
      2e-08   34.4   0.0    4.1e-08   33.3   0.0    1.4  1  KR            KR domain
  ------ inclusion threshold ------
       0.11   12.4   0.1       0.18   11.7   0.1    1.3  1  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.6   0.0   2.7e-48   1.2e-44       4     232 ..      17     259 ..      12     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 152.6 bits;  conditional E-value: 2.7e-48
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE..E..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae..v..lecDVtdeeqvealveevvekfgklDilvn 75 
                                       sg+G a A+ala+eG +vv+  ++e++ +++v+e++++   +  v     D td+e++ealve+ ve+fg+lD lv 
  gi|313122496|ref|YP_004038383.1|  17 SGLGNASARALAQEGVNVVMNGRDEDRlESAVAEVQADAADDatVvgQTGDLTDPEDIEALVERPVEEFGRLDHLVT 93 
                                       9***********************************9998664446999**************************** PP

                                       -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalea 150
                                       +ag  p+  gpf+et+++++ +a d  + s+++ ++aa+ ++++g  g ivn++s + + ++++    + ++ ++++
  gi|313122496|ref|YP_004038383.1|  94 SAGGPPS--GPFMETTDDDWYEAYDLLVMSVVRSVRAAADHLRAGdgGTIVNITSRSVKEAIDGLVLSNSVRMGVIG 168
                                       *******..*******************************8888778****************************** PP

                                       HHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT..........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSG CS
                      adh_short_C2 151 ltrylAvelgpkgiRvNavspgpikTlaasgikg..........fdelleelearaplgrlgtpeevaeaalfLasd 217
                                       l ++l +el+p ++R Nav pg  +T+  +++ +           ++ l+ + + +p+g++g+p + ++++++L s+
  gi|313122496|ref|YP_004038383.1| 169 LEKTLSKELAP-EVRANAVLPGSHETPRIEELIEqgvergeyedYEDGLDDWGQGIPVGHIGDPMDLGRTVAYLSSP 244
                                       ***********.9**********9999855432223333444446779999************************** PP

                                       GGTT--SEEEEESTT CS
                      adh_short_C2 218 easyitGqtlvvDgG 232
                                       +++yi+G  + +DgG
  gi|313122496|ref|YP_004038383.1| 245 QSEYINGVAVPIDGG 259
                                       **************9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   0.0   3.3e-42   1.5e-38       2     190 ..       9     199 ..       8     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 3.3e-42
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT...TSEEEEEE-TTTSHHHHHHHHHHHHHHH CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee...gakalaiqvDvtdreevealvekavkkl 75 
                                       ++lvt  ssG+G a a++la+eG++vv+ +r e++le +++e++++    a+++  ++D+td e++ealve+ v+++
  gi|313122496|ref|YP_004038383.1|   9 AALVTASSSGLGNASARALAQEGVNVVMNGRDEDRLESAVAEVQADaadDATVVGQTGDLTDPEDIEALVERPVEEF 85 
                                       79******************************************998666678999********************* PP

                                       SSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                         adh_short  76 gkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152
                                       g+ld Lv+ AG   sgpf e+++++w + +++ +++v+  +ra+++++ ++ +G+Ivn++S   k++  g++   + 
  gi|313122496|ref|YP_004038383.1|  86 GRLDHLVTSAGGPPSGPFMETTDDDWYEAYDLLVMSVVRSVRAAADHLRAGDGGTIVNITSRSVKEAIDGLVLSNSV 162
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                         +v+gl ++l+kelap+ +r nav PG  +T+  +el
  gi|313122496|ref|YP_004038383.1| 163 RMGVIGLEKTLSKELAPE-VRANAVLPGSHETPRIEEL 199
                                       *****************8.************9876665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   9.1e-12   4.1e-08       4     109 ..      11     115 ..       9     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 9.1e-12
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       l+t    gLG + ar la++g  ++v+ +R++   e++ a++++ +a +a+v     D++d++++eal+e+  +e++
  gi|313122496|ref|YP_004038383.1|  11 LVTASSSGLGNASARALAQEGV-NVVMNGRDEDRLESAVAEVQADAADDATVVGQTGDLTDPEDIEALVERPVEEFG 86 
                                       7888999**************7.7999****88888888899999999***************************** PP

                                       ---EEEE---------TTT--HHHHHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvl 109
                                       ++   + +Ag    ++++e+t++d+ +++
  gi|313122496|ref|YP_004038383.1|  87 RLDHLVTSAGGPPSGPFMETTDDDWYEAY 115
                                       *************************8875 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     4e-05      0.18      10      48 ..      19      57 ..      16      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4e-05
                                      CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHC CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekiekslek 48
                                      +G+  a ++a++g++Vv+  ++e++le+a +++++  + 
  gi|313122496|ref|YP_004038383.1| 19 LGNASARALAQEGVNVVMNGRDEDRLESAVAEVQADAAD 57
                                      69999**************************99986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1657.42
//
Query:       gi|313122497|ref|YP_004038384.1|  [L=63]
Description: hypothetical protein Hbor_37310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.48
# Mc/sec: 394.65
//
Query:       gi|313122498|ref|YP_004038385.1|  [L=199]
Description: transcriptional regulator, TetR family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-13   50.3   0.9    3.8e-13   49.7   0.9    1.3  1  TetR_C_6   BetI-type transcriptional repressor, C-terminal
    3.4e-13   49.1   0.2    7.2e-13   48.1   0.1    1.6  2  TetR_N     Bacterial regulatory proteins, tetR family
    0.00015   22.0   0.0    0.00035   20.9   0.0    1.6  1  TetR_C_25  Tetracyclin repressor-like, C-terminal domain
     0.0003   21.0   0.1    0.00054   20.2   0.1    1.4  1  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
    0.00039   20.7   1.1    0.00067   20.0   1.1    1.5  1  TetR_C_11  Tetracyclin repressor-like, C-terminal domain
    0.00067   19.7   0.0    0.00089   19.3   0.0    1.3  1  TetR_C_29  Tetracyclin repressor-like, C-terminal domain
     0.0033   17.5   0.1     0.0084   16.1   0.1    1.7  1  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.042   13.8   0.0    1.3  1  TetR_C_13  Tetracyclin repressor-like, C-terminal domain
      0.051   13.5   0.0       0.12   12.3   0.0    1.5  1  MarR_2     MarR family
      0.065   13.1   0.1       0.19   11.6   0.0    1.7  2  HTH_10     HTH DNA binding domain
      0.065   12.8   0.0       0.12   12.0   0.0    1.4  1  HTH_24     Winged helix-turn-helix DNA-binding
       0.13   12.4   0.0       0.21   11.7   0.0    1.4  1  TetR_C_17  Tetracyclin repressor-like, C-terminal domain
       0.14   12.0   0.1       0.36   10.7   0.1    1.7  1  LacI       Bacterial regulatory proteins, lacI family
       0.21   11.9   0.0       0.33   11.2   0.0    1.3  1  UPF0122    Putative helix-turn-helix protein, YlxM / p13 like


Domain annotation for each model (and alignments):
>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.9   2.9e-16   3.8e-13       1     114 [.      75     189 ..      75     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 2.9e-16
                                       HHHHHHHHHHCC.ST.HSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH.TTSCTTSTHHH CS
                          TetR_C_6   1 prerlraileal.lp.ldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelae.gglradadaea 74 
                                       p+e+l  ++e++ lp +d++ +++ ++ l++ a+a++d++++e+++++++++ +++r +la+++e g +r+d+ +++
  gi|313122498|ref|YP_004038385.1|  75 PAEQLLSLIETVmLPpADDDPHEFRTALLEIEAQAPYDESFRERLERFDDAFTERIRSILAAGVEdGTFREDVAPDE 151
                                       678888888775156244444567778************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHT CS
                          TetR_C_6  75 aAerlaAlidGLwlraalapeeldaeraralvrrhldall 114
                                       aA+ +a  + G  ++ +    +++ +    + r ++++ l
  gi|313122498|ref|YP_004038385.1| 152 AASFVATYVRGARTQNVAV--GTPLDDSLSAFRSYVESTL 189
                                       ***************9988..6777788888888888765 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.1   5.6e-16   7.2e-13       1      45 [.       9      53 ..       9      55 .. 0.96
   2 ?   -3.2   0.0         6   7.7e+03      25      33 ..     135     143 ..     134     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 5.6e-16
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                      I+d++   +  +Gy+a+t+++IA++AG+sk+al+++F+ K +Ll+
  gi|313122498|ref|YP_004038385.1|  9 IMDGTHSALRTHGYAALTMQDIADEAGLSKAALHYHFDCKHDLLL 53
                                      8999999************************************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                                       HHTSSHHHH CS
                            TetR_N  25 rAGvskgal 33 
                                       +AGv  g++
  gi|313122498|ref|YP_004038385.1| 135 AAGVEDGTF 143
                                       699999986 PP

>> TetR_C_25  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.7e-07   0.00035      24      96 ..     122     192 ..     117     199 .] 0.92

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.7e-07
                         TetR_C_25  24 llehmvedaeayleegvaaGtirpsrdpkarArylalsslGalllelqlheeedptdlravlreylermvlPa 96 
                                       + +++ e ++++l++gv++Gt r+   p + A ++a++  Ga + ++++ +    +d  +++r+y+e ++lPa
  gi|313122498|ref|YP_004038385.1| 122 FDDAFTERIRSILAAGVEDGTFREDVAPDEAASFVATYVRGARTQNVAVGT--PLDDSLSAFRSYVESTLLPA 192
                                       6678899999**************************************999..9999***************8 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   4.2e-07   0.00054       2      82 ..      73     158 ..      72     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.2e-07
                                       SSHHHHHHHHHHHHHHHHHHTH.HHHHHHHHHGGG...S-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB.-SS-H CS
                         TetR_C_24   2 gspaerLralvrahveviaeer.eeaavllrelra...LspehreeiralrreyerllrdlieeGvaagef.edldp 73 
                                       ++pae+L +l+++++   a+++  e++  l e++a    ++  re++ +  +++++++r+++++Gv++g+f ed+ p
  gi|313122498|ref|YP_004038385.1|  73 DDPAEQLLSLIETVMLPPADDDpHEFRTALLEIEAqapYDESFRERLERFDDAFTERIRSILAAGVEDGTFrEDVAP 149
                                       6888888888888888766554144555555544411145566889999999*******************999999 PP

                                       HHHHHHHHH CS
                         TetR_C_24  74 klaalailg 82 
                                       + aa ++ +
  gi|313122498|ref|YP_004038385.1| 150 DEAASFVAT 158
                                       998877765 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.1   5.2e-07   0.00067      27      91 ..      98     161 ..      69     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.2e-07
                         TetR_C_11  27 agallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadvelvldlllgpll 91 
                                        + +l  + a+a  d+ ++e+l++ + +  ++++r +l+ +v+ G  r+d+ ++ +++ ++  ++
  gi|313122498|ref|YP_004038385.1|  98 FRTALLEIEAQAPYDESFRERLER-FDDAFTERIRSILAAGVEDGTFREDVAPDEAASFVATYVR 161
                                       56677777788999********99.*******************************999987776 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     7e-07   0.00089      39      77 ..     115     153 ..      75     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7e-07
                                       TS--SS-.THHHHHHHHHHHHHHHHTTSS-SS--HHHHH CS
                         TetR_C_29  39 ksesirelnspliekleeilerGqaagvFrpgvdaldly 77 
                                        +e+++++ ++++e++++il+ G+++g Fr++v + +  
  gi|313122498|ref|YP_004038385.1| 115 FRERLERFDDAFTERIRSILAAGVEDGTFREDVAPDEAA 153
                                       4678889999***********************998765 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   6.6e-06    0.0084      20      78 ..      91     157 ..      75     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.6e-06
                                       HHH-HHHHHHHHHHHHH-HHHHHHHHHHH.......HHHHHHHHHHHHHCT-STT-.-HHHHHHHHH CS
                         TetR_C_27  20 arddpelFatyvvlieeelevvekhieel.......eeqlaeIireGvaaGeFkaa.dpeaaaravf 78 
                                       a ddp+ F+t +  ie++  + e+++e+l       +e + +I+++Gv++G+F+++  p++aa+ v+
  gi|313122498|ref|YP_004038385.1|  91 ADDDPHEFRTALLEIEAQAPYDESFRERLerfddafTERIRSILAAGVEDGTFREDvAPDEAASFVA 157
                                       67788888888777777766666666655222222268999************98735666666655 PP

>> TetR_C_13  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.3e-05     0.042      38     110 ..     111     181 ..     102     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                                       S-TTHHHHHHHHHHHHHHHHHHHHHHHHCTTSS-TTS-HHHHHHHHHHHHHHHHHHHHHHTSSHHHHHHHHHH CS
                         TetR_C_13  38 lpesfrerleevledwqkrvaacleeaqeageiaadadaeelaeffwigWeGAvlRaklerstqPlelfletf 110
                                        +esfrerle+   ++ +r+ ++l +  e+g+ ++d  ++e a+f+ +   GA  R++ +   +Pl+  l+ f
  gi|313122498|ref|YP_004038385.1| 111 YDESFRERLERFDDAFTERIRSILAAGVEDGTFREDVAPDEAASFVATYVRGA--RTQNVAVGTPLDDSLSAF 181
                                       589*******************************************9999998..666677777777666666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.4e-05      0.12      14      40 ..      17      43 ..      15      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.4e-05
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHH CS
                            MarR_2 14 Lgrrpgrdltvgelarrlglsksavsr 40
                                      L+ ++   lt++++a++ glsk+a+++
  gi|313122498|ref|YP_004038385.1| 17 LRTHGYAALTMQDIADEAGLSKAALHY 43
                                      555554479***************987 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.19      25      43 ..      26      44 ..      23      46 .. 0.92
   2 ?   -2.8   0.0       4.5   5.8e+03       1      16 [.     126     141 ..     126     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                            HTH_10 25 tlkeLAkelGIskstlseh 43
                                      t++++A+e G+sk++l++h
  gi|313122498|ref|YP_004038385.1| 26 TMQDIADEAGLSKAALHYH 44
                                      889***************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                            HTH_10   1 LTdkqlevlklAyemG 16 
                                       +T++ +++l++ +e G
  gi|313122498|ref|YP_004038385.1| 126 FTERIRSILAAGVEDG 141
                                       6888888888877766 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.2e-05      0.12      18      37 ..      25      44 ..      23      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.2e-05
                            HTH_24 18 isqreLAerlglSpstvnrr 37
                                      ++++++A++ glS+++++++
  gi|313122498|ref|YP_004038385.1| 25 LTMQDIADEAGLSKAALHYH 44
                                      89****************99 PP

>> TetR_C_17  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.21      43      94 ..     120     172 ..      98     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                       HHHHH.HHHHHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHHHHHHHHHS-H CS
                         TetR_C_17  43 eRyer.lvealkellqeGvergEfkPqlplesiakylisfldGliletlalge 94 
                                       eR++  + e++ ++l +Gve g f+     ++ a+++  ++ G  ++++a+g+
  gi|313122498|ref|YP_004038385.1| 120 ERFDDaFTERIRSILAAGVEDGTFREDVAPDEAASFVATYVRGARTQNVAVGT 172
                                       3443315688999*****************************99999998886 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00028      0.36       1      15 [.      26      40 ..      26      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                                      -HHHHHHHCTS-HHH CS
                              LacI  1 tikDVArlAGVSkaT 15
                                      t++D+A++AG Ska+
  gi|313122498|ref|YP_004038385.1| 26 TMQDIADEAGLSKAA 40
                                      9***********985 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.33      32      68 ..      23      59 ..      13      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                           UPF0122 32 dDlSlsEiAeefnvsrqavydnikrtekllekyEekL 68
                                        l +++iA+e  +s+ a++ +    ++ll+++ ++L
  gi|313122498|ref|YP_004038385.1| 23 AALTMQDIADEAGLSKAALHYHFDCKHDLLLSFLDRL 59
                                      5689**************************9997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1320.57
//
Query:       gi|313122499|ref|YP_004038386.1|  [L=490]
Description: efflux protein, MATE family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-62  210.5  36.7    4.1e-38  130.6  10.8    2.5  3  MatE             MatE
  ------ inclusion threshold ------
      0.031   14.5   1.0       0.64   10.3   0.1    3.3  2  Pmp3             Proteolipid membrane potential modulator
      0.043   13.1   0.0      0.061   12.6   0.0    1.1  1  Glyco_hydro_43   Glycosyl hydrolases family 43
       0.62   10.1  49.5       0.05   13.7  21.7    4.9  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6  10.8   9.2e-42   4.1e-38       1     161 []      34     194 ..      34     194 .. 0.99
   2 ?   -3.8   0.2         2     9e+03      83      99 ..     227     243 ..     218     248 .. 0.59
   3 !   90.6  12.8   1.8e-29   7.9e-26      14     160 ..     293     440 ..     280     441 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 9.2e-42
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       Pi+++nll++ ++l+dt+++gr++++alAa+s+a++ ++ll++f++gls+a ++lv+q  Ga+  ++a+ a+ q++ 
  gi|313122499|ref|YP_004038386.1|  34 PIVVTNLLQTAYNLADTYWIGRFSTDALAAISFAFPMVFLLISFGMGLSVAGSVLVAQHTGAGEEDEAEYAASQTVT 110
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       ++l+ sl++ +l+++   ++l +++++++vl+la++y++i+ lg+p+++ ++v+ + +rg+g+t +p+ +++ s++l
  gi|313122499|ref|YP_004038386.1| 111 FSLVGSLFLGVLGYVAVGPFLGILGASPDVLPLARDYMQIISLGLPFMFGFFVFVALMRGYGDTITPMLVMFGSVVL 187
                                       ***************************************************************************** PP

                              MatE 155 niplnyl 161
                                       ni l+++
  gi|313122499|ref|YP_004038386.1| 188 NIALDPI 194
                                       ****986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                              MatE  83 sliiallvllfseqils 99 
                                       +++ a+++++fs+ ++ 
  gi|313122499|ref|YP_004038386.1| 227 GIAGAAIATVFSRSLAL 243
                                       45555555555555554 PP

  == domain 3  score: 90.6 bits;  conditional E-value: 1.8e-29
                              MatE  14 lidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallv 90 
                                        ++ ++vg+++++ +Aa++i+ +++s++f+++++++ +++t++gq++Ga+++ ra++a++++ ++++++  ++ +++
  gi|313122499|ref|YP_004038386.1| 293 NLLLIVVGMFPTTVVAAYGIGVRVFSVIFLPAIAVARGVETMTGQNIGAGKPARAERAANIAAMAMFGILTLAGVIA 369
                                       677899*********************************************************************** PP

                              MatE  91 llfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llniplny 160
                                       ++ +e+i+ +ft+d++v+ ++ ++l +++++  ++++   ++g +rgag+t ++++i+++ l  +++p++y
  gi|313122499|ref|YP_004038386.1| 370 FVAAEPIIAVFTNDPDVIRVGVDFLYWVAPTFGFIGIMRSYTGSFRGAGETLTAAAIAVLMLgFIRLPFAY 440
                                       **********************************************************************9 PP

>> Pmp3  Proteolipid membrane potential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00014      0.64      19      46 ..     283     310 ..     274     312 .. 0.91
   2 ?    0.5   0.1      0.16   7.3e+02       4      17 ..     315     328 ..     314     335 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                              Pmp3  19 ksGcsadllinilLtllgylPgviHAfy 46 
                                       + G++ +l +n+lL + g++P ++ A y
  gi|313122499|ref|YP_004038386.1| 283 IEGTGRALSVNLLLIVVGMFPTTVVAAY 310
                                       68999******************99998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.16
                              Pmp3   4 lillaiilPPlaVa 17 
                                       +++  i+lP +aVa
  gi|313122499|ref|YP_004038386.1| 315 RVFSVIFLPAIAVA 328
                                       566789******98 PP

>> Glyco_hydro_43  Glycosyl hydrolases family 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.4e-05     0.061       3      35 ..     374     404 ..     372     412 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                       SESBCSSEESEEEEEETTC.EEEEEEEBTEESEE CS
                    Glyco_hydro_43   3 nPvlsgfypDpsilrvged.yYlvtstfewfpgl 35 
                                        P+++ f++Dp+++rvg d  Y+v++tf     +
  gi|313122499|ref|YP_004038386.1| 374 EPIIAVFTNDPDVIRVGVDfLYWVAPTFG---FI 404
                                       7******************99******94...33 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   3.5      0.21   9.5e+02      91     137 ..      69     127 ..      34     133 .. 0.66
   2 ?   13.7  21.7   1.1e-05      0.05       1     135 [.     147     318 ..     147     329 .. 0.77
   3 ?   -8.7   9.5         4   1.8e+04      94     104 ..     351     361 ..     289     381 .. 0.45
   4 ?   11.9   1.6     4e-05      0.18       2      85 ..     394     480 ..     393     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.21
                   Polysacc_synt_C  91 llkpllaalvmgivvylllllllglllla............alalllavlvgalvYlll 137
                                        ++ ll++++mg+ v + +l+   +  ++            +++l+ ++++g+l Y+++
  gi|313122499|ref|YP_004038386.1|  69 PMVFLLISFGMGLSVAGSVLVAQHTGAGEedeaeyaasqtvTFSLVGSLFLGVLGYVAV 127
                                       34678888888888665555444444444899999999876668999999999999876 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.1e-05
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgi...................... 55 
                                       +++i++l+++f++ + v+ +++ g g + +++++++ +++++++l  +li  f +                      
  gi|313122499|ref|YP_004038386.1| 147 YMQIISLGLPFMFGFFVFVALMRGYGDTITPMLVMFGSVVLNIALDPILIFGFEAnplftmlglgnlqsqlfamtgy 223
                                       69************************************************87777888888**************** PP

                   Polysacc_synt_C  56 .....vGaaiatvlallvvavln...lyalrrllgikl.......ellrrllkpllaalvmgiv.vylllllllgll 116
                                             Gaaiatv++  +++++    ++  +r ++i+l       ++l rll + + a + g   ++ ++lll+ + 
  gi|313122499|ref|YP_004038386.1| 224 tgsgiAGAAIATVFSRSLALIVGlyiMFDGSRGVQIHLwqmspnfDFLERLLSIGIPASIEGTGrALSVNLLLIVVG 300
                                       ***************98888777222455577788888888877777777777777777777775332344433333 PP

                   Polysacc_synt_C 117 llaalalllavlvgalvYl 135
                                       + +  ++++a ++g+ v+ 
  gi|313122499|ref|YP_004038386.1| 301 MFP-TTVVAAYGIGVRVFS 318
                                       333.234444445555553 PP

  == domain 3  score: -8.7 bits;  conditional E-value: 4
                   Polysacc_synt_C  94 pllaalvmgiv 104
                                         +aa++m+++
  gi|313122499|ref|YP_004038386.1| 351 ANIAAMAMFGI 361
                                       33444444444 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 4e-05
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalv.igalvklilnllliplf..givGaaiatvlallvvavlnly 75 
                                       L ++a+++ f+++++ +++ + g g++ +a+ ++v    ++ l + ++   +f  g +G+ +a +++ +++av+ + 
  gi|313122499|ref|YP_004038386.1| 394 LYWVAPTFGFIGIMRSYTGSFRGAGETLTAAAIAVlMLGFIRLPFAYFASQSFdhGSTGIWMAFTVSNVAGAVIAYA 470
                                       7899**********************977665555055569*********9998899******************** PP

                   Polysacc_synt_C  76 alrrllgikl 85 
                                       + rr +  + 
  gi|313122499|ref|YP_004038386.1| 471 WYRRSTWRDK 480
                                       9999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3565.47
//
Query:       gi|313122500|ref|YP_004038387.1|  [L=361]
Description: membrane-associated Zn-dependent protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-13   50.7   7.5    3.4e-07   29.8   0.3    2.5  2  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   2.5   2.1e-09   3.8e-05       2     108 ..     122     200 ..     121     226 .. 0.90
   2 !   29.8   0.3   1.9e-11   3.4e-07     186     228 ..     239     281 ..     213     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.1e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp....LGGyVkmageepeeelsee 74 
                                       f ++++ ++ vHElGH+++ + ++v+                  +++Y+++l      +G++++m+++ p+++    
  gi|313122500|ref|YP_004038387.1| 122 FTVAVLGVLGVHELGHYVASRYHDVQA-----------------SLPYFLPLPTllgtMGAVIRMNDTLPDRK---- 177
                                       88999999*****************99.................789999999999999***********999.... PP

                                       ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  75 eakaflkkspwqrllivlAGplanfilailvfvv 108
                                                  + + i +AGpla++  +++v +v
  gi|313122500|ref|YP_004038387.1| 178 -----------SLFDIGVAGPLAGLGATVIVTAV 200
                                       ...........999***********999999887 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.9e-11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 186 aglssflqllalisvnLgilNLlPipvLDGghllfalleairr 228
                                       + + +++ +  +++  +++lNLlP+ +LDGgh+++a++ +  +
  gi|313122500|ref|YP_004038387.1| 239 SLMANPVVVGGWVGAFVTFLNLLPVGQLDGGHIVRAMFGRAHG 281
                                       3455999999**************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2737.00
//
Query:       gi|313122501|ref|YP_004038388.1|  [L=79]
Description: hypothetical protein Hbor_37350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.013   15.3   0.1    1.5  2  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5


Domain annotation for each model (and alignments):
>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   7.4e-07     0.013       4      23 ..       4      23 ..       1      26 [. 0.89
   2 ?   -3.1   0.1      0.43   7.7e+03      36      41 ..      28      33 ..      28      34 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.4e-07
                             RHH_5  4 vnvtLPeelleeLeewAdee 23
                                      v vtLP+ell e+e++ dee
  gi|313122501|ref|YP_004038388.1|  4 VEVTLPDELLTEFEQLVDEE 23
                                      89**************9998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.43
                             RHH_5 36 ekalre 41
                                      e+a++e
  gi|313122501|ref|YP_004038388.1| 28 EQAVEE 33
                                      788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 603.06
//
Query:       gi|313122502|ref|YP_004038389.1|  [L=147]
Description: hypothetical protein Hbor_37360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.32   11.6   2.5       0.42   11.2   1.0    1.7  2  Cadherin-like  Cadherin-like beta sandwich domain


Domain annotation for each model (and alignments):
>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   2.4e-05      0.42      18      82 ..       6      70 ..       2      72 .. 0.89
   2 ?   -1.0   0.0      0.14   2.6e+03      29      49 ..      87     110 ..      81     116 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.4e-05
                     Cadherin-like 18 YtvdVdedvdsvtitataedsvatvtvngvaveegstetkdvsLneGrnk.ieikvtaedgsttrt 82
                                       t++V+ +v + ++  +a  s + v++ +v+v+e+   + ++s+ +G+   +e+ v+  dg+t +t
  gi|313122502|ref|YP_004038389.1|  6 DTARVPVNVLRQQVADAAGVSASLVEIENVDVDEN-VLSVSFSVPDGDAPmVEVLVEHPDGRTDST 70
                                      5788999999999999999999***********96.***********999***********88764 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.14
                     Cadherin-like  29 vtitatae...dsvatvtvngvav 49 
                                       ++i+++ +    +++ vtv+ +++
  gi|313122502|ref|YP_004038389.1|  87 IRIEYAGRdseTDDILVTVDQRRG 110
                                       555555554444556666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 983.34
//
Query:       gi|313122503|ref|YP_004038390.1|  [L=262]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-18   66.1   0.1    2.9e-18   65.5   0.1    1.3  1  TrmB       Sugar-specific transcriptional regulator TrmB
      0.002   18.2   0.0     0.0047   16.9   0.0    1.6  1  E2F_TDP    E2F/DP family winged-helix DNA-binding domain
  ------ inclusion threshold ------
      0.047   13.6   0.0       0.11   12.5   0.0    1.6  1  PadR       Transcriptional regulator PadR-like family
      0.099   12.6   0.0       0.21   11.6   0.0    1.5  1  Blo-t-5    Mite allergen Blo t 5
       0.13   11.9   0.0       0.15   11.7   0.0    1.1  1  SusD_RagB  SusD family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.1   8.2e-22   2.9e-18       1      68 []       4      71 ..       4      71 .. 0.99

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 8.2e-22
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                      L++lGLs+yE kvY +Ll  g ata+e++ ++ vp+ ++Y+vL+ Le + l++ +   p++Y avdpe
  gi|313122503|ref|YP_004038390.1|  4 LSELGLSSYEEKVYRTLLVTGTATATELSAASSVPKGRIYDVLNGLEARTLIQSQSTDPTRYIAVDPE 71
                                      789***************************************************************97 PP

>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.3e-06    0.0047      24      66 ..      22      62 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                           E2F_TDP 24 lslneaakeLvdkkdekvkkRRiYDilNVLealglieKeskne 66
                                      ++ ++ a+eL   ++  v k RiYD+lN Lea  li+ +s   
  gi|313122503|ref|YP_004038390.1| 22 VTGTATATELS--AASSVPKGRIYDVLNGLEARTLIQSQSTDP 62
                                      56678899999..9999*******************9987655 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     3e-05      0.11      26      53 ..      34      61 ..      22      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                                      -CCTTHHHHHHHHHHHHHTTSEEEEEE- CS
                              PadR 26 llelseGslYpaLkrLekeglvesewee 53
                                      +  + +G++Y++L+ Le+  l++s+ ++
  gi|313122503|ref|YP_004038390.1| 34 ASSVPKGRIYDVLNGLEARTLIQSQSTD 61
                                      357889******************9876 PP

>> Blo-t-5  Mite allergen Blo t 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.9e-05      0.21      11      75 ..     153     220 ..     146     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                                       XXXXXXXXXXX-HHHH...HHHHHHHHHHHHHHHHHHHHHH--SSHHHHHHHHHHHHHHHHHHHHHHH CS
                           Blo-t-5  11 efReefDrllieelee...kleklekallklseqvkelektkskelkeqilreltialnfiegakgfl 75 
                                        +R+efD ++ ++ ++    l   ++ l +l e + el k+ks ++   +l e+ ++ ++i+ +  ++
  gi|313122503|ref|YP_004038390.1| 153 TLRSEFDAFFGAMQTDvsvSLIFSDEVLTTLPETFPELVKSKSVDISISVLPEIPVSFDIIDQTTTMI 220
                                       678999988655444311155667899**********************************9987766 PP

>> SusD_RagB  SusD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.1e-05      0.15     196     233 ..      59      96 ..      30     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                                       --CGCSBT......HHHHHHHHHHHHHHHTTTTT-HHHHHH CS
                         SusD_RagB 196 ltdaaykttv...skdelikaildERrrElagEgnRwfDLr 233
                                       +td +    +   + +++ + +l ER+ El  E+nR+++L+
  gi|313122503|ref|YP_004038390.1|  59 STDPTR---YiavDPETAVDRLLAERTDELQREWNRYHELA 96 
                                       333333...134599***********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1708.15
//
Query:       gi|313122504|ref|YP_004038391.1|  [L=110]
Description: cation/cationic drug transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-26   91.6   4.0      5e-26   91.2   4.0    1.1  1  Multi_Drug_Res  Small Multidrug Resistance protein
     0.0052   17.0   7.2     0.0052   17.0   7.2    1.7  2  EamA            EamA-like transporter family


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   4.0   5.6e-30     5e-26       3      93 .]       4      94 ..       2      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 5.6e-30
                                      -HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH--- CS
                    Multi_Drug_Res  3 wvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgillfges 81
                                      ++llv Ai++ev+g+++L+lsegf+k  psl+v++gygi+f+l s+++++lp++v+Y +w+++G+v+i+ +gi++f+es
  gi|313122504|ref|YP_004038391.1|  4 YLLLVSAIIAEVIGTTALRLSEGFSKPLPSLGVLLGYGIAFYLVSLTMEELPIGVVYGTWAALGIVGIAGIGIVFFDES 82
                                      89***************************************************************************** PP

                                      -----HHHHHHH CS
                    Multi_Drug_Res 82 lslkkliglali 93
                                      ++l++++g+ li
  gi|313122504|ref|YP_004038391.1| 83 IDLAGVLGILLI 94
                                      *********998 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   6.3    0.0011       9.9       3      80 ..       3      79 ..       1      79 [. 0.86
   2 !   17.0   7.2   5.8e-07    0.0052      71     136 ..      36     102 ..      30     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0011
                              EamA  3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80
                                      ++ll++ a +   i++++ +    +  pl  ++v +  + ++ l+ + ++e ++    +  w++l ++g+ g+ ++f+
  gi|313122504|ref|YP_004038391.1|  3 PYLLLVSAIIAEVIGTTALRLSEGFSKPLPSLGVLLGYGIAFYLVSLTMEELPI-GVVYGTWAALGIVGIAGIGIVFF 79
                                      5677777888888888888998888899*****999999999999999988888.*****************999985 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.8e-07
                              EamA  71 gllgtvlafllffyalkktsasna.slitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        llg  +af+l    +++++ +++ +   +l  v ++ ++++++ e++ l  +lgi+li++Gv+ i+
  gi|313122504|ref|YP_004038391.1|  36 VLLGYGIAFYLVSLTMEELPIGVVyGTWAALGIVGIAGIGIVFFDESIDLAGVLGILLIVVGVYCIN 102
                                       469999**************996626779***********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 790.37
//
Query:       gi|313122505|ref|YP_004038392.1|  [L=537]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-09   35.9   0.4    1.4e-07   31.4   0.0    2.5  2  DUF772         Transposase domain (DUF772)
    8.1e-08   32.2   0.2    1.5e-07   31.3   0.2    1.4  1  DDE_Tnp_1      Transposase DDE domain
      0.004   15.6   0.0     0.0082   14.6   0.0    1.4  2  PhageP22-tail  Salmonella phage P22 tail-spike
  ------ inclusion threshold ------
      0.013   15.9   0.1      0.053   13.9   0.1    2.0  2  DDE_Tnp_1_2    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   3.1e-11   1.4e-07       4      68 ..      64     127 ..      62     132 .. 0.90
   2 ?    1.9   0.1     0.051   2.3e+02      25      65 ..     399     436 ..     390     446 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3.1e-11
                            DUF772   4 ayppelmlkllllqylygl.SdreleealrenlsfrwflgldleedpvpdhstlsrfRk.rlee.ler 68 
                                        yp + +++++ll+ l+g   + +l+e l+ ++s+   lg    ++++pd+stl+r+ + r+++ +++
  gi|313122505|ref|YP_004038392.1|  64 QYPMAQLFRAFLLKALHGWsHETALVEYLQQRPSLGEQLG----SETLPDQSTLWRTWNqRFTTeVQE 127
                                       69*****************9********************....699*********998888877555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.051
                            DUF772  25 releealrenlsfrwflgldleedpvpdhstlsrfRkrlee 65 
                                       r+l+e   ++ s+ + l l    d  ++++tl+  Rk+  e
  gi|313122505|ref|YP_004038392.1| 399 RQLCEHDIDRQSVDRGLHL--G-DDEWHETTLVYRRKENSE 436
                                       4555555555555555554..4.558********9998766 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.2   3.4e-11   1.5e-07      29     196 ..     308     481 ..     283     499 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.4e-11
                         DDE_Tnp_1  29 ggkykygyklhiavdtrsglilsvvitpgnvhdskglkq..lldelrpr.kgklvlaDaGYasaelldtleekgvdy 102
                                       +++ +y y   ++    + ++l ++  p ++ d++  +   lld+++++   + vl+D+ ++s+ +l+++ +++++y
  gi|313122505|ref|YP_004038392.1| 308 EKTDEYAYQWATVQLVGNAVPLVLDARPVRKGDTRLEIVrdLLDSAEEMvMVDDVLMDREFDSQHVLEEISSRRLQY 384
                                       55555666666666666677777777777777777666666****9999*9************************** PP

                         DDE_Tnp_1 103 iirlkkntklyrk......gaeskrrgrlrkhdrnkiltksqkrrnk.....................skkekgdvy 152
                                       +++ +  t ++++      +           ++ ++                                +++ +++ y
  gi|313122505|ref|YP_004038392.1| 385 VVPKRMRTSEKETarqlceH-----------DIDRQ----------SvdrglhlgddewhettlvyrrKENSEHTDY 440
                                       **986666666554434330...........22222..........2333333333366666666666666666777 PP

                         DDE_Tnp_1 153 yvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryr 196
                                       + +++  + ++ e +   y  Rw+iE+  k++kr f   ++ ++
  gi|313122505|ref|YP_004038392.1| 441 RQYSVFMTNYETEAIG-KYGSRWEIESGYKSIKR-FM-AATTSK 481
                                       7777777777777765.7899*************.66.344444 PP

>> PhageP22-tail  Salmonella phage P22 tail-spike
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0      0.67     3e+03     297     314 ..      59      76 ..      54      79 .. 0.73
   2 !   14.6   0.0   1.8e-06    0.0082     243     296 ..     463     519 ..     448     526 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.67
                                       S--TTTSTTT------EE CS
                     PhageP22-tail 297 dlpvsqyplhqlplnhlv 314
                                           +qyp+ ql    l+
  gi|313122505|ref|YP_004038392.1|  59 YSVSTQYPMAQLFRAFLL 76 
                                       44558******9887776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.8e-06
                                       -SS-SEEE--SEETTEE--EBS-EE...EEEEEES-SSESEEE-SSSSSSTSSSBTT CS
                     PhageP22-tail 243 agesgvktwqgsvgattsrnynlqf...rdsvvlspvwdgfdlgadtdmapeedrpg 296
                                         esg+k+ +  + atts+n+ l+f     +  l+ +w   dl  + ++a e drp 
  gi|313122505|ref|YP_004038392.1| 463 EIESGYKSIKRFMAATTSKNFVLRFfyfAFACLLYSIWRSVDLLVQVELAGEYDRPP 519
                                       469*******************98722256789**********************95 PP

>> DDE_Tnp_1_2  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.2e-05     0.053       1      55 [.     362     414 ..     362     417 .. 0.94
   2 ?   -2.2   0.0       1.3   5.8e+03      44      62 ..     456     474 ..     450     479 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                       DDE_Tnp_1_2   1 vlaDrgYrsralrealkergIrasipplgrpaknkaapkkqarederarnvvErs 55 
                                       vl Dr ++s++++e++  r+ + ++p++ r+++  ++  +q +e ++ r  v+r 
  gi|313122505|ref|YP_004038392.1| 362 VLMDREFDSQHVLEEISSRRLQYVVPKRMRTSE--KETARQLCEHDIDRQSVDRG 414
                                       689*****************************8..99999************995 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                       DDE_Tnp_1_2  44 ederarnvvErsfgwlkrr 62 
                                         +  r+ +E  +  +kr+
  gi|313122505|ref|YP_004038392.1| 456 GKYGSRWEIESGYKSIKRF 474
                                       56889*****999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3603.36
//
Query:       gi|313122506|ref|YP_004038393.1|  [L=108]
Description: hypothetical protein Hbor_37400 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 740.42
//
Query:       gi|313122507|ref|YP_004038394.1|  [L=120]
Description: hypothetical protein Hbor_37410 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 880.32
//
Query:       gi|313122508|ref|YP_004038395.1|  [L=225]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-32  111.5   0.0    6.6e-32  110.7   0.0    1.4  1  DDE_Tnp_IS240  DDE domain
    4.1e-07   29.7   0.3    8.8e-07   28.6   0.3    1.6  1  rve_3          Integrase core domain
  ------ inclusion threshold ------
      0.031   14.5   0.1       0.06   13.5   0.1    1.7  1  rve            Integrase core domain
      0.037   13.8   0.0        1.5    8.6   0.0    2.2  2  DDE_3          DDE superfamily endonuclease
       0.05   13.1   0.1       0.11   12.0   0.1    1.5  1  DDE_Tnp_IS66   Transposase IS66 family


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.0   1.8e-35   6.6e-32       2     140 .]      80     212 ..      79     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.8e-35
                     DDE_Tnp_IS240   2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkel 77 
                                       k+++vDET+vki+G+w++ly+a+D e++ ild+ ++ r +t++a+afl+++ +k++l+++++++D+++ y++al++l
  gi|313122508|ref|YP_004038395.1|  80 KRVAVDETAVKINGEWSWLYAAIDIETKlILDVELFGRHGTDPAAAFLHRLSEKHDLSDAVFLVDGYG-YQTALSRL 155
                                       789*****************************************************************.******** PP

                     DDE_Tnp_IS240  78 kregelfdevshvqvkylnnriEsdhrtlKkrl..rptrgfkslksaaktlagfeavknlrkghk 140
                                       + +g+ +d+       +++n iE+++ tlK+r+  ++++++ s  s++++  +f+ ++n++++h+
  gi|313122508|ref|YP_004038395.1| 156 GLSGR-LDY-------VERNLIEKWFHTLKMRVdrFHNSWVGSHGSVREWFIQFAQYYNFQRPHQ 212
                                       **887.455.......789**************9889**************************95 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.3   2.5e-10   8.8e-07      34      67 .]     186     219 ..     165     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.5e-10
                             rve_3  34 elfrslaearekleawredYNteRPHssLgykTP 67 
                                       ++  s   +re+  ++ ++YN +RPH+sL+++TP
  gi|313122508|ref|YP_004038395.1| 186 SWVGSHGSVREWFIQFAQYYNFQRPHQSLNGRTP 219
                                       336677889************************9 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.7e-05      0.06       6      73 ..      80     144 ..      75     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                               rve   6 elwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsD 73 
                                       +++ vD t v+i   g++++l++++d  ++lil + l  ++ ++ ++a+l+r  ++   +   ++l D
  gi|313122508|ref|YP_004038395.1|  80 KRVAVDETAVKIN--GEWSWLYAAIDIETKLILDVELFGRHGTDPAAAFLHRLSEKHDLS-DAVFLVD 144
                                       6788999*99955..447*********************************999887776.4666666 PP

>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00041       1.5      29      91 ..      87     149 ..      70     153 .. 0.87
   2 ?    2.8   0.2     0.026        92     120     135 ..     167     182 ..     165     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00041
                             DDE_3  29 leeygrrgrvnligaldekgglaf.vtfeetlnaedfaeflerlletalqakkivlilDnasiH 91 
                                        + +++++  +l++a+d +++l++ v   ++  ++  a+fl rl e+++ +   v+++D+ ++ 
  gi|313122508|ref|YP_004038395.1|  87 TAVKINGEWSWLYAAIDIETKLILdVELFGRHGTDPAAAFLHRLSEKHDLS-DAVFLVDGYGYQ 149
                                       5667888999**************9999999999999*************8.999999988775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.026
                             DDE_3 120 NpiEivwsklkrellk 135
                                       N iE++++ lk ++ +
  gi|313122508|ref|YP_004038395.1| 167 NLIEKWFHTLKMRVDR 182
                                       9**********98876 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     3e-05      0.11      13     135 ..      31     148 ..      27     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                      DDE_Tnp_IS66  13 lvlkyadhlPlyRqeeilarlGvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkgkk 89 
                                       +v+ +a +++l+  +eil+ lGve s +++ +wv+r a+   +  ea        +++++DET ++       +g+ 
  gi|313122508|ref|YP_004038395.1|  31 AVQLHATGCSLRETKEILRILGVERSHQAVWQWVHRLADSGHNPPEATP------KRVAVDETAVK------INGEW 95 
                                       57789999*******************************9877777755......56789******......78888 PP

                      DDE_Tnp_IS66  90 sylWvyvtdkrkpavlfeysp.sRg.gevaealLag.......fkGvlvsDgyag 135
                                       s+l++++  ++    +++++  +R  ++ a a+L            v  +Dgy+ 
  gi|313122508|ref|YP_004038395.1|  96 SWLYAAIDIET--KLILDVELfGRHgTDPAAAFLHRlsekhdlSDAVFLVDGYGY 148
                                       88888887774..222233222333133445554444445655446777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1573.25
//
Query:       gi|313122509|ref|YP_004038396.1|  [L=59]
Description: hypothetical protein Hbor_37430 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 404.38
//
Query:       gi|313122510|ref|YP_004038397.1|  [L=73]
Description: hypothetical protein Hbor_37440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0093   16.1   3.6      0.011   15.9   3.6    1.1  1  DUF3792          Protein of unknown function (DUF3792)
  ------ inclusion threshold ------
      0.088   12.8   1.9      0.092   12.7   1.9    1.1  1  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
       0.15   12.1   1.3       0.16   12.0   1.3    1.0  1  DUF3043          Protein of unknown function (DUF3043)
       0.23   11.2   5.3       0.46   10.2   0.5    2.1  2  FeoB_C           Ferrous iron transport protein B C terminus
       0.58   10.0   4.9       0.48   10.3   2.1    2.0  2  LapA_dom         Lipopolysaccharide assembly protein A domain
        8.1    6.6  12.8         31    4.7   0.4    3.7  4  Myco_arth_vir_N  Mycoplasma virulence signal region (Myco_art


Domain annotation for each model (and alignments):
>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.6   3.7e-06     0.011       9      62 ..      13      66 ..       7      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.7e-06
                           DUF3792  9 llialvitlilllilalllyftslsekvlsililiililsvfigGflagkkakk 62
                                        i  ++t++++++la ++  ++ +  ++s +++++++  ++ig++++ kk k+
  gi|313122510|ref|YP_004038397.1| 13 AYILSLFTALIVAMLAGVVVGGNAEPRTISRAVVVLVFFTTLIGSMIFLKKYKN 66
                                      444556667777777777999***************************999987 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.9   3.1e-05     0.092      67     118 ..      10      68 ..       2      73 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                         RseC_MucC  67 allvYllPllllilgallgsall.......gssellaalgallglvlgflivrllskrl 118
                                       a+ +Y+l l++ +++a+l+ +++       + s ++++l+ +  l+ ++++++++++++
  gi|313122510|ref|YP_004038397.1|  10 AVGAYILSLFTALIVAMLAGVVVggnaeprTISRAVVVLVFFTTLIGSMIFLKKYKNEV 68 
                                       56689999999888888888888888889988999999999999999999999998875 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.3   5.4e-05      0.16      78     137 ..      15      72 ..       6      73 .] 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-05
                           DUF3043  78 lgelflplalvvlvlllvslvkvpevqavvsllllvllllvvidgillgrkvkkkvrekF 137
                                       + +lf  l++++l+ ++v    ++e + +   ++++++++++i ++++  k k++v   F
  gi|313122510|ref|YP_004038397.1|  15 ILSLFTALIVAMLAGVVV--GGNAEPRTISRAVVVLVFFTTLIGSMIFLKKYKNEVFSTF 72 
                                       555666666666666555..345555667788888999999************9998777 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00015      0.46       2      30 ..      11      38 ..      10      41 .. 0.83
   2 ?    3.7   0.5     0.016        48       4      29 ..      45      70 ..      44      73 .] 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                            FeoB_C  2 fslYllgilvallvalllkkttlkgepsp 30
                                      ++ Y+l+++ al+va+l+  +   g+++p
  gi|313122510|ref|YP_004038397.1| 11 VGAYILSLFTALIVAMLAGVV-VGGNAEP 38
                                      789**************9886.7776655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                            FeoB_C  4 lYllgilvallvalll.kkttlkgep.s 29
                                      + +l ++ +l+ ++++ kk   k e  s
  gi|313122510|ref|YP_004038397.1| 45 VVVLVFFTTLIGSMIFlKK--YKNEVfS 70
                                      5788999999999999454..6766555 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.1   0.00016      0.48      16      35 ..      15      34 ..       7      36 .. 0.88
   2 ?    0.4   0.0      0.19   5.8e+02      21      29 ..      47      55 ..      41      67 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00016
                          LapA_dom 16 elpLsllllvafgiGallgw 35
                                       l+L + l+va+++G+++g+
  gi|313122510|ref|YP_004038397.1| 15 ILSLFTALIVAMLAGVVVGG 34
                                      589**************996 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.19
                          LapA_dom 21 llllvafgi 29
                                      +l++++ +i
  gi|313122510|ref|YP_004038397.1| 47 VLVFFTTLI 55
                                      333333333 PP

>> Myco_arth_vir_N  Mycoplasma virulence signal region (Myco_arth_vir_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.4     0.011        31      12      24 ..      10      22 ..      10      25 .. 0.88
   2 ?    4.0   1.8     0.018        54      15      28 ..      21      34 ..      18      35 .. 0.90
   3 ?    2.8   0.1     0.043   1.3e+02      10      21 ..      44      55 ..      43      57 .. 0.84
   4 ?    4.4   0.3     0.013        40       1       9 [.      58      66 ..      58      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                   Myco_arth_vir_N 12 ltlalvaaLlaal 24
                                      +++a + +L++al
  gi|313122510|ref|YP_004038397.1| 10 AVGAYILSLFTAL 22
                                      699*********8 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.018
                   Myco_arth_vir_N 15 alvaaLlaaltfgG 28
                                      al++a la + +gG
  gi|313122510|ref|YP_004038397.1| 21 ALIVAMLAGVVVGG 34
                                      9*********9998 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.043
                   Myco_arth_vir_N 10 kIltlalvaaLl 21
                                      ++++l+  ++L 
  gi|313122510|ref|YP_004038397.1| 44 AVVVLVFFTTLI 55
                                      789*******97 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.013
                   Myco_arth_vir_N  1 MsflKKKKi 9 
                                      M flKK K+
  gi|313122510|ref|YP_004038397.1| 58 MIFLKKYKN 66
                                      99******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 515.18
//
Query:       gi|313122511|ref|YP_004038398.1|  [L=144]
Description: hypothetical protein Hbor_37450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1132.51
//
Query:       gi|313122512|ref|YP_004038399.1|  [L=471]
Description: ABC-type dipeptide transport system, periplasmic component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-65  220.5   0.8    3.9e-65  220.3   0.8    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.3   0.8   2.2e-69   3.9e-65       2     374 ..      38     380 ..      37     383 .. 0.94

  Alignments for each domain:
  == domain 1  score: 220.3 bits;  conditional E-value: 2.2e-69
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                        +p LA++ w  + D +t+ f LR++v+F++G++ltA++vv sf+r+ ++ +  +         ++++v+avddytv
  gi|313122512|ref|YP_004038399.1|  38 TEPLLATE-WR-TVDETTWDFSLREDVTFHNGDQLTADAVVRSFDRVFEQWSWVPGWIGV----EPDGVTAVDDYTV 108
                                       58******.45.8999*********************************98877777776....7************ PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSEE CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldri 155
                                       rf +++p++ f+ ++++    i             dt +kpvgtGP+++++++ +q ++l   ++ +  g p++  +
  gi|313122512|ref|YP_004038399.1| 109 RFQTAEPFPAFPGTISHNYFGIQ----------HPDTTDKPVGTGPFQVAHVEEEQAVTLAPYDEHR-DGTPNPATL 174
                                       *******9999999999888777..........578889**************************87.9******** PP

                                       EEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS- CS
                         SBP_bac_5 156 efkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAiD 232
                                       +fk i+d+++r+++lq G id+++  p s + +l ea  + +  ++  ++ +++a+N +k p  d+ +R+Al+ A+D
  gi|313122512|ref|YP_004038399.1| 175 TFKWIKDPNTRVLSLQEGSIDVAQKTPKSKASSLAEAAETAI-ETQLAPEAGFVAVNLYKSPTTDEQLRKALNWAVD 250
                                       ******************************************.********************************** PP

                                       HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSHH CS
                         SBP_bac_5 233 reeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasgspa 309
                                       ++++v+ vl+g ++pa +++++++p+a  +  p y   d + A++l +e  y++            l +l++s++++
  gi|313122512|ref|YP_004038399.1| 251 QNQLVESVLNGIGEPARGPISSVIPWAIHDDLPTYG-PDRDRARELVAESEYDGET----------LSILINSENTD 316
                                       *******************99999999888888776.5****************97..........*********** PP

                                       HHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTC CS
                         SBP_bac_5 310 ekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsssg 374
                                       ++ ia+++   l++i+++ e+++vd+ a ++++ ++g+  + l g+g++++  d+ + ++++s+g
  gi|313122512|ref|YP_004038399.1| 317 DRTIAQILSGWLEDINVDSEIRQVDP-ASFYDKFTSGESHLTLVGFGSNSAACDYLIRAMFHSKG 380
                                       **************************.8999*****************99999998888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3144.33
//
Query:       gi|313122513|ref|YP_004038400.1|  [L=316]
Description: ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-38  129.9  10.7    8.7e-38  129.9  10.7    1.7  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.15   12.0   0.3        2.4    8.1   0.1    2.3  2  GTP_EFTU_D4   Elongation factor Tu domain 4
       0.38   11.4   0.1       0.38   11.4   0.1    2.7  3  Renin_r       Renin receptor-like protein
       0.41   10.7   5.0       0.45   10.6   0.1    3.0  3  DUF3561       Protein of unknown function (DUF3561)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9  10.7   1.9e-41   8.7e-38       1     183 [.     119     309 ..     119     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.9e-41
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.........vilsilghlilpviillllsaapyv 68 
                                       ++++Gi +a+n++++ld+  ++ + v+ s+P f+l+ ll+  +         +  ++l +l+lp+++l+  +aa+++
  gi|313122513|ref|YP_004038400.1| 119 AVPAGIASAVNPGSRLDYTAQFGSLVGVSMPNFWLGYLLIITCslwldifpvAGAGGLEYLVLPALTLGSGMAAIIT 195
                                       589***********************************997779999****************************** PP

                      BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleai 145
                                       rl+r a+l++l+  ++++a  +G++++ +++k++++nal p++t ++l++ ++l+gav++e +++ pGlgtll++ai
  gi|313122513|ref|YP_004038400.1| 196 RLVRTAMLDVLDAAYIRTAQSKGLRERIVIYKHAFRNALVPVVTIIGLQLSYVLNGAVVVEAVFQRPGLGTLLVDAI 272
                                       ***************************************************************************** PP

                      BPD_transp_1 146 lgydyseisnggvlalviavlllnlvadilqrlldprv 183
                                        ++dy+ i+ g++l ++++++l n+++d+ +  ldpr+
  gi|313122513|ref|YP_004038400.1| 273 FARDYPIIQ-GVTLLIGVIFVLTNFAVDLTYSRLDPRI 309
                                       *********.***************************8 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.073   3.3e+02      50      83 ..      98     132 ..      92     135 .. 0.76
   2 ?    8.1   0.1   0.00054       2.4       1      31 [.     261     291 ..     261     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.073
                                       EEETTEEESEEETT-EEEEEEESS-.TTTS--TT- CS
                       GTP_EFTU_D4  50 iqdkgkkleeakaGqevaisiegki.vGrqikegd 83 
                                       +q+  +++  a a + vai+i  +  +   ++ g 
  gi|313122513|ref|YP_004038400.1|  98 VQRLPNTVALAVASMLVAITIAVPAgIASAVNPGS 132
                                       66777889999999999999988877777777665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00054
                                       S-CEEEEEEEEEEETCCCEEEEEEEEEEEEE CS
                       GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvik 31 
                                       rPg  ++l + +f r  p+i Gv++l Gvi 
  gi|313122513|ref|YP_004038400.1| 261 RPGLGTLLVDAIFARDYPIIQGVTLLIGVIF 291
                                       688889999*******************995 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.5   6.7e+03      60      82 ..      11      33 ..       9      35 .. 0.75
   2 ?   -1.7   0.2         1   4.5e+03      63      76 ..     105     118 ..      81     133 .. 0.58
   3 ?   11.4   0.1   8.6e-05      0.38      46      81 ..     272     307 ..     248     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                           Renin_r 60 wlvvvlvlaliaivvalasmdPg 82
                                        + v++l + +++++++ + Pg
  gi|313122513|ref|YP_004038400.1| 11 LTMGVVLLGVSLLTYGMIFVTPG 33
                                      55667778888888999888887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                           Renin_r  63 vvlvlaliaivval 76 
                                       v+l++a +++++++
  gi|313122513|ref|YP_004038400.1| 105 VALAVASMLVAITI 118
                                       44444444333333 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 8.6e-05
                           Renin_r  46 kyssdYpaiFniiLwlvvvlvlaliaivvalasmdP 81 
                                        +  dYp+i  + L + v++vl+ +a+ ++  ++dP
  gi|313122513|ref|YP_004038400.1| 272 IFARDYPIIQGVTLLIGVIFVLTNFAVDLTYSRLDP 307
                                       5678***************************99999 PP

>> DUF3561  Protein of unknown function (DUF3561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.15   6.9e+02      62     103 ..     113     156 ..     101     161 .. 0.72
   2 ?   -0.7   0.6      0.32   1.4e+03      52      80 ..     155     183 ..     143     206 .. 0.72
   3 ?   10.6   0.1    0.0001      0.45      54      88 ..     224     258 ..     221     274 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                           DUF3561  62 lallPvsvlvGvalsvllrgkllysilatllavvll..fwllfl 103
                                       l  + ++v  G+a  v   ++l y+  +  l+ v++  fwl +l
  gi|313122513|ref|YP_004038400.1| 113 LVAITIAVPAGIASAVNPGSRLDYTAQFGSLVGVSMpnFWLGYL 156
                                       44566778889999999999999998887766555534776555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.32
                           DUF3561  52 ffllytWPfflallPvsvlvGvalsvllr 80 
                                       ++l+ t  ++l ++Pv+   G+ + vl +
  gi|313122513|ref|YP_004038400.1| 155 YLLIITCSLWLDIFPVAGAGGLEYLVLPA 183
                                       56788999999999999888877666544 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0001
                           DUF3561  54 llytWPfflallPvsvlvGvalsvllrgkllysil 88 
                                       ++y   f  al+Pv  ++G+ ls +l+g ++   +
  gi|313122513|ref|YP_004038400.1| 224 VIYKHAFRNALVPVVTIIGLQLSYVLNGAVVVEAV 258
                                       689999**********************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1826.14
//
Query:       gi|313122514|ref|YP_004038401.1|  [L=290]
Description: ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-31  107.8   9.7    5.2e-31  107.8   9.7    1.5  2  BPD_transp_1  Binding-protein-dependent transport system inne
      5e-06   26.4   0.2      5e-06   26.4   0.2    3.0  3  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1      0.57   5.1e+03     157     166 ..      27      36 ..      11      45 .. 0.55
   2 !  107.8   9.7   5.8e-35   5.2e-31       2     181 ..     102     281 ..     101     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.57
                      BPD_transp_1 157 gvlalviavl 166
                                       +v++++++vl
  gi|313122514|ref|YP_004038401.1|  27 VVVVFGLLVL 36 
                                       2333333222 PP

  == domain 2  score: 107.8 bits;  conditional E-value: 5.8e-35
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilpviillllsaapyvrlirraalr 77 
                                         +G++a+ + ++++d++l++l+++ll++P ++la+++       +ilg +l+ ++++l+++++a y+rl+r+++l+
  gi|313122514|ref|YP_004038401.1| 102 AAVGLVAG-YAGGWVDEALMRLVDTLLAFPGIILALVIA------GILGpSLVNMMLALAVVGWASYARLVRSSVLS 171
                                       679*****.******************************......****666666********************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                        +++++v a+r+lG sr ++   +++Pn++ p++ ++ l +gg++ g++ l+flg    lg +  ++++g +++++ 
  gi|313122514|ref|YP_004038401.1| 172 LREREFVTASRLLGRSRLHVATSHLIPNIVAPVVVLATLDIGGVILGTAGLSFLG----LGAQPPTPEWGTMLASGR 244
                                       *******************************************************....***************999 PP

                      BPD_transp_1 155 ..........nggvlalviavlllnlvadilqrlldp 181
                                                 n++ + + +avl +nl+ d l + l+p
  gi|313122514|ref|YP_004038401.1| 245 nylrqawwlvNAPGICIMLAVLGFNLLGDRLRETLSP 281
                                       *****************************99988877 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.2   5.6e-10     5e-06      13      51 .]      20      60 ..      19      60 .. 0.92
   2 ?    2.3   1.2     0.019   1.7e+02      22      37 ..     132     147 ..     130     157 .. 0.88
   3 ?   -4.0   0.6       1.7   1.5e+04       2       8 ..     246     252 ..     245     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5.6e-10
                            OppC_N 13 NklAvvglvilllllliaifaPliaPydp..qdliqnllpP 51
                                      N+l  +g v++  ll++a+f+P+++Pydp  q+l ++l+pP
  gi|313122514|ref|YP_004038401.1| 20 NRLTQFGVVVVFGLLVLAVFGPMVSPYDPveQHLLNRLQPP 60
                                      88889999*********************98888778***9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.019
                            OppC_N  22 illlllliaifaPlia 37 
                                       i+l+l+++ i++P ++
  gi|313122514|ref|YP_004038401.1| 132 IILALVIAGILGPSLV 147
                                       8999*********984 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 1.7
                            OppC_N   2 lwqdawr 8  
                                       ++++aw+
  gi|313122514|ref|YP_004038401.1| 246 YLRQAWW 252
                                       899***5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.55
# Mc/sec: 1591.61
//
Query:       gi|313122515|ref|YP_004038402.1|  [L=365]
Description: ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-27   96.7   0.0    2.2e-27   96.2   0.0    1.2  1  ABC_tran   ABC transporter
    3.1e-15   56.4   0.3      6e-15   55.5   0.3    1.5  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    4.6e-07   30.0   0.7    0.00012   22.0   0.7    2.1  1  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    1.5e-05   25.3   0.2     0.0014   19.0   0.2    2.2  1  AAA_22     AAA domain
    0.00065   20.1   1.1     0.0026   18.2   1.1    2.1  1  AAA_16     AAA ATPase domain
     0.0091   15.5   0.2       0.22   11.0   0.2    2.1  1  SMC_N      RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.026   14.3   0.1    1.4  1  AAA_29     P-loop containing region of AAA domain
      0.031   14.2   0.0      0.063   13.2   0.0    1.4  1  HetR_C     Heterocyst differentiation regulator C-terminal Ho
      0.091   12.3   0.0       0.15   11.6   0.0    1.2  1  AAA_7      P-loop containing dynein motor region
       0.21   10.9   0.2        0.5    9.7   0.0    1.7  2  AIG1       AIG1 family


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   1.2e-30   2.2e-27       2     136 ..      26     200 ..      25     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.2e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke....qeleslrkeigvlpqe..pq 69 
                                       + v++++ +ge+v+++Ge+G+GKS  ++ +++l++p   t G+i++dg++l++    + +++  +ei++++q+  ++
  gi|313122515|ref|YP_004038402.1|  26 DGVTFSVDRGEIVGLIGESGSGKSVTAQSILRLEDPgriTDGTIRFDGTELTTadeaTLRRIRGNEISMVFQDptET 102
                                       789**************************************************988777888889********9999 PP

                                       S-TTSBHHHH................................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHH CS
                                       xxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  70 lfpeltvren................................esdeeiekalsklglkelkdtvvksspssLSgGqk 114
                                       l+p  +v+e+                                +++e++ ++l+++++++ ++++ +  p+++SgG +
  gi|313122515|ref|YP_004038402.1| 103 LNPVFSVGEQiaeavrihetdsrqrlldflgvplfrnrsawaDARERAIELLEQMDIPN-PESRSSAYPHEFSGGLR 178
                                       *********************************99999997777777999999999999.555556999******** PP

                                       HHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 115 qrvalarallkkpkllllDEpt 136
                                       qr +la al+++p ll++DEpt
  gi|313122515|ref|YP_004038402.1| 179 QRAVLAIALASDPALLVADEPT 200
                                       *********************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.3   3.4e-18     6e-15       1      65 []     252     316 ..     252     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3.4e-18
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E gp+++++++p HPYT++Ll++  r++++ +++++++ ++ +    ++GCpFa+RC++a+++C
  gi|313122515|ref|YP_004038402.1| 252 MEAGPVDQVLTDPEHPYTRTLLDCSVRNRAPGERVRSVERTPVDSIGGHKGCPFADRCQHATSAC 316
                                       79*******************************8999999988********************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.7   6.9e-08   0.00012     160     302 ..     125     236 ..      37     237 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.9e-08
                            AAA_21 160 glrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelpare 236
                                        +r+ +++   +f++   +a+ ++++ +l+ + + +++e + +                               ++e
  gi|313122515|ref|YP_004038402.1| 125 RQRLLDFLGVPLFRNRSAWADARERAIELLEQMDIPNPESRSS-----------------------------AYPHE 172
                                       3333377777777777777777777777777777777777777.............................56788 PP

                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       +S G ++  a+l++ l+ ++  +ll+ DEp + L+   ++ +l+ +++l++ +g+ v+l +H+  ++
  gi|313122515|ref|YP_004038402.1| 173 FSGGLRQR-AVLAIALASDP--ALLVADEPTTALDTTTQADILRRIRALRDeRGIGVLLISHDIGVI 236
                                       9*******.66666666555..9***********************9999999*********98776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   7.6e-07    0.0014       7     128 ..      37     229 ..      32     234 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.6e-07
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee....................................erpevv..fv 45 
                                       i+ ++GesG+GK+++++ +l+  d     +                                     +++  v   +
  gi|313122515|ref|YP_004038402.1|  37 IVGLIGESGSGKSVTAQSILRLEDPGRITDGtirfdgtelttadeatlrrirgneismvfqdptetlNPVFSVgeQI 113
                                       6669******************9877665557777777777777777777766666666665555443333333222 PP

                            AAA_22  46 tlpsstsskdllrellralglelka.......................erlsseellealeqalrarav........ 91 
                                         ++    +d +++ll +lg++l +                       ++ +s+++ + +   lr+rav        
  gi|313122515|ref|YP_004038402.1| 114 AEAVRIHETDSRQRLLDFLGVPLFRnrsawadareraielleqmdipnPESRSSAYPHEFSGGLRQRAVlaialasd 190
                                       22222255555555555555555558888999999999999999999755666666688888888888888888888 PP

                            AAA_22  92 ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       ++ll+ DE    l+   ++++l+ +r l +  + g+ ++L+
  gi|313122515|ref|YP_004038402.1| 191 PALLVADEPTTaLDtttQADILRRIRALRD--ERGIGVLLI 229
                                       899999999998988655999999999999..999999997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.1   1.4e-06    0.0026      23     107 ..      34     159 ..      23     332 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif...lrgkcdqlesa........................ipy... 69 
                                       r+e+v l+GesG+GKs  ++++l +le+ g i+   +r + ++l++a                         p    
  gi|313122515|ref|YP_004038402.1|  34 RGEIVGLIGESGSGKSVTAQSIL-RLEDPGRITdgtIRFDGTELTTAdeatlrrirgneismvfqdptetlNPVfsv 109
                                       55899******************.79999776675555555555222333444444444444444443333222222 PP

                            AAA_16  70 ......sa.laqalareellrqlldeaesaeleawrekleeala......a 107
                                             ++ + ++ +r + l + l  +  ++++aw+++ e+a++      +
  gi|313122515|ref|YP_004038402.1| 110 geqiaeAVrIHETDSR-QRLLDFLGVPLFRNRSAWADARERAIElleqmdI 159
                                       2221111113333322.2222222235555555555555555555555552 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.2   0.00012      0.22     135     212 ..     162     247 ..      27     253 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                       T.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                             SMC_N 135 e.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislree 200
                                                 ++SgG ++ + la+ +A    +  +l + De   aLD +  + + +++++ +++    ++ is++ +
  gi|313122515|ref|YP_004038402.1| 162 PesrssayphEFSGGLRQRAVLAIALA----SDPALLVADEPTTALDTTTQADILRRIRALRDErgIGVLLISHDIG 234
                                       245555555588888776666655555....55679999********************888775588999999998 PP

                                       HCCC-.SCEEEEE CS
                                       xxxxx.xxxxxxx RF
                             SMC_N 201 mleka.dklvgvt 212
                                       ++++  d++v v+
  gi|313122515|ref|YP_004038402.1| 235 VIAQTcDRVVVVY 247
                                       8877657777776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.4e-05     0.026      11      37 ..      24      50 ..      22      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKST 37
                                        dg t+++d+ +++ l+G+sGsGKS 
  gi|313122515|ref|YP_004038402.1| 24 AVDGVTFSVDRGEIVGLIGESGSGKSV 50
                                      678999****877*************6 PP

>> HetR_C  Heterocyst differentiation regulator C-terminal Hood domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.5e-05     0.063      17      42 ..     137     162 ..     133     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.5e-05
                            HetR_C  17 frlmrdwaerkpkvlrvleeldippe 42 
                                       fr    wa+ +++++ +le++dip+ 
  gi|313122515|ref|YP_004038402.1| 137 FRNRSAWADARERAIELLEQMDIPNP 162
                                       899999*****************974 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.2e-05      0.15      30      69 ..      32      71 ..      24      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.2e-05
                             AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinf 69
                                      ++++  v l+G++G+GK+v+++++l+  d+ +++  ti f
  gi|313122515|ref|YP_004038402.1| 32 VDRGEIVGLIGESGSGKSVTAQSILRLEDPGRITDGTIRF 71
                                      556677889****************999888888777777 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00028       0.5       5      22 ..      40      57 ..      36      95 .. 0.88
   2 ?   -2.1   0.0       1.1     2e+03      52     111 ..     194     247 ..     181     257 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                                      EESSTTSSHHHHHHHHHT CS
                              AIG1  5 lvGktgnGkSaTgNsilg 22
                                      l+G +g+GkS T+ sil+
  gi|313122515|ref|YP_004038402.1| 40 LIGESGSGKSVTAQSILR 57
                                      89**************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                       EEEE--SC.CCTTCCHHCHHHHHHHHHHHCTT-ESEEEEEEETTB-SHHHHHHHHHHHHHH CS
                              AIG1  52 nViDTPgl.fdlsvsadkiskeivrclllseegihalllvlslgrfteedekalktlkelF 111
                                        V D P   +d+ ++ad i + i    l  e gi +ll+  ++g +     ++  ++  ++
  gi|313122515|ref|YP_004038402.1| 194 LVADEPTTaLDTTTQAD-ILRRIR--ALRDERGIGVLLISHDIGVIA----QTCDRVVVVY 247
                                       55566654344444444.444444..366788888888888888776....4445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2293.04
//
Query:       gi|313122516|ref|YP_004038403.1|  [L=356]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-30  104.9   0.0    6.5e-30  104.4   0.0    1.2  1  ABC_tran         ABC transporter
    7.6e-20   71.2   1.3    1.5e-19   70.3   1.3    1.5  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    5.2e-08   33.1   0.9    7.1e-06   26.0   0.1    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.3e-07   30.2   0.7    1.4e-06   28.8   0.6    1.8  1  AAA_16           AAA ATPase domain
    1.5e-05   25.3   0.0    3.3e-05   24.2   0.0    1.6  1  AAA_22           AAA domain
     0.0023   17.9   0.0     0.0052   16.7   0.0    1.5  2  RsgA_GTPase      RsgA GTPase
     0.0044   17.0   0.4        0.2   11.7   0.2    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.013   15.9   0.1       0.11   12.9   0.1    2.2  1  AAA              ATPase family associated with various cellul
       0.02   14.6   0.0       0.61    9.8   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain
      0.032   14.6   0.0      0.067   13.6   0.0    1.5  1  RNA_helicase     RNA helicase
      0.033   14.3   0.0      0.069   13.2   0.0    1.5  1  MMR_HSR1         50S ribosome-binding GTPase
      0.034   14.4   0.1        0.1   12.8   0.1    1.8  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.035   13.7   0.1      0.075   12.6   0.1    1.7  1  AAA_25           AAA domain
      0.039   13.6   0.0      0.039   13.6   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.054   12.9   0.0       0.18   11.2   0.0    1.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.055   13.2   0.3        1.9    8.2   0.1    2.1  2  IstB_IS21        IstB-like ATP binding protein
      0.057   12.7   0.1       0.11   11.7   0.1    1.4  1  Zeta_toxin       Zeta toxin
      0.088   13.0   0.0       0.18   12.0   0.0    1.6  1  AAA_33           AAA domain
       0.09   11.4   0.0        0.3    9.7   0.0    1.7  2  AAA_13           AAA domain
       0.11   12.3   0.1       0.19   11.5   0.1    1.3  1  AAA_29           P-loop containing region of AAA domain
       0.12   13.0   0.0       0.21   12.2   0.0    1.4  1  AAA_18           AAA domain
       0.13   12.1   0.2       0.24   11.3   0.2    1.4  1  APS_kinase       Adenylylsulphate kinase
       0.15   11.9   0.2       0.29   11.0   0.2    1.5  1  NACHT            NACHT domain
       0.19   11.4   0.1        2.1    8.0   0.1    2.0  2  CoaE             Dephospho-CoA kinase
       0.21   11.1   0.0       0.33   10.5   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
       0.21   10.7   0.1       0.35   10.0   0.1    1.2  1  NB-ARC           NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   9.5e-33   6.5e-30       3     136 ..      49     198 ..      47     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 9.5e-33
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpelt 75 
                                       + sl ++ ge+v++vGe+G+GKStL+kll+g+l+p+ G++lldg+ +    ++ +  r++igv++q+  ++++p+  
  gi|313122516|ref|YP_004038403.1|  49 DASLAVRDGETVGLVGESGCGKSTLAKLLTGQLTPDHGQVLLDGTCVGGysDRSPAQRRRIGVVFQHvrQSFDPRWP 125
                                       57999******************************************99889999************9777888887 PP

                                       HHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       + ++            e+ ++++ +   l+ + l+ +++++ p++LSgGq qrvalaral+  p++++lDEp 
  gi|313122516|ref|YP_004038403.1| 126 ISRSltealddsgtdtEDGSDLDGIDGLLQSVSLPSHIADRYPRELSGGQLQRVALARALAHSPDVIVLDEPV 198
                                       777799999999888766666666666666666777999999******************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   1.3   2.2e-22   1.5e-19       1      65 []     250     314 ..     250     314 .. 0.99

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2.2e-22
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+gp+++lf++p HPYT+aLlr++p+ d++++  + ++g++p++ ++++GCpF+pRC  a++eC
  gi|313122516|ref|YP_004038403.1| 250 VETGPANELFRHPSHPYTEALLRAIPSDDPRDEHPTPLRGDPPDPADRPAGCPFHPRCSAATAEC 314
                                       8**************************************************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.016        11       3      20 ..      61      78 ..      60      93 .. 0.87
   2 !   26.0   0.1     1e-08   7.1e-06     180     301 ..     125     233 ..      98     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.016
                            AAA_21  3 vliGpNgsGKSnLLdald 20
                                      +l+G  g+GKS+L ++l 
  gi|313122516|ref|YP_004038403.1| 61 GLVGESGCGKSTLAKLLT 78
                                      69***********99995 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1e-08
                            AAA_21 180 kekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralk 256
                                       ++ r l++ ++ + ++    sdl+  + l  sv+++           ++  ++ +relS G+++  al+ al+  + 
  gi|313122516|ref|YP_004038403.1| 125 PISRSLTEALDDSGTDTEDGSDLDGIDGLLQSVSLP-----------SHIADRYPRELSGGQLQRVALARALAHSP- 189
                                       555555555555555556666666666666666655...........68889999*********999999999888. PP

                            AAA_21 257 kgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                         +++++DEp +gL+ + ++++l ll++ ++  g+  ++ +H+  +
  gi|313122516|ref|YP_004038403.1| 190 --DVIVLDEPVSGLDMATQATILNLLEDVQQrFGVGYVFISHDLDV 233
                                       ..************************77777799********9765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.6     2e-09   1.4e-06      18     165 ..      53     219 ..      38     227 .. 0.63

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2e-09
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa.................ipysalaqal 76 
                                       +vr+g  e v l+GesG+GKs+l++ l  +l+ d+g + l g+c+   s+                  ++++ + + 
  gi|313122516|ref|YP_004038403.1|  53 AVRDG--ETVGLVGESGCGKSTLAKLLTGQLTPDHGQVlLDGTCVGGYSDrspaqrrrigvvfqhvrQSFDPRWPIS 127
                                       56666..67999**********************7666677777766333223334444444444443334444444 PP

                            AAA_16  77 areellrqlldeaesaeleawrekleealaavpelagaea.....srllellkrll.allsrderplvlvlDd.lqw 146
                                        r +l ++l+d  +++e + + + +++ l+ + +l++ +a     +    +l+r + a++   ++p v+vlD+ +  
  gi|313122516|ref|YP_004038403.1| 128 -R-SLTEALDDSGTDTEDGSDLDGIDGLLQ-SVSLPSHIAdryprELSGGQLQRVAlARALA-HSPDVIVLDEpVSG 200
                                       .3.555555555666666666666666666.6666666665666433333445555455555.55789999963567 PP

                            AAA_16 147 adeaslqllaaLlrllesk 165
                                       +d a+++ + +Ll++++++
  gi|313122516|ref|YP_004038403.1| 201 LDMATQATILNLLEDVQQR 219
                                       7777777788888887774 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   4.8e-08   3.3e-05      10     129 ..      62     228 ..      55     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.8e-08
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee...................erpevvfvtlpsst.sskdllrellralgl 66 
                                       ++GesG+GK+tl++ l+ ql+  +++ +                   +r +vvf  + +s   +  + r l +al++
  gi|313122516|ref|YP_004038403.1|  62 LVGESGCGKSTLAKLLTGQLT--PDHGQvlldgtcvggysdrspaqrRRIGVVFQHVRQSFdPRWPISRSLTEALDD 136
                                       79******************6..4455588**************887777788777777773333567777777777 PP

                            AAA_22  67 elka............................erlsseellealeqalrarav...ielliiDEaqh.lr...seea 108
                                       ++ +                            ++ls      +l++ + ara    + ++++DE    l+   ++++
  gi|313122516|ref|YP_004038403.1| 137 SGTDtedgsdldgidgllqsvslpshiadrypRELSG----GQLQRVALARALahsPDVIVLDEPVSgLDmatQATI 209
                                       7777999********************7444444444....55555555555556666******9999988766999 PP

                            AAA_22 109 leeLrsllnlsrkgvqliLvG 129
                                       l+ L + +   r+gv  +++ 
  gi|313122516|ref|YP_004038403.1| 210 LNLLEDVQQ--RFGVGYVFIS 228
                                       999988888..9999999885 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   7.5e-06    0.0052      98     126 ..      56      84 ..      42      92 .. 0.82
   2 ?   -3.1   0.0       9.3   6.4e+03      56      85 ..     201     230 ..     175     244 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.5e-06
                                       TTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelk 126
                                       +++t+ lvG+SG GKStL + l+++l+  
  gi|313122516|ref|YP_004038403.1|  56 DGETVGLVGESGCGKSTLAKLLTGQLTPD 84 
                                       458999****************9997655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.3
                                       GGG--HHHHHHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase  56 iDlleeeeeleelkeelealgyevllvsak 85 
                                       +D++++++ l+ l++  +++g+  +++s +
  gi|313122516|ref|YP_004038403.1| 201 LDMATQATILNLLEDVQQRFGVGYVFISHD 230
                                       456666665555555566666666666554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   0.00029       0.2       4      22 ..      62      80 ..      59      90 .. 0.84
   2 ?    3.3   0.0      0.11        76      56      91 ..     178     215 ..     162     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                      EE--SSSSHHHHHHHGGGG CS
                             AAA_5  4 LvGppGtgKselaerlaaa 22
                                      LvG++G+gKs+la+ l   
  gi|313122516|ref|YP_004038403.1| 62 LVGESGCGKSTLAKLLTGQ 80
                                      9*************99765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
                                       .--------.G-SEEEEES.GGG--HHHHHHHHHHHHS CS
                             AAA_5  56 dsplvraar.egeilvlDE.veraesevlnsLlsllee 91 
                                         +l ra   +++++vlDE v  ++ +++++ l+lle+
  gi|313122516|ref|YP_004038403.1| 178 RVALARALAhSPDVIVLDEpVSGLDMATQATILNLLED 215
                                       455666665799*******6666669999999999998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00016      0.11       3      24 ..      62      83 ..      60     244 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                                      EESSTTSSHHHHHHHHHHHHTH CS
                               AAA  3 lyGppGtGKTllakavakelgv 24
                                      l+G  G+GK++lak +  +l  
  gi|313122516|ref|YP_004038403.1| 62 LVGESGCGKSTLAKLLTGQLTP 83
                                      89**************999842 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00088      0.61      15      44 ..      50      79 ..      37      94 .. 0.78
   2 ?    2.5   0.0      0.15     1e+02      96     121 ..     191     217 ..     183     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00088
                                      HHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 15 ikkvaktdlsvlitGesGtGKellaraihe 44
                                      ++ +++   +v ++GesG+GK++la+++  
  gi|313122516|ref|YP_004038403.1| 50 ASLAVRDGETVGLVGESGCGKSTLAKLLTG 79
                                      5556666788999************99865 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                                       EEEEET.GGGS-HHHHHHHHHHHHHSE CS
                   Sigma54_activat  96 tlfLDe.igelplelQekLlrvlqege 121
                                       ++ LDe ++ l++++Q+ +l++l++ +
  gi|313122516|ref|YP_004038403.1| 191 VIVLDEpVSGLDMATQATILNLLEDVQ 217
                                       6889998999*************9754 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.7e-05     0.067       3      23 ..      62      82 ..      60     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.7e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakall 23
                                      l+G+sg+GKStlak L+ +l+
  gi|313122516|ref|YP_004038403.1| 62 LVGESGCGKSTLAKLLTGQLT 82
                                      79*************998887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.069       2      22 ..      60      80 ..      59      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      v++vG +  GKStL + ltg+
  gi|313122516|ref|YP_004038403.1| 60 VGLVGESGCGKSTLAKLLTGQ 80
                                      99*****************97 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00015       0.1      61      89 ..     186     214 ..     164     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                           SbcCD_C  61 epalrlvfLDEAFsklDeesiatllelle 89 
                                        +++++++LDE  s+lD  ++at+l+lle
  gi|313122516|ref|YP_004038403.1| 186 AHSPDVIVLDEPVSGLDMATQATILNLLE 214
                                       46899**********************97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011     0.075      30      98 ..      54     142 ..      29     229 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            AAA_25  30 lpagelallaGapgtGKttlaldlalava..tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal....... 97 
                                       ++ ge++ l+G +g+GK+tla  l   ++   G+ +l+      g+++     d+    rrR+  v++++       
  gi|313122516|ref|YP_004038403.1|  54 VRDGETVGLVGESGCGKSTLAKLLTGQLTpdHGQVLLD------GTCVGGYS-DRSPAQRRRIGVVFQHVrqsfdpr 123
                                       46799999*************99999999776666655......33333333.333366666666666664433333 PP

                            AAA_25  98 ..................r 98 
                                                         +
  gi|313122516|ref|YP_004038403.1| 124 wpisrsltealddsgtdtE 142
                                       3332222233444444432 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.6e-05     0.039       4      38 ..      47      81 ..      44     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-05
                                      HHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  4 vlDalfpivqGqrtlipgafgvGktvisqslskqs 38
                                      v Da + +  G++++++g++g+Gk+++++ l+ q 
  gi|313122516|ref|YP_004038403.1| 47 VCDASLAVRDGETVGLVGESGCGKSTLAKLLTGQL 81
                                      789999**********************9988775 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.18      17      60 ..      52      95 ..      41     120 .. 0.79
   2 ?   -1.5   0.0       1.9   1.3e+03       6      37 ..     172     203 ..     158     244 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                      Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevaki 60
                                      +a+  g  + lvG +G+GK+ lak l++ l+p + +  l+ + +
  gi|313122516|ref|YP_004038403.1| 52 LAVRDGETVGLVGESGCGKSTLAKLLTGQLTPDHGQVLLDGTCV 95
                                      56666777889****************99999887777776655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                      Mg_chelatase   6 kGqeeakraleiaaaGgHnlllvGppGsGKtm 37 
                                        G + ++ al  a a + +++++  p sG  m
  gi|313122516|ref|YP_004038403.1| 172 SGGQLQRVALARALAHSPDVIVLDEPVSGLDM 203
                                       34444444555555555555555555555544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0028       1.9      44      70 ..      54      80 ..      44      90 .. 0.83
   2 ?    3.0   0.0      0.11        77     104     154 ..     183     236 ..     169     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialgve 70
                                      +++ e + l+G sG GKs la  l  +
  gi|313122516|ref|YP_004038403.1| 54 VRDGETVGLVGESGCGKSTLAKLLTGQ 80
                                      67889999*************887655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                         IstB_IS21 104 krllkv.dllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpfaew 154
                                       ++l+++ d+++lD+   gl    qa   +l+e +++r++   + i+ +l + ++
  gi|313122516|ref|YP_004038403.1| 183 RALAHSpDVIVLDEpvSGLDMATQATILNLLEDVQQRFGVGYVFISHDLDVVQY 236
                                       34444349*****95457777778888888888889998888888888777665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00016      0.11      21      51 ..      62      92 ..      55      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldp 51
                                      l+G +G+GKs+la+ll+ +l+++ + v ld+
  gi|313122516|ref|YP_004038403.1| 62 LVGESGCGKSTLAKLLTGQLTPDHGQVLLDG 92
                                      89*******************9998888886 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00026      0.18       4      25 ..      62      86 ..      60     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                            AAA_33  4 lvGlpGsGKstlaerllkklg...a 25
                                      lvG +G+GKstla+ l  +l+   +
  gi|313122516|ref|YP_004038403.1| 62 LVGESGCGKSTLAKLLTGQLTpdhG 86
                                      79*************9999986663 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.67   4.6e+02      23      39 ..      64      80 ..      62      88 .. 0.83
   2 ?    9.7   0.0   0.00044       0.3     526     579 ..     188     239 ..     176     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.67
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G  G GK+tL++ll  +
  gi|313122516|ref|YP_004038403.1| 64 GESGCGKSTLAKLLTGQ 80
                                      7789*********9864 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00044
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkk 579
                                          ++v+D PvS LD   +  + +l++++  ++  +  +fi+ H l+  +++ +
  gi|313122516|ref|YP_004038403.1| 188 SPDVIVLDEPVSGLDMATQATILNLLEDVQ-QRFGVGYVFIS-HDLDVVQYLAD 239
                                       5689************************97.88999999997.88877777765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00027      0.19      23      39 ..      57      74 ..      48      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                            AAA_29 23 g.atlltGpsGsGKSTll 39
                                      g ++ l+G+sG GKSTl 
  gi|313122516|ref|YP_004038403.1| 57 GeTVGLVGESGCGKSTLA 74
                                      447789**********95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0003      0.21       1      44 [.      60     101 ..      60     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                       ++l G +G+GK+tlak L   l     +++v+ ++ ++ ++ + 
  gi|313122516|ref|YP_004038403.1|  60 VGLVGESGCGKSTLAKLLTGQL--TPDHGQVLLDGTCVGGYSDR 101
                                       6799**************7776..66777777777777666666 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00035      0.24       2      40 ..      57      94 ..      56      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                      g +v l G sg GKst+a+ l  +L+ +  + +lLdG  
  gi|313122516|ref|YP_004038403.1| 57 GETVGLVGESGCGKSTLAKLLTGQLTPDHGQ-VLLDGTC 94
                                      5688899******************987655.4688865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00043      0.29       2      21 ..      59      78 ..      58      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      +v l Ge+G+GK+tL++ l 
  gi|313122516|ref|YP_004038403.1| 59 TVGLVGESGCGKSTLAKLLT 78
                                      67899**********99776 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1     0.003       2.1       2      21 ..      59      78 ..      58      92 .. 0.89
   2 ?    0.9   0.0      0.45   3.1e+02      47      74 ..     162     187 ..     155     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.003
                                      EEEEEESTTSSHHHHHHHHH CS
                              CoaE  2 ivgltGgiasGKstvanlfa 21
                                       vgl G  ++GKst+a+l++
  gi|313122516|ref|YP_004038403.1| 59 TVGLVGESGCGKSTLAKLLT 78
                                      59***************997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.45
                                       HHHHHHGGGCB.TTSSE-HHHHHHHHHT CS
                              CoaE  47 kiveeFgeeildedGeLdReaLrkkvFa 74 
                                       +i+++++ e+  + G+L+R aL++ + +
  gi|313122516|ref|YP_004038403.1| 162 HIADRYPREL--SGGQLQRVALARALAH 187
                                       6888999998..89********987655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00047      0.33      28      61 ..      52      85 ..      48      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00047
                             AAA_7 28 lllknkkpvllvGptGtGKtviikdllkkldkek 61
                                      l ++ +  v lvG++G+GK++++k l+ +l +++
  gi|313122516|ref|YP_004038403.1| 52 LAVRDGETVGLVGESGCGKSTLAKLLTGQLTPDH 85
                                      5678889999**************9999988765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00051      0.35      22      38 ..      59      75 ..      46      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00051
                                      EEEEEESTTSSHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlak 38
                                       v+lvG  G+GK+tlak
  gi|313122516|ref|YP_004038403.1| 59 TVGLVGESGCGKSTLAK 75
                                      79*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2209.16
//
Query:       gi|313122517|ref|YP_004038404.1|  [L=240]
Description: thioredoxin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-11   42.4   1.1    1.2e-05   24.8   0.0    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.8e-07   30.0   0.3     0.0041   16.3   0.0    2.2  2  FAD_binding_2  FAD binding domain
    2.7e-06   27.5   0.2    5.9e-06   26.4   0.2    1.5  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    3.2e-06   26.6   0.1      0.093   12.0   0.0    3.1  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    9.3e-06   24.6   0.0    0.00011   21.1   0.0    2.0  2  HI0933_like    HI0933-like protein
    7.5e-05   22.0   0.0    0.00011   21.4   0.0    1.3  1  GIDA           Glucose inhibited division protein A
    0.00031   20.1   0.0     0.0011   18.2   0.0    1.8  2  FAD_binding_3  FAD binding domain
    0.00086   18.8   0.2     0.0018   17.7   0.2    1.5  1  FAD_oxidored   FAD dependent oxidoreductase
     0.0017   18.0   1.2      0.013   15.1   0.1    2.1  2  DAO            FAD dependent oxidoreductase
     0.0056   16.0   0.0       0.01   15.1   0.0    1.4  1  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.019   14.2   0.0    1.3  1  2-ph_phosp     2-phosphosulpholactate phosphatase
      0.046   13.7   0.8        1.5    8.8   0.0    2.6  3  NAD_binding_9  FAD-NAD(P)-binding
       0.09   12.4   0.0       0.19   11.4   0.0    1.5  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.096   12.6   0.0       0.21   11.5   0.0    1.6  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   9.1e-09   1.2e-05       1      42 [.      12      52 ..      12      80 .. 0.83
   2 !   16.8   0.2   2.4e-06    0.0031     202     291 ..      84     174 ..      63     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 9.1e-09
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll 42
                                      +d++++GgGpAG aa  +la+a ++v+l+ + g+  +++c  
  gi|313122517|ref|YP_004038404.1| 12 YDIAIVGGGPAGSAAGVFLARADFEVLLF-DHGQSTLQKCAF 52
                                      69***************************.888888888876 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.4e-06
                                       ESCEEEEEEETTE.EEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE...EETTEE...E--TTSBESSTTE CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx...xxxxxxxxxxxxx RF
                       Pyr_redox_2 202 lgtsvkeidgnge.klevvledgeeidadlvvvavGvrpstelleeklglel...derggi...vvdeflrtnvpgi 271
                                       l++ v++i + ++   +v+ + + ++ +++v+v  + + +   l   lg+e+   ++ g +    +d+ ++t+v+g+
  gi|313122517|ref|YP_004038404.1|  84 LEAAVERISETSDgGFRVH-SREGTYGTRYVLVTSWAETDY--L-SPLGVETvpeKHPGEVqvvMTDDDGETTVDGV 156
                                       5788888888887555544.444557999999999988885..4.567777765566666644467*********** PP

                                       EE-GGGCTECCSS--HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 272 yaiGDvaggkggpelaqaAv 291
                                       ya+G v+  ++  + +++A 
  gi|313122517|ref|YP_004038404.1| 157 YAAGRVT--ETYHQAIVNAG 174
                                       *******..55555556655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.2e-06    0.0041       1      34 [.      13      46 ..      13      61 .. 0.93
   2 !   12.3   0.1   5.1e-05     0.065     325     409 ..      83     169 ..      63     179 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.2e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqef 34
                                      D+ ++G+G AG aA++ +a+a  +v++ + +q++
  gi|313122517|ref|YP_004038404.1| 13 DIAIVGGGPAGSAAGVFLARADFEVLLFDHGQST 46
                                      899**************************99984 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.1e-05
                                       HHHHHSHHHHHHHHHCCT......S-TTTS............EEE.......EEEEEEEES-EEEBETTSBESTTEE CS
                     FAD_binding_2 325 gleatleaineeaangldkdfgrgidpadr............pipgpfyavkvvpaqhytmgGvetdengrvldadg 389
                                        lea +e+i e+ + g+ ++  r+++  +r               +p+    v  ++++    v td++g++     
  gi|313122517|ref|YP_004038404.1|  83 RLEAAVERISETSDGGFRVH-SREGTYGTRyvlvtswaetdyL--SPLGVETVPEKHPGEVQVVMTDDDGET----- 151
                                       56666666666666666644.3333333333433332222221..333333333333455555677777777..... PP

                                       ESSBTEEE-STCEESSSSTT CS
                     FAD_binding_2 390 qpipGLYAaGevaaggvhga 409
                                        +++G YAaG v+   +h a
  gi|313122517|ref|YP_004038404.1| 152 -TVDGVYAAGRVT-ETYHQA 169
                                       .************.888865 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.2   4.6e-09   5.9e-06       1      29 [.      16      44 ..      16      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.6e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      IvG+G +G++a  +La+a+f+vll+++++
  gi|313122517|ref|YP_004038404.1| 16 IVGGGPAGSAAGVFLARADFEVLLFDHGQ 44
                                      9*************************987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   7.3e-05     0.093       2      31 ..      16      44 ..      15      55 .. 0.89
   2 !    8.1   0.0    0.0011       1.4     100     130 ..      84     115 ..      72     128 .. 0.90
   3 ?    3.2   0.0     0.033        42     286     305 .]     141     160 ..     121     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgn 31
                                      I+G+GPaG aa++ l +a++ ++l  + g+
  gi|313122517|ref|YP_004038404.1| 16 IVGGGPAGSAAGVFLARADF-EVLLFDHGQ 44
                                      9*******************.688888876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                       Pyr_redox_3 100 lfeeVesvkk.edegfevetsketyeAkkvii 130
                                       l+  Ve++++ +d+gf+v+++++ty +++v++
  gi|313122517|ref|YP_004038404.1|  84 LEAAVERISEtSDGGFRVHSREGTYGTRYVLV 115
                                       56789***9956888***************97 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.033
                       Pyr_redox_3 286 rpvlteeteetnvpglflaG 305
                                       ++v+t+++ et+v+g++ aG
  gi|313122517|ref|YP_004038404.1| 141 QVVMTDDDGETTVDGVYAAG 160
                                       57899*************99 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.5e-08   0.00011       1      39 [.      12      50 ..      12      52 .. 0.95
   2 ?    1.5   0.0     0.076        97     124     168 ..      80     119 ..      60     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.5e-08
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHH CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKi 39
                                      +d++++GgG+AG  a + +a+++ +Vll+++++++++K 
  gi|313122517|ref|YP_004038404.1| 12 YDIAIVGGGPAGSAAGVFLARADFEVLLFDHGQSTLQKC 50
                                      589********************************9996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.076
                                       -EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-G CS
                       HI0933_like 124 vklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiP 168
                                          rle +v+++++++dg frv+   e+++ +++++++    S++
  gi|313122517|ref|YP_004038404.1|  80 GCNRLEAAVERISETSDGGFRVHS-REGTYGTRYVLVT----SWA 119
                                       45588999***************9.8999999999998....555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   8.6e-08   0.00011       1      46 [.      13      58 ..      13      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.6e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsigg 46
                                      d+ ++GgG AG++A + +ar+ ++vlL+ h  +t+ +++  ++  g
  gi|313122517|ref|YP_004038404.1| 13 DIAIVGGGPAGSAAGVFLARADFEVLLFDHGQSTLQKCAFLENYLG 58
                                      789*************************999999988876666555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.9e-07    0.0011       2      37 ..      12      47 ..      11      50 .. 0.87
   2 ?   -0.8   0.0      0.55     7e+02     204     235 ..      89     121 ..      70     180 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.9e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37
                                      +d++IVG+GpaG  ++ +L++a  +v+l +  ++t 
  gi|313122517|ref|YP_004038404.1| 12 YDIAIVGGGPAGSAAGVFLARADFEVLLFDHGQSTL 47
                                      6899******************99999988877765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.55
                                       EEEEECCTTEEEEEECCE.TEEEEEEEEECCE- CS
                     FAD_binding_3 204 vlilsaesrgvmviPlen.tlerfyvqvearae 235
                                       + i +++++g+ v ++e    +r++++ ++ ++
  gi|313122517|ref|YP_004038404.1|  89 ERISETSDGGFRVHSREGtYGTRYVLVTSWAET 121
                                       456677777777777777555666666666554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   1.4e-06    0.0018       1      31 [.      13      43 ..      13      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      D+ +vGGgpaG aA +  ara+ +vlL +  
  gi|313122517|ref|YP_004038404.1| 13 DIAIVGGGPAGSAAGVFLARADFEVLLFDHG 43
                                      9**************************8865 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     1e-05     0.013       1      29 [.      13      43 ..      13      49 .. 0.93
   2 ?    2.1   0.2     0.094   1.2e+02     168     242 ..      87     158 ..      64     231 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      d++i+GGG +G+++  +Lar+   V+l++ g
  gi|313122517|ref|YP_004038404.1| 13 DIAIVGGGPAGSAAGVFLARADfeVLLFDHG 43
                                      8******************99999***9976 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.094
                                       CEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTT.CTTTSEEEEEEEEEEEEEECCTHSTGSGCSE CS
                               DAO 168 evtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgll.keldlpispvrgqvlvlkplseklvspaail 241
                                        v++++e+++++ +v  +++ g+  + ++v ++  a +d l++l  ++++ + +p   qv++++   e++v    ++
  gi|313122517|ref|YP_004038404.1|  87 AVERISETSDGGFRV--HSReGTYGT-RYVLVTSWAETDyLSPLGvETVPEK-HPGEVQVVMTDDDGETTVDG--VY 157
                                       666776655566666..333354333.6777777666664442222333333.67777777775555544433..22 PP

                                       E CS
                               DAO 242 p 242
                                       +
  gi|313122517|ref|YP_004038404.1| 158 A 158
                                       2 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.8e-06      0.01      18      49 ..      12      42 ..       1      46 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.8e-06
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       D++ivG+G++G +a+  la++ d++v+++++
  gi|313122517|ref|YP_004038404.1| 12 YDIAIVGGGPAGSAAGVFLARA-DFEVLLFDH 42
                                      59********************.****99875 PP

>> 2-ph_phosp  2-phosphosulpholactate phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.019     128     182 ..     132     186 ..     127     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                       HHHHTSS.EEEEE--BTTB--HHHHHHHHHHHHHHHHHS.SEE-HHHHHHHHHHHC CS
                        2-ph_phosp 128 lkelake.vvivcaGtegefsleDtlcAgalveelekeeelelsDaalaalalyes 182
                                       + e+++  v +v+   +ge++++ +++Ag + e+ ++   +++ D+a++a +++e+
  gi|313122517|ref|YP_004038404.1| 132 VPEKHPGeVQVVMTDDDGETTVDGVYAAGRVTETYHQ-AIVNAGDGARVARSIIER 186
                                       56667766****************************9.589**********99987 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011       1.5       1      35 [.      15      45 ..      15      55 .. 0.81
   2 ?    2.6   0.0     0.092   1.2e+02     104     150 ..      68     114 ..      66     117 .. 0.79
   3 ?   -2.3   0.0       3.1     4e+03     133     150 ..     140     157 ..     130     162 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.se 35
                                      aivG+Gp+G a+   L++      ++e+ lfd  ++
  gi|313122517|ref|YP_004038404.1| 15 AIVGGGPAGSAAGVFLARA-----DFEVLLFDHgQS 45
                                      8*********999999888.....699999998444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.092
                     NAD_binding_9 104 feellarlpegvtvevhraevvdleeradgqavlladgaslaadaVv 150
                                       f+el+++  + v  + ++a v++++e+ dg   + +++ ++  ++V 
  gi|313122517|ref|YP_004038404.1|  68 FRELTREHTDAVGCNRLEAAVERISETSDGGFRVHSREGTYGTRYVL 114
                                       7888999999999***************9986666666666666665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.1
                     NAD_binding_9 133 gqavlladgaslaadaVv 150
                                        q v+++d+ ++++d V 
  gi|313122517|ref|YP_004038404.1| 140 VQVVMTDDDGETTVDGVY 157
                                       245666666777777765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.19       1      34 [.      14      48 ..      14      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rle 34
                                      iai+G G  Gs  ++ La+a  +v l ++++  l+
  gi|313122517|ref|YP_004038404.1| 14 IAIVGGGPAGSAAGVFLARADFEVLLFDHGQsTLQ 48
                                      89***************************997766 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.21       2      38 ..      14      50 ..      13      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                                      +a++G G  G+     +a+a++eV l+d  +++l+k+
  gi|313122517|ref|YP_004038404.1| 14 IAIVGGGPAGSAAGVFLARADFEVLLFDHGQSTLQKC 50
                                      8****************************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1488.29
//
Query:       gi|313122518|ref|YP_004038405.1|  [L=241]
Description: sugar phosphate isomerase/epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-16   60.8   1.7    2.7e-16   59.6   1.7    1.5  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.019   13.8   0.0      0.031   13.1   0.0    1.3  1  UxuA          D-mannonate dehydratase (UxuA)
       0.14   12.4   0.2        4.2    7.6   0.0    2.6  2  DUF3234       Protein of unknown function (DUF3234)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   1.7   4.6e-20   2.7e-16      28     209 ..      39     198 ..       8     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 4.6e-20
                                       HHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHH CS
                      AP_endonuc_2  28 eelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpGtagagpkgseee 104
                                       +e+++++  ld+++l +a+++    +                d++ ++++  ++LG+++ v++   + ++   +  e
  gi|313122518|ref|YP_004038405.1|  39 DEADDIADTLDRTDLGVAGVHVGLESL--------------EDNFAETVDVWSQLGIETFVVP---WADPKHFETHE 98 
                                       344555666666666655544444333..............578999****************...5588999999* PP

                                       HHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHG CS
                      AP_endonuc_2 105 awerlaeslneladyaekegvklalEtlagsgvelgdeelarlldavdspnvgvclDtgHlliaeedvddalralad 181
                                       ++e lae+l ++a++++++g  l +++++ ++v l de ++++l +   p vg+ lD g++ +a++ + ++++ +ad
  gi|313122518|ref|YP_004038405.1|  99 TIEALAERLSAIAAKLDQRGYSLHYHNHDHEFVTLDDEYALEILAENA-PEVGLELDLGWAGAAGAEPLSLVESYAD 174
                                       ********************************9988677777777765.78************************** PP

                                       GEEEEEE.EESSTTTTSSTTEESTTSSS CS
                      AP_endonuc_2 182 rikhvHikDakgdlgagrdrhvpigeGe 209
                                       ri ++H+kD++       +  + +geG+
  gi|313122518|ref|YP_004038405.1| 175 RIDLLHVKDYDT----ETGSPAKVGEGD 198
                                       ***********9....677777777776 PP

>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.2e-06     0.031     233     311 ..     144     217 ..     129     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-06
                                       --STTEEEEEEHHHHTTSTT--HHHHHHHHGGGEEEEE--EEEE-SSTT-EEEE-TTSSSS-HHHHHHHHHHHHHHH CS
                              UxuA 233 vdspangitlCtGslgaradndlvemikefadriyFahlRnikreedeksFveaahleGsvdlaevvkalleeeyrr 309
                                       ++ p+ g+ l  G  ga  ++   ++++++adri   h+++  +e +      a+  eG++dla v  a+ e + ++
  gi|313122518|ref|YP_004038405.1| 144 ENAPEVGLELDLGWAGAAGAEP-LSLVESYADRIDLLHVKDYDTETG----SPAKVGEGDLDLAGVASAVREYDIEW 215
                                       5667777777777777777555.5899**************998854....5899******************9999 PP

                                       -E CS
                              UxuA 310 yl 311
                                        +
  gi|313122518|ref|YP_004038405.1| 216 LI 217
                                       65 PP

>> DUF3234  Protein of unknown function (DUF3234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.038   2.3e+02       9      28 ..      52      71 ..      48      88 .. 0.79
   2 ?    7.6   0.0    0.0007       4.2       9      35 ..      90     116 ..      82     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.038
                                      ST...T-BEEEEETTEEEEE CS
                           DUF3234  9 dpnvaGehlvlealGqrlsl 28
                                      d  vaG h+ le+l + ++ 
  gi|313122518|ref|YP_004038405.1| 52 DLGVAGVHVGLESLEDNFAE 71
                                      56699**********99985 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0007
                                       ST...T-BEEEEETTEEEEEEBSSHHH CS
                           DUF3234   9 dpnvaGehlvlealGqrlsliwtsree 35 
                                       dp+    h ++eal +rls+i    ++
  gi|313122518|ref|YP_004038405.1|  90 DPKHFETHETIEALAERLSAIAAKLDQ 116
                                       9999999*************9776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1668.44
//
Query:       gi|313122519|ref|YP_004038406.1|  [L=155]
Description: universal stress family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-07   30.8   0.6    6.4e-07   30.0   0.6    1.4  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.6   3.6e-11   6.4e-07       6     132 ..       5     142 ..       1     150 [. 0.89

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.6e-11
                                       EEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...........H CS
                               Usp   6 lVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada...........a 71 
                                       +V +D++e+ +++l  A+e a++ +ael ll+++d+++++++ +  e+ +  e +   a ++ +a            
  gi|313122519|ref|YP_004038406.1|   5 VVTIDDTESHRELLCEAAEHAESADAELLLLRFLDEKTYEQEIETLETIGNIENVNYTADEVTEAvtantrelaevV 81 
                                       899**********************************************************9999**9999998766 PP

                                       HHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHH CS
                               Usp  72 kaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrh 132
                                        ++ +    + + v+ ++  a+ ++e+  ++d+d   +    rs   ++l+G+++++v+ +
  gi|313122519|ref|YP_004038406.1|  82 LEEFDVDFNVAVSVTSDKRRADRLIETGAAHDCDHAFIVGESRSPTGKALFGDFAQNVILN 142
                                       6666666666677777788889999999*******99999999***************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 981.75
//
Query:       gi|313122520|ref|YP_004038407.1|  [L=366]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-29  103.2   0.0    2.1e-29  102.8   0.0    1.2  1  ABC_tran   ABC transporter
    3.9e-14   52.9   0.2    6.9e-14   52.1   0.2    1.4  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    0.00093   19.5   0.7      0.017   15.4   0.7    2.2  1  AAA_22     AAA domain
  ------ inclusion threshold ------
      0.015   15.1   0.4          4    7.1   0.1    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
      0.017   14.3   0.1      0.027   13.7   0.1    1.2  1  NB-ARC     NB-ARC domain
      0.062   13.2   0.0       0.11   12.3   0.0    1.4  1  MobB       Molybdopterin guanine dinucleotide synthesis prote
      0.067   12.9   0.1       0.12   12.1   0.1    1.4  1  AAA_29     P-loop containing region of AAA domain
      0.077   12.7   0.0       0.13   11.9   0.0    1.3  1  IstB_IS21  IstB-like ATP binding protein
       0.11   12.3   0.0       0.16   11.7   0.0    1.2  1  PduV-EutP  Ethanolamine utilisation - propanediol utilisation
       0.14   12.5   0.0        0.3   11.5   0.0    1.5  1  AAA        ATPase family associated with various cellular act
       0.16   12.4   0.2       0.34   11.3   0.2    1.6  1  AAA_16     AAA ATPase domain
       0.22   10.8   0.0       0.67    9.2   0.0    1.7  2  ATPase     KaiC


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.0   1.4e-32   2.1e-29       2     136 ..      43     202 ..      42     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 1.4e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx.. RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.........qeleslrkeigvlpqe.. 67 
                                       + vs++++e+ ++ +vGe+G+GK+tL k ++gl +pt G+i+++g+d+ e         ++++ +r ++++++q+  
  gi|313122520|ref|YP_004038407.1|  43 DGVSFDVEENDVISLVGESGCGKTTLGKSVIGLQRPTGGTINYRGHDMWEirdgtsdanIDWKDVRTSLQIIHQDpg 119
                                       78*********************************************999999*****9****************77 PP

                                       --S-TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSE CS
                                       xxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkl 129
                                       ++l+p+ ++                  e++e+i+ +l+++g++  +++ +++ p++LSgG++qrval+rall +p++
  gi|313122520|ref|YP_004038407.1| 120 SSLNPNRRLIAIlseplrqthpelsagEKRERIYSLLERVGMNP-AADFAERYPHQLSGGEQQRVALCRALLMNPDV 195
                                       667776653333788**************************999.888889************************** PP

                                       EEEESTT CS
                                       xxxxxxx RF
                          ABC_tran 130 lllDEpt 136
                                       +l+DE+ 
  gi|313122520|ref|YP_004038407.1| 196 ILADEAI 202
                                       *****96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.2   4.6e-17   6.9e-14       2      65 .]     259     323 ..     258     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 4.6e-17
                         oligo_HPY   2 ErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfaleeC 65 
                                       E gp+++++++p+HPYTk L  ++p l ++k+ +l+  k + p++ + ++GC+F++RCp a++ C
  gi|313122520|ref|YP_004038407.1| 259 EFGPAEDVINDPQHPYTKVLRWATPNLSERKTgRLPMRKIDIPDPVNPPAGCRFHTRCPEARAVC 323
                                       99******************************99999*************************999 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.7   1.2e-05     0.017       6     127 ..      53     230 ..      49     236 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee........................erpevvfvtlpsstsskdllr 58 
                                        ++ ++GesG+GKTtl + +                                    +                d+++
  gi|313122520|ref|YP_004038407.1|  53 DVISLVGESGCGKTTLGKSVIGLQRPT----GgtinyrghdmweirdgtsdanidwK----------------DVRT 109
                                       6789**************998765322....12344655555555555555555552................4433 PP

                            AAA_22  59 ellralglelka.................................................erlsseellealeqal 86 
                                        l  + ++++++                                                 ++++++   ++    +
  gi|313122520|ref|YP_004038407.1| 110 SLQIIHQDPGSSlnpnrrliailseplrqthpelsagekreriysllervgmnpaadfaerYPHQLSGGEQQRVALC 186
                                       33333333333322222222222222222554555455555555555555555555554443333322222222222 PP

                            AAA_22  87 rarav.ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliL 127
                                       ra  + + +++ DEa   l+   + e++    +l++  ++g++ ++
  gi|313122520|ref|YP_004038407.1| 187 RALLMnPDVILADEAISaLDvslRVEMMDLMLDLQE--EFGTSYVF 230
                                       222225557777777666666333666666666666..66666665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0047         7       3      49 ..      56      98 ..      54     118 .. 0.71
   2 ?    7.1   0.1    0.0027         4     179     299 ..     123     235 ..     100     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0047
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll 49
                                       l+G  g+GK++L +   +l+r     +g+t++ +g+ ++ + ++ +
  gi|313122520|ref|YP_004038407.1| 56 SLVGESGCGKTTLGKSVIGLQR----PTGGTINYRGHDMWEIRDGTS 98
                                      59*************9999886....455555555555555555554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0027
                            AAA_21 179 akekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallral 255
                                       ++++rl+  l+ +l++ ++els+ +++e+ + +         v  +   d  e+ +++lS G ++  al  all  +
  gi|313122520|ref|YP_004038407.1| 123 NPNRRLIAILSEPLRQTHPELSAGEKRERIYSLLE------RVGMNPAADFAERYPHQLSGGEQQRVALCRALLMNP 193
                                       66777777777777777777777776666655555......678889999999*************9*******999 PP

                            AAA_21 256 kkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                          +++l DE  + L+ +l  + ++l+ ++ ++ g+  ++ +H+ 
  gi|313122520|ref|YP_004038407.1| 194 ---DVILADEAISALDVSLRVEMMDLMlDLQEEFGTSYVFISHDL 235
                                       ...9********************999544444899999999985 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.8e-05     0.027      17      41 ..      51      73 ..      38      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                      TSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqil 41
                                      e   +v++lvG  G+GKttl k+++
  gi|313122520|ref|YP_004038407.1| 51 EN--DVISLVGESGCGKTTLGKSVI 73
                                      44..4***************99886 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.7e-05      0.11       1      32 [.      54      85 ..      54     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-05
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrvgt 32
                                      v+++vg sg+GKTtL + +i   +  g ++++
  gi|313122520|ref|YP_004038407.1| 54 VISLVGESGCGKTTLGKSVIGLQRPTGGTINY 85
                                      689*****************998888877665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.3e-05      0.12      13      38 ..      43      68 ..      40      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                      dg ++++++++++ l+G+sG GK+Tl
  gi|313122520|ref|YP_004038407.1| 43 DGVSFDVEENDVISLVGESGCGKTTL 68
                                      77889999999**************8 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.9e-05      0.13      29      66 ..      33      71 ..      14      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.9e-05
                         IstB_IS21 29 sldkrkvkeLatlsf.iekkenivllGpsGvGKshlaia 66
                                      ++d+r v+++ + sf +e+++ i l+G sG GK+ l  +
  gi|313122520|ref|YP_004038407.1| 33 GSDPRVVRAVDGVSFdVEENDVISLVGESGCGKTTLGKS 71
                                      57999**********899999*************99765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.16       4      23 ..      55      74 ..      52     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      i l+G++g+GKttL +++ g
  gi|313122520|ref|YP_004038407.1| 55 ISLVGESGCGKTTLGKSVIG 74
                                      679***********998866 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002       0.3       3      20 ..      57      74 ..      55     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      l+G  G+GKT+l k+v+ 
  gi|313122520|ref|YP_004038407.1| 57 LVGESGCGKTTLGKSVIG 74
                                      89*************986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00023      0.34      26      50 ..      54      77 ..      40     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                            AAA_16 26 lvllsGesGvGKsslvrellralek 50
                                      ++ l+GesG+GK++l +++   l++
  gi|313122520|ref|YP_004038407.1| 54 VISLVGESGCGKTTLGKSVI-GLQR 77
                                      6889***********88776.4444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00045      0.67      18      38 ..      51      71 ..      46     127 .. 0.89
   2 ?   -1.7   0.0      0.97   1.5e+03     139     175 ..     208     245 ..     201     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00045
                            ATPase 18 egrvvlitGepGtGKtifalq 38
                                      e+ v+ ++Ge+G+GKt++++ 
  gi|313122520|ref|YP_004038407.1| 51 ENDVISLVGESGCGKTTLGKS 71
                                      67899*************985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.97
                            ATPase 139 vaReilrqlvrvl.kklgvTailvsekssseeaaggyg 175
                                        +R +++ l+  l ++ g+  +++s   s+++ ++++g
  gi|313122520|ref|YP_004038407.1| 208 SLRVEMMDLMLDLqEEFGTSYVFISHDLSNARYFSQHG 245
                                       57999999999998888999999999888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2430.39
//
Query:       gi|313122521|ref|YP_004038408.1|  [L=360]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-23   84.0   0.0    1.8e-23   83.5   0.0    1.2  1  ABC_tran         ABC transporter
    4.2e-20   72.0   0.2    8.1e-20   71.1   0.2    1.5  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    8.4e-10   38.9   0.1    9.7e-07   28.9   0.1    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00094   18.7   1.0          1    8.8   0.1    2.3  2  SMC_N            RecF/RecN/SMC N terminal domain
     0.0016   18.8   0.2     0.0034   17.8   0.2    1.7  1  AAA_16           AAA ATPase domain
     0.0027   18.0   0.0      0.011   16.0   0.0    1.8  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.012   15.3   0.2        1.4    8.6   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
      0.026   14.3   0.1      0.051   13.3   0.1    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.028   14.9   0.0      0.044   14.3   0.0    1.2  1  AAA_23           AAA domain
      0.069   13.2   0.0       0.19   11.7   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
      0.088   11.8   0.0       0.12   11.3   0.0    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.098   12.6   0.0       0.19   11.6   0.0    1.5  1  NACHT            NACHT domain
       0.15   11.4   0.1       0.33   10.3   0.1    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.57    9.9   0.0       0.57    9.9   0.0    1.6  2  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.0   1.4e-26   1.8e-23       1     137 []      36     197 ..      36     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 1.4e-26
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEE........EETTCEGGG.......B-HHHCC. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx........xxxxxxxxx.......xxxxxxx. RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp...teGei........lldgkdlke.......qeleslr. 58 
                                       l++vsl+l +ge+++ivGe+G+GKS L+++++    +    +Gei                        +el+s+r 
  gi|313122521|ref|YP_004038408.1|  36 LNDVSLDLGRGEILGIVGESGSGKSMLAEAMLDAIPDpgvLQGEIiyrpdsdtD-------IdilelnkNELRSMRw 105
                                       799***************************999876668888999444433332.......2556666645444443 PP

                                       HCEEEE-SS..--S-TTSBHHHH..........HHHTC..HHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHH CS
                                       xxxxxxxxx..xxxxxxxxxxxx..........xxxxx..xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  59 keigvlpqe..pqlfpeltvren..........esdee..iekalsklglke.lkdtvvksspssLSgGqkqrvala 120
                                       ++i++++q   ++++p+++v+ +          +   +  +++a++ l +++ ++++v++s p++LSgG++qr  +a
  gi|313122521|ref|YP_004038408.1| 106 EQISMVFQGamSSFNPTMKVGAHfretiqahdaDV--KagMSRAREALADVYlDPERVLDSYPHELSGGMQQRALIA 180
                                       89******999999999999999988888764433..24477777777776644588888999************** PP

                                       HHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxx RF
                          ABC_tran 121 rallkkpkllllDEpta 137
                                        +++ +p++l++DEpta
  gi|313122521|ref|YP_004038408.1| 181 LSIVLEPDILVMDEPTA 197
                                       ***************97 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.2   6.3e-23   8.1e-20       1      65 []     248     312 ..     248     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 6.3e-23
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE gp+++++d+++HPYT+aLl+s+p ld++ ++++ i+g+ p++ + ++GC ++pRCp a e+C
  gi|313122521|ref|YP_004038408.1| 248 VEAGPTDEIIDHAAHPYTRALLNSTPNLDAPLEEMRPIAGQSPAPINVPSGCSYHPRCPLADEQC 312
                                       8**************************************************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0015       1.9       2      50 ..      49      96 ..      48     111 .. 0.69
   2 !   28.9   0.1   7.6e-10   9.7e-07     233     301 ..     165     232 ..     123     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslld 50
                                       +++G  gsGKS L +a+  +   d+ v ++ ++ ++ +++++++ +l+
  gi|313122521|ref|YP_004038408.1| 49 LGIVGESGSGKSMLAEAMLDAIP-DPGVLQGEIIYRPDSDTDIDILELN 96
                                      579***************65533.6666666655555555555555554 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 7.6e-10
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS.pll 301
                                        ++elS G+++ + +++++   +   ++l+ DEp + L+  ++r++l ll++l++  +   ++ TH+ pl+
  gi|313122521|ref|YP_004038408.1| 165 YPHELSGGMQQRALIALSIVLEP---DILVMDEPTAALDLLMQRSILLLLEDLKEkYDLTMVFITHDlPLV 232
                                       67999*******88888888777...9***********************66666699*********6665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00079         1      26      44 ..      48      66 ..      26      70 .. 0.82
   2 !    8.4   0.1     0.001       1.3     136     200 ..     168     230 ..      86     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00079
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                      +  ivG+ GSGKs l +A+
  gi|313122521|ref|YP_004038408.1| 48 ILGIVGESGSGKSMLAEAM 66
                                      567**************98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.001
                                       CS-HH..HHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                             SMC_N 136 lLSgG..ektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislree 200
                                       +LSgG  +++L+al++++     +p  + ++De  aaLD    + +  ll+  +++    ++ i+++  
  gi|313122521|ref|YP_004038408.1| 168 ELSGGmqQRALIALSIVL-----EPD-ILVMDEPTAALDLLMQRSILLLLEDLKEKydLTMVFITHDLP 230
                                       89**96667788888874.....454.789**********99999999999777762244555566554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   2.6e-06    0.0034      22      56 ..      44      76 ..      36     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdggifl 56
                                      gr+e++ ++GesG+GKs l+++ l+a+ + g  +l
  gi|313122521|ref|YP_004038408.1| 44 GRGEILGIVGESGSGKSMLAEAMLDAIPDPG--VL 76
                                      78899*******************9999884..33 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.5e-06     0.011       6      44 ..      47      80 ..      42     108 .. 0.77
   2 ?   -1.0   0.1       1.6     2e+03      91     128 ..     183     225 ..     145     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.5e-06
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...f 44
                                       il ++GesG+GK++l++ +l+  +        +p+v+    
  gi|313122521|ref|YP_004038408.1| 47 EILGIVGESGSGKSMLAEAMLDAIP--------DPGVLqgeI 80
                                      57889***************99886........666665554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                            AAA_22  91 v...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                           + +l+ DE    l+   +  +l  L +l +  +++++++++
  gi|313122521|ref|YP_004038408.1| 183 IvlePDILVMDEPTAaLDllmQRSILLLLEDLKE--KYDLTMVFI 225
                                       3556778888887666655555555555555555..777777766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0011       1.4      47      67 ..      46      66 ..      39      74 .. 0.86
   2 ?    4.6   0.1     0.019        24     101     151 ..     179     231 ..     145     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                         IstB_IS21 47 kenivllGpsGvGKshlaial 67
                                       e + ++G sG GKs la a+
  gi|313122521|ref|YP_004038408.1| 46 GEILGIVGESGSGKSMLAEAM 66
                                      667789**************8 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                         IstB_IS21 101 ralkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                        al+ +l++d+l++D+   +l  l q +  ll+e ++++y+ + + it +lp+
  gi|313122521|ref|YP_004038408.1| 179 IALSIVLEPDILVMDEptAALDLLMQRSILLLLEDLKEKYDLTMVFITHDLPL 231
                                       456778899******954467778899999999***************99986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     4e-05     0.051      16      42 ..      40      66 ..      32      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAi 42
                                      ++++ + ++  ++G+sGsGKS l  A+
  gi|313122521|ref|YP_004038408.1| 40 SLDLGRGEILGIVGESGSGKSMLAEAM 66
                                      55666455888**********987776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-05     0.044       9      40 ..      33      67 ..      25      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                            AAA_23  9 sf..rdqeidFsk.gltlItGpNGaGKTTildAik 40
                                      sf  +d+++d+++  +  I+G+ G+GK+ + +A+ 
  gi|313122521|ref|YP_004038408.1| 33 SFvlNDVSLDLGRgEILGIVGESGSGKSMLAEAML 67
                                      677788999997735889***************86 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.19       4      26 ..      51      73 ..      49      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                                      EE--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5  4 LvGppGtgKselaerlaaalnre 26
                                      +vG++G+gKs+lae ++ a+ ++
  gi|313122521|ref|YP_004038408.1| 51 IVGESGSGKSMLAEAMLDAIPDP 73
                                      69***************999654 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.7e-05      0.12      18      56 ..      35      73 ..      24     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.7e-05
                                      HHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCT CS
                              MeaB 18 llerllakaGraqvvGltGvPGaGkstlvealglelrrr 56
                                      +l+ ++ + Gr + +G+ G  G+Gks l ea+   + + 
  gi|313122521|ref|YP_004038408.1| 35 VLNDVSLDLGRGEILGIVGESGSGKSMLAEAMLDAIPDP 73
                                      688899999*********************998776655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.19       5      26 ..      51      72 ..      47      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                      EEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  5 lqGeaGsGKTtLlqklalawae 26
                                      + Ge+GsGK++L++ + +a+ +
  gi|313122521|ref|YP_004038408.1| 51 IVGESGSGKSMLAEAMLDAIPD 72
                                      89***********999888765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00026      0.33      27      48 ..      51      72 ..      42      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllpp 48
                                      +vG +GsGK+mla+++   +p+
  gi|313122521|ref|YP_004038408.1| 51 IVGESGSGKSMLAEAMLDAIPD 72
                                      79*************9988886 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00044      0.57      27      44 ..      51      68 ..      43      75 .. 0.88
   2 ?   -3.5   0.4       5.8   7.4e+03      97     119 ..     190     213 ..     188     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00044
                                      EECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 27 itGesGtGKellaraihe 44
                                      i+GesG+GK++la+a+ +
  gi|313122521|ref|YP_004038408.1| 51 IVGESGSGKSMLAEAMLD 68
                                      89************9976 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.8
                                       EEEET.GGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  97 lfLDe.igelplelQekLlrvlqe 119
                                       l +De  + l+l +Q  +l +l++
  gi|313122521|ref|YP_004038408.1| 190 LVMDEpTAALDLLMQRSILLLLED 213
                                       677774467999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2721.08
//
Query:       gi|313122522|ref|YP_004038409.1|  [L=341]
Description: ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-23   82.9  17.1    2.3e-23   82.9  17.1    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2     0.069   1.2e+03      52      52 ..      97      97 ..      43     131 .. 0.53
   2 !   82.9  17.1   1.3e-27   2.3e-23       2     184 ..     130     317 ..     129     318 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.069
                      BPD_transp_1 52 l 52
                                      +
  gi|313122522|ref|YP_004038409.1| 97 T 97
                                      2 PP

  == domain 2  score: 82.9 bits;  conditional E-value: 1.3e-27
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                       +++G +a+ ++++ +d+ll+  ++v +s+P + l+++l +v     +  + il +i++++ ++a++ r ir+++l +
  gi|313122522|ref|YP_004038409.1| 130 LVIGTVAG-YKGGSIDRLLTSASDVAMSIPGLPLIMVLAVV----FSPENPILIGILITINYWAGLGRAIRSQVLTI 201
                                       799*****.****************************9965....78899*************************** PP

                      BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis. 154
                                       +  ++vea+r++G+s+ +i+ k ++Pn++p+++ ++++a+ +++ ++v l+flg  p ++tl + ++l+  y+ +  
  gi|313122522|ref|YP_004038409.1| 202 RGNSYVEASRTMGVSTTRILTKDIIPNLMPYVLVSFVNAARYVIFASVGLYFLGILP-FSTLNWGVTLNLAYTTGGa 277
                                       ******************************************************444.777777777777777666* PP

                      BPD_transp_1 155 ..........nggvlalviavlllnlvadilqrlldprvr 184
                                                 +++++a+  + l+++l+a  l r+++prvr
  gi|313122522|ref|YP_004038409.1| 278 lylpslaywlIAPMVAIMGLSLAMILLAQGLDRVFNPRVR 317
                                       **************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 2137.99
//
Query:       gi|313122523|ref|YP_004038410.1|  [L=334]
Description: ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-36  123.7  11.5    6.9e-36  123.7  11.5    2.0  3  BPD_transp_1    Binding-protein-dependent transport system in
  ------ inclusion threshold ------
       0.81    9.8   0.0       0.81    9.8   0.0    3.1  4  Fumarate_red_C  Fumarate reductase subunit C


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       0.6   5.3e+03     165     178 ..      16      29 ..      12      53 .. 0.55
   2 !    3.9   0.7    0.0044        39     138     178 ..      90     129 ..      73     129 .. 0.76
   3 !  123.7  11.5   7.7e-40   6.9e-36       1     184 [.     120     326 ..     120     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.6
                      BPD_transp_1 165 vlllnlvadilqrl 178
                                       v+l++++++ + rl
  gi|313122523|ref|YP_004038410.1|  16 VWLVITLTFGMIRL 29 
                                       33333333333333 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0044
                      BPD_transp_1 138 gtllleailgydyseisnggvlalviavlllnlvadilqrl 178
                                        ++++++i++  +++++ +++++++i+++++ +v+ +lq++
  gi|313122523|ref|YP_004038410.1|  90 YDRTVTSIIAEALPWTI-FVMVTATILMFAVGVVIGALQAY 129
                                       45677788888888888.99999999999999999888875 PP

  == domain 3  score: 123.7 bits;  conditional E-value: 7.7e-40
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf........................vilsilghli 53 
                                       g+++G+l a++ ++++d ++++ +i+l+slP+++l+i+lv+++                        ++ s+l+h++
  gi|313122523|ref|YP_004038410.1| 120 GVVIGALQAYKEGSRFDSAMSVTSIILSSLPFYILGIVLVYILgyqlnvfptggqvasgvdpelsltFFVSALKHAM 196
                                       89*************************************************************************** PP

                      BPD_transp_1  54 lpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllef 130
                                       lp+i +++++a+  ++ +r + +++l +d+v++ar++G+s+ +i  ++v +na+ p+ t+++  +g++lgg+v+le 
  gi|313122523|ref|YP_004038410.1| 197 LPIISIVITQAGVQALTMRGNSIQILGEDYVRVARLRGLSDNRISLRYVARNAILPMYTSFLTLIGFNLGGSVILER 273
                                       ***************************************************************************** PP

                      BPD_transp_1 131 lgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       ++ +pG+g  +++a++++dy++++ g++l+++ a++  + +ad+ + ++dprv+
  gi|313122523|ref|YP_004038410.1| 274 VFKYPGVGWYMFNALQARDYPLMM-GIFLIITTALVFAVYIADLTYGIIDPRVS 326
                                       ************************.***************************96 PP

>> Fumarate_red_C  Fumarate reductase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   9.1e-05      0.81      23      51 ..       4      32 ..       1      47 [. 0.90
   2 ?   -0.6   0.5      0.15   1.3e+03     103     126 ..      95     118 ..      86     126 .. 0.71
   3 ?   -1.9   0.0      0.36   3.2e+03      54      74 ..     184     204 ..     146     213 .. 0.65
   4 ?   -1.1   0.1      0.21   1.9e+03      29      45 ..     304     320 ..     285     327 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.1e-05
                    Fumarate_red_C 23 fYmlrEatavlvalfalvlllgllaLaqg 51
                                      +Y+ r + a+l+++ +++l++g+++L  g
  gi|313122523|ref|YP_004038410.1|  4 YYLKRTGRAILTVWLVITLTFGMIRLLPG 32
                                      7999*********************9766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.15
                    Fumarate_red_C 103 peevivkalwaalvvvsvvvlvlv 126
                                       ++ +  +  w+++v+v+  +l+++
  gi|313122523|ref|YP_004038410.1|  95 TSIIAEALPWTIFVMVTATILMFA 118
                                       444555566888888888888765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.36
                    Fumarate_red_C  54 ayeafleflqnPlvlllniia 74 
                                       + + f+++l++ ++ ++ i++
  gi|313122523|ref|YP_004038410.1| 184 SLTFFVSALKHAMLPIISIVI 204
                                       455677777777777776665 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.21
                    Fumarate_red_C  29 atavlvalfalvlllgl 45 
                                       +ta++ a++ + l++g+
  gi|313122523|ref|YP_004038410.1| 304 TTALVFAVYIADLTYGI 320
                                       35666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1951.40
//
Query:       gi|313122524|ref|YP_004038411.1|  [L=613]
Description: extracellular solute-binding protein, family 5 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.8e-38  130.1   5.6    1.5e-37  129.5   5.6    1.2  1  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
  ------ inclusion threshold ------
       0.12   12.2   1.1        0.2   11.5   1.1    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   5.6   1.6e-41   1.5e-37      12     371 ..     119     494 ..     112     499 .. 0.83

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 1.6e-41
                                       EEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEEESSETT. CS
                         SBP_bac_5  12 evsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrftlkkpna. 87 
                                       +v++   + t+++R+g+++ +G+p+t+ D++  fe    +++++g  + +      ++ve + d++++++l++ ++ 
  gi|313122524|ref|YP_004038411.1| 119 TVEPE--QATITIRDGLTWFNGDPVTSRDIKTQFEL---QKYTGGELWQY-----AESVEMDGDTKLVINLAQETNp 185
                                       44444..579**********************8885...67788888888.....59*****************554 PP

                                       TTTTHCHHHHHHHGC..................CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTT CS
                         SBP_bac_5  88 lfltllaavpasiak..................kaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwg 146
                                       +   ++ a++++++                   ++ +  ++ +++ +++p g G++  ++ ++ q+++++rnpd  +
  gi|313122524|ref|YP_004038411.1| 186 TIVKHTIAYNYTSVPhsvygeylkkiqeaeseeEENKAIAELTEFAPTDPLGCGAFEKQSADK-QQAIYTRNPDHPD 261
                                       455555555555555567778999******99977777888899*******************.**********657 PP

                                       TSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHH CS
                         SBP_bac_5 147 ggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrv 223
                                       +++ +++r + ++   ++a+ +al+sG++d +  +++++    +  ++  v  + p+++ + la N +k p+ + + 
  gi|313122524|ref|YP_004038411.1| 262 AENINFERYRSNYTGGNQATWQALLSGKVDAAYTLFTPSRIVDQLPDHWRV-GKPPSNWGYGLAPNYNKSPLGKREM 337
                                       7888**********9999999999*****9888777777777666666666.9999********************* PP

                                       HHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH.............SHHHHHHHHHHHTT-BCS CS
                         SBP_bac_5 224 RqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka.............ydpekAkklLkeaGykdg 287
                                       Rq ++y ++r++iv+++  + ++    +++   ++   +                        kA++ ++eaG+++ 
  gi|313122524|ref|YP_004038411.1| 338 RQGIMYVLNRKQIVNNAAPNSKIYPEIPTAIAASQQERYL-----GdeidtfesygadkTMTSKAEAKFEEAGLTKE 409
                                       *****************65544333333333223333333.....123335777776555599************** PP

                                       STSCEETC..EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTT CS
                         SBP_bac_5 288 dggglrek..klkltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdp 362
                                       +g++ ++   + +l +l++sg++++  +a+  ++ql   G++ ++ + d+  t l+++++g+f ++ + w ++ +  
  gi|313122524|ref|YP_004038411.1| 410 GGQWKDSSgsVVELPILVPSGWSDWVTAAQTAADQLSSFGFNSSLVSKDF-GTVLKDWSNGNFTLASFYWLPGGARS 485
                                       ***99999******************************************.*********************99998 PP

                                       HHHHHHHHS CS
                         SBP_bac_5 363 dnflnpfls 371
                                        + + p+ +
  gi|313122524|ref|YP_004038411.1| 486 AFPYFPIAH 494
                                       888887766 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.1   2.3e-05       0.2       2      25 ..      12      34 ..      11      36 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.3e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      +SRR F+  +++ +A a l+gc++
  gi|313122524|ref|YP_004038411.1| 12 VSRRRFIELTGVSGATA-LAGCSG 34
                                      7************9777.555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 4020.85
//
Query:       gi|313122525|ref|YP_004038412.1|  [L=83]
Description: hypothetical protein Hbor_37590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.081   13.5   0.5       0.71   10.5   0.1    2.0  2  DUF565    Protein of unknown function (DUF565)


Domain annotation for each model (and alignments):
>> DUF565  Protein of unknown function (DUF565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   3.9e-05      0.71      34      58 ..       9      33 ..       4      35 .. 0.85
   2 ?    1.5   0.0     0.025   4.4e+02       5      24 ..      51      70 ..      49      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.9e-05
                            DUF565 34 sllveilNtlKiGllygLfleAFkL 58
                                      s++++  + l+iG+++gL+l  F +
  gi|313122525|ref|YP_004038412.1|  9 SIVCDYQDQLRIGFMLGLLLLVFTV 33
                                      567888899**********998876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.025
                            DUF565  5 wDvivaalivlftEvlsrli 24
                                      +D+i++++++++t +  +  
  gi|313122525|ref|YP_004038412.1| 51 IDLILVLFLIVATGGAHWCC 70
                                      69999999999988777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 611.64
//
Query:       gi|313122526|ref|YP_004038413.1|  [L=302]
Description: Adaptin N terminal region protein, partial [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-16   59.4  18.9    1.5e-06   28.5   0.3    4.3  5  HEAT_2      HEAT repeats
    9.9e-11   41.0   7.5       0.52   10.7   0.1    5.8  5  HEAT        HEAT repeat
    2.4e-08   34.2   0.7    4.5e-05   23.6   0.4    2.6  3  Cnd1        non-SMC mitotic condensation complex subunit 1
    4.9e-06   25.4   2.6    0.00055   18.6   0.6    2.1  2  Adaptin_N   Adaptin N terminal region
    1.1e-05   25.8  16.3       0.19   12.3   0.6    4.7  4  HEAT_EZ     HEAT-like repeat
    0.00013   21.9   2.6      0.026   14.5   0.2    3.1  3  Nipped-B_C  Sister chromatid cohesion C-terminus
    0.00092   19.7   9.9        1.2   10.0   0.1    6.1  6  HEAT_PBS    PBS lyase HEAT-like repeat
  ------ inclusion threshold ------
      0.058   13.7   0.0       0.11   12.8   0.0    1.4  1  TINF2_N     TERF1-interacting nuclear factor 2 N-terminus
      0.093   12.8   4.1       0.11   12.6   0.0    3.1  4  Arm         Armadillo/beta-catenin-like repeat
       0.16   11.3   0.1        0.4   10.1   0.0    1.6  2  DUF5578     Family of unknown function (DUF5578)


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.3    0.0016       2.9      32      61 ..      21      50 ..       6      59 .. 0.70
   2 !   16.5   2.0   4.5e-06     0.008       1      56 [.      22      82 ..      22      91 .. 0.89
   3 !   20.8   0.7   2.2e-07   0.00039       2      74 ..      60     143 ..      57     155 .. 0.73
   4 !   17.5   0.9   2.2e-06     0.004      22      75 ..     186     251 ..     172     252 .. 0.74
   5 !   28.5   0.3   8.2e-10   1.5e-06       1      63 [.     240     302 .]     240     302 .] 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                            HEAT_2 32 alpaLvellededpavRraaaeaLgaigdp 61
                                      ++p+L+ +l+d++  vR  aa   + ++d+
  gi|313122526|ref|YP_004038413.1| 21 TIPTLRAALTDDENLVRDRAAAVCVTFADE 50
                                      467777777777777777777666666555 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.5e-06
                            HEAT_2  1 ldaLlqalendpdpevrraairaLgrignpea......lpaLvellededpavRraaaeaLg 56
                                      +++L +al +d +  vr +a+ +  +++++++      lpa+v +++de+ +v   a++ L 
  gi|313122526|ref|YP_004038413.1| 22 IPTLRAAL-TDDENLVRDRAAAVCVTFADEDVevvlplLPAIVTAARDENVNVALKAVTVLN 82
                                      57899999.78888****************88888888*********************996 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 2.2e-07
                            HEAT_2   2 daLlqalendpdpevrraairaLg...rignp...ealpaLvellededpavRraaaeaLgaigd..pe....alpa 66 
                                       +a + a+ +d++ +v+ +a+ +L    +++++   ea ++L  ll+++ p+v+  aa+a   ig   pe      + 
  gi|313122526|ref|YP_004038413.1|  60 PAIVTAA-RDENVNVALKAVTVLNvvaQQQPTelnEATETLATLLTHDLPRVQLFAAKAVQTIGAehPEwftsHPEP 135
                                       5666677.8***************7764443368899************************9995223333333345 PP

                            HEAT_2  67 Lkellddd 74 
                                       L+e+l+ d
  gi|313122526|ref|YP_004038413.1| 136 LLEALRAD 143
                                       55555544 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 2.2e-06
                            HEAT_2  22 raLgrignpea......lpaLvellededpavRraaaeaLgaig......dpealpaLkelldddd 75 
                                         L +i++++        pa+ ++l+ ed +v + aae Lg+ig      + + +p L e+ld+++
  gi|313122526|ref|YP_004038413.1| 186 NLLIEIADRDPaaiapyAPAIMDALTAEDLNVVACAAEILGRIGqmeavdTAALVPPLVECLDSES 251
                                       444444443222246669*************************966555346678*****999876 PP

  == domain 5  score: 28.5 bits;  conditional E-value: 8.2e-10
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpea 63 
                                       +++L++ l +++++ v+++ i aLg ig+ +a++ L++++ + ++ + R+ a++++ ++++++a
  gi|313122526|ref|YP_004038413.1| 240 VPPLVECL-DSESEVVAARSITALGHIGSATAVEPLRSAAkRYDNGDLRELAVRTADWLDRERA 302
                                       58999*9*.9******************************555789**********99998875 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00029      0.52       2      28 ..      22      48 ..      22      50 .. 0.93
   2 !    7.8   0.1    0.0025       4.4       1      29 [.      58      86 ..      58      88 .. 0.93
   3 ?    4.3   0.0     0.034        61       4      27 ..      98     121 ..      97     125 .. 0.88
   4 !    7.6   0.1    0.0029       5.1       3      29 ..     204     230 ..     203     231 .. 0.94
   5 !   10.0   0.0   0.00051      0.91       1      28 [.     239     266 ..     239     268 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                      HHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT  2 lPlllkllsDpspeVReaAakaLgala 28
                                      +P+l  +l+D++  VR+ Aa  ++++a
  gi|313122526|ref|YP_004038413.1| 22 IPTLRAALTDDENLVRDRAAAVCVTFA 48
                                      7999*****************999987 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0025
                                      HHHHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT  1 llPlllkllsDpspeVReaAakaLgalae 29
                                      llP+++++ +D++ +V   A+  L  +a+
  gi|313122526|ref|YP_004038413.1| 58 LLPAIVTAARDENVNVALKAVTVLNVVAQ 86
                                      89********************9999887 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.034
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l +ll+++ p+V   Aaka+ ++
  gi|313122526|ref|YP_004038413.1|  98 TLATLLTHDLPRVQLFAAKAVQTI 121
                                       5788999*************9988 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0029
                                       HHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgalae 29 
                                       P+++ +l+ ++ +V + Aa+ Lg++ +
  gi|313122526|ref|YP_004038413.1| 204 PAIMDALTAEDLNVVACAAEILGRIGQ 230
                                       8999********************975 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   1 llPlllkllsDpspeVReaAakaLgala 28 
                                       l+P+l+++l ++s  V + ++ aLg++ 
  gi|313122526|ref|YP_004038413.1| 239 LVPPLVECLDSESEVVAARSITALGHIG 266
                                       79***********************997 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.4   2.5e-08   4.5e-05      22     110 ..      21     109 ..      18     180 .. 0.80
   2 ?    1.3   0.0      0.17   3.1e+02      73     105 ..     179     211 ..     171     215 .. 0.88
   3 !    8.2   0.0    0.0013       2.4      16      87 ..     196     267 ..     192     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.5e-08
                              Cnd1  22 lvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseksenaiynllp 98 
                                       +++ Lr++L+D++  VR  aa v+    ++d+  +  +l  + ++ +Den +V   a+++l+ +++++++++ + + 
  gi|313122526|ref|YP_004038413.1|  21 TIPTLRAALTDDENLVRDRAAAVCVTFADEDVEVVLPLLPAIVTAARDENVNVALKAVTVLNVVAQQQPTELNEATE 97 
                                       6889***************************************************************9988888888 PP

                              Cnd1  99 diisklsdalne 110
                                       +++  l ++l  
  gi|313122526|ref|YP_004038413.1|  98 TLATLLTHDLPR 109
                                       877777764443 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
                              Cnd1  73 rVvanalaalteiseksenaiynllpdiiskls 105
                                       +V+a a ++l ei+++++ ai    p i+  l 
  gi|313122526|ref|YP_004038413.1| 179 SVQATAGNLLIEIADRDPAAIAPYAPAIMDALT 211
                                       699999**************9999999988776 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0013
                              Cnd1  16 pnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteise 87 
                                       p+ + ++ + +  +L+ ed  V  +aa ++ ++ +++ v    ++  l ++l+ e++ V a +++al  i +
  gi|313122526|ref|YP_004038413.1| 196 PAAIAPYAPAIMDALTAEDLNVVACAAEILGRIGQMEAVDTAALVPPLVECLDSESEVVAARSITALGHIGS 267
                                       567889999999******************************************************998865 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6     3e-07   0.00055     116     206 ..      22     108 ..       6     152 .. 0.77
   2 !    6.2   0.1    0.0018       3.1      82     141 ..     204     265 ..     187     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3e-07
                                       HHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHHHCCCCCCCHHHHH CS
                         Adaptin_N 116 apaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleeikkndrlllkllpk 192
                                        p+++++l+d+++ vr  Aa   ++  + d + + + l++ i+ +  d+++ v l Av++l  +  +++   + l++
  gi|313122526|ref|YP_004038413.1|  22 IPTLRAALTDDENLVRDRAAAVCVTFADEDVEVVLP-LLPAIVTAARDENVNVALKAVTVLNVV-AQQQP--TELNE 94 
                                       578999999999999999999999999999999988.699999999999999999999999999.44444..44555 PP

                                       HHCCHHHHHHCS-H CS
                         Adaptin_N 193 lvrrLcnllteldp 206
                                        ++ L +llt   p
  gi|313122526|ref|YP_004038413.1|  95 ATETLATLLTHDLP 108
                                       55555555544444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0018
                                       HHHHHHCCSSSHHHHHHHHHHHCCC--CCCH..HHHHHHHHHHHT-SSHHHHHHHHHHHHHC CS
                         Adaptin_N  82 nslqkDlkdpnqlirglALrvLssirvpela..edlapaikkllkdrspyvrkkAalailkl 141
                                        +++ +l+  + ++++ A   L++i++ e +   +l+p + ++l ++s +v   +++a+ ++
  gi|313122526|ref|YP_004038413.1| 204 PAIMDALTAEDLNVVACAAEILGRIGQMEAVdtAALVPPLVECLDSESEVVAARSITALGHI 265
                                       56888888888888888888888888887775567788888888888888888888887776 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2   0.00052      0.93      30      49 ..      22      41 ..      19      44 .. 0.85
   2 !    7.3   0.5    0.0037       6.6       8      51 ..      71     117 ..      64     123 .. 0.75
   3 !    9.5   0.5   0.00077       1.4      14      55 .]     191     228 ..     179     228 .. 0.88
   4 !   12.3   0.6    0.0001      0.19       5      55 .]     219     265 ..     216     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00052
                           HEAT_EZ 30 lpaLlalLnddsdeVRaaAa 49
                                      +p L a+L+dd+ +VR  Aa
  gi|313122526|ref|YP_004038413.1| 22 IPTLRAALTDDENLVRDRAA 41
                                      89*************76665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0037
                           HEAT_EZ   8 aw.aLGr..laggepellqplvpeilpaLlalLnddsdeVRaaAaga 51 
                                       ++ aL +  ++++ ++++++++ e+   L+ lL++d ++V+  Aa a
  gi|313122526|ref|YP_004038413.1|  71 VNvALKAvtVLNVVAQQQPTELNEATETLATLLTHDLPRVQLFAAKA 117
                                       5555555558899999999****************999995444444 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00077
                           HEAT_EZ  14 laggepellqplvpeilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       +a   p +++p+ p+i++aL       +d +V a Aa  Lg++
  gi|313122526|ref|YP_004038413.1| 191 IADRDPAAIAPYAPAIMDALT-----AEDlNVVACAAEILGRI 228
                                       77889999*************.....***************97 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.0001
                           HEAT_EZ   5 raAawaLGrlaggepellqplvpeilpaLlalLnddsdeV.RaaAagaLgnl 55 
                                       + Aa  LGr+ ++e+ + + lvp ++ +L      +++eV  a ++ aLg +
  gi|313122526|ref|YP_004038413.1| 219 ACAAEILGRIGQMEAVDTAALVPPLVECLD-----SESEVvAARSITALGHI 265
                                       457779*************99999999999.....99999999999999976 PP

>> Nipped-B_C  Sister chromatid cohesion C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.078   1.4e+02      45      68 ..      21      44 ..      15      50 .. 0.86
   2 !   14.5   0.2   1.4e-05     0.026       9      81 ..      59     131 ..      53     134 .. 0.94
   3 ?    3.5   0.1     0.032        58       7      71 ..     201     265 ..     197     269 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.078
                                      THHHHHHHTT-SSHHHHHHHHHHH CS
                        Nipped-B_C 45 cvptLialetdpdesirsrAdkll 68
                                      ++ptL a  td+++ +r+rA ++ 
  gi|313122526|ref|YP_004038413.1| 21 TIPTLRAALTDDENLVRDRAAAVC 44
                                      79******************9875 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHTSS-HHHHHHHHHHHHHHHHHT-S-GGGTHHHHHHHTT-SSHHHHHHHHHHHHHHHHHSHHHHHH CS
                        Nipped-B_C   9 lkdilecalspdsqvrlaAlevvslilrqGLvhPvqcvptLialetdpdesirsrAdkllqeleekyegfles 81 
                                       l+ i+ +a +++ +v+l+A++v++++++q  +   ++  tL +l t + + ++  A k +q++   +++ + s
  gi|313122526|ref|YP_004038413.1|  59 LPAIVTAARDENVNVALKAVTVLNVVAQQQPTELNEATETLATLLTHDLPRVQLFAAKAVQTIGAEHPEWFTS 131
                                       78999************************************************************99988765 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHTSS-HHHHHHHHHHHHHHHHHT-S-GGGTHHHHHHHTT-SSHHHHHHHHHHHHHH CS
                        Nipped-B_C   7 rYlkdilecalspdsqvrlaAlevvslilrqGLvhPvqcvptLialetdpdesirsrAdkllqel 71 
                                        Y + i+++ + +d +v   A e++  i +   v     vp L+ +  +++e ++ r +  l ++
  gi|313122526|ref|YP_004038413.1| 201 PYAPAIMDALTAEDLNVVACAAEILGRIGQMEAVDTAALVPPLVECLDSESEVVAARSITALGHI 265
                                       699*****************************************999999999999988877665 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.95   1.7e+03      17      27 .]      21      31 ..      18      31 .. 0.84
   2 ?   -0.3   0.0       1.4   2.5e+03       1      22 [.      36      59 ..      36      64 .. 0.72
   3 ?    1.1   0.1      0.51   9.2e+02       1      15 [.     110     126 ..     110     142 .. 0.64
   4 ?   -1.4   0.1       3.3     6e+03      11      19 ..     190     200 ..     180     211 .. 0.56
   5 !    8.0   0.0     0.003       5.3       5      26 ..     221     248 ..     221     249 .. 0.86
   6 !   10.0   0.1   0.00067       1.2       3      26 ..     256     279 ..     254     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.95
                                      GHHHHHHHCTC CS
                          HEAT_PBS 17 aipaLleaLqd 27
                                       ip+L++aL d
  gi|313122526|ref|YP_004038413.1| 21 TIPTLRAALTD 31
                                      599*****976 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHCTS..GGGHHHHH CS
                          HEAT_PBS  1 vRraAakaLgqlgd..eeaipaLl 22
                                      vR +Aa    ++ d   e++ +Ll
  gi|313122526|ref|YP_004038413.1| 36 VRDRAAAVCVTFADedVEVVLPLL 59
                                      788899888888887766666666 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHCTS..G CS
                          HEAT_PBS   1 vRraAakaLgqlgd..e 15 
                                       v+  Aaka  ++g+  +
  gi|313122526|ref|YP_004038413.1| 110 VQLFAAKAVQTIGAehP 126
                                       66779999999988551 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3.3
                                       HCTS..GGGHH CS
                          HEAT_PBS  11 qlgd..eeaip 19 
                                       ++ d  ++ai+
  gi|313122526|ref|YP_004038413.1| 190 EIADrdPAAIA 200
                                       55555544443 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.003
                                       HHHHHHHCTS......GGGHHHHHHHCT CS
                          HEAT_PBS   5 AakaLgqlgd......eeaipaLleaLq 26 
                                       Aa+ Lg++g        + +p+L+e+L+
  gi|313122526|ref|YP_004038413.1| 221 AAEILGRIGQmeavdtAALVPPLVECLD 248
                                       89********888888888888888887 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.00067
                                       HHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   3 raAakaLgqlgdeeaipaLleaLq 26 
                                       ++ + aLg +g+  a+++L+ a +
  gi|313122526|ref|YP_004038413.1| 256 ARSITALGHIGSATAVEPLRSAAK 279
                                       56789***************9975 PP

>> TINF2_N  TERF1-interacting nuclear factor 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.2e-05      0.11      17      71 ..      50     104 ..      45     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-05
                           TINF2_N  17 efvslvteavPeLlssrqkakLilGLrarlilellrkekaadlkaiqshlerlra 71 
                                       e v++v  ++P +++  + +++ + L+a ++l+++ ++++++l++ ++ l +l +
  gi|313122526|ref|YP_004038413.1|  50 EDVEVVLPLLPAIVTAARDENVNVALKAVTVLNVVAQQQPTELNEATETLATLLT 104
                                       558999*********************************9999998888877655 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.3   9.6e+03      14      29 ..      22      37 ..      22      42 .. 0.62
   2 ?   -1.8   0.2       2.1   3.7e+03      13      35 ..      58      80 ..      53      81 .. 0.70
   3 ?   -1.2   0.0       1.4   2.5e+03      15      29 ..      97     111 ..      93     119 .. 0.78
   4 ?   12.6   0.0   6.2e-05      0.11      14      39 ..     240     265 ..     237     267 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.3
                                      HHHHHHHTTTSSHHHH CS
                               Arm 14 vppLvrLLssedeevq 29
                                      +p L + L+++   v+
  gi|313122526|ref|YP_004038413.1| 22 IPTLRAALTDDENLVR 37
                                      6778887875555554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                                      HHHHHHHHTTTSSHHHHHHHHHH CS
                               Arm 13 avppLvrLLssedeevqeeAawA 35
                                       +p+ v+  ++e+++v   A++ 
  gi|313122526|ref|YP_004038413.1| 58 LLPAIVTAARDENVNVALKAVTV 80
                                      46777777778888887777765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.4
                                       HHHHHHTTTSSHHHH CS
                               Arm  15 ppLvrLLssedeevq 29 
                                       + L +LL+++ ++vq
  gi|313122526|ref|YP_004038413.1|  97 ETLATLLTHDLPRVQ 111
                                       678899999999888 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm  14 vppLvrLLssedeevqeeAawALsNL 39 
                                       vppLv++L+se+e v   + +AL+++
  gi|313122526|ref|YP_004038413.1| 240 VPPLVECLDSESEVVAARSITALGHI 265
                                       9**********************998 PP

>> DUF5578  Family of unknown function (DUF5578)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00022       0.4     164     248 ..      73     157 ..      61     168 .. 0.88
   2 ?   -2.0   0.0         1   1.9e+03     221     254 ..     200     233 ..     163     249 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                           DUF5578 164 tqeeaqklleslaegnPkyqkqvykgliallacsspkaqqlalqtlrvvqeivkeakpsivepllelLkslhlevqy 240
                                       +  +a ++l+ +a+  P   +   ++l +ll+ + p+ q +a+++++++    +e  +s  eplle+L+   ++  +
  gi|313122526|ref|YP_004038413.1|  73 VALKAVTVLNVVAQQQPTELNEATETLATLLTHDLPRVQLFAAKAVQTIGAEHPEWFTSHPEPLLEALRADITDPTS 149
                                       455677899999**********************************************************9999999 PP

                           DUF5578 241 eaielike 248
                                       ea+el  +
  gi|313122526|ref|YP_004038413.1| 150 EATELTGT 157
                                       99998765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                           DUF5578 221 psivepllelLkslhlevqyeaielikelmstev 254
                                            +++++L+  +l+v + a e++  + ++e 
  gi|313122526|ref|YP_004038413.1| 200 APYAPAIMDALTAEDLNVVACAAEILGRIGQMEA 233
                                       3334457777888888888888888777766643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1973.98
//
Query:       gi|313122527|ref|YP_004038414.1|  [L=382]
Description: galactonate dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-60  203.6   0.0    3.4e-60  203.3   0.0    1.1  1  MR_MLE_C  Enolase C-terminal domain-like
    7.8e-27   93.8   0.0    1.6e-26   92.8   0.0    1.5  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N
  ------ inclusion threshold ------
      0.046   12.9   0.1      0.086   12.0   0.1    1.4  1  NanE      Putative N-acetylmannosamine-6-phosphate epimerase
       0.16   12.2   0.0       0.38   11.0   0.0    1.6  1  DUF4777   Domain of unknown function (DUF4777)


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.3   0.0   7.6e-64   3.4e-60       2     219 ..     129     355 ..     128     357 .. 0.95

  Alignments for each domain:
  == domain 1  score: 203.3 bits;  conditional E-value: 7.6e-64
                                       HHHHHHHHHHHHT-SEEEEETSSS........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHG CS
                          MR_MLE_C   2 laeearelvaeqgfravKlkvggd........dvaedvervravreavgpgddvdlmvDanqawdlatAirvarele 70 
                                       l +ea++lv + g++a+K++ ++          ++  ver+  vr+++  gd+vdl+vD+ +++  ++A +++ ele
  gi|313122527|ref|YP_004038414.1| 129 LIAEAEKLVNA-GYTAIKMDATERtahidtpaAIDTIVERISGVRKEI--GDEVDLCVDFRGRVAKPMAKQLLSELE 202
                                       56889886665.********8888************************..5577**********************9 PP

                                       GGTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHH CS
                          MR_MLE_C  71 eldllwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalae 146
                                       +++++++EEP+ pe+  ++la ++ ++ ++pia+gE++ysr+df++l+e+gavd++qp+vs++gGi+e+r++a +ae
  gi|313122527|ref|YP_004038414.1| 203 SVRPMFVEEPLLPEH-SDQLANVA-THsTVPIATGERMYSRWDFKPLFEDGAVDVIQPNVSHAGGISEVRRIASMAE 277
                                       9************76.999*****.6679************************************************ PP

                                       HTT-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGH.....TSGCSBSSSSEEETTEEECTSSSBTSSEB-H CS
                          MR_MLE_C 147 afgvpvapHsgsgglglaaslhlaaaipnllileyfldael.....leeelleeplevedGrvtvpdgpGlGvelde 218
                                       a++v vap ++ g+++laasl++++a+pnll++++ +d e       ++ l+ + +e+edG++   d+pGlG+++d+
  gi|313122527|ref|YP_004038414.1| 278 AYNVAVAPNCPLGPIALAASLQVSTATPNLLVQDQGFDIESgrrnnGSNYLAGSGFEFEDGYLIPTDQPGLGITPDR 354
                                       **********889**************************9999999999***************************6 PP

                                       H CS
                          MR_MLE_C 219 e 219
                                       +
  gi|313122527|ref|YP_004038414.1| 355 D 355
                                       5 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   3.5e-30   1.6e-26      29     117 .]      16     108 ..      13     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.5e-30
                                       EEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS.....CHHHHHHHHHHH CS
                          MR_MLE_N  29 vlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg.....nmsAkaaidmAl 100
                                        +++iet++G+vG+ge+  +g ra+t+k ++ + +  +l+gkd+++i+d +q ++r  ++      msA a+id+Al
  gi|313122527|ref|YP_004038414.1|  16 LFLRIETDDGLVGWGEPIVEG-RAKTVKTAVTEVMDGYLLGKDPQRIQDHWQAMYRGGFYrggpvLMSAMAGIDQAL 91 
                                       689******************.**************************************9**************** PP

                                       HHHHHHHTTSBHHHHTT CS
                          MR_MLE_N 101 wDlkakalnlpladLlG 117
                                       wD+k+k+ ++p+++LlG
  gi|313122527|ref|YP_004038414.1|  92 WDIKGKRYDAPVYELLG 108
                                       ****************9 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.9e-05     0.086      54      90 ..     130     166 ..     125     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHH CS
                              NanE  54 lkdideLaaagadiialDatdrerpvtieelikkike 90 
                                       + + ++L++ag + i +Dat+r+ +++  + i +i e
  gi|313122527|ref|YP_004038414.1| 130 IAEAEKLVNAGYTAIKMDATERTAHIDTPAAIDTIVE 166
                                       7899*******************99666555555544 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.5e-05      0.38      15      44 ..     154     183 ..     150     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.5e-05
                           DUF4777  15 vlnrPaTldEivervaerydlseeelkkvV 44 
                                        +++Pa++d+iver++ ++++  +e+   V
  gi|313122527|ref|YP_004038414.1| 154 HIDTPAAIDTIVERISGVRKEIGDEVDLCV 183
                                       689***************999999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2703.68
//
Query:       gi|313122528|ref|YP_004038415.1|  [L=244]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-23   82.3   0.0    3.7e-23   81.7   0.0    1.3  1  IclR            Bacterial transcriptional regulator
    7.9e-13   48.0   0.3    9.6e-12   44.5   0.2    2.3  2  HTH_IclR        IclR helix-turn-helix domain
      1e-06   28.7   0.0    2.4e-06   27.5   0.0    1.6  1  HTH_20          Helix-turn-helix domain
    1.7e-06   27.8   0.0    7.5e-06   25.7   0.0    2.1  3  TrmB            Sugar-specific transcriptional regulator TrmB
    1.9e-06   27.7   0.0    4.3e-06   26.5   0.0    1.7  2  HTH_5           Bacterial regulatory protein, arsR family
    2.9e-05   23.9   0.0      5e-05   23.2   0.0    1.4  1  MarR            MarR family
    9.3e-05   21.9   0.0     0.0002   20.8   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00042   20.2   0.0    0.00098   19.0   0.0    1.7  1  MarR_2          MarR family
     0.0033   17.6   0.0     0.0064   16.7   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0096   16.3   0.0      0.021   15.1   0.0    1.5  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.021   14.6   0.0      0.043   13.6   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.022   14.8   0.0      0.044   13.8   0.0    1.5  1  z-alpha         Adenosine deaminase z-alpha domain
      0.023   14.5   0.0      0.051   13.4   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.036   14.1   0.0      0.067   13.2   0.0    1.4  1  HTH_45          Winged helix-turn-helix
      0.051   13.3   0.1       0.26   11.0   0.0    2.1  2  Sigma70_r4_2    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   3.1e-26   3.7e-23      10     121 ..     122     231 ..     115     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 3.1e-26
                                       T-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEEE CS
                              IclR  10 GtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciAapi 86 
                                       G +  l++ta GKa+La l++e++++++ +++l +lt++Tit++ +L++eLa++R++G+a+dreE+  g+r +A p+
  gi|313122528|ref|YP_004038415.1| 122 GLSKYLHSTAPGKAILAKLPDERVDEIVDQHGLPALTPHTITTRSALEDELARIRDRGIAFDREENRTGMRGVAIPV 198
                                       556679**********************************************************************9 PP

                                       E-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHH CS
                              IclR  87 fdasgevvaAvsvsgptarlteeelkeellalvre 121
                                               +A  v+gp+ rlt + ++e++  +++ 
  gi|313122528|ref|YP_004038415.1| 199 VH--DGIRGAMYVVGPQRRLTGKWFNENIPGIIIS 231
                                       87..67889999*********99999977776665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.2     8e-15   9.6e-12       6      50 ..       9      52 ..       4      54 .. 0.94
   2 ?    1.0   0.0      0.32   3.8e+02      11      31 ..     136     155 ..     135     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 8e-15
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++iL+al+e +++ +++e A+++++pkSt+h +L+tL +lGyv+ 
  gi|313122528|ref|YP_004038415.1|  9 FDILQALRELGGA-GVTETAEHLDIPKSTAHKHLHTLAQLGYVTN 52
                                      89**********8.9****************************86 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.32
                                       T-CTTBSS-BHHHHHHHHTS- CS
                          HTH_IclR  11 alaeapqeltlselArrtglp 31 
                                       +la+ p e ++ e+ ++ glp
  gi|313122528|ref|YP_004038415.1| 136 ILAKLPDE-RVDEIVDQHGLP 155
                                       57888888.9**********9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0     2e-09   2.4e-06      10      56 ..       6      52 ..       3      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2e-09
                                      HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ++  +il+aL++ +g+ ++e ae ld++k+t+++HL++L++ g+v+ 
  gi|313122528|ref|YP_004038415.1|  6 ETSFDILQALRELGGAGVTETAEHLDIPKSTAHKHLHTLAQLGYVTN 52
                                      6789***************************************9985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   6.3e-09   7.5e-06       5      59 ..       3      57 ..       1      69 [. 0.92
   2 ?   -2.1   0.0       3.2   3.8e+03      17      35 ..     137     155 ..     135     158 .. 0.77
   3 ?   -3.0   0.0       5.8   6.9e+03      40      60 ..     169     189 ..     164     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.3e-09
                                      HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                      G +e+ +++ +aL +lg a ++e ae+l++p+s++ + L  L + G+V+ e+g++
  gi|313122528|ref|YP_004038415.1|  3 GATETSFDILQALRELGGAGVTETAEHLDIPKSTAHKHLHTLAQLGYVTNEDGTY 57
                                      55788889999****************************************9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                                       HHHHCCCHHCHHCCCTTSS CS
                              TrmB  17 Llklgpatadeiaeelgvp 35 
                                       L kl   ++dei  + g+p
  gi|313122528|ref|YP_004038415.1| 137 LAKLPDERVDEIVDQHGLP 155
                                       5577788899999988887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.8
                                       HHHHHHHHHCTSEEEESSTTT CS
                              TrmB  40 YevLrsLedkGlVerekgrpk 60 
                                        + L +  d+G+   ++++++
  gi|313122528|ref|YP_004038415.1| 169 EDELARIRDRGIAFDREENRT 189
                                       566788889999888888765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   3.6e-09   4.3e-06       6      46 ..      10      51 ..       5      52 .. 0.95
   2 ?   -3.3   0.0       7.4   8.8e+03      29      44 ..     165     180 ..     163     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.6e-09
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +IL++L+e g + v+e ae+l++++st   HL  L ++G+V+
  gi|313122528|ref|YP_004038415.1| 10 DILQALRElGGAGVTETAEHLDIPKSTAHKHLHTLAQLGYVT 51
                                      7***************************************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.4
                                       HHHHHHHHHHHHHTTS CS
                             HTH_5  29 qstvShHLkkLreaGL 44 
                                       +s++   L++ r+ G+
  gi|313122528|ref|YP_004038415.1| 165 RSALEDELARIRDRGI 180
                                       6777777888888887 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.2e-08     5e-05       2      48 ..       5      51 ..       4      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.2e-08
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      t+t f+iL  l+e g++ v+e a++l + kst+ + l++L + G+++
  gi|313122528|ref|YP_004038415.1|  5 TETSFDILQALRELGGAGVTETAEHLDIPKSTAHKHLHTLAQLGYVT 51
                                      89*******************************************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.7e-07    0.0002       3      48 .]       6      51 ..       5      51 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.7e-07
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      et ++IL++L++ ++   +e Ae+l++++st +++l  L + G+++
  gi|313122528|ref|YP_004038415.1|  6 ETSFDILQALRELGGAGVTETAEHLDIPKSTAHKHLHTLAQLGYVT 51
                                      799*****************************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.2e-07   0.00098       5      56 ..       6      55 ..       2      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.2e-07
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                       + +++L aL+  +g    v+e a++l+++ks+++++l  L + G+v+ ++g
  gi|313122528|ref|YP_004038415.1|  6 ETSFDILQALRELGG--AGVTETAEHLDIPKSTAHKHLHTLAQLGYVTNEDG 55
                                      578999********9..89****************************98876 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.4e-06    0.0064      13      54 ..      11      52 ..      10      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.4e-06
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54
                                      I+++  e + +++++ ae L++ +s++ + l  L++ Gyv  
  gi|313122528|ref|YP_004038415.1| 11 ILQALRELGGAGVTETAEHLDIPKSTAHKHLHTLAQLGYVTN 52
                                      666777888999****************************75 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.8e-05     0.021      26      61 ..      21      56 ..       4      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                      + ++e ae+ +i++s + k l++L++ g+v+ + G 
  gi|313122528|ref|YP_004038415.1| 21 AGVTETAEHLDIPKSTAHKHLHTLAQLGYVTNEDGT 56
                                      568999*************************99986 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.6e-05     0.043       5      46 ..      11      52 ..       9      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                          HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      il+ l++ g   v+e +e+l++ + T+ + L +L++ g +t 
  gi|313122528|ref|YP_004038415.1| 11 ILQALRELGGAGVTETAEHLDIPKSTAHKHLHTLAQLGYVTN 52
                                      9***********************************999875 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.7e-05     0.044       8      57 ..      10      56 ..       4      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEEESSS CS
                           z-alpha  8 kilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvyredgt 57
                                       il++L+elg + ++t+ a  +++   k  + + L  l+++g v  edgt
  gi|313122528|ref|YP_004038415.1| 10 DILQALRELG-GAGVTETAEHLDIP--KSTAHKHLHTLAQLGYVTNEDGT 56
                                      69********.*****999887776..9********************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.3e-05     0.051      10      41 ..      11      44 ..       9      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrwlkry 41
                                      il++l+e  G+ v+e A++L+++++T  + l++ 
  gi|313122528|ref|YP_004038415.1| 11 ILQALRElgGAGVTETAEHLDIPKSTAHKHLHTL 44
                                      89999*9*******************99887775 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.6e-05     0.067       6      58 ..       6      59 ..       3      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-05
                            HTH_45  6 eIiadILeais.egeakkTkimykanLsykllnkYLdmLvekglikkskekYvl 58
                                      e  +dIL+a++  g+a  T+   + ++  ++++k L++L + g++++++++Y l
  gi|313122528|ref|YP_004038415.1|  6 ETSFDILQALReLGGAGVTETAEHLDIPKSTAHKHLHTLAQLGYVTNEDGTYDL 59
                                      5569******9789**************************************76 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00022      0.26      21      48 ..      15      42 ..      14      43 .. 0.93
   2 ?   -0.8   0.1       1.1   1.3e+03      39      48 ..     232     241 ..     231     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                                      HHHTS---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrls 48
                                      lr+l g    E+Ae l+i+ +t  ++l+
  gi|313122528|ref|YP_004038415.1| 15 LRELGGAGVTETAEHLDIPKSTAHKHLH 42
                                      7889999999****************98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                       -HHHHHHHHH CS
                      Sigma70_r4_2  39 segtVksrls 48 
                                       s++tV++rl+
  gi|313122528|ref|YP_004038415.1| 232 SVKTVEQRLR 241
                                       899****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1790.69
//
Query:       gi|313122529|ref|YP_004038416.1|  [L=323]
Description: acetyltransferase (GNAT) family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-09   38.4   0.0    2.8e-07   30.8   0.0    2.2  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.8e-05   23.0   0.0    0.00012   21.9   0.0    1.6  1  FR47             FR47-like protein
    0.00074   19.9   0.0     0.0015   19.0   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0067   16.4   0.0      0.027   14.4   0.0    2.0  1  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0041        18      24      90 ..      39     111 ..      11     128 .. 0.77
   2 !   30.8   0.0   6.3e-11   2.8e-07      19     117 .]     203     311 ..     184     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0041
                                       HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET.....TSTTEEEEEEEEESGGG.TTSSHHHHHHHHHHHHHH CS
                    Acetyltransf_1  24 feesfsleaegllvaeedgeliGfisllkipd.....ekggvayieslaVspey.rgkGlGsaLlealeerar 90 
                                        +  + +++ +++ ++++ el+ f+ l++ +      e++++a++  +a  p+  r + l + Ll++++++  
  gi|313122529|ref|YP_004038416.1|  39 LFAPLPDIEVRCYGGYDEHELVSFAVLKQLDSpvrefEDTDTAWLSLFAFEPDSeRARTLSKDLLTTVVDKHV 111
                                       33335556668888999999*********************************999999***99999998655 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 6.3e-11
                                       HHHHHHHHHHHSTTC..EEEEEEETTEEEEEEEEEEEET............TSTTEEEEEEEEESGGGTTSSHHHHH CS
                    Acetyltransf_1  19 aseeefeesfsleae..gllvaeedgeliGfisllkipd............ekggvayieslaVspeyrgkGlGsaL 81 
                                       ++++e +++ +++ +   +++ ++dg ++Gf++ +  +             +++ ++ +  l +++e +g+G G  +
  gi|313122529|ref|YP_004038416.1| 203 RWYYEARNICRIPGGaaDYWLLRWDGDVVGFARSNRWDGsyrgpnvnwgwrLSNVYCGVGPLGIHEEQQGRGWGLFM 279
                                       444444444555666668999***********9999988998888888888888899999***************** PP

                                       HHHHHHHHHHTTESEEEE.EEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  82 lealeerareegikkivl.aveedndaairlYeklGF 117
                                       ++++++r+++ g++ +v+ +++ +     ++YeklGF
  gi|313122529|ref|YP_004038416.1| 280 ITKIVQRLKQDGYDTMVIdWTDIP-----GYYEKLGF 311
                                       *************99899556555.....599****9 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.8e-08   0.00012      13      83 ..     250     317 ..     241     320 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.8e-08
                                       EEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEEE CS
                              FR47  13 aawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekieet 83 
                                        +w+l + +  +g l +++e ++rG+g  ++ ++ +++ + g++ ++ +  ++ p    yeklGfe    +
  gi|313122529|ref|YP_004038416.1| 250 WGWRLSNVYCGVGPLGIHEEQQGRGWGLFMITKIVQRLKQDGYDTMV-IDWTDIP--GYYEKLGFERWISY 317
                                       58******************************************876.4555555..68******986555 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.2e-07    0.0015       3      76 .]     219     313 ..     217     313 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.2e-07
                                       EEEEEEEETTEEEEEEEEEEES................TCTEE.....EEE-GGGTTSSHHHHHHHH..TT...SEE CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld................aeitr.....laVdpeyrgkGiGraLlea..ae...kgi 53 
                                       + +++++ dg +vGf++  + d                    +     l +++e +g+G G  +++   ++    g+
  gi|313122529|ref|YP_004038416.1| 219 ADYWLLRWDGDVVGFARSNRWDgsyrgpnvnwgwrlsnV---YcgvgpLGIHEEQQGRGWGLFMITKivQRlkqDGY 292
                                       568999999999999987777799999988777665542...03446799***************963311333443 PP

                                       EEE.EEEETHHHHHH.HHHHTTEEE CS
                    Acetyltransf_7  54 ile.qlelnaekaik.fYeklGFee 76 
                                        +    ++     i+ +YeklGFe+
  gi|313122529|ref|YP_004038416.1| 293 DTMvIDWT----DIPgYYEKLGFER 313
                                       21112233....3555*******95 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.9e-06     0.027      30     108 ..     218     313 ..     197     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.9e-06
                   Acetyltransf_10  30 ealllvaeeggkivGviel.rdgs..................hisllfVdpeyrgqGigkaLleaveeeaekdgikl 87 
                                       +a ++++ ++g +vG+++  r ++                   ++ l +++e++g+G g  ++ ++ +++++dg+  
  gi|313122529|ref|YP_004038416.1| 218 AADYWLLRWDGDVVGFARSnRWDGsyrgpnvnwgwrlsnvycGVGPLGIHEEQQGRGWGLFMITKIVQRLKQDGYD- 293
                                       555666666777777775544444566666666676666555667788**********************888775. PP

                   Acetyltransf_10  88 eltvnaspyavpfYeklGFka 108
                                        + v   +   ++YeklGF++
  gi|313122529|ref|YP_004038416.1| 294 -TMVIDWTDIPGYYEKLGFER 313
                                       .888889999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1699.54
//
Query:       gi|313122530|ref|YP_004038417.1|  [L=100]
Description: hypothetical protein Hbor_37640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.036   14.1   0.5      0.069   13.2   0.1    1.6  2  Phenol_hyd_sub  Phenol hydroxylase subunit


Domain annotation for each model (and alignments):
>> Phenol_hyd_sub  Phenol hydroxylase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.15   2.6e+03      25      34 ..      61      71 ..      59      74 .. 0.70
   2 ?   13.2   0.1   3.9e-06     0.069      27      41 ..      76      90 ..      70      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.15
                    Phenol_hyd_sub 25 eFaiGeP.eLa 34
                                       Fa GeP eL 
  gi|313122530|ref|YP_004038417.1| 61 PFAFGEPiELE 71
                                      59999995555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.9e-06
                    Phenol_hyd_sub 27 aiGePeLavELlLpe 41
                                       +G+PeL vEL Lp 
  gi|313122530|ref|YP_004038417.1| 76 GVGDPELEVELSLPG 90
                                      69***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 588.20
//
Query:       gi|313122531|ref|YP_004038418.1|  [L=181]
Description: DNA-binding ferritin-like protein (oxidative damage protectant) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-30  106.1   6.8    1.6e-30  105.9   6.8    1.0  1  Ferritin  Ferritin-like domain
  ------ inclusion threshold ------
      0.023   14.8   0.4      0.072   13.2   0.3    1.9  2  DUF2959   Protein of unknown function (DUF2959)
      0.089   13.1   0.5      0.089   13.1   0.5    3.3  3  Osmo_CC   Osmosensory transporter coiled coil
       0.82    9.7   5.4        3.3    7.7   0.9    2.3  2  DUF1451   Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   6.8   3.5e-34   1.6e-30       2     139 ..      31     172 ..      30     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 3.5e-34
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH...C-SS CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee...ieap 75 
                                       +aLn  lad +++++q ++++w+v+g + ++++ f++e +e+  + ad++aeri++lGg+p ++   l+e   +ea+
  gi|313122531|ref|YP_004038418.1|  31 DALNTDLADAYVLYHQLHKHHWNVEGAEHRDIHIFLQEAYEDVEDAADDVAERIQTLGGVPHASMTALSEaatVEAE 107
                                       79****************************************************************99998887777 PP

                                       SS.CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  76 ke.fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                       +e + +++  l ++le++ +++es+re iel e  gD+at ++l + l + eeh++ ++++le+ 
  gi|313122531|ref|YP_004038418.1| 108 DEdVYDIRTSLSNDLEMYGDIIESYREHIELIEGLGDYATGEMLREQLMDIEEHAHVIDHYLEDD 172
                                       77544*********************************************************986 PP

>> DUF2959  Protein of unknown function (DUF2959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.6e-05     0.072      42      86 ..      49      93 ..      21     131 .. 0.83
   2 ?   -0.4   0.0      0.25   1.1e+03      43      83 ..     102     142 ..      92     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                           DUF2959 42 kavvefdggeLekeyeklnkeyeesekaaeevrerieaveevaea 86
                                      k+  +++g+e ++ +  l+++ye+ e+aa++v+eri+++  v +a
  gi|313122531|ref|YP_004038418.1| 49 KHHWNVEGAEHRDIHIFLQEAYEDVEDAADDVAERIQTLGGVPHA 93
                                      45678899999999999********************99888766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.25
                           DUF2959  43 avvefdggeLekeyeklnkeyeesekaaeevrerieaveev 83 
                                       a ve+++ ++ + + +l++++e   +  e+ re ie +e  
  gi|313122531|ref|YP_004038418.1| 102 ATVEAEDEDVYDIRTSLSNDLEMYGDIIESYREHIELIEGL 142
                                       45677888888888888888888888888888888888765 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.17   7.4e+02      15      30 ..      24      39 ..      22      55 .. 0.78
   2 ?   13.1   0.5     2e-05     0.089       9      31 ..      65      87 ..      58      89 .. 0.92
   3 ?    1.3   0.7     0.091   4.1e+02       8      28 ..     149     169 ..     147     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.17
                                      THHHHHHHHHHHHHHH CS
                           Osmo_CC 15 dnIEqkvedideeIaa 30
                                      d++Eq v+ +++++a+
  gi|313122531|ref|YP_004038418.1| 24 DKVEQIVDALNTDLAD 39
                                      7889999988888775 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2e-05
                                      XXXXXXTHHHHHHHHHHHHHHHH CS
                           Osmo_CC  9 lLqehYdnIEqkvedideeIaaL 31
                                       Lqe+Y+++E   +d+ e I+ L
  gi|313122531|ref|YP_004038418.1| 65 FLQEAYEDVEDAADDVAERIQTL 87
                                      69******************988 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.091
                                       XXXXXXXTHHHHHHHHHHHHH CS
                           Osmo_CC   8 elLqehYdnIEqkvedideeI 28 
                                       e+L+e+  +IE+    id+ +
  gi|313122531|ref|YP_004038418.1| 149 EMLREQLMDIEEHAHVIDHYL 169
                                       7999*******9999998765 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9   0.00075       3.3      30      85 ..      20      78 ..       4      88 .. 0.74
   2 ?    4.1   0.3    0.0097        43      26      94 ..     101     169 ..      82     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00075
                           DUF1451 30 eltkeelelvaeylkrDleeaarsleeske...eleewlsldlelieesllealasiaD 85
                                      +l+++++e++ ++l+ Dl++a+  +++ ++   ++e  ++ d+++  ++++e   + aD
  gi|313122531|ref|YP_004038418.1| 20 RLDEDKVEQIVDALNTDLADAYVLYHQLHKhhwNVEGAEHRDIHIFLQEAYEDVEDAAD 78
                                      58899****************99999988844455555566666555555555555555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0097
                           DUF1451  26 seaeeltkeelelvaeylkrDleeaarsleeskeeleewlsldlelieesllealasiaDktqvelael 94 
                                       +++ e+++e++  ++  l++Dle +++ +e+ +e++e  + l   +  e l e+l++i + ++v  + l
  gi|313122531|ref|YP_004038418.1| 101 AATVEAEDEDVYDIRTSLSNDLEMYGDIIESYREHIELIEGLGDYATGEMLREQLMDIEEHAHVIDHYL 169
                                       4556778899999**************999999988888888777888888888888877777655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1154.92
//
Query:       gi|313122532|ref|YP_004038419.1|  [L=88]
Description: hypothetical protein Hbor_37660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 612.00
//
Query:       gi|313122533|ref|YP_004038420.1|  [L=77]
Description: hypothetical protein Hbor_37670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 594.52
//
Query:       gi|313122534|ref|YP_004038421.1|  [L=42]
Description: hypothetical protein Hbor_37680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 317.27
//
Query:       gi|313122535|ref|YP_004038422.1|  [L=802]
Description: PAS domain S-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-44  149.6   0.5      1e-19   70.7   0.1    3.6  3  PAS_9       PAS domain
    1.9e-40  138.3   4.1    5.8e-40  136.7   4.1    1.9  1  BAT         GAF and HTH_10 associated domain
    1.6e-35  121.5   1.9    2.5e-16   59.7   0.1    3.3  3  PAS         PAS fold
    1.5e-31  108.9   8.5    7.6e-14   51.9   0.1    3.9  4  PAS_4       PAS fold
    4.1e-25   87.9   0.4    8.1e-11   42.1   0.1    3.6  3  PAS_3       PAS fold
    1.7e-23   82.2   0.1    4.1e-08   33.1   0.0    3.7  3  PAS_8       PAS domain
    4.2e-18   64.9   0.0    8.8e-18   63.9   0.0    1.6  1  HTH_10      HTH DNA binding domain
    8.3e-17   61.8   0.6    5.4e-16   59.2   0.2    2.5  2  GAF_2       GAF domain
    1.1e-06   29.3   0.0    3.2e-06   27.8   0.0    1.8  1  GAF         GAF domain
    4.1e-05   23.9   0.0    8.9e-05   22.8   0.0    1.6  1  GAF_3       GAF domain
    0.00014   22.0   1.4       0.29   11.3   0.0    3.6  3  PAS_7       PAS fold
     0.0031   18.1   0.0          2    9.0   0.0    3.2  2  PAS_10      PAS domain
  ------ inclusion threshold ------
      0.021   14.3   2.3       0.14   11.7   0.0    3.2  3  Sigma70_r4  Sigma-70, region 4
       0.03   14.0   0.0        3.3    7.3   0.0    2.7  2  PAS_12      UPF0242 C-terminal PAS-like domain
       0.14   12.3   0.0       0.42   10.7   0.0    1.9  1  HTH_22      HTH domain


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   1.2e-14   1.5e-11       2     104 .]      42     146 ..      41     146 .. 0.87
   2 !   31.0   0.0     2e-10   2.4e-07      11     104 .]     177     267 ..     165     267 .. 0.86
   3 !   70.7   0.1   8.8e-23     1e-19       3     104 .]     288     389 ..     286     389 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.2e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk..kerevevvlirknge 74 
                                       +g l +++d +i++aN+a++r+lGy+p+e++g+++ +l+    d+++ + +++++e+g++     +v+   ++k+g 
  gi|313122535|ref|YP_004038422.1|  42 EGLLTVDEDSTIVFANPAVERILGYQPNELVGQPLLTLVpdRLDQQHTRAFQQYIETGERqmDWDDVDFPARHKDGH 118
                                       7888899********************************9977888888888888888888889************* PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                       +++v ++++    d+++l+   +ilrD t+
  gi|313122535|ref|YP_004038422.1| 119 EVPVSIRFREHSHDGQRLFT--GILRDNTD 146
                                       ***88877666666666666..*****985 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2e-10
                             PAS_9  11 grilyaNeaalrllG.yspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvk 86 
                                       g+ +  N+a++++l  +s e++l++   d++  dp++++ +++ l++      ++e+  ++ +get+w+ +ta++  
  gi|313122535|ref|YP_004038422.1| 177 GTFVEGNTALREMLDvTSMEALLQQGPADFY-ADPDERQIFQERLREDG-VISDEELKVQTATGETIWTSITAIRRE 251
                                       677888*********777*************.77777777777777777.68999*************999999998 PP

                             PAS_9  87 dddgelvgiivilrDite 104
                                       ++++ ++   ++ +Dite
  gi|313122535|ref|YP_004038422.1| 252 EQGEVYID--GVAEDITE 267
                                       88888888..*******8 PP

  == domain 3  score: 70.7 bits;  conditional E-value: 8.8e-23
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       +i ++++dg+i+y+N+a+++++Gys+ee  g   + l   ++++e   +l++ +++g+  ++++ev+++rk+ge++ 
  gi|313122535|ref|YP_004038422.1| 288 SIYMTDTDGTIEYVNPAFEDITGYSEEEACGETPRLLSsgEHNDEFYADLWETIRSGE--VWQGEVTNQRKTGERYV 362
                                       688899********************************88888888888888888888..***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       v+ t++pv dddge+ ++++++ Dit+
  gi|313122535|ref|YP_004038422.1| 363 VNQTIAPVTDDDGEIERFVAVSADITD 389
                                       *************************96 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.7   4.1   4.8e-43   5.8e-40       1     150 [.     581     729 ..     581     735 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 4.8e-43
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+vveLe++ +++++++v++++eldcr+el+ +vp+s++ +l++ +vdg++pe+v++ +++ + ve+ rvv++++++
  gi|313122535|ref|YP_004038422.1| 581 DTVVELEFKTSSAESIFVRVSEELDCRLELKTIVPTSENAYLCYTSVDGVSPEAVATKLSSSPVVENPRVVDATGTS 657
                                       9**************************************************************************** PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrt 150
                                        ++e +v ++s+++tl e+G+tv sa +e+g+ ++v e++p+ad R+++++++++ypd++ +a+r ++rpvr+
  gi|313122535|ref|YP_004038422.1| 658 GTVEYKV-SQSPVTTLLEYGATVTSAIIESGDETVVGEIAPDADSRKIISGIQAAYPDTTFIAKRSVDRPVRS 729
                                       *******.899************************************************************98 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   1.6e-15   1.9e-12       3     112 ..      33     143 ..      31     143 .. 0.88
   2 !   12.7   0.1   7.8e-05     0.093       1     113 []     155     265 ..     155     265 .. 0.90
   3 !   59.7   0.1   2.1e-19   2.5e-16       3     112 ..     278     386 ..     276     387 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.6e-15
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                        +a++ ++ ++ + vDed  i+++N+a e++lG++++e++g++ll l++   d+++ ++++q++e+ge++ +++   
  gi|313122535|ref|YP_004038422.1|  33 CQALVANTSEGLLTVDEDSTIVFANPAVERILGYQPNELVGQPLLTLVPDRLDQQHTRAFQQYIETGERQMDWDDVD 109
                                       5899********************************************97766688889999999998888887544 PP

                                       EC...TTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  80 kl...rdgrpihlevraspvrdaggeilgflgvlrd 112
                                            +dg ++++ +r +   + g++   f g+lrd
  gi|313122535|ref|YP_004038422.1| 110 FParhKDGHEVPVSIRFREHSHDGQR--LFTGILRD 143
                                       44799999999999999999999988..88888887 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.8e-05
                                       HHHHHHHHHSSSEEEEEE..TTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECC CS
                               PAS   1 edlraileslpdpifvvD..edgrilyvNaaaeellGlsr.eevlgkslldliheeddaelaelleqlleqgeesra 74 
                                       e+++ i+ +lp++i  +     g +++ N+a +e+l  +  e +l +   d++  +d    +++++++l++    ++
  gi|313122535|ref|YP_004038422.1| 155 ERYEDIITHLPEGIYRTEacSGGTFVEGNTALREMLDVTSmEALLQQGPADFYADPD---ERQIFQERLREDGVISD 228
                                       5899999999999999999999********************************998...9999999********** PP

                                       CCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  75 geisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +e ++ +  g++i+  ++a  + + g+ + ++ gv+ di
  gi|313122535|ref|YP_004038422.1| 229 EELKVQTATGETIWTSITAIRREEQGE-V-YIDGVAEDI 265
                                       **99999***********998877755.4.777776665 PP

  == domain 3  score: 59.7 bits;  conditional E-value: 2.1e-19
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       +r+ +e++   i ++D dg i yvN+a+e+++G+s+ee++g++   l + e+++e+++ l++ +++ge ++++ ++ 
  gi|313122535|ref|YP_004038422.1| 278 FREAVEQAGHSIYMTDTDGTIEYVNPAFEDITGYSEEEACGETPRLLSSGEHNDEFYADLWETIRSGEVWQGEVTNQ 354
                                       7899********************************************************************99999 PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrd 112
                                       ++  g+ + + ++ +pv+d +gei  f+ v  d
  gi|313122535|ref|YP_004038422.1| 355 RK-TGERYVVNQTIAPVTDDDGEIERFVAVSAD 386
                                       99.*********************999987655 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.3   1.9e-15   2.3e-12       3     109 ..      39     148 ..      37     149 .. 0.96
   2 !   13.1   0.2   7.4e-05     0.088      14     110 .]     176     270 ..     162     270 .. 0.77
   3 !   51.9   0.1   6.4e-17   7.6e-14       2     109 ..     283     391 ..     282     392 .. 0.94
   4 ?   -2.6   0.0       5.5   6.6e+03      77     104 ..     519     545 ..     478     546 .. 0.71

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.9e-15
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..... 74 
                                       +++++l+ +d+d+++++aN+a ++++g++p el+G++l  l+p+++ +++ ra ++ +e++e++ +++ +++     
  gi|313122535|ref|YP_004038422.1|  39 NTSEGLLTVDEDSTIVFANPAVERILGYQPNELVGQPLLTLVPDRLDQQHTRAFQQYIETGERQMDWDDVDFparhk 115
                                       78999************************************************************************ PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +g e+++++r++    ++G+ + + +i+rD T+r+
  gi|313122535|ref|YP_004038422.1| 116 DGHEVPVSIRFREH-SHDGQ-RLFTGILRDNTDRE 148
                                       ************98.67999.999********997 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.4e-05
                             PAS_4  14 dgrvlyaNaaaae.lfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pgeerhyelrllP 87 
                                        g+++  N+a +e l   + e+ll + +a+++ +   ++ +++ ++ l+++ +i+++e  +    ge+ + ++++++
  gi|313122535|ref|YP_004038422.1| 176 GGTFVEGNTALREmLDVTSMEALLQQGPADFYAD---PDERQIFQERLREDGVISDEELKVQtaTGETIWTSITAIR 249
                                       5899999999999666777788899999998886...555555555555666666666555559************9 PP

                             PAS_4  88 lrdesGevigvlvisrDiTerrr 110
                                         +e+Ge + + +++ DiTer++
  gi|313122535|ref|YP_004038422.1| 250 R-EEQGE-VYIDGVAEDITERKE 270
                                       6.89999.9************85 PP

  == domain 3  score: 51.9 bits;  conditional E-value: 6.4e-17
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       ++    +++ d+dg+++y+N+a++++ g++ ee+ G+t++ l + e+ +++ ++l + ++++e+++ + +  +  ge
  gi|313122535|ref|YP_004038422.1| 283 EQAGHSIYMTDTDGTIEYVNPAFEDITGYSEEEACGETPRLLSSGEHNDEFYADLWETIRSGEVWQGEVTNQRkTGE 359
                                       566678999*******************************888888*********************9999999999 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       + +++ ++ P+ d++Ge+  ++++s DiT+++
  gi|313122535|ref|YP_004038422.1| 360 RYVVNQTIAPVTDDDGEIERFVAVSADITDQK 391
                                       999999***********************997 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 5.5
                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrD 104
                                       ++ + +  ++P+ + +G+v gv+++  D
  gi|313122535|ref|YP_004038422.1| 519 DGGYQSSAAIPV-AFDGTVYGVIGVYSD 545
                                       344444455888.678999999988776 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   3.2e-11   3.8e-08       1      82 [.      53     135 ..      53     141 .. 0.87
   2 !    8.6   0.0    0.0019       2.3      39      88 ..     213     261 ..     184     262 .. 0.81
   3 !   42.1   0.1   6.7e-14   8.1e-11       2      88 ..     299     383 ..     298     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3.2e-11
                             PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge...py.egeyRirrkdGeyrwvearar 73 
                                       i++++++ve+ilGy+p+el g+   +l lv     ++  +a+q+++++ge   ++ ++++  r+kdG+ + v+ r r
  gi|313122535|ref|YP_004038422.1|  53 IVFANPAVERILGYQPNELVGQ--PLLTLVPDRLDQQHTRAFQQYIETGErqmDWdDVDFPARHKDGHEVPVSIRFR 127
                                       589*******************..******9999************9999834455555*************99988 PP

                             PAS_3  74 virdengkp 82 
                                        + + +g+ 
  gi|313122535|ref|YP_004038422.1| 128 EH-SHDGQR 135
                                       77.666665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0019
                             PAS_3  39 realqealkkgepy.egeyRirrkdGeyrwveararvi.rdengkpvrvigv 88 
                                       r+ +qe l++++++ ++e +++++ Ge++w + +  +i r e+g++ ++ gv
  gi|313122535|ref|YP_004038422.1| 213 RQIFQERLREDGVIsDEELKVQTATGETIWTSIT--AIrREEQGEV-YIDGV 261
                                       788999999999886888**********997766..5524666655.47766 PP

  == domain 3  score: 42.1 bits;  conditional E-value: 6.7e-14
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                        yv++++e+i+Gys+ee  g   + + l   e  ++++++l+e +++ge+++ge+  +rk Ge + v  ++ ++ d+
  gi|313122535|ref|YP_004038422.1| 299 EYVNPAFEDITGYSEEEACGE--TPRLLSSGEHNDEFYADLWETIRSGEVWQGEVTNQRKTGERYVVNQTIAPVTDD 373
                                       59*******************..999999999999****************************************** PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g++ r+++v
  gi|313122535|ref|YP_004038422.1| 374 DGEIERFVAV 383
                                       *******987 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   3.4e-11   4.1e-08       3      59 ..      33      91 ..      31     100 .. 0.87
   2 !   18.0   0.0   1.8e-06    0.0021       1      57 [.     155     211 ..     155     225 .. 0.81
   3 !   26.7   0.0   3.4e-09   4.1e-06       2      55 ..     274     330 ..     273     344 .. 0.68

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.4e-11
                             PAS_8  3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle.da 59
                                       +al+ + ++g++ vd++ +iv++N+a +++lGy  ++l g++l +l+p+  +  + +a
  gi|313122535|ref|YP_004038422.1| 33 CQALVANTSEGLLTVDEDSTIVFANPAVERILGYQpNELVGQPLLTLVPDRLDQQHtRA 91
                                      589*************7778*************************99999888776555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.8e-06
                             PAS_8   1 erlralfesspdgiavvd..lgdrivdvNqaalellGysadlkgellgqllpvlrplle 57 
                                       er++ ++ ++p+gi  +    g+++v+ N a  e+l ++  + ++ll+q + +++   +
  gi|313122535|ref|YP_004038422.1| 155 ERYEDIITHLPEGIYRTEacSGGTFVEGNTALREMLDVT--SMEALLQQGPADFYADPD 211
                                       79*************987785556*************99..******977777766655 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 3.4e-09
                             PAS_8   2 rlral...fesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       rlra+   +e++  +i ++d + ++i +vN+a+++++Gys ++  ge+  +ll   + +
  gi|313122535|ref|YP_004038422.1| 274 RLRAFreaVEQAGHSIYMTDtD-GTIEYVNPAFEDITGYSeEEACGETP-RLLSSGEHN 330
                                       6666444499**********55.55*************99666655555.333333333 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   7.3e-21   8.8e-18       1      53 []     741     793 ..     741     793 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 7.3e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LTd+q+evl lAy++G+F+ PR  t +eLA++lGI+ +t++ h+rka++k++e
  gi|313122535|ref|YP_004038422.1| 741 LTDRQREVLELAYRAGFFESPRCSTGDELADALGITSPTFYLHVRKATRKVLE 793
                                       9*************************************************985 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   1.7e+03      22      52 ..     287     322 ..     269     383 .. 0.59
   2 !   59.2   0.2   4.5e-19   5.4e-16       3     137 ..     426     569 ..     424     569 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                                       EEEEEEE-TTS-EEEE......EEEES-TTSTT-S-B CS
                             GAF_2  22 lgyillvdddgglrla......awgeaeeefgaaldr 52 
                                       +  i++ d dg ++++        g+ eee +++++r
  gi|313122535|ref|YP_004038422.1| 287 H-SIYMTDTDGTIEYVnpafedITGYSEEEACGETPR 322
                                       3.45555666765555555555444444444444433 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 4.5e-19
                                       HHHHHHHHHHHHHHHSS...EEEEEE.E-TTS-EEEEEEEES-TTSTT-S-B--.....-TTHHHHHHHHTS-EEES CS
                             GAF_2   3 dleelldlvldelvelg.aalgyill.vdddgglrlaawgeaeeefgaaldrpl.....geglvgealrtgrpviln 72 
                                       + +e+ + v+++l+  +   +++++  + ++++++   w+e e+e  + +          +g+vg+a+++       
  gi|313122535|ref|YP_004038422.1| 426 TRDEIEQVVCEQLAASDaYLFAWYGDyIPEREQVTPQEWAEIEDECLDDFAVTTnegdsVRGPVGRAVHSCDVQAAR 502
                                       6799*********9977566999999544667777778988888887777552255665899********9999999 PP

                                       -GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  73 dleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       ++ +dp + +l+  a + g++s++a+P+  +g v+Gv+++y+++p+afde ++ lL+el+e i+ ai
  gi|313122535|ref|YP_004038422.1| 503 NILTDPLSESLHknALDGGYQSSAAIPVAFDGTVYGVIGVYSDRPNAFDEYEQGLLRELGERIGHAI 569
                                       99999999999999**************9999*********************************98 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.6e-09   3.2e-06      12     133 .]     433     569 ..     427     569 .. 0.62

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.6e-09
                                       HHHHHHTESEEEEEEEEETTEEECEEEEECC....................EEEETTSHHHHHHHHHSSSEEESTGG CS
                               GAF  12 elrellgadrvalylpdydGlhydipqasrw....................lfmkngrgicgqvlatgqplvipdst 68 
                                        ++e l+a  + l+   + G +y ip+  +                      +   +rg +g+++++ ++    ++ 
  gi|313122535|ref|YP_004038422.1| 433 VVCEQLAASDAYLFA--WYG-DY-IPEREQVtpqewaeiedeclddfavttNEGDSVRGPVGRAVHSCDVQAARNIL 505
                                       566666666666654..444.44.33333333333333444444434332223333455455444443333333333 PP

                                       TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  69 pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvaval 133
                                       +dp       ++ +   g++ss+++P+  dg ++G++ +++ +p  f+++e  ll++l+++++ a+
  gi|313122535|ref|YP_004038422.1| 506 TDPLSES--LHKNALDGGYQSSAAIPVAFDGTVYGVIGVYSDRPnAFDEYEQGLLRELGERIGHAI 569
                                       5555444..455677899***********************99989****************9886 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   7.4e-08   8.9e-05      81     127 ..     523     569 ..     462     571 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.4e-08
                             GAF_3  81 raalavPLvagr.qviGvlalastkprafdaedlelleslArqiatai 127
                                       ++  a+P++  + +v+Gv++++s++p afd+ ++ ll++l+ +i+ ai
  gi|313122535|ref|YP_004038422.1| 523 QSSAAIPVAF-DgTVYGVIGVYSDRPNAFDEYEQGLLRELGERIGHAI 569
                                       56789*****.66********************************998 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00024      0.29       2      55 ..      38      90 ..      37     124 .. 0.80
   2 ?    0.2   0.2      0.68   8.1e+02      96     115 .]     251     273 ..     184     273 .. 0.60
   3 !    6.8   0.0    0.0062       7.4       2     114 ..     283     394 ..     282     395 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                             PAS_7  2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg 55
                                       n s+G++ +D+d  +v+ N  + ++l++ ++ + vg pl +l+  + ++++ +
  gi|313122535|ref|YP_004038422.1| 38 ANTSEGLLTVDEDSTIVFANPAVERILGYQPNEL-VGQPLLTLVPDRLDQQHTR 90
                                      6899*************************99888.8999888876666655554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.68
                             PAS_7  96 pdgGfVt...tytDiTerrraee 115
                                       ++ G V    + +DiTer++ ee
  gi|313122535|ref|YP_004038422.1| 251 EEQGEVYidgVAEDITERKEREE 273
                                       55555552224689999999875 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0062
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeve.rrlaaaragkphs 77 
                                       e+  + i + D d+ +  +N  + ++ +++ee ++  +p   ll    ++ ef a+  e     ++ +   ++++++
  gi|313122535|ref|YP_004038422.1| 283 EQAGHSIYMTDTDGTIEYVNPAFEDITGYSEEEACGETP--RLLSSGEHNDEFYADLWETIRSgEVWQGEVTNQRKT 357
                                       66778899***********************99944444..567777777777744444443212334444467777 PP

                             PAS_7  78 fererpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                        er   + ++  v+    +   fV++  DiT++++ e
  gi|313122535|ref|YP_004038422.1| 358 GERYVVNQTIAPVTDDDGEIERFVAVSADITDQKERE 394
                                       7888888888888888888888999999999999877 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0017         2       3      68 ..      35     102 ..      33     125 .. 0.79
   2 ?    5.3   0.0     0.024        29      51     106 .]     330     388 ..     283     388 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                            PAS_10   3 nlLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpk.kavknveeviealrtgekd 68 
                                        l  +t  +l+ +D++  i + +pa ++++ ++p++ vG pl +++p+   +++++ + + + tge++
  gi|313122535|ref|YP_004038422.1|  35 ALVANTSEGLLTVDEDSTIVFANPAVERILGYQPNElVGQPLLTLVPDrLDQQHTRAFQQYIETGERQ 102
                                       577889999***********************998758**********44555555566666666664 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.024
                            PAS_10  51 avknveeviealrtgek..devevvvpkngkw.vlvrylpyrdedgeiaGvvetfvDit 106
                                       + +   ++ e++r+ge    ev+ ++++ +++ v +++ p+ d+dgei+  v +  Dit
  gi|313122535|ref|YP_004038422.1| 330 NDEFYADLWETIRSGEVwqGEVTNQRKTGERYvVNQTIAPVTDDDGEIERFVAVSADIT 388
                                       44555667788888887324444444455555367899***********9999999996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.55   6.6e+02       6      17 ..     209     220 ..     209     238 .. 0.81
   2 ?   -0.9   0.1         1   1.2e+03      32      40 ..     402     410 ..     398     413 .. 0.80
   3 ?   11.7   0.0   0.00012      0.14       5      33 ..     741     776 ..     736     793 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.55
                                       -HHHHHHHHHHH CS
                        Sigma70_r4   6 pererevlelrf 17 
                                       +++er++++ r 
  gi|313122535|ref|YP_004038422.1| 209 DPDERQIFQERL 220
                                       699******997 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                       S-HHHHHHH CS
                        Sigma70_r4  32 iSrerVrqi 40 
                                       + +erV+qi
  gi|313122535|ref|YP_004038422.1| 402 VALERVKQI 410
                                       5689****9 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00012
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS- CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiS 33 
                                       L++r+revlel +        +  T  E+++ lgi+
  gi|313122535|ref|YP_004038422.1| 741 LTDRQREVLELAYragffesPRCSTGDELADALGIT 776
                                       8************99998664445888999999987 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0028       3.3      64      89 ..      48      73 ..      17     125 .. 0.78
   2 ?    3.6   0.0      0.04        48      57      98 ..     286     327 ..     278     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0028
                            PAS_12 64 qkenkllfaNaqirallGwssdkflq 89
                                        +  ++faN  ++++lG+++++++ 
  gi|313122535|ref|YP_004038422.1| 48 DEDSTIVFANPAVERILGYQPNELVG 73
                                      56789****************99984 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.04
                            PAS_12  57 gailvysqkenkllfaNaqirallGwssdkflqdfseivqeg 98 
                                       g  +  +  +  + ++N  +++++G+s+++   +   +++ g
  gi|313122535|ref|YP_004038422.1| 286 GHSIYMTDTDGTIEYVNPAFEDITGYSEEEACGETPRLLSSG 327
                                       55555566777889**************99877766666655 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00035      0.42      16      62 ..     736     784 ..     723     785 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                            HTH_22  16 pverltkeekieivraLdekGiFllkg..avekvAekLgiSraTvYryL 62 
                                       ++++l +++ +e+ +  +++G+F+  +  + +++A++Lgi+ +T Y + 
  gi|313122535|ref|YP_004038422.1| 736 ALDELLTDRQREVLELAYRAGFFESPRcsTGDELADALGITSPTFYLHV 784
                                       56788889999999**********98644789**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (802 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 5128.68
//
Query:       gi|313122536|ref|YP_004038423.1|  [L=471]
Description: FAD/FMN-dependent dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-37  128.2   3.1    2.8e-37  127.6   3.1    1.3  1  FAD_binding_4  FAD binding domain
    5.3e-08   32.8   0.1    1.1e-07   31.8   0.1    1.5  1  BBE            Berberine and berberine like


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.6   3.1   3.1e-41   2.8e-37       1     138 [.      45     179 ..      45     180 .. 0.98

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 3.1e-41
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdl 77 
                                       pa++vr++ +++v+aa+++a+e+++ v vrGgG++++g+av+++g+v+dls++++ + +d++++ta+v+aG+t++dl
  gi|313122536|ref|YP_004038423.1|  45 PALIVRCQGVADVVAAVNFARENDVLVAVRGGGHNVSGNAVCDDGLVIDLSEMTG-VRVDPAAQTAWVQAGATWADL 120
                                       799**********************************99999*************.89******************* PP

                                       HHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  78 vealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       +++++  gl+++   g +++++++G+++++++G+ + kyGl++dn++++e+v+adGe +++
  gi|313122536|ref|YP_004038423.1| 121 DRETQLFGLATP--GGVVSDTGIAGLTLGGGIGHLRCKYGLSCDNLRSVELVTADGEFLTA 179
                                       ************..*******************************************9986 PP

>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   1.2e-11   1.1e-07       2      45 ..     418     462 ..     417     463 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.2e-11
                                       -TTS--GGG-H.HHHHHHHGGGHHHHHHHHHHH-TT--S--TT-- CS
                               BBE   2 YvNyrdldlgk.ewgerYFggNferLvkvKtkyDPdNvFrneqsI 45 
                                       Y+N++ + +   +  ++ Fg  +erL+++K +yDP+N F  +q+I
  gi|313122536|ref|YP_004038423.1| 418 YLNFPGFFEEGdDMMRTTFGPAYERLAELKDEYDPTNRFSLNQNI 462
                                       999999999855999*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 3215.12
//
Query:       gi|313122537|ref|YP_004038424.1|  [L=231]
Description: hypothetical protein Hbor_37710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-07   29.8   0.8        5.1    7.5   0.0    5.0  5  DUF4968    Domain of unknown function (DUF4968)
    0.00098   19.6   0.2          1    9.8   0.0    2.7  2  HtaA       Htaa
     0.0067   16.2   2.4        1.2    8.8   0.1    2.9  2  DUF2807    Putative auto-transporter adhesin, head GIN domain
     0.0079   15.3   0.9      0.046   12.8   0.9    2.0  1  DUF945     Bacterial protein of unknown function (DUF945)
  ------ inclusion threshold ------
      0.019   15.6   0.0         42    4.9   0.1    3.8  4  FecR       FecR protein
       0.11   12.9   1.1         21    5.5   1.1    3.6  1  PCC_BT     Propionyl-coenzyme A carboxylase BT domain
       0.13   12.4   6.8        0.5   10.5   0.8    3.3  4  HSP20      Hsp20/alpha crystallin family
       0.17   12.9   1.4         12    7.0   0.1    3.4  2  CS         CS domain
       0.65   10.0   4.8         10    6.2   0.1    3.9  3  MinE       Septum formation topological specificity factor Mi
        2.2    8.7   4.7         15    6.0   0.1    3.8  3  GNAT_like  GCN5-related N-acetyltransferase like domain
        3.4    8.0   9.2       0.64   10.4   0.2    3.4  3  Big_3      Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> DUF4968  Domain of unknown function (DUF4968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0043         7      49      84 ..      33      68 ..      23      71 .. 0.84
   2 !    7.4   0.0    0.0033       5.4      49      81 ..      65      97 ..      58     103 .. 0.86
   3 ?    0.4   0.0      0.49     8e+02      49      75 ..     101     127 ..      95     138 .. 0.69
   4 !    7.5   0.0    0.0031       5.1      42      81 ..     131     167 ..     115     181 .. 0.75
   5 ?    3.9   0.1     0.041        67      49      74 ..     202     227 ..     164     230 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0043
                           DUF4968 49 ektefeveekedevvikTekltvkieksplrisfyd 84
                                        +++ev++k+d ++++T++  +    +  +i+  d
  gi|313122537|ref|YP_004038424.1| 33 HRNSVEVSHKGDRIEVETNDFDIDLRSDRAEIDTQD 68
                                      67899***************9999998888887766 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0033
                           DUF4968 49 ektefeveekedevvikTekltvkieksplris 81
                                      ++ ++++e ++d v+i +++l v+i+ s+ +++
  gi|313122537|ref|YP_004038424.1| 65 DTQDVDYEFEGDRVEIDSDDLDVEIDGSNIEVE 97
                                      578999999*****************9888775 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.49
                           DUF4968  49 ektefeveekedevvikTekltvkiek 75 
                                        + +fe+ +++d + +++++  ++   
  gi|313122537|ref|YP_004038424.1| 101 HNLDFELRDDGDDLDVESDDFDIEFRD 127
                                       667888888888888888877776554 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0031
                           DUF4968  42 avvkkadektefeveekedevvikTekltvkieksplris 81 
                                        v+       ++e+e  +d+v+i++++  ++i +   +i+
  gi|313122537|ref|YP_004038424.1| 131 EVES---HDSDLEIESHGDSVEIEGDSFDIEIFRGHVEID 167
                                       4444...457888899999999999999999887777666 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.041
                           DUF4968  49 ektefeveekedevvikTekltvkie 74 
                                       +  ++++e ++++  i+T++l +k++
  gi|313122537|ref|YP_004038424.1| 202 DDPDLDLEFDGQNADIETDTLDIKMA 227
                                       66788888899999999999999875 PP

>> HtaA  Htaa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00063         1      29      78 ..      60     109 ..      24     133 .. 0.64
   2 !    7.7   0.0    0.0028       4.5      31      97 ..     146     213 ..     109     228 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00063
                              HtaA  29 ggakan.kggafqFpvasgsvdkdtkkgeirfkGs.vhftghngaLdltlsn 78 
                                       + a+ + ++ +++F+ ++  v+ d+++++++ +Gs ++++g ++ Ld +l +
  gi|313122537|ref|YP_004038424.1|  60 DRAEIDtQDVDYEFEGDR--VEIDSDDLDVEIDGSnIEVEGREHNLDFELRD 109
                                       344444344555555555..55566677888888888888875555555433 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0028
                              HtaA  31 akan.kggafqFpvasgsvdkdtk..kgeirfkGsvhftghngaLdltlsnpkievsgetgtLladvssk 97 
                                       ++ + +g++f+ +  +g v+ d++  + +i+ +G+++ +   + +d++++np+++++ +   L  +++++
  gi|313122537|ref|YP_004038424.1| 146 DSVEiEGDSFDIEIFRGHVEIDSRdfEIDIESDGEIEIET--DNFDVEYENPTLDLESDDPDLDLEFDGQ 213
                                       2222244555555533344333332355555566665555..6778888888887777777776666653 PP

>> DUF2807  Putative auto-transporter adhesin, head GIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00076       1.2      94     136 ..      72     112 ..      19     124 .. 0.69
   2 !    6.4   0.3    0.0043       7.1      82     111 ..     154     191 ..     118     228 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00076
                                       ECSEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEEEEECCEE CS
                           DUF2807  94 agsgditlkldaeelsveasgsgdielsGtadrlevsvaGsGe 136
                                       + +gd ++++d+++l+ve++gs +ie++G+  +l++++  +G+
  gi|313122537|ref|YP_004038424.1|  72 EFEGD-RVEIDSDDLDVEIDGS-NIEVEGREHNLDFELRDDGD 112
                                       33444.5679999999999986.57999999999999887775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0043
                                       S..........-EEEEEEEEEEECSEEEEEEEEEEEEEEE CS
                           DUF2807  82 g..........tlkadklelniagsgditlkldaeelsve 111
                                       +          ++ ++++e++i+++g+i++  ++++++ve
  gi|313122537|ref|YP_004038424.1| 154 SfdieifrghvEIDSRDFEIDIESDGEIEI--ETDNFDVE 191
                                       133333333334445555555555555555..34444443 PP

>> DUF945  Bacterial protein of unknown function (DUF945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.9   2.8e-05     0.046     145     271 ..      69     199 ..      20     230 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                            DUF945 145 tsseltlpafelkeeggklewsggkvkvdlskdlkklsgegnldglkleadndeslelkgltlssdlkrgkeglyl. 220
                                       ++ e++   +e+++++ ++e +g +++v+ +++  ++ ++ + d l++e+d d ++e+ + +++++++ ++ +++  
  gi|313122537|ref|YP_004038424.1|  69 VDYEFEGDRVEIDSDDLDVEIDGSNIEVEGREHNLDFELRDDGDDLDVESD-DFDIEFRDGRWEVESHDSDLEIESh 144
                                       333333344444555555555577777777766666667777777777777.8888888888888887554443336 PP

                            DUF945 221 Gds...............slkiasltvssedqega.elknlsld..sssteegdllnstlkyslkslkl 271
                                       Gds                              +  +  ++++d  s+ ++e ++ n+++ y+  +l l
  gi|313122537|ref|YP_004038424.1| 145 GDSveiegdsfdieifrgH--------------VEiDSRDFEIDieSDGEIEIETDNFDVEYENPTLDL 199
                                       6666333332333333332..............223333333332222222223333333333333333 PP

>> FecR  FecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.025        42      56      89 ..      29      65 ..      21      90 .. 0.63
   2 ?    0.9   0.0      0.43     7e+02      59      83 ..      83     111 ..      69     118 .. 0.57
   3 ?    3.7   0.0     0.059        97      71      95 ..     124     164 ..     102     166 .. 0.44
   4 ?    3.5   0.0     0.067   1.1e+02      85      95 ..     154     164 ..     122     203 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.025
                              FecR 56 dkkrp...fevktpsatigvrgtefrvrksdkqteva 89
                                       ++ +    ev+ +  +i+v   +f+++ +++++e+ 
  gi|313122537|ref|YP_004038424.1| 29 VAASHrnsVEVSHKGDRIEVETNDFDIDLRSDRAEID 65
                                      4442222467777777777777777666555555544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.43
                              FecR  59 rpfevktpsatigvrgt....efrvrksd 83 
                                       +++ v+   ++i+v g     +f++r+++
  gi|313122537|ref|YP_004038424.1|  83 DDLDVEIDGSNIEVEGRehnlDFELRDDG 111
                                       24667777777777775233333445555 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.059
                              FecR  71 gvrgtefrvrksdkqte................vavleGeV 95 
                                       + r  + +v+++d+ +e                +++++G+V
  gi|313122537|ref|YP_004038424.1| 124 EFRDGRWEVESHDSDLEieshgdsveiegdsfdIEIFRGHV 164
                                       44444444433333333111111111222222266666665 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.067
                              FecR  85 qtevavleGeV 95 
                                       ++ +++++G+V
  gi|313122537|ref|YP_004038424.1| 154 SFDIEIFRGHV 164
                                       33333333333 PP

>> PCC_BT  Propionyl-coenzyme A carboxylase BT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.1     0.013        21      56      67 ..      85      96 ..      19     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                            PCC_BT 56 vevkvdgksvkv 67
                                      ++v++dg++++v
  gi|313122537|ref|YP_004038424.1| 85 LDVEIDGSNIEV 96
                                      333333333333 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.75   1.2e+03      21      37 ..      35      51 ..      22      76 .. 0.66
   2 ?   10.5   0.8   0.00031       0.5       4      40 ..      66     106 ..      63     126 .. 0.78
   3 ?    3.4   0.3     0.053        87      20      56 ..     136     154 ..     112     183 .. 0.64
   4 ?    2.7   0.2     0.084   1.4e+02      20      39 ..     136     155 ..     130     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.75
                                      CCEEEEEETTEEEEEEE CS
                             HSP20 21 eelkvkvednrvlvkge 37
                                      + ++v+ +++r+ v+ +
  gi|313122537|ref|YP_004038424.1| 35 NSVEVSHKGDRIEVETN 51
                                      56666666666666544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00031
                                       SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..... CS
                             HSP20   4 eeeeefevkldvpglkkeelkvkvednrvlvkgehe....e 40 
                                        ++  +e++ d  +++ ++l+v++++ ++ v+g ++    e
  gi|313122537|ref|YP_004038424.1|  66 TQDVDYEFEGDRVEIDSDDLDVEIDGSNIEVEGREHnldfE 106
                                       5677899999999********************98856543 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.053
                                       CCCEEEEEETTEEEEEEE--..---TT----SS---E CS
                             HSP20  20 keelkvkvednrvlvkgeheeeeedekglikerssrk 56 
                                        ++l+++ ++++v ++g                   +
  gi|313122537|ref|YP_004038424.1| 136 DSDLEIESHGDSVEIEGD------------------S 154
                                       345556666666655554..................3 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.084
                                       CCCEEEEEETTEEEEEEE-- CS
                             HSP20  20 keelkvkvednrvlvkgehe 39 
                                        ++l+++ ++++v ++g   
  gi|313122537|ref|YP_004038424.1| 136 DSDLEIESHGDSVEIEGDSF 155
                                       57999999999999999765 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0072        12      12      72 ..      20      80 ..      19      82 .. 0.82
   2 ?    2.8   0.2      0.15   2.4e+02      10      10 ..     153     153 ..      81     217 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0072
                                      EEEEEE-TTC.TTTTTCEEEEEETTEEEEEETS.CEEEEECEBSS-BETTTEEEEEETTEEEE CS
                                CS 12 Vvvtiyvkkv.nikkkdvkvefkerslkvkigk.eklliegeLfgpIdpeesswtieskkvei 72
                                      +vv ++v+ v     ++v+v+ k ++++v+ ++ +  l ++  +++Id+++  + +e+++vei
  gi|313122537|ref|YP_004038424.1| 20 IVVAFTVQPVaASHRNSVEVSHKGDRIEVETNDfDIDLRSD--RAEIDTQDVDYEFEGDRVEI 80
                                      56778887776777788999999999999986666667777..99****************98 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                                       T CS
                                CS  10 d 10 
                                       d
  gi|313122537|ref|YP_004038424.1| 153 D 153
                                       1 PP

>> MinE  Septum formation topological specificity factor MinE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   2.1e+03      40      54 ..      46      60 ..      44      71 .. 0.66
   2 ?    2.9   0.2     0.065   1.1e+02      40      54 ..      78      93 ..      76     105 .. 0.81
   3 ?    6.2   0.1    0.0061        10      33      55 ..     157     180 ..     157     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                                      H-..-SEEEEEEE-- CS
                              MinE 40 veideekvevkleke 54
                                      +e+++++ +++l ++
  gi|313122537|ref|YP_004038424.1| 46 IEVETNDFDIDLRSD 60
                                      567777777777744 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.065
                                      H-..-SEEEEEEE.-- CS
                              MinE 40 veideekvevkle.ke 54
                                      veid+++++v+++ ++
  gi|313122537|ref|YP_004038424.1| 78 VEIDSDDLDVEIDgSN 93
                                      79*********99444 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0061
                                       HHHHHHHH-..-SEEEEEEE--.- CS
                              MinE  33 leviskYveideekvevkleke.k 55 
                                       +e+ + +veid+ + e+++e++ +
  gi|313122537|ref|YP_004038424.1| 157 IEIFRGHVEIDSRDFEIDIESDgE 180
                                       567788**************6533 PP

>> GNAT_like  GCN5-related N-acetyltransferase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3      0.13   2.2e+02       6      18 ..      87      99 ..      34     116 .. 0.75
   2 ?    6.0   0.1    0.0093        15       2      25 ..     128     156 ..     127     157 .. 0.80
   3 ?   -1.3   0.0       1.8     3e+03      14      14 ..     198     198 ..     163     224 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.13
                         GNAT_like  6 vevdggaltvsgt 18
                                      ve+dg  ++v+g+
  gi|313122537|ref|YP_004038424.1| 87 VEIDGSNIEVEGR 99
                                      4555555555555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0093
                         GNAT_like   2 ggWrvevdggaltvsgtga.....gdpld 25 
                                       g W+ve ++ +l++++ g+     gd+ d
  gi|313122537|ref|YP_004038424.1| 128 GRWEVESHDSDLEIESHGDsveieGDSFD 156
                                       68***************854556677666 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.8
                         GNAT_like  14 t 14 
                                        
  gi|313122537|ref|YP_004038424.1| 198 D 198
                                       3 PP

>> Big_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00039      0.64      27      64 ..      42      80 ..      34      93 .. 0.84
   2 ?   -0.2   0.8      0.77   1.3e+03      11      41 ..     111     141 ..     109     158 .. 0.66
   3 ?    1.2   0.4      0.28   4.5e+02      24      49 ..     191     216 ..     143     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                             Big_3 27 dGdae.vpfddvevsgsvdstkaGeytvtvtykgvsatf 64
                                      +Gd+  v+  d ++++  d ++ ++++v++ ++g ++ +
  gi|313122537|ref|YP_004038424.1| 42 KGDRIeVETNDFDIDLRSDRAEIDTQDVDYEFEGDRVEI 80
                                      566546999999**********************66554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.77
                             Big_3  11 GDkldaedlfvsatykdGdaevpfddvevsg 41 
                                       GD+ld e   +   ++dG+ ev+  d ++++
  gi|313122537|ref|YP_004038424.1| 111 GDDLDVESDDFDIEFRDGRWEVESHDSDLEI 141
                                       7777777444445667777667666666655 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.28
                             Big_3  24 tykdGdaevpfddvevsgsvdstkaG 49 
                                        y++ + +++ dd ++++++d + a+
  gi|313122537|ref|YP_004038424.1| 191 EYENPTLDLESDDPDLDLEFDGQNAD 216
                                       34444444788888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1473.99
//
Query:       gi|313122538|ref|YP_004038425.1|  [L=309]
Description: nucleoside-diphosphate sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-13   49.4   0.0    1.2e-12   47.9   0.0    1.7  1  NmrA            NmrA-like family
    4.7e-11   42.9   0.0    1.5e-10   41.3   0.0    1.8  1  NAD_binding_10  NAD(P)H-binding
    2.9e-09   36.8   0.0    9.5e-08   31.8   0.0    2.1  2  Epimerase       NAD dependent epimerase/dehydratase family
     0.0001   21.4   0.0    0.00018   20.6   0.0    1.3  1  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase


Domain annotation for each model (and alignments):
>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   2.8e-16   1.2e-12       1     229 [.      15     240 ..      15     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2.8e-16
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT........-HHHHHHHHTT-SEEE CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdld........dkeslvealkgvdvvf 69 
                                       +lv GaTG++G++ v a+ ++g  vral R ++ e++ +        v  d+d        d + l+ + +g dvvf
  gi|313122538|ref|YP_004038425.1|  15 VLVAGATGYLGRYAVCAFKRRGCWVRALSRPQSVEKLSTPGRFLEPAVRSDIDdlfvgtatDSDTLDGLCDGIDVVF 91 
                                       79****************************8855544444443344466666677777777**************** PP

                                       E---GG.....S-HHHHH..HHHHHHHHHHS-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEE CS
                              NmrA  70 svtgfy.....skeiedg..kklvdAakeaGvkhfiySslgddndrsnaeepavphfdsKaeieeyvralgipytfv 139
                                       s++g++     + e+++g   +l d a  aGv++f++ s+++ +   + +ep  ++ d+       +  + i  t v
  gi|313122538|ref|YP_004038425.1|  92 SSLGVTrqqasHWEVDYGanRTLLDLALDAGVERFVFVSVFAPELWGSLVEPREQFVDE-------LYDAEISQTVV 161
                                       ***9989999977888882256*******************999666666666665554.......55678****** PP

                                       EE-EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHH CS
                              NmrA 140 yagffmenflsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgne 216
                                       +++ + + ++ ++           +  v+l g+gn+ + ++ + +D +a+ + +++d r+  ++      +t +++e
  gi|313122538|ref|YP_004038425.1| 162 RPTGYFSDMTEFFEM-----A--RRARVFLVGDGNARINPI-HGADLAAACADAVSDDREEFAV---GGPETFTYDE 227
                                       ***999999996666.....3..33469*******999999.**************97765433...3457888888 PP

                                       HHHHHHHHHTS-E CS
                              NmrA 217 ivelfekkigktv 229
                                       i++l ++ ++ +v
  gi|313122538|ref|YP_004038425.1| 228 IAALASRTLDGRV 240
                                       8888888776666 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   3.4e-14   1.5e-10       1     183 [.      19     210 ..      19     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.4e-14
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTH..HHCH........HHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnp..ekla........eleaeeglevvegdvtdvedlaealkgadaVvsa 67 
                                       GAtG  Gr++v    +r g  v+al R +  ekl+        +++ ++  ++++g +td+++l   ++g+d+V+s+
  gi|313122538|ref|YP_004038425.1|  19 GATGYLGRYAVCAFKRR-GCWVRALSRPQsvEKLStpgrflepAVR-SDIDDLFVGTATDSDTLDGLCDGIDVVFSS 93 
                                       9**********999999.59******97522566655554333332.355579************************ PP

                                       ---TCC.......HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSE CS
                    NAD_binding_10  68 lggggk.......deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgld 137
                                       lg +++       d  + ++++d a  agv+Rfv+vs +  +             l+++ ++  ++  ++l + ++ 
  gi|313122538|ref|YP_004038425.1|  94 LGVTRQqashwevDYGANRTLLDLALDAGVERFVFVSVFAPE-------------LWGSLVEPREQFVDELYDAEIS 157
                                       *8777744444455555*********************9865.............3466777888888999999999 PP

                                       EEEEEE-CEE-ST--SEEEE.......ETTSS----EEEHHHHHHHHHHHCTX CS
                    NAD_binding_10 138 wTivrpggLtdepttkyrvv.......ekgepfkggsisradVAdvlvavldd 183
                                        T+vrp+g   + t  ++++        ++ + + + i  ad+A++++++++d
  gi|313122538|ref|YP_004038425.1| 158 QTVVRPTGYFSDMTEFFEMArrarvflVGDGNARINPIHGADLAAACADAVSD 210
                                       99999999766544444444111111123334455689999999999998876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   2.1e-11   9.5e-08       1     114 [.      15     130 ..      15     155 .. 0.89
   2 ?    2.9   0.0     0.014        62     194     228 ..     177     210 ..     162     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.1e-11
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..........EEEE--TT-HHHHHHHHHHHT-SE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl..........elveldltdrsalerlfkeeqpda 67 
                                       +lV+GatG++G++ v a++++g  v +l+r +s ++ +   +           +l  +  td++ l+ l++  ++d+
  gi|313122538|ref|YP_004038425.1|  15 VLVAGATGYLGRYAVCAFKRRGCWVRALSRPQSVEKLSTPGRFlepavrsdidDLFVGTATDSDTLDGLCD--GIDV 89 
                                       79*****************************9999888877779***************************..9*** PP

                                       EEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEE CS
                         Epimerase  68 vihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllfls 114
                                       v+      gv +   ++a  +e +   +++ll+ a +agv+r++f+s
  gi|313122538|ref|YP_004038425.1|  90 VFSS---LGVTR---QQASHWEVDYGANRTLLDLALDAGVERFVFVS 130
                                       **99...34444...2333588999********************98 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.014
                                       HTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                         Epimerase 194 legkqevtllgdgtalRdflyveDvaeaillvleh 228
                                       +++   v l+gdg+a+   ++  D+a a+  ++  
  gi|313122538|ref|YP_004038425.1| 177 ARRA-RVFLVGDGNARINPIHGADLAAACADAVSD 210
                                       3344.799********************9877665 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.9e-08   0.00018       1     116 [.      16     131 ..      16     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.9e-08
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD.......lrespelleelskvnvkkviegDvtdkdkleealegvdvv 70 
                                       +v G++G+lGr+ v ++ r++    vr+l        l +  + le + +++++++  g  td d+l+  ++g+dvv
  gi|313122538|ref|YP_004038425.1|  16 LVAGATGYLGRYAVCAFKRRGC--WVRALSrpqsvekLSTPGRFLEPAVRSDIDDLFVGTATDSDTLDGLCDGIDVV 90 
                                       699**************99995..6888776666555556667788999999999********************** PP

                         3Beta_HSD  71 ihlaslvdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSs 116
                                       +   +++       + +  +v +   r++l+ +++agv+++v++S 
  gi|313122538|ref|YP_004038425.1|  91 FSSLGVTRQ-----QASHWEVDYGANRTLLDLALDAGVERFVFVSV 131
                                       988555443.....34568999**********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1982.64
//
Query:       gi|313122539|ref|YP_004038426.1|  [L=181]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-05   24.8   0.0    3.9e-05   23.4   0.0    1.8  1  HTH_IclR        IclR helix-turn-helix domain
    3.7e-05   23.5   0.0    0.00011   22.0   0.0    1.8  2  MarR_2          MarR family
    0.00024   21.5   0.0    0.00072   20.0   0.0    1.7  1  HTH_27          Winged helix DNA-binding domain
    0.00089   19.1   0.1      0.002   18.0   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0029   17.5   0.0      0.007   16.3   0.0    1.6  1  MarR            MarR family
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.015   14.8   0.0    1.1  1  NBP1            Fungal Nap binding protein NBP1
      0.017   15.2   0.0      0.045   13.8   0.0    1.7  1  HTH_20          Helix-turn-helix domain
      0.017   14.6   0.0      0.041   13.5   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.018   14.7   0.0      0.051   13.2   0.0    1.7  1  GntR            Bacterial regulatory proteins, gntR family
      0.024   14.5   0.0      0.059   13.2   0.0    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
      0.024   14.7   0.4      0.074   13.2   0.1    1.9  2  DUF4363         Domain of unknown function (DUF4363)
      0.072   11.8   0.1      0.099   11.4   0.1    1.1  1  Glyco_hydro_15  Glycosyl hydrolases family 15
      0.099   12.8   0.4       0.19   11.9   0.2    1.5  2  SesA            N-terminal domain on NACHT_NTPase and P-loop 
       0.13   12.5   0.8       0.26   11.6   0.8    1.4  1  Rx_N            Rx N-terminal domain


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     3e-08   3.9e-05      12      50 ..      39      75 ..      36      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3e-08
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +a +p   +l elA++tg +kStv++ + tL++  +v +
  gi|313122539|ref|YP_004038426.1| 39 FAGGPK--SLDELAEETGYAKSTVSNAMGTLERYHLVHR 75
                                      555555..69***********************999876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.5e-08   0.00011       2      61 ..      25      83 ..      24      84 .. 0.94
   2 ?   -2.0   0.0       2.7   3.5e+03       8      20 ..      94     106 ..      94     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.5e-08
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      gl+++  rv ++L+ ++g++ +  ela+++g+ ks+vs++   L++  Lv rr++p+ +R
  gi|313122539|ref|YP_004038426.1| 25 GLNRSYGRVYGFLYFAGGPK-SLDELAEETGYAKSTVSNAMGTLERYHLVHRRSAPGEGR 83
                                      88999999999*******98.********************************9999888 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                                       HHHHHHHHCTTTS CS
                            MarR_2   8 arvLaaLgrrpgr 20 
                                       + vL +L  r+gr
  gi|313122539|ref|YP_004038426.1|  94 WTVLTELFEREGR 106
                                       6789999888887 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   5.6e-07   0.00072      16      63 ..      41      88 ..      36      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.6e-07
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvr 63
                                      +++k+l +l++ + + +s++s+++  L++++Lv+r   + ++r + ++
  gi|313122539|ref|YP_004038426.1| 41 GGPKSLDELAEETGYAKSTVSNAMGTLERYHLVHRRSAPGEGRKVYFE 88
                                      689************************************999998876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.5e-06     0.002       4      62 ..      24      86 ..      22      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                                      CHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST...TTEE CS
                              TrmB  4 lGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr...pklY 62
                                      +GL+    +vY  L  + gp++ de+aee+g  +s+v +++  Le+  lV+r+      +k+Y
  gi|313122539|ref|YP_004038426.1| 24 YGLNRSYGRVYGFLYfAGGPKSLDELAEETGYAKSTVSNAMGTLERYHLVHRRSAPgegRKVY 86
                                      5666666678888877889*********************************98666666666 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.5e-06     0.007      16      59 .]      42      85 ..      39      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.5e-06
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTSE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRev 59
                                      gp s+ eLa+  g  kstv+++  +Le+  l++R+  p+  R+v
  gi|313122539|ref|YP_004038426.1| 42 GPKSLDELAEETGYAKSTVSNAMGTLERYHLVHRRSAPGEGRKV 85
                                      688999********************************999987 PP

>> NBP1  Fungal Nap binding protein NBP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.1e-05     0.015      91     148 ..      89     145 ..      40     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                              NBP1  91 slrsllesiksvFsne.eqdlkrmknasenlnallpseelksreerkklkdrilrseaF 148
                                         + ++  ++++F  e +++++ m++a en +++l  ee  ++ee+k++++ri++ + +
  gi|313122539|ref|YP_004038426.1|  89 AETDFWTVLTELFEREgRREIRIMRRALENAQETL--EEAPETEETKRAEERIEQLQQL 145
                                       45789*********985689************999..57889999********976655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05     0.045      21      57 ..      40      76 ..      32      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                                      TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                       +++ ++ elae+ + +k+t+s+ + +Le+  Lv+++
  gi|313122539|ref|YP_004038426.1| 40 AGGPKSLDELAEETGYAKSTVSNAMGTLERYHLVHRR 76
                                      57899*************************9999987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.2e-05     0.041      19      43 ..      45      69 ..      41      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLee 43
                                      s  eLAe++g  +stv+  +  Le+
  gi|313122539|ref|YP_004038426.1| 45 SLDELAEETGYAKSTVSNAMGTLER 69
                                      667********************98 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     4e-05     0.051      27      58 ..      46      77 ..      42      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverrq 58
                                        eLa+e g  ++tv  A+ +Le+  lv+rr+
  gi|313122539|ref|YP_004038426.1| 46 LDELAEETGYAKSTVSNAMGTLERYHLVHRRS 77
                                      579***************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.6e-05     0.059      10      34 ..      38      62 ..      36      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                                      HHTTSSEEHHHHHHHHTS-HHHHHH CS
                             HTH_5 10 lLaegelcvcelaeelglsqstvSh 34
                                      + a g+++  elaee+g  +stvS 
  gi|313122539|ref|YP_004038426.1| 38 YFAGGPKSLDELAEETGYAKSTVSN 62
                                      56889******************95 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.9   2.5e+03      76      92 ..       3      19 ..       1      28 [. 0.60
   2 ?   13.2   0.1   5.8e-05     0.074      14      56 ..     116     158 ..     106     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                           DUF4363 76 tedkeealaelaelkfl 92
                                      +e ++ea  e+a +   
  gi|313122539|ref|YP_004038426.1|  3 EEAYDEARTEIADAMAR 19
                                      45566666666665554 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.8e-05
                           DUF4363  14 lsekleeleeaienedweeakekleelekeWekkkkklsifie 56 
                                       l++  e+leea e e+ + a+e +e+l++ +++ +++l++f+e
  gi|313122539|ref|YP_004038426.1| 116 LENAQETLEEAPETEETKRAEERIEQLQQLYRQSERVLEFFTE 158
                                       4444455666669***************************987 PP

>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   7.7e-05     0.099     301     408 ..      47     148 ..      43     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.7e-05
                                       HHHHHHSGGGTT-STTS...--SBTT--CGSSSBSCT--BHHHH...HHHHHHHHHHHHHHHHHTE-EEEECCCHHH CS
                    Glyco_hydro_15 301 dsllsegflavgeldpl...vrRysedvkpdklglsGrpyylct...lwtvetlldelyekagkgrlwglvryalgl 371
                                       d+l +e+  a++++++      Ry    + +   ++Gr++y      +w   t+l+el e++g+ + ++++r+al+ 
  gi|313122539|ref|YP_004038426.1|  47 DELAEETGYAKSTVSNAmgtLERYHLVHR-RSAPGEGRKVYFEAetdFW---TVLTELFEREGRRE-IRIMRRALEN 118
                                       66777777777777777777899999988.699********96522267...99**********55.9999999998 PP

                                       HHHHTTTTTGGGSSEEETCHHHHHHHHHHHHHHHHHH CS
                    Glyco_hydro_15 372 leklveskqltvGlpperesvisaplpveeladlive 408
                                        +++ e+       +pe+e+++ a + +e+l++l+ +
  gi|313122539|ref|YP_004038426.1| 119 AQETLEE-------APETEETKRAEERIEQLQQLYRQ 148
                                       8888888.......999**************999866 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.1   6.5e+03      84     101 ..      59      76 ..      44      85 .. 0.51
   2 ?   11.9   0.2   0.00015      0.19      32      81 ..     106     154 ..      95     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.1
                              SesA  84 apapadsrleryrkavrs 101
                                       + ++a  +lery+ + r+
  gi|313122539|ref|YP_004038426.1|  59 TVSNAMGTLERYHLVHRR 76 
                                       334444566777666555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                              SesA  32 gkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeife 81 
                                        +++ + + +Le a+++le++ + e+t+  +++ +e+ ++  ++ e+++e
  gi|313122539|ref|YP_004038426.1| 106 RREIRIMRRALENAQETLEEAPETEETKR-AEERIEQLQQLYRQSERVLE 154
                                       5789999*******************998.99999999998877777765 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8    0.0002      0.26      22      75 ..     104     156 ..      94     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                              Rx_N  22 gvkeeleklkdeLesiqavLedaeerqikdeavkeWlkelrdlaydaeDvlDef 75 
                                       + ++e++ +++ Le+ q  Le+a e ++  + ++e +++l++l  + e vl+ f
  gi|313122539|ref|YP_004038426.1| 104 EGRREIRIMRRALENAQETLEEAPETEE-TKRAEERIEQLQQLYRQSERVLEFF 156
                                       55899*******************9875.677899*********9999999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1561  (0.0870656); expected 358.6 (0.02)
Passed bias filter:                      890  (0.0496402); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1222.81
//
Query:       gi|313122540|ref|YP_004038427.1|  [L=180]
Description: hypothetical protein Hbor_37740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.7  12.4       0.58   10.4  12.8    1.8  1  TctB      Tripartite tricarboxylate transporter TctB family


Domain annotation for each model (and alignments):
>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  12.8   3.2e-05      0.58      45     125 ..      56     155 ..      23     158 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.2e-05
                              TctB  45 lllv..............aadgekeekearedwrkllklvlallaalllyalllepl.........Gfilatalfll 98 
                                       +  v               a +   +++++  w+ +  +v a l  ++l a+l+e++         Gf++ +a+++l
  gi|313122540|ref|YP_004038427.1|  56 VA-VfaldiaggivanttDAGARWWHRSSQGPWDHFG-FVSAHLHPFVL-AVLFETVtwyesaliyGFLIVSAALVL 129
                                       22.1245555555666743333344444444555555.88886666665.777888767777777899999998884 PP

                              TctB  99 lllgreerkwlkalilavvlallvyll 125
                                       l   +++r+++ +l+++v++ ++++l+
  gi|313122540|ref|YP_004038427.1| 130 LSP-HRFRRPVGMLLVSVGVLVGLMLV 155
                                       444.6799***************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1373.72
//
Query:       gi|313122541|ref|YP_004038428.1|  [L=318]
Description: Zn-dependent oxidoreductase, NADPH:quinone reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-27   95.0   0.0    1.2e-26   94.3   0.0    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    1.6e-17   63.7   0.0    5.1e-17   62.1   0.0    1.7  2  ADH_zinc_N    Zinc-binding dehydrogenase
    3.9e-08   33.1   0.0    2.4e-07   30.6   0.0    2.2  3  ADH_N         Alcohol dehydrogenase GroES-like domain
      0.004   16.9   0.0      0.006   16.4   0.0    1.2  1  DUF2855       Protein of unknown function (DUF2855)
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.44   10.5   0.0    1.9  2  ADH_N_2       N-terminal domain of oxidoreductase


Domain annotation for each model (and alignments):
>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.0   3.4e-30   1.2e-26       1     133 []     188     311 ..     188     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 3.4e-30
                                       TT-SEEEETTSTTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE-- CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyef 77 
                                       lG+de++dyr+++fe+++ ++ +Dv+ld+vgge+l e+s++v+ +gGr+v++ +p  s+++  +a+++  r+ ++ +
  gi|313122541|ref|YP_004038428.1| 188 LGVDEFVDYRNQSFEDEL-SD-IDVILDAVGGETL-EQSIDVITHGGRIVTLPKP-PSQNVVTNARNE--RNASIDW 258
                                       8*************9777.45.***********99.*******888*****9975.666677776755..6666666 PP

                                       GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  78 lfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                       +  ++++  a  l e+ +l+e G+l ++v+  +pl+ea  Ahr+ + g++rGK+Vl
  gi|313122541|ref|YP_004038428.1| 259 FS-VEPD-AAA-LSEIRTLVENGHLSVTVSDAWPLSEAHAAHRASQRGHVRGKLVL 311
                                       66.8888.777.*******************************************8 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.66   2.4e+03      64     104 ..      66     113 ..      65     120 .. 0.63
   2 !   62.1   0.0   1.4e-20   5.1e-17       1      95 [.     157     244 ..     157     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.66
                                       ESSCSHHHHHHHHHCEEEE.EEEEECSCTSSEEE......EEHHHHHH CS
                        ADH_zinc_N  64 ecvGsgatleaalkllkpg.GrlvvvGggkgeee......fdlrnlll 104
                                       + +G+ a + +++++ +pg   + +vG++  ++       +++ +++l
  gi|313122541|ref|YP_004038428.1|  66 DLSGVVADVGTSVSAFAPGdEVFGLVGMPDPGNAyaeyatVPAEDVVL 113
                                       667888889999999999945555677733333333455555555555 PP

  == domain 2  score: 62.1 bits;  conditional E-value: 1.4e-20
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG++avqlA ++Ga vi+++s ++   ++++lG+de+++y++ ++++++       ++dv++++vG g+tle++++
  gi|313122541|ref|YP_004038428.1| 157 GVGHIAVQLASHAGASVIGTASARN-EGFLRELGVDEFVDYRNQSFEDELS------DIDVILDAVG-GETLEQSID 225
                                       9******************998886.59*************4425555553......899*******.********* PP

                                       CEEEEEEEEECSC.TSSEE CS
                        ADH_zinc_N  78 llkpgGrlvvvGg.gkgee 95 
                                       ++++gGr+v+    ++++ 
  gi|313122541|ref|YP_004038428.1| 226 VITHGGRIVTLPKpPSQNV 244
                                       *********9877555444 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   6.7e-11   2.4e-07       2      61 ..      28      89 ..      27     101 .. 0.91
   2 ?   -2.1   0.0         1   3.6e+03      94     107 ..      99     112 ..      88     113 .. 0.77
   3 ?   -1.2   0.0      0.51   1.8e+03      50      64 ..     140     154 ..     120     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 6.7e-11
                                      TEEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE CS
                             ADH_N  2 gevlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvv 61
                                      +e+l++v+aag++  D ++ +g   + l  +lp ++G +++G+v++vg +v+ ++ Gd+V+ 
  gi|313122541|ref|YP_004038428.1| 28 DELLVRVHAAGVNPIDWMVREGYadNALDPSLPYVPGWDLSGVVADVGTSVSAFAPGDEVFG 89
                                      799**************99999877889999****************************986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                                       SSBSEEEECGGGEE CS
                             ADH_N  94 gfaeyvvvpekklv 107
                                       ++aey +vp++++v
  gi|313122541|ref|YP_004038428.1|  99 AYAEYATVPAEDVV 112
                                       699******98876 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.51
                                       -CS--TT-EEEE-SE CS
                             ADH_N  50 vkklkvGdrVvvepl 64 
                                       v +++ G+rV+v+++
  gi|313122541|ref|YP_004038428.1| 140 VGDVRSGQRVLVHAA 154
                                       556888999988765 PP

>> DUF2855  Protein of unknown function (DUF2855)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.7e-06     0.006      95     228 ..      98     224 ..      93     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                           DUF2855  95 piYnrylrvsedpay.esdeeealtallrplfetsflledflfddadlsgakvvvllsASsKTAlslayllrkrrka 170
                                       + Y +y +v++++ + +sd   + +a + p+   +    + lf+ +d+++ ++v++ +A++  +  +a +l++++  
  gi|313122541|ref|YP_004038428.1|  98 NAYAEYATVPAEDVVlKSDALTHEEAAAIPM--VALTARRALFEVGDVRSGQRVLVHAAAGGVGH-IAVQLASHAG- 170
                                       5799999999999986666666666666665..567899*******999999*******999997.5666666666. PP

                           DUF2855 171 eegplklvglTSaknrafveslglydkvvsYddlesleaakkv.vivDfagrdellekl 228
                                            +++g +Sa+n++f ++lg+ d+ v+Y + + +++ + + vi+D  g ++l +++
  gi|313122541|ref|YP_004038428.1| 171 ----ASVIGTASARNEGFLRELGV-DEFVDYRNQSFEDELSDIdVILDAVGGETLEQSI 224
                                       ....48*****************7.8999****99999999988999*99999888765 PP

>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.44      15      95 ..      12      94 ..       3     106 .. 0.77
   2 ?   -2.7   0.0       1.5   5.4e+03      23      41 ..     263     281 ..     252     283 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                           ADH_N_2 15 esdfeleeeelpelkdGevlvralylSvDPy...mR.grmndaksyvepvelgdvmrggavgeVveSknpdfkvGdlVv 89
                                      ++ ++ e+ + pe++++e+lvr++  +v P     R g+ ++a +   p+  g  + g +v++V  S  ++f++Gd V 
  gi|313122541|ref|YP_004038428.1| 12 ADVLTHEDIPRPEPAADELLVRVHAAGVNPIdwmVReGYADNALDPSLPYVPGWDLSG-VVADVGTSV-SAFAPGDEVF 88
                                      555666777889999*************996222453455556666669999999976.799999886.68*******9 PP

                           ADH_N_2 90 gllgwq 95
                                      gl+g+ 
  gi|313122541|ref|YP_004038428.1| 89 GLVGMP 94
                                      999875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                           ADH_N_2  23 eelpelkdGevlvralylS 41 
                                        + ++l +   lv++ +lS
  gi|313122541|ref|YP_004038428.1| 263 PDAAALSEIRTLVENGHLS 281
                                       3344444455556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2248.87
//
Query:       gi|313122542|ref|YP_004038429.1|  [L=325]
Description: hypothetical protein Hbor_37770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2299.49
//
Query:       gi|313122543|ref|YP_004038430.1|  [L=917]
Description: PAS domain S-box [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-40  139.1   7.4    1.1e-40  139.1   7.4    2.9  2  BAT       GAF and HTH_10 associated domain
    2.4e-19   68.9   0.0    5.7e-19   67.7   0.0    1.7  1  HTH_10    HTH DNA binding domain
    3.9e-18   66.1   1.5    3.8e-11   43.4   0.1    2.8  2  GAF_2     GAF domain
    1.3e-17   64.0   4.7    8.4e-10   38.9   0.2    3.3  3  PAS_4     PAS fold
    4.5e-17   62.1   0.5    6.2e-13   48.7   0.1    3.0  2  PAS       PAS fold
    9.9e-16   57.9   0.0    9.3e-13   48.3   0.1    2.8  2  PAS_9     PAS domain
      8e-12   44.9   0.4    6.8e-07   29.2   0.1    3.5  3  PAS_8     PAS domain
    4.4e-06   26.8   4.5     0.0036   17.4   0.1    3.7  3  PAS_7     PAS fold
    0.00018   22.2   0.1       0.14   12.8   0.0    3.0  3  GAF       GAF domain
     0.0013   18.6   0.0     0.0035   17.2   0.0    1.7  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0022   18.0   0.0       0.01   15.9   0.0    2.2  1  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.8   0.0        2.8    8.3   0.0    3.1  2  GAF_3     GAF domain
      0.063   13.6   0.0       0.36   11.1   0.0    2.2  2  PAS_3     PAS fold
        6.7    6.8  10.4        0.7   10.0   0.2    3.5  3  MLTR_LBD  MmyB-like transcription regulator ligand binding do


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5       2.3     3e+03      65      99 ..      58      95 ..      37     111 .. 0.64
   2 !  139.1   7.4   8.4e-44   1.1e-40       2     156 .]     700     854 ..     699     854 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                               BAT 65 vedvrvvseeddg...tlleltvsgpslastlaehGgt 99
                                       ++v+vvs++ dg    ++ l +++ +++s+  + G+t
  gi|313122543|ref|YP_004038430.1| 58 CTSVDVVSATPDGqapVVVVLSTADNDVISRAYSAGAT 95
                                      35666666666655555666666666666666666665 PP

  == domain 2  score: 139.1 bits;  conditional E-value: 8.4e-44
                               BAT   2 avveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgt 78 
                                       + veL+++i++++++l ++a++ld++v+leg+v+++ g++l+++tv++ d+ + ++++++l  +e+vr +++++++t
  gi|313122543|ref|YP_004038430.1| 700 SFVELDVHITSQNEPLLRIAQALDATVQLEGSVQQTSGSALLYLTVSESDTTRNAEILSSLTVIEQVREIAARENET 776
                                       78*************************************************************************** PP

                               BAT  79 lleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrrefr 155
                                       ++e++++ + l s+la+ G++ r+++a+++  ++v+e+P+g ++R++ve+l+e yp++eL a+r+rer+ +t+++fr
  gi|313122543|ref|YP_004038430.1| 777 VVEVQLAAEALPSRLADFGAVARTLTARPDALTVVIELPSGSEIRKFVEYLREWYPGTELNAKRTRERSIETQQSFR 853
                                       ****************************************************************************9 PP

                               BAT 156 a 156
                                       a
  gi|313122543|ref|YP_004038430.1| 854 A 854
                                       6 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   4.4e-22   5.7e-19       1      52 [.     860     911 ..     860     912 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 4.4e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd+q+e+l++Ay +GYF +PR+ t++e+A  l+I+++t+s hLr ae+kl+
  gi|313122543|ref|YP_004038430.1| 860 LTDRQFEALRTAYFSGYFAWPRERTASEIATSLDIAQPTFSRHLRVAEQKLF 911
                                       9**************************************************8 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   2.2e-07   0.00029       6     137 ..     374     501 ..     369     502 .. 0.75
   2 !   43.4   0.1     3e-14   3.8e-11       2     137 ..     545     687 ..     544     688 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHHS.S..EEEEEEE-TT.S-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EE.ES-GGG-S- CS
                             GAF_2   6 elldlvldelvel.gaalgyillvddd.gglrlaawgeaeeefgaaldrplgeglvgealrtgrpvi.lndleedpd 79 
                                        + ++vl++++++   + +++ l+d+  g+lr +aw +++   +  +    g+g++++++ + ++v   +d ++ ++
  gi|313122543|ref|YP_004038430.1| 374 AVGERVLNTATQIlELESVVVFLYDESvGELRPVAWEGTGSPPSIGP----GDGVLWTCFVECESVHlRTDEQTLDR 446
                                       67899*******65888666666664437799999999987777777....***99********9995555888777 PP

                                       HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  80 kkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +++l+   ++a  + ++a+Pl   g  +Gvl+ ++++++a  + + +l  +la+ +  a+
  gi|313122543|ref|YP_004038430.1| 447 WDRLEavDSDASNGESVAIPL---G-EHGVLATSSSGENA-PRNQSTLTHLLAANAEAAL 501
                                       7777744666666666*****...8.9*****99999988.4556666666777766666 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 3e-14
                                       HHHHHHHHHHHHHHHHSS....EEEEEEE-.TTS-EEEE...EEEES-TTSTT-S-B--...-TTHHHHHHHHTS-E CS
                             GAF_2   2 adleelldlvldelvelg..aalgyillvd.ddgglrla...awgeaeeefgaaldrpl...geglvgealrtgrpv 69 
                                        + ee+ ++v+++lve g  +a+++++ +d  d+        aw++ae++  ++l+ ++   +  +     rt + +
  gi|313122543|ref|YP_004038430.1| 545 DSREEIERAVCERLVE-GpaIAFAWVGAYDrVDEA---IgsrAWAGAERGYLDCLSESPaefRTEPSVVTTRTHETT 617
                                       6889************.6557799****9943344...1355********999998877455555544556666899 PP

                                       EES-GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  70 ilndleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +++++ ++   ++++  a ++g++s ++vPl++++  +G l++ya++p+afd + + ++eel+ + a ai
  gi|313122543|ref|YP_004038430.1| 618 VVDNVGQEIQAHQWRrdALDRGFASVASVPLTYNEFSYGTLTIYATEPNAFDKQMRLMFEELGVTTANAI 687
                                       9999***8888888888****************878********************************99 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.8   1.3e-08   1.6e-05       5     109 ..     136     228 ..     133     229 .. 0.90
   2 !   38.9   0.2   6.6e-13   8.4e-10       1     110 []     241     351 ..     241     351 .. 0.92
   3 ?   -2.5   0.0       4.8   6.2e+03      16      40 ..     355     379 ..     353     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.3e-08
                             PAS_4   5 pdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhy 81 
                                       +da +vld++ rv+ a aa++e fga+p +l G+ l+   p   ++  +r +r+vl+g+++ +++++    +++r +
  gi|313122543|ref|YP_004038430.1| 136 NDAACVLDRQWRVVEATAAFCEFFGADP-TLDGENLWATCPN-TRTTADRCWRAVLTGDDAEFEVTF----RDGRRV 206
                                       799*******************888887.699*****98888.***************987777774....566*** PP

                             PAS_4  82 elrllPlrdesGevigvlvisrDiTerr 109
                                        ++++Plrd      g+ +  rD++er 
  gi|313122543|ref|YP_004038430.1| 207 AVNAVPLRD------GLALRYRDVSERT 228
                                       ********9......***********96 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 6.6e-13
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..p 75 
                                       l+ + d++++ld+++++ ++N+a  e+ g+++e+l+G++   l+ e++  + +++++r l+ge +  +l++ l   +
  gi|313122543|ref|YP_004038430.1| 241 LETIDDGIYILDENFQIAAVNEAVLEMTGYDRETLVGEHATMLADESVIIEASAIIQRILTGELSDGRLDVELEtaD 317
                                       67899************************************99999999999********99866655655555899 PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       g++ ++e+r++ lr  +G+ +g+++++rDi++rr+
  gi|313122543|ref|YP_004038430.1| 318 GSRLPVETRFSALRFNDGT-HGTVGVIRDISDRRQ 351
                                       *******************.*************96 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.8
                             PAS_4  16 rvlyaNaaaaelfgappeellGktl 40 
                                       + +++N +a+elf  + + ++G+++
  gi|313122543|ref|YP_004038430.1| 355 TLTALNSSAHELFNSQTKPAVGERV 379
                                       6678888888888888888888765 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00044      0.56      11      38 ..     136     163 ..     131     218 .. 0.71
   2 !   48.7   0.1   4.9e-16   6.2e-13       2     113 .]     236     346 ..     235     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00044
                                       SSEEEEEETTSBEEEECHHHHHHHSSTH CS
                               PAS  11 pdpifvvDedgrilyvNaaaeellGlsr 38 
                                        d+ +v+D++ r++++ aa++e++G ++
  gi|313122543|ref|YP_004038430.1| 136 NDAACVLDRQWRVVEATAAFCEFFGADP 163
                                       6899*********************986 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 4.9e-16
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECC.CC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesra.ge 76 
                                       ++++ile+++d+i ++De+  i  vN+a  e++G++re ++g++  +l  e     + a+++ q++++ge s +  +
  gi|313122543|ref|YP_004038430.1| 236 RYKRILETIDDGIYILDENFQIAAVNEAVLEMTGYDRETLVGEHATMLADES--ViIEASAIIQRILTGELSDGrLD 310
                                       79*****************************************999999543..46899999999999987655156 PP

                                       EEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  77 isfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + +++ dg+  ++e+r s +r+ +g++ g +gv+rdi
  gi|313122543|ref|YP_004038430.1| 311 VELETADGSRLPVETRFSALRFNDGTH-GTVGVIRDI 346
                                       77777********************97.********8 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0069       8.8       6      88 ..     141     216 ..     136     226 .. 0.74
   2 !   48.3   0.1   7.3e-16   9.3e-13       1     104 []     245     348 ..     245     348 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0069
                             PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                       + + + r++ a  a+++++G +p  + g +++ ++   p+++ + ++++++   +  + e + + ++g+++   ++a
  gi|313122543|ref|YP_004038430.1| 141 VLDRQWRVVEATAAFCEFFGADPT-LDGENLWATC---PNTRTTADRCWRAVL-TGDDAEFEVTFRDGRRVA--VNA 210
                                       444666899***********8877.8*********...666666666666666.566666666667776666..999 PP

                             PAS_9  83 spvkdd 88 
                                       +p++d+
  gi|313122543|ref|YP_004038430.1| 211 VPLRDG 216
                                       999875 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 7.3e-16
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirknge 74 
                                       +dgi i ++++ i  +Nea+l+++Gy++e ++g + t+l   d++   + +a+++++ +   +  + +v+l + +g+
  gi|313122543|ref|YP_004038430.1| 245 DDGIYILDENFQIAAVNEAVLEMTGYDRETLVGEHATMLA--DESVIIEASAIIQRILTgelSDGRLDVELETADGS 319
                                       689***99********************************..99999999999999999999*************** PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                       +++v+ ++s+++ +dg+    ++++rDi++
  gi|313122543|ref|YP_004038430.1| 320 RLPVETRFSALRFNDGTHGT-VGVIRDISD 348
                                       ***********888777765.7******96 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00049      0.63      11      46 ..     136     171 ..     131     193 .. 0.74
   2 !   29.2   0.1   5.3e-10   6.8e-07       2      44 ..     236     275 ..     235     296 .. 0.80
   3 ?    1.2   0.0      0.31     4e+02      12      40 ..     340     369 ..     326     393 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00049
                             PAS_8  11 pdgiavvdlgdrivdvNqaalellGysadlkgellg 46 
                                       +d+ +v+d+++r+v++  a++e++G ++ l+ge l+
  gi|313122543|ref|YP_004038430.1| 136 NDAACVLDRQWRVVEATAAFCEFFGADPTLDGENLW 171
                                       57889999888**************66666666665 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 5.3e-10
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgel 44 
                                       r++ ++e+++dgi ++d +  +i  vN+a le++Gy+ +     l
  gi|313122543|ref|YP_004038430.1| 236 RYKRILETIDDGIYILDeNF-QIAAVNEAVLEMTGYDrE----TL 275
                                       9****************555.5*************9842....22 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.31
                             PAS_8  12 dgiavvd.lgd.....rivdvNqaalellGysadl 40 
                                       +g++  d  ++     +++  N +a el+     +
  gi|313122543|ref|YP_004038430.1| 340 VGVI-RDiSDRrqyeqTLTALNSSAHELFN----S 369
                                       6788.565555334445************7....3 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.8   6.2e+03       7      30 ..     138     161 ..     135     165 .. 0.82
   2 !    9.1   0.0    0.0011       1.4      62     114 ..     180     231 ..     171     232 .. 0.87
   3 !   17.4   0.1   2.8e-06    0.0036       1     115 []     241     354 ..     241     354 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.8
                             PAS_7   7 GisvfDadlrLvawNrrylelldl 30 
                                       + +v+D++ r+v     ++e ++ 
  gi|313122543|ref|YP_004038430.1| 138 AACVLDRQWRVVEATAAFCEFFGA 161
                                       569*********999999998875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                             PAS_7  62 everrlaaaragkphsfererpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                       +++r+ +a+ +g+   fe++ +dgr + v++ pl d G+   y D++er ++e
  gi|313122543|ref|YP_004038430.1| 180 TADRCWRAVLTGDDAEFEVTFRDGRRVAVNAVPLRD-GLALRYRDVSERTETE 231
                                       566777888899999*******************98.68899*******9998 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 2.8e-06
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphs 77 
                                       le +++Gi ++D++ ++ a+N+ +le+ ++ +e + vg + +    ++a++  +   +++a ++r+l+   ++ +  
  gi|313122543|ref|YP_004038430.1| 241 LETIDDGIYILDENFQIAAVNEAVLEMTGYDRETL-VGEHAT----MLADESVII--EASAIIQRILTGELSDGRLD 310
                                       799******************************99.666554....444555554..67889999999999999999 PP

                             PAS_7  78 fererpdgrvievrgnpl......pdgGfVttytDiTerrraee 115
                                       +e e++dg  + v+++           G+V +  Di++rr+ e+
  gi|313122543|ref|YP_004038430.1| 311 VELETADGSRLPVETRFSalrfndGTHGTVGVIRDISDRRQYEQ 354
                                       99999999999998886644664444699999999999999875 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.8   6.1e+03      12      27 ..     263     290 ..     258     369 .. 0.51
   2 ?    5.9   0.0     0.015        19       7      96 ..     377     468 ..     374     496 .. 0.71
   3 !   12.8   0.0   0.00011      0.14      56     133 .]     611     687 ..     548     687 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.8
                                       HHHHHHTESEEEEEE............E CS
                               GAF  12 elrellgadrvalyl............p 27 
                                        + e++g+dr +l               
  gi|313122543|ref|YP_004038430.1| 263 AVLEMTGYDRETLVGehatmladesviI 290
                                       5668888888555332222232222220 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHTESEEEEEE.EEETTEEECEEEEECC......EEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTT CS
                               GAF   7 dtvveelrellgadrvalyl.pdydGlhydipqasrw......lfmkngrgicgqvlatgqplvipdstpdprfaqy 76 
                                       ++v++++ ++l+++ v+++l +++ G +       +w      + + +g+g+  +++ + +++++    +d++ +++
  gi|313122543|ref|YP_004038430.1| 377 ERVLNTATQILELESVVVFLyDESVG-EL---RPVAWegtgspPSIGPGDGVLWTCFVECESVHLR---TDEQTLDR 446
                                       68999*************99444455.22...2222234443444444999999************...78777765 PP

                                       .HHHHHHHHTTES.EEEEEEEE CS
                               GAF  77 .nrrdllenmgir.sslvvPlv 96 
                                         r++ ++   ++  s+++Pl 
  gi|313122543|ref|YP_004038430.1| 447 wDRLEAVDSDASNgESVAIPLG 468
                                       5444444444444477777775 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00011
                                       HHHSSSEEESTGGTSTTHHTT.HHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHH CS
                               GAF  56 latgqplvipdstpdprfaqy.nrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqva 130
                                        +t ++ v+++    ++  q+  +r+ +   g+ s+++vPl+ ++  +G+l+++ + p  f+++ + ++++l+   a
  gi|313122543|ref|YP_004038430.1| 611 TRTHETTVVDN---VGQEIQAhQWRRDALDRGFASVASVPLTYNEFSYGTLTIYATEPnAFDKQMRLMFEELGVTTA 684
                                       34667777774...44433334488999999************************9997788888888799999888 PP

                                       HHH CS
                               GAF 131 val 133
                                       +a+
  gi|313122543|ref|YP_004038430.1| 685 NAI 687
                                       886 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0035      14      38 ..     881     905 ..     878     907 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                                       SSEEHHHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  14 gelcvcelaeelglsqstvShHLkk 38 
                                       +e++++e+a  l++ q+t S+HL++
  gi|313122543|ref|YP_004038430.1| 881 RERTASEIATSLDIAQPTFSRHLRV 905
                                       699********************95 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.8e-06      0.01      23      47 ..     881     905 ..     866     908 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.8e-06
                                       TTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  23 egltaselaerldlskntlsyHLrv 47 
                                       +++tase+a  ld+++ t s+HLrv
  gi|313122543|ref|YP_004038430.1| 881 RERTASEIATSLDIAQPTFSRHLRV 905
                                       789********************97 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.051        66       9      45 ..     379     414 ..     375     480 .. 0.82
   2 ?    8.3   0.0    0.0022       2.8      81     127 ..     641     687 ..     604     688 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.051
                             GAF_3   9 llkllvkllgaevgalllldedgnklqvaagwdgkpa 45 
                                       +l  + ++l +e+++++l+de   +l+++a w+g  +
  gi|313122543|ref|YP_004038430.1| 379 VLNTATQILELESVVVFLYDESVGELRPVA-WEGTGS 414
                                       5677889*************9988999998.434444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0022
                             GAF_3  81 raalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       +++  vPL+  + ++G+l ++ t+p afd + + ++e+l+  +a+ai
  gi|313122543|ref|YP_004038430.1| 641 ASVASVPLTYNEFSYGTLTIYATEPNAFDKQMRLMFEELGVTTANAI 687
                                       45566*****99********************************998 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.9   2.4e+03       4      57 ..     151     201 ..     148     204 .. 0.67
   2 ?   11.1   0.0   0.00028      0.36       3      81 ..     259     336 ..     257     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyR 57 
                                       + ++++e +G +p  l g  + w  +  p  r  + +++ ++l+++  ++e+ +R
  gi|313122543|ref|YP_004038430.1| 151 ATAAFCEFFGADPT-LDGE-NLW--ATCPNTRTTADRCWRAVLTGDDaEFEVTFR 201
                                       56677777777764.4444.233..356888888999999999777767777776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00028
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                        v+e+v e++Gy++e l g    ++ ++  e  + ++ + +q++l++   +   ++ + ++dG+   ve+r +++r 
  gi|313122543|ref|YP_004038430.1| 259 AVNEAVLEMTGYDRETLVGE---HATMLADESvIIEASAIIQRILTGELsDGRLDVELETADGSRLPVETRFSALRF 332
                                       689*****************...666666666466677777777744446667889999999999999999999988 PP

                             PAS_3  78 engk 81 
                                       ++g 
  gi|313122543|ref|YP_004038430.1| 333 NDGT 336
                                       8876 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00055       0.7      16      45 ..     138     167 ..     132     234 .. 0.79
   2 ?    2.1   0.0      0.15   1.9e+02       7      43 ..     239     274 ..     233     284 .. 0.78
   3 ?   -1.4   0.4       1.8   2.3e+03      51     104 ..     778     833 ..     766     870 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                          MLTR_LBD  16 PAlVldrrwdvlaaNraaraLlgdpaalpe 45 
                                       +A+Vldr+w v+ a +a+  ++g+ ++l +
  gi|313122543|ref|YP_004038430.1| 138 AACVLDRQWRVVEATAAFCEFFGADPTLDG 167
                                       69*********************9544433 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.15
                          MLTR_LBD   7 rlLdalepvPAlVldrrwdvlaaNraaraLlgdpaal 43 
                                       r+L+ + +   ++ld ++++ a N+a+  + g   + 
  gi|313122543|ref|YP_004038430.1| 239 RILETI-DDGIYILDENFQIAAVNEAVLEMTGYDRET 274
                                       666666.45689****************999985544 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.8
                          MLTR_LBD  51 lrlvfldpglrpliedweevaralvarLra..eaarrpddpalaalvaeLsaaspe 104
                                       +   ++ ++l ++++d  +var+l ar  a   + + p  ++++++v+ L++++p 
  gi|313122543|ref|YP_004038430.1| 778 VEVQLAAEALPSRLADFGAVARTLTARPDAltVVIELPSGSEIRKFVEYLREWYPG 833
                                       55566777888888888889998888765511346677777888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (917 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 6581.27
//
Query:       gi|313122544|ref|YP_004038431.1|  [L=94]
Description: hypothetical protein Hbor_37790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-17   62.3   0.1    4.4e-17   62.1   0.1    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   2.4e-21   4.4e-17       7      74 ..      18      86 ..      12      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.4e-21
                            HalOD1  7 taVveavaavegvdptel.epLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVe 74
                                       ++++ava+++gv+p ++ + L+d iD dA  +Lf    d+++ ++g+vsFt +g+eVt+++  +i V 
  gi|313122544|ref|YP_004038431.1| 18 WRIITAVADAKGVEPLDIdDRLHDIIDVDAVKQLFVGMPDKRSMTEGRVSFTLDGCEVTINERWDINVN 86
                                      68****************666*****************************************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 698.94
//
Query:       gi|313122545|ref|YP_004038432.1|  [L=1186]
Description: type I restriction-modification system methyltransferase subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-06   27.4   0.0     0.0068   15.7   0.0    2.6  2  N6_Mtase  N-6 DNA Methylase
    8.8e-05   23.0   0.0    0.00015   22.2   0.0    1.4  1  Eco57I    Eco57I restriction-modification methylase
     0.0023   18.0   0.0     0.0063   16.6   0.0    1.7  1  TaqI_C    TaqI-like C-terminal specificity domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-06    0.0068      19      96 ..     408     528 ..     384     534 .. 0.78
   2 !    8.7   0.0   0.00016      0.95     124     204 ..     601     688 ..     580     712 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                          N6_Mtase  19 eeegksgGeffTPrevsklivell.........................epksgesvyDpacGsggllvqaekvlke 70 
                                       ++  k +G f+TP++v++ ++  +                              + v+Dpa+G g llv +++ l +
  gi|313122545|ref|YP_004038432.1| 408 TTRRKTNGSFYTPESVVTYLAAQTagslvrdartaasdesatnvaadvrTRLLSRRVVDPAMGGGTLLVAVARRLAS 484
                                       3456889*********9998887779999************999997653344567*****************9987 PP

                          N6_Mtase  71 e..................dgktkelsiyGqeknettyrLakmN 96 
                                                               +  +yG++ n+ ++ +a++ 
  gi|313122545|ref|YP_004038432.1| 485 GirraarhadapvesfasiRRAVVSQCLYGVDRNPAATTVARLV 528
                                       78888888888888887666666677788888888888888765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00016
                          N6_Mtase 124 kkfdvvvaNppfnqkew.........kektlekde..rfrea....vapksnadlafllhiieslkpkGraavvlan 185
                                         fd+vv Npp+  +                  d   ++r+a      p+ n   afl  +   l+p+G +a+v+++
  gi|313122545|ref|YP_004038432.1| 601 VGFDAVVGNPPWKGTAGradisaridG------DTsaYLRKAfdstNGPQPNLYAAFLERAC-RLAPDGYVAFVVPD 670
                                       579*********988545664433322......22223333344437777888888988876.69999********* PP

                          N6_Mtase 186 gvLfrggkegkIrkalvek 204
                                         L r ++    r+ l++ 
  gi|313122545|ref|YP_004038432.1| 671 ALLVRLSVAS-ARRFLLDS 688
                                       **99976643.35555555 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.6e-08   0.00015       3      78 ..     603     694 ..     601     713 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.6e-08
                            Eco57I   3 fdviiGNPPYqeseakkelkaleek................akdiyqkFvekalkle.dkylaliiparflasgkgl 62 
                                       fd+++GNPP++ +  + + +a                    + ++y  F+e+a +l+ d+y+a+++p   l     +
  gi|313122545|ref|YP_004038432.1| 603 FDAVVGNPPWKGTAGRADISARIDGdtsaylrkafdstngpQPNLYAAFLERACRLApDGYVAFVVPDALL-VRLSV 678
                                       9**********999777766554448899************9***************99********9887.55666 PP

                            Eco57I  63 kefrekllkdkklkkl 78 
                                       ++ r++ll++  l++l
  gi|313122545|ref|YP_004038432.1| 679 ASARRFLLDSGGLTHL 694
                                       6667777776666655 PP

>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-06    0.0063       9     120 .]     823     959 ..     815     959 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-06
                            TaqI_C   9 ikrysieikgnYldlikkklknekakelfeekpKilvrdiskkldaaydekayyvlntlylliakdele........ 77 
                                       ++ry ++ ++  ++++++   +   k ++   pK+l+r++++ l+ ++d++++  l+++y    +  ++        
  gi|313122545|ref|YP_004038432.1| 823 VRRYALSARK--IRYVPEVAVS---KTVYD-PPKLLCRQTGRFLVGTLDTEGVANLKSVYDAHVRPRVDdgadddds 893
                                       5555555552..3444433333...56898.*****************************988888888889***** PP

                            TaqI_C  78 .......................vslkyllgiLNSklikfyykkiystlrggysrlkrkeleklPi 120
                                                                l  llg+LNS ++++y+    +     +++  +++ e lP+
  gi|313122545|ref|YP_004038432.1| 894 vadragnhdsvddgadadaadeeRLLLHLLGLLNSAVYNYYHYVRRNAYPAEFPQNNQRNYETLPV 959
                                       *******************98876677899*********887655555566788888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 7179.27
//
Query:       gi|313122546|ref|YP_004038433.1|  [L=418]
Description: hypothetical protein Hbor_37810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-07   29.7   0.7      0.054   12.6   0.0    3.3  3  Glyco_hydro_88  Glycosyl Hydrolase Family 88
    0.00013   21.6   0.9      0.002   17.7   0.0    2.4  2  Glyco_hydro_76  Glycosyl hydrolase family 76


Domain annotation for each model (and alignments):
>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00021       1.9      32      67 ..      80     115 ..      77     198 .. 0.83
   2 !   10.4   0.0   2.7e-05      0.24     212     298 ..     227     312 ..     222     317 .. 0.87
   3 !   12.6   0.0     6e-06     0.054      47     142 ..     293     399 ..     269     412 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS- CS
                    Glyco_hydro_88  32 Gvflsglleayeatgdkeyldyakawadslideggk 67 
                                       G+f s+ l++yeatg+++yl  a++   +l ++  +
  gi|313122546|ref|YP_004038433.1|  80 GLFASACLRLYEATGKETYLTEAEQLLGWLTEQTSP 115
                                       8999******************99977777776665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 2.7e-05
                                       -TTHHHHHHHHHHHHHHHHCTS-TTSSEBSBTT-TTTTSSBEHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH CS
                    Glyco_hydro_88 212 ekarqelinllrdlvkalaklqdeeglWhqilddgskesylEtSatalfvygLakgvnkglldkkkykkvaqkawka 288
                                       +++ ++l    ++l++++   qd++g W+ ++  ++++ + ++  t++++++L ++    +l +++ +k+++ +++ 
  gi|313122546|ref|YP_004038433.1| 227 YTDDESLSGRATELFEFVLHAQDDSGAWYYSMPASDSHLSHDNFHTGFVLESL-HEYATSDLGNDRARKAYEDGLEF 302
                                       566777888889999*********************99***************.88888888899999999999888 PP

                                       HHHCEE-TTS CS
                    Glyco_hydro_88 289 llkkaveedG 298
                                        +++  e dG
  gi|313122546|ref|YP_004038433.1| 303 YVRELFEADG 312
                                       8888777776 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 6e-06
                                       -HHHHHHHHHHHHHCCCTTS-......CTTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B.TTS.B. CS
                    Glyco_hydro_88  47 dkeyldyakawadslideggk......telelDdidigllllllyeltkderykeaaeeladyvlakpprtseGgfw 117
                                       +k+y d ++ ++++l++ +g       t++  D+++ ++ l++l  + +d++++e a +++d+ +a+ ++ seG f 
  gi|313122546|ref|YP_004038433.1| 293 RKAYEDGLEFYVRELFEADGApkfesdTSKPYDAHASAQALITL-IQSDDSDANEVAARVYDWSIANLYD-SEGYFY 367
                                       34466666669999999999999999999999*****9999887.57899999*****************.99**** PP

                                       S......BTTSTTEEETHH.HHHHHHHHHHHH CS
                    Glyco_hydro_88 118 h......kkkepeqlWlDg.LfMaipllakls 142
                                       +       ++ p+  W  g +  a+  la++ 
  gi|313122546|ref|YP_004038433.1| 368 RrigrffDDETPYIRWSQGwMTLALATLARAQ 399
                                       99999998888888887762233444455555 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.3e-07     0.002     157     188 ..      80     111 ..      75     125 .. 0.88
   2 ?    1.8   0.1     0.015   1.3e+02     175     203 ..     344     370 ..     326     411 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHHHHHHH--CHHHHHHHHHHHHHHH CS
                    Glyco_hydro_76 157 gplfqlaarLarytgnetYlewAekvwdWved 188
                                       g ++ +++rL+++tg+etYl+ Ae+   W+++
  gi|313122546|ref|YP_004038433.1|  80 GLFASACLRLYEATGKETYLTEAEQLLGWLTE 111
                                       78999************************986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHSCSBTTTS-B-SEE CS
                    Glyco_hydro_76 175 YlewAekvwdWvedvgliddedwlvyDga 203
                                         e+A +v+dW+ + +l  d+++++y ++
  gi|313122546|ref|YP_004038433.1| 344 ANEVAARVYDWSIA-NLY-DSEGYFYRRI 370
                                       45789999999999.676.7777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3256.60
//
Query:       gi|313122547|ref|YP_004038434.1|  [L=46]
Description: hypothetical protein Hbor_37820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       165  (0.00920297); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 319.83
//
Query:       gi|313122548|ref|YP_004038435.1|  [L=341]
Description: membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-77  258.6   5.6    8.8e-77  258.4   5.6    1.0  1  DUF1616      Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
       0.02   14.7   0.3       0.02   14.7   0.3    2.0  2  DUF2976      Protein of unknown function (DUF2976)
      0.048   13.8   0.0      0.087   13.0   0.0    1.3  1  Transglut_C  Transglutaminase family, C-terminal ig like doma


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.4   5.6   1.5e-80   8.8e-77       3     293 .]      13     322 ..      11     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 258.4 bits;  conditional E-value: 1.5e-80
                           DUF1616   3 vlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPe.....................krdidgieRlaL 58 
                                        +al++ ++++v +l+  + R++l+ +lvLflPGYal +++FP+                     + ++  +eR+aL
  gi|313122548|ref|YP_004038435.1|  13 TIALTAGAILAVLNLPPVTARAALAGILVLFLPGYALTTLVFPAtketrlsvgdvpsafvgnntkHAGVPFLERAAL 89 
                                       5778888888999999*************************************************99********** PP

                           DUF1616  59 SfglSiaivpliglvlnvtpwgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleekses 135
                                       S+glS+a+vpl+++ l+v+ +++ +  +++++ +f +++al++ vrR+r+ +e r+ vp+ + +++ +++ +++  s
  gi|313122548|ref|YP_004038435.1|  90 SIGLSVALVPLFAWSLEVSGVEFLAPNVAAACGGFAIVAALLGGVRRLRTAAETRYVVPIGT-VAAYRNAAHDR--S 163
                                       **********************************************************9876.77788888885..5 PP

                           DUF1616 136 rldkalnvlLvvsivlavaalgyavvaPke..gekfTelyllgedgd.elvaenypteltagesqevivgieNhEhe 209
                                       + d++lnv+Lv ++v+a++ + +a+v+P++  + ++T+ +ll+e +d  lva++yp++lt+ges e+++ +eN+E+e
  gi|313122548|ref|YP_004038435.1| 164 NWDNVLNVALVGAVVVATVVVTFALVSPASvaSASYTQASLLTEADDgSLVASDYPQNLTVGESGELVLLVENYEQE 240
                                       68*************************99877899****************************************** PP

                           DUF1616 210 evnYtvvvllqevtdeeevevlerteldrrevtladnetweqelevepeatgenlrleflLYkdevpeeptteeayr 286
                                       ++ Ytvv++lq+v  e+++ev++++e+dr++ t++ +++w+ ++ev+p+ +genlrl++l Yk+++pe+pt+e++yr
  gi|313122548|ref|YP_004038435.1| 241 TTRYTVVAQLQRV--ESNGEVTATSEIDRFSETVETGDRWQLTHEVAPSIPGENLRLTYLVYKGDAPENPTIESSYR 315
                                       ***********96..555777799***************************************************** PP

                           DUF1616 287 slhlwVn 293
                                       ++ lw++
  gi|313122548|ref|YP_004038435.1| 316 HVTLWMD 322
                                       *****85 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.4       1.5   9.1e+03      30      43 ..      11      24 ..       5      27 .. 0.57
   2 ?   14.7   0.3   3.3e-06      0.02      41      79 ..     145     183 ..     120     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.5
                           DUF2976 30 llgLvlaavaflaV 43
                                      ++ ++l a a+laV
  gi|313122548|ref|YP_004038435.1| 11 VATIALTAGAILAV 24
                                      34455555566665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.3e-06
                           DUF2976  41 laVakaalkkfneisegkaewgkfgltlvvGvvllvvvi 79 
                                       ++V   +++ ++++ +++++w ++  +++vG+v+++ v+
  gi|313122548|ref|YP_004038435.1| 145 YVVPIGTVAAYRNAAHDRSNWDNVLNVALVGAVVVATVV 183
                                       567788999*************************98776 PP

>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.087       8      81 ..     219     291 ..     217     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                                       SSCEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-HHSHEE CS
                       Transglut_C   8 lesavlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlkilpskyGe 81 
                                       ++++ +g + ++++l+ N  +e+ ++ ++    q ve+nG + a ++ + +  t+e +   +++ ++ ps  Ge
  gi|313122548|ref|YP_004038435.1| 219 PQNLTVGESGELVLLVENYEQET-TRYTVVAQLQRVESNGEVTATSEIDRFSETVETGDRWQLTHEVAPSIPGE 291
                                       68999**************8888.888999999********************************999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2342.18
//
Query:       gi|313117185|ref|YP_004044168.1|  [L=316]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-25   89.8   0.0    3.4e-25   89.1   0.0    1.3  1  ABC_tran      ABC transporter
    2.4e-14   53.9   0.2    2.6e-08   34.0   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.4e-06   28.2   0.0    6.1e-06   26.9   0.0    1.7  2  DUF4162       Domain of unknown function (DUF4162)
    0.00021   21.0   0.1    0.00047   19.8   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0012   18.3   0.0       0.61    9.5   0.0    2.3  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0022   18.5   0.0     0.0033   18.0   0.0    1.3  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.023   13.7   0.0      0.038   13.0   0.0    1.2  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.048   12.6   0.0       0.28   10.0   0.0    2.0  2  AAA_10        AAA-like domain
      0.064   13.0   0.0       0.17   11.6   0.0    1.6  2  AAA_15        AAA ATPase domain
       0.12   12.4   0.0       0.24   11.4   0.0    1.5  1  SicP-binding  SicP binding
       0.17   11.8   0.0       0.26   11.2   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
       0.19   11.1   0.0        4.7    6.5   0.0    2.2  2  Mg_chelatase  Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   2.3e-28   3.4e-25       1     136 [.      19     157 ..      19     158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 2.3e-28
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ +++++++ge+ +++G+nG+GKSt + +l+g   pt+G+  + g d +e + +  r++ gv+p   ++ p+ t r
  gi|313117185|ref|YP_004044168.1|  19 LDSLEMSIENGEVFGFLGPNGSGKSTTIDILLGFIYPTSGSASVFGIDPTE-NATAIRQRTGVVPDGYEVMPDWTGR 94 
                                       68899*********************************************9.9************************ PP

                                       HH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++        + d++++++l+++gl e++d+v+    + +S G++qr+ l +a + +p+llllDEpt
  gi|313117185|ref|YP_004044168.1|  95 DHvefeldsrNVDDDPDALLDRFGLLEDADRVA----TGYSRGMRQRLLLSMAAAGEPDLLLLDEPT 157
                                       99***9999888899*****************9....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.4e-06    0.0021       2      22 ..      32      52 ..      31      85 .. 0.78
   2 !   34.0   0.0   1.8e-11   2.6e-08     231     297 ..     124     187 ..      91     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       ++ GpNgsGKS+ +d+l ++
  gi|313117185|ref|YP_004044168.1| 32 FGFLGPNGSGKSTTIDILLGF 52
                                      5789**************765 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 1.8e-11
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++ a+  S G+++ l l  a +   ++ +lll+DEp +gL+P  +r   e++++++++ga +++++H
  gi|313117185|ref|YP_004044168.1| 124 DRVATGYSRGMRQRLLLSMAAA--GEP-DLLLLDEPTTGLDPNGIRLMREFIRDERARGATIFFSSH 187
                                       4556667899999844444444..444.***************999999****************** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.6   1.1e+04      38      55 ..      95     115 ..      82     119 .. 0.61
   2 !   26.9   0.0   4.1e-09   6.1e-06       2      80 ..     212     296 ..     212     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.6
                                       S-EEEEE-..-.--------- CS
                           DUF4162  38 gelelkle..d.eeaanellk 55 
                                       +++e++l+  + ++++ +ll+
  gi|313117185|ref|YP_004044168.1|  95 DHVEFELDsrNvDDDPDALLD 115
                                       455555554355566666665 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 4.1e-09
                                       -HHHHHTTS-SSEEE.EE.....-------..---EEEE-TTS-EEEEE-------------.----EEEEEEEE-- CS
                           DUF4162   2 tleeiKrsygknrie.ve.....adaeelleepgveeveeeggelelkledeeaanellkal.tsgveirsFeeeeP 71 
                                       +++ ++++ g n+i  v+     +d ++l +++g+e +e  g++l++++ ++    + l++l + g++ ++Fe e +
  gi|313117185|ref|YP_004044168.1| 212 SIDSLRNAVGDNTILqVSvdhvpDDIDSLTTLDGIENLEVSGTTLRVQCAHGRHL-DALNHLdRLGATPQRFETETA 287
                                       5799*****99999989998998889999999**********9999999986555.5566775689*********** PP

                                       -HHHHHHHH CS
                           DUF4162  72 sLndIFiek 80 
                                       sL+dIF  +
  gi|313117185|ref|YP_004044168.1| 288 SLEDIFSAY 296
                                       ******765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   3.1e-07   0.00047      16      50 ..      23      57 ..      15      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.1e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +++i+  +++ + Gp+GsGKST +D +   ++p++
  gi|313117185|ref|YP_004044168.1| 23 EMSIENGEVFGFLGPNGSGKSTTIDILLGFIYPTS 57
                                      56777455999**************8888888765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00041      0.61      29      44 ..      34      49 ..      19      56 .. 0.83
   2 !    6.4   0.0    0.0037       5.5     149     212 ..     138     202 ..     125     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00041
                                      EEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 29 ivGpNGSGKsnlldAi 44
                                       +GpNGSGKs  +d +
  gi|313117185|ref|YP_004044168.1| 34 FLGPNGSGKSTTIDIL 49
                                      57********999965 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0037
                                       HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                       Ll+++ ++    l llDe    LD + ++ + e+++ ++ + a ++  s+r  ++e +   vg+ 
  gi|313117185|ref|YP_004044168.1| 138 LLLSMAAAGEPDLLLLDEPTTGLDPNGIRLMREFIRDERARgATIFFSSHRLAQVESVCDRVGIL 202
                                       7888888888899***********************6655549999999*999999887777775 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0033      20      47 ..      30      57 ..      13     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                            AAA_23 20 gltlItGpNGaGKTTildAiklaLyget 47
                                       ++ + GpNG+GK+T +d +    y  +
  gi|313117185|ref|YP_004044168.1| 30 EVFGFLGPNGSGKSTTIDILLGFIYPTS 57
                                      6899**************9987777644 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.5e-05     0.038      19      71 ..      19      71 ..       8      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                                      HHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------ CS
                              MeaB 19 lerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspf 71
                                      l+ l  +  + +v G+ G  G+Gkst+++ l   +       +v  +DP+ + 
  gi|313117185|ref|YP_004044168.1| 19 LDSLEMSIENGEVFGFLGPNGSGKSTTIDILLGFIYPTSGSASVFGIDPTENA 71
                                      666777777899******************999999999999*******9765 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00019      0.28      19      66 ..      27      76 ..      16     127 .. 0.76
   2 ?   -0.0   0.0      0.21   3.2e+02     256     286 ..     162     192 ..     147     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                            AAA_10 19 tnasasliiGdlGnGKSvlakllvlyisllg..gkaliiDpkkerekfke 66
                                      +n     ++G+ G GKS ++ +l  +i        ++ iDp+++    ++
  gi|313117185|ref|YP_004044168.1| 27 ENGEVFGFLGPNGSGKSTTIDILLGFIYPTSgsASVFGIDPTENATAIRQ 76
                                      455555799*************9877776652267888****99766554 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.21
                            AAA_10 256 aeGkkllkelvRiGRsynaavylvtqsadDv 286
                                       ++G +l++e +R+ R+  a +++ ++    v
  gi|313117185|ref|YP_004044168.1| 162 PNGIRLMREFIRDERARGATIFFSSHRLAQV 192
                                       57999******************99987655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.17      18      47 ..      23      53 ..      18      88 .. 0.82
   2 ?   -1.7   0.0       1.2   1.8e+03     304     349 ..     133     173 ..     122     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsilealdlFl 47
                                      e+++++  +  + G+N+sGKS+ +++l  F+
  gi|313117185|ref|YP_004044168.1| 23 EMSIENGeVFGFLGPNGSGKSTTIDILLGFI 53
                                      5555555577899*************98776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                            AAA_15 304 llllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllk 349
                                        +   ll+ +a  +     ++++ll++EP + L p+  + + + ++
  gi|313117185|ref|YP_004044168.1| 133 GMRQRLLLSMAAAG-----EPDLLLLDEPTTGLDPNGIRLMREFIR 173
                                       44444444555555.....8899999**999998887777766665 PP

>> SicP-binding  SicP binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.24      45      66 ..       7      28 ..       4      31 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                      HHHHHTTSCHHHHHHHHHHHH- CS
                      SicP-binding 45 laLskkyGeeavkdaldysair 66
                                      ++L+k+yGe+++ d+l++s  +
  gi|313117185|ref|YP_004044168.1|  7 HSLTKRYGETTALDSLEMSIEN 28
                                      89****************9765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.26      82     121 ..      11      51 ..       1      76 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                       --TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  82 vsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        +  ++++l++l+  +++ ++  ++G+ G GKSt i+ ll+
  gi|313117185|ref|YP_004044168.1|  11 KRYGETTALDSLEMSIENgEVFGFLGPNGSGKSTTIDILLG 51 
                                       55566788999*****9999****************99876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0031       4.7       6      49 ..      13      56 ..       8      76 .. 0.84
   2 ?    2.2   0.0     0.068     1e+02      11      34 ..     136     159 ..     131     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0031
                      Mg_chelatase  6 kGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                       G+++a   le+++  g  + ++Gp GsGK+  +  l + + p 
  gi|313117185|ref|YP_004044168.1| 13 YGETTALDSLEMSIENGEVFGFLGPNGSGKSTTIDILLGFIYPT 56
                                      578888899999999999999**********9999887766554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.068
                      Mg_chelatase  11 akraleiaaaGgHnlllvGppGsG 34 
                                       ++  l +aaaG+ +lll+  p +G
  gi|313117185|ref|YP_004044168.1| 136 QRLLLSMAAAGEPDLLLLDEPTTG 159
                                       567899************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2295.39
//
Query:       gi|313117186|ref|YP_004044169.1|  [L=318]
Description: hypothetical protein Hbor_29690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-23   81.1   5.9    9.3e-22   77.6   5.9    1.9  1  ABC2_membrane_2  ABC-2 family transporter protein
    9.5e-05   22.0   1.2    0.00017   21.2   1.2    1.5  1  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.01   15.8   2.2       0.01   15.8   2.2    1.5  2  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   5.9   1.6e-25   9.3e-22      80     288 .]      86     317 ..      30     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 1.6e-25
                   ABC2_membrane_2  80 imavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivl 156
                                       ++ +++ + a ++g+ +++g+ ++g ++l L +P++R+++++ Kf+g  ++  +i v+ lat ++++ai+ +l  ++
  gi|313117186|ref|YP_004044169.1|  86 AIRLFGILGASVAGYSLVTGDQASGRIRLILKLPHTRWKYVFEKFLGEGLA--LITVTSLAT-ITGFAISTILYGPP 159
                                       34444444499************************************9998..455666666.669*********** PP

                   ABC2_membrane_2 157 aledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindfl 233
                                       ++   + ++++   +ll  v l+++++ S+ +++sr+a+a+ ++l++    +++ v   ++    + ++   +++f 
  gi|313117186|ref|YP_004044169.1| 160 PVLPAVEVLIVQEGFLL--VWLSIATATSMAVKTSRRAIAVPVALYLSA-WAWKRVMNSILRGIGEQSI--AVRLFA 231
                                       **999999999998888..78************************9876.9999999998888888888..99**** PP

                   ABC2_membrane_2 234 sllsptsayntllneilagsdlna................................lgstatnllilllllavllvl 278
                                         l p +ayn+ +n+i++  + ++                                 +s + ++l+l+l+ +v++ l
  gi|313117186|ref|YP_004044169.1| 232 YRLEPSRAYNVTVNWIFNLPN-SDlmapllmehvdpngstiigprivselvgdvpwFLSEWVSALVLVLWGTVPMLL 307
                                       *****************9984.33588************************************************** PP

                   ABC2_membrane_2 279 gyvlFkrkDl 288
                                       +y +F + D+
  gi|313117186|ref|YP_004044169.1| 308 AYRRFATTDI 317
                                       *****99885 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.2   2.8e-08   0.00017      41     145 ..      88     193 ..      40     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.8e-08
                   ABC2_membrane_5  41 silslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlf.vlililiailitlllliiavlikgnvtisev 116
                                        ++ ++ +++   +++  D+ s+  +++l LP tr+++V +K+l+ +l li++++l t+  ++i+++++g+  + ++
  gi|313117186|ref|YP_004044169.1|  88 RLFGILGASVAGYSLVTGDQASGRIRLILKLPHTRWKYVFEKFLGeGLALITVTSLATITGFAISTILYGPPPVLPA 164
                                       444455555556689999**************************95677777777777777889*******888888 PP

                   ABC2_membrane_5 117 llsiliglvialiflaivlPlyfkfgvek 145
                                       + ++++  ++ l++l+i        ++++
  gi|313117186|ref|YP_004044169.1| 165 VEVLIVQEGFLLVWLSIATATSMAVKTSR 193
                                       88888888888888888766666655444 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   2.2   1.7e-06      0.01       8     171 ..      40     202 ..      38     206 .. 0.72
   2 ?   -3.3   0.0       1.2   7.2e+03     136     156 ..     286     306 ..     278     313 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-06
                   ABC2_membrane_4   8 KlkrskivwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknL 84 
                                       Klk +   wl  ++++++ + a +      ++g +  + y  ++f + + l+  l   + +  l++  + ++ ++ +
  gi|313117186|ref|YP_004044169.1|  40 KLKNR-YYWLYGFIIFVAGMGAATDLLFNPASGYQGGSAYVIATFAWAIRLFGILGASVAGYSLVTGDQASGRIRLI 115
                                       77766.56777777777766666666666789999**************999999999999999999********** PP

                   ABC2_membrane_4  85 ltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvg..fsvklvlellkkclelgllvffavlpiialv 159
                                       l +P +r k+++ K++   l  + ++ ++++  ++++ ++ +++  + +  vl++   +l++ l +  a++  +a+ 
  gi|313117186|ref|YP_004044169.1| 116 LKLPHTRWKYVFEKFLGEGLALITVTSLATITGFAISTILYGPPpvLPAVEVLIVQEGFLLVWLSI--ATATSMAVK 190
                                       ****************99988887777777777887777776541233333443333333333322..333335666 PP

                   ABC2_membrane_4 160 llkksyvlplil 171
                                       +  +  ++p++l
  gi|313117186|ref|YP_004044169.1| 191 TSRRAIAVPVAL 202
                                       777777777766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.2
                   ABC2_membrane_4 136 ellkkclelgllvffavlpii 156
                                       ++l +++   +lv+  ++p++
  gi|313117186|ref|YP_004044169.1| 286 WFLSEWVSALVLVLWGTVPML 306
                                       555555555555665666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2279.33
//
Query:       gi|313117187|ref|YP_004044170.1|  [L=128]
Description: hypothetical protein Hbor_29700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 981.34
//
Query:       gi|313117188|ref|YP_004044171.1|  [L=101]
Description: hypothetical protein Hbor_29710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-12   46.8   0.0    4.3e-12   46.4   0.0    1.2  1  DDE_Tnp_IS240  DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   2.4e-16   4.3e-12       2      47 ..      27      73 ..      26      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.4e-16
                     DDE_Tnp_IS240  2 kswrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaf 47
                                      k+++vDE +vki+G+w++ly+a+D e++ ild+ ++ r +t++a+a+
  gi|313117188|ref|YP_004044171.1| 27 KRVAVDEAAVKINGEWSWLYAAIDTETKlILDVELFGRHGTDPAAAL 73
                                      799****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 800.60
//
Query:       gi|313117189|ref|YP_004044172.1|  [L=148]
Description: hypothetical protein Hbor_29720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-09   37.6  27.7    2.4e-09   37.3  27.7    1.1  1  DUF5518          Family of unknown function (DUF5518)
     0.0064   16.6  11.3     0.0091   16.2  11.3    1.3  1  DUF3792          Protein of unknown function (DUF3792)
  ------ inclusion threshold ------
      0.093   11.5   1.7      0.096   11.5   1.7    1.1  1  ALMT             Aluminium activated malate transporter
       0.11   12.7   8.5       0.28   11.4   4.8    2.1  2  YbjM             Putative inner membrane protein of Enterobac
       0.13   12.6  11.4       0.06   13.7   8.9    1.7  2  MgtC             MgtC family


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3  27.7   6.8e-13   2.4e-09       1     117 [.      14     131 ..      14     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 6.8e-13
                           DUF5518   1 wraaliGavvaivlslllg......lllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvl 71 
                                       wr aliGa++++++ ++++      ++l++ ++++g ++gG++a+  + +   +g++aG+l G+i+++ ++v ++ +
  gi|313117189|ref|YP_004044172.1|  14 WRFALIGALASLPVAAVVNslpnseATLGGGVMIIGAFIGGAIAAIRSASPDAAGLRAGFLGGVIAVLTFIVTVVSA 90 
                                       9******************9999*99*******************99999988888888888888877776666666 PP

                           DUF5518  72 llglvaaigglagfvallvalllvvllllvvllvilgaiGGaiGgl 117
                                       +       g++a  +++ +++ ++  +l+++++ i+g+ +G++Gg+
  gi|313117189|ref|YP_004044172.1|  91 A-----SSGTVAAWTLSRIVFWVAGGVLVLCVAPIFGLGCGRVGGW 131
                                       6.....46777777778888888889999****************9 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  11.3   2.5e-06    0.0091      14     109 ..      18     112 ..      10     132 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                           DUF3792  14 vitlilllilalllyftslsekvlsililiililsvfigGflagkkakk...kgllnGllvGllyflillllsllik 87 
                                       +i ++++l +a++++    se+   +l   ++i+++figG +a+ ++ +    gl  G+l G++ +l  +++++++ 
  gi|313117189|ref|YP_004044172.1|  18 LIGALASLPVAAVVNSLPNSEA---TLGGGVMIIGAFIGGAIAAIRSASpdaAGLRAGFLGGVIAVLT-FIVTVVSA 90 
                                       4455555555555544444443...45777899999*******9998653338999999999998888.88888886 PP

                           DUF3792  88 ksgsafslkllikllllllaga 109
                                        s+ + ++++l ++++ +++g+
  gi|313117189|ref|YP_004044172.1|  91 ASSGTVAAWTLSRIVFWVAGGV 112
                                       6666556666655555444443 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7   2.7e-05     0.096     123     166 ..      75     118 ..      18     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                              ALMT 123 gvlvflLTFclvvvsgyrtdevielAvkRfltiaiGaliclivs 166
                                       g ++ +LTF++ vvs   +++v   + +R++  + G++++l+v 
  gi|313117189|ref|YP_004044172.1|  75 GGVIAVLTFIVTVVSAASSGTVAAWTLSRIVFWVAGGVLVLCVA 118
                                       789*****************************999999999875 PP

>> YbjM  Putative inner membrane protein of Enterobacteriaceae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.025        91      62      80 ..      16      34 ..       6      42 .. 0.81
   2 ?   11.4   4.8   7.7e-05      0.28      46     112 ..      52     118 ..      36     122 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.025
                              YbjM 62 vpllGallaapvcllvlkl 80
                                       +l+Gal+++pv  +v +l
  gi|313117189|ref|YP_004044172.1| 16 FALIGALASLPVAAVVNSL 34
                                      699*********9999877 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.7e-05
                              YbjM  46 lPGivaallskekrllvpllGallaapvcllvlklvlaseeslwqelayllS.avFWcalGallvlll 112
                                       + G++aa+ s++       +G l ++   +l + ++++s+ s   + a++lS  vFW a G l+++++
  gi|313117189|ref|YP_004044172.1|  52 IGGAIAAIRSASPDAAGLRAGFLGGVI-AVLTFIVTVVSAASSGTVAAWTLSrIVFWVAGGVLVLCVA 118
                                       567777777766655544455444443.3444445567778888999****95589999888877665 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.1   3.8e+03      84      94 ..      14      24 ..       9      36 .. 0.54
   2 ?   13.7   8.9   1.7e-05      0.06       1      66 [.      46     113 ..      46     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                              MgtC 84 wvtaaiGllvg 94
                                      w  a+iG+l+ 
  gi|313117189|ref|YP_004044172.1| 14 WRFALIGALAS 24
                                      44455555443 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.7e-05
                              MgtC   1 LllAlllGlliGleRelrekaaGlRTfaLvalgaalfvllslelae..srvaaqvvsgigflgagvil 66 
                                       +++ +++G++i + R+ +  aaGlR   L +++a+l  ++++  a+    vaa+++s i+f +ag +l
  gi|313117189|ref|YP_004044172.1|  46 MIIGAFIGGAIAAIRSASPDAAGLRAGFLGGVIAVLTFIVTVVSAAssGTVAAWTLSRIVFWVAGGVL 113
                                       678999***********************999999999996666557867777777777777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1046.08
//
Query:       gi|313117190|ref|YP_004044173.1|  [L=49]
Description: hypothetical protein Hbor_29730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 327.10
//
Query:       gi|313117191|ref|YP_004044174.1|  [L=185]
Description: hypothetical protein Hbor_29740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.4   3.5       0.22   12.1   2.2    1.7  2  FadA      Adhesion protein FadA


Domain annotation for each model (and alignments):
>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.2   1.2e-05      0.22      36      79 ..      30      73 ..      28      81 .. 0.79
   2 ?   -1.5   0.0       0.2   3.7e+03      32      52 ..     102     122 ..      94     132 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                              FadA 36 kkkelkakieeklakleadsevrfykdeYkellkeyksllkele 79
                                      ++++ ++ +e++++  +a +++r+++++Y ++  + +++ ++ +
  gi|313117191|ref|YP_004044174.1| 30 QRQAGEEIVEQQMDAEKALENYRWFRSQYHDIEAQREQVENSYD 73
                                      456666667777777677**************999888888766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.2
                              FadA  32 aklakkkelkakieeklakle 52 
                                       +++  ++++ +++ ++++   
  gi|313117191|ref|YP_004044174.1| 102 ERITGNQNMLESMVAEYNARS 122
                                       444555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1380.67
//
Query:       gi|313117192|ref|YP_004044175.1|  [L=220]
Description: hypothetical protein Hbor_29750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1561.49
//
Query:       gi|313117193|ref|YP_004044176.1|  [L=158]
Description: hypothetical protein Hbor_29760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1134.75
//
Query:       gi|313117194|ref|YP_004044177.1|  [L=98]
Description: hypothetical protein Hbor_29770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 750.11
//
Query:       gi|313117195|ref|YP_004044178.1|  [L=148]
Description: universal stress protein UspA-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-31  109.4   0.0    2.1e-31  109.3   0.0    1.0  1  Usp             Universal stress protein family
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.051   13.6   0.0    1.2  1  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.0   2.4e-35   2.1e-31       1     138 [.       9     146 ..       9     148 .] 0.98

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 2.4e-35
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my +IlV++Dgs+ +++ le++ ela+++ga+l++l v+d++ +g+++++ + ++   ++   ae  a+   ++a +
  gi|313117195|ref|YP_004044178.1|   9 MYTNILVPTDGSDLAERGLEHGMELAREHGAHLHILFVVDESVYGSTPALSSYEAFLDKMADDAEDLAEDFIEEATE 85 
                                       9*******************************************************9999999999999999***** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVl 138
                                       +g++ +  v+ g p eeil + +e+++d iV+G+rg  g+    +GSv+++v+r+a++pV+
  gi|313117195|ref|YP_004044178.1|  86 QGIDSTMSVLRGVPHEEILNYTQENNIDAIVMGKRGAAGVGYPHIGSVTDRVIREAEVPVI 146
                                       ************************************************************8 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.6e-06     0.051      18      95 ..      32     118 ..      26     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-06
                                       HHHHCTTSEEEEEEEE-HH..HHTCG.S-CHHHHHHHHHHHHHHHHHH....HHTT..--EEEEESSHHHHHHHHHH CS
                    DNA_photolyase  18 aaAaasgepvipvfvldpe..kahkl.rvgaarvdfllesLadLdeeL....relg..irLvvrrgdpadvlpelak 85 
                                       + A+++g++++ +fv+d++  ++ +      a  d ++   +dL+e++     e+g  +++ v+rg p++++ ++ +
  gi|313117195|ref|YP_004044178.1|  32 ELAREHGAHLHILFVVDESvyGSTPAlSSYEAFLDKMADDAEDLAEDFieeaTEQGidSTMSVLRGVPHEEILNYTQ 108
                                       56999**************75222225556777778888888888888777745555599***************** PP

                                       HCTECEEEEE CS
                    DNA_photolyase  86 elgasavvan 95 
                                       e++++a+v+ 
  gi|313117195|ref|YP_004044178.1| 109 ENNIDAIVMG 118
                                       ******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1046.99
//
Query:       gi|313117196|ref|YP_004044179.1|  [L=313]
Description: hypothetical protein Hbor_29800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2315.78
//
Query:       gi|313117197|ref|YP_004044180.1|  [L=60]
Description: hypothetical protein Hbor_29810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.21   11.6   0.6       0.24   11.4   0.6    1.1  1  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   1.3e-05      0.24      18      37 ..      33      54 ..      28      59 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.3e-05
                                      XXXXXXXXXXXXXXXXX..XXX CS
                   Gram_pos_anchor 18 ifltaaGllallggllL..lvk 37
                                      +f+ +++l +l gg+l+  +v+
  gi|313117197|ref|YP_004044180.1| 33 LFFSIGALVILGGGALFvgYVR 54
                                      6888888888888888876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 441.67
//
Query:       gi|313117198|ref|YP_004044181.1|  [L=130]
Description: hypothetical protein Hbor_29820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-10   39.3  10.1    5.2e-10   39.1  10.1    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00049   20.1   4.3    0.00049   20.1   4.3    1.7  2  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.27   10.3  12.4       0.42    9.7  12.4    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1  10.1   8.7e-14   5.2e-10      99     207 ..       2     105 ..       1     125 [. 0.76

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 8.7e-14
                   ABC2_membrane_2  99 gEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvlllllv 175
                                       gE+e+gTlkl L +P++++++ll+K++++l +   ++v+ll  +++  +++ ++   ++l ++ l++   +++    
  gi|313117198|ref|YP_004044181.1|   2 GERESGTLKLRLGLPATKRDVLLAKLVSRLSL---VVVTLLPLFVVLGVLMSSVYGGIPLVAFGLTAGWLLFYTS-- 73 
                                       8*******************************...6666666655555666666667777777766555554444.. PP

                   ABC2_membrane_2 176 vflalglllSsvarssreaaalalglfvvlai 207
                                       v +++ +++S+ + s  + +a+  g +++++ 
  gi|313117198|ref|YP_004044181.1|  74 VWTTFVVGVSAAFTSPFRVLAAICGTYLFFSP 105
                                       7799******9999987777777777777754 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   4.3   8.2e-08   0.00049      75     165 ..       3     100 ..       1     109 [. 0.70
   2 ?    0.6   4.1     0.082   4.9e+02     124     158 ..      76     109 ..      58     129 .. 0.36

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.2e-08
                   ABC2_membrane_4  75 EeqndtlknLltiPvsrtklllaKlivllllsvllml.vtflitvlfallsgfvg.fsvkl.....vlellkkclel 144
                                       E++++tlk  l +P +++ +llaKl+  l l+v+ +l +++++ vl++ + g+++ + ++l     ++++ ++++ +
  gi|313117198|ref|YP_004044181.1|   3 ERESGTLKLRLGLPATKRDVLLAKLVSRLSLVVVTLLpLFVVLGVLMSSVYGGIPlVAFGLtagwlLFYTSVWTTFV 79 
                                       99***********************9877766665552666888999999888762333322233345555566666 PP

                   ABC2_membrane_4 145 gllvffavlpiialvllkksy 165
                                       + +++++++p  +l+++  +y
  gi|313117198|ref|YP_004044181.1|  80 VGVSAAFTSPFRVLAAICGTY 100
                                       666677777777776665555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.082
                   ABC2_membrane_4 124 sgfvgfsvklvlellkkclelgllvffavlpiial 158
                                        +fv + v++ + + +++l  + +++++++p+  +
  gi|313117198|ref|YP_004044181.1|  76 TTFV-VGVSAAFTSPFRVLAAICGTYLFFSPVTRI 109
                                       2222.222333333333333333333333333222 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  12.4   7.1e-05      0.42     186     281 ..       3     104 ..       1     128 [. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7.1e-05
                   ABC2_membrane_3 186 Ekesrikelqlvsgvsplqywlskilg...dflvyllqlllill.l...afglgipfgnlglllllfllfglayial 255
                                       E+es++++l l  + ++   +l+k+++   +++v ll+l+++l+ l   ++g gip   +gl+  ++l++  + +++
  gi|313117198|ref|YP_004044181.1|   3 ERESGTLKLRLGLPATKRDVLLAKLVSrlsLVVVTLLPLFVVLGvLmssVYG-GIPLVAFGLTAGWLLFYTSVWTTF 78 
                                       9999999999999999999999998651115666666666666533566666.9*********************** PP

                   ABC2_membrane_3 256 gyllsslfknsetaqilifivillls 281
                                       +  +s++f+++  + ++i+ + l++s
  gi|313117198|ref|YP_004044181.1|  79 VVGVSAAFTSPFRVLAAICGTYLFFS 104
                                       ***********998888877777443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 944.89
//
Query:       gi|313117199|ref|YP_004044182.1|  [L=333]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-17   63.6   0.0    7.3e-17   61.4   0.0    2.1  2  Glycos_transf_1  Glycosyl transferases group 1
    1.9e-15   57.3   0.0    3.4e-15   56.4   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.6e-13   50.5   0.0    3.6e-12   46.9   0.0    2.4  3  Glyco_trans_1_4  Glycosyl transferases group 1
    6.7e-09   36.0   0.0    1.4e-08   35.0   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    4.6e-07   30.4   0.0    8.6e-07   29.5   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.45   1.6e+03      85     102 ..      96     113 ..      88     123 .. 0.85
   2 !   61.4   0.0     2e-20   7.3e-17      72     171 ..     216     311 ..     151     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.45
                                       SHHHHHHCESEEEEEESS CS
                   Glycos_transf_1  85 dleellknadifvlpsis 102
                                        ++ ++k+ad +++ps++
  gi|313117199|ref|YP_004044182.1|  96 YVDFFYKRADHLIAPSEY 113
                                       57889**********987 PP

  == domain 2  score: 61.4 bits;  conditional E-value: 2e-20
                                       TCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHH CS
                   Glycos_transf_1  72 sdnviflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaeal 148
                                         n+ f g+ +  d+  ++ ++d+f++p  sE  Gi+++EA ++g+p+++ +++ +  ++++g    + k  ++e++
  gi|313117199|ref|YP_004044182.1| 216 PSNCVFPGFAD--DVRDVYAASDVFFFPTKSETEGISIIEAAYCGIPIVTRDIPVYEPLLEHGT--HCLKGSSVEEF 288
                                       45899*****9..***************************************************..6888889**** PP

                                       HHHHHHHHHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 149 aeairklledeelrerlgenark 171
                                       +++i+ l +d+elr+rlgenar+
  gi|313117199|ref|YP_004044182.1| 289 KNHIKLLQNDPELRKRLGENARE 311
                                       *********************97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   9.6e-19   3.4e-15      72     170 .]      41     138 ..      14     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 9.6e-19
                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglye.krllkarlkplsrllralerrllrradrviavSeatade 147
                                       +  ++H + p +  ++ l+ ++r gip+V + H   e      + +  +s+++r++  ++++rad++ia+Se++++ 
  gi|313117199|ref|YP_004044182.1|  41 DAEILHLNVPTPRTYVQLRRAKRAGIPVVMHTHEIGEnFQESFRLSTTFSPIVRRYVDFFYKRADHLIAPSEYAKRV 117
                                       77899999999988887777779*************97444455667899*************************** PP

                    Glyco_transf_4 148 lrerygvppekitVipnGvDler 170
                                       l++  g++  +i V+ nG+D++r
  gi|313117199|ref|YP_004044182.1| 118 LKQ-RGLN-TPISVVTNGIDPDR 138
                                       ***.**99.9***********97 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.6   5.7e+03      90     102 ..      61      73 ..      56      89 .. 0.76
   2 ?    0.6   0.0       0.2   7.2e+02      66      81 ..      97     112 ..      73     131 .. 0.72
   3 !   46.9   0.0     1e-15   3.6e-12      13     131 ..     173     295 ..     162     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                       HHHTT-EEEE-TG CS
                   Glyco_trans_1_4  90 amaaglpvVatdv 102
                                       a  ag+pvV+ + 
  gi|313117199|ref|YP_004044182.1|  61 AKRAGIPVVMHTH 73 
                                       5568999999876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                                       HHHHHHH-SEEEE--- CS
                   Glyco_trans_1_4  66 laellaaadvfvaPse 81 
                                       ++ ++++ad ++aPse
  gi|313117199|ref|YP_004044182.1|  97 VDFFYKRADHLIAPSE 112
                                       6778***********5 PP

  == domain 3  score: 46.9 bits;  conditional E-value: 1e-15
                                       G.GTHHHHHHHHHHHH.HHEEEEEES---........HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEEE--..- CS
                   Glyco_trans_1_4  13 nvkgvdllleavpllrkkdvrlvivGdgp..rp....eeleelaagleerveftGfvedlaellaaadvfvaPs..e 81 
                                       ++kg+  +   + +l+  dv++   G  p  ++    +++++ +++  ++++f Gf +d+++++aa+dvf +P+  e
  gi|313117199|ref|YP_004044182.1| 173 ERKGLSDFTAVARQLQ--DVNFAWFG--PrfNRfltgSSVDKTIQQAPSNCVFPGFADDVRDVYAASDVFFFPTksE 245
                                       5688888888888888..67888888..3223344444444444444478************************998 PP

                                       --SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE-.-TT-HHHHHHHHHHH CS
                   Glyco_trans_1_4  82 gfglkllEamaaglpvVatdvggiaevvgengllv.ppgdpealaeailrL 131
                                       + g++++Ea+ +g+p+V+ d++   e + e+g  + +  ++e++ ++i  L
  gi|313117199|ref|YP_004044182.1| 246 TEGISIIEAAYCGIPIVTRDIPV-YEPLLEHGTHClKGSSVEEFKNHIKLL 295
                                       99*******************65.664434443331334689998888766 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0     4e-12   1.4e-08       8      77 ..     244     313 ..     237     322 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 4e-12
                   Glyco_trans_1_2   8 sespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarerv 77 
                                       se+    + Eaa cG++++t d++ +e l++ g++++  +++ee+  +i+ l ++pe+r++++e+are +
  gi|313117199|ref|YP_004044182.1| 244 SETEGISIIEAAYCGIPIVTRDIPVYEPLLEHGTHCLKGSSVEEFKNHIKLLQNDPELRKRLGENARELA 313
                                       555556679*****************************99***********999*************975 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   2.4e-10   8.6e-07      73     160 .]      41     133 ..      20     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.4e-10
                   Glyco_trans_4_4  73 rpdvvhahsptaglaa..rlarrrrgiplvvtlhgll..lrrg...sgavrrlyralerrllrradavlvvseaeae 142
                                          ++h++ pt   ++  r+a+ r+gip+v + h+    +++    s+   +++r+  ++ ++rad+++++se+  +
  gi|313117199|ref|YP_004044182.1|  41 DAEILHLNVPTPRTYVqlRRAK-RAGIPVVMHTHEIGenFQESfrlSTTFSPIVRRYVDFFYKRADHLIAPSEYAKR 116
                                       5679999998744444125555.89*********6332244333336777788899999****************** PP

                   Glyco_trans_4_4 143 elralgvpadrvvvvpng 160
                                        l ++g+  + + vv ng
  gi|313117199|ref|YP_004044182.1| 117 VLKQRGLN-TPISVVTNG 133
                                       ******97.899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2636.61
//
Query:       gi|313117200|ref|YP_004044183.1|  [L=66]
Description: hypothetical protein Hbor_29840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 446.20
//
Query:       gi|313117201|ref|YP_004044184.1|  [L=248]
Description: hypothetical protein Hbor_29850 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1938.96
//
Query:       gi|313117202|ref|YP_004044185.1|  [L=95]
Description: hypothetical protein Hbor_29860 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.7   4.8       0.22   11.7   4.9    1.6  1  DUF3325   Protein of unknown function (DUF3325)
        1.7    8.9   5.4       0.55   10.5   0.4    1.9  2  DUF3784   Domain of unknown function (DUF3784)


Domain annotation for each model (and alignments):
>> DUF3325  Protein of unknown function (DUF3325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.9   2.4e-05      0.22      30      76 ..      17      63 ..       6      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                           DUF3325 30 lsaarrrllrlaGwlllllslalavaawgwavGlvlwlgllslaAll 76
                                       s++ r  l ++G+++l+++++  va++ ++ G+++++++l++a l 
  gi|313117202|ref|YP_004044185.1| 17 DSKRMRSILAVVGVGTLVIGAWKLVAGNPVTAGSMFVFTTLCVANLR 63
                                      57889999***********************************9875 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   6.1e-05      0.55      43      88 ..      18      62 ..      12      69 .. 0.73
   2 ?    1.3   0.4     0.044     4e+02      69      88 ..      73      92 ..      64      94 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.1e-05
                           DUF3784 43 srfmgivllligilflllgllsaiesealliialiviiiiviyliv 88
                                      s++m+ +l ++g+ +l++g+++ +  + ++++ ++v+  +++ + +
  gi|313117202|ref|YP_004044185.1| 18 SKRMRSILAVVGVGTLVIGAWKLVAGNPVTAGSMFVFTTLCV-ANL 62
                                      6899*****************555555555555555555554.444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.044
                           DUF3784 69 ealliialiviiiiviyliv 88
                                      ++ +++ +++i ++v+++++
  gi|313117202|ref|YP_004044185.1| 73 DHPIVVLIALIPVAVVGVVA 92
                                      56666666677777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 692.66
//
Query:       gi|313117203|ref|YP_004044186.1|  [L=291]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.9e-28   98.1   0.0    9.8e-28   97.4   0.0    1.4  1  ABC_tran     ABC transporter
    3.1e-11   43.7   0.2    2.9e-06   27.3   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.6e-05   25.5   0.0    4.5e-05   24.0   0.0    1.7  3  AAA_23       AAA domain
    6.9e-05   22.5   0.0    0.00013   21.6   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00011   21.7   0.0     0.0048   16.4   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0029   17.4   0.0       0.25   11.0   0.0    2.2  2  AAA_15       AAA ATPase domain
     0.0087   16.2   0.0      0.035   14.3   0.0    1.9  1  AAA_33       AAA domain
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.021   14.6   0.1    1.4  1  MukB         MukB N-terminal
       0.02   14.8   0.2      0.056   13.3   0.1    1.8  2  RsgA_GTPase  RsgA GTPase
      0.038   13.6   0.0      0.063   12.9   0.0    1.3  1  AAA_27       AAA domain
       0.04   14.3   0.0      0.073   13.4   0.0    1.4  1  AAA_16       AAA ATPase domain
      0.053   12.4   0.0      0.099   11.5   0.0    1.4  1  AAA_PrkA     PrkA AAA domain
      0.072   12.8   0.1       0.16   11.7   0.1    1.7  1  AAA_30       AAA domain
       0.12   11.6   0.0       0.28   10.4   0.0    1.6  1  Zeta_toxin   Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.0   7.7e-31   9.8e-28       2     136 ..      20     161 ..      19     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 7.7e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n++l+l  g +++++G+nGaGKS+L+++++  ++pt+G+i+++g+d+ + +    r+ +g+lpq+  + p+lt++e
  gi|313117203|ref|YP_004044186.1|  20 RNIDLELDTG-VHGLLGPNGAGKSSLMRMITTVMEPTKGSIRWNGTDVLD-SPGTIRSVLGYLPQDFGVYPDLTLEE 94 
                                       5777777777.78*************************************.88899******************999 PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     +  ++i+++++  +l++ +d+++    +++SgG++qr  +a+all++p ll++DEpt
  gi|313117203|ref|YP_004044186.1|  95 FleyvgalrsvdskTVAARIDELIALTNLEQARDRKL----KTFSGGMRQRAGIAQALLNDPGLLVVDEPT 161
                                       9********9987777777999999999999999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   2.3e-05     0.029       2      19 ..      31      48 ..      30      69 .. 0.86
   2 !   27.3   0.0   2.3e-09   2.9e-06     232     297 ..     129     190 ..     102     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       +l GpNg+GKS+L++ +
  gi|313117203|ref|YP_004044186.1| 31 HGLLGPNGAGKSSLMRMI 48
                                      579************987 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.3e-09
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       + +  +S G+++ ++++ all ++   +ll++DEp  gL+P+   r+  ++++ls+ +  vil+TH
  gi|313117203|ref|YP_004044186.1| 129 RKLKTFSGGMRQRAGIAQALLNDP---GLLVVDEPTVGLDPEERVRFRNIISDLSS-DRVVILSTH 190
                                       445568*******9*******999...*****************************.9999***** PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.5e-08   4.5e-05       1      42 [.       2      51 ..       2      69 .. 0.86
   2 ?   -2.6   0.0       5.3   6.7e+03     101     171 ..     107     130 ..      73     143 .. 0.59
   3 ?   -3.4   0.0       9.2   1.2e+04     102     120 ..     227     245 ..     203     260 .. 0.56

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.5e-08
                            AAA_23  1 kLkienfrsf........rdqeidFskgltlItGpNGaGKTTildAikla 42
                                      +L+i+n+++         r+ +++++ g+  + GpNGaGK+++++ i+ +
  gi|313117203|ref|YP_004044186.1|  2 SLSIQNLGKRytedvwgvRNIDLELDTGVHGLLGPNGAGKSSLMRMITTV 51
                                      5788888776687777667777888**********************976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.3
                            AAA_23 101 gkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkl 171
                                       +kt+                                                 r++el+  ++ +++++++
  gi|313117203|ref|YP_004044186.1| 107 SKTVAA-----------------------------------------------RIDELIALTNLEQARDRK 130
                                       333333...............................................333333333333333333 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 9.2
                            AAA_23 102 kttkkaklelleideleqf 120
                                       ++t+ ++ ++l++  ++q+
  gi|313117203|ref|YP_004044186.1| 227 VYTYTTDQSNLDKIRSDQI 245
                                       3333333333333333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     1e-07   0.00013      18      55 ..      25      62 ..      17      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1e-07
                            AAA_29 18 eidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      e+d  g++ l Gp+G+GKS+l+  i++++ p+k ++r+N
  gi|313117203|ref|YP_004044186.1| 25 ELD-TGVHGLLGPNGAGKSSLMRMITTVMEPTKgSIRWN 62
                                      344.347889**********************9999988 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.7e-06    0.0048      17      50 ..      21      54 ..      16      67 .. 0.83
   2 ?    3.2   0.0     0.039        50     158     202 ..     151     195 ..     112     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.7e-06
                                      EEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 17 tvilpfsksftaivGpNGSGKsnlldAilFvLGe 50
                                      +++l++++++  ++GpNG+GKs+l+  i  v+  
  gi|313117203|ref|YP_004044186.1| 21 NIDLELDTGVHGLLGPNGAGKSSLMRMITTVMEP 54
                                      6789999******************999888764 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.039
                                       --SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 158 paplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                          l ++De    LD +++ ++ +++   s++  +i  ++    +
  gi|313117203|ref|YP_004044186.1| 151 DPGLLVVDEPTVGLDPEERVRFRNIISDLSSDRVVILSTHIVPDI 195
                                       556899************************999999888865555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0002      0.25      15      46 ..      20      51 ..      18      84 .. 0.86
   2 ?    4.2   0.0     0.023        30     322     364 ..     150     190 ..     137     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                            AAA_15 15 kdveidlseeltvliGkNnsGKSsilealdlF 46
                                      ++++++l+  +  l G+N++GKSs+++++   
  gi|313117203|ref|YP_004044186.1| 20 RNIDLELDTGVHGLLGPNGAGKSSLMRMITTV 51
                                      6788889999999***************9765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.023
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++ +l+++EP + L p+    + + + +l++d    vi++TH
  gi|313117203|ref|YP_004044186.1| 150 NDPGLLVVDEPTVGLDPEERVRFRNIISDLSSDRV--VILSTH 190
                                       57889*****************************6..****** PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.7e-05     0.035       4     106 ..      33     189 ..      30     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                            AAA_33   4 lvGlpGsGKstlaerl...lkklg.......avllssdt...................................... 32 
                                       l G++G+GKs l + +   +++++       + +l+s+                                       
  gi|313117203|ref|YP_004044186.1|  33 LLGPNGAGKSSLMRMIttvMEPTKgsirwngTDVLDSPGtirsvlgylpqdfgvypdltleefleyvgalrsvdskt 109
                                       579********999875554444455555547777777799999999999999999999999999999999999999 PP

                            AAA_33  33 ......lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat..nlsrrerarflklarrlgvpvri 101
                                             ++ +l++ +q +++++++++  ++q+  ++a+  l   + +++d +   l+++er rf+++ ++l+  +r+
  gi|313117203|ref|YP_004044186.1| 110 vaaridELIALTNLEQARDRKLKTFSGGMRQRA-GIAQALLNDPGLLVVDEPtvGLDPEERVRFRNIISDLS-SDRV 184
                                       888888777888888888889999999999997.******************555669**************.7888 PP

                            AAA_33 102 vvvet 106
                                       v+++t
  gi|313117203|ref|YP_004044186.1| 185 VILST 189
                                       88876 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.7e-05     0.021      22      62 ..      24      64 ..      16     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                                      E-HHHHHHHHHS--SHHHHHHHHHHHHHHS--TTT------ CS
                              MukB 22 fdldelvttlsGgnGaGksttmaafvtaliPdlsllhfrnt 62
                                       +ld+ v  l G nGaGks  m  + t++ P    +++  t
  gi|313117203|ref|YP_004044186.1| 24 LELDTGVHGLLGPNGAGKSSLMRMITTVMEPTKGSIRWNGT 64
                                      689*************************9999888887655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.4e-05     0.056      89     129 ..      18      58 ..       9      65 .. 0.82
   2 ?   -3.9   0.0       8.5   1.1e+04      13      58 ..     111     125 ..     103     136 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                                       THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallpelelktge 129
                                       g++++  +l+  +  l+G+ G+GKS+L+ +++  +e   g+
  gi|313117203|ref|YP_004044186.1|  18 GVRNIDLELDTGVHGLLGPNGAGKSSLMRMITTVMEPTKGS 58 
                                       67888889999999***************998876655555 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8.5
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDl 58 
                                       +a +d+l+ ++ l+                                
  gi|313117203|ref|YP_004044186.1| 111 AARIDELIALTNLE-------------------------------Q 125
                                       44445444444443...............................3 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.9e-05     0.063      19      48 ..      22      50 ..      17      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.9e-05
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisd 48
                                      +d++  ++++h ++GpN AGKs+++r i+ 
  gi|313117203|ref|YP_004044186.1| 22 IDLE-LDTGVHGLLGPNGAGKSSLMRMITT 50
                                      5555.46899***************99876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.7e-05     0.073      29     126 ..      33     179 ..      27     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-05
                            AAA_16  29 lsGesGvGKsslvrellralekd.......................ggiflrgkcdql.....esaipysalaqala 77 
                                       l G+ G GKssl+r++ + +e +                       +   l +++  +     e+ ++y+  ++  +
  gi|313117203|ref|YP_004044186.1|  33 LLGPNGAGKSSLMRMITTVMEPTkgsirwngtdvldspgtirsvlgY---LPQDFGVYpdltlEEFLEYVGALRSVD 106
                                       78***************988888666777777777766555432220...333333334444444488888777777 PP

                            AAA_16  78 reellrqlldeaesaeleawrekleeala........................avpelagaeasrllellkrl 126
                                        +++ + +++  + ++le++r++ +++++                        ++  l+++e+ r+++ +++l
  gi|313117203|ref|YP_004044186.1| 107 SKTVAARIDELIALTNLEQARDRKLKTFSggmrqragiaqallndpgllvvdePTVGLDPEERVRFRNIISDL 179
                                       7677777777788888888888888888899999999999999999999888877777777774444444433 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.7e-05     0.099      89     115 ..      29      55 ..      20      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.7e-05
                          AAA_PrkA  89 qilyllGPvggGksslverlkklleaa 115
                                        +  llGP g+Gkssl+ ++ +++e +
  gi|313117203|ref|YP_004044186.1|  29 GVHGLLGPNGAGKSSLMRMITTVMEPT 55 
                                       56679*******************965 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012      0.16      20      48 ..      30      58 ..      24     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggr 48
                                      v+ l Gp G+GK+ +++ ++ ++e  +g+
  gi|313117203|ref|YP_004044186.1| 30 VHGLLGPNGAGKSSLMRMITTVMEPTKGS 58
                                      77899*****************9988544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00022      0.28      23      53 ..      35      65 ..      30      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                        Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldpDd 53
                                      G  GAGKs+l++++++ +e++++ +r +++d
  gi|313117203|ref|YP_004044186.1| 35 GPNGAGKSSLMRMITTVMEPTKGSIRWNGTD 65
                                      778******************9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1958.27
//
Query:       gi|313117204|ref|YP_004044187.1|  [L=534]
Description: hypothetical protein Hbor_29890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-05   23.6   4.4    3.2e-05   23.6   4.4    3.0  3  ABC2_membrane_5  ABC-2 family transporter protein
    0.00021   20.5   9.2    0.00021   20.5   9.2    2.5  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1         1   9.1e+03     149     158 ..      22      31 ..      15      44 .. 0.48
   2 !   23.6   4.4   3.6e-09   3.2e-05      37     156 ..      70     194 ..      62     233 .. 0.72
   3 ?   -9.2  14.8         2   1.8e+04     102     198 ..     428     526 ..     381     529 .. 0.56

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1
                   ABC2_membrane_5 149 vliiiifgii 158
                                       ++++++++  
  gi|313117204|ref|YP_004044187.1|  22 IALLAFVIYL 31 
                                       2222222222 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 3.6e-09
                   ABC2_membrane_5  37 llifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlf.vlililiailitlllliiavlikgn.. 110
                                        l++s++++++ ++l+ ++l+ D+  +++ +l ++P+++  +   K l+ ++ l+li+++++l ++ ++++++g   
  gi|313117204|ref|YP_004044187.1|  70 GLTGSFFVVFVGFYLVKNSLYRDRSTEVSELLASMPISNPRYLLGKWLSnGAYLGLIVSVLGLSAV-VVHVVHGVgp 145
                                       57899*******************************************844555555555554444.4455554444 PP

                   ABC2_membrane_5 111 .vtisevllsiliglvialiflaivlPlyfk..fgvekgrivliiiifg 156
                                          i+ +l ++l+++  a++++ + l +     + +  g+i++++  ++
  gi|313117204|ref|YP_004044187.1| 146 tNPIKLLLPVVLLAIPTAFFIGGVALLVETVepLNNTAGNILYFFGTLA 194
                                       477899**************99888876554224444455544444444 PP

  == domain 3  score: -9.2 bits;  conditional E-value: 2
                   ABC2_membrane_5 102 iiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgri.vliiiifgiifllvai.fslsklelslid 176
                                       +i+ ++ g+ +  ++ll+++ +l+  ++++ +v  l +  g + gr  ++ +++++i+f+++a  ++   ++++  +
  gi|313117204|ref|YP_004044187.1| 428 TIIAVLVGSSIGLTALLTSTPVLLGYVAAILFVPSLALSVGIWSGRSeLFEVLYLVIWFVGPANgLKPVVFTATEAT 504
                                       22223333333344444444444444444444445555555555555333344444555555431222333444333 PP

                   ABC2_membrane_5 177 lsnyilliillviillliivSy 198
                                         +++++i+++ ++l+l+++S+
  gi|313117204|ref|YP_004044187.1| 505 ALSTVSVIVYICLGLCLFVASF 526
                                       3334444445555666777775 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   9.2   2.3e-08   0.00021     169     298 ..      75     210 ..      51     285 .. 0.72
   2 ?   -1.4  12.0      0.11   9.5e+02     168     256 ..     382     464 ..     379     527 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.3e-08
                   ABC2_membrane_3 169 iilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..lafgl..gipfg....n 237
                                       ++++f++++ + +s+ +++++ + el+ ++++s+  y+l+k l+ ++   l++ ++ l  +++++  g+  +     
  gi|313117204|ref|YP_004044187.1|  75 FFVVFVGFYLVKNSLYRDRSTEVSELLASMPISNPRYLLGKWLSNGAYLGLIVSVLGLsaVVVHVvhGVGPTnpikL 151
                                       455777777777899*******************************9999998888775456666774555522325 PP

                   ABC2_membrane_3 238 lglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalk 298
                                       l+ ++ll ++ ++ +  +++l+ ++     ta  ++ ++  l+++ +++++++   ++ ++
  gi|313117204|ref|YP_004044187.1| 152 LLPVVLLAIPTAFFIGGVALLVETVEPLNNTAGNILYFFGTLALMNVFYTGTVA--NGVVS 210
                                       67799********************77555544444444444444444444333..23333 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.11
                   ABC2_membrane_3 168 liilifitasfiavsi.veEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglgipfgnlgll 241
                                       l+ +++i ++f+++s+ v+  ++r+  l+++s  s+++++++  +  +++ ++ +   ++l  ++    +   lg++
  gi|313117204|ref|YP_004044187.1| 382 LL-IALIWPIFVLSSMgVRAQRHRMEPLIFSS-NSAYTQLFAEWIVGVTIIAVLVGSSIGLtaLLT--STPVLLGYV 454
                                       33.34444444455554999999*********.999999999876666666666655555543444..444444444 PP

                   ABC2_membrane_3 242 l.llfllfglayialg 256
                                         +lf++      +l+
  gi|313117204|ref|YP_004044187.1| 455 AaILFVP------SLA 464
                                       4333333......222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3411.45
//
Query:       gi|313117205|ref|YP_004044188.1|  [L=55]
Description: hypothetical protein Hbor_29900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 394.33
//
Query:       gi|313117206|ref|YP_004044189.1|  [L=418]
Description: F420-dependent methylene-tetrahydromethanopterin reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-31  108.0   0.4    1.3e-25   90.5   0.0    2.4  2  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.0   7.2e-30   1.3e-25      20     153 ..      39     181 ..      22     192 .. 0.90
   2 !   15.3   0.1   5.6e-07      0.01     150     308 ..     216     405 ..     206     409 .. 0.59

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 7.2e-30
                    Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpgga..ldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLd 94 
                                       ++l + v+ a++aE+ Gf++++ aehh+   ++  ++++ + +a+a +T+ irl+ ++ +l++++P++lA++  +Ld
  gi|313117206|ref|YP_004044189.1|  39 EALSQSVATAVEAESMGFEYIVHAEHHSELVTNnsPNPILTQTAIARETQEIRLLQMANILPWHEPVRLAEMLSMLD 115
                                       578999*********************9655559******************************************* PP

                    Bac_luciferase  95 hlsgGRfglglgtggpaveerrfGv.......dhderyarlrEfvevlrrlwrgeevdfeGeffsv 153
                                        ls+GR+++g+g g++ + ++  G+       + ++  + ++E  e+l ++w+++ v+++Gef++v
  gi|313117206|ref|YP_004044189.1| 116 ILSDGRVDVGVGGGSRDIATATLGQywggssaHEPKNEKSFEEKFEILVKAWTEDLVSYHGEFHQV 181
                                       ***********************999999*988899999*************66666******997 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.6e-07
                    Bac_luciferase 150 ffsvkgalllprpgqgpiP.vyvaaaspaglelaarhadglllageppeeaaelierlragaae............. 212
                                       +++++g+ ++p+p+q+p+P ++  a s  +  +aar++  + +++ +  +  e+++ +  +a+              
  gi|313117206|ref|YP_004044189.1| 216 TITLEGLPVIPQPEQEPHPqLWRPALSSSSSTWAARRGINVCTHLLSISQTNEVVDAYYTAAKDaewpdrqtdytge 292
                                       56789999*********99****************************************977776666666666666 PP

                    Bac_luciferase 213 .......agrdpadirvgi..sltvivadteeeAraea..raliagld..fyaldsegagreaeaaeiqeeedanlw 276
                                              a r +  + ++i    t +++d + e +++   r      d  + ++d +++ + +e+ +++ +   ++ 
  gi|313117206|ref|YP_004044189.1| 293 afnygwdAQRNR-GVGIIIsmFNTEVADDGAIERWKRSfkR------DeqQRRNDLSEPINVDEQIQERTAPLYGDA 362
                                       666554422222.2222221022222222222222222221......022333344444433333333333333333 PP

                    Bac_luciferase 277 agaadavpdelvaatal...........vG.tpeqvaerlaaya 308
                                       a+  + + +e+++++al           vG t+e+ +e+++a+a
  gi|313117206|ref|YP_004044189.1| 363 AELINGL-AEVIEECALddaliicnphsVGlTHEERREQIRAFA 405
                                       3333333.455555555555556666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3340.41
//
Query:       gi|313117207|ref|YP_004044190.1|  [L=172]
Description: carbonic anhydrase/acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.7e-15   54.4  10.8    1.3e-06   27.9   1.0    3.5  3  Hexapep     Bacterial transferase hexapeptide (six repeats)
    1.6e-06   27.7  10.5      1e-05   25.2   1.1    4.1  4  Hexapep_2   Hexapeptide repeat of succinyl-transferase
     0.0016   17.5   0.0      0.002   17.2   0.0    1.2  1  Fucokinase  L-fucokinase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   1.7e-05       0.1       9      36 .]      21      48 ..      11      48 .. 0.80
   2 !   19.4   0.7     1e-07   0.00061       1      35 [.      52      85 ..      52      86 .. 0.92
   3 !   27.9   1.0   2.2e-10   1.3e-06       2      34 ..      87     119 ..      86     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                      EE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  9 lIgpfaviggnVkIGdnvkIgagvvigg 36
                                      ++   +++ g+V +  n+ +++gvv++g
  gi|313117207|ref|YP_004044190.1| 21 HVSQMSTLVGDVRVAANASVWPGVVLRG 48
                                      444468999****************986 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1e-07
                                      TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep  1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                      s++IG  +++  +av+ +  +IG++v +g+g+v++
  gi|313117207|ref|YP_004044190.1| 52 SVRIGAESHVADNAVL-HASTIGNRVMVGHGSVLN 85
                                      689*************.8888************86 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 2.2e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       +v+++ +lIg +a+i  +V++G++++++ag+v+
  gi|313117207|ref|YP_004044190.1|  87 AVVEDSTLIGFNATINTDVTVGERSIVAAGCVV 119
                                       7999****************************9 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.1   6.3e+02      18      32 ..      32      46 ..      26      47 .. 0.65
   2 ?    2.5   0.0     0.021   1.2e+02      16      32 ..      50      67 ..      48      69 .. 0.78
   3 ?    3.1   0.1     0.014        81      20      32 ..      72      84 ..      70      86 .. 0.56
   4 !   25.2   1.1   1.7e-09     1e-05       3      32 ..      88     119 ..      86     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                                      EEE-TT-EE-TT-EE CS
                         Hexapep_2 18 vslGdncvvgaGvvi 32
                                      v +  n+ v +Gvv+
  gi|313117207|ref|YP_004044190.1| 32 VRVAANASVWPGVVL 46
                                      566667777777775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.021
                                      ES.EEE-TT-EE-TT-EE CS
                         Hexapep_2 16 iG.vslGdncvvgaGvvi 32
                                      iG v +G +++v+ + v+
  gi|313117207|ref|YP_004044190.1| 50 IGsVRIGAESHVADNAVL 67
                                      655999999999988887 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.014
                                      E-TT-EE-TT-EE CS
                         Hexapep_2 20 lGdncvvgaGvvi 32
                                      +G+++ vg G+v+
  gi|313117207|ref|YP_004044190.1| 72 IGNRVMVGHGSVL 84
                                      5555555555555 PP

  == domain 4  score: 25.2 bits;  conditional E-value: 1.7e-09
                                       EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvi 32 
                                        ++d +liG na+i   v++G++++v+aG+v+
  gi|313117207|ref|YP_004044190.1|  88 VVEDSTLIGFNATIntDVTVGERSIVAAGCVV 119
                                       6899*********988***************8 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.3e-07     0.002     265     335 ..      56     136 ..      20     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.3e-07
                        Fucokinase 265 nkkekkkesavvinSvlessvsvgegsvie............hsslkgnvsigsnsivs.glelesseeslelpddt 328
                                        ++++ +++av + S + ++v vg gsv+             + +++ +v++g++siv  g+ + ++ +   +p ++
  gi|313117207|ref|YP_004044190.1|  56 GAESHVADNAVLHASTIGNRVMVGHGSVLNeavvedstligfNATINTDVTVGERSIVAaGCVVPEGRD---IPPES 129
                                       34455599999999999999999999998888888999999999999***********64888888766...***** PP

                        Fucokinase 329 ilqtlsl 335
                                       ++ +++ 
  gi|313117207|ref|YP_004044190.1| 130 FVRGVPA 136
                                       *999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1374.85
//
Query:       gi|313117208|ref|YP_004044191.1|  [L=102]
Description: hypothetical protein Hbor_29930 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.053   13.6   0.0       0.08   13.0   0.0    1.3  1  AbrB-like  AbrB-like transcriptional regulator


Domain annotation for each model (and alignments):
>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.4e-06      0.08      29      59 ..      60      90 ..      43     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.4e-06
                         AbrB-like 29 asYrvsVqknGnLliGsaYTkklgLkpGdef 59
                                      a+++++Vq+ G++ i  a  + l+++ Gd  
  gi|313117208|ref|YP_004044191.1| 60 ATFKTRVQSGGRISIPDAERETLDIEEGDIV 90
                                      89**************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 770.77
//
Query:       gi|313117209|ref|YP_004044192.1|  [L=155]
Description: hypothetical protein Hbor_29940 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00058   20.1   3.9       0.15   12.3   0.3    2.3  2  Phasin_2   Phasin protein
  ------ inclusion threshold ------
      0.029   14.8   1.0      0.095   13.1   0.3    2.1  2  GCK        GCK domain
      0.036   14.4   0.5      0.065   13.6   0.5    1.4  1  DUF2383    Domain of unknown function (DUF2383)
       0.37   11.5   4.4       0.25   12.0   1.2    2.0  2  PMC2NT     PMC2NT (NUC016) domain
        1.5    8.7   7.2        3.1    7.7   0.9    2.5  2  PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_B


Domain annotation for each model (and alignments):
>> Phasin_2  Phasin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   1.8   0.00078       2.8      11      55 ..       6      50 ..       1      71 [. 0.77
   2 !   12.3   0.3   4.3e-05      0.15       9      84 ..      65     142 ..      57     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00078
                          Phasin_2 11 lealealaslalegaeklaelqleaarasleeslaaakallsakd 55
                                      +e+ ++l  ++++ a +++e+++++ +++++   + + a  s++ 
  gi|313117209|ref|YP_004044192.1|  6 IETTFDLQHQSVKQAREIVEQNVKLQQSMMQSVPDGMDAQRSVQH 50
                                      789999999999999999999999999999999988888887775 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.3e-05
                          Phasin_2   9 knlealealaslalegaeklaelqleaarasleeslaaakallsakd..pqellelqselaqpalekavayarklae 83 
                                       +++ea+   a+ ++e + + ++  +++ ++sl++  ++ +++++     + e+++ q  ++ ++++++++   ++ e
  gi|313117209|ref|YP_004044192.1|  65 EAIEAASPEAEMSFEDMHQAIDDGFDMFNESLDDMWDYYEQIVDMNVeaYDEFADTQLNFVHDSFDAFLESYEAVEE 141
                                       677888888899999999999999******************98754459*****************9998887776 PP

                          Phasin_2  84 l 84 
                                        
  gi|313117209|ref|YP_004044192.1| 142 Q 142
                                       5 PP

>> GCK  GCK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   2.6e-05     0.095      20      71 ..      66     117 ..      59     120 .. 0.89
   2 ?   -0.8   0.0      0.59   2.1e+03      56      71 ..     128     143 ..     125     148 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                               GCK  20 awekcveeaeknkedlvekcaevtatlkkCmeahsdYYePiLaaekaaeeev 71 
                                       a e    eae + ed+++   + ++++++ +++  dYYe i  ++ +a++e+
  gi|313117209|ref|YP_004044192.1|  66 AIEAASPEAEMSFEDMHQAIDDGFDMFNESLDDMWDYYEQIVDMNVEAYDEF 117
                                       556677899**9******************************9999988876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.59
                               GCK  56 YYePiLaaekaaeeev 71 
                                        ++++L++ +a+ee++
  gi|313117209|ref|YP_004044192.1| 128 SFDAFLESYEAVEEQT 143
                                       4566666666666654 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   1.8e-05     0.065      13     103 ..      56     145 ..      51     148 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----------------------------HHH CS
                           DUF2383  13 lkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralggepedggslagklhrawvdlksaltsndeea 89 
                                       +k + ++y ea+e +  p+ +  +e++ ++  +  + +++ + ++ +  e+  ++++++   ++d    + +++ +a
  gi|313117209|ref|YP_004044192.1|  56 SKQALHTYAEAIEAAS-PEAEMSFEDMHQAIDDGFDMFNESLDDMWDYYEQIVDMNVEAYDEFADTQLNFVHDSFDA 131
                                       67899********998.************************************************************ PP

                                       HHHHHHHHHHHHHH CS
                           DUF2383  90 ileeleegEdkale 103
                                       +le+ e +E++++e
  gi|313117209|ref|YP_004044192.1| 132 FLESYEAVEEQTIE 145
                                       **********9986 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.2   7.1e-05      0.25       2      90 ..      15      99 ..      14     101 .. 0.78
   2 ?    0.3   0.1      0.33   1.2e+03      68      82 ..     121     135 ..     102     148 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                            PMC2NT  2 eatraanaLpaeDldfyrsldpefaksldeq...serllslinsllklaaskseisassklededdveekfksvvdvvD 77
                                      + ++ a+++ +++++ ++s+ +++ + +d+q   ++r  +l ++ l+  a+  e+ ++    ++   e +f+++  ++D
  gi|313117209|ref|YP_004044192.1| 15 QSVKQAREIVEQNVKLQQSMMQSVPDGMDAQrsvQHRASDLSKQALHTYAEAIEAASP----EA---EMSFEDMHQAID 86
                                      57999*******************9999998222346666666666666666666333....33...56********** PP

                            PMC2NT 78 sllEkadtcLDel 90
                                      + ++  + +LD +
  gi|313117209|ref|YP_004044192.1| 87 DGFDMFNESLDDM 99
                                      **********975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.33
                            PMC2NT  68 kfksvvdvvDsllEk 82 
                                       + + v d  D  lE+
  gi|313117209|ref|YP_004044192.1| 121 QLNFVHDSFDAFLES 135
                                       555555555555554 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9   0.00087       3.1     109     140 ..       3      34 ..       1      50 [. 0.89
   2 ?    4.1   0.5     0.011        40      10      55 ..      96     141 ..      90     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00087
                         PhaP_Bmeg 109 lspsKssldllkkaeeqleetvkslieqqkkr 140
                                        +p+ +++dl +++ +q  e v++ ++ q+  
  gi|313117209|ref|YP_004044192.1|   3 SNPIETTFDLQHQSVKQAREIVEQNVKLQQSM 34 
                                       589***********************999975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                         PhaP_Bmeg  10 vdafWdqweeslerfaslskqvEqltLkalkqqqdlvkeltkalse 55 
                                       +d +Wd +e+ ++   ++ ++  ++ L+ + +  d+  e  +a++e
  gi|313117209|ref|YP_004044192.1|  96 LDDMWDYYEQIVDMNVEAYDEFADTQLNFVHDSFDAFLESYEAVEE 141
                                       5778888888888888888888888877777777766555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1505  (0.0839422); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1251.84
//
Query:       gi|313117210|ref|YP_004044193.1|  [L=184]
Description: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-10   39.2   1.0    1.4e-09   37.5   0.3    1.9  2  PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subuni
  ------ inclusion threshold ------
      0.026   14.5   0.3      0.076   13.0   0.1    2.0  2  Phasin           Poly(hydroxyalcanoate) granule associated pr
      0.044   13.2   0.0       0.19   11.1   0.0    1.8  2  FliD_C           Flagellar hook-associated protein 2 C-termin
      0.064   13.1   0.9        6.2    6.6   0.1    2.3  2  Nsp1_C           Nsp1-like C-terminal region


Domain annotation for each model (and alignments):
>> PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.3    0.0054        24     215     252 ..      17      52 ..      13      66 .. 0.76
   2 !   37.5   0.3   3.1e-13   1.4e-09     184     312 ..      40     169 ..      37     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0054
                   PHA_synth_III_E 215 verlreklqeaaekgkqiksaralfdlWveaaeevyae 252
                                       +e+lre + e  e+  +i++ +a+ + W +a++e   +
  gi|313117210|ref|YP_004044193.1|  17 FEQLREAYMEGFER--NIEAQSAFVEAWQDAVDETMLS 52 
                                       78888888888777..9999999999999999875443 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 3.1e-13
                   PHA_synth_III_E 184 eqlqelvravvdyqqasqeYqalla...avgvksverlreklqeaaekgkqiksaralfdlWveaaeevyaevvase 257
                                       e +q++v+  +  ++a+q+ ++ +    +v +++ e+  +++++a  +gk ++ ++++ d+W eaa+++++e ++++
  gi|313117210|ref|YP_004044193.1|  40 EAWQDAVDETMLSEEAMQDSIEGYVgayEVWMDAAEASLSRMSSA-YEGKDVD-ISNFRDIWLEAANDAFKEIASTQ 114
                                       569999999999999999877766511145555555555555544.4567776.677889***************** PP

                   PHA_synth_III_E 258 eyakiygrlvnaqmalkaemqrlveevlealnlPtRsEldtlhkriqelrrevrr 312
                                        +a + g+ v     l+    ++  e+l++l++Pt s +d++ +r+ e +r+ ++
  gi|313117210|ref|YP_004044193.1| 115 GFATMTGQTVEESFGLRGDFGEIQRETLRNLGVPTESDIDEIGERLLEFERRQHK 169
                                       **************************************************98775 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.49   2.2e+03      85      85 ..      53      53 ..      18      91 .. 0.56
   2 ?   13.0   0.1   1.7e-05     0.076      88     124 ..     134     170 ..      86     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.49
                            Phasin 85 e 85
                                      e
  gi|313117210|ref|YP_004044193.1| 53 E 53
                                      1 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.7e-05
                            Phasin  88 fdervakaLsrlgvpsredveaLsarvdeLtkelekl 124
                                       f e   ++L++lgvp+++d++++ +r+ e +++ +k+
  gi|313117210|ref|YP_004044193.1| 134 FGEIQRETLRNLGVPTESDIDEIGERLLEFERRQHKV 170
                                       44555789*******************9999988776 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.12   5.3e+02      50      75 ..      54      79 ..      34      96 .. 0.79
   2 ?   11.1   0.0   4.2e-05      0.19     163     238 ..     106     181 ..      68     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.12
                                      CCCCCCHCHHHHHHHHCCCCCCCCCS CS
                            FliD_C 50 dkikealkeFVdaYNalvteinektk 75
                                      ++++++++ +V aY   ++  +++++
  gi|313117210|ref|YP_004044193.1| 54 EAMQDSIEGYVGAYEVWMDAAEASLS 79
                                      67888888889888877777776666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.2e-05
                                       .......SXSHHHHHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH CS
                            FliD_C 163 qektvtsdsglatrlenllksyvkssngtlqtasknltkqikdldkkiedldkrletleerlkkqfaalekavskl 238
                                       + k++ s++g+at++ + +++  + +++  + + ++l +    ++++i+++ +rl + e+r +k  ++l+++++ l
  gi|313117210|ref|YP_004044193.1| 106 AFKEIASTQGFATMTGQTVEESFGLRGDFGEIQRETLRNLGVPTESDIDEIGERLLEFERRQHKVEQKLDEVLNAL 181
                                       447899*****************88877777777777777777777777777777777777777777777776654 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1    0.0048        22      64     108 ..      34      78 ..      29      89 .. 0.80
   2 ?    6.6   0.1    0.0014       6.2      57      85 ..     151     179 ..     144     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0048
                            Nsp1_C  64 sevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellskl 108
                                        +   +e+ q ++d+++   e+ qd +e ++  yE  +++  ++l
  gi|313117210|ref|YP_004044193.1|  34 AQSAFVEAWQDAVDETMLSEEAMQDSIEGYVGAYEVWMDAAEASL 78 
                                       566779999*************************98777666554 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0014
                            Nsp1_C  57 ekIskLysevleaeqeqnkidqeLeyies 85 
                                       + I ++ + +le e+ q+k++q+L+ + +
  gi|313117210|ref|YP_004044193.1| 151 SDIDEIGERLLEFERRQHKVEQKLDEVLN 179
                                       57889999999*************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1294.32
//
Query:       gi|313117211|ref|YP_004044194.1|  [L=446]
Description: poly(R)-hydroxyalkanoic acid synthase subunit PhaC [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-24   86.2   0.0    5.1e-24   85.3   0.0    1.4  1  Abhydrolase_1    alpha/beta hydrolase fold
    8.5e-13   48.3   0.0    1.5e-12   47.5   0.0    1.4  1  PhaC_N           Poly-beta-hydroxybutyrate polymerase (PhaC) 
    5.9e-10   38.2   0.0    3.1e-09   35.8   0.1    1.8  2  DUF3141          Protein of unknown function (DUF3141)
    3.9e-09   37.0   0.0    8.1e-09   36.0   0.0    1.5  1  HHH_5            Helix-hairpin-helix domain
    2.3e-08   33.6   0.0    0.00029   20.2   0.0    2.5  2  Hydrolase_4      Serine aminopeptidase, S33
    1.9e-05   24.4   0.0     0.0046   16.5   0.0    2.3  2  DLH              Dienelactone hydrolase family
    6.4e-05   22.7   0.0     0.0099   15.6   0.0    2.3  2  FSH1             Serine hydrolase (FSH1)
    9.6e-05   22.2   0.0       0.16   11.7   0.0    2.3  2  Abhydrolase_5    Alpha/beta hydrolase family
    0.00028   20.6   0.0     0.0008   19.2   0.0    1.8  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0013   18.9   0.2      0.016   15.4   0.2    2.2  1  DUF4332          Domain of unknown function (DUF4332)
     0.0019   17.7   0.0     0.0055   16.2   0.0    1.8  2  PHB_depo_C       PHB de-polymerase C-terminus
     0.0063   16.7   0.0      0.013   15.8   0.0    1.5  1  Cdd1             Pathogenicity locus
  ------ inclusion threshold ------
      0.027   15.4   0.2        0.1   13.6   0.2    1.9  1  RNAse_A_bac      Bacterial CdiA-CT RNAse A domain
      0.093   12.4   0.0       0.16   11.7   0.0    1.4  1  PGAP1            PGAP1-like protein
       0.12   12.7   0.9       0.23   11.8   0.0    2.0  2  HTH_Tnp_1        Transposase


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   4.3e-27   5.1e-24       2     252 ..      70     336 ..      69     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 4.3e-27
                                       EEEEE-STTT...CGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSE CS
                     Abhydrolase_1   2 vlvilhGlpg...ssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkl 75 
                                       +++i+ +l +    +d++ +r+++++L ++g dv+l+D+  + + +++++   ddy +  +++++d ++d+ ++d++
  gi|313117211|ref|YP_004044194.1|  70 PILIVYALINrpyILDLQPNRSVVRTLLDQGLDVYLIDWGEPSRLDASLTL--DDYVNRYIENCVDVVRDRSDQDSI 144
                                       78899999998888899**********************************..************************ PP

                                       EEEEETHHHHHHHHHHHHHGGGEEEEEEESE...CSSCCHHHHHHHHHHHHHHCH...HCHHHHHHHHHHHHHHHHC CS
                     Abhydrolase_1  76 tlvGhSmGGmialayaaeyperVkalvllga...idpaaslieaqrqqaksfpdf...fdgyaadcarnpagpllad 146
                                       +++G++mGG+++++y a++pe+V++l l+++    ++   + e +    +  p++     g+++ ++  ++  l++ 
  gi|313117211|ref|YP_004044194.1| 145 NVLGYCMGGTMSAMYTALHPEKVRNLGLMASglcFNDTGGTLEFWGDEEYYNPEAvtdVSGNVPSEFLDVGFALMDP 221
                                       *******************************7773333333333333333333321114566777777777777777 PP

                                       CSCHHHHHHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC........THHHHSEEE CS
                     Abhydrolase_1 147 elaaleqrhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre........lknvlaptl 215
                                         + l+ + rl   l++ +++ +f +++ + + + +  +  + +  ++ + +++l + +         l n+  p++
  gi|313117211|ref|YP_004044194.1| 222 VDNYLTKYIRLFENLDNDSFVENFARMEKWLSDGIDVAGETYNQFLQDIYQDNKLVNGELmlgeqhvdLANIDMPVI 298
                                       7777777777777777799999999999999999999999999999999999999887779**************** PP

                                       EEEETTCSSSCH.HHHHHHHHCHTSEEEEEEETCSSSH CS
                     Abhydrolase_1 216 visgtsDplvpp.kaledlaqllpkkrlvvisdagHla 252
                                        i+g++D+l+pp +++ ++++  ++ + v+++++gH+ 
  gi|313117211|ref|YP_004044194.1| 299 QIIGEHDHLIPPeSSIPFNDAIASDDTMVIEFPTGHIG 336
                                       ************77777777777779**********86 PP

>> PhaC_N  Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.3e-15   1.5e-12     116     171 ..      39      94 ..      13      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.3e-15
                            PhaC_N 116 nvattpGkvvfrnelleliqykpttekvlkrPllivPplinkfYilDLkpenslvr 171
                                       +v+ tp +vv+ ++ l+l++y+p t+++l+ P+liv +lin+ YilDL+p++s+vr
  gi|313117211|ref|YP_004044194.1|  39 EVGQTPSEVVYSENKLDLLHYEPRTDEQLDVPILIVYALINRPYILDLQPNRSVVR 94 
                                       6889**************************************************98 PP

>> DUF3141  Protein of unknown function (DUF3141)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.24   2.8e+02     117     165 ..     119     167 ..      89     184 .. 0.63
   2 !   35.8   0.1   2.6e-12   3.1e-09     218     320 ..     214     317 ..     201     351 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.24
                           DUF3141 117 tledvveaeaaflrkvaelhpeaekPvvignCqaGwavlmlaalapelv 165
                                       tl+d v+   +    v++  ++++   v+g C +G    m +al+pe v
  gi|313117211|ref|YP_004044194.1| 119 TLDDYVNRYIENCVDVVRDRSDQDSINVLGYCMGGTMSAMYTALHPEKV 167
                                       4555544444444455555666667789999999999999999999876 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 2.6e-12
                           DUF3141 218 qnfeklnPantlwskqynlyakvdtea..erylefekwWGghvllnkeeieyivdnLfvGnrlatgelvtsdgvriD 292
                                         f  ++P +++ +k+ +l+++ d+++  e +  +ekw  + + + +e  +   ++++  n+l++gel+   ++++D
  gi|313117211|ref|YP_004044194.1| 214 VGFALMDPVDNYLTKYIRLFENLDNDSfvENFARMEKWLSDGIDVAGETYNQFLQDIYQDNKLVNGELML-GEQHVD 289
                                       568999*****************99865589************************************966.5689** PP

                           DUF3141 293 lrnirsPivvfaskgDnitPPqqalnWi 320
                                       l ni  P++    + D + PP+ ++ + 
  gi|313117211|ref|YP_004044194.1| 290 LANIDMPVIQIIGEHDHLIPPESSIPFN 317
                                       **********************998653 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   6.7e-12   8.1e-09       2      56 ..     386     439 ..     385     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 6.7e-12
                                       HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                        eL ++ GiGp++A +l + Gie++edla+a+v    +i ++++ + +++i+e+ 
  gi|313117211|ref|YP_004044194.1| 386 AELEDITGIGPAYATRLRESGIETFEDLASAEVSIAEQI-DVSESQFQQWIDEAN 439
                                       5899***********************************.************996 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.5e-07   0.00029      23     111 ..      92     177 ..      89     193 .. 0.80
   2 !   10.9   0.0   0.00017       0.2     187     228 ..     290     331 ..     224     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.5e-07
                       Hydrolase_4  23 laeaLaaqGfavyalDhrGhGrsegkrghvpsfddyv.dDlaafvekvkeehpelplfllGhSmGGliallyllryp 98 
                                       +++ L +qG +vy +D+   G+     + +  +ddyv + ++  v+ v++++ +  + +lG  mGG++++ y++ +p
  gi|313117211|ref|YP_004044194.1|  92 VVRTLLDQGLDVYLIDW---GEPSRLDASL-TLDDYVnRYIENCVDVVRDRSDQDSINVLGYCMGGTMSAMYTALHP 164
                                       67899999999999996...6665555544.445555144556689999999999********************** PP

                       Hydrolase_4  99 dkvaglilsaPal 111
                                       +kv+ l l+a+ l
  gi|313117211|ref|YP_004044194.1| 165 EKVRNLGLMASGL 177
                                       ****888888765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00017
                       Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgskdktlklyp 228
                                        a+i++P++ ++Ge+D++++pe s  + ++++s+d  +  +p
  gi|313117211|ref|YP_004044194.1| 290 LANIDMPVIQIIGEHDHLIPPESSIPFNDAIASDDTMVIEFP 331
                                       45699****************************988777666 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.9e-06    0.0046      78     119 ..     124     163 ..     114     170 .. 0.79
   2 ?    5.3   0.0      0.01        12     136     171 ..     286     321 ..     279     346 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.9e-06
                               DLH  78 vlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaev 119
                                       v + ++  v+ ++ ++  +++ + v G+CmGG+++  + a  
  gi|313117211|ref|YP_004044194.1| 124 VNRYIENCVDVVRDRS--DQDSINVLGYCMGGTMSAMYTALH 163
                                       5566678888899999..888*************88777665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                               DLH 136 eleeaakikapilalfgeeDefipadevekleealk 171
                                       ++ + a+i  p++ ++ge+D+ ip ++   ++ a++
  gi|313117211|ref|YP_004044194.1| 286 QHVDLANIDMPVIQIIGEHDHLIPPESSIPFNDAIA 321
                                       5667789*****************999888888873 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.017        20      85     128 ..     127     168 ..     106     208 .. 0.76
   2 !   15.6   0.0   8.3e-06    0.0099     157     200 ..     290     334 ..     261     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.017
                              FSH1  85 gleesldavkdyikengpfdGiiGFSqGaalaallaslleellk 128
                                        +e+++d+v+d  ++      ++G+  G++++a++++l  e+ +
  gi|313117211|ref|YP_004044194.1| 127 YIENCVDVVRDRSDQDS--INVLGYCMGGTMSAMYTALHPEKVR 168
                                       45666666666655554..789**************99887665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 8.3e-06
                              FSH1 157 edkiqtptLhvlGelDtvvdeerseaLaeafkns.skvlkHpggH 200
                                         +i +p++ ++Ge D ++++e s  + +a++++ + v+++p gH
  gi|313117211|ref|YP_004044194.1| 290 LANIDMPVIQIIGEHDHLIPPESSIPFNDAIASDdTMVIEFPTGH 334
                                       56789****************************99********** PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0016       1.9      45      89 ..     130     175 ..      92     187 .. 0.89
   2 !   11.7   0.0   0.00013      0.16      46     133 ..     238     327 ..     226     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                     Abhydrolase_5  45 kaeeiikeapklekfvvgGhslGGvvasrfaaee.ekiegvvflas 89 
                                       +  +++++  +++   v G+ +GG +++ ++a + ek+  + ++as
  gi|313117211|ref|YP_004044194.1| 130 NCVDVVRDRSDQDSINVLGYCMGGTMSAMYTALHpEKVRNLGLMAS 175
                                       556899999999******************9977579998888887 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00013
                     Abhydrolase_5  46 aeeiikeapklekfvvgGhslGGvvasrfaa....eeekiegvvflasYPekdelselskkvlsivgteDgvlnvks 118
                                        ++ +++   +ek++  G  + G    +f +    +++ ++g ++l+      +l +  ++v+ i+g++D +++ +s
  gi|313117211|ref|YP_004044194.1| 238 NDSFVENFARMEKWLSDGIDVAGETYNQFLQdiyqDNKLVNGELMLGEQHV--DLANIDMPVIQIIGEHDHLIPPES 312
                                       567788889999999999999999999998877757789********9774..7*******************9998 PP

                     Abhydrolase_5 119 lekakkflpkdtkvv 133
                                           ++ ++ d ++v
  gi|313117211|ref|YP_004044194.1| 313 SIPFNDAIASDDTMV 327
                                       766666665555544 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   6.7e-07    0.0008       2      30 ..     387     415 ..     386     430 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.7e-07
                   DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwyakGirtledlra 30 
                                       ++  ++G+Gp+ A ++ + Gi t+edl  
  gi|313117211|ref|YP_004044194.1| 387 ELEDITGIGPAYATRLRESGIETFEDLAS 415
                                       5789***********************88 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.4e-05     0.016      25      84 ..     358     417 ..     353     441 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                           DUF4332  25 lgktekgrkalaeklgisernvlklanlAdLarikgigeeyaeLLeaaGvdsvaeLaqrn 84 
                                       ++++e+++ + ae++   + +  +  + A+L  i gig++ya  L ++G+++ ++La  +
  gi|313117211|ref|YP_004044194.1| 358 RSQHEETESTSAEATDEPATESAAVEESAELEDITGIGPAYATRLRESGIETFEDLASAE 417
                                       566667777777788888888888888999999999999999999999999999999865 PP

>> PHB_depo_C  PHB de-polymerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.6e-06    0.0055      93     197 ..     254     353 ..     210     359 .. 0.72
   2 ?   -2.8   0.0         3   3.6e+03     142     157 ..     386     401 ..     375     411 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.6e-06
                        PHB_depo_C  93 avlDltaefylqtveevfqefalakgklkvegkrvdlkkikrvalltveGenDDisglGqtkaaldlctgipesrka 169
                                         +D++ e y q +++++q+ +l +g+l+   ++vdl +i ++ ++ + Ge+D +  +  +        +i  +  +
  gi|313117211|ref|YP_004044194.1| 254 DGIDVAGETYNQFLQDIYQDNKLVNGELMLGEQHVDLANI-DMPVIQIIGEHDHLIPPESSIPF---NDAIASD-DT 325
                                       479************************************9.6899999*****98765444333...3333322.34 PP

                        PHB_depo_C 170 hylqegvGhyGvfsGsrfreeivPrvrd 197
                                         ++  +Gh G+   s+ + e+ P+v d
  gi|313117211|ref|YP_004044194.1| 326 MVIEFPTGHIGLSVSSKSHAELWPQVCD 353
                                       4556666777777777777777777766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3
                        PHB_depo_C 142 GenDDisglGqtkaal 157
                                        e +Di+g+G + a++
  gi|313117211|ref|YP_004044194.1| 386 AELEDITGIGPAYATR 401
                                       5889******998875 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05     0.013       4      37 ..     384     417 ..     381     437 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                              Cdd1   4 alkelqdiPniGkalaedlvelGirsveelkged 37 
                                       + +el+di +iG+a a  l+e Gi+++e+l+  +
  gi|313117211|ref|YP_004044194.1| 384 ESAELEDITGIGPAYATRLRESGIETFEDLASAE 417
                                       6789**************************9765 PP

>> RNAse_A_bac  Bacterial CdiA-CT RNAse A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   8.4e-05       0.1      27      62 ..     406     441 ..     397     445 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-05
                       RNAse_A_bac  27 aastFtdlatAekavsealranseeikkwlkeaakd 62 
                                          tF+dla+Ae  ++e+++  +++ ++w++ea+++
  gi|313117211|ref|YP_004044194.1| 406 GIETFEDLASAEVSIAEQIDVSESQFQQWIDEANER 441
                                       5669***************************74443 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.16      70     121 ..     122     169 ..      87     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                             PGAP1  70 eylndaIkyIlslysssekeptsviliGHSmGGivaraaltlknyikqsvnt 121
                                       +y+n  I++  ++    + ++ s+ ++G  mGG ++    ++ ++ +++v++
  gi|313117211|ref|YP_004044194.1| 122 DYVNRYIENCVDVV-RDRSDQDSINVLGYCMGGTMSA---MYTALHPEKVRN 169
                                       89999999999999.89999***************93...333344555555 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.4       8.3   9.9e+03      46      69 ..     360     384 ..     357     388 .. 0.48
   2 ?   11.8   0.0    0.0002      0.23      27      51 ..     418     442 ..     408     446 .] 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.3
                         HTH_Tnp_1  46 qyr.egeeaspaefeltaleeenre 69 
                                       q++  ++++++a++e++ +++ ++e
  gi|313117211|ref|YP_004044194.1| 360 QHEeTESTSAEATDEPATESAAVEE 384
                                       5532223333333666666655554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0002
                         HTH_Tnp_1  27 sevArrhgvspnqLykWrrqyrege 51 
                                       +++A++ +vs++q+ +W+ ++ e +
  gi|313117211|ref|YP_004044194.1| 418 VSIAEQIDVSESQFQQWIDEANERL 442
                                       579****************997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2992.40
//
Query:       gi|313117212|ref|YP_004044195.1|  [L=163]
Description: hypothetical protein Hbor_29970 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   12.6   0.0       0.11   11.8   0.0    1.3  1  CcmH      Cytochrome C biogenesis protein


Domain annotation for each model (and alignments):
>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.9e-06      0.11      55      97 ..      21      63 ..      12      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.9e-06
                                      HHHHHHHHHHHHHT--HHHHHHHHHHHHTTT-EE---XXXXXX CS
                              CcmH 55 kdlrrevremlkaGksdeeivdylvarYGdfVlykPpvkastl 97
                                       d  + + e+l++ +sd +i +y v+ +G  + ++P ++ +t+
  gi|313117212|ref|YP_004044195.1| 21 YDRPESIIERLDQLESDGKINEYTVDVWGRSINTSPSCSVTTA 63
                                      5666789*******************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1069.90
//
Query:       gi|313117213|ref|YP_004044196.1|  [L=221]
Description: acyl dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-19   67.7   0.0    9.5e-19   67.2   0.0    1.2  1  MaoC_dehydratas  MaoC like domain
    2.8e-07   30.7   0.0    3.2e-06   27.3   0.0    2.3  2  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.0   1.1e-22   9.5e-19      15     103 ..      96     181 ..      86     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.1e-22
                                       EEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--BT CS
                   MaoC_dehydratas  15 eitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVlp 91 
                                       + +++ +d+  +a++sgD+np+H+d+efAk ++fg+pI+hG l ++++++++++  g    + + ++++ F +   p
  gi|313117213|ref|YP_004044196.1|  96 TKQLSSEDVSAFATISGDTNPLHLDDEFAKRTRFGTPIVHGTLISGLISAALARFPGV---TIYLSQDLEFLSAAEP 169
                                       678899**********************************************999888...77************** PP

                                       TCEEEEEEEEEE CS
                   MaoC_dehydratas  92 gdtlkvelevvg 103
                                       g tl+++ e ++
  gi|313117213|ref|YP_004044196.1| 170 GGTLTATCEITE 181
                                       ******999887 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.016   1.4e+02      67     101 ..      60     100 ..      26     101 .. 0.74
   2 !   27.3   0.0   3.6e-10   3.2e-06      13     102 ..      98     181 ..      89     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.016
                   MaoC_dehydrat_N  67 algidlsrllhgeqefeyhe......piraGDelttesria 101
                                       + g++l  +l +  ++ +++      ++ +G+++++++++ 
  gi|313117213|ref|YP_004044196.1|  60 DEGVELDSILETRHQWSFERsvnryeELGVGERVSFTKQLS 100
                                       44788889999999999977555566888999999999985 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3.6e-10
                   MaoC_dehydrat_N  13 evereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhgeqefeyhepir 89 
                                       +++ e+v  fa   g+tnp++ld+e a++++++++i+  t+ + l  +a  l +  g+    ++ ++q +e+   + 
  gi|313117213|ref|YP_004044196.1|  98 QLSSEDVSAFATISGDTNPLHLDDEFAKRTRFGTPIVHGTLISGLISAA--LARFPGV----TIYLSQDLEFLSAAE 168
                                       67899******************************************99..4444444....56789999******* PP

                   MaoC_dehydrat_N  90 aGDelttesriad 102
                                       +G++lt +++i++
  gi|313117213|ref|YP_004044196.1| 169 PGGTLTATCEITE 181
                                       *********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1467.62
//
Query:       gi|313117214|ref|YP_004044197.1|  [L=56]
Description: hypothetical protein Hbor_29990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00017   21.4   9.2    0.00017   21.4   9.2    2.0  2  C1_1             Phorbol esters/diacylglycerol binding domain
     0.0072   16.2  14.5      0.052   13.5  14.6    1.9  1  Prok-RING_1      Prokaryotic RING finger family 1
  ------ inclusion threshold ------
       0.11   12.5  20.2       0.21   11.6   0.2    2.9  3  YhfH             YhfH-like protein
       0.41   10.3  13.2       0.81    9.4   0.1    3.2  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        0.5   10.7  15.4       0.48   10.8   7.6    2.1  2  C1_2             C1 domain
       0.53   10.4  12.9        1.3    9.2  12.9    1.5  1  Zf_RING          KIAA1045 RING finger
        1.3    9.5  14.1        1.9    8.9  14.0    1.4  1  zf-RING_2        Ring finger domain
        5.1    7.1  13.0         18    5.3   0.3    2.8  2  zf-HIT           HIT zinc finger
        9.1    5.5   7.4        2.8    7.1   3.0    1.9  2  Gmx_para_CXXCG   Protein of unknown function (Gmx_para_CXXCG)


Domain annotation for each model (and alignments):
>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   9.2   8.5e-08   0.00017      10      48 ..       3      39 ..       1      41 [. 0.90
   2 ?    4.1   0.4     0.021        42      26      35 ..      37      46 ..      35      48 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.5e-08
                                      S--B-TTT-SB--SSSS-EEEETTT--EE-CCCCTTS-S CS
                              C1_1 10 qptfCkhCgeflwgkekqglkCswCkllvHkkChekvpk 48
                                      + ++C+ Cge l   ek+   C+ C++ +H++C+e  ++
  gi|313117214|ref|YP_004044197.1|  3 MGNKCTVCGERL--TEKHVRDCTICGCQMHNQCMEYFQT 39
                                      5689********..********************98765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                                      S-EEEETTT- CS
                              C1_1 26 kqglkCswCk 35
                                      +q + C++C+
  gi|313117214|ref|YP_004044197.1| 37 FQTYECQTCG 46
                                      6888899996 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5  14.6   2.6e-05     0.052       3      39 ..       3      38 ..       1      49 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                       Prok-RING_1  3 tgkkCpvCgkelkeedDiVvCpeCgtpyHraCyekag 39
                                       g+kC+vCg++l+e+  +  C+ Cg   H +C e++ 
  gi|313117214|ref|YP_004044197.1|  3 MGNKCTVCGERLTEK-HVRDCTICGCQMHNQCMEYFQ 38
                                      589**********98.7999************98764 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2    0.0001      0.21      15      27 ..       6      18 ..       4      19 .. 0.92
   2 ?    3.0  13.8     0.051     1e+02      15      37 .]      21      45 ..      19      45 .. 0.90
   3 ?    4.0   1.3     0.024        49      15      22 ..      41      48 ..      39      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                              YhfH 15 kCteCGkeieEqa 27
                                      kCt CG+ + E++
  gi|313117214|ref|YP_004044197.1|  6 KCTVCGERLTEKH 18
                                      7**********98 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.051
                              YhfH 15 kCteCGkeieEqaecYgn..eCekC 37
                                       Ct CG +++ q+  Y++  eC++C
  gi|313117214|ref|YP_004044197.1| 21 DCTICGCQMHNQCMEYFQtyECQTC 45
                                      6***************985569999 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.024
                              YhfH 15 kCteCGke 22
                                      +C++CG+e
  gi|313117214|ref|YP_004044197.1| 41 ECQTCGDE 48
                                      7*****86 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.8    0.0042       8.3       8      14 ..       6      12 ..       3      15 .. 0.90
   2 ?    2.2   1.6      0.07   1.4e+02       8      13 ..      21      26 ..      14      29 .. 0.81
   3 ?    9.4   0.1    0.0004      0.81       4      15 ..      37      48 ..      34      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0042
                                      E-TTT-- CS
                   Desulfoferrod_N  8 kCevCGn 14
                                      kC+vCG+
  gi|313117214|ref|YP_004044197.1|  6 KCTVCGE 12
                                      9*****6 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.07
                                      E-TTT- CS
                   Desulfoferrod_N  8 kCevCG 13
                                       C++CG
  gi|313117214|ref|YP_004044197.1| 21 DCTICG 26
                                      5****9 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0004
                                      T-EEE-TTT--E CS
                   Desulfoferrod_N  4 levYkCevCGni 15
                                       + Y C+ CG++
  gi|313117214|ref|YP_004044197.1| 37 FQTYECQTCGDE 48
                                      699*******85 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   7.6   0.00024      0.48      20      47 .]       6      34 ..       3      34 .. 0.91
   2 ?    5.3   0.9     0.012        25      31      38 ..      37      45 ..      34      50 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                              C1_2 20 nCsaCgrkidgff.YsCseCdfslhvrCa 47
                                      +C +Cg+  ++++   C++C  ++h +C+
  gi|313117214|ref|YP_004044197.1|  6 KCTVCGERLTEKHvRDCTICGCQMHNQCM 34
                                      8*******888888**************6 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                              C1_2 31 ff.YsCseC 38
                                      f+ Y+C++C
  gi|313117214|ref|YP_004044197.1| 37 FQtYECQTC 45
                                      445666666 PP

>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  12.9   0.00064       1.3       7      40 ..       6      40 ..       2      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00064
                           Zf_RING  7 lCeiC.evytaeelypCRvCtkvfHegClrklgyl 40
                                       C++C e  t ++   C +C   +H++C++ ++  
  gi|313117214|ref|YP_004044197.1|  6 KCTVCgERLTEKHVRDCTICGCQMHNQCMEYFQTY 40
                                      6****8899999999**************987655 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  14.0   0.00095       1.9       1      43 [.       5      45 ..       5      46 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00095
                         zf-RING_2  1 deCpICleelssadsvlll.pCgHvfhreClerwlrssstCPlC 43
                                      ++C++C e+l+ +++v+ +  Cg  +h +C+ +++ ++ +C +C
  gi|313117214|ref|YP_004044197.1|  5 NKCTVCGERLT-EKHVRDCtICGCQMHNQCM-EYF-QTYECQTC 45
                                      68****99996.5888855358877*****6.556.55567766 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.009        18       4      10 ..       6      12 ..       3      21 .. 0.78
   2 ?    4.0   7.0     0.023        46       5      21 ..      27      47 ..      18      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.009
                                      B-TTT-S CS
                            zf-HIT  4 lCgvCgf 10
                                      +C vCg+
  gi|313117214|ref|YP_004044197.1|  6 KCTVCGE 12
                                      7999997 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.023
                                      -TT...T-S.B-SEE-TTT-- CS
                            zf-HIT  5 Cgv...Cgf.pakYkCpkCnt 21
                                      C++   C + +  Y C +C+ 
  gi|313117214|ref|YP_004044197.1| 27 CQMhnqCMEyFQTYECQTCGD 47
                                      4448889999*********95 PP

>> Gmx_para_CXXCG  Protein of unknown function (Gmx_para_CXXCG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.8      0.23   4.5e+02      27      36 ..       4      13 ..       1      25 [. 0.63
   2 ?    7.1   3.0    0.0014       2.8     158     180 ..      27      49 ..      21      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.23
                    Gmx_para_CXXCG 27 gveCptcgat 36
                                      g +C++cg+ 
  gi|313117214|ref|YP_004044197.1|  4 GNKCTVCGER 13
                                      5556666653 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0014
                    Gmx_para_CXXCG 158 grlhpdclpedreppCetCGres 180
                                        ++h++c+   ++  C+tCG e+
  gi|313117214|ref|YP_004044197.1|  27 CQMHNQCMEYFQTYECQTCGDET 49 
                                       589*****************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 383.43
//
Query:       gi|313117215|ref|YP_004044198.1|  [L=152]
Description: nucleic acid-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-06   27.3   0.7    4.9e-06   26.5   0.7    1.4  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.7   2.7e-10   4.9e-06       5      64 ..      52     125 ..      49     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.7e-10
                                       -G.G-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT......-EE-EEEEEEES..............TT-B-EEE- CS
                     OB_aCoA_assoc   5 sg.rGtvysftvvhrappgfaeeaPyvvgvVeLde...gvrimarlvgvdpde............vriGmrVravf 64 
                                       s  ++tv ++tv  + p   + ++P +v++Ve+d     vr +++l  + + +            v iG++Vr v+
  gi|313117215|ref|YP_004044198.1|  52 SEyTATVLTWTVSTATP--SGVRRPNPVAIVEFDIdgeSVRAIGQLATAGDFDdgsgtdeemsvdVAIGDEVRPVY 125
                                       5559*************..889************976677777777655432246677799999999******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 1010.92
//
Query:       gi|313117216|ref|YP_004044199.1|  [L=385]
Description: acetyl-CoA acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-56  191.3   0.0    2.6e-56  190.9   0.0    1.2  1  Thiolase_N       Thiolase, N-terminal domain
    2.3e-07   30.5   0.1    6.2e-07   29.1   0.0    1.7  2  Thiolase_C       Thiolase, C-terminal domain
     0.0063   16.5   0.1         17    5.4   0.0    3.3  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
  ------ inclusion threshold ------
      0.067   12.7   0.9       0.26   10.8   0.7    1.9  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.9   0.0   5.9e-60   2.6e-56       1     260 []       4     223 ..       4     223 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.9 bits;  conditional E-value: 5.9e-60
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TT CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipee 75 
                                       v+++sa++t++g+     +   + +Llaea++a+l+++gv+p++vd+++v+n++++ +egq+ i +++a+++ +  +
  gi|313117216|ref|YP_004044199.1|   4 VAVISASMTQFGN----REGQFILDLLAEAGEACLDDVGVSPDSVDHLYVSNMASGeFEGQTgIPNALAHDLSM-LP 75 
                                       79***********....666779********************************99*****************.** PP

                                       SEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTT CS
                        Thiolase_N  76 vpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafne 152
                                       ++++++++++sSg ++v++a+qsia+g++++++++G+E+m++++ta++td++++++++ e+++++++p+        
  gi|313117216|ref|YP_004044199.1|  76 AYTTRIDQTSSSGGAGVYAAWQSIASGASEMTLLVGGEKMTHRSTADTTDIIASITHPVEYKHGITLPT-------- 144
                                       *********************************************************************........ PP

                                       SEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS CS
                        Thiolase_N 153 ehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLakl 229
                                        ++Glta++++++y+++Re+++++Avk+h++++++++a+ F++ei              + ++a++++v a++L+ +
  gi|313117216|ref|YP_004044199.1| 145 -FAGLTARRYLHEYDAPRESLARVAVKNHANGVDNPHAQ-FRKEI--------------TLEDALEAPVIADPLRLY 205
                                       .**************************************.*****..............899*************** PP

                                       -BSSSTTSS-BTTSB--BEEEEEEEEEEEHH CS
                        Thiolase_N 230 kpaFkkeGtvtAgnasqisDGaaavllmses 260
                                                    ++++isDG+aa+l+++es
  gi|313117216|ref|YP_004044199.1| 206 -------------DFCPISDGSAALLFCPES 223
                                       .............***************986 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         1   4.6e+03      27      45 ..      29      47 ..      18      53 .. 0.82
   2 !   29.1   0.0   1.4e-10   6.2e-07      29     120 ..     264     377 ..     244     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1
                                      HHHHHHHHHT--GGGESEE CS
                        Thiolase_C 27 aikkvlkkagltvedidlf 45
                                      a +++l+++g++ +++d +
  gi|313117216|ref|YP_004044199.1| 29 AGEACLDDVGVSPDSVDHL 47
                                      6678999999999999976 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 1.4e-10
                                       HHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHHH CS
                        Thiolase_C  29 kkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasGa 87 
                                       + + + ag +  did+ E+++ F+   +   ++l++ +                    +N  GG  + GHPlGasG+
  gi|313117216|ref|YP_004044199.1| 264 NIAYEMAGRNPGDIDVAELHDMFSILEFLQSEDLGFFEkgegwkavedgithrdgdLPINTSGGLKSKGHPLGASGV 340
                                       5567889999*************************9999**************99888******************* PP

                                       HHHHHHHHHHHHCTT....SEEEEEEEETTTEEEEEE CS
                        Thiolase_C  88 Rivvtllselkkegg....klgvaalCigggqgvalv 120
                                        ++  + ++++++ g       v   C+ gg g+ ++
  gi|313117216|ref|YP_004044199.1| 341 AQAYEIHKQVTNDAGprqvDADVGLTCNVGGFGNCVI 377
                                       *999999999887651111455666899999998876 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.037   1.6e+02      26      48 ..      26      48 ..       4      56 .. 0.75
   2 !    4.9   0.0    0.0057        25       1      51 [.     232     284 ..     232     288 .. 0.74
   3 !    5.4   0.0    0.0039        17      87     115 ..     331     359 ..     315     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.037
                                      HHHHHHHHHHHHT--GGGEEEEE CS
                   Ketoacyl-synt_C 26 qaraiekalaeagvdpedvdyve 48
                                      +a+a e++l+++gv+p++vd++ 
  gi|313117216|ref|YP_004044199.1| 26 LAEAGEACLDDVGVSPDSVDHLY 48
                                      5678899************9764 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0057
                                       SEEEEEEEEEE--STSSSTSTTHHHHHHHHHH...HHHHHT--GGGEEEEE-SS CS
                   Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiek...alaeagvdpedvdyveahg 51 
                                       y+v++g++    + h    + ++  ++ ++e+   a+++ag +p d+d+ e h+
  gi|313117216|ref|YP_004044199.1| 232 YSVVTGVGGAT-DTHVVHERSDPTTMRGVVESgniAYEMAGRNPGDIDVAELHD 284
                                       67788888777.556666666666666665443339***************997 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0039
                                       H-B-GGGHHHHHHHHHHHHHHHTEE--BT CS
                   Ketoacyl-synt_C  87 iGHleaAaGvaelikvvlalkhgvipptl 115
                                        GH ++A+Gva++  + +++ +++ p ++
  gi|313117216|ref|YP_004044199.1| 331 KGHPLGASGVAQAYEIHKQVTNDAGPRQV 359
                                       5************9999998888777665 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.2     9e+02      91     124 ..      25      58 ..      19      83 .. 0.74
   2 ?   10.8   0.7   5.8e-05      0.26     171     211 ..      81     121 ..      46     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESST CS
                     ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgag 124
                                       ll ea + +l d g++p+++d+  v +++  + +
  gi|313117216|ref|YP_004044199.1|  25 LLAEAGEACLDDVGVSPDSVDHLYVSNMASGEFE 58 
                                       67788899999******99998777666655555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5.8e-05
                                       EESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHH CS
                     ketoacyl-synt 171 vdtACsSslvavhaavqslrsgeadvalaGGvellltpeav 211
                                       +d   sS+ + v aa+qs+ sg +++ l  G e +++ ++ 
  gi|313117216|ref|YP_004044199.1|  81 IDQTSSSGGAGVYAAWQSIASGASEMTLLVGGEKMTHRSTA 121
                                       566678889**********************9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2659.12
//
Query:       gi|313117217|ref|YP_004044200.1|  [L=247]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-66  222.2   1.1    7.9e-66  221.9   1.1    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.8e-60  203.1   2.0    3.3e-60  202.9   2.0    1.1  1  adh_short        short chain dehydrogenase
    5.1e-21   75.4   0.3    7.2e-21   74.9   0.3    1.2  1  KR               KR domain
    0.00025   20.6   0.2    0.00033   20.2   0.2    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00055   19.9   0.3    0.00071   19.5   0.3    1.3  1  NAD_binding_10   NAD(P)H-binding
     0.0023   17.1   0.2     0.0028   16.8   0.2    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
       0.13   12.7   0.1       0.47   11.0   0.0    1.9  2  CoA_binding_2    CoA binding domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.9   1.1   3.1e-69   7.9e-66       1     231 [.      12     243 ..      12     245 .. 0.95

  Alignments for each domain:
  == domain 1  score: 221.9 bits;  conditional E-value: 3.1e-69
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v.lecDVtdeeqvealveevvekfgklDilv 74 
                                       Ga +gIGrai k+l + Ga+v++ +++ e+ + +v+e  ee g + v +++DV+d +qv+a+ ++v  +fg++D+lv
  gi|313117217|ref|YP_004044200.1|  12 GASRGIGRAITKELGQSGANVIVNYRSSESaAYDVAESIEENGGTaVpVQADVSDISQVKAMRDTVHGEFGSIDVLV 88 
                                       999**************************9977777777776655379***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaale 149
                                       nnagi+ +  + f++++++++++++dvnl ++f+++k + + + k++ g+++n+ssv ++++  +++ y+a+K ++ 
  gi|313117217|ref|YP_004044200.1|  89 NNAGITVD--KTFTNMTEADWKQVIDVNLGGVFNCTKTFYEdIKKANeGRLINISSVIGKQGNYGQSNYAASKSGML 163
                                       ********..*******************************7665557***************************** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqt 226
                                       ++tr++A el++ g + N+v+pg+++T+++++++  ++++++l++++pl+r+++pee+a+++ fLas+e+sy+tG++
  gi|313117217|ref|YP_004044200.1| 164 GFTRSIALELASSGSTANCVAPGYTRTDMVDDVP--EDIQDKLRSKIPLNRFAEPEEIANVVRFLASEESSYMTGEV 238
                                       *********************************9..9**************************************** PP

                                       EEEST CS
                      adh_short_C2 227 lvvDg 231
                                       + v+g
  gi|313117217|ref|YP_004044200.1| 239 IDVNG 243
                                       ***98 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.9   2.0   1.3e-63   3.3e-60       2     193 ..       7     199 ..       6     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 202.9 bits;  conditional E-value: 1.3e-63
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       + ++tGas+GIGrai kel ++Ga+v+v + +se+++  va++++e+g +a+++q+Dv+d ++v+a+ +++  ++g+
  gi|313117217|ref|YP_004044200.1|   7 TCVITGASRGIGRAITKELGQSGANVIVnYRSSESAAYDVAESIEENGGTAVPVQADVSDISQVKAMRDTVHGEFGS 83 
                                       679*************************9999999999*************************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       +dvLvnNAGit +++f +++e++w++vi+vNl gvf++t+++++ ++k+++Gr +n+sSv+gk+++ g++ Y+AsK 
  gi|313117217|ref|YP_004044200.1|  84 IDVLVNNAGITVDKTFTNMTEADWKQVIDVNLGGVFNCTKTFYEDIKKANEGRLINISSVIGKQGNYGQSNYAASKS 160
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                       ++ g+trs+a ela++g + n+vaPG+++Tdm+ ++ e+
  gi|313117217|ref|YP_004044200.1| 161 GMLGFTRSIALELASSGSTANCVAPGYTRTDMVDDVPED 199
                                       ********************************9988776 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.3   2.8e-24   7.2e-21       3     156 ..       8     162 ..       7     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 2.8e-24
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        +itG+  g+G+++++ l ++ga+ +v   Rs  +++++ +  +++e++g +   v+aDvsd ++v+a+ ++++ e+
  gi|313117217|ref|YP_004044200.1|   8 CVITGASRGIGRAITKELGQSGANVIVNY-RS--SESAAYDVAESIEENGGTAVPVQADVSDISQVKAMRDTVHGEF 81 
                                       68********************9877765.66..45666678999******************************** PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaa 152
                                       ++i   ++ Ag++ dk++++mt++d++qv+   + G+ n  +++ +     +   ++ +SS+ g  g+ gq+nYaa 
  gi|313117217|ref|YP_004044200.1|  82 GSIDVLVNNAGITVDKTFTNMTEADWKQVIDVNLGGVFNCTKTFYEdikkANEGRLINISSVIGKQGNYGQSNYAAS 158
                                       ***************************************9999877676577789*********************8 PP

                                       HHHH CS
                                KR 153 Nafl 156
                                        + +
  gi|313117217|ref|YP_004044200.1| 159 KSGM 162
                                       7655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   1.3e-07   0.00033       2     121 ..       9     146 ..       8     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HH...HHHHHHHHH..T-S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrs...alerlfkee..qpd 66 
                                       ++tGa+  iG+a++k+l + g +vi+  r s++ +    e +         v++d+ d s   a+++ ++ e   +d
  gi|313117217|ref|YP_004044200.1|   9 VITGASRGIGRAITKELGQSGANVIVNYRSSESAAYDVAESIeenggtaVPVQADVSDISqvkAMRDTVHGEfgSID 85 
                                       79****************************999999998888******96677777777644466666666667899 PP

                                       EEEE--S..---HHHHHHSH..HHHHHHHTHHHHHHHHHHH....HHTCTEEEEEEEGGGGTS CS
                         Epimerase  67 avihlAa..vggvaassedp..adfieknlqgtlnlleaar....kagvkrllflsSsevYGk 121
                                       + ++ A+  v    ++++++  +++i+ nl g+ n  +       ka+  rl+++sS  v Gk
  gi|313117217|ref|YP_004044200.1|  86 VLVNNAGitVDKTFTNMTEAdwKQVIDVNLGGVFNCTKTFYedikKANEGRLINISS--VIGK 146
                                       999998854444445554442257899999888887777662222445558998888..5555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   2.8e-07   0.00071       1      98 [.      12     142 ..      12     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.8e-07
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH.....HHHCT.TTCEEEE--TT-CCHHHHHHT.......T-SEE CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla.....eleae.eglevvegdvtdvedlaealk.......gadaV 64 
                                       GA+ ++Gr+++kel ++g  +v +  R++e++a     ++e++   +  v++dv+d +++++  +        +d+ 
  gi|313117217|ref|YP_004044200.1|  12 GASRGIGRAITKELGQSG-ANVIVNYRSSESAAydvaeSIEENgGTAVPVQADVSDISQVKAMRDtvhgefgSIDVL 87 
                                       9****************5.9********9998755555677773445569999998665543322222444355666 PP

                                       EES---TCC....HHHH...................HHHHHHHHHHCT--EEEEEEE CS
                    NAD_binding_10  65 vsalggggk....deeg...................aknivdaakeagvkRfvlvsa 98 
                                       v ++g + +    +  +                   +k+  +  k+a+  R++ +s+
  gi|313117217|ref|YP_004044200.1|  88 VNNAGITVDktftN--MteadwkqvidvnlggvfncTKTFYEDIKKANEGRLINISS 142
                                       66665443323320..13334444555555666666666666666666666666666 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   1.1e-06    0.0028       2     111 ..       9     121 ..       8     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-06
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.... CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel.. 76 
                                       ++tGa+  iG+++++++ ++ ++ i+ + ++E + y++++++ee+  +  +   + + + d+ + + ++++++    
  gi|313117217|ref|YP_004044200.1|   9 VITGASRGIGRAITKELGQSGANVIVNYRSSESAAYDVAESIEENGGT-AV--PVQADVSDISQVKAMRDTVHGEfg 82 
                                       79**************************************99654443.33..444566666666666665543222 PP

                                       T-SEEEE----...--.HHHHHHSHHHHHHHHHHHHHHH CS
                   Polysacc_synt_2  77 kvdvvfhaAAl...Kh.VPlveenpleaiktNvlgtenv 111
                                       ++dv+++ A +   K    + e  + ++i+ N  g  n+
  gi|313117217|ref|YP_004044200.1|  83 SIDVLVNNAGItvdKTfTNMTEADWKQVIDVNLGGVFNC 121
                                       566666666542223213455666666666666665555 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.47      11      65 ..      38      90 ..      29      96 .. 0.89
   2 ?   -2.7   0.0       3.1   7.9e+03      53      53 ..     205     205 ..     167     231 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                      -TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-H CS
                     CoA_binding_2 11 npgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftpp 65
                                       +++++y v++ + e+g + vpV+   + i  +k+ +++    ++  ++dv+++ 
  gi|313117217|ref|YP_004044200.1| 38 SSESAAYDVAESIEENGGTAVPVQADVSDISQVKAMRDTV--HGEFGSIDVLVNN 90
                                      56899**********************************9..3788899888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.1
                                       . CS
                     CoA_binding_2  53 p 53 
                                        
  gi|313117217|ref|YP_004044200.1| 205 R 205
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1673.20
//
Query:       gi|313117218|ref|YP_004044201.1|  [L=514]
Description: propionyl-CoA carboxylase carboxyltransferase subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.1e-196  652.1   0.1   5.7e-196  651.9   0.1    1.0  1  Carboxyl_trans  Carboxyl transferase domain
     0.0007   19.1   0.5     0.0013   18.3   0.1    1.6  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.9   0.1  6.4e-200  5.7e-196       1     493 [.      26     511 ..      26     512 .. 0.99

  Alignments for each domain:
  == domain 1  score: 651.9 bits;  conditional E-value: 6.4e-200
                                       SSCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSG CS
                    Carboxyl_trans   1 kehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgp 76 
                                       k+h++Gkltareri++lld+gsF+e++++++h++ ++g+  + +p+d+vvtg G+v+Gr  +v+a+d+tv+ggs++ 
  gi|313117218|ref|YP_004044201.1|  26 KQHDKGKLTARERISYLLDEGSFVEVDAFAEHQCRNFGMeDRTVPGDAVVTGHGTVNGRPIVVFAHDFTVFGGSVSS 102
                                       69*************************************8889********************************** PP

                                       GGCEEECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHH CS
                    Carboxyl_trans  77 akgekllkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpal 153
                                       + +ek+ k++++ai+ag+p++g+ndsgGa  riqegv+sl+g++++f++n+kasg++pqis ++g+caGg++Y+pal
  gi|313117218|ref|YP_004044201.1| 103 VVAEKINKIVDTAIEAGVPVVGLNDSGGA--RIQEGVDSLDGFANLFRRNTKASGVVPQISCIMGPCAGGAVYSPAL 177
                                       *****************************..********************************************** PP

                                       TSEEEEETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGG CS
                    Carboxyl_trans 154 gdrvimveetskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnr 230
                                       +d+++mv++ts++++tGpdvi++v+g e+vt++elgGa++h++ksGvah ++ dde+al++ir+llsylP    nn+
  gi|313117218|ref|YP_004044201.1| 178 TDFTFMVQDTSHMMITGPDVIETVTG-EQVTMDELGGANAHTSKSGVAHKAFRDDEAALDSIRELLSYLP---ANNM 250
                                       **************************.*******************************************...999* PP

                                       SS----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--S CS
                    Carboxyl_trans 231 esaPivetadepdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetr 304
                                       e++P+ve++d+p+r+   li+i+P+++kkpyD+ evi+ +vd g+F E++e+yAk++VvGfArl+G+++GvvAn++r
  gi|313117218|ref|YP_004044201.1| 251 EDPPRVEPWDDPNRRddeLIDIIPEEPKKPYDMTEVIQHIVDVGSFYETHENYAKNLVVGFARLDGRSIGVVANQPR 327
                                       **************999999********************************************************* PP

                                       EEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEH CS
                    Carboxyl_trans 305 veaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayG 381
                                       v+aG  l+i +++K arf+r+cda+n+P+++++dv+Gf++G++qe+ggi+khGakl++a+ ea+vP +tv++rkayG
  gi|313117218|ref|YP_004044201.1| 328 VNAG-TLDIAASEKGARFVRFCDAFNIPILTFVDVPGFMPGTDQEHGGIIKHGAKLIYAYGEATVPLLTVVTRKAYG 403
                                       ****.************************************************************************ PP

                                       HHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Carboxyl_trans 382 GayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargf 458
                                       Gay+vm sk +gad+++awpta++aV+gp gav++l r+e+a+a+    +++a+r++ ++e++ee+++py+a++ g 
  gi|313117218|ref|YP_004044201.1| 404 GAYIVMASKGLGADVNYAWPTAELAVMGPRGAVNVLHRREIAKAD----NPEAKRQELIDEFREEFAHPYRASEKGH 476
                                       ********************************************9....99************************** PP

                                       HHTTSSHHHHHHTTSSSEEEHGGGHHHHHHHHHHH CS
                    Carboxyl_trans 459 aDavidpsetraklvialelewkkarklparkrrn 493
                                       +D+vidp+etr +l+++l+l ++k+ ++p++ ++n
  gi|313117218|ref|YP_004044201.1| 477 IDDVIDPRETRPRLIKDLQLRETKRAENPPKTHGN 511
                                       *********************************98 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.38   3.4e+03      55      74 ..     112     129 ..      69     178 .. 0.56
   2 !   18.3   0.1   1.4e-07    0.0013      28     151 ..     315     439 ..     296     447 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.38
                                       HHHHHTSSS--EEEEEEEE- CS
                              MdcE  55 VleaieraekrpilvlvDva 74 
                                       V+ ai  +   p++ l D+ 
  gi|313117218|ref|YP_004044201.1| 112 VDTAI--EAGVPVVGLNDSG 129
                                       33333..2223444444444 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.4e-07
                                       EEEEEEE---TTSS-B-HHHHHHHHHHHHHHH..TSSS--EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHH CS
                              MdcE  28 svrfvaVigdankgevGvdealaLaaaVleai..eraekrpilvlvDvasQrlgrrdEllGihealahlakalarAr 102
                                       ++r + V+++  + + G ++ +a +++    +    a + pil  vDv++   g  +E  Gi +  a l+ a+  A 
  gi|313117218|ref|YP_004044201.1| 315 DGRSIGVVANQPRVNAGTLD-IAASEKGARFVrfCDAFNIPILTFVDVPGFMPGTDQEHGGIIKHGAKLIYAYGEAT 390
                                       55666666666666666554.2223333333322345678**********************************998 PP

                                       HHT--EEEEEEEEEEHHHHH...HTTTT-SEEEEEET-EEESS-HHHHHHHH CS
                              MdcE 103 laGhpvigllvGkavsGafl...ahglqanrlialpgvqvavmdkasaArvT 151
                                       +   p+++++  ka  Ga++   + gl a++  a p ++ avm+ + a  v 
  gi|313117218|ref|YP_004044201.1| 391 V---PLLTVVTRKAYGGAYIvmaSKGLGADVNYAWPTAELAVMGPRGAVNVL 439
                                       6...9*************98555679******************99887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3602.24
//
Query:       gi|313117219|ref|YP_004044202.1|  [L=148]
Description: hypothetical protein Hbor_30040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0019   18.8  20.5     0.0038   17.9   9.6    3.6  4  ACC_epsilon  Acyl-CoA carboxylase epsilon subunit
  ------ inclusion threshold ------
        6.1    7.5  15.6        3.3    8.3  12.1    2.4  2  OAD_gamma    Oxaloacetate decarboxylase, gamma chain


Domain annotation for each model (and alignments):
>> ACC_epsilon  Acyl-CoA carboxylase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.14   1.3e+03      19      40 ..       8      29 ..       8      34 .. 0.77
   2 !    5.8   0.2    0.0026        23      20      40 ..      35      55 ..      33      63 .. 0.85
   3 !   17.9   9.6   4.2e-07    0.0038       9      56 ..      75     127 ..      72     130 .. 0.72
   4 ?    3.2   0.6     0.016   1.4e+02      25      49 ..     118     143 ..     116     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.14
                       ACC_epsilon 19 taVLaaraaaaaaaaaepapag 40
                                      ta++++r +++ +a+++++p++
  gi|313117219|ref|YP_004044202.1|  8 TAAVLQRPDEKDDAESDEKPRP 29
                                      7888888888888888888876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0026
                       ACC_epsilon 20 aVLaaraaaaaaaaaepapag 40
                                      aVL+ r a++a++++e++p++
  gi|313117219|ref|YP_004044202.1| 35 AVLLEREATKAEEPEETQPPK 55
                                      9*************9999875 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 4.2e-07
                       ACC_epsilon   9 nPtdeELAALtaVLaaraaaaaaaaaepapag..saWarper...rlrrplrp 56 
                                       ++t+ E+AA+ta+++a  +a++aaa+e + ++  + W+   r   +++rp+r 
  gi|313117219|ref|YP_004044202.1|  75 AATEAEVAAITAAVSAHLSAEQAAAEENQSKSesDPWQMSGRyrtATGRPART 127
                                       689***********998888887777777766797777666622255555555 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.016
                       ACC_epsilon  25 raaaaaaaaaepapag.saWarperr 49 
                                       r+a+ ++a+++p+ ++ s+W+  +++
  gi|313117219|ref|YP_004044202.1| 118 RTATGRPARTPPHLTTqSGWKLAAQA 143
                                       67888888888888889***987765 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  12.1   0.00037       3.3      37      76 ..      43      91 ..       5      92 .. 0.75
   2 ?   -1.1   0.1      0.34   3.1e+03      46      53 ..      97     104 ..      93     123 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00037
                         OAD_gamma 37 kkkkkkakaaaaaaaaaaaaa..............eldddeelvAvIaaAiaay 76
                                       k++++++++++++      a               ++ +e  vA+I+aA++a+
  gi|313117219|ref|YP_004044202.1| 43 TKAEEPEETQPPKQD-----ArqvsigknagdltvPDAATEAEVAAITAAVSAH 91
                                      222222222222222.....13346789999****889999***********99 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.34
                         OAD_gamma  46 aaaaaaaa 53 
                                       aaa+++++
  gi|313117219|ref|YP_004044202.1|  97 AAAEENQS 104
                                       11111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1037.32
//
Query:       gi|313117220|ref|YP_004044203.1|  [L=446]
Description: ATPase component of various ABC-type transport systems with duplicated ATPase domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-35  120.9   0.0      8e-35  120.3   0.0    1.3  1  ABC_tran         ABC transporter
    5.3e-18   65.3   0.0    1.3e-17   64.1   0.0    1.7  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    2.9e-07   30.6   0.1    0.00068   19.5   0.1    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    9.1e-06   26.0   0.0     0.0001   22.6   0.0    2.1  1  AAA_22           AAA domain
      3e-05   23.5   0.0    6.3e-05   22.5   0.0    1.5  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0043   17.5   0.3      0.011   16.1   0.1    2.0  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.032   14.0   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.017   14.9   0.0      0.026   14.3   0.0    1.2  1  AAA_15           AAA ATPase domain
      0.019   14.4   0.0        2.5    7.5   0.0    2.3  2  TniB             Bacterial TniB protein
      0.039   13.1   0.0      0.047   12.9   0.0    1.1  1  G-alpha          G-protein alpha subunit
      0.087   12.7   0.0       0.17   11.8   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
       0.12   11.7   0.0          2    7.7   0.0    2.1  2  AIG1             AIG1 family
       0.13   11.9   0.0       0.13   11.9   0.0    1.4  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.15   11.3   0.0       0.27   10.5   0.0    1.3  1  Zeta_toxin       Zeta toxin
       0.18   11.5   0.1       0.52   10.0   0.0    1.7  2  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0   6.7e-38     8e-35       2     136 ..      46     196 ..      45     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 6.7e-38
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + +s+++++ge+v++vGe+G+GKSt ++++++l++pt G+i++d++d++e   +el+s+r+e ++++q+  ++++p+
  gi|313117220|ref|YP_004044203.1|  46 DGISFEIERGETVGLVGESGCGKSTAAEAILRLEEPTDGTITFDDEDITEyddTELKSFRREAQMIFQNpdSSFDPR 122
                                       789***********************************************9999***************98999*** PP

                                       SBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++++e+            ++ +++ a + l+ ++l+++ v++ p++LSgGqkqrvalaral+ +p+l+++DEp 
  gi|313117220|ref|YP_004044203.1| 123 MSIGESiteplrihgvgPREHRLAIASDLLERVGLNASDVDRYPHELSGGQKQRVALARALVVNPRLIVADEPV 196
                                       ***************9977777777777777777777999999******************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   1.1e-20   1.3e-17       1      62 [.     248     310 ..     248     312 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.1e-20
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfal 62 
                                       vE++++++lf++p+HPYT+aLlr++p +d++ +   + + g++p++++ ++GC F++RCp ++
  gi|313117220|ref|YP_004044203.1| 248 VEIADTETLFEDPQHPYTRALLRAIPTIDAGTRgIDAALSGDVPNPSDPPTGCNFYTRCPEVV 310
                                       8********************************888999*********************876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00097       1.2       3      55 ..      59      99 ..      58     130 .. 0.78
   2 !   19.5   0.1   5.7e-07   0.00068     227     302 ..     159     232 ..     124     233 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00097
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpe 55
                                      +l+G  g+GKS+  +a+  l            e++  g+i+ ++  +++yd++
  gi|313117220|ref|YP_004044203.1| 59 GLVGESGCGKSTAAEAILRL------------EEPTDGTITFDDEDITEYDDT 99
                                      69***************998............666666666666666666654 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 5.7e-07
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                        ++ ++ ++elS G+k+  al+ al   +   +l++ DEp + L+ ++++++l+ll ++ ++ +  +++ +H+ +++
  gi|313117220|ref|YP_004044203.1| 159 ASDVDRYPHELSGGQKQRVALARALVVNP---RLIVADEPVSALDVSVQAEVLTLLkDIQTEFDLSILFISHDMSVV 232
                                       345567899*********9*******999...************************5555559**********8775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   8.4e-08    0.0001      10     128 ..      60     225 ..      53     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.4e-08
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglelka........... 70 
                                       ++GesG+GK+t ++ +l+  +       + ++++      +t   +t++k+++re   +++++ ++           
  gi|313117220|ref|YP_004044203.1|  60 LVGESGCGKSTAAEAILRLEE-------PTDGTItfddeDITEYDDTELKSFRREAQMIFQNPDSSfdprmsigesi 129
                                       79****************975.......46777766777888888889999999999999999999999******** PP

                            AAA_22  71 .................................erlsseellealeqalrarav...ielliiDEaqh.lr...see 107
                                                                         r   e    + ++ + ara    ++l++ DE    l+   ++e
  gi|313117220|ref|YP_004044203.1| 130 teplrihgvgprehrlaiasdllervglnasdvDRYPHELSGGQKQRVALARALvvnPRLIVADEPVSaLDvsvQAE 206
                                       ***********999999999999999999988633333333366666666666678999******8877989655** PP

                            AAA_22 108 aleeLrsllnlsrkgvqliLv 128
                                       +l+ L++++   +++++++++
  gi|313117220|ref|YP_004044203.1| 207 VLTLLKDIQT--EFDLSILFI 225
                                       **********..****99987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.2e-08   6.3e-05      27     211 ..      58     241 ..      38     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.2e-08
                                       EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                         +vG+ G+GKs   +Ai   L e +  ++   + +d+  + +++ ++ + e +++f+n+d++    ++++si  ++
  gi|313117220|ref|YP_004044203.1|  58 VGLVGESGCGKSTAAEAI-LRLEEPTDGTIT-FDDEDITEYDDTELKSFRREAQMIFQNPDSS---FDPRMSIGESI 129
                                       459***************.678876665555.455788888899999999999*********9...78889999888 PP

                                       ETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 104 krkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                        +  +  + +  +e + +  s+lle++g++ +       +LSgG+k+ vala  + +   +p  l + De  +aLD 
  gi|313117220|ref|YP_004044203.1| 130 TEPLR-IHGVGPREHRLAIASDLLERVGLNASdvdryphELSGGQKQRVALARALVV---NP-RLIVADEPVSALDV 201
                                       87777.667777888888889999999999999999999********9999877544...44.48999********* PP

                                       HHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkekskn..aQfivislreemlekadklvgv 211
                                       +  ++v +llk  +++    ++ is++  ++++   +v v
  gi|313117220|ref|YP_004044203.1| 202 SVQAEVLTLLKDIQTEfdLSILFISHDMSVVREICDTVAV 241
                                       ***********77776336788899998888887555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   9.2e-06     0.011      23      52 ..      54      82 ..      39     261 .. 0.80
   2 ?   -2.0   0.0       3.3     4e+03      99     128 ..     364     394 ..     334     422 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.2e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdg 52
                                      r+e v l+GesG+GKs+ ++++lr le+  
  gi|313117220|ref|YP_004044203.1| 54 RGETVGLVGESGCGKSTAAEAILR-LEEPT 82
                                      457899*****************5.66652 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.3
                            AAA_16  99 ekleealaavpelagaea.srllellkrlla 128
                                       ++l+++  + p+l++++a s l e+l ++++
  gi|313117220|ref|YP_004044203.1| 364 AELRREHDIPPSLTDSAAeSVLEEALDEIVR 394
                                       3333444455555555554444444444443 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.6e-05     0.032      13      45 ..      46      78 ..      43      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqal 45
                                      dg ++ei++ +++ l+G+sG GKST   Ai  l
  gi|313117220|ref|YP_004044203.1| 46 DGISFEIERGETVGLVGESGCGKSTAAEAILRL 78
                                      56678898777999***********99998876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.1e-05     0.026      17      72 ..      50     100 ..      47     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                            AAA_15  17 veidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenis 72 
                                       +ei+  e +  l+G+ ++GKS+++ea+  + + +    + +i++++ed+ ++++++
  gi|313117220|ref|YP_004044203.1|  50 FEIERGE-TVGLVGESGCGKSTAAEAILRLEEPT----DGTITFDDEDITEYDDTE 100
                                       5566556.778****************8888877....789999999998887665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.017        21      34      63 ..      54      83 ..      50      93 .. 0.83
   2 ?    7.5   0.0    0.0021       2.5     107     159 ..     174     224 ..     140     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.017
                              TniB 34 rmpnlllvGdsnnGKtmivekFarlhppek 63
                                      r + + lvG+s +GK++ +e   rl++p++
  gi|313117220|ref|YP_004044203.1| 54 RGETVGLVGESGCGKSTAAEAILRLEEPTD 83
                                      5567789************99999888775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0021
                              TniB 107 leqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       +++ +l+    +++r+++ DE  ++l   ++ q e+l +lk ++ e++++i  
  gi|313117220|ref|YP_004044203.1| 174 KQRVALARALVVNPRLIVADEPVSAL--DVSVQAEVLTLLKDIQTEFDLSILF 224
                                       44444444456899*******99999..788899**************99975 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.9e-05     0.047      26      81 ..      58     118 ..      41     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                                       EEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHHHHHHHHHHHHHHHHHHHHHT CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg.....fseeelatwraviqlnivrsiktilealesl 81 
                                       + l+G+s++GKsT  + + +l++++     f++e++ ++ +   + + r +++i+++ +s+
  gi|313117220|ref|YP_004044203.1|  58 VGLVGESGCGKSTAAEAILRLEEPTdgtitFDDEDITEYDDTELKSFRREAQMIFQNPDSS 118
                                       5599******************99999*********99*9999999999999999988773 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.17      84     120 ..      39      76 ..      10      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                       TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       + + ++++ ++ +++  +t+ lvG+SG GKSt  +a+l
  gi|313117220|ref|YP_004044203.1|  39 VGRVKAVDGISFEIERgETVGLVGESGCGKSTAAEAIL 76 
                                       555677888888888779999***********888776 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0016         2       3      22 ..      58      77 ..      56      92 .. 0.89
   2 ?    1.5   0.0      0.13   1.6e+02      32      65 ..     229     262 ..     221     286 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0016
                                      EEEESSTTSSHHHHHHHHHT CS
                              AIG1  3 ivlvGktgnGkSaTgNsilg 22
                                      + lvG +g+GkS+++ +il+
  gi|313117220|ref|YP_004044203.1| 58 VGLVGESGCGKSTAAEAILR 77
                                      669***************97 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                                       TS---SS-EEEEEEETTEEEEEEE--SCCCTTCC CS
                              AIG1  32 aqsvtkkcqkksrtwdgkkinViDTPglfdlsvs 65 
                                        + v + c ++  +  g+++++ DT  lf+  ++
  gi|313117220|ref|YP_004044203.1| 229 MSVVREICDTVAVMYLGQIVEIADTETLFEDPQH 262
                                       5567778999999***************987654 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.13       3      39 ..      43      80 ..      41     423 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      HHHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHSS CS
                                      xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  3 rvlDal.fpivqGqrtlipgafgvGktvisqslskqsn 39
                                      +++D + f i +G++++++g++g+Gk++ ++++++  +
  gi|313117220|ref|YP_004044203.1| 43 KAVDGIsFEIERGETVGLVGESGCGKSTAAEAILRLEE 80
                                      56665437899*******************99998765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00022      0.27      19      57 ..      58      96 ..      48     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                      + l+G +G+GKs++ae++ +  e++++ +++d  d+ e+
  gi|313117220|ref|YP_004044203.1| 58 VGLVGESGCGKSTAAEAILRLEEPTDGTITFDDEDITEY 96
                                      6689***************999999***99999888665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00044      0.52      22      51 ..      55      84 ..      36      98 .. 0.81
   2 ?   -2.4   0.1       2.7   3.2e+03     102     119 ..     196     213 ..     189     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00044
                                      SS-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                   Sigma54_activat 22 dlsvlitGesGtGKellaraiheaskrkek 51
                                        +v ++GesG+GK++ a+ai + ++ +++
  gi|313117220|ref|YP_004044203.1| 55 GETVGLVGESGCGKSTAAEAILRLEEPTDG 84
                                      5678899**************998776655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                                       GGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat 102 igelplelQekLlrvlqe 119
                                       ++ l++++Q+++l++l++
  gi|313117220|ref|YP_004044203.1| 196 VSALDVSVQAEVLTLLKD 213
                                       789999*******99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 3097.24
//
Query:       gi|313117221|ref|YP_004044204.1|  [L=369]
Description: dipeptide/oligopeptide/nickel ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.3e-28   97.6   0.0    1.3e-27   97.0   0.0    1.3  1  ABC_tran   ABC transporter
    7.2e-17   61.7   0.7    1.5e-16   60.7   0.3    1.8  2  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    1.8e-06   28.0   1.1    1.1e-05   25.4   0.1    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    0.00013   21.5   0.1    0.00037   20.0   0.1    1.6  1  SMC_N      RecF/RecN/SMC N terminal domain
     0.0059   16.4   0.0     0.0089   15.8   0.0    1.3  1  PRK        Phosphoribulokinase / Uridine kinase family
  ------ inclusion threshold ------
      0.019   15.3   0.5        0.1   12.9   0.5    2.1  1  AAA_22     AAA domain
      0.037   13.8   0.0      0.079   12.7   0.0    1.5  1  AAA_29     P-loop containing region of AAA domain
      0.061   12.8   0.0        0.1   12.1   0.0    1.3  1  AAA_7      P-loop containing dynein motor region
      0.088   13.2   0.1       0.28   11.6   0.1    1.8  2  AAA_16     AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.0   6.7e-31   1.3e-27       2     136 ..      26     185 ..      25     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 6.7e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx.. RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke....qeleslrkeigvlpqe.. 67 
                                       + vs+++++ge+vaivGe+G+GK+   + +++ l+       eG+i++dg dl+e    q   +  ++i+ ++q+  
  gi|313117221|ref|YP_004044204.1|  26 DSVSFDVNPGETVAIVGESGSGKTVTSESITKILDMppgeiVEGTITFDGMDLTEmsekQLQDIRGNRISHIFQNpq 102
                                       78*******************************9997888888999*****99998885555667789*******87 PP

                                       --S-TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSE CS
                                       xxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkl 129
                                       + l+p ++v+++               e ++++ ++l++ g++e + ++v++ p+++SgG+kqrv +a+al+++++l
  gi|313117221|ref|YP_004044204.1| 103 NGLNPVYKVGRQigetlrihrddlpkaEIRDRVIDLLDRTGIPE-ASSRVDDYPHEFSGGMKQRVLIAMALACDSDL 178
                                       789999999999*************9999999************.888889************************** PP

                                       EEEESTT CS
                                       xxxxxxx RF
                          ABC_tran 130 lllDEpt 136
                                       l++DEpt
  gi|313117221|ref|YP_004044204.1| 179 LIADEPT 185
                                       ******9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.3   7.5e-20   1.5e-16       1      65 []     237     298 ..     237     298 .. 0.96
   2 ?   -3.1   0.0       6.2   1.2e+04      49      55 ..     310     322 ..     301     323 .. 0.52

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 7.5e-20
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E+g++++++++p+HPYTkaL++++p   +  +   +i+g  ps+++ +eGC+F++RC++a++ C
  gi|313117221|ref|YP_004044204.1| 237 MEKGSVEEVIHNPAHPYTKALIECLPGRGSSMK---RIDGALPSVTEPPEGCRFNSRCEHAVSDC 298
                                       7*************************8877777...9**************************99 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.2
                         oligo_HPY  49 de......GCpFa 55 
                                       d        C+++
  gi|313117221|ref|YP_004044204.1| 310 DGsqthraSCVYY 322
                                       3333344479986 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.12   2.4e+02       3      16 ..      39      52 ..      38     105 .. 0.83
   2 !   25.4   0.1   5.5e-09   1.1e-05     200     302 ..     136     221 ..      81     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.12
                            AAA_21  3 vliGpNgsGKSnLL 16
                                      +++G  gsGK+   
  gi|313117221|ref|YP_004044204.1| 39 AIVGESGSGKTVTS 52
                                      79*********755 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 5.5e-09
                            AAA_21 200 sdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllr 276
                                        dl+++   +               e +++ +  ++e+S G+k+   ++ al+ +    +ll+ DEp + L+  +++
  gi|313117221|ref|YP_004044204.1| 136 IDLLDRTGIP---------------EASSRVDDYPHEFSGGMKQRVLIAMALACDS---DLLIADEPTTALDVTIQA 194
                                       3333333333...............344555556999*******966666666555...9***************** PP

                            AAA_21 277 rllellkelsr.ngaQviltTHSplll 302
                                        +l+ll++ ++  +  ++++TH+  ++
  gi|313117221|ref|YP_004044204.1| 195 QILQLLEDVQAeYNMSILFVTHDLGVV 221
                                       ******77777799********98776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.9e-07   0.00037      17     213 ..      27     233 ..      22     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.9e-07
                                       EEEEETTSS.EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--.BTTCSSTTEEEEEEEEEETTE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  17 tvilpfsks.ftaivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihk.skekasvkkaeveitfdnedk 88 
                                       +v+ +++++   aivG+ GSGK+   ++i  +L     + +  + +    dl    +k+ + +   +++ +f+n+++
  gi|313117221|ref|YP_004044204.1|  27 SVSFDVNPGeTVAIVGESGSGKTVTSESITKILDMPPGEIVEGTITfdgMDLTEMsEKQLQDIRGNRISHIFQNPQN 103
                                       5556666651458********************9887755555543111355555566778888999*********9 PP

                                       ESSSSSSCEEEEEEEETTSEEEEEETTEEE-H....HHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxx RF
                             SMC_N  89 klkiekeevsisrrvkrkgeseykingkevtk....kevsellesagiske.........lLSgGektLvalaLlfA 152
                                            ++ +++ r++ ++ +    i + +  k      v +ll ++gi +          ++SgG k+ v +a+ +A
  gi|313117221|ref|YP_004044204.1| 104 G---LNPVYKVGRQIGETLR----IHRDDLPKaeirDRVIDLLDRTGIPEAssrvddyphEFSGGMKQRVLIAMALA 173
                                       9...6677777777766555....555555550012446678999999888899999999******99999999988 PP

                                       HHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC-.SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 153 iqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemleka.dklvgvtk 213
                                             + l + De   aLD +  +++ +ll+  +++ n+ ++ ++++ +++++  d++v ++ 
  gi|313117221|ref|YP_004044204.1| 174 CD----SDLLIADEPTTALDVTIQAQILQLLEdvQAEYNMSILFVTHDLGVVSEIaDRVVVMYA 233
                                       75....5799**********************555666799999***99998876366666554 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.5e-06    0.0089       2      86 ..      38     120 ..      37     125 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.5e-06
                               PRK   2 IgvagsSGaGkttvarklekifgrekvkaaei.eg.dsflrldraekdleleerkrakekevsflspeandfdllye 76 
                                       +++ g+SG+Gkt +++ ++ki+    +++ ei eg + f  +d  e++ +  +   ++++    ++   n ++ +y+
  gi|313117221|ref|YP_004044204.1|  38 VAIVGESGSGKTVTSESITKILD---MPPGEIvEGtITFDGMDLTEMSEKQLQD-IRGNRISHIFQNPQNGLNPVYK 110
                                       689********************...4544443441445556666666554443.3344444445666677888888 PP

                               PRK  77 vlkelkegkk 86 
                                       v ++ +e+ +
  gi|313117221|ref|YP_004044204.1| 111 VGRQIGETLR 120
                                       8888777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   5.2e-05       0.1       8      30 ..      38      60 ..      33     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                      ++++GesG+GKT++ + +++ ld
  gi|313117221|ref|YP_004044204.1| 38 VAIVGESGSGKTVTSESITKILD 60
                                      689************99999886 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     4e-05     0.079      13      43 ..      26      56 ..      22      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiq 43
                                      d  ++++++ +++ ++G+sGsGK+    +i+
  gi|313117221|ref|YP_004044204.1| 26 DSVSFDVNPGETVAIVGESGSGKTVTSESIT 56
                                      56788999989************97655555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.2e-05       0.1      33      71 ..      35      75 ..      21     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
                             AAA_7 33 kkpvllvGptGtGKtviikdllkkld..kekylsltinfsa 71
                                      +  v +vG++G+GKtv+ ++++k ld  + +++  ti+f  
  gi|313117221|ref|YP_004044204.1| 35 GETVAIVGESGSGKTVTSESITKILDmpPGEIVEGTITFDG 75
                                      67899**************9777665336777777777764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00014      0.28      22      48 ..      35      59 ..      24     141 .. 0.84
   2 ?   -1.1   0.0       1.1   2.1e+03      90      90 ..     246     246 ..     141     317 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                            AAA_16 22 grpelvllsGesGvGKsslvrellral 48
                                      g  e v ++GesG+GK+   +++ + l
  gi|313117221|ref|YP_004044204.1| 35 G--ETVAIVGESGSGKTVTSESITKIL 59
                                      3..789************999988755 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                            AAA_16  90 e 90 
                                        
  gi|313117221|ref|YP_004044204.1| 246 I 246
                                       0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1998.85
//
Query:       gi|313117222|ref|YP_004044205.1|  [L=387]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-19   70.7  10.8    1.3e-19   70.7  10.8    2.6  2  BPD_transp_1  Binding-protein-dependent transport system inne
    1.5e-09   37.7   1.9    1.5e-09   37.7   1.9    3.4  3  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.2      0.13   1.2e+03     147     174 ..      90     119 ..      36     126 .. 0.52
   2 !   70.7  10.8   1.4e-23   1.3e-19       3     183 ..     196     379 ..     194     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.13
                      BPD_transp_1 147 gydyseis......nggvlalviavlllnlvadi 174
                                       ++++ +        +    ++++++l++++v+ i
  gi|313117222|ref|YP_004044205.1|  90 MRQFYWRRfkknriA----VIALVYLAVVFVIGI 119
                                       223222224422223....444444444444333 PP

  == domain 2  score: 70.7 bits;  conditional E-value: 1.4e-23
                      BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraa 75 
                                       l+G++aa       ++ d++l++++++ + +P+f+l++llv        +g   ++ +++ +++++ +++r +r +a
  gi|313117222|ref|YP_004044205.1| 196 LVGSVAAlatATDIGWMDEVLMRYTDIQSVFPVFILLLLLV------YLFGAELWMiIALYGFFGWEGIARTVRGEA 266
                                       566666666656669**************************......78996666648888899************* PP

                      BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyse 152
                                       l+  ++ +++aara Ga+   i+r++++Pn++ ++i ++ + ++g++ g + l flg      +   ++++g+ +s+
  gi|313117222|ref|YP_004044205.1| 267 LQRSSEAYIKAARASGANMLYIVRTHLIPNSANSVIISASVLIPGFILGEATLAFLG-----FSDPSTFSWGRTISA 338
                                       *********************************************************.....888999999999999 PP

                      BPD_transp_1 153 is..........nggvlalviavlllnlvadilqrlldprv 183
                                       ++           ++ l+l + vl +  v  ++ ++ dpr 
  gi|313117222|ref|YP_004044205.1| 339 GQanieqawwisTIPGLFLFFTVLSFYYVGEAMRDAMDPRQ 379
                                       9999999*999999999********************9996 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.41   3.7e+03      26      33 ..      37      44 ..      34      65 .. 0.56
   2 !   37.7   1.9   1.7e-13   1.5e-09       5      50 ..      92     138 ..      89     139 .. 0.76
   3 ?   -2.2   3.3      0.48   4.3e+03      21      33 ..     228     240 ..     225     254 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.41
                            OppC_N 26 llliaifa 33
                                      ll++a+fa
  gi|313117222|ref|YP_004044205.1| 37 LLIVALFA 44
                                      44555554 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 1.7e-13
                            OppC_N   5 da.wrrFkrNklAvvglvilllllliaifaPliaPydp.....qdliqn.llp 50 
                                       ++ wrrFk+N++Av++lv l+++++i i++Pl+   dp     +    n  lp
  gi|313117222|ref|YP_004044205.1|  92 QFyWRRFKKNRIAVIALVYLAVVFVIGILGPLV--VDPpqvrfT----NrILP 138
                                       555******************************..555423222....22455 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.48
                            OppC_N  21 villlllliaifa 33 
                                       v++lllll+ +f+
  gi|313117222|ref|YP_004044205.1| 228 VFILLLLLVYLFG 240
                                       5677777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2361.55
//
Query:       gi|313117223|ref|YP_004044206.1|  [L=326]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-33  114.6  12.7    4.4e-33  114.6  12.7    2.1  3  BPD_transp_1   Binding-protein-dependent transport system inn
     0.0038   17.2   3.8      0.023   14.6   0.0    2.8  2  60KD_IMP       60Kd inner membrane protein
  ------ inclusion threshold ------
      0.091   12.7   0.1       0.21   11.6   0.1    1.5  1  DUF1471        Protein of unknown function (DUF1471)
       0.13   12.5   0.6       0.75   10.0   0.2    2.2  2  Lipoprotein_3  Lipoprotein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.45     2e+03     114     140 ..      18      27 ..       3      46 .. 0.48
   2 ?   -1.2   0.0      0.33   1.5e+03     154     171 ..      79     116 ..      58     117 .. 0.59
   3 !  114.6  12.7   9.8e-37   4.4e-33       1     184 [.     118     322 ..     118     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.45
                      BPD_transp_1 114 lilafggllggavlleflgswpGlgtl 140
                                       ++l+++                 +g+ 
  gi|313117223|ref|YP_004044206.1|  18 IALTVT-----------------FGLI 27 
                                       222222.................2222 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.33
                      BPD_transp_1 154 s....................nggvlalviavlllnlv 171
                                       +                    + +++ ++i vl++++v
  gi|313117223|ref|YP_004044206.1|  79 TlnwgwsdsrsqyvipalldaWKYTAQYAIPVLVISTV 116
                                       44444444444444444456666666667777776665 PP

  == domain 3  score: 114.6 bits;  conditional E-value: 9.8e-37
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilpv 56 
                                       g+ lG+++a+++    d++ +++ +++ s+P f++ai+l++++                     + +  +++l lp+
  gi|313117223|ref|YP_004044206.1| 118 GYALGLYSAYKPYTLSDYAGSFVAFFGISIPNFWFAIILIMLLgvrfeslpvyyqsgipqqqgwFSIANIKQLLLPI 194
                                       6789************************************999*******************998888999****** PP

                      BPD_transp_1  57 iillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggl.lggavlleflg 132
                                        +ll+ s+a+ +r+ r++al+++++++v++a+a+Gas+ ++++ +vl++a+ p+ t+++ ++ g+ + g+v++e ++
  gi|313117223|ref|YP_004044206.1| 195 TVLLTASFAFQTRYSRAQALEQMNQEFVKVAKAKGASHYRLMVWHVLRMAAVPLSTSFVGRMLGIfFAGSVVIEQIF 271
                                       **********************************************************999998889********** PP

                      BPD_transp_1 133 swpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       s pGlg ++ +ai ++d+++ + +++l++v++ ++ nl+ di + lldpr+ 
  gi|313117223|ref|YP_004044206.1| 272 SIPGLGFMTYTAIVEQDTTLVL-ATTLITVFLAIIGNLLEDIAYVLLDPRID 322
                                       **********************.***************************96 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.1e-06     0.023       6      67 ..      18      78 ..      14      82 .. 0.95
   2 ?    1.2   1.8     0.068     3e+02      40      64 ..     204     230 ..     150     305 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.1e-06
                          60KD_IMP  6 illtiivrlillpltlkqlkssakmqelqPelkeiqekykkdkqklqqemmklYkkegvnpl 67
                                      i lt+++ li+   ++ q+ks++  ++   + +e +e++  ++++l q  ++ Yk++ +n++
  gi|313117223|ref|YP_004044206.1| 18 IALTVTFGLITASPNQAQMKSMMSCAATGDNPEECKERF-REQHNLDQSATERYKNYMINMA 78
                                      899************************************.77899***************85 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.068
                          60KD_IMP  40 iqekykkdk..qklqqemmklYkkegv 64 
                                        q +y+  +  ++++qe  k+ k +g+
  gi|313117223|ref|YP_004044206.1| 204 FQTRYSRAQalEQMNQEFVKVAKAKGA 230
                                       344444332234455555555444444 PP

>> DUF1471  Protein of unknown function (DUF1471)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.6e-05      0.21      12      36 ..     210     234 ..     205     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                                       S-SSHHHHHHHHHHHHHHCT-SEEE CS
                           DUF1471  12 vfgspsdledalskkAdekGAkyYr 36 
                                       ++ ++++++++  k A++kGA++Yr
  gi|313117223|ref|YP_004044206.1| 210 RAQALEQMNQEFVKVAKAKGASHYR 234
                                       788999******************9 PP

>> Lipoprotein_3  Lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00017      0.75      14      55 ..      60     103 ..      53     107 .. 0.72
   2 ?   -0.4   0.0      0.31   1.4e+03      18      76 ..     210     229 ..     195     234 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                     Lipoprotein_3  14 kyaeknkelelnKknlit..iLkeaye.sdpkgtvkvLldgWkyt 55 
                                       + ++++   e+ K+ +i+  +L  +++ s ++  + +Lld+Wkyt
  gi|313117223|ref|YP_004044206.1|  60 HNLDQSAT-ERYKNYMINmaTLNWGWSdSRSQYVIPALLDAWKYT 103
                                       45556655.788888987334777775256778899********9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.31
                     Lipoprotein_3  18 knkelelnKknlitiLkeayesdpkgtvkvLldgWkytLldqkiLek.eldvsrFvkaFG 76 
                                       + +                                         Le+ ++++++ +ka G
  gi|313117223|ref|YP_004044206.1| 210 RAQ----------------------------------------ALEQmNQEFVKVAKAKG 229
                                       444........................................45554555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 2459.28
//
Query:       gi|313117224|ref|YP_004044207.1|  [L=653]
Description: extracellular solute-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-56  191.6   8.2    2.6e-56  191.2   8.2    1.1  1  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
     0.0021   17.8   2.0     0.0041   16.9   2.0    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
      0.048   13.1   0.0        0.1   12.0   0.0    1.6  1  SBP_bac_3   Bacterial extracellular solute-binding proteins, 


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.2   8.2   4.4e-60   2.6e-56       4     372 ..     119     557 ..     116     562 .. 0.86

  Alignments for each domain:
  == domain 1  score: 191.2 bits;  conditional E-value: 4.4e-60
                                       ESSEEEEEEEETTTTEEEEEE-TT-B-TTS.SB-SHHHHHHHHHHHHTGGGHCTTHHHHHC...TCTEEEEEEEETT CS
                         SBP_bac_5   4 paLAeswwevsdDgktytfkLRkgvkFsDG.tpltAeDvvfsferlldpdtasgyasllee...dqdikkveavddy 76 
                                       p   e++ +v++   ++++kLR++++F     +ltA+D+ + ++++++ d+as ++ + ++    +++  +e+vd+y
  gi|313117224|ref|YP_004044207.1| 119 PLWFEDV-TVEQPVNQIEIKLRENLQFGEEyGELTADDYLWCIDNIWKADWASFAYANDFYvgkEDKPIQFEKVDKY 194
                                       6777885.89999999**************99**********************99999889*************** PP

                                       EEEEEESSETT.........TTTTHCHHHHHHHGC.........CHTCTCTTTTTGTTTSE-B.SSSEEEEEEETTT CS
                         SBP_bac_5  77 tvrftlkkpna.........lfltllaavpasiak.........kaaekeddkdkdtnekpvg.tGPYklkefkpgq 134
                                       t+r t ++ ++         + +++         k         + ae  +++d+  ++ + g  GP+ lk++k+++
  gi|313117224|ref|YP_004044207.1| 195 TIRETIPSSRPffpyneplsYQFPIP--------KelakpyveeQDAEGLEKDDSIMRATFNGnLGPWDLKNWKQQS 263
                                       ******99988766654333333333........134446666655555555566666666669************* PP

                                       EEEEEE-TTST..............TTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE CS
                         SBP_bac_5 135 kivlernpdYw..............gggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv 197
                                        +++er +dY+               +++p +d+ +++++ +++++++alq+ ei d a++p + i ++k+++glk+
  gi|313117224|ref|YP_004044207.1| 264 VMEFERAEDYYlrkwakeddrvpdvFAEAPFFDEYHLQYFDKQQTARQALQADEI-DTAYIPSTKISSYKQKEGLKL 339
                                       *********977777******999777999**********6666666666*****.888999999999999999999 PP

                                       EEEEEEEEEEEEEETTT...STGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSH CS
                         SBP_bac_5 198 lyespgggvtylafNtk...kppfddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpaykayd 271
                                        ++  +++++yl++N++   +  +++k+vR+A+++ ++++ iv+++l+g a+++n+l+p + p+++++  +   ++ 
  gi|313117224|ref|YP_004044207.1| 340 YKNPYRSWSGYLGINQRangWSQLRNKKVRHAMAHIYNNDFIVNNILKGRAEVQNTLHPAWGPYSPDDVVTF--DGS 414
                                       667779************9999******************************************99999987..468 PP

                                       HHHHHHHHHHTT-BCSSTSCEETC....EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH........ CS
                         SBP_bac_5 272 pekAkklLkeaGykdgdggglrek....klkltlllasgspaekaiaeliqqqlkkiGikvevktvdwa........ 336
                                       +ekAk+lLke    d ++ g +      +++ ++l+++++++++  a+++++ l k+Gik++ +t++w         
  gi|313117224|ref|YP_004044207.1| 415 LEKAKQLLKEGTSSDYGYSGDKFVgpdgEQVELTLVYQSDELDDLRAAYLKKRLGKVGIKLTQQTTSWPslmknyfn 491
                                       ****************9999877799****************************************9999****999 PP

                                       .............................HHHHHHHHCTTESEEEEEEECT.TSTTHHHHHHHHST CS
                         SBP_bac_5 337 .............................atylervkdgdfdmillgwgad.ypdpdnflnpflss 372
                                                                      ++++v+++ +d++l+  ++  + +p   + +++s+
  gi|313117224|ref|YP_004044207.1| 492 ctnpaegvsdaenlgygengkdhpsiynhGPWDKAVSSKSWDFMLTLGFSYgPLTPAGTIASLFSE 557
                                       999999999999999999999999999999999999999999999855554155555555555554 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.0   6.8e-07    0.0041       2      25 ..      13      36 ..      12      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.8e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      + RR ++K  AA++ A+ l+gc++
  gi|313117224|ref|YP_004044207.1| 13 FGRRRLIKYLAATGVATSLAGCSG 36
                                      56********************98 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.7e-05       0.1     131     200 ..     280     365 ..     225     381 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                                       C................TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCGCCEEEEECGGCECEEEEEE CS
                                       x................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 131 k................gaeivefdtleealqaLkngrvdavvadspvlaylvkknpdkkvvlveeplsseeyaiav 191
                                       k                +  +++fd ++ a qaL+++++d +   s+ +  + +k++ k  +  +  + s +++i  
  gi|313117224|ref|YP_004044207.1| 280 KeddrvpdvfaeapffdEYHLQYFDKQQTARQALQADEIDTAYIPSTKISSYKQKEGLKLYKN-PYRSWSGYLGINQ 355
                                       33444444433334444556699*********************************9999998.5555555555554 PP

                                       ET.TTHHHHH CS
                                       xx.xxxxxxx RF
                         SBP_bac_3 192 rk.gdseLrk 200
                                       r  g s+Lr+
  gi|313117224|ref|YP_004044207.1| 356 RAnGWSQLRN 365
                                       4324455553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 5112.41
//
Query:       gi|313117225|ref|YP_004044208.1|  [L=347]
Description: oligopeptide ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-36  126.4   0.0    1.4e-36  126.0   0.0    1.2  1  ABC_tran      ABC transporter
    8.6e-15   55.0   0.7    1.8e-14   54.0   0.2    1.9  2  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    3.3e-07   30.4   0.2    0.00068   19.5   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.3e-06   28.7   0.2    1.9e-05   24.9   0.2    2.1  1  AAA_22        AAA domain
     0.0015   18.9   0.1      0.004   17.6   0.1    1.7  2  AAA_16        AAA ATPase domain
     0.0027   16.9   0.0     0.0033   16.6   0.0    1.1  1  G-alpha       G-protein alpha subunit
     0.0084   15.8   0.0     0.0085   15.8   0.0    1.2  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.022   14.7   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.025   14.3   0.1      0.047   13.4   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.039   13.4   0.1        9.3    5.6   0.0    2.3  2  TniB          Bacterial TniB protein
      0.087   12.9   0.0       0.14   12.2   0.0    1.3  1  AAA_14        AAA domain
        0.1   11.8   0.0       0.18   11.0   0.0    1.3  1  NB-ARC        NB-ARC domain
       0.12   12.7   0.0       0.23   11.9   0.0    1.5  1  RNA_helicase  RNA helicase
       0.14   11.9   0.0       0.21   11.3   0.0    1.3  1  PRK           Phosphoribulokinase / Uridine kinase family
       0.14   11.4   0.0       0.21   10.8   0.0    1.2  1  Septin        Septin
       0.34   10.8   1.0       0.99    9.3   1.0    1.9  1  NACHT         NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.0   1.3e-39   1.4e-36       2     137 .]      55     206 ..      54     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 1.3e-39
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + vs++++ege++++vGe+G+GKStL k+l++l++ t G+i +dg+d+++    +++slr+ i++++q+  ++l+p+
  gi|313117225|ref|YP_004044208.1|  55 DGVSFSIQEGETLGLVGESGCGKSTLGKTLMRLHDATDGSIYFDGEDITDasrSQMRSLRRDIQIIFQDpgSSLNPR 131
                                       78************************************************999999*************999***** PP

                                       SBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +tv++            +++++ +++++ ++ ++l+++++k+ p+++SgGq+qrva+aral  +p+++++DEpt+
  gi|313117225|ref|YP_004044208.1| 132 MTVADLitepmraltdwDREKRQARLHELVNEVDLQENHLKRAPHEFSGGQQQRVAIARALSVNPQMIVADEPTS 206
                                       ***************9855555666677777777777999999******************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.9   1.1e+04      23      47 ..     143     169 ..     142     172 .. 0.62
   2 !   54.0   0.2   1.6e-17   1.8e-14       2      60 ..     258     317 ..     257     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.9
                         oligo_HPY  23 rsvprldrekd..klekikgeapsler 47 
                                       r++ + drek+  +l+++ +e+++ e+
  gi|313117225|ref|YP_004044208.1| 143 RALTDWDREKRqaRLHELVNEVDLQEN 169
                                       566667777775557777666666555 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 1.6e-17
                         oligo_HPY   2 ErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpf 60 
                                       E +ps++lf++p+HPYT+aLl+ +pr ++e       ++g++ps+e  ++GC+F++RC+ 
  gi|313117225|ref|YP_004044208.1| 258 EVAPSRELFENPKHPYTQALLSGIPRATPEPMtDRIILEGDVPSPESPPDGCRFHTRCQE 317
                                       899************************99988567788********************85 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0012       1.4       3      28 ..      68      94 ..      67     119 .. 0.71
   2 !   19.5   0.1     6e-07   0.00068     197     302 ..     146     241 ..     108     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl.drd 28
                                      +l+G  g+GKS+L ++l  l+++ d++
  gi|313117225|ref|YP_004044208.1| 68 GLVGESGCGKSTLGKTLMRLHDAtDGS 94
                                      69***************9998765222 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 6e-07
                            AAA_21 197 ielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                         ++ ++ + +l+++v+e++++        ++  ++ ++e+S G+++  a++ al   +     ++ DEp + L+ +
  gi|313117225|ref|YP_004044208.1| 146 TDWDREKRQARLHELVNEVDLQ--------ENHLKRAPHEFSGGQQQRVAIARALSVNP---QMIVADEPTSALDVS 211
                                       4555555555555555555555........666678899*******9988888888877...99************* PP

                            AAA_21 274 llrrllellkelsr.ngaQviltTHSplll 302
                                       +++++l l+++l++  +   ++ +H+ +++
  gi|313117225|ref|YP_004044208.1| 212 VQAKILNLMEDLQDtYDLTYLFISHDISVI 241
                                       *********999999**********98776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   1.7e-08   1.9e-05      10     128 ..      69     234 ..      62     243 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-08
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglelka........... 70 
                                       ++GesG+GK+tl ++l++ +d+        ++ +      +t +s +  ++l+r++  ++++++++           
  gi|313117225|ref|YP_004044208.1|  69 LVGESGCGKSTLGKTLMRLHDA-------TDGSIyfdgeDITDASRSQMRSLRRDIQIIFQDPGSSlnprmtvadli 138
                                       89******************86.......444443576667777777899999999999999999988888888888 PP

                            AAA_22  71 .................................erlsseellealeqalrarav......................i 92 
                                                                        +                   +                      +
  gi|313117225|ref|YP_004044208.1| 139 tepmraltdwdrekrqarlhelvnevdlqenhlK-------------------RaphefsggqqqrvaiaralsvnP 196
                                       8888888889888877766666666444444321...................122222223333444455667899 PP

                            AAA_22  93 elliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       ++++ DE    l+   ++++l+   +l++  +++++ +++
  gi|313117225|ref|YP_004044208.1| 197 QMIVADEPTSaLDvsvQAKILNLMEDLQD--TYDLTYLFI 234
                                       99999999998888554777777777777..666665554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   3.5e-06     0.004      23      91 ..      63     126 ..      53     234 .. 0.54
   2 ?   -2.0   0.0       3.7   4.1e+03      93     131 ..     277     324 ..     222     333 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd.g.giflrgkcdql.esaipysalaqalareellrqlldeaes 91 
                                       ++e + l+GesG+GKs+l ++l+r   ++ g ++f  g+     +++       + l  ++ ++ + +++ s
  gi|313117225|ref|YP_004044208.1|  63 EGETLGLVGESGCGKSTLGKTLMRLHDATdGsIYF-DGEDITDaSRS-----QMRSL--RRDIQIIFQDPGS 126
                                       4577889****************744444442444.33332221111.....22222..2555555555333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                            AAA_16  93 eleawrekleeala.........avpelagaeasrllellkrll.alls 131
                                       +l+  +++ +e ++         + ++ ++ +  r++  +++ + + ++
  gi|313117225|ref|YP_004044208.1| 277 LLSGIPRATPEPMTdriilegdvP-SPESPPDGCRFHTRCQEYIgDICE 324
                                       333333333333334443333322.222222236777777777655555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     3e-06    0.0033      26     120 ..      67     190 ..      56     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-06
                                       EEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT............... CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg.....fseeelatwraviqlnivrsiktilealesleselsesf........ 89 
                                       l l+G+s++GKsT+ k l +l++ +     f+ e++       +  + r+i+ i++   s   +l++++        
  gi|313117225|ref|YP_004044208.1|  67 LGLVGESGCGKSTLGKTLMRLHDATdgsiyFDGEDITDASRSQMRSLRRDIQIIFQDPGS---SLNPRMtvadlite 140
                                       669*******************88888**9999988776666667777777777776666...44444456678888 PP

                                       ........HHHC-SS-SCCCS-HCHHHH.....................H CS
                           G-alpha  90 ........elqelkerldplkkveasliaklssateee...........q 120
                                               + +++++rl++l +  +   ++l+ a  e            +
  gi|313117225|ref|YP_004044208.1| 141 pmraltdwDREKRQARLHELVNEVDLQENHLKRAPHEFsggqqqrvaiaR 190
                                       88999999999999999999766555544444444333566554455441 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.6e-06    0.0085       3      47 ..      52      97 ..      50     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.6e-06
                                      HHHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEE CS
                                      xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  3 rvlDal.fpivqGqrtlipgafgvGktvisqslskqsnsddaiiyv 47
                                      +++D + f+i +G++++++g++g+Gk+++ ++l++ ++++d +iy 
  gi|313117225|ref|YP_004044208.1| 52 KAVDGVsFSIQEGETLGLVGESGCGKSTLGKTLMRLHDATDGSIYF 97
                                      6677543899************************998777777775 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.9e-05     0.022      87     122 ..      51      87 ..      35     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                        ++++ ++  +++ +t  lvG+SG GKStL ++l+  
  gi|313117225|ref|YP_004044208.1|  51 VKAVDGVSFSIQEgETLGLVGESGCGKSTLGKTLMRL 87 
                                       566777778888779999************9998764 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.2e-05     0.047      12      38 ..      54      80 ..      46      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.2e-05
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTl 38
                                       dg +++i++ ++  l+G+sG GKSTl
  gi|313117225|ref|YP_004044208.1| 54 VDGVSFSIQEGETLGLVGESGCGKSTL 80
                                      577888998666778***********8 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0083       9.3      37      63 ..      66      92 ..      60     111 .. 0.88
   2 ?    5.3   0.0      0.01        12     109     156 ..     185     230 ..     165     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0083
                              TniB 37 nlllvGdsnnGKtmivekFarlhppek 63
                                       l lvG+s +GK+++ +  +rlh +++
  gi|313117225|ref|YP_004044208.1| 66 TLGLVGESGCGKSTLGKTLMRLHDATD 92
                                      5679***************99998875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                              TniB 109 qqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkip 156
                                       + +++   ++++++++ DE  ++l   ++ q ++ln++  L+++++++
  gi|313117225|ref|YP_004044208.1| 185 RVAIARALSVNPQMIVADEPTSAL--DVSVQAKILNLMEDLQDTYDLT 230
                                       3344444568899***********..6778999*****9999988765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.14       4      50 ..      66     111 ..      63     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe 50 
                                        l ++G   +GK+tl k+l++ +    +  +y++ +d +d+++++ +
  gi|313117225|ref|YP_004044208.1|  66 TLGLVGESGCGKSTLGKTLMRLHD-ATDGSIYFDGEDITDASRSQMR 111
                                       567889999***********9998.899*********9997666543 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00016      0.18      22      51 ..      66      97 ..      51     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                                      EEEEEESTTSSHHHHHHHHCCSHCCCCC..CB CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnksdeveg..rF 51
                                       ++lvG  G+GK+tl k  ++ +d ++g   F
  gi|313117225|ref|YP_004044208.1| 66 TLGLVGESGCGKSTLGKTLMRLHDATDGsiYF 97
                                      689***************99999888874445 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.23       3      20 ..      69      86 ..      67     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                      RNA_helicase  3 lyGpsgeGKStlakeLak 20
                                      l+G+sg+GKStl k+L++
  gi|313117225|ref|YP_004044208.1| 69 LVGESGCGKSTLGKTLMR 86
                                      78*************665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.21       3      91 ..      68     155 ..      66     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                               PRK   3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyevlk 79 
                                       g+ g+SG+Gk+t+ ++l  +   ++  + + +g  ++   r +++   ++ +  ++   s l+p+    dl+ e ++
  gi|313117225|ref|YP_004044208.1|  68 GLVGESGCGKSTLGKTLMRLHD-ATDGSIYFDGEDITDASRSQMRSLRRDIQIIFQDPGSSLNPRMTVADLITEPMR 143
                                       899*************998776.555568889999999999999988888888888888888888888888888888 PP

                               PRK  80 elkegkkvdkpi 91 
                                       +l +  + ++  
  gi|313117225|ref|YP_004044208.1| 144 ALTDWDREKRQA 155
                                       887766655555 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.21       6      33 ..      66     100 ..      63     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                                       EEEEEEBTTSSCCCCCCTTSSSS----.......- CS
                            Septin   6 tlmvvGesglGkttlintlfetdliee.......e 33 
                                       tl +vGesg Gk+tl +tl++ ++ ++       e
  gi|313117225|ref|YP_004044208.1|  66 TLGLVGESGCGKSTLGKTLMRLHDATDgsiyfdgE 100
                                       5678****************998888755555442 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.0   0.00089      0.99       3      23 ..      67      87 ..      65     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00089
                                      EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklala 23
                                      + l Ge+G+GK+tL + l+++
  gi|313117225|ref|YP_004044208.1| 67 LGLVGESGCGKSTLGKTLMRL 87
                                      6689**********9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 2710.74
//
Query:       gi|313117226|ref|YP_004044209.1|  [L=354]
Description: dipeptide/oligopeptide/nickel ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-26   93.1   0.0    2.8e-26   92.7   0.0    1.2  1  ABC_tran   ABC transporter
      4e-18   65.7   0.2    7.6e-18   64.8   0.2    1.5  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    0.00031   20.6   0.6      0.003   17.4   0.1    2.0  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
  ------ inclusion threshold ------
      0.013   15.0   0.3      0.051   13.0   0.3    1.8  1  SMC_N      RecF/RecN/SMC N terminal domain
       0.17   12.2   2.5        2.9    8.2   2.5    2.2  1  AAA_22     AAA domain
       0.29   11.5   0.9       0.92    9.9   0.9    2.0  1  AAA_16     AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.0   9.4e-30   2.8e-26       1     136 [.      25     184 ..      25     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 9.4e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx. RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke....qeleslrkeigvlpqe. 67 
                                       l+ vs+++ ++e+v+++Ge+G+GKS  +   +gll+      + G+i++dg+dl e    +  e+    i ++ q+ 
  gi|313117226|ref|YP_004044209.1|  25 LDGVSITVGRDEVVGVIGESGCGKSVTALSTMGLLQSppakiERGSIRYDGQDLLElsksELNEIRGDDITMIYQDp 101
                                       789**********************99999999888779999*************99997777888899*******9 PP

                                       .--S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSE CS
                                       .xxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 .pqlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkl 129
                                        ++l+p lt++++              e++ e++++l+ +gl + +++ + + p+ LSgG++qrv++a+al+++p+l
  gi|313117226|ref|YP_004044209.1| 102 mSSLNPVLTIGKQiiepllahrdisksEARTEAKRMLEAVGLAD-AERLLAEYPEALSGGMRQRVVIAMALITEPDL 177
                                       99*********************997777777************.889999************************** PP

                                       EEEESTT CS
                                       xxxxxxx RF
                          ABC_tran 130 lllDEpt 136
                                       l++DEpt
  gi|313117226|ref|YP_004044209.1| 178 LIADEPT 184
                                       ******9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.2   2.5e-21   7.6e-18       1      61 [.     236     296 ..     236     301 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2.5e-21
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfa 61 
                                       vE+  +++lf+ plHPYT++L++s+p++ +  d+l++i+g++p+l + ++GC+Fa+RCp+ 
  gi|313117226|ref|YP_004044209.1| 236 VETCAMRELFEAPLHPYTRKLAESIPKVGEVADRLPTIEGTVPELIDPPQGCRFASRCPQY 296
                                       89999******************************************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.06   1.8e+02       2      61 ..      38      82 ..      37      99 .. 0.74
   2 !   17.4   0.1     1e-06     0.003     220     301 ..     140     220 ..      89     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.06
                            AAA_21  2 nvliGpNgsGKS.nLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefe 61
                                       ++iG  g+GKS + L ++ ll++                +++ki++ + +yd     e++
  gi|313117226|ref|YP_004044209.1| 38 VGVIGESGCGKSvTALSTMGLLQS----------------PPAKIERGSIRYDGQDLLELS 82
                                      679*********778999988887................666666666666665555554 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1e-06
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                        v + + ++     +  lS G+++   ++++ l + +  +ll+ DEp + L+  +++ +++ll++l++  g  v++ 
  gi|313117226|ref|YP_004044209.1| 140 AVGLADAERLLAEYPEALSGGMRQR-VVIAMALITEP--DLLIADEPTTALDVTIQAQIVDLLRDLREeFGMSVLFI 213
                                       5555555555566677789999999.55555555555..9***********************9999999******* PP

                            AAA_21 296 THS.pll 301
                                       +H+ p++
  gi|313117226|ref|YP_004044209.1| 214 SHDlPVI 220
                                       ***7776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.7e-05     0.051      27     212 ..      38     230 ..      27     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                       EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH...CCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrse...klsdlihk.skekasvkkaeveitfdnedkklkiekeevsi 99 
                                         ++G+ G+GKs    + + +L    ak  r +   + +dl+   ++e +++   +++++++++ ++    ++ ++i
  gi|313117226|ref|YP_004044209.1|  38 VGVIGESGCGKSVTALSTMGLLQSPPAKIERGSiryDGQDLLELsKSELNEIRGDDITMIYQDPMSS---LNPVLTI 111
                                       5667777777775555554444444443223221112356666633344444555677777666666...5566666 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HH..HHHHHHHHHHHHHHCCS--SEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiske.........lLSgG..ektLvalaLlfAiqkvkpaplyllD 165
                                        +++++    +  i ++e++ +e +++le +g+            +LSgG  ++ ++a+aL+          l + D
  gi|313117226|ref|YP_004044209.1| 112 GKQIIEPLLAHRDISKSEAR-TEAKRMLEAVGLADAerllaeypeALSGGmrQRVVIAMALI------TEPDLLIAD 181
                                       66666666666666666554.456677777777665777777777*****545556666666......44458899* PP

                                       TTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 166 eidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvt 212
                                       e   aLD +  +++++ll+  +++  + ++ is++  ++++    + v+
  gi|313117226|ref|YP_004044209.1| 182 EPTTALDVTIQAQIVDLLRDLREEfgMSVLFISHDLPVISEIADRMAVM 230
                                       *******************999996678899999998888764444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.5   0.00096       2.9      10      38 ..      40      82 ..      33     217 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00096
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaee..............e 38
                                      v+GesG+GK++++   +  l+  ++  e               
  gi|313117226|ref|YP_004044209.1| 40 VIGESGCGKSVTALSTMGLLQSPPAKIErgsirydgqdllelS 82
                                      89*********99887777754444433555555444444440 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.9   0.00031      0.92      22      51 ..      33      61 ..      20     213 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                      gr e+v ++GesG+GKs  + + +  l ++
  gi|313117226|ref|YP_004044209.1| 33 GRDEVVGVIGESGCGKSVTALSTMG-LLQS 61
                                      4458999**********99977774.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 2800.03
//
Query:       gi|313117227|ref|YP_004044210.1|  [L=316]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-28  100.4  13.7    1.4e-28   99.9   9.6    2.0  2  BPD_transp_1   Binding-protein-dependent transport system inn
    4.3e-14   52.2   0.3    4.3e-14   52.2   0.3    2.8  4  OppC_N         N-terminal TM domain of oligopeptide transport
  ------ inclusion threshold ------
       0.42   10.1   6.6       0.46   10.0   0.0    2.5  3  E1-E2_ATPase   E1-E2 ATPase


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.015        90      18     176 ..      43      71 ..      32     129 .. 0.65
   2 !   99.9   9.6   2.4e-32   1.4e-28       1     183 [.     132     314 ..     132     316 .] 0.99

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.015
                      BPD_transp_1  18 kllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasr 94 
                                        +lr+++  ++++  +v+++ll+                                                      
  gi|313117227|ref|YP_004044210.1|  43 TVLRRVMKNWFAMFGLVVVVLLI------------------------------------------------------ 65 
                                       45555555555555555333333...................................................... PP

                      BPD_transp_1  95 wqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlv 171
                                                                                                                   +
  gi|313117227|ref|YP_004044210.1|  66 ----------------------------------------------------------------------------L 66 
                                       ............................................................................3 PP

                      BPD_transp_1 172 adilq 176
                                       + i++
  gi|313117227|ref|YP_004044210.1|  67 TAIFA 71 
                                       33333 PP

  == domain 2  score: 99.9 bits;  conditional E-value: 2.4e-32
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g++lG++a+ ++++++  ++++++++ ls+P +vla+ +       + lg + +p +i+++l+++ +++rl+r ++ 
  gi|313117227|ref|YP_004044210.1| 132 GVTLGLVAG-YYGGWTESIIMRIVDISLSIPALVLALAIA------GMLGGGLFPlIIAVSLVGWRGFARLVRGDVK 201
                                       899******.******************************......*********9********************* PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       ++++++++  a a G+s+++i+ ++vlPna+++ii    l+++ ++  ++ l+flg    +g +  ++++g  ++++
  gi|313117227|ref|YP_004044210.1| 202 SVIEEEYIDSANAAGLSDFRIITRYVLPNAASSIIVYSTLTIPTVILWSAGLSFLG----MGVQPPRPEWGAILAAG 274
                                       ********************************************************....***************99 PP

                      BPD_transp_1 154 s..........nggvlalviavlllnlvadilqrlldprv 183
                                                   ++ la+ i v+++n + d l ++ldpr 
  gi|313117227|ref|YP_004044210.1| 275 RgeidsawwiaTFPGLAIMITVIAFNGLGDGLRDALDPRQ 314
                                       9*************************************95 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.3   7.2e-18   4.3e-14       4      51 .]      42      91 ..      40      91 .. 0.91
   2 ?   -0.8   0.1      0.25   1.5e+03       3      25 ..     103     126 ..     101     145 .. 0.65
   3 ?   -4.0   2.5       2.5   1.5e+04      26      33 ..     164     171 ..     156     188 .. 0.49
   4 ?   -4.0   0.3       2.6   1.6e+04      19      28 ..     289     298 ..     289     300 .. 0.59

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 7.2e-18
                            OppC_N  4 qdawrrFkrNklAvvglvilllllliaifaPliaPydp..qdliqnllpP 51
                                      + ++rr  +N  A++glv+++ll+l aifaPliaP+dp  q++++  +pP
  gi|313117227|ref|YP_004044210.1| 42 KTVLRRVMKNWFAMFGLVVVVLLILTAIFAPLIAPHDPteQNYDALSQPP 91
                                      5689**********************************887776569999 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.25
                            OppC_N   3 wqdaw.rrFkrNklAvvglvilll 25 
                                       ++d++ r  +  + Av+  v+++ 
  gi|313117227|ref|YP_004044210.1| 103 GRDVFsRVVFGSRYAVFLGVVIVG 126
                                       555542455666777777777664 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 2.5
                            OppC_N  26 llliaifa 33 
                                       +l++ai +
  gi|313117227|ref|YP_004044210.1| 164 VLALAIAG 171
                                       44444432 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 2.6
                            OppC_N  19 glvillllll 28 
                                       gl+i +++++
  gi|313117227|ref|YP_004044210.1| 289 GLAIMITVIA 298
                                       5666666554 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   7.7e-05      0.46      85     140 ..      17      74 ..      10      88 .. 0.79
   2 ?    1.4   2.6     0.034     2e+02     118     174 ..     120     174 ..     114     178 .. 0.77
   3 ?   -4.1   0.1       1.6   9.7e+03     162     175 ..     289     302 ..     284     305 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.7e-05
                                       EEE-TTTSTTTTTSTTS----..----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STT CS
                      E1-E2_ATPase  85 Vtatgedtelgkiarlveeak..skktplqkkldklgkvlvpvvlliallvflialll 140
                                       V + + +++ +++ ++ve+ +  ++kt l + +++ ++++ +vv+++++l++++a+l+
  gi|313117227|ref|YP_004044210.1|  17 VSNEAGSSRGAQAPKMVETGRvaRTKTVLRRVMKNWFAMFGLVVVVLLILTAIFAPLI 74 
                                       55556666777777888887777999****************9999999999988764 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHH CS
                      E1-E2_ATPase 118 lgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplavplalalg 174
                                       lg v+v + +li++++ l+a ++g+++  +++r++++ +++ P aL+la+ +a +lg
  gi|313117227|ref|YP_004044210.1| 120 LGVVIVGIEMLIGVTLGLVAGYYGGWTESIIMRIVDISLSI-P-ALVLALAIAGMLG 174
                                       4566788889999999999999***9988888888887654.4.6777777777666 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 1.6
                                       THHHHHHHHHHHHH CS
                      E1-E2_ATPase 162 aLplavplalalga 175
                                       +L+++++++ ++g+
  gi|313117227|ref|YP_004044210.1| 289 GLAIMITVIAFNGL 302
                                       67777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 2105.65
//
Query:       gi|313117228|ref|YP_004044211.1|  [L=313]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-45  152.7  14.5      9e-45  152.7  14.5    1.9  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.25   4.5e+03     126     127 ..      21      22 ..       7      44 .. 0.53
   2 ?   -1.2   0.1     0.081   1.5e+03     101     121 ..      93     113 ..      84     114 .. 0.75
   3 !  152.7  14.5     5e-49     9e-45       2     184 ..     114     311 ..     113     312 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.25
                      BPD_transp_1 126 vl 127
                                       ++
  gi|313117228|ref|YP_004044211.1|  21 IV 22 
                                       11 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.081
                      BPD_transp_1 101 vvlPnalppiitglilafggl 121
                                        +lP++l  ++++++l+f+++
  gi|313117228|ref|YP_004044211.1|  93 NRLPATLELALSSMVLTFIIA 113
                                       568888888888888888876 PP

  == domain 3  score: 152.7 bits;  conditional E-value: 5e-49
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf................vilsilghlilpviillll 62 
                                       ++lG+++a+++  + d+l++ + i++ s+Psf+la++l+l+f                +   +l +lilp++++++ 
  gi|313117228|ref|YP_004044211.1| 114 LPLGVISAVKQYTWADNLSMLFAIFWISMPSFWLALILILLFsvqwslfpisgratpvFTTAWLVSLILPAVATGTR 190
                                       89*******************************************************77777777************ PP

                      BPD_transp_1  63 saapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgt 139
                                        a+ ++r++r+++l++l++d++++ar +G +++ ++++++++na++p+it+++l++++++gg+v++e+++swpG+g+
  gi|313117228|ref|YP_004044211.1| 191 RAGLLTRITRSSMLEVLNEDYIRTARGKGIGEKSVIYTHAMKNAMIPVITLIGLQIPAIFGGSVIIETVFSWPGMGR 267
                                       ***************************************************************************** PP

                      BPD_transp_1 140 llleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       ll+++ l++dy+  + g+vl+++i+v++ nl++d+ + ++dpr++
  gi|313117228|ref|YP_004044211.1| 268 LLVNSVLQRDYPVVQ-GLVLVYAIIVVASNLLVDVAYGYFDPRIE 311
                                       ***************.***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2293.92
//
Query:       gi|313117229|ref|YP_004044212.1|  [L=563]
Description: dipeptide ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-68  228.8   1.2    1.3e-67  228.5   1.2    1.1  1  SBP_bac_5        Bacterial extracellular solute-binding prote
  ------ inclusion threshold ------
       0.15   11.9   0.0         13    5.7   0.0    2.8  2  Retrotran_gag_3  gag-polypeptide of LTR copia-type
       0.76   10.0   5.3        2.7    8.3   0.0    3.4  3  PRODH            Proline utilization A proline dehydrogenase 


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.5   1.2   2.1e-71   1.3e-67       1     360 [.     100     460 ..     100     474 .. 0.93

  Alignments for each domain:
  == domain 1  score: 228.5 bits;  conditional E-value: 2.1e-71
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddyt 77 
                                       e+vp+LA++ ++v++D++++ f + +gv+F++G++ltAe vv+++er++++ ++s+  s +      k++ea+ +y+
  gi|313117229|ref|YP_004044212.1| 100 EPVPHLAAD-YSVNEDATEFVFQIEQGVTFHNGDELTAEEVVYNWERFVENSPSSYLLSPA------KAFEATGEYE 169
                                       689******.8*********************************************99998......8********* PP

                                       EEEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTS.T......TT CS
                         SBP_bac_5  78 vrftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdY.w......gg 147
                                       v++t+ +p++l++++l+++   +++ +++ e++ +++  +  vgtGPY+ k++++g  ivl ++++Y w      ++
  gi|313117229|ref|YP_004044212.1| 170 VTVTFDAPYPLLPRYLTDPLTGFVS-KRAVEEAGESYGQDIAVGTGPYQWKNWEHGTAIVLSKFEEYgWgpefaaNQ 245
                                       ************************5.77777888**********************************999999888 PP

                                       SCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHH CS
                         SBP_bac_5 148 gkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvR 224
                                       g+ ++++++f++ p++++ +++l sG ++  +++++sd +++++a+++++ +++++++ +yla+N +k+p d+++vR
  gi|313117229|ref|YP_004044212.1| 246 GPGNPEQFRFEIHPEATTLLNELTSGGVHGSSYITLSDTKEVEQADSTNL-IRKQYTRPGYLAINVEKKPTDNVHVR 321
                                       888***********************************************.************************** PP

                                       HHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH..SHHHHHHHHHHHTT-BCSSTSCEETC..EE CS
                         SBP_bac_5 225 qAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka..ydpekAkklLkeaGykdgdggglrek..kl 297
                                       +A+++A+ ++ +++a+l+g + p  s++pp+   a +e k ++       ekA+k L++aG++++++g++r+k  ++
  gi|313117229|ref|YP_004044212.1| 322 RAITHAVRKQPVIEAALGGEGYPIWSIVPPVAVNALDEEKAKELGqtVSQEKARKELDAAGWTNSKQGEVRTKngEE 398
                                       ***************************77766665555555433356669***********************9777 PP

                                       EEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTS CS
                         SBP_bac_5 298 kltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadyp 360
                                       + ++++a + p  k++  +++  l ++Gik+e++ +++  t ++  ++g++++  +++g++++
  gi|313117229|ref|YP_004044212.1| 399 LKLTFYAFTIPRYKKMGKVVAPLLGEVGIKAELEILEA-GTLYKNLQSGNHNITTMAYGGNWA 460
                                       77777777788888***********************9.9****************9999874 PP

>> Retrotran_gag_3  gag-polypeptide of LTR copia-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.014        86      11      26 ..     334     349 ..     331     357 .. 0.82
   2 ?    5.7   0.0    0.0021        13      16      37 ..     477     498 ..     473     499 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                   Retrotran_gag_3  11 vsvqLdgdNYssWkra 26 
                                       +   L g++Y +W+++
  gi|313117229|ref|YP_004044212.1| 334 IEAALGGEGYPIWSIV 349
                                       566799********85 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0021
                   Retrotran_gag_3  16 dgdNYssWkramrlaLsvKnkl 37 
                                        g+NYs W++  +  L+ K k+
  gi|313117229|ref|YP_004044212.1| 477 GGTNYSLWQNDEFDSLLEKAKT 498
                                       58*******9988888887775 PP

>> PRODH  Proline utilization A proline dehydrogenase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00045       2.7       7      24 ..      73      90 ..      71     109 .. 0.86
   2 ?    0.6   0.2      0.11   6.6e+02       3      12 ..     320     329 ..     319     331 .. 0.88
   3 ?    1.1   0.2      0.08   4.8e+02      22      35 ..     492     505 ..     490     509 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00045
                             PRODH  7 ItaayRrpEaecVapLle 24
                                      I  a+RrpE++++ +L e
  gi|313117229|ref|YP_004044212.1| 73 IHKATRRPEETVLSALHE 90
                                      899***********9976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
                             PRODH   3 LRqaItaayR 12 
                                        R+aIt+a R
  gi|313117229|ref|YP_004044212.1| 320 VRRAITHAVR 329
                                       69******99 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.08
                             PRODH  22 LleaArlpeaeraa 35 
                                       Lle A+ +++++++
  gi|313117229|ref|YP_004044212.1| 492 LLEKAKTSPEQATR 505
                                       9*********8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.21s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 3831.91
//
Query:       gi|313117230|ref|YP_004044213.1|  [L=256]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-26   91.9   0.4    4.7e-25   87.9   0.1    2.1  2  IclR            Bacterial transcriptional regulator
    1.1e-06   28.3   0.1    2.6e-06   27.1   0.1    1.6  1  HTH_IclR        IclR helix-turn-helix domain
    1.8e-05   24.2   0.0    4.3e-05   23.0   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00024   20.9   0.1    0.00055   19.7   0.1    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0032   17.3   0.1     0.0087   15.9   0.0    1.7  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.013   15.2   0.0       0.03   14.1   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.015   15.5   0.3      0.049   13.9   0.1    1.8  2  DUF5304         Family of unknown function (DUF5304)
      0.017   15.2   0.1      0.037   14.1   0.1    1.5  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.018   14.9   0.1      0.048   13.6   0.1    1.7  1  MarR            MarR family
      0.022   14.7   0.0      0.083   12.9   0.0    1.9  1  HTH_46          Winged helix-turn-helix DNA binding
      0.032   14.4   0.0      0.084   13.0   0.0    1.7  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.051   13.5   0.0        0.2   11.6   0.0    2.0  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.054   13.5   0.0       0.11   12.5   0.0    1.5  1  DUF1803         Domain of unknown function (DUF1803)
      0.055   13.7   0.5       0.17   12.1   0.1    2.1  2  DUF4148         Domain of unknown function (DUF4148)
      0.058   13.5   0.1       0.15   12.2   0.1    1.7  1  HTH_20          Helix-turn-helix domain
      0.061   13.4   0.0       0.17   12.0   0.0    1.8  1  cNMP_binding    Cyclic nucleotide-binding domain
      0.083   13.1   0.0       0.23   11.7   0.0    1.7  2  Rio2_N          Rio2, N-terminal
      0.086   12.9   0.2       0.28   11.3   0.1    1.9  2  SpoIIID         Stage III sporulation protein D
      0.095   12.5   0.1       0.41   10.5   0.0    2.0  2  HTH_10          HTH DNA binding domain
        0.1   12.6   0.0       0.31   11.0   0.0    1.8  2  HTH_11          HTH domain


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.19   1.7e+02      45      75 ..      32      62 ..      18      68 .. 0.84
   2 !   87.9   0.1   5.3e-28   4.7e-25       9     127 ..     128     246 ..     121     248 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.19
                                      SSTTS--SHHHHHHHHHHHHHHTSEEEESSS CS
                              IclR 45 lterTitdpeeLleeLakvReqGyavdreEe 75
                                      l e+T   + + ++ L++ R+++y v+++E 
  gi|313117230|ref|YP_004044213.1| 32 LVEETGLAKSTVHKHLSTLRANDYIVKEGER 62
                                      5677777889999**************9996 PP

  == domain 2  score: 87.9 bits;  conditional E-value: 5.3e-28
                                       TT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEE CS
                              IclR   9 iGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciAap 85 
                                        Gt++ l+ ta+GKa+La   + +++++l +++l + t++Ti ++e+L++eL++vRe+Gya++++E  eg r ++ +
  gi|313117230|ref|YP_004044213.1| 128 TGTEFFLHNTAAGKAILATYADSKRDEILDTQGLPATTNKTIQSREALHAELEQVRENGYALNDGECVEGYRTVSSV 204
                                       7999************************************************************************* PP

                                       EE-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  86 ifdasgevvaAvsvsgptarlteeelkeellalvreaArkis 127
                                       i + +g+ ++A+s  gp++r+++++lk+el+  vr a ++++
  gi|313117230|ref|YP_004044213.1| 205 IKRPNGSALGAISAGGPAYRIDQSRLKNELADHVRSATAEVT 246
                                       ***********************************9988875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   2.9e-09   2.6e-06       6      51 ..      15      59 ..      13      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.9e-09
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      l+iL+++  ++  +tl+ l ++tgl+kStvh +L+tL    y+ ++
  gi|313117230|ref|YP_004044213.1| 15 LHILELIVDHGW-VTLRGLVEETGLAKSTVHKHLSTLRANDYIVKE 59
                                      789999999988.7************************99998765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   4.8e-08   4.3e-05       4      47 ..      13      56 ..      11      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.8e-08
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      t + ILel+ +++  + r L e++gl +stv+++l  L  + +I
  gi|313117230|ref|YP_004044213.1| 13 TSLHILELIVDHGWVTLRGLVEETGLAKSTVHKHLSTLRANDYI 56
                                      7899***************************************9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   6.2e-07   0.00055       7      45 ..      17      56 ..      12      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.2e-07
                                      HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  7 ILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      IL l  + g  +   l+ee+gl +stv  HL+ Lr  +++
  gi|313117230|ref|YP_004044213.1| 17 ILELIVDhGWVTLRGLVEETGLAKSTVHKHLSTLRANDYI 56
                                      666666666678889********************99887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.7e-06    0.0087       4      54 ..      11      59 ..       8      63 .. 0.90
   2 ?   -3.1   0.0       8.4   7.6e+03      11      25 ..     213     228 ..     211     248 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-06
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      t + +++L  + +++   +t + l++++gl ks+v+++l  L a  +++++
  gi|313117230|ref|YP_004044213.1| 11 TATSLHILELIVDHGW--VTLRGLVEETGLAKSTVHKHLSTLRANDYIVKE 59
                                      5778899999999996..9*****************************886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.4
                                       HHHHHCTTTS.EEEHH CS
                            MarR_2  11 LaaLgrrpgr.dltvg 25 
                                       L+a+ ++++  ++ ++
  gi|313117230|ref|YP_004044213.1| 213 LGAISAGGPAyRIDQS 228
                                       6777777765633333 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.3e-05      0.03       5      46 ..      17      58 ..      15      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                          HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      ilel+ ++g +++  lve+ g ++ T+ + L++L + + +++
  gi|313117230|ref|YP_004044213.1| 17 ILELIVDHGWVTLRGLVEETGLAKSTVHKHLSTLRANDYIVK 58
                                      9*********************************99888766 PP

>> DUF5304  Family of unknown function (DUF5304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.4e-05     0.049      26     104 ..      70     149 ..      51     188 .. 0.78
   2 ?   -0.6   0.1       1.6   1.4e+03      11      56 ..     173     220 ..     167     252 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                           DUF5304  26 aepGsaaeelrklvdavadklsglqspllgavaspaaqqv.vrqvveqakaavepviernPdvfdhLaaaGsellaa 101
                                        + G+ a e+r   + v +k+ +l+s+  ++v  ++ ++     + e a a+ e+      + f h +aaG+ +la 
  gi|313117230|ref|YP_004044213.1|  70 LTVGKRAVEFRESYQLVEQKVRELGSRTDAEVDFTVEENGrLILMFEAAGATNESTFGTGTEFFLHNTAAGKAILAT 146
                                       567999*********************99987766554431445668899999************************ PP

                           DUF5304 102 YRs 104
                                       Y  
  gi|313117230|ref|YP_004044213.1| 147 YAD 149
                                       *64 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                           DUF5304  11 eDlaaekaRrr.aeegaepGsaaeelrklvdavad.klsglqspllga 56 
                                       e l+ae +  r + ++ + G+  e  r +  ++   + s l++  +g 
  gi|313117230|ref|YP_004044213.1| 173 EALHAELEQVReNGYALNDGECVEGYRTVSSVIKRpNGSALGAISAGG 220
                                       556666666663445666666666666655554431223344433333 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.1e-05     0.037      18      51 ..      17      50 ..      13      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                                      HHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHH CS
                             HTH_9 18 VvetLlrkgrltlrelvkktkLsldqVkksLvvL 51
                                      + e+++++g  tlr lv++t+L ++ V+k L++L
  gi|313117230|ref|YP_004044213.1| 17 ILELIVDHGWVTLRGLVEETGLAKSTVHKHLSTL 50
                                      7899***************************998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.4e-05     0.048       2      48 ..      11      57 ..      10      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      t+t ++iL+++ ++g  ++  L +  g+ kstv + l +L  +++i 
  gi|313117230|ref|YP_004044213.1| 11 TATSLHILELIVDHGWVTLRGLVEETGLAKSTVHKHLSTLRANDYIV 57
                                      899************************************99998885 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.2e-05     0.083      31      54 ..      34      57 ..      32      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-05
                            HTH_46 31 krtnLSrSsimkvLseLkkggyIe 54
                                      + t L +S++ k Ls L+ ++yI 
  gi|313117230|ref|YP_004044213.1| 34 EETGLAKSTVHKHLSTLRANDYIV 57
                                      679*******************95 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.3e-05     0.084       4      51 ..      14      59 ..      11      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.3e-05
                    B-block_TFIIIC  4 qfklLelIassRysGitqsdLakeskqdprslfyrlksLekkgLIvkq 51
                                      +  +LelI+ +++  +t ++L+ e++  ++ ++++l +L  + +Ivk 
  gi|313117230|ref|YP_004044213.1| 14 SLHILELIVDHGW--VTLRGLVEETGLAKSTVHKHLSTLRANDYIVKE 59
                                      5679999999999..8******************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022       0.2      16      60 ..      20      64 ..      13      71 .. 0.90
   2 ?   -3.0   0.0       7.9   7.1e+03      17      38 ..     144     165 ..     142     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                       ++ +g  t + + ee+g+ +s+v + L+ L   +++ +e +r++
  gi|313117230|ref|YP_004044213.1| 20 LIVDHGWVTLRGLVEETGLAKSTVHKHLSTLRANDYIVKEGERYT 64
                                      56789999*******************************999876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.9
                                       HHHHCCCHHCHHCCCTTSSCHC CS
                              TrmB  17 Llklgpatadeiaeelgvprsk 38 
                                       L ++  ++ dei    g+p ++
  gi|313117230|ref|YP_004044213.1| 144 LATYADSKRDEILDTQGLPATT 165
                                       5678888999999999999775 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.11      15      82 ..      15      83 ..       4      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                           DUF1803 15 keLieyLaehddviLRelkkeFa.dqkkldrlldelidaglikRenkrYklnlpifeieeaaelileee 82
                                       +++e + +h  v+LR l +e    ++ + + l+ l ++++i +e  rY+l l + ++ + a    e++
  gi|313117230|ref|YP_004044213.1| 15 LHILELIVDHGWVTLRGLVEETGlAKSTVHKHLSTLRANDYIVKEGERYTLGLYFLTVGKRAVEFRESY 83
                                      567788889999****9987764166789************************9988766655555544 PP

>> DUF4148  Domain of unknown function (DUF4148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00019      0.17      21      47 ..     148     189 ..     116     198 .. 0.77
   2 ?   -1.7   0.1       3.8   3.4e+03      31      42 ..     243     254 ..     211     255 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                           DUF4148  21 a...............ahskspkTRAqVraELaqaeaaGylp 47 
                                       a                 +k+  +R+   aEL+q + +Gy  
  gi|313117230|ref|YP_004044213.1| 148 AdskrdeildtqglpaTTNKTIQSREALHAELEQVRENGYAL 189
                                       366666666666666656777889***************865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.8
                           DUF4148  31 AqVraELaqaea 42 
                                       A+V + L++a++
  gi|313117230|ref|YP_004044213.1| 243 AEVTESLVEAQS 254
                                       777777888775 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00016      0.15      11      60 ..      13      62 ..       7      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      + + il ++ + + +t+  l e+ +l+k+t+++HL +L+  +++  ++e+
  gi|313117230|ref|YP_004044213.1| 13 TSLHILELIVDHGWVTLRGLVEETGLAKSTVHKHLSTLRANDYIVKEGER 62
                                      6677777777777788888889999**************9***9999887 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.17       3      43 ..      49      91 ..      47      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                      EE-TT-EEE-TTSB-S.EEEEEEES-EEE.EEEETTS.EEEEE CS
                      cNMP_binding  3 sfkagevifrqGdpad.slyivlsGevrv.yrlsedgkevvla 43
                                       ++a+++i+++G++ + +ly+++ G+ +v +r s +  e+ ++
  gi|313117230|ref|YP_004044213.1| 49 TLRANDYIVKEGERYTlGLYFLTVGKRAVeFRESYQLVEQKVR 91
                                      589***********888*********77723444444455555 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.23      21      62 ..      23      64 ..      13      73 .. 0.90
   2 ?   -2.7   0.0       8.1   7.2e+03      43      66 ..     177     189 ..     151     200 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                            Rio2_N 21 nhevVptelieeisrlkeeevkkrlsrllkaklisrktakyd 62
                                      +h +V  + + e ++l ++ v+k+ls+l  ++ i+++  +y+
  gi|313117230|ref|YP_004044213.1| 23 DHGWVTLRGLVEETGLAKSTVHKHLSTLRANDYIVKEGERYT 64
                                      699*********************************998885 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.1
                            Rio2_N  43 krlsrllkaklisrktakydGYkL 66 
                                         l+++ +           +GY+L
  gi|313117230|ref|YP_004044213.1| 177 AELEQVRE-----------NGYAL 189
                                       33333333...........34443 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00031      0.28       9      41 ..      15      48 ..      10      59 .. 0.84
   2 ?   -2.2   0.0       5.1   4.6e+03       2      21 ..     236     255 ..     235     256 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                           SpoIIID  9 leiakyivesk.atvRkaakvfgvskstvhkDvt 41
                                      l+i + iv++   t+R   ++ g++kstvhk ++
  gi|313117230|ref|YP_004044213.1| 15 LHILELIVDHGwVTLRGLVEETGLAKSTVHKHLS 48
                                      67778888886479*****************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.1
                           SpoIIID   2 dyieeRvleiakyiveskat 21 
                                       d+++  + e+++ +ve ++t
  gi|313117230|ref|YP_004044213.1| 236 DHVRSATAEVTESLVEAQST 255
                                       56778888899999998887 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00046      0.41      24      45 ..      27      48 ..      26      53 .. 0.90
   2 ?   -1.3   0.0       2.2     2e+03      37      51 ..     231     245 ..     231     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00046
                            HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                                      vtl+ L +e G++kst+++hL+
  gi|313117230|ref|YP_004044213.1| 27 VTLRGLVEETGLAKSTVHKHLS 48
                                      6899999**************7 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                            HTH_10  37 kstlsehLrkaeskl 51 
                                       k+ l +h+r+a+  +
  gi|313117230|ref|YP_004044213.1| 231 KNELADHVRSATAEV 245
                                       567889999998766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00035      0.31       3      43 ..      15      54 ..      13      66 .. 0.82
   2 ?   -2.3   0.0       4.9   4.4e+03      28      44 ..     171     187 ..     169     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      l+ilel+   +g ++   L ee+++ ++tv++++ +L++  
  gi|313117230|ref|YP_004044213.1| 15 LHILELI-VDHGWVTLRGLVEETGLAKSTVHKHLSTLRAND 54
                                      5788888.555569************************974 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.9
                            HTH_11  28 SrrtvrrdIkaLeelgv 44 
                                       Sr + +  +++ +e g+
  gi|313117230|ref|YP_004044213.1| 171 SREALHAELEQVRENGY 187
                                       67777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1713.02
//
Query:       gi|313117231|ref|YP_004044214.1|  [L=488]
Description: acyl-CoA synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-69  234.1   0.1    3.5e-69  233.4   0.1    1.2  1  AMP-binding    AMP-binding enzyme
    8.7e-14   52.3   0.0    1.6e-13   51.4   0.0    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.4   0.1   3.9e-73   3.5e-69      17     422 ..      21     390 ..       7     391 .. 0.83

  Alignments for each domain:
  == domain 1  score: 233.4 bits;  conditional E-value: 3.9e-73
                                       CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHH CS
                       AMP-binding  17 sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayileds 93 
                                       s+++++ TY+e  e++ +lA  Lr++Gv +g++V ++++n+p+++ +l+ai  +Gav+ p+n +l++e++ay +e s
  gi|313117231|ref|YP_004044214.1|  21 SDGNRHQTYHETAENAAQLATELRNRGVSEGSVVSVAAWNTPRFFELLYAITGIGAVIYPVNVNLPPEQIAYTIERS 97 
                                       4689********************99*************************************************** PP

                                       TESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--S CS
                       AMP-binding  94 eakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGT 170
                                       +a +l+  +ds+  + l+e  +             d+++  + +++ee +        +e ++ +dd+a+i++TSGT
  gi|313117231|ref|YP_004044214.1|  98 DADMLL--YDSDF-DGLAESFEG------------DAISIPALEYAEE-A--------TELSAAQDDPAVILFTSGT 150
                                       ******..66655.444444432............2222121222222.1........2224678************ PP

                                       SSS-EEEEEEHHHHHHHHHHHH..HHHC...SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHH CS
                       AMP-binding 171 TGkPKGVmlshrnlvanvaslk..letr...fklkeddvvlsilplahifglilelllallsGatvvllpkdaaldp 242
                                       TG+PK+V ++h+++v++   ++  + ++     l+ +d+v+   p++h +++   +++a + Ga ++l+ ++++   
  gi|313117231|ref|YP_004044214.1| 151 TGMPKAVRYTHAQIVHSSLGMAhqMAEYqtpAALSGEDTVFPGIPMYHLLAW-GTTIFAPYLGADLMLAGRFDP--- 223
                                       **************99999987776655443334449***************.777777777******997755... PP

                                       HHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGG CS
                       AMP-binding 243 klllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTE 319
                                       ++l ++ e  ++t  ++vP+++ ++le g        +dls+l l l+gg+ + + l++++r+ +   +  +YG T 
  gi|313117231|ref|YP_004044214.1| 224 QRLGAAAESGEATWSCLVPTMAVQVLETG--------HDLSGLTL-LTGGSVVKRGLTERLRDAGVS-FATIYGGTD 290
                                       678899999******************73........49*****9.79****************876.********* PP

                                       GSSECEE.....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE CS
                       AMP-binding 320 ttgvvtv.....lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds 391
                                       +++v ++     ++ +e  +++ +   p+p vevki De  g+    +  Gellvr+p++  gY+  pe   +a++ 
  gi|313117231|ref|YP_004044214.1| 291 MLAVGITlwtkhAR-REGYEYVRRSTHPIPAVEVKI-DERAGQ----DGMGELLVRSPWLPDGYYDAPEGKDDAYV- 360
                                       *****665677544.44446777889**********.555344....456*************************9. PP

                                       TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 392 egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                        ++w+rTGDlgr+ +dG + i++R+ d ik+
  gi|313117231|ref|YP_004044214.1| 361 -DGWFRTGDLGRRLPDGGITILDRLTDAIKS 390
                                       .57**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   1.8e-17   1.6e-13       2      76 .]     400     475 ..     399     475 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.8e-17
                                       HHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.-.--HHHHHHHHHHH.HT-TTTS-SEEEE-S---B-TTS CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.s.ealeeeLkahvrk.elgpyavpkkvvfvdelpktrsG 75 
                                       +Es++++ ++V+++aV +++d+ +Ge++va++    + + e l+++L+++ r+ ++++++ p++v+fv+e+p+t +G
  gi|313117231|ref|YP_004044214.1| 400 LESVISETDGVENVAVLAKSDAEWGERPVAVISG--DvTaETLQADLRSKSRDgRIESWWIPDDVRFVEEMPLTSTG 474
                                       6******************************997..423234888888888768*********************** PP

                                       - CS
                     AMP-binding_C  76 K 76 
                                       K
  gi|313117231|ref|YP_004044214.1| 475 K 475
                                       9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 3213.79
//
Query:       gi|313117232|ref|YP_004044215.1|  [L=586]
Description: acyl-CoA dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-33  115.4   1.7    2.4e-33  115.4   1.7    2.0  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      2e-20   73.3   0.0    6.8e-20   71.6   0.0    1.9  1  AidB_N         Adaptive response protein AidB N-terminal doma
      7e-18   64.6   0.0    1.4e-17   63.7   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    8.2e-10   39.1   6.6    1.7e-09   38.1   0.7    2.3  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   1.7   5.4e-37   2.4e-33       2     149 ..     288     444 ..     287     444 .. 0.98
   2 ?   -0.8   0.1      0.36   1.6e+03      54      85 ..     502     533 ..     496     542 .. 0.84

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 5.4e-37
                                       BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                     Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaeal 78 
                                       +Gfr++ e ln eRl +a+++ g + r l e+  +a +r+ fgk+l +h+l+r+ laema++ eaa + +++a+eal
  gi|313117232|ref|YP_004044215.1| 288 NGFRQMSEMLNAERLYNAIGSCGSMGRSLLESKVHAANREVFGKRLDEHPLMRRDLAEMATDHEAALAFTFEAVEAL 364
                                       7***************************************************************************9 PP

                                       ------.........HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHH CS
                     Acyl-CoA_dh_1  79 dagkpd.........raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniia 146
                                       ++ + +         r  +  aK++++++a++ a+ am++ Gg+Gy ee    rl+r+a+vl+i+eG+s+++ +++ 
  gi|313117232|ref|YP_004044215.1| 365 HRREREnddeahrlmRILVPTAKYRTARMAVDTASYAMEIKGGNGYVEEFVHPRLLRNAQVLPIWEGASNVMALDVL 441
                                       999999999*****************************************************************999 PP

                                       HHH CS
                     Acyl-CoA_dh_1 147 rrl 149
                                       r++
  gi|313117232|ref|YP_004044215.1| 442 RSM 444
                                       976 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHHHHHH--------H CS
                     Acyl-CoA_dh_1  54 reklaemaaeleaarllvyraaealdagkpdr 85 
                                       +++l ++  +++ a  lv++a ++ld ++++r
  gi|313117232|ref|YP_004044215.1| 502 AKELTDYIFDVTTAAILVEQAQWQLDVDGDAR 533
                                       567888999999*************9998874 PP

>> AidB_N  Adaptive response protein AidB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.0   1.5e-23   6.8e-20       8     155 ..      15     171 ..      11     172 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 1.5e-23
                            AidB_N   8 dvnlfasdpaLqeavaregaaea....aeelaalGellgsaevlelarlanrnpPrlrthDrfGrRiDevefhpayh 80 
                                       + n ++ dp Lq  ++r ++ e+    +++l+++G+++g+ +v++ a+ a+ npP+lrth+++G+ i+e+e hpa  
  gi|313117232|ref|YP_004044215.1|  15 HCNYYTYDPSLQFELRRRCDPEEldwgESNLREFGAMIGH-TVADNADVADDNPPKLRTHNKHGEVINEIEHHPAHI 90 
                                       5799***********999996666676*************.************************************ PP

                            AidB_N  81 almaaaveaglhasawe....earegahvaraallyllaqvea.GhlCPltmThAavpaL.kaepalaeewlpklls 151
                                       +  ++  eag+ a  +e    ++++ +   ++ ++yl+  + + G +CP +mT +a+ +L k +    +++ + l++
  gi|313117232|ref|YP_004044215.1|  91 ENERLVYEAGVIADVFEsppgREDPVSFPYHFGQFYLMEYASSvGLSCPGAMTGGAALVLdKFDDGSLQRFYDGLTA 167
                                       *****************9988888999999*******98765449***************77899999********* PP

                            AidB_N 152 rdYd 155
                                       rdYd
  gi|313117232|ref|YP_004044215.1| 168 RDYD 171
                                       ***9 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0     3e-21   1.4e-17       1      96 [.     177     277 ..     177     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 3e-21
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE..TS-------EEEEEEE..GG.... CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar..tekpdrarglslflvprdap.... 71 
                                       a+ lTE+q+G+dv +++ ta ++++g y l+GeK++++n  +++ alvlar  +  pd+++glslflv +++     
  gi|313117232|ref|YP_004044215.1| 177 AMFLTEKQGGTDVGANEVTAEPQEDGTYELYGEKWFCSNI-DSEAALVLARrpA-APDGTEGLSLFLVSTHDRdgep 251
                                       6889**************99999999**************.99********733.3447**********55444778 PP

                                       .GEEE-----BSS-TTS-EEEEEEE. CS
                     Acyl-CoA_dh_M  72 .gvsvrrieeklGlrglptgelvfed 96 
                                        + ++rr+++klG+ ++ptge+vfe 
  gi|313117232|ref|YP_004044215.1| 252 tNYRFRRLKDKLGTVTVPTGEVVFEG 277
                                       9***********************85 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.7   3.8e-13   1.7e-09      21     131 ..     322     431 ..     305     434 .. 0.84
   2 ?    3.9   0.7     0.013        58      16     103 ..     484     570 ..     480     573 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.8e-13
                                       HHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTT----HHHHHHHHHHHHHHHHHHHH CS
                     Acyl-CoA_dh_2  21 larervrassgekladdpatqlalaeaaarldAAralleraaaraeal.aaagkevtvedraearraaalavelaia 96 
                                       +a++r    +g++l+++p +   lae+a++ +AA a++ +a+++  +  +++++e    +r    +a+ +++++a++
  gi|313117232|ref|YP_004044215.1| 322 HAANREV--FGKRLDEHPLMRRDLAEMATDHEAALAFTFEAVEALHRReRENDDEAHRLMRILVPTAKYRTARMAVD 396
                                       4555555..9********************************9966544666666677777777888********** PP

                                       HHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGG CS
                     Acyl-CoA_dh_2  97 avdalfeaaGgsalrkesplqRlwRDahaaaaHaa 131
                                        ++ ++e+ Gg+++ +e +  Rl+R+a+++ ++++
  gi|313117232|ref|YP_004044215.1| 397 TASYAMEIKGGNGYVEEFVHPRLLRNAQVLPIWEG 431
                                       ****************************9877765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHH CS
                     Acyl-CoA_dh_2  16 aefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraearraaalave 92 
                                       a ++  +++  + ++++++++ + + + +++aa  +++A+  l  + ++ +al+ ++  v+  +r   +r  +   e
  gi|313117232|ref|YP_004044215.1| 484 ANAITAVGTSDGEYAQTQAKELTDYIFDVTTAAILVEQAQWQLDVDGDARKALVTRQ-FVNSYLREHDARGITGGGE 559
                                       5666677777778999****************************9999977655544.3455566655566666666 PP

                                       HHHHHHHHHHH CS
                     Acyl-CoA_dh_2  93 laiaavdalfe 103
                                       l+++a da+++
  gi|313117232|ref|YP_004044215.1| 560 LSTEAFDAVVR 570
                                       66666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3904.76
//
Query:       gi|313117233|ref|YP_004044216.1|  [L=258]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-35  121.4   0.2      5e-35  120.2   0.0    1.7  2  IclR            Bacterial transcriptional regulator
    4.2e-10   39.3   0.3    2.9e-09   36.6   0.2    2.2  2  HTH_IclR        IclR helix-turn-helix domain
    2.8e-07   30.3   0.0      7e-07   29.0   0.0    1.7  2  HTH_5           Bacterial regulatory protein, arsR family
    3.4e-07   30.1   0.1      1e-06   28.5   0.1    1.8  1  MarR_2          MarR family
    8.1e-06   25.3   0.0    2.7e-05   23.6   0.0    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
    3.3e-05   23.8   0.1    7.4e-05   22.7   0.1    1.6  1  HTH_20          Helix-turn-helix domain
    3.5e-05   23.6   0.0    7.7e-05   22.5   0.0    1.6  1  MarR            MarR family
    0.00043   20.4   0.2     0.0054   16.9   0.0    2.2  2  HTH_34          Winged helix DNA-binding domain
    0.00048   19.8   0.1     0.0011   18.7   0.1    1.6  1  HTH_38          Helix-turn-helix domain
    0.00073   20.0   0.7     0.0026   18.2   0.1    2.1  2  HTH_27          Winged helix DNA-binding domain
     0.0014   18.3   0.1     0.0035   17.0   0.1    1.7  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.005   16.8   0.8      0.095   12.7   0.1    2.7  3  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.011   15.9   0.1      0.027   14.7   0.1    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.015   15.1   0.0      0.031   14.1   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.023   14.9   0.1        6.8    7.0   0.0    2.3  2  DUF1257         Protein of unknown function (DUF1257)
      0.071   13.0   0.0       0.17   11.8   0.0    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.5   3.9e+03      42      73 ..      32      63 ..      21      71 .. 0.64
   2 !  120.2   0.0   4.4e-38     5e-35       6     127 ..     130     251 ..     125     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.5
                                      ---SSTTS--SHHHHHHHHHHHHHHTSEEEES CS
                              IclR 42 lkrlterTitdpeeLleeLakvReqGyavdre 73
                                      +++l ++  + + ++++ L++  +q y v ++
  gi|313117233|ref|YP_004044216.1| 32 VTELADTLDKAKSTIHRHLSTLEAQEYVVREG 63
                                      45555555556677777788877777777654 PP

  == domain 2  score: 120.2 bits;  conditional E-value: 4.4e-38
                                       TTSTT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEE CS
                              IclR   6 vsaiGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrci 82 
                                       +s+ G+ +plyata+GKa+L+  ++e++e++l +  l +lte+Tit++ +L++e++++ ++Gy+v+reE+ +g++++
  gi|313117233|ref|YP_004044216.1| 130 NSKAGEGVPLYATAAGKAILSCYPKEKVERILDEISLVALTENTITQKSALHDEIDAIQKRGYSVNREENVNGIHAV 206
                                       6889************************************************************************* PP

                                       EEEEE-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  83 AapifdasgevvaAvsvsgptarlteeelkeellalvreaArkis 127
                                       ++p+++ +g +++A+s+sgp++rl+ e l+e+l al+ e+A++++
  gi|313117233|ref|YP_004044216.1| 207 GVPVRRTNGWPIGALSISGPAYRLQGELLEETLPALLLETANELE 251
                                       ******************************************987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.2   2.5e-12   2.9e-09       6      51 ..      18      62 ..      14      63 .. 0.94
   2 ?   -0.2   0.0      0.79   8.8e+02      20      29 ..      92     101 ..      79     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.5e-12
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      ++i++al++  ++ +++elA+ ++ +kSt hR+L+tL+ + yv ++
  gi|313117233|ref|YP_004044216.1| 18 FEIIEALRAMEGA-RVTELADTLDKAKSTIHRHLSTLEAQEYVVRE 62
                                      899****999997.*****************************987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.79
                                       BHHHHHHHHT CS
                          HTH_IclR  20 tlselArrtg 29 
                                       +++elA++t+
  gi|313117233|ref|YP_004044216.1|  92 KVKELAEKTD 101
                                       899****997 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   6.3e-10     7e-07       2      45 ..      15      59 ..      14      60 .. 0.93
   2 ?   -3.6   0.0       9.5   1.1e+04      17      25 ..      92     100 ..      92     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 6.3e-10
                                      HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  2 ptRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +t  +I+ +L+  e + v+ela+ l++ +st+ +HL+ L+ + +V
  gi|313117233|ref|YP_004044216.1| 15 ETVFEIIEALRAMEgARVTELADTLDKAKSTIHRHLSTLEAQEYV 59
                                      67889*******666***************************998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.5
                                       EHHHHHHHH CS
                             HTH_5  17 cvcelaeel 25 
                                       +v elae++
  gi|313117233|ref|YP_004044216.1|  92 KVKELAEKT 100
                                       589999987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   9.2e-10     1e-06       6      57 ..      16      65 ..      13      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 9.2e-10
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                      + + ++ aL++ +g   +v+ela++l+  ks+++r+l  L+a+ +v+r+ ++
  gi|313117233|ref|YP_004044216.1| 16 TVFEIIEALRAMEG--ARVTELADTLDKAKSTIHRHLSTLEAQEYVVREGDE 65
                                      6678999*******..9*******************************9775 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.4e-08   2.7e-05       3      47 ..      15      59 ..      13      60 .. 0.96
   2 ?   -2.1   0.0       2.7     3e+03      21      27 ..      94     100 ..      92     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.4e-08
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      et ++I+e+L++  +   +eLA+ l+  +st++r+l  Le ++++
  gi|313117233|ref|YP_004044216.1| 15 ETVFEIIEALRAMEGARVTELADTLDKAKSTIHRHLSTLEAQEYV 59
                                      7899***************************************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                            HTH_24  21 reLAerl 27 
                                       +eLAe++
  gi|313117233|ref|YP_004044216.1|  94 KELAEKT 100
                                       89**997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   6.6e-08   7.4e-05      13      58 ..      18      63 ..      13      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.6e-08
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                       +i  aL+  eg+ ++ela++ld +k+t+++HL +Le  ++v +++
  gi|313117233|ref|YP_004044216.1| 18 FEIIEALRAMEGARVTELADTLDKAKSTIHRHLSTLEAQEYVVREG 63
                                      5799999999***************************999998776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   6.9e-08   7.7e-05       2      53 ..      14      65 ..      13      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.9e-08
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                      t+t f+i++ l+ +++++v+eLa+ l   kst+ r l +Le ++++ R+ ++
  gi|313117233|ref|YP_004044216.1| 14 TETVFEIIEALRAMEGARVTELADTLDKAKSTIHRHLSTLEAQEYVVREGDE 65
                                      7899*******************************************98766 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.8e-06    0.0054       3      47 ..      18      62 ..      17      66 .. 0.95
   2 ?    0.9   0.0      0.48   5.4e+02      13      44 ..     162     193 ..     160     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-06
                            HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievd 47
                                      ++++  L + + a  +el ++l   ++ +  hl++Le+++Y++++
  gi|313117233|ref|YP_004044216.1| 18 FEIIEALRAMEGARVTELADTLDKAKSTIHRHLSTLEAQEYVVRE 62
                                      78999*************************************876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.48
                            HTH_34  13 deadfvelkealeatdgnLsvhlkkLekagYi 44 
                                       de++ v l e + + +++L  ++++++k gY 
  gi|313117233|ref|YP_004044216.1| 162 DEISLVALTENTITQKSALHDEIDAIQKRGYS 193
                                       6778888999999999**************94 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1     1e-06    0.0011      12      41 ..      20      50 ..      19      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1e-06
                            HTH_38 12 eIerlla.eGlslreIArrLgrspsTIsREl 41
                                       Ie+l+a eG  + e A  L++++sTI+R+l
  gi|313117233|ref|YP_004044216.1| 20 IIEALRAmEGARVTELADTLDKAKSTIHRHL 50
                                      69***988*********************98 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.3e-06    0.0026       9      64 ..      21      75 ..      13      77 .. 0.86
   2 ?   -1.1   0.0       2.4   2.7e+03      23      47 ..     168     192 ..     159     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64
                                      ++ +r  +++++ ++l+++l+  +s+i+  l+ L+++++v+r+gde d + ++++l
  gi|313117233|ref|YP_004044216.1| 21 IEALR-AMEGARVTELADTLDKAKSTIHRHLSTLEAQEYVVREGDEYDIGLRFLSL 75
                                      45555.7889999*********************************9887777765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                            HTH_27  23 dlcgrlnvedshisyslkkLtekGL 47 
                                       +l + + +++s+ +  +++  ++G+
  gi|313117233|ref|YP_004044216.1| 168 ALTENTITQKSALHDEIDAIQKRGY 192
                                       6778888999999999999999998 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.2e-06    0.0035       4      46 ..      19      61 ..      18      63 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.2e-06
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +i+e l+     +v+el++ l+ ++ Ti R L++Le+q  ++R
  gi|313117233|ref|YP_004044216.1| 19 EIIEALRAMEGARVTELADTLDKAKSTIHRHLSTLEAQEYVVR 61
                                      69999*********************************99887 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   8.5e-05     0.095       3      43 ..      18      57 ..      16      61 .. 0.84
   2 ?   -2.7   0.0       5.4   6.1e+03      18      26 ..      93     101 ..      92     103 .. 0.80
   3 ?    1.3   0.0       0.3   3.3e+02      44      54 ..     182     192 ..     171     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.5e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      + i+e L +a +     eLA+ L+  ++t++r++ +Le++ 
  gi|313117233|ref|YP_004044216.1| 18 FEIIEAL-RAMEGARVTELADTLDKAKSTIHRHLSTLEAQE 57
                                      5789999.555558999*********************975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.4
                            HTH_11  18 geeLAeeLn 26 
                                        +eLAe+++
  gi|313117233|ref|YP_004044216.1|  93 VKELAEKTD 101
                                       589**9975 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.3
                            HTH_11  44 vpIesepgrGY 54 
                                       ++I++ ++rGY
  gi|313117233|ref|YP_004044216.1| 182 DEIDAIQKRGY 192
                                       789*******9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.4e-05     0.027       7      56 ..      15      63 ..      10      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress  7 EdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                      E + e I  l    + +++++la  L+ ++s++   l+ Le ++yv+ e+
  gi|313117233|ref|YP_004044216.1| 15 ETVFEIIEALR-AMEGARVTELADTLDKAKSTIHRHLSTLEAQEYVVREG 63
                                      44444443333.4556899***************************9776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-05     0.031       8      41 ..      18      53 ..      12      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                            HTH_23  8 lrillllae..GlsvreIAreLgvsrrTvyrwlkry 41
                                      ++i+ +l+   G++v+e A+ L+  ++T+ r l++ 
  gi|313117233|ref|YP_004044216.1| 18 FEIIEALRAmeGARVTELADTLDKAKSTIHRHLSTL 53
                                      68999999777********************98875 PP

>> DUF1257  Protein of unknown function (DUF1257)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0061       6.8       9      48 ..      39      78 ..      32      80 .. 0.80
   2 ?    5.6   0.0     0.017        19      68      95 ..     172     199 ..     155     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0061
                           DUF1257  9 vkegeeevrgyrgqtrsaevvirqkngydigFrwngegeY 48
                                       ++ +++++ + ++ +  e+v+r+  +ydig r  + geY
  gi|313117233|ref|YP_004044216.1| 39 LDKAKSTIHRHLSTLEAQEYVVREGDEYDIGLRFLSLGEY 78
                                      555666778888888899*************999888887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                           DUF1257  68 nkltqrYAyktvlaeaekeGftveeeek 95 
                                       n +tq+ A +  +++++k+G++v  ee+
  gi|313117233|ref|YP_004044216.1| 172 NTITQKSALHDEIDAIQKRGYSVNREEN 199
                                       569********************99987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.17      17      58 ..      24      65 ..      14      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      L + + a+++e+a  l+  +s++ + L+ Le   +V re  +
  gi|313117233|ref|YP_004044216.1| 24 LRAMEGARVTELADTLDKAKSTIHRHLSTLEAQEYVVREGDE 65
                                      5567899*****************************999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1834.79
//
Query:       gi|313117234|ref|YP_004044217.1|  [L=730]
Description: PAS domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-28   98.8   0.1    4.8e-28   97.9   0.1    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.7e-12   47.4   0.0    1.8e-11   44.2   0.0    2.7  3  PAS_3        PAS fold
      1e-10   41.5   0.4    4.6e-10   39.4   0.1    2.3  2  HisKA        His Kinase A (phospho-acceptor) domain
    3.3e-10   39.9   0.0    1.3e-09   38.0   0.0    2.0  2  PAS          PAS fold
    4.1e-08   33.5   0.0    1.2e-07   31.9   0.0    1.9  1  HAMP         HAMP domain
    2.7e-06   27.6   0.4    1.4e-05   25.3   0.0    2.3  2  PAS_4        PAS fold
    3.2e-06   27.3   0.0    1.9e-05   24.8   0.0    2.3  2  PAS_9        PAS domain
    9.5e-06   25.5   0.0    2.6e-05   24.1   0.0    1.8  2  HATPase_c_5  GHKL domain
     0.0015   18.5   0.0     0.0034   17.3   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0038   17.1   0.0     0.0078   16.0   0.0    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.056   13.6   0.3       0.13   12.3   0.3    1.6  1  FxsA         FxsA cytoplasmic membrane protein
        1.3    8.3   4.7       0.17   11.2   0.1    1.8  2  CorA         CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.1   3.2e-31   4.8e-28       2     110 ..     622     728 ..     621     730 .] 0.90

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 3.2e-31
                                       HHHHHHHHHHHHHHHHHHHHS.TTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfat.kageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75 
                                       de +Lrq+++nl++Na+++a+ + +ei++  +  e  d +++sveDnG Gip+++++k+fe f q   ++ + +gtG
  gi|313117234|ref|YP_004044217.1| 622 DENQLRQVFQNLIKNAIEHAGeDPPEIHIGFT--ElpDAYRFSVEDNGVGIPENQQEKIFEIFEQ---ASGEESGTG 693
                                       899****************6655556777666..5568***************************...667789*** PP

                                       HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  76 lGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       +Gl+++k++ve++gG+iwves+ g+ ttf+ft+ +
  gi|313117234|ref|YP_004044217.1| 694 IGLAVCKRIVERHGGDIWVESSVGKQTTFYFTISK 728
                                       *******************************9875 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.2e-14   1.8e-11       2      82 ..     405     479 ..     404     486 .. 0.85
   2 ?   -3.2   0.0       7.3   1.1e+04      15      47 ..     523     555 ..     514     568 .. 0.75
   3 ?   -1.3   0.0       1.8   2.7e+03      57      71 ..     701     715 ..     671     717 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.2e-14
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       ++ s++   ilGy+pe++ g+   +l++vhp+D + v +al     ++e p  +e+R++ +dG++r +e +++ +  
  gi|313117234|ref|YP_004044217.1| 405 TFQSPSSHAILGYDPEQMDGT--PLLSYVHPDDKSTVDSALS----DDEnPRRIEFRMQDADGDWRVLEGTCEKV-T 474
                                       57799999*************..**********888888887....4444889*******************999.5 PP

                             PAS_3  78 engkp 82 
                                       +n  +
  gi|313117234|ref|YP_004044217.1| 475 DNPFV 479
                                       55555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.3
                             PAS_3  15 speellgkveswldlvhpeDrervrealqealk 47 
                                       + +e l  v+s+ldl+  e  +r+ e+ +e+++
  gi|313117234|ref|YP_004044217.1| 523 DLQEPLRMVSSYLDLLSSEYGDRLDEEANEYIE 555
                                       556777778899999999999999888888874 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.8
                             PAS_3  57 RirrkdGeyrwvear 71 
                                       Ri+ ++G+ +wve++
  gi|313117234|ref|YP_004044217.1| 701 RIVERHGGDIWVESS 715
                                       99999*******987 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.1   4.6e+03      11      29 ..      70      88 ..      53     103 .. 0.66
   2 !   39.4   0.1   3.1e-13   4.6e-10       2      65 ..     513     578 ..     512     580 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.1
                                      HHHHHHHHHHHHHHHHHHC CS
                             HisKA 11 HELrtPLsailgnaeaLkr 29
                                      HE +  L+++l ++++ ++
  gi|313117234|ref|YP_004044217.1| 70 HEQNKRLTGVLTATDVVRN 88
                                      4444446777777776655 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 3.1e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l++f+   +H+L  PL  ++ ++++L+ e  ++l+ee  ey+e ++++a+r++++++ lL++sr  
  gi|313117234|ref|YP_004044217.1| 513 LQQFAYIASHDLQEPLRMVSSYLDLLSSEygDRLDEEANEYIEFAVDGAERMRNMIDGLLTYSRVK 578
                                       78999*********************666699*******************************975 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   8.8e-13   1.3e-09       4     113 .]     385     489 ..     382     489 .. 0.96
   2 ?   -2.1   0.0       2.4   3.6e+03      66      92 ..     683     715 ..     670     718 .. 0.56

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 8.8e-13
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       +a+++++ d i  vDe+g+i++ +++   +lG+++e++ g +ll ++h++    +++ +  +l++ e++r  e +  
  gi|313117234|ref|YP_004044217.1| 385 SALIDNASDLITQVDENGDITFQSPSSHAILGYDPEQMDGTPLLSYVHPD----DKSTVDSALSDDENPRRIEFRMQ 457
                                       699*********************************************99....99******************999 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         dg  + le ++ +v+d    ++g++++++di
  gi|313117234|ref|YP_004044217.1| 458 DADGDWRVLEGTCEKVTDNPF-VTGVVVTCHDI 489
                                       9******************98.78********8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                                       HHHTT-ECCCCEEEEC......TTSSEEEEEEE CS
                               PAS  66 leqgeesrageisfkl......rdgrpihlevr 92 
                                       ++++ e+++  i + +      r+g+ i++e  
  gi|313117234|ref|YP_004044217.1| 683 EQASGEESGTGIGLAVckriveRHGGDIWVESS 715
                                       333344444444444455778899999999865 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   8.3e-11   1.2e-07       3      48 ..     330     375 ..     328     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 8.3e-11
                                       HHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHH CS
                              HAMP   3 arrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMl 48 
                                        r++   + rL+r a ri +Gd+d++ ++++ D iG+L rafN+M+
  gi|313117234|ref|YP_004044217.1| 330 GRNTAVAVDRLTRKAGRIESGDFDVDFETNRIDNIGQLYRAFNEMQ 375
                                       677777789************************************7 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6   2.4e+03      31      58 ..      72     100 ..      55     103 .. 0.81
   2 !   25.3   0.0   9.2e-09   1.4e-05       2     109 ..     389     493 ..     388     494 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                             PAS_4  31 ppeellGktla.ellpeedaarleralrr 58 
                                       + ++l+G   a +++  +d ++++r+lr+
  gi|313117234|ref|YP_004044217.1|  72 QNKRLTGVLTAtDVVRNRDPEAIQRHLRQ 100
                                       56788888888889999999999999887 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 9.2e-09
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       d+ +d+++ +d++g +++ ++++++++g++pe++ G +l +++ ++d+  +++al    + e p + +  + + +g+
  gi|313117234|ref|YP_004044217.1| 389 DNASDLITQVDENGDITFQSPSSHAILGYDPEQMDGTPLLSYVHPDDKSTVDSALS---DDENPRRIEFRMQDaDGD 462
                                       8999************************************9988877777777665...677777777777779*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +r++e ++  + d +  v gv+v+++DiT+r 
  gi|313117234|ref|YP_004044217.1| 463 WRVLEGTCEKVTD-NPFVTGVVVTCHDITDRI 493
                                       ********99955.4449***********995 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         2     3e+03       5      29 ..     104     128 ..     101     153 .. 0.75
   2 !   24.8   0.0   1.3e-08   1.9e-05       4     104 .]     395     491 ..     392     491 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2
                             PAS_9   5 lidnpdgrilyaNeaalrllGyspe 29 
                                       ++ +  + i y+N++ +r+l  ++e
  gi|313117234|ref|YP_004044217.1| 104 FFPDATHSIDYVNTTNNRILAGTRE 128
                                       5555677799*****9999865543 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.3e-08
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                       i  ++++g i++ +++   +lGy+pe++ g+++   +  +p+++++++ al + + ++r+ e  +++ +g     + 
  gi|313117234|ref|YP_004044217.1| 395 ITQVDENGDITFQSPSSHAILGYDPEQMDGTPLLSYV--HPDDKSTVDSALSDDE-NPRRIEFRMQDADGDWRVLEG 468
                                       55589***************************99999..9***************.9*****************99* PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       t+  v d+   ++g++v+++Dit+
  gi|313117234|ref|YP_004044217.1| 469 TCEKVTDN-PFVTGVVVTCHDITD 491
                                       *****765.3477799*******6 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.1   1.2e+04      13      31 ..     387     404 ..     385     410 .. 0.74
   2 !   24.1   0.0   1.7e-08   2.6e-05       3      90 ..     623     715 ..     621     727 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.1
                       HATPase_c_5  13 lLdNAieacskieeekrfI 31 
                                       l+dNA +  ++++e +  I
  gi|313117234|ref|YP_004044217.1| 387 LIDNASDLITQVDE-NGDI 404
                                       89999998888885.5555 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.7e-08
                       HATPase_c_5   3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkkle....sskskkeehGiGl 71 
                                       ++ l  ++ nl+ NAie + + +   ++I++ ++e  +++ +s+e +  g    +++k++    + + +++  GiGl
  gi|313117234|ref|YP_004044217.1| 623 ENQLRQVFQNLIKNAIEHAGEDP---PEIHIGFTELPDAYRFSVEDNGVGipenQQEKIFeifeQASGEESGTGIGL 696
                                       678999************99866...9*****************98844434335555443333668889999**** PP

                       HATPase_c_5  72 ksireivkkykgnlsieae 90 
                                          ++iv++++g++++e +
  gi|313117234|ref|YP_004044217.1| 697 AVCKRIVERHGGDIWVESS 715
                                       **************99875 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.3e-06    0.0034      35     110 ..     629     704 ..     614     723 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                       HATPase_c_2  35 aveEactNavehayleapegpvevrlesdeealtvevaDsGpg..fdpetlpdpteeepkeslkegGrGlalikglv 109
                                       + + ++ Na+eha ++ p  ++++ ++  ++a +++v+D+G g   + +++  +  e++++++   G+Gla+ k++v
  gi|313117234|ref|YP_004044217.1| 629 VFQNLIKNAIEHAGEDPP--EIHIGFTELPDAYRFSVEDNGVGipENQQEKIFEIFEQASGEESGTGIGLAVCKRIV 703
                                       5555778*******8766..9999******************95333334444445555677777778888888877 PP

                       HATPase_c_2 110 D 110
                                       +
  gi|313117234|ref|YP_004044217.1| 704 E 704
                                       6 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.2e-06    0.0078       7      63 ..     630     688 ..     624     708 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.2e-06
                       HATPase_c_3   7 laelvdNsld.Adaen...vkievnknrgktgeivieDdGkGmseeelknalrlatsskea 63 
                                          l++N+++ A  e    ++i + + + ++ ++++eD+G G++e++ ++ +++ +++  +
  gi|313117234|ref|YP_004044217.1| 630 FQNLIKNAIEhA-GEDppeIHIGFTELP-DAYRFSVEDNGVGIPENQQEKIFEIFEQASGE 688
                                       5689*****954.333344888888876.799**************999999998887763 PP

>> FxsA  FxsA cytoplasmic membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3     9e-05      0.13       7      52 ..     296     340 ..     290     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9e-05
                              FxsA   7 pvlEilllvlvasaiGvlatllllvltallGallvrrqgrralrrl 52 
                                         ++ + +v+ ++++G l+t++ ++l +++Ga+l r++ +  + rl
  gi|313117234|ref|YP_004044217.1| 296 STVDSYGFVRAVQQYGTLVTVVSVLLIGVVGAILGRNTAVA-VDRL 340
                                       5688999**************************99976654.4444 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   1.0       3.9   5.8e+03     237     259 ..     314     334 ..     312     335 .. 0.83
   2 ?   11.2   0.1   0.00011      0.17     130     211 ..     486     571 ..     460     577 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.9
                              CorA 237 LTvltaiflPlTlitGiyGmNfk 259
                                        Tv++++++   +++ i+G N++
  gi|313117234|ref|YP_004044217.1| 314 VTVVSVLLIG--VVGAILGRNTA 334
                                       5899999988..99*****9986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00011
                              CorA 130 leeeldeledeledstkkeilrelaqlrrrlvkl..rralapnrevlk..rllakaddkllddedkeylrdlldele 202
                                        ++ +d++e++ e +++k +l++  +  ++ +++  ++   p+r v +  +ll+++ +++ld+e++ey++   d +e
  gi|313117234|ref|YP_004044217.1| 486 CHDITDRIERQAELEETKRELERSNEALQQFAYIasHDLQEPLRMVSSylDLLSSEYGDRLDEEANEYIEFAVDGAE 562
                                       5677899999996666666666666655555555458888888888744455569********************** PP

                              CorA 203 rllemleal 211
                                       r+ +m++ l
  gi|313117234|ref|YP_004044217.1| 563 RMRNMIDGL 571
                                       ******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 4939.64
//
Query:       gi|313117235|ref|YP_004044218.1|  [L=431]
Description: sugar ABC transporter periplasmic protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.2e-21   75.3   2.2    3.5e-20   73.2   2.2    1.8  1  SBP_bac_1  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.032   14.4   0.0        7.6    6.7   0.0    2.4  2  ApbA_C     Ketopantoate reductase PanE/ApbA C terminal
      0.091   12.6   0.0       0.16   11.7   0.0    1.3  1  SpoVIF     Stage VI sporulation protein F


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   2.2   5.9e-24   3.5e-20       2     315 .]      37     345 ..      36     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 5.9e-24
                                       GSHHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHH CS
                         SBP_bac_1   2 gsltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyv 78 
                                       +++ eg+ ++ l  ++f ++++gi+V++e  ++++l+++ ++ +a  + + D++++d+ w++++a+   l+p+  y+
  gi|313117235|ref|YP_004044218.1|  37 ATEGEGRLFRRLT-DEFVADETGIEVNVELKPYDALYEQNRKLLAEQNDEFDLVFIDDPWFPQFASD--LEPIRQYL 110
                                       67788999*****.************************8888888888899*************999..99999999 PP

                                       HHTTECTTCCTEEEEHHHHTHHHHCE.EE.................ES.EEEEE.EEEEEEETTTHHCTTGGGSHBH CS
                         SBP_bac_1  79 kaylapgvkdaadklsssvlpkilds.kv.................ly.vPlya.argliYNkdlfekagldppwtW 135
                                        +  + +           + +++ld+  +                 l  + + + ++ ++YN ++f++ g dpp+t+
  gi|313117235|ref|YP_004044218.1| 111 PDGVPAE-----------YIQTTLDIaHWptprgplppevsdedpvLRgLVVVGnTQIFAYNATYFDQVGYDPPETY 176
                                       9998888...........4555555544456666777777999999666667788********************** PP

                                       HHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT.HHCSHHHHSHHHHHHHHHHHHHHHH CS
                         SBP_bac_1 136 delveaakklkekgkkpiggarggsasgtayyfalalakslggkvfdkdgg.gldnpegvtaatylvklyavanltk 211
                                       ++++ea++ +++   ++ g + +g++++    ++ ++  s +g+ fd+d++ +  ++egv+a+ +lv         +
  gi|313117235|ref|YP_004044218.1| 177 QDVLEAGRAIDAEIDGTHGYVIRGAQGNPIVTNFFPVGFSQAGRMFDADWRfQWGSREGVEAVRFLVQEL------A 247
                                       *****************88888888888888888888888888*****9987656666666666666666......8 PP

                                       HHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE.EEEE CS
                         SBP_bac_1 212 elkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi.lgay 287
                                       + ++++++ ++++++++ +++G++a a  +++          ++ ++a  ++   +l ++ +P   +g ++   g++
  gi|313117235|ref|YP_004044218.1| 248 DISPADVTKYNEDEVVTTLSQGTVAQASTWPGT---------ASLAIAENSPSARDLKFTVIPSNADGRRAPqQGNW 315
                                       **************************9888877.........77777777777788889999999999999999*** PP

                                       EEEEBTTCST..HHHHHHHHHHHTSHHHHH CS
                         SBP_bac_1 288 glaipkgskn..peaAkkFldfllspeaqa 315
                                        ++i++++++  ++a  k+++ + s+e+q+
  gi|313117235|ref|YP_004044218.1| 316 IVGINSHTSEaaKKAGGKVIQSFVSKEGQE 345
                                       **********88888************996 PP

>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0013       7.6      63     107 ..     157     204 ..     138     212 .. 0.81
   2 ?    5.0   0.0    0.0045        27      17      77 ..     216     276 ..     209     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0013
                            ApbA_C  63 leeaveavlektaanrsSMlqD.veagr..ktEidyinGavvklAekl 107
                                       + ++ +++++++    + ++qD +eagr    Eid + G+v++ A+ +
  gi|313117235|ref|YP_004044218.1| 157 IFAYNATYFDQVGYDPPETYQDvLEAGRaiDAEIDGTHGYVIRGAQGN 204
                                       666677777777778999****7789997888***********99865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0045
                            ApbA_C  17 npltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaan 77 
                                       ++ + ++d++ +  + s+e+ + vr l++E+ ++  a+  +++e+++  ++ + + ++a +
  gi|313117235|ref|YP_004044218.1| 216 SQAGRMFDADWRFQWGSREGVEAVRFLVQELADISPADVTKYNEDEVVTTLSQGTVAQAST 276
                                       566667899999999********************999988***99999888877776665 PP

>> SpoVIF  Stage VI sporulation protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.7e-05      0.16      32      64 ..     238     270 ..     235     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                            SpoVIF  32 tlRqlikqvsklankpvskekedkivkaivndk 64 
                                        +R l+++++++   +v+k +ed++v +  +  
  gi|313117235|ref|YP_004044218.1| 238 AVRFLVQELADISPADVTKYNEDEVVTTLSQGT 270
                                       79************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2875.83
//
Query:       gi|313117236|ref|YP_004044219.1|  [L=414]
Description: amino acid ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-38  131.4   8.7    8.2e-38  130.9   8.7    1.1  1  Peripla_BP_6  Periplasmic binding protein
    6.1e-20   71.6   0.0      9e-19   67.8   0.0    2.0  1  ANF_receptor  Receptor family ligand binding region
    3.9e-07   29.4   0.1    1.2e-06   27.8   0.1    1.7  2  Peripla_BP_5  Periplasmic binding protein domain
  ------ inclusion threshold ------
      0.019   14.8   2.8      0.019   14.8   2.8    2.5  2  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   8.7   1.8e-41   8.2e-38       1     312 [.      37     341 ..      37     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 1.8e-41
                                       EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-B CS
                      Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgpl 77 
                                       p+++G++ pl+G +  +g+   ++++ a+ +iN+aGGi+Gr++el++ D + ++d+a+e +++lvd +gv ++vg+l
  gi|313117236|ref|YP_004044219.1|  37 PVRFGVVLPLTGSLEKVGTHGKRAVEQAVSDINQAGGILGRPVELTTIDSKASADVAVEGYKKLVD-EGVVGFVGAL 112
                                       79****************************************************************.********** PP

                                       SHHHHHHHHHHHHHHT-EEEESS-HH......CC.TTSTTEEESS--HHHHHHHHHHHHH...HHTTSCEEEEEEES CS
                      Peripla_BP_6  78 ssavaaavaevlakdgvpvigpaglt......ge.kcspyvfslgpsysaqasalveyla...kelggkkvalvyad 144
                                        s++ +a+a+++a+dg+  ++pa+++      g  ++  y+ ++ ps+  qa a+++  +   + +g+ +v l++ d
  gi|313117236|ref|YP_004044219.1| 113 ASDTSLALAPKAAEDGIMEVSPASTNpqlsnaGRsDGRKYFGRTVPSDILQAVAMAKV-LdapQYVGAESVSLLAID 188
                                       *********************9965533322232377778889999999999888885.42336789********** PP

                                       SHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEE CS
                      Peripla_BP_6 145 yafgregiaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakril 221
                                       + fg ++++ ++ ++     +vv+++++++++++f+++++++ a  +dav +++++++   ++ a+ + ++da+   
  gi|313117236|ref|YP_004044219.1| 189 NGFGSALADEIGSSLD---ADVVADVRYDPSASSFDSVLDEVFAGSPDAVGFVSVPGQEKGIVDAYTASDYDAP--W 260
                                       **************99...569999************************************************8..6 PP

                                       EECCC-CHHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTH CS
                      Peripla_BP_6 222 lvswsgseedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaags 298
                                       ++s +++ +d+ +      +g++++    ++  ++    +++++ + ++ a     +++++y+a+ l+++a++ ag+
  gi|313117236|ref|YP_004044219.1| 261 VFSAGMFGNDVPSSY----NGFYSA--SLSSVRTDGYFTLSRRLSDIAPLA----PYSSNAYDALFLMAAAAEMAGE 327
                                       78999****996665....577766..556777888888899999989976....799******************* PP

                                       CCHHHHHHHHHHS- CS
                      Peripla_BP_6 299 ltreavraaleslg 312
                                        ++ a++++++s++
  gi|313117236|ref|YP_004044219.1| 328 ASGPAIADTIRSVS 341
                                       ***********985 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0     2e-22     9e-19       3     351 ..      58     393 ..      56     396 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 2e-22
                                       HHHHHHHHHHHHT-TTSSTTEEEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEEE CS
                      ANF_receptor   3 leAmklAveeinsdpnllpgiklgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvis 79 
                                       + A++ Av++in+ +++l++  ++++ id++ +   a+e   +++   vv+++G+  s++s a+a  a++  i  +s
  gi|313117236|ref|YP_004044219.1|  58 KRAVEQAVSDINQAGGILGR-PVELTTIDSKASADVAVEGYKKLVDEGVVGFVGALASDTSLALAPKAAEDGIMEVS 133
                                       679***********999975.*************************66***************************** PP

                                       SS---GGGG-TTTTT...TEEESS--CHHHHHHHHHHHH...HTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EE CS
                      ANF_receptor  80 ygstspelsdknryp...tflrtvpsdtsqaqAivdilk...hfgWkkvaliysdddygesglqaleeeleergicv 150
                                       ++st+p ls+  r++   +f rtvpsd  qa A++++l    + g  +v+l++ d+  g  +++++  +l++    v
  gi|313117236|ref|YP_004044219.1| 134 PASTNPQLSNAGRSDgrkYFGRTVPSDILQAVAMAKVLDapqYVGAESVSLLAIDNGFGSALADEIGSSLDA---DV 207
                                       **********9998533378*****************9555499************************9988...45 PP

                                       EEEEEEST.CHHHCHHHHHHHHHHTTT--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC.. CS
                      ANF_receptor 151 alkekipe.ssnddevvrkllkeikskarvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpelt 226
                                       +   ++++ +s++d+v++++    + +++++ +++ +   + ++ a     ++ + +v+                  
  gi|313117236|ref|YP_004044219.1| 208 VADVRYDPsASSFDSVLDEVF---AGSPDAVGFVSVPGQEKGIVDAYTASDYDAP-WVFS----------------- 263
                                       555555555779********9...4444555555555666679999999999986.5555................. PP

                                       HHHHHTT-EEEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHH...... CS
                      ANF_receptor 227 gleaaegvlgfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkk...... 297
                                          ++++ +  +++   s+++s+++  +  ++ ++  +  +   ++s++a   Yda +l+a A++ ++++       
  gi|313117236|ref|YP_004044219.1| 264 -AGMFGNDVPSSYNGFYSASLSSVR-TDGYFTLSRRLSDIAPLAPYSSNA---YDALFLMAAAAEMAGEASgpaiad 335
                                       .234444444444444444444444.111122223333333455566777...***************999999999 PP

                                       ..SSSHCCB-HHHH..CCHHHHHHHHHHHT-EEEETTSCEEB-TTSBBE-EEEEEEEE CS
                      ANF_receptor 298 ..kpgralscntlk..pweggqkllrylrnvnfeGltGdvkfdengdrvptydilnlq 351
                                          +++ ++ +t +  ++ + ++l+++ rn+n++G +  v++ ++ +   +y i  ++
  gi|313117236|ref|YP_004044219.1| 336 tiRSVSGGNGHTVSvgDFGSLKLLVDAGRNLNYQGASSGVDLTADLEPLSSYLIKGVT 393
                                       995555555555555699999***************9999999988888888776665 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   2.7e-10   1.2e-06       2      79 ..      39     115 ..      38     126 .. 0.91
   2 ?   -1.7   0.0      0.24   1.1e+03     279     308 ..     309     338 ..     295     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.7e-10
                      Peripla_BP_5   2 kvGvLhSlsGtmaisekslkdaallaieeinaagGvlgrkieavvvdpasdwelfaekaeklieedkvevvfGcwtS 78 
                                       + Gv+  l+G++  + ++ k+a+  a+++in+agG+lgr +e  + d+++ +++  e  +kl++ ++v   +G+  S
  gi|313117236|ref|YP_004044219.1|  39 RFGVVLPLTGSLEKVGTHGKRAVEQAVSDINQAGGILGRPVELTTIDSKASADVAVEGYKKLVD-EGVVGFVGALAS 114
                                       789**********************************************************998.778788888777 PP

                      Peripla_BP_5  79 a 79 
                                        
  gi|313117236|ref|YP_004044219.1| 115 D 115
                                       5 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.24
                      Peripla_BP_5 279 eaayiqvklwaqAvekagstdvekvreall 308
                                         ay ++ l+a+A e ag+++  ++ ++++
  gi|313117236|ref|YP_004044219.1| 309 SNAYDALFLMAAAAEMAGEASGPAIADTIR 338
                                       579999************999988888776 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   2.8   4.2e-06     0.019       2      25 ..       5      28 ..       4      29 .. 0.94
   2 ?   -4.0   1.8       3.6   1.6e+04      15      19 ..     318     322 ..     317     328 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.2e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                       SRR  L++++ + A++ l+gc++
  gi|313117236|ref|YP_004044219.1|  5 YSRRGVLRAAGSTVALGSLAGCTG 28
                                      6*********************86 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.6
                        TAT_signal  15 aAAaa 19 
                                       +AAaa
  gi|313117236|ref|YP_004044219.1| 318 MAAAA 322
                                       45554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2555.31
//
Query:       gi|313117237|ref|YP_004044220.1|  [L=811]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-43  148.5  26.3    1.6e-43  148.5  26.3    4.6  5  MCPsignal     Methyl-accepting chemotaxis protein (MCP) signa
    4.1e-11   43.2   0.0    4.1e-11   43.2   0.0    4.4  5  dCache_1      Cache domain
    4.3e-06   27.0  19.9    1.4e-05   25.4   0.0    5.8  7  HAMP          HAMP domain
     0.0054   17.0  33.2        1.9    8.9   1.1    6.0  5  BLOC1_2       Biogenesis of lysosome-related organelles compl
     0.0078   16.5  41.3      0.075   13.3   1.5    7.0  7  DUF948        Bacterial protein of unknown function (DUF948)
  ------ inclusion threshold ------
      0.031   14.6  21.9       0.15   12.4   0.1    5.0  4  KxDL          Uncharacterized conserved protein
      0.079   12.9   0.0      0.079   12.9   0.0    1.8  1  OppC_N        N-terminal TM domain of oligopeptide transport 
       0.13   12.3  42.1      0.025   14.6   6.6    4.6  4  Laminin_II    Laminin Domain II
        1.4    8.9  38.3        3.1    7.8   1.2    5.9  5  DUF1664       Protein of unknown function (DUF1664)
        1.7    7.4  51.0        1.8    7.3  19.0    2.3  2  Mitofilin     Mitochondrial inner membrane protein
          2    8.2  10.4        1.3    8.8   1.3    3.1  2  Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
        2.8    6.9   9.2          2    7.4   2.2    2.3  2  IIGP          Interferon-inducible GTPase (IIGP)
          4    8.0  23.8       0.13   12.8   1.6    5.3  5  NPV_P10       Nucleopolyhedrovirus P10 protein
        5.6    7.1  27.2        2.7    8.2   3.5    4.5  4  Fib_alpha     Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       6.7   8.6e+03     125     139 ..      57      71 ..      52      90 .. 0.55
   2 !    7.6   6.9    0.0024       3.1     118     170 ..     449     501 ..     402     503 .. 0.78
   3 !    7.5  13.9    0.0026       3.4      75     167 ..     469     554 ..     466     559 .. 0.71
   4 !  148.5  26.3   1.3e-46   1.6e-43      10     171 ..     565     726 ..     552     727 .. 0.93
   5 ?    4.3   1.4     0.024        31     133     169 ..     723     759 ..     719     774 .. 0.52

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.7
                                       HHCCHHHHHHHHHHH CS
                         MCPsignal 125 etgealkeiveavae 139
                                       +t+e+++ i+e+ a+
  gi|313117237|ref|YP_004044220.1|  57 QTKEEIRGIAESQAR 71 
                                       455555555554332 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 118 egselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevak 170
                                          e++++ +e ++e+ ++vaev++  + +aaasee +as++e+ +a  ev++
  gi|313117237|ref|YP_004044220.1| 449 AMNEMARSFNEMISELEATVAEVTEFAETVAAASEEVTASAQEIERASREVSE 501
                                       44567777788888888888889998899999999999999999888888765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                        EV + Ae  a a++e++a      +ei+++ + ++e++q ++eg+++ +   e+l++ + ++++++++++e+a+++
  gi|313117237|ref|YP_004044220.1| 469 AEVTEFAETVAAASEEVTASA----QEIERASREVSESTQVMAEGAHEQQ---ETLQQTTGETSNLSATIEEVASSA 538
                                       48999***********99999....6667777777777777777765444...446666777777777777777777 PP

                                       HHHHHHHHHHHHHHHH CS
                         MCPsignal 152 eeqsasieevnqavee 167
                                       +e+ +++e++ +a ee
  gi|313117237|ref|YP_004044220.1| 539 TELEHTAEHTLEASEE 554
                                       7777777776666654 PP

  == domain 4  score: 148.5 bits;  conditional E-value: 1.3e-46
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  10 eAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAersaq 86 
                                       + ee + +  ++ ++++e+e++ +ei +i+e i++iadQTN+LALNA iEAARAGe+G+GF+VVA+EV++LA ++++
  gi|313117237|ref|YP_004044220.1| 565 TIEEVESKTTQTATRIKELESRMEEIGEIVELITNIADQTNILALNANIEAARAGEAGEGFSVVANEVKQLAGETKE 641
                                       44455677788899999999********************************************************* PP

                                       HHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  87 aakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnq 163
                                       +a+eiea i+e+q  +  sve + et++ ve+g+e ve+++++l +iv++v   +d v+ei+++++eq+as eev++
  gi|313117237|ref|YP_004044220.1| 642 SAEEIEATIQEVQSTSAASVEEMRETQKAVESGVEAVENARDSLDTIVDNVRATKDGVDEISRTTDEQAASTEEVAS 718
                                       ***************************************************************************** PP

                                       HHHHHHHH CS
                         MCPsignal 164 aveevakv 171
                                        +++v+++
  gi|313117237|ref|YP_004044220.1| 719 MMDRVTEI 726
                                       **999987 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 133 iveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                       ++e  +e ++  + +aaa+eeq+as++ev+++ +e+a
  gi|313117237|ref|YP_004044220.1| 723 VTEISDETSQRAESVAAAAEEQTASLSEVSDGTDELA 759
                                       3333333344444555555555555555555544443 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   3.2e-14   4.1e-11       3     248 ..      54     286 ..      53     287 .. 0.72
   2 ?   -0.5   0.6      0.67   8.6e+02      17      67 ..     406     464 ..     399     495 .. 0.48
   3 ?   -4.2   5.7         9   1.2e+04       8      53 ..     450     500 ..     443     558 .. 0.59
   4 ?   -1.7   0.1       1.6     2e+03      15      41 ..     573     602 ..     558     619 .. 0.51
   5 ?    3.8   1.0     0.034        44       9      78 ..     633     703 ..     626     773 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3.2e-14
                          dCache_1   3 ieeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallks.ilksnpdisgvy 78 
                                       +e+q++e+  g+ae+ a ++ ++ +s e++a +la +     l++ p    + +  + ++ l++ + +  +d++++ 
  gi|313117237|ref|YP_004044220.1|  54 VEQQTKEEIRGIAESQARSVAEWTTSKESSASFLAAS-----LADRPA---NTTATDHERWLEQkLIELPNDVRSLH 122
                                       589*******************************886.....333333...33334444444442445557889**9 PP

                          dCache_1  79 lvdadGqviassdpssppnlegtddpadrdw...ykealaggggkpvisdpyvdqtggkpvitiavpiyddsgkfiG 152
                                       +v+ad + +++s+++  +++       + +w    +e ++ +  +++  +py d++ g+pvi++++p+  ++    G
  gi|313117237|ref|YP_004044220.1| 123 YVNADTGTVVASTTDGVGGQS--ISSLSAPWtgrATELAQMN--DVTTLQPY-DAN-GEPVIAFVAPVTETD----G 189
                                       999876666666666554443..5555667766667777777..999*****.788.9**********9875....8 PP

                          dCache_1 153 vlaadldldnlqdllsniklgetgyvfivdsdGniiahpdkdllgknlrdelkaq.ealekalakiesgvssvk.ln 227
                                        +++  +l+  ++ + +  +  tg + +v+s+G+i+ ++ k+ l +    + +++ + +e+a  k ++g   v+ ++
  gi|313117237|ref|YP_004044220.1| 190 FVVLTASLEARSHEFGSP-I-ATGDTKVVTSEGTILLDNRKSSLLEQYTASGSESvTEIESA-LKGQGGYKLVGaRT 263
                                       999999999999988854.3.589***************98776544444444447444444.35566666555355 PP

                          dCache_1 228 g...eeylvayapiptglgWylvv 248
                                       g    ey +ayap+  g++W l++
  gi|313117237|ref|YP_004044220.1| 264 GmesGEYAMAYAPVT-GTDWVLMY 286
                                       55445999******6.6***9976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.67
                          dCache_1  17 qlanniedvldslenlaetlasn......pslqdlleepnra..neasreslqallksi 67 
                                       q+ +++e+ + +le+ ae+++++       +l + ++e+  +  ++++ +s+++++ ++
  gi|313117237|ref|YP_004044220.1| 406 QTHEDLEALIVELETKAEMFGETmaaaaeGDLTGRMQEDADNeaMNEMARSFNEMISEL 464
                                       55566666666666555555443222222444444444333345444444444444433 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 9
                          dCache_1   8 eeqllglaeqlanniedvldslenlaetl.asnpslqdlleepnra....n 53 
                                       ++++  + +++ +++e+++++++ +aet+ a ++++  +++e++ra    +
  gi|313117237|ref|YP_004044220.1| 450 MNEMARSFNEMISELEATVAEVTEFAETVaAASEEVTASAQEIERAsrevS 500
                                       555555666666666666666666666664444446666666665533330 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.6
                          dCache_1  15 aeqlan...niedvldslenlaetlasnps 41 
                                        +q+a    ++e+ ++++  ++e++++  +
  gi|313117237|ref|YP_004044220.1| 573 TTQTATrikELESRMEEIGEIVELITNIAD 602
                                       333333011345555666666666655333 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.034
                          dCache_1   9 eqllglaeqlanniedvldsle.nlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvy 78 
                                       +ql g  ++ a++ie+++++++ ++a  + ++ + q+++e+   a e+ r+sl+ +++++ ++++++++++
  gi|313117237|ref|YP_004044220.1| 633 KQLAGETKESAEEIEATIQEVQsTSAASVEEMRETQKAVESGVEAVENARDSLDTIVDNVRATKDGVDEIS 703
                                       45666667777888888888544777777888888887777444477789999999999999999888875 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.8   3.6e+03       8      19 ..       3      14 ..       1      15 [. 0.81
   2 !   25.4   0.0   1.1e-08   1.4e-05       3      51 ..     323     372 ..     321     374 .. 0.91
   3 ?   -1.0   0.0       1.9   2.4e+03      12      31 ..     374     393 ..     370     402 .. 0.74
   4 !   10.1   2.3   0.00065      0.83      15      52 ..     427     465 ..     426     466 .. 0.93
   5 ?   -2.1   0.1       4.1   5.2e+03      12      46 ..     498     533 ..     494     544 .. 0.51
   6 ?   -0.6   0.1       1.4   1.8e+03       8      22 ..     578     592 ..     573     623 .. 0.68
   7 ?   -1.7   0.1       3.2   4.1e+03      23      38 ..     743     759 ..     716     760 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.8
                                      HHHHHHHHHHHH CS
                              HAMP  8 rPLrrLaraarr 19
                                       PL+rLa++ ++
  gi|313117237|ref|YP_004044220.1|  3 SPLKRLASSLEQ 14
                                      69****998876 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.1e-08
                                       HHTTHHHHHHHHHHHHHHTTTBTSSTCCT.TSSSHHHHHHHHHHHHHHHH CS
                              HAMP   3 arrilrPLrrLaraarriaaGdldtrlpv.sgrDEiGeLarafNaMldrL 51 
                                        r +  +L  ++++a++ia+G++d ++p  ++ DE+G+L  af +M+  L
  gi|313117237|ref|YP_004044220.1| 323 GRGTATSLATVTKSADAIASGEVDGDIPSsNRIDEMGRLYDAFGEMQSYL 372
                                       677888999********************99***************9765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.9
                                       HHHHHHHHHTTTBTSSTCCT CS
                              HAMP  12 rLaraarriaaGdldtrlpv 31 
                                        +a +a+++aa ++d ++ +
  gi|313117237|ref|YP_004044220.1| 374 TVAGQAEALAAKEFDDPVLE 393
                                       678899*****999999544 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00065
                                       HHHHHHTTTBTSSTCCTTSSSH.HHHHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtrlpvsgrDE.iGeLarafNaMldrLr 52 
                                       +++++ a+Gdl+ r  ++ ++E + e+ar+fN+M+ +L+
  gi|313117237|ref|YP_004044220.1| 427 ETMAAAAEGDLTGRMQEDADNEaMNEMARSFNEMISELE 465
                                       589999****************88***********9997 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 4.1
                                       HHHHHHHHHTTT......BTSSTCCT.TSSSHHHHHHHHHHH CS
                              HAMP  12 rLaraarriaaG......dldtrlpv.sgrDEiGeLarafNa 46 
                                       +++++++ +a+G                +  E   L +++++
  gi|313117237|ref|YP_004044220.1| 498 EVSESTQVMAEGaheqqeT------LqQTTGETSNLSATIEE 533
                                       6666677777774333331......22333444444444333 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHTT CS
                              HAMP   8 rPLrrLaraarriaa 22 
                                        ++++L++ +++i++
  gi|313117237|ref|YP_004044220.1| 578 TRIKELESRMEEIGE 592
                                       567777777777764 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 3.2
                                       TBTSSTCCT.TSSSHHH CS
                              HAMP  23 Gdldtrlpv.sgrDEiG 38 
                                        +  +  +v +g DE++
  gi|313117237|ref|YP_004044220.1| 743 EQTASLSEVsDGTDELA 759
                                       24444466767777775 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   1.4    0.0096        12      23      75 ..     448     500 ..     426     508 .. 0.72
   2 !    8.8   2.6    0.0015       1.9      29      82 ..     492     546 ..     477     552 .. 0.76
   3 !    8.9   1.1    0.0015       1.9      34      81 ..     564     611 ..     560     613 .. 0.89
   4 !    7.3   1.9    0.0046       5.9      11      80 ..     635     705 ..     626     708 .. 0.77
   5 ?    4.7   0.9     0.029        37      32      88 ..     712     769 ..     706     776 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0096
                           BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvt 75 
                                       + ++++ ++ +e + +l+  +a++++++e + + +ee+    q+i++  ++v+
  gi|313117237|ref|YP_004044220.1| 448 EAMNEMARSFNEMISELEATVAEVTEFAETVAAASEEVTASAQEIERASREVS 500
                                       55666667777777777888888888888888888888887777777766666 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                           BLOC1_2  29 Neaasekykklkd.vaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                        e+as+++ + ++ +a++++++ e l+++  e +++   i+++  + teLe++++
  gi|313117237|ref|YP_004044220.1| 492 IERASREVSESTQvMAEGAHEQQETLQQTTGETSNLSATIEEVASSATELEHTAE 546
                                       4555555555544267899999999999999********************9997 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0015
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                         ++++++++ ++++ +++l+++ ee+ + ++ i +i +q++ L  ++
  gi|313117237|ref|YP_004044220.1| 564 DTIEEVESKTTQTATRIKELESRMEEIGEIVELITNIADQTNILALNA 611
                                       5678999*********************************99887655 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0046
                           BLOC1_2  11 leaeleatvedyk.lLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       l +e++ ++e+++ +++++  ++++ ++++++  + +e+ +e++++  ++l+  ++++ + ++ v+e+  +
  gi|313117237|ref|YP_004044220.1| 635 LAGETKESAEEIEaTIQEVQSTSAASVEEMRETQKAVESGVEAVENARDSLDTIVDNVRATKDGVDEISRT 705
                                       55666666666653678888888899999999999999999999999999999999999888888887766 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.029
                           BLOC1_2  32 asekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLDeys 88 
                                       ++e+++++ d++ +++++ ++  e  + + +++  ++ ++ + ++eL + +++L + +
  gi|313117237|ref|YP_004044220.1| 712 STEEVASMMDRVTEISDETSQRAESVAaAAEEQTASLSEVSDGTDELASQAEHLMSLV 769
                                       6677788888888887777666655544777888888888888888888887775555 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.43   5.5e+02       8      43 ..     308     338 ..     303     375 .. 0.63
   2 !   13.3   1.5   5.9e-05     0.075      32      87 ..     447     502 ..     440     504 .. 0.92
   3 !   10.7   2.3   0.00038      0.49      30      88 ..     477     535 ..     474     536 .. 0.87
   4 ?    0.4   7.0      0.64   8.1e+02      24      80 ..     527     600 ..     510     611 .. 0.54
   5 !   10.8   3.7   0.00035      0.44      24      87 ..     639     702 ..     621     704 .. 0.78
   6 ?    4.7   4.2     0.029        37      24      73 ..     702     751 ..     684     773 .. 0.48
   7 ?    2.4   0.2      0.15   1.9e+02      26      83 ..     739     796 ..     735     799 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                            DUF948   8 iAFvvLviflivvllklkktldeaaatieelekqvd 43 
                                       iAF++ ++fl+ v +      + +a+++++++k +d
  gi|313117237|ref|YP_004044220.1| 308 IAFAIGALFLVGVTIG-----RGTATSLATVTKSAD 338
                                       5555555555544332.....223344444444444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.9e-05
                            DUF948  32 aatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +++++e+ +  ++++ e+e+++a+v e +e v   +e+v +  ++++ +++ vse 
  gi|313117237|ref|YP_004044220.1| 447 NEAMNEMARSFNEMISELEATVAEVTEFAETVAAASEEVTASAQEIERASREVSES 502
                                       78999**********************************************99985 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00038
                            DUF948  30 eaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                        +aa+ ee++  +++i + ++++ + +++++e+ +e+ e++++ t +  +l+++++e+ 
  gi|313117237|ref|YP_004044220.1| 477 TVAAASEEVTASAQEIERASREVSESTQVMAEGAHEQQETLQQTTGETSNLSATIEEVA 535
                                       56677788888888888889999999999**************************9986 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.64
                            DUF948  24 lkktldeaaatieele.................kqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                       l+ t++e+a++ +ele                  ++  +++eve  ++++ +  +++++++e++ +++e + ++
  gi|313117237|ref|YP_004044220.1| 527 LSATIEEVASSATELEhtaehtleaseeghsatVDAIDTIEEVESKTTQTATRIKELESRMEEIGEIVELITNI 600
                                       45555555555555553333333333333333333334444555444444444555555555555555555555 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.00035
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                        k+ ++e++ati+e+++   + ++e++++ + v+  +e v++  +++d+++++v+ + + v e+
  gi|313117237|ref|YP_004044220.1| 639 TKESAEEIEATIQEVQSTSAASVEEMRETQKAVESGVEAVENARDSLDTIVDNVRATKDGVDEI 702
                                       4667788888999999999999999999999999999999999999999999998887776665 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.029
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpl 73 
                                       +++t de aa+ ee+ + +d +++ ++++ + ++ +++  +e+++++ ++
  gi|313117237|ref|YP_004044220.1| 702 ISRTTDEQAASTEEVASMMDRVTEISDETSQRAESVAAAAEEQTASLSEV 751
                                       33444444444444333333333333333333333333333333333333 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.15
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvne.klekvdpl.teavadlges 83 
                                         ++e +a++ e+ + +d++  ++e l++ v     dvn  +  +vd++ te+v+ +  s
  gi|313117237|ref|YP_004044220.1| 739 AAAEEQTASLSEVSDGTDELASQAEHLMSLVSS--FDVNAgQNRNVDSIdTEHVESAESS 796
                                       566788999999999999999999999998888..6666546666666655666666555 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.9    0.0058       7.5       2      60 ..     441     499 ..     440     504 .. 0.90
   2 ?    1.1   1.9      0.39     5e+02      10      56 ..     505     551 ..     500     576 .. 0.84
   3 ?   12.4   0.1   0.00012      0.15      19      75 ..     640     696 ..     627     700 .. 0.91
   4 ?    5.5   0.5     0.016        20      10      62 ..     701     753 ..     698     771 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0058
                              KxDL   2 ltsavdsedldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkev 60 
                                       +++  d+e+++e+ +  +++  +l+++ +e++e+ + + +  ++++a  ++  ++++ev
  gi|313117237|ref|YP_004044220.1| 441 MQEDADNEAMNEMARSFNEMISELEATVAEVTEFAETVAAASEEVTASAQEIERASREV 499
                                       6667899************************************9999999988888887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.39
                              KxDL  10 dldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkl 56 
                                        + e  + Q++t+++   ++  L++ ++++ +  ++l++  +   ++
  gi|313117237|ref|YP_004044220.1| 505 VMAEGAHEQQETLQQTTGETSNLSATIEEVASSATELEHTAEHTLEA 551
                                       56778899********************9999999988776665555 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00012
                              KxDL  19 aqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslk 75 
                                       ++   +++++ +e++   a s e++ ++++ +++g++++ + ++ L++i  ++r+ k
  gi|313117237|ref|YP_004044220.1| 640 KESAEEIEATIQEVQSTSAASVEEMRETQKAVESGVEAVENARDSLDTIVDNVRATK 696
                                       567789*********************************************999865 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.016
                              KxDL  10 dldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkk 62 
                                       +++++ + Qa    +  +   +++e+ +++++r +++ a  +++t  l+ev +
  gi|313117237|ref|YP_004044220.1| 701 EISRTTDEQAASTEEVASMMDRVTEISDETSQRAESVAAAAEEQTASLSEVSD 753
                                       689999****************************************9999976 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.2e-05     0.079      11      39 ..      21      48 ..      19      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-05
                            OppC_N 11 krNklAvvglvilllllliaifaPliaPy 39
                                      +r  +A +glv+l+++l++++++ +i  +
  gi|313117237|ref|YP_004044220.1| 21 RRRYAAKFGLVLLAIILVMSAVGAFI-HF 48
                                      78889********************9.34 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.2    0.0045       5.8       9      66 ..     447     504 ..     440     508 .. 0.82
   2 ?   14.6   6.6     2e-05     0.025       5     103 ..     510     601 ..     506     617 .. 0.86
   3 ?    4.8   5.6      0.02        25       4      63 ..     628     687 ..     626     697 .. 0.85
   4 ?    2.5   4.3       0.1   1.3e+02       5      73 ..     699     767 ..     686     787 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0045
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-- CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLek 66 
                                       ne ++e  +  +++  +le t +++ e++++v+   e+v ++ + i+ A+r+v++ ++
  gi|313117237|ref|YP_004044220.1| 447 NEAMNEMARSFNEMISELEATVAEVTEFAETVAAASEEVTASAQEIERASREVSESTQ 504
                                       5667788888999999999999999999999999999999999999999999987555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       a+e +et++++   + +ls+ +e++ +++ e++ ++e+t e  ++   a++dA + + ++e +  q   ++kel+ +
  gi|313117237|ref|YP_004044220.1| 510 AHEQQETLQQTTGETSNLSATIEEVASSATELEHTAEHTLEASEEGHSATVDAIDTIEEVESKTTQTATRIKELESR 586
                                       778899****************************************************************9999999 PP

                                       HHH...HHHHHHHHHHHHHHHH CS
                        Laminin_II  82 eeassslsdniseikelIaqAR 103
                                        e+       i ei elI    
  gi|313117237|ref|YP_004044220.1| 587 MEE-------IGEIVELITNIA 601
                                       888.......555555554444 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkk 63 
                                       +a+e+++ a e++e  +++++ ++++++      ++++et++ v++  +a++ Ar+s  +
  gi|313117237|ref|YP_004044220.1| 628 VANEVKQLAGETKESAEEIEATIQEVQSTSAASVEEMRETQKAVESGVEAVENARDSLDT 687
                                       578899999999999999999999999888888888899999999999999999998765 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.1
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld 73 
                                       ++e++ t+ e  + +++++  ++++ e   e  + +e + + +++ +  + ++++   +L  +a+ L++
  gi|313117237|ref|YP_004044220.1| 699 VDEISRTTDEQAASTEEVASMMDRVTEISDETSQRAESVAAAAEEQTASLSEVSDGTDELASQAEHLMS 767
                                       444444444444444444444444444444444444444555555555555555555555555555544 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.2    0.0024       3.1      27     121 ..     399     493 ..     398     496 .. 0.84
   2 ?    7.1   3.5    0.0041       5.3      40     108 ..     475     543 ..     470     554 .. 0.55
   3 ?    5.0   1.8     0.019        24      66     110 ..     558     601 ..     541     609 .. 0.76
   4 ?    6.6   5.0    0.0057       7.3      44     120 ..     626     702 ..     622     709 .. 0.77
   5 ?    5.6   5.5     0.012        15      42     108 ..     677     739 ..     675     799 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0024
                           DUF1664  27 klsdlmfvTkrslsdavesvskqleqvseslaat.krhLssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                       ++ + m  T   l+  + ++ ++ e + e++aa+   +L+ r+++ d+  ++++e++++ +e ++e++  ++e+ e 
  gi|313117237|ref|YP_004044220.1| 399 SFGEAMGQTHEDLEALIVELETKAEMFGETMAAAaEGDLTGRMQE-DADNEAMNEMARSFNEMISELEATVAEVTEF 474
                                       577788889999999999999999999999986515699999998.8888999999999999999999999999999 PP

                           DUF1664 103 vesvkeaveglesklerie 121
                                        e+v +a e++ ++ ++ie
  gi|313117237|ref|YP_004044220.1| 475 AETVAAASEEVTASAQEIE 493
                                       9999999888888888877 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0041
                           DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                       ++ v+  s++++   ++++++ r+ s+  + + +   eq+e+ ++++ e ++++  ++e+ +  +++++
  gi|313117237|ref|YP_004044220.1| 475 AETVAAASEEVTASAQEIERASREVSESTQVMAEGAHEQQETLQQTTGETSNLSATIEEVASSATELEH 543
                                       344445555555555555555555555555555555555555555555555555555555555555544 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.019
                           DUF1664  66 sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       + +d +d +++e++  +++++  ++e+++ ++eige ve + ++ 
  gi|313117237|ref|YP_004044220.1| 558 ATVDAID-TIEEVESKTTQTATRIKELESRMEEIGEIVELITNIA 601
                                       5555555.6888888999999999999999999999999888765 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0057
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       + v+++++q+  + ++  +++++ i++v+++  ++ e  +e+++ v++  e +++ ++ ++++ + v+  +  +++i
  gi|313117237|ref|YP_004044220.1| 626 SVVANEVKQLAGETKESAEEIEATIQEVQSTSAASVEEMRETQKAVESGVEAVENARDSLDTIVDNVRATKDGVDEI 702
                                       67889999999999999999999999999988777777777777777777777777777777777777666666666 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.012
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                       ave+   +l+++ ++++atk+   ++i r  +++ +++e  +++ + vte+++++s+  e   sv +
  gi|313117237|ref|YP_004044220.1| 677 AVENARDSLDTIVDNVRATKDGV-DEISRTTDEQAASTEEVASMMDRVTEISDETSQRAE---SVAA 739
                                       78888889999999999999875.345555555555666666666666666666665444...4444 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  24.1     0.005       6.4     117     289 ..     435     617 ..     393     621 .. 0.62
   2 ?    7.3  19.0    0.0014       1.8     118     268 ..     638     788 ..     621     801 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.005
                         Mitofilin 117 a.....qqpkseqekekaleevlkealskaekataaakeakde...akkavkeavdklkeasdteeksrekardtal 185
                                              q+++  e+ ++ + + +e +s+ e  +a+++e+ +    a + v+++++++++as + ++s + +++ a+
  gi|313117237|ref|YP_004044220.1| 435 GdltgrMQEDADNEAMNEMARSFNEMISELEATVAEVTEFAETvaaASEEVTASAQEIERASREVSESTQVMAEGAH 511
                                       13444434444455555555556666777777766666666552225556666666666667677777777777777 PP

                         Mitofilin 186 eaaeaaaek..eleklkevielakqseee...aakplldaaeetlekliehlkkveekvekaqslaklvekykelve 257
                                       e++e + +   e  +l  +ie+  +s +e    a+ +l+a+ee  ++++++++ +ee + k     + ++++kel++
  gi|313117237|ref|YP_004044220.1| 512 EQQETLQQTtgETSNLSATIEEVASSATElehTAEHTLEASEEGHSATVDAIDTIEEVESKT---TQTATRIKELES 585
                                       77777776699777777777766665443110444555555555666666666666666666...555667777777 PP

                         Mitofilin 258 eerevFqqelesiipei..itnlkednkklskdd 289
                                         +e+   e++++i++i  +tn+ + n+++++++
  gi|313117237|ref|YP_004044220.1| 586 RMEEI--GEIVELITNIadQTNILALNANIEAAR 617
                                       77777..788888888833346667777777665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                         Mitofilin 118 qqpkseqekekaleevlkealskaekataaakeakdeakkavkeavdklkeasdteeksrekardtaleaaeaaaek 194
                                       ++ +s++e+e+ ++ev+++ ++++e+  + +++a ++ ++av+ a d+l+  +d+  + ++   ++ +++ e+aa  
  gi|313117237|ref|YP_004044220.1| 638 ETKESAEEIEATIQEVQSTSAASVEEMRE-TQKAVESGVEAVENARDSLDTIVDNVRATKDGVDEISRTTDEQAAST 713
                                       346889999***************99988.6677789999************9888888888878888887777766 PP

                         Mitofilin 195 .eleklkevielakqseeeaakplldaaeetlekliehlkkveekvekaqslaklvekykelveeerevFqqele 268
                                        e++ +   +++   + ++ a++ ++aaee+ ++l+e  +   e   +a+ l +lv++  +++ ++r+v+  ++e
  gi|313117237|ref|YP_004044220.1| 714 eEVASMMDRVTEISDETSQRAESVAAAAEEQTASLSEVSDGTDELASQAEHLMSLVSSFDVNAGQNRNVDSIDTE 788
                                       79999****************************************************************766655 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.3    0.0011       1.3      41     158 ..     434     554 ..     424     576 .. 0.78
   2 ?    4.1   0.9     0.029        38     101     158 ..     637     694 ..     623     712 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                      Bacillus_HBL  41 nkellsklnqh.qklakanakewlnevkPqliktiqdiigYstkFqsyyktlveav..dkkdkaellellekLqeei 114
                                       + +l ++++++  + a  ++++  ne+  +l  t  ++ ++ ++ ++  +++ +++   + ++ e++e  + + e++
  gi|313117237|ref|YP_004044220.1| 434 EGDLTGRMQEDaDNEAMNEMARSFNEMISELEATVAEVTEFAETVAAASEEVTASAqeIERASREVSESTQVMAEGA 510
                                       56777777777445677788888899999999999999999999999999999999444577789999999999999 PP

                      Bacillus_HBL 115 qqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsg 158
                                        ++q++ +q+ +e ++l   +++  ++ ++   +++ +l++++ 
  gi|313117237|ref|YP_004044220.1| 511 HEQQETLQQTTGETSNLSATIEEVASSATELEHTAEHTLEASEE 554
                                       99999999999999999999988888877777788888876653 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.029
                      Bacillus_HBL 101 aellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsg 158
                                        e +e  e+++++iq+ q ++ ++++e+++ ++++++ ++  +++ d l+ i+ +  +
  gi|313117237|ref|YP_004044220.1| 637 GETKESAEEIEATIQEVQSTSAASVEEMRETQKAVESGVEAVENARDSLDTIVDNVRA 694
                                       4668888999999999999999999999999999999999999999999999877555 PP

>> IIGP  Interferon-inducible GTPase (IIGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.7     0.025        31     283     371 ..     440     527 ..     404     531 .. 0.76
   2 ?    7.4   2.2    0.0016         2       5      67 ..     580     644 ..     576     659 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.025
                                       HHHTT-SHHHHHHHHHHTTS-HHHHHCTSSGGGTSSTBSSSHHHHHHHHHHHHHHHHHTTSSSTT-B--HHHHHHHH CS
                              IIGP 283 rkvFGlDdeslqevArdlgaevkdlkaelkslelfkltkddsilerltravkaflrvkgyleavvtllrklyykrkl 359
                                       r     D+e+++e+Ar+++  +++l+a++     f++t      e++t  ++++ r+ + ++ +++++ +  +++++
  gi|313117237|ref|YP_004044220.1| 440 RMQEDADNEAMNEMARSFNEMISELEATVAEVTEFAETVA-AASEEVTASAQEIERASREVSESTQVMAEGAHEQQE 515
                                       55556799******************99988777777655.45667888899999****999999999999999999 PP

                                       HHHHHHHHHHHH CS
                              IIGP 360 fldivaedakel 371
                                        l+ ++ ++ +l
  gi|313117237|ref|YP_004044220.1| 516 TLQQTTGETSNL 527
                                       999999888775 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHH.T-HHHHHHHHHHHHHHHH.T--EEEEEEESTTSSHHHHHHHHTT--TTSTTS-- CS
                              IIGP   5 ikliekalke.gnlqkvvsiikeaikeie.saklkiavtGdsGnGkssFinaLRliGheeedsAp 67 
                                       ik++e +++e g+++++++ i ++ + +  +a+++ a  G++G+G s   n ++ +  e ++sA+
  gi|313117237|ref|YP_004044220.1| 580 IKELESRMEEiGEIVELITNIADQTNILAlNANIEAARAGEAGEGFSVVANEVKQLAGETKESAE 644
                                       788899998879*********999886543889******************************97 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4      0.23     3e+02      20      59 ..     461     500 ..     445     547 .. 0.65
   2 ?    5.7   0.9     0.016        20      11      52 ..     564     605 ..     557     616 .. 0.80
   3 ?   -2.7   0.1       6.6   8.4e+03      52      62 ..     644     654 ..     626     667 .. 0.49
   4 ?   12.8   1.6   9.8e-05      0.13      12      64 ..     674     726 ..     668     731 .. 0.86
   5 ?    0.3   0.2      0.77   9.8e+02      17      56 ..     731     770 ..     728     797 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.23
                           NPV_P10  20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                       ++ l++ v++v+e  ++v   +e++ a +++++  + +v+
  gi|313117237|ref|YP_004044220.1| 461 ISELEATVAEVTEFAETVAAASEEVTASAQEIERASREVS 500
                                       4444555555555545544444444444444444444444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                       + i++v++k +   ++++++++ ++++ e+ e + ++++q +
  gi|313117237|ref|YP_004044220.1| 564 DTIEEVESKTTQTATRIKELESRMEEIGEIVELITNIADQTN 605
                                       568899999999999999999999999998888877777654 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.6
                           NPV_P10  52 aeletkvenIq 62 
                                       +e+e++++++q
  gi|313117237|ref|YP_004044220.1| 644 EEIEATIQEVQ 654
                                       23333333333 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 9.8e-05
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                        ++av++  d+l++ vd+v++    v+e++   d+q+a+ +e+ + ++ +++i
  gi|313117237|ref|YP_004044220.1| 674 GVEAVENARDSLDTIVDNVRATKDGVDEISRTTDEQAASTEEVASMMDRVTEI 726
                                       689999999***************************99998888866666655 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.77
                           NPV_P10  17 ddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                       +++ +++ ++ ++ ++ l +v++ +++L +q++ L +l +
  gi|313117237|ref|YP_004044220.1| 731 SQRAESVAAAAEEQTASLSEVSDGTDELASQAEHLMSLVS 770
                                       5666666677777777788888888888888888887765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.5    0.0021       2.7      24     123 ..     448     543 ..     447     551 .. 0.76
   2 ?    4.3   4.4     0.033        42      28     110 ..     529     612 ..     515     618 .. 0.56
   3 ?    3.7   1.2     0.052        66      57     106 ..     635     684 ..     625     703 .. 0.36
   4 ?    5.3   1.1     0.016        20      25     110 ..     687     771 ..     684     782 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0021
                                       HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCC CS
                         Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaq 100
                                       ++++++ +++++ +++le +++e+++  +++   ++e++ s +e ++ +++    +++s++ + e   + +et++++
  gi|313117237|ref|YP_004044220.1| 448 EAMNEMARSFNEMISELEATVAEVTEFAETVAAASEEVTASAQEIERASRE----VSESTQVMAEGAHEQQETLQQT 520
                                       5799999****************9999999999999999998888888875....5666666665666666666666 PP

                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 101 esnirvLqnvlesneqkiqkLeq 123
                                         +  +L  ++e+  ++ ++Le 
  gi|313117237|ref|YP_004044220.1| 521 TGETSNLSATIEEVASSATELEH 543
                                       67777777777777777777766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.033
                                       CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH..H CS
                         Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe..s 102
                                        + ++v  + ++le++ e+  + ++e ++ +++  d+++e +++++++ + ik++++++e ei ++ e i++    +
  gi|313117237|ref|YP_004044220.1| 529 ATIEEVASSATELEHTAEHTLEASEEGHSATVDAIDTIEEVESKTTQTATRIKELESRME-EIGEIVELITNIAdqT 604
                                       444555555666666665555555444444444444444444444446777777777777.7777777776655335 PP

                                       HHHHHHHH CS
                         Fib_alpha 103 nirvLqnv 110
                                       ni +L  +
  gi|313117237|ref|YP_004044220.1| 605 NILALNAN 612
                                       55555555 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                         Fib_alpha  57 lvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                                       l  e+k+s +e +++ ++ +++   s +e++e +  ++  + a e+    
  gi|313117237|ref|YP_004044220.1| 635 LAGETKESAEEIEATIQEVQSTSAASVEEMRETQKAVESGVEAVENARDS 684
                                       22223333333333333222222222222222222222222222222222 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.016
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe 101
                                       ++ +  + +k+ ++++ ++ +e + st+e+ +++ +++++  e+ + ++    + ++ + +l  e+++  +++ +q 
  gi|313117237|ref|YP_004044220.1| 687 TIVDNVRATKDGVDEISRTTDEQAASTEEVASMMDRVTEISDETSQRAESVAAAAEEQTASLS-EVSDGTDELASQA 762
                                       566667788899999999999999999999999999999998888888877888888888888.8888888888887 PP

                                       HHHHHHHHH CS
                         Fib_alpha 102 snirvLqnv 110
                                       +++  L + 
  gi|313117237|ref|YP_004044220.1| 763 EHLMSLVSS 771
                                       777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (811 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2485  (0.138602); expected 358.6 (0.02)
Passed bias filter:                      829  (0.0462379); expected 358.6 (0.02)
Passed Vit filter:                       168  (0.00937029); expected 17.9 (0.001)
Passed Fwd filter:                       114  (0.00635841); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 2.06u 0.40s 00:00:02.46 Elapsed: 00:00:00.75
# Mc/sec: 3251.65
//
Query:       gi|313117238|ref|YP_004044221.1|  [L=161]
Description: hypothetical protein Hbor_30230 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-08   34.3   0.7      6e-08   33.5   0.3    1.6  2  Pilin_N   Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.076   13.5   2.6      0.064   13.7   0.9    1.7  2  DUF2190   Uncharacterized conserved protein (DUF2190)


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.3   6.7e-12     6e-08      12      77 ..       1      64 [.       1      68 [. 0.89
   2 ?   -2.7   0.0       1.3   1.2e+04      33      40 ..      94     101 ..      74     116 .. 0.61

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 6.7e-12
                           Pilin_N 12 mvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidtkdlkivln 77
                                      mv ++vIla+ +a++  g+a++++ apq+s+++++ +++++  +++ ++ + G +++t++l ++ +
  gi|313117238|ref|YP_004044221.1|  1 MVGVVVILASSLAVYFWGVADEQTPAPQISVSHSLVEDDGE--QTIAVTFDAGSAVQTDQLYVIGS 64
                                      9******************************9996666654..56***************999865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                           Pilin_N  33 neekapqa 40 
                                         ++ pq+
  gi|313117238|ref|YP_004044221.1|  94 SGSNPPQV 101
                                       33344444 PP

>> DUF2190  Uncharacterized conserved protein (DUF2190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.92   8.2e+03      26      36 ..       9      22 ..       3      28 .. 0.51
   2 ?   13.7   0.9   7.2e-06     0.064       3      76 ..      39     122 ..      38     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.92
                           DUF2190 26 ga.l..kvlGVAat 36
                                       + l   + GVA++
  gi|313117238|ref|YP_004044221.1|  9 ASsLavYFWGVADE 22
                                      33313456788854 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.2e-06
                           DUF2190   3 dgk.sldvtvaaaaaitagqvvvlga..lkvlGVAatdaaaGetvtvaveGvf.........veaaaaiavGdkVyw 67 
                                       dg+ ++ vt++a++a+   q++v+g+  l++ G  + da+a e ++ ++e  +         v  ++++++ ++Vy 
  gi|313117238|ref|YP_004044221.1|  39 DGEqTIAVTFDAGSAVQTDQLYVIGSkkLDIGGSPDSDAPATEAYASKREKFTessgsnppqVGIGETWEAAETVYL 115
                                       67779********************9552557788779999999888777766999999**9999************ PP

                           DUF2190  68 dasgkvltt 76 
                                       d +g v  +
  gi|313117238|ref|YP_004044221.1| 116 DPEGSV--D 122
                                       ****98..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1067.28
//
Query:       gi|313117239|ref|YP_004044222.1|  [L=146]
Description: hypothetical protein Hbor_30240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.056   13.3   7.4      0.068   13.1   7.4    1.2  1  7TMR-DISM_7TM  7TM diverse intracellular signalling
      0.091   13.2   7.8       0.13   12.7   7.8    1.2  1  MerC           MerC mercury resistance protein
        2.5    8.1   6.8        7.3    6.6   0.1    2.3  2  RseC_MucC      Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   7.4   1.1e-05     0.068      95     184 ..       8     105 ..       2     130 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                     7TMR-DISM_7TM  95 rllklllllavllsllllllpllpyteslslaq........llallvillllligikawrkgnkparyfliawllll 163
                                       r+ k+ l+l+v  ++++++l+++p  + +sl++        +++++v l l +++++ +r  +++   ++i+ l +l
  gi|313117239|ref|YP_004044222.1|   8 RVRKVELALSVTSLVTIVVLSAIPPIHLSSLSStvvgraiaFVIWMVPLALSAVVLYRVRASKRSRSTYVIGGLSVL 84 
                                       66677777777777777776666554444444445688877777777777777788888999999999999999999 PP

                     7TMR-DISM_7TM 164 igvlidilsllgllpsn.ffte 184
                                       +++li +l +  ++ s  f+t+
  gi|313117239|ref|YP_004044222.1|  85 TAALI-LLDTQTVIVSEgFLTH 105
                                       99999.3444445555557765 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   7.8   2.1e-05      0.13      13     111 ..      18     127 ..      14     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                              MerC  13 vhClllPvllallpllglsflasellhqvllil..vvaigllalvvgyrrhrktsvlvlgalGllillvalflg... 84 
                                       v  l++ v+l++ p + ls l s  + + ++++  +v+++l a+v+   r  k+s  +  ++Gl +l +al+l    
  gi|313117239|ref|YP_004044222.1|  18 VTSLVTIVVLSAIPPIHLSSLSSTVVGRAIAFViwMVPLALSAVVLYRVRASKRSRSTYVIGGLSVLTAALILLdtq 94 
                                       6679999************97766654444433369***********9************************99554 PP

                              MerC  85 .............teaeetllfgslwqvltvlGaalLaia 111
                                                    t+a            + v++  lLa+a
  gi|313117239|ref|YP_004044222.1|  95 tvivsegflthsgTGA-------FSRPLIAVVAGSLLATA 127
                                       4444443333322111.......12223455555555655 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.5    0.0047        28      66     111 ..      47      91 ..      37      96 .. 0.82
   2 ?    6.6   0.1    0.0012       7.3      56      96 ..      96     135 ..      92     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0047
                         RseC_MucC  66 aallvYllPllllilgallgsallgssellaalgallglvlgfliv 111
                                        a++++++Pl+l  +++  + a    s  + ++g+l +l ++++++
  gi|313117239|ref|YP_004044222.1|  47 IAFVIWMVPLALSAVVLYRVRAS-KRSRSTYVIGGLSVLTAALILL 91 
                                       58899999999999988888888.6999999999999999988876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0012
                         RseC_MucC  56 vgieeksllkaallvYllPllllilgallgsallgssella 96 
                                       v ++e  l ++   ++  Pl+++++g ll++a+ + +el++
  gi|313117239|ref|YP_004044222.1|  96 VIVSEGFLTHSGTGAFSRPLIAVVAGSLLATAV-VIKELVS 135
                                       66788888889999999***************9.4666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 994.10
//
Query:       gi|313117240|ref|YP_004044223.1|  [L=131]
Description: hypothetical protein Hbor_30250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.088   13.3   0.1       0.13   12.8   0.1    1.3  1  LPAM_1    Prokaryotic membrane lipoprotein lipid attachment s


Domain annotation for each model (and alignments):
>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   7.5e-06      0.13       3      18 .]       5      20 ..       4      20 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.5e-06
                            LPAM_1  3 KillalgalllLsGCs 18
                                      K+ +a++a ++LsGCs
  gi|313117240|ref|YP_004044223.1|  5 KLHFAIVAFVVLSGCS 20
                                      6669***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 869.74
//
Query:       gi|313117241|ref|YP_004044224.1|  [L=34]
Description: hypothetical protein Hbor_30260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      130  (0.00725082); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 242.87
//
Query:       gi|313117242|ref|YP_004044225.1|  [L=294]
Description: hypothetical protein Hbor_30270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-30  106.7  16.9    1.7e-30  106.3  13.9    1.9  2  ABC2_membrane_2  ABC-2 family transporter protein
    3.1e-09   37.0   9.3    3.1e-09   37.0   9.3    1.9  2  ABC2_membrane_4  ABC-2 family transporter protein
    5.9e-07   28.9  17.3    7.6e-07   28.5  17.3    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
    0.00023   20.8   7.1    0.00047   19.8   7.1    1.5  1  ABC2_membrane_5  ABC-2 family transporter protein
    0.00041   19.8  13.1    0.00069   19.1  13.1    1.5  1  ABC2_membrane    ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.039   1.4e+02       3      27 ..       6      30 ..       4      52 .. 0.87
   2 !  106.3  13.9   4.8e-34   1.7e-30      81     288 .]      55     293 ..      40     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.039
                   ABC2_membrane_2  3 iakkEfrdlvrsrrfllltvllpli 27
                                      +a+ E r  ++s+  ++l+vl++l 
  gi|313117242|ref|YP_004044225.1|  6 LARSECRTVLTSKGAWILAVLIVLK 30
                                      7999*****************9985 PP

  == domain 2  score: 106.3 bits;  conditional E-value: 4.8e-34
                   ABC2_membrane_2  81 mavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivla 157
                                       +++++p+  +l++++++  E+++g++k+lL++P++R+++l+gK+ g++a+   i  ++la+ l+  +i l+    ++
  gi|313117242|ref|YP_004044225.1|  55 VSLFLPIGVLLLTYQSLISERTSGSIKFLLALPITRAQLLFGKVAGRFAA---IGASILAAILALSGIGLIEHGGFS 128
                                       6899**********************************************...99999999999999999999**** PP

                   ABC2_membrane_2 158 ledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlyg....vaellagpavp..qe 228
                                       + +++ +v+a++ll+   vf+ lg+l+S+v++ +++a+ala++ ++++ ++++ ++ +    va  + +p++     
  gi|313117242|ref|YP_004044225.1| 129 VLQFVETVLATLLLIG--VFVVLGILVSTVTQRTVTATALAFA-YFLTDLFWDSIVMKlytaVAGVPVDPYNApaSG 202
                                       ************7777..99************88888888877.566779***999884444555555555546333 PP

                   ABC2_membrane_2 229 indflsllsptsayntllneilagsdlna...............................lgstatnllilllllav 274
                                          + + l+p+ ayn+l+n+il  ++  +                               ++  a +l+ill++l+v
  gi|313117242|ref|YP_004044225.1| 203 PLFLALRLTPGGAYNVLTNWILGVGNSAEllttvyiklkpgtginafvveaafesgavpwYLHPALSLAILLAWLVV 279
                                       33344679*****************6555************************************************ PP

                   ABC2_membrane_2 275 llvlgyvlFkrkDl 288
                                       +lvl+  lF r D+
  gi|313117242|ref|YP_004044225.1| 280 PLVLARRLFTRGDI 293
                                       ***********985 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   9.3   8.6e-13   3.1e-09      50     177 ..      49     172 ..       8     174 .. 0.71
   2 ?    0.2   0.1      0.18   6.4e+02     127     158 ..     253     284 ..     233     294 .] 0.74

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 8.6e-13
                   ABC2_membrane_4  50 svfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgf 126
                                         +++++ l+lp+ + +++ +++  E++++ +k Ll +P++r++ll++K++  +  + + +l+ +++++     +g 
  gi|313117242|ref|YP_004044225.1|  49 GYIQIGVSLFLPIGVLLLTYQSLISERTSGSIKFLLALPITRAQLLFGKVAGRFAAIGASILA-AILALS---GIGL 121
                                       34678899******************************************9998865555444.333333...3444 PP

                   ABC2_membrane_4 127 vgfsvklvlellkkclelgllvffavlpiialvllkksyvlpliltlvyti 177
                                       ++  + +vl+++  +l + ll+ ++v+  i+++++++  v++ +l++ y++
  gi|313117242|ref|YP_004044225.1| 122 IEHGGFSVLQFVETVLATLLLIGVFVVLGILVSTVTQRTVTATALAFAYFL 172
                                       4444445666677777777777777777788999*************9986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                   ABC2_membrane_4 127 vgfsvklvlellkkclelgllvffavlpiial 158
                                       ++f++++v + l   l l++l++ +v+p+++ 
  gi|313117242|ref|YP_004044225.1| 253 AAFESGAVPWYLHPALSLAILLAWLVVPLVLA 284
                                       45778888888888888888888888887654 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5  17.3   2.1e-10   7.6e-07     160     342 ..      49     283 ..      33     285 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.1e-10
                   ABC2_membrane_3 160 asflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill.l.afgl... 231
                                        ++ +g+ l+++i + ++ + +s+++E++s+ ++++l  +++++q++++k+ g f++   ++l ++l l  +gl   
  gi|313117242|ref|YP_004044225.1|  49 GYIQIGVSLFLPIGVLLL-TYQSLISERTSGSIKFLLALPITRAQLLFGKVAGRFAAIGASILAAILaLsGIGLieh 124
                                       344455667777776666.7789**************************************9999883455555899 PP

                   ABC2_membrane_3 232 .gipfgnlglllllfllfglayialgyllsslfknsetaqilifivil.......llsgffgglfp.....ledlp. 294
                                        g+++ +++ ++l  ll + ++++lg l+s+++++++ta +l+f+ +l       + + +++++        ++++ 
  gi|313117242|ref|YP_004044225.1| 125 gGFSVLQFVETVLATLLLIGVFVVLGILVSTVTQRTVTATALAFAYFLtdlfwdsIVMKLYTAVAGvpvdpYNAPAs 201
                                       999999******************************************88777775555555552212332333335 PP

                   ABC2_membrane_3 295 salkwifsiiPffapglgllrlitgd.plwe..................................illsliilalfa 336
                                       ++l  ++++ P  a+ + l++ i g+ + +e                                   +lsl+il++  
  gi|313117242|ref|YP_004044225.1| 202 GPLFLALRLTPGGAYNV-LTNWILGVgNSAEllttvyiklkpgtginafvveaafesgavpwylhPALSLAILLAWL 277
                                       55666677777666443.33444344224446666666666666666666666666666666666556666666666 PP

                   ABC2_membrane_3 337 vvylll 342
                                       vv l+l
  gi|313117242|ref|YP_004044225.1| 278 VVPLVL 283
                                       666665 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   7.1   1.3e-07   0.00047      39     142 ..      55     158 ..      39     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.3e-07
                   ABC2_membrane_5  39 ifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn.vtis 114
                                       + ++l++ ++ +++++++s ++ s++ k+ll LP+tr ++   K  + +  i ++il  +l+l  ++li++  + + 
  gi|313117242|ref|YP_004044225.1|  55 VSLFLPIGVLLLTYQSLIS-ERTSGSIKFLLALPITRAQLLFGKVAGRFAAIGASILAAILALSGIGLIEHGgFSVL 130
                                       3344555555666778888.***************************999999999999999887777777766666 PP

                   ABC2_membrane_5 115 evllsiliglvialiflaivlPlyfkfg 142
                                       +++ ++l+ l+++ +f+++ + +   + 
  gi|313117242|ref|YP_004044225.1| 131 QFVETVLATLLLIGVFVVLGILVSTVTQ 158
                                       6666666666555555444444444333 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  13.1   1.9e-07   0.00069      44     171 ..      43     173 ..       9     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.9e-07
                     ABC2_membrane  44 g.nsedglnrpgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlve..lpvsllqalifll 117
                                       g n + g+  +g+  f+ + +   +lt +++++er+ g+++ +l+ p+ +++  +++kv++   ++ + ++a+i+ l
  gi|313117242|ref|YP_004044225.1|  43 GqNITIGYIQIGVSLFLPIGVL--LLTYQSLISERTSGSIKFLLALPI-TRAQLLFGKVAGRfaAIGASILAAILAL 116
                                       2333333333777777777777..7888889*****************.**********887423334444444444 PP

                     ABC2_membrane 118 ivyflv...gldlsrfflflllllltalaasslgllisalapsfedasqlaslvllp 171
                                         + l+   g+ + +f+  +l++ll++ +++ lg+l+s++++   +a+ la++ +l 
  gi|313117242|ref|YP_004044225.1| 117 SGIGLIehgGFSVLQFVETVLATLLLIGVFVVLGILVSTVTQRTVTATALAFAYFLT 173
                                       5555556667777799**********************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2047.68
//
Query:       gi|313117243|ref|YP_004044226.1|  [L=251]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-30  104.2   0.0    1.1e-29  103.7   0.0    1.2  1  ABC_tran     ABC transporter
    1.2e-12   48.3   0.1    1.5e-08   34.8   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.023   15.1   0.0    1.3  1  AAA_16       AAA ATPase domain
      0.015   15.8   0.0       0.02   15.4   0.0    1.3  1  AAA_23       AAA domain
      0.026   14.7   0.0      0.085   13.1   0.0    2.0  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.042   13.6   0.1      0.079   12.7   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.053   13.1   0.0        0.4   10.2   0.0    2.0  2  AAA_27       AAA domain
      0.056   12.9   0.0        9.3    5.6   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
       0.13   12.1   0.0       0.23   11.2   0.0    1.4  1  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.17   11.8   0.0        0.3   11.0   0.0    1.4  1  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.0     6e-33   1.1e-29       1     137 []      23     162 ..      23     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 6e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++n++l+++ ge+++++G+nGaGKSt + +l+  l+pt+G++++ g+d ++ +  + +++igvlp    l ++ t+r
  gi|313117243|ref|YP_004044226.1|  23 VDNLDLTVESGEIYGFLGPNGAGKSTTIGMLLDYLRPTSGTMRVFGQDPQT-DAVKIHERIGVLPDRFGLYEDRTAR 98 
                                       589************************************************.99999******************** PP

                                       HH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++        +sd+++e++l+++gl++  d+      s++S+G+ qr+ala++l+ +p+ll+lDEp++
  gi|313117243|ref|YP_004044226.1|  99 QHvrfitemkQSDDDPETLLERVGLSDAIDDDT----SEYSHGMEQRLALAMSLVGNPDLLILDEPFN 162
                                       *********999999************666666....*****************************86 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   3.8e-05     0.068       2      83 ..      36     114 ..      35     136 .. 0.61
   2 !   34.8   0.0   8.6e-12   1.5e-08     196     297 ..     111     191 ..     101     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++ GpNg+GKS+ +  l      ++ +  +  + ++ ++ ++ +++  +  p+  + +e++ +  q+vr+  ++++
  gi|313117243|ref|YP_004044226.1|  36 YGFLGPNGAGKSTTIGMLLDYL--RPTSGTMRVFGQDPQTDAVKIHERIGVLPDRFGLYEDR-TARQHVRFITEMKQ 109
                                       5789*******99887664433..45555555555555555556666666666666666666.66666666666655 PP

                            AAA_21  79 ersqv 83 
                                        +++ 
  gi|313117243|ref|YP_004044226.1| 110 SDDDP 114
                                       55555 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 8.6e-12
                            AAA_21 196 eielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP 272
                                       ++ +++l+e++ l++ +d++                    e S G+ + lal+ +l   +   +ll++DEp ngL+P
  gi|313117243|ref|YP_004044226.1| 111 DDDPETLLERVGLSDAIDDDTS------------------EYSHGMEQRLALAMSLVGNP---DLLILDEPFNGLDP 166
                                       5555555555555555555543..................3588887777*******999...9************* PP

                            AAA_21 273 kllrrllellkelsrngaQviltTH 297
                                       + +rr+ e++ e++++ga v++++H
  gi|313117243|ref|YP_004044226.1| 167 HGVRRVREIVHEENERGATVFFSSH 191
                                       **********666666********* PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.3e-05     0.023      19     132 ..      30     151 ..      18     187 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqllde..... 88 
                                       v sg  e+  + G+ G GKs+ + +ll++l+ + g   + g+  q   a+     +  + +r +l+++  ++     
  gi|313117243|ref|YP_004044226.1|  30 VESG--EIYGFLGPNGAGKSTTIGMLLDYLRPTSGTMrVFGQDPQT-DAVKIHErIGVLPDRFGLYEDRTARqhvrf 103
                                       4444..677789***************9999984333344444444.222222212222222233333333355555 PP

                            AAA_16  89 .aesaeleawrekleealaavpelagaea...srllellkrllallsr 132
                                        +e ++ ++++e+l+e+++ +++++++ +   + + + l+ +++l  +
  gi|313117243|ref|YP_004044226.1| 104 iTEMKQSDDDPETLLERVGLSDAIDDDTSeysHGMEQRLALAMSLVGN 151
                                       544466677777777777733333333333334444444444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.1e-05      0.02      13      66 ..      26      79 ..      16     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                            AAA_23 13 qeidF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveie 66
                                       ++   s  ++ + GpNGaGK+T +  +   L    +++ r  g++  ++ v+i+
  gi|313117243|ref|YP_004044226.1| 26 LDLTVeSGEIYGFLGPNGAGKSTTIGMLLDYLRPT-SGTMRVFGQDPQTDAVKIH 79
                                      344445567999***********987666655543.3344444555555555555 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.7e-05     0.085      63      88 ..     151     176 ..      95     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                           SbcCD_C  63 alrlvfLDEAFsklDeesiatllell 88 
                                       +++l++LDE F++lD++ ++++ e++
  gi|313117243|ref|YP_004044226.1| 151 NPDLLILDEPFNGLDPHGVRRVREIV 176
                                       589**************999988776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.4e-05     0.079      17      39 ..      28      50 ..      21      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-05
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      ++++  +++ + Gp+G+GKST +
  gi|313117243|ref|YP_004044226.1| 28 LTVESGEIYGFLGPNGAGKSTTI 50
                                      55664448889**********87 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00023       0.4      10      49 ..      16      56 ..      11      62 .. 0.81
   2 ?    0.3   0.0      0.24   4.3e+02     135     169 ..     173     207 ..     162     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                            AAA_27 10 ryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      +yG +    +ld+  e+ ++   +GpN AGKst++  + d 
  gi|313117243|ref|YP_004044226.1| 16 QYGDIRAvDNLDLTVESGEIYGFLGPNGAGKSTTIGMLLDY 56
                                      577765524788888889999999**********9887776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.24
                            AAA_27 135 ealleaegelgqlLfeasaGlaslrevleaLeaea 169
                                       ++++++e+e g ++f +s  l +++ v +++   +
  gi|313117243|ref|YP_004044226.1| 173 REIVHEENERGATVFFSSHVLGQVEIVCDRIGILH 207
                                       68999999999999999999999888887765555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.007        13      29      41 ..      38      50 ..      24      66 .. 0.81
   2 ?    5.6   0.0    0.0052       9.3     149     211 ..     142     205 ..     136     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.007
                                      EEESTTSSHHHHH CS
                                      xxxxxxxxxxxxx RF
                             SMC_N 29 ivGpNGSGKsnll 41
                                       +GpNG+GKs  +
  gi|313117243|ref|YP_004044226.1| 38 FLGPNGAGKSTTI 50
                                      58********876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0052
                                       HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgv 211
                                       L +A+  v    l +lDe    LD + v++v e+++e++++ a ++  s+  +++e +   +g+
  gi|313117243|ref|YP_004044226.1| 142 LALAMSLVGNPDLLILDEPFNGLDPHGVRRVREIVHEENERgATVFFSSHVLGQVEIVCDRIGI 205
                                       66778888888899**********************9887768888888877777766655555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.23       2      40 ..      39      77 ..      38      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelp 40
                                      +Gp G+GK+t +g l ++l+ +  +++v   DP  ++++
  gi|313117243|ref|YP_004044226.1| 39 LGPNGAGKSTTIGMLLDYLRPTSGTMRVFGQDPQTDAVK 77
                                      7*******************9999999999999887665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017       0.3      86     122 ..      19      56 ..       4      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       + +++++l   +++ ++  ++G+ G+GKSt i +ll  
  gi|313117243|ref|YP_004044226.1|  19 DIRAVDNLDLTVESgEIYGFLGPNGAGKSTTIGMLLDY 56 
                                       5567778887787779999***********99888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 1635.13
//
Query:       gi|313117244|ref|YP_004044227.1|  [L=192]
Description: hypothetical protein Hbor_30290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.4   0.1        8.6    6.5   0.0    2.4  2  BsuPI     Intracellular proteinase inhibitor
      0.068   13.4   0.0        3.8    7.8   0.0    2.3  2  CARDB     CARDB


Domain annotation for each model (and alignments):
>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0   0.00096       8.6       6      30 ..      49      73 ..      40      75 .. 0.76
   2 ?    4.5   0.0    0.0039        35      67      91 ..     130     156 ..     124     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00096
                                      EEEE-SS-EEEEEEEEE-SSS-EEE CS
                             BsuPI  6 eaeasgeavelaltvtNesdeavtl 30
                                      + +  + + e++lt++N+++++v++
  gi|313117244|ref|YP_004044227.1| 49 ANAVIEHPAEFTLTIENTGNDPVRI 73
                                      444455699*************987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0039
                                       EE-TT-EEEEEEEE..S---.SEEEEE CS
                             BsuPI  67 tlepgesatyeetwd.edle.pGeYtl 91 
                                        lepge++t + +++ edl+ +G+Y+ 
  gi|313117244|ref|YP_004044227.1| 130 ALEPGETVTRQYKLHgEDLSsAGTYYT 156
                                       69************9745543899975 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00042       3.8       4      33 ..      40      69 ..      37      73 .. 0.92
   2 ?    3.4   0.0      0.01        91      41      78 ..     114     154 ..     105     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00042
                                      EEE.EEEC-SEEETTSEEEEEEEEEE-SSS CS
                             CARDB  4 LtvtntlnpseafvgeentitvtvkNqGta 33
                                      L v++ l++++a+ +   ++t+t++N+G++
  gi|313117244|ref|YP_004044227.1| 40 LSVSVDLTAANAVIEHPAEFTLTIENTGND 69
                                      78899999********************96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                                       EEEETTEEE.EEEEESEE-CTEEEEEEEEEE-S..-S-CEE CS
                             CARDB  41 alyldgelv.gtvtvpsLaagesttvsftwtte..ategev 78 
                                       ++  +g +  ++  + +L++ge++t++++   e   ++g++
  gi|313117244|ref|YP_004044227.1| 114 EVKPNGMSLsSEPLIRALEPGETVTRQYKLHGEdlSSAGTY 154
                                       4555565554555679**********999877764444544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1279.13
//
Query:       gi|313117245|ref|YP_004044228.1|  [L=324]
Description: DMT(drug/metabolite transporter) superfamily permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-35  119.9  27.8    2.9e-18   66.3   9.4    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.015   14.6   5.3       0.02   14.2   2.0    2.2  2  TPT       Triose-phosphate Transporter family
      0.028   13.9   7.3      0.049   13.1   7.3    1.4  1  SLC35F    Solute carrier family 35
        5.9    6.2  13.7       0.29   10.5   6.9    2.0  2  DUF373    Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   9.4   6.6e-22   2.9e-18       6     136 ..      16     146 ..      12     147 .. 0.96
   2 !   59.8  10.3   6.7e-20     3e-16       2     136 ..     160     297 ..     159     298 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 6.6e-22
                              EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllf 82 
                                        ++    +w+++f++++i++++++pl ++++r+ ++g ++l++a+ +  +l   +++++l ++++g + +  ++  +
  gi|313117245|ref|YP_004044228.1|  16 AIVGLGALWGAGFPAIDIVVEQLPPLGAAGIRYAVSGCIVLAYAAATTDRLLPKTWRELLGIAVIGGFMFGGYQAGL 92 
                                       57778899***************************************99998889999******************* PP

                              EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       +++ +++s ++as++t+++Pv++++ +v +lge+ ++++++g++++++Gv++++
  gi|313117245|ref|YP_004044228.1|  93 YMGTTYVSGAVASVVTTMSPVVAAVVAVPILGESRGILDIIGFFVGIAGVFVLS 146
                                       ***************************************************986 PP

  == domain 2  score: 59.8 bits;  conditional E-value: 6.7e-20
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllgt 75 
                                       +g+ l++l++ ++a++ v+++ + ++++  +l ++ +++++ ll++ a+ +++     ++ls+ ++ +ll++ l+++
  gi|313117245|ref|YP_004044228.1| 160 IGVGLVFLGTTLFAVGSVTIQLFDEELPAESLQGWAMVVGAGLLFFGAAARGEAVpalRSLSPLALGSLLYITLIAG 236
                                       68899*********************************988888888777777778999999999************ PP

                              EamA  76 vlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       + ++ll+f ++++++a++ +l+ +leP+ +++ sv+++ ++l  ++++g++ + +G  li+
  gi|313117245|ref|YP_004044228.1| 237 AGGYLLYFRLVRRVGATETTLVAYLEPLSATFVSVVFFDQTLDETTVIGFLAVAAGFTLIS 297
                                       *********************************************************9997 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.0   4.5e-06      0.02     215     289 ..      71     145 ..      46     146 .. 0.88
   2 ?    1.3   0.1     0.038   1.7e+02      96     136 ..     257     297 ..     216     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-06
                               TPT 215 lkevllllllsgvlfhlynqvaymvLervspvthsvantvKrvvvIvlsvlvfknpvsllnaiGtavaivGvflY 289
                                       ++e+l   ++ g++f  y+   ym    vs    sv  t+  vv  v++v +++++  +l++iG  v+i+Gvf+ 
  gi|313117245|ref|YP_004044228.1|  71 WRELLGIAVIGGFMFGGYQAGLYMGTTYVSGAVASVVTTMSPVVAAVVAVPILGESRGILDIIGFFVGIAGVFVL 145
                                       67777788999**************************************************************85 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.038
                               TPT  96 tvKasePiFtvilsrlllgeklsllvylsLlpivgGvalas 136
                                        v  +eP+ +  +s +++ ++l  + ++  l + +G +l s
  gi|313117245|ref|YP_004044228.1| 257 LVAYLEPLSATFVSVVFFDQTLDETTVIGFLAVAAGFTLIS 297
                                       56667888888888888888888888888888888887766 PP

>> SLC35F  Solute carrier family 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   7.3   1.1e-05     0.049     115     297 ..     117     296 ..      89     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                            SLC35F 115 vlswlflkvryrlvkiigvvvcilGvvllvvsdvlagrransgsnpvlGdllvlaGatlyavsnvleeylvkklslv 191
                                       v++  +l     ++ iig +v i+Gv +l    v +     s s + +G  lv++G+tl+av  v+ + + ++l+  
  gi|313117245|ref|YP_004044228.1| 117 VVAVPILGESRGILDIIGFFVGIAGVFVLSQPSVGT----ASVSSTAIGVGLVFLGTTLFAVGSVTIQLFDEELPAE 189
                                       444455666667889**********98776666654....36788999999************************99 PP

                            SLC35F 192 ellgllglfGaiisaiqlai..lerkelkaihWdaeiallfvgfalvlfllysllpilikktsatsvnlslltsdly 266
                                        l g   + Ga +     a       +l+++   a   ll+++ +++    y l   l++  +at  +l      l 
  gi|313117245|ref|YP_004044228.1| 190 SLQGWAMVVGAGLLFFGAAArgEAVPALRSLSPLALGSLLYITLIAGAG-GYLLYFRLVRRVGATETTLVAYLEPLS 265
                                       9998888777755444433300334566666666666677777766653.355556678999*******9999**** PP

                            SLC35F 267 slliglflfhykvswlyllafvviliGlily 297
                                       + ++ +  f++ ++   ++ f  ++ G+ l 
  gi|313117245|ref|YP_004044228.1| 266 ATFVSVVFFDQTLDETTVIGFLAVAAGFTLI 296
                                       **************************99875 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.5      0.19   8.6e+02     162     203 ..      52      94 ..      37     124 .. 0.45
   2 ?   10.5   6.9   6.5e-05      0.29     155     288 ..     127     253 ..     124     300 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.19
                            DUF373 162 Glllliyallll..lglpelalaiillllGlylllrGfgldell 203
                                       G ++l ya++++  l + ++   + ++++G++++  G++   ++
  gi|313117245|ref|YP_004044228.1|  52 GCIVLAYAAATTdrLLPKTWRELLGIAVIGGFMF-GGYQAGLYM 94 
                                       5555555555554322222333333444444432.333333322 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.5e-05
                            DUF373 155 ktiLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallll 231
                                       + iL ++G+++ i ++++l +++  ++++ ++++G+ l++ G  l  + + +++ + e l ++++   ++vv++ ll
  gi|313117245|ref|YP_004044228.1| 127 RGILDIIGFFVGIAGVFVLSQPSVGTASVSSTAIGVGLVFLGTTLFAVGSVTIQLFDEELPAESLQGWAMVVGAGLL 203
                                       568999**************999999*************************************************** PP

                            DUF373 232 ligiisgyislesvss.asvssglltlilafiygavewlalailtaslgkiideylkr 288
                                       ++g+++  +++ +++s ++ + g l +        ++++a a+ +++  +++ ++ ++
  gi|313117245|ref|YP_004044228.1| 204 FFGAAARGEAVPALRSlSPLALGSLLY--------ITLIAGAGGYLLYFRLVRRVGAT 253
                                       ****99988888888733333333333........33444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2241.92
//
Query:       gi|313117246|ref|YP_004044229.1|  [L=161]
Description: AsnC family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-09   37.1   0.7    3.6e-09   36.5   0.2    1.6  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    5.3e-08   32.3   0.0    9.8e-08   31.4   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0002   21.1   0.0    0.00041   20.1   0.0    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00045   20.0   0.0    0.00078   19.3   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00059   19.6   0.0     0.0037   17.0   0.0    2.1  2  HTH_IclR        IclR helix-turn-helix domain
     0.0011   19.4   0.1     0.0025   18.3   0.1    1.6  1  HTH_27          Winged helix DNA-binding domain
     0.0033   17.5   0.0     0.0067   16.5   0.0    1.5  1  HTH_20          Helix-turn-helix domain
     0.0094   15.8   0.0      0.018   14.9   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.045   13.7   0.0    1.7  2  GYD             GYD domain
      0.038   14.0   0.2        0.8    9.7   0.0    2.2  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.088   12.9   0.0       0.16   12.1   0.0    1.5  1  DUF2250         Uncharacterized protein conserved in archaea 
        0.1   12.8   0.0        3.2    8.1   0.0    2.3  2  Rio2_N          Rio2, N-terminal
       0.17   11.7   0.0       0.42   10.4   0.0    1.7  1  MerR            MerR family regulatory protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.4   6.1e+03      45      53 ..      10      18 ..       7      25 .. 0.60
   2 !   36.5   0.2   2.6e-12   3.6e-09       2      74 ..      68     137 ..      65     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.4
                                      SSHHHHHHH CS
                    AsnC_trans_reg 45 rdlealerf 53
                                      +++e+le+ 
  gi|313117246|ref|YP_004044229.1| 10 KSMEDLETT 18
                                      456666553 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 2.6e-12
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       +v +++  + +++e  + + e++ V+ ++ + G+ d+++ ++ +d ++ er++++ + +l+ vart++++v+ 
  gi|313117246|ref|YP_004044229.1|  68 EVFTKD--DRNHTESGRIISEVEGVTKVFFTMGSTDFIALARLPDSDSVERLISD-FEELDAVARTDSTFVID 137
                                       444443..3488999999*************************************.***************86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   7.1e-11   9.8e-08       1      48 []       1      48 [.       1      48 [. 0.98

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 7.1e-11
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +de+d +IL+ +++   +s   +++++g+++st+++rl++L e G+Ik
  gi|313117246|ref|YP_004044229.1|  1 MDEKDVQILKSMEDLETTSTEAVSDATGIPISTIHYRLNKLRETGVIK 48
                                      89*********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     3e-07   0.00041       1      42 []       1      42 [.       1      42 [. 0.99

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +De D +IL+ ++    +s +++++++G+  st++ R+++L+
  gi|313117246|ref|YP_004044229.1|  1 MDEKDVQILKSMEDLETTSTEAVSDATGIPISTIHYRLNKLR 42
                                      9****************************************7 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.6e-07   0.00078       1      46 [.       2      48 ..       2      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.6e-07
                                      SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      d++ ++ILk++++ + ++    ++++g++ st+ + L+kLre G+++
  gi|313117246|ref|YP_004044229.1|  2 DEKDVQILKSMEDlETTSTEAVSDATGIPISTIHYRLNKLRETGVIK 48
                                      56669********555777779**********************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.7e-06    0.0037       7      51 ..       7      50 ..       3      51 .. 0.83
   2 ?   -0.0   0.0      0.56   7.8e+02      34      50 ..     113     129 ..      97     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.7e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +iL+  +      +   ++++tg+p St h  L+ L e G ++ d
  gi|313117246|ref|YP_004044229.1|  7 QILKSMEDLETT-STEAVSDATGIPISTIHYRLNKLRETGVIKND 50
                                      666666666665.77889**********************99987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHTTSEE. CS
                          HTH_IclR  34 tvhRlLqtLvelGyveq 50 
                                       +v Rl++ ++el  v +
  gi|313117246|ref|YP_004044229.1| 113 SVERLISDFEELDAVAR 129
                                       78899999999988876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.8e-06    0.0025       4      58 ..       4      51 ..       1      53 [. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                            HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                       ++++L +++  +++ + +++++++ +  s+i+y l+kL e G++      +++r
  gi|313117246|ref|YP_004044229.1|  4 KDVQILKSME-DLETTSTEAVSDATGIPISTIHYRLNKLRETGVI------KNDR 51
                                      6899999*99.9999999***************************......5555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.9e-06    0.0067      23      55 ..      16      48 ..       6      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.9e-06
                                      TTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 23 egltaselaerldlskntlsyHLrvLeeagLve 55
                                      e  + +++ ++ +++ +t++y+L++L+e g ++
  gi|313117246|ref|YP_004044229.1| 16 ETTSTEAVSDATGIPISTIHYRLNKLRETGVIK 48
                                      678899999999******************997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.3e-05     0.018       8      54 ..       3      49 ..       1      53 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                      HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      e ++++ + +  l+  +++ ++ ++g+p s++   L++L + G+++ 
  gi|313117246|ref|YP_004044229.1|  3 EKDVQILKSMEDLETTSTEAVSDATGIPISTIHYRLNKLRETGVIKN 49
                                      667777888888899999*************************9986 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.9     4e+03      16      34 ..      10      28 ..       3      38 .. 0.51
   2 ?   13.7   0.0   3.3e-05     0.045      31      64 ..      85     117 ..      67     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.9
                               GYD 16 kdsperreeakealveslG 34
                                      k++++ +++  ea+  + G
  gi|313117246|ref|YP_004044229.1| 10 KSMEDLETTSTEAVSDATG 28
                                      4444444444444433345 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.3e-05
                               GYD  31 eslGgkleslyatlGeyDvvvivEapDdetaaal 64 
                                       ++++g + ++++t+G  D++++  +pD++++++l
  gi|313117246|ref|YP_004044229.1|  85 SEVEG-VTKVFFTMGSTDFIALARLPDSDSVERL 117
                                       66654.5689********************9987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00058       0.8      23      59 ..      19      54 ..       7      60 .. 0.83
   2 ?    2.0   0.0      0.15     2e+02      37      61 ..     113     137 ..     111     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00058
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrgrriri 59
                                      + e  ++  G+  +t+   l++L++ g+i++ r + i
  gi|313117246|ref|YP_004044229.1| 19 STEAVSDATGIPISTIHYRLNKLRETGVIKNDR-LDI 54
                                      567788999*********************765.444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHTTSEEE.TEEEEES- CS
                         HTH_Crp_2  37 tvsrilseLkreglisr.grririld 61 
                                       +v r++s++++   + r      + d
  gi|313117246|ref|YP_004044229.1| 113 SVERLISDFEELDAVARtDS-TFVID 137
                                       799*********99996234.44444 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.16       7      55 ..       2      50 ..       1      54 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                           DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerv 55
                                      de+++++lk ++ ++      +++ + ip++ ++  l+kL+e+G +++ 
  gi|313117246|ref|YP_004044229.1|  2 DEKDVQILKSMEDLETTSTEAVSDATGIPISTIHYRLNKLRETGVIKND 50
                                      577899***************************************9875 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0023       3.2       8      57 ..       5      50 ..       1      59 [. 0.82
   2 ?    2.5   0.0      0.13   1.8e+02      10      58 ..      82     131 ..      77     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0023
                            Rio2_N  8 dfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrk 57
                                      d ++L++    m + e  +te ++  +++  + +++rl++l +++ i+ +
  gi|313117246|ref|YP_004044229.1|  5 DVQILKS----MEDLETTSTEAVSDATGIPISTIHYRLNKLRETGVIKND 50
                                      5555554....55789999*************************999875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                            Rio2_N  10 rvLtavEmgmrnhevVptelieeisrlk.eeevkkrlsrllkaklisrkt 58 
                                       r+++ vE   + +  + ++    ++rl  +++v++ +s+  + + ++r++
  gi|313117246|ref|YP_004044229.1|  82 RIISEVEGVTKVFFTMGSTDFIALARLPdSDSVERLISDFEELDAVARTD 131
                                       88888999999988888888999999997888999999999999999865 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00031      0.42       4      18 ..      22      36 ..      19      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                                      HHHHHHTTTHHHHHH CS
                              MerR  4 evAeltGvsprtLRy 18
                                       v+++tG++++t++y
  gi|313117246|ref|YP_004044229.1| 22 AVSDATGIPISTIHY 36
                                      69***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1098.46
//
Query:       gi|313117247|ref|YP_004044230.1|  [L=220]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-18   65.7   0.0    4.4e-18   64.8   0.0    1.5  1  HTH_10         HTH DNA binding domain
    9.3e-08   31.6   0.2      2e-06   27.4   0.0    2.6  2  Sigma70_r4_2   Sigma-70, region 4
    7.2e-06   25.5   0.0    3.9e-05   23.1   0.0    2.0  1  GerE           Bacterial regulatory proteins, luxR family
     0.0003   20.2   0.0    0.00064   19.2   0.0    1.6  1  Sigma70_r4     Sigma-70, region 4
    0.00039   20.1   0.0     0.0056   16.4   0.0    2.3  1  HTH_38         Helix-turn-helix domain
    0.00084   19.1   0.0      0.002   17.9   0.0    1.6  1  LexA_DNA_bind  LexA DNA binding domain
     0.0071   16.4   0.1      0.019   15.0   0.1    1.7  1  HTH_20         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   14.4   0.0      0.055   13.0   0.0    1.8  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.03   14.1   0.0      0.077   12.8   0.0    1.7  1  HTH_23         Homeodomain-like domain
      0.098   12.6   0.2       0.48   10.4   0.0    2.1  2  MarR_2         MarR family


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0   2.5e-21   4.4e-18       1      52 [.     162     213 ..     162     214 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2.5e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd+q+ev+ +A e+GY+d+PR +t +e+A el+ +++t++ hL+kae kl+
  gi|313117247|ref|YP_004044230.1| 162 LTDRQREVIEVARENGYYDQPRGTTHAEIAAELDCAPNTVTTHLQKAEAKLV 213
                                       9*************************************************97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.8     1e+04       3      13 ..     129     139 ..     129     141 .. 0.74
   2 !   27.4   0.0   1.1e-09     2e-06      11      54 .]     162     212 ..     160     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.8
                                       HHHHHHTTS-H CS
                      Sigma70_r4_2   3 alrealaeLpe 13 
                                       al+ea+++ p+
  gi|313117247|ref|YP_004044230.1| 129 ALQEAIEQTPP 139
                                       68999998555 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.1e-09
                                       S-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  11 Lperqreifllrylegl.......sykEIAellgisegtVksrlsRArkkL 54 
                                       L+ rqre+++  +++g+       +++EIA++l++ ++tV ++l++A +kL
  gi|313117247|ref|YP_004044230.1| 162 LTDRQREVIEVARENGYydqprgtTHAEIAAELDCAPNTVTTHLQKAEAKL 212
                                       777888888888888765555555***********************9998 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.2e-08   3.9e-05      16      45 ..     183     212 ..     160     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.2e-08
                                       TTS-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  16 eGksnkeIAeelniSekTVkvhksnimkKL 45 
                                        G +  eIA+el+++++TV++h++ +  KL
  gi|313117247|ref|YP_004044230.1| 183 RGTTHAEIAAELDCAPNTVTTHLQKAEAKL 212
                                       49999*******************999998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.6e-07   0.00064       4      48 ..     161     212 ..     160     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.6e-07
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                        L++r+rev+e  +        +g T++EI+++l+    +V  ++ +A  kL
  gi|313117247|ref|YP_004044230.1| 161 GLTDRQREVIEVARengyydqPRGTTHAEIAAELDCAPNTVTTHLQKAEAKL 212
                                       69***************99888999***********9999999999997777 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.1e-06    0.0056       3      42 ..     160     206 ..     159     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.1e-06
                            HTH_38   3 khLsleeReeIerllaeG.lslr......eIArrLgrspsTIsRElk 42 
                                       + L+  +Re+Ie  ++ G + +       eIA +L+++p+T+  +l+
  gi|313117247|ref|YP_004044230.1| 160 RGLTDRQREVIEVARENGyYDQPrgtthaEIAAELDCAPNTVTTHLQ 206
                                       56999999999999999843333455555*************98876 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-06     0.002       2      53 ..     160     211 ..     159     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                       X---HHHHHHHHHHHHHHHHHS.S---HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind   2 kkLTerQrevldlikasieetg.ypPsireiaralglkSpsaveehLkaLerK 53 
                                       ++LT+rQrev+++ +++    +    + +eia +l  + p++v  hL++ e K
  gi|313117247|ref|YP_004044230.1| 160 RGLTDRQREVIEVARENGYYDQpRGTTHAEIAAELDCA-PNTVTTHLQKAEAK 211
                                       68************99865444156789*********9.********987766 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.1e-05     0.019      22      54 ..     182     213 ..     179     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                       CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20  22 aegltaselaerldlskntlsyHLrvLeeagLv 54 
                                       ++g t +e+a++ld+++nt+  HL++  ea Lv
  gi|313117247|ref|YP_004044230.1| 182 PRGTTHAEIAAELDCAPNTVTTHLQKA-EAKLV 213
                                       5789999*****************984.66666 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     3e-05     0.055      15      43 ..     181     210 ..     162     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                            HTH_24  15 npr.isqreLAerlglSpstvnrrlkrLee 43 
                                       +pr ++ +e+A +l+  p+tv+++l++ e 
  gi|313117247|ref|YP_004044230.1| 181 QPRgTTHAEIAAELDCAPNTVTTHLQKAEA 210
                                       67779*********************9886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.3e-05     0.077      15      40 ..     180     207 ..     168     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
                            HTH_23  15 ae..GlsvreIAreLgvsrrTvyrwlkr 40 
                                       ++  G + +eIA+eL++ ++Tv   l++
  gi|313117247|ref|YP_004044230.1| 180 DQprGTTHAEIAAELDCAPNTVTTHLQK 207
                                       5677999***************876665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.9   1.6e+03      47      55 ..     103     111 ..      99     119 .. 0.76
   2 ?   10.4   0.0   0.00027      0.48      20      48 ..     178     211 ..     160     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.9
                                       HTTSEEEEE CS
                            MarR_2  47 aaGLverrp 55 
                                       +aGLv+r+p
  gi|313117247|ref|YP_004044230.1| 103 RAGLVVRKP 111
                                       69***9987 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00027
                                       S.....EEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  20 r.....dltvgelarrlglsksavsrilkrLvaa 48 
                                       +       t +e+a++l+  + +v+ +l++++a+
  gi|313117247|ref|YP_004044230.1| 178 YydqprGTTHAEIAAELDCAPNTVTTHLQKAEAK 211
                                       4454444599*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 1479.93
//
Query:       gi|313117248|ref|YP_004044231.1|  [L=488]
Description: cytosine deaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-49  167.7   0.0    5.1e-49  167.4   0.0    1.1  1  Amidohydro_1  Amidohydrolase family
    1.3e-18   67.7   1.1      2e-13   50.7   0.1    2.2  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.4   0.0   5.7e-53   5.1e-49       1     344 []      59     415 ..      59     415 .. 0.91

  Alignments for each domain:
  == domain 1  score: 167.4 bits;  conditional E-value: 5.7e-53
                                       EEEE-EEEEEEECETTECSSS....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSST CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.............vppetaaealesgiktalksGtttvadmgatts 60 
                                       +vlPGlI+aH+Hle ++l ga    ++ +++             + +  a++++e ++  +l++G+tt++ m     
  gi|313117248|ref|YP_004044231.1|  59 LVLPGLINAHTHLEVTPLIGAfsdlDFAEMMgsmtalcnqlaggELDYLASAGYELAALNFLNGGVTTTNSMDV--- 132
                                       59******************99988777777999999*************************************... PP

                                       HHHHHHHHHHHTSSSEEEEEEESSEGGS....GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHH CS
                      Amidohydro_1  61 tgiealleaaeelplglrilggkvsldr....gsaetskasreklkagaaetikgkadgvvkvalapheapafsdee 133
                                          ++ +e + e+  glr ++g  + d      ++e++   r  +     et +++ dg++ +++ ph ++++++e+
  gi|313117248|ref|YP_004044231.1| 133 -RPSLGAETFGEA--GLRGFFGPAISDLfwdiPVEEQFSRARSFI-----ETYHDTYDGRIRATICPHDDWSCTREL 201
                                       .788899999998..999999966666677754444444333333.....4449999******************** PP

                                       HHHHHHHHHHH.TTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHH CS
                      Amidohydro_1 134 lkealkeakkr.dlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellker 209
                                        +  ++ a+++ +l v++H+le+++ +++a+  +       + le + ++gll++ +l+ ah    + +++++++e 
  gi|313117248|ref|YP_004044231.1| 202 WERTAEFADEYpGLLVHTHLLELEASNKMARSNGS-----DGSLELLAEVGLLND-RLLGAHYRIADEDDIRRTAES 272
                                       ***************************99999999.....78999**********.9999999999999******** PP

                                       HHHHCEEHHHHHHHH....SEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHH CS
                      Amidohydro_1 210 lkeagvahcpfsnsi....lrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglsl 282
                                         +++vahcp+  s+     ++++ ++ ++ d+Gv vglg D++   +s n++ e r+a + ++    ++++g++s 
  gi|313117248|ref|YP_004044231.1| 273 --GVSVAHCPSIFSYwnpdGETQWTPVPELRDAGVDVGLGIDDHYWHDSYNMFGEARQARLAAN---LKRSAGQFSS 344
                                       ..****************9*************************999********999994444...33679***** PP

                                       HHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.CT........CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 283 kealrmaTingAkalglddkvGsievGkdADlvvvdl.di........laafvglkkdgnvkkvivkGklv 344
                                       +e++rm Ti gA+alg+dd+vGs+evGk+AD+ v+d  ++         a++++++ +  v +v+++G++v
  gi|313117248|ref|YP_004044231.1| 345 MELVRMLTIEGARALGIDDEVGSLEVGKRADMLVLDVdKPkfvpltniPAHVANNATPADVETVVIDGNVV 415
                                       *************************************744677788889*******************998 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   7.4e-07    0.0066       2      21 ..      52      71 ..      51     112 .. 0.89
   2 !   50.7   0.1   2.2e-17     2e-13     312     473 .]     256     416 ..     239     416 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.4e-07
                      Amidohydro_3  2 viDakGrlvlPGFvDsHtHl 21
                                      +iD  G+lvlPG++ +HtHl
  gi|313117248|ref|YP_004044231.1| 52 TIDGAGKLVLPGLINAHTHL 71
                                      79*****************6 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 2.2e-17
                      Amidohydro_3 312 ehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprig 388
                                       +h ++ +e++i+r a+ +v  + +p   f      s  +p   ++ tpv el++agv v lg D      d++++  
  gi|313117248|ref|YP_004044231.1| 256 AHYRIADEDDIRRTAESGVSVAHCPS-IF------SYWNPDGETQWTPVPELRDAGVDVGLGID------DHYWHDS 319
                                       67777788888888888888887732.23......23335666677******************......8877777 PP

                      Amidohydro_3 389 aavmrktrrgg...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.....adpldvdppel 457
                                       ++  +++r      ++ r    +s  e+++++T ++A+alg +d+ G+LevG++AD  vld          v+ +++
  gi|313117248|ref|YP_004044231.1| 320 YNMFGEARQARlaaNLKRSAGQFSSMELVRMLTIEGARALGIDDEVGSLEVGKRADMLVLDvdkpkF----VPLTNI 392
                                       77777776555899***********************************************744441....333444 PP

                      Amidohydro_3 458 aear........vrltvvdGrvvy 473
                                          +        v+ +v+dG+vv+
  gi|313117248|ref|YP_004044231.1| 393 PAHVannatpadVETVVIDGNVVV 416
                                       433366668888**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3216.98
//
Query:       gi|313117249|ref|YP_004044232.1|  [L=228]
Description: hypothetical protein Hbor_30340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-11   41.4   1.8    1.7e-10   40.5   1.8    1.4  1  Cupin_2       Cupin domain
     0.0019   18.1   0.0     0.0028   17.5   0.0    1.4  1  AraC_binding  AraC-like ligand binding domain
     0.0093   15.6   0.1      0.019   14.6   0.1    1.4  1  Cupin_3       Protein of unknown function (DUF861)
     0.0094   15.6   0.0      0.016   14.8   0.0    1.3  1  Cupin_1       Cupin


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   1.8   3.7e-14   1.7e-10       7      67 ..      72     132 ..      68     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 3.7e-14
                                       TTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEE CS
                           Cupin_2   7 pGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparl 67 
                                        Ge  p+h+H g +e f V++Ge++++++ge ++l++Gd + +p+ t H ++  gd   + 
  gi|313117249|ref|YP_004044232.1|  72 NGEGPPPHYHVGYEESFEVIRGEFVVEMEGESHHLSRGDEISVPPETAHSLEAVGDSIGVA 132
                                       47899**************************************************985555 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.3e-07    0.0028      29      76 ..      90     138 ..      69     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.3e-07
                                       EEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTS.EEEEEEEEE CS
                      AraC_binding  29 vteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsed.gweyrwlyf 76 
                                       v++G+  ++ +g+ ++l+ Gd + +pp++ H++e+ ++  g +++++++
  gi|313117249|ref|YP_004044232.1|  90 VIRGEFVVEMEGESHHLSRGDEISVPPETAHSLEAVGDSiGVALTTVRP 138
                                       899**********************************888888887765 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   4.3e-06     0.019      22      61 ..      81     119 ..      77     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-06
                                       CESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                           Cupin_3  22 tyeedEfcyileGevkvtpeggetvelraGDlvvlpkgls 61 
                                       +++++E + +++Ge  v+  +ge ++l+ GD + +p+ + 
  gi|313117249|ref|YP_004044232.1|  81 HVGYEESFEVIRGEFVVEM-EGESHHLSRGDEISVPPETA 119
                                       5678999************.**************999875 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.6e-06     0.016      47     130 ..      77     152 ..      71     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-06
                                       EEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEEEESSSTT-EEH CS
                           Cupin_1  47 lPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaivvfdtnnpgnqsv 123
                                       +Phyh  ++e + v+ Ge  v++  +       +  l++Gd + vP+  +h   + gd+ +va+  +  +++ + +v
  gi|313117249|ref|YP_004044232.1|  77 PPHYHVGYEESFEVIRGEFVVEMEGE-------SHHLSRGDEISVPPETAHSLEAVGDSIGVALTTVRPAAQ-TFTV 145
                                       8****************998665444.......458*********************999999988887777.4445 PP

                                       SCEHHHH CS
                           Cupin_1 124 laalfsv 130
                                        +++f++
  gi|313117249|ref|YP_004044232.1| 146 VSTQFGL 152
                                       5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1637.85
//
Query:       gi|313117250|ref|YP_004044233.1|  [L=533]
Description: myosin-crossreactive antigen [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   7.5e-216  717.7   0.0   8.5e-216  717.5   0.0    1.0  1  MCRA           MCRA family
      3e-05   24.1   0.1    7.6e-05   22.9   0.1    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00038   20.2   0.0    0.00097   18.8   0.0    1.7  1  DAO            FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  717.5   0.0  1.4e-219  8.5e-216       2     496 .]      15     502 ..      14     502 .. 0.98

  Alignments for each domain:
  == domain 1  score: 717.5 bits;  conditional E-value: 1.4e-219
                                       -EEEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-----------------CCC----B.-TT-HHHHHHHTTSB CS
                              MCRA   2 kkaylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdpekGyvlrggrel.eehyeclwdLlssip 77 
                                       ++ay+vG+GiasLa+A++L+rda+vpgenihile+l+v+gg+ldg+g+pe+Gyv+rggr++ +++yec+wdLl+s+p
  gi|313117250|ref|YP_004044233.1|  15 RDAYFVGGGIASLAGAAFLVRDAGVPGENIHILEKLDVMGGALDGSGTPEDGYVIRGGRMFnYPTYECTWDLLESVP 91 
                                       78***********************************************************9*************** PP

                                       -SSSTTSBHHHHHHHHHHHS----S--EEETTTEE-TTTT----C.CHHHHHHHHHCS-GGGCTT-BHHHHS-HHHH CS
                              MCRA  78 SleepgasvldeieelnkedknkskarlvekrgeeavddkklglskkdrlellkLlltkeekLedkrIedvfseeff 154
                                       Sle+p++s+   + e+n++ ++++++rl+++ ++e+ d++++++++++rl+ll+L+lt+e+kL+d++Ie++fse+ff
  gi|313117250|ref|YP_004044233.1|  92 SLEDPDRSIKAVMDEFNERYESYAETRLMDE-EQEILDASSYDFEMEHRLSLLQLALTPERKLGDTTIEEWFSESFF 167
                                       *******************************.78******************************************* PP

                                       TSHHHHHHHHHHT--TTSBHHHHHHHHHHTGGGGGGSTT-TT-B--SS-HHHHCCHHHHHHHHHTT-EEE-SEEEEE CS
                              MCRA 155 esnFWllwsttFafqkwhSalElrrylrrfiheisgledlsglkrtkynqyeslilPlvkyLkeqgVdfqfntkVtd 231
                                       +++FW+lw+ttFafq+whS++E+rry++rf+he+++l++l+g++rtkynqy+s+++Plv++Lke++V+f+ +++Vt 
  gi|313117250|ref|YP_004044233.1| 168 DTTFWYLWATTFAFQPWHSVVEMRRYMHRFMHEFPRLDTLEGVDRTKYNQYDSIVRPLVQWLKERDVEFRGGCEVTA 244
                                       ***************************************************************************** PP

                                       EEEEEE.TTEEEEEEEEEEE.TTEEEEEE--TTEEEEEE---SSTT-EE-BTTB------.---HHHHHHHHHHCC- CS
                              MCRA 232 iefeeeeedkktvteielekeegeeetieleedDlvfvtnGsitessslGdndtpakleekeadesweLWkklaaks 308
                                       +++++  +  ktv++i++e+ +++ +ti++ ++DlvfvtnGs+t++sslG++d++++l++  +++s+eLWk++ +++
  gi|313117250|ref|YP_004044233.1| 245 LDITSM-RGGKTVEAIHYES-DETPNTIDVAPSDLVFVTNGSMTDGSSLGSMDEAPTLDT--TGASFELWKSIVEDH 317
                                       ****77.669*********8.66888********************************98..58************* PP

                                       GGG--THHHHSS--TTS-EEEEEEE-SSTTHHHHHHHHTS-TSSSS-EEETT-TT-EEEE--SS-SSTT--TT-EEE CS
                              MCRA 309 pkfGnPekFcsdieeskwesfTvtlkdeklleriekltknepgtgglvtlkdSnwllsivvnrqphfkeQpedvtvl 385
                                       p+fGnP++F ++++e+kwesfTvtl++++lle+i ++t++ep  +glvt++dSnwl+sivv+ qphf++Qpedv+v+
  gi|313117250|ref|YP_004044233.1| 318 PEFGNPSAFADHVQETKWESFTVTLDEPDLLEYIIEVTREEP-GNGLVTFTDSNWLMSIVVAGQPHFANQPEDVKVF 393
                                       ******************************************.788******************************* PP

                                       EEEES-SSSB-SSS-SBGGG--HHHHHHHHHHHHT--HHHHHHHCTTTEEEEEEE-TTTTGGGS---TTSS-BSS-T CS
                              MCRA 386 wgYglfpekeGdyvkKpmlectGeEileEllyhLgvpeekieellkssvntipcvmPyitalflpRakgdRPkvvPe 462
                                       wgYglfpe++G+y++K+m +ctGeEileEl+yhLg++ ++ +++++s+ ++ipc+mP+it++f+pR+ gdRP+vvP+
  gi|313117250|ref|YP_004044233.1| 394 WGYGLFPEAKGNYIEKRMEDCTGEEILEELCYHLGCS-DRSSSFIESA-TCIPCMMPFITSQFMPRTPGDRPDVVPA 468
                                       ************************************7.7788899877.**************************** PP

                                       TBSSEEEESTTSB-S---SSSHHHHHHHHHHHHH CS
                              MCRA 463 gskNlAliGqFveiprdtvftveysvrtaqeAvY 496
                                       +s+NlA++GqF+e+p+d+vftveysvr+a++AvY
  gi|313117250|ref|YP_004044233.1| 469 RSNNLAFLGQFAELPNDVVFTVEYSVRSAMVAVY 502
                                       *********************************9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   1.3e-08   7.6e-05       2      66 ..      20      88 ..      20      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-08
                                      E--SHHHHHHHHHHHCC....TEEEEEE-SSSSSSGGG-EECETT.CEECTS---EEETTHHHHCHHHHC CS
                     NAD_binding_8  2 vGaGlsGlvaAylLaka....gfdvlllekrdrlGGraasyevpg.vrvdygahifhgsgyypnvrrllr 66
                                      vG+G+++l+ A++L ++    g ++++lek d  GG +     p+   v  g + f+ +  y+ +++ll+
  gi|313117250|ref|YP_004044233.1| 20 VGGGIASLAGAAFLVRDagvpGENIHILEKLDVMGGALDGSGTPEdGYVIRGGRMFNYP-TYECTWDLLE 88
                                      9*************9977555559**************977664324445677888875.5899998876 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.6e-07   0.00097       5     227 ..      20     309 ..      18     407 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-07
                                       ECTSHHHHHHHHHHHHT.T.....EEEEESSSSTTSSGGGSSE.....EEEESSS.STHHSTH.............. CS
                               DAO   5 iGGGiiGlstAyeLarr.g.....VtllekgdiagsgaSgrns.....gllhsgl.rylpeas.............. 55 
                                       +GGGi+ l+ A +L r  g     + +lek d  g ga  +++      ++++g   ++p ++              
  gi|313117250|ref|YP_004044233.1|  20 VGGGIASLAGAAFLVRDaGvpgenIHILEKLDVMG-GALDGSGtpedgYVIRGGRmFNYPTYEctwdllesvpsled 95 
                                       8*************987756679********9988.99888886666345555557334444478888988888888 PP

                                       .........HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEES.SHHHHHHHHHHHHHHHHTTT.TEEEEEHHHH CS
                               DAO  56 .........elarlslealeelreleeelgididyrrtGllslaa.deeelealdkllallleagl.daelldaeev 121
                                                +      e +e+++ ++e+ +  +  +++  l   + d   +e ++ +l ll ++ l +++ l    +
  gi|313117250|ref|YP_004044233.1|  96 pdrsikavmD------EFNERYESYAET-R--LMDEEQEILDASSyD---FE-MEHRLSLL-QLALtPERKLGDTTI 158
                                       8874333331......333333444443.2..223334444443212...11.22222222.233324455666557 PP

                                       HHHSTTST..TTSEEEEETTEEEEEHHHHHHH...................................HHHHHHHTT- CS
                               DAO 122 relepalp..gllgalfypdtgqvdpakltaa...................................laraaealGv 161
                                       +e+++  +  +++ +++  +t  ++p++ +                                     l + ++++ v
  gi|313117250|ref|YP_004044233.1| 159 EEWFSE-SffDTTFWYLWATTFAFQPWHSVVEmrrymhrfmhefprldtlegvdrtkynqydsivrpLVQWLKERDV 234
                                       777764.134555555555556666666666666666668888888888888888888888888888********** PP

                                       EEEESECEEEEEEEE.TCEEEEE......EECT.EEEE.EEEEEEE--GGGHH.HH.HTTCTTTSEEEEEEEEEEEE CS
                               DAO 162 eilegtevtgleeed.gkvwgve......rttp.gend.aadavVnaaGawsd.ll.gllkeldlpispvrgqvlvl 227
                                       e++ g+evt+l+ ++  ++++ve      ++tp  + +   d v +++G  +d  + g + e   p+  + g ++ l
  gi|313117250|ref|YP_004044233.1| 235 EFRGGCEVTALDITSmRGGKTVEaihyesDETPnTIDVaPSDLVFVTNGSMTDgSSlGSMDE--APTLDTTGASFEL 309
                                       ***********87667455677777798877773443244377**********844333322..3666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3677.90
//
Query:       gi|313117251|ref|YP_004044234.1|  [L=91]
Description: PadR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-15   57.1   1.0    1.6e-15   56.8   1.0    1.1  1  PadR            Transcriptional regulator PadR-like family
     0.0029   17.5   0.2     0.0043   17.0   0.2    1.4  1  HTH_45          Winged helix-turn-helix
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.029   14.2   0.0    1.2  1  DUF1495         Winged helix DNA-binding domain (DUF1495)
      0.025   14.7   0.0      0.057   13.6   0.0    1.6  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.13   12.2   0.0       0.33   10.9   0.0    1.7  1  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   1.0   4.5e-19   1.6e-15       2      74 ..      12      79 ..      11      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 4.5e-19
                                      HHHH.CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  2 Lall.eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      L+++ +  + +G+++++elee++e  +++++G+lYp+L++L ++gl+e+   ++    +++yY+ T++Grre++
  gi|313117251|ref|YP_004044234.1| 12 LMVIaGLDEPHGLAVKDELEEYYE--TKIHHGRLYPNLDTLVEKGLIEKGTIDQ----RTNYYTTTRRGRREIN 79
                                      6777344677************86..6***********************9986....9************986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   1.2e-06    0.0043      28      70 ..      35      82 ..      24      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-06
                            HTH_45 28 kanLsykllnkYLdmLvekgli.....kkskekYvlTekGlelleklk 70
                                      +  +   +l   Ld+Lvekgli     +++++ Y++T +G++ ++  +
  gi|313117251|ref|YP_004044234.1| 35 ETKIHHGRLYPNLDTLVEKGLIekgtiDQRTNYYTTTRRGRREINARQ 82
                                      555666677777999999999877777999**********98766555 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     8e-06     0.029      53      85 ..      44      76 ..      39      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8e-06
                           DUF1495 53 ynsessLielGLveeeeeseglklYklteeGie 85
                                      y + + L+e+GL+e+ + ++ +++Y+ t +G++
  gi|313117251|ref|YP_004044234.1| 44 YPNLDTLVEKGLIEKGTIDQRTNYYTTTRRGRR 76
                                      777789*******99999*************97 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.057      25      57 ..      33      65 ..       5      72 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                    B-block_TFIIIC 25 akeskqdprslfyrlksLekkgLIvkqsiidsa 57
                                      + e+k+    l+  l++L +kgLI+k +i +++
  gi|313117251|ref|YP_004044234.1| 33 YYETKIHHGRLYPNLDTLVEKGLIEKGTIDQRT 65
                                      3578899*********************94444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.3e-05      0.33       2      55 ..       3      60 ..       2      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.3e-05
                                      T--HHHHHHHHHHHCTTTS.EEEHH.HHHH..HHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgr.dltvg.elar..rlglsksavsrilkrLvaaGLverrp 55
                                      +lt+ q+++L++++  +++  l+v+ el++  ++++ ++++   l+ Lv++GL+e+ +
  gi|313117251|ref|YP_004044234.1|  3 DLTGFQRDLLMVIAGLDEPhGLAVKdELEEyyETKIHHGRLYPNLDTLVEKGLIEKGT 60
                                      7888899999999999999966665267779999999999999***********9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 661.35
//
Query:       gi|313117252|ref|YP_004044235.1|  [L=438]
Description: major facilitator superfamily transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-13   48.1  33.7    7.4e-13   48.1  33.7    1.9  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.22   11.4   0.1       0.37   10.7   0.1    1.2  1  UPF0227   Uncharacterised protein family (UPF0227)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1  33.7   8.2e-17   7.4e-13      10     344 ..      25     377 ..      23     383 .. 0.73
   2 !    6.9  19.1   0.00028       2.5      34     178 ..     284     425 ..     256     435 .. 0.71

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 8.2e-17
                             MFS_1  10 larsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fassl 85 
                                       l+ ++++p+++l+l ++  ++ +++g+l +ly+++++ + +p+G+++dr+Grr  lll++++++ + l+++ ++ ++
  gi|313117252|ref|YP_004044235.1|  25 LSVGFITPIFTLFLLRS--LTFTQVGTLSALYSVFSVGGEIPTGYVGDRLGRRASLLLSVAFTIGS-LVGFvVVKGF 98 
                                       778899******99999..56*********************************************.6666234999 PP

                             MFS_1  86 wlllvlrvlqGlgagalfpagaaliadwfpkeergrai....gllsagfslGailgpllggllasslgWravfyila 158
                                        + ++l +l +l+  +   ++ a++ d+  ++  +  +    g   a  +  a++ +++ggll+  l  +++f+++ 
  gi|313117252|ref|YP_004044235.1|  99 LWYAFLYALWALALTFRSGSMDAWLYDILDERLDSGRFshvrGRGDAVQNWTAAVSMVVGGLLY-GLHPTYPFVAAV 174
                                       99*****************************7444444144477777*****************.666788888888 PP

                             MFS_1 159 ivsllafv.lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvl..w....illialllfffgfsg..l 226
                                       ++  l+f+ l  l lp ++   +      +  + g  +++++ +  l++p+l  +     l++a+++++  + +  +
  gi|313117252|ref|YP_004044235.1| 175 AFNSLGFItL--LSLPKNRQYAGCGDANVD--RLGLLEAFTVVRGYLTKPPLrsLvvyvGLFYAVVGVSHTYVQpmA 247
                                       8888888844..666666666666666666..455555555778888888774413334455555555433333764 PP

                             MFS_1 227 ltllplylqevlgls...................glllaglllallalvgailallagrlsdrlgrrrrlllallll 284
                                       + +l  y  + +g                     + l +g+++a l +v+ +++  ag++ drlg rr+ ll  +++
  gi|313117252|ref|YP_004044235.1| 248 VETLAPY-ATGFGVQmvtgdataaarsgdagatmA-LGLGAMYASLTAVSSVGGYYAGAVEDRLGIRRAVLLVPAIT 322
                                       4444445.8888888999999*********77654.55555666666666666999999999999744444443333 PP

                             MFS_1 285 llaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfnta 344
                                       ++a++  +++a+     l+l  ++ + +++ +v+p+++ +++d++    ++t++++++++
  gi|313117252|ref|YP_004044235.1| 323 AIALIVPLWVAL-----LALPTFASMRTAMPLVQPIANGYINDHIEGVGRATLLSAVSMF 377
                                       333333333333.....57778888999*****************444444555555554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00028
                             MFS_1  34 igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGl..gagalfpagaa 108
                                       +g +++  +++++v+ + +G++ dr+G rr +ll  +++a++l+++l++    +ll+l  ++++  ++ ++ p+++ 
  gi|313117252|ref|YP_004044235.1| 284 LGAMYASLTAVSSVGGYYAGAVEDRLGIRRAVLLVPAITAIALIVPLWV----ALLALPTFASMrtAMPLVQPIANG 356
                                       455777778888***************9995555555555553666642....3444444444411335677***** PP

                             MFS_1 109 liadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178
                                       +i d   +  r+  ++ +s+++       +l +g++a++   ++++ +l++++l+++   ++ l +  pe
  gi|313117252|ref|YP_004044235.1| 357 YINDHIEGVGRATLLSAVSMFYMTLRTPLALSAGIVADATTATVAMAALGGLFLVVGGA-VWILGDVVPE 425
                                       **********************99999999999****9999999988888888888553.1333333333 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   4.1e-05      0.37      66      92 ..     295     322 ..     286     329 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.1e-05
                           UPF0227  66 ssLGGyyatrlgerfglrq.vllnPalk 92 
                                       ss GGyya  +  r g+r  vll Pa++
  gi|313117252|ref|YP_004044235.1| 295 SSVGGYYAGAVEDRLGIRRaVLLVPAIT 322
                                       89***************877*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2918.62
//
Query:       gi|313117253|ref|YP_004044236.1|  [L=947]
Description: ATP-dependent exonuclase V beta subunit, helicase and exonuclease domain-containing [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-49  168.4   0.1    8.6e-49  166.7   0.1    1.8  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    5.4e-29  101.6   0.0    1.1e-17   64.5   0.0    2.2  2  UvrD_C           UvrD-like helicase C-terminal domain
    7.2e-25   88.0   0.0    4.8e-24   85.4   0.0    2.2  1  AAA_19           AAA domain
    6.9e-09   35.4   0.1     0.0028   17.5   0.1    2.7  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    1.5e-07   31.6   0.1    8.3e-06   25.9   0.0    2.7  2  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    2.4e-06   27.4   0.0    1.3e-05   25.0   0.0    2.1  2  AAA_30           AAA domain
      0.002   18.0   0.0        0.6    9.9   0.0    2.3  2  AAA_11           AAA domain
     0.0025   17.1   0.0     0.0048   16.2   0.0    1.4  1  DUF2800          Protein of unknown function (DUF2800)
     0.0052   16.4   0.0       0.14   11.8   0.0    2.5  2  AAA_12           AAA domain
  ------ inclusion threshold ------
      0.031   14.0   2.8         29    4.3   0.1    4.1  4  Viral_helicase1  Viral (Superfamily 1) RNA helicase
        0.1   12.4   0.3       0.51   10.2   0.0    2.4  3  TetR_N           Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.7   0.1   5.3e-52   8.6e-49       2     313 ..       5     359 ..       4     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 166.7 bits;  conditional E-value: 5.3e-52
                                       SHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT CS
                     UvrD-helicase   2 npeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessd 78 
                                       n+ q++ i s+ g  +v A+AG+GKTf+++ r+++ +++ e+ p ++l+vTFTn Aa E+k Ri ++++        
  gi|313117253|ref|YP_004044236.1|   5 NDHQQDLIDSTDGIHVVDAGAGTGKTFTVTRRYAEIVDQDEVAPADVLLVTFTNNAATEMKDRIVSHCGYGM----- 76 
                                       7899**************************************************************999764..... PP

                                       -HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT........SHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTT CS
                     UvrD-helicase  79 derlrlalqnlseanisTlHsfcqkilkkeanrig........ldpnfrildeedeedlkqqellkelleksaddsl 147
                                               ++ls+a i+T+Hs+c+ +l+++ +++         +    ril++e+ e+    + + e + +  dd +
  gi|313117253|ref|YP_004044236.1|  77 --------RELSDAPIQTFHSLCHDLLMEHGFEAPthlgiddrITGSTRILEDETVEK----AQFREFIRRFSDD-H 140
                                       ........579**********************9999999999888999999999543....3444444332233.5 PP

                                       THHHHHHHHHHHHHHCCCCCH..................................................HHHCCC CS
                     UvrD-helicase 148 nldkkkleklikelsksrnik..................................................keelsl 174
                                           +++++         +++                                                  k     
  gi|313117253|ref|YP_004044236.1| 141 AAYDDFFRAIED------PVEllglltqlaskgvfptadgwyrngerhldgdfeafselfdelnqprnggsK----- 206
                                       555555553321......222335556777888999999999999777777777777776665444444442..... PP

                                       HHHHHCHHHHHHHHHHHTTCCTTHHCHSS.............................TSCSHHHHHHHHHHHHHHH CS
                     UvrD-helicase 175 skskaeelrelvskakekqlspkelkkaf.............................ekasdlqkkiaeflkeyqe 222
                                              lr  +s++  ++                                       e   dl++++ +++ ey+e
  gi|313117253|ref|YP_004044236.1| 207 ----QSRLRSKLSRYGRNKC--------YlpdapdkstirggrgekqvpadvarrafeEDRADLKQFVHDVYFEYLE 271
                                       ....2222222222222222........0222222224555555555788899999999999*************** PP

                                       HHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGG CS
                     UvrD-helicase 223 qkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgF 299
                                           +n l f  l +++  ll ++++l++++   +++++iDE+QD ++iQ+++  lla ++ +l++vGD kQsIY+F
  gi|313117253|ref|YP_004044236.1| 272 FALSRNYLNFGFLQLFAFVLLCDDHSLRDDVA--FEYVMIDEFQDSSEIQFKLALLLADTN-NLCVVGDWKQSIYSF 345
                                       *****************************986..788****************99999887.9************** PP

                                       GTB-THHHHHHHHH CS
                     UvrD-helicase 300 RgAdielflkkkkd 313
                                       + A +e++ +++++
  gi|313117253|ref|YP_004044236.1| 346 QYAAVENITEFESR 359
                                       **********9987 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   5.6e-12   9.1e-09       1     126 [.     384     529 ..     384     547 .. 0.82
   2 !   64.5   0.0   6.7e-21   1.1e-17     238     346 ..     589     736 ..     549     739 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 5.6e-12
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   1 ivLekNyRStksLlkaankflenilnr..ralekek...........ktvekgekivvleaeteeeEaekiaatika 64 
                                       i L +NyRSt+ +l+ +++ l     +  ++    +           +++++ e    +ea ++e+E+e i  +i++
  gi|313117253|ref|YP_004044236.1| 384 IELVENYRSTQAILDFSEHSLVTPAAStdKV----DveevqdrivslSANTPCE-NSNIEAIQHEDEHEAILTKIQE 455
                                       6799***************993322221222....1222444677764444444.4446788899************ PP

                                       xx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  65 ll............ekneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllank 126
                                       ++             + +++ d+avL+R+    +++  a  + g+p+   ++ ++F+    k +la l++l+ +
  gi|313117253|ref|YP_004044236.1| 456 IAgnedyqveedgeLRPPEYGDVAVLTRTRDFGRELLSAAAEYGLPMSYEGGIELFRSDPAKLLLAWLRILDAD 529
                                       *********999888889******************************999******************99866 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 6.7e-21
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 238 lenlreLysllkelekkeeeeeveeklneileiatLseseleeskkk...ekipiiTiHqAKGlEFdvVflagleeg 311
                                         + + L+++++++     ++  + +l +++e   +++++ +e++     +++++ TiH+AKGlE ++V+l++++  
  gi|313117253|ref|YP_004044236.1| 589 GAHADVLLTTVQSIHS--ATTVTRGDLIQFIERG-IENGSTQEVHASagvNSVTVQTIHAAKGLEHPIVILVNMNSH 662
                                       4566677788888888..77778889******98.999999999888899*************************** PP

                                       xxx..................................xxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 312 tfP..................................syrskk.........ekrleEEkRlfYVaiTRAkkrLfis 345
                                       +fP                                  +               +  +EE+Rl+YV +TRA + L++s
  gi|313117253|ref|YP_004044236.1| 663 RFPpsggnsntitfddpiglrqrkryaddygyphihdN----WrtdvlrtclPRGYDEERRLLYVSMTRAESHLVFS 735
                                       *********99999999999888888888877777663....03345777778899******************998 PP

                                       x RF
                            UvrD_C 346 y 346
                                       +
  gi|313117253|ref|YP_004044236.1| 736 A 736
                                       7 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   2.9e-27   4.8e-24       5     146 .]      12     346 ..       8     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.9e-27
                            AAA_19   5 vealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae............a 69 
                                       + ++++++ +v aG+GtGKT +++ + a++v++ +v+p+++llv+ft+ Aa e+++r+ +   +            +
  gi|313117253|ref|YP_004044236.1|  12 I-DSTDGIHVVDAGAGTGKTFTVTRRYAEIVDQDEVAPADVLLVTFTNNAATEMKDRIVS---HcgygmrelsdapI 84 
                                       5.67788999**********************************************9943...2345888999999* PP

                            AAA_19  70 tTiHrlal..................................................................... 77 
                                       +T+H+l                                                                       
  gi|313117253|ref|YP_004044236.1|  85 QTFHSLCHdllmehgfeapthlgiddritgstriledetvekaqfrefirrfsddhaayddffraiedpvellgllt 161
                                       ******88********************************************************************* PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|313117253|ref|YP_004044236.1| 162 qlaskgvfptadgwyrngerhldgdfeafselfdelnqprnggskqsrlrsklsrygrnkcylpdapdkstirggrg 238
                                       ***************************************************************************** PP

                            AAA_19  78 ........................................ldfddlltealelle.........eaeeekklqeeel 105
                                                                               l+f  l        +         +++ ++++ + e+
  gi|313117253|ref|YP_004044236.1| 239 ekqvpadvarrafeedradlkqfvhdvyfeylefalsrnyLNFGFL--------QlfafvllcdDHSLRDDV-AFEY 306
                                       *********************9999999999887766665444444........344444444655566666.566* PP

                            AAA_19 106 livDEfqdvdelqyrLlkallgekkklllvGDpdQliyvfr 146
                                       +++DEfqd +e q++L   l+ ++++l++vGD +Q+iy+f+
  gi|313117253|ref|YP_004044236.1| 307 VMIDEFQDSSEIQFKLALLLA-DTNNLCVVGDWKQSIYSFQ 346
                                       ****************99999.5666*************95 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.6e-06     0.014       2      25 ..     638     661 ..     637     668 .. 0.85
   2 !   17.5   0.1   1.7e-06    0.0028      30      50 ..     713     733 ..     705     735 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-06
                          UvrD_C_2   2 ayaltihkaQGsefpaVivfdpdl 25 
                                       +++ tih a+G+e p+Vi+++++ 
  gi|313117253|ref|YP_004044236.1| 638 VTVQTIHAAKGLEHPIVILVNMNS 661
                                       6788***************98874 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.7e-06
                          UvrD_C_2  30 mgelrrrlLYtavTRArekli 50 
                                       ++++ rrlLY+ +TRA  +l+
  gi|313117253|ref|YP_004044236.1| 713 GYDEERRLLYVSMTRAESHLV 733
                                       45668************9998 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.053        87      35      68 ..     805     841 ..     791     854 .. 0.77
   2 !   25.9   0.0   5.1e-09   8.3e-06     124     197 ..     855     923 ..     840     946 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.053
                          PDDEXK_1  35 dlGtlvHaaleefye..wkkldke.dleelleeavee 68 
                                       ++Gt+vH+ +e++      +++k+ d e +l+++++ 
  gi|313117253|ref|YP_004044236.1| 805 EFGTQVHEFAERYALgaDVEPSKGnDDESHLKTLIDS 841
                                       79***********997755566667777777777765 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 5.1e-09
                          PDDEXK_1 124 g....gekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylr 196
                                            ge+v++ G +D+v    ++++iiD+Kt +    +++  e +++ Ql +Y  +l+e    +e+  ++ a+++ 
  gi|313117253|ref|YP_004044236.1| 855 PltvdGERVTISGVVDLVHILPDTVEIIDFKTDR---GRHA--EAEYRKQLSVYYHVLHEC--FPER--DVTAAIFY 922
                                       1445479************66666********99...7777..889999*********999..4444..33333333 PP

                          PDDEXK_1 197 l 197
                                        
  gi|313117253|ref|YP_004044236.1| 923 T 923
                                       3 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   8.2e-09   1.3e-05      12      82 ..      10     109 ..       3     142 .. 0.68
   2 ?   -1.0   0.0      0.77   1.3e+03      90     127 ..     305     340 ..     288     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 8.2e-09
                            AAA_30  12 alltsgdrvavltGpAGtGKttalk.alreaweaag...grviglAptgkaAkvLa............eelgieast 72 
                                        l+ s+d ++v+ ++AGtGKt++++  ++e++++++    +v++++ t++aA +++            e ++++ +t
  gi|313117253|ref|YP_004044236.1|  10 DLIDSTDGIHVVDAGAGTGKTFTVTrRYAEIVDQDEvapADVLLVTFTNNAATEMKdrivshcgygmrELSDAPIQT 86 
                                       46678899*************8875156999988877889****************444444333333233358888 PP

                            AAA_30  73 iakllkrlk.............g 82 
                                        ++l + l              +
  gi|313117253|ref|YP_004044236.1|  87 FHSLCHDLLmehgfeapthlgiD 109
                                       88888766665556555555432 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.77
                            AAA_30  90 tllivDEagmvdtkqlaallkaaekagakvilvGDerQ 127
                                       + +++DE    +  q++  l  a++    + +vGD +Q
  gi|313117253|ref|YP_004044236.1| 305 EYVMIDEFQDSSEIQFKLALLLADT--NNLCVVGDWKQ 340
                                       6789999988888888777766655..88999****99 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00037       0.6      16      76 ..      15      70 ..       3     134 .. 0.88
   2 !    5.6   0.1    0.0074        12     212     253 ..     299     340 ..     290     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00037
                            AAA_11 16 eseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr 76
                                      +++i ++    GtgKT+t++  ++++      ++++ a++ +L+ + +N+A  e+ +r+++
  gi|313117253|ref|YP_004044236.1| 15 TDGIHVVDAGAGTGKTFTVTRRYAEI-----VDQDEVAPADVLLVTFTNNAATEMKDRIVS 70
                                      45577899999***************.....567899*******************99998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0074
                            AAA_11 212 eklakkfdvviIDEAaqavEpstliPlrlga.kkvvLvGDpkQ 253
                                       ++    f++v IDE   + E++   +l+l+  +++  vGD kQ
  gi|313117253|ref|YP_004044236.1| 299 RDDV-AFEYVMIDEFQDSSEIQFKLALLLADtNNLCVVGDWKQ 340
                                       4443.8********************96654499********9 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.9e-06    0.0048      95     151 ..     843     903 ..     831     911 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.9e-06
                           DUF2800  95 dalvlvEqrvdfskyvpe....gfGtaDvviiaddvLeviDlKyGkgvkVsaekNpQlalY 151
                                       d+++ vE+ v +   v+       G  D+v i  d++e+iD+K  +g +++ae  +Ql +Y
  gi|313117253|ref|YP_004044236.1| 843 DGEIRVEEDVYLPLTVDGervtISGVVDLVHILPDTVEIIDFKTDRGRHAEAEYRKQLSVY 903
                                       789999999999877765588899***********************************99 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.11   1.8e+02      19      42 ..     385     408 ..     370     467 .. 0.68
   2 !   11.8   0.0   8.5e-05      0.14     137     193 ..     627     733 ..     598     737 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                            AAA_12  19 lLdtqYRmhpeIsrfpsklfYkgk 42 
                                        L ++YR+ ++I++f+++ +   +
  gi|313117253|ref|YP_004044236.1| 385 ELVENYRSTQAILDFSEHSLVTPA 408
                                       6889************99775544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.5e-05
                            AAA_12 137 ekseke.....ievntvdgfQGrekdviilslVRsn....ekk.................................. 170
                                       ++ + +     ++v+t+ +  G e  ++il    s+    + +                                  
  gi|313117253|ref|YP_004044236.1| 627 QEVHASagvnsVTVQTIHAAKGLEHPIVILVNMNSHrfppS-Ggnsntitfddpiglrqrkryaddygyphihdnwr 702
                                       33332255556*******************99999755540.14556788889999999999*************** PP

                            AAA_12 171 ........eigflkderrlNValTRAkskli 193
                                                 g  +++r l V++TRA s+l+
  gi|313117253|ref|YP_004044236.1| 703 tdvlrtclPRGYDEERRLLYVSMTRAESHLV 733
                                       ****9998899999**************997 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.075   1.2e+02       2      21 ..      20      39 ..      19      79 .. 0.76
   2 ?    4.3   0.1     0.018        29      60     114 ..     301     350 ..     292     370 .. 0.72
   3 ?    2.4   0.0     0.065   1.1e+02     172     203 ..     625     658 ..     571     668 .. 0.77
   4 ?    1.6   0.1      0.12     2e+02     213     232 ..     715     734 ..     703     736 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.075
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                      vv++ +G GK+  + + + +
  gi|313117253|ref|YP_004044236.1| 20 VVDAGAGTGKTFTVTRRYAE 39
                                      8**********999888877 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                   Viral_helicase1  60 stkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasfllahl 114
                                       +  ++++ +DE++     +++l++ l+   +++++GD +Q+ ++      ++a  
  gi|313117253|ref|YP_004044236.1| 301 DVAFEYVMIDEFQDSSEIQFKLALLLADTNNLCVVGDWKQSIYSF-----QYAAV 350
                                       456899******9998666666888889999*********98884.....44433 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.065
                   Viral_helicase1 172 ftqalkealgvr..evttvhevqGltfdkVtlvl 203
                                        tq+  ++ gv+   v t h + Gl+ + V+lv 
  gi|313117253|ref|YP_004044236.1| 625 STQEVHASAGVNsvTVQTIHAAKGLEHPIVILVN 658
                                       57778888888888899***************96 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.12
                   Viral_helicase1 213 sesrenllvAlTRhrkslvi 232
                                        e+r  l+v +TR+ + lv+
  gi|313117253|ref|YP_004044236.1| 715 DEERRLLYVSMTRAESHLVF 734
                                       45799***********9987 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.1   6.6e+03       8      16 ..      94     102 ..      92     106 .. 0.83
   2 ?   -3.7   0.0       6.6   1.1e+04       5      16 ..     578     589 ..     577     592 .. 0.84
   3 ?   10.2   0.0   0.00031      0.51       8      32 ..     615     639 ..     613     640 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.1
                                       HHHHHHTTT CS
                            TetR_N   8 lfaerGyda 16 
                                       l+ e+G++a
  gi|313117253|ref|YP_004044236.1|  94 LLMEHGFEA 102
                                       899****98 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.6
                                       HHHHHHHHHTTT CS
                            TetR_N   5 ArelfaerGyda 16 
                                       A ++f+++ yd+
  gi|313117253|ref|YP_004044236.1| 578 AQRVFSRYNYDG 589
                                       7899***99997 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00031
                                       HHHHHHTTT--HHHHHHHHTSSHHH CS
                            TetR_N   8 lfaerGydattvreIAkrAGvskga 32 
                                        f+erG+++ +++e+ ++AGv+  +
  gi|313117253|ref|YP_004044236.1| 615 QFIERGIENGSTQEVHASAGVNSVT 639
                                       69*******************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (947 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 6067.94
//
Query:       gi|313117254|ref|YP_004044237.1|  [L=862]
Description: hypothetical protein Hbor_30390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-13   50.6   0.1    8.6e-13   48.8   0.1    2.1  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   4.8e-17   8.6e-13       1     231 [.     480     737 ..     480     838 .. 0.68

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 4.8e-17
                          PDDEXK_1   1 rlSvsrletfleCplrfflryllglreeeeleapdlGtlvHaaleefye.wkkldkedleelleeaveelwpellle 76 
                                       ++S+s+l+t+ + p+ +f+++ll  +++  +++   G+l+H+ +e ++       + + +e l+e++e +++e +  
  gi|313117254|ref|YP_004044237.1| 480 TISQSSLNTYVNSPRDYFFSRLLDTPDKDYFRE---GNLLHDFAEYYVAhP----ESVTDETLAEVAEIILDEVDPF 549
                                       58***********************99999999...********7555543....3333333324444444443333 PP

                          PDDEXK_1  77 eeilessarlrylaeklkevlekl.ve..rlaeeleakrg....frpvalelefg..................gekv 128
                                        + +  + r+  ++  l+ ++e l  +  +  e  + ++g    f                            ++++
  gi|313117254|ref|YP_004044237.1| 550 LRGVDREVRHTKYRLGLQTIVEFLdTNppHGDEFVAGNDGwgrnF---------FaeyydrpidtphterwfeNSDL 617
                                       323333334433333333333333211112222222222243333.........03333455668899999965889 PP

                          PDDEXK_1 129 rLkGriDrvddkegelriiDyKtgsappkskelaelkegl..........QlllYllalaegeelkeegepagalyl 195
                                        LkG+iD+v d  +   ++DyK+gs   k+ + + +k++           Q llYl+  ++   ++++  +++ +++
  gi|313117254|ref|YP_004044237.1| 618 GLKGKIDLVHDSTH---LLDYKSGS---KKSAHSIVKHSAldppsdkpnfQALLYLAHQRTV--QPDQ--ELQFTFF 684
                                       9********87777...********...4444335555557888999999****99887777..5544..8888888 PP

                          PDDEXK_1 196 rleepkvk.................deevvkkmalteeeleallqeleelaee 231
                                       ++ e+  +                  ++++++ ++te+ +++l++e+ + +++
  gi|313117254|ref|YP_004044237.1| 685 HFLETLDDivageaslddclttvtyYPHTFAEYVATEAVFNELKSEAANDCNK 737
                                       88443333666666666666666665555555566666665555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (862 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 5248.06
//
Query:       gi|313117255|ref|YP_004044238.1|  [L=128]
Description: acyl dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-09   35.4   0.1    1.7e-07   31.4   0.1    2.0  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
    0.00016   21.2   0.1    0.00082   18.9   0.1    1.9  1  MaoC_dehydratas  MaoC like domain
  ------ inclusion threshold ------
      0.076   13.4   0.0       0.13   12.7   0.0    1.4  1  4HBT             Thioesterase superfamily


Domain annotation for each model (and alignments):
>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   2.9e-11   1.7e-07      11     131 ..      13     117 ..       7     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.9e-11
                   MaoC_dehydrat_N  11 kaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhgeqefeyhep 87 
                                       + + + e+v++fa+  g+++p++++++        + ++ + +l+++  ++      lg+d  ++l  ++efe+h+p
  gi|313117255|ref|YP_004044238.1|  13 ERTFTVEEVQQFAELSGDAQPRHTEPDED------GRVMVQGLLTATMPTK------LGGD-DGVLASNMEFEFHQP 76 
                                       56778999******************995......4555555554444444......6666.5899*********** PP

                   MaoC_dehydrat_N  88 iraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                       ++ G+++t++s+ + v +++     ef + + ++ n++Gepv t
  gi|313117255|ref|YP_004044238.1|  77 VYTGESVTCTSTYDTVVERD--NRYEF-SADVVCENADGEPVLT 117
                                       *******************7..57776.7789999******976 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.4e-07   0.00082      14     100 ..      12      88 ..       2     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-07
                                       EEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--B CS
                   MaoC_dehydratas  14 keitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVl 90 
                                        e+t t +++ ++a +sgD +p H+ p+       g + ++G+lt+ + +kl  +++           ++ F +pV+
  gi|313117255|ref|YP_004044238.1|  12 FERTFTVEEVQQFAELSGDAQPRHTEPDE-----DGRVMVQGLLTATMPTKLGGDDGVL-----ASNMEFEFHQPVY 78 
                                       48899999*****************9983.....4567799999999999998888888.....7888899999999 PP

                                       TTCEEEEEEE CS
                   MaoC_dehydratas  91 pgdtlkvele 100
                                       +g+ ++ + +
  gi|313117255|ref|YP_004044238.1|  79 TGESVTCTST 88 
                                       9999887655 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05      0.13      24      54 ..      58      87 ..      44      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                      TTSTTEEEEEEEEEEEESS-BBTTCEEEEEE CS
                              4HBT 24 lggrgilvvvvelsidflrpvrlgdeltvea 54
                                      lgg + +v +++++ +f+ pv  g+ +t++ 
  gi|313117255|ref|YP_004044238.1| 58 LGG-DDGVLASNMEFEFHQPVYTGESVTCTS 87
                                      444.5899*********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 881.03
//
Query:       gi|313117256|ref|YP_004044239.1|  [L=127]
Description: Fe2+/Zn2+ uptake regulation protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-11   45.0   0.0    1.3e-11   44.9   0.0    1.1  1  Penicillinase_R  Penicillinase repressor
    3.5e-05   23.9   0.1    4.4e-05   23.6   0.1    1.1  1  FUR              Ferric uptake regulator family
     0.0019   17.9   0.4     0.0029   17.3   0.4    1.2  1  Arg_repressor    Arginine repressor, DNA binding domain
     0.0027   17.8   0.0     0.0031   17.6   0.0    1.2  1  DUF480           Protein of unknown function, DUF480
     0.0086   16.5   1.0       0.02   15.4   0.7    1.9  2  HTH_27           Winged helix DNA-binding domain
     0.0097   15.9   0.1      0.014   15.4   0.1    1.2  1  PadR             Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.013   15.4   3.4      0.044   13.7   1.8    2.4  2  MarR_2           MarR family
      0.042   13.6   0.0      0.054   13.2   0.0    1.1  1  DUF4364          Domain of unknown function (DUF4364)
      0.058   13.7   0.2       0.12   12.7   0.2    1.5  1  HTH_Tnp_Tc3_2    Transposase
      0.064   13.9   2.1       0.12   13.1   0.3    2.2  3  HTH_32           Homeodomain-like domain
      0.095   12.6   0.5       0.21   11.5   0.5    1.7  1  TrmB             Sugar-specific transcriptional regulator Trm
       0.14   12.1   1.1       0.21   11.6   0.6    1.5  2  HTH_12           Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   8.4e-15   1.3e-11       1      86 [.       6      95 ..       6     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 8.4e-15
                                      ---S-SHHHHHHHHHS-.EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE----XXXXXXXX CS
                   Penicillinase_R  1 lgelEaevmeilwekge.atvkevveeleee.kelaysTVktllrrLvkKgllsreke..grafiYsplvseeeavasa 75
                                      lg++E+e + il+++++ +t++ev+ el e+  ++ ysTV  +l rLv+K l++r +e    + +Y+ +   +++  + 
  gi|313117256|ref|YP_004044239.1|  6 LGPREKELLAILRRSEQsLTSREVQRELREDgVDVVYSTVSATLDRLVEKRLVDRTEEmqRGSPRYRHTFAADQYAGEL 84
                                      699***********9999************99**********************9998634456899999999999999 PP

                                      XXXXXXXXXXX CS
                   Penicillinase_R 76 vkqlldklfeg 86
                                      ++++++ + e 
  gi|313117256|ref|YP_004044239.1| 85 LDSIVEDVSEV 95
                                      99988887765 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   2.9e-08   4.4e-05       8      71 ..       8      72 ..       4      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.9e-08
                                      HHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET.TSEEEEE CS
                               FUR  8 kqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefe.dgesrye 71
                                      +  +++l++l++se+ l+  ev++el+e++ ++  +TV  tL+ l e  lv+++e    g+ ry+
  gi|313117256|ref|YP_004044239.1|  8 PREKELLAILRRSEQSLTSREVQRELREDGVDVVYSTVSATLDRLVEKRLVDRTEEMqRGSPRYR 72
                                      455789**********************************************9975426777776 PP

>> Arg_repressor  Arginine repressor, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   1.9e-06    0.0029       6      50 ..       9      54 ..       6      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
                                      HHHHHHHHHHH.S---SHHHHHHHHHTTT----HHHHHHHHHHHT- CS
                     Arg_repressor  6 rqklikkiike.ekissQkelvelLkeeGidvtQatvSRdLkelgl 50
                                      r k +++i+ + e+  +  e++ +L+e+G+dv+ +tvS  L+ l  
  gi|313117256|ref|YP_004044239.1|  9 REKELLAILRRsEQSLTSREVQRELREDGVDVVYSTVSATLDRLVE 54
                                      7788889997515556889*******************99998755 PP

>> DUF480  Protein of unknown function, DUF480
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.1e-06    0.0031      29      83 ..      23      77 ..      19     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.1e-06
                                      HHHHHHT-SSS-SS-----HHHHHHHHHHHHHTTSEEEE..--SS--EEEE-HHH CS
                            DUF480 29 alvaacNQkssRePvmelsesevqealdeLkkkklvseaseagsRvekyehrlee 83
                                      +l++   Q+  Re  +++  s+v+++ld+L +k+lv +++e++  + +y+h+++ 
  gi|313117256|ref|YP_004044239.1| 23 SLTSREVQRELREDGVDVVYSTVSATLDRLVEKRLVDRTEEMQRGSPRYRHTFAA 77
                                      5666667888999999999********************9************976 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.7   1.4e-05      0.02      28      65 ..      38      74 ..       6      76 .. 0.83
   2 ?   -2.4   0.0       4.6   6.9e+03      21      32 ..      88     100 ..      86     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                            HTH_27 28 lnvedshisyslkkLtekGLvertgdeadrrekrvrlT 65
                                      ++v +s++s  l++L+ek Lv rt+  + r++ r+r T
  gi|313117256|ref|YP_004044239.1| 38 VDVVYSTVSATLDRLVEKRLVDRTEE-MQRGSPRYRHT 74
                                      478899***************88888.99999999977 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.6
                            HTH_27  21 l.adlcgrlnved 32 
                                       + +d++++l ++ 
  gi|313117256|ref|YP_004044239.1|  88 IvEDVSEVLGTDG 100
                                       4488888888765 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   9.2e-06     0.014       1      60 [.      13      70 ..      13      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.2e-06
                                      HHHHH..CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-E CS
                              PadR  1 iLall..eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegppr 60
                                      +La+l  +eq +   e+ +el+e   g +++ ++++  +L+rL +++lv++++e + +g pr
  gi|313117256|ref|YP_004044239.1| 13 LLAILrrSEQSLTSREVQRELRED--G-VDVVYSTVSATLDRLVEKRLVDRTEEMQ-RGSPR 70
                                      57888434588899999*******..9.8***********************9996.56665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.8   2.9e-05     0.044       7      55 ..      10      62 ..       5      67 .. 0.72
   2 ?   -1.4   0.0       1.5   2.2e+03      39      48 ..     102     111 ..      92     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHHHCTTTSEEEHHHHHHHH.....TSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrl.....glsksavsrilkrLvaaGLverrp 55
                                      +  +La L+r++   lt +e+ r+l     ++  s+vs +l+rLv++ Lv r++
  gi|313117256|ref|YP_004044239.1| 10 EKELLAILRRSEQS-LTSREVQRELredgvDVVYSTVSATLDRLVEKRLVDRTE 62
                                      55677777777764.7777777755333115667****************9984 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                                       HHHHHHHHHT CS
                            MarR_2  39 srilkrLvaa 48 
                                       + +++r++a 
  gi|313117256|ref|YP_004044239.1| 102 TGLVRRAEAM 111
                                       6667777765 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.6e-05     0.054       7      83 ..      15      94 ..      13      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                           DUF4364  7 Yllkkvkfpltnsqlseiileney.tnYfdlqqalseLvesglieee..ekenktlykiTekGketlelfenripksir 82
                                       +l++ +++lt  ++ + + e+++ + Y +++ +l+ Lve+ l++ +   ++++ +y+ T + ++ + ++ ++i +++ 
  gi|313117256|ref|YP_004044239.1| 15 AILRRSEQSLTSREVQRELREDGVdVVYSTVSATLDRLVEKRLVDRTeeMQRGSPRYRHTFAADQYAGELLDSIVEDVS 93
                                      589999999999999999887775499*****************9884345999*******999999999999988876 PP

                           DUF4364 83 e 83
                                      e
  gi|313117256|ref|YP_004044239.1| 94 E 94
                                      5 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   7.9e-05      0.12      10      40 ..      20      50 ..      11      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                     HTH_Tnp_Tc3_2 10 kdPritlreLanelkeeGksvsreTirrrLr 40
                                       + + t+re+++el e+G+ v  +T++ +L 
  gi|313117256|ref|YP_004044239.1| 20 SEQSLTSREVQRELREDGVDVVYSTVSATLD 50
                                      44559*********999**********9995 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   7.7e-05      0.12      30      73 .]       7      49 ..       4      49 .. 0.78
   2 ?    1.3   0.0      0.36   5.3e+02       1      28 [.      44      72 ..      44      95 .. 0.52
   3 ?   -1.4   0.0       2.5   3.7e+03      12      18 ..      99     105 ..      70     116 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-05
                            HTH_32 30 sdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73
                                       +++++ +  l+r+e  ++ r+++++l +++gv+v +stv   L
  gi|313117256|ref|YP_004044239.1|  7 GPREKELLAILRRSEQSLTSREVQREL-REDGVDVVYSTVSATL 49
                                      56666666666655779**********.8889********8765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.36
                            HTH_32  1 TvsrwlkRyneeGlegLkdr...prrgrpr.k 28
                                      Tvs +l R  e     L dr    +rg pr +
  gi|313117256|ref|YP_004044239.1| 44 TVSATLDRLVEK---RLVDRteeMQRGSPRyR 72
                                      566666665555...44544333334455443 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.5
                            HTH_32  12 eGlegLk 18 
                                       +Gl gL 
  gi|313117256|ref|YP_004044239.1|  99 DGLTGLV 105
                                       4555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   0.00014      0.21      19      58 ..      20      64 ..       6      77 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                      HHCCCHHCHHCCC.....TTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 19 klgpatadeiaee.....lgvprskvYevLrsLedkGlVerekgr 58
                                      +++++t +e+ +e     ++v +s+v  +L +L++k lV+r ++ 
  gi|313117256|ref|YP_004044239.1| 20 SEQSLTSREVQRElredgVDVVYSTVSATLDRLVEKRLVDRTEEM 64
                                      5556666666665222225899*******************9876 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   0.00014      0.21       2      51 ..      12      61 ..      11      68 .. 0.91
   2 ?   -3.4   0.0       6.8     1e+04      45      54 ..      99     108 ..      95     111 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrv 51
                                      e L+il +s++ + ++e+  eL++ g d+   +v   L  l e+ l+ r 
  gi|313117256|ref|YP_004044239.1| 12 ELLAILRRSEQSLTSREVQRELREDGVDVVYSTVSATLDRLVEKRLVDRT 61
                                      689**************************999999999999999999886 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.8
                            HTH_12  45 rgltrrvgya 54 
                                       +glt  v++a
  gi|313117256|ref|YP_004044239.1|  99 DGLTGLVRRA 108
                                       5555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 879.24
//
Query:       gi|313117257|ref|YP_004044240.1|  [L=171]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-18   64.8   1.7    1.7e-17   63.7   1.7    1.6  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
     0.0022   18.1   2.7      0.044   13.9   2.8    2.2  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
       0.19   11.7   1.3       0.45   10.5   0.1    2.1  3  CBM_20        Starch binding domain
       0.41   10.4   2.0        4.5    7.1   0.1    2.2  2  PKD_3         PKD-like domain


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   1.7   3.7e-21   1.7e-17       6      98 ..      67     170 ..      62     171 .] 0.87

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 3.7e-21
                                       EETTET.SEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTC..........EEEEBSTTEEEE CS
                       Copper-bind   6 gvesgd.lqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaed..........etkliggGekds 71 
                                       +v+ +d l+F +k+i+v++g++vt++n  ++gH v   +d++p+g+  +++   d          ++  +++G +++
  gi|313117257|ref|YP_004044240.1|  67 TVDMNDeLKFAPKRIKVESGTTVTWKNVGAVGHTVTAYEDEIPDGATYFASGGFDsekaakdgypDKGNVTEGGTYE 143
                                       5778888********************************99999988777655555567777898555677899*** PP

                                       EEEESSEEEEEEETTTTTTTSEEEEEE CS
                       Copper-bind  72 vtfdeagtYkffCsPHaaagMkgkvtv 98 
                                        tf+++gtYk++C PH +  M+g v+v
  gi|313117257|ref|YP_004044240.1| 144 HTFETKGTYKYYCVPHEMNAMVGYVKV 170
                                       *************************98 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.8   9.7e-06     0.044      18      96 ..      61     160 ..      30     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                      Cupredoxin_1  18 aaektveitvkdg.gfePskievkagekvklkiknkdktpeefesed........................lgeekv 69 
                                       + +kt ++ ++d+ +f P++i+v++g+  ++++kn ++  +++++++                           + +
  gi|313117257|ref|YP_004044240.1|  61 KWTKTDTVDMNDElKFAPKRIKVESGT--TVTWKNVGAVGHTVTAYEdeipdgatyfasggfdsekaakdgYPDKGN 135
                                       445667888888789***********9..899******988887777777777777777776666677766556678 PP

                      Cupredoxin_1  70 lapgktttitiaplkpGeYeftcdmhm 96 
                                       ++ g t++ t+  +++G+Y+++c  h+
  gi|313117257|ref|YP_004044240.1| 136 VTEGGTYEHTF--ETKGTYKYYCVPHE 160
                                       99999999999..89999999997554 PP

>> CBM_20  Starch binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.62   2.8e+03      16      28 ..      12      24 ..       5      27 .. 0.84
   2 ?   10.5   0.1    0.0001      0.45      40      81 ..      52      95 ..      39     107 .. 0.77
   3 ?   -1.9   0.0      0.74   3.3e+03      59      70 ..     147     158 ..     133     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.62
                            CBM_20 16 esvyivGsiseLG 28
                                      +++ i+G ++ LG
  gi|313117257|ref|YP_004044240.1| 12 KQIGITGTVALLG 24
                                      7899***999999 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0001
                            CBM_20 40 aseqtssyplWst..tvslpagtkieYkyikkdsdgsvtWesge 81
                                      ++ ++s+ + W+   tv+++ + k+  k ik++s  +vtW++  
  gi|313117257|ref|YP_004044240.1| 52 PKDSSSDGEKWTKtdTVDMNDELKFAPKRIKVESGTTVTWKNVG 95
                                      334456788999878999999999****************9854 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.74
                            CBM_20  59 gtkieYkyikkd 70 
                                       +tk  Yky+ + 
  gi|313117257|ref|YP_004044240.1| 147 ETKGTYKYYCVP 158
                                       455668887765 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.001       4.5      14      43 ..      67      97 ..      63     108 .. 0.85
   2 ?    2.7   0.3     0.025   1.1e+02      44      61 ..     136     153 ..     129     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.001
                             PKD_3 14 kvkvgreltiaPtvenaenaa.faWtieGki 43
                                      +v ++ el++aP+  ++e  +   W+  G++
  gi|313117257|ref|YP_004044240.1| 67 TVDMNDELKFAPKRIKVESGTtVTWKNVGAV 97
                                      6899*********99999998899*988865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.025
                             PKD_3  44 vsteptytfteeelgsye 61 
                                       v +  ty+ t+e++g+y+
  gi|313117257|ref|YP_004044240.1| 136 VTEGGTYEHTFETKGTYK 153
                                       777889999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1274.79
//
Query:       gi|313117258|ref|YP_004044241.1|  [L=672]
Description: nitrous oxide reductase apoprotein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-33  113.4   0.0    1.1e-32  112.2   0.0    1.7  1  nos_propeller_2  Nitrous oxide reductase propeller repeat 2
    8.5e-29   99.3   0.6    2.7e-27   94.5   0.2    3.1  3  nos_propeller    Nitrous oxide reductase propeller repeat
      2e-07   31.1   0.0    4.9e-07   29.8   0.0    1.7  1  Cupredoxin_1     Cupredoxin-like domain
    1.5e-05   24.6   3.6    2.3e-05   24.0   3.6    1.3  1  TAT_signal       TAT (twin-arginine translocation) pathway si
      3e-05   23.9   0.0    8.6e-05   22.4   0.0    1.7  1  COX2             Cytochrome C oxidase subunit II, periplasmic
  ------ inclusion threshold ------
      0.068   14.1   0.8         28    5.8   0.0    4.0  4  WD40             WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> nos_propeller_2  Nitrous oxide reductase propeller repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.0   3.6e-36   1.1e-32       1      69 [.     212     279 ..     212     280 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 3.6e-36
                   nos_propeller_2   1 iPNvqaiHGlrvqkvPktkyvfangEfrvPlpndGrdlddpekyvslfsaidaetmevawqviVdGNLD 69 
                                       +PNvq++HG+++q  P+t+yvfangEfr+PlpndGrd+ddp+kyvslfsaid+e+m+v wqv V+GNLD
  gi|313117258|ref|YP_004044241.1| 212 VPNVQSVHGCCIQ-SPDTEYVFANGEFRAPLPNDGRDVDDPSKYVSLFSAIDPESMDVLWQVKVSGNLD 279
                                       8************.6*****************************************************9 PP

>> nos_propeller  Nitrous oxide reductase propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.37   1.1e+03      20      53 ..     180     212 ..     164     217 .. 0.75
   2 ?    0.3   0.0      0.23   6.8e+02      19      33 ..     370     384 ..     363     387 .. 0.85
   3 !   94.5   0.2   8.9e-31   2.7e-27       1      71 []     458     534 ..     458     534 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.37
                     nos_propeller  20 epdGkylvalnKlskdrflpvGplkpeneqLidi 53 
                                       + dG+yl++  K + +r ++v  +  e++ ++d+
  gi|313117258|ref|YP_004044241.1| 180 KYDGEYLFVNDK-ANGRVARVNLKYFETDAILDV 212
                                       568999999888.678888888888888888876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.23
                     nos_propeller  19 kepdGkylvalnKls 33 
                                       ++pdGky ++  Kls
  gi|313117258|ref|YP_004044241.1| 370 VTPDGKYGIVAGKLS 384
                                       68********99998 PP

  == domain 3  score: 94.5 bits;  conditional E-value: 8.9e-31
                     nos_propeller   1 kvdvhYniGHlsaaegdtkepdGkylvalnKlskdrflpvGplkpeneqLidisgek......mklladaptlgEPH 71 
                                       k+dvhYn+GH++a+++ ++ep+G++lv+lnKlskdrflpvGp +p+n+qLi i ++k      m+l++d+p+++EPH
  gi|313117258|ref|YP_004044241.1| 458 KIDVHYNPGHIQAVQAMSVEPTGDWLVVLNKLSKDRFLPVGPIHPDNDQLIYIGNDKdnetggMELVSDHPVYPEPH 534
                                       79*************************************************999887778888************** PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.6e-10   4.9e-07      19      94 ..     573     653 ..     561     668 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.6e-10
                      Cupredoxin_1  19 aektveitvkdg..gfePskievkagekvklkiknkdktp...eefesedlgeekvlapgktttitiaplkpGeYef 90 
                                       ++ tve+ ++++  +f   + +vk+g +v+++++n  k+p   + + +++ +++  lap++t ++t+a+++pG Y +
  gi|313117258|ref|YP_004044241.1| 573 DDSTVEVNMSSKrsEFGLREFTVKEGDEVQMTVTNIEKSPdiiHGVAIPEHDINLALAPQDTREVTFAADDPGVYWI 649
                                       55566666555444999**********************9999********************************** PP

                      Cupredoxin_1  91 tcdm 94 
                                       +c +
  gi|313117258|ref|YP_004044241.1| 650 YCTY 653
                                       **85 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   3.6   7.8e-09   2.3e-05       4      25 ..      59      80 ..      56      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.8e-09
                        TAT_signal  4 RRdFLKgsAAaaAAaalggcaa 25
                                      RRdF+K++AA++ ++ ++gca+
  gi|313117258|ref|YP_004044241.1| 59 RRDFMKAGAAVGVLGSVAGCAG 80
                                      ********************97 PP

>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.9e-08   8.6e-05      53     113 ..     602     662 ..     585     669 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.9e-08
                              COX2  53 etkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssm 113
                                       ++++  +  + d++h  a+p   +     p    +v++ +d +Gv++  c+ +c ++h  m
  gi|313117258|ref|YP_004044241.1| 602 QMTVTNIEKSPDIIHGVAIPEHDINLALAPQDTREVTFAADDPGVYWIYCTYFCSALHLEM 662
                                       44555566689***********************************************888 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         6   1.8e+04      13      26 ..     218     232 ..     214     235 .. 0.68
   2 ?    2.7   0.1      0.09   2.7e+02      18      30 ..     283     295 ..     267     298 .. 0.80
   3 ?    0.3   0.0      0.52   1.5e+03      14      36 ..     366     389 ..     357     391 .. 0.78
   4 ?    5.8   0.0    0.0095        28       8      26 ..     465     484 ..     457     494 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6
                                       EEEEE.EETTSSEEE CS
                              WD40  13 vtsla.fspdgawla 26 
                                       v++++  spd  +++
  gi|313117258|ref|YP_004044241.1| 218 VHGCCiQSPDTEYVF 232
                                       654444899988875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.09
                                       EETTSSEEEEEET CS
                              WD40  18 fspdgawlasGsd 30 
                                        ++dg+wl+s+s+
  gi|313117258|ref|YP_004044241.1| 283 SDKDGRWLLSSSY 295
                                       799******9984 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.52
                                       EEEEEETTSSE.EEEEETTSEEEE CS
                              WD40  14 tslafspdgaw.lasGsdDgtvri 36 
                                       +++ + pdg++ +++G   +tv i
  gi|313117258|ref|YP_004044241.1| 366 HCVEVTPDGKYgIVAGKLSPTVSI 389
                                       7999*******9877844666665 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0095
                                       ESS.SSEEEEEEETTSSEEE CS
                              WD40   8 tGH.ssvtslafspdgawla 26 
                                        GH + v ++++ p g+wl+
  gi|313117258|ref|YP_004044241.1| 465 PGHiQAVQAMSVEPTGDWLV 484
                                       59999999999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 4494.79
//
Query:       gi|313117259|ref|YP_004044242.1|  [L=254]
Description: hypothetical protein Hbor_30440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1758.49
//
Query:       gi|313117260|ref|YP_004044243.1|  [L=460]
Description: nitrous oxidase accessory protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-56  190.2  15.0    9.6e-54  182.2  14.2    2.1  2  NosD        Periplasmic copper-binding protein (NosD)
    1.1e-26   93.6  15.9    4.5e-19   68.9   3.9    2.3  2  Beta_helix  Right handed beta helix region
    1.3e-05   24.6   6.7       0.05   12.9   0.0    2.3  2  DUF1565     Protein of unknown function (DUF1565)
  ------ inclusion threshold ------
      0.019   15.5   0.4      0.019   15.5   0.4    3.0  3  VCBS        Repeat domain in Vibrio, Colwellia, Bradyrhizobiu
       0.13   12.1   0.0       0.27   11.0   0.0    1.5  1  Lsm_C       Lsm C-terminal


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   7.3e-05      0.26      37     103 ..     116     187 ..      85     191 .. 0.67
   2 !  182.2  14.2   2.7e-57   9.6e-54       2     236 ..     181     406 ..     180     411 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.3e-05
                              NosD  37 srdgilldnssnntitgntienl.......ryGihlensesntiedntlssnesGialmsssnntlenNtisnn 103
                                       ++d++   +++++t+++  i+n+       ++Gi++++++  +i d+ l++ + Gi++    +  l+nNti + 
  gi|313117260|ref|YP_004044243.1| 116 TEDAL-TIDADGVTVRRIWIHNSgrdtgsnDAGIWVNGTDA-RILDSRLTDVTFGIWVNGVDDVLLRNNTIVGR 187
                                       44444.55566666666666666666666677777777776.77777777777777777777667777777664 PP

  == domain 2  score: 182.2 bits;  conditional E-value: 2.7e-57
                              NosD   2 nnaisgdevlvsa..rgngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedn 76 
                                       nn+i g+e ++    rgngiql+++++ ++ +n+i+++rdg++++++sn+t ++nt+++lryG+h+++s+++++++n
  gi|313117260|ref|YP_004044243.1| 181 NNTIVGREAVRPLsyRGNGIQLWKTTDTRVVENRITDVRDGLYYSWASNVTARENTMWELRYGVHYMYSDDCRLQNN 257
                                       789999996555589************************************************************** PP

                              NosD  77 tlssnesGialmsssnntlenNtisnnen...yGillsdssnntisnNtisnnnkGiflensssntitgNriesnqk 150
                                       t ++n+ G+alm s++  + +N++ nn++   +Gill++++++ +++N+++ n++Gi++ ns +n++ +N + +n +
  gi|313117260|ref|YP_004044243.1| 258 TSFDNDVGYALMLSEHIEVVDNVAVNNTGvsgHGILLKRIDDSVVRGNHFVGNDRGIYVLNSVRNVMANNLVMEN-G 333
                                       *****************999*******************************************************.* PP

                              NosD 151 iGilllsssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYei 227
                                       iG++l++++e+ ++++N+F+nn  +v  ++++   Wn ++            +GNyWs  d +D d+DGi+D+ Y++
  gi|313117260|ref|YP_004044243.1| 334 IGVHLTAGTEDERVFGNSFVNNDRSVFAVTGELAVWNASE------------RGNYWSSADAADIDNDGISDVRYRP 398
                                       ****************************************............***********************99 PP

                              NosD 228 ndgviDylp 236
                                       ++ v   l+
  gi|313117260|ref|YP_004044243.1| 399 SGLV-EHLI 406
                                       8876.5555 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   3.9   1.2e-22   4.5e-19       7     157 ..     124     280 ..     118     285 .. 0.87
   2 !   30.0   7.7   1.1e-10     4e-07      59     140 ..     276     357 ..     271     390 .. 0.57

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1.2e-22
                                       SS-E.EEESEEEES-......SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---........S CS
                        Beta_helix   7 gssnvtiknntisns......ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn........g 69 
                                        +++ t++   i+ns      +++Gi+++g++  +i ++++++  ++Gi+++g++++ ++nnti +          g
  gi|313117260|ref|YP_004044243.1| 124 ADGV-TVRRIWIHNSgrdtgsNDAGIWVNGTDA-RILDSRLTD-VTFGIWVNGVDDVLLRNNTIVGREavrplsyrG 197
                                       4455.8888888888999999999999999999.777799999.999999999999999999997777777777777 PP

                                       EEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT CS
                        Beta_helix  70 ggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvg 146
                                        gi l ++  + +  n+itd ++ G+y + +sn+t ++N++ + + +G+++++s+ +++ +nNt ++n+ +G a++ 
  gi|313117260|ref|YP_004044243.1| 198 NGIQLWKTTDTRVVENRITDVRD-GLYYSWASNVTARENTMWELR-YGVHYMYSD-DCRLQNNTSFDND-VGYALML 270
                                       89999999999999999999999.999988999999999999999.999999999.9999999999998.9999999 PP

                                       -SS--EEES-E CS
                        Beta_helix 147 sssnvtvrnNt 157
                                       s + ++v+ N+
  gi|313117260|ref|YP_004044243.1| 271 SEH-IEVVDNV 280
                                       999.8888886 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 1.1e-10
                                       EES-EEE---...SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES- CS
                        Beta_helix  59 isnntisdnn...gggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnN 132
                                       + +n+  +n+   g gi l+  + +++++n++  n++ Giy+ +s +n++ nN + +n+  G++++++  + +v++N
  gi|313117260|ref|YP_004044243.1| 276 VVDNVAVNNTgvsGHGILLKRIDDSVVRGNHFVGNDR-GIYVLNSVRNVMANNLVMENG-IGVHLTAGTEDERVFGN 350
                                       4444444444454555555555555555555555554.555555555555555555555.55555555544444555 PP

                                       EEES-SSE CS
                        Beta_helix 133 titnnkga 140
                                       +++nn+  
  gi|313117260|ref|YP_004044243.1| 351 SFVNND-R 357
                                       555554.2 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.4e-05      0.05      96     194 ..     123     245 ..      80     265 .. 0.74
   2 !   10.7   5.6   6.7e-05      0.24     116     221 ..     266     358 ..     252     380 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                           DUF1565  96 laneatiaGvtitNp...nilkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGns....ilfek 165
                                        a+ +t++ + i N    +  ++ g++++++ a+i +  +t+ +  Gi v+  +      +n+i+G +    +  + 
  gi|313117260|ref|YP_004044243.1| 123 DADGVTVRRIWIHNSgrdTGSNDAGIWVNGTDARILDSRLTD-VTFGIWVNGVD-DVLLRNNTIVGREavrpLSYRG 197
                                       456688888999999553238999******************.589*******7.999999*****99443333555 PP

                           DUF1565 166 nGiaisgasaa..venkien.................NiivkNliGvv 194
                                       nGi+  +++ +  ven+i +                 N++ + ++Gv 
  gi|313117260|ref|YP_004044243.1| 198 NGIQLWKTTDTrvVENRITDvrdglyyswasnvtareNTMWELRYGVH 245
                                       577655555444455666556677777777755555555555555666 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.7e-05
                           DUF1565 116 tgvliesasakianNtitgniadGievsiyeaktgaggniisGnsilfeknGiaisgasaavenkienNiivkNliG 192
                                       +++++++  +++ +N   +n   G++ +   + + + + ++ Gn+   + +Gi      ++v n + nN++++N iG
  gi|313117260|ref|YP_004044243.1| 266 YALMLSE-HIEVVDNVAVNN--TGVSGHGI-LLKRIDDSVVRGNHFVGNDRGIYVL---NSVRNVMANNLVMENGIG 335
                                       4444433.556666666664..68888888.5788999***************864...5677899*********** PP

                           DUF1565 193 vvanalalDlGsgsegsaGnNifsnnaea 221
                                       v    +a   G++ e   G N f nn + 
  gi|313117260|ref|YP_004044243.1| 336 VHL--TA---GTEDERVFG-NSFVNNDRS 358
                                       993..34...777776666.888888765 PP

>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.1      0.19   6.8e+02       2      27 ..     111     138 ..     111     168 .. 0.60
   2 ?   -2.6   0.1       2.4   8.6e+03       6      28 ..     173     200 ..     172     222 .. 0.61
   3 ?   15.5   0.4   5.3e-06     0.019      35      59 ..     369     394 ..     345     395 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                              VCBS   2 ldgDGrlDlvvandgglrv...yrnngdG 27 
                                       +dgD   D + ++ +g++v   +++n +G
  gi|313117260|ref|YP_004044243.1| 111 IDGDETEDALTIDADGVTVrriWIHN-SG 138
                                       699********996665554333333.22 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                              VCBS   6 GrlDlvva.....ndgglrvyrnngdGt 28 
                                       G +D+++      +++++r + ++g+G 
  gi|313117260|ref|YP_004044243.1| 173 GVDDVLLRnntivGREAVRPLSYRGNGI 200
                                       5667776644443445566666666664 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 5.3e-06
                              VCBS  35 tslgg.sgggtgvavgDlDgDGdlDl 59 
                                       +  ++ ++++ +++++D+D+DG  D+
  gi|313117260|ref|YP_004044243.1| 369 WNASErGNYWSSADAADIDNDGISDV 394
                                       333442667779**********9996 PP

>> Lsm_C  Lsm C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.7e-05      0.27      27      52 ..     273     298 ..     270     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.7e-05
                                       EEEETTTEEEETTEEE--SHHHHHHH CS
                             Lsm_C  27 vvvvldrikVsekGVeGsGplAervy 52 
                                        ++v d++ V + GV G G l +r+ 
  gi|313117260|ref|YP_004044243.1| 273 HIEVVDNVAVNNTGVSGHGILLKRID 298
                                       699******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 3190.73
//
Query:       gi|313117261|ref|YP_004044244.1|  [L=322]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-32  110.8   0.0    5.5e-31  107.9   0.0    2.0  2  ABC_tran     ABC transporter
    1.8e-12   47.7   0.4    3.8e-08   33.5   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0013   19.4   0.0     0.0023   18.6   0.0    1.5  1  DUF4162      Domain of unknown function (DUF4162)
     0.0063   16.9   0.0      0.012   16.0   0.0    1.5  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.019   15.0   0.3       0.28   11.3   0.3    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
      0.019   14.9   0.1      0.033   14.1   0.1    1.3  1  RsgA_GTPase  RsgA GTPase
      0.026   14.2   0.6      0.056   13.2   0.6    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.049   13.1   0.0         10    5.5   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   2.5e-34   5.5e-31       1     137 []      19     161 ..      19     161 .. 0.98
   2 ?    0.6   0.0      0.34   7.5e+02      81     134 ..     192     249 ..     171     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 2.5e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ +sl++++g++ +++G nGaGKStL+kl+ g+++p+ G++ + g+++++   +  r+e+g+lp+++ + p lt r
  gi|313117261|ref|YP_004044244.1|  19 LDGLSLSIEPGTTFGLLGTNGAGKSTLFKLVVGHVRPDTGTVSVAGQNVET-AGPAIRSEVGYLPEHAGFPPALTGR 94 
                                       6899**********************************************9.99*********************99 PP

                                       HH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e            ++d++ie +ls +gl + +d++       +S G+ +r+ la all++p++lllDEpta
  gi|313117261|ref|YP_004044244.1|  95 EVlefhakmrgldDADDRIESVLSLVGLRDAADRRT----GGYSNGMNRRLGLATALLSRPTILLLDEPTA 161
                                       99**********99999*************999999....*****************************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.34
                                       HHTCHHHHHHHSTTGG....TTCBGESTTS....GGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxxxxxxxxxxx....xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  81 sdeeiekalsklglke....lkdtvvkssp....ssLSgGqkqrvalarallkkpkllllDE 134
                                         +e+ek+ +++g+++     +            + L  G ++rv la a   +    ++DE
  gi|313117261|ref|YP_004044244.1| 192 VLSEVEKLCDTVGIVHngrlRAGGS----VealkRDLIDGVRVRVRLADAGSMADATSVVDE 249
                                       5567888888888888443333333....2444599999999***99999877777777776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   4.2e-05     0.095       3      39 ..      33      63 ..      32      77 .. 0.82
   2 !   33.5   0.0   1.7e-11   3.8e-08     189     297 ..     103     191 ..      83     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsgg 39
                                      +l G Ng+GKS+L+++        ++v+++t + s  
  gi|313117261|ref|YP_004044244.1| 33 GLLGTNGAGKSTLFKLV------VGHVRPDTGTVSVA 63
                                      699************99......77777777776655 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 1.7e-11
                            AAA_21 189 vrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDE 265
                                       +r+l++++++++  +  + l + +d+r  +                   S G+ r l+l+tall+++   ++ll+DE
  gi|313117261|ref|YP_004044244.1| 103 MRGLDDADDRIESVLSLVGLRDAADRRTGG------------------YSNGMNRRLGLATALLSRP---TILLLDE 158
                                       666677777777777776666666666544..................7******************...******* PP

                            AAA_21 266 pEngLHPkllrrllellkelsr.ngaQviltTH 297
                                       p +gL+P+ ++ + +++++l+r  +  v+l++H
  gi|313117261|ref|YP_004044244.1| 159 PTAGLDPRGVAAFHDVVERLARdDDLTVVLSSH 191
                                       *******9999999***888888********** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     1e-06    0.0023       1      77 [.     215     298 ..     215     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1e-06
                                       E-HHHHHTTS.-SSEEEEE.-------..--.-EEE.....E-TTS-EEEEE-----------------EEEEEEEE CS
                           DUF4162   1 GtleeiKrsy.gknrieve.adaeelleepg.veev.....eeeggelelkledeeaanellkaltsgveirsFeee 69 
                                       G++e +Kr +  + r++v+ ada+++++  + v e      ++ ++e+++++++ e+++ ll+ l++ +++  +e++
  gi|313117261|ref|YP_004044244.1| 215 GSVEALKRDLiDGVRVRVRlADAGSMADATSvVDEHdgairSQSNREFTVECSS-EVPPGLLDDLMDAASLSGYEVT 290
                                       89999999999999999**99999999887756665665434444667777776.8********************* PP

                                       ---HHHHH CS
                           DUF4162  70 ePsLndIF 77 
                                       eP L+ +F
  gi|313117261|ref|YP_004044244.1| 291 EPGLEQVF 298
                                       ******** PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.2e-06     0.012      29     143 ..      34     158 ..      18     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.2e-06
                            AAA_16  29 lsGesGvGKsslvrellralekdggif.lrgkcdql.....esaipy...sa.laqalareellrqlldeaesaele 95 
                                       l G  G GKs+l + +  +++ d g + ++g++++      +s++ y    a +  al+ +e+l+  + +   + l+
  gi|313117261|ref|YP_004044244.1|  34 LLGTNGAGKSTLFKLVVGHVRPDTGTVsVAGQNVETagpaiRSEVGYlpeHAgFPPALTGREVLEFHAKM---RGLD 107
                                       789********************777779999999866555555555666555*******9999999999...8999 PP

                            AAA_16  96 awrekleeala......avpelagaea......srllellkrllallsrderplvlvlDd 143
                                       ++++++e++l+      a      a++      + +++ l  + allsr   p++l+lD+
  gi|313117261|ref|YP_004044244.1| 108 DADDRIESVLSlvglrdA------ADRrtggysNGMNRRLGLATALLSR---PTILLLDE 158
                                       999999999995544332......3335555656666666666666676...89999996 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00012      0.28       2      27 ..      32      58 ..      31     264 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHHTS.TEEES CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivs 27
                                      ++++G   +GKStL++  +g  +  ++
  gi|313117261|ref|YP_004044244.1| 32 FGLLGTNGAGKSTLFKLVVGHvRPDTG 58
                                      5899*************9996433332 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.5e-05     0.033      90     132 ..      19      62 ..       2      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgevse 132
                                       l+ l+  ++   t  l+G  G+GKStL + ++++ +  tg vs 
  gi|313117261|ref|YP_004044244.1|  19 LDGLSLSIEPgTTFGLLGTNGAGKSTLFKLVVGHVRPDTGTVSV 62 
                                       5566666666467779************************9996 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   2.5e-05     0.056      13      39 ..      20      46 ..      17      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      dg +++i++  ++ l G++G+GKSTl+
  gi|313117261|ref|YP_004044244.1| 20 DGLSLSIEPGTTFGLLGTNGAGKSTLF 46
                                      56677888777888***********96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0053        12      25      41 ..      29      46 ..      19      51 .. 0.76
   2 ?    5.5   0.0    0.0045        10     149     208 ..     141     199 ..     131     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0053
                                      SEEE.EEESTTSSHHHHH CS
                                      xxxx.xxxxxxxxxxxxx RF
                             SMC_N 25 sfta.ivGpNGSGKsnll 41
                                      + t+ ++G NG+GKs l+
  gi|313117261|ref|YP_004044244.1| 29 GTTFgLLGTNGAGKSTLF 46
                                      5544389********987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0045
                                       HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadkl 208
                                       L +A+   ++  + llDe  a LD + v+++ +++++   +  + v+ l++++l++++kl
  gi|313117261|ref|YP_004044244.1| 141 LGLATALLSRPTILLLDEPTAGLDPRGVAAFHDVVERLARDDDLTVV-LSSHVLSEVEKL 199
                                       55788888888999*********************987765444433.333444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 2124.42
//
Query:       gi|313117262|ref|YP_004044245.1|  [L=289]
Description: hypothetical protein Hbor_30470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-19   68.0  25.6    1.3e-17   64.1  25.6    2.0  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.072   12.6   9.9       0.22   11.1   9.7    1.9  1  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1  25.6   1.4e-21   1.3e-17       2     283 ..      30     284 ..      29     289 .] 0.82

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.4e-21
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       ++a+ Efr +vr+r+ ++l++l+ l+       + + ++  s+++ ++++++ ++++                    
  gi|313117262|ref|YP_004044245.1|  30 TVAGMEFRLSVRNRWAVALAALFTLF------ASLIVGFGASSVGPVRADAVIVSMA-S------------------ 81 
                                       78999*********************......3444556666677777766665333.2.................. PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                        +++ l+p+ a++fg+da++g +erg l + +++PvsR+ +++g  +g+++    ++ a+ +++ ++ ++  ++  +
  gi|313117262|ref|YP_004044245.1|  82 -LATYLLPLAALVFGFDAVVGAEERGWLDIVFALPVSRARVVVGSYLGRAVT---LVAATSIGFGIGGILLFSVASS 154
                                       .7899***********************************************...7777777766766666666666 PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindf 232
                                        ++  + ++++ sv+l+l   fla+g+++Ssv+ +++ a+ +al ++v +++  +++++g   l ag + pq+    
  gi|313117262|ref|YP_004044245.1| 155 ANTVLYATFLLGSVALGL--GFLAVGVFVSSVVGEKTHALGAALLVWVWFVFGHDLLALG---LVAGSKLPQSALSV 226
                                       677777777888888888..67************************************99...66677777778999 PP

                   ABC2_membrane_2 233 lsllsptsayntllneilagsdlna.......lgstatnllilllllavllvlgyvlF 283
                                       + l +p s++++ + + + +++           +s +  +++  ++ +v+++ ++ + 
  gi|313117262|ref|YP_004044245.1| 227 MVLSNPVSVFRVFVLSGIDSTGGGLatvvgesTLSMPLLAVAATVWVVVPVAAAARAV 284
                                       9999******976655554443233689999999999999999999999999998654 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.7   2.4e-05      0.22      60     161 ..     103     204 ..      50     247 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.4e-05
                   ABC2_membrane_5  60 ekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgnvtisevlls..iliglvialiflaiv 134
                                       e  +w  +++ LPv+r  +V   Yl+ ++  ++a+ i++ ++ i  +   +   ++vl++  +l +++++l fla+ 
  gi|313117262|ref|YP_004044245.1| 103 EERGWLDIVFALPVSRARVVVGSYLGRAVTLVAATSIGFGIGGILLFSVASS-ANTVLYAtfLLGSVALGLGFLAVG 178
                                       5589**********************************99998755544443.345555411444444667777776 PP

                   ABC2_membrane_5 135 lPlyfkfgvekgrivliiiifgiifll 161
                                         +    g ek+  +  ++ + ++f++
  gi|313117262|ref|YP_004044245.1| 179 VFVSSVVG-EKTHALGAALLVWVWFVF 204
                                       66666666.555543333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1914.33
//
Query:       gi|313117263|ref|YP_004044246.1|  [L=368]
Description: hypothetical protein Hbor_30480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-07   31.5   6.5      0.013   16.0   0.3    4.3  4  HtaA             Htaa
    4.4e-06   26.2   0.0        1.3    8.3   0.0    4.1  4  Sarcoglycan_1    Sarcoglycan complex subunit protein
    8.2e-05   21.9   9.2       0.97    8.5   6.3    3.9  3  DUF945           Bacterial protein of unknown function (DUF94
    8.6e-05   22.3   7.0       0.37   10.6   0.0    5.8  6  YabP             YabP family
    0.00024   21.4   7.3       0.49   10.7   0.4    6.4  6  DUF4968          Domain of unknown function (DUF4968)
    0.00026   20.9   0.0       0.89    9.4   0.0    3.2  3  DUF2345          Uncharacterized protein conserved in bacteri
    0.00035   20.4  11.4        3.3    7.7   0.1    7.2  8  Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal dom
     0.0043   16.9  16.0      0.075   12.8   7.8    3.1  2  DUF2807          Putative auto-transporter adhesin, head GIN 
  ------ inclusion threshold ------
      0.023   14.9   5.3        7.1    6.9   0.1    5.3  7  Imm50            Immunity protein 50
       0.03   14.1   2.4         71    3.3   0.0    5.1  5  DUF3868          Domain of unknown function, B. Theta Gene de
      0.041   14.6   1.5       0.56   10.9   0.1    3.5  3  Ribosomal_L6     Ribosomal protein L6
      0.061   13.9   0.0         42    4.8   0.0    3.9  3  LEA_2            Late embryogenesis abundant protein
      0.063   13.4   6.0        2.1    8.5   0.1    4.3  4  DNA_pol3_beta    DNA polymerase III beta subunit, N-terminal 
      0.069   13.5  11.2        7.6    6.9   0.1    5.8  3  PCC_BT           Propionyl-coenzyme A carboxylase BT domain
      0.098   13.0   0.4         73    3.8   0.0    4.6  4  DUF108           Domain of unknown function DUF108
       0.21   11.5   2.0       0.59   10.0   0.3    2.4  3  DUF4302          Domain of unknown function (DUF4302)
       0.33   11.1   1.9         39    4.4   0.2    3.4  3  MelC1            Tyrosinase co-factor MelC1
        4.3    7.5  22.8        4.1    7.6   0.8    6.0  7  HSP20            Hsp20/alpha crystallin family
        4.8    7.5  11.7         22    5.4   0.1    5.4  6  DUF2850          Protein of unknown function (DUF2850)


Domain annotation for each model (and alignments):
>> HtaA  Htaa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00037      0.35      23     108 ..      19     102 ..      10     124 .. 0.69
   2 ?    3.6   0.0     0.091        86      36      92 ..     101     158 ..      89     163 .. 0.61
   3 !   16.0   0.3   1.4e-05     0.013      28     140 ..     161     270 ..     154     277 .. 0.70
   4 ?    5.0   0.6     0.033        31      35      96 ..     244     323 ..     236     353 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                              HtaA  23 gswelsggakankggafqFpv.asgsvdkdtkkgeirfkGs.vhftghngaLdltlsnpkievsgetgtLladvssk 97 
                                         +e+s+   + +g++f+ ++ + g v+ ++++++i+++G  +  ++  +  ++++   +iev+g +g+L+ dv+ +
  gi|313117263|ref|YP_004044246.1|  19 FDVETSDERVELDGDDFDIEFrSDGRVEIEGDDFDIELDGDrIDLES--DDVEVEINGNEIEVEGRSGSLTLDVEYN 93 
                                       45666665544466777777744467777777888888887677666..7889999999**************9943 PP

                              HtaA  98 dkeggekvtke 108
                                        ++   +v+ +
  gi|313117263|ref|YP_004044246.1|  94 GND--LEVDSD 102
                                       222..233444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.091
                              HtaA  36 ggafqFpvasgsvdkdtk..kgeirfkGs.vhftghngaLdltlsnpkievsgetgtLla 92 
                                       +++f+ + ++g +d +++  +++i+ +G  v+ +g    +d+++   +ie++ +   + +
  gi|313117263|ref|YP_004044246.1| 101 SDDFEIERKNGEYDVESDneNLDIESDGDrVEIEGD--EFDIEFDGDTIEIQTDDFDVEI 158
                                       4666666677788544444599***99999999996..4555555555555444443333 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.4e-05
                              HtaA  28 sggakankggafqFpvasgsvdkdtkkgeirfkGs.vhftghngaLdltl...snpkievsgetgtLladvsskdke 100
                                       +g  +  ++++f+F+++ ++ d ++++++++f+G  ++++g +g ++ tl    n +++++g++    +d++ +d e
  gi|313117263|ref|YP_004044246.1| 161 DGDIEV-ETNDFDFEYDGSTLDLESDDFDVEFDGDrIEVEGDDGDFEFTLdtdDNGNVVFDGGR-D--VDIELDDIE 233
                                       444444.779******999***********************6666666622247788887743.2..333333566 PP

                              HtaA 101 ggekvtkedvalatldlsgakvkdgsvslsgapatltaeG 140
                                       ++  +++ +v+  +ld+++   +d+ v+++g +  +  +G
  gi|313117263|ref|YP_004044246.1| 234 VERDNDRAEVETDDLDFES---DDDRVDVEGDDFEIERDG 270
                                       6666666777777777755...677777777766666665 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.033
                              HtaA  35 kggafqFpvasgsvdkdtkkgeirfkGs.vhftgh.................ngaLdltlsnpkievsgetgtLlad 93 
                                       ++++++F+++   vd +++++ei+ +G   ++++                   g +d+++ + ++ev+ +   +  d
  gi|313117263|ref|YP_004044246.1| 244 ETDDLDFESDDDRVDVEGDDFEIERDGDrAEVESDdlefdsddgrvefefdgSGGIDIEIRDGRVEVETDDHDIEHD 320
                                       45666677766666666667777766666666666666666666666666688888888888888888887777777 PP

                              HtaA  94 vss 96 
                                        +s
  gi|313117263|ref|YP_004044246.1| 321 GDS 323
                                       553 PP

>> Sarcoglycan_1  Sarcoglycan complex subunit protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0014       1.3     166     223 ..      25      82 ..      15     111 .. 0.79
   2 !    7.0   0.0    0.0034       3.3     165     212 ..     118     165 ..     113     170 .. 0.79
   3 ?    2.3   0.0     0.092        87     166     223 ..     177     232 ..     165     245 .. 0.76
   4 ?    3.8   0.0     0.033        32     166     214 ..     245     292 ..     207     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0014
                     Sarcoglycan_1 166 dedLklesdtr.lslrgnegvrieakageieatslkdikLkssnGsivLdakgiflknl 223
                                       de  +l++d   +++r   +v+ie+ + +ie +  ++i L+s + ++ +++++i ++ +
  gi|313117263|ref|YP_004044246.1|  25 DERVELDGDDFdIEFRSDGRVEIEGDDFDIELD-GDRIDLESDDVEVEINGNEIEVEGR 82 
                                       666777777777888888888888888888888.8888888888888888887766554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0034
                     Sarcoglycan_1 165 adedLklesdtr.lslrgne.gvrieakageieatslkdikLkssn.Gsiv 212
                                        +e+L +esd++ ++++g e ++++++ ++ei+++   d++++    G i 
  gi|313117263|ref|YP_004044246.1| 118 DNENLDIESDGDrVEIEGDEfDIEFDGDTIEIQTD-DFDVEID--AdGDIE 165
                                       4799*******99*****9989**********999.4455544..335665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.092
                     Sarcoglycan_1 166 dedLklesdtr.lslrgnegvrieakageieatslkdikLkssn.GsivLdak...giflknl 223
                                       +++L lesd   ++++g  ++++e+ +g++e t      L++ + G++v+d++    i l++ 
  gi|313117263|ref|YP_004044246.1| 177 GSTLDLESDDFdVEFDGD-RIEVEGDDGDFEFT------LDTDDnGNVVFDGGrdvDIELDDI 232
                                       578999999988888886.58999999999988......777777999999987665555554 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.033
                     Sarcoglycan_1 166 dedLklesdtr.lslrgne.gvrieakageieatslkdikLkssnGsivLd 214
                                        +dL +esd + ++++g   +++ ++ + e+e +   d++++s +G++ ++
  gi|313117263|ref|YP_004044246.1| 245 TDDLDFESDDDrVDVEGDDfEIERDGDRAEVESD---DLEFDSDDGRVEFE 292
                                       4689999999989999976588888888888888...99999999999875 PP

>> DUF945  Bacterial protein of unknown function (DUF945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1     0.003       2.8     154     220 ..      19      90 ..      11     108 .. 0.63
   2 !    8.5   6.3     0.001      0.97     167     239 ..     108     180 ..      83     341 .. 0.60
   3 ?    2.2   0.1     0.084        79     138     210 ..     290     359 ..     274     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.003
                            DUF945 154 felkeeggklewsggkvkvdls......kdlkklsgegnldglkleadndeslelkgltlssdlkrgkeglyl 220
                                       f+++  ++++e +g +++++++         +++++e++ d ++le+d d+ +e++g +++++ + g+ +l++
  gi|313117263|ref|YP_004044246.1|  19 FDVETSDERVELDGDDFDIEFRsdgrveIEGDDFDIELDGDRIDLESD-DVEVEINGNEIEVEGRSGSLTLDV 90 
                                       555555566666655555555533333334677888888888888888.888888888888887777666655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.001
                            DUF945 167 ggkvkvdlskdlkklsgegnldglkleadndeslelkgltlssdlkrgkeglyl...Gdsslkiasltvssedqeg 239
                                         +++ d+++d ++l++e + d +++e+d + ++e++g t++ ++   ++++++   Gd +++ +++++  +++  
  gi|313117263|ref|YP_004044246.1| 108 RKNGEYDVESDNENLDIESDGDRVEIEGD-EFDIEFDGDTIEIQTD--DFDVEIdadGDIEVETNDFDFEYDGSTL 180
                                       44444444445555555555555555555.5555555555444442..3333334444444444444444433331 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.084
                            DUF945 138 rvgysgstsseltlpafel..keeggklewsggkvkvdlskdlkklsgegnldglkleadndeslelkgltlssd 210
                                        + ++gs+ +++++  +++  + ++ ++e +g +++v+ +    ++++e + d  ++e+d d ++e +g  l+++
  gi|313117263|ref|YP_004044246.1| 290 EFEFDGSGGIDIEIRDGRVevETDDHDIEHDGDSLEVETD----DFDFESDDDRTEFEDD-DHDIEHDGGDLDVE 359
                                       5788888888888888888777777888888888888877....7888888888888888.77776666555554 PP

>> YabP  YabP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00039      0.37      25      58 ..      17      50 ..      13      54 .. 0.92
   2 ?    4.8   0.2     0.025        24      21      47 ..      55      81 ..      54      95 .. 0.83
   3 ?    3.7   0.3     0.055        52      29      46 ..     124     141 ..     115     166 .. 0.52
   4 ?   -1.9   0.0       3.1   2.9e+03      21      30 ..     190     199 ..     173     206 .. 0.57
   5 ?   -1.1   0.0       1.8   1.7e+03      30      46 ..     251     267 ..     242     273 .. 0.78
   6 ?    0.5   0.0      0.57   5.4e+02      20      46 ..     301     327 ..     286     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                              YabP 25 eeirletkkgkltIkGenLhikklskgelkieGk 58
                                       ++ +et++ ++++ G+++ i+  s+g ++ieG+
  gi|313117263|ref|YP_004044246.1| 17 SNFDVETSDERVELDGDDFDIEFRSDGRVEIEGD 50
                                      56889****************************5 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.025
                              YabP 21 sfdeeeirletkkgkltIkGenLhikk 47
                                      + d ++i le+++ +++I+G++ +++ 
  gi|313117263|ref|YP_004044246.1| 55 ELDGDRIDLESDDVEVEINGNEIEVEG 81
                                      67889999************9999875 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.055
                              YabP  29 letkkgkltIkGenLhik 46 
                                       +e++  +++I+G+++ i+
  gi|313117263|ref|YP_004044246.1| 124 IESDGDRVEIEGDEFDIE 141
                                       555555555555555543 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3.1
                              YabP  21 sfdeeeirle 30 
                                       +fd ++i +e
  gi|313117263|ref|YP_004044246.1| 190 EFDGDRIEVE 199
                                       3444444443 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 1.8
                              YabP  30 etkkgkltIkGenLhik 46 
                                       e+++ ++ ++G++++i+
  gi|313117263|ref|YP_004044246.1| 251 ESDDDRVDVEGDDFEIE 267
                                       56667788999999987 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.57
                              YabP  20 lsfdeeeirletkkgkltIkGenLhik 46 
                                       ++  + ++ +et++  ++  G++L+++
  gi|313117263|ref|YP_004044246.1| 301 IEIRDGRVEVETDDHDIEHDGDSLEVE 327
                                       478889999*****9999999999987 PP

>> DUF4968  Domain of unknown function (DUF4968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.32     3e+02      49      78 ..      15      43 ..       6      48 .. 0.53
   2 ?    2.8   0.0      0.16   1.5e+02      52      80 ..      51      79 ..      45      88 .. 0.86
   3 !   10.7   0.4   0.00052      0.49      48      82 ..     129     166 ..      91     173 .. 0.77
   4 ?   -0.6   0.0       1.8   1.7e+03      49      65 ..     183     199 ..     163     220 .. 0.59
   5 ?    1.9   0.1      0.29   2.7e+02      54      70 ..     233     249 ..     195     297 .. 0.68
   6 ?    0.0   0.0       1.2   1.1e+03      50      68 ..     312     330 ..     288     347 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.32
                           DUF4968 49 ektefeveekedevvikTekltvkiekspl 78
                                      +  +f+ve  ++ v++ +++  ++   s++
  gi|313117263|ref|YP_004044246.1| 15 RSSNFDVETSDERVELDGDDFDIEFR-SDG 43
                                      34455555555555555555555544.444 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.16
                           DUF4968 52 efeveekedevvikTekltvkieksplri 80
                                      +f++e ++d + +++++++v+i+ ++ ++
  gi|313117263|ref|YP_004044246.1| 51 DFDIELDGDRIDLESDDVEVEINGNEIEV 79
                                      78999999**************9887765 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00052
                           DUF4968  48 d....ektefeveekedevvikTekltvkieksplrisf 82 
                                       d    e  ef++e ++d+++i+T++  v+i+ +++ i++
  gi|313117263|ref|YP_004044246.1| 129 DrveiEGDEFDIEFDGDTIEIQTDDFDVEID-ADGDIEV 166
                                       25555677899999999*******9999999.8888877 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.8
                           DUF4968  49 ektefeveekedevvik 65 
                                       e  +f+ve ++d ++++
  gi|313117263|ref|YP_004044246.1| 183 ESDDFDVEFDGDRIEVE 199
                                       34444444444444444 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.29
                           DUF4968  54 eveekedevvikTeklt 70 
                                       eve ++d  +++T++l 
  gi|313117263|ref|YP_004044246.1| 233 EVERDNDRAEVETDDLD 249
                                       45555555555555543 PP

  == domain 6  score: 0.0 bits;  conditional E-value: 1.2
                           DUF4968  50 ktefeveekedevvikTek 68 
                                       + + ++e+++d+++++T++
  gi|313117263|ref|YP_004044246.1| 312 TDDHDIEHDGDSLEVETDD 330
                                       4455667788888888876 PP

>> DUF2345  Uncharacterized protein conserved in bacteria (DUF2345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0     0.005       4.7      80     134 ..      28      81 ..      21      90 .. 0.80
   2 !    9.4   0.0   0.00094      0.89      78     147 ..     102     173 ..      85     176 .. 0.83
   3 ?   -0.4   0.0      0.99   9.4e+02     116     135 ..     293     313 ..     260     322 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.005
                           DUF2345  80 veiqAqsdalellAkkdvtvtStegkieisAkkeillaaggayirleggnIelgt 134
                                       ve+   + ++e  ++ +v+++  + +ie+  + +i l++ +  ++++g++Ie+++
  gi|313117263|ref|YP_004044246.1|  28 VELDGDDFDIEFRSDGRVEIEGDDFDIELDGD-RIDLESDDVEVEINGNEIEVEG 81 
                                       56666666788888999999999999999998.8999999999999999999876 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00094
                           DUF2345  78 gkveiqAqsdalellAk.kdvtvtStegkieisAkk.eillaaggayirleggnIelgtpGkievkaashsf 147
                                       ++ ei+ ++++ ++ ++ +++ ++S  +++ei+ ++  i++ +    i+ ++ ++e+ + G+iev++++++f
  gi|313117263|ref|YP_004044246.1| 102 DDFEIERKNGEYDVESDnENLDIESDGDRVEIEGDEfDIEFDGDTIEIQTDDFDVEIDADGDIEVETNDFDF 173
                                       5667777788888888625899************95478888877788889999***********9998887 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.99
                           DUF2345 116 laagga.yirleggnIelgtp 135
                                       + ++g+  i++ +g++e++t 
  gi|313117263|ref|YP_004044246.1| 293 FDGSGGiDIEIRDGRVEVETD 313
                                       445566688888999888886 PP

>> Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.022        21      21      51 .]      52      79 ..      13      79 .. 0.80
   2 !    7.7   0.1    0.0035       3.3      21      50 ..      68      98 ..      64      99 .. 0.89
   3 ?    2.9   0.0      0.11   1.1e+02      23      50 ..     104     132 ..     103     133 .. 0.88
   4 ?    0.7   0.0      0.55   5.2e+02      11      45 ..     137     169 ..     132     175 .. 0.69
   5 ?    4.2   0.1     0.044        42      12      44 ..     187     229 ..     181     236 .. 0.72
   6 ?    2.4   0.1      0.16   1.5e+02      21      51 .]     280     310 ..     248     310 .. 0.84
   7 ?    3.6   0.2     0.069        65      21      50 ..     299     325 ..     288     330 .. 0.74
   8 ?   -2.4   0.0         5   4.7e+03      36      44 ..     351     360 ..     331     364 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
                                      EEEEEESSEEEEEEESSSTEEEEETTEEEEE CS
                   Glyco_hydro_65C 21 LrVrvtpeevtvtlesgepltievyGeevtL 51
                                      ++++++ +++ ++      +++e++G+e+++
  gi|313117263|ref|YP_004044246.1| 52 FDIELDGDRIDLESD---DVEVEINGNEIEV 79
                                      556666665555555...7999999999875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0035
                                      EEEEEESSEEEEEEESSS.TEEEEETTEEEE CS
                   Glyco_hydro_65C 21 LrVrvtpeevtvtlesge.pltievyGeevt 50
                                      ++V+++ +e++v+ +sg+  l++e +G++++
  gi|313117263|ref|YP_004044246.1| 68 VEVEINGNEIEVEGRSGSlTLDVEYNGNDLE 98
                                      69**************888999999998876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.11
                                       EEEESSEEEEEEES.SSTEEEEETTEEEE CS
                   Glyco_hydro_65C  23 Vrvtpeevtvtles.gepltievyGeevt 50 
                                        ++++++ ++ +es  e+l+ie  G +v+
  gi|313117263|ref|YP_004044246.1| 104 FEIERKNGEYDVESdNENLDIESDGDRVE 132
                                       58999999*****8799*****9999986 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.55
                                       EEEEEETTEEEEEEEESSEEEEEEESSSTEEEEET CS
                   Glyco_hydro_65C  11 sFrlryRGrrLrVrvtpeevtvtlesgepltievy 45 
                                       +F + + G +++++ ++  v++ +     +++e +
  gi|313117263|ref|YP_004044246.1| 137 EFDIEFDGDTIEIQTDDFDVEIDAD--GDIEVETN 169
                                       5777777777887777777777776..35777666 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.044
                                       EEEEETTEEEEEEEESSEEEEEEESSS..........TEEEEE CS
                   Glyco_hydro_65C  12 FrlryRGrrLrVrvtpeevtvtlesge..........pltiev 44 
                                       F + + G r++V+ +++  ++tl +++           ++ie+
  gi|313117263|ref|YP_004044246.1| 187 FDVEFDGDRIEVEGDDGDFEFTLDTDDngnvvfdggrDVDIEL 229
                                       78889999***************98663334444444555555 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.16
                                       EEEEEESSEEEEEEESSSTEEEEETTEEEEE CS
                   Glyco_hydro_65C  21 LrVrvtpeevtvtlesgepltievyGeevtL 51 
                                       L+ + ++++v+++      ++ie+++ +v++
  gi|313117263|ref|YP_004044246.1| 280 LEFDSDDGRVEFEFDGSGGIDIEIRDGRVEV 310
                                       5566677788888887667999999999875 PP

  == domain 7  score: 3.6 bits;  conditional E-value: 0.069
                                       EEEEEESSEEEEEEESSSTEEEEETTEEEE CS
                   Glyco_hydro_65C  21 LrVrvtpeevtvtlesgepltievyGeevt 50 
                                       +++++++++v+v+  +    +ie+ G +++
  gi|313117263|ref|YP_004044246.1| 299 IDIEIRDGRVEVETDD---HDIEHDGDSLE 325
                                       7899999999999985...55666665554 PP

  == domain 8  score: -2.4 bits;  conditional E-value: 5
                                       S.SSTEEEEE CS
                   Glyco_hydro_65C  36 s.gepltiev 44 
                                       + g  l++e+
  gi|313117263|ref|YP_004044246.1| 351 HdGGDLDVEH 360
                                       1244455555 PP

>> DUF2807  Putative auto-transporter adhesin, head GIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   7.8   7.9e-05     0.075      15     133 ..      47     177 ..      13     190 .. 0.70
   2 !    7.3   1.1     0.004       3.7       9     114 ..     203     314 ..     189     354 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.9e-05
                                       EEE-SS-EEEEEEEHHHH..CCEEEEEETTEEEEEE-.......TTTTSSB.EEEEEEES--SEEEEECCEEEEE-S CS
                           DUF2807  15 vtqgdeqsvviegdenll..ekvevevedgtLkirle.......kefestktlkvtvtvpnleelelsgsgsieveg 82 
                                       + +gd + +++ gd+  l  ++veve+++++++++          e+++++   ++v + ++e  + +g++++e+++
  gi|313117263|ref|YP_004044246.1|  47 I-EGDDFDIELDGDRIDLesDDVEVEINGNEIEVEGRsgsltldVEYNGND---LEVDSDDFEIERKNGEYDVESDN 119
                                       3.4777888888887665224677777788888877766666555666666...99999999999999999999999 PP

                                       ............-EEEEEEEEEEECSEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEEEEEC CS
                           DUF2807  83 ............tlkadklelniagsgditlkldaeelsveasgsgdielsGtadrlevsvaG 133
                                                   ++++d+++++  g+   t+++++++++ve++  gdie++  +++++++ +G
  gi|313117263|ref|YP_004044246.1| 120 enldiesdgdrvEIEGDEFDIEFDGD---TIEIQTDDFDVEIDADGDIEVE--TNDFDFEYDG 177
                                       99999999999966666666666655...3556666666666666666654..3444444443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.004
                                       CCEEEEEEE-SS-EEEEEEEHHH...HCCEEEEEETTEEEEEE-.TTTTSSB.EEEEEEES--SEEEEECCEEEEE- CS
                           DUF2807   9 gsidvevtqgdeqsvviegdenl...lekvevevedgtLkirle.kefestktlkvtvtvpnleelelsgsgsieve 81 
                                       g +++++   d+ +vv  g +++   l+++eve ++++ +++++  +fes +  +v v+  ++e  +  + +++e++
  gi|313117263|ref|YP_004044246.1| 203 GDFEFTLDTDDNGNVVFDGGRDVdieLDDIEVERDNDRAEVETDdLDFESDD-DRVDVEGDDFEIERDGDRAEVESD 278
                                       4567777788888888888877544489999999999999999988888888.899999999999999999999999 PP

                                       S-EEEE....EEEEEEECSEEEEEEEEEEEEEEEEEC CS
                           DUF2807  82 gtlkad....klelniagsgditlkldaeelsveasg 114
                                       + l++d    ++e++  gsg i++++   +++ve ++
  gi|313117263|ref|YP_004044246.1| 279 D-LEFDsddgRVEFEFDGSGGIDIEIRDGRVEVETDD 314
                                       9.55441111567777999999999988888888765 PP

>> Imm50  Immunity protein 50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.8   1.7e+03      84     108 ..      19      42 ..       9      50 .. 0.70
   2 ?    0.8   0.0      0.58   5.4e+02      82     114 ..      35      65 ..      20      69 .. 0.75
   3 ?    2.1   0.1      0.23   2.2e+02      70     114 ..      92     135 ..      43     138 .. 0.72
   4 ?    1.7   0.0      0.31   2.9e+02      88     113 ..     126     150 ..     112     153 .. 0.80
   5 ?    0.0   0.0      0.99   9.3e+02      81     114 ..     170     200 ..     155     203 .. 0.70
   6 ?    0.2   0.1      0.87   8.2e+02      18      33 ..     227     242 ..     204     277 .. 0.61
   7 ?    6.9   0.1    0.0075       7.1      76     113 ..     274     311 ..     225     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                             Imm50  84 iskedsdlkvsiessegleislkcs 108
                                       ++ e+sd +v++++++ ++i+++ +
  gi|313117263|ref|YP_004044246.1|  19 FDVETSDERVELDGDD-FDIEFRSD 42 
                                       4455555669999999.99999876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.58
                             Imm50  82 ieiskedsdlkvsiessegleislkcssieies 114
                                       ++i+  +++ +v+ie+++ ++i+l  ++i +es
  gi|313117263|ref|YP_004044246.1|  35 FDIEFRSDG-RVEIEGDD-FDIELDGDRIDLES 65 
                                       555544444.89999999.99999999988876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.23
                             Imm50  70 isgfgteniidkieiskedsdlkvsiessegleislkcssieies 114
                                        +g   e   d++ei+++++++ v+ ++++ l+i+   +++eie+
  gi|313117263|ref|YP_004044246.1|  92 YNGNDLEVDSDDFEIERKNGEYDVESDNEN-LDIESDGDRVEIEG 135
                                       444445555678888888888888888888.88888888888775 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.31
                             Imm50  88 dsdlkvsiessegleislkcssieie 113
                                       +++ +v+ie++e ++i++  ++iei+
  gi|313117263|ref|YP_004044246.1| 126 SDGDRVEIEGDE-FDIEFDGDTIEIQ 150
                                       333579******.*********9997 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 0.99
                             Imm50  81 kieiskedsdlkvsiessegleislkcssieies 114
                                       +++++++     +++es++ +++++  ++ie+e+
  gi|313117263|ref|YP_004044246.1| 170 DFDFEYDG--STLDLESDD-FDVEFDGDRIEVEG 200
                                       34444433..458888888.99999999999985 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.87
                             Imm50  18 aeltsvllkregstls 33 
                                       +el++++++r++ + +
  gi|313117263|ref|YP_004044246.1| 227 IELDDIEVERDNDRAE 242
                                       4555555555322222 PP

  == domain 7  score: 6.9 bits;  conditional E-value: 0.0075
                             Imm50  76 eniidkieiskedsdlkvsiessegleislkcssieie 113
                                       e   d++e++++d+++++++++s g++i+++  ++e+e
  gi|313117263|ref|YP_004044246.1| 274 EVESDDLEFDSDDGRVEFEFDGSGGIDIEIRDGRVEVE 311
                                       556689**********************9998888887 PP

>> DUF3868  Domain of unknown function, B. Theta Gene description (DUF3868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.33   3.2e+02      12      49 ..       3      40 ..       1      49 [. 0.77
   2 ?    3.0   0.0     0.088        83      27      60 ..      69     102 ..      55     104 .. 0.87
   3 ?    1.0   0.0      0.39   3.6e+02      26      49 ..     113     136 ..     103     160 .. 0.68
   4 ?   -2.1   0.0       3.5   3.3e+03      28      48 ..     225     245 ..     223     258 .. 0.74
   5 ?    3.3   0.0     0.075        71      28      49 ..     308     329 ..     302     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.33
                           DUF3868 12 vlslnigeaeaq.rsyegkisvkpvqleqkGdslhidid 49
                                      ++ ++     a  rs + +++  + ++e +Gd   i++ 
  gi|313117263|ref|YP_004044246.1|  3 LSVMV-APVAAShRSSNFDVETSDERVELDGDDFDIEFR 40
                                      44444.4445555999****************9999875 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.088
                           DUF3868  27 egkisvkpvqleqkGdslhidididlenvkvksa 60 
                                       e++i+ +++++e + +sl +d++++ ++++v s 
  gi|313117263|ref|YP_004044246.1|  69 EVEINGNEIEVEGRSGSLTLDVEYNGNDLEVDSD 102
                                       6788889999999999********9999999885 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.39
                           DUF3868  26 yegkisvkpvqleqkGdslhidid 49 
                                       y+++ + +++ +e +Gd + i+ d
  gi|313117263|ref|YP_004044246.1| 113 YDVESDNENLDIESDGDRVEIEGD 136
                                       666666677777777777777654 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.5
                           DUF3868  28 gkisvkpvqleqkGdslhidi 48 
                                       ++i++ ++++e++ d   ++ 
  gi|313117263|ref|YP_004044246.1| 225 VDIELDDIEVERDNDRAEVET 245
                                       567778888888887777765 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.075
                           DUF3868  28 gkisvkpvqleqkGdslhidid 49 
                                       ++++  ++ +e++Gdsl ++ d
  gi|313117263|ref|YP_004044246.1| 308 VEVETDDHDIEHDGDSLEVETD 329
                                       4577889************975 PP

>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00059      0.56       4      35 ..      67      98 ..      65     121 .. 0.82
   2 ?   -0.9   0.0       2.9   2.7e+03       8      28 ..     190     209 ..     185     245 .. 0.56
   3 ?   -0.6   0.0       2.3   2.2e+03      23      47 ..     298     312 ..     272     322 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00059
                                      TEEEEEETTTEEEEEESSEEEEEE-CTT.SEEE CS
                      Ribosomal_L6  4 gvrvsikggqlvlvlGpkgeltreipeg.vtve 35
                                      +v+v+i+g + + v G +g+lt+++ ++  ++e
  gi|313117263|ref|YP_004044246.1| 67 DVEVEING-NEIEVEGRSGSLTLDVEYNgNDLE 98
                                      79*****8.*************99987644444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.9
                                       EEETTTEEEEEESSEEEEEE- CS
                      Ribosomal_L6   8 sikggqlvlvlGpkgeltrei 28 
                                       + +g   + v G  g  ++++
  gi|313117263|ref|YP_004044246.1| 190 EFDG-DRIEVEGDDGDFEFTL 209
                                       5554.5555555555544443 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.3
                                       EEEEE-CTTSEEEEEECSTEEEEEE CS
                      Ribosomal_L6  23 eltreipegvtvevkvegnkvtviv 47 
                                        + +ei++g           v+v++
  gi|313117263|ref|YP_004044246.1| 298 GIDIEIRDG----------RVEVET 312
                                       233344444..........333333 PP

>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.5   2.4e+03      70      83 ..      33      46 ..       3      60 .. 0.63
   2 ?    4.1   0.0     0.073        69      15      43 ..      84     110 ..      44     167 .. 0.67
   3 ?    4.8   0.0     0.044        42       8      28 ..     169     189 ..     168     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.5
                                      CCSEEEEEEEEEEE CS
                             LEA_2 70 vgleleytlrgrlk 83
                                      +++++e++ +gr++
  gi|313117263|ref|YP_004044246.1| 33 DDFDIEFRSDGRVE 46
                                      45666666666665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.073
                                       EEEEEEEEESSSEEEEEEECE-EEESSSC CS
                             LEA_2  15 dgleldlsyngqrlasgtspqgfsqparg 43 
                                        +l+ld++yng+ l   + ++ f +++++
  gi|313117263|ref|YP_004044246.1|  84 GSLTLDVEYNGNDLE--VDSDDFEIERKN 110
                                       455666666666666..455555555544 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.044
                                       SSS-EEEEEEEEEEEESSSEE CS
                             LEA_2   8 Nsfgvrydgleldlsyngqrl 28 
                                       N+f+++ydg++ldl+ ++  +
  gi|313117263|ref|YP_004044246.1| 169 NDFDFEYDGSTLDLESDDFDV 189
                                       99*********9999877655 PP

>> DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0022       2.1      32     100 ..      18      80 ..      16     105 .. 0.81
   2 ?    3.5   0.3     0.078        73      35      65 ..     124     161 ..     119     214 .. 0.49
   3 ?    1.3   0.1      0.37   3.5e+02      39     100 ..     177     244 ..     168     265 .. 0.61
   4 ?   -0.9   0.0       1.8   1.7e+03      36      58 ..     274     296 ..     272     313 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0022
                                       EEEEEEETTEEEEEEE-SSEEEEEEEESEEEEE-EEEEEEHHHHHHHHHHSSTTSEEEEEEETTEEEEE CS
                     DNA_pol3_beta  32 gvllevkdsqlsltgtDleisiestisaeseeeegkvlvparllldivkaLpndkkvkisvneqkllii 100
                                       +  +e +d+++ l g D +i+++s    e+e  ++ + + +  +      L+   +v++++n+++ ++ 
  gi|313117263|ref|YP_004044246.1|  18 NFDVETSDERVELDGDDFDIEFRSDGRVEIEGDDFDIELDGDRI-----DLES-DDVEVEINGNEIEVE 80 
                                       56678899***********************999*999999775.....4666.677777777777766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.078
                                       EEEETTEEEEEEE-SSEEEE.EEEESEEE......EE- CS
                     DNA_pol3_beta  35 levkdsqlsltgtDleisie.stisaese......eee 65 
                                       +e + +++ + g + +i++  +ti+++ +      + +
  gi|313117263|ref|YP_004044246.1| 124 IESDGDRVEIEGDEFDIEFDgDTIEIQTDdfdveiDAD 161
                                       55555666666666666665234444444222222222 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.37
                                       TTEEEEEEE-SSEEEE.EEEESEEEEE-EEEEE....EHHHHHHHHHHSSTT.SEEEEEEETTEEEEE CS
                     DNA_pol3_beta  39 dsqlsltgtDleisie.stisaeseeeegkvlv....parllldivkaLpnd.kkvkisvneqkllii 100
                                        s+l l + D ++++  ++i+ e ++ ++++++    ++  ++d  +  + +  +++++ +++++++ 
  gi|313117263|ref|YP_004044246.1| 177 GSTLDLESDDFDVEFDgDRIEVEGDDGDFEFTLdtddNGNVVFDGGRDVDIElDDIEVERDNDRAEVE 244
                                       56777778888888762456666665555555522222334444444443221346666666776666 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.8
                                       EEETTEEEEEEE-SSEEEEEEEE CS
                     DNA_pol3_beta  36 evkdsqlsltgtDleisiestis 58 
                                       ev+++ l + + D  +++e   s
  gi|313117263|ref|YP_004044246.1| 274 EVESDDLEFDSDDGRVEFEFDGS 296
                                       68899999999999999987654 PP

>> PCC_BT  Propionyl-coenzyme A carboxylase BT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.008       7.6      39      84 ..      48      94 ..       7     109 .. 0.50
   2 ?    4.2   0.3     0.053        50      32      69 ..     111     151 ..      98     161 .. 0.55
   3 ?    0.4   3.9       0.8   7.6e+02      69      69 ..     200     200 ..     145     336 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.008
                            PCC_BT 39 dgedetvtvkve...eaadevevkvdgksvkvssdwklgqplirgtvdg 84
                                      +g+d +++++ +    ++d+vev+++g++++v++  + g+ +++++ +g
  gi|313117263|ref|YP_004044246.1| 48 EGDDFDIELDGDridLESDDVEVEINGNEIEVEG--RSGSLTLDVEYNG 94
                                      3333333333221113334444444444444443..2233333333333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.053
                            PCC_BT  32 kdwvvtvdgedetvtvk...veeaadevevkvdgksvkvss 69 
                                        +++v+ d+e+ +++ +   ve ++de+++++dg ++++++
  gi|313117263|ref|YP_004044246.1| 111 GEYDVESDNENLDIESDgdrVEIEGDEFDIEFDGDTIEIQT 151
                                       34444444444443322111234456666666776666665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.8
                            PCC_BT  69 s 69 
                                       +
  gi|313117263|ref|YP_004044246.1| 200 G 200
                                       3 PP

>> DUF108  Domain of unknown function DUF108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.077        73      46      70 ..      67      91 ..      54      98 .. 0.84
   2 ?   -0.9   0.0       2.4   2.2e+03      36      61 ..     151     178 ..     146     186 .. 0.66
   3 ?    2.6   0.0      0.19   1.8e+02      54      70 ..     194     210 ..     185     216 .. 0.81
   4 ?   -1.8   0.0       4.3     4e+03      49      66 ..     310     327 ..     307     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.077
                                      ETT-SSEEEEEEEEETTEEEEEEEE CS
                            DUF108 46 dpnldkniheieveGsfgefsleve 70
                                      d +++ n  eieveG++g+++l ve
  gi|313117263|ref|YP_004044246.1| 67 DVEVEINGNEIEVEGRSGSLTLDVE 91
                                      556788999**********999887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.4
                                       CCGEEEEEEEETT-..SSEEEEEEEEET CS
                            DUF108  36 fdrvkvelvadpnl..dkniheieveGs 61 
                                        d+ +ve+ ad ++  + n  + e  Gs
  gi|313117263|ref|YP_004044246.1| 151 TDDFDVEIDADGDIevETNDFDFEYDGS 178
                                       6788899999887733455555555555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.19
                                       EEEEEEETTEEEEEEEE CS
                            DUF108  54 heieveGsfgefsleve 70 
                                        +ieveG+ g+f++++ 
  gi|313117263|ref|YP_004044246.1| 194 DRIEVEGDDGDFEFTLD 210
                                       68***********9976 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 4.3
                                       -SSEEEEEEEEETTEEEE CS
                            DUF108  49 ldkniheieveGsfgefs 66 
                                       ++ + h+ie  G++ e++
  gi|313117263|ref|YP_004044246.1| 310 VETDDHDIEHDGDSLEVE 327
                                       6778899*9999977665 PP

>> DUF4302  Domain of unknown function (DUF4302)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.8   6.4e+03      48      64 ..      34      50 ..      21      55 .. 0.70
   2 ?   -0.3   0.0      0.86   8.1e+02     161     192 ..     117     149 ..      76     184 .. 0.63
   3 ?   10.0   0.3   0.00062      0.59     107     135 ..     197     224 ..     181     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.8
                           DUF4302 48 tflmkFsedgkVtmasd 64
                                       f ++F  dg+V++  d
  gi|313117263|ref|YP_004044246.1| 34 DFDIEFRSDGRVEIEGD 50
                                      55567888888888766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.86
                           DUF4302 161 a.dnvlnfekyykqltikgeeyevsfgsdaksk 192
                                       + +++l +e+   +++i+g e+++ f++d+   
  gi|313117263|ref|YP_004044246.1| 117 SdNENLDIESDGDRVEIEGDEFDIEFDGDTIEI 149
                                       224444455556677777777777777665444 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00062
                           DUF4302 107 egkGleGdfeFlilgkdeddkivLkGkkn 135
                                       e +G  GdfeF+ +  d+++++v+ G + 
  gi|313117263|ref|YP_004044246.1| 197 EVEGDDGDFEFTLD-TDDNGNVVFDGGRD 224
                                       6799**********.555*******9765 PP

>> MelC1  Tyrosinase co-factor MelC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.061        58      29      77 ..      21      79 ..       2      99 .. 0.61
   2 ?   -0.6   0.1       1.4   1.3e+03      35      48 ..     135     148 ..     124     180 .. 0.68
   3 ?    4.4   0.2     0.041        39      35      49 ..     184     198 ..     172     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.061
                             MelC1 29 aegsae.....pesFDevyr..Gr.RiqGlpaegg..ahghaehgagyqvlidGreLhv 77
                                      +e+s e     +++FD ++r  Gr  i+G   +    +   + ++   +v i+G e++v
  gi|313117263|ref|YP_004044246.1| 21 VETSDErveldGDDFDIEFRsdGRvEIEGDDFDIEldGDRIDLESDDVEVEINGNEIEV 79
                                      33333334444888888887445544777666555224445556667777777777766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                             MelC1  35 pesFDevyrGrRiq 48 
                                       +++FD ++ G  i+
  gi|313117263|ref|YP_004044246.1| 135 GDEFDIEFDGDTIE 148
                                       66777777776654 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.041
                             MelC1  35 pesFDevyrGrRiqG 49 
                                        ++FD+++ G Ri+ 
  gi|313117263|ref|YP_004044246.1| 184 SDDFDVEFDGDRIEV 198
                                       789**********75 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.2   4.9e+03      22      38 ..      18      34 ..      13      56 .. 0.60
   2 ?    7.6   0.8    0.0043       4.1       8      39 ..      51      84 ..      44     115 .. 0.73
   3 ?   -0.7   0.1       1.7   1.6e+03      23      39 ..      88     104 ..      77     125 .. 0.61
   4 ?    2.5   0.4      0.17   1.6e+02      19      39 ..     118     138 ..     105     159 .. 0.79
   5 ?    4.9   0.1      0.03        28       2      38 ..     164     202 ..     163     220 .. 0.79
   6 ?    3.1   0.8      0.11     1e+02      14      46 ..     239     271 ..     226     285 .. 0.70
   7 ?    1.4   0.2      0.37   3.5e+02      23      51 ..     299     327 ..     291     345 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.2
                                      CEEEEEETTEEEEEEE- CS
                             HSP20 22 elkvkvednrvlvkgeh 38
                                      + +v++ d+rv   g  
  gi|313117263|ref|YP_004044246.1| 18 NFDVETSDERVELDGDD 34
                                      55666666666666654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0043
                                      EEEEEEE-T..T--CCCEEEEEETTEEEEEEE-- CS
                             HSP20  8 efevkldvp..glkkeelkvkvednrvlvkgehe 39
                                       f ++ld    +l+ ++++v++++n++ v+g   
  gi|313117263|ref|YP_004044246.1| 51 DFDIELDGDriDLESDDVEVEINGNEIEVEGRSG 84
                                      5555555441156799**************9865 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.7
                                       EEEEEETTEEEEEEE-- CS
                             HSP20  23 lkvkvednrvlvkgehe 39 
                                       l+v++++n + v +   
  gi|313117263|ref|YP_004044246.1|  88 LDVEYNGNDLEVDSDDF 104
                                       56677777777766554 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.17
                                       -CCCEEEEEETTEEEEEEE-- CS
                             HSP20  19 kkeelkvkvednrvlvkgehe 39 
                                       ++e+l+++ +++rv ++g + 
  gi|313117263|ref|YP_004044246.1| 118 DNENLDIESDGDRVEIEGDEF 138
                                       478999999999999999875 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.03
                                       --SSEEEEEEEEE-TT--..CCCEEEEEETTEEEEEEE- CS
                             HSP20   2 ikeeeeefevkldvpglk..keelkvkvednrvlvkgeh 38 
                                       i +e + f ++ d + l+   ++ +v+ +++r+ v+g  
  gi|313117263|ref|YP_004044246.1| 164 IEVETNDFDFEYDGSTLDleSDDFDVEFDGDRIEVEGDD 202
                                       6677788888888776554388**************986 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.11
                                       E-TT--CCCEEEEEETTEEEEEEE--..---TT CS
                             HSP20  14 dvpglkkeelkvkvednrvlvkgeheeeeedek 46 
                                       d +++++++l+ + +d+rv v+g   e e d++
  gi|313117263|ref|YP_004044246.1| 239 DRAEVETDDLDFESDDDRVDVEGDDFEIERDGD 271
                                       556788899999999999999998774444444 PP

  == domain 7  score: 1.4 bits;  conditional E-value: 0.37
                                       EEEEEETTEEEEEEE--..---TT----S CS
                             HSP20  23 lkvkvednrvlvkgeheeeeedekglike 51 
                                       ++++++d+rv v+   ++ e+d++ l  e
  gi|313117263|ref|YP_004044246.1| 299 IDIEIRDGRVEVETDDHDIEHDGDSLEVE 327
                                       67777777777777766555555544443 PP

>> DUF2850  Protein of unknown function (DUF2850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.2   1.1e+03      33      49 ..      86     102 ..      66     129 .. 0.70
   2 ?    3.0   0.1      0.14   1.3e+02      37      50 ..     140     153 ..     112     165 .. 0.84
   3 ?    1.7   0.1      0.33   3.1e+02      36      48 ..     172     184 ..     164     189 .. 0.84
   4 ?    5.4   0.1     0.023        22      38      62 ..     190     214 ..     184     219 .. 0.87
   5 ?   -1.0   0.1       2.4   2.3e+03      36      42 ..     290     296 ..     288     317 .. 0.71
   6 ?   -1.1   0.0       2.6   2.4e+03      38      50 ..     318     330 ..     303     343 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.2
                           DUF2850  33 vsTsfefdGktleykvg 49 
                                       ++ + e++G++le+   
  gi|313117263|ref|YP_004044246.1|  86 LTLDVEYNGNDLEVDSD 102
                                       55677899999987654 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                           DUF2850  37 fefdGktleykvgs 50 
                                        efdG+t+e+++ +
  gi|313117263|ref|YP_004044246.1| 140 IEFDGDTIEIQTDD 153
                                       58********9976 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.33
                           DUF2850  36 sfefdGktleykv 48 
                                       +fe+dG+tl ++ 
  gi|313117263|ref|YP_004044246.1| 172 DFEYDGSTLDLES 184
                                       69******98875 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.023
                           DUF2850  38 efdGktleykvgseeyiyqllgeek 62 
                                       efdG+++e++  ++ + ++l  +++
  gi|313117263|ref|YP_004044246.1| 190 EFDGDRIEVEGDDGDFEFTLDTDDN 214
                                       8*****************9987766 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.4
                           DUF2850  36 sfefdGk 42 
                                       +fefdG+
  gi|313117263|ref|YP_004044246.1| 290 EFEFDGS 296
                                       79***97 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 2.6
                           DUF2850  38 efdGktleykvgs 50 
                                       e+dG++le+++ +
  gi|313117263|ref|YP_004044246.1| 318 EHDGDSLEVETDD 330
                                       7899999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.88u 0.35s 00:00:01.23 Elapsed: 00:00:00.52
# Mc/sec: 2122.07
//
Query:       gi|313117264|ref|YP_004044247.1|  [L=174]
Description: hypothetical protein Hbor_30490 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-05   23.1   0.0         16    6.2   0.0    5.2  5  MORN_2         MORN repeat variant
  ------ inclusion threshold ------
      0.022   15.0   0.2      0.054   13.8   0.2    1.7  1  zinc_ribbon_9  zinc-ribbon
       0.16   11.9   2.2         24    4.9   0.3    3.5  3  DUF1936        Domain of unknown function (DUF1936)


Domain annotation for each model (and alignments):
>> MORN_2  MORN repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.011        67       4      17 ..      60      73 ..      60      75 .. 0.85
   2 ?    0.7   0.0      0.16   9.4e+02       8      15 ..      87      94 ..      79      98 .. 0.79
   3 ?    0.9   0.0      0.13   7.8e+02       4      17 ..     106     119 ..     106     121 .. 0.81
   4 !    6.2   0.0    0.0026        16       5      15 ..     130     140 ..     129     141 .. 0.88
   5 ?    3.4   0.0      0.02   1.2e+02       5      16 ..     153     164 ..     152     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.011
                            MORN_2  4 eekeYyenGklkee 17
                                      e++e++ nG ++++
  gi|313117264|ref|YP_004044247.1| 60 ERTEFDRNGIVRYR 73
                                      679*******9987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                            MORN_2  8 YyenGklk 15
                                      Y+ nG+l+
  gi|313117264|ref|YP_004044247.1| 87 YDGNGTLR 94
                                      88899887 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.13
                            MORN_2   4 eekeYyenGklkee 17 
                                       ee+ Y+ nG+l+ +
  gi|313117264|ref|YP_004044247.1| 106 EERIYDVNGTLRFQ 119
                                       5788999****987 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0026
                            MORN_2   5 ekeYyenGklk 15 
                                       e++Y+e+G+l+
  gi|313117264|ref|YP_004044247.1| 130 ERWYDETGTLR 140
                                       79******997 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.02
                            MORN_2   5 ekeYyenGklke 16 
                                       ++ Y++nG l e
  gi|313117264|ref|YP_004044247.1| 153 RRVYDANGILIE 164
                                       689*****9975 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2     9e-06     0.054       8      34 ..      25      52 ..      24      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-06
                     zinc_ribbon_9  8 CdrfVsvspdedsdv.lCPhCgggFVEe 34
                                      C+rfV  ++++ ++  +C   +ggFVEe
  gi|313117264|ref|YP_004044247.1| 25 CRRFVKYETTDGEEFeSCIGPDGGFVEE 52
                                      *******9986666447**********9 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3    0.0041        24      11      34 .]      84     107 ..      80     107 .. 0.87
   2 ?    1.0   0.1     0.069   4.1e+02      11      31 ..     107     127 ..     105     130 .. 0.84
   3 ?    3.7   0.0    0.0097        58      14      31 ..     133     150 ..     128     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0041
                                       EEEE-TTS-EEEEEES-TT---EE CS
                           DUF1936  11 EPVYNekGEIKvFRCdredCdYiE 34 
                                       E +Y  +G ++v+R + ed d +E
  gi|313117264|ref|YP_004044247.1|  84 EWIYDGNGTLRVYREEEEDDDEEE 107
                                       669***********9999977665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.069
                                       EEEE-TTS-EEEEEES-TT-- CS
                           DUF1936  11 EPVYNekGEIKvFRCdredCd 31 
                                       E +Y  +G +++ R + +d d
  gi|313117264|ref|YP_004044247.1| 107 ERIYDVNGTLRFQRTEDDDGD 127
                                       668999********9988866 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0097
                                       E-TTS-EEEEEES-TT-- CS
                           DUF1936  14 YNekGEIKvFRCdredCd 31 
                                       Y e G ++vF  d ed d
  gi|313117264|ref|YP_004044247.1| 133 YDETGTLRVFQKDDEDGD 150
                                       9**********9999966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 1325.79
//
Query:       gi|313117265|ref|YP_004044248.1|  [L=117]
Description: pterin-4-alpha-carbinolamine dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-26   92.6   0.2    1.6e-26   92.3   0.2    1.1  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
  ------ inclusion threshold ------
       0.21   10.4   0.2       0.26   10.1   0.2    1.0  1  SerH       Cell surface immobilisation antigen SerH


Domain annotation for each model (and alignments):
>> Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.2   1.7e-30   1.6e-26       2      91 .]      19     110 ..      18     110 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 1.7e-30
                         Pterin_4a   2 klseeeiqkllael..pgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilvsynkvtvrltThdagg 76 
                                       +l+e+e +++l+el  + W+  ++  le +++f+df++a++f+ ++++laeee+Hhpdi+++++kv+v+++Th++ g
  gi|313117265|ref|YP_004044248.1|  19 PLTEDEYANYLTELddSVWEVVDEYYLEGTYEFEDFRDALEFTYEIGELAEEEWHHPDIHLTWGKVRVEMWTHKIDG 95 
                                       89*********888767***658889*************************************************** PP

                         Pterin_4a  77 ltenDfklAakidel 91 
                                       l++ Df +Aa++d++
  gi|313117265|ref|YP_004044248.1|  96 LHKTDFVMAARMDRI 110
                                       *************85 PP

>> SerH  Cell surface immobilisation antigen SerH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   2.9e-05      0.26     152     177 ..       2      27 ..       1      30 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.9e-05
                              SerH 152 tsgltDanCaaCattaspkgknvfAn 177
                                       +s+l+D++C+aC+++ +p +++ +An
  gi|313117265|ref|YP_004044248.1|   2 ASTLADQECEACTSADEPLTEDEYAN 27 
                                       57888888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.37
# Mc/sec: 945.73
//
Query:       gi|313117266|ref|YP_004044249.1|  [L=1010]
Description: FAD/FMN-dependent dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-60  203.5   0.6    8.2e-60  202.5   0.6    1.5  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    1.1e-37  128.9   0.6    4.1e-37  127.0   0.3    2.1  2  FAD_binding_4  FAD binding domain
    3.2e-10   40.4   4.7    5.9e-10   39.6   4.7    1.4  1  Fer4_17        4Fe-4S dicluster domain
    4.8e-10   39.7   5.3    1.1e-09   38.6   5.3    1.5  1  Fer4_8         4Fe-4S dicluster domain
    2.3e-05   24.5   0.0     0.0029   17.8   0.0    2.7  2  CCG            Cysteine-rich domain
    3.5e-05   23.8   4.4      0.014   15.5   0.4    2.4  2  Fer4_10        4Fe-4S dicluster domain
    0.00031   21.3   4.9    0.00068   20.2   4.9    1.6  1  Fer4_7         4Fe-4S dicluster domain
    0.00046   20.3   4.4     0.0014   18.7   4.5    1.8  1  Fer4_9         4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   16.0   2.9      0.096   12.8   0.2    2.4  2  Fer4_21        4Fe-4S dicluster domain
      0.012   15.7   9.5       0.47   10.7   1.7    2.5  2  Fer4_2         4Fe-4S binding domain
      0.012   15.4  12.7      0.083   12.7   3.6    2.5  2  Fer4           4Fe-4S binding domain
      0.081   13.5  12.5       0.11   13.0   2.4    2.5  2  Fer4_4         4Fe-4S binding domain
       0.21   11.2   0.3         11    5.7   0.1    2.6  2  ChitinaseA_N   Chitinase A, N-terminal domain
       0.29   11.3  11.9       0.55   10.4   2.8    2.4  2  Fer4_6         4Fe-4S binding domain
        0.3   11.3   2.8       0.48   10.6   1.0    2.2  2  Fer4_18        4Fe-4S dicluster domain
        3.1    8.8   6.3        9.5    7.2   1.9    1.9  2  Fer4_16        4Fe-4S double cluster binding domain
        3.9    8.1   5.8        5.9    7.5   0.1    3.2  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.5   0.6   7.8e-63   8.2e-60       2     250 .]     298     547 ..     297     547 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.5 bits;  conditional E-value: 7.8e-63
                                       -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SS...TTS-TTT-EEEEEEEEE-HHHH CS
                     FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgak...kglpdeeealllvefegddeee 75 
                                       pe++a+al  f+++  a++av+ + +   +++a+elmd++ ++l+++ +g +   +++p++++a+ll+ef++  ++ 
  gi|313117266|ref|YP_004044249.1| 298 PEETALALYCFDDLVTAMEAVPVALEY--DVSAVELMDDEVFRLAANSDGYAeyvEPIPEGTDAALLLEFDSELHDD 372
                                       999*******************99999..*********************************************877 PP

                                       HHHHHHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHH CS
                     FAD-oxidase_C  76 aeeelealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikal 152
                                        e+++ a+ e+  ++++a +v+ a+++a+++ +wk+Rkaa+p+l ++ ++a++++++eD +vP+++la++v++++a 
  gi|313117266|ref|YP_004044249.1| 373 FEAAIDATTERFIHDGAAFEVVEAYTDADQADIWKLRKAAIPLLMSLEGDAKPYPFIEDATVPPAELAAYVQKFEAV 449
                                       77777779999999999999********************************************************* PP

                                       HHHHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THH CS
                     FAD-oxidase_C 153 ldkyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeegl 229
                                       ld++++++++f+Hag g lh++++++l++e  +e ++ + d+v+dl++e++Gs sgEHG G+++ ++ ++++ge+++
  gi|313117266|ref|YP_004044249.1| 450 LDDHDTSAAYFAHAGSGTLHIRPILNLKSESGVEDMHSITDDVTDLVLEHHGSFSGEHGDGMARTEFNPKMYGETLW 526
                                       ***************************************************************************** PP

                                       HHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 230 almrriKaalDPkgiLNPgkv 250
                                       ++++r+K a+DP++ + Pg+v
  gi|313117266|ref|YP_004044249.1| 527 DAFKRVKTAFDPEWWMHPGNV 547
                                       *******************86 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.6   3.8e+03      63      81 ..      35      53 ..      29      58 .. 0.81
   2 !  127.0   0.3   3.9e-40   4.1e-37       1     137 [.      65     202 ..      65     204 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.6
                                      TTEEEEETTSBHHHHHHHH CS
                     FAD_binding_4 63 egtatveaGvtlgdlveal 81
                                      + +a+ve+Gv +++ ++ l
  gi|313117266|ref|YP_004044249.1| 35 DLRARVEGGVEFDEYAQIL 53
                                      7899******999877665 PP

  == domain 2  score: 127.0 bits;  conditional E-value: 3.9e-40
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETT.S--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsr.lnrileideeegtatveaGvtlgd 76 
                                       pa+vv+p+++ +v+aa+++a+++++p+l+rG+Gssl+gq v  g+vvld+sr +++ilei ++e+++++++Gv+ +d
  gi|313117266|ref|YP_004044249.1|  65 PAGVVFPTDTSDVQAAVEVATSHEVPILPRGTGSSLAGQTVGPGCVVLDVSRhMDDILEIRPDEKRVRIQPGVVQDD 141
                                       799*************************************99*********99************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvr 137
                                       l++al+++gl + ++p+s +++tvGG i +n+ G +s +yG +  + + +++vl+dG++++
  gi|313117266|ref|YP_004044249.1| 142 LDAALSEYGLKFAPDPASSNRATVGGGIGNNSTGAHSVRYGITDAYTETVTAVLSDGSLLQ 202
                                       *********************************************************9986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   4.7   5.6e-13   5.9e-10       2      61 .]     602     678 ..     601     678 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 5.6e-13
                           Fer4_17   2 CiqCgyClp.....eCpsyeaydnepkkllraakl............glleeaekeekaslCieCgeCerkCPqgld 61 
                                       C++Cg C++     +Cp+y+a ++e ++++ +a+l            +++ e  +ee+ +lCi+C++C+++CP g+d
  gi|313117266|ref|YP_004044249.1| 602 CNGCGTCRQtgqevMCPTYRASREEVQTTRGRANLlrsaisgdlrpdEIHSERFQEEVLDLCIGCKGCKSDCPTGVD 678
                                       *********************999999899888888888877655543444444558*****************997 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   5.3     1e-12   1.1e-09       4      65 .]     601     677 ..     599     677 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1e-12
                            Fer4_8   4 kCieCgaCq.....saCpvlrrtkkhlldargeaae...........dvqeeqvlee.......eealwsCttcgaC 57 
                                        C++Cg C+      +Cp++r+++++ +++rg+a+            d        e       ee l+ C +c+ C
  gi|313117266|ref|YP_004044249.1| 601 LCNGCGTCRqtgqeVMCPTYRASREEVQTTRGRANLlrsaisgdlrpD--------EihserfqEEVLDLCIGCKGC 669
                                       6********9998889*****************999888777765552........033334559************ PP

                            Fer4_8  58 tevCpvgi 65 
                                       ++ Cp+g+
  gi|313117266|ref|YP_004044249.1| 670 KSDCPTGV 677
                                       *****986 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.077        81      10      65 ..     782     837 ..     775     854 .. 0.87
   2 !   17.8   0.0   2.7e-06    0.0029      21      84 ..     924     989 ..     908     990 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.077
                               CCG  10 lraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnveta 65 
                                        +++yp+ +ka   +lea+ v++ ++++    G +++ +g+ ++a++ a+ n + +
  gi|313117266|ref|YP_004044249.1| 782 TNYSYPAAGKAAVTVLEAADVHVSIPDDTAPSGRAAYSTGMLDRAKERAQSNTDRL 837
                                       5788*************************************999999999988765 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.7e-06
                               CCG  21 lkkllealgveleelekesCCGagggrsgkee...laealakrnvetaeetgadaivtacpgCllql 84 
                                          +l++ g ++++l + +CCG +g +  ++e   l++a++   +++++  + d +v++ ++C  ql
  gi|313117266|ref|YP_004044249.1| 924 AVGVLRRVGYDVDPL-DTTCCGMAGSFGYHDEhyaLSKAIGSILFDAVDASDGDRVVAPGGSCRSQL 989
                                       344667778888877.*************999999999**************************998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.3    0.0011       1.2       7      32 ..     600     626 ..     597     644 .. 0.73
   2 !   15.5   0.4   1.3e-05     0.014       7      36 ..     661     687 ..     656     699 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                           Fer4_10   7 dtCirCgkCvk.....aCPadltsvgakgea 32 
                                       + C +Cg+C++     +CP++     a+ e+
  gi|313117266|ref|YP_004044249.1| 600 ELCNGCGTCRQtgqevMCPTYR----ASREE 626
                                       67*************88***44....22222 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.3e-05
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakgeaseee 36 
                                       d Ci+C+ C++ CP+   +v+  + + e +
  gi|313117266|ref|YP_004044249.1| 661 DLCIGCKGCKSDCPT---GVDMAKLKAEVK 687
                                       89*************...444444444433 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   4.9   6.4e-07   0.00068       2      52 .]     602     677 ..     601     677 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.4e-07
                            Fer4_7   2 CigCgaCv.....aaCpvkaieldeeenekgtekv....................eidpekClgCgaCvavCPtga 52 
                                       C gCg C      ++Cp++  + +e++  +g++ +                    e + + C+gC+ C + CPtg+
  gi|313117266|ref|YP_004044249.1| 602 CNGCGTCRqtgqeVMCPTYRASREEVQTTRGRANLlrsaisgdlrpdeihserfqEEVLDLCIGCKGCKSDCPTGV 677
                                       *******74444478*******999998887644444445555555655555554556788*************96 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   4.5   1.4e-06    0.0014       2      49 ..     602     676 ..     601     678 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                            Fer4_9   2 CtgCgaC.....veaCpagvvvedaaerkarlraase........................eaCigCgaCveaCpkg 49 
                                       C+gCg+C     + +Cp+  ++++++++++   +                           + CigC+ C   Cp+g
  gi|313117266|ref|YP_004044249.1| 602 CNGCGTCrqtgqEVMCPTYRASREEVQTTRGRAN--LlrsaisgdlrpdeihserfqeevlDLCIGCKGCKSDCPTG 676
                                       *******888877779999998888887765433..245799999******************************98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.12   1.3e+02      33      49 ..     594     610 ..     577     622 .. 0.70
   2 ?   12.8   0.2   9.1e-05     0.096      30      53 ..     652     675 ..     639     689 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                           Fer4_21  33 vlkvvedeCvGCnlCss 49 
                                        +  + + C GC  C +
  gi|313117266|ref|YP_004044249.1| 594 GFSQLVELCNGCGTCRQ 610
                                       55666788999999975 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.1e-05
                           Fer4_21  30 aktvlkvvedeCvGCnlCssvCPv 53 
                                       +++  + v d C+GC+ C s CP+
  gi|313117266|ref|YP_004044249.1| 652 SERFQEEVLDLCIGCKGCKSDCPT 675
                                       55566677899***********96 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.7   0.00044      0.47       8      21 ..     600     618 ..     595     619 .. 0.71
   2 ?    9.1   1.2    0.0014       1.5       7      22 .]     660     675 ..     654     675 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00044
                            Fer4_2   8 drCigCgaCv....sa.CP 21 
                                       + C+gCg+C+     + CP
  gi|313117266|ref|YP_004044249.1| 600 ELCNGCGTCRqtgqEVmCP 618
                                       78*******6333355677 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                        d CigC+ C s CP+
  gi|313117266|ref|YP_004044249.1| 660 LDLCIGCKGCKSDCPT 675
                                       589****99*888**7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.7    0.0044       4.6       6      14 ..     600     608 ..     599     611 .. 0.88
   2 ?   12.7   3.6   7.8e-05     0.083       6      21 ..     661     676 ..     659     677 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0044
                                       TTSSS-THH CS
                              Fer4   6 ekCigCGaC 14 
                                       e+C gCG+C
  gi|313117266|ref|YP_004044249.1| 600 ELCNGCGTC 608
                                       89******* PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.8e-05
                                       TTSSS-THHHHHSTTT CS
                              Fer4   6 ekCigCGaCvevCPvg 21 
                                       ++CigC+ C + CP+g
  gi|313117266|ref|YP_004044249.1| 661 DLCIGCKGCKSDCPTG 676
                                       89*************9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.7     0.036        38       2      11 ..     600     609 ..     600     620 .. 0.79
   2 ?   13.0   2.4   0.00011      0.11       2      17 .]     661     676 ..     660     676 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.036
                            Fer4_4   2 erCigCgsCv 11 
                                       e C+gCg C+
  gi|313117266|ref|YP_004044249.1| 600 ELCNGCGTCR 609
                                       57*******8 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + CigC+ C + CP+g
  gi|313117266|ref|YP_004044249.1| 661 DLCIGCKGCKSDCPTG 676
                                       78************86 PP

>> ChitinaseA_N  Chitinase A, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.1   1.1e+02      13      46 ..     289     326 ..     283     338 .. 0.80
   2 ?    5.7   0.1      0.01        11      72     103 ..     582     613 ..     570     619 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
                      ChitinaseA_N  13 etkfalievdqeat....sYnslvkvkdeaevsvewnv 46 
                                       e +++l+ v +e+      +++lv+  ++++v +e++v
  gi|313117266|ref|YP_004044249.1| 289 EAELSLVTVPEETAlalyCFDDLVTAMEAVPVALEYDV 326
                                       567888888777655434579***************98 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.01
                      ChitinaseA_N  72 kesatfkvkkgGryqlevelCdaeGCsksapk 103
                                       + ++t++++  G ++  velC++ G  + + +
  gi|313117266|ref|YP_004044249.1| 582 EPQTTLDFTDEGGFSQLVELCNGCGTCRQTGQ 613
                                       56889999**************9995555544 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.8     0.018        19       7      21 ..     600     619 ..     599     622 .. 0.74
   2 ?   10.4   2.8   0.00052      0.55       7      23 ..     661     677 ..     660     677 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                            Fer4_6   7 dkCigCgdC.....vrvCPe 21 
                                       ++C+gCg C     ++ CP+
  gi|313117266|ref|YP_004044249.1| 600 ELCNGCGTCrqtgqEVMCPT 619
                                       79*******76664444775 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00052
                            Fer4_6   7 dkCigCgdCvrvCPega 23 
                                       d+CigC  C + CP+g+
  gi|313117266|ref|YP_004044249.1| 661 DLCIGCKGCKSDCPTGV 677
                                       89************986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.1   5.3e+03      13      37 ..     444     467 ..     439     490 .. 0.69
   2 ?   10.6   1.0   0.00045      0.48      50      78 ..     652     680 ..     614     685 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.1
                           Fer4_18  13 arvqsvlydeetllvvydakrGeki 37 
                                        ++ +vl d++t ++ + a+ G ++
  gi|313117266|ref|YP_004044249.1| 444 QKFEAVLDDHDTSAAYF-AHAGSGT 467
                                       58899999999877655.4455554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00045
                           Fer4_18  50 keerkekgagdcidcescvkvcPtgidir 78 
                                       +e+ +e+    ci c+ c + cPtg+d+ 
  gi|313117266|ref|YP_004044249.1| 652 SERFQEEVLDLCIGCKGCKSDCPTGVDMA 680
                                       34445556667****************86 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.4     0.011        11       2      66 ..     602     675 ..     601     676 .. 0.65
   2 ?    7.2   1.9     0.009       9.5       2      16 ..     663     677 ..     662     694 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                           Fer4_16   2 CgtCgkCae.....vCPtnaikekkekeiearecisy.......ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C +Cg C +     +CPt   + ++ ++ + r+   +        +   ++++ ++++++    ++gC+ C+  CP 
  gi|313117266|ref|YP_004044249.1| 602 CNGCGTCRQtgqevMCPTYRASREEVQTTRGRA---NllrsaisGDLRPDEIHSERFQEEVLDLCIGCKGCKSDCPT 675
                                       999999986333336***888777333333333...22334343455567777777888878999***********6 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.009
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C++C+ C + CPt++
  gi|313117266|ref|YP_004044249.1| 663 CIGCKGCKSDCPTGV 677
                                       *************87 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.6      0.37   3.9e+02       5      17 ..     601     613 ..     599     630 .. 0.85
   2 ?    7.5   0.1    0.0056       5.9       4      36 ..     661     691 ..     660     709 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.37
                           Fer4_13   5 tCiacgaCvelaP 17 
                                        C +cg+C+++  
  gi|313117266|ref|YP_004044249.1| 601 LCNGCGTCRQTGQ 613
                                       6********9855 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0056
                           Fer4_13   4 dtCiacgaCvelaPdvFeeddeggasvvaeqpt 36 
                                       d Ci+c+ C + +P   ++ +   ++ v++q +
  gi|313117266|ref|YP_004044249.1| 661 DLCIGCKGCKSDCPTGVDMAK--LKAEVKHQHH 691
                                       57************9877775..4666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1010 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 7464.02
//
Query:       gi|313117267|ref|YP_004044250.1|  [L=125]
Description: lactoylglutathione lyase-like lyase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-16   59.6   0.2      4e-16   59.4   0.2    1.1  1  Glyoxalase     Glyoxalase/Bleomycin resistance protein/Dioxyg
    1.2e-13   51.3   0.1    5.8e-11   42.6   0.1    2.0  2  Glyoxalase_4   Glyoxalase/Bleomycin resistance protein/Dioxyg
    8.9e-08   32.9   0.2    1.1e-07   32.6   0.2    1.1  1  Glyoxalase_6   Glyoxalase-like domain
    0.00016   21.8   0.0      0.002   18.2   0.0    2.0  1  Glyoxalase_3   Glyoxalase-like domain
  ------ inclusion threshold ------
      0.017   15.0   0.0       0.03   14.3   0.0    1.7  1  Glyoxalase_2   Glyoxalase-like domain
      0.028   14.2   0.1       0.44   10.3   0.0    2.1  2  Phage_Mu_Gp45  Bacteriophage Mu Gp45 protein


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.2   1.4e-19     4e-16       2     128 .]       6     120 ..       5     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.4e-19
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEEST.EEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteet.eglriaffhaggghielvlneapsgaakhvkkieetvhhv 77 
                                       i h+ l+v+d++++++FY++ +Gf+ ++++     t +g +  +  ++g+ +el l e+++  +         + + 
  gi|313117267|ref|YP_004044250.1|   6 ILHTCLNVADAAEAIEFYKQ-FGFTESWQFT----TpDGRTTNYYVSDGDGVELQLSETDGETDFEM------GTGW 71 
                                       88******************.**********....43666667778888889999999999888888......89** PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                        ++al vedv+++++r+   g  v +epg ++    y++++rDpdG+ +e+
  gi|313117267|ref|YP_004044250.1|  72 DHLALGVEDVDQTVERINHYG--VEKEPGPQPEAEAYTAFIRDPDGHVVEL 120
                                       *****************9988..88999999999999999********996 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1   1.9e-14   5.8e-11       2      92 ..       8      94 ..       7      97 .. 0.96
   2 !    7.5   0.0    0.0016       4.7      27      57 ..      96     125 .]      92     125 .] 0.84

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.9e-14
                                      EEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEEES-HH CS
                      Glyoxalase_4  2 QigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflaehgeglhhlaywvddld 80
                                      ++++ V D  +a++++++ +G++++++++ ++ + +++ +  g+g v+++L e++ +++f  e g+g  hla+ v+d+d
  gi|313117267|ref|YP_004044250.1|  8 HTCLNVADAAEAIEFYKQ-FGFTESWQFTTPDGRTTNYYVSDGDG-VELQLSETDGETDF--EMGTGWDHLALGVEDVD 82
                                      89999************8.*************************9.*************9..9**************** PP

                                      HHHHHHCTTTEE CS
                      Glyoxalase_4 81 aavarleeqGfe 92
                                      ++v+r   +G+e
  gi|313117267|ref|YP_004044250.1| 83 QTVERINHYGVE 94
                                      *******99986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0016
                                       S--E.EETTTTEEEEEEEETTEEEEEEEESS CS
                      Glyoxalase_4  27 qryrdepqevdlafallgsgsvqieLieple 57 
                                       ++ +++++e+ +af +  +g   +eLiepl+
  gi|313117267|ref|YP_004044250.1|  96 EPGPQPEAEAYTAFIRDPDG-HVVELIEPLD 125
                                       45677889999********9.57******86 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.2   3.5e-11   1.1e-07       2     106 ..       9     120 ..       8     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.5e-11
                      Glyoxalase_6   2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe.........paknrvHldlavedl 69 
                                        +l++ad+a++++F+++ +g++ +++  +++d ++ +    d+  + +q  ++         +++   Hl l ved+
  gi|313117267|ref|YP_004044250.1|   9 TCLNVADAAEAIEFYKQ-FGFTESWQF-TTPDGRTTNYYVSDGDGVELQLSETdgetdfemgTGW--DHLALGVEDV 81 
                                       5899***********98.678888877.5566665555556666666666665559999877777..5********* PP

                      Glyoxalase_6  70 daevarlvalGArvlreprdgthgr..vlaDPeGneFcv 106
                                       d++v+r+   G ++   p+ ++++    ++DP+G++  +
  gi|313117267|ref|YP_004044250.1|  82 DQTVERINHYGVEKEPGPQPEAEAYtaFIRDPDGHVVEL 120
                                       ***********9999777766654489********9876 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   6.8e-07     0.002       3     102 ..       8      98 ..       6     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.8e-07
                      Glyoxalase_3   3 HvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdgYlEllavdpeapaperprlfgldrlakgeglh 79 
                                       H+ l v d +ea++ + ++ Gft       p++ t N+ v  gdg +El   + + ++          +++ g g+ 
  gi|313117267|ref|YP_004044250.1|   8 HTCLNVADAAEAIEFY-KQFGFTESWQFTTPDGRTTNYYVSDGDG-VELQLSETDGET----------DFEMGTGWD 72 
                                       8999999999999977.8999999999999999999999987776.788777777776..........567899*** PP

                      Glyoxalase_3  80 tlalrtddidataarlraaGvd...e 102
                                       +lal ++d+d+t++r    Gv+    
  gi|313117267|ref|YP_004044250.1|  73 HLALGVEDVDQTVERINHYGVEkepG 98 
                                       *****************999875330 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05      0.03      64     117 ..      73     124 ..       9     125 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                                       EEEEEES-HHHHHHHH..GGGS-EEEEEEE-TTS-EEEEEE-TT--EEEEEE-- CS
                      Glyoxalase_2  64 eLyFevedvdaflqklkeaeniellhelkekpWgqrvirfyDpDkhiiEigesl 117
                                       +L   vedvd++++++++++ +e    ++ ++    ++ + DpD+h++E+ e+l
  gi|313117267|ref|YP_004044250.1|  73 HLALGVEDVDQTVERINHYG-VEKEPGPQPEA-EAYTAFIRDPDGHVVELIEPL 124
                                       4566789*********9998.76544444333.44578899*********9988 PP

>> Phage_Mu_Gp45  Bacteriophage Mu Gp45 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.069   2.1e+02      26      39 ..      16      29 ..       7      50 .. 0.84
   2 ?   10.3   0.0   0.00015      0.44      25      61 ..      80     118 ..      73     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.069
                                      XXXXXXXXXXXXXX CS
                     Phage_Mu_Gp45 26 tlddverfqpyGft 39
                                        +++e ++++Gft
  gi|313117267|ref|YP_004044250.1| 16 AAEAIEFYKQFGFT 29
                                      567899*******9 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00015
                                       XXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXX CS
                     Phage_Mu_Gp45  25 etlddverfqpyGftS..vppaGaeaivlavgGdrshgv 61 
                                       ++ + ver+++yG+     p++ aea  +++ +  +h+v
  gi|313117267|ref|YP_004044250.1|  80 DVDQTVERINHYGVEKepGPQPEAEAYTAFIRDPDGHVV 118
                                       56789*********983456799********99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1004.27
//
Query:       gi|313117268|ref|YP_004044251.1|  [L=434]
Description: citrate lyase subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.6e-09   34.7   0.0    3.5e-08   32.8   0.0    1.9  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0     2e-12   3.5e-08      15     214 ..      37     255 ..      27     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2e-12
                                       HHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGG............ CS
                         HpcH_HpaI  15 ekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdle............ 79 
                                       + + ++ +D+ + D Eda+a   +d+  +++ e++ +  a  + + e+  R+ ++ +  + +               
  gi|313117268|ref|YP_004044251.1|  37 QLTGMQAPDVWVPDNEDATAPSMRDEGVENIVEVVSEYGA--DFPGEIHPRIVWHRDDPATRYQGfqhmleiadpan 111
                                       4445667788899999999999999999999999999888..44557777777766555443211224112112223 PP

                                       HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHH...HHTHHHHH.....TSTTEEEEE CS
                         HpcH_HpaI  80 vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaeg...vknaeeIa.....avegldgvf 148
                                        + + +++++vP v   ++ +++++ +  +e++ + +++++ + + +Es ++   + +++  +     ++e+l  ++
  gi|313117268|ref|YP_004044251.1| 112 GAIEHIDGFVVPEVGDIDDWKKADEFITIVENEHGLEEGSLSMSVIVESGAAelaLGDLRTEMgkpanNLERLFLLV 188
                                       3335799******************************************8752226666555544224445888999 PP

                                       E-HHHHHHHTT-TT.STTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEH CS
                         HpcH_HpaI 149 lGaeDlsadlgtkr.spegtevldareriltaaraagiaaldtvasdiddaegflaegalfvalGfd 214
                                        G+ D++ d+++   + e +e+ + r++    a aag+ a+d+ + di+d++g+ ++ ++  a G+ 
  gi|313117268|ref|YP_004044251.1| 189 DGEVDYTKDMRAMTpTGELPEWPELRHNTSRGASAAGLVAVDGPYDDIRDVDGYNERMTENQAKGMI 255
                                       9**********865266789**********************************9999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2748.32
//
Query:       gi|313117269|ref|YP_004044252.1|  [L=254]
Description: IclR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-32  111.3   0.4    8.7e-32  109.7   0.1    1.8  2  IclR            Bacterial transcriptional regulator
      2e-06   27.8   0.1    4.9e-06   26.5   0.1    1.6  1  HTH_20          Helix-turn-helix domain
    6.4e-06   25.9   0.2    1.9e-05   24.3   0.2    1.8  1  HTH_IclR        IclR helix-turn-helix domain
      8e-05   22.4   0.0    0.00016   21.5   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0004   20.2   0.0    0.00092   19.1   0.0    1.6  1  MarR_2          MarR family
     0.0015   18.4   0.1      0.006   16.5   0.0    2.0  2  MarR            MarR family
     0.0017   18.2   0.0     0.0036   17.1   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0043   17.5   0.5      0.019   15.5   0.0    2.3  2  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.049   13.4   0.0    1.7  1  LexA_DNA_bind   LexA DNA binding domain
      0.025   14.1   0.0       0.05   13.2   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.036   14.0   1.2      0.057   13.4   0.1    1.9  1  PadR            Transcriptional regulator PadR-like family
      0.047   13.6   0.0        0.1   12.5   0.0    1.5  1  HTH_11          HTH domain
      0.048   13.8   0.0        0.1   12.8   0.0    1.5  1  HTH_34          Winged helix DNA-binding domain
      0.092   12.9   0.0        0.2   11.9   0.0    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.13   12.7   0.2       0.96   10.0   0.0    2.3  2  HTH_40          Helix-turn-helix domain
       0.13   11.9   0.0        0.3   10.7   0.0    1.5  1  RP-C            Replication protein C N-terminal domain


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.2e+03      41      82 ..      30      72 ..      22      73 .. 0.75
   2 !  109.7   0.1   7.8e-35   8.7e-32       4     127 ..     126     248 ..     123     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                                      T---SSTTS--SHHHHHHHHHHHHHHTSE.EEESSSSTTEEEE CS
                              IclR 41 elkrlterTitdpeeLleeLakvReqGya.vdreEeeegvrci 82
                                      +l++lt++    + ++ + L++  + G   + ++E+  g+rc+
  gi|313117269|ref|YP_004044252.1| 30 TLAELTDELEFAKSTIYKHLNTLEKGGLVvMRDNEYLIGLRCL 72
                                      5667777777778888888999988886515678888899996 PP

  == domain 2  score: 109.7 bits;  conditional E-value: 7.8e-35
                                       EETTSTT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEE CS
                              IclR   4 ravsaiGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvr 80 
                                        + +++G+r+ l+ taiGKalL+  ++e++e++l r++l   t++Titd+e+L+eeL+++R++G+a+d+eE  +g+ 
  gi|313117269|ref|YP_004044252.1| 126 NLDTSLGKRVHLHQTAIGKALLSSFSDERVEEILDRHGLPGETDNTITDREALFEELETIRAEGIAYDKEERVNGTG 202
                                       56789************************************************************************ PP

                                       EEEEEEE-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  81 ciAapifdasgevvaAvsvsgptarlteeelkeellalvreaArkis 127
                                       c+++p+     +  aA+s+++p++r+   e ++e++  v++aA+ i+
  gi|313117269|ref|YP_004044252.1| 203 CVGVPVET-GDRREAAISITAPINRMAAPERESEIIDTVKQAANVIE 248
                                       ******77.78889******************************997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   4.4e-09   4.9e-06      11      57 ..      14      61 ..      10      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.4e-09
                                      HHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 11 vRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      + +++l+ + + ++g+t++el ++l+ +k+t+++HL++Le+ gLv  +
  gi|313117269|ref|YP_004044252.1| 14 TSLAVLSGIeTLGGGATLAELTDELEFAKSTIYKHLNTLEKGGLVVMR 61
                                      6677777778889*******************************9776 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.2   1.7e-08   1.9e-05       6      48 ..      16      58 ..      11      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.7e-08
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      la+L  +++ +++ tl+el +++  +kSt + +L+tL++ G+v
  gi|313117269|ref|YP_004044252.1| 16 LAVLSGIETLGGGATLAELTDELEFAKSTIYKHLNTLEKGGLV 58
                                      8999999**********************************99 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.4e-07   0.00016      16      45 ..      29      58 ..      16      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.4e-07
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5 16 lcvcelaeelglsqstvShHLkkLreaGLV 45
                                      ++  el++el+  +st+  HL+ L++ GLV
  gi|313117269|ref|YP_004044252.1| 29 ATLAELTDELEFAKSTIYKHLNTLEKGGLV 58
                                      5778*************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   8.2e-07   0.00092      10      56 ..      18      63 ..      12      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.2e-07
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      vL  +   +g+  t +el+++l   ks++ ++l+ L++ GLv+ r++
  gi|313117269|ref|YP_004044252.1| 18 VLSGIETLGGG-ATLAELTDELEFAKSTIYKHLNTLEKGGLVVMRDN 63
                                      66666667776.7*****************************99987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.4e-06     0.006       2      47 ..      12      58 ..      11      64 .. 0.94
   2 ?   -1.5   0.0       2.2   2.4e+03      22      37 ..     130     145 ..     123     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.4e-06
                                      -HHHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  2 tltqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGli 47
                                      t+t + +L  +++ g+ ++++eL + l+  kst+ + l +Lek Gl+
  gi|313117269|ref|YP_004044252.1| 12 TETSLAVLSGIETLGGgATLAELTDELEFAKSTIYKHLNTLEKGGLV 58
                                      88999*********999****************************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                                       HHHHHHTS-HHHHHHH CS
                              MarR  22 eLakklgvskstvtrv 37 
                                        L+k+++++++++ ++
  gi|313117269|ref|YP_004044252.1| 130 SLGKRVHLHQTAIGKA 145
                                       79999***99998765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.2e-06    0.0036      21      58 ..      27      64 ..      25      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.2e-06
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      g at  e+  el+  +s++Y+ L+ Le+ GlV  ++ +
  gi|313117269|ref|YP_004044252.1| 27 GGATLAELTDELEFAKSTIYKHLNTLEKGGLVVMRDNE 64
                                      679999*************************9877665 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-05     0.019       7      51 ..      17      61 ..      11      65 .. 0.88
   2 ?   -1.8   0.0       4.1   4.6e+03      56      66 ..     212     222 ..     209     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                      +vL  i+  +++++la+l + l + +s+i + l+ L++ GLv++ 
  gi|313117269|ref|YP_004044252.1| 17 AVLSGIETLGGGATLAELTDELEFAKSTIYKHLNTLEKGGLVVMR 61
                                      5778888889999*****************************876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.1
                            HTH_27  56 drrekrvrlTd 66 
                                       drre  +++T+
  gi|313117269|ref|YP_004044252.1| 212 DRREAAISITA 222
                                       89*******97 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.4e-05     0.049      20      61 ..      23      63 ..      16      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                                      HHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                     LexA_DNA_bind 20 eetgypPsireiaralglkSpsaveehLkaLerKGyierdpg 61
                                      e+ g   + +e+ ++l ++  s++ +hL++Le+ G++ + ++
  gi|313117269|ref|YP_004044252.1| 23 ETLGGGATLAELTDELEFA-KSTIYKHLNTLEKGGLVVMRDN 63
                                      555666799*********9.9**************9988775 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.5e-05      0.05      16      47 ..      27      58 ..      22      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                            HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++ + +eL ++l   +st+ ++l+ Le+ Gl+
  gi|313117269|ref|YP_004044252.1| 27 GGATLAELTDELEFAKSTIYKHLNTLEKGGLV 58
                                      6899**************************98 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.1e-05     0.057      19      51 ..      31      62 ..      28      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                                      HHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEE CS
                              PadR 19 leelsegllelseGslYpaLkrLekeglvesew 51
                                      l+el+++ le+ ++++Y+ L++Lek glv+ + 
  gi|313117269|ref|YP_004044252.1| 31 LAELTDE-LEFAKSTIYKHLNTLEKGGLVVMRD 62
                                      6788665.9********************9775 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.2e-05       0.1      16      45 ..      29      58 ..      22      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                            HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                       + +eL +eL+  ++t+++++ +Le+ g+ 
  gi|313117269|ref|YP_004044252.1| 29 ATLAELTDELEFAKSTIYKHLNTLEKGGLV 58
                                      5899*********************98854 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.1e-05       0.1       4      46 ..      17      60 ..      14      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.1e-05
                            HTH_34  4 avlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYiev 46
                                      avls   +    a+ +el ++le  ++ +++hl++Lek g +++
  gi|313117269|ref|YP_004044252.1| 17 AVLSGIETlGGGATLAELTDELEFAKSTIYKHLNTLEKGGLVVM 60
                                      556655555678999***********************998876 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017       0.2      18      51 ..      28      61 ..      26      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                    B-block_TFIIIC 18 GitqsdLakeskqdprslfyrlksLekkgLIvkq 51
                                      G t  +L  e++  ++ ++++l++Lek gL+v++
  gi|313117269|ref|YP_004044252.1| 28 GATLAELTDELEFAKSTIYKHLNTLEKGGLVVMR 61
                                      8899999*************************97 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00085      0.96      11      40 ..      27      56 ..      21      74 .. 0.85
   2 ?   -0.5   0.1       1.5   1.7e+03      44      64 ..     223     243 ..     215     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00085
                            HTH_40 11 eglsieeIAkerglkesTIegHLaelieeg 40
                                       g +++e  +e ++++sTI++HL  l + g
  gi|313117269|ref|YP_004044252.1| 27 GGATLAELTDELEFAKSTIYKHLNTLEKGG 56
                                      5899*******************8876655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                            HTH_40  44 dlerlvseeeekeIeeaiekv 64 
                                       +++r+  +e+e+eI+++++++
  gi|313117269|ref|YP_004044252.1| 223 PINRMAAPERESEIIDTVKQA 243
                                       678888899999999999875 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00026       0.3      76     106 ..      33      63 ..      30      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                              RP-C  76 qLsralglsestlrrhlaaLveaGliirrDs 106
                                       +L  +l +++st+ +hl  L + Gl+++rD+
  gi|313117269|ref|YP_004044252.1|  33 ELTDELEFAKSTIYKHLNTLEKGGLVVMRDN 63 
                                       6788999***********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1772.41
//
Query:       gi|313117270|ref|YP_004044253.1|  [L=1159]
Description: hypothetical protein Hbor_30550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-27   94.9  44.6    4.1e-15   56.3  19.5   10.3 11  Big_9       Bacterial Ig domain
    2.2e-16   60.2  37.0    1.5e-09   38.3  11.9   10.7  8  Cadherin_4  Bacterial cadherin-like domain
    6.2e-09   35.7  29.5    1.9e-06   27.7  11.3    6.4  6  Cadherin_5  Cadherin-like domain
      0.005   17.3   0.1      0.056   13.9   0.0    2.9  2  MG2         MG2 domain
  ------ inclusion threshold ------
      0.023   14.7   4.7      0.047   13.7   4.7    1.5  1  PGF-CTERM   PGF-CTERM motif
      0.034   14.4   0.0      0.034   14.4   0.0    5.3  6  Gmad2       Immunoglobulin-like domain of bacterial spore ger
       0.48    9.9   5.2       0.11   11.9   0.5    2.4  2  SoxE        Sulfocyanin (SoxE) domain


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -11.8  20.2         7   1.8e+04      24      84 ..      77     151 ..      14     151 .. 0.57
   2 ?   -0.5  10.9      0.87   2.2e+03      14      73 ..     110     173 ..     102     192 .. 0.80
   3 !   53.9  17.2   8.9e-18   2.3e-14       4      90 .]     208     295 ..     206     295 .. 0.83
   4 !   56.3  19.5   1.6e-18   4.1e-15       1      90 []     300     390 ..     300     390 .. 0.86
   5 ?   -1.8   1.3       2.2   5.6e+03       2      21 ..     396     418 ..     395     494 .. 0.37
   6 ?   -1.8   0.8       2.1   5.4e+03      11      73 ..     507     567 ..     500     584 .. 0.47
   7 ?   -1.1   1.6       1.2   3.2e+03       5      41 ..     587     637 ..     566     692 .. 0.53
   8 ?   -1.7   0.9       1.9   4.9e+03      22      34 ..     775     789 ..     711     805 .. 0.59
   9 ?   -1.9   0.0       2.2   5.7e+03      59      78 ..     898     917 ..     877     930 .. 0.76
  10 ?   -3.0   4.2         5   1.3e+04      53      81 ..    1030    1066 ..     904    1073 .. 0.64
  11 ?  -12.2  17.9         7   1.8e+04       4      74 ..    1078    1124 ..    1052    1140 .. 0.47

  Alignments for each domain:
  == domain 1  score: -11.8 bits;  conditional E-value: 7
                             Big_9  24 vtedsv..............landtdpdgdaltvtsltvtlvta.panGtvtin.adgtltytpnagfsgtdsftYt 84 
                                       ++e ++                 d+d dg+ +    +tvt ++  +++   +i+  dg++t   +++ s + ++ Yt
  gi|313117270|ref|YP_004044253.1|  77 INEAETktgdgtnksftvgrSIVDSDLDGNLDDE--VTVTNTSDgSTYNVSSIDpIDGNVTVENAPNSSTEIEIAYT 151
                                       3322223333334444434322455566555543..33333333245555555556888888888888888777776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.87
                             Big_9  14 aPvavdds....vtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpna 73 
                                         +++++s    ++v++ ++++  + +++ + + t++ ++ +tap+   + +++dgt+t t  +
  gi|313117270|ref|YP_004044253.1| 110 EVTVTNTSdgstYNVSSIDPIDGNVTVENAPNSSTEIEIAYTTAPEAQNIDLSGDGTVTATIGT 173
                                       44455544555588888888999999999999999999********************999765 PP

  == domain 3  score: 53.9 bits;  conditional E-value: 8.9e-18
                             Big_9   4 vtvtvtpvndaPvavddsvtvtedsv.....landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagf 75 
                                       +t  vt++n+aP+a+dd++tvt++++     l+nd   d+ +l+  + +vt+v+ p+ G  t++++g++tyt +a+ 
  gi|313117270|ref|YP_004044253.1| 208 ATASVTAANTAPTANDDTTTVTKGESvtipvLDND--EDDGSLN--TSSVTVVSEPSEGETTVHSNGSITYTHTADS 280
                                       67788899**************9999444334344..4445555..4567889************************ PP

                             Big_9  76 sgtdsftYtvsDgsg 90 
                                         +dsftY v D++g
  gi|313117270|ref|YP_004044253.1| 281 EANDSFTYEVADDQG 295
                                       ************997 PP

  == domain 4  score: 56.3 bits;  conditional E-value: 1.6e-18
                             Big_9   1 tatvtvtvtpvndaPvavddsvtvtedsv.....landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpn 72 
                                       ta+v vtv+ +n+aP+a+dd++tv+++++     l+nd+d    + t+++ ++ +v++p+ G  t+n+dgt+tyt +
  gi|313117270|ref|YP_004044253.1| 300 TANVDVTVEVANTAPTANDDTTTVNKGETvtvpvLDNDVD----DGTFDNSSLIVVSGPSEGETTVNSDGTITYTHT 372
                                       899**********************888855555556654....444555677889********************* PP

                             Big_9  73 agfsgtdsftYtvsDgsg 90 
                                       a+   +dsf+Y+v+D++g
  gi|313117270|ref|YP_004044253.1| 373 ADRVADDSFKYKVEDDQG 390
                                       ***************997 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 2.2
                             Big_9   2 atvtvtvtp...vndaPvavdds 21 
                                       atv vtv+     n+aP   + +
  gi|313117270|ref|YP_004044253.1| 396 ATVDVTVETavpDNTAPKYLASA 418
                                       56666666444444444433322 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 2.1
                             Big_9  11 vndaPvavddsvtvtedsv...landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpna 73 
                                        n   v+++ +v+ +e ++   + + + + gd+ + t   v++v++  +   t   d++ +y  ++
  gi|313117270|ref|YP_004044253.1| 507 GNKSVVVAPVTVSEAERNLnvyIGTKIAVVGDSPN-TP--VEIVNGDYQAGSTG--DNSHVYIFDT 567
                                       56666666666666666666664444444444443.22..23333322222222..2233333333 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 1.2
                             Big_9   5 tvtvtpvndaPvavddsvtvtedsv..............landtdpdgdal 41 
                                       +v v   n a  +  d+ +vted++              +    d dgd  
  gi|313117270|ref|YP_004044253.1| 587 EVEVILRNLALDIDIDDRNVTEDETiegmvsskdgnrpvTLELLDDDGDVV 637
                                       333333444444444444444444433322222223333223333344443 PP

  == domain 8  score: -1.7 bits;  conditional E-value: 1.9
                             Big_9  22 vtvt..edsvlandt 34 
                                       ++++  edsv++ d+
  gi|313117270|ref|YP_004044253.1| 775 YSTNnsEDSVTDADV 789
                                       233223444444444 PP

  == domain 9  score: -1.9 bits;  conditional E-value: 2.2
                             Big_9  59 vtinadgtltytpnagfsgt 78 
                                       +++++dg +++t ++   g+
  gi|313117270|ref|YP_004044253.1| 898 FELSDDGDISFTVEQADPGP 917
                                       67788888888887766665 PP

  == domain 10  score: -3.0 bits;  conditional E-value: 5
                             Big_9   53 a.......panGtvtinadgtltytpna.gfsgtdsf 81  
                                        +        + Gt+ +++dgt+  t +   +s +d+f
  gi|313117270|ref|YP_004044253.1| 1030 SgdtrppfVKTGTAYVSEDGTFESTVDFsEQSVNDTF 1066
                                        0334444456788888888888877776455566666 PP

  == domain 11  score: -12.2 bits;  conditional E-value: 7
                             Big_9    4 vtvtvtpvndaPvavddsvtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnag 74  
                                        vt+  + v+d  + +++++ +t+                        +++++  t t +++ t t tp++ 
  gi|313117270|ref|YP_004044253.1| 1078 VTIEGNVVDDGETPTPTDTPITS------------------------TSTTTTDTSTDTPTPTKTATPTDT 1124
                                        33333334443333333333333........................333333333333333333333333 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -23.6  31.4         7   1.8e+04      19      57 ..      73     120 ..      14     199 .. 0.57
   2 !   38.3  11.9     6e-13   1.5e-09       3      72 .]     208     274 ..     206     274 .. 0.88
   3 !   37.2  17.1   1.3e-12   3.3e-09       1      72 []     301     369 ..     301     369 .. 0.90
   4 ?    1.2   1.9      0.23   5.9e+02       1      68 [.     396     477 ..     396     480 .. 0.66
   5 ?   -1.7   1.7       1.8   4.7e+03      19      46 ..     602     639 ..     584     675 .. 0.57
   6 ?   -2.1   3.1       2.5   6.5e+03      19      65 ..     722     769 ..     712     802 .. 0.74
   7 ?   -1.3   2.8       1.3   3.5e+03      59      70 ..    1022    1051 ..     847    1052 .. 0.69
   8 ?   -4.5   8.0         7   1.8e+04      21      54 ..    1090    1123 ..    1054    1138 .. 0.65

  Alignments for each domain:
  == domain 1  score: -23.6 bits;  conditional E-value: 7
                        Cadherin_4  19 dsatvtedtplt.......itagnvl....andtDvd..gdd.ltvtavtvag 57 
                                         +t++e ++ t       +     +      d+D d   dd +tvt ++   
  gi|313117270|ref|YP_004044253.1|  73 SDGTINEAETKTgdgtnksF-----TvgrsIVDSDLDgnLDDeVTVTNTSDGS 120
                                       22222221111111111112.....0222222333332222236666665222 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 6e-13
                        Cadherin_4   3 vtitvtgvndaPvavddsatvtedtpltitagnvlandtDvdgdd.ltvtavtvagtyGtltlnadGsftY 72 
                                       +t +vt++n aP+a+dd+ tvt ++++ti+   vl+nd D  +    +vt v+  ++ G+ t++++Gs+tY
  gi|313117270|ref|YP_004044253.1| 208 ATASVTAANTAPTANDDTTTVTKGESVTIP---VLDNDEDDGSLNtSSVTVVS-EPSEGETTVHSNGSITY 274
                                       6789*************************6...**999986544436777777.9***************9 PP

  == domain 3  score: 37.2 bits;  conditional E-value: 1.3e-12
                        Cadherin_4   1 atvtitvtgvndaPvavddsatvtedtpltitagnvlandtDvdgdd.ltvtavtvagtyGtltlnadGsftY 72 
                                       a+v++tv+ +n aP+a+dd+ tv+ ++++t++   vl+nd+D  + d  +   v+  ++ G+ t+n+dG++tY
  gi|313117270|ref|YP_004044253.1| 301 ANVDVTVEVANTAPTANDDTTTVNKGETVTVP---VLDNDVDDGTFDnSSLIVVS-GPSEGETTVNSDGTITY 369
                                       78*****************************6...**999997665546667777.89**************9 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.23
                        Cadherin_4   1 atvtitvt...gvndaPv....avddsatvtedtpltitagnvlandtD....vdgdd...ltvtavtvagtyGtlt 63 
                                       atv++tv+   + n aP     a  d  + + dt +  +     +n  D    ++gd+   l+  a++++ t+G  +
  gi|313117270|ref|YP_004044253.1| 396 ATVDVTVEtavPDNTAPKylasAHYDEDEGDGDTEIELSFSEPVENLGDseiyINGDPkgtLSGYAASIDHTGGRYV 472
                                       89999997444558899876444446667777887776445555665552233557777668989999999999877 PP

                        Cadherin_4  64 lnadG 68 
                                          dG
  gi|313117270|ref|YP_004044253.1| 473 ATLDG 477
                                       76666 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 1.8
                        Cadherin_4  19 dsatvtedtplt.............itagnvlandtDvdgd 46 
                                       d  +vted+++                   +l++d Dv  +
  gi|313117270|ref|YP_004044253.1| 602 DDRNVTEDETIEgmvsskdgnrpvtL---ELLDDDGDVVKG 639
                                       33444444444322222221111004...566555555433 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 2.5
                        Cadherin_4  19 dsatvtedtpltitagnvlandtDvdgdd.ltvtavtvagtyGtltln 65 
                                       d+at + +++  +   nv+  d + dg   l +++ +v+g  G+l+ +
  gi|313117270|ref|YP_004044253.1| 722 DTATLAIGNSDKGFRSNVTVKDGNEDGRVeLLFNTYAVTGLEGELSDS 769
                                       555555555555545688888888888888888888888888877644 PP

  == domain 7  score: -1.3 bits;  conditional E-value: 1.3
                        Cadherin_4   59 y..................GtltlnadGsf 70  
                                        +                  Gt ++++dG+f
  gi|313117270|ref|YP_004044253.1| 1022 QidilirdsgdtrppfvktGTAYVSEDGTF 1051
                                        033333333333444444488889999888 PP

  == domain 8  score: -4.5 bits;  conditional E-value: 7
                        Cadherin_4   21 atvtedtpltitagnvlandtDvdgdd..ltvtavt 54  
                                          ++ dtp+t t  + +++dt  d+ +   t+t ++
  gi|313117270|ref|YP_004044253.1| 1090 TPTPTDTPITST--STTTTDTSTDTPTptKTATPTD 1123
                                        335667777776..4445555555444224444443 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.4      0.68   1.7e+03      52      85 ..      29      60 ..      15      68 .. 0.67
   2 ?    2.5   3.6     0.054   1.4e+02      31      81 ..     100     152 ..      72     170 .. 0.78
   3 !   27.7  11.3   7.5e-10   1.9e-06       2      98 .]     216     306 ..     208     308 .. 0.68
   4 !   23.3  10.2   1.8e-08   4.7e-05       2      97 ..     311     402 ..     310     403 .. 0.77
   5 ?   -1.2   0.2      0.77     2e+03      76      98 .]     667     689 ..     600     689 .. 0.67
   6 ?   -2.5   0.1         2   5.2e+03      59      71 ..     902     914 ..     846     945 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.68
                        Cadherin_5 52 nGtvvdngdGtftftpeanynGevtlsYtvsDge 85
                                       Gt v+   Gt+t  p+++ +  ++ ++tv+D+ 
  gi|313117270|ref|YP_004044253.1| 29 AGTAVA-DTGTVT-APAEDVEVGTDANFTVEDTD 60
                                      344443.456655.69999999999999999975 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.054
                        Cadherin_5  31 anasDvd.gdtLsvsslta.daenGtvvdngdGtftftpeanynGevtlsYtv 81 
                                         + D + +d+++v++ +  ++ n + +d  dG++t++ + n + e+++ Yt 
  gi|313117270|ref|YP_004044253.1| 100 DSDLDGNlDDEVTVTNTSDgSTYNVSSIDPIDGNVTVENAPNSSTEIEIAYTT 152
                                       44555555578****995324456666799*********************85 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 7.5e-10
                        Cadherin_5   2 ndaPvvssevtlaagseDtaltitaaqLLanasDvd.gdtLsvssltadaenGtvvdngdGtftftpeanynGevtl 77 
                                       n aP+++++  ++++++++++ti    +L n+ D    +t sv+ ++ + ++G+++ +++G++t+t +a+ + + ++
  gi|313117270|ref|YP_004044253.1| 216 NTAPTANDD--TTTVTKGESVTIP---VLDNDEDDGsLNTSSVTVVS-EPSEGETTVHSNGSITYTHTADSEANDSF 286
                                       556655554..3345566666665...66665554423444555554.5669************************* PP

                        Cadherin_5  78 sYtvsDgeggtttatasltva 98 
                                       +Y+v D++g+ +++ta+++v+
  gi|313117270|ref|YP_004044253.1| 287 TYEVADDQGE-VSNTANVDVT 306
                                       *******976.4455555553 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 1.8e-08
                        Cadherin_5   2 ndaPvvssevtlaagseDtaltitaaqLLanasD...vdgdtLsvssltadaenGtvvdngdGtftftpeanynGev 75 
                                       n aP+++++  ++++++++++t+    +L n+ D   +d+ +L v+s     ++G+++ n+dGt+t+t +a+   + 
  gi|313117270|ref|YP_004044253.1| 311 NTAPTANDD--TTTVNKGETVTVP---VLDNDVDdgtFDNSSLIVVSG---PSEGETTVNSDGTITYTHTADRVADD 379
                                       889988876..4467777888887...888887744446666777665...347*********************** PP

                        Cadherin_5  76 tlsYtvsDgegg.tttatasltv 97 
                                       +++Y+v+D++g  +  at+++tv
  gi|313117270|ref|YP_004044253.1| 380 SFKYKVEDDQGVeSNIATVDVTV 402
                                       *********98635556666665 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.77
                        Cadherin_5  76 tlsYtvsDgeggtttatasltva 98 
                                       + + +v+D+++g+ +++ ++tv+
  gi|313117270|ref|YP_004044253.1| 667 EYNLRVTDDQSGVQEESRDITVT 689
                                       44567999999999999888885 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 2
                        Cadherin_5  59 gdGtftftpeany 71 
                                        dG+++ft e+  
  gi|313117270|ref|YP_004044253.1| 902 DDGDISFTVEQAD 914
                                       3455555554444 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.3   3.4e+03      43      81 ..     231     273 ..     207     309 .. 0.58
   2 !   13.9   0.0   2.2e-05     0.056      33      95 ..     617     687 ..     584     688 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                                       TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEE....E CS
                               MG2  43 pdgkevkelplatdetggaesefalpeaaklGeysvel....s 81 
                                        ++ ++  l+ + d+ ++  s++++ ++++ Ge +v       
  gi|313117270|ref|YP_004044253.1| 231 GESVTIPVLDNDEDDGSLNTSSVTVVSEPSEGETTVHSngsiT 273
                                       5555555555555555555555555555555555544433331 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.2e-05
                                       -.....EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT-...-SEEEEEEEEECSTTT-EEEEEEE CS
                               MG2  33 k.....lplkltirdpdgkevkelplatdetggaesefalpeaa...klGeysvelsadsaeeslssgsfr 95 
                                       +     +p++l++ d+dg +vk  +++ + +g ae+ef l +++     Gey++++ +d+ + + +s ++ 
  gi|313117270|ref|YP_004044253.1| 617 SskdgnRPVTLELLDDDGDVVKGSTITGRFDGQAEYEFSLDASSldlDPGEYNLRVTDDQSGVQEESRDIT 687
                                       3445569**********************************98733358*******888777777776665 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.7   1.8e-05     0.047       1      23 []    1136    1158 ..    1136    1158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                         PGF-CTERM    1 tPGFGavlAlaGLLaaalLaRRr 23  
                                        tPGFG+ +A+++ LaaalL+ Rr
  gi|313117270|ref|YP_004044253.1| 1136 TPGFGIPIAVVAFLAAALLVSRR 1158
                                        9*******************998 PP

>> Gmad2  Immunoglobulin-like domain of bacterial spore germination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3         1   2.6e+03       4      58 ..      39      91 ..      36     120 .. 0.57
   2 ?   -1.8   0.2       1.5   3.9e+03      44      86 .]     209     247 ..     201     247 .. 0.79
   3 ?   -0.5   0.3       0.6   1.5e+03      29      47 ..     285     303 ..     255     341 .. 0.70
   4 ?   -0.9   0.1       0.8     2e+03       2      41 ..     349     392 ..     348     433 .. 0.71
   5 ?   14.4   0.0   1.3e-05     0.034      11      81 ..     604     675 ..     601     679 .. 0.73
   6 ?   -0.1   0.0      0.44   1.1e+03      53      69 ..    1045    1061 ..    1024    1070 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1
                             Gmad2  4 vtaPapgaevts..pvkvsGkarvFEatvnvrlrddagevlaegfvtAdegapkfgd 58
                                      vtaPa++ ev++   ++v+ + +   a++     d++g++ +e+ + +++g  +   
  gi|313117270|ref|YP_004044253.1| 39 VTAPAEDVEVGTdaNFTVEDTDNPNPAKIV-YFSDSDGTI-NEAETKTGDG--TNKS 91
                                      788888888885336666555555555543.345666655.5666666665..4444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                             Gmad2  44 egfvtAdegapkfgdFeatvefkapepgkgtlevyelsakdGs 86 
                                       +++vtA++ ap+ +d  +tv+      ++ t+ v+  ++ dGs
  gi|313117270|ref|YP_004044253.1| 209 TASVTAANTAPTANDDTTTVTKG----ESVTIPVLDNDEDDGS 247
                                       56788888888888877777766....7899999999999987 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.6
                             Gmad2  29 tvnvrlrddagevlaegfv 47 
                                       ++++++ dd+gev ++++v
  gi|313117270|ref|YP_004044253.1| 285 SFTYEVADDQGEVSNTANV 303
                                       7899999999999666655 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.8
                             Gmad2   2 ievtaPapgae.vtspvkvsG..kar.vFEatvnvrlrddagev 41 
                                       i+v+ P +g++ v+s  +++   +a  v   ++ ++++dd+g+ 
  gi|313117270|ref|YP_004044253.1| 349 IVVSGPSEGETtVNSDGTITYthTADrVADDSFKYKVEDDQGVE 392
                                       77888887765144544444322443588889999999999875 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 1.3e-05
                             Gmad2  11 aevtspvkvsGkarvFEa..tvnvrlrddagevlaegfvtAdegapkfgdFeatvefkape..pgkgtlevyels 81 
                                         vt+  +++G  ++  +   v+++l dd+g v++ + +t+   ++++ ++e++++ + +   pg++ l+v +++
  gi|313117270|ref|YP_004044253.1| 604 RNVTEDETIEGMVSSKDGnrPVTLELLDDDGDVVKGSTITGR--FDGQAEYEFSLDASSLDldPGEYNLRV-TDD 675
                                       6788999999988888884468999********976655544..56666666666666665548*******.444 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.44
                             Gmad2   53 apkfgdFeatvefkape 69  
                                        + + g+Fe tv+f++++
  gi|313117270|ref|YP_004044253.1| 1045 VSEDGTFESTVDFSEQS 1061
                                        66789********9764 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   4.5e-05      0.11      54     121 ..     137     208 ..     112     220 .. 0.77
   2 ?   -2.3   0.4       1.1   2.8e+03      21      75 ..     278     331 ..     266     369 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                              SoxE  54 vneeslphnlvlvqnntaiPnsleissdGkillivGattsnyav.sGi...ssGqsasGlledlsaGtywla 121
                                        n    + ++ +   +++  +++++s dG +  ++G+++sn ++ +Gi   ++G++ +  + d saG y  a
  gi|313117270|ref|YP_004044253.1| 137 ENAPNSSTEIEIAYTTAPEAQNIDLSGDGTVTATIGTAKSNANTdDGIlkvAAGDTLTAAYWDASAGVYRSA 208
                                       4444555567777788888999******************98762576222689999999999999999765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                              SoxE  21 vsssasnlfnfnGtsnGqlkiyiPagwsvlvklvneeslphnlvlvqnntaiPns 75 
                                       + s a++ f ++ + + q ++   a+ +v+v++ n+ ++  + +   n+ ++   
  gi|313117270|ref|YP_004044253.1| 278 ADSEANDSFTYEVA-DDQGEVSNTANVDVTVEVANTAPTANDDTTTVNKGETVTV 331
                                       55666666666643.3444555678888888888888887776666666555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 6855.21
//
Query:       gi|313117271|ref|YP_004044254.1|  [L=221]
Description: 4-amino-5-aminomethyl-2-methylpyrimidine deaminase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.1e-50  169.4   0.0    1.1e-49  169.1   0.0    1.0  1  TENA_THI-4  TENA/THI-4/PQQC family


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   0.0   6.3e-54   1.1e-49       4     209 ..      11     215 ..       9     216 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 6.3e-54
                                       CHHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHHH CS
                        TENA_THI-4   4 lrpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielhl 80 
                                       ++p w+ ++ Hp v++l  Gtl++e f ++v qdy yl+++ rv+a ++++++dl+ +  +++ +  ++++e++lh+
  gi|313117271|ref|YP_004044254.1|  11 ADPVWDAIVAHPMVEQLGAGTLSTEPFEYWVRQDYVYLVDYSRVFAYGAATAPDLDKMGTFAELLDSTINTEMDLHR 87 
                                       5799******************************************************8888888889999****** PP

                                       HHHHHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHHH CS
                        TENA_THI-4  81 rlaealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvke 157
                                        +a ++G+s+ el++t+ sp+t+ay+++l+++a +g++ ++va llpc ++ +e+a+rl ++   ++ + y ew+++
  gi|313117271|ref|YP_004044254.1|  88 AYAAEFGISEAELEATEASPTTRAYTDFLVRVAATGTFGDLVAVLLPCMWGFNETAKRLESEGM-PDDDRYAEWIQT 163
                                       **************************************************************99.************ PP

                                       HCSHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        TENA_THI-4 158 yaseefraaveeakrllerllakvsdeqleelqeiflkalefetsfltmald 209
                                       ya eef++  ++ k+l++ +    sd + e+ ++ f+++ ++e+ f+++a++
  gi|313117271|ref|YP_004044254.1| 164 YAGEEFTELTTWCKELMNDVAVGRSDAERERFRNLFETSARYEYRFWDAAWR 215
                                       ************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1562.29
//
Query:       gi|313117272|ref|YP_004044255.1|  [L=255]
Description: putative transcription activator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-24   87.4   0.0    1.4e-24   87.0   0.0    1.1  1  TENA_THI-4     TENA/THI-4/PQQC family


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0     8e-29   1.4e-24       3     209 ..      34     238 ..      32     239 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 8e-29
                                       HCHHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHH CS
                        TENA_THI-4   3 qlrpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielh 79 
                                       + +p w+ ++ H F++ l   +l+ e+f+ y++qdy +l + v  ++ ++  +++ ++  +l + +     +e++ +
  gi|313117272|ref|YP_004044255.1|  34 RSQPDWDAATTHRFTRELGADELDDEVFRRYLVQDYAFLETLVGLVGHAVGDAPTMAAKSQLTEFLGTLTADENDYF 110
                                       56788******************************************************88888888888888**** PP

                                       HHHHHHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHH CS
                        TENA_THI-4  80 lrlaealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvk 156
                                       +r  ealG+++e  +    +p+t a  ++l + ar+g +ae++a + p ++ y+e a+ ++ +   ++     ew++
  gi|313117272|ref|YP_004044255.1| 111 ERSFEALGVPPETYTDPDLTPTTMAMEDLLERAAREGGYAETLAVFVPAEWIYREWATAVANE--SPSRFYLAEWIE 185
                                       *********************************************************999977..45777789**** PP

                                       HHCSHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        TENA_THI-4 157 eyaseefraaveeakrllerllakvsdeqleelqeiflkalefetsfltmald 209
                                        +a eef+a v+++++ l+r  a +++++ ++l++ f ++  +e+ f ++a+d
  gi|313117272|ref|YP_004044255.1| 186 LHAVEEFQAVVGWLRDELDREGAAAAPQRRRRLERLFRRTASLEVAFFDAAYD 238
                                       **************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1678.43
//
Query:       gi|313117273|ref|YP_004044256.1|  [L=526]
Description: Na+/proline symporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-31  108.0  29.0    6.4e-31  107.6  29.0    1.2  1  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
       0.23   11.6   3.6       0.39   10.9   0.1    2.6  2  TMEM191C  TMEM191C family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6  29.0   7.2e-35   6.4e-31       9     406 .]      44     428 ..      36     428 .. 0.83

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 7.2e-35
                               SSF   9 tgfvlglslaasnisaasfvGlaGavaasGlavvl.lelgalllvlllllllaerlr..nagalTlpdylskRfkgk 82 
                                       +  ++ ++l as ++ + ++  + a+a++G+a v+ + +g  +  +l++  l++r r        l +y+ +R++g 
  gi|313117273|ref|YP_004044256.1|  44 GEGQMSATLIASVMGVWILLSAPEAGALYGIAAVIgYGIGEAV-PMLAYSRLGPRIRelIPEGHSLTEYAYARYGGA 119
                                       456899*************************876526777655.56778888999995533567899*********9 PP

                               SSF  83 rilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlvgal 159
                                            + +++++l++++ l+++l g    ++++ G+   +  +l+++ + lYt  GGl+A+++tdtiq++++l  ++
  gi|313117273|ref|YP_004044256.1| 120 M--YAFVIVVSVLYMFVFLAAELTGISLALNHVAGIPQWQTAVLVGGFVLLYTGYGGLRASIFTDTIQTMVILPLLV 194
                                       9..666777788899999******************99888889999**************************9999 PP

                               SSF 160 illiivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvagl....philvRflaakdak 232
                                       + +  v+l +Gg  ++ + + ea+     ll p+        + +l ++++lv+ v g+    +   +R++aa d+ 
  gi|313117273|ref|YP_004044256.1| 195 LSVAAVILTLGGPGAIHQGVVEANA---TLLDPGF-------VPGLRFGIALVFAVLGAelvnQTWWQRIYAATDSG 261
                                       99999*****************999...5555554.......5666677777777776666689999********** PP

                               SSF 233 ailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaimstl 309
                                        + +g++ +t+  +l+l+++  +++ a   a +v    g+e+ ++ ia+  L   +++++l   +l  +l  +mst 
  gi|313117273|ref|YP_004044256.1| 262 VLERGFRTATVANGLILVLATLLGVVAVGNADVVT-QLGSENYNAGIAFFVLLEGVFGEWLVLGVLLLALTLVMSTA 337
                                       *******************9999999998888865.6799********************986666788999***** PP

                               SSF 310 tslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavil 386
                                       ++l+++ ss++t Dl   +     ++ ++l  ++  +v+ v+++a+      + + vl l  ++++ l++av+  ++
  gi|313117273|ref|YP_004044256.1| 338 DTLFNALSSLVTADLPRLLNDPD-DRTLRLGARAVTVVVAVAAIAV---SLRARS-VLRL-FFVADLLGAAVGFPLV 408
                                       ***************98887777.5555554444444444444433...333334.4555.5899************ PP

                               SSF 387 lalfwkrvneqGAlagliiG 406
                                        +lf  r+   GAla++i+G
  gi|313117273|ref|YP_004044256.1| 409 YGLFTGRLSGAGALASSITG 428
                                       ******************98 PP

>> TMEM191C  TMEM191C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   4.4e-05      0.39      52      93 ..     174     216 ..     163     232 .. 0.83
   2 ?    0.4   0.5     0.079   7.1e+02      38      95 ..     292     348 ..     282     371 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.4e-05
                          TMEM191C  52 alrlwal.galqtllllPlgflalpllylvlvksdavraglps 93 
                                       +lr  ++  ++qt+++lPl+ l+++ ++l+l  ++a+++g+ +
  gi|313117273|ref|YP_004044256.1| 174 GLRASIFtDTIQTMVILPLLVLSVAAVILTLGGPGAIHQGVVE 216
                                       55554441589****************************9865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.079
                          TMEM191C  38 adcekrlfGgagaaalrlwal..galqtllllPlgflalpllylvlvksdavraglpsls 95 
                                       ad  ++l      a++  ++l  g++   l+l +++lal+l++    + d++ + l sl 
  gi|313117273|ref|YP_004044256.1| 292 ADVVTQLGSENYNAGIAFFVLleGVFGEWLVLGVLLLALTLVM---STADTLFNALSSLV 348
                                       5555555555555555555554466677777777777776654...44444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 3583.70
//
Query:       gi|313117274|ref|YP_004044257.1|  [L=41]
Description: hypothetical protein Hbor_30590 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.22s 00:00:00.52 Elapsed: 00:00:00.38
# Mc/sec: 323.57
//
Query:       gi|313117275|ref|YP_004044258.1|  [L=440]
Description: Mn2+/Fe2_ transporter, NRAMP family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-64  216.9  35.5    3.9e-64  216.9  35.5    1.8  2  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.9  35.5   2.2e-68   3.9e-64       2     350 ..      39     372 ..      38     380 .. 0.93
   2 ?   -2.4   2.4       0.1   1.8e+03      68     105 ..     391     429 ..     374     436 .. 0.61

  Alignments for each domain:
  == domain 1  score: 216.9 bits;  conditional E-value: 2.2e-68
                             Nramp   2 atdlqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviG 78 
                                       a+ ++aGa fGy+Llwv+lls +++ + q+l++rLGl +g+g++ l++ +l++ ++++l++++++a+ +++l  +  
  gi|313117275|ref|YP_004044258.1|  39 ASLITAGAGFGYSLLWVVLLSAVAGTVAQYLAMRLGLLSGQGIVTLVESYLGESWAWILVVDVVVAAGVAQLVIMKT 115
                                       899************************************************************************** PP

                             Nramp  79 aAialnllfgipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgevlkglvvPslp 155
                                       +A +  +++gi+  ++++i+av+ l+ l+   +gyr lE + +alv++++l+F+a++f+v++d g++++gl+ P+lp
  gi|313117275|ref|YP_004044258.1| 116 VASVSATITGIDARIWGVIWAVILLAGLA--GRGYRFLELAAKALVAAVVLAFVASAFIVPIDAGSAVQGLI-PTLP 189
                                       *****************************..***************************************99.**** PP

                             Nramp 156 gkeslllavgilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiial.ivaflinlailivaAavlysg 231
                                       + + +l+a+gilG  v+++ + +hs++++ r+++     ++  +  +++D+i+++ +++++++++i++vaA+vl + 
  gi|313117275|ref|YP_004044258.1| 190 S-NGALVAAGILGGAVHITLITMHSYTMRARGWDE----SD--YGLATFDVIASMlVAFGIYSISIFLVAASVLSDP 259
                                       *.******************************776....78..************5666789*************55 PP

                             Nramp 232 gkdvesledaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralafvpali 308
                                       +    +  +aa+aL pl+G + a++lF +gL +a++s++  +t+   +v+++ lg+   ++ +r    + af  + +
  gi|313117275|ref|YP_004044258.1| 260 NL---TTVGAAQALGPLVG-PNAKWLFLLGLGGAAVSTLGGNTIVPPFVVADKLGWGTTVEDSRYRALLAAFALLSA 332
                                       54...7889**********.7***************************************88886665556666655 PP

                             Nramp 309 villigaelelvkllvlsqvllslllPfaliplllltsskkl 350
                                         ++ig ++     lvl+ +l  +++Pfa++++l+l++s+++
  gi|313117275|ref|YP_004044258.1| 333 PGAFIGGQVI--GQLVLVLALGTVGTPFAIAVVLYLLNSEAV 372
                                       5555555555..99*************************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.1
                             Nramp  68 iiatdlaeviGa.Aialnllfgipllvgvlitavlvlll 105
                                         a  ++ v G  A +++ll+g  l  +v++ +++v+ll
  gi|313117275|ref|YP_004044258.1| 391 SGALAANFVRGQiAGGVELLSGAVLAFAVILGVAIVVLL 429
                                       444444445554488888888665555555544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2629.27
//
Query:       gi|313117276|ref|YP_004044259.1|  [L=57]
Description: hypothetical protein Hbor_30610 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.13   12.1   0.0    1.1  1  PAZ       PAZ domain


Domain annotation for each model (and alignments):
>> PAZ  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.3e-06      0.13      67      92 ..      11      36 ..       6      57 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.3e-06
                                      CECCHHHHCCT---ST-TT--EEEEE CS
                               PAZ 67 itfaeYfkkkYnieikdqdqplldvd 92
                                      i   eY ++ Y+ie++d+dq++  v 
  gi|313117276|ref|YP_004044259.1| 11 IECDEYTHTDYGIELYDEDQFVAFVP 36
                                      6678****************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.41
# Mc/sec: 417.26
//
Query:       gi|313117277|ref|YP_004044260.1|  [L=230]
Description: DNA-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-77  257.5   0.3    8.4e-77  257.3   0.3    1.0  1  PIN_5     PINc domain ribonuclease


Domain annotation for each model (and alignments):
>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.3   0.3   4.7e-81   8.4e-77       1     206 []       9     220 ..       9     220 .. 0.95

  Alignments for each domain:
  == domain 1  score: 257.3 bits;  conditional E-value: 4.7e-81
                             PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyippsvykElkeflkreeveeeviakldtwlv 77 
                                       +fvlDTs+++++e+r+  ++e+leeav +ll+l+a arl+l+isc++pps+++El  +l+++ev eev++kldtw+v
  gi|313117277|ref|YP_004044260.1|   9 QFVLDTSLFITEEIRR--EDESLEEAVLHLLELVAMARLELNISCHMPPSIHDELAAMLRDREVGEEVFTKLDTWVV 83 
                                       5***************..99********************************************************* PP

                             PIN_5  78 kkspdryevkipaeilyeyveevrerinkGlrvaEeavreaaeesekl......ekee....eeeevgelikklRek 144
                                       +kspdry v+ipa+i+y++v+e+++r+++Glrv+Eea+re ++   +       e  +     ++e +++++k+R+k
  gi|313117277|ref|YP_004044260.1|  84 RKSPDRYGVTIPANIVYNFVDEMSDRVDRGLRVSEEAIREVEQLDPENlaattgE--DgteaYMTEADRVLSKMRDK 158
                                       *****************************************99887665554441..1555599************* PP

                             PIN_5 145 YrealRkGilDsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeylk 206
                                       Yr+alR+G+lDs+eD+d+l+LA+EL+a+vv++D+Gi +wa+++Glr+v++ +fp++l+eyl+
  gi|313117277|ref|YP_004044260.1| 159 YRRALRRGVLDSREDFDLLVLARELNAGVVTEDRGIISWADEFGLRYVRGGRFPTLLEEYLR 220
                                       ************************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1547.66
//
Query:       gi|313117278|ref|YP_004044261.1|  [L=375]
Description: ATP-dependent DNA ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.1e-45  152.3   0.3    1.4e-44  151.1   0.2    1.7  2  Lig_C       Ligase Pab1020 C-terminal region
    8.6e-10   39.2   0.0    1.5e-09   38.4   0.0    1.4  1  RNA_ligase  RNA ligase


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.83   7.5e+03      75      90 ..      15      30 ..       9      35 .. 0.79
   2 !  151.1   0.2   1.6e-48   1.4e-44       1     125 []     248     371 ..     248     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.83
                                      HHHHHHHHHHHCTT-- CS
                             Lig_C 75 enieellehLrrlgvk 90
                                      e+ +el+eh+ r +++
  gi|313117278|ref|YP_004044261.1| 15 ETPDELFEHFSRRSID 30
                                      6678999999998876 PP

  == domain 2  score: 151.1 bits;  conditional E-value: 1.6e-48
                                       HHCCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHH CS
                             Lig_C   1 vafsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeeni 77 
                                       +afs++f+ grdF+fsRviReafqavef+e++e+lr+ra++LGes+L p veti++v+++++++e+++vr +d+e+i
  gi|313117278|ref|YP_004044261.1| 248 YAFSLPFDRGRDFFFSRVIREAFQAVEFDEDDERLRDRAHDLGESVLLPAVETIREVQAGKTAGERHTVR-GDSESI 323
                                       8*********************************************************************.****** PP

                                       HHHHHHHHCTT--EEEEEEE..TTEEEEE..EE-HHHHHHHHHHHTT- CS
                             Lig_C  78 eellehLrrlgvkaeveekekedgelvvkfkkiaqsttdkikslLeGg 125
                                       ++ll+hLr++++++e+e++++edge++v+f k+a+st+++++++L+Gg
  gi|313117278|ref|YP_004044261.1| 324 DALLDHLRNHSLTVEIESDRREDGERIVEFVKVAESTMGRTQYYLDGG 371
                                       **********************************************96 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.7e-13   1.5e-09       2     160 ..      83     236 ..      82     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.7e-13
                                       EEEEEEE-SSEEEEEEEETT.EEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH.........ECCEEEEEEEES. CS
                        RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqilpfgeekfkefkrwaaalrkklkekla.......neelilyGEligh 70 
                                       +vv++EKl+G n+ri  v e + +++ ++  p  ++++            ++++ l+        ++++l+ Elig+
  gi|313117278|ref|YP_004044261.1|  83 TVVAEEKLNGFNVRIADVGEpLAFTKGGHVCP--YTTS------------RVRDLLDlssffadYPKMMLCAELIGP 145
                                       79*************98844355555555554..1121............33333333345558888*********6 PP

                                       SS.......TT.SS.EEEEEEEEEEECTTBECE--HHHHHHHHHCCT..B..EEEEE.SS.HHHHHCCC..HHHHTC CS
                        RNA_ligase  71 si.....kygg.lpkefyvFdifdirdkeeqrylspdevealakglg..tvpvlyegkfl.aaeellell.lskgnk 137
                                               y+g + +   vF i    ++ +++ l+ + +++l++++g  + ++++ ++     e ++e + + ++  
  gi|313117278|ref|YP_004044261.1| 146 ETpytthDYEGiDSNAVRVFGIR---NRATGEPLPVESRRDLCDEYGfpQPRLFGWYSQGaVVEGVREAIsELDDAG 219
                                       66234445555555588888888...677***************99996333333333335444444442225888* PP

                                       --EEEEEESSSSBETTEBSEEEE CS
                        RNA_ligase 138 rEGlVikpeselyknkgraifKv 160
                                       rEG+V+k++++        ++K+
  gi|313117278|ref|YP_004044261.1| 220 REGVVMKSADG------TEMVKY 236
                                       *******8888......566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 2870.09
//
Query:       gi|313117279|ref|YP_004044262.1|  [L=140]
Description: hypothetical protein Hbor_30640 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-26   90.0   5.7    6.3e-14   52.2   0.2    2.4  3  CBS       CBS domain
  ------ inclusion threshold ------
       0.11   12.2   0.8       0.51   10.0   0.1    2.0  2  DAGK_cat  Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.2   7.1e-18   6.3e-14       1      52 [.       3      53 ..       3      54 .. 0.97
   2 !   39.9   1.0   4.9e-14   4.4e-10       1      51 [.      68     118 ..      68     121 .. 0.94
   3 ?   -2.5   0.0      0.85   7.6e+03      10      23 ..     121     134 ..     119     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 7.1e-18
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52
                                      V+d+m+++vvt++pdt  +e++++mr+++v+++ VV+ d+++ Givt+rDl+
  gi|313117279|ref|YP_004044262.1|  3 VSDLMRKNVVTATPDTAASELAQQMRDENVGSV-VVEADNRPAGIVTDRDLA 53
                                      89*******************************.**9999**********96 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 4.9e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                       ++d+mt+d+ tv+ dt + e+ +++ e+ v+r+PVVd+dg l Givtl Dl
  gi|313117279|ref|YP_004044262.1|  68 AEDVMTSDLTTVTTDTGVMELCDELCEASVRRMPVVDGDGTLAGIVTLDDL 118
                                       579*********************85666*********************8 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.85
                                       EEEETTSBHHHHHH CS
                               CBS  10 vtvppdttleeale 23 
                                       ++++++++l +++e
  gi|313117279|ref|YP_004044262.1| 121 LFAREQQNLTDVIE 134
                                       56778888888876 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.043   3.9e+02      35      61 ..      11      37 ..       2      39 .. 0.67
   2 ?   10.0   0.1   5.7e-05      0.51      31      72 ..      72     113 ..      59     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.043
                                      EEE--STTHHHHHHHHHHHCC-SEEEE CS
                          DAGK_cat 35 lieteepgdakelakeakeegvdlivv 61
                                      +++ + +  a ela+++++e+v  +vv
  gi|313117279|ref|YP_004044262.1| 11 VVTATPDTAASELAQQMRDENVGSVVV 37
                                      444455666788888888887766665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 5.7e-05
                                       CEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHH CS
                          DAGK_cat  31 velelieteepgdakelakeakeegvdlivvaGGDGtvsevl 72 
                                       ++ +l++++ +    el+ e+ e++v++  v+ GDGt+  ++
  gi|313117279|ref|YP_004044262.1|  72 MTSDLTTVTTDTGVMELCDELCEASVRRMPVVDGDGTLAGIV 113
                                       466778888888899***********************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 1136.10
//
Query:       gi|313117280|ref|YP_004044263.1|  [L=617]
Description: sodium/proton antiporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-34  117.5  42.7    7.7e-34  117.1  42.7    1.1  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
    1.1e-28   99.8   0.8    1.1e-28   99.8   0.8    2.0  2  TrkA_N           TrkA-N domain
    8.4e-09   35.1   0.0    2.8e-08   33.5   0.0    2.0  1  TrkA_C           TrkA-C domain
    1.3e-05   25.6   0.2    2.8e-05   24.5   0.2    1.6  1  NAD_binding_7    Putative NAD(P)-binding
    0.00066   20.2   1.4     0.0015   19.1   0.2    2.3  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00085   18.9   0.0     0.0015   18.2   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.001   19.0   1.2     0.0021   18.0   1.2    1.5  1  NAD_binding_10   NAD(P)H-binding
     0.0013   18.9   0.3     0.0041   17.4   0.3    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0014   18.3   0.1     0.0035   17.0   0.1    1.7  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0022   17.5   0.3     0.0034   16.9   0.3    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.003   16.9   0.1     0.0041   16.4   0.1    1.2  1  FAD_binding_3    FAD binding domain
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.036   14.2   0.1    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.025   13.9   0.3      0.098   12.0   0.0    2.0  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.063   13.8   0.1       0.17   12.4   0.1    1.8  1  XdhC_C           XdhC Rossmann domain
      0.077   13.2   4.2        1.7    8.9   0.1    3.0  2  DMT_6            Putative member of DMT superfamily (DUF486)


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1  42.7   6.4e-37   7.7e-34       3     373 ..       9     387 ..       7     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 6.4e-37
                                       HHHHHHHHHHH...H.HHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGC CS
                    Na_H_Exchanger   3 llillallvgl...l.arrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelr 73 
                                       ++++++l +g+   + a rl++p++++li+aG+ +Gp glg+i p    + l  +  l + +++F+ +++l++++lr
  gi|313117280|ref|YP_004044263.1|   9 VIVVTILGLGVaaqViADRLRVPSVMFLILAGIAVGPEGLGVITPAvfGDGLPAIVGLSVAIIVFEGAFHLNFERLR 85 
                                       4444444444468966*************************999999*9**************************** PP

                                       CTHHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHH CS
                    Na_H_Exchanger  74 knlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvl 150
                                       +  ++++ l ++g +i+++++++++++   l+ +++ a+l+g++l at p v+++i+ +   v++r++t+l+ e+v+
  gi|313117280|ref|YP_004044263.1|  86 EAPRETFRLVTIGAVISLIGTATVVRF--ALDASWSVAFLIGSLLIATGPTVITPIM-NVVPVRNRVATTLETEGVV 159
                                       ********************9999996..89**************************.******************* PP

                                       HHHHCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS....CTHHHHHHHHHHHHH CS
                    Na_H_Exchanger 151 nDavavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft....dddrelevllvllla 223
                                       nD++a +l +v+ +++     ++ +  +l+ +f   ++gg+l+g v+  ++++++r++    ++ ++   l+vl+ +
  gi|313117280|ref|YP_004044263.1| 160 NDVTAAILAFVMFEFV---LLETQGFPTLIREFGMRLGGGILVGSVVAGIVWYLLRHVslsvENAPQNARLIVLVAS 233
                                       ***************9...5566666677777777777777777777666666666666666*************** PP

                                       HHHHHHHHTS.XXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH...HHHHHHHHHHHHHHSXHHHHHXXHHHHHHH CS
                    Na_H_Exchanger 224 llaallaell.gvsgilgaflaGlvlseyefsnklseklesfre...glfnplfFvlvGlsldlkvlnnhlsvlilv 296
                                       l+++++ae++    gi ++   G +l++ e     + ++e f      l++ ++F+ +   l l  +  +l    +v
  gi|313117280|ref|YP_004044263.1| 234 LVMYGIAEIVaPEAGIAAVATGGFTLGNAEIPY--RGDIERFKGditLLVISFVFITLASLLSLRDIL-SLGIGGVV 307
                                       **********77777777888889999776666..4667777777779999************99996.99999999 PP

                                       HHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHH....XHHHHTT.SSTTTCSTSXHH CS
                    Na_H_Exchanger 297 llilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpal....gllarel.yallivvvlftv 368
                                       ++i+va  ++r++ v l++   +l++ e+l+i++ g  rg + + +a l+ ++    +  a+++ + ++++v++ tv
  gi|313117280|ref|YP_004044263.1| 308 VVIVVAG-VIRPALVILCTVGDRLTFDERLYISAIGP-RGIIPASVATLFALElqsqNPQAATMlVGTVFLVIVSTV 382
                                       9999999.7**********999***************.************999655544444666677777777776 PP

                                       HHHHH CS
                    Na_H_Exchanger 369 lvqGl 373
                                       ++ G+
  gi|313117280|ref|YP_004044263.1| 383 VFEGG 387
                                       66665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.2   2.7e+03       2      18 ..      13      29 ..      12      37 .. 0.86
   2 !   99.8   0.8   9.4e-32   1.1e-28       2     110 ..     404     512 ..     403     517 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.2
                                      EEES-SHHHHHHHHHHH CS
                            TrkA_N  2 iiiGlGrvGrslaeeLs 18
                                       i+GlG  ++ +a++L+
  gi|313117280|ref|YP_004044263.1| 13 TILGLGVAAQVIADRLR 29
                                      69************997 PP

  == domain 2  score: 99.8 bits;  conditional E-value: 9.4e-32
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanil 78 
                                       +iiG GrvG++l+e+L+e+ ++v++id+d+++ve+lr++g+ v +gd+t++evLe+ag+++a++v aatg d++n+l
  gi|313117280|ref|YP_004044263.1| 404 LIIGGGRVGQALTERLEERDEEVLIIDNDDQTVETLRADGFSVRHGDGTQQEVLESAGANNARVVAAATGTDDVNLL 480
                                       7*****************6667******************************************************* PP

                                       HHHHHHHHTSSSEEEEEESSGGGHHHHHHHTT CS
                            TrkA_N  79 avllakelnpkkkiiaraqdpehaellkklga 110
                                       +++lak+ ++  +++ar+++p +++++++l +
  gi|313117280|ref|YP_004044263.1| 481 VAQLAKNTFGVERVVARVNQPGNIDAFEDLDI 512
                                       ***************************99876 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   2.3e-11   2.8e-08       2      65 ..     548     611 ..     547     615 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.3e-11
                                       EEEEEE--GGGTTSBHHHHT..HHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkeln..lrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlael 65 
                                        e++v+ +  +vG t++el   l++ ++ ++ + R++   +p +++++e GD+l+++g  ++++++
  gi|313117280|ref|YP_004044263.1| 548 QEIEVT-NVAIVGETISELMaeLPE-DCHLALLSRDETNQLPHPEDTIERGDHLTFIGRTEAVRQA 611
                                       578887.888********4444777.************************************9986 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2   2.3e-08   2.8e-05       5      85 ..     398     491 ..     395     507 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.3e-08
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk..........laeeel..ekdlegadlviaat 69 
                                       +   + l++GgG+v++   ++l e + +v +++++  + +e +++           +++e+  ++  ++a +v aat
  gi|313117280|ref|YP_004044263.1| 398 VIPMRTLIIGGGRVGQALTERLEERDEEVLIIDND-DQTVE-TLRadgfsvrhgdGTQQEVleSAGANNARVVAAAT 472
                                       556789*****************************.33333.22212222211111233332224488899****** PP

                     NAD_binding_7  70 ddrelneriaeaaka...r 85 
                                         +++n  +a++ak+    
  gi|313117280|ref|YP_004044263.1| 473 GTDDVNLLVAQLAKNtfgV 491
                                       *************974433 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.1   3.8e+03       2      18 ..      12      28 ..      11      30 .. 0.89
   2 !   19.1   0.2   1.3e-06    0.0015       4      85 ..     405     488 ..     402     500 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.1
                                      EEEETTSHHHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgl 18
                                      + i+G G  ++ +a +l
  gi|313117280|ref|YP_004044263.1| 12 VTILGLGVAAQVIADRL 28
                                      689**********9987 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.3e-06
                                       EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHH.HHHC-EEECECHHHHHH.....H-SEEEE-S-HHHH CS
                     F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeela.eelgvkvtavdneeaae.....eadvvvlavkpedv 74 
                                       iiG+G++g+al+++l +++   +e++++ +++ +++e l+ + ++v+   ++++e++e     +a vv  a  + dv
  gi|313117280|ref|YP_004044263.1| 405 IIGGGRVGQALTERLEERD---EEVLII-DNDDQTVETLRaDGFSVRHGDGTQQEVLEsaganNARVVAAATGTDDV 477
                                       89*****************...****99.888888888873445555544555555443333367777777777777 PP

                                       HHHHHHCGHHH CS
                     F420_oxidored  75 eevlselakda 85 
                                         ++++lak++
  gi|313117280|ref|YP_004044263.1| 478 NLLVAQLAKNT 488
                                       77777776665 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.2e-06    0.0015       1      50 [.     401     450 ..     401     480 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TT CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepg 50 
                                       m+  +iG G vG      l e+  ev+++D+d+++v++l+++ +++ + +
  gi|313117280|ref|YP_004044263.1| 401 MRTLIIGGGRVGQALTERLEERDEEVLIIDNDDQTVETLRADGFSVRHGD 450
                                       67789************************************999987754 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.2   1.7e-06    0.0021       3      80 ..     408     483 ..     407     517 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                                       TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC....HH CS
                    NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk....de 75 
                                        G+vG++l+++l +r + e ++++ n +++ e  +++g +v +gd t++e l++a ++   Vv+a+ g+++      
  gi|313117280|ref|YP_004044263.1| 408 GGRVGQALTERLEER-DEE-VLIIDNDDQTVETLRADGFSVRHGDGTQQEVLESAGANNARVVAAATGTDDvnllV- 481
                                       59*************.556.5888888777665568*********************9999999998777623332. PP

                                       HHHHH CS
                    NAD_binding_10  76 egakn 80 
                                          ++
  gi|313117280|ref|YP_004044263.1| 482 ---AQ 483
                                       ...22 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   3.4e-06    0.0041       2      73 ..     404     467 ..     403     500 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-06
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEE CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlv 73 
                                       liiG+G+vGqa++e l+++++   e+ ++d +++ +e l a+     f+ +  d  ++e  L+++ + +  v
  gi|313117280|ref|YP_004044263.1| 404 LIIGGGRVGQALTERLEERDE---EVLIIDNDDQTVETLRAD----GFSVRHGDGTQQEV-LESAGANNARV 467
                                       89****************976...6********998877654....34444444444433.44444444444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.9e-06    0.0035       2      56 ..     404     460 ..     403     482 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.9e-06
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECE CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppe 56 
                                       +i+G G +G+ l  +L +  ++v +i++++  +e+l+ +G++++  + +++ +++++
  gi|313117280|ref|YP_004044263.1| 404 LIIGGGRVGQALTERLEERDEEVLIIDNDDqTVETLRADGFSVRHGDgTQQEVLESA 460
                                       79*****************************************99998666666555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   2.8e-06    0.0034       2      80 ..     404     478 ..     403     502 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.8e-06
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       l++G+ G +G+al+++l+e++ ev+ +d++ ++ +t r +  ++ ++d t+++ le + ++   +a + +Aa g+ +
  gi|313117280|ref|YP_004044263.1| 404 LIIGG-GRVGQALTERLEERDEEVLIIDNDDQTVETLRADGFSVRHGDGTQQEVLESAGAN---NARVVAAATGTDD 476
                                       78888.*******************************99999***********99999985...3555555566666 PP

                                       HH CS
                         Epimerase  79 as 80 
                                       ++
  gi|313117280|ref|YP_004044263.1| 477 VN 478
                                       55 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.5e-06    0.0041       3      49 ..     402     448 ..     400     530 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHH CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrt 49 
                                        +lI+G+G +G  l+  L e+  +v++++  ++tv++ radg++ r 
  gi|313117280|ref|YP_004044263.1| 402 RTLIIGGGRVGQALTERLEERDEEVLIIDNDDQTVETLRADGFSVRH 448
                                       579******************99*******************99874 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     3e-05     0.036       4      78 ..     405     486 ..     403     503 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHC....SEEEE-SSSHHHHHHHH CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...akaaesieelvasl....dvvitmvkagkavdevi 73 
                                       +iG G  G+ + ++l++++ +v +++ + + ve+l a+g    ++  + +e+++s+      v+   + +++v+ ++
  gi|313117280|ref|YP_004044263.1| 405 IIGGGRVGQALTERLEERDEEVLIIDNDDQTVETLRADGfsvRHGDGTQQEVLESAgannARVVAAATGTDDVNLLV 481
                                       69************************************966533444566777776666666666666677777777 PP

                                       HSHCC CS
                     NAD_binding_2  74 eglle 78 
                                        +l++
  gi|313117280|ref|YP_004044263.1| 482 AQLAK 486
                                       77665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.4   1.6e+03      39      56 ..      12      29 ..       5      38 .. 0.86
   2 ?   12.0   0.0   8.2e-05     0.098      37      80 ..     401     444 ..     384     460 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                                      EEEES-SHHHHHHHHHHH CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlk 56
                                      v i+GlG  +q +a+rl+
  gi|313117280|ref|YP_004044263.1| 12 VTILGLGVAAQVIADRLR 29
                                      88************9987 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.2e-05
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80 
                                       ++  iiG Gr+Gqa+ +rl++ + +v+++d   ++ e+ ++ g+
  gi|313117280|ref|YP_004044263.1| 401 MRTLIIGGGRVGQALTERLEERDEEVLIIDNDDQTVETLRADGF 444
                                       6778**************************99987776666665 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00015      0.17       2      93 ..     404     489 ..     403     505 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE-EEEE--S-HHHHHHHHHHHSSS--SEEEESS-H CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeadetavvvlthdhklDaealeaalrkkaayigllGSr 78 
                                       +i+G+g v+qal + +++ + +v ++d+++++   e +     +    + h+  + +e+le a +++a+ +++   +
  gi|313117280|ref|YP_004044263.1| 404 LIIGGGRVGQALTERLEERDEEVLIIDNDDQTV--ETLR----ADGFSVRHGDGTQQEVLESAGANNARVVAAATGT 474
                                       69****************************744..4444....2234445555555555555555555555544444 PP

                                       HHHHHHCTTS.--.. CS
                            XdhC_C  79 kkaarrlerlraagl 93 
                                          + ++++l+++ +
  gi|313117280|ref|YP_004044263.1| 475 DDVNLLVAQLAKNTF 489
                                       445555555544444 PP

>> DMT_6  Putative member of DMT superfamily (DUF486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0014       1.7      27     101 ..      60     133 ..      53     137 .. 0.91
   2 ?    3.7   1.4     0.057        68       2      55 ..     277     334 ..     276     384 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                             DMT_6  27 lllvilvsWgialfEYllqvpAnriGaeenlslaqlkiiqevitlvvfvlfsvlllkeklklnhlvaflllvlav 101
                                       l +++ +s +i +fE ++++  +r+  +   +++ l +i  vi+l+  +++  ++l+ ++++ +l++ ll++++ 
  gi|313117280|ref|YP_004044263.1|  60 LPAIVGLSVAIIVFEGAFHLNFERLREAP-RETFRLVTIGAVISLIGTATVVRFALDASWSVAFLIGSLLIATGP 133
                                       567889999****************9998.89**************************************99875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.057
                             DMT_6   2 illlilsnvfmtlAWyghLk..lkkk....plllvilvsWgialfEYllqvpAnriGaee 55 
                                       i+ll++s vf+tlA    L+  l  +     +++vi+v+ +i  +  +l    +r+ ++e
  gi|313117280|ref|YP_004044263.1| 277 ITLLVISFVFITLASLLSLRdiL--SlgigGVVVVIVVAGVIRPALVILCTVGDRLTFDE 334
                                       789***********999999642..22344777777777666544445555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 3671.45
//
Query:       gi|313117281|ref|YP_004044264.1|  [L=298]
Description: universal stress protein UspA-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-64  215.6   6.9    4.2e-33  114.8   2.1    2.0  2  Usp             Universal stress protein family
  ------ inclusion threshold ------
      0.015   15.1   0.9       0.54   10.1   0.1    2.8  3  DUF5615         Domain of unknown function (DUF5615)
      0.032   14.5   0.5       0.33   11.2   0.1    2.5  3  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
       0.23   11.4   1.2         10    6.2   0.1    2.7  3  FR47            FR47-like protein


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   2.1   9.4e-37   4.2e-33       1     141 []       1     141 [.       1     141 [. 0.99
   2 !  103.8   0.2   2.4e-33   1.1e-29       2     140 ..     152     290 ..     151     291 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 9.4e-37
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my++Il+++Dgse++ +A+e++  la+ ++a++++++v+d +a g v da    ee  + l+++ ++  +++aa  +
  gi|313117281|ref|YP_004044264.1|   1 MYETILIPTDGSEHAVRAAEHGQYLARLFDATVHIVNVVDVQAAGGVFDAGGVDEEFVSRLKAKGERTIEEAAAVID 77 
                                       9***************************************************************999999******* PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       + ++ ++ v+ g p+eeile+a e+++d +V+G++gr+gl+r++ GSv+e+v+r a++pVl Vr
  gi|313117281|ref|YP_004044264.1|  78 ETESIQTAVLKGRPDEEILEYAAEHGVDALVMGTHGRTGLRRYIAGSVTERVVRLADIPVLTVR 141
                                       *************************************************************998 PP

  == domain 2  score: 103.8 bits;  conditional E-value: 2.4e-33
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       y+ +l+++Dgse + +A+e++l+ a+++ga++++++++d  + +a++++  ++e   + ++e e + ++ + +a+++
  gi|313117281|ref|YP_004044264.1| 152 YDEVLIPTDGSEPASAAVEHGLAIAEKSGARVHAVNIVDVGNVSASPTYTLPSEVIGQLESEGETVTEEIASQARER 228
                                       789***********************************************99999999999999999999******* PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       g + +++v+eg pa ++l++a+e+d++li +G+ gr+gl r+llGS++e+++r++++pVl+V
  gi|313117281|ref|YP_004044264.1| 229 GLEAVTEVREGFPAKTLLDYANENDISLIAMGTAGRTGLNRYLLGSTTERIIRQSDVPVLAV 290
                                       ************************************************************99 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00012      0.54      24      48 ..      79     103 ..      66     105 .. 0.86
   2 ?   -3.1   0.0       1.5   6.7e+03      18      37 ..     131     151 ..     125     154 .. 0.69
   3 ?    2.6   0.0     0.026   1.2e+02      11      52 ..     219     257 ..     215     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                           DUF5615  24 vlhvrelglegasDeeileyAkeed 48 
                                       + +++ + l+g +DeeileyA e++
  gi|313117281|ref|YP_004044264.1|  79 TESIQTAVLKGRPDEEILEYAAEHG 103
                                       567888899*************997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                           DUF5615  18 reaghdvlhvrelgleg.asD 37 
                                       r a + vl+vr++++++ a+D
  gi|313117281|ref|YP_004044264.1| 131 RLADIPVLTVRSTDQSQvAED 151
                                       556677888888887764555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.026
                           DUF5615  11 prlvellreaghdvlhvrelglegasDeeileyAkeedriiv 52 
                                        +++ + re+g+++++  +   eg + ++ l+yA+e+d  ++
  gi|313117281|ref|YP_004044264.1| 219 EEIASQARERGLEAVTEVR---EGFPAKTLLDYANENDISLI 257
                                       6677888888886655433...5577899********98776 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.74   3.3e+03      53      73 ..      35      65 ..      23      89 .. 0.59
   2 ?   11.2   0.1   7.4e-05      0.33      12      72 ..      92     154 ..      85     197 .. 0.77
   3 ?    0.3   0.0      0.18     8e+02      39      76 ..     212     253 ..     206     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.74
                                      -EEEEEESSSBS-----H............. CS
                    Asparaginase_C 53 ivvvatsqcpsgsvsnseye..........a 73
                                      iv v+ +q   g ++++ ++          +
  gi|313117281|ref|YP_004044264.1| 35 IVNVVDVQAAGGVFDAGGVDeefvsrlkakG 65
                                      5666667777777777655444443333333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.4e-05
                                       -HHHHHHHHHTT--EEEEEEBTTTB--H.....HHHHHHHHHHTTT-EEEEEESSSBS-----H.. CS
                    Asparaginase_C  12 dtkvlkallkkgakGvvlegtGvGnlps.....allealkeakargivvvatsqcpsgsvsnseye 72 
                                       d+++l+++ ++g++++v+ + G+++l       ++ ++++    ++i+v  +  + + +v++++ e
  gi|313117281|ref|YP_004044264.1|  92 DEEILEYAAEHGVDALVMGTHGRTGLRRyiagsVTERVVRL---ADIPVLTVRSTDQSQVAEDYDE 154
                                       7899***********************87655333333333...59**999999999999888543 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.18
                                       H....HHHHHHHHHHTTT-EEEEEESSSBS-----H.....H CS
                    Asparaginase_C  39 s....allealkeakargivvvatsqcpsgsvsnseyeagke 76 
                                       s    ++ e +++a++rg   v  +++ +   +   y+++++
  gi|313117281|ref|YP_004044264.1| 212 SegetVTEEIASQARERGLEAVTEVREGFPAKTLLDYANEND 253
                                       444458889999999999999999999887777776765555 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0023        10      30      66 ..     109     145 ..     105     149 .. 0.90
   2 ?   -2.7   0.0       1.3     6e+03      40      58 ..     215     233 ..     214     239 .. 0.66
   3 ?    3.3   0.0     0.018        79      33      66 ..     262     295 ..     254     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0023
                                       -GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-H CS
                              FR47  30 lpehrrrGlgsrlvkalakeiaergktvllvvvasNt 66 
                                         +h r Gl + ++ ++++++++  ++++l v+ +++
  gi|313117281|ref|YP_004044264.1| 109 MGTHGRTGLRRYIAGSVTERVVRLADIPVLTVRSTDQ 145
                                       56899***************************99886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHS-S-EE CS
                              FR47  40 srlvkalakeiaergktvl 58 
                                         +++++a + +erg +++
  gi|313117281|ref|YP_004044264.1| 215 ETVTEEIASQARERGLEAV 233
                                       5677778888777776665 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.018
                                       G-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-H CS
                              FR47  33 hrrrGlgsrlvkalakeiaergktvllvvvasNt 66 
                                       + r Gl + l  + +++i+++ + ++l v+a ++
  gi|313117281|ref|YP_004044264.1| 262 AGRTGLNRYLLGSTTERIIRQSDVPVLAVNARDE 295
                                       6699*************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 2105.67
//
Query:       gi|313117282|ref|YP_004044265.1|  [L=141]
Description: IclR-like transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-10   39.9   0.3    4.9e-10   39.3   0.3    1.3  1  HTH_20    Helix-turn-helix domain
    6.1e-07   29.1   0.4      2e-06   27.5   0.3    2.0  2  HTH_IclR  IclR helix-turn-helix domain
    0.00038   20.3   0.0    0.00065   19.5   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0014   18.5   0.1     0.0034   17.2   0.1    1.6  1  MarR_2    MarR family
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.029   13.9   0.0    1.3  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.029   14.2   0.0      0.052   13.4   0.0    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
      0.037   13.8   0.2      0.042   13.7   0.2    1.3  1  DUF742    Protein of unknown function (DUF742)
      0.038   14.1   0.0      0.068   13.3   0.0    1.5  1  FUR       Ferric uptake regulator family
       0.14   11.7   0.0       0.18   11.4   0.0    1.1  1  ArsR      ArsR transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.3   2.5e-13   4.9e-10       2      59 ..      28      84 ..      27      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.5e-13
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      ++++A+ +   r+il+a  ++e+l+ase+ e++dl+ +t ++ L++L +agL+e ++ 
  gi|313117282|ref|YP_004044265.1| 28 DLLDAFNDAGCRAILDAT-SGEALSASEVSEACDLPLSTTYRKLDQLTDAGLLEERTR 84
                                      67888889999*******.***********************************9985 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.3   9.8e-10     2e-06      18      50 ..      39      81 ..      27      83 .. 0.79
   2 ?   -2.6   0.0       2.5     5e+03      26      42 ..      86     102 ..      86     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 9.8e-10
                                      S..........-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 18 e..........ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +          l+ se++++++lp St++R L  L+  G++e 
  gi|313117282|ref|YP_004044265.1| 39 RaildatsgeaLSASEVSEACDLPLSTTYRKLDQLTDAGLLEE 81
                                      44444444455******************************96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                       HHHTS-HHHHHHHHHHH CS
                          HTH_IclR  26 rrtglpkStvhRlLqtL 42 
                                       rr+g + S   Rl+  +
  gi|313117282|ref|YP_004044265.1|  86 RRSGKHASEYARLVEDM 102
                                       68888889888888766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.3e-07   0.00065      21      56 ..      48      83 ..      40     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.3e-07
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      + ++a+e++e+ ++p s+ Y+ L +L d+Gl e + 
  gi|313117282|ref|YP_004044265.1| 48 EALSASEVSEACDLPLSTTYRKLDQLTDAGLLEERT 83
                                      5689***************************99876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.7e-06    0.0034      10      55 ..      41      83 ..      35      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-06
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +L a   +    l+++e+ ++++l+ s++ r l+ L +aGL+e+r+
  gi|313117282|ref|YP_004044265.1| 41 ILDATSGEA---LSASEVSEACDLPLSTTYRKLDQLTDAGLLEERT 83
                                      555555555...9******************************996 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.5e-05     0.029      18      47 ..      50      79 ..      41      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +s +e++e+++l++st+ r l++L+++Gl+
  gi|313117282|ref|YP_004044265.1| 50 LSASEVSEACDLPLSTTYRKLDQLTDAGLL 79
                                      7899************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.052       7      46 ..      41      80 ..      39      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                      HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      IL + + + l+++e +e+ +l+ st+ + L +L +aGL+e
  gi|313117282|ref|YP_004044265.1| 41 ILDATSGEALSASEVSEACDLPLSTTYRKLDQLTDAGLLE 80
                                      5666666679****************************87 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   2.1e-05     0.042      25      98 ..      16      91 ..       2     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                            DUF742 25 letlvvaeagape..aarlqpehrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltvrapvtdraaeq 98
                                       et+v  e +  +  +a     +rail+ ++   ls  e++ + +lP++++   l  L dagll+ r+ + ++ +++
  gi|313117282|ref|YP_004044265.1| 16 SETVVRNEDAVQDllDAFNDAGCRAILDATSGeALSASEVSEACDLPLSTTYRKLDQLTDAGLLEERTRIRRS-GKH 91
                                      567776666555333455556799****999989******************************998877762.222 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.4e-05     0.068      34      62 ..      55      83 ..      43     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                                      HHTTTT--HHHHHHHHHHHHHTTSEEEEE CS
                               FUR 34 keedpeislaTVYrtLklleeaglvkele 62
                                      ++e  ++ l+T Yr L++l++agl++e +
  gi|313117282|ref|YP_004044265.1| 55 VSEACDLPLSTTYRKLDQLTDAGLLEERT 83
                                      56778899*****************8754 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.3e-05      0.18      10     100 ..      29     118 ..      23     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.3e-05
                              ArsR  10 llqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsqWrmpepgekpekeYhtsYskvqa 83 
                                       ll +f+++  + ++++ s e l+++e++e ++     + + l+ L  ++l+E++ r+ + g++      + Y ++  
  gi|313117282|ref|YP_004044265.1|  29 LLDAFNDAGCRAILDATSGEALSASEVSEACDLPlstTYRKLDQLTDAGLLEERTRIRRSGKH-----ASEYARLVE 100
                                       899****************************9654347789999*************996654.....456777777 PP

                              ArsR  84 nfqcsledlsdi.ievaf 100
                                       ++++sl++ +++ ++v++
  gi|313117282|ref|YP_004044265.1| 101 DMVISLDECGEMeLRVSL 118
                                       777777777776444544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 983.76
//
Query:       gi|313117283|ref|YP_004044266.1|  [L=211]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-22   77.8   0.2    5.9e-22   77.2   0.2    1.3  1  HTH_10          HTH DNA binding domain
    1.4e-05   25.0   0.5    4.1e-05   23.5   0.5    1.9  1  BAT             GAF and HTH_10 associated domain
     0.0016   18.3   0.0     0.0049   16.7   0.0    1.8  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0065   16.3   0.0      0.014   15.3   0.0    1.6  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.024   14.2   0.1       0.94    9.1   0.0    2.2  2  GerE            Bacterial regulatory proteins, luxR family
      0.034   13.7   0.1        0.1   12.2   0.1    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.064   13.2   0.1       0.19   11.7   0.1    1.8  1  MarR            MarR family
      0.077   13.2   0.0       0.13   12.5   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.085   13.0   0.5       0.18   11.9   0.1    1.8  2  Sigma70_r3      Sigma-70 region 3
       0.11   12.6   0.1       0.22   11.6   0.1    1.5  1  HTH_20          Helix-turn-helix domain
       0.12   12.2   0.1        0.3   10.9   0.1    1.6  1  Homeodomain     Homeodomain
       0.16   11.8   1.1        1.3    8.8   1.1    2.2  1  LexA_DNA_bind   LexA DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.2   3.9e-25   5.9e-22       1      53 []     156     208 ..     156     208 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 3.9e-25
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT +qlevl++Ay+mGYF++PRr+++ e+A el+I +stl+ehL +aeskl+e
  gi|313117283|ref|YP_004044266.1| 156 LTTRQLEVLQTAYDMGYFERPRRANATEIAAELDINPSTLTEHLAAAESKLLE 208
                                       9**************************************************85 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.5   2.7e-08   4.1e-05      61     138 ..      54     133 ..       6     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.7e-08
                               BAT  61 dldavedvrvvseeddgtlleltvs..gpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypd 135
                                       d d+ +d++ +  ++ + ++++t +    ++ + l + G  v + +a+dg  +lv + ++ +++Rsvv  l++r+pd
  gi|313117283|ref|YP_004044266.1|  54 DADSETDLTPIFSHGPTNRYRFTHDdgVNCPCECLGQFGCPVARYVAQDGHLTLVFHAADYEELRSVVAELRDRFPD 130
                                       45555666666666666777777542235677789999999************************************ PP

                               BAT 136 veL 138
                                       v+ 
  gi|313117283|ref|YP_004044266.1| 131 VDI 133
                                       *96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       8.9   1.3e+04      20      30 ..      15      25 ..      15      26 .. 0.76
   2 !   16.7   0.0   3.3e-06    0.0049      17      37 ..     180     200 ..     173     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8.9
                                      HHHHHHTS-HH CS
                             HTH_5 20 elaeelglsqs 30
                                      +l+ +++ls +
  gi|313117283|ref|YP_004044266.1| 15 DLCPIVELSDA 25
                                      68888899876 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.3e-06
                                       EHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  17 cvcelaeelglsqstvShHLk 37 
                                        ++e+a+el++++st+ +HL+
  gi|313117283|ref|YP_004044266.1| 180 NATEIAAELDINPSTLTEHLA 200
                                       679*****************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.3e-06     0.014      17      48 ..     175     205 ..     155     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.3e-06
                                       TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  17 rpgrdltvgelarrlglsksavsrilkrLvaa 48 
                                       rp r+ +++e+a++l++ +s+++ +l+ ++++
  gi|313117283|ref|YP_004044266.1| 175 RP-RRANATEIAAELDINPSTLTEHLAAAESK 205
                                       34.468********************999875 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.052        78       2      14 ..     155     167 ..     154     169 .. 0.85
   2 ?    9.1   0.0   0.00063      0.94      21      45 ..     182     206 ..     179     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.052
                                       SS-HHHHHHHHHH CS
                              GerE   2 sLskRErevLrll 14 
                                        L+ R++evL+  
  gi|313117283|ref|YP_004044266.1| 155 KLTTRQLEVLQTA 167
                                       69********975 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00063
                                       HHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  21 keIAeelniSekTVkvhksnimkKL 45 
                                       +eIA+el+i + T + h++ + +KL
  gi|313117283|ref|YP_004044266.1| 182 TEIAAELDINPSTLTEHLAAAESKL 206
                                       69*****************999997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.9   4.3e+03      21      34 ..      20      33 ..      17      37 .. 0.59
   2 ?   12.2   0.1   6.9e-05       0.1      17      43 ..     178     204 ..     174     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.9
                            HTH_24 21 reLAerlglSpstv 34
                                       eL+++  +++  v
  gi|313117283|ref|YP_004044266.1| 20 VELSDAAEITVDSV 33
                                      57777666665555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.9e-05
                            HTH_24  17 risqreLAerlglSpstvnrrlkrLee 43 
                                       r + +e+A +l++ pst++++l   e+
  gi|313117283|ref|YP_004044266.1| 178 RANATEIAAELDINPSTLTEHLAAAES 204
                                       57889****************987765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012      0.19       1      39 [.     156     200 ..     156     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                       --HHHHHHHHHHHHST......TEEHHHHHHHHTS-HHHHHHHHH CS
                              MarR   1 ltltqfviLrilyeqg......plsvseLakklgvskstvtrvld 39 
                                       lt  q+++L + y++g       ++ +e+a  l +++st+t+ l 
  gi|313117283|ref|YP_004044266.1| 156 LTTRQLEVLQTAYDMGyferprRANATEIAAELDINPSTLTEHLA 200
                                       577777888888777644444458899**************9986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.5e-05      0.13       2      43 ..     156     199 ..     155     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-05
                                       --HHHHHHHHHHHHHHH..HHSSB-HHHHHHHHTS-HHHHHHHH CS
                    Fe_dep_repress   2 LvestEdYLetIYtlse..ekkvvktkdlaerLnvspssVseml 43 
                                       L+++  ++L+t Y++        +  +++a +L++ ps+ +e l
  gi|313117283|ref|YP_004044266.1| 156 LTTRQLEVLQTAYDMGYfeRPRRANATEIAAELDINPSTLTEHL 199
                                       77777788899998875425678999***************976 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.1   6.1e+03      33      50 ..      29      35 ..      20      60 .. 0.50
   2 ?   11.9   0.1   0.00012      0.18      17      46 ..     175     204 ..     160     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.1
                                      XHHHHHHHHHHHXXXEET CS
                        Sigma70_r3 33 seekVrevleaarepvSl 50
                                      +++ V           + 
  gi|313117283|ref|YP_004044266.1| 29 TVDSV-----------AT 35
                                      33333...........33 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00012
                                       HSSXXXHHHHHHHHTXXHHHHHHHHHHHXX CS
                        Sigma70_r3  17 lgrePtpeEiAeeLglseekVrevleaare 46 
                                         r ++++EiA+eL++ ++ + e l aa++
  gi|313117283|ref|YP_004044266.1| 175 RPRRANATEIAAELDINPSTLTEHLAAAES 204
                                       5699****************9999988875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00015      0.22      23      47 ..     177     201 ..     159     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                       TTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  23 egltaselaerldlskntlsyHLrv 47 
                                       + + a+e+a++ld+ ++tl  HL++
  gi|313117283|ref|YP_004044266.1| 177 RRANATEIAAELDINPSTLTEHLAA 201
                                       56679******************86 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0002       0.3       4      42 ..     153     193 ..     152     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                       SSSS-HHHHHHHHHHHHH..SSS-SHHHHHHHHHHHTS-HH CS
                       Homeodomain   4 RttftkeqleeLeklFee..nrypsaeereeLAkklgLeer 42 
                                       R  +t+ qle+L++++ +   + p ++  +e+A++l+++ +
  gi|313117283|ref|YP_004044266.1| 153 RSKLTTRQLEVLQTAYDMgyFERPRRANATEIAAELDINPS 193
                                       8889*************87799**************99865 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.1    0.0009       1.3       2      53 ..     154     205 ..     153     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0009
                                       X---HHHHHHHHHHHHH.HHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind   2 kkLTerQrevldlikas.ieetgypPsireiaralglkSpsaveehLkaLerK 53 
                                       +kLT rQ evl+   +    e+       eia +l ++ ps+  ehL+a e K
  gi|313117283|ref|YP_004044266.1| 154 SKLTTRQLEVLQTAYDMgYFERPRRANATEIAAELDIN-PSTLTEHLAAAESK 205
                                       689999999999876641223333445679*******9.********998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1537.55
//
Query:       gi|313117284|ref|YP_004044267.1|  [L=56]
Description: hypothetical protein Hbor_30700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00029   20.9   0.3    0.00036   20.6   0.3    1.1  1  Zn-ribbon_8  Zinc ribbon domain
     0.0013   18.7   0.2     0.0013   18.7   0.2    1.1  1  Elf1         Transcription elongation factor Elf1 like
     0.0058   16.0   0.3        3.5    7.2   0.1    2.2  2  zf-ribbon_3  zinc-ribbon domain
  ------ inclusion threshold ------
      0.033   14.2   0.3      0.042   13.9   0.3    1.2  1  DZR          Double zinc ribbon
      0.092   12.4   0.2       0.25   11.0   0.1    1.7  2  zf_UBZ       Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.3     1e-07   0.00036       4      36 ..       9      42 ..       8      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1e-07
                       Zn-ribbon_8  4 YeYrCeeCghefevlqsisdaplta.CPeCgsev 36
                                      Y + C eC++  ev  s++da  +  C  Cg+ v
  gi|313117284|ref|YP_004044267.1|  9 YTFTCPECDEALEVNGSMKDALIERgCVICGAGV 42
                                      99*****************9999999*****955 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   3.7e-07    0.0013      17      58 ..       6      45 ..       1      54 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.7e-07
                              Elf1 17 klptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetk 58
                                      k + +F+Cp C++   +ev+ + k+   e  C +Cg+ ++t+
  gi|313117284|ref|YP_004044267.1|  6 KEEYTFTCPECDEA--LEVNGSMKDALIERGCVICGAGVTTD 45
                                      45789******988..9*******************998876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1   0.00097       3.5       3      10 ..      11      18 ..      10      23 .. 0.77
   2 !    7.2   0.0   0.00098       3.5       5      15 ..      35      45 ..      31      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00097
                       zf-ribbon_3  3 vrCPnCGa 10
                                       +CP+C++
  gi|313117284|ref|YP_004044267.1| 11 FTCPECDE 18
                                      68****97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00098
                       zf-ribbon_3  5 CPnCGa.plssd 15
                                      C  CGa + ++d
  gi|313117284|ref|YP_004044267.1| 35 CVICGAgV-TTD 45
                                      ******88.766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   1.2e-05     0.042      13      41 ..      11      45 ..       3      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                               DZR 13 rfCseCgtklkavaa......edrCpsCgekvdpe 41
                                       +C+eC ++l+   +      e+ C+ Cg+ v+ +
  gi|313117284|ref|YP_004044267.1| 11 FTCPECDEALEVNGSmkdaliERGCVICGAGVTTD 45
                                      48*******986666999**99*******998766 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.9e-05      0.25       2      14 ..      10      22 ..       9      27 .. 0.85
   2 ?   -1.0   0.0      0.39   1.4e+03       5      15 ..      35      45 ..      35      48 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.9e-05
                            zf_UBZ  2 tylCerCgkeipe 14
                                      t++C++C++ +++
  gi|313117284|ref|YP_004044267.1| 10 TFTCPECDEALEV 22
                                      89******98876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.39
                            zf_UBZ  5 CerCgkeipes 15
                                      C  Cg+ + ++
  gi|313117284|ref|YP_004044267.1| 35 CVICGAGVTTD 45
                                      77899877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 439.05
//
Query:       gi|313117285|ref|YP_004044268.1|  [L=476]
Description: amino acid transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-40  137.6  35.6    6.1e-40  137.3  35.6    1.0  1  AA_permease_2   Amino acid permease
    2.5e-35  122.0  34.2    3.2e-35  121.6  34.2    1.1  1  AA_permease     Amino acid permease
     0.0045   15.9   1.1     0.0045   15.9   1.1    3.2  4  Spore_permease  Spore germination protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3  35.6     1e-43   6.1e-40       1     403 [.      43     445 ..      43     468 .. 0.83

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 1e-43
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       ++l++ +a+ +g++ig+gifv +  +a+ +gp ++l++ +++++  l v+l   El++a+p sgG y + ++++g++
  gi|313117285|ref|YP_004044268.1|  43 IGLRGGVAIGVGTMIGAGIFVFPglAAGRAGPGAALSFALGAVVA-LLVALPTSELATAMPQSGGGYYFISRGIGNP 118
                                       6888999**************99977777***************9.89***************************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgp.....dlqgntwltyliaiaililvalinirgikesakiqnil 147
                                        + +++ ++w++ +++ a++l+ +++y + +l++     d+    + +  +a+++ ++++  +i g+  +ak+qn +
  gi|313117285|ref|YP_004044268.1| 119 YGAVVGLSLWLGLIFASAFYLVGFGQYAAAILAEigleiDV---GTVAPALAVLVGVGLTGASIAGTENTAKLQNSI 192
                                       *******************************9986553332...346677889999999****************** PP

                     AA_permease_2 148 gilkillpliiliilglitvdgggfsslstetdtffpn.gwpg.v...llgllivlwsfdGfesaanvseevkk..k 217
                                       + l + ++ ++l+  gl  +   gf      +  ++p+ + p+ v   l + + v+ ++ Gf  +a v+  +k+  +
  gi|313117285|ref|YP_004044268.1| 193 VGLLLGILTLFLVYGGLDSL---GFF-----GRETVPEaFAPFgVfpiLTTTAFVFTAYLGFAQVATVAGDIKRpsR 261
                                       *****755555554444444...444.....333455547776542325555669999*************998879 PP

                     AA_permease_2 218 dvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavg.gkvvaiivvilialsllgaintavi 293
                                       ++p+a++ ++++v+vl++++ ++++ + +  ++a+ +++  ++++    vg g++v+i+  +++ l+ + ++n+ ++
  gi|313117285|ref|YP_004044268.1| 262 NLPLAMIGSVVLVAVLNVVTILVATSAFGSAQLATYGETA-LVEVARSFVGiGGAVTIL--VAGLLATVSSANASIL 335
                                       *********************************9888854.455555555523344444..458889999******* PP

                     AA_permease_2 294 gssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliiga 369
                                       +ssr l+al+rd   P      n k+++p  a+ l    + ++l+lf       + +l++v+s++++++y+l+ +++
  gi|313117285|ref|YP_004044268.1| 336 SSSRALYALSRDALVPAKAGTLNrKYNTPHIALSLAGGPV-LFLVLFG-----PVEVLAEVASFLHLLMYGLMCVTL 406
                                       ***************************************9.7766774.....38********************** PP

                     AA_permease_2 370 lilrkkrphlkr.....pgkilvaiigalfllfllvalf 403
                                       +ilr+++p++       pg++++ i+ga++++ llv++ 
  gi|313117285|ref|YP_004044268.1| 407 VILRRRSPDWYDpdyriPGYPVLPILGAVTSFSLLVLMQ 445
                                       ********9944446688889999***999999998765 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6  34.2   5.4e-39   3.2e-35       3     429 ..      49     444 ..      47     466 .. 0.85

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 5.4e-39
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviG 79 
                                       + i +g +iG+g+fv  g +++ aGp ga l+++l+ vv +lv+l ++e+at++p+sgg y+++sr +g   G v+G
  gi|313117285|ref|YP_004044268.1|  49 VAIGVGTMIGAGIFVFPGLAAGRAGP-GAALSFALGAVVALLVALPTSELATAMPQSGGGYYFISRGIGNPYGAVVG 124
                                       6799**********************.777*********************************************** PP

                       AA_permease  80 lnylfswitvlaleltaasiliqfwelvtdlpkawvt...........gavflvvlliinlvgvkvygeaefilali 145
                                       l++++  i++ a+      +l++f ++  +++ +++            ++++ v l++ +++g +  ++ +  +  +
  gi|313117285|ref|YP_004044268.1| 125 LSLWLGLIFASAF------YLVGFGQYAAAILAEIGLeidvgtvapalAVLVGVGLTGASIAGTENTAKLQNSIVGL 195
                                       **66555555555......5666665556666555556666999999544444559999999999999999999999 PP

                       AA_permease 146 kiiaiiafiivg...iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielva 219
                                       ++ ++  f++ g     + +g ++ ++                + p         +  ++   ++v+ a+ G+  va
  gi|313117285|ref|YP_004044268.1| 196 LLGILTLFLVYGgldSLGFFGRETVPE---------------AFAPF-------GVFPILTTTAFVFTAYLGFAQVA 250
                                       999999999999666556666666666...............45555.......4889******************* PP

                       AA_permease 220 iiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinavi 296
                                       ++ag++k P++++P a++  v++++++ v  +l++++ ++   l    ++a    +++++ ++ g+ ++ ++++a++
  gi|313117285|ref|YP_004044268.1| 251 TVAGDIKRPSRNLPLAMIGSVVLVAVLNVVTILVATSAFGSAQLATYGETA----LVEVARSFVGIGGAVTILVAGL 323
                                       *****************************************9999988777....89************99999997 PP

                       AA_permease 297 ltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllais 372
                                       l a++ssan+s+ s+sR+ly+l++d l P k ++   k++ P+ a+ l    +l+++l   +        ++l  ++
  gi|313117285|ref|YP_004044268.1| 324 L-ATVSSANASILSSSRALYALSRDALVPaKAGTLNRKYNTPHIALSLAGGPVLFLVLFGPV--------EVLAEVA 391
                                       6.6789***********************99999999******9988888888887755555........4558999 PP

                       AA_permease 373 aliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillil 429
                                        +  l++++l++++++ +R+    +  ++ +  ++++++p ++il+ +   ++l+++
  gi|313117285|ref|YP_004044268.1| 392 SFLHLLMYGLMCVTLVILRRR---SPDWY-DPDYRIPGYPVLPILGAVTSFSLLVLM 444
                                       999****************99...88989.99************9876555554443 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.1   7.5e-07    0.0045      12     102 ..      53     144 ..      45     152 .. 0.91
   2 ?   -1.0   1.1       0.1   6.2e+02     115     159 ..     191     240 ..     182     281 .. 0.75
   3 ?   -0.6   0.6     0.075   4.5e+02     174     239 ..     228     294 ..     224     310 .. 0.65
   4 ?   -0.3   0.2     0.062   3.7e+02     113     165 ..     364     415 ..     361     441 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.5e-07
                    Spore_permease  12 vsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpek.tliellkkilgkwLGsllsilfil 87 
                                       v +++G+gi ++p+ +a +a+p + +s  l+++++l+++l +++l   +p++   + +++ ++g + G + ++ + l
  gi|313117285|ref|YP_004044268.1|  53 VGTMIGAGIFVFPGLAAGRAGPGAALSFALGAVVALLVALPTSELATAMPQSgGGYYFISRGIGNPYGAVVGLSLWL 129
                                       789*********************************************99762578899****************** PP

                    Spore_permease  88 yFlllaafelRefse 102
                                         ++ +af l  f++
  gi|313117285|ref|YP_004044268.1| 130 GLIFASAFYLVGFGQ 144
                                       *****9999887775 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.1
                    Spore_permease 115 wiiilllllvilYlvvkGieslar.....eflfiivilliilllillfsl 159
                                        i+ lll +++l+lv++G++sl       +   ++++ ++++l+++ f++
  gi|313117285|ref|YP_004044268.1| 191 SIVGLLLGILTLFLVYGGLDSLGFfgretVPEAFAPFGVFPILTTTAFVF 240
                                       57778888889999999998886333354445666677777776666665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.075
                    Spore_permease 174 gikpvlkslkttslsflgveillllvpflkdkkkvkkaallgvlistllyll.ttlivilvlsveql 239
                                       g+ p+l  +  +  ++lg+  +  +   +k + + +  a++g ++ + ++ + t+l++ ++++  ql
  gi|313117285|ref|YP_004044268.1| 228 GVFPILTTTAFVFTAYLGFAQVATVAGDIKRPSRNLPLAMIGSVVLVAVLNVvTILVATSAFGSAQL 294
                                       5567777777777777777777777777777777777777765555544444044445566666655 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.062
                    Spore_permease 113 plwiiilllllvilYlvvkGieslareflfiivilliilllillfslklaeik 165
                                       p +++ l    v  +++++ +e+la e++ ++  l+  l+ ++l++l+   ++
  gi|313117285|ref|YP_004044268.1| 364 PHIALSLAGGPVLFLVLFGPVEVLA-EVASFLHLLMYGLMCVTLVILRRRSPD 415
                                       5555555555677888999999999.888888888888888888888766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3389.29
//
Query:       gi|313117286|ref|YP_004044269.1|  [L=261]
Description: universal stress family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-09   36.6   7.1      2e-05   25.1   2.4    2.8  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.15   11.9   1.8         14    5.5   0.1    2.7  2  T2SSM_b   Type II secretion system (T2SS), protein M subtype 


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.2   1.6e-05      0.15      44     109 ..      52     110 ..      21     114 .. 0.72
   2 !   25.1   2.4   2.3e-09     2e-05       3     141 .]     118     242 ..     116     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                                       CCCCCCCHHHHHHHHHHHHHHHHHHHH...HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEE CS
                               Usp  44 sgavsdadeeaeeeeleleeaeleada...akaaaeaggvkvevvveegdpaeeilevaeeedadliVv 109
                                              +e+a+++  e+++ e        a+a ++agg ++  vv  gd+ ++  ++a ee+ad i++
  gi|313117286|ref|YP_004044269.1|  52 A------PEQARTQFGEQARSE----LddvAEAFRNAGGDVEARVVFTGDATQTFERIAVEEKADAILL 110
                                       2......222222222222222....12235677899*****************************986 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 2.3e-09
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       +rI Va+ +  ++++ +e   +la  ++ +++l hv  +++  a+++   +     l +++             a +
  gi|313117286|ref|YP_004044269.1| 118 ERIFVALSEGINTERIAELTSALATGTDVTVTLFHVATSEDERAAGEQLLDKTARILSEKGV------------ATD 182
                                       68999999999999*************99999999988777666655544444444444442............457 PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        +++ v ++  p + + +va e d dl+V+G ++  ++++l++G  se+ ++++  p lvVr
  gi|313117286|ref|YP_004044269.1| 183 DIEREVAVSDAPVQLLSDVASE-DSDLVVLGESR-PTVRELVFGEPSERMAERTLAPILVVR 242
                                       7888888888888888888887.99*********.**************************8 PP

>> T2SSM_b  Type II secretion system (T2SS), protein M subtype b
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0023        21      21      57 ..      69     105 ..      46     109 .. 0.71
   2 ?    5.5   0.1    0.0016        14       8      48 ..     155     195 ..     152     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0023
                           T2SSM_b  21 qrvralvsaaggsltssqvlpageegkvrriavrvsl 57 
                                       + v++++ +agg++++  v   ++ ++++riav+ ++
  gi|313117286|ref|YP_004044269.1|  69 DDVAEAFRNAGGDVEARVVFTGDATQTFERIAVEEKA 105
                                       4456666677****9988888888888*****98655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0016
                           T2SSM_b   8 egataslagaalqqrvralvsaaggsltssqvlpageegkv 48 
                                       ++++  +ag++l+++ ++++s+ g+ ++  ++  a++++ v
  gi|313117286|ref|YP_004044269.1| 155 TSEDERAAGEQLLDKTARILSEKGVATDDIEREVAVSDAPV 195
                                       678999*********************99999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1641.81
//
Query:       gi|313117287|ref|YP_004044270.1|  [L=229]
Description: plastocyanin [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-19   68.5   0.1    1.3e-18   67.2   0.1    1.6  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    7.8e-05   22.7   0.0      0.049   13.7   0.0    2.2  2  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
       0.15   12.2   0.6       0.59   10.3   0.0    1.9  2  DUF3493       Low psii accumulation1 / Rep27


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.1   2.2e-22   1.3e-18       6      98 ..      64     171 ..      60     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 2.2e-22
                                       EETTET.SEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTC..............EEEEBSTT CS
                       Copper-bind   6 gvesgd.lqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaed..............etkliggG 67 
                                       +ve +d l+Fe+ +it+++g++v++ n  ++gH v   +d +p+g+d +++   d              e   i+gG
  gi|313117287|ref|YP_004044270.1|  64 TVEMTDgLVFEPDAITIAPGDTVVWENVGSIGHSVTAYEDDIPEGADYFASGGFDsedaarsaysagdpESGDIAGG 140
                                       6777888********************************99999999988766556678999999999977789*** PP

                                       EEEEEEEESSEEEEEEETTTTTTTSEEEEEE CS
                       Copper-bind  68 ekdsvtfdeagtYkffCsPHaaagMkgkvtv 98 
                                       e+++ tf+++gt+++fC PH ++gM+g vtv
  gi|313117287|ref|YP_004044270.1| 141 ESYEHTFETEGTFEYFCIPHETVGMVGSVTV 171
                                       ******************************9 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   8.2e-06     0.049       7      61 ..      47     100 ..      40     110 .. 0.76
   2 !    7.0   0.0     0.001         6      68     104 .]     135     171 ..     118     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.2e-06
                      Cupredoxin_1   7 vllllsskaaaaaektveitvkdg.gfePskievkagekvklkiknkdktpeefes 61 
                                       +l + + +aaa++ ++++++++dg  feP+ i++  g   ++ ++n ++  +++++
  gi|313117287|ref|YP_004044270.1|  47 ALSAATGTAAAQEGQQHTVEMTDGlVFEPDAITIAPGD--TVVWENVGSIGHSVTA 100
                                       3334444666889999********89***********9..7788887777777765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.001
                      Cupredoxin_1  68 kvlapgktttitiaplkpGeYeftcdmhmd..akGkliV 104
                                        ++a g++++ t+  +++G++e++c  h++  + G ++V
  gi|313117287|ref|YP_004044270.1| 135 GDIAGGESYEHTF--ETEGTFEYFCIPHETvgMVGSVTV 171
                                       68999********..9*********99985467777776 PP

>> DUF3493  Low psii accumulation1 / Rep27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.23   1.4e+03      34      50 ..      47      63 ..      36      71 .. 0.49
   2 ?   10.3   0.0   9.8e-05      0.59      30      70 ..     164     204 ..     159     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.23
                           DUF3493 34 alifllrllaaragaes 50
                                      al +++ ++aa++g+++
  gi|313117287|ref|YP_004044270.1| 47 ALSAATGTAAAQEGQQH 63
                                      23334444444444444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.8e-05
                           DUF3493  30 aliGalifllrllaaragaesapeleealenlaiqvgaval 70 
                                       +++G +++++  +a ++g++ ap++ ++ + lai +++ + 
  gi|313117287|ref|YP_004044270.1| 164 GMVGSVTVTPGGAAEENGGPAAPQVPDSAKTLAIATTIALT 204
                                       899*******************************9887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1483.37
//
Query:       gi|313117288|ref|YP_004044271.1|  [L=305]
Description: K+dependent Na+ exchanger related-protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-38  131.2  32.2    7.3e-23   81.2  12.9    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein
  ------ inclusion threshold ------
      0.022   15.0   1.0      0.022   15.0   1.0    3.0  3  DUF4730   Domain of unknown function (DUF4730)


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2  12.9   8.1e-27   7.3e-23       4     146 ..       6     139 ..       3     140 .. 0.86
   2 !   56.2  11.3     4e-19   3.6e-15       6     143 ..     169     299 ..     165     305 .] 0.93

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 8.1e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       ++f+++l ++ v+ad+ v+sa+e+a + g+s  ++G+t++++g+s+pE+++s++aa  g +dl++gn++Gs ++ ++
  gi|313117288|ref|YP_004044271.1|   6 GGFVVGLGILLVGADRTVRSAAELALYYGVSNFFVGVTVVSIGTSIPEMTTSLYAAYYGAGDLVVGNIVGSETAQIT 82 
                                       78***********************99************************************************** PP

                                       THHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalyl 146
                                       l+iG++ali++++ ++++  l  g+   ++ll++++++l l     +  +t+ eg++++l+Ya+++
  gi|313117288|ref|YP_004044271.1|  83 LGIGIVALISPIVAERKN-VLVYGG---AMLLSMIIMILTL-----EDGITRSEGILMMLAYAIFI 139
                                       *********996666555.344444...3333333333323.....39****************97 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 4e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTH CS
                          Na_Ca_ex   6 filslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllv 82 
                                       ++++lll++ + +++v +  ++a+ lgi++ v+G+ l  lg+++pE++++ iaa++g   +++g++lGsni +  + 
  gi|313117288|ref|YP_004044271.1| 169 VLFGLLLVVGGGQVMVTNGVALATLLGIPPYVVGI-LTGLGTTAPEIVVAGIAARSGRSGISVGSLLGSNITDPVFS 244
                                       67899999***************999*********.***************************************** PP

                                       HHHHHHHHH.BTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHH CS
                          Na_Ca_ex  83 iGlialigs.lkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYa 143
                                       +G+ al++     d+es++++++++l+v+l++++++++        + +++  ++ +lllY+
  gi|313117288|ref|YP_004044271.1| 245 LGIGALVADvTLSDPESVTMSVSYMLFVSLIVIAVLYW-R------RGIDRRSAIGCLLLYL 299
                                       *******9955999999***************887777.6......99************97 PP

>> DUF4730  Domain of unknown function (DUF4730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.5      0.43   3.9e+03      11      28 ..     108     125 ..      99     139 .. 0.61
   2 ?   15.0   1.0   2.4e-06     0.022       9      51 ..     167     209 ..     163     212 .. 0.90
   3 ?   -1.8   0.8      0.45     4e+03       3      21 ..     261     279 ..     260     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.43
                           DUF4730  11 vllslllvipgvEAklda 28 
                                        lls++ +i   E  ++ 
  gi|313117288|ref|YP_004044271.1| 108 MLLSMIIMILTLEDGITR 125
                                       455555555555555544 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.4e-06
                           DUF4730   9 livllslllvipgvEAkldaGDaiALlLGivltilGiCACLGi 51 
                                         vl+ lllv+ g    ++ G a+A lLGi   ++Gi   LG 
  gi|313117288|ref|YP_004044271.1| 167 PWVLFGLLLVVGGGQVMVTNGVALATLLGIPPYVVGILTGLGT 209
                                       569****************************999999999996 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.45
                           DUF4730   3 avlrallivllslllvipg 21 
                                       +v   ++  l++ l vi++
  gi|313117288|ref|YP_004044271.1| 261 SVTMSVSYMLFVSLIVIAV 279
                                       6667777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 2239.36
//
Query:       gi|313117289|ref|YP_004044272.1|  [L=405]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-31  108.9  18.4    9.6e-10   38.8   1.6    4.5  4  CBS              CBS domain
  ------ inclusion threshold ------
       0.05   14.4   0.0       0.13   13.0   0.0    1.8  1  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma
       0.15   11.9   0.1       0.31   10.9   0.1    1.5  1  DUF1508          Domain of unknown function (DUF1508)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   3.7e-05      0.22       3      52 ..       5      52 ..       3      56 .. 0.89
   2 !   30.6   0.3   5.7e-11   3.4e-07       9      55 ..      69     114 ..      62     116 .. 0.89
   3 !   37.8   0.7   3.1e-13   1.9e-09       1      53 [.     123     174 ..     123     178 .. 0.92
   4 !   38.8   1.6   1.6e-13   9.6e-10       1      54 [.     223     275 ..     223     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                                      HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS  3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52
                                      di ++++  v+p+t +++++  + +  v ++  V  d ++ G+vt+r l+
  gi|313117289|ref|YP_004044272.1|  5 DIVSEEYEAVSPETRVSKLVGVFDDPTVKGV-LVQ-DTQFEGVVTRRQLA 52
                                      678889999**************8888****.995.777********997 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 5.7e-11
                                       CEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHHH CS
                               CBS   9 vvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllral 55 
                                       v+ + pd++++++++lm++++ s+l PV ++d+ +vG+v+  D+l+a+
  gi|313117289|ref|YP_004044272.1|  69 VPRLAPDEDVRKVARLMIDSD-SQLlPVFEGDD-VVGVVSADDILEAV 114
                                       46899*************998.7998***9999.***********997 PP

  == domain 3  score: 37.8 bits;  conditional E-value: 3.1e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       Vgd+ t+++v+v  +tt +ea+ ++re+++++lPVV++d   vGi++l D ++
  gi|313117289|ref|YP_004044272.1| 123 VGDVYTDELVSVESETTAGEAVTRFREHHITHLPVVEDDA-AVGILSLYDMVD 174
                                       89**********************************5555.*********876 PP

  == domain 4  score: 38.8 bits;  conditional E-value: 1.6e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+d+m ++v t++pd+tle a+e m e++ s+l VV ed+ +vGivt++D+l+ 
  gi|313117289|ref|YP_004044272.1| 223 VRDVMVSPVRTIRPDETLETAVEAMFETDGSSLVVV-EDDCPVGIVTKTDILDS 275
                                       89**********************646554799778.8999**********986 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05      0.13      30      83 ..     319     380 ..     300     383 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                                       -EEEEEEE...EE......EEEEEEEEECTTEEEEEEEEESSHHHHHHHHHHHHHHHHHHCHH CS
                   Ribosomal_S30AE  30 ieadVtls...kk......kkvevtirlakgkviraeeesedlyaaidlavdklerqlrkyke 83 
                                        +a+V+l+   +k        + +++++ +g  i a+ e     +a+++a+d +erq+r  k+
  gi|313117289|ref|YP_004044272.1| 319 LDAKVHLHehdEKrrgtplVLARIRLYTDSGLYI-ASGEGYGARQALNEACDIVERQIRDEKT 380
                                       7899999986622568877777777755455544.55677********************998 PP

>> DUF1508  Domain of unknown function (DUF1508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   5.2e-05      0.31       7      44 ..     341     378 ..     340     381 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.2e-05
                                       EEEEE-TTS-EEEEEEEBSSHHHHHHHHHHHHHHTTTC CS
                           DUF1508   7 rFrLkaaNgevIatsegYsskaaaenGIesVkknapda 44 
                                       r rL+ + g  Ia++egY +++a  ++ + V ++  d+
  gi|313117289|ref|YP_004044272.1| 341 RIRLYTDSGLYIASGEGYGARQALNEACDIVERQIRDE 378
                                       77999999999*************99999888876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 2500.48
//
Query:       gi|313117290|ref|YP_004044273.1|  [L=259]
Description: GMP synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-20   71.3   0.0    1.2e-19   70.8   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    1.5e-06   28.1   0.1    9.8e-06   25.5   0.1    2.3  1  Peptidase_C26  Peptidase C26
     0.0082   15.1   0.0      0.015   14.2   0.0    1.4  1  HTS            Homoserine O-succinyltransferase


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0     2e-23   1.2e-19      39     177 ..      46     181 ..       7     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 2e-23
                                       THHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEE.EEEE CS
                            GATase  39 llknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekekehhggtm.rlgd 109
                                        +  +dg+++sg   s++     ++g+ e  ++a  +++P LG+C G+Q +a+++g+ vv ++e+e    t+ r+gd
  gi|313117290|ref|YP_004044273.1|  46 RAWVYDGVVISGSQISVYddndwIHGATEWFRRAQAAGVPTLGVCWGHQFIAQAVGGRVVDMHEYELGYRTItRVGD 122
                                       46789*********9999999******************************************88888887625566 PP

                                       TTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTST CS
                            GATase 110 detallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststp 177
                                         + l++g ++++++   H++ v +   +p g + +a+++ +  + +++   +  +gvQFHPE+  ++
  gi|313117290|ref|YP_004044273.1| 123 --SPLFEGVPRRFTAFETHSDRVAE---LPPGAVTLARNDFG--VQAFRVGGS--YGVQFHPEYDRET 181
                                       ..78*********************...****9999999555..666666665..********98665 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.1   1.6e-09   9.8e-06      98     216 .]      76     176 ..      17     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.6e-09
                     Peptidase_C26  98 iraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslH 174
                                       +r+a ++gvP lg+C G+q+++ a+GG+++   e             +   ++++ + +s l e +  +++     H
  gi|313117290|ref|YP_004044273.1|  76 FRRAQAAGVPTLGVCWGHQFIAQAVGGRVVDMHE------------YELGYRTITRVGDSPLFEGVP-RRFTAFETH 139
                                       688999*********************9864333............345567888888888888888.79999999* PP

                     Peptidase_C26 175 hqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       +  + el ++    A+  D  + a+++       +gvQ+HPE
  gi|313117290|ref|YP_004044273.1| 140 SDRVAELPPGAVTLARN-DFGVQAFRVGG----SYGVQFHPE 176
                                       **********9888876.55689**9999....48******9 PP

>> HTS  Homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.6e-06     0.015      98     221 ..      49     163 ..      44     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-06
                                       -EEEEEE---S-TTS-GGGSTTHHHHHHHHHHHHHHEEEEEEETHHHHHHHHHHH----EEEEEEEEEEEEEEES.S CS
                               HTS  98 kfDgliiTGApveqlefeevkYWeelteildwakenvtstlfiCwaaqaalyylygvekkklpeKlfGvfehkvlke 174
                                        +Dg++i G++++   +++ ++ +  te +  a+   + tl +Cw+ q  ++   g + ++++e   G +++ ++  
  gi|313117290|ref|YP_004044273.1|  49 VYDGVVISGSQISV--YDDNDWIHGATEWFRRAQAAGVPTLGVCWGHQF-IAQAVGGRVVDMHEYELG-YRTITRVG 121
                                       59********9985..89****************************997.566666677778888888.67777888 PP

                                       --GGGTT--SEEEEEEEEEEE--HHHHTT-TTEEEEEEETTTEEEEE CS
                               HTS 175 kspllrgfddeflvphsRytevkeedieekkelevLaeseeaGvsll 221
                                       +spl++g++++f++        ++++++e +   v    ++ Gv+ +
  gi|313117290|ref|YP_004044273.1| 122 DSPLFEGVPRRFTAFET-----HSDRVAELPPGAVTLARNDFGVQAF 163
                                       99999999998876433.....2222333333333334445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1635.00
//
Query:       gi|313117291|ref|YP_004044274.1|  [L=140]
Description: hypothetical protein Hbor_30770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 987.04
//
Query:       gi|313117292|ref|YP_004044275.1|  [L=130]
Description: hypothetical protein Hbor_30780 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-38  130.5   0.0    3.6e-38  130.2   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.2   0.0     2e-42   3.6e-38       1     114 [.      15     126 ..      15     127 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.2 bits;  conditional E-value: 2e-42
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssl 76 
                                       d+t++v+++v   ++++G+++vf++htta++++nE+ ++++++Dle++le+l+p+  +Y h+ e +dnadaH++++l
  gi|313117292|ref|YP_004044275.1|  15 DVTSDVAATVP-DDLDTGVCTVFVPHTTAGIIVNEH-ERRLMSDLERLLEHLAPRGdDYAHD-EIDDNADAHMRAAL 88 
                                       79999999965.68*********************9.******************99*****.8999********** PP

                                       H-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEE CS
                           UPF0047  77 lgssltipvedgklalGtwqsiylveldgpreRkvvvq 114
                                       lgss++ipve+g+l lGtwqs++++e+dgpr+R++ v+
  gi|313117292|ref|YP_004044275.1|  89 LGSSVSIPVENGELGLGTWQSVMFAECDGPRTRELRVT 126
                                       **********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 954.23
//
Query:       gi|313117293|ref|YP_004044276.1|  [L=148]
Description: universal stress protein UspA-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-26   93.8   0.4    1.5e-26   93.6   0.4    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.05   13.9   0.1       0.71   10.2   0.1    2.3  2  TPR_12    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.4   1.6e-30   1.5e-26       1     141 []       1     148 []       1     148 [] 0.96

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.6e-30
                                       S-SEEEEEE-SSHHHHHHHHHHHH.HHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...... CS
                               Usp   1 mykrIlVavDgseeskkAlewAle.lakargaelillhvidprasgavsdadeeaeeeeleleeaeleada...... 70 
                                       m k++lV+vDgs  s  Al++Al  + +   a +++lhv+d +++g+  +++ e+ +e+l+ +e+ +e+++      
  gi|313117293|ref|YP_004044276.1|   1 MAKHVLVPVDGSALSWSALRYALGeFPE---ASITALHVVDLFEPGYGTYPEFETTYEPLMGSEEWYERAEevserl 74 
                                       89*********************94444...45************************************99****** PP

                                       ...HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  71 ...akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                          a+a a +++ +v +  e gd +++i+++ e+ed+d iV+G++gr+   r+++GSv+e v+r+a + V++Vr
  gi|313117293|ref|YP_004044276.1|  75 lseAEAIAGDHDRTVATASEIGDSKRVIVDYSEAEDVDQIVLGAHGRGEEGRAVFGSVAEIVVRRARVTVTLVR 148
                                       **999********************************************************************8 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.062   5.5e+02      10      34 ..      17      41 ..      11      48 .. 0.68
   2 ?   10.2   0.1     8e-05      0.71      19      66 ..      64     110 ..      60     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.062
                            TPR_12 10 aavlrrlgrydeAlellekaleiar 34
                                       a+ ++lg++ eA     +++++++
  gi|313117293|ref|YP_004044276.1| 17 SALRYALGEFPEASITALHVVDLFE 41
                                      5566778888888777777777766 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 8e-05
                            TPR_12  19 ydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                       y+ A+e  e+ l  a+++  +dh+ t++t   +g+  r   +y eA++
  gi|313117293|ref|YP_004044276.1|  64 YERAEEVSERLLSEAEAIA-GDHDRTVATASEIGDSKRVIVDYSEAED 110
                                       8899999999999999996.58*************9886668888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 1144.62
//
Query:       gi|313117294|ref|YP_004044277.1|  [L=111]
Description: hypothetical protein Hbor_30800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.032   14.0   0.1      0.038   13.8   0.1    1.1  1  Porin_OmpG  Outer membrane protein G (OmpG)


Domain annotation for each model (and alignments):
>> Porin_OmpG  Outer membrane protein G (OmpG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.1e-06     0.038     115     181 ..      34      99 ..      20     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-06
                        Porin_OmpG 115 qPdweiklsddlkfegWlalyqyindleenglsdkeletEtGltykfndtlsvklnyyldrgwnkns 181
                                       +Pd+ ++++  ++f+  l+ly +++  e+ng    ++e   G ++   d  ++ ++ yld    +++
  gi|313117294|ref|YP_004044277.1|  34 RPDGTLRIE-ITEFSRGLSLYWWVDVYERNGDDWTQIEVGLGTSFTSADDAAAAVQSYLDETERSGE 99 
                                       699999986.5789999*******************************************8655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 747.37
//
Query:       gi|313117295|ref|YP_004044278.1|  [L=810]
Description: copper/silver-translocating P-type ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-45  154.9   0.5    1.5e-45  154.9   0.5    2.0  2  E1-E2_ATPase  E1-E2 ATPase
    3.2e-34  119.1   2.4    6.2e-34  118.1   2.4    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
    3.8e-08   33.6   0.0    1.2e-07   32.0   0.0    2.0  1  HMA           Heavy-metal-associated domain
     0.0016   18.3   0.1     0.0026   17.6   0.1    1.2  1  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.034   13.9   4.0       0.06   13.1   1.7    2.7  2  HCV_NS4a      Hepatitis C virus non-structural protein NS4a


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.8   2.2         5   1.8e+04     129     155 ..     261     285 ..     254     292 .. 0.32
   2 !  154.9   0.5   4.2e-49   1.5e-45       7     180 ..     319     492 ..     313     493 .. 0.95

  Alignments for each domain:
  == domain 1  score: -5.8 bits;  conditional E-value: 5
                                       HHHHHHHS-STTTSSTT..HHHHHHHHHH CS
                      E1-E2_ATPase 129 iallvflialllgksla..eallralall 155
                                       +a++vf +  ++    +  + +++ ++++
  gi|313117295|ref|YP_004044278.1| 261 VAAYVFSVGSMV----VgrTHVYFDVSVA 285
                                       222222222222....1222333323322 PP

  == domain 2  score: 154.9 bits;  conditional E-value: 4.2e-49
                                       EEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEE CS
                      E1-E2_ATPase   7 akvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeak 82 
                                       a+++  dg++e+++++ ++p+D +l+++g+rvp+Dg++veg a vdes++TGEs p ++e gd+v++G+vv+++ ++
  gi|313117295|ref|YP_004044278.1| 319 ATRLsDDGRTESVPVESIRPDDRILVRPGERVPVDGVVVEGRAAVDESLVTGESIPTTREPGDSVIGGSVVTDDALT 395
                                       5555599********************************************************************** PP

                                       EEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS CS
                      E1-E2_ATPase  83 avVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaai 159
                                       ++V   + +++l+++++l+ e +s++   q+ +dkl+ v+vp+vl++++l+ + +l+lg s+++all++l++l++++
  gi|313117295|ref|YP_004044278.1| 396 VEVGDDA-TSTLDRLVELLWEIQSSRGGAQRLADKLATVFVPLVLALSVLTTAGFLVLGSSPTDALLNGLTVLIVSC 471
                                       **98765.788****************************************************************** PP

                                       -TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 160 PcaLplavplalalgarrlak 180
                                       PcaL+la+pla+a g+r +a+
  gi|313117295|ref|YP_004044278.1| 472 PCALGLATPLAVASGVRDAAD 492
                                       *****************9985 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   2.4   1.7e-37   6.2e-34       2     210 .]     510     720 ..     509     720 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 1.7e-37
                                       SEEEEESBTTTBCHHHHHHHHHHHH.....CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa.....alalaaaletgsehpigkalvaaakarsgaltgfatfigrg...... 67 
                                       +t++fDk+GTLt+g+++v+ v+  a     al+laaa e  + hp+++alv  a +r + +t+ ++   rg      
  gi|313117295|ref|YP_004044278.1| 510 DTIIFDKTGTLTDGRMRVRGVTTAAadettALELAAAVERYASHPLAEALVQCAPDRLPTVTDSTV-HQRGvtgrvd 585
                                       79***********************9999999999999999****************999999988.666678888* PP

                                       ..HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEE CS
                                       ..xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ..ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievv 138
                                          + +g p +l++   ++p++l +a +s  ++gr  +++  +  a+avf + d   +++   e++ +L a   e+v
  gi|313117295|ref|YP_004044278.1| 586 gtDIVVGHPSLLREAgvTVPDELASAGESVRDAGRVPVFVgwDRSARAVFDVGDA--PREMWDETLSELGAE-RELV 659
                                       ******************************************99***********..************965.77** PP

                                       EEESSEHHHHHHHHHH.TTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 139 lltgdnpetaeraanq.lGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +ltgd+++ a    ++ +            +e++a++ pe+k +++++++ +   vamVGDg nDa+alaaA+
  gi|313117295|ref|YP_004044278.1| 660 VLTGDDERAAAQFRSHpAV-----------DEVFAGVPPEAKAETVERFR-SRGTVAMVGDGSNDAPALAAAD 720
                                       *******999988888455...........888****************5.5559*****************8 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   3.4e-11   1.2e-07       2      61 ..      99     158 ..      98     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3.4e-11
                               HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                       ++v+gmhCa C+  +e++  + +gV++++ ++at+ + V++d+++t+l  ++  +   gy
  gi|313117295|ref|YP_004044278.1|  99 LSVDGMHCATCETFIESTAVGDDGVYAAEASYATDMLRVTYDPDETDLDGLVGRLGRYGY 158
                                       579******************************************777666666655555 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   7.1e-07    0.0026     205     243 ..     702     740 ..     695     749 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.1e-07
                                       GEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE CS
                       Hydrolase_3 205 eviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvt 243
                                        v+ +GDg ND + L aa++g+A g++++ + +aAd ++
  gi|313117295|ref|YP_004044278.1| 702 TVAMVGDGSNDAPALAAADVGIAFGSGTDLAGSAADAII 740
                                       68899*******************************997 PP

>> HCV_NS4a  Hepatitis C virus non-structural protein NS4a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.7   1.7e-05      0.06       8      29 ..     256     277 ..     255     298 .. 0.79
   2 ?   -2.5   0.0       1.2   4.4e+03      40      55 ..     336     352 ..     316     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                          HCV_NS4a   8 lalAglAiyalttGSvvvvtrw 29 
                                       +alA++A+y  ++GS+vv ++ 
  gi|313117295|ref|YP_004044278.1| 256 VALAAVAAYVFSVGSMVVGRTH 277
                                       69**************996654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                          HCV_NS4a  40 vvpdeevlyq.geemee 55 
                                       + pd+ +l + ge+++ 
  gi|313117295|ref|YP_004044278.1| 336 IRPDDRILVRpGERVPV 352
                                       45899999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (810 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.24s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 5126.02
//
Query:       gi|313117296|ref|YP_004044279.1|  [L=266]
Description: hypothetical protein Hbor_30820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-43  149.3  14.4    1.5e-43  149.1  14.4    1.0  1  DsbD_2     Cytochrome C biogenesis protein transmembrane regi


Domain annotation for each model (and alignments):
>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.1  14.4   8.4e-48   1.5e-43       2     198 ..      22     240 ..      21     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 149.1 bits;  conditional E-value: 8.4e-48
                            DsbD_2   2 afllgLlgslhClgmCggivlalslsk......pk....ral.alllynlGRilsYallGalvgllgsvlqlagel. 66 
                                       ++++g lg++hClgmCg++v+ +++++       +    r++ +++l+nlGR + Ya++Ga+++++g+v   a ++ 
  gi|313117296|ref|YP_004044279.1|  22 FLVVGVLGGAHCLGMCGPLVSVYADRLratddtDAeltvRQVrQHTLFNLGRAAGYAVVGAILAAIGAVTVGALDAv 98 
                                       789********************999955444301333466658**************************9888777 PP

                            DsbD_2  67 ....eglrallgvllgllllllglklllkkkllkl....erlgkllsrllkklakkl...kslasalllGllnGllp 132
                                           +g+ra+ gvl+g+l+++ g+++l+++ + ++    +rl++ ++r+ + l++++    +  ++++lG+ +++lp
  gi|313117296|ref|YP_004044279.1|  99 vaigTGVRATTGVLVGVLIMATGVSYLRGG-AGSVvrlpGRLSNAFRRVSSVLTNRVdalVGDTRIVGLGVGHAFLP 174
                                       788888********************9644.33430113444444444444445554666999************** PP

                            DsbD_2 133 CglvysalllalasgsaleGalvmlaFgLGTlpalllfglllgllskklrkkllrlagvllillgl 198
                                       C++ y+a+l+a+a++++++ a+++ ++gLGT+p+l+++g++lg ls+  r++l+r++g+++++lg+
  gi|313117296|ref|YP_004044279.1| 175 CPITYPAYLYAFATADPVRAAFLLSLLGLGTIPTLFVYGTALGSLSAGRRRSLHRVLGAVFLVLGY 240
                                       ****************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1860.43
//
Query:       gi|313117297|ref|YP_004044280.1|  [L=66]
Description: hypothetical protein Hbor_30830 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 452.80
//
Query:       gi|313117298|ref|YP_004044281.1|  [L=94]
Description: hypothetical protein Hbor_30840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 647.08
//
Query:       gi|313117299|ref|YP_004044282.1|  [L=171]
Description: heme/copper-type cytochrome/quinol oxidase subunit 2 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-10   41.5   0.1    1.4e-10   41.1   0.1    1.2  1  COX2            Cytochrome C oxidase subunit II, periplasmic 
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.016   15.3   0.0    1.3  1  Cupredoxin_1    Cupredoxin-like domain
       0.02   14.6   0.6      0.038   13.8   0.6    1.4  1  COX2-transmemb  Cytochrome C oxidase subunit II, transmembran
        0.2   11.0   0.6        0.4   10.1   0.6    1.5  1  UCR_Fe-S_N      Ubiquitinol-cytochrome C reductase Fe-S subun


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   3.2e-14   1.4e-10      44     115 ..      83     154 ..      66     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.2e-14
                              COX2  44 vdnrvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssmpi 115
                                       + + + +p ++++ + vt+ dv+h + +      + a+pG+++q+++  d    +   c e cG+ h +m  
  gi|313117299|ref|YP_004044282.1|  83 TSDPIRVPANSEVTFHVTSRDVIHGYEIVGTNANTMAIPGQVSQMTVKFDEAKEYGLLCNEYCGAAHHAMEG 154
                                       567889********************************************99999889**********9964 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.5e-06     0.016      35     104 .]      85     158 ..      55     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-06
                      Cupredoxin_1  35 skievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeftcd.....mhmdakGkliV 104
                                       + i v+a+ +v+++++ +d   +  e+   + ++   pg+ +++t++ +++ eY + c       h  ++Gk++V
  gi|313117299|ref|YP_004044282.1|  85 DPIRVPANSEVTFHVTSRDV-IHGYEIVGTNANTMAIPGQVSQMTVKFDEAKEYGLLCNeycgaAHHAMEGKIVV 158
                                       5699*****99999988874.599999999**************************9988555444459999998 PP

>> COX2-transmemb  Cytochrome C oxidase subunit II, transmembrane
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.6   8.4e-06     0.038      10      33 ..       4      27 ..       2      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                    COX2-transmemb 10 LAYEKGWLAFsLAmLFvFiALiAY 33
                                        YEK WLA +L ++  FiA + Y
  gi|313117299|ref|YP_004044282.1|  4 HKYEKIWLAGALLLIVGFIATVSY 27
                                      56*******************999 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6   8.9e-05       0.4      16      29 ..      21      34 ..      21      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.9e-05
                        UCR_Fe-S_N 16 yiATgavgaVGaaa 29
                                      +iAT++ gaVGa+ 
  gi|313117299|ref|YP_004044282.1| 21 FIATVSYGAVGAGI 34
                                      69**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1107.40
//
Query:       gi|313117300|ref|YP_004044283.1|  [L=573]
Description: heme/copper-type cytochrome/quinol oxidase, subunit 1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-92  308.3  64.4      1e-90  304.7  62.8    2.0  2  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.7  62.8   5.7e-95     1e-90       2     423 ..      14     462 ..      13     470 .. 0.90
   2 !    3.4   0.0    0.0016        29     120     176 ..     471     542 ..     465     567 .. 0.72

  Alignments for each domain:
  == domain 1  score: 304.7 bits;  conditional E-value: 5.7e-95
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S CS
                              COX1   2 igllylilalvlllvggllgllirlqlafp....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardla 74 
                                       ++ + l++a+++l +g ++gl+++l++++     ++  y++++t Hg+l++++f+++f++g++ ++v + l +r+l 
  gi|313117300|ref|YP_004044283.1|  14 VVQASLAVAFIALGIGAFFGLIQALHRTNIiriiSSVDYYTVLTGHGVLLALVFTIFFLVGLFTWAVTRSL-ERPLP 89 
                                       6777899********************86455667899********************************9.99*** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHH........CSS-STTTTTTTC.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              COX1  75 fprlnalsfwlvvlgvvllllsll........gaattgwteYaplsevdlwllglllvvvssllgainfivtilkrr 143
                                       + rl ++ f l++ g+++ ++++l         +a++++t+Yapl++++++++gl++++++++++++  + ++ ++r
  gi|313117300|ref|YP_004044283.1|  90 DIRLTWAWFGLMTTGATITAVTILaglfpdipMSADVLYTFYAPLQAHPAFYIGLAMFIIGTWMAGADWFLAYREWR 166
                                       **********777777776666664333554444******************************************* PP

                                       HHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSCE-HHHHHHHHHHHHTHHHHHHHHHHHHH CS
                              COX1 144 apgmtvaklplfvwavlatailillalpvlalalllllldrslgkffspgdplldqhlfWffgHpeVyililpalgi 220
                                       ++++  +++pl +++vl+t+i++ ++++++a+++++ l+++s+g +++ ++pll ++lfW+fgHp+Vy++++pa+ +
  gi|313117300|ref|YP_004044283.1| 167 SENP-DERIPLQTFMVLTTMIMWYISTLGVAVSVVFFLIPWSMG-LVDSVNPLLTRTLFWYFGHPVVYFWLMPAYLM 241
                                       9999.889***********************************7.8899**************************** PP

                                       HHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTS.SS-HHHHHHHHHHHHHTHHHHHH............ CS
                              COX1 221 vyyilpkfagrplfsyklsvlafililflsflvwaHHlftt.glpewlkalgsvfslliavPsgl............ 284
                                       +y++lpk++g +lfs+ l+++ f+l+l+ls++v++HH++ + g+ e +k+++++ ++++ +Ps+l            
  gi|313117300|ref|YP_004044283.1| 242 WYTVLPKLSGGRLFSDPLARVVFVLFLLLSTPVGIHHQYLDpGIAEGFKFIAMTNTMFLLLPSLLtaftvvasmehg 318
                                       *****************************************************************999999999999 PP

                                       .......CCCHHHHCC.TTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHH CS
                              COX1 285 .......kvfnwlatl.wrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvf 353
                                              + ++wl+tl wr ++ f+ ++l    ++++f +gG++G+++a  ++ny++hnt wv++HfH+++ +av++
  gi|313117300|ref|YP_004044283.1| 319 arqrggeGYLGWLGTLpWR-DPAFTGMAL----AGLMFAAGGFSGMINAGMNINYLIHNTIWVPGHFHMTVGTAVAL 390
                                       9999999889999999443.555555555....78888*************************************** PP

                                       HHHHHHHHHHHHHH.SB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST..--SCCCCHHHCHHHH CS
                              COX1 354 llfaaiyyllpklt.grmlserlaklhfwllfiGlvlmflpmhilGllgmprraad..yksfletvpelqpln 423
                                       +++a++y+llp++t ++ +s+ ++ l+++++f+G+v+m+ +mh  Gllg+prr+a+  y ++++ v+++  ++
  gi|313117300|ref|YP_004044283.1| 391 TMMAGTYWLLPQITgKKVYSRPIGLLQVVMWFVGMVFMSNAMHRGGLLGIPRRTAEpqY-TNFDFVTAIGSIW 462
                                       **************77788************************************5224.4455555555555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHH...............HHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHH CS
                              COX1 120 glllvvvssllgainfivtilk...............rrapgmtvaklplfvwavlatailillalpvlala 176
                                       g +l+ +s++l+++n+++t++                  a+g  v   +l++w+ +a++++il +++ la  
  gi|313117300|ref|YP_004044283.1| 471 GGTLLFISVVLFLFNVAATWADdrsetpvddylpeplSDASGSPVILDNLALWTGIAVVLVILAYTLPLASI 542
                                       445666899999*********955555555555555444444444477888888888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3574.24
//
Query:       gi|313117301|ref|YP_004044284.1|  [L=60]
Description: hypothetical protein Hbor_30870 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 405.27
//
Query:       gi|313117302|ref|YP_004044285.1|  [L=220]
Description: hypothetical protein Hbor_30880 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1527.64
//
Query:       gi|313117303|ref|YP_004044286.1|  [L=75]
Description: hypothetical protein Hbor_30890 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.40
# Mc/sec: 561.71
//
Query:       gi|313117304|ref|YP_004044287.1|  [L=242]
Description: hypothetical protein Hbor_30900 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-23   83.1   5.7    2.1e-23   83.1   5.7    2.4  2  SNARE_assoc      SNARE associated Golgi protein
  ------ inclusion threshold ------
        9.6    6.3  12.4       0.32   11.1   6.3    1.6  2  CD20             CD20-like family


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.16   1.4e+03      58      77 ..      57      76 ..      14      84 .. 0.66
   2 !   83.1   5.7   2.3e-27   2.1e-23       1     118 [.      86     202 ..      86     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.16
                       SNARE_assoc 58 alerlverygflallllrll 77
                                      +l ++++ ygf+a l+l +l
  gi|313117304|ref|YP_004044287.1| 57 ELRAFIQGYGFWAPLVLVIL 76
                                      25566666777775555544 PP

  == domain 2  score: 83.1 bits;  conditional E-value: 2.3e-27
                       SNARE_assoc   1 lPsevllvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrll 77 
                                       +P++vl+++aG+lfg ++gt++ ++g+++G+++a++l+r++g +a +++++ e+ + ++++    +  l+l+l+ l+
  gi|313117304|ref|YP_004044287.1|  86 IPGQVLALVAGYLFGAWWGTVYNVIGITIGSTVAFWLARRFG-RAYVERIVHEDVLAQFDSIDPTHARLTLFLFFLV 161
                                       8*****************************************.888888999999999*****99************ PP

                       SNARE_assoc  78 pivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylG 118
                                       p++P+d+++++ Glt++++++ ++ ++iG  p+ +++ ++G
  gi|313117304|ref|YP_004044287.1| 162 PGLPDDILCFAGGLTKIPLWQLVALAIIGRTPAFFLTNVVG 202
                                       ***********************************998887 PP

>> CD20  CD20-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.3   3.6e-05      0.32       4      88 ..      28     122 ..      27     132 .. 0.88
   2 ?   -2.8   0.4      0.65   5.8e+03      72      81 ..     213     222 ..     195     230 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
                              CD20   4 vvQillGllslvlGilllsvsss........tllasgypfWgGivfiisGvlgiaaekrst..kllvklslllnlvs 70 
                                       +v++l++l++l+ +++ll  +            +  gy fW+ +v +i  +l ++a   ++    lv ++l+    +
  gi|313117304|ref|YP_004044287.1|  28 LVHLLVALVVLSIAVVLLRRHLEfltnaaelRAFIQGYGFWAPLVLVILQSLQVVAAPIPGqvLALVAGYLFGAWWG 104
                                       69***************9999999999**999999**************************4444556778888889 PP

                              CD20  71 lvlalaGiillilslall 88 
                                        v +++Gi +++ ++++l
  gi|313117304|ref|YP_004044287.1| 105 TVYNVIGITIGSTVAFWL 122
                                       999999999999888776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.65
                              CD20  72 vlalaGiill 81 
                                       +l la++i+ 
  gi|313117304|ref|YP_004044287.1| 213 ALGLAALIIA 222
                                       3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1577.61
//
Query:       gi|313117305|ref|YP_004044288.1|  [L=982]
Description: methyl-accepting chemotaxis protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-42  144.3  26.7    3.1e-42  144.3  26.7    4.0  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    3.5e-24   85.9   1.0    3.5e-24   85.9   1.0    6.3  6  dCache_1         Cache domain
    1.4e-13   51.0   0.4    1.4e-13   51.0   0.4    4.1  4  HAMP             HAMP domain
    4.4e-13   49.2   3.5    5.5e-11   42.3   0.6    4.9  6  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
    6.6e-07   28.8  17.5    1.3e-06   27.9   0.3    4.5  4  dCache_2         Cache domain
    1.2e-06   28.5   1.2    1.2e-06   28.5   1.2    4.4  4  sCache_2         Single Cache domain 2
  ------ inclusion threshold ------
      0.037   14.3  50.1       0.06   13.6   3.2    5.8  5  DUF948           Bacterial protein of unknown function (DUF94
      0.056   11.6  32.5     0.0058   14.9  15.2    2.5  2  EzrA             Septation ring formation regulator, EzrA
      0.076   13.0  42.5      0.019   15.0   4.7    4.9  5  Laminin_II       Laminin Domain II
       0.54    9.5  25.8        1.4    8.2   5.8    3.9  4  CorA             CorA-like Mg2+ transporter protein
       0.87    9.2  41.7        5.2    6.7  12.2    3.9  3  YkyA             Putative cell-wall binding lipoprotein
        1.6    9.2   8.4       0.19   12.2   1.6    2.8  3  DUF3106          Protein of unknown function (DUF3106)
        3.7    7.2  40.5        1.3    8.7  10.0    3.8  3  Laminin_I        Laminin Domain I


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       4.6   6.3e+03      25      40 ..      54      69 ..      32      80 .. 0.49
   2 !    7.9  11.6    0.0018       2.4      76     156 ..     641     721 ..     638     726 .. 0.90
   3 !  144.3  26.7   2.2e-45   3.1e-42       3     171 ..     729     897 ..     720     898 .. 0.96
   4 ?    3.0   5.6     0.057        79     132     169 ..     893     930 ..     890     933 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.6
                                      HHHHHHHHHHHHHHHH CS
                         MCPsignal 25 meeieksskeisdiie 40
                                       ++++ + ++i+++++
  gi|313117305|ref|YP_004044288.1| 54 NNTVTARREQIQNVLD 69
                                      1223333444444444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  76 EVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaase 152
                                       EV+++A++ a+ + e+    +ei++ ++ +++s+ee  + +e+ +e+ + + +++++++++++eva++ + +  +++
  gi|313117305|ref|YP_004044288.1| 641 EVHDVADQFADVSSETVVSAEEIEAASQATAQSVEEIAHGAEQQTEQLQAASDEMNNLSATIEEVAASADGVVETAN 717
                                       89999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       HHHH CS
                         MCPsignal 153 eqsa 156
                                       e ++
  gi|313117305|ref|YP_004044288.1| 718 EAAS 721
                                       8876 PP

  == domain 3  score: 144.3 bits;  conditional E-value: 2.2e-45
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHH CS
                         MCPsignal   3 laeeaseeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrk 79 
                                        a +a+ee +  + e   +v+q+e ++++ +ei+++++ i+ei++QT lLALNA+iEAARAGe G+GFaVVA+E++ 
  gi|313117305|ref|YP_004044288.1| 729 HAADATEEISAIEDETTTAVEQVEGLSERIEEINEVVQLITEITEQTDLLALNASIEAARAGEVGKGFAVVANEIKM 805
                                       577788888888999999*********************************************************** PP

                                       HHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  80 LAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsa 156
                                       LA+++ +a++++e+li+eiq +++d+ve +++ r+rve+g+e++e++ e + +i+ea ++ +d+v+ei++++e+q++
  gi|313117305|ref|YP_004044288.1| 806 LANQAEDATEQVEELITEIQDDTDDTVEDIQSMRERVESGAETIEDAIEMFDDIAEASEKAEDEVKEISKSTEDQAT 882
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHH CS
                         MCPsignal 157 sieevnqaveevakv 171
                                       s eev   v+ev++v
  gi|313117305|ref|YP_004044288.1| 883 STEEVVAMVDEVSSV 897
                                       **********99987 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.057
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 132 eiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                       e+++  ++ a++ + ++aa+eeq+asi+ev+q+++ v+
  gi|313117305|ref|YP_004044288.1| 893 EVSSVSEQTASEASTVSAATEEQTASINEVTQNIQTVS 930
                                       44555566677778888888889999998888888776 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.0     0.012        17       3      45 ..      45      87 ..      44     127 .. 0.84
   2 !    8.9   0.1   0.00084       1.2     165     246 ..     169     265 ..     165     268 .. 0.58
   3 !   85.9   1.0   2.6e-27   3.5e-24      53     246 ..     279     491 ..     267     494 .. 0.84
   4 ?   -2.6   4.6       2.8   3.8e+03      16      40 ..     682     706 ..     659     787 .. 0.61
   5 ?    2.0   2.4       0.1   1.4e+02       5      54 ..     811     864 ..     797     900 .. 0.57
   6 ?   -0.5   0.6      0.65   8.9e+02       5      32 ..     909     936 ..     892     956 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                          dCache_1  3 ieeqaeeqllglaeqlanniedvldslenlaetlasnpslqdl 45
                                      +e+q++ +l ++++   ++i++vld ++  a+ la ++ +q++
  gi|313117305|ref|YP_004044288.1| 45 METQVTGELNNTVTARREQIQNVLDVRRVDARSLADSSPVQNY 87
                                      78999*****************************999888876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00084
                          dCache_1 165 dllsniklgetgyvfivdsdGniiahpd.kdl..........lgknlrdelkaq........ealekalakiesgvs 222
                                       ++++   +g+tgy++i d+d n+++h + +d           +    ++e +++           e+++ + e +++
  gi|313117305|ref|YP_004044288.1| 169 KIFQPGYIGDTGYAYITDGDSNVVVHHKiHDGfnlvddasltV----FNEVESTiqndpavrSGSEWRIVEYEWEDT 241
                                       56777779*****************988766644444433331....233333255555555333333333333333 PP

                          dCache_1 223 svklng.eeylvayapiptglgWyl 246
                                       ++  n  ee++vaya  + +++W l
  gi|313117305|ref|YP_004044288.1| 242 TQAGNPvEEKFVAYAYYE-DFDWVL 265
                                       333333456677777776.588876 PP

  == domain 3  score: 85.9 bits;  conditional E-value: 2.6e-27
                          dCache_1  53 neasreslqallksilksn.........pdisgvylvdadGqviassdpssppnleg.....tddpadrdwykeala 115
                                       +e+ ++++++ ++++l++          p ++++ l d+dG  +++  +  +++  +     +  +ad++w++  ++
  gi|313117305|ref|YP_004044288.1| 279 SESAKNRINDSFENYLNTRsvsvqgeerPAYDEIILTDEDGHGVVRAERT-DGSV-VtesveNTSYADTEWFNSSRS 353
                                       5778899999999999999999999999999*******888876643333.2222.23567889************* PP

                          dCache_1 116 ggggkpvisdpyvdqtggkpvitiavpiyddsgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpd 192
                                        ++g+++++d+ +  + g pvi++++p+y  +g+f G++a+ +d   l+ l + + +g+tg++ iv+++G++++hp+
  gi|313117305|ref|YP_004044288.1| 354 MEKGEVHVGDVRT--VNGAPVIYLSTPVYQ-NGEFAGTIALRFDYGILTALTNGVTVGDTGHLSIVNDEGRVLSHPN 427
                                       ***********94..4489**********9.6********************************************* PP

                          dCache_1 193 kdllgknlrdelkaq..........ealekalakiesgvssvklnge....eylvayapip.tglgWyl 246
                                       ++ +     ++++++          +++e ++   e g s+++++ +    ey+v yap++ +++   l
  gi|313117305|ref|YP_004044288.1| 428 STVV-----ETESSIvneeyagglaGIAEERILTGEHGLSTYTRQTDgenaEYYVGYAPLDfGDKQFAL 491
                                       9998.....5555555556799***9*****************99965677*********976666655 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.8
                          dCache_1  16 eqlanniedvldslenlaetlasnp 40 
                                       eq ++++++  d+++nl+ t+ +  
  gi|313117305|ref|YP_004044288.1| 682 EQQTEQLQAASDEMNNLSATIEEVA 706
                                       2222222222233444444332222 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.1
                          dCache_1   5 eqaeeqllglaeqlanniedvldslenlaetlasn.pslqdlleepnra...ne 54 
                                       e+a+eq+++l++++ ++ +d+++ +++  e++ s  +++ d+ e+++     +e
  gi|313117305|ref|YP_004044288.1| 811 EDATEQVEELITEIQDDTDDTVEDIQSMRERVESGaETIEDAIEMFDDIaeaSE 864
                                       556666666666666666666655554444442221234444444444333333 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 0.65
                          dCache_1   5 eqaeeqllglaeqlanniedvldslenl 32 
                                       ++a+e+++++++++++ni++v +++++l
  gi|313117305|ref|YP_004044288.1| 909 SAATEEQTASINEVTQNIQTVSEEAQSL 936
                                       4455566666666666666666555532 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.4   9.8e-17   1.4e-13       2      52 ..     540     591 ..     539     592 .. 0.96
   2 !    6.9   0.3    0.0057       7.9      11      42 ..     595     626 ..     593     637 .. 0.88
   3 ?   -0.7   0.4       1.4   1.9e+03      14      48 ..     671     706 ..     669     711 .. 0.66
   4 ?   -2.9   0.1       7.1   9.7e+03      10      38 ..     761     793 ..     758     794 .. 0.69

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 9.8e-17
                                       HHHTTHHHHHHHHHHHHHHTTTBTSSTCCT.TSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   2 larrilrPLrrLaraarriaaGdldtrlpv.sgrDEiGeLarafNaMldrLr 52 
                                        +r+ +rP+++L+++a+++a+G++d ++++  ++DEiGeL++af +M+++Lr
  gi|313117305|ref|YP_004044288.1| 540 ASRYFSRPIEQLRDHAAALAEGRFDDDIEIsASDDEIGELVEAFGEMQRNLR 591
                                       689***************************99******************97 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHH CS
                              HAMP  11 rrLaraarriaaGdldtrlpvsgrDEiGeLar 42 
                                        +L+++ +++++G ld+++ ++ + E+G++  
  gi|313117305|ref|YP_004044288.1| 595 AELRAVSEELGEGTLDQDVRTDLPGEFGAIMS 626
                                       6899************************9865 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.4
                                       HHHHHHHTTT......BTSSTCCTTSSSHHHHHHHHHHHHH CS
                              HAMP  14 araarriaaG......dldtrlpvsgrDEiGeLarafNaMl 48 
                                       a+++++ia+G      +l +       DE+  L +++++ +
  gi|313117305|ref|YP_004044288.1| 671 AQSVEEIAHGaeqqteQLQA-----ASDEMNNLSATIEEVA 706
                                       56778888886554443333.....5788888888887766 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 7.1
                                       HHHHHHHHHHHTTT....BTSSTCCTTSSSHHH CS
                              HAMP  10 LrrLaraarriaaG....dldtrlpvsgrDEiG 38 
                                       ++++++ + +i +      l+++++  +  E+G
  gi|313117305|ref|YP_004044288.1| 761 INEVVQLITEITEQtdllALNASIEAARAGEVG 793
                                       566677777777655555677778888888887 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       1.8   2.5e+03      32      58 ..      96     122 ..      80     133 .. 0.56
   2 !   42.3   0.6     4e-14   5.5e-11     177     288 ..     160     280 ..     140     284 .. 0.85
   3 !   16.7   0.1   2.5e-06    0.0034     136     265 ..     354     481 ..     330     509 .. 0.77
   4 ?   -1.6   0.4      0.95   1.3e+03      23      51 ..     680     708 ..     658     780 .. 0.48
   5 ?   -3.4   4.4       3.2   4.4e+03      17      46 ..     891     920 ..     810     939 .. 0.59
   6 ?   -1.3   0.0      0.77   1.1e+03     178     205 ..     930     957 ..     926     971 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                   Cache_3-Cache_2  32 ellrekverdlnvfakllsnewrvdnq 58 
                                       +l++++ +++l  +a +++++++ ++q
  gi|313117305|ref|YP_004044288.1|  96 KLVQRQSQTQLGHMALQMRSTIESTKQ 122
                                       555555555555555554444433333 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 4e-14
                   Cache_3-Cache_2 177 qsealkslrkelkklkvGktGylyvldgkgdkkgkliihptlk.gknvldlkdadgesvvkkllkk........ksg 244
                                       q+ a  s +k ++   +G+tGy+y++dg+     ++++h + + g n++d ++    + v+  +++        + +
  gi|313117305|ref|YP_004044288.1| 160 QTTAAGSASKIFQPGYIGDTGYAYITDGD----SNVVVHHKIHdGFNLVDDASLTVFNEVESTIQNdpavrsgsEWR 232
                                       5566667777777788*************....89999999888*****98444444888888888*******9999 PP

                   Cache_3-Cache_2 245 sleyelk....kdekgreklavftyfepwdWvivasvyedefqeevnr 288
                                        +eye++    + +  +ek++++ y+e +dWv++ svy  e+q ++++
  gi|313117305|ref|YP_004044288.1| 233 IVEYEWEdttqAGNPVEEKFVAYAYYEDFDWVLAPSVYYYELQTTASE 280
                                       9******999999999*************************9988765 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 2.5e-06
                   Cache_3-Cache_2 136 vlagetYvGra.kvfgkwYvTaYePikdadgkViGilyVgvdqsealkslrkelkklkvGktGylyvldgkgdkkgk 211
                                       + +ge  vG + +v+g+  +   +P+  ++g+  G +   +d+      l+   + ++vG+tG+l +++++    g+
  gi|313117305|ref|YP_004044288.1| 354 MEKGEVHVGDVrTVNGAPVIYLSTPVY-QNGEFAGTIALRFDY----GILTALTNGVTVGDTGHLSIVNDE----GR 421
                                       567777788762577888888999999.*********999999....5577777899**************....** PP

                   Cache_3-Cache_2 212 liihptlk....gknvldlkdadge..svvkkllkkksgsleyelkkdekgreklavfty 265
                                       ++ hp ++      ++++ + a g    + +++l  + g  +y+ ++d +++e+++ +  
  gi|313117305|ref|YP_004044288.1| 422 VLSHPNSTvvetESSIVNEEYAGGLagIAEERILTGEHGLSTYTRQTDGENAEYYVGYAP 481
                                       *******99877777777655555555566677777999999977766666666666654 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.95
                   Cache_3-Cache_2  23 laetletqdellrekverdlnvfakllsn 51 
                                        ae+   q ++++ ++++++ ++++  ++
  gi|313117305|ref|YP_004044288.1| 680 GAEQQTEQLQAASDEMNNLSATIEEVAAS 708
                                       22222223333333334443333333333 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 3.2
                   Cache_3-Cache_2  17 ekevedlaetletqdellrekverdlnvfa 46 
                                         ev+++ e++++  +++++++e ++  ++
  gi|313117305|ref|YP_004044288.1| 891 VDEVSSVSEQTASEASTVSAATEEQTASIN 920
                                       223333333333333333333333333333 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 0.77
                   Cache_3-Cache_2 178 sealkslrkelkklkvGktGylyvldgk 205
                                       se+ +sl++  k++ vGk+G + + +++
  gi|313117305|ref|YP_004044288.1| 930 SEEAQSLQELVKRFDVGKHGSASASQSS 957
                                       678899**************99877666 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.3   9.3e-10   1.3e-06     202     294 ..     176     273 ..     161     275 .. 0.79
   2 !    6.1   0.0    0.0038       5.2      84     119 ..     400     435 ..     395     475 .. 0.76
   3 ?   -0.8   6.2      0.51     7e+02       4      74 ..     804     875 ..     799     902 .. 0.61
   4 ?   -2.0   2.6       1.2   1.6e+03      44      93 ..     881     931 ..     865     942 .. 0.48

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 9.3e-10
                          dCache_2 202 ygnngyifiydtdgniilhplkkelngknllevkdkkgkl...lqelleaakkkge....gfveYkwpkpsgd..ke 269
                                       +g++gy++i d d+n+++h   k  +g nl+  +d++ ++   +++ +++  + ++     +veY w +++++    
  gi|313117305|ref|YP_004044288.1| 176 IGDTGYAYITDGDSNVVVHH--KIHDGFNLV--DDASLTVfneVESTIQNDPAVRSgsewRIVEYEWEDTTQAgnPV 248
                                       689*****************..777787777..4444444445666666533322234799********99998788 PP

                          dCache_2 270 rkKisyvryfppwdWiigtgvylde 294
                                       ++K + + y++++dW+++ +vy  e
  gi|313117305|ref|YP_004044288.1| 249 EEKFVAYAYYEDFDWVLAPSVYYYE 273
                                       9999999**************9876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0038
                          dCache_2  84 alrsirydggegyyfiidskgtlilhpdspsleGkn 119
                                       al++   +g++g++ i++++g+++ hp+s+ +e  +
  gi|313117305|ref|YP_004044288.1| 400 ALTNGVTVGDTGHLSIVNDEGRVLSHPNSTVVETES 435
                                       444444499*******************98887643 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.51
                          dCache_2   4 dfkeeiekleeetikerkellksevdsaielieyeknsleeslkesLksrveeaysiaeeiyek.......yknels 73 
                                       ++ +++++  +e+++e  +++++++d+ +e i++ ++++e s  e++ + +e++ +iae   +              
  gi|313117305|ref|YP_004044288.1| 804 KMLANQAEDATEQVEELITEIQDDTDDTVEDIQSMRERVE-SGAETIEDAIEMFDDIAEASEKAedevkeiS----- 874
                                       5666777777888888888888888888888885555554.4566777777776666665555433322222..... PP

                          dCache_2  74 e 74 
                                       +
  gi|313117305|ref|YP_004044288.1| 875 K 875
                                       2 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.2
                          dCache_2  44 eslkesLksrveeaysiaeeiyekykn.elseeeakklikealrsirydgg 93 
                                       ++ +e++ + v+e+ s+ e+   +      + ee + +i e+ ++i+ + +
  gi|313117305|ref|YP_004044288.1| 881 ATSTEEVVAMVDEVSSVSEQTASEASTvSAATEEQTASINEVTQNIQTVSE 931
                                       334444444555555555555555444444444444444444444443333 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   1.2   8.7e-10   1.2e-06      22     153 ..     127     282 ..     106     284 .. 0.79
   2 ?    0.9   0.0      0.26   3.6e+02      45      78 ..     402     434 ..     373     451 .. 0.78
   3 ?   -1.1   0.2       1.1   1.5e+03       5      69 ..     743     808 ..     739     820 .. 0.72
   4 ?    3.3   0.4     0.047        65       8      47 ..     823     862 ..     813     875 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 8.7e-10
                          sCache_2  22 avykqvesgkiteeeaqeevkelvnglkfgdG.....................kgYffvldedgtllvhPfnpqleG 77 
                                       + y      ++t +e q++vke+v+++  g                        gY +++d d +++vh        
  gi|313117305|ref|YP_004044288.1| 127 EEYNGRSWAELTPAE-QQRVKEKVERIIAGTAgnqttaagsaskifqpgyigdTGYAYITDGDSNVVVH-----HKI 197
                                       445555556666666.556777777777776667779********************************.....345 PP

                          sCache_2  78 knasnlkDanGkyiirelvkeak.......kkgggfvtylwkkpge..geveeklayvkyfepWdwvigtgvylddi 145
                                        +  nl D    ++++e+ ++++       +++ ++v+y+w++  +  + veek+++ +y+e +dwv+   vy+ ++
  gi|313117305|ref|YP_004044288.1| 198 HDGFNLVDDASLTVFNEVESTIQndpavrsGSEWRIVEYEWEDTTQagNPVEEKFVAYAYYEDFDWVLAPSVYYYEL 274
                                       78888888889999999999988544443446779******998877799**************************9 PP

                          sCache_2 146 nkavekil 153
                                       + ++ + +
  gi|313117305|ref|YP_004044288.1| 275 QTTASESA 282
                                       99987765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.26
                          sCache_2  45 vnglkfgdGkgYffvldedgtllvhPfnpqleGk 78 
                                        ng + gd  g + +++++g +l hP ++ +e +
  gi|313117305|ref|YP_004044288.1| 402 TNGVTVGD-TGHLSIVNDEGRVLSHPNSTVVETE 434
                                       45556666.999**************97666555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                          sCache_2   5 keaelknqvetaislieavykqves.gkiteeeaqeevkelvnglkfgdG.kgYffvldedgtllvh 69 
                                       + +   +qve++ + ie++++ v+   +ite+         +++ + g+  kg f v++++ ++l++
  gi|313117305|ref|YP_004044288.1| 743 ETTTAVEQVEGLSERIEEINEVVQLiTEITEQTDLLALNASIEAARAGEVgKG-FAVVANEIKMLAN 808
                                       55666788999999999999888864678888888888888888888874377.7777777777776 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.047
                          sCache_2   8 elknqvetaislieavykqvesgkiteeeaqeevkelvng 47 
                                       e++  ++++++ i+ ++++vesg+ t e+a e + ++ ++
  gi|313117305|ref|YP_004044288.1| 823 EIQDDTDDTVEDIQSMRERVESGAETIEDAIEMFDDIAEA 862
                                       677778899999******************9988877665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       3.8   5.2e+03      42      66 ..      39      63 ..      27      71 .. 0.54
   2 ?    7.7   3.8     0.003       4.1      21      87 ..     639     705 ..     634     707 .. 0.88
   3 ?    8.1   1.9    0.0022         3      21      83 ..     716     774 ..     711     779 .. 0.77
   4 ?   13.6   3.2   4.4e-05      0.06      19      83 ..     798     862 ..     794     875 .. 0.50
   5 ?    9.6   8.9    0.0008       1.1      23      88 ..     872     937 ..     868     938 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
                            DUF948 42 vdpilkevedllakvnelledvnek 66
                                      ++++++  ++++ + n+++   +e+
  gi|313117305|ref|YP_004044288.1| 39 TQSTTHMETQVTGELNNTVTARREQ 63
                                      4555555555555555533333333 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.003
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       l+++ +++d++a+   e+   +++i   ++++ + v+e++ + ++++e++++  +++++l+++++e+
  gi|313117305|ref|YP_004044288.1| 639 LVEVHDVADQFADVSSETVVSAEEIEAASQATAQSVEEIAHGAEQQTEQLQAASDEMNNLSATIEEV 705
                                       77788888888888888889999999999999999999999***********************987 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0022
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                        +++++++d+ +++ ++ ++++ +i +e+++++++v+     ++e++e+++++++ + +++e+
  gi|313117305|ref|YP_004044288.1| 716 ANEAASLADRGREHAADATEEISAIEDETTTAVEQVEG----LSERIEEINEVVQLITEITEQ 774
                                       55667788888999999999999999999999999988....666777777777777777765 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 4.4e-05
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                       vv +++k ++++a+++ e++e+ +++i ++++d+++ ++ + e v++  e+++  +e + d++e+
  gi|313117305|ref|YP_004044288.1| 798 VVANEIKMLANQAEDATEQVEELITEIQDDTDDTVEDIQSMRERVESGAETIEDAIEMFDDIAEA 862
                                       44455555555555555555555555555555555555555555555555555554444444443 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0008
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +++k  +  a++ ee+   vd+++  +e++ +++ ++ +  +e++++++++t+++++++e  ++l+
  gi|313117305|ref|YP_004044288.1| 872 EISKSTEDQATSTEEVVAMVDEVSSVSEQTASEASTVSAATEEQTASINEVTQNIQTVSEEAQSLQ 937
                                       566667777788889999999999999**********************************99986 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   9.2      0.04        55     111     217 ..     661     772 ..     625     779 .. 0.55
   2 ?   14.9  15.2   4.2e-06    0.0058      96     222 ..     807     935 ..     799     943 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH-------------. CS
                              EzrA 111 deveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeelten. 186
                                       +e+e+ +++  + ++e+ +  e++ e+ +++ ++  +l+ ++++  +s   ++e+ ++  +  ++  ++  ++te+ 
  gi|313117305|ref|YP_004044288.1| 661 EEIEAASQATAQSVEEIAHGAEQQTEQLQAASDEMNNLSATIEEVAASADGVVETANEAASLADRGREHAADATEEi 737
                                       34555555566666666666666666666666666666666666666666666666666666666666666665531 PP

                                       ....---HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 187 ....gdyveakeilkkleeeideleevieeiPell 217
                                            + ++a e+++ l+e+i+e++ev++ i e+ 
  gi|313117305|ref|YP_004044288.1| 738 saieDETTTAVEQVEGLSERIEEINEVVQLITEIT 772
                                       11113334444444444444444444444444443 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.2e-06
                                       HHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHH CS
                              EzrA  96 fkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqlen 172
                                        ++a+ + +++ee ++e++ ++++  e+++ ++e  e   e ie++ e ++++ +  ++ +++ +e+ ++ e+q   
  gi|313117305|ref|YP_004044288.1| 807 ANQAEDATEQVEELITEIQDDTDDTVEDIQSMRERVESGAETIEDAIEMFDDIAEASEKAEDEVKEISKSTEDQATS 883
                                       5789999********************************************************************** PP

                                       H------------..----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTT CS
                              EzrA 173 iekefsefeelte..ngdyveakeilkkleeeideleevieeiPelleelkk 222
                                        e+  +  +e+ +  ++  +ea+ +  ++ee++++++ev+++i ++ ee+++
  gi|313117305|ref|YP_004044288.1| 884 TEEVVAMVDEVSSvsEQTASEASTVSAATEEQTASINEVTQNIQTVSEEAQS 935
                                       ******99998752267789************************99999875 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   5.0     0.021        29      27      71 ..     661     705 ..     632     725 .. 0.59
   2 ?    3.8  12.4     0.038        52       3     100 ..     669     766 ..     659     774 .. 0.73
   3 ?    7.4   2.2    0.0031       4.3       2      50 ..     727     775 ..     726     788 .. 0.86
   4 ?   15.0   4.7   1.4e-05     0.019       2      71 ..     804     873 ..     803     880 .. 0.93
   5 ?    1.7   8.3      0.17   2.3e+02      10      69 ..     882     941 ..     874     947 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.021
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II  27 entkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       e++++  +  ++svee+ + +++ +++++ A++++ +L  +++++
  gi|313117305|ref|YP_004044288.1| 661 EEIEAASQATAQSVEEIAHGAEQQTEQLQAASDEMNNLSATIEEV 705
                                       445555555666666666667777777777777777776666554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.038
                                       XXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH CS
                        Laminin_II   3 elaaeanetakevleqlaplsq...nlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklk 76 
                                       ++a++++e+a   ++q+++l++   +++n+++ ++e+++s++ + e +++a    +  r+   + ++++  ++d   
  gi|313117305|ref|YP_004044288.1| 669 ATAQSVEEIAHGAEQQTEQLQAasdEMNNLSATIEEVAASADGVVETANEAASLADRGREHAADATEEISAIEDETT 745
                                       66666677766666666665532227888888888888888888888888888888888888888888888888866 PP

                                       HHHHHHHH...HHHHHHHHHHHHH CS
                        Laminin_II  77 elkqleeassslsdniseikelIa 100
                                       +  ++ e+   ls+ i+ei e ++
  gi|313117305|ref|YP_004044288.1| 746 TAVEQVEG---LSERIEEINEVVQ 766
                                       66666666...8888888888775 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0031
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkda 50 
                                       +e aa+a e ++++++ ++   +++e ++e ++ein+ v+ ++e  ++ 
  gi|313117305|ref|YP_004044288.1| 727 REHAADATEEISAIEDETTTAVEQVEGLSERIEEINEVVQLITEITEQT 775
                                       678999********************************99999877654 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 1.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       k la++a++ +++v+e +++++ +++ t e+++++++ ve   e ++da ++ +d  +++ k e ++ ++
  gi|313117305|ref|YP_004044288.1| 804 KMLANQAEDATEQVEELITEIQDDTDDTVEDIQSMRERVESGAETIEDAIEMFDDIAEASEKAEDEVKEI 873
                                       77899*************************************************9999999999888776 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.17
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                        +++ev + + ++s   e+t +++s++ +  ee ++ +++ ++ i+ ++++ + L++l+ 
  gi|313117305|ref|YP_004044288.1| 882 TSTEEVVAMVDEVSSVSEQTASEASTVSAATEEQTASINEVTQNIQTVSEEAQSLQELVK 941
                                       567889999999999999999999999999999999999999999999999999988775 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.4    0.0016       2.3     150     223 ..     629     703 ..     581     709 .. 0.78
   2 ?    4.8   0.4     0.011        15     178     222 ..     723     765 ..     701     776 .. 0.79
   3 ?    8.2   5.8     0.001       1.4     120     224 ..     744     851 ..     724     856 .. 0.75
   4 ?    3.6  10.7     0.026        36      94     215 ..     799     940 ..     794     944 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                              CorA 150 lrelaqlrrrlvklrralapnrevlkrlla.kaddkllddedkeylrdlldelerllemlealrerleslqdtys 223
                                        + + ++rr+lv++++++ +  +v ++ +   ++ +  +++ ++  +++   +e+  e+l+a ++ +++l+ t+ 
  gi|313117305|ref|YP_004044288.1| 629 DDGIEKIRRSLVEVHDVADQFADVSSETVVsAEEIEAASQATAQSVEEIAHGAEQQTEQLQAASDEMNNLSATIE 703
                                       444556999999999999999999997666578888888888888999999999999999999999999887765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                              CorA 178 lakaddkllddedkeylrdlldelerllemlealrerleslqdty 222
                                          +++ ++ +++ e ++ ++de++ ++e++e l+er+e +++  
  gi|313117305|ref|YP_004044288.1| 723 A--DRGREHAADATEEISAIEDETTTAVEQVEGLSERIEEINEVV 765
                                       3..4666666677779***********************999876 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.001
                              CorA 120 vdrlfellekleeeldeledeledstkkeilrelaqlr.....rrlvklrralapnrevlkrllakaddkllddedk 191
                                       + +  e++e l+e+++e+ + ++  t+  +  +l++l       r++++ + +a   + + ++la + ++  +++ +
  gi|313117305|ref|YP_004044288.1| 744 TTTAVEQVEGLSERIEEINEVVQLITEITEQTDLLALNasieaARAGEVGKGFAVVANEI-KMLA-NQAEDATEQVE 818
                                       556678899999999999999966666666666666663322344555555555555555.6666.88888888889 PP

                              CorA 192 eylrdlldelerllemlealrerleslqdtyss 224
                                       e++ +++d+++  +e+++++rer+es  +t+  
  gi|313117305|ref|YP_004044288.1| 819 ELITEIQDDTDDTVEDIQSMRERVESGAETIED 851
                                       99***********************98888765 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.026
                              CorA  94 vikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledel.edstkkeilrelaqlr....rrlvklrr 165
                                       v++++k   ++ ++++e +++l+ ei d+ ++++e++ + ++++e+     +   e+++++a+       ++ ++ +
  gi|313117305|ref|YP_004044288.1| 799 VANEIKMLANQAEDATEQVEELITEIQDDTDDTVEDIQSMRERVESGAeTIEDAIEMFDDIAEASekaeDEVKEISK 875
                                       55666666688999999999999999999999999999999999999965555567888888877544444555544 PP

                              CorA 166 alapnrevlk...............rllakaddkllddedkeylrdlldelerllemlealrerl 215
                                       +  ++ +  +               +  + +  +  ++e+   ++++ ++++ ++e++++l+e++
  gi|313117305|ref|YP_004044288.1| 876 STEDQATSTEevvamvdevssvseqTASEASTVSAATEEQTASINEVTQNIQTVSEEAQSLQELV 940
                                       44444444442222555554444432333555666666666667777777777777777777766 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.37   5.2e+02     145     171 ..     625     651 ..     622     666 .. 0.89
   2 ?    6.7  12.2    0.0038       5.2      11     115 ..     672     773 ..     659     780 .. 0.74
   3 ?    4.3  21.9     0.021        29      25     169 ..     801     943 ..     782     946 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.37
                              YkyA 145 leeleeqiekiNesyeevkeaneqFne 171
                                       + +l+++ieki +s  ev++  +qF +
  gi|313117305|ref|YP_004044288.1| 625 MSDLDDGIEKIRRSLVEVHDVADQFAD 651
                                       6799*********************86 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0038
                              YkyA  11 eeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefeki 87 
                                       ++++e+  + e+q e+L+ +  + ++l   i e      d +++ ++ea ++++  +e+ +   e i++ ++e +++
  gi|313117305|ref|YP_004044288.1| 672 QSVEEIAHGAEQQTEQLQAASDEMNNLSATIEE-VAASADGVVETANEAASLADRGREHAADATEEISAIEDETTTA 747
                                       344455567777778888888777777777755.55666************************************** PP

                              YkyA  88 keeieeiedeelkkeaeelieameerye 115
                                        e++e + +    +e++e+++ + e +e
  gi|313117305|ref|YP_004044288.1| 748 VEQVEGLSER--IEEINEVVQLITEITE 773
                                       *******655..5555555555444333 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.021
                              YkyA  25 ekLtelekkeqelyeeiielgmde.fdkikklsdealenveeReellekekesieeakeefekikeeieeiede..e 98 
                                       ++++ l ++ ++  e++      e   +i++  d+ +e ++  +e++e+  e ie+a e f++i e  e+ ede  e
  gi|313117305|ref|YP_004044288.1| 801 NEIKMLANQAEDATEQVE-----ElITEIQDDTDDTVEDIQSMRERVESGAETIEDAIEMFDDIAEASEKAEDEvkE 872
                                       444444444444444442.....224456666777777777777777777777777777777777777777665445 PP

                              YkyA  99 lkkeaeelieameeryeaydklykaYkealeldkeLYemLkkeeltleeleeqiekiNesyeevkeaneqF 169
                                       + k +e+ +++ ee  +  d++ +  +++ ++  +     +++ ++++e+++ i+++ e+ + ++e ++ F
  gi|313117305|ref|YP_004044288.1| 873 ISKSTEDQATSTEEVVAMVDEVSSVSEQTASEASTVSAATEEQTASINEVTQNIQTVSEEAQSLQELVKRF 943
                                       56677777777778888888888888888888889999999999999999999999999999999999888 PP

>> DUF3106  Protein of unknown function (DUF3106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.6   0.00014      0.19      16      73 ..      92     152 ..      82     165 .. 0.66
   2 ?   -1.5   0.1       2.5   3.4e+03      61      78 ..     683     700 ..     663     750 .. 0.58
   3 ?   -1.7   0.1       2.9     4e+03      57      89 ..     910     941 ..     896     944 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                           DUF3106  16 aeewnelspeqreklleiaerykkltpe.eqkrlqerm..eewakLspeqreqarenyqkl 73 
                                       a +w+ ++ + + +l ++a ++++  +  +q+ l+e +  ++wa+L+p+++++++e+++++
  gi|313117305|ref|YP_004044288.1|  92 AGQWKLVQRQSQTQLGHMALQMRSTIEStKQTILEEEYngRSWAELTPAEQQRVKEKVERI 152
                                       5677777777777777777777665444044444554445677777777777777777665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                           DUF3106  61 eqreqarenyqklkqLpp 78 
                                       +q eq+++  +++++L++
  gi|313117305|ref|YP_004044288.1| 683 QQTEQLQAASDEMNNLSA 700
                                       333333333333333332 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.9
                           DUF3106  57 kLspeqreqarenyqklkqLppeereelrekwe 89 
                                       + ++eq + + e  q++++++ e + +l+e  +
  gi|313117305|ref|YP_004044288.1| 910 AATEEQTASINEVTQNIQTVSEEAQ-SLQELVK 941
                                       4456666666666666666666666.5555555 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  10.0   0.00093       1.3      15     111 ..     661     759 ..     649     766 .. 0.64
   2 ?    6.1   4.9    0.0057       7.9      48     128 ..     767     843 ..     759     849 .. 0.88
   3 ?    0.7  12.9      0.25   3.4e+02      41     114 ..     862     935 ..     833     940 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00093
                         Laminin_I  15 ykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaeki 91 
                                       ++i+a  + +++  +e     +++ ++++ +  e+++L   +ee +  a  v + a++    ++r  ++a ++ e+i
  gi|313117305|ref|YP_004044288.1| 661 EEIEAASQATAQSVEEIAHGAEQQTEQLQAASDEMNNLSATIEEVAASADGVVETANEAASLADRGREHAADATEEI 737
                                       56666666666667776666677777777777777777777777777777777777777777777777777777777 PP

                         Laminin_I  92 kkladnikeilekvatlne..n 111
                                        +++d+ + ++e+v+ l+e  +
  gi|313117305|ref|YP_004044288.1| 738 SAIEDETTTAVEQVEGLSEriE 759
                                       7777777777777776666332 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0057
                         Laminin_I  48 elesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlneneealpssklseel 124
                                        ++++ ++t+ L+  a    a+a +v +      n++k La ++++  ++++e++  +    +++ +  +++++++ 
  gi|313117305|ref|YP_004044288.1| 767 LITEITEQTDLLALNASIEAARAGEVGKGFAVVANEIKMLANQAEDATEQVEELITEI----QDDTDDTVEDIQSMR 839
                                       578999**************************************************99....556677777888777 PP

                         Laminin_I 125 aeaq 128
                                       + ++
  gi|313117305|ref|YP_004044288.1| 840 ERVE 843
                                       7665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.25
                         Laminin_I  41 kieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlneneea 114
                                         e +e e++++ + te  ++  ++v a   +v   se+t ++a++  ++ ++  ++i+e+++ ++t++e+++ 
  gi|313117305|ref|YP_004044288.1| 862 ASEKAEDEVKEISKSTEDQATSTEEVVAMVDEVSSVSEQTASEASTVSAATEEQTASINEVTQNIQTVSEEAQS 935
                                       55788999************************************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (982 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2705  (0.150873); expected 358.6 (0.02)
Passed bias filter:                      840  (0.0468515); expected 358.6 (0.02)
Passed Vit filter:                       166  (0.00925874); expected 17.9 (0.001)
Passed Fwd filter:                       109  (0.00607954); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.85u 0.40s 00:00:02.25 Elapsed: 00:00:00.63
# Mc/sec: 4663.94
//
Query:       gi|313117306|ref|YP_004044289.1|  [L=362]
Description: hypothetical protein Hbor_30920 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-30  106.6   0.1    1.5e-30  106.2   0.1    1.2  1  DUF21     Cyclin M transmembrane N-terminal domain
    7.9e-13   48.7   2.1    3.1e-07   30.7   0.0    2.5  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.1   1.7e-34   1.5e-30       3     160 ..      13     200 ..      11     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.7e-34
                             DUF21   3 ivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvell 79 
                                        ++ll+++a+f+  E+A+++++++   e+  +g+++ +r++++++++e +Ls +++g+t+++++l+++a+++++ +l
  gi|313117306|ref|YP_004044289.1|  13 GIVLLFGNAYFVTIEFAMTRVRQFS--ESEFQGSRGLERAWDMTERLEIFLSGCQLGITICSVGLGVVAEPALTAVL 87 
                                       58999******************99..56666779****************************************** PP

                             DUF21  80 ae..................galavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwll 138
                                        +                  +ala+v ++ ++ ll+l +gE +P  l++++++++a++ ap+l++++++++P+++l 
  gi|313117306|ref|YP_004044289.1|  88 DPavsalglqslsgtgsnghTALAAVTSLGVINLLHLTVGEQAPTYLGIERSKQVAKYGAPILYWWTRVFSPVIRLA 164
                                       *9****************9888888999999********************************************** PP

                             DUF21 139 skllnlil..............esesepavseeelk 160
                                       ++ ++ +l              e e e++ +++el 
  gi|313117306|ref|YP_004044289.1| 165 DWTAKSLLsvigvtitrswaeeEMEGEKPGTRQELL 200
                                       ********9888888887777766666777777765 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   7.5e-07    0.0067       2      56 ..     232     289 ..     231     290 .. 0.85
   2 !   30.7   0.0   3.5e-11   3.1e-07       3      55 ..     300     350 ..     296     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.5e-07
                                       HHH..SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdi..mtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllrall 56 
                                       gdi   ++d+v v+ + ++e  le++r++ ++r+P V ++ + ++G + l+ l+r + 
  gi|313117306|ref|YP_004044289.1| 232 GDImvDREDIVAVSTERSVEANLETIRSNSYTRFPLVgESVDDIIGTIYLMSLIRSID 289
                                       77744556******************6666******9877778***********9875 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 3.5e-11
                                       HH.SBSSCEEEETTSBHHHHHHHHHHHT..SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   3 di.mtrdvvtvppdttleealelmrekg..vsrlPVVdedgklvGivtlrDllral 55 
                                       di m   ++tvppd +++e+++++  ++  + ++ VV e+++ vG+vt +D ++a+
  gi|313117306|ref|YP_004044289.1| 300 DIaM--SPMTVPPDIPVSELIDEFQAADqeI-AF-VV-ESDRTVGLVTATDAFEAI 350
                                       5656..569***************6443447.88.**.8999*********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 2346.51
//
Query:       gi|313117307|ref|YP_004044290.1|  [L=216]
Description: phosphoribosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-26   91.8   0.0    5.2e-26   91.1   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0011   18.5   0.0     0.0019   17.7   0.0    1.6  1  UPRTase       Uracil phosphoribosyltransferase
      0.008   15.7   0.0      0.021   14.3   0.0    1.7  2  PRTase_2      Phosphoribosyl transferase
  ------ inclusion threshold ------
      0.076   12.4   1.8       0.15   11.4   0.3    1.9  2  PALP          Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   1.2e-29   5.2e-26      19     156 ..      20     199 ..       8     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 1.2e-29
                                       TEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........................ CS
                      Pribosyltran  19 aaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes................ 79 
                                       + ++l+e +   d+v++i+rgG+p++  +ad+L +pl++v  +k  +++++e+a+g+++                  
  gi|313117307|ref|YP_004044290.1|  20 LGDALREEGVDADIVLAIPRGGLPLGRMVADALHAPLDIVATQKIGAPNNPEFAIGAVAADgsawlneevierrgid 96 
                                       4455556577889*********************************************999**************** PP

                                       .........................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHH CS
                      Pribosyltran  80 .........................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpatee 131
                                                                  l+d+ gk+V++VDD+++tG T +a l ++ ++ pe+v++av+v  p    
  gi|313117307|ref|YP_004044290.1|  97 reyierirseeaenarekaetyrddGSLPDLSGKTVVVVDDGVATGATARACLSRVNAAAPERVIFAVPVGSPRAIS 173
                                       *************************99************************************************** PP

                                       HHHHH-TTS......EEEEEEE-SEE CS
                      Pribosyltran 132 evdknakrvfsls.pdnfvavvgfel 156
                                       + +  a++v++ls p+ f+av +f+ 
  gi|313117307|ref|YP_004044290.1| 174 DLEGLADEVVCLSaPSVFHAVGQFYE 199
                                       ***********************986 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.2e-07    0.0019     115     171 ..     124     177 ..      11     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.2e-07
                           UPRTase 115 LPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlae 171
                                       LP+ ++ +tv+++D  +aTG++a a+++++    +  e+++++  + s+ +++ l  
  gi|313117307|ref|YP_004044290.1| 124 LPD-LSGKTVVVVDDGVATGATARACLSRVNA--AAPERVIFAVPVGSPRAISDLEG 177
                                       554.57889***********************..889************99988765 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.35   1.6e+03      33      79 ..      14      56 ..       6      72 .. 0.68
   2 !   14.3   0.0   4.7e-06     0.021     121     154 ..     129     162 ..     105     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.35
                          PRTase_2 33 reagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadaleeea 79
                                      ++ag++L++ l+    ee  +  +v+++      Lg+ vadal++  
  gi|313117307|ref|YP_004044290.1| 14 ESAGKQLGDALR----EEGVDADIVLAIPRGGLPLGRMVADALHAPL 56
                                      567777777777....3444555667777888888888888885544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.7e-06
                          PRTase_2 121 akelvLvDDEistGktalnliralqeklprkryv 154
                                        k++v+vDD ++tG ta + ++++++++p++ + 
  gi|313117307|ref|YP_004044290.1| 129 GKTVVVVDDGVATGATARACLSRVNAAAPERVIF 162
                                       589***********************99987665 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.059   2.7e+02     156     223 ..      27      85 ..      13     137 .. 0.57
   2 ?   11.4   0.3   3.4e-05      0.15     164     252 ..     138     213 ..     115     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.059
                                       TTEEE.EEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS CS
                              PALP 156 gkpda.vvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg 223
                                       + +da +v+++  Ggl  G + + + + p   +++ +  g++   +++          +  +adg a  
  gi|313117307|ref|YP_004044290.1|  27 EGVDAdIVLAIPRGGLPLGRMVADALHAP-LDIVATQKIGAPNNPEFA---------IGAVAADGSAWL 85 
                                       44553399999999999998877777777.477777777777666665.........233344444444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.4e-05
                                       E-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEE CS
                              PALP 164 pvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvdei 240
                                       +v +G+++ ++   + ++ p+ rvi++ p+gs+   + l           + +ad + +  +++ +f ++ ++  ++
  gi|313117307|ref|YP_004044290.1| 138 GVATGATARACLSRVNAAAPE-RVIFAVPVGSPRAISDL-----------EGLADEVVCL-SAPSVFHAVGQFYERF 201
                                       788999999999999999999.999999***********...........9999999999.7888888899999999 PP

                                       EEEEHHHHHHHH CS
                              PALP 241 vtvsdeealeam 252
                                        +v+deea++ +
  gi|313117307|ref|YP_004044290.1| 202 GQVTDEEAMAYI 213
                                       99*****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1522.09
//
Query:       gi|313117308|ref|YP_004044291.1|  [L=216]
Description: dienelactone hydrolase-like enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-08   34.2   0.1     0.0036   16.6   0.0    2.3  2  Hydrolase_4    Serine aminopeptidase, S33
    4.8e-08   33.9   0.9     0.0039   17.8   0.0    2.1  2  Abhydrolase_6  Alpha/beta hydrolase family
    2.1e-07   30.9   0.0     0.0041   16.8   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    4.1e-07   29.8   0.0      1e-06   28.5   0.0    1.6  1  DLH            Dienelactone hydrolase family
    6.2e-05   22.6   0.7       0.27   10.7   0.2    2.9  3  Peptidase_S9   Prolyl oligopeptidase family
    0.00025   21.0   0.0       0.12   12.3   0.0    2.1  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
     0.0012   18.5   0.1      0.031   13.9   0.1    2.0  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
      0.046   13.5   0.0        3.4    7.4   0.0    2.1  2  Abhydrolase_2  Phospholipase/Carboxylesterase
       0.14   10.7   0.0        7.8    4.9   0.0    2.0  2  PAF-AH_p_II    Platelet-activating factor acetylhydrolase, is


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.2e-06    0.0064       3     109 ..      28     137 ..      26     146 .. 0.76
   2 !   16.6   0.0   1.8e-06    0.0036     187     237 ..     146     194 ..     137     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.2e-06
                       Hydrolase_4   3 pkavvvlvHGlae..hsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfd..dyvdDlaafvekvkeehpe 75 
                                       + ++vv++HG ++  hs r + +a +L ++G a++ +D      ++  r + ++fd   ++d l a++e ++++  +
  gi|313117308|ref|YP_004044291.1|  28 ASGIVVFAHGSGSsrHSPRNNFVAGRLHEAGLATLLFDLLT---EDEDRSRENRFDipLLTDRLVAVTEWLRQRDDT 101
                                       6799*****98754499*********************984...445555556655213455566666777766666 PP

                       Hydrolase_4  76 l..plfllGhSmGGliallyllrypdkvaglilsaP 109
                                       +   +  +G S+G++ al++++    +v++++  + 
  gi|313117308|ref|YP_004044291.1| 102 AelTIGYFGSSTGAAAALRATASDDTSVDAVVSRGG 137
                                       6347778**************999999999997665 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.8e-06
                       Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnE 237
                                        + it+P+ll+ G++D+ v + ++ e++++l+   k+l++ pg+ H   +E
  gi|313117308|ref|YP_004044291.1| 146 LDTITAPTLLIVGGNDESVRRLNQ-EAHAKLSC-SKSLHVVPGAGHLFEGE 194
                                       57899***************6665.66666764.8***********87666 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.6   1.2e-05     0.023       1      87 [.      32     126 ..      32     147 .. 0.66
   2 !   17.8   0.0     2e-06    0.0039     165     212 ..     145     194 ..     125     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                                       EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTS..TS-GGCS--HHHCHHH.HHHHCCTT....TTSE.EE. CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDlpGh..Grsdpppldledladl.aalldelaa..gggpv.vl. 69 
                                       v+++HG+gss++s +  ++a +l++   ++l +Dl      rs    +d + l d  +a+ + l++  ++ +  ++ 
  gi|313117308|ref|YP_004044291.1|  32 VVFAHGSGSSRHSPRNNFVAGRLHEAgLATLLFDLLTEdeDRSRENRFDIPLLTDRlVAVTEWLRQrdDTAELtIGy 108
                                       8********99998544555555555666689***999433455555666665444588888887766455557556 PP

                                       EEETCHHHHHHHHHHCC. CS
                     Abhydrolase_6  70 vGHSlGGalalaaaplal 87 
                                       +G S G+a al+a ++ +
  gi|313117308|ref|YP_004044291.1| 109 FGSSTGAAAALRATASDD 126
                                       ************655552 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2e-06
                                       HHTT-TTGC.EEECTT-CHHHHCHHCCCH..STTEEETCE...SSS-HHHH CS
                     Abhydrolase_6 165 awadlpvpl.lvlggeDplvprllerlla..qagarlpvvlpgaGHlphle 212
                                        + ++++p+ l++gg+D++v+rl ++++a  + ++ l +v+pgaGHl+  e
  gi|313117308|ref|YP_004044291.1| 145 VLDTITAPTlLIVGGNDESVRRLNQEAHAklSCSKSL-HVVPGAGHLFEGE 194
                                       4555666663455****************98888888.********76554 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.1e-06    0.0041       2     108 ..      31     140 ..      30     148 .. 0.85
   2 !   13.4   0.0   2.2e-05     0.044     207     251 ..     146     190 ..     135     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.1e-06
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHH..SHHHHHHHHHHHHHHCTTSSEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddy..gtasvaddldrildalgddklt 76 
                                        +v+ hG + s ++++++++a  L ++g  ++l+Dl+  ++ + + +  +      t+ + ++ ++++++ +  +lt
  gi|313117308|ref|YP_004044291.1|  31 IVVFAHGSGSSRHSPRNNFVAGRLHEAGLATLLFDLLTEDEDRSRENRFD--IplLTDRLVAVTEWLRQRDDTAELT 105
                                       79****************************************99999844..4224556778888997777777777 PP

                                       ..EEEETHHHHHHHHHHHHHGGGEEEEEEESE.CS CS
                     Abhydrolase_1  77 ..lvGhSmGGmialayaaeyperVkalvllga.id 108
                                         + G S G + al + a  + +V+a+v+ g+ +d
  gi|313117308|ref|YP_004044291.1| 106 igYFGSSTGAAAALRATASDDTSVDAVVSRGGrVD 140
                                       67***************************999644 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.2e-05
                                       THHHHSEEEEEEETTCSSSCHHHHHHHHHC.HTSEEEEEEETCSSS CS
                     Abhydrolase_1 207 lknvlaptlvisgtsDplvppkaledlaql.lpkkrlvvisdagHl 251
                                       l+ ++aptl+i g +D  v   ++e  a+l ++k +l+v+++agHl
  gi|313117308|ref|YP_004044291.1| 146 LDTITAPTLLIVGGNDESVRRLNQEAHAKLsCSK-SLHVVPGAGHL 190
                                       678999**********************998888.**********7 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   5.1e-10     1e-06       8     201 ..      25     203 ..      18     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.1e-10
                               DLH   8 pknakkpvvvviqeifGvn.....dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvl 79 
                                       p +a   ++vv+    G       +n   ++ rl e+G + l+ dl++ ++    ++++++++            ++
  gi|313117308|ref|YP_004044291.1|  25 PRDA--SGIVVFAHGSGSSrhsprNN--FVAGRLHEAGLATLLFDLLTEDE--DRSRENRFDIP----------LLT 85 
                                       5555..67777777777776664333..37888888888888888888777..33334444443..........345 PP

                               DLH  80 ddlkaavaylksvpevstkkvgvvGfCmGGalalllaaev.pevdaavafYGlspekeleeaakikapilalfgeeD 155
                                       d+l a  ++l+++ ++ +  +g  G   G+a al   a +   vda+v+  G +++   +  + i ap l ++g++D
  gi|313117308|ref|YP_004044291.1|  86 DRLVAVTEWLRQRDDTAELTIGYFGSSTGAAAALRATASDdTSVDAVVSRGG-RVDMADAVLDTITAPTLLIVGGND 161
                                       667788899999999999****************988877689*****9988.************************ PP

                               DLH 156 efipadevekleealkaanvdlelkvYpgagHaFandsresyneea 201
                                       e++   +    +ea ++      l+v pgagH F  + + ++++  
  gi|313117308|ref|YP_004044291.1| 162 ESVRRLN----QEAHAKLSCSKSLHVVPGAGHLFEGEGELEEVADV 203
                                       ***9885....4555556788899999*******887766555555 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.3     6e+02      11      29 ..      26      44 ..      18      54 .. 0.83
   2 !   10.7   0.2   0.00014      0.27      48     108 ..      88     148 ..      84     151 .. 0.91
   3 !   10.1   0.0    0.0002       0.4     139     211 ..     144     214 ..     139     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.3
                                      HCCT-EEEEE--TTSSTTH CS
                      Peptidase_S9 11 adrGyvvvvanirGsggyG 29
                                      +d+  +vv+a++ Gs+ ++
  gi|313117308|ref|YP_004044291.1| 26 RDASGIVVFAHGSGSSRHS 44
                                      688899********98765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE---CCCHHCST CS
                      Peptidase_S9  48 fiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavaevpvvdvlrydsdt 108
                                       ++a++e+l +++ + +  ++ +G S G   ++ a ++ +   +a+v+  + vd+    +dt
  gi|313117308|ref|YP_004044291.1|  88 LVAVTEWLRQRDDTAELTIGYFGSSTGAAAALRATASDDTSVDAVVSRGGRVDMADAVLDT 148
                                       6899********************************999999***********98877765 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0002
                                       G--..---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHHCT- CS
                      Peptidase_S9 139 nvk..aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkealgk 211
                                       +v   +++p+Lli+G +D+ v   + +   a+L        l++ p++gH +  +    e     +++++e+lg+
  gi|313117308|ref|YP_004044291.1| 144 AVLdtITAPTLLIVGGNDESVRRLNQE-AHAKLSC---SKSLHVVPGAGHLFEGEGELEEVADVAADWFAEHLGN 214
                                       55556899*************654443.3445552...3479********99977777777777889*****985 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   5.9e-05      0.12      10      54 ..      92     137 ..      90     146 .. 0.89
   2 !    6.8   0.0    0.0029       5.8     113     165 ..     148     193 ..     142     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                                       HHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSS.SEEEEEEES- CS
                            BAAT_C  10 inyllrhpkvkkdkigllGiSkGgelalllasflk.kisavvling 54 
                                        ++l+++  +++  ig  G S G+  al  ++  + +++avv+  g
  gi|313117308|ref|YP_004044291.1|  92 TEWLRQRDDTAELTIGYFGSSTGAAAALRATASDDtSVDAVVSRGG 137
                                       58**************************998888889****98765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0029
                                       G--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S---S CS
                            BAAT_C 113 kakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHliep 165
                                        + +p ll+vg +D++++    +++a ++L  ++   +++++  p+aGHl+e 
  gi|313117308|ref|YP_004044291.1| 148 TITAPTLLIVGGNDESVR--RLNQEAHAKLSCSK---SLHVV--PGAGHLFEG 193
                                       678999*********997..67788999998654...45888..******985 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   1.5e-05     0.031      87     140 ..      89     143 ..      85     146 .. 0.93
   2 ?    3.1   0.0      0.03        59     224     261 ..     146     184 ..     142     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCC CS
                     Peptidase_S15  87 advidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyd 140
                                       ++v +Wl++  + ++ ++g +G+S ++  +l a a+++  ++a+v+  + +d++d
  gi|313117308|ref|YP_004044291.1|  89 VAVTEWLRQRdDTAELTIGYFGSSTGAAAALRATASDDTSVDAVVSRGGRVDMAD 143
                                       7899*****999***********************************99999988 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.03
                                       HCT--S-EEEEEECCSSTTCCHHHHHHHHHCCTT-.EEE CS
                     Peptidase_S15 224 adkvkapvllvgGwnDwnvkngaiklyealkapgv.kli 261
                                       +d+++ap+ll+ G nD+ v++ + +++ +l+  ++ +++
  gi|313117308|ref|YP_004044291.1| 146 LDTITAPTLLIVGGNDESVRRLNQEAHAKLSCSKSlHVV 184
                                       5899************99999999999999988854333 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.017        33      13      29 ..      28      44 ..      22      52 .. 0.84
   2 ?    7.4   0.0    0.0017       3.4     107     199 ..     106     189 ..      63     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.017
                                      --EEEEEE--TT--SHH CS
                     Abhydrolase_2 13 aqavviflHGlGdsgha 29
                                      a+ +v+f HG G+s h+
  gi|313117308|ref|YP_004044291.1| 28 ASGIVVFAHGSGSSRHS 44
                                      6789**********997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0017
                                       EEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHH CS
                     Abhydrolase_2 107 iiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklpilqiHgeeDpvvplalgkaakevlk 183
                                       i  +G S Gaa al ++ +  + +  +v+ +g++ ++ ++ +  t ++   p l+i g  D+ v      + +e++ 
  gi|313117308|ref|YP_004044291.1| 106 IGYFGSSTGAAAALRATASDDTSVDAVVSRGGRVDMADAVLD--TITA---PTLLIVGGNDESVR----RLNQEAHA 173
                                       3346889***************************99999996..4444...78999999999874....33344444 PP

                                       TTS-GEEEEEETT--S CS
                     Abhydrolase_2 184 kllkkvelksyeglaH 199
                                       kl    +l++++g +H
  gi|313117308|ref|YP_004044291.1| 174 KLSCSKSLHVVPGAGH 189
                                       4444456777777777 PP

>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.008        16      90     113 ..      19      42 ..       5      45 .. 0.86
   2 ?    4.9   0.0    0.0039       7.8     229     284 ..     105     160 ..      81     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.008
                                       ET--B--SS-EEEEEEE--TT--T CS
                       PAF-AH_p_II  90 knellktkekyPlivFsHGLgafR 113
                                       ++el+ +++   ++vF+HG g++R
  gi|313117308|ref|YP_004044291.1|  19 EGELIVPRDASGIVVFAHGSGSSR 42 
                                       677888999999**********99 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0039
                                       EEEEEEETHHHHHHHHHHHH-TTS-EEEEES---TTS-GGGGGG--S-EEEEEETT CS
                       PAF-AH_p_II 229 kvaviGHsFGgAtvikslsedteFrcaialDaWmlPveeevyskvrqPllfinsek 284
                                        +   G s G+A ++++ + d     a++  +    + + v++++  P+l+i   +
  gi|313117308|ref|YP_004044291.1| 105 TIGYFGSSTGAAAALRATASDDTSVDAVVSRGGRVDMADAVLDTITAPTLLIVGGN 160
                                       466689**********99999999999**9*********************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1386.81
//
Query:       gi|313117309|ref|YP_004044292.1|  [L=467]
Description: carbohydrate ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-49  168.1   9.6    5.1e-49  167.6   9.6    1.2  1  SBP_bac_8    Bacterial extracellular solute-binding protein
      6e-30  105.3  11.2    8.7e-30  104.7  11.2    1.2  1  SBP_bac_1    Bacterial extracellular solute-binding protein
    0.00012   21.6   0.1      0.073   12.5   0.0    2.3  2  SBP_bac_6    Bacterial extracellular solute-binding protein
     0.0015   18.4   0.8       0.57    9.9   0.1    2.5  2  SBP_bac_11   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.02   14.7   0.1      0.051   13.4   0.1    1.7  1  TAT_signal   TAT (twin-arginine translocation) pathway signal
      0.069   12.5   0.0       0.13   11.7   0.0    1.4  1  Helo_like_N  Fungal N-terminal domain of STAND proteins


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.6   9.6   1.7e-52   5.1e-49       2     280 ..      75     398 ..      74     400 .. 0.83

  Alignments for each domain:
  == domain 1  score: 167.6 bits;  conditional E-value: 1.7e-52
                                       HHHHHHHH-.TEEEEEEE-.-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG.....GSTTHHH- CS
                         SBP_bac_8   2 lakefekkt.gvkvnvvta.asndleqklkaalaagtapdidvvwanedalatlaeeglladls.....dldnlddl 71 
                                       la+ef+++  g+++++++  ++ ++ + +++a+++g+ p+i +++  + +la  +++g++ +++     d  n dd+
  gi|313117309|ref|YP_004044292.1|  75 LASEFQQQAdGIELEATKKgSYRETLNATTSAVQSGNPPAIAQIFEIGTQLA--IDSGVFTPVEdiipkDAVNFDDY 149
                                       799****9999*******99********************999999887755..999*******6666544666665 PP

                                       .HHHHHTT--TS.----EEEEEEE-EEEEEHHHHHHS......---BHHHHHHHHHHHH..HH-....SEGG---GG CS
                         SBP_bac_8  72 .tdalaavgydgklygvPyasetpyvliynkdlleka.....edpktwdellaaakklk..gkf....glpdpasgw 136
                                        +++l+++ +dgkl ++P++s++  +++ynk ++e+a     ++p++++++ +aak+l+  g +    ++p+ ++++
  gi|313117309|ref|YP_004044292.1| 150 lDSVLNYYRIDGKLHSMPFNSSN-AIFYYNKNAFEEAgldpeNPPTSYEGVMDAAKTLTdaGVVdkgtTWPNHSWFV 225
                                       36699999***************.6***********9999999*************996433336666********* PP

                                       GGGGTHHETTEE---H.............HHH.HHHHHHHHHHHHTT-EE....-S..--SSTTTTTSBSEEEE-TT CS
                         SBP_bac_8 137 lqaallakdgksldddg...........gkdglkealellkklkdngkty....dtgadavsefanGevaftingsw 198
                                        q+++ + ++  +++ +           ++++ k+++e++++l++ g+++    +++++a+++f +++  +  ++++
  gi|313117309|ref|YP_004044292.1| 226 EQWFAEQ-NQTLVNNGNgrngratkanfESEASKNIFEWWTDLYNEGQYLnpgiEAWSEAQQAFLTQKTGMLGYSTS 301
                                       *******.5555533333543442233456666**************9667777********************999 PP

                                       HHHHHH....-TTTSEEEE.--.....S--EEEEEEEEEEBTTS-HHHH.HHHHHHHHHTTSHHHHHHHHHH---BS CS
                         SBP_bac_8 199 diaaaq....kagkklgai.vp.....kqgsfaggkglavpknaknedl.aAldFlkwltspenqaalaektgyipv 264
                                       +ia  +    k+g++lg + +p     +qg+++gg++l+ p++ ++e++ aA +F+ wlt pe+q+ ++++tgy+pv
  gi|313117309|ref|YP_004044292.1| 302 SIAPMAkgakKNGFELGTMqLPtpngkRQGVVIGGASLWTPASLSAEKKkAAGEFIAWLTKPEQQKRWHTNTGYFPV 378
                                       99965556658899**99976676877799**************999999*************************** PP

                                       -S-TTT....HHHHHH-HHH CS
                         SBP_bac_8 265 nksaal....spevkkdpal 280
                                       nk a        ++ ++p++
  gi|313117309|ref|YP_004044292.1| 379 NKRAISqledEGFYEENPDF 398
                                       **998434333446666665 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7  11.2   2.9e-33   8.7e-30       9     315 .]      71     367 ..      64     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 2.9e-33
                                       HHHHHHHHHHHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTT CS
                         SBP_bac_1   9 alqalvakafekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkayl 82 
                                        ++ l+  +f+++  gi+ e   +  gs+++   + t a+++G++p  +++++   +   +++g+++p+ +++ +++
  gi|313117309|ref|YP_004044292.1|  71 FIDTLA-SEFQQQADGIELE--ATKKGSYREtlnATTSAVQSGNPP-AIAQIFEIGTQLAIDSGVFTPVEDIIPKDA 143
                                       566666.8898877555555..555599999887888888888855.*****888888999***************9 PP

                                       ECTTCCTEEEEHHHHTHHHHCEEE.ES.EEEEE.EEEEEEETTTHHCTTGGG...SHBHHHHHHHHHHHHHHCTCTH CS
                         SBP_bac_1  83 apgvkdaadklsssvlpkildskv.ly.vPlya.argliYNkdlfekagldp...pwtWdelveaakklkekgkkpi 153
                                       ++ +    d+l+s vl +++ + + l  +P+++ +  ++YNk  fe+agldp   p++++ +++aak l+++g  + 
  gi|313117309|ref|YP_004044292.1| 144 VNFD----DYLDS-VLNYYRID-GkLHsMPFNSsNAIFYYNKNAFEEAGLDPenpPTSYEGVMDAAKTLTDAGVVD- 213
                                       9884....44444.34444442.36999****76******************************************. PP

                                       CCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT........HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSS CS
                         SBP_bac_1 154 ggarggsasgtayyfalalakslggkvfdkdgg........gldnpegvtaatylvklyavanltkelkgkgaenkd 222
                                            g+ + + ++f +++++  +++++++ +g        ++++++ ++ ++++++ly     + ++ ++g e   
  gi|313117309|ref|YP_004044292.1| 214 ----KGTTWPNHSWFVEQWFAEQNQTLVNNGNGrngratkaNFESEASKNIFEWWTDLY----NEGQYLNPGIEA-- 280
                                       ....*************************9999*****999999999999*********....566666666665.. PP

                                       HHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE.EEEEEEEEBTTCST. CS
                         SBP_bac_1 223 gaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi.lgayglaipkgskn. 297
                                       +++a+++f + +++m+  ++++          +++a+ ++k+++elg   lP+  g+  g  +g+  l+ p++ +  
  gi|313117309|ref|YP_004044292.1| 281 WSEAQQAFLTQKTGMLGYSTSS---------IAPMAKGAKKNGFELGTMQLPTPNGKRQGVvIGGASLWTPASLSAe 348
                                       555669****************.........8999999999999999999998877777779777776666554443 PP

                                       .HHHHHHHHHHHTSHHHHH CS
                         SBP_bac_1 298 .peaAkkFldfllspeaqa 315
                                        ++aA +F+++l+ pe+q+
  gi|313117309|ref|YP_004044292.1| 349 kKKAAGEFIAWLTKPEQQK 367
                                       4888*************96 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0014       4.1      17      77 ..     125     196 ..     122     201 .. 0.74
   2 !   12.5   0.0   2.5e-05     0.073     187     220 ..     344     383 ..     328     405 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0014
                         SBP_bac_6  17 kfieeglfqpld...panlpnvnkdfa.eeglkdpdgkyy..pygvgplvlavnkdrlkgrpv.....PksW 77 
                                        +i+ g+f+p++   p+ + n+++ ++   ++   dgk    p++ + +++++nk ++++  +     P+s+
  gi|313117309|ref|YP_004044292.1| 125 LAIDSGVFTPVEdiiPKDAVNFDDYLDsVLNYYRIDGKLHsmPFNSSNAIFYYNKNAFEEAGLdpenpPTSY 196
                                       58999******9777555555554444656666666766677****************99888856656666 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.5e-05
                         SBP_bac_6 187 g...kkkelakafidfllspevqailakaggvfPvv...t 220
                                       +   +kk+ a +fi +l++pe q+ +  ++g fPv+    
  gi|313117309|ref|YP_004044292.1| 344 SlsaEKKKAAGEFIAWLTKPEQQKRWHTNTGYFPVNkraI 383
                                       334459****************************965431 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0017       5.2       4      37 ..      63      97 ..      62     131 .. 0.78
   2 !    9.9   0.1   0.00019      0.57     200     225 ..     341     370 ..     188     375 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0017
                                      EE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHH CS
                        SBP_bac_11  4 aaagslaaalrelaaaF.eahtgvkvevsaggsgk 37
                                      a++g+l a ++ la +F +++ g+++e +++gs++
  gi|313117309|ref|YP_004044292.1| 63 AMGGDLGAFIDTLASEFqQQADGIELEATKKGSYR 97
                                      57899************666899*********953 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00019
                                       E....-TT--HHHHHHHHHTTSHHHHHHHH CS
                        SBP_bac_11 200 k....kaakreaAraFlafLrspeaqailr 225
                                       +    +a k++aA +F+a+L+ pe+q++++
  gi|313117309|ref|YP_004044292.1| 341 TpaslSAEKKKAAGEFIAWLTKPEQQKRWH 370
                                       3333456899*****************985 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.7e-05     0.051       2      23 ..       5      25 ..       4      27 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggc 23
                                       +RR F+K+ +A++ A+++g c
  gi|313117309|ref|YP_004044292.1|  5 NTRRRFIKTVGATGIAGLAG-C 25
                                      59***********9877554.4 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.2e-05      0.13     139     181 ..     421     463 ..     391     467 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.2e-05
                       Helo_like_N 139 rkskvtaevleeykeliedttsdLeehLedideklealtekse 181
                                         +kv + v e y ++i+d +++ e+ L +id+++e++ ++ +
  gi|313117309|ref|YP_004044292.1| 421 TFTKVRTIVEEGYVSMIQDSSTNVEDALGSIDSQVEEVLKSYN 463
                                       457788888999************************9986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2906.18
//
Query:       gi|313117310|ref|YP_004044293.1|  [L=297]
Description: carbohydrate ABC transporter membrane protein 1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-13   49.9  13.5    2.9e-13   49.9  13.5    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   7.5      0.66   1.2e+04     154     178 ..      51      95 ..       8     102 .. 0.48
   2 !   49.9  13.5   1.6e-17   2.9e-13      27     169 ..     114     283 ..     105     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 0.66
                      BPD_transp_1 154 s....................nggvlalviavlllnlvadilqrl 178
                                       +                    +++++ +++av++ +l++ ++  +
  gi|313117310|ref|YP_004044293.1|  51 QqfvgienyvalatsaeyqksIVISFLFAAAVVVGTLAVSLFISY 95 
                                       233333333444444455555334444444444444444444433 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 1.6e-17
                      BPD_transp_1  27 llslPsfvlaillvlvf...................vilsilghlilpviillllsaapyvrlirraalrslpkdlv 84 
                                       +++lP+ v a +l++++                    ++++   ++l +++++++ +++y++++  aal+++p+ l 
  gi|313117310|ref|YP_004044293.1| 114 PYALPTAVAATILLFMLhptlgivthyleaatgltfDWFTSGPLAFLVLALVAIWKQLGYNIIFLVAALNNIPDTLT 190
                                       789*********99999****************766555555566666789999*********************** PP

                      BPD_transp_1  85 eaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydyseis..... 154
                                       e a ++G++r +++++v +P++ p++  +++++ ++++ ga+ l  l++++G    t ll + l++d  e +     
  gi|313117310|ref|YP_004044293.1| 191 ESAQLDGVGRLRMLFRVYIPLISPTLTFLVVMNTIYAFFGAFPLVDLMTSGGpnNATNLLIFKLYRDAFEFNslgla 267
                                       *************************************7777766666666666855555555555555555534333 PP

                      BPD_transp_1 155 .nggvlalviavllln 169
                                        + +++ ++i+ +l+ 
  gi|313117310|ref|YP_004044293.1| 268 sAESTVLFGIVSILMY 283
                                       3444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1973.36
//
Query:       gi|313117311|ref|YP_004044294.1|  [L=289]
Description: carbohydrate ABC transporter membrane protein 2 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-17   61.6  17.4      8e-17   61.6  17.4    1.9  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6  17.4   4.5e-21     8e-17       3     176 ..     100     277 ..      98     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 4.5e-21
                      BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfv.laillvlvfvilsilghlilpviillllsaapyvrlirraa 75 
                                        l++laa   +++++++ +++ ++i ++l +P+ v +++l++    ++ +lg++   ++i++ + a +++++++r+ 
  gi|313117311|ref|YP_004044294.1| 100 ALSLLAAlalVYYRFPFERAVFGFILLTLLVPVPVrIVPLFQ----LMADLGWADSLIAITGPYIASATAVFLFRQH 172
                                       6778888889*************************8888888....56***************************** PP

                      BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.....lgtllleailg 147
                                       + s+p++lve ar++G+++ + +++v++P+++ +i+   +++f++++++++++++++s++      +g  +l+  ++
  gi|313117311|ref|YP_004044294.1| 173 FMSIPESLVENARLDGVGPLTFLVQVLIPMSKGMIAGVSVITFIYAWNQYLWPLIVISDQSkqviqVGIKFLQGASQ 249
                                       **********************************************************9989999999999999999 PP

                      BPD_transp_1 148 ydyseisnggvlalviavlllnlvadilq 176
                                       + ++++   +++ +via+++ ++v+ +l+
  gi|313117311|ref|YP_004044294.1| 250 SGLTQWG-LIMAGAVIALIPPLAVLLVLH 277
                                       9998888.899999999998888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 2072.94
//
Query:       gi|313117312|ref|YP_004044295.1|  [L=383]
Description: sugar ABC transporter ATP-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-33  113.6   0.0    1.6e-32  112.9   0.0    1.3  1  ABC_tran         ABC transporter
    3.5e-11   43.8   0.2    1.5e-10   41.8   0.2    2.2  1  OB_MalK          MalK OB fold domain
    1.9e-10   40.8   0.5    1.9e-09   37.6   0.1    2.4  2  TOBE_2           TOBE domain
    4.7e-07   29.9   0.4      0.022   14.6   0.1    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    8.2e-05   23.1   0.0    0.00079   19.9   0.0    2.5  2  CysA_C_terminal  CysA C-terminal regulatory domain
    0.00051   20.0   0.0    0.00083   19.3   0.0    1.2  1  Rad17            Rad17 P-loop domain
     0.0016   18.8   0.2     0.0028   18.0   0.2    1.6  1  AAA_22           AAA domain
     0.0019   18.6   0.1     0.0034   17.8   0.1    1.6  1  AAA_16           AAA ATPase domain
     0.0035   16.8   0.0      0.061   12.7   0.0    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0051   16.7   0.0     0.0089   16.0   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
      0.016   15.5   0.4      0.046   14.0   0.1    2.0  2  TOBE             TOBE domain
       0.02   14.3   0.0      0.054   12.9   0.0    1.7  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.02   15.0   0.0      0.045   13.9   0.0    1.7  1  AAA_33           AAA domain
      0.029   14.1   0.1      0.054   13.2   0.1    1.6  1  AAA_30           AAA domain
      0.052   14.0   0.0       0.11   13.0   0.0    1.5  1  AAA              ATPase family associated with various cellul
      0.059   13.1   0.0       0.12   12.1   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.094   12.3   0.0        0.2   11.2   0.0    1.5  1  AAA_25           AAA domain
       0.11   12.4   0.4        0.5   10.4   0.1    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
       0.14   12.4   0.1       0.41   10.9   0.0    1.8  2  AAA_28           AAA domain
       0.26   11.8   0.0       0.43   11.0   0.0    1.3  1  AAA_23           AAA domain
        0.3   10.7   0.0       0.49   10.0   0.0    1.2  1  AAA_15           AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.0   1.9e-35   1.6e-32       2     136 ..      20     162 ..      19     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 1.9e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       k ++l ++ege +++vG++G+GKSt l+++agl++ teG++ + ++ +++  l+  ++ +++++q+  l p++t++e
  gi|313117312|ref|YP_004044295.1|  20 KGIDLAVQEGEFLVLVGPSGCGKSTTLRMIAGLESITEGTLSFGETVVND--LPPHERDVAMVFQNYALYPHMTAAE 94 
                                       7899*************************************999988888..************************* PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n               +de++ +++++lg+++l d++     ++LSgG++qrva+ rall++p+++llDEp 
  gi|313117312|ref|YP_004044295.1|  95 NmtfgldstglfrnsGDDERVRDVAETLGITDLLDRKP----KELSGGERQRVAIGRALLREPEVFLLDEPL 162
                                       *************9999999************999998....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.2   1.7e-13   1.5e-10       1      53 []     236     290 ..     236     290 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.7e-13
                           OB_MalK   1 GSPaMNflpatveedg....vlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       GSPaMN++pa+++ ++    +++  +g+ +plp++    l + +g +  lG+RPE+i
  gi|313117312|ref|YP_004044295.1| 236 GSPAMNIVPAEIVSGKgengAIARCDGFNVPLPDAP--GLDNLVGSQASLGVRPEDI 290
                                       9**********9855569999***************..******************8 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.72   6.1e+02      48      66 ..     188     207 ..     178     213 .. 0.71
   2 !   37.6   0.1   2.2e-12   1.9e-09       1      76 []     283     356 ..     283     356 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.72
                            TOBE_2  48 rqpnadr.dsalapGdtVel 66 
                                        + ++++  +a++ Gd+V++
  gi|313117312|ref|YP_004044295.1| 188 TVYVTHDqTEAMTLGDRVAV 207
                                       34444443579*******98 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 2.2e-12
                            TOBE_2   1 laiRPEklrlaaagg.an.glsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavv 75 
                                       l++RPE+++la++ + ++ ++  t + +e lG+s++++++ ++ ql +v+ ++++    + +Gd +e+++d d++++
  gi|313117312|ref|YP_004044295.1| 283 LGVRPEDISLAENLPtQTaTFDVTATVTEPLGESLLVHCTSGDRQL-LVKAEPRS---SISAGDVIEVGVDEDRLHL 355
                                       79********944443555999999999****************99.77888887...8*****************9 PP

                            TOBE_2  76 l 76 
                                       +
  gi|313117312|ref|YP_004044295.1| 356 F 356
                                       8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   5.5e-05     0.047       1      25 [.      31      55 ..      31      76 .. 0.78
   2 !   14.6   0.1   2.5e-05     0.022     229     298 ..     127     194 ..      93     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.5e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      + vl+Gp g+GKS+ L+ + +l ++
  gi|313117312|ref|YP_004044295.1| 31 FLVLVGPSGCGKSTTLRMIAGLESI 55
                                      579****************999543 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.5e-05
                            AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHS 298
                                         ++ + elS G ++  a+  allr +    ++l+DEp ++L+ kl  +   ell+++++  +  + +TH+
  gi|313117312|ref|YP_004044295.1| 127 LLDRKPKELSGGERQRVAIGRALLREP---EVFLLDEPLSNLDAKLRVEMRaELLEIHRELQTTTVYVTHD 194
                                       455566788999999999999999999...9****************999999999999999999*****8 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0         2   1.7e+03       8      22 ..      56      71 ..      54      81 .. 0.74
   2 !   19.9   0.0   9.3e-07   0.00079       8      42 ..     253     291 ..     248     292 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2
                   CysA_C_terminal  8 edGklriGglalp.vP 22
                                       +G+l +G++ +  +P
  gi|313117312|ref|YP_004044295.1| 56 TEGTLSFGETVVNdLP 71
                                      689******9988788 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 9.3e-07
                   CysA_C_terminal   8 edGk.lriGglalpvP...elagadgqevvayVRPhDle 42 
                                       e+G  +r +g+ +p+P    l++  g+++ ++VRP+D+ 
  gi|313117312|ref|YP_004044295.1| 253 ENGAiARCDGFNVPLPdapGLDNLVGSQASLGVRPEDIS 291
                                       566437889*******55555555*************97 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.7e-07   0.00083      39      66 ..      23      50 ..      11      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.7e-07
                             Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLs 66
                                       L  ++ + L++ GPsGCgkst++++++
  gi|313117312|ref|YP_004044295.1| 23 DLAVQEGEFLVLVGPSGCGKSTTLRMIA 50
                                      566677789***************9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   3.2e-06    0.0028       5      29 ..      29      53 ..      26     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.2e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                        +lv++G+sG+GK+t+lr+++   
  gi|313117312|ref|YP_004044295.1| 29 GEFLVLVGPSGCGKSTTLRMIAGLE 53
                                      679****************987654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1     4e-06    0.0034      23      46 ..      28      51 ..       5     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellr 46
                                      ++e ++l+G+sG+GKs+ +r+++ 
  gi|313117312|ref|YP_004044295.1| 28 EGEFLVLVGPSGCGKSTTLRMIAG 51
                                      3389****************9983 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   7.2e-05     0.061      25     205 ..      30     199 ..      17     214 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.2e-05
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       +f ++vGp G+GKs  l  i    G +s ++   +  + +++        ++ +v+++f+n     ++       + 
  gi|313117312|ref|YP_004044295.1|  30 EFLVLVGPSGCGKSTTLRMI---AGLESITEGTLSFGETVVND----LPPHERDVAMVFQNYALYPHM---TAAENM 96 
                                       68899999999999998888...66666654444455555554....566667788888887777222...222233 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                       +   + +  ++  g + + ++v+e l  +++   ++++LSgGe++ va+     +   +   ++llDe  ++LD+k 
  gi|313117312|ref|YP_004044295.1|  97 TFGLDSTGLFRNSGDDERVRDVAETLGITDLldrKPKELSGGERQRVAIGRA--L--LREPEVFLLDEPLSNLDAKL 169
                                       33444444566667777778888888776663336789******98887533..2..34455789*********986 PP

                                       H.HHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 176 v.kkvaellkeksknaQfivislreemleka 205
                                       + +  aell+ ++ + Q   + ++++++e +
  gi|313117312|ref|YP_004044295.1| 170 RvEMRAELLEIHR-ELQTTTVYVTHDQTEAM 199
                                       5055566666555.77877777766666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     1e-05    0.0089      88     125 ..      17      55 ..       1      64 [. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelel 125
                                       e+++ +  ++++ ++ vlvG+SG GKSt + ++++ +++
  gi|313117312|ref|YP_004044295.1|  17 EAVKGIDLAVQEgEFLVLVGPSGCGKSTTLRMIAGLESI 55 
                                       556666666666699***************999986555 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         9   7.7e+03      35      53 ..     189     205 ..     175     208 .. 0.72
   2 ?   14.0   0.1   5.4e-05     0.046       5      64 .]     301     355 ..     297     355 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9
                              TOBE  35 ArvtrrsaeeLgLapGeeV 53 
                                       + vt ++ e+  ++ G++V
  gi|313117312|ref|YP_004044295.1| 189 VYVTHDQTEA--MTLGDRV 205
                                       4466677777..7777776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.4e-05
                              TOBE   5 NqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       +++ +t +v eplg + +V+ + g+ + L ++  +rs  +    +G+ + + ++  ++hl
  gi|313117312|ref|YP_004044295.1| 301 ATFDVTATVTEPLGESLLVHCTSGDRQ-LLVKAEPRSSIS----AGDVIEVGVDEDRLHL 355
                                       68999**********************.************....**********999997 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.3e-05     0.054       5      84 ..      12      91 ..       8     103 .. 0.73
   2 ?   -2.6   0.0       3.4   2.9e+03      88     107 ..     274     295 ..     237     295 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.3e-05
                      Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphh 83
                                        G+ ea + +++a+  g  l+lvGp+G+GK+   + +++l +  + + ++  + ++ +  ++++ +++ +     ph 
  gi|313117312|ref|YP_004044295.1| 12 YFGDVEAVKGIDLAVQEGEFLVLVGPSGCGKSTTLRMIAGLESITEGTLSFGETVVNDLPPHERDVAMVFQNYALYPHM 90
                                      5688899999**********************99999988866666555565666665555555555555555555555 PP

                      Mg_chelatase 84 s 84
                                      +
  gi|313117312|ref|YP_004044295.1| 91 T 91
                                      5 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.4
                      Mg_chelatase  88 aalvGggs..kpkpGeislahn 107
                                         lvG+++   ++p +isla+n
  gi|313117312|ref|YP_004044295.1| 274 DNLVGSQAslGVRPEDISLAEN 295
                                       5689987745689999999975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.2e-05     0.045       2      97 ..      32     124 ..      31     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrr..rlfgtdqqsktdytrvldrlyqilnelarkalsagrnvild 76 
                                       ++lvG++G+GKst ++ ++   g + +++ tl++  +++++ +++++d + v ++ y  l      +++++ ++ ld
  gi|313117312|ref|YP_004044295.1|  32 LVLVGPSGCGKSTTLRMIA---GLESITEGTLSFgeTVVNDLPPHERDVAMVFQN-Y-ALYPHM--TAAENMTFGLD 101
                                       589*************998...899999999888756666666676665555443.2.222333..24556666677 PP

                            AAA_33  77 atnlsrrer..arflklarrlgv 97 
                                       +t l+r+    +r++ +a+ lg 
  gi|313117312|ref|YP_004044295.1| 102 STGLFRNSGddERVRDVAETLGI 124
                                       77444433322577777776665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.3e-05     0.054      13      43 ..      25      54 ..      18     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-05
                            AAA_30 13 lltsgdrvavltGpAGtGKttalkalreawe 43
                                      ++++g  + vl+Gp G GK+t+l+ ++ +  
  gi|313117312|ref|YP_004044295.1| 25 AVQEG-EFLVLVGPSGCGKSTTLRMIAGLES 54
                                      44455.599***************9986654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012      0.11       2      22 ..      33      53 ..      32      87 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                      EEESSTTSSHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel 22
                                      +l+Gp G+GK+++ + +a   
  gi|313117312|ref|YP_004044295.1| 33 VLVGPSGCGKSTTLRMIAGLE 53
                                      79***************9864 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.12      18      39 ..      25      46 ..      17      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                       +++ ++ +l+GpsG GKST l
  gi|313117312|ref|YP_004044295.1| 25 AVQEGEFLVLVGPSGCGKSTTL 46
                                      455444899***********75 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023       0.2      30      50 ..      26      46 ..      19      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + +ge+ +l+G++g+GK+t +
  gi|313117312|ref|YP_004044295.1| 26 VQEGEFLVLVGPSGCGKSTTL 46
                                      579***************976 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00059       0.5       2      20 ..      32      50 ..      31      56 .. 0.89
   2 ?   -0.8   0.0       1.6   1.4e+03      49      72 ..     185     209 ..     168     269 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00059
                                      EEEE--SSSSHHHHHHHGG CS
                             AAA_5  2 vlLvGppGtgKselaerla 20
                                      ++LvGp+G+gKs+  + +a
  gi|313117312|ref|YP_004044295.1| 32 LVLVGPSGCGKSTTLRMIA 50
                                      68***********999877 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                                       ........--------.G-SEEEEE CS
                             AAA_5  49 ngttslvdsplvraar.egeilvlD 72 
                                       + tt++v    ++a++   +++vl+
  gi|313117312|ref|YP_004044295.1| 185 QTTTVYVTHDQTEAMTlGDRVAVLN 209
                                       4444444444444444322233332 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00048      0.41       3      21 ..      33      51 ..      31      86 .. 0.79
   2 ?   -1.9   0.0       4.1   3.5e+03     112     143 ..     155     186 ..     132     199 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                            AAA_28  3 vitGgestGKTtlleaLaa 21
                                      v++G++++GK+t+l+ +a 
  gi|313117312|ref|YP_004044295.1| 33 VLVGPSGCGKSTTLRMIAG 51
                                      99************99983 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                            AAA_28 112 vfllp.papeidddgeRredleereaiderlre 143
                                       vfll+ p   + d + R e  +e  +i++ l+ 
  gi|313117312|ref|YP_004044295.1| 155 VFLLDePLSNL-DAKLRVEMRAELLEIHRELQT 186
                                       45554224444.555555555555555555544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00051      0.43      15      39 ..      22      49 ..       9      52 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                      id+   +  + +++Gp G+GK+T l+ i
  gi|313117312|ref|YP_004044295.1| 22 IDLavqEGEFLVLVGPSGCGKSTTLRMI 49
                                      5666655567799***********9987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00057      0.49      23      44 ..      28      50 ..      18      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00057
                            AAA_15 23 ee.ltvliGkNnsGKSsileald 44
                                      e  + vl+G+ ++GKS+ l+++ 
  gi|313117312|ref|YP_004044295.1| 28 EGeFLVLVGPSGCGKSTTLRMIA 50
                                      43599***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2610.79
//
Query:       gi|313117313|ref|YP_004044296.1|  [L=231]
Description: hypothetical protein Hbor_30990 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.74    8.5   5.8        2.9    6.5   0.8    2.0  2  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3   0.00042       7.6     355     433 ..      16      92 ..       2     110 .. 0.56
   2 ?    6.5   0.8   0.00016       2.9     374     432 ..     138     194 ..     106     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.00042
                           DUF2207 355 kalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfs 431
                                        a ++ + a+++ +   +d+  +k l  +++ + ++++l+ +l+++++  +++ ++ l+ ++++++++++++ + ++
  gi|313117313|ref|YP_004044296.1|  16 IARDEARVALER-QLSTLDDIDSKALSVFRLNIALVGLLLSALSFAGASDMAT-VTALVNPVVGVGVASFVLSATAA 90 
                                       555555555555.4444444444455555555555555555555555555555.66666666666666666655554 PP

                           DUF2207 432 rl 433
                                       +l
  gi|313117313|ref|YP_004044296.1|  91 GL 92 
                                       43 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00016
                           DUF2207 374 kkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsr 432
                                       +  k+ l +ls+lg++++ l+l+++++++l+    + + ++++l++l+ a++v+ l+s 
  gi|313117313|ref|YP_004044296.1| 138 NVRKALLVTLSVLGTVGGALALAVGTVSALTGR--FLGPAVVALAVLVTAAGVAGLPSQ 194
                                       334666777788888888888887777776655..999999999999999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1570.27
//
Query:       gi|313117314|ref|YP_004044297.1|  [L=268]
Description: hypothetical protein Hbor_31000 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1696.23
//
Query:       gi|313117315|ref|YP_004044298.1|  [L=305]
Description: hypothetical protein Hbor_31010 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.37   10.7   2.6        9.7    6.1   0.3    2.2  2  Lipase_chap  Proteobacterial lipase chaperone protein


Domain annotation for each model (and alignments):
>> Lipase_chap  Proteobacterial lipase chaperone protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3   0.00054       9.7      63      92 ..      41      70 ..      37      99 .. 0.85
   2 ?    4.7   0.1    0.0015        27      64      94 ..     166     196 ..     164     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00054
                       Lipase_chap 63 alarlaiaqdsslsaeekqqrlaalraqlP 92
                                       ++r  iaq ++  ae+ + +l +++++lP
  gi|313117315|ref|YP_004044298.1| 41 RFERRVIAQSAARAAEQYRTALRRYDSRLP 70
                                      58999************************8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0015
                       Lipase_chap  64 larlaiaqdsslsaeekqqrlaalraqlPes 94 
                                       l+ +ai+ d++l++ e+++ l ++ a+lP  
  gi|313117315|ref|YP_004044298.1| 166 LESMAIELDTQLTQTEQANVLSRAAARLPSP 196
                                       799*************************864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1985.76
//
Query:       gi|313117316|ref|YP_004044299.1|  [L=410]
Description: ferrichrome-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-12   46.1   0.0    6.1e-12   45.6   0.0    1.2  1  Peripla_BP_2     Periplasmic binding protein
  ------ inclusion threshold ------
      0.072   12.9   0.0       0.11   12.4   0.0    1.2  1  Glyco_hyd_65N_2  Glycosyl hydrolase family 65, N-terminal dom
      0.085   12.4   0.1       0.13   11.8   0.1    1.3  1  Amelotin         Amelotin


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0     1e-15   6.1e-12      57     236 ..     147     351 ..     134     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1e-15
                                       HH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS.....................HHHHHHHHHHHHHTT-HH CS
                      Peripla_BP_2  57 alkPDlvilskglgltdedeellksgiptvivessntg.....................eslkeqiralgellgled 112
                                       +l+ D+ + ++ +  ++  e+l+++++  + +  ++++                     +sl e ++ +++++   +
  gi|313117316|ref|YP_004044299.1| 147 ELDSDVHLTDPAY--ASTLEQLDEADVAEISDKIGPWFgnyysdkrrdppqswadeyryYSLWEIFERVAQVFRAGS 221
                                       6788888888888..88899999999999999999999999999999999999999999****************** PP

                                       HHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTSTTTHHHHT.S--EESTTT--.STT-EEE- CS
                      Peripla_BP_2 113 eaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvvagsnsyigdllda.lgieniaaesk.kseyeeis 185
                                       +a++l   ++s    ++s ++     p+ +l+f g+++ ++v+  + +++   +   l++ +++a+   +++  +++
  gi|313117316|ref|YP_004044299.1| 222 RADALRDVHESMRSTIESNLPPTeeRPTVALTFEGKEDTFWVYRLNANGFLTAHTRpLDATDAFADVTfEGAQTQVD 298
                                       ********************999888999999***********98877777777777******99998999999*** PP

                                       HHHHHHH--SEEEEEEH..HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 186 aEqilasdpdvifvsgr..aeadnktgleflkenpllaelpAvkngrVyalds 236
                                        E++l++dpdvi+v  +   + + + + e+l+++p+ +e+ Avkn rVya ++
  gi|313117316|ref|YP_004044299.1| 299 YEAMLEADPDVILVLFTmsSSYSISDVREALESSPVGSEIAAVKNDRVYAQGA 351
                                       ************99988888999**************************8766 PP

>> Glyco_hyd_65N_2  Glycosyl hydrolase family 65, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.8e-05      0.11     101     185 ..     266     351 ..     198     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                   Glyco_hyd_65N_2 101 sgdsskvtnYrReLDlstaiatveYsvegvtytrevfaSapdqVlvvrlsaskagkl.nltvsleselekktketvk 176
                                         +++  t  +R LD ++a a+v+++  ++++  e+   a  +V+ v ++ s+  ++ +++ +les+   ++  +vk
  gi|313117316|ref|YP_004044299.1| 266 LNANGFLTAHTRPLDATDAFADVTFEGAQTQVDYEAMLEADPDVILVLFTMSSSYSIsDVREALESSPVGSEIAAVK 342
                                       45566678899*****************************8888888888888889989*99999999999999999 PP

                   Glyco_hyd_65N_2 177 gntltlrga 185
                                       ++ ++ +ga
  gi|313117316|ref|YP_004044299.1| 343 NDRVYAQGA 351
                                       998888876 PP

>> Amelotin  Amelotin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.3e-05      0.13     141     194 ..      36      90 ..      21      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                          Amelotin 141 lPagqaGvnpaiqgtpeghlptpsgtdddfevt.tPaGiqRgtktteetttesPn 194
                                       l ag aG n +    +  ++ tp+  dd + vt  PaG     ++ e+  t+ Pn
  gi|313117316|ref|YP_004044299.1|  36 LLAGCAGENGSQSVPAGTPSETPTAKDDSYSVTmEPAGTVEFDHVPENVYTGLPN 90 
                                       668999999887777777889*********99956*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 2940.44
//
Query:       gi|313117317|ref|YP_004044300.1|  [L=340]
Description: HEAT repeat containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-14   52.5  19.4    3.8e-07   30.4   2.3    3.7  3  HEAT_2         HEAT repeats
    5.7e-12   45.9  12.4     0.0017   18.8   0.6    5.2  5  HEAT_EZ        HEAT-like repeat
    1.5e-07   31.1   8.5      0.018   15.3   0.1    5.1  6  HEAT           HEAT repeat
    1.5e-07   31.6   0.0      0.014   15.4   0.0    3.0  3  Cnd1           non-SMC mitotic condensation complex subunit 1
    0.00019   20.1   0.0    0.00096   17.8   0.0    2.1  2  Adaptin_N      Adaptin N terminal region
     0.0049   16.9   0.9     0.0099   15.9   0.9    1.5  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.015   14.7   6.6      0.053   12.9   6.6    2.0  1  zf-ribbon_3    zinc-ribbon domain
      0.036   14.2   0.0        0.6   10.3   0.0    2.6  2  RTP1_C1        Required for nuclear transport of RNA pol II C
      0.078   12.5   0.0       0.15   11.6   0.0    1.5  1  CLASP_N        CLASP N terminal
      0.089   12.5   4.0       0.41   10.4   4.0    2.2  1  zinc_ribbon_2  zinc-ribbon domain
       0.13   13.0  12.9        7.6    7.5   1.1    4.9  4  HEAT_PBS       PBS lyase HEAT-like repeat
        8.1    6.7   8.0         20    5.4   0.6    2.6  2  Zn-ribbon_8    Zinc ribbon domain


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   2.3   2.5e-10   3.8e-07      13      88 .]      36     124 ..      22     124 .. 0.80
   2 !   27.3   1.4   2.3e-09   3.4e-06       3      81 ..     101     193 ..      99     200 .. 0.80
   3 !   20.1   1.4   4.1e-07   0.00062      10      84 ..     185     270 ..     177     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.5e-10
                            HEAT_2  13 dpevrraairaLgri..gnpea....lpaLvellededpavRraaaeaLgaig......dpealpaLkellddddd. 76 
                                         + rr+a+r++ ++  + p+a    lpaL+++l+d+++ +R   a+  + ++       ++a++ L+++l+d+d+ 
  gi|313117317|ref|YP_004044300.1|  36 PVDERREALRTIRSLleHRPSAldplLPALTSFLTDSERSIRLRTAKIFVSVAenaplaAESAVSPLAARLADEDEf 112
                                       56789********6533345555666999******************888775333333588***********9998 PP

                            HEAT_2  77 dvvReaAaeaLa 88 
                                       ++vR++AaeaL+
  gi|313117317|ref|YP_004044300.1| 113 YYVRARAAEALG 124
                                       **********96 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.3e-09
                            HEAT_2   3 aLlqalen.dpdpevrraairaLg........rignpealpaLvellededpavRraaaeaL..gaigdpe....al 64 
                                       +L ++l++ d++++vr++a++aLg          ++pe+l+ L+  l+ + ++v +  a+aL  +a+g+p      l
  gi|313117317|ref|YP_004044300.1| 101 PLAARLADeDEFYYVRARAAEALGyvalecpdAVASPEILAELRVGLSFDAREVKEKLAKALeyVALGNPGrlrhQL 177
                                       566667445***************9999888778899*************************443667666444489 PP

                            HEAT_2  65 paLkellddddddvvRe 81 
                                       ++L e ++d+ +++vR 
  gi|313117317|ref|YP_004044300.1| 178 SSLSEHFADE-SELVRY 193
                                       9*****9865.566675 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 4.1e-07
                            HEAT_2  10 ndpdpevrraairaLg..rignp....ealpaLvellededpavRraaaeaLgaig.........dpealpaLkell 71 
                                        d+++ vr++ + + +   +  p    ++ +aL+  l+de+p vR  aaeaLg +g          ++ ++aL+   
  gi|313117317|ref|YP_004044300.1| 185 ADESELVRYHLVTTAAvvGCECPealvSVCAALTAQLDDESPFVRGRAAEALGVLGrstvadwspPNAKIAALE--- 258
                                       6999999999999999665555544555599999999***************9888333322221233444444... PP

                            HEAT_2  72 ddddddvvReaAa 84 
                                        +ddd++v e+A 
  gi|313117317|ref|YP_004044300.1| 259 -TDDDAFVAERAR 270
                                       .567777777765 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   5.3e-06    0.0079       3      49 ..      39      81 ..      37      86 .. 0.81
   2 !    9.5   0.3   0.00093       1.4      23      54 ..      92     125 ..      80     126 .. 0.78
   3 !   18.8   0.6   1.1e-06    0.0017       3      53 ..     115     163 ..     113     165 .. 0.95
   4 ?    3.3   0.0     0.083   1.2e+02      10      46 ..     161     193 ..     158     198 .. 0.84
   5 !   12.8   0.2   8.5e-05      0.13      24      55 .]     208     239 ..     196     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.3e-06
                           HEAT_EZ  3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAa 49
                                      +Rr A++++ +l++++p +l      +lpaL ++L+d++ ++R  +a
  gi|313117317|ref|YP_004044300.1| 39 ERREALRTIRSLLEHRPSALD----PLLPALTSFLTDSERSIRLRTA 81
                                      7********779999999999....7777777777777779987665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00093
                           HEAT_EZ  23 qplvpeilpaLlalLnddsd..eVRaaAagaLgn 54 
                                       +++ + ++ +L+a+L d++    VRa Aa aLg 
  gi|313117317|ref|YP_004044300.1|  92 PLAAESAVSPLAARLADEDEfyYVRARAAEALGY 125
                                       44556788888888888888*999********95 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 1.1e-06
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLg 53 
                                       vR+ Aa aLG +a ++p++++   peil++L  +L+ d  eV+++ a aL+
  gi|313117317|ref|YP_004044300.1| 115 VRARAAEALGYVALECPDAVA--SPEILAELRVGLSFDAREVKEKLAKALE 163
                                       9**********9999****99..**********************999997 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.083
                           HEAT_EZ  10 aLGr.laggepellqplvpeilpaLlalLnddsd.eVRa 46 
                                       aL + +a g+p  l+ +++ +   ++     d++ +VR+
  gi|313117317|ref|YP_004044300.1| 161 AL-EyVALGNPGRLRHQLSSLSEHFA-----DESeLVRY 193
                                       66.458899*****************.....99977797 PP

  == domain 5  score: 12.8 bits;  conditional E-value: 8.5e-05
                           HEAT_EZ  24 plvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                        ++  + +aL a L d+s+ VR+ Aa aLg l
  gi|313117317|ref|YP_004044300.1| 208 EALVSVCAALTAQLDDESPFVRGRAAEALGVL 239
                                       3444667889999999999**********975 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       8.4   1.3e+04      17      30 ..      40      53 ..      40      53 .. 0.79
   2 !    8.7   0.0    0.0016       2.4       1      30 [.      61      90 ..      61      91 .. 0.94
   3 !    8.4   0.1    0.0019       2.8       7      28 ..     105     127 ..      99     130 .. 0.78
   4 ?   -0.7   0.0       1.6   2.4e+03       5      18 ..     180     193 ..     177     197 .. 0.81
   5 !   15.3   0.1   1.2e-05     0.018       5      28 ..     217     240 ..     213     242 .. 0.87
   6 ?   -2.3   0.1       5.3   7.9e+03       9      25 ..     257     274 ..     254     276 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.4
                                      HHHHHHHHHHHHHC CS
                              HEAT 17 ReaAakaLgalaev 30
                                      R+ A++++  l+e+
  gi|313117317|ref|YP_004044300.1| 40 RREALRTIRSLLEH 53
                                      77799999998875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                                      HHHHHHHHHT-SSHHHHHHHHHHHHHHHHC CS
                              HEAT  1 llPlllkllsDpspeVReaAakaLgalaev 30
                                      llP+l + l+D++ ++R  +ak ++ +ae+
  gi|313117317|ref|YP_004044300.1| 61 LLPALTSFLTDSERSIRLRTAKIFVSVAEN 90
                                      89*********************9999986 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0019
                                       HHH.T-SSHHHHHHHHHHHHHHH CS
                              HEAT   7 kll.sDpspeVReaAakaLgala 28 
                                       +l  +D+   VR+ Aa+aLg +a
  gi|313117317|ref|YP_004044300.1| 105 RLAdEDEFYYVRARAAEALGYVA 127
                                       555578999**********9665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.6
                                       HHHHHT-SSHHHHH CS
                              HEAT   5 llkllsDpspeVRe 18 
                                       l +   D+s  VR+
  gi|313117317|ref|YP_004044300.1| 180 LSEHFADESELVRY 193
                                       667788******96 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 1.2e-05
                                       HHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgala 28 
                                       l   l D+sp+VR  Aa+aLg l 
  gi|313117317|ref|YP_004044300.1| 217 LTAQLDDESPFVRGRAAEALGVLG 240
                                       56679****************985 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 5.3
                                       H.T-SSHHHHHHHHHHHH CS
                              HEAT   9 l.sDpspeVReaAakaLg 25 
                                       l +D++++V e A  a++
  gi|313117317|ref|YP_004044300.1| 257 LeTDDDAFVAERARFAVA 274
                                       448999998877766655 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00012      0.18       6      72 ..      43     111 ..      40     132 .. 0.83
   2 !    7.0   0.0    0.0038       5.7      19      82 ..      95     162 ..      90     191 .. 0.77
   3 !   15.4   0.0   9.4e-06     0.014       7      93 ..     196     283 ..     190     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                              Cnd1   6 airtlg..cirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenp 72 
                                       a+rt+     + p+ +++l++ L++ L+D++  +R  +a ++  + +n     +  +s la  l De++
  gi|313117317|ref|YP_004044300.1|  43 ALRTIRslLEHRPSALDPLLPALTSFLTDSERSIRLRTAKIFVSVAENAPLAAESAVSPLAARLADEDE 111
                                       677777555567899*************************************************99885 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0038
                              Cnd1  19 veylvepLrkrLkDedp..yVRktaaivvakL..ilndmvkekgflselaklleDenprVvanalaal 82 
                                        e  v+pL +rL Ded+  yVR  aa ++  +    +d v + ++l+el+  l+ + ++V +    al
  gi|313117317|ref|YP_004044300.1|  95 AESAVSPLAARLADEDEfyYVRARAAEALGYValECPDAVASPEILAELRVGLSFDAREVKEKLAKAL 162
                                       68899*********99666******9988887546678888888888888777666666666555555 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 9.4e-06
                              Cnd1   7 irtlg..cirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaa 81 
                                       + t +   +  p+ +  ++  L+++L De+p VR  aa ++  L + ++  ++   +++a l +D+++ V + a++a
  gi|313117317|ref|YP_004044300.1| 196 VTTAAvvGCECPEALVSVCAALTAQLDDESPFVRGRAAEALGVLGRSTVADWSPPNAKIAALETDDDAFVAERARFA 272
                                       55555444556777778999********************************************************* PP

                              Cnd1  82 lteiseksenai 93 
                                          + + + n++
  gi|313117317|ref|YP_004044300.1| 273 VAALDDDE-NTT 283
                                       99998886.443 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.4e-07   0.00096     330     520 ..      15     239 ..       2     243 .. 0.87
   2 ?    3.4   0.0     0.015        22     114     179 ..     212     276 ..     206     283 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.4e-07
                                       CCXXTTTHHHHHHHHHHHTTSSXXHHHHHHHHHHHHHHHHHSCCHHHHHHHHHHHHHTTXXHHHHHHHHHHHHHHHH CS
                         Adaptin_N 330 klvdesNvkeivkeLkkyvkevadedfksklvkaIgrlaekfatdaewvldvllellslsgesvkdeivevirdliq 406
                                       + +des  +  v+    +  +v   d +++++++I++l e  ++  +  l+ l  +l++s+ s++   ++ +  + +
  gi|313117317|ref|YP_004044300.1|  15 DVLDESAYEDAVEYVERFQ-SV-PVDERREALRTIRSLLEHRPSALDPLLPALTSFLTDSERSIRLRTAKIFVSVAE 89 
                                       5555555555555555554.44.344699************************************************ PP

                                       HSTTTSTTCHHHHCCTCCG.XXSHHHHHHHHHHHHHTTTTXTT.................................. CS
                         Adaptin_N 407 kvpelheeiiekLaellek.ieseearaaaiWllGeygelvsn.................................. 448
                                       + p   e++++ La+ l +  e+  +ra+a+  lG  + + ++                                  
  gi|313117317|ref|YP_004044300.1|  90 NAPLAAESAVSPLAARLADeDEFYYVRARAAEALGYVALECPDavaspeilaelrvglsfdarevkeklakaleyva 166
                                       *************8888877999999999999999999999999999****************************** PP

                                       ......HHHHHHCTTTTTTTSXHHHHHHHHHHHHHHHHCXGCC.THXHHHHHHHHHHHXXSHHHHHHHHHHHHHH CS
                         Adaptin_N 449 ..te.sasdllrslaekfvlesekvklqiltalvKlyltspdketqekliqlvlslatssdlevrdRaveylqll 520
                                         +  ++ ++l+sl e f +ese v++ ++t+++  +   p++    +++  ++  +++++  vr Ra e l +l
  gi|313117317|ref|YP_004044300.1| 167 lgNPgRLRHQLSSLSEHFADESELVRYHLVTTAAVVGCECPEA--LVSVCAALTAQLDDESPFVRGRAAEALGVL 239
                                       **999********************************999955..459**********99********9998776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHH CS
                         Adaptin_N 114 dlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleei 179
                                       +++ a+++ l d+sp+vr  Aa a+  l +++    ++    +i  l +d+d  v   A  +   +
  gi|313117317|ref|YP_004044300.1| 212 SVCAALTAQLDDESPFVRGRAAEALGVLGRSTVADWSPP-NAKIAALETDDDAFVAERARFAVAAL 276
                                       678889999999999999999999888888876666665.67777777777777776666555555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.9   6.6e-06    0.0099       8      37 ..     311     339 ..     308     340 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.6e-06
                               DZR   8 lppdarfCseCgtklkavaaedrCpsCgek 37 
                                       +++ +  C++Cg +l+ +a + +Cp+Cg++
  gi|313117317|ref|YP_004044300.1| 311 ITSPDSACPNCGLALP-EAGPPMCPQCGAP 339
                                       5666788********6.67799*****986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   6.6   3.6e-05     0.053       5      25 ..     318     339 ..     314     339 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
                       zf-ribbon_3   5 CPnCGa.plssddnvCpyCGtk 25 
                                       CPnCG  +++++ ++Cp CG++
  gi|313117317|ref|YP_004044300.1| 318 CPNCGLaLPEAGPPMCPQCGAP 339
                                       ******99************86 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0004       0.6       6      72 ..      30     131 ..      25     163 .. 0.66
   2 ?    0.2   0.0      0.56   8.4e+02      41      68 ..     213     240 ..     174     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0004
                           RTP1_C1   6 kdlqdpllpvrahglvlLrkliekkske.................................avldiekilkllleaL 49 
                                       +  q+  +  r ++l+++r+l+e++ +                                  a l +e+ ++ l   L
  gi|313117317|ref|YP_004044300.1|  30 ERFQSVPVDERREALRTIRSLLEHRPSAldpllpaltsfltdsersirlrtakifvsvaenAPLAAESAVSPLAARL 106
                                       5566777777999**********997556666666666666666666666666666666665666666666666666 PP

                           RTP1_C1  50 kdedsYvYLn..aikgLvaLadvfp 72 
                                       +ded++ Y+   a ++L  +a  +p
  gi|313117317|ref|YP_004044300.1| 107 ADEDEFYYVRarAAEALGYVALECP 131
                                       6666666654113445555555554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.56
                           RTP1_C1  41 ilkllleaLkdedsYvYLnaikgLvaLa 68 
                                       +   l  +L de ++v   a ++L  L+
  gi|313117317|ref|YP_004044300.1| 213 VCAALTAQLDDESPFVRGRAAEALGVLG 240
                                       5556666777777777777766666665 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.15     172     220 ..      56     104 ..      37     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                           CLASP_N 172 llldliekslkkgleDanptVRetaRstfweffkvwPsrAksllssldp 220
                                       + ld + ++l+++l+D++ ++R  + + f+++++++P  A+s +s l  
  gi|313117317|ref|YP_004044300.1|  56 SALDPLLPALTSFLTDSERSIRLRTAKIFVSVAENAPLAAESAVSPLAA 104
                                       3579999**********************************98877765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.0   0.00027      0.41       2      22 ..     318     339 ..     317     340 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                     zinc_ribbon_2   2 CpnCGaelqdnakF.CpyCGtp 22 
                                       CpnCG  l++  +  Cp+CG+p
  gi|313117317|ref|YP_004044300.1| 318 CPNCGLALPEAGPPmCPQCGAP 339
                                       ********9855555*****98 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.033        50       8      25 ..      43      65 ..      42      67 .. 0.92
   2 ?   -1.9   0.2       5.8   8.6e+03      13      27 .]      94     108 ..      91     108 .. 0.79
   3 ?    7.5   1.1    0.0051       7.6       1      15 [.     115     137 ..     115     164 .. 0.80
   4 ?    5.8   0.1     0.019        28       1      14 [.     228     241 ..     228     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.033
                                      HHHHCTS.....GGGHHHHHHHC CS
                          HEAT_PBS  8 aLgqlgd.....eeaipaLleaL 25
                                      aL ++++     + a+++Ll aL
  gi|313117317|ref|YP_004044300.1| 43 ALRTIRSllehrPSALDPLLPAL 65
                                      9999****************998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.8
                                       TSGGGHHHHHHHCTC CS
                          HEAT_PBS  13 gdeeaipaLleaLqd 27 
                                        +e a+ +L + L+d
  gi|313117317|ref|YP_004044300.1|  94 AAESAVSPLAARLAD 108
                                       568899999998876 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHCTS........G CS
                          HEAT_PBS   1 vRraAakaLgqlgd........e 15 
                                       vR++Aa+aLg +          +
  gi|313117317|ref|YP_004044300.1| 115 VRARAAEALGYVALecpdavasP 137
                                       9*********9999775554444 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHCTS CS
                          HEAT_PBS   1 vRraAakaLgqlgd 14 
                                       vR +Aa+aLg lg 
  gi|313117317|ref|YP_004044300.1| 228 VRGRAAEALGVLGR 241
                                       8*********8886 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.6     0.013        20      24      34 ..     313     323 ..     302     327 .. 0.79
   2 ?    4.6   1.5     0.024        36      26      34 ..     330     338 ..     324     340 .] 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.013
                       Zn-ribbon_8  24 apltaCPeCgs 34 
                                       +p+ aCP+Cg 
  gi|313117317|ref|YP_004044300.1| 313 SPDSACPNCGL 323
                                       57889****96 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                       Zn-ribbon_8  26 ltaCPeCgs 34 
                                       ++ CP+Cg+
  gi|313117317|ref|YP_004044300.1| 330 PPMCPQCGA 338
                                       456*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2244.06
//
Query:       gi|313117318|ref|YP_004044301.1|  [L=398]
Description: ORC complex protein Cdc6/Orc1 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-15   56.4   0.0    5.1e-15   55.2   0.0    1.6  1  Cdc6_C           CDC6, C terminal winged helix domain
    3.5e-10   40.3   0.0    7.6e-10   39.2   0.0    1.5  1  AAA_22           AAA domain
    2.7e-09   37.6   0.1    1.9e-08   34.9   0.0    2.3  2  AAA_16           AAA ATPase domain
     0.0021   16.9   0.2       0.11   11.3   0.0    2.1  2  AAA_32           AAA domain
     0.0025   18.2   0.0     0.0088   16.5   0.0    2.0  1  AAA              ATPase family associated with various cellul
     0.0043   17.4   0.0     0.0088   16.4   0.0    1.5  1  RNA_helicase     RNA helicase
     0.0087   16.0   0.0      0.018   14.9   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.075   12.5   0.0    1.9  2  AAA_7            P-loop containing dynein motor region
      0.024   13.8   0.0      0.051   12.7   0.0    1.4  2  PIF1             PIF1-like helicase
      0.027   13.6   0.0       0.05   12.8   0.0    1.4  1  NB-ARC           NB-ARC domain
      0.031   13.3   0.0      0.062   12.4   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
      0.032   13.9   0.1      0.071   12.8   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
      0.037   13.9   0.0      0.099   12.5   0.0    1.7  1  RsgA_GTPase      RsgA GTPase
      0.041   13.7   0.0        1.1    9.0   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
      0.057   12.3   0.0      0.088   11.7   0.0    1.3  1  Kinesin          Kinesin motor domain
      0.065   13.1   0.0       0.16   11.9   0.0    1.6  1  NACHT            NACHT domain
        0.1   11.5   0.0       0.95    8.3   0.0    2.0  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.11   12.5   0.0       0.46   10.5   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
       0.11   12.1   0.0       0.18   11.5   0.0    1.4  1  AAA_24           AAA domain
       0.13   12.2   0.0       0.24   11.4   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   5.7e-18   5.1e-15       1      84 []     306     389 ..     306     389 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 5.7e-18
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----H.HHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltq.revsdllseLemlgileleksskGrregrtrkisLnv 76 
                                       L ++++l+  ++k++ +++e+ +vY+++++++++dplt+ ++++++l  Lemlg+l+ ++ + G+r+g +  ++L+v
  gi|313117318|ref|YP_004044301.1| 306 LESVARLEC-EEKTPSRSKEIRNVYETVADHYAYDPLTSlKSIQNHLGTLEMLGFLSKTEYNDGKRGGSYFVYELSV 381
                                       78999**99.******************************************************************* PP

                                       SCHHHHHH CS
                            Cdc6_C  77 dpddvlea 84 
                                       d d v ea
  gi|313117318|ref|YP_004044301.1| 382 DADAVFEA 389
                                       ***99876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   8.5e-13   7.6e-10       5     118 ..      51     171 ..      48     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 8.5e-13
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelka....erlss 75 
                                        + ++v+G +G+GKT + + +l+ l++e + +e   +++v  ++++ ++      r l+++l  e ++     +ls+
  gi|313117318|ref|YP_004044301.1|  51 PSNIFVYGKTGVGKTAVTNYMLQALEAETEKREeaDDVHVRIYNCNRGS-VYGAVRSLVNKLRGEDEDpfpkTGLST 126
                                       57799********************888777776555555588887777.555555555555555555566699999 PP

                            AAA_22  76 eellealeqalraravielliiDEaqhlrs..eealeeL.rsllnl 118
                                          +e+l++ +++ + + l+++DE++hl s  +e+l e+ r ++n 
  gi|313117318|ref|YP_004044301.1| 127 NIAFETLYEKMDDIGGTFLFVLDEIDHL-SdaDELLYEFpRARANG 171
                                       9999************9***********.65688888887877774 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   2.2e-11   1.9e-08       4     157 ..      30     163 ..      27     174 .. 0.71
   2 ?   -2.2   0.0       5.2   4.7e+03     124     124 ..     260     260 ..     211     328 .. 0.59

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.2e-11
                            AAA_16   4 GReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd........ggif.lrgkcdqlesaipys 70 
                                        R++e+++ ++al++v  gr  ++++++G  GvGK+++ +  l+ale++        ++++ ++  ++ +       
  gi|313117318|ref|YP_004044301.1|  30 ERDDEIRAYRDALKDVLFGRNpSNIFVYGKTGVGKTAVTNYMLQALEAEtekreeadDVHVrIYNCNRGS------- 99 
                                       6*************99999988**********************99999655555544555444444444....... PP

                            AAA_16  71 alaqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwa 147
                                        +  a  r +l+++l  e    + ++++++                 + + ++  l +++   + ++++vlD+++ +
  gi|313117318|ref|YP_004044301.1| 100 -VYGAV-R-SLVNKLRGE----DEDPFPKTG---------------LSTNIAFETLYEKMDDIGGTFLFVLDEIDHL 154
                                       .55555.5.777777777....333444422...............3466666666666666666799999999999 PP

                            AAA_16 148 deaslqllaa 157
                                        +a+  ll++
  gi|313117318|ref|YP_004044301.1| 155 SDADE-LLYE 163
                                       88654.4454 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.2
                            AAA_16 124 k 124
                                       +
  gi|313117318|ref|YP_004044301.1| 260 R 260
                                       1 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00012      0.11      32      62 ..      53      83 ..      29      96 .. 0.81
   2 ?    3.7   0.1     0.024        22     478     510 ..     253     285 ..     219     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                            AAA_32 32 NifvlGesgtGrttlvkrlleeiakkeptpd 62
                                      Nifv G++g+G+t +++ +l++ +++ ++ +
  gi|313117318|ref|YP_004044301.1| 53 NIFVYGKTGVGKTAVTNYMLQALEAETEKRE 83
                                      9************999999988776665543 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.024
                            AAA_32 478 seiadllrEAdywakkegaevveaehVekAlee 510
                                       ++  dllr    +a++eg+++v++eh+++A e+
  gi|313117318|ref|YP_004044301.1| 253 RQALDLLRTGGDLAESEGDSMVTDEHIQDAREK 285
                                       567899999999******************765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.8e-06    0.0088       2     128 ..      55     206 ..      54     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.8e-06
                                       EEESSTTSSHHHHHHHHHHHHTHE.............EEEEETTTCSSS..............STTHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakelgve.............fleisgsellsk..............yvgesekkirelfk 51 
                                        +yG  G+GKT++ + + + l++e             +++ +  ++                  + ++  +++  f+
  gi|313117318|ref|YP_004044301.1|  55 FVYGKTGVGKTAVTNYMLQALEAEtekreeaddvhvrIYNCNRGSVYGAvrslvnklrgededPFPKTGLSTNIAFE 131
                                       68******************854433344444444445555555555445666666666677755555556666676 PP

                                       HHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS....SSTEEEEEEESS...GGGSTH CS
                               AAA  52 eakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk....eskvivigatnr...pdkldp 117
                                       ++ ek     ++  +++DEid l  ++             +Ll e+ + + +    eskv vig++n+    d+l+p
  gi|313117318|ref|YP_004044301.1| 132 TLYEKMddigGTFLFVLDEIDHLSDAD-------------ELLYEFPRARANghitESKVGVIGISNNyrfRDSLSP 195
                                       65444457866688889******6666.............5555555555555666999********9888889998 PP

                                       HHHSTTSSEEE CS
                               AAA 118 allrgRfdrki 128
                                       +++   ++++i
  gi|313117318|ref|YP_004044301.1| 196 KVRDTLMEKEI 206
                                       88845555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.9e-06    0.0088       1      28 [.      54      82 ..      54     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.9e-06
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl.kl 28
                                      i++yG++g+GK+ +++++ +al+ +  k 
  gi|313117318|ref|YP_004044301.1| 54 IFVYGKTGVGKTAVTNYMLQALEAETeKR 82
                                      79********************9777322 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     2e-05     0.018      12      48 ..      43      79 ..      29     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                          ATPase_2 12 eeilerepneiyfiYGpegsGKtaLlkeiienledkd 48
                                      + +l   + + +f+YG  g+GKta+ + +++ le   
  gi|313117318|ref|YP_004044301.1| 43 KDVLFGRNPSNIFVYGKTGVGKTAVTNYMLQALEAET 79
                                      455555566678*************999998885543 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.4e-05     0.075      32      60 ..      50      78 ..      40      83 .. 0.86
   2 ?   -1.0   0.0       1.2   1.1e+03      60      89 ..     199     227 ..     178     264 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                             AAA_7 32 nkkpvllvGptGtGKtviikdllkkldke 60
                                      n  +++++G+tG+GKt++++ +l++l+ e
  gi|313117318|ref|YP_004044301.1| 50 NPSNIFVYGKTGVGKTAVTNYMLQALEAE 78
                                      5678999*****************99966 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                             AAA_7  60 ekylsltinfsaqtsanqlqdiiesklekr 89 
                                       ++++ + i+fs + +an+l++i++++ ek 
  gi|313117318|ref|YP_004044301.1| 199 DTLMEKEISFSPY-DANELRSILDKRAEKA 227
                                       5566666666654.5667777776666664 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.6e-05     0.051      11      51 ..      39      80 ..      31      84 .. 0.78
   2 ?   -4.0   0.0       7.2   6.4e+03     182     205 ..     304     327 ..     298     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                                      HHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCC CS
                              PIF1 11 daiiea.vlnekgklfFvtGsgGtgKtflwkallkklrsegk 51
                                      + +++  ++ +++ ++Fv+G  G gKt + + +l++l++e +
  gi|313117318|ref|YP_004044301.1| 39 RDALKDvLFGRNPSNIFVYGKTGVGKTAVTNYMLQALEAETE 80
                                      444444055699***********************9998765 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 7.2
                                       EEE-S-STTTT...........HH CS
                              PIF1 182 lkLtknmRllsesldetekkelke 205
                                       l L+++ Rl++e+++ + +ke+++
  gi|313117318|ref|YP_004044301.1| 304 LVLESVARLECEEKTPSRSKEIRN 327
                                       779999999999999999999876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05      0.05       6     126 ..      40     165 ..      36     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                                       HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHH...HHCCSHCCCCC.CBTEEEEEEEESXXHHHHHHHXXHHHHHC CS
                            NB-ARC   6 ekviekLlekdelqslvvalvGmgGvGKttlak...qilnksdeveg.rFdsvawvvvsktdkseeiletilkeLsl 78 
                                       +++++ L+   ++    ++++G+ GvGKt + +   q+l+   e ++   d+++ +   +  + +  +++++++L  
  gi|313117318|ref|YP_004044301.1|  40 DALKDVLF-GRNPS--NIFVYGKTGVGKTAVTNymlQALEAETEKREeADDVHVRIYNCNRGSVYGAVRSLVNKLRG 113
                                       67888888.77777..79***********997722245555455555244588999989999999999999999966 PP

                                       CCTTSSSS-STTS...HHHHHHHHCCCT..TEEEEEEEE-SHHHH.....HHH CS
                            NB-ARC  79 seddleekeeves...lkrklvrlLltk..rfllvlDDVweeedwdkigvvlp 126
                                       +++d   k+ + s   + + l++ + +    fl+vlD + +  d d++   +p
  gi|313117318|ref|YP_004044301.1| 114 EDEDPFPKT-GLStniAFETLYEKMDDIggTFLFVLDEIDHLSDADELLYEFP 165
                                       644443333.3334667788888887766799999999987777777776666 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.9e-05     0.062     128     158 ..      50      80 ..      17      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                             T2SSE 128 erglilvsGgTgsGKttllyallkeinksde 158
                                       +  +i v G Tg GKt +++ +l+ +++++e
  gi|313117318|ref|YP_004044301.1|  50 NPSNIFVYGKTGVGKTAVTNYMLQALEAETE 80 
                                       5579**********************99865 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.9e-05     0.071       5      45 ..      32      79 ..      28     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.9e-05
                                      SHHHHHHHHHHHHHC..TSSS-EEEECSTTSSHHHHHHHHHH.....H CS
                   Sigma54_activat  5 sealkelleqikkva..ktdlsvlitGesGtGKellaraihe.....a 45
                                      ++++++ ++ +k v   ++++++++ G++G+GK+ + + + +     +
  gi|313117318|ref|YP_004044301.1| 32 DDEIRAYRDALKDVLfgRNPSNIFVYGKTGVGKTAVTNYMLQaleaeT 79
                                      566666667777766435679******************998444332 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.099      93     132 ..      42      84 ..      14      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                       HHHHCTT...SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase  93 lkellkd...ktsvlvGqSGvGKStLinallpelelktgevse 132
                                       lk++l +   + +++ G++GvGK+++ n +l+ le++t++  e
  gi|313117318|ref|YP_004044301.1|  42 LKDVLFGrnpSNIFVYGKTGVGKTAVTNYMLQALEAETEKREE 84 
                                       4555443222456788*****************9999987555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0012       1.1      15      41 ..      52      80 ..      36      97 .. 0.72
   2 ?    2.3   0.0      0.14   1.3e+02     124     136 ..     145     157 ..     125     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                                      CEEEEEESTTSSHHHH..HHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTla..flipvlqivye 41
                                       +++v ++TG GKT++  +++ +l++ +e
  gi|313117318|ref|YP_004044301.1| 52 SNIFVYGKTGVGKTAVtnYMLQALEAETE 80
                                      6899***********95566666654444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                                       EEEEETHHHHHHT CS
                                       xxxxxxxxxxxxx RF
                              DEAD 124 flVlDEadrlldq 136
                                       ++VlDE+d l+d 
  gi|313117318|ref|YP_004044301.1| 145 LFVLDEIDHLSDA 157
                                       79********996 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.8e-05     0.088      62      89 ..      37      65 ..       6     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                                      HHHHHHHHHHTTSE.EEEEEEESTTSSHH CS
                           Kinesin 62 takplvesvleGyn.atifaYGqtgsGKT 89
                                      + ++ +++vl G n + if YG+tg GKT
  gi|313117318|ref|YP_004044301.1| 37 AYRDALKDVLFGRNpSNIFVYGKTGVGKT 65
                                      34678999999999567***********9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.16       3      97 ..      54     158 ..      52     173 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC..-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C...... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqga..fklvFflslrelsrsgnarsladllfsqlpepaapvse...... 71 
                                       +++ G+ G+GKT+    + +a+ +++ ++++    +v   ++ + s  g++rsl + l+ +  +p  +         
  gi|313117318|ref|YP_004044301.1|  54 IFVYGKTGVGKTAVTNYMLQALEAETEKREEadDVHVRIYNCNRGSVYGAVRSLVNKLRGEDEDPFPKTGLstniaf 130
                                       799*******************9999998885544455556666666666666666666655554333322456644 PP

                                       ..CHHHHCCSCCCEEEEEE-STT-SS-T CS
                             NACHT  72 ..vwavllelperlLlilDglDelvtdl 97 
                                           + +  +    L++lD +D l++ +
  gi|313117318|ref|YP_004044301.1| 131 etLYEKMDDIGGTFLFVLDEIDHLSDAD 158
                                       4444444444455569999999998765 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0011      0.95      16      44 ..      52      80 ..      47      85 .. 0.87
   2 ?    0.7   0.0      0.22   1.9e+02     245     273 ..     144     172 ..     124     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                     TrwB_AAD_bind 16 qhilivGttGsGKtqalekllrairargd 44
                                      + i++ G tG GKt +++ +l+a++a  +
  gi|313117318|ref|YP_004044301.1| 52 SNIFVYGKTGVGKTAVTNYMLQALEAETE 80
                                      67999*****************9998765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.22
                     TrwB_AAD_bind 245 lWfflDElpaLgrleelksllaegRkfGg 273
                                         f+lDE+++L   +el     ++R  G 
  gi|313117318|ref|YP_004044301.1| 144 FLFVLDEIDHLSDADELLYEFPRARANGH 172
                                       5699*************999999999885 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00051      0.46       1      28 [.      53      80 ..      53      88 .. 0.89
   2 ?   -1.6   0.0       2.7   2.4e+03      69      78 ..     146     155 ..     132     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00051
                                      EEEEE--SSSSHHHHHHHGGGGBS--EE CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaalnreve 28
                                      ++++ G++G+gK+ ++ ++++al++e+e
  gi|313117318|ref|YP_004044301.1| 53 NIFVYGKTGVGKTAVTNYMLQALEAETE 80
                                      57999******************77764 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                                       EEEESGGG-- CS
                             AAA_5  69 lvlDEverae 78 
                                       +vlDE+++++
  gi|313117318|ref|YP_004044301.1| 146 FVLDEIDHLS 155
                                       5777777655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.18       3      34 ..      52      82 ..      50     166 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                            AAA_24  3 lkiliyGpsgiGKTtlakelgpkplfidtekG 34
                                       +i++yG+ g+GKT + + +  ++l   tek 
  gi|313117318|ref|YP_004044301.1| 52 SNIFVYGKTGVGKTAVTNYM-LQALEAETEKR 82
                                      5899***************9.99999999983 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027      0.24       6      46 ..      34      78 ..      29      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                      HHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  6 etealgkklakal....gdvilLeGdLGaGKTtlvrglakalgve 46
                                      e++a   +l+++l     + i+ +G+ G+GKT+ +  +++al+ e
  gi|313117318|ref|YP_004044301.1| 34 EIRAYRDALKDVLfgrnPSNIFVYGKTGVGKTAVTNYMLQALEAE 78
                                      566666666665564434459********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2727.94
//
Query:       gi|313117319|ref|YP_004044302.1|  [L=553]
Description: aldehyde:ferredoxin oxidoreductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-77  261.3   0.1    2.3e-77  260.6   0.1    1.3  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    5.1e-60  202.7   0.3    8.5e-60  202.0   0.3    1.4  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.6   0.1   2.6e-81   2.3e-77       8     374 ..     221     548 ..     214     551 .. 0.90

  Alignments for each domain:
  == domain 1  score: 260.6 bits;  conditional E-value: 2.6e-81
                                       HHHHHSH.HHH.HHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE. CS
                            AFOR_C   8 keiksspqvta.elrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrevkv 83 
                                       +e +++    +  +++ GT +++++ane + lp ++f+e+tfe++e i+g a++   + k++ C sC  aC+  +k 
  gi|313117319|ref|YP_004044302.1| 221 REAATD----DhIMKEQGTVAVMDLANEVSGLPSYYFSEQTFEGVEGINGSAVAS-KKYKKGTCSSCAFACKLPTKD 292
                                       333333....3379************************************88887.4455545************96 PP

                                       .....ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT CS
                            AFOR_C  84 eegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefg 160
                                       +e   +++egpe+e ++a+Gsn g+dd+  ++k n+lcd++GlD isaGn++a +  +                efg
  gi|313117319|ref|YP_004044302.1| 293 DERG-IETEGPEFEVAMAFGSNAGVDDIVDVMKSNQLCDDYGLDAISAGNVVASYLAAED--------------EFG 354
                                       5555.679*********************************************9998755..............59* PP

                                       -THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG-TH CS
                            AFOR_C 161 daeallellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlrayli 237
                                       + e + +l+ekiA+reg+gd+lAeG+ r  eklg e++  +vkG++++a++ r + g++l+Ya++nrGa+H+ a+++
  gi|313117319|ref|YP_004044302.1| 355 NRELIWDLVEKIAHREGVGDTLAEGIDRTHEKLGVENW--TVKGMDFAAHEGRVLHGQGLSYAVANRGADHMYATFY 429
                                       **********************************9886..89*********************************** PP

                                       HHH.......S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHH CS
                            AFOR_C 238 ale.......ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaG 307
                                       ++e       ++vdp  t gka  ++  ++l+al ds ++Ckf++  ++     + ++ ++   G+  + e+ll +G
  gi|313117319|ref|YP_004044302.1| 430 SVEyplvpqdQAVDPEGTLGKADTLIERENLMALNDSGVVCKFSR--DY-----MTPERYETLFGV--DFEDLLNVG 497
                                       ******9999888888889**************************..34.....566667777776..679****** PP

                                       HHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---H CS
                            AFOR_C 308 eRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtk 374
                                        R ++leR fn++ G++r+dd+lp  l +                +e++ldeyY++rGW+  Gv+  
  gi|313117319|ref|YP_004044302.1| 498 ARTVTLERHFNNQRGFNRDDDRLPYELPD----------------FETALDEYYAARGWTNGGVVPD 548
                                       ************************99872................9**************9998765 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.0   0.3   9.5e-64   8.5e-60       3     197 ..       8     204 ..       6     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 9.5e-64
                                       EEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-T CS
                            AFOR_N   3 ilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksP 79 
                                       +l +++ +++++  +++ +++e+y+Ggrg+a++l ++++p +vdp++ en+++f+tGp++ ++++ +gr++++a+sP
  gi|313117319|ref|YP_004044302.1|   8 LLSINVGERETNAVDVS-DVLESYIGGRGVATRLAHERIPYDVDPYGSENRVLFTTGPMQASKMSFTGRMNCTAVSP 83 
                                       799**************.79********************************************************* PP

                                       TTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS...EEE CS
                            AFOR_N  80 ltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd...kva 153
                                       lt++l +snaGg+++ +++ +G +a+ + G++++ v+++++d++ve+e + +l g ++ et e+l +e+g    ++a
  gi|313117319|ref|YP_004044302.1|  84 LTEGLLSSNAGGFMSRHFAATGNSAVEFVGESDELVVVHVSDQGVEFEAVPNLAGATVPETVEYLDSEHGIgadQTA 160
                                       *******************************************************************8887888*** PP

                                       EE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 154 viGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                        iGpaGen+vrfAsi+++++ra+grgGlGav+gsKn+ka+++ g
  gi|313117319|ref|YP_004044302.1| 161 IIGPAGENRVRFASIMTSEERAFGRGGLGAVLGSKNVKAVTFGG 204
                                       ***************888***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 3706.23
//
Query:       gi|313117320|ref|YP_004044303.1|  [L=379]
Description: Fe3+ ABC transporter periplasmic protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-17   63.4   0.0    3.5e-17   62.6   0.0    1.2  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    2.4e-17   63.6   0.7    4.4e-17   62.8   0.7    1.4  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    9.7e-15   55.3   3.3      1e-14   55.3   1.2    1.8  2  SBP_bac_1   Bacterial extracellular solute-binding protein
    8.1e-11   42.1   0.0      2e-10   40.9   0.0    1.6  1  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   7.8e-21   3.5e-17      18     227 ..     125     341 ..     124     351 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 7.8e-21
                         SBP_bac_6  18 fieeglfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpv..PksWaDLldPeykgkvalp 92 
                                       +++eg+ ++++pan+++v+     e+lk ++g+ ++ +  ++ + + kd +++r +  P++W+DLl+P+     al 
  gi|313117320|ref|YP_004044303.1| 125 AMNEGFTTGYKPANWDKVP-----EKLKTDNGHMTATRRMTTAVTYRKDIYEERGLkePETWDDLLHPDIVQDLALQ 196
                                       5789***************.....***************************************************** PP

                         SBP_bac_6  93 gnngsdlfealllalyk....dfg.edgvkkllrnlkanlhpaqmvkaagslesgepavsvvpyffadilpekkkgk 164
                                       ++   +   a++l ++     + + +++v ++ +++k ++   + ++ +++  +ge a+ +  ++++ +l+++++  
  gi|313117320|ref|YP_004044303.1| 197 TPTA-AVGLATALSVNNarggSLDdLQPVIDYYEEIKSGGAEFT-DNFLAQFTKGEYATFLRYDYSGLNLKYNNDDI 271
                                       *998.88888888888888**7777***************9999.***********888888888888888887444 PP

                         SBP_bac_6 165 ........nlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvvtnpavlne 227
                                                lk +   +Ga+  p+   + kg +++e +k f+d+ ls e+q+ + +a+   P+  +p+++ +
  gi|313117320|ref|YP_004044303.1| 272 deekvgvaLLKGTDGSKGAFNQPYGFGMLKGaPNPEACKLFMDYVLSTEGQRKFLDAYV-RPI-RAPELEMP 341
                                       899774433333333449****************************************5.999.66666554 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.7   9.8e-21   4.4e-17       3     275 ..      78     345 ..      68     350 .. 0.74

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 9.8e-21
                                       HHHHHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-HHHHHTT- CS
                         SBP_bac_8   3 akefekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddltdalaavg 79 
                                       +++fe k+gv +n    +s+++   +++ ++  +a+ +  + ++++ + +++e g +    +  n+d+++ +l+  +
  gi|313117320|ref|YP_004044303.1|  78 MDAFESKYGVPLNDDDRSSGEALKHMRSHAQ--NADHSAYNGGYTYGIIAMNE-GFTTG-YKPANWDKVPEKLK--T 148
                                       5566666666666655566666666666443..33333445555555554443.33332.34466777777666..4 PP

                                       -TS.----EEEEEEE-EEEEEHHHHHHS...---BHHHHHHHHHHHHHH-SEGG---GGGGGGTHH...ETTEE--- CS
                         SBP_bac_8  80 ydgklygvPyasetpyvliynkdlleka..edpktwdellaaakklkgkfglpdpasgwlqaalla...kdgksldd 151
                                        +g         + ++++ y+kd++e+   + p+twd+ll+  +++ +  +l +p++ +++a++l    + g sldd
  gi|313117320|ref|YP_004044303.1| 149 DNG--HMTATRRM-TTAVTYRKDIYEERglKEPETWDDLLH--PDIVQDLALQTPTAAVGLATALSvnnARGGSLDD 220
                                       667..44444444.589*********97888**********..9999999******999988888877777777776 PP

                                       H..HHH.HHHHHHHHHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH...-TTT....SEEEE--.....S CS
                         SBP_bac_8 152 dggkdglkealellkklkdngktydtgadavsefanGevaftingswdiaaaq...kagk....klgaivp.....k 216
                                                +++++ ++k  g   +  +++ + f++Ge+a+++ ++ +  +++   +  +    k+g++++      
  gi|313117320|ref|YP_004044303.1| 221 L------QPVIDYYEEIKSGGA--EFTDNFLAQFTKGEYATFLRYDYSGLNLKynnD--DideeKVGVALLkgtdgS 287
                                       5......99*********7774..444899*************99988888886541..223459****99444333 PP

                                       --EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHHHH CS
                         SBP_bac_8 217 qgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaalspevk 275
                                       +g+f +  g+ ++k+a+n++ a++ F+ +++s e+q+++ +++  +   ++++ ++e+ 
  gi|313117320|ref|YP_004044303.1| 288 KGAFNQPYGFGMLKGAPNPE-ACKLFMDYVLSTEGQRKFLDAYVRPIRAPELEMPDEFP 345
                                       57******************.6*******************998887777777666665 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.16   7.1e+02     213     272 ..      64     136 ..      22     140 .. 0.73
   2 !   55.3   1.2   2.3e-18     1e-14      87     314 ..     140     322 ..     129     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                                       HHTTEEECSSHHHHHHHHH.............TTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEEC CS
                         SBP_bac_1 213 lkgkgaenkdgaaalalfe.............aGeaamaivglwaalaamkvapkvafaadkekpkeelgvap 272
                                         ++++ +++++++ ++fe             +Gea   + ++ +  ++   ++++ + +++++ ++ +g+ p
  gi|313117320|ref|YP_004044303.1|  64 VYCVQSGWSNWPSLMDAFEskygvplndddrsSGEALKHMRSHAQNADHSAYNGGYTYGIIAMNEGFTTGYKP 136
                                       5577788888888888888777777777777777777777777777777777777777777777777777766 PP

  == domain 2  score: 55.3 bits;  conditional E-value: 2.3e-18
                                       CCTEEEEHHHHTHHHHCE.EEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHH CS
                         SBP_bac_1  87 kdaadklsssvlpkilds.kvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsas 162
                                       ++   kl  ++++ + +           ++++ Y+kd++e+ gl++p+tWd+l++++   + +  +p          
  gi|313117320|ref|YP_004044303.1| 140 DKVPEKLKTDNGHMTATRrM--------TTAVTYRKDIYEERGLKEPETWDDLLHPDIVQDLALQTP---------- 198
                                       44445555566666666544........99*************************************.......... PP

                                       HHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEE CS
                         SBP_bac_1 163 gtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamai 239
                                         +++  la a+s +           ++++g+ ++ + v  y+      e    g ++++++++ a+f++Ge a ++
  gi|313117320|ref|YP_004044303.1| 199 --TAAVGLATALSVN-----------NARGGSLDDLQPVIDYY------EEIKSGGAEFTDNFL-AQFTKGEYATFL 255
                                       ..5555555555555...........77778886666666662......556678899999996.56999******* PP

                                       EEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 240 vglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                        + ++       +++ ++++d+ +  e++gva l +++g k++    yg++++kg++npea k F+d++ls e+q
  gi|313117320|ref|YP_004044303.1| 256 RYDYS-------GLNLKYNNDDIDE-EKVGVALLKGTDGSKGAFNQPYGFGMLKGAPNPEACKLFMDYVLSTEGQ 322
                                       **999.......6666777776666.569999999888888888*****************************99 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   4.4e-14     2e-10      18     227 ..      79     328 ..      74     331 .. 0.68

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 4.4e-14
                                       HHHHHHH---EEEEESSHHHHHHHHHHH...-SEEEESS.H.HHHHHHHHGGGGG...............GG-EEEE CS
                        SBP_bac_11  18 aaFeahtgvkvevsaggsgklarqiadga.rpDvwipas.sawlellaaaglvqa...............esavpla 77 
                                       +aFe+++gv ++   ++sg++++ ++++a  +D  +     ++   + ++g+++                +++   a
  gi|313117320|ref|YP_004044303.1|  79 DAFESKYGVPLNDDDRSSGEALKHMRSHAqNADHSAYNGgYTYGIIAMNEGFTTGykpanwdkvpeklktDNGHMTA 155
                                       66666666666666666666666665555455554444412222223444555545555555555555555777777 PP

                                       EEEEEEEESTT-.......TT---SHHHHHHSS-..-EEEE--T-TTTTHH.HHHHGGG.--........HHHHHHH CS
                        SBP_bac_11  78 ssplviavpkgn.......pkkikgwadLlkpgl..klavadPttspsGlaalalleaa.ga........qellkal 136
                                       + ++  av   +        k + +w+dLl+p++   la+ +P t+++Gla+   +++a g+         ++++++
  gi|313117320|ref|YP_004044303.1| 156 TRRMTTAVTYRKdiyeergLKEPETWDDLLHPDIvqDLALQTP-TAAVGLATALSVNNArGGslddlqpvIDYYEEI 231
                                       777766664444334444337899**********988******.889999888777766342555554444455555 PP

                                       HHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHH...H.......HSTTSSEEEE--TTT--....EEEEEEEE-TT- CS
                        SBP_bac_11 137 ekkvvklgessrqlltaveageadagivyesea...kaa.....engdkleavylpeglnl.dpldypaavlkkaak 204
                                       +++ + +   +++ l+++  ge++ ++ y  +    k++     e++ ++ ++   +g       +y++++lk+a++
  gi|313117320|ref|YP_004044303.1| 232 KSGGAEF---TDNFLAQFTKGEYATFLRYDYSGlnlKYNnddidEEKVGVALLKGTDGSKGaFNQPYGFGMLKGAPN 305
                                       5444433...3678888**********88655545533367776889999999******99999************* PP

                                       -HHHHHHHHHTTSHHHHHHHHHT CS
                        SBP_bac_11 205 reaAraFlafLrspeaqailrky 227
                                       +ea + F+++++s e+q+ + ++
  gi|313117320|ref|YP_004044303.1| 306 PEACKLFMDYVLSTEGQRKFLDA 328
                                       ******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2653.12
//
Query:       gi|313117321|ref|YP_004044304.1|  [L=320]
Description: Fe3+ ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-11   42.1  15.5    1.2e-10   41.4  15.5    1.4  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4  15.5   6.8e-15   1.2e-10      13     171 ..     134     307 ..     103     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 6.8e-15
                      BPD_transp_1  13 nkkldkllrpliivllslPsfvlaillvlvf.................vilsilghlilpviillllsaapyvrlir 72 
                                         ++   l +l  ++ slP +v a+++++++                 +i+ ++ +++ ++++++ +s++p ++l+ 
  gi|313117321|ref|YP_004044304.1| 134 DLPFEGTLVTLLSFPVSLPGIVAAFMIIVLLgntglltnaaawfsgqsAIDLAVATGVVGLFVAYCYSMIPRALLLL 210
                                       55566678889999999999998888887779****************9999************************* PP

                      BPD_transp_1  73 raalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgyd 149
                                       r+   ++++  +eaar lGas+ ++f++v+lP+++p +i  +il+f  +l  +  +++l       +++++ ++ y 
  gi|313117321|ref|YP_004044304.1| 211 RGSYAEVNTRAEEAARSLGASPARTFYHVTLPQVKPGLIGAFILTFRTALAIFGTVLILQ-----AMRVWTYEIDYA 282
                                       **********************************************99999999999999.....555555555555 PP

                      BPD_transp_1 150 yseis...nggvlalviavlllnlv 171
                                       +s++     +++ a+v +v++l + 
  gi|313117321|ref|YP_004044304.1| 283 LSNGFdiqLAAAMATVWFVFVLGFT 307
                                       5555555533333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 2064.93
//
Query:       gi|313117322|ref|YP_004044305.1|  [L=298]
Description: spermidine/putrescine ABC transporter permease II [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-09   36.4  11.7    4.3e-09   36.4  11.7    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   4.3     0.099   1.8e+03      16      49 ..      19      46 ..       5     101 .. 0.62
   2 !   36.4  11.7   2.4e-13   4.3e-09       1     168 [.     118     282 ..     114     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.099
                      BPD_transp_1 16 ldkllrpliivllslPsfvlaillvlvfvilsil 49
                                      + +l+  l+ ++l +P++v ++  +         
  gi|313117322|ref|YP_004044305.1| 19 IVRLVFALTLLFLIFPIVVTFVASF------ARE 46
                                      3344444444444555554444433......222 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 2.4e-13
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       g+++++ +a +++++++++l  l  ++l+  +++ ++ ++        l  + +++ii + l  ap+++l +++ ++
  gi|313117322|ref|YP_004044305.1| 118 GVPIAYAVA-RYRFRGREWLNALAVLPLAPGIIL-GVAFLR---AYPELSGTDFGLIIGYSLLKAPFMVLAVQSSFE 189
                                       678888888.999999999999999888755555.444332...225556688999********************* PP

                      BPD_transp_1  78 slp.kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydys 151
                                       ++p ++l+e ar lGas  ++f  v++Pna++ i++g+i+ ++++  ++ + + ++s ++  l ++l   i+++ + 
  gi|313117322|ref|YP_004044305.1| 190 AMPlRQLEESARSLGASWLETFLFVIVPNAKRGIVSGAIICWALAAAEFNFSYVVFSRGArpLALFLKANISNSSFL 266
                                       **97799*************************************************997754443333333333333 PP

                      BPD_transp_1 152 eisnggvlalviavlll 168
                                        +s ++v ++ ++v+ +
  gi|313117322|ref|YP_004044305.1| 267 TTS-AAVSVFFLLVAGV 282
                                       333.2333333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1943.98
//
Query:       gi|313117323|ref|YP_004044306.1|  [L=248]
Description: spermidine/putrescine ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-37  126.9   0.0    9.8e-37  126.5   0.0    1.2  1  ABC_tran  ABC transporter
    7.7e-09   35.8   0.2    0.00021   21.2   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00085   19.3   0.0     0.0014   18.6   0.0    1.3  1  Rad17     Rad17 P-loop domain
     0.0079   16.5   0.1      0.021   15.1   0.0    1.7  2  AAA_22    AAA domain
     0.0094   15.4   0.5       0.61    9.5   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.016   15.6   1.8      0.052   13.9   1.8    1.9  1  AAA_16    AAA ATPase domain
      0.067   12.9   1.0       0.13   12.0   0.6    1.6  2  PRK       Phosphoribulokinase / Uridine kinase family
       0.11   13.0   0.4       0.19   12.2   0.4    1.4  1  AAA_23    AAA domain
       0.12   12.8   1.5        1.1    9.7   1.0    2.3  2  AAA       ATPase family associated with various cellular acti
       0.15   12.1   0.0       0.28   11.2   0.0    1.5  1  AAA_14    AAA domain
       0.17   11.0   0.2       0.29   10.3   0.2    1.3  1  NB-ARC    NB-ARC domain
       0.21   11.4   0.4       0.41   10.4   0.4    1.4  1  AAA_29    P-loop containing region of AAA domain
       0.21   11.3   0.1       0.35   10.6   0.1    1.3  1  AAA_24    AAA domain
       0.27   11.4   0.7       0.91    9.7   0.7    2.0  1  AAA_33    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.0   7.6e-40   9.8e-37       2     136 ..      20     161 ..      19     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 7.6e-40
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + vsl++  ge+++ivG++G+GK+t l+++ g ++pt+G+il+d++d+++   +  r+++g ++q   lf+++tvre
  gi|313117323|ref|YP_004044306.1|  20 DGVSLSIDDGEILGIVGPSGCGKTTTLRTIGGFETPTSGRILFDDDDVTR--VPPERRNVGLVFQSYALFDNMTVRE 94 
                                       789***********************************************..9************************ PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e++++++++ls lg+ +l d+      s+LSgGq+qrv laral+ +p++lllDEp+
  gi|313117323|ref|YP_004044306.1|  95 NvqfgpkmqgvprqERRDRADRLLSMLGIGDLSDRDP----STLSGGQQQRVGLARALAVEPRILLLDEPM 161
                                       ************9999999************999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   5.8e-05     0.074       2      37 ..      32      58 ..      31     101 .. 0.68
   2 !   21.2   0.0   1.6e-07   0.00021     226     300 ..     123     195 ..      95     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdels 37
                                       +++Gp g+GK++ L+++ ++         +t++++
  gi|313117323|ref|YP_004044306.1| 32 LGIVGPSGCGKTTTLRTIGGF---------ETPTSG 58
                                      579***************766.........333333 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.6e-07
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpl 300
                                        gd  +++++ lS G+++  +l+ al+  +   ++ll+DEp +gL+ +l rrl + + ++l++ ++  + +TH+ +
  gi|313117323|ref|YP_004044306.1| 123 IGDLSDRDPSTLSGGQQQRVGLARALAVEP---RILLLDEPMTGLDAQLKRRLRDEIgSLLTELDVTALYVTHDQV 195
                                       4555566778899**999999999999999...*********************999999999**********965 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0014      34      65 ..      18      49 ..      11      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                             Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvL 65
                                      +++  +L     +iL i GPsGCgk+t+++ +
  gi|313117323|ref|YP_004044306.1| 18 AIDGVSLSIDDGEILGIVGPSGCGKTTTLRTI 49
                                      6677778888889***************9875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.021       6      25 ..      30      49 ..      26      87 .. 0.88
   2 ?   -1.7   0.0       2.5   3.2e+03      80      99 ..     137     159 ..     101     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrl 25
                                       il ++G+sG+GKTt+lr++
  gi|313117323|ref|YP_004044306.1| 30 EILGIVGPSGCGKTTTLRTI 49
                                      67889************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                            AAA_22  80 ealeqalrarav...ielliiDE 99 
                                        + ++   ara    +++l++DE
  gi|313117323|ref|YP_004044306.1| 137 GQQQRVGLARALavePRILLLDE 159
                                       44444444444455667777776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.018        23      26      43 ..      31      48 ..      17      51 .. 0.83
   2 !    9.5   0.0   0.00048      0.61     134     217 ..     131     210 ..      82     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.018
                                      EEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldA 43
                                      +  ivGp G+GK+  l  
  gi|313117323|ref|YP_004044306.1| 31 ILGIVGPSGCGKTTTLRT 48
                                      567*********987765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00048
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvg 210
                                       +++LSgG+++ v la  +A++    + + llDe    LD++  +++ + + +  ++  +    ++++++e ++ + +
  gi|313117323|ref|YP_004044306.1| 131 PSTLSGGQQQRVGLARALAVEP---R-ILLLDEPMTGLDAQLKRRLRDEIGSLLTELDVTALYVTHDQVEAMEMCDR 203
                                       459*************999864...3.7899**99999999999999999998888888888888888888888888 PP

                                       EEEEETT CS
                                       xxxxxxx RF
                             SMC_N 211 vtkveng 217
                                       +   ++g
  gi|313117323|ref|YP_004044306.1| 204 IAVMNDG 210
                                       7766555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.8   4.1e-05     0.052      21      45 ..      26      50 ..      16     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrell 45
                                       +++e++ ++G+sG+GK++ +r++ 
  gi|313117323|ref|YP_004044306.1| 26 IDDGEILGIVGPSGCGKTTTLRTIG 50
                                      45679999*************9985 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   9.8e-05      0.13       1      19 [.      31      49 ..      31      54 .. 0.92
   2 ?   -2.6   0.0         3   3.9e+03      19      47 ..     176     204 ..     171     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.8e-05
                               PRK  1 vIgvagsSGaGkttvarkl 19
                                      ++g+ g+SG+Gktt+ r++
  gi|313117323|ref|YP_004044306.1| 31 ILGIVGPSGCGKTTTLRTI 49
                                      789*************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                               PRK  19 lekifgrekvkaaeiegdsflrldraekd 47 
                                       + +++ +  v+a ++++d++  ++ ++  
  gi|313117323|ref|YP_004044306.1| 176 IGSLLTELDVTALYVTHDQVEAMEMCDRI 204
                                       66777888888888888888888887765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00015      0.19      21      39 ..      31      49 ..      12      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                      +  I+Gp G+GKTT l+ i
  gi|313117323|ref|YP_004044306.1| 31 ILGIVGPSGCGKTTTLRTI 49
                                      668***********99876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.0   0.00086       1.1       3      18 ..      34      49 ..      32      54 .. 0.89
   2 ?    1.0   0.0      0.42   5.4e+02      51      74 ..     143     171 ..     132     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00086
                                      EESSTTSSHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakav 18
                                      ++Gp G+GKT++ + +
  gi|313117323|ref|YP_004044306.1| 34 IVGPSGCGKTTTLRTI 49
                                      68**********9987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.42
                                       HHHHHTS.TSEEEEEET....GGGHHHHH CS
                               AAA  51 keakeka.kpsilfiDE....idalaksr 74 
                                         a++ a +p il++DE    +da  k+r
  gi|313117323|ref|YP_004044306.1| 143 GLARALAvEPRILLLDEpmtgLDAQLKRR 171
                                       45666677899*****9444444444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.28       3      23 ..      30      50 ..      28      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                            AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                      +il i+G+  +GKTt l+++ 
  gi|313117323|ref|YP_004044306.1| 30 EILGIVGPSGCGKTTTLRTIG 50
                                      7999*************9986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00022      0.29      17      40 ..      28      49 ..      18      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                                      TSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                      + +  ++++vG  G+GKtt ++ i
  gi|313117323|ref|YP_004044306.1| 28 DGE--ILGIVGPSGCGKTTTLRTI 49
                                      555..9*************88766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00032      0.41      12      39 ..      19      46 ..      16      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                      +dg +++id  ++  ++GpsG GK+T l
  gi|313117323|ref|YP_004044306.1| 19 IDGVSLSIDDGEILGIVGPSGCGKTTTL 46
                                      577889999666999**********976 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00027      0.35       6      22 ..      33      49 ..      29      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                            AAA_24  6 liyGpsgiGKTtlakel 22
                                       i+Gpsg GKTt+++++
  gi|313117323|ref|YP_004044306.1| 33 GIVGPSGCGKTTTLRTI 49
                                      69************998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.7   0.00071      0.91       4      19 ..      34      49 ..      31     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00071
                            AAA_33  4 lvGlpGsGKstlaerl 19
                                      +vG++G+GK+t ++ +
  gi|313117323|ref|YP_004044306.1| 34 IVGPSGCGKTTTLRTI 49
                                      69*********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1603.60
//
Query:       gi|313117324|ref|YP_004044307.1|  [L=411]
Description: WD-40 repeat-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-37  128.4  13.9    1.1e-19   70.9   3.1    2.3  2  PQQ_2     PQQ-like domain
    2.8e-22   78.5  28.7     0.0035   17.8   0.0    8.9  8  PQQ_3     PQQ-like domain
    3.2e-18   64.7  16.0    0.00036   20.3   0.1    7.9  8  PQQ       PQQ enzyme repeat
  ------ inclusion threshold ------
       0.96    9.3   2.8         28    4.6   0.0    3.1  3  DUF1391   Protein of unknown function (DUF1391)


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   3.3   8.1e-21   3.6e-17      11     178 ..      60     216 ..      53     223 .. 0.73
   2 !   70.9   3.1   2.5e-23   1.1e-19       4     183 ..     225     399 ..     222     408 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 8.1e-21
                             PQQ_2  11 atGaelWrvdlarplgggvsravlsggtlfva....tgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvva 83 
                                         G+++W+++    ++     +v ++gt++++    +++g  +alda +G++ W+ttl g+  +   + +gr + va
  gi|313117324|ref|YP_004044307.1|  60 SRGNLVWTSEA---FTQWE--PVIADGTVYTTnfapSKEGSAIALDAQDGSEQWRTTLGGKDSNGRVLVGGR-FIVA 130
                                       35899999965...55555..577999999997777799999999999999999999977633333444444.4555 PP

                             PQQ_2  84 sdgqlialdaedGkrlWstqqrseepaelrssaspava...gdtvvvgessgklvaldpkdGkvlWerelaaprgts 157
                                        d +l+ald ++G+ +W++ +++ ep  l+ssa+   a   ++tv+v+  s +l a++++dG+++We+    ++ t 
  gi|313117324|ref|YP_004044307.1| 131 HDSRLVALDPQNGDIVWQRSLAGLEPSGLGSSAELLAAderSGTVIVPY-SDGLKAFQAEDGQRRWET----GEITG 202
                                       7999999999999999999999999999888888887789999999999.777999999999999998....33222 PP

                             PQQ_2 158 elsrvgdisgrpvvaegtVya 178
                                       +l        +p + +gtVy 
  gi|313117324|ref|YP_004044307.1| 203 QL-------NTPAIYDGTVYT 216
                                       22.......455555566665 PP

  == domain 2  score: 70.9 bits;  conditional E-value: 2.5e-23
                             PQQ_2   4 vvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvga...plvaeg 77 
                                       +++al+ ++G++ W++ l++p++g +     ++g+l+v  +g++lv  d++tG  + e +l +  +g+      ++g
  gi|313117324|ref|YP_004044307.1| 225 SLVALALDDGTIRWTTALEDPSDGDP--VATDQGVLVV--DGNTLVVHDRETGDRRSEIELVSDELGSlttIAADGG 297
                                       56699999**********99999999..7779999999..8********************66666665557999** PP

                             PQQ_2  78 rvvvvasdgqlialdaedGkrlWstqqrse..epae.lrssaspava...gdtvvvgessgklvaldpkdGkvlWer 148
                                        ++v++ ++ l a+d+e+G+++W+ +++s+   +a  +++  + +++   + + v  + +  ++a+d ++G+v+W++
  gi|313117324|ref|YP_004044307.1| 298 TAFVATYERGLFAVDIETGTTQWQ-YDDSAhdDSAFgVCVGIETVISivdKPESVSSTYGKTVTAFDRETGDVRWNY 373
                                       ************************.66664344444888777777777755555555558899************** PP

                             PQQ_2 149 elaaprgtselsrvgdisgrpvvaegtVyassgqg 183
                                       +l   +          ++ rp++a+g+V++++ + 
  gi|313117324|ref|YP_004044307.1| 374 ALDGYH---------ALTIRPILADGAVFFATDSI 399
                                       **6655.........689***********999776 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0003       1.4      16      40 .]      75     103 ..      57     103 .. 0.83
   2 !   17.8   0.0   7.7e-07    0.0035       1      39 [.     104     141 ..     104     142 .. 0.78
   3 ?    4.5   0.0     0.011        51       1      31 [.     143     182 ..     143     190 .. 0.70
   4 !   16.3   0.5   2.2e-06      0.01       1      36 [.     191     229 ..     191     233 .. 0.84
   5 !   12.6   0.3   3.3e-05      0.15       1      37 [.     234     269 ..     234     272 .. 0.74
   6 !   17.2   0.4   1.2e-06    0.0054      15      40 .]     290     315 ..     282     315 .. 0.86
   7 ?    3.5   0.1     0.024   1.1e+02      26      40 .]     352     366 ..     316     366 .. 0.57
   8 !   11.4   0.2   7.9e-05      0.35       1      32 [.     367     401 ..     367     406 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0003
                             PQQ_3  16 spavdgglvyvgtg....dGtlyAlDaet 40 
                                        p++++g+vy++       G+  AlDa++
  gi|313117324|ref|YP_004044307.1|  75 EPVIADGTVYTTNFapskEGSAIALDAQD 103
                                       59*********999************986 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 7.7e-07
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       G ++W+++l+g + n+ ++v+g+ +++   d +l+AlD++
  gi|313117324|ref|YP_004044307.1| 104 GSEQWRTTLGGkDSNGRVLVGGRFIVA-H-DSRLVALDPQ 141
                                       889********8887766776665544.4.59******97 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.011
                             PQQ_3   1 GevlWsvqlpgpvnssp.......avdg..glvyvgtgdG 31 
                                       G+++W+++l g   s++       a+d+  g+v v  +dG
  gi|313117324|ref|YP_004044307.1| 143 GDIVWQRSLAGLEPSGLgssaellAADErsGTVIVPYSDG 182
                                       99*****998844455555559977776556888877644 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 2.2e-06
                             PQQ_3   1 GevlWsv.qlpgpvnsspavdgglvyvgtg...dGtlyAl 36 
                                       G+++W++ ++ g++n +pa+++g+vy+ +      +l+Al
  gi|313117324|ref|YP_004044307.1| 191 GQRRWETgEITGQLN-TPAIYDGTVYTIGRvdgVDSLVAL 229
                                       99*****999**995.8**********9998776666666 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 3.3e-05
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlD 37 
                                       G+++W++ l +p  + p++ +  v v++g +tl+  D
  gi|313117324|ref|YP_004044307.1| 234 GTIRWTTALEDPSDGDPVATDQGVLVVDG-NTLVVHD 269
                                       99*******99999999666666666676.6655555 PP

  == domain 6  score: 17.2 bits;  conditional E-value: 1.2e-06
                             PQQ_3  15 sspavdgglvyvgtgdGtlyAlDaet 40 
                                       ++ a+dgg+ +v+t+  +l+A+D et
  gi|313117324|ref|YP_004044307.1| 290 TTIAADGGTAFVATYERGLFAVDIET 315
                                       4569********************98 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.024
                             PQQ_3  26 vgtgdGtlyAlDaet 40 
                                        +t+  t++A+D et
  gi|313117324|ref|YP_004044307.1| 352 SSTYGKTVTAFDRET 366
                                       457788999999887 PP

  == domain 8  score: 11.4 bits;  conditional E-value: 7.9e-05
                             PQQ_3   1 GevlWsvqlpg..pvnsspavdgglvyvgtg.dGt 32 
                                       G+v+W++ l+g  +++  p +++g v+++t+  G 
  gi|313117324|ref|YP_004044307.1| 367 GDVRWNYALDGyhALTIRPILADGAVFFATDsIGA 401
                                       99*******98888888899999999999975555 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.7e-05     0.077       2      33 ..      86     117 ..      85     121 .. 0.92
   2 !    6.8   0.0    0.0016         7       4      27 ..     129     150 ..     124     154 .. 0.81
   3 ?    3.7   0.0     0.014        64       2      26 ..     174     197 ..     173     207 .. 0.81
   4 ?   -2.1   0.3      0.97   4.4e+03       8      20 ..     210     222 ..     210     222 .. 0.83
   5 !    9.4   0.1   0.00022         1      12      37 ..     226     251 ..     224     252 .. 0.88
   6 ?   -0.6   0.0      0.33   1.5e+03       8      25 ..     261     278 ..     256     288 .. 0.73
   7 !   20.3   0.1     8e-08   0.00036       1      36 [.     297     332 ..     297     334 .. 0.93
   8 !   15.2   0.3   3.2e-06     0.015       7      29 ..     354     376 ..     351     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSCGS CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvl 33 
                                       +++++s+ G   AlDa +G + Wr+ +gg++ 
  gi|313117324|ref|YP_004044307.1|  86 TNFAPSKEGSAIALDAQDGSEQWRTTLGGKDS 117
                                       78999***********************9986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0016
                                       EEEETTSEEEEEETTTCCEEEEEE CS
                               PQQ   4 ylgsadGylyAlDadTGkvlWrfk 27 
                                       +++  d +l+AlD  +G+++W+  
  gi|313117324|ref|YP_004044307.1| 129 VAH--DSRLVALDPQNGDIVWQRS 150
                                       444..89**************965 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.014
                                       EEEEEETTSEEEEEETTTCCEEEEE CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrf 26 
                                       +v+++  d  l A+ a++G+ +W++
  gi|313117324|ref|YP_004044307.1| 174 TVIVPYSD-GLKAFQAEDGQRRWET 197
                                       66666444.699999********97 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.97
                                       TTSEEEEEETTTC CS
                               PQQ   8 adGylyAlDadTG 20 
                                       +dG++y + + +G
  gi|313117324|ref|YP_004044307.1| 210 YDGTVYTIGRVDG 222
                                       79****9987776 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.00022
                                       EEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ  12 lyAlDadTGkvlWrfktggpvlslpi 37 
                                       l+Al +d+G+++W++ +++p +++p+
  gi|313117324|ref|YP_004044307.1| 226 LVALALDDGTIRWTTALEDPSDGDPV 251
                                       5677788****************997 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.33
                                       TTSEEEEEETTTCCEEEE CS
                               PQQ   8 adGylyAlDadTGkvlWr 25 
                                       ++++l+  D++TG+ + +
  gi|313117324|ref|YP_004044307.1| 261 DGNTLVVHDRETGDRRSE 278
                                       567777789999998765 PP

  == domain 7  score: 20.3 bits;  conditional E-value: 8e-08
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvlslp 36 
                                       g+ +++++   l+A+D++TG+  W+++ +++++s +
  gi|313117324|ref|YP_004044307.1| 297 GTAFVATYERGLFAVDIETGTTQWQYDDSAHDDSAF 332
                                       67899****************************986 PP

  == domain 8  score: 15.2 bits;  conditional E-value: 3.2e-06
                                       ETTSEEEEEETTTCCEEEEEESS CS
                               PQQ   7 sadGylyAlDadTGkvlWrfktg 29 
                                       +++ ++ A+D++TG+v+W + ++
  gi|313117324|ref|YP_004044307.1| 354 TYGKTVTAFDRETGDVRWNYALD 376
                                       78899*************99876 PP

>> DUF1391  Protein of unknown function (DUF1391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0062        28      32      43 ..     184     195 ..     173     198 .. 0.90
   2 ?   -3.0   0.1       1.5   6.7e+03      34      43 ..     311     320 ..     295     321 .. 0.64
   3 ?    3.4   0.2     0.015        67      27      43 ..     354     371 ..     350     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0062
                           DUF1391  32 ktfktetGarrW 43 
                                       k+f++e G rrW
  gi|313117324|ref|YP_004044307.1| 184 KAFQAEDGQRRW 195
                                       89********** PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                           DUF1391  34 fktetGarrW 43 
                                          etG  +W
  gi|313117324|ref|YP_004044307.1| 311 VDIETGTTQW 320
                                       4568999888 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.015
                           DUF1391  27 tytkskt.fktetGarrW 43 
                                       ty k+ t f  etG  rW
  gi|313117324|ref|YP_004044307.1| 354 TYGKTVTaFDRETGDVRW 371
                                       899987669********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2706.90
//
Query:       gi|313117325|ref|YP_004044308.1|  [L=148]
Description: hypothetical protein Hbor_31120 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 995.33
//
Query:       gi|313117326|ref|YP_004044309.1|  [L=313]
Description: hypothetical protein Hbor_31130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-13   50.2   5.8    7.1e-12   45.2   5.8    2.1  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.2e-05   25.3   0.3    2.6e-05   24.2   0.0    1.6  2  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
          3    7.4   5.2       0.39   10.3   1.1    1.5  2  Ycf4             Ycf4


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   5.8   1.2e-15   7.1e-12       2     287 ..       7     310 ..       6     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.2e-15
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                        iak+Ef++ v+sr ++lltv ++l  + l +l ++  +  +  ++++  +++    +                   
  gi|313117326|ref|YP_004044309.1|   7 PIAKHEFSEVVKSRLVWLLTVPIVLD-GLLNVLTSQ--TAIQHLGNLRYIASF----QR------------------ 58 
                                       79******************998887.666665433..223333333333333....22.................. PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                         m ++ip+  +++ga a+ g +  g l     +PvsR+++l+gK+ g+      ++v l  ++ l+ +  + +g+ 
  gi|313117326|ref|YP_004044309.1|  59 -GMGLVIPIACIILGARAVGGARGKGFLTNTALQPVSRGDVLVGKAAGRTSG---LLVPLSTGLALGYIHGAMNGDI 131
                                       .899************************************************...99999999999*********** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlyg.....vaellagpavp. 226
                                       ++l   + + +a +++l  +  + + ++lS++++++   a  a++l   ++++++ +l                   
  gi|313117326|ref|YP_004044309.1| 132 PPLLPTIGFWLANIVYLGSL--MFAMIGLSAFFKEALAPAGFAFILGGGTFLFYDELLPIplkaiY---------Gv 197
                                       *****999999999777744..5556899*****88888888888888888888777733222221.........13 PP

                   ABC2_membrane_2 227 ....................qeindflsllsptsayntllneilagsdlna.......................... 257
                                                             +  fls l+pt+a ++l+n++l   + ++                          
  gi|313117326|ref|YP_004044309.1| 198 tkaspstsgvsmtweqpdapLGLVAFLSRLPPTNAHQALTNWPLGLPNSDSlsifvirqlepdfiapsvvilgdayg 274
                                       34566677888888888888**********************9998865559************************* PP

                   ABC2_membrane_2 258 ......lgstatnllilllllavllvlgyvlFkrkD 287
                                             ++    + ++ll+  +++++lgy+ F++ D
  gi|313117326|ref|YP_004044309.1| 275 gqpvpfYLHPLVSGVVLLVFSTAVFALGYYTFNNTD 310
                                       *****97777777788888888889*******9988 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   4.4e-09   2.6e-05       4     175 ..      11     175 ..       8     178 .. 0.79
   2 ?   -2.5   0.1      0.69   4.1e+03     146     158 ..     289     301 ..     278     311 .. 0.49

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.4e-09
                   ABC2_membrane_4   4 tEflKlkrskivwllvlaallvpllallyfnllgktgldpaefys.lsvfgftlllllplilgiiasylifrEeqnd 79 
                                        Ef  + +s++vwll + ++l  ll +l+    ++t++++ +     ++f+ ++ l++p+  +i++++ +   + ++
  gi|313117326|ref|YP_004044309.1|  11 HEFSEVVKSRLVWLLTVPIVLDGLLNVLT----SQTAIQHLGNLRyIASFQRGMGLVIPIACIILGARAVGGARGKG 83 
                                       67777788899999555555444444443....5567776444441579999999********************** PP

                   ABC2_membrane_4  80 tlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpii 156
                                        l n  + Pvsr  +l++K +       ll  v +   ++++ + g ++ ++ ++l ++  +l  ++++  ++ ++i
  gi|313117326|ref|YP_004044309.1|  84 FLTNTALQPVSRGDVLVGKAAGRTSG--LL--VPLSTGLALGYIHGAMNGDIPPLLPTIGFWLANIVYLGSLMFAMI 156
                                       *******************9976432..22..223344567788899999999999999999999999999999*** PP

                   ABC2_membrane_4 157 alvllkksyvlpliltlvy 175
                                        l++++k+ ++p ++++++
  gi|313117326|ref|YP_004044309.1| 157 GLSAFFKEALAPAGFAFIL 175
                                       *****************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.69
                   ABC2_membrane_4 146 llvffavlpiial 158
                                       +++++++++++al
  gi|313117326|ref|YP_004044309.1| 289 VVLLVFSTAVFAL 301
                                       2222223333332 PP

>> Ycf4  Ycf4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.1   6.4e-05      0.39      17      46 ..     140     169 ..     137     189 .. 0.81
   2 ?   -3.9   0.2       1.5   8.7e+03      57      75 ..     287     305 ..     282     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.4e-05
                              Ycf4  17 ylwavvvllGglgfllagissylkvnllpi 46 
                                       +++a +v lG+l f + g+s+++k  l p 
  gi|313117326|ref|YP_004044309.1| 140 FWLANIVYLGSLMFAMIGLSAFFKEALAPA 169
                                       899*********************998654 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.5
                              Ycf4  57 qGlvllfYgvaglllslyl 75 
                                        G+vll++++a + l  y+
  gi|313117326|ref|YP_004044309.1| 287 SGVVLLVFSTAVFALGYYT 305
                                       5899999999988888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2026.53
//
Query:       gi|313117327|ref|YP_004044310.1|  [L=300]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-27   97.3   0.0    2.8e-27   95.9   0.0    1.6  2  ABC_tran  ABC transporter
    1.3e-09   38.3   4.3    2.1e-06   27.8   0.0    2.4  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    8.5e-05   23.2   0.3    0.00014   22.5   0.3    1.4  1  DUF4162   Domain of unknown function (DUF4162)
  ------ inclusion threshold ------
      0.013   15.2   0.2      0.026   14.3   0.2    1.4  1  AAA_29    P-loop containing region of AAA domain
      0.014   15.8   0.0      0.027   14.8   0.0    1.5  1  AAA_16    AAA ATPase domain
      0.054   14.0   0.5        0.1   13.1   0.5    1.4  1  AAA_23    AAA domain
      0.083   12.3   0.4        2.9    7.3   0.1    2.5  3  SMC_N     RecF/RecN/SMC N terminal domain
       0.11   12.2   0.4       0.17   11.5   0.4    1.3  1  DUF2529   Domain of unknown function (DUF2529)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0   1.2e-30   2.8e-27       2     136 ..      21     158 ..      20     159 .. 0.96
   2 ?   -1.6   0.0       1.6   3.6e+03      62      63 ..     240     241 ..     181     285 .. 0.54

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.2e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + ++l +++g++ +++G+nG+GKSt + +l+gl +pt G+  l g+d +e +  s+r+++gvlp+  +  p lt re
  gi|313117327|ref|YP_004044310.1|  21 DAINLAIERGTVFGFLGPNGSGKSTTIGMLLGLIHPTGGTAALAGHDPQE-DPVSVRSNVGVLPEGFTPYPSLTGRE 96 
                                       789***********************************************.8899********************** PP

                                       H........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +         ++ ++e+als++glk+ +d+ +    + +S+G+ qr+ la+al+ +p++l+lDEp+
  gi|313117327|ref|YP_004044310.1|  97 HltyiaelrGEEIDPEAALSEVGLKDAQDRAA----TAYSKGMTQRLGLAMALIGRPPILVLDEPF 158
                                       ***99988777777************999999....*****************************7 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                                       EE CS
                                       xx RF
                          ABC_tran  62 gv 63 
                                       +v
  gi|313117327|ref|YP_004044310.1| 240 EV 241
                                       22 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.5   8.5e-05      0.19       2      22 ..      33      53 ..      32      76 .. 0.82
   2 !   27.8   0.0   9.2e-10   2.1e-06     227     297 ..     121     188 ..      92     190 .. 0.84
   3 ?   -3.7   0.1       3.7   8.2e+03     288     299 ..     225     236 ..     211     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       ++ GpNgsGKS+ +  l +l
  gi|313117327|ref|YP_004044310.1| 33 FGFLGPNGSGKSTTIGMLLGL 53
                                      5789*********99888776 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 9.2e-10
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +d q++ a+  S G+ + l+l+ al+ ++   ++l++DEp +gL+P     + +++ +++++g+ +++++H
  gi|313117327|ref|YP_004044310.1| 121 KDAQDRAATAYSKGMTQRLGLAMALIGRP---PILVLDEPFTGLDPDGAQLVRDIVMRERERGTTILFSSH 188
                                       78899999999***99999********99...**************6666666666777778********* PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.7
                            AAA_21 288 ngaQviltTHSp 299
                                       + +Q+ ++THS 
  gi|313117327|ref|YP_004044310.1| 225 THTQLEIATHSD 236
                                       457898999996 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   6.2e-08   0.00014      13      80 ..     227     299 ..     212     300 .] 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.2e-08
                                       SEEEEE...-------..--.-EEEE-TTS-EEEEE-------------.----EEEEEEEE---HHHHHHHH CS
                           DUF4162  13 nrieve...adaeelleepg.veeveeeggelelkledeeaanellkal.tsgveirsFeeeePsLndIFiek 80 
                                       +++e+    + a e+l+  + v+ev++++++++++ +++++  +l ++l ++g++ ++ +++ P+ +dI+ e 
  gi|313117327|ref|YP_004044310.1| 227 TQLEIAthsDSAVEVLTDAEsVQEVTKKDKTVVVEHDSNTSHLALVRQLeANGITAVNATVQAPTVEDIYREF 299
                                       555655664335555555444****************************77******************9985 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.1e-05     0.026      19      43 ..      27      51 ..      16      62 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                            AAA_29 19 idlkg.atlltGpsGsGKSTllDAiq 43
                                      i+ +g ++ + Gp+GsGKST +  + 
  gi|313117327|ref|YP_004044310.1| 27 IE-RGtVFGFLGPNGSGKSTTIGMLL 51
                                      55.34477899*********985555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-05     0.027      29     155 ..      35     169 ..      18     185 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                            AAA_16  29 lsGesGvGKsslvrellralekdggif.lrgkcdql..esa............ipysalaqalareellrqlldeae 90 
                                       + G+ G+GKs+ + +ll  +  +gg + l+g+  q     +            +py  l+      +++++l  e+ 
  gi|313117327|ref|YP_004044310.1|  35 FLGPNGSGKSTTIGMLLGLIHPTGGTAaLAGHDPQEdpV-SvrsnvgvlpegfTPYPSLTGREHL-TYIAELRGEE- 108
                                       78*********************8666466666665440.1444577777777777444444423.5666665552. PP

                            AAA_16  91 saeleawrekleealaavpelagaeasrllellkrll.allsrderplvlvlDd.lqwadeaslqll 155
                                           ++ ++  e  l+   ++ + +a++    +++ l   ++  +rp +lvlD+ +  +d++ +ql 
  gi|313117327|ref|YP_004044310.1| 109 ---IDPEAALSEVGLK---DAQDRAATAYSKGMTQRLgLAMALIGRPPILVLDEpFTGLDPDGAQLV 169
                                       ...2233332223223...222222244444444444322233355889999953667777777764 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   4.6e-05       0.1      19      36 ..      30      47 ..      13      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                            AAA_23 19 kgltlItGpNGaGKTTil 36
                                        ++ + GpNG+GK+T +
  gi|313117327|ref|YP_004044310.1| 30 GTVFGFLGPNGSGKSTTI 47
                                      46899***********76 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0013       2.9      29      41 ..      35      47 ..      16      54 .. 0.80
   2 ?    2.3   0.0     0.042        93     149     191 ..     139     181 ..     135     204 .. 0.83
   3 ?   -2.2   0.1         1   2.3e+03      79      97 ..     239     257 ..     218     282 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0013
                                      EEESTTSSHHHHH CS
                                      xxxxxxxxxxxxx RF
                             SMC_N 29 ivGpNGSGKsnll 41
                                       +GpNGSGKs  +
  gi|313117327|ref|YP_004044310.1| 35 FLGPNGSGKSTTI 47
                                      57********765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.042
                                       HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQ 191
                                       L +A+  + + p+ +lDe    LD    + v +++ +++++  
  gi|313117327|ref|YP_004044310.1| 139 LGLAMALIGRPPILVLDEPFTGLDPDGAQLVRDIVMRERERGT 181
                                       56788889999*******************9999987776644 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1
                                       EEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N  79 veitfdnedkklkiekeev 97 
                                       ve++ d e+ +++++k+++
  gi|313117327|ref|YP_004044310.1| 239 VEVLTDAESVQEVTKKDKT 257
                                       3333333333333333332 PP

>> DUF2529  Domain of unknown function (DUF2529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   7.8e-05      0.17      55     112 ..     231     287 ..     207     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.8e-05
                                       HHHCSTT--TTEEE--TT----TT-EEEEEES-S--HHHHHHHHHHHHHT--EEEEES CS
                           DUF2529  55 ealegkeklpsvkkleeekeltetDrvllfsresndkealklakkleekgievvavss 112
                                        a++++  ++  + +e+ +e+t++D+ +++ ++sn+ + l+l+++le++gi++v  + 
  gi|313117327|ref|YP_004044310.1| 231 IATHSDSAVEVLTDAESVQEVTKKDKTVVVEHDSNT-SHLALVRQLEANGITAVNATV 287
                                       3566677777778888888************99999.899***********9987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1982.09
//
Query:       gi|313117328|ref|YP_004044311.1|  [L=119]
Description: hypothetical protein Hbor_31150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 859.78
//
Query:       gi|313117329|ref|YP_004044312.1|  [L=40]
Description: hypothetical protein Hbor_31160 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        85  (0.00474092); expected 358.6 (0.02)
Passed bias filter:                       78  (0.00435049); expected 358.6 (0.02)
Passed Vit filter:                         0  (0); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 261.66
//
Query:       gi|313117330|ref|YP_004044313.1|  [L=660]
Description: hypothetical protein Hbor_31170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-36  124.8  37.9    3.5e-21   75.7  10.8    3.1  2  ABC2_membrane_2  ABC-2 family transporter protein
    2.1e-07   30.4  45.6    1.9e-05   23.9  18.4    2.5  2  ABC2_membrane_3  ABC-2 family transporter protein
    6.2e-05   23.0   5.2    6.2e-05   23.0   5.2    2.9  3  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.17   12.0   3.5        6.2    7.0   0.2    3.6  3  Ldr_toxin        Toxin Ldr, type I toxin-antitoxin system


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4  19.1   4.2e-17   1.9e-13       3     288 .]      23     309 ..      21     309 .. 0.81
   2 !   75.7  10.8   7.8e-25   3.5e-21       2     288 .]     361     659 ..     360     659 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 4.2e-17
                   ABC2_membrane_2   3 iakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvst 79 
                                       ++++Ef  lvr ++++++t +++l+          g+s  + +++++  t    +v+a                 s 
  gi|313117330|ref|YP_004044313.1|  23 LIQREFWLLVRLKWLWIVTPVVVLV----------GNSFITPFGNEVTVTGGWIAVAA-----------------SE 72 
                                       5666666666666666666666666..........44444555555555555444433.................22 PP

                   ABC2_membrane_2  80 imavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivl 156
                                        +  +   +a+  ++ +i   + +g +++   +P +R+ei++g + g+ ++   +   +l +v+     il++    
  gi|313117330|ref|YP_004044313.1|  73 TAVAFASYFAVPVAFRSIIHSRQSGNIRITAGTPLTRSEIIIGTAFGRGLA---LFCPVLMGVVG--TAILGWNHYG 144
                                       455667789******************************************...88888888666..4556677777 PP

                   ABC2_membrane_2 157 aledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp......q 227
                                       +l  +ll+ + +v+ l++++++a  +++S+v+ s++ a a++ + ++v a   +iv+ ++ +  +   v+       
  gi|313117330|ref|YP_004044313.1| 145 TLPVFLLIGYTVVTALFILAVVATITAISAVVESTVHAVACSTVCVIVMAYWTDIVA-AIHQFITSQNVSigqppqS 220
                                       7777888888877777777679**************************988777777.6666666666667788867 PP

                   ABC2_membrane_2 228 eindflsllsptsayntllneilagsdlna............................lgstatnllilllllavll 276
                                        i +  + l+p++++ +++n+++  +++++                             +s + ++lil+++++v++
  gi|313117330|ref|YP_004044313.1| 221 VILLVARRLTPINSFFVVVNTLTGVGNTDSnfvdsiqyglqgeagyhvgalfgsgypiVLSPWVSVLILIAWIIVPI 297
                                       7888889*******************8777*********************************************** PP

                   ABC2_membrane_2 277 vlgyvlFkrkDl 288
                                       +++  +F r Dl
  gi|313117330|ref|YP_004044313.1| 298 AFASAVFSRLDL 309
                                       *********997 PP

  == domain 2  score: 75.7 bits;  conditional E-value: 7.8e-25
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                        ia++Ef d++rs    ll+ l+     ++ayl +l + +++   +i++ ++a    +a                 +
  gi|313117330|ref|YP_004044313.1| 361 PIARREFTDILRSLAAPLLFGLV-----VMAYLYSLTTISPNISSQIGQQLPAAVGQQA-----------------V 415
                                       79***********8776666554.....4567777777777777777777777444444.................3 PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                       ti+ +++pv+   +g+ +ia+E+e+gT++    +P sR ++l+gK  g   +   + v+++ ++++ +ai  +   +
  gi|313117330|ref|YP_004044313.1| 416 TIFGLVGPVF---LGYRSIAEERESGTIRYTAGLPPSRTSVLIGKGAGLWFA---LSVIIGYALIVCFAIGSIQTGS 486
                                       5777777776...8**************************************...********************** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp...... 226
                                       ++  ++  ++va+++++   + +a+ ++lSs++  + +aa  a ++++++++++++++  + +   g +++      
  gi|313117330|ref|YP_004044313.1| 487 FPSVAFSGTLVATIMYIG--TNTAIVVALSSFFS-RGVAAVSAAIVYLFFVLFWSGIHPIIWDSIFGYSYIiqpppp 560
                                       **************9999..77***********9.9**********************8866666666666788888 PP

                   ABC2_membrane_2 227 ....................................qeindflsllsptsayntllneilagsdlna.lgstatnll 266
                                                                            +i++ ++  +  +  + l+  ++ ++++   ++s +++++
  gi|313117330|ref|YP_004044313.1| 561 dslyfltrrlsprqavtvlwnwaigvgnsgssytmvLHIENAVTSPNLNALTHSLVVDVSYSDGQVPiILSPVASVG 637
                                       666666666666666666666666666666666666666666666666666666666666666544499******** PP

                   ABC2_membrane_2 267 illlllavllvlgyvlFkrkDl 288
                                       +l ++ +++++l++ +F++ Dl
  gi|313117330|ref|YP_004044313.1| 638 TLAVWGIIPFALALRRFQTSDL 659
                                       *******************997 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9  18.0     1e-05     0.045     168     343 ..      75     300 ..      54     302 .. 0.74
   2 !   23.9  18.4   4.3e-09   1.9e-05     163     289 ..     409     542 ..     385     651 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                   ABC2_membrane_3 168 liilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..lafgl....gipfgnl 238
                                       +++++++ + ++ +si++ ++s+ + +   +++++++++++  +g +l+ + ++l  ++   ++g      +p++ l
  gi|313117330|ref|YP_004044313.1|  75 VAFASYFAVPVAFRSIIHSRQSGNIRITAGTPLTRSEIIIGTAFGRGLALFCPVLMGVVgtAILGWnhygTLPVFLL 151
                                       445555555556679************************************99986555455788555566777777 PP

                   ABC2_membrane_3 239 glllllfllfglayialgyllsslfkns......etaqilifivil....llsgffgglfp....ledlp..salkw 299
                                       +   ++  lf+la++a ++++s+++ ++      +   ++++iv+     +  ++  ++ +    + ++p   +l +
  gi|313117330|ref|YP_004044313.1| 152 IGYTVVTALFILAVVATITAISAVVESTvhavacS---TVCVIVMAywtdIVAAIHQFITSqnvsIGQPPqsVILLV 225
                                       7777**********************996663333...444444445557666665555445655788886533445 PP

                   ABC2_membrane_3 300 ifsiiPffapglgllrli...tgdplwe..............................illsliilalfavvyllla 343
                                       + ++ P+++++++  +l    ++d  ++                               + s++il++ ++v +++a
  gi|313117330|ref|YP_004044313.1| 226 ARRLTPINSFFVVVNTLTgvgNTD--SNfvdsiqyglqgeagyhvgalfgsgypivlsPWVSVLILIAWIIVPIAFA 300
                                       566777777777776664433444..224558889999999999999999999999888888888888888877665 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.3e-09
                   ABC2_membrane_3 163 lvg..liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl...... 231
                                       +vg  ++ i+ +  +++   +si+eE+es+++      + s+++ +++k  g++++  +++  +l+++f++      
  gi|313117330|ref|YP_004044313.1| 409 AVGqqAVTIFGLVGPVFLGYRSIAEERESGTIRYTAGLPPSRTSVLIGKGAGLWFALSVIIGYALIVCFAIgsiqtg 485
                                       444566667777778888889********988776555558889**********************99999978886 PP

                   ABC2_membrane_3 232 gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp 289
                                       ++p   +  +l+  ++++ + +a++ +lss+f++ ++a +++++ ++ + +f+ g+ p
  gi|313117330|ref|YP_004044313.1| 486 SFPSVAFSGTLVATIMYIGTNTAIVVALSSFFSRGVAAVSAAIVYLF-FVLFWSGIHP 542
                                       66666888899************************888876666666.7777666644 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8  10.3    0.0026        12       1     177 [.      23     191 ..      23     193 .. 0.77
   2 ?   -2.7   0.3       1.1   5.1e+03     144     159 ..     286     301 ..     273     311 .. 0.51
   3 !   23.0   5.2   1.4e-08   6.2e-05      21     178 ..     376     533 ..     364     534 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0026
                   ABC2_membrane_4   1 liktEflKlkrskivwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgi.iasylifrEe 76 
                                       li+ Ef+ l r k +w++  +++lv    ++    +g++ + + ++   +++++ +   +   +++ +a ++i   +
  gi|313117330|ref|YP_004044313.1|  23 LIQREFWLLVRLKWLWIVTPVVVLVGNSFITP---FGNEVTVTGGWIAVAASETAV--AFASYFAVpVAFRSIIHSR 94 
                                       7999*********9999887777765544444...466666667777766666443..3444444446677888889 PP

                   ABC2_membrane_4  77 qndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavl 153
                                       q++ ++     P +r +++++  +   l  ++ +l    + v+ + ++g+  + + +v+ l+  +++++l+++++v+
  gi|313117330|ref|YP_004044313.1|  95 QSGNIRITAGTPLTRSEIIIGTAFGRGLALFCPVL----MGVVGTAILGWNHYGTLPVFLLIGYTVVTALFILAVVA 167
                                       ********************988888776444444....456666777888889999999999999999*9999999 PP

                   ABC2_membrane_4 154 piialvllkksyvlpliltlvyti 177
                                        i a++++ +s v +++ + v +i
  gi|313117330|ref|YP_004044313.1| 168 TITAISAVVESTVHAVACSTVCVI 191
                                       9*************9998888776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                   ABC2_membrane_4 144 lgllvffavlpiialv 159
                                       + +l++ +++pi + +
  gi|313117330|ref|YP_004044313.1| 286 VLILIAWIIVPIAFAS 301
                                       3333344444443333 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 1.4e-08
                   ABC2_membrane_4  21 aallv..pllallyfnllgktgldpaefysl.svfgftlllllplilgi.iasylifrEeqndtlknLltiPvsrtk 93 
                                       a+ll+  +++a ly+ +  +++++ +   +l +++g ++++++ l+  + ++ ++i +E++++t+++   +P srt+
  gi|313117330|ref|YP_004044313.1| 376 APLLFglVVMAYLYSLTTISPNISSQIGQQLpAAVGQQAVTIFGLVGPVfLGYRSIAEERESGTIRYTAGLPPSRTS 452
                                       3444311334555555555555554333332356666666666666666246789********************** PP

                   ABC2_membrane_4  94 lllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkksyvlpli 170
                                       +l++K + l +   +++  +++++++++ + +++  sv+    +   ++ +++++   ++ ++al+++++  v+++ 
  gi|313117330|ref|YP_004044313.1| 453 VLIGKGAGLWFALSVIIGYALIVCFAIGSIQTGSFPSVA----FSGTLVATIMYIGTNTAIVVALSSFFSRGVAAVS 525
                                       *****8866544333333444444555444444322222....2222222222222233344678999999999**9 PP

                   ABC2_membrane_4 171 ltlvytia 178
                                        ++vy ++
  gi|313117330|ref|YP_004044313.1| 526 AAIVYLFF 533
                                       99999986 PP

>> Ldr_toxin  Toxin Ldr, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0014       6.2      15      30 ..     125     140 ..     114     142 .. 0.82
   2 ?    2.5   0.0     0.034   1.5e+02       6      18 ..     191     203 ..     187     210 .. 0.82
   3 ?    0.3   0.0      0.17   7.7e+02      14      23 ..     374     383 ..     372     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHH CS
                         Ldr_toxin  15 AAPvlAGIlaaaIVnW 30 
                                         Pvl G++  aI +W
  gi|313117330|ref|YP_004044313.1| 125 FCPVLMGVVGTAILGW 140
                                       37************** PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHH CS
                         Ldr_toxin   6 laMaFWHDLAAPv 18 
                                       + Ma+W D+ A +
  gi|313117330|ref|YP_004044313.1| 191 IVMAYWTDIVAAI 203
                                       67******98866 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.17
                                       HHHHHHHHHH CS
                         Ldr_toxin  14 LAAPvlAGIl 23 
                                       LAAP+l G++
  gi|313117330|ref|YP_004044313.1| 374 LAAPLLFGLV 383
                                       9*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 3855.77
//
Query:       gi|313117331|ref|YP_004044314.1|  [L=300]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-28   99.6   0.0    3.8e-28   98.7   0.0    1.4  1  ABC_tran      ABC transporter
    7.5e-13   49.0   0.1    3.3e-07   30.4   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.5e-05   24.6   0.0    2.9e-05   23.7   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00039   21.1   0.0    0.00089   19.9   0.0    1.6  1  DUF4162       Domain of unknown function (DUF4162)
     0.0023   18.5   0.2     0.0038   17.7   0.2    1.3  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.024   14.5   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.019   14.7   0.0      0.035   13.8   0.0    1.5  1  AAA_30        AAA domain
      0.025   14.1   0.0      0.044   13.3   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
      0.029   13.8   0.0       0.11   11.9   0.0    1.8  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.053   13.5   0.1       0.09   12.7   0.1    1.4  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
       0.06   12.3   0.0       0.22   10.5   0.0    1.8  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.066   12.8   0.0       0.11   12.1   0.0    1.4  1  SRP54         SRP54-type protein, GTPase domain
      0.085   12.4   0.0       0.14   11.7   0.0    1.4  1  AAA_27        AAA domain
      0.092   12.6   0.0       0.25   11.2   0.0    1.7  1  DUF3215       Protein of unknown function (DUF3215)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0   2.9e-31   3.8e-28       2     136 ..      20     157 ..      19     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 2.9e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + ++l++kege+++++G+nGaGKSt + +l++  +pt+G+i++ g d +e + +++++++g+lp +  +  +lt r+
  gi|313117331|ref|YP_004044314.1|  20 DGLNLSVKEGEVYGFLGPNGAGKSTTIDALMNYIQPTSGQIEIFGLDARE-DASQVHSRVGILPDQFDVYARLTGRQ 95 
                                       789*********************************************99.99********************9999 PP

                                       H........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +          d + +++l+++gl++ kd+++    +s+S+G++qr+ la+al+ +p+ll+lDEp+
  gi|313117331|ref|YP_004044314.1|  96 HiefvantkGVDINTDTLLNRVGLEDAKDSPA----QSYSKGMQQRLGLAMALVGDPDLLILDEPF 157
                                       999987755555559***********999999....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   4.2e-06    0.0054       3      34 ..      33      58 ..      31     108 .. 0.73
   2 !   30.4   0.0   2.6e-10   3.3e-07     227     297 ..     120     187 ..      90     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.2e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltd 34
                                      ++ GpNg+GKS+ +dal      +++++++  
  gi|313117331|ref|YP_004044314.1| 33 GFLGPNGAGKSTTIDAL------MNYIQPTSG 58
                                      689**************......444444433 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 2.6e-10
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +d ++ pa + S G+++ l+l+ al  ++   +ll++DEp +gL+P  +  + +++   +++g+ v++++H
  gi|313117331|ref|YP_004044314.1| 120 EDAKDSPAQSYSKGMQQRLGLAMALVGDP---DLLILDEPFSGLDPFGTQLVRDIVMTQTNRGTTVFFSSH 187
                                       46677789999****************99...9*************6666666666555555********* PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.3e-08   2.9e-05      15      50 ..      22      57 ..      17      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.3e-08
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                        +++++ +++ + Gp+G+GKST +DA++  + p++
  gi|313117331|ref|YP_004044314.1| 22 LNLSVKEGEVYGFLGPNGAGKSTTIDALMNYIQPTS 57
                                      5566775558999***************99888876 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     7e-07   0.00089       1      80 [.     211     297 ..     211     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7e-07
                                       E-HHHHHTTS.-SSEEEEE.....-------..---EEEE-TT.S-EEEEE-----------------EEEEEEEE- CS
                           DUF4162   1 GtleeiKrsy.gknrieve.....adaeelleepgveeveeeg.gelelkledeeaanellkaltsgveirsFeeee 70 
                                       G+++ei++s   k r++v      ++  e++++++v++v+ +g g+l++  e+ ++  ++l++l+s  ei+ F +e 
  gi|313117331|ref|YP_004044314.1| 211 GKPREIRASAdVKPRLVVAlaqpkKGLTEVQDIDSVSDVNIDGdGYLSVVSESAHVFTTVLNRLDSTNEIQWFDVEF 287
                                       99********8899999999754444666666677777788884555555556************************ PP

                                       --HHHHHHHH CS
                           DUF4162  71 PsLndIFiek 80 
                                        +++d Fie 
  gi|313117331|ref|YP_004044314.1| 288 GTIEDAFIEN 297
                                       ********95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2     3e-06    0.0038      20      39 ..      30      49 ..       6      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3e-06
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       ++ + GpNGaGK+T +dA+
  gi|313117331|ref|YP_004044314.1| 30 EVYGFLGPNGAGKSTTIDAL 49
                                      577899*************8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.9e-05     0.024      75     127 ..       4      57 ..       1      64 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                       TTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  75 lgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       ++++ ++ + k++++++ l+  +k+ ++  ++G+ G+GKSt i+al++  +   
  gi|313117331|ref|YP_004044314.1|   4 IDITNFTKEYKSTTAVDGLNLSVKEgEVYGFLGPNGAGKSTTIDALMNYIQPTS 57 
                                       566666777778888999999998889***************999988765555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.7e-05     0.035      19      82 ..      30     114 ..      22     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgka.AkvLaeelgi...eastiakllkrlk.......... 81 
                                        v    Gp G+GK+t++ al + ++   g++ ++   ++  A ++   +gi   + +  a+l+ r+           
  gi|313117331|ref|YP_004044314.1|  30 EVYGFLGPNGAGKSTTIDALMNYIQPTSGQIEIFGLDAREdASQVHSRVGIlpdQFDVYARLTGRQHiefvantkgv 106
                                       477788****************9999976777666665532555666777655555555555555555555555444 PP

                            AAA_30  82 .......g 82 
                                               
  gi|313117331|ref|YP_004044314.1| 107 dintdtlL 114
                                       44444440 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.4e-05     0.044      27      79 ..      23      75 ..      11      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlq 79
                                      +l +k++    + Gp G GK+++i  l++ +++++ ++ ++ + a+ +a+q+ 
  gi|313117331|ref|YP_004044314.1| 23 NLSVKEGEVYGFLGPNGAGKSTTIDALMNYIQPTSGQIEIFGLDAREDASQVH 75
                                      667788888889********************************999999986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.5e-05      0.11      25      45 ..      30      50 ..       1      59 [. 0.67
   2 ?   -1.0   0.0      0.78   9.9e+02     151     203 ..     140     193 ..     134     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.5e-05
                                      SEEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAil 45
                                      ++   +GpNG+GKs  +dA++
  gi|313117331|ref|YP_004044314.1| 30 EVYGFLGPNGAGKSTTIDALM 50
                                      355678*************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.78
                                       HHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                             SMC_N 151 fAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemle 203
                                       +A+  v    l +lDe  + LD   ++ v +++ +++++ + ++  s+  e++e
  gi|313117331|ref|YP_004044314.1| 140 LAMALVGDPDLLILDEPFSGLDPFGTQLVRDIVMTQTNRgTTVFFSSHVLEQVE 193
                                       55666666668999999999**99999999999988766466666666555554 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     7e-05      0.09       1      17 [.     206     222 ..     206     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-05
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrV 17 
                                       ++ AeG+P E+r+  +V
  gi|313117331|ref|YP_004044314.1| 206 QLVAEGKPREIRASADV 222
                                       679**********9888 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00017      0.22      28      66 ..      28      66 ..       5      85 .. 0.81
   2 ?   -1.2   0.0      0.63   8.1e+02     161     192 ..     233     270 ..     221     284 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                      + +v G+ G  GaGkst+++al+  ++    ++ +  +D
  gi|313117331|ref|YP_004044314.1| 28 EGEVYGFLGPNGAGKSTTIDALMNYIQPTSGQIEIFGLD 66
                                      56789*****************99988777777777666 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.63
                                       --CCCHHH-SEEEEE---......HHHHHHHHHHHHHH CS
                              MeaB 161 ikkGileiaDiivvnkaD......kkeaekaarelraa 192
                                        kkG+ e+ Di  v   +      ++ ++++a+ ++++
  gi|313117331|ref|YP_004044314.1| 233 PKKGLTEVQDIDSVSDVNidgdgyLSVVSESAHVFTTV 270
                                       58999999998766543322334444455555555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.9e-05      0.11       4      39 ..      32      67 ..      30     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      + ++G++GaGK tt+  L ++++    ++ +  +D 
  gi|313117331|ref|YP_004044314.1| 32 YGFLGPNGAGKSTTIDALMNYIQPTSGQIEIFGLDA 67
                                      5689******************99988888887775 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.14      25      49 ..      28      52 ..      18      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                            AAA_27 25 eadlhliyGpNEAGKstalrAisdl 49
                                      e ++   +GpN AGKst+++A+ + 
  gi|313117331|ref|YP_004044314.1| 28 EGEVYGFLGPNGAGKSTTIDALMNY 52
                                      55555568*************9875 PP

>> DUF3215  Protein of unknown function (DUF3215)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.25      27      58 ..     236     268 ..     223     278 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                       GGCTHHHHHHHCCHH-STCCE.EEEESSSEEEE CS
                           DUF3215  27 GkerieDilelsqveldkeGy.avledsdvlvh 58 
                                       G ++++Di  +s+v++d +Gy +v+++s ++  
  gi|313117331|ref|YP_004044314.1| 236 GLTEVQDIDSVSDVNIDGDGYlSVVSESAHVFT 268
                                       4589*****************988888766543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2205.46
//
Query:       gi|313117332|ref|YP_004044315.1|  [L=203]
Description: hypothetical protein Hbor_31190 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1386.07
//
Query:       gi|313117333|ref|YP_004044316.1|  [L=84]
Description: hypothetical protein Hbor_31200 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 560.72
//
Query:       gi|313117334|ref|YP_004044317.1|  [L=212]
Description: hypothetical protein Hbor_31210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1381.06
//
Query:       gi|313117335|ref|YP_004044318.1|  [L=392]
Description: cell division GTPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-28   99.4   0.0    4.4e-28   98.8   0.0    1.3  1  Tubulin    Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
      0.048   12.8   1.3       0.18   11.0   0.3    2.2  3  Tubulin_2  Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   0.0   4.9e-32   4.4e-28       2     194 ..       3     174 ..       2     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 4.9e-32
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE- CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklll 78 
                                       ++ +g+Gq+G++i++++ e    e                + ++++i  +va++t + +l+e+       +++++l+
  gi|313117335|ref|YP_004044318.1|   3 LVLLGIGQAGGKIVDRFLE---YER---------------QTEQDFIEGAVAFNTARADLKELSHV---PEHHRQLF 58 
                                       6899***************...442...............44689999*******77777776665...566999** PP

                                       -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE...SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEE CS
                           Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcds..lqgffitaslgGGTGSGlgpvilevlkeeypkalvvtv 153
                                       g+ +a+++g+g++ e ++ +ae+ ++++ +++++  +  +++f+++a+lgGGTGSG++pv++  l + y +++v++ 
  gi|313117335|ref|YP_004044318.1|  59 GEVDAKGHGVGADTEFAADLAEQDAQQLIRSLDDIPTsrADAFLVVAGLGGGTGSGAAPVLANELDRIY-EKPVYGL 134
                                       *********************************865544999**************************9.779**** PP

                                       EEE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHC CS
                           Tubulin 154 vvlPsefsevvvepynailalkelieesdavividNdaLlk 194
                                        vlP ++ e+ v  yna+ + ++l++++d ++++dNd +lk
  gi|313117335|ref|YP_004044318.1| 135 GVLPASE-EEDVFAYNAVRSFRTLVNHVDNLLLFDNDTWLK 174
                                       *****98.99999************************9987 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0     0.076   6.9e+02       2      48 ..       5      50 ..       4      93 .. 0.58
   2 ?   11.0   0.3     2e-05      0.18     157     186 ..     100     129 ..      75     164 .. 0.72
   3 ?   -1.7   0.0      0.14   1.3e+03     318     333 ..     216     242 ..     170     253 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.076
                         Tubulin_2  2 viGLGGtGgkvlaelrrrlreelgslelpdkvqFlyiDtdeneknrl 48
                                      + G+G  Ggk+++++ +  r++  ++  +  v+F  +  d +e+++ 
  gi|313117335|ref|YP_004044318.1|  5 LLGIGQAGGKIVDRFLEYERQTE-QDFIEGAVAFNTARADLKELSHV 50
                                      67888888888888755444444.33344555554444444444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2e-05
                         Tubulin_2 157 nvfVvgSLaGGTGSGiflDvayllrkilke 186
                                        + Vv +L GGTGSG +  +a  l  i+++
  gi|313117335|ref|YP_004044318.1| 100 AFLVVAGLGGGTGSGAAPVLANELDRIYEK 129
                                       578************987776666666655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.14
                         Tubulin_2 318 a...........ystfGlasieiPvde 333
                                       +           +st+G as ++P d+
  gi|313117335|ref|YP_004044318.1| 216 SseiintlrgggVSTIGHASSTLPTDD 242
                                       123334467778999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2627.20
//
Query:       gi|313117336|ref|YP_004044319.1|  [L=334]
Description: membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.3e-115  385.0   1.3   2.7e-115  384.8   1.3    1.0  1  DUF1616   Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
        2.7    7.6  10.1        5.8    6.5   0.1    3.0  2  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.8   1.3    3e-119  2.7e-115       1     293 []      21     329 ..      21     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 384.8 bits;  conditional E-value: 3e-119
                           DUF1616   1 vlvlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPe...............krdidgieRlaLSfgl 62 
                                       vlvl++l+++a+++pv++ tp+Ri+lglp +Lf+PGYal+aaLFPe               +++idgieR+aLSfgl
  gi|313117336|ref|YP_004044319.1|  21 VLVLVVLTVAAATIPVIKGTPIRIILGLPYLLFIPGYALVAALFPEaaerstrmddneteiESGIDGIERVALSFGL 97 
                                       689************************************************************************** PP

                           DUF1616  63 SiaivpliglvlnvtpwgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleeksesrldk 139
                                       Sia+vpligl+ln+tpwg+rl pi++++s+ft++l++vA  rR++l+e +rf vp++++i+++k+el+  ++sr+d+
  gi|313117336|ref|YP_004044319.1|  98 SIAVVPLIGLLLNFTPWGMRLIPIVAIVSAFTVILTFVASRRRQALNETDRFVVPYERWITDAKAELFA-PDSRADA 173
                                       *********************************************************************.899**** PP

                           DUF1616 140 alnvlLvvsivlavaalgyavvaPkegekfTelyllgedgd.elvaenypteltagesqevivgieNhEheevnYtv 215
                                       alnvlLvvsi+la++++gya+ +P+ ge+f+elyll+ed++ +lva++ypte+ +ge +++ +gi NhE++ev+Ytv
  gi|313117336|ref|YP_004044319.1| 174 ALNVLLVVSILLAAGSTGYAIFVPPPGEQFSELYLLTEDESgDLVADEYPTEFIRGEAKPLHIGIGNHEGREVQYTV 250
                                       ***************************************************************************** PP

                           DUF1616 216 vvllqev.tdeeevevlerteldrrevtladnetweqelevepeatgenlrleflLYkdevpeeptteeayrslhlw 291
                                       v++l++v  +++ + v ertel+r + t+ +n tw+++ +v+p++tg++lrl++lLYk+++pe+pt+++ayr+ hlw
  gi|313117336|ref|YP_004044319.1| 251 VAQLHRVeRQNNATVVRERTELHRYTQTVGANSTWSTKTTVSPSMTGDRLRLTYLLYKGSAPENPTIDNAYRENHLW 327
                                       *******64444555679*********************************************************** PP

                           DUF1616 292 Vn 293
                                       Vn
  gi|313117336|ref|YP_004044319.1| 328 VN 329
                                       *7 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1   0.00064       5.8       3      75 ..      14      85 ..      12      94 .. 0.73
   2 ?    1.7   5.9      0.02   1.8e+02       7     141 ..     121     315 ..      91     317 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00064
                           DUF4131  3 lplalvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqllesgqeviveGvv 75
                                      lp  l ++++l++l+++++ +   + ++ +++l l +ll++ +++++ a+ p+a + s+ ++ ++e+++e  +
  gi|313117336|ref|YP_004044319.1| 14 LPADLGAVLVLVVLTVAAATIPVIKGTPIRIILGLPYLLFIPGYALVAALFPEAAERSTRMD-DNETEIESGI 85
                                      56666667777777777777766677777777777788888888999999999999999998.7888777655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.02
                           DUF4131   7 lvllalllllllllllllrr.......................rprrrv............llllllllllallgfa 48 
                                       +v++++++ ++l+ ++  rr                            +            ll++++ll++++ g+a
  gi|313117336|ref|YP_004044319.1| 121 IVAIVSAFTVILTFVASRRRqalnetdrfvvpyerwitdakaeL----FapdsradaalnvLLVVSILLAAGSTGYA 193
                                       45555555555555555444666665555555544444444440....04444445555558888888888888888 PP

                           DUF4131  49 lrapqpnandlsqlles....gqevi.......veGvv......aslpeltgsgtrfvlevervlsagktkpvsgrv 108
                                       + +p p+++  + +l      g  v+       ++G+         + e ++ +  +v++ +rv ++++   v++r 
  gi|313117336|ref|YP_004044319.1| 194 IFVPPPGEQFSELYLLTedesGDLVAdeyptefIRGEAkplhigIGNHEGREVQYTVVAQLHRVERQNNATVVRERT 270
                                       88888888444444443557633333555555644444444433333333333334555555555555555555555 PP

                           DUF4131 109 lvtvpkspae............glrpGdrlrltgrlkrprpatNp 141
                                        +  + ++                  Gdrlrlt  l++ +++ Np
  gi|313117336|ref|YP_004044319.1| 271 ELHRYTQTVGanstwstkttvsPSMTGDRLRLTYLLYKGSAPENP 315
                                       555444444444555555533344488999999999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 2346.72
//
Query:       gi|313117337|ref|YP_004044320.1|  [L=736]
Description: hypothetical protein Hbor_31240 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-05   25.4  18.1      0.023   14.9   3.8    4.7  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    2.8e-05   24.2   2.6      0.047   13.8   0.2    3.2  2  MG4              Macroglobulin domain MG4
    6.5e-05   23.1   1.2    0.00046   20.4   1.2    2.6  1  DUF4129          Domain of unknown function (DUF4129)
     0.0021   18.0   3.3        2.4    8.2   0.0    4.0  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
     0.0072   16.5   0.2      0.017   15.3   0.2    1.5  1  CaMBD            Calmodulin binding domain
  ------ inclusion threshold ------
       0.79   10.3   3.2        9.3    6.9   0.0    3.1  3  EF-G-binding_N   Elongation factor G-binding protein, N-termi


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.018        55       4      43 ..     281     318 ..     278     364 .. 0.73
   2 ?   -2.1   0.0       1.6   4.9e+03      15      28 ..     357     370 ..     349     374 .. 0.73
   3 !   14.9   3.8   7.8e-06     0.023       3      51 ..     379     422 ..     377     458 .. 0.78
   4 !   12.6   2.0   4.2e-05      0.13       1      54 [.     472     527 ..     472     547 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.018
                   CarboxypepD_reg   4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlr 43 
                                       Gr      +++a+ ++ v    +++  +t+tda+G+f l 
  gi|313117337|ref|YP_004044320.1| 281 GRLATNESKAVANRAINVL--VGEQLLRTQTDAEGRFDLV 318
                                       6666666778888888888..5677899*********886 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                   CarboxypepD_reg  15 agatVtvtnadtgt 28 
                                       ++a+Vtv+++d+++
  gi|313117337|ref|YP_004044320.1| 357 TNASVTVSRSDETA 370
                                       57888888766655 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 7.8e-06
                   CarboxypepD_reg   3 sGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtys 51 
                                       +GrV  a g+ +a++ V+v+   ++ ++++tt a+G+f+++ lp  + s
  gi|313117337|ref|YP_004044320.1| 379 TGRVS-AAGRDVANVPVRVS--LGERSRTVTTTANGTFSVP-LPV-PAS 422
                                       68887.689***********..68899*************9.654.333 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 4.2e-05
                   CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtgtvastttdadGafrlr.glpp..gtysvtv 54 
                                       +isG+ t  sg+p++  ++ ++  +++tv++  tda G  + + gl+   g+ +vt+
  gi|313117337|ref|YP_004044320.1| 472 QISGQLTTDSGQPVSSQQIQIR-VGGTTVKTLSTDARGMVQSTiGLEEanGSVTVTA 527
                                       69********************.789999*********7765545666445555555 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2   0.00051       1.5      25      67 ..     384     422 ..     378     458 .. 0.80
   2 !   13.8   0.2   1.6e-05     0.047      22      78 ..     477     530 ..     472     544 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00051
                               MG4  25 pdgspaknvpVkiealkseteekeslttdedGtakfsintped 67 
                                       + g+ ++nvpV++++ +   e+ +++tt ++Gt ++ + +p++
  gi|313117337|ref|YP_004044320.1| 384 AAGRDVANVPVRVSL-G---ERSRTVTTTANGTFSVPLPVPAS 422
                                       568899*********.5...68999********9998888875 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.6e-05
                               MG4  22 vkdpdgspaknvpVkiealkseteekeslttdedGtakfsintpedaksltitvktk 78 
                                       ++   g+p++  +++i++ +   +  ++l td+ G+++ +i ++e + s+t+t+ ++
  gi|313117337|ref|YP_004044320.1| 477 LTTDSGQPVSSQQIQIRV-G--GTTVKTLSTDARGMVQSTIGLEEANGSVTVTAAYD 530
                                       67789*************.4..6888999***********************99886 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.2   1.5e-07   0.00046      18      66 ..     674     724 ..     667     727 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                           DUF4129  18 pgeTprEyarrv..riapspaaalaalaelfeearYGgrpasaeeyrrlve 66 
                                        + T  E++++v  +++ + +a + +l+ ++e+a Y+++p+ ++ + +l+e
  gi|313117337|ref|YP_004044320.1| 674 KSLTHWELLEHVraEASEDVSAIFTELTSAYEQAAYAPEPVQRDRALELLE 724
                                       678*********87777778999999******************9988876 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00081       2.4       5      39 ..     283     318 ..     279     325 .. 0.74
   2 !    6.2   0.1    0.0033        10       2      63 ..     379     435 ..     378     466 .. 0.58
   3 ?    1.0   0.7      0.15   4.4e+02       1      34 [.     473     508 ..     473     526 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00081
                   CarbopepD_reg_2   5 Vvdketkeplpg..atVyvkgtkkgtvTdenGnFelk 39 
                                         ++e+ ++++   ++V+v ++   t+Td++G+F l 
  gi|313117337|ref|YP_004044320.1| 283 LATNES-KAVANraINVLVGEQLLRTQTDAEGRFDLV 318
                                       555554.344443369******************995 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0033
                   CarbopepD_reg_2   2 sGtVvdketkeplpg..atVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvt 63 
                                       +G+V+ ++    ++   + V++ + ++ ++T +nG+F++  lp     L   +vG +t++  v 
  gi|313117337|ref|YP_004044320.1| 379 TGRVSAAGR--DVANvpVRVSLGERSRTVTTTANGTFSVP-LPVP-ASL---AVGTQTANAAVA 435
                                       688887765..44442268888999999**********97.4432.222...344444444444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.15
                   CarbopepD_reg_2   1 isGtVvdketkeplpg..atVyvkgtkkgtv.TdenG 34 
                                       isG+ ++++ ++p+    +++ v gt+++t  Td+ G
  gi|313117337|ref|YP_004044320.1| 473 ISGQLTTDS-GQPVSSqqIQIRVGGTTVKTLsTDARG 508
                                       799999865.689987335666688887775489888 PP

>> CaMBD  Calmodulin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   5.6e-06     0.017      34      67 ..     159     192 ..     153     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.6e-06
                             CaMBD  34 qsrvrkhqRklLqAihrlRkvkmeqrklnDqant 67 
                                        +++r+ qR + +A++ +R++k +  + +++ nt
  gi|313117337|ref|YP_004044320.1| 159 FNKTRTQQRSYIEAVNDFRETKSKYERARESGNT 192
                                       6789**************************9998 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.068     2e+02      45      72 ..     159     187 ..     147     189 .. 0.82
   2 ?   -2.8   0.1       3.1   9.3e+03      46      59 ..     242     255 ..     215     270 .. 0.55
   3 ?    6.9   0.0    0.0031       9.3       7      52 ..     659     704 ..     657     710 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.068
                    EF-G-binding_N  45 fpelseeqkelLeqiddik.tkekaeklL 72 
                                       f++  ++q++++e+++d + tk+k e++ 
  gi|313117337|ref|YP_004044320.1| 159 FNKTRTQQRSYIEAVNDFReTKSKYERAR 187
                                       78888999***********9999999875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.1
                    EF-G-binding_N  46 pelseeqkelLeqi 59 
                                       +e ++e+ e ++++
  gi|313117337|ref|YP_004044320.1| 242 VENTTETSEQIREL 255
                                       22333333333333 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0031
                    EF-G-binding_N   7 YnfIkkqveqllnayrsvnDkkvveavkalaaekIlelfpelseeq 52 
                                       Y  I+ ++++ l + +s +  + +e v+a+a e++  +f+el+ + 
  gi|313117337|ref|YP_004044320.1| 659 YETIRTKMTDSLGVEKSLTHWELLEHVRAEASEDVSAIFTELTSAY 704
                                       9999**************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 4442.11
//
Query:       gi|313117338|ref|YP_004044321.1|  [L=480]
Description: hypothetical protein Hbor_31250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-19   70.3   0.0    2.8e-19   69.2   0.0    1.6  1  DUF58     Protein of unknown function DUF58
     0.0015   19.2   0.0     0.0038   17.8   0.0    1.7  1  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.0   3.1e-23   2.8e-19       1      86 []     195     280 ..     195     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 3.1e-23
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarql 77 
                                       gl++a++R Yv gD+++rIdWkatAR++++++r++e  + r++ l++d +++   g+ g++kl+ + ++a++ ++++
  gi|313117338|ref|YP_004044321.1| 195 GLEPAEIRRYVYGDDISRIDWKATARLNHPHIRDYEMPTVRQTALIVDHRASTADGTPGETKLDFLREIALAFVNSA 271
                                       689***********************************************************************999 PP

                             DUF58  78 ldegdrvgl 86 
                                        +  d++gl
  gi|313117338|ref|YP_004044321.1| 272 DSLDDPIGL 280
                                       988888876 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.3e-07    0.0038       2      80 ..     238     322 ..     237     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.3e-07
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallksl.p.gdrvglvtfsd.gpevliplt...kdkakilnalrnleak 72 
                                        +++D  +S ++g+ g+t+l+ +++++ a+++s    +d +gl t++d g +  +p+    + +++i++ lrnle++
  gi|313117338|ref|YP_004044321.1| 238 ALIVDHRASTADGTPGETKLDFLREIALAFVNSAdSlDDPIGLYTVGDeGTTNTAPPRaseRQYRSIRSTLRNLEPT 314
                                       68999999************************9854689*********667777888544588*************9 PP

                             VWA_2  73 gggtnlaa 80 
                                       +g++  a+
  gi|313117338|ref|YP_004044321.1| 315 TGESGAAD 322
                                       77765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 3491.70
//
Query:       gi|313117339|ref|YP_004044322.1|  [L=157]
Description: hypothetical protein Hbor_31260 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        3.9    6.7   6.8        1.2    8.4   2.2    1.9  2  7tm_1       7 transmembrane receptor (rhodopsin family)


Domain annotation for each model (and alignments):
>> 7tm_1  7 transmembrane receptor (rhodopsin family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2     0.016   2.8e+02     207     230 ..      38      61 ..      34      77 .. 0.78
   2 ?    8.4   2.2   6.7e-05       1.2      18      68 ..      96     142 ..      82     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                             7tm_1 207 lgivvavfivcwlPftiiyllqal 230
                                       l+ v++  +v+w+P  +++   a+
  gi|313117339|ref|YP_004044322.1|  38 LLSVLVGIAVAWTPRVFAVAFGAV 61 
                                       677888899999999988888777 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHHHHHHHHHCHHHHHHHHHCHSSCHSHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             7tm_1  18 stnyfilsLaiaDlllgllvlpfaivyelttgewlfgevlCklwlsldvfl 68 
                                           +il+ a + +ll++l + + +    tt+ wl+g +lC l  + ++++
  gi|313117339|ref|YP_004044322.1|  96 WRRALILNIAACAILLSVLAVSWQL----TTNLWLLGAILCCLCAVAFYTI 142
                                       5567999999999999886666555....5677********9999888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 997.83
//
Query:       gi|313117340|ref|YP_004044323.1|  [L=303]
Description: hypothetical protein Hbor_31270 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1844.88
//
Query:       gi|313117341|ref|YP_004044324.1|  [L=334]
Description: MoxR-like ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-61  205.3   0.5    6.3e-61  204.0   0.2    1.8  2  AAA_3            ATPase family associated with various cellul
    5.2e-20   71.1   0.2    1.3e-19   69.8   0.2    1.7  1  AAA_lid_2        AAA lid domain
    1.7e-13   50.7   0.0    3.1e-13   49.9   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    8.1e-06   25.4   0.5     0.0081   15.6   0.1    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    8.1e-06   25.1   0.0    1.3e-05   24.5   0.0    1.2  1  MCM              MCM P-loop domain
    3.7e-05   23.5   0.1    0.00017   21.3   0.1    1.9  1  Sigma54_activat  Sigma-54 interaction domain
    0.00012   21.8   0.2     0.0013   18.5   0.2    2.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00026   21.4   1.4    0.00055   20.4   0.2    2.1  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.056   13.8   0.1       0.31   11.4   0.1    2.1  2  AAA_16           AAA ATPase domain
      0.065   12.9   1.2       0.55    9.9   1.2    2.3  1  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.0   0.2   3.5e-64   6.3e-61       1     130 [.      38     167 ..      38     168 .. 0.99
   2 ?   -2.9   0.0       3.2   5.7e+03       8      25 ..     270     287 ..     267     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 204.0 bits;  conditional E-value: 3.5e-64
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       h+llegvPG+akt+l+ a+a++ +l+ +riq+tpdllP+di+Gt++++e++  fe+++Gpvf+nl++adeinra+pk
  gi|313117341|ref|YP_004044324.1|  38 HLLLEGVPGVAKTTLAAAFAQTTGLQGRRIQMTPDLLPADITGTKIYREDTGAFELERGPVFSNLVIADEINRATPK 114
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                       tqsalleam+e+qvt+eget +lp+pf+v+atqnPie+eGt+ lpeaq drf 
  gi|313117341|ref|YP_004044324.1| 115 TQSALLEAMQETQVTIEGETLNLPTPFMVVATQNPIEMEGTFGLPEAQRDRFQ 167
                                       ****************************************************7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                             AAA_3   8 PGlaktllvkalakaldl 25 
                                       P   ktl+v+ala+ l l
  gi|313117341|ref|YP_004044324.1| 270 PDDVKTLAVSALAHRLVL 287
                                       666799999999988765 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.2     7e-23   1.3e-19       5      71 ..     236     303 ..     232     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 7e-23
                         AAA_lid_2   5 ahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeive 71 
                                       + + ++ g+s+r ++l+ll+aA+A+Aa+egr+yV+p+Dvk++a  +LaHRl+   ++e  +++ e+i+e
  gi|313117341|ref|YP_004044324.1| 236 ETPDVSHGISPR-GSLHLLQAAKAHAAIEGRHYVIPDDVKTLAVSALAHRLVlsTDAEIGDVEPEAIIE 303
                                       5678999*****.***************************************98888877788888877 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   1.7e-16   3.1e-13       1     138 []      38     166 ..      38     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.7e-16
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       ++lL G pG++K++la  +a+ ++ +   +q+t d+ ++d++g   ++   g  +l+ +p+      + +++ DE++
  gi|313117341|ref|YP_004044324.1|  38 HLLLEGVPGVAKTTLAAAFAQTTGLQGRRIQMTPDLLPADITGTKIYRedTGAFELERGPVF-----SNLVIADEIN 109
                                       79******************************************9999889999999*****.....99******** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra ++++++Ll  + e ++   eg +l    +      f+v+at np +  +   l +a r+Rf
  gi|313117341|ref|YP_004044324.1| 110 RATPKTQSALLEAMQETQVT-IEGETLNLPTP------FMVVATQNPIEmEGTFGLPEAQRDRF 166
                                       ******************99.77888887777......***********999999999999998 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.5e-06    0.0081       5      43 ..      19      57 ..      16      62 .. 0.92
   2 !    7.8   0.0     0.001       1.9     110     160 ..     103     151 ..      98     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.5e-06
                      Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlp 43
                                      ++Gqe+a + l+i+   + +lll G pG  Kt la++++
  gi|313117341|ref|YP_004044324.1| 19 LIGQEDALKRLTISLLTQSHLLLEGVPGVAKTTLAAAFA 57
                                      58*********************************9875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.001
                      Mg_chelatase 110 LfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcp 160
                                       ++ DE+   + k+  +L e +++++vti+   ++++ p+ f++va+ Np  
  gi|313117341|ref|YP_004044324.1| 103 VIADEINRATPKTQSALLEAMQETQVTIEG--ETLNLPTPFMVVATQNPIE 151
                                       5679************************85..67888***********975 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     7e-09   1.3e-05      48     175 ..      27     151 ..       9     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7e-09
                                       BSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS..SSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTT CS
                               MCM  48 ledktklrgdinvllvgdpgtaKsqlLkyvekla..pravytsgkgssaagLtaavvrdeetgefvleaGalvladk 122
                                       ++  ++l ++ ++ll g pg+aK++l  + ++++  +            a++t +    e+tg f le G +     
  gi|313117341|ref|YP_004044324.1|  27 KRLTISLLTQSHLLLEGVPGVAKTTLAAAFAQTTglQGRRIQMTPDLLPADITGTKIYREDTGAFELERGPVFSN-- 101
                                       4445678899****************9988776521344455556677899999999999**********98764.. PP

                                       SEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                               MCM 123 GvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                        +++ De+++ + +++sal+Eam + +++i   G +  L++   v+a  np++
  gi|313117341|ref|YP_004044324.1| 102 -LVIADEINRATPKTQSALLEAMQETQVTIE--GETLNLPTPFMVVATQNPIE 151
                                       .8999************************98..55689999999******984 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   9.7e-08   0.00017      11     142 ..      25     148 ..      19     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.7e-08
                                       HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEH CS
                   Sigma54_activat  11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkG 87 
                                       +l++++    t++++l++G  G+ K++la a  +++  + ++ +++    +p+++  ++++    GaF      ++G
  gi|313117341|ref|YP_004044324.1|  25 ALKRLTISLLTQSHLLLEGVPGVAKTTLAAAFAQTTGLQ-GRRIQMTPDLLPADITGTKIYREDTGAFE----LERG 96 
                                       5566666778999****************9988877755.55788888899999999999999988885....4455 PP

                                       HHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  88 lfekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                        +       +  Dei++ ++++Q+ Ll+++qe +v+  G++ + ++ ++++a+ n
  gi|313117341|ref|YP_004044324.1|  97 PVF---SNLVIADEINRATPKTQSALLEAMQETQVTIEGETLNLPTPFMVVATQN 148
                                       554...357889********************************99998886544 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2     7e-07    0.0013      33     115 ..      36     130 ..      11     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7e-07
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklk.itsgPvlekagdlaallt........nleek....dvlfideihrl 96 
                                         h+ll G PG+ kttla+  a+  g + + i  +P l  ++d+++           +le++    +++  dei r 
  gi|313117341|ref|YP_004044324.1|  36 QSHLLLEGVPGVAKTTLAAAFAQTTGLQGRrIQMTPDLL-PADITGTKIyredtgafELERGpvfsNLVIADEINRA 111
                                       57*********************9987754145556553.4444443211111111145554112255677999999 PP

                            RuvB_N  97 sraveevlysamedfrldi 115
                                       +++++  l  am++ ++ i
  gi|313117341|ref|YP_004044324.1| 112 TPKTQSALLEAMQETQVTI 130
                                       9999999999999988766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   3.1e-07   0.00055       1     130 [.      39     172 ..      39     174 .. 0.72
   2 ?   -3.9   0.1       9.7   1.7e+04      11      22 ..     274     285 ..     274     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.1e-07
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHH.HHHHHHHHHHHHTS.TSEEEEEETGGGHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvgese.kkirelfkeakeka.kpsilfiDEidalaks 73 
                                       +ll G pG+ KT+la a a+++g +  +i++ ++ll  ++ g +  ++  + f+  ++       ++ DEi + +++
  gi|313117341|ref|YP_004044324.1|  39 LLLEGVPGVAKTTLAAAFAQTTGLQGRRIQMtPDLLpADITGTKIyREDTGAFEL-ERGPvFSNLVIADEINRATPK 114
                                       699*******************988777765246664444443330222333333.333243378999*******99 PP

                                       HTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEET CS
                               AAA  74 rsgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkiei 130
                                                   +++Ll+++++ +            +++v+++ n         l++a + +Rf+ ki i
  gi|313117341|ref|YP_004044324.1| 115 T-----------QSALLEAMQETQVTiegetlnlPTPFMVVATQNPiemegTFGLPEAQR-DRFQFKIAI 172
                                       9...........999999999999999999999866688888888844433344888888.999988876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9.7
                                       HHHHHHHHHHHH CS
                               AAA  11 KTllakavakel 22 
                                       KTl+++a+a+ l
  gi|313117341|ref|YP_004044324.1| 274 KTLAVSALAHRL 285
                                       999999999875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00017      0.31       8      47 ..      25      59 ..      18      91 .. 0.74
   2 ?   -0.9   0.0         1   1.8e+03     138     162 ..     102     126 ..      92     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                            AAA_16  8 eleqLlsalervrsgrp..elvllsGesGvGKsslvrellra 47
                                       l++L+  l          + +ll G +Gv K++l+ ++++ 
  gi|313117341|ref|YP_004044324.1| 25 ALKRLTISL-------LtqSHLLLEGVPGVAKTTLAAAFAQT 59
                                      444443322.......22279****************99974 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                            AAA_16 138 vlvlDdlqwadeaslqllaaLlrll 162
                                       +++ D++ +a + ++++l + ++++
  gi|313117341|ref|YP_004044324.1| 102 LVIADEINRATPKTQSALLEAMQET 126
                                       5788999999999999955555543 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.2   0.00031      0.55       6      51 ..      22      69 ..      19     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                            AAA_30  6 Qaaaveallts..gdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                      Q++a+++l+ s  ++   +l+G++G  Ktt+ +a +++   +g+r+ +
  gi|313117341|ref|YP_004044324.1| 22 QEDALKRLTISllTQSHLLLEGVPGVAKTTLAAAFAQTTGLQGRRIQM 69
                                      6666666654422344689*****************999999887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2103.04
//
Query:       gi|313117342|ref|YP_004044325.1|  [L=350]
Description: hypothetical protein Hbor_31290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-12   48.0   9.5    4.3e-09   36.7   0.2    3.6  4  DUF4350         Domain of unknown function (DUF4350)
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.023   14.2   0.0    1.3  1  ABC_transp_aux  ABC-type uncharacterized transport system
      0.043   13.2   0.0       0.14   11.6   0.0    1.8  2  DUF4159         Domain of unknown function (DUF4159)


Domain annotation for each model (and alignments):
>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2   7.3e-13   4.3e-09       1      69 []      39     108 ..      39     108 .. 0.92
   2 !    4.5   0.5    0.0078        46      25      50 ..     140     167 ..     120     172 .. 0.77
   3 !   11.6   0.1   4.8e-05      0.28       4      67 ..     172     240 ..     170     242 .. 0.84
   4 ?   -3.5   0.0       2.5   1.5e+04      48      60 ..     309     321 ..     305     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 7.3e-13
                           DUF4350   1 skspnGtralaelLeaqGvevrrvrkpfdalegedgtl.lvvapdlrlteeelaallewvarGntlvlaa 69 
                                       + ++nG++ ++ +++++G++ ++++ + +a+ ++++t+ ++++pd  +t +e+++++e+v++G+t+v+a+
  gi|313117342|ref|YP_004044325.1|  39 NSAWNGAADVQPVASETGATFSVATELETAYREPNNTVsIILSPDQAYTRAEAQRVREFVEQGGTVVVAD 108
                                       679*******************99999999977666665*****************************96 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0078
                           DUF4350  25 rkp.fd.alegedgtllvvapdlrltee 50 
                                       ++p f+ a + +++t+l+++++l l++ 
  gi|313117342|ref|YP_004044325.1| 140 TTPnFSeATTTPNATFLNTDQTLTLNHG 167
                                       44444425678***********999884 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 4.8e-05
                           DUF4350   4 pnGtralaelLeaqGvevrrvrkpfd..aleg.........edgtllvvapdlrlteeelaallewvarGntlvl 67 
                                        nGt +la+  e + v+  r ++++d  al +         +dgt++vv++   +    ++a+le  + Gn+ ++
  gi|313117342|ref|YP_004044325.1| 172 ANGTTVLARSSEFSYVDSNRNYQLDDseALGSrpiatqesvGDGTIVVVSDPSMF----INAMLE--REGNRAFV 240
                                       79*********************9888566558999999999*********9555....568888..58888887 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 2.5
                           DUF4350  48 teeelaallewva 60 
                                       t+++++al++++a
  gi|313117342|ref|YP_004044325.1| 309 TPVDADALRAYLA 321
                                       6689999998875 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.8e-06     0.023     169     229 ..      51     109 ..      17     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-06
                    ABC_transp_aux 169 fleeleenYnveevdldsedilpedidvlviakptkdlseeelykldqflmnGgkllvfld 229
                                       + +e ++ ++v + +l++  + + +  v +i  p ++++  e +++++f+++Gg ++v+ d
  gi|313117342|ref|YP_004044325.1|  51 VASETGATFSVAT-ELETAYR-EPNNTVSIILSPDQAYTRAEAQRVREFVEQGGTVVVADD 109
                                       5556666666654.5665655.44666777778************************9977 PP

>> DUF4159  Domain of unknown function (DUF4159)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.3e-05      0.14      61      92 ..      82     112 ..      78     130 .. 0.80
   2 ?   -2.6   0.0      0.49   2.9e+03      68      78 ..     311     321 ..     304     342 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                                       S------HHHHHHHHHHHTT-EEEEEE-SSSS CS
                           DUF4159  61 gnvkfssaeakaLraYlrkGGfLliDdrgyga 92 
                                       ++++++ aea+++r+++++GG++++ d + g+
  gi|313117342|ref|YP_004044325.1|  82 PDQAYTRAEAQRVREFVEQGGTVVVAD-DFGP 112
                                       5678899***************98877.3444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHH CS
                           DUF4159  68 aeakaLraYlr 78 
                                        +a+aLraYl+
  gi|313117342|ref|YP_004044325.1| 311 VDADALRAYLA 321
                                       56667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2292.46
//
Query:       gi|313117343|ref|YP_004044326.1|  [L=91]
Description: hypothetical protein Hbor_31300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.2   2.9      0.012   15.9   2.9    1.1  1  DUF3429   Protein of unknown function (DUF3429)
      0.073   13.3   3.1       0.17   12.2   3.3    1.5  1  DMT_YdcZ  Putative inner membrane exporter, YdcZ
        0.2   11.7   4.4        6.8    6.8   1.8    2.3  2  TPPK_C    Thiamine pyrophosphokinase C terminal
       0.22   11.7   6.6        0.3   11.4   6.6    1.2  1  DUF2537   Protein of unknown function (DUF2537)


Domain annotation for each model (and alignments):
>> DUF3429  Protein of unknown function (DUF3429)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   2.9   2.7e-06     0.012      72     136 ..       6      72 ..       2      80 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                           DUF3429  72 rtrlalsvvpsllawlalllpse.aalallil..gflllllvDrraaragwlpswylklRfvltavvv 136
                                       r +++ ++v+s+la +++l   e  +l l+++  ++++l+ v+   a  + +p+w  +lR+++ a+ +
  gi|313117343|ref|YP_004044326.1|   6 RHQFVHAQVASMLAVAVVLTLLEsLSLELFFVvsLIAFLVNVE-LTAPFRITPRWRRRLRWIILAGLI 72 
                                       4588999999999988855544445555555531555555577.66688999*********9877664 PP

>> DMT_YdcZ  Putative inner membrane exporter, YdcZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.3   3.8e-05      0.17      36      83 ..      34      81 ..       9      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                          DMT_YdcZ 36 vsflvGlivllllllllrksaalaalksvpwwallGGllGavfvtlni 83
                                      + f+v+li++l+ + l+     + ++++   w+ l+Gl+G ++v+++ 
  gi|313117343|ref|YP_004044326.1| 34 LFFVVSLIAFLVNVELTAPFRITPRWRRRLRWIILAGLIGFAYVVVQR 81
                                      457888888888888888767788899999**************9875 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.8    0.0015       6.8      15      44 ..       8      38 ..       3      45 .. 0.82
   2 ?    5.5   0.0    0.0039        18      17      32 ..      64      79 ..      58      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                            TPPK_C 15 allllvlAaLvAvavallvspagq.sfldll 44
                                      + + + +A ++Avav+l +  + + +++ ++
  gi|313117343|ref|YP_004044326.1|  8 QFVHAQVASMLAVAVVLTLLESLSlELFFVV 38
                                      6778889**********99888877777665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0039
                            TPPK_C 17 lllvlAaLvAvavall 32
                                       +++lA+L++ a +++
  gi|313117343|ref|YP_004044326.1| 64 RWIILAGLIGFAYVVV 79
                                      5*********998876 PP

>> DUF2537  Protein of unknown function (DUF2537)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.6   6.6e-05       0.3       9      75 ..      14      78 ..       9      83 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
                           DUF2537  9 vavfvavvvava.vvalslalaevhpllavvvnvvvvaGlaPtvwllrrvpvlRWvvlGvaaGvlvgw 75
                                      va ++av v+++ + +lsl+l  v  l+a +vnv  +a +  t  ++rr+  lRW++l  ++G +   
  gi|313117343|ref|YP_004044326.1| 14 VASMLAVAVVLTlLESLSLELFFVVSLIAFLVNVELTAPFRITP-RWRRR--LRWIILAGLIGFAYVV 78
                                      55555554444404468888888888888888888887666553.45554..8****99999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 624.54
//
Query:       gi|313117344|ref|YP_004044327.1|  [L=163]
Description: hypothetical protein Hbor_31310 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1117.40
//
Query:       gi|313117345|ref|YP_004044328.1|  [L=1852]
Description: CARDB domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-24   85.1  91.0    5.3e-08   33.0   6.8   10.7 12  CARDB            CARDB
    4.6e-11   42.3   2.4    2.9e-05   23.2   0.1    2.8  3  TED_complement   A-macroglobulin TED domain
    1.7e-06   27.6   5.8        6.4    6.6   0.2    5.4  5  Prenyltrans      Prenyltransferase and squalene oxidase repea
    0.00014   21.1  13.9     0.0087   15.2   1.2    3.2  3  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
     0.0032   17.5   0.9        6.3    7.0   0.1    5.2  4  Fn3-like         Fibronectin type III-like domain
  ------ inclusion threshold ------
      0.049   13.6   0.8        6.7    6.7   0.0    4.5  4  Y_Y_Y            Y_Y_Y domain
      0.059   13.4   0.0         17    5.4   0.0    3.3  3  DUF2393          Protein of unknown function (DUF2393)
       0.15   12.5   3.0        4.1    7.9   0.0    4.4  3  Inhibitor_I42    Chagasin family peptidase inhibitor I42
       0.21   11.2   1.2        2.3    7.8   0.1    2.3  2  Lysyl_oxidase    Lysyl oxidase
       0.33   10.0   3.5        9.6    5.2   0.1    3.3  4  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
        8.6    7.0  21.0        8.8    7.0   0.1    7.6  7  YtkA             YtkA-like


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       6.7   1.1e+04      44      87 ..     114     158 ..     113     160 .. 0.74
   2 ?   -0.8   2.1       1.2   1.9e+03       8      71 ..     395     458 ..     390     476 .. 0.66
   3 !    8.7   0.1    0.0013       2.1      10      80 ..     485     552 ..     475     556 .. 0.88
   4 !   17.2   0.3   2.9e-06    0.0046       9      80 ..     576     643 ..     567     647 .. 0.85
   5 !   26.1   0.2   4.6e-09   7.5e-06       9      79 ..     667     734 ..     658     743 .. 0.87
   6 !   33.0   6.8   3.3e-11   5.3e-08       2      99 ..     750     850 ..     749     853 .. 0.87
   7 ?   -2.7   0.2       4.5   7.3e+03      31      77 ..     870     916 ..     868     927 .. 0.71
   8 ?   -2.0   0.2       2.7   4.5e+03      18      54 ..     942     984 ..     935    1027 .. 0.55
   9 !   29.1   4.0   5.6e-10   9.1e-07      12     100 ..    1068    1172 ..    1058    1174 .. 0.85
  10 !   19.3   3.4   6.4e-07     0.001      11      86 ..    1189    1263 ..    1182    1270 .. 0.89
  11 ?    4.7   5.1     0.022        36      13      85 ..    1354    1424 ..    1348    1430 .. 0.80
  12 ?   -3.3   1.3       6.9   1.1e+04      40      88 ..    1747    1799 ..    1740    1810 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.7
                                       ETTEEEEEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT CS
                             CARDB  44 ldgelvgtvtvpsLaagesttvsftwtte..ategevtltvvvDpd 87 
                                       +d+e v+tv +  L+ g+++  s+ +  +  + + +++ ++  D++
  gi|313117345|ref|YP_004044328.1| 114 IDDERVQTVAI-RLKEGAEKPDSIEHISRyiTDSENTHARIINDTT 158
                                       78888999998.8999999999999888884444445588777765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE- CS
                             CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtt 71 
                                        +l++++++v++   +t+tv+N+  ++++  +++++  ge+    ++ tv   +++es+t +++  +
  gi|313117345|ref|YP_004044328.1| 395 LNLAANNTTVRQGTPVTFTVTNE--EDEPVANANVTYAGETYttgADGTV-TFSPKESATATVSKEP 458
                                       567788899999999999999*8..5555555555555544434544555.6777777777777655 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0013
                                       EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEE CS
                             CARDB  10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtl 80 
                                       l+ +e++  e++ ++ tv+N G+  +g ++ +l  dg+  +++tv ++a+g+++  sf +t + ++g+ ++
  gi|313117345|ref|YP_004044328.1| 485 LSTTELSSDETLVVNGTVQNVGDF-EGYFTFELKRDGQIIDEQTV-QVAPGQTAAASFDVTFD-QTGQFDI 552
                                       5678889999999********976.6899****************.89**************9.9999876 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 2.9e-06
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtl 80 
                                        ++ +++  g+++t+++tv+N+G++  g+ +++++ +g+  ++ +   L ages+t+sft t +  +g+++l
  gi|313117345|ref|YP_004044328.1| 576 DVSSTDVDLGDSVTVSATVENNGSGP-GEYNASFVKNGDI-TDYQNGTLGAGESKTISFTKTLA--PGTYDL 643
                                       55667788899************985.899**********.789999*************9986..888876 PP

  == domain 5  score: 26.1 bits;  conditional E-value: 4.6e-09
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevt 79 
                                       +++p+++  ge++t ++tv+N+G +++g++ va+ +d+e+ +t +v sL++ge+t+vsft       g++t
  gi|313117345|ref|YP_004044328.1| 667 EVSPDTVALGESITANATVENTG-GQAGSFLVAFAVDDEVLETRNV-SLDSGETTNVSFTADSL-GIGDHT 734
                                       678899999*************9.568*******************.9***********98765.555555 PP

  == domain 6  score: 33.0 bits;  conditional E-value: 3.3e-11
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEE....SEE-CTEEEEEEEEEE-S- CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtv....psLaagesttvsftwttea 73 
                                       pDL  t+t +pse+++g  + +++tv+N G+a+ ++ +v l +  e   + +++      L++g+sttv++  t + 
  gi|313117345|ref|YP_004044328.1| 750 PDLAATVTNTPSEVSEG-VVPVEATVSNVGNAEVTDATVVLDAQPEGGsNYTQLtnesVTLSPGSSTTVTAELTRA- 824
                                       9****999999999988.589************999999999877665433334566669***************8. PP

                                       S-CEEEEEEEESTT-SS--SSCCCSE CS
                             CARDB  74 tegevtltvvvDpdnevaEsnEtNNe 99 
                                       ++ ++t++v +D+d++ +E +E+NN 
  gi|313117345|ref|YP_004044328.1| 825 EARNYTVRVRADADDQFTEPDEQNNI 850
                                       *************************6 PP

  == domain 7  score: -2.7 bits;  conditional E-value: 4.5
                                       SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CE CS
                             CARDB  31 GtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteatege 77 
                                       G+aa+ ++  +++ldg +v+ v+ +  + +++ +v ++ tte + g 
  gi|313117345|ref|YP_004044328.1| 870 GDAAADDVVYSFVLDGLNVTAVNGAVTNDNGTFYVPANATTEQNVGY 916
                                       88999999999999999987776666677777777777777644444 PP

  == domain 8  score: -2.0 bits;  conditional E-value: 2.7
                                       TSEEEEEEEEEE-SSS-EEEE...EEEEE.ETTEEE..EEEEE CS
                             CARDB  18 geentitvtvkNqGtaasgat...kvaly.ldgelv..gtvtv 54 
                                        +++    +v+N Gt + ++    +v+++  dg+ v  +tvtv
  gi|313117345|ref|YP_004044328.1| 942 LTTVPAVTNVSNIGTFDLPNAgvlNVTVVdQDGDPVegATVTV 984
                                       5666667789999998755541113333214666663333333 PP

  == domain 9  score: 29.1 bits;  conditional E-value: 5.6e-10
                                        -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE..........SEE-CTEEEEEEEEEE-S.... CS
                             CARDB   12 pseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv..........psLaagesttvsftwtte.... 72  
                                        +++   g+++t +vtv+N G  +  + +v+l +   + +t t+          +  a++++ + +ft+++e    
  gi|313117345|ref|YP_004044328.1| 1068 ERQQRFGDNVTANVTVSNDGLVDVDNATVDLRIRSASGETKTLtkhtgfvanrTDSANETELSFDFTDFAEdnll 1142
                                        455566899****************************9999999******9887777888888899999997666 PP

                                        ..-S-CEEEEEEEESTT-SS--SSCCCSEE CS
                             CARDB   73 ..ategevtltvvvDpdnevaEsnEtNNel 100 
                                          ++ g+  +tv vDp+ne++E++E NN  
  gi|313117345|ref|YP_004044328.1| 1143 gdLADGNARVTVIVDPNNEITETDEGNNIA 1172
                                        66666***********************75 PP

  == domain 10  score: 19.3 bits;  conditional E-value: 6.4e-07
                                        C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEES CS
                             CARDB   11 npseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvvvD 85  
                                         p+++ + +  +  v vkN+Gta   + ++a+   + +++tv++  ++a+++ t ++ +t++ + g++t+t++vD
  gi|313117345|ref|YP_004044328.1| 1189 VPKNTLASTPTNTVVFVKNNGTAPILNATAAVDYGDGSNTTVDLGRINASQTNTTRAPHTYN-SGGDYTVTATVD 1262
                                        5677777777778889********999999998888888**********************9.***********9 PP

                                        T CS
                             CARDB   86 p 86  
                                         
  gi|313117345|ref|YP_004044328.1| 1263 D 1263
                                        6 PP

  == domain 11  score: 4.7 bits;  conditional E-value: 0.022
                                        SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEES CS
                             CARDB   13 seafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvvvD 85  
                                        +++++ ++ +++vt k +G+ +s +t+++l + +   ++++ + L++g+  +v++    + t+ ++t++v+v 
  gi|313117345|ref|YP_004044328.1| 1354 NTTEDVSDAQVNVTTKAHGQTSSASTTLNLSVPKIRLTDTNATTLSSGS-DNVTVDLSSA-TTYDHTVNVTVQ 1424
                                        567778899************************************9985.4666666665.666666666654 PP

  == domain 12  score: -3.3 bits;  conditional E-value: 6.9
                                        EEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S....-S-CEEEEEEEESTT- CS
                             CARDB   40 valyldgelvgtvtvpsLaagesttvsftwtte....ategevtltvvvDpdn 88  
                                        v +y ++ + g++  +++a ++ tt +   +t+     t g vt t++vD++ 
  gi|313117345|ref|YP_004044328.1| 1747 VGVYDSDGSFGNTRATGVAINALTTADQRGVTPqtvdVTVGGVTKTASVDSST 1799
                                        66777777777777777777777777777666644455668888888888765 PP

>> TED_complement  A-macroglobulin TED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   1.8e-08   2.9e-05      17     139 ..    1433    1577 ..    1419    1594 .. 0.75
   2 ?    0.5   0.1      0.15   2.4e+02     120     146 ..    1615    1641 ..    1587    1672 .. 0.71
   3 !   17.0   0.4   1.5e-06    0.0024      77     214 ..    1625    1774 ..    1620    1782 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.8e-08
                                        THHHHHSSS--SSHHHHGGGTHHHHHHHHHHHHTTGTTTSHHHHHHHHHHHHHHHHHTC...........BETTS CS
                    TED_complement   17 enlesLlrlPygcgEqnmvllapnvyvlkYLekteqltkeikkkaleklekgyqrqlsy...........kkadg 80  
                                         +le L   Pygc Eq+ +++   + + +Y ++ +  ++  +++a +++e g+ +  +            +++dg
  gi|313117345|ref|YP_004044328.1| 1433 AGLEYLFTYPYGCVEQTTSQMMGALRTDQYYRSGDIPNNYNRQRANDTIEIGVEKLGTNqassliwpdlaQNEDG 1507
                                        58899**********************************************9987543211112333333789** PP

                                        EBBSSS...SS-BEHHHHHHHHHHHHH.CHHHST.........--HHHHHHHHHHHHTTB-TTS-B--SS CS
                    TED_complement   81 sysafgkd.ssegstWLtAfvlkvlaq.akefif.........ideeeiseslewLlseQkedGsFkeeg 139 
                                        s+s++g     eg    t   l+     a++ ++         i+  + s+s+ewL+ +Q++dGs   + 
  gi|313117345|ref|YP_004044328.1| 1508 SWSMYGGAfYDEGDLYYTTAALQGVTSvANDEVQgtraevsddIQTVNASRSIEWLSDHQRADGSVPATD 1577
                                        ******44566777776666666555524444446777777779999999**************976655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.15
                                        HHHHHHHTTB-TTS-B--SS-SS-TTC CS
                    TED_complement  120 eslewLlseQkedGsFkeegsllnrkm 146 
                                        ++  +L+++Q+ dGs+ +++s  + + 
  gi|313117345|ref|YP_004044328.1| 1615 DAAVFLIENQNSDGSWASDRSQSDISQ 1641
                                        456688888888888887776665544 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 1.5e-06
                                        ETTSEBBSSS...SS-BEHHHHHHHHHHHHHCHHHST..........--.HHHHHHHHHHHHTTB-TTS-B--SS CS
                    TED_complement   77 kadgsysafgkd.ssegstWLtAfvlkvlaqakefif..........id.eeeiseslewLlseQkedGsFkeeg 139 
                                        ++dgs++  +++ + ++    tA+ l+ la ++e              d  ++i +  +wL+ +Q++dGs+   +
  gi|313117345|ref|YP_004044328.1| 1625 NSDGSWASDRSQsDISQKPQATALALRGLATVNESAAlrqrvnqqtdTDlSTAIDNGSQWLIDNQNADGSWDAYR 1699
                                        6677776666332333344468888888888555544455555554455246899******************** PP

                                        -SS-TTCSSSTHCHHHHHHHHHHHHHHHHTTCS.HHHHHHHHHHHHHHHHHH..HHHHS---HHHHHHHHHHHHH CS
                    TED_complement  140 sllnrkmkggvekevtLtAyvliaLleakeile.lkkkvelsiskAleyLee..kqaeelesvyalAilaYalal 211 
                                        + +  + +g+v +    t + ++aL+e++ +++   +  + s++ A+ yL    ++  ++ ++ a  ++  al++
  gi|313117345|ref|YP_004044328.1| 1700 NSFFWSSNGEVTR---ATGHSILALNETQGVTTqGTSDAADSVEDATDYLVGvyDSDGSFGNTRATGVAINALTT 1771
                                        9999999999765...59**********9999878888999*********8877777777777777777777777 PP

                                        TT- CS
                    TED_complement  212 aks 214 
                                        a++
  gi|313117345|ref|YP_004044328.1| 1772 ADQ 1774
                                        776 PP

>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.6    0.0079        13      14      39 ..    1503    1531 ..    1502    1533 .. 0.86
   2 ?    4.1   0.0     0.024        40       7      19 ..    1560    1572 ..    1555    1572 .. 0.90
   3 ?    4.9   0.0     0.013        21       9      23 ..    1619    1633 ..    1614    1641 .. 0.87
   4 !    6.6   0.2    0.0039       6.4       8      20 ..    1683    1695 ..    1677    1707 .. 0.88
   5 ?    3.8   0.0     0.031        50       3      21 ..    1739    1757 ..    1737    1758 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0079
                                        SHTTS-BBSSTTS....SBBHHHHHHHHHH CS
                       Prenyltrans   14 QnedGGwggrpgs....esdtyytywalaa 39  
                                        QnedG+w+    +    e d+yyt  al++
  gi|313117345|ref|YP_004044328.1| 1503 QNEDGSWSMYG-GafydEGDLYYTTAALQG 1531
                                        99*******95.459999999999999875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.024
                                        HHHHHHHSHTTS- CS
                       Prenyltrans    7 vefLlscQnedGG 19  
                                        +e+L  +Q++dG+
  gi|313117345|ref|YP_004044328.1| 1560 IEWLSDHQRADGS 1572
                                        89**********8 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.013
                                        HHHHHSHTTS-BBSS CS
                       Prenyltrans    9 fLlscQnedGGwggr 23  
                                        fL+  Qn dG+w+++
  gi|313117345|ref|YP_004044328.1| 1619 FLIENQNSDGSWASD 1633
                                        89999*******987 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0039
                                        HHHHHHSHTTS-B CS
                       Prenyltrans    8 efLlscQnedGGw 20  
                                        ++L+  Qn+dG+w
  gi|313117345|ref|YP_004044328.1| 1683 QWLIDNQNADGSW 1695
                                        8************ PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.031
                                        HHHHHHHHHHHSHTTS-BB CS
                       Prenyltrans    3 vekavefLlscQnedGGwg 21  
                                        ve a+++L    + dG++g
  gi|313117345|ref|YP_004044328.1| 1739 VEDATDYLVGVYDSDGSFG 1757
                                        899***************8 PP

>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   2.8   6.3e-05       0.1     171     288 ..    1502    1634 ..    1489    1638 .. 0.70
   2 !   15.2   1.2   5.4e-06    0.0087     199     286 ..    1603    1697 ..    1599    1703 .. 0.62
   3 !    5.2   0.1    0.0059       9.6      74     162 ..    1717    1805 ..    1712    1819 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.3e-05
                                        HS-TTS----SSBSSH....HHHHHHHHHHHHHTT--............TTSHHHHHHHHHHHTT--TTSSBB-- CS
                   SQHop_cyclase_C  171 eqepdGsWfGrWGvny....iyGtwsvlsalaavged............leepvirkavdWlksvqnedGGWGes 229 
                                         q++dGsW    G+ y    +y t ++l+++++v++d             ++    ++++Wl+++q++dG    +
  gi|313117345|ref|YP_004044328.1| 1502 AQNEDGSWSMYGGAFYdegdLYYTTAALQGVTSVANDevqgtraevsddIQTVNASRSIEWLSDHQRADGSVPAT 1576
                                        6889999977777777666688899999999888776322211111000233345699************98776 PP

                                        GGGGT-GGGTT-SSBBHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHH--TTS-----S CS
                   SQHop_cyclase_C  230 aesykdpklagkgestasqtaWallallaageveseavkrGiaylletqkedGtWeeea 288 
                                            +d+      +  a + a   l   a+ ++e   v     +l+e+q++dG+W  ++
  gi|313117345|ref|YP_004044328.1| 1577 DYFLRDQFSSTGYTMVAFDRAEPHLNSSATQTAEDFRVDAA-VFLIENQNSDGSWASDR 1634
                                        65555655555556677788888888877777777777655.59***********8765 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.4e-06
                                        HTT--TTSHHHHHHHHHHHTT--TTSSBB--GG.GGT..-G...GGTT-SSBBHHHHHHHHHHHHHTTGGG...S CS
                   SQHop_cyclase_C  199 avgedleepvirkavdWlksvqnedGGWGesae.syk..dp...klagkgestasqtaWallallaageve...s 264 
                                        + +++++e++   a+ +l + qn+dG W  + + s    +p   +la +g +t ++ a   l +    +++   s
  gi|313117345|ref|YP_004044328.1| 1603 SSATQTAEDFRVDAAVFLIENQNSDGSWASDRSqSDIsqKPqatALALRGLATVNESA--ALRQRVNQQTDtdlS 1675
                                        55667777777889999***********876431332112211123333445544443..333333333321126 PP

                                        HHHHHHHHHHHHH--TTS---- CS
                   SQHop_cyclase_C  265 eavkrGiaylletqkedGtWee 286 
                                         a+  G ++l+++q++dG+W+ 
  gi|313117345|ref|YP_004044328.1| 1676 TAIDNGSQWLIDNQNADGSWDA 1697
                                        7999****************86 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0059
                                        HHHHHTT-...--STHHHHHHHHHHHHHHHHHTB-TTSSB-SSSSSB--SGGGGSTT-SSS-SSB--BHHHHHHH CS
                   SQHop_cyclase_C   74 vvlalkrv...rlkeekkkeeaiaraveWilglqsknGGwaafdkdntkellnkiPfadhealldpptadvtarv 145 
                                         +lal+++   +++ +++ +++++ a+++++g+  ++G ++   +  t   +n++  ad+  +  p t+dvt   
  gi|313117345|ref|YP_004044328.1| 1717 SILALNETqgvTTQGTSDAADSVEDATDYLVGVYDSDGSFGN--TRATGVAINALTTADQRGV-TPQTVDVTVGG 1788
                                        5667766522146677888999******************96..56688899*******9885.699*****988 PP

                                        HHHHHHHT--TTSHHHH CS
                   SQHop_cyclase_C  146 lellaqlgeeedsealk 162 
                                        +   a++++++++++++
  gi|313117345|ref|YP_004044328.1| 1789 VTKTASVDSSTTTDTVT 1805
                                        88888888877766654 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.19   3.1e+02      26      50 ..     527     551 ..     523     565 .. 0.83
   2 ?    0.3   0.0      0.48   7.8e+02      24      40 ..     617     633 ..     613     637 .. 0.84
   3 ?    0.6   0.0      0.39   6.3e+02      26      42 ..     710     726 ..     709     728 .. 0.89
   4 !    7.0   0.1    0.0039       6.3      26      51 ..     806     831 ..     803     842 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                                       EEEE-TT-EEEEEEEEECGGG-EEE CS
                          Fn3-like  26 kveLapGesktvtftldrkdlsvwd 50 
                                        v++apG+++ ++f+++ +++  +d
  gi|313117345|ref|YP_004044328.1| 527 TVQVAPGQTAAASFDVTFDQTGQFD 551
                                       689*************988877666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                                       EEEEEE-TT-EEEEEEE CS
                          Fn3-like  24 FekveLapGesktvtft 40 
                                       ++  +L +Geskt++ft
  gi|313117345|ref|YP_004044328.1| 617 YQNGTLGAGESKTISFT 633
                                       6667899********98 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.39
                                       EEEE-TT-EEEEEEEEE CS
                          Fn3-like  26 kveLapGesktvtftld 42 
                                        v+L  Ge++ v+ft d
  gi|313117345|ref|YP_004044328.1| 710 NVSLDSGETTNVSFTAD 726
                                       589***********987 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0039
                                       EEEE-TT-EEEEEEEEECGGG-EEET CS
                          Fn3-like  26 kveLapGesktvtftldrkdlsvwde 51 
                                        v+L pG s+tvt +l+r + + + +
  gi|313117345|ref|YP_004044328.1| 806 SVTLSPGSSTTVTAELTRAEARNYTV 831
                                       699**************987766655 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0041       6.7      29      53 ..     163     188 ..     147     192 .. 0.82
   2 ?   -2.0   0.0       2.2   3.6e+03      26      44 ..     626     644 ..     614     648 .. 0.71
   3 ?   -2.1   0.0       2.5     4e+03      40      57 ..     828     845 ..     809     850 .. 0.73
   4 ?    0.7   0.0      0.32   5.1e+02      26      50 ..    1239    1264 ..    1231    1279 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0041
                                       ..EEEEES--SEEEEEEEEEEETTS- CS
                             Y_Y_Y  29 q.easytnlppGdYtlkVkakdndgq 53 
                                       +  + +t+ ++G+Y++ V++  n +q
  gi|313117345|ref|YP_004044328.1| 163 KnYFRFTPQKSGQYVFAVAIVENGSQ 188
                                       1489***************9999887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                       STS.EEEEES.--SEEEEEE CS
                             Y_Y_Y  26 dysqeasytn.lppGdYtlk 44 
                                       ++  ++s+t  l pG+Y l 
  gi|313117345|ref|YP_004044328.1| 626 ESK-TISFTKtLAPGTYDLG 644
                                       344.888885489****875 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.5
                                       EEEEEEEEEETTS-B-SS CS
                             Y_Y_Y  40 dYtlkVkakdndgqwnyd 57 
                                       +Yt++V+a  +d+  ++d
  gi|313117345|ref|YP_004044328.1| 828 NYTVRVRADADDQFTEPD 845
                                       8******98777665555 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.32
                                        STS..EEEEES--SEEEEEEEEEEET CS
                             Y_Y_Y   26 dysq.easytnlppGdYtlkVkakdn 50  
                                          ++  a  t ++ GdYt+++ + d 
  gi|313117345|ref|YP_004044328.1| 1239 QTNTtRAPHTYNSGGDYTVTATVDDA 1264
                                        33445888999********9988775 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.01        17      52      76 ..     485     509 ..     480     516 .. 0.91
   2 ?    3.4   0.0     0.044        71      58     126 ..     762     831 ..     754     839 .. 0.83
   3 ?   -1.5   0.0       1.4   2.3e+03      58      93 ..    1072    1107 ..    1065    1126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.01
                           DUF2393  52 lsqkrllyteafvvdgtitNeGkft 76 
                                       ls + l+++e++vv gt++N G+f+
  gi|313117345|ref|YP_004044328.1| 485 LSTTELSSDETLVVNGTVQNVGDFE 509
                                       5678899***************986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.044
                           DUF2393  58 lyteafv.vdgtitNeGkftikeCkleiklvnkshnkkskellkklkplv.sksevikedlkpgeskeFrv 126
                                        ++e +v v+ t+ N G+ +++  ++ ++  +++  + +++l+++ ++l+  +s+++ ++l++ e ++++v
  gi|313117345|ref|YP_004044328.1| 762 EVSEGVVpVEATVSNVGNAEVTDATVVLDAQPEGGSN-YTQLTNESVTLSpGSSTTVTAELTRAEARNYTV 831
                                       55555544899**************************.999999888776257788999999999999987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.4
                           DUF2393   58 lyteafvvdgtitNeGkftikeCkleiklvnkshnk 93  
                                         + + + + +t+ N+G  ++ + ++ +++  +s ++
  gi|313117345|ref|YP_004044328.1| 1072 RFGDNVTANVTVSNDGLVDVDNATVDLRIRSASGET 1107
                                        578899999****************99998877776 PP

>> Inhibitor_I42  Chagasin family peptidase inhibitor I42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0025       4.1      37      68 ..     140     178 ..     126     191 .. 0.85
   2 ?    0.0   0.1       0.7   1.1e+03      38      68 ..     612     643 ..     584     651 .. 0.76
   3 ?    0.2   0.1      0.63     1e+03      17      64 ..    1297    1357 ..    1289    1385 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0025
                                       TTCECCECCE.......STTSSEEEEEEEEESSSEEEEE CS
                     Inhibitor_I42  37 eeyipdesde.......lvGaggthvwtfkalkpGetti 68 
                                       ++yi+d++++       + G +g+  ++f+ +k+G++ +
  gi|313117345|ref|YP_004044328.1| 140 SRYITDSENThariindTTGEPGKNYFRFTPQKSGQYVF 178
                                       57888888889999999******************9855 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.7
                                       TCECCECCESTTSSE.EEEEEEEESSSEEEEE CS
                     Inhibitor_I42  38 eyipdesdelvGagg.thvwtfkalkpGetti 68 
                                       + i+d+++ ++Gag  ++++  k l+pG++++
  gi|313117345|ref|YP_004044328.1| 612 GDITDYQNGTLGAGEsKTISFTKTLAPGTYDL 643
                                       33555555599***956666666779999875 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.63
                                        CCT-EEEEEE-..............-TTTEEE-T.TTCECCECCESTTSSEEEEEEEEESSSE CS
                     Inhibitor_I42   17 ttGYsWtvdas..............dseglklls.eeyipdesdelvGaggthvwtfkalkpG 64  
                                        t G + t++a                ++gl+l+  e+ ++d +  +  +ggt  w+++++ + 
  gi|313117345|ref|YP_004044328.1| 1297 TNGTTFTATARfqtnypttvnatleLPDGLELVAsENASKDVP--ASATGGTAAWKVRVNTTE 1357
                                        5555555554444455555555566779999999555555555..899999****99988543 PP

>> Lysyl_oxidase  Lysyl oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.13   2.1e+02     156     185 ..     821     850 ..     816     856 .. 0.90
   2 ?    7.8   0.1    0.0014       2.3     158     195 ..    1144    1183 ..    1140    1189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
                     Lysyl_oxidase 156 itdvkpgeyilkvevnpefkvaEsdfenNa 185
                                       +t  ++ +y+++v+ + + + +E d +nN+
  gi|313117345|ref|YP_004044328.1| 821 LTRAEARNYTVRVRADADDQFTEPDEQNNI 850
                                       6888999**********************7 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0014
                     Lysyl_oxidase  158 dvkpgeyilkvevnpefkvaEsdfenNavkce..lrytgs 195 
                                        d+ +g+  + v v+p+++++E+d  nN+++ +  +ry + 
  gi|313117345|ref|YP_004044328.1| 1144 DLADGNARVTVIVDPNNEITETDEGNNIAVNStlVRYADA 1183
                                        8899999********************9865412455555 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.072   1.2e+02      57      79 ..    1502    1527 ..    1491    1532 .. 0.77
   2 ?   -3.3   0.0       2.4   3.8e+03      46      63 ..    1555    1572 ..    1547    1576 .. 0.67
   3 ?    1.7   0.0      0.07   1.1e+02      45      66 ..    1611    1632 ..    1600    1665 .. 0.73
   4 ?    5.2   0.1    0.0059       9.6      44      69 ..    1675    1700 ..    1649    1706 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.072
                   SQHop_cyclase_N   57 qqredGgWelypg...gpgdlsttve 79  
                                         q+edG+W++y g   ++gdl  t  
  gi|313117345|ref|YP_004044328.1| 1502 AQNEDGSWSMYGGafyDEGDLYYTTA 1527
                                        69********9762224677777765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.4
                   SQHop_cyclase_N   46 eeekiakylrsqqredGg 63  
                                        ++++  ++l ++qr+dG+
  gi|313117345|ref|YP_004044328.1| 1555 NASRSIEWLSDHQRADGS 1572
                                        556667777777777776 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.07
                   SQHop_cyclase_N   45 eeeekiakylrsqqredGgWel 66  
                                        + +  +a +l ++q++dG+W+ 
  gi|313117345|ref|YP_004044328.1| 1611 DFRVDAAVFLIENQNSDGSWAS 1632
                                        45567889999*********75 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.0059
                   SQHop_cyclase_N   44 eeeeekiakylrsqqredGgWelypg 69  
                                        ++ +++  ++l ++q++dG+W  y +
  gi|313117345|ref|YP_004044328.1| 1675 STAIDNGSQWLIDNQNADGSWDAYRN 1700
                                        33444556788888888888888765 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.5   2.4e+03      56      79 ..     163     186 ..     143     187 .. 0.76
   2 ?    3.6   0.2     0.062     1e+02       7      44 ..     393     431 ..     387     451 .. 0.73
   3 ?   -1.5   0.0       2.4   3.9e+03      51      71 ..     585     606 ..     512     611 .. 0.70
   4 ?    2.0   0.3      0.19   3.1e+02      11      51 ..     756     796 ..     746     812 .. 0.75
   5 ?    7.0   0.1    0.0054       8.8      25      54 ..     966     997 ..     958    1012 .. 0.67
   6 ?    1.3   0.2      0.33   5.4e+02      12      47 ..    1189    1225 ..    1179    1264 .. 0.63
   7 ?    0.2   0.2      0.72   1.2e+03      14      45 ..    1339    1369 ..    1333    1382 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.5
                              YtkA  56 ttkvelkesedGvYeaevnfsmeG 79 
                                       +     ++++ G+Y + v + ++G
  gi|313117345|ref|YP_004044328.1| 163 KNYFRFTPQKSGQYVFAVAIVENG 186
                                       55556678899*****99999998 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.062
                              YtkA   7 levelvspeepkagentivvt.vtqggkpVedadvkvef 44 
                                       ++ +l  +++ + + + +++t  +++++pV +a+v+  +
  gi|313117345|ref|YP_004044328.1| 393 VQLNLAANNTTVRQGTPVTFTvTNEEDEPVANANVTYAG 431
                                       5556666555555555677774669*********98765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.4
                              YtkA  51 Gmeemttkvelke..sedGvYea 71 
                                       G++  t+ +++++  s++G+Y a
  gi|313117345|ref|YP_004044328.1| 585 GDS-VTVSATVENngSGPGEYNA 606
                                       333.5677777777788888876 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.19
                              YtkA  11 lv.speepkagentivvt.vtqggkpVedadvkvefwmpameG 51 
                                       ++ +p+e+++g   +++t  + g+++V+da+v +++  +  +G
  gi|313117345|ref|YP_004044328.1| 756 VTnTPSEVSEGVVPVEATvSNVGNAEVTDATVVLDAQPE--GG 796
                                       443677999999999998677999******998877655..34 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0054
                              YtkA  25 vvt.vtqggkpVedadvkv.efwmpameGmee 54 
                                        vt v+q+g+pVe+a+v+v ++  +a  G  e
  gi|313117345|ref|YP_004044328.1| 966 NVTvVDQDGDPVEGATVTVvHRNNDAITGITE 997
                                       45559**********97651555555556664 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.33
                              YtkA   12 vspeep.kagentivvtvtqggkpVedadvkvefwmp 47  
                                        v+++++ +++ nt+v++++ g +p+ +a+  v+  + 
  gi|313117345|ref|YP_004044328.1| 1189 VPKNTLaSTPTNTVVFVKNNGTAPILNATAAVDYGDG 1225
                                        3344557899999***********9999877766554 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 0.72
                              YtkA   14 peepkagentivvtvtqggkpVedadvkvefw 45  
                                        p +++ g ++++v+v+ + + V+da v v+  
  gi|313117345|ref|YP_004044328.1| 1339 PASATGGTAAWKVRVN-TTEDVSDAQVNVTTK 1369
                                        4455778888999988.5788****9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1852 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 10039.28
//
Query:       gi|313117346|ref|YP_004044329.1|  [L=413]
Description: dockerin-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-09   37.7   3.1    1.8e-09   37.7   3.1    2.8  2  Dockerin_1  Dockerin type I domain
      0.005   16.7   2.0       0.23   11.4   0.2    3.2  3  PEGA        PEGA domain
  ------ inclusion threshold ------
      0.022   15.4   8.7          4    8.1   0.2    4.2  4  YtkA        YtkA-like


Domain annotation for each model (and alignments):
>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4      0.11   6.4e+02      27      44 ..     185     202 ..     161     204 .. 0.83
   2 !   37.7   3.1   2.9e-13   1.8e-09       4      56 ..     354     400 ..     351     401 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                                       BTTSCCCHGGGSTT-SSC CS
                        Dockerin_1  27 gqssssngkaaDvNgDGr 44 
                                        +++ +   +aDv+ DG+
  gi|313117346|ref|YP_004044329.1| 185 VDTDGNAVSNADVSIDGN 202
                                       56777888999**99997 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 2.9e-13
                                       TTSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHH CS
                        Dockerin_1   4 VNgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallviny 56 
                                       VN+D +V+a+Da ++   +       + + +++aDvN DGrv+a+Da+ + +y
  gi|313117346|ref|YP_004044329.1| 354 VNRDDTVDATDASAVSADVA------KGQSPEYADVNDDGRVSAIDAMFIAQY 400
                                       9*******************......9999******************99876 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1   6.3e+03      37      52 ..     141     156 ..     134     168 .. 0.61
   2 !   11.4   0.2   3.8e-05      0.23      11      41 ..     193     222 ..     189     226 .. 0.89
   3 ?    3.0   0.0     0.015        92      35      57 ..     339     363 ..     329     376 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                              PEGA  37 slrvekeGYedlektv 52 
                                        ++v  +G ++++++v
  gi|313117346|ref|YP_004044329.1| 141 NVTVDTPGSTTVSADV 156
                                       3555555555555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.8e-05
                              PEGA  11 eGatVyidGkylGkTPvtlsleaGnyslrve 41 
                                       ++a V+idG+ +G++  +++l +G++++ v+
  gi|313117346|ref|YP_004044329.1| 193 SNADVSIDGNAVGSSVSETVL-EGEHTVSVS 222
                                       79************9777777.9*****997 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.015
                              PEGA  35 nyslrvekeGYe..dlektvtvtag 57 
                                       + ++++e+eGYe  +++++ tv+a+
  gi|313117346|ref|YP_004044329.1| 339 TTQVDLEYEGYElgNVNRDDTVDAT 363
                                       669********85566666666655 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0011       6.8       2      31 ..      40      70 ..      39      88 .. 0.80
   2 ?   -2.8   0.0       1.7     1e+04      69      83 ..     138     152 ..     126     157 .. 0.59
   3 ?    8.1   0.2   0.00068         4      18      45 ..     174     202 ..     161     220 .. 0.79
   4 ?    2.5   0.4     0.037   2.2e+02      21      67 ..     262     311 ..     239     322 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                              YtkA  2 aesddlevelvspeep.kagentivvtvtqg 31
                                      a++d+++ve+v p+ + ++g++t++v+vt +
  gi|313117346|ref|YP_004044329.1| 40 AQQDPYTVEVVAPDDFsTNGNQTLTVRVTNN 70
                                      689*************788888999986644 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                              YtkA  69 YeaevnfsmeGtWqv 83 
                                       Y ++v+   +G  +v
  gi|313117346|ref|YP_004044329.1| 138 YHFNVTVDTPGSTTV 152
                                       555555555555444 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00068
                              YtkA  18 kagentivvt.vtqggkpVedadvkvefw 45 
                                       + g  t++++ v+ +g++V++adv++++ 
  gi|313117346|ref|YP_004044329.1| 174 ALGTGTVSANvVDTDGNAVSNADVSIDGN 202
                                       56778999966**************9875 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.037
                              YtkA  21 entivv..tvtqggkpVe..dadvkvefwmpameGmeemttkvelkesedG 67 
                                       e+ ivv  t + +g++V+  + +v+++f+++   +  e +++  +++ +dG
  gi|313117346|ref|YP_004044329.1| 262 ETNIVVssTSRTEGSAVSpvNTTVSFTFSKDSGTAVYEVQEPSVATK-GDG 311
                                       33344433567888888854556999999996333344444444444.777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2741.88
//
Query:       gi|313117347|ref|YP_004044330.1|  [L=286]
Description: hypothetical protein Hbor_31340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-08   31.8   7.5      2e-07   30.8   7.5    1.6  1  PGF-CTERM        PGF-CTERM motif


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   7.5   1.1e-11     2e-07       1      23 []     263     285 ..     263     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.1e-11
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       tPGFG+v A+++LLaaalLa Rr
  gi|313117347|ref|YP_004044330.1| 263 TPGFGVVAAITALLAAALLAVRR 285
                                       9********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1902.89
//
Query:       gi|313117348|ref|YP_004044331.1|  [L=78]
Description: hypothetical protein Hbor_31350 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 532.04
//
Query:       gi|313117349|ref|YP_004044332.1|  [L=369]
Description: hypothetical protein Hbor_31360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-06   27.4   1.4      0.059   13.5   0.1    2.7  2  DUF3244   Domain of unknown function (DUF3244)
  ------ inclusion threshold ------
      0.061   12.5  20.4      0.082   12.1  20.4    1.1  1  SOG2      RAM signalling pathway protein
       0.11   12.6   0.8       0.42   10.8   0.0    2.3  3  PAC3      Proteasome assembly chaperone 3
       0.13   11.9   1.2        1.4    8.6   0.0    2.3  2  FAM176    FAM176 family
        3.7    7.4  15.2        9.2    6.1  15.2    1.6  1  Velvet    Velvet factor


Domain annotation for each model (and alignments):
>> DUF3244  Domain of unknown function (DUF3244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   3.4e-05      0.12      30      94 ..      61     123 ..      28     125 .. 0.82
   2 !   13.5   0.1   1.6e-05     0.059      25      97 ..     150     222 ..     130     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                                       ETTEEEEEESS--.SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS-EE CS
                           DUF3244  30 egnilsiefespl.sdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskggyl 94 
                                        g+++s++ + p  ++ t+ i ++ + e ++++  v +  ++  ++l+ +++g+Y + +  +++ +
  gi|313117349|ref|YP_004044332.1|  61 TGDYVSVTTNAPSdKEYTVRIINS-EQELMHSNPGVGD--DESRFELDRYDPGTYAVAIMNGSEEV 123
                                       68889998888761567*******.799********99..99*****************9777655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.6e-05
                                       EEEEEETTEEEEEESS--SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEE.ESS-EEEEE CS
                           DUF3244  25 itasiegnilsiefesplsdvtitikdeetgevvyestivnasgstisidlsgeesgeYklelt.skggylyGe 97 
                                       +++s+e + +s +   p  +v++ + d+ t+ v ++ t  ++ + t ++dls++++g+Y++  t  +++ + Ge
  gi|313117349|ref|YP_004044332.1| 150 MEVSVELTKVSNDVSPPPATVEVVVGDD-TDSVRTTATKQSDLTYTATVDLSSLSTGDYRVYSTvRRDNEVFGE 222
                                       3444444444555555555668888888.899999999999999*****************9988888888886 PP

>> SOG2  RAM signalling pathway protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  20.4   2.3e-05     0.082     182     364 ..     183     352 ..     115     367 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                              SOG2 182 ttssgssstlvssaesstesrassvtyta..................rtRhagsfsaqdveqGaaltplrsdqipfn 240
                                       tt+ ++                s  tyta                  r R + +f  +++     +  + s+q++  
  gi|313117349|ref|YP_004044332.1| 183 TTATKQ----------------SDLTYTAtvdlsslstgdyrvystvR-RDNEVFGEKEL-----IGLSDSQQLS-- 235
                                       222111................11111112222222222222222213.77777763222.....2233344333.. PP

                              SOG2 241 lsrsrrssssgnsaspaangaqsetsersasssgvqssasstPlgegstsppgalsrqslsttgststltsssksrs 317
                                         ++ ++ s++ +++p++ +++ +++         ++++++tP +++s ++ g++++   s+ ++t  +tss+  + 
  gi|313117349|ref|YP_004044332.1| 236 --VVAEQPSTPSTTEPQSPTETESPTA------TPTTTPTTTPTTSESAPN-GQQPAGGDSADEDTDATTSSPADST 303
                                       ..3444444433444444333222222......234556666666655544.9999999999999999999999988 PP

                              SOG2 318 ssrsntnasastprslattpappasaesfastltasrintlaa..vDeq 364
                                       +++++  +s+ +p+  + t+ p+ +a+s+a+++  ++++t +    D  
  gi|313117349|ref|YP_004044332.1| 304 TEQVTDTTSTEPPQNTTATTMPTQTASSTAPSTAVQTTTTETPvlPDIS 352
                                       8888767777778777777777777777533333333333332445555 PP

>> PAC3  Proteasome assembly chaperone 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.2   4.3e+03       3      32 ..      53      80 ..      52      82 .. 0.56
   2 ?   10.8   0.0   0.00012      0.42      13      47 ..     152     186 ..     148     193 .. 0.87
   3 ?   -3.7   0.0       3.8   1.4e+04      32      46 ..     223     238 ..     213     240 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.2
                              PAC3  3 iTqigki..Gtlvsvtpdsksdelseptytvr 32
                                      +T+igk   G  vsvt     +  s+  ytvr
  gi|313117349|ref|YP_004044332.1| 53 VTDIGKYqtGDYVSVT----TNAPSDKEYTVR 80
                                      8999986224455555....444455556555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                              PAC3  13 vsvtpdsksdelseptytvrvllGkdddllrvyar 47 
                                       vsv+  + s++ s p+ tv+v+ G+d+d +r  a+
  gi|313117349|ref|YP_004044332.1| 152 VSVELTKVSNDVSPPPATVEVVVGDDTDSVRTTAT 186
                                       4566669999********************99886 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.8
                              PAC3  32 rvllGk.dddllrvya 46 
                                       + l+G  d++ l v+a
  gi|313117349|ref|YP_004044332.1| 223 KELIGLsDSQQLSVVA 238
                                       5678888888888877 PP

>> FAM176  FAM176 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00039       1.4      30      52 ..       6      28 ..       3      82 .. 0.82
   2 ?    1.4   0.6     0.064   2.3e+02      66      96 ..     284     311 ..     257     336 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00039
                            FAM176 30 vcvGLlltLcllviriscrkdle 52
                                      vc+G +l++cll + +s  + + 
  gi|313117349|ref|YP_004044332.1|  6 VCLGVFLAVCLLTVPVSIGQTAD 28
                                      9**************99877655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.064
                            FAM176  66 ekasededeeeeeeeedsseseaeeelsefe 96 
                                         +s ded  ++ ++++ ++s++ e++++++
  gi|313117349|ref|YP_004044332.1| 284 GGDSADED--TDATTSSPADSTT-EQVTDTT 311
                                       22233333..3333333333332.2222222 PP

>> Velvet  Velvet factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  15.2    0.0026       9.2      27     153 ..     166     329 ..     158     353 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0026
                                       S--EEEEEEEETTT-SB--GGG---TTEEEEEEEEETT.SSSB--EE.............................. CS
                            Velvet  27 PppvvqLrvtdaetnsevdveeldssffvvtvdLwsed.gtkevnlv.............................. 72 
                                       Pp+ v+++v d  +   +  ++ ++ ++++tvdL s + g+  v +                               
  gi|313117349|ref|YP_004044332.1| 166 PPATVEVVVGDDTDSVRTTATKQSDLTYTATVDLSSLStGDYRVYSTvrrdnevfgekeliglsdsqqlsvvaeqps 242
                                       7778*******5444445566678889*********44333333222577777779999999877766555554443 PP

                                       .......--.---------.---------------------------------------.................. CS
                            Velvet  73 .......kssssasssisseasssssqsseesssspksqassaessapsssaapsaqee.................. 124
                                              +             s+++++s       p+  ++++++++p++s+++ + ++                  
  gi|313117349|ref|YP_004044332.1| 243 tpsttepQ-------------SPTETES-------PTATPTTTPTTTPTTSESAPNGQQpaggdsadedtdattssp 299
                                       32222221.............1111111.......111111222222221111111111233334444444444444 PP

                                       .-------------------EESEEE--EE CS
                            Velvet 125 .kekkeatlssssnqasskltrnLiGslva 153
                                        ++++e+ ++++s+++ +++t + + +++a
  gi|313117349|ref|YP_004044332.1| 300 aDSTTEQVTDTTSTEPPQNTTATTMPTQTA 329
                                       433333333333333334444444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 2388.81
//
Query:       gi|313117350|ref|YP_004044333.1|  [L=939]
Description: hypothetical protein Hbor_31370 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-07   31.5   7.1    2.4e-07   30.5   7.1    1.5  1  PGF-CTERM  PGF-CTERM motif
     0.0013   19.2   2.5        1.9    9.0   0.2    4.3  5  MG2        MG2 domain
  ------ inclusion threshold ------
      0.029   14.5   0.2       0.12   12.5   0.2    2.1  1  DUF4581    Domain of unknown function (DUF4581)
      0.068   13.0   0.1       0.38   10.6   0.0    2.4  2  KH_1       KH domain
        1.7    8.6  10.3          1    9.3   0.8    4.8  6  DUF4251    Domain of unknown function (DUF4251)


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   7.1   6.6e-11   2.4e-07       1      23 []     916     938 ..     916     938 .. 0.98

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 6.6e-11
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       tPGFG+v+A+++LLaaalLa Rr
  gi|313117350|ref|YP_004044333.1| 916 TPGFGVVVAVTALLAAALLAVRR 938
                                       9********************98 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.5   5.5e+03      31      59 ..      84     112 ..      75     123 .. 0.71
   2 ?   -3.3   0.0       3.5   1.3e+04      25      74 ..     193     243 ..     191     250 .. 0.72
   3 !    9.0   0.2   0.00053       1.9      33      83 ..     307     358 ..     293     367 .. 0.81
   4 !    6.6   0.0    0.0029        11      31      69 ..     393     431 ..     379     459 .. 0.82
   5 ?   -2.4   0.0       1.9   6.9e+03      13      52 ..     793     828 ..     789     851 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                                       ---EEEEEEEE-TTSSEEEEEEEEE-CTT CS
                               MG2  31 laklplkltirdpdgkevkelplatdetg 59 
                                       +++++  l+i++++g ++ + +++ +++ 
  gi|313117350|ref|YP_004044333.1|  84 VTFANSNLVIENASGTQIGTGSVTLTNND 112
                                       55577889999999999999888655553 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.5
                                       STTCSB---EEEEEEEE-TTSS.EEEEEEEEE-CTTEEEEEEE--TT--SE CS
                               MG2  25 detlqglaklplkltirdpdgk.evkelplatdetggaesefalpeaaklG 74 
                                       d++ ++ ++++l+l ++ p +  e + + l  de+ +a+s++ l ++ + G
  gi|313117350|ref|YP_004044333.1| 193 DNDTSASEDAELELAFNEPIKDiEKSDFNLYVDEEPIADSKISLDQKGSSG 243
                                       566677777888888888855426666777888888888888888887777 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00053
                                       -.EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEEC CS
                               MG2  33 k.lplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsad 83 
                                       + +++++t++ +d++++++++  ++ t++  + f + +++++G+y+++l+ +
  gi|313117350|ref|YP_004044333.1| 307 DkTQTEITVEASDDEDFDSFQEGNTGTNSQVYVFSTTDDTETGQYNITLKGE 358
                                       34899999999999999999998888889999*****************332 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0029
                                       ---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--T CS
                               MG2  31 laklplkltirdpdgkevkelplatdetggaesefalpe 69 
                                       + ++p++l++ d+dg +v++ +++ + +  +e++f+ +e
  gi|313117350|ref|YP_004044333.1| 393 AGNRPVRLELLDSDGDTVEQRDVELSGQRKYEFSFNASE 431
                                       3459*******************9999999999998765 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 1.9
                                       TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEE CS
                               MG2  13 PgetVslkallrdetlqglaklplkltirdpdgkevkelp 52 
                                       Pg +Vs++a + + + q+   +p++++++    +++++ +
  gi|313117350|ref|YP_004044333.1| 793 PGTEVSVRARS-TGDTQPSFLKPATVYVTE---NQTFSAT 828
                                       55556655555.345555555666666654...3344444 PP

>> DUF4581  Domain of unknown function (DUF4581)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   3.4e-05      0.12      48     111 ..     697     763 ..     685     777 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                           DUF4581  48 tggtdnfhvwsesedclpflqlaqdyisscgkktl.levlekvfksfrpllglpdvddd.tf.eeyn 111
                                         gtdn  vw++s++   f++   d +++  +      vle  f  +     l dvdd  t+ +ey+
  gi|313117350|ref|YP_004044333.1| 697 ELGTDNTTVWADSDNNTYFIKYDTDQVTTTERSIDkDHVLEANFTVYEDEGNLTDVDDGeTVkDEYE 763
                                       558*************************99987651579******************9514313343 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.4     5e+03      33      55 ..      41      68 ..      36      76 .. 0.65
   2 ?   10.6   0.0   0.00011      0.38      14      57 ..     294     346 ..     280     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                                      EEEES.STT.......T.-EEEEEE.SHH CS
                              KH_1 33 Ikvpk.sedeg....sderevtisG.spe 55
                                      +++ + + deg    +++  v isG + +
  gi|313117350|ref|YP_004044333.1| 41 VTFSPtDVDEGetgsQHNVNVSISGyT-N 68
                                      666644444446778899999999944.3 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
                                       HHTGGGHHHHHHHHHHT-EEEEESSTT............T.-EEEEEESHHHH CS
                              KH_1  14 iIGkgGsnIkeIreetgakIkvpksedeg.........sderevtisGspeav 57 
                                       i   +GsnI  I ++t++ I+v+ s+de+         +++++v ++ + ++ 
  gi|313117350|ref|YP_004044333.1| 294 INAYQGSNIAVITDKTQTEITVEASDDEDfdsfqegntGTNSQVYVFSTTDDT 346
                                       55569****************99555555678888888888888887755555 PP

>> DUF4251  Domain of unknown function (DUF4251)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.71   2.6e+03      54     109 ..      26      77 ..      22     101 .. 0.59
   2 ?   -1.9   0.0      0.84     3e+03     107     124 ..     105     123 ..      89     136 .. 0.73
   3 ?    9.3   0.8   0.00029         1      56     122 ..     297     367 ..     292     374 .. 0.74
   4 ?   -1.6   0.0      0.65   2.3e+03      96     120 ..     475     499 ..     439     503 .. 0.82
   5 ?    0.4   0.0      0.16   5.7e+02      16      51 ..     675     724 ..     662     726 .. 0.76
   6 ?   -1.0   0.0      0.44   1.6e+03      82     110 ..     818     846 ..     811     856 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.71
                                       ESSCCC-----..-----EEEEEEEEEEEEEE-TT--EEEEEEEE-SS-EEEEEEE CS
                           DUF4251  54 LpYfgraysgpygngkggitfkgkisdykikkdkkgnveiefsvkgkeesytvtlt 109
                                       +++ g+a  ++  +    +tf+ +  d + ++  ++nv++++s  ++++ +  t++
  gi|313117350|ref|YP_004044333.1|  26 IAFAGSAAAVS--GASK-VTFSPTDVD-EGETGSQHNVNVSISGYTNADGAADTIN 77 
                                       66667776655..4444.777444444.5566666667777766444444433333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.84
                                       EEEE-T.SSEEEEEEEETS CS
                           DUF4251 107 tltlyk.ngkaslsvnsnn 124
                                       ++tl++ + +a +s+n+ +
  gi|313117350|ref|YP_004044333.1| 105 SVTLTNnDASAEISINPAS 123
                                       5677777788888888865 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00029
                                       SCCC-----..-----EEEEEEEEE..EEEEE-TT--..EEEEEEEE-SS-EEEEEEEE-TSSEEEEEEEE CS
                           DUF4251  56 Yfgraysgpygngkggitfkgkisd..ykikkdkkgn..veiefsvkgkeesytvtltlykngkaslsvns 122
                                       Y g++  +  ++++  it++++  +   ++++ ++g+    + fs+++++e+ ++++tl  +g+a+++v +
  gi|313117350|ref|YP_004044333.1| 297 YQGSNIAVITDKTQTEITVEASDDEdfDSFQEGNTGTnsQVYVFSTTDDTETGQYNITLKGEGSAQVNVRN 367
                                       555555555566666777777766555333444444336899**************************975 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.65
                                       EEE-SS-EEEEEEEE-TSSEEEEEE CS
                           DUF4251  96 svkgkeesytvtltlykngkaslsv 120
                                        v + ++++++t+++ ++  a+ls+
  gi|313117350|ref|YP_004044333.1| 475 FVDQRGDVANITINVENSDFATLSL 499
                                       5678889999999999999999886 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.16
                                       TT-EEEEEEEEEET..............TS-EEE--TTTSEEEEETTEEE CS
                           DUF4251  16 skeFkieadraypk..............rgrsinltsntyfvkvkgdsvs 51 
                                       ++ F++ +++a+p                   ++ ++ntyf+k + d+v+
  gi|313117350|ref|YP_004044333.1| 675 DGAFELTVEQANPGanrdpyelelgtdnTTVWADSDNNTYFIKYDTDQVT 724
                                       67888999999988888888888877655555666789999999999986 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 0.44
                                       EEEE-TT--EEEEEEEE-SS-EEEEEEEE CS
                           DUF4251  82 kikkdkkgnveiefsvkgkeesytvtltl 110
                                        ++++++ + ++ fs +  +++y++t++ 
  gi|313117350|ref|YP_004044333.1| 818 YVTENQTFSATLDFSEQAVGDTYEITIDG 846
                                       56777777889999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (939 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 5983.79
//
Query:       gi|313117351|ref|YP_004044334.1|  [L=264]
Description: hypothetical protein Hbor_31380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1826.29
//
Query:       gi|313117352|ref|YP_004044335.1|  [L=998]
Description: lipoprotein release ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-05   25.3  12.1      3e-05   24.2   1.2    4.1  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0012   18.8   1.6      0.031   14.3   0.1    2.8  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
     0.0019   18.6   5.0     0.0019   18.6   5.0    5.1  6  FtsX             FtsX-like permease family
  ------ inclusion threshold ------
      0.013   15.3   6.2      0.051   13.5   0.5    3.9  4  PEGA             PEGA domain
      0.025   14.8   0.1       0.21   11.9   0.1    2.6  1  Big_6            Bacterial Ig domain
       0.29   11.4   2.5       0.37   11.1   0.4    2.3  2  CARDB            CARDB


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.014        41      48      76 ..     578     607 ..     557     614 .. 0.75
   2 ?    2.0   0.2     0.083   2.5e+02      13      54 ..     594     637 ..     583     646 .. 0.67
   3 !   24.2   1.2     1e-08     3e-05      10      77 ..     676     737 ..     670     742 .. 0.88
   4 ?    1.2   0.2      0.15   4.5e+02      44      78 ..     807     840 ..     806     844 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                   CarboxypepD_reg  48 gtysvtv..sapGyatatreevtltagqttt 76 
                                        ty++tv  +  G + at ++vt++a++ t+
  gi|313117352|ref|YP_004044335.1| 578 HTYTLTVrgENLGKKAAT-RNVTVRADNRTR 607
                                       689999944455666777.58****999775 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.083
                   CarboxypepD_reg  13 piagatVtvtnadtgtvastttdadGafrlrglpp..gtysvtv 54 
                                       +  ++tV++ n   + + s+  +++Ga  + +  +  gt+++t+
  gi|313117352|ref|YP_004044335.1| 594 ATRNVTVRADNRTRSRTLSVGPGESGAADVGFTFAepGTHTITA 637
                                       44677777777777777777778888776665544448887777 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 1e-08
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglpp..gtysvtvsapGyatatreevtltagqtttl 77 
                                       + +p++gatVt+        ++ tt+++G+  +r +p+  g+y++t+++++y + +r +++++++ +++l
  gi|313117352|ref|YP_004044335.1| 676 NETPVTGATVTLG------DRQGTTNEQGTVLMR-VPTepGEYTLTIEKQNYTSERR-TLVVEEDAPQRL 737
                                       789**********......799*********998.77778****************7.599999988876 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.15
                   CarboxypepD_reg  44 glppgtysvtvsapGyatatreevtltagqtttld 78 
                                       +l+pgty+++  ++    at  + ++t ++ +t +
  gi|313117352|ref|YP_004044335.1| 807 SLTPGTYDLRLVSDEIVLATT-TYRVTGDERVTAT 840
                                       699********9999999995.5888865544443 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.049   1.5e+02      28      71 ..     564     607 ..     556     613 .. 0.74
   2 !   14.3   0.1     1e-05     0.031       9      69 ..     675     734 ..     672     745 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.049
                   CarbopepD_reg_2  28 tvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektld 71 
                                       +vT+ +G+ +++  +  + t++ + +G k ++++vtv  ++++ 
  gi|313117352|ref|YP_004044335.1| 564 VVTELSGSSSVEVNHTYTLTVRGENLGKKAATRNVTVRADNRTR 607
                                       5688888888875554555555567************9988765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1e-05
                   CarbopepD_reg_2   9 etkeplpgatVyvkgtkkgtvTdenGnFelknlpa.gkytLvvsyvGyktqekkvtvskekt 69 
                                        +++p+ gatV++ +  ++ +T+e+G+  ++ +++ g+ytL+++   y+++ +++ v+++  
  gi|313117352|ref|YP_004044335.1| 675 RNETPVTGATVTLGD--RQGTTNEQGTVLMRVPTEpGEYTLTIEKQNYTSERRTLVVEEDAP 734
                                       5678********944..45679*****9998544359*****************99998755 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.55   1.6e+03      25      46 ..      16      37 ..       7      59 .. 0.63
   2 ?   -1.7   0.2       1.4   4.2e+03      70      94 ..     207     231 ..     183     233 .. 0.59
   3 ?    2.8   8.4     0.053   1.6e+02       3      93 ..     239     332 ..     237     335 .. 0.83
   4 ?   -3.0   6.4       3.6   1.1e+04      25      86 ..     308     392 ..     300     401 .. 0.49
   5 ?   -4.1   0.4         6   1.8e+04      21      35 ..     867     881 ..     862     888 .. 0.48
   6 !   18.6   5.0   6.3e-07    0.0019       1      79 [.     895     973 ..     895     988 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.55
                              FtsX 25 illitlvalviGlglgllaaql 46
                                      +l ++++a   ++++g++++ l
  gi|313117352|ref|YP_004044335.1| 16 WLSVAVIAVTTAFLIGSAVLLL 37
                                      4455555555555555444333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                              FtsX  70 liiivlllllallagllsiskilkk 94 
                                       + ++ ++ +   l +l+ +++++++
  gi|313117352|ref|YP_004044335.1| 207 IRTLTIAAVGGGLLILVVVYNVTRM 231
                                       3333333333333334455555555 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.053
                              FtsX   3 eigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs..selkisidli.tvliiivll 76 
                                       ei + ra G +  +++ +l + +l ++  + ++G+++gl+ ++++ +          +++ ++ d++ +vl i ++l
  gi|313117352|ref|YP_004044335.1| 239 EIRVARATGISPIRLFAVLQGRVLGLVGTGVILGFAIGLITTKAVINAATYAGLPvtIRAVVTSDILwAVLQIGGFL 315
                                       999*****************************************888876665547755555555551578899999 PP

                              FtsX  77 lllallagllsiskilk 93 
                                       l + +lag+l++  + +
  gi|313117352|ref|YP_004044335.1| 316 LGMGVLAGVLASVPVVR 332
                                       99999*99999987766 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 3.6
                              FtsX  25 illitlvalviGlglgllaaqllsdvllssvf....................s...selkisidlitvliiivllll 78 
                                       +l i+ + l +G+++g+la+ ++  +  +  +                    +         +++ t ++++vl++l
  gi|313117352|ref|YP_004044335.1| 308 VLQIGGFLLGMGVLAGVLASVPVVRGSPATIGrstnttqsiatrvrerlslvQptfVDWRAVVPTTTTVAVFVLVIL 384
                                       44445555555566666666666666655533333344444444444432221322333334555555666666666 PP

                              FtsX  79 lallagll 86 
                                       l++++g +
  gi|313117352|ref|YP_004044335.1| 385 LTTAIGGA 392
                                       66666544 PP

  == domain 5  score: -4.1 bits;  conditional E-value: 6
                              FtsX  21 llteillitlvalvi 35 
                                       l++ +++++ v++v 
  gi|313117352|ref|YP_004044335.1| 867 LFLVMIALAGVSTVG 881
                                       333444444444443 PP

  == domain 6  score: 18.6 bits;  conditional E-value: 6.3e-07
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlll 77 
                                       +r igi+ra G++++q+l++l + ++ ++l+a++i++g ++ ++++l      + f++ l+   +++ +l + + +l
  gi|313117352|ref|YP_004044335.1| 895 RRRIGIFRATGASRRQLLGVLAVDAVKLSLPAIAIAFGTAFTVIYVLARSDVLVIFGIKLHAPQSVELLLGTGLGAL 971
                                       689*********************************99999888886655555555544444444444444444444 PP

                              FtsX  78 ll 79 
                                        l
  gi|313117352|ref|YP_004044335.1| 972 AL 973
                                       44 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.54   1.6e+03      22      55 ..     338     373 ..     335     381 .. 0.77
   2 ?   -2.5   0.1       1.6   4.9e+03      36      60 ..     580     606 ..     575     611 .. 0.63
   3 ?   13.5   0.5   1.7e-05     0.051      10      66 ..     680     741 ..     675     744 .. 0.78
   4 ?    1.7   0.0     0.083   2.5e+02      30      64 ..     807     841 ..     804     845 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.54
                              PEGA  22 lG.kTPvtls.leaGnyslrvekeGYedlektvtvt 55 
                                       +G +T++t s     + +l ++++ + d+++ v  t
  gi|313117352|ref|YP_004044335.1| 338 IGrSTNTTQSiATRVRERLSLVQPTFVDWRAVVPTT 373
                                       5667888888555667789**********9998776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                              PEGA  36 yslrveke..GYedlektvtvtagetv 60 
                                       y+l+v  e  G + +++ vtv+a+  +
  gi|313117352|ref|YP_004044335.1| 580 YTLTVRGEnlGKKAATRNVTVRADNRT 606
                                       555555442233567888888877665 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.7e-05
                              PEGA  10 peGatVyidGkylGkTP.....vtls.leaGnyslrvekeGYedlektvtvtagetvklnltL 66 
                                         GatV++ G   G T+     ++ +  e+G+y+l++ek +Y+  ++t  v+++  ++l  +L
  gi|313117352|ref|YP_004044335.1| 680 VTGATVTL-GDRQGTTNeqgtvLMRVpTEPGEYTLTIEKQNYTSERRTLVVEEDAPQRLIGRL 741
                                       6799****.88999777444433333489**************99999999988877776666 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.083
                              PEGA  30 sleaGnyslrvekeGYedlektvtvtagetvklnl 64 
                                       sl +G+y lr++ +    +++t  vt +e v+++l
  gi|313117352|ref|YP_004044335.1| 807 SLTPGTYDLRLVSDEIVLATTTYRVTGDERVTATL 841
                                       5889**********999999999999999988775 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.9e-05      0.21      23      68 ..     681     732 ..     673     736 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                             Big_6  23 agatVtvkdadgtvlgtgta.....dadGeFsvtlepaqangetls.vvatD 68 
                                       +gatVt+ d +gt+  +gt+     ++ Ge+++t+e+++ + e+ + vv +D
  gi|313117352|ref|YP_004044335.1| 681 TGATVTLGDRQGTTNEQGTVlmrvpTEPGEYTLTIEKQNYTSERRTlVVEED 732
                                       79****************999998999********99985555544045555 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00012      0.37       5      82 ..     564     637 ..     561     642 .. 0.84
   2 ?   -3.2   0.1       3.4     1e+04      66      82 ..     699     715 ..     676     724 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       EE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEE CS
                             CARDB   5 tvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtlt 81 
                                       +vt+ ++ s+++v+ ++t+tv  +N G++a++  +v++ +d  +  + t+ s+ +ges   ++ +t + ++g++t+t
  gi|313117352|ref|YP_004044335.1| 564 VVTELSGSSSVEVNHTYTLTVRGENLGKKAATR-NVTVRADNRT-RSRTL-SVGPGESGAADVGFTFA-EPGTHTIT 636
                                       56899999********************99876.6777777777.44555.67999999999999998.99999998 PP

                                       E CS
                             CARDB  82 v 82 
                                       +
  gi|313117352|ref|YP_004044335.1| 637 A 637
                                       7 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.4
                                       EEEEE-S-S-CEEEEEE CS
                             CARDB  66 sftwtteategevtltv 82 
                                       ++ + +++++ge+tlt+
  gi|313117352|ref|YP_004044335.1| 699 TVLMRVPTEPGEYTLTI 715
                                       33333335677776653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (998 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.79u 0.29s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 5824.52
//
Query:       gi|313117353|ref|YP_004044336.1|  [L=232]
Description: antimicrobial peptide ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-30  104.8   0.0    6.5e-30  104.4   0.0    1.1  1  ABC_tran     ABC transporter
    1.6e-06   28.1   0.7     0.0057   16.5   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.3e-05   24.0   0.1    7.2e-05   23.2   0.1    1.3  1  AAA_16       AAA ATPase domain
     0.0035   17.0   0.2     0.0087   15.8   0.2    1.7  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.02   13.9   0.1      0.035   13.2   0.1    1.4  1  T2SSE        Type II/IV secretion system protein
       0.02   14.8   0.1      0.045   13.7   0.1    1.5  1  RsgA_GTPase  RsgA GTPase
      0.026   14.0   0.0       0.29   10.6   0.0    2.0  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.029   14.6   0.1       0.29   11.4   0.0    2.1  2  AAA_22       AAA domain
      0.066   13.1   0.0      0.096   12.6   0.0    1.2  1  Rad17        Rad17 P-loop domain
      0.071   13.6   0.0       0.11   13.0   0.0    1.3  1  AAA_23       AAA domain
      0.074   13.3   0.1        1.3    9.3   0.1    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.096   12.6   0.3        2.2    8.2   0.1    2.2  2  NACHT        NACHT domain
       0.19   11.9   0.2       0.33   11.1   0.2    1.7  1  AAA_33       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   4.7e-33   6.5e-30       1     136 [.      20     165 ..      20     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 4.7e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ +sl++  ++ + + G++GaGK+tL+++l  l++pt+G++ ++g+d ++    ++  + r  ig+++q+ ql p+
  gi|313117353|ref|YP_004044336.1|  20 LDGISLDVADDTSLLVRGPSGAGKTTLFNVLGLLSTPTSGSLFVNGEDASSlperKRAAIRRDTIGFVFQDFQLIPD 96 
                                       789**********************************************999998999999**************** PP

                                       SBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       l++ +n           +++++e++ + l++++l+++      ++LSgG+kqrva+aral++kp+++l+DEpt
  gi|313117353|ref|YP_004044336.1|  97 LSAWDNaalpqdhtgsRDESWLETLFDALDITDLREQYP----TTLSGGEKQRVAIARALANKPDVVLADEPT 165
                                       ************99988888899999****999999998....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.4   0.00037      0.51       6      36 ..      37      67 ..      33      98 .. 0.74
   2 !   16.5   0.0   4.2e-06    0.0057     212     299 ..     113     198 ..      89     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00037
                            AAA_21  6 GpNgsGKSnLLdaldllarldrdvegltdel 36
                                      Gp g+GK++L+  l ll+   + + + + e+
  gi|313117353|ref|YP_004044336.1| 37 GPSGAGKTTLFNVLGLLSTPTSGSLFVNGED 67
                                      9*************99975444444444333 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.2e-06
                            AAA_21 212 vderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsr 287
                                       +de ++e  +  l+ +d +e  ++ lS G k+  a++ al+  +   +++l DEp   L+P   +r+l+ll + +++
  gi|313117353|ref|YP_004044336.1| 113 RDESWLETLFDALDITDLREQYPTTLSGGEKQRVAIARALANKP---DVVLADEPTGQLDPNTAERVLDLLfRVKAQ 186
                                       333333336666777788999999********977777777766...*********************999888888 PP

                            AAA_21 288 ngaQviltTHSp 299
                                       +++ ++l +H+ 
  gi|313117353|ref|YP_004044336.1| 187 TDTALVLISHDR 198
                                       89********85 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   5.3e-08   7.2e-05      25     139 ..      31     193 ..      21     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.3e-08
                            AAA_16  25 elvllsGesGvGKsslvrellralekd..ggiflrgkcdql.....esaipysalaqalareellrqlldeaesael 94 
                                        ++l++G+sG GK++l + l   l++   g +f++g+  ++     ++ai+++++  ++   +l+ +l + +++ +l
  gi|313117353|ref|YP_004044336.1|  31 TSLLVRGPSGAGKTTLFNVLG-LLSTPtsGSLFVNGEDASSlperkRAAIRRDTIGFVFQDFQLIPDLSAWDNA-AL 105
                                       689**************8888.5555545788888888888886644447778899999889999999988555.44 PP

                            AAA_16  95 eawrekleeala..............................................avpelagaeasrllellkr 125
                                       +++++  +++                                                ++++l++  a+r+l+ll r
  gi|313117353|ref|YP_004044336.1| 106 PQDHTGSRDESWletlfdalditdlreqypttlsggekqrvaiaralankpdvvladePTGQLDPNTAERVLDLLFR 182
                                       44555444444457888888899999999999999999999999999999999999998899999888888888655 PP

                            AAA_16 126 llallsrderplvl 139
                                           +++ +  lvl
  gi|313117353|ref|YP_004044336.1| 183 VK--AQT-DTALVL 193
                                       44..554.334665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   6.3e-06    0.0087      17      50 ..      25      58 ..      13      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.3e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +++  + + l+ GpsG+GK+Tl+  +  l +p++
  gi|313117353|ref|YP_004044336.1| 25 LDVADDTSLLVRGPSGAGKTTLFNVLGLLSTPTS 58
                                      445434489999**********987777777766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.6e-05     0.035     122     167 ..      23      69 ..      11      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                             T2SSE 122 lrkavrerglilvsGgTgsGKttllyal.lkeinksderivtvEDpv 167
                                       ++  v+   ++lv G+ g GKttl ++l l   ++s   +v  ED+ 
  gi|313117353|ref|YP_004044336.1|  23 ISLDVADDTSLLVRGPSGAGKTTLFNVLgLLSTPTSGSLFVNGEDAS 69 
                                       5666788999**************99863445555566666667665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.2e-05     0.045      96     119 ..      26      50 ..      10      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-05
                                       HCTTSEEEEE.CSTTSSHHHHHHHH CS
                       RsgA_GTPase  96 llkdktsvlv.GqSGvGKStLinal 119
                                        ++d+ts+lv G+SG+GK+tL n+l
  gi|313117353|ref|YP_004044336.1|  26 DVADDTSLLVrGPSGAGKTTLFNVL 50 
                                       55665555544************98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.13   1.8e+02      28      43 ..      34      49 ..      20      58 .. 0.79
   2 ?   10.6   0.0   0.00021      0.29     135     201 ..     136     200 ..      62     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
                                      EEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnlldA 43
                                       + Gp G+GK+ l++ 
  gi|313117353|ref|YP_004044336.1| 34 LVRGPSGAGKTTLFNV 49
                                      577********99875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreem 201
                                       ++LSgGek+ va+a  +A    kp  ++l De   +LD +  ++v +ll   ++++++ ++ is+++++
  gi|313117353|ref|YP_004044336.1| 136 TTLSGGEKQRVAIARALAN---KP-DVVLADEPTGQLDPNTAERVLDLLFrvKAQTDTALVLISHDRGL 200
                                       48**********9988773...34.46788****************99873445556778888887765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.29       5      24 ..      30      49 ..      27      71 .. 0.87
   2 ?    1.1   0.0      0.32   4.4e+02      81     133 ..     147     200 ..     109     204 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                            AAA_22  5 agilvvtGesGtGKTtllrr 24
                                      +++l+v G+sG+GKTtl + 
  gi|313117353|ref|YP_004044336.1| 30 DTSLLVRGPSGAGKTTLFNV 49
                                      6799************9875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.32
                            AAA_22  81 aleqalraravielliiDEaqh.lr..s.eealeeLrsllnl.srkgvqliLvGtp.el 133
                                       a+++al ++ +  +++ DE    l+  + e++l  L   + + ++++++l+L+ +  +l
  gi|313117353|ref|YP_004044336.1| 147 AIARALANKPD--VVLADEPTGqLDpnTaERVLDLL---FRVkAQTDTALVLISHDrGL 200
                                       45555555555..88888887778543223333333...33356899999988766555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.9e-05     0.096      35      66 ..      20      51 ..      17      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.9e-05
                             Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      l+  +L+ +    LL+ GPsG gk+t  +vL 
  gi|313117353|ref|YP_004044336.1| 20 LDGISLDVADDTSLLVRGPSGAGKTTLFNVLG 51
                                      6667888888899*************999986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.8e-05      0.11      23      43 ..      34      54 ..      20      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.8e-05
                            AAA_23 23 lItGpNGaGKTTildAiklaL 43
                                      l+ Gp GaGKTT+++ + l  
  gi|313117353|ref|YP_004044336.1| 34 LVRGPSGAGKTTLFNVLGLLS 54
                                      778***********9987765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00095       1.3      32      88 ..     137     180 ..     126     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00095
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       tlSGGekq    +a+a     ++ +      ++++v+ DE  ++lD+++++++l+ll
  gi|313117353|ref|YP_004044336.1| 137 TLSGGEKQR---VAIA----RALAN------KPDVVLADEPTGQLDPNTAERVLDLL 180
                                       678888843...3333....33333......5889999**********999999987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0016       2.2       3      18 ..      33      48 ..      31      55 .. 0.87
   2 ?    2.3   0.0       0.1   1.4e+02      93     138 ..     164     204 ..     141     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                                      EEEEC-TTTCHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlq 18
                                      ++++G++G GKTtL  
  gi|313117353|ref|YP_004044336.1| 33 LLVRGPSGAGKTTLFN 48
                                      689**********975 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                                       -SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTT CS
                             NACHT  93 lvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeq 138
                                          +l   +++ ++++L  l+r k  + + l+l+++ r+l  +++ 
  gi|313117353|ref|YP_004044336.1| 164 PTGQL---DPNTAERVLDLLFRVKAQTDTALVLISHDRGL--APRF 204
                                       44444...458888999999***************99998..4444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00024      0.33       3      19 ..      34      50 ..      33     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                            AAA_33  3 llvGlpGsGKstlaerl 19
                                      l+ G++G+GK+tl   l
  gi|313117353|ref|YP_004044336.1| 34 LVRGPSGAGKTTLFNVL 50
                                      789*********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 1561.44
//
Query:       gi|313117354|ref|YP_004044337.1|  [L=172]
Description: membrane-bound metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   40.8   7.3    1.9e-10   40.3   7.3    1.2  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
      0.072   13.2   1.0        0.1   12.7   1.0    1.2  1  UPF0242   Uncharacterised protein family (UPF0242) N-terminus


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   7.3   2.1e-14   1.9e-10       1     162 [.       1     155 [.       1     167 [. 0.74

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.1e-14
                              YdjM   1 MdgltHallGaalglalaallgaake.avllavavlgAllPD.iDhpsstlgrklgllskklaklvgHRgftHSllf 75 
                                       M ++ H++l+ +  +++a  +  +    + la++v+++ lPD +D p ++    +g ls+        R++ HSl++
  gi|313117354|ref|YP_004044337.1|   1 MYPIGHLALAYLSYVLYARVTDIQLPhGRPLAILVVASQLPDlVDKPLVY----IGVLSS-------GRSLAHSLVV 66 
                                       88899*************9999987789**************99*55555....456667.......9********* PP

                              YdjM  76 lallalvlllllrlfgrsalrlglllllgvlsHlllDl....ltkyGvpl...lwPfskkkvrlsllfiiidplltl 145
                                       l+ + l++  +l++++r+   l+ +l +g lsH+l+D+    lt++ ++l   lwP+     +++ +   i p+++l
  gi|313117354|ref|YP_004044337.1|  67 LVPVLLLVGTILVHLERR--PLWPILSVGTLSHVLGDSyrlvLTQQWTELrflLWPV---FPAINYPNDGIPPWVRL 138
                                       *******99999999999..899**************83332455444333248888...46666666666777666 PP

                              YdjM 146 lsrrglvalelvllvly 162
                                       l+   ++ + + +++++
  gi|313117354|ref|YP_004044337.1| 139 LNHGFGLGMRVQFSLAI 155
                                       64444443444444433 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   1.2e-05       0.1      10      58 ..      64     112 ..      58     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                           UPF0242  10 flYllPllllaiysiqllseqksWsllsiGlllaaaGsLlllllllkwe 58 
                                       ++ l+P+lll+   + +l  +  W +ls+G l  + G    l+l  +w 
  gi|313117354|ref|YP_004044337.1|  64 LVVLVPVLLLVGTILVHLERRPLWPILSVGTLSHVLGDSYRLVLTQQWT 112
                                       67799**********************************9****99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 1262.72
//
Query:       gi|313117355|ref|YP_004044338.1|  [L=552]
Description: hypothetical protein Hbor_31420 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.034   14.4   0.6      0.034   14.4   0.6    3.4  4  Spore_YabQ  Spore cortex protein YabQ (Spore_YabQ)


Domain annotation for each model (and alignments):
>> Spore_YabQ  Spore cortex protein YabQ (Spore_YabQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.6   1.9e-06     0.034      34      71 ..     148     185 ..     131     192 .. 0.87
   2 ?   -1.1   0.4      0.13   2.2e+03      63      75 ..     220     232 ..     194     235 .. 0.74
   3 ?   -2.2   0.7      0.29   5.1e+03      40      60 ..     260     280 ..     256     299 .. 0.56
   4 ?   -2.7   0.2      0.39   7.1e+03      59      72 ..     347     360 ..     340     364 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-06
                        Spore_YabQ  34 eDilfwllaallvflfllrinygelrlylflgillGal 71 
                                       e+i+  ll+ ++  ++ + +  g+ r+y ++g+llG++
  gi|313117355|ref|YP_004044338.1| 148 EEIVAILLSLIVAVSLHYAFRTGQRRWYGIVGLLLGIF 185
                                       77888999****************************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.13
                        Spore_YabQ  63 flgillGallyrl 75 
                                        +g++ G+++y +
  gi|313117355|ref|YP_004044338.1| 220 GVGLAGGFWAYIA 232
                                       4577778888865 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.29
                        Spore_YabQ  40 llaallvflfllrinygelrl 60 
                                       +++++++ + +++i++  lr+
  gi|313117355|ref|YP_004044338.1| 260 VAWGIVLVIGVVWIQHTSLRI 280
                                       455555555555555555554 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 0.39
                        Spore_YabQ  59 rlylflgillGall 72 
                                        l+  +++++G+ l
  gi|313117355|ref|YP_004044338.1| 347 ALFSAPAVIIGFSL 360
                                       57888889999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 4044.14
//
Query:       gi|313117356|ref|YP_004044339.1|  [L=992]
Description: antimicrobial peptide ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-11   43.7  13.0    2.1e-07   31.3   2.0    5.2  6  FtsX             FtsX-like permease family
      0.004   17.4   4.7      0.004   17.4   4.7    4.8  5  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
       0.42   11.7   2.6       0.93   10.6   0.3    2.7  2  CopC             CopC domain
        4.2    7.3   7.1        2.2    8.2   1.0    3.3  2  DUF5325          Family of unknown function (DUF5325)


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.076   3.4e+02      11      45 ..      10      36 ..       3      75 .. 0.59
   2 ?   -2.0   0.4       1.1   5.1e+03      58      83 ..     190     215 ..     174     219 .. 0.62
   3 !   31.3   2.0   4.7e-11   2.1e-07       3      96 .]     225     321 ..     223     321 .. 0.73
   4 ?   -0.4   0.2      0.37   1.6e+03      15      34 ..     364     383 ..     343     388 .. 0.59
   5 ?   -0.8   0.3      0.49   2.2e+03      66      83 ..     844     861 ..     818     872 .. 0.59
   6 !   26.9   3.5   1.1e-09   4.9e-06       1      89 [.     876     964 ..     876     971 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.076
                              FtsX 11 GmkkkqvlllllteillitlvalviGlglgllaaq 45
                                      G+ ++++l ++++ + + +lv++        +++ 
  gi|313117356|ref|YP_004044339.1| 10 GWARRDTLAVVVIALTVSFLVGA--------AVLG 36
                                      55555555555554444444443........3332 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                              FtsX  58 selkisidlitvliiivlllllalla 83 
                                       +el   + l tv+++i++++ +++++
  gi|313117356|ref|YP_004044339.1| 190 GELVRLLRLATVAAGILVAVTIYSVV 215
                                       66666667777777777777777666 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 4.7e-11
                              FtsX   3 eigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs..selkisid.litvliiivll 76 
                                        i++lr+ G++ +qvl+l+ + ++ +t+v++++G+g+gl++  ++ +           +++is + l+ ++ ++vl+
  gi|313117356|ref|YP_004044339.1| 225 DIAVLRSTGATPRQVLQLFALRAVTLTAVGTAVGYGFGLILVRVVVNAAIYGGLPtsLSAQISQPvLSVLVPAVVLF 301
                                       69****************************************99666544433333333444433144445556666 PP

                              FtsX  77 lllallagllsiskilkkep 96 
                                       l++  l+gll+++k + +ep
  gi|313117356|ref|YP_004044339.1| 302 LVVGGLSGLLAAYKGATQEP 321
                                       67777888998888777665 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.37
                              FtsX  15 kqvlllllteillitlvalv 34 
                                       +++l +++  +ll+t+va +
  gi|313117356|ref|YP_004044339.1| 364 ASTLTVFMCALLLLTAVAGA 383
                                       33334444444444444444 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.49
                              FtsX  66 litvliiivlllllalla 83 
                                        i vl+++v++ll ++ +
  gi|313117356|ref|YP_004044339.1| 844 NIEVLVLAVVALLSVMTV 861
                                       444444444444444444 PP

  == domain 6  score: 26.9 bits;  conditional E-value: 1.1e-09
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlll 77 
                                       kreigi+ra G++ + +l  +++ +l i+  a+v++ ++++ +   l +v++  vf+  l + i + +v++++v ++
  gi|313117356|ref|YP_004044339.1| 876 KREIGIRRATGASPWAILTDVIVDTLKIGTTATVLAGVIAFGVVSGLLSVGELRVFGVVLEPVITPTAVVAALVGGV 952
                                       79*******************************************************88888888888888888888 PP

                              FtsX  78 llallagllsis 89 
                                        la++++ l++ 
  gi|313117356|ref|YP_004044339.1| 953 ALAVISATLATA 964
                                       888877666543 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.7   3.1e+03      15      54 ..     482     519 ..     477     525 .. 0.76
   2 ?   -1.5   0.2       0.7   3.2e+03      43      76 ..     559     592 ..     545     606 .. 0.69
   3 !   17.4   4.7     9e-07     0.004       9      77 ..     664     724 ..     659     731 .. 0.80
   4 ?    1.0   0.0      0.12   5.3e+02      52      81 ..     759     786 ..     754     787 .. 0.78
   5 ?    3.2   0.6     0.024   1.1e+02      41      71 ..     785     814 ..     783     822 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.7
                   CarboxypepD_reg  15 agatVtvtnadtgtvastttdadGafrlrglppgtysvtv 54 
                                       +g tV++   +++t + ++ + +G+f+ +g++ ++  v +
  gi|313117356|ref|YP_004044339.1| 482 PGETVVIG--GSTTASVARFNITGTFTGTGIQDDQLLVSI 519
                                       56677777..666777788899999998888887777665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.7
                   CarboxypepD_reg  43 rglpp.gtysvtvsapGyatatreevtltagqttt 76 
                                       r++   +  sv v+  G  +atr e+++  g t++
  gi|313117356|ref|YP_004044339.1| 559 RNVNNrTGVSVAVTNLGLSEATR-EFEIKLGSTVR 592
                                       55555555677778888888886.47666666654 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 9e-07
                   CarboxypepD_reg   9 asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttl 77 
                                       + ++p+a+at+++        +++tt++ G  rl+   +g+ +++++++G +++t  +vt++++  + l
  gi|313117356|ref|YP_004044339.1| 664 HGDTPVANATISLG------AQTVTTNDRGLARLALNSTGNATLVATSNGERETT--TVTVRDDAVRAL 724
                                       3568**********......8*************96666*************999..488887765433 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.12
                   CarboxypepD_reg  52 vtvsapGyatatreevtltagqtttlditL 81 
                                       ++v+ p  +  +   vt++ g+t+t++++L
  gi|313117356|ref|YP_004044339.1| 759 LRVTGPSVEKKR--PVTVESGETATVRARL 786
                                       666666666666..5***********9987 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.024
                   CarboxypepD_reg  41 rlrglppgtysvtvsapGyatatreevtlta 71 
                                       rl+  p+g+y+v+++ +  + +t +  t++ 
  gi|313117356|ref|YP_004044339.1| 785 RLPRRPAGSYTVEATTTAGQRVTAT-YTVQG 814
                                       5677799*******99999999974.88774 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   5.8e+03      23      72 ..     584     620 ..     567     637 .. 0.56
   2 ?   10.6   0.3   0.00021      0.93      32      73 ..     754     797 ..     728     811 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                              CopC  23 tLtFsepvelskvkvtdpdgkeevetvdaktveaelkvplpelaaGtYtV 72 
                                       +++   +v++++v+v +             ++++++ vp++e+++Gt+t+
  gi|313117356|ref|YP_004044339.1| 584 EIKLGSTVRKRSVTVGS-------------QQSTRVFVPFDETPSGTHTL 620
                                       33333333333333333.............33444555555666666554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                              CopC  32 l..skvkvtdpdgke.evetvdaktveaelkvplpelaaGtYtVe 73 
                                       +  s+++vt+p+ ++ ++  + ++ ++a+++++lp+ +aG+YtVe
  gi|313117356|ref|YP_004044339.1| 754 TvqSSLRVTGPSVEKkRP-VTVESGETATVRARLPRRPAGSYTVE 797
                                       144999******766444.3444445899***************7 PP

>> DUF5325  Family of unknown function (DUF5325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.6       0.2   8.8e+02      10      33 ..     242     264 ..     237     277 .. 0.65
   2 ?    8.2   1.0   0.00048       2.2      24      51 ..     838     865 ..     834     871 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                           DUF5325  10 lyAilAvaslmgiGiaigersilg 33 
                                       l+A+ Av  l+++G a+g    l+
  gi|313117356|ref|YP_004044339.1| 242 LFALRAV-TLTAVGTAVGYGFGLI 264
                                       6777665.6899999999764443 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00048
                           DUF5325  24 iaigersilgiiiaivalivvmGlGFkt 51 
                                       i ++  +i ++++a+val  vm +G +t
  gi|313117356|ref|YP_004044339.1| 838 IQVAFGNIEVLVLAVVALLSVMTVGSTT 865
                                       889*********************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (992 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 6581.11
//
Query:       gi|313117357|ref|YP_004044340.1|  [L=370]
Description: glycosyl transferase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-23   82.9   0.0    3.4e-23   82.3   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
      0.002   18.0   0.0     0.0025   17.7   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   3.8e-27   3.4e-23       1     167 [.       3     163 ..       3     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 3.8e-27
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       s v+pt Nee+ ++e++ + ++  ++ +    ivv D+StD+t+ei+e+      + +v+  ++  G++ a+  +++
  gi|313117357|ref|YP_004044340.1|   3 SLVMPTLNEEEGIEECIGRMKNAlEELQITGEIVVSDSSTDRTPEIAESM-----GAIVVEPDKP-GYGYAYQYAFD 73 
                                       78*********************888888899******************.....99******99.*********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTT CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsf 153
                                       +a+gd i++ DaD+++d + l+kl+e   +++ad+++g+r   + +++ +++ ++ +  ++l +k  + +++ ++s+
  gi|313117357|ref|YP_004044340.1|  74 HARGDAIAIGDADTTYDFEELPKLYELVANGDADMAMGSRLNGEIKDGAMPPLHQ-YVGNPLLTKFLNVFYGAGVSD 149
                                       ****************************************************999.7******************** PP

                                       CSTCCCEEEEHHHH CS
                   Glycos_transf_2 154 eigsaallrreale 167
                                        ++++++l++ea e
  gi|313117357|ref|YP_004044340.1| 150 AHSGMRVLSKEAWE 163
                                       **********9865 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.8e-07    0.0025       4     123 ..       2     112 ..       1     185 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-07
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesll.aqey.prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       l+++ pt+nee+ ++e++     a e+   +  +vv d s++ t e ae      ++    +vv ++++g   + +a
  gi|313117357|ref|YP_004044340.1|   2 LSLVMPTLNEEEGIEECIGRMKnALEElQITGEIVVSDSSTDRTPEIAES----MGA----IVVEPDKPG---YGYA 67 
                                       79999*************99985666534466677778888888998875....455....455666577...5557 PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtp 123
                                       ++ a++++++d +++ D+Dt  + + l++l  +++  +++++ ++
  gi|313117357|ref|YP_004044340.1|  68 YQYAFDHARGDAIAIGDADTTYDFEELPKLYELVANGDADMAMGS 112
                                       7*******************9999999888888855556665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2327.53
//
Query:       gi|313117358|ref|YP_004044341.1|  [L=521]
Description: PAS domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-14   54.2   0.0      3e-14   53.5   0.0    1.4  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    8.8e-14   51.3   1.4    8.8e-14   51.3   1.4    2.3  2  HisKA         His Kinase A (phospho-acceptor) domain
    1.7e-13   50.7   0.1    5.9e-13   49.0   0.0    2.0  2  Response_reg  Response regulator receiver domain
    6.7e-12   45.6   0.3    6.8e-11   42.4   0.1    2.6  2  PAS_4         PAS fold
    5.3e-10   39.3   0.0    1.4e-09   37.9   0.0    1.8  1  PAS           PAS fold
    2.7e-06   27.6   0.0    9.3e-06   25.8   0.0    2.0  2  PAS_9         PAS domain
    1.1e-05   25.3   0.0    5.7e-05   23.0   0.0    2.2  2  PAS_8         PAS domain
    0.00015   22.0   0.1     0.0055   17.0   0.0    2.9  2  PAS_3         PAS fold
    0.00041   20.5   0.0      0.002   18.3   0.0    2.2  1  PAS_7         PAS fold
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.031   14.1   0.0    1.4  1  VIT1          VIT family
      0.055   13.8   0.8        1.2    9.5   0.2    2.6  2  DUF2524       Protein of unknown function (DUF2524)


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   1.9e-17     3e-14       3     107 ..     419     514 ..     417     517 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.9e-17
                                       HHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHH CS
                         HATPase_c   3 ekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGl 78 
                                         rL+q++ nl++Na+++   ++ +++++   + +  + v D+G+ ip++ ++k+fe  +s+         gtG+Gl
  gi|313117358|ref|YP_004044341.1| 419 RCRLQQLFENLLQNAIDH--GGDGVTITVG--SCEDGFYVADDGPSIPEDRREKIFEaGYST------HMNGTGIGL 485
                                       569**************9..5677888888..4478899******************88888......679****** PP

                                       HHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  79 sivkklvelmgGeiwvesepgrGttftft 107
                                       siv  +++ +g +++ +++  +G +f +t
  gi|313117358|ref|YP_004044341.1| 486 SIVADIATAHGWKLKATESAAGGARFEIT 514
                                       *****9999*******99999***99875 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   1.4   5.4e-17   8.8e-14       2      66 ..     320     379 ..     319     380 .. 0.96
   2 ?   -2.0   0.1       2.3   3.7e+03      50      60 ..     421     431 ..     408     434 .. 0.68

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 5.4e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l rf++ v+H+Lr+PL++ +g +e+L++     e   e l  +++  +r+ +l++dlL+l+r ++
  gi|313117358|ref|YP_004044341.1| 320 LDRFVSVVSHDLRNPLNVAIGRTELLQN-----EYDSEHLTEAQQALDRMAELIDDLLTLARNGQ 379
                                       78************************99.....999*************************9875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHH CS
                             HisKA  50 rldhlvedlLd 60 
                                       rl++l e+lL+
  gi|313117358|ref|YP_004044341.1| 421 RLQQLFENLLQ 431
                                       77777777764 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   3.6e-16   5.9e-13       1     105 [.      67     174 ..      67     179 .. 0.92
   2 ?   -3.6   0.0       7.7   1.2e+04      49      61 ..     265     277 ..     257     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 3.6e-16
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHH..ESEEEEESSCSSSEHHHHHHHHHHCTTTSE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeek..vdlillDinmpgmdGlellkeireedpelp 73 
                                       +l vdD+   r+l++++l   +e + +v   + +++a++ l +++  +++++   ++p+ +Glell ++ree p+lp
  gi|313117358|ref|YP_004044341.1|  67 ILYVDDNNEHRDLVADALVqfDERF-DVILERGASDAIDRLAADDeaIHCLISEYELPDQTGLELLATVREEFPQLP 142
                                       799**************99888999.888889999999999665556****************************** PP

                                       EEEEESSTSHHHHHHHHHCTESEEEESSG-HH CS
                      Response_reg  74 viiltahseeedavealkagaddflsKpfdpe 105
                                        i++t+ ++e+ a ea+++g+ ++l K ++++
  gi|313117358|ref|YP_004044341.1| 143 FILFTGVGSEALASEAISMGVTEYLPKRYEET 174
                                       ***************************98765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.7
                                       EESSCSSSEHHHH CS
                      Response_reg  49 lDinmpgmdGlel 61 
                                       +D+ m ++ G+++
  gi|313117358|ref|YP_004044341.1| 265 TDMWMGRCRGMTV 277
                                       7999*99999976 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.1   4.2e-14   6.8e-11       1     108 [.     203     306 ..     203     308 .. 0.84
   2 ?    0.1   0.0      0.58   9.4e+02       4      19 ..     402     417 ..     401     436 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4.2e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       l++  +++ +ld+dgr++y+N a+a+l+ ++pee+lG+++  l+pe+  +r+++ +r  l++ + +       + +g
  gi|313117358|ref|YP_004044341.1| 203 LEAATQGISILDADGRYRYVNDAFADLYNCTPEEILGEHWTGLYPEPEVTRFQQEVRPRLDETDMWMGRCRGMTvDG 279
                                       6788999*************************************************988888655555555555788 PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTer 108
                                          +   +++ l+     + g+++++r +Te+
  gi|313117358|ref|YP_004044341.1| 280 TIFPERASVTQLD-----TGGYVCVVRPVTEL 306
                                       8888888888884.....36788888888885 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.58
                             PAS_4   4 lpdalavldpdgrvly 19 
                                       + d ++v+d+d+++++
  gi|313117358|ref|YP_004044341.1| 402 SDDSTLVIDTDLVIRA 417
                                       57899********997 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   8.8e-13   1.4e-09       3     113 .]     199     303 ..     197     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 8.8e-13
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       + + le+++ +i ++D+dgr  yvN+a+++l + ++ee+lg++  +l++e++   ++++++ +l ++ ++ + ++  
  gi|313117358|ref|YP_004044341.1| 199 VYEALEAATQGISILDADGRYRYVNDAFADLYNCTPEEILGEHWTGLYPEPEVTRFQQEVRPRLDETDMWMGRCRGM 275
                                       56789**********************************************55555555555555555555555555 PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++ dg++++ +  ++ +  +     g+++v+r++
  gi|313117358|ref|YP_004044341.1| 276 TV-DGTIFPERASVTQLDTG-----GYVCVVRPV 303
                                       55.******99999999888.....899998875 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   5.7e-09   9.3e-06       3     104 .]     209     305 ..     207     305 .. 0.85
   2 ?   -3.8   0.0       9.5   1.6e+04      43      74 ..     350     379 ..     342     382 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.7e-09
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       gi i + dgr  y+N+a+++l+  +pee+lg ++t l+   +  + ++++r  l++ +   + +    ++ +g+ f+
  gi|313117358|ref|YP_004044341.1| 209 GISILDADGRYRYVNDAFADLYNCTPEEILGEHWTGLYpePEVTRFQQEVRPRLDETD--MWMGRCRGMTVDGTIFP 283
                                       899999***999*********9999*************77777777777777777777..9999999999999**** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                        +++++ +  +     g+++++r +te
  gi|313117358|ref|YP_004044341.1| 284 ERASVTQLDTG-----GYVCVVRPVTE 305
                                       99*****9333.....35588888876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.5
                             PAS_9  43 dpeanerlraaleqgrkkerevevvlirknge 74 
                                       d+e+  + ++al+++   e  +++    +ng+
  gi|313117358|ref|YP_004044341.1| 350 DSEHLTEAQQALDRMA--ELIDDLLTLARNGQ 379
                                       5666677777777777..77777777777776 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.5e-08   5.7e-05       6      58 ..     202     253 ..     197     264 .. 0.79
   2 ?   -3.0   0.0       5.1   8.3e+03       2      10 ..     421     429 ..     421     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.5e-08
                             PAS_8   6 lfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpvlrplle..d 58 
                                       ++e++ +gi ++d+++r ++vN+a+++l+  +    +e lg+ +++l+p+ e  +
  gi|313117358|ref|YP_004044341.1| 202 ALEAATQGISILDADGRYRYVNDAFADLYNCT---PEEILGEHWTGLYPEPEvtR 253
                                       689**********8888************755...66777888888888888753 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.1
                             PAS_8   2 rlralfess 10 
                                       rl++lfe++
  gi|313117358|ref|YP_004044341.1| 421 RLQQLFENL 429
                                       789999976 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.082   1.3e+02      25      66 ..     186     220 ..     173     222 .. 0.63
   2 !   17.0   0.0   3.3e-06    0.0055       3      73 ..     221     289 ..     219     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.082
                             PAS_3  25 swldlvhpeDrervrealqealkkgepyegeyRirrkdGeyr 66 
                                        + +    +Dr+rv+eal++a ++ +       i+ +dG yr
  gi|313117358|ref|YP_004044341.1| 186 AVSQSRIEQDRDRVYEALEAATQGIS-------ILDADGRYR 220
                                       55666678899999999997764433.......444444444 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.3e-06
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwvearar 73 
                                       yv++++ +++  +pee+lg   +w  l    +  r+++++   l++   + g  R ++ dG+++  +a+++
  gi|313117358|ref|YP_004044341.1| 221 YVNDAFADLYNCTPEEILGE--HWTGLYPEPEVTRFQQEVRPRLDETDMWMGRCRGMTVDGTIFPERASVT 289
                                       99******************..**********************99999*************977666655 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06     0.002       1      34 [.     203     236 ..     203     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeel 34 
                                       le  +qGis++Dad+r + +N+ + +l++ ++e 
  gi|313117358|ref|YP_004044341.1| 203 LEAATQGISILDADGRYRYVNDAFADLYNCTPEE 236
                                       67889************************87654 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.031      35      92 ..     146     205 ..     133     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                              VIT1  35 laGl..aellAGaiSMgiGeYlsvkserdlekaerkreeeeleedpeegeaeelaeilea 92 
                                       ++G+    l + aiSMg+ eYl  + e+ + ++  +r  ++++++  e++++ + e lea
  gi|313117358|ref|YP_004044341.1| 146 FTGVgsEALASEAISMGVTEYLPKRYEETQHERLGNRILDAVSQSRIEQDRDRVYEALEA 205
                                       555531467889*********************999999999999656667777777765 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       0.2   3.3e+02      62      75 ..     314     327 ..     306     338 .. 0.68
   2 ?    9.5   0.2   0.00071       1.2      31      65 ..     346     380 ..     340     385 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.2
                           DUF2524  62 dqQreqLeRarlql 75 
                                       +qQ eqL+R    +
  gi|313117358|ref|YP_004044341.1| 314 EQQNEQLDRFVSVV 327
                                       57888888876554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00071
                           DUF2524  31 qehyndeeYteAqlkLEeavneLeklaksandqQr 65 
                                       q++y+ e  teAq+ L+ + + +++l++ a + Qr
  gi|313117358|ref|YP_004044341.1| 346 QNEYDSEHLTEAQQALDRMAELIDDLLTLARNGQR 380
                                       899***************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 3993.61
//
Query:       gi|313117359|ref|YP_004044342.1|  [L=147]
Description: ADP-ribose pyrophosphatase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-11   43.4   0.0    3.9e-11   43.1   0.0    1.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   2.2e-15   3.9e-11       5     111 ..      22     129 ..      18     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.2e-15
                                       EEEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   5 avgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd 80 
                                       +v +v+  + g +Ll  r + p +g W +PgG+v +gE++ +A++R + EE+G+++   + lg +++++ + +++g 
  gi|313117359|ref|YP_004044342.1|  22 SVDLVVKHDGG-ILLGMRENEPAKGeWFVPGGTVLKGESLTDAVHRVATEELGVDVTINDRLGTFEHFYDTSEVDGI 97 
                                       45555555554.9**99998999999***************************988777777755555555555444 PP

                                       .EEEEEEEEEEEECSGCSSTSTTTEEEEEEEE CS
                             NUDIX  81 .eheilyvfleevegelepndenevsevrwvp 111
                                         ++++ + +    +++++n +  +s ++ ++
  gi|313117359|ref|YP_004044342.1|  98 dSKHYVATAFVVTPDTNKLNTDTQHSRFQVFE 129
                                       65555555556777777777677777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 951.02
//
Query:       gi|313117360|ref|YP_004044343.1|  [L=307]
Description: dTDP-glucose 4,6-dehydratase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-81  272.7   0.0    5.5e-81  272.5   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      7e-67  225.4   0.0    8.6e-67  225.1   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.5e-24   84.7   0.0    7.3e-24   84.2   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.2e-22   78.6   0.0    4.9e-22   78.4   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    9.4e-21   74.2   0.0    1.7e-19   70.1   0.0    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.3e-14   53.2   0.0      5e-13   48.8   0.0    2.4  1  NAD_binding_4    Male sterility protein
    6.2e-12   45.8   0.0    9.7e-12   45.1   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    3.1e-07   30.2   0.1      5e-07   29.5   0.1    1.3  1  NmrA             NmrA-like family
    0.00077   19.0   0.0      0.071   12.6   0.0    2.6  3  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
       0.01   16.1   0.2      0.028   14.7   0.1    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.09   12.9   0.6        1.6    8.9   0.2    2.3  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.16   11.9   0.0       0.47   10.4   0.0    1.8  1  KR               KR domain


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.5   0.0   3.7e-84   5.5e-81       1     332 []       4     301 ..       4     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: 272.5 bits;  conditional E-value: 3.7e-84
                                       EEETTTSHHHHHHHHHHHHC.T-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT- CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlek.gyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqp 76 
                                       L+TG+aGfiGs+++++ +e+ + ev+ ++ ++++ + +++e + ++p      + ++++gD++D++ +++l+a+v  
  gi|313117360|ref|YP_004044343.1|   4 LVTGGAGFIGSNFVHYVIEQyDDEVVTLDALTYAGSKENLEGVLDNP------RHEFIEGDIRDEELVRDLVADV-- 72 
                                       9******************9345666666666666666666666655......668*****************99.. PP

                                       SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHH CS
                     GDP_Man_Dehyd  77 devynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPY 153
                                       d+v+n+AA+shVd+s+e ++ ++e+nv Gt++LL+a+++ g+e   rf+q+St+EvYG+  + +++E+ p++Pr+PY
  gi|313117360|ref|YP_004044343.1|  73 DTVVNFAAESHVDRSIEGAKPFVETNVQGTQTLLDAAKDSGIE---RFLQISTDEVYGQILDGKFSEDDPLNPRNPY 146
                                       9****************************************97...9****************************** PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       +a+K++ad+++++++ +++l+++++++ n+ +pr+    ++++i++++ ++ +gk + +++G+++++R w +++D +
  gi|313117360|ref|YP_004044343.1| 147 SATKASADHLAKSFETTHDLPVLITRTCNNFGPRQ---HPEKLIPKFIKNASEGK-SLPVYGDGSNVREWIYAEDNC 219
                                       **********************************7...689*************9.8899***************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       +a++++l++++        ge +++++++e+++le+ + i              + g ++  ++++ +r g++++++
  gi|313117360|ref|YP_004044343.1| 220 RALDTVLREGE-------IGEIYNIGSHAEKTNLEVTEAILD------------AVGADKALIEFVEDRAGHDQRYA 277
                                       *********99.......7*****************988754............4577889999************* PP

                                       B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvrem 332
                                        +++k++  LgW+p ++fee+++e+
  gi|313117360|ref|YP_004044343.1| 278 LETEKIE-SLGWEPAYTFEEGLEET 301
                                       ******9.9*************986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.1   0.0   5.8e-70   8.6e-67       1     241 []       3     238 ..       3     238 .. 0.97

  Alignments for each domain:
  == domain 1  score: 225.1 bits;  conditional E-value: 5.8e-70
                                       EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl......elveldltdrsalerlfkeeqpdavih 70 
                                       ilVtG++GfiGs++v+++ e+  + v++ld l++a+ +++le +      e++e+d++d++ +++l++  ++d+v++
  gi|313117360|ref|YP_004044343.1|   3 ILVTGGAGFIGSNFVHYVIEQYDDeVVTLDALTYAGSKENLEGVldnprhEFIEGDIRDEELVRDLVA--DVDTVVN 77 
                                       8********************9666******************9************************..89***** PP

                                       --S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHH CS
                         Epimerase  71 lAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKl 147
                                       +Aa+++v++s+e ++ f+e+n+qgt++ll+aa+++g++r+l++s++evYG+  +   +e+    pl+p++pY+a+K+
  gi|313117360|ref|YP_004044343.1|  78 FAAESHVDRSIEGAKPFVETNVQGTQTLLDAAKDSGIERFLQISTDEVYGQILDGKFSEDD---PLNPRNPYSATKA 151
                                       **************************************************87774466666...************* PP

                                       HHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHH CS
                         Epimerase 148 ageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaill 224
                                        +++l++++  +++l+++i+r +n++Gpr   ++++++ip++i+++ egk ++ ++gdg+++R+++y+eD ++a+ +
  gi|313117360|ref|YP_004044343.1| 152 SADHLAKSFETTHDLPVLITRTCNNFGPR---QHPEKLIPKFIKNASEGK-SLPVYGDGSNVREWIYAEDNCRALDT 224
                                       *****************************...99****************.************************** PP

                                       HHHHHTT-STTEEEEES CS
                         Epimerase 225 vlehvdagdkgeiyniG 241
                                       vl++   g+ geiyniG
  gi|313117360|ref|YP_004044343.1| 225 VLRE---GEIGEIYNIG 238
                                       ****...999******9 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   4.9e-27   7.3e-24       1     220 [.       4     217 ..       4     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 4.9e-27
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegvdvvihla 74 
                                       +vtGgaGF+G++ v+ +++  +  ev  lD    + s+e le +    ++++iegD++d++ +++ + +vd v+  a
  gi|313117360|ref|YP_004044343.1|   4 LVTGGAGFIGSNFVHYVIEQYD-DEVVTLDaltYAGSKENLEGVLDNPRHEFIEGDIRDEELVRDLVADVDTVVNFA 79 
                                       69****************9986.8888888554666777778888888888************************** PP

                         3Beta_HSD  75 slvdvagklt.edeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesK 150
                                       + + v   ++  + + + nv+GT+++l+a++++g+++++  S+ ev g+      il+g+ ++  + ++ ++y+ +K
  gi|313117360|ref|YP_004044343.1|  80 AESHVDRSIEgAKPFVETNVQGTQTLLDAAKDSGIERFLQISTDEVYGQ------ILDGKFSEDDPLNPRNPYSATK 150
                                       *****98555166799******************************999......999******************* PP

                         3Beta_HSD 151 alaEklvlkaNgrtlknggrlyTcaLRpagiyGegd..kllvpllkqlaklglalfkigdeevlsdrvYvgN 220
                                       a a++l ++          +l     R    +G+++  ++l p + + a  g++l  +gd +++ +++Y++ 
  gi|313117360|ref|YP_004044343.1| 151 ASADHLAKSFET-----THDLPVLITRTCNNFGPRQhpEKLIPKFIKNASEGKSLPVYGDGSNVREWIYAED 217
                                       ****99765554.....567777788********9733467788888888899*****************95 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0   3.3e-25   4.9e-22       1     284 [.       1     304 [.       1     307 [] 0.87

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 3.3e-25
                                       EEEEEESTTSHHHHHHHHHCTT.TSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEE CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlae.eglevlaltre.....................eldltdaeavaellkeakpdvv 55 
                                       m+ilvtG+ G +Gs+ ++ + e  + ev++l+                       e d++d+e v++l+++   d v
  gi|313117360|ref|YP_004044343.1|   1 MRILVTGGAGFIGSNFVHYVIEqYDDEVVTLDALtyagskenlegvldnprhefiEGDIRDEELVRDLVAD--VDTV 75 
                                       99*************99987652566888886667889********************************9..778* PP

                                       EE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHH CS
                     RmlD_sub_bind  56 vnaAAytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPlnvYGrtKla 131
                                       vn AA   vD+  +  +   + n++++++l +aa+  g+  ++++StD V+    + +++edd+ +P+n Y +tK+ 
  gi|313117360|ref|YP_004044343.1|  76 VNFAAESHVDRSIEGAKPFVETNVQGTQTLLDAAKDSGIErFLQISTDEVYGQILDGKFSEDDPLNPRNPYSATKAS 152
                                       **************************************9549*********9999********************** PP

                                       HHHHHHH....H-SSEEEEEE-SEESS..SSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH CS
                     RmlD_sub_bind 132 GEqavla....agkkalivRtswvyge..kgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaae 202
                                         +  ++    +   +li Rt   +g   + + ++ ++++ a+e ++l v  D      +    Ae    +l++ ++
  gi|313117360|ref|YP_004044343.1| 153 ADHLAKSfettHDLPVLITRTCNNFGPrqHPEKLIPKFIKNASEGKSLPVYGDGSNVREWI--YAEDNCRALDTVLR 227
                                       **999985543344679********9766899********************965544443..34555555555555 PP

                                       .GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHH CS
                     RmlD_sub_bind 203 ekelagvyHlanegetswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealk 279
                                       e e+ ++y +++++e + le+ +ail+++gad++ ++ +      ++A   ++ +L+tek+e+ +  ++ +++e+l+
  gi|313117360|ref|YP_004044343.1| 228 EGEIGEIYNIGSHAEKTNLEVTEAILDAVGADKALIEFV-----EDRAGHDQRYALETEKIESLGWEPAYTFEEGLE 299
                                       5567*****************************999988.....46677778889*********99999*******9 PP

                                       HHHHH CS
                     RmlD_sub_bind 280 evlke 284
                                       e+++ 
  gi|313117360|ref|YP_004044343.1| 300 ETVEY 304
                                       99875 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   1.1e-22   1.7e-19       1     230 [.       3     239 ..       3     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.1e-22
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +lvtG++G iGs++v+ ++++   +++ l+   ++  + + e    l++ + ++    + gd+rd+e +++++   +
  gi|313117360|ref|YP_004044343.1|   3 ILVTGGAGFIGSNFVHYVIEQYDDEVVTLDALTYAGSKENLE--GVLDNPRHEF----IEGDIRDEELVRDLVA--D 71 
                                       89***************************9987766554444..3455544433....47**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG..............SS--SHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA..............vnPtnvmGa 140
                                       vd+v++ AA  hV    e +   ++tNv gt+++++aa+++g+++++ iStD                 nP n + a
  gi|313117360|ref|YP_004044343.1|  72 VDTVVNFAAESHVDRSIEGAKPFVETNVQGTQTLLDAAKDSGIERFLQISTDEVygqildgkfseddpLNPRNPYSA 148
                                       ***************************************************9753333333333333369******* PP

                                       HHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGTT...SSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHHHHH CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekktkfvvvRfGNVlgSrG...SviplFkkqikeggpvtv.TdpemtRyfmtieeavqLv 213
                                       tK+ a+ l+ ++++++   +  ++++R  N +g r     +ip+F k  +eg++++v  d + +R ++  e+ ++ +
  gi|313117360|ref|YP_004044343.1| 149 TKASADHLAKSFETTH---DLPVLITRTCNNFGPRQhpeKLIPKFIKNASEGKSLPVyGDGSNVREWIYAEDNCRAL 222
                                       **********999998...899***********9963337****************945788999999999999999 PP

                                       HHHHHH--SS-EEEE-- CS
                   Polysacc_synt_2 214 lqalalakggeifvldm 230
                                        + l +++ gei+    
  gi|313117360|ref|YP_004044343.1| 223 DTVLREGEIGEIYNIGS 239
                                       99999999999985544 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   3.3e-16     5e-13       1     203 [.       5     173 ..       5     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.3e-16
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G+ +++  +++ ++ ++            ++ l+ +  k +l+ +l      r +++eGD+ +++    
  gi|313117360|ref|YP_004044343.1|   5 VTGGAGFIGSNFVHYVIEQYDD-EV----------VTLDALTYAGSKENLEGVLD---NPRHEFIEGDIRDEE---- 63 
                                       7999999999999999999875.33..........34455666666777777776...8999*******9876.... PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                          +++l++ vd +++ aA  ++d++++    ++++Nv+Gt+ +l+ ak       +l++ST  v+g+         
  gi|313117360|ref|YP_004044343.1|  64 --LVRDLVADVDTVVNFAAESHVDRSIEGakpFVETNVQGTQTLLDAAKDSGIE-RFLQISTDEVYGQIL------- 130
                                       ..59********************99876344789**************99888.*******87777777....... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRp 203
                                                + + ++++  +  n Y+ +Ka a++l ++    ++lpv+i R 
  gi|313117360|ref|YP_004044343.1| 131 ---------DGKFSEDDPLNPRNPYSATKASADHLAKSFETTHDLPVLITRT 173
                                       .........446678899999*****************************96 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   6.5e-15   9.7e-12       1     134 [.       7     159 ..       7     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 6.5e-15
                                       TTTSHHHHHHHHHHHHC-T-EEEE...E..ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevta...l..vRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalgggg 72 
                                       G+ G +G+  v+  +++ + ev+    l  + ++e l+ + ++++ e +egd+ d+e +++ ++++d+Vv  ++ ++
  gi|313117360|ref|YP_004044343.1|   7 GGAGFIGSNFVHYVIEQYDDEVVTldaLtyAGSKENLEGVLDNPRHEFIEGDIRDEELVRDLVADVDTVVNFAAESH 83 
                                       89999*****9999999955554312232255799999999**************************8877775555 PP

                                       CHHHH.............HHHHHHHHHHCT--EEEEEEETTTTSG.CGCHHHHHHHHCCHHHHHHHHHHHHHHHHS CS
                    NAD_binding_10  73 kdeeg.............aknivdaakeagvkRfvlvsaigvgde.vpgefgewnkellkaylaakraaeellras 134
                                        d+ +             +++++daak +g++Rf+ +s+  v+ +  +g+f+e +  + ++ + a +a++++l +s
  gi|313117360|ref|YP_004044343.1|  84 VDRSIegakpfvetnvqgTQTLLDAAKDSGIERFLQISTDEVYGQiLDGKFSEDDPLNPRNPYSATKASADHLAKS 159
                                       543334445555555667************************9762578899988888888888877777777665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   3.4e-10     5e-07       1      98 [.       3     118 ..       3     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.4e-10
                                       EEESSTTSHHHHHHHHHHHH....HT-EEEEEES-S-SHHHHHHHHST.TEEEES-TT-HHHHHHHHTT-SEEEE-- CS
                              NmrA   1 IlviGaTGrqGksvvrallk....aghkvralvRdtkselakslkeaG.velvkgdlddkeslvealkgvdvvfsvt 72 
                                       Ilv+G++G +G+ +v+++++    +  +  al+   ++e+++ + +++  e+++gd+ d+e+++ ++ +vd+v    
  gi|313117360|ref|YP_004044343.1|   3 ILVTGGAGFIGSNFVHYVIEqyddEVVTLDALTYAGSKENLEGVLDNPrHEFIEGDIRDEELVRDLVADVDTVVNFA 79 
                                       9******************98765556678999999*****999999935899*******************98777 PP

                                       -GG.............S-HHHHHHHHHHHHHHHS-SEEE CS
                              NmrA  73 gfy.............skeiedgkklvdAakeaGvkhfi 98 
                                       +               +++++  ++l dAak  G+++f+
  gi|313117360|ref|YP_004044343.1|  80 AEShvdrsiegakpfvETNVQGTQTLLDAAKDSGIERFL 118
                                       665789********99999**99***************7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   4.7e-05     0.071       3      72 ..       3      73 ..       1     122 [. 0.77
   2 ?    3.4   0.0      0.03        44     146     164 ..     143     161 ..     134     168 .. 0.84
   3 ?   -1.9   0.0       1.3   1.9e+03     122     143 ..     225     246 ..     219     251 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.7e-05
                                      EEEESTTSHHHHHHHHHHHHT.T-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelake.Gakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekav 72
                                      +lvtG+++ IG ++++ ++++ + +vv +d      +  +++l+    + +  +i++D++d+e v++lv+++ 
  gi|313117360|ref|YP_004044343.1|  3 ILVTGGAGFIGSNFVHYVIEQyDDEVVTLDALTY--AGSKENLEGVldNPRHEFIEGDIRDEELVRDLVADVD 73
                                      89**************999872445555555433..34555555555578899****************9884 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.03
                                       BHHHHHHHHHHHHHHHHHH CS
                         adh_short 146 vaaYsAsKaavagltrsla 164
                                         +YsA+Ka  ++l++s+ 
  gi|313117360|ref|YP_004044343.1| 143 RNPYSATKASADHLAKSFE 161
                                       679************9976 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                                       HHHHCTTEEEEEEEEGGGTSB- CS
                         adh_short 122 amlkqssGrIvnvsSvagkvpv 143
                                        + +++ G+I n++S a k  +
  gi|313117360|ref|YP_004044343.1| 225 VLREGEIGEIYNIGSHAEKTNL 246
                                       3557899********9987665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.9e-05     0.028       3      78 ..       5      80 ..       3     104 .. 0.78
   2 ?   -2.0   0.0       2.7   4.1e+03      93     117 ..     218     254 ..     213     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                                      EE--.SHHHHHHHHHHHCTCCT-GEEEEEES.....SHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE CS
                   Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadr.....skeklealaakalgvrfeaialdaenyeavLaallkegdlvvn 75
                                      + G+ G++G+ +++++ ++ d   e++  d      ske+le ++    ++r+e+i+ d+ ++e  +  l+++ d vvn
  gi|313117360|ref|YP_004044343.1|  5 VTGGaGFIGSNFVHYVIEQYDD--EVVTLDAltyagSKENLEGVL---DNPRHEFIEGDIRDEEL-VRDLVADVDTVVN 77
                                      55555***********999988..555555411111333334443...89**************9.************* PP

                                      -SS CS
                   Sacchrp_dh_NADP 76 lsp 78
                                       + 
  gi|313117360|ref|YP_004044343.1| 78 FAA 80
                                      886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                                       T-EEEESS-............BCGCCSCHCCSHHHHH CS
                   Sacchrp_dh_NADP  93 gvhyvdtsi............skeertnyalreavlk 117
                                        ++ +dt+             s +e+tn +++ea+l+
  gi|313117360|ref|YP_004044343.1| 218 NCRALDTVLregeigeiynigSHAEKTNLEVTEAILD 254
                                       5666777777777777777777778888888877776 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2    0.0011       1.6       1      87 [.       1      91 [.       1     119 [. 0.63
   2 ?    1.9   0.0      0.15   2.3e+02      13      76 ..     206     267 ..     202     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEE..EETTC..STTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaa..vdrke..selegkdagellglgklgvavtddleevlekadvliDFT 75
                                      ++++v+G +G +G++ v+ v e+ d e+v    +   +  ++leg       ++ + ++  ++ + ++++++d ++ F 
  gi|313117360|ref|YP_004044343.1|  1 MRILVTGGAGFIGSNFVHYVIEQYDDEVVTLdaLTYAGskENLEGVLDNPRHEFIEGDIRDEELVRDLVADVDTVVNFA 79
                                      89****************9999877666654003333311222222222222222444444566777888899999998 PP

                                      -HHHHHHHHHHH CS
                            DapB_N 76 tpeavlenlkla 87
                                      + + v   ++ a
  gi|313117360|ref|YP_004044343.1| 80 AESHVDRSIEGA 91
                                      887777666554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S- CS
                            DapB_N  13 GkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTt 76 
                                       G++v + + ++++++    v r+++  e  ++g+  + +k++++vt+ + +++ +   li+F  
  gi|313117360|ref|YP_004044343.1| 206 GSNVREWIYAEDNCRALDTVLREGEIGEIYNIGS--HAEKTNLEVTEAILDAVGADKALIEFVE 267
                                       7778888888888888888888884444444443..3336778888888888888889999965 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00031      0.47       4      76 ..       4      73 ..       2     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                                      EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                                      l+tGG+G +G  +++  +e+   ++v l     + + sk++++ + + + + e+++ D+ d++ v+ l+++++
  gi|313117360|ref|YP_004044343.1|  4 LVTGGAGFIGSNFVHYVIEQYDDEVVTLDAL--TYAGSKENLEGVLD-NPRHEFIEGDIRDEELVRDLVADVD 73
                                      9*********************999999877..55666656665555.4567888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2005.40
//
Query:       gi|313117361|ref|YP_004044344.1|  [L=301]
Description: dTDP-4-dehydrorhamnose reductase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-70  235.8   0.0    5.9e-70  235.6   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    3.1e-25   89.0   0.0    4.3e-25   88.6   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.7e-15   56.2   0.0      8e-15   55.1   0.0    1.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.2e-07   29.8   0.2    1.1e-06   28.0   0.1    2.0  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.4e-06   26.8   0.3    4.7e-06   25.8   0.3    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    3.1e-06   26.6   0.0    6.3e-06   25.6   0.0    1.6  1  NAD_binding_4    Male sterility protein
      0.004   17.1   0.0     0.0059   16.5   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.6   0.0   2.3e-73   5.9e-70       1     283 [.       1     293 [.       1     297 [. 0.96

  Alignments for each domain:
  == domain 1  score: 235.6 bits;  conditional E-value: 2.3e-73
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHHHHHHHHHHH--SEEEE------HHHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre..........eldltdaeavaellkeakpdvvvnaAAytavDka 67 
                                       m++l++GanG+lGs+++ +++ +g+ ++++  +          ++d+t+ +av+++l+e++pd+vvn+AA t+vD +
  gi|313117361|ref|YP_004044344.1|   1 MQLLILGANGLLGSNVVTAAQDRGWRTTGTYHSerptfdiplhQIDITNTDAVQRVLSEVEPDWVVNCAAMTDVDGC 77 
                                       89****************************666699***************************************** PP

                                       HHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEE CS
                     RmlD_sub_bind  68 EseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkal 144
                                       E++ e+a++vna+a++++A ++ +  + ++hvStDyVFdG+ +  Yeedd+++P+  YG++K aGE+ v +  ++al
  gi|313117361|ref|YP_004044344.1|  78 EENTEHAHEVNARAPGEIASQCVESSIRFLHVSTDYVFDGTVNGVYEEDDAPQPIQEYGKSKFAGENEVVERDPDAL 154
                                       ***************************************************************************** PP

                                       EEEE-SEESS.....SSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS CS
                     RmlD_sub_bind 145 ivRtswvyge.....kgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlaneg 216
                                       i R s vyg      +   f + +  ++ + e+  ++ Dq+ +PT a + Ae + +l+++  +     g++H+a++ 
  gi|313117361|ref|YP_004044344.1| 155 ITRLSFVYGMhrgsdQLTGFPAWVRGRLLDGEQTPLFTDQHVTPTRAGQAAETICDLIDADES-----GLFHVAAQS 226
                                       ********985444445679999999********************************99985.....********* PP

                                       -EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHH CS
                     RmlD_sub_bind 217 etswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlk 283
                                        t+ +ef+ ai+ ++g+d++ ++  s++++++pA+RP++ +L+ +k+e+t g   ++  ++l ++ +
  gi|313117361|ref|YP_004044344.1| 227 CTTPYEFGAAIAGQLGMDETLLTQGSQSDVNRPAERPSRTCLNVSKVEETLGRAQPTLTTDLDAISD 293
                                       ****************************************************999999999887766 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   1.7e-28   4.3e-25       2     205 ..       4     193 ..       3     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 1.7e-28
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       l++Ga+G++Gs++v a +++g++ +g  +      +    d+ l+++d+t+ +a++r+++e++pd v+++Aa  +v+
  gi|313117361|ref|YP_004044344.1|   4 LILGANGLLGSNVVTAAQDRGWRTTGTYHS-----ERPTFDIPLHQIDITNTDAVQRVLSEVEPDWVVNCAAMTDVD 75 
                                       8*****************************.....33334558********************************** PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                          e+ +   e n++   ++++ + ++ + r+l++s++ v+    +   ee+      +p + Y+ +K age+ v +
  gi|313117361|ref|YP_004044344.1|  76 GCEENTEHAHEVNARAPGEIASQCVESSI-RFLHVSTDYVFDGTVNGVYEEDD---APQPIQEYGKSKFAGENEVVE 148
                                       *****************************.***********866663388888...789****************96 PP

                                       HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETT CS
                         Epimerase 156 yaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgd 205
                                            + +a+i+rl+ +yG ++g ++ +++ + +  ++l+g+ +  l+ d
  gi|313117361|ref|YP_004044344.1| 149 R----DPDALITRLSFVYGMHRGSDQLTGFPAWVRGRLLDGE-QTPLFTD 193
                                       4....4578**********************99999****99.7776664 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   3.1e-18     8e-15      52     270 ..      38     245 ..       4     288 .. 0.75

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 3.1e-18
                                       CCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEE CS
                     GDP_Man_Dehyd  52 enlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaS 128
                                        ++ lh+ D+t++++++r+l+ev+pd v+n AA+  Vd   e+ e   evn+ +  ++   +    +e+++rf+++S
  gi|313117361|ref|YP_004044344.1|  38 FDIPLHQIDITNTDAVQRVLSEVEPDWVVNCAAMTDVDGCEENTEHAHEVNARAPGEIASQC----VESSIRFLHVS 110
                                       2578***************************************************9887766....45789****** PP

                                       EGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHH CS
                     GDP_Man_Dehyd 129 tsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravaria 205
                                       t+ v+  + +  ++E+   +P   Y+ +K + +  vv+     +  a++++l+  ++ +rg +  t     +  r +
  gi|313117361|ref|YP_004044344.1| 111 TDYVFDGTVNGVYEEDDAPQPIQEYGKSKFAGENEVVE----RDPDALITRLSFVYGMHRGSDQLTGFPAWVRGRLL 183
                                       *****77778999*******************999976....45577888888888888888877777777777888 PP

                                       TTS-C-EEC.TTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHH CS
                     GDP_Man_Dehyd 206 lgkqevlyl.GnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgkti 270
                                        g+q+ l    +  ++R  + ++ +++ +++    d++  + +a +  ++  ef  + + +lg++ 
  gi|313117361|ref|YP_004044344.1| 184 DGEQTPLFTdQHVTPTRAGQAAETICDLIDA----DESGLFHVAAQSCTTPYEFGAAIAGQLGMDE 245
                                       8888777664566778888888888877775....7777788888888888888777777777643 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         1   2.7e+03       2      18 ..       4      20 ..       3      33 .. 0.83
   2 !   28.0   0.1   4.2e-10   1.1e-06      58     131 ..      42     114 ..      25     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1
                                      EEETTTSHHHHHHHHHH CS
                   Polysacc_synt_2  2 lvtGagGsiGselvrqi 18
                                      l+ Ga G +Gs++v+  
  gi|313117361|ref|YP_004044344.1|  4 LILGANGLLGSNVVTAA 20
                                      89999999999998765 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 4.2e-10
                                       ..E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG CS
                   Polysacc_synt_2  58 pvigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA 131
                                           d+++++ ++++l+e+++d v+++AA+  V  +een+ +a + N  +  ++++ ++e+ + +++ +StD  
  gi|313117361|ref|YP_004044344.1|  42 LHQIDITNTDAVQRVLSEVEPDWVVNCAAMTDVDGCEENTEHAHEVNARAPGEIASQCVESSI-RFLHVSTDYV 114
                                       45579********************************************************99.699****965 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.3   1.8e-09   4.7e-06      43     158 ..      37     147 ..       4     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.8e-09
                         3Beta_HSD  43 kvnvkkviegDvtdkdkleealegv..dvvihlaslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSs 116
                                       ++++  +++ D+t++d ++++l +v  d v+  a+++dv g + ++++  +vn +   ++ + cv++++r+l ++ s
  gi|313117361|ref|YP_004044344.1|  37 TFDIP-LHQIDITNTDAVQRVLSEVepDWVVNCAAMTDVDGcEENTEHAHEVNARAPGEIASQCVESSIRFL-HV-S 110
                                       55555.89***************984468************8889999*********************987.45.5 PP

                         3Beta_HSD 117 aevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvl 158
                                        + v++       +ng  e+   +++ + y +sK   E+ v+
  gi|313117361|ref|YP_004044344.1| 111 TDYVFD-----GTVNGVYEEDDAPQPIQEYGKSKFAGENEVV 147
                                       578888.....3456666666777777888888888887775 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.4e-09   6.3e-06      83     213 ..      55     173 ..      39     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.4e-09
                                       HHHHH-..-EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H. CS
                     NAD_binding_4  83 elaeev..dviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyee 154
                                       ++ +ev  d ++++aA +++d+   +++ + +vN ++  e+ + + + +    +lhvST yv +   + v       
  gi|313117361|ref|YP_004044344.1|  55 RVLSEVepDWVVNCAAMTDVDGceeNTEHAHEVNARAPGEIASQCVESSI--RFLHVSTDYVFDGTVNGV------- 122
                                       5555543389*********9864448889************999997655..5******77777777666....... PP

                                       .....HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.....-SSST CS
                     NAD_binding_4 155 gekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.....esktG 213
                                                 e+++  +  ++Y +sK+++E+ v e        ++i R+s ++g     +  tG
  gi|313117361|ref|YP_004044344.1| 123 ---------YEEDDAPQPIQEYGKSKFAGENEVVERD----PDALITRLSFVYGmhrgsDQLTG 173
                                       .........356677778889*********9998877....3478*******998777744444 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.3e-06    0.0059       1     142 [.       7     157 ..       7     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S..EEEES-....... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgad..aVvsal....... 68 
                                       GA+G  G+ +v+ + +rg +++t    ++  + +      + + ++d+t++++++++l+ ++   Vv ++       
  gi|313117361|ref|YP_004044344.1|   7 GANGLLGSNVVTAAQDRG-WRTTGTYHSERPTFD------IPLHQIDITNTDAVQRVLSEVEpdWVVNCAamtdvdg 76 
                                       9****************5.999988776666654......5699***************995556666663555543 PP

                                       ......--TCCHHHH.......HHHHHHHHHHCT--EEEEEEETTTTS.GCGCHHHHHHH.HCCHHHHHHHHHHHHH CS
                    NAD_binding_10  69 ......ggggkdeeg.......aknivdaakeagvkRfvlvsaigvgd.evpgefgewnk.ellkaylaakraaeel 130
                                                     +          i+  + e+ + Rf+ vs+  v d  v+g  +e +  + +++y + k a e++
  gi|313117361|ref|YP_004044344.1|  77 ceenteH-------AhevnaraPGEIASQCVESSI-RFLHVSTDYVFDgTVNGVYEEDDApQPIQEYGKSKFAGENE 145
                                       3322221.......134443337778899999999.99999998886624555544433326889999999999999 PP

                                       HHHSSSEEEEEE CS
                    NAD_binding_10 131 lrasgldwTivr 142
                                       + +++ d  i r
  gi|313117361|ref|YP_004044344.1| 146 VVERDPDALITR 157
                                       888877776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1958.55
//
Query:       gi|313117362|ref|YP_004044345.1|  [L=59]
Description: hypothetical protein Hbor_31490 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00017   21.6   0.9    0.00053   20.0   0.1    2.0  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
  ------ inclusion threshold ------
      0.011   15.8   2.9       0.02   14.9   2.9    1.5  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.012   15.5   1.4      0.018   15.0   1.4    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.027   13.9   0.8      0.054   12.9   0.1    1.8  2  zf-ribbon_3     zinc-ribbon domain
       0.03   13.9   0.6      0.079   12.6   0.1    1.9  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.033   13.7   0.1      0.033   13.7   0.1    2.0  3  TF_Zn_Ribbon    TFIIB zinc-binding
      0.068   13.4   0.7       0.69   10.2   1.1    1.9  2  IBR             IBR domain, a half RING-finger domain
      0.079   13.0   3.3       0.14   12.3   0.2    2.6  3  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.4e-07   0.00053       2      19 ..       6      23 ..       6      24 .. 0.94
   2 ?   -0.1   0.1      0.46     1e+03       3       6 ..      27      30 ..      26      36 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-07
                            zf-ACC  2 tKCpsCgemlykkeLern 19
                                      t Cp+Cg+++ ++eLe n
  gi|313117362|ref|YP_004044345.1|  6 TTCPECGTVVAANELESN 23
                                      68**************98 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.46
                            zf-ACC  3 KCps 6 
                                      KCp+
  gi|313117362|ref|YP_004044345.1| 27 KCPG 30
                                      8884 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.9   9.1e-06      0.02       1      25 [.       7      33 ..       7      34 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.1e-06
                    DNA_ligase_ZBD  1 hCPvCGsavvRee..geaiyRCtnlsC 25
                                      +CP+CG+ v  +e     +  C++  C
  gi|313117362|ref|YP_004044345.1|  7 TCPECGTVVAANEleSNRVMKCPGFGC 33
                                      7*********7663357779***9999 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.4     8e-06     0.018      29      54 ..       6      35 ..       5      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8e-06
                    OrfB_Zn_ribbon 29 ktCseCgsknke..alsgrtfkCpn..Cgf 54
                                      +tC+eCg ++      s+r++kCp   C +
  gi|313117362|ref|YP_004044345.1|  6 TTCPECGTVVAAneLESNRVMKCPGfgCEH 35
                                      69*******99998899*******855554 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.4e-05     0.054       2      12 ..       5      15 ..       4      19 .. 0.77
   2 ?   -1.4   0.0      0.79   1.8e+03      16      20 ..      25      29 ..      22      29 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                       zf-ribbon_3  2 tvrCPnCGapl 12
                                      t++CP+CG+++
  gi|313117362|ref|YP_004044345.1|  5 TTTCPECGTVV 15
                                      68899999965 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.79
                       zf-ribbon_3 16 dnvCp 20
                                      +++Cp
  gi|313117362|ref|YP_004044345.1| 25 VMKCP 29
                                      56776 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.5e-05     0.079       3      18 ..       6      21 ..       5      22 .. 0.87
   2 ?   -1.1   0.1      0.68   1.5e+03      16      20 ..      45      49 ..      39      49 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                            zf_UBZ  3 ylCerCgkeipeselq 18
                                       +C++Cg+ +  +el+
  gi|313117362|ref|YP_004044345.1|  6 TTCPECGTVVAANELE 21
                                      69*********99986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.68
                            zf_UBZ 16 elqEH 20
                                      e qEH
  gi|313117362|ref|YP_004044345.1| 45 EAQEH 49
                                      78999 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.5e-05     0.033      20      36 ..       6      22 ..       5      25 .. 0.82
   2 ?   -1.2   0.1      0.67   1.5e+03       1       4 [.      26      29 ..      26      39 .. 0.81
   3 ?   -2.3   0.0       1.5   3.4e+03      10      19 ..      49      58 ..      45      59 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                      EEESSSSBEEEECCCCC CS
                      TF_Zn_Ribbon 20 lvCtdCGlVlednside 36
                                      ++C++CG+V+  n  ++
  gi|313117362|ref|YP_004044345.1|  6 TTCPECGTVVAANELES 22
                                      79*******99887766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.67
                                      EEET CS
                      TF_Zn_Ribbon  1 ykCP 4 
                                      +kCP
  gi|313117362|ref|YP_004044345.1| 26 MKCP 29
                                      6888 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.5
                                      ECHEETSTTC CS
                      TF_Zn_Ribbon 10 nlveDperge 19
                                      +++e+ +r e
  gi|313117362|ref|YP_004044345.1| 49 HFLENKDRYE 58
                                      4788888877 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1   0.00031      0.69      19      44 ..       6      33 ..       3      36 .. 0.75
   2 ?    8.4   0.0    0.0011       2.5      11      35 ..      19      42 ..      15      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                               IBR 19 kwCprpdCeaiiekseg.cks..vtCsk..C 44
                                      + Cp  +C++++  +e  + +  ++C+   C
  gi|313117362|ref|YP_004044345.1|  6 TTCP--ECGTVVAANELeS-NrvMKCPGfgC 33
                                      78*9..9*****9999953.34699996555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                               IBR 11 slesdpnlkwCprpdCeaiiekseg 35
                                      +les++ + +Cp  +Ce++ + se 
  gi|313117362|ref|YP_004044345.1| 19 ELESNR-VMKCPGFGCEHVHRFSEL 42
                                      567766.89********99887765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   6.3e-05      0.14       2      13 ..       7      18 ..       6      20 .. 0.81
   2 ?   -0.1   0.2      0.45     1e+03       2       5 ..      27      30 ..      26      36 .. 0.66
   3 ?   -0.7   0.0      0.69   1.5e+03       9      16 ..      41      48 ..      37      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.3e-05
                           UPF0547  2 vCPeCeakvPva 13
                                      +CPeC + v+++
  gi|313117362|ref|YP_004044345.1|  7 TCPECGTVVAAN 18
                                      688888888876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.45
                           UPF0547  2 vCPe 5 
                                      +CP+
  gi|313117362|ref|YP_004044345.1| 27 KCPG 30
                                      5774 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.69
                           UPF0547  9 kvPvaaqf 16
                                      ++Pv aq+
  gi|313117362|ref|YP_004044345.1| 41 ELPVEAQE 48
                                      78999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 411.85
//
Query:       gi|313117363|ref|YP_004044346.1|  [L=357]
Description: glucose-1-phosphate thymidylyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-55  187.6   0.0    3.4e-55  187.3   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    4.4e-10   40.1   0.0    7.5e-10   39.4   0.0    1.4  1  NTP_transf_3     MobA-like NTP transferase domain
    3.8e-06   26.4   1.5     0.0074   16.0   0.1    3.4  3  Hexapep          Bacterial transferase hexapeptide (six repea
     0.0081   15.9   0.0      0.015   15.1   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.3   0.0   7.6e-59   3.4e-55       1     247 [.       2     237 ..       2     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 7.6e-59
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       k+v+L+GG+G+RL+P+t+t +k+lvpv++k +++++ ++ l ++gi+ei v+l ++ ++ ++e l++gsk+gv++++
  gi|313117363|ref|YP_004044346.1|   2 KGVLLSGGTGSRLRPITHTGPKQLVPVANK-PVLEYAIEDLKEAGITEIGVILGHKGREDIQELLGDGSKYGVDITY 77 
                                       69****************************.********************************************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       +++ ++ g+A+A   a+++++d++    v++Lg+++l k  ++++v+++++ +    + +++++v++++++G++ +d
  gi|313117363|ref|YP_004044346.1|  78 IVQGNPLGLAHAAGCARDFVGDDDF---VMYLGDNIL-KSGVTDLVESFESGDY--GAGIALQEVDNPQAFGIADVD 148
                                       ************************6...888877665.66*********99999..99******************* PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       ++++v++++EKP+ ++ ++la  G Yvf + v++ + +dle+++rge eitd+++ +le+g++  +++ +++  W+D
  gi|313117363|ref|YP_004044346.1| 149 DQQNVTELIEKPDDPP-TNLALIGMYVFSPAVFDAI-DDLEPSWRGELEITDAIQHLLEDGHEIDSHVVTGW--WKD 221
                                       ****************.*******************.89********************************6..*** PP

                                       XSSHHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleaneklae 247
                                       +G+++++lean+ ++e
  gi|313117363|ref|YP_004044346.1| 222 TGKPEDILEANRLVLE 237
                                       ***********98765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   1.7e-13   7.5e-10       1     121 [.       3     132 ..       3     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.7e-13
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTC....TS-EEE- CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd...eevlaalarl....gvrvved 65 
                                       +v+L GG +sR+      g+K+l+p+++kp+le++++ l++ag+ e+ v+ g+   e+++ +l +     gv++++ 
  gi|313117363|ref|YP_004044346.1|   3 GVLLSGGTGSRLRpithtGPKQLVPVANKPVLEYAIEDLKEAGITEIGVILGHkgrEDIQ-ELLGDgskyGVDITYI 78 
                                       79**********6554447*******************************9995533444.3444411114444333 PP

                                       TT.SS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEE CS
                      NTP_transf_3  66 ed.pgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvp 121
                                        +    g +++  +a + + ++d +++ ++D +l  ++ v  l++++++ ++ + ++
  gi|313117363|ref|YP_004044346.1|  79 VQgNPLGLAHAAGCARDFV-GDDDFVMYLGDNIL--KSGVTDLVESFESGDYGAGIA 132
                                       2101244445444444555.89999999999987..677888888887666655554 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.7e-06    0.0074       7      35 ..     262     290 ..     256     291 .. 0.91
   2 !    8.5   0.2   0.00039       1.7       5      29 ..     290     313 ..     288     315 .. 0.54
   3 ?   -3.6   0.0       2.4   1.1e+04       3       8 ..     348     353 ..     347     355 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                                       TEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   7 nvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                        ++I  +av++g++ I +n++I +g+++g
  gi|313117363|ref|YP_004044346.1| 262 SAVIEDGAVVRGPASIAENTTIKSGTYVG 290
                                       5799**********************998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00039
                                       ETTEEE-TTEEEETTEEE-TTEEEE CS
                           Hexapep   5 GsnvlIgpfaviggnVkIGdnvkIg 29 
                                       G  + Ig+++++ ++++I + v+Ig
  gi|313117363|ref|YP_004044346.1| 290 GPYTSIGANSTL-ADTHIENSVVIG 313
                                       666666665555.555555555554 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.4
                                       EEETTE CS
                           Hexapep   3 vIGsnv 8  
                                       v+G+n+
  gi|313117363|ref|YP_004044346.1| 348 VVGENS 353
                                       445554 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.3e-06     0.015       4      66 ..       4      70 ..       1      83 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-06
                                      EEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG..C CS
                              IspD  4 vipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld..k 66
                                      v+   G+G+R++      pKq++ ++++++le +++ l +   + +i v++ ++ +e +++ll+d  k
  gi|313117363|ref|YP_004044346.1|  4 VLLSGGTGSRLRpitHTGPKQLVPVANKPVLEYAIEDLKE-AGITEIGVILGHKGREDIQELLGDgsK 70
                                      666789999985332678*******************999.678888888888888*******99551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2423.37
//
Query:       gi|313117364|ref|YP_004044347.1|  [L=156]
Description: dTDP-4-dehydrorhamnose 35-epimerase-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-17   62.8   0.0    4.1e-17   62.4   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
    0.00014   21.6   0.0    0.00019   21.1   0.0    1.3  1  FdtA             WxcM-like, C-terminal
      0.006   16.3   0.3      0.061   13.1   0.3    2.1  1  Cupin_2          Cupin domain


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   6.8e-21   4.1e-17       3     153 ..       3     151 ..       2     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 6.8e-21
                                       SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEE CS
                   dTDP_sugar_isom   3 eiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldv 79 
                                       +i++v + + +v +D+RG  +e+f+e+ ++e  ++   +   +s++  gv+R  H + e  +q     + +G++   
  gi|313117364|ref|YP_004044347.1|   3 NIHDVEVRDLQVNADQRGHLVEVFRED-WDEYDID--PAMSYYSMTYPGVVRAWHRHLE--GQIDHFVCPKGRITVG 74 
                                       588999999***************965.5666666..89999*************7766..9999999********* PP

                                       EEE-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEE..EEES.S---GGGEEEE-TT-TTTT---S CS
                   dTDP_sugar_isom  80 aVDlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevl..Ykvt.eyyapesergirwnDpelgidwe 153
                                       + D R++Spt g+  ++ + ++n++ + ip  + hGf ++ de  +l  Y ++   y+  +e+ i ++D ++  dw+
  gi|313117364|ref|YP_004044347.1|  75 IYDDRQDSPTNGELDTFVIGEHNQQVIRIPGDCWHGFKAIGDEPAFLinYPTNlYDYEDPDEERIPYDDDRIPYDWN 151
                                       ****************************************999776522666654577779***************4 PP

>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.2e-08   0.00019       2     115 ..       6     130 ..       5     138 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.2e-08
                                       T-EEEEEEEEEETTEEEE.EEEBTTT.BSS--SEEEEEES--TTTEEEEEEESS.--EEEEEEES-EEEEEE-SS-E CS
                              FdtA   2 nvklielpkikdergnLs.vieeeke.vpfeikrvyyvydvpegeerGeHahkk.leqllialsGsvevllddgkkk 75 
                                       +v++ +l+  +d+rg+L+ v+ e+++  + ++++ yy++  p  + r  H h + +   +++ +G+++v + d ++ 
  gi|313117364|ref|YP_004044347.1|   6 DVEVRDLQVNADQRGHLVeVFREDWDeYDIDPAMSYYSMTYPGVV-RAWHRHLEgQIDHFVCPKGRITVGIYDDRQD 81 
                                       788999*********99834455555699999*****99988665.******8735689**********98776654 PP

                                       .......EEEEE.-STTEEEEE-TT-EEEEE---TT.-EEEEEESS--- CS
                              FdtA  76 .......keill.dspskglyipkmiWrelinfsed.avllvlasesyd 115
                                               ++++ +++++ + ip  +W+       + a l+    + yd
  gi|313117364|ref|YP_004044347.1|  82 sptngelDTFVIgEHNQQVIRIPGDCWHGFKAIGDEpAFLINYPTNLYD 130
                                       1211111223331344566667777776666655554555555555555 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.3     1e-05     0.061      42      68 ..      96     122 ..      42     125 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                                       ETTEEEEE-TT-EEEEEE-SSS-EEEE CS
                           Cupin_2  42 eaGdsvyfpagtpHrfrNtgdeparll 68 
                                       +  +++ +p   +H+f+  gdepa l+
  gi|313117364|ref|YP_004044347.1|  96 HNQQVIRIPGDCWHGFKAIGDEPAFLI 122
                                       456899*****************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1074.21
//
Query:       gi|313117365|ref|YP_004044348.1|  [L=474]
Description: membrane protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-26   92.2  13.5      3e-26   92.2  13.5    3.6  2  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    1.2e-22   80.5  11.8    1.2e-22   80.5  11.8    2.3  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    7.1e-21   74.8  36.5    9.7e-19   67.8  15.9    2.2  2  Polysacc_synt    Polysaccharide biosynthesis protein
    9.4e-11   41.0  12.5    9.4e-11   41.0  12.5    2.0  2  MurJ             Lipid II flippase MurJ
    2.1e-10   40.5   6.7    2.1e-10   40.5   6.7    3.5  4  MatE             MatE


Domain annotation for each model (and alignments):
>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.8   9.0         5   1.8e+04      93      93 ..      83      83 ..       9     130 .. 0.53
   2 !   92.2  13.5   8.2e-30     3e-26       1     142 [.     319     457 ..     319     458 .. 0.90

  Alignments for each domain:
  == domain 1  score: -7.8 bits;  conditional E-value: 5
                   Polysacc_synt_C 93 k 93
                                      k
  gi|313117365|ref|YP_004044348.1| 83 K 83
                                      1 PP

  == domain 2  score: 92.2 bits;  conditional E-value: 8.2e-30
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfg.ivGaaiatvlallvvavlnlya 76 
                                       vL+il+   i++s++++l+  Lqg++r+++a++a+v++++++liln++li +f+ ivGaa+at++++++ +vl+ y+
  gi|313117365|ref|YP_004044348.1| 319 VLVILTGEKILQSVHIILGRALQGIDRPDLAAWATVVSVALNLILNVVLILSFNdIVGAACATAISFALNTVLHAYF 395
                                       7999***********************************************9955********************** PP

                   Polysacc_synt_C  77 lrrllgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                       l+++l i++  +  +   ++++++m++++    + ++++ +l+  +l+lav++ga+ Y++++ll+r
  gi|313117365|ref|YP_004044348.1| 396 LSKYLTIRP-PYAEIGWCVFSSVMMALLLE-GIQTIVTVETLP--QLFLAVIFGAVTYGFFILLFR 457
                                       *********.79999887888877777755.444455555555..9*****************997 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5  11.8   3.2e-26   1.2e-22       3     289 ..      29     314 ..      27     318 .. 0.92
   2 ?    0.2   2.3     0.094   3.4e+02     125     157 ..     412     444 ..     362     461 .. 0.84

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 3.2e-26
                   Polysacc_synt_3   3 ARLLspedFGvvaialvvislanlfvdmGlssaliqkedltee...dlstvftfnlvlgllialvlfllapliasfy 76 
                                       AR L  +  Gv  +  ++++++ + +d+Gl  a+ ++ +  e+    ls++  ++l+  +li l ++l++ +i s++
  gi|313117365|ref|YP_004044348.1|  29 ARELGASQMGVFFLFQALLGMLAIPADFGLRGAVEKRISEGESpgaFLSSAVLLKLIPLALIVLGILLFRSWINSYL 105
                                       899999999************************966655544445599***************************** PP

                   Polysacc_synt_3  77 nqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllsslls 153
                                       + + +v     lal ++l+ + ++    l+ el+  ++++ +l+  +  v  + +l++ gl + AL+++ l    ++
  gi|313117365|ref|YP_004044348.1| 106 GADLAV----WLALAIVLQEAAQLAVVVLKGELRVGETAVLKLARRISWVGGGALLVVSGLKAEALIYSLLGGMCVI 178
                                       988665....689**************************************************************** PP

                   Polysacc_synt_3 154 lvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeits 230
                                       lv  w+ s+  ++   s +++++lf ++ + ++s++  y+++ +d  +iG +l++a++G Y++a r++++ +  ++ 
  gi|313117365|ref|YP_004044348.1| 179 LVWGWYKSSISLQR-PSASHARSLFDYSRYNVISSIGGYFYSWMDVAIIGLFLTQADVGAYETAWRVTTI-TMLFSR 253
                                       *********99876.5789***********************************************9876.6689** PP

                   Polysacc_synt_3 231 viakVlfPalSrl..qddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWl 289
                                       +ia+ +fP +S+    d+k+++++++++++  ++++v+P+++g++v++++++ +++G ++ 
  gi|313117365|ref|YP_004044348.1| 254 AIASTIFPQVSQWntEDEKDRIESVINNSMVPSMVLVIPAFFGTIVFSREILGLVFGTEFA 314
                                       ***********8622688999************************************9875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.094
                   Polysacc_synt_3 125 gvivaivlAllglgvwALvigtllssllslvll 157
                                        v++++++All+ g+  +v+ + l +l+ +v++
  gi|313117365|ref|YP_004044348.1| 412 CVFSSVMMALLLEGIQTIVTVETLPQLFLAVIF 444
                                       47899*************987777666666654 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8  15.9   2.7e-22   9.7e-19       3     272 ..       5     265 ..       3     267 .. 0.81
   2 !   13.1  12.9   1.3e-05     0.045      69     244 ..     271     452 ..     263     463 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 2.7e-22
                     Polysacc_synt   3 kgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.kelvslil 78 
                                       + +  l+l+++i+++++f+ ++ +ar lg+ + G + l +a++++l i +d+Gl  a+ ++i++ ++    l+s  l
  gi|313117365|ref|YP_004044348.1|   5 RSSVKLFLANVISAGIQFLGITFFARELGASQMGVFFLFQALLGMLAIPADFGLRGAVEKRISEGESPgAFLSSAVL 81 
                                       6677799*********************************************************9984333333444 PP

                     Polysacc_synt  79 lnvllvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvil 155
                                       l+++ + l+++ + l+  +i   + + +lav    lal+++ l   a++ +  ++g  r   +av  +++++s v  
  gi|313117365|ref|YP_004044348.1|  82 LKLIPLALIVLGILLFRSWI-NSYLGADLAV---WLALAIV-LQEAAQLAVVVLKGELRVGETAVLKLARRISWVGG 153
                                       44444444444444444444.3555555544...3344444.66789999999999********************* PP

                     Polysacc_synt 156 vliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsill 232
                                        +++v  +l+  a++ +++ ++ v ++ +++ +      +   +s ++ r l+ +s + +iss+++++y ++d+ ++
  gi|313117365|ref|YP_004044348.1| 154 GALLVVSGLKAEALIYSLLGGMCVILVWGWYKSS----ISLQRPSASHARSLFDYSRYNVISSIGGYFYSWMDVAII 226
                                       *********8888888888888888888888888....44444445579**************************** PP

                     Polysacc_synt 233 glllgaeavGiYnaayqllvaisgllapivtaalfPvfse 272
                                       gl+l   +vG Y  a +++++   +  +i++ ++fP  s+
  gi|313117365|ref|YP_004044348.1| 227 GLFLTQADVGAYETAWRVTTITMLFSRAIAS-TIFPQVSQ 265
                                       *****************99998888888888.****9987 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.3e-05
                     Polysacc_synt  69 ekkelvslillnvllvllvlvllfllllliaa.....flglpelavlylilalmll..llvgvasfrrglfqglerm 138
                                       e k+++ + ++n+++ ++vlv+ +++   ++      +  ++e+a+  ++l +     +l +v +  +  +qg  r 
  gi|313117365|ref|YP_004044348.1| 271 E-KDRIESVINNSMVPSMVLVIPAFFGTIVFSreilgLVFGTEFAIASVVLVILTGekILQSVHIILGRALQGIDRP 346
                                       3.5888999999999999999888777777777888877778888888888777777******************** PP

                     Polysacc_synt 139 kyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr..prfvilslklvrellsfsap 213
                                         aa+ +vv++   +il +++++ f+div+a+ +++++  ++ ++ +++l k+++  p+ + +    +  + s+ + 
  gi|313117365|ref|YP_004044348.1| 347 DLAAWATVVSVALNLILNVVLILSFNDIVGAACATAISFALNTVLHAYFLSKYLTirPPYAEI---GWCVFSSVMMA 420
                                       ***************************************************999543444444...55555555555 PP

                     Polysacc_synt 214 ltissl.aillytyidsillglllgaeavGiY 244
                                       l +  + +i    ++ +++l+ + ga+++G++
  gi|313117365|ref|YP_004044348.1| 421 LLLEGIqTIVTVETLPQLFLAVIFGAVTYGFF 452
                                       55555522333456666777777777777766 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.7      0.29     1e+03     143     180 ..      92     129 ..      71     150 .. 0.63
   2 !   41.0  12.5   2.6e-14   9.4e-11     227     425 ..     229     423 ..     212     450 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.29
                              MurJ 143 ltllllanklgeeaila..LaiGvliGgvlqllvqlpalk 180
                                       l++ll++  ++  + l+  La+ + ++ vlq ++ql+ ++
  gi|313117365|ref|YP_004044348.1|  92 LGILLFRSWIN--SYLGadLAVWLALAIVLQEAAQLAVVV 129
                                       34444444444..222224777777777777777776654 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 2.6e-14
                              MurJ 227 flaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpi 303
                                       fl +  v +++ a+r+ ++   lf+ +i+++++P++S+   e+++d +++ +++++  +++l+ip+ fg +v+s++i
  gi|313117365|ref|YP_004044348.1| 229 FLTQADVGAYETAWRVTTIT-MLFSRAIASTIFPQVSQWNTEDEKDRIESVINNSMVPSMVLVIPAFFGTIVFSREI 304
                                       56666677889999998775.5******************************************************* PP

                              MurJ 304 vsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnillsllllpplg.vv 379
                                       + l+f       +++++++ vL +     i  ++  +l r++    +   ++ ++++s+ ln++l+++l+ ++   v
  gi|313117365|ref|YP_004044348.1| 305 LGLVF------GTEFAIASVVLVILTGEKILQSVHIILGRALQGIDRPDLAAWATVVSVALNLILNVVLILSFNdIV 375
                                       *****......578889999999999999*************************************88777775389 PP

                              MurJ 380 glalatslsaliglvllyvllrkrlkltea.rgiktflak.lvvllal 425
                                       g a at++s+ +++vl  ++l k l + +   +i   + + ++++l+l
  gi|313117365|ref|YP_004044348.1| 376 GAACATAISFALNTVLHAYFLSKYLTIRPPyAEIGWCVFSsVMMALLL 423
                                       ***********************9996543122333333312333333 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   6.7       2.1   7.5e+03       5     105 ..      13     109 ..      10     133 .. 0.57
   2 ?   -1.7   0.1      0.56     2e+03       3      43 ..     114     154 ..     113     160 .. 0.80
   3 !   40.5   6.7   5.7e-14   2.1e-10       5     161 .]     211     366 ..     209     366 .. 0.96
   4 ?   -3.2   0.5       1.6   5.7e+03     114     114 ..     438     438 ..     411     461 .. 0.50

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.1
                              MatE   5 enllesllsli.dtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglill 79 
                                       +n++   ++++ +t+++ +lg++ +++  +++ +l +l +   +gl  a++ +++           +  l  +++l 
  gi|313117365|ref|YP_004044348.1|  13 ANVISAGIQFLgITFFARELGASQMGVFFLFQALLGMLAIpADFGLRGAVEKRISEGES------PGAFLSSAVLLK 83 
                                       55566666665245556666888888777777777777775557777777777664322......222333333333 PP

                              MatE  80 lllsliiallvllfseqilslftqde 105
                                       l+  ++i+l +llf+ +i s++++d 
  gi|313117365|ref|YP_004044348.1|  84 LIPLALIVLGILLFRSWINSYLGADL 109
                                       33333333444566666666666655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
                              MatE   3 alenllesllslidtllvgrlgskalAavsialsilsllfv 43 
                                       al+ +l+   +l++++l g+l   + A++ +a +i+++ + 
  gi|313117365|ref|YP_004044348.1| 114 ALAIVLQEAAQLAVVVLKGELRVGETAVLKLARRISWVGGG 154
                                       67888999999999999999988888889999888887765 PP

  == domain 3  score: 40.5 bits;  conditional E-value: 5.7e-14
                              MatE   5 enllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                       +++  +++s  d+ ++g +  + +++a+  a++++ ++++f+ ++++ + + v+q   +  ++r++ +++ +++ ++
  gi|313117365|ref|YP_004044348.1| 211 SSIGGYFYSWMDVAIIGLFlTQADVGAYETAWRVTTITMLFSRAIASTIFPQVSQWNTEDEKDRIESVINNSMVPSM 287
                                       6666789999******************************************************************* PP

                              MatE  81 llsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnip 157
                                       +l +++++ +++fs+ il l+  +e   ++a+  l il    ++++++++l ++l+g+ ++ +++ ++++s+ ln++
  gi|313117365|ref|YP_004044348.1| 288 VLVIPAFFGTIVFSREILGLVFGTE--FAIASVVLVILTGEKILQSVHIILGRALQGIDRPDLAAWATVVSVALNLI 362
                                       ********************98888..799*********************************************** PP

                              MatE 158 lnyl 161
                                       ln++
  gi|313117365|ref|YP_004044348.1| 363 LNVV 366
                                       *985 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.6
                              MatE 114 y 114
                                       +
  gi|313117365|ref|YP_004044348.1| 438 L 438
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2835.77
//
Query:       gi|313117366|ref|YP_004044349.1|  [L=619]
Description: hypothetical protein Hbor_31530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3755.43
//
Query:       gi|313117367|ref|YP_004044350.1|  [L=416]
Description: arylsulfatase A family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-18   65.6   0.0      6e-18   65.3   0.0    1.1  1  Sulfatase     Sulfatase
  ------ inclusion threshold ------
      0.014   15.0   0.9      0.022   14.3   0.4    1.7  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
       0.12   11.0   0.0       0.18   10.4   0.0    1.2  1  DUF229        Protein of unknown function (DUF229)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0     1e-21     6e-18       3     307 ..       5     323 ..       3     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1e-21
                                       EEEEEESSE-TT..GSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT.. CS
                         Sulfatase   3 vvliladdlgag..dlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg.. 75 
                                       v+li +d+++ +  + +++  + +    +   +   +rf n++s++ ++  + + +  g +++ +g   ++  +   
  gi|313117367|ref|YP_004044350.1|   5 VILISIDTVRQDvfNEKCFPKSWPV---I---TSDFTRFPNAISSGVATPHAFPGIIAGTPAIDDGKFKSGTSTIae 75 
                                       6788888887776666666666553...4...47789***************************9965555433377 PP

                                       ..HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCC.TTT CS
                         Sulfatase  76 ..gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrv.ppe 149
                                         +g+    ++ + l  ++GY  ++     +++   q+ +++  f+r+++  ++++ ++ +  ++++ +   + p++
  gi|313117367|ref|YP_004044350.1|  76 lfDGRTVAFTNNGHLRADRGYSRGVDDFADTSLPTHQNKASGSLFERIVEIEHVKNSQTLKRLYSWYKSLSESpPYS 152
                                       88888888888888888888888888888888888888778999999999999999999999999999887655666 PP

                                       TCSHHHHHHHHHHHHHHCCC.TSSEEEEEEE-TTSSST......CTCGGHTCCGSTTTTCCCCCCH........... CS
                         Sulfatase 150 ggysddrlldealefllarn.dkpfflylatlapHapp......eapdeyakkyatffddgseaar........... 208
                                       +   d+++   + ++lla++ d p fl+ +++  H p+        p+  ++k            +           
  gi|313117367|ref|YP_004044350.1| 153 KPAKDADV---VTDWLLAETrDPPEFLWAHYMDAHKPFiperaiDGPKVTVTKE-----------Klgylndyered 215
                                       66666555...5566644555**************9553333221222222222...........122333344455 PP

                                       .........HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEE CS
                         Sulfatase 209 .........qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvP 276
                                                 l e y + v+y D ++gr l +L+ +  +d++l++  SDhg+  +e ++  ++    +  e+ + vP
  gi|313117367|ref|YP_004044350.1| 216 dppskehqdLLWELYEANVRYLDRGLGRALLELQSQDWYDDALIILASDHGELFGEHGYMWHPMTI-DPVEELIDVP 291
                                       666666667999****************************************99885555555554.788******* PP

                                       EEEEETTTSHC.EEECSEEEGGGHHHHHHHHT CS
                         Sulfatase 277 llvwwpgekap.rvseelvshiDlfptildla 307
                                       l v +p e+++  +++  v h D+ +t+++++
  gi|313117367|ref|YP_004044350.1| 292 LAVKFPSENHAgDIVQHRVQHADIPATVASVL 323
                                       ****************************9887 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.59   3.5e+03       1      16 [.       5      20 ..       5      24 .. 0.88
   2 ?   14.3   0.4   3.7e-06     0.022     197     234 ..     230     267 ..     133     378 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.59
                                      EEEEEETT-BTTHHHH CS
                      Phosphodiest  1 vlvislDGlradlldr 16
                                      v++is+D +r d +++
  gi|313117367|ref|YP_004044350.1|  5 VILISIDTVRQDVFNE 20
                                      79********999876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.7e-06
                                       HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES--- CS
                      Phosphodiest 197 vedalrrvDkaigdLlealderglsaetniilvSDHGm 234
                                        e+++r++D+ +g+ l +l+ +  +++  iil+SDHG 
  gi|313117367|ref|YP_004044350.1| 230 YEANVRYLDRGLGRALLELQSQDWYDDALIILASDHGE 267
                                       799**********************************5 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     3e-05      0.18     312     351 ..     235     274 ..     216     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3e-05
                            DUF229 312 ealDedllkylkklekkgllentlvlllsDHGlrfgklrk 351
                                       + lD  l + l +l+ ++  ++ l++l sDHG  fg++  
  gi|313117367|ref|YP_004044350.1| 235 RYLDRGLGRALLELQSQDWYDDALIILASDHGELFGEHGY 274
                                       5569999999**********************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2474.85
//
Query:       gi|313117368|ref|YP_004044351.1|  [L=298]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-18   66.0   0.0    4.8e-18   65.5   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
      3e-12   46.9   0.0    5.5e-12   46.1   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00027   20.7   0.5     0.0018   18.0   0.1    2.4  2  Glyco_tranf_2_5  Glycosyltransferase like family


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   8.1e-22   4.8e-18       3     168 ..       9     179 ..       9     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 8.1e-22
                                       EEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH-- CS
                   Glycos_transf_2   3 viptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraat 79 
                                       +i   N +k   e+l+sl +  +y +f+ iv+D+gStD++ e ++e    +p++ v++ ++n G+ag++n g+ +a 
  gi|313117368|ref|YP_004044351.1|   9 IILNWNNYKDTSECLRSLNSL-EYRNFTPIVIDNGSTDGSGEKIREE---FPDIDVCQTNQNLGFAGGMNVGINKAL 81 
                                       566778899999*********.*******************999999...69************************* PP

                                       SS...EEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.....EEEECCHCCCCHCCC CS
                   Glycos_transf_2  80 gd...yilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeiernkrv.....generlyfkerkrsl 147
                                        +   yi++l+ D+ +++d  l  l++ le+ ++++++  ++r + ++  i+  k+       +  + ++    +s+
  gi|313117368|ref|YP_004044351.1|  82 EEefsYIWILNNDVLFSDDnVLGSLIQTLEAVPDAGAVTPIVRDETDSSGIWFKKGEinwktATAVHSNQDSATNSD 158
                                       ********************************************999999999988777766666666666666666 PP

                                       CCCSTTCSTCCCEEEEHHHHH CS
                   Glycos_transf_2 148 kgnlsfeigsaallrrealee 168
                                        ++ +++  + al+  ++++e
  gi|313117368|ref|YP_004044351.1| 159 LIENQYIPLCSALFPASVFRE 179
                                       666666666666666666666 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   9.3e-16   5.5e-12       2     203 ..       4     209 ..       3     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 9.3e-16
                   Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       +d+a ++ ++n+ ++  e+l+sl + ey ++  +v++++s+++  e ++e   ++pd+  +v ++ +nlg+   + +
  gi|313117368|ref|YP_004044351.1|   4 PDVAGIILNWNNYKDTSECLRSLNSLEYRNFTPIVIDNGSTDGSGEKIRE---EFPDI--DVCQTNQNLGF---AGG 72 
                                       358899*************************************9999998...****7..67788888886...555 PP

                   Glyco_tranf_2_3  79 lnealravk...sdlvllvDdDtvv.ePdtlkrllqff.ltpkvgavgtpvfllnrstl.........vsalgalef 141
                                       +n +++ +    + ++++++ D++  ++++l +l q++ + p++gav+  v+ + +s+          +  ++a++ 
  gi|313117368|ref|YP_004044351.1|  73 MNVGINKALeeeFSYIWILNNDVLFsDDNVLGSLIQTLeAVPDAGAVTPIVRDETDSSGiwfkkgeinWKTATAVHS 149
                                       66666643224499***********89999********9999******66655554433348888888999999999 PP

                   Glyco_tranf_2_3 142 aerhlrflaarralgv.ltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtay 203
                                       +++ + ++ + +   + l+      l++++v++e ++l +  f   +D+e+g+r+r++g+++ +
  gi|313117368|ref|YP_004044351.1| 150 NQDSATNSDLIENQYIpLC----SALFPASVFREVGLLPEdYFMYYEDLEYGVRVRNHGYKIFT 209
                                       9999966666555555233....589*********98888999999**************9875 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.2   1.2e+03       2      23 ..       9      30 ..       8      35 .. 0.87
   2 !   18.0   0.1     3e-07    0.0018      40     199 ..      72     227 ..      56     274 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.2
                   Glyco_tranf_2_5  2 fivcvnneelyeeclsylenle 23
                                      +i+  nn +  +ecl+ l++le
  gi|313117368|ref|YP_004044351.1|  9 IILNWNNYKDTSECLRSLNSLE 30
                                      788889999999*****99998 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-07
                   Glyco_tranf_2_5  40 siaeaynkalsasdakykvYlhqDvliinkdfikdlleiFkkdkkiGmiGvvGakslpesgvwweskkkvgkviets 116
                                        +  + nkal++ ++ y   l++Dvl+   +++  l++ ++  ++ G +  + ++++ +sg+w+++     +++ ++
  gi|313117368|ref|YP_004044351.1|  72 GMNVGINKALEE-EFSYIWILNNDVLFSDDNVLGSLIQTLEAVPDAGAVTPIVRDETDSSGIWFKKG----EINWKT 143
                                       566777888877.9999999********************************************444....444443 PP

                   Glyco_tranf_2_5 117 keeakelraeeeeseyeeVeai...dGllmat.qydv.pwredlftgfhfYdvsqslefekagykvvVpnqekpWvi 188
                                       ++ ++  ++++++s+ +e + i     l+ a   ++v    ed    +++ d++  ++++++gyk++  + ++  +i
  gi|313117368|ref|YP_004044351.1| 144 ATAVHSNQDSATNSDLIENQYIplcSALFPASvFREVgLLPEDY--FMYYEDLEYGVRVRNHGYKIFTKTSTS--II 216
                                       33333333344444444444430002222221122333455562..245558888888888888888755444..45 PP

                   Glyco_tranf_2_5 189 hdsgfkklkey 199
                                       hd+g  + ++y
  gi|313117368|ref|YP_004044351.1| 217 HDQGGTAGDQY 227
                                       77665554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1907.96
//
Query:       gi|313117369|ref|YP_004044352.1|  [L=362]
Description: hypothetical protein Hbor_31560 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-12   48.1   0.0    2.7e-12   47.3   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    4.5e-06   27.0   0.0    9.8e-06   25.9   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00062   19.3   0.0     0.0012   18.5   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
     0.0065   16.5   0.0     0.0096   15.9   0.0    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0     6e-16   2.7e-12       3     133 ..     197     326 ..     195     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 6e-16
                                       EEEEES--.-GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEEE CS
                   Glyco_trans_1_4   3 vilfvGrl.eenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfvedlaellaaadvfva 78 
                                       + +fvG+  ++n+++v  ++  + +  ++ v+ +i+G+   + ++ e    + ++++++Gfv++++++++ +d++++
  gi|313117369|ref|YP_004044352.1| 197 IACFVGNDhYPNIEAVNEIASMARRTTDDGVQYLIIGNV-CD-QFSED--SVPPNMHLLGFVDSIEPYYSLSDIALN 269
                                       5689**99778*999999999999999666*******44.43.45422..4679********99************* PP

                                       --...---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  79 Ps...egfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrLle 133
                                       P+    g+++k+lE++  g+ + +t+  g++  v  e g+  ++ d + + e+i++L +
  gi|313117369|ref|YP_004044352.1| 270 PIcsgSGVNIKMLEYFQQGVTTLSTPF-GARG-VeAEPGVHYAQSDISNFPEKIVHLKN 326
                                       **9877*********************.6344.447999999999*********99865 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.2e-09   9.8e-06       1      90 [.     266     355 ..     266     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.2e-09
                   Glyco_trans_1_2   1 ivLnpsrs.espnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaare 75 
                                       i+Lnp  s  ++n +++E+   G++ l+++  + +   +pg  v +++ d  ++ eki +l +np er+ ++ +a+ 
  gi|313117369|ref|YP_004044352.1| 266 IALNPICSgSGVNIKMLEYFQQGVTTLSTPFGARGVEAEPG--VHYAQsDISNFPEKIVHLKNNPSEREDMSSNAKL 340
                                       67886556366******************554444445666..555558**************************** PP

                   Glyco_trans_1_2  76 rvlaehtydhraeql 90 
                                        ++++++++   ++l
  gi|313117369|ref|YP_004044352.1| 341 LIQEKLNWETVSKNL 355
                                       ********9877665 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.6e-07    0.0012      12     170 ..     192     339 ..     187     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.6e-07
                                       TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHH CS
                   Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredlee 88 
                                       ++ + i+++vg+  ++ +++ + + +   ++++++ v+++i+G      ++ ++  e  +  n ++lg+v+   +e 
  gi|313117369|ref|YP_004044352.1| 192 DSSDFIACFVGND-HYPNIEAVNEIASMARRTTDDGVQYLIIG------NVCDQFSEDSVPPNMHLLGFVD--SIEP 259
                                       5666677777764.457888888888888888999********......6888999999***********9..9*** PP

                                       HHHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHH CS
                   Glycos_transf_1  89 llknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrer 164
                                       +++ +di++ p  s  g  i  lE+++ g+ ++++  g      ++g+   ++++ ++  + e+i  l +++ +re+
  gi|313117369|ref|YP_004044352.1| 260 YYSLSDIALNPICSgSGVNIKMLEYFQQGVTTLSTPFGARGVEAEPGV---HYAQSDISNFPEKIVHLKNNPSERED 333
                                       ***********9999999******************998887666655...9************************* PP

                                       HHHHHH CS
                   Glycos_transf_1 165 lgenar 170
                                       ++ na+
  gi|313117369|ref|YP_004044352.1| 334 MSSNAK 339
                                       ****98 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-06    0.0096      73     163 ..      78     169 ..      54     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                    Glyco_transf_4  73 pDvvHahspaalgaallalrrrlgiplVltvHglye....krllkarlkplsrllralerrllrradrviavSeata 145
                                        Dvv +  p+ +   ++a r  ++ plV++ H+ +     +    +  k l   +r le+ ++  ad +i++S   +
  gi|313117369|ref|YP_004044352.1|  78 ADVVVVDRPWQV--PYIAERVDHDTPLVYSSHNVESelysHLDSSYLTKGLLTTVRDLEQNAIETADLTITISSRDK 152
                                       588877777666..555666679************99887444444555666788899999**************** PP

                    Glyco_transf_4 146 delrerygvppekitVip 163
                                       + ++ +++ +   i+V p
  gi|313117369|ref|YP_004044352.1| 153 NIYQNKFD-KCGEIHVAP 169
                                       ****9887.337888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 2640.94
//
Query:       gi|313117370|ref|YP_004044353.1|  [L=382]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-27   93.8   0.0    1.3e-26   93.1   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    6.7e-24   84.8   0.0    1.1e-23   84.2   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    4.3e-12   46.4   1.5    1.2e-11   45.0   0.6    2.1  2  Glyco_transf_4   Glycosyltransferase Family 4
    5.3e-07   30.2   0.0    9.6e-07   29.4   0.0    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0016   18.5   0.2      0.033   14.2   0.2    2.2  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.038   14.4   0.0       0.11   12.9   0.0    1.8  2  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.0   4.5e-30   1.3e-26       5     172 .]     195     361 ..     192     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 4.5e-30
                                       HHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECC CS
                   Glycos_transf_1   5 krkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgev 81 
                                       ++++  + + ++ il+v+r +++Kg++++++++a +    + +v + ++G g++ ++lk+l e l+++d+v flg+v
  gi|313117370|ref|YP_004044353.1| 195 NKFEPTEGHIENRILTVARHVEKKGIEYALRSIANI----DTKVDYRVIGTGPRTEYLKELTEDLKIKDQVSFLGRV 267
                                       5666666677899*********************87....789********************************** PP

                                       HSSSHHHHHHCESEEEEEESS......BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHH CS
                   Glycos_transf_1  82 sredleellknadifvlpsis......EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeai 152
                                       s+e+l+  +  a +f+lp+        +g ++++ EAma ++p +++ ++g++e+v +   G+l +p+++e+l + i
  gi|313117370|ref|YP_004044353.1| 268 SDERLKREMDEAQLFLLPCVVakngdrDGVPVSIKEAMAMKTPPVTTTVSGIPEIVDESC-GYLSPPKDVESLCNSI 343
                                       ******************************************************997766.**************** PP

                                       HHHHHSHHHHHHHHHHHHHH CS
                   Glycos_transf_1 153 rklledeelrerlgenarkr 172
                                       ++ l+++  ++++g+na++r
  gi|313117370|ref|YP_004044353.1| 344 KEGLNSR--SNDIGRNAQQR 361
                                       ******9..********986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   3.6e-27   1.1e-23       2     132 ..     206     347 ..     205     349 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 3.6e-27
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaa..gleerveftGfv..edlaellaaad 74 
                                       ++il+v r +e+ kg+++ l+ ++ +  k v   ++G gpr e l+el++  +++++v+f+G+v  e l++ +++a+
  gi|313117370|ref|YP_004044353.1| 206 NRILTVARHVEK-KGIEYALRSIANIDTK-VDYRVIGTGPRTEYLKELTEdlKIKDQVSFLGRVsdERLKREMDEAQ 280
                                       689*****9655.**************66.99*******9667999888768999*********7545********* PP

                                       EEEE--........---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  75 vfvaPs........egfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrLl 132
                                       +f++P          g+++++ Eama+++p V+t+v+gi+e+v +  g+l pp+d+e+l + i + l
  gi|313117370|ref|YP_004044353.1| 281 LFLLPCvvakngdrDGVPVSIKEAMAMKTPPVTTTVSGIPEIVdESCGYLSPPKDVESLCNSIKEGL 347
                                       *******99877644****************************999**************9998765 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.6   3.9e-15   1.2e-11       5     168 ..      15     194 ..      14     196 .. 0.75
   2 ?   -1.9   0.0      0.99     3e+03       5      24 ..     205     224 ..     204     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 3.9e-15
                    Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpgddgpleeev.......................elvvrvprvplpllk..rllr 56 
                                       e+ v + + +L++rGh+V v++++ ++++ +e                        +l   +    l+ ++  r  +
  gi|313117370|ref|YP_004044353.1|  15 ETWVKNEISELRKRGHQVAVFSHHAPDEPSDELadihsftppepslkgfrhlefseVLNPTFYQTLLWTKNplRQAY 91 
                                       78899999******************99999999***********99999888875333333333333222003334 PP

                    Glyco_transf_4  57 slaflrrlrrllkre..kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrll 131
                                       s+ +++++   ++    ++D +H h++++  + + + +r +++p+ l  H  +          ++        ++l+
  gi|313117370|ref|YP_004044353.1|  92 SIYYASYASSYVDSLpfDIDHIHGHFAMPPQVPANYVARLYDLPHTLMTHAYD----------LYGFDHTPTREYLY 158
                                       5566666677777776677778888888877777777778*************..........34444444445678 PP

                    Glyco_transf_4 132 rradrviavSeatadelrerygvppekitVipnGvDl 168
                                       r++dr++++Se+ ++++++  ++   ++ V+p   D 
  gi|313117370|ref|YP_004044353.1| 159 RHSDRILTISEYNREYMEKEANCT-LDVNVVPACFDA 194
                                       89*****************99988.589999977775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.99
                    Glyco_transf_4   5 erhvleLaraLarrGheVtv 24 
                                       e+ +l++ar+  ++G+e  +
  gi|313117370|ref|YP_004044353.1| 205 ENRILTVARHVEKKGIEYAL 224
                                       78899999999999998766 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.2e-10   9.6e-07      11     158 ..      22     189 ..      15     191 .. 0.59

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.2e-10
                   Glyco_trans_4_4  11 araLaarGheVtvlt.papapgapeleedgvrvhrlpvp.rrpspladlaal...................ralrrl 66 
                                       +++L++rGh+V v+   ap+++++    + + +h++  p ++ ++++ l+++                   +     
  gi|313117370|ref|YP_004044353.1|  22 ISELRKRGHQVAVFShHAPDEPSD----ELADIHSFTPPePSLKGFRHLEFSevlnptfyqtllwtknplrQ----- 89 
                                       679************433444444....67889987433134468888888766674444433333333320..... PP

                   Glyco_trans_4_4  67 lrqr................rerpdvvhahspt.aglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrl 126
                                          +                 + +d +h h  +    +a   +r  ++p+ +  h+ +l    g+++   ++   +l
  gi|313117370|ref|YP_004044353.1|  90 ---AysiyyasyassyvdslPFDIDHIHGHFAMpPQVPANYVARLYDLPHTLMTHAYDLY---GFDH---TPTREYL 157
                                       ...133333333333333225555556666555244445444448899999998886553...2222...3445689 PP

                   Glyco_trans_4_4 127 lrradavlvvseaeaeelra.lgvpadrvvvvp 158
                                       +r+ d++l++se+ +e+++   +    +v vvp
  gi|313117370|ref|YP_004044353.1| 158 YRHSDRILTISEYNREYMEKeANCT-LDVNVVP 189
                                       ******************9834333.4555555 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   1.1e-05     0.033       8      53 ..      13      56 ..       4     168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                   Glyco_trans_4_2  8 lssvhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd 53
                                      ls++ +++ ++eL+krg++V+v++ + +  de  +e + +h+++ +
  gi|313117370|ref|YP_004044353.1| 13 LSETWVKNEISELRKRGHQVAVFSHHAP--DEPSDELADIHSFTPP 56
                                      45677888899***************99..6677777788888433 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       3.8   1.1e+04      58      80 ..     156     178 ..     153     182 .. 0.74
   2 ?   12.9   0.0   3.6e-05      0.11      15      90 ..     301     374 ..     281     376 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.8
                   Glyco_trans_1_2  58 yllanpeerraiaeaarervlae 80 
                                       yl ++ +++  i+e +re +++e
  gi|313117370|ref|YP_004044353.1| 156 YLYRHSDRILTISEYNREYMEKE 178
                                       67788888888888888877766 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.6e-05
                   Glyco_trans_1_2  15 lfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaehtydhraeql 90 
                                       + Ea+a+ ++ +t+  +g++e++++ +  +    d+e+l   i++ l+++   + i+++a++r+ + h  ++ +++l
  gi|313117370|ref|YP_004044353.1| 301 IKEAMAMKTPPVTTTVSGIPEIVDESCGYLSPPkDVESLCNSIKEGLNSRS--NDIGRNAQQRI-QSHKSEKVVDDL 374
                                       67************99*******8886666555777777777777776555..59********5.677777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2262.61
//
Query:       gi|313117371|ref|YP_004044354.1|  [L=447]
Description: arylsulfatase A family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-15   54.9   1.7    3.9e-13   49.5   1.7    2.2  1  Sulfatase     Sulfatase
     0.0043   16.7   5.6      0.033   13.8   5.6    2.1  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
     0.0053   17.0   0.1     0.0094   16.2   0.1    1.3  1  acVLRF1       Actinobacteria/chloroflexi VLRF1 release factor


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   1.7   6.6e-17   3.9e-13      38     303 ..      78     338 ..      70     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6.6e-17
                                       EESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT.....HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGG CS
                         Sulfatase  38 rftnfysaaplcspsraalltgryphnsgvasntevgg.....gglpqteatLpellkeaGYntaaigkwhlgwssr 109
                                        f ++++ ++ + p+  +l tg+yph++g+ ++t++ +     +++ ++ +tL+ ++ +aGY t             
  gi|313117371|ref|YP_004044354.1|  78 EFGRAITPGSWTFPAITSLHTGQYPHEHGSIAHTPPEEedhaiPKQYESRNTLAHVFESAGYST--------YSG-- 144
                                       67789999999*************************99****999*******************........212.. PP

                                       GSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCCTTTTCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSST CS
                         Sulfatase 110 qsvyknrgfdrflgfptgsaalkdpekseyngevlrvppeggysddrlldealefllarndkpfflylatlapHapp 186
                                                  ++ f +++  ++++    y             s + +    l +  +r++   f yl++   H p 
  gi|313117371|ref|YP_004044354.1| 145 -C-------AFIVPFLATNGWYEQNR--VYA----------DKSAQTVISDYLSW--RRKHSRTFGYLHLGDLHNPI 199
                                       .2.......12333333333333333..332..........25667777777777..667999************** PP

                                       CTCGGHTCCGSTTTTCCCCCCH......................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGE CS
                         Sulfatase 187 eapdeyakkyatffddgseaar......................qlleaylnsveyvDdligrvlaaLeenglldnt 241
                                       e p +y +k    + +                            + +  y +++ yv d ++++++++      ++t
  gi|313117371|ref|YP_004044354.1| 200 EPPSKYIDKHDIDTTM-----FlsefgkwtdeydggeeaqryrrERMKLYHAALDYVSDEVNKLIDEI-----QNDT 266
                                       ********95444333.....14445566677777777888889************************.....99** PP

                                       EEEEEESSSSCCCG.............HHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHH CS
                         Sulfatase 242 lvvftSDhgaslee.............sngplrggkganayeggtrvPllvwwpgekaprvseelvshiDlfpti 303
                                       ++v+ +Dhg+   e             s g+ +gg   +  ++  rvP  +  p++     + +  s+iD+  ti
  gi|313117371|ref|YP_004044354.1| 267 MIVVGGDHGEPHFEhwqrdqritdsrpSYGVGHGG---TPFDELARVPVSIQTPDGETYLPEGGWGSLIDIPNTI 338
                                       ************99888888888864433333333...4477777777777777766655555555555555555 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   5.6   5.5e-06     0.033      43     234 ..      87     276 ..      84     291 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-06
                                       -SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEEEETTTTGGGGGCTT.S-HHHHHHHTHTTCEEEESE.TTTTS CS
                      Phosphodiest  43 tlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvvfvtededaprwwqg.epiwdtaakarglkaaalfw.pgsev 117
                                       + Tfp+ +sl TG+yP eHG ++     ++ ++ +  ++++++     ++  ++++ a     + ++++f  p    
  gi|313117371|ref|YP_004044354.1|  87 SWTFPAITSLHTGQYPHEHGSIA--HTPPEEEDHAIPKQYESR-----NTlAHVFESAGYS-TY-SGCAFIvPFLAT 154
                                       56*********************..778888885444444333.....3346666666666.33.667777575555 PP

                                       EBTTCT.SC.TBHHSBTCT..CSTTSCHHHHHHHHHHHHHHHCHTHSHHHHHCT...SSESE.EEEEECCCHHHHHH CS
                      Phosphodiest 118 dystyyylvsetppryled.dfnakvpledkvdkavlqtwldaafakvvlekel...ekpdl.llvyleetDtvgHk 189
                                       +   +y +   + ++++++   ++++++++k ++  +  +l + + ++ +e  +   +k d  +++ l+e ++   +
  gi|313117371|ref|YP_004044354.1| 155 NG--WYEQN-RVYADKSAQtVISDYLSWRRKHSR-TF-GYLHLGDLHNPIEPPSkyiDKHDIdTTMFLSEFGKWTDE 226
                                       55..33333.333333334366777799998886.45.588888877666533344533333122223344444444 PP

                                       H-TTSHH...........HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES--- CS
                      Phosphodiest 190 fGpdspe...........vedalrrvDkaigdLlealderglsaetniilvSDHGm 234
                                       +    +e             +al +v + +++L+++++ +     t i++ +DHG 
  gi|313117371|ref|YP_004044354.1| 227 Y-DGGEEaqryrrermklYHAALDYVSDEVNKLIDEIQND-----TMIVVGGDHGE 276
                                       4.223336788888899999******************99.....99*******95 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.6e-06    0.0094      40      83 ..     229     274 ..     224     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-06
                           acVLRF1  40 GGwSqqRfaRrrenqadalleavaeaaarllaeesae..vvlgGdr 83 
                                       GG   qR+ R r +   a+l+ v +++++l++e +++  +v+gGd+
  gi|313117371|ref|YP_004044354.1| 229 GGEEAQRYRRERMKLYHAALDYVSDEVNKLIDEIQNDtmIVVGGDH 274
                                       77778**************************77777799******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2897.95
//
Query:       gi|313117372|ref|YP_004044355.1|  [L=344]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-17   61.6   0.0    1.3e-16   61.0   0.0    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.7e-14   53.1   0.1    1.3e-13   50.9   0.1    2.1  1  Glycos_transf_1  Glycosyl transferases group 1
    9.2e-14   52.0   0.0    2.7e-13   50.5   0.0    1.8  2  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00014   22.3   0.0    0.00021   21.8   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0018   18.0   0.0     0.0031   17.2   0.0    1.4  1  Glyco_transf_5   Starch synthase catalytic domain
     0.0044   17.0   0.2      0.082   12.9   0.0    2.2  2  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.026   14.9   0.0      0.064   13.7   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   5.2e-20   1.3e-16       2     169 ..      16     188 ..      15     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 5.2e-20
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvv...tpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrr...llkre 71 
                                       GG+  h+ +L ++ + +Gh+Vtv+   +p++  +le+ev +   ++  +p  + +r +++l ++ +l+    +l+  
  gi|313117372|ref|YP_004044355.1|  16 GGISYHLKNLYNEIQNLGHNVTVLagkCPQSWNELEKEVdP---NINVIPVEFGYRKGYYLLYPVSLWSklvRLDTS 89 
                                       9***********************77777777777777442...223333333333333333333333300035555 PP

                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglye..........krllkarlkplsrllralerrllrradrvi 138
                                       k+D+  +h+p ++       +   ++ l++ +H+             +++ k   ++l+++++++ +  l+++d+ i
  gi|313117372|ref|YP_004044355.1|  90 KYDIAITHTPLPF-------KI-PHLNLITKYHDCVTetrpyirdglSTFGKIGDSFLHPIRKRIDQTSLHKSDKGI 158
                                       ************9.......44.6999*******************9999999************************ PP

                    Glyco_transf_4 139 avSeatadelrerygvppekitVipnGvDle 169
                                        vSe  ++ ++++y  +     Vi+nGvD++
  gi|313117372|ref|YP_004044355.1| 159 FVSELNKNAWEKHYEAQ-LETDVIYNGVDVD 188
                                       ***************88.79*********98 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1     5e-17   1.3e-13      18     139 ..     200     301 ..     188     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 5e-17
                                       EEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCES CS
                   Glycos_transf_1  18 ilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknad 94 
                                       +l+vg  e+ Kg++ ++k ++        ++ ++i+G             e e ++n+i +g+vs+e+l el++ a 
  gi|313117372|ref|YP_004044355.1| 200 VLFVGSSER-KGISKVLKYAE------SGEYTVHIVG-----------DTEVE-NNNIITHGRVSQEKLRELYSGAL 257
                                       555555554.66666666655......3556666666...........22333.4899******************* PP

                                       EEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEE CS
                   Glycos_transf_1  95 ifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGll 139
                                       ++++p   E+fG  +lE++++g+pvi++n +g+ ev++++  G++
  gi|313117372|ref|YP_004044355.1| 258 ATIHPTKFEAFGNIVLESLSCGTPVITTNKCGAGEVLTEET-GII 301
                                       ************************************99876.554 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.4   6.2e+03      21      55 ..      22      56 ..      13      63 .. 0.51
   2 !   50.5   0.0   1.1e-16   2.7e-13       4     117 ..     200     303 ..     197     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                                      HHHH.HHHH.H.HEEEEEES---...HHHHHHHTT-T. CS
                   Glyco_trans_1_4 21 leav.pllrkk.dvrlvivGdgprp.eeleelaaglee 55
                                      l+++  ++++  +   v++G+ p++ +ele++++   +
  gi|313117372|ref|YP_004044355.1| 22 LKNLyNEIQNLgHNVTVLAGKCPQSwNELEKEVD---P 56
                                      4444444442222346777765533356665553...4 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 1.1e-16
                                       EEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE CS
                   Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvfva 78 
                                       +lfvG+   ++kg+  +l+ ++      ++++ivGd     e+e      +++++ +G+v  e+l+el++ a  ++ 
  gi|313117372|ref|YP_004044355.1| 200 VLFVGSS--ERKGISKVLKYAESGE---YTVHIVGDT----EVE------NNNIITHGRVsqEKLRELYSGALATIH 261
                                       7888877..4588887777776665...89*****43....676......279*******9777************* PP

                                       --..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE-- CS
                   Glyco_trans_1_4  79 Ps..egfglkllEamaaglpvVatdvggiaevv.gengllvp 117
                                       P+  e fg+ +lE++++g+pv++t+  g+ ev+ +e+g++ +
  gi|313117372|ref|YP_004044355.1| 262 PTkfEAFGNIVLESLSCGTPVITTNKCGAGEVLtEETGIITN 303
                                       ***99*******************877989*99999*99875 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   8.1e-08   0.00021       1     160 []      16     184 ..      16     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.1e-08
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvlt...papapgapeleedgvrvhrlpvprrps..pladlaalralrrllrqrre 72 
                                       gGi+ +  +l  + + +Gh Vtvl+   p+  ++ + ++ + + v+++ +++r +  +l+ ++    l    r +  
  gi|313117372|ref|YP_004044355.1|  16 GGISYHLKNLYNEIQNLGHNVTVLAgkcPQSWNELEKEVDPNINVIPVEFGYRKGyyLLYPVSLWSKLV---RLDTS 89 
                                       8************************66655555566688999********9998522444444444455...559** PP

                   Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlh..............glllrrgsgavrrlyralerrllrradavlv 135
                                       ++d+ ++h+p   l+ ++      + l+  +h              ++ +  g ++++++++++++++l+  d  + 
  gi|313117372|ref|YP_004044355.1|  90 KYDIAITHTP---LPFKIPH----LNLITKYHdcvtetrpyirdglSTFGKIGDSFLHPIRKRIDQTSLHKSDKGIF 159
                                       *********9...4444444....34555555333322233332214445556999999999999999999999999 PP

                   Glyco_trans_4_4 136 vseaeaeelralgvpadrvvvvpng 160
                                       vse    + + ++ ++  ++v+ ng
  gi|313117372|ref|YP_004044355.1| 160 VSELNKNAWEKHYEAQLETDVIYNG 184
                                       9998888877766666666777776 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.2e-06    0.0031       2      56 ..       3      53 ..       2     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-06
                    Glyco_transf_5  2 ilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleev 56
                                      il+++ E++p +  GG++ +++ L +++++lgh+v+v+  ++++  +e    e+ 
  gi|313117372|ref|YP_004044355.1|  3 ILVISREFPP-YVLGGISYHLKNLYNEIQNLGHNVTVLAGKCPQSWNEL---EKE 53
                                      9*********.99**************************9995555443...222 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   3.2e-05     0.082      10      85 ..      19     101 ..      13     118 .. 0.76
   2 ?    1.9   0.0     0.083   2.1e+02       2      36 ..     200     234 ..     199     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                   Glyco_trans_4_2  10 svhtlrlakeLakrgyeVhvitpkkga....kdeleaegihvhrlkvd.rkg..pleylkaf.klkklikkikPDvv 78 
                                       s+h+++l +e+++ g++V+v+  k ++     +++++++i+v++++ + rkg   l  +++  kl++l +  k+D+ 
  gi|313117372|ref|YP_004044355.1|  19 SYHLKNLYNEIQNLGHNVTVLAGKCPQswneLEKEVDPNINVIPVEFGyRKGyyLLYPVSLWsKLVRL-DTSKYDIA 94 
                                       89******************966544433245677899*******98854445344445543377775.78899999 PP

                   Glyco_trans_4_2  79 hahyakp 85 
                                       ++h++ p
  gi|313117372|ref|YP_004044355.1|  95 ITHTPLP 101
                                       9999866 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.083
                   Glyco_trans_4_2   2 illlanlssvhtlrlakeLakrgyeVhvitpkkga 36 
                                       +l+++   +   +++ k++ +  y+Vh++  ++ +
  gi|313117372|ref|YP_004044355.1| 200 VLFVGSSERKGISKVLKYAESGEYTVHIVGDTEVE 234
                                       678888888888999*************9987773 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-05     0.064       9      72 ..     266     326 ..     256     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaea 72 
                                       e +   ++E + cG++++t+   g +e +t++ ++i+     e +e+i+     ++e+r++ae+
  gi|313117372|ref|YP_004044355.1| 266 EAFGNIVLESLSCGTPVITTNKCGAGEVLTEE-TGIITNKISEGLERIEST--KEQECRKVAEN 326
                                       55666689************99*******999.666667777888888874..77788877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2236.34
//
Query:       gi|313117373|ref|YP_004044356.1|  [L=383]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-26   93.5   0.0    1.6e-26   92.8   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-23   84.1   0.0    2.8e-23   82.8   0.0    1.7  2  Glyco_trans_1_4  Glycosyl transferases group 1
      2e-23   83.2   0.7    3.4e-23   82.5   0.7    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    7.5e-18   65.5   1.8    7.5e-18   65.5   1.8    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   3.7e-30   1.6e-26      14     161 ..     206     351 ..     197     362 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.7e-30
                                       T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSSHHHH CS
                   Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs.redleel 89 
                                         + +l+ grl   K+v++li+af+++ +   +++ l i+G+g e+++l+++a+     d+v+flg+++ +ed+   
  gi|313117373|ref|YP_004044356.1| 206 SGYDVLFAGRLIADKNVSVLIDAFDSVAE--SHDATLGIIGDGLEFDRLQRQAQRIDHADRVTFLGFLDaYEDVLGH 280
                                       56779*********************986..6********************************************* PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeel 161
                                       +++ad+f+ ps++EgfGi+  EAmaa + vi   ++  a   + g+ G+l +p+ +e+ ae ++++le +  
  gi|313117373|ref|YP_004044356.1| 281 MRAADVFASPSTREGFGITYAEAMAADCTVIGATHPESAASEVIGDAGYLAEPT-VESVAESLARALEGDTP 351
                                       *******************************87755555555555567******.************98744 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   5.7e+03      85     100 ..     112     127 ..      48     144 .. 0.68
   2 !   82.8   0.0   6.2e-27   2.8e-23       3     132 ..     209     346 ..     207     348 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                       HHHHHHHHTT-EEEE- CS
                   Glyco_trans_1_4  85 lkllEamaaglpvVat 100
                                        + l a+  ++p+V+t
  gi|313117373|ref|YP_004044356.1| 112 SAKLAALGTETPIVST 127
                                       3445666677777777 PP

  == domain 2  score: 82.8 bits;  conditional E-value: 6.2e-27
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---...HHHHHHHT..T-T.TEEEE---...THHHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgprp.eeleelaa..gleerveftGfv...edlaellaa 72 
                                       ++lf Grl +  k+v +l++a+  ++++ d++l i+Gdg  + ++l+++a+  + ++rv+f+Gf+   ed+  +++a
  gi|313117373|ref|YP_004044356.1| 209 DVLFAGRLIAD-KNVSVLIDAFDSVAEShDATLGIIGDG-LEfDRLQRQAQriDHADRVTFLGFLdayEDVLGHMRA 283
                                       69******655.*************98856*******99.555799988875655699*******99999******* PP

                                       -SEEEE--..---SHHHHHHHHTT-EEEE-TGG..GTTT--TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  73 advfvaPs..egfglkllEamaaglpvVatdvg..giaevvgengllvppgdpealaeailrLl 132
                                       advf  Ps  egfg++  Eamaa + v+  + +  +++ev+g++g+l++p  +e+ ae ++r l
  gi|313117373|ref|YP_004044356.1| 284 ADVFASPStrEGFGITYAEAMAADCTVIGATHPesAASEVIGDAGYLAEP-TVESVAESLARAL 346
                                       *********99******************998633579999*******87.5888888888776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.7   7.7e-27   3.4e-23       2     169 ..      16     192 ..      15     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 7.7e-27
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvv..tpgddgpleeev.....elvvrvprvplpllkrllrslaflrrl....rrl 67 
                                       GG+e  ++e+  +La+rGh+Vt++   + +dgp e        + v  ++  ++  ++     + f+ rl     ++
  gi|313117373|ref|YP_004044356.1|  16 GGAEKRIHEIGTRLAARGHDVTIYgrHF-WDGPKETTHegvtlRAVAPGTDLYTDDRRSITEAIDFAARLayplSKQ 91 
                                       9***********************7522.333333332355664444444444444444444555554442222799 PP

                    Glyco_transf_4  68 lkrekpDvv.HahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSea 143
                                       l+r++ D+v  + +p++ ++++  +++ +  p+V t H  + + ++  +l+ l ++ + +e  ++r  ++ iavS  
  gi|313117373|ref|YP_004044356.1|  92 LRRNEHDLVvASVFPYFPVLSAKLAALGTETPIVSTWHEVW-RDYWDDYLGTLAPFGKVVEHLTARTPQHPIAVSGI 167
                                       *********5344444444444333337*************.89********************************* PP

                    Glyco_transf_4 144 tadelrerygvppekitVipnGvDle 169
                                       tad+l e  g ++++i+V+pnG+D+e
  gi|313117373|ref|YP_004044356.1| 168 TADRLTE-IGPSRDDIEVVPNGIDVE 192
                                       *******.**9*************98 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   1.8   1.7e-21   7.5e-18       1     160 []      16     188 ..      16     188 .. 0.81
   2 ?   -1.8   0.1      0.82   3.7e+03      29      29 ..     292     292 ..     221     354 .. 0.66

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.7e-21
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpsplad........laalralrrll.. 67 
                                       gG++++++e+  +LaarGh+Vt++ ++   g+ e +++gv+++ +  +      +d         +++++l+  l  
  gi|313117373|ref|YP_004044356.1|  16 GGAEKRIHEIGTRLAARGHDVTIYGRHFWDGPKETTHEGVTLRAVAPGTDL--YTDdrrsiteaIDFAARLAYPLsk 90 
                                       8*************************99999999*******9876433332..222111122224444555444465 PP

                   Glyco_trans_4_4  68 rqrrerpdvvhahs.pt.aglaarlarrrrgiplvvtlhgll...lrrgsgavrrlyralerrllrradavlvvsea 139
                                       + rr   d+v+a   p+   l a+la++++ +p+v t+h+ +   ++++ g ++++ + +e++++r   + ++vs  
  gi|313117373|ref|YP_004044356.1|  91 QLRRNEHDLVVASVfPYfPVLSAKLAALGTETPIVSTWHEVWrdyWDDYLGTLAPFGKVVEHLTARTPQHPIAVSGI 167
                                       44**********99555566888999999**********87634455669999************************ PP

                   Glyco_trans_4_4 140 eaeelralgvpadrvvvvpng 160
                                        a++l++ g  +d+++vvpng
  gi|313117373|ref|YP_004044356.1| 168 TADRLTEIGPSRDDIEVVPNG 188
                                       ********************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.82
                   Glyco_trans_4_4  29 a 29 
                                       +
  gi|313117373|ref|YP_004044356.1| 292 T 292
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2419.46
//
Query:       gi|313117374|ref|YP_004044357.1|  [L=243]
Description: dTDP-glucose pyrophosphorylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-44  149.9   0.0      1e-43  149.7   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    3.1e-14   53.6   0.0    3.8e-14   53.4   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0003   20.6   0.0     0.0015   18.4   0.0    2.0  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
       0.21   11.0   0.0       0.32   10.4   0.0    1.2  1  RecA             recA bacterial DNA recombination protein


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.7   0.0   2.3e-47     1e-43       1     245 [.       2     234 ..       2     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 2.3e-47
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kav+LaGG+GtRL+PLt + +k +v v +k +++ +++++la+ g +e +vv+  + ++++ e+++++   g+ +++
  gi|313117374|ref|YP_004044357.1|   2 KAVVLAGGEGTRLRPLTEDKPKGMVEVNEK-PILTHCFEQLAELGADE-LVVVVGYLKERIIEYYGDEF-QGIPITY 75 
                                       79****************************.*****************.78888899999999999987.589**** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       a+++e+kg+A+A++ ++e ++d++    +l+Lg++ +++ +++++v++ +e++a+   ++  vp+eea++yGv  ++
  gi|313117374|ref|YP_004044357.1|  76 AHQREQKGLAHALLTVEEHIDDDF----MLMLGDN-IFNANLTDVVNRQQEQRADAAFLVEEVPWEEASRYGVCDTN 147
                                       *********************999....6777666.5666**************999999***************** PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE. CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs. 230
                                       + g++++ vEKP+ ++ s+l+ +G Y+f++e+++   + +++++r e ei++++  ++++g+   a +  +  +W+ 
  gi|313117374|ref|YP_004044357.1| 148 KYGEITDVVEKPEDPP-SNLVMTGFYTFTPEIFHAC-HLVQPSNRNEYEISEAIDLLIHSGRTIDA-IGIK--GWRi 219
                                       ****************.*****************99.89*********************977655.5555..5866 PP

                                       EXSSHHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleanekl 245
                                       D+G +++  ea+++l
  gi|313117374|ref|YP_004044357.1| 220 DIGYPEDRDEAEKRL 234
                                       ***999877777665 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   8.4e-18   3.8e-14       1     123 [.       3     131 ..       3     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 8.4e-18
                                       EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC....TS-EEE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggd..eevlaalarl....gvrvvede 66 
                                       av+LAGG+++R+    +  +K ++++++kp+l +++++l+++g+de+vvv+g+  e + +++ +     ++++++++
  gi|313117374|ref|YP_004044357.1|   3 AVVLAGGEGTRLRpltEdkPKGMVEVNEKPILTHCFEQLAELGADELVVVVGYlkERIIEYYGDEfqgiPITYAHQR 79 
                                       79**********6444145**********************************876666655443442145555554 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEES CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpty 123
                                        ++kg +++l++  +++  +d ++++++D ++   + +  ++++ ++++ad+++++ 
  gi|313117374|ref|YP_004044357.1|  80 -EQKGLAHALLTVEEHI--DDDFMLMLGDNIF--NANLTDVVNRQQEQRADAAFLVE 131
                                       .489************9..799999*****99..45566777777777777776665 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.2e-07    0.0015       2      88 ..       2      91 ..       1     236 [. 0.60

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.2e-07
                                      EEEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG..CCEEEEE--S CS
                              IspD  2 vvvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld..ksiqlvaGGd 75
                                       +v+ A G+G+R+    +++pK  +e++ +++l+h  + l++ +a + +vvv   ++  ++ +  +d  + i +    +
  gi|313117374|ref|YP_004044357.1|  2 KAVVLAGGEGTRLrplTEDKPKGMVEVNEKPILTHCFEQLAELGADELVVVVGYLKE--RIIEYYGDefQGIPITYAHQ 78
                                      699*********733369**********************99887777776655444..44444444444455555555 PP

                                      SHHHHHHHHHHTT CS
                              IspD 76 eRaesVlnglkal 88
                                        ++   ++l  +
  gi|313117374|ref|YP_004044357.1| 79 REQKGLAHALLTV 91
                                      5555555555555 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.1e-05      0.32      40     107 ..      45     109 ..      37     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.1e-05
                                       HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--GGG CS
                              RecA  40 aldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvdide 107
                                       + d  + + G+ k riie yG e  G     +    + ++kg   a++ +e  +d ++   lG +i +
  gi|313117374|ref|YP_004044357.1|  45 GADELVVVVGYLKERIIEYYGDEFQGI---PITYAHQREQKGLAHALLTVEEHIDDDFMLMLGDNIFN 109
                                       5677778899**************995...4555567788899999*************999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1732.77
//
Query:       gi|313117375|ref|YP_004044358.1|  [L=270]
Description: hypothetical protein Hbor_31620 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0092   15.9   1.7      0.019   14.9   1.7    1.5  1  PGF-CTERM  PGF-CTERM motif


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.7   1.1e-06     0.019       1      17 [.     245     261 ..     245     267 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-06
                         PGF-CTERM   1 tPGFGavlAlaGLLaaa 17 
                                       tPGFG+++++ + L ++
  gi|313117375|ref|YP_004044358.1| 245 TPGFGIAVTVLATLVVV 261
                                       9*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1679.79
//
Query:       gi|313117376|ref|YP_004044359.1|  [L=1822]
Description: subtilisin-like serine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-43  146.7   7.1    8.3e-43  146.7   7.1    3.2  2  Peptidase_S8     Subtilase family
    4.9e-10   39.3   1.2    1.8e-09   37.5   0.3    2.6  2  CarbopepD_reg_2  CarboxypepD_reg-like domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   7.1   9.2e-47   8.3e-43       1     298 []     388     667 ..     388     667 .. 0.86
   2 ?   -0.9   1.1     0.089     8e+02      51     130 ..    1284    1355 ..    1137    1397 .. 0.78

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 9.2e-47
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGE.ETT-SS-TT-SC-SSS....HHHHHHHHHH-B. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfng.adsettstnwarddngnsieHGthvAGiaaana 76 
                                       g g +vavlDtG+d +hpdl+  +++++   d+ +  +a+f++ +d  t+st +a+++      HGthv G++a++ 
  gi|313117376|ref|YP_004044359.1| 388 GAGAKVAVLDTGIDVGHPDLE-LYTEDPG-NDTYPGGWAEFDTnGDRVTGSTPHATSG------HGTHVSGTVAGG- 455
                                       6799*****************.4444444.3455555555554156667777777777......************. PP

                                       .SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  77 peegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnk 153
                                         +g++ gvap+a++    vl++  gs    +++i+++++a+e+++dvi+mslg    ++ +++ +    i++a+ +
  gi|313117376|ref|YP_004044359.1| 456 TASGKAIGVAPDADMMHGLVLPDGTGSF---AQIIGGMQWAVEEDADVISMSLG---ADGFYSTLVT--PIRNAE-D 523
                                       9999************999998888877...9**********************...8899999988..9*****.9 PP

                                       CT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxx RF
                      Peptidase_S8 154 kgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssd...............gklkp 215
                                        g++vv++aGN g         ++  +p++   ++tvga  ++ +iapfSs G ++                + + p
  gi|313117376|ref|YP_004044359.1| 524 AGTVVVAAAGNHG--------PETAPSPGSIYDSLTVGASGPNRDIAPFSS-GDVVRterdwgdaapsdwpdEYVMP 591
                                       9************........455678999999****************95.555544666777777777777799* PP

                                       -EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT.--HHHHHHHHHCCS-EE......S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 216 divapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk.ltpetvraallntAqdlgkadnie 291
                                       di+apG++ +st +  +        y  +sGTSmA+P+++g++Al+ sa     +pe++r+al ++A+   +a++  
  gi|313117376|ref|YP_004044359.1| 592 DIAAPGVDTYSTLPGGK--------YGEKSGTSMATPHVSGVVALMVSASGGdASPEEIRTALRKSATKPDDAPAKK 660
                                       ********888888888........***********************88888**************9999999999 PP

                                       SSSSSTT CS
                                       xxxxxxx RF
                      Peptidase_S8 292 sfaqGaG 298
                                       + ++G+G
  gi|313117376|ref|YP_004044359.1| 661 DIRYGNG 667
                                       9999998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.089
                                        TT-SC-SSS....HHHHHHHHHH-B..SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   51 tnwarddngnsieHGthvAGiaaanapeegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvi 125 
                                        ++ ++++    + HG  + G     ++     + +  ga++l++ v  ++  +    + +++a++    +++dv+
  gi|313117376|ref|YP_004044359.1| 1284 RHVSVSG----TSHGVLIGGAGSTADDAVVHDVNISDGADLLAIGVTVGEADN----AHVYNATISGQDSGADVY 1350
                                        3333333....339988888777778888888889999999977777555544....689999999999999988 PP

                                        EE-EE CS
                                        xxxxx RF
                      Peptidase_S8  126 nmslg 130 
                                          s +
  gi|313117376|ref|YP_004044359.1| 1351 TSSGT 1355
                                        77755 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.3     2e-13   1.8e-09       1      78 [.     684     758 ..     684     764 .. 0.88
   2 ?   -3.7   0.0       1.4   1.2e+04      19      31 ..    1530    1542 ..    1528    1543 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2e-13
                   CarbopepD_reg_2   1 isGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillk 77 
                                       isG +++++ +epl ga+V + ++++ t+Td+nG + +++l +g+y  +vs  Gy + + +vtv++++ ++ +++lk
  gi|313117376|ref|YP_004044359.1| 684 ISGSISNTG-GEPLSGASVRL-DSGAATATDANGDYLIRTL-SGTYNTTVSEFGYASSTATVTVTGGSMTTHDVSLK 757
                                       89**99986.69********9.67999***********866.7*********************9987766666666 PP

                   CarbopepD_reg_2  78 e 78 
                                       +
  gi|313117376|ref|YP_004044359.1| 758 P 758
                                       5 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.4
                   CarbopepD_reg_2   19 VyvkgtkkgtvTd 31  
                                        V+v gt+++tv+d
  gi|313117376|ref|YP_004044359.1| 1530 VSVPGTTRQTVSD 1542
                                        899********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1822 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.06u 0.32s 00:00:01.38 Elapsed: 00:00:00.52
# Mc/sec: 10636.92
//
Query:       gi|313117377|ref|YP_004044360.1|  [L=305]
Description: nucleoside-diphosphate-sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-44  150.9   0.1    4.8e-44  150.6   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.4e-43  147.9   1.1      3e-42  145.2   1.1    2.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.4e-13   50.6   0.1    1.8e-13   50.2   0.1    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    6.3e-11   41.8   0.1    3.4e-10   39.4   0.1    2.0  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.1e-10   38.5   0.2    6.3e-07   28.8   0.0    2.8  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
      6e-08   32.2   0.0    8.4e-06   25.1   0.1    2.6  2  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
       0.14   11.7   0.1        5.7    6.4   0.0    2.4  2  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.1   1.9e-47   4.8e-44       1     241 []       6     234 ..       6     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 1.9e-47
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       +lVtG++GfiGs+l++al+    +vi++d    + +++++  +e+v++ ++d++    l    ++d+v+hlAa +++
  gi|313117377|ref|YP_004044360.1|   6 VLVTGGAGFIGSNLANALAPD-NDVIAIDDCYLGTPENLDSGVEFVDASVLDED----LPT--DVDVVFHLAALSSY 75 
                                       79****************976.59******988888888888899999999988....555..79************ PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                       +   +dp+  ++ n++g +n +e ark g++ ++++s+s++YG  +e p  e++    ++ ++ Y a+Kla e+++e
  gi|313117377|ref|YP_004044360.1|  76 QMHEQDPTTGARVNVEGFVNTVEQARKDGCETVVYASTSSIYGSRTE-PSPESM---AIEARTGYEASKLAREQYAE 148
                                       **********************************************9.877777...79****************** PP

                                       HHHHHHT-EEEEEEESEEESTT....S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHH CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGpr....ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvle 227
                                       ++ + y+l    +r f++y  +    +++ge ++ ++++ +ki++g+ +  l+gdg++ Rdf +v+D++++++l++e
  gi|313117377|ref|YP_004044360.1| 149 YFYNHYDLTLAGMRFFSVYQGFggaeEHKGEYANTVAQFTEKIANGE-QPELFGDGSQTRDFTHVDDIVRGLVLAAE 224
                                       *******************444466699999****************.***************************** PP

                                       HHTT-STTEEEEES CS
                         Epimerase 228 hvdagdkgeiyniG 241
                                       h    + +++yn+G
  gi|313117377|ref|YP_004044360.1| 225 H----ELNGVYNLG 234
                                       *....567899998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.2   1.1   1.2e-45     3e-42       1     331 [.       7     297 ..       7     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 1.2e-45
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+la+ L     +v+ i+ +    ++g+ e+l +         ++++ + + D++        +++d
  gi|313117377|ref|YP_004044360.1|   7 LVTGGAGFIGSNLANALAPD-NDVIAID-D---CYLGTPENLDS--------GVEFVDASVLDEDL------PTDVD 64 
                                       9****************987.6787764.3...45566666643........46799999999773......4567* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        v++LAA s  +   ++P + a+vnv G ++ +e +r+ g+e    ++ aSts +YG+ +  p  E+  +++r  Y 
  gi|313117377|ref|YP_004044360.1|  65 VVFHLAALSSYQMHEQDPTTGARVNVEGFVNTVEQARKDGCE---TVVYASTSSIYGSRT-EPSPESMAIEARTGYE 137
                                       ***************************************997...6889*********97.6899************ PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT....SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrget....fvtrkitravarialgkqevlylGnldakRdwghvk 227
                                       a+Kl+ ++ ++ +++ y+l     ++f  +    g++       +++ ++  +ia+g+q+ l +G+++++Rd++hv+
  gi|313117377|ref|YP_004044360.1| 138 ASKLAREQYAEYFYNHYDLTLAGMRFFSVYQGFGGAEehkgEYANTVAQFTEKIANGEQPEL-FGDGSQTRDFTHVD 213
                                       ****************************98887776523334678999999*********99.8************* PP

                                       HHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--S CS
                     GDP_Man_Dehyd 228 Dyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevd 304
                                       D+v++++l+ +++ +  y+++tge++s +e+v + ++ lg ++e +               ++ ++d      + v+
  gi|313117377|ref|YP_004044360.1| 214 DIVRGLVLAAEHELNGVYNLGTGESYSFNEMVAMINEVLGTDVEPK--------------YIENPLD------EYVH 270
                                       **************************************99876543..............2223333......3367 PP

                                       B--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 305 lllgdaskakeeLgWkpkvsfeelvre 331
                                        +++d++k+ke  gW+p++sfee+v++
  gi|313117377|ref|YP_004044360.1| 271 DTMADPTKMKEATGWEPEISFEEGVQR 297
                                       789*********************986 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.1   7.2e-17   1.8e-13       2     235 ..       5     256 ..       4     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 7.2e-17
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..........eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                       ++lvtG+ G +Gs+La++la ++ +v+a++             +++ da+ ++e l   + dvv ++AA       E
  gi|313117377|ref|YP_004044360.1|   5 QVLVTGGAGFIGSNLANALAPDN-DVIAIDDCylgtpenldsGVEFVDASVLDEDLPT-DVDVVFHLAALSSYQMHE 79 
                                       69******************998.*****87788888877766777777777777765.889*************** PP

                                       HSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH....H- CS
                     RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla....ag 140
                                       +++   ++vn+e+  +  e+a++ g  ++++ St  ++ G++++p  e+ + + ++ Y ++Kla Eq  +     + 
  gi|313117377|ref|YP_004044360.1|  80 QDPTTGARVNVEGFVNTVEQARKDGCeTVVYASTSSIY-GSRTEPSPESMAIEARTGYEASKLAREQYAEYfynhYD 155
                                       *************************84699*******9.6669999*********************9887542233 PP

                                       SSEEEEEE-SEESS.........SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG CS
                     RmlD_sub_bind 141 kkalivRtswvyge.........kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekel 206
                                        + + +R+  vy           +  n v+++ ++ ++ e+ +++ D  q++  T+++d+ + l+ ++e++++    
  gi|313117377|ref|YP_004044360.1| 156 LTLAGMRFFSVYQGfggaeehkgEYANTVAQFTEKIANGEQPELFGDgsQTRDFTHVDDIVRGLVLAAEHELN---- 228
                                       455568******766777886544467888888888877777777665599**************99999996.... PP

                                       -EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 207 agvyHlanegetswlefArailkeagads 235
                                        gvy l+  ++ s  e+   i + +g+d 
  gi|313117377|ref|YP_004044360.1| 229 -GVYNLGTGESYSFNEMVAMINEVLGTDV 256
                                       .***************9999999988866 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.1   1.3e-13   3.4e-10       1     155 [.       7     145 ..       7     229 .. 0.67

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.3e-13
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G++l ++L   ++   v ++D     +   e   ++v+ ++ + v+d+d       +vdvv+hla+l+
  gi|313117377|ref|YP_004044360.1|   7 LVTGGAGFIGSNLANALAPDND---VIAIDDCYLGTP--ENLDSGVE-FVDASVLDEDL----PTDVDVVFHLAALS 73 
                                       69***************98885...555554444444..46677888.78888888753....579*********99 PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                         +  ++   +  +vnv+G  n +e ++k g +++vY S+ ++ g   + e+     E++ +e      y  sK   
  gi|313117377|ref|YP_004044360.1|  74 SYQMhEQDPTTGARVNVEGFVNTVEQARKDGCETVVYASTSSIYGS--RTEPSP---ESMAIEA--RTGYEASKLAR 143
                                       8877356677789***************************999988..433332...4444433..34455555555 PP

                         3Beta_HSD 154 Ek 155
                                       E+
  gi|313117377|ref|YP_004044360.1| 144 EQ 145
                                       55 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0019       4.9       1      19 [.       6      24 ..       6      33 .. 0.87
   2 !   28.8   0.0   2.5e-10   6.3e-07      73     129 ..      59     114 ..      47     268 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0019
                                      EEEETTTSHHHHHHHHHHH CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqil 19
                                      vlvtG++G iGs+l + ++
  gi|313117377|ref|YP_004044360.1|  6 VLVTGGAGFIGSNLANALA 24
                                      8*************98765 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 2.5e-10
                                       TT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG CS
                   Polysacc_synt_2  73 leelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD 129
                                       l  ++vdvvfh AAl    + e+ p+ + + Nv g  n++e a + g ++vv+ St 
  gi|313117377|ref|YP_004044360.1|  59 LP-TDVDVVFHLAALSSYQMHEQDPTTGARVNVEGFVNTVEQARKDGCETVVYASTS 114
                                       54.689*************************************************96 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.0    0.0081        21       1      19 [.       8      26 ..       8      34 .. 0.82
   2 !   25.1   0.1   3.3e-09   8.4e-06      84     197 ..      59     157 ..      55     219 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0081
                                      EE-TTSHHHHHHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrt 19
                                      +TG+ GF+G+ L + L  +
  gi|313117377|ref|YP_004044360.1|  8 VTGGAGFIGSNLANALAPD 26
                                      7**********99888655 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 3.3e-09
                                       HHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.... CS
                     NAD_binding_4  84 laeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegek 157
                                       l   vdv++h aA  +++    +  +  rvNveG ++ +e a+k     ++++ ST+ ++g r++   e +  e ++
  gi|313117377|ref|YP_004044360.1|  59 LPTDVDVVFHLAALSSYQMheqDPTTGARVNVEGFVNTVEQARKDGCE-TVVYASTSSIYGSRTEPSPESMAIEART 134
                                       5678*********987665111555689***************99888.************9997765655554444 PP

                                       ..HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH--- CS
                     NAD_binding_4 158 eekldederaklkglpntYeqsKalaEklvrearrrsglp 197
                                                        +Ye sK + E+  +   ++ +l 
  gi|313117377|ref|YP_004044360.1| 135 -----------------GYEASKLAREQYAEYFYNHYDLT 157
                                       .................44444444444444444444444 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.023        58       1      23 [.       6      27 ..       6     112 .. 0.79
   2 ?    6.4   0.0    0.0022       5.7     150     229 ..     182     256 ..     170     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.023
                                      EEESSTTSHHHHHHHHHHHHHT- CS
                              NmrA  1 IlviGaTGrqGksvvrallkagh 23
                                      +lv+G++G +G+ +++al+ + +
  gi|313117377|ref|YP_004044360.1|  6 VLVTGGAGFIGSNLANALAPD-N 27
                                      79************9998754.3 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0022
                                       SSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHT CS
                              NmrA 150 sllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkig 226
                                        ++aq ++++ a++ ++ +l g+g+    +  +++Di +  + ++  +++l+g++   +g+ +s+ne+v+++++++g
  gi|313117377|ref|YP_004044360.1| 182 NTVAQ-FTEKIANG-EQPELFGDGSQTRDFT-HVDDIVRGLVLAA--EHELNGVYNLGTGESYSFNEMVAMINEVLG 253
                                       45555.33333333.3577899999777777.8888876665555..5688*************************9 PP

                                       S-E CS
                              NmrA 227 ktv 229
                                         v
  gi|313117377|ref|YP_004044360.1| 254 TDV 256
                                       987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1932.80
//
Query:       gi|313117378|ref|YP_004044361.1|  [L=182]
Description: response regulator with CheY-like receiver domain and winged-helix DNA-binding domain [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-17   62.4   0.3    7.2e-17   61.6   0.3    1.4  1  Response_reg   Response regulator receiver domain
    6.5e-17   61.6   6.3    1.3e-16   60.7   6.3    1.5  1  HalX           HalX domain
  ------ inclusion threshold ------
      0.022   14.8   1.6       0.04   14.0   1.6    1.4  1  TolA_bind_tri  TolA binding protein trimerisation
       0.04   13.2   0.7      0.055   12.8   0.7    1.2  1  AIG1           AIG1 family
      0.067   11.6   0.2      0.086   11.2   0.2    1.2  1  Orbi_VP5       Orbivirus outer capsid protein VP5
      0.088   12.7   0.1        5.9    6.8   0.0    2.7  3  DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
       0.11   11.7   0.5       0.46    9.6   0.0    1.8  2  IF-2B          Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.3   2.8e-20   7.2e-17       2     111 ..       2     105 ..       1     106 [. 0.94

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 2.8e-20
                                       EEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEE CS
                      Response_reg   2 livdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviilt 78 
                                       l+vdD++++++l +++l   +y +v+ a +g++ale l+e  v +++lD +mp+ +G e+l+eir++  ++ v ++t
  gi|313117378|ref|YP_004044361.1|   2 LVVDDERAIADLYATWLA-TDY-TVEIAYNGSSALEVLDET-VSVVILDRRMPNTSGDEVLDEIRARGFDCHVAMIT 75 
                                       8*****************.889.9**************986.*********************************** PP

                                       SSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  79 ahseeedavealkagaddflsKpfdpeeLlkal 111
                                       a + +    + l++g d +l Kp+++e++++ +
  gi|313117378|ref|YP_004044361.1|  76 AVDPD---YDILEMGFDTYLKKPVKEEDIKAVV 105
                                       88864...46799****************9877 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   6.3     5e-20   1.3e-16       1      68 []     110     176 ..     110     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 5e-20
                              HalX   1 trseYdeelqelfaLasKravLeaekseaeLadseeYqeLearleelraqldetldelddaddfealf 68 
                                       +rs+Y e+l+ lf+  sKr +L+a+k+ aeL    +Yq+L ++++elraq d+ l +ld+ +dfea+f
  gi|313117378|ref|YP_004044361.1| 110 RRSRYAESLTALFRKLSKREALKAQKPVAELKRQSQYQQLIDEIAELRAQSDRHLHQLDN-EDFEAMF 176
                                       69**********************************************************.*****98 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.6   1.5e-05      0.04      18      49 ..     137     168 ..     114     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                     TolA_bind_tri  18 qlllelqqqlealqqelreLRGqiEelqyqle 49 
                                        + l+ q+q ++l  e++eLR q +++ +ql+
  gi|313117378|ref|YP_004044361.1| 137 VAELKRQSQYQQLIDEIAELRAQSDRHLHQLD 168
                                       5677789***********************97 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   2.1e-05     0.055     141     194 ..     113     166 ..      92     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                                       HH-HHHHHHHHHTTTSEEEEETTHHHHHHHHHHHHHHHHHHHHHHHHTTTT--B CS
                              AIG1 141 sspeaLkevlkecgnRvvlfnnktaskeekeeQvkellelveaivkenggkpyt 194
                                       +  e+L+ +++++++R  l   k  ++ ++++Q ++l++ +++++ +++ + ++
  gi|313117378|ref|YP_004044361.1| 113 RYAESLTALFRKLSKREALKAQKPVAELKRQSQYQQLIDEIAELRAQSDRHLHQ 166
                                       44689***************************************9998766654 PP

>> Orbi_VP5  Orbivirus outer capsid protein VP5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   3.4e-05     0.086     133     220 ..      72     159 ..      46     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                          Orbi_VP5 133 keveaveeqytmlckavdsy.ekilkeedskmailaralqreaaersedeikmvkeyrqkidalksaieierdgmqe 208
                                         + av+ +y +l    d+y +k +keed k a++   l+r     s   +      r+ + a k   e++r+   +
  gi|313117378|ref|YP_004044361.1|  72 AMITAVDPDYDILEMGFDTYlKKPVKEEDIK-AVVENLLRRSRYAESLTALFRKLSKREALKAQKPVAELKRQSQYQ 147
                                       56789***************44579999998.67788888887777777766666779999**************** PP

                          Orbi_VP5 209 eaiqeiagmtad 220
                                       + i+eia + a+
  gi|313117378|ref|YP_004044361.1| 148 QLIDEIAELRAQ 159
                                       *******98875 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0023       5.9       2      30 ..      43      71 ..      43      73 .. 0.93
   2 ?    2.7   0.0     0.044   1.1e+02       5      21 ..      92     108 ..      91     112 .. 0.88
   3 ?   -2.6   0.1         2   5.1e+03      11      24 ..     143     156 ..     141     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0023
                     DAHP_snth_FXD  2 IivmkkgateeqieevierieelGlkvhv 30
                                      ++++ + + +   +ev+++i++ G+++hv
  gi|313117378|ref|YP_004044361.1| 43 VVILDRRMPNTSGDEVLDEIRARGFDCHV 71
                                      7999999999******************8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.044
                     DAHP_snth_FXD   5 mkkgateeqieevieri 21 
                                       +kk ++ee+i++v+e++
  gi|313117378|ref|YP_004044361.1|  92 LKKPVKEEDIKAVVENL 108
                                       68999*********976 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2
                     DAHP_snth_FXD  11 eeqieevierieel 24 
                                       ++q +++i++i el
  gi|313117378|ref|YP_004044361.1| 143 QSQYQQLIDEIAEL 156
                                       67889999998875 PP

>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00018      0.46      94     170 ..       7      78 ..       3      81 .. 0.87
   2 ?    0.1   0.1      0.14   3.6e+02      35      91 ..     101     154 ..      88     173 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXT.TTTHHHTHHHHHHHTTXEEEEEEGGGH CS
                             IF-2B  94 dekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsr.PrlqGrltakeLvqagipvtlitdsav 169
                                       +++i+d +a+ +  + t+    n +++levl + ++      V+ ++ r P+++G +++ e++  g ++ +++++av
  gi|313117378|ref|YP_004044361.1|   7 ERAIADLYATWLATDYTVEIAYNGSSALEVLDETVS------VVILDRRmPNTSGDEVLDEIRARGFDCHVAMITAV 77 
                                       688999999999999999999999999999999887......66666554**************************9 PP

                                       H CS
                             IF-2B 170 a 170
                                       +
  gi|313117378|ref|YP_004044361.1|  78 D 78 
                                       6 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                                       HHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHHHHHHHHHHH CS
                             IF-2B  35 lrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliekikelikeie 91 
                                       ++  ++ L      a sl    r l k  ++lk +++v e k +  ++ ++li+ei 
  gi|313117378|ref|YP_004044361.1| 101 IKAVVENLLRRSRYAESLTALFRKLSK-REALKAQKPVAELKRQ--SQYQQLIDEIA 154
                                       555554444444456677777777777.4666777777666654..23333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1262  (0.0703888); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1276.90
//
Query:       gi|313117379|ref|YP_004044362.1|  [L=315]
Description: hypothetical protein Hbor_31660 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2099.45
//
Query:       gi|313117380|ref|YP_004044363.1|  [L=404]
Description: hypothetical protein Hbor_31670 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-05   23.3  10.5    6.1e-05   23.3  10.5    2.8  2  ATG16            Autophagy protein 16 (ATG16)
     0.0025   15.4   8.6     0.0036   14.9   8.6    1.2  1  DUF3584          Protein of unknown function (DUF3584)
     0.0056   16.7   4.4     0.0056   16.7   4.4    2.2  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
  ------ inclusion threshold ------
      0.012   15.7  11.0       0.28   11.2   0.8    2.5  2  DUF1664          Protein of unknown function (DUF1664)
      0.024   14.9   4.2      0.024   14.9   4.2    2.5  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.04   13.8  15.0       0.23   11.3  12.3    2.1  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
      0.041   14.3   0.2      0.041   14.3   0.2    3.0  1  KELK             KELK-motif containing domain of MRCK Ser/Thr
      0.044   12.9   7.2       0.12   11.4   7.3    1.6  1  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.046   13.3   2.5      0.071   12.7   2.5    1.2  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.048   13.7   9.8       0.13   12.3   9.8    1.7  1  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
       0.06   13.2   7.9       0.96    9.2   1.7    2.3  2  DUF724           Protein of unknown function (DUF724)
      0.073   11.9  16.5       0.64    8.8   7.0    2.0  2  Spc7             Spc7 kinetochore protein
      0.079   13.1  10.6      0.033   14.3   1.3    2.7  2  Nup54            Nucleoporin complex subunit 54
        0.1   12.6  15.2        4.7    7.2   0.8    4.0  3  Prefoldin_2      Prefoldin subunit
       0.11   12.0  13.4      0.017   14.7   7.1    2.0  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.18   11.2  13.4      0.025   14.0   6.1    2.4  2  Tropomyosin      Tropomyosin
       0.23   11.6  13.2        3.1    7.9   0.7    3.2  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
       0.25   11.4  18.3       0.13   12.3   9.7    2.7  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.27   10.5  13.6       0.18   11.1   0.9    2.3  2  DUF2353          Uncharacterized coiled-coil protein (DUF2353
       0.28   11.6  13.4       0.16   12.4   3.6    3.0  3  Snapin_Pallidin  Snapin/Pallidin
       0.39    8.6   3.6       0.57    8.1   3.6    1.3  1  Prominin         Prominin
        0.4   10.7   7.7        0.5   10.4   4.1    2.7  2  Med28            Mediator complex subunit 28
       0.69    8.0  13.9      0.081   11.1   0.5    1.9  2  EzrA             Septation ring formation regulator, EzrA
       0.76   10.3  13.0       0.07   13.6   1.7    3.4  3  HSCB_C           HSCB C-terminal oligomerisation domain
       0.78   10.0  18.3        2.3    8.5   2.1    4.5  3  ABC_tran_CTD     ABC transporter C-terminal domain
       0.83    9.1   6.5        1.9    7.9   6.5    1.6  1  MIF4G_like_2     MIF4G like
       0.87    9.8   9.0       0.63   10.2   5.5    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
        0.9    9.9  13.4       0.22   11.8   6.5    2.9  2  DUF4164          Domain of unknown function (DUF4164)
        1.4    9.6   7.3       0.46   11.1   0.2    3.0  3  GTP-bdg_M        GTP-binding GTPase Middle Region
        1.8    9.1  15.3         47    4.5   0.3    3.7  3  NPV_P10          Nucleopolyhedrovirus P10 protein
        2.2    7.5   9.9        3.8    6.7   9.4    1.8  1  CorA             CorA-like Mg2+ transporter protein
        2.3    7.5  10.8         92    2.3  11.1    2.3  1  GAS              Growth-arrest specific micro-tubule binding
        2.3    8.7  11.8       0.51   10.8   3.1    2.6  2  CENP-H           Centromere protein H (CENP-H)
        2.3    8.7  20.7       0.34   11.4   3.0    3.3  2  APG6_N           Apg6 coiled-coil region
        2.5    9.0  16.2        2.9    8.9   6.6    3.0  2  PRKG1_interact   cGMP-dependent protein kinase interacting do
        2.9    7.1   5.8       0.68    9.1   1.7    1.8  2  TMPIT            TMPIT-like protein
        3.4    7.7   8.3       0.29   11.2   0.2    2.6  2  SPATA1_C         Spermatogenesis-associated C-terminus
        4.1    8.1  14.6        2.4    8.8   1.1    3.0  2  YabA             Initiation control protein YabA
        4.6    6.7  20.5        1.1    8.8  16.3    2.0  2  MscS_porin       Mechanosensitive ion channel porin domain
          5    7.3  16.7    1.1e+02    2.9  16.8    2.8  1  Tropomyosin_1    Tropomyosin like
        5.4    7.9  11.4       0.88   10.4   4.5    3.1  2  FliT             Flagellar protein FliT
        5.5    6.8  10.0        3.4    7.6   3.0    2.7  2  Sec34            Sec34-like family
        7.1    4.4   6.4         14    3.4   6.2    1.5  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        7.7    6.9  16.0       0.73   10.2   1.9    3.2  2  CCDC-167         Coiled-coil domain-containing protein 167
        8.7    6.2   7.5       0.69    9.8   0.6    2.4  2  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans


Domain annotation for each model (and alignments):
>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3  10.5   1.5e-07   6.1e-05      13     174 ..      33     196 ..      22     204 .. 0.76
   2 ?   -1.7   0.4       7.3   2.9e+03      37      66 ..     291     319 ..     276     371 .. 0.53

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.5e-07
                             ATG16  13 qekafaeliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlree 89 
                                       +e++f++li+ y  L + +++l++ +++   +  s + s + ++++ e+ ++ ++  ++ ++++ +l +++++++ e
  gi|313117380|ref|YP_004044363.1|  33 REELFEQLISSYWTLNEISQLLNETTENN--SLGSLELSGPANTVDGESDTTGET--ETVTDQLDTLRERITEIQVE 105
                                       5999******************9998887..333333344444444444444444..78889*************** PP

                             ATG16  90 laelyksrgelaqrllelneelqkleekl.....kedeerlaeleaeraaletklk.dreeelrekeklvqdlqDEl 160
                                       l+ +  +r+e ++ + el+  l +lee+l     +e + +l+++e++ +a + ++k +++ ++ + ++ +q l +E 
  gi|313117380|ref|YP_004044363.1| 106 LESVVDRRSEIESEIGELTGRLTELEEQLgdtgdSEIQDELESIESQLSAEQAEIKaQLQSRFGDVQTILQYLIEET 182
                                       ***************************87442223445555555555555555554366777888999999999*** PP

                             ATG16 161 saLqlqlnqaEekl 174
                                       ++L  q++ + ++ 
  gi|313117380|ref|YP_004044363.1| 183 DSLDAQVTEVQQQQ 196
                                       ******99998886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.3
                             ATG16  37 enaklekaaasakssksskksakekeasas 66 
                                       e+++l +a  +++  ++ +++++e e+s  
  gi|313117380|ref|YP_004044363.1| 291 EQEQLGSADRASE-GTADESKTSEGERSDG 319
                                       4555533322222.2222222222222222 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   8.6   9.1e-06    0.0036     600     721 ..      91     211 ..      54     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.1e-06
                           DUF3584 600 seeeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaia 676
                                       + ++Lrer+  ++ +l+s  ++++++e+e+ +l   l+e+++++ +      + +d+le ++++  +e+ +++++++
  gi|313117380|ref|YP_004044363.1|  91 QLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTG--DSEIQDELESIESQLSAEQAEIKAQLQ 165
                                       335999999999999999999999999999999999999999887654..456678889999999999999999999 PP

                           DUF3584 677 erkqqaeeqlqkldaqlkqleeqqkaaleelk..edlseerlekkak 721
                                       +r   +++ lq l ++ + l++q  ++++++   e++++er +k + 
  gi|313117380|ref|YP_004044363.1| 166 SRFGDVQTILQYLIEETDSLDAQVTEVQQQQGviEQVENER-DKLQR 211
                                       99999999999999999999999999887763224444444.44444 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.4   1.4e-05    0.0056       1      95 [.      47     154 ..      47     155 .. 0.79
   2 ?    6.1   4.0     0.028        11      23      91 ..     151     193 ..     141     219 .. 0.37

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-05
                      Baculo_PEP_C   1 ladvqqL....nggggnqfldLtnvLnairlqnvqi..laqlatlldaietqLnalsedlkslla...eldtrldtl 68 
                                       l+++ qL    + +++ + l+L+   n++   + ++  +  ++ +ld++ +++++++ +l+s++    e+++++ +l
  gi|313117380|ref|YP_004044363.1|  47 LNEISQLlnetTENNSLGSLELSGPANTVDGESDTTgeTETVTDQLDTLRERITEIQVELESVVDrrsEIESEIGEL 123
                                       57788888877899999**********996554444225678999999999*********99875222566699999 PP

                      Baculo_PEP_C  69 ltnLtdalnalq....dtlrneLtnlnsilt 95 
                                       + +Lt+   +l      +++ eL++++s+l+
  gi|313117380|ref|YP_004044363.1| 124 TGRLTELEEQLGdtgdSEIQDELESIESQLS 154
                                       99999999999877777899********986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.028
                      Baculo_PEP_C  23 nairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnln 91 
                                       +++ + +++i aql++ + +++t L+ l e+  sl a+                           t ++
  gi|313117380|ref|YP_004044363.1| 151 SQLSAEQAEIKAQLQSRFGDVQTILQYLIEETDSLDAQ--------------------------VTEVQ 193
                                       11222222333333333333333333333333333222..........................22222 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   0.00071      0.28      69     115 ..      86     132 ..      45     141 .. 0.57
   2 ?    8.5   3.8    0.0049       1.9      48     100 ..     151     200 ..     137     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00071
                           DUF1664  69 drvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       ++v ++ld   e ++ei+ e+++v +  sei++++ ++    ++le+
  gi|313117380|ref|YP_004044363.1|  86 ETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEE 132
                                       33444444444444444444444444444444444444444444444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0049
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseig 100
                                       +   q+s++ a+ k +L+sr   v++ l+  +e + +++++vtev+++   i+
  gi|313117380|ref|YP_004044363.1| 151 S---QLSAEQAEIKAQLQSRFGDVQTILQYLIEETDSLDAQVTEVQQQQGVIE 200
                                       3...3455566779999999999999999999999999999999998744333 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   4.2     6e-05     0.024      22     102 ..      83     165 ..      73     167 .. 0.84
   2 ?    1.3   2.1         1     4e+02      15      52 ..     161     196 ..     159     233 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-05
                                       TCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCC.HHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  22 gedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaev.kelkeelkaleaelkeleae 96 
                                       ge +   d+l  l e+  e+qvele++  +r e+  eIg++  +  e  e+l + + +e+++el+ +e +l++ +ae
  gi|313117380|ref|YP_004044363.1|  83 GETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLtELEEQLGDTGdSEIQDELESIESQLSAEQAE 159
                                       667788999**********************************9954444554443268****************** PP

                                       HHHHHC CS
                      Seryl_tRNA_N  97 leklll 102
                                       +++ l+
  gi|313117380|ref|YP_004044363.1| 160 IKAQLQ 165
                                       998775 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1
                                       HHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  15 keklkkRgedkadvdelleldekrrelqveleelqaer 52 
                                       k++l++R++d++++ +   l e+  +l +++ e+q+++
  gi|313117380|ref|YP_004044363.1| 161 KAQLQSRFGDVQTILQ--YLIEETDSLDAQVTEVQQQQ 196
                                       5566666644433321..12333333333333333322 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  12.3   0.00058      0.23       5      96 ..     105     195 ..     101     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00058
                                       CCCCHHHHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHH CS
                    Apolipoprotein   5 sldelkayaeeleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapytee 81 
                                        l++++ +++e+e+ +++l+ +l +  ++  +    +++ ele+  ++l++  +e+++ql+++  +++  l+ ++ee
  gi|313117380|ref|YP_004044363.1| 105 ELESVVDRRSEIESEIGELTGRLTELEEQLGDTGDSEIQDELESIESQLSAEQAEIKAQLQSRFGDVQTILQYLIEE 181
                                       56778888888888888888866666666666777888999999999999999999999999999999999888888 PP

                                       HHHHHHHCHHCCHHC CS
                    Apolipoprotein  82 lrerlaadaeelqeq 96 
                                         ++l+a++ e+q+q
  gi|313117380|ref|YP_004044363.1| 182 T-DSLDAQVTEVQQQ 195
                                       8.7788888888887 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2    0.0001     0.041      14      64 ..      83     133 ..      79     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.0001
                              KELK  14 qEkeelqkelaeaqErlksqkkeLkdaisqrklamqefsevneklselrsq 64 
                                        E e ++ +l  ++Er+ + + eL   + +r     e  e++ +l+el +q
  gi|313117380|ref|YP_004044363.1|  83 GETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQ 133
                                       58899999****************************************998 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   7.3    0.0003      0.12      50     179 ..      55     207 ..      33     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                             Atg14  50 egke..................eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakls 108
                                       ++++                    ++++ + ++ +++l++l+ +i +++ +l+ + d++s+  +ei e   +l +l 
  gi|313117380|ref|YP_004044363.1|  55 NETTennslgslelsgpantvdGESDTTGETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELE 131
                                       33333444444444446677765556667777777888888888888888888888888888888888888888888 PP

                             Atg14 109 dklk.....kRrsdleslqneleerrkkqiaklqdaikrieqklsslssktlesrsslcselaklyglrrtsyerg 179
                                       ++l      + + +les++++l+++++++ a+lq+    ++  l+ l  +t + +++  +   +   + ++++er+
  gi|313117380|ref|YP_004044363.1| 132 EQLGdtgdsEIQDELESIESQLSAEQAEIKAQLQSRFGDVQTILQYLIEETDSLDAQVTEVQQQQGVIEQVENERD 207
                                       8888888878999*********************999888888777777777666666666666666666666666 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.5   0.00018     0.071     136     257 ..      86     217 ..      80     234 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                      Exonuc_VII_L 136 elvvpdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerk.....rqrldeleerleralkkql 207
                                       e v+ + ++l+e++ e++ +le+ ++r+ e  ++++ +l+ rl++ ee+l +      +++l+++e++l++++++  
  gi|313117380|ref|YP_004044363.1|  86 ETVTDQLDTLRERITEIQVELESVVDRRSEI-ESEIGELTGRLTELEEQLGDTgdseiQDELESIESQLSAEQAEIK 161
                                       6778888888999999999999988877642.234444444443333333222100023334444444444433333 PP

                      Exonuc_VII_L 208 kkkrerleelkerlk...ekleekkerlkklkerle...lleekkerleeleekle 257
                                       ++ ++r+  +++ l+   e++++ ++++++++++     ++e+++++l++l+++ +
  gi|313117380|ref|YP_004044363.1| 162 AQLQSRFGDVQTILQyliEETDSLDAQVTEVQQQQGvieQVENERDKLQRLKREAS 217
                                       33344444444333334433444444443332222233367777777777766554 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   9.8   0.00033      0.13       9     116 ..      86     195 ..      79     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00033
                         ApoLp-III   9 ksvkkqlnlpsqeevvetiKensenlvdqlkqvikslqeelkkksdeleeal.....kevkkkieetadklseenPe 80 
                                       ++v++ql      e  ++i+ + e++vd+ +++ +++ e   + + elee l     +e+++++e +  +ls+e++e
  gi|313117380|ref|YP_004044363.1|  86 ETVTDQLD--TLRERITEIQVELESVVDRRSEIESEIGELTGRLT-ELEEQLgdtgdSEIQDELESIESQLSAEQAE 159
                                       56777755..77888899999999999988777777755444444.677776222234678888888888888**** PP

                         ApoLp-III  81 vkkkaqelqekvQsgvqslvkesqklaeslkensqe 116
                                       +k ++q     vQ+ +q l++e++ l++++ e  q+
  gi|313117380|ref|YP_004044363.1| 160 IKAQLQSRFGDVQTILQYLIEETDSLDAQVTEVQQQ 195
                                       ******************************975443 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.7    0.0024      0.96     102     177 ..      90     167 ..      83     176 .. 0.72
   2 ?    5.7   4.7      0.03        12     109     173 ..     159     222 ..     141     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0024
                            DUF724 102 deqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk..ekkeaadkeiarlkseaekleeeled 176
                                       d+ + l+e++ +++ ++e   ++++++e+ei el  +  ele+ql  +   e +++ ++  ++l++e+++++ +l++
  gi|313117380|ref|YP_004044363.1|  90 DQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTGdsEIQDELESIESQLSAEQAEIKAQLQS 166
                                       56667788888899999999999999999999999999999999997775333333333335666667777777666 PP

                            DUF724 177 v 177
                                        
  gi|313117380|ref|YP_004044363.1| 167 R 167
                                       5 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.03
                            DUF724 109 eerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleee 173
                                       e + +l++++ + ++  + l ee d l+ ++ e+++q+ ++  + e++  ++ rlk ea+++  +
  gi|313117380|ref|YP_004044363.1| 159 EIKAQLQSRFGDVQTILQYLIEETDSLDAQVTEVQQQQGVIE-QVENERDKLQRLKREASDVGSY 222
                                       3344566677777788888899999*************9776.7778888899999999887665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.0    0.0016      0.64     196     268 ..      87     160 ..      33     162 .. 0.55
   2 ?    4.7   8.1     0.028        11     139     211 ..     141     219 ..     139     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                              Spc7 196 idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksel.eeeiaeaervleeckgwsesev 268
                                          ++L +lre+++e+++e+e+  ++ +e ++++ el+ +++el+eq  ++  +ei+ + + +e + + ++ e+
  gi|313117380|ref|YP_004044363.1|  87 TVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTgDSEIQDELESIESQLSAEQAEI 160
                                       22567777777777777777777777777777777777777777777654424566655555555555555555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                              Spc7 139 gLkegleenlegleedkelLekqee....eldellpeleeekaeleeeleklqeaaeelesid..keeLeelreela 209
                                       +++++le++ ++l ++++++++q +     ++++l+ l ee ++l +++++ q+++  +e+++  +++L+ l++e +
  gi|313117380|ref|YP_004044363.1| 141 EIQDELESIESQLSAEQAEIKAQLQsrfgDVQTILQYLIEETDSLDAQVTEVQQQQGVIEQVEneRDKLQRLKREAS 217
                                       56677777777777776666665552222578888888888888888888888888777776545788888888876 PP

                              Spc7 210 el 211
                                       ++
  gi|313117380|ref|YP_004044363.1| 218 DV 219
                                       65 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.3   8.3e-05     0.033      68     139 ..      79     152 ..      46     181 .. 0.84
   2 ?    2.5   2.5      0.37   1.5e+02      39      64 ..     186     211 ..     180     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHHHS-H..HH.HHHHHHHHHH CS
                             Nup54  68 letsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletleaqlndp..aqlkgrvnelwar 139
                                        +t+ + e++  +  +l +R++++ + le +  r++ ++ e  el +rl +le+ql d   ++++  ++ + ++
  gi|313117380|ref|YP_004044363.1|  79 SDTTGETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTgdSEIQDELESIESQ 152
                                       56788888999999999999999999999888999999999999999999999999985447777777766655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  39 kaQqkevaqhrerlkeisdrleeleq 64 
                                       +aQ +ev+q++  +++++++ ++l++
  gi|313117380|ref|YP_004044363.1| 186 DAQVTEVQQQQGVIEQVENERDKLQR 211
                                       79******************999995 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.041        16      76     102 ..      83     109 ..      78     113 .. 0.82
   2 ?    5.2   1.9     0.048        19      79     104 ..     144     169 ..     126     171 .. 0.69
   3 ?    7.2   0.8     0.012       4.7       2      34 ..     187     219 ..     186     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                       Prefoldin_2  76 keiktlekqleklekeleelkeelqkk 102
                                        e +t+++ql++l+++++e++ el + 
  gi|313117380|ref|YP_004044363.1|  83 GETETVTDQLDTLRERITEIQVELESV 109
                                       578999999999999999999999865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.048
                                       HHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  79 ktlekqleklekeleelkeelqkklq 104
                                       ++le+ +++l +e +e+k++lq++++
  gi|313117380|ref|YP_004044363.1| 144 DELESIESQLSAEQAEIKAQLQSRFG 169
                                       46777777788888888888888887 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   2 elinkfqqlqqqlqqlaqqikqletqlkelelv 34 
                                       +++ + qq q  ++q+++++++l++ ++e+ +v
  gi|313117380|ref|YP_004044363.1| 187 AQVTEVQQQQGVIEQVENERDKLQRLKREASDV 219
                                       678999***********************9998 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   7.1   4.4e-05     0.017      29     164 ..      40     181 ..      13     185 .. 0.84
   2 ?    0.6   0.6      0.86   3.4e+02      62      87 ..     191     216 ..     179     224 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-05
                      HAUS-augmin3  29 elqayeeLkksGkpiLegeaLeeaLktie.psdlkq.edvellevileeeeesleaLeqelqeLqkekalklkrlnk 103
                                        +  y  L++  + +L++++ +  L ++e ++  ++ + ++ ++ ++e  +++l  L++ + e q e ++   r+++
  gi|313117380|ref|YP_004044363.1|  40 LISSYWTLNEISQ-LLNETTENNSLGSLElSGPANTvDGESDTTGETETVTDQLDTLRERITEIQVELESVVDRRSE 115
                                       5566777777777.999999999999999855555556666677778888899************************ PP

                      HAUS-augmin3 104 Lqvqaaslqqelrkleeee.....keakkklkeaqeelraenaetnavLqqlteeakqlaeyfeea 164
                                       ++  + +l+ +l +lee+      +e + +l+ ++++l+ae ae++a+Lq+    ++ + +y+ e+
  gi|313117380|ref|YP_004044363.1| 116 IESEIGELTGRLTELEEQLgdtgdSEIQDELESIESQLSAEQAEIKAQLQSRFGDVQTILQYLIEE 181
                                       ***************99863333367899****************************999998665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.86
                      HAUS-augmin3  62 kqedvellevileeeeesleaLeqel 87 
                                       + ++++ + +++e+e+++l+ L++e+
  gi|313117380|ref|YP_004044363.1| 191 EVQQQQGVIEQVENERDKLQRLKREA 216
                                       22444444455555555555555554 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   6.1   6.2e-05     0.025       5      65 ..      87     148 ..      84     167 .. 0.79
   2 ?   -1.2   2.7       2.7   1.1e+03      22      57 ..     176     211 ..     156     224 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.2e-05
                       Tropomyosin   5 qveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteer.leealek 65 
                                       +v ++ld+ +er ++++ +le+  +++ + e+E   l+ r++ lee+l  t +  +++ le 
  gi|313117380|ref|YP_004044363.1|  87 TVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTGDSeIQDELES 148
                                       7899********************************************87754303333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.7
                       Tropomyosin  22 kkleeaekkaekaeaEvaalnrriqlleeelertee 57 
                                       + l e+++  + + +Ev + +  i+++e+e ++ + 
  gi|313117380|ref|YP_004044363.1| 176 QYLIEETDSLDAQVTEVQQQQGVIEQVENERDKLQR 211
                                       445555555555666666666666666666666554 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.7    0.0078       3.1       9      55 ..      89     135 ..      83     139 .. 0.91
   2 ?    6.3   6.0     0.026        10       9      61 ..     143     202 ..     139     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0078
                       Cep57_CLD_2   9 qnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaeve 55 
                                        ++Ld l++++ + + el+++   R++ ++ +g+   +l eL +++ 
  gi|313117380|ref|YP_004044363.1|  89 TDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLG 135
                                       579***************************************99875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.026
                       Cep57_CLD_2   9 qnrLdsltrklqvheeelkrLnkERdsalrqLgv.AyeelneLkaevealrkE......L 61 
                                       q++L+s++++l++ + e+k+  + R ++++ + +  +ee+++L a+v   +++       
  gi|313117380|ref|YP_004044363.1| 143 QDELESIESQLSAEQAEIKAQLQSRFGDVQTILQyLIEETDSLDAQVTEVQQQqgvieqV 202
                                       99****************************98777*************999986666551 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   9.7   0.00033      0.13      52     132 ..      83     165 ..      74     180 .. 0.74
   2 ?    2.6   1.8      0.32   1.3e+02      29      61 ..     185     216 ..     172     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00033
                    CENP-F_leu_zip  52 aevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlle..ekEqekvqmkeeska 126
                                        e et+ +++++l+e+ +e++++L+++   + e+e e+ +   r  eLe+   ++       e+E  + q++ e+ +
  gi|313117380|ref|YP_004044363.1|  83 GETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTGDSEIqdELESIESQLSAEQAE 159
                                       5899*********************************************9877764332200223223333333333 PP

                    CENP-F_leu_zip 127 aveeLq 132
                                          +Lq
  gi|313117380|ref|YP_004044363.1| 160 IKAQLQ 165
                                       333333 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.32
                    CENP-F_leu_zip  29 LerelemseenqekvileaEtskaevetlkeei 61 
                                       L++++ +++ +q+ vi ++E+++ +++ lk e 
  gi|313117380|ref|YP_004044363.1| 185 LDAQVTEVQ-QQQGVIEQVENERDKLQRLKREA 216
                                       455554444.46789999999999999999875 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   0.00045      0.18     116     177 ..      73     134 ..       9     137 .. 0.79
   2 ?    2.9   7.0      0.14        57      75     152 ..     148     219 ..     131     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00045
                           DUF2353 116 dlletrhssaeereelvkqlEklkekiqqlerdlkavldekeelvterdaykeKaerLnqeL 177
                                       ++++ +  +  e e +  ql +l+e+i++++ +l++v+d ++e++ e  +   +   L ++L
  gi|313117380|ref|YP_004044363.1|  73 NTVDGESDTTGETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQL 134
                                       44555566688999999****************************99777766666666665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                           DUF2353  75 eenkalkleveeLrqklkeaqgDiklLReqlarqrlglkdedlletrhssaeereelvkqlEklkekiqqlerdlka 151
                                         +++l+ e  e++ +l+   gD++++ + l       ++ d+l+++ ++ ++++ +++q+E+ + k q l+r+  +
  gi|313117380|ref|YP_004044363.1| 148 SIESQLSAEQAEIKAQLQSRFGDVQTILQYLI------EETDSLDAQVTEVQQQQGVIEQVENERDKLQRLKREASD 218
                                       44567888888888888888888888764333......345667788888999******************998766 PP

                           DUF2353 152 v 152
                                       v
  gi|313117380|ref|YP_004044363.1| 219 V 219
                                       5 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8      0.17        69       8      49 ..      92     133 ..      89     155 .. 0.85
   2 ?   -0.9   0.9       5.6   2.2e+03      24      38 ..     152     166 ..     123     181 .. 0.56
   3 ?   12.4   3.6   0.00041      0.16       7      51 ..     174     217 ..     171     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.17
                   Snapin_Pallidin   8 lellepkldeldeklkelrqsQeeLleqldrlnekLkeleea 49 
                                       l++l   ++e++ +l+++ +  +e  +++ +l+ +L+elee 
  gi|313117380|ref|YP_004044363.1|  92 LDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQ 133
                                       567788888999999999999999999999999999988875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 5.6
                   Snapin_Pallidin  24 elrqsQeeLleqldr 38 
                                       +l ++Q e ++ql++
  gi|313117380|ref|YP_004044363.1| 152 QLSAEQAEIKAQLQS 166
                                       344455555555544 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00041
                   Snapin_Pallidin   7 llellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                       +l+ l  + d ld+++ e++q+Q  + eq++++++kL++l+++++
  gi|313117380|ref|YP_004044363.1| 174 ILQYLIEETDSLDAQVTEVQQQQG-VIEQVENERDKLQRLKREAS 217
                                       677777788999999999998665.67999999999999998765 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.6    0.0014      0.57     235     339 ..      86     189 ..      30     221 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0014
                          Prominin 235 lpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldts 311
                                         + ++l++l e ++e++ +Le+v +  +e+ ++  +L   l++  ++l ++  +++q  e ++i+s+l++e+ + +
  gi|313117380|ref|YP_004044363.1|  86 ETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTGDSEIQ-DELESIESQLSAEQAEIK 161
                                       4566778888888888888888888888888888888888888888888888888887.666666666666666666 PP

                          Prominin 312 kcl.dqlpnvdevlealeevletnlssiv 339
                                       ++l +   +v+++l+ l e   ++l+ +v
  gi|313117380|ref|YP_004044363.1| 162 AQLqSRFGDVQTILQYLIEE-TDSLDAQV 189
                                       66664444444444433222.11222222 PP

>> Med28  Mediator complex subunit 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.1    0.0013       0.5      26     129 ..     109     212 ..      88     217 .. 0.88
   2 ?   -0.4   0.0       2.8   1.1e+03       5      30 ..     252     277 ..     250     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                             Med28  26 vlekrneLsasvsdlkkelerkaekykvapeellmkHlqktseqlatqlkalrekgqnvfgdg.tkidstidylekl 101
                                       v+++r e+  ++ +l  +l +  e+   + ++ ++  l++   ql+++   ++ + q  fgd  t ++  i+  + l
  gi|313117380|ref|YP_004044363.1| 109 VVDRRSEIESEIGELTGRLTELEEQLGDTGDSEIQDELESIESQLSAEQAEIKAQLQSRFGDVqTILQYLIEETDSL 185
                                       688999999999*******99999**************************************625668899999*** PP

                             Med28 102 kqvlsdaedvykvrdevlnearqrlael 129
                                         +++++++++ v+++v ne r++l  l
  gi|313117380|ref|YP_004044363.1| 186 DAQVTEVQQQQGVIEQVENE-RDKLQRL 212
                                       *****************985.6666665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.8
                             Med28   5 yleqlsqkFvllDviRekktfvlekr 30 
                                       ++eq s+ Fvl + + ++k  v++ +
  gi|313117380|ref|YP_004044363.1| 252 GVEQRSKWFVLSEAVIKTKSSVIDNE 277
                                       699*******9999988888888765 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5    0.0002     0.081     309     397 ..      48     136 ..      45     140 .. 0.81
   2 ?    1.2   6.9      0.19        78     348     424 ..     141     217 ..     137     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                       SSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHH CS
                              EzrA 309 kelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleele 385
                                       +e+++ l++++++n+  + el+   ++ + + + + + + ++++l++l++++ e++ +le+     Se+++e+ el+
  gi|313117380|ref|YP_004044363.1|  48 NEISQLLNETTENNSLGSLELSGPANTVDGESDTTGETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELT 124
                                       56777777777777777777777777777778888899999999999999999999999999999999999999999 PP

                                       HHHHHHHHHHHH CS
                              EzrA 386 ekleeieekqee 397
                                        +l+e+ee++ +
  gi|313117380|ref|YP_004044363.1| 125 GRLTELEEQLGD 136
                                       999999999866 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHS-S.S---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 348 elekelkelekdyeeleekleek.kvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkel 423
                                       e+++el+++e+++   + +++++ +  + ++q  l+ l e+ + ++ ++ e++++ + +++ E++ r++l+++k+e 
  gi|313117380|ref|YP_004044363.1| 141 EIQDELESIESQLSAEQAEIKAQlQSRFGDVQTILQYLIEETDSLDAQVTEVQQQQGVIEQVENE-RDKLQRLKREA 216
                                       78999999999999999999887466799999999999999999999999999999999999988.89999988876 PP

                                       H CS
                              EzrA 424 k 424
                                       +
  gi|313117380|ref|YP_004044363.1| 217 S 217
                                       5 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.9      0.34   1.3e+02      12      48 ..      95     129 ..      84     131 .. 0.81
   2 ?   13.6   1.7   0.00018      0.07      11      63 ..     129     179 ..     127     185 .. 0.87
   3 ?   -0.2   0.2       3.7   1.5e+03      16      35 ..     199     216 ..     186     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.34
                                       HHHHHHCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HSCB_C  12 lrEeleeaeeaadkeeleelkaeveerieeleaelee 48 
                                       lrE++ e+ +  + e + + ++e+e++i el+ +l e
  gi|313117380|ref|YP_004044363.1|  95 LRERITEI-QV-ELESVVDRRSEIESEIGELTGRLTE 129
                                       79999999.34.6799999999999999998888766 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00018
                                       HHHHHHHCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                            HSCB_C  11 elrEeleeaeeaadkeeleelkaeveerieeleaeleeafekkdleaaadllr 63 
                                       el E+l +  +++ ++ele ++++++++++e+ a+l++ f   d++++ + l+
  gi|313117380|ref|YP_004044363.1| 129 ELEEQLGDTGDSEIQDELESIESQLSAEQAEIKAQLQSRF--GDVQTILQYLI 179
                                       789999999555455*************************..49999988876 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 3.7
                                       HHCGGGSSSHHHHHHHHHHH CS
                            HSCB_C  16 leeaeeaadkeeleelkaev 35 
                                       +e++e  ++ ++l++lk+e 
  gi|313117380|ref|YP_004044363.1| 199 IEQVE--NERDKLQRLKREA 216
                                       67773..3568999998885 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.1    0.0059       2.3       9      57 ..      84     134 ..      81     135 .. 0.73
   2 ?    8.4   8.1    0.0065       2.6      11      58 ..     114     154 ..     103     166 .. 0.77
   3 ?   -1.3   9.7         7   2.8e+03       7      56 ..     143     195 ..     140     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0059
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeL 57 
                                       e e++ ++++ L e+i+e++ el++      +   ++ el+ +l+ele++L
  gi|313117380|ref|YP_004044363.1|  84 ETETVTDQLDTLRERITEIQVELESVVDRRSEieSEIGELTGRLTELEEQL 134
                                       567777888888888888888888765443334577999999999999987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0065
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLe 58 
                                        e+e+eI +L  +++ele++l d +        +e++ ele +e++L 
  gi|313117380|ref|YP_004044363.1| 114 SEIESEIGELTGRLTELEEQLGDTG-------DSEIQDELESIESQLS 154
                                       37********************998.......4577777777777775 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 7
                      ABC_tran_CTD   7 qreleeleaeIeaLEeei.aeleaeladpelysdp..eklaelsaeleeleae 56 
                                       q ele +e+++ a ++ei a+l+ ++ d +   ++  e+   l a+ +e++++
  gi|313117380|ref|YP_004044363.1| 143 QDELESIESQLSAEQAEIkAQLQSRFGDVQTILQYliEETDSLDAQVTEVQQQ 195
                                       67899999888887777624677788888777777777777777777777765 PP

>> MIF4G_like_2  MIF4G like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.5    0.0049       1.9     152     245 ..      87     200 ..      78     219 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0049
                      MIF4G_like_2 152 llkrtlskvnkrvkkvrqeleelkkkeeeekakeeed......................keeeeeleraeekleaaq 206
                                        +   l+++  r+++++ ele++ ++++e       +                      +e ++ele++e++l+a+q
  gi|313117380|ref|YP_004044363.1|  87 TVTDQLDTLRERITEIQVELESVVDRRSEI------EseigeltgrlteleeqlgdtgdSEIQDELESIESQLSAEQ 157
                                       444445555555555555554444443333......112333444444455667777778899************** PP

                      MIF4G_like_2 207 keqkelflivferlveilsesleeletsgseentevie....e 245
                                       +e k+ ++  f   ++il+  +ee ++ + +  +++++    e
  gi|313117380|ref|YP_004044363.1| 158 AEIKAQLQSRFGDVQTILQYLIEETDSLDAQVTEVQQQqgviE 200
                                       *********************7766554444333222244452 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.5    0.0016      0.63      25     130 ..      87     194 ..      81     197 .. 0.89
   2 ?    6.7   4.8     0.019       7.6      35     124 ..     125     215 ..     122     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCC CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaq 100
                                       +++++  ++++++++++ ele++ ++ +e+e+ + e++  l+e +++  d+ d+ i++  +++e++ +  +++i+aq
  gi|313117380|ref|YP_004044363.1|  87 TVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTgDSEIQDELESIESQLSAEQAEIKAQ 163
                                       5667788999*********************************9999998889999999999999999999999999 PP

                                       H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 101 e.snirvLqnvlesneqkiqkLeqdidqker 130
                                         s+    q++l+ + ++   L  ++++ ++
  gi|313117380|ref|YP_004044363.1| 164 LqSRFGDVQTILQYLIEETDSLDAQVTEVQQ 194
                                       9899999999999999999999888876554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqesnirvLqnv 110
                                        +l++le++l +  +  +e+++  ++i+++l ++q++ k + ++ + ++++ l+   ++  +++daq++++++ q+v
  gi|313117380|ref|YP_004044363.1| 125 GRLTELEEQLGDTGD--SEIQDELESIESQLSAEQAEIKAQlQSRFGDVQTILQ-YLIEETDSLDAQVTEVQQQQGV 198
                                       577888888887654..5788888999999999999988878999999999999.7777788899999999999988 PP

                                       HHHH...HHHHHHHHHH CS
                         Fib_alpha 111 lesn...eqkiqkLeqd 124
                                       +e+    + k+q+L+ +
  gi|313117380|ref|YP_004044363.1| 199 IEQVeneRDKLQRLKRE 215
                                       76651115577777765 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.5   0.00055      0.22       2      88 ..      88     176 ..      87     177 .. 0.82
   2 ?    0.7   0.6       1.7   6.7e+02      34      72 ..     199     216 ..     178     220 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00055
                           DUF4164   2 vtkeleaaltrLeaaldsLEkavdrrleaerkrdeleaeiealged.....rsRLaeeLdqaearaarleevnrEvs 73 
                                       vt++l+   +r+++   +LE+ vdrr e e + +el  ++++l+e       s + +eL      +++l++ ++E++
  gi|313117380|ref|YP_004044363.1|  88 VTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQlgdtgDSEIQDELE---SIESQLSAEQAEIK 161
                                       789999999******************************999987522222344444444...4467899******* PP

                           DUF4164  74 rrLkaaietiravLa 88 
                                        +L++    ++++L+
  gi|313117380|ref|YP_004044363.1| 162 AQLQSRFGDVQTILQ 176
                                       ************996 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.7
                           DUF4164  34 rdeleaeiealgedrsRLaeeLdqaearaarleevnrEv 72 
                                                              q+e++  +l++++rE+
  gi|313117380|ref|YP_004044363.1| 199 I---------------------EQVENERDKLQRLKREA 216
                                       2.....................34455555555555554 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2    0.0012      0.46      40      74 ..      80     115 ..      50     120 .. 0.77
   2 ?    1.6   0.7       1.1   4.3e+02      21      65 ..     121     164 ..     114     168 .. 0.50
   3 ?   -1.2   0.1       8.2   3.3e+03      34      35 ..     196     197 ..     161     220 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0012
                                       XXXXXXXXHHHH.HHHHHHHHHHHHHHHHHHHHHH. CS
                         GTP-bdg_M  40 rGpGetkleldr.rlireriaklkkeLekvkkkrel 74 
                                          Get++ +d+  ++reri++++ eLe+v  +r++
  gi|313117380|ref|YP_004044363.1|  80 DTTGETETVTDQlDTLRERITEIQVELESVVDRRSE 115
                                       446777776665389***************999976 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1.1
                                       HHHCXXXXXXXXX..X..XXXXXX..XXXHHHHHHHHHHHHHHHHHH CS
                         GTP-bdg_M  21 prLeglgkelsrqgGgigtrGpGe..tkleldrrlireriaklkkeL 65 
                                         L+g+ +el++q G     G  e   +le+ + +++   a++k +L
  gi|313117380|ref|YP_004044363.1| 121 GELTGRLTELEEQLGD---TGDSEiqDELESIESQLSAEQAEIKAQL 164
                                       5677777888888665...2222211334444444444444444444 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 8.2
                                       .. CS
                         GTP-bdg_M  34 gG 35 
                                       +G
  gi|313117380|ref|YP_004044363.1| 196 QG 197
                                       22 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3      0.12        47      38      59 ..      86     107 ..      73     113 .. 0.57
   2 ?    0.7  10.4       1.9   7.4e+02      16      66 ..      88     154 ..      83     201 .. 0.67
   3 ?    4.4   3.2      0.13        51       3      38 ..     172     210 ..     170     223 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.12
                           NPV_P10  38 telnekLdaqsaqLaeletkve 59 
                                       + ++++Ld + + ++e++ ++e
  gi|313117380|ref|YP_004044363.1|  86 ETVTDQLDTLRERITEIQVELE 107
                                       4445555555555555554444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.9
                           NPV_P10  16 vddkVdalqqqvddvqenlpdv....telnekLdaqsaqLaelet............kvenIqdiLn 66 
                                       v d++d l ++++++q +l+ v    +e+++++ +++  L+ele+            ++e+I++ L+
  gi|313117380|ref|YP_004044363.1|  88 VTDQLDTLRERITEIQVELESVvdrrSEIESEIGELTGRLTELEEqlgdtgdseiqdELESIESQLS 154
                                       5555555555555555555554333346777777777777777775555555555556666666655 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.13
                           NPV_P10   3 qniLlvIradikavddkVdalqqq...vddvqenlpdvt 38 
                                       q iL    ++   +d +V+ +qqq   +++v+++  +++
  gi|313117380|ref|YP_004044363.1| 172 QTILQYLIEETDSLDAQVTEVQQQqgvIEQVENERDKLQ 210
                                       678888888888888888888887222244444333333 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   9.4    0.0096       3.8     120     222 ..      85     196 ..      81     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0096
                              CorA 120 vdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnre..vlkrlla.....kaddklld 187
                                       ++++ ++l++l e++ e++ el    +++ ei +e+ +l  rl++l+++l ++ +  + ++l +     +a++ +++
  gi|313117380|ref|YP_004044363.1|  85 TETVTDQLDTLRERITEIQVELesVVDRRSEIESEIGELTGRLTELEEQLGDTGDseIQDELESiesqlSAEQAEIK 161
                                       5778899***************8877888899999999999999998888665431133322223346679****** PP

                              CorA 188 dedkeylrdlldelerllemlealrerleslqdty 222
                                       ++ + ++ d++  l+ l+e++++l  +++ +q++ 
  gi|313117380|ref|YP_004044363.1| 162 AQLQSRFGDVQTILQYLIEETDSLDAQVTEVQQQQ 196
                                       ******************************99875 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  11.1      0.23        92      29     123 ..      93     197 ..      84     219 .. 0.51

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.23
                               GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeev.....eeLrkqlknyekd.....kqslknlkarlk 95 
                                       ++l+e i+e++ + e+   + sei++e  +l+  L+++ee++      e + +l+  e++      +  ++l++r  
  gi|313117380|ref|YP_004044363.1|  93 DTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLgdtgdSEIQDELESIESQlsaeqAEIKAQLQSRFG 169
                                       55666666666666666666666666666666666666665522222234444443333210000233344445555 PP

                               GAS  96 elekelkdlkwehevleqrfekvekerd 123
                                       +++  l+ l +e ++l  ++++v+++  
  gi|313117380|ref|YP_004044363.1| 170 DVQTILQYLIEETDSLDAQVTEVQQQQG 197
                                       5666666666666666666555555433 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.1    0.0013      0.51      11      83 ..      88     161 ..      80     165 .. 0.85
   2 ?    2.6   7.6      0.44   1.7e+02      18      91 ..     142     218 ..     140     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0013
                            CENP-H  11 lssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek.eklkeelekleaelkksrqrwr 83 
                                       +  +l  l + ++e+q el++v   + +++ +  el+ +l+el+++   +  ++ ++ele++e++l +++++++
  gi|313117380|ref|YP_004044363.1|  88 VTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTGdSEIQDELESIESQLSAEQAEIK 161
                                       5566777888899999999999999999999999999999999999888888999***********99998765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.44
                            CENP-H  18 lsqelrelqeeltevekenlrlkrknrelaael.lelakekesek..eklkeelekleaelkksrqrwrvvknvasa 91 
                                       ++ el++++++l+  ++e+++  +     ++++ + l +e++s +   ++ ++++ + ++++++r++ + +k+ as 
  gi|313117380|ref|YP_004044363.1| 142 IQDELESIESQLSAEQAEIKAQLQSRFGDVQTIlQYLIEETDSLDaqVTEVQQQQGVIEQVENERDKLQRLKREASD 218
                                       6889999***********99999999999****66999999999988668899999*************99998886 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.0   0.00086      0.34      44      97 ..      63     133 ..      10     137 .. 0.81
   2 ?    4.4   5.9      0.12        49      78     132 ..     140     195 ..     136     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00086
                            APG6_N  44 k.................qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                                         +  e+e   ++l++l++   e + eL+ + + r+e+e+e+ +l+  l +lee+
  gi|313117380|ref|YP_004044363.1|  63 LgslelsgpantvdgesdTTGETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQ 133
                                       144555555555555555667999999*****************************************997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.12
                            APG6_N  78 eeleaelaaleeelealeee.eerfwreynelqlelleleeeldsleaqyehaqnq 132
                                       +e+++el+++e++l+a ++e +++  +++ + q+ l+ l ee dsl+aq++  q+q
  gi|313117380|ref|YP_004044363.1| 140 SEIQDELESIESQLSAEQAEiKAQLQSRFGDVQTILQYLIEETDSLDAQVTEVQQQ 195
                                       6889999999999999888834455566778******************9998887 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.5     0.069        27      11      44 ..      83     116 ..      79     137 .. 0.74
   2 ?    8.9   6.6    0.0072       2.9      14      87 ..     140     210 ..     131     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.069
                    PRKG1_interact  11 eenerLkreLeelekelselkseleklkqqrqes 44 
                                        e+e+  ++L++l+++++e++ ele++  +r+e 
  gi|313117380|ref|YP_004044363.1|  83 GETETVTDQLDTLRERITEIQVELESVVDRRSEI 116
                                       68999999*****************998766552 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0072
                    PRKG1_interact  14 erLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkeleeLraenqrLk 87 
                                       +++++eLe++e +ls  ++e++      q+++ + +++l+   +e  sl+ +++e+++++ ++e++ +e ++L+
  gi|313117380|ref|YP_004044363.1| 140 SEIQDELESIESQLSAEQAEIKAQL---QSRFGDVQTILQYLIEETDSLDAQVTEVQQQQGVIEQVENERDKLQ 210
                                       5678999999999999999888755...568999999999999999********99999988877776655543 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.7    0.0017      0.68       3      84 ..      84     163 ..      82     183 .. 0.74
   2 ?   -1.0   3.3         2   7.9e+02      34      70 ..     170     211 ..     141     235 .. 0.35

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0017
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       e e++++++++l+e+ +e++ +le++    s++ +ei + + rl+el+++l ++  s   e ++e+e+++++l+ ++
  gi|313117380|ref|YP_004044363.1|  84 ETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTGDS---EIQDELESIESQLSAEQ 157
                                       67788999999999999999****************************999998766...34444444444444444 PP

                             TMPIT  80 kvlk.e 84 
                                       + +k +
  gi|313117380|ref|YP_004044363.1| 158 AEIKaQ 163
                                       443322 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2
                             TMPIT  34 kcskeikkqkkrlkelksslkklkksvk.....eeeeeevee 70 
                                       ++++ ++   ++  +l++++++++++++     e+e++++++
  gi|313117380|ref|YP_004044363.1| 170 DVQTILQYLIEETDSLDAQVTEVQQQQGvieqvENERDKLQR 211
                                       111111122222222222222222221111111222222222 PP

>> SPATA1_C  Spermatogenesis-associated C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00073      0.29      98     149 ..      77     128 ..      24     131 .. 0.83
   2 ?   -0.6   0.2         3   1.2e+03     109     134 ..     142     167 ..     139     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00073
                          SPATA1_C  98 lkneliiqiiaaqheidelkrkledakmklvaElklRkqaaeelkaLraels 149
                                        +++++ +  +++ ++d l++++++ +++l + + +R ++++e+ +L   l+
  gi|313117380|ref|YP_004044363.1|  77 GESDTTGETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLT 128
                                       56777888889999********************************988776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3
                          SPATA1_C 109 aqheidelkrkledakmklvaElklR 134
                                        q e++ +  +l + ++++ a l+ R
  gi|313117380|ref|YP_004044363.1| 142 IQDELESIESQLSAEQAEIKAQLQSR 167
                                       56777777777777777777666666 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.1    0.0061       2.4       9      58 ..      84     133 ..      77     151 .. 0.68
   2 ?    6.2   4.1      0.04        16       5      77 ..     141     213 ..     137     221 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0061
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXX CS
                              YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekk 58 
                                       + e++++ql++l e+++e++ el++++++ +e+e e  +l  rl+e e++
  gi|313117380|ref|YP_004044363.1|  84 ETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQ 133
                                       55677888888888888888888888888888888888888888443332 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   5 elfdkleeleeqleelleele.elkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlY 77 
                                       e+ d+le++e+ql++ ++e++ +l++++ ++    + L  e ++l  ++ +e ++++   +++++ +++L+rl 
  gi|313117380|ref|YP_004044363.1| 141 EIQDELESIESQLSAEQAEIKaQLQSRFGDVQTILQYLIEETDSLDAQV-TEVQQQQGVIEQVENERDKLQRLK 213
                                       7788888888888877777753566666666666666666667776666.455555556666666666666664 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       5.6   2.2e+03     122     140 ..      40      58 ..      28      68 .. 0.59
   2 ?    8.8  16.3    0.0028       1.1      80     189 ..      92     205 ..      79     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.6
                        MscS_porin 122 ltearqrlqeirnrLnsta 140
                                       l + +  l+ei++ Ln+t 
  gi|313117380|ref|YP_004044363.1|  40 LISSYWTLNEISQLLNETT 58 
                                       4444444555555555553 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0028
                        MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqql.....tearqrlqeirnrLnstaaagealsqaqr 151
                                       l++L  r+++ + +l+++  ++++++s++ el  r++++ +ql     +e + +l+ i+++L++ +a+ +a  q++ 
  gi|313117380|ref|YP_004044363.1|  92 LDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLgdtgdSEIQDELESIESQLSAEQAEIKAQLQSRF 168
                                       56667777777777777777777777777777777777777766666666677777777777777666667777777 PP

                        MscS_porin 152 talqaelaaleaqieeleqellsnnnrqeLlklqrdll 189
                                          q+ l++l  +++ l+ +    +++q  ++ q +  
  gi|313117380|ref|YP_004044363.1| 169 GDVQTILQYLIEETDSLDAQVTEVQQQQGVIE-QVENE 205
                                       77777777777777777666666666555544.33333 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  16.8      0.28   1.1e+02       2     102 ..      99     195 ..      84     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.28
                     Tropomyosin_1   2 lnsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnneal 78 
                                       ++++++e e+ +++ +e+e+++ el  + +e e+++ +  +  +++++e+e +e++l+   e+ae ++++++    +
  gi|313117380|ref|YP_004044363.1|  99 ITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGD--TGDSEIQDELESIESQLSA--EQAEIKAQLQSRFGDV 171
                                       67788899999999999999999999999999999886..4568899999999999976..5677788888999999 PP

                     Tropomyosin_1  79 trkiqlLEeeleesdkkLkettek 102
                                       +  +q L ee ++ d++++e  ++
  gi|313117380|ref|YP_004044363.1| 172 QTILQYLIEETDSLDAQVTEVQQQ 195
                                       9999***99999999999998765 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.5    0.0022      0.88      11      73 ..     111     176 ..     104     187 .. 0.86
   2 ?   -0.4   0.1       5.2   2.1e+03      58      80 ..     175     197 ..     172     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHHHHHHCS-...-ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              FliT  11 delaaleaerqqlverlreld...aaplspaereekrellrrilandaeirallqprldelqkllg 73 
                                       d+ ++ e e  +l  rl+el+    +  +++ + e++ + +++ a+ aei+a+lq r   +q  l+
  gi|313117380|ref|YP_004044363.1| 111 DRRSEIESEIGELTGRLTELEeqlGDTGDSEIQDELESIESQLSAEQAEIKAQLQSRFGDVQTILQ 176
                                       777889999999999*****988888888888888888888****************999998776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 5.2
                                       HHHHHHHHHHHHHHHCHTHHHHH CS
                              FliT  58 rallqprldelqkllgalrrqrk 80 
                                        + l ++ d+l ++++++++q+ 
  gi|313117380|ref|YP_004044363.1| 175 LQYLIEETDSLDAQVTEVQQQQG 197
                                       55666788889999999988885 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.0    0.0084       3.4      10     106 ..      83     176 ..      78     189 .. 0.68
   2 ?    2.7   1.9      0.26     1e+02      23      59 ..     172     211 ..     150     235 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0084
                             Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkLnspgs 86 
                                        e++++ +q+d++ e ++e++ + +sv ++ s+++++  +l+   ++lee   +   + ++ +el++i+++L++ ++
  gi|313117380|ref|YP_004044363.1|  83 GETETVTDQLDTLRERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTG-DSEIQDELESIESQLSAEQA 158
                                       56777888888888888888888888888888888888777766666655544433.34788999999999999999 PP

                             Sec34  87 slvksesFlemLkklDecle 106
                                       +   + + ++    + + l+
  gi|313117380|ref|YP_004044363.1| 159 E--IKAQLQSRFGDVQTILQ 176
                                       8..34445555555555555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.26
                             Sec34  23 leqLeeleekfksvsektsslhea...ceqlleeqkrlee 59 
                                       ++ L+ l e+ +s +++ ++++++    eq+ +e+++l++
  gi|313117380|ref|YP_004044363.1| 172 QTILQYLIEETDSLDAQVTEVQQQqgvIEQVENERDKLQR 211
                                       4444444444444444444443331212333333333333 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   6.2     0.035        14      16     119 ..      97     209 ..      83     234 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.035
                        V_ATPase_I  16 edvnafqrkfvkevrrcdemerklrfleeeieklekavikeeea.........eesleapeekeldeleeeleklee 83 
                                       e ++++q +  + v r  e+e ++  l+  +++le++   + ++         e++l+a++++   +l++++ ++++
  gi|313117380|ref|YP_004044363.1|  97 ERITEIQVELESVVDRRSEIESEIGELTGRLTELEEQLGDTGDSeiqdelesiESQLSAEQAEIKAQLQSRFGDVQT 173
                                       55555566666666666666666666666666655555544444555665675666666666666788999999999 PP

                        V_ATPase_I  84 elkelnenleklkkelnelvelkavlekakefleee 119
                                        l+ l e++++l ++++e+++++ v+e++++  ++ 
  gi|313117380|ref|YP_004044363.1| 174 ILQYLIEETDSLDAQVTEVQQQQGVIEQVENERDKL 209
                                       999999999999999999999999999988766543 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9    0.0018      0.73       5      58 ..      84     134 ..      81     137 .. 0.84
   2 ?    0.4   6.5       2.1   8.4e+02      15      61 ..     141     212 ..     138     218 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0018
                          CCDC-167   5 eIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeL 58 
                                       e +++ ++l  +rer+ ++  +l+++    ++R ++e E ++l+++l+e e++L
  gi|313117380|ref|YP_004044363.1|  84 ETETVTDQLDTLRERITEIQVELESV---VDRRSEIESEIGELTGRLTELEEQL 134
                                       56777888888888888888888766...478*********************9 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.1
                          CCDC-167  15 screrLeaverrlrkeelseee...................Resle......eEeaslkeqleenekeLksL 61 
                                       +++++Le++e++l  e+ + ++                    +sl       + ++ + eq+e++  +L++L
  gi|313117380|ref|YP_004044363.1| 141 EIQDELESIESQLSAEQAEIKAqlqsrfgdvqtilqylieeTDSLDaqvtevQQQQGVIEQVENERDKLQRL 212
                                       578999999999999999888877787777777655554442222233322333344444555555555555 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.6    0.0017      0.69       3      52 ..     115     165 ..     113     174 .. 0.87
   2 ?   -0.2   0.2       2.1   8.4e+02      16      46 ..     183     215 ..     168     224 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                              ACCA   3 dfekpiaeleekieelkkl.aeesevdlseeieklekkleklkkeiyknlt 52 
                                       ++e++i el+ +++el+++  ++ + ++++e+e++e++l++ ++ei+++l+
  gi|313117380|ref|YP_004044363.1| 115 EIESEIGELTGRLTELEEQlGDTGDSEIQDELESIESQLSAEQAEIKAQLQ 165
                                       7899***********987725667889********************9986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.1
                              ACCA  16 eelkklaee..sevdlseeieklekkleklkke 46 
                                       ++l+++ +e  +++ + e++e+ ++kl++lk+e
  gi|313117380|ref|YP_004044363.1| 183 DSLDAQVTEvqQQQGVIEQVENERDKLQRLKRE 215
                                       333333222113333455555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1765  (0.0984439); expected 358.6 (0.02)
Passed bias filter:                      864  (0.0481901); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                        67  (0.00373696); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 1.03u 0.30s 00:00:01.33 Elapsed: 00:00:00.53
# Mc/sec: 2276.84
//
Query:       gi|313117381|ref|YP_004044364.1|  [L=524]
Description: hypothetical protein Hbor_31680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-05   23.2   7.2      0.049   13.9   1.2    2.9  3  T2SSN          Type II secretion system (T2SS), protein N
    0.00047   19.6  13.7       0.33   10.3   0.6    4.4  3  Sarcoglycan_1  Sarcoglycan complex subunit protein
  ------ inclusion threshold ------
      0.087   13.0   1.4       0.31   11.3   0.1    2.6  2  ASH            Abnormal spindle-like microcephaly-assoc'd, AS
      0.098   11.7   3.3       0.22   10.6   3.3    1.7  1  DUF945         Bacterial protein of unknown function (DUF945)
       0.13   12.5   1.4        1.6    9.0   0.2    3.1  2  Poly_export    Polysaccharide biosynthesis/export protein
       0.89    9.1   3.0        5.5    6.5   0.3    3.0  3  DUF3971        Protein of unknown function


Domain annotation for each model (and alignments):
>> T2SSN  Type II secretion system (T2SS), protein N
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.4   4.2e+03     131     131 ..     121     121 ..      44     159 .. 0.56
   2 !   12.5   0.6   4.3e-05      0.13      74     192 ..     282     364 ..     216     392 .. 0.61
   3 !   13.9   1.2   1.6e-05     0.049      62     168 ..     387     493 ..     357     503 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                             T2SSN 131 l 131
                                       +
  gi|313117381|ref|YP_004044364.1| 121 P 121
                                       2 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.3e-05
                             T2SSN  74 gglqlenvrlrlpaalla..n.plsas.Gdvsldldelrfgrg.gcqalqGtlnwrnaevsslsgslplgd.....l 140
                                         +++e+++++l a+++   n +++++ G+++++ +++r +++ ++ a qG++++++a+v s++g++++        
  gi|313117381|ref|YP_004044364.1| 282 VSIEAEDGEVSLAASTIDtkNgKVEVKgGRIDAQNSQFRSNTKiELTAEQGSVSLSGATVDSVNGKVEVVGrsvsaP 358
                                       24566666666666666643144554315666666666666666666666666666666666666665443232233 PP

                             T2SSN 141 raelsceggqltltlsdqsgpLslegqgslnaagtyrvagtlkptaeappaL 192
                                       +a++s                                               
  gi|313117381|ref|YP_004044364.1| 359 NADIS----------------------------------------------T 364
                                       33333..............................................2 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 1.6e-05
                             T2SSN  62 kgrlaatlagssgglqlenvrlrlpaallanplsasGdvsldldelrfgrggcqal.qGtlnwrnaevsslsgslpl 137
                                       +g++a  ++g    + ++n++++++ + ++n  + +G ++l ++++r ++g+++   +G l  + a+v+++s  ++l
  gi|313117381|ref|YP_004044364.1| 387 NGQVA--VYGN--SISARNAEITTNSEIVLN--TENGHIDLVDSTVRSTNGEIKISsDGLLDATRATVETNSD-ISL 456
                                       23443..3333..366666666666666665..689***************666555**********977775.999 PP

                             T2SSN 138 gd......lraelsceggqltltlsdqsgpLslegqg 168
                                       g+       +a++s  +g +t++ls +s+ Ls++g++
  gi|313117381|ref|YP_004044364.1| 457 GSvgdmtlTEATVSTVNGGITAQLSRDSATLSVDGTV 493
                                       9987788778899999******************987 PP

>> Sarcoglycan_1  Sarcoglycan complex subunit protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   1.2    0.0027         8     174     218 ..     273     298 ..     181     312 .. 0.47
   2 !    9.5   2.1   0.00019      0.57     131     223 ..     274     360 ..     270     379 .. 0.62
   3 !   10.3   0.6   0.00011      0.33     186     229 ..     396     437 ..     381     459 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0027
                     Sarcoglycan_1 174 dtrlslrgnegvrieakageieatslkdikLkssnGsivLdakgi 218
                                       +   +++ n+                 ++++++++G++ L a++i
  gi|313117381|ref|YP_004044364.1| 273 R--STFETNR-----------------EVSIEAEDGEVSLAASTI 298
                                       1..1333344.................444444444444444433 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                     Sarcoglycan_1 131 tlFsadreevtvgldkgvkkLrvksvetprirseadedLklesdtrlslrgnegvrieakageieatslkdikLkss 207
                                        +F ++re v +++++g  +L+++ + t++ + e++   +++++++ ++r n ++++ a++g+++ +     + +s 
  gi|313117381|ref|YP_004044364.1| 274 STFETNRE-VSIEAEDGEVSLAASTIDTKNGKVEVKGG-RIDAQNS-QFRSNTKIELTAEQGSVSLS---GATVDSV 344
                                       55666666.66666666666666666666655555444.6666664.66666666666666666666...5666666 PP

                     Sarcoglycan_1 208 nGsivLdakgiflknl 223
                                       nG++ + ++++  +n+
  gi|313117381|ref|YP_004044364.1| 345 NGKVEVVGRSVSAPNA 360
                                       6666666666666666 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00011
                     Sarcoglycan_1 186 rieakageieatslkdikLkssnGsivLdakgiflknlrlpiss 229
                                        i+a++ ei+++   +i+L+++nG+i L  ++++ +n +++iss
  gi|313117381|ref|YP_004044364.1| 396 SISARNAEITTN--SEIVLNTENGHIDLVDSTVRSTNGEIKISS 437
                                       699*********..**************9999999999999998 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00011      0.31      22      92 ..      65     136 ..      63     141 .. 0.93
   2 ?   -2.2   0.1       1.6   4.8e+03      55      70 ..     397     412 ..     359     436 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                       EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  22 GssaerlLtveNpseepaevkvskvpaaekgfsveete..levqpgesvtltvtwtPteegavrevLqflvnd 92 
                                       G+s ++   ++N+ + + +v ++ ++ ++ ++s+++t+  ++++ g++  +  + +P   g+ +++L+++vn+
  gi|313117381|ref|YP_004044364.1|  65 GNSGTAIASLVNNLDSDMTVSYEASV-DTDAVSLKTTSetTTIDRGSQERIFASCNPPNGGSGTATLTVTVNE 136
                                       7888899999***************9.9999999999989*******************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                                       XXXXXXXXXXXXXXXX CS
                               ASH  55 veetelevqpgesvtl 70 
                                       +++++ e++ +++++l
  gi|313117381|ref|YP_004044364.1| 397 ISARNAEITTNSEIVL 412
                                       4444444444444444 PP

>> DUF945  Bacterial protein of unknown function (DUF945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.3   7.4e-05      0.22     146     263 ..     288     420 ..     261     438 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.4e-05
                            DUF945 146 sseltlpafelkeeggklewsggkvkvdls..kdlkklsgegnldglkleadn....deslelkgltlssdlkrgke 216
                                       ++e++l+a +++ ++gk+e +gg ++ + s  +  +k+ ++++  +++l++++    ++++e+ g + s+ +   ++
  gi|313117381|ref|YP_004044364.1| 288 DGEVSLAASTIDTKNGKVEVKGGRIDAQNSqfRSNTKIELTAEQGSVSLSGATvdsvNGKVEVVGRSVSAPNADIST 364
                                       46677777777778888888899999999955444555555555555666666888899999999999887777766 PP

                            DUF945 217 glyl...Gdsslkiasltvssedqega......elknlsldsssteegdllnstlk 263
                                       + ++   G++ +++   tv+s+++++a      +  n +++++s++  ++ n++++
  gi|313117381|ref|YP_004044364.1| 365 NSEIsliGSNAVTLTGATVDSTNGQVAvygnsiSARNAEITTNSEIVLNTENGHID 420
                                       6666667******************9999999999999999888877776666665 PP

>> Poly_export  Polysaccharide biosynthesis/export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.33     1e+03      48      66 ..     346     364 ..     333     414 .. 0.69
   2 ?    9.0   0.2   0.00053       1.6      32      78 ..     444     488 ..     404     493 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.33
                       Poly_export  48 GkikvaGltveelreeiee 66 
                                       Gk++v G++v+  +++i++
  gi|313117381|ref|YP_004044364.1| 346 GKVEVVGRSVSAPNADIST 364
                                       5566666666555555544 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00053
                       Poly_export  32 qgylVdpdGtIslPllGkikvaGltveelreeieeklskylkdpqvt 78 
                                       ++ +V  + +Isl  +G++ +   tv+ ++  i+++ls+   + +++
  gi|313117381|ref|YP_004044364.1| 444 TRATVETNSDISLGSVGDMTLTEATVSTVNGGITAQLSR--DSATLS 488
                                       5789*********************************77..455544 PP

>> DUF3971  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.22   6.5e+02     193     232 ..     236     275 ..     226     296 .. 0.73
   2 ?    6.5   0.3    0.0018       5.5     173     227 ..     302     356 ..     286     402 .. 0.78
   3 ?    0.6   0.1      0.11   3.3e+02     189     218 ..     404     432 ..     378     482 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.22
                           DUF3971 193 npdleltnvsGeleFdnegltaknlsanllgqplnltikt 232
                                       n d+++++ sG ++F+++g+++ n   ++ g  +  + +t
  gi|313117381|ref|YP_004044364.1| 236 NRDVSIETESGGVTFVDSGVSTTNGEIEIEGSSVVASRST 275
                                       3788999999999999999998887776666666555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0018
                           DUF3971 173 geevkvs.GevtlknnnlslknpdleltnvsGeleFdnegltaknlsanllgqpln 227
                                       +++v+v+ G ++ +n++++ +n+++elt+ +G +++  + +++ n + +++g+ ++
  gi|313117381|ref|YP_004044364.1| 302 NGKVEVKgGRIDAQNSQFR-SNTKIELTAEQGSVSLSGATVDSVNGKVEVVGRSVS 356
                                       3334444268999999999.559999999999999999999999888888887764 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.11
                           DUF3971 189 lslknpdleltnvsGeleFdnegltaknls 218
                                       ++ +n ++ l++ +G ++++++ +++ n  
  gi|313117381|ref|YP_004044364.1| 404 IT-TNSEIVLNTENGHIDLVDSTVRSTNGE 432
                                       33.235555666666666655555554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3095.39
//
Query:       gi|313117382|ref|YP_004044365.1|  [L=386]
Description: signal peptidase I [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-08   31.9   0.5    2.3e-07   30.6   0.0    1.9  2  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
        6.2    7.1  23.3      0.093   13.0   4.0    3.6  4  TrbC           TrbC/VIRB2 family


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   2.6e-11   2.3e-07       1      59 [.      36      99 ..      36     107 .. 0.85
   2 ?   -2.5   0.1      0.59   5.3e+03      27      36 ..     126     135 ..     125     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.6e-11
                                      EXXSSTTCCTXXTTXEEEEECTS...---TTSEEEEEETTCE..-EEEEEEEEETTEEEEE.SS CS
                     Peptidase_S24  1 rvpGdSMeptlldGdlilVdkfs...epkrGdivvfrlpgee..eayiKrviglpgdrvllasn 59
                                      +v+ +SMept+++Gd  +  + +    p++Gd+vvf+  +     ++ +r+++++++ + ++ +
  gi|313117382|ref|YP_004044365.1| 36 YVETGSMEPTMEPGDGFIAVPAVvtpPPESGDVVVFQATELHngGLTTHRIVRRTDEGYITRGD 99
                                      6999***********99999888899**********766666667***********99986654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.59
                                       TTSEEEEEET CS
                     Peptidase_S24  27 rGdivvfrlp 36 
                                       +G++vv+r+ 
  gi|313117382|ref|YP_004044365.1| 126 NGQVVVIRDL 135
                                       7999999975 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.2     0.013   1.2e+02      53      72 ..       7      26 ..       3      37 .. 0.82
   2 ?   13.0   4.0     1e-05     0.093      42      89 ..     135     182 ..     120     184 .. 0.94
   3 ?    4.4   0.1    0.0049        44       6      35 ..     201     230 ..     196     239 .. 0.79
   4 ?   -3.5   0.4       1.4   1.3e+04      24      55 ..     351     356 ..     336     363 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.013
                              TrbC 53 lakviatiaiivaGimlafg 72
                                      + +++ +i i+++G+ml+ +
  gi|313117382|ref|YP_004044365.1|  7 IQYGVLIILIVAVGAMLFGQ 26
                                      7789999********99876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1e-05
                              TrbC  42 lqnivdfltgplakviatiaiivaGimlafgrlswrtlvmvviGivii 89 
                                       l ++ + ++gpl+ +i++i+ ++ + +l++g+ s ++lv + +G++i+
  gi|313117382|ref|YP_004044365.1| 135 LGTVSQIVQGPLVGTIGLIGSAIGSSGLLAGGSSAQSLVFLGVGLIIV 182
                                       67899*****************************************98 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0049
                              TrbC   6 skarrlllalalalvllllaspalAqaagg 35 
                                       + ++  +++++l++++ll+  pa A+    
  gi|313117382|ref|YP_004044365.1| 201 RRSNYIKTTTFLFILSLLVLAPATASMVAP 230
                                       667888999999**********99987654 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 1.4
                              TrbC  24 laspalAqaaggdpvetvlqnivdfltgplak 55 
                                       +                          g +a+
  gi|313117382|ref|YP_004044365.1| 351 I--------------------------GTVAF 356
                                       2..........................22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2381.59
//
Query:       gi|313117383|ref|YP_004044366.1|  [L=199]
Description: hypothetical protein Hbor_31700 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.04   14.2   0.8      0.057   13.7   0.1    1.7  2  DUF3446        Early growth response N-terminal domain
       0.11   12.6   9.9       0.52   10.5   3.3    2.7  2  DUF4232        Protein of unknown function (DUF4232)
          3    8.4   7.3       0.65   10.6   2.4    2.3  3  Cadherin-like  Cadherin-like beta sandwich domain


Domain annotation for each model (and alignments):
>> DUF3446  Early growth response N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.1   6.6e+03      40      43 ..      37      40 ..      20      51 .. 0.43
   2 ?   13.7   0.1   9.6e-06     0.057       7      60 ..      74     127 ..      65     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                           DUF3446 40 ssss 43
                                       s+s
  gi|313117383|ref|YP_004044366.1| 37 VSVS 40
                                      1111 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9.6e-06
                           DUF3446   7 pqtsgsnslwaeellslvsglvgvanppsspsssssssssssssssspslscsv 60 
                                       p  + + s ++ee +  ++++v+++n++s  ss+++  s   ++ +s++ s+++
  gi|313117383|ref|YP_004044366.1|  74 PDGNDGASGFNEEAITTLTDVVTITNNASDGSSATVGVSTDGAADASANGSATL 127
                                       455666899****99999***************999999999999999999887 PP

>> DUF4232  Protein of unknown function (DUF4232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.5    0.0064        38      43     105 ..      15      81 ..      11     113 .. 0.74
   2 ?   10.5   3.3   8.7e-05      0.52      16      98 ..     102     191 ..      89     199 .] 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0064
                           DUF4232  43 lldadgqqvgaaaeregpaavpvtLapGesAyaglrwtnaggdgdgecta..aglrvt.pp.dgtks 105
                                       l+++ g+ vg+ a  + +a+ +v ++  + A+a l++t  +++ ++++ +   +++   p+ ++ +s
  gi|313117383|ref|YP_004044366.1|  15 LVGGGGALVGTGAFTTVSAERTVSVSTAGDASAFLTITGDDEYVTDDSGDgtLTIDLGgPDgNDGAS 81 
                                       7799999999999999999999*********************999999966666666565444444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8.7e-05
                           DUF4232  16 agsryvtltltNtgsrtCtldGyPgVslldadgqqvgaaaeregpaavp......vtLapGesAyaglrwtnaggdg 86 
                                        +   +t+ +   g ++ + +G +++ l d++ + ++ + + +g ++++       tLa GesAy ++++ + +++ 
  gi|313117383|ref|YP_004044366.1| 102 SDGSSATVGVSTDGAADASANGSATLLLQDGNTDVAEVTFSVGGEDTNSigsgsaKTLATGESAYLDVKIDTRQDTL 178
                                       55566777778888888888888888888777655554444444455557777779****************99999 PP

                           DUF4232  87 dgecta.aglrvt 98 
                                       d+  ++   l+++
  gi|313117383|ref|YP_004044366.1| 179 DNSNADtGDLTIV 191
                                       9988887666665 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.4   2.4e+03      39      47 ..      46      54 ..      27      85 .. 0.50
   2 ?   10.6   2.4   0.00011      0.65      26      79 ..      92     147 ..      85     153 .. 0.73
   3 ?    0.6   0.3      0.14   8.4e+02      39      72 ..     138     171 ..     134     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.4
                     Cadherin-like 39 vatvtvngv 47
                                       a +t+ g+
  gi|313117383|ref|YP_004044366.1| 46 SAFLTITGD 54
                                      222233222 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
                     Cadherin-like  26 vdsvtitatae...dsvatvtvngvaveegstetkdvsLneGrnkieikvtaedgst 79 
                                       +d vtit  a+   ++++ v+++g a  +  ++++++ L++G++++  ++++  g++
  gi|313117383|ref|YP_004044366.1|  92 TDVVTITNNASdgsSATVGVSTDGAADAS-ANGSATLLLQDGNTDVAEVTFSVGGED 147
                                       67799999998766677777777776665.69**********888555555555444 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.14
                     Cadherin-like  39 vatvtvngvaveegstetkdvsLneGrnk.ieikv 72 
                                        +t +v g+++++  +  ++ +L  G++  +++k+
  gi|313117383|ref|YP_004044366.1| 138 EVTFSVGGEDTNS-IGSGSAKTLATGESAyLDVKI 171
                                       5677788888887.477777777777776755554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1414.23
//
Query:       gi|313117384|ref|YP_004044367.1|  [L=248]
Description: hypothetical protein Hbor_31710 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1613.31
//
Query:       gi|313117385|ref|YP_004044368.1|  [L=204]
Description: hypothetical protein Hbor_31720 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1384.82
//
Query:       gi|313117386|ref|YP_004044369.1|  [L=188]
Description: hypothetical protein Hbor_31730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   13.9   0.4      0.047   13.4   0.4    1.2  1  HlyIII    Haemolysin-III related


Domain annotation for each model (and alignments):
>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   2.6e-06     0.047      27      67 ..     137     178 ..     121     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-06
                            HlyIII  27 llslaevken.sklakvvvlvfllgallcllcSalyHtlsih 67 
                                       ++++a+++    +++ +++lv+   +++++++Sa+yHt++  
  gi|313117386|ref|YP_004044369.1| 137 CVIIAALWLEvLPTDSIPMLVYPTLIVVLFTVSAVYHTVDNY 178
                                       2333333333457889**********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1397.36
//
Query:       gi|313117387|ref|YP_004044370.1|  [L=340]
Description: hypothetical protein Hbor_31740 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-46  158.5   0.2    7.6e-45  153.0   0.0    2.2  2  DUF5305   Family of unknown function (DUF5305)
  ------ inclusion threshold ------
      0.053   13.6   0.2        2.2    8.3   0.1    2.2  2  T2SSM     Type II secretion system (T2SS), protein M
       0.12   12.1   0.7        0.3   10.7   0.4    1.8  2  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   0.1    0.0074        45     111     148 ..      13      51 ..       4      62 .. 0.68
   2 !  153.0   0.0   1.3e-48   7.6e-45       1     219 []     125     327 ..     125     327 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0074
                           DUF5305 111 pslae.gilliilgllaliglvvlirriiftsskaekye 148
                                       ++++e +++l+++g+++li++ +++++   t   ++   
  gi|313117387|ref|YP_004044370.1|  13 RQTRElVAVLVLAGIICLIAAGYIFLTPTTTVVSEDTNL 51 
                                       555666778888888888888888777666555555555 PP

  == domain 2  score: 153.0 bits;  conditional E-value: 1.3e-48
                           DUF5305   1 Wekeeplasettqeveskeltisesvsinlseyndrieeieeelglsvgtseltvvlevnvegeidgesieesktsr 77 
                                       ++++++l++++t++++++   ++++++in s++++r++e+++e+g +vg+ +++++l+v++e     +++e++ ++ 
  gi|313117387|ref|YP_004044370.1| 125 YRTNRTLIDRQTTVTDGN---ATAEATINASALRQRLQEMRTEVG-GVGQFQVELDLNVSYES----DRYEGTLKDG 193
                                       8999*********99988...999*********************.999**************....********** PP

                           DUF5305  78 lpiplteqtyeikkdetdeengeitetvtvkespslaegilliilgllaliglvvlirriiftsskaekyeleleki 154
                                        p+ l++q+y +++ +++++++++ +t++++++p+++e +++ +lgl+  +gl++++r+     ++a+ ++l+++ i
  gi|313117387|ref|YP_004044370.1| 194 SPLALSGQAYYLEDGLQADTTRRTPVTKEIQQPPTMLEYGGIGVLGLVL-FGLAAVARN---VGRDADTERLRTNII 266
                                       **************************************55555555554.556665566...68899999******* PP

                           DUF5305 155 lkeYdewIvkgslppdlgdekvievdsledLvdvaielnepvlydeeedeegkFvvvddevvYvY 219
                                       ++++dewI++g+ p++ +++ +i++ +ledLvdvai+++++v++d++ d    ++v+d++++Y+Y
  gi|313117387|ref|YP_004044370.1| 267 HDRHDEWISRGEFPTESEKQ-YISILTLEDLVDVAIDSGRRVIFDPDLD---AYAVIDGDEIYHY 327
                                       *****************877.****************************...************9 PP

>> T2SSM  Type II secretion system (T2SS), protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.016        94      10      65 ..      12      69 ..       7      82 .. 0.69
   2 ?    8.3   0.1   0.00037       2.2      72     114 ..     134     176 ..     125     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.016
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXX CS
                             T2SSM 10 glspRErrllaalglvlllallylllwqPlse..rieraqaelqklraqlawveeqaa 65
                                      ++++RE  ++++l+ +++l    +++++P ++   +++  +++++  ++ a v+ + +
  gi|313117387|ref|YP_004044370.1| 12 ARQTRELVAVLVLAGIICLIAAGYIFLTPTTTvvSEDTNLQTFETDVKTSAVVTGNTT 69
                                      6899*****9999999999888888888877622345555566666666666665555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00037
                                       XXXXXXXXX--HHHHHHHHHHHCT--EEEEEEETT.EEEEEE- CS
                             T2SSM  72 aapasalsgaaleqvvtrsarqagLalarlqpqgdgsvqvwle 114
                                       ++ +++  +a  e+ +++sa ++ L+  r +  g g++qv+l+
  gi|313117387|ref|YP_004044370.1| 134 RQTTVTDGNATAEATINASALRQRLQEMRTEVGGVGQFQVELD 176
                                       5677778888999****************************98 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4     5e-05       0.3      27     118 ..      16     105 ..       7     117 .. 0.74
   2 ?   -2.3   0.0      0.52   3.1e+03      10      24 ..     235     249 ..     227     264 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5e-05
                           DUF4131  27 rprrrvllllllllllallgfalrapqpnandlsqllesgqeviveGvvaslpeltgsgtrfvlevervlsagktkp 103
                                       r    vl+l+++++l+a+++++l+  ++ +++  +l + +++v   +vv+ +  l+++g   +l+ ++v   ++t +
  gi|313117387|ref|YP_004044370.1|  16 RELVAVLVLAGIICLIAAGYIFLTPTTTVVSEDTNLQTFETDVKTSAVVTGNTTLYERGE--TLQNRSVYFISATPN 90 
                                       444456888888888888888887777666555444444999999999999999999999..778888888888888 PP

                           DUF4131 104 vsgrvlvtvpkspae 118
                                       v+ +v+ +vp +++ 
  gi|313117387|ref|YP_004044370.1|  91 VTFQVRTSVPPDQRV 105
                                       888888888877765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.52
                           DUF4131  10 lalllllllllllll 24 
                                       +++l+l+l+ l+++ 
  gi|313117387|ref|YP_004044370.1| 235 IGVLGLVLFGLAAVA 249
                                       444555555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2150.90
//
Query:       gi|313117388|ref|YP_004044371.1|  [L=299]
Description: hypothetical protein Hbor_31750 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.6   0.8        1.2    9.2   0.0    2.3  2  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2     0.058     1e+03      18      35 ..      31      49 ..      28      62 .. 0.66
   2 ?    9.2   0.0   6.5e-05       1.2       4      37 ..     113     146 ..     110     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.058
                            OppC_N 18 vglvilll.llliaifaPl 35
                                      +gl++  + l++++i a l
  gi|313117388|ref|YP_004044371.1| 31 FGLFFTGVgLVIVSIAAFL 49
                                      6777777756666665533 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 6.5e-05
                            OppC_N   4 qdawrrFkrNklAvvglvilllllliaifaPlia 37 
                                       q  w+  ++N   vvgl  l +++++a  +  ++
  gi|313117388|ref|YP_004044371.1| 113 QIYWQHWFQNSSFVVGLYALGAVIVVATAGTALS 146
                                       677999********************98887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1801.10
//
Query:       gi|313117389|ref|YP_004044372.1|  [L=395]
Description: hypothetical protein Hbor_31760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0016   18.9   0.0      0.005   17.2   0.0    1.8  2  FtsA        Cell division protein FtsA
  ------ inclusion threshold ------
        5.9    5.6   8.0          8    5.1   8.0    1.2  1  NPR3        Nitrogen Permease regulator of amino acid transpo


Domain annotation for each model (and alignments):
>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.45     4e+03      70      86 ..      61     104 ..      26     130 .. 0.59
   2 !   17.2   0.0   5.6e-07     0.005       3     103 .]     171     316 ..     169     316 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.45
                                       H...........................GGGGSTTHHHHHHHHH CS
                                       x...........................xxxxxxxxxxxxxxxx RF
                              FtsA  70 s...........................ggsalpnleelaeral 86 
                                                                   ++sa+p ++ + e+++
  gi|313117389|ref|YP_004044372.1|  61 VgddalnfanifnketrrpmeqgilsseEASAIPMIKLITEQVV 104
                                       04444444444444555555555555666777777777777773 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.6e-07
                                       EEE-SSSEEEEEEETTEEEEEEEES-....-HHHHHHHHHHHHT--HHHHHHHHHHH--S--............... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                              FtsA   3 vDiGagktdvavaedgalvhlrvigv....ggngitkdiakalrtaveeAerikikyGsala............... 60 
                                       v +Gag+t++ +       ++ v ++    gg+ i+k +a+a +t+v++  +ik +                     
  gi|313117389|ref|YP_004044372.1| 171 VSFGAGMTNICLSYY----AVPVMKFsiarGGDWIDKQAAQATGTPVDKVTSIKED-----Dfvldfrtdvggiega 238
                                       667888887777777....33444444455************************32.....1223355555555555 PP

                                       ................EEEEEHHHHH...................GGGGSTTHHHHHHHHH....T-.....HH.HT CS
                                       ................xxxxxxxxxx...................xxxxxxxxxxxxxxxx....xxx...xxx.xx RF
                              FtsA  61 ................ekeigrkels...................ggsalpnleelaeral....spk...lee.vs 94 
                                                                +                   g+s   ++eel+++ l     p    +++ v+
  gi|313117389|ref|YP_004044372.1| 239 lsiyyenlldyvveniA--------AqvdegdveeeldvpvvvtgGTSRPDGFEELFAKHLedveIPFsisDVQsVD 307
                                       55566666666655553........0444555558888999999****************855552226665666** PP

                                       -GGGHHHHH CS
                                       xxxxxxxxx RF
                              FtsA  95 dpeyasalg 103
                                       dp y++a g
  gi|313117389|ref|YP_004044372.1| 308 DPLYSVARG 316
                                       ****99976 PP

>> NPR3  Nitrogen Permease regulator of amino acid transport activity 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   8.0   0.00089         8      52     102 ..     337     387 ..     298     395 .] 0.43

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00089
                              NPR3  52 kkskrkrssrskekkskesskksesssksesseekksskeseeseekesne 102
                                       ++  r++s++++++++++ss+++++ss+s+ss+++ s+++s+++++++++e
  gi|313117389|ref|YP_004044372.1| 337 SSGTRSSSGKRSSASKRSSSTSTSTSSSSTSSTSTPSTNSSSADNSTSTSE 387
                                       222333333333333333333333333332222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1489  (0.0830498); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                       161  (0.00897987); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2456.12
//
Query:       gi|313117390|ref|YP_004044373.1|  [L=121]
Description: hypothetical protein Hbor_31770 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00068   19.4   2.5     0.0015   18.3   2.5    1.6  1  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
    0.00079   18.7   1.5     0.0015   17.8   1.5    1.5  1  zf-TFIIB         Transcription factor zinc-finger
  ------ inclusion threshold ------
      0.016   15.6   0.5      0.023   15.0   0.5    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.026   14.5   0.8      0.042   13.8   0.8    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.059   13.2   0.1      0.075   12.9   0.1    1.3  1  zf-RING_6        zf-RING of BARD1-type protein


Domain annotation for each model (and alignments):
>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   2.5   4.2e-07    0.0015       4      27 ..       3      27 ..       3      28 .. 0.98

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.2e-07
                                      -TTT--BBEEEEC.TTEEEEE-TTT CS
                      zf-FPG_IleRS  4 CpRCwryiervgq.agrstyfCprC 27
                                      CpRC + ++++++ +g   ++C rC
  gi|313117390|ref|YP_004044373.1|  3 CPRCENSLSTIVIqGGGEAVYCKRC 27
                                      ************************* PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.5   4.3e-07    0.0015       1      26 [.       2      28 ..       2      28 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.3e-07
                          zf-TFIIB  1 kCPkCqdeleeser.ggveidyCpqCr 26
                                      +CP+C ++l ++   gg e  yC +Cr
  gi|313117390|ref|YP_004044373.1|  2 DCPRCENSLSTIVIqGGGEAVYCKRCR 28
                                      6*******996666377*********8 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.5   6.6e-06     0.023       5      56 ..       2      51 ..       1      57 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.6e-06
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga..stpwfkiaedeaeaekeaie 56
                                      +CP C +    +  q++ +     vyC+ C +  ++++++  +   e+ ++ai 
  gi|313117390|ref|YP_004044373.1|  2 DCPRCENSLSTIVIQGGGE----AVYCKRCRYadVESEYEPSDTPRETWDDAIR 51
                                      6*************99999....9********7766666666666666666665 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   1.2e-05     0.042      21      45 ..       3      29 ..       1      30 [. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                     Zn_Tnp_IS1595 21 CPhCgsr.kayrikt.rglfqCkeCrk 45
                                      CP+C+++ + + i++  +   Ck+Cr+
  gi|313117390|ref|YP_004044373.1|  3 CPRCENSlSTIVIQGgGEAVYCKRCRY 29
                                      ***************988999****98 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.1e-05     0.075       9      36 ..       2      29 ..       1      59 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                         zf-RING_6  9 rcsrctdilrepvclggcehifcsncis 36
                                       c rc + l   v  gg e ++c  c  
  gi|313117390|ref|YP_004044373.1|  2 DCPRCENSLSTIVIQGGGEAVYCKRCRY 29
                                      69***********************964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 806.23
//
Query:       gi|313117391|ref|YP_004044374.1|  [L=697]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-22   79.2   0.0    6.1e-22   77.2   0.0    2.2  2  HTH_10      HTH DNA binding domain
    3.2e-19   69.3   3.8    3.2e-19   69.3   3.8    2.9  4  BAT         GAF and HTH_10 associated domain
    7.9e-13   48.9   3.5    3.2e-08   34.0   0.2    2.7  2  GAF_2       GAF domain
    2.3e-08   34.4   0.7     0.0089   16.4   0.1    2.6  2  GAF_3       GAF domain
    6.3e-05   22.8   0.0    0.00027   20.8   0.0    2.2  1  HTH_1       Bacterial regulatory helix-turn-helix protein, ly
    0.00012   22.8   0.2    0.00048   20.8   0.1    2.1  2  GAF         GAF domain
    0.00039   19.9   0.0     0.0012   18.3   0.0    1.9  1  Sigma70_r4  Sigma-70, region 4
     0.0017   17.9   0.0       0.13   11.8   0.0    3.1  2  GerE        Bacterial regulatory proteins, luxR family
     0.0053   16.6   0.0      0.013   15.3   0.0    1.6  1  HTH_5       Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.033   13.7   0.0      0.083   12.5   0.0    1.7  1  HTH_24      Winged helix-turn-helix DNA-binding
      0.039   13.9   0.0        0.1   12.5   0.0    1.7  2  DUF5119     Domain of unknown function (DUF5119)
       0.17   11.3   0.2       0.27   10.6   0.2    1.3  1  MSC         Man1-Src1p-C-terminal domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.9   4.4e+03       1      10 [.     446     455 ..     446     459 .. 0.89
   2 !   77.2   0.0   4.1e-25   6.1e-22       1      52 [.     637     688 ..     637     689 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.9
                            HTH_10   1 LTdkqlevlk 10 
                                       +T+++l+vl 
  gi|313117391|ref|YP_004044374.1| 446 FTERELSVLN 455
                                       7******996 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 4.1e-25
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd+q+evl+ A+++GY+d+PR+ ++k++A+ l+Is++t+s+hLr+ae+kl+
  gi|313117391|ref|YP_004044374.1| 637 LTDRQYEVLRCAFDNGYYDWPRNKSAKDVAEMLDISQPTFSQHLRAAEQKLL 688
                                       9*************************************************98 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.2   3.2e+03      53      84 ..      27      58 ..      20      63 .. 0.66
   2 ?   -1.8   0.1       1.7   2.5e+03      69      85 ..     148     164 ..     114     197 .. 0.77
   3 ?   -2.4   0.2       2.6   3.9e+03      58      78 ..     398     417 ..     356     432 .. 0.69
   4 !   69.3   3.8   2.2e-22   3.2e-19       4     141 ..     480     616 ..     478     625 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                               BAT 53 eevrdaaedldavedvrvvseeddgtlleltv 84
                                       e++ +a+ ++ ++d  v+ + d++++ +l+ 
  gi|313117391|ref|YP_004044374.1| 27 REATYLADGIVEIDDNLVIVDADEKARARLEA 58
                                      55666777777777777777777776666654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                               BAT  69 rvvseeddgtlleltvs 85 
                                       ++++e+dd+ l el+++
  gi|313117391|ref|YP_004044374.1| 148 ELLRERDDDRLAELALD 164
                                       67889999999999873 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.6
                               BAT  58 aaedldavedvrvvseeddgt 78 
                                       +a++ ++ve+   ++++d+ +
  gi|313117391|ref|YP_004044374.1| 398 VAQNAVSVEEWKRIETTDT-A 417
                                       4556666777777766665.3 PP

  == domain 4  score: 69.3 bits;  conditional E-value: 2.2e-22
                               BAT   4 veLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtll 80 
                                       ++L+++++d++++lv++++  +  + ++++  ++ ++  v+f ++g+ +e++ d + ++dav+  +vv+ + dg+l+
  gi|313117391|ref|YP_004044374.1| 480 IQLKVRVNDDTHPLVEVSRFDETDIVVDHIEFDHANGIQVYFDTAGERAERFLDELGEHDAVAGSEVVTNRRDGALV 556
                                       78*************************************************************************** PP

                               BAT  81 eltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvar 141
                                        l + +++l+++l + +  + s+ a++ ++ +++ vP+++  R ++ alee+++dv+Lv+r
  gi|313117391|ref|YP_004044374.1| 557 NLVL-TDDLLTALISLDLHIASVKADEQGVIVTLTVPQNVSPRGILTALEEQFSDVSLVSR 616
                                       ****.789****************************************************8 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   1.5e-05     0.023       3     134 ..     154     279 ..     152     282 .. 0.66
   2 !   34.0   0.2   2.1e-11   3.2e-08       3     137 ..     326     465 ..     324     465 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHHH.SS..EEEEEEE-.TTS-....EEEEEEEES-TTSTT-S-B--..-TTHHHHHHHHTS-EEE CS
                             GAF_2   3 dleelldlvldelve.lgaalgyillvd.ddgg....lrlaawgeaeeefgaaldrpl..geglvgealrtgrpvil 71 
                                       d + l++l+ld++v   +a  g i+l d d+++    ++   ++ a+ ++ +  ++p+  ge++++e+l+ g+  + 
  gi|313117391|ref|YP_004044374.1| 154 DDDRLAELALDAIVGdSNALSGRIYLADwDETErrseVT--LRAAATVGDEQPYPDPIerGESVIWEVLKLGQQRY- 227
                                       5678999******88347889999998864433333333..34444444444444455447778999999998555. PP

                                       S-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES.......--HHHHHHHHHHHHHHH CS
                             GAF_2  72 ndleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppa.fdeedlelLeelaeqia 134
                                              ++ ++  + ++ +++l+vP+   g  +Gvl+l ++ ++  f e++ +  + +a++ a
  gi|313117391|ref|YP_004044374.1| 228 -------RSLSADVSSEPDAAELFVPI---G-RYGVLVLRSSSEQItF-EQHEHATSIVASLTA 279
                                       .......34455578899999******...9.*******555554424.666666666665544 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 2.1e-11
                                       HHHHHHHHHHHHHHHS.S...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--....-TT.HHHHHHHHTS-EEES CS
                             GAF_2   3 dleelldlvldelvel.g.aalgyillvdddgglrlaawgeaeeefgaaldrpl....geg.lvgealrtgrpviln 72 
                                        ++ell+ v+++l ++ +  a ++  ++   + l ++++++a  + ++++  +l      + l ++al  + +v+ +
  gi|313117391|ref|YP_004044374.1| 326 RIDELLQCVVEQLSDTeTyYASAFARYDPVSETLSYVTSSGALSFTDDEI--ALadetPLSdLGQRALDRQSAVVAQ 400
                                       789************97755556666655667777775555555555555..33212222335569999999***99 PP

                                       -.GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  73 d.leedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       + +  ++ k+ +  + a++ s +a+P+++ + v+Gv  l +++ ++f+e++l++L+el++ ++ a+
  gi|313117391|ref|YP_004044374.1| 401 NaVSVEEWKRIETTDTAAVESVAALPVVHHNLVYGVCYL-FAETDSFTERELSVLNELSSMLGYAV 465
                                       97666666666669999999*********889******9.788888**************999885 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.7e-06     0.013      31     112 ..     190     266 ..     160     282 .. 0.81
   2 !   16.4   0.1     6e-06    0.0089      49     126 ..     376     464 ..     326     465 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.7e-06
                             GAF_3  31 gnklqvaagw.dgkpalsesldedsalarralssgevvsepsfaeedglpdraalavPLvagrqviGvlalastkpr 106
                                       + +l++aa   d++p +   +++++++++++l+ g+  +   +a+ ++ pd+a l+vP+ +    +Gvl+l+s++++
  gi|313117391|ref|YP_004044374.1| 190 EVTLRAAATVgDEQPYP-DPIERGESVIWEVLKLGQQRYRSLSADVSSEPDAAELFVPIGR----YGVLVLRSSSEQ 261
                                       34566666667888887.6****************98777777999***************....********9966 PP

                             GAF_3 107 afdaed 112
                                        ++ e+
  gi|313117391|ref|YP_004044374.1| 262 -ITFEQ 266
                                       .65554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6e-06
                             GAF_3  49 sldedsalar...ralssgevvse.........psfaeedglpdraalavPLvagrqviGvlalastkprafdaedl 113
                                       +l  +++l++   ral+++ +v++         ++ + +d+   +++ a+P+v+++ v+Gv +l    + +f++++l
  gi|313117391|ref|YP_004044374.1| 376 ALADETPLSDlgqRALDRQSAVVAqnavsveewKRIETTDTAAVESVAALPVVHHNLVYGVCYLFAETD-SFTEREL 451
                                       44445555544446666666555544433334444467888999999*******99*******977664.5****** PP

                             GAF_3 114 elleslArqiata 126
                                       + l++l++ ++ a
  gi|313117391|ref|YP_004044374.1| 452 SVLNELSSMLGYA 464
                                       *******988866 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.8e-07   0.00027      12      47 ..     658     693 ..     657     696 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.8e-07
                                       HHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEE CS
                             HTH_1  12 eegsftrAAeeLglsqpavsrqikrLEeelgvpLfe 47 
                                       +++s    Ae L +sqp+ s+++++ E+ l ++Lf+
  gi|313117391|ref|YP_004044374.1| 658 RNKSAKDVAEMLDISQPTFSQHLRAAEQKLLDQLFT 693
                                       57889999**************************97 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         3   4.4e+03     102     125 ..     250     277 ..     183     284 .. 0.76
   2 !   20.8   0.1   3.2e-07   0.00048       3     132 ..     328     464 ..     310     465 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3
                                       EEEEEEEESSS..CS..HHHHHHHHHHH CS
                               GAF 102 wGllvlhnpsp..pf..treelellqvl 125
                                       +G+lvl + s+   f  ++++  ++ +l
  gi|313117391|ref|YP_004044374.1| 250 YGVLVLRSSSEqiTFeqHEHATSIVASL 277
                                       6888888866656554455555555444 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3.2e-07
                                       HHHHHHHHHHHHHHHTESEEEEEE...EEETTEEE.CEEEEECC......EEEETTSHHHH........HHHHHSSS CS
                               GAF   3 eelldtvveelrellgadrvalyl...pdydGlhy.dipqasrw......lfmkngrgicg........qvlatgqp 61 
                                       +ell+ vve+l+++  + +++++    p ++ l y   + a+++      l         +        q +  +q+
  gi|313117391|ref|YP_004044374.1| 328 DELLQCVVEQLSDTETY-YASAFArydPVSETLSYvTSSGALSFtddeiaLA--------DetplsdlgQRALDRQS 395
                                       55666666666655444.3333221223333333331222333333333211........11112223388888999 PP

                                       EEESTGGTSTTHHTT.HHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCSHHHHHHHHHHHHHHHHHH CS
                               GAF  62 lvipdstpdprfaqy.nrrdllenmgirsslvvPlvndgelwGllvlhnpsppftreelellqvladqvava 132
                                        v++   +     +  +r ++ +   + s++++P+v+++ ++G+ +l  ++++ft+ el +l +l+++++ a
  gi|313117391|ref|YP_004044374.1| 396 AVVA---QNAVSVEEwKRIETTDTAAVESVAALPVVHHNLVYGVCYLFAETDSFTERELSVLNELSSMLGYA 464
                                       9999...444444444669999***************************9999*************999877 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.1e-07    0.0012       4      48 ..     636     687 ..     635     688 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.1e-07
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                        L++r+ evl++ f        ++ + ++++e+l+iS+ + +q+++ A +kL
  gi|313117391|ref|YP_004044374.1| 636 ALTDRQYEVLRCAFdngyydwPRNKSAKDVAEMLDISQPTFSQHLRAAEQKL 687
                                       79***************99988999**********************99987 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0       0.1   1.5e+02       1      14 [.     444     457 ..     444     465 .. 0.89
   2 !   11.8   0.0   8.8e-05      0.13       2      45 ..     636     687 ..     635     688 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.1
                                       CSS-HHHHHHHHHH CS
                              GerE   1 ssLskRErevLrll 14 
                                       +s+++RE++vL  l
  gi|313117391|ref|YP_004044374.1| 444 DSFTERELSVLNEL 457
                                       589********876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.8e-05
                                       SS-HHHHHHHHHHCT.T.......S-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE   2 sLskRErevLrllae.G.......ksnkeIAeelniSekTVkvhksnimkKL 45 
                                        L++R+ evLr+  + G       ks k++Ae l+iS+ T + h++ + +KL
  gi|313117391|ref|YP_004044374.1| 636 ALTDRQYEVLRCAFDnGyydwprnKSAKDVAEMLDISQPTFSQHLRAAEQKL 687
                                       58888888888866423333333389***********************998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.8e-06     0.013      16      38 ..     660     682 ..     657     684 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.8e-06
                                       EEHHHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  16 lcvcelaeelglsqstvShHLkk 38 
                                       +++ + ae+l++sq+t S+HL++
  gi|313117391|ref|YP_004044374.1| 660 KSAKDVAEMLDISQPTFSQHLRA 682
                                       678999***************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.5e-05     0.083      19      43 ..     661     685 ..     657     686 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                            HTH_24  19 sqreLAerlglSpstvnrrlkrLee 43 
                                       s +++Ae+l++S++t +++l+  e+
  gi|313117391|ref|YP_004044374.1| 661 SAKDVAEMLDISQPTFSQHLRAAEQ 685
                                       779******************9887 PP

>> DUF5119  Domain of unknown function (DUF5119)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.9e-05       0.1      56     109 ..     240     292 ..     223     313 .. 0.80
   2 ?   -3.0   0.0       3.9   5.8e+03      29      43 ..     495     526 ..     470     538 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.9e-05
                           DUF5119  56 ggevslpeGrYrvvvyNndtesvlirgedsyetieaytrtaasklsskgeese..e 109
                                         e+ +p GrY v+v+ ++ e++++++ ++ ++i a  + a   l+ +g+e +  e
  gi|313117391|ref|YP_004044374.1| 240 AAELFVPIGRYGVLVLRSSSEQITFEQHEHATSIVASLTAA---LETAGHERQlrE 292
                                       478899*****************************999998...555555554433 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.9
                           DUF5119  29 e..................PegmrvifYpkdgg 43 
                                       e                  ++g++v+f ++ g+
  gi|313117391|ref|YP_004044374.1| 495 EvsrfdetdivvdhiefdhANGIQVYF-DTAGE 526
                                       333444444444445555567888876.44444 PP

>> MSC  Man1-Src1p-C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00018      0.27      98     178 ..     267     347 ..     262     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                               MSC  98 erkvkevakkalelLreknakvecgeskddeekakksglseeeLkeslsekksksiskeefeelwkealkeLkkeee 174
                                        ++   ++ +++  L++   +++ +e+++  e +k++ l+++ L e l+e +++ i  + ++el++ ++++L+++e 
  gi|313117391|ref|YP_004044374.1| 267 HEHATSIVASLTAALETAGHERQLREQQAVLERQKRKLLTVARLNELLREVNRSIIGADRIDELLQCVVEQLSDTET 343
                                       67778899999999999999*******9999889****************999********************9987 PP

                               MSC 175 ivvr 178
                                        + +
  gi|313117391|ref|YP_004044374.1| 344 YYAS 347
                                       6544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 4343.54
//
Query:       gi|313117392|ref|YP_004044375.1|  [L=98]
Description: hypothetical protein Hbor_31790 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-18   64.3   0.0    1.1e-17   64.1   0.0    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   5.9e-22   1.1e-17       3      73 ..      22      93 ..      20      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 5.9e-22
                            HalOD1  3 espstaVveavaavegvdptelepLydaiDpdALdaLfasradgearad.gsvsFtyegyeVtVrsdgeieV 73
                                      e++s+aV+eav++++ +d  +l+pL d i+  AL++Lf  +  ++ + + g+++Fty+g++VtV++ g i+V
  gi|313117392|ref|YP_004044375.1| 22 EPVSEAVIEAVSELKACDKNDLPPLSDRINRSALNSLFGGEGPQQPKINrGELTFTYDGVRVTVDAIGMIRV 93
                                      89**************************************5554433335********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 763.99
//
Query:       gi|313117393|ref|YP_004044376.1|  [L=642]
Description: Chromosome segregation protein (Spc25, Csm1, Pcs1) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-06   28.0  63.0    0.00029   21.0   6.1    5.6  6  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
    3.8e-06   27.6  24.8    3.8e-06   27.6  24.8    4.8  2  AAA_23           AAA domain
    4.1e-05   23.1  56.1     0.0059   16.0  24.4    3.2  3  DUF4407          Domain of unknown function (DUF4407)
    6.3e-05   22.0  80.2     0.0098   14.8  27.0    4.1  4  Spc7             Spc7 kinetochore protein
    0.00012   22.2  44.8      0.025   14.6   4.4    6.0  6  DUF1664          Protein of unknown function (DUF1664)
    0.00014   21.8  77.9     0.0069   16.2  30.1    2.4  2  ERM              Ezrin/radixin/moesin family
     0.0016   17.9  71.0     0.0035   16.7  11.6    4.1  4  GAS              Growth-arrest specific micro-tubule binding
     0.0038   16.6  11.7     0.0038   16.6  11.7    4.3  4  HemX             HemX, putative uroporphyrinogen-III C-methyl
     0.0059   16.9  87.3      0.038   14.2  27.6    5.2  4  ATG16            Autophagy protein 16 (ATG16)
     0.0094   16.1  14.2     0.0094   16.1  14.2    4.9  4  UPF0242          Uncharacterised protein family (UPF0242) N-t
  ------ inclusion threshold ------
      0.027   13.6  64.3       0.22   10.6   4.0    4.2  4  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.077   13.4  55.8      0.038   14.4   5.8    6.2  6  Snapin_Pallidin  Snapin/Pallidin
      0.095   12.8  92.2          1    9.4  21.2    5.4  5  DHR10            Designed helical repeat protein 10 domain
       0.15   11.9   0.2       0.15   11.9   0.2    5.7  5  HSBP1            Heat shock factor binding protein 1
       0.22   11.3  63.3        2.1    8.1  13.8    4.9  4  DUF4201          Domain of unknown function (DUF4201)
       0.35   10.9  46.0       0.19   11.8   2.5    4.9  5  Laminin_II       Laminin Domain II
          1    9.9  98.0       0.22   12.1  41.3    5.6  5  APG6_N           Apg6 coiled-coil region
        1.2    9.4  27.3        1.5    9.1   1.9    5.5  4  DUF948           Bacterial protein of unknown function (DUF94
        1.4    7.5  52.6      0.037   12.7  12.9    2.6  2  MAP65_ASE1       Microtubule associated protein (MAP65/ASE1 f
        2.1    8.4  82.3       0.99    9.5   7.0    5.1  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        2.5    6.3  68.0        1.8    6.8  21.3    2.4  2  MAD              Mitotic checkpoint protein
        3.4    8.1   8.6         24    5.4   0.1    4.4  4  IMPa_helical     Immunomodulating metalloprotease helical dom
        4.3    7.7  52.4       0.96    9.8   4.1    6.3  6  BLOC1_2          Biogenesis of lysosome-related organelles co
        4.6    4.6  72.1       0.51    7.8  24.2    2.6  3  DUF3584          Protein of unknown function (DUF3584)
          5    7.7  37.7        3.6    8.1   1.3    6.6  4  NPV_P10          Nucleopolyhedrovirus P10 protein
        5.4    6.4  84.0        1.6    8.2  30.1    3.7  4  Golgin_A5        Golgin subfamily A member 5
        7.4    6.2  37.5         15    5.1  19.5    3.2  2  AAA_15           AAA ATPase domain
        8.9    6.3  88.1       0.21   11.6  10.7    4.6  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
        9.6    4.9  74.7        5.3    5.8  21.8    2.2  2  CALCOCO1         Calcium binding and coiled-coil domain (CALC


Domain annotation for each model (and alignments):
>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   6.1   4.7e-07   0.00029      22      99 ..     118     196 ..     111     202 .. 0.90
   2 !   12.2   8.2   0.00025      0.16      29      98 ..     164     233 ..     161     239 .. 0.90
   3 ?    3.2   7.5      0.16        99      44     104 ..     224     284 ..     195     287 .. 0.45
   4 !    8.8   1.7    0.0029       1.8      12      63 ..     237     288 ..     224     313 .. 0.77
   5 ?    6.2  13.8      0.02        12      39     103 ..     352     416 ..     333     433 .. 0.53
   6 !   10.5  13.4   0.00089      0.55      29      97 ..     433     501 ..     428     507 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.7e-07
                                       T.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  22 g.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleael 97 
                                         ++ ad+ e+l       ++++e+++l++er ++  eI++++  ++++  l ++ +++ke +++l ++ +el+ae+
  gi|313117393|ref|YP_004044376.1| 118 AvVAGADLREILMRPVDTVAIESEIQSLKSERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAEI 194
                                       35677888899999999999********************************************************9 PP

                                       HH CS
                      Seryl_tRNA_N  98 ek 99 
                                       e+
  gi|313117393|ref|YP_004044376.1| 195 EA 196
                                       86 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaele 98 
                                       de+  l+++r +++ ++eel  +r el++eI+   ++  + +e +ae +e+ e+l+ +  +lk ++ +le
  gi|313117393|ref|YP_004044376.1| 164 DEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQTENKAELDEILEKLQSARSDLKSVRFRLE 233
                                       799999****************************999999999*************99999999876665 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  44 eleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                       +l +++ +  +  ++I+++ ++  ++++ ++  +e   e+k++e + ++ + ++++l ++i
  gi|313117393|ref|YP_004044376.1| 224 DLKSVRFRLESERESIESLRDERTETSDELDALSETDYETKQIESQIEQTRGRIDELNRTI 284
                                       3333333334444444444444444444444444444444444444444444444444444 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0029
                                       HHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC CS
                      Seryl_tRNA_N  12 eavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkak 63 
                                       e ++    +R e + ++d+l e d + +++++++e+ + +  el+++I  + 
  gi|313117393|ref|YP_004044376.1| 237 ESIESLRDERTETSDELDALSETDYETKQIESQIEQTRGRIDELNRTITDLQ 288
                                       4444445567799999999999999999999999999999999999998765 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  39 relqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekllla 103
                                        e++ + eel+++  el  e  +  +++   eel ++ + l +e+++ +a+++el++e ++l  +
  gi|313117393|ref|YP_004044376.1| 352 DEHRERREELRNRLEELDSELREVNEQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQEQ 416
                                       33333445555555555555555555555555555555555555555555555555555554433 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00089
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleael 97 
                                        el+e  ++r e +++l++ + e   +++e +++ ++ e +eel+++ +++ke+l+++  + + +e++ 
  gi|313117393|ref|YP_004044376.1| 433 TELIERHKQRNEYEFKLDQKRDELEDITAELAEKQDELERREELKQRREQVKEQLAETRSRIESIETNA 501
                                       699**********************************************************99999865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6  24.8   6.1e-09   3.8e-06       2     199 ..      12     225 ..      11     289 .. 0.47
   2 ?    0.7  26.5         1   6.4e+02     113     197 ..     409     499 ..     399     502 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.1e-09
                            AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese......gkvk 72 
                                       + +en++ ++d +++F +g+t++tG N +  T++l+ i  +L+ +   l+++   ++ + + +i  e      +   
  gi|313117393|ref|YP_004044376.1|  12 VDVENIGGIEDADVQFQQGITVLTGRNATNRTSFLRSIAAGLGSDDVSLKSD--ADSGHVELKIDGEsytrslT--- 83 
                                       5689***************************************987777774..44555555554443333222... PP

                            AAA_23  73 ayveltfenkdgry.............................................trsiererelskkkgktt 104
                                                k+g+                                              t+ ie e++  k++ +++
  gi|313117393|ref|YP_004044376.1|  84 --------QKRGTVtfdgdpyledstiadlfafllgsnearravvagadlreilmrpvdTVAIESEIQSLKSERDQI 152
                                       ........222222222223356666666666666666666677777777777777777444444444444444444 PP

                            AAA_23 105 kkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkllekl.eqeke 180
                                       + ++++l ++++   +i +l +++++i + i  l+++r                    +el++e++  ++   ++ e
  gi|313117393|ref|YP_004044376.1| 153 DSEIKQLSSVED---EIHTLEQRRNSIKETIEELADKR--------------------DELTAEIEAEDRSlSEQTE 206
                                       333333333321...11111112222222222222222....................2222222222222112222 PP

                            AAA_23 181 kekeleeleeeleeilkel 199
                                       +++el+e+ e+l+++ ++l
  gi|313117393|ref|YP_004044376.1| 207 NKAELDEILEKLQSARSDL 225
                                       2222222222222222222 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
                            AAA_23 113 eideleqfisellgskki......ilnlilflgqerfeefelkdkkerleelekeleeledekkllekleqe.keke 182
                                       e del++++++ l+s+ +      + +li  ++q ++ ef+l +k ++le+++ el e++de +  e+l+q+ ++ +
  gi|313117393|ref|YP_004044376.1| 409 ERDELQEQVES-LESEADelrdqtQTELIERHKQRNEYEFKLDQKRDELEDITAELAEKQDELERREELKQRrEQVK 484
                                       44777777775.34333356677799***********9***********************9999999965515567 PP

                            AAA_23 183 keleeleeeleeilk 197
                                       ++l e ++++e+i+ 
  gi|313117393|ref|YP_004044376.1| 485 EQLAETRSRIESIET 499
                                       799999999999875 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  14.2     0.015       9.4     111     229 ..     141     256 ..     131     264 .. 0.66
   2 !   10.4   8.2    0.0005      0.31     119     239 ..     262     384 ..     255     397 .. 0.74
   3 !   16.0  24.4   9.5e-06    0.0059     123     234 ..     381     498 ..     374     511 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                           DUF4407 111 elaeeqqeeakelkeqlaaa......ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGk 181
                                       e+++ ++e     ++q++++       ++e+ +le+++++++++i+++ +++d+l+ae ++e     +++t     +
  gi|313117393|ref|YP_004044376.1| 141 EIQSLKSE-----RDQIDSEikqlssVEDEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDR-SLSEQT----EN 207
                                       33333333.....333333333335688999999999999999999999999999999988744.344443....35 PP

                           DUF4407 182 gpaakekkaqldaaqaelaelkakld.atarlaalraelaeleaerake 229
                                        ++ +e  ++l+ a+ +l++++ +l+ +++ +++lr+e++e  +e+++ 
  gi|313117393|ref|YP_004044376.1| 208 KAELDEILEKLQSARSDLKSVRFRLEsERESIESLRDERTETSDELDAL 256
                                       6777777777777777777777776677778888888888777776655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0005
                           DUF4407 119 eakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.........gtgttgvaGkgpaak 186
                                       e+k++++q++ + + +++el++ i++lq+ i+  ++ l+ + + +++ ld +                         
  gi|313117393|ref|YP_004044376.1| 262 ETKQIESQIE-QTRGRIDELNRTITDLQTIIEYNSDVLAGKSDVVADALDEDAagsvtdqlvD-------------- 323
                                       4555655655.4679999999999999999999999999999999999997666444444442.............. PP

                           DUF4407 187 e...........kkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaa 239
                                       +            ++q ++ + +l +l+++   ++r+++lr++l+el++e+++ +++ ++++ +
  gi|313117393|ref|YP_004044376.1| 324 StitcwtcgtnvEQSQVEETTDRLRSLRDE--HRERREELRNRLEELDSELREVNEQERRQE-E 384
                                       033444466666889***************..***************999988777766644.3 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 9.5e-06
                           DUF4407 123 lkeqlaaa..........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekk 189
                                        +e+l++            ta+++el++++++lq++++++e+++d+lr++ q el        ++++ ++   ++k+
  gi|313117393|ref|YP_004044376.1| 381 RQEELTNRlsrledeieeRTATVEELQDERDELQEQVESLESEADELRDQTQTELIER----HKQRNEYEFKLDQKR 453
                                       2233333333334456668888888999999999999999999999999999988853....33478899999**** PP

                           DUF4407 190 aqldaaqaelaelkakldatarlaalraelaeleaerakeraasq 234
                                       ++l++++aelae +++l+++++l+++r++ +e  ae+++++++ +
  gi|313117393|ref|YP_004044376.1| 454 DELEDITAELAEKQDELERREELKQRREQVKEQLAETRSRIESIE 498
                                       ************999988888888887777776666666555444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8  11.3   0.00053      0.33     199     264 ..     143     208 ..     129     210 .. 0.84
   2 !   10.1   9.9   0.00043      0.26     174     259 ..     206     293 ..     201     305 .. 0.48
   3 !   14.8  27.0   1.6e-05    0.0098     153     265 ..     335     444 ..     330     448 .. 0.87
   4 ?    1.0  16.7      0.26   1.6e+02     195     247 ..     443     495 ..     429     514 .. 0.34

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00053
                              Spc7 199 eeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgws 264
                                       ++L++ r+++++  +++++ ++e+ +l++++++++e+ieel+++++el +ei++++r l e+ + +
  gi|313117393|ref|YP_004044376.1| 143 QSLKSERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQTENK 208
                                       4566677777777777788899***********************************999988766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00043
                              Spc7 174 eekaeleeeleklqeaaeeles......idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqks 244
                                       e+kael e leklq+a+ +l+s      +++e++e+lr+e +e + e++     l+e   + +++e++ie+++ +++
  gi|313117393|ref|YP_004044376.1| 206 ENKAELDEILEKLQSARSDLKSvrfrleSERESIESLRDERTETSDELD----ALSETDYETKQIESQIEQTRGRID 278
                                       4444455555555554444444333333445555555555555555555....444444444444444444444444 PP

                              Spc7 245 eleeeiaeaervlee 259
                                       el+  i   + ++e 
  gi|313117393|ref|YP_004044376.1| 279 ELNRTITDLQTIIEY 293
                                       444444444444443 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.6e-05
                              Spc7 153 edkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                        +++++e+  + l +l +e +e+++el+++le+l ++ +e+++  + + eel ++l++l+ eiee+ + ++elq+++
  gi|313117393|ref|YP_004044376.1| 335 VEQSQVEETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQ-ERRQEELTNRLSRLEDEIEERTATVEELQDER 410
                                       578999******************************99997775.455589999*********************** PP

                              Spc7 230 eeleekieelkeqkseleeeiaeaervleeckgwse 265
                                       +el+e++e+l+++ +el+++++   +++e++k+ +e
  gi|313117393|ref|YP_004044376.1| 411 DELQEQVESLESEADELRDQTQ--TELIERHKQRNE 444
                                       *******************999..555555555555 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.26
                              Spc7 195 sidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksele 247
                                       +  + +L + r+el+++ ae++ek++el++++e +++ e+  e+l+e +s++e
  gi|313117393|ref|YP_004044376.1| 443 NEYEFKLDQKRDELEDITAELAEKQDELERREELKQRREQVKEQLAETRSRIE 495
                                       22233444444444444444444444443222222222111111111111111 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.9      0.17   1.1e+02      84     120 ..     137     176 ..     130     179 .. 0.69
   2 !   14.6   4.4   4.1e-05     0.025      48     113 ..     174     242 ..     167     249 .. 0.78
   3 ?    4.8   0.7     0.045        28      49     114 ..     252     288 ..     236     296 .. 0.38
   4 !   12.5   7.6   0.00019      0.12      42     122 ..     339     422 ..     334     423 .. 0.83
   5 !   11.0   3.2   0.00054      0.33      61     109 ..     382     430 ..     378     437 .. 0.89
   6 ?    6.9   3.9      0.01       6.2      48     106 ..     454     512 ..     439     520 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                           DUF1664  84 eikeevtevredlseigedves...vkeavegleskleri 120
                                       +i++e+++++++ ++i++++++   v++ +++le++ ++i
  gi|313117393|ref|YP_004044376.1| 137 AIESEIQSLKSERDQIDSEIKQlssVEDEIHTLEQRRNSI 176
                                       6788888888888888887765111556677777776666 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.1e-05
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeik...eevtevredlseigedvesvkeavegl 113
                                       +++++  e+la+ +++L+++i+  d++l eq+e ++e++   e+++++r+dl++++  +es +e +e+l
  gi|313117393|ref|YP_004044376.1| 174 NSIKETIEELADKRDELTAEIEAEDRSLSEQTENKAELDeilEKLQSARSDLKSVRFRLESERESIESL 242
                                       67889999**********************999877544111677777788888888888877777776 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.045
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       +l+ +                             +e++ e +++++++++++  ++++++++++l+
  gi|313117393|ref|YP_004044376.1| 252 ELDAL-----------------------------SETDYETKQIESQIEQTRGRIDELNRTITDLQ 288
                                       22222.............................23333333333333333333333333333333 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00019
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkklde...qkeiskeikeevtevredlseigedvesvkeavegles 115
                                        ve+ + +l ++ ++ ++ +++L +r++++d++l e   q++ ++e+++ +++++++++e    ve++++   +l++
  gi|313117393|ref|YP_004044376.1| 339 QVEETTDRLRSLRDEHRERREELRNRLEELDSELREvneQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQE 415
                                       5778889999999999999************9876511155567889999999999999999999999999999999 PP

                           DUF1664 116 kleriee 122
                                       ++e++e+
  gi|313117393|ref|YP_004044376.1| 416 QVESLES 422
                                       9999986 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.00054
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       +++L++r+ r++++++e +++ +e+++e +e++e++++++++ +++++ 
  gi|313117393|ref|YP_004044376.1| 382 QEELTNRLSRLEDEIEERTATVEELQDERDELQEQVESLESEADELRDQ 430
                                       689************************************9999988765 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.01
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevred.lseigedvesv 106
                                        +le++ ++la+ +++L++r +++ ++ +++ke  +e+++ +++++ + +++++e++e+v
  gi|313117393|ref|YP_004044376.1| 454 DELEDITAELAEKQDELERR-EELKQRREQVKEQLAETRSRIESIETNaIEAFNEEMETV 512
                                       34555666666666666544.556666666666666666666666544245555555555 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  30.1   1.1e-05    0.0069      12     201 ..     143     375 ..     139     379 .. 0.84
   2 !    9.9  41.7   0.00093      0.58       2     137 ..     377     521 ..     376     572 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                               ERM  12 erLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreae 88 
                                       + Lk+ +++++   ++L+  e++++ L++++   +e  e+L+ k+ e+++ei++  +s +++ e+k++l + l++ +
  gi|313117393|ref|YP_004044376.1| 143 QSLKSERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQTENKAELDEILEKLQ 219
                                       6788889999999***************************************************************9 PP

                               ERM  89 leaarleeeserkeeeaerLkeeleeareaeeeakekllealstpskseseenveeseteeeeensee......... 156
                                       +  ++l++ + r e+e    +e +e  r++ +e++ +l ++++t +++++ e++ e+++   +e + +         
  gi|313117393|ref|YP_004044376.1| 220 SARSDLKSVRFRLESE----RESIESLRDERTETSDELDALSETDYETKQIESQIEQTRGRIDELNRTitdlqtiie 292
                                       9999999999999998....568899999999999999999999987755444444444333333333678999999 PP

                               ERM 157 ......................................esaeletdeveklsleieeeRvtylekskrlqeqLkeLk 195
                                                                               +++e+ +ve+++++    R +  e+ ++l+++L+eL 
  gi|313117393|ref|YP_004044376.1| 293 ynsdvlagksdvvadaldedaagsvtdqlvdstitcwtCGTNVEQSQVEETTDRLRSLRDEHRERREELRNRLEELD 369
                                       9999999999999999999999988888887777666533555566688889999999******************* PP

                               ERM 196 seleql 201
                                       sel ++
  gi|313117393|ref|YP_004044376.1| 370 SELREV 375
                                       ***986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00093
                               ERM   2 eaerekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaa.ea.eeeiqrlke..saekee 74 
                                       e er+++el +rL +l++e+e++ +  +e +++ ++L+e+ + +e ea++L  + + e+ e+ +qr +   +  ++ 
  gi|313117393|ref|YP_004044376.1| 377 EQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQEQVESLESEADELRDQTQtELiERHKQRNEYefKLDQKR 453
                                       68**********************************************99976654144344444444300445566 PP

                               ERM  75 eekeklerklreaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstpsks.....e 137
                                        e e++ ++l+e++ e++r ee ++r+e+ +e+L e   +++  e++a e+  e ++t  +      +
  gi|313117393|ref|YP_004044376.1| 454 DELEDITAELAEKQDELERREELKQRREQVKEQLAETRSRIESIETNAIEAFNEEMETVLNLldyenI 521
                                       77888888999999999999999999999999999888888888877777777777666433555441 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   4.9    0.0028       1.7      26      76 ..     143     193 ..     133     197 .. 0.39
   2 !   16.7  11.6   5.6e-06    0.0035      27     161 ..     179     312 ..     178     315 .. 0.92
   3 !   10.9  25.5   0.00035      0.22      37     139 ..     339     442 ..     334     446 .. 0.89
   4 ?   -0.2  14.3      0.88   5.4e+02      38      98 ..     438     498 ..     432     517 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0028
                               GAS  26 elIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkq 76 
                                       +  ks +++i    k+  + e e++ ++q+ +++ke+++++  +++eL ++
  gi|313117393|ref|YP_004044376.1| 143 QSLKSERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAE 193
                                       222222333333333333333444444444444444444444444444333 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.6e-06
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                       +I++l ++  el ++ e+ ++ lse ++++ +l e L+k++  +  L+    + e++++s+++l+ + +e+ +el +
  gi|313117393|ref|YP_004044376.1| 179 TIEELADKRDELTAEIEAEDRSLSEQTENKAELDEILEKLQSARSDLKSVRFRLESERESIESLRDERTETSDELDA 255
                                       799999999******************************************************************** PP

                               GAS 104 lkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkk 161
                                       l++ +   +q  +++e+ r ++  + +++i ++q  ++ ++ +L  k + + ++l++ 
  gi|313117393|ref|YP_004044376.1| 256 LSETDYETKQIESQIEQTRGRID-ELNRTITDLQTIIEYNSDVLAGKSDVVADALDED 312
                                       ******************99995.5778899999999999999999988888888865 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00035
                               GAS  37 elkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleq 113
                                       + ++  +r + + +e+ ++ ++l+  L++++ e+ e ++q +++e+  ++l +l+ +++e +  +++l+ e + l++
  gi|313117393|ref|YP_004044376.1| 339 QVEETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQE 415
                                       66777888899999*************************************************************** PP

                               GAS 114 rfekvekerdelykkfeaa.iqevqqk 139
                                       ++e++e+e del+++ ++  i+  +q+
  gi|313117393|ref|YP_004044376.1| 416 QVESLESEADELRDQTQTElIERHKQR 442
                                       ************987665426666665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.88
                               GAS  38 lkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkele 98 
                                         k+ ++ e +l++   e ++++ +L + + e+e+ ++  ++ e+ k++l+++++r+++ e
  gi|313117393|ref|YP_004044376.1| 438 RHKQRNEYEFKLDQKRDELEDITAELAEKQDELERREELKQRREQVKEQLAETRSRIESIE 498
                                       4444444444444444444444445555544444444444444444555555555444444 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   8.2      0.02        13      34      92 ..     156     218 ..     128     228 .. 0.40
   2 ?    2.6   5.3      0.11        66      45      99 ..     230     287 ..     204     302 .. 0.48
   3 !   16.6  11.7   6.2e-06    0.0038      33     104 ..     354     425 ..     330     436 .. 0.84
   4 ?    0.1  10.0      0.61   3.8e+02      27      99 ..     439     512 ..     429     520 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.02
                              HemX  34 taevaelqqqlaaleqqlaq....veaekeqkqeleerlqqlaeklealekeleqlqkqleel 92 
                                        ++ +++++++++leq  ++    +e+++ + +el++++++ + +l+++++++++l++ le+l
  gi|313117393|ref|YP_004044376.1| 156 IKQLSSVEDEIHTLEQRRNSiketIEELADKRDELTAEIEAEDRSLSEQTENKAELDEILEKL 218
                                       122222222333333222222222222333333333333333333333333333333333333 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                              HemX  45 aaleqqlaqveaekeqkqeleerlqql...aeklealekeleqlqkqleelqqqlskv 99 
                                         le++ +++e+++ + +e++++l++l   + ++++ e+++eq+  +++el++ ++++
  gi|313117393|ref|YP_004044376.1| 230 FRLESERESIESLRDERTETSDELDALsetDYETKQIESQIEQTRGRIDELNRTITDL 287
                                       2233333334444444444443333332224455555555555555555555555544 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 6.2e-06
                              HemX  33 ltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgaer 104
                                       ++ + +el+++l++l+++l +v++++++++el++rl  l++++e++++++e+lq + +elq+q++ ++++  
  gi|313117393|ref|YP_004044376.1| 354 HRERREELRNRLEELDSELREVNEQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQEQVESLESEAD 425
                                       3344499***********************************************************999844 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.61
                              HemX  27 qqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleq.lqkqleelqqqlskv 99 
                                       ++q +e++ + ++ +++l+ + ++la+ + e e+ +el++r +q +e+l+++++++e+  ++++e+ ++++++v
  gi|313117393|ref|YP_004044376.1| 439 HKQRNEYEFKLDQKRDELEDITAELAEKQDELERREELKQRREQVKEQLAETRSRIESiETNAIEAFNEEMETV 512
                                       33444444445555555555555555555555666666666666666666666555541345566666666665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2  19.8      0.59   3.6e+02      61     159 ..     144     245 ..     130     256 .. 0.54
   2 !   10.6   5.1   0.00078      0.49      90     160 ..     239     312 ..     231     318 .. 0.77
   3 !   14.2  27.6   6.2e-05     0.038     100     178 ..     343     428 ..     330     430 .. 0.78
   4 ?    1.6  20.4      0.44   2.7e+02      79     162 ..     424     511 ..     422     517 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.59
                             ATG16  61 keasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraalet 137
                                       +++s++++  ++ ++++s e+++++l +       + +ela++  el++e+++ +++l+e++e+ ael +  ++l+ 
  gi|313117393|ref|YP_004044376.1| 144 SLKSERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQTENKAELDEILEKLQS 220
                                       33344443344445555555555555555555555555555555566666666665555555555555555555554 PP

                             ATG16 138 klkdr...eeelrekeklvqdlqDE 159
                                       +++d+   + +l+  ++ ++ l+DE
  gi|313117393|ref|YP_004044376.1| 221 ARSDLksvRFRLESERESIESLRDE 245
                                       4444411144667777777777776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00078
                             ATG16  90 laelyksrgelaqrllelne...elqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEl 160
                                        + l  +r+e+++ l +l+e   e ++ e+++++ + r++el++++++l+t ++ + + l++k  +v d  DE 
  gi|313117393|ref|YP_004044376.1| 239 IESLRDERTETSDELDALSEtdyETKQIESQIEQTRGRIDELNRTITDLQTIIEYNSDVLAGKSDVVADALDED 312
                                       444444555555555555442227899999*****************************************995 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 6.2e-05
                             ATG16 100 laqrllelneelqklee.......klkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnq 169
                                       +++rl++l +e+++++e       +l ++ ++++e e++ ++l+ +l+++e+e++e++++v++lqDE + Lq q+++
  gi|313117393|ref|YP_004044376.1| 343 TTDRLRSLRDEHRERREelrnrleELDSELREVNEQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQEQVES 419
                                       5556666666555555511111115566777888999999************************************* PP

                             ATG16 170 aEeklrkle 178
                                       +E++ ++l+
  gi|313117393|ref|YP_004044376.1| 420 LESEADELR 428
                                       *****9986 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.44
                             ATG16  79 leqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerla...eleaeraaletklkdreeelreke.k 151
                                        ++++ q+++el e +k+r+e + +l ++ +el++  ++l e++ +l+   el+++r++++++l++ + +++  e +
  gi|313117393|ref|YP_004044376.1| 424 ADELRDQTQTELIERHKQRNEYEFKLDQKRDELEDITAELAEKQDELErreELKQRREQVKEQLAETRSRIESIEtN 500
                                       678889**********************************9999887522267777777777777777777764315 PP

                             ATG16 152 lvqdlqDElsa 162
                                       +++++ +E+++
  gi|313117393|ref|YP_004044376.1| 501 AIEAFNEEMET 511
                                       66777777765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  11.4     0.062        38      66     122 ..     148     211 ..     129     212 .. 0.67
   2 !   16.1  14.2   1.5e-05    0.0094      69     167 ..     193     293 ..     191     299 .. 0.90
   3 ?    2.1  36.9      0.29   1.8e+02      66     165 ..     371     470 ..     318     473 .. 0.52
   4 ?    2.4  13.2      0.24   1.5e+02      84     144 ..     449     513 ..     446     519 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.062
                           UPF0242  66 ekskleekeaklteldeglktkee.......aleelqeeeeeLkeeldakeeelerlkeenqqL 122
                                       e  ++++++++l++ +++++t e+       ++eel ++ +eL  e++a ++ l + +e++++L
  gi|313117393|ref|YP_004044376.1| 148 ERDQIDSEIKQLSSVEDEIHTLEQrrnsikeTIEELADKRDELTAEIEAEDRSLSEQTENKAEL 211
                                       5555555555555555444444434444444999999999999999999999999999998887 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-05
                           UPF0242  69 kleekeaklteldeglktkeealeelqeeeeeLkee...ldakeeelerlkeenqqLqekleaiaedfeelklelee 142
                                       ++e++ + l+e+ e+ ++ +e le+lq+   +Lk     l++  e +e l+ e  + + +l a + + +   +++e+
  gi|313117393|ref|YP_004044376.1| 193 EIEAEDRSLSEQTENKAELDEILEKLQSARSDLKSVrfrLESERESIESLRDERTETSDELDALS-ETDYETKQIES 268
                                       689999***************************997788*******************9999955.56666788*** PP

                           UPF0242 143 qLaekqellqeyqetieeqrsvlek 167
                                       q+++ + +++e+++ti++++  +e 
  gi|313117393|ref|YP_004044376.1| 269 QIEQTRGRIDELNRTITDLQTIIEY 293
                                       ********************99985 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.29
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklelee 142
                                       e  +++e+e+   el + l+  e+++ee+++  eeL++e d+ +e++e l+ e  +L+ +++    + ++++ e+e 
  gi|313117393|ref|YP_004044376.1| 371 ELREVNEQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQEQVESLESEADELRDQTQTELIERHKQRNEYEF 447
                                       33334444444444444555555555555555555555555555555555555555555555555555555555555 PP

                           UPF0242 143 qLaekqellqeyqetieeqrsvl 165
                                       +L++k+  l++  +++ e++ +l
  gi|313117393|ref|YP_004044376.1| 448 KLDQKRDELEDITAELAEKQDEL 470
                                       55555555555555555555555 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.24
                           UPF0242  84 lktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae....dfeelkleleeqL 144
                                       l++k+++le+ ++e  e ++el+ +ee+ +r+++ ++qL e  + i       +e++  e+e  L
  gi|313117393|ref|YP_004044376.1| 449 LDQKRDELEDITAELAEKQDELERREELKQRREQVKEQLAETRSRIESietnAIEAFNEEMETVL 513
                                       78999**********************************98888877666667888888888776 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  17.5   0.00083      0.51      30     146 ..     141     252 ..     135     259 .. 0.63
   2 ?   10.6   4.0   0.00036      0.22      27     111 ..     218     305 ..     215     324 .. 0.50
   3 ?    7.2  15.1    0.0037       2.3      12      97 ..     327     431 ..     317     433 .. 0.60
   4 ?    6.4  20.4    0.0066       4.1      24     134 ..     396     496 ..     393     531 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00083
                             Atg14  30 rlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieek...kkk 103
                                       ++++lkse++++ ++i+++ + ++       +i ++ ++ +++k +i++l ++  el + ++  ++++ e+   k++
  gi|313117393|ref|YP_004044376.1| 141 EIQSLKSERDQIDSEIKQLSSVED-------EIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQtenKAE 210
                                       456777777777777776655555.......6677777777777777777777666666666666666544111444 PP

                             Atg14 104 laklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqk 146
                                       l +  +kl   rsdl+s++++le++r++ i++l d+  ++++ 
  gi|313117393|ref|YP_004044376.1| 211 LDEILEKLQSARSDLKSVRFRLESERES-IESLRDERTETSDE 252
                                       44444444499***********988765.56666665555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00036
                             Atg14  27 lrerlaklksekeslkkkiekalegke...eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieek 100
                                       l+    +lks ++ l+++ e +++ ++   e++++ d++  +    +++ s+i+++r r+ el+ +++ l+  ie  
  gi|313117393|ref|YP_004044376.1| 218 LQSARSDLKSVRFRLESERESIESLRDertETSDELDALSETDYETKQIESQIEQTRGRIDELNRTITDLQTIIEYN 294
                                       44444455555555555555555555522233333344444444445555555555555555555555555555555 PP

                             Atg14 101 kkklaklsdkl 111
                                       +  la++sd +
  gi|313117393|ref|YP_004044376.1| 295 SDVLAGKSDVV 305
                                       55555555544 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0037
                             Atg14  12 iCesClrng...................perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakl 69 
                                       +C +C  n                    +er +elr rl  l se  ++ ++  + +e +++ ++led+i+ ++a +
  gi|313117393|ref|YP_004044376.1| 327 TCWTCGTNVeqsqveettdrlrslrdehRERREELRNRLEELDSELREVNEQERRQEELTNRLSRLEDEIEERTATV 403
                                       56666333333355555555555555555666666666666666666666666666666666666666666666666 PP

                             Atg14  70 eelksliadlrerlqelkdklsqlkkei 97 
                                       eel+ ++ +l+e+++ l+   ++l++++
  gi|313117393|ref|YP_004044376.1| 404 EELQDERDELQEQVESLESEADELRDQT 431
                                       6666666666666666666666666655 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0066
                             Atg14  24 lyelrerlaklksekeslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeiee 99 
                                       ++e    +  l+ e+++l++++e ++++ +   +q+       ++ l e  +++ + + +l + +d l+  ++e++e
  gi|313117393|ref|YP_004044376.1| 396 IEERTATVEELQDERDELQEQVESLESEADeLRDQT-------QTELIERHKQRNEYEFKLDQKRDELEDITAELAE 465
                                       556666677788888888888887777777222222.......3333334444444444444444444444444444 PP

                             Atg14 100 kkkklaklsdklkkRrsdleslqneleerrkkqia 134
                                       k+ +l+++ ++lk+Rr++   ++++l+e r ++ +
  gi|313117393|ref|YP_004044376.1| 466 KQDELERR-EELKQRREQ---VKEQLAETRSRIES 496
                                       44444432.233444444...44444444433222 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.7      0.34   2.1e+02      44      83 ..     143     177 ..     134     178 .. 0.63
   2 ?   14.4   5.8   6.1e-05     0.038      16      84 ..     174     237 ..     166     243 .. 0.86
   3 ?    6.0   1.0     0.027        16      15      79 ..     225     291 ..     224     298 .. 0.79
   4 ?    5.5   5.0     0.038        23      12      53 ..     337     383 ..     333     391 .. 0.76
   5 ?   11.2  11.6   0.00061      0.38       8      87 ..     389     471 ..     383     472 .. 0.83
   6 ?   -0.7   4.5       3.2     2e+03      25      75 ..     463     497 ..     449     517 .. 0.48

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.34
                   Snapin_Pallidin  44 keleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklk 83 
                                       ++l+ +       ++++ +k L++++ ++++l++r +++k
  gi|313117393|ref|YP_004044376.1| 143 QSLKSER-----DQIDSEIKQLSSVEDEIHTLEQRRNSIK 177
                                       2223333.....3677778888888888888887777766 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.1e-05
                   Snapin_Pallidin  16 deldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkk 84 
                                       + ++e+++el ++ +eL+++++ + ++L e  e++      +l+e ++KL++++ +++s+  rl++ ++
  gi|313117393|ref|YP_004044376.1| 174 NSIKETIEELADKRDELTAEIEAEDRSLSEQTENKA-----ELDEILEKLQSARSDLKSVRFRLESERE 237
                                       57899***********************98777777.....9******************999987655 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.027
                   Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmsslnerl 79 
                                       l+ ++ +l++ r+s e L+++ ++ +++L+ l+e++   +++ +++++ + ++ ++ + ++ l++++
  gi|313117393|ref|YP_004044376.1| 225 LKSVRFRLESERESIESLRDERTETSDELDALSETDYetKQIESQIEQTRGRIDELNRTITDLQTII 291
                                       6677777888888888899999999999999998887644555789999999999999999998876 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.038
                   Snapin_Pallidin  12 epkldeldeklkelr....qsQeeLleqldrlnekLkeleeaqe.ae 53 
                                       +++++e++++l++lr    +  eeL+++l++l ++L+e++e +  +e
  gi|313117393|ref|YP_004044376.1| 337 QSQVEETTDRLRSLRdehrERREELRNRLEELDSELREVNEQERrQE 383
                                       567888888888776111156799****************9988554 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.00061
                   Snapin_Pallidin   8 lellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlk...eyakKLvnikkrmsslnerlqk 81 
                                       l+ le +++e +++++el+++ +eL+eq+++l ++ +el++ +++e++++ k   ey  KL + + +++ +   l +
  gi|313117393|ref|YP_004044376.1| 389 LSRLEDEIEERTATVEELQDERDELQEQVESLESEADELRDQTQTELIERHKqrnEYEFKLDQKRDELEDITAELAE 465
                                       566899*********************************99999666655541116889999999999999999988 PP

                   Snapin_Pallidin  82 lkkRae 87 
                                        ++ +e
  gi|313117393|ref|YP_004044376.1| 466 KQDELE 471
                                       888776 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 3.2
                   Snapin_Pallidin  25 lrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmssl 75 
                                       l ++Q+eL              e+ +e  + ++ ++ ++ L++ + r++s+
  gi|313117393|ref|YP_004044376.1| 463 LAEKQDEL--------------ERREE--LKQRREQVKEQLAETRSRIESI 497
                                       23333333..............22222..2223333333444444444433 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  12.1     0.028        17      25      91 ..     142     209 ..     136     210 .. 0.79
   2 ?    7.8  15.5    0.0055       3.4       3     100 ..     193     290 ..     191     298 .. 0.95
   3 ?    9.1   3.8    0.0021       1.3      84     115 ..     337     368 ..     334     370 .. 0.95
   4 ?    9.4  21.2    0.0017         1      42     104 ..     372     434 ..     370     446 .. 0.92
   5 ?    3.8  15.5     0.094        58      51     101 ..     448     501 ..     441     512 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.028
                             DHR10  25 idalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeiel.relerkeerlqrqlenae 91 
                                       i +l+    ++ s ik+l  +e+e+  le+ +  +ke+ ++l++k+ el +e+e++ + l  q en+ 
  gi|313117393|ref|YP_004044376.1| 142 IQSLKSERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELtAEIEAEDRSLSEQTENKA 209
                                       55666666677888999999999999999999999999999999988863689999999999999875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0055
                             DHR10   3 slaeekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerk 79 
                                       ++++e ++l+e+ ++  el + ++ lq +  dl+s+   le   + +++l++++ + ++  dal+e   e++++e++
  gi|313117393|ref|YP_004044376.1| 193 EIEAEDRSLSEQTENKAELDEILEKLQSARSDLKSVRFRLESERESIESLRDERTETSDELDALSETDYETKQIESQ 269
                                       67899999********************************************************************* PP

                             DHR10  80 eerlqrqlenaeeklerlreq 100
                                       +e+ + +++  ++ ++ l+  
  gi|313117393|ref|YP_004044376.1| 270 IEQTRGRIDELNRTITDLQTI 290
                                       *************99999975 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0021
                             DHR10  84 qrqlenaeeklerlreqaeekreaakarleel 115
                                       q q+e  +++l  lr +++e+re+ ++rleel
  gi|313117393|ref|YP_004044376.1| 337 QSQVEETTDRLRSLRDEHRERREELRNRLEEL 368
                                       789***************************98 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0017
                             DHR10  42 leeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeek 104
                                       l e++++ +++ee   +l++l+d++ee++++++el+ +++ lq q+e+ e + + lr q +++
  gi|313117393|ref|YP_004044376.1| 372 LREVNEQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQEQVESLESEADELRDQTQTE 434
                                       789999****************************************************99875 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.094
                             DHR10  51 kleeakkklkelrdaleekeie...lrelerkeerlqrqlenaeeklerlreqa 101
                                       kl++ +++l++  ++l+ek+ e   ++el++++e+++ ql+  + ++e  + +a
  gi|313117393|ref|YP_004044376.1| 448 KLDQKRDELEDITAELAEKQDElerREELKQRREQVKEQLAETRSRIESIETNA 501
                                       6788888899999999988877222579********************998776 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00025      0.15      22      48 ..     263     289 ..     261     290 .. 0.93
   2 ?    1.7   1.1      0.38   2.4e+02      16      50 ..     345     379 ..     333     380 .. 0.79
   3 ?   -0.6   2.8         2   1.3e+03      30      49 ..     411     430 ..     383     432 .. 0.60
   4 ?   -2.0   0.1       5.5   3.4e+03      18      35 ..     456     473 ..     449     473 .. 0.65
   5 ?    0.7   0.1      0.78   4.8e+02      24      42 ..     482     500 ..     479     508 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                             HSBP1  22 sdqilsriDdMssriDdLEksiadlmt 48 
                                       ++qi s+i++   riD+L ++i+dl t
  gi|313117393|ref|YP_004044376.1| 263 TKQIESQIEQTRGRIDELNRTITDLQT 289
                                       57999*******************976 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.38
                             HSBP1  16 dkFqtmsdqilsriDdMssriDdLEksiadlmtqa 50 
                                       d+  ++ d+  +r +++ +r+++L+  + ++ +q+
  gi|313117393|ref|YP_004044376.1| 345 DRLRSLRDEHRERREELRNRLEELDSELREVNEQE 379
                                       5666666666778899***********99999886 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2
                             HSBP1  30 DdMssriDdLEksiadlmtq 49 
                                       D++++ +++LE   ++l +q
  gi|313117393|ref|YP_004044376.1| 411 DELQEQVESLESEADELRDQ 430
                                       66666666666666666665 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 5.5
                             HSBP1  18 FqtmsdqilsriDdMssr 35 
                                        ++++ ++ ++ D++++r
  gi|313117393|ref|YP_004044376.1| 456 LEDITAELAEKQDELERR 473
                                       456777777777777766 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.78
                             HSBP1  24 qilsriDdMssriDdLEks 42 
                                       q+ +++ +  sri+++E++
  gi|313117393|ref|YP_004044376.1| 482 QVKEQLAETRSRIESIETN 500
                                       6777889999*******98 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  12.7    0.0075       4.7      46     133 ..     144     234 ..     139     240 .. 0.82
   2 ?    6.6   3.3    0.0092       5.7       6      79 ..     223     298 ..     222     300 .. 0.84
   3 ?    8.1  13.8    0.0033       2.1      78     174 ..     325     423 ..     324     426 .. 0.88
   4 ?    4.3  12.3     0.047        29      83     157 ..     439     515 ..     427     520 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0075
                           DUF4201  46 qlqienqalnkkIeern...keLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkl 119
                                       +l+ e  + + +I   +   +e++ l ++ ++   ++++l +k+++l++e ++   +l+e++e++a+l++ l+k++ 
  gi|313117393|ref|YP_004044376.1| 144 SLKSERDQIDSEIKQLSsveDEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQTENKAELDEILEKLQS 220
                                       666666666666655532227999999999999999***************************************** PP

                           DUF4201 120 erdklrkqneklkq 133
                                        r+ l+  + +l++
  gi|313117393|ref|YP_004044376.1| 221 ARSDLKSVRFRLES 234
                                       ****9988777665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0092
                           DUF4201   6 nelsklrlklislkhqlakiqeklekkeelgegLtlidFeqlqie..nqalnkkIeernkeLkrlkkkttktvhal 79 
                                        +l+ +r +l s +++++ ++++  +  +  ++L++ d+e+ qie  +++ + +I+e n  +  l+  + +++ +l
  gi|313117393|ref|YP_004044376.1| 223 SDLKSVRFRLESERESIESLRDERTETSDELDALSETDYETKQIEsqIEQTRGRIDELNRTITDLQTIIEYNSDVL 298
                                       67888999999999999999999999999999*******988887225699999*******999999888876655 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0033
                           DUF4201  78 althlkeklhmleselselkkelkekeerlaklrkely.kvklerdklrkqneklkqqggllrv.PaLlkDYdktke 152
                                       ++t++ + ++  +s+++e  ++l+++ ++ ++ r+el  ++++  + lr+ ne+ ++q +l ++   L  + +++ +
  gi|313117393|ref|YP_004044376.1| 325 TITCWTCGTNVEQSQVEETTDRLRSLRDEHRERREELRnRLEELDSELREVNEQERRQEELTNRlSRLEDEIEERTA 401
                                       68999********************99999999999962677778899999999999999987636788999***** PP

                           DUF4201 153 kveekrksvkkLrrkvkilemr 174
                                        vee++++ ++L+++v++le+ 
  gi|313117393|ref|YP_004044376.1| 402 TVEELQDERDELQEQVESLESE 423
                                       *****************99975 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.047
                           DUF4201  83 keklhmleselselkkelkekeerlaklrkely...kvklerdklrkqneklkqqggllrvPaLlkDYdktkekvee 156
                                       ++ ++++e +l ++++el++++++la+ ++el+   ++k++r+++++q ++ +++ + ++  a+   + +++e v +
  gi|313117393|ref|YP_004044376.1| 439 HKQRNEYEFKLDQKRDELEDITAELAEKQDELErreELKQRREQVKEQLAETRSRIESIETNAIEA-FNEEMETVLN 514
                                       577899999**********************973336999*****************999999998.9999998866 PP

                           DUF4201 157 k 157
                                       +
  gi|313117393|ref|YP_004044376.1| 515 L 515
                                       5 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   8.8     0.008         5      33     128 ..     142     247 ..     132     250 .. 0.65
   2 ?   11.8   2.5    0.0003      0.19       2      79 ..     208     281 ..     207     294 .. 0.77
   3 ?    3.6   0.2       0.1        62      12      47 ..     256     291 ..     253     311 .. 0.66
   4 ?    4.0   4.4     0.075        46      23      83 ..     337     397 ..     332     401 .. 0.80
   5 ?    5.8  12.9      0.02        13       6     109 ..     397     497 ..     393     504 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.008
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.................HHHHHHHH CS
                        Laminin_II  33 lseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss..............lsdnisei 95 
                                       +++++++     +++++  k++ ++++++ +Le+  + + + ++el  ++++  +               +++++ei
  gi|313117393|ref|YP_004044376.1| 142 IQSLKSE----RDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAeieaedrslseqteNKAELDEI 214
                                       3333333....445555555555566666666666666666666665555555555555555544444447899*** PP

                                       HHHHHHHHHHHHT---EEEEES--EEEE----S CS
                        Laminin_II  96 kelIaqARkaAnkikvsvsfdgdsivelrppek 128
                                        e  + AR+   +++   +++++si  lr ++ 
  gi|313117393|ref|YP_004044376.1| 215 LEKLQSARSDLKSVRFRLESERESIESLRDERT 247
                                       ************************999987765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0003
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       k+ ++e++e++++  ++l+ +  +le ++e++++++++  et +++++++++      + k++e +++q   ++ el
  gi|313117393|ref|YP_004044376.1| 208 KAELDEILEKLQSARSDLKSVRFRLESERESIESLRDERTETSDELDALSET----DYETKQIESQIEQTRGRIDEL 280
                                       7889**********************************88888777766554....444555555555555555555 PP

                                       H CS
                        Laminin_II  79 k 79 
                                       +
  gi|313117393|ref|YP_004044376.1| 281 N 281
                                       4 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.1
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekv 47 
                                       ++e+   +++++ ++e+t+  + e+nr++   +  +
  gi|313117393|ref|YP_004044376.1| 256 LSETDYETKQIESQIEQTRGRIDELNRTITDLQTII 291
                                       456666677777777777777777777765554444 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.075
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II  23 sqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       + ++e+t + l +++++ +e  e++++  + +++  r+v + e+  ++L ++l++l+   e
  gi|313117393|ref|YP_004044376.1| 337 QSQVEETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQERRQEELTNRLSRLEDEIE 397
                                       5678888888888888888888888888888888888888888888888888888887655 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsve.etnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       +e   t++e ++   +l++++e +++++ e++++ + e  e  k+ n+      ++  +Le    +L +k  el+ +
  gi|313117393|ref|YP_004044376.1| 397 EERTATVEELQDERDELQEQVESLESEADELRDQTQtELIERHKQRNEYEFKLDQKRDELEDITAELAEKQDELERR 473
                                       55566777888888899999999999999998883213344445666666666677777777666677765555544 PP

                                       HHH...HHHHHHHHHHHHHHHHHHHHT- CS
                        Laminin_II  82 eeassslsdniseikelIaqARkaAnki 109
                                       ee    l++  +++ke+ a +R+   +i
  gi|313117393|ref|YP_004044376.1| 474 EE----LKQRREQVKEQLAETRSRIESI 497
                                       43....799*************988777 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   9.7     0.026        16      68     126 ..     140     194 ..     134     196 .. 0.58
   2 ?    5.2  15.8     0.045        28      15      95 ..     198     281 ..     194     295 .. 0.72
   3 ?    0.1  14.1       1.7   1.1e+03      15      95 ..     267     383 ..     264     385 .. 0.60
   4 ?   12.1  41.3   0.00035      0.22      12     133 .]     345     470 ..     340     470 .. 0.86
   5 ?   -1.4  20.2       5.2   3.2e+03      45     116 ..     445     519 ..     437     523 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
                            APG6_N  68 eeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqy 126
                                       +e++ l++er+++++e+++l++ +++++  e+r    +n+ + + +el +++d l+a++
  gi|313117393|ref|YP_004044376.1| 140 SEIQSLKSERDQIDSEIKQLSSVEDEIHTLEQR----RNSIKETIEELADKRDELTAEI 194
                                       566666666666666666666666666665544....4555556666666666665554 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.045
                            APG6_N  15 dkqleqaekerdaYeeflkklkkekkeeek...qdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                       d+ l+++++ + ++ e l+kl++ +++ ++     e+++e+ e+l++ + e ++ l  L e++ e +++e+++++ +
  gi|313117393|ref|YP_004044376.1| 198 DRSLSEQTENKAELDEILEKLQSARSDLKSvrfRLESERESIESLRDERTETSDELDALSETDYETKQIESQIEQTR 274
                                       67788888888888888888888866665566655555666667777777777777777777778888888888877 PP

                            APG6_N  89 eeleale 95 
                                          ++l+
  gi|313117393|ref|YP_004044376.1| 275 GRIDELN 281
                                       7776665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.7
                            APG6_N  15 dkqleqaekerdaYeeflkklkkekkeeek....................................qdeeleeleee 55 
                                       ++q+eq++  +d++++    l++  + +++                                    ++ e  + ee 
  gi|313117393|ref|YP_004044376.1| 267 ESQIEQTRGRIDELNRTITDLQTIIEYNSDvlagksdvvadaldedaagsvtdqlvdstitcwtcgTNVEQSQVEET 343
                                       56666666666666666666665544443366666666666666666666666666666666666645555566666 PP

                            APG6_N  56 leklekeeeelleeLkelekereeleaelaaleeeleale 95 
                                        ++l++ ++e  e  +el +  eel++el++  e++++ e
  gi|313117393|ref|YP_004044376.1| 344 TDRLRSLRDEHRERREELRNRLEELDSELREVNEQERRQE 383
                                       6666666666666667777777777777777777776655 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00035
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                       ++l +  ++ ++ r+++++ l++l++e +e ++q+   eel ++l++le+e ee  +  +el++er+el++++++le
  gi|313117393|ref|YP_004044376.1| 345 DRLRSLRDEHRERREELRNRLEELDSELREVNEQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQEQVESLE 421
                                       555666677788888889999999988888887888999************************************** PP

                            APG6_N  89 eelealeeeee....rfwreynelqlelleleeeldsleaqyehaqnql 133
                                       +e+++l ++ +    +  +++ne++ +l ++ +el+ ++a+++  q++l
  gi|313117393|ref|YP_004044376.1| 422 SEADELRDQTQteliERHKQRNEYEFKLDQKRDELEDITAELAEKQDEL 470
                                       ****9987766222256789999********************999986 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 5.2
                            APG6_N  45 qdeeleeleeeleklekeeeelleeL...kelekereeleaelaaleeelealeeeeerfwreynelqlellele 116
                                        + +l++ ++ele++ +e +e++ eL   +el++ re+++++la+ ++  e +e +  + ++e  e  l+ll+ e
  gi|313117393|ref|YP_004044376.1| 445 YEFKLDQKRDELEDITAELAEKQDELerrEELKQRREQVKEQLAETRSRIESIETNAIEAFNEEMETVLNLLDYE 519
                                       455777778888888888777777772225788888899999999888888888888888888887777777665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.9    0.0025       1.5      27      88 ..     158     219 ..     142     220 .. 0.93
   2 ?    4.4   0.3     0.073        45      23      80 ..     227     287 ..     224     305 .. 0.63
   3 ?    4.4   0.5     0.074        46      27      85 ..     339     397 ..     327     400 .. 0.82
   4 ?    3.4   7.0      0.15        92      21      66 ..     389     434 ..     385     512 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                        l+++++ i++le++ ++i + +e+l +k  el+++++ +  ++ + te+ a+l e +++l+
  gi|313117393|ref|YP_004044376.1| 158 QLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQTENKAELDEILEKLQ 219
                                       6789999*******************************************999998888775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.073
                            DUF948  23 klkktldeaaatieelekqvdpilkevedlla...kvnelledvneklekvdplteavadl 80 
                                       +++  l++ +++ie+l+++ +++++e+++l +   +++++ +++++   ++d+l   + dl
  gi|313117393|ref|YP_004044376.1| 227 SVRFRLESERESIESLRDERTETSDELDALSEtdyETKQIESQIEQTRGRIDELNRTITDL 287
                                       5556677778888888888888888887665511134445555555444444444444444 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.074
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                        ++e+++++++l+++ ++  +e+++ l++    l +vne+  + ++lt+ +  l + ++
  gi|313117393|ref|YP_004044376.1| 339 QVEETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQERRQEELTNRLSRLEDEIE 397
                                       57888899999999999999999999999999899999998888888888887777665 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.15
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvnek 66 
                                       l +l++ ++e +at+eel+++ d++ ++ve l +++ el ++ + +
  gi|313117393|ref|YP_004044376.1| 389 LSRLEDEIEERTATVEELQDERDELQEQVESLESEADELRDQTQTE 434
                                       6688999999999999999999999999999999999988887765 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  12.9     6e-05     0.037      43     205 ..     123     293 ..     117     313 .. 0.73
   2 ?    0.6  30.7      0.28   1.7e+02       5     147 ..     357     500 ..     353     565 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                                       HHHHHHST-----....-SS--SHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHHHHHTS...--- CS
                        MAP65_ASE1  43 sglksiLheepvdvpqsekkelsLlqkkkkldtaleel......rkekaerlaeflelleqlqklceelge...epl 110
                                       ++l++iL + pvd +  e +  sL++++ ++d+++++l         +++r+++++e +e+l +  +el      ++
  gi|313117393|ref|YP_004044376.1| 123 ADLREILMR-PVDTVAIESEIQSLKSERDQIDSEIKQLssvedeIHTLEQRRNSIKETIEELADKRDELTAeieAED 198
                                       578899999.888888888899***********9999933333346899**********999999999988565455 PP

                                       SS--TSS--HHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHHHHHT----SHHHHHHHCT-TTTS-. CS
                        MAP65_ASE1 111 sllidslpkleeleslrkhleelke.......ekerRleeikelkkqIkslmeeLglepktsieedllkesednskk 180
                                         l+++ ++ +el++++++l+ ++          e+  e+i++l+++  + + eL+   +t+ e ++++++ ++   
  gi|313117393|ref|YP_004044376.1| 199 RSLSEQTENKAELDEILEKLQSARSdlksvrfRLESERESIESLRDERTETSDELDALSETDYETKQIESQIEQT-- 273
                                       555556666666555555555555555555558888899**************************9995544444.. PP

                                       ...TSHHHHHHHHHHHHHHHHHHHH CS
                        MAP65_ASE1 181 lkpltretikkLkllkkeleeqkse 205
                                            r +i++L+ ++  l+ + + 
  gi|313117393|ref|YP_004044376.1| 274 -----RGRIDELNRTITDLQTIIEY 293
                                       .....55555555555555444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHH...HHST-----....-SS--SHHHHHHHHHHH CS
                        MAP65_ASE1   5 keklisesiknffedl..lseeneieqkilneIaelraeasglk...siLheepvdvpqsekkelsLlqkkkkldta 76 
                                       + + ++++ +++ ++l  ++e++++++++ n+++ l++e+++ +   ++L+ e+ +    +++  sL ++  +l+++
  gi|313117393|ref|YP_004044376.1| 357 RREELRNRLEELDSELreVNEQERRQEELTNRLSRLEDEIEERTatvEELQDERDE---LQEQVESLESEADELRDQ 430
                                       5556677777777777999********************99988344555554433...3444579**********9 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---SS--TSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        MAP65_ASE1  77 leelrkekaerlaeflelleqlqklceelgeeplsllidslpkleeleslrkhleelkeekerRleeikel 147
                                        +  + e  ++++e++ +l+q ++ +e +   +l + +d+l+  eel++ r++++e+ +e  +R+e+i++ 
  gi|313117393|ref|YP_004044376.1| 431 TQTELIERHKQRNEYEFKLDQKRDELEDITA-ELAEKQDELERREELKQRREQVKEQLAETRSRIESIETN 500
                                       9999999999999999999999998888888.67799******************************9864 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  14.7    0.0079       4.9      32     117 ..     139     227 ..     137     229 .. 0.86
   2 ?    9.5   7.0    0.0016      0.99      54     117 ..     220     282 ..     212     289 .. 0.86
   3 ?    5.1  28.2     0.036        22       3     114 ..     337     444 ..     335     447 .. 0.94
   4 ?    3.0  30.1      0.17     1e+02       5     115 ..     391     497 ..     389     502 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0079
                        TPR_MLP1_2  32 ekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeq...keelekel 105
                                       e++ +++k   ++  +e+ + ++  +e+ +l ++ n++k++i+el +++++++ae+e++  s++eq   k el++ l
  gi|313117393|ref|YP_004044376.1| 139 ESEIQSLKSERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQtenKAELDEIL 215
                                       56677788888888899999999999999999999**************************9998744467899999 PP

                        TPR_MLP1_2 106 selekriedlne 117
                                       ++l++ + dl++
  gi|313117393|ref|YP_004044376.1| 216 EKLQSARSDLKS 227
                                       999999999986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                        TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlne 117
                                       ++  +l+++r +l++ ++ i++l++e+ +++ el++  e    + +++e+++++++ ri++ln 
  gi|313117393|ref|YP_004044376.1| 220 SARSDLKSVRFRLESERESIESLRDERTETSDELDALSETDY-ETKQIESQIEQTRGRIDELNR 282
                                       5667899999999*********************99877655.55689**************85 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.036
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                        +++ee+ ++l++  +e++++ ++l++ le+  ++++e ++    +   ++e ++ l++l +e++e +a+++el++e
  gi|313117393|ref|YP_004044376.1| 337 QSQVEETTDRLRSLRDEHRERREELRNRLEELDSELREVNE----QERRQEELTNRLSRLEDEIEERTATVEELQDE 409
                                       5789999*********************************9....778899************************** PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelselekried 114
                                       ++++++++e  e++ +e +++ ++el e  k++++
  gi|313117393|ref|YP_004044376.1| 410 RDELQEQVESLESEADELRDQTQTELIERHKQRNE 444
                                       **************************998888877 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.17
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                       +le+ei++ ++  ee++++  +lqe++e+ +++a e  ++ ++el++     k+ +++  +l++ ++e+++++ae+ 
  gi|313117393|ref|YP_004044376.1| 391 RLEDEIEERTATVEELQDERDELQEQVESLESEADELRDQTQTELIERH---KQRNEYEFKLDQKRDELEDITAELA 464
                                       5666666666666666666666666666666666666666666666443...4444555666666666666666666 PP

                        TPR_MLP1_2  82 sakaeleeseesweeqkeelekelselekriedl 115
                                       + + ele+ e ++++++e+ +++l+e+++rie +
  gi|313117393|ref|YP_004044376.1| 465 EKQDELERRE-ELKQRREQVKEQLAETRSRIESI 497
                                       6666665543.46666666666666666666654 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  21.3    0.0029       1.8       8     179 ..     146     291 ..     133     304 .. 0.59
   2 ?    4.9  38.7     0.011       6.8      19     178 ..     336     500 ..     320     517 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                               MAD   8 kaaleqlknelkqkelehkrarielekkasalkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkkn 84 
                                       k                             + ++q++ e ++  +++++i+ le+r +  +e+ +e + +   ++  
  gi|313117393|ref|YP_004044376.1| 146 K-----------------------------SERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAE 193
                                       2.............................33556777777777777777777777777777777777777777777 PP

                               MAD  85 lealnkkekekesklaearevisalknelaelkr...qiekqelelsekeseleelqerldllkkklseleqliqql 158
                                        ea ++ ++e+++++ae+ e+ ++l+   ++lk     +e +   +++ + e  e   +ld l ++  e++q  +q 
  gi|313117393|ref|YP_004044376.1| 194 IEAEDRSLSEQTENKAELDEILEKLQSARSDLKSvrfRLESERESIESLRDERTETSDELDALSETDYETKQIESQI 270
                                       77777777777777777777766665544444331114555555555666666666666666666555555555666 PP

                               MAD 159 ekkqkelaeaeqrikeLefei 179
                                       e+      e + +i +L+  i
  gi|313117393|ref|YP_004044376.1| 271 EQTRGRIDELNRTITDLQTII 291
                                       666666666666666665443 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.011
                               MAD  19 kqkelehkrarielekkasalkrqleeesdrnqelqkrikllekreeekee......alreqiElarl.kkknleal 88 
                                       +q ++e+  +r+ + +   + ++  ee ++r +el+ ++++++++e  +ee       l+++iE+  +  +  +++ 
  gi|313117393|ref|YP_004044376.1| 336 EQSQVEETTDRLRSLRD--EHRERREELRNRLEELDSELREVNEQERRQEEltnrlsRLEDEIEERTAtVEELQDER 410
                                       55555555555555555..3334445556666666666666666664444311111122344444333033444677 PP

                               MAD  89 nkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkel 165
                                       ++++++ es + ea e+ ++ + el e+++q ++ e +l +k+ ele++  +l +++ +l+  e+l+q  e+ +++l
  gi|313117393|ref|YP_004044376.1| 411 DELQEQVESLESEADELRDQTQTELIERHKQRNEYEFKLDQKRDELEDITAELAEKQDELERREELKQRREQVKEQL 487
                                       778888899999999999*******************************************9999999999999999 PP

                               MAD 166 aeaeqrikeLefe 178
                                       ae   ri  +e +
  gi|313117393|ref|YP_004044376.1| 488 AETRSRIESIETN 500
                                       9999999999875 PP

>> IMPa_helical  Immunomodulating metalloprotease helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       5.1   3.1e+03      21      51 ..     154     184 ..     103     198 .. 0.65
   2 ?    5.4   0.1     0.039        24      24      63 ..     342     381 ..     319     394 .. 0.79
   3 ?    1.0   0.2      0.91   5.7e+02      28      65 ..     398     435 ..     381     444 .. 0.75
   4 ?    3.6   0.2      0.14        88      11      66 ..     458     513 ..     449     517 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.1
                                       EETEE-TTSTTH.HHHHHHHHHHHHHHHHHH CS
                      IMPa_helical  21 snvksCdeeaklkeefkkaaesirsaleald 51 
                                       s++k+ +++++  ++++++ +si++++e+l 
  gi|313117393|ref|YP_004044376.1| 154 SEIKQLSSVEDEIHTLEQRRNSIKETIEELA 184
                                       3333333333333444455555555555554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.039
                                       EE-TTSTTH.HHHHHHHHHHHHHHHHHHHTT--GGGSSS- CS
                      IMPa_helical  24 ksCdeeaklkeefkkaaesirsalealdsskidlfaeegy 63 
                                       ++ d   +l++e +++ e++r++le+lds+  ++ ++e+ 
  gi|313117393|ref|YP_004044376.1| 342 ETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQERR 381
                                       4566778999*******************99999887754 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.91
                                       TSTTH.HHHHHHHHHHHHHHHHHHHTT--GGGSSS-HH CS
                      IMPa_helical  28 eeaklkeefkkaaesirsalealdsskidlfaeegyrl 65 
                                       e+ +  ee+++  +++++++e+l+s++ +l ++++++l
  gi|313117393|ref|YP_004044376.1| 398 ERTATVEELQDERDELQEQVESLESEADELRDQTQTEL 435
                                       55667788888999999999999998888877776655 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.14
                                       -----GGG-EEETEE-TTSTTH.HHHHHHHHHHHHHHHHHHHTT--GGGSSS-HHH CS
                      IMPa_helical  11 sftvdlskCdsnvksCdeeaklkeefkkaaesirsalealdsskidlfaeegyrle 66 
                                       + t++l++ +++ +  +e ++ +e+ k++ ++ rs++e+ ++++i+ f+ee  +++
  gi|313117393|ref|YP_004044376.1| 458 DITAELAEKQDELERREELKQRREQVKEQLAETRSRIESIETNAIEAFNEEMETVL 513
                                       5566777777777777788888999999*********************9976665 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.1    0.0016      0.96      45      94 ..     137     186 ..     133     188 .. 0.89
   2 ?    1.0   1.8      0.84   5.2e+02      51      92 ..     181     219 ..     173     235 .. 0.48
   3 ?    7.9   3.4    0.0059       3.7      16      87 ..     219     290 ..     212     293 .. 0.79
   4 ?    8.9   8.8     0.003       1.8      19      95 ..     341     417 ..     331     418 .. 0.87
   5 ?    3.9   1.8      0.11        67      58      85 ..     401     428 ..     398     440 .. 0.70
   6 ?    1.5   4.5      0.62   3.8e+02      36      79 ..     453     499 ..     448     517 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                           BLOC1_2  45 slekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                        +e++++ l+++ +++++ ++q+  +e+++ +Le+  + + e + eL +k
  gi|313117393|ref|YP_004044376.1| 137 AIESEIQSLKSERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADK 186
                                       68999*****************************9999998888888765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.84
                           BLOC1_2  51 eklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       e+l     + +++  +i++ +++++e +e+ +eLDe+  +L+
  gi|313117393|ref|YP_004044376.1| 181 EELAD---KRDELTAEIEAEDRSLSEQTENKAELDEILEKLQ 219
                                       22222...2233333444444444444444444444444443 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0059
                           BLOC1_2  16 eatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87 
                                       +++++d+k +    e+  e +++l+d+  +++++l++l+e++ e ++  +qi+q   +++eL  ++  L ++
  gi|313117393|ref|YP_004044376.1| 219 QSARSDLKSVRFRLESERESIESLRDERTETSDELDALSETDYETKQIESQIEQTRGRIDELNRTITDLQTI 290
                                       555556666665566677788899999999999999999999999999999999999999999999888765 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.003
                           BLOC1_2  19 vedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                        e  + L  l  +  e+ ++l++++++l ++l ++ne++   +++ +++ ++e++++e +++v+eL     eL++++
  gi|313117393|ref|YP_004044376.1| 341 EETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQEQV 417
                                       455667777888889999************************************************88888887765 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.11
                           BLOC1_2  58 eelqpylqqidqiekqvteLeeavseLD 85 
                                       ++++++ ++ d++++qv++Le+ ++eL 
  gi|313117393|ref|YP_004044376.1| 401 ATVEELQDERDELQEQVESLESEADELR 428
                                       5566667777888888888888888883 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.62
                           BLOC1_2  36 ykklkdvaaslekkleklnekye...elqpylqqidqiekqvteLee 79 
                                        ++l+d++a+l++k ++l++++e     ++ ++q+ +   +++++e+
  gi|313117393|ref|YP_004044376.1| 453 RDELEDITAELAEKQDELERREElkqRREQVKEQLAETRSRIESIET 499
                                       56677777777777776666322111444455555566666666665 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  24.2   0.00082      0.51     239     390 ..     141     293 ..     133     320 .. 0.82
   2 ?    4.3  29.7    0.0091       5.6     393     529 ..     337     466 ..     327     471 .. 0.70
   3 ?    3.5  23.7     0.016       9.8     808     940 ..     401     525 ..     396     546 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00082
                           DUF3584 239 aiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeai..delnqe 313
                                       +i++ + e +++  e++ql s+e ++ +l++   + +e ++e   +++e  ae++++ r+l ++ ++++  de  ++
  gi|313117393|ref|YP_004044376.1| 141 EIQSLKSERDQIDSEIKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQTENKAelDEILEK 217
                                       68888899999999999999999999999999999999999999999999999999999988888877533788999 PP

                           DUF3584 314 lsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkike 390
                                       l+ a+ +l+  + +le   e+ +   d++ e+ + +ld+l ++  e +++e +++   +++ ++++    ++  i+ 
  gi|313117393|ref|YP_004044376.1| 218 LQSARSDLKSVRFRLESERESIESLRDERTET-SDELDALSETDYETKQIESQIEQTRGRIDELNRTITDLQTIIEY 293
                                       99999999999999999999999999999987.57899999999999999999999999999998888777665543 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0091
                           DUF3584 393 eeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEeleq 469
                                       + ++e+  +rl  +r+e  +++++ ++ le+l s+lr     + +e +++++el++rls+l+  +++ tat Eel++
  gi|313117393|ref|YP_004044376.1| 337 QSQVEETTDRLRSLRDEHRERREELRNRLEELDSELR-----EVNEQERRQEELTNRLSRLEDEIEERTATVEELQD 408
                                       667888999999999999999****************.....667777889999****************9999988 PP

                           DUF3584 470 ie.eadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqaleel 529
                                        + e +e++e  ++e+ + +++    q+e+ +  k+r+e + +l + ++ le+  ++l+e 
  gi|313117393|ref|YP_004044376.1| 409 ERdELQEQVESLESEADELRDQT---QTELIERHKQRNEYEFKLDQKRDELEDITAELAEK 466
                                       65245666766666666555544...44444444444444444444444444444444332 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.016
                           DUF3584 808 lkvdslaeerpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqldqldenlrklrdllsklaelk 884
                                       + v++l++er++l+eqve+les+a el+++ ++   + +++r++ e +++  ++ l+ ++++l + +d+l++  elk
  gi|313117393|ref|YP_004044376.1| 401 ATVEELQDERDELQEQVESLESEADELRDQTQTELIERHKQRNEYEFKLDQKRDELEDITAELAEKQDELERREELK 477
                                       56789999999999999999999999998888888888888888999999999999999999988888888888887 PP

                           DUF3584 885 ldadaeqaegelaerlaaleelkrkrerlsedvkkalerfkgvlkdksgsglaetw 940
                                         +++ +++  lae+        r+++ + +++++++e++++vl+     ++++ w
  gi|313117393|ref|YP_004044376.1| 478 QRREQVKEQ--LAET------RSRIESIETNAIEAFNEEMETVLNLLDYENIDRVW 525
                                       776666666..3333......34455666778888888888888777666666666 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   9.3         3   1.9e+03       8      27 ..     175     194 ..     130     259 .. 0.62
   2 ?    8.1   1.3    0.0058       3.6      10      66 ..     243     299 ..     232     310 .. 0.63
   3 ?   -0.3  10.2       2.5   1.6e+03      20      63 ..     365     408 ..     337     474 .. 0.71
   4 ?    2.7   1.2      0.28   1.7e+02      21      62 ..     457     498 ..     446     517 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3
                           NPV_P10   8 vIradikavddkVdalqqqv 27 
                                        I++ i+++ dk d l +++
  gi|313117393|ref|YP_004044376.1| 175 SIKETIEELADKRDELTAEI 194
                                       24444444444444444444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0058
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       r++ ++++d +dal++   + ++   ++++   ++d+++ ++++l+t +e  +d+L 
  gi|313117393|ref|YP_004044376.1| 243 RDERTETSDELDALSETDYETKQIESQIEQTRGRIDELNRTITDLQTIIEYNSDVLA 299
                                       444455666666666655444444445555667777777777777777777666665 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.5
                           NPV_P10  20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       ++ l++++ +v+e+ +  +el+++L ++ ++++e  ++ve+ qd
  gi|313117393|ref|YP_004044376.1| 365 LEELDSELREVNEQERRQEELTNRLSRLEDEIEERTATVEELQD 408
                                       55555555555555555555555555555555555555555443 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.28
                           NPV_P10  21 dalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                       + + +++++ q++l+  +el+++ ++  +qLae  + +e+I+
  gi|313117393|ref|YP_004044376.1| 457 EDITAELAEKQDELERREELKQRREQVKEQLAETRSRIESIE 498
                                       333445555666777778999999999999999999888886 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  27.1     0.075        46      27     157 ..     142     272 ..     136     292 .. 0.82
   2 ?    5.2  35.8      0.02        13      29     213 ..     241     430 ..     239     433 .. 0.69
   3 ?    8.2  30.1    0.0025       1.6      46     153 ..     393     499 ..     390     517 .. 0.89
   4 ?    3.0  18.3     0.096        59      80     153 ..     427     499 ..     425     546 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.075
                         Golgin_A5  27 iasLkegsgeegle..sstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeq 101
                                       i+sLk++  + ++e      +++e+  l+q+r+ ++e +++l  + ++l +e+ + e++  +e+ + + +l e+ e+
  gi|313117393|ref|YP_004044376.1| 142 IQSLKSERDQIDSEikQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAEI-EAEDRSLSEQTENKAELDEILEK 217
                                       8999997655554411455678899999************************6.7899999999999********** PP

                         Golgin_A5 102 leeerkakeeveaelerlkeelryleeelvrskatlqsrikdrekeieklrnqltt 157
                                       l++ r+  ++v+  le+ +e +++l++e +++  +l   + + + e +++++q+ +
  gi|313117393|ref|YP_004044376.1| 218 LQSARSDLKSVRFRLESERESIESLRDERTETSDELD-ALSETDYETKQIESQIEQ 272
                                       ****************************998877765.466778777777777764 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.02
                         Golgin_A5  29 sLkegsgeeglesstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleee 105
                                       sL+++ +e++      + ++l+e+  e +++++++++++++i++l   + dl++  + +++ l  +   + ++l+e+
  gi|313117393|ref|YP_004044376.1| 241 SLRDERTETSD-----ELDALSETDYETKQIESQIEQTRGRIDELNRTITDLQTIIEYNSDVLAGKSDVVADALDED 312
                                       55544433332.....3356677788899999999999999999999999999999999999999888888888877 PP

                         Golgin_A5 106 rkak...eeveaeler.......lkeelryleeelvrskatlqsrikdrekeieklrnqlttkslsssseselesRl 172
                                        + +   + v++ +          + +++ + + l+  + + ++r ++  + +e+l ++l   + ++  ++el +Rl
  gi|313117393|ref|YP_004044376.1| 313 AAGSvtdQLVDSTITCwtcgtnvEQSQVEETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQERRQEELTNRL 389
                                       655411133444443211110002223333333333444444444555555677788888888888999******** PP

                         Golgin_A5 173 kqLtesLiqKQtvlEalsteknslvlQLeRleqqikevqse 213
                                         L + + ++ +++E+l+ e++ l+ Q+e le ++ e+  +
  gi|313117393|ref|YP_004044376.1| 390 SRLEDEIEERTATVEELQDERDELQEQVESLESEADELRDQ 430
                                       **********************************9998765 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0025
                         Golgin_A5  46 saeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkee 122
                                       ++e++e ++  + l++e  +l++q+e+l +e ++l +q+q+e  + ++q +e+e +l+++r + e++ ael+++++e
  gi|313117393|ref|YP_004044376.1| 393 EDEIEERTATVEELQDERDELQEQVESLESEADELRDQTQTELIERHKQRNEYEFKLDQKRDELEDITAELAEKQDE 469
                                       67889999999999999999999999*****99******************************************** PP

                         Golgin_A5 123 lryleeelvrskatlqsrikdrekeieklrn 153
                                       l++ +eel++ ++++++++ +  + ie+++ 
  gi|313117393|ref|YP_004044376.1| 470 LER-REELKQRREQVKEQLAETRSRIESIET 499
                                       *86.7899999********999999998654 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.096
                         Golgin_A5  80 leaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatlqsrikdrekeieklrn 153
                                       l +q+q+e  + ++q +e+e +l+++r + e++ ael+++++el++ +eel++ ++++++++ +  + ie+++ 
  gi|313117393|ref|YP_004044376.1| 427 LRDQTQTELIERHKQRNEYEFKLDQKRDELEDITAELAEKQDELER-REELKQRREQVKEQLAETRSRIESIET 499
                                       5566666666666666666666666666666666666666666664.556666666666666666666665443 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  19.5     0.025        15       5     262 ..      11     411 ..      10     427 .. 0.64
   2 ?   -2.9  20.8       7.1   4.4e+03     129     288 ..     366     536 ..     335     561 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.025
                            AAA_15   5 kikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn........................... 54 
                                       ++ ++N + ++d++++++  +tvl G+N++  +s+l+ +   l  + + +                           
  gi|313117393|ref|YP_004044376.1|  11 QVDVENIGGIEDADVQFQQGITVLTGRNATNRTSFLRSIAAGLGSD-DVSlksdadsghvelkidgesytrsltqkr 86 
                                       6889***********************************8877755.333567888898988889988888888888 PP

                            AAA_15  55 ............................................................................. 54 
                                                                                                                    
  gi|313117393|ref|YP_004044376.1|  87 gtvtfdgdpyledstiadlfafllgsnearravvagadlreilmrpvdtvaieseiqslkserdqidseikqlssve 163
                                       88888888888888888888888888888888888888888888777777777776666666666666665555555 PP

                            AAA_15  55 ......kkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklk 125
                                             ++  +  ke +e+  ++  + + +I+ e           ++++++e k +  ++ +k ++  + +k+  + 
  gi|313117393|ref|YP_004044376.1| 164 deihtlEQRRNSIKETIEELADKRDELTAEIEAED---------RSLSEQTENKAELDEILEKLQSARSDLKSVRFR 231
                                       43333322222333333333333333333333333.........344444444444445566666666666666666 PP

                            AAA_15 126 lkknelsdekisvekkkskkelpkekeeklekekeelkid.....kedlkklikkleeslkkee............. 184
                                       l++++ s e+  +e  + + el+ ++e + e+++ e +i+      ++l+++i +l++++++++             
  gi|313117393|ref|YP_004044376.1| 232 LESERESIESLRDERTETSDELDALSETDYETKQIESQIEqtrgrIDELNRTITDLQTIIEYNSdvlagksdvvada 308
                                       67777777777777777777777777777777777777765555456677777777777777778888888888888 PP

                            AAA_15 185 .....................elknvlksai..iklllisakRnvsdedsekkssllgklkekileealqekleeel 238
                                                            + + + ++++  ++++   + R+   e+ e+ ++ l++l++++ e + qe+  eel
  gi|313117393|ref|YP_004044376.1| 309 ldedaagsvtdqlvdstitcwTCGTNVEQSQveETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQERRQEEL 385
                                       88888888777777777777733333333331134555666677777777777777777777777766666666666 PP

                            AAA_15 239 teklkeiqeklkeidkklaeelk...k 262
                                       t  l++++++++e   +++e l+   +
  gi|313117393|ref|YP_004044376.1| 386 TNRLSRLEDEIEERTATVEE-LQderD 411
                                       66666666666666666633.222443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.1
                            AAA_15 129 nelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee.elknvlksaiiklllisakR 204
                                       +el++e  +v++++ ++e  +++ + le e+ee   + e+l++  ++l+e++++ e e +++  + +++l   +++R
  gi|313117393|ref|YP_004044376.1| 366 EELDSELREVNEQERRQEELTNRLSRLEDEIEERTATVEELQDERDELQEQVESLEsEADELRDQTQTELIERHKQR 442
                                       35566666777777788888888888888888887787777777777777777766555555566666666666666 PP

                            AAA_15 205 nvsdedsekkssllgklkekileealqekl.........eeelteklkeiqeklkeidkklaeelkkilkkkidkik 272
                                       n  + + ++k++ l+ ++ ++ e+  q++l         +e+++e+l e+ + ++ i+ +  e  +++++  ++ ++
  gi|313117393|ref|YP_004044376.1| 443 NEYEFKLDQKRDELEDITAELAEK--QDELerreelkqrREQVKEQLAETRSRIESIETNAIEAFNEEMETVLNLLD 517
                                       666666677777777777777774..666678667777777777777777777777777777777788888888888 PP

                            AAA_15 273 kfnykgkkneeieik...d 288
                                       ++n+ +++ e ++i    +
  gi|313117393|ref|YP_004044376.1| 518 YENIDRVWIERKNIGsgkS 536
                                       8888888888888875551 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  12.9    0.0019       1.2      71     139 ..     138     209 ..     126     210 .. 0.87
   2 ?   11.6  10.7   0.00034      0.21      31     111 ..     209     292 ..     206     297 .. 0.90
   3 ?   -0.2  20.6       1.5   9.3e+02      58     140 .]     337     415 ..     333     415 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                    CENP-F_leu_zip  71 leldLvalrsekeeLe...kelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtqlkeln 139
                                       +e+++++l+se+++++   k+l    +++++Le+++ s+++++ee+ +++ ++  e +a+  +L+ q ++ +
  gi|313117393|ref|YP_004044376.1| 138 IESEIQSLKSERDQIDseiKQLSSVEDEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDRSLSEQTENKA 209
                                       799************933334556789*********************************999999988766 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00034
                    CENP-F_leu_zip  31 relemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr...sekeeLekelqkkqervseLeslns 104
                                       +el ++ e+++++  +  + +  +e+ +e ie l+ e++e + +L+al+    e +++e ++++ + r++eL+++  
  gi|313117393|ref|YP_004044376.1| 209 AELDEILEKLQSARSDLKSVRFRLESERESIESLRDERTETSDELDALSetdYETKQIESQIEQTRGRIDELNRTIT 285
                                       5888888999999999999999999999999999999999999999999555699********************** PP

                    CENP-F_leu_zip 105 slenlle 111
                                       +l+ ++e
  gi|313117393|ref|YP_004044376.1| 286 DLQTIIE 292
                                       **99987 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.5
                    CENP-F_leu_zip  58 keeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtq 134
                                       ++++ee + +lr l+ +  + r+e  +  +el  + ++v+e e+++++l+n l+++E+e     ee  a+veeLq +
  gi|313117393|ref|YP_004044376.1| 337 QSQVEETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQERRQEELTNRLSRLEDEI----EERTATVEELQDE 409
                                       5688999999999999988888887777789999999********************985....6778899999999 PP

                    CENP-F_leu_zip 135 lkelne 140
                                         el+e
  gi|313117393|ref|YP_004044376.1| 410 RDELQE 415
                                       999987 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  21.8    0.0086       5.3      59     257 ..     140     288 ..     124     311 .. 0.42
   2 ?    4.8  44.8     0.018        11      53     278 ..     336     550 ..     332     557 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0086
                          CALCOCO1  59 kekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeeksalleakeesearirELE 135
                                        e +  k++r+++d+e k+l+                                                      +E
  gi|313117393|ref|YP_004044376.1| 140 SEIQSLKSERDQIDSEIKQLS-----------------------------------------------------SVE 163
                                       333333444444443333332.....................................................224 PP

                          CALCOCO1 136 eDiktltqralekEteLeRlkerakkalaqrkeee...aerkqlqakleqseeelrslskelqelrnslaerdtqvl 209
                                       ++i+tl qr       +e l ++   ++a    e+   +e+ + +a+l++  e l+s  ++l+++r  l+    ++ 
  gi|313117393|ref|YP_004044376.1| 164 DEIHTLEQRRNSIKETIEELADKRDELTAEIEAEDrslSEQTENKAELDEILEKLQSARSDLKSVRFRLESERESIE 240
                                       44444444444433334444443333333222221111233333334444444444444444444444444444444 PP

                          CALCOCO1 210 qLqdtittltqkLttAqrkeaenEallkelrslqerlaaSerkvegLk 257
                                        L+d+ t++ ++L++      e+ ++  ++  ++ r+   +r+ + L+
  gi|313117393|ref|YP_004044376.1| 241 SLRDERTETSDELDALSETDYETKQIESQIEQTRGRIDELNRTITDLQ 288
                                       444444444444444444444444444444444443333333333332 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.018
                          CALCOCO1  53 anrqrekekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeeksalleakeesea 129
                                        + q+e+   + ++ r+e  ++r+el++r+eel +el+e++e+           er +eel+++ s+l ++ ee++a
  gi|313117393|ref|YP_004044376.1| 336 EQSQVEETTDRLRSLRDEHRERREELRNRLEELDSELREVNEQ-----------ERRQEELTNRLSRLEDEIEERTA 401
                                       5667788888888888888888888888888888887776654...........4566799999999********** PP

                          CALCOCO1 130 rirELEeDiktltqralekEteLeRlkerakkalaqrkeeeaerkqlqakleqseeelrslskelqelrnslaerdt 206
                                        + EL ++   l +++   E e + l+++ +  l    e +++r++++ kl+q ++el+ +++el e ++ l++r+ 
  gi|313117393|ref|YP_004044376.1| 402 TVEELQDERDELQEQVESLESEADELRDQTQTELI---ERHKQRNEYEFKLDQKRDELEDITAELAEKQDELERREE 475
                                       ****************************9876555...5667889999*******************9999988874 PP

                          CALCOCO1 207 qvl...qLqdtittltqkLttAqrkeaenEallkelrslqerlaaSe.rkvegLkeeLssvaaqrdrtqa.eLHqaR 278
                                         +   q++++++++++++++ +      Ea  +e+ ++ ++l   +  +v   ++++ s  + r++  a eLH +R
  gi|313117393|ref|YP_004044376.1| 476 LKQrreQVKEQLAETRSRIESIET--NAIEAFNEEMETVLNLLDYENiDRVWIERKNIGSGKSNRNSQSAfELHIVR 550
                                       332111555666666666665543..456899999999999988765234555567777777777654444777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3324  (0.185398); expected 358.6 (0.02)
Passed bias filter:                      939  (0.0523733); expected 358.6 (0.02)
Passed Vit filter:                       336  (0.0187406); expected 17.9 (0.001)
Passed Fwd filter:                       212  (0.0118244); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 3.21u 0.36s 00:00:03.57 Elapsed: 00:00:00.91
# Mc/sec: 2124.20
//
Query:       gi|313117394|ref|YP_004044377.1|  [L=206]
Description: hypothetical protein Hbor_31810 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1374.45
//
Query:       gi|313117395|ref|YP_004044378.1|  [L=207]
Description: hypothetical protein Hbor_31820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1546.99
//
Query:       gi|313117396|ref|YP_004044379.1|  [L=104]
Description: HalX domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-12   46.1  13.2    1.3e-11   44.6  12.8    1.9  1  HalX      HalX domain
     0.0012   18.8   0.8     0.0015   18.6   0.8    1.1  1  Erp_C     Erp protein C-terminus
     0.0032   17.3   3.4     0.0046   16.8   3.4    1.3  1  SPAM      Salmonella surface presentation of antigen gene typ
  ------ inclusion threshold ------
       0.46   11.1   4.6       0.28   11.8   1.7    1.9  2  ADSL_C    Adenylosuccinate lyase C-terminus
       0.75    8.8   7.8        0.8    8.7   7.8    1.1  1  Atg14     Vacuolar sorting 38 and autophagy-related subunit 1


Domain annotation for each model (and alignments):
>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6  12.8   3.7e-15   1.3e-11       2      65 ..      26      89 ..      12      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 3.7e-15
                              HalX  2 rseYdeelqelfaLasKravLeaekseaeLadseeYqeLearleelraqldetldelddaddfe 65
                                      rse+  e++ l+aL++K avL+ +kseaeL +s +Y++L+a +ee ++ ld++ ++l d+++f 
  gi|313117396|ref|YP_004044379.1| 26 RSEFAAEIRSLYALQNKAAVLRESKSEAELKQSLAYSQLQAAIEERKSSLDAERERLADDHEFI 89
                                      9*******************************************************99988885 PP

>> Erp_C  Erp protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.8   4.1e-07    0.0015      66     131 ..      22      89 ..       9     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.1e-07
                             Erp_C  66 llkelsdtrdelrtklnegnkayivlek..epklkenvnvseikedleklkskleevkkylkdedkfe 131
                                        l   s+   e+r+    +nka +  e   e +lk+++  s+++  +e+ ks l+  ++ l d+++f 
  gi|313117396|ref|YP_004044379.1|  22 QLLSRSEFAAEIRSLYALQNKAAVLRESksEAELKQSLAYSQLQAAIEERKSSLDAERERLADDHEFI 89 
                                       4444577778999999999**9998876679********************************99984 PP

>> SPAM  Salmonella surface presentation of antigen gene type M protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   3.4   1.3e-06    0.0046      40     105 ..      12      86 ..       8      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                              SPAM  40 qragLkeLLdlqrpegk.sldreelyallrkqaivrrqlkeLeLql........vaiqekrselqkekeelskks 105
                                       +r++L+ L++ + + ++   +   lyal+ k a++r    e eL+          ai+e++s l+ e+e+l   +
  gi|313117396|ref|YP_004044379.1|  12 KRQELRDLVQQLLSRSEfAAEIRSLYALQNKAAVLRESKSEAELKQslaysqlqAAIEERKSSLDAERERLADDH 86 
                                       677888888866444431366789***************9999985323322225899***********998765 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.7   7.7e-05      0.28      11      61 ..       6      63 ..       5      71 .. 0.77
   2 ?    0.5   0.2      0.25     9e+02      35      48 ..      74      90 ..      59     101 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.7e-05
                                      HHHHTH-HHHHHHHHHHHHHHHHHC....HHHHHHT-HHHH.C..HHCHHHHHT-GGG CS
                            ADSL_C 11 aLvkglgReeAyelVqeaamkawee....llelLaadpevk.k..seeeldalfdpay 61
                                       L+k + R+e ++lVq++  ++        l +L++ ++v  +  se+el++ + +++
  gi|313117396|ref|YP_004044379.1|  6 YLTKPIKRQELRDLVQQLLSRSEFAaeirSLYALQNKAAVLrEskSEAELKQSLAYSQ 63
                                      58899*************9998755678844566677777645799999998887765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                                      C...HHHHHHT-HHHHC CS
                            ADSL_C 35 e...llelLaadpevkk 48
                                      +    +e+La d e+  
  gi|313117396|ref|YP_004044379.1| 74 SldaERERLADDHEFIS 90
                                      14445677777766653 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   7.8   0.00022       0.8      38     117 ..      13      95 ..       7     104 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00022
                             Atg14  38 keslkkkiekalegke..eaeqledkiknkkakleelksliadlre.rlqelkdklsqlkkeieekkkklaklsdkl 111
                                       +++l+  ++++l++ e  +  ++  +++nk+a l+e ks+ +++++   ++l++ ++++k+++++ +++la   + +
  gi|313117396|ref|YP_004044379.1|  13 RQELRDLVQQLLSRSEfaAEIRSLYALQNKAAVLRESKSEAELKQSlAYSQLQAAIEERKSSLDAERERLADDHEFI 89 
                                       556666667777777765455666799*************999887469**********************988888 PP

                             Atg14 112 kkRrsd 117
                                       ++ r  
  gi|313117396|ref|YP_004044379.1|  90 SQIRDI 95 
                                       765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1639  (0.0914161); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 693.29
//
Query:       gi|313117397|ref|YP_004044380.1|  [L=98]
Description: response regulator with CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-13   50.8   0.2      2e-13   50.5   0.2    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.2   1.1e-17     2e-13       1      80 [.       8      84 ..       8      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.1e-17
                                      EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEES CS
                      Response_reg  1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviilta 79
                                      vliv+Dd  v++  + +l  ++y +v+ a  g+eal+ ++   +d+illD +mpg++G e+l++i+e+d ++ v i++a
  gi|313117397|ref|YP_004044380.1|  8 VLIVEDDLQVAKTYEHWLS-ADY-RVELAMGGREALDAVHDA-IDVILLDRRMPGVSGDEVLERIHERDIDCYVAIVSA 83
                                      8*****************9.99*.***************876.**********************************98 PP

                                      S CS
                      Response_reg 80 h 80
                                       
  gi|313117397|ref|YP_004044380.1| 84 V 84
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 630.37
//
Query:       gi|313117398|ref|YP_004044381.1|  [L=282]
Description: hypothetical protein Hbor_31850 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 2078.98
//
Query:       gi|313117399|ref|YP_004044382.1|  [L=456]
Description: PAS domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.9e-23   80.5   0.5    1.5e-12   47.7   0.1    2.5  2  PAS_4        PAS fold
    4.1e-19   69.1   0.0    7.6e-19   68.3   0.0    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.7e-11   43.2   0.0    0.00041   20.6   0.0    2.8  2  PAS_9        PAS domain
    1.3e-10   41.2   0.0    2.3e-08   34.0   0.0    2.7  2  PAS          PAS fold
    4.7e-07   29.8   0.7    4.7e-07   29.8   0.7    2.1  2  HisKA        His Kinase A (phospho-acceptor) domain
    6.1e-07   29.4   0.1    1.6e-06   28.1   0.1    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
    3.3e-06   26.7   1.1    7.6e-06   25.6   1.1    1.6  1  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain
    5.6e-06   26.2   0.0    1.3e-05   25.0   0.0    1.6  1  HATPase_c_5  GHKL domain
      2e-05   24.2   0.0    4.2e-05   23.2   0.0    1.5  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
     0.0004   20.9   0.0       0.67   10.6   0.0    2.8  2  PAS_10       PAS domain
      0.007   16.6   0.1        1.1    9.6   0.0    2.6  2  PAS_3        PAS fold
  ------ inclusion threshold ------
       0.02   14.7   0.2       0.21   11.3   0.0    2.2  2  dCache_1     Cache domain
      0.024   14.7   1.4       0.84    9.8   0.1    3.1  3  YojJ         Bacterial membrane-spanning protein N-terminus
       0.11   12.6   0.0       0.49   10.5   0.0    2.1  1  PAS_8        PAS domain
       0.25   11.3   4.6      0.075   13.0   1.6    1.6  2  AIF-MLS      Mitochondria Localisation Sequence


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.4e-10   2.8e-07      11     108 ..      31     125 ..      28     127 .. 0.93
   2 !   47.7   0.1   1.3e-15   1.5e-12       1     110 []     129     231 ..     129     231 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.4e-10
                             PAS_4  11 ldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllP 87 
                                       +d+++r +++ +     +g++ ee++Gkt+ael+++ + +++++a r+++e+e ++e++ +  ++ ++  y + + P
  gi|313117399|ref|YP_004044382.1|  31 VDTELRHTWVAKP---TLGVSKEEIIGKTDAELFTDAVSGPVMEAKREAIETESHVEREFTSIHSSRQNRYRIAAEP 104
                                       6888888888887...578********************************************************** PP

                             PAS_4  88 lrdesGevigvlvisrDiTer 108
                                       + d++ +  g+++ ++D++ +
  gi|313117399|ref|YP_004044382.1| 105 IYDTDDKLEGAMCAAIDLSGQ 125
                                       *****************9866 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 1.3e-15
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l+++ d ++ +d+d +v+++N+++ae   ++p e++G+  ++++ e+  ++l ++ rrv+e++ep+e++++l  ++ 
  gi|313117399|ref|YP_004044382.1| 129 LERTTDSVFTVDSDWNVTFWNERIAERTDIEPGEIVGENIWDVYEERIPTELKAQFRRVMETGEPAETEQYLP-EPF 204
                                       678899**************************************************************99555.5** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       + ++e+r++  +d      g+ v+sr+iTer++
  gi|313117399|ref|YP_004044382.1| 205 GYWVEIRMFADDD------GLSVYSREITERKE 231
                                       **********655......9***********85 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   6.4e-22   7.6e-19       8     110 ..     355     454 ..     349     456 .] 0.89

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 6.4e-22
                                       HHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHH CS
                         HATPase_c   8 qiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkk 83 
                                        +++nl++Nav ++  + +ei+v+i+ ++d++ ++v DnG+Gip ++ +k+f+k  +      +++gtG+Gl++v+ 
  gi|313117399|ref|YP_004044382.1| 355 SVFRNLLKNAVLHNDkQVPEITVTIDERDDEIIVRVADNGPGIPDNQKEKIFGKGEK----GLDSEGTGIGLYLVQT 427
                                       699**********44577799*****8779***********************7666....44589*********** PP

                                       HHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  84 lvelmgGeiwvesepgrGttftftlpl 110
                                       lve +gG+i+ve+++ +G  f +tlp+
  gi|313117399|ref|YP_004044382.1| 428 LVEGYGGSIEVEDNEPEGAVFSVTLPK 454
                                       *************************97 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.4e-07   0.00076      23     103 ..      44     123 ..      40     124 .. 0.85
   2 !   20.6   0.0   3.4e-07   0.00041       2      83 ..     134     213 ..     133     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.4e-07
                             PAS_9  23 llGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiiv 97 
                                        lG s+ee++gk   +lf  + +    e +r+a+e+ +    e+e + i++++ +  +++ a p++d+d++l g+ +
  gi|313117399|ref|YP_004044382.1|  44 TLGVSKEEIIGKTDAELFtdAVSGPVMEAKREAIETES--HVEREFTSIHSSR-QNRYRIAAEPIYDTDDKLEGAMC 117
                                       5899**************77777777777777777777..8888888888876.66669****************** PP

                             PAS_9  98 ilrDit 103
                                         +D++
  gi|313117399|ref|YP_004044382.1| 118 AAIDLS 123
                                       *99987 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.4e-07
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       d+++ +++d +++++Ne  ++ +   p e++g +i+d++  +++   +l+a++++  ++ +  e++ + ++   +wv
  gi|313117399|ref|YP_004044382.1| 134 DSVFTVDSDWNVTFWNERIAERTDIEPGEIVGENIWDVY--EERIPTELKAQFRRVMETGEPAETEQYLPEPFGYWV 208
                                       6889888999*****************************..888888888888888865555555555555555776 PP

                             PAS_9  79 lltas 83 
                                       +++++
  gi|313117399|ref|YP_004044382.1| 209 EIRMF 213
                                       66654 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.037        44      34     112 ..      45     121 ..      41     122 .. 0.66
   2 !   34.0   0.0   1.9e-11   2.3e-08       6      78 ..     128     200 ..     126     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.037
                                       HSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC.TTSSEEEEEEEEEEEEETTEEEEEEEEE CS
                               PAS  34 lGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl.rdgrpihlevraspvrdaggeilgflgv 109
                                       lG s ee++gk+  +l+    +  + e+ ++   + e ++++e+ f+     r    ++ a p++d ++++ g+++ 
  gi|313117399|ref|YP_004044382.1|  45 LGVSKEEIIGKTDAELFTDAVSGPVMEAKRE---AIETESHVEREFTSiHSSRQNRYRIAAEPIYDTDDKLEGAMCA 118
                                       8999999999999988865422134444444...4455555555555553355555567899999999999999998 PP

                                       EEE CS
                               PAS 110 lrd 112
                                       + d
  gi|313117399|ref|YP_004044382.1| 119 AID 121
                                       877 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 1.9e-11
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +le ++d +f vD d +++++N+ ++e + +++ e++g+++ d++ e  + el++++++++e+ge++++++  
  gi|313117399|ref|YP_004044382.1| 128 FLERTTDSVFTVDSDWNVTFWNERIAERTDIEPGEIVGENIWDVYEERIPTELKAQFRRVMETGEPAETEQYL 200
                                       688999***************************************************************9976 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.5   5.3e+03      44      64 ..       6      26 ..       4      28 .. 0.61
   2 !   29.8   0.7   3.9e-10   4.7e-07       6      62 ..     247     301 ..     232     303 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.5
                                      HHHHHHHHHHHHHHHHHHCCH CS
                             HisKA 44 iesearrldhlvedlLdlsri 64
                                      +++e +r ++ +e +L+ +r+
  gi|313117399|ref|YP_004044382.1|  6 LRRELQRTERFLELVLETGRM 26
                                      556666666666666666665 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 3.9e-10
                                       HHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHC CS
                             HisKA   6 lagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdls 62 
                                        + + H++r+ L  ++g+a+++ +  +l+ee k+y+eti++ a++  +l  + +++s
  gi|313117399|ref|YP_004044382.1| 247 NQVLRHDIRNDLQMVSGYADLIAE--QLDEEDKAYVETIQKRAEHAVELTRTAREIS 301
                                       56789*****************99..7******************999999888876 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   1.3e-09   1.6e-06      41     113 ..     362     435 ..     358     451 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.3e-09
                       HATPase_c_2  41 tNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvDev..e 113
                                        Nav h+ ++ p  +++v+++ +++++ v+vaD+Gpg  d ++ +  ++ e+  + +  G+Gl+l+++lv+ +  +
  gi|313117399|ref|YP_004044382.1| 362 KNAVLHNDKQVP--EITVTIDERDDEIIVRVADNGPGiPDNQKEKIFGKGEKGLDSEGTGIGLYLVQTLVEGYggS 435
                                       69*******999..666667799**************99999999999999999***************9876553 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   1.1   6.3e-09   7.6e-06       3      54 ..     233     288 ..     231     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.3e-09
                            SPOB_a   3 keeikelkeliklL.rsqRHDflNhLQvIsGylqL..gky.dkaeeyieevvkelk 54 
                                       +++++++++ +++L +++RHD  N+LQ +sGy +L  +++ ++ ++y+e + k ++
  gi|313117399|ref|YP_004044382.1| 233 EQQLESQRDTLDILnQVLRHDIRNDLQMVSGYADLiaEQLdEEDKAYVETIQKRAE 288
                                       678999********99*****************98443331334456666666555 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.1e-08   1.3e-05       6      91 ..     353     442 ..     348     453 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.1e-08
                       HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkkle...sskskkeehGiGlksir 75 
                                       l +++ nlL NA+   +k+    ++I++t+ e+++ +i+++  +  g    +k+k++   ++  ++e  GiGl  ++
  gi|313117399|ref|YP_004044382.1| 353 LPSVFRNLLKNAVLHNDKQV---PEITVTIDERDDEIIVRVADNGPGipdnQKEKIFgkgEKGLDSEGTGIGLYLVQ 426
                                       5689*********9998866...89***********9999988755544446677665556678999********** PP

                       HATPase_c_5  76 eivkkykgnlsieaed 91 
                                        +v+ y+g++++e ++
  gi|313117399|ref|YP_004044382.1| 427 TLVEGYGGSIEVEDNE 442
                                       **********998776 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.5e-08   4.2e-05     131     163 ..     237     269 ..     226     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.5e-08
                         HisKA_4TM 131 krisdalafvndlirhdlrndlvvirgyaeaie 163
                                       +   d+l  +n+++rhd+rndl+++ gya+ i+
  gi|313117399|ref|YP_004044382.1| 237 ESQRDTLDILNQVLRHDIRNDLQMVSGYADLIA 269
                                       56679************************9996 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0057       6.8       4     105 ..      20     122 ..      17     123 .. 0.63
   2 !   10.6   0.0   0.00056      0.67       4      87 ..     128     214 ..     126     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0057
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipadvGrpladihpk....kavknveeviealrtgekdevevvvpk 76 
                                       +L++  ++  f+D++l+ ++  +   +l   +++ +G + a++ ++      ++  +e ie+ +  e++  +++  +
  gi|313117399|ref|YP_004044382.1|  20 VLETGRMNGSFVDTELRHTWVAKP--TLGVSKEEIIGKTDAELFTDavsgPVMEAKREAIETESHVEREFTSIHS-S 93 
                                       566666666677777777766555..5666666667766666655521113344444455555555555555443.6 PP

                            PAS_10  77 ngkwvlvrylpyrdedgeiaGvvetfvDi 105
                                       +++ + +   p++d+d++ +G++   +D+
  gi|313117399|ref|YP_004044382.1|  94 RQNRYRIAAEPIYDTDDKLEGAMCAAIDL 122
                                       77779999***************999997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00056
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknveevi.ealrtgekdevevvvp.kn 77 
                                       +L+ t  ++  +D++ +++++++++++  ++ p++ vG+++ d+ ++++ ++++  +   + tge  e e + p   
  gi|313117399|ref|YP_004044382.1| 128 FLERTTDSVFTVDSDWNVTFWNERIAERTDIEPGEiVGENIWDVYEERIPTELKAQFrRVMETGEPAETEQYLPePF 204
                                       67778888889********************998648**************99876515566777788888887455 PP

                            PAS_10  78 gkwvlvrylp 87 
                                       g wv +r+++
  gi|313117399|ref|YP_004044382.1| 205 GYWVEIRMFA 214
                                       9999999876 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.037        44      11      81 ..      44     111 ..      41     119 .. 0.81
   2 !    9.6   0.0   0.00094       1.1       2      56 ..     146     198 ..     145     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                             PAS_3  11 ilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengk 81 
                                       +lG+s+ee++gk  + ++l        v+ea  ea+++ +++e e+  ++ + + r+ +  a++i+d + k
  gi|313117399|ref|YP_004044382.1|  44 TLGVSKEEIIGK--TDAELFTDAVSGPVMEAKREAIETESHVEREFTSIHSSRQNRY-RIAAEPIYDTDDK 111
                                       79**********..889999999999*******************999998877764.4445666666655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00094
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegey 56 
                                       ++++er+ e ++++p e+ g   ++ d+       ++++++ +++++gep e+e 
  gi|313117399|ref|YP_004044382.1| 146 TFWNERIAERTDIEPGEIVGE--NIWDVYEERIPTELKAQFRRVMETGEPAETEQ 198
                                       79*******************..99999999999999999999999999998874 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.21     124     167 ..      88     129 ..      39     151 .. 0.77
   2 ?    1.0   0.2      0.25     3e+02       6      81 ..     230     307 ..     212     385 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                          dCache_1 124 sdpyvdqtggkpvitiavpiyddsgkfiGvlaadldldnlqdll 167
                                       + ++++ + ++ +   a+piyd++ k +G+++a++dl+  +++l
  gi|313117399|ref|YP_004044382.1|  88 TSIHSS-R-QNRYRIAAEPIYDTDDKLEGAMCAAIDLSGQYQFL 129
                                       455543.4.56777889*****99************98655555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.25
                          dCache_1   6 qaeeqllglaeqlanniedvl.dslenlaetlasnps.lqdlleepnra.neasreslqallksilksnpdisgvyl 79 
                                       + +eq+l++ + + + ++ vl + ++n +++++   + +++ l+e ++a  e ++++++++++ +  + + is+v +
  gi|313117399|ref|YP_004044382.1| 230 KEYEQQLESQRDTLDILNQVLrHDIRNDLQMVSGYADlIAEQLDEEDKAyVETIQKRAEHAVELTRTA-REISEVLF 305
                                       44555555555555666666655577777777666665666777766665555555555555544333.34555554 PP

                          dCache_1  80 vd 81 
                                       +d
  gi|313117399|ref|YP_004044382.1| 306 AD 307
                                       44 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00071      0.84       6      37 ..     246     277 ..     242     298 .. 0.86
   2 ?    2.3   0.0      0.15   1.8e+02      33      51 ..     314     332 ..     292     338 .. 0.81
   3 ?   -2.3   0.0       4.2     5e+03      10      37 ..     357     384 ..     351     387 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00071
                              YojJ   6 leeelkeklkeeLeqiekeleevlkaldeede 37 
                                       l++ l+ ++++ L+ +++ ++ + ++ldeed+
  gi|313117399|ref|YP_004044382.1| 246 LNQVLRHDIRNDLQMVSGYADLIAEQLDEEDK 277
                                       67789*************************97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                              YojJ  33 deedeClLcelesirekfa 51 
                                       +e +e lL+e e+ir   +
  gi|313117399|ref|YP_004044382.1| 314 EELQESLLSEVEDIRAANS 332
                                       6789999******997655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.2
                              YojJ  10 lkeklkeeLeqiekeleevlkaldeede 37 
                                       +++ lk+   +  k++ e+  ++de d+
  gi|313117399|ref|YP_004044382.1| 357 FRNLLKNAVLHNDKQVPEITVTIDERDD 384
                                       5666666666777899999999999986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00041      0.49       5      51 ..     127     173 ..     126     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                             PAS_8   5 alfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpv 51 
                                       +++e   d+++ vd +++++++N++ +e +  +  ++ ge ++ ++ +
  gi|313117399|ref|YP_004044382.1| 127 QFLERTTDSVFTVDSDWNVTFWNERIAERTDIEpGEIVGENIW-DVYE 173
                                       5788889*******999*************9886777776663.2222 PP

>> AIF-MLS  Mitochondria Localisation Sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       5.4   6.4e+03     143     159 ..      69      85 ..      45      98 .. 0.46
   2 ?   13.0   1.6   6.2e-05     0.075      80     149 ..     271     340 ..     264     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.4
                           AIF-MLS 143 aeaapvettavsaetep 159
                                       +  a+ e+ + ++++e 
  gi|313117399|ref|YP_004044382.1|  69 VMEAKREAIETESHVER 85 
                                       22222333344444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.2e-05
                           AIF-MLS  80 nlkektkaelqplqgekenvaeaekasseapevsvveaevvdaeevpdataavaeeasacpddaeaapve 149
                                       +l e+ ka ++ +q   e+++e  +++ e +ev  +++++ ++ee+ ++     e+ +a+ +da  +  e
  gi|313117399|ref|YP_004044382.1| 271 QLDEEDKAYVETIQKRAEHAVELTRTAREISEVLFADVSETGTEELQESLLSEVEDIRAANSDAVVTVDE 340
                                       6899*******************************************99988888877776665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 3784.82
//
Query:       gi|313117400|ref|YP_004044383.1|  [L=447]
Description: cytochrome P450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.3e-91  305.2   0.0    8.3e-91  305.0   0.0    1.0  1  p450       Cytochrome P450
  ------ inclusion threshold ------
      0.083   12.3   0.0       0.16   11.4   0.0    1.5  1  Pr_beta_C  Proteasome beta subunits C terminal


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.0   0.0   9.2e-95   8.3e-91       1     449 [.       8     426 ..       8     438 .. 0.90

  Alignments for each domain:
  == domain 1  score: 305.0 bits;  conditional E-value: 9.2e-95
                                       --SESEHHCCHCHHHHTTTCCHHHHHHHHHHHH-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHH CS
                              p450   1 Ppgptplplvgnllqlgrkeelhevlrklqkkygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallat 77 
                                       Ppg   lp+vgn ++l+  + + e+++ l+++yg i + ++ ++++ ++ +pea++++l  ++ + + +  + +l+ 
  gi|313117400|ref|YP_004044383.1|   8 PPGDGGLPVVGNTVELS--RDILEFYEGLRNEYGRIASYRVFGTDACMVADPEAIRQILLEDH-DAYEK-GD-VLTR 79 
                                       788889**********9..689999*************************************6.66665.34.4555 PP

                                       HHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTT.THHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHH CS
                              p450  78 srkpfkgkgvlfangekwkklRrfltptltsfgkl.sleelveeeaedlveklrkkagesselditellskaaldvi 153
                                       s +  +g g+++++ge+w+++R+++ p++     l ++++ + + a++ ++ ++++a     +++ + ++ +++dv+
  gi|313117400|ref|YP_004044383.1|  80 SLGDAMGDGLFLSAGEQWHRQRTRMQPAFYRE-RLdTYVPAMRDTASQSLDDWHDEAV----IEVNDAMTAMTIDVL 151
                                       5789**************************99.8889999999999999999987654....66************* PP

                                       HHHHHSSHHHTTTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              p450 154 gsilFgarfdlledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerret 230
                                       g++lFg+   + +++      +a ++++  +++++  ++ + p  + +pt+++r++++  ++l +++d l  +rr+ 
  gi|313117400|ref|YP_004044383.1| 152 GRTLFGVD--VADEPV---VTDASDAILARFDTNR--FWSFLP--DSVPTPTNRRYRREIERLREFVDGLADQRRRR 219
                                       *******7..446665...5666666655565555..899999..558***************************** PP

                                       HCHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHC CS
                              p450 231 ldsakksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevl 307
                                        +++  +  d+l++l+     ++g+  l++ e + +++++lfaG++Tt+ +l+++ ++La+nP+ qe++r E+d+v 
  gi|313117400|ref|YP_004044383.1| 220 PREE--RGDDLLSILVGFV--ESGD--LTMSEFRDNLITFLFAGHETTALGLTYTVLCLARNPDEQERIRAEVDSVC 290
                                       ****..9***********7..6666..************************************************** PP

                                       CTTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS-- CS
                              p450 308 gdkreptyddlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFd 384
                                        +  ++t +dl +l+ +  +i E+LRl+p+v+ l  Re+ +dv++ gy ip Gt+ +++++ +hrd + +++P++++
  gi|313117400|ref|YP_004044383.1| 291 DG--SVTAADLPELEQTGRAIDEALRLYPPVY-LFFRETARDVKLAGYRIPNGTTLVLSPWVVHRDSAWWDDPQTYR 364
                                       77..59**************************.999***************************************** PP

                                       GGGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSGGEEESS CS
                              p450 385 peRFldekgnskrksfaflPFGaGpRnCiGerlArmelklflatlLqnFevelqpetdpppilek 449
                                       p+RF  e+    r+++a++PFG GpR CiG+r+Arme+k ++a++L+++e+el ++ dp+ i   
  gi|313117400|ref|YP_004044383.1| 365 PDRFAGESD---RPEYAYFPFGGGPRHCIGMRFARMEMKTVIASILRRYEFELVSDPDPELIASS 426
                                       *******75...9****************************************887777766554 PP

>> Pr_beta_C  Proteasome beta subunits C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.8e-05      0.16       4      22 ..     328     346 ..     326     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.8e-05
                                       -S--SS-----TTSS-EEE CS
                         Pr_beta_C   4 kgeRqgsYkfkrGTTaVLk 22 
                                       + +++  Y+++ GTT VL+
  gi|313117400|ref|YP_004044383.1| 328 RDVKLAGYRIPNGTTLVLS 346
                                       6789999***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 3452.06
//
Query:       gi|313117401|ref|YP_004044384.1|  [L=225]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-18   66.8   0.0    2.1e-18   65.9   0.0    1.5  1  HTH_10        HTH DNA binding domain
     0.0063   16.2   0.1       0.35   10.6   0.1    2.4  2  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
      0.015   15.1   0.1      0.067   13.0   0.0    2.3  2  HTH_38        Helix-turn-helix domain
      0.028   13.9   0.1       0.14   11.7   0.0    2.1  2  Sigma70_r4    Sigma-70, region 4
      0.034   14.2   0.0      0.092   12.8   0.0    1.8  1  HTH_20        Helix-turn-helix domain
      0.063   12.8   0.1        1.1    8.9   0.0    2.5  2  GerE          Bacterial regulatory proteins, luxR family
      0.089   12.6   0.0       0.18   11.7   0.0    1.5  1  HTH_23        Homeodomain-like domain
       0.11   12.6   0.0        0.2   11.8   0.0    1.4  1  SpoIIID       Stage III sporulation protein D


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   9.2e-22   2.1e-18       1      52 [.     165     216 ..     165     217 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 9.2e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++q+ev+ +A e GY+d+PR++ ++++A++l+ skst+ +hLrkae +l+
  gi|313117401|ref|YP_004044384.1| 165 LTERQREVVSVAREIGYYDVPRNAGVRDVADRLDCSKSTTANHLRKAEARLV 216
                                       9************************************************997 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.031        69       8      21 ..     162     175 ..     159     181 .. 0.81
   2 !   10.6   0.1   0.00016      0.35      30      54 .]     191     215 ..     189     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.031
                                       HTTS-HHHHHHHHH CS
                      Sigma70_r4_2   8 laeLperqreifll 21 
                                       +a L+erqre++  
  gi|313117401|ref|YP_004044384.1| 162 VAVLTERQREVVSV 175
                                       577********965 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                                       HHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  30 kEIAellgisegtVksrlsRArkkL 54 
                                       +++A +l++s +t  ++l++A ++L
  gi|313117401|ref|YP_004044384.1| 191 RDVADRLDCSKSTTANHLRKAEARL 215
                                       689******************9887 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.1   4.8e+03      37      42 ..      95     100 ..      93     100 .. 0.70
   2 ?   13.0   0.0     3e-05     0.067      19      43 ..     186     210 ..     165     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.1
                            HTH_38  37 IsRElk 42 
                                       I+REl+
  gi|313117401|ref|YP_004044384.1|  95 IARELR 100
                                       667775 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3e-05
                            HTH_38  19 eGlslreIArrLgrspsTIsRElkR 43 
                                       ++ ++r++A rL++s+sT +++l++
  gi|313117401|ref|YP_004044384.1| 186 RNAGVRDVADRLDCSKSTTANHLRK 210
                                       57899*************9999985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.96   2.2e+03       9      24 ..      24      39 ..      23      40 .. 0.84
   2 ?   11.7   0.0   6.2e-05      0.14       3      47 ..     163     214 ..     162     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.96
                                      HHHHHHHHHTTT--HH CS
                        Sigma70_r4  9 erevlelrfgeglTle 24
                                      e+e ++  +++ ++++
  gi|313117401|ref|YP_004044384.1| 24 EQELIRRAYLRHWNFS 39
                                      8999999999998876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.2e-05
                                       HHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4   3 asLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrk 47 
                                       a+L+er+rev++  +        ++    ++++rl+ S+++   ++++A  +
  gi|313117401|ref|YP_004044384.1| 163 AVLTERQREVVSVAReigyydvPRNAGVRDVADRLDCSKSTTANHLRKAEAR 214
                                       68*************9*988776666799***********999999998665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-05     0.092      29      56 ..     192     218 ..     188     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                                       HHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  29 elaerldlskntlsyHLrvLeeagLvev 56 
                                       ++a+rld+sk+t  +HLr+  ea Lv +
  gi|313117401|ref|YP_004044384.1| 192 DVADRLDCSKSTTANHLRKA-EARLVAL 218
                                       68****************95.7777765 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.14   3.1e+02       2      11 ..     164     173 ..     163     177 .. 0.86
   2 ?    8.9   0.0   0.00049       1.1      21      45 ..     191     215 ..     188     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.14
                                       SS-HHHHHHH CS
                              GerE   2 sLskRErevL 11 
                                       +L++R+rev 
  gi|313117401|ref|YP_004044384.1| 164 VLTERQREVV 173
                                       8*******95 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00049
                                       HHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  21 keIAeelniSekTVkvhksnimkKL 45 
                                        ++A++l++S+ T  +h++ +  +L
  gi|313117401|ref|YP_004044384.1| 191 RDVADRLDCSKSTTANHLRKAEARL 215
                                       789***************9987776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.8e-05      0.18      18      46 ..     188     215 ..     175     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.8e-05
                            HTH_23  18 lsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                       + vr++A++L++s++T  + l++  e  l
  gi|313117401|ref|YP_004044384.1| 188 AGVRDVADRLDCSKSTTANHLRKA-EARL 215
                                       5689************99888883.6655 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.9e-05       0.2       8      38 ..     176     206 ..     169     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.9e-05
                           SpoIIID   8 vleiakyiveskatvRkaakvfgvskstvhk 38 
                                       + ei++y v ++a vR++a  ++ skst  +
  gi|313117401|ref|YP_004044384.1| 176 AREIGYYDVPRNAGVRDVADRLDCSKSTTAN 206
                                       568999**********************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1534.84
//
Query:       gi|313117402|ref|YP_004044385.1|  [L=334]
Description: metal ion ABC transporter substrate-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-41  142.6   0.1    1.7e-41  142.3   0.1    1.0  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.3   0.1   9.7e-46   1.7e-41       2     224 ..      32     276 ..      32     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 9.7e-46
                                       EESSHHHHHHHHHHHGG.GCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCE.E CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                              ZnuA   2 vattsplgdlvrqvaGd.rvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrv.e 76 
                                       va+++  +d++r+va d  ve++ L+p+g   H ++p ++  +k+ eAd ++++g ++++w d++++ ++++++  +
  gi|313117402|ref|YP_004044385.1|  32 VASFFSFYDFARKVARDtPVEIENLIPTGLHGHGWKPNASITKKIIEADAFIHVGEDFQPWADRAIKTIKGDNVDtQ 108
                                       89*************76379**********************************************99976333358 PP

                                       EEETTTTCCSEBCSS...............ESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHH.HHH CS
                                       xxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                              ZnuA  77 vidlsegveeeeeee...............DpHiWlspknaiamveniadaLveadpanadtyeanaaayiek.Lee 137
                                       +i++ eg+e  + +                DpH+Wl+p++a++ v+niad+L+++ p+++d++++na++y++  L++
  gi|313117402|ref|YP_004044385.1| 109 LINVREGIELVDLAAsldpeeegigenrgkDPHFWLDPNRAAQSVDNIADGLAKLAPEHEDAFRKNAETYKTDvLDR 185
                                       888888774444444555555677788888****************************************76538** PP

                                       HHHHHHHHHTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEE.SSSSS....HHHHHHHHHHHHHTT-SEEEEETTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 138 ldaeireelaeipeekrklvtthdafgylarayglevagia.giste....aaqiaalieeikeagvkaifveplas 209
                                       +d+++++ ++++ ++  + + +h+af+yl  +yg+e+  ++ ++ ++    + +i++ ++ i+e++++ i +   ++
  gi|313117402|ref|YP_004044385.1| 186 IDQDYADIFDRADRDV-VQLAAHNAFQYLGVTYGVEMRPLVvNLAASgdvkPTDITEAKRVIQENDINHIGAAVFET 261
                                       **********888655.7789*****************99887777788***********************99999 PP

                                       THHHHHHHHHHT-EE CS
                                       xxxxxxxxxxxxxxx RF
                              ZnuA 210 pklaetlaeeagvkv 224
                                        + a++l  e+ v+ 
  gi|313117402|ref|YP_004044385.1| 262 RRPAQQLLTETDVES 276
                                       999*****9999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2062.49
//
Query:       gi|313117403|ref|YP_004044386.1|  [L=266]
Description: Mn/Zn ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-31  108.1   0.0    6.5e-31  107.7   0.0    1.2  1  ABC_tran     ABC transporter
      1e-11   45.3   0.5      6e-05   23.0   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.9e-05   23.6   0.4      0.001   18.6   0.4    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
      8e-05   22.3   0.1    0.00017   21.3   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00067   20.0   0.3     0.0092   16.3   0.3    2.1  1  AAA_22       AAA domain
     0.0011   18.8   0.0     0.0019   18.0   0.0    1.3  1  AAA_15       AAA ATPase domain
     0.0015   18.3   0.0      0.003   17.3   0.0    1.5  1  AAA_30       AAA domain
     0.0015   17.4   0.4       0.39    9.4   0.1    3.0  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.005   17.2   0.0     0.0085   16.5   0.0    1.5  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.021   15.3   0.0      0.032   14.7   0.0    1.3  1  AAA_23       AAA domain
      0.027   14.4   0.1       0.16   11.9   0.1    2.0  1  NTPase_1     NTPase
      0.049   13.9   0.3       0.89    9.8   0.3    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.062   12.3   0.0      0.085   11.8   0.0    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.072   12.0   0.0       0.11   11.5   0.0    1.2  1  Spore_IV_A   Stage IV sporulation protein A (spore_IV_A)
      0.075   13.1   0.1       0.21   11.7   0.1    1.8  1  MMR_HSR1     50S ribosome-binding GTPase
      0.083   13.0   0.1       0.14   12.3   0.1    1.6  1  AAA_33       AAA domain
      0.085   12.9   0.2       0.22   11.6   0.1    1.7  2  DUF87        Helicase HerA, central domain
      0.089   12.7   0.0       0.16   11.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.15   11.3   0.0         13    5.0   0.0    2.1  2  Septin       Septin
       0.16   11.5   0.0       0.29   10.7   0.0    1.3  1  AAA_27       AAA domain
        0.2   10.7   0.0        0.3   10.0   0.0    1.2  1  DUF3987      Protein of unknown function (DUF3987)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.0   7.7e-34   6.5e-31       1     136 [.      42     188 ..      42     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 7.7e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TT..SB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpe..lt 75 
                                       +k++sl++  ge  a+vG+nG+GKStL+kl++gll+p++G  +l g+++++       ++ig++ q+++  ++  +t
  gi|313117403|ref|YP_004044386.1|  42 VKDISLQIDSGEYAAVVGPNGSGKSTLMKLMLGLLRPDKGVTKLFGEPSHQ---FDDGSRIGYVAQHASASKDmpIT 115
                                       589**********************************************99...88899********5555551156 PP

                                       HHHH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       vre                 e+ + +++al+++g++ +++++v    ++LSgGq+qr  +aral+++++ll+lDEpt
  gi|313117403|ref|YP_004044386.1| 116 VREVvkmgrfphvgfgrlsdEDWQIVDRALDTVGMTAFANRRV----TQLSGGQRQRAFIARALASEADLLVLDEPT 188
                                       8888************998666666******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0     7e-08     6e-05       2      33 ..      55      86 ..      54     102 .. 0.76
   2 !   21.1   0.1   2.6e-07   0.00022     221     295 ..     145     216 ..      81     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 7e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdveglt 33
                                      ++++GpNgsGKS+L++++ +l r d+ v+ l 
  gi|313117403|ref|YP_004044386.1| 55 AAVVGPNGSGKSTLMKLMLGLLRPDKGVTKLF 86
                                      589***************99987654444444 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.6e-07
                            AAA_21 221 vvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                       + ++ ++   ++ +++lS G+++  a+++  l+     +ll++DEp  g + + ++++++ll++l++ g+ ++l 
  gi|313117403|ref|YP_004044386.1| 145 LDTVGMTAFANRRVTQLSGGQRQR-AFIARALASEA--DLLVLDEPTVGVDIESVESFYDLLDSLNEDGITILLI 216
                                       555556666778899*********.55555554443..9**************************9999999875 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.4   1.2e-06     0.001      25     198 ..      53     219 ..      40     236 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHC.CCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrsek.lsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                       +  a+vGpNGSGKs l+  +   LG      lr +k +++l  +  ++++ +  ++  + ++ +++    k+   + 
  gi|313117403|ref|YP_004044386.1|  53 EYAAVVGPNGSGKSTLMKLM---LG-----LLRPDKgVTKLFGE-PSHQFDDGSRIGYVAQHASAS----KDMPITV 116
                                       4789************9877...88.....36665514444444.555555555555553333333....3333333 PP

                                       EEEETTSE.EEEEETTEEE-H.HHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTT CS
                                       xxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkge.seykingkevtk.kevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeida 169
                                       r+v++ g+  ++ + + + +  + v + l ++g++        +LSgG+++ + +a  +A    + a l +lDe   
  gi|313117403|ref|YP_004044386.1| 117 REVVKMGRfPHVGFGRLSDEDwQIVDRALDTVGMTAFanrrvtQLSGGQRQRAFIARALA----SEADLLVLDEPTV 189
                                       344444441222222222222234444455555443333344478888877665555554....4567788888888 PP

                                       TS-HHHHHHHHHHHHHHCTT.SEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N 170 aLDeknvkkvaellkekskn.aQfivislr 198
                                         D + v+ + +ll++ +++   ++ i ++
  gi|313117403|ref|YP_004044386.1| 190 GVDIESVESFYDLLDSLNEDgITILLIEHD 219
                                       888888888888877776654555555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1     2e-07   0.00017      17      50 ..      47      80 ..      40      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++id  +   ++Gp+GsGKSTl+  +  lL p+k
  gi|313117403|ref|YP_004044386.1| 47 LQIDSGEYAAVVGPNGSGKSTLMKLMLGLLRPDK 80
                                      6777555999*************99999988887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   1.1e-05    0.0092       8     128 ..      55     216 ..      49     221 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.........erpevvfvtlpsstsskdllrellralglelka..... 70 
                                        +v+G+ G+GK+tl++ +l  l  ++  ++          + + + + +++ + skd+   + + ++ ++       
  gi|313117403|ref|YP_004044386.1|  55 AAVVGPNGSGKSTLMKLMLGLLRPDKGVTKlfgepshqfDDGSRIGYVAQHASASKDMPITVREVVKMGRFPhvgfg 131
                                       689****************9997766666688877777644444455555555555555555554444444466666 PP

                            AAA_22  71 ............................erlsseellealeqalraravielliiDEaqh.lr..seealeeLrsll 116
                                                                   +    ++ ++ +++al + a+  ll++DE    ++  s e + +L + l
  gi|313117403|ref|YP_004044386.1| 132 rlsdedwqivdraldtvgmtafanrrvtQLSGGQRQRAFIARALASEAD--LLVLDEPTVgVDieSVESFYDLLDSL 206
                                       6666677777766666666677555554444444444444455555544..88888877767555566666666666 PP

                            AAA_22 117 nlsrkgvqliLv 128
                                       n  ++g++++L+
  gi|313117403|ref|YP_004044386.1| 207 N--EDGITILLI 216
                                       6..888888776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0019      15      66 ..      43      91 ..      41     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedle 66
                                      kd+++++++  +  ++G+N+sGKS++++++  +l  +    k v+k+  e  +
  gi|313117403|ref|YP_004044386.1| 43 KDISLQIDSGeYAAVVGPNGSGKSTLMKLMLGLLRPD----KGVTKLFGEPSH 91
                                      6777777776799****************99888877....445554444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.5e-06     0.003      16     121 ..      51     215 ..      44     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.5e-06
                            AAA_30  16 sgdrvavltGpAGtGKttalkalreaweaa.g...............grviglAptgkaAkvLa............. 63 
                                       sg  +a+++Gp G+GK+t++k +  +++ + g                r+  +A  + a+k++              
  gi|313117403|ref|YP_004044386.1|  51 SG-EYAAVVGPNGSGKSTLMKLMLGLLRPDkGvtklfgepshqfddgSRIGYVAQHASASKDMPitvrevvkmgrfp 126
                                       44.4899****************9999999569************99999999999999999998888888888887 PP

                            AAA_30  64 ...................eelgieastiakllkrlk...........grarlepgtllivDEagmv....dtkqla 106
                                                          + +g++a    +++   +           +ra  ++++ll+ DE  +     + +++ 
  gi|313117403|ref|YP_004044386.1| 127 hvgfgrlsdedwqivdralDTVGMTAFANRRVT---QlsggqrqrafiARALASEADLLVLDEPTVGvdieSVESFY 200
                                       777777776555555544444444444333333...03347779999865666666999999977644444555555 PP

                            AAA_30 107 allkaaekagakvil 121
                                       +ll++++++g++++l
  gi|313117403|ref|YP_004044386.1| 201 DLLDSLNEDGITILL 215
                                       666777777777766 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.064        55     245     262 ..      52      70 ..      37      74 .. 0.84
   2 !    9.4   0.1   0.00046      0.39     324     412 ..     162     234 ..     149     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.064
                                       S.EEEEEE-TTSSHHHHHH CS
                        ABC_ATPase 245 G.vtlIvGggfhGKsTLLe 262
                                       G   ++vG++  GKsTL++
  gi|313117403|ref|YP_004044386.1|  52 GeYAAVVGPNGSGKSTLMK 70 
                                       555689***********97 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00046
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                                       SG   q a i++al  +a+ll++DE t                  + e ++++ d++ +l ++ g++++l+   +++
  gi|313117403|ref|YP_004044386.1| 162 SGGQRQRAFIARALASEADLLVLDEPTV---------------GVDIESVESFYDLLDSL-NEDGITILLIEHDLSA 222
                                       6666666777777777777777777654...............33678999999999999.8889999999999999 PP

                                       CTTT-SEEEEEE CS
                        ABC_ATPase 401 yldvAdtvilme 412
                                        +++Ad+vi ++
  gi|313117403|ref|YP_004044386.1| 223 VTEHADRVICLN 234
                                       999999999987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.9e-06    0.0085      23      63 ..      51      92 ..      42     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.9e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                      ++e+  ++G+ G+GKs+l++  l  l+ d+g++ l g+  + 
  gi|313117403|ref|YP_004044386.1| 51 SGEYAAVVGPNGSGKSTLMKLMLGLLRPDKGVTkLFGEPSHQ 92
                                      558899*****************9999998888777766665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.8e-05     0.032      23      37 ..      56      70 ..      35      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                            AAA_23 23 lItGpNGaGKTTild 37
                                      +++GpNG+GK+T++ 
  gi|313117403|ref|YP_004044386.1| 56 AVVGPNGSGKSTLMK 70
                                      679**********97 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00018      0.16       4      61 ..      57     115 ..      54     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                                       EE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-.------EEEEEET.T--EEEEE CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlellkssgvkvgGfyteevr.eggrrigFkivdlasgeegiLa 61 
                                       + Gp G+GK+Tl+k +l ll+ +    + f  + ++ ++g+rig+     +  +  ++ 
  gi|313117403|ref|YP_004044386.1|  57 VVGPNGSGKSTLMKLMLGLLRPDKGVTKLFGEPSHQfDDGSRIGYVAQHASASKDMPIT 115
                                       78******************988777777888888889999999987777555555554 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3     0.001      0.89      26      88 ..     154     203 ..     138     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.001
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                        +r++++lSGG++q ++          l s+        +l++LDE   ++D es+++  +ll
  gi|313117403|ref|YP_004044386.1| 154 ANRRVTQLSGGQRQRAFIARA------LASE-------ADLLVLDEPTVGVDIESVESFYDLL 203
                                       678999999999976653222......2233.......3678888888888888888877776 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.9e-05     0.085      15     102 ..      38     124 ..      18     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.9e-05
                                       HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTT CS
                              MeaB  15 akellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdeg 91 
                                       a ++++ ++ +    +   + G  G+Gkstl+ +l+l l r  k v+ l  +Ps +f  Gs +G   + ++ ++d  
  gi|313117403|ref|YP_004044386.1|  38 AASVVKDISLQIDSGEYAAVVGPNGSGKSTLM-KLMLGLLRPDKGVTKLFGEPSHQFDDGSRIGYVAQHASASKDMP 113
                                       56666667666667777789999*******98.68889999999********************9999999999999 PP

                                       EEEEEE----- CS
                              MeaB  92 vfiRslpsrGa 102
                                       + +R +   G+
  gi|313117403|ref|YP_004044386.1| 114 ITVREVVKMGR 124
                                       99998887776 PP

>> Spore_IV_A  Stage IV sporulation protein A (spore_IV_A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.11       4      38 ..      39      73 ..      36      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                        Spore_IV_A  4 ldiykdiaertngdiyigvvGpvRtGKStfikrfm 38
                                       +++kdi+ + +   y +vvGp  +GKSt++k ++
  gi|313117403|ref|YP_004044386.1| 39 ASVVKDISLQIDSGEYAAVVGPNGSGKSTLMKLML 73
                                      6799**************************99776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00024      0.21       2      22 ..      55      83 ..      54     217 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                      EEEEESTTSSHHHHHHHHHT........S CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg........e 22
                                      +a+vG   +GKStL++ ++g        +
  gi|313117403|ref|YP_004044386.1| 55 AAVVGPNGSGKSTLMKLMLGllrpdkgvT 83
                                      589*************9997444433330 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00017      0.14       4      28 ..      57      76 ..      55     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                            AAA_33  4 lvGlpGsGKstlaerllkklgavll 28
                                      +vG++GsGKstl + +l      ll
  gi|313117403|ref|YP_004044386.1| 57 VVGPNGSGKSTLMKLML-----GLL 76
                                      79**********99776.....344 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00026      0.22      26      47 ..      55      76 ..      32      85 .. 0.79
   2 ?   -1.6   0.0       2.8   2.4e+03     187     218 ..     200     230 ..     156     233 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                             DUF87 26 lAilgsTGsGKSntvavLleel 47
                                       A++g  GsGKS++++++l  l
  gi|313117403|ref|YP_004044386.1| 55 AAVVGPNGSGKSTLMKLMLGLL 76
                                      69***************99655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                             DUF87 187 tdliallleklekegkitii....dlsgvdelaqql 218
                                       +dl+++l     +e  iti+    dls v e a ++
  gi|313117403|ref|YP_004044386.1| 200 YDLLDSL-----NEDGITILliehDLSAVTEHADRV 230
                                       3333333.....555566655677777777766555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.16      86     121 ..      38      74 ..       6      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                         + +++++ ++++ + +++vG+ G GKStL++ +l+
  gi|313117403|ref|YP_004044386.1|  38 AASVVKDISLQIDSgEYAAVVGPNGSGKSTLMKLMLG 74 
                                       445677788888877999*************998765 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.015        13       9      25 ..      57      73 ..      54     108 .. 0.89
   2 ?    4.4   0.0     0.023        20      63     125 ..     180     245 ..     164     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.015
                                      EEEBTTSSCCCCCCTTS CS
                            Septin  9 vvGesglGkttlintlf 25
                                      vvG +g Gk+tl++ ++
  gi|313117403|ref|YP_004044386.1| 57 VVGPNGSGKSTLMKLML 73
                                      9************9775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.023
                                       EEEEEE---BSSSSSHHCCCHHHHHHHHHHHHHHHHHCTSS--SS-----EEEE...EEEE-TTSS CS
                            Septin  63 nltviDtpgfGdavdnskswepiveyideqfeeylreesklkRkkivDkRvHac...lyfisPtgh 125
                                        l v+D p  G  ++  +s+  +++ ++e   ++l  e+ l+  +   +Rv ++   +yf  Pt++
  gi|313117403|ref|YP_004044386.1| 180 DLLVLDEPTVGVDIESVESFYDLLDSLNEDGITILLIEHDLSAVTEHADRVICLnreIYFDGPTSE 245
                                       688****************************************99999999997666788888765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00034      0.29      18      50 ..      46      76 ..      38      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      sl++  ++ +   ++GpN +GKst+++ +  ll
  gi|313117403|ref|YP_004044386.1| 46 SLQI--DSGEYAAVVGPNGSGKSTLMKLMLGLL 76
                                      4444..4677889************99877665 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00036       0.3      38      62 ..      54      78 ..      43      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00036
                           DUF3987 38 ytlvvapsGerKSpvdklvlrplee 62
                                      y +vv+p G++KS+++kl+l +l++
  gi|313117403|ref|YP_004044386.1| 54 YAAVVGPNGSGKSTLMKLMLGLLRP 78
                                      789*****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1591.92
//
Query:       gi|313117404|ref|YP_004044387.1|  [L=336]
Description: Mn2+/Zn2+ ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-55  189.1  40.6    1.2e-55  188.9  40.6    1.0  1  ABC-3      ABC 3 transport family
    0.00033   19.8  36.9    0.00033   19.8  36.9    1.8  1  FecCD      FecCD transport family
  ------ inclusion threshold ------
       0.11   12.7   1.0       0.28   11.4   1.0    1.6  1  DUF2407_C  DUF2407 C-terminal domain


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.9  40.6     2e-59   1.2e-55       1     256 [.      45     307 ..      45     309 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.9 bits;  conditional E-value: 2e-59
                             ABC-3   1 qyeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvn......lllgailvgliaaval 71 
                                       qy f+ ra+l+++ ++++++l+g+f+v r+ +l+gdal+H  ++Gva++++l+        ++l a++v++iaa+ +
  gi|313117404|ref|YP_004044387.1|  45 QYGFMHRAILVGLCIGVMAPLIGTFLVHRQLALIGDALAHTGFAGVAVGLFLNAVldlgvsPYLTAVIVAMIAALLI 121
                                       689*************************************************988888888**************** PP

                             ABC-3  72 ellkrktklkedtaigivlsvflalglvlvslikk.skvdldsyLfGniltisqedliliaiieavvllllllfwke 147
                                       el++++t  ++d++++ivls+++alg  l+s++ +  +v+++++LfGn+ t+s +   +++++ av++ ++ l + +
  gi|313117404|ref|YP_004044387.1| 122 ELISEATDAYNDVSMAIVLSTGFALGTTLISINAGgLAVGVKQFLFGNLSTVSPDSAAILLVLFAVIIGVVGLTRNQ 198
                                       **********************************99***************************************** PP

                             ABC-3 148 lllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvs 224
                                       ll +tfde+ A+v+glsv+ ++ ++++l+a+ vv a+q++GviLv+a+l++P a A +++rs+++ l+v+++l+ ++
  gi|313117404|ref|YP_004044387.1| 199 LLYVTFDETAAAVSGLSVSWYNRIMVMLTAMVVVGAMQIMGVILVAAMLVVPVAGAAQVSRSFNESLLVSVVLAELA 275
                                       ***************************************************************************** PP

                             ABC-3 225 vvaGlllSyyldlatGavivlvatllfllall 256
                                       v++G+  Syy ++ +G+vivl a++++++ +l
  gi|313117404|ref|YP_004044387.1| 276 VILGIGASYYGKATAGGVIVLTAVAIYIVTIL 307
                                       ****************************9886 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  36.9   5.5e-08   0.00033      86     308 ..      89     305 ..      80     310 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.5e-08
                             FecCD  86 gavlalllllgslsl.falplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneeale 161
                                       g++++l+l    l l ++  l a++ a++a+ll+ l+++ +   + +++    i++s+ ++  t+l+ ++     + 
  gi|313117404|ref|YP_004044387.1|  89 GVAVGLFLN-AVLDLgVSPYLTAVIVAMIAALLIELISEATDAYNDVSM---AIVLSTGFALGTTLISIN-AGGLAV 160
                                       444444443.333330345577889**********9*966666666555...566777776667777766.556788 PP

                             FecCD 162 silfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavaval 238
                                        +++ l+G+ls++s +++++llvl+++++ ++ l +++l  ++++++ A+  G++v  ++ ++++l+a+++  a+ +
  gi|313117404|ref|YP_004044387.1| 161 GVKQFLFGNLSTVSPDSAAILLVLFAVIIGVVGLTRNQLLYVTFDETAAAVSGLSVSWYNRIMVMLTAMVVVGAMQI 237
                                       9**************************************************************************** PP

                             FecCD 239 vGpigFvG.LivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiy 308
                                       +G+i   + L+vP    + v++++   l++s++l+ l ++l    a ++ + t    g+++ +  a++ + 
  gi|313117404|ref|YP_004044387.1| 238 MGVILVAAmLVVPVAGAAQVSRSFNESLLVSVVLAELAVILGI-GASYYGKAT--AGGVIVLTAVAIYIVT 305
                                       ****887746789999999999999999999999888777653.333333333..3455555555555444 PP

>> DUF2407_C  DUF2407 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   4.6e-05      0.28      89     138 ..      49      98 ..      41     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.6e-05
                         DUF2407_C  89 anedlliGlliGfflglfalllllkeegllnkrqkmaviaGvlvnlvlgl 138
                                       +++ +l+Gl+iG++ +l++ +l+ ++ +l+        +aGv+v l+l +
  gi|313117404|ref|YP_004044387.1|  49 MHRAILVGLCIGVMAPLIGTFLVHRQLALIGDALAHTGFAGVAVGLFLNA 98 
                                       57889**************7777777799888888888888877777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2193.80
//
Query:       gi|313117405|ref|YP_004044388.1|  [L=239]
Description: Mn-dependent transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-20   73.0   0.3    3.2e-20   72.0   0.3    1.6  1  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
      9e-17   61.0   0.0    1.8e-16   60.1   0.0    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    1.3e-11   44.3   0.3    2.8e-10   40.0   0.2    2.5  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    1.5e-10   40.8   0.3    9.3e-09   35.1   0.0    2.8  2  MarR_2           MarR family
    7.5e-09   35.7   0.1    1.8e-08   34.5   0.1    1.7  1  FeoA             FeoA domain
    1.3e-08   34.7   0.3    5.4e-08   32.6   0.1    2.0  2  MarR             MarR family
      4e-08   32.7   0.1    8.6e-08   31.6   0.1    1.6  1  HTH_24           Winged helix-turn-helix DNA-binding
    9.8e-08   31.7   6.2      3e-07   30.1   0.1    3.3  3  HTH_IclR         IclR helix-turn-helix domain
    7.4e-07   29.1   0.0      5e-05   23.3   0.1    2.8  3  HTH_20           Helix-turn-helix domain
    4.4e-06   27.1   0.6    1.2e-05   25.7   0.1    1.9  1  HTH_27           Winged helix DNA-binding domain
    8.2e-06   25.4   0.4    1.8e-05   24.3   0.1    1.7  1  Crp              Bacterial regulatory proteins, crp family
    1.3e-05   25.1   0.2    2.2e-05   24.3   0.2    1.3  1  HTH_11           HTH domain
    1.6e-05   24.7   0.3    8.4e-05   22.4   0.0    2.3  2  TrmB             Sugar-specific transcriptional regulator Trm
    5.6e-05   22.6   0.2       0.23   11.0   0.0    2.8  2  Sigma70_r4       Sigma-70, region 4
    7.5e-05   23.0   0.0    0.00042   20.6   0.0    2.2  2  Rrf2             Transcriptional regulator
    0.00021   21.0   0.0    0.00082   19.1   0.0    2.0  1  HTH_23           Homeodomain-like domain
    0.00041   19.9   0.1    0.00079   19.0   0.1    1.5  1  GntR             Bacterial regulatory proteins, gntR family
    0.00076   19.0   0.3     0.0018   17.8   0.2    1.7  1  HTH_CodY         CodY helix-turn-helix domain
    0.00093   19.0   0.0      0.003   17.4   0.0    1.9  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0011   18.7   0.1     0.0032   17.3   0.1    1.7  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0036   17.3   0.1     0.0086   16.1   0.1    1.6  1  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
     0.0036   17.2   0.0     0.0058   16.6   0.0    1.3  1  HTH_36           Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.018   15.1   0.1    1.5  1  HTH_29           Winged helix-turn helix
       0.01   15.9   0.0      0.025   14.6   0.0    1.6  1  FeoC             FeoC like transcriptional regulator
      0.015   15.6   0.0      0.031   14.7   0.0    1.5  1  FaeA             FaeA-like protein
      0.017   15.2   0.5      0.062   13.4   0.1    2.1  2  Sigma70_r3       Sigma-70 region 3
      0.028   14.2   0.5      0.086   12.6   0.2    2.0  2  LacI             Bacterial regulatory proteins, lacI family
      0.028   14.1   0.0      0.042   13.6   0.0    1.3  1  DUF4423          Domain of unknown function (DUF4423)
       0.03   14.2   0.0      0.055   13.3   0.0    1.4  1  TFIIE_alpha      TFIIE alpha subunit
      0.041   13.6   0.0       0.17   11.7   0.0    2.1  1  LexA_DNA_bind    LexA DNA binding domain
      0.045   13.5   0.3       0.51   10.2   0.0    2.3  2  TetR_N           Bacterial regulatory proteins, tetR family
      0.066   13.3   0.0       0.15   12.2   0.0    1.6  1  DUF2250          Uncharacterized protein conserved in archaea
      0.081   13.0   0.0       0.71   10.0   0.0    2.5  2  HTH_3            Helix-turn-helix
       0.11   12.3   0.1       0.35   10.7   0.1    2.0  1  HTH_38           Helix-turn-helix domain
       0.11   12.5   0.0        0.2   11.7   0.0    1.4  1  TBPIP            TBPIP/Hop2 winged helix domain
       0.11   12.2   0.0       0.49   10.1   0.0    2.2  1  Sigma70_r4_2     Sigma-70, region 4
       0.12   12.3   0.0        1.1    9.2   0.0    2.3  2  YdaS_antitoxin   Putative antitoxin of bacterial toxin-antito
       0.14   11.4   0.0       0.26   10.5   0.0    1.4  1  EAP30            EAP30/Vps36 family
       0.15   12.0   0.3       0.87    9.6   0.0    2.5  1  HTH_1            Bacterial regulatory helix-turn-helix protei
       0.18   11.8   0.0       0.73    9.9   0.0    1.8  2  Phage_terminase  Phage terminase small subunit
       0.22   11.7   0.1       0.72   10.1   0.0    1.8  2  SgrR_N           Sugar transport-related sRNA regulator N-ter


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.3   7.2e-23   3.2e-20       1      70 []      80     149 ..      80     149 .. 0.99

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 7.2e-23
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B--- CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpipd 70 
                                       T++G e A+ ++rrhrl+e++L++ +++  +e++ eA  lEh+ls++l +++++ l+ p+ +Phgdpipd
  gi|313117405|ref|YP_004044388.1|  80 TDDGVEHALGVIRRHRLVETMLSELFDYTISEVDAEADVLEHHLSPRLCREIERELDMPDIDPHGDPIPD 149
                                       99******************************************************************95 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   4.1e-19   1.8e-16       2      58 ..      18      75 ..      17      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 4.1e-19
                                      --HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                    Fe_dep_repress  2 LvestEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekyk 58
                                      L++++EdYL+ IY+l+  +++ v+++d+a rL+v  ++Vs ml  L++ G++e e y+
  gi|313117405|ref|YP_004044388.1| 18 LTPKMEDYLRHIYRLEQeSNSRVSNSDIADRLGVTRATVSSMLDTLSESGLIERERYR 75
                                      899************998*************************************998 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.2   6.4e-13   2.8e-10       9      61 ..      31      81 ..      24      83 .. 0.82
   2 ?    1.3   0.0      0.79   3.5e+02      26      44 ..     162     180 ..     142     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 6.4e-13
                                      HHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.TEE.EEES- CS
                         HTH_Crp_2  9 rlaeraggeielpltqeelAsmlGltretvsrilseLkreglisr.grr.irild 61
                                      rl+++     + ++++ ++A++lG+tr tvs +l  L++ gli+r ++r ir++d
  gi|313117405|ref|YP_004044388.1| 31 RLEQE----SNSRVSNSDIADRLGVTRATVSSMLDTLSESGLIEReRYRpIRLTD 81
                                      44443....35799******************************635678*9998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.79
                                       HHHHHTTSSHHHHHHHHHH CS
                         HTH_Crp_2  26 elAsmlGltretvsrilse 44 
                                        lA+   ++ + v+ril++
  gi|313117405|ref|YP_004044388.1| 162 SLAEVAESSCVEVTRILTQ 180
                                       699999**********986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   2.1e-11   9.3e-09       9      55 ..      24      73 ..      17      76 .. 0.89
   2 ?    2.7   0.0      0.28   1.2e+02      22      45 ..     212     235 ..     198     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.1e-11
                                      HHHHHHHCTTTS...EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  9 rvLaaLgrrpgr...dltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      + L +++r + +   +++ +++a+rlg+++++vs +l+ L++ GL+er++
  gi|313117405|ref|YP_004044388.1| 24 DYLRHIYRLEQEsnsRVSNSDIADRLGVTRATVSSMLDTLSESGLIERER 73
                                      77889999988899999*******************************95 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.28
                                       EEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2  22 ltvgelarrlglsksavsrilkrL 45 
                                       +tv e  r +gl+++ +s+il  +
  gi|313117405|ref|YP_004044388.1| 212 VTVVETGRQMGLPRPVASQILVTA 235
                                       577777899***********9655 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   4.1e-11   1.8e-08       2      73 ..     162     234 ..     161     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 4.1e-11
                                       EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEET..TEEEEE-HHHHTTEEEE CS
                              FeoA   2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvg..dtrvaLgreeAqaIlVe 73 
                                       +L+++ e   +e++ri  +d+e+l +L + G+ p  r+ + ++ p  g+l+v v   + ++ L+r++A++IlV+
  gi|313117405|ref|YP_004044388.1| 162 SLAEVAESSCVEVTRILTQDDETLEYLVSAGIEPSVRLCLDEKTPI-GMLTVTVVetGRQMGLPRPVASQILVT 234
                                       79999************************************99998.899998852355788***********8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   1.2e-10   5.4e-08      18      51 ..      40      73 ..      21      74 .. 0.81
   2 ?   -1.0   0.0         4   1.7e+03      21      39 ..     161     179 ..     156     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.2e-10
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                       s+s++a++lgv+++tv+ +ld+L + GlieR++
  gi|313117405|ref|YP_004044388.1| 40 VSNSDIADRLGVTRATVSSMLDTLSESGLIERER 73
                                      4555****************************87 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4
                                       HHHHHHHTS-HHHHHHHHH CS
                              MarR  21 seLakklgvskstvtrvld 39 
                                       + La+  + s+  vtr+l+
  gi|313117405|ref|YP_004044388.1| 161 TSLAEVAESSCVEVTRILT 179
                                       5677777888888888886 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1     2e-10   8.6e-08      11      48 .]      32      70 ..      22      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2e-10
                            HTH_24 11 lLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      l q+ n+r s++++A+rlg++++tv+  l+ L e+GlI+
  gi|313117405|ref|YP_004044388.1| 32 LEQEsNSRVSNSDIADRLGVTRATVSSMLDTLSESGLIE 70
                                      55557*********************************7 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1     7e-10     3e-07      15      51 ..      36      72 ..      26      73 .. 0.88
   2 ?   -2.0   0.1       7.6   3.3e+03      17      27 ..     159     169 ..     156     170 .. 0.72
   3 ?    3.5   0.0      0.15        64      25      41 ..     218     234 ..     204     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7e-10
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                       + ++++s++A+r+g++++tv+ +L tL e G++e++
  gi|313117405|ref|YP_004044388.1| 36 SNSRVSNSDIADRLGVTRATVSSMLDTLSESGLIERE 72
                                      455699****************************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.6
                                       SS-BHHHHHHH CS
                          HTH_IclR  17 qeltlselArr 27 
                                        + +l+e+A+ 
  gi|313117405|ref|YP_004044388.1| 159 DATSLAEVAES 169
                                       45699***986 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.15
                                       HHHHTS-HHHHHHHHHH CS
                          HTH_IclR  25 ArrtglpkStvhRlLqt 41 
                                        r+ glp++ ++ +L t
  gi|313117405|ref|YP_004044388.1| 218 GRQMGLPRPVASQILVT 234
                                       5999*********9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   1.2e-07     5e-05      22      58 ..      37      73 ..      21      76 .. 0.85
   2 ?    2.1   0.0      0.46     2e+02      17      37 ..     121     138 ..      84     153 .. 0.81
   3 ?    2.7   0.0       0.3   1.3e+02      10      20 ..     126     156 ..     114     174 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.2e-07
                                      CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 22 aegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +  ++ s++a+rl+++++t+s  L++L+e gL+e++r
  gi|313117405|ref|YP_004044388.1| 37 NSRVSNSDIADRLGVTRATVSSMLDTLSESGLIERER 73
                                      5567789****************************98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.46
                                       HHHSTCTTB-HHHHHHHHTS- CS
                            HTH_20  17 raLaraegltaselaerldls 37 
                                        +L    ++ + e+ ++ld++
  gi|313117405|ref|YP_004044388.1| 121 HHL---SPRLCREIERELDMP 138
                                       344...788888999998755 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.3
                                       HHHHHHHHHH....................S CS
                            HTH_20  10 PvRrrilraL....................a 20 
                                       +  r+i+r+L                    +
  gi|313117405|ref|YP_004044388.1| 126 RLCREIERELdmpdidphgdpipdanldipH 156
                                       3445555555555555555555555555555 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   2.6e-08   1.2e-05       8      68 .]      25      83 ..      24      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.6e-08
                            HTH_27  8 vLhlir....hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +L++i+    + + r++ +d+++rl v+ +++s++l+ L e GL+er+      r++ +rlTd G
  gi|313117405|ref|YP_004044388.1| 25 YLRHIYrleqESNSRVSNSDIADRLGVTRATVSSMLDTLSESGLIERE------RYRPIRLTDDG 83
                                      589999998899999999***************************555......55699999988 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1     4e-08   1.8e-05       2      32 .]      39      69 ..      39      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4e-08
                                      E--HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                               Crp  2 pmSRqdIAdylGlTrETVSRlLtrLrekGLI 32
                                      ++S+ dIAd lG Tr TVS +L  L e+GLI
  gi|313117405|ref|YP_004044388.1| 39 RVSNSDIADRLGVTRATVSSMLDTLSESGLI 69
                                      69****************************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.2     5e-08   2.2e-05       4      47 ..      28      70 ..      26      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5e-08
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIe 47
                                      +i++l  e+++ +s +++A++L+v+r+tv   +++L+e+g  Ie
  gi|313117405|ref|YP_004044388.1| 28 HIYRLEQESNSRVSNSDIADRLGVTRATVSSMLDTLSESG-LIE 70
                                      566666667777***************************9.555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.9e-07   8.4e-05      23      60 ..      40      77 ..      36      80 .. 0.88
   2 ?   -2.2   0.0       8.8   3.9e+03      24      43 ..     213     232 ..     211     233 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.9e-07
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                       + ++ia +lgv r++v ++L  L++ Gl+ere+ rp 
  gi|313117405|ref|YP_004044388.1| 40 VSNSDIADRLGVTRATVSSMLDTLSESGLIERERYRPI 77
                                      5678*****************************88775 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.8
                                       HHCHHCCCTTSSCHCHHHHH CS
                              TrmB  24 tadeiaeelgvprskvYevL 43 
                                       t+ e  ++ g+pr+ + ++L
  gi|313117405|ref|YP_004044388.1| 213 TVVETGRQMGLPRPVASQIL 232
                                       77788899999999887776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00052      0.23      24      39 ..      43      58 ..      18      62 .. 0.84
   2 !    8.7   0.0    0.0027       1.2      22      45 ..     213     236 ..     211     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00052
                                      HHHHHHHTS-HHHHHH CS
                        Sigma70_r4 24 eEIgerlgiSrerVrq 39
                                      ++I++rlg++r +V++
  gi|313117405|ref|YP_004044388.1| 43 SDIADRLGVTRATVSS 58
                                      79************98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0027
                                       -HHHHHHHHTS-HHHHHHHHHHHH CS
                        Sigma70_r4  22 TleEIgerlgiSrerVrqiekrAl 45 
                                       T  E+g+++g++r  ++qi+  A+
  gi|313117405|ref|YP_004044388.1| 213 TVVETGRQMGLPRPVASQILVTAV 236
                                       899****************99886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   9.7e-07   0.00042       4      58 ..      19      72 ..      17      74 .. 0.90
   2 ?   -1.6   0.0       8.3   3.6e+03      26      38 ..     161     173 ..     153     192 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.7e-07
                                      -HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2  4 sskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      + k+e  l+ ++ L++e++++ vs ++ia+r ++ +  ++ +l +L+++gl++ +
  gi|313117405|ref|YP_004044388.1| 19 TPKMEDYLRHIYRLEQESNSR-VSNSDIADRLGVTRATVSSMLDTLSESGLIERE 72
                                      567777889999999999998.******************************976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 8.3
                                       B-HHHHHHHHTS- CS
                              Rrf2  26 vsseeiaerqnis 38 
                                        s++e+ae+  ++
  gi|313117405|ref|YP_004044388.1| 161 TSLAEVAESSCVE 173
                                       6777777776665 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.9e-06   0.00082      16      46 ..      34      68 ..      28      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.9e-06
                            HTH_23 16 e....GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      +    + s ++IA++Lgv+r Tv+  l +  e+Gl
  gi|313117405|ref|YP_004044388.1| 34 QesnsRVSNSDIADRLGVTRATVSSMLDTLSESGL 68
                                      345568899*****************999999996 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.8e-06   0.00079      13      62 ..      29      77 ..      23      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                                      HHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 13 IlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                      I + e + +++  s +++a+++gV+r tv   L++L++ gl+er++ r +
  gi|313117405|ref|YP_004044388.1| 29 IYRLEQESNSRV-SNSDIADRLGVTRATVSSMLDTLSESGLIERERYRPI 77
                                      566666778888.9999***************************987765 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   4.2e-06    0.0018       4      35 ..      39      70 ..      36      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.2e-06
                          HTH_CodY  4 rLtaskiaDriGitrsvivnaLrkLesaGiie 35
                                      r+  s iaDr+G+tr+ +   L  L  +G+ie
  gi|313117405|ref|YP_004044388.1| 39 RVSNSDIADRLGVTRATVSSMLDTLSESGLIE 70
                                      7789***************************9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.8e-06     0.003      17      46 ..      41      70 ..      32      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.8e-06
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLVe 46
                                      + +++a+ lg++++tvS  L  L e+GL+e
  gi|313117405|ref|YP_004044388.1| 41 SNSDIADRLGVTRATVSSMLDTLSESGLIE 70
                                      579*************************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   7.3e-06    0.0032      14      35 ..      36      57 ..      30      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.3e-06
                     HTH_AsnC-type 14 edaRisyaeLAervGlSestvl 35
                                       ++R s++++A+r+G++++tv 
  gi|313117405|ref|YP_004044388.1| 36 SNSRVSNSDIADRLGVTRATVS 57
                                      579*****************96 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1     2e-05    0.0086      13      44 ..      25      56 ..      22      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-05
                                      HHHHHHHHHHTT--EE-HHHHHHHCTS-HHHH CS
                    Put_DNA-bind_N 13 YlryLeelkeegveriSSteLaealgvtaaqv 44
                                      Ylr + +l++e  +r+S +++a++lgvt a+v
  gi|313117405|ref|YP_004044388.1| 25 YLRHIYRLEQESNSRVSNSDIADRLGVTRATV 56
                                      ****************************9998 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-05    0.0058      27      55 .]      41      69 ..      29      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s++++a rlg+ + Tvs+ ++ L + G+i
  gi|313117405|ref|YP_004044388.1| 41 SNSDIADRLGVTRATVSSMLDTLSESGLI 69
                                      9************************9998 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1     4e-05     0.018      12      62 ..      37      85 ..      27      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4e-05
                            HTH_29 12 vs..tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeqe 62
                                       s  + s+iA +lg++r tv   l+   e G   l++r r  rp ++ ++++e
  gi|313117405|ref|YP_004044388.1| 37 NSrvSNSDIADRLGVTRATVSSMLDTLSESG---LIERER-YRPIRLTDDGVE 85
                                      444459*************************...777544.555555666655 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.7e-05     0.025      10      47 ..      35      72 ..      24      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-05
                              FeoC 10 eergrvslkeLsrhfkaspealeamLeqwvrkGrvekv 47
                                      e + rvs ++++ ++ ++ +++ +mL+++   G +e++
  gi|313117405|ref|YP_004044388.1| 35 ESNSRVSNSDIADRLGVTRATVSSMLDTLSESGLIERE 72
                                      4688*****************************99986 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     7e-05     0.031       3      49 ..      23      73 ..      21      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7e-05
                                      HHHHHHHHH.....S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE- CS
                              FaeA  3 eeIleylnsi....kapckTreiAdalglsaYQaRyYLeqLekegkikrsp 49
                                      e+ l ++ ++    ++ +  ++iAd lg++   + + L +L   g i+r  
  gi|313117405|ref|YP_004044388.1| 23 EDYLRHIYRLeqesNSRVSNSDIADRLGVTRATVSSMLDTLSESGLIERER 73
                                      66788888888887888999****************************965 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00014     0.062       6      43 ..      25      62 ..      21      72 .. 0.87
   2 ?   -1.8   0.1       7.8   3.4e+03      23      37 ..     163     177 ..     153     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHH CS
                        Sigma70_r3  6 ikraqreLeqelgrePtpeEiAeeLglseekVrevlea 43
                                      + r + +Leqe +   ++ +iA++Lg++ + V ++l+ 
  gi|313117405|ref|YP_004044388.1| 25 YLRHIYRLEQESNSRVSNSDIADRLGVTRATVSSMLDT 62
                                      678889***************************99975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.8
                                       HHHHHHHHTXXHHHH CS
                        Sigma70_r3  23 peEiAeeLglseekV 37 
                                        +E+Ae+  +++ ++
  gi|313117405|ref|YP_004044388.1| 163 LAEVAESSCVEVTRI 177
                                       578888777766554 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2    0.0002     0.086       4      20 ..      44      60 ..      43      65 .. 0.92
   2 ?   -2.2   0.0       8.8   3.9e+03       3      17 ..     164     175 ..     162     186 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                                      HHHHHCTS-HHHHHHHC CS
                              LacI  4 DVArlAGVSkaTVSrvL 20
                                      D+A++ GV+ aTVS +L
  gi|313117405|ref|YP_004044388.1| 44 DIADRLGVTRATVSSML 60
                                      9*************988 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.8
                                       HHHHHHCTS-HHHHH CS
                              LacI   3 kDVArlAGVSkaTVS 17 
                                        +VA+ + V    V+
  gi|313117405|ref|YP_004044388.1| 164 AEVAESSCV---EVT 175
                                       455554433...344 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.6e-05     0.042      39      81 ..      42      82 ..      25     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.6e-05
                           DUF4423 39 peelakrlrpkisaeevekalefLlklgllkkdedgkyrqtek 81
                                       + +a+rl+  ++ + v++ l++L ++gl+++++   +r t+ 
  gi|313117405|ref|YP_004044388.1| 42 NSDIADRLG--VTRATVSSMLDTLSESGLIERERYRPIRLTDD 82
                                      578******..*********************98766666665 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00013     0.055      24      65 ..      36      80 ..      32     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                                      CTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE...T CS
                       TFIIE_alpha 24 ekgevteedlakelkidlnelrklLnrLyearlvkykrrrd...e 65
                                      +++ v++ d+a  l++ +  + ++L  L e +l++  r r     
  gi|313117405|ref|YP_004044388.1| 36 SNSRVSNSDIADRLGVTRATVSSMLDTLSESGLIERERYRPirlT 80
                                      5899******************************99998765554 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00039      0.17       4      62 ..      18      75 ..      15      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00039
                                      --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG- CS
                     LexA_DNA_bind  4 LTerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdpgk 62
                                      LT++ ++ l+ i +  +e     s  +ia++lg++  ++v + L +L+  G+ier+  +
  gi|313117405|ref|YP_004044388.1| 18 LTPKMEDYLRHIYRLEQESNSRVSNSDIADRLGVT-RATVSSMLDTLSESGLIERERYR 75
                                      666666666666666666666678899********.99****************98765 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0012      0.51      15      33 ..      38      56 ..      32      58 .. 0.87
   2 ?    0.9   0.1      0.93   4.1e+02      15      26 ..     159     170 ..     157     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                      TT--HHHHHHHHTSSHHHH CS
                            TetR_N 15 dattvreIAkrAGvskgal 33
                                      ++++ ++IA+r+Gv+++++
  gi|313117405|ref|YP_004044388.1| 38 SRVSNSDIADRLGVTRATV 56
                                      578899***********97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.93
                                       TT--HHHHHHHH CS
                            TetR_N  15 dattvreIAkrA 26 
                                       dat+++e+A++ 
  gi|313117405|ref|YP_004044388.1| 159 DATSLAEVAESS 170
                                       79*******975 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00035      0.15      28      71 ..      45      88 ..      23      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00035
                           DUF2250 28 iakeleipleevrellkkLeelGLlervegktikrteaklKkks 71
                                      ia++l + +  v+++l+ L e GL+er   + i+ t+    ++ 
  gi|313117405|ref|YP_004044388.1| 45 IADRLGVTRATVSSMLDTLSESGLIERERYRPIRLTDDGVEHAL 88
                                      89999***********************9999998877666555 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0016      0.71      11      28 ..      41      58 ..      31      60 .. 0.89
   2 ?   -0.6   0.0       3.4   1.5e+03      12      38 ..     109     140 ..     103     141 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                                      HHHHHHHHHTSSHHHHHH CS
                             HTH_3 11 sqeeLAeklGvsrstisr 28
                                      s  ++A++lGv+r+t+s 
  gi|313117405|ref|YP_004044388.1| 41 SNSDIADRLGVTRATVSS 58
                                      6789************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.4
                                       HHHHHHHHT.....SSHHHHHHHHTTSSCSBH CS
                             HTH_3  12 qeeLAeklG.....vsrstisriEnGernPsl 38 
                                       + e+ ++++     +s++  + iE+   +P++
  gi|313117405|ref|YP_004044388.1| 109 ISEVDAEADvlehhLSPRLCREIERELDMPDI 140
                                       55555555555555777777788888777776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0008      0.35      21      38 ..      40      57 ..      27      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0008
                            HTH_38 21 lslreIArrLgrspsTIs 38
                                       s+++IA rLg+ + T+s
  gi|313117405|ref|YP_004044388.1| 40 VSNSDIADRLGVTRATVS 57
                                      5889************98 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00045       0.2       5      53 ..      28      74 ..      24      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00045
                             TBPIP  5 lvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkiieKey 53
                                       ++++ qe+n   s +d+++ l  +++ ++v   Ld+L+++g+i    y
  gi|313117405|ref|YP_004044388.1| 28 HIYRLEQESNSRVSNSDIADRL--GVTRATVSSMLDTLSESGLIERERY 74
                                      6888889999999999**9999..59*****************987655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0011      0.49      28      47 ..      41      60 ..      38      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                                      -HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrl 47
                                      s  +IA +lg++ +tV s+l
  gi|313117405|ref|YP_004044388.1| 41 SNSDIADRLGVTRATVSSML 60
                                      889*************9986 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0024       1.1      10      31 ..      41      62 ..      28      81 .. 0.81
   2 ?   -0.0   0.0       1.9   8.3e+02      35      45 ..     123     133 ..     117     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0024
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkg 31
                                      + +  A++lgv++++Vs +l++
  gi|313117405|ref|YP_004044388.1| 41 SNSDIADRLGVTRATVSSMLDT 62
                                      56789*************9975 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.9
                    YdaS_antitoxin  35 vpaervpeIek 45 
                                       ++++ ++eIe+
  gi|313117405|ref|YP_004044388.1| 123 LSPRLCREIER 133
                                       6899******8 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0006      0.26     194     234 ..      34      71 ..      14      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0006
                             EAP30 194 kssgggvtaselaeeeenlgwsvarakeaLeelereGllwv 234
                                       ++s++ v+ s++a++   lg+++a + ++L++l ++Gl+ +
  gi|313117405|ref|YP_004044388.1|  34 QESNSRVSNSDIADR---LGVTRATVSSMLDTLSESGLIER 71 
                                       233468******777...*******************9865 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0     0.002      0.87      20      59 ..      46      83 ..      41      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.002
                                      HHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE.EEE-HHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEeelgvpLfeRtgrg.lrLTeaG 59
                                      A++Lg++ ++vs ++ +L e     L+eR   + +rLT+ G
  gi|313117405|ref|YP_004044388.1| 46 ADRLGVTRATVSSMLDTLSE---SGLIERERYRpIRLTDDG 83
                                      89************999976...479999554459999988 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0017      0.73      13      40 ..      30      57 ..      27      59 .. 0.91
   2 ?   -1.6   0.0       6.6   2.9e+03      24      36 ..     127     139 ..     119     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                   Phage_terminase 13 yelykEsggtlklkdIAkvLdvsestvr 40
                                      y+l +Es   + + dIA+ L+v   tv+
  gi|313117405|ref|YP_004044388.1| 30 YRLEQESNSRVSNSDIADRLGVTRATVS 57
                                      778899********************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.6
                   Phage_terminase  24 klkdIAkvLdvse 36 
                                       ++++I  +Ld+++
  gi|313117405|ref|YP_004044388.1| 127 LCREIERELDMPD 139
                                       79*******9985 PP

>> SgrR_N  Sugar transport-related sRNA regulator N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0016      0.72       4      50 ..      24      70 ..      21      73 .. 0.86
   2 ?   -2.1   0.0        10   4.4e+03      17      29 ..     158     170 ..     154     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                            SgrR_N  4 eqyerLlqhfegkevevtLqelAdvlfCsrRhartlLkkmqeegwle 50
                                      ++   +++  ++++++v+ +++Ad+l  +r  + ++L  ++e g++e
  gi|313117405|ref|YP_004044388.1| 24 DYLRHIYRLEQESNSRVSNSDIADRLGVTRATVSSMLDTLSESGLIE 70
                                      44455777888999******************************996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 10
                            SgrR_N  17 evevtLqelAdvl 29 
                                       e +++L+e+A+  
  gi|313117405|ref|YP_004044388.1| 158 EDATSLAEVAESS 170
                                       5678888888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1575.45
//
Query:       gi|313117406|ref|YP_004044389.1|  [L=163]
Description: phosphatidylglycerophosphatase A [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-29  101.7   1.6    3.8e-29  101.6   1.6    1.0  1  PgpA      Phosphatidylglycerophosphatase A


Domain annotation for each model (and alignments):
>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   1.6   2.1e-33   3.8e-29       6     142 ..       2     153 ..       1     154 [. 0.81

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 2.1e-33
                                       HHHHTT......--HHHHHHHHHHHTT.....HHHHH.HHHHHHHHHHHHHHHHHHHHHT.-S-HHT-TT--HHHHT CS
                              PgpA   6 tlfgsGllpvaPgtvgslaalllallll....lleslslllllilllflvGiwackktek.elgekDpgeiviDEvv 77 
                                       t+ g+G++pvaPgt+gsl  +++al++l     +++l+ +l+ ++l++ v++   ++ ++ ++g kDp  +v DE +
  gi|313117406|ref|YP_004044389.1|   2 TVGGLGHAPVAPGTFGSLPPVAVALVFLttplPIWQLNVVLPTLALVLSVACVRFGHWAEgYWGCKDPRTVVADEAI 78 
                                       67899*************8888887776555544444344466666777777666666666**************** PP

                                       THHHHH...................TTHHHHHHHHHHHHS--THHHHTSSS.-S---TTHHHHHHHHHHHHHHHHH CS
                              PgpA  78 gqwiallllpa...........tllalllafilFrlfDivKpgpigwldrklkgglgvmlDDllAgiaaalvlali 142
                                       gq + ll+lp+           ++l l++a+++FrlfD +K  p ++l+r l+gg+g+++DDl+Ag++a + ++l+
  gi|313117406|ref|YP_004044389.1|  79 GQTLPLLFLPWhhwgygemalwNVLLLFTAVTTFRLFDVTKLPPMRMLER-LSGGWGILIDDLVAGVYATVFSHLL 153
                                       *********886666666665444466899******************99.7******************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1072.12
//
Query:       gi|313117407|ref|YP_004044390.1|  [L=274]
Description: nitrate/sulfonate/bicarbonate ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-31  107.5   0.0    1.4e-30  106.6   0.0    1.4  1  ABC_tran      ABC transporter
    3.1e-07   30.5   0.1      0.012   15.5   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.6e-06   27.4   0.3    5.5e-05   23.6   0.2    2.5  2  AAA           ATPase family associated with various cellular 
     0.0011   19.1   0.0     0.0024   18.0   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0011   19.3   0.2     0.0045   17.4   0.0    1.9  2  AAA_16        AAA ATPase domain
     0.0013   18.7   1.2      0.031   14.3   0.1    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0051   17.1   0.3      0.016   15.5   0.3    2.0  1  AAA_22        AAA domain
     0.0055   16.6   0.0       0.01   15.7   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.019   15.4   0.0      0.043   14.3   0.0    1.5  1  AAA_23        AAA domain
       0.02   14.7   0.0      0.041   13.6   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
       0.02   15.1   0.3      0.075   13.2   0.3    2.0  1  AAA_33        AAA domain
      0.022   14.5   0.0      0.048   13.4   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
      0.025   14.5   0.0      0.052   13.5   0.0    1.5  1  Rad17         Rad17 P-loop domain
      0.026   13.7   0.0      0.043   13.0   0.0    1.3  1  NB-ARC        NB-ARC domain
      0.032   14.5   0.6       0.16   12.2   0.1    2.1  2  AAA_28        AAA domain
      0.033   13.0   0.1       0.08   11.7   0.0    1.5  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.037   13.8   0.3        1.2    8.8   0.0    2.3  2  AAA_24        AAA domain
      0.063   13.5   0.1       0.26   11.5   0.1    1.9  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.063   12.8   0.2       0.23   11.0   0.0    1.9  2  AAA_25        AAA domain
      0.072   12.5   0.0        5.8    6.3   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.073   13.1   0.0       0.13   12.3   0.0    1.3  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.081   12.8   0.1       0.18   11.7   0.0    1.6  1  NACHT         NACHT domain
      0.099   12.0   0.0       0.22   10.9   0.0    1.5  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.12   12.1   0.0       0.35   10.6   0.0    1.7  2  AAA_30        AAA domain
       0.15   11.9   0.0       0.35   10.8   0.0    1.5  1  ATPase_2      ATPase domain predominantly from Archaea
       0.16   12.5   0.7       0.33   11.5   0.3    1.7  1  AAA_18        AAA domain
       0.17   11.6   0.0       0.36   10.6   0.0    1.4  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.18   11.8   0.5        2.4    8.2   0.1    2.6  3  AAA_14        AAA domain
        0.2   11.1   0.0       0.33   10.4   0.0    1.3  1  AAA_7         P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   2.3e-33   1.4e-30       1     136 [.      41     180 ..      41     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 2.3e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++vsl+++ ge v +vG++G+GK+tL++++agl+ pt+G++ + g +++           g+++qe +lfp  tv+
  gi|313117407|ref|YP_004044390.1|  41 LRDVSLTVEDGEFVCLVGPSGCGKTTLFRIVAGLEPPTSGDVFVTGSPVTG-----PGIDRGMVFQEYNLFPWRTVE 112
                                       689***************************************999999999.....99999**************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        n             + ++++e++++ +gl++++d       ++LSgG+kqrva+aral+ +p++lllDEp+
  gi|313117407|ref|YP_004044390.1| 113 GNvrfgleqpacdcpDCTARVEELIDLVGLTGFEDAYP----KELSGGMKQRVAVARALAVDPEILLLDEPF 180
                                       **************999***************999998....*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.9e-05     0.012       1      22 [.      53      74 ..      53     101 .. 0.83
   2 !   13.1   0.0   9.9e-05     0.061     235     297 ..     151     211 ..     127     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + +l+Gp g+GK++L+++  +l
  gi|313117407|ref|YP_004044390.1| 53 FVCLVGPSGCGKTTLFRIVAGL 74
                                      679****************988 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.9e-05
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQviltTH 297
                                        elS G+k+  a++ al+ ++    +ll+DEp  +++     +l+r+ll++  e+++    ++++TH
  gi|313117407|ref|YP_004044390.1| 151 KELSGGMKQRVAVARALAVDP---EILLLDEPFGSIDAqtrdHLQRELLDIWQETEK---TILFVTH 211
                                       578*****9999999999999...9***************************99999...******* PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   8.8e-08   5.5e-05       1     100 [.      54     219 ..      54     243 .. 0.65
   2 ?   -2.0   0.0       7.4   4.6e+03      60      74 ..     252     266 ..     229     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.8e-08
                                       EEEESSTTSSHHHHHHHHHHH............HTHE................................EEEEETTT CS
                               AAA   1 vllyGppGtGKTllakavake............lgve................................fleisgse 33 
                                       v+l+Gp G+GKT+l + va              +  +                                        
  gi|313117407|ref|YP_004044390.1|  54 VCLVGPSGCGKTTLFRIVAGLepptsgdvfvtgS--PvtgpgidrgmvfqeynlfpwrtvegnvrfgleQ------- 121
                                       79******************96665444443220..1334444444444444444444444444444441....... PP

                                       CSSS..........................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHH CS
                               AAA  34 llsk..........................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeee 83 
                                                                     y +e +  +++ ++ a++ a +p il++DE    + ++       ++
  gi|313117407|ref|YP_004044390.1| 122 ---PacdcpdctarveelidlvgltgfedaYPKELSGGMKQRVAVARALAvDPEILLLDEPFGSIDAQ------TRD 189
                                       ...044444555556666666666666666****************9999999*******54444555......678 PP

                                       HHHHHHHHHHHHTTTS.............S CS
                               AAA  84 rvvnqLlteldgvkkk.............e 100
                                        ++ +Ll  +++ +k               
  gi|313117407|ref|YP_004044390.1| 190 HLQRELLDIWQETEKTilfvtheieeavtL 219
                                       899999999999988544444444444442 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.4
                                       EEEEEETGGGHHHHH CS
                               AAA  60 silfiDEidalaksr 74 
                                        + +i+E+ +l+++r
  gi|313117407|ref|YP_004044390.1| 252 FVSLIEEVRELIEQR 266
                                       556788888888887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.8e-06    0.0024       2     111 ..      54     209 ..      53     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.8e-06
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE............................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke............................... 47 
                                       v++vG +  GK+tL++   g +  +s   ++T  +++g    +                                  
  gi|313117407|ref|YP_004044390.1|  54 VCLVGPSGCGKTTLFRIVAGLEPPTSGDVFVTGSPVTGPGIDR--Gmvfqeynlfpwrtvegnvrfgleqpacdcpd 128
                                       89******************999999999******99976522..12345566777777778888888888888888 PP

                                       .....EEEEECGGCS..SHHHHHH...HHHHHHHHHHC..TSEEEEEEETT......TTCSHHHHHHHHHHHHHTTS CS
                          MMR_HSR1  48 .....ielvDtpGli..egaseek...glgkaflalee..adlillvvdas......eeklkpldeeleelleeakk 106
                                             el+D++Gl   e+a  ++   g++++++  +   +d  +l++d +       ++ ++l++el ++ +e++k
  gi|313117407|ref|YP_004044390.1| 129 ctarvEELIDLVGLTgfEDAYPKElsgGMKQRVAVARAlaVDPEILLLD-EpfgsidAQTRDHLQRELLDIWQETEK 204
                                       88887899*****743332322333444544444333343577788887.335555422345566666666666666 PP

                                       EEEEE CS
                          MMR_HSR1 107 plilv 111
                                        +++v
  gi|313117407|ref|YP_004044390.1| 205 TILFV 209
                                       65554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   7.3e-06    0.0045       8      44 ..      37      71 ..      34      93 .. 0.82
   2 ?   -0.5   0.1       2.3   1.4e+03     127     135 ..     195     204 ..     131     272 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.3e-06
                            AAA_16  8 eleqLlsalervrsgrpelvllsGesGvGKsslvrel 44
                                       +++L+++  +v +g  e v l+G+sG+GK++l r +
  gi|313117407|ref|YP_004044390.1| 37 TVDALRDVSLTVEDG--EFVCLVGPSGCGKTTLFRIV 71
                                      577788877788888..78**************8766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.3
                            AAA_16 127 l.allsrder 135
                                       l +  +++e+
  gi|313117407|ref|YP_004044390.1| 195 LlDIWQETEK 204
                                       3333333333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   4.9e-05     0.031       2      20 ..      54      72 ..      53      80 .. 0.90
   2 ?    3.0   0.2      0.15        95      39     101 ..     193     268 ..     183     273 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-05
                                      EEEE--SSSSHHHHHHHGG CS
                             AAA_5  2 vlLvGppGtgKselaerla 20
                                      v+LvGp+G+gK++l + +a
  gi|313117407|ref|YP_004044390.1| 54 VCLVGPSGCGKTTLFRIVA 72
                                      8*************99876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.15
                                       HHHH--B--.........--------.............G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSS CS
                             AAA_5  39 edlkgrreikngttslvdsplvraar.............egeilvlDEveraesevlnsLlslleerrllleegge 101
                                       ++l+  ++ +++t  +v  ++ +a++              + ++v+ +ver ++ +++++ sl+ee r l+e++g+
  gi|313117407|ref|YP_004044390.1| 193 RELLDIWQETEKTILFVTHEIEEAVTladrivvlgsnpdDSITTVDIDVERPRDRTAPEFVSLIEEVRELIEQRGR 268
                                       556666665566666666666666666666666666774444455559*****************99888777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   2.6e-05     0.016       4      28 ..      50      74 ..      47     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      +  +++++G+sG+GKTtl r ++  
  gi|313117407|ref|YP_004044390.1| 50 DGEFVCLVGPSGCGKTTLFRIVAGL 74
                                      56799*************9977655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-05      0.01      81     120 ..      32      72 ..      17      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       + + +t ++l++++  ++d ++++lvG+SG GK+tL   ++
  gi|313117407|ref|YP_004044390.1|  32 YDNRQTVDALRDVSLTVEDgEFVCLVGPSGCGKTTLFRIVA 72 
                                       55667778888888888888****************87665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.9e-05     0.043      18      37 ..      50      69 ..      30      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.9e-05
                            AAA_23 18 skgltlItGpNGaGKTTild 37
                                      +  +++++Gp G+GKTT+++
  gi|313117407|ref|YP_004044390.1| 50 DGEFVCLVGPSGCGKTTLFR 69
                                      446889************97 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.7e-05     0.041      29      63 ..      31      67 ..      25      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-05
                         IstB_IS21 29 sldkrk.vkeLatlsf.iekkenivllGpsGvGKshl 63
                                       +d+r+ v++L+  s  +e+ e ++l+GpsG GK+ l
  gi|313117407|ref|YP_004044390.1| 31 RYDNRQtVDALRDVSLtVEDGEFVCLVGPSGCGKTTL 67
                                      455554167999988647899**************87 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   0.00012     0.075       2      21 ..      54      73 ..      53     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                            AAA_33  2 vllvGlpGsGKstlaerllk 21
                                      v lvG++G+GK+tl + ++ 
  gi|313117407|ref|YP_004044390.1| 54 VCLVGPSGCGKTTLFRIVAG 73
                                      679***********997764 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.8e-05     0.048      12      39 ..      38      68 ..      32      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-05
                            AAA_29 12 fdg.htieidlkg..atlltGpsGsGKSTll 39
                                       d  +++++++++  ++ l+GpsG GK+Tl+
  gi|313117407|ref|YP_004044390.1| 38 VDAlRDVSLTVEDgeFVCLVGPSGCGKTTLF 68
                                      55555666665555799************97 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.4e-05     0.052      36      66 ..      42      72 ..      31      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.4e-05
                             Rad17 36 kadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      +  +L  +  + + + GPsGCgk+t  ++++
  gi|313117407|ref|YP_004044390.1| 42 RDVSLTVEDGEFVCLVGPSGCGKTTLFRIVA 72
                                      5556666667788899*********999976 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     7e-05     0.043       4      39 ..      37      70 ..      34      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                                      HHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHH CS
                            NB-ARC  4 svekviekLlekdelqslvvalvGmgGvGKttlakq 39
                                      +v+++ +  l  ++ +  +v lvG  G+GKttl++ 
  gi|313117407|ref|YP_004044390.1| 37 TVDALRDVSLTVEDGE--FVCLVGPSGCGKTTLFRI 70
                                      5666666555466777..9**************975 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00026      0.16       2      21 ..      54      73 ..      53      90 .. 0.84
   2 ?   -0.1   0.0       1.5   9.5e+02     130     154 ..     184     208 ..     146     217 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      ++++G++++GKTtl +  a 
  gi|313117407|ref|YP_004044390.1| 54 VCLVGPSGCGKTTLFRIVAG 73
                                      89************998775 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                            AAA_28 130 dleereaiderlrealrelgipvii 154
                                       d + r  +++ l+++++e    ++ 
  gi|313117407|ref|YP_004044390.1| 184 DAQTRDHLQRELLDIWQETEKTILF 208
                                       3334444555555555555555444 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.3   1.4e+03     246     262 ..      53      69 ..      46      81 .. 0.76
   2 ?   11.7   0.0   0.00013      0.08     323     398 ..     153     228 ..     145     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.3
                                       EEEEEE-TTSSHHHHHH CS
                        ABC_ATPase 246 vtlIvGggfhGKsTLLe 262
                                        + +vG+   GK+TL +
  gi|313117407|ref|YP_004044390.1|  53 FVCLVGPSGCGKTTLFR 69 
                                       5678999999*****87 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00013
                                       --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS- CS
                        ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggs 398
                                        SG + q +++++al ++ ++lL+DE         rD++ +el+  ++e+ ++++   +e+ + + +   +vv gs
  gi|313117407|ref|YP_004044390.1| 153 LSGGMKQRVAVARALAVDPEILLLDEPFGSIDAQTRDHLQRELLDIWQETEKTILFVTHEIEEAVTLADRIVVLGS 228
                                       59****************************************************9999999988888766655443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0     0.002       1.2       5      20 ..      54      69 ..      51      79 .. 0.87
   2 ?    2.8   0.1      0.14        84     112     139 ..     193     220 ..     186     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.002
                            AAA_24  5 iliyGpsgiGKTtlak 20
                                      ++++Gpsg GKTtl +
  gi|313117407|ref|YP_004044390.1| 54 VCLVGPSGCGKTTLFR 69
                                      79***********975 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                            AAA_24 112 rrllkklqelrknvifiahektrkdedp 139
                                       r+ll+  qe+ k++ f+ he ++ ++  
  gi|313117407|ref|YP_004044390.1| 193 RELLDIWQETEKTILFVTHEIEEAVTLA 220
                                       7889999999************999876 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00042      0.26      62      84 ..     169     191 ..     147     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatl 84 
                                        ++++++LDE F+++D+++++ l
  gi|313117407|ref|YP_004044390.1| 169 VDPEILLLDEPFGSIDAQTRDHL 191
                                       4689**************98865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00038      0.23      31      49 ..      49      67 ..      40      72 .. 0.90
   2 ?   -0.9   0.1       1.7     1e+03      67     108 ..     199     239 ..     185     268 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                            AAA_25 31 pagelallaGapgtGKttl 49
                                        ge++ l+G++g+GKttl
  gi|313117407|ref|YP_004044390.1| 49 EDGEFVCLVGPSGCGKTTL 67
                                      6799**************8 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                            AAA_25  67 vapeqgkVlyvsaEdsed.elrrRlravgealrddarllvldl 108
                                       ++ +  + l+v  E  e+ +l+ R+  +g +   d+  + +d+
  gi|313117407|ref|YP_004044390.1| 199 WQETEKTILFVTHEIEEAvTLADRIVVLGSNP--DDSITTVDI 239
                                       44455556666666653336666666555553..333344443 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0093       5.8      24      41 ..      51      68 ..      40      72 .. 0.84
   2 ?    4.1   0.0     0.044        27     133     209 ..     149     224 ..     127     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0093
                                      SSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnll 41
                                       +f ++vGp G+GK+ l+
  gi|313117407|ref|YP_004044390.1| 51 GEFVCLVGPSGCGKTTLF 68
                                      4699***********987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.044
                                       STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH...HHCTTSEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 133 skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk...eksknaQfivislreemlekad 206
                                       ++++LSgG k+ va+a  +A+    p+ + llDe    +D++ +  + + l    ++++++ ++v+   ee ++ ad
  gi|313117407|ref|YP_004044390.1| 149 YPKELSGGMKQRVAVARALAVD---PE-ILLLDEPFGSIDAQTRDHLQRELLdiwQETEKTILFVTHEIEEAVTLAD 221
                                       5679************999874...44.6688888888888887777654332434555555555555566666666 PP

                                       CEE CS
                                       xxx RF
                             SMC_N 207 klv 209
                                       ++v
  gi|313117407|ref|YP_004044390.1| 222 RIV 224
                                       665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.13      13      40 ..      43      72 ..      31      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                      HHHHCH..TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 13 klakal..gdvilLeGdLGaGKTtlvrgla 40
                                      ++  ++  g++++L G+ G+GKTtl r +a
  gi|313117407|ref|YP_004044390.1| 43 DVSLTVedGEFVCLVGPSGCGKTTLFRIVA 72
                                      33333355788**************99765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00029      0.18       3      20 ..      54      71 ..      52      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                      v+l G++G+GKTtL + +
  gi|313117407|ref|YP_004044390.1| 54 VCLVGPSGCGKTTLFRIV 71
                                      89************8755 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00035      0.22      19      50 ..      48      79 ..      35      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                      Mg_chelatase 19 aaGgHnlllvGppGsGKtmlakrlpsllppls 50
                                      +  g  + lvGp+G+GKt l + +++l pp s
  gi|313117407|ref|YP_004044390.1| 48 VEDGEFVCLVGPSGCGKTTLFRIVAGLEPPTS 79
                                      55566689******************999976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00057      0.35      16      40 ..      49      73 ..      35      87 .. 0.80
   2 ?   -1.9   0.0       3.8   2.3e+03      37      71 ..     194     228 ..     186     261 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00057
                            AAA_30 16 sgdrvavltGpAGtGKttalkalre 40
                                      ++  +++l+Gp G GKtt+ + ++ 
  gi|313117407|ref|YP_004044390.1| 49 EDGEFVCLVGPSGCGKTTLFRIVAG 73
                                      444599*************998875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
                            AAA_30  37 alreaweaaggrviglAptgkaAkvLaeelgieas 71 
                                       +l ++w++ +++++ ++++ + A +La+ + + +s
  gi|313117407|ref|YP_004044390.1| 194 ELLDIWQETEKTILFVTHEIEEAVTLADRIVVLGS 228
                                       55677888888888888888888888876655444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00056      0.35      18      40 ..      49      71 ..      35      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00056
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkei 40
                                      e  e++ + Gp g+GKt+L++ +
  gi|313117407|ref|YP_004044390.1| 49 EDGEFVCLVGPSGCGKTTLFRIV 71
                                      446788899**********9865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00053      0.33       1      19 [.      54      72 ..      54      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00053
                            AAA_18  1 IlltGtpGvGKttlakeLs 19
                                      ++l G++G+GKttl + ++
  gi|313117407|ref|YP_004044390.1| 54 VCLVGPSGCGKTTLFRIVA 72
                                      79************98775 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00058      0.36       4      23 ..      54      73 ..      52      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00058
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      + l+G++g+GKttL + + g
  gi|313117407|ref|YP_004044390.1| 54 VCLVGPSGCGKTTLFRIVAG 73
                                      789***********987766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0038       2.4       3      21 ..      52      70 ..      50      84 .. 0.84
   2 ?    0.4   0.0      0.99   6.1e+02      69     105 ..     195     233 ..     174     249 .. 0.74
   3 ?   -1.2   0.0       3.2     2e+03      30      58 ..     231     261 ..     218     268 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0038
                            AAA_14  3 kilvitGaRrvGKTtllkq 21
                                      + ++++G+  +GKTtl + 
  gi|313117407|ref|YP_004044390.1| 52 EFVCLVGPSGCGKTTLFRI 70
                                      6789************764 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.99
                            AAA_14  69 flDEiqevpewekalkslvdeg..knldvivtGSnskll 105
                                       +lD +qe ++   ++ + ++e      +++v GSn  + 
  gi|313117407|ref|YP_004044390.1| 195 LLDIWQETEKTILFVTHEIEEAvtLADRIVVLGSNPDDS 233
                                       577778888888888888886644344899999987655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.2
                            AAA_14  30 kesilyinldderdkkladpe..kllelile 58 
                                       ++si  +++d er ++++ pe  +l+e+++e
  gi|313117407|ref|YP_004044390.1| 231 DDSITTVDIDVERPRDRTAPEfvSLIEEVRE 261
                                       4455555555444444443332255555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00054      0.33      26      51 ..      44      69 ..      34      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00054
                             AAA_7 26 lelllknkkpvllvGptGtGKtviik 51
                                      ++l ++ +  v+lvGp+G+GKt++ +
  gi|313117407|ref|YP_004044390.1| 44 VSLTVEDGEFVCLVGPSGCGKTTLFR 69
                                      5678899999************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1707.19
//
Query:       gi|313117408|ref|YP_004044391.1|  [L=281]
Description: nitrate/sulfonate/bicarbonate ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-16   58.7  11.0    1.1e-15   57.8  11.0    1.6  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8  11.0   6.4e-20   1.1e-15       1     182 [.     107     275 ..      82     278 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 6.4e-20
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       g+++G++++  +  + d + +p++ vl+ +P ++++ + +       ++g + +++ ++++++a++++++  ++++r
  gi|313117408|ref|YP_004044391.1| 107 GNGAGLVIG--YATRADAIATPVVRVLRPIPELAWIAFAI------VWFGIGHTGATFIVAIGALWINYYAAYSGVR 175
                                       556677777..889********************888888......799**************************** PP

                      BPD_transp_1  78 slpkdlveaaralGa.srwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                        + ++++e+a  lG  ++  ++r+v+lP+a p i+ g++ ++g+ l   v +e++g  pG+g+ +l+a+++ d++  
  gi|313117408|ref|YP_004044391.1| 176 GVRDGYKEVAASLGIrTHVGMLRYVILPAASPAIVNGFRTSIGRCLMIVVGAELFG-APGVGYEILNASNNLDMA-- 249
                                       **************944689************************************.789***************.. PP

                      BPD_transp_1 154 snggvlalviavlllnlvadilqrlldpr 182
                                           + a+ +++ ++ +++d  +++l+ r
  gi|313117408|ref|YP_004044391.1| 250 ---RSMAYMLLISAVYICVDGGYAALESR 275
                                       ...56688888899999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1859.04
//
Query:       gi|313117409|ref|YP_004044392.1|  [L=337]
Description: nitrate/sulfonate/bicarbonate ABC transporter periplasmic protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-47  162.8   0.7      2e-47  162.0   0.2    1.5  2  NMT1_2          NMT1-like family
     0.0095   15.5   0.2       0.02   14.5   0.1    1.6  2  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   0.2   2.3e-51     2e-47       2     252 ..      31     276 ..      30     277 .. 0.96
   2 ?   -1.9   0.0      0.24   2.1e+03      41      62 ..     300     323 ..     289     328 .. 0.79

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 2.3e-51
                            NMT1_2   2 apekeqlklGfialtdaaplvvakekglfakeGltvelekqaswaelrdkllagelDaahv.ltpapllidlGigga 77 
                                       ++++eql++G+++++ +++++v++e++++a+ + ++++++++s+++++++++ag+lD++++ +tpa++l+d+G+   
  gi|313117409|ref|YP_004044392.1|  31 QENSEQLHVGWVPIYPNVQHFVMSERDYYAELDAELSTTEFSSGPAAVKAFAAGDLDIGFFgVTPAMVLTDNGV--- 104
                                       6889**********************************************************************... PP

                            NMT1_2  78 kadmkvlaslnlnGqaitlsnklkdkkvsdakalkdlvakkkas..kplkiavtfpgsthdlllrywLaaaGldp.. 150
                                         d +vl+++++nG +++++++++d   + +++  d++++++a+  +++ +++  +gs +d+++ryw+ +++l+   
  gi|313117409|ref|YP_004044392.1| 105 --DADVLVANSKNGFKMIATDGFAD---RYDDDGGDAFQSYTADhgTKPIWGTAPDGSVPDIITRYWI-ERDLEAga 175
                                       ..***********************...8999999*********************************.9****999 PP

                            NMT1_2 151 .eadvklvvvpppqmvanlkagtidgfcvgePwnaqavaegiG.vtaltsqelwkdhPekvlgvredfveknpntar 225
                                        ++ v+ ++vpp+++++++++g+i g++v+eP+ a++vae+ G +++ +s+++++dhP++v +v +++     ++ r
  gi|313117409|ref|YP_004044392.1| 176 tTDVVNKAKVPPAKTPQAAQSGDIVGTTVQEPY-ATLVAEMDGyRQIEWSGTVLPDHPVTVAFVANSV---SNELKR 248
                                       88999****************************.9********88999********************...4489** PP

                            NMT1_2 226 alvkalleAtkwlda.kkenraeaakll 252
                                        +v+++++At+ + +  + ++++aa++l
  gi|313117409|ref|YP_004044392.1| 249 GFVEQHIRATNAVYDdPTGAAQDAAAVL 276
                                       **************98999999999887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.24
                            NMT1_2  41 kqaswaelrdkll..agelDaahv 62 
                                       + +s +e++ k++   g++D+a+ 
  gi|313117409|ref|YP_004044392.1| 300 EITSQSETMSKFVaeVGNIDGAMS 323
                                       557889999999977799999976 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   2.2e-06      0.02      27      81 ..      62     116 ..      59     140 .. 0.83
   2 ?   -3.2   0.0      0.58   5.2e+03     183     199 ..     220     236 ..     192     253 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-06
                                       HSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS.-EEEEEEEEETT- CS
                    Phosphonate-bd  27 lGvevelvvatdyaavvealragqvDiaflgplayvqardqa.gveplatrvrsdG 81 
                                       l+ e  ++ +++  a+v+a++ag +Di+f+g  +++++ d+  ++++l+++++ +G
  gi|313117409|ref|YP_004044392.1|  62 LDAELSTTEFSSGPAAVKAFAAGDLDIGFFGVTPAMVLTDNGvDADVLVANSK-NG 116
                                       555656666667789***********************9995599**999986.55 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.58
                                       EEEEEEEEEE--EEEEE CS
                    Phosphonate-bd 183 rviassppipndpvvvr 199
                                       ++ +s  ++p +pv v 
  gi|313117409|ref|YP_004044392.1| 220 QIEWSGTVLPDHPVTVA 236
                                       34466667777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2261.17
//
Query:       gi|313117410|ref|YP_004044393.1|  [L=324]
Description: deoxyhypusine synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.1e-100  335.7   0.0   2.4e-100  335.5   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.5   0.0  1.3e-104  2.4e-100       1     286 [.      36     319 ..      36     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 335.5 bits;  conditional E-value: 1.3e-104
                                DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       e+l+sye++gfqat+l+ea++i ++m ++ ++t++l++tsn+issGlre +a+lv+e++vdv++tT g+i+eD+ik+
  gi|313117410|ref|YP_004044393.1|  36 EMLSSYETTGFQATQLAEAVEIAEEM-QEADATVYLTFTSNIISSGLREAVAYLVREGYVDVLITTSGSITEDVIKT 111
                                       6899**********************.78899********************************************* PP

                                DS  78 lgkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSily 154
                                        ++ + +g++++d+++Lre+ginR+gn++vp+++y  +e+++ +++d++ +e+k+++p+ + +elG+ ++de+S+l+
  gi|313117410|ref|YP_004044393.1| 112 AKP-FKMGEWDADEAALREQGINRLGNIFVPSDRYVWLEEYLYDFFDDFFAEKKIRTPTAFARELGETLDDEDSVLK 187
                                       ***.************************************************************************* PP

                                DS 155 wAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlmr 231
                                       +A++nd+pvfcpaltD ++G  +l++++   ++++ ++i++D+++l +  l +++tg+i +GGGvpKhh++ +nl+r
  gi|313117410|ref|YP_004044393.1| 188 QAADNDVPVFCPALTDAEVGN-FLYYYRQGYDSEVGIEILDDYDKLIENGLLSDTTGLIAVGGGVPKHHAIMTNLFR 263
                                       *********************.777775558899******************************************* PP

                                DS 232 ngadyavyittaqefdGslsgatldEavSwgkika.eaksvkvyaDaTivlPLlva 286
                                        gadya+yi+t+ e dGslsga ++EavSwgkik+ +++ +++ a+aT+v+P+l+a
  gi|313117410|ref|YP_004044393.1| 264 GGADYAIYISTGMEGDGSLSGAPPNEAVSWGKIKEeDKNYTQIEAEATLVFPMLIA 319
                                       **********************************9445889*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2241.56
//
Query:       gi|313117411|ref|YP_004044394.1|  [L=326]
Description: multidrug ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-29  103.3   0.0    3.2e-29  102.2   0.0    1.6  2  ABC_tran     ABC transporter
    1.3e-10   41.6   6.6    2.8e-07   30.7   0.2    2.6  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.6e-07   31.2   1.0    7.1e-07   29.9   1.0    1.8  1  DUF4162      Domain of unknown function (DUF4162)
    0.00024   21.6   0.2    0.00091   19.6   0.0    1.9  2  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.016   14.9   0.3      0.045   13.5   0.3    1.7  1  AAA_29       P-loop containing region of AAA domain
      0.017   15.4   0.6       0.15   12.3   0.6    2.2  1  AAA_22       AAA domain
       0.02   15.4   1.5      0.039   14.5   1.5    1.8  1  AAA_23       AAA domain
      0.026   14.9   0.1      0.081   13.4   0.1    2.1  1  AAA          ATPase family associated with various cellular a
      0.035   13.8   0.1       0.08   12.7   0.1    1.5  1  AAA_30       AAA domain
       0.05   13.5   0.0       0.15   12.0   0.0    1.8  1  NTPase_1     NTPase
      0.054   13.8   0.1      0.086   13.2   0.1    1.7  1  AAA_19       AAA domain
      0.072   12.8   0.0       0.17   11.6   0.0    1.7  2  AAA_24       AAA domain
       0.08   12.7   0.1       0.22   11.3   0.1    1.7  2  MukB         MukB N-terminal
      0.097   12.3   0.1       0.19   11.3   0.1    1.5  1  SRP54        SRP54-type protein, GTPase domain
       0.13   11.7   0.8       0.56    9.6   0.8    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
          1    9.7   3.4        2.1    8.7   3.2    1.7  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   2.9e-32   3.2e-29       2     136 ..      35     178 ..      34     179 .. 0.98
   2 ?   -2.3   0.0       5.2   5.8e+03      48      48 ..     255     255 ..     213     308 .. 0.54

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 2.9e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + vs++++ g++v+++G+nGaGK+t +k ++gl++p++G++++dg d+ e++++ +++  ++l+   +   +ltvre
  gi|313117411|ref|YP_004044394.1|  35 DGVSFTIESGSVVGLLGPNGAGKTTTIKSILGLVRPDAGTVRIDGIDTAENPRQAFNRVDAMLEGARNDYWRLTVRE 111
                                       78*************************************************************************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             + +++ +++l++l+l+e++d++v    + LS G+kq+v+la +l+++ ++ +lDEpt
  gi|313117411|ref|YP_004044394.1| 112 NlryfaaiggddpaAVSDRHDQLLDTLELSEKADEPV----RDLSRGMKQKVSLASVLASDVSVAFLDEPT 178
                                       *************999999******************....*****************************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.2
                                       E CS
                                       x RF
                          ABC_tran  48 d 48 
                                       d
  gi|313117411|ref|YP_004044394.1| 255 D 255
                                       2 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3     2e-05     0.023       2      23 ..      47      68 ..      46     102 .. 0.78
   2 !   30.7   0.2   2.5e-10   2.8e-07     205     302 ..     120     214 ..      78     215 .. 0.77
   3 ?   -2.0   0.1       2.3   2.5e+03     197     234 ..     247     284 ..     232     307 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       +l GpNg+GK++ ++ + +l 
  gi|313117411|ref|YP_004044394.1| 47 VGLLGPNGAGKTTTIKSILGLV 68
                                      689***************8884 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 2.5e-10
                            AAA_21 205 geeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrr 277
                                       g +++a v++r ++  + +le +   + p+r+lS G+k+   l++ l+++    s+ ++DEp +gL+      l r+
  gi|313117411|ref|YP_004044394.1| 120 GGDDPAAVSDRHDQ-LLDTLELSEKADEPVRDLSRGMKQKVSLASVLASDV---SVAFLDEPTLGLDVesslTLRRE 192
                                       44455555555555.89999999999***********************99...**************555444455 PP

                            AAA_21 278 llellkelsrngaQviltTHSplll 302
                                       l +++    +++  v+l++H+  ++
  gi|313117411|ref|YP_004044394.1| 193 LRRIV---DERDLTVVLSSHDMDVI 214
                                       55555...33579*******97766 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.3
                            AAA_21 197 ielsdlgegeeliasvderlrergvvflengdgqelpa 234
                                       +++s++++ ++   +  er + +++ ++++  + e++a
  gi|313117411|ref|YP_004044394.1| 247 FRISLNDVDSDTLSLLRERYDVSDIDQFDRRTRFEVTA 284
                                       44444444444444444443333444444433333333 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   1.0   6.3e-10   7.1e-07       3      81 .]     235     321 ..     234     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6.3e-10
                                       HHHHHTTS-SSEEEEE.....-------..--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE-- CS
                           DUF4162   3 leeiKrsygknrieve.....adaeelleepg.veeveeeggelelkled.eeaanellkal.tsgveirsFeeeeP 71 
                                       + e+ +++ ++r++++     +d  +ll+e   v+++++++++ +++++  +e+  +l++a+ +++v++ s+e ++P
  gi|313117411|ref|YP_004044394.1| 235 VAELLEQFETQRFRISlndvdSDTLSLLRERYdVSDIDQFDRRTRFEVTAdNETFYRLIDAIaEADVTLDSVETIQP 311
                                       78999***********98866557777777666********888998885589*********78************* PP

                                       -HHHHHHHHH CS
                           DUF4162  72 sLndIFiekv 81 
                                        L+d+F+e +
  gi|313117411|ref|YP_004044394.1| 312 DLEDVFLEIT 321
                                       *******975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   8.2e-07   0.00091      24     136 ..      44     147 ..      37     205 .. 0.82
   2 ?   -0.4   0.1       1.2   1.3e+03      71      99 ..     237     264 ..     185     317 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.2e-07
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       +++v l G+ G GK++ ++++l  l + ++ ++r +  +            a   ++ ++ +++++e a  ++wr +
  gi|313117411|ref|YP_004044394.1|  44 GSVVGLLGPNGAGKTTTIKSILG-LVRPDAGTVRIDGIDT-----------AENPRQAFNRVDAMLEGARNDYWRLT 108
                                       378889****************6.5555588888888888...........33355888888888888999999999 PP

                            AAA_16 101 leeala...avpelagaeasrllellkrllallsrderp 136
                                        +e+l+   a++ +++a+ s+ +++l + l+l+++ ++p
  gi|313117411|ref|YP_004044394.1| 109 VRENLRyfaAIGGDDPAAVSDRHDQLLDTLELSEKADEP 147
                                       999999888777777777788888888888777776655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                            AAA_16  71 alaqalareellrqlldeaesaeleawre 99 
                                        l++++++ + +r  l++ +s+ l+  re
  gi|313117411|ref|YP_004044394.1| 237 ELLEQFET-QRFRISLNDVDSDTLSLLRE 264
                                       35555533.55555555544444444433 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3     4e-05     0.045      13      49 ..      35      71 ..      32      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      dg +++i+  +++ l Gp+G+GK+T + +i  l  p+
  gi|313117411|ref|YP_004044394.1| 35 DGVSFTIESGSVVGLLGPNGAGKTTTIKSILGLVRPD 71
                                      67788888555999************99988887776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   0.00013      0.15       7     127 ..      46     206 ..      41     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka............ 70 
                                       ++ + G+ G+GKTt+++ +l           +++++v+++      ++++ ++++   l+  +++            
  gi|313117411|ref|YP_004044394.1|  46 VVGLLGPNGAGKTTTIKSILGLVR-------PDAGTVRIDGIDTAeNPRQAFNRVDAMLEGARNDywrltvrenlry 115
                                       55678***************9984.......4777777776666667777777777777766666777777777677 PP

                            AAA_22  71 ............................erlsseellealeqalrarav....ielliiDEaqh.lr...seealee 111
                                                                   +    ++l + + q ++ ++v    +++  +DE    l+   s ++ +e
  gi|313117411|ref|YP_004044394.1| 116 faaiggddpaavsdrhdqlldtlelsekADEPVRDLSRGMKQKVSLASVlasdVSVAFLDEPTLgLDvesSLTLRRE 192
                                       77777777777777777666655555443444444444444443333336778888888888888888755888888 PP

                            AAA_22 112 LrsllnlsrkgvqliL 127
                                       Lr++++  + +++++L
  gi|313117411|ref|YP_004044394.1| 193 LRRIVD--ERDLTVVL 206
                                       888888..88888887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.5   3.5e-05     0.039      20      40 ..      45      65 ..      31     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-05
                            AAA_23 20 gltlItGpNGaGKTTildAik 40
                                       ++ + GpNGaGKTT +  i 
  gi|313117411|ref|YP_004044394.1| 45 SVVGLLGPNGAGKTTTIKSIL 65
                                      577899*********998884 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.2e-05     0.081       3      35 ..      49      83 ..      47     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-05
                                      EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelg..vefleisgsell 35
                                      l Gp G GKT+++k++   +   +  ++i+g +  
  gi|313117411|ref|YP_004044394.1| 49 LLGPNGAGKTTTIKSILGLVRpdAGTVRIDGIDTA 83
                                      89**************9988533667777777776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.1e-05      0.08      15      49 ..      42      75 ..      35      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                      +sg  v+ l Gp G+GKtt++k++  +++ + g+v
  gi|313117411|ref|YP_004044394.1| 42 ESG-SVVGLLGPNGAGKTTTIKSILGLVRPDAGTV 75
                                      445.5999**************9988877665555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.15       3      40 ..      48      87 ..      46     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      EEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-- CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevre 40
                                       + Gp G GKtT +k +l l++ +   v+++G+ t e  +
  gi|313117411|ref|YP_004044394.1| 48 GLLGPNGAGKTTTIKSILGLVRPDagTVRIDGIDTAENPR 87
                                      677******************876547999***9998654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.7e-05     0.086      10      62 ..      44      97 ..      37     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.7e-05
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallv.elggvkpeeillvaftgrAakelrerl 62
                                       +v+ ++++ G GKT+++k i+ l+  ++g+v  + i  +   ++A +++   l
  gi|313117411|ref|YP_004044394.1| 44 GSVVGLLGPNGAGKTTTIKSILGLVRpDAGTVRIDGIDTAENPRQAFNRVDAML 97
                                      578899***************987652566677777777777777777777666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.17       4      43 ..      46      82 ..      43     130 .. 0.79
   2 ?   -2.9   0.0       4.1   4.6e+03     152     169 ..     206     223 ..     189     255 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkf 43
                                       + + Gp+g+GKTt++k++     ++  ++G+ ++d+++ 
  gi|313117411|ref|YP_004044394.1| 46 VVGLLGPNGAGKTTTIKSI---LGLVRPDAGTVRIDGIDT 82
                                      57899************99...556666666666666654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.1
                            AAA_24 152 lgkktanelkeevDlvlr 169
                                       l++ +++ ++  +D v+ 
  gi|313117411|ref|YP_004044394.1| 206 LSSHDMDVIEDVCDRVII 223
                                       333334444444444433 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00019      0.22      27      59 ..      45      77 ..      36      92 .. 0.83
   2 ?   -2.8   0.0       3.9   4.4e+03     186     202 ..     279     295 ..     276     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                                      HHHHHHS--SHHHHHHHHHHHHHHS--TTT--- CS
                              MukB 27 lvttlsGgnGaGksttmaafvtaliPdlsllhf 59
                                       v  l G nGaGk+tt+ +++  + Pd   ++ 
  gi|313117411|ref|YP_004044394.1| 45 SVVGLLGPNGAGKTTTIKSILGLVRPDAGTVRI 77
                                      578899***************9999*9887765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.9
                                       ---SHHHHHHHHHHHHH CS
                              MukB 186 rlrssedrskfyrliea 202
                                       r++  +d + fyrli+a
  gi|313117411|ref|YP_004044394.1| 279 RFEVTADNETFYRLIDA 295
                                       5566789999****998 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00017      0.19       3      32 ..      46      75 ..      44      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkv 32
                                      v+ l+G++GaGKTtt+  +  l++ ++ +v
  gi|313117411|ref|YP_004044394.1| 46 VVGLLGPNGAGKTTTIKSILGLVRPDAGTV 75
                                      67799***********88776666655555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.8    0.0005      0.56      26     152 ..      46     166 ..      37     230 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0005
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsis 100
                                       +  ++GpNG+GK+  + +i   LG      +r +  +  i    ++e++++ + +v+ +++   ++    + + +++
  gi|313117411|ref|YP_004044394.1|  46 VVGLLGPNGAGKTTTIKSI---LGL-----VRPDAGTVRIDGidTAENPRQAFNRVDAMLEGARNDYWRLTVRENLR 114
                                       66789*************9...663.....22222222222222245555555566655544444433333333333 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfA 152
                                         +  +g+   ++ +++ +  +  el e+a+     LS+G k+ v+la ++A
  gi|313117411|ref|YP_004044394.1| 115 YFAAIGGDDPAAVSDRHDQLLDTLELSEKADEPVRDLSRGMKQKVSLASVLA 166
                                       4444444444455555555555555555555555566666666666666555 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.2    0.0019       2.1      55     142 ..     175     301 ..     119     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                                       STGGGSTTHHHHHHHHHHTC..CCTEEEEEEECSSCHG....................HHHHHHHHHTT-SEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  55 gepllypdfvellerlakla..vpgiritvetngtlpd....................eeklerllelgvdrvslgl 109
                                       +ep+l  d +  l  +++l+  v+++ +tv+ + +  d                     e++e+l + ++ r+ ++l
  gi|313117411|ref|YP_004044394.1| 175 DEPTLGLDVESSLTLRRELRriVDERDLTVVLSSHDMDviedvcdrviimsdgeiiinSEVAELLEQFETQRFRISL 251
                                       68888888888888888888887777777777777777888888888888888888889999999999999999999 PP

                                       BSSSHH...............HHHHHHT..CTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxx...............xxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 110 eaadde...............kvlklmn..rghtfeevlealeklreagi 142
                                       + +d++               ++ ++++   + ++e +++++++++ea++
  gi|313117411|ref|YP_004044394.1| 252 NDVDSDtlsllrerydvsdidQFDRRTRfeVTADNETFYRLIDAIAEADV 301
                                       99999977777777777777777777766677777888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2159.85
//
Query:       gi|313117412|ref|YP_004044395.1|  [L=264]
Description: ABC transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00064   18.9  27.3     0.0021   17.2  27.3    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.27   10.5  21.0       0.58    9.4  17.3    2.5  2  ABC2_membrane_2  ABC-2 family transporter protein
       0.45   10.7  10.3       0.51   10.5   9.3    1.6  1  PIG-F            GPI biosynthesis protein family Pig-F


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2  27.3   3.5e-07    0.0021     155     344 ..      59     245 ..      18     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.5e-07
                   ABC2_membrane_3 155 elsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl 231
                                        ++++a  +vg++l+ l+  +++ ++  i eE + +++e+ ++s+      ++ k ++ +l +l+++l +l++++  
  gi|313117412|ref|YP_004044395.1|  59 FSDSAAGLVVGYFLWSLVGQSYQGTIGIITEEASWGTLERHFISPFGFNRVLFIKAIARMLRALFVSLAVLAMMVI- 134
                                       45677778888************999999999999*********************************99997555. PP

                   ABC2_membrane_3 232 gipfg....nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp.ledlpsalkwifsi 303
                                        ++ +    +++ +l  +ll  l+++ lg++++ +   ++  +++  +++l+++g++g+ ++ ++        ++++
  gi|313117412|ref|YP_004044395.1| 135 -LTGTqlqmHVITVLSILLLTTLSVVGLGFAMGGVAVLYKRISSFSQLFSLVILGLVGAPVLdIP--------WLRV 202
                                       .44442214557777888888********************999999999966666666665444........9*** PP

                   ABC2_membrane_3 304 iPffapglgllrli.tgdplweil.lsliilalfavvylllal 344
                                       +P ++ + +l + + +g+ lw++  ++++il++ ++vy+ +++
  gi|313117412|ref|YP_004044395.1| 203 LPVVQGSAMLQQTMrSGVRLWQFDgIDIGILVGVTLVYFGIGF 245
                                       **************88889999655**************9875 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.22   1.3e+03     191     209 ..      30      48 ..      23      64 .. 0.67
   2 ?    9.4  17.3   9.8e-05      0.58      93     183 ..      83     171 ..      55     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.22
                   ABC2_membrane_2 191 sreaaalalglfvvlailv 209
                                        ++aa +++g f+++a+++
  gi|313117412|ref|YP_004044395.1|  30 PVNAASVVFGQFFFFALIF 48 
                                       4566666666666666543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 9.8e-05
                   ABC2_membrane_2  93 gadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasv 169
                                       ++ +i++E   gTl++ + +P     +l+ K+i++++ +l++ +a+la +++  + +l+  + + l+ lll+ +++v
  gi|313117412|ref|YP_004044395.1|  83 TIGIITEEASWGTLERHFISPFGFNRVLFIKAIARMLRALFVSLAVLAMMVILTGTQLQMHVITVLSILLLTTLSVV 159
                                       5789**********************************888888888887776677777777777777777777777 PP

                   ABC2_membrane_2 170 lllllvvflalgll 183
                                        l++++   ++++l
  gi|313117412|ref|YP_004044395.1| 160 GLGFAM--GGVAVL 171
                                       776644..333333 PP

>> PIG-F  GPI biosynthesis protein family Pig-F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   9.3   8.6e-05      0.51      56     140 ..     111     194 ..      66     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.6e-05
                             PIG-F  56 ivlallsllltlllatlllaillvlfGApllthlleTlllalhlslltvlpllyvlgvdaeawkevvsleepldevl 132
                                       +++a++++l +l+++  +la++++l G  l  h+  T+l  l+l++l+v+ l +++g  a  +k++ s+++ ++ v+
  gi|313117412|ref|YP_004044395.1| 111 FIKAIARMLRALFVSLAVLAMMVILTGTQLQMHV-ITVLSILLLTTLSVVGLGFAMGGVAVLYKRISSFSQLFSLVI 186
                                       6789999999999999***********9997776.599999*******************************99999 PP

                             PIG-F 133 ggllgtvv 140
                                        gl+g+ v
  gi|313117412|ref|YP_004044395.1| 187 LGLVGAPV 194
                                       99998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1585.78
//
Query:       gi|313117413|ref|YP_004044396.1|  [L=740]
Description: PAS domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-33  112.4   1.6    7.1e-18   64.7   0.2    2.5  2  PAS_3           PAS fold
    6.7e-17   61.7   0.2    7.6e-08   32.5   0.0    3.7  3  PAS_9           PAS domain
    1.1e-16   61.3   0.1    2.4e-16   60.2   0.1    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    6.9e-15   54.8   2.2    2.7e-14   52.9   0.1    3.0  3  HisKA           His Kinase A (phospho-acceptor) domain
    1.5e-13   51.0   5.2    1.2e-05   25.6   0.3    3.7  3  PAS_4           PAS fold
    1.4e-08   35.2   0.8    1.5e-07   31.8   0.2    2.7  2  GAF_2           GAF domain
      7e-06   26.0   3.3      0.007   16.3   0.1    3.3  4  PAS             PAS fold
    6.1e-05   22.9   0.4      0.016   15.3   0.0    3.2  3  PAS_8           PAS domain
     0.0033   17.3   0.0     0.0095   15.8   0.0    1.7  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
      0.005   17.2   0.0       0.01   16.1   0.0    1.5  1  GAF_3           GAF domain
     0.0057   17.1   6.0       0.19   12.2   0.0    3.9  4  ZapB            Cell division protein ZapB
     0.0088   16.2   0.2       0.13   12.5   0.0    2.8  2  PAS_7           PAS fold
     0.0095   16.2   1.1       0.85    9.9   0.1    2.9  3  Retrotrans_gag  Retrotransposon gag protein
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.034   14.1   0.0    1.7  1  HATPase_c_2     Histidine kinase-like ATPase domain
      0.016   14.5   0.0      0.055   12.8   0.0    1.9  2  CCB2_CCB4       Cofactor assembly of complex C subunit B, CCB
      0.055   13.2   0.0       0.16   11.7   0.0    1.8  1  SPOB_a          Sensor_kinase_SpoOB-type, alpha-helical domai
      0.062   12.9   0.0        0.1   12.1   0.0    1.3  1  HisKA_4TM       Archaeal 4TM region of histidine kinase


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   2.9e-15   3.1e-12       2      82 ..     139     219 ..     138     225 .. 0.87
   2 !   64.7   0.2   6.8e-21   7.1e-18       3      87 ..     268     354 ..     266     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2.9e-15
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvi.rd 77 
                                       + +s+ +++i G++ e  + ++e++++++hp+Dre++ + +++al+++e  ++e Ri r+dGe+r v+a ++ + + 
  gi|313117413|ref|YP_004044396.1| 139 LRWSDGIYRIHGIDLE-YEPTLEDVIEFCHPDDREQIASFFNQALEGQETNSIETRITRADGEVRDVRAWCELVeKE 214
                                       68***********997.555558**********************999999**********************9555 PP

                             PAS_3  78 engkp 82 
                                       ++g+ 
  gi|313117413|ref|YP_004044396.1| 215 RSGET 219
                                       55554 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 6.8e-21
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy..egeyRirrkdGeyrwveararvird 77 
                                       +++ + ee++G+++++l+++++ wl+++hp+D+e vr+++++  ++ +++  ++e+Ri+++  ++rwv++ra +i +
  gi|313117413|ref|YP_004044396.1| 268 FMNSATEEMYGVTEQQLRQDPKAWLERIHPDDIEAVRSDIEAQQTTEAEWpqHQEFRIQHPERGVRWVRSRAHPITN 344
                                       899**************************************88877776665999********************** PP

                             PAS_3  78 engkpvrvig 87 
                                       ++g + ++ +
  gi|313117413|ref|YP_004044396.1| 345 DDGVVKQIAS 354
                                       ***9998876 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.8e-05      0.05       6      76 ..       3      79 ..       1     103 [. 0.60
   2 !   11.1   0.1   0.00034      0.36      39     104 .]     165     230 ..     128     230 .. 0.81
   3 !   32.5   0.0   7.3e-11   7.6e-08       2     103 ..     254     360 ..     253     361 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                             PAS_9  6 idnpdgrilyaNeaalrllG..yspeevlgksitdlf.......vtdpeanerlraaleqgrkkerevevvlirknget 75
                                      + ++  +i+ aNea+ +++    sp++++g++++ +        ++++    rl+++l + +      + +l   +g+t
  gi|313117413|ref|YP_004044396.1|  3 VEDETREIIAANEALHDIIDlsGSPDDLVGQNCEAVAedlkqqfADPEGFITRLEEILADQE---TVLNEELALADGRT 78
                                      4456668***********885456**********9997777666566666666666665555...33333333333444 PP

                             PAS_9 76 f 76
                                      +
  gi|313117413|ref|YP_004044396.1| 79 V 79
                                      4 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00034
                             PAS_9  39 lf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdd.dgelvgiivilrDite 104
                                       ++  ++ ++ ++++++ale  +    + e+ ++r +ge   v++ +  v  + +ge v + ++l+Dit+
  gi|313117413|ref|YP_004044396.1| 165 FChpDDREQIASFFNQALEGQE--TNSIETRITRADGEVRDVRAWCELVEKErSGETV-LRGVLQDITT 230
                                       3367788889999999999999..*************************888788877.59******95 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 7.3e-11
                             PAS_9   2 dgilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirkng 73 
                                       ++++++ pd   + ++N a ++++G +++++ + +  +l   +p++ e +r  +e+ ++     ++++e  ++++++
  gi|313117413|ref|YP_004044396.1| 254 HAFFLVPPDYSEVsFMNSATEEMYGVTEQQLRQDPKAWLERIHPDDIEAVRSDIEAQQTteaeWPQHQEFRIQHPER 330
                                       67899889996666*********************9999955666666666666666666999999*********** PP

                             PAS_9  74 etfwvlltaspvkdddgelvgiivilrDit 103
                                       +  wv+ +a p+ +ddg ++ i++i++D+t
  gi|313117413|ref|YP_004044396.1| 331 GVRWVRSRAHPITNDDGVVKQIASISTDVT 360
                                       *****************************9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.1   2.3e-19   2.4e-16       6     106 ..     643     736 ..     638     738 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 2.3e-19
                                       HHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsiv 81 
                                       L++++ nl  Nav++   +++++v++ + + +  + veDnG Gip+e+++ +fe  +++      ++ggtG+Gl+iv
  gi|313117413|ref|YP_004044396.1| 643 LTELFENLFRNAVEH--GGEDVTVNVGKLDRTDGFYVEDNGTGIPPEKREDVFEyGYTT------NQGGTGFGLAIV 711
                                       899***********9..6888999998644689999******************99999......9*********** PP

                                       HHHHHHTTTEEEEEEETTTEEEEEE CS
                         HATPase_c  82 kklvelmgGeiwvesepgrGttftf 106
                                         +++ +g +i+++ ++++Gt+f f
  gi|313117413|ref|YP_004044396.1| 712 ADIANAHGWSISLTASSEGGTRFEF 736
                                       *************99999*****98 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       4.2   4.4e+03      33      49 ..     230     246 ..     208     252 .. 0.68
   2 ?   -0.9   0.0       1.6   1.7e+03      27      46 ..     362     381 ..     352     385 .. 0.60
   3 !   52.9   0.1   2.6e-17   2.7e-14       2      64 ..     540     597 ..     539     600 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.2
                                       -HSSCHHHHHHHHHHHH CS
                             HisKA  33 lteelkeyletiesear 49 
                                       +  e+++ l++++++ r
  gi|313117413|ref|YP_004044396.1| 230 TLKEQERTLRQAHQQFR 246
                                       34566667777776654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.6
                                       HHC..T-HSSCHHHHHHHHH CS
                             HisKA  27 Lkregklteelkeyleties 46 
                                        +++++  e+l++y  ++++
  gi|313117413|ref|YP_004044396.1| 362 AEEYKRKLERLQQYTSRLID 381
                                       34444456777777777665 PP

  == domain 3  score: 52.9 bits;  conditional E-value: 2.6e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsri 64 
                                       l++f++ v+H+Lr+PLs+ +g++e+ ++        key+e+i s  +r++ l+edlL ls+ 
  gi|313117413|ref|YP_004044396.1| 540 LEKFASIVSHDLRNPLSVARGYIELAEE-----KGEKEYFEKINSALNRMEGLIEDLLVLSKA 597
                                       679***********************99.....799*************************97 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.6e-07   0.00017      12     109 ..       5     105 ..       1     106 [. 0.90
   2 ?    4.0   0.1     0.053        56      43      83 ..     165     206 ..     155     233 .. 0.74
   3 !   25.6   0.3   1.1e-08   1.2e-05      17     109 ..     266     363 ..     250     364 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-07
                             PAS_4  12 dpdgrvlyaNaaaaelf..gappeellGktlaellpee.....daarleralrrvlegeepiefleelllpgeerhy 81 
                                       d+   +++aN+a ++++    +p++l+G+ ++ ++ +      d +++ + l++ l+ +e++  +e  l   ++r++
  gi|313117413|ref|YP_004044396.1|   5 DETREIIAANEALHDIIdlSGSPDDLVGQNCEAVAEDLkqqfaDPEGFITRLEEILADQETVLNEELALA--DGRTV 79 
                                       89999*******99965125689*********988888999************************98888..99*** PP

                             PAS_4  82 elrllPlrdesGevigvlvisrDiTerr 109
                                       e +++    ++G+  g +++ rDiTe++
  gi|313117413|ref|YP_004044396.1|  80 ERSYVSYQLPEGR--GNIWLYRDITEQK 105
                                       ****99999****..***********97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.053
                             PAS_4  43 llpeedaarleralrrvlegeepiefleelll.pgeerhyel 83 
                                       +  ++d++++++  +++leg+e+ + ++  ++ +ge r +  
  gi|313117413|ref|YP_004044396.1| 165 FCHPDDREQIASFFNQALEGQETNSIETRITRaDGEVRDVRA 206
                                       55567*********************9999999888776555 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 1.1e-08
                             PAS_4  17 vlyaNaaaaelfgappeellGktla...ellpeedaarleralrrvlegeepiefleelll...pgeerhyelrllP 87 
                                       v ++N a +e++g++ ++l+  + a    ++p+ d +++++++++  ++e+ + +++e +    +++ r++  r++P
  gi|313117413|ref|YP_004044396.1| 266 VSFMNSATEEMYGVTEQQLRQDPKAwleRIHPD-DIEAVRSDIEAQQTTEAEWPQHQEFRIqhpERGVRWVRSRAHP 341
                                       6789*****************998888558887.5555555555555444444444444434458************ PP

                             PAS_4  88 lrdesGevigvlvisrDiTerr 109
                                       + +++G v  +  is+D+T  +
  gi|313117413|ref|YP_004044396.1| 342 ITNDDGVVKQIASISTDVTSAE 363
                                       *******************865 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.64   6.7e+02       5      46 ..     235     276 ..     232     367 .. 0.56
   2 !   31.8   0.2   1.4e-10   1.5e-07       4     137 ..     385     517 ..     382     518 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHHS..S..EEEEEEE-TTS-EEEE.....EEEES-TTS CS
                             GAF_2   5 eelldlvldelvel..gaalgyillvdddgglrla.....awgeaeeef 46 
                                       e +l++++++ +++  +++++++l++ d  +  ++     +     ee 
  gi|313117413|ref|YP_004044396.1| 235 ERTLRQAHQQFRTFaeNVDHAFFLVPPDYSE--VSfmnsaT-----EEM 276
                                       5678899999999775599999999775555..44333321.....222 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.4e-10
                                       HHHHHHHHHHHHHHS.S..EEEEEEE-TTS-.EEEE.......EEEES-TTSTT-S-B---TTHHHHHHHHTS-EEE CS
                             GAF_2   4 leelldlvldelvel.gaalgyillvdddgg.lrla.......awgeaeeefgaaldrplgeglvgealrtgrpvil 71 
                                        +e ++l +++++++ +++++ i+l  +  + lr         +  +++ + + +++ ++ ++lv+++++tg    +
  gi|313117413|ref|YP_004044396.1| 385 TDEAAELGVEAATDIlDVEFCGIHLQTG--SeLRQTaftdatgSEHFTPSTYDREAEGDPVSSLVWDVFETGDQRTI 459
                                       68999*********66*********663..3234224554455444555555666656667889********99999 PP

                                       S-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  72 ndleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +d+ e    ++  a+h ++rs ++ Pl    + +Gv+ +++  p+af++ d++l+++l+e +  a+
  gi|313117413|ref|YP_004044396.1| 460 DDINE----QSTLADHTPVRSAIVHPL----EEHGVVIVSSLSPDAFSAVDQTLVTLLGEALTGAL 517
                                       99555....45557*************....59**************************9887766 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.9     3e+03      16      47 ..       3      36 ..       1      72 [. 0.79
   2 !    8.9   0.1    0.0014       1.5      46     113 .]     162     228 ..     141     228 .. 0.72
   3 !   16.3   0.1   6.7e-06     0.007       2     107 ..     244     353 ..     243     359 .. 0.79
   4 ?   -3.0   0.0       6.9   7.3e+03       3      55 ..     486     539 ..     484     548 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.9
                                      EEETTSBEEEECHHHHHHHSSTH..HHCTTSBGG CS
                               PAS 16 vvDedgrilyvNaaaeellGlsr..eevlgksll 47
                                      v De  +i+ +N+a  ++  ls   ++++g++  
  gi|313117413|ref|YP_004044396.1|  3 VEDETREIIAANEALHDIIDLSGspDDLVGQNCE 36
                                      5588899999999999988888777888888855 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                                       GGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  46 lldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++++ h++d+++ a+ + q+le +e +++ e+++++ dg+++ ++ ++  v  + +  + + gvl+di
  gi|313117413|ref|YP_004044396.1| 162 VIEFCHPDDREQIASFFNQALEGQETNSI-ETRITRADGEVRDVRAWCELVEKERSGETVLRGVLQDI 228
                                       56666666665555555555555555555.5556666********99998888877777888888876 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 6.7e-06
                                       HHHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTHHHCTT..SBGGGGBSTTHHHHHHHHHHHHHHHTT-.ECC CS
                               PAS   2 dlraileslpdpifvvD.edgrilyvNaaaeellGlsreevlg..kslldliheeddaelaelleqlleqgee.sra 74 
                                       ++r++ e+ + + f+v     +++++N+a+ee+ G +++++    k  l+ ih++d + +++ +e +  +  e +++
  gi|313117413|ref|YP_004044396.1| 244 QFRTFAENVDHAFFLVPpDYSEVSFMNSATEEMYGVTEQQLRQdpKAWLERIHPDDIEAVRSDIEAQQTTEAEwPQH 320
                                       6788888888888888888899*******************974456778887777666666666666555551577 PP

                                       CCEEEECTTSSEEEEEEEEEEEEETTEEEEEEE CS
                               PAS  75 geisfklrdgrpihlevraspvrdaggeilgfl 107
                                       +e ++  +  ++++++ ra+p+++ +g ++++ 
  gi|313117413|ref|YP_004044396.1| 321 QEFRIQHPERGVRWVRSRAHPITNDDGVVKQIA 353
                                       7777777*******************9888775 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 6.9
                                       HHHHHHH.SSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHH CS
                               PAS   3 lrailes.lpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedd 55 
                                        + i++s +pd+  +vD   + l+  a +  l+ ++r+ +l+    +l   +d+
  gi|313117413|ref|YP_004044396.1| 486 GVVIVSSlSPDAFSAVDQTLVTLLGEALTGALTRIERSKLLRDRERELQKQNDR 539
                                       566777777888888887777776666667777777776666666655555554 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.044        46      18      62 ..       5      52 ..       1      58 [. 0.72
   2 ?   -2.9   0.0       7.2   7.6e+03      29      58 ..     206     234 ..     205     241 .. 0.61
   3 !   15.3   0.0   1.5e-05     0.016       1      56 [.     243     295 ..     243     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.044
                             PAS_8 18 dlgdrivdvNqaalellGys...adlkgellgqllpvlrplledaeql 62
                                      d+ + i+ +N+a  ++  +s   +dl g+ +  + ++l+  ++d e +
  gi|313117413|ref|YP_004044396.1|  5 DETREIIAANEALHDIIDLSgspDDLVGQNCEAVAEDLKQQFADPEGF 52
                                      32225************9888889999988887777777777666555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.2
                             PAS_8  29 aalellGysadlkgellg.qllpvlrplled 58 
                                       a++el    ++ +ge++   +l++++ l+e 
  gi|313117413|ref|YP_004044396.1| 206 AWCELVE--KERSGETVLrGVLQDITTLKEQ 234
                                       8888888..5588888855666666555553 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.5e-05
                             PAS_8   1 erlralfesspdgiavv..dlgdrivdvNqaalellGysadlkgellgqllpvlrpll 56 
                                       +++r++ e+++ + ++v  d    + ++N a++e++G    + ++ l+q+++   + +
  gi|313117413|ref|YP_004044396.1| 243 QQFRTFAENVDHAFFLVppDYS-EVSFMNSATEEMYG----VTEQQLRQDPKAWLERI 295
                                       689************9755444.5*************....55655554444333333 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     9e-06    0.0095      10      62 ..     650     701 ..     644     717 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9e-06
                       HATPase_c_3  10 lvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                                       l +N+++   e v+++v k +  t+ + +eD+G+G+++e+ +++++++ ++++
  gi|313117413|ref|YP_004044396.1| 650 LFRNAVEHGGEDVTVNVGKLD-RTDGFYVEDNGTGIPPEKREDVFEYGYTTNQ 701
                                       67899999999*******986.79****************9999999987776 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.9e-06      0.01       3     129 .]     386     519 ..     385     519 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.9e-06
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagw..dgkpalse.......sldedsalarralssgevvsep 70 
                                       de +e  ++++ ++l++e++ ++l ++   +l+ +a +  +g++ +         + d  s+l + ++++g   +  
  gi|313117413|ref|YP_004044396.1| 386 DEAAELGVEAATDILDVEFCGIHLQTGS--ELRQTAFTdaTGSEHFTPstydreaEGDPVSSLVWDVFETGDQRTID 460
                                       5667778999*************99955..66444333134444443355766555556677777888999888887 PP

                             GAF_3  71 sfaeedg....lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                       +  e+++    +p r+a+++PL       Gv+ + s +p af+a+d+ l+  l+  +  a+ r
  gi|313117413|ref|YP_004044396.1| 461 DINEQSTladhTPVRSAIVHPLEE----HGVVIVSSLSPDAFSAVDQTLVTLLGEALTGALTR 519
                                       777766611115556666666665....9****************************999976 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.8   6.1e+03      42      67 ..      36      61 ..       6      62 .. 0.76
   2 !   12.2   0.0   0.00018      0.19      17      62 ..     225     295 ..     218     297 .. 0.91
   3 ?   -1.8   0.0       4.2   4.4e+03       6      15 ..     369     378 ..     354     385 .. 0.55
   4 ?    4.4   1.3     0.048        50      17      62 ..     520     584 ..     518     591 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.8
                              ZapB 42 releeeneqlkeereawqerlkkLLg 67
                                      +++ e ++q  +++e +  rl+ +L+
  gi|313117413|ref|YP_004044396.1| 36 EAVAEDLKQQFADPEGFITRLEEILA 61
                                      45567888888888888888888875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00018
                              ZapB  17 idtitlLqmeieeLkeeneelkeenrele.........................eeneqlkeereawqerl 62 
                                       ++ it+L+++ + L++ +++    ++++                             +ql+++++aw er+
  gi|313117413|ref|YP_004044396.1| 225 LQDITTLKEQERTLRQAHQQFRTFAENVDhafflvppdysevsfmnsateemygVTEQQLRQDPKAWLERI 295
                                       678999999999999999999999999999********************9999999*************9 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.2
                              ZapB   6 LeqLEskiqk 15 
                                       Le+L++  + 
  gi|313117413|ref|YP_004044396.1| 369 LERLQQYTSR 378
                                       3333333333 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.048
                              ZapB  17 idtitlLqmeieeLkeeneelkeenrele................eeneqlk...eereawqerl 62 
                                       i++ +lL+ + +eL+++n  l++ +  ++                +e + +k   e  ++  +r+
  gi|313117413|ref|YP_004044396.1| 520 IERSKLLRDRERELQKQNDRLEKFASIVShdlrnplsvargyielAEEKGEKeyfEKINSALNRM 584
                                       77888999999999999999998777777777777777766644433332222333333444444 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00012      0.13      10     114 ..       3     108 ..       1     109 [. 0.66
   2 ?    0.3   0.0      0.71   7.5e+02      16     104 ..     265     352 ..     250     366 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                             PAS_7  10 vfDadlrLvawNrrylelldl...peelvqvgvpleellrynaergefgagdveaeverrlaaa.ragkphsferer 82 
                                       v D++ +++a N+   ++ dl   p++lv  g + e++ + ++++ +    d+e +++r  + +  +++  + e   
  gi|313117413|ref|YP_004044396.1|   3 VEDETREIIAANEALHDIIDLsgsPDDLV--GQNCEAVAEDLKQQFA----DPEGFITRLEEILaDQETVLNEELAL 73 
                                       66889999999998887777733355665..8889998888855544....44555544433330334445556778 PP

                             PAS_7  83 pdgrvievrgnpl...pdgGfVttytDiTerrrae 114
                                       +dgr++e         +++G +  y DiTe+++ e
  gi|313117413|ref|YP_004044396.1|  74 ADGRTVERSYVSYqlpEGRGNIWLYRDITEQKKRE 108
                                       9*****9554333222668************9987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.71
                             PAS_7  16 rLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpdgrvievrg 92 
                                       ++ ++N+   e+++++e+ +++  p + l r+  +  e  ++d+ea+ ++  a++ + ++ ++++ ++  r+++ r+
  gi|313117413|ref|YP_004044396.1| 265 EVSFMNSATEEMYGVTEQQLRQD-PKAWLERIHPDDIEAVRSDIEAQQTT-EAEWPQHQEFRIQHPERGVRWVRSRA 339
                                       56677888888888888877443.33333344333444444555554222.23444445555555555556666666 PP

                             PAS_7  93 npl.pdgGfVtty 104
                                        p+  d G+V   
  gi|313117413|ref|YP_004044396.1| 340 HPItNDDGVVKQI 352
                                       6663456776554 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00081      0.85      38      81 ..     213     259 ..     176     273 .. 0.71
   2 ?   -2.9   0.0       7.9   8.4e+03       6      25 ..     283     302 ..     280     314 .. 0.81
   3 ?    3.7   0.0      0.07        73      47      79 ..     346     378 ..     334     392 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00081
                    Retrotrans_gag  38 ktflpserkdqleeelsslrQgtesvreYvtrfktladqlde...vl 81 
                                       k+   + + +   +++ +l+++++++r+++++f+t+a ++d+    +
  gi|313117413|ref|YP_004044396.1| 213 KERSGETVLRGVLQDITTLKEQERTLRQAHQQFRTFAENVDHaffLV 259
                                       455555566667789**************************966555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.9
                    Retrotrans_gag   6 slegaAkswlkslvarsida 25 
                                       +l+ + k+wl+++ +++i+a
  gi|313117413|ref|YP_004044396.1| 283 QLRQDPKAWLERIHPDDIEA 302
                                       68888999999999988876 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.07
                    Retrotrans_gag  47 dqleeelsslrQgtesvreYvtrfktladqlde 79 
                                       d   +++ s++ +  s +eY +++++l ++  +
  gi|313117413|ref|YP_004044396.1| 346 DGVVKQIASISTDVTSAEEYKRKLERLQQYTSR 378
                                       566778999999999*************99886 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.2e-05     0.034      40     111 ..     651     717 ..     639     734 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDe 111
                                       + Naveh+      ++v+v +   +++  + v+D+G g +pe+++d  e ++++++   G+Gla+++ +++ 
  gi|313117413|ref|YP_004044396.1| 651 FRNAVEHGG-----EDVTVNVGKLDRTDGFYVEDNGTGIPPEKREDVFEYGYTTNQGGTGFGLAIVADIANA 717
                                       456666665.....67888888888888999***********************************999876 PP

>> CCB2_CCB4  Cofactor assembly of complex C subunit B, CCB2/CCB4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.4   2.5e+03      36      87 ..     269     320 ..     266     321 .. 0.72
   2 ?   12.8   0.0   5.2e-05     0.055     158     195 ..     475     512 ..     464     513 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                         CCB2_CCB4  36 llaavlilvgllwkrlkpkppeavelegaeevfelaedlsdalkeeLaWase 87 
                                       + +a+  + g+++++l+  p+   e +  + + ++ +d+++++ +e +W  +
  gi|313117413|ref|YP_004044396.1| 269 MNSATEEMYGVTEQQLRQDPKAWLERIHPDDIEAVRSDIEAQQTTEAEWPQH 320
                                       5667777788888888866655555555568889999999999999999665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.2e-05
                         CCB2_CCB4 158 qsvlvqplgdegvlilgsntpraftkkdeaWiaaiAek 195
                                       +s +v+pl+++gv+i+ s +p af+  d++ ++ ++e 
  gi|313117413|ref|YP_004044396.1| 475 RSAIVHPLEEHGVVIVSSLSPDAFSAVDQTLVTLLGEA 512
                                       799***************************99988775 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.16      17      57 ..     545     585 ..     529     590 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                            SPOB_a  17 rsqRHDflNhLQvIsGylqLgkydkaeeyieevvkelkees 57 
                                       +   HD  N L v +Gy++L +    +ey e++  +l++++
  gi|313117413|ref|YP_004044396.1| 545 SIVSHDLRNPLSVARGYIELAEEKGEKEYFEKINSALNRME 585
                                       5668*******************************999886 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.8e-05       0.1     102     161 ..     504     564 ..     495     567 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-05
                         HisKA_4TM 102 vlvaaevGavaGllaGylaararadasra.krisdalafvndlirhdlrndlvvirgyaea 161
                                       +lv+    a++G l+   + +   d +r  ++  d l    +++ hdlrn l v rgy e 
  gi|313117413|ref|YP_004044396.1| 504 TLVTLLGEALTGALTRIERSKLLRDRERElQKQNDRLEKFASIVSHDLRNPLSVARGYIEL 564
                                       677777779*************99999863778999**********************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (740 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 4625.95
//
Query:       gi|313117414|ref|YP_004044397.1|  [L=681]
Description: PAS domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-30  103.3   6.0    4.8e-14   52.5   0.2    4.0  3  PAS_4            PAS fold
      7e-15   55.2   0.2    1.5e-14   54.1   0.2    1.6  1  Response_reg     Response regulator receiver domain
    2.6e-14   53.2   0.5    6.3e-06   26.2   0.0    3.7  2  PAS              PAS fold
    8.9e-12   45.2   0.0      1e-05   25.7   0.0    2.8  2  PAS_9            PAS domain
    3.6e-11   42.8   0.2     0.0027   17.7   0.0    4.1  3  PAS_8            PAS domain
    1.6e-10   41.4   0.8    3.8e-10   40.2   0.2    2.0  2  GAF_2            GAF domain
    1.2e-07   32.1   0.0    4.1e-07   30.4   0.0    1.9  1  GAF_3            GAF domain
    0.00014   22.1   0.3      0.001   19.3   0.3    2.4  2  OKR_DC_1_N       Orn/Lys/Arg decarboxylase, N-terminal domain
  ------ inclusion threshold ------
       0.15   12.2   0.5        2.7    8.2   0.0    3.2  3  PAS_7            PAS fold
       0.23   11.5   3.6       0.22   11.6   1.3    2.0  2  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.2   2.7e-17   4.8e-14       1     110 []     152     254 ..     152     254 .. 0.94
   2 !   42.1   1.0   4.6e-14   8.2e-11       1     110 []     266     387 ..     266     387 .. 0.81
   3 !    8.6   0.0    0.0012       2.1       4      43 ..     560     595 ..     557     627 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2.7e-17
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l+++ da++++d++ r++y+N+++ae +g++pe+++G  l+e +p  ++++le+ +r ++e++ p++f+++    + 
  gi|313117414|ref|YP_004044397.1| 152 LERTTDAIYAVDTEWRIEYMNEQMAERVGRDPEAVIGANLWEEFPFTVGTELEEKYRTAIETGSPVTFEQHIGG-PL 227
                                       68899************************************99***************************7777.** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       + ++++r++P +       g+ v+s++iT++r+
  gi|313117414|ref|YP_004044397.1| 228 DYWVQVRAFPDE------NGLTVFSHEITDERE 254
                                       **********54......489********9985 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 4.6e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaae.lfgappeellGktlaellpee....daarleralrrvlegeepiefleel 72 
                                       l ++ da++vld+ +++++aNaaaa+   +  p++l G+ l +++ +     d +++ +a ++vl   e  ++  ++
  gi|313117414|ref|YP_004044397.1| 266 LKNIHDAVFVLDETSTIQFANAAAAQaFDRTGPDQLEGEQLKDIVGDAvsrsDIREFNQAFEEVLHAAEEDDSSATP 342
                                       56899******************999788999**********77666666679999999999888654432222222 PP

                             PAS_4  73 ll.........pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        +         p e+r +++rl+Pl  ++Ge   vlv++rD+Te+++
  gi|313117414|ref|YP_004044397.1| 343 YDcdlhfelgtPLERRCFDTRLTPL-QADGE-PQVLVVARDVTEQKQ 387
                                       22245677788**************.79***.99**********985 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0012
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlael 43 
                                       +p  l+++d++gr +++++   +    +p++++Gkt+ e 
  gi|313117414|ref|YP_004044397.1| 560 VPIHLFIKDREGRHQWMSRGLVD----DPDQYIGKTDVEA 595
                                       67789999************999....*********9973 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.2   8.1e-18   1.5e-14       1      99 [.      14     113 ..      14     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 8.1e-18
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl v D+ ++ +l+ + +e  ++++ ++ +ae   eale+l ++ +d++++  ++p+ +G++l++ ir+ed+elpvi
  gi|313117414|ref|YP_004044397.1|  14 VLYVNDSYAFTDLVCEDIEttNSEI-NCVTAECVGEALEILSSHPIDCVVTAYELPDRTGIDLIESIRAEDDELPVI 89 
                                       7889999999999999999766777.888************************************************ PP

                                       EEESSTSHHHHHHHHHCTESEEEE CS
                      Response_reg  76 iltahseeedavealkagaddfls 99 
                                       +lt +++e++a++a +a++ d++ 
  gi|313117414|ref|YP_004044397.1|  90 LLTEQGNENVATAATQADVTDYIP 113
                                       **********************96 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.5e-09   6.3e-06       2      76 ..     147     221 ..     146     233 .. 0.94
   2 !   22.8   0.1   3.9e-08   6.9e-05       2      73 ..     261     337 ..     260     382 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.5e-09
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrage 76 
                                       ++++ le ++d+i +vD   ri y+N+ ++e  G ++e v+g +l ++++ +   el e++++++e+g++ + ++
  gi|313117414|ref|YP_004044397.1| 147 HVQRTLERTTDAIYAVDTEWRIEYMNEQMAERVGRDPEAVIGANLWEEFPFTVGTELEEKYRTAIETGSPVTFEQ 221
                                       8999***********************************************9777*************9987665 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.9e-08
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBSTTHHH.....HHHHHHHHHHHHTT-E CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsr.eevlgkslldliheedda.....elaelleqlleqgees 72 
                                       + +++l +++d++fv+De   i ++Naaa++ +  +  +++ g+ l d +     +     e+++++e++l+++ee 
  gi|313117414|ref|YP_004044397.1| 261 RNETVLKNIHDAVFVLDETSTIQFANAAAAQAFDRTGpDQLEGEQLKDIVGDAV-SrsdirEFNQAFEEVLHAAEED 336
                                       568899*****************************9989999999885553333.2477788888888888877765 PP

                                       C CS
                               PAS  73 r 73 
                                        
  gi|313117414|ref|YP_004044397.1| 337 D 337
                                       4 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     4e-06    0.0072       4      84 ..     159     237 ..     156     251 .. 0.82
   2 !   25.7   0.0   5.7e-09     1e-05       2     104 .]     271     384 ..     270     384 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4e-06
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       i  ++++ ri+y+Ne++++  G +pe+v+g ++++ f      e +e+ r a+e+g+  + ++e ++  + +  +wv
  gi|313117414|ref|YP_004044397.1| 159 IYAVDTEWRIEYMNEQMAERVGRDPEAVIGANLWEEFpfTVGTELEEKYRTAIETGS--PVTFEQHIGGPLD--YWV 231
                                       554567889*************************99999999999999999999999..8888888888855..887 PP

                             PAS_9  79 lltasp 84 
                                       +++a+p
  gi|313117414|ref|YP_004044397.1| 232 QVRAFP 237
                                       777766 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 5.7e-09
                             PAS_9   2 dgilidnpdgrilyaNeaalrllG.yspeevlgksitdlfvtdpeanerlraaleqgrk..........kerevevv 67 
                                       d++++ ++  +i +aN aa++ +  ++p+++ g +++d++ +d+ +++++r++ ++ ++          ++  ++ +
  gi|313117414|ref|YP_004044397.1| 271 DAVFVLDETSTIQFANAAAAQAFDrTGPDQLEGEQLKDIV-GDAVSRSDIREFNQAFEEvlhaaeeddsSATPYDCD 346
                                       7889888999999***********666*************.888888888888888873333344444445555555 PP

                             PAS_9  68 lirkngetfw...vlltaspvkdddgelvgiivilrDite 104
                                       l  + g+++    ++ +++p++ d++  v+  v+ rD+te
  gi|313117414|ref|YP_004044397.1| 347 LHFELGTPLErrcFDTRLTPLQADGEPQVL--VVARDVTE 384
                                       555555444444355666777665555555..******98 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.3e-05     0.041       8      53 ..     153     196 ..     147     211 .. 0.81
   2 !   17.7   0.0   1.5e-06    0.0027       2      48 ..     261     309 ..     260     316 .. 0.78
   3 !    6.5   0.0    0.0049       8.9      21      41 ..     318     339 ..     308     363 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                             PAS_8   8 esspdgiavvdlgdrivdvNqaalellGysadlkgellg.qllpvlr 53 
                                       e   d+i  vd+ +ri ++N++++e  G +  + ++++g +l+++++
  gi|313117414|ref|YP_004044397.1| 153 ERTTDAIYAVDTEWRIEYMNEQMAERVG-R--DPEAVIGaNLWEEFP 196
                                       56789******777**************.5..577777778877776 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.5e-06
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys..adlkgellgql 48 
                                       r ++++ +++d+++v+d+  +i ++N aa++ +  +  ++l ge l ++
  gi|313117414|ref|YP_004044397.1| 261 RNETVLKNIHDAVFVLDETSTIQFANAAAAQAFDRTgpDQLEGEQLKDI 309
                                       6689*************4446************8667666666666544 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0049
                             PAS_8  21 drivdvNqaalellGys..adlk 41 
                                       d i++ Nqa++e l+    +d++
  gi|313117414|ref|YP_004044397.1| 318 D-IREFNQAFEEVLHAAeeDDSS 339
                                       6.99**********955433333 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.2   2.1e-13   3.8e-10       2     136 ..     406     536 ..     405     537 .. 0.82
   2 ?   -3.7   0.0       7.6   1.4e+04      29      68 ..     583     620 ..     579     621 .. 0.43

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.1e-13
                                       HHHHHHHHHHHHHHHHS.S...EEEEEEE-TTS-EEEE.EEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GG CS
                             GAF_2   2 adleelldlvldelvel.gaa.lgyillvdddgglrla.awgeaeeefgaaldrplgeglvgealrtgrpvilndle 75 
                                       +++ e+ ++ +++++++  ++  g+  +++ +++l+ +   + a+e+f+  ++ p+ge+l++ea+++g+  +++d+ 
  gi|313117414|ref|YP_004044397.1| 406 SSPAEVGEIGVEAVADIlEFEiTGVWTYDERENELVPEtETAAAQEQFDTLPRIPPGESLAWEAFESGEVQYCSDVS 482
                                       6788999999******6589955555555666666666555556666666666699*******************77 PP

                                       G-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHH CS
                             GAF_2  76 edpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaia 136
                                       +    + + a +  ++s+++vPl   g  +G+l  +++ +++f e+++ l++ l++++  a
  gi|313117414|ref|YP_004044397.1| 483 S---VDESYAHGTEIHSEIVVPL---G-EYGILLAATTAEQTFAERQIGLFKILGATVKAA 536
                                       7...56677899***********...8.9*****99999999*************998766 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.6
                                       -TTS-EEEE.....EEEES-TTSTT-S-B---TTHHHHHHHHTS- CS
                             GAF_2  29 dddgglrla.....awgeaeeefgaaldrplgeglvgealrtgrp 68 
                                       d+d++  +      a ++a eef+ ++    +e+l  +++++g+p
  gi|313117414|ref|YP_004044397.1| 583 DPDQY--IGktdveADAGASEEFSKRT---HAESL--RVIEQGEP 620
                                       33333..22311114444444444444...24446..77777766 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   2.3e-10   4.1e-07       2     121 ..     408     531 ..     407     536 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.3e-10
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse.....sldedsalarralssgevvse..ps 71 
                                       + e+ e+ +++++++l +e+  ++ +de++n+l++   +  ++a+++      ++ +++la++a++sgev++    s
  gi|313117414|ref|YP_004044397.1| 408 PAEVGEIGVEAVADILEFEITGVWTYDERENELVPETET--AAAQEQfdtlpRIPPGESLAWEAFESGEVQYCsdVS 482
                                       56777899*************************999998..55555566576777**************96653444 PP

                             GAF_3  72 faeedg...lpdraalavPLvagrqviGvlalastkprafdaedlelleslAr 121
                                       + +e++   ++ ++ ++vPL      +G+l++a+t ++ f +++  l++ l++
  gi|313117414|ref|YP_004044397.1| 483 SVDESYahgTEIHSEIVVPLGE----YGILLAATTAEQTFAERQIGLFKILGA 531
                                       44554422267788899*9999....***********************9986 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3   5.7e-07     0.001      15      94 ..      35     116 ..      22     130 .. 0.85
   2 ?   -2.2   0.0       2.7   4.8e+03      57      75 ..     553     571 ..     534     580 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.7e-07
                        OKR_DC_1_N  15 kegfevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlreidg 88 
                                       + ++++v+++ ++++l+++++ + i++vv +++       +l++ ir+   +lPv ll+e+ +++ ++a   + ++ 
  gi|313117414|ref|YP_004044397.1|  35 NSEINCVTAECVGEALEILSS-HPIDCVVTAYElpdRTGIDLIESIRAEDDELPVILLTEQGNENVATAATQADVTD 110
                                       3567899*************9.78**********999999********************88888888888888888 PP

                        OKR_DC_1_N  89 fielle 94 
                                       +i + +
  gi|313117414|ref|YP_004044397.1| 111 YIPIRS 116
                                       876655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                        OKR_DC_1_N  57 irernedlPvFllaetrts 75 
                                       ++ + e +P+ l++++r+ 
  gi|313117414|ref|YP_004044397.1| 553 LDTIFEYVPIHLFIKDREG 571
                                       55667899**999997755 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.42   7.5e+02       2      28 ..     153     179 ..     152     257 .. 0.72
   2 ?    8.2   0.0    0.0015       2.7       1      76 [.     266     339 ..     266     390 .. 0.87
   3 ?   -3.6   0.0       7.1   1.3e+04      29      51 ..     406     429 ..     400     455 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.42
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylell 28 
                                       e  +++i  +D + r+  +N+++ e  
  gi|313117414|ref|YP_004044397.1| 153 ERTTDAIYAVDTEWRIEYMNEQMAERV 179
                                       566777888888888888888877644 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkph 76 
                                       l+n+++++ v+D++  + + N    + +d +      g +l++++   ++r +++  + ++++e++l+aa++++++
  gi|313117414|ref|YP_004044397.1| 266 LKNIHDAVFVLDETSTIQFANAAAAQAFDRTGPDQLEGEQLKDIVGDAVSRSDIR--EFNQAFEEVLHAAEEDDSS 339
                                       789**************************98777779****************99..7888888988777776544 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 7.1
                             PAS_7  29 dlpeelvqvgvp.leellrynaer 51 
                                       + p+e+ ++gv+ ++++l++  + 
  gi|313117414|ref|YP_004044397.1| 406 SSPAEVGEIGVEaVADILEFEITG 429
                                       567888888888788888877543 PP

>> Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.3   0.00012      0.22      60     119 ..     103     162 ..      92     175 .. 0.86
   2 ?   -1.6   0.0       1.4   2.6e+03      57      84 ..     251     278 ..     235     282 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                   Spore_YhcN_YlaJ  60 etaqniaqrverlegVedarvlvtgndvlVavqtdesdnekvkkkVketVekvvddiknV 119
                                        t  ++++ +    +V+d++ l++  + +V    d+++  +++++V++t e ++d i++V
  gi|313117414|ref|YP_004044397.1| 103 ATQADVTDYIPIRSDVDDCNLLINRIRTFVEAARDRKRASQLENHVQRTLERTTDAIYAV 162
                                       555666777777789***************999999*********************999 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                   Spore_YhcN_YlaJ  57 ydgetaqniaqrverlegVedarvlvtg 84 
                                       +++e+ q+++++ + l++++da  +  +
  gi|313117414|ref|YP_004044397.1| 251 DERERKQELERNETVLKNIHDAVFVLDE 278
                                       3467788888888889999999777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 4807.83
//
Query:       gi|313117415|ref|YP_004044398.1|  [L=63]
Description: hypothetical protein Hbor_32020 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.072   12.4   0.0      0.072   12.4   0.0    1.0  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     4e-06     0.072     258     287 ..      32      61 ..       8      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-06
                   ABC2_membrane_2 258 lgstatnllilllllavllvlgyvlFkrkD 287
                                         + ++++l+l ++++v  ++gy  F++++
  gi|313117415|ref|YP_004044398.1|  32 AHQSWFTVLVLMVWTVVAPAVGYLKFRTME 61 
                                       5678**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 422.92
//
Query:       gi|313117416|ref|YP_004044399.1|  [L=923]
Description: PAS domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-36  123.1   0.0      9e-36  123.1   0.0    2.9  4  BAT           GAF and HTH_10 associated domain
    9.6e-31  106.9   0.7    6.6e-20   71.8   0.0    2.8  2  GAF_2         GAF domain
    8.8e-25   87.9   0.1    3.9e-13   50.2   0.1    3.0  2  GAF           GAF domain
    3.1e-21   74.9   0.0    1.1e-20   73.1   0.0    2.0  2  HTH_10        HTH DNA binding domain
      5e-21   75.0   1.3    1.1e-09   38.5   0.4    3.0  2  PAS_4         PAS fold
    4.9e-20   71.6   0.1    9.6e-11   41.7   0.0    2.8  2  PAS           PAS fold
    3.8e-19   68.9   0.0    1.1e-10   41.7   0.0    2.7  2  PAS_9         PAS domain
    1.1e-13   51.6   0.0    1.6e-05   25.3   0.0    2.5  2  GAF_3         GAF domain
    1.1e-10   41.7   0.0    4.7e-08   33.2   0.0    2.9  2  PAS_3         PAS fold
    2.9e-09   36.7   0.1    1.7e-05   24.7   0.0    3.0  2  PAS_8         PAS domain
    6.8e-05   23.0   4.1       0.05   13.8   0.0    3.4  3  PAS_7         PAS fold
    0.00027   20.4   0.8      0.014   14.9   0.0    3.2  3  Sigma70_r4    Sigma-70, region 4
    0.00046   20.2   0.4       0.03   14.4   0.2    2.7  2  HTH_20        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.0   0.0        1.4    8.7   0.0    2.6  2  Sigma70_r4_2  Sigma-70, region 4
      0.015   15.2   3.7        1.7    8.6   0.2    3.4  3  MarR_2        MarR family
      0.021   14.4   0.0       0.21   11.2   0.0    2.4  2  HTH_24        Winged helix-turn-helix DNA-binding
      0.028   14.3   0.0       0.14   12.1   0.0    2.2  2  TrmB          Sugar-specific transcriptional regulator TrmB
      0.037   13.8   0.4       0.41   10.5   0.2    2.4  2  HTH_IclR      IclR helix-turn-helix domain
       0.08   12.9   0.0       0.81    9.7   0.0    2.5  2  HTH_1         Bacterial regulatory helix-turn-helix protein, 
       0.14   12.3   0.0        1.1    9.4   0.0    2.6  2  HTH_22        HTH domain
        1.2    9.2   4.7        4.3    7.4   0.1    3.2  3  HTH_Crp_2     Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       3.9   3.3e+03      69     113 ..     153     202 ..     105     210 .. 0.65
   2 ?   -2.7   0.1       5.7   4.9e+03     131     148 ..     200     217 ..     196     222 .. 0.78
   3 ?   -2.9   0.2       6.7   5.7e+03     127     144 ..     500     517 ..     498     529 .. 0.80
   4 !  123.1   0.0   1.1e-38     9e-36       1     155 [.     695     847 ..     695     848 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.9
                               BAT  69 rvvseeddg...tlleltvsgpslas..tlaehGgtvrsaeaedgrarlv 113
                                       rv+++++++    ++e++v++ +  +  +l  + g ++s    +gr+++ 
  gi|313117416|ref|YP_004044399.1| 153 RVLATYEQEtgtERFECRVTSGDGREerWLEHRSGPIESGPYAGGRVEVY 202
                                       45555555434477888876544332336666666666666666666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.7
                               BAT 131 erypdveLvarrererpv 148
                                       e y dv+++ rrer  ++
  gi|313117416|ref|YP_004044399.1| 200 EVYYDVTYRKRRERKLRE 217
                                       56889********98544 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.7
                               BAT 127 ealeerypdveLvarrer 144
                                       +a++++ ++ eLv++rer
  gi|313117416|ref|YP_004044399.1| 500 SAIARHADERELVRQRER 517
                                       678888899999999987 PP

  == domain 4  score: 123.1 bits;  conditional E-value: 1.1e-38
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+v+e+ ++i d  ++l  + ++ ++r+++++++p +d+++l++++++g++ ++vr+++e+l+ +e+v++ +e+++ 
  gi|313117416|ref|YP_004044399.1| 695 DDVIEIAFQIPDVFEAL-NAESNQNGRISFDHMMPIEDERYLLYGSATGDAIDNVRSIVEQLPYWESVSFHDEGKK- 769
                                       99***************.67888899**********************************************8877. PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                       t +e+++s+p+++s++a+ Gg++++a++edg++ ++v+v+p+ad+R++++++ee+yp ++L+ +r+++r+++t++++
  gi|313117416|ref|YP_004044399.1| 770 TDFEAQLSNPPVLSVVASAGGSIKQAVIEDGDYNITVHVAPTADIRQITKTIEETYPMAQLLKHRQVTRRDNTTNRI 846
                                       ***********************************************************************999876 PP

                               BAT 155 r 155
                                       +
  gi|313117416|ref|YP_004044399.1| 847 Q 847
                                       5 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.3   9.3e-11   7.9e-08       2     138 .]     362     503 ..     361     503 .. 0.81
   2 !   71.8   0.0   7.7e-23   6.6e-20       2     138 .]     539     684 ..     538     684 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 9.3e-11
                                       HHHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-.EEEE.EEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-G CS
                             GAF_2   2 adleelldlvldelve.lgaalgyillvdddgg.lrla.awgeaeeefgaaldrplgeg.lvgealrtgrpvilndl 74 
                                       +d+++ll ++++++++ lg +++ il +d+d + l l+   g  ++ +g+a+ +++++   +++ lrt +pv+++dl
  gi|313117416|ref|YP_004044399.1| 362 RDIDTLLTEATRQVANtLGNDYCKILDLDADADeLLLRqGVGWHDGIVGSATVSAVADDsQAAHTLRTDQPVVVSDL 438
                                       79************9956999**99998866553333368888888888888888877747***************9 PP

                                       GG-S-HHHHH.HHHHTT--EEEEEE-T.TS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglp.aghaglrsflavPlis.egrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       e++ + +g   ++++++rs+++  +++  + + G+l+   +   +f+  d+ +++++a+ +a ai+
  gi|313117416|ref|YP_004044399.1| 439 ETETRFSGPDlLREHDVRSGIST-IVGpSDDPWGILGTHDTAAKSFSTHDVNFVQSVANILASAIA 503
                                       99888888885777777777665.5566678******87666777*******************95 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 7.7e-23
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEE.......EEEES-TTSTT-S-B--...-TTHHHHHHHHTS CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgglrla.......awgeaeeefgaaldrpl...geglvgealrtgr 67 
                                       ++ ee+ ++v++ l++ +  ++++++ vd   +   +       + g+ ++ +  ++d+     ++g++g+a++tg+
  gi|313117416|ref|YP_004044399.1| 539 STREEIEETVCEFLAKSDsYSFAWVGDVDTTSK--RVnvrtkagTKGYLDDIV-ISVDP-NderSNGPTGRAFKTGE 611
                                       6889**********9987688******996655..223445563444444444.44433.1345888********** PP

                                       -EEES-GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  68 pvilndleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                           +++++dp++++++   +++ +rs++a+P+i+e+ ++Gvln+y+++ +af+ e+++++e+l+e i+ ai+
  gi|313117416|ref|YP_004044399.1| 612 IQTTQNIDQDPSHDPWRehIEAHEFRSSAAIPIIHEDAIYGVLNVYSKRLNAFEGEERAVVEQLGEIIGHAIA 684
                                       999**************99999999999*******99**********************************95 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.1   4.6e-16   3.9e-13       1     133 []     363     502 ..     363     502 .. 0.82
   2 !   34.4   0.0   3.3e-11   2.8e-08      46     133 .]     599     683 ..     544     683 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 4.6e-16
                                       SHHHHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC.........EEEETTSHHHH.....HHHHHSSSEE CS
                               GAF   1 dleelldtvveelrellgadrvalylpdydGlhydipqasrw.........lfmkngrgicg.....qvlatgqplv 63 
                                       d+++ll +++++++ +lg d++ ++  d+d  +  + q+  w         +     + +++     ++l+t+qp+v
  gi|313117416|ref|YP_004044399.1| 363 DIDTLLTEATRQVANTLGNDYCKILDLDADADELLLRQGVGWhdgivgsatV-----SAVADdsqaaHTLRTDQPVV 434
                                       799*********************8744455322478888885554332222.....2222255566********** PP

                                       ESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  64 ipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvaval 133
                                       ++d+ ++ rf+    +dll+++ +rs ++  +   ++ wG+l  h++ + +f++++++++q++a+ +a a+
  gi|313117416|ref|YP_004044399.1| 435 VSDLETETRFSG---PDLLREHDVRSGISTIVGPSDDPWGILGTHDTAAkSFSTHDVNFVQSVANILASAI 502
                                       ************...99********99998888899**********87789**************999987 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 3.3e-11
                                       ETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHH CS
                               GAF  46 kngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelel 121
                                       +ng    g++++tg++ + +++++dp + +  +r+++e++++rss+++P+++++ ++G+l +++++   f  ee+++
  gi|313117416|ref|YP_004044399.1| 599 SNG--PTGRAFKTGEIQTTQNIDQDPSHDP--WREHIEAHEFRSSAAIPIIHEDAIYGVLNVYSKRLnAFEGEERAV 671
                                       332..3369*********************..99******************************76678******** PP

                                       HHHHHHHHHHHH CS
                               GAF 122 lqvladqvaval 133
                                       +++l++ ++ a+
  gi|313117416|ref|YP_004044399.1| 672 VEQLGEIIGHAI 683
                                       ****99998776 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.9     5e+03       2      19 ..     569     586 ..     569     587 .. 0.82
   2 !   73.1   0.0   1.3e-23   1.1e-20       1      52 [.     854     905 ..     854     906 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.9
                            HTH_10   2 TdkqlevlklAyemGYFd 19 
                                       T k ++v ++A  +GY d
  gi|313117416|ref|YP_004044399.1| 569 TSKRVNVRTKAGTKGYLD 586
                                       667778889999****98 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 1.3e-23
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++q+++l +Ay++G+F +PR++t + +A+ lG+s++t+++hLrkae+k++
  gi|313117416|ref|YP_004044399.1| 854 LTERQRTALEAAYHAGFFQWPRETTGEGVAESLGVSPPTFHQHLRKAEQKVF 905
                                       9*************************************************98 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.4   1.3e-12   1.1e-09       2     110 .]      94     210 ..      93     210 .. 0.87
   2 !   34.2   0.0   2.8e-11   2.4e-08       2     108 ..     227     334 ..     226     336 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.3e-12
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee...daarleralrrvlegeepiefleelll. 74 
                                       +++ ++++vld+d+ v +a++a +++fg+++ +l+G+   el+      + ++ er  +rvl++ e  + +e   + 
  gi|313117416|ref|YP_004044399.1|  94 SRVDVGVFVLDEDFEVAWASEAVERYFGIDRSQLVGREKPELVESTvapVIDNAERFTERVLATYEQETGTERFECr 170
                                       56789***********************************9888888887777777777777777777777766666 PP

                             PAS_4  75 .....pgeerhyelrllPlrdesGe.vigvlvisrDiTerrr 110
                                            ++eer++e r  P+  esG  + g +++ +D+T r+r
  gi|313117416|ref|YP_004044399.1| 171 vtsgdGREERWLEHRSGPI--ESGPyAGGRVEVYYDVTYRKR 210
                                       669****************..8999999**********9986 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 2.8e-11
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelll..p 75 
                                       d + d+++++++++ ++ +N  ++el g+++eellG+++  ++  +   +r+e+ l+ v+++++   + e   +  +
  gi|313117416|ref|YP_004044399.1| 227 DTVEDGIYAVNEEMEFVVVNDGFCELTGYDREELLGSHVSMVHDNDkIMPRVESKLQTVIDTDRESARIELDIRtkS 303
                                       7789************************************9999999**************976555554333368* PP

                             PAS_4  76 geerhyelrl..lPlrdesGevigvlvisrDiTer 108
                                       ge +++e r+  +Pl+ + G+    ++++rD+++r
  gi|313117416|ref|YP_004044399.1| 304 GEKVPCESRFalFPLEGSYGR----CGVVRDVSDR 334
                                       *********9999**998888....9999999987 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   4.2e-09   3.6e-06       6      82 ..      92     174 ..      85     195 .. 0.82
   2 !   41.7   0.0   1.1e-13   9.6e-11       2     113 .]     221     331 ..     220     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.2e-09
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH...HHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda...elaelleqlleqgeesrageisf 79 
                                       +l+  ++++fv+Ded ++ ++++a e+ +G++r++++g+   +l+  +  a   + ae+++++ +++ e+++g  +f
  gi|313117416|ref|YP_004044399.1|  92 VLSRVDVGVFVLDEDFEVAWASEAVERYFGIDRSQLVGREKPELVEST-VApviDNAERFTERVLATYEQETGTERF 167
                                       455689************************************999654.4479999999999999999999999998 PP

                                       EC....T CS
                               PAS  80 kl....r 82 
                                       +      
  gi|313117416|ref|YP_004044399.1| 168 ECrvtsG 174
                                       8766552 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 1.1e-13
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH..HHHHHHHHHHHHTT-ECCCC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda..elaelleqlleqgeesrage 76 
                                       ++++i+++  d+i +v+e  +++ vN+ ++el+G++ree+lg++++++ h +d     + ++l++++ + +es   e
  gi|313117416|ref|YP_004044399.1| 221 QYETIVDTVEDGIYAVNEEMEFVVVNDGFCELTGYDREELLGSHVSMV-HDNDKImpRVESKLQTVIDTDRESARIE 296
                                       89********************************************44.44444589******************** PP

                                       EEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  77 isfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        +++++ g+++++e r + +  +g+   g +gv+rd+
  gi|313117416|ref|YP_004044399.1| 297 LDIRTKSGEKVPCESRFALFPLEGSY--GRCGVVRDV 331
                                       **************998877777665..777777775 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.2e-08   2.8e-05       1     103 [.      97     206 ..      97     206 .. 0.76
   2 !   41.7   0.0   1.2e-13   1.1e-10       2     104 .]     231     333 ..     230     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.2e-08
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf........vtdpeanerlraaleqgrkkerevevvli 69 
                                       ++g+++ ++d+++ +a+ea++r +G ++ +++g+   +l+        +++++  er+ a +eq +   +++e   +
  gi|313117416|ref|YP_004044399.1|  97 DVGVFVLDEDFEVAWASEAVERYFGIDRSQLVGREKPELVestvapviDNAERFTERVLATYEQET-GTERFECRVT 172
                                       57999999********************************99998666666666666666666666.5555665555 PP

                             PAS_9  70 rkng.etfwvlltaspvkdddgelvg.iivilrDit 103
                                         +g e+ w + +  p+  ++g + g  + +  D+t
  gi|313117416|ref|YP_004044399.1| 173 SGDGrEERWLEHRSGPI--ESGPYAGgRVEVYYDVT 206
                                       55557999999999999..46666665556666665 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 1.2e-13
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirknget 75 
                                       dgi  +n++ + + +N+++++l+Gy++ee+lg +++++    +  p+ +++l+ ++++ r +  + e+++++k+ge+
  gi|313117416|ref|YP_004044399.1| 231 DGIYAVNEEMEFVVVNDGFCELTGYDREELLGSHVSMVHdndKIMPRVESKLQTVIDTDR-ESARIELDIRTKSGEK 306
                                       7888889999*****************************888888888888888888888.99************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                       ++++ +++ +  ++    g  +++rD+++
  gi|313117416|ref|YP_004044399.1| 307 VPCESRFALFPLEG--SYGRCGVVRDVSD 333
                                       ****8887776553..3444579999985 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.8e-08   1.6e-05       1     129 []     363     504 ..     363     504 .. 0.80
   2 !   24.0   0.0   4.6e-08   3.9e-05      21     128 ..     560     684 ..     541     685 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.8e-08
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse....sldedsalarralssgevvsepsfa 73 
                                       ++d ll ++ ++++++lg +++ +l ld+d ++l  + g + ++ ++     s ++d++ a+ +l ++++v++ + +
  gi|313117416|ref|YP_004044399.1| 363 DIDTLLTEATRQVANTLGNDYCKILDLDADADELLLRQGVGWHDGIVGsatvSAVADDSQAAHTLRTDQPVVVSDLE 439
                                       6789999*****************99****9999888777445555444455444888889999999***9998877 PP

                             GAF_3  74 eedg........lpdraalavPLvagr.qviGvlalastkprafdaedlelleslArqiataier 129
                                        e++         +d    +  +v ++  + G+l+ + t  ++f+  d+ +++s+A+ +a+ai+r
  gi|313117416|ref|YP_004044399.1| 440 TETRfsgpdllrEHDVRSGISTIVGPSdDPWGILGTHDTAAKSFSTHDVNFVQSVANILASAIAR 504
                                       7766555555444455555555777779***********************************87 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 4.6e-08
                             GAF_3  21 vgalllldedgnklqvaagwdgkpalse...sld....edsalarralssgevvsepsfaeedg..........lpd 80 
                                       ++ ++ +d+  ++++v+ + + k  l     s+d    + +  + ra+++ge+++++  ++ ++          ++ 
  gi|313117416|ref|YP_004044399.1| 560 FAWVGDVDTTSKRVNVRTKAGTKGYLDDiviSVDpndeRSNGPTGRAFKTGEIQTTQNIDQDPShdpwrehieaHEF 636
                                       5555556666666666655544444444555665522344444559********99888775554444444444778 PP

                             GAF_3  81 raalavPLvagrqviGvlalastkprafdaedlelleslArqiataie 128
                                       r+  a+P+++++  +Gvl ++s++  af  e+++ +e l+  i+ ai+
  gi|313117416|ref|YP_004044399.1| 637 RSSAAIPIIHEDAIYGVLNVYSKRLNAFEGEERAVVEQLGEIIGHAIA 684
                                       ********************************************9996 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0      0.03        25       3      75 ..     111     189 ..     109     194 .. 0.72
   2 !   33.2   0.0   5.6e-11   4.7e-08       2      75 ..     243     316 ..     242     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.03
                             PAS_3   3 yvserveeilGyspeellgk..veswldlvhpeD..rervrealqealkkge.pyegeyRirrkdG.eyrwvearar 73 
                                        +se+ve+++G+++++l g+  +e + + v p     er+ e + +  ++ +    +e R+   dG e rw+e r  
  gi|313117416|ref|YP_004044399.1| 111 WASEAVERYFGIDRSQLVGRekPELVESTVAPVIdnAERFTERVLATYEQETgTERFECRVTSGDGrEERWLEHRSG 187
                                       589*****************977777777777533366666666666655553447788888887646788888877 PP

                             PAS_3  74 vi 75 
                                       +i
  gi|313117416|ref|YP_004044399.1| 188 PI 189
                                       77 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 5.6e-11
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD..rervrealqealkkge.pyegeyRirrkdGeyrwveararvi 75 
                                       + v++ ++e++Gy++eellg+   + ++vh  D   +rv+++lq+++++++ +  +e  ir+k+Ge +  e+r   +
  gi|313117416|ref|YP_004044399.1| 243 VVVNDGFCELTGYDREELLGS---HVSMVHDNDkiMPRVESKLQTVIDTDReSARIELDIRTKSGEKVPCESRFALF 316
                                       679******************...***********************9999789************99999997765 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0     0.002       1.7      10      45 ..      96     127 ..      87     159 .. 0.73
   2 !   24.7   0.0     2e-08   1.7e-05       2      55 ..     221     277 ..     220     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.002
                             PAS_8  10 spdgiavvdlgdrivdvNqaalellGysadlkgell 45 
                                       +++g++v+d++  + ++ +a ++ +G +    ++ l
  gi|313117416|ref|YP_004044399.1|  96 VDVGVFVLDEDFEVAWASEAVERYFGID----RSQL 127
                                       689******5446*************55....4333 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2e-08
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg..qllpvlrpl 55 
                                       +++++++++ dgi  v+ +   +v vN+ ++el+Gy+ ++l+g+ +    + + ++p 
  gi|313117416|ref|YP_004044399.1| 221 QYETIVDTVEDGIYAVNeEM-EFVVVNDGFCELTGYDrEELLGSHVSmvHDNDKIMPR 277
                                       79**************9444.5***************888888766444444444444 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   5.9e-05      0.05       2     114 ..      94     212 ..      93     213 .. 0.73
   2 !    9.2   0.0    0.0016       1.3       1      35 [.     226     260 ..     226     304 .. 0.87
   3 ?   -2.5   0.1       6.6   5.6e+03      43      72 ..     501     530 ..     487     550 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-05
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaara...... 72 
                                       + ++ G+ v+D+d ++    + + + +++ ++ + vg++  el++ +++    +   +e + er+la +++      
  gi|313117416|ref|YP_004044399.1|  94 SRVDVGVFVLDEDFEVAWASEAVERYFGIDRSQL-VGREKPELVESTVAPVIDN---AERFTERVLATYEQetgter 166
                                       67889**************************999.9***999999997766655...45555555555544211111 PP

                             PAS_7  73 gkphsfererpdgrvievrgnpl....pdgGfVttytDiTerrrae 114
                                       ++   +    +++r++e r+ p+      gG V +y D+T r+r e
  gi|313117416|ref|YP_004044399.1| 167 FECRVTSGDGREERWLEHRSGPIesgpYAGGRVEVYYDVTYRKRRE 212
                                       33333333445568*********5443358*************998 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelv 35 
                                       ++ +++Gi  ++++++ v++N+ ++el ++ +e +
  gi|313117416|ref|YP_004044399.1| 226 VDTVEDGIYAVNEEMEFVVVNDGFCELTGYDREEL 260
                                       57899***********************9988765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.6
                             PAS_7  43 ellrynaergefgagdveaeverrlaaara 72 
                                       ++ r+  er+ ++++++ a+++   + +r+
  gi|313117416|ref|YP_004044399.1| 501 AIARHADERELVRQRERLAALNSLNEVVRE 530
                                       444555555555544444444444444443 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.17   1.4e+02       8      34 ..       9      37 ..       4      40 .. 0.75
   2 ?   -1.6   0.2       2.4   2.1e+03      34      44 ..     509     519 ..     509     522 .. 0.84
   3 !   14.9   0.0   1.6e-05     0.014       4      47 ..     853     903 ..     852     906 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.17
                                      HHHHHHHHHH..TTT--HHHHHHHHTS-H CS
                        Sigma70_r4  8 rerevlelrf..geglTleEIgerlgiSr 34
                                        re l l    g +lT  EI++ l + r
  gi|313117416|ref|YP_004044399.1|  9 ALRETLALFEqsGTPLTTTEIADCLELGR 37
                                      55555666557799*********998876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrA 44 
                                       re Vrq+e+ A
  gi|313117416|ref|YP_004044399.1| 509 RELVRQRERLA 519
                                       788*****976 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 1.6e-05
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrk 47 
                                       +L+er+r+ le  +        ++ T e ++e lg+S  + +q++++A +k
  gi|313117416|ref|YP_004044399.1| 853 QLTERQRTALEAAYhagffqwPRETTGEGVAESLGVSPPTFHQHLRKAEQK 903
                                       8*******************98999**********************9777 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   3.6e-05      0.03      19      60 ..      16      59 ..       6      60 .. 0.86
   2 ?    3.0   0.0      0.13   1.1e+02      30      47 ..     882     899 ..     854     902 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                                      H..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 19 L..araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      L   ++ +lt +e+a++l+l + + +++L+ L+ +g +e+ ++g
  gi|313117416|ref|YP_004044399.1| 16 LfeQSGTPLTTTEIADCLELGRRSTYDRLDRLVNHGRLETKKVG 59
                                      2566789*****************************99998876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                                       HHHHHTS-HHHHHHHHHH CS
                            HTH_20  30 laerldlskntlsyHLrv 47 
                                       +ae l++s+ t ++HLr+
  gi|313117416|ref|YP_004044399.1| 882 VAESLGVSPPTFHQHLRK 899
                                       78999***********97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.075        64       9      23 ..     852     866 ..     845     870 .. 0.87
   2 ?    8.7   0.0    0.0016       1.4      32      53 ..     882     903 ..     876     904 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.075
                                       TTS-HHHHHHHHHHH CS
                      Sigma70_r4_2   9 aeLperqreifllry 23 
                                       ++L+erqr++++  y
  gi|313117416|ref|YP_004044399.1| 852 NQLTERQRTALEAAY 866
                                       79*********9876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                                       HHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2  32 IAellgisegtVksrlsRArkk 53 
                                       +Ae lg+s+ t  ++l++A +k
  gi|313117416|ref|YP_004044399.1| 882 VAESLGVSPPTFHQHLRKAEQK 903
                                       7******************887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2     0.002       1.7      13      58 ..      18      60 ..       5      63 .. 0.78
   2 ?   -2.6   0.2       6.4   5.5e+03      39      55 ..     500     516 ..     499     521 .. 0.80
   3 ?    5.9   0.0     0.013        11      26      47 ..     881     902 ..     852     903 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.002
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                      +    p   lt +e+a+ l l + ++  +l+rLv +G +e+++  +
  gi|313117416|ref|YP_004044399.1| 18 EQSGTP---LTTTEIADCLELGRRSTYDRLDRLVNHGRLETKKVGA 60
                                      333333...9***************************999986555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.4
                                       HHHHHHHHHTTSEEEEE CS
                            MarR_2  39 srilkrLvaaGLverrp 55 
                                       s i + + ++ Lv++r+
  gi|313117416|ref|YP_004044399.1| 500 SAIARHADERELVRQRE 516
                                       78999999999999985 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.013
                                       HHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  26 elarrlglsksavsrilkrLva 47 
                                        +a+ lg+s+++ +++l+++++
  gi|313117416|ref|YP_004044399.1| 881 GVAESLGVSPPTFHQHLRKAEQ 902
                                       5799***************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.77   6.6e+02      18      45 ..      24      51 ..      10      54 .. 0.82
   2 ?   11.2   0.0   0.00024      0.21      23      44 ..     882     903 ..     877     903 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.77
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeG 45
                                      ++ +e+A+ l l +  +  rl+rL++ G
  gi|313117416|ref|YP_004044399.1| 24 LTTTEIADCLELGRRSTYDRLDRLVNHG 51
                                      8999****9999999999******9877 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00024
                            HTH_24  23 LAerlglSpstvnrrlkrLeee 44 
                                       +Ae lg+Sp+t +++l++ e++
  gi|313117416|ref|YP_004044399.1| 882 VAESLGVSPPTFHQHLRKAEQK 903
                                       69****************9975 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.14      21      57 ..      22      58 ..      14      72 .. 0.85
   2 ?   -2.4   0.0       5.2   4.4e+03      23      45 ..     877     899 ..     875     903 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                       p+t++eia +l++ r + Y+ L +L++ G  e++k 
  gi|313117416|ref|YP_004044399.1| 22 TPLTTTEIADCLELGRRSTYDRLDRLVNHGRLETKKV 58
                                      589***************************9998875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.2
                                       CHHCHHCCCTTSSCHCHHHHHHH CS
                              TrmB  23 atadeiaeelgvprskvYevLrs 45 
                                        t + +ae lgv+ ++  + Lr+
  gi|313117416|ref|YP_004044399.1| 877 TTGEGVAESLGVSPPTFHQHLRK 899
                                       68899*******99987777766 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00048      0.41       9      50 ..      14      55 ..      13      57 .. 0.94
   2 ?    0.5   0.0      0.65   5.5e+02      24      40 ..     882     898 ..     875     899 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00048
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      L ++++ + +lt +e+A+ + l + +++  L  Lv++G +e+
  gi|313117416|ref|YP_004044399.1| 14 LALFEQSGTPLTTTEIADCLELGRRSTYDRLDRLVNHGRLET 55
                                      78999*********************************8875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.65
                                       HHHHHTS-HHHHHHHHH CS
                          HTH_IclR  24 lArrtglpkStvhRlLq 40 
                                       +A+ +g++++t h +L+
  gi|313117416|ref|YP_004044399.1| 882 VAESLGVSPPTFHQHLR 898
                                       79***********9986 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.3     2e+03      17      30 ..     421     434 ..     421     445 .. 0.87
   2 ?    9.7   0.0   0.00095      0.81      19      46 ..     882     909 ..     876     915 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.3
                                       HHHHHHHTS-HHHH CS
                             HTH_1  17 trAAeeLglsqpav 30 
                                       ++AA  L++ qp v
  gi|313117416|ref|YP_004044399.1| 421 SQAAHTLRTDQPVV 434
                                       68**********88 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00095
                                       HHHHHTS-HHHHHHHHHHHHHHHTS-SE CS
                             HTH_1  19 AAeeLglsqpavsrqikrLEeelgvpLf 46 
                                        Ae Lg+s+p+  +++++ E+ + + L+
  gi|313117416|ref|YP_004044399.1| 882 VAESLGVSPPTFHQHLRKAEQKVFDHLL 909
                                       69******************99877665 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       7.7   6.6e+03       4      34 ..     496     526 ..     494     526 .. 0.77
   2 ?    9.4   0.0    0.0012       1.1      23      63 .]     856     898 ..     838     898 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.7
                            HTH_22   4 siieevladlgkpverltkeekieivraLde 34 
                                       +i+++++a+++ + e   + e++++  +L+e
  gi|313117416|ref|YP_004044399.1| 496 NILASAIARHADERELVRQRERLAALNSLNE 526
                                       5667777777777788899999999999986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                            HTH_22  23 eekieivraLdekGiFllkg..avekvAekLgiSraTvYryLr 63 
                                       e+ +++ +a +++G+F+  +  + e vAe Lg+S +T   +Lr
  gi|313117416|ref|YP_004044399.1| 856 ERQRTALEAAYHAGFFQWPRetTGEGVAESLGVSPPTFHQHLR 898
                                       56677788889999999865337899***********999986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.005       4.3      20      54 ..      22      56 ..       8      63 .. 0.86
   2 ?   -1.7   0.5       3.5     3e+03      44      65 ..     344     367 ..     339     369 .. 0.80
   3 ?    2.0   0.0      0.24   2.1e+02      23      46 ..     878     901 ..     845     904 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.005
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrg 54
                                       plt +e+A++l l r ++   l +L ++g ++++
  gi|313117416|ref|YP_004044399.1| 22 TPLTTTEIADCLELGRRSTYDRLDRLVNHGRLETK 56
                                      59****************************99854 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.5
                                       HHHHTTSEE.ETEE.EEES-HHHH CS
                         HTH_Crp_2  44 eLkreglis.rgrr.irildleaL 65 
                                       + ++++ i+  gr+ ++++d++ L
  gi|313117416|ref|YP_004044399.1| 344 RIRQQKSITkLGRQaLEVRDIDTL 367
                                       667888899668778*****9988 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.24
                                       HHHHHHHHTTSSHHHHHHHHHHHH CS
                         HTH_Crp_2  23 tqeelAsmlGltretvsrilseLk 46 
                                       t e  A+ lG+++ t+ + l++ +
  gi|313117416|ref|YP_004044399.1| 878 TGEGVAESLGVSPPTFHQHLRKAE 901
                                       55678*************999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (923 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 5889.00
//
Query:       gi|313117417|ref|YP_004044400.1|  [L=138]
Description: hypothetical protein Hbor_32040 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.081   13.1   1.5       0.11   12.6   1.5    1.2  1  CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal


Domain annotation for each model (and alignments):
>> CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.5   6.3e-06      0.11      36     123 ..      31     118 ..       4     129 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-06
                         CPSF100_C  36 eaeeeekeeeeeeeeeeeeeeeaskkqklaeksekeaseeeseekkeslptldvlpankasvrsaaqpl...fvGdl 109
                                       +++ +e+ee++++++++++ +++s++q +  +   + +++  ++ ++++p+    ++++a+ r a ++l   f G++
  gi|313117417|ref|YP_004044400.1|  31 AETTTESEERTSTTADTTDTDDESRTQSM--QIPYKFRRDGVQDGRSRVPLFLQSETKTAE-RDALRELedrFDGNV 104
                                       11111111111111112222222222222..223333333344444444433333333333.5566666666***** PP

                         CPSF100_C 110 rLadLkkallssgi 123
                                        L+dL++al   g+
  gi|313117417|ref|YP_004044400.1| 105 SLTDLREALVMVGL 118
                                       ********987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 952.38
//
Query:       gi|313117418|ref|YP_004044401.1|  [L=295]
Description: chromosome partitioning ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-20   71.7   0.0    9.9e-20   71.2   0.0    1.1  1  AAA_31       AAA domain
      9e-10   38.7   0.0    9.5e-10   38.6   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    5.5e-07   29.1   0.0    8.7e-07   28.4   0.0    1.2  1  ArsA_ATPase  Anion-transporting ATPase
    4.3e-05   23.1   0.0    0.00012   21.6   0.0    1.7  2  ParA         NUBPL iron-transfer P-loop NTPase
    0.00024   20.5   0.0      0.016   14.5   0.0    2.2  2  MipZ         ATPase MipZ
     0.0035   16.8   0.0     0.0053   16.2   0.0    1.3  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.022   14.2   0.0    1.4  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
      0.019   14.6   0.0      0.041   13.5   0.0    1.5  1  SRP54        SRP54-type protein, GTPase domain
       0.21   11.3   0.0       0.42   10.4   0.0    1.4  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0     5e-23   9.9e-20       7     161 ..      11     183 ..       7     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 5e-23
                            AAA_31   7 anqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQ.anattglgiekne...iektlyevli.eeknikeaiiktkv 78 
                                       +   GGvGKTTt+ nla+a a++g k L+v lDpQ + ++  +g+++++   +++ + +++   + + ++++   +v
  gi|313117418|ref|YP_004044401.1|  11 YSEAGGVGKTTTAANLAVAHARAGLKPLVVPLDPQdGDLSRLFGVDHERtesVDNIVRHMIRrPKGEFDDLVR--TV 85 
                                       6678*******************************45788889997665333555555555556778888888..78 PP

                            AAA_31  79 enldlipssidLaeaeielvelekk..........eeilkellek..vkdeYDyiiiDcpPsLglltenaLvasdsv 143
                                       e +d++p +  L+++   l++ +++          + +l ++l++  v ++YD+ i D p + g  + na+ a  s+
  gi|313117418|ref|YP_004044401.1|  86 EGVDIVPEHNMLSDLAEYLQREKDQaeamgeafgmHAQLLRVLREagVPETYDVLICDPPATEGPHLYNAINATRSL 162
                                       999****************99999977777666665557777755337899************************** PP

                            AAA_31 144 iipvqaea...yaleGleqll 161
                                       +ipv+++a    a+eGle+l+
  gi|313117418|ref|YP_004044401.1| 163 VIPVEPSAkgrAAVEGLESLV 183
                                       *****9865557888888886 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   4.8e-13   9.5e-10       5      55 ..      12     103 ..       8     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 4.8e-13
                                       ESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                              CbiA   5 stkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                       s  GGvGKTt+aanLa+a ar+gl+ l+v +Dpq   l+ l+g+  ++ +                           
  gi|313117418|ref|YP_004044401.1|  12 SEAGGVGKTTTAANLAVAHARAGLKPLVVPLDPQDGDLSRLFGVDHERTEsvdnivrhmirrpkgefddlvrtvegv 88 
                                       789*******************************9999889999888888666666666666666555555555555 PP

                                       ..............C CS
                                       ..............x RF
                              CbiA  55 ..............d 55 
                                                      
  gi|313117418|ref|YP_004044401.1|  89 divpehnmlsdlaeY 103
                                       555555544444440 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   4.4e-10   8.7e-07       9     135 ..      14     147 ..       8     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.4e-10
                                       STTSSHHHHHHHHHHHHHHTTS-EEEEE-STTT.HHHHHHTS--BSS-EEETSSEEEEE--HH.HHHHHHHCCH..H CS
                       ArsA_ATPase   9 KGGVGKttvsaatavklsekgkkvllistDPAh.slsDsfdqklgkeptkvkeNLsavEidpe.veleeakqev..q 81 
                                        GGVGKtt +a +av  ++ g k l++ +DP    ls  f     +e t   +N++   i     e +   + v   
  gi|313117418|ref|YP_004044401.1|  14 AGGVGKTTTAANLAVAHARAGLKPLVVPLDPQDgDLSRLFGV--DHERTESVDNIVRHMIRRPkGEFDDLVRTVegV 88 
                                       5******************************8648*****99..677777778888888865445555444333113 PP

                                       GGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHH.HHHHHHHH....CSSSSEEEEESBSC CS
                       ArsA_ATPase  82 keeeallgleeledvlaeelaslPGideilsf.eellkyvk....eeeydvvvlDtaPT 135
                                       +   +  +l+ l + l+ e      + e++ + ++ll+ ++     e+ydv++ D + T
  gi|313117418|ref|YP_004044401.1|  89 DIVPEHNMLSDLAEYLQREKDQAEAMGEAFGMhAQLLRVLReagvPETYDVLICDPPAT 147
                                       334445566788888888888889999999862467777775556789******97665 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     6e-08   0.00012       9      62 ..      11      64 ..       3      76 .. 0.88
   2 ?   -2.1   0.0       1.1   2.1e+03     110     127 ..     135     151 ..     103     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 6e-08
                              ParA  9 lSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqse 62
                                       S  GGVGK+t+a+nlA+a a+ glk  ++ +D    ++ rl+gv++e++e+ +
  gi|313117418|ref|YP_004044401.1| 11 YSEAGGVGKTTTAANLAVAHARAGLKPLVVPLDPQDGDLSRLFGVDHERTESVD 64
                                      6778******************************************99877665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                              ParA 110 gelDyLiiDlPPGtgDeq 127
                                       ++ D+Li D PP t   +
  gi|313117418|ref|YP_004044401.1| 135 ETYDVLICD-PPATEGPH 151
                                       667999999.77776555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     8e-06     0.016       8      54 ..      13      59 ..       9      72 .. 0.86
   2 ?    3.4   0.0      0.02        39      74     132 ..     109     169 ..      90     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8e-06
                                      SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHH CS
                              MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraat 54
                                      e GG Gk+tta  +ava +++G++  ++ ld +   l+r ++   ++
  gi|313117418|ref|YP_004044401.1| 13 EAGGVGKTTTAANLAVAHARAGLKPLVVPLDPQDGDLSRLFGVDHER 59
                                      89*****************************9999999988755544 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.02
                                       HHHHTTS-HHHHHHHHHHHHHH..HHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESS CS
                              MipZ  74 eeaeveeeeeaevaeleelvad..leaeldfividtPGsdsalsrlahsladtlvtPlnds 132
                                       ++ae+ +e+    a+l +++++  + +++d+++ d P ++ +    a +   +lv P+  s
  gi|313117418|ref|YP_004044401.1| 109 DQAEAMGEAFGMHAQLLRVLREagVPETYDVLICDPPATEGPHLYNAINATRSLVIPVEPS 169
                                       4555555555556677777665224689****************************99765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.7e-06    0.0053       8      48 ..      14      54 ..       8      93 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-06
                         Fer4_NifH  8 kGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllg 48
                                       GG+Gk+tt++nl+ a a+ g k l+v  DP+    + l+g
  gi|313117418|ref|YP_004044401.1| 14 AGGVGKTTTAANLAVAHARAGLKPLVVPLDPQDGDLSRLFG 54
                                      59*****************************9754444443 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.022      11     144 ..      15     164 ..      13     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                          CBP_BcsQ  11 GGvGttsllaaLawalhelgesvlviDlspdn.lLrlhFnvdieqregw...araeldgap.wrqaaleyapgldll 82 
                                       GGvG+t+ +a La a  + g + lv+ l p++  L   F vd+e++e+    +r ++ + +   +  ++  +g+d++
  gi|313117418|ref|YP_004044401.1|  15 GGVGKTTTAANLAVAHARAGLKPLVVPLDPQDgDLSRLFGVDHERTESVdniVRHMIRRPKgEFDDLVRTVEGVDIV 91 
                                       9***************************9976369999****99887651114444433221235678899999999 PP

                          CBP_BcsQ  83 PfGelnveekenlqq.......laekaeallaalkelk.....eqyrwillDlpagasaltrellaladlvllv 144
                                       P  ++ ++ +e lq        + e+ +  ++ l+ l+     e+y+ ++ D pa + +   ++++ a+++l +
  gi|313117418|ref|YP_004044401.1|  92 PEHNMLSDLAEYLQRekdqaeaMGEAFGMHAQLLRVLReagvpETYDVLICDPPATEGPHLYNAIN-ATRSLVI 164
                                       976655444333333101000133333444444444547778889999999999999998888888.4444433 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.1e-05     0.041      11      38 ..      16      43 ..      13      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                      TSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54 11 GaGKTttlaKLaallkkegkkvllvaaD 38
                                      G+GKTtt+a La    + g k+l+v +D
  gi|313117418|ref|YP_004044401.1| 16 GVGKTTTAANLAVAHARAGLKPLVVPLD 43
                                      9***********************9988 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00021      0.42       4      38 ..      16      50 ..      14      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvGqseis 38
                                       +GK+T a++L+   +r+g kp++v lD+ ++++s
  gi|313117418|ref|YP_004044401.1| 16 GVGKTTTAANLAVAHARAGLKPLVVPLDPQDGDLS 50
                                      59***************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1953.31
//
Query:       gi|313117419|ref|YP_004044402.1|  [L=99]
Description: hypothetical protein Hbor_32060 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 668.87
//
Query:       gi|313117420|ref|YP_004044403.1|  [L=221]
Description: hypothetical protein Hbor_32090 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-10   41.9   0.8    1.7e-10   41.2   0.8    1.3  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.8   9.3e-15   1.7e-10       6     121 ..      30     131 ..      27     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 9.3e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH...HH CS
                                HD   6 leVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld...le 79 
                                        +V  +a rla++ + + dr++l +aa lHDiG ++++         ++k+ +H ++g   + +++ ++g++   + 
  gi|313117420|ref|YP_004044403.1|  30 NRVRDVAIRLANECENNVDRDVLSAAAWLHDIGRPRER---------VGKIGNHDEWGTAEAAALLADEGVPtdhIA 97 
                                       56777788888888889*******************77.........589999****************99999*** PP

                                       HHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  80 dvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       ++ + ir h+ ++          +++ ++ea+++ +aD+l+a
  gi|313117420|ref|YP_004044403.1|  98 AIKHCIRTHSIRSS--------SPEPETIEAKLLFDADKLDA 131
                                       *************8........679***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 1511.85
//
Query:       gi|313117421|ref|YP_004044404.1|  [L=117]
Description: hypothetical protein Hbor_32100 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        4.3    7.0   7.6        4.9    6.8   7.6    1.1  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   7.6   0.00028       4.9      35     102 ..      36     103 ..      10     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00028
                                       ..................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  35 lacllsesaedpailaillivvGvllfllgflGcigalkenkcllltfsllllvlfllelaagilgfv 102
                                           ++e a+   +   +++v+ +l ++l+ +G+iga+  +   l++  +lllvl +l l +g++ ++
  gi|313117421|ref|YP_004044404.1|  36 TLPSSTEPATGLESGNPFILVLAALPIFLSAVGLIGAYYGRPEALAIGGVLLLVLGVLGLNIGFFYLA 103
                                       33334455566666667899**********************99999999999997776666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 818.31
//
Query:       gi|313117422|ref|YP_004044405.1|  [L=353]
Description: nitrate/sulfonate/bicarbonate ABC transporter periplasmic protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-21   75.8   0.0    5.1e-21   75.5   0.0    1.1  1  NMT1_2          NMT1-like family
    0.00025   21.1   0.0    0.00048   20.1   0.0    1.4  1  NMT1            NMT1/THI5 like
    0.00093   18.9   0.0     0.0013   18.4   0.0    1.3  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   8.5e-25   5.1e-21       6     249 ..      44     285 ..      39     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 8.5e-25
                            NMT1_2   6 eqlklGfialtdaaplvvakekglfakeGltvelekqas.waelrdkllagelDaahv.ltpapllidlGiggakad 80 
                                        +l++++ +     +  ++ ++g+f++ G +ve + +a  + +++++ ++g++D+a++  tp++   ++Gi     +
  gi|313117422|ref|YP_004044405.1|  44 DTLNVAYKPVFPFLQRHIMDQQGFFDELGPSVEQTNFADkGLTIVKAYADGDIDLAFMgITPVIKMKHKGI-----P 115
                                       6799999999999999****************77777751668889999**********************.....9 PP

                            NMT1_2  81 mkvlaslnlnGqaitlsnklkdkkvsdakalkdlvakkkas..kplkiavtfpgsthdlllrywLaa.aGldpeadv 154
                                        kv a++++nG   ++++++ +      k  +d+++k +++  +++++ +  +gs   +l++ywL++  G+ p + v
  gi|313117422|ref|YP_004044405.1| 116 GKVTAANHKNGFVAMAHEEFVS---LWEKHGADAFQKFREQngRKFRFSTFPKGSVAYILVQYWLREeLGVSP-DVV 188
                                       9***********9999998777...4555555666666655568******99*************85269999.999 PP

                            NMT1_2 155 klvvvpp.pqmvanlkagtidgfcvgePwnaqavaegiGvtal.tsqelwkdhPekvlgvredfveknpntaralvk 229
                                       ++ ++ +   + + l +g+ dg++  eP +  +  + + +  l +s+e   ++P+ v++++ ++ ++ p++a+ +v+
  gi|313117422|ref|YP_004044405.1| 189 EIETLGGaGPVRQSLLTGNADGTFIMEPIPTALQLKDAPFEWLtWSGEFMSGQPGGVMFMHDRLWKDSPDLAQSIVE 265
                                       99999996777889***************9999888888877659******************************** PP

                            NMT1_2 230 alleAtkwldakkenraeaa 249
                                        +++At+++++k++++a+a+
  gi|313117422|ref|YP_004044405.1| 266 KHVRATQLINNKPDTAAKAV 285
                                       ***********999998886 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.1e-08   0.00048      12     216 .]      64     281 ..      61     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.1e-08
                                       HTTHHHHTTEEEEEE--SSTT.HHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEE........EE-S--EEEEE CS
                              NMT1  12 ekGYFkeeGldVeivepadps.datelvasgkadfgvsyqesllaarakglpvvsvaa........llqeplsgliv 79 
                                       ++G+F e G +Ve    ad++ + +++ a g+ d+++   + ++  ++kg+p +  aa        + +e++ +l  
  gi|313117422|ref|YP_004044405.1|  64 QQGFFDELGPSVEQTNFADKGlTIVKAYADGDIDLAFMGITPVIKMKHKGIPGKVTAAnhkngfvaMAHEEFVSLWE 140
                                       79**********88877666516789**************************8876661111111144555555566 PP

                                       ECCC-.-SSGGGGTTSEEEE-S-TT...HHHHHHHHHHHT.T--GGG-EEEE-.TT-.HHHHHHCTSSSEEECEETT CS
                              NMT1  80 lkdsg.ikspkDLkGkrigyvgspf...ekallkallakd.ggdpsdvtlvnvggts.lakalltgkvDaaiggyen 150
                                       + +++  +++++ +G++  ++  p+   + +l++  l+++ g++p+ v++ + gg   + ++lltg++D ++ ++e 
  gi|313117422|ref|YP_004044405.1| 141 KHGADaFQKFREQNGRKFRFSTFPKgsvAYILVQYWLREElGVSPDVVEIETLGGAGpVRQSLLTGNADGTF-IMEP 216
                                       66777899*********99877655333778889888776377*******99998862556********999.7776 PP

                                       THHHHHHHTT--EEEE-GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHHHH CS
                              NMT1 151 wegvelesegkelrifaladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyalahPeea 216
                                            l+++  + + +  +   +      v++ ++ l k++p+l++++++   ++++ + ++P+ a
  gi|313117422|ref|YP_004044405.1| 217 -IPTALQLKDAPFEWLTWSGEFMSGQPGGVMFMHDRLWKDSPDLAQSIVEKHVRATQLINNKPDTA 281
                                       .67777888889999999999988999************************************987 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.1e-07    0.0013      40     167 ..      85     217 ..      42     294 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHTTS-SEEE--HHHHHHHHHHS.-EEEEEEEEETT-.....-SEEEEEEEEETTSS--SHHHHGG-EEEE CS
                    Phosphonate-bd  40 aavvealragqvDiaflgplayvqardqa.gveplatrvrsdG.....sasyrsviivradsdiqsledLkgktiaf 110
                                        ++v+a + g +D+af+g  ++++++ +    +++a++ + +G      +++ s++  +  ++ q++ + +g+++ f
  gi|313117422|ref|YP_004044405.1|  85 LTIVKAYADGDIDLAFMGITPVIKMKHKGiPGKVTAANHK-NGfvamaHEEFVSLWEKHGADAFQKFREQNGRKFRF 160
                                       568999********************997689******97.997654446888888888888899999999998887 PP

                                       --.TT-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEEHHH CS
                    Phosphonate-bd 111 vs.psStsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavsada 167
                                          p+   +y++ +++L +e g+ p+   + +  g+   + +++l g+ad  ++ + +
  gi|313117422|ref|YP_004044405.1| 161 STfPKGSVAYILVQYWLREELGVSPD-VVEIETLGGAGPVRQSLLTGNADGTFIMEPI 217
                                       653444446*********99***986.678889*****************99976544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2240.04
//
Query:       gi|313117423|ref|YP_004044406.1|  [L=274]
Description: nitrate/sulfonate/bicarbonate ABC transporter permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-21   75.5   7.6    5.6e-21   75.1   7.6    1.2  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   7.6   3.1e-25   5.6e-21       2     183 ..      97     269 ..      92     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 3.1e-25
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                       +++G+ ++  +  +  ld++ +p+i +l+ +P+++++++ +       ++g +  +++++++++a+++++++ ++++
  gi|313117423|ref|YP_004044406.1|  97 VTVGSAVGiaVGWSDALDDACTPIIRILRPIPPLAWIVFAI------IWFGLGHSGAAFIVFIGAFWITFYNAYSGV 167
                                       4445555566779**********************999999......99**************************** PP

                      BPD_transp_1  77 rslpkdlveaaralGa.srwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyse 152
                                       +s +++l+e+a++lG+ ++w+++r+vvlP a p ++tgl+ ++g  +   +++e++g  pG+g+ +++++++  +  
  gi|313117423|ref|YP_004044406.1| 168 ESASRELMEVAETLGVdTDWRLIRRVVLPDATPELLTGLRTSVGQCWMMVIAAELFG-APGVGYEIITSSNNLATE- 242
                                       ***************9568**************************************.789************999. PP

                      BPD_transp_1 153 isnggvlalviavlllnlvadilqrlldprv 183
                                            ++a+ + + ++ lv+d+ +r l+ r+
  gi|313117423|ref|YP_004044406.1| 243 ----RSVAYMLTISAVFLVSDWGVRRLEARL 269
                                       ....889********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1741.85
//
Query:       gi|313117424|ref|YP_004044407.1|  [L=262]
Description: nitrate/sulfonate/bicarbonate ABC transporter ATPase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.3e-32  111.0   0.0    9.4e-32  110.4   0.0    1.3  1  ABC_tran     ABC transporter
    8.3e-06   25.8   0.0        0.1   12.4   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00063   20.2   0.0     0.0045   17.4   0.0    2.1  1  AAA          ATPase family associated with various cellular a
    0.00066   20.1   0.4    0.00088   19.7   0.4    1.6  1  AAA_16       AAA ATPase domain
     0.0018   18.6   0.2     0.0035   17.6   0.2    1.8  1  AAA_22       AAA domain
     0.0022   17.9   0.1     0.0037   17.2   0.1    1.3  1  RsgA_GTPase  RsgA GTPase
     0.0059   16.8   0.0      0.011   15.9   0.0    1.6  1  AAA_33       AAA domain
  ------ inclusion threshold ------
      0.017   15.4   0.4       0.53   10.5   0.0    2.5  3  AAA_28       AAA domain
      0.022   14.5   0.2       0.25   11.1   0.1    2.0  2  AAA_30       AAA domain
      0.043   14.0   0.0       0.12   12.7   0.0    1.7  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.05   13.2   0.1       0.44   10.1   0.1    2.1  2  AAA_25       AAA domain
      0.055   13.2   0.1       0.11   12.3   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.071   12.5   0.1        3.8    6.9   0.1    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.077   12.9   0.1       0.13   12.2   0.1    1.3  1  Rad17        Rad17 P-loop domain
      0.081   12.1   0.2       0.14   11.3   0.2    1.3  1  NB-ARC       NB-ARC domain
       0.11   13.0   0.5       0.18   12.3   0.5    1.3  1  AAA_23       AAA domain
       0.11   12.4   0.1       0.21   11.5   0.1    1.4  1  ATPase_2     ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.0   8.9e-35   9.4e-32       1     136 [.      32     171 ..      32     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 8.9e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l n+s+++  ge v +vG++G+GK+tL++l+ gl++pt+G +++dg+ ++       + + ++++qe++lfp ltvr
  gi|313117424|ref|YP_004044407.1|  32 LTNISFSVASGEFVTVVGPSGCGKTTLIRLVGGLESPTSGAVRVDGRTVSG-----PSPNRAMVFQEHRLFPWLTVR 103
                                       689********************************************9999.....888999*************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             +++e+ +++l+ +gl+e  d       + LSgG+kqrv laral+ +p++ll+DEp+
  gi|313117424|ref|YP_004044407.1| 104 ENiafglveagvperTRTERTDELLELVGLVEYSDMYP----TALSGGMKQRVGLARALAVDPDILLMDEPF 171
                                       ************99999999************777666....*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   9.8e-05       0.1       2      23 ..      45      66 ..      44      98 .. 0.73
   2 !   11.7   0.0   0.00016      0.17     235     298 ..     142     203 ..     104     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.8e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                        ++Gp g+GK++L+++  +l 
  gi|313117424|ref|YP_004044407.1| 45 VTVVGPSGCGKTTLIRLVGGLE 66
                                      679*************998883 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00016
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHS 298
                                       + lS G+k+  +l+ al+ ++   ++ll DEp  + + +  r+l  ell++ +++g  v+++TH+
  gi|313117424|ref|YP_004044407.1| 142 TALSGGMKQRVGLARALAVDP---DILLMDEPFGSVDAQTRRTLQgELLDIWRETGKTVLFVTHD 203
                                       56799***999*******999...9*************9999999777777777899*******8 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.2e-06    0.0045       2      98 ..      46     195 ..      45     221 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.2e-06
                                       EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS....................................... CS
                               AAA   2 llyGppGtGKTllakavakelg..vefleisgsellsk....................................... 37 
                                        ++Gp G+GKT+l++ v    +  +  ++++g ++                                          
  gi|313117424|ref|YP_004044407.1|  46 TVVGPSGCGKTTLIRLVGGLESptSGAVRVDGRTVSGPspnramvfqehrlfpwltvreniafglveagvpertrte 122
                                       689**************987322233445554444422344445555555555555555555555555666666666 PP

                                       .................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
                               AAA  38 .................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                                                        y  + +  +++ +  a++ a +p il++DE    + ++       +++++ +Ll  + + 
  gi|313117424|ref|YP_004044407.1| 123 rtdellelvglveysdmYPTALSGGMKQRVGLARALAvDPDILLMDEPFGSVDAQ------TRRTLQGELLDIWRET 193
                                       7777777777777777777777777777777777777778888888855554555......5666666666666655 PP

                                       TT CS
                               AAA  97 kk 98 
                                        k
  gi|313117424|ref|YP_004044407.1| 194 GK 195
                                       55 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.4   8.4e-07   0.00088      18      45 ..      38      63 ..      29     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.4e-07
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrell 45
                                      +v+sg  e v ++G+sG+GK++l+r + 
  gi|313117424|ref|YP_004044407.1| 38 SVASG--EFVTVVGPSGCGKTTLIRLVG 63
                                      45556..79***************9886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   3.4e-06    0.0035       6      29 ..      43      66 ..      39     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.4e-06
                            AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                       +++v+G+sG+GKTtl+r +    
  gi|313117424|ref|YP_004044407.1| 43 EFVTVVGPSGCGKTTLIRLVGGLE 66
                                      6899*************9987654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   3.5e-06    0.0037      72     121 ..      14      64 ..       2      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.5e-06
                                       HHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  72 lealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       le+++ +   ++ + +++l++++  +++ +++++vG+SG GK+tLi  + +
  gi|313117424|ref|YP_004044407.1|  14 LENVDKRYESTNGSGTDALTNISFSVASgEFVTVVGPSGCGKTTLIRLVGG 64 
                                       56666666666677778888999888877*****************87655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05     0.011       2      33 ..      45     110 ..      44     220 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                            AAA_33   2 vllvGlpGsGKstlaerl..lkklg..avllssdt..............................l 33 
                                       v +vG++G+GK+tl++ +  l+  +  av+++  t                              l
  gi|313117424|ref|YP_004044407.1|  45 VTVVGPSGCGKTTLIRLVggLESPTsgAVRVDGRTvsgpspnramvfqehrlfpwltvreniafgL 110
                                       679************988665444477888888776666666666666666655555555544441 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0005      0.53       2      18 ..      45      61 ..      44      97 .. 0.85
   2 ?    2.5   0.0      0.14   1.5e+02     130     162 ..     175     206 ..     151     207 .. 0.87
   3 ?   -2.8   0.0       6.2   6.5e+03     127     148 ..     236     257 ..     215     260 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                            AAA_28  2 ivitGgestGKTtllea 18
                                      + ++G++++GKTtl++ 
  gi|313117424|ref|YP_004044407.1| 45 VTVVGPSGCGKTTLIRL 61
                                      6799**********986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                            AAA_28 130 dleereaiderlrealrelgipviivpsgdvee 162
                                       d + r+ ++  l++++re g  v+ v + dvee
  gi|313117424|ref|YP_004044407.1| 175 DAQTRRTLQGELLDIWRETGKTVLFV-THDVEE 206
                                       667788889999**************.999997 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.2
                            AAA_28 127 Rredleereaiderlrealrel 148
                                       R+ + ee +a+++r++++l++ 
  gi|313117424|ref|YP_004044407.1| 236 RTGQREELAALETRVLDLLNKS 257
                                       4456677777888888887765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00023      0.25      15      39 ..      40      63 ..      33      90 .. 0.79
   2 ?    0.8   0.0      0.32   3.3e+02      37      66 ..     185     214 ..     180     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalr 39
                                      +sg+ +++++Gp G GKtt+++ + 
  gi|313117424|ref|YP_004044407.1| 40 ASGE-FVTVVGPSGCGKTTLIRLVG 63
                                      4554.899*************9875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.32
                            AAA_30  37 alreaweaaggrviglAptgkaAkvLaeel 66 
                                       +l ++w++ g++v+ +++  + A +L++ l
  gi|313117424|ref|YP_004044407.1| 185 ELLDIWRETGKTVLFVTHDVEEAVRLGDRL 214
                                       567899999999999999999999999866 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011      0.12      45      84 ..     143     182 ..     135     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                           SbcCD_C  45 alaaalaalyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                       al  ++ + ++ a++   +++++++DE F+++D+++++tl
  gi|313117424|ref|YP_004044407.1| 143 ALSGGMKQRVGLARALAVDPDILLMDEPFGSVDAQTRRTL 182
                                       56666777777766566789****************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00042      0.44      31      49 ..      40      58 ..      35      62 .. 0.90
   2 ?    0.6   0.0      0.34   3.6e+02     172     188 ..     186     202 ..     173     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                            AAA_25 31 pagelallaGapgtGKttl 49
                                      + ge++ ++G++g+GKttl
  gi|313117424|ref|YP_004044407.1| 40 ASGEFVTVVGPSGCGKTTL 58
                                      5699**************9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.34
                            AAA_25 172 leriarrtgaavllvhH 188
                                       l +i r+tg +vl+v H
  gi|313117424|ref|YP_004044407.1| 186 LLDIWRETGKTVLFVTH 202
                                       55566778888888877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1    0.0001      0.11      17      39 ..      35      59 ..      19      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            AAA_29 17 ieidlkg..atlltGpsGsGKSTll 39
                                      i++++++  ++ ++GpsG GK+Tl+
  gi|313117424|ref|YP_004044407.1| 35 ISFSVASgeFVTVVGPSGCGKTTLI 59
                                      455544436999************8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0036       3.8      24      41 ..      42      59 ..      32      63 .. 0.85
   2 ?    3.6   0.0     0.036        38     122     172 ..     129     175 ..     117     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0036
                                      SSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnll 41
                                       +f  +vGp G+GK+ l+
  gi|313117424|ref|YP_004044407.1| 42 GEFVTVVGPSGCGKTTLI 59
                                      57999**********987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.036
                                       HHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 122 evsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                       e+  l+e +++++++LSgG k+ v la  +A+    p  + l+De     D
  gi|313117424|ref|YP_004044407.1| 129 ELVGLVEYSDMYPTALSGGMKQRVGLARALAVD---PD-ILLMDEPFGSVD 175
                                       67778889999999************9999864...22.445555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012      0.13      47      64 ..      44      61 ..      29      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                             Rad17 47 iLLisGPsGCgkstvvkv 64
                                       + + GPsGCgk+t ++ 
  gi|313117424|ref|YP_004044407.1| 44 FVTVVGPSGCGKTTLIRL 61
                                      56789**********986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00013      0.14      21      38 ..      43      60 ..      31      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                      EEEEEEESTTSSHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlak 38
                                       +v++vG  G+GKttl++
  gi|313117424|ref|YP_004044407.1| 43 EFVTVVGPSGCGKTTLIR 60
                                      489*************86 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   0.00017      0.18      14      37 ..      34      60 ..      24      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                            AAA_23 14 eidF...skgltlItGpNGaGKTTild 37
                                      +i F   s  ++ ++Gp G+GKTT+++
  gi|313117424|ref|YP_004044407.1| 34 NISFsvaSGEFVTVVGPSGCGKTTLIR 60
                                      57787777788999***********97 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0002      0.21      21      38 ..      43      60 ..      31      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                          ATPase_2 21 eiyfiYGpegsGKtaLlk 38
                                      e++ + Gp g+GKt+L++
  gi|313117424|ref|YP_004044407.1| 43 EFVTVVGPSGCGKTTLIR 60
                                      678899**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1614.62
//
Query:       gi|313117425|ref|YP_004044408.1|  [L=560]
Description: acyl-CoA synthetase/AMP-acid ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-90  302.3   0.0    5.5e-90  302.0   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.3e-20   74.2   0.7    2.8e-20   73.0   0.7    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.0   0.0   6.1e-94   5.5e-90       6     421 ..      45     454 ..      40     456 .. 0.89

  Alignments for each domain:
  == domain 1  score: 302.0 bits;  conditional E-value: 6.1e-94
                                       HHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                       AMP-binding   6 aktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                       a+ +++val++   +ge +++T+ el +r++++A++L +lGv++gdrV  ++p+ pe++val+++lk Gav   +n 
  gi|313117425|ref|YP_004044408.1|  45 ATDRERVALYQvdtDGELTKMTFWELADRSSQFANVLDRLGVEQGDRVFSYMPRIPEHYVALIGTLKHGAVWGSVNE 121
                                       46678999977999999************************************************************ PP

                                       TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS- CS
                       AMP-binding  80 tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeel 156
                                       +++++ +ay l+d++akv++  + +++ e +++a ++ +av++vi +d+++ +  e++ +++  + ++ k+ e++e+
  gi|313117425|ref|YP_004044408.1| 122 RFGPDGIAYRLDDCDAKVVV--TTTDNRETVADALDDAPAVEHVITVDRGGGAPVEDVVFNTALDGAS-KEYEAAET 195
                                       ********************..65666678888888889999******99887777777777666555.47788899 PP

                                       BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEE CS
                       AMP-binding 157 kpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllallsGatvv 232
                                         +d a++ YTSGTTG  KGV +++r ++  +a++k   +  +l+++d ++s+ +l + +g  +++l+a ++G ++ 
  gi|313117425|ref|YP_004044408.1| 196 GGEDNALLYYTSGTTGLAKGVLHKQRWVAGVAATQK---YaVDLQPGDLYWSTGDLGWLTGA-INTLGAWFWGTSLF 268
                                       99***********************99877666643...4355789***************8.************** PP

                                       E-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHHHHH CS
                       AMP-binding 233 llpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlss.lrlvllggeplspellrffralf 307
                                        ++++  +dp+ +++l++++ vtv+++vP+++++l e ++ l+      d    lr++l+ gepls+ ++++ ++ +
  gi|313117425|ref|YP_004044408.1| 269 TYEGE--FDPTEWADLLDEFPVTVLFSVPTAYRMLREkEDVLD------DVDLdLRHALSIGEPLSAGVVEWGKENL 337
                                       99966..67999***********************99554454......66666*********************** PP

                                       TCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBTT-H CS
                       AMP-binding 308 geevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYlkkp 382
                                       g ++l++YG+TEt+ ++++ + ++ + ++gs Gkplpg+e+ ivD++tge +p+ge+Ge+  rg   + +  Y++kp
  gi|313117425|ref|YP_004044408.1| 338 GVTILDTYGQTETGNMIIN-NYPTMELRPGSMGKPLPGIEADIVDPDTGEVLPPGETGEIAERGDypCFFAEYWNKP 413
                                       ****************985.334455589***********************************8779********* PP

                                       HHHHHHEEET..CCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                       AMP-binding 383 eataeafdse..grwlrTGDlgrldedGyleivgRkkdlik 421
                                       e+ta  f+++  g+w+ +GDl++ dedGy+++ gR++d+i 
  gi|313117425|ref|YP_004044408.1| 414 EKTAACFVEGdsGEWYLSGDLAYKDEDGYFWFEGRADDVIL 454
                                       ********734456*************************96 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.7   3.2e-24   2.8e-20       1      76 []     464     542 ..     464     542 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 3.2e-24
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEs l +h+aVae aVv +p++ +G++++a+Vvl++g+e+   l+e++k +v++ l ++  p++++f delpkt +
  gi|313117425|ref|YP_004044408.1| 464 EVESSLGEHEAVAESAVVPKPHPERGNIVKAYVVLSEGTEPsesLKEDIKNKVKSDLSAHEYPREIEFRDELPKTVT 540
                                       8**********************************988533457********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|313117425|ref|YP_004044408.1| 541 GK 542
                                       *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3644.81
//
Query:       gi|313117426|ref|YP_004044409.1|  [L=941]
Description: aconitase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     1e-170  568.7   0.0   1.4e-170  568.3   0.0    1.2  1  Aconitase    Aconitase family (aconitate hydratase)
    8.3e-42  142.6   0.0    1.4e-41  141.9   0.0    1.4  1  Aconitase_C  Aconitase C-terminal domain
     0.0018   18.2   7.1      0.002   18.0   0.3    3.4  4  BAT          GAF and HTH_10 associated domain


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.3   0.0  2.3e-174  1.4e-170       4     461 .]      70     606 ..      57     606 .. 0.94

  Alignments for each domain:
  == domain 1  score: 568.3 bits;  conditional E-value: 2.3e-174
                         Aconitase   4 wdahlveeegiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealekn 75 
                                       w+  + ++e +++ p+rv+lqd tgv+a+vdlaa r++v r g++++ +++ +p dlvidhsv     g+ +a+ekn
  gi|313117426|ref|YP_004044409.1|  70 WKPDVPDTE-VPFSPSRVVLQDLTGVPAVVDLAALRSEVDRKGRDPTLVEPEIPCDLVIDHSVqvdyfGTGDAYEKN 145
                                       444434444.999*******************************************************9******** PP

                         Aconitase  76 ledefernkeryefLksaakaf.girvvppgqGIvHqvnlEy.............glalpgktvvgtDSHTtmiggl 138
                                       +e e+ern+ery+++k+a++af +++vvppg+GIvHqvnlE+             +++lp+ t+vgtDSHT+migg+
  gi|313117426|ref|YP_004044409.1| 146 VELEYERNAERYRAIKWAQNAFeNFNVVPPGTGIVHQVNLEHlgrvvhererdgaEWLLPD-TLVGTDSHTPMIGGI 221
                                       *************************************************9999777*****.*************** PP

                         Aconitase 139 GvlaiGvGgieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsle 215
                                       Gv+++GvGgieaea++lgqp+++k+p+vvgv+l+G+l++g+ta+Dlvl+++++lr  gvv+++vEffG+gve+Ls+ 
  gi|313117426|ref|YP_004044409.1| 222 GVVGWGVGGIEAEAAMLGQPITMKLPEVVGVRLDGELPDGATATDLVLHITEQLRDVGVVDRFVEFFGPGVENLSVP 298
                                       ***************************************************************************** PP

                         Aconitase 216 draTiaNMaaEvGAttglfpvdektleYLkatgreeaav.lveaydkaqalfelaadedaeydkvleldlstlepsv 291
                                       draTiaNMa+E G+t+++fpvde+tl+YL++tgr+++++  v++y +aq+lf    ++++ey++v+e+dlst+eps+
  gi|313117426|ref|YP_004044409.1| 299 DRATIANMAPEQGSTISVFPVDETTLDYLELTGRDPEHIeVVREYLEAQGLF---GEQEPEYTEVVEFDLSTVEPSL 372
                                       ***************************************999********88...57789***************** PP

                         Aconitase 292 agpkrPqdavplselvkkefkeele.................................................... 316
                                       ag krPqd++p+ ++vk++f++ ++                                                    
  gi|313117426|ref|YP_004044409.1| 373 AGHKRPQDRIPM-GDVKHSFRSLIHgefedelgdidedalrrwlgdgggataetdggdvetqargdvqlddsggtel 448
                                       ************.66665788777788889999****************************************9997 PP

                         Aconitase 317 .keaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaaglla.kavekglkvkpgvktsvaPGSevvkayl 391
                                          +++ ++e+ ++e+ ++ +g+v + ai+SCTN+sn++v++aaglla +ave+gl v ++vkts+aPGS+vv++yl
  gi|313117426|ref|YP_004044409.1| 449 gPLTKRVTVEL-DDEEIEIGHGDVLVSAITSCTNTSNPSVMMAAGLLArNAVERGLDVPSYVKTSLAPGSRVVTEYL 524
                                       64455555555.5679************************************************************* PP

                         Aconitase 392 eaeGlleiLekaGfevvgagCstCignsdrle........ege...aivsssNRNFegRqgpntra.yLaSPelvva 456
                                       ea+Gll++Lek+G++vvg+gC+tCign+++l+        +++   ++v+s+NRNFe+R++p+ ra yLaSP+lvva
  gi|313117426|ref|YP_004044409.1| 525 EASGLLDSLEKLGYDVVGYGCTTCIGNAGPLPdpieaaidTHDlwtTSVLSGNRNFEARIHPKIRAnYLASPPLVVA 601
                                       *******************************988877765444999******************************* PP

                         Aconitase 457 aAlaG 461
                                       + laG
  gi|313117426|ref|YP_004044409.1| 602 YGLAG 606
                                       ***98 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.9   0.0   2.4e-45   1.4e-41       5     129 ..     738     862 ..     734     864 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.9 bits;  conditional E-value: 2.4e-45
                                       CCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE-- CS
                       Aconitase_C   5 lklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviag 81 
                                       l+ +G+++++++ +++++++++++++gt+an++++n+++++++ + t++ ++ e++ v++a +ry++e+++lvv+ag
  gi|313117426|ref|YP_004044409.1| 738 LRDHGVEPHEFNTYGSRRGNHEVMMRGTFANVRIENQMLDDVEGGYTIHHPTDEQTTVYEASQRYREEEIPLVVLAG 814
                                       6779************************************************************************* PP

                                       SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
                       Aconitase_C  82 knfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefk 129
                                       ++fG+GSSR++AAk++ llG++a iaeS+erI+++nl+++g+Lpl+f+
  gi|313117426|ref|YP_004044409.1| 815 EEFGTGSSRDWAAKGTDLLGVRATIAESYERIYRDNLVGMGVLPLQFH 862
                                       **********************************************96 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.54   3.2e+03     110     139 ..     252     281 ..     250     283 .. 0.86
   2 ?   -3.0   0.0         1     6e+03      38      58 ..     320     340 ..     312     348 .. 0.78
   3 ?    2.3   0.0     0.023   1.4e+02      19      64 ..     603     647 ..     594     664 .. 0.88
   4 !   18.0   0.3   3.4e-07     0.002      48     100 ..     873     928 ..     867     931 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.54
                               BAT 110 arlvvevPpgadvRsvvealeerypdveLv 139
                                       +rl  e+P+ga +  +v  ++e+  dv +v
  gi|313117426|ref|YP_004044409.1| 252 VRLDGELPDGATATDLVLHITEQLRDVGVV 281
                                       678889***********9999999998777 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1
                               BAT  38 dgevlvfftvdgadpeevrda 58 
                                       d+++l +++++g dpe ++ +
  gi|313117426|ref|YP_004044409.1| 320 DETTLDYLELTGRDPEHIEVV 340
                                       789999999999999987654 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.023
                               BAT  19 alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedlda 64 
                                        la + d  +e e l +++ ge+++++ +   d++ev++a +d ++
  gi|313117426|ref|YP_004044409.1| 603 GLAGRMDIDLETEPLGTDESGEPVYLADIWP-DADEVQAAIHDSVS 647
                                       7999********************9999998.669***99998765 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 3.4e-07
                               BAT  48 dgadpeevrdaaedldavedvrvvseeddgtlleltvs...gpslastlaehGgtv 100
                                       dg+++ ++r +a+ ld +++++vv+e+ddg+++e+ v+   g++ a t+ ehGg +
  gi|313117426|ref|YP_004044409.1| 873 DGTEVFTIRGLADGLDVMDELTVVAERDDGSTVEFPVTaqvGTPAAVTYIEHGGIL 928
                                       77888899****************************98666667777*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 6365.52
//
Query:       gi|313117427|ref|YP_004044410.1|  [L=91]
Description: hypothetical protein Hbor_32170 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 621.81
//
Query:       gi|313117428|ref|YP_004044411.1|  [L=403]
Description: hypothetical protein Hbor_32180 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.22   11.4   0.0    1.4  1  RACo_linker  RACo linker region


Domain annotation for each model (and alignments):
>> RACo_linker  RACo linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.2e-05      0.22      36      71 ..     247     286 ..     242     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.2e-05
                       RACo_linker  36 eaLekqw..d..leidlsvLrkLpevLrkgnwkVtvalhe 71 
                                       e+L+++   d  +e+++ v + +p+ Lr+++w+V ++ + 
  gi|313117428|ref|YP_004044411.1| 247 EELAENSpdDceIEFQVDVPSSMPDSLREAQWTVNATKYV 286
                                       55666665324599999*******************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2596.54
//
Query:       gi|313117429|ref|YP_004044412.1|  [L=1039]
Description: PAS domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-38  131.6   8.6    2.3e-15   56.8   0.3    5.0  4  PAS_4         PAS fold
    3.3e-35  120.5   2.9      1e-16   60.9   0.1    3.8  3  PAS           PAS fold
    1.3e-27   96.0   0.3    1.3e-13   51.1   0.0    3.8  3  PAS_9         PAS domain
    3.6e-24   85.6   2.1    6.4e-12   45.9   0.1    4.8  5  GAF_2         GAF domain
    2.2e-18   65.8   0.1    9.1e-07   28.8   0.0    4.0  3  PAS_8         PAS domain
    1.5e-16   60.9   0.4    3.8e-16   59.6   0.4    1.7  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    1.1e-15   58.1   0.0    1.5e-07   31.8   0.0    4.3  5  GAF_3         GAF domain
      2e-15   57.6   0.0    3.6e-07   30.9   0.0    3.9  3  GAF           GAF domain
    8.2e-13   48.5   0.3    8.2e-13   48.5   0.3    3.0  3  Response_reg  Response regulator receiver domain
    4.2e-12   45.9   0.2    4.2e-12   45.9   0.2    3.6  3  HisKA         His Kinase A (phospho-acceptor) domain
    1.1e-05   25.6   0.1    0.00073   19.8   0.0    2.8  2  PAS_3         PAS fold
      0.001   19.3   0.6     0.0049   17.1   0.5    2.3  1  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain
     0.0077   16.4   1.3        0.5   10.5   0.0    4.2  5  PAS_7         PAS fold
     0.0092   15.6   0.0      0.059   13.0   0.0    2.3  3  PAS_12        UPF0242 C-terminal PAS-like domain
  ------ inclusion threshold ------
      0.025   14.4   0.0      0.066   13.0   0.0    1.7  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
        0.1   13.2   0.0       0.81   10.3   0.0    2.7  1  PAS_10        PAS domain
       0.56   10.3   3.2         19    5.4   0.1    3.5  3  GIT1_C        G protein-coupled receptor kinase-interacting p


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.3   2.2e-18   2.3e-15       1     110 []     149     251 ..     149     251 .. 0.95
   2 !   31.4   0.2   1.6e-10   1.7e-07       3     109 ..     265     382 ..     263     383 .. 0.82
   3 !   44.5   0.1   1.4e-14   1.5e-11       2     110 .]     565     673 ..     564     673 .. 0.94
   4 ?   -0.6   0.0       1.5   1.6e+03      35      72 ..     799     839 ..     788     865 .. 0.68

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.2e-18
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l+++ da++++d++ r++y+N+++a+ +g++pe+++G  l+e +p+  ++ le+++r ++e++epi+f+++l   + 
  gi|313117429|ref|YP_004044412.1| 149 LERTADAIYAVDTEWRIEYMNEQMADRVGRDPETVVGTVLWEEFPTITGTKLEEQYRTAMETGEPISFEQYLEE-PF 224
                                       67889************************************99***************************7777.** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       + ++ +r++P +d      g+ v+sr+iT++r+
  gi|313117429|ref|YP_004044412.1| 225 DYWVKVRAFPDED------GLTVFSREITDERE 251
                                       **********655......99********9985 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.6e-10
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee....daarleralrrvleg...eepiefleel 72 
                                       ++ d+++v+++dgr+++aN aaa+++ +++e+l  ++l  +++ +    da+++ +a+++ l++   +  ++ l   
  gi|313117429|ref|YP_004044412.1| 265 KIHDVVFVINEDGRIQFANSAAARVLERSRESLEEERLSGIVSSRvsdsDAREFKSAVTETLQEidgDGGVTGLYDF 341
                                       6789***********************************66666666669999999999999761113345555544 PP

                             PAS_4  73 ll......pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +l      + ++r++++rl+P+  +  +   vlv++rD+Te++
  gi|313117429|ref|YP_004044412.1| 342 DLqlglrvGTKRRVFDVRLTPFQSTMNR--QVLVVARDVTEQS 382
                                       4477779***************665555..***********86 PP

  == domain 3  score: 44.5 bits;  conditional E-value: 1.4e-14
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       ++ p  +  +d+dg vl +N+ a+++fg+++ee++G+    ++p+e + ++ ++ +++l+ge+    ++ + + +ge
  gi|313117429|ref|YP_004044412.1| 565 EAAPLTIMEIDRDGEVLLWNRGAEQMFGWSREEVVGEFNP-IVPKEGQSEFKQHRQQALRGERIRGKEIQRQTkDGE 640
                                       5677888899**************************9877.9*******************9998888888889999 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +  ++l++ P+ ++ Gev  +++++ D+Te++r
  gi|313117429|ref|YP_004044412.1| 641 RLDLLLSVAPITEAGGEVTSIIAVLDDTTEQKR 673
                                       999***************************986 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.5
                             PAS_4  35 llGktlaellpee...daarleralrrvlegeepiefleel 72 
                                        +G+++ e   +    ++a +e+al+r+ ++ee  ++ e l
  gi|313117429|ref|YP_004044412.1| 799 TVGQRYSETEVDLfriLGATVEAALARADREEELRRQNERL 839
                                       55555553222223447888888888888888877776655 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   2.3e-08   2.4e-05       2      79 ..     144     221 ..     143     238 .. 0.92
   2 !   33.6   0.2   3.1e-11   3.2e-08       2     113 .]     258     378 ..     257     378 .. 0.80
   3 !   60.9   0.1   9.6e-20     1e-16       2     112 ..     559     667 ..     558     668 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.3e-08
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++++ le ++d+i +vD   ri y+N+ +++  G ++e v+g  l +++++ +  +l e++++++e+ge+ + ++  
  gi|313117429|ref|YP_004044412.1| 144 RFQRTLERTADAIYAVDTEWRIEYMNEQMADRVGRDPETVVGTVLWEEFPTITGTKLEEQYRTAMETGEPISFEQYL 220
                                       7999************************************************999**************98888776 PP

                                       E CS
                               PAS  79 f 79 
                                       +
  gi|313117429|ref|YP_004044412.1| 221 E 221
                                       5 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 3.1e-11
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTH...HHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsr...eevlgkslldliheedda.elaelleqlleqgeesra 74 
                                       + +ail+ ++d +fv++edgri ++N+aa++ l  sr   ee   + ++ +++ ++da e+++++++ l++     +
  gi|313117429|ref|YP_004044412.1| 258 RNEAILQKIHDVVFVINEDGRIQFANSAAARVLERSReslEEERLSGIVSSRVSDSDArEFKSAVTETLQEIDGDGG 334
                                       679**********************************5444444444455666666668999999999887666666 PP

                                       CCEEEEC.......TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  75 geisfkl.......rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +    ++       +  + + ++vr +p+ +   +  ++l+v+rd+
  gi|313117429|ref|YP_004044412.1| 335 VTGLYDFdlqlglrVGTKRRVFDVRLTPFQSTMNR--QVLVVARDV 378
                                       66666666699998888888899999999999988..999999997 PP

  == domain 3  score: 60.9 bits;  conditional E-value: 9.6e-20
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +l++++e++p  i+ +D+dg++l++N+ ae+++G+sreev+g+   ++  e +     ++ +q+++ ge+ r++ei 
  gi|313117429|ref|YP_004044412.1| 559 RLESLIEAAPLTIMEIDRDGEVLLWNRGAEQMFGWSREEVVGEFNPIVPKEGQ--SEFKQHRQQALRGERIRGKEIQ 633
                                       789***************************************96665555555..59999***************** PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrd 112
                                       + ++dg+   l++ ++p+++agge++ ++ vl d
  gi|313117429|ref|YP_004044412.1| 634 RQTKDGERLDLLLSVAPITEAGGEVTSIIAVLDD 667
                                       ******************************9987 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.2e-05     0.024       4      90 ..     156     238 ..     153     248 .. 0.78
   2 !   25.8   0.0   9.1e-09   9.6e-06       2     104 .]     268     380 ..     267     380 .. 0.89
   3 !   51.1   0.0   1.2e-16   1.3e-13       4     104 .]     571     670 ..     568     670 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                       i  ++++ ri+y+Ne++++  G +pe v+g+ +++ f  +  +  +l++++++    e  +++ +    +e+f + +
  gi|313117429|ref|YP_004044412.1| 156 IYAVDTEWRIEYMNEQMADRVGRDPETVVGTVLWEEF--PTITGTKLEEQYRTAM--ETGEPISFEQYLEEPFDYWV 228
                                       444567779****************************..8888888888888888..88888888888888888888 PP

                             PAS_9  81 taspvkdddg 90 
                                       +++++ d+dg
  gi|313117429|ref|YP_004044412.1| 229 KVRAFPDEDG 238
                                       8888887763 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 9.1e-09
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrk........kerevevv 67 
                                       d ++++n+dgri +aN aa+r+l  s+e +   +++ ++   v+d++a+e+++a+ e++++          ++++++
  gi|313117429|ref|YP_004044412.1| 268 DVVFVINEDGRIQFANSAAARVLERSRESLEEERLSGIVssrVSDSDAREFKSAVTETLQEidgdggvtGLYDFDLQ 344
                                       5677788********************************9999999999999999999999999*****99999999 PP

                             PAS_9  68 lirkngetfwvl.ltaspvkdddgelvgiivilrDite 104
                                       l  + g++  v  ++++p++++ ++ v+  v+ rD+te
  gi|313117429|ref|YP_004044412.1| 345 LGLRVGTKRRVFdVRLTPFQSTMNRQVL--VVARDVTE 380
                                       9999998888777******988656666..9******8 PP

  == domain 3  score: 51.1 bits;  conditional E-value: 1.2e-16
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       i+ ++ dg++l +N++a++++G s+eev+g   ++ +   ++ +e ++  ++al+  r   r +e++ ++k+ge++ 
  gi|313117429|ref|YP_004044412.1| 571 IMEIDRDGEVLLWNRGAEQMFGWSREEVVG--EFNPIvpkEGQSEFKQHRQQALRGER--IRGKEIQRQTKDGERLD 643
                                       34367*************************..77777688888888888889999999..***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                        ll+++p+ +++ge+++ii++l D te
  gi|313117429|ref|YP_004044412.1| 644 LLLSVAPITEAGGEVTSIIAVLDDTTE 670
                                       *************************98 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.7   3.9e+03       3      31 ..     314     342 ..     312     397 .. 0.60
   2 !   32.6   0.0   7.9e-11   8.3e-08       3     134 ..     408     541 ..     406     544 .. 0.80
   3 ?    3.0   0.0      0.11   1.1e+02      95     136 ..     648     691 ..     616     693 .. 0.81
   4 !   45.9   0.1   6.1e-15   6.4e-12       1     137 [.     691     823 ..     691     824 .. 0.85
   5 ?   -1.7   0.0         3   3.2e+03       5      50 ..     943     996 ..     941    1018 .. 0.49

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHHHSS..EEEEEEE-TT CS
                             GAF_2   3 dleelldlvldelvelgaalgyillvddd 31 
                                       d +e+ ++v+++l+e++ + g+ +l+d d
  gi|313117429|ref|YP_004044412.1| 314 DAREFKSAVTETLQEIDGDGGVTGLYDFD 342
                                       56667778999999998899999998822 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 7.9e-11
                                       HHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B.---TTHHHHHHHHTS-EEES-.GGG CS
                             GAF_2   3 dleelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldr.plgeglvgealrtgrpvilnd.lee 76 
                                       + ++ l ++l+  +++ g ++g+i  +++d++  ++ + +++++  +  dr +l++  ++ ++++   + ++d + +
  gi|313117429|ref|YP_004044412.1| 408 STDDRLTELLEVGCQTtGLEIGIISKIEGDKY--TVRSVHTPDGSIETGDRfDLESTYCEVVVAQDSVCAFSDaISA 482
                                       567778899999999658**********9998..6655555555555555547777789999999888889997777 PP

                                       -S-HHHHHHHHHTT--EEEEEE-TTS---EEEEE..S......--HHHHHHHHHHHHHHH CS
                             GAF_2  77 dpdkkglpaghaglrsflavPlisegrvvGvlnl..yankppafdeedlelLeelaeqia 134
                                         +++++  ++  l s ++vPl+ +g+ +G ln+   ++++++f   +++++e+lae+++
  gi|313117429|ref|YP_004044412.1| 483 GKSSHPA-YQQFELESYIGVPLVVDGNRYGTLNFssPTTRESEFGTLERTFVELLAELVS 541
                                       4444444.59999***********99********543777777*************9986 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.11
                                       EEEE-T.TS---EEEEE..S......--HHHHHHHHHHHHHHHHH CS
                             GAF_2  95 avPlis.egrvvGvlnl..yankppafdeedlelLeelaeqiaia 136
                                       + P+++ +g+v  ++++   ++++ ++ e +l+ L+e a+q+++a
  gi|313117429|ref|YP_004044412.1| 648 VAPITEaGGEVTSIIAVldDTTEQKRL-ENQLRALQETAQQLSVA 691
                                       579*9999**99999996434444444.**************987 PP

  == domain 4  score: 45.9 bits;  conditional E-value: 6.1e-15
                                       HHHHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-.EEEE.EEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-G CS
                             GAF_2   1 aadleelldlvldelve.lgaalgyillvdddgg.lrla.awgeaeeefgaaldrplgeglvgealrtgrpvilndl 74 
                                       a++ ee+ d++++++v+ lg+++  i+ +dd+++ l+     + a+e+f+++++  +g++l++e++++++  +++d+
  gi|313117429|ref|YP_004044412.1| 691 ARSREEIGDIAVEAAVDvLGFDITGIWRHDDRENaLVPItETTAARERFSESPRFTPGDSLAWEVFESREIHVCDDV 767
                                       5899*************66*9966666666555534433788899999999998899***********988889999 PP

                                       GG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       e+   +++      +++s+++vPl   g  +G ++ +++  ++++e++++l++ l++++  a+
  gi|313117429|ref|YP_004044412.1| 768 ET---SSSVYNPNTQIKSEIYVPL---G-DHGLISTGSTVGQRYSETEVDLFRILGATVEAAL 823
                                       99...44444578***********...9.9*****************************9998 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHHS.S...EEEEEEE-TTS-EEEE......EEEES-TTSTT-S CS
                             GAF_2   5 eelldlvldelvel.gaa.lgyillvdddgglrla......awgeaeeefgaal 50 
                                       ++l++++++ +ve  g +    ++ +dd++g++++      ++ ++e+ f + +
  gi|313117429|ref|YP_004044412.1| 943 TQLFENLFRNAVEHgGTDvTITVGGLDDREGFYVEddgqgiSPERREDVFEHGV 996
                                       567777777777763344222444455555555444444443333333333333 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.017       2      53 ..     144     193 ..     143     208 .. 0.75
   2 !   17.1   0.0   3.8e-06     0.004       2      47 ..     258     300 ..     257     324 .. 0.74
   3 !   28.8   0.0   8.7e-10   9.1e-07       1      44 [.     558     602 ..     558     626 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg.qllpvlr 53 
                                       r++  +e  +d+i  vd+ +ri ++N+++++  G + + +     g +l+++++
  gi|313117429|ref|YP_004044412.1| 144 RFQRTLERTADAIYAVDTEWRIEYMNEQMADRVGRDpETVV----GtVLWEEFP 193
                                       89999999*********777**************3333333....444444443 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.8e-06
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgq 47 
                                       r +a++  ++d ++v+++++ri ++N aa++ l  s ++++e   +
  gi|313117429|ref|YP_004044412.1| 258 RNEAILQKIHDVVFVINEDGRIQFANSAAARVLERSRESLEE---E 300
                                       66899999*********8888************944333332...3 PP

  == domain 3  score: 28.8 bits;  conditional E-value: 8.7e-10
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgel 44 
                                       +rl++l+e++p  i+ +d+++ ++ +N+ a++++G+s +++ ge 
  gi|313117429|ref|YP_004044412.1| 558 QRLESLIEAAPLTIMEIDRDGEVLLWNRGAEQMFGWSrEEVVGEF 602
                                       79****************6666*************9966666543 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.4   3.6e-19   3.8e-16       2     107 ..     938    1036 ..     937    1039 .] 0.90

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 3.6e-19
                                        HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSH CS
                         HATPase_c    2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGl 76  
                                        +  rL+q++ nl  Nav++   ++++++++   +d+  + veD+G+Gi++e ++ +fe+ ++     +++ggtG+
  gi|313117429|ref|YP_004044412.1|  938 NAGRLTQLFENLFRNAVEH--GGTDVTITVGGLDDREGFYVEDDGQGISPERREDVFEHGVT-----SNKGGTGF 1005
                                        678***************9..67888888885458***********************7777.....699***** PP

                                        HHHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c   77 GlsivkklvelmgGeiwvesepgrGttftft 107 
                                        Glsiv  +++ +g +++v +  ++G +f+f+
  gi|313117429|ref|YP_004044412.1| 1006 GLSIVADIARAHGWTVSVAEGTDGGARFVFE 1036
                                        ******************99999*****996 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.66     7e+02      53      76 ..     200     223 ..     186     237 .. 0.83
   2 !   31.8   0.0   1.4e-10   1.5e-07       2     129 .]     409     546 ..     408     546 .. 0.87
   3 ?   -1.0   0.0         2   2.1e+03      93     125 ..     657     690 ..     613     691 .. 0.80
   4 !   19.4   0.0   9.5e-07     0.001       3     123 ..     695     819 ..     693     825 .. 0.87
   5 ?   -2.4   0.0       5.3   5.6e+03      99     128 ..     822     851 ..     821     852 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.66
                             GAF_3  53 dsalarralssgevvsepsfaeed 76 
                                        +  +r+a+++ge++s+ ++ ee+
  gi|313117429|ref|YP_004044412.1| 200 LEEQYRTAMETGEPISFEQYLEEP 223
                                       566789***********9998876 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.4e-10
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvse........p 70 
                                        d+ l +ll+ +++++g+e+g++   ++d+ +++ ++  dg+      +d +s  +  +++++ v ++         
  gi|313117429|ref|YP_004044412.1| 409 TDDRLTELLEVGCQTTGLEIGIISKIEGDKYTVRSVHTPDGSIETGDRFDLESTYCEVVVAQDSVCAFsdaisagkS 485
                                       68999****************************99999999999999***999999*99999999777444444433 PP

                             GAF_3  71 sfaeedglpdraalavPLvagr.qviGvlalastkpra..fdaedlelleslArqiataier 129
                                       s ++ +  ++++++ vPLv+ + + +G+l + s+ +r+  f+  ++ ++e lA +++++++r
  gi|313117429|ref|YP_004044412.1| 486 SHPAYQQFELESYIGVPLVV-DgNRYGTLNFSSPTTREseFGTLERTFVELLAELVSSELSR 546
                                       3355677888**********.66*********99988778******************9986 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2
                             GAF_3  93 qviGvlal.astkprafdaedlelleslArqiat 125
                                       +v  ++a+   t +++ ++ +l+ l++ A+q++ 
  gi|313117429|ref|YP_004044412.1| 657 EVTSIIAVlDDTTEQKRLENQLRALQETAQQLSV 690
                                       66667775367778889999**********9985 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 9.5e-07
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagw.dgkpalse..sldedsalarralssgevvsepsfae.. 74 
                                       +e+ +++++++v++lg+++  ++  d+++n l+++  +  + +++se   ++ +++la+++++s+e+++  +++   
  gi|313117429|ref|YP_004044412.1| 695 EEIGDIAVEAAVDVLGFDITGIWRHDDRENALVPITETtAARERFSEspRFTPGDSLAWEVFESREIHVCDDVETss 771
                                       688899****************9999999999999999899999*9965566**************98776655533 PP

                             GAF_3  75 ...edglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqi 123
                                           ++++  + ++vPL +     G++  +st ++ +++++++l++ l++ +
  gi|313117429|ref|YP_004044412.1| 772 svyNPNTQIKSEIYVPLGD----HGLISTGSTVGQRYSETEVDLFRILGATV 819
                                       333588*************....9***********************99865 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 5.3
                             GAF_3  99 alastkprafdaedlelleslArqiataie 128
                                       ala+ + ++ ++++ e l+++A+++a  + 
  gi|313117429|ref|YP_004044412.1| 822 ALARADREEELRRQNERLNEFASVVAHDLR 851
                                       57777888899999999******9997665 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   3.4e-10   3.6e-07       3     133 .]     410     544 ..     408     544 .. 0.75
   2 ?    3.7   0.0     0.087        92      92     132 ..     648     691 ..     621     691 .. 0.86
   3 !   18.2   0.0   2.8e-06    0.0029       2     133 .]     694     823 ..     693     823 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.4e-10
                                       HHHHHHHHHHHHHHHTESEEEEEEEEETTEEE..........CEEEEECCEEEETTSHHHHHHHHHSSSEEEST..G CS
                               GAF   3 eelldtvveelrellgadrvalylpdydGlhy..........dipqasrwlfmkngrgicgqvlatgqplvipd..s 67 
                                       ++ l +++e  ++++g++ +++ +   +G  y           i+ ++r+  + + +  c  v+a++ ++ ++d  s
  gi|313117429|ref|YP_004044412.1| 410 DDRLTELLEVGCQTTGLEIGIISK--IEGDKYtvrsvhtpdgSIETGDRF--DLESTY-CEVVVAQDSVCAFSDaiS 481
                                       667889999999**********88..445333344443333345556665..444445.777888788888888643 PP

                                       G...TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  68 t...pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvladqvaval 133
                                       +    +p ++q         ++  s+++vPlv+dg+ +G+l + +p++   +f + e+ +++ la++v+ +l
  gi|313117429|ref|YP_004044412.1| 482 AgksSHPAYQQ---------FELESYIGVPLVVDGNRYGTLNFSSPTTresEFGTLERTFVELLAELVSSEL 544
                                       35456666666.........*************************6666799***************99876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.087
                                       EEEEEE.TTEEEEEEEEEE..SSS.CSHHHHHHHHHHHHHHHHHH CS
                               GAF  92 vvPlvn.dgelwGllvlhn..psp.pftreelellqvladqvava 132
                                       v+P++  +ge+  ++++ +  + + + ++++l+ lq+ a+q++va
  gi|313117429|ref|YP_004044412.1| 648 VAPITEaGGEVTSIIAVLDdtT-EqKRLENQLRALQETAQQLSVA 691
                                       7899955999999999999642.3467***************997 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHHHHHHHHHHTESEEEEEEEEETTEEE......CEEEEECCEEEET...TSHHHHHHHHHSSSEEESTGG. CS
                               GAF   2 leelldtvveelrellgadrvalylpdydGlhy......dipqasrwlfmkn...grgicgqvlatgqplvipdst. 68 
                                       +ee+ d++ve + ++lg d   ++++d    ++       + +  r+++ +    g++++ +v++++++ v++d+  
  gi|313117429|ref|YP_004044412.1| 694 REEIGDIAVEAAVDVLGFDITGIWRHDDRE-NAlvpiteTTAARERFSESPRftpGDSLAWEVFESREIHVCDDVEt 769
                                       79999********************32222.123444333444555555555555777788****888888888542 PP

                                       TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  69 pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvaval 133
                                        ++ +++        n++i+s + vPl ++    Gl++  ++   ++++ e++l++ l++ v+ al
  gi|313117429|ref|YP_004044412.1| 770 SSSVYNP--------NTQIKSEIYVPLGDH----GLISTGSTVGqRYSETEVDLFRILGATVEAAL 823
                                       5555777........8************95....899999954457999*****999999999886 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.3   7.8e-16   8.2e-13       1     104 [.      11     115 ..      11     123 .. 0.89
   2 ?   -0.0   0.4      0.92   9.7e+02       3      51 ..     663     713 ..     661     714 .. 0.82
   3 ?   -1.1   0.1       1.9     2e+03      17      50 ..     899     930 ..     887     932 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 7.8e-16
                                       EEEESSSHHHHHHHHHHHHHTTEEEEE..EESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeeva..eaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl v  d+++ el+++ l +++  +++   a++++ a+e +  e++d++++  ++ + +G++l++ ir++d++lp++
  gi|313117429|ref|YP_004044412.1|  11 VLYVNTDEDFTELVQTKLCQADA-DIEfiHATNARTAVETVSVERIDCVVTAYSLADETGIDLTESIRQQDEDLPIV 86 
                                       67888999999999998885555.444449*********************************************** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-H CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdp 104
                                       ++t++++ee+a e  +ag+ d+++   d+
  gi|313117429|ref|YP_004044412.1|  87 LFTGQGSEEVASESTRAGITDYITIRTDR 115
                                       ***********************866655 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.92
                                       EESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEES CS
                      Response_reg   3 ivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDi 51 
                                        v Dd + ++ l+++l+  +e  ++  +a++ +e  +++ e +vd++  Di
  gi|313117429|ref|YP_004044412.1| 663 AVLDDTTEQKRLENQLRalQETAQQLSVARSREEIGDIAVEAAVDVLGFDI 713
                                       4556677777888888878888899********************998887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.9
                                       HHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEE CS
                      Response_reg  17 lleeegyeevaeaedgkealellkeekvdlillD 50 
                                       l+e  + e++  ++ ++ea+ ++++++  l ++D
  gi|313117429|ref|YP_004044412.1| 899 LIE--DTEQINLTDIATEAWGYVDTSQATLTVCD 930
                                       444..55669999**************9999999 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       3.5   3.7e+03      21      56 ..     534     565 ..     530     569 .. 0.50
   2 ?   -1.5   0.2       2.5   2.7e+03      33      52 ..     670     689 ..     658     691 .. 0.69
   3 !   45.9   0.2     4e-15   4.2e-12       2      66 ..     839     898 ..     838     899 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                                       HHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHH CS
                             HisKA  21 lgnaeaLkregklteelkeyletiesearrldhlve 56 
                                        + ae+ + e     +  +    +e+  +rl++l+e
  gi|313117429|ref|YP_004044412.1| 534 ELLAELVSSE----LSRDRSRTELEQTNQRLESLIE 565
                                       3333333331....2222255566666677777776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                                       -HSSCHHHHHHHHHHHHHHH CS
                             HisKA  33 lteelkeyletiesearrld 52 
                                          +l+ +l+ +++ a++l+
  gi|313117429|ref|YP_004044412.1| 670 EQKRLENQLRALQETAQQLS 689
                                       23567779999999999885 PP

  == domain 3  score: 45.9 bits;  conditional E-value: 4e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++f++ vaH+Lr+PL+  +g++e+ k+      +     e+ies   r+++l++dlL+l+r e+
  gi|313117429|ref|YP_004044412.1| 839 LNEFASVVAHDLRNPLTIASGFLEVVKE-----TDDPTHYEKIESAHSRIERLIDDLLTLARGET 898
                                       789*************************.....7888889*********************9875 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.13   1.4e+02       2      55 ..     166     217 ..     165     234 .. 0.79
   2 !   19.8   0.0   6.9e-07   0.00073       2      88 ..     581     664 ..     580     665 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyege 55 
                                        y++e++ + +G +pe + g+   w ++       +++e++ +a+++gep+++e
  gi|313117429|ref|YP_004044412.1| 166 EYMNEQMADRVGRDPETVVGT-VLWEEFPTITG-TKLEEQYRTAMETGEPISFE 217
                                       599******************.88888765554.66666666677777777666 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 6.9e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + +++  e+++G+s+ee+ g    +  +v  e +++++++ q+al++ +    e+++++kdGe   +  ++ +i   
  gi|313117429|ref|YP_004044412.1| 581 LLWNRGAEQMFGWSREEVVGE---FNPIVPKEGQSEFKQHRQQALRGERIRGKEIQRQTKDGERLDLLLSVAPITEA 654
                                       67*******************...889999999************666666999*********99999999999888 PP

                             PAS_3  79 ngkpvrvigv 88 
                                        g+++ +i+v
  gi|313117429|ref|YP_004044412.1| 655 GGEVTSIIAV 664
                                       8888888876 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.5   4.6e-06    0.0049      18      99 ..      35     118 ..      18     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
                        OKR_DC_1_N  18 fevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlreidgfie 91 
                                       +e + +t+   +++ ++   ri++vv +++   +   +l + ir+  edlP+ l++ + ++e ++    + i+ +i 
  gi|313117429|ref|YP_004044412.1|  35 IEFIHATNARTAVETVSV-ERIDCVVTAYSladETGIDLTESIRQQDEDLPIVLFTGQGSEEVASESTRAGITDYIT 110
                                       666777777777777776.8********999999999*******************988999889999999999999 PP

                        OKR_DC_1_N  92 lledtpef 99 
                                       +  d  +f
  gi|313117429|ref|YP_004044412.1| 111 IRTDRDNF 118
                                       97776665 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.3   3.4e+03       2      26 ..     150     174 ..     149     190 .. 0.80
   2 ?   -3.1   0.0       7.9   8.4e+03      69     114 ..     207     253 ..     195     254 .. 0.55
   3 ?    1.1   0.0      0.41   4.4e+02       1      35 [.     263     297 ..     263     332 .. 0.79
   4 !   10.5   0.0   0.00048       0.5       8      88 ..     571     642 ..     564     676 .. 0.58
   5 ?   -2.5   0.0       5.4   5.7e+03       7      53 ..     822     869 ..     818     892 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.3
                             PAS_7   2 enmsqGisvfDadlrLvawNrryle 26 
                                       e   ++i  +D + r+  +N+++ +
  gi|313117429|ref|YP_004044412.1| 150 ERTADAIYAVDTEWRIEYMNEQMAD 174
                                       667789999***********99876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.9
                             PAS_7  69 aaragkphsfererpdgrvievrgnplpd.gGfVttytDiTerrrae 114
                                       a+++g+p sfe+  ++     v+ ++ pd  G+ +   +iT++r+ +
  gi|313117429|ref|YP_004044412.1| 207 AMETGEPISFEQYLEEPFDYWVKVRAFPDeDGLTVFSREITDERERQ 253
                                       45556666666554444333444444444234444556788888776 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.41
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelv 35 
                                       l+++++ + v+++d+r+ + N+   ++l+ ++e +
  gi|313117429|ref|YP_004044412.1| 263 LQKIHDVVFVINEDGRIQFANSAAARVLERSRESL 297
                                       567888899*************9999998887766 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00048
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpd 84 
                                       i+ +D+d+++++wNr   +++++++e v vg +++ ++     + ef++++++a   +r+      + + ++r+++d
  gi|313117429|ref|YP_004044412.1| 571 IMEIDRDGEVLLWNRGAEQMFGWSREEV-VG-EFNPIVPKE-GQSEFKQHRQQALRGERI------RGKEIQRQTKD 638
                                       7789********************9988.33.344444433.333344333333333333......34455555555 PP

                             PAS_7  85 grvi 88 
                                       g+ +
  gi|313117429|ref|YP_004044412.1| 639 GERL 642
                                       5554 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 5.4
                             PAS_7   7 GisvfDadlrLvawNrrylelldlpeelvqvgvp.leellrynaerge 53 
                                       +++  D++++L+  N+r  e  ++ ++ ++   +  + +l++ +e+ +
  gi|313117429|ref|YP_004044412.1| 822 ALARADREEELRRQNERLNEFASVVAHDLRNPLTiASGFLEVVKETDD 869
                                       556668888888888888777776666665555523345555555555 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.4   2.5e+03      61      88 ..     156     184 ..     147     188 .. 0.79
   2 ?   -3.5   0.0       6.7     7e+03      63      88 ..     273     298 ..     266     308 .. 0.71
   3 !   13.0   0.0   5.6e-05     0.059      66     150 ..     577     664 ..     561     666 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.4
                            PAS_12  61 vys.qkenkllfaNaqirallGwssdkfl 88 
                                       +y+   e ++ ++N+q+ + +G  +++++
  gi|313117429|ref|YP_004044412.1| 156 IYAvDTEWRIEYMNEQMADRVGRDPETVV 184
                                       5552568899**********999999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.7
                            PAS_12  63 sqkenkllfaNaqirallGwssdkfl 88 
                                        + + ++ faN+   ++l  s + + 
  gi|313117429|ref|YP_004044412.1| 273 INEDGRIQFANSAAARVLERSRESLE 298
                                       45677999999998888877777765 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 5.6e-05
                            PAS_12  66 enkllfaNaqirallGwssdkflqdfseiv.qegleeWkralak.lsskteskirlvlKtKagqevllncllg.iip 139
                                       +  +l  N+  +++ Gws ++++ +f+ iv +eg  e+k++ ++ l  +  +  +++ +tK g+ + l   +  i +
  gi|313117429|ref|YP_004044412.1| 577 DGEVLLWNRGAEQMFGWSREEVVGEFNPIVpKEGQSEFKQHRQQaLRGERIRGKEIQRQTKDGERLDLLLSVApITE 653
                                       5679999***********************77999999998754155555566789999999999988777762445 PP

                            PAS_12 140 sGiFrnhvigv 150
                                        G   +++i+v
  gi|313117429|ref|YP_004044412.1| 654 AGGEVTSIIAV 664
                                       56666666666 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.2e-05     0.066      10      61 ..     949     999 ..     945    1019 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                       HATPase_c_3  10 lvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatssk 61 
                                       l +N+++   + v+i+v   + + + + +eDdG+G+s+e  +++++ + +s+
  gi|313117429|ref|YP_004044412.1| 949 LFRNAVEHGGTDVTITVGGLD-DREGFYVEDDGQGISPERREDVFEHGVTSN 999
                                       678999999999*****9975.789**************9888887666555 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00077      0.81       1      79 [.     560     640 ..     560     669 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00077
                            PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklipadvGrpladihpkkavknveeviealrtgek.devevvvp. 75 
                                       l+ l++++p+ ++ +D++ +++ +++ a+++f   +++v  + + i+pk+ ++++++  ++  +ge+   +e++++ 
  gi|313117429|ref|YP_004044412.1| 560 LESLIEAAPLTIMEIDRDGEVLLWNRGAEQMFGWSREEVVGEFNPIVPKEGQSEFKQHRQQALRGERiRGKEIQRQt 636
                                       6789999********************************9***************9999988888884445555544 PP

                            PAS_10  76 kngk 79 
                                       k+g+
  gi|313117429|ref|YP_004044412.1| 637 KDGE 640
                                       4443 PP

>> GIT1_C  G protein-coupled receptor kinase-interacting protein 1 C term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.088        92      13      33 ..     119     139 ..     112     169 .. 0.83
   2 ?    5.4   0.1     0.018        19      45      77 ..     658     690 ..     630     701 .. 0.87
   3 ?   -1.6   0.0       2.7   2.9e+03      29      68 ..     871     911 ..     856     916 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.088
                            GIT1_C  13 eqitkriqeLlqaaqeekkes 33 
                                       e+++ riq+L+qaa+e++  +
  gi|313117429|ref|YP_004044412.1| 119 ELLVHRIQTLVQAARERRAAE 139
                                       78999**********988654 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                            GIT1_C  45 VqdlvalfpenlseetlrtaLkqLtssaerLqe 77 
                                       V++++a+  ++++++ l+++L++L++ a++L +
  gi|313117429|ref|YP_004044412.1| 658 VTSIIAVLDDTTEQKRLENQLRALQETAQQLSV 690
                                       999***************************975 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.7
                            GIT1_C  29 ekkesfvpcaerIqsaVqdlvalfpenlseetlrt.aLkqL 68 
                                       ++ e++ +  +rI++ ++dl++l   ++  e+ ++  L+++
  gi|313117429|ref|YP_004044412.1| 871 THYEKIESAHSRIERLIDDLLTLARGETLIEDTEQiNLTDI 911
                                       45567777788999999999999875444444444356555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1039 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.86u 0.34s 00:00:01.20 Elapsed: 00:00:00.48
# Mc/sec: 6521.38
//
Query:       gi|313117430|ref|YP_004044413.1|  [L=530]
Description: transporter, NhaC family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-64  217.5  24.6    3.4e-64  217.0   5.6    2.3  2  Na_H_antiporter  Na+/H+ antiporter family
  ------ inclusion threshold ------
      0.038   13.6   0.2      0.038   13.6   0.2    2.1  2  SseC             Secretion system effector C (SseC) like fami
       0.49   10.2   3.0        1.7    8.4   0.1    3.2  2  DUF4516          Domain of unknown function (DUF4516)


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0  10.3    0.0005         3     111     248 ..      16     151 ..       3     158 .. 0.76
   2 !  217.0   5.6   5.7e-68   3.4e-64       7     297 ..     163     475 ..     157     481 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0005
                   Na_H_antiporter 111 afivalafqntdvatalvvgalaglivatllela.....slseidkllnrGiksmlgaililllAwgiggvlealgv 182
                                       a+++   + + +v+ +l++g+++g ++ ++ + +     sl+ + +++++ ++s l +++  l ++ +g+++   g 
  gi|313117430|ref|YP_004044413.1|  16 AIVMT--LVSRQVLLSLFTGIWIGATILVGWNPIegaahSLQMVINSVTASFNSKL-LLFTFLSGAMLGMIFLSGG- 88 
                                       22222..55667999***************99999744444444444444444443.3444555666788888888. PP

                   Na_H_antiporter 183 teslvsslakgvvskgllplilflvallvafatGtswgtigIilpiavplaaklgisllalvrave 248
                                        ++l + + +++++++ + l + ++++l+ +    s+++  I++ +++p+ ++++is+  l+ ++ 
  gi|313117430|ref|YP_004044413.1|  89 MSALAQRIISRIQTRKQAELGTGILGMLIFV---DSYASTMITGSVMRPITDQFDISREKLAYLLD 151
                                       ****************************977...9***********************88776655 PP

  == domain 2  score: 217.0 bits;  conditional E-value: 5.7e-68
                   Na_H_antiporter   7 kssplsdtvgliagilktdlieeiaalgmlvqsipanvysifallvvglvvlllrdigamlraeaear......... 74 
                                       +s++++++vgli   ++++     +a+ +++qsip+++ys++a+++v++++    d+g+m++ae++a          
  gi|313117430|ref|YP_004044413.1| 163 VSTWVGFEVGLIRDQINSISSIDQSAFMVFLQSIPFRFYSLLAVTLVFILIVMDWDFGPMKQAEKRAKeegkvlgdd 239
                                       79***********999887655555699***************************************9999999998 PP

                   Na_H_antiporter  75 .....eleekeltk............lpiavliiltlskmpytgalalvaivkafivalafqntdvatalvvgalag 134
                                            e  e+++              +pi+ l+++t ++ +y g+      +ka + a  ++++  a+a+++g +++
  gi|313117430|ref|YP_004044413.1| 240 adpliETREEDIDTpdhvdprwwyfaVPIVSLVAVTGFGLLYSGGWP----SKAPVEA--LKGAATADAILWGVFSA 310
                                       88877444444444666778888888*******************99....5444433..58888899999998865 PP

                   Na_H_antiporter 135 ..livatllela..slseidkllnrGiksmlgaililllAwgiggvlealgvteslvsslakgvvskgllplilflv 207
                                         l+ a+l++ a  +l+e+ +++ +G+k++++ +++l lAw+ig+v ealg ++ +v s+++g++++ +lp+++f++
  gi|313117430|ref|YP_004044413.1| 311 caLLLAILVGHArvELEEVSDSIFEGFKMVMFPVAVLSLAWTIGSVSEALG-VGPYVVSISQGIITAPMLPAVVFIS 386
                                       11444444444468*************************************.************************* PP

                   Na_H_antiporter 208 allvafatGtswgtigIilpiavplaaklgisllalvraveaggtlgdhlsPisdttilsstglnadhidhvsytql 284
                                       a++++fa+Gtswgt+gI+ p+avpla++lg  l+   +a+++g+ +gdh+sPisdtt++ss++++adh+dhv+ tq+
  gi|313117430|ref|YP_004044413.1| 387 AAIISFAIGTSWGTMGIMFPVAVPLAVQLGAPLPGATGAILTGSLFGDHCSPISDTTVMSSMFAGADHVDHVN-TQI 462
                                       *************************************************************************.*** PP

                   Na_H_antiporter 285 pyallvapitail 297
                                       pyall  ++++ l
  gi|313117430|ref|YP_004044413.1| 463 PYALLCGVVATGL 475
                                       ****988554433 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   6.4e-06     0.038     102     180 ..      76     156 ..      28     164 .. 0.79
   2 ?   -4.8   4.8       2.5   1.5e+04      68     151 ..     388     508 ..     381     515 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-06
                              SseC 102 adevvaaattkslideemqpimdvv...dkaqlageivgavvaavavvaavvavgsaakgaaaavksgaaklaeava 175
                                        +++  ++     +++ +q i+  +   ++a+l++ i+g+++ +v+  a  +++gs++  ++++++ + +kla  + 
  gi|313117430|ref|YP_004044413.1|  76 SGAMLGMIFLSGGMSALAQRIISRIqtrKQAELGTGILGMLI-FVDSYASTMITGSVMRPITDQFDISREKLAYLLD 151
                                       45555666666677777799999999**************65.********************99888999888777 PP

                              SseC 176 eaigk 180
                                       ++++ 
  gi|313117430|ref|YP_004044413.1| 152 STTSP 156
                                       77765 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 2.5
                              SseC  68 aivsvvagalkvgaslll.aavgvAgglmdaalgiadevvaaattkslideemqpimdvv................. 126
                                       ai+s+ +g+  +  + +  +av +A     +++   ++  a  t+ sl +  + pi+d +                 
  gi|313117430|ref|YP_004044413.1| 388 AIISFAIGTSWGTMGIMFpVAVPLA---VQLGAPLPGATGAILTG-SLFGDHCSPISDTTvmssmfagadhvdhvnt 460
                                       5667777777777777776666666...33345566666666666.7777777888888888888888855555555 PP

                              SseC 127 .......................dkaqlageivgavvaavavvaavva 151
                                                              +++ + g  vg +v++va vaa ++
  gi|313117430|ref|YP_004044413.1| 461 qipyallcgvvatglflaggygvSSLTVFGYTVGPLVLLVAGVAALFV 508
                                       555556666666666666666666666666666666666666665555 PP

>> DUF4516  Domain of unknown function (DUF4516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.5      0.14   8.1e+02      12      26 ..     383     397 ..     376     412 .. 0.76
   2 ?    8.4   0.1   0.00029       1.7      15      28 ..     442     455 ..     441     458 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                           DUF4516  12 kfvtasllsMlaGAq 26 
                                        f++a+++s ++G +
  gi|313117430|ref|YP_004044413.1| 383 VFISAAIISFAIGTS 397
                                       577788888887754 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00029
                           DUF4516  15 tasllsMlaGAqvV 28 
                                       t++++sM+aGA  V
  gi|313117430|ref|YP_004044413.1| 442 TTVMSSMFAGADHV 455
                                       689********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3388.68
//
Query:       gi|313117431|ref|YP_004044414.1|  [L=92]
Description: hypothetical protein Hbor_32210 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.015   15.1   0.1    1.1  1  TAT_signal   TAT (twin-arginine translocation) pathway signal
       0.12   11.7   4.2       0.12   11.8   4.2    1.0  1  SDA1         SDA1
       0.16   10.2   5.1       0.16   10.2   5.1    1.0  1  Nop14        Nop14-like family
       0.98    9.4   8.2        1.2    9.1   8.2    1.1  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)
        1.8    6.6  13.8          2    6.4  13.8    1.0  1  DNA_pol_phi  DNA polymerase phi
        5.9    6.6   9.2        7.2    6.3   9.2    1.1  1  DUF4637      Domain of unknown function (DUF4637)
        6.1    5.9  12.5        6.8    5.7  12.5    1.1  1  DUF2457      Protein of unknown function (DUF2457)
        9.2    4.4   6.9         10    4.3   6.9    1.0  1  CDC45        CDC45-like protein


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   6.7e-06     0.015       3      25 ..       9      31 ..       8      32 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.7e-06
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      +RR++L+g +++  +++l gca+
  gi|313117431|ref|YP_004044414.1|  9 DRRSLLRGIGVTLLGVGLSGCAG 31
                                      6********************98 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.2   5.3e-05      0.12      93     137 ..      34      71 ..       8      85 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.3e-05
                              SDA1  93 edsddeddeedwevesdddseedseggwidvesdeeeieesdese 137
                                       ++++ e+de+d ev+++ d e++ eg+       e++++ +d +e
  gi|313117431|ref|YP_004044414.1|  34 DEENGEEDENDGEVDDEADGENEGEGD-------EDRESGDDGEE 71 
                                       112223333333333332222222222.......11111111111 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.1     7e-05      0.16     343     386 ..      33      72 ..       8      85 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7e-05
                             Nop14 343 taeeeeeededdfeedddlveseseeeeeeeeedeeeeedeeee 386
                                        +ee++eede+d e dd+++ +++     e +ed e+ +d eee
  gi|313117431|ref|YP_004044414.1|  33 DDEENGEEDENDGEVDDEADGENEG----EGDEDRESGDDGEEE 72 
                                       2222344444444444411111111....111111111111111 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   8.2   0.00053       1.2      45      98 ..      27      81 ..      15      88 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00053
                       Trypan_PARP 45 kgtkvsdddtngtdpepepepepepepepepepepetepeeepepepe.pepepe 98
                                       g    dd+ ng + e + e + e + e e e +++ e  +++e+e +  +p pe
  gi|313117431|ref|YP_004044414.1| 27 SGCAGPDDEENGEEDENDGEVDDEADGENEGEGDEDRESGDDGEEEDGrVNPLPE 81
                                      5667778999999888888888888888887777777776666666541344444 PP

>> DNA_pol_phi  DNA polymerase phi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  13.8   0.00089         2     642     682 ..      33      75 ..      26      88 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00089
                       DNA_pol_phi 642 dedeeddeeeeeeddeededseedddeeesdedee..dedded 682
                                       d++e  +e+e++ + +++ d e++ + +e+ e  +  +e+d+ 
  gi|313117431|ref|YP_004044414.1|  33 DDEENGEEDENDGEVDDEADGENEGEGDEDRESGDdgEEEDGR 75 
                                       3333334444444444444444333333333333311444444 PP

>> DUF4637  Domain of unknown function (DUF4637)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   9.2    0.0032       7.2      18      59 ..      33      74 ..      28      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0032
                           DUF4637 18 eeeeaeeeseeedeeedraeeesaaegeeesreaeeaegrek 59
                                      ++ee+ ee+e++ e +d+a+ e++ eg+e++++ +++e ++ 
  gi|313117431|ref|YP_004044414.1| 33 DDEENGEEDENDGEVDDEADGENEGEGDEDRESGDDGEEEDG 74
                                      456666777777777788999999999988888888877654 PP

>> DUF2457  Protein of unknown function (DUF2457)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  12.5    0.0031       6.8      47      83 ..      35      71 ..      23      86 .. 0.44

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0031
                           DUF2457 47 eeEaeeeeeeeeddeedeeddddddddedddedddee 83
                                      ee  ee+e++ e d+e + +++ + d++ +  dd ee
  gi|313117431|ref|YP_004044414.1| 35 EENGEEDENDGEVDDEADGENEGEGDEDRESGDDGEE 71
                                      3333333333333333222222222222222222111 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   6.9    0.0046        10     142     183 ..      34      75 ..      27      91 .. 0.45

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0046
                             CDC45 142 eddddeeeeeeeeedeedeeedeeeskkkrksksdeeeesdd 183
                                       ++++ ee+e++ e d+e + e+e e +++r+s +d eee+ +
  gi|313117431|ref|YP_004044414.1|  34 DEENGEEDENDGEVDDEADGENEGEGDEDRESGDDGEEEDGR 75 
                                       222223333333333333333333334444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 614.76
//
Query:       gi|313117432|ref|YP_004044415.1|  [L=286]
Description: dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-36  126.0   2.5    2.5e-36  125.4   2.5    1.2  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    6.1e-32  110.7   1.5    7.4e-32  110.4   1.5    1.1  1  adh_short      short chain dehydrogenase
    0.00011   22.2   2.0    0.00024   21.1   2.0    1.6  1  KR             KR domain
     0.0011   18.5   0.6     0.0015   18.0   0.2    1.4  2  Epimerase      NAD dependent epimerase/dehydratase family
      0.003   17.0   0.2      0.004   16.6   0.2    1.1  1  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
  ------ inclusion threshold ------
       0.06   13.8   0.3       0.19   12.2   0.3    1.8  1  MCR_alpha      Methyl-coenzyme M reductase alpha subunit, C-t
       0.55    9.3   2.3       0.76    8.8   2.3    1.1  1  RmlD_sub_bind  RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   2.5   9.7e-40   2.5e-36       1     234 []      35     282 ..      35     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 9.7e-40
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE..E..EE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae..v..lecDVtdeeqvealveevvekfgklDil 73 
                                       GaasgIG+a+A ala++G +v+ +d+++++  ++ +la+++  +  +  + +D td+++vea++e ++++ g+l ++
  gi|313117432|ref|YP_004044415.1|  35 GAASGIGQATAVALAANGLSVIGADIDDDGLTETVDLADDIAVAgtIhpVTTDLTDDADVEAMIEVAADQ-GELRYV 110
                                       9*****************************8899999999996655589***************977766.9***** PP

                                       EE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC....CEEEEEEEGGGTSBSTTTTHHHHHHH CS
                      adh_short_C2  74 vnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg....gsivnlssvgaervvpnynaygaaKa 146
                                        n ag+ +   +++ e++ e++d ++d+ l++ fl+ak a+p+++++    g+i n+ssv+++ ++++  ay +aK+
  gi|313117432|ref|YP_004044415.1| 111 ANIAGMQHI--ASIPEFPMEKYDFIVDIMLRAPFLTAKLAMPHIRATddgvGAIANMSSVHGHYATQDKPAYITAKH 185
                                       *******99..*******************************66655567*************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEE--BHCTG.GGGSTT.HHH.........HHHHHHHHSTTSS-B-HHHHHHHHH CS
                      adh_short_C2 147 alealtrylAvelgpkgiRvNavspgpikTla.asgikg.fde.........lleelearaplgrlgtpeevaeaal 212
                                       +le+ltr++A+e      R  +vs g++ T++ +++i+g + +         +++ +  +a  ++++tp eva++ +
  gi|313117432|ref|YP_004044415.1| 186 GLEGLTRAIAAEGEG-TLRGFSVSVGYVLTPLmVNQIEGtA-DergiskrevVEDVMLGQARTKEMMTPAEVANLFV 260
                                       ************777.9*************87677777741.223333333477778888999999*********** PP

                                       HHCSGGGTT--SEEEEESTTGG CS
                      adh_short_C2 213 fLasdeasyitGqtlvvDgGlt 234
                                       f +s + +  +G ++  DgG+t
  gi|313117432|ref|YP_004044415.1| 261 FGFSGHGKHLNGGDMLWDGGYT 282
                                       *********************8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   1.5   2.9e-35   7.4e-32       2     190 ..      30     220 ..      29     225 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 2.9e-35
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklg 76 
                                       +++vtGa+sGIG+a+a +la++G +v+ +d+ ++ l e+++   +   + +++++++D+td ++vea++e a ++ g
  gi|313117432|ref|YP_004044415.1|  30 TAVVTGAASGIGQATAVALAANGLSVIGADIDDDGLTETVDLADDIavAGTIHPVTTDLTDDADVEAMIEVA-ADQG 105
                                       79****************************************999999999******************988.777* PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH..HCTTEEEEEEEEGGGTSB-TTBHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml..kqssGrIvnvsSvagkvpvagvaaYsA 151
                                       +l  + n AG+++ +++ e+  e+++ ++++ l ++fl++++++p++   +   G+I n+sSv+g+++    +aY +
  gi|313117432|ref|YP_004044415.1| 106 ELRYVANIAGMQHIASIPEFPMEKYDFIVDIMLRAPFLTAKLAMPHIRatDDGVGAIANMSSVHGHYATQDKPAYIT 182
                                       **********************************************8888999************************ PP

                                       HHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 152 sKaavagltrslakelaptgirvnavaPGlvdTdmakel 190
                                       +K++++gltr++a e + t  r  +v  G+v T+++ ++
  gi|313117432|ref|YP_004044415.1| 183 AKHGLEGLTRAIAAEGEGT-LRGFSVSVGYVLTPLMVNQ 220
                                       ***************9998.9999999999999987665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.0   9.4e-08   0.00024       2     168 ..      30     199 ..      29     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.4e-08
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-..EEEE----TT-HHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga..evevvaaDvsdkdavealleeik 76 
                                       t ++tG++ g+G+++a  la++g +   +++ +   d+  +++++   +  +  +++ v  D++d ++vea++e + 
  gi|313117432|ref|YP_004044415.1|  30 TAVVTGAASGIGQATAVALAANGLS---VIGAD-IDDDGLTETVDLADDIAVagTIHPVTTDLTDDADVEAMIEVAA 102
                                       679*****************99955...66666.444444445555555444558******************9886 PP

                                       HHSS---EEEE---------TTT--HHHHHHHH.....TTTTHHHHHHHHHTTT.S--SEEEEEEEHHHHH--TT-H CS
                                KR  77 aeeppikGvihaAgvlrdklleemtaedleqvl.....apKvkGawnLhelled.esldffvlfSSiagllgsagqa 147
                                        ++++++ v + Ag+ + + + e  +e+++ ++     ap +++   + ++ +  + +  +  +SS+ g + ++ + 
  gi|313117432|ref|YP_004044415.1| 103 -DQGELRYVANIAGMQHIASIPEFPMEKYDFIVdimlrAPFLTAKLAMPHIRATdDGVGAIANMSSVHGHYATQDKP 178
                                       .6679999999999999999988888877654411122445555555544433336677777777777777777777 PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                                KR 148 nYaaaNaflDalaeyrrsqgl 168
                                       +Y +a + l++l +  +++g+
  gi|313117432|ref|YP_004044415.1| 179 AYITAKHGLEGLTRAIAAEGE 199
                                       777777777777777666664 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2     6e-07    0.0015       2      78 ..      32     120 ..      31     139 .. 0.80
   2 ?   -3.9   0.0       2.9   7.4e+03     140     160 ..     178     198 ..     166     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6e-07
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..........EEEE--TT-HH...HHHHHHHHH.T CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl..........elveldltdrs...alerlfkee.q 64 
                                       +VtGa+  iG+a++ al+++g  vig d + ++  +    dl          + v+ dltd++   a+ ++ +++ +
  gi|313117432|ref|YP_004044415.1|  32 VVTGAASGIGQATAVALAANGLSVIGADIDDDGLTETV--DLaddiavagtiHPVTTDLTDDAdveAMIEVAADQgE 106
                                       8*************************999944433322..2245789***99999******9955555566667778 PP

                                       -SEEEE--S---HH CS
                         Epimerase  65 pdavihlAavggva 78 
                                         +v ++A+ +++a
  gi|313117432|ref|YP_004044415.1| 107 LRYVANIAGMQHIA 120
                                       99999999988876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.9
                                       SHHHHHHHHHHHHHHHHHHHH CS
                         Epimerase 140 spYaaaKlageklveayaaqy 160
                                        +Y  aK+  e l++a+aa++
  gi|313117432|ref|YP_004044415.1| 178 PAYITAKHGLEGLTRAIAAEG 198
                                       568888988888888888776 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   1.5e-06     0.004       2     100 ..      33     131 ..      32     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.... CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.... 74 
                                       +TG a  iG+ +a  L ++g  v+g + +++   t++++ la+d    + ++++ +  DltD + +e +++ +    
  gi|313117432|ref|YP_004044415.1|  33 VTGAASGIGQATAVALAANGLSVIGADIDDDG-LTETVD-LADDI--AVAGTIHPVTTDLTDDADVEAMIEVAadqg 105
                                       9************************8766554.556665.56654..4789****************9997654445 PP

                                       T-SEEEE--S---HHHHTTSHHHHHH CS
                     GDP_Man_Dehyd  75 qpdevynLAAqshVdvsfekPeytae 100
                                       + + v n A++ h++   e P + ++
  gi|313117432|ref|YP_004044415.1| 106 ELRYVANIAGMQHIASIPEFPMEKYD 131
                                       899***********988888877665 PP

>> MCR_alpha  Methyl-coenzyme M reductase alpha subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   7.5e-05      0.19      78     111 ..      20      54 ..      14      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                         MCR_alpha  78 led.hfGGsqraavlaaaagistalatgnsnaGln 111
                                       led hfG    a v+ aa+gi+ a a + + +Gl+
  gi|313117432|ref|YP_004044415.1|  20 LEDpHFGPETTAVVTGAASGIGQATAVALAANGLS 54 
                                       55559***************************997 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.3    0.0003      0.76       3      87 ..      31     121 ..      29     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0003
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHH CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre......eldltdaeavaellkeakpdvvvnaAAytavDkaEseeea 73 
                                        +vtGa   +G++ a +la++gl+v++ + +      ++dl+d  ava +++ +  d+  +a     +  a ++ e+
  gi|313117432|ref|YP_004044415.1|  31 AVVTGAASGIGQATAVALAANGLSVIGADIDddglteTVDLADDIAVAGTIHPVTTDLTDDADVEAMIEVAADQGEL 107
                                       589*************************888889999**************************************** PP

                                       HHHHHTHHHHHHHH CS
                     RmlD_sub_bind  74 ayavnaeavealAe 87 
                                       +y +n  + +++A 
  gi|313117432|ref|YP_004044415.1| 108 RYVANIAGMQHIAS 121
                                       ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1756.65
//
Query:       gi|313117433|ref|YP_004044416.1|  [L=321]
Description: alpha/beta hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-15   57.9   2.5      3e-14   53.7   2.5    2.2  1  Patatin   Patatin-like phospholipase


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   2.5   1.7e-18     3e-14       2     203 ..      12     207 ..      11     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1.7e-18
                           Patatin   2 vlsGGGsrgafslgalkaL..kkelgerfdiisGtSaGAiialllalg...rdpaalvddlrnlllnkifdrdl... 70 
                                       + +GGGs  af++g+lk L  +++  + +  isGtS+GA++al+  +g    d++++ + l++++++ ++d  +   
  gi|313117433|ref|YP_004044416.1|  12 ACQGGGSHTAFTAGVLKGLlrEWNNDHELVGISGTSGGAFNALAAWYGlvtADADRSIELLDAFWSDIAADTATdki 88 
                                       568***************779*********************55555577778888888888899888888887888 PP

                           Patatin  71 .......lirelaan.laarlsgllgkgglfdaealrellrkvladktlkrl.sarlgklpllkslftanqavpait 138
                                              + r ++++ + ++ls + ++g+ +  e +re+l+++++++++ +l  ++++ l                 
  gi|313117433|ref|YP_004044416.1|  89 tndwvvgMFRLESNGfPLPQLSPYQTPGSDLGKERIREILERHIDFDEIPDLcDRDAPDL----------------- 148
                                       888888744444444144566777777777777788888888887777665413334444................. PP

                           Patatin 139 tataatastanranglytedddddvdla.davraSsafPglfppvsldgelyvDGGilsNvPilaa 203
                                                ++ + ++   ++ +d+++  +av+aS+a+P +f++v++++   +DG ++ N Pi+ +
  gi|313117433|ref|YP_004044416.1| 149 -------VIGTVNINAGKFETFNDENVTpQAVLASAAVPNFFEAVEINDHFHWDGLFSQNPPIHDL 207
                                       .......55677777777777777777537********************99***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2047.03
//
Query:       gi|313117434|ref|YP_004044417.1|  [L=453]
Description: pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-53  181.7   4.2    3.1e-53  180.9   4.2    1.3  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.5e-28   99.2   1.0    3.1e-28   98.2   1.0    1.5  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    2.6e-15   56.7   5.5    1.6e-14   54.2   0.2    3.3  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    2.9e-12   46.5   1.3    1.2e-11   44.4   1.3    1.9  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    5.4e-07   29.1   0.0    0.00032   20.0   0.0    2.4  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    3.5e-06   26.4   5.4    1.1e-05   24.7   4.2    2.3  2  GIDA           Glucose inhibited division protein A
    5.1e-05   22.8   1.1    8.5e-05   22.1   0.2    1.9  2  FAD_oxidored   FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.065   11.9   0.8         11    4.6   0.3    3.1  3  HI0933_like    HI0933-like protein
       0.12   11.4   8.8       0.35    9.9   8.8    2.2  1  FAD_binding_2  FAD binding domain
       0.15   11.9   1.3         14    5.6   0.1    2.4  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
        1.6    9.0   5.0         13    6.1   0.2    3.2  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   4.2   1.9e-56   3.1e-53       1     279 [.       4     313 ..       4     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 1.9e-56
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias................. 57 
                                       +dv+v+GgG +  ++a  +a ag++++lve   l+gtcln+gc +sk l ++a +a+ ++                 
  gi|313117434|ref|YP_004044417.1|   4 FDVIVVGGGSGN-NVAAAAADAGLDTALVEpgpLGGTCLNRGCNPSKMLIQAANAANSVRdaakfhvdatvneidqa 79 
                                       59*******865.555667778********9*************************99999*******999999999 PP

                                       .............HHHHCHHHHCCCCHC.CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC. CS
                                       .............xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .............evvkklnqgielllg.eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGva 120
                                                           +++e +++ +e +++ ++  ++++e + + d+  ++++k+v+AtGs+p  ++i+G+ 
  gi|313117434|ref|YP_004044417.1|  80 avidemddllggiA------EDMEARYReKEHLTLFKEYTEFVDERTLKLDGDAVTAEKVVVATGSRPIVPPIDGL- 149
                                       99987775444430......3433333323366666666666666666667789**********************. PP

                                       TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 121 envgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeG 197
                                           +++++l+s eal+l ++p+++v+ GgGyi+vEl  al ++g +vt+ve +d l++  d +++aa +++  ++ 
  gi|313117434|ref|YP_004044417.1| 150 ----DNIDYLTSQEALNLRETPESLVILGGGYIAVELGYALQSMGTDVTIVEMLDSLVPREDGDIAAAFTKVAAER- 221
                                       ....44599*************************************************777777777777766664. PP

                                       EEEEESCEEEEEEETTE....EEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESST CS
                                       xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 198 vevklgtsvkeidgnge....klevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvp 269
                                        +v++g++v+++++++e    ++e++ +d+ +++ + v+va G++p+++ l+ +++g+e++erg+i+++e+l+t+ +
  gi|313117434|ref|YP_004044417.1| 222 HDVYTGHRVTAVEEHSEgyavHAETEAGDKLTVEGSEVLVALGRQPNSDDLGlDAAGIEVTERGFIETNEYLETTAE 298
                                       48899*********999996444488888888********************************************* PP

                                       TEEE-GGGC.....T CS
                                       xxxxxxxxx.....x RF
                       Pyr_redox_2 270 giyaiGDva.....g 279
                                       +++a GDva     +
  gi|313117434|ref|YP_004044417.1| 299 NVWAQGDVAgnalfK 313
                                       *********655551 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   1.0   1.9e-31   3.1e-28       1     107 [.     340     445 ..     340     448 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.9e-31
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p ++ft+p++a vG tee+++++g e++vg++ f++++  +a++ ++gf+K++a   +g++lG h +G++a+ l++
  gi|313117434|ref|YP_004044417.1| 340 MPHTIFTEPQIAGVGATEEDLQEEGTEYVVGRAAFAESAMGRAKKLEDGFMKVLAAP-DGEILGSHAIGYEASTLLH 415
                                       699**************************************************7766.******************* PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGH CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealk 107
                                       e+ +a++ gl+v+d+a+tih+hPtls +++
  gi|313117434|ref|YP_004044417.1| 416 EAVIAMRHGLSVADVAETIHAHPTLSKVVE 445
                                       **************************5554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3     0.073   1.2e+02       2      31 ..       6      34 ..       5      42 .. 0.87
   2 ?   -1.5   0.0       2.4   3.9e+03      24      45 ..      78      99 ..      62     109 .. 0.66
   3 !   54.2   0.2   9.6e-18   1.6e-14       1      78 [.     169     244 ..     169     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.073
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      v+vvGgG +g  +A+a+a+ g ++ +ve +
  gi|313117434|ref|YP_004044417.1|  6 VIVVGGG-SGNNVAAAAADAGLDTALVEPG 34
                                      7899988.799999999**99999999975 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                                      EEEEEESSSSSSTTSSHHHHHH CS
                         Pyr_redox 24 kVtvversdkllrllDeeaski 45
                                      +  v++ +d ll ++ e+++++
  gi|313117434|ref|YP_004044417.1| 78 QAAVIDEMDDLLGGIAEDMEAR 99
                                      4456777777776655555555 PP

  == domain 3  score: 54.2 bits;  conditional E-value: 9.6e-18
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       ++v++GgGyi++El+ al+ +g +Vt+ve+ d l + +D ++++++++   ++  +v+++++v+++e++++g ++v+
  gi|313117434|ref|YP_004044417.1| 169 SLVILGGGYIAVELGYALQSMGTDVTIVEMLDSLVPREDGDIAAAFTKVAAER-HDVYTGHRVTAVEEHSEG-YAVH 243
                                       58*********************************************999888.8**************998.4455 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                        
  gi|313117434|ref|YP_004044417.1| 244 A 244
                                       4 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   1.3   7.6e-15   1.2e-11       1     303 [.       7     302 ..       6     304 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 7.6e-15
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyrypke.mtfispsftsekleipdlnaiseetspafslkee 76 
                                       i++G+G  G ++a ++ +agl d   +E g +g +  +   +  +++ ++  +   ++ d   ++ ++   +   ++
  gi|313117434|ref|YP_004044417.1|   7 IVVGGG-SGNNVAAAAADAGL-DTALVEPGPLGGTCLNRGCNpSKMLIQA-ANAANSVRDAAKFHVDAT--VNEIDQ 78 
                                       445544.68888888888888.5678888877666555433313333322.333334444444333332..222344 PP

                       Pyr_redox_3  77 klsrkealeYlrevaksfelpiklfeeVesvkked...egfevetsketyeAkkviiAtGefdkPnklnipGeeklv 150
                                        +  +e+ + l  +a+  e + +++e+ +  k+     ++ +++ + + ++A+kv++AtG   +P ++ i G ++  
  gi|313117434|ref|YP_004044417.1|  79 AAVIDEMDDLLGGIAEDMEARYREKEHLTLFKEYTefvDERTLKLDGDAVTAEKVVVATGS--RPIVPPIDGLDNID 153
                                       455677888888888888888888888877776331225678899999************9..**********9655 PP

                       Pyr_redox_3 151 khyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeeki 227
                                         +s+       + + +v+ Gg+  av+  + l ++g +Vt+v   +++  +e         di   + ++ + e+ 
  gi|313117434|ref|YP_004044417.1| 154 YLTSQEALNLRETPESLVILGGGYIAVELGYALQSMGTDVTIVEMLDSLVPRE-------DGDIAAAFTKVAA-ERH 222
                                       54444442224457889999***********************9998766665.......5778888888766.558 PP

                       Pyr_redox_3 228 kvlfnaevkeikekeeeykvk..tedgkkvev.kddvvlatGykpdlsf..lkkslfeldedgrpvlteeteetnvp 299
                                       +v++ ++v++++e++e y v+  te g+k++v  ++v++a+G +p+ +   l+++++e +e g+++ +e   et+ +
  gi|313117434|ref|YP_004044417.1| 223 DVYTGHRVTAVEEHSEGYAVHaeTEAGDKLTVeGSEVLVALGRQPNSDDlgLDAAGIEVTERGFIETNE-YLETTAE 298
                                       9*****************9986688899999944667777******998345569****9999998765.5667788 PP

                       Pyr_redox_3 300 glfl 303
                                       +++ 
  gi|313117434|ref|YP_004044417.1| 299 NVWA 302
                                       8775 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.9e-07   0.00032     141     233 ..     122     207 ..      98     218 .. 0.79
   2 !    6.6   0.1    0.0023       3.8     111     161 ..     223     268 ..     212     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.9e-07
                       K_oxygenase 141 egeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkv 217
                                       + + + ++a+++v+++G++p +P++ + l++  + + s+e+l+ +   ++++++++ G+G  a e+ + l +  +  
  gi|313117434|ref|YP_004044417.1| 122 KLDGDAVTAEKVVVATGSRPIVPPI-DGLDN-IDYLTSQEALNLR---ETPESLVILGGGYIAVELGYALQSMGT-- 191
                                       44567899***************96.66774.8899999999887...79******************9998876.. PP

                       K_oxygenase 218 elklvtrsealepldd 233
                                       ++++v   ++l p +d
  gi|313117434|ref|YP_004044417.1| 192 DVTIVEMLDSLVPRED 207
                                       5555555555555555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0023
                       K_oxygenase 111 eqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepk 161
                                       + v  g++v++ve ++e     + v+ ++++g++ ++e  +++++ G +p+
  gi|313117434|ref|YP_004044417.1| 223 D-VYTGHRVTAVEEHSE----GYAVHAETEAGDKLTVEGSEVLVALGRQPN 268
                                       4.677899999999887....4999*999*******************996 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   4.2     7e-09   1.1e-05       1     150 [.       5     139 ..       5     176 .. 0.76
   2 ?   -1.5   0.0      0.62     1e+03       2      28 ..     170     196 ..     169     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 7e-09
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT....-SHHHHHHHHE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalg....gliikaadkag 71 
                                       dviV+GgG +G   A+aaa +G++++L+   +  +t+++ +Cnps   i +++  + ++          ++ +d+a+
  gi|313117434|ref|YP_004044417.1|   5 DVIVVGGG-SGNNVAAAAADAGLDTALVepGPLGGTCLNRGCNPSKMLIQAANAANSVRDAAkfhvDATVNEIDQAA 80 
                                       79*****9.6999999************98899****************7777777776633000123333334444 PP

                                       EEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE-- CS
                              GIDA  72 iqfrilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviat 148
                                       +   i        ++ l        ++++++++ +++++l++++e  e ++         ++ dg +++a++vv+at
  gi|313117434|ref|YP_004044417.1|  81 V---I------DEMDDL-----LGGIAEDMEARYREKEHLTLFKEYTEFVDE------RTLKLDGDAVTAEKVVVAT 137
                                       4...1......222222.....467899999999999999999887777744......6677899999999999999 PP

                                       TT CS
                              GIDA 149 Gt 150
                                       G+
  gi|313117434|ref|YP_004044417.1| 138 GS 139
                                       98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.62
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                       ++++GgG   +e  +a+  +G +v+++
  gi|313117434|ref|YP_004044417.1| 170 LVILGGGYIAVELGYALQSMGTDVTIV 196
                                       5899********************998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   5.2e-08   8.5e-05       1      50 [.       5      52 ..       5     161 .. 0.68
   2 ?   -2.5   0.1       1.5   2.5e+03      93     136 ..     214     256 ..     205     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.2e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignk 50
                                      Dv+VvGGg++  +AA aAa aG  ++Lve+ + lGG+  + + ++  +  
  gi|313117434|ref|YP_004044417.1|  5 DVIVVGGGSGNNVAA-AAADAGLDTALVEPGP-LGGTCLNRGCNPSKMLI 52
                                      9*******9988887.7899**********88.89999888887776633 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                      FAD_oxidored  93 leemlaeagvtvllntrlvevekegkriesvtveskeg.rktirA 136
                                       + ++ ae + +v++++r+++ve    +  +v +e+++g + t+++
  gi|313117434|ref|YP_004044417.1| 214 FTKVAAE-RHDVYTGHRVTAVEEHS-EGYAVHAETEAGdKLTVEG 256
                                       5555555.88999999999999864.5677777777765777766 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3    0.0066        11       1      32 [.       4      34 ..       4      72 .. 0.88
   2 ?    1.4   0.0     0.064     1e+02     143     165 ..     119     140 ..      91     149 .. 0.82
   3 ?    2.4   0.0     0.032        52     117     165 ..     215     266 ..     205     289 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0066
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dviv+GgG +G   A++aa++g +++l+e +
  gi|313117434|ref|YP_004044417.1|  4 FDVIVVGGG-SGNNVAAAAADAGLDTALVEPG 34
                                      589****99.67778888889****9999976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.064
                                       EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 143 frvktkseeeleadklvlAtGGl 165
                                        ++k+ ++++++a+k+v+AtG+ 
  gi|313117434|ref|YP_004044417.1| 119 RTLKL-DGDAVTAEKVVVATGSR 140
                                       46777.899************86 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.032
                                       HHHHHHT-EEE-S--EEEEECETTE.EEEEE.....TTEEEEESEEEE----S CS
                       HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktk....seeeleadklvlAtGGl 165
                                       +++ +++ ++++ ++v++ve++++g + v+++    ++ ++e +++++A+G +
  gi|313117434|ref|YP_004044417.1| 215 TKVAAERHDVYTGHRVTAVEEHSEG-YAVHAEteagDKLTVEGSEVLVALGRQ 266
                                       56677778999********988887.88877434446668999******9976 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   8.8   0.00022      0.35       1      75 [.       5      78 ..       5     382 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS....GGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg....atawsqGgidavlspeqkkagikdspelhrtdtlkalde 75
                                      DviV+G+G +  +AA+ aa+aGl++a+ve ++  g         s   i+a++    +++ ++d  + h+  t+++ d+
  gi|313117434|ref|YP_004044417.1|  5 DVIVVGGGSGNNVAAA-AADAGLDTALVEPGPLGGTclnrGCNPSKMLIQAAN----AANSVRDAAKFHVDATVNEIDQ 78
                                      9*******96555555.99***********99744433222223333444444....3344667777777777777665 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0083        14       2      56 ..       6      62 ..       5     120 .. 0.66
   2 ?    5.2   0.1      0.01        17       3      52 ..     171     220 ..     169     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0083
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S...-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi...seealekalekieksleklvekgklk 56
                                      v v+G G  G+ +aa++a agl++ lv+        l+++ +  +  ++ + +++++ 
  gi|313117434|ref|YP_004044417.1|  6 VIVVGGGS-GNNVAAAAADAGLDTALVEPgplGGTCLNRGCNPSKMLIQAANAANSVR 62
                                      78999997.******************9844444555555555555444444444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTT CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvek 52 
                                        ++G G +  ++ +++ s g +V++v++ ++ + +    i++ + k++++
  gi|313117434|ref|YP_004044417.1| 171 VILGGGYIAVELGYALQSMGTDVTIVEMLDSLVPREDGDIAAAFTKVAAE 220
                                       699*************************9999999999999988877654 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.053        86       1      35 [.       8      40 ..       8      51 .. 0.79
   2 ?    6.1   0.2    0.0081        13       1      30 [.     172     201 ..     172     203 .. 0.94
   3 ?   -1.6   0.0         2   3.3e+03      14      29 ..     218     237 ..     208     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.053
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      +vG+G sG   A+++a+ag+d  l+e ++ lGG +
  gi|313117434|ref|YP_004044417.1|  8 VVGGG-SGNNVAAAAADAGLDTALVEPGP-LGGTC 40
                                      78888.777778888889******99985.66655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0081
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                       I+G+G  +  + y+L+  g dv+++e+ d+
  gi|313117434|ref|YP_004044417.1| 172 ILGGGYIAVELGYALQSMGTDVTIVEMLDS 201
                                       89************************9876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                                       HHHCC....TEEEEEE-SSS CS
                     NAD_binding_8  14 lLaka....gfdvlllekrd 29 
                                       ++ ++    g++v+ +e ++
  gi|313117434|ref|YP_004044417.1| 218 AAERHdvytGHRVTAVEEHS 237
                                       33343445799999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 2968.61
//
Query:       gi|313117435|ref|YP_004044418.1|  [L=197]
Description: putative transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-10   39.5   0.0    1.3e-09   37.8   0.0    1.8  2  MarR_2           MarR family
    2.1e-08   33.8   0.0    8.8e-08   31.8   0.0    2.0  3  HTH_IclR         IclR helix-turn-helix domain
    7.8e-07   28.9   0.0    1.3e-06   28.2   0.0    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    3.1e-06   27.1   0.0    6.4e-06   26.1   0.0    1.5  1  HTH_20           Helix-turn-helix domain
    5.1e-06   26.3   0.0    1.5e-05   24.8   0.0    1.7  2  MarR             MarR family
    1.3e-05   24.7   0.0    2.6e-05   23.7   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    5.5e-05   23.6   0.1     0.0013   19.1   0.0    2.3  2  HTH_27           Winged helix DNA-binding domain
    0.00012   21.9   0.0     0.0002   21.3   0.0    1.3  1  Dimerisation2    Dimerisation domain
    0.00014   21.7   0.0    0.00022   21.0   0.0    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    0.00031   20.6   0.0    0.00059   19.8   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0061   16.5   0.0       0.01   15.8   0.0    1.3  1  HTH_36           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.045   14.1   0.0       0.12   12.8   0.0    1.7  1  HTH_31           Helix-turn-helix domain
      0.062   13.5   0.0       0.28   11.4   0.0    1.9  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.067   13.2   0.0       0.12   12.4   0.0    1.4  1  HTH_29           Winged helix-turn helix
        0.1   12.8   0.0       0.26   11.5   0.0    1.7  1  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
       0.12   12.1   0.1        0.2   11.3   0.1    1.3  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.16   11.8   0.0       0.38   10.7   0.0    1.6  2  TFIIE_alpha      TFIIE alpha subunit
       0.18   11.5   0.0        0.4   10.4   0.0    1.5  1  GntR             Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   1.3e-12   1.3e-09      11      55 ..      87     129 ..      85     134 .. 0.89
   2 ?   -1.9   0.0       3.3   3.3e+03      44      56 ..     171     183 ..     163     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.3e-12
                                       HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE.E CS
                            MarR_2  11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr.p 55 
                                       L+++g++p   l+++e+a++lg+++s+++r l++Lv+ GL++r+  
  gi|313117435|ref|YP_004044418.1|  87 LYVIGDGP---LSASEVAETLGYDRSTMTRYLNKLVDLGLLRRSeL 129
                                       88999999...9*******************************944 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                                       HHHHTTSEEEEES CS
                            MarR_2  44 rLvaaGLverrpg 56 
                                        L ++ ++er p+
  gi|313117435|ref|YP_004044418.1| 171 NLTKQDYLERNPD 183
                                       4667777777765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.8   6.8e+03      26      33 ..      74      81 ..      72      81 .. 0.80
   2 !   31.8   0.0   8.9e-11   8.8e-08      16      51 ..      92     127 ..      90     128 .. 0.95
   3 ?   -1.8   0.0       2.9   2.8e+03      42      52 .]     172     182 ..     170     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.8
                                      HHHTS-HH CS
                          HTH_IclR 26 rrtglpkS 33
                                      +++glpk+
  gi|313117435|ref|YP_004044418.1| 74 QAFGLPKA 81
                                      789***96 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 8.9e-11
                                       BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  16 pqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       +++l+ se+A+ +g  +St  R+L+ Lv lG++++ 
  gi|313117435|ref|YP_004044418.1|  92 DGPLSASEVAETLGYDRSTMTRYLNKLVDLGLLRRS 127
                                       789*******************************85 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.9
                                       HHHTTSEE... CS
                          HTH_IclR  42 LvelGyveqdg 52 
                                       L+++ y+e+++
  gi|313117435|ref|YP_004044418.1| 172 LTKQDYLERNP 182
                                       89999***997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.3e-09   1.3e-06       2      66 ..      74     144 ..      73     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                                       HHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE-- CS
                              TrmB   2 qklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYravd 66 
                                       q++GL +   ++ l+++  gp++a+e+ae lg +rs+  ++L++L+d Gl +r++ +       ++Y+ vd
  gi|313117435|ref|YP_004044418.1|  74 QAFGLPKAGLDICLYVIGDGPLSASEVAETLGYDRSTMTRYLNKLVDLGLLRRSELNredggvVNMYHSVD 144
                                       5788888888888889999**********************************997767777777777776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   6.4e-09   6.4e-06      13      56 ..      83     126 ..      70     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.4e-09
                                       HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56 
                                       ++i+ +  ++++l+ase+ae+l+ +++t+ + L++L++ gL+++
  gi|313117435|ref|YP_004044418.1|  83 LDICLYVIGDGPLSASEVAETLGYDRSTMTRYLNKLVDLGLLRR 126
                                       577788889*********************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.5e-08   1.5e-05      16      51 ..      93     128 ..      86     132 .. 0.93
   2 ?   -2.3   0.0       4.3   4.3e+03      41      54 ..     172     185 ..     171     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.5e-08
                                       TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       gpls se a+ lg ++st+tr l +L++ Gl++Rs 
  gi|313117435|ref|YP_004044418.1|  93 GPLSASEVAETLGYDRSTMTRYLNKLVDLGLLRRSE 128
                                       789*******************************96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.3
                                       HHHTTSEEEEEETT CS
                              MarR  41 LekkGlieRskspe 54 
                                       L k++++eR +++e
  gi|313117435|ref|YP_004044418.1| 172 LTKQDYLERNPDKE 185
                                       77999999999875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.6e-08   2.6e-05      13      48 .]      90     125 ..      83     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.6e-08
                            HTH_24  13 qknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                         ++ +s +e+Ae lg  +st +r+l++L++ Gl++
  gi|313117435|ref|YP_004044418.1|  90 IGDGPLSASEVAETLGYDRSTMTRYLNKLVDLGLLR 125
                                       56999****************************975 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.3e-06    0.0013       9      58 ..      87     134 ..      84     143 .. 0.85
   2 ?    2.1   0.0      0.29   2.9e+02      41      54 ..     171     184 ..     163     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                            HTH_27   9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58 
                                       L +i+  +++ ++++++++l ++ s++   l+kL+  GL+ r++  ++++
  gi|313117435|ref|YP_004044418.1|  87 LYVIG--DGPLSASEVAETLGYDRSTMTRYLNKLVDLGLLRRSELNREDG 134
                                       77888..9********************************7776544444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.29
                            HTH_27  41 kLtekGLvertgde 54 
                                        Lt+++++er++d+
  gi|313117435|ref|YP_004044418.1| 171 NLTKQDYLERNPDK 184
                                       599*******9996 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     2e-07    0.0002      30      69 ..      92     131 ..      69     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2e-07
                     Dimerisation2  30 eeplsaeevaeelgasvkGterLldacvaLgLLerekkee 69 
                                       ++plsa+evae+lg + + ++r l+ +v LgLL+r++ ++
  gi|313117435|ref|YP_004044418.1|  92 DGPLSASEVAETLGYDRSTMTRYLNKLVDLGLLRRSELNR 131
                                       589*******************************885544 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.2e-07   0.00022      13      46 ..      92     125 ..      83     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.2e-07
                                       TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  13 egelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       +g+l+++e ae lg  +st  ++L+kL ++GL++
  gi|313117435|ref|YP_004044418.1|  92 DGPLSASEVAETLGYDRSTMTRYLNKLVDLGLLR 125
                                       5*******************************85 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.9e-07   0.00059      21      54 ..      94     127 ..      78     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.9e-07
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglisrg 54 
                                       pl+  e A+ lG  r+t++r l++L + gl++r+
  gi|313117435|ref|YP_004044418.1|  94 PLSASEVAETLGYDRSTMTRYLNKLVDLGLLRRS 127
                                       8999***************************964 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-05      0.01      28      55 .]      97     124 ..      94     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                            HTH_36  28 qetlakrlglsknTvsraikeLeqlGyi 55 
                                        +  a+ lg +++T  r++++L++lG++
  gi|313117435|ref|YP_004044418.1|  97 ASEVAETLGYDRSTMTRYLNKLVDLGLL 124
                                       5677999*******************97 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012      0.12      15      36 ..      95     116 ..      91     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                            HTH_31  15 LsqeevAerlgvsestlsrlEq 36 
                                       Ls  evAe lg+ +st++r+ +
  gi|313117435|ref|YP_004044418.1|  95 LSASEVAETLGYDRSTMTRYLN 116
                                       899*****************98 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00028      0.28      22      53 ..      94     125 ..      89     128 .. 0.90
   2 ?   -1.1   0.0       2.2   2.2e+03      46      58 ..     172     184 ..     170     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                                       SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  22 vvktkdlaerLnvspssVsemlkkLekdGyve 53 
                                       + + +++ae L+   s+ +  l+kL + G++ 
  gi|313117435|ref|YP_004044418.1|  94 PLSASEVAETLGYDRSTMTRYLNKLVDLGLLR 125
                                       66889*********************999985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                                       HHHTTSEEEETTT CS
                    Fe_dep_repress  46 LekdGyveyekyk 58 
                                       L k+ y+e +++k
  gi|313117435|ref|YP_004044418.1| 172 LTKQDYLERNPDK 184
                                       6677777777766 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.12      14      46 ..      96     125 ..      90     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            HTH_29  14 tvsqiAkllglsrrtvyrwlkrfeegGlaalld 46 
                                       + s++A+ lg++r+t  r+l+  +  G   ll+
  gi|313117435|ref|YP_004044418.1|  96 SASEVAETLGYDRSTMTRYLNKLVDLG---LLR 125
                                       489*******************99999...444 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.26      13      40 ..      94     126 ..      91     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                           AbiEi_4  13 lfttrelea.aGispsa....lrrLvrkGwLvr 40 
                                        ++ +e+++ +G ++s+    l++Lv+ G+L r
  gi|313117435|ref|YP_004044418.1|  94 PLSASEVAEtLGYDRSTmtryLNKLVDLGLLRR 126
                                       57889**********888************988 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0002       0.2       6      34 ..      26      54 ..      22      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                      EEE-TTT--EEEECC--SS-EEETTEE-E CS
                   Desulfoferrod_N  6 vYkCevCGniVeVleaGgGeLVCCgepMk 34
                                       + C  C niV     G     C gepM+
  gi|313117435|ref|YP_004044418.1| 26 LFECATCDNIVLSFGRGDKPISCHGEPMQ 54
                                      589*******9888888888********7 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.2   1.2e+03      36      50 ..      60      74 ..      49      83 .. 0.81
   2 ?   10.7   0.0   0.00038      0.38       5      79 ..      70     146 ..      66     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                                      HHTS-HHHHHHHHHH CS
                       TFIIE_alpha 36 elkidlnelrklLnr 50
                                      e++i+ + +r++L++
  gi|313117435|ref|YP_004044418.1| 60 EMNIKSPDIRQVLFQ 74
                                      67899999***9987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00038
                                       HHHHHCS-..HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECC CS
                       TFIIE_alpha   5 evvrkfyg..eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinye 79 
                                        v+++++g  +    +   ++ +g ++  ++a+ l+ d+  + + Ln+L + +l        e+ ++ + y+ ++ +
  gi|313117435|ref|YP_004044418.1|  70 QVLFQAFGlpKAGLDICLYVIGDGPLSASEVAETLGYDRSTMTRYLNKLVDLGLLRRSELNREDGGVVNMYHSVDLD 146
                                       6777777765555566666667999*****************************98877777888888888887766 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0004       0.4      23      56 ..      94     126 ..      90     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                                       B---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR  23 kLPsereLaaefgVsrttvReALrrLeaeglver 56 
                                       +L s +e+a+ +g +r+t  + L++L+  gl+ r
  gi|313117435|ref|YP_004044418.1|  94 PL-SASEVAETLGYDRSTMTRYLNKLVDLGLLRR 126
                                       57.889*************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1312.75
//
Query:       gi|313117436|ref|YP_004044419.1|  [L=202]
Description: transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-14   53.9   0.5    2.6e-14   53.4   0.5    1.3  1  TetR_C_6   BetI-type transcriptional repressor, C-terminal
    1.3e-06   28.1   0.0    2.3e-06   27.3   0.0    1.5  1  TetR_N     Bacterial regulatory proteins, tetR family
    6.6e-06   26.3   0.2    1.1e-05   25.5   0.2    1.4  1  TetR_C_31  Tetracyclin repressor-like, C-terminal domain
    0.00011   22.2   0.0    0.00028   20.9   0.0    1.7  2  TetR_C_17  Tetracyclin repressor-like, C-terminal domain
    0.00018   21.8   0.0    0.00031   21.0   0.0    1.4  1  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
    0.00048   20.1   0.3    0.00088   19.3   0.3    1.5  1  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.023   15.0   0.5      0.032   14.5   0.5    1.3  1  TetR_C_11  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.5     1e-17   2.6e-14       3     111 ..      86     195 ..      84     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1e-17
                                       HHHHHHHHCCST..HSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHHHH CS
                          TetR_C_6   3 erlraileallp..ldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglradadaeaaAe 77 
                                       e l+ il+ +l+  l++err+++++ +++ ++aa++p++++++   ++ ++++++a+++++ e+g++ ++ a+ +A+
  gi|313117436|ref|YP_004044419.1|  86 EHLDSILDHVLAtpLSPERRQFATAIVELRGQAAHNPRYRDHFTCHDQFFHDQIAAIIEAGIEDGEFNAVSADVFAW 162
                                       6677777777754499************************************************************* PP

                                       HHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHH CS
                          TetR_C_6  78 rlaAlidGLwlraalapeeldaeraralvrrhld 111
                                        l+ +i+G  ++ +++ +  + + +ra ++r + 
  gi|313117436|ref|YP_004044419.1| 163 FLVTVINGAMTQRVTS-DADTTAMVRAQIDRCIG 195
                                       ***************9.55555777777777665 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0     9e-10   2.3e-06       1      45 [.      18      62 ..      18      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9e-10
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                      I+ a+   + e+Gy+ +t+++I ++   sk+++Y+++++K+eLl+
  gi|313117436|ref|YP_004044419.1| 18 IIRATYLALCEYGYADLTIQRIGEQFPKSKSLIYHHYDGKDELLL 62
                                      566666667799*******************************97 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2   4.5e-09   1.1e-05      12     105 ..      94     194 ..      79     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.5e-09
                                       HHCCCCCT..THHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHHCSS-HH.H......HHHHHHHHHH CS
                         TetR_C_31  12 dlldrala..drertlAryelfleaarrPeLraalarlrralrealaallaalGlpdpe.e......aarllvaald 79 
                                        +l+  l+  +r+   A  el+ +aa++P+ r+ ++ + + +++++aa+ + +G +d e         a+ lv +++
  gi|313117436|ref|YP_004044419.1|  94 HVLATPLSpeRRQFATAIVELRGQAAHNPRYRDHFTCHDQFFHDQIAAIIE-AGIEDGEfNavsadvFAWFLVTVIN 169
                                       333444447778888999*******************99999999999999.88876764223222255559***** PP

                                       HHHHHHHHSGTS-HHHHHHHHHHHHT CS
                         TetR_C_31  80 GllldrLagpaadpraevrellrall 105
                                       G++ +r++ + ad++a vr+ +++ +
  gi|313117436|ref|YP_004044419.1| 170 GAMTQRVTSD-ADTTAMVRAQIDRCI 194
                                       *********8.677788888887766 PP

>> TetR_C_17  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.69   1.8e+03      36      70 ..      45      80 ..      16     110 .. 0.71
   2 !   20.9   0.0   1.1e-07   0.00028      44      98 ..     131     184 ..      87     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.69
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHTTS.---SS- CS
                         TetR_C_17 36 errayleeRyerlvealkellqeGvergE.fkPqlp 70
                                      ++++++ + y+   e l ++l+   +r E + P  +
  gi|313117436|ref|YP_004044419.1| 45 KSKSLIYHHYDGKDELLLDFLEFALDRFEgLVPFDD 80
                                      556677788888888888888777777664555555 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHHHHHHHHHS-HHHH- CS
                         TetR_C_17  44 RyerlvealkellqeGvergEfkPqlplesiakylisfldGliletlalgeektk 98 
                                         + + +++ +++++G+e gEf+ + +++  a +l+ +++G ++++++ ++++t+
  gi|313117436|ref|YP_004044419.1| 131 HDQFFHDQIAAIIEAGIEDGEFN-AVSADVFAWFLVTVINGAMTQRVTSDADTTA 184
                                       45556799**************9.56899*********************99986 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.2e-07   0.00031      23      87 ..     107     171 ..      84     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHHCH CS
                         TetR_C_24  23 reeaavllrelraLspehreeiralrreyerllrdlieeGvaagefedldpklaalailgmlnwv 87 
                                       +++a v lr   a +p +r++++   + ++++++++ie+G+++gef+++ +++ a ++++++n+ 
  gi|313117436|ref|YP_004044419.1| 107 FATAIVELRGQAAHNPRYRDHFTCHDQFFHDQIAAIIEAGIEDGEFNAVSADVFAWFLVTVINGA 171
                                       5667777788888899999999999999********************************99975 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3   3.4e-07   0.00088      39      82 ..     126     169 ..     117     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.4e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHCT-STT--HHHHHHHHHHHSG CS
                         TetR_C_27  39 evvekhieeleeqlaeIireGvaaGeFkaadpeaaaravfdata 82 
                                       +    h +  ++q+a Ii++G+++GeF+a  +++ a  ++++++
  gi|313117436|ref|YP_004044419.1| 126 DHFTCHDQFFHDQIAAIIEAGIEDGEFNAVSADVFAWFLVTVIN 169
                                       55566777789*******************99999988877665 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   1.3e-05     0.032      26      99 ..     106     181 ..      78     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                         TetR_C_11  26 ragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelra...dadvelvldlllgpllyrllltge 99 
                                       + + ++  l ++a+++p+ ++ +     +  +++++a+++ +++ Ge  a   d+ + +++ ++ g++ +r+  + +
  gi|313117436|ref|YP_004044419.1| 106 QFATAIVELRGQAAHNPRYRDHFTC-HDQFFHDQIAAIIEAGIEDGEFNAvsaDVFAWFLVTVINGAMTQRVTSDAD 181
                                       3455566667778888888888877.677789***************765211555567888888888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1434.11
//
Query:       gi|313117437|ref|YP_004044420.1|  [L=495]
Description: putative efflux protein, MATE family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-64  214.9  48.1      3e-36  124.5  12.8    3.0  3  MatE             MatE
    2.7e-06   27.5  32.8    3.7e-05   23.8  16.4    5.6  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
        0.1   12.1   0.1        0.1   12.1   0.1    2.8  3  TRAP-gamma       Translocon-associated protein, gamma subunit
        1.1    7.8  37.3        5.1    5.6  35.6    3.1  1  MurJ             Lipid II flippase MurJ


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5  12.8   6.6e-40     3e-36       1     160 [.      28     189 ..      28     190 .. 0.99
   2 ?   -1.1   1.5      0.29   1.3e+03      50      89 ..     204     244 ..     199     255 .. 0.73
   3 !  103.0  18.4   2.7e-33   1.2e-29       1     160 [.     276     439 ..     276     440 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 6.6e-40
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       Pi+l+n+l++ ++l+dt++vgrlg++a++a+s+++ i++l+++++ g+ +a t+lv+q+ Ga+n +r++ ++ q++ 
  gi|313117437|ref|YP_004044420.1|  28 PIVLTNMLQVAYNLADTFWVGRLGQDAVSALSFSWAIVFLIITLAAGFTVAGTVLVAQNKGAGNLDRISDVAGQTIA 104
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee..vlelakrylrililgipalalqlvlsgilrgagktkvplyislisl 152
                                       ++++ls+++++l++++++++l+l+++++   v  l+ +y r ++lgip+ + ++++++ l+g g+tk+ply++l+++
  gi|313117437|ref|YP_004044420.1| 105 FVVALSVVFSVLGYVLAPWLLQLIGATPGteVFRLSITYTRTMFLGIPFVFAFFIFQSLLQGWGDTKTPLYLMLLGV 181
                                       ***************************9888********************************************** PP

                              MatE 153 llniplny 160
                                       +ln+++++
  gi|313117437|ref|YP_004044420.1| 182 ILNVVIDP 189
                                       *****986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.29
                              MatE  50 talttlvgqalGaknfkrakealr.qglilllllsliiall 89 
                                       t+lttl ++ + a  f +++++   +++i++ +++++ia+ 
  gi|313117437|ref|YP_004044420.1| 204 TGLTTLQSNLYAATEFGGFGVQGAaIATITARGIGAVIAVG 244
                                       79999999999999999999875414555666666666654 PP

  == domain 3  score: 103.0 bits;  conditional E-value: 2.7e-33
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+ +e+ ++s+  +++t lv+  g++a+Aa +i+++i+sl+++++lgl+ +++t vgq+lGak+  rak+a++ +  
  gi|313117437|ref|YP_004044420.1| 276 PASIEMSTQSFGITVMTALVALAGAEAVAAFGIGTRITSLVVLPALGLARGTETAVGQNLGAKQAGRAKQAVFASAG 352
                                       999************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee...vlelakrylrililgipalalqlvlsgilrgagktkvplyislis 151
                                       + +++ ++i++lv+l++  i+s+f + +e   v++++++ylr++++++++l+++ v +g++rg g t++++++ +i+
  gi|313117437|ref|YP_004044420.1| 353 IIAGVLVVISVLVYLNAATIVSIFITGQEaatVIAIGADYLRVVGVTYVFLGVFYVVQGAYRGSGSTRLAMIFGIIG 429
                                       **************************99999********************************************** PP

                              MatE 152 l.llniplny 160
                                       l +l++p +y
  gi|313117437|ref|YP_004044420.1| 430 LiVLRVPPAY 439
                                       *******998 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   5.7      0.87   3.9e+03      91     141 ..      67     125 ..      49     127 .. 0.50
   2 !   23.8  16.4   8.2e-09   3.7e-05       4     138 ..     146     310 ..     143     316 .. 0.79
   3 ?   -8.0  11.1         4   1.8e+04      94     127 ..     347     375 ..     286     390 .. 0.61
   4 !   17.8   8.3   6.1e-07    0.0027       1      77 [.     392     471 ..     392     478 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.87
                   Polysacc_synt_C  91 llkpllaalvmgivvylllllllglllla............alalllavlvgalvYlllllll 141
                                       l+ +l+a++ +++ v+  ++   g    +            a++++l+v++ +l Y+l+ +ll
  gi|313117437|ref|YP_004044420.1|  67 LIITLAAGFTVAGTVLVAQNKGAG----NldrisdvagqtiAFVVALSVVFSVLGYVLAPWLL 125
                                       222222332222222222222222....23356777777655577777777777777766665 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 8.2e-09
                   Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgi......................... 55 
                                        + l+i+f + + +++s+Lqg g +k++l+ +++g+++++++  +li  f+                          
  gi|313117437|ref|YP_004044420.1| 146 TMFLGIPFVFAFFIFQSLLQGWGDTKTPLYLMLLGVILNVVIDPFLILGFQDnllfevtglttlqsnlyaatefggf 222
                                       57899******************************************87764567888999**************** PP

                   Polysacc_synt_C  56 ..vGaaiatvlallvvavln.lyalrrllgikl.....ellrrll.kpllaalvmgivvylllllllgllllaalal 123
                                          Gaaiat+ a  ++av+    +l+ ++gi+l     +l r ++ k++ +++  +i    +  + +g++ +    +
  gi|313117437|ref|YP_004044420.1| 223 gvQGAAIATITARGIGAVIAvGLLLSGRVGIHLapsdfVLTRETVsKIFTIGAPASIE---MSTQSFGITVMT-ALV 295
                                       *******************955566669999999998755666655666666666666...444444444433.345 PP

                   Polysacc_synt_C 124 llavlvgalvYllll 138
                                       +la++ +++++++ +
  gi|313117437|ref|YP_004044420.1| 296 ALAGAEAVAAFGIGT 310
                                       555556666666655 PP

  == domain 3  score: -8.0 bits;  conditional E-value: 4
                   Polysacc_synt_C  94 pllaalvmgivvylllllllgllllaalalllav 127
                                       ++++a ++++v + + ++l+ l+     a+++++
  gi|313117437|ref|YP_004044420.1| 347 VFASAGIIAGV-LVVISVLVYLNA----ATIVSI 375
                                       33333333333.212222222222....333333 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 6.1e-07
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllliplf..givGaaiatvlallvvavlnl 74 
                                       +L+++ ++ +fl+++ v+++   g g +++a+++ +ig++ + +   + l+ +f  g++G+ +++++a +++ vl  
  gi|313117437|ref|YP_004044420.1| 392 YLRVVGVTYVFLGVFYVVQGAYRGSGSTRLAMIFGIIGLIvLRVPPAYALVAWFdmGAMGVWYGIAAANVLIVVLSG 468
                                       5899999*******************************99689********99966789988888888888888884 PP

                   Polysacc_synt_C  75 yal 77 
                                       ++ 
  gi|313117437|ref|YP_004044420.1| 469 VYF 471
                                       443 PP

>> TRAP-gamma  Translocon-associated protein, gamma subunit (TRAP-gamma)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2      0.63   2.8e+03      48      63 ..      63      78 ..      57      86 .. 0.79
   2 ?   12.1   0.1   2.3e-05       0.1     118     147 ..     134     163 ..     130     167 .. 0.91
   3 ?   -1.6   0.9      0.37   1.7e+03     130     165 ..     352     387 ..     343     391 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.63
                        TRAP-gamma 48 lilfvivtllstylla 63
                                      +i+f+i+tl++ +++a
  gi|313117437|ref|YP_004044420.1| 63 AIVFLIITLAAGFTVA 78
                                      6888888888888775 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.3e-05
                        TRAP-gamma 118 yEsttfsifynNalflalllvlsfyllksf 147
                                       +E   +si y+ ++fl + +v++f++++s+
  gi|313117437|ref|YP_004044420.1| 134 TEVFRLSITYTRTMFLGIPFVFAFFIFQSL 163
                                       57889**********************986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.37
                        TRAP-gamma 130 alflalllvlsfyllksfsptvnyilsvvvasglva 165
                                        +   +l+v+s++++ + +++v + ++   a++++a
  gi|313117437|ref|YP_004044420.1| 352 GIIAGVLVVISVLVYLNAATIVSIFITGQEAATVIA 387
                                       555566777777777777777777777666666666 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  35.6    0.0011       5.1      30     393 ..      72     462 ..      49     486 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0011
                              MurJ  30 egalssaFvPvlaeak.kkdeekaaefvrkvltllilvlllvtligilaapllirllatgfdeetlelavsllrill 105
                                        ++++ a     a+ k + + ++ + ++++++ +++++ +++ ++g ++ap+l +l+  +   e ++l ++ +r ++
  gi|313117437|ref|YP_004044420.1|  72 AAGFTVAGTVLVAQNKgAGNLDRISDVAGQTIAFVVALSVVFSVLGYVLAPWLLQLIGATPGTEVFRLSITYTRTMF 148
                                       4445444444444445556889999999************************************************* PP

                              MurJ 106 pylllvslsavfgavLnarkkFfap...afsPvllNvsvIltllllanklgeeail..................... 158
                                       + + +v+   +f+++L+ ++    p   ++  v+lNv++  +l+l  +     +++                     
  gi|313117437|ref|YP_004044420.1| 149 LGIPFVFAFFIFQSLLQGWGDTKTPlylMLLGVILNVVIDPFLILGFQDNLLFEVTglttlqsnlyaatefggfgvq 225
                                       *****************998765542227889999*9986666665554443444477888999*******999998 PP

                              MurJ 159 aLaiGvl..iGgvlqllvqlpalkkaglllkpr.fafrdeglkkflklllptllgvsvsqlnllvdtalAsflaegs 232
                                       + ai+++   G  + ++v l    + g++l p  f  + e + k+++  +p+ + +s++  +  v tal   + + +
  gi|313117437|ref|YP_004044420.1| 226 GAAIATItaRGIGAVIAVGLLLSGRVGIHLAPSdFVLTRETVSKIFTIGAPASIEMSTQSFGITVMTALVALAGAEA 302
                                       45665552246666677777777777777666426678889******************************999*** PP

                              MurJ 233 vsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllfe 309
                                       v++   + ri  l + l ++ ++     ++ ++  +k+   +++ +  +  +++ +l+++s+++ + +  ivs++  
  gi|313117437|ref|YP_004044420.1| 303 VAAFGIGTRITSLVV-LPALGLARGTETAVGQNLGAKQAGRAKQAVFASAGIIAGVLVVISVLVYLNAATIVSIF-I 377
                                       **********99964.66777777777899999999999999**************************9999875.5 PP

                              MurJ 310 rGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnills.llllpplgvvglalat 385
                                        G+  ++ +++ a  L++ +++ +++ ++++++ ++  ++ t+ +++ ++i l++  +   + l+  + + ++++ +
  gi|313117437|ref|YP_004044420.1| 378 TGQEAATVIAIGADYLRVVGVTYVFLGVFYVVQGAYRGSGSTRLAMIFGIIGLIVLRVPPaYALVAWFDMGAMGVWY 454
                                       ************************************************99988765443334444444333333333 PP

                              MurJ 386 slsaligl 393
                                       +++a   l
  gi|313117437|ref|YP_004044420.1| 455 GIAAANVL 462
                                       33332111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 3133.46
//
Query:       gi|313117438|ref|YP_004044421.1|  [L=295]
Description: nucleoside-diphosphate sugar epimerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-13   50.8   0.0    6.1e-13   49.1   0.0    1.9  1  NAD_binding_10  NAD(P)H-binding
    1.5e-12   47.6   0.0    2.1e-12   47.1   0.0    1.2  1  NmrA            NmrA-like family
    0.00065   19.2   0.0     0.0034   16.9   0.0    2.1  2  Epimerase       NAD dependent epimerase/dehydratase family
     0.0028   16.9   0.0     0.0048   16.1   0.0    1.4  1  NAD_binding_4   Male sterility protein
  ------ inclusion threshold ------
      0.024   14.4   0.0      0.058   13.2   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.081   12.5   0.0       0.16   11.6   0.0    1.3  1  GerE            Bacterial regulatory proteins, luxR family
      0.083   12.0   0.0       0.14   11.3   0.0    1.3  1  RmlD_sub_bind   RmlD substrate binding domain
       0.11   11.5   0.0       0.26   10.3   0.0    1.6  2  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
       0.12   11.8   0.0       0.19   11.2   0.0    1.3  1  adh_short       short chain dehydrogenase


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   3.1e-16   6.1e-13       1     183 [.      19     191 ..      19     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 3.1e-16
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHHH CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdeeg 77 
                                       GAtG vG+ lv++ll+    +v++ + +p+ + e    ++ e ve d++ +e+  +al++++  +  + +  +  + 
  gi|313117438|ref|YP_004044421.1|  19 GATGTVGKPLVTRLLDT-LAQVRVATTSPQTARERF-GNAPEYVEFDFERPETWGSALEQINRMFLLFPPAVG-VTP 92 
                                       9****************.5************98755.4799***********************999965444.578 PP

                                       HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE-CEE-S.T.-- CS
                    NAD_binding_10  78 aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTivrpggLtde.p.tt 152
                                       ++  +daa++ gv ++ ++s +g+++     ++             +r+ e++l + +l +T++r ++++++    +
  gi|313117438|ref|YP_004044421.1|  93 VREFIDAADRVGVGHVAYLSILGAEK-----LPV----------LPHRRLEKHLVRADLAYTFLRASWFMQNlSgIH 154
                                       ************************94.....433..........4699*********************99843356 PP

                                       SEEEEETTS...S---...-EEEHHHHHHHHHHHCTX CS
                    NAD_binding_10 153 kyrvvekge...pfkg...gsisradVAdvlvavldd 183
                                       + ++++++e   p ++   g +  +dVA+v++ vl++
  gi|313117438|ref|YP_004044421.1| 155 RPEITADDEiyiPAGDgrlGFVDTSDVAAVAATVLTE 191
                                       778887776444333323369*************986 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0     1e-15   2.1e-12       1     232 [.      15     227 ..      15     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1e-15
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GGS- CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfysk 77 
                                       Ilv+GaTG  Gk +v  ll+   +vr+ +  +++   + + +a+ e v+ d +  e   +al++ + +f+ ++    
  gi|313117438|ref|YP_004044421.1|  15 ILVTGATGTVGKPLVTRLLDTLAQVRVATTSPQTA-RERFGNAP-EYVEFDFERPETWGSALEQINRMFLLFP-PAV 88 
                                       9*************************999888754.46677766.899************************9.789 PP

                                       HHHHHHHHHHHHHHHS-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEEE-EEGGG-BSSS-S CS
                              NmrA  78 eiedgkklvdAakeaGvkhfiySslgddndrsnaeepavphfdsKaeieeyvralgipytfvyagffmenflsllaq 154
                                        +    + +dAa + Gv h+ y s+  +++      p +ph     + e+++  + + ytf++a  fm+n+++   +
  gi|313117438|ref|YP_004044421.1|  89 GVTPVREFIDAADRVGVGHVAYLSILGAEK-----LPVLPH----RRLEKHLVRADLAYTFLRASWFMQNLSGIHRP 156
                                       99999**********************993.....456666....355666666899****************8888 PP

                                       S-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-S.EEE-HHHHHHHHHHHHTS-EE CS
                              NmrA 155 lkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklag.ntlsgneivelfekkigktvk 230
                                          + ta +e  ++  g+g     ++ ++ D++a+ + +l + + ++++ ++l+g + + ++ ++++f+ +++++++
  gi|313117438|ref|YP_004044421.1| 157 ---EITADDE-IYIPAGDGR--LGFV-DTSDVAAVAATVLTE-AGYENRTLDLTGpESMDFDAVAAVFSDVLDRRIT 225
                                       ...6666666.677777777..7787.*****9877776666.55555555555437789***************** PP

                                       EE CS
                              NmrA 231 Yt 232
                                       Y 
  gi|313117438|ref|YP_004044421.1| 226 YA 227
                                       96 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.7e-06    0.0034       1      61 [.      15      75 ..      15     103 .. 0.75
   2 ?   -0.7   0.0      0.39   7.7e+02     201     228 ..     164     191 ..     143     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-06
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHH CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfk 61
                                      ilVtGatG +G+ lv +ll+   +v + +  +++ ++   +  e ve d+  ++ +  +++
  gi|313117438|ref|YP_004044421.1| 15 ILVTGATGTVGKPLVTRLLDTLAQVRVATTSPQTARERFGNAPEYVEFDFERPETWGSALE 75
                                      8*******************99776666666444444333333788888877777666666 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.39
                                       EEETTST-EEEEEEHHHHHHHHHHHHHH CS
                         Epimerase 201 tllgdgtalRdflyveDvaeaillvleh 228
                                       +++  g+ +  f++ +Dva +  +vl++
  gi|313117438|ref|YP_004044421.1| 164 IYIPAGDGRLGFVDTSDVAAVAATVLTE 191
                                       455578888899*********9999998 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.4e-06    0.0048       1      41 [.      17      53 ..      17      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRl 41
                                      +TGaTG +Gk L+ +LL+t ++v+    v ++s ++a+eR+
  gi|313117438|ref|YP_004044421.1| 17 VTGATGTVGKPLVTRLLDTLAQVR----VATTSPQTARERF 53
                                      7******************99744....4455666666666 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.9e-05     0.058       8      36 ..     255     283 ..     253     287 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                            HTH_23   8 lrillllaeGlsvreIAreLgvsrrTvyr 36 
                                       ++i++l   G ++ ++A+ L++s+rTv++
  gi|313117438|ref|YP_004044421.1| 255 YSIVRLGVSGRTTDDVATVLDRSPRTVRQ 283
                                       578899999******************97 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.8e-05      0.16       7      35 ..     254     282 ..     254     286 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.8e-05
                                       HHHHHHHHCTTS-HHHHHHHHTS-HHHHH CS
                              GerE   7 ErevLrllaeGksnkeIAeelniSekTVk 35 
                                       E ++ rl ++G ++ ++A  l+ S++TV+
  gi|313117438|ref|YP_004044421.1| 254 EYSIVRLGVSGRTTDDVATVLDRSPRTVR 282
                                       66788999********************7 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.8e-05      0.14       1      50 [.      13      77 ..      13      83 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.8e-05
                                      EEEEEESTTSHHHHHHHHHCTTTSEEE.EEE-TT..............T--TTSHHHHHHHHHHH CS
                     RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglev.laltre..............eldltdaeavaellkea 50
                                      m+ilvtGa+G +G+ L+ +l    ++v +a+t++              e+d++++e+  ++l+++
  gi|313117438|ref|YP_004044421.1| 13 MRILVTGATGTVGKPLVTRLLDTLAQVrVATTSPqtarerfgnapeyvEFDFERPETWGSALEQI 77
                                      99*************99887765555524444445677777777777777777777777666665 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00013      0.26       1      69 [.      16      79 ..      16     105 .. 0.76
   2 ?   -2.0   0.0      0.71   1.4e+03     213     232 ..     100     119 ..      93     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleealegvdv 69
                                      +vtG++G +G+ lv +L+++    +vrv+     p++    ++++++  ++e D    ++   ale+++ 
  gi|313117438|ref|YP_004044421.1| 16 LVTGATGTVGKPLVTRLLDTL--AQVRVATTS--PQT--ARERFGNAPeYVEFDFERPETWGSALEQINR 79
                                      69***************9875..79**98544..333..2233333333788888888888888877765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.71
                         3Beta_HSD 213 sdrvYvgNvawahilAaral 232
                                       +drv vg va+  il a +l
  gi|313117438|ref|YP_004044421.1| 100 ADRVGVGHVAYLSILGAEKL 119
                                       68899999999999988877 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.5e-05      0.19       3      72 ..      15      78 ..      13      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.5e-05
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekav 72
                                      +lvtGa++ +G+ ++ +l+   a+v v+  s+++++e   +         ++++D +  e +  ++e++ 
  gi|313117438|ref|YP_004044421.1| 15 ILVTGATGTVGKPLVTRLLDTLAQVRVATTSPQTARERFGNAP------EYVEFDFERPETWGSALEQIN 78
                                      89*************************9999888855555544......588888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1926.86
//
Query:       gi|313117439|ref|YP_004044422.1|  [L=145]
Description: universal stress protein UspA-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-29  101.0   0.8    8.7e-29  100.8   0.8    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.8   4.9e-33   8.7e-29       1     140 [.       1     138 [.       1     139 [. 0.96

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 4.9e-33
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+ Il+++Dg e+ +++  + l+la++++a++++l+vid+ra+ + +    +   +ele +++e+   a  ++ e 
  gi|313117439|ref|YP_004044422.1|   1 MYDDILLPTDGDESMDNVYAHTLDLAQRHDATVHILYVIDDRAFLTLASDVVDNVVSELEATGEEATTIA-LDRIES 76 
                                       9*****************************************************9999999999988665.99**** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       g+v+ +  ++ g+paeei+++ e+ed+d++ +G++g s+ ++ ++GSvs +v++ ap+pVl V
  gi|313117439|ref|YP_004044422.1|  77 GDVEATAAIRRGNPAEEIIDYIEREDIDIVTMGTHG-SNYQENMVGSVSARVVADAPVPVLTV 138
                                       ************************************.9999999*****************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 1117.76
//
Query:       gi|313117440|ref|YP_004044423.1|  [L=107]
Description: hypothetical protein Hbor_32300 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.8   0.1      0.026   15.1   0.1    1.3  1  ASCH      ASCH domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.4e-06     0.026      50      96 ..      49      96 ..      48     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-06
                                      EEEEEEEEEHHHHHHHHHCHCC--.-HCHHHHHHHCCHHHHHCCEEEE CS
                              ASCH 50 vevtkvevkpfeevteehalkege.sleewrevheefyeeeseeyede 96
                                      +++t+ve +++ + t+e+a+ eg  sl+  ++ +++  ++ +e  e  
  gi|313117440|ref|YP_004044423.1| 49 FTITSVEHRTLGDFTDEDAKREGSeSLDAYKQRMKRVHPGDFEWDESS 96
                                      579**********************************99988733344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 691.06
//
Query:       gi|313117441|ref|YP_004044424.1|  [L=594]
Description: subtilisin-like serine protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-48  165.5   8.8    1.6e-48  165.5   8.8    1.6  2  Peptidase_S8  Subtilase family
     0.0057   16.2   0.1      0.012   15.2   0.1    1.4  1  DUF4225       Protein of unknown function (DUF4225)
     0.0095   16.6   0.1      0.021   15.5   0.1    1.6  1  Inhibitor_I9  Peptidase inhibitor I9
  ------ inclusion threshold ------
      0.024   15.6   0.3      0.088   13.8   0.3    2.0  1  CHRD          CHRD domain
      0.082   13.3   0.0       0.25   11.7   0.0    1.9  1  fn3           Fibronectin type III domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.88   3.2e+03       4      50 ..      19      64 ..      17      73 .. 0.76
   2 !  165.5   8.8   4.5e-52   1.6e-48       1     295 [.     129     370 ..     129     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.88
                                      -EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  4 vlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsetts 50
                                      v ++++ tG+  +    ++t d+ r++v ++++ g +++g+ +++ +
  gi|313117441|ref|YP_004044424.1| 19 VGIGIASTGF-IGTGSAQETSDNSRHVVGTKSRYGVDVAGQRADAVD 64
                                      6688888888.667777888899999998888888888887776665 PP

  == domain 2  score: 165.5 bits;  conditional E-value: 4.5e-52
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g g  vavlDtG++++hpdl  t+             g g++  ds+ +++ w++d       HGth+AG+++a  +
  gi|313117441|ref|YP_004044424.1| 129 GTGADVAVLDTGIESTHPDLTRTL-------------GEGYAVVDSDRGEEPWNDDHT-----HGTHCAGTIGAV-N 186
                                       56788****************554.............445667789999999998875.....************.* PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnkk 154
                                       + ++++gvapg+++ ++k+l+++g+   tg +++++i++aa ++ dv++ms+g +ts +++ ++    a+++a  +k
  gi|313117441|ref|YP_004044424.1| 187 NGQGVVGVAPGVTLHAIKALNGDGSG--TGGDIAEGIRWAADQGYDVLSMSIG-ATSPSSVIED----AVKYAY-DK 255
                                       ********************888866..58***********************.6666666655....9*****.99 PP

                                       T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 155 gvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrq 231
                                       gvl+v++aGN+g      ++   +++p+ ++ v++v+++t ++++++fSs+Gp++      di+apG++i st+   
  gi|313117441|ref|YP_004044424.1| 256 GVLLVAAAGNEG------PCDDCIHYPAAYDDVVAVSSTTIDDELSEFSSTGPEV------DIAAPGSDITSTVIGG 320
                                       ************......8888*******************************98......6*************** PP

                                       CHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 232 snnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaq 295
                                       +        y ++sGTSmA+P+++g+ A+l+   +  ++++ r+ l  tA+d+       ++++
  gi|313117441|ref|YP_004044424.1| 321 G--------YRAFSGTSMATPHVSGVGAVLM--ANGASNTEARKRLTETAEDI----GLDQNEM 370
                                       *........**********************..5668999**********998....2333444 PP

>> DUF4225  Protein of unknown function (DUF4225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   3.2e-06     0.012      45      99 ..     316     364 ..     313     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-06
                           DUF4225  45 gvVagglqivaGvalvskasetvvgavaGalLilhGannvvenisyllgreektG 99 
                                        v+ gg   ++G  ++     t +++++Ga+L+++Ga+n+ e+ ++l +  e +G
  gi|313117441|ref|YP_004044424.1| 316 TVIGGGYRAFSGTSMA-----TPHVSGVGAVLMANGASNT-EARKRLTETAEDIG 364
                                       7999************.....9*****************6.77777777666666 PP

>> Inhibitor_I9  Peptidase inhibitor I9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.8e-06     0.021      50      81 ..      74     105 ..      32     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.8e-06
                                       SEEEEEE-GGGHHHHHTSTTEEEEEEEEEEEE CS
                      Inhibitor_I9  50 nGfavklteeqaeklrkrpeVesVepDqsvrl 81 
                                       ++  + +++e + +l+ r++V++Ve+D +v++
  gi|313117441|ref|YP_004044424.1|  74 KAVVGDFSDEALAELESRDDVRYVERDVTVQT 105
                                       677899************************98 PP

>> CHRD  CHRD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   2.5e-05     0.088      13     110 ..     445     580 ..     435     586 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                              CHRD  13 pavttgasGtavltldddgktlsysvtvsgls...dvtaaHiheg.aagengpvvvtleetekekesaetvp..... 80 
                                       + ++++++Gt++ t+++ +    y++    +    +vt++ +    +  +++pvv tl++t+ e e+ae        
  gi|313117441|ref|YP_004044424.1| 445 EVGSESSAGTFTTTVEELEADTDYQFRAYATAdddTVTGSAVAFStSEPAEAPVVKTLSPTDIEHEEAELRGevvsl 521
                                       446667889999999888888888888877755553333322222233499********999988766666699999 PP

                              CHRD  81 .............................gaatlteeqlaalkagelyvnvhteefpgG 110
                                                                    ++ +  +e+ ++l++ge yv v+t + p+G
  gi|313117441|ref|YP_004044424.1| 522 gdadevtpgficwekgdrddaeyiedfdtDEPEEFDEDIEDLDDGETYVAVATVTTPDG 580
                                       99999999999998888887777776665333333455556999*************96 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     7e-05      0.25      35      76 ..     429     475 ..     401     480 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7e-05
                                       EEEEETTSTS.....TEEEEEECSTSSEEEEESSSTTEEEEEEEEEE CS
                               fn3  35 veyrekgsee.....ewneftvprtttsvtltgLkpgteYevrVqav 76 
                                       vey+ +g e+     +++    ++ t + t++ L+++t+Y++r +a 
  gi|313117441|ref|YP_004044424.1| 429 VEYWVDGAEHdsattVEVGSESSAGTFTTTVEELEADTDYQFRAYAT 475
                                       7888888888644333333334445779***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 4471.70
//
Query:       gi|313117442|ref|YP_004044425.1|  [L=54]
Description: YHS domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-06   26.1   0.7    1.4e-05   25.0   0.4    1.7  2  YHS       YHS domain
     0.0069   16.3   0.4       0.59   10.2   0.1    2.1  2  DUF2116   Uncharacterized protein containing a Zn-ribbon (DUF
  ------ inclusion threshold ------
      0.032   14.2   4.3       0.12   12.3   4.3    1.9  1  zf-FCS    MYM-type Zinc finger with FCS sequence motif
      0.081   13.1   0.5        8.9    6.5   0.1    2.1  2  SR1P      SR1 protein
       0.16   11.5   6.4       0.52    9.8   6.4    1.9  1  zf-FLZ    zinc-finger of the FCS-type, C2-C2


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3   4.5e+03      25      26 ..      16      17 ..       6      22 .. 0.57
   2 !   25.0   0.4     4e-09   1.4e-05      24      41 ..      30      47 ..      30      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                               YHS 25 eY 26
                                      +Y
  gi|313117442|ref|YP_004044425.1| 16 WY 17
                                      44 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 4e-09
                               YHS 24 keYyFcSegCkdkFedeP 41
                                      ++Y FcSe+C+++F+deP
  gi|313117442|ref|YP_004044425.1| 30 QTYAFCSEHCRSEFLDEP 47
                                      69***************9 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0     0.008        29       6      17 ..       4      15 ..       2      18 .. 0.87
   2 !   10.2   0.1   0.00016      0.59      18      28 ..      33      43 ..      28      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.008
                           DUF2116  6 CivCGkaIplde 17
                                      C++CG  I+  e
  gi|313117442|ref|YP_004044425.1|  4 CANCGDVIDRSE 15
                                      ********9877 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                           DUF2116 18 sfCsekCqeey 28
                                       fCse+C++e+
  gi|313117442|ref|YP_004044425.1| 33 AFCSEHCRSEF 43
                                      69*******99 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.3   3.4e-05      0.12      28      41 .]      30      43 ..       1      43 [. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.4e-05
                            zf-FCS 28 vvgqFCStsCldsY 41
                                      +++ FCS++C++++
  gi|313117442|ref|YP_004044425.1| 30 QTYAFCSEHCRSEF 43
                                      7889********98 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0071        25       6      15 ..       4      13 ..       2      18 .. 0.88
   2 ?    6.5   0.1    0.0025       8.9      17      35 ..      24      41 ..      21      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0071
                              SR1P  6 CqtCnatIdh 15
                                      C +C+ +Id 
  gi|313117442|ref|YP_004044425.1|  4 CANCGDVIDR 13
                                      ********96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0025
                              SR1P 17 edekVttLYgtCnqceCkk 35
                                      ++++V   Y++C    C++
  gi|313117442|ref|YP_004044425.1| 24 DEDGVLQTYAFCS-EHCRS 41
                                      68999999****7.77876 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.4   0.00015      0.52      37      48 ..      33      44 ..       1      48 [. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                            zf-FLZ 37 aFCSeeCRqqqi 48
                                      aFCSe CR++ +
  gi|313117442|ref|YP_004044425.1| 33 AFCSEHCRSEFL 44
                                      9*******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.28u 0.20s 00:00:00.48 Elapsed: 00:00:00.36
# Mc/sec: 454.74
//
Query:       gi|313117443|ref|YP_004044426.1|  [L=886]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-41  140.1   1.8    5.4e-41  140.1   1.8    2.5  2  BAT           GAF and HTH_10 associated domain
    6.6e-33  113.9   0.5    2.4e-14   53.8   0.0    3.3  3  GAF_2         GAF domain
    3.6e-21   74.7   0.0    1.7e-20   72.6   0.0    2.2  2  HTH_10        HTH DNA binding domain
    1.5e-12   47.7   0.4    5.4e-12   45.9   0.1    2.2  2  Response_reg  Response regulator receiver domain
      1e-09   38.8   0.0     0.0028   18.0   0.0    3.8  3  GAF_3         GAF domain
    7.1e-09   36.4   0.4     0.0021   18.7   0.0    4.0  5  GAF           GAF domain
     0.0095   15.4   0.5      0.037   13.6   0.2    2.2  2  Sigma70_r4    Sigma-70, region 4
  ------ inclusion threshold ------
       0.01   15.4   0.0      0.022   14.3   0.0    1.6  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.012   15.2   0.0      0.058   13.0   0.0    2.0  2  SatD          SatD family (SatD)
      0.018   15.4   0.1       0.35   11.2   0.0    3.1  3  FleQ          Flagellar regulatory protein FleQ


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.7       1.4   2.4e+03      16      64 ..     371     418 ..     362     433 .. 0.63
   2 !  140.1   1.8     3e-44   5.4e-41       1     154 [.     667     820 ..     667     822 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                               BAT  16 vlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedlda 64 
                                       +++a  + ++c+ e  ++ p++ ++v+  + v+g++ + v+d+ ++  +
  gi|313117443|ref|YP_004044426.1| 371 PVAATPELAECAAENPSVGPDTTDSVVWDVFVSGDT-ALVEDLQTTDAT 418
                                       555666667888888889999999988555555522.444444444333 PP

  == domain 2  score: 140.1 bits;  conditional E-value: 3e-44
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+v+e++l+i+++d+vl+++a+++++ ve+e ++p+ +++++v+f+v+ ++ ee+ ++a++  ++e++++v++++++
  gi|313117443|ref|YP_004044426.1| 667 DEVTEIKLKIHESDSVLNRIARKANASVEFEAVIPQPGNKTRVLFSVATDSIEEILSVADEFISIESITHVRQTGEK 743
                                       99*************************************************************************** PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                        l+e+t++g+++a+ l ++G ++++++a++++ + v+e+P+ advR+vve le++y ++eL++rr rer+++t ref
  gi|313117443|ref|YP_004044426.1| 744 QLFEATTTGSVVAQPLINYGTYPQEITADQSTIHAVIELPQFADVREVVELLENNYGKTELISRRDRERSRKTNREF 820
                                       ***************************************************************************99 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.6e-10   2.9e-07       5     135 ..     170     307 ..     166     310 .. 0.78
   2 !   26.1   0.1   4.9e-09   8.7e-06       3     137 ..     336     470 ..     334     471 .. 0.78
   3 !   53.8   0.0   1.4e-17   2.4e-14       1     137 [.     513     655 ..     513     656 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.6e-10
                                       HHHHHHHHHHHHHSS...EE.EEEEE-TTS-EEEEEEEES-TTSTT-S-B...---TT.HHHHHHHHTS-EEES-.G CS
                             GAF_2   5 eelldlvldelvelg.aalg.yillvdddgglrlaawgeaeeefgaaldr...plgeg.lvgealrtgrpvilnd.l 74 
                                       +e+ ++++d l+     +++ ++ +  ++g ++ ++w++ e+   + +     +l e  ++++a rt ++v++++ +
  gi|313117443|ref|YP_004044426.1| 170 KEVEQAICDCLTAESpYEFAaICSFSSEAGTFTPVTWAGCERDELDDAIEateKLCEQdPLAMANRT-QEVQFQNiP 245
                                       67888888888553337755266667789999999999776666555544354556666********.889999977 PP

                                       GG-S-HHHHH.HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglp.aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiai 135
                                        e ++ +g+   ++ + +s + vPli +  v+G+l+l++ + ++++e++++ + el++ i++
  gi|313117443|ref|YP_004044426.1| 246 GELAAVSGETkTSDDQRKSVITVPLIFGSTVHGILTLFRGQSHSLSERERDAFGELGSIIGL 307
                                       77777777776777777777*******999****************************9997 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 4.9e-09
                                       HHHHHHHHHHHHHHHS.S...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--.....-TTHHHHHHHHTS-EEES CS
                             GAF_2   3 dleelldlvldelvel.g.aalgyillvdddgglrlaawgeaeeefgaaldrpl.....geglvgealrtgrpviln 72 
                                       + +++++lv+++ + + + ++++++ +++ ++   l++ + ++e   +a++ p       +++v++++ +g   +++
  gi|313117443|ref|YP_004044426.1| 336 TKSDVAELVVNTGRVIlDlSHVAIFCIDETQNV--LEPVAATPELAECAAENPSvgpdtTDSVVWDVFVSGDTALVE 410
                                       6789***********66*999999999887666..5555555555555554422355657779************** PP

                                       -GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  73 dleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       dl++ ++    + ++ +  s+l+vP+   g   Gvl+      ++fd   + l+ +la++   a+
  gi|313117443|ref|YP_004044426.1| 411 DLQTTDATFEMA-QRTDAESGLFVPI---G-DRGVLVTLCGSVESFDTHTRKLVGMLAATTEAAL 470
                                       *99977777776.*************...5.66666655578888**************999887 PP

  == domain 3  score: 53.8 bits;  conditional E-value: 1.4e-17
                                       HHHHHHHHHHHHHHHHHS.S..EEEEEEE-TT.S-EEEEEEEES-TTSTT-S-B--.-TT.HHHHHHHHTS-EEES- CS
                             GAF_2   1 aadleelldlvldelvel.gaalgyillvddd.gglrlaawgeaeeefgaaldrpl.geg.lvgealrtgrpvilnd 73 
                                       aa+ ee+ ++v++ l e  g+ +++i++ d   g++  +aw + +    ++++ ++ +++ ++ + l +g  +++ +
  gi|313117443|ref|YP_004044426.1| 513 AASREEIEEAVCEKLNESgGFPFVWIGERDSIsGSISPRAWVNNGSDYLDQVSFDIdDSSePAVQTLTSGTMTVIPN 589
                                       5789***********99845********773313355559998888888888666675555999************* PP

                                       GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       ++++ +  +++  a   g++s +++Pl++e+  +G+l++yan+++afde  +e+Leel+ ++a ai
  gi|313117443|ref|YP_004044426.1| 590 VADNLREEPWRqkALTNGYQSVISIPLVYEDVRYGILTVYANQQSAFDELVREVLEELGCTVAYAI 655
                                       ***88888888889***************99*********************************99 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.9   3.4e+03      22      38 ..      27      43 ..      25      47 .. 0.83
   2 !   72.6   0.0   9.3e-24   1.7e-20       1      52 [.     828     879 ..     828     880 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                            HTH_10 22 RrvtlkeLAkelGIsks 38
                                      R+ +l+ +A+ ++++ +
  gi|313117443|ref|YP_004044426.1| 27 RKSQLQGVAESIDVTHT 43
                                      8899999******9876 PP

  == domain 2  score: 72.6 bits;  conditional E-value: 9.3e-24
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++q+evl++Aye+G+F++PR++t +e+A+ +GIs+st+  hLr ae+kl+
  gi|313117443|ref|YP_004044426.1| 828 LTERQYEVLRTAYESGFFEEPREITGQEVADLIGISQSTFNHHLRGAERKLF 879
                                       9*************************************************97 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.1     3e-15   5.4e-12       1     111 [.       9     126 ..       9     127 .. 0.83
   2 ?   -2.8   0.0       3.8   6.9e+03      10      32 ..     636     657 ..     631     662 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 3e-15
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEE......ESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTT CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevae......aedgkealellkeekvdlillDinmpgmdGlellkeireedpe 71 
                                       vl++d dp+ ++ ++ +l++++++ vae      +e+ +e  + l   ++dl+++ + +p+ + le++++i  + p 
  gi|313117443|ref|YP_004044426.1|   9 VLLIDQDPDDAHFITHYLRKSQLQGVAEsidvthTETLSEGEARLSGTEYDLVMVALGLPEYEDLETTRRIASQAPA 85 
                                       7999999999999999999777755554111111666777777777777**************************** PP

                                       SEEEEEESSTSHHHHHHHHHCTESEEEESSG.-HHHHHHHH CS
                      Response_reg  72 lpviiltahseeedavealkagaddflsKpf.dpeeLlkal 111
                                       +p+i+l  +se ++a++al+ ga+d+l K+  d+++Ll  +
  gi|313117443|ref|YP_004044426.1|  86 VPIIVLAERSERDTAIQALQNGAQDYLIKDRiDIDQLLRSI 126
                                       *****************************844888888765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHTTEEEEEEESSH CS
                      Response_reg  10 vrellrqlleeegyeevaeaedg 32 
                                       + el+r++lee g+ +va a +g
  gi|313117443|ref|YP_004044426.1| 636 FDELVREVLEELGC-TVAYAING 657
                                       5689999*******.88877666 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0003      0.53      70     125 ..     251     307 ..     205     311 .. 0.76
   2 ?    5.6   0.0     0.011        20      10      92 ..     345     438 ..     337     465 .. 0.74
   3 !   18.0   0.0   1.6e-06    0.0028      40     127 ..     554     655 ..     516     656 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                             GAF_3  70 psfaeedglpdraa.lavPLvagrqviGvlalastkprafdaedlelleslArqiat 125
                                        s++ +++ ++r+  + vPL+ g++v G+l l + +  ++++++++ + +l++ i++
  gi|313117443|ref|YP_004044426.1| 251 VSGETKTSDDQRKSvITVPLIFGSTVHGILTLFRGQSHSLSERERDAFGELGSIIGL 307
                                       34444555555555166****************999999*********999999887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                             GAF_3  10 lkllvkllgaevgalllldedgnklqvaagwdgkpalse......sl.d..edsalarralssgevvse......ps 71 
                                       +  +  +l+++ +a++  de +n l ++a++   p l e      s+ +  +ds +++  +s + +++e      ++
  gi|313117443|ref|YP_004044426.1| 345 VNTGRVILDLSHVAIFCIDETQNVLEPVAAT---PELAEcaaenpSVgPdtTDSVVWDVFVSGDTALVEdlqttdAT 418
                                       55567799*********************99...3333334446644334677777777777777776677777777 PP

                             GAF_3  72 faeedglpdraalavPLvagr 92 
                                       f+++++++ ++ l+vP+ + r
  gi|313117443|ref|YP_004044426.1| 419 FEMAQRTDAESGLFVPIGD-R 438
                                       7888888888888888887.4 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.6e-06
                             GAF_3  40 w.dgkpalse...sld.edsalarralssgevvsepsfae..edglpd.......raalavPLvagrqviGvlalas 102
                                         +g++ l +    +d   +++ +++ s  + v+ + ++   e+ +++       ++++ +PLv ++  +G+l ++ 
  gi|313117443|ref|YP_004044426.1| 554 VnNGSDYLDQvsfDIDdSSEPAVQTLTSGTMTVIPNVADNlrEEPWRQkaltngyQSVISIPLVYEDVRYGILTVYA 630
                                       355555555552255556666666666666777775543333555555555556688899***************** PP

                             GAF_3 103 tkprafdaedlelleslArqiatai 127
                                       ++ +afd+  +e le+l+  +a ai
  gi|313117443|ref|YP_004044426.1| 631 NQQSAFDELVREVLEELGCTVAYAI 655
                                       *****************99998887 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       7.9   1.4e+04      19      52 ..      58      89 ..      54     138 .. 0.54
   2 ?    5.3   0.0     0.016        28      86     124 ..     261     300 ..     206     307 .. 0.78
   3 !    7.5   0.2    0.0035       6.2       5     132 ..     340     469 ..     337     470 .. 0.63
   4 !   18.7   0.0   1.2e-06    0.0021      48     133 .]     572     655 ..     516     655 .. 0.76
   5 ?   -3.5   0.0       8.4   1.5e+04      72      97 ..     736     761 ..     706     782 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.9
                                      ESEEEEEE..EEETTEEECEEEEECCEEEETTSHHH CS
                               GAF 19 adrvalyl..pdydGlhydipqasrwlfmkngrgic 52
                                      +d v++ l  p+y++l    +  +r   + +  +i+
  gi|313117443|ref|YP_004044426.1| 58 YDLVMVALglPEYEDL----ETTRRIASQAPAVPII 89
                                      6666664433444443....3333332223333333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                                       TESEEEEEEEEETTEEEEEEEEEE.SSSCSHHHHHHHHHH CS
                               GAF  86 girsslvvPlvndgelwGllvlhn.psppftreelellqv 124
                                       + +s+++vPl+ +  + G+l+l + +s++ ++ e++ + +
  gi|313117443|ref|YP_004044426.1| 261 QRKSVITVPLIFGSTVHGILTLFRgQSHSLSERERDAFGE 300
                                       5579*******************96444677777766655 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHTESEEEEEEEEETTEEE.....CEEEEECC...........EEEET.TSHHHHHHHHHSSSEEE CS
                               GAF   5 lldtvveelrellgadrvalylpdydGlhy.....dipqasrw...........lfmkn.grgicgqvlatgqplvi 64 
                                       +++ vv++ r +l++ +va++  d+  +                          + + +  ++++  v+ +g++ ++
  gi|313117443|ref|YP_004044426.1| 340 VAELVVNTGRVILDLSHVAIFCIDETQNVLepvaaT------PelaecaaenpsVGP-DtTDSVVWDVFVSGDTALV 409
                                       667788888889999999998733333222233321......222333333332222.23555777*********** PP

                                       ST.GGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCSHHHHHHHHHHHHHHHHHH CS
                               GAF  65 pd.stpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsppftreelellqvladqvava 132
                                       +d +t+d  f        ++++   s l vP+ ++g l   ++l    ++f+++ + l+ +la+  + a
  gi|313117443|ref|YP_004044426.1| 410 EDlQTTDATFEM------AQRTDAESGLFVPIGDRGVL---VTLCGSVESFDTHTRKLVGMLAATTEAA 469
                                       *94445555544......6789999********99763...3333333379999999999999877666 PP

  == domain 4  score: 18.7 bits;  conditional E-value: 1.2e-06
                                       TSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHH CS
                               GAF  48 grgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellq 123
                                        ++ + q+l++g   vip++++  r  +  +r+ +   g++s++++Plv ++  +G+l+++  ++  f++  +e+l+
  gi|313117443|ref|YP_004044426.1| 572 SEP-AVQTLTSGTMTVIPNVADNLREEP--WRQKALTNGYQSVISIPLVYEDVRYGILTVYANQQsAFDELVREVLE 645
                                       333.4499**********8654444444..66688899************************55557********** PP

                                       HHHHHHHHHH CS
                               GAF 124 vladqvaval 133
                                       +l+  va a+
  gi|313117443|ref|YP_004044426.1| 646 ELGCTVAYAI 655
                                       *998888776 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 8.4
                                       THHTTHHHHHHHHTTESEEEEEEEEE CS
                               GAF  72 rfaqynrrdllenmgirsslvvPlvn 97 
                                       +  q+ +++l+e++ + s+++ Pl+n
  gi|313117443|ref|YP_004044426.1| 736 HVRQTGEKQLFEATTTGSVVAQPLIN 761
                                       33333356788888888888888887 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   2.2e+03       4      12 ..     289     297 ..     288     298 .. 0.83
   2 !   13.6   0.2   2.1e-05     0.037       4      47 ..     827     877 ..     826     879 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                                       HS-HHHHHH CS
                        Sigma70_r4   4 sLpererev 12 
                                       sL+erer+ 
  gi|313117443|ref|YP_004044426.1| 289 SLSERERDA 297
                                       8******85 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.1e-05
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrk 47 
                                       +L+er+ evl+  +        ++ T +E+++  giS+++   +++ A rk
  gi|313117443|ref|YP_004044426.1| 827 QLTERQYEVLRTAYesgffeePREITGQEVADLIGISQSTFNHHLRGAERK 877
                                       8*****************9888889*************9966666666555 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05     0.022      14      39 ..     846     872 ..     828     877 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                            HTH_24  14 knpr.isqreLAerlglSpstvnrrlk 39 
                                       ++pr i+ +e+A+ +g+S+st n +l+
  gi|313117443|ref|YP_004044426.1| 846 EEPReITGQEVADLIGISQSTFNHHLR 872
                                       48999********************98 PP

>> SatD  SatD family (SatD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.82   1.5e+03       4      74 ..     304     371 ..     303     374 .. 0.77
   2 ?   13.0   0.0   3.3e-05     0.058     101     201 ..     783     880 ..     759     882 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.82
                              SatD   4 liGdiinskqiterskvqkklkklleelnkkyaeeliskftitlGdefqallkvekkifqiideiqlalkd 74 
                                       +iG  i + + +er+++  +l+++  +l ++ +++ ++++ + +G      l  ++   + ide q  l +
  gi|313117443|ref|YP_004044426.1| 304 IIGLWITAADRKEREQILTTLHHATRQLLHTETKSDVAELVVNTGRVI---LDLSHVAIFCIDETQNVLEP 371
                                       899999999999999999999999999999999988899999888654...44444445567777766655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.3e-05
                              SatD 101 PayweareaidyihdkndyGttklalrledkeldkvlnallaagdfikskwrasqlevletllekkiyee..kfdqk 175
                                       P + + re ++ +  +n+yG+t+l  r + +   k+   ++++      + +  q+evl t  e +++ee  + + +
  gi|313117443|ref|YP_004044426.1| 783 PQFADVREVVELL--ENNYGKTELISRRDRERSRKTNREFITTF---EEQLTERQYEVLRTAYESGFFEEprEITGQ 854
                                       6677777777776..588*****977776666666666777765...578999****************9656899* PP

                              SatD 176 klaeklklsasalskrlkssglkiyl 201
                                       ++a+ + +s+s+++  l+ ++ k+++
  gi|313117443|ref|YP_004044426.1| 855 EVADLIGISQSTFNHHLRGAERKLFV 880
                                       ******************99999875 PP

>> FleQ  Flagellar regulatory protein FleQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.35       1      81 [.       8      97 ..       8     131 .. 0.80
   2 ?   -3.3   0.0       6.4   1.2e+04      56      91 ..     214     248 ..     209     250 .. 0.72
   3 ?   -0.4   0.0      0.83   1.5e+03      46      81 ..     509     544 ..     494     549 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                              FleQ  1 kiLvidddaerrrdleti.....LeFlgeeveavsseel...saaleesssealavilgsvs.sleealealaekdphl 70
                                      ++L+id+d + ++ ++       L+ + e++ ++  e l   +a l+ ++ ++++v lg  + +  e+ +++a+++p +
  gi|313117443|ref|YP_004044426.1|  8 RVLLIDQDPDDAHFITHYlrksqLQGVAESIDVTHTETLsegEARLSGTEYDLVMVALGLPEyEDLETTRRIASQAPAV 86
                                      5889999999888887651111156677888888888888878888889999999999999988999************ PP

                              FleQ 71 Pvlllgesdea 81
                                      P+++l e++e+
  gi|313117443|ref|YP_004044426.1| 87 PIIVLAERSER 97
                                      ******99887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.4
                              FleQ  56 leealealaekdphlPvlllgesdeaeelanvigel 91 
                                       l++a+ea  +  ++ P+ ++++++e  + +n+ gel
  gi|313117443|ref|YP_004044426.1| 214 LDDAIEATEKLCEQDPLAMANRTQEV-QFQNIPGEL 248
                                       56677777777777788888888888.888877766 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.83
                              FleQ  46 lavilgsvssleealealaekdphlPvlllgesdea 81 
                                       +++ + s ++ eea+ + ++++  +P++ +ge+d+ 
  gi|313117443|ref|YP_004044426.1| 509 VLIQAASREEIEEAVCEKLNESGGFPFVWIGERDSI 544
                                       455555566788999999999999********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 6455.43
//
Query:       gi|313117444|ref|YP_004044427.1|  [L=206]
Description: hypothetical protein Hbor_32340 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.5   0.0        1.3    9.1   0.0    2.1  2  SH3_14    Dda helicase SH3 domain


Domain annotation for each model (and alignments):
>> SH3_14  Dda helicase SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.026   4.7e+02      83     110 ..       9      36 ..       3      39 .. 0.85
   2 ?    9.1   0.0   7.2e-05       1.3      49      83 ..     151     188 ..     133     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.026
                                       E--SHHHHHHHHHHHHHHHHHHHS--SS CS
                            SH3_14  83 vlsddeekekfalflakaaetykslrkg 110
                                       ++ + + + k+++fl    + yks++ +
  gi|313117444|ref|YP_004044427.1|   9 LIAERLGRVKYDRFLFYLMGPYKSFNLN 36 
                                       5677788899**************9865 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 7.2e-05
                                       EE--TTSSS-EEE...EEEEEEEEEESSS---EEEEEE CS
                            SH3_14  49 fvkaktvdGellk...rafdlavetvedeeyyvekikv 83 
                                       fv++  v   +++     +dl vet+e ee  v k++ 
  gi|313117444|ref|YP_004044427.1| 151 FVHEDDVTSAMIRsarVRWDLRVETYETEEELVSKLRF 188
                                       666666666665545468*************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 1745.93
//
Query:       gi|313117445|ref|YP_004044428.1|  [L=137]
Description: ArsR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-12   45.1   0.1    1.7e-11   44.0   0.1    1.5  1  HTH_20          Helix-turn-helix domain
    3.3e-08   33.3   0.0    4.5e-08   32.8   0.0    1.2  1  HTH_5           Bacterial regulatory protein, arsR family
    3.9e-08   33.1   0.0    5.9e-08   32.5   0.0    1.2  1  MarR_2          MarR family
    2.3e-07   30.6   0.0    3.7e-07   30.0   0.0    1.3  1  MarR            MarR family
    7.9e-07   28.9   0.1    1.2e-06   28.3   0.1    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    5.6e-05   23.2   0.0    8.2e-05   22.7   0.0    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0004   19.9   0.0    0.00058   19.4   0.0    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00068   19.4   0.0     0.0012   18.6   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
     0.0011   18.9   0.0     0.0015   18.4   0.0    1.2  1  TFIIE_alpha     TFIIE alpha subunit
     0.0016   18.9   0.2     0.0027   18.2   0.2    1.4  1  HTH_27          Winged helix DNA-binding domain
     0.0023   17.9   1.1      0.012   15.6   0.2    2.0  2  PadR            Transcriptional regulator PadR-like family
     0.0038   17.0   0.0     0.0048   16.7   0.0    1.2  1  HxlR            HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.018   15.2   0.0    1.3  1  HTH_34          Winged helix DNA-binding domain
      0.018   14.7   0.0      0.027   14.1   0.0    1.2  1  RP-C            Replication protein C N-terminal domain
      0.026   14.6   0.3       0.13   12.3   0.2    2.1  2  TFIIA_gamma_N   Transcription initiation factor IIA, gamma su
      0.042   12.7   0.0      0.042   12.7   0.0    1.0  1  HTH_micro       HTH-like


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.1   1.5e-14   1.7e-11       4      57 ..      36      89 ..      31      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.5e-14
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      + A++h++R+++l  L   + ++++el e++d++++tl+yHL++L+++gLve +
  gi|313117445|ref|YP_004044428.1| 36 HAAVGHRTRYEVLYRLVHSGDMSPKELEEAIDIDDSTLHYHLNKLVDVGLVEKR 89
                                      679************************************************976 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0     4e-11   4.5e-08       3      47 .]      43      88 ..      41      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4e-11
                                      HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      tR ++L+ L   g ++  el e++++  st+ +HL+kL + GLVek
  gi|313117445|ref|YP_004044428.1| 43 TRYEVLYRLVHsGDMSPKELEEAIDIDDSTLHYHLNKLVDVGLVEK 88
                                      8999***99999********************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   5.3e-11   5.9e-08       5      55 ..      42      90 ..      38      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 5.3e-11
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      ++ + vL+ L ++++  ++++el+++ +++ s+++++l++Lv+ GLve+r 
  gi|313117445|ref|YP_004044428.1| 42 RTRYEVLYRLVHSGD--MSPKELEEAIDIDDSTLHYHLNKLVDVGLVEKRQ 90
                                      57899*********9..*******************************995 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   3.3e-10   3.7e-07       3      53 ..      42      92 ..      41      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.3e-10
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                      +t++++L+ l ++g++s +eL +++ ++ st+   l +L++ Gl+e+++ +
  gi|313117445|ref|YP_004044428.1| 42 RTRYEVLYRLVHSGDMSPKELEEAIDIDDSTLHYHLNKLVDVGLVEKRQLT 92
                                      589********************************************9976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1     1e-09   1.2e-06      12      65 ..      46     106 ..      43     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1e-09
                                       CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE- CS
                              TrmB  12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYrav 65 
                                       +v   L+ +g ++ +e+ e+++++ s+    L++L+d GlVe+++ +       +++Yra+
  gi|313117445|ref|YP_004044428.1|  46 EVLYRLVHSGDMSPKELEEAIDIDDSTLHYHLNKLVDVGLVEKRQLTergqdglYTYYRAT 106
                                       57788***************************************97778999999999985 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   7.4e-08   8.2e-05      22      61 ..      60      95 ..      42     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.4e-08
                    B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqsiidsatkks 61
                                      ++L  ++++d + l+y+l++L + gL++k+++    t+++
  gi|313117445|ref|YP_004044428.1| 60 KELEEAIDIDDSTLHYHLNKLVDVGLVEKRQL----TERG 95
                                      57778899***********************9....5544 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.2e-07   0.00058       3      48 .]      42      87 ..      41      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.2e-07
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +t++++L  L   +++s +eL e++++  st++++l++L++ Gl++
  gi|313117445|ref|YP_004044428.1| 42 RTRYEVLYRLVHSGDMSPKELEEAIDIDDSTLHYHLNKLVDVGLVE 87
                                      577888888888999**************************99986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0012      16      50 ..      54      88 ..      48      90 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       ++++ +el +++++  St h +L+ Lv  G+ve+
  gi|313117445|ref|YP_004044428.1| 54 SGDMSPKELEEAIDIDDSTLHYHLNKLVDVGLVEK 88
                                      688******************************97 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0015      15      73 ..      44     103 ..      32     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE.TTTEEEEEE CS
                       TFIIE_alpha  15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd.eekswykyy 73 
                                         +vl  L+  g ++  +l++ + id   l   Ln+L + +lv+ ++  +  + + y+yy
  gi|313117445|ref|YP_004044428.1|  44 RYEVLYRLVHSGDMSPKELEEAIDIDDSTLHYHLNKLVDVGLVEKRQLTErGQDGLYTYY 103
                                       5789*******************************************9994444555554 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   2.4e-06    0.0027      19      65 ..      57     106 ..      42     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.4e-06
                            HTH_27  19 kkladlcgrlnvedshisyslkkLtekGLvertgdeadrre....krvrlT 65 
                                       ++ ++l ++ +++ds+ +y l+kL+  GLve+ +  ++r++    + +r+T
  gi|313117445|ref|YP_004044428.1|  57 MSPKELEEAIDIDDSTLHYHLNKLVDVGLVEKRQL-TERGQdglyTYYRAT 106
                                       44478999**********************65544.344444444888877 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.32   3.6e+02      20      45 ..      30      55 ..      27      64 .. 0.74
   2 !   15.6   0.2   1.1e-05     0.012      19      74 ..      62     114 ..      58     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.32
                                      HCCSTT-CCTTHHHHHHHHHHHHHTT CS
                              PadR 20 eelsegllelseGslYpaLkrLekeg 45
                                      +e++  + ++ + + Y +L rL  +g
  gi|313117445|ref|YP_004044428.1| 30 DEYLAMHAAVGHRTRYEVLYRLVHSG 55
                                      55666666777888899999999877 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.1e-05
                                       HHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEEESHCCCHHHH CS
                              PadR  19 leelsegllelseGslYpaLkrLekeglvesewees.gegpprkyYrlTdaGrrela 74 
                                       l    e+++++ +++l   L++L + glve+++ ++ g+++   yYr T  G+ +l+
  gi|313117445|ref|YP_004044428.1|  62 L----EEAIDIDDSTLHYHLNKLVDVGLVEKRQLTErGQDGLYTYYRATVFGEVTLT 114
                                       3....4458999***********************999999********99998876 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.3e-06    0.0048       2      77 ..      39     118 ..      38     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.3e-06
                                       HHSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-...EEEEEE-TCGG.GGH CS
                              HxlR   2 iggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPp...kveYsltekGr.sle 73 
                                       +g++ +  +l+ l++ g +  +el++a+ +i  ++L  +L +L   gl+e++ + e ++      Y+ t +G+ +l+
  gi|313117445|ref|YP_004044428.1|  39 VGHRTRYEVLYRLVHsGDMSPKELEEAI-DIDDSTLHYHLNKLVDVGLVEKRQLTERGQdglYTYYRATVFGEvTLT 114
                                       677778889****999************.*********************999887665111566778888873455 PP

                                       HHHH CS
                              HxlR  74 pvlq 77 
                                       + ++
  gi|313117445|ref|YP_004044428.1| 115 EGVD 118
                                       5555 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.6e-05     0.018       2      52 ..      44      94 ..      43     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkg 52
                                      R +vl  L+    ++++el ea+ + d+ L  hl+kL + g +e +   + 
  gi|313117445|ref|YP_004044428.1| 44 RYEVLYRLVHSGDMSPKELEEAIDIDDSTLHYHLNKLVDVGLVEKRQLTER 94
                                      889999**********************************99986654444 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.4e-05     0.027      73     104 ..      58      89 ..      56      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                              RP-C  73 sNaqLsralglsestlrrhlaaLveaGliirr 104
                                       s ++L +a+++ +stl +hl +Lv++Gl+  r
  gi|313117445|ref|YP_004044428.1|  58 SPKELEEAIDIDDSTLHYHLNKLVDVGLVEKR 89 
                                       668999**********************9776 PP

>> TFIIA_gamma_N  Transcription initiation factor IIA, gamma subunit, helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.7   1.9e+03      18      30 ..      48      60 ..      45      67 .. 0.73
   2 ?   12.3   0.2   0.00012      0.13       2      24 ..     100     123 ..      99     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                     TFIIA_gamma_N 18 LDeliqegkIspq 30
                                      L  l+++g++sp+
  gi|313117445|ref|YP_004044428.1| 48 LYRLVHSGDMSPK 60
                                      6678888888875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                     TFIIA_gamma_N   2 YelYRrstlGt.aLtdaLDeliqe 24 
                                       Y  YR +  G+ +Lt+ +Deli+ 
  gi|313117445|ref|YP_004044428.1| 100 YTYYRATVFGEvTLTEGVDELIRG 123
                                       999*******659*********85 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.042      93     140 ..      44      90 ..      31     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                         HTH_micro  93 yykivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqkt 140
                                        y+++  lv++ d  + +el + ++id  +l+Y ++kL   gl+e+++
  gi|313117445|ref|YP_004044428.1|  44 RYEVLYRLVHSGDM-SPKELEEAIDIDDSTLHYHLNKLVDVGLVEKRQ 90 
                                       58888889988886.5689**************************543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 920.26
//
Query:       gi|313117446|ref|YP_004044429.1|  [L=272]
Description: hypothetical protein Hbor_32360 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1789.88
//
Query:       gi|313117447|ref|YP_004044430.1|  [L=278]
Description: hypothetical protein Hbor_32380 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1782.39
//
Query:       gi|313117448|ref|YP_004044431.1|  [L=214]
Description: hypothetical protein Hbor_32390 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1432.94
//
Query:       gi|313117449|ref|YP_004044432.1|  [L=277]
Description: beta-lactamase superfamily metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-06   26.2   0.1    8.6e-06   25.4   0.1    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00019   21.5   4.7    0.00035   20.6   4.7    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   9.6e-10   8.6e-06       3      82 ..      33     106 ..      32     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9.6e-10
                                       EEES--TT..HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGH CS
                     Lactamase_B_2   3 iLiDagpd..lrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvy 76 
                                       +L+D+g +  ++       ++++l+  +   d ++l+h H+DH+agl+ +   + +   ++y +++++ +  + +++
  gi|313117449|ref|YP_004044432.1|  33 VLFDTGQSdaVV-------HNARLLGLPTTFDDIVLSHTHFDHTAGLDQFLDpMNQ--PRVYLHPEIWTHRYSTGPP 100
                                       566666664222.......33334555668999*****************996433..3599****99999998888 PP

                                       HHCHTT CS
                     Lactamase_B_2  77 laleee 82 
                                       +    +
  gi|313117449|ref|YP_004044432.1| 101 NGGSFP 106
                                       766655 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   4.7   3.9e-08   0.00035      18      78 ..      33      89 ..      31     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.9e-08
                                      EEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B 18 iLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78
                                      +L+DtG s +    a+    l   p   d+++l+H H+DH++gl+ + +  + p ++ + e
  gi|313117449|ref|YP_004044432.1| 33 VLFDTGQSDAVVHNAR----LLGLPTTFDDIVLSHTHFDHTAGLDQFLDPMNQPRVYLHPE 89
                                      899*****99999985....99999*********************998755554444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2052.56
//
Query:       gi|313117450|ref|YP_004044433.1|  [L=243]
Description: maleate cis-trans isomerase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-37  129.8   0.0    1.4e-37  129.5   0.0    1.0  1  Amdase        Arylmalonate decarboxylase
    4.1e-13   49.7   0.0    5.1e-13   49.4   0.0    1.1  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase
  ------ inclusion threshold ------
      0.069   12.5   0.0        1.9    7.9   0.1    2.8  2  AroM          AroM protein
      0.099   13.0   0.0        0.2   12.0   0.0    1.5  1  YnfE          Uncharacterized YnfE-like


Domain annotation for each model (and alignments):
>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   0.0   3.1e-41   1.4e-37      10     208 ..      28     227 ..      20     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 3.1e-41
                            Amdase  10 pe.vrFeAeGLglkelskegydevidrvveaArelaerGaqavslmGtsLsFyRGaafneeLvarleeatgLPattm 85 
                                       pe v+ +A  + l++++++  d++ d  v++A +l ++ +++v+   t  s   G+ f++eL+ +l+ea+g+Pa   
  gi|313117450|ref|YP_004044433.1|  28 PEgVSVHAARMPLESVTPDELDAMADAAVDCADRLSHADVDVVAYACTTGSLLHGPGFDRELELSLAEAAGVPAVAT 104
                                       4458999999******************************************************************* PP

                            Amdase  86 ssavvealralgarRvAvataYidevnerLvayLeesglevaalesLdiedveavakvtaeelvelgkkavaaapea 162
                                       + +v +al+ lga+R+ v+t Y++e+n+r ++yLe++g++v +l++L+ie+ +++ + t e+    ++  +++ape+
  gi|313117450|ref|YP_004044433.1| 105 ALSVKRALHVLGAERLGVVTPYTEELNQRETDYLESAGYDVITLDGLGIESNTEIGEQTPENAYRQTRMCLDTAPEV 181
                                       ***************************************************************************** PP

                            Amdase 163 dallisCGGLrtldvvreledelglpvvssalAGlwdavrlaglda 208
                                       da+++sC   rtl+++++le++  +pvv+s  A lwda+++a+ ++
  gi|313117450|ref|YP_004044433.1| 182 DAVFVSCTNYRTLPMIERLERDCDVPVVTSNGATLWDALQRADVST 227
                                       ***************************************9998764 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0   1.1e-16   5.1e-13      32     223 ..      31     219 ..      10     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.1e-16
                                       EEEE-CCS-TCHHHHHCH.T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHH.HHH........HH-SSEEEECH CS
                      Asp_Glu_race  32 ivlndsaipdrteaieeesgddpvlklleaakkLekagadaiviaCnTahavad.elq........kkikiPvlgiv 99 
                                       + ++ +++p   e+   ++ d  +    ++a++L++a++d++++aC+T + ++  +++        +++ +P +   
  gi|313117450|ref|YP_004044433.1|  31 VSVHAARMP--LESVTPDELDAMADAAVDCADRLSHADVDVVAYACTTGSLLHGpGFDrelelslaEAAGVPAVA-T 104
                                       555666667..344444455656679***********************87653122244444454555555555.3 PP

                                       HHHHHHHHH.HSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCHHCCHCHHHHTT-TTSH.HHHHHHH CS
                      Asp_Glu_race 100 eataealka.tgvkkvglLgTrgtlksglyqkeleanqgievvvpseelqssvnqaiyeelkaGevtee.arrailk 174
                                         +++ +    g++++g+++++++  ++   + le+ +g++v++ +   ++s           Ge t+e a+r+ + 
  gi|313117450|ref|YP_004044433.1| 105 ALSVKRALHvLGAERLGVVTPYTEELNQRETDYLES-AGYDVITLDGLGIESN-------TEIGEQTPEnAYRQTRM 173
                                       3334444447**************************.6**9999988876553.......34788888857777777 PP

                                       HHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHHHHH CS
                      Asp_Glu_race 175 llerlaergadaviLGCTelplllekaealekeksvpvidptdilaret 223
                                       +l+     ++dav++ CT++++l + +e+le++ +vpv+ ++ ++ + +
  gi|313117450|ref|YP_004044433.1| 174 CLD--TAPEVDAVFVSCTNYRTL-PMIERLERDCDVPVVTSNGATLWDA 219
                                       777..589*************88.********98********9999875 PP

>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.016        71     126     204 ..       7     102 ..       3     115 .. 0.48
   2 ?    7.9   0.1   0.00041       1.9     121     206 ..     114     211 ..      49     216 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.016
                              AroM 126 qlgvivPleeqaeqaekkweelakevvvavaspy..gse.........eelaeaarelaeqgadlivldci...... 185
                                       +lg +vP+ + +   e ++  +a e v ++a ++  +s          ++  + a +l+++++d++   c       
  gi|313117450|ref|YP_004044433.1|   7 RLGAVVPSSNTTV--EGEFTTYAPEGVSVHAARMplESVtpdeldamaDAAVDCADRLSHADVDVVAYACTtgsllh 81 
                                       6777777555443..55555555544444443332122244444222233333455667777777755443222222 PP

                              AroM 186 ..GYteemkaavaealgkpVl 204
                                         G+++e    +aea+g+p +
  gi|313117450|ref|YP_004044433.1|  82 gpGFDRELELSLAEAAGVPAV 102
                                       225666666666666666655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00041
                              AroM 121 lvkkkqlgvivPleeqaeqaekkweelak.evvvavaspygse.........eelaeaarela.eqgadlivldciG 186
                                       +++ ++lgv++P  e+ +q e+++ e a  +v +     ++s+         ++ +++   l  + ++d + + c  
  gi|313117450|ref|YP_004044433.1| 114 VLGAERLGVVTPYTEELNQRETDYLESAGyDVITLDGLGIESNteigeqtpeNAYRQTRMCLDtAPEVDAVFVSCTN 190
                                       566899**************999998876433333333333331122112211222222222212356666666666 PP

                              AroM 187 Y.teemkaavaealgkpVlla 206
                                       Y t  m +++++ +++pV+++
  gi|313117450|ref|YP_004044433.1| 191 YrTLPMIERLERDCDVPVVTS 211
                                       633356666666666666666 PP

>> YnfE  Uncharacterized YnfE-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.5e-05       0.2      43      65 ..      38      60 ..      28      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                              YnfE 43 LkqesssdedfDevvdavvkcAa 65
                                      +  es+++++ D ++da+v+cA 
  gi|313117450|ref|YP_004044433.1| 38 MPLESVTPDELDAMADAAVDCAD 60
                                      556899***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1586.37
//
Query:       gi|313117451|ref|YP_004044434.1|  [L=539]
Description: N-methylhydantoinase B/acetone carboxylase subunit alpha [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.2e-208  692.9   6.3   2.5e-208  692.7   6.3    1.0  1  Hydantoinase_B  Hydantoinase B/oxoprolinase


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.7   6.3  1.4e-212  2.5e-208       1     516 []      10     520 ..      10     520 .. 0.97

  Alignments for each domain:
  == domain 1  score: 692.7 bits;  conditional E-value: 1.4e-212
                    Hydantoinase_B   1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfege 77 
                                       D+itle++rn+++s+aeemg++l+ +++Spniker+D+s+alfdadg+lvaqa+hipvhlg+m+eav++vl  +  +
  gi|313117451|ref|YP_004044434.1|  10 DAITLEIMRNQFESVAEEMGQVLITSSYSPNIKERRDCSTALFDADGRLVAQAEHIPVHLGAMPEAVQTVLG-Y--D 83 
                                       89*********************************************************************3.3..6 PP

                    Hydantoinase_B  78 lkpGDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklvee 154
                                        kpGDv+++NdP++ggtHlpD+t+++P   +ge+++fv+sraHhaD+GG++pGsmp+ a+ei++EGlr+ppv+lve+
  gi|313117451|ref|YP_004044434.1|  84 PKPGDVFVLNDPFEGGTHLPDVTMVSPLSLDGEILGFVVSRAHHADVGGMAPGSMPAGAREIYQEGLRLPPVRLVEG 160
                                       79*************************************************************************** PP

                    Hydantoinase_B 155 geleedvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgt 231
                                       ge ++dv+++llanvR+p ++++D++Aqiaan+++e+rl +l+ee+G+ +v aa+d+++++++ +v a+l++lpdg+
  gi|313117451|ref|YP_004044434.1| 161 GEVNDDVMSVLLANVRNPGERRADIRAQIAANERAEERLGDLVEEHGKPQVVAAFDAVMAYSRDRVTAELRALPDGE 237
                                       ***************************************************************************** PP

                    Hydantoinase_B 232 yeaedyldd.g.....ipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrp 302
                                       y+a+d+l+  g     ipi+vtv+ dg+++ vDf+gt+pqv+gn+Naplav++sav++v+rc++d++ip N+Gc++p
  gi|313117451|ref|YP_004044434.1| 238 YHARDVLEGdGvtdedIPIEVTVSTDGETVAVDFDGTAPQVAGNVNAPLAVAKSAVYFVVRCVTDPEIPPNQGCYDP 314
                                       *******6544555559******99**************************************************** PP

                    Hydantoinase_B 303 ievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetia 379
                                       i+v +peg+llnp+ paavvggnvetsqrv+dvv+ ala+a+p+rv+A++qgtmnnlt+g +   g+e f+yyeti+
  gi|313117451|ref|YP_004044434.1| 315 ITVSVPEGTLLNPNAPAAVVGGNVETSQRVTDVVFTALAEAAPDRVPAQGQGTMNNLTIGSRAG-GSEGFTYYETIG 390
                                       ************************************************************6554.57888******* PP

                    Hydantoinase_B 380 gGaGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilse 456
                                       gG G+r+ +dG+++v+v mtnt nt++E+lE++yP+ ve+++lr++sgG+G+yrGG+G+vr+++++++ +tvs+l+e
  gi|313117451|ref|YP_004044434.1| 391 GGFGGRASGDGMDGVQVGMTNTLNTPIEALEAEYPLFVEEYSLRENSGGRGRYRGGLGIVRSVTIEAD-ATVSLLTE 466
                                       *******************************************************************7.******** PP

                    Hydantoinase_B 457 rrvfapwGlaGGepGargrvvlnllvrgeeenlggkatvelkagdvlvietpGGGGyGdp 516
                                       rr++ap G+aGGe+Ga+g+   nl+   + e++++k+t ++ ag +++++tpGGGG+G p
  gi|313117451|ref|YP_004044434.1| 467 RRRVAPKGIAGGEDGATGQ---NLV---DGESVPAKTTRDVLAGTTVTVRTPGGGGHGTP 520
                                       *******************...765...45666789999*******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3653.18
//
Query:       gi|313117452|ref|YP_004044435.1|  [L=669]
Description: N-methylhydantoinase A/acetone carboxylase subunit beta [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-99  332.1  12.4    7.2e-98  327.4   8.2    2.2  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    2.6e-52  177.1   3.0    1.3e-51  174.8   0.7    2.5  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    6.7e-05   21.7   3.9     0.0096   14.6   0.9    2.5  2  MutL            MutL protein
     0.0076   15.8   3.7       0.12   11.8   3.6    2.9  1  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1   0.00083       3.7      80      97 ..       5      22 ..       1      45 [. 0.77
   2 !  327.4   8.2  1.6e-101   7.2e-98       1     290 [.     201     487 ..     201     488 .. 0.99

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00083
                    Hydantoinase_A 80 kvItfDmGGTstDvslik 97
                                        I++D+GGT tDv+l+ 
  gi|313117452|ref|YP_004044435.1|  5 TRIGVDVGGTFTDVALLT 22
                                      569************998 PP

  == domain 2  score: 327.4 bits;  conditional E-value: 1.6e-101
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       rt+t+vv+Ay++p + +yl ++e++ ++ ++ +  ++mq++Gg+++a+++r++ v t +SGPaaGvvgaa+t++ ++
  gi|313117452|ref|YP_004044435.1| 201 RTSTTVVDAYVTPAIDAYLGRLEERAAEMDV-PVPQIMQANGGIAPASTVREHAVTTTMSGPAAGVVGAAETATSDD 276
                                       89**************************988.7779***************************************** PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpa 154
                                        + ++tfDmGGTs Dvsl++dgeve++++ ei + +++ p++d++tvgagGgsi++vd g++lrvgp+s ga+pgpa
  gi|313117452|ref|YP_004044435.1| 277 LDGLVTFDMGGTSSDVSLVRDGEVERTTDAEINERPIKTPMVDVNTVGAGGGSIAWVDAGNALRVGPRSSGANPGPA 353
                                       ***************************************************************************** PP

                    Hydantoinase_A 155 cyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlk.veevAegilsvavenmanavr 230
                                       cy++Ggte+tvTDan+vLG++  ++ l   +g+ +ldv++a+ a+++la+e +l+ +  +A g+++va+ nm +a+r
  gi|313117452|ref|YP_004044435.1| 354 CYGRGGTEPTVTDANVVLGYIGGSSAL---GGELSLDVDAAHDALANLADEAGLDgALAAARGVYRVANANMTRAIR 427
                                       ************************999...***********************9989999***************** PP

                    Hydantoinase_A 231 klsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290
                                        ++verg+dp+e+ lv+fGGaG++haaalae+l+v +v+vp+++gvlsa+G+++Ad++++
  gi|313117452|ref|YP_004044435.1| 428 AVTVERGHDPREFGLVAFGGAGPMHAAALAESLDVGTVVVPRACGVLSAYGLLAADQKHD 487
                                       *********************************************************987 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.8   0.7   2.9e-55   1.3e-51       1     177 [.       6     181 ..       6     182 .. 0.97
   2 ?    1.5   0.1     0.048   2.1e+02       3      24 ..     282     302 ..     280     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: 174.8 bits;  conditional E-value: 2.9e-55
                        Hydant_A_N   1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkge 77 
                                       rig+DvGGTfTD+ +l+++ +e++++K++st d+++ g+++ +e++ +e+ +++s++d+  ++ Tv +Nalle +g+
  gi|313117452|ref|YP_004044435.1|   6 RIGVDVGGTFTDVALLTPE-NELVTAKVPST-DDQSVGVVRGFEKACDEAEIDPSDVDAFTHAMTVSVNALLEENGA 80 
                                       79***************99.88*********.********************************************* PP

                        Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagves 152
                                       ++aL+tt+gfrd+leigrq+rpdl++ +     plv++++++ev+er ++d  v + +de+evr+++++++a+++es
  gi|313117452|ref|YP_004044435.1|  81 KTALVTTEGFRDVLEIGRQARPDLYDVTADkpAPLVPRRRRFEVTERATID-GVETTVDESEVRSIAENIRASDAES 156
                                       **************************888778899***************8.7999********************* PP

                        Hydant_A_N 153 iavvllhSylnpehElrvaeiarei 177
                                       +av+llh+y  pe+E++va+++re+
  gi|313117452|ref|YP_004044435.1| 157 VAVSLLHAYQHPENEQIVADVLREE 181
                                       ***********************97 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.048
                        Hydant_A_N   3 gIDvGGTfTDavaldekeeeva 24 
                                         D+GGT  D+ +++++ e+ +
  gi|313117452|ref|YP_004044435.1| 282 TFDMGGTSSDVSLVRDG-EVER 302
                                       56***********9966.5444 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1   0.00032       1.4       4      54 ..       9      56 ..       7      78 .. 0.81
   2 !   14.6   0.9   2.1e-06    0.0096     201     273 ..     230     304 ..     187     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00032
                              MutL  4 iDiGSttTkvtlvdlekvderllgqaeapTtvee.edvleGleealeeleek 54
                                      +D+G t+T v+l++ e+     l +a+ p+t ++   v++G+e+a +e e  
  gi|313117452|ref|YP_004044435.1|  9 VDVGGTFTDVALLTPEN----ELVTAKVPSTDDQsVGVVRGFEKACDEAEID 56
                                      89***********9955....678999999999888999****999987655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.1e-06
                              MutL 201 evFlehivkakg....lskleelvsaeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekek 273
                                       +v + +i++a g     s+++e++ ++ m  PaA + ++   a+  +++l++l+++D+GG+++dv  v +g+ e+++
  gi|313117452|ref|YP_004044435.1| 230 DVPVPQIMQANGgiapASTVREHAVTTTMSGPAAGVVGAAETAT--SDDLDGLVTFDMGGTSSDVSLVRDGEVERTT 304
                                       55566777666533334677888888888889998888877777..45689*****************877766544 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   3.6   2.7e-05      0.12       1      71 [.       7      69 ..       7     502 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                                      EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEES CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtg 71
                                      +G+D+G+T t ++l++ + e+++  +  s+  +sv+       +++ +++a+++a+ +++d++     +t 
  gi|313117452|ref|YP_004044435.1|  7 IGVDVGGTFTDVALLTPENELVTAKV-PSTDDQSVG-------VVRGFEKACDEAEIDPSDVDAFTHAMTV 69
                                      7*****************99555544.454555566.......6788888888888888887655333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 4167.45
//
Query:       gi|313117453|ref|YP_004044436.1|  [L=409]
Description: Mn2+/Fe2_ transporter, NRAMP family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-95  318.3  25.9    7.8e-95  317.9  25.9    1.2  1  Nramp       Natural resistance-associated macrophage protein
  ------ inclusion threshold ------
       0.11   11.9   2.7       0.13   11.7   0.3    2.1  2  Ceramidase  Ceramidase


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.9  25.9   8.7e-99   7.8e-95       1     357 [.      30     377 ..      30     378 .. 0.94

  Alignments for each domain:
  == domain 1  score: 317.9 bits;  conditional E-value: 8.7e-99
                             Nramp   1 iatdlqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerl.....pkkvsillwilaelaiiatd 72 
                                       ++t++  GaqfGy+L+w++ +s++++i+lqe+sarLGlv+++gl e++r ++     +    +l++ ++ ++++a++
  gi|313117453|ref|YP_004044436.1|  30 VTTASVTGAQFGYALIWTIAFSIIATIVLQEMSARLGLVSREGLGEALRSQFdnevaSAFSIALVVSAIGIGTAAYE 106
                                       6899************************************************77775666667777888999***** PP

                             Nramp  73 laeviGaAialnllfgipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgevlkgl 149
                                        ++++G+A++l+ l+gi+ +++++++++++ +ll+  +g+y+ +E+++++lv+++alsF++ ++++ pd+g+++ g+
  gi|313117453|ref|YP_004044436.1| 107 TGNILGGAAGLEGLTGISANIWGPVMGLIAGALLW--SGKYKLIEKALVGLVSLMALSFLVDAIIIGPDLGALAMGF 181
                                       ***********************************..***************************************9 PP

                             Nramp 150 vvPslpgkeslllavgilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiialivaflinlailivaAa 226
                                       v Ps+p+ +s +l++g++G+tv+ +nlflh+ +vqer+  +    +e  l+ +r Dt+++++v++li++ail++aAa
  gi|313117453|ref|YP_004044436.1| 182 V-PSVPQ-GSEFLITGLVGTTVVGYNLFLHAGSVQERWAGP----DE--LNESRADTVLSIVVGGLITIAILVTAAA 250
                                       9.*****.******************************665....55..**************************** PP

                             Nramp 227 vlysggkdvesledaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralaf 303
                                       ++   g+++++++ +ae++epl+G+  a+vlF+igL+aaG+ S++t++lag+y+++g+lg++ +l       ++++f
  gi|313117453|ref|YP_004044436.1| 251 AFP-VGTEIQNVSTMAEQIEPLVGT-HAKVLFGIGLFAAGFTSATTAPLAGAYATAGALGWDTDL-------QSTKF 318
                                       ***.55679***************5.***************************************.......56667 PP

                             Nramp 304 vpalivilligaele.....lvkllvlsqvllslllPfaliplllltsskklMGefkns 357
                                       ++++ +ill+g  ++     +v+++v++qv++++llP+++i+l++++++++++G+++n+
  gi|313117453|ref|YP_004044436.1| 319 RAVWGTILLTGIVFSalgysPVQAIVFAQVANGILLPIVAIFLIYVMNDRDILGSYVNN 377
                                       77777777777777777777*************************************97 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1     0.086   7.7e+02     131     185 ..      33     100 ..      14     107 .. 0.55
   2 ?   11.7   0.3   1.4e-05      0.13     102     175 ..     312     384 ..     291     399 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.086
                        Ceramidase 131 kepvlhqvafalltvlvllrsiyliekkv.............dksdeaakkevkklallgliifllgf 185
                                         ++  q+ +al+ +++   ++ ++ +++             +  +++ ++ev++ + ++l++ ++g+
  gi|313117453|ref|YP_004044436.1|  33 ASVTGAQFGYALIWTIAFSIIATIVLQEMsarlglvsreglgEALRSQFDNEVASAFSIALVVSAIGI 100
                                       44445555555555554444444444444445566666666644455666666666666666665555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.4e-05
                        Ceramidase 102 ekksrstrvllgvlltalavvvtllylvlkepvlhqvafalltvlvllrsiyliekkv..dksdeaakkevkklal 175
                                       + +s+++r++ g++l++ +v+ +l y  ++  v+ qva ++l  +v++  iy+++ +       + ++++v++++ 
  gi|313117453|ref|YP_004044436.1| 312 DLQSTKFRAVWGTILLTGIVFSALGYSPVQAIVFAQVANGILLPIVAIFLIYVMNDRDilG---SYVNNTVQNVVG 384
                                       4678999***********************************************6554331...333344433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2464.84
//
Query:       gi|313117454|ref|YP_004044437.1|  [L=181]
Description: CopG family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-06   26.0   0.1    1.4e-05   24.9   0.1    1.6  1  RHH_1     Ribbon-helix-helix protein, copG family
     0.0002   21.2   0.0    0.00045   20.1   0.0    1.5  1  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.5e-09   1.4e-05       1      36 [.       5      40 ..       5      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.5e-09
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlrey 36
                                      r++++ld++   +Ld l  r+++ +Sel+ReAl +y
  gi|313117454|ref|YP_004044437.1|  5 RITVSLDDDAQGALDSLSNRTDKAQSELVREALVFY 40
                                      8*******************************9776 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.1e-08   0.00045       4      36 ..       5      37 ..       4      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.1e-08
                             RHH_3  4 rttvsidpelaekLkaLSekTrIprSklldeAi 36
                                      r+tvs+d++    L+ LS++T  ++S+l++eA+
  gi|313117454|ref|YP_004044437.1|  5 RITVSLDDDAQGALDSLSNRTDKAQSELVREAL 37
                                      89******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1190.20
//
Query:       gi|313117455|ref|YP_004044438.1|  [L=289]
Description: hypothetical protein Hbor_32460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-05   24.9   0.0    5.3e-05   23.2   0.0    1.9  2  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.9e-09   5.3e-05       1      49 [.      11      62 ..      11      62 .. 0.95
   2 ?   -3.1   0.0      0.49   8.9e+03      24      42 ..     127     145 ..     126     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.9e-09
                                      HHHHHHHS-HHHHHHHHHH..STCTTB-HHHHHHHHTS-HHH.HHHHHHHHH CS
                            HTH_20  1 dqiaeALahPvRrrilraL..araegltaselaerldlsknt.lsyHLrvLe 49
                                      d ++ +La++ R +ilr L    +e l++s+l   +d++++   +yHL+vL+
  gi|313117455|ref|YP_004044438.1| 11 DSVFGLLANELRIEILRTLwaQHPESLSFSDLRSSVDIRDSGkFNYHLDVLV 62
                                      57899**************9999***************************95 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.49
                                       TB-HHHHHHHHTS-HHHHH CS
                            HTH_20  24 gltaselaerldlskntls 42 
                                       ++ + +l  r+ +++nt+ 
  gi|313117455|ref|YP_004044438.1| 127 CAACDDLITRMPIPPNTVA 145
                                       5677888888889999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1892.17
//
Query:       gi|313117456|ref|YP_004044439.1|  [L=239]
Description: hypothetical protein Hbor_32470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0032   17.7   0.1     0.0057   16.9   0.1    1.4  1  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
  ------ inclusion threshold ------
      0.019   15.3   0.2      0.038   14.4   0.2    1.5  1  zf-met       Zinc-finger of C2H2 type
      0.022   13.5   0.0      0.027   13.2   0.0    1.2  1  DUF4764      Domain of unknown function (DUF4764)
       0.04   14.8   1.5      0.067   14.1   0.5    1.8  2  zf-C2H2_4    C2H2-type zinc finger
       0.18   11.5   0.0       0.34   10.5   0.0    1.4  1  DUF4747      Domain of unknown function (DUF4747)


Domain annotation for each model (and alignments):
>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.6e-06    0.0057       2      21 ..     110     129 ..     109     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                                       CBBTTTTBBBSSHHHHHCCT CS
                       zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHl 21 
                                       + C++C++ F s++al+ H+
  gi|313117456|ref|YP_004044439.1| 110 WTCPTCERKFLSHQALQRHY 129
                                       57*****************7 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.1e-05     0.038       1      20 [.     110     129 ..     110     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                            zf-met   1 fyCelCnvtfnsesqlksHl 20 
                                       ++C+ C ++f s ++l+ H+
  gi|313117456|ref|YP_004044439.1| 110 WTCPTCERKFLSHQALQRHY 129
                                       99*****************9 PP

>> DUF4764  Domain of unknown function (DUF4764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.5e-06     0.027     187     218 ..     106     137 ..      61     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.5e-06
                           DUF4764 187 rPktFkCqtCeKSYIGkGGLARHyKLNPgHge 218
                                       +   + C tCe+ ++    L RHy  NP+H +
  gi|313117456|ref|YP_004044439.1| 106 KSERWTCPTCERKFLSHQALQRHYGTNPEHPQ 137
                                       666789************************75 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.3   1.2e+04      13      20 ..      33      40 ..      31      41 .. 0.80
   2 ?   14.1   0.5   1.9e-05     0.067       2      20 ..     111     129 ..     110     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.3
                         zf-C2H2_4 13 kkaLlrHl 20
                                       +aL++Hl
  gi|313117456|ref|YP_004044439.1| 33 LDALSNHL 40
                                      57899**7 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.9e-05
                         zf-C2H2_4   2 kCpiCgksFsskkaLlrHl 20 
                                       +Cp C + F s++aL+rH 
  gi|313117456|ref|YP_004044439.1| 111 TCPTCERKFLSHQALQRHY 129
                                       7*****************6 PP

>> DUF4747  Domain of unknown function (DUF4747)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.4e-05      0.34     148     191 ..     164     208 ..     158     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.4e-05
                           DUF4747 148 esieriLalpk.lkklkieitfsNpDdlrelekeleqrlkemnvr 191
                                       + +e++L+lp  ++   ie+t s +D+  e++ e+e+ ++++ + 
  gi|313117456|ref|YP_004044439.1| 164 DRVETFLTLPDkIEADDIEVTHSPSDECVEISGEYEETIDTNSIT 208
                                       789*******99***************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1535.50
//
Query:       gi|313117457|ref|YP_004044440.1|  [L=463]
Description: FAD/FMN-dependent dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-34  118.8   2.6    2.3e-34  118.1   2.6    1.3  1  FAD_binding_4  FAD binding domain
    1.2e-15   57.3   1.0    3.5e-15   55.8   1.0    1.8  1  BBE            Berberine and berberine like


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   2.6   2.6e-38   2.3e-34       1     138 [.      47     181 ..      47     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 2.6e-38
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdl 77 
                                       p+++++++++++v+aa+++ +e++l   vrGgG++  g a+ ++g+v+dls++++ + +d++++t+++e+G+t+gd+
  gi|313117457|ref|YP_004044440.1|  47 PRLIAQCATVADVIAAVNFGREHDLATAVRGGGHNGPGLALVDSGLVIDLSEMTG-IRVDPSAKTVRAEPGCTWGDV 122
                                       7899************************************99*************.89******************* PP

                                       HHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  78 vealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       ++a++a gl+++   g ++++++GG+++++++Gy  +k+Gl+ dn+++++vvladG++v++
  gi|313117457|ref|YP_004044440.1| 123 DHATHAFGLATP--SGIISTTGIGGLTLGGGHGYLTRKHGLTIDNLVSADVVLADGRLVHA 181
                                       ************..9*******************************************997 PP

>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   1.0   3.9e-19   3.5e-15       1      46 []     416     460 ..     416     460 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 3.9e-19
                                       --TTS--GGG-HHHHHHHHGGGHHHHHHHHHHH-TT--S--TT--- CS
                               BBE   1 aYvNyrdldlgkewgerYFggNferLvkvKtkyDPdNvFrneqsIp 46 
                                       +YvN++ ++   +++++++ +N+erL++vK+kyDPdN+F+ +q+I+
  gi|313117457|ref|YP_004044440.1| 416 SYVNFMMEEGE-SRVQAAYRDNYERLQQVKAKYDPDNFFHINQNIE 460
                                       6*****99999.********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3059.70
//
Query:       gi|313117458|ref|YP_004044441.1|  [L=96]
Description: gas vesicle protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-12   47.0   6.3    2.4e-12   46.8   6.3    1.1  1  Gas_vesicle      Gas vesicle protein
  ------ inclusion threshold ------
      0.084   12.1   0.0      0.097   11.9   0.0    1.0  1  O_anti_polymase  Putative O-antigen polymerase


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   6.3   2.7e-16   2.4e-12       1      39 []      14      52 ..      14      52 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.7e-16
                       Gas_vesicle  1 sLaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                      ++++ +D++L  G+V+++d++++va+i+L++i+Lr++iA
  gi|313117458|ref|YP_004044441.1| 14 AIVEFVDVLLRDGAVLQADVIVTVADIPLIGISLRAAIA 52
                                      589***********************************8 PP

>> O_anti_polymase  Putative O-antigen polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.1e-05     0.097      69     120 ..      11      63 ..       2      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.1e-05
                   O_anti_polymase  69 nekkvekiglilvliGillfiinllivggiPlfdpslraklntkltalsy.lf 120
                                       + + +++++ +l+  G +l++  ++ v +iPl+  slra+++   t+  y lf
  gi|313117458|ref|YP_004044441.1|  11 DTHAIVEFVDVLLRDGAVLQADVIVTVADIPLIGISLRAAIAGMTTMTEYgLF 63 
                                       445667788889999********************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 704.00
//
Query:       gi|313117459|ref|YP_004044442.1|  [L=288]
Description: Gas vesicle synthesis protein GvpL/GvpF [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-72  243.7   0.1      3e-72  243.5   0.1    1.0  1  GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF


Domain annotation for each model (and alignments):
>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.5   0.1   1.7e-76     3e-72       1     244 []      32     285 ..      32     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 243.5 bits;  conditional E-value: 1.7e-76
                         GvpL_GvpF   1 glYvYgivdadsddseaad.tGvdgepVrlvragglaavvsdvpeeeydaerleqverwllaHqrVvealm.aegtv 75 
                                       g+Y+Y++vd++s ds++ +  Gv++++V++++ ++++a+v+d+ e+ yd+e  eqv +w+l+Hq+Vv+a++  +gt+
  gi|313117459|ref|YP_004044442.1|  32 GRYLYCFVDTESADSNDLSvLGVGESSVYVIETESVGAAVHDC-EAVYDTESPEQVTQWVLRHQHVVDAAGeVFGTP 107
                                       79***********9999889***********************.7**************************88**** PP

                         GvpL_GvpF  76 lPlrFgtvlkdeeav.relLeeeadelreaLerlagkvEygvkvlwdeealleelleedpelrelreeieaasesgt 151
                                       lP+rF+t++++++a   ++++e++d++reaL+++ag++Ey+++++wd +a+++e++++d++l++l++++++a++ gt
  gi|313117459|ref|YP_004044442.1| 108 LPMRFNTIIEGGDASiSQWVHENHDTIREALTSFAGTWEYRIRLHWDSSAFEAEIADQDDQLQDLQRRRKQAGS-GT 183
                                       **************99*******************************************************999.9* PP

                         GvpL_GvpF 152 ayllrkrlgqrleealeerreelaeeleeaLaplaeevrerepqd..........eemvlnaafLvdrdreeefgea 218
                                       ++ll+k++++rl+e  ++rr +l+++l+e+++p++ e+ e++p++          +e v ++a+L+d+++e e+g++
  gi|313117459|ref|YP_004044442.1| 184 SFLLEKQYDKRLRELKQQRRSDLTATLRESISPVVTEMIEQDPSSpltddttaidGEPVARVAVLADEADETELGNR 260
                                       ***************************************************************************** PP

                         GvpL_GvpF 219 veelaarldglevrltGPwpPYsFvp 244
                                       ++  a++ +g+++++tGPwpPY+F+p
  gi|313117459|ref|YP_004044442.1| 261 LDGPAEQ-EGVSIKFTGPWPPYTFAP 285
                                       *******.9***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1743.18
//
Query:       gi|313117460|ref|YP_004044443.1|  [L=115]
Description: gas vesicle protein K [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-26   91.0   7.3    4.4e-26   90.7   7.3    1.1  1  GvpK             Gas vesicle protein K
     0.0052   17.1   4.2     0.0076   16.6   4.0    1.4  1  Csm1_N           Csm1 N-terminal domain
  ------ inclusion threshold ------
      0.018   15.4   0.3      0.022   15.1   0.3    1.2  1  Ribosomal_S13    Ribosomal protein S13/S18
      0.019   14.7   0.5      0.023   14.5   0.5    1.1  1  LTV              Low temperature viability protein
      0.022   14.7   1.5      0.031   14.3   1.5    1.3  1  FlxA             FlxA-like protein
      0.037   13.5   0.2      0.042   13.3   0.2    1.1  1  Not3             Not1 N-terminal domain, CCR4-Not complex com
      0.037   14.2   0.6      0.042   14.0   0.6    1.1  1  End3             Actin cytoskeleton-regulatory complex protei
      0.046   13.8   0.1       0.06   13.5   0.1    1.3  1  DUF2730          Protein of unknown function (DUF2730)
      0.058   13.7   1.4       0.16   12.3   1.4    1.7  1  Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
      0.067   13.0   1.2       0.13   12.0   1.2    1.4  1  DivIC            Septum formation initiator
      0.099   12.8   1.8       0.16   12.1   0.8    1.9  2  MbeD_MobD        MbeD/MobD like
        0.1   12.7   0.1       0.12   12.4   0.1    1.2  1  PARP_reg         Poly(ADP-ribose) polymerase, regulatory doma
       0.16   12.3   0.4       0.31   11.4   0.1    1.7  1  HHA              Haemolysin expression modulating protein
       0.37   11.2   2.2       0.63   10.5   0.8    2.2  2  LPP              Lipoprotein leucine-zipper
        1.9    9.2   6.3        3.2    8.4   4.9    2.0  2  SlyX             SlyX
        4.1    7.5   7.9        1.7    8.8   3.3    2.4  2  DUF1192          Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> GvpK  Gas vesicle protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   7.3     4e-29   4.4e-26       2      82 ..       5      87 ..       4      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 4e-29
                              GvpK  2 ldadpesverglakLvLtvveLlrqllErqaiRRmeagdlsdeeierlgetLmkleeeleelkesfgleee..dLnldL 78
                                      ld ++++v+ gl++Lv+tvveLl+++lE++a+RRmeagdls++eierlg++L++leee+e+lk++ ++ +e   ++ dL
  gi|313117460|ref|YP_004044443.1|  5 LDGEADDVQGGLTALVVTVVELLVEALEQEAVRRMEAGDLSAAEIERLGQQLQTLEEEVERLKQQEDIGDEvaAFKSDL 83
                                      68899****************************************************************9999****** PP

                              GvpK 79 gplg 82
                                      +++ 
  gi|313117460|ref|YP_004044443.1| 84 DHVV 87
                                      *997 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   4.0   6.8e-06    0.0076      19      65 ..      25      71 ..      23      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.8e-06
                            Csm1_N 19 dllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrk 65
                                      +llv+ l +E +  +++ +    eie+L +ql++lee+v++l+++++
  gi|313117460|ref|YP_004044443.1| 25 ELLVEALEQEAVRRMEAGDLSAAEIERLGQQLQTLEEEVERLKQQED 71
                                      89*****************************************9987 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3     2e-05     0.022      39     101 ..      37      95 ..      16     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                     Ribosomal_S13  39 edkrigelteeeiekieeivenkaqykipnwinrqkdikdGkdshvvendlrrklredieRlk 101
                                       +++ +g+l+  eie++ + ++   +++++  + +q+di  G++    ++dl++ +r++ie l 
  gi|313117460|ref|YP_004044443.1|  37 RRMEAGDLSAAEIERLGQQLQT-LEEEVE-RLKQQEDI--GDEVAAFKSDLDHVVRDAIEQLS 95 
                                       46789****************9.444444.45788887..7789999************9875 PP

>> LTV  Low temperature viability protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5     2e-05     0.023     120     166 ..      50      95 ..      19     106 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                               LTV 120 lllpssvlpsefeekvtlqdqqkvpdeiaGfqpDmDPrLRevleaLe 166
                                       ++l ++    e ee + l++q+++ de+a f+ D+D  +R+ +e L 
  gi|313117460|ref|YP_004044443.1|  50 ERLGQQLQTLE-EEVERLKQQEDIGDEVAAFKSDLDHVVRDAIEQLS 95 
                                       34555544444.56666788************************996 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.5   2.7e-05     0.031      10      44 ..      40      74 ..      33     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                              FlxA 10 ssssgsasqiasLqkQiknlqkqLkelsesdeltk 44
                                      + ++ sa++i++L +Q+++l+++++ l+++++  +
  gi|313117460|ref|YP_004044443.1| 40 EAGDLSAAEIERLGQQLQTLEEEVERLKQQEDIGD 74
                                      56777999*********************955444 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.8e-05     0.042     114     163 ..      31      81 ..      15     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                              Not3 114 ldpkekekeearewlkdaideLneqvekleaeieklsskkkkkkk.skeka 163
                                       l+++  +++ea +     i+ L +q+++le+e+e+l++++   ++ ++ k+
  gi|313117460|ref|YP_004044443.1|  31 LEQEAVRRMEAGDLSAAEIERLGQQLQTLEEEVERLKQQEDIGDEvAAFKS 81 
                                       5667778999999999*********************99876665444444 PP

>> End3  Actin cytoskeleton-regulatory complex protein END3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   3.7e-05     0.042      94     151 ..      44     101 ..      24     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                              End3  94 gtdweevrLkreLaeLeeklekveeeaekrkekereessksalvkreleqLLkYKeeq 151
                                           e  rL ++L+ Lee++e+++++++  +e    +s+ +++v++ +eqL  +   q
  gi|313117460|ref|YP_004044443.1|  44 LSAAEIERLGQQLQTLEEEVERLKQQEDIGDEVAAFKSDLDHVVRDAIEQLSGHEASQ 101
                                       4567999*****************9888666666666777799999999997665555 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.3e-05      0.06      11      66 ..      17      73 ..      12      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.3e-05
                           DUF2730 11 lavisvvvavilllldskYakredlekla.ekveendkrlteletkvenLPtakdle 66
                                      +a++ +vv +++  l++  ++r +   l   ++e+  ++l++le +ve L  ++d+ 
  gi|313117460|ref|YP_004044443.1| 17 TALVVTVVELLVEALEQEAVRRMEAGDLSaAEIERLGQQLQTLEEEVERLKQQEDIG 73
                                      57888899999999*************9525789999*************9998864 PP

>> Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.4   0.00014      0.16       3      25 ..      46      68 ..      44      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                   Val_tRNA-synt_C  3 ekeraRLeKeLaklekeiervqk 25
                                      ++e++RL  +L+ le e+er+++
  gi|313117460|ref|YP_004044443.1| 46 AAEIERLGQQLQTLEEEVERLKQ 68
                                      68******************975 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.2   0.00012      0.13      31      61 ..      47      77 ..      43      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      HHHHHHHHHHHHHHHHHCC-XXXXXXXXXXX CS
                             DivIC 31 aelaklkaeneeLeaevkdLksdedyieerA 61
                                      ae+++l ++ + Le+ev++Lk++ed  +e+A
  gi|313117460|ref|YP_004044443.1| 47 AEIERLGQQLQTLEEEVERLKQQEDIGDEVA 77
                                      7999999999999999999998888777766 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   0.00014      0.16      42      69 ..      39      67 ..      27      68 .. 0.80
   2 ?   -2.0   0.0       3.7   4.1e+03       8      17 ..      87      96 ..      81     102 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                         MbeD_MobD 42 renaaLs.eqvtgLsqQVesLseqvrRls 69
                                       e + Ls + +++L qQ + L e+v+Rl 
  gi|313117460|ref|YP_004044443.1| 39 MEAGDLSaAEIERLGQQLQTLEEEVERLK 67
                                      455677725799***************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                         MbeD_MobD  8 LLsAlEqLQq 17
                                         A+EqL  
  gi|313117460|ref|YP_004044443.1| 87 VRDAIEQLSG 96
                                      5568888764 PP

>> PARP_reg  Poly(ADP-ribose) polymerase, regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00011      0.12      31      66 ..      36      82 ..      21     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                          PARP_reg 31 lkkmPLGkLskeqikkgyevLkelselikkkekae...........k 66
                                      +++m  G Ls ++i++  + L++l+e +++ +++e           +
  gi|313117460|ref|YP_004044443.1| 36 VRRMEAGDLSAAEIERLGQQLQTLEEEVERLKQQEdigdevaafksD 82
                                      578999************************99976555544444330 PP

>> HHA  Haemolysin expression modulating protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00027      0.31       8      37 ..      55      85 ..      50      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                      -HHHHHHHHHHHHHHS-HH.HHHHHHHHHTH CS
                               HHA  8 sidtlEkvieklkyeltdd.EllefysAaDH 37
                                       ++tlE  +e+lk++ +   E+++f+s  DH
  gi|313117460|ref|YP_004044443.1| 55 QLQTLEEEVERLKQQEDIGdEVAAFKSDLDH 85
                                      689**********9988655*********** PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.7   5.3e+03      30      39 ..      28      37 ..      21      38 .. 0.78
   2 ?   10.5   0.8   0.00056      0.63       2      37 ..      49      90 ..      48      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.7
                               LPP 30 aqaakeEAaR 39
                                      ++a  +EA R
  gi|313117460|ref|YP_004044443.1| 28 VEALEQEAVR 37
                                      5677889887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00056
                               LPP  2 ldeLssqVsqLkskvdqlssd......vnsakaaaqaakeEA 37
                                      ++ L +q+++L+++v+ l+++      v++ k++++ +  +A
  gi|313117460|ref|YP_004044443.1| 49 IERLGQQLQTLEEEVERLKQQedigdeVAAFKSDLDHVVRDA 90
                                      678999999999999999987777777888888888777666 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.9    0.0029       3.2      16      60 ..      25      69 ..      20      77 .. 0.72
   2 ?   -1.1   0.0       2.7     3e+03      17      29 ..      89     101 ..      83     105 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0029
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXX CS
                              SlyX 16 edtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseae 60
                                      e ++e+L ++ ++  +  d   +++++l ++l++lee+ ++ +++
  gi|313117460|ref|YP_004044443.1| 25 ELLVEALEQEAVRRMEAGDLSAAEIERLGQQLQTLEEEVERLKQQ 69
                                      677888888888888888888888888888888888777654443 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHH CS
                              SlyX  17 dtieeLndvvaeq 29 
                                       d+ie+L+   a q
  gi|313117460|ref|YP_004044443.1|  89 DAIEQLSGHEASQ 101
                                       5666666544444 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.81   9.1e+02      26      38 ..      25      37 ..      12      42 .. 0.72
   2 ?    8.8   3.3    0.0015       1.7      16      42 ..      43      69 ..      37      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.81
                           DUF1192 26 eerIalLeaEIaR 38
                                      e  +++Le+E  R
  gi|313117460|ref|YP_004044443.1| 25 ELLVEALEQEAVR 37
                                      5568999999877 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                           DUF1192 16 DLslLSveELeerIalLeaEIaRleaa 42
                                      DLs+  +e L +  ++Le+E++Rl+++
  gi|313117460|ref|YP_004044443.1| 43 DLSAAEIERLGQQLQTLEEEVERLKQQ 69
                                      888888899999************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1533  (0.0855039); expected 358.6 (0.02)
Passed bias filter:                      942  (0.0525406); expected 358.6 (0.02)
Passed Vit filter:                       148  (0.00825478); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 847.29
//
Query:       gi|313117461|ref|YP_004044444.1|  [L=113]
Description: gas vesicle protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-15   57.4   3.0    1.4e-15   57.1   3.0    1.1  1  Gas_vesicle  Gas vesicle protein
  ------ inclusion threshold ------
      0.015   15.8   1.7      0.037   14.5   1.8    1.6  1  SASP_gamma   Small, acid-soluble spore protein, gamma-type


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   3.0   1.6e-19   1.4e-15       2      39 .]      13      50 ..      12      50 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.6e-19
                       Gas_vesicle  2 LaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                      La++L+++LdkGvVI++di +sv ++eLl+i+Lr+++A
  gi|313117461|ref|YP_004044444.1| 13 LAEMLEMLLDKGVVINADIAVSVGDTELLGIQLRAAVA 50
                                      89***********************************8 PP

>> SASP_gamma  Small, acid-soluble spore protein, gamma-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.8   4.1e-06     0.037      12      64 ..      50      98 ..      41     106 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-06
                        SASP_gamma 12 aqsaagagsfGtefasetnaqevrqqnaqsaakkaaassasagqfGtefaset 64
                                      a s   a ++G ef + t+ ++v  +   s     a+ + s++q  te a et
  gi|313117461|ref|YP_004044444.1| 50 A-SFETAAQYGLEFPTGTDMKRVETAAGVSS---DASDANSETQPETEPARET 98
                                      2.33556667777777777777766665555...3333444566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.89
# Mc/sec: 385.67
//
Query:       gi|313117462|ref|YP_004044445.1|  [L=139]
Description: hypothetical protein Hbor_32530 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        4.8    6.4   7.4        4.7    6.5   7.4    1.2  1  DUF4407       Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   7.4   0.00026       4.7     190     243 ..       6      61 ..       1     118 [. 0.63

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00026
                           DUF4407 190 aqldaaqaelaelkakld...atarlaalraelaeleaerakeraasqaaaaaddGl 243
                                       +q  +++a+   +ka+l+   a+++l ++r+++a+ +++r++ +++sq++++++dG 
  gi|313117462|ref|YP_004044445.1|   6 QQKRKQKARQILAKAQLSrdtARQKLLQQRRKIAQ-RRKRNRHQSESQRDRDENDGT 61 
                                       22222222222333333333444444444444444.344444444444445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2075  (0.115734); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1064.55
//
Query:       gi|313117463|ref|YP_004044446.1|  [L=192]
Description: GvpH protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-48  163.5  11.0    6.1e-48  163.2  11.0    1.0  1  GvpH      GvpH


Domain annotation for each model (and alignments):
>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.2  11.0   3.4e-52   6.1e-48       4     172 ..      17     189 ..      11     192 .] 0.88

  Alignments for each domain:
  == domain 1  score: 163.2 bits;  conditional E-value: 3.4e-52
                              GvpH   4 ddqsdrlsGlldqlsrlvevlaele.eegGerhessridrGraridydydvsiGlG.dadssstdeenaddasdaeq 78 
                                       d + d +sGll+ql+ +v  lae+e eegG+r +s++id+G ++idydy+vsiGlG d +++  ++ +a+d s++ +
  gi|313117463|ref|YP_004044446.1|  17 DKRPDSPSGLLEQLRAIVASLAEIEsEEGGHRRGSGQIDQGSSQIDYDYEVSIGLGsDDRTAESPHRSASDHSRTGE 93 
                                       677899******************956799**************************99999999**********996 PP

                              GvpH  79 rsgqqrttedsihvetrasddsdelvvvadlpGvtd....edvdvaletdeqaltlrvdddvverlvlddpdvaitd 151
                                        ++qq  t +s+hvetr  +  +e +v+adl Gvtd    +d+dv+l+td  al l+ d + v r++ld+pd++itd
  gi|313117463|ref|YP_004044446.1|  94 SNSQQGDT-ESVHVETRECS-HNERIVIADLLGVTDsesdDDLDVTLDTDAPALVLSADGETVGRVALDHPDMTITD 168
                                       66666555.69******975.5678899******974443679********************************** PP

                              GvpH 152 ltlrnqvlelrlarsedsdga 172
                                       + l+nq+le+rl r ++s  +
  gi|313117463|ref|YP_004044446.1| 169 VELNNQILEIRLVRRNESTEG 189
                                       ***********9987665433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 1460.78
//
Query:       gi|313117464|ref|YP_004044447.1|  [L=83]
Description: hypothetical protein Hbor_32550 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0037   17.4   1.9     0.0042   17.2   1.9    1.0  1  Mod_r          Modifier of rudimentary (Mod(r)) protein
     0.0051   16.8   1.8      0.006   16.6   1.8    1.1  1  GvpG           Gas vesicle protein G
     0.0081   16.4   0.0     0.0093   16.2   0.0    1.1  1  Orthopox_A49R  Orthopoxvirus A49R protein
  ------ inclusion threshold ------
      0.027   14.8   3.4      0.031   14.6   3.4    1.1  1  THOC7          Tho complex subunit 7
      0.073   12.8   4.2       0.13   12.0   2.1    2.3  2  SHOCT          Short C-terminal domain


Domain annotation for each model (and alignments):
>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.9   1.2e-06    0.0042       9      78 ..       5      76 ..       3      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-06
                             Mod_r  9 qellede.eklealvktl..pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefe 78
                                       +ll ++   l  +++t+  +e+ + ++ ++++ +en+ l e    +++e+++ ++el+++l+++k+++++++
  gi|313117464|ref|YP_004044447.1|  5 DDLLVNPfLSLVDILHTMalDEMYDTEAIQDDI-KENRLLYEIGERSKEEYQQRKQELEAQLDTAKQVKSQMR 76
                                      566666655566666744348899999999999.************************************987 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.8   1.7e-06     0.006       6      73 ..       9      73 ..       4      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                              GvpG  6 laPvrgviWiaeqvqeraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLealerlea 73
                                      + P  +++   + ++  a  +++d e+++  + +  +  + Ge ++ee+++r +el  +L++ ++++ 
  gi|313117464|ref|YP_004044447.1|  9 VNPFLSLV---DILHTMALDEMYDTEAIQDDIKENRLLYEIGERSKEEYQQRKQELEAQLDTAKQVKS 73
                                      55554444...456788999*****************************************9998765 PP

>> Orthopox_A49R  Orthopoxvirus A49R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.6e-06    0.0093      57     114 ..       8      69 ..       2      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.6e-06
                                       TTSHHHHHHHHHHHHHTCHHHHHHHHH.T--HHHHHHHHHHHHGGGG...SS-HHHHHHHHH CS
                     Orthopox_A49R  57 ldnpfisfldtvytiidqeiyqtelin.slddnkiidcivnkfmsfy...kdnlenivdaii 114
                                       l npf+s++d ++t+  +e+y+te i+  + +n+++  i ++    y   k++le  +d+  
  gi|313117464|ref|YP_004044447.1|   8 LVNPFLSLVDILHTMALDEMYDTEAIQdDIKENRLLYEIGERSKEEYqqrKQELEAQLDTAK 69 
                                       78**********************99626899999998888777666222445665555554 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   3.4   8.6e-06     0.031      48      99 ..      29      80 ..      18      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.6e-06
                             THOC7 48 dfaafelsierlqllakanerereryeaekeeieseieavreeieelkaqLe 99
                                      d +a +  i+   ll +  er +e+y++ k+e+e+++  +++  ++++ + e
  gi|313117464|ref|YP_004044447.1| 29 DTEAIQDDIKENRLLYEIGERSKEEYQQRKQELEAQLDTAKQVKSQMRGRVE 80
                                      778889999999******************************9999998865 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.2   7.2e+02       6      15 ..      24      33 ..      23      36 .. 0.76
   2 ?   12.0   2.1   3.7e-05      0.13      16      27 ..      50      61 ..      42      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.2
                             SHOCT  6 LkeLyarGeI 15
                                      L+e+y+  +I
  gi|313117464|ref|YP_004044447.1| 24 LDEMYDTEAI 33
                                      89***96555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.7e-05
                             SHOCT 16 teEEFeakKakL 27
                                      ++EE++++K++L
  gi|313117464|ref|YP_004044447.1| 50 SKEEYQQRKQEL 61
                                      89*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1522  (0.0848904); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 513.83
//
Query:       gi|313117465|ref|YP_004044448.1|  [L=213]
Description: Gas vesicle synthesis protein GvpL/GvpF [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-41  141.9   0.7    7.9e-22   78.4   0.1    2.0  2  GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF


Domain annotation for each model (and alignments):
>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.1   4.4e-26   7.9e-22       2     122 ..       5     122 ..       4     126 .. 0.90
   2 !   62.3   0.1   3.5e-21   6.2e-17     171     244 .]     128     202 ..     127     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 4.4e-26
                         GvpL_GvpF   2 lYvYgivdadsddseaadtGv.dgepVrlvragglaavvsdvpeeeydaerleqverwllaHqrVvealma...egt 74 
                                       lY Yg++++ +d + +   Gv + e+V++v ++ l+avvsd+++ + + ++++     + aH++V++++++    +t
  gi|313117465|ref|YP_004044448.1|   5 LYTYGVIEQ-EDIELEV-DGVgEAERVYTVDYRTLSAVVSDIDTTDPERTDED-----IEAHNNVLQTVLEydgGRT 74 
                                       7******44.4444455.899899******************99999999999.....************656778* PP

                         GvpL_GvpF  75 vlPlrFgtvlkdeeavrelLeeeadelreaLerlagkvEygvkvlwde 122
                                       ++P+ Fg+ +k+ ++++ +L+  ++ lr+aL  ++g+vE+gvk+ +  
  gi|313117465|ref|YP_004044448.1|  75 IVPMSFGMAFKGARTLKGVLRGARRPLRSALNDIEGTVELGVKIIAPA 122
                                       ********************************************9876 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 3.5e-21
                         GvpL_GvpF 171 reelaeeleeaLaplaeevrerepqdeemvlnaafLvdrdreeefgeaveelaarldg.levrltGPwpPYsFvp 244
                                       r+e+++++ ++L++++ + +e++  +++ ++n ++Lv+r++ ++f++a+++++a +d+ l+v++tGPw+PY+Fv+
  gi|313117465|ref|YP_004044448.1| 128 RDEIQADVTDRLSEVSLNETENDLFSDRLIVNKSYLVEREHRDDFDAAIDAIEAAYDDeLRVQYTGPWAPYNFVD 202
                                       68999**************************************************9889**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1479.31
//
Query:       gi|313117466|ref|YP_004044449.1|  [L=192]
Description: PadR family transcriptional regulator [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-09   36.5   0.0    8.3e-09   35.3   0.0    1.6  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
       0.01   16.3   0.0       0.02   15.3   0.0    1.5  1  HTH_40    Helix-turn-helix domain
      0.014   15.5   0.0       0.02   15.0   0.0    1.3  1  FUR       Ferric uptake regulator family
      0.024   14.5   0.0        0.1   12.5   0.0    2.0  1  HTH_5     Bacterial regulatory protein, arsR family
       0.11   12.1   0.0         12    5.7   0.0    2.4  2  HTH_33    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   2.3e-12   8.3e-09       2      68 ..      90     149 ..      87     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.3e-12
                                       HHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHC CS
                              PadR   2 LalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTda 68 
                                       L ++ +++  G e+ ++l++l+ g ++ls+G++Yp L++L +eg+++ ++ +     +rk+Yr++da
  gi|313117466|ref|YP_004044449.1|  90 LLIAVRGEACGKELLQDLRRLF-G-VDLSPGTVYPHLNDLADEGMLDMTELT-----KRKIYRIADA 149
                                       555578999************8.7.8***********************998.....6******997 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   5.7e-06      0.02      23      66 ..     114     155 ..     112     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.7e-06
                            HTH_40  23 glkesTIegHLaelieegeeidlerlvseeeekeIeeaiekvgs 66 
                                        l+++T++ HL +l+ eg  +d+++l +++++ +I++a + ++s
  gi|313117466|ref|YP_004044449.1| 114 DLSPGTVYPHLNDLADEGM-LDMTEL-TKRKIYRIADAEATFNS 155
                                       599***************8.***998.78888889988777664 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   5.6e-06      0.02      38      92 ..     113     166 ..      85     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.6e-06
                                       TT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSEEEEEETTT--EEEE CS
                               FUR  38 peislaTVYrtLklleeaglvkelefedgesryelakkehhdhlicekCgkvief 92 
                                        ++s  TVY  L+ l+++g+++ +e++ +++ y++a++e   + ++   ++ i f
  gi|313117466|ref|YP_004044449.1| 113 VDLSPGTVYPHLNDLADEGMLDMTELT-KRKIYRIADAEATFNSVEPAVNRLITF 166
                                       678999********************9.999*****9998888888777777766 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.9e-05       0.1      25      45 ..     113     133 ..      86     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                                       HTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  25 lglsqstvShHLkkLreaGLV 45 
                                       ++ls++tv  HL+ L ++G++
  gi|313117466|ref|YP_004044449.1| 113 VDLSPGTVYPHLNDLADEGML 133
                                       58*****************86 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.012        44       8      32 ..       6      30 ..       5      31 .. 0.90
   2 ?    5.7   0.0    0.0032        12      14      32 ..     107     125 ..     101     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.012
                            HTH_33  8 arlaqlieerfgvsysvsgvyrlLk 32
                                      ++l++ i+ ++ +s++vs v+ lL 
  gi|313117466|ref|YP_004044449.1|  6 KELHEEIRMETELSFTVSAVRSLLA 30
                                      6889999**************9996 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0032
                            HTH_33  14 ieerfgvsysvsgvyrlLk 32 
                                       +++ fgv++s+ +vy  L 
  gi|313117466|ref|YP_004044449.1| 107 LRRLFGVDLSPGTVYPHLN 125
                                       7899**********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1306.91
//
Query:       gi|313117467|ref|YP_004044450.1|  [L=537]
Description: recombinase A [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.5e-233  773.9   0.0   7.7e-233  773.4   0.0    1.2  1  GvpD      GvpD gas vesicle protein
      4e-12   46.0   0.0    8.7e-09   35.1   0.0    2.4  2  ATPase    KaiC
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.033   14.6   0.0    1.6  1  AAA_16    AAA ATPase domain
      0.036   13.7   0.1       0.14   11.7   0.1    2.0  1  AAA_25    AAA domain
      0.062   13.5   0.0       0.19   11.9   0.0    1.8  1  AAA_33    AAA domain
       0.19   10.8   0.1       0.33   10.0   0.1    1.3  1  PAXNEB    PAXNEB protein
        0.2   10.8   0.0        0.3   10.3   0.0    1.2  1  DUF2075   Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  773.4   0.0    3e-236  7.7e-233       1     484 []      23     537 .]      23     537 .] 0.94

  Alignments for each domain:
  == domain 1  score: 773.4 bits;  conditional E-value: 3e-236
                              GvpD   1 leqffdgeaGktllikGaPGtGktlftlrgldvlrresdvlyvstrvddetvseayfsgeaeldktalldllkdple 77 
                                       +++ff+g++G++ll+kGaPGtGktlft+rgldvl+r++dvlyvstrvd++tv+e+yf+++ +ldkt +ldl++dp+e
  gi|313117467|ref|YP_004044450.1|  23 ISRFFTGDPGHALLVKGAPGTGKTLFTIRGLDVLERDGDVLYVSTRVDQDTVHEMYFEEHFSLDKTSILDLSQDPFE 99 
                                       689************************************************************************** PP

                              GvpD  78 ldldvdvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvl 154
                                       l+ld+dvP+e+ldl++lle++++++a++++l+ia+dswel+yeyla+r+d+P+di+tv+ +lv+lar++++rl+lv+
  gi|313117467|ref|YP_004044450.1| 100 LPLDMDVPFERLDLDALLEWIQQVKAASKRLTIAFDSWELIYEYLATRHDEPPDIETVTTQLVALARQEDIRLLLVS 176
                                       ***************************************************************************** PP

                              GvpD 155 etaansrleyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftladGkfksitrvelvtidtvtdeakye 231
                                       eta  s+leyivdGvvtl+v ed+rgr+rr+lrleklrGvrignrlqP tla+G+f++it+vel t++t+t+ ++++
  gi|313117467|ref|YP_004044450.1| 177 ETADSSPLEYIVDGVVTLQVAEDERGRTRRHLRLEKLRGVRIGNRLQPITLANGQFQAITPVELPTVHTGTGSGTWK 253
                                       ***************************************************************************** PP

                              GvpD 232 PlandkakfsvglrdldkllseGtdrGsvvildlgkdlsrdawsvlvlaairdflsqemgvavvppkegspgllknd 308
                                       P  n+kakfs+g+ dld +ls+G++rGsvv+l+lg+dlsrdaw vl+l++ir+fl +emgvavvpp+egspgll+nd
  gi|313117467|ref|YP_004044450.1| 254 PRPNSKAKFSTGISDLDPILSGGYNRGSVVHLELGTDLSRDAWCVLTLPTIRNFLVNEMGVAVVPPREGSPGLLHND 330
                                       ***************************************************************************** PP

                              GvpD 309 lnivlskavidvtasvfetyagllksl........................aekylenaittskddaidP....... 354
                                       ln vl+  v+d++++vfetyag+++s+                                                  
  gi|313117467|ref|YP_004044450.1| 331 LNSVLTPRVFDTYCHVFETYAGPSRSKdtyenddqseapsgtsravsksdvD-----------------Ssigigat 390
                                       **************************97777666644444444444444440.................24555555 PP

                              GvpD 355 ...............drltgsd..yvisleggrlkydiyiaivervreesegPllyvismdtayeafetrlgdfany 414
                                                      +r t  d   ++++egg+l y++y+++ve+vr++s+gPll+vismdta  +fet lgdfany
  gi|313117467|ref|YP_004044450.1| 391 rreeqsrtsddvverNRSTTIDerLESPVEGGQLDYEPYMEYVEQVRKQSDGPLLHVISMDTARSTFETWLGDFANY 467
                                       5555544443333336666666889**************************************************** PP

                              GvpD 415 valrndavilivkdgtelrtradrvadmhirlelsgdaivlygenkltsllgigvsdskriPkitlieiv 484
                                       val+nd++ili+k+gtelr radrvadmh+rle+sg+ai+lygen+lts+lgig+++s++iP+itl+e+v
  gi|313117467|ref|YP_004044450.1| 468 VALHNDLAILITKPGTELRKRADRVADMHLRLERSGKAIMLYGENPLTSMLGIGIDQSQSIPRITLTEMV 537
                                       *********************************************************************7 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   3.4e-12   8.7e-09      19     221 ..      32     229 ..      29     238 .. 0.81
   2 !    8.3   0.0    0.0005       1.3       2      24 ..     263     285 ..     262     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.4e-12
                            ATPase  19 grvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaees 95 
                                       g++ l+ G pGtGKt+f  + l   +e+ +  +++v++  ++  ++e        +e+  + +k  i+d+s++  e 
  gi|313117467|ref|YP_004044450.1|  32 GHALLVKGAPGTGKTLFTIRGL-DVLER-DGDVLYVSTRVDQDTVHEM------YFEEHFSLDKTSILDLSQDPFEL 100
                                       6789************998866.33355.999**********999985......46666666667888888888887 PP

                            ATPase  96 aee....kdkedleelieelaeaikeikakrvviDsitgl.aye....ekeavaReilrqlvrvlkklgvTailvse 163
                                       + +     ++ dl++l+e ++++ ++ k   +  Ds + + +y     +++  + +   qlv   ++ ++  +lvse
  gi|313117467|ref|YP_004044450.1| 101 PLDmdvpFERLDLDALLEWIQQVKAASKRLTIAFDSWELIyEYLatrhDEPPDIETVTTQLVALARQEDIRLLLVSE 177
                                       77777778899************99999999*****88775554111134455888999999999************ PP

                            ATPase 164 kssseeaaggygveefivdgvivLdlkeiee.elvRtleivkmRgtkhskkehpfeIte 221
                                         +s          e+ivdgv+ L++ e e  +++R+l+  k+Rg ++ ++  p++  +
  gi|313117467|ref|YP_004044450.1| 178 TADS------S-PLEYIVDGVVTLQVAEDERgRTRRHLRLEKLRGVRIGNRLQPITLAN 229
                                       4333......2.3578*********99988879***************99998887766 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0005
                            ATPase   2 ktgIeglDeilkgGipegrvvli 24 
                                       +tgI  lD il+gG+ +g+vv++
  gi|313117467|ref|YP_004044450.1| 263 STGISDLDPILSGGYNRGSVVHL 285
                                       6*******************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.3e-05     0.033      17      64 ..      24      73 ..      16     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                            AAA_16 17 ervrsgrp.elvllsGesGvGKsslvrellralekdg.giflrgkcdqle 64
                                      +r  +g+p +++l+ G++G+GK+    + l+ le+dg +++++++ dq +
  gi|313117467|ref|YP_004044450.1| 24 SRFFTGDPgHALLVKGAPGTGKTLFTIRGLDVLERDGdVLYVSTRVDQDT 73
                                      567789999***************99777779999988999999999983 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.6e-05      0.14      33     141 ..      32     124 ..      20     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                            AAA_25  33 gelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldla 109
                                       g+  l+ GapgtGKt +++        G  +l+    + g Vlyvs+  ++d++++ +    e++   ++  +ldl 
  gi|313117467|ref|YP_004044450.1|  32 GHALLVKGAPGTGKTLFTIR-------GLDVLE----RDGDVLYVSTRVDQDTVHEMYF--EEHF-SLDKTSILDLS 94 
                                       6778899*********9985.......554444....6799**********99998877..4444.45888899998 PP

                            AAA_25 110 gv.eslpLfakdrggtlltadvdaleaaieeve 141
                                       +   +lpL ++d   ++   d+dal ++i++v+
  gi|313117467|ref|YP_004044450.1|  95 QDpFELPL-DMDVPFER--LDLDALLEWIQQVK 124
                                       87777777.33433333..45667888877765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.3e-05      0.19       3      44 ..      36      89 ..      35     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.3e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklg........avllssdtlrrrlfg....tdqqs 44
                                      l+ G+pG+GK+ +  r l  l          +++++dt+++++f+     d++s
  gi|313117467|ref|YP_004044450.1| 36 LVKGAPGTGKTLFTIRGLDVLErdgdvlyvSTRVDQDTVHEMYFEehfsLDKTS 89
                                      678**********999655555555***98899*****9999998444433334 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00013      0.33      10      43 ..     254     286 ..     247     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                            PAXNEB  10 pSphdgqlltStGtpsLDklLgGGLplGsillie 43 
                                       p p +++   StG+++LD +L+GG   Gs++ +e
  gi|313117467|ref|YP_004044450.1| 254 PRP-NSKAKFSTGISDLDPILSGGYNRGSVVHLE 286
                                       555.889999***************999998665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012       0.3       3      23 ..      34      54 ..      32      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                           DUF2075  3 vvlVtGvaGtGKtvvllnlla 23
                                       +lV+G++GtGKt+  ++ l 
  gi|313117467|ref|YP_004044450.1| 34 ALLVKGAPGTGKTLFTIRGLD 54
                                      689***********9877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3443.70
//
Query:       gi|313117468|ref|YP_004044451.1|  [L=78]
Description: gas vesicle protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-14   53.8   5.7      2e-14   53.4   5.7    1.2  1  Gas_vesicle  Gas vesicle protein


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   5.7   1.1e-18     2e-14       1      39 []       8      46 ..       8      46 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.1e-18
                       Gas_vesicle  1 sLaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                      sLa++LDrvLdkGvV+d + ++s++gie+lt+++r+v A
  gi|313117468|ref|YP_004044451.1|  8 SLAEVLDRVLDKGVVVDVWARVSLVGIEILTVEARVVAA 46
                                      8***********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 529.80
//
Query:       gi|313117469|ref|YP_004044452.1|  [L=274]
Description: gas vesicle protein C (GVPC) family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-68  224.5  81.6    2.5e-12   46.7   3.8    7.3  7  Halo_GVPC        Halobacterial gas vesicle protein C (GVPC) r
    5.3e-07   29.2   4.0     0.0012   18.2   0.1    3.8  4  GAS              Growth-arrest specific micro-tubule binding
    6.1e-07   29.6  10.7     0.0028   17.7   0.3    3.3  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    5.1e-06   25.4   7.5    5.1e-06   25.4   7.5    1.5  2  AAA_13           AAA domain
    1.6e-05   24.4  10.7    3.2e-05   23.4   4.0    2.2  2  CorA             CorA-like Mg2+ transporter protein
      3e-05   23.3   8.5        1.6    7.7   0.1    3.6  2  APG17            Autophagy protein Apg17
    5.2e-05   23.7   2.3       0.11   13.0   0.1    3.1  3  DUF16            Protein of unknown function DUF16
    8.8e-05   22.2   8.5     0.0019   17.8   3.0    2.2  2  Vps5             Vps5 C terminal like
    9.5e-05   22.4   1.7      0.084   12.9   0.2    3.2  3  DUF1664          Protein of unknown function (DUF1664)
    0.00013   22.3   4.3        0.2   12.1   0.1    4.4  4  ZapB             Cell division protein ZapB
    0.00014   21.7   4.0        0.4   10.5   0.1    3.4  3  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
    0.00014   22.0   8.8     0.0036   17.6   0.3    3.8  4  Tup_N            Tup N-terminal
    0.00028   20.1   1.4    0.00038   19.7   1.1    1.4  1  AIP3             Actin interacting protein 3
    0.00067   20.0  15.2        0.1   13.0   0.6    3.3  3  OmpH             Outer membrane protein (OmpH-like)
    0.00092   19.2   3.4        4.2    7.4   0.2    3.7  4  LOH1CR12         Tumour suppressor protein
    0.00098   18.8  12.4     0.0022   17.6  12.4    1.7  1  Filament         Intermediate filament protein
    0.00098   19.5   0.3        1.7    9.1   0.2    3.0  2  HsbA             Hydrophobic surface binding protein A
      0.001   19.3   5.3        1.3    9.3   0.1    3.8  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0012   17.8   6.9      0.066   12.1   1.1    2.8  3  Spc7             Spc7 kinetochore protein
      0.002   17.9   2.2       0.04   13.6   1.4    2.3  2  SHE3             SWI5-dependent HO expression protein 3
     0.0027   17.9   0.3       0.24   11.6   0.1    2.9  2  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0031   17.8  36.6      0.032   14.6   1.9    6.2  6  HalX             HalX domain
     0.0053   16.6  10.0      0.057   13.2   0.8    2.9  2  TACC_C           Transforming acidic coiled-coil-containing p
     0.0053   17.1   6.0       0.33   11.4   0.1    4.5  4  YgaB             YgaB-like protein
     0.0059   16.4   0.9        3.9    7.2   0.3    3.8  2  Lectin_N         Hepatic lectin, N-terminal domain
     0.0073   16.4   3.1          2    8.5   0.3    3.2  3  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
     0.0086   16.1   0.3       0.94    9.6   0.0    3.7  3  Med9             RNA polymerase II transcription mediator com
     0.0093   15.4  13.7       0.38   10.1   9.6    2.7  2  DUF4407          Domain of unknown function (DUF4407)
     0.0096   15.7  20.2       0.15   11.8  13.3    2.9  3  FAM184           Family with sequence similarity 184, A and B
  ------ inclusion threshold ------
      0.011   15.8   1.7        7.3    6.6   0.0    3.3  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.019   14.5   6.5        1.2    8.6   0.7    2.4  2  Golgin_A5        Golgin subfamily A member 5
      0.023   14.3   3.0       0.05   13.2   1.7    2.0  2  CagZ             CagZ
      0.025   14.6   5.6         15    5.7   0.4    3.9  4  NYD-SP28         Sperm tail
      0.025   15.0   6.4       0.32   11.4   2.5    2.3  2  Fez1             Fez1
      0.038   12.9   4.6       0.17   10.7   1.1    2.3  2  CALCOCO1         Calcium binding and coiled-coil domain (CALC
      0.039   14.6   6.8        7.4    7.3   0.5    4.0  5  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
       0.05   13.4   3.5        2.2    8.0   0.1    3.5  3  She9_MDM33       She9 / Mdm33 family
       0.05   12.8   5.5       0.12   11.6   0.7    2.3  2  HAP1_N           HAP1 N-terminal conserved region
      0.053   13.4   7.4        1.7    8.4   0.6    2.7  2  DUF724           Protein of unknown function (DUF724)
      0.064   13.4  13.9        1.4    9.1   0.7    3.7  3  DUF848           Gammaherpesvirus protein of unknown function
      0.064   13.4   5.3       0.72   10.0   0.7    3.0  4  CREPT            Cell-cycle alteration and expression-elevate
       0.08   13.5   0.5       0.08   13.5   0.5    3.3  3  ECM11            Extracellular mutant protein 11
      0.081   13.4  16.3       0.51   10.9   3.3    3.1  3  APG6_N           Apg6 coiled-coil region
      0.092   12.6   7.6        0.4   10.5   2.5    2.3  2  PIN_8            PIN like domain
      0.099   11.8   7.0        5.3    6.1   0.4    3.1  3  Tmemb_cc2        Predicted transmembrane and coiled-coil 2 pr
       0.11   12.3   0.4        2.4    8.0   0.0    2.8  4  CHD5             CHD5-like protein
       0.12   12.8  14.5       0.19   12.2   1.1    4.0  4  DUF4200          Domain of unknown function (DUF4200)
       0.12   11.9   1.4         12    5.5   0.1    3.4  2  DUF3452          Domain of unknown function (DUF3452)
       0.13   12.7   0.1          2    8.8   0.1    2.6  1  EHN              Epoxide hydrolase N terminus
       0.13   12.3   8.5        2.8    8.0   3.3    2.9  2  GldM_N           GldM N-terminal domain
       0.16   11.2   7.6        1.2    8.4   2.6    2.2  2  DUF3450          Protein of unknown function (DUF3450)
       0.16   11.7   6.8        1.3    8.8   0.8    3.0  2  DASH_Spc34       DASH complex subunit Spc34
       0.17   12.0   1.2        9.5    6.4   0.0    3.4  3  DUF2384          Protein of unknown function (DUF2384)
       0.19   11.8   8.2        3.2    7.8   1.2    2.8  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.21   11.7   4.4       0.65   10.1   0.7    2.3  2  Octopine_DH      NAD/NADP octopine/nopaline dehydrogenase, al
       0.23   12.0  10.4        4.2    7.9   0.9    4.3  4  Spectrin         Spectrin repeat
       0.26   11.3   5.4        3.3    7.7   1.6    3.3  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.28   11.6   6.6        9.4    6.6   1.6    2.9  2  T4SS             Type IV secretion system proteins
       0.28   11.9  10.8        3.8    8.2   0.5    3.2  3  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.44   10.5   3.5        5.1    7.1   0.0    3.2  3  DUF2605          Protein of unknown function (DUF2605)
       0.48   10.7  18.1        1.4    9.2   1.3    4.5  6  WXG100           Proteins of 100 residues with WXG
       0.57   10.4  11.7        7.9    6.7   4.4    3.2  3  ATG16            Autophagy protein 16 (ATG16)
       0.61   10.3   3.9        7.3    6.8   0.1    3.7  4  Cnn_1N           Centrosomin N-terminal motif 1
       0.64    9.6   3.8         17    4.9   0.2    2.7  2  AAA_25           AAA domain
       0.67   10.2  16.5        6.9    6.9   0.1    5.4  5  DUF2508          Protein of unknown function (DUF2508)
       0.72   10.0   6.0         17    5.6   0.2    3.8  3  DMPK_coil        DMPK coiled coil domain like
       0.82   10.1   5.5         48    4.4   0.4    4.0  5  Goodbye          fungal STAND N-terminal Goodbye domain
       0.88    8.9   6.3        1.2    8.5   2.4    2.2  2  Rab5-bind        Rabaptin-like protein
       0.93    9.5  12.3        3.3    7.7   1.0    3.0  3  MSA-2c           Merozoite surface antigen 2c
        1.1    8.0   5.1        4.1    6.1   2.1    2.4  3  HAUS5            HAUS augmin-like complex subunit 5
        1.3    9.0   8.8        7.6    6.6   0.1    3.6  4  Phasin           Poly(hydroxyalcanoate) granule associated pr
        1.3    9.1  12.1       0.79    9.8   0.6    3.8  3  DHR10            Designed helical repeat protein 10 domain
        1.3    7.3   7.1       0.16   10.3   0.3    2.2  2  MAD              Mitotic checkpoint protein
        1.6    8.8   6.9        5.1    7.2   0.5    3.2  3  DUF4715          Domain of unknown function (DUF4715)
        1.8    7.0  12.3         32    2.9  12.2    2.1  1  FUSC             Fusaric acid resistance protein family
        2.4    8.4   8.9        6.1    7.1   1.2    3.4  4  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        2.4    8.1   6.5         39    4.2   0.7    3.1  2  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
        3.2    8.2  15.3        2.4    8.6   0.1    5.2  4  LPP              Lipoprotein leucine-zipper
        3.6    8.2  13.9        8.1    7.1   1.0    3.3  3  CCP_MauG         Di-haem cytochrome c peroxidase
        3.6    8.6  16.4         15    6.6   0.2    4.2  4  Rotamase         PPIC-type PPIASE domain
        7.4    5.9  14.8        1.2    8.4   0.5    3.1  3  TraF_2           F plasmid transfer operon, TraF, protein


Domain annotation for each model (and alignments):
>> Halo_GVPC  Halobacterial gas vesicle protein C (GVPC) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   9.9   9.5e-09   2.1e-06       1      32 []       3      34 ..       3      34 .. 0.97
   2 !   46.7   3.8   1.2e-14   2.5e-12       1      32 []      41      72 ..      41      72 .. 0.98
   3 !   44.7   1.0     5e-14   1.1e-11       1      32 []      73     104 ..      73     104 .. 0.98
   4 !   42.8   3.8     2e-13   4.4e-11       1      32 []     111     142 ..     111     142 .. 0.98
   5 !   44.8   5.3   4.6e-14     1e-11       1      32 []     149     180 ..     149     180 .. 0.99
   6 !   17.7   4.3   1.5e-05    0.0032       6      30 ..     179     203 ..     179     204 .. 0.97
   7 !   38.9   8.5   3.3e-12   7.4e-10       1      32 []     207     238 ..     207     238 .. 0.98

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 9.5e-09
                         Halo_GVPC  1 VsaLlaaIaafreefdatqdaFeaYadeFaaD 32
                                      V+++++ + a+reef++ q++F+aYa +FaaD
  gi|313117469|ref|YP_004044452.1|  3 VRDKREKMTATREEFADAQQEFAAYAADFAAD 34
                                      8999***************************8 PP

  == domain 2  score: 46.7 bits;  conditional E-value: 1.2e-14
                         Halo_GVPC  1 VsaLlaaIaafreefdatqdaFeaYadeFaaD 32
                                      Vs+Ll+aI+a+r+e+++t daF+aY++eFaa+
  gi|313117469|ref|YP_004044452.1| 41 VSSLLDAIDALRAEIEETGDAFDAYNQEFAAE 72
                                      9*****************************95 PP

  == domain 3  score: 44.7 bits;  conditional E-value: 5e-14
                         Halo_GVPC   1 VsaLlaaIaafreefdatqdaFeaYadeFaaD 32 
                                       Vs+L+++I ++re+ ++++d F+aYa++F++D
  gi|313117469|ref|YP_004044452.1|  73 VSHLQTEIGEQREALREMRDIFDAYAETFESD 104
                                       9****************************987 PP

  == domain 4  score: 42.8 bits;  conditional E-value: 2e-13
                         Halo_GVPC   1 VsaLlaaIaafreefdatqdaFeaYadeFaaD 32 
                                       Vs+LlaaI+++r+e+d t++aF+aY  eF +D
  gi|313117469|ref|YP_004044452.1| 111 VSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTD 142
                                       9****************************998 PP

  == domain 5  score: 44.8 bits;  conditional E-value: 4.6e-14
                         Halo_GVPC   1 VsaLlaaIaafreefdatqdaFeaYadeFaaD 32 
                                       Vs+LlaaI++++ ef+a+q++F++Y d+F+aD
  gi|313117469|ref|YP_004044452.1| 149 VSDLLAAIEELQLEFGAVQAEFDDYTDDFDAD 180
                                       9******************************8 PP

  == domain 6  score: 17.7 bits;  conditional E-value: 1.5e-05
                         Halo_GVPC   6 aaIaafreefdatqdaFeaYadeFa 30 
                                       a+I++fr++ ++ +da ++Y++eF+
  gi|313117469|ref|YP_004044452.1| 179 ADIERFRNAVAEQRDAVAEYREEFH 203
                                       8***********************9 PP

  == domain 7  score: 38.9 bits;  conditional E-value: 3.3e-12
                         Halo_GVPC   1 VsaLlaaIaafreefdatqdaFeaYadeFaaD 32 
                                       V+a+l+aIa+f++e+d+++++Fe+++++F+a+
  gi|313117469|ref|YP_004044452.1| 207 VQAMLNAIADFQQEIDDFRAEFETTEESFDAF 238
                                       99****************************97 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0     0.002      0.44      58     122 ..       5      69 ..       2      71 .. 0.94
   2 !   18.2   0.1   5.4e-06    0.0012      24     121 ..      44     138 ..      41     148 .. 0.91
   3 ?    5.3   0.0      0.05        11     101     136 ..     149     184 ..     143     192 .. 0.84
   4 ?    2.0   0.1       0.5   1.1e+02      86     117 ..     206     237 ..     181     248 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.002
                               GAS  58 rlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekveker 122
                                       + +e++++ +ee +  +++ + y  d+++  ++k+ +++l + + +l+ e e   + f++  +e+
  gi|313117469|ref|YP_004044452.1|   5 DKREKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEF 69 
                                       56899*************************************************99999998886 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 5.4e-06
                               GAS  24 NLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkeleke 100
                                        L+ I+ l+ eiee     ++ +   +e ++e ++l+ ++ +++e + e+r     y + ++s  ++k+ +++l   
  gi|313117469|ref|YP_004044452.1|  44 LLDAIDALRAEIEETGDAFDAYN---QEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSDLLAA 117
                                       69999999999999877766665...56789********************************************** PP

                               GAS 101 lkdlkwehevleqrfekveke 121
                                       ++dl+ e +  ++ f++  +e
  gi|313117469|ref|YP_004044452.1| 118 IEDLRAEMDTTHEAFDAYTNE 138
                                       ***************998877 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.05
                               GAS 101 lkdlkwehevleqrfekvekerdelykkfeaaiqev 136
                                       ++dl    e l+ +f +v++e+d+ ++ f+a i+  
  gi|313117469|ref|YP_004044452.1| 149 VSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERF 184
                                       5677777899*******************9998765 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.5
                               GAS  86 slknlkarlkelekelkdlkwehevleqrfek 117
                                       + +++ + + + ++e+ d + e e  e+ f++
  gi|313117469|ref|YP_004044452.1| 206 EVQAMLNAIADFQQEIDDFRAEFETTEESFDA 237
                                       33344444555555555555555555555554 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   3.0   0.00065      0.14      27     115 ..       6      90 ..       2     103 .. 0.88
   2 !   17.7   0.3   1.3e-05    0.0028      17     109 ..     107     199 ..      92     208 .. 0.80
   3 ?    4.4   0.2      0.17        37      53      94 ..     189     235 ..     182     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00065
                        TPR_MLP1_2  27 lqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelek 103
                                        +e++++ +e+ ++aqq    e    a+d  +  +++ ++++l + i  l+ae e++  ++++  ++ + + ++l++
  gi|313117469|ref|YP_004044452.1|   6 KREKMTATREEFADAQQ----EFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQT 78 
                                       57899999999999999....777777777777789999************************************** PP

                        TPR_MLP1_2 104 elselekriedl 115
                                       e+ e ++ + ++
  gi|313117469|ref|YP_004044452.1|  79 EIGEQREALREM 90 
                                       ***999988876 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.3e-05
                        TPR_MLP1_2  17 keeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleesees 93 
                                       +++  ++l ++ edl+++ + + ea + Y +e v   ++++++++l + ++el+ e   ++ae ++ + ++++  e 
  gi|313117469|ref|YP_004044452.1| 107 AKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIER 183
                                       4445566778899**************************************************99998888777666 PP

                        TPR_MLP1_2  94 weeqkeelekelsele 109
                                         +   e ++ ++e +
  gi|313117469|ref|YP_004044452.1| 184 FRNAVAEQRDAVAEYR 199
                                       6655555555555555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.17
                        TPR_MLP1_2  53 aedvkelqalreel.....nelkaeiaelkaeaesakaeleeseesw 94 
                                       ae+ ++++++ree+     + + + ia++++e ++ +ae+e+ ees 
  gi|313117469|ref|YP_004044452.1| 189 AEQRDAVAEYREEFhgvevQAMLNAIADFQQEIDDFRAEFETTEESF 235
                                       66667777777777666666666778888888888888888888775 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   1.8    0.0014      0.32     381     482 ..       6     108 ..       2     112 .. 0.77
   2 !   25.4   7.5   2.3e-08   5.1e-06     276     445 ..      64     234 ..      47     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                            AAA_13 381 hNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleee....ikeLekql 453
                                         ek++   ee ++a++++ + +++++ ++++  k+++++l +ai  l +e++e  ++  ++++e    ++ L++++
  gi|313117469|ref|YP_004044452.1|   6 KREKMTATREEFADAQQEFAA-YAADFAADIE-TKRDVSSLLDAIDALRAEIEETGDAFDAYNQEfaaeVSHLQTEI 80 
                                       556777778888888888888.5667888885.777888888888888888888887777776665555******** PP

                            AAA_13 454 rdekpaaeeinkeLkafGlgeleLkfeee 482
                                        ++++a  e+ ++  a+  + +e ++e++
  gi|313117469|ref|YP_004044452.1|  81 GEQREALREMRDIFDAY-AETFESDVEAK 108
                                       *************9999.77777666655 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 2.3e-08
                            AAA_13 276 hFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepf 352
                                        +++ef++++++L+  i +  ++ +e+ + ++a +++ + + ++++d+++l a++e l++++++  +a +a  +e +
  gi|313117469|ref|YP_004044452.1|  64 AYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFV 140
                                       45777777777777777777777777777777777776667788999****************************** PP

                            AAA_13 353 ksve.lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaie 426
                                       ++v  l +v++ + +i++l+ e+ ++ a++  ++++++++ e+ ++++  ++  v+e+++e++  +  ++++ +ai 
  gi|313117469|ref|YP_004044452.1| 141 TDVAaLRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRdaVAEYREEFHGVE--VQAMLNAIA 215
                                       *87758******************************************865444999999999777..888888999 PP

                            AAA_13 427 klekelkeeeaelkkleee 445
                                       + ++e+++  ae ++ ee 
  gi|313117469|ref|YP_004044452.1| 216 DFQQEIDDFRAEFETTEES 234
                                       9999999888888777765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   4.0   1.4e-07   3.2e-05     120     224 ..      41     141 ..       2     146 .. 0.87
   2 ?    4.7   0.3      0.07        15     119     179 ..     180     240 ..     174     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.4e-07
                              CorA 120 vdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrd 196
                                       v +l++++++l +e++e  d + d  ++e++ e++ l++++++ r+al+++r++++++ + ++++ ++  +k+  +d
  gi|313117469|ref|YP_004044452.1|  41 VSSLLDAIDALRAEIEETGDAF-DAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAE-TFESDVE--AKQDVSD 113
                                       5678899999999999999999.99999***************************66666.5555444..4458*** PP

                              CorA 197 lldelerllemlealrerleslqdtyss 224
                                       ll  +e l  ++++++e  +   +++ +
  gi|313117469|ref|YP_004044452.1| 114 LLAAIEDLRAEMDTTHEAFDAYTNEFVT 141
                                       *****************99999998865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.07
                              CorA 119 ivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrlla 179
                                        ++r+++++ +  + + e+ +e++  + + +l+ +a+ ++++  +r  + +++e ++++ +
  gi|313117469|ref|YP_004044452.1| 180 DIERFRNAVAEQRDAVAEYREEFHGVEVQAMLNAIADFQQEIDDFRAEFETTEESFDAFAR 240
                                       5678888888888888888888888888888888888888888888888888888855555 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0075       1.6     119     161 ..     147     189 ..     145     206 .. 0.83
   2 ?    0.2   0.0       1.4   3.1e+02     121     152 ..     207     238 ..     203     254 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0075
                                       TTTTHHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH- CS
                             APG17 119 dsveelkealkesidelqaaqkkldssllefdtdlrelkkels 161
                                       ++v++l  a++e++ e+ a+q+++d+++  fd d++  +++++
  gi|313117469|ref|YP_004044452.1| 147 RDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVA 189
                                       5789999*****************************9999983 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.4
                                       TTHHHHHHHHHHHHHHHHHHHHHTTHH..HHH CS
                             APG17 121 veelkealkesidelqaaqkkldssllefdtd 152
                                       v+++ +a+ + ++e+++ +++++++ ++fd  
  gi|313117469|ref|YP_004044452.1| 207 VQAMLNAIADFQQEIDDFRAEFETTEESFDAF 238
                                       55666666666666666666666666666644 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3     0.026       5.7      23      88 ..      22     104 ..       4     120 .. 0.54
   2 ?    2.0   0.0       1.3   2.8e+02      54     103 ..     108     157 ..     100     158 .. 0.77
   3 !   13.0   0.1   0.00049      0.11      22      79 ..     167     236 ..     165     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.026
                                       HHHHHB-........BHHHHHHHHHHHH...HHHHHHHHHHHHHH....HHHHHHHHHHHHHHH............. CS
                             DUF16  23 kqlnefkds......nkqrLkkieakvdklgeqinkleqkvekqg....ekikelkveqkaqgeeln.......kvd 82 
                                       +++  +  +      +k ++  + + +d+l  +i++  ++ ++ +    +++++l+ e+  q+e+l        +  
  gi|313117469|ref|YP_004044452.1|  22 QEFAAYAADfaadieTKRDVSSLLDAIDALRAEIEETGDAFDAYNqefaAEVSHLQTEIGEQREALRemrdifdAYA 98 
                                       34444444455556666666666666666666666555555443211114677777777777777773333333444 PP

                                       .HHHHH CS
                             DUF16  83 etleli 88 
                                       et+e+ 
  gi|313117469|ref|YP_004044452.1|  99 ETFESD 104
                                       444444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                             DUF16  54 eqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                       +q v+ + + i++l++e+++ +e++++  + +   + +L ++++ l  ie
  gi|313117469|ref|YP_004044452.1| 108 KQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIE 157
                                       67788888899999999999999999877777777777777777776665 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00049
                                       HHHHHHB-..BHHHHHHHHHHHH...............HHHHHHHHHHHHHHHHHHHHHHHHHHHHH... CS
                             DUF16  22 rkqlnefkdsnkqrLkkieakvd............klgeqinkleqkvekqgekikelkveqkaqgeeln 79 
                                       + +++++ d+ +++++++ + v+             +g++++++ +++   +++i++ ++e ++ +e+++
  gi|313117469|ref|YP_004044452.1| 167 QAEFDDYTDDFDADIERFRNAVAeqrdavaeyreeFHGVEVQAMLNAIADFQQEIDDFRAEFETTEESFD 236
                                       569********************77777776666666667777767776666677777766666666665 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   3.0   8.7e-06    0.0019      48     171 ..       8     138 ..       3     141 .. 0.83
   2 !    7.9   0.3    0.0093       2.1      98     189 ..     141     231 ..     136     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.7e-06
                              Vps5  48 ellvsqrkelasataelakslesLa.slelskslsralsqlaeveerike......llerqaeqdvltLgetideyl 117
                                       e + + r+e+a a +e+a+ ++ +a ++e ++++s++l+++  + ++i+e       ++++  ++v +L++ i e+ 
  gi|313117469|ref|YP_004044452.1|   8 EKMTATREEFADAQQEFAAYAADFAaDIETKRDVSSLLDAIDALRAEIEEtgdafdAYNQEFAAEVSHLQTEIGEQR 84 
                                       667899*************999996269*************888888886222222567788899************ PP

                              Vps5 118 rligsvksvfeqRvklwqkwqsaeqelskkkeqleKlekaaksqqdklqqlkke 171
                                        ++  ++++f++ ++++++ ++a+q++s   ++ e l+++  + ++ +++ ++e
  gi|313117469|ref|YP_004044452.1|  85 EALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNE 138
                                       **************************9988777777777766666666666655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0093
                              Vps5  98 lerqaeqdvltLgetideylrligsvksvfeqRvklwq.kwqsaeqelskkkeqleKlekaaksqqdklqqlkkeve 173
                                       ++  a  dv +L   i+e    +g+v++ f++ ++ +   ++++ + ++ ++++++ ++ + +     +q++ + ++
  gi|313117469|ref|YP_004044452.1| 141 TDVAALRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDaDIERFRNAVAEQRDAVAEYREEFHGV--EVQAMLNAIA 215
                                       56779999***********************999988527999***************9997776..7888888888 PP

                              Vps5 174 elerkvqeaekeFeei 189
                                       + ++ +++++ eFe+ 
  gi|313117469|ref|YP_004044452.1| 216 DFQQEIDDFRAEFETT 231
                                       8888888888888764 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1    0.0011      0.24      32     109 ..      10      93 ..       6     109 .. 0.51
   2 !   12.9   0.2   0.00038     0.084      38     118 ..      43     126 ..      35     137 .. 0.83
   3 ?    6.3   0.0     0.042       9.3      42     117 ..     155     221 ..     139     240 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0011
                           DUF1664  32 mfvTkrslsdavesvskqleqvseslaatkr..hLssridrvdkkldeq....keiskeikeevtevredlseiged 102
                                       m +T+  ++da ++ +    ++ +++++ ++   L + id + ++++e+     +  +e ++ev++++ ++ e +e 
  gi|313117469|ref|YP_004044452.1|  10 MTATREEFADAQQEFAAYAADFAADIETKRDvsSLLDAIDALRAEIEETgdafDAYNQEFAAEVSHLQTEIGEQREA 86 
                                       67777777777777777777777777543322234444444444444431111233444444455555554444444 PP

                           DUF1664 103 vesvkea 109
                                       +++++++
  gi|313117469|ref|YP_004044452.1|  87 LREMRDI 93 
                                       4444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00038
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls...eigedvesvkeave 111
                                       sl da++ +  ++e+  ++  a  +++++++ ++++++ eq e+ +e+++  ++  e  +   e ++dv+ + +a+e
  gi|313117469|ref|YP_004044452.1|  43 SLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFEsdvEAKQDVSDLLAAIE 119
                                       6889*******************************************998777666655422246788888888888 PP

                           DUF1664 112 gleskle 118
                                       +l ++++
  gi|313117469|ref|YP_004044452.1| 120 DLRAEMD 126
                                       8887776 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.042
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       a+e++  +   v+++  +  +++ ++i+r  + + eq ++ +e +       e+ + +  +v+++ +a+ ++++++
  gi|313117469|ref|YP_004044452.1| 155 AIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYR-------EEFHGV--EVQAMLNAIADFQQEI 221
                                       333333444444444444444555555554444444444444444.......443322..2333333333333333 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00091       0.2      13      63 ..      41      88 ..      35      95 .. 0.73
   2 ?    0.5   0.0       3.8   8.5e+02      13      31 ..     111     129 ..      97     139 .. 0.71
   3 ?    2.4   0.0         1   2.2e+02      13      39 ..     149     175 ..     147     201 .. 0.76
   4 ?    5.1   0.0      0.14        30      13      40 ..     207     234 ..     205     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00091
                              ZapB 13 iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlk 63
                                      +++++d i++L+ eiee      ++++   e  +e+++l++e  +++e l+
  gi|313117469|ref|YP_004044452.1| 41 VSSLLDAIDALRAEIEETGDAFDAYNQ---EFAAEVSHLQTEIGEQREALR 88
                                      89*************997766666555...666677777765555555554 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 3.8
                              ZapB  13 iqkaidtitlLqmeieeLk 31 
                                       ++ ++  i+ L+ e++   
  gi|313117469|ref|YP_004044452.1| 111 VSDLLAAIEDLRAEMDTTH 129
                                       5667777777777776655 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 1
                              ZapB  13 iqkaidtitlLqmeieeLkeeneelke 39 
                                       ++ ++  i++Lq e  ++++e   +++
  gi|313117469|ref|YP_004044452.1| 149 VSDLLAAIEELQLEFGAVQAEFDDYTD 175
                                       6789999*******9999998766655 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.14
                              ZapB  13 iqkaidtitlLqmeieeLkeeneelkee 40 
                                       +q++++ i+  q+ei++ ++e e+ +e 
  gi|313117469|ref|YP_004044452.1| 207 VQAMLNAIADFQQEIDDFRAEFETTEES 234
                                       899*****************99988875 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1       0.2        45      81     120 ..      21      61 ..       8      89 .. 0.65
   2 !   10.5   0.1    0.0018       0.4      66     122 ..      76     133 ..      67     141 .. 0.80
   3 !    8.4   0.3    0.0077       1.7      83     174 ..     131     221 ..     126     228 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.2
                      Bacillus_HBL  81 stkFqsyyktlveav.dkkdkaellellekLqeeiqqnqke 120
                                       +++F++y+ +  + +  k d  +ll+++ +L++ei +   +
  gi|313117469|ref|YP_004044452.1|  21 QQEFAAYAADFAADIeTKRDVSSLLDAIDALRAEIEETGDA 61 
                                       56788888888888855667778888888888888765443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0018
                      Bacillus_HBL  66 vkPqliktiqdiigYstkFqsyyktlveav.dkkdkaellellekLqeeiqqnqkevk 122
                                       ++ ++ +  + + +  ++F++y++t ++ v  k+d  +ll+++e+L++e+ +  ++ +
  gi|313117469|ref|YP_004044452.1|  76 LQTEIGEQREALREMRDIFDAYAETFESDVeAKQDVSDLLAAIEDLRAEMDTTHEAFD 133
                                       556666666667778899************7788999999999***999988877766 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0077
                      Bacillus_HBL  83 kFqsyyktlveav.dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilag... 155
                                        F++y ++ v  v         l ++++L + i + q e  ++ +e  ++ +++++d + F ++v+e    +a    
  gi|313117469|ref|YP_004044452.1| 131 AFDAYTNEFVTDVaA-------LRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEyre 200
                                       455565555555533.......4445555566666666666666666777777777777777777333222221011 PP

                      Bacillus_HBL 156 ..dsgvisqlqneiedlqgki 174
                                          + +++++ n+i+d+q++i
  gi|313117469|ref|YP_004044452.1| 201 efHGVEVQAMLNAIADFQQEI 221
                                       112244556666666666665 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   1.6e-05    0.0036       4      75 ..       8      82 ..       7      85 .. 0.93
   2 ?    0.1   0.0       4.8   1.1e+03      39      49 ..     116     126 ..      84     151 .. 0.52
   3 ?    2.4   0.2      0.89     2e+02      44      67 ..     159     182 ..     110     192 .. 0.54
   4 ?    5.4   1.1       0.1        23      16      62 ..     188     235 ..     149     240 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-05
                             Tup_N  4 elLdavkqEfdalsqeasslka.qkdeyelk..iqsqiqElqqirqtlyeLeeahrkikqqYEeeiarLkaeLes 75
                                      e + a ++Ef  ++qe   + a    ++e+k  ++s ++ ++++r ++ e   a+ +  q++  e+++L++e+ +
  gi|313117469|ref|YP_004044452.1|  8 EKMTATREEFADAQQEFAAYAAdFAADIETKrdVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGE 82
                                      667789*************9997899*****99***************************************965 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 4.8
                             Tup_N  39 qElqqirqtly 49 
                                       + ++ +r ++ 
  gi|313117469|ref|YP_004044452.1| 116 AAIEDLRAEMD 126
                                       22222222222 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.89
                             Tup_N  44 irqtlyeLeeahrkikqqYEeeia 67 
                                       ++ ++   ++++ +  + ++ +i+
  gi|313117469|ref|YP_004044452.1| 159 LQLEFGAVQAEFDDYTDDFDADIE 182
                                       222333333333333333444444 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.1
                             Tup_N  16 lsqeasslkaqkdeyelk.iqsqiqElqqirqtlyeLeeahrkikqqY 62 
                                       ++++   + + ++e+    +q+ ++ ++ ++q++ +  ++++   +++
  gi|313117469|ref|YP_004044452.1| 188 VAEQRDAVAEYREEFHGVeVQAMLNAIADFQQEIDDFRAEFETTEESF 235
                                       334444455566666544467777777777777777776666666655 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.1   1.7e-06   0.00038      73     253 ..      54     234 ..      19     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.7e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXX CS
                              AIP3  73 pldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavlrq 149
                                       +++e  + +d  ++++++e+ +l+++i +q+++l+e+++     a++ +s++ ak++ ++ l+ +++lr ++ ++ +
  gi|313117469|ref|YP_004044452.1|  54 EIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHE 130
                                       5677778999999999********************999988888888999999999******************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXX CS
                              AIP3 150 lysefkseikeslselrekakkvkeaslastkkssnrayiekgkkkLseesdklvtkvddLqDlvedlrkDVvqRgv 226
                                         ++ ++e+ + +++lr+  + + +++  + + ++ +a  ++  + ++++ ++  + v +  D v + r+     +v
  gi|313117469|ref|YP_004044452.1| 131 AFDAYTNEFVTDVAALRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREEFHGVEV 207
                                       *****************9999999777778888999***************************************** PP

                                       XXXHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 227 rpskkqlesvakeikkakkelkkleey 253
                                       +   + + + ++ei++ ++e ++ ee 
  gi|313117469|ref|YP_004044452.1| 208 QAMLNAIADFQQEIDDFRAEFETTEES 234
                                       ******************999987765 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.8       0.2        44      61      87 ..      13      39 ..       2      62 .. 0.46
   2 !   11.9   1.3   0.00094      0.21      15      89 ..      60     138 ..      52     148 .. 0.69
   3 !   13.0   0.6   0.00045       0.1      11      86 ..     146     227 ..     139     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.2
                                      HHHHHHHHHHHHHHHHHHHH.HHHHHHH CS
                              OmpH 61 keqelqkkeqelqqkqqqka.qelqkkq 87
                                       ++e+++ +qe+ + +++++  +++ k+
  gi|313117469|ref|YP_004044452.1| 13 TREEFADAQQEFAA-YAADFaADIETKR 39
                                      23335555555555.3333334444444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00094
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.....-HHHHHH...HHHHHHHHHHHHHHHHHHHH CS
                              OmpH  15 pegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e...keekeqe...lqkkeqelqqkqqqkaqelq 84 
                                       +++ a +++++++ + lq+e+ +++++l+++++ ++++a++  +    ++   +   l +  ++l+++++ + + + 
  gi|313117469|ref|YP_004044452.1|  60 DAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFeSdveAKQ---DvsdLLAAIEDLRAEMDTTHEAFD 133
                                       56778889999999999999999999999999999888877533443333...334466666666666666556555 PP

                                       HHHHH CS
                              OmpH  85 kkqqe 89 
                                       +  +e
  gi|313117469|ref|YP_004044452.1| 134 AYTNE 138
                                       55554 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00045
                                       HHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHH......HHHHHHHHHHHHHHHH CS
                              OmpH  11 leespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqe......lqkkeqelqqkqqqka 80 
                                       l++  +  aa e+l+ +f + qae+++  +++++ +e++ ++ +++ +  ++++e      +q++ +++ + +qq+ 
  gi|313117469|ref|YP_004044452.1| 146 LRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQrDAVAEYREefhgveVQAMLNAIAD-FQQEI 221
                                       5566666788899999***********************98777765544444446788889999999999.77777 PP

                                       HHHHHH CS
                              OmpH  81 qelqkk 86 
                                        +++++
  gi|313117469|ref|YP_004044452.1| 222 DDFRAE 227
                                       665554 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1      0.11        24      62     105 ..       7      50 ..       1      67 [. 0.76
   2 ?    7.4   0.2     0.019       4.2      52     112 ..      67     127 ..      51     135 .. 0.82
   3 ?    1.4   0.0       1.3     3e+02      63     100 ..     116     157 ..     104     162 .. 0.63
   4 ?    5.8   0.1     0.061        14      51     114 ..     167     232 ..     157     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.11
                          LOH1CR12  62 dakiitllaelrekqkqyasyaealskvnelsdqlsriqiiled 105
                                        +k++   +e+ + q+++a ya+ ++   e + ++s++ + ++ 
  gi|313117469|ref|YP_004044452.1|   7 REKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDA 50 
                                       578999999**************998776777777766665554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.019
                          LOH1CR12  52 aklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEt 112
                                       ++ ++++ +++++i +  + lre+++ ++ yae+++   e ++++s +   +ed  + ++t
  gi|313117469|ref|YP_004044452.1|  67 QEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDT 127
                                       5677888889999999999****************99888899998888888887777766 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.3
                          LOH1CR12  63 akiitllaelrekqkqyasyaeal....skvnelsdqlsriq 100
                                       a i+ l ae+   ++ ++ y +++    + ++++sd l+ i+
  gi|313117469|ref|YP_004044452.1| 116 AAIEDLRAEMDTTHEAFDAYTNEFvtdvAALRDVSDLLAAIE 157
                                       456666777777777777766554222156777777777665 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.061
                          LOH1CR12  51 qaklverikevdakiitllaelrekqkqyasyaealskv..nelsdqlsriqiiledivpllEtln 114
                                       qa+  + + + da+i++  + + e+++  a+y e++ +v  + + + ++  q+ ++d  +  Et  
  gi|313117469|ref|YP_004044452.1| 167 QAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREEFHGVevQAMLNAIADFQQEIDDFRAEFETTE 232
                                       6777777888999****999999*************986225688889999999988877777665 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6  12.4     1e-05    0.0022      93     310 ..       9     232 ..       2     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXX CS
                          Filament  93 kelnkreevEaelkalrkdldeatlarvdLekkvesLkeelaflkkvheeEvkelqkqvseqvlvevda..arkldL 167
                                       k ++ ree  ++ +++     +   a ++  + v sL + ++ l+   ee  + + +   ++   ev +  ++  + 
  gi|313117469|ref|YP_004044452.1|   9 KMTATREEFADAQQEFAAYA-ADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYN-QEFAAEVSHlqTEIGEQ 83 
                                       44444444333333333222.22344456666689999999999999988777777777.66666665311444568 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXX-HHHH.HH..HHHHHHHHHHHHHHHH CS
                          Filament 168 teilkeiraqyeelaeknreeaeewyk.....skleelqeaaeknsealrsakeei.te..lrrqiqsleieleslk 236
                                        e+l+e+r+ +++ ae+ ++++e+        + +e+l+ ++++ +ea  +  +e  t+  + r +  l + +e+l+
  gi|313117469|ref|YP_004044452.1|  84 REALREMRDIFDAYAETFESDVEAKQDvsdllAAIEDLRAEMDTTHEAFDAYTNEFvTDvaALRDVSDLLAAIEELQ 160
                                       99******************9998765222226799************99988885244224589999********* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-XX CS
                          Filament 237 kqkasleaqlaeleerleaeleklqeklseleeelaeireemarqlreYqeLLdvKlaLdiEIatYRkLLEGee 310
                                        +  +++a+  +  + ++a++e+++++++e  +++ae ree   +  e q +L+      +EI+ +R   E  e
  gi|313117469|ref|YP_004044452.1| 161 LEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREEF--HGVEVQAMLNAIADFQQEIDDFRAEFETTE 232
                                       ****************************************87..67899**************99998777655 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2    0.0076       1.7      13     108 ..      15     109 ..       7     118 .. 0.77
   2 ?    6.5   0.0      0.05        11       2      49 ..     112     160 ..     111     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0076
                                       HHHHHHHHHHHH--SH...HHHHHHHHHHHHHHHHHHHHHHHTS----HHHHHHHHHHHHHCHHHHHHHHHHHHHTH CS
                              HsbA  13 tavtaldtavnafnGg.asalpilsasnalvsaikkattdaqasapltdeealalaqavqtLepdvkaaldaliaKk 88 
                                       +   + ++  +a+  + a  ++ + ++++l +ai++ ++ ++ ++   d+  +++a++v+ L++++    +al + +
  gi|313117469|ref|YP_004044452.1|  15 EEFADAQQEFAAYAADfAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMR 91 
                                       556666777777755555668888999999****************999999************************* PP

                                       HHHHHHT-HHHHHHHHHHHH CS
                              HsbA  89 pafdkagltslvlssLqdlk 108
                                       + fd   ++ +  s+++  +
  gi|313117469|ref|YP_004044452.1|  92 DIFD--AYAETFESDVEAKQ 109
                                       9999..44566666655544 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHHHHHHHHHHHH--SH...HHHHHHHHHHHHHHHHHHH CS
                              HsbA   2 atvisdittistavtaldtavnafnGg.asalpilsasnalvsaikkat 49 
                                       +++ ++i+++ + +++ ++a +a+++   + ++ l ++++l +ai++  
  gi|313117469|ref|YP_004044452.1| 112 SDLLAAIEDLRAEMDTTHEAFDAYTNEfVTDVAALRDVSDLLAAIEELQ 160
                                       5678999999**************9955556777778888888877655 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4     0.051        11      35      99 ..       7      71 ..       2      84 .. 0.74
   2 ?    6.9   0.2     0.032         7      30      96 ..      72     138 ..      66     146 .. 0.74
   3 !    9.3   0.1    0.0057       1.3       7      98 ..      90     178 ..      87     188 .. 0.74
   4 ?    3.6   0.1      0.35        77      67     101 ..     205     239 ..     179     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.051
                                      HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N 35 dekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99
                                       ek+ +++ e+ ++q+e  + ++ ++  ++ k d ++l++ +++l +e++++ ++ ++ ++e+ +
  gi|313117469|ref|YP_004044452.1|  7 REKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAA 71
                                      56667777777788888888888888888888888888888888888888887777777766655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleae 96 
                                       e+ +l+++  e + +l e++    + ++++++  ++k+d ++l+a +++l +e++++ ++ ++ ++e
  gi|313117469|ref|YP_004044452.1|  72 EVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNE 138
                                       5556666666666677777777777777778888888888888888888888888888888887776 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0057
                                       HHH-HHHHHHHHCCCTCCCHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHH CS
                      Seryl_tRNA_N   7 irenpeavkeklkkRgedkadvdelleldek.rrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkee 82 
                                       +r+ ++a++e  ++  e+k+dv +ll++ e  r e+ ++ e++ a  Ne    ++ +     d ++l+a ++el+ e
  gi|313117469|ref|YP_004044452.1|  90 MRDIFDAYAETFESDVEAKQDVSDLLAAIEDlRAEMDTTHEAFDAYTNEFVTDVAALR----DVSDLLAAIEELQLE 162
                                       5667888888888888888888888876655155677888888888999888888887....567888888888888 PP

                                       HHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  83 lkaleaelkeleaele 98 
                                       + a++ae ++ +++++
  gi|313117469|ref|YP_004044452.1| 163 FGAVQAEFDDYTDDFD 178
                                       8888888777777665 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.35
                                       S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  67 edaeeliaevkelkeelkaleaelkeleaelekll 101
                                        + +++++ +++ ++e+++  ae ++ e+ +++++
  gi|313117469|ref|YP_004044452.1| 205 VEVQAMLNAIADFQQEIDDFRAEFETTEESFDAFA 239
                                       7889999999999*******999999999988775 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.22        49     198     248 ..       7      57 ..       2      61 .. 0.68
   2 !   12.1   1.1    0.0003     0.066     150     242 ..      47     138 ..      36     151 .. 0.84
   3 !    9.0   0.2    0.0026      0.57     140     254 ..     121     232 ..     116     247 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.22
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkselee 248
                                       +e++ ++ree+a++++e ++  ++ a   e + ++++ ++++++ ++e+ee
  gi|313117469|ref|YP_004044452.1|   7 REKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEE 57 
                                       567777777777777777777777777777777777666666666666655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0003
                              Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelq 226
                                       ++++ ++++e+  + +d++ +e+ +e + l+ e+ +++ea +e+ +i  ++ e++ ++++ +k++++ + + +++l+
  gi|313117469|ref|YP_004044452.1|  47 AIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVE-AKQDVSDLLAAIEDLR 122
                                       5555678899999999*******************************9999999999875.6889999999999999 PP

                              Spc7 227 eqleeleekieelkeq 242
                                       +++++  e++++ +++
  gi|313117469|ref|YP_004044452.1| 123 AEMDTTHEAFDAYTNE 138
                                       9999999999888765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0026
                              Spc7 140 LkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeie 216
                                       L+ +++ + e++++  ++   + + l ++ + l +  +el+ e+   q++ ++ ++   +++e +r+++ae+   ++
  gi|313117469|ref|YP_004044452.1| 121 LRAEMDTTHEAFDAYTNEFVTDVAALRDVSD-LLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVA 196
                                       5555555555555555555555555555543.344456677777777776666666557788888888888888888 PP

                              Spc7 217 ekkkelaelqeqleeleekieelkeqkseleeeiaeae 254
                                       e ++e   +  ++++  ++i++ +++++++++e +  e
  gi|313117469|ref|YP_004044452.1| 197 EYREEFHGV--EVQAMLNAIADFQQEIDDFRAEFETTE 232
                                       777777644..344445555555555555555554444 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   1.4   0.00018      0.04     109     216 ..      47     160 ..       6     202 .. 0.69
   2 ?    4.5   0.1      0.11        25     108     178 ..     154     228 ..     150     234 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHSSSXXXXXXX...XXXX.XXXXXXXXXXXXXX CS
                              SHE3 109 elerlkvqYdalvdsqkeYkehYqqeieeLkesleklk...lenekqleelqeri...ssndkdidtkldsynnkkk 179
                                        ++ l+++ +   d+   Y + +  e+++L++++++ +   +e +  ++ + e+    ++ ++d+  +l   ++ ++
  gi|313117469|ref|YP_004044452.1|  47 AIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQRealREMRDIFDAYAETFesdVEAKQDVSDLLAAIEDLRA 123
                                       4555555555566777778888888888888877765522234444444444444111445679************* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 180 nlesieeeknkkllkkleslaseldleswlelykelk 216
                                       +++  +e  + + ++ ++ +a++ d++ +l+  +el+
  gi|313117469|ref|YP_004044452.1| 124 EMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIEELQ 160
                                       ******************9999999777666555543 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSXXX....XXXXXXXX.XXXXXXXXXXXXX CS
                              SHE3 108 eelerlkvqYdalvdsqkeYkehYqqeieeLkesleklklenekqleel....qerissndkdidtkldsynnkk 178
                                       + +e+l+ ++ a+ +    Y + ++ +ie+ ++++ + +    ++ ee+     + + +   d+++++d++   +
  gi|313117469|ref|YP_004044452.1| 154 AAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREEFhgveVQAMLNAIADFQQEIDDFRAEF 228
                                       567888888888888888888888888888888776655443333333211113344444456666666666555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1    0.0011      0.24      24     112 ..      60     151 ..      57     163 .. 0.87
   2 ?    2.9   0.0       0.5   1.1e+02      25      53 ..     169     197 ..     163     231 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0011
                                       HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHH CS
                         Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketi 97 
                                       d+++ y++++  ++++l+ e+ e ++  +e++++  +  ++ +++ + k+d      +i++++ e+++ ++ +++  
  gi|313117469|ref|YP_004044452.1|  60 DAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVsdlLAAIEDLRAEMDTTHEAFDAYT 136
                                       67899*************************99999999999999888888764447899*****************9 PP

                                       HCCHHHHHHHHHHHH CS
                         Fib_alpha  98 daqesnirvLqnvle 112
                                       ++ ++ + +L++v +
  gi|313117469|ref|YP_004044452.1| 137 NEFVTDVAALRDVSD 151
                                       9999******99754 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.5
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstke 53 
                                        +++y  d++ d+e+ +n ++e ++   e
  gi|313117469|ref|YP_004044452.1| 169 EFDDYTDDFDADIERFRNAVAEQRDAVAE 197
                                       45555555555555555555554444333 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2       4.1     9e+02       1      14 [.      13      26 ..       2      32 .. 0.56
   2 !   13.1   0.9   0.00042     0.092      36      66 ..      40      71 ..      32      73 .. 0.83
   3 ?    2.9   1.0      0.64   1.4e+02      36      60 ..      72      96 ..      67     103 .. 0.52
   4 !   14.6   1.9   0.00014     0.032      25      65 ..      99     140 ..      97     143 .. 0.89
   5 ?    3.5   3.3      0.41        90      38      66 ..     150     179 ..     141     204 .. 0.85
   6 ?    5.7   0.2     0.081        18      39      64 ..     216     242 ..     209     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 4.1
                              HalX  1 trseYdeelqelfa 14
                                      tr e+ +  qe+ a
  gi|313117469|ref|YP_004044452.1| 13 TREEFADAQQEFAA 26
                                      34444444444444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00042
                              HalX 36 eYqeLearleelraqldetldeldd.addfea 66
                                        + L + +++lra+++et d++d+  ++f+a
  gi|313117469|ref|YP_004044452.1| 40 DVSSLLDAIDALRAEIEETGDAFDAyNQEFAA 71
                                      567899******************98888876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.64
                              HalX 36 eYqeLearleelraqldetldeldd 60
                                      e + L++++ e r+ l e  d +d+
  gi|313117469|ref|YP_004044452.1| 72 EVSHLQTEIGEQREALREMRDIFDA 96
                                      3444555555555555555555444 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 0.00014
                              HalX  25 ekseaeLadseeYqeLearleelraqldetldeldd.addfe 65 
                                       e  e++ ++ +  ++L a +e+lra+ d+t +++d+ + +f 
  gi|313117469|ref|YP_004044452.1|  99 ETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAyTNEFV 140
                                       66688999**************************99877775 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.41
                              HalX  38 qeLearleelraqldetldeldd.addfea 66 
                                       ++L a +eel+ +  ++ +e+dd +ddf+a
  gi|313117469|ref|YP_004044452.1| 150 SDLLAAIEELQLEFGAVQAEFDDyTDDFDA 179
                                       677888888888888888888888888875 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.081
                              HalX  39 eLearleelraqldetldeldd.addf 64 
                                       + ++++++ ra+ ++t +++d+ a+df
  gi|313117469|ref|YP_004044452.1| 216 DFQQEIDDFRAEFETTEESFDAfARDF 242
                                       56899**************99998888 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.8   0.00026     0.057       9      72 ..      58     120 ..      47     141 .. 0.75
   2 !    8.1   0.3    0.0097       2.1       4      66 ..     175     235 ..     173     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00026
                            TACC_C   9 alekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqk 72 
                                          ++++ ++e   e+++l+ ++ e+++  +em++i++++ +t +  +e kq  +    + i+ 
  gi|313117469|ref|YP_004044452.1|  58 TGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVS-DLLAAIED 120
                                       44556677788899****************************9998888775443.34444555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0097
                            TACC_C   4 kdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkela 66 
                                        d da +e++++ v e+   ++e++++ +    e+q m + +a+f + i ++ +e ++++e++
  gi|313117469|ref|YP_004044452.1| 175 DDFDADIERFRNAVAEQRDAVAEYREEFHG--VEVQAMLNAIADFQQEIDDFRAEFETTEESF 235
                                       699*************99999999988765..57899***************99999988765 PP

>> YgaB  YgaB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       4.5     1e+03      36      64 ..      35      63 ..       8      68 .. 0.77
   2 !   11.4   0.1    0.0015      0.33      37      67 ..      68      98 ..      62     103 .. 0.87
   3 ?    3.4   0.0      0.45        99      37      71 ..     106     140 ..      98     145 .. 0.86
   4 ?    0.5   0.1       3.6     8e+02      37      63 ..     206     235 ..     191     240 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 4.5
                              YgaB 36 lekeaklesiqeeikrkkkeLkeiqkvFe 64
                                      +e +  ++s+ + i+ ++ e++e  + F+
  gi|313117469|ref|YP_004044452.1| 35 IETKRDVSSLLDAIDALRAEIEETGDAFD 63
                                      45566677888888888888888777776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0015
                              YgaB 37 ekeaklesiqeeikrkkkeLkeiqkvFekQt 67
                                      e  a+++++q ei ++++ L+e++++F+   
  gi|313117469|ref|YP_004044452.1| 68 EFAAEVSHLQTEIGEQREALREMRDIFDAYA 98
                                      5579999********************8755 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.45
                              YgaB  37 ekeaklesiqeeikrkkkeLkeiqkvFekQteevi 71 
                                       e +  ++++ + i+ ++ e+   ++ F+  t+e +
  gi|313117469|ref|YP_004044452.1| 106 EAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFV 140
                                       56677889999*****************9999976 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 3.6
                              YgaB  37 ekeakle...siqeeikrkkkeLkeiqkvF 63 
                                       e +a+l+   + q+ei+  + e +  ++ F
  gi|313117469|ref|YP_004044452.1| 206 EVQAMLNaiaDFQQEIDDFRAEFETTEESF 235
                                       445554411155778888888887777766 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3     0.018       3.9      53     122 ..      51     126 ..       7     129 .. 0.76
   2 ?    5.8   0.0     0.047        10      53      81 ..     121     155 ..     116     242 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.018
                          Lectin_N  53 LqreLetLketfsnfssstlaeiqalss....qggslsekvtsleaklekkqq..dlkadhselllhvkqlvkdLr 122
                                       L+ e+e   ++f+   ++  ae+++l++    q + l e+   ++a  e  +   + k+d s+ll  +  l++++ 
  gi|313117469|ref|YP_004044452.1|  51 LRAEIEETGDAFDAYNQEFAAEVSHLQTeigeQREALREMRDIFDAYAETFESdvEAKQDVSDLLAAIEDLRAEMD 126
                                       7888888888899999999999999998555433334444444455555444400557799999999999988875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.047
                          Lectin_N  53 LqreLetLketfsnfssstlaeiqalss......q 81 
                                       L+ e+ t +e+f+  +++  +++ al+       +
  gi|313117469|ref|YP_004044452.1| 121 LRAEMDTTHEAFDAYTNEFVTDVAALRDvsdllaA 155
                                       67777777777777777777777777653333331 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.053        12      48      92 ..      36      80 ..       2      89 .. 0.71
   2 !    8.5   0.3     0.009         2      35     123 ..      48     134 ..      29     154 .. 0.52
   3 ?    6.1   0.1     0.048        11      38     110 ..     159     235 ..     149     242 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.053
                         ApoLp-III 48 elkkksdeleealkevkkkieetadklseenPevkkkaqelqekv 92
                                      e k+  + l  a++ ++++ieet d + + n e + +++ lq+++
  gi|313117469|ref|YP_004044452.1| 36 ETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEI 80
                                      445555667777777778888888888777777777777777766 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.009
                         ApoLp-III  35 vdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesq..klaes 109
                                       +d l++ i+++ ++   +++e++  ++ ++++i e ++ l+e    +    +++ e++ s v++    s+  ++ e+
  gi|313117469|ref|YP_004044452.1|  48 IDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALRE----MRDIFDAYAETFESDVEAKQDVSDllAAIED 120
                                       233333344444455556666666666666666666666665....5555555666665555544333331133345 PP

                         ApoLp-III 110 lkensqeakeklak 123
                                       l +++ ++ e   +
  gi|313117469|ref|YP_004044452.1| 121 LRAEMDTTHEAFDA 134
                                       55555555555555 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.048
                         ApoLp-III  38 lkqvikslqeelkkksdeleealkevkkkieetadklse....enPevkkkaqelqekvQsgvqslvkesqklaesl 110
                                       l+  ++ +q e  +++d ++  ++ ++++++e +d + e     +   ++++ +  + +Q+ +     e +++ es+
  gi|313117469|ref|YP_004044452.1| 159 LQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEyreeFHGVEVQAMLNAIADFQQEIDDFRAEFETTEESF 235
                                       44445556666666777777777777777777666666644431222234444455667777777777776666666 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       6.7   1.5e+03      51      77 ..      40      66 ..      34      69 .. 0.72
   2 !    9.6   0.0    0.0043      0.94      21      78 ..      66     137 ..      43     139 .. 0.87
   3 ?    1.6   0.0       1.4   3.1e+02      55      78 ..     177     200 ..     169     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 6.7
                              Med9 51 sveeqeaeieeleeqlakKrelLkkyk 77
                                       v + ++ i++l+ +++   + +  y+
  gi|313117469|ref|YP_004044452.1| 40 DVSSLLDAIDALRAEIEETGDAFDAYN 66
                                      566677888888888887776666665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0043
                              Med9  21 skdletktgelrhkLkkarelirelpg..............idrsveeqeaeieeleeqlakKrelLkkykn 78 
                                        +++ ++++ l++ + + re++re+ +                  v + +a ie+l+ ++++  e +  y n
  gi|313117469|ref|YP_004044452.1|  66 NQEFAAEVSHLQTEIGEQREALREMRDifdayaetfesdveAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTN 137
                                       589999*********************999999999999888889999999999999999998888887766 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 1.4
                              Med9  55 qeaeieeleeqlakKrelLkkykn 78 
                                        +a ie  ++ +a +r+  ++y++
  gi|313117469|ref|YP_004044452.1| 177 FDADIERFRNAVAEQRDAVAEYRE 200
                                       568899999*********999998 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   9.6    0.0017      0.38     114     243 ..      18     139 ..       3     190 .. 0.63
   2 ?    7.0   0.5     0.014       3.2     136     239 ..     150     241 ..     137     256 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                           DUF4407 114 eeqqeeakelkeqlaaa..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakek 188
                                       + +q+e +++ +  aa+   + +++ l + i+al+aei++  +++da ++e+++e++   +t+       g+  ++ 
  gi|313117469|ref|YP_004044452.1|  18 ADAQQEFAAYAADFAADieTKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHL-QTE----I--GEQREAL 87 
                                       34444445555555555777778888889999999999999999999999999999863.333....2..3333344 PP

                           DUF4407 189 kaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGl 243
                                       +++ d  +a  ++++++++a++++++l a +++l+ae++++++a++a +++   +
  gi|313117469|ref|YP_004044452.1|  88 REMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNE---F 139
                                       444444444444444444477777777777777777777777777664443...3 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                           DUF4407 136 aeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakldatarl 212
                                       ++l a i++lq e+ a +a++d+ ++++++ ++               a  e +++ +++++e   ++ +     ++
  gi|313117469|ref|YP_004044452.1| 150 SDLLAAIEELQLEFGAVQAEFDDYTDDFDADIER-----------FRNAVAEQRDAVAEYREEFHGVEVQ-AMLNAI 214
                                       4555555555555555555555555555555443...........1222333344444444444444444.344555 PP

                           DUF4407 213 aalraelaeleaerakeraasqaaaaa 239
                                       a+ ++e+++ +ae ++++++++a a++
  gi|313117469|ref|YP_004044452.1| 215 ADFQQEIDDFRAEFETTEESFDAFARD 241
                                       555555555555555555555555554 PP

>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.0     0.027       6.1      96     172 ..       8      82 ..       2      88 .. 0.50
   2 !   11.8  13.3   0.00067      0.15       9     159 ..      66     221 ..      66     237 .. 0.84
   3 ?    2.8   2.1      0.39        86      87     120 ..     210     243 ..     189     253 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.027
                            FAM184  96 qkvvelsreveevkrkFeeklrqfaqlqeqle................qekekaLeelrkkhreeveeLlkeqeaqs 156
                                       +k+++  +e  +++++F +   +fa   e++                 +                  e  ++ +a +
  gi|313117469|ref|YP_004044452.1|   8 EKMTATREEFADAQQEFAAYAADFAADIETKRdvsslldaidalraeiE------------------ETGDAFDAYN 66 
                                       5666666666666666666666665544433334444444444444444..................5555555555 PP

                            FAM184 157 ekllkeqekleekhka 172
                                       +++++e ++l+ ++ +
  gi|313117469|ref|YP_004044452.1|  67 QEFAAEVSHLQTEIGE 82 
                                       5555555555444333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00067
                            FAM184   9 NdeheaeiqalkeaHeeeiqqilaetrekilqykskveeeldlkqkiaeleesleqhekekrqalaefeqykrrvee 85 
                                       N e+ ae+++l++   e+  + l+e+r+   +y +  e++ + kq ++ l  ++e+  +e + ++  f++y ++   
  gi|313117469|ref|YP_004044452.1|  66 NQEFAAEVSHLQTEIGEQR-EALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVT 141
                                       7889999999998877765.5689************************************************99766 PP

                            FAM184  86 rel..kleaehsqkvvelsreveevkrkFeeklrqfaqlqeqle...qekekaLeelrkk.hreeveeLlkeqeaqs 156
                                         +   + ++  + + el+ e  +v+++F++   +f    e++    +e++ a+ e r++ h  ev+ +l++  + +
  gi|313117469|ref|YP_004044452.1| 142 DVAalRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRnavAEQRDAVAEYREEfHGVEVQAMLNAIADFQ 218
                                       555005568999*************************9999999899999999999998746789999998876655 PP

                            FAM184 157 ekl 159
                                       +++
  gi|313117469|ref|YP_004044452.1| 219 QEI 221
                                       554 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.39
                            FAM184  87 elkleaehsqkvvelsreveevkrkFeeklrqfa 120
                                        l++ a+++q +  + +e e+ ++ F++  r+f 
  gi|313117469|ref|YP_004044452.1| 210 MLNAIADFQQEIDDFRAEFETTEESFDAFARDFY 243
                                       3445566666666666666666666666666664 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.5     0.097        22      18     100 ..      41     117 ..      28     146 .. 0.40
   2 ?    6.6   0.0     0.033       7.3      17      81 ..     148     222 ..     145     242 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.097
                      Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsil 94 
                                       ++ +L+ai ++ ++i    +++ da +   +++++++++l +e+ ++  ++l ++ d   a ++t++++ ++ ++++
  gi|313117469|ref|YP_004044452.1|  41 VSSLLDAIDALRAEI----EETGDAFDAYNQEFAAEVSHLQTEIGEQ-REALREMRDIFDAYAETFESDVEA-KQDV 111
                                       444444442222222....2222222222222222222222222222.112222222222222333333332.2233 PP

                      Baculo_PEP_C  95 tnLlss 100
                                       ++Ll+ 
  gi|313117469|ref|YP_004044452.1| 112 SDLLAA 117
                                       333333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.033
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt.......rldtl.ltnLtdalnalq...d 81 
                                       d++++L+ai  ++ +  +++++ +d+    ++a  e++++++ae+++       +++ + ++++ +a++ +q   d
  gi|313117469|ref|YP_004044452.1| 148 DVSDLLAAIEELQLEF-GAVQAEFDDYTDDFDADIERFRNAVAEQRDavaeyreEFHGVeVQAMLNAIADFQqeiD 222
                                       6667777777777776.77777777666666666666666666666633333332222113334444444444444 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.5    0.0076       1.7      60     121 ..      38      99 ..       2     115 .. 0.59
   2 ?    8.6   0.7    0.0053       1.2      44     158 ..     120     231 ..     102     241 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0076
                         Golgin_A5  60 reelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlke 121
                                       + ++ +l  +i+ lr+e++++ + + a  +++  ++++l++++ e+r+a +e+++    + e
  gi|313117469|ref|YP_004044452.1|  38 KRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAE 99 
                                       34555566666666666666666666666666666666666666666666666554444444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0053
                         Golgin_A5  44 alsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlk 120
                                        l ae+d +++  d++++e      +++++   l+ +e+ q  e+  ++ +  ++ + ++++ +   ++++ +++++
  gi|313117469|ref|YP_004044452.1| 120 DLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIEELQ-LEFGAVQAEFDDYTDDFDADIE---RFRNAVAEQR 192
                                       35566666666666666666666666666666666666654.6777777777777777775444...4456666677 PP

                         Golgin_A5 121 eelryleeelvrskatlq.srikdrekeieklrnqlttk 158
                                       + +   +ee + + ++ + + i d ++ei++ r++  t 
  gi|313117469|ref|YP_004044452.1| 193 DAVAEYREEFHGVEVQAMlNAIADFQQEIDDFRAEFETT 231
                                       777777777777666544256777777777777776654 PP

>> CagZ  CagZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       3.5   7.7e+02      30      71 ..      26      67 ..       6      75 .. 0.78
   2 ?   13.2   1.7   0.00023      0.05      25     157 ..      91     224 ..      77     235 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.5
                              CagZ 30 kfiqnyasslkdsndpqdflrrvqelrinmqknfisfdvyyn 71
                                       +  ++a+ +    d   +l  ++ lr +++    +fd y +
  gi|313117469|ref|YP_004044452.1| 26 AYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQ 67
                                      456678888888889999999999999999999999998865 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00023
                              CagZ  25 nevrdkfiqnyasslkdsndpqdflrrvqelrinmqknfisfdvyynylnnlvlasynrckqektfaestikneltl 101
                                        ++ d + + + s +   +d  d+l  +++lr +m+    +fd y n +   v a  +      ++       +l +
  gi|313117469|ref|YP_004044452.1|  91 RDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIE----ELQLEF 163
                                       45667788899999999****************************9988777766555444333333....345566 PP

                              CagZ 102 gefvaeisdnfnnfmcd......evarisdlvasylpreylppfidgnmmgvafqilgiddf 157
                                       g + ae  d  ++f +d       va   d va y   e+    ++  +  +a     iddf
  gi|313117469|ref|YP_004044452.1| 164 GAVQAEFDDYTDDFDADierfrnAVAEQRDAVAEYR-EEFHGVEVQAMLNAIADFQQEIDDF 224
                                       666677666666665542111114555555555553.2333334444444444444455555 PP

>> NYD-SP28  Sperm tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4     0.067        15       9      80 ..       6      77 ..       2      83 .. 0.73
   2 ?    5.0   0.1      0.11        25      51      88 ..      73     110 ..      68     115 .. 0.92
   3 ?    4.6   0.0      0.15        33      22      84 ..     119     182 ..     114     197 .. 0.80
   4 ?   -1.0   0.0       8.3   1.8e+03      71      88 ..     216     233 ..     205     240 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.067
                          NYD-SP28  9 rrreeeelrqerkekleeeaksseekfeeinekWreilrknkpqeLrkeleeqkqaceelideKdklikelq 80
                                      +r++   +r+e  +  +e a+ +++  ++i+ k +     +    Lr+e+ee   a+++  +e  + ++ lq
  gi|313117469|ref|YP_004044452.1|  6 KREKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQ 77
                                      677788888888888888888888888888888888888888888888888888888876555555555555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.11
                          NYD-SP28  51 pqeLrkeleeqkqaceelideKdklikelqeeLkekde 88 
                                          L+ e+ eq++a  e+ d  d+  ++++ ++++k++
  gi|313117469|ref|YP_004044452.1|  73 VSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQD 110
                                       6789******************************9987 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.15
                          NYD-SP28  22 ekleeeaksseekfeeinekWr.eilrknkpqeLrkeleeqkqaceelideKdklikelqeeLk 84 
                                       e l +e ++++e f++ ++++   + +  +  +L +++ee++  + ++ +e d+  +++  +++
  gi|313117469|ref|YP_004044452.1| 119 EDLRAEMDTTHEAFDAYTNEFVtDVAALRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIE 182
                                       6788899999999999888875489999999999999999999998888888877777777765 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 8.3
                          NYD-SP28  71 eKdklikelqeeLkekde 88 
                                       +  + i++++ e++  +e
  gi|313117469|ref|YP_004044452.1| 216 DFQQEIDDFRAEFETTEE 233
                                       333334444444444444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.8    0.0065       1.4      41     158 ..       4     139 ..       1     144 [. 0.53
   2 ?   11.4   2.5    0.0014      0.32      24     159 ..      71     203 ..      67     246 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0065
                              Fez1  41 relrakleekeeeikeleesleektle.................levcenelqrk....kseaellrekvekleeel 96 
                                       r+ r+k++++ ee  ++++++   +++                 ++ + +e++++     + ++ +  +v++l++e+
  gi|313117469|ref|YP_004044452.1|   4 RDKREKMTATREEFADAQQEFAAYAADfaadietkrdvsslldaIDALRAEIEETgdafDAYNQEFAAEVSHLQTEI 80 
                                       45555555555555555555544444444444444444444444555555555554444333333344466666666 PP

                              Fez1  97 kelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassF 158
                                        e re+l+e+    +   +e+ e     ++++++++l + +e lrae+ + +++ ++ +++F
  gi|313117469|ref|YP_004044452.1|  81 GEQREALREMRDIFDAY-AETFE--SDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEF 139
                                       66666666644332222.22222..2333356788999999999999999998888877777 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0014
                              Fez1  24 aevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelr 100
                                       aev++   ei + +  lre+r   ++  e+ ++  e+ ++ ++ l  +e+  +++ +++e ++  ++++ ++++ lr
  gi|313117469|ref|YP_004044452.1|  71 AEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALR 147
                                       55666666666666666666665555555544443333344444444444444444455555555556666666666 PP

                              Fez1 101 eelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFe 159
                                       + +s+l +  ee +le  +  +q +  + +++ ++++er r++++e+r++  e +++F+
  gi|313117469|ref|YP_004044452.1| 148 D-VSDLLAAIEELQLEFGA--VQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREEFH 203
                                       6.44444444444433333..23333344555555555555555555555544444443 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00078      0.17      38     138 ..      36     143 ..      32     150 .. 0.71
   2 ?    3.7   0.1       0.1        23      45     100 ..     151     206 ..     141     241 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00078
                          CALCOCO1  38 eclreraeLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesre....kveeleekqkelerls 110
                                       e++r+ + Ll a +a + + e+    +    +e+  e++ l+ ++ e +e+l+e+r+      e+ e+  ++++++s
  gi|313117469|ref|YP_004044452.1|  36 ETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDifdaYAETFESDVEAKQDVS 112
                                       67899999***************99******************************9977763344444444444444 PP

                          CALCOCO1 111 eelae...eksalleakeesearirELEeDi 138
                                       + la+    ++ + + +e+  a   E   D+
  gi|313117469|ref|YP_004044452.1| 113 DLLAAiedLRAEMDTTHEAFDAYTNEFVTDV 143
                                       4444400044444444444445555555555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                          CALCOCO1  45 eLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesrekveele 100
                                       +Ll a e  + +    + e+    +++d   + +++ v+e +++++e+re+ + +e
  gi|313117469|ref|YP_004044452.1| 151 DLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREEFHGVE 206
                                       44444444444444444444444444444444444444444444444444333332 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1       1.1   2.5e+02      47      94 ..       3      50 ..       1      55 [. 0.79
   2 ?    7.3   0.5     0.033       7.4      20      88 ..      46     114 ..      29     126 .. 0.50
   3 ?    2.6   0.0      0.93   2.1e+02      11      58 ..     100     147 ..      92     164 .. 0.65
   4 ?    6.6   0.1     0.054        12      23      76 ..     150     203 ..     136     223 .. 0.85
   5 ?    2.9   0.1      0.75   1.7e+02      24      75 ..     180     235 ..     178     241 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 1.1
                    HIP1_clath_bdg 47 leeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqa 94
                                      +++++e++ + ++e+++ ++e+a   +  +   +++ ++ss l+a++a
  gi|313117469|ref|YP_004044452.1|  3 VRDKREKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDA 50
                                      678889999999999999999999999998888888888888877665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.033
                    HIP1_clath_bdg  20 qaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlk.......ssLesseqsgeqlssq 88 
                                               + + l  e+e+  +  +   +e + e+ +L++e+ ++r+ l +++       ++ es  ++++++s  
  gi|313117469|ref|YP_004044452.1|  46 D-------AIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRdifdayaETFESDVEAKQDVSDL 114
                                       3.......34445555555555555555555566666666666666666555500000004555555555555444 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.93
                    HIP1_clath_bdg  11 vtkqlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLk 58 
                                       +      a+q  +++ ++ ++l  e++  +e  +  ++e  + + +L+
  gi|313117469|ref|YP_004044452.1| 100 TFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALR 147
                                       555555677777777777777777777777776666666655555554 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.054
                    HIP1_clath_bdg  23 eeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLe 76 
                                       +++ ++ +el+ e+ ++++e +  +++    +e++++ ++++r+ +a+ ++  +
  gi|313117469|ref|YP_004044452.1| 150 SDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREEFH 203
                                       6889999*************************************9999887665 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.75
                    HIP1_clath_bdg  24 everekkeleeelerlkeeaer....kleeqkeelekLkreleakraelarlkssL 75 
                                       ++er ++ ++e+ +++ e +e+    +++     +  +++e+ + rae+++ ++s 
  gi|313117469|ref|YP_004044452.1| 180 DIERFRNAVAEQRDAVAEYREEfhgvEVQAMLNAIADFQQEIDDFRAEFETTEESF 235
                                       67777777777766666555431111333444556667777777777777766665 PP

>> She9_MDM33  She9 / Mdm33 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.62   1.4e+02      40      79 ..       4      46 ..       1      55 [. 0.71
   2 ?    8.0   0.1    0.0099       2.2      35      80 ..      69     117 ..      46     171 .. 0.73
   3 ?    3.1   0.1      0.33        73      11      54 ..     158     203 ..     118     240 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.62
                        She9_MDM33 40 eeleeeleeakeevreakea...yeeaiekrsksqrevneLLq 79
                                      +++ e++++++ee  +a+++   y++  ++  +++r+v +LL+
  gi|313117469|ref|YP_004044452.1|  4 RDKREKMTATREEFADAQQEfaaYAADFAADIETKRDVSSLLD 46
                                      5566778888888887777511155566777889999999986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0099
                        She9_MDM33  35 lkksieeleeeleeakeevreake...ayeeaiekrsksqrevneLLqR 80 
                                       + +++++l++e+ e++e++re+++   ay+e+ e+  +++++v +LL+ 
  gi|313117469|ref|YP_004044452.1|  69 FAAEVSHLQTEIGEQREALREMRDifdAYAETFESDVEAKQDVSDLLAA 117
                                       45677788999999999998888533388999999999999***99974 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.33
                        She9_MDM33  11 slqetlltaskalndvtG.Y.seieklkksieeleeeleeakeevr 54 
                                       +lq ++  ++ +++d t  +  +ie+++++++e+ + ++e +ee +
  gi|313117469|ref|YP_004044452.1| 158 ELQLEFGAVQAEFDDYTDdFdADIERFRNAVAEQRDAVAEYREEFH 203
                                       3344444444444444431113455555555555555555555544 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   0.00053      0.12     205     303 ..      11     112 ..       2     117 .. 0.84
   2 ?    3.8   1.3      0.13        28     204     296 ..     111     212 ..      99     238 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00053
                            HAP1_N 205 ldcveqlseanqqiaelseelarkleele...rqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLt 278
                                       +   e++++a+q+ a  + + a   e+++      + i  L+a+i +    +  +++e     +hL+ +   qr+  
  gi|313117469|ref|YP_004044452.1|  11 TATREEFADAQQEFAAYAADFAADIETKRdvsSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREAL 87 
                                       5566899999999999988888877765411155678999************************************* PP

                            HAP1_N 279 aELqdlqekyaevegmLheaqeevk 303
                                        E++d+ + yae+ +   ea+++v 
  gi|313117469|ref|YP_004044452.1|  88 REMRDIFDAYAETFESDVEAKQDVS 112
                                       ************9999999988876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                            HAP1_N 204 vldcveqlseanqqiaelseelarkleeler...qqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqL 277
                                       v+d+ + +++ ++++++ +e  +  ++e  +     +++s Lla i +lq  +  +++e ++ +    a  e  r+ 
  gi|313117469|ref|YP_004044452.1| 111 VSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTdvaALRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNA 187
                                       55555555555556666665555555554331113466777777777777777777777777666666666666666 PP

                            HAP1_N 278 taE....Lqdlqekya..evegmLh 296
                                        aE    + +++e ++  ev+ mL+
  gi|313117469|ref|YP_004044452.1| 188 VAEqrdaVAEYREEFHgvEVQAMLN 212
                                       6664444555555543224555554 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.6    0.0079       1.7      95     185 ..       8      98 ..       2     100 .. 0.92
   2 ?    7.0   1.2     0.021       4.6     126     185 ..     175     232 ..     104     240 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0079
                            DUF724  95 nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekle 171
                                       +k+ + ++e + +++e  ++  +++ + + kr +++ +d ++   +e+e+  +++ + +++ ++e+++l++e  + +
  gi|313117469|ref|YP_004044452.1|   8 EKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQR 84 
                                       788889999999999999999999999999*********************************************** PP

                            DUF724 172 eeledveqeFeava 185
                                       e+l+++++ F+a a
  gi|313117469|ref|YP_004044452.1|  85 EALREMRDIFDAYA 98 
                                       *******9998865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.021
                            DUF724 126 rkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeava 185
                                         ++++i+ + ++++e +  +a++  ++e +  e+ ++    +++++e++d + eFe++ 
  gi|313117469|ref|YP_004044452.1| 175 DDFDADIERFRNAVAEQR--DAVAEYREEFHGVEVQAMLNAIADFQQEIDDFRAEFETTE 232
                                       334455555555555433..3334455666777777777777777777777777777764 PP

>> DUF848  Gammaherpesvirus protein of unknown function (DUF848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.7    0.0062       1.4      63     129 ..      11      81 ..       2      95 .. 0.72
   2 ?    7.8   1.3     0.015       3.3      83     132 ..     104     153 ..      82     163 .. 0.84
   3 ?    2.8   1.7      0.52   1.2e+02      88     117 ..     186     216 ..     146     252 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0062
                            DUF848  63 eavdteieakkkelslLkk...lnrkkvarveeLtdkvlelkeevsleldsleeaqeeyqeg.essetsip 129
                                       +a  +e+ + ++e++   +    + +   +v  L d++  l++e++   d+++++++e   +  + +t+i 
  gi|313117469|ref|YP_004044452.1|  11 TATREEFADAQQEFAAYAAdfaADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEvSHLQTEIG 81 
                                       44455555555555554433224667777899999999999999999999999999998888788888875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.015
                            DUF848  83 nrkkvarveeLtdkvlelkeevsleldsleeaqeeyqegessetsipDtl 132
                                       + ++ ++v +L  ++++l++e++   ++++++ +e + +     ++ D+l
  gi|313117469|ref|YP_004044452.1| 104 DVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLL 153
                                       66677899**************************9998877777888866 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.52
                            DUF848  88 arveeLtdkvlelkeevs.leldsleeaqee 117
                                       ++v e +d+v+e +ee++ +e++++ +a  +
  gi|313117469|ref|YP_004044452.1| 186 NAVAEQRDAVAEYREEFHgVEVQAMLNAIAD 216
                                       3455666777777777654555555444333 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.7    0.0032      0.72      41     123 ..       4      87 ..       1      93 [. 0.79
   2 ?    5.7   0.2     0.068        15      49     118 ..      51     127 ..      46     136 .. 0.60
   3 ?    2.1   0.2      0.89     2e+02      58     103 ..      92     136 ..      82     159 .. 0.68
   4 ?    2.2   0.1      0.81   1.8e+02      31      93 ..     140     203 ..     134     235 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0032
                             CREPT  41 kdk.eeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkek.lekvksvrke 115
                                       +dk e+ ++  ++  +a++  a Y +  +a++e  + ++++l+  + a++++++++    + +++  +++v++ ++e
  gi|313117469|ref|YP_004044452.1|   4 RDKrEKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLD-AIDALRAEIEETGDAFDAYNQEfAAEVSHLQTE 79 
                                       5541455666788999**********************98885.678899999999999999987625789999999 PP

                             CREPT 116 lkshiqsL 123
                                       + ++ + L
  gi|313117469|ref|YP_004044452.1|  80 IGEQREAL 87 
                                       87776665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.068
                             CREPT  49 llkqveealellaeYnkrLeael.......eeRkklakmledfleaqkellakaeekleelkeklekvksvrkelks 118
                                       l  ++ee   + + Yn+  +ae+        e ++  + ++d++ a  e+ +   e  +++ + l+ ++  r+e+++
  gi|313117469|ref|YP_004044452.1|  51 LRAEIEETGDAFDAYNQEFAAEVshlqteiGEQREALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDT 127
                                       56666666666777776655555111111134444444456666666677777777777777777777777777765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.89
                             CREPT  58 ellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelk 103
                                        + + Y +  e+++e  + ++ +l++ +e +++++++++e  + + 
  gi|313117469|ref|YP_004044452.1|  92 DIFDAYAETFESDVEAKQDVSDLLAA-IEDLRAEMDTTHEAFDAYT 136
                                       45667777777888887777777754.4556666666666666655 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.81
                             CREPT  31 vsdvsllekikdk.eeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkella 93 
                                       v+dv+ l+ ++d  ++ e+l+ +    ++  ++Y+   +a++e  ++     +d ++  +e+ +
  gi|313117469|ref|YP_004044452.1| 140 VTDVAALRDVSDLlAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREEFH 203
                                       5667777777765144567777777777788888888888888744444444555555555443 PP

>> ECM11  Extracellular mutant protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       9.4   2.1e+03      85     114 ..       9      38 ..       3      62 .. 0.61
   2 ?   13.5   0.5   0.00036      0.08      71     116 ..      65     110 ..      55     127 .. 0.86
   3 ?    0.0   0.1       5.3   1.2e+03      98     119 ..     175     196 ..     171     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 9.4
                             ECM11  85 klkeaRrakrktaaefeaeierReeavrkk 114
                                       k+ ++R++  +  +ef a  ++ ++++++k
  gi|313117469|ref|YP_004044452.1|   9 KMTATREEFADAQQEFAAYAADFAADIETK 38 
                                       444455555555555555555555555544 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00036
                             ECM11  71 aGdwlldqfsellkklkeaRrakrktaaefeaeierReeavrkkge 116
                                         ++++ ++s+l +++ e+R+a+r++   f a  e  e++v++k++
  gi|313117469|ref|YP_004044452.1|  65 YNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQD 110
                                       5689**************************************9975 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 5.3
                             ECM11  98 aefeaeierReeavrkkgeeld 119
                                         f a ier  +av ++++++ 
  gi|313117469|ref|YP_004044452.1| 175 DDFDADIERFRNAVAEQRDAVA 196
                                       4566666666666666655443 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.3    0.0023      0.51      40     121 ..       8      89 ..       2      96 .. 0.89
   2 ?    2.5   1.4      0.87   1.9e+02      19      66 ..      85     128 ..      82     148 .. 0.59
   3 ?    7.0   2.6     0.035       7.8      10      82 ..     155     233 ..     118     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0023
                            APG6_N  40 keeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlellele 116
                                       ++ ++++ee +++++e+++  ++ ++ +e  +++ +  ++++a +a++ee+ +a ++ +++f  e + lq+e  e  
  gi|313117469|ref|YP_004044452.1|   8 EKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQR 84 
                                       333336899***************************************************************99999 PP

                            APG6_N 117 eelds 121
                                       e l+ 
  gi|313117469|ref|YP_004044452.1|  85 EALRE 89 
                                       88765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.87
                            APG6_N  19 eqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeel 66 
                                       e++++ rd + ++ ++++++ + +    +++ +l   +e+l++e ++ 
  gi|313117469|ref|YP_004044452.1|  85 EALREMRDIFDAYAETFESDVEAK----QDVSDLLAAIEDLRAEMDTT 128
                                       455555666666666666663332....36666666666666665444 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.035
                            APG6_N  10 LleeldkqleqaekerdaYe.eflkklkkekkeeekqdeeleeleee.....leklekeeeelleeLkelekereel 80 
                                        +eel+ ++ ++++e d+Y+ +f + +++ ++   +q++ ++e +ee     ++++ ++ ++ ++e+++  +e e  
  gi|313117469|ref|YP_004044452.1| 155 AIEELQLEFGAVQAEFDDYTdDFDADIERFRNAVAEQRDAVAEYREEfhgveVQAMLNAIADFQQEIDDFRAEFETT 231
                                       48999999999999999997359999997766665566777777777555554445555555555555544444444 PP

                            APG6_N  81 ea 82 
                                       e+
  gi|313117469|ref|YP_004044452.1| 232 EE 233
                                       44 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.5    0.0018       0.4      48     156 ..       6     119 ..       2     128 .. 0.75
   2 ?    5.6   0.3     0.055        12      75     142 ..     134     207 ..     113     246 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0018
                             PIN_8  48 resviskekkayedlekeleklkkaaekkleealkkwakkkald.teelrkelkkqleelkeel....kaeleelkk 119
                                       +++ +   ++ + d+++e+++  +++++++e++ + ++  +a+d  +   +e+ ++++++++e+    ++ ++e+ +
  gi|313117469|ref|YP_004044452.1|   6 KREKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDaLRAEIEETGDAFDAYNQEFaaevSHLQTEIGE 82 
                                       55556667888888888998888888888888888888888888766666777778888888885544555555566 PP

                             PIN_8 120 sskadkeedpilkkleellegkigealskeeleelvk 156
                                       + +a +e+ +i+++++e++e  + ++ + ++l ++++
  gi|313117469|ref|YP_004044452.1|  83 QREALREMRDIFDAYAETFESDVEAKQDVSDLLAAIE 119
                                       6666667799*************99999988866655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.055
                             PIN_8  75 kkleealkkwakkkald........teelrkelkkqleelkeelkaeleelkksskadkeedpilkkleellegki 142
                                       + ++e++++ a+ + ++         +    +++++++++++++ a+ e++++++ +++  d + +  ee+ + ++
  gi|313117469|ref|YP_004044452.1| 134 AYTNEFVTDVAALRDVSdllaaieeLQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQR--DAVAEYREEFHGVEV 207
                                       33333333333333333333333343333344444555555555555555555555554..444444444433333 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4     0.024       5.3     208     266 ..      29      87 ..       2      99 .. 0.75
   2 ?    2.8   0.1      0.24        53     212     255 ..     103     146 ..      85     149 .. 0.85
   3 ?    5.6   0.3     0.033       7.4     219     272 ..     148     202 ..     141     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.024
                         Tmemb_cc2 208 asksaesesqeklekileelqeikeeqerleeelerlkeqlkkelkllkqaLqeeryry 266
                                       a+ +a+ e++++++++l+++  +++e e+  + +++ ++++  e++ l++ + e+r   
  gi|313117469|ref|YP_004044452.1|  29 ADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREAL 87 
                                       256788899999**********************************9999999988655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                         Tmemb_cc2 212 aesesqeklekileelqeikeeqerleeelerlkeqlkkelkll 255
                                       ++ e++++++ +l +++++++e++  +e +++  +++ ++++ l
  gi|313117469|ref|YP_004044452.1| 103 SDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAAL 146
                                       566788999************************99999998876 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.033
                         Tmemb_cc2 219 klekileelqeikeeqerleeelerlkeqlkkelkllkqaLqeeryryerL.Eeq 272
                                       +++ +l +++e++ e   +++e+++  ++++ +++ +++a+ e+r  + +  Ee 
  gi|313117469|ref|YP_004044452.1| 148 DVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYrEEF 202
                                       67789999999999999*****************999999999986655443333 PP

>> CHD5  CHD5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.011       2.4      43      98 ..       5      65 ..       2      76 .. 0.85
   2 ?    1.4   0.0       1.2   2.6e+02      70     100 ..     107     137 ..      64     147 .. 0.63
   3 ?    0.7   0.0       1.9   4.2e+02      75     100 ..     112     137 ..      93     177 .. 0.71
   4 ?   -1.5   0.0       9.1     2e+03      96      96 ..     171     171 ..     128     214 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.011
                              CHD5 43 klkkellklkeelnsisaqDefAkWaK.......lnRkldkleeeleklkkelsaskssfkkk 98
                                      ++++++ +++ee +  +aq efA +a         +R ++ l + +++l++e++++ ++f+++
  gi|313117469|ref|YP_004044452.1|  5 DKREKMTATREEFA--DAQQEFAAYAAdfaadieTKRDVSSLLDAIDALRAEIEETGDAFDAY 65
                                      55566666666655..79**************************************9999976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.2
                              CHD5  70 lnRkldkleeeleklkkelsaskssfkkklk 100
                                       ++  +++l + +e+l++e++++ ++f+++ +
  gi|313117469|ref|YP_004044452.1| 107 AKQDVSDLLAAIEDLRAEMDTTHEAFDAYTN 137
                                       4556777888888888888888888887765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.9
                              CHD5  75 dkleeeleklkkelsaskssfkkklk 100
                                       ++l + +e+l++e++++ ++f+++ +
  gi|313117469|ref|YP_004044452.1| 112 SDLLAAIEDLRAEMDTTHEAFDAYTN 137
                                       45566666666666666666665554 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 9.1
                              CHD5  96 k 96 
                                       +
  gi|313117469|ref|YP_004044452.1| 171 D 171
                                       2 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.8     0.012       2.6      16     107 ..       4      98 ..       1     103 [. 0.77
   2 ?   12.2   1.1   0.00085      0.19       2     102 ..      35     131 ..      35     141 .. 0.76
   3 ?    5.7   0.7     0.085        19       5      88 ..     122     208 ..     105     211 .. 0.76
   4 ?    2.7   0.1      0.71   1.6e+02       8      31 ..     214     237 ..     212     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.012
                           DUF4200  16 eakkeeiqrleealkqreeelekkeqeleedl...lkfdkflkendakraralkkaeeerklkkekeaeikklkaei 89 
                                         k+e++  + e+++++++e+ +  + +  d+     +   l  +da ra+ ++  +     ++e +ae+  l++ei
  gi|313117469|ref|YP_004044452.1|   4 RDKREKMTATREEFADAQQEFAAYAADFAADIetkRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEI 80 
                                       56788888888888888888888888887776222356778888889999999999999999999999999999999 PP

                           DUF4200  90 etlkseiekleekleeyk 107
                                        + ++ ++++ ++ + y 
  gi|313117469|ref|YP_004044452.1|  81 GEQREALREMRDIFDAYA 98 
                                       999888888888887775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00085
                           DUF4200   2 lekkremfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkek 78 
                                       +e+kr+++ +  a++a ++ei+++ +a++   +e+ ++ + l+ ++ +  + l+e  +      +  e+  ++k++ 
  gi|313117469|ref|YP_004044452.1|  35 IETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDV 111
                                       799*********************************************99999999877766666666666666554 PP

                           DUF4200  79 eaeikklkaeietlkseiekleek 102
                                            +l a ie+l++e++ + e+
  gi|313117469|ref|YP_004044452.1| 112 ----SDLLAAIEDLRAEMDTTHEA 131
                                       ....44444444444444444443 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.085
                           DUF4200   5 kremfevqealeakkeeiqrleealkqreeel...ekkeqeleedllkfdkflkendakraralkkaeeerklkkek 78 
                                       + em+ ++ea +a  +e+ +   al++  + l   e+ + e+    ++fd +  + da  +r +  ++e+r++  e+
  gi|313117469|ref|YP_004044452.1| 122 RAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLaaiEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEY 198
                                       56888888888888888888777666666554100444455555558899999999999999999999999999999 PP

                           DUF4200  79 eaeikklkae 88 
                                        +e +  +++
  gi|313117469|ref|YP_004044452.1| 199 REEFHGVEVQ 208
                                       9987766655 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.71
                           DUF4200   8 mfevqealeakkeeiqrleealkq 31 
                                       + + q++++  ++e++++ee+++ 
  gi|313117469|ref|YP_004044452.1| 214 IADFQQEIDDFRAEFETTEESFDA 237
                                       567899999999999999998876 PP

>> DUF3452  Domain of unknown function (DUF3452)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2       0.2        43      44      69 ..      71      96 ..      30     205 .. 0.69
   2 ?    5.5   0.1     0.052        12      32      67 ..     207     242 ..     177     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.2
                           DUF3452 44 qeieelernfsvttvifkkYrqiFee 69
                                       e+++l++++ +     ++ r+iF+ 
  gi|313117469|ref|YP_004044452.1| 71 AEVSHLQTEIGEQREALREMRDIFDA 96
                                      33333333333333333333333322 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.052
                           DUF3452  32 wadmanldeelrqeieelernfsvttvifkkYrqiF 67 
                                       +++m n  ++++qei++ +++f++t   f  + + F
  gi|313117469|ref|YP_004044452.1| 207 VQAMLNAIADFQQEIDDFRAEFETTEESFDAFARDF 242
                                       57899999*****************99999998887 PP

>> EHN  Epoxide hydrolase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1     0.009         2      43      85 ..     189     231 ..      36     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.009
                               EHN  43 delkelldyWkeeydWraeearlnsfpqfkteidgldihFihl 85 
                                       +e ++++++++ee+   +++a ln++  f+ eid+++  F  +
  gi|313117469|ref|YP_004044452.1| 189 AEQRDAVAEYREEFHGVEVQAMLNAIADFQQEIDDFRAEFETT 231
                                       4556777888889999999999999999999998888777555 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.7     0.029       6.3      29      86 ..      12      71 ..       2      82 .. 0.68
   2 ?    8.0   3.3     0.013       2.8       5     131 ..      61     181 ..      60     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.029
                            GldM_N 29 asleakaeenpekakewlekAkevkkk..sdelynyiealKeeivkeaggkdedvgeika 86
                                      a+ e+ a  ++e a+ +++ A ++++k   ++l + i+al++ei++  +  d+  +e++a
  gi|313117469|ref|YP_004044452.1| 12 ATREEFADAQQEFAAYAADFAADIETKrdVSSLLDAIDALRAEIEETGDAFDAYNQEFAA 71
                                      44444444444444446666666655522679*****************99998777765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.013
                            GldM_N   5 aFglvneslersnenasekNaalyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkdedv 81 
                                       aF   n+++ +  + ++++  +  ++l++ +++  + ++e++e   e+k+  ++l + ie+l++e+ +  +  d+ +
  gi|313117469|ref|YP_004044452.1|  61 AFDAYNQEFAAEVSHLQTEIGEQREALRE-MRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYT 136
                                       56666666666666666666666666665.6777788999**************************99999999998 PP

                            GldM_N  82 geikak.dnldaaselmlaegksgkGkeLkkkineyreellklvndlakda 131
                                       +e+ +    l  +s l+ a       +eL+ +  + + e  ++ +d ++d 
  gi|313117469|ref|YP_004044452.1| 137 NEFVTDvAALRDVSDLLAA-I-----EELQLEFGAVQAEFDDYTDDFDADI 181
                                       8876653466666666663.2.....4555555555555555555544444 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.6    0.0053       1.2      17     105 ..      37     125 ..       3     137 .. 0.69
   2 ?    5.6   0.2     0.039       8.7      16      92 ..     147     225 ..     134     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0053
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       t +++ +   ++ a +a++++  d+ d   qe +ae+  l++e+ + +   ++++++ ++  ++++s  e +++++ 
  gi|313117469|ref|YP_004044452.1|  37 TKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSD 113
                                       34455666667777777777777777777777777777777777777777777777777777777777777777776 PP

                           DUF3450  94 ierelvpllekm 105
                                       + ++++ l  +m
  gi|313117469|ref|YP_004044452.1| 114 LLAAIEDLRAEM 125
                                       666666655555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.039
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyral.keeleslevyneqlerl.vasqeqeiasleeqiee 90 
                                        +++++l++ e+ + +  ++q++ d+++d+ +   +++r++  e+ ++ + y+e+   + v+++ + ia+ +++i++
  gi|313117469|ref|YP_004044452.1| 147 RDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAvAEQRDAVAEYREEFHGVeVQAMLNAIADFQQEIDD 223
                                       56677777777888888899999999999999999999976155667778888888765477888999999999998 PP

                           DUF3450  91 ie 92 
                                       ++
  gi|313117469|ref|YP_004044452.1| 224 FR 225
                                       65 PP

>> DASH_Spc34  DASH complex subunit Spc34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.7     0.016       3.6     174     238 ..      56     115 ..       5     120 .. 0.67
   2 ?    8.8   0.8    0.0057       1.3     106     202 ..      98     203 ..      91     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.016
                        DASH_Spc34 174 leakekieelreeYeelseeieeleaeiaeQkkqLeaqnknesessseddsesetskskdvdeli 238
                                       +e  ++++++ +e   + +e+ +l+ ei eQ++ L +++   ++  ++ +  s+ + ++dv++l+
  gi|313117469|ref|YP_004044452.1|  56 EETGDAFDAYNQE---FAAEVSHLQTEIGEQREALREMRDIFDAYAETFE--SDVEAKQDVSDLL 115
                                       3444455555555...568999****************998887766654..4444566666666 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0057
                        DASH_Spc34 106 levlakkfksdkqirqlllalqngsvttgedsgsssekanrrktafvedfdvelllkvleelltkyplleake.... 178
                                        e+ ++ ++ ++ +++ll+a+++    +++++++  +++n + t +++  dv++ll  +eel  ++   +a+     
  gi|313117469|ref|YP_004044452.1|  98 AETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIEELQLEFGAVQAEFddyt 174
                                       45666777788889999999999888888888888888899*********************999987665544566 PP

                        DASH_Spc34 179 .....kieelreeYeelseeieeleaeia 202
                                            +ie++r+  +e+++ ++e+++e +
  gi|313117469|ref|YP_004044452.1| 175 ddfdaDIERFRNAVAEQRDAVAEYREEFH 203
                                       66666666666666666666666666543 PP

>> DUF2384  Protein of unknown function (DUF2384)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       1.7   3.9e+02      34      49 ..      34      49 ..      25      50 .. 0.77
   2 ?    0.7   0.0       2.4   5.4e+02      39      49 ..     109     119 ..     102     120 .. 0.87
   3 ?    6.4   0.0     0.043       9.5      30      49 ..     138     157 ..     125     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.7
                           DUF2384 34 teaGarlVedyLdrir 49
                                       ++  r V+ +Ld+i+
  gi|313117469|ref|YP_004044452.1| 34 DIETKRDVSSLLDAID 49
                                      5566689*******97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.4
                           DUF2384  39 rlVedyLdrir 49 
                                       + V+d+L++i+
  gi|313117469|ref|YP_004044452.1| 109 QDVSDLLAAIE 119
                                       78********8 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.043
                           DUF2384  30 dlldteaGarlVedyLdrir 49 
                                       ++++ +a +r V+d+L++i+
  gi|313117469|ref|YP_004044452.1| 138 EFVTDVAALRDVSDLLAAIE 157
                                       67788999***********8 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.2      0.02       4.5      81     167 ..      38     127 ..       2     134 .. 0.48
   2 ?    7.8   1.2     0.014       3.2      82     185 ..     109     227 ..      98     231 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.02
                           UPF0242  81 deglktkeealeelqeeeeeLkeeldakeeelerlkeenq.qLqekleaiae...dfeelkleleeqLaekqellqe 153
                                       + +++   +a+  l++e ee  + +da ++e +      q ++ e+ ea  e    f+++    e+ ++ kq  +++
  gi|313117469|ref|YP_004044452.1|  38 KRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQtEIGEQREALREmrdIFDAYAETFESDVEAKQD-VSD 113
                                       1233333335555555555555555555554433222222234444333333332567777777777777665.455 PP

                           UPF0242 154 yqetieeqrsvlek 167
                                       + + ie++r++++ 
  gi|313117469|ref|YP_004044452.1| 114 LLAAIEDLRAEMDT 127
                                       56678888887775 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.014
                           UPF0242  82 eglktkeealeelqeeeeeLkee.................ldakeeelerlkeenqqLqekleaiaedfeelklele 141
                                       ++++    a+e+l++e +  +e                  ++    ++e+l+ e   +q +  +   df++      
  gi|313117469|ref|YP_004044452.1| 109 QDVSDLLAAIEDLRAEMDTTHEAfdaytnefvtdvaalrdVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFR 185
                                       35666677899999999999998666666666554444444444444444444444444444444444444444444 PP

                           UPF0242 142 eqLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyE 185
                                       +++ae++  + ey+e+++    +++   + i++ +  + D   E
  gi|313117469|ref|YP_004044452.1| 186 NAVAEQRDAVAEYREEFHGV--EVQAMLNAIADFQQEIDDFRAE 227
                                       45555555555555554422..3444555666666666666555 PP

>> Octopine_DH  NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.7     0.003      0.65      27      98 ..      53     119 ..      37     139 .. 0.79
   2 ?    2.9   0.3      0.48   1.1e+02      34      86 ..     168     223 ..     124     262 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.003
                       Octopine_DH  27 srieetegdfslyyegitpsvaevlealdeErlaiakalglevlplaerlldaYgdeikdksslaevirtne 98 
                                       ++ieet+  f+ y++++  +v+++++++ e r a+++  ++     ++ ++++++ +++ k+++ + +++ e
  gi|313117469|ref|YP_004044452.1|  53 AEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDI-----FDAYAETFESDVEAKQDVSDLLAAIE 119
                                       78999***************************999998877.....66777777777776666666555443 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.48
                       Octopine_DH  34 gdfslyyegitpsvaevlealdeErlaiakal....glevlplaerlldaYgdeikd 86 
                                        +f+ y ++++  + ++ +a+ e r a+a+      g+ev+ +   ++d+  +ei+d
  gi|313117469|ref|YP_004044452.1| 168 AEFDDYTDDFDADIERFRNAVAEQRDAVAEYReefhGVEVQAMLNAIADFQ-QEIDD 223
                                       456669999999999999999999999998777778666654444433322.33332 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.9     0.019       4.2      50      95 ..      45      90 ..       2      99 .. 0.70
   2 ?    3.0   0.8      0.62   1.4e+02       7      52 ..      70     107 ..      67     154 .. 0.45
   3 ?    1.3   0.1       2.2   4.9e+02      28      58 ..     148     178 ..     137     202 .. 0.63
   4 ?    5.0   0.3      0.15        34       6      63 ..     177     234 ..     174     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.019
                                      HHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin 50 laaqqervkalnelaeklldeghsaseeieerleelnerWeeLkel 95
                                      l+a +    +++e+++++ +++++ ++e+++ + e+ e+ e+L+e+
  gi|313117469|ref|YP_004044452.1| 45 LDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREM 90
                                      3344444455667777776666677777777777777777777764 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.62
                                       HHHHHHHHHHHHHHHHHH.CCSSC.SSSHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin   7 aqdadeleeWieekeell.ssedl.gkdleevqallkkhkaleaelaa 52 
                                       a ++++l+  i e++e l + +d+     e+ ++ ++          a
  gi|313117469|ref|YP_004044452.1|  70 AAEVSHLQTEIGEQREALrEMRDIfDAYAETFESDVE----------A 107
                                       5555555555555544442222222222222222222..........2 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 2.2
                                       SCSSSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  28 dlgkdleevqallkkhkaleaelaaqqervk 58 
                                       d++  l+++++l+ ++ a++ae++++ + ++
  gi|313117469|ref|YP_004044452.1| 148 DVSDLLAAIEELQLEFGAVQAEFDDYTDDFD 178
                                       4444555566666666666666665555554 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin   6 faqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnel 63 
                                       f  d++ + +   e++  +++ + + +  evqa+l++  ++++e+++ + ++++ +e 
  gi|313117469|ref|YP_004044452.1| 177 FDADIERFRNAVAEQRDAVAEYREEFHGVEVQAMLNAIADFQQEIDDFRAEFETTEES 234
                                       5556666666666666666555555555677777778888888887777777766654 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.6     0.015       3.3      14      77 ..      36      96 ..      34     128 .. 0.76
   2 ?    1.1   0.9       1.6   3.5e+02      27      61 ..      99     132 ..      82     168 .. 0.56
   3 ?    1.0   0.2       1.8     4e+02      26      39 ..     118     131 ..     102     199 .. 0.54
   4 ?    2.1   0.1      0.84   1.9e+02      51      80 ..     204     233 ..     180     242 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.015
                    CENP-F_leu_zip 14 eserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLva 77
                                      e++r+ +sL d +++L +e+e+ +   ++   e     aev+ l++ei e +e lre++  ++a
  gi|313117469|ref|YP_004044452.1| 36 ETKRDVSSLLDAIDALRAEIEETGDAFDAYNQE---FAAEVSHLQTEIGEQREALREMRDIFDA 96
                                      6899999*************9999886665544...4689999999999999999998765554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.6
                    CENP-F_leu_zip  27 enLerelemseenqekvileaEtskaevetlkeei 61 
                                       e  e+++e  +   +++    E+ +ae+ t +e  
  gi|313117469|ref|YP_004044452.1|  99 ETFESDVEAKQD-VSDLLAAIEDLRAEMDTTHEAF 132
                                       444444443332.2444444555555544444333 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.8
                    CENP-F_leu_zip  26 venLerelemseen 39 
                                       +e L +e+ +  e 
  gi|313117469|ref|YP_004044452.1| 118 IEDLRAEMDTTHEA 131
                                       22222222222222 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.84
                    CENP-F_leu_zip  51 kaevetlkeeieelaeelreleldLvalrs 80 
                                         ev+++ + i   ++e  +++++++++ +
  gi|313117469|ref|YP_004044452.1| 204 GVEVQAMLNAIADFQQEIDDFRAEFETTEE 233
                                       446666666666666666666666666554 PP

>> T4SS  Type IV secretion system proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.6     0.042       9.4     107     155 ..      15      62 ..       2      80 .. 0.76
   2 ?    6.0   1.0     0.063        14       9      94 ..      96     177 ..      63     234 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.042
                              T4SS 107 eqaskaceqaankaaqdkalaeqaydkankrlkqiqkLadqinnatDpK 155
                                       e++ ++ +q++ + a+d a   ++++ +++ l+ i++L+++i  + D+ 
  gi|313117469|ref|YP_004044452.1|  15 EEF-ADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAF 62 
                                       233.78899999999999999999*********************9974 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.063
                              T4SS   9 aiaqaikqvkeaaqqltqlkqqleqakqqlesltgarglrdvgalLndpk.lrkllPaewqdvkdlvksggasgsls 84 
                                       a+a++ ++ +ea+q ++ l + +e ++   + + +a +     +++ d + lr+ ++  ++ +++l+ +   +g+++
  gi|313117469|ref|YP_004044452.1|  96 AYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDA-YTNEFVTDVAaLRD-VSDLLAAIEELQLE---FGAVQ 167
                                       455666666666665555555555555555555555555.44455555555555.33333333333333...33444 PP

                              T4SS  85 saaqslrdkn 94 
                                       ++++++ d++
  gi|313117469|ref|YP_004044452.1| 168 AEFDDYTDDF 177
                                       4444444443 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5       0.1        23      15      73 ..       3      59 ..       1      73 [. 0.67
   2 ?    5.2   0.8      0.15        34       9      83 ..      84     153 ..      66     160 .. 0.54
   3 ?    8.2   0.5     0.017       3.8      11      92 ..     145     223 ..     140     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.1
                           DUF2203 15 lkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelG 73
                                      ++++ e++ a+r+e++++++e ++  a+ ++    e ++++++l + i++l +eiee+G
  gi|313117469|ref|YP_004044452.1|  3 VRDKREKMTATREEFADAQQEFAAYAADFAA--DIETKRDVSSLLDAIDALRAEIEETG 59
                                      4445555555555555555555555554332..77888888888888998888888887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.15
                           DUF2203   9 nalLpllkelleelralrkeleeleeeleeakaeaekse........aaeleaeleeleaeieelveeieelGvevk 77 
                                       ++ L ++++++++++++ +   e++             +         + l+ae+++  + ++++++e+    + ++
  gi|313117469|ref|YP_004044452.1|  84 REALREMRDIFDAYAETFESDVEAK-------------QdvsdllaaIEDLRAEMDTTHEAFDAYTNEFVTDVAALR 147
                                       3333333333333333333333333.............133334444667777777777777777777777777777 PP

                           DUF2203  78 dleagl 83 
                                       d++ +l
  gi|313117469|ref|YP_004044452.1| 148 DVSDLL 153
                                       766555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.017
                           DUF2203  11 lLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvDFp 87 
                                        L  +++ll+++ +l+ e+  +++e ++ +++ +  + ++ +++++e ++ + e+ ee++  Gvev+ + + + DF 
  gi|313117469|ref|YP_004044452.1| 145 ALRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFD-ADIERFRNAVAEQRDAVAEYREEFH--GVEVQAMLNAIADFQ 218
                                       5777888888888888888888888888888854.5588888888888888888888885..899999999999**9 PP

                           DUF2203  88 akldg 92 
                                        ++d+
  gi|313117469|ref|YP_004044452.1| 219 QEIDD 223
                                       99886 PP

>> DUF2605  Protein of unknown function (DUF2605)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       2.3   5.2e+02      39      77 ..      38      76 ..      15      79 .. 0.84
   2 ?    7.1   0.0     0.023       5.1      35      90 ..     104     159 ..      83     165 .. 0.85
   3 ?    1.7   0.2       1.1   2.4e+02      34      68 ..     200     233 ..     167     239 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.3
                           DUF2605 39 eeeqadllarvkeaqqeveaakaLfkatdgqvgvevevl 77
                                      +++ ++ll+ ++  ++e+e +   f a +++ + ev+ l
  gi|313117469|ref|YP_004044452.1| 38 KRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHL 76
                                      556688999999999999999999999999999988876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.023
                           DUF2605  35 sflseeeqadllarvkeaqqeveaakaLfkatdgqvgvevevlvpWHqLvtecwqv 90 
                                       ++ ++++ +dlla +++ ++e+ +++  f a  ++   +v++l    +L++ + ++
  gi|313117469|ref|YP_004044452.1| 104 DVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIEEL 159
                                       555678899********************************999988888877666 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 1.1
                           DUF2605  34 lsflseeeqadllarvkeaqqeveaakaLfkatdg 68 
                                        +f    e +++l+ + + qqe+   +a f++t++
  gi|313117469|ref|YP_004044452.1| 200 EEFHG-VEVQAMLNAIADFQQEIDDFRAEFETTEE 233
                                       22222.24467788888888888888888887776 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.7       2.6   5.7e+02      45      65 ..      13      33 ..      10      40 .. 0.81
   2 ?    4.3   5.1      0.21        46      19      81 ..      31     101 ..      18     106 .. 0.51
   3 ?    5.1   1.6      0.12        28      46      80 ..      59      93 ..      54     137 .. 0.75
   4 ?    2.1   0.1         1   2.3e+02      44      66 ..     130     152 ..     105     172 .. 0.51
   5 ?    4.9   0.2      0.14        30      40      81 ..     160     202 ..     123     206 .. 0.63
   6 ?    9.2   1.3    0.0063       1.4       9      85 ..     170     246 ..     165     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.6
                                      HCHHHHHHHHHHHHHHHHHHH CS
                            WXG100 45 aadafqaefeewkqaaqklvd 65
                                      ++++f+++++e+ + a+++++
  gi|313117469|ref|YP_004044452.1| 13 TREEFADAQQEFAAYAADFAA 33
                                      788999999999999988765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.21
                                       HHHHHHHHHH..HHHHHHHHCGCGCT..HHHCHHHHHHHH.H...HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  19 qaeeledelq..rlkaevdalqsgWs..Gaaadafqaefe.e...wkqaaqklvdaLeeisealkqaanaf 81 
                                        a+++e+  +  +l   +dal++  +  G+a da+++ef+ e   ++ ++ +  +aL e+++  ++ a++f
  gi|313117469|ref|YP_004044452.1|  31 FAADIETKRDvsSLLDAIDALRAEIEetGDAFDAYNQEFAaEvshLQTEIGEQREALREMRDIFDAYAETF 101
                                       44444433222255555666655554347777776666665411134444455566666666555555555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.12
                                      CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 46 adafqaefeewkqaaqklvdaLeeisealkqaana 80
                                      +daf+a  +e+ +++  l+++  e +eal++  + 
  gi|313117469|ref|YP_004044452.1| 59 GDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDI 93
                                      56666666666666666666666666666655444 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 1
                                       HHCHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  44 aaadafqaefeewkqaaqklvda 66 
                                       +a da+ +ef    +a++++ d+
  gi|313117469|ref|YP_004044452.1| 130 EAFDAYTNEFVTDVAALRDVSDL 152
                                       23333333333333344444444 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.14
                                       GCT.HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  40 gWs.GaaadafqaefeewkqaaqklvdaLeeisealkqaanaf 81 
                                       + + Ga + +f++  + +++ ++++ +a +e ++a+ +  ++f
  gi|313117469|ref|YP_004044452.1| 160 QLEfGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREEF 202
                                       4455888899999999999999999999999988887766666 PP

  == domain 6  score: 9.2 bits;  conditional E-value: 0.0063
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   9 lrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                        ++   +f++  e+ ++++++ +  v++ ++ + G   +a  ++++ ++q+++++ +++e+++e+ ++ a+ f  a+
  gi|313117469|ref|YP_004044452.1| 170 FDDYTDDFDADIERFRNAVAEQRDAVAEYREEFHGVEVQAMLNAIADFQQEIDDFRAEFETTEESFDAFARDFYGAE 246
                                       566677899999999999***********************************************999999987776 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.4     0.036       7.9      70     154 ..      11      95 ..       2     134 .. 0.52
   2 ?    4.2   0.3       0.2        45      96     158 ..     103     161 ..      95     173 .. 0.74
   3 ?    4.2   0.8      0.21        46     117     174 ..     176     235 ..     148     241 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.036
                             ATG16  70 skqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeel 146
                                       ++++++ ++ +q+ a+  ++ a+   ++ + ++ l +  +  ++ ee+  + ++  +e  ae+++l+t++ +++e+l
  gi|313117469|ref|YP_004044452.1|  11 TATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREAL 87 
                                       34555556666666666666666666666655555555555555555555555555666666666666666666666 PP

                             ATG16 147 rekeklvq 154
                                       re +   +
  gi|313117469|ref|YP_004044452.1|  88 REMRDIFD 95 
                                       66655544 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.2
                             ATG16  96 srgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqD 158
                                       s  e +q + +l +++++l++++ +  e+ ++ ++e  +   +l+d  + l+     +++lq 
  gi|313117469|ref|YP_004044452.1| 103 SDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAA----IEELQL 161
                                       66688899999999999999999999999999999998888888887777654....444444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.21
                             ATG16 117 klkedeerlaeleaeraaletklkdreeelrekeklvq..dlqDElsaLqlqlnqaEekl 174
                                          +d er +++ ae ++   ++++  + ++ ++ l+   d+q E++  + +++  Ee  
  gi|313117469|ref|YP_004044452.1| 176 DFDADIERFRNAVAEQRDAVAEYREEFHGVEVQAMLNAiaDFQQEIDDFRAEFETTEESF 235
                                       555555555555555555555555555555545444434499**********99999975 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       3.8   8.5e+02      45      69 ..      34      58 ..       3      62 .. 0.72
   2 ?    6.8   0.1     0.033       7.3      35      69 ..      56      90 ..      40      94 .. 0.82
   3 ?    2.4   0.2      0.79   1.7e+02      29      70 ..      86     129 ..      84     139 .. 0.73
   4 ?    0.5   0.0         3   6.7e+02      36      64 ..     205     233 ..     169     241 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.8
                            Cnn_1N 45 nielkveveslqkelkekkkllrea 69
                                       ie k +v sl + +++++ +++e 
  gi|313117469|ref|YP_004044452.1| 34 DIETKRDVSSLLDAIDALRAEIEET 58
                                      5788888888888888888777765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.033
                            Cnn_1N 35 eeqkeellkenielkveveslqkelkekkkllrea 69
                                      ee+ ++  + n e   ev +lq e+ e ++ lre+
  gi|313117469|ref|YP_004044452.1| 56 EETGDAFDAYNQEFAAEVSHLQTEIGEQREALREM 90
                                      477778888899********************997 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.79
                            Cnn_1N  29 rleklse..eqkeellkenielkveveslqkelkekkkllreae 70 
                                       +l ++++  +   e+ ++ +e k++v +l   ++ ++ +++  +
  gi|313117469|ref|YP_004044452.1|  86 ALREMRDifDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTH 129
                                       56666666666677888888888888888888888887776655 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 3
                            Cnn_1N  36 eqkeellkenielkveveslqkelkekkk 64 
                                        +++++l+   + ++e+ + + e ++ ++
  gi|313117469|ref|YP_004044452.1| 205 VEVQAMLNAIADFQQEIDDFRAEFETTEE 233
                                       45566666666667777777766666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5     0.082        18      87     142 ..       7      60 ..       2      64 .. 0.82
   2 ?    4.9   0.2     0.077        17     147     182 ..      93     128 ..      67     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.082
                            AAA_25  87 rrRlravgealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaieeveg 142
                                       r+++ a++e+++d +++++ ++a++  ++    ++r+ + l  ++dal+a+iee+ +
  gi|313117469|ref|YP_004044452.1|   7 REKMTATREEFADAQQEFAAYAADFaADIE---TKRDVSSLLDAIDALRAEIEETGD 60 
                                       67899999999*************988874...556666666789********9765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.077
                            AAA_25 147 viDplsralggdensnsdvgalvealeriarrtgaa 182
                                       ++D  +++++ d +++ dv+ l++a+e+++++ + +
  gi|313117469|ref|YP_004044452.1|  93 IFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTT 128
                                       8999*************************9998765 PP

>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.82   1.8e+02      16      37 ..      42      63 ..      32      66 .. 0.81
   2 ?    5.1   0.2      0.11        25      13      45 ..      64      97 ..      61     109 .. 0.78
   3 ?    6.9   0.1     0.031       6.9      15      40 ..     111     136 ..     101     147 .. 0.83
   4 ?    3.2   0.3      0.45     1e+02      17      46 ..     151     181 ..     146     199 .. 0.79
   5 ?    1.6   0.1       1.5   3.2e+02      16      39 ..     208     231 ..     204     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.82
                           DUF2508 16 eeLleeIektkeelesakslfe 37
                                        Ll++I+ ++ e+e+  ++f+
  gi|313117469|ref|YP_004044452.1| 42 SSLLDAIDALRAEIEETGDAFD 63
                                      579***********99877766 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.11
                           DUF2508 13 eedeeLleeIektkeelesakslfensvD.lsde 45
                                      ++++e+ +e+  +++e+ +++++++   D  + +
  gi|313117469|ref|YP_004044452.1| 64 AYNQEFAAEVSHLQTEIGEQREALREMRDiFDAY 97
                                      5889999999999999999999999999944443 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.031
                           DUF2508  15 deeLleeIektkeelesakslfensv 40 
                                         +Ll++Ie+++ e+++  ++f++ +
  gi|313117469|ref|YP_004044452.1| 111 VSDLLAAIEDLRAEMDTTHEAFDAYT 136
                                       568**************999998865 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.45
                           DUF2508  17 eLleeIektkeelesakslfensvD.lsdel 46 
                                       +Ll++Ie+++ e  + ++ f+  +D  + ++
  gi|313117469|ref|YP_004044452.1| 151 DLLAAIEELQLEFGAVQAEFDDYTDdFDADI 181
                                       699*********9999999999888766444 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 1.5
                           DUF2508  16 eeLleeIektkeelesakslfens 39 
                                       +  l++I++ ++e++  ++ fe++
  gi|313117469|ref|YP_004044452.1| 208 QAMLNAIADFQQEIDDFRAEFETT 231
                                       567899999999999999988887 PP

>> DMPK_coil  DMPK coiled coil domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.075        17       8      59 ..      33      84 ..      31      86 .. 0.85
   2 ?    4.5   0.1      0.17        37       6      25 ..     101     120 ..      98     130 .. 0.73
   3 ?   -1.0   0.0       8.6   1.9e+03      42      61 .]     208     227 ..     205     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.075
                         DMPK_coil  8 aEirakQslqeeLekvkaanlafeskLkeaEkknreLeeeleqLkkemEelr 59
                                      a i +k  ++  L ++ a   + e       + n+e  +e+ +L+ e+ e r
  gi|313117469|ref|YP_004044452.1| 33 ADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQR 84
                                      678888888888888888888888888888999************9998766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.17
                         DMPK_coil   6 LeaEirakQslqeeLekvka 25 
                                        e  + akQ +++ L ++ +
  gi|313117469|ref|YP_004044452.1| 101 FESDVEAKQDVSDLLAAIED 120
                                       57778888888888887765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 8.6
                         DMPK_coil  42 reLeeeleqLkkemEelrar 61 
                                       +++++ ++  ++e++ +ra+
  gi|313117469|ref|YP_004044452.1| 208 QAMLNAIADFQQEIDDFRAE 227
                                       56777788888888888875 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.43        95      91     121 .]      35      65 ..       3      65 .. 0.84
   2 ?    4.4   0.4      0.22        48     103     121 .]      47      65 ..      19     135 .. 0.62
   3 ?    3.9   0.1      0.32        70      23     121 .]     107     135 ..      90     171 .. 0.52
   4 ?    1.3   0.0         2   4.5e+02       7      47 ..     131     169 ..     125     191 .. 0.65
   5 ?    2.0   0.1       1.2   2.7e+02       4      47 ..     194     234 ..     191     243 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.43
                           Goodbye  91 ikaakkvseiydaieeLfeelsdflerleiY 121
                                       i++ ++vs+  dai++L  e++++   ++ Y
  gi|313117469|ref|YP_004044452.1|  35 IETKRDVSSLLDAIDALRAEIEETGDAFDAY 65 
                                       6777888888888888888888888877777 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.22
                           Goodbye 103 aieeLfeelsdflerleiY 121
                                       ai++L  e++++   ++ Y
  gi|313117469|ref|YP_004044452.1|  47 AIDALRAEIEETGDAFDAY 65 
                                       4444444444443333333 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.32
                           Goodbye  23 elssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqgasmaFgPaslcfnAvsyLikaakkvse 99 
                                       + + v dll+ ie+ ++                                                            
  gi|313117469|ref|YP_004044452.1| 107 AKQDVSDLLAAIEDLRA------------------------------------------------------------ 123
                                       33333333333333333............................................................ PP

                           Goodbye 100 iydaieeLfeelsdflerleiY 121
                                                 e+  + e ++ Y
  gi|313117469|ref|YP_004044452.1| 124 ----------EMDTTHEAFDAY 135
                                       ..........222222222222 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 2
                           Goodbye   7 eyekeTgkdlkdealkelssvedllkqieaekdkfeefrek 47 
                                        + + T++ +  ++  +l+ v dll+ ie+ + +f   +++
  gi|313117469|ref|YP_004044452.1| 131 AFDAYTNEFV--TDVAALRDVSDLLAAIEELQLEFGAVQAE 169
                                       4555555555..55577778888888888877766555544 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 1.2
                           Goodbye   4 Alkeyeke.Tgkdlkdealkelssvedllkqieaekdkfeefrek 47 
                                       A++ey++e  g ++    +  l+ + d++++i++ +++fe+ +e+
  gi|313117469|ref|YP_004044452.1| 194 AVAEYREEfHGVEV----QAMLNAIADFQQEIDDFRAEFETTEES 234
                                       55566555333344....444455555566666555555554443 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.4    0.0052       1.2     136     266 ..      35     161 ..      29     170 .. 0.80
   2 ?    4.9   0.6     0.066        15      37     102 ..     119     187 ..     101     209 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0052
                         Rab5-bind 136 idlPddveeLqelvlklrEeliesRtakdHlEekLkaEillLkeqiqaEkalkEnlEetlqleierlkeelasissl 212
                                       i+   dv  L   +  lr e+ e+  a d  +++  aE+  L+ +i + + +  ++ + + +  e + +++++    
  gi|313117469|ref|YP_004044452.1|  35 IETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEA---- 107
                                       5556678888888888999999999999999999999999999999999999999999999999999999988.... PP

                         Rab5-bind 213 kveleeikvekeslekslaektrqldklqtikselEeqlkelekekaaveqlvl 266
                                       k +++++++  e+l++ +  + +++d + +  +   + l+++++  aa+e+l l
  gi|313117469|ref|YP_004044452.1| 108 KQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIEELQL 161
                                       777888888888888888888888888776655555667777777777777655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.066
                         Rab5-bind  37 eqLekerk.dkkeLedslkelseets..kqvselakrvkksEllleeLqqafskakrniqeqlavlvks 102
                                       e+L +e++  ++  + + +e  ++++  + vs+l+ ++++  l +  +q++f++ + ++  +++  ++ 
  gi|313117469|ref|YP_004044452.1| 119 EDLRAEMDtTHEAFDAYTNEFVTDVAalRDVSDLLAAIEELQLEFGAVQAEFDDYTDDFDADIERFRNA 187
                                       556666651456688899999988762258899988888888888888888888888877766554433 PP

>> MSA-2c  Merozoite surface antigen 2c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       1.5   3.3e+02     107     144 ..      10      44 ..       3      61 .. 0.63
   2 ?    7.4   1.3     0.018       3.9      88     146 ..      98     154 ..      36     169 .. 0.52
   3 ?    7.7   1.0     0.015       3.3      67     135 ..     175     242 ..     164     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.5
                            MSA-2c 107 lvkvckeflddesefyklvelykafatdiaalkdvtee 144
                                       ++   +ef d + ef   +     fa+di + +dv+  
  gi|313117469|ref|YP_004044452.1|  10 MTATREEFADAQQEFAAYAAD---FAADIETKRDVSSL 44 
                                       566677899999999843333...55566666655543 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.018
                            MSA-2c  88 vkYykkhiyakenvkdvtglvkvckeflddesefyklvelykafa....tdiaalkdvteeLl 146
                                        + +  ++ ak++v d+   +       d ++e     e ++a++    td+aal+dv++ L 
  gi|313117469|ref|YP_004044452.1|  98 AETFESDVEAKQDVSDLLAAI------EDLRAEMDTTHEAFDAYTnefvTDVAALRDVSDLLA 154
                                       233444455454444443333......2333333334556666545555**********9886 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.015
                            MSA-2c  67 nkflkelrknsdkleeDkekvvkYykkhiyakenvkdvtglvkvckeflddesefyklvelykafatdi 135
                                       + f  ++ +  + + e ++ v + y+++    e    ++ ++++ +e  d ++ef    e+++afa d 
  gi|313117469|ref|YP_004044452.1| 175 DDFDADIERFRNAVAEQRDAVAE-YREEFHGVEVQAMLNAIADFQQEIDDFRAEFETTEESFDAFARDF 242
                                       44555555666677777766666.577777666667789999999999999***************774 PP

>> HAUS5  HAUS augmin-like complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.1     0.018       4.1      79     167 ..      63     151 ..      36     198 .. 0.67
   2 ?    1.5   0.1      0.44        98      86     128 ..     178     218 ..     171     225 .. 0.77
   3 ?   -0.6   0.0       1.9   4.1e+02     399     427 ..     207     235 ..     199     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.018
                             HAUS5  79 aaereelekeverLraeirrldkeleareeelsreeaevkraldeisdsrhrqvlLeaydqqceeaakilaedtkrl 155
                                       +a  +e ++ev++L++ei ++++ l+ + +   +  ++ +  ++ ++d+    + +e  ++ ++ +++ +  +t   
  gi|313117469|ref|YP_004044452.1|  63 DAYNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEF 139
                                       55556677777777777777777777777777666666666666666666666666666777777777777777777 PP

                             HAUS5 156 qeqvqqlrdaer 167
                                          v++lrd++ 
  gi|313117469|ref|YP_004044452.1| 140 VTDVAALRDVSD 151
                                       777777777654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.44
                             HAUS5  86 ekeverLraeirrldkeleareeelsreeaevkraldeisdsr 128
                                        +++er r+ +++++  ++   ee     +ev+++l+ i+d +
  gi|313117469|ref|YP_004044452.1| 178 DADIERFRNAVAEQRDAVAEYREEFHG--VEVQAMLNAIADFQ 218
                                       578999999999999999998888764..55667777776665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.9
                             HAUS5 399 rkealrsLqkkwkkIldFrarvseleeii 427
                                        + +l++    +++I dFra  + +ee  
  gi|313117469|ref|YP_004044452.1| 207 VQAMLNAIADFQQEIDDFRAEFETTEESF 235
                                       57777888888999999999888888865 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.034       7.6     100     123 ..      34      57 ..       7      60 .. 0.94
   2 ?    5.3   0.4     0.084        19      63     123 ..      66     127 ..      58     130 .. 0.66
   3 ?    0.4   0.1       2.9   6.3e+02      88     121 ..     132     163 ..     124     168 .. 0.71
   4 ?   -0.6   0.0       5.6   1.2e+03      65      88 ..     176     199 ..     164     236 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.034
                            Phasin 100 gvpsredveaLsarvdeLtkelek 123
                                       ++ +++dv++L + +d+L++e+e+
  gi|313117469|ref|YP_004044452.1|  34 DIETKRDVSSLLDAIDALRAEIEE 57 
                                       799******************997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.084
                            Phasin  63 resvkskveevkekaeeqwd...klekafdervakaLsrlgvpsredveaLsarvdeLtkelek 123
                                       +++  ++v+++++++ eq +   ++  +fd    ++ +  +v  ++dv++L a ++ L++e++ 
  gi|313117469|ref|YP_004044452.1|  66 NQEFAAEVSHLQTEIGEQREalrEMRDIFDAYA-ETFE-SDVEAKQDVSDLLAAIEDLRAEMDT 127
                                       555556666666666555541115555666543.3443.4899*****************9986 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.9
                            Phasin  88 fdervakaLsrlgvpsredveaLsarvdeLtkel 121
                                       fd   ++ ++  +v+  +dv++L a ++eL+ e 
  gi|313117469|ref|YP_004044452.1| 132 FDAYTNEFVT--DVAALRDVSDLLAAIEELQLEF 163
                                       5555555544..6888899*********998765 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 5.6
                            Phasin  65 svkskveevkekaeeqwdklekaf 88 
                                         ++++e+ ++ ++eq d + +  
  gi|313117469|ref|YP_004044452.1| 176 DFDADIERFRNAVAEQRDAVAEYR 199
                                       555555555555555555443332 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   3.4      0.91     2e+02      11      62 ..      45      97 ..       7     112 .. 0.64
   2 ?    9.8   0.6    0.0035      0.79      11      92 ..     115     193 ..     105     204 .. 0.80
   3 ?    0.9   0.3       2.1   4.6e+02      59      79 ..     188     208 ..     174     237 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.91
                             DHR10 11 laelErkarelqakidalqvvekdlrscikllee.ieaelakleeakkklkel 62
                                      l++ ++   e++++ da++ + +++++ +  l++ i ++ ++l+e ++  ++ 
  gi|313117469|ref|YP_004044452.1| 45 LDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTeIGEQREALREMRDIFDAY 97
                                      34444445556666666666666666666665543555555555555544444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0035
                             DHR10  11 laelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrql 87 
                                       la+ E    e+ ++++a++ +++++   +++l ++++ la+ ee + +  + +++ ++ +    + ++ +er +  +
  gi|313117469|ref|YP_004044452.1| 115 LAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIEELQLEFGAVQAEFDDYTD---DFDADIERFRNAV 188
                                       677788888999*******************************************999876...5555555555555 PP

                             DHR10  88 enaee 92 
                                       +  ++
  gi|313117469|ref|YP_004044452.1| 189 AEQRD 193
                                       55555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 2.1
                             DHR10  59 lkelrdaleekeielrelerk 79 
                                       ++e+rda++e ++e + +e +
  gi|313117469|ref|YP_004044452.1| 188 VAEQRDAVAEYREEFHGVEVQ 208
                                       455555555555555544443 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00072      0.16     498     574 ..      65     139 ..      58     146 .. 0.90
   2 ?   -0.3   0.1       1.2   2.6e+02     135     175 ..     182     224 ..     141     241 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00072
                               MAD 498 akqqkkeqlekLqaEierlkellkkleedkekkvaslpessltlafkevleLrkelesaelkiqrlKevFkakiqEF 574
                                       ++q  ++++ +Lq Ei   +e l+++++  +  +++++++    a++ v +L + +e+  + +    e F a ++EF
  gi|313117469|ref|YP_004044452.1|  65 YNQEFAAEVSHLQTEIGEQREALREMRDIFDAYAETFESD--VEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEF 139
                                       567778999******************9999888889888..66899*****************************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                               MAD 135 eelqerldllkkklseleqli..qqlekkqkelaeaeqrikeL 175
                                       e+++++  +++  ++e+ + +   + ++  +  a+ +q i + 
  gi|313117469|ref|YP_004044452.1| 182 ERFRNAVAEQRDAVAEYREEFhgVEVQAMLNAIADFQQEIDDF 224
                                       2333333333333333333332222222222222222222222 PP

>> DUF4715  Domain of unknown function (DUF4715)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.52   1.1e+02      54      91 ..      72     108 ..      35     128 .. 0.79
   2 ?    7.2   0.5     0.023       5.1      46      93 ..     154     201 ..     142     209 .. 0.90
   3 ?    1.2   0.0       1.6   3.5e+02      48      69 ..     207     228 ..     202     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.52
                           DUF4715  54 kvagvqreledfkkealkaihrledaycemsralveqe 91 
                                        v+ +q e+ + ++eal+ +  + day e  ++ ve +
  gi|313117469|ref|YP_004044452.1|  72 EVSHLQTEIGE-QREALREMRDIFDAYAETFESDVEAK 108
                                       56667777765.689************99877766654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.023
                           DUF4715  46 adleillqkvagvqreledfkkealkaihrledaycemsralveqeeq 93 
                                       a +e l+     vq e++d+ ++    i r+ +a  e   a++e  e+
  gi|313117469|ref|YP_004044452.1| 154 AAIEELQLEFGAVQAEFDDYTDDFDADIERFRNAVAEQRDAVAEYREE 201
                                       568999*************************************98876 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.6
                           DUF4715  48 leillqkvagvqreledfkkea 69 
                                       ++ +l+ +a  q+e++df+ e 
  gi|313117469|ref|YP_004044452.1| 207 VQAMLNAIADFQQEIDDFRAEF 228
                                       5678889999********9885 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  12.2      0.15        32     164     328 ..      19     170 ..       7     262 .. 0.48

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.15
                              FUSC 164 allrdalalaaaalageegaeareaararlaadilalealrsqaayesprirararalrrllsrmlallallsslar 240
                                        + ++++a+aa+  a  e+++++++ + ++ a  +++e+  ++  + +++++a++ +l+   +++ ++l+ ++ + +
  gi|313117469|ref|YP_004044452.1|  19 DAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQEFAAEVSHLQTEIGEQREALREMRDIFD 95 
                                       44444444444444444444444444444444444444444444444444444444444444444444444444444 PP

                              FUSC 241 llarlraeeaaavpelaallaelaal..eaaaaaealeaalaalrarlralrraleadadtaalllarlaellaela 315
                                         a+  +++ +a +++++lla++++l  e    +ea +a+ +++ ++++alr                  +lla+  
  gi|313117469|ref|YP_004044452.1|  96 AYAETFESDVEAKQDVSDLLAAIEDLraEMDTTHEAFDAYTNEFVTDVAALRDV---------------SDLLAAIE 157
                                       444444444444444444444444443322222222222222222222222222...............22222222 PP

                              FUSC 316 qllaslraleaai 328
                                       +l+ ++ a +a+ 
  gi|313117469|ref|YP_004044452.1| 158 ELQLEFGAVQAEF 170
                                       2222222222222 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.9      0.79   1.7e+02      20      78 ..       2      60 ..       1      89 [. 0.71
   2 ?    5.3   2.9       0.1        23      33     106 ..      39     116 ..      36     130 .. 0.54
   3 ?    7.1   1.2     0.027       6.1      26      88 ..      71     133 ..      65     159 .. 0.71
   4 ?    1.1   0.1         2   4.5e+02      58      83 ..     206     231 ..     148     237 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.79
                       TMF_TATA_bd 20 eirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqe 78
                                      ++r +   +++++ee +  ++e  + +++ ++ +++  ++++l + ++ l++e+ee  +
  gi|313117469|ref|YP_004044452.1|  2 TVRDKREKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGD 60
                                      56777777788888888888888888888888888888888888888888887777654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.1
                       TMF_TATA_bd  33 eelerleaerdeareeivklmkeneelk.elkkeleelekeleelqeryetlLellG...eksEeveELraDvaDlK 105
                                       +++++l    d++r+ei +     ++ + e ++e+++l++e+ e +e + ++  ++    e  E   E ++Dv+Dl 
  gi|313117469|ref|YP_004044452.1|  39 RDVSSLLDAIDALRAEIEETGDAFDAYNqEFAAEVSHLQTEIGEQREALREMRDIFDayaETFESDVEAKQDVSDLL 115
                                       55556666666666666666666665441345667777776666666666665555411133344446666666664 PP

                       TMF_TATA_bd 106 e 106
                                       +
  gi|313117469|ref|YP_004044452.1| 116 A 116
                                       3 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.027
                       TMF_TATA_bd  26 gElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellG 88 
                                       +E+++l++e+ +  +  +e+r+   +  ++ e+  e+k+++++l + +e+l+ + +t+ e + 
  gi|313117469|ref|YP_004044452.1|  71 AEVSHLQTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFD 133
                                       577777777777777777777766666677777778888888888888888888888877765 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 2
                       TMF_TATA_bd  58 elkelkkeleelekeleelqeryetl 83 
                                       e++++ + +++ ++e+++ + + et+
  gi|313117469|ref|YP_004044452.1| 206 EVQAMLNAIADFQQEIDDFRAEFETT 231
                                       34455566666666666666666665 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.18        41     109     137 ..      63      91 ..      50      94 .. 0.84
   2 ?    4.2   0.7      0.18        39      75     134 ..     172     229 ..     101     235 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.18
                          MIP-T3_C 109 eealeplkaqlaeleeaIkdqkekisnvr 137
                                       +   ++  a+++ l+ +I +q+e + ++r
  gi|313117469|ref|YP_004044452.1|  63 DAYNQEFAAEVSHLQTEIGEQREALREMR 91 
                                       55679999****************99998 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.18
                          MIP-T3_C  75 fiqdDidsMqrELemWrseyrqqaeelaeerratee.aleplkaqlaeleeaIkdqkekis 134
                                          dD+d    ++e+ r+   +q  ++ae r++ ++ +++ + + +a+ +++I d + + +
  gi|313117469|ref|YP_004044452.1| 172 DYTDDFD---ADIERFRNAVAEQRDAVAEYREEFHGvEVQAMLNAIADFQQEIDDFRAEFE 229
                                       3344444...467777777777777777777665542578888888888888888776655 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1     0.011       2.4       7      36 ..      39      68 ..      36      72 .. 0.91
   2 ?    1.3   0.0       2.1   4.7e+02       4      28 ..      68      92 ..      66     100 .. 0.73
   3 ?    4.5   0.1       0.2        45       7      36 ..     109     138 ..     106     140 .. 0.90
   4 ?    1.4   0.3       1.9   4.2e+02       8      32 ..     148     172 ..     146     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.011
                               LPP  7 sqVsqLkskvdqlssdvnsakaaaqaakeE 36
                                       +Vs+L + +d+l ++++++ +a +a  +E
  gi|313117469|ref|YP_004044452.1| 39 RDVSSLLDAIDALRAEIEETGDAFDAYNQE 68
                                      69*********************9998877 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 2.1
                               LPP  4 eLssqVsqLkskvdqlssdvnsaka 28
                                      e +++Vs+L++++ +  + + ++++
  gi|313117469|ref|YP_004044452.1| 68 EFAAEVSHLQTEIGEQREALREMRD 92
                                      5678899999999887777777765 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.2
                               LPP   7 sqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                       ++Vs+L + ++ l ++++ +++a +a  +E
  gi|313117469|ref|YP_004044452.1| 109 QDVSDLLAAIEDLRAEMDTTHEAFDAYTNE 138
                                       79******************9999987776 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 1.9
                               LPP   8 qVsqLkskvdqlssdvnsakaaaqa 32 
                                       +Vs+L + +++l+ +  +++a+ ++
  gi|313117469|ref|YP_004044452.1| 148 DVSDLLAAIEELQLEFGAVQAEFDD 172
                                       6777777777776665555555444 PP

>> CCP_MauG  Di-haem cytochrome c peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.2      0.38        83      87     146 ..       8      67 ..       2      71 .. 0.83
   2 ?    4.8   0.5      0.19        41     105     146 ..      96     137 ..      71     179 .. 0.61
   3 ?    7.1   1.0     0.037       8.1      98     142 ..     186     229 ..     158     241 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.38
                                       TTH.SSHHHHHHHHHTSHHHHHHHHHHCTSCCSHHHHHHHHHHHHTT--STTSHHHHHHT CS
                          CCP_MauG  87 emgnaskeevverlaaspeYaelfeaafgekitfaniakAiaayertlvsaeskfDrylk 146
                                       e  +a++ee ++  ++ ++Ya+ f+a  ++k  ++ + +Ai a   ++ ++   fD+y +
  gi|313117469|ref|YP_004044452.1|   8 EKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDAIDALRAEIEETGDAFDAYNQ 67 
                                       4445888899999999999******99998789999999999999999999999999865 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.19
                                       HHHHHHHHHCTSCCSHHHHHHHHHHHHTT--STTSHHHHHHT CS
                          CCP_MauG 105 eYaelfeaafgekitfaniakAiaayertlvsaeskfDrylk 146
                                       +Yae+fe+ ++ k  ++++  Ai+    ++ +++  fD+y +
  gi|313117469|ref|YP_004044452.1|  96 AYAETFESDVEAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTN 137
                                       366666666664455666666666666666666666666543 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.037
                                       HHHHTSHHHHHHHHHHCTSCCSHHHHHHHHHHHHTT--STTSHHH CS
                          CCP_MauG  98 erlaaspeYaelfeaafgekitfaniakAiaayertlvsaeskfD 142
                                       + +a++ +  +++++ f+  + ++++ +Aia +++++   +++f+
  gi|313117469|ref|YP_004044452.1| 186 NAVAEQRDAVAEYREEFHG-VEVQAMLNAIADFQQEIDDFRAEFE 229
                                       3444555555566666654.6889999999999998877665554 PP

>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   5.7       2.3   5.2e+02      19      71 ..       7      72 ..       2     105 .. 0.62
   2 ?    3.2   0.6      0.77   1.7e+02      19      70 ..      77     127 ..      61     143 .. 0.61
   3 ?    4.7   0.2      0.28        61      10      69 ..     106     164 ..      88     177 .. 0.80
   4 ?    6.6   0.2     0.067        15      13      56 ..     212     253 ..     202     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 2.3
                                      HHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEEEC.EETT.............TS-CCCHHH CS
                          Rotamase 19 kakaeeileqlksgedtFeelArkySddknsakngGdlgw.vekg.............qlppefeka 71
                                      ++k+++ +e+    +++F+++A +++ d +++++  +l + ++                +++ef+  
  gi|313117469|ref|YP_004044452.1|  7 REKMTATREEFADAQQEFAAYAADFAADIETKRDVSSLLDaID-AlraeieetgdafdAYNQEFAAE 72
                                      5666777777777777777777777777777666555543111.11222333344444444444444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.77
                                       HHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEEECEETTTS-CCCHH CS
                          Rotamase  19 kakaeeileqlksgedtFeelArkySddknsakngGdlgwvekgqlppefek 70 
                                       ++++ e +e l++  d F+++A+ +  d + +++  dl   + ++l++e+++
  gi|313117469|ref|YP_004044452.1|  77 QTEIGEQREALREMRDIFDAYAETFESDVEAKQDVSDLL-AAIEDLRAEMDT 127
                                       566666666777777777777776655666666666665.444444444433 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.28
                                       E----HHHHHHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEEECEETTTS-CCCH CS
                          Rotamase  10 asekeraeakakaeeileqlksgedtFeelArkySddknsakngGdlgwvekgqlppefe 69 
                                       + +++  +  a +e++++++ + +++F+++ +++ +d +  ++  dl   + ++l+ ef 
  gi|313117469|ref|YP_004044452.1| 106 EAKQDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLL-AAIEELQLEFG 164
                                       457788888999*******************99999988877777776.55555555554 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.067
                                       --HHHHHHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEE CS
                          Rotamase  13 keraeakakaeeileqlksgedtFeelArkySddknsakngGdl 56 
                                       ++ a+ ++++++ +++ ++ e++F++ Ar++   ++ a++ Gd 
  gi|313117469|ref|YP_004044452.1| 212 NAIADFQQEIDDFRAEFETTEESFDAFARDFY--GAEASDSGDA 253
                                       5678899**********************997..5556666664 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5    0.0056       1.2      31      78 ..      39      90 ..      18     105 .. 0.76
   2 ?    5.2   0.7     0.052        11      31      82 ..     109     160 ..     103     168 .. 0.84
   3 ?    0.4   3.3       1.6   3.5e+02      26      77 ..     163     223 ..     147     243 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0056
                            TraF_2 31 gdvdnlvDkiDdlsdildgleaavnaasad...etq.vdeaaddlnalLedl 78
                                      +dv+ l+D iD+l +++++  +a +a +++   e++ ++ ++ + +++L+++
  gi|313117469|ref|YP_004044452.1| 39 RDVSSLLDAIDALRAEIEETGDAFDAYNQEfaaEVShLQTEIGEQREALREM 90
                                      79****************8888888887776543334444444444455555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.052
                            TraF_2  31 gdvdnlvDkiDdlsdildgleaavnaasadetqvdeaaddlnalLedlggdg 82 
                                       +dv++l+  i+dl +++d+  +a +a + + +   +a++d+ +lL+++++ +
  gi|313117469|ref|YP_004044452.1| 109 QDVSDLLAAIEDLRAEMDTTHEAFDAYTNEFVTDVAALRDVSDLLAAIEELQ 160
                                       699***************9999999988886668888999999999988766 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.6
                            TraF_2  26 vgvevgdvdnlvDkiD.dlsdildgleaavnaasad...........etq.vdeaaddlnalLed 77 
                                       +g+   + d+ +D++D d++   ++++++ +                e+q + +a++d++++++d
  gi|313117469|ref|YP_004044452.1| 163 FGAVQAEFDDYTDDFDaDIERFRNAVAEQRD----AvaeyreefhgvEVQaMLNAIADFQQEIDD 223
                                       3333333444444444444444443333333....234446667666333444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1217  (0.0678789); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        89  (0.00496402); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              81  [number of targets reported over threshold]
# CPU time: 1.23u 0.35s 00:00:01.58 Elapsed: 00:00:00.54
# Mc/sec: 1522.94
//
Query:       gi|313117470|ref|YP_004044453.1|  [L=79]
Description: ROS/MUCR transcriptional regulator protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-08   32.6   0.0    8.2e-08   32.3   0.0    1.1  1  ROS_MUCR  ROS/MUCR transcriptional regulator protein
  ------ inclusion threshold ------
       0.15   10.7   0.1       0.16   10.6   0.1    1.0  1  Cas_Csd1  CRISPR-associated protein (Cas_Csd1)


Domain annotation for each model (and alignments):
>> ROS_MUCR  ROS/MUCR transcriptional regulator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   9.2e-12   8.2e-08      43      99 ..      12      68 ..       3      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 9.2e-12
                          ROS_MUCR 43 eeeaaeeeekepavpikksvtpdaiicledGkklksL.krhLasahgltpeeYrakwg 99
                                      ++ea+++ e+  +++ ++   +  i cl +G+ ++ + + hL ++h++t++eYr+ +g
  gi|313117470|ref|YP_004044453.1| 12 TREAENAVEEDEETEADEDAPEGMIQCLVCGEYYQAItEPHL-QTHDMTIQEYREEYG 68
                                      344445566677777888888999*************999**.*************98 PP

>> Cas_Csd1  CRISPR-associated protein (Cas_Csd1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   1.8e-05      0.16     155     198 ..       9      54 ..       2      66 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.8e-05
                          Cas_Csd1 155 lwedpaireawadyyaskeseeekkda....glClvtGek.apiarlh.p 198
                                       + + +++ +a+++  ++ e++e+   a     +Clv+Ge+ ++i++ h +
  gi|313117470|ref|YP_004044453.1|   9 TEDTREAENAVEE-DEETEADED---ApegmIQCLVCGEYyQAITEPHlQ 54 
                                       5566777777777.333333333...334467********9999998844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 480.40
//
Query:       gi|313117471|ref|YP_004044454.1|  [L=347]
Description: gas vesicle protein GvpN [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-18   66.9   0.0    4.7e-17   62.3   0.0    2.5  1  AAA_5            AAA domain (dynein-related subfamily)
      1e-05   26.0   0.0      7e-05   23.3   0.0    2.3  1  AAA_16           AAA ATPase domain
      2e-05   25.0   0.0    5.8e-05   23.5   0.0    2.0  1  AAA              ATPase family associated with various cellul
    5.3e-05   23.1   0.0     0.0095   15.8   0.0    2.4  1  AAA_3            ATPase family associated with various cellul
    0.00011   21.8   0.0     0.0002   20.9   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
    0.00013   21.8   0.0    0.00033   20.4   0.0    1.7  2  IstB_IS21        IstB-like ATP binding protein
     0.0017   17.9   0.0     0.0075   15.9   0.0    2.1  2  AAA_25           AAA domain
     0.0059   16.3   0.0       0.13   12.0   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
      0.006   16.5   0.0       0.02   14.8   0.0    1.9  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0094   16.5   0.1      0.019   15.5   0.0    1.8  1  ABC_tran         ABC transporter
  ------ inclusion threshold ------
      0.013   15.7   2.6      0.046   13.9   0.0    2.8  3  AAA_33           AAA domain
      0.018   15.0   0.0      0.055   13.4   0.0    1.9  2  NACHT            NACHT domain
      0.019   14.2   0.0      0.042   13.0   0.0    1.5  1  TIP49            TIP49 P-loop domain
       0.02   14.3   0.0      0.033   13.6   0.0    1.4  1  IPT              Isopentenyl transferase
      0.022   14.2   0.0       0.11   11.9   0.0    2.1  3  PhoH             PhoH-like protein
      0.024   14.7   0.0      0.088   12.9   0.0    2.0  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.029   14.6   0.0      0.099   12.9   0.0    1.9  2  AAA_22           AAA domain
      0.038   13.7   0.0       0.28   10.9   0.0    2.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.07   12.3   0.1       0.33   10.1   0.0    2.0  2  NB-ARC           NB-ARC domain
      0.094   12.3   1.0       0.16   11.5   1.0    1.3  1  DUF2201_N        Putative metallopeptidase domain
        0.1   12.6   0.0       0.22   11.6   0.0    1.6  1  AAA_14           AAA domain
        1.2    9.1   4.9       0.84    9.6   2.7    1.7  2  DUF4192          Domain of unknown function (DUF4192)


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   5.8e-20   4.7e-17       2     138 .]      87     240 ..      86     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 5.8e-20
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........................---- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..................ngttslvdsplv 60 
                                       v L+Gp+G+gK+ la+++a+   r+v+ +++ +d+t++dl+g++  k                    + ++v++pl+
  gi|313117471|ref|YP_004044454.1|  87 VHLIGPTGCGKTALAMHVAHERDRPVVWINGDADLTTSDLVGEYAEKeriserdkyihnvikskdIIRDRWVNNPLT 163
                                       77******************************************987999999999999998755557899999999 PP

                                       ----G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHT CS
                             AAA_5  61 raaregeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrs 136
                                        a++eg++lv +E+ r ++ + n+Lls++ee  l l+  +++ +       ++fr i t+n+++  +++e + al++
  gi|313117471|ref|YP_004044454.1| 164 VAVQEGATLVYNEFSRTKPVANNVLLSVFEEGVLELPGQRGESRYVD--VHSDFRAILTSNSVEyAGVHEPQDALLD 238
                                       9999*******************************999888876554..5677***********999999999**99 PP

                                       T- CS
                             AAA_5 137 Rf 138
                                       R+
  gi|313117471|ref|YP_004044454.1| 239 RL 240
                                       95 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   8.6e-08     7e-05       9      66 ..      70     125 ..      66     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.6e-08
                            AAA_16   9 leqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesa 66 
                                       ++q+++ ++r+ + + + v l+G+ G+GK++l+ +++++  +  +++++g++d  +s+
  gi|313117471|ref|YP_004044454.1|  70 VAQVETRMSRWLDVG-RPVHLIGPTGCGKTALAMHVAHERDRP-VVWINGDADLTTSD 125
                                       677777777777776.89*******************866655.888****9998555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   7.1e-08   5.8e-05       2      38 ..      88     135 ..      87     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7.1e-08
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS..SS.........S CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsell..sk.........y 38 
                                        l+Gp G+GKT+la  va+e +++++ i+g   l  s+          
  gi|313117471|ref|YP_004044454.1|  88 HLIGPTGCGKTALAMHVAHERDRPVVWINGDADLttSDlvgeyaekeR 135
                                       699*************************99765524554444444444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-05    0.0095       7     129 ..      92     240 ..      87     242 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                             AAA_3   7 vPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..................kefefkkGpvfanl 65 
                                         G +kt l+ ++a+  d  +  i   +dl  sd++G    +e+                      +  + p+   +
  gi|313117471|ref|YP_004044454.1|  92 PTGCGKTALAMHVAHERDRPVVWINGDADLTTSDLVGEYAEKERIserdkyihnvikskdiirD--RWVNNPLTVAV 166
                                       5577777777777777777777777777777777777543333222333355544444333221..22233333222 PP

                             AAA_3  66 .....lladeinrappktqsalleameerqvtveget.....hklpepflvlatqnPieqeGtyplpeaqldrf 129
                                            l+ +e  r++p ++  ll + ee  + + g++      ++++ f  + t n +e+ G+++  +a ldr+
  gi|313117471|ref|YP_004044454.1| 167 qegatLVYNEFSRTKPVANNVLLSVFEEGVLELPGQRgesryVDVHSDFRAILTSNSVEYAGVHEPQDALLDRL 240
                                       222227789********************998866542222257899**************************7 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.4e-07    0.0002      10      58 ..      61     109 ..      54     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.4e-07
                             AAA_7  10 seilVptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkld 58 
                                       ++ +V+t   +++++ ++  l+ ++pv l+GptG+GKt++++++ ++ d
  gi|313117471|ref|YP_004044454.1|  61 EQPFVETEAVAQVETRMSRWLDVGRPVHLIGPTGCGKTALAMHVAHERD 109
                                       6779************************************999877655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     4e-07   0.00033      30     123 ..      65     163 ..      40     180 .. 0.75
   2 ?   -3.0   0.0       6.5   5.3e+03     165     172 ..     234     241 ..     229     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4e-07
                         IstB_IS21  30 ldkrkvkeL..atlsfiekkenivllGpsGvGKshlaialgveavraglsvlfv......rvedLveelkrarrdgk 98 
                                       ++ ++v+++  +   +++    + l+Gp+G GK+ la+ +++e   ++  v+++      +++dLv e + ++r  +
  gi|313117471|ref|YP_004044454.1|  65 VETEAVAQVetRMSRWLDVGRPVHLIGPTGCGKTALAMHVAHE---RDRPVVWIngdadlTTSDLVGEYAEKERISE 138
                                       444444443226689**********************988776...5666766533333378899999999999999 PP

                         IstB_IS21  99 laralkrllkvdllilDdlgllpld 123
                                         + +++++k++ +i D +  +pl 
  gi|313117471|ref|YP_004044454.1| 139 RDKYIHNVIKSKDIIRDRWVNNPLT 163
                                       9999999999999998888777765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.5
                         IstB_IS21 165 tAilDRlv 172
                                       +A+lDRlv
  gi|313117471|ref|YP_004044454.1| 234 DALLDRLV 241
                                       89*****8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.2e-06    0.0075      20      55 ..      71     106 ..      55     121 .. 0.88
   2 ?   -1.9   0.0       2.5     2e+03     161     181 ..     265     285 ..     245     300 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.2e-06
                            AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlal 55 
                                       ++++  + ++l  g  + l+G++g+GKt+la+++a+
  gi|313117471|ref|YP_004044454.1|  71 AQVETRMSRWLDVGRPVHLIGPTGCGKTALAMHVAH 106
                                       567888999************************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                            AAA_25 161 snsdvgalvealeriarrtga 181
                                       +++ ++++ve ++++++r+++
  gi|313117471|ref|YP_004044454.1| 265 DAENIEQIVELMRELRERLDI 285
                                       444455666666666655554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00016      0.13       5      57 ..      67     116 ..      64     130 .. 0.76
   2 ?    1.9   0.0      0.19   1.6e+02      92     135 ..     167     211 ..     162     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                       SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
                   Sigma54_activat   5 sealkelleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavn 57 
                                       +ea++++ +++++  +   +v + G +G+GK+ la ++ +   ++++p+v +n
  gi|313117471|ref|YP_004044454.1|  67 TEAVAQVETRMSRWLDVGRPVHLIGPTGCGKTALAMHVAH---ERDRPVVWIN 116
                                       677888999999999999**************99865543...3455666666 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.19
                                       TTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSS.SEEE--E CS
                   Sigma54_activat  92 adgGtlfLDeigelplelQekLlrvlqegevervGss.keikvdv 135
                                        +g tl  +e ++ ++ + + Ll v +eg +e  G++ +++ vdv
  gi|313117471|ref|YP_004044454.1| 167 QEGATLVYNEFSRTKPVANNVLLSVFEEGVLELPGQRgESRYVDV 211
                                       57899*************************998887633444544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.5e-05      0.02      21      88 ..      85     149 ..      69     183 .. 0.71
   2 ?   -1.8   0.0         3   2.4e+03     188     203 ..     244     259 ..     206     280 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpk 88 
                                       +++ + Gp g+GKtaL ++++ ++   d  v++++   +  +s l    +e+e  ++ +k++ +++++
  gi|313117471|ref|YP_004044454.1|  85 RPVHLIGPTGCGKTALAMHVAHER---DRPVVWINGDADLTTSDLVGEYAEKERISERDKYIHNVIKS 149
                                       577788***************999...44777777655555555555444555555555555555554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                          ATPase_2 188 lvddldketalnflke 203
                                       ++d  d++t +++++ 
  gi|313117471|ref|YP_004044454.1| 244 YMDFYDRDTEVEIVQS 259
                                       5555555555555444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.3e-05     0.019       9      50 ..      82     127 ..      75     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlk 50 
                                         g+ v ++G++G+GK+ L++ +a++ +      +G+  l   dl 
  gi|313117471|ref|YP_004044454.1|  82 DVGRPVHLIGPTGCGKTALAMHVAHERDRpvvwINGDADLTTSDLV 127
                                       5688899***************999987645556666655544444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.8       4.3   3.5e+03     108     132 ..      20      44 ..      15      53 .. 0.76
   2 ?   13.9   0.0   5.6e-05     0.046       2      39 ..      87     128 ..      87     181 .. 0.69
   3 ?   -0.5   0.0       1.6   1.3e+03     109     137 ..     316     343 ..     307     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.3
                            AAA_33 108 eetlkeRlakRaangddrsevpeea 132
                                       +e+ +++++ R +++++r e  e++
  gi|313117471|ref|YP_004044454.1|  20 DEKQEQNVRNRREKERQRLEKQESH 44 
                                       6777888888888888777776665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.6e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt......lrrrlfg 39 
                                       v l+G+ G+GK+ la +++ +++  +v ++ d+      l    +g
  gi|313117471|ref|YP_004044454.1|  87 VHLIGPTGCGKTALAMHVAHERDrpVVWINGDAdlttsdL----VG 128
                                       5689*************99888888888999986544442....33 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.6
                            AAA_33 109 etlkeRlakRaangddrsevpeealdrqk 137
                                       ++l++++a+R++ ++ r +v e+a++++ 
  gi|313117471|ref|YP_004044454.1| 316 DVLASKVAQRSEVSELR-DVVESAIQDME 343
                                       688999*****998866.89999999885 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.8e-05     0.055       1      23 [.      85     107 ..      85     113 .. 0.90
   2 ?   -2.8   0.0       6.5   5.3e+03     107     147 ..     171     211 ..     165     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-05
                                       SCEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   1 rlvilqGeaGsGKTtLlqklala 23 
                                       r+v l G+ G+GKT+L+ ++a++
  gi|313117471|ref|YP_004044454.1|  85 RPVHLIGPTGCGKTALAMHVAHE 107
                                       67899***************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.5
                                       ..HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEE CS
                             NACHT 107 tlLselirkkllpeasllltvrpralrdleeqleeaivlev 147
                                       tl  + ++++ +  + +ll+v  +++ +l+ q  e++++ v
  gi|313117471|ref|YP_004044454.1| 171 TLVYNEFSRTKPVANNVLLSVFEEGVLELPGQRGESRYVDV 211
                                       66666677888888899999999999999888888877776 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.2e-05     0.042      49      79 ..      83     111 ..      66     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  49 aGravLlaGpsgtGktalaiaiskelgedvp 79 
                                        Gr v l Gp+g Gktala+ +++e  +  p
  gi|313117471|ref|YP_004044454.1|  83 VGRPVHLIGPTGCGKTALAMHVAHERDR--P 111
                                       4899*******************98543..4 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-05     0.033       6      32 ..      89     115 ..      85     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                               IPT   6 ifGatttGKtaeaiklaketgapvivl 32 
                                       + G+t+ GKta a+++a+e+  pv+ +
  gi|313117471|ref|YP_004044454.1|  89 LIGPTGCGKTALAMHVAHERDRPVVWI 115
                                       45**********************964 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.11      22      40 ..      87     105 ..      68     109 .. 0.84
   2 ?   -1.7   0.0         2   1.6e+03     173     198 ..     134     159 ..     117     164 .. 0.74
   3 ?   -3.1   0.0       5.4   4.4e+03      55      98 ..     289     333 ..     279     342 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                       EEEE--TTSSTTHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavala 40 
                                       v  iGp+G+GKt la+ +a
  gi|313117471|ref|YP_004044454.1|  87 VHLIGPTGCGKTALAMHVA 105
                                       778*************998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                                       HHTTT-TTEEEEE--GGG----HHHH CS
                              PhoH 173 evlknvegieivelkkkdvvRhplvk 198
                                       e++++ ++  +  +k+kd++R++ v+
  gi|313117471|ref|YP_004044454.1| 134 ERISERDKYIHNVIKSKDIIRDRWVN 159
                                       55666667777789999999998876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.4
                                       EE-S--TT----SS-------.--TTTHHHHHHHTTTS-TTCHHH CS
                              PhoH  55 trpaveageelGflpgdleek.vdpylrplydaLkdllgaekvek 98 
                                       tr+a++a e +G ++   +    d+ +  l +++ +  + +++++
  gi|313117471|ref|YP_004044454.1| 289 TRAAIMAAEGIGTVDDRNQSVlTDICVDVLASKVAQRSEVSELRD 333
                                       677777777777766544333134555555555555555555554 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.088       4      47 ..      67     110 ..      64     181 .. 0.85
   2 ?   -1.4   0.0       2.9   2.4e+03      56      98 ..     239     280 ..     227     313 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                       -HHHHHHHHHHHHHHT-SS-EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2   4 saaiqelkerLeqaaqsklpvfltGekGsgkelvArlLhknsgp 47 
                                       ++a+++ ++r+        pv+l+G+ G+gk+  A   ++++ +
  gi|313117471|ref|YP_004044454.1|  67 TEAVAQVETRMSRWLDVGRPVHLIGPTGCGKTALAMHVAHERDR 110
                                       5677777888888888889*************999888777665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.9
                                       HHHH-HHHHHHHTTTSEEEEEE-TT--HHHHHHHHHHHHHHTT CS
                   Sigma54_activ_2  56 rlaklpldlleqakggtLylkdiadlskaeqkeLlellakaek 98 
                                       rl+ l +d+ ++ +++ ++   ++ l++++  ++ el+++  +
  gi|313117471|ref|YP_004044454.1| 239 RLVGLYMDFYDRDTEVEIVQSHVDGLDAENIEQIVELMREL-R 280
                                       45556677777777777788888888888888888888776.3 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.099      10      57 ..      89     127 ..      82     140 .. 0.79
   2 ?   -1.9   0.0       4.6   3.7e+03     109     118 ..     276     285 ..     262     341 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdll 57 
                                       ++G++G+GKT l+  ++++          +++vv ++  ++ + +dl 
  gi|313117471|ref|YP_004044454.1|  89 LIGPTGCGKTALAMHVAHER---------DRPVVWINGDADLTTSDLV 127
                                       89****************98.........7777777766666666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.6
                            AAA_22 109 leeLrsllnl 118
                                       ++eLr++l++
  gi|313117471|ref|YP_004044454.1| 276 MRELRERLDI 285
                                       4444443332 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00034      0.28      36      74 ..      87     125 ..      65     140 .. 0.81
   2 ?   -0.1   0.0      0.84   6.8e+02      80     120 ..     164     204 ..     147     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvlekagd 74 
                                       v l+Gp G Gkt+la+ +a+e +  +    g +   ++d
  gi|313117471|ref|YP_004044454.1|  87 VHLIGPTGCGKTALAMHVAHERDRPVVWINGDADLTTSD 125
                                       6799*****************988777666665555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.84
                            RuvB_N  80 tnleekdvlfideihrlsraveevlysamedfrldivigkG 120
                                       + ++e+  l  +e  r ++++++vl s +e+  l++  ++G
  gi|313117471|ref|YP_004044454.1| 164 VAVQEGATLVYNEFSRTKPVANNVLLSVFEEGVLELPGQRG 204
                                       567888999999****************9999888765555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0004      0.33       5      44 ..      70     108 ..      66     150 .. 0.86
   2 ?   -0.5   0.1      0.72   5.8e+02     115     191 ..     266     339 ..     262     342 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC   5 vekviekLlekdelqslvvalvGmgGvGKttlakqilnks 44 
                                       v +v  ++++  +++   v l G  G+GKt la ++ ++ 
  gi|313117471|ref|YP_004044454.1|  70 VAQVETRMSRWLDVG-RPVHLIGPTGCGKTALAMHVAHER 108
                                       667777777777777.6799***************99884 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.72
                                       HHHH.....HHHHCHTTSEEEEEESBCCCCCCS-S-EEEEEESS--HHHHHHHHHHCCTS-GGCHH..CHHHHHHHH CS
                            NB-ARC 115 eedwdkigvvlparenrlrvllTTRdeevanavsatsekievelLekdeawellenkvfekkleekesleevakeiv 191
                                        e+ ++i   + +  +rl + + TR   +a +  +t +    ++   d + ++l +kv +++  ++  l++v ++ +
  gi|313117471|ref|YP_004044454.1| 266 AENIEQIVELMRELRERLDINVGTRAAIMAAEGIGTVDDR-NQSVLTDICVDVLASKVAQRSEVSE--LRDVVESAI 339
                                       5667777777777888888889999888877777754444.4444568899999999998887755..777777665 PP

>> DUF2201_N  Putative metallopeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0    0.0002      0.16     139     196 ..      21      78 ..      13      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                         DUF2201_N 139 rdgekkgdgekaakkkrsdspesarvgalatgfeadleesekgksseeeeseearewr 196
                                       +++e++ + +++++++r ++ es r+g++a++f +  +++e++  ++e++++++  ++
  gi|313117471|ref|YP_004044454.1|  21 EKQEQNVRNRREKERQRLEKQESHRAGNGAAQFDDRFMPEEQPFVETEAVAQVETRMS 78 
                                       3344445556666666777899******************999999999998875444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00027      0.22       3      45 ..      85     124 ..      83     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk 45 
                                       +++ + G+  +GKT l+ ++++e+    + ++ in d + +++
  gi|313117471|ref|YP_004044454.1|  85 RPVHLIGPTGCGKTALAMHVAHERD---RPVVWINGDADLTTS 124
                                       67889****************9988...999999999865532 PP

>> DUF4192  Domain of unknown function (DUF4192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.7     0.001      0.84     139     248 ..      10     119 ..       5     133 .. 0.74
   2 ?   -1.4   0.0       2.4   1.9e+03     257     272 ..     277     294 ..     246     344 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                           DUF4192 139 laGrvvegsReelearlapvegaaaraaqrraaeraaaaleralarprdaerrsdpaevrraaleavraalarvaag 215
                                       ++G++++ sR+e +++    +    +++++r +++ ++++   +a+++d+   ++++ v  +a+++v++ + r  + 
  gi|313117471|ref|YP_004044454.1|  10 VRGSQIRSSRDEKQEQNVRNRR---EKERQRLEKQESHRAGNGAAQFDDRFMPEEQPFVETEAVAQVETRMSRWLDV 83 
                                       68*********88777665333...3334444556666666677777666555889*****************9995 PP

                           DUF4192 216 aglsda...eeaarlavaLtdvrvRDaalalalgee 248
                                        ++        + + a+a++  + RD+ + ++ g+ 
  gi|313117471|ref|YP_004044454.1|  84 GRPVHLigpTGCGKTALAMHVAHERDRPVVWINGDA 119
                                       554444677899999999999999999888887665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                           DUF4192 257 lalarrlpgpl..rAaal 272
                                       ++l +rl  ++  rAa +
  gi|313117471|ref|YP_004044454.1| 277 RELRERLDINVgtRAAIM 294
                                       333333333332222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.87
# Mc/sec: 1205.37
//
Query:       gi|313117472|ref|YP_004044455.1|  [L=140]
Description: Gas vesicle synthesis protein GvpO [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-34  115.4   0.3    1.3e-33  114.8   0.3    1.2  1  GvpO      Gas vesicle synthesis protein GvpO
  ------ inclusion threshold ------
      0.055   13.5   0.3      0.079   12.9   0.3    1.3  1  PGA2      Protein trafficking PGA2


Domain annotation for each model (and alignments):
>> GvpO  Gas vesicle synthesis protein GvpO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   0.3   1.4e-37   1.3e-33       3      94 .]      45     137 ..      43     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 1.4e-37
                              GvpO   3 eeeseeeesrleaaeaarkareqlaeLlgrelegvssverted.gWrvevevlElervPdttdilasYeveldeege 78 
                                       ++ +++++s +++++a+++are+++eLl+ ++eg++++e+t+d +Wr++vev+E+++vPdt+di+++Ye++lde+g+
  gi|313117472|ref|YP_004044455.1|  45 AMPNQSSDSPIGLGDAQKRAREVAEELLEYKFEGIIKIEATDDdSWRTVVEVVERSAVPDTQDIIGCYEITLDETGS 121
                                       567889999*******************************98879******************************** PP

                              GvpO  79 ltgYrrvrRYrRgrad 94 
                                       +t+Y+++rRYrRg+++
  gi|313117472|ref|YP_004044455.1| 122 VTSYELLRRYRRGDMK 137
                                       *************996 PP

>> PGA2  Protein trafficking PGA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   8.8e-06     0.079      61     120 ..      15      75 ..       2      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.8e-06
                              PGA2  61 kakvspnalRggeaksgesdedddegeeeed.vakasgvpewg.kkarkrqkkvlkkleeea 120
                                       +  vsp ++ g  ++ +++d++ +e++++ + + ++s+ +  g   a+kr ++v ++l+e +
  gi|313117472|ref|YP_004044455.1|  15 NDVVSPTEIEGMPSA-EHVDDESSEQATSAEaMPNQSSDSPIGlGDAQKRAREVAEELLEYK 75 
                                       55799******9875.778888777777766687777777777469***********99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 931.55
//
Query:       gi|313117473|ref|YP_004044456.1|  [L=575]
Description: formate-tetrahydrofolate ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.7e-242  804.5   0.0   4.2e-242  804.3   0.0    1.0  1  FTHFS     Formate--tetrahydrofolate ligase


Domain annotation for each model (and alignments):
>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  804.3   0.0  2.3e-246  4.2e-242       2     554 .]      13     575 .]      12     575 .] 0.98

  Alignments for each domain:
  == domain 1  score: 804.3 bits;  conditional E-value: 2.3e-246
                                       -HHHHHHCS----HHHHHHCTT--CCCEEEBSTTEEEE-CHHCCTCTTTS-...-EEEEEEESS--TT--SHHHHHH CS
                             FTHFS   2 sdieiaqeaklkpieeiaeklglkeeelelyGkykakvslkvlerllkekkk..gklilvtaitPtplGeGKtttti 76 
                                       sd+eiaq++++ pi +  e  +l++++l+  G+ykak++++++erl +++ +   +l+lvt++tPtplGeGKt+tt+
  gi|313117473|ref|YP_004044456.1|  13 SDYEIAQSTEMVPIWDFLEPWDLDSSDLQYSGEYKAKIEHHAVERLRDDAADraQNLVLVTGMTPTPLGEGKTVTTV 89 
                                       8******************************************9987766544599********************* PP

                                       HHHHHHHHTT--EEEEE----SHHHHCST--SCEETTEEEESHHHHHTTTTSHHHHHHHHHHHHHHHHHHHHHTTTT CS
                             FTHFS  77 gLaqalnklgkkavaalRepslGPvfgiKGgAaGGGysqvvPmedinLhltGDihaitaannllaalidnrifhene 153
                                       gL q+l +lgk+av+a+RepslGP+fg+KGgAaGGGysqv+PmedinLh+tGD+ha+t+a+nl+aa++d++i +++e
  gi|313117473|ref|YP_004044456.1|  90 GLGQTLDHLGKEAVIAIREPSLGPIFGVKGGAAGGGYSQVLPMEDINLHFTGDLHALTSAHNLIAAMLDAKISQGSE 166
                                       ***************************************************************************** PP

                                       T-EECCCE---EEESS--GGGSSEEES-SSTTS---EEE-EEEGGGSHHHHHHHH-SSHHHHHHHHHC-EEEEETTS CS
                             FTHFS 154 ldidpkkitwkrvlDvndraLRkivvglggkekgvpretgfditvasEimailaLakdledlkerlgrivvaytkdg 230
                                       l+id++ ++w r+lD+ndr+LR+ vvglggk+ g+pre+gf +t+asE+ma+l+La+dl dlker++ri+vay+ +g
  gi|313117473|ref|YP_004044456.1| 167 LEIDVNDVEWPRALDMNDRVLRETVVGLGGKTGGTPREDGFLLTAASELMAVLCLASDLGDLKERIARIIVAYDDEG 243
                                       ***************************************************************************** PP

                                       -EEECCCCT-HHHHHHHTTTTTS-EEEEETT--EEEE-----SSSS--B--HHHHHHHHHH-SEEEEEBSSSTTTHH CS
                             FTHFS 231 epvtaedlkvagalavllkdaikPnlvqtlegtpalvHggPFAniahGcnsviatklalkladyvvtEaGFgadlga 307
                                       +pvt++d++++g +++ll+daikPn+vqt+egtpa+vHggPFAniahG+ns+ia+k+a+ + dy vtEaGFg+dlga
  gi|313117473|ref|YP_004044456.1| 244 DPVTVDDIEATGPVTMLLRDAIKPNIVQTIEGTPAFVHGGPFANIAHGTNSLIADKAAFGMGDYLVTEAGFGSDLGA 320
                                       ***************************************************************************** PP

                                       HHHHHTHHHHHT---SEEEEEEEHHHHHHHTT....--CCCTTS--HHHHHHHHHHHHHHHHHHCTTT--EEEEEE- CS
                             FTHFS 308 ekfldikcrasglkpdavvlvatvraLklhgg....vekeelkeenlealekGlanlekhienvkkfgvpvvvaink 380
                                       ekf++i cr ++++p++ vlva+vraLk+hg     ++ ++++e  ++a+e+G++nl+kh++n+++fgvpvvva+n+
  gi|313117473|ref|YP_004044456.1| 321 EKFMNIVCRFGEMTPNVLVLVASVRALKYHGLdmwpTDYDAIAEAGVDAIERGFENLDKHVQNLQQFGVPVVVAVNR 397
                                       *******************************878755569************************************* PP

                                       -TT--HHHHHHHHHHH.HCTTSEEEEE-HHHHGGGGGHHHHHHHHHHCC..-.-.---SS-TTS-HHHHHHHHHHHT CS
                             FTHFS 381 fktDteaelelvkela.eakavevalsevwakGgeGalelaeavveale..e.kefkflYdlelsieekietiakei 453
                                       f++Dt++e+++v +++ ++ +v++a s+v+a+GgeG+++lae+++e +e  + ++f flY++++si+ekiet+a+e+
  gi|313117473|ref|YP_004044456.1| 398 FPNDTDEEIQTVLDHCrDDIGVKAAESTVFADGGEGGVDLAENIIEEVEtnDpDDFAFLYEDDASIKEKIETVATEM 474
                                       ****************9999****************************9653477********************** PP

                                       T--SEEEE-HHHHHHHHHHHHTTCTTS-EEEE--SSSSSSSTT--SS--S-EEEEEEEEEETTTTEEEEESST--SS CS
                             FTHFS 454 YgadgvelseeakkklkklekqgldklpvciaKtqySlsddpklkgapegftltvrevrlsaGagfivalageimtm 530
                                       Ygadgv+++ +a+++++++e+ g+ ++pvc++Kt  Slsdd+++kgap++++l+vrev  saGagf+val+g++ tm
  gi|313117473|ref|YP_004044456.1| 475 YGADGVTYTGTASEDIERMEELGFAEYPVCLSKTFHSLSDDSSKKGAPTDWSLEVREVYPSAGAGFLVALTGDVLTM 551
                                       ***************************************************************************** PP

                                       ----SS-GGGC-EE-TTSEEES-- CS
                             FTHFS 531 PGlpkkpaaekidvdeegkieGlf 554
                                       PGlp++paa ++d+d+eg+i+Glf
  gi|313117473|ref|YP_004044456.1| 552 PGLPADPAAADMDIDAEGNISGLF 575
                                       ***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 3929.30
//
Query:       gi|313117474|ref|YP_004044457.1|  [L=352]
Description: signal transduction histidine kinase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-17   63.7   0.0    1.4e-16   61.0   0.0    2.2  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.7e-07   30.4   0.0    4.2e-07   29.8   0.0    1.3  1  HATPase_c_5  GHKL domain
    1.6e-06   28.1   0.1    4.1e-06   26.8   0.0    1.7  2  HATPase_c_2  Histidine kinase-like ATPase domain
      2e-06   27.5   0.1    3.6e-06   26.7   0.1    1.5  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
    2.9e-05   24.0   0.4    7.5e-05   22.7   0.4    1.7  1  HisKA        His Kinase A (phospho-acceptor) domain
  ------ inclusion threshold ------
      0.025   14.3   0.0       0.05   13.3   0.0    1.4  1  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.7   2.1e+03      71      92 ..       2      23 ..       1      37 [. 0.81
   2 !   61.0   0.0   4.6e-20   1.4e-16       6     111 ..     250     350 ..     247     351 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.7
                                      STSSSH.HHHHHHHHHHHTTTEE CS
                         HATPase_c 71 gggtGl.GlsivkklvelmgGei 92
                                      g+g+Gl G+s+++ l + m G+i
  gi|313117474|ref|YP_004044457.1|  2 GFGVGLvGVSLAEILLR-MSGRI 23
                                      57888669999998888.88877 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 4.6e-20
                                       HHHHHHHHHHHHHHHHSTTTEEEEEEEE..EETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfatkageieveika..seddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGls 79 
                                       L++++snl++Nav++ +++++ +v+ ++  ++d+  +++eDnG+G+p+  +  lf++ ++ d        ++GlGl 
  gi|313117474|ref|YP_004044457.1| 250 LKRLLSNLLENAVEH-NPDERPWVSAEVsvTDDTAAVRIEDNGPGVPETVQSDLFKPAQKwD-------DRHGLGLL 318
                                       899************.66666666666544468**********************9777742.......5******* PP

                                       HHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  80 ivkklvelmgGeiwvesepgrGttftftlple 111
                                       ivk+l+++++G+i+++++   G+ ft++lpl+
  gi|313117474|ref|YP_004044457.1| 319 IVKRLANRYDGRIELTETGPDGSVFTVELPLA 350
                                       ***************99999**********96 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.4e-10   4.2e-07       6      89 ..     250     335 ..     245     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.4e-10
                       HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ekkklesskskkeehGiGlksirei 77 
                                       l ++l+nlL+NA+e      +e++ ++ +v+ ++++  ++ie +  g     +++ ++  ++ +++hG+Gl  ++++
  gi|313117474|ref|YP_004044457.1| 250 LKRLLSNLLENAVEHNP---DERPWVSAEVSVTDDTAAVRIEDNGPGvpetvQSDLFKPAQKWDDRHGLGLLIVKRL 323
                                       6789********99754...468*******************99888554433344556678899************ PP

                       HATPase_c_5  78 vkkykgnlsiea 89 
                                       +++y+g ++++ 
  gi|313117474|ref|YP_004044457.1| 324 ANRYDGRIELTE 335
                                       ******998544 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.9   5.5e+03       2      27 ..     132     157 ..     132     161 .. 0.77
   2 !   26.8   0.0   1.4e-09   4.1e-06      40     112 ..     258     327 ..     238     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                       HATPase_c_2   2 sadpehvrtvrevaeavlrraglsee 27 
                                       sa++e+ r++ ++++a+lr+  l+++
  gi|313117474|ref|YP_004044457.1| 132 SAELEERRELLNYLNALLRHEVLNTA 157
                                       57889999999999999998766655 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.4e-09
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikglvDev 112
                                       + Naveh+ +e+p   v+ ++++++++  v+++D+Gpg + + + d  +++ +  ++++G+Gl+++k+l++ +
  gi|313117474|ref|YP_004044457.1| 258 LENAVEHNPDERP--WVSAEVSVTDDTAAVRIEDNGPGVPETVQSDLFKPA-QKWDDRHGLGLLIVKRLANRY 327
                                       5699999999999..677777799**************7776666665554.57999************9987 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   1.2e-09   3.6e-06      42     161 ..      39     166 ..       2     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.2e-09
                         HisKA_4TM  42 lalglvyagyrlastdlpaeqewtvlvwslgGavvvgavigltvlvrllegrtiaePvfvvlvaaevGavaGllaGy 118
                                        al l+ +gy+l+++d+p  +   vl+ +++G + +g+    t++   + +  i + + ++    +vG+ +Gll  +
  gi|313117474|ref|YP_004044457.1|  39 FALYLMIGGYWLKRSDVPEVRYPRVLAITMTGMMFLGGFF--TIIGVTFRQVGIVQTLSPIRWGLSVGGGSGLLLAF 113
                                       58999*************99999**************986..44555566777889999999999*******98777 PP

                         HisKA_4TM 119 laa.rarad.as.....r.a..krisdalafvndlirhdlrndlvvirgyaea 161
                                       l+a r  ++ as     r a  +   + l ++n l+rh++ n  +vi+gya+ 
  gi|313117474|ref|YP_004044457.1| 114 LNAqRIEKElASereliRsAelEERRELLNYLNALLRHEVLNTANVIEGYATG 166
                                       77624433322211111212113345789**********************85 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.4   2.5e-08   7.5e-05       5      63 ..     145     201 ..     141     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.5e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                             HisKA   5 flagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsr 63 
                                       + a + HE  +  ++i g+a  L++  +l+ + k++ +ti+++ar l+ +++d++ l r
  gi|313117474|ref|YP_004044457.1| 145 LNALLRHEVLNTANVIEGYATGLME--SLDGDEKDNAATIRRQARELTVIIDDVRFLLR 201
                                       778899*****************99..7**************************98755 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.7e-05      0.05       4      34 ..     133     164 ..     131     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                            SPOB_a   4 eeikelkeliklL.rsqRHDflNhLQvIsGyl 34 
                                        e++e +el+++L   +RH+ lN   vI Gy 
  gi|313117474|ref|YP_004044457.1| 133 AELEERRELLNYLnALLRHEVLNTANVIEGYA 164
                                       578999*******5568**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 2615.40
//
Query:       gi|313117475|ref|YP_004044458.1|  [L=500]
Description: PAS domain-containing protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-48  161.0   0.1    1.1e-18   67.3   0.0    3.4  3  PAS_3            PAS fold
      2e-41  140.7   1.1    2.4e-16   59.9   0.1    3.5  4  PAS_4            PAS fold
      8e-38  128.9   0.3    1.1e-14   54.3   0.0    3.2  3  PAS              PAS fold
    1.7e-31  108.5   0.1    5.4e-12   45.9   0.0    3.3  3  PAS_9            PAS domain
    1.1e-20   73.9   0.0    2.7e-20   72.6   0.0    1.7  1  Response_reg     Response regulator receiver domain
    3.6e-16   58.8   0.7    0.00011   22.1   0.0    3.4  3  PAS_8            PAS domain
    2.2e-06   27.8   0.0     0.0002   21.5   0.0    3.0  3  PAS_11           PAS domain
     0.0009   19.4   4.2          3    8.0   0.0    4.6  4  PAS_7            PAS fold
     0.0027   17.4   0.0       0.22   11.1   0.1    2.2  2  PAS_12           UPF0242 C-terminal PAS-like domain
      0.009   16.3   0.0      0.026   14.8   0.0    1.8  1  OKR_DC_1_N       Orn/Lys/Arg decarboxylase, N-terminal domain
  ------ inclusion threshold ------
      0.046   14.2   0.1        0.5   10.9   0.1    2.5  2  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   5.8e-18   9.4e-15       2      89 .]     157     243 ..     156     243 .. 0.97
   2 !   35.3   0.0   6.6e-12   1.1e-08       3      89 .]     285     368 ..     283     368 .. 0.96
   3 !   67.3   0.0   6.6e-22   1.1e-18       2      74 ..     402     473 ..     401     484 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 5.8e-18
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +y++ ++e+i+G s e l ++++++l  vhp+Dre+v +a++++  +g p + eyR+       rw++ +a++i d+
  gi|313117475|ref|YP_004044458.1| 157 LYINSAYEDIWGRSTETLAAQPRDFLHGVHPDDREQVTAAMNQLS-NGNPADLEYRVNEDENYQRWIWVQAEPITDS 232
                                       79****************************************985.9999*************************** PP

                             PAS_3  79 ngkpvrvigva 89 
                                        g ++r+ g+a
  gi|313117475|ref|YP_004044458.1| 233 AGTVTRIAGFA 243
                                       ********985 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 6.6e-12
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                        ++e+  e +Gy+++e+ +   + +++   ++rerv ea++eal++g+  ++e  +++k+Gey+  e ++  + d +
  gi|313117475|ref|YP_004044458.1| 285 RWNETALERTGYTDAEISEM--QAIEFFPEDERERVGEAIEEALTTGS-ATVEANVLTKHGEYIPHEFTGARLTDPE 358
                                       69******************..*************************9.79******************99999*** PP

                             PAS_3  80 gkpvrvigva 89 
                                       g+ + ++g+a
  gi|313117475|ref|YP_004044458.1| 359 GNLTGLVGIA 368
                                       *******986 PP

  == domain 3  score: 67.3 bits;  conditional E-value: 6.6e-22
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararv 74 
                                       +y s++ve++lGy+pe llg   +  +++hpeDr++v+e++ ea+++ e   ++e R+r+kdG++rw+ea ++ 
  gi|313117475|ref|YP_004044458.1| 402 LYQSPSVEHVLGYEPEALLGE--NAFEYIHPEDRQEVMETFSEAVSNPEmTPTVECRFRHKDGSWRWIEAVGNN 473
                                       689******************..**************************666******************9876 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.6   9.2e+03      18      58 ..      61     101 ..      59     106 .. 0.82
   2 !   26.7   0.1   3.3e-09   5.3e-06      16     109 ..     155     250 ..     139     251 .. 0.85
   3 !   59.9   0.1   1.5e-19   2.4e-16       1     109 [.     267     375 ..     267     376 .. 0.98
   4 !   51.1   0.0   8.4e-17   1.4e-13       2     109 ..     386     494 ..     385     495 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.6
                             PAS_4  18 lyaNaaaaelfgappeellGktlaellpeedaarleralrr 58 
                                       +++Na  +++  +p+  ++Gk  ++++++   a++ ++l++
  gi|313117475|ref|YP_004044458.1|  61 EFLNAVREDYPSLPFILFTGKGSESIASDAISAGVTDYLQK 101
                                       67888888899999999999999999999888888888876 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 3.3e-09
                             PAS_4  16 rvlyaNaaaaelfgappeellGktla...ellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPl 88 
                                         ly+N a++++ g++ e+l  ++      ++p+ d++++ +a++++  g  p++ +  ++  +  +r++ +++ P+
  gi|313117475|ref|YP_004044458.1| 155 ELLYINSAYEDIWGRSTETLAAQPRDflhGVHPD-DREQVTAAMNQLSNG-NPADLEYRVNEdENYQRWIWVQAEPI 229
                                       579********99999999988876655346665.***********9888.6**********9999*********** PP

                             PAS_4  89 rdesGevigvlvisrDiTerr 109
                                        d+ G+v  + +++rDiTer+
  gi|313117475|ref|YP_004044458.1| 230 TDSAGTVTRIAGFARDITERK 250
                                       ********************8 PP

  == domain 3  score: 59.9 bits;  conditional E-value: 1.5e-19
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l++l da++v++pdg+++++N++a e  g++++e+  +   e++pe+ ++r+ +a++++l+++ +  ++ +l+  ge
  gi|313117475|ref|YP_004044458.1| 267 LNALDDAFYVINPDGTMRRWNETALERTGYTDAEISEMQAIEFFPEDERERVGEAIEEALTTGSATVEANVLTKHGE 343
                                       6899***********************************************************99999999999*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                         ++e++  +l d++G   g+++i+rDi+er+
  gi|313117475|ref|YP_004044458.1| 344 YIPHEFTGARLTDPEGNLTGLVGIARDISERK 375
                                       *******************************8 PP

  == domain 4  score: 51.1 bits;  conditional E-value: 8.4e-17
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pg 76 
                                       +++ d+++vld+dg++ly +++ ++++g++pe+llG+  +e+  +ed++++++   ++++  e   ++e++ +  +g
  gi|313117475|ref|YP_004044458.1| 386 ENSTDIIVVLDEDGTYLYQSPSVEHVLGYEPEALLGENAFEYIHPEDRQEVMETFSEAVSNPEMTPTVECRFRhkDG 462
                                       799**************************************99999**************988777776666666** PP

                             PAS_4  77 eerhyelrl.lPlrdesGevigvlvisrDiTerr 109
                                       ++r++e    + l+++   v g+++ srDiTer+
  gi|313117475|ref|YP_004044458.1| 463 SWRWIEAVGnNQLDNP--AVEGFVINSRDITERK 494
                                       *********7777655..566************8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.1e-08   3.4e-05      22     113 .]     155     246 ..     133     246 .. 0.86
   2 !   47.6   0.0   8.8e-16   1.4e-12       4     113 .]     264     371 ..     262     371 .. 0.94
   3 !   54.3   0.0   6.9e-18   1.1e-14       1     113 []     379     490 ..     379     490 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.1e-08
                                       BEEEECHHHHHHHSSTHHHCTTSB..GGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC..TTSSEEEEEEEEE CS
                               PAS  22 rilyvNaaaeellGlsreevlgks..lldliheeddaelaelleqlleqgeesrageisfkl..rdgrpihlevras 94 
                                       + ly+N+a+e++ G s e +  ++  +l+ +h++    ++e+++ +++q ++++  +   ++    +  +++ v+a 
  gi|313117475|ref|YP_004044458.1| 155 ELLYINSAYEDIWGRSTETLAAQPrdFLHGVHPD----DREQVTAAMNQLSNGNPADLEYRVneDENYQRWIWVQAE 227
                                       569**************99998753378888887....8999999999999999999999999999*********** PP

                                       EEEETTEEEEEEEEEEEES CS
                               PAS  95 pvrdaggeilgflgvlrdi 113
                                       p++d  g+++ + g++rdi
  gi|313117475|ref|YP_004044458.1| 228 PITDSAGTVTRIAGFARDI 246
                                       ******************8 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 8.8e-16
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       ++ l++l+d+  v++ dg +  +N++a e +G++  e++    +++++e++++ + e++e++l +g+     ++ ++
  gi|313117475|ref|YP_004044458.1| 264 DQALNALDDAFYVINPDGTMRRWNETALERTGYTDAEISEMQAIEFFPEDERERVGEAIEEALTTGSATVEANV-LT 339
                                       6889**********************************************999999*******99999888888.44 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + +g++i+ e + + ++d++g+++g++g++rdi
  gi|313117475|ref|YP_004044458.1| 340 K-HGEYIPHEFTGARLTDPEGNLTGLVGIARDI 371
                                       4.9*****************************8 PP

  == domain 3  score: 54.3 bits;  conditional E-value: 6.9e-18
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e+++a++e+++d i+v+Dedg  ly +++ e  lG+++e +lg++ +++ih+ed++e+ e ++++ ++ e+  ++e 
  gi|313117475|ref|YP_004044458.1| 379 ERFQAFIENSTDIIVVLDEDGTYLYQSPSVEHVLGYEPEALLGENAFEYIHPEDRQEVMETFSEAVSNPEMTPTVEC 455
                                       689************************************************************************** PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +f+ +dg+ +++e   +  +d      gf+   rdi
  gi|313117475|ref|YP_004044458.1| 456 RFRHKDGSWRWIEAVGNNQLDNPAV-EGFVINSRDI 490
                                       *************998888777763.4777777665 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.7e-08   2.8e-05      12     104 .]     155     248 ..     144     248 .. 0.83
   2 !   45.9   0.0   3.3e-15   5.4e-12       2     104 .]     272     373 ..     271     373 .. 0.89
   3 !   34.8   0.0   9.5e-12   1.5e-08       2     104 .]     390     492 ..     389     492 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.7e-08
                             PAS_9  12 rilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrk.kerevevvlirkngetfwvlltaspvk 86 
                                       ++ly+N a +++ G s e +  ++ +d++   +p+++e + aa++q+++ ++ + e+    +++ + w+ + a p+ 
  gi|313117475|ref|YP_004044458.1| 155 ELLYINSAYEDIWGRSTETLAAQP-RDFLhGVHPDDREQVTAAMNQLSNgNPADLEYRVNEDENYQRWIWVQAEPIT 230
                                       478***********8877766655.666667777777777777777777779999999999999999999******* PP

                             PAS_9  87 dddgelvgiivilrDite 104
                                       d+ g++++i+++ rDite
  gi|313117475|ref|YP_004044458.1| 231 DSAGTVTRIAGFARDITE 248
                                       *****************8 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 3.3e-15
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       d++ ++npdg++ ++Ne+al+ +Gy+ +e+   +  ++f  +++++er+ +a+e+  +    +ve    +k ge+++
  gi|313117475|ref|YP_004044458.1| 272 DAFYVINPDGTMRRWNETALERTGYTDAEISEMQAIEFF--PEDERERVGEAIEEALTtGSATVEANVLTKHGEYIP 346
                                       7888999***999**************************..6666666666666666667799************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                        ++t +++ d +g+l+g+++i rDi+e
  gi|313117475|ref|YP_004044458.1| 347 HEFTGARLTDPEGNLTGLVGIARDISE 373
                                       *************************98 PP

  == domain 3  score: 34.8 bits;  conditional E-value: 9.5e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetf 76 
                                       d i++ ++dg+ ly +++++ +lGy pe++lg + ++ + ++++++e ++ + e+ ++     +ve  +++k+g+  
  gi|313117475|ref|YP_004044458.1| 390 DIIVVLDEDGTYLYQSPSVEHVLGYEPEALLGENAFEYI-HPEDRQEVMETFSEAVSNpeMTPTVECRFRHKDGSWR 465
                                       6788889********************************.999999999999999999998899************* PP

                             PAS_9  77 wvlltaspv.kdddgelvgiivilrDite 104
                                       w+++      + d+  + g+++ +rDite
  gi|313117475|ref|YP_004044458.1| 466 WIEAVG--NnQLDNPAVEGFVINSRDITE 492
                                       *77544..32335777999*********8 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   1.6e-23   2.7e-20       2     103 ..       2     104 ..       1     113 [. 0.94

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.6e-23
                                       EEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEE CS
                      Response_reg   2 livdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvii 76 
                                       l vdD+p++++l +++le  ++ + +v++a+++ + l+ l +e++d+++ D +mp+ +G+e+l+ +re+ p+lp i+
  gi|313117475|ref|YP_004044458.1|   2 LHVDDEPDFATLAADFLEreNDSF-VVETATTAGAGLDVLATEDIDCVVSDYDMPEQNGIEFLNAVREDYPSLPFIL 77 
                                       669***************844566.**************************************************** PP

                                       EESSTSHHHHHHHHHCTESEEEESSG- CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfd 103
                                       +t++++e+ a +a++ag+ d+l+K+  
  gi|313117475|ref|YP_004044458.1|  78 FTGKGSESIASDAISAGVTDYLQKQAG 104
                                       ************************976 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   3.9e-05     0.064       2      55 ..     134     188 ..     133     200 .. 0.67
   2 !   20.0   0.0   3.2e-07   0.00052       4      59 ..     264     321 ..     261     330 .. 0.84
   3 !   22.1   0.0   6.7e-08   0.00011       1      63 [.     379     440 ..     379     444 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.9e-05
                             PAS_8   2 rlralfesspdgiavvdlgd.rivdvNqaalellGysadlkgellg....qllpvlrpl 55 
                                       rl+ l e+s+d ++++  ++  ++++N a+++++G     ++e+l     ++l++++p 
  gi|313117475|ref|YP_004044458.1| 134 RLQELSEASNDVLWMFSSDWdELLYINSAYEDIWG----RSTETLAaqprDFLHGVHPD 188
                                       888999*********5444455*************....44444432122444444444 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.2e-07
                             PAS_8   4 ralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle.da 59 
                                        +++++++d+  v++ +g+  + +N++ale +Gy+ a+++++   +++p+ + +++ +a
  gi|313117475|ref|YP_004044458.1| 264 DQALNALDDAFYVINpDGT-MRRWNETALERTGYTdAEISEMQAIEFFPEDERERVgEA 321
                                       6789***********6666.999******************999999999998887743 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 6.7e-08
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg.qllpvlrplle.daeqll 63 
                                       er++a++e+s d i+v+d +g + ++  ++ ++ lGy+    ++llg + ++ ++p+ + + ++++
  gi|313117475|ref|YP_004044458.1| 379 ERFQAFIENSTDIIVVLDeDG-TYLYQSPSVEHVLGYE---PEALLGeNAFEYIHPEDRqEVMETF 440
                                       7*****************555.5*************99...6688877999999999887666665 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.15   2.4e+02      44      86 ..     185     227 ..     169     230 .. 0.88
   2 ?   -0.6   0.0      0.86   1.4e+03      27      67 ..     293     332 ..     288     348 .. 0.87
   3 !   21.5   0.0   1.2e-07    0.0002       8      89 ..     395     473 ..     389     489 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.15
                            PAS_11  44 chpqdlstlkshlrevissngeatsslyRLrl..sqdkfvkvktk 86 
                                       +hp+d+++++ +  +    ng+ + + yR     + +++++v+++
  gi|313117475|ref|YP_004044458.1| 185 VHPDDREQVTAAMNQLS--NGNPADLEYRVNEdeNYQRWIWVQAE 227
                                       69999999999999987..9999*******997777899**9985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.86
                            PAS_11  27 slglekeelvgrsiydLchpqdlstlkshlrevissngeat 67 
                                       ++g+++ e++++ + +++ +++++++ ++ +e + ++g at
  gi|313117475|ref|YP_004044458.1| 293 RTGYTDAEISEMQAIEFFPEDERERVGEAIEEAL-TTGSAT 332
                                       57999******************99999999999.777766 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.2e-07
                            PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvk 84 
                                       ld dg  +   +   + +++lg+e e l+g  +++ +hp+d++++++ ++e +s+++++ +   R+r +++ + ++ 
  gi|313117475|ref|YP_004044458.1| 395 LDEDGTYLYQSP---SVEHVLGYEPEALLGENAFEYIHPEDRQEVMETFSEAVSNPEMTPTVECRFRHKDGSWRWIE 468
                                       666666666666...8899**********************************8888888888*********99999 PP

                            PAS_11  85 tkskl 89 
                                       +++  
  gi|313117475|ref|YP_004044458.1| 469 AVGNN 473
                                       88765 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1         1   1.6e+03      42      81 ..      96     134 ..      89     141 .. 0.62
   2 !    6.5   0.1    0.0054       8.8      58     114 ..     188     253 ..     140     254 .. 0.69
   3 ?    2.6   0.0     0.089   1.5e+02       2      36 ..     268     302 ..     267     379 .. 0.55
   4 !    8.0   0.0    0.0018         3      73     115 .]     452     498 ..     385     498 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                             PAS_7  42 eellrynaergefgagdveaeverrlaaara.gkphsfere 81 
                                       ++ l+ +a +g+++    ++ ++++++++ra ++++++er+
  gi|313117475|ref|YP_004044458.1|  96 TDYLQKQAGTGQYK--LLANRIKNVVSQYRAeQQATKTERR 134
                                       55566666666666..5667777777777763444555554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0054
                             PAS_7  58 dveaeverrlaaara....gkphsfererpdgrvievrgnplpd.gGfVtty....tDiTerrrae 114
                                       d +++v++ ++++++    + +++++  ++  r+i v+++p+ d  G+Vt       DiTer++ e
  gi|313117475|ref|YP_004044458.1| 188 DDREQVTAAMNQLSNgnpaDLEYRVNEDENYQRWIWVQAEPITDsAGTVTRIagfaRDITERKKRE 253
                                       334445555555555111155566666777789*********775799997533337*****9987 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.089
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvq 36 
                                       + +++++ v++ d+ ++ wN+  le  ++++  + 
  gi|313117475|ref|YP_004044458.1| 268 NALDDAFYVINPDGTMRRWNETALERTGYTDAEIS 302
                                       66778888888888888888888887777766553 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0018
                             PAS_7  73 gkphsfererpdgrvievrgnpl....pdgGfVttytDiTerrraee 115
                                         + +f ++  + r+ie  gn      +  GfV+   DiTer+++e+
  gi|313117475|ref|YP_004044458.1| 452 TVECRFRHKDGSWRWIEAVGNNQldnpAVEGFVINSRDITERKKHEQ 498
                                       334445555555677887776553553458*************9986 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00014      0.22      18      96 ..     101     183 ..      94     212 .. 0.71
   2 ?    3.8   0.0     0.024        39      54      90 ..     386     422 ..     383     460 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                            PAS_12  18 kitgansftneksrfrdl....sldnyaldlRrLfDsLrsEnlgailvysqkenkllfaNaqirallGwssdkflqd 90 
                                       k+ g+ +++  + r +++     +++ a    r   +L +  + ++ ++s   + ll++N+  +++ G s++++  +
  gi|313117475|ref|YP_004044458.1| 101 KQAGTGQYKLLANRIKNVvsqyRAEQQATKTERRLQELSEASNDVLWMFSSDWDELLYINSAYEDIWGRSTETLAAQ 177
                                       55555555544444444311112345555555555789999999*****************************9987 PP

                            PAS_12  91 fseivq 96 
                                         + ++
  gi|313117475|ref|YP_004044458.1| 178 PRDFLH 183
                                       777665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.024
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflqd 90 
                                       En++ i+v    +   l+    ++++lG++++ +l +
  gi|313117475|ref|YP_004044458.1| 386 ENSTDIIVVLDEDGTYLYQSPSVEHVLGYEPEALLGE 422
                                       89999999999999******************99743 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.6e-05     0.026      15     111 .]      22     122 ..      10     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                        OKR_DC_1_N  15 kegfevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlreidg 88 
                                       +++f v ++t+ + +l v+ +  +i++vv ++d   ++  e+l+++re  + lP  l++ + ++  ++  + + ++ 
  gi|313117475|ref|YP_004044458.1|  22 NDSFVVETATTAGAGLDVLAT-EDIDCVVSDYDmpeQNGIEFLNAVREDYPSLPFILFTGKGSESIASDAISAGVTD 97 
                                       345666666666666666665.9*******************************99999865666666666666777 PP

                        OKR_DC_1_N  89 fielledtpe..fiarqieaaakkY 111
                                       +++ + +t +   +a++i+  +++Y
  gi|313117475|ref|YP_004044458.1|  98 YLQKQAGTGQykLLANRIKNVVSQY 122
                                       7776555543114566666666555 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00031       0.5      33      89 ..      95     162 ..      85     167 .. 0.60
   2 ?   -0.3   0.0      0.95   1.6e+03      50      87 ..     369     404 ..     348     412 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                   Glyco_tranf_2_4  33 trailkelpe...vkllhvd.....ksy..ederrqve.llkallaryaeadwvlvvDaDEflvvpds 89 
                                       ++++l++++    +kll ++     ++y  e+++++ e +l++l +  ++  w++  D DE+l ++++
  gi|313117475|ref|YP_004044458.1|  95 VTDYLQKQAGtgqYKLLANRiknvvSQYraEQQATKTErRLQELSEASNDVLWMFSSDWDELLYINSA 162
                                       555665543322233333333333355522445555433888888888899************98875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.95
                   Glyco_tranf_2_4  50 ksyederrqvellkallaryaeadwvlvvDaDEflvvp 87 
                                        ++++++ q e+ +a++++   +d ++v+D D  + ++
  gi|313117475|ref|YP_004044458.1| 369 RDISERKAQQERFQAFIEN--STDIIVVLDEDGTYLYQ 404
                                       4566666777888888865..59999999999766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3208.71
//
Query:       gi|313117476|ref|YP_004044459.1|  [L=1098]
Description: formate dehydrogenase, alpha subunit, archaeal-type [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-85  285.8   0.0    7.3e-85  285.5   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    1.9e-31  108.3   0.0    3.8e-31  107.4   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    1.2e-26   92.6   0.8    2.6e-26   91.5   0.8    1.6  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    2.8e-12   46.0   1.1    9.9e-12   44.2   1.1    2.1  1  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    4.4e-10   40.0   8.0    3.9e-07   30.5   8.7    3.5  3  Fer4_7           4Fe-4S dicluster domain
    1.7e-09   37.5   0.0      6e-09   35.8   0.0    2.1  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    2.4e-09   37.2   9.0    2.4e-09   37.2   9.0    2.8  3  Fer4_21          4Fe-4S dicluster domain
    3.6e-07   30.0  20.7    4.8e-05   23.2   2.7    3.7  3  Fer4_6           4Fe-4S binding domain
    6.4e-07   28.9  23.0    0.00027   20.6   2.7    3.6  3  Fer4             4Fe-4S binding domain
    3.4e-06   27.1   8.1    3.4e-06   27.1   8.1    3.7  3  Fer4_9           4Fe-4S dicluster domain
    3.2e-05   24.3   7.3    3.2e-05   24.3   7.3    3.4  3  Fer4_8           4Fe-4S dicluster domain
    0.00038   20.5  13.5    0.00038   20.5  13.5    3.4  3  Fer4_10          4Fe-4S dicluster domain
      0.005   17.7   2.4      0.005   17.7   2.4    3.4  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0088   16.2   0.0      0.021   15.0   0.0    1.7  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
  ------ inclusion threshold ------
      0.012   16.5  11.2       0.63   10.9   2.1    3.8  3  Fer4_22          4Fe-4S dicluster domain
      0.015   15.3   2.5      0.015   15.3   2.5    4.4  4  Fer4_2           4Fe-4S binding domain
      0.018   15.2  13.3      0.068   13.4   2.0    2.6  2  Fer4_18          4Fe-4S dicluster domain
        0.3   11.7  15.3       0.92   10.1   3.7    2.8  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
       0.42   11.4  16.6        5.4    7.8  11.7    4.1  3  Fer4_15          4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.5   0.0   7.7e-88   7.3e-85       1     431 [.     446     871 ..     446     872 .. 0.96

  Alignments for each domain:
  == domain 1  score: 285.5 bits;  conditional E-value: 7.7e-88
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl++P+vR   +++G+F++ sW+ Al+++a++l ++++++g d+v   +s++ + +e+ ++ +k+++ + g  ++++
  gi|313117476|ref|YP_004044459.1| 446 RLTRPLVR---NDAGEFEPTSWENALDYVADRLSEIQDEHGVDTVGCLASSKGT-NEEAYLVQKFARQVLG--TKNI 516
                                       9*******...99*********************************98888998.9***************..9*** PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d++a+l+++s++    qt+g++      ++   ed+ ++d+ ++ GsN  e +p+l +ri + ++ + a +iv++pr
  gi|313117476|ref|YP_004044459.1| 517 DNCARLCHSSTVaalqQTLGYGAM----TNRINEDIGHADAYLISGSNTTESHPVLATRIKQNVRDG-ADLIVFDPR 588
                                       **********99555555555544....444445**********************99999999885.********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                       +  ++++ad++  ++pg d+a ++++  +++++ ++d++f+++ t+g+e +++ +++ ++e++++  +v  +     
  gi|313117476|ref|YP_004044459.1| 589 KVGIAEHADQYTRTRPGYDVAWLNGLIRYLIENDLHDTAFIERNTKGFESVKKKVQAFTPERVEELAGVSPDELAAA 665
                                       ***************************************************************************** PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       a+ +a++++   + + +g++++++g++++ a++ Lal +g+vg++g+g   ++Gq++++g++ ++g+lp  l+ ++ 
  gi|313117476|ref|YP_004044459.1| 666 AETLAAADT-VVFGWAMGMTQSSHGTENLIAMADLALTLGQVGKEGAGLSPFRGQNNVQGGGGDMGTLPGSLPGYQD 741
                                       *********.9999*******************************************************99999999 PP

                                       TT...HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSH CS
                     Molybdopterin 305 ke...ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrlts 378
                                       +      +kfa  + +  +  p+ ++ e+   ++++++k +y++g+np  + +d  +  +ale+ d++ v d+++t+
  gi|313117476|ref|YP_004044459.1| 742 PAdddVGEKFAEAWGERPPEEPGLKVPEMFSEIHEGNLKGMYIVGENPALSEPDVTHAAEALEQIDFLAVQDIFVTE 818
                                       988998899******************************************************************** PP

                                       HHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 379 talyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                       ta+yaD+iLPaat  Ek++++tn+e+r+q+ ++  +ppgea++dw+I +aLa+
  gi|313117476|ref|YP_004044459.1| 819 TAEYADVILPAATSPEKHGTFTNTERRIQRVRPSSDPPGEARQDWEITQALAN 871
                                       ***************************************************97 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.0     4e-34   3.8e-31       2     109 ..     963    1066 ..     962    1068 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 4e-34
                                        EEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEE CS
                   Molydop_binding    2 rLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvf 75  
                                        +L++gr+l+++h++  tr+v+ l ++ + ++vei+pe+Aa+ G++dG+ V+vesrrG+++v+a +t+rv  G++f
  gi|313117476|ref|YP_004044459.1|  963 TLTSGRVLYHWHTGQITRRVEGLMSHVGeSFVEISPETAAQIGVEDGEYVRVESRRGAIVVKATITDRVGNGTLF 1037
                                        79************************************************************************* PP

                                        EESSHCC.....S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding   76 mpfgwweagekggnaNaltddatdplsgtpefks 109 
                                        +p+++ +     g++N+lt++ +dp++g+pe+k+
  gi|313117476|ref|YP_004044459.1| 1038 IPMHFAA-----GAVNKLTQENFDPQTGIPEYKV 1066
                                        *****99.....********************96 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.8   2.8e-29   2.6e-26       2      81 ..      42     140 ..      41     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 2.8e-29
                            Fer2_4   2 rpvtltfDGkevtvpeGdtvasAllang................vdvprsckygrp...rgelcaggeCrnClVeve 59 
                                       +++tl+++++ vtvp+G+tv++A++a++                +dvp++c+y+r+   ++e+++++eCr+C+Ve++
  gi|313117476|ref|YP_004044459.1|  42 ASTTLRVNDELVTVPPGSTVIDAMQAASdqtvtvspgadvlhddADVPALCYYDREgdcSDEVGPRSECRTCIVETD 118
                                       689************************************************************************** PP

                            Fer2_4  60 gepnvracstpvedGlkvetqt 81 
                                       +++ v++cs+p+edGl+v+t+t
  gi|313117476|ref|YP_004044459.1| 119 EHGLVPSCSFPAEDGLRVRTDT 140
                                       ********************97 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   1.1   1.1e-14   9.9e-12       1      40 []     147     186 ..     147     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.1e-14
                   NADH-G_4Fe-4S_3   1 RktilellLanHpldCltCdknGnCeLQdlayelgveesr 40 
                                       R  +l+l L+nH+l C+tC  nG+CeLQ++a    ve+ r
  gi|313117476|ref|YP_004044459.1| 147 RSVNLDLVLSNHNLRCTTCNGNGRCELQETAIGADVEHPR 186
                                       6789***************************999999976 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.5   3.3e+03      37      42 ..     161     166 ..     133     173 .. 0.69
   2 !   30.5   8.7   4.1e-10   3.9e-07       1      51 [.     212     270 ..     212     271 .. 0.69
   3 ?    4.3   0.0     0.067        63       4      13 ..     392     424 ..     391     527 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.5
                            Fer4_7  37 kClgCg 42 
                                       +C++C+
  gi|313117476|ref|YP_004044459.1| 161 RCTTCN 166
                                       566663 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 4.1e-10
                            Fer4_7   1 rCigCgaCvaaCp....vkaieldeeenekgt.....ekveidpekClgCgaCvavCPtg 51 
                                       +Ci C++Cv+aC      ++++++ +  +  +     +  ++  ++C++Cg+C++vCPtg
  gi|313117476|ref|YP_004044459.1| 212 KCILCNRCVEACNdvqvEGVLRIEGSGPDT-RigfqsDAETMADSECVSCGHCATVCPTG 270
                                       7***********844444455554432222.123343555889999************98 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.067
                            Fer4_7   4 gCgaCvaaC.......................p 13 
                                        Cg+C++ C                       p
  gi|313117476|ref|YP_004044459.1| 392 TCGFCAVGCrfemwgkdgdslgvvpiedpdsaP 424
                                       6********665555555555555555544441 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   6.4e-12     6e-09       4      54 ..     389     442 ..     386     443 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 6.4e-12
                                       EEEE-SSBTT--EEEEEEETTEEE...EEEE-TTSTTTTT---HHHHTCHHCCC CS
                    Molybdop_Fe4S4   4 vktaCpyCgvgCglevhvkdgkiv...kvegdpdhpvnegrlCvKGrtllervy 54 
                                       + t+C +C vgC +e++ kdg       +e  +++p+n+  +CvKG++++e+ +
  gi|313117476|ref|YP_004044459.1| 389 AETTCGFCAVGCRFEMWGKDGDSLgvvPIEDPDSAPANNFSTCVKGKFGHEFAN 442
                                       67*******************98755588888999****************988 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   9.0   2.6e-12   2.4e-09       2      58 ..     207     273 ..     206     274 .. 0.78
   2 ?   -2.4   0.7       5.7   5.4e+03      10      19 ..     392     401 ..     390     403 .. 0.80
   3 ?   -2.8   0.1       7.8   7.4e+03      13      27 ..     518     532 ..     515     541 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.6e-12
                           Fer4_21   2 ridedkCigCgkCliaCedtshqai..........eidaktvl.......kvvedeCvGCnlCssvCPvedcie 58 
                                       +id++kCi C++C+ aC+d  ++ +          +      +       ++ ++eCv C  C++vCP+ + i+
  gi|313117476|ref|YP_004044459.1| 207 QIDRNKCILCNRCVEACNDVQVEGVlriegsgpdtR------IgfqsdaeTMADSECVSCGHCATVCPT-GSIT 273
                                       69******************9999987765544442......2333444377799*************6.7775 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.7
                           Fer4_21  10 gCgkCliaCe 19 
                                        Cg C++ C+
  gi|313117476|ref|YP_004044459.1| 392 TCGFCAVGCR 401
                                       5899998886 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.8
                           Fer4_21  13 kCliaCedtshqaie 27 
                                       +C+  C+ +++ a++
  gi|313117476|ref|YP_004044459.1| 518 NCARLCHSSTVAALQ 532
                                       799999988888775 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   2.7   5.1e-08   4.8e-05       1      20 [.     205     224 ..     205     232 .. 0.89
   2 !   16.4   3.3   7.6e-06    0.0071       9      24 .]     257     272 ..     254     272 .. 0.91
   3 ?   -0.9   0.6       2.1     2e+03      12      20 ..     393     401 ..     391     405 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.1e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCP 20 
                                       +++id++kCi C++Cv +C 
  gi|313117476|ref|YP_004044459.1| 205 FIQIDRNKCILCNRCVEACN 224
                                       689****************5 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.6e-06
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C++Cg C++vCP+g i
  gi|313117476|ref|YP_004044459.1| 257 CVSCGHCATVCPTGSI 272
                                       *************965 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.1
                            Fer4_6  12 CgdCvrvCP 20 
                                       Cg C++ C 
  gi|313117476|ref|YP_004044459.1| 393 CGFCAVGCR 401
                                       *****9996 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   4.3   1.2e-06    0.0011       1      18 [.     206     223 ..     206     223 .. 0.96
   2 !   20.6   2.7   2.8e-07   0.00027       6      24 .]     255     273 ..     254     273 .. 0.92
   3 ?   -0.1   1.2         1   9.7e+02      11      20 ..     393     402 ..     391     404 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                                       EEEETTTSSS-THHHHHS CS
                              Fer4   1 vvideekCigCGaCvevC 18 
                                       ++id +kCi C++Cve+C
  gi|313117476|ref|YP_004044459.1| 206 IQIDRNKCILCNRCVEAC 223
                                       68**************** PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.8e-07
                                       TTSSS-THHHHHSTTTEEE CS
                              Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                       + C+ CG C+ vCP+g It
  gi|313117476|ref|YP_004044459.1| 255 SECVSCGHCATVCPTGSIT 273
                                       68**************996 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1
                                       -THHHHHSTT CS
                              Fer4  11 CGaCvevCPv 20 
                                       CG C+  C +
  gi|313117476|ref|YP_004044459.1| 393 CGFCAVGCRF 402
                                       *****99965 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  12.9     0.098        92       2      47 ..     162     224 ..     107     228 .. 0.75
   2 !   27.1   8.1   3.6e-09   3.4e-06       1      50 [.     212     271 ..     212     272 .. 0.75
   3 ?    1.5   0.2      0.35   3.3e+02       3      20 ..     391     408 ..     389     432 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.098
                            Fer4_9   2 CtgC...gaCveaCpagvvvedaaerkarlraase..................eaCigCgaCveaCp 47 
                                       Ct C   g+C+   + +++  d      r+  +++                  ++Ci C++CveaC+
  gi|313117476|ref|YP_004044459.1| 162 CTTCngnGRCEL--QETAIGADVE--HPRYGVFDDraeyeplddtssfiqidrNKCILCNRCVEACN 224
                                       555533334555..2222222222..12222222233457788888889999999***********7 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 3.6e-09
                            Fer4_9   1 kCtgCgaCveaC....pagvvvedaaerkarlraase......eaCigCgaCveaCpkga 50 
                                       kC+ C++CveaC      gv + + ++   r+  +s+      ++C++Cg C+ +Cp+g 
  gi|313117476|ref|YP_004044459.1| 212 KCILCNRCVEACndvqVEGVLRIEGSGPDTRIGFQSDaetmadSECVSCGHCATVCPTGS 271
                                       7***********999844555555555555555555567777778************985 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.35
                            Fer4_9   3 tgCgaCveaCpagvvved 20 
                                       t Cg C   C ++++ +d
  gi|313117476|ref|YP_004044459.1| 391 TTCGFCAVGCRFEMWGKD 408
                                       569999999988887766 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.9       1.2   1.1e+03       2      12 ..     162     172 ..     109     177 .. 0.79
   2 !   24.3   7.3   3.3e-08   3.2e-05       3      64 ..     211     270 ..     209     271 .. 0.78
   3 ?    0.3   0.1         1   9.8e+02       7      16 ..     392     401 ..     391     458 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.2
                            Fer4_8   2 lekCieCgaCq 12 
                                       +  C+++g+C+
  gi|313117476|ref|YP_004044459.1| 162 CTTCNGNGRCE 172
                                       45666777775 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.3e-08
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk..khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       +kCi C +C +aC  ++ ++  +   + ++ +++  q++ +     a  +C++cg+C++vCp+g
  gi|313117476|ref|YP_004044459.1| 211 NKCILCNRCVEACNDVQVEGvlRIEGSGPDTRIG-FQSDAE---TMADSECVSCGHCATVCPTG 270
                                       69***********977776654777888888888.444444...24569*************86 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1
                            Fer4_8   7 eCgaCqsaCp 16 
                                        Cg+C   C 
  gi|313117476|ref|YP_004044459.1| 392 TCGFCAVGCR 401
                                       5777777773 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3       3.4   3.2e+03      44      48 ..     161     165 ..     151     173 .. 0.57
   2 !   20.5  13.5     4e-07   0.00038       2      56 .]     206     268 ..     205     268 .. 0.81
   3 !   13.4   2.4   6.9e-05     0.065       6      23 ..     254     271 ..     249     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.4
                           Fer4_10  44 kCtgc 48 
                                       +Ct+c
  gi|313117476|ref|YP_004044459.1| 161 RCTTC 165
                                       34444 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl.........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++id+++Ci C++Cv+aC  d+          s   + +  +++a+  + ++C  cg C+ +CP
  gi|313117476|ref|YP_004044459.1| 206 IQIDRNKCILCNRCVEAC-NDVqvegvlrieGSGPDTRIGFQSDAETMADSECVSCGHCATVCP 268
                                       689***************.5559*****9964444455556666666688*************9 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 6.9e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadl 23 
                                       d+ C+ Cg C ++CP+  
  gi|313117476|ref|YP_004044459.1| 254 DSECVSCGHCATVCPTGS 271
                                       678************943 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.3     0.015        14       1      12 [.     212     223 ..     208     233 .. 0.88
   2 !   17.7   2.4   5.3e-06     0.005       2      20 ..     257     275 ..     256     280 .. 0.93
   3 ?   -2.1   0.4       8.5     8e+03      55      64 ..     391     400 ..     384     403 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                           Fer4_16   1 rCgtCgkCaevC 12 
                                       +C+ C++C+e+C
  gi|313117476|ref|YP_004044459.1| 212 KCILCNRCVEAC 223
                                       599999999999 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 5.3e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++Cg Ca vCPt+ i+ek
  gi|313117476|ref|YP_004044459.1| 257 CVSCGHCATVCPTGSITEK 275
                                       ****************997 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 8.5
                           Fer4_16  55 tgCdiCqdvC 64 
                                       t C+ C+  C
  gi|313117476|ref|YP_004044459.1| 391 TTCGFCAVGC 400
                                       5566666555 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.2e-05     0.021      10      57 ..     987    1033 ..     979    1040 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                                        -CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTST.TT CS
                           CDC48_N   10 edvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepede.gk 57  
                                        ++vg + v i+pe+ +++g+e g++v++e +r   aiv+ a   d+ g+
  gi|313117476|ref|YP_004044459.1|  987 SHVGESFVEISPETAAQIGVEDGEYVRVESRR--GAIVVKATITDRvGN 1033
                                        489**************************988..677777766666555 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.77   7.2e+02      72      89 ..     155     172 ..     124     177 .. 0.73
   2 ?    7.9   0.2    0.0057       5.4      76      93 ..     207     224 ..     191     227 .. 0.85
   3 ?   10.9   2.1   0.00067      0.63       1      15 [.     256     270 ..     247     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.77
                           Fer4_22  72 efkekfgesgCvGCgRCi 89 
                                         +++   ++C G gRC+
  gi|313117476|ref|YP_004044459.1| 155 LSNHNLRCTTCNGNGRCE 172
                                       45566678899******7 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0057
                           Fer4_22  76 kfgesgCvGCgRCieacp 93 
                                       ++++++C+ C+RC+eac+
  gi|313117476|ref|YP_004044459.1| 207 QIDRNKCILCNRCVEACN 224
                                       67999************7 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00067
                           Fer4_22   1 rClsCgaCtlvCptC 15 
                                       +C+sCg+C++vCpt 
  gi|313117476|ref|YP_004044459.1| 256 ECVSCGHCATVCPTG 270
                                       589999999999985 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.4       7.5     7e+03      12      17 ..     109     114 ..     108     115 .. 0.79
   2 ?   -2.3   1.8       6.7   6.3e+03       9      16 ..     161     171 ..     158     173 .. 0.71
   3 ?   15.3   2.5   1.6e-05     0.015       3      20 ..     206     223 ..     204     224 .. 0.94
   4 ?   13.5   4.6   6.2e-05     0.059       5      22 .]     253     269 ..     250     269 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.5
                            Fer4_2  12 gCgaCv 17 
                                       +C++C+
  gi|313117476|ref|YP_004044459.1| 109 ECRTCI 114
                                       799995 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.7
                            Fer4_2   9 rCigC...gaC 16 
                                       rC+ C   g C
  gi|313117476|ref|YP_004044459.1| 161 RCTTCngnGRC 171
                                       79999544577 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.6e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       +++d+++Ci C+ Cv aC
  gi|313117476|ref|YP_004044459.1| 206 IQIDRNKCILCNRCVEAC 223
                                       789*************** PP

  == domain 4  score: 13.5 bits;  conditional E-value: 6.2e-05
                            Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                       +d++ C++Cg C ++CP+
  gi|313117476|ref|YP_004044459.1| 253 ADSE-CVSCGHCATVCPT 269
                                       5777.************7 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   3.8     0.012        11      84      98 ..     212     226 ..     205     235 .. 0.86
   2 ?   13.4   2.0   7.2e-05     0.068      53      78 ..     249     274 ..     234     278 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                           Fer4_18  84 eciscllcidacdkv 98 
                                       +ci c +c++ac++v
  gi|313117476|ref|YP_004044459.1| 212 KCILCNRCVEACNDV 226
                                       7***********998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.2e-05
                           Fer4_18  53 rkekgagdcidcescvkvcPtgidir 78 
                                        ++ ++++c++c++c +vcPtg    
  gi|313117476|ref|YP_004044459.1| 249 AETMADSECVSCGHCATVCPTGSITE 274
                                       4567889**************96555 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.7   0.00098      0.92       1      19 [.     208     226 ..     208     229 .. 0.95
   2 ?    6.3   3.9     0.015        14       2      17 ..     254     268 ..     253     270 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00098
                           Fer4_13   1 VDrdtCiacgaCvelaPdv 19 
                                       +Dr++Ci c+ Cve++ dv
  gi|313117476|ref|YP_004044459.1| 208 IDRNKCILCNRCVEACNDV 226
                                       8***************997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       D ++C++cg C+ ++P
  gi|313117476|ref|YP_004044459.1| 254 D-SECVSCGHCATVCP 268
                                       5.89************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  11.7    0.0058       5.4       1      64 [.     206     272 ..     206     272 .. 0.79
   2 ?    4.1   1.7     0.084        79       6      20 ..     255     269 ..     251     311 .. 0.80
   3 ?   -2.5   0.0       9.6   9.1e+03      21      47 ..     934     958 ..     928     961 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0058
                           Fer4_15   1 VvvDrdaCigcglCvaea.....pevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64 
                                       + +Dr++Ci c++Cv+++     + v ++++ g ++ ++ +++   ++ +d e       a +CP++ I
  gi|313117476|ref|YP_004044459.1| 206 IQIDRNKCILCNRCVEACndvqvEGVLRIEGSGPDTRIGFQSD--AETMADSECVSCGHCATVCPTGSI 272
                                       68****************8888888888888888877765444..568888888888888888888765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.084
                           Fer4_15   6 daCigcglCvaeape 20 
                                       ++C +cg C++++p+
  gi|313117476|ref|YP_004044459.1| 255 SECVSCGHCATVCPT 269
                                       58***********85 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 9.6
                           Fer4_15  21 vfeldedglasvllddgeiaegevpdd 47 
                                        f +d dgla+++ +dg    ge+pd+
  gi|313117476|ref|YP_004044459.1| 934 NFNFD-DGLARFVPADGG-HPGELPDE 958
                                       57777.9***99955444.56788886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1098 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 6827.62
//
Query:       gi|313117477|ref|YP_004044460.1|  [L=90]
Description: hypothetical protein Hbor_32680 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.2   0.4       0.35   10.6   0.4    1.3  1  WW_1      WW domain


Domain annotation for each model (and alignments):
>> WW_1  WW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4     2e-05      0.35       5      15 ..      29      39 ..      28      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2e-05
                              WW_1  5 iihENGrPmYY 15
                                      ++hENGr  YY
  gi|313117477|ref|YP_004044460.1| 29 LVHENGRHEYY 39
                                      69*****9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 617.06
//
Query:       gi|313117478|ref|YP_004044461.1|  [L=66]
Description: hypothetical protein Hbor_32690 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0062   16.6   0.5     0.0062   16.6   0.5    1.6  2  Zn-ribbon_8    Zinc ribbon domain
      0.008   16.1   0.1      0.017   15.0   0.1    1.6  1  zinc_ribbon_4  zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.3   4.2       0.15   11.6   0.9    2.3  2  TF_Zn_Ribbon   TFIIB zinc-binding
       0.05   13.8   1.7      0.087   13.0   0.1    2.1  2  zf-RING_7      C4-type zinc ribbon domain
      0.083   12.3   0.1      0.083   12.3   0.1    1.9  2  zf-ribbon_3    zinc-ribbon domain
       0.13   12.5   0.3       0.13   12.5   0.3    2.4  2  zinc_ribbon_9  zinc-ribbon
        7.1    6.6   8.0         73    3.4   8.0    2.3  1  Prok-RING_1    Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       2.4   6.1e+03      29      33 ..       5       9 ..       3      12 .. 0.57
   2 !   16.6   0.5   2.4e-06    0.0062       9      35 ..      34      64 ..      34      66 .] 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.4
                       Zn-ribbon_8 29 CPeCg 33
                                      C  C+
  gi|313117478|ref|YP_004044461.1|  5 CYFCH 9 
                                      44454 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.4e-06
                       Zn-ribbon_8  9 eeCghefevlqsisdap...ltaCPeCgs.e 35
                                      eeC + +e + +++++p   +++CPeCg+ e
  gi|313117478|ref|YP_004044461.1| 34 EECARGYELVDESDEDPgdvKVTCPECGAvE 64
                                      5899*******999777896666*****966 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   6.6e-06     0.017       7      34 ..      35      63 ..      34      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.6e-06
                     zinc_ribbon_4  7 sCkakyeiddek.lpakgvkvrCskCghv 34
                                      +C   ye+ de    ++ vkv+C+ Cg+v
  gi|313117478|ref|YP_004044461.1| 35 ECARGYELVDESdEDPGDVKVTCPECGAV 63
                                      7888899877773559999*******986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0068        17      22      32 ..       5      16 ..       4      20 .. 0.90
   2 ?   11.6   0.9   5.8e-05      0.15      13      28 ..      48      63 ..      35      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0068
                                      ESSS.SBEEEEC CS
                      TF_Zn_Ribbon 22 CtdC.GlVledn 32
                                      C +C GlVl d+
  gi|313117478|ref|YP_004044461.1|  5 CYFChGLVLPDE 16
                                      999******997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.8e-05
                                      EETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon 13 eDpergelvCtdCGlV 28
                                      eDp    ++C++CG+V
  gi|313117478|ref|YP_004044461.1| 48 EDPGDVKVTCPECGAV 63
                                      577777789*****99 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.37   9.4e+02      20      31 ..      27      38 ..       5      38 .. 0.54
   2 ?   13.0   0.1   3.4e-05     0.087      16      31 ..      45      62 ..      41      63 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.37
                                      STB-EE-TTT-- CS
                         zf-RING_7 20 gdevvtCpeCGR 31
                                         v+  +eC R
  gi|313117478|ref|YP_004044461.1| 27 EHRVFLHEECAR 38
                                      244666677755 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.4e-05
                                      HHCCS.TB-.EE-TTT-- CS
                         zf-RING_7 16 elrag.dev.vtCpeCGR 31
                                      e++   ++v vtCpeCG+
  gi|313117478|ref|YP_004044461.1| 45 ESDEDpGDVkVTCPECGA 62
                                      5555555566*******7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   1.9       6.8   1.7e+04      19      22 ..       5       8 ..       5       8 .. 0.78
   2 ?   12.3   0.1   3.2e-05     0.083       2      11 ..      54      63 ..      53      66 .] 0.80

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 6.8
                       zf-ribbon_3 19 CpyC 22
                                      C+ C
  gi|313117478|ref|YP_004044461.1|  5 CYFC 8 
                                      8888 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.2e-05
                       zf-ribbon_3  2 tvrCPnCGap 11
                                      +v+CP+CGa+
  gi|313117478|ref|YP_004044461.1| 54 KVTCPECGAV 63
                                      689*****97 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   2.2      0.27     7e+02       3       6 ..       6       9 ..       4      21 .. 0.80
   2 ?   12.5   0.3   5.2e-05      0.13       7      28 ..      35      61 ..      35      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.27
                     zinc_ribbon_9 3 yWCh 6
                                     y+Ch
  gi|313117478|ref|YP_004044461.1| 6 YFCH 9
                                     7777 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.2e-05
                     zinc_ribbon_9  7 qCdrfVsvspdedsd.....vlCPhCg 28
                                      +C+r  ++  ++d+d     v+CP+Cg
  gi|313117478|ref|YP_004044461.1| 35 ECARGYELVDESDEDpgdvkVTCPECG 61
                                      5888888877778888887669****8 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   8.0     0.029        73      18      29 ..      51      63 ..       1      64 [. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.029
                       Prok-RING_1 18 dDi.VvCpeCgtp 29
                                       D+ V+CpeCg++
  gi|313117478|ref|YP_004044461.1| 51 GDVkVTCPECGAV 63
                                      455499*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 473.51
//
Query:       gi|313117479|ref|YP_004044462.1|  [L=287]
Description: serine acetyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-10   40.5   6.6    4.5e-06   26.2   1.9    2.4  2  Hexapep    Bacterial transferase hexapeptide (six repeats)
    5.1e-06   26.8   0.0    8.7e-06   26.1   0.0    1.3  1  SATase_N   Serine acetyltransferase, N-terminal
     0.0045   16.7   0.9     0.0045   16.7   0.9    2.5  2  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   7.6e-07    0.0046       2      35 ..     174     209 ..     170     210 .. 0.92
   2 !   26.2   1.9   7.5e-10   4.5e-06       4      34 ..     233     263 ..     230     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.6e-07
                                       EEEETTEEE-T..TEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgp..faviggnVkIGdnvkIgagvvig 35 
                                       + IG+  +I++  ++vig+ +++Gd v+I   v++g
  gi|313117479|ref|YP_004044462.1| 174 AEIGEYFFIDHgtGVVIGETATVGDWVRIYQDVTLG 209
                                       789**************************9999887 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 7.5e-10
                                       EETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       IG++v+Ig++++++g +++Gd+v +ga++ +
  gi|313117479|ref|YP_004044462.1| 233 IGDHVVIGAGTKVLGAITVGDHVSVGANSWV 263
                                       9***************************977 PP

>> SATase_N  Serine acetyltransferase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.5e-09   8.7e-06      57     103 ..      91     137 ..      85     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHH-THHHHHHHHHHHHHHHH-TT---THHHHHH-HHHHHH CS
                          SATase_N  57 elfeealeadpeiveaaraDlkAvlerDpAcksylepllyfKGFhAl 103
                                       +++e++l++ p+i++++++D++A ++ DpA+k+y+e++  + GF A+
  gi|313117479|ref|YP_004044462.1|  91 RTVEQILNELPKIRATLKKDVEAAYKGDPAAKTYMEIIRSYPGFLAI 137
                                       578999***************************************98 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.6     0.037   2.2e+02      16      27 ..     186     197 ..     170     210 .. 0.67
   2 !   16.7   0.9   7.5e-07    0.0045       4      32 ..     233     263 ..     232     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.037
                                       ESEEE-TT-EE- CS
                         Hexapep_2  16 iGvslGdncvvg 27 
                                       +Gv +G+ ++vg
  gi|313117479|ref|YP_004044462.1| 186 TGVVIGETATVG 197
                                       356666555554 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.5e-07
                                       E-TT-EE-TT-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2   4 IGdnCliGanagi.G.vslGdncvvgaGvvi 32 
                                       IGd ++iGa   + G +++Gd + vga++ +
  gi|313117479|ref|YP_004044462.1| 233 IGDHVVIGAGTKVlGaITVGDHVSVGANSWV 263
                                       9***********8899************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1953.40
//
Query:       gi|313117480|ref|YP_004044463.1|  [L=896]
Description: P-type ATPase, translocating [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-56  190.5   3.7    1.8e-56  190.5   3.7    2.9  3  E1-E2_ATPase     E1-E2 ATPase
    1.7e-34  119.1   6.4    1.7e-34  119.1   6.4    2.3  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    4.2e-28   99.1   4.8      2e-27   96.9   4.8    2.2  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.2e-17   62.0   0.0    6.5e-17   61.0   0.0    1.6  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    6.2e-14   51.8   0.0    1.8e-13   50.4   0.0    1.8  1  Cation_ATPase    Cation transport ATPase (P-type)
    4.7e-06   26.5   0.2    0.00016   21.5   0.6    2.2  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.035   14.5   3.0      0.043   14.2   0.7    2.3  2  HAD              haloacid dehalogenase-like hydrolase
       0.05   12.3   2.7      0.087   11.5   2.7    1.3  1  EMP70            Endomembrane protein 70
        4.1    6.7   5.3        4.6    6.6   3.8    1.7  2  DUF2417          Region of unknown function (DUF2417)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.021        42     106     140 ..      43      77 ..      37      91 .. 0.63
   2 !  190.5   3.7   8.9e-60   1.8e-56       2     180 ..     110     302 ..     109     303 .. 0.96
   3 ?   -2.8   1.2         2     4e+03     121     126 ..     782     787 ..     744     829 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.021
                                       ----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STT CS
                      E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvflialll 140
                                       +++ pl  +l ++++ l++v ll+a+l f i  ++
  gi|313117480|ref|YP_004044463.1|  43 RQRGPLRIFLAQFSSALIWVLLLAAVLSFSIGHTV 77 
                                       56677777777777777777777777777665443 PP

  == domain 2  score: 190.5 bits;  conditional E-value: 8.9e-60
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............G CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............e 65 
                                       l+ pt++v+rdg e++++a elvpGDiv++ +gd+vpaD+r+ve ++ e+desaLTGEs+pv+k            e
  gi|313117480|ref|YP_004044463.1| 110 LTTPTVTVRRDGDEQSVEATELVPGDIVVVGQGDVVPADCRLVEAQNmEIDESALTGESVPVKKtteavnadtplaE 186
                                       7899************************************************************************* PP

                                       -TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTS CS
                      E1-E2_ATPase  66 kgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgk 142
                                       +++m++ Gt+v++g+ +avV+ tg++te+g ia+++++a+  +tplq+ ld+lg+ l + v++++++++ +++++g+
  gi|313117480|ref|YP_004044463.1| 187 RESMAYKGTNVTRGRGVAVVVSTGMETEVGSIAEALSSAEDLQTPLQQDLDRLGRRLGLGVVALSAVLVPLLVFVGG 263
                                       ***********************************************************999999999988888776 PP

                                       STT.HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 143 sla.eallralallvaaiPcaLplavplalalgarrlak 180
                                           ++ l a++l+vaa+P++Lp++v+l+lalg+rr+a+
  gi|313117480|ref|YP_004044463.1| 264 RSLvQSGLTAVSLAVAAVPEGLPAVVTLTLALGVRRMAD 302
                                       6666*********************************97 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2
                                       HHHHHH CS
                      E1-E2_ATPase 121 vlvpvv 126
                                       + +++v
  gi|313117480|ref|YP_004044463.1| 782 YAMTMV 787
                                       222222 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.2   2.5e+03     129     161 ..     245     275 ..     232     295 .. 0.62
   2 ?   -2.2   0.2       1.4   2.9e+03     119     146 ..     669     697 ..     658     701 .. 0.73
   3 !  119.1   6.4   8.4e-38   1.7e-34       2     178 ..     703     869 ..     702     872 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                   Cation_ATPase_C 129 llaillslllqvlivyvpglnavfgtaplslee 161
                                       l++++ls++l+ l+v+v  ++++   + l++ +
  gi|313117480|ref|YP_004044463.1| 245 LGVVALSAVLVPLLVFVG-GRSL-VQSGLTAVS 275
                                       677889999999999993.3333.333333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                   Cation_ATPase_C 119 fsglfsnkllllaillsl.llqvlivyvp 146
                                        + +f n + ++a lls+ +  vl+v++ 
  gi|313117480|ref|YP_004044463.1| 669 GRTIFDNVWKFVAYLLSAnVAEVLVVFIA 697
                                       45678999999999999988888888873 PP

  == domain 3  score: 119.1 bits;  conditional E-value: 8.4e-38
                   Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgi 78 
                                       l+l a+q+LwinL+tD+lpalaL+++p   d+m+r Pr++   +i++ ml  i + g++++++ l ++f+tl   g+
  gi|313117480|ref|YP_004044463.1| 703 LILPAVQLLWINLLTDGLPALALGTDPSG-DVMDRTPRDRVTGIIDRMMLELISGAGVTVTVLMLGLMFYTLN--GA 776
                                       67899*********************986.******************************************9..54 PP

                   Cation_ATPase_C  79 sekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgta 155
                                        + +      ya+tm+F+ +vl+++++++++r ++e       +fsn +l +a+++slllq++++y+p l+++fgt+
  gi|313117480|ref|YP_004044463.1| 777 PSVT-----PYAMTMVFTGFVLFEFVKLYVVRWTKE-----TPTFSNAWLAVAVVASLLLQLAVLYTP-LRTYFGTV 842
                                       5544.....47**********************444.....7889**********************9.******** PP

                   Cation_ATPase_C 156 plsleew...lialllalvvllv.del 178
                                       pls+++w     +ll ++ vl++ + +
  gi|313117480|ref|YP_004044463.1| 843 PLSVSDWgllGAVLLTGAPVLVLvGWV 869
                                       *******77544466666665552444 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   4.8     1e-30     2e-27       1     210 []     319     633 ..     319     633 .. 0.71

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 1e-30
                                       SSEEEEESBTTTBCHHHHHHHHHHHH......................................CHHHHHHHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx......................................xxxxxxxxxxx.. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa......................................alalaaaletg.. 37 
                                       +++v+ Dk+GTLt+ge++v+ ++v+                                       +    + le+g  
  gi|313117480|ref|YP_004044463.1| 319 VDVVCTDKTGTLTEGEMRVRGAWVYGqafdigrdsagnpaekatsesadkgrdkpadeeageraDERFDRLLEIGal 395
                                       689***********************777777777777776666666666666666666666664444444444455 PP

                                       .......HHCHHHHHHHHHHHHH............HHHHHHHHHETTTE..................HHHHTHHH.. CS
                                       .......xxxxxxxxxxxxxxxx............xxxxxxxxxxxxxx..................xxxxxxxx.. RF
                         Hydrolase  38 .......sehpigkalvaaakar............sgaltgfatfigrg..................ayaigkpe.. 75 
                                                 p  +alvaaa+ r            +                               +y +g p+  
  gi|313117480|ref|YP_004044463.1| 396 cndatteEGDPTERALVAAAERRfdvaarraerprR------------DevpfsserkrmatihddvVYVKGAPDei 460
                                       555566666777777777777775444444433330............23444444444444444556666666644 PP

                                       ......HHHHH...HCHHHHHHHHHHHHHHCHHHHHH.................TTHHHHHHHHHHTHHBHTTHHHH CS
                                       ......xxxxx...xxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  76 ......wltal...dippdlgaaigsaqsqgrtvall.................qaralavftiadplkvkpeaaea 126
                                              lta+   ++ +d++ +i +  ++    al                  +   +++  + dp  +++e+++a
  gi|313117480|ref|YP_004044463.1| 461 lrrttrVLTAEgitTMDDDVRTRIRDQIDEFAADALRvlafaykdrdddggpeeNLIFVGLQGLIDP--PREEVRDA 535
                                       333333444445665556666666655555555555599999****9999988777888899999**..******** PP

                                       HHHHHHTTEEEEEEESSEHHHHHHHHHHTT..GGGE.SEEEEHHCES...........STTTSHHHHHHHHHHHTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxxxxxxxx...........xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 127 vasLkaagievvlltgdnpetaeraanqlG..ddyf.daviasdiet...........vakpspegkvaaireLqgk 189
                                       ++  k+agi+v ++tgd+p+t +++a+q+G   d +  a ++s +e            +a ++p++kv++++ Lq++
  gi|313117480|ref|YP_004044463.1| 536 IEDTKRAGIDVKVITGDHPTTGQAIASQVGveSDVLsGADVDSMDEDelrervedvdvFARAEPSHKVRILKSLQAN 612
                                       ******************************99444445555555555688888889999999*************** PP

                                       GGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 190 peevamVGDgvnDaaalaaAg 210
                                       +++vam GDg+nDa+al++A+
  gi|313117480|ref|YP_004044463.1| 613 GHRVAMTGDGINDAPALKNAD 633
                                       *******************98 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   3.3e-20   6.5e-17       1      69 []       3      70 ..       3      70 .. 0.99

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.3e-20
                   Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      +ha ++ee +e+L+ +  +GL+  +aaer ++ GpNe++ ++++  ++++l qf++ l+++Ll aa++s
  gi|313117480|ref|YP_004044463.1|  3 WHARDPEESYEELD-TTASGLSATDAAERYETVGPNEITGERQRGPLRIFLAQFSSALIWVLLLAAVLS 70
                                      9************9.89**************************************************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   9.1e-17   1.8e-13      16      90 ..     399     466 ..     361     467 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 9.1e-17
                     Cation_ATPase  16 evkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCth 90 
                                       +++  G++tE AL+ +ae+   d+   r+e ++  e+pF+s+rKrm++++        ++yvKGAp+ il+r t+
  gi|313117480|ref|YP_004044463.1| 399 ATTEEGDPTERALVAAAERR-FDVAARRAERPRRDEVPFSSERKRMATIHDD------VVYVKGAPDEILRRTTR 466
                                       55577**************9.******************************6......7************9886 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.056   1.1e+02      18      66 ..     530     576 ..     526     593 .. 0.84
   2 !   21.5   0.6   8.1e-08   0.00016     195     251 ..     605     662 ..     602     666 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali 66 
                                       e+ ++ai+  k +gi v + TG ++++ + ++ ++g+++ v++  Ga +
  gi|313117480|ref|YP_004044463.1| 530 EEVRDAIEDTKRAGIDVKVITGDHPTTGQAIASQVGVESDVLS--GADV 576
                                       7899********************************9976665..6655 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 8.1e-08
                                       HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET.TS-HHHHHHSSEEE--GGGTHH CS
                       Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmg.naseevkkaAdyvtksnnedGV 251
                                       ++k l+ +  +v+  GDg ND + L+ a++g+Amg  +++ +k+a+d +  + n   +
  gi|313117480|ref|YP_004044463.1| 605 ILKSLQANGHRVAMTGDGINDAPALKNADVGIAMGvRGTDVAKQASDIILLDDNYATI 662
                                       7899******************************956888888888887776665555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.84   1.7e+03      43     123 ..     389     469 ..     367     520 .. 0.57
   2 ?   14.2   0.7   2.2e-05     0.043      85     188 .]     524     630 ..     446     630 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.84
                               HAD  43 frellrldraglaelleallaglseelaaelerfvaevirpklldp.galellaahraaGdrvvvvSgglrplvepl 118
                                       + e++ l ++++ e  + + ++l ++ +++++ + +++ rp+  d+  +    ++ +  +d vv v g+++++++++
  gi|313117480|ref|YP_004044463.1| 389 LLEIGALCNDATTEEGDPTERALVAAAERRFDVAARRAERPR-RDEvPFSSERKRMATIHDDVVYVKGAPDEILRRT 464
                                       556666666666666666666666666666666666666666.4444333333322245555555555555555555 PP

                               HAD 119 laelg 123
                                        + l 
  gi|313117480|ref|YP_004044463.1| 465 TRVLT 469
                                       54444 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.2e-05
                               HAD  85 lldp...galellaahraaGdrvvvvSgglrplvepllaelg..adevlatelevdd..rltgelglegkpvrgegk 154
                                       l+dp   +++++++  ++aG+ v v++g +    ++++ ++g  +d + + ++++ d   l  +  +e+ +v+ ++ 
  gi|313117480|ref|YP_004044463.1| 524 LIDPpreEVRDAIEDTKRAGIDVKVITGDHPTTGQAIASQVGveSDVLSGADVDSMDedELRER--VEDVDVFARAE 598
                                       5555566***********************************9777777777777778655555..66666666555 PP

                               HAD 155 vaalrewlaaegegidleevvayGDspsDlpllr 188
                                       +++  +    ++  +  ++v   GD+++D p+l+
  gi|313117480|ref|YP_004044463.1| 599 PSHKVR--ILKSLQANGHRVAMTGDGINDAPALK 630
                                       544444..333344444557777*********96 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.7   4.3e-05     0.087     256     346 ..     736     832 ..     730     841 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.3e-05
                             EMP70 256 rpPkn.......sllLsvlvGsGvqlllmalvtlllallgflspsnrgslltvalllyvllgliaGYvsarlyktfg 325
                                       r+P+        +++L ++ G Gv +++++l++++ +l g   ps +   +t++++ +vl+ +++ Yv  ++ +t  
  gi|313117480|ref|YP_004044463.1| 736 RTPRDrvtgiidRMMLELISGAGVTVTVLMLGLMFYTLNGA--PSVTPYAMTMVFTGFVLFEFVKLYVVRWTKETPT 810
                                       55555566666689***********************9888..99999**********************9988765 PP

                             EMP70 326 .gekwkkntlltalllpgllfl 346
                                        ++ w   +++ +lll + ++ 
  gi|313117480|ref|YP_004044463.1| 811 fSNAWLAVAVVASLLLQLAVLY 832
                                       2369999999999998877765 PP

>> DUF2417  Region of unknown function (DUF2417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.6   3.2e+03     171     205 ..      40      73 ..      26      89 .. 0.73
   2 ?    6.6   3.8    0.0023       4.6      87     158 ..     759     829 ..     753     836 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                           DUF2417 171 tgreetrhtlkewlsilvrniikllllvvlilltl 205
                                       tg+  +r +l+ +l+ + + +i +lll++++ +++
  gi|313117480|ref|YP_004044463.1|  40 TGE-RQRGPLRIFLAQFSSALIWVLLLAAVLSFSI 73 
                                       444.4677788888888888888888888877765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0023
                           DUF2417  87 lslianllnllf...fglpSkldrvlnivlavLllvnllllllvkytReregfvgiasvlWaaltfllgilldry 158
                                       ++++ ++l l+f    g pS   + + +v ++++l++++ l++v+ t+e   f +    +W a+ ++ ++ll+  
  gi|313117480|ref|YP_004044463.1| 759 VTVTVLMLGLMFytlNGAPSVTPYAMTMVFTGFVLFEFVKLYVVRWTKETPTFSN----AWLAVAVVASLLLQLA 829
                                       678888999999888899******************************9876655....4555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (896 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.74u 0.27s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 5462.65
//
Query:       gi|313117481|ref|YP_004044464.1|  [L=193]
Description: VIT family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-09   37.7   2.3    1.9e-09   37.7   2.3    2.0  2  VIT1      VIT family
  ------ inclusion threshold ------
          4    7.6   8.5         85    3.3   6.6    3.4  2  GPHR_N    The Golgi pH Regulator (GPHR) Family N-terminal


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   3.1      0.13   1.2e+03       4      42 ..      25      63 ..      22      69 .. 0.81
   2 !   37.7   2.3   2.2e-13   1.9e-09     113     212 ..      87     190 ..      72     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.13
                              VIT1  4 avlGanDGLvspfalvaGlsaaslgssktvllaGlaell 42
                                      +v    DG ++ +++++G + +++ +  tv+  G+  ++
  gi|313117481|ref|YP_004044464.1| 25 FVSNGFDGTLTSIGIIVGAVLSGIPDGFTVVKIGVGAAV 63
                                      566677999999999999999999899999999987766 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 2.2e-13
                              VIT1 113 allelmlreelgpsa.seelasplkaAlssalsfliGgliPllpylfve...svglalvvsiavtllalllfGavka 185
                                       +l+++ml +  + +  +++      +A  s+l+ liG l+Pl+p+ f     s+ +a +v +a+ + +l++fGa  +
  gi|313117481|ref|YP_004044464.1|  87 RLERAMLVDLDDTQIeRKKRGARTVHATLSGLGPLIGILVPLVPFAFEGsvfSMAEAGFVGVALGTGILAVFGAYMG 163
                                       34444444333333313344667889********************9665677888888888*************** PP

                              VIT1 186 lltgssklvsalrmlliGalAaaaayl 212
                                        ++g+++ vsa+rm+l G++ a++ ++
  gi|313117481|ref|YP_004044464.1| 164 SISGQRWYVSAFRMALAGLVVAGINVV 190
                                       **********************99876 PP

>> GPHR_N  The Golgi pH Regulator (GPHR) Family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   6.6    0.0094        85      12      56 ..      35      94 ..      32     106 .. 0.70
   2 ?   -0.3   0.0      0.13   1.2e+03      17      26 ..     110     119 ..     110     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0094
                            GPHR_N 12 sviGvtlmAiLSG...........fGa.v....stpyetfslfkrpvteadinslearleh 56
                                      + iG+++ A+LSG           +Ga v    s+++++++  +r  t+adi++le+++  
  gi|313117481|ref|YP_004044464.1| 35 TSIGIIVGAVLSGipdgftvvkigVGAaVglgtSAVWSVWEI-ERAETRADIRRLERAMLV 94
                                      569**********88888888888555223333777777775.888899999999987654 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.13
                            GPHR_N  17 tlmAiLSGfG 26 
                                       t+ A LSG G
  gi|313117481|ref|YP_004044464.1| 110 TVHATLSGLG 119
                                       788*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1249.59
//
Query:       gi|313117482|ref|YP_004044465.1|  [L=96]
Description: hypothetical protein Hbor_32730 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-34  115.4   0.6    1.1e-33  115.3   0.6    1.0  1  DUF211    Uncharacterized ArCR, COG1888


Domain annotation for each model (and alignments):
>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.6   5.9e-38   1.1e-33       2      88 ..       4      90 ..       3      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 5.9e-38
                                      EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEE CS
                            DUF211  2 irrlvLDvlkphepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevva 80
                                       rr+vLDvlkph+p + ++++++a+ e+vd+++ +++e+D+e++n+kit+eG+ +dy +iee+ie+lgg++hS+D+v+ 
  gi|313117482|ref|YP_004044465.1|  4 ARRIVLDVLKPHDPPLRKFTEHIADAETVDAATGSLIELDQEVQNVKITVEGTALDYVAIEESIENLGGTVHSVDQVAY 82
                                      59***************************************************************************** PP

                                      ESS----- CS
                            DUF211 81 Gkkiveev 88
                                      G++ive++
  gi|313117482|ref|YP_004044465.1| 83 GEYIVEDH 90
                                      ******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 603.34
//
Query:       gi|313117483|ref|YP_004044466.1|  [L=384]
Description: site-specific recombinase XerD [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-09   36.6   0.0      5e-08   32.9   0.0    2.6  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.029   14.7   0.0    1.4  1  Phage_int_SAM_5  Phage integrase SAM-like domain
      0.039   14.3   0.0       0.28   11.6   0.0    2.2  2  FdsD             NADH-dependant formate dehydrogenase delta s


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   8.3e-12     5e-08      18     170 ..     173     370 ..     151     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 8.3e-12
                                       HHHHHHHHHHHHHHHHT--HHHHTT...........-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHH CS
                   Phage_integrase  18 slkirdklllellyetGlRisElls...........LrvkdldlengvilvheregKgskeravplseealellkel 83 
                                        +++rd++l+ +l  tG+R +E+ +           L++  +d++  +++v    gK +    v ++++a e+l+++
  gi|313117483|ref|YP_004044466.1| 173 RQEVRDRALVHVLAYTGVRGAEVFRvsgdnregrqgLTWARVDTDAWTFRV---WGKAQEWEDVSVPKQAREALRRW 246
                                       689*******************97523333333333788888888888888...9999999**************** PP

                                       HHHHCHCCTTTS.BSSBET....................................TSSB--HHHHHHHHHHHHHHCT CS
                   Phage_integrase  84 lskaleeaekse.llfask....................................rgkplsrqtvrkafkraveeag 123
                                         +     ++ e  +f+ +                                    +   ++++ +r++++r++  ag
  gi|313117483|ref|YP_004044466.1| 247 RTVL--DPPSAEwPVFPTAhapskyaavrdalgtddanarldgaevddvlrdedvAPPAITTEGARRVLERIADTAG 321
                                       **99..33333332444445555555555577777777777777888888887778888****************** PP

                                       -S...SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHH.HHHHCCC CS
                   Phage_integrase 124 ie...kpltpHtlRhsfataLleagvdlrvvqkllGHssistt.qiYthva 170
                                       ++   kp+ pH  R+ ++ +L +        q++l H+s+stt + Y h +
  gi|313117483|ref|YP_004044466.1| 322 VDidgKPPLPHGARRGLGDELFRTD--RGLAQDVLRHKSLSTTkEAYSHID 370
                                       **********************986..7789*****************987 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.9e-06     0.029      17      93 ..      39     123 ..      26     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.9e-06
                                       S.-HHHHHHHHHHHHHTTTS-....S-..--TTT--HHHHHHHHHHH...HHTS---HHHHHHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5  17 g.skgtlrnykstlkhlkkFl..kkkd..itfeeidkefleeFedYL...kkkkglsentiskyfkklkavlnkAik 85 
                                       g s ++ ++ +s+l +++ +l  ++kd    fe+  +++l+++ d L    +  g+s +++++y++ +  +l  +++
  gi|313117483|ref|YP_004044466.1|  39 GdSSQYRSTAESVLSKFETWLrrRGKDtfDAFEDEGEQLLRRYSDRLaqrVEADGISASSAQTYYNVISGFLGFCVR 115
                                       335567777788888888888653344456788888889999999997665566*********************** PP

                                       TTS--S-H CS
                   Phage_int_SAM_5  86 egilkknp 93 
                                       +g l++np
  gi|313117483|ref|YP_004044466.1| 116 DGALTRNP 123
                                       *******9 PP

>> FdsD  NADH-dependant formate dehydrogenase delta subunit FdsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.33     2e+03       6      32 ..      28      54 ..      25      78 .. 0.71
   2 ?   11.6   0.0   4.6e-05      0.28      28      49 ..     139     160 ..     132     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.33
                              FdsD  6 aNqIaaffesqpdreeavegvadHikk 32
                                      a  Ia++++s +d+++  +  ++ + k
  gi|313117483|ref|YP_004044466.1| 28 AAAIARYLRSNGDSSQYRSTAESVLSK 54
                                      667999999999888876555555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.6e-05
                              FdsD  28 dHikkfWeprMRraLlayleag 49 
                                       dH ++fW+++ Rr+L+++ +++
  gi|313117483|ref|YP_004044466.1| 139 DHSQQFWTREVRRKLVQHTNDA 160
                                       899***************9554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2511.27
//
Query:       gi|313117484|ref|YP_004044467.1|  [L=374]
Description: biotin synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-15   55.2   0.0    1.3e-14   54.1   0.0    1.6  1  BATS         Biotin and Thiamin Synthesis associated domain
    2.8e-14   53.8   0.2    4.1e-12   46.8   0.0    2.3  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.096   12.3   0.2       0.23   11.1   0.2    1.6  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   2.1e-18   1.3e-14       1      86 []     238     333 ..     238     333 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.1e-18
                                       E--B----TCCCC...............HHHHHHHHHHSTTSE.CCCTCHH-HHHHHH..HHHCCT--EEE-C---T CS
                              BATS   1 siprlrpikdtpl...............lkiiaalRlllPkag.illsgResaefrdq..lllklGansisagskte 59 
                                       +++ l+p+ +t+l               l++ia++Rll P+a+ +l +gRe + + d+    +++Ga+ i +g+   
  gi|313117484|ref|YP_004044467.1| 238 PVNVLNPVAGTDLgdqfgdsatisteelLQTIAVYRLLHPNARvRLTGGREVNLDTDEqhRPFEAGADGILTGD--- 311
                                       89******99999999999999999999***********************999877768889***********... PP

                                       TTGGGSESSTT-TCCCCHHHHHHTT-E CS
                              BATS  60 vggyaflttdgrsleedvkmleelGle 86 
                                            +ltt+g+s+ +d++ +e++Gl+
  gi|313117484|ref|YP_004044467.1| 312 -----YLTTEGQSPGDDIEIVERAGLQ 333
                                       .....********************96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   6.8e-16   4.1e-12       6     159 ..      67     221 ..      65     229 .. 0.85
   2 !    4.9   0.0    0.0051        30      22     101 ..     253     331 ..     242     358 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 6.8e-16
                                       EESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE...SSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilg...ggepllypdfvellerlaklavpg 77 
                                        C+ +C fCa++ +     +++ +l +ee+l+ +k++ +++g  ++ i++   g     +p++ e++ ++++l  ++
  gi|313117484|ref|YP_004044467.1|  67 NCAEDCGFCAQSVHfDTGIDTYGFLGPEEVLAAAKRA-ERDGaQRFGIVVaekGVSKEKRPEEWEEVIQAIRLVRDE 142
                                       5**************9*********************.9***5555555555555555557777777777777699* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpG 154
                                         + v ++ + ++ee +e l+  g++++++++e+     + + +  +h+f +++e+le++++ag++  + +++++ G
  gi|313117484|ref|YP_004044467.1| 143 TDVEVDASLGILTEEEAEILASEGINHYNHNIETSPAY-FPEVV-STHSFADRVETLERAKAAGMD-LCAGVILGMG 216
                                       **************************************.*****.99*******************.7777777766 PP

                                       TSHHH CS
                                       xxxxx RF
                       Radical_SAM 155 endee 159
                                       e   +
  gi|313117484|ref|YP_004044467.1| 217 EAPTD 221
                                       65555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTEEEEEEECSSCHGHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  22 regrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlakla...vpgiritvetngtlpdeekl 94 
                                       + g+++++s+ee+l+ +  ++  ++++++ + gg e++l+ d++   +++ +      +     ++t g  p  + +
  gi|313117484|ref|YP_004044467.1| 253 QFGDSATISTEELLQTIAVYRlLHPNARVRLTGGREVNLDTDEQHRPFEAGADGiltGD----YLTTEGQSP-GDDI 324
                                       5788999**************87877999999999*****9999998888887333222....344444444.4445 PP

                                       HHHHHTT CS
                                       xxxxxxx RF
                       Radical_SAM  95 erllelg 101
                                       e   ++g
  gi|313117484|ref|YP_004044467.1| 325 EIVERAG 331
                                       5555555 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   3.9e-05      0.23      10      76 ..      83     147 ..      78     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.9e-05
                                       TCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEE CS
                       Pterin_bind  10 sfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpi 76 
                                          d+  f+ ++++la+a++  ++GA+   i +++   g +     ee+e v++ ++ +rde+dv +
  gi|313117484|ref|YP_004044467.1|  83 TGIDTYGFLGPEEVLAAAKRAERDGAQRFGIVVAEK--GVSKEKRPEEWEEVIQAIRLVRDETDVEV 147
                                       55677778999********************99999..89999999***************976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2590.19
//
Query:       gi|313117485|ref|YP_004044468.1|  [L=357]
Description: hypothetical protein Hbor_32760 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00046   20.0   0.1     0.0009   19.0   0.1    1.5  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
     0.0089   16.9   3.3       0.04   14.8   0.2    2.9  3  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1     1e-07    0.0009      26      85 ..      12      72 ..       5     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-07
                                      TTS-STTEEEEEE--SHHHHHHHHHHHHC.T-EEEEEEESSEEEEETTEE-HHHHHHHHHC CS
                     ELFV_dehydrog 26 kldslegkrvaisGsGnvgsyaallltel.gakvvavsDssGviydpeGldieellelkee 85
                                       ++++++ r+a+ G G +g  +   ++++   + va  D +Gv +d +Gld++ell+  e 
  gi|313117485|ref|YP_004044468.1| 12 TTTTMDEIRFAVLGTGGIGRRTLDVSKQKpELTPVAACDRHGVAIDHDGLDVDELLSATEG 72
                                      45578999******************99867799*********************998654 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   4.4e-06      0.04       1      76 [.      19     128 ..      19     147 .. 0.68
   2 ?   -2.8   0.0       1.2   1.1e+04      21      35 ..     237     250 ..     225     262 .. 0.66
   3 ?   -3.7   0.1         2   1.8e+04      92      99 ..     290     297 ..     290     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.4e-06
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH..........HHHTTHEEESS.............. CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav..........aesfgveaysd.............. 53 
                                       +r+a+ G+G ig++ l  + ++++++  va++d++  + ++                     +              
  gi|313117485|ref|YP_004044468.1|  19 IRFAVLGTGGIGRRTL-DVSKQKPELTPVAACDRHGVAIDHDgldvdellsaT---------Egniasdggttavke 85 
                                       689************9.666666888777777776655554333333322220.........123333345555555 PP

                                       ...................HHHHHTCT.TESEEEE-S-GGGHH CS
                      GFO_IDH_MocA  54 ...................leelladp.eidavivatpngthe 76 
                                                          ++++ a++ +idav++a pn +h 
  gi|313117485|ref|YP_004044468.1|  86 sgenkgvaassqavstetpIDDVIAESdAIDAVLIALPNFEHD 128
                                       66667777777788888899988888879**********9985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                       HTTTTEEEEEEECSS CS
                      GFO_IDH_MocA  21 esqrleevvalldpd 35 
                                       e  ++ee+ a++d++
  gi|313117485|ref|YP_004044468.1| 237 EM-SDEEIEAVIDEH 250
                                       33.555666666655 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2
                                       ESSS-SSH CS
                      GFO_IDH_MocA  92 EKPlattv 99 
                                       EKP +ttv
  gi|313117485|ref|YP_004044468.1| 290 EKPTTTTV 297
                                       9*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2438.21
//
Query:       gi|313117486|ref|YP_004044469.1|  [L=419]
Description: 7-keto-8-aminopelargonate synthetase-like enzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-61  208.4   0.0    2.1e-61  208.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0018   17.0   0.0     0.0026   16.5   0.0    1.2  1  Aminotran_3      Aminotransferase class-III
     0.0035   15.9   0.0      0.009   14.6   0.0    1.5  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0079   15.5   0.5       0.03   13.7   0.9    1.8  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1   0.0   4.6e-65   2.1e-61       2     362 ..      70     408 ..      69     409 .. 0.95

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 4.6e-65
                                       EEEESSSSSTTSTTSS.HHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgk.ptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsG 76 
                                       ++i +++n+ylg+++   ++ ++++a+   g +ag ++  +g++ ++  le +la+  g        +e+a++++sG
  gi|313117486|ref|YP_004044469.1|  70 EQIVFAANNYLGLTQDeRVVRAAREAAEAvGTGAGASRLVTGDTGLHRGLERDLADAKG--------TERALLFSSG 138
                                       6899*********9995556665555555******************************........********** PP

                                       HHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTE..TEEE CS
                     Aminotran_1_2  77 agaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnk..ktkv 151
                                       + a+  ++ +l      d+++++++++as+++++rls++e v y        h+d+++l +a ++ +  +      +
  gi|313117486|ref|YP_004044469.1| 139 YAANVGTIGALDP----DVVFSDALNHASIIDGCRLSDAETVVYD-------HCDADSLAAAMADRSRSSTpdDSWL 204
                                       ****999998886....9***************************.......************9877777777889 PP

                                       EEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG CS
                     Aminotran_1_2 152 ilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGe 228
                                       i++ s+++++G+va+l++++++   a++y+++++vDea+a++ ++  + v+ r +++++++ + +g+lsKa+++ G 
  gi|313117486|ref|YP_004044469.1| 205 IVTDSVFSMDGDVAPLADICDV---AERYGAWVMVDEAHATGLYDGGGIVQ-REGLSDRVH-VQMGTLSKALASQG- 275
                                       **********************...********************888877.*********.**************. PP

                                       -EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCS CS
                     Aminotran_1_2 229 RvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsg 305
                                         Gy++g+ a+v+ql++++r+f +s+ l + ++ a++ al++  + e++ ++l++r  +lr++L++lg +vl+  + 
  gi|313117486|ref|YP_004044469.1| 276 --GYVAGSTALVEQLANAARSFVFSTGLTPPAVGAAREALRI-AREEKRHEQLWDRVSRLRSGLEALGYDVLGT-TQ 348
                                       ..**********************999999999999999976.599***************************7.** PP

                                       SEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHHH CS
                     Aminotran_1_2 306 mflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelvea 362
                                       +++++ +++++a +l++ L+e+ g++  +++++tv   ++r+R+++ A++te+++++ ++a
  gi|313117486|ref|YP_004044469.1| 349 ILPVVIGDRSDAVALAERLRER-GIVAPAIRPPTVpegTSRIRVSPmATHTEADIDRCLDA 408
                                       **********************.*************9999****************99987 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.8e-07    0.0026     216     404 ..     221     411 ..     210     412 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.8e-07
                                       HHHHHHHHHHT-EEEEE-T.TTTTTTTSSSSGGGGC..TS--SEEEE-GGGG..TTSS-EEEEEEHHHHTTS-TTSB CS
                       Aminotran_3 216 aklrelckkhdvllivDEv.qtGfGrTGklfAleha..gvspDlmtlaKalt..gGlplsavlataevmqalapgsh 287
                                       a + ++++++++ ++vDE  +tG+   G +   e +   v+  + tl+Kal+  gG+ +  ++  +++++a ++   
  gi|313117486|ref|YP_004044469.1| 221 ADICDVAERYGAWVMVDEAhATGLYDGGGIVQREGLsdRVHVQMGTLSKALAsqGGYVAGSTALVEQLANAARSFVF 297
                                       4444556799999999998569999989888888766689999********85456999999999999999855555 PP

                                       --TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHH CS
                       Aminotran_3 288 gsTfgGnplacavalavleiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeil 364
                                       ++     p a  +a+++l+i+ eek  e+  +  ++l++gLe+l   y+v+++   + ++i+     +++    +++
  gi|313117486|ref|YP_004044469.1| 298 STGL--TPPAVGAAREALRIAREEKRHEQLWDRVSRLRSGLEALG--YDVLGTTQILPVVIGD----RSD--AVALA 364
                                       5444..599************************************..7677777766666664....444..2379* PP

                                       HHHHHCTEE.......-EEETTTEEEE---TT--HHHHHHHHHHHHH CS
                       Aminotran_3 365 kkakekGvl.......ilsaGdnvirllppliitdeeidelleilkk 404
                                       ++++e G++       + + G + ir+ p+ + t+++id +l+++++
  gi|313117486|ref|YP_004044469.1| 365 ERLRERGIVapairppTVPEGTSRIRVSPMATHTEADIDRCLDAFEA 411
                                       ********9333222223456699*******************9986 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     2e-06     0.009      55     180 ..     117     244 ..     110     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TS CS
                   Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sd 126
                                       + le+ +a+ +g+e+al++ssG aA   +i al     ++v sd l   +     ++     + ++++d      + 
  gi|313117486|ref|YP_004044469.1| 117 RGLERDLADAKGTERALLFSSGYAANVGTIGAL---DPDVVFSDALNHASIIDGCRLSDAETVVYDHCDAdslaaAM 190
                                       669***********************6666555...45677777776666555555555555555555551111033 PP

                                       HHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTT CS
                   Cys_Met_Meta_PP 127 leelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspl 180
                                       +++ ++   +   l+ ++++ +   +v+ +++i+++a   g+ v+vD + a++l
  gi|313117486|ref|YP_004044469.1| 191 ADRSRSSTPDDSWLIVTDSVFSMDGDVAPLADICDVAERYGAWVMVDEAHATGL 244
                                       33334444446779999********************************99997 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.9   6.6e-06      0.03      26     155 ..     117     248 ..      91     270 .. 0.74
   2 ?   -4.3   0.0       1.8   8.2e+03     289     308 ..     359     378 ..     349     383 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-06
                                       HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-.B-TTTSSB-G CS
                   DegT_DnrJ_EryC1  26 eeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvD.vdpdtynidp 101
                                       + +E+++a+  g++ a+ +ssG aA+  ++ al+ +    V   +l+ ++ +   + + a++v  D  d+d++    
  gi|313117486|ref|YP_004044469.1| 117 RGLERDLADAKGTERALLFSSGYAANVGTIGALDPD---VVFSDALNHASIIDGCRLSDAETVVYDhCDADSLAAAM 190
                                       567888888888888888888888888777777654...66666777777778888888888887734556666666 PP

                                       GGCGGG--TTEEEEEEB-....GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1 102 aaieaaitertkaIlpVh....lyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       a+  +  t+  +  ++ +    + G+va ++ + ++a+++g +v+ D AhA G    g
  gi|313117486|ref|YP_004044469.1| 191 ADRSRSSTPDDSWLIVTDsvfsMDGDVAPLADICDVAERYGAWVMVDEAHATGLYDGG 248
                                       6666666666666555542222679****************************87666 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.8
                                       CHHHHHHHHHHCCEE-B-SG CS
                   DegT_DnrJ_EryC1 289 krdelvealkeegigtrvhy 308
                                       +  +l+e+l+e+gi + +++
  gi|313117486|ref|YP_004044469.1| 359 DAVALAERLRERGIVAPAIR 378
                                       46778899999998877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2640.34
//
Query:       gi|313117487|ref|YP_004044470.1|  [L=226]
Description: dethiobiotin synthase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-33  115.5   0.0    3.3e-33  115.2   0.0    1.0  1  AAA_26    AAA domain
      5e-07   29.8   0.0    1.3e-06   28.5   0.0    1.7  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
      2e-06   27.2   0.9    1.1e-05   24.8   0.9    2.3  1  DUF1611   Domain of unknown function (DUF1611_C) P-loop domai
  ------ inclusion threshold ------
      0.087   12.7   0.0        0.2   11.6   0.0    1.6  2  MobB      Molybdopterin guanine dinucleotide synthesis protei
       0.11   10.7   0.3       0.15   10.2   0.3    1.1  1  FTHFS     Formate--tetrahydrofolate ligase


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   0.0   9.1e-37   3.3e-33       3     185 ..      11     199 ..       9     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 9.1e-37
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspelaa 79 
                                       + v+gtdtgvGKTvv++gLv al++ g  +  +KP qtg   d+d+++++ ++g++++   +   +l+ +l+pe+aa
  gi|313117487|ref|YP_004044470.1|  11 FAVVGTDTGVGKTVVTAGLVGALREAGHDACAIKPAQTGYPPDDDAAFVADICGTEAAATCL--RRLEPALAPEVAA 85 
                                       569**************************************************999887755..678999******* PP

                            AAA_26  80 rqegedidlekiv...kelekdadivvVEGagglgvpiteellnadiaknlgapvilVargglgtinqllltiealr 153
                                       +  g++++ e+i     e  ++++i v EG+ggl+vp+++++ ++d++  lg+p ++Var+glgt+n+++l+++alr
  gi|313117487|ref|YP_004044470.1|  86 DVAGVELEYESIReetAEHLAAHEIGVLEGIGGLRVPLADGREVIDLVSDLGIPAVVVARSGLGTLNHTALSVSALR 162
                                       ************9988778889******************************************************* PP

                            AAA_26 154 qknvrvlGvilNkvrnp.....envetlekksgipvl 185
                                       ++++ v +v+lN+   +     +n + l +++  pv+
  gi|313117487|ref|YP_004044470.1| 163 NRGIDVPAVVLNEYEGEslaarTNPDVLAEMTDCPVV 199
                                       *************766644443477777777777765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   3.7e-10   1.3e-06       2     102 ..      12     194 ..      11     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.7e-10
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE.EEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvD.aDpqannlaileglendiep....................... 54 
                                       a+++t  GvGKT+++a+L  al ++g++  +++ a++  + +     +                             
  gi|313117487|ref|YP_004044470.1|  12 AVVGTDTGVGKTVVTAGLVGALREAGHDACAIKpAQTGYPPDD----D-----Aafvadicgteaaatclrrlepal 79 
                                       89*******************************7777755544....2.....223444677778888899999999 PP

                                       ...............................................................CCHCCCHHHHHHCH CS
                                       ...............................................................xxxxxxxxxxxxxx RF
                              CbiA  55 ...............................................................dlkrllellealgk 68 
                                                                                                       + ++l++l++   
  gi|313117487|ref|YP_004044470.1|  80 apevaadvagveleyesireetaehlaaheigvlegigglrvpladgrevidlvsdlgipavvVARSGLGTLNHTAL 156
                                       99999999999999999999999999999999999999999999999999999999999999944444555544444 PP

                                       CHHHH......EEEEEEEEESS...-TTCHHHHHHHHH CS
                                       xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  69 kkall....lkiagvvlnrvdgeneetllkealeelkq 102
                                       +++ l    +++  vvln ++ge   ++ + ++  ++ 
  gi|313117487|ref|YP_004044470.1| 157 SVSALrnrgIDVPAVVLNEYEGESLAARTNPDVLAEMT 194
                                       44444577899999999999999888888777766654 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.9   3.1e-09   1.1e-05       9      94 ..       5      91 ..       1     208 [. 0.89

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.1e-09
                           DUF1611  9 evkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili.agegvvldavvvdfvaGaveglvkkaaeee 86
                                      e++ +  +vvGTd  vGK + +  l  al+e+G +a  +   qtg     ++ +v+d    + +a  + +l +++a e 
  gi|313117487|ref|YP_004044470.1|  5 ELPDDAFAVVGTDTGVGKTVVTAGLVGALREAGHDACAIKPAQTGYPPdDDAAFVADICGTEAAATCLRRLEPALAPEV 83
                                      56667789****************************************9999*****9999999999988888888777 PP

                           DUF1611 87 epdlilve 94
                                       +d+  ve
  gi|313117487|ref|YP_004044470.1| 84 AADVAGVE 91
                                      77776665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.5e-05       0.2       3      44 ..      12      54 ..      10      68 .. 0.89
   2 ?   -2.9   0.0       1.7   5.9e+03       5      31 ..     143     169 ..     141     172 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.5e-05
                              MobB  3 givgk.sgsGKTtLleklipelkarglrvgtiKhahhgfdvdk 44
                                      ++vg+  g GKT     l+ +l++ g   ++iK a+ g+  d+
  gi|313117487|ref|YP_004044470.1| 12 AVVGTdTGVGKTVVTAGLVGALREAGHDACAIKPAQTGYPPDD 54
                                      677764799*************************999988776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                              MobB   5 vgksgsGKTtLleklipelkarglrvg 31 
                                       v++sg G        +++l++rg+ v 
  gi|313117487|ref|YP_004044470.1| 143 VARSGLGTLNHTALSVSALRNRGIDVP 169
                                       566666655555566778888888775 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   4.2e-05      0.15      61      91 ..      12      42 ..      10      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.2e-05
                                      ESS--TT--SHHHHHHHHHHHHHHTT--EEE CS
                             FTHFS 61 aitPtplGeGKttttigLaqalnklgkkava 91
                                      a+  t +G GKt++t gL+ al+++g+ a+a
  gi|313117487|ref|YP_004044470.1| 12 AVVGTDTGVGKTVVTAGLVGALREAGHDACA 42
                                      67789*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1472.55
//
Query:       gi|313117488|ref|YP_004044471.1|  [L=272]
Description: CAAX amino terminal protease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-16   59.1   7.3    4.2e-16   59.1   7.3    2.6  3  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   2.8      0.22   3.9e+03      23      55 ..      67      95 ..      20     109 .. 0.63
   2 !   59.1   7.3   2.3e-20   4.2e-16       4      90 ..     120     225 ..     117     226 .. 0.85
   3 ?   -3.1   0.1      0.58     1e+04      65      73 ..     248     256 ..     233     263 .. 0.45

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.22
                                      HTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG CS
                              CPBP 23 fRglllqllqergsstlailissilFglaHlpn 55
                                       R++l +  +     + a+l+  ++++l+ l+ 
  gi|313117488|ref|YP_004044471.1| 67 PRSILSPVRSL----LSALLVVTVFWVLYNLVA 95
                                      44444332222....346666666666665554 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 2.3e-20
                                       THHHHHHHHHHHHHHHHHHHTTCHHHHHHHH..S-.....HHHHHHHHHHHHHCSGGG..HHHH............. CS
                              CPBP   4 lllvfllalllapllEEllfRglllqllqer.gss.....tlailissilFglaHlpn..gpsv............. 59 
                                        l+ f+  +l++++ EEl+fRg+l++++ +  g++     ++ + i++ilF+l+Hlp      +             
  gi|313117488|ref|YP_004044471.1| 120 YLAAFVSSVLFTAIPEELVFRGYLQSKFVSLaGGKtgkavAVGVGITAILFALFHLPRwfL--Msghgvgaalatrl 194
                                       57889999*******************99997333578899****************9550..34555555555555 PP

                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              CPBP  60 llaalaGlvlgylylktgsllaaillHalln 90 
                                       l ++l+Gl++g++y  t++l+ ++l+Ha +n
  gi|313117488|ref|YP_004044471.1| 195 LGLTLMGLAYGLVYALTRNLWLVALFHATMN 225
                                       ****************************998 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.58
                                       HHHHHHHHH CS
                              CPBP  65 aGlvlgyly 73 
                                       +  ++++++
  gi|313117488|ref|YP_004044471.1| 248 FAAIVTVVF 256
                                       333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 2066.39
//
Query:       gi|313117489|ref|YP_004044472.1|  [L=117]
Description: hypothetical protein Hbor_32800 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0037   17.1   1.1      0.004   17.0   1.1    1.1  1  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
  ------ inclusion threshold ------
       0.14   11.3   0.0       0.16   11.1   0.0    1.1  1  AC_N          Adenylyl cyclase N-terminal extracellular and t
        5.2    6.9   6.2        6.4    6.6   0.5    2.3  2  FixS          Cytochrome oxidase maturation protein cbb3-type


Domain annotation for each model (and alignments):
>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.1   6.7e-07     0.004      31      93 ..      12      74 ..       2      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.7e-07
                      Trp_oprn_chp 31 prtvalsGadwapaltalAlvllAaavAvlavrglgrrvvgvllalagagaavaalslltdpa 93
                                       +t ++sG ++a +l a  l +l  +  v av  ++r+ +++l a ++++++v  +++ t+++
  gi|313117489|ref|YP_004044472.1| 12 RKTFEISGTSLAHLLYAATLGCLVLLTMVWAVDSFARVPLAILFASLAIAMIVGLWRAKTGRD 74
                                      67899***********************************************99988877765 PP

>> AC_N  Adenylyl cyclase N-terminal extracellular and transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.6e-05      0.16     180     240 ..       3      65 ..       1      86 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.6e-05
                              AC_N 180 seklerlyqryffrlnqssltmlmavlvlvcvvmlaf.haargplevsyvvvl.slaillilv 240
                                       +++l   y r  f +  +sl+ l+    l c+v+l++  a+ + ++v+  +++ slai +i+ 
  gi|313117489|ref|YP_004044472.1|   3 TDQLVSGYMRKTFEISGTSLAHLLYAATLGCLVLLTMvWAVDSFARVPLAILFaSLAIAMIVG 65 
                                       57788889*************************997626777888998776662456665553 PP

>> FixS  Cytochrome oxidase maturation protein cbb3-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.5    0.0011       6.4      10      27 ..      28      45 ..      22      45 .. 0.87
   2 ?    3.1   0.8     0.013        77       7      21 ..      49      63 ..      46      72 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0011
                              FixS 10 SlllgllalaaFlWavks 27
                                      +  lg+l+l+ ++Wav s
  gi|313117489|ref|YP_004044472.1| 28 AATLGCLVLLTMVWAVDS 45
                                      6689************86 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.013
                              FixS  7 iplSlllgllalaaF 21
                                      +pl++l++ la+a+ 
  gi|313117489|ref|YP_004044472.1| 49 VPLAILFASLAIAMI 63
                                      789999988887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 893.21
//
Query:       gi|313117490|ref|YP_004044473.1|  [L=106]
Description: hypothetical protein Hbor_32820 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 725.79
//
Query:       gi|313117491|ref|YP_004044474.1|  [L=407]
Description: ferrichrome-binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-18   64.7   0.0    1.5e-17   64.0   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein
    0.00022   21.0   0.1     0.0004   20.1   0.1    1.5  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.25   11.5   0.0    1.4  1  Cupin_5       Cupin superfamily (DUF985)


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   2.5e-21   1.5e-17      55     232 ..     139     348 ..     112     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 2.5e-21
                                       HHHH--SEEEE-GGG....GGGHHHHHHHS-EEE----TTS...............HHHHHHHHHHHHHTT-HHHHH CS
                      Peripla_BP_2  55 laalkPDlvilskgl.gltdedeellksgiptvivessntg...............eslkeqiralgellgledeae 115
                                         + +PD++++++++ + t  d+  +ks+ + +  +  +++               +s +e ++ l+el+++ +++e
  gi|313117491|ref|YP_004044474.1| 139 FYEQDPDVILMDPNYmHKTGWDKSWDKSDTNEISENVAPFFgnnilrrrdwhdyklYSMYEALERLAELFQERERYE 215
                                       55679***********888888888888888888888888888888999**************************** PP

                                       HHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE....EEEE-TTSTTTHH..HHTS--EESTTT--STT-EEE-H CS
                      Peripla_BP_2 116 klvaeidsklaaaksaidse..kpkpvlvfggade..ggyvvagsnsyigdl..ldalgieniaaeskkseyeeisa 186
                                       +l++ + s  ++++s+++ +   p+++l+ + +++  g+++ + ++ ++ +l   ++l+i++++ +  + e+++i+ 
  gi|313117491|ref|YP_004044474.1| 216 ALAEVHASVQDEIQSRLPPAdeRPEIALINSASNPneGTFYPMRTQDEGVELkpYRDLDIRSAFTAD-HIEAGTIDY 291
                                       ********************8666677777666668777777777776666644677******9888.********* PP

                                       HHHHHH--SEEEEEEH...........HHHT-S--HHHHT-SHHHHTSHHHHTT-EE CS
                      Peripla_BP_2 187 Eqilasdpdvifvsgr...........aeadnktgleflkenpllaelpAvkngrVy 232
                                       E++l+ dp++++v++            ++a++ +++  ++e+p+ ++l+Av++g+Vy
  gi|313117491|ref|YP_004044474.1| 292 ETLLEVDPEILVVHWGisttgdqdtfsPKAFREQFVTPFEEDPTGSQLTAVQEGNVY 348
                                       ********************************************************9 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   6.6e-08    0.0004       2      25 ..      11      34 ..      10      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.6e-08
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      l+RRd +K ++A+  +++l+gc++
  gi|313117491|ref|YP_004044474.1| 11 LTRRDYMKYGGAVVGGGLLAGCSS 34
                                      79********************97 PP

>> Cupin_5  Cupin superfamily (DUF985)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.1e-05      0.25     100     138 ..      79     116 ..      57     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                                       SEEEE-TTSEE.EEEESSSSTSSEEEEEEEESSC--GGGE CS
                           Cupin_5 100 lqlvVpagkwk.aaellgddeeeylLvsctvaPGFefedf 138
                                        +++V++g+w   a+ lg+  ++++L s  ++PGF fe f
  gi|313117491|ref|YP_004044474.1|  79 ETYMVNNGEWAdMAFALGQ--RDGFLTSAYMIPGFLFEPF 116
                                       4689******835666664..89*************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 3120.16
//
Query:       gi|313117492|ref|YP_004044475.1|  [L=299]
Description: hypothetical protein Hbor_32840 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-21   75.4   8.5    8.5e-21   74.5   8.5    1.5  1  ABC2_membrane_2  ABC-2 family transporter protein
    4.5e-07   29.6   4.5    4.5e-07   29.6   4.5    1.5  2  ABC2_membrane_5  ABC-2 family transporter protein
     0.0005   19.3  12.3    0.00058   19.1  12.3    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.029   14.4   0.4      0.029   14.4   0.4    2.1  2  DUF2561          Protein of unknown function (DUF2561)


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   8.5   1.9e-24   8.5e-21      80     288 .]      69     298 ..      15     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1.9e-24
                   ABC2_membrane_2  80 imavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivl 156
                                        +a ++ +ia+ +g+ +++ + ++g ++llL +P+ R+ +++ K +g  ++  ++  ++la+ l +l +++    ++
  gi|313117492|ref|YP_004044475.1|  69 NIAYFGSLIAIFAGYASVTSDQASGRIRLLLKLPYARWRYVFEKYLGEGLA--LGTFTALAI-LGGLTVSATIYGQP 142
                                       5899*******************************************9888..466677777.77777777666666 PP

                   ABC2_membrane_2 157 aledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindfl 233
                                       ++   +++ ++s+ +l+  v l+++++ S+va++ r+a++++++++++  +++++v  +v+ l  +  +   + +f+
  gi|313117492|ref|YP_004044475.1| 143 PVLTAVTVPLLSIGYLF--VWLSFAVATSVVAKTGRQAITVVISVYLLP-MAWTLVTPAVSWLVGDDPA---LFLFV 213
                                       65555555556666777..57**************************99.8999999776555554444...9999* PP

                   ABC2_membrane_2 234 sllsptsayntllneilagsdlna..............................lgstatnllilllllavllvlgy 280
                                       + l p +ay +++n+ +   +                                  +s + ++l+l+++ +v++ l+ 
  gi|313117492|ref|YP_004044475.1| 214 ERLLPMNAYFAATNWAIGVPNSHGpardvltkvltdiprpttiivselfesvpwFLSGWVSVLVLVIWGLVPMLLAC 290
                                       ***************9988854449999************************************************* PP

                   ABC2_membrane_2 281 vlFkrkDl 288
                                        +F ++D+
  gi|313117492|ref|YP_004044475.1| 291 RRFATADI 298
                                       ***99995 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   4.5     1e-10   4.5e-07      31     159 ..      66     190 ..      61     224 .. 0.75
   2 ?   -4.0   0.3       1.9   8.7e+03      94     100 ..     272     278 ..     256     288 .. 0.51

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1e-10
                   ABC2_membrane_5  31 flndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlf.vlililiailitlllliiavl 106
                                       + +++++ ++s+++++  +     ++  D+ s+  ++ll LP+ r+ +V +KYl+ +l l++++ l +l  l+++  
  gi|313117492|ref|YP_004044475.1|  66 I-QSNIAYFGSLIAIFAGYA----SVTSDQASGRIRLLLKLPYARWRYVFEKYLGeGLALGTFTALAILGGLTVSAT 137
                                       3.455666666666555555....7778**************************86788888888888888899999 PP

                   ABC2_membrane_5 107 ikgnvtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiif 159
                                       i+g+  + +++++ l+++++ +++l++        ++ +  i ++i+++++ +
  gi|313117492|ref|YP_004044475.1| 138 IYGQPPVLTAVTVPLLSIGYLFVWLSFAVATSVVAKTGRQAITVVISVYLLPM 190
                                       99997777777777777777777777776666666655555555555555544 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.9
                   ABC2_membrane_5  94 ilitlll 100
                                       ++ +l+l
  gi|313117492|ref|YP_004044475.1| 272 WVSVLVL 278
                                       2222222 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  12.3   1.3e-07   0.00058     154     343 ..      54     289 ..      18     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-07
                   ABC2_membrane_3 154 eelsnvasflvg...liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill. 226
                                       ++ +++++ +v+    i+++ ++i ++   +s+ ++  s+ + l+l  +  ++ y++ k+lg +l+  ++++l++l 
  gi|313117492|ref|YP_004044475.1|  54 NYDPGSEHGFVIiqsNIAYFGSLIAIFAGYASVTSDQASGRIRLLLKLPYARWRYVFEKYLGEGLALGTFTALAILg 130
                                       6666777766666777888888888777778999998886666666777***********************99987 PP

                   ABC2_membrane_3 227 .l.....afglgipfgnlglll.llfllfglayialgyllsslfknsetaqilifivilllsgffggl....fpled 292
                                        l     ++g   p     +++ ll++ ++++ ++++ + s++ k+ + a+++++ v ll+++  +++    +++ d
  gi|313117492|ref|YP_004044475.1| 131 gLtvsatIYG--QPPVLTAVTVpLLSIGYLFVWLSFAVATSVVAKTGRQAITVVISVYLLPMAWTLVTpavsWLVGD 205
                                       8633444444..44444455559******************************999999888887777654455999 PP

                   ABC2_membrane_3 293 lpsalkwifsiiPffapglgllrlitgdplwe..................................illsliilalf 335
                                        p  +  + +++P++a++ +    i g+p++                                    + s+++l++ 
  gi|313117492|ref|YP_004044475.1| 206 DPALFLFVERLLPMNAYFAATNWAI-GVPNSHgpardvltkvltdiprpttiivselfesvpwflsGWVSVLVLVIW 281
                                       ******************9986665.443333456677788888888888888888888888888666888888888 PP

                   ABC2_membrane_3 336 avvyllla 343
                                       ++v +lla
  gi|313117492|ref|YP_004044475.1| 282 GLVPMLLA 289
                                       88887776 PP

>> DUF2561  Protein of unknown function (DUF2561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   2.9       1.1   5.1e+03     167     202 ..     164     202 ..     124     203 .. 0.64
   2 ?   14.4   0.4   6.5e-06     0.029      61      94 ..     264     297 ..     244     299 .] 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                           DUF2561 167 vaaatyLma.vgkdgasWv..lyglaGvvtagmpvieWl 202
                                        a+at ++a  g+++ + v  +y l  + t++ p++ Wl
  gi|313117492|ref|YP_004044475.1| 164 FAVATSVVAkTGRQAITVVisVYLLPMAWTLVTPAVSWL 202
                                       344555444234444333322456666666666666665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.5e-06
                           DUF2561  61 httwvLyavivvsalvivgavPlLLrarrvaeae 94 
                                         +w L   + v +lvi g vP+LL  rr a+a+
  gi|313117492|ref|YP_004044475.1| 264 SVPWFLSGWVSVLVLVIWGLVPMLLACRRFATAD 297
                                       468***************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1897.58
//
Query:       gi|313117493|ref|YP_004044476.1|  [L=396]
Description: hypothetical protein Hbor_32850 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-28  100.5   6.7    1.1e-16   61.2   4.1    3.0  2  PQQ_2            PQQ-like domain
      3e-21   75.3  15.9    0.00082   19.8   0.3    7.7  8  PQQ_3            PQQ-like domain
    2.9e-17   61.7   1.0      0.018   14.9   0.0    6.4  6  PQQ              PQQ enzyme repeat
  ------ inclusion threshold ------
      0.055   13.6   0.0        0.1   12.7   0.0    1.4  1  EFhand_Ca_insen  Ca2+ insensitive EF hand


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   4.1   2.4e-20   1.1e-16      44     236 ..     109     281 ..      65     282 .. 0.77
   2 !   37.1   0.0   5.4e-13   2.4e-09      28     129 ..     291     387 ..     284     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 2.4e-20
                             PQQ_2  44 gggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepaelrssaspav 120
                                       g+ r   ld ++G+ +  ++l +   ++p++a++ v+v +  + ++a+d ++Gk+ W+ ++ ++  ae     +p++
  gi|313117493|ref|YP_004044476.1| 109 GEYRSFTLDSSSGSWTVDYKLGK---STPTIAGNAVFVST-AEFVAAYDVRNGKLCWRADDGGSGGAE----NAPIL 177
                                       55555667777777555555544...479*******9997.99***************5555535555....99999 PP

                             PQQ_2 121 agdtvvvgessgklvaldpkdGkvlWerelaaprgtselsrvgdisgrpvvaegtVyassgqgrllaldlatgrrlw 197
                                       a +t++  +  + ++++dp++G+++W++ + +                pv  +gt y ++  g  +a+d ++g+++w
  gi|313117493|ref|YP_004044476.1| 178 AEGTLLDYT-TSTVNGRDPATGEKRWQYGVDDSL------------VPPVTRDGTAYTATETG-AAAFDPKSGEEVW 240
                                       999999999.99****************776644............8899998*******999.5778******99* PP

                             PQQ_2 198 .skeissinglpildgdllyvvsa.gelialdratGavlWk 236
                                        + ++ +  +  ++ ++ ly++ + + l+al++ +Ga++W+
  gi|313117493|ref|YP_004044476.1| 241 rQADLPESSAPLAVGDNHLYYSAKgEDLYALSLDDGASQWQ 281
                                       6666555566588888899999989***************8 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 5.4e-13
                             PQQ_2  28 gvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvga.plvaegrvvvvasdgqlialdaedGkrlWstq 103
                                        + +a  s+gtl v +  g ++a+da +G+ +  ++le+ ++ + p va++  +   +d++l+a+d e+G+ +Ws  
  gi|313117493|ref|YP_004044476.1| 291 SHYTAI-SDGTLHVQSADGVVAAFDAVDGSKKYIKQLEADLRQRpPVVADDTRFSL-GDETLYAFDVETGDIQWSLP 365
                                       344477.9*********************************999559999999888.7*****************88 PP

                             PQQ_2 104 qrseepaelrssaspavagdtvvvge 129
                                       +++ ep++    + p+++g++++++ 
  gi|313117493|ref|YP_004044476.1| 366 LDT-EPVS---GGVPSIRGEELYFVS 387
                                       888.5555...788999999999876 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.9   1.7e+04      23      36 ..      10      23 ..       9      23 .. 0.78
   2 !    9.7   0.2   0.00027       1.2       6      39 ..     124     155 ..     122     156 .. 0.80
   3 !    5.1   0.1    0.0075        34       1      24 [.     157     182 ..     157     183 .. 0.83
   4 !   19.8   0.3   1.8e-07   0.00082       1      40 []     198     235 ..     198     235 .. 0.92
   5 !   16.3   0.0   2.2e-06    0.0099       1      39 [.     236     274 ..     236     275 .. 0.88
   6 !   15.1   0.1   5.5e-06     0.025       2      38 ..     277     315 ..     276     317 .. 0.76
   7 !    7.4   0.0    0.0015       6.6      15      40 .]     333     357 ..     323     357 .. 0.76
   8 !    6.7   0.0    0.0023        10       1      30 [.     358     389 ..     358     394 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.9
                             PQQ_3 23 lvyvgtgdGtlyAl 36
                                      +v ++tg  tl++l
  gi|313117493|ref|YP_004044476.1| 10 KVLAATGAATLTSL 23
                                      68889999988876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00027
                             PQQ_3   6 svqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       +v+    ++s+p+++g+ v+v+t    + A+D +
  gi|313117493|ref|YP_004044476.1| 124 TVDYK-LGKSTPTIAGNAVFVSTA-EFVAAYDVR 155
                                       44433.45699************9.******987 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0075
                             PQQ_3   1 GevlWsvqlpg..pvnsspavdgglv 24 
                                       G+++W+ + +g   +  +p +++g++
  gi|313117493|ref|YP_004044476.1| 157 GKLCWRADDGGsgGAENAPILAEGTL 182
                                       9******9998666668889999987 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 1.8e-07
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       Ge +W++++++ +  +p++ +g+ y++t+  +  A+D+++
  gi|313117493|ref|YP_004044476.1| 198 GEKRWQYGVDDSL-VPPVTRDGTAYTATE-TGAAAFDPKS 235
                                       99********988.589***********9.9999999975 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 2.2e-06
                             PQQ_3   1 GevlWsv.qlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       Ge++W++ +lp+   +++av+++++y ++    lyAl  +
  gi|313117493|ref|YP_004044476.1| 236 GEEVWRQaDLPESS-APLAVGDNHLYYSAKGEDLYALSLD 274
                                       9******9999764.677******************9865 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 5.5e-06
                             PQQ_3   2 evlWsvqlp..gpvnssp..avdgglvyvgtgdGtlyAlDa 38 
                                         +W+ ++p  +++      a+++g++ v + dG + A+Da
  gi|313117493|ref|YP_004044476.1| 277 ASQWQASIPlsERGS--HytAISDGTLHVQSADGVVAAFDA 315
                                       567999665114544..445********************9 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.0015
                             PQQ_3  15 sspavdgglvyvgtgdGtlyAlDaet 40 
                                       ++p+v++++ +  + d tlyA+D et
  gi|313117493|ref|YP_004044476.1| 333 RPPVVADDTRFSLG-DETLYAFDVET 357
                                       56677777776654.7*******998 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.0023
                             PQQ_3   1 GevlWsvqlpg.pvnssp.avdgglvyvgtgd 30 
                                       G+++Ws +l+  pv +++  + g  +y+++  
  gi|313117493|ref|YP_004044476.1| 358 GDIQWSLPLDTePVSGGVpSIRGEELYFVSNS 389
                                       99*******8879997777*999999999964 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   7.6e-06     0.034      11      29 ..     148     166 ..     138     169 .. 0.80
   2 !    6.2   0.0    0.0024        11      18      30 ..     196     208 ..     194     213 .. 0.86
   3 ?    3.2   0.0     0.021        92      14      26 ..     230     242 ..     228     249 .. 0.90
   4 ?    1.5   0.0     0.072   3.2e+02       4      25 ..     260     281 ..     257     285 .. 0.73
   5 !   13.5   0.0   1.1e-05     0.051       1      31 [.     299     329 ..     299     336 .. 0.84
   6 !   14.9   0.0   4.1e-06     0.018       9      35 ..     347     373 ..     345     376 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.6e-06
                                       EEEEEETTTCCEEEEEESS CS
                               PQQ  11 ylyAlDadTGkvlWrfktg 29 
                                        + A+D+++Gk++Wr + g
  gi|313117493|ref|YP_004044476.1| 148 FVAAYDVRNGKLCWRADDG 166
                                       689************8866 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0024
                                       TTCCEEEEEESSS CS
                               PQQ  18 dTGkvlWrfktgg 30 
                                       +TG+++W++ +++
  gi|313117493|ref|YP_004044476.1| 196 ATGEKRWQYGVDD 208
                                       6********9875 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.021
                                       EEETTTCCEEEEE CS
                               PQQ  14 AlDadTGkvlWrf 26 
                                       A+D ++G+++Wr 
  gi|313117493|ref|YP_004044476.1| 230 AFDPKSGEEVWRQ 242
                                       88999******95 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.072
                                       EEEETTSEEEEEETTTCCEEEE CS
                               PQQ   4 ylgsadGylyAlDadTGkvlWr 25 
                                       y+  ++  lyAl +d+G   W+
  gi|313117493|ref|YP_004044476.1| 260 YYSAKGEDLYALSLDDGASQWQ 281
                                       555566679********76665 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 1.1e-05
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSC CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggp 31 
                                       g++ + sadG++ A+Da +G ++  ++++++
  gi|313117493|ref|YP_004044476.1| 299 GTLHVQSADGVVAAFDAVDGSKKYIKQLEAD 329
                                       567788****************998888876 PP

  == domain 6  score: 14.9 bits;  conditional E-value: 4.1e-06
                                       TSEEEEEETTTCCEEEEEESSSCGSSE CS
                               PQQ   9 dGylyAlDadTGkvlWrfktggpvlsl 35 
                                       d +lyA+D++TG++ W+ +++ +++s 
  gi|313117493|ref|YP_004044476.1| 347 DETLYAFDVETGDIQWSLPLDTEPVSG 373
                                       668****************99999886 PP

>> EFhand_Ca_insen  Ca2+ insensitive EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05       0.1       2      26 ..     303     327 ..     302     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                       -STHHHHHCHHHHHCTTSSSEEHHH CS
                   EFhand_Ca_insen   2 vdsaeqveeaFralaggKpYvTeed 26 
                                       v+sa+ v++aF a+ g K+Y+ +++
  gi|313117493|ref|YP_004044476.1| 303 VQSADGVVAAFDAVDGSKKYIKQLE 327
                                       79*******************7664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2881.56
//
Query:       gi|313122550|ref|YP_004044477.1|  [L=529]
Description: choline-glycine betaine transporter [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.4e-115  385.8  50.5   2.8e-115  385.5  50.5    1.0  1  BCCT      BCCT, betaine/carnitine/choline family transporter
  ------ inclusion threshold ------
      0.081   12.9   0.9        4.4    7.3   0.0    3.4  3  Ninjurin  Ninjurin
       0.09   12.7   2.7       0.26   11.2   0.2    2.9  2  DUF1360   Protein of unknown function (DUF1360)


Domain annotation for each model (and alignments):
>> BCCT  BCCT, betaine/carnitine/choline family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.5  50.5  4.7e-119  2.8e-115       2     482 ..      20     499 ..      19     502 .. 0.95

  Alignments for each domain:
  == domain 1  score: 385.5 bits;  conditional E-value: 4.7e-119
                              BCCT   2 flvslliivlfvllalvfpealeevlsslnswilekfgwlylllvllflvfllvlafskygkikLGkddekpefstl 78 
                                       f+v++ +++++  ++l++p+ l+++l  +++w+l++fgw+++ll +++l+++l+++fs+yg++++G++d++pef+ +
  gi|313122550|ref|YP_004044477.1|  20 FVVAMSVMLALGGFGLLNPSLLSSTLIGAKTWVLNYFGWWFILLGFVLLIVVLLMVFSQYGHLRIGGPDAEPEFDLF 96 
                                       8999************************************************************************* PP

                              BCCT  79 sWfamlfaaglgigllfwgvaEplahylspppgaeagteeaa.qeAlaytffhwGlhaWaiy.alvalalayfayrk 153
                                       sW++m+f+ g+g+++l+wgvaEp++++ +ppp+  + + +++  +Ala++f+h  + + a++   va+a++ ++y+ 
  gi|313122550|ref|YP_004044477.1|  97 SWLSMVFTVGFGASILIWGVAEPISIVSNPPPKPYPVQGASVeAMALAFMFIHEVFPGLAMWyLPVAIAFGIIVYTD 173
                                       *******************************99988888888799***************97588***********8 PP

                              BCCT 154 glp.ltissalypllge.ringllgkvvDvlavlatvfGvatslGlgvlqinaglselfgieesltvqlaiivvita 228
                                       g   ++iss+l+ ++ e ri g l  +v+++av+at+ G++t+lG+ +++++a+l ++f++e + ++++a++++i +
  gi|313122550|ref|YP_004044477.1| 174 GVGdYKISSMLTAIVDEdRIPG-LYWMVNLAAVVATIGGISTTLGFSAQTMAAILGRVFNLEAT-VLTYAVFALIGV 248
                                       87449***********945555.679***********************************755.8899******** PP

                              BCCT 229 latvsavsGldkGikrlSnlnlvlalllllfvllvGptlfilntfvqslgdylqnlvalslatdaaeeaeewlasWT 305
                                       +++  +++Gl+kGi+  ++++++l+ + ++++++vGpt+f++++ ++++g +l+++++lsl+t+++++ + w a+WT
  gi|313122550|ref|YP_004044477.1| 249 VFLGDVWLGLRKGIRNAARATMFLIGVSMALLVVVGPTIFMFELGLDATGVWLSEMLRLSLYTAPTSAGN-WAANWT 324
                                       *****************************************************************99888.****** PP

                              BCCT 306 vFyWawwiawapfvGlFiAriSrGRtiRefilgvllvptlvtflwftvlGgtaielelegeaelaeaaeasveaalf 382
                                        F+Waww aw++fvG F+Ar+S+GRtiRe+ +++++vpt++t++   ++Gg+ ++   +++++    a+a+ +aa+ 
  gi|313122550|ref|YP_004044477.1| 325 GFWWAWWAAWSIFVGSFVARVSKGRTIREMFVVLVVVPTFLTWIQHLLIGGWVLAPGYQQPVADIM-AAAGKPAAVA 400
                                       ******************************************************999988763333.699******* PP

                              BCCT 383 alleqlplgsilsvlavvliiiffvTsaDSatlvlatltsggdenpprkqrvfWgvllgavaavlllagglealqsa 459
                                       + l+ +plg++l+vl+v++i+ +++Ts DSa+++++++t g +enp+ ++r++Wg ll+ + ++ l + +++++qs+
  gi|313122550|ref|YP_004044477.1| 401 KALQITPLGAVLAVLFVFVIAGYIITSLDSAVFMISAITLG-NENPNPRNRAWWGALLAFFGMMSLELKEFSSIQSL 476
                                       **************************************998.9********************************** PP

                              BCCT 460 siiaalPftlvlllmvvsllkal 482
                                       s+++alPf+l+ll++++  +  +
  gi|313122550|ref|YP_004044477.1| 477 SVTMALPFSLLLLVILYGSYVVA 499
                                       ***************99877655 PP

>> Ninjurin  Ninjurin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.043   2.6e+02      23      85 ..      37      99 ..      33     113 .. 0.69
   2 ?    7.3   0.0   0.00074       4.4      41      63 ..     267     289 ..     257     338 .. 0.89
   3 ?   -1.0   0.1      0.29   1.7e+03      47      65 ..     482     499 ..     469     519 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.043
                          Ninjurin 23 NasqLkavlesgekskfyiallvLislSllLqvvvgilliliasklnlekekkerrlnklnna 85
                                      N s L + l   + + + ++   +i+l  +L +vv ++++ + ++l +   + e +++++  +
  gi|313122550|ref|YP_004044477.1| 37 NPSLLSSTLIGAKTWVLNYFGWWFILLGFVLLIVVLLMVFSQYGHLRIGGPDAEPEFDLFSWL 99
                                      556666666666666667888889999999999998887775556666555555555555555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00074
                          Ninjurin  41 iallvLislSllLqvvvgillil 63 
                                        a + Li++S++L vvvg ++++
  gi|313122550|ref|YP_004044477.1| 267 RATMFLIGVSMALLVVVGPTIFM 289
                                       5789*************977765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.29
                          Ninjurin  47 islSllLqvvvgillilia 65 
                                       + +SllL v+++   ++ a
  gi|313122550|ref|YP_004044477.1| 482 LPFSLLLLVILYGSYVV-A 499
                                       44677777777776666.2 PP

>> DUF1360  Protein of unknown function (DUF1360)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.14   8.4e+02      63      82 ..     297     316 ..     296     325 .. 0.87
   2 ?   11.2   0.2   4.4e-05      0.26      46      97 ..     348     398 ..     335     404 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.14
                           DUF1360  63 lgvWvaaalvlglvlaPrlt 82 
                                       +gvW++ +l l+l++aP+ +
  gi|313122550|ref|YP_004044477.1| 297 TGVWLSEMLRLSLYTAPTSA 316
                                       79***************865 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.4e-05
                           DUF1360  46 gkgvrkaiGeLlsCpfClgvWvaaalvlglvlaPrltrlvalilaiagaadi 97 
                                       g+ +r+++  L+  p  +  W+  +l+ g+vlaP + ++va i+a+ag  ++
  gi|313122550|ref|YP_004044477.1| 348 GRTIREMFVVLVVVPT-FLTWIQHLLIGGWVLAPGYQQPVADIMAAAGKPAA 398
                                       5555555555555553.347**************************997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 3095.71
//
Query:       gi|313122551|ref|YP_004044478.1|  [L=81]
Description: glycosyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 544.11
//
Query:       gi|313122552|ref|YP_004044479.1|  [L=173]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1207.35
//
Query:       gi|313122553|ref|YP_004044480.1|  [L=271]
Description: ABC-type spermidine/putrescine transport system, permease component II [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-15   54.9  15.0      9e-15   54.9  15.0    2.2  2  BPD_transp_1   Binding-protein-dependent transport system inn
  ------ inclusion threshold ------
      0.021   14.9   2.5      0.088   12.9   0.5    2.4  2  Herpes_UL49_5  Herpesvirus UL49.5 envelope/tegument protein
       0.76    9.7   4.2        1.8    8.5   0.7    2.2  2  TraS           Plasmid conjugative transfer entry exclusion p


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   3.3      0.15   8.9e+02      31     119 ..      32      92 ..       6     102 .. 0.43
   2 !   54.9  15.0   1.5e-18     9e-15       4     173 ..      92     259 ..      88     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
                      BPD_transp_1  31 Psfvlaillvlvf................vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralG 91 
                                       P + l+i  ++                  +                                            alG
  gi|313122553|ref|YP_004044480.1|  32 PLLSLVIASFYDGrffsivdyeftlhwyeA--------------------------------------------ALG 64 
                                       333322222222233333333333333330............................................333 PP

                      BPD_transp_1  92 asrwqifrkvvlPnalppiitglilafg 119
                                        + ++  +  +++ a+p++i + i+  g
  gi|313122553|ref|YP_004044480.1|  65 SGSIRSAFMNTVRIAVPVTIISTIIGTG 92 
                                       3333444444444444444444444444 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 1.5e-18
                      BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslp 80 
                                       +G++a +++ ++ ++ +  l  ++  +P ++l++ + +++++  +lg+++lp+i+  l+ + p+v+++++     ++
  gi|313122553|ref|YP_004044480.1|  92 GGAIAYTRHEFPYQDKFKLLALLPIFFPLILLGLGMSMWASVV-GLGYGVLPAIVGELVWISPIVMFVVSITALGVD 167
                                       4555558999999999999999999999999999999886666.99******************************* PP

                      BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..n 155
                                        + +eaar lGa  ++++ k+vlP+++  +++g+i+af+++++++ ++++l    G+ +++++ i g++++  +  +
  gi|313122553|ref|YP_004044480.1| 168 PNVEEAARDLGADSITLYTKIVLPLIKDGVVSGAIFAFVLAWNNYYIVSYLS---GVESTITTWIHGRMTQGFTpvV 241
                                       ****************************************************...9999999999999999777864 PP

                      BPD_transp_1 156 ggvlalviavlllnlvad 173
                                        +v+ l+++v ll++v  
  gi|313122553|ref|YP_004044480.1| 242 PAVASLIFYVSLLLVVGA 259
                                       555555555555555544 PP

>> Herpes_UL49_5  Herpesvirus UL49.5 envelope/tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.067     4e+02       5      48 ..      18      62 ..      15      83 .. 0.73
   2 ?   12.9   0.5   1.5e-05     0.088      51      78 ..     234     261 ..     202     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.067
                     Herpes_UL49_5  5 aersvvlllavvvllllalvraasgdgal.diareeeredFwhaa 48
                                      +   v+l+++ +vl ll+lv a + dg+  +i+  e   ++++aa
  gi|313122553|ref|YP_004044480.1| 18 WYAYVALVALFFVLPLLSLVIASFYDGRFfSIVDYEFTLHWYEAA 62
                                      566678888888888999999888887651333444445556655 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.5e-05
                     Herpes_UL49_5  51 arGvsiaessaasvlFYisLlavlvall 78 
                                        +G+  + ++ as++FY+sLl v+ a++
  gi|313122553|ref|YP_004044480.1| 234 TQGFTPVVPAVASLIFYVSLLLVVGAVI 261
                                       68999999*************9998886 PP

>> TraS  Plasmid conjugative transfer entry exclusion protein TraS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.027   1.6e+02      60      84 ..      12      38 ..       8      54 .. 0.72
   2 ?    8.5   0.7    0.0003       1.8      21      95 ..     193     266 ..     180     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.027
                              TraS 60 kfskgiwyvimpvcsl..lspllslmi 84
                                      k+  g wy  + +++l  + pllsl+i
  gi|313122553|ref|YP_004044480.1| 12 KLKAGSWYAYVALVALffVLPLLSLVI 38
                                      677899998888877622579999988 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0003
                              TraS  21 aewgvaetgiillfvllwqglfiwlfiqirk.knnisdefkfskgiwyvimpvcsllspllslmifiggtlyelrr 95 
                                        + gv  +g i+ fvl w+  +i  ++   +         ++++g   v+  v+sl+   +sl++++g+++ e+r 
  gi|313122553|ref|YP_004044480.1| 193 IKDGVV-SGAIFAFVLAWNNYYIVSYLSGVEsTITTWIHGRMTQGFTPVVPAVASLI-FYVSLLLVVGAVIIEFRE 266
                                       555665.68899***********9998754404444456789999999988888877.5789********999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1774.85
//
Query:       gi|313122554|ref|YP_004044481.1|  [L=312]
Description: ABC-type spermidine/putrescine transport system, permease component I [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-08   32.6  23.9    6.2e-08   32.6  23.9    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.018   14.3   0.1      0.025   13.9   0.1    1.4  1  DUF1101       Protein of unknown function (DUF1101)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   2.4     0.071   6.3e+02      49      72 ..      28      51 ..      20      62 .. 0.71
   2 !   32.6  23.9   6.9e-12   6.2e-08      29     174 ..     109     296 ..      75     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.071
                      BPD_transp_1 49 lghlilpviillllsaapyvrlir 72
                                       +  +lp+ +lll++++++++ i+
  gi|313122554|ref|YP_004044481.1| 28 PYLFMLPLTVLLLFMFVGPMVAIV 51
                                      566788877888888777777765 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 6.9e-12
                      BPD_transp_1  29 slPsfv.............laillvlvf.............................vilsilghlilpviilllls 63 
                                       s P                l++l++ +f                             ++  +  +  + +i+ +++ 
  gi|313122554|ref|YP_004044481.1| 109 SYPAAYalarkikryklvfLLMLIIPLFtsvnirvfgwalflvqngvldsivglfgiSNYPSMMYQRWTIILGTTYV 185
                                       44444455555555553332333332235555555555555666999999999987755555667788899999*** PP

                      BPD_transp_1  64 aapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtl 140
                                       ++p++++ ++  l s+++   eaa  lGa++ ++frk++lP+++p ii g +++f++ lg+ v + +lg+++ + t+
  gi|313122554|ref|YP_004044481.1| 186 YMPFMLFPIYLSLLSIEDTTFEAAADLGANKLTMFRKILLPLSMPGIIIGSLFVFILTLGADVEAQILGGGS-VYTM 261
                                       *********************************************************************887.**** PP

                      BPD_transp_1 141 lleailgydyseis.nggvlalviavlllnlvadi 174
                                         +++ ++ ys++   g++ a++++++ +++ + i
  gi|313122554|ref|YP_004044481.1| 262 ASNINYSFGYSQNWpLGSAQAVGLLLITVVAGVII 296
                                       ***********999633333333333333333333 PP

>> DUF1101  Protein of unknown function (DUF1101)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.8e-06     0.025     289     327 ..     169     207 ..      83     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-06
                           DUF1101 289 lsmmyirailimvmikdyspiklvplylnaleiedpaym 327
                                        smmy r  +i+     y p  l p+yl  l ied ++ 
  gi|313122554|ref|YP_004044481.1| 169 PSMMYQRWTIILGTTYVYMPFMLFPIYLSLLSIEDTTFE 207
                                       59*********************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1954.86
//
Query:       gi|313122555|ref|YP_004044482.1|  [L=353]
Description: ABC-type spermidine/putrescine transport system, ATPase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-37  127.3   0.0      1e-36  126.4   0.0    1.4  1  ABC_tran      ABC transporter
    2.2e-10   40.9   0.1    2.4e-05   24.3   0.1    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.7e-06   25.2   0.0      0.011   15.2   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    2.4e-05   24.6   0.1    7.4e-05   23.0   0.1    1.9  2  AAA_22        AAA domain
     0.0001   22.8   0.0    0.00067   20.1   0.0    2.1  1  AAA           ATPase family associated with various cellular 
    0.00017   21.5   0.0       0.17   11.5   0.0    2.1  2  AAA_15        AAA ATPase domain
     0.0004   20.8   0.2    0.00078   19.9   0.2    1.6  1  AAA_16        AAA ATPase domain
    0.00091   19.2   0.0     0.0015   18.5   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
     0.0018   18.2   0.0     0.0028   17.6   0.0    1.3  1  Rad17         Rad17 P-loop domain
      0.005   16.8   0.4      0.074   13.0   0.0    2.2  2  NACHT         NACHT domain
     0.0068   16.4   0.0      0.019   15.0   0.0    1.7  2  AAA_14        AAA domain
     0.0093   16.2   0.2      0.023   15.0   0.2    1.6  1  AAA_28        AAA domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.019   14.9   0.0    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
      0.015   15.0   0.0      0.036   13.8   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
      0.017   15.6   0.1      0.026   15.0   0.1    1.4  1  AAA_23        AAA domain
      0.018   15.4   0.0      0.039   14.4   0.0    1.5  1  RNA_helicase  RNA helicase
      0.019   15.1   0.1      0.036   14.2   0.1    1.6  1  AAA_33        AAA domain
      0.024   14.3   0.0      0.047   13.4   0.0    1.4  1  AAA_30        AAA domain
      0.027   14.0   0.0      0.066   12.8   0.0    1.6  1  AAA_25        AAA domain
       0.04   14.5   0.0      0.095   13.2   0.0    1.7  1  AAA_18        AAA domain
      0.052   13.7   0.1       0.18   12.0   0.1    2.0  1  TOBE_2        TOBE domain
      0.053   12.9   0.2       0.59    9.5   0.1    2.0  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.059   13.4   0.0       0.18   11.8   0.0    1.8  1  AAA_5         AAA domain (dynein-related subfamily)
       0.11   11.7   0.0       0.21   10.8   0.0    1.4  1  Zeta_toxin    Zeta toxin
       0.14   11.9   0.0       0.23   11.2   0.0    1.3  1  AAA_24        AAA domain
       0.17   11.8   0.0       0.37   10.7   0.0    1.6  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.22   11.3   0.2        0.6    9.8   0.0    1.8  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.22   10.7   0.9       0.36   10.0   0.0    1.7  2  NB-ARC        NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.0   1.6e-39     1e-36       2     136 ..      18     158 ..      17     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 1.6e-39
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++v+l+++ ge   ivG++G+GK+tLl++lag+l+pt+Gei+ldg+d+++  ++  ++  + ++q   lfp++tvre
  gi|313122555|ref|YP_004044482.1|  18 NDVDLEIETGEFATIVGPSGCGKTTLLRMLAGHLEPTAGEINLDGQDITY--TSPQKRPTSLVFQSWALFPHMTVRE 92 
                                       89************************************************..78888899***************** PP

                                       H..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n          e + ++e++l++++l+   + ++++++++LSgGqkqrvalar+l+ +p++lllDEp 
  gi|313122555|ref|YP_004044482.1|  93 NiefpikntgrEVNGQVEELLEQVRLDP--EVHADKQATELSGGQKQRVALARSLAYDPDILLLDEPL 158
                                       *******999999999*********998..88889999*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.1e-05     0.026       1      23 [.      29      51 ..      29      78 .. 0.73
   2 !   24.3   0.1   3.7e-08   2.4e-05     231     299 ..     125     191 ..      85     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      ++ ++Gp g+GK++LL+ l +  
  gi|313122555|ref|YP_004044482.1| 29 FATIVGPSGCGKTTLLRMLAGHL 51
                                      678***************96543 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.7e-08
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                       + +a+elS G+k+  al+ +l++++   ++ll+DEp ++L++ l++rl + l +++ + +  +i +THS 
  gi|313122555|ref|YP_004044482.1| 125 DKQATELSGGQKQRVALARSLAYDP---DILLLDEPLASLDYVLQKRLQRELaDLNVELDMTFIYVTHSL 191
                                       4468899****************99...9*************999999966657777789*********7 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0032         2      25      41 ..      28      44 ..      15      51 .. 0.81
   2 !   15.2   0.0   1.7e-05     0.011     103     201 ..      88     193 ..      63     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0032
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      +f  ivGp G+GK+ ll
  gi|313122555|ref|YP_004044482.1| 28 EFATIVGPSGCGKTTLL 44
                                      699***********987 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.7e-05
                                       EETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtk.kevsellesagiske........lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                       +   ++ e+ i+++  +   +v+elle++++++e        +LSgG+k+ vala  +A   ++p  + llDe  a 
  gi|313122555|ref|YP_004044482.1|  88 MTVRENIEFPIKNTGREVnGQVEELLEQVRLDPEvhadkqatELSGGQKQRVALARSLA---YDPD-ILLLDEPLAS 160
                                       5555566666665555543799*********************************9877...6776.6799****** PP

                                       S-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkekskn..aQfivislreem 201
                                       LD    k++ + l   + +  + fi ++++ e 
  gi|313122555|ref|YP_004044482.1| 161 LDYVLQKRLQRELADLNVEldMTFIYVTHSLEA 193
                                       ****99999999986655433778888887655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   1.2e-07   7.4e-05       4      99 ..      26     156 ..      23     197 .. 0.62
   2 ?   -2.1   0.0       6.8   4.4e+03      83     103 ..     188     210 ..     158     221 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.2e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............................erpevv..fvtlpss 50 
                                       t  + +++G+sG+GKTtllr+l+  l+  a   e                            +   +v   ++ p +
  gi|313122555|ref|YP_004044482.1|  26 TGEFATIVGPSGCGKTTLLRMLAGHLEPTAG--EinldgqditytspqkrptslvfqswalfP-HMTVreNIEFPIK 99 
                                       67899*******************9965444..345887777777777544444444444431.1111233333333 PP

                            AAA_22  51 tsskdllrellralglelka....erlsseell.ealeqalrarav...ielliiDE 99 
                                       ++ +++  ++ + l++ + +    + ++  el   + ++ + ar+    + +l++DE
  gi|313122555|ref|YP_004044482.1| 100 NTGREVNGQVEELLEQVRLDpevhADKQATELSgGQKQRVALARSLaydPDILLLDE 156
                                       333333333333333333335556555666666666666666666666666777766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.8
                            AAA_22  83 eqalrarav..ielliiDEaqhl 103
                                       ++ l+a+ v   +l+++D+ + +
  gi|313122555|ref|YP_004044482.1| 188 THSLEAALVmsDKLFVLDDGDTV 210
                                       33333333344458888887766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     1e-06   0.00067       3      38 ..      32     101 ..      30     195 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-06
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS................................S CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk................................y 38 
                                       ++Gp G+GKT+l + +a +l+  +  ++++g +++                                  +
  gi|313122555|ref|YP_004044482.1|  32 IVGPSGCGKTTLLRMLAGHLEptAGEINLDGQDITYTspqkrptslvfqswalfphmtvreniefpiknT 101
                                       79******************73344588888888822345555555555555555555555555555550 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00027      0.17      17      43 ..      22      47 ..      16      73 .. 0.82
   2 !    7.8   0.0    0.0038       2.4     323     365 ..     148     190 ..     134     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                            AAA_15 17 veidlseeltvliGkNnsGKSsileal 43
                                       ei+  e + +++G+ ++GK+++l++l
  gi|313122555|ref|YP_004044482.1| 22 LEIETGE-FATIVGPSGCGKTTLLRML 47
                                      5666667.*****************99 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0038
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++ill++EP a+L + +qk l + l++l  + ++  i+ THS
  gi|313122555|ref|YP_004044482.1| 148 DPDILLLDEPLASLDYVLQKRLQRELADLNVELDMTFIYVTHS 190
                                       789******************************99*******9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   1.2e-06   0.00078      25      51 ..      28      54 ..      16     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                      e   ++G+sG+GK++l+r+l+ +le +
  gi|313122555|ref|YP_004044482.1| 28 EFATIVGPSGCGKTTLLRMLAGHLEPT 54
                                      67789****************999988 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-06    0.0015      99     131 ..      26      59 ..      11      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                                       T.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                         +++++vG+SG GK+tL+ +l+++le   ge+ 
  gi|313122555|ref|YP_004044482.1|  26 TgEFATIVGPSGCGKTTLLRMLAGHLEPTAGEIN 59 
                                       448899*******************999999886 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.3e-06    0.0028      48      91 ..      30      74 ..      16     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.3e-06
                             Rad17 48 LLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqksd 91
                                        i GPsGCgk+t +++L+  l +   e +l++  +  ++ qk  
  gi|313122555|ref|YP_004044482.1| 30 ATIVGPSGCGKTTLLRMLAGHLEPTAGEiNLDGQDITYTSPQKRP 74
                                      5699***************99988776535666666666666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00012     0.074       4      23 ..      31      50 ..      28      57 .. 0.87
   2 ?    1.8   0.1       0.3   1.9e+02      53      99 ..     164     216 ..     109     236 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                      EEEC-TTTCHHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklala 23
                                       + G++G+GKTtLl+ la  
  gi|313122555|ref|YP_004044482.1| 31 TIVGPSGCGKTTLLRMLAGH 50
                                      589************99865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.3
                                       -HCHHHCCCCTS--SSS-CCHHHHCCSCCCEE......EEEE-STT-SS-TCH CS
                             NACHT  53 sladllfsqlpepaapvsevwavllelperlL......lilDglDelvtdlgq 99 
                                        l++ l ++l +++ + +  +++++   e +L      ++lD+ D ++t +++
  gi|313122555|ref|YP_004044482.1| 164 VLQKRLQRELADLNVELDMTFIYVTHSLEAALvmsdklFVLDDGDTVQTGPPE 216
                                       44444555555555555556666666666666688888*******99998877 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     3e-05     0.019       4      44 ..      29      66 ..      26      85 .. 0.77
   2 ?   -2.9   0.0       9.8   6.3e+03     100     122 ..     160     182 ..     142     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdk 44
                                        +i+G+  +GKTtll+ l+ +l        +inld ++ +
  gi|313122555|ref|YP_004044482.1| 29 FATIVGPSGCGKTTLLRMLAGHLE---PTAGEINLDGQDIT 66
                                      678****************98877...77777777776553 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.8
                            AAA_14 100 Snskllskeiatslagrvaeiel 122
                                       S+ ++l+k+++ +la+   e+++
  gi|313122555|ref|YP_004044482.1| 160 SLDYVLQKRLQRELADLNVELDM 182
                                       66667777777777776666666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   3.6e-05     0.023       4      27 ..      32      55 ..      30      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-05
                            AAA_28  4 itGgestGKTtlleaLaargypvv 27
                                      i+G++++GKTtll+ La +  p+ 
  gi|313122555|ref|YP_004044482.1| 32 IVGPSGCGKTTLLRMLAGHLEPTA 55
                                      89***************8865555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.9e-05     0.019      16      44 ..      23      51 ..      18     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienl 44
                                      e e+ e+  i Gp g+GKt+Ll+ ++  l
  gi|313122555|ref|YP_004044482.1| 23 EIETGEFATIVGPSGCGKTTLLRMLAGHL 51
                                      67889999**************9887665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.6e-05     0.036      14      39 ..      19      44 ..      15      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                      + ++ei++ ++  ++GpsG GK+Tll
  gi|313122555|ref|YP_004044482.1| 19 DVDLEIETGEFATIVGPSGCGKTTLL 44
                                      567888877799*************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1     4e-05     0.026      20      39 ..      28      47 ..       9     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-05
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       +  I+Gp G+GKTT+l+ +
  gi|313122555|ref|YP_004044482.1| 28 EFATIVGPSGCGKTTLLRML 47
                                      4567*************876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     6e-05     0.039       3      36 ..      32      68 ..      30      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakall...kklklkkkdsvys 36
                                      ++Gpsg+GK+tl + La +l+   ++++l+ +d +y+
  gi|313122555|ref|YP_004044482.1| 32 IVGPSGCGKTTLLRMLAGHLEptaGEINLDGQDITYT 68
                                      89**************999985555556666666666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.6e-05     0.036       4      24 ..      32      52 ..      30     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-05
                            AAA_33  4 lvGlpGsGKstlaerllkklg 24
                                      +vG++G+GK+tl++ l+ +l 
  gi|313122555|ref|YP_004044482.1| 32 IVGPSGCGKTTLLRMLAGHLE 52
                                      69************9998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.4e-05     0.047      19      46 ..      28      56 ..      21      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.4e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g 46
                                       +a+++Gp G GKtt+l+ l+ ++e   g
  gi|313122555|ref|YP_004044482.1| 28 EFATIVGPSGCGKTTLLRMLAGHLEPTaG 56
                                      4899****************999887733 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0001     0.066      31      55 ..      25      49 ..      20      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                            AAA_25 31 pagelallaGapgtGKttlaldlal 55
                                        ge+a ++G++g+GKttl+  la 
  gi|313122555|ref|YP_004044482.1| 25 ETGEFATIVGPSGCGKTTLLRMLAG 49
                                      679****************987775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00015     0.095       3      25 ..      32      62 ..      31     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00015
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf........g 25
                                      + G++G+GKttl + L+ +l+         g
  gi|313122555|ref|YP_004044482.1| 32 IVGPSGCGKTTLLRMLAGHLEPtageinldG 62
                                      89**************988722344444442 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00028      0.18      16      74 ..     288     349 ..     268     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                            TOBE_2  16 an.glsGtVedveylGsstryvvelag.gqlvvvrqpnadr.dsalapGdtVelswdpddav 74 
                                        + g++ +V+++  +G+++++  + +   q+ v++++ +     +la+Gdt  l+wd+++ +
  gi|313122555|ref|YP_004044482.1| 288 KDfGAEVHVDNILVRGNTVLIEGSADHsDQDYVAEVDFEKFeGVDLAVGDTAYLQWDARKSI 349
                                       3568999***************6666526777777777776559*************98765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00093      0.59      27      83 ..      32      88 ..      24      93 .. 0.79
   2 ?    2.3   0.0      0.15        93      44     154 ..      83     197 ..      75     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00093
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphh 83
                                      +vGp+G+GKt l + l++ l p   e  l+ + i+  + +k+ ++l+ +     ph 
  gi|313122555|ref|YP_004044482.1| 32 IVGPSGCGKTTLLRMLAGHLEPTAGEINLDGQDITYTSPQKRPTSLVFQSWALFPHM 88
                                      79******************9999999998888887777666666666655555665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                      Mg_chelatase  44 sllpplseeealevakiasvag.kkeeekllkrrpfr.aphhsaskaalvGggskpkpGeislahn.GvLfLDE.lp 116
                                       +l+p+++ +e +e    ++  + + + e+ll++  +  + h    ++ l Gg+++    + sla    +L+LDE l+
  gi|313122555|ref|YP_004044482.1|  83 ALFPHMTVRENIEFPIKNTGREvNGQVEELLEQVRLDpEVHADKQATELSGGQKQRVALARSLAYDpDILLLDEpLA 159
                                       6788888899988866655555344555555555554145666667778899999999999999763799***9445 PP

                      Mg_chelatase 117 efkrkvlevLRePledgevtisrakakvefparfqlva 154
                                        ++    + L + l d +v++  +   v++  +  lv+
  gi|313122555|ref|YP_004044482.1| 160 SLDYVLQKRLQRELADLNVELDMTFIYVTHSLEAALVM 197
                                       55555556788888888888777777777777776666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028      0.18       4      24 ..      32      52 ..      30      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                                      EE--SSSSHHHHHHHGGGGBS CS
                             AAA_5  4 LvGppGtgKselaerlaaaln 24
                                      +vGp+G+gK++l + la  l+
  gi|313122555|ref|YP_004044482.1| 32 IVGPSGCGKTTLLRMLAGHLE 52
                                      79**************99883 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00033      0.21      21      54 ..      32      65 ..      25      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldpDdl 54
                                      ++G +G+GK++l+++l+  le++ + + ld+ d+
  gi|313122555|ref|YP_004044482.1| 32 IVGPSGCGKTTLLRMLAGHLEPTAGEINLDGQDI 65
                                      7899*****************9999999999887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00035      0.23       6      33 ..      31      62 ..      29     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                            AAA_24  6 liyGpsgiGKTtlakel....gpkplfidtek 33
                                       i+Gpsg GKTtl+++l    +p++  i++++
  gi|313122555|ref|YP_004044482.1| 31 TIVGPSGCGKTTLLRMLaghlEPTAGEINLDG 62
                                      599************99877777777777665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00057      0.37       3      24 ..      31      52 ..      29      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00057
                              MobB  3 givgksgsGKTtLleklipelk 24
                                      +ivg sg+GKTtLl  l  +l+
  gi|313122555|ref|YP_004044482.1| 31 TIVGPSGCGKTTLLRMLAGHLE 52
                                      69************99988776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00094       0.6       6      23 ..      32      49 ..      29      72 .. 0.84
   2 ?   -3.0   0.0       8.7   5.5e+03      46      70 ..     162     186 ..     161     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00094
                         PduV-EutP  6 liGkvgsGKttLtqalkg 23
                                      ++G++g+GKttL + l g
  gi|313122555|ref|YP_004044482.1| 32 IVGPSGCGKTTLLRMLAG 49
                                      79***********99987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.7
                         PduV-EutP  46 eylenrklysalivtsaeadvialv 70 
                                       +y+ +++l + l+ + +e d+  + 
  gi|313122555|ref|YP_004044482.1| 162 DYVLQKRLQRELADLNVELDMTFIY 186
                                       5888999999999999998876654 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00057      0.36      22      40 ..      29      47 ..      15      58 .. 0.82
   2 ?   -2.3   0.2       3.2   2.1e+03      75     111 ..     168     206 ..     162     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00057
                                      EEEEEESTTSSHHHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlakqi 40
                                      + ++vG  G+GKttl++  
  gi|313122555|ref|YP_004044482.1| 29 FATIVGPSGCGKTTLLRML 47
                                      679************9865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                       HHHCCCTTSSSS-STTS..HHHHHHHHCCCTTEEEEEEE CS
                            NB-ARC  75 eLslseddleekeeves..lkrklvrlLltkrfllvlDD 111
                                       +L+++ +dl+   +       + l  +L     l+vlDD
  gi|313122555|ref|YP_004044482.1| 168 RLQRELADLNVELDMTFiyVTHSLEAALVMSDKLFVLDD 206
                                       444444444433333324477888889999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2025.02
//
Query:       gi|313122556|ref|YP_004044483.1|  [L=409]
Description: hypothetical protein Hbor_38130 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-10   41.0   6.9    2.9e-10   40.4   6.9    1.2  1  SBP_bac_8  Bacterial extracellular solute-binding protein
    9.3e-07   28.5   1.2      2e-06   27.4   0.7    1.7  2  SBP_bac_6  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.72    9.8   6.2        7.1    6.7   0.1    2.3  2  LPD16      Large polyvalent protein-associated domain 16


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   6.9   4.9e-14   2.9e-10      30     256 ..     108     347 ..     100     370 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.9e-14
                                       HHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH...................-HHHHHTT......--T CS
                         SBP_bac_8  30 aalaagtapdidvvwanedalatlaeeglladlsdldnldd...................ltdalaav......gyd 81 
                                       + l++g+  ++ +++++ +++++lae+gl+ ++s++d+  +                   +      +      ++d
  gi|313122556|ref|YP_004044483.1| 108 NRLKSGEWKQFHQATFDMAWIPRLAEAGLIRPISYEDWKPYtfdqyidvfqkqngykyafV------NeddytfDLD 178
                                       557788888899999999****************655444455667777766666555552......044445599* PP

                                       S.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-SEGG---GGG.GGGTHHETTEE---H..HHH CS
                         SBP_bac_8  82 gklygvPyasetpyvliynkdllekaedpktwdellaaakklkgkfglpdpasgwl.qaallakdgksldddggkdg 157
                                       gk yg P   +    +++nkd +++  d kt+d+ ++  +++   +g +d   +w+ q+++l  +g ++ +  ++++
  gi|313122556|ref|YP_004044483.1| 179 GKMYGAPQRFGW-ASFVVNKDTVSAD-DYKTYDAAWS--EEY--DVGVYDL-MFWGiQIIMLR-EGIDPYKEHTDEE 247
                                       *******99997.79*********75.**********..**9..5666553.33432455555.6777766558999 PP

                                       .HHHHHHHHHHHHTT-EE.-S..--SSTTTTTSBSEEE.E-TTHHHHHH-TT.TSEEEE--S--EEEEEEEEEEBTT CS
                         SBP_bac_8 158 lkealellkklkdngkty.dtgadavsefanGevafti.ngswdiaaaqkag.kklgaivpkqgsfaggkglavpkn 231
                                       ++++++   +l dn kt+ ++ a++++++++Ge+ +++ +g+w+  +++  g  +++a vp +g +++++++a  k+
  gi|313122556|ref|YP_004044483.1| 248 VEQVRQATFDLFDNAKTLlPDFASMNQALKSGEIDIGFiSGNWINGTLRRGGnLQFEAHVPEEGGVIWVETTAFVKG 324
                                       98888777666677665559****************98789999999998752599999***********9988887 PP

                                       S-HHHHHHHHHHHHHTTSHHHHHHH CS
                         SBP_bac_8 232 aknedlaAldFlkwltspenqaala 256
                                              +   l ++ + en  +l+
  gi|313122556|ref|YP_004044483.1| 325 EQPTV--SDSYLAYMQQGENALKLS 347
                                       66665..777788887777777644 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.7   3.3e-10     2e-06      10     199 ..     123     336 ..      94     347 .. 0.77
   2 ?   -1.2   0.0      0.19   1.1e+03     154     178 ..     335     357 ..     326     360 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.3e-10
                         SBP_bac_6  10 fdkdflekfieeglfqpld...............panlpnvnkdfa.eeglkdp.dgkyy..pygvgplvlavnkdr 67 
                                       fd  ++ +++e+gl+ p+                 ++++ ++  f  e +++ + dgk y  p + g+++++vnkd 
  gi|313122556|ref|YP_004044483.1| 123 FDMAWIPRLAEAGLIRPISyedwkpytfdqyidvFQKQNGYKYAFVnEDDYTFDlDGKMYgaPQRFGWASFVVNKDT 199
                                       89999***********************999999777777777788899999999********************** PP

                         SBP_bac_6  68 lkgrpvPksWaDLldPeykgkvalpgnng.sdlfealllalyk.....dfgedgvkkllrnlkanlhpaq..mvkaa 136
                                       + + ++ k+++  +++ey   v++ +    + ++ +l   +       d+ +++v++ + +l++n +        + 
  gi|313122556|ref|YP_004044483.1| 200 VSADDY-KTYDAAWSEEYD--VGVYDLMFwGIQIIMLREGIDPykehtDEEVEQVRQATFDLFDNAKTLLpdFASMN 273
                                       ******.***********5..55555444336666666666558899766688888888888888888878755666 PP

                         SBP_bac_6 137 gslesgepavs...vvpyffadilpekkkgknlkvvwPedGalvspifmlvkkgkkkelakafidf 199
                                       ++l+sge  ++   ++ ++ + +l++   + +++  +Pe+G+++++++ + +kg+++   + ++ +
  gi|313122556|ref|YP_004044483.1| 274 QALKSGE--IDigfISGNWINGTLRRGG-NLQFEAHVPEEGGVIWVETTAFVKGEQPTVSDSYLAY 336
                                       6677777..4400155678888887774.55999**************999999555555555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.19
                         SBP_bac_6 154 adilpekkkgknlkvvwPed.Galvs 178
                                       a + +  +    lk+ wP++ G+ v+
  gi|313122556|ref|YP_004044483.1| 335 AYMQQGEN---ALKLSWPTSgGTNVV 357
                                       44444444...999999999555555 PP

>> LPD16  Large polyvalent protein-associated domain 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.3    0.0049        29      13      46 ..     151     186 ..     148     188 .. 0.89
   2 ?    6.7   0.1    0.0012       7.1      26      76 ..     204     260 ..     191     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0049
                             LPD16  13 dqYlhiqeceeGydytlYdkd.yr.eldgGqldnpd 46 
                                       dqY+ +  +++Gy y++ ++d y+  ldg  + +p+
  gi|313122556|ref|YP_004044483.1| 151 DQYIDVFQKQNGYKYAFVNEDdYTfDLDGKMYGAPQ 186
                                       7999999**************987589999998886 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0012
                             LPD16  26 dytlYdkd.yreldgGqld.....npdltieeaadeiladedlkgkkaekvdleele 76 
                                       dy  Yd +  +e d G++d      + ++++e +d++ +  d++ +++++++++ ++
  gi|313122556|ref|YP_004044483.1| 204 DYKTYDAAwSEEYDVGVYDlmfwgIQIIMLREGIDPYKEHTDEEVEQVRQATFDLFD 260
                                       9********************997677999999999999999988888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2445.16
//
Query:       gi|313122557|ref|YP_004044484.1|  [L=391]
Description: alcohol dehydrogenase, class IV [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.5e-115  384.7   2.4   3.9e-115  384.5   2.4    1.0  1  Fe-ADH    Iron-containing alcohol dehydrogenase
    7.8e-17   61.8   2.1      2e-09   37.6   0.1    2.2  2  Fe-ADH_2  Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.5   2.4  4.4e-119  3.9e-115       1     364 []       5     373 ..       5     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 384.5 bits;  conditional E-value: 4.4e-119
                                       -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaala 77 
                                       P+ri+fg g+++e+g++l+++ga+ralivtd+g+  ++g+ld vl+++e+ag +++vfdgv p+pt++ v+eaa+++
  gi|313122557|ref|YP_004044484.1|   5 PNRILFGHGTAAETGTYLESFGAERALIVTDEGVR-AAGVLDPVLDAIEDAGKDYAVFDGVVPDPTDTVVHEAAEMY 80 
                                       99*******************************65.***************************************** PP

                                       -TT.--EEEEEESHHHHHHHHHHHHHTT...................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  78 reegadvviavGGGsviDtAKaialllanpe.vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegek 153
                                        +++ad++i++GGGs++DtAKa+++l++n++ +  y+g+ ++ + +++p i  PTt+G+Gsev +++++ d+e+  k
  gi|313122557|ref|YP_004044484.1|  81 DKADADMLIGIGGGSSMDTAKAASILATNGGhILNYEGVSNV-EYDTPPTIYMPTTSGSGSEVGHWCIVRDSETDIK 156
                                       *****************************966*****77766.66779***************************** PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHH.H CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadge.d 229
                                        +i+d ell+dla++Dp+lt+++P+ v aatg+D+l+ha+Ea+vs ka+  +  lal +i+ + k+l+rav+  + d
  gi|313122557|ref|YP_004044484.1| 157 EEIGDVELLADLALIDPQLTASAPAPVKAATGMDVLTHAIEAFVSIKAQSQTSSLALDSIEKVGKYLPRAVEYRGgD 233
                                       *********************************************999999999*******************555* PP

                                       HHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT....... CS
                            Fe-ADH 230 leareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralgge... 303
                                        ea  +m+ as  ag+af+ aglgavHa++h++g++fg+phgl+nai+lp+v+++n+++ pe+++ +a+ lg++   
  gi|313122557|ref|YP_004044484.1| 234 DEALGKMARASSQAGMAFNGAGLGAVHAISHQVGGKFGVPHGLINAIVLPYVMEYNLPQVPEKFVAVAERLGEDidh 310
                                       ***************************************************************************** PP

                                       .....T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-TSGGGGSSS---HHHH CS
                            Fe-ADH 304 ..sdeeaaeeliealrellkelglptsLselgvdeedldklaeaalkdrslannpreltaedv 364
                                           +++a ++++a rel +++ +p +L++ + +++++++la++al+d+sl +npr++ +ed+
  gi|313122557|ref|YP_004044484.1| 311 naPVRREAYKAVRAARELGDSVRIPETLADTDAERDAIPELAANALNDGSLTGNPRQTRQEDI 373
                                       999999*****************************************************9997 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1   2.2e-13     2e-09       2      97 ..      10     106 ..       9     110 .. 0.95
   2 !   23.7   0.4   3.6e-09   3.2e-05     140     246 ..     170     275 ..     164     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 2.2e-13
                          Fe-ADH_2   2 igegaleklgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketd 77 
                                       +g+g+  ++g +l++ +++++l+v+de++ +a + + v +++++ag + +v++ v ++++ + v + +e   ++++d
  gi|313122557|ref|YP_004044484.1|  10 FGHGTAAETGTYLESFGAERALIVTDEGVRAAgVLDPVLDAIEDAGKDYAVFDGVVPDPTDTVVHEAAEMYDKADAD 86 
                                       58999*************************99899*****************************999999999**** PP

                          Fe-ADH_2  78 lvvavGgGtiiDiakyvsak 97 
                                       +++++GgG+ +D+ak +s  
  gi|313122557|ref|YP_004044484.1|  87 MLIGIGGGSSMDTAKAASIL 106
                                       ****************9975 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.6e-09
                          Fe-ADH_2 140 iaDldvlaeAPrrllasGvGDllgkytaladwklanevseplaklsaamvqeaaeklve.dkketealeellealal 215
                                       ++D ++ a AP+   a+   D+l   +  + +  a++ + +la+ s+++v + + ++ve  ++++eal ++++a+  
  gi|313122557|ref|YP_004044484.1| 170 LIDPQLTASAPAPVKAATGMDVLTHAIEAFVSIKAQSQTSSLALDSIEKVGKYLPRAVEyRGGDDEALGKMARASSQ 246
                                       68***************999****999888888888888999****************967889************* PP

                          Fe-ADH_2 216 sgigisrpaSGsEHliSHaldmlalkqalHG 246
                                       +g+++  ++ G+ H iSH    ++   + HG
  gi|313122557|ref|YP_004044484.1| 247 AGMAFNGAGLGAVHAISHQVGGKF--GVPHG 275
                                       ******************998888..77777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 2862.18
//
Query:       gi|313122558|ref|YP_004044485.1|  [L=493]
Description: hypothetical protein Hbor_38150 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-88  294.6   1.6    9.4e-88  294.2   1.6    1.2  1  DUF1485   Metallopeptidase family M81
    2.6e-60  203.6   0.1    3.9e-60  203.0   0.1    1.3  1  MlrC_C    MlrC C-terminus


Domain annotation for each model (and alignments):
>> DUF1485  Metallopeptidase family M81
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.2   1.6     1e-91   9.4e-88       2     287 ..       6     291 ..       5     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 294.2 bits;  conditional E-value: 1e-91
                                       EEEEEEE--EETT--S-B-GGGEE...EEETHHHHHHHHTS-SHHHHHHHHHHHTT-EEEEEEEEEE-SEE-B-HHH CS
                           DUF1485   2 iaiaglahEtntFspvrttledFea..vlrGeelleafrgtntelggfidaaeaagvelvpllvaralPgGpvtrda 76 
                                       ++++++ hEtntFs  +t++++F++  +++G+++  +frg+nt++ggf+++a+++++++vp+++a a+PgG+vt+da
  gi|313122558|ref|YP_004044485.1|   6 VVLGQIEHETNTFSSLPTGIDQFADasLHYGDTIPPEFRGSNTAIGGFLRVADEKNWNVVPTVAADATPGGIVTADA 82 
                                       67899************************************************************************ PP

                                       HHHHHHHHHHHHHHS-.-SEEEEEE-S---BSS-SSHHHHHHHHHHHHHTTTSEEEEEE-TT----HHHHHH-SEEE CS
                           DUF1485  77 yeelkaeilerlkaalplDgvlldlHGAmvveglddaEgelleriRavvGpdvpiaaslDlHgnvserlveaadllv 153
                                        ++l +e+l+++++  p D+vll+lHGAmv e+++d++g +ler+R+++G d+p++aslDlH+n+ser+ve+ad l+
  gi|313122558|ref|YP_004044485.1|  83 LSSLLDEVLTGIEKSEP-DAVLLALHGAMVSEDHPDGDGYILERVREAAG-DIPVMASLDLHANISERMVEHADGLF 157
                                       **************876.*******************************6.9************************* PP

                                       E---SS---HHHHHHHH.HHHHHHTTT-SS-EEEEEEE-B--BS-.--SSSSHHHHHHHHHHHHHTSTT--EEEEE- CS
                           DUF1485 154 ayrtaPHvDmaetgeraarllvellkgekrpvkalvkvpillpgektsTrdePakslyarleeleaeegvldasvlv 230
                                       +y t+PHvD+ +tge aar ++++l+g   p +++ + p+l p+   +T++eP++sl++++++ ea+    d+sv++
  gi|313122558|ref|YP_004044485.1| 158 GYDTYPHVDIGDTGETAARAMAATLSGDLDPQVVVERAPLLPPLPPLQTDIEPMESLLQQAAASEAK-FRPDVSVFG 233
                                       ******************************************************************8.99******* PP

                                       --TT---SS-SEEEEEEESSS..SSHHHHHHHHHHHHHHTGGGSB---B-HHHHHHHH CS
                           DUF1485 231 GFpwaDvpragasvvvvgddee.aaaeaaaeelaralwdaraefvaptgsleealarA 287
                                       GF++aDv++ag+svv v+d++  ++ +a++++la++++++r+ef  ++ s+ +a+++A
  gi|313122558|ref|YP_004044485.1| 234 GFAYADVEEAGFSVVGVSDTHVaEETRATCKALAESAYERRHEFDHDYTSVGDAVEAA 291
                                       *******************987689999***************************998 PP

>> MlrC_C  MlrC C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.0   0.1   4.4e-64   3.9e-60       1     178 []     305     481 ..     305     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 203.0 bits;  conditional E-value: 4.4e-64
                                       EEEGGG-GGGT------HHHHHHHHH-TT--EEEEEE-HHHHHHHHHH-TT-EEEEEES-SS-TTS.--EEEEEEEE CS
                            MlrC_C   1 laDsgDNpgaGgsgdvtalLrellargekkvlvasivDpeavaaaaaagvGatveltlGgkvdalhgepveltgtVe 77 
                                       laD +DNpg+G++ d+t++L+ ll++g++++++a+ivDp+avaaa++agvG+tv ++lGg++++  g+p+ ++g+V+
  gi|313122558|ref|YP_004044485.1| 305 LADLADNPGGGSAEDGTFILESLLDAGIEDAALALIVDPDAVAAAVEAGVGNTVAVDLGGHIEDN-GDPLAVEGRVR 380
                                       79**************************************************************8.*********** PP

                                       EEEEEEEE--SSTTTT-EEEEEEEEEEEETTEEEEEESS-----STHHHHHTT--GGG-SEEEES-SSTTHHHHTTT CS
                            MlrC_C  78 alsdgrytaegpmltgqevdlgrtavlrvggvdvvvtsrrkqphdleqftslgidpeeadivvvKsgvylraefapi 154
                                        +sdg y++ gpm +g +v+lgrtavl+++g+dv+v s r+qp+d+e f+++gi pe+++++v+Ks+v++ra+f+p+
  gi|313122558|ref|YP_004044485.1| 381 LISDGSYRNYGPMSRGLRVNLGRTAVLEIDGIDVIVGSHRQQPYDPEAFRRMGITPERQRVLVLKSTVHYRAAFEPM 457
                                       ***************************************************************************** PP

                                       E.EEEEE---STTSS-GGGS--ST CS
                            MlrC_C 155 aadiimaltpGvvdqdlarlpykr 178
                                       a +i ++++pG + +dl++++y++
  gi|313122558|ref|YP_004044485.1| 458 AGAIREVAAPGLCHPDLTQFDYEH 481
                                       *********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3098.09
//
Query:       gi|313122559|ref|YP_004044486.1|  [L=481]
Description: NAD-dependent aldehyde dehydrogenase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.7e-158  526.5   0.4   5.7e-158  526.2   0.4    1.0  1  Aldedh    Aldehyde dehydrogenase family
     0.0046   16.0   0.0     0.0097   15.0   0.0    1.5  2  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.2   0.4  6.4e-162  5.7e-158       6     462 .]      15     469 ..      11     469 .. 0.98

  Alignments for each domain:
  == domain 1  score: 526.2 bits;  conditional E-value: 6.4e-162
                                       SSEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH--- CS
                            Aldedh   6 setievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkp 82 
                                       +e++ v  Patg+v+++v+++ta++  +a++aA++a ++w+  +++eR++ L+++ad +e++++e+ael+++etGk 
  gi|313122559|ref|YP_004044486.1|  15 EERLSVDAPATGDVLGTVASGTAAQTADAIEAAQRAAREWRYSDPSERSAPLAAVADRIEDEADEIAELLSRETGKC 91 
                                       3679999********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEE CS
                            Aldedh  83 laearaeveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvl 159
                                       la a++ev+e++  +r+ya+  +k++g+++p+ ++++++++r P+Gv++ I+PWN+Plll ++++a+ala+GNtvv 
  gi|313122559|ref|YP_004044486.1|  92 LATAEGEVAETVAQFRFYAGVTDKVRGDTVPTPSNRFNYTKRVPYGVTAHIVPWNYPLLLGSRSIAAALATGNTVVA 168
                                       ********************************88******************************************* PP

                                       EE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE CS
                            Aldedh 160 KPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlEl 236
                                       K  +++pl+++   e++ e ++P+gv+n+++g+gsevg +l ++ +vd++sftGst vg++++++aak++ +v +El
  gi|313122559|ref|YP_004044486.1| 169 KAPSQAPLTTMWYGEFLVE-EFPDGVVNLLSGPGSEVGGELSDNANVDAISFTGSTMVGQHVLESAAKHIIPVDVEL 244
                                       *******************.********************************************************* PP

                                       ---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SS CS
                            Aldedh 237 GGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPlis 313
                                       GGk+p+ivl+daD ++a+ ++++g+f+n+GQ+C+a srl+v+e+i +e+v+++v++a+++++g + d++td+G++is
  gi|313122559|ref|YP_004044486.1| 245 GGKAPAIVLPDADPKNAAVGVATGIFSNTGQNCVAQSRLIVHEDIKEEVVDEIVAQAEAITLGPGTDPETDMGAVIS 321
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHH CS
                            Aldedh 314 eaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaiei 389
                                       e++le + +y+e +k+ega+ll+Gg+  ++++l++g+f+ePtv+++vt+dmriaqeEiFGPVlsvi+++++eeaie+
  gi|313122559|ref|YP_004044486.1| 322 EDALEDMLNYIEVGKKEGATLLTGGKrPDDPELADGNFLEPTVFDDVTNDMRIAQEEIFGPVLSVITVSSVEEAIEL 398
                                       **************************999************************************************ PP

                                       HHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                            Aldedh 390 aNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                       aNd++++Laa+++t +l  a r+a+rl+ G v +N+  ++ +++ p+gG k+Sg+Gregg eg+e++t+v +v
  gi|313122559|ref|YP_004044486.1| 399 ANDSNFALAASLWTGSL-DATRYADRLDHGLVAVNTFPVSMPQS-PWGGNKRSGIGREGGLEGVEAFTTVNSV 469
                                       **************985.6899***************9999999.***********************99876 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-06    0.0097      81     246 ..     127     286 ..     120     332 .. 0.66
   2 ?   -4.0   0.0      0.65   5.8e+03     319     342 ..     376     399 ..     372     400 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-06
                              LuxC  81 eksyekaqprglvlhvlsgNvpl.lpvmsilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvyf 156
                                         +y k++p g++ h+++ N pl l+  si+ +l ++n  + k +s+ p +++     l++  ++        vv+ 
  gi|313122559|ref|YP_004044486.1| 127 RFNYTKRVPYGVTAHIVPWNYPLlLGSRSIAAALATGNTVVAKAPSQAPLTTMWYGEFLVEEFPD-------GVVNL 196
                                       457*******************736899******************9999887655555555554.......22222 PP

                              LuxC 157 .ksgdtkleeeiv..qnaDvvvawGgeeaikaise.klkpgk.qlikfGakvSfavvdkealeeealdkaaeraAkD 228
                                        +++  ++  e++  +n+D+++  G+    + + e  +k     +++ G k   a+v ++a    + ++aa  +A+ 
  gi|313122559|ref|YP_004044486.1| 197 lSGPGSEVGGELSdnANVDAISFTGSTMVGQHVLEsAAKHIIpVDVELGGKAP-AIVLPDA----DPKNAAVGVATG 268
                                       24555555555554445566666666666666666333332213455666654.3333444....455566666666 PP

                              LuxC 229 iivfdQqAClspqvvfve 246
                                       i +   q C++   + v 
  gi|313122559|ref|YP_004044486.1| 269 IFSNTGQNCVAQSRLIVH 286
                                       666666666665555555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 0.65
                              LuxC 319 qeelnePlnrtvnvkavdsledvv 342
                                       qee++ P+  +++v  v+++ +++
  gi|313122559|ref|YP_004044486.1| 376 QEEIFGPVLSVITVSSVEEAIELA 399
                                       578999999999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 3383.70
//
Query:       gi|313122560|ref|YP_004044487.1|  [L=442]
Description: glutamine synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.1e-103  346.8   0.0     3e-103  345.4   0.0    1.6  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    2.5e-10   40.2   0.0    4.4e-10   39.4   0.0    1.4  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain
    4.4e-05   23.1   0.0     0.0047   16.6   0.0    2.3  2  Gln-synt_N    Glutamine synthetase, beta-Grasp domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.4   0.0  5.1e-107    3e-103       2     345 .]     102     438 ..     101     438 .. 0.93

  Alignments for each domain:
  == domain 1  score: 345.4 bits;  conditional E-value: 5.1e-107
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                        +PRs lk +++ +++ G++++vg+E EF l+  ++d+     +          p + +  ++++++d+ +dl++  
  gi|313122560|ref|YP_004044487.1| 102 LCPRSALKSVVEDVRDAGFEPFVGVETEFSLLAPDDDNG----W---------VPFNYRCSYDMDALDQSADLMHAW 165
                                       69*******************************998855....3.........34455789**************** PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                        +a++a g++v  +h+E+ +gQ+E+n++++da+++aD v++f+++vk++ r++gl+at mp+p +g+ ++g+H hlS
  gi|313122560|ref|YP_004044487.1| 166 SDAMNAGGYNVLGIHQESQPGQYEVNIEYDDAVTTADGVMFFRHMVKALSRNEGLKATMMPRPHSGEDANGLHYHLS 242
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGG...........G..B-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEE CS
                        Gln-synt_C 156 lwdkdgknlfadeddey...........a..lselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawg 219
                                       lw   ++n fa+ dd++           +  +s++ar+f+gGll+h+kalta++aptvnSYkRl+pg +aPv++awg
  gi|313122560|ref|YP_004044487.1| 243 LW-DGDENCFAGGDDAEdlqfpagkhphGagISDTARYFMGGLLEHMKALTAVCAPTVNSYKRLIPGIWAPVNIAWG 318
                                       **.5559***9988754222222222222347********************************************* PP

                                       SS-TTCSEEEE-TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTHTSS-B--SS CS
                        Gln-synt_C 220 arNRsallRipaskekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeerkgieelPas 296
                                        +NRs++lR p + + a+r+E+R+ d++aNPYL +Aa+laAgldGien+++pge + +++ye + e      +lP++
  gi|313122560|ref|YP_004044487.1| 319 PDNRSTVLRLPPELGPATRIEHRVTDSAANPYLSMAATLAAGLDGIENEIDPGEGTLSNAYEEDYE------NLPRT 389
                                       **************************************************************9996......5**** PP

                                       HHHHHHHHHCSHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 297 leeAlealeedellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       l  Al +le+d++l+++lge++++++++lkr+E+++++ +v+dwe+e+y
  gi|313122560|ref|YP_004044487.1| 390 LPGALAHLENDAVLRDALGEDLVSEFVKLKRDEFDRYQNHVTDWEREEY 438
                                       **********************************************988 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   7.3e-14   4.4e-10      11     105 ..       3      98 ..       1     100 [. 0.94

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 7.3e-14
                                       ------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SS.S--EEEEE-GGG-EEE CS
                      Gln-synt_N_2  11 eekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgp.vGelrLvpdPasaval 86 
                                        +k+ + i+++ +dl+Gv rG ++p ++L++   +G+G+ +   +l+ +  + +  ++gp +G++  v+d  s   l
  gi|313122560|ref|YP_004044487.1|   3 STKEFDTIRLVWTDLNGVARGISIPASELDNAAEEGVGFANGVAELTLEPGLLDDPKYGPqHGDMMAVADLDSVTPL 79 
                                       5788899****************************************999999888998768*************** PP

                                       ---SSTTSEEEEEE-TTS- CS
                      Gln-synt_N_2  87 pyaPdaaallgdlvevdgt 105
                                           + aa+++dl+ vdg 
  gi|313122560|ref|YP_004044487.1|  80 SWHENMAAVFTDLTTVDGK 98 
                                       *****************96 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.8e-07    0.0047       3      37 ..       8      41 ..       6      42 .. 0.94
   2 !    4.1   0.0    0.0065        39      50      80 ..      64      92 ..      61      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.8e-07
                                      -EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEE CS
                        Gln-synt_N  3 kfvdlqFtDikgklkhvtipadelsedaleegvsF 37
                                        ++l +tD++g  + ++ipa+el ++a eegv+F
  gi|313122560|ref|YP_004044487.1|  8 DTIRLVWTDLNGVARGISIPASEL-DNAAEEGVGF 41
                                      579*********************.********98 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0065
                                      --EEEEEEEGGGEEE-SS-SS-.EEEEEEEE CS
                        Gln-synt_N 50 eSDmlLkPdlstavidPfreekktarvicdv 80
                                      + Dm+ + dl++++++ ++e+  +a v+ d 
  gi|313122560|ref|YP_004044487.1| 64 HGDMMAVADLDSVTPLSWHEN--MAAVFTDL 92
                                      56*****************74..68887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 3151.62
//
Query:       gi|313122561|ref|YP_004044488.1|  [L=87]
Description: membrane protein involved in the export of O- antigen and teichoic acid [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 567.92
//
Query:       gi|313122562|ref|YP_004044489.1|  [L=700]
Description: phosphodiesterase/alkaline phosphatase D [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-51  174.8   0.0    4.6e-51  173.9   0.0    1.4  1  PhoD             PhoD-like phosphatase
    2.7e-18   66.3   4.1    6.4e-18   65.1   4.1    1.7  1  PhoD_N           PhoD-like phosphatase, N-terminal domain
    4.1e-18   65.6   0.0    1.1e-17   64.2   0.0    1.7  1  Laminin_B        Laminin B (Domain IV)
    7.2e-09   36.1   6.5    2.7e-08   34.3   6.5    2.0  1  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
  ------ inclusion threshold ------
      0.053   13.9   1.8       0.16   12.3   1.0    2.3  2  fn3              Fibronectin type III domain
      0.058   13.3   0.5       0.14   12.1   0.5    1.7  1  TAT_signal       TAT (twin-arginine translocation) pathway si


Domain annotation for each model (and alignments):
>> PhoD  PhoD-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.9   0.0   1.5e-54   4.6e-51      13     302 ..     203     458 ..     186     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 1.5e-54
                              PhoD  13 yfnayrelaeeedlDlvlhlGDyiYeygpgeyaseaaelgreveppkeivtladYReryaqyktdadlqa....... 82 
                                        f+  +++ae+ ++D++l+ GD+iY+++       ++  gr + +++ +  l+ YR +y++ +  ++  a       
  gi|313122562|ref|YP_004044489.1| 203 PFEGLQTIAER-QPDFFLYHGDTIYADA-------KTPAGRVTSDTSLADALDIYRGKYKEMRVPPESVAeqtylrs 271
                                       47888999**9.***************5.......4455555566677899**********9987775554555555 PP

                              PhoD  83 ahaaapfivvwDDHEvaNnswsggaenhqeetegdfekrkaaAlqAyfEwmPireakp...geeeriyrsfeyGdla 156
                                       + aa++++ +wDDHEv+Nn ++g           ++e +  +++qA++E+ Pi ++++   +e+ r+yrsf++G+ +
  gi|313122562|ref|YP_004044489.1| 272 LLAATSVVSIWDDHEVQNN-FAG-----------SIEPLMPSGRQAFIEYWPIDQSQQvtgTEASRLYRSFRWGAHL 336
                                       *******************.666...........6788889************99853355899************* PP

                              PhoD 157 dlflLDtRqyrrdqavsyegdeleaaeaevkdpartlLGeeQeqwLkaeLkasrarWkvlaqqvlmskvdldaelae 233
                                       +lf+LDtRqyr+++                  +++tlLG+eQ++wLk++L+as+a+Wkv+a+ +++++ +   ++a+
  gi|313122562|ref|YP_004044489.1| 337 ELFVLDTRQYRDPNLE---------------LKQKTLLGREQLEWLKSSLSASDATWKVIASPAPLGQPS--DTWAT 396
                                       ************9974...............4678*********************************99..45544 PP

                              PhoD 234 galpvnlDawdGypaeRerlletikeakirnvVvLtGDvHaawandldykdpdgeavgvEfvtgsvssg 302
                                       ++         Gy+ae  +l++ i+ ++i+nvV+++GDvH++ ++ +d +d dge+ + E v+g++ + 
  gi|313122562|ref|YP_004044489.1| 397 PT------ERTGYEAELVELISYINTEEIANVVSVAGDVHYSQVSGFDPND-DGEFEFYEAVAGPLGAY 458
                                       44......789************************************5444.4469999*999999873 PP

>> PhoD_N  PhoD-like phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   4.1   2.1e-21   6.4e-18       1      82 [.      71     146 ..      71     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.1e-21
                            PhoD_N   1 hGVasGDptadsvilWTRvapeseerpvrvevevaedeafkkvvrkgtalatseldytvkvevtgLkpgqeyfYrfr 77 
                                       hGVasGD+ta+ +++W+R+a     ++++++v++++d++f +++r+ t+++  ++dyt +v++t+L+p+++y+Yr+ 
  gi|313122562|ref|YP_004044489.1|  71 HGVASGDVTATTAVVWARTA-----DTATLQVQYSTDDEFDSTQRQ-TTTVADSTDYTGHVRLTELQPATRYYYRVW 141
                                       9*******************.....99*************888855.55666789*********************8 PP

                            PhoD_N  78 agses 82 
                                       a + +
  gi|313122562|ref|YP_004044489.1| 142 ATAGT 146
                                       54433 PP

>> Laminin_B  Laminin B (Domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   3.7e-21   1.1e-17       1     120 [.     573     698 ..     573     699 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 3.7e-21
                         Laminin_B   1 ywsaPekflGnkltSYGgkLkytvryekeargesekep...dvileGngltlsysese.esspspsqettysvrLre 73 
                                       y++aP kflG +   YGg+L + +r+e+++++  +  p   d++l G+g+tl y+ +  +s+p+    t+++v L  
  gi|313122562|ref|YP_004044489.1| 573 YYQAPFKFLGPRDAFYGGTLAFDLRQEETDQQFDAALPvggDIVLSGSGMTLVYEFRGdNSKPET-DWTSFEVSLSA 648
                                       89*************************43333332335666*************98543555555.5889*****99 PP

                         Laminin_B  74 e.nwrh...sdglpvsredfmrvLanltallIrasystgqsessLssvsLd 120
                                       +  w +   +d+  ++ ++f  vL++lt+++Ir+ y+tg ++s+L++v L+
  gi|313122562|ref|YP_004044489.1| 649 DdDWINidsQDPF-ATEDEFRAVLSDLTQFRIRGEYRTGLDQSRLDNVVLT 698
                                       6689444324444.**********************************997 PP

>> Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   6.5   9.1e-12   2.7e-08      11      89 ..      77     149 ..      68     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 9.1e-12
                   Pur_ac_phosph_N  11 dtstsmtvsWitpektkksvvrygtssdalestaeatsstyettnyksgyshkatltgLepgttYyYrvgddeggwS 87 
                                       d + + +v W  +++t++ +v+y+t+++ ++++ + t+       + + y+ +++lt+L+p t+YyYrv ++  g+S
  gi|313122562|ref|YP_004044489.1|  77 DVTATTAVVWARTADTATLQVQYSTDDEFDSTQRQTTT-----VADSTDYTGHVRLTELQPATRYYYRVWATA-GTS 147
                                       366778899******9**********988766655444.....46899*********************8886.455 PP

                   Pur_ac_phosph_N  88 ev 89 
                                       ++
  gi|313122562|ref|YP_004044489.1| 148 DE 149
                                       54 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.0   5.5e-05      0.16      32      79 ..      94     146 ..      77     152 .. 0.74
   2 ?   -3.1   0.0       3.4     1e+04      27      42 ..     636     651 ..     632     676 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                                       EEEEEEEETTSTS..TEEEEEECST...SSEEEEESSSTTEEEEEEEEEEETS CS
                               fn3  32 gYeveyrekgsee..ewneftvprt...ttsvtltgLkpgteYevrVqavngg 79 
                                         +v+y+++++ +  + ++ tv  +   t +v lt L+p t+Y  rV a  g 
  gi|313122562|ref|YP_004044489.1|  94 TLQVQYSTDDEFDstQRQTTTVADStdyTGHVRLTELQPATRYYYRVWATAGT 146
                                       5689999999999653333333333344559****************987766 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.4
                                       SSTEEEEEEEEEETTS CS
                               fn3  27 ggpitgYeveyrekgs 42 
                                       + ++t++ev ++ +++
  gi|313122562|ref|YP_004044489.1| 636 ETDWTSFEVSLSADDD 651
                                       5667777777666543 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   4.6e-05      0.14       3      24 ..      15      37 ..      13      39 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.6e-05
                        TAT_signal  3 SRRdFLKgsAAaa.AAaalggca 24
                                      +RR+FL++ +  + AAa+l g +
  gi|313122562|ref|YP_004044489.1| 15 NRRTFLQAVGSSTvAAAGLSGTV 37
                                      8******8877776666677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (700 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 3851.98
//
Query:       gi|313122563|ref|YP_004044490.1|  [L=114]
Description: haloacid dehalogenase superfamily enzyme, subfamily IA [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.38
# Mc/sec: 900.28
//
Query:       gi|313122564|ref|YP_004044491.1|  [L=556]
Description: glycosyl transferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-19   70.5  35.9    4.1e-09   36.5   5.7    3.4  3  Beta_helix       Right handed beta helix region
    2.4e-16   60.2   3.5    2.4e-16   60.2   3.5    3.7  4  Pectate_lyase_3  Pectate lyase superfamily protein
    2.4e-11   43.4  23.7    4.7e-05   22.8   1.3    3.9  3  NosD             Periplasmic copper-binding protein (NosD)
  ------ inclusion threshold ------
      0.019   14.6   0.2      0.072   12.8   0.0    2.1  2  End_N_terminal   N terminal extension of bacteriophage endosi


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8  16.7   1.3e-11   5.7e-08      18     158 .]     160     309 ..     126     309 .. 0.78
   2 !   26.0   2.0   1.5e-09   6.9e-06      77     146 ..     275     351 ..     271     360 .. 0.90
   3 !   36.5   5.7   9.2e-13   4.1e-09      12     156 ..     365     505 ..     356     506 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.3e-11
                                       EES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-S CS
                        Beta_helix  18 isnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsG 94 
                                       +s+s++ G +++ + n ++ n    n++g+G+++ g +++ +s++ +++n    i+++g sn+ +++n ++++ + G
  gi|313122564|ref|YP_004044491.1| 160 LSGSSDGGNFVQLGANSTLHNVWSVNSTGDGVETVG-DGVSVSDCLFRNNEKRDIHIRG-SNTSVNDNLCENCQE-G 233
                                       333355555555555555555444448999999987.*********************5.5699*********87.7 PP

                                       EE-T.T........-S--EEES-EEESTT--SEE---TT...---EEES-EEES-SSEEEE-TT-SS--EEES-E. CS
                        Beta_helix  95 iyln.y........ssnntienNiidnnagsGividdss...snvtvtnNtitnnkgaGiavvgsssnvtvrnNti 158
                                       + ++ +         s + i++N+idn    Gi+i + s   ++ t+  N+i++++g+Gi   + + ++++++Nt+
  gi|313122564|ref|YP_004044491.1| 234 FAIKvGtattekgnISTVEITDNVIDNPVTGGISIGQKSawaTDATIVSNRIVDSGGHGIRSETAAKGLEIAGNTV 309
                                       77774366666555555*******************************************9999999*******96 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.5e-09
                                       -S--EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---TT......---EEES-EEES-SSEEEE-TT CS
                        Beta_helix  77 asnnlienneitdnggsGiyln.yssnntienNiidnnagsGividdss......snvtvtnNtitnnkgaGiavvg 146
                                       a   +i  n+i d gg+Gi+ +  ++ + i +N++   a++Gi+++ ++       +  vtnNt+ ++++ Giav +
  gi|313122564|ref|YP_004044491.1| 275 ATDATIVSNRIVDSGGHGIRSEtAAKGLEIAGNTVVKSAKDGIHVTVTErsaadcIRPQVTNNTVRDSGNSGIAVSN 351
                                       5678999************99966999**********************99*99977778*************9876 PP

  == domain 3  score: 36.5 bits;  conditional E-value: 9.2e-13
                                       EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEE CS
                        Beta_helix  12 tiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneit 88 
                                        ik+n++ ++g+++  + ++++ +i++n++++++  G++++  s +t+s+ +i+dn             +i+nn   
  gi|313122564|ref|YP_004044491.1| 365 RIKDNDVFGAGQAACRVSNTDDPRIDSNTFEGSQKQGLHVT--SSVTLSRVRIRDND------------IIDNNQAD 427
                                       69***************************************..67777777777776............77777777 PP

                                       S-SS-SEE-TT-S-.....-EEES-EEESTT....--SEE---TT...---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  89 dnggsGiylnyssn.....ntienNiidnna....gsGividdss...snvtvtnNtitnnkgaGiavvgsssnvtv 153
                                          + Gi+++ ++n     ++i++N id+++    + Gi+i d++   s+v  ++Nt+ n   ++  + +s++  +v
  gi|313122564|ref|YP_004044491.1| 428 SSFD-GIRTY-ADNasisaLVIRGNEIDSVGepqhQRGISIWDGAgsySSVHLRDNTVMNQTEVAYGISESDWYSVV 502
                                       7766.77665.222234456667777777777777777777777777777777777777777444444444444455 PP

                                       ES- CS
                        Beta_helix 154 rnN 156
                                       r+N
  gi|313122564|ref|YP_004044491.1| 503 RGN 505
                                       555 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   3.5   5.4e-20   2.4e-16       2     205 ..      48     247 ..      47     267 .. 0.80
   2 ?    1.5   2.7      0.05   2.3e+02     151     214 ..     244     317 ..     235     347 .. 0.49
   3 ?    3.5   1.5     0.013        57     105     187 ..     301     396 ..     270     419 .. 0.46
   4 !    4.4   1.0    0.0066        30     104     165 ..     417     485 ..     366     509 .. 0.46

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 5.4e-20
                                       EEGGGGT---EEEEE-HHHHHHHH......HTSS-EEE-SEEEEESS-E........EE-SSEEEEES-TTTEEEEE CS
                   Pectate_lyase_3   2 rnVkdyGakgDGvtDdtaaiqkaiscasatttgavVYfPaGtYlvsspi........ilksgvqLvGdgngrpvlka 70 
                                       +nVk  GakgDG+t+dt ai++a+ +  ++++g+  +fPaGtY+v +           +k + +++G g   + +ka
  gi|313122564|ref|YP_004044491.1|  48 VNVKAWGAKGDGSTNDTQAIRDAL-SYLKEEGGGRLFFPAGTYVVCENSgpektfdlTDKPNLEICGVG-YASHIKA 122
                                       9***********************.899999**************99998899999999**********.8999*** PP

                                       -TT-SS--SEEES-TT.T-..-EEEEEEEEEEEGGGG-SS---SSEEE.....ES-E.EEEEEEEEEES-SSEEE-S CS
                   Pectate_lyase_3  71 aaafvgaglidgdpyv.sggsealiatnnfyrqirnlkiditavapga.....tgih.wqtaqatslenvefemsea 140
                                       ++++  a  +d+  +  +gg+    +      +i +l++d ++ ++g+     +g + +q + + +l+nv   +s++
  gi|313122564|ref|YP_004044491.1| 123 KDGV--AEGVDAGVVIfHGGE----N-----ADIHDLRVDGRRSTQGKlsgssDGGNfVQLGANSTLHNVWSVNSTG 188
                                       9954..455555555534433....2.....46888888888886666666665545499**********8888888 PP

                                       SS---TT---SS--EEEEES-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE-TT-EEEEEEE CS
                   Pectate_lyase_3 141 sgtkhqgifiengsggflndlvfsglgdigiavgnqqftvrnitfnnattgievlwgwgwtlknv 205
                                       +g     +    g g  ++d+ f+++++  i ++  +  v+++ ++n+++g+ ++ g++ t k++
  gi|313122564|ref|YP_004044491.1| 189 DG-----VE-TVGDGVSVSDCLFRNNEKRDIHIRGSNTSVNDNLCENCQEGFAIKVGTATTEKGN 247
                                       84.....32.23556668***************999****************9999988777744 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.05
                                       SS--EEEE..ES-EEES-SS-SEEES-EEEEEES-EEE-......S--SEEE-T.T-EEEEEEEEE.ESSSEEE CS
                   Pectate_lyase_3 151 engsggfl..ndlvfsglgdigiavgnqqftvrnitfnn......attgievlw.gwgwtlknvki.nncegGi 214
                                       e+g+ +++  +d v+++    gi +g++ +++++ t+ +       + gi+ ++  +g  ++++++ +++++Gi
  gi|313122564|ref|YP_004044491.1| 244 EKGNISTVeiTDNVIDNPVTGGISIGQKSAWATDATIVSnrivdsGGHGIRSETaAKGLEIAGNTVvKSAKDGI 317
                                       44444444444444444333333333222222222222222222245555555533335555443324444444 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.013
                                       GG-SS---S.SEEEES-EEE...EEEEEEEES-SSEEE-SSS---TT---SS--EEEE.........ES-EEES-SS CS
                   Pectate_lyase_3 105 nlkiditav.apgatgihwq...taqatslenvefemseasgtkhqgifiengsggfl.........ndlvfsglgd 168
                                        l i  + v +++++gih++    + a+++  ++++++  +   ++gi ++n  ++ +         +d  + g g+
  gi|313122564|ref|YP_004044491.1| 301 GLEIAGNTVvKSAKDGIHVTvteRSAADCIRPQVTNNTVRD-SGNSGIAVSNLTQERVsaavaspriKDNDVFGAGQ 376
                                       33444333323333555544222233333444444444444.45555555554442221222233334555555566 PP

                                       -SEEES.-EEEEEES-EEE- CS
                   Pectate_lyase_3 169 igiavg.nqqftvrnitfnn 187
                                        + +v+ +++  + ++tf++
  gi|313122564|ref|YP_004044491.1| 377 AACRVSnTDDPRIDSNTFEG 396
                                       66666313344445555555 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.0066
                                       GGG-SS---SSEEEES-EEEEEEEEEEES-SSEEE-SSS...---T.T---SS--EEEE....ES-EEES CS
                   Pectate_lyase_3 104 rnlkiditavapgatgihwqtaqatslenvefemseasg...tkhq.gifiengsggfl....ndlvfsg 165
                                        n +id ++++++ +gi+ ++a+++s+++ +++ +e +     +hq gi i +g+g++     +d ++ +
  gi|313122564|ref|YP_004044491.1| 417 DNDIIDNNQADSSFDGIR-TYADNASISALVIRGNEIDSvgePQHQrGISIWDGAGSYSsvhlRDNTVMN 485
                                       233344444444444433.355555555555533333322234444456655555543333332333322 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   9.5   2.8e-08   0.00013      34     154 ..     184     318 ..     132     327 .. 0.45
   2 !   22.8   1.3   1.1e-08   4.7e-05      94     174 ..     333     425 ..     326     427 .. 0.87
   3 !    9.6   1.7   0.00011       0.5      69     147 ..     417     509 ..     412     526 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.8e-08
                              NosD  34 isnsrdgilldnssnntitgntienl.ryGihlensesntiedntlssnesGialmsss......nn.tle..nNti 100
                                       ++++ dg+  +  ++++++++ ++n+ +  ih+ +s+   ++dn ++++++G+a++  +      n  t+e  +N+i
  gi|313122564|ref|YP_004044491.1| 184 VNSTGDGV-ETVGDGVSVSDCLFRNNeKRDIHIRGSNT-SVNDNLCENCQEGFAIKVGTattekgNIsTVEitDNVI 258
                                       23333333.33344444444444444444444444444.44444444444443333322122211112221224444 PP

                              NosD 101 snnenyGillsdssn....ntisnNtis.nnnkGiflens.ssntitgNriesnqkiGil 154
                                        n  + Gi++ + s      ti  N+i+ + + Gi+ e + ++ +i gN++ ++ k Gi+
  gi|313122564|ref|YP_004044491.1| 259 DNPVTGGISIGQKSAwatdATIVSNRIVdSGGHGIRSETAaKGLEIAGNTVVKSAKDGIH 318
                                       443333443333222222244444444444444444444434444444444444444444 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.1e-08
                              NosD  94 tlenNtisnnenyGillsdssn.........ntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsss. 159
                                        ++nNt++++ n Gi +s+ ++           i++N +    +++ +++n+++ +i +N++e++qk G++++ss  
  gi|313122564|ref|YP_004044491.1| 333 QVTNNTVRDSGNSGIAVSNLTQervsaavasPRIKDNDVFgAGQAACRVSNTDDPRIDSNTFEGSQKQGLHVTSSVt 409
                                       589*****************9977777766656999999*9******************************666654 PP

                              NosD 160 .egntiynNyFinnse 174
                                        ++ +i +N+ i+n++
  gi|313122564|ref|YP_004044491.1| 410 lSRVRIRDNDIIDNNQ 425
                                       4569999**9999985 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00011
                              NosD  69 esntiedntlssnesGialmsss....nntlenNtisnnen....yGillsdssn....ntisnNtis.nnnkGifl 132
                                       ++++i +n+++s+ +Gi  +  +    + ++++N+i +  +     Gi++ d ++      +++Nt++ +++ +  +
  gi|313122564|ref|YP_004044491.1| 417 DNDIIDNNQADSSFDGIRTYADNasisALVIRGNEIDSVGEpqhqRGISIWDGAGsyssVHLRDNTVMnQTEVAYGI 493
                                       56778888888888888888777666445788888887766777778888888774443448999998777777777 PP

                              NosD 133 ens.ssntitgNries 147
                                       ++s  +++++gN+ ++
  gi|313122564|ref|YP_004044491.1| 494 SESdWYSVVRGNYPSE 509
                                       7777888888887554 PP

>> End_N_terminal  N terminal extension of bacteriophage endosialidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.072       1      19 [.      55      73 ..      55      87 .. 0.89
   2 ?   -2.7   0.1       1.1   4.9e+03       3      23 ..     188     210 ..     186     221 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                                      ---EEEEE-HHHHHHHHHH CS
                    End_N_terminal  1 akGDGvtdDtdalsevlaa 19
                                      akGDG t+Dt+a+ ++l+ 
  gi|313122564|ref|YP_004044491.1| 55 AKGDGSTNDTQAIRDALSY 73
                                      89**************985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                       -EEEEE..-HHHHHHHHHHS-TT CS
                    End_N_terminal   3 GDGvtd..Dtdalsevlaaapvg 23 
                                       GDGv    D  ++s+ l    + 
  gi|313122564|ref|YP_004044491.1| 188 GDGVETvgDGVSVSDCLFRNNEK 210
                                       77775322666666666665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3488.38
//
Query:       gi|313122565|ref|YP_004044492.1|  [L=41]
Description: TIM-barrel fold metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.18s 00:00:00.49 Elapsed: 00:00:00.35
# Mc/sec: 349.79
//
Query:       gi|313122566|ref|YP_004044493.1|  [L=66]
Description: enoyl-CoA hydratase/carnithine racemase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 449.05
//
Query:       gi|313122567|ref|YP_004044494.1|  [L=119]
Description: DNA binding protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.12   12.4   0.5       0.32   11.1   0.5    1.8  1  HTH_20        Helix-turn-helix domain
       0.14   11.8   0.0       0.36   10.5   0.0    1.7  2  Thymopoietin  Thymopoietin protein


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   3.5e-05      0.32       5      35 ..      13      43 ..       9      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
                                      HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHT CS
                            HTH_20  5 eALahPvRrrilraLaraegltaselaerld 35
                                      e+ ahP Rrr+l  L r   l+++++a++l 
  gi|313122567|ref|YP_004044494.1| 13 ELHAHPYRRRLLICLDRHITLSVADIADELA 43
                                      5669************************994 PP

>> Thymopoietin  Thymopoietin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       0.4   3.6e+03      16      22 ..      11      17 ..      11      18 .. 0.88
   2 ?   10.5   0.0     4e-05      0.36      28      44 ..      55      71 ..      44      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.4
                      Thymopoietin 16 KSeLvah 22
                                      +SeL ah
  gi|313122567|ref|YP_004044494.1| 11 RSELHAH 17
                                      79**999 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 4e-05
                      Thymopoietin 28 pgesrKdVYVqLYLkhl 44
                                      p+e  Kd+Y +LY  hl
  gi|313122567|ref|YP_004044494.1| 55 PAEDVKDIYMELYHTHL 71
                                      7999*********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 786.77
//
Query:       gi|313122568|ref|YP_004044495.1|  [L=109]
Description: hypothetical protein Hbor_38250 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.23s 00:00:00.52 Elapsed: 00:00:00.38
# Mc/sec: 853.49
//
Query:       gi|313122569|ref|YP_004044496.1|  [L=143]
Description: universal stress protein UspA-like protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-26   92.9   1.2    2.9e-26   92.7   1.2    1.0  1  Usp             Universal stress protein family
     0.0025   18.1   1.2      0.012   15.9   1.2    1.9  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.023   14.1   0.0      0.028   13.9   0.0    1.1  1  ATP-grasp_5     ATP-grasp domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   1.2   4.8e-30   2.9e-26       4     141 .]       5     143 .]       3     143 .] 0.92

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 4.8e-30
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCT CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeag 78 
                                       ++lV++Dgs+ +++Al +A++   ++++++++l+v+ p +s+++  +     e++ e + +++ ++   a+++a++ 
  gi|313122569|ref|YP_004044496.1|   5 HVLVPLDGSPLADEALAHAID---TFDCPVTVLNVVTPLDSSMSEGGIVGNDESRREAAHERANELIetARRRAAES 78 
                                       79*******************...68999*********99999998888888877777777776666779******* PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCC..SSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrg..rsglsrlllGSvseyvlrhapcpVlvVr 141
                                       g + ++ ve+g+pae+ile+++++d+d i++G +g  +s l  +llG v+  v+ +ap+ V+vVr
  gi|313122569|ref|YP_004044496.1|  79 GRNLDTAVEMGEPAETILEYVDDHDVDHIIMGGHGgsQSELVSRLLGTVATTVVSEAPVTVTVVR 143
                                       ***********************************9999999999*******************8 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.2     2e-06     0.012      73     124 ..      88     139 ..      44     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                    baeRF_family10  73 lkevAellaklleergverlvlgGdeeetaalldrlpkalrarvvgtlplpv 124
                                       + e Ae++ +++++++v+++++gG+    ++l++rl   ++  vv + p+ v
  gi|313122569|ref|YP_004044496.1|  88 MGEPAETILEYVDDHDVDHIIMGGHGGSQSELVSRLLGTVATTVVSEAPVTV 139
                                       556799999************************************9988765 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.7e-06     0.028      39     141 ..      21     122 ..      15     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-06
                       ATP-grasp_5  39 veaaeeigypv.vlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkekspeariegvlVqemakrggrEli 114
                                       ++a+++++ pv vl +v p  +  ++ g v  + + +e+ ++ a+e++e+++++++e+  +  + +em +    E i
  gi|313122569|ref|YP_004044496.1|  21 AHAIDTFDCPVtVLNVVTPLDSSMSEGGIVGNDESRREAAHERANELIETARRRAAESGRNLDTAVEMGE--PAETI 95 
                                       567778888852566666666666666666666668899999***********99998877777778866..69*** PP

                       ATP-grasp_5 115 vgvteDpvFGpvilfGlGGtavevlkd 141
                                       + + +D     +i+ G+GG++ e+++ 
  gi|313122569|ref|YP_004044496.1|  96 LEYVDDHDVDHIIMGGHGGSQSELVSR 122
                                       **********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:02.92
# Mc/sec: 148.54
//
Query:       gi|313122570|ref|YP_004044497.1|  [L=401]
Description: phosphate/sulfate permease [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-40  138.9  31.3    2.7e-40  138.4  31.3    1.2  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4  31.3   1.5e-44   2.7e-40       2     336 ..      25     387 ..      24     388 .. 0.78

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 1.5e-44
                              PHO4   2 GanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwll 78 
                                       Gan  +  fa+++g++a+++++A++l +i+ +lGa+ +G++++et++ g++d      ++  l+++a ll+a+++++
  gi|313122570|ref|YP_004044497.1|  25 GANSNSPPFAPAIGANAISTMRAAFLIGILAALGALAQGGSISETVGAGLID----GVAITSLAATAGLLTATAFMA 97 
                                       9**************************************************5....3334459************** PP

                              PHO4  79 latvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrl......ilvkek 149
                                       + +++g+Pv  +++++Ga++G++l ++g+ a+   +  +i+++w+l P ++g +a+l+++l++r             
  gi|313122570|ref|YP_004044497.1|  98 FGVYTGYPVPAAFATTGAMVGVGLSLGGTPAL--ATYRRIAIFWMLVPPVSGSLAYLTATLLRRDdipetvG----- 167
                                       *************************8775444..45689*************************94444330..... PP

                              PHO4 150 lknalralpvlvlvt.........................................iailalsilfkgesk....kd 181
                                              +p+l+ ++                                         i++++++++  g+ +    + 
  gi|313122570|ref|YP_004044497.1| 168 -------VPLLAGIVgsivanvrlsvipapggakqnslagfvsgvmpapsiagvdpIVVIVTVLVGAGSFQyirrRT 237
                                       .......3433333322222222233333333333333333333334444444444333333333333222322345 PP

                              PHO4 182 deeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykask.evplw.vlllgglaialGlllgGkrvikt 256
                                         ++ k +k+++vv +++v+f+ G+++v  a+Gpl   l+     ++   p + + +lg ++i+ G ++g++r+ ++
  gi|313122570|ref|YP_004044497.1| 238 IASVDKGVKTFLVVLGSVVAFSSGGSQVGLATGPL-ENLYG----TElGLPGIvLSALGSIGILGGAWMGAPRLLQA 309
                                       5666777****************************.65643....4556675516699******************* PP

                              PHO4 257 vGekitkkltpsrGfaaelaaaltvl.lasklglPvStThvlvgavvGvGlakkresavnwklvrnivlaWvlTlpv 332
                                        ++++  +l   r++ a+l+  ++++ la  lg+P+S++++++++v+G Gla  ++++v+++ ++ +++ W++Tl+ 
  gi|313122570|ref|YP_004044497.1| 310 TSREYA-QLGIRRSI-AALVPGFIIAqLAIELGIPISFNNIIISGVIGGGLAG-GSAGVSRRKIGVTLAFWLFTLVT 383
                                       ******.5******9.66777777777**************************.68********************* PP

                              PHO4 333 sall 336
                                       s+++
  gi|313122570|ref|YP_004044497.1| 384 SVAI 387
                                       9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2557.90
//
Query:       gi|313122571|ref|YP_004044498.1|  [L=348]
Description: WD40-like repeat protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-39  135.7  12.5    1.4e-26   93.5   6.1    2.2  2  PQQ_2           PQQ-like domain
    4.7e-36  122.4  16.6    1.4e-06   28.6   0.2    8.1  8  PQQ_3           PQQ-like domain
      3e-26   90.1   4.2    8.9e-05   22.2   0.1    7.3  8  PQQ             PQQ enzyme repeat
  ------ inclusion threshold ------
      0.013   15.8   0.4      0.027   14.8   0.4    1.5  1  CBM_6           Carbohydrate binding module (family 6)
      0.055   12.4   0.0       0.11   11.4   0.0    1.4  1  Arylsulfotrans  Arylsulfotransferase (ASST)


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   6.1   3.9e-30   1.4e-26       9     235 ..      15     240 ..       9     241 .. 0.86
   2 !   51.4   0.7     3e-17   1.1e-13       5     128 ..     229     345 ..     225     348 .] 0.80

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 3.9e-30
                             PQQ_2   9 daatGaelWrvdlarplgggvsravlsggtlfvat........gggrlvaldaatGkvlWettlegpvvgaplvaeg 77 
                                        +++ +++W+++l++   + +  + l +g+l+v +         + r++al+aatG+++W++ l+++  ++p v+++
  gi|313122571|ref|YP_004044498.1|  15 GPTDPETVWTTELEQVRATQT--PALVDGRLYVPSnavsdtarHRYRIHALSAATGAERWQVPLRSEPNAPPAVSGN 89 
                                       5667799****9966544445..7779999*999556666677999*********************9********* PP

                             PQQ_2  78 rvvvva....sdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerel 150
                                       +++v a    + g+++ + ++dG++ W  ++ +     +r +a p+v  + v++++ +g+++al++++G+vlW+r +
  gi|313122571|ref|YP_004044498.1|  90 QIIVTArrslEQGRIVCFQKRDGDEEWL-VDVN-----ARLTAPPTVNNGIVYIPDWRGRVHALSVSNGSVLWSRLV 160
                                       ******9998888***************.5555.....78999********************************99 PP

                             PQQ_2 151 aaprgtselsrvgdisgrpvvaeg.tVyassgqgr..llaldlatgrrlwskeissinglpildgdllyvvsageli 224
                                        a +        g+++ +pv +++ t+y  s++g+  ++ald++tg+++w+k+  +++g p++  + ++v+s+  +i
  gi|313122571|ref|YP_004044498.1| 161 DASE-------SGRTFTEPVAVNNeTLYLGSQSGTtgIVALDATTGETRWTKPTPAVTGGPVVHTNGIIVQSHHLVI 230
                                       6644.......47778888888777******9997568***************778888899999999999977777 PP

                             PQQ_2 225 aldratGavlW 235
                                       a+d a+G+ +W
  gi|313122571|ref|YP_004044498.1| 231 AFD-ADGTCRW 240
                                       777.5777777 PP

  == domain 2  score: 51.4 bits;  conditional E-value: 3e-17
                             PQQ_2   5 vsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvv 81 
                                       v a+da +G+  W+++   p ++ +  av ++++++v  +++ l+a+d  tG+  We++++g+ vg p+va++ v+ 
  gi|313122571|ref|YP_004044498.1| 229 VIAFDA-DGTCRWSFNA--PGDAVRPIAV-DDRHVYVS-TRNALYAID-WTGEKAWEYEPSGTQVGMPTVAGDTVLI 299
                                       78***8.8*******87..5566665677.99999996.*********.**************************88 PP

                             PQQ_2  82 vasdgqlialdaedGkrlWstqqrseepaelrssaspava..gdtvvvg 128
                                       + + ++l+al++ +G+++W+t+ + +  a + + a  ++   g+ v+++
  gi|313122571|ref|YP_004044498.1| 300 R-GSNHLTALSSVTGEKQWTTHPAVSGRAVVTPEA--IFMsaGGAVIAH 345
                                       8.79****************877775444433322..222346666666 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.2e-05     0.043       2      40 .]      20      67 ..      20      67 .. 0.85
   2 !   17.6   0.0   1.1e-06     0.004       1      38 [.      68     109 ..      68     111 .. 0.93
   3 !   22.4   0.1   3.4e-08   0.00012       1      37 [.     112     148 ..     112     151 .. 0.94
   4 !   15.3   0.3   5.9e-06     0.021       1      40 []     152     198 ..     152     198 .. 0.83
   5 !   17.2   0.0   1.5e-06    0.0053       1      39 [.     199     235 ..     199     235 .. 0.94
   6 !   28.6   0.2   3.9e-10   1.4e-06       1      37 [.     236     271 ..     236     273 .. 0.94
   7 !   11.0   0.0   0.00013      0.47       1      36 [.     274     308 ..     274     312 .. 0.85
   8 ?    0.7   0.1      0.23   8.1e+02       2      25 ..     314     329 ..     310     346 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                             PQQ_3  2 evlWsvqlpg.pvnsspavdgglvyvgtg........dGtlyAlDaet 40
                                      e++W+++l   +++ +pa+++g++yv +           +++Al a+t
  gi|313122571|ref|YP_004044498.1| 20 ETVWTTELEQvRATQTPALVDGRLYVPSNavsdtarhRYRIHALSAAT 67
                                      579*****999999*************998887777777777777766 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.1e-06
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg....dGtlyAlDa 38 
                                       G ++W+v+l ++ n++pav+g+ + v++     +G+++++  
  gi|313122571|ref|YP_004044498.1|  68 GAERWQVPLRSEPNAPPAVSGNQIIVTARrsleQGRIVCFQK 109
                                       899********999************999**********965 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 3.4e-08
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlD 37 
                                       G++ W v++ ++++++p+v +g+vy+ ++ G+++Al 
  gi|313122571|ref|YP_004044498.1| 112 GDEEWLVDVNARLTAPPTVNNGIVYIPDWRGRVHALS 148
                                       8899*******************************96 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 5.9e-06
                             PQQ_3   1 GevlWsv....qlpgpvnssp.avdgglvyvgtg..dGtlyAlDaet 40 
                                       G vlWs+    +  g++ + p av + ++y g+     +++AlDa+t
  gi|313122571|ref|YP_004044498.1| 152 GSVLWSRlvdaSESGRTFTEPvAVNNETLYLGSQsgTTGIVALDATT 198
                                       889****8755444566666669999*******************98 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 1.5e-06
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       Ge++W++++p +v+++p+v  + + v ++ + + A+Da+
  gi|313122571|ref|YP_004044498.1| 199 GETRWTKPTP-AVTGGPVVHTNGIIVQSH-HLVIAFDAD 235
                                       9*********.699**********9*998.*******95 PP

  == domain 6  score: 28.6 bits;  conditional E-value: 3.9e-10
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlD 37 
                                       G+ +Ws++ pg+++++ avd+++vyv+t  + lyA+D
  gi|313122571|ref|YP_004044498.1| 236 GTCRWSFNAPGDAVRPIAVDDRHVYVSTR-NALYAID 271
                                       6669************************8.******9 PP

  == domain 7  score: 11.0 bits;  conditional E-value: 0.00013
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtgdGtlyAl 36 
                                       Ge  W+++  g +v + p+v+g++v + ++ ++l+Al
  gi|313122571|ref|YP_004044498.1| 274 GEKAWEYEPSGtQV-GMPTVAGDTVLIRGS-NHLTAL 308
                                       8999***8776355.778**********99.999998 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 0.23
                             PQQ_3   2 evlWsvqlpgpvnsspavdgglvy 25 
                                       e +W++         pav+g+ v+
  gi|313122571|ref|YP_004044498.1| 314 EKQWTT--------HPAVSGRAVV 329
                                       444444........4555555443 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       3.5   1.2e+04      21      30 ..      20      29 ..      20      31 .. 0.79
   2 !   18.7   0.0   3.3e-07    0.0012      10      37 ..      58      85 ..      56      86 .. 0.93
   3 ?   -1.1   0.0       0.6   2.1e+03      10      24 ..     102     116 ..     102     124 .. 0.75
   4 !   15.8   0.0   2.6e-06    0.0094       1      25 [.     133     157 ..     133     158 .. 0.95
   5 !   22.2   0.1   2.5e-08   8.9e-05       3      35 ..     180     214 ..     179     217 .. 0.83
   6 !    5.8   0.0     0.004        14      12      32 ..     229     248 ..     219     253 .. 0.87
   7 !   17.4   0.1   8.6e-07    0.0031       2      36 ..     258     290 ..     257     292 .. 0.86
   8 ?    3.5   0.0     0.021        75       9      26 ..     302     319 ..     296     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.5
                                      CEEEEEESSS CS
                               PQQ 21 kvlWrfktgg 30
                                      + +W++++++
  gi|313122571|ref|YP_004044498.1| 20 ETVWTTELEQ 29
                                      579*999987 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.3e-07
                                      SEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ 10 GylyAlDadTGkvlWrfktggpvlslpi 37
                                      +++ Al a+TG ++W++++ +++++ p+
  gi|313122571|ref|YP_004044498.1| 58 YRIHALSAATGAERWQVPLRSEPNAPPA 85
                                      699*********************9997 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.6
                                       SEEEEEETTTCCEEE CS
                               PQQ  10 GylyAlDadTGkvlW 24 
                                       G+++ +  ++G++ W
  gi|313122571|ref|YP_004044498.1| 102 GRIVCFQKRDGDEEW 116
                                       6677777899***** PP

  == domain 4  score: 15.8 bits;  conditional E-value: 2.6e-06
                                       TEEEEEETTSEEEEEETTTCCEEEE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWr 25 
                                       g vy+++  G++ Al +++G vlW+
  gi|313122571|ref|YP_004044498.1| 133 GIVYIPDWRGRVHALSVSNGSVLWS 157
                                       689*********************7 PP

  == domain 5  score: 22.2 bits;  conditional E-value: 2.5e-08
                                       EEEE..ETTSEEEEEETTTCCEEEEEESSSCGSSE CS
                               PQQ   3 vylg..sadGylyAlDadTGkvlWrfktggpvlsl 35 
                                       +ylg  s  + ++AlDa+TG+ +W+++t+++  + 
  gi|313122571|ref|YP_004044498.1| 180 LYLGsqSGTTGIVALDATTGETRWTKPTPAVTGGP 214
                                       56776677788*****************9988775 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.004
                                       EEEEETTTCCEEEEEESSSCG CS
                               PQQ  12 lyAlDadTGkvlWrfktggpv 32 
                                       + A+D ++G+ +W+f+++g+ 
  gi|313122571|ref|YP_004044498.1| 229 VIAFD-ADGTCRWSFNAPGDA 248
                                       789**.***********9976 PP

  == domain 7  score: 17.4 bits;  conditional E-value: 8.6e-07
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvlslp 36 
                                       +vy+ +++  lyA+D  TG++ W+++++g  +++p
  gi|313122571|ref|YP_004044498.1| 258 HVYVSTRN-ALYAID-WTGEKAWEYEPSGTQVGMP 290
                                       56666666.9*****.**************99998 PP

  == domain 8  score: 3.5 bits;  conditional E-value: 0.021
                                       TSEEEEEETTTCCEEEEE CS
                               PQQ   9 dGylyAlDadTGkvlWrf 26 
                                        ++l Al   TG++ W++
  gi|313122571|ref|YP_004044498.1| 302 SNHLTALSSVTGEKQWTT 319
                                       689***********9986 PP

>> CBM_6  Carbohydrate binding module (family 6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.4   7.5e-06     0.027      21     111 ..     142     226 ..     131     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.5e-06
                                       TSEEEE---TT-EEEEEE.EEESSTEEEEEEEEEEESSSEEEEEEEESSTTSSEEEEEEE---SSTTEEEEEEEEEE CS
                             CBM_6  21 ggkavgyinnGdwlaYkd.vdfgsggaysvearvasgaaggsielrldsatgtlvgtvsvpstggwqtyvtvsanvt 96 
                                       g ++  +++nG+ + +++ vd  ++g  +++  va ++++    l+l+s ++   g v++ +t g + +++ + +vt
  gi|313122571|ref|YP_004044498.1| 142 GRVHALSVSNGS-VLWSRlVDASESGR-TFTEPVAVNNET----LYLGS-QSGTTGIVALDATTGETRWTKPTPAVT 211
                                       556677889999.55555499999998.9*********98....*****.77778999******************* PP

                                       E-SEEEEEEEEEECS CS
                             CBM_6  97 lptGvhdlylvftgg 111
                                           vh+  + ++ +
  gi|313122571|ref|YP_004044498.1| 212 GGPVVHTNGIIVQSH 226
                                       ***999988888775 PP

>> Arylsulfotrans  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05      0.11      25      82 ..     224     280 ..     177     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                    Arylsulfotrans  25 dekknnlivDtkGevrWyldqdkisdnklkrlkngkllilsgqklaefdllGrvikey 82 
                                       ++   ++++D++G  rW ++      +    +++ ++++ +++ l+ +d +G    ey
  gi|313122571|ref|YP_004044498.1| 224 QSHHLVIAFDADGTCRWSFNAPGDAVRP-IAVDDRHVYVSTRNALYAIDWTGEKAWEY 280
                                       5567889*****************9986.8999*******************976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2063.99
//
Query:       gi|313122572|ref|YP_004044499.1|  [L=323]
Description: hypothetical protein Hbor_38290 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-10   38.8  38.6     0.0097   16.0  14.3    6.3  7  Pentapeptide_3  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.26   4.7e+03      23      28 ..      99     104 ..      94     107 .. 0.61
   2 !    9.2   0.0   7.3e-05       1.3      11      39 ..     130     159 ..     127     161 .. 0.89
   3 !    7.7   4.9   0.00023         4      17      44 ..     200     231 ..     177     235 .. 0.55
   4 !    6.7   8.5   0.00045       8.1       9      39 ..     202     237 ..     200     252 .. 0.79
   5 !   13.8  10.4   2.8e-06      0.05       9      47 ..     228     273 ..     226     278 .. 0.78
   6 !   16.0  14.3   5.4e-07    0.0097       1      39 [.     258     300 ..     258     303 .. 0.81
   7 !   12.6  13.3   6.3e-06      0.11       1      42 [.     270     316 ..     270     323 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.26
                    Pentapeptide_3  23 FsnadF 28 
                                       F +a+F
  gi|313122572|ref|YP_004044499.1|  99 FIGATF 104
                                       444444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 7.3e-05
                    Pentapeptide_3  11 dFrgatFsgaasFsnadF.gsadFsgarFt 39 
                                        F++a+F+g+ s ++ +F + ++ + ++F+
  gi|313122572|ref|YP_004044499.1| 130 VFDHAVFKGGLSAQDVVFqQPIRACYTQFD 159
                                       6999*************9779999999997 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00023
                    Pentapeptide_3  17 FsgaasFsnadF...gsadFsgarFtgd..vdF 44 
                                        +  ++F++a F   g+++F ga  t d  v+F
  gi|313122572|ref|YP_004044499.1| 200 YEA-VNFRHAEFtndGTVRFGGAAVTADgqVRF 231
                                       222.26777777775677777776665544555 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.00045
                    Pentapeptide_3   9 aadFrgatFsgaa..sFsnadF...gsadFsgarFt 39 
                                       a++Fr+a F+++   +F +a     g ++F+g++F 
  gi|313122572|ref|YP_004044499.1| 202 AVNFRHAEFTNDGtvRFGGAAVtadGQVRFDGVTFR 237
                                       789999999999877799999999779999999996 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 2.8e-06
                    Pentapeptide_3   9 aadFrgatFsgaa..sFsnadF...g.sadFsgarFtgd.vdFsga 47 
                                        ++F+g+tF+ +   sF  ++F   +  ++F+g+ Ftgd v+Fs++
  gi|313122572|ref|YP_004044499.1| 228 QVRFDGVTFRTDGgvSFAATRFqngEyIVTFRGSSFTGDtVSFSNS 273
                                       5688888887666668999999888778999999999998888887 PP

  == domain 6  score: 16.0 bits;  conditional E-value: 5.4e-07
                    Pentapeptide_3   1 FsganFsga.adFrgatFsgaa..sFsnadF.gsadFsgarFt 39 
                                       F+g++F+g+ ++F+++ F+g+    F++++F + ++F +a F+
  gi|313122572|ref|YP_004044499.1| 258 FRGSSFTGDtVSFSNSEFHGSGttEFTGTTFnTHVRFTDAEFN 300
                                       8899999996699999999997545999999669999999997 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 6.3e-06
                    Pentapeptide_3   1 FsganFsga..adFrgatFsgaasFsnadF...gsadFsgarFtgdv 42 
                                       Fs+++F+g+  + F+g+tF+  ++F++a F   g+++F  +rF g++
  gi|313122572|ref|YP_004044499.1| 270 FSNSEFHGSgtTEFTGTTFNTHVRFTDAEFnttGGVSFISCRFRGNA 316
                                       999999999956********************77*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 2498.13
//
Query:       gi|313122573|ref|YP_004044500.1|  [L=235]
Description: pentapeptide repeat protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-07   29.8   2.6    5.9e-07   29.0   0.6    2.1  2  Pentapeptide  Pentapeptide repeats (8 copies)
  ------ inclusion threshold ------
      0.079   13.2   1.7       0.13   12.5   0.2    2.0  2  YqjK          YqjK-like protein


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.6   6.6e-11   5.9e-07      12      40 .]       2      30 ..       1      32 [. 0.56
   2 ?    0.3   0.0     0.065   5.9e+02       3      10 ..      38      45 ..      36      49 .. 0.41

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 6.6e-11
                                      CCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide 12 nLsganlsgAnLtgAnlsgAdLsganLsg 40
                                      +Lsga++s+AnLtg+nl+++d s a+L++
  gi|313122573|ref|YP_004044500.1|  2 DLSGADCSDANLTGVNLRKTDVSSADLRD 30
                                      45555555555555555555555555554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.065
                                      -TT-B-CC CS
                      Pentapeptide  3 LsgAnLsg 10
                                      + gAn+  
  gi|313122573|ref|YP_004044500.1| 38 CDGANFAK 45
                                      33444433 PP

>> YqjK  YqjK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.4e-05      0.13       5      39 ..      56      90 ..      54      93 .. 0.94
   2 ?   -1.4   0.1      0.31   2.8e+03      38      49 ..     153     164 ..     125     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                              YqjK  5 ieqQRldLaqaaepwekalapvDrgwqtlrslrkh 39
                                      ie+QR+++ +  ++w +  +  Dr+ ++++ lr+ 
  gi|313122573|ref|YP_004044500.1| 56 IEHQRALFGRGVRQWGRDAEDHDRTARGVHALREA 90
                                      99******************************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.31
                              YqjK  38 khlilvsgllal 49 
                                       +++ l++gl+a+
  gi|313122573|ref|YP_004044500.1| 153 RPAFLMIGLIAV 164
                                       445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 1873.79
//
Query:       gi|313122574|ref|YP_004044501.1|  [L=507]
Description: aldehyde dehydrogenase (acceptor) [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.6e-172  571.8   0.2   9.8e-172  571.6   0.2    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  571.6   0.2  5.4e-176  9.8e-172       1     462 []      40     502 ..      40     502 .. 0.99

  Alignments for each domain:
  == domain 1  score: 571.6 bits;  conditional E-value: 5.4e-176
                                       EET-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH.HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHH CS
                            Aldedh   1 wveses.etievinPatgeviakvpaataedvdaavaaAkeafk.awaklpaeeRaeiLrkaadlleerkeelaele 75 
                                       wv+s+s et+e+ +P+tge++a+ +a+ ++d+d+av+aA + ++  +++ + ++R+++L+++ad +e++ke +a+le
  gi|313122574|ref|YP_004044501.1|  40 WVRSASgETFETRDPTTGETLATLQAGVEADIDNAVEAAWKGYNtVYSDYSTADRQALLQEIADRVEANKEAFAQLE 116
                                       899999788********************************99967******************************* PP

                                       HHHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHH CS
                            Aldedh  76 tletGkplaearaeveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapala 152
                                       +l++Gkp++ear ++e ++d++ry+a+la+  +ge++++++++   +++eP+Gvvg+I+PWNfPll+aawklapala
  gi|313122574|ref|YP_004044501.1| 117 SLDNGKPITEARIDIELVVDHFRYFAGLARSHKGETIETDDSRSVQTYNEPYGVVGQIIPWNFPLLMAAWKLAPALA 193
                                       ***************************************999*********************************** PP

                                       TT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTT CS
                            Aldedh 153 aGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknl 229
                                       aGN+vvlKPaeetpls+l+l+e + +  +P+gv+nvvtg g e+g+ l++h++++kv+ftGstevg +++k+aa+n+
  gi|313122574|ref|YP_004044501.1| 194 AGNAVVLKPAEETPLSVLKLMEEAGD-VIPDGVVNVVTGFGTEAGAPLASHEDIRKVAFTGSTEVGSEVMKSAAENI 269
                                       **********************9999.7************************************************* PP

                                       SEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT- CS
                            Aldedh 230 krvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedt 306
                                       + +tlElGGk+pl+v++daDl++av+ +++++f+n+G+ C+a+srl+v+e++  ef+++l++aa++l vgdpl e+t
  gi|313122574|ref|YP_004044501.1| 270 TDITLELGGKSPLVVFPDADLEQAVRTTITAIFFNTGECCCAGSRLFVHEDVKTEFLDELAAAAAELVVGDPLLEST 346
                                       ***************************************************************************** PP

                                       SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESS CS
                            Aldedh 307 dvGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkd 382
                                       d+GP +se+q+++ ++y+eea++ ga  l+Gg+  +++ l++g+fv+Pt+++++++++r +qeEiFGPV  v++ +d
  gi|313122574|ref|YP_004044501.1| 347 DIGPKVSEEQVKNTMSYIEEARDSGASFLTGGAqPDDEALADGCFVTPTLIDEIDHNNRAVQEEIFGPVQEVFTWSD 423
                                       ********************************999999*************************************** PP

                                       HHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEE CS
                            Aldedh 383 eeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytev 459
                                        +e+ie+aNd +yGLaag+ t+dl++a+++a+++eaGn+++N+++++ a + pfgG+k+Sg+Gre++++++++yt++
  gi|313122574|ref|YP_004044501.1| 424 YDEMIELANDVDYGLAAGILTQDLTKAHQCAKDIEAGNIWVNTYNDFPAGQ-PFGGYKKSGIGRETSQKAIDHYTQT 499
                                       **********************************************99999.************************* PP

                                       EEE CS
                            Aldedh 460 ktv 462
                                       ktv
  gi|313122574|ref|YP_004044501.1| 500 KTV 502
                                       *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3229.84
//
Query:       gi|313122575|ref|YP_004044502.1|  [L=313]
Description: phenylacetate-CoA ligase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0078   16.1   0.4       0.54   10.1   0.4    2.5  1  TraB        TraB family
  ------ inclusion threshold ------
       0.18   11.7   3.9       0.32   10.9   3.9    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.4     6e-05      0.54     169     245 ..     199     290 ..      39     297 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6e-05
                              TraB 169 etldeleeakdlle..elveaykegdleal....e..le........aeaeeefpel.........kevlldeRnrr 220
                                       et+   e+++++l+   l+e+yk+ ++       +  ++        +                    +  ++Rn r
  gi|313122575|ref|YP_004044502.1| 199 ETV---EQEQQRLNegSLLEHYKRLNMLNSessvWqnDQqlyatafeN--------SdpgeytmvkLMTAWTQRNLR 264
                                       233...233333333478888888777777433323311444434321........022223333444567899999 PP

                              TraB 221 waekieallkep.gsvfvaVGagHla 245
                                        a++i +  + + ++++v+ G  H++
  gi|313122575|ref|YP_004044502.1| 265 IASNIWNVPNADdQRTLVIYGSSHVP 290
                                       99999998844449999999999987 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.9   3.5e-05      0.32       2      23 ..       1      21 [.       1      24 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.5e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggc 23
                                      ++RR+F  ++AAaa A+++g c
  gi|313122575|ref|YP_004044502.1|  1 MDRRSFVGATAAAAIAGLAG-C 21
                                      79******888887666554.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2003.52
//
Query:       gi|313122576|ref|YP_004044503.1|  [L=71]
Description: ABC-type branched-chain amino acid transport system, ATPase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 500.08
//
Query:       gi|313122577|ref|YP_004044504.1|  [L=687]
Description: siderophore synthetase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-56  190.8   0.0    4.1e-56  190.2   0.0    1.3  1  IucA_IucC  IucA / IucC family
    1.7e-31  109.9   0.0    5.5e-31  108.2   0.0    1.9  2  FhuF       Ferric iron reductase FhuF-like transporter
  ------ inclusion threshold ------
      0.037   12.9   0.0       0.05   12.5   0.0    1.1  1  Mus7       Mus7/MMS22 family


Domain annotation for each model (and alignments):
>> IucA_IucC  IucA / IucC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.2   0.0   6.9e-60   4.1e-56       3     238 ..     228     476 ..     226     477 .. 0.93

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 6.9e-60
                                       HHHHHH-----SS-S-S---BT--HHHHHHH-GGG---B--EEEEEETTTEEESTT-HHH...HHHHHH-HHHHHHH CS
                         IucA_IucC   3 lalEqllleGHpfhpaaKsRlgfseedaaaysPEfaasfrlrwvavhrelvtfssaeeeraqellaaeldpstraaf 79 
                                       +++++l++ GHp+hp aK R+++s++++ +++PEf  s++lr+vav++ ++   sa+  +  +  +  ++p   aa+
  gi|313122577|ref|YP_004044504.1| 228 AFFDRLVIGGHPIHPGAKLRRNMSPTESLSFAPEFTDSIQLRFVAVRNPHTLSVSADGIS-LTERLYSVFPGLAAAV 303
                                       6899*******************************************9999998888544.677889999******* PP

                                       HHHHCTT--GGGEEEEEE-HHHHHHTHHHHSHHHHHTTSEEEEEE-SS-EEE-TTSSEEEESS-TT.....-EEEE- CS
                         IucA_IucC  80 aaelksgldpedyvllpvHPwQwehliaplfaaeiakgrlvdlgesgdeylPtqSvRTlvnidrpa.....phvKls 151
                                       ++ l++g+ +e+y++lpvHPwQ++h+++ ++a+++++gr+v++ e +++++P++S+RT+v+ +++      ph+Kl+
  gi|313122577|ref|YP_004044504.1| 304 DESLPAGHGREEYAVLPVHPWQFRHVVPDRYADACQAGRVVPISEYSRSATPLLSLRTVVPSSAETslatpPHLKLA 380
                                       *****************************************************************9*********** PP

                                       EEEEETTEEE---HHHHHHHHHHHHHHHHHHHT-HHHHC--EE--EEEEEEE-..............-...T-SEEE CS
                         IucA_IucC 152 LsvritnsvRglspaeleaGpavsrlleellaadaflrerfkllrEvagiavthp........ayeel...ellgvl 217
                                       ++v++tn+vR+lsp+ +++Gp++ r++++ +++++f   rf +  E+a++ + +p            +   ++lg+l
  gi|313122577|ref|YP_004044504.1| 381 IGVQTTNAVRTLSPNVVADGPQLGRIVKQKCENESFE--RFGVRSEPAAACYYPPdgphpdgdG---YdavRHLGAL 452
                                       ***********************************98..7***************666554444...1666****** PP

                                       EE--CCCT-..T..-EEEEGGGGG CS
                         IucA_IucC 218 wRenpesll..g.deravplaaLl 238
                                       +R  p+++   g  e+av++a++l
  gi|313122577|ref|YP_004044504.1| 453 IRPHPATHPivGdSEQAVTAASVL 476
                                       *****888788779*******987 PP

>> FhuF  Ferric iron reductase FhuF-like transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.1   6.7e+03      53      89 ..      28      68 ..      17      71 .. 0.63
   2 !  108.2   0.0   9.2e-35   5.5e-31       2     157 ..     509     668 ..     508     673 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                                      ....TTT-EES-TT----.TTSGGGB----GGGSHHHHIII CS
                              FhuF 53 v...slkaellpelpalp.eevkrlltddpeelreevfygl 89
                                          +++ +  ++l++ p ee +r+l+ ++  +re+v+ gl
  gi|313122577|ref|YP_004044504.1| 28 AlpaAYHYAEQYDLSTPPdEEYRRTLVPARRSVRERVLGGL 68
                                      34444555555666666667777777777777777777766 PP

  == domain 2  score: 108.2 bits;  conditional E-value: 9.2e-35
                                       HHHHHHHHHHHHHHHHHHHHH-EE---STTTEEEEEETTEEEEEEE---....TTT-EES-TT----TTSGGGB--- CS
                              FhuF   2 lWlkrYfglllpPllhllleygialeahlqNvllvlddgrpvrlllrdfegv.slkaellpelpalpeevkrlltdd 77 
                                       ++l+ Y+++++p  l ll ++gi+leahlqN+ +v+d+g p+++l+ df++v +l+++l   ++  p++   ++t+d
  gi|313122577|ref|YP_004044504.1| 509 QFLSSYLDAVVPGPLTLLIKHGIGLEAHLQNTAVVFDNGQPTGALVSDFGDVrLLEPRLDVSFDPYPGSD--VCTRD 583
                                       7999*********************************************888744444444444444322..9**** PP

                                       -GGGSHHHHIIIIIIIHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHS......GGGHHHHHHT-TT-SEE-.-- CS
                              FhuF  78 peelreevfyglfvnhlapliealaaagglsekllWsnvaellewylael......pelaerfaqalLfaptlpgka 148
                                       pe+ re++ y+lf+nhl++l+++l+a+ ++se++ Ws v++++e++++ l      p+    ++++ Lfap+l  ++
  gi|313122577|ref|YP_004044504.1| 584 PEAAREKLWYALFQNHLGELVARLTATEPISETDCWSLVRRCCENVFDNLaadgsvPDDRVSADRDSLFAPKLG-HK 659
                                       **************************************************76654433333333777****999.88 PP

                                       -HHHHHH-X CS
                              FhuF 149 nllrvrlad 157
                                        l+ +r   
  gi|313122577|ref|YP_004044504.1| 660 PLTAMRISG 668
                                       888888765 PP

>> Mus7  Mus7/MMS22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.4e-06      0.05       2      46 ..     589     632 ..     588     646 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-06
                              Mus7   2 EslWqklftllplsevdangitqagarlkenWslvkrllsrvler 46 
                                       E+lW+ lf++  l e+ a ++++ +++++++Wslv r  ++v+++
  gi|313122577|ref|YP_004044504.1| 589 EKLWYALFQNH-LGELVARLTATEPISETDCWSLVRRCCENVFDN 632
                                       99******875.6777777777777777**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (687 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 4267.18
//
Query:       gi|313122578|ref|YP_004044505.1|  [L=638]
Description: ABC-type multidrug transport system, ATPase and permease component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-41  141.8   1.0      4e-41  141.5   1.0    1.1  1  ABC_membrane    ABC transporter transmembrane region
    1.4e-34  119.5   0.0    2.9e-34  118.5   0.0    1.5  1  ABC_tran        ABC transporter
    4.3e-05   24.0   4.0    0.00033   21.1   4.0    2.1  1  AAA_16          AAA ATPase domain
    0.00035   20.9   0.4     0.0027   18.0   0.3    2.4  1  AAA_22          AAA domain
    0.00089   19.7   0.0      0.016   15.6   0.0    2.4  1  AAA             ATPase family associated with various cellula
     0.0012   18.2   0.1     0.0029   16.9   0.1    1.6  1  Zeta_toxin      Zeta toxin
     0.0015   18.6   0.2       0.01   15.8   0.2    2.3  1  AAA_5           AAA domain (dynein-related subfamily)
     0.0019   18.0   0.0     0.0034   17.1   0.0    1.4  1  AAA_24          AAA domain
      0.003   17.7   0.0     0.0098   16.1   0.0    1.9  1  AAA_33          AAA domain
     0.0035   17.3   0.0     0.0089   15.9   0.0    1.6  1  RsgA_GTPase     RsgA GTPase
     0.0039   17.7   0.0      0.015   15.9   0.0    2.1  1  AAA_18          AAA domain
     0.0065   15.9   0.1       0.21   11.0   0.1    2.1  1  SMC_N           RecF/RecN/SMC N terminal domain
     0.0077   16.2   0.2        1.2    9.1   0.0    2.4  2  NTPase_1        NTPase
     0.0095   15.9   0.0       0.58   10.2   0.0    2.4  2  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.037   13.9   0.0    1.6  1  APS_kinase      Adenylylsulphate kinase
      0.028   14.2   0.0      0.074   12.8   0.0    1.7  1  AAA_29          P-loop containing region of AAA domain
       0.03   14.1   3.3       0.16   11.7   3.3    2.1  1  AAA_30          AAA domain
      0.036   13.8   0.1       0.21   11.3   0.0    2.2  2  IstB_IS21       IstB-like ATP binding protein
      0.036   13.9   0.1       0.35   10.6   0.0    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
      0.055   12.5   0.0       0.28   10.2   0.0    2.0  2  T2SSE           Type II/IV secretion system protein
      0.061   13.0   0.0       0.12   12.1   0.0    1.5  1  Cytidylate_kin  Cytidylate kinase
      0.062   13.4   0.2       0.17   12.0   0.1    1.7  2  DUF87           Helicase HerA, central domain
       0.18   11.5   0.0       0.35   10.5   0.0    1.4  1  Guanylate_kin   Guanylate kinase
       0.18   11.4   1.5       0.93    9.0   0.1    2.5  2  AAA_25          AAA domain
        0.2   11.4   0.9        2.6    7.8   0.9    2.1  1  DEAD            DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5   1.0   5.6e-44     4e-41       1     274 []      39     334 ..      39     334 .. 0.93

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 5.6e-44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH..............HHHHHHHHHHHHHHHH..HHHHHHHH CS
                      ABC_membrane   1 liliillailagvlsplfplvlgrildtlldkgdpet..............ealnvysllllllgla..qfilallq 61 
                                       l+l++l+++ a+++ +++plvlg  +d +++ +dp+               +++ +++ + l+++ +   + l++++
  gi|313122578|ref|YP_004044505.1|  39 LTLGLLASLGAHGATLVTPLVLGTTIDAVFT-SDPSPyrlplvpvawlptkQTTQFWLSAALVAASLvtTASLTWVR 114
                                       57899*************************9.777778***********7644444444444444330034467899 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane  62 syllnvtgerlskrlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfy 138
                                          +nv + ++  ++r+++++++ r++msffd++++Ge++s l nd+s+l+ +l + l++ ++ ++++vg+ + +f 
  gi|313122578|ref|YP_004044505.1| 115 GVAMNVFAYKVLYEIRTDAYERLQRLDMSFFDNTQTGEIMSVLDNDASNLERFLDNALSQSVRIFAIVVGISAALFH 191
                                       9999************************************************************************* PP

                                       HSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 139 lgwkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakk 215
                                       ++ +l++v+l+ +p ++ +++++++++++   +   +++++++ +e  +sgi+ Vk  +  + ++e+ ++ + +  +
  gi|313122578|ref|YP_004044505.1| 192 TNTQLAVVTLVAVPFLVGFTWWFMRLVEPRYARLRAEIGNLNTQIENGISGIELVKTANTAAHENERMDEVSHNLFE 268
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.......SSTHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 216 agikkaianglligitqllgllsyalalwfGttlvisg.......elsvgdlvvflslfailfgal 274
                                       a + + +++ l  + + ll+ +s ++++++G+++v sg       elsvgd+vvf++l  +l+ +l
  gi|313122578|ref|YP_004044505.1| 269 ARVDVSKLTFLYRPGMKLLTGASLLATFVVGGVWVFSGpppgfsgELSVGDFVVFILLVQQLTAPL 334
                                       *************************************99***********************9886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.0     4e-37   2.9e-34       1     137 []     396     545 ..     396     545 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 4e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ v+++ ++ge++a+vG++GaGKSt++kll++l++ + G +++dg+d+++++l  lr++ig+++q + lf+++ v+
  gi|313122578|ref|YP_004044505.1| 396 LNGVDFTAQPGETIALVGPTGAGKSTVAKLLLRLYDADTGAVRVDGHDVRDIRLGDLRESIGYVSQGTVLFDGT-VA 471
                                       789***********************************************************************.** PP

                                       HH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       en                ++ +e+++++++l+  +  dt v++++ +LSgGq+qr+alara+l++p++++lDE+ta
  gi|313122578|ref|YP_004044505.1| 472 ENirygrfevsdeavreaARVAEAHAFIEELSSGY--DTQVGERGVKLSGGQRQRIALARAVLQDPDIIVLDEATA 545
                                       ********998877765555555888888888777..99999********************************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   4.0   4.6e-07   0.00033      23     152 ..     404     598 ..     393     605 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.6e-07
                            AAA_16  23 rp.elvllsGesGvGKsslvrellralekdggif.lrgkcdql......esaipy........sa.laqalareell 82 
                                       +p e + l+G+ G GKs++++ llr + +d g + + g+ ++       +++i y        +  +a+ + r + +
  gi|313122578|ref|YP_004044505.1| 404 QPgETIALVGPTGAGKSTVAKLLLRLYDADTGAVrVDGHDVRDirlgdlRESIGYvsqgtvlfDGtVAENI-RYGRF 479
                                       334899******************99999955555777777774443332223333333333334355555.44555 PP

                            AAA_16  83 rqllde.aesaeleawrekleeala..................................................av 108
                                       +  +++  e+a ++++++++ee  +                                                  ++
  gi|313122578|ref|YP_004044505.1| 480 EVSDEAvREAARVAEAHAFIEELSSgydtqvgergvklsggqrqrialaravlqdpdiivldeatasvdtetealIQ 556
                                       44444444444455555555554449999888888888888888888888888888888888888888888778777 PP

                            AAA_16 109 pelagaeasrllellkrllallsrderplvlvlDdlqwadeasl 152
                                       ++l++  a r   ++++ l+ ++  ++ ++lvlDd q ++ +s+
  gi|313122578|ref|YP_004044505.1| 557 RSLERVTADRTTVAIAHRLSTIKD-AD-IILVLDDGQIVERGSH 598
                                       777887778888888888877776.77.9999999887666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   3.7e-06    0.0027       8      36 ..     409     437 ..     403     586 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.7e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakae 36 
                                       ++++G++G+GK+t+++ ll+ +d++  a 
  gi|313122578|ref|YP_004044505.1| 409 IALVGPTGAGKSTVAKLLLRLYDADTGAV 437
                                       89*******************98644333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.3e-05     0.016       2     115 ..     410     578 ..     409     587 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                                       EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS....................................... CS
                               AAA   2 llyGppGtGKTllakavakelg..vefleisgsellsk....................................... 37 
                                        l+Gp G GK+++ak + +  +  +  ++++g+++++                                        
  gi|313122578|ref|YP_004044505.1| 410 ALVGPTGAGKSTVAKLLLRLYDadTGAVRVDGHDVRDIrlgdlresigyvsqgtvlfdgtvaenirygrfevsdeav 486
                                       699****************9752255677777777744677777779999999999999999999999888888888 PP

                                       ............................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHH CS
                               AAA  38 ............................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervv 86 
                                                                   +   + ++ r  +++a  + +p i+++DE+ a + ++          + 
  gi|313122578|ref|YP_004044505.1| 487 reaarvaeahafieelssgydtqvgergVKLSGGQRQRIALARAVLQ-DPDIIVLDEATASVDTE----------TE 552
                                       88888888888888888888885555533333333444444444333.58888888888888777..........33 PP

                                       HHHHHHHHHTTTSSSTEEEEEEESSGGGS CS
                               AAA  87 nqLlteldgvkkkeskvivigatnrpdkl 115
                                       + + + l++v+    + + +++++r +++
  gi|313122578|ref|YP_004044505.1| 553 ALIQRSLERVTA---DRTTVAIAHRLSTI 578
                                       334444555555...23455555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1     4e-06    0.0029      19      56 ..     409     446 ..     402     448 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4e-06
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56 
                                       i l+G +GAGKs++a+ll +  +++ ++vr+d+ d+R 
  gi|313122578|ref|YP_004044505.1| 409 IALVGPTGAGKSTVAKLLLRLYDADTGAVRVDGHDVRD 446
                                       7799******************************9996 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.4e-05      0.01       3      82 ..     410     493 ..     408     568 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                                       EEE--SSSSHHHHHHHGGGGB..S--EEEEE--..TT--HHHHH--B--.........--------G-SEEEEESGG CS
                             AAA_5   3 lLvGppGtgKselaerlaaal..nreveyvqlt..rdtteedlkgrreikngttslvdsplvraaregeilvlDEve 75 
                                        LvGp+G gKs++a+ l++++   +  + v ++  rd++  dl+ ++ + +++t+l d+ + +++r g+  v DE  
  gi|313122578|ref|YP_004044505.1| 410 ALVGPTGAGKSTVAKLLLRLYdaDTGAVRVDGHdvRDIRLGDLRESIGYVSQGTVLFDGTVAENIRYGRFEVSDEAV 486
                                       59*******************76556666666655789999999999999999999999999999998888888887 PP

                                       G--HHHH CS
                             AAA_5  76 raesevl 82 
                                       r    v+
  gi|313122578|ref|YP_004044505.1| 487 REAARVA 493
                                       7655554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.8e-06    0.0034       4      87 ..     408     556 ..     406     565 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.8e-06
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.........swedfldevvel............ 59 
                                        i+++Gp g+GK+t+ak l     + d + G+ ++d++++ di+                    +            
  gi|313122578|ref|YP_004044505.1| 408 TIALVGPTGAGKSTVAKLL---LRLYDADTGAVRVDGHDVRDIRlgdlresigY----------Vsqgtvlfdgtva 471
                                       699****************...8899*****************66655554440..........3333444455555 PP

                            AAA_24  60 .........................................................aaeladyktlviDtidelee 79 
                                                                                                +a l+d +++v+D ++  ++
  gi|313122578|ref|YP_004044505.1| 472 enirygrfevsdeavreaarvaeahafieelssgydtqvgergvklsggqrqrialaRAVLQDPDIIVLDEATASVD 548
                                       55555555555555555566667777776667778888888888888888888888877888888888888877777 PP

                            AAA_24  80 lclaevir 87 
                                         ++ +i+
  gi|313122578|ref|YP_004044505.1| 549 TETEALIQ 556
                                       66666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-05    0.0098       3      47 ..     410     458 ..     409     505 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdtlrrrlfgtdqqsktd 47 
                                        lvG+ G+GKst+a+ ll+  +    av+++  ++r+   g+ ++s+ +
  gi|313122578|ref|YP_004044505.1| 410 ALVGPTGAGKSTVAKLLLRLYDadtgAVRVDGHDVRDIRLGDLRESIGY 458
                                       68*************99865556678*****999999555566666654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-05    0.0089      93     132 ..     399     439 ..     370     445 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                                       HHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinallpelelktgevse 132
                                       +    +  +t++lvG++G+GKSt+ + ll   ++ tg+v+ 
  gi|313122578|ref|YP_004044505.1| 399 VDFTAQPgETIALVGPTGAGKSTVAKLLLRLYDADTGAVRV 439
                                       4444444599*******************999999999985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     2e-05     0.015       1      25 [.     409     441 ..     409     568 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..........g 25 
                                       I+l G+ G+GK+t+ak L ++  +          g
  gi|313122578|ref|YP_004044505.1| 409 IALVGPTGAGKSTVAKLLLRL--YdadtgavrvdG 441
                                       89****************766..333554444442 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00029      0.21     109     208 ..     435     584 ..     395     591 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                       EEEEETTEEE-HHHHHHHHHCTT-STT.................................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................. RF
                             SMC_N 109 seykingkevtkkevsellesagiske.................................................. 135
                                         ++++g++v+   + +l es g  ++                                                  
  gi|313122578|ref|YP_004044505.1| 435 GAVRVDGHDVRDIRLGDLRESIGYVSQgtvlfdgtvaenirygrfevsdeavreaarvaeahafieelssgydtqvg 511
                                       45555555555555555555555555566666666666666666666666666666666666666666666667777 PP

                                       ....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCE CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadkl 208
                                            LSgG+++ +ala        +   + +lDe  a  D +  + + + l++ + +   + i++r  ++++ad +
  gi|313122578|ref|YP_004044505.1| 512 ergvKLSGGQRQRIALAR----AVLQDPDIIVLDEATASVDTETEALIQRSLERVTADRTTVAIAHRLSTIKDADII 584
                                       77778******9877764....345566699**************************************99999865 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0016       1.2       2      77 ..     409     482 ..     408     497 .. 0.71
   2 ?    5.3   0.1     0.023        17      65     104 ..     504     543 ..     464     594 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                                       EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvv 76 
                                       +++ Gp G GK+T+ k +l+l + +   v+v+G  ++++r g+ r    +v+      + L      +++r g++ v
  gi|313122578|ref|YP_004044505.1| 409 IALVGPTGAGKSTVAKLLLRLYDADtgAVRVDGHDVRDIRLGDLRESIGYVSQ----GTVLFDGTVAENIRYGRFEV 481
                                       7899************9999987654479999999999998887766555543....33444444455555555555 PP

                                       - CS
                          NTPase_1  77 d 77 
                                        
  gi|313122578|ref|YP_004044505.1| 482 S 482
                                       5 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.023
                                       ---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE--- CS
                          NTPase_1  65 akreprvgkyvvdvesfeelalealrkalseadviviDEi 104
                                       +    +vg+  v++   ++  ++  r  l+++d+iv+DE 
  gi|313122578|ref|YP_004044505.1| 504 SGYDTQVGERGVKLSGGQRQRIALARAVLQDPDIIVLDEA 543
                                       56678999999**9999998888888888**********5 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.13        92      43      61 ..      13      33 ..      10      42 .. 0.76
   2 !   10.2   0.0   0.00081      0.58      16      44 ..     403     431 ..     390     439 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                                      TT--..----TTTTSEEEEEE CS
                              TsaE 43 lgve..evkSPTFtlveeYel 61
                                      lg +   v+SP F l++eY  
  gi|313122578|ref|YP_004044505.1| 13 LGAHqeLVTSPLFRLFREYGR 33
                                      5554457************65 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00081
                                       HCHTEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  16 kalgdvilLeGdLGaGKTtlvrglakalg 44 
                                       ++ g++i+L G+ GaGK+t ++ l++ ++
  gi|313122578|ref|YP_004044505.1| 403 AQPGETIALVGPTGAGKSTVAKLLLRLYD 431
                                       334789****************9998765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.2e-05     0.037       2      43 ..     406     446 ..     405     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTT CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRh 43 
                                       g ++ l G +g+GKst+a+ l  +L +  + ++++dG  vR 
  gi|313122578|ref|YP_004044505.1| 406 GETIALVGPTGAGKSTVAKLLL-RLYDADTGAVRVDGHDVRD 446
                                       56899*************9998.6999999999******996 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0001     0.074      13      38 ..     397     422 ..     393     427 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                            AAA_29  13 dghtieidlkgatlltGpsGsGKSTl 38 
                                       +g +++ ++ +++ l+Gp+G+GKST+
  gi|313122578|ref|YP_004044505.1| 397 NGVDFTAQPGETIALVGPTGAGKSTV 422
                                       5667778888899************6 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.3   0.00022      0.16      12     108 ..     400     554 ..     391     602 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                            AAA_30  12 alltsgdrvavltGpAGtGKttalkalreaweaa.g..............grviglAptgkaAkvLaeelgieasti 73 
                                        +++++  + +l+Gp G+GK+t+ k l ++++a+ g              g             +L+e++g  ++ +
  gi|313122578|ref|YP_004044505.1| 400 DFTAQPGETIALVGPTGAGKSTVAKLLLRLYDADtGavrvdghdvrdirlG-------------DLRESIGYVSQGT 463
                                       56677778999*********************9944533333333333330.............3554444322222 PP

                            AAA_30  74 akllkrlk........................................................grarlepgtlliv 94 
                                         +  + +                                                        +ra l++ ++++ 
  gi|313122578|ref|YP_004044505.1| 464 VLFDGTVAenirygrfevsdeavreaarvaeahafieelssgydtqvgergvklsggqrqrialARAVLQDPDIIVL 540
                                       22222222222222333333333333333333345555556666666666666666777777775566666677777 PP

                            AAA_30  95 DEagmvdtkqlaal 108
                                       DEa     ++++al
  gi|313122578|ref|YP_004044505.1| 541 DEATASVDTETEAL 554
                                       77765544444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.21      37      67 ..     395     426 ..     379     507 .. 0.81
   2 ?   -0.8   0.1       1.6   1.1e+03     100     136 ..     526     561 ..     518     592 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                         IstB_IS21  37 eLatlsfiek.kenivllGpsGvGKshlaial 67 
                                        L + +f+++  e i+l+Gp+G+GKs +a  l
  gi|313122578|ref|YP_004044505.1| 395 VLNGVDFTAQpGETIALVGPTGAGKSTVAKLL 426
                                       57788888663799************999755 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                         IstB_IS21 100 aralkrllkvdllilDdlgllpldqaeaellfeviek 136
                                       a a + l+ +d+++lD+     +d + ++l+ + +e+
  gi|313122578|ref|YP_004044505.1| 526 ALARAVLQDPDIIVLDEAT-ASVDTETEALIQRSLER 561
                                       5555667777888888854.45555555555555544 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00049      0.35       3      26 ..     410     436 ..     409     459 .. 0.75
   2 ?    0.3   0.0      0.67   4.8e+02     223     265 ..     501     542 ..     457     572 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00049
                            AAA_21   3 vliGpNgsGKSnLLdaldllarl...d 26 
                                       +l+Gp g+GKS++ ++l  l ++   +
  gi|313122578|ref|YP_004044505.1| 410 ALVGPTGAGKSTVAKLLLRLYDAdtgA 436
                                       79***************9998764431 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.67
                            AAA_21 223 flengdgqelparel..SdGtkrllalltallralkkgsllliDE 265
                                        l  g++ ++  r +  S G+++ +al+ a+l+++   +++++DE
  gi|313122578|ref|YP_004044505.1| 501 ELSSGYDTQVGERGVklSGGQRQRIALARAVLQDP---DIIVLDE 542
                                       4444444444444446699***9999999999999...9*****9 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00039      0.28      98     156 ..     375     433 ..     358     451 .. 0.82
   2 ?   -1.5   0.0       1.4     1e+03     193     207 ..     528     542 ..     515     556 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00039
                             T2SSE  98 ksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                       +++ ++++dd+ +e ++ e++ + +    +   +i + G+Tg GK+t++  ll   +++
  gi|313122578|ref|YP_004044505.1| 375 SANGRIEYDDVNFEYDDGEQVLNGVDFTAQPGETIALVGPTGAGKSTVAKLLLRLYDAD 433
                                       556677888888888888888887777777799999*************9999877665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                             T2SSE 193 raaLRlrPDrimvGE 207
                                         a+ ++PD+i++ E
  gi|313122578|ref|YP_004044505.1| 528 ARAVLQDPDIIVLDE 542
                                       444559*****9977 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.12       1      20 [.     409     428 ..     409     511 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                       EEEE-STTSSHHHHHHHHHH CS
                    Cytidylate_kin   1 iaiDGPagsGKssvaralae 20 
                                       ia+ GP+g+GKs+va++l +
  gi|313122578|ref|YP_004044505.1| 409 IALVGPTGAGKSTVAKLLLR 428
                                       8999************9965 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.5   5.4e+03      92     128 ..     140     175 ..     124     192 .. 0.65
   2 ?   12.0   0.1   0.00024      0.17      26      45 ..     409     428 ..     406     439 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.5
                             DUF87  92 inpwsldpeelldlleeddkpaaavqrsvleealdqa 128
                                       ++++ +d  +  +++ +  +++a++++++l++al+q 
  gi|313122578|ref|YP_004044505.1| 140 LDMSFFDNTQTGEIMSV-LDNDASNLERFLDNALSQS 175
                                       44444554545555555.4456677888888887775 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00024
                             DUF87  26 lAilgsTGsGKSntvavLle 45 
                                       +A +g TG+GKS+ +++Ll+
  gi|313122578|ref|YP_004044505.1| 409 IALVGPTGAGKSTVAKLLLR 428
                                       799**************997 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00049      0.35       4      45 ..     408     451 ..     406     474 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                                       EEEEESTTTSSHHHHHHHHHHHSTTTEE.E--.EEESS---TTS CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg.vsv.shtTrdprkge 45 
                                       ++ lvgp+gaGks++ k Ll+ +    g v v  h  rd+r g+
  gi|313122578|ref|YP_004044505.1| 408 TIALVGPTGAGKSTVAKLLLRLYDADTGaVRVdGHDVRDIRLGD 451
                                       789******************99988876877347788888766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0013      0.93      32      50 ..     405     423 ..     395     429 .. 0.89
   2 ?    0.2   0.1      0.65   4.6e+02     131     156 ..     525     548 ..     461     575 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                            AAA_25  32 agelallaGapgtGKttla 50 
                                        ge+++l+G++g+GK+t+a
  gi|313122578|ref|YP_004044505.1| 405 PGETIALVGPTGAGKSTVA 423
                                       5999*************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.65
                            AAA_25 131 daleaaieevegvrlvviDplsralg 156
                                        al++a+ +  +++ +v+D  ++ ++
  gi|313122578|ref|YP_004044505.1| 525 IALARAVLQ--DPDIIVLDEATASVD 548
                                       245555555..699999998887655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9    0.0036       2.6      14     149 ..     406     562 ..     395     572 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0036
                                       TCEEEEEESTTSSHHHHHHHHHHHHHHHS................TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                              DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyet................kgktgpkalivePtreLaeqtlnnlkkfkky. 73 
                                       g+ + + ++TG+GK++++ + +   +y+                  g+ +  + +v+  + L   t+ +  +++ + 
  gi|313122578|ref|YP_004044505.1| 406 GETIALVGPTGAGKSTVAKLLLR--LYDAdtgavrvdghdvrdirLGDLRESIGYVSQGTVLFDGTVAENIRYGRFe 480
                                       56677888888888888766665..6554446666655555555434444677778888888887777777777753 PP

                                       ST...SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH.....CTTEEEEEEETHHHHHHTTTHHHH CS
                                       xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  74 id...lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln.....lsqvrflVlDEadrlldqgfsdfi 142
                                       ++   +r+       +a+  +++l++g+d  vg  g  ++  +++++      l++  ++VlDEa    d + +  i
  gi|313122578|ref|YP_004044505.1| 481 VSdeaVREA--ARVAEAHAFIEELSSGYDTQVGERGVKLSGGQRQRIAlaravLQDPDIIVLDEATASVDTETEALI 555
                                       222333333..333455666777777888888888777776655555444555999999******999999999999 PP

                                       HHHHHHS CS
                                       xxxxxxx RF
                              DEAD 143 nrilnql 149
                                       +r l+++
  gi|313122578|ref|YP_004044505.1| 556 QRSLERV 562
                                       9999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 4063.11
//
Query:       gi|313122579|ref|YP_004044506.1|  [L=146]
Description: ABC-type branched-chain amino acid transport system, periplasmic component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 928.39
//
Query:       gi|313122580|ref|YP_004044507.1|  [L=617]
Description: siderophore synthetase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-71  239.8   0.0      4e-71  239.3   0.0    1.2  1  IucA_IucC  IucA / IucC family
    1.3e-37  129.7   0.4      3e-37  128.5   0.4    1.7  1  FhuF       Ferric iron reductase FhuF-like transporter


Domain annotation for each model (and alignments):
>> IucA_IucC  IucA / IucC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.3   0.0   4.5e-75     4e-71       2     239 .]     155     403 ..     154     403 .. 0.95

  Alignments for each domain:
  == domain 1  score: 239.3 bits;  conditional E-value: 4.5e-75
                                       HHHHHHH-----SS-S-S---BT--HHHHHHH-GGG---B--EEEEEETTTEEESTT-HHH...HHHHHH-HHHHHH CS
                         IucA_IucC   2 flalEqllleGHpfhpaaKsRlgfseedaaaysPEfaasfrlrwvavhrelvtfssaeeeraqellaaeldpstraa 78 
                                       ++++E+ + eGHp+  ++K+R+gf+++d+ +y+PE +++ rl wvav re+ tf+s e  ++++l+a+el  + +++
  gi|313122580|ref|YP_004044507.1| 155 YAEVEGEM-EGHPWYTYNKGRIGFGYDDYLQYAPESKEPQRLSWVAVSRERGTFQSVEGLEHTALIADEL-GEYYEQ 229
                                       8999****.*************************************************888889******.789999 PP

                                       HHHHHC.TT--GGGEEEEEE-HHHHHHTHHHHSHHHHHTTSEEEEEE-SS-EEE-TTSSEEEESS-TT.-EEEE-EE CS
                         IucA_IucC  79 faaelk.sgldpedyvllpvHPwQwehliaplfaaeiakgrlvdlgesgdeylPtqSvRTlvnidrpa.phvKlsLs 153
                                       f+++l  +gldp+ y++lpvH+wQw++ i +lfa +ia+  +v+lg+++deylP+qS+RT+ n+++p+ +hvKl++ 
  gi|313122580|ref|YP_004044507.1| 230 FREQLLdRGLDPAAYLFLPVHDWQWNDSIVQLFAGDIATDAIVPLGKGPDEYLPQQSIRTFSNTTTPEkHHVKLPIR 306
                                       9999976********************************************************************** PP

                                       EEETTEEE---HHHHHHHHHHHHHHHHHHHT-HHHHC..--EE--EEEEEEE-.........-........T-SEEE CS
                         IucA_IucC 154 vritnsvRglspaeleaGpavsrlleellaadaflre..rfkllrEvagiavthp...ayeel........ellgvl 217
                                       v++tn++Rg+  +++ea+p v++++++++++d+flr+  ++ l +E+a+i+++hp   +   +        ellg++
  gi|313122580|ref|YP_004044507.1| 307 VLNTNVYRGILGEQAEAAPGVTAFIKSVRDNDTFLRDdcELLLPGEIASINYEHPlfsQ---FddapyqyhELLGCV 380
                                       *******************************************************6662...344466777****** PP

                                       EE--CCCT-T..-EEEEGGGGG- CS
                         IucA_IucC 218 wRenpesllg.deravplaaLla 239
                                       wRe++ sl++ der+++laaLl+
  gi|313122580|ref|YP_004044507.1| 381 WRESVLSLIDdDERPLTLAALLH 403
                                       *****9999779*********97 PP

>> FhuF  Ferric iron reductase FhuF-like transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.5   0.4   3.4e-41     3e-37       2     160 ..     425     592 ..     424     595 .. 0.90

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 3.4e-41
                                       HHHHHHHHHHHHHHHHHHHHH-EE---STTTEEEEEETTEEEEEEE---....TTT-EES-TT----TTSGG..... CS
                              FhuF   2 lWlkrYfglllpPllhllleygialeahlqNvllvlddgrpvrlllrdf.egvslkaellpelpalpeevkr..... 72 
                                       +W+++++++ll Pllh l++yg+++++h+ Nv+l +ddgrp+r++++df ++v++ ++++pel+a+ +++ r     
  gi|313122580|ref|YP_004044507.1| 425 AWIDEFLEVLLNPLLHYLYKYGLVFMPHGTNVVLIHDDGRPTRIAVKDFvDEVAITDRDFPELAAALPDELRdddry 501
                                       7****************************************************888888888877775555557888 PP

                                       ....GB----GGGSHHHHIIIIIIIHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHSGGGHHHHHHT-TT-SEE- CS
                              FhuF  73 ....lltddpeelreevfyglfvnhlapliealaaagglsekllWsnvaellewylaelpelaerfaqalLfaptlp 145
                                           l   +pe l ++++ +lfv ++++++++la++++++e+++W++v+ ++++y+ ++pe  +rf  ++L++p + 
  gi|313122580|ref|YP_004044507.1| 502 khhiLHQIPPESLCHRMVGTLFVGVFRYVADLLARHHDYPEERFWGQVRSAMDAYQSRFPEFEDRFSLFDLYQPRFK 578
                                       8886555555555588************************************************************* PP

                                       .---HHHHHH-XXXX CS
                              FhuF 146 gkanllrvrladeae 160
                                        k +l+r r++++++
  gi|313122580|ref|YP_004044507.1| 579 -KYCLNRNRMVRHGY 592
                                       .*********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 4604.68
//
Query:       gi|313122581|ref|YP_004044508.1|  [L=446]
Description: glutamine synthetase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-98  328.5   0.0    5.1e-98  328.3   0.0    1.1  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    6.2e-14   51.7   0.0    1.2e-13   50.8   0.0    1.4  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain
  ------ inclusion threshold ------
      0.038   13.7   0.0       0.96    9.2   0.0    2.9  3  Gln-synt_N    Glutamine synthetase, beta-Grasp domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.3   0.0  8.5e-102   5.1e-98       3     344 ..     111     441 ..     109     442 .. 0.96

  Alignments for each domain:
  == domain 1  score: 328.3 bits;  conditional E-value: 8.5e-102
                                       -HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHH CS
                        Gln-synt_C   3 dPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreiv 79 
                                       d Rs l+  ++ la+ Gl+++v++E EF lf++ +++e              ++ +++g++ +a+++e+++++  iv
  gi|313122581|ref|YP_004044508.1| 111 DARSSLRALERDLADAGLSPNVAFESEFHLFKQGPNEE-------------VQRVDERGAYATASTRETHETILAIV 174
                                       89******************************999955.............345677899***************** PP

                                       HHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEE CS
                        Gln-synt_C  80 ealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSl 156
                                       +al+a+ i+ve+   E+a g +Ei + + + l+a+D+ v+++++v +vAr+hg++ tF+pKp+  ++++g+H+h+Sl
  gi|313122581|ref|YP_004044508.1| 175 DALKAQDISVEKYYPEYAAGKHEIVTGHRSGLRAVDEYVLLRETVDSVARDHGYQSTFVPKPFD-NSTNGCHIHVSL 250
                                       **************************************************************98.789********* PP

                                       EECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-.. CS
                        Gln-synt_C 157 wdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa.. 231
                                       w  d+ n+++d++ +++ls+++r+fi+G+l+ha+ l+altaptvnSY Rl p+  a++ ++wg +NR+al+R+pa  
  gi|313122581|ref|YP_004044508.1| 251 W--DDGNAMYDPE-QKELSQTGRQFIAGILEHAPGLCALTAPTVNSYARLRPQIGAAAFVCWGRENREALVRVPApd 324
                                       *..888******9.579**********************************************************99 PP

                                       ..TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHH CS
                        Gln-synt_C 232 ..skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAleal 304
                                         + e ++r+E+R++d +aNPY al  llaAgldG+e+ lep+epv+ d  +ls++er  +g+++lP++l +Al+al
  gi|313122581|ref|YP_004044508.1| 325 sgDPEGSTRIEFRAADNTANPYVALLGLLAAGLDGVERDLEPPEPVTVDPGNLSEKERtdRGVNRLPRTLGQALDAL 401
                                       8777889***************************************************99***************** PP

                                       HCSHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHH CS
                        Gln-synt_C 305 eedellkevlgeevieaylalkraEleeleeevsdweler 344
                                       e+d+ l+++lg ++++ayl +kr+ +e+++++ ++w+++r
  gi|313122581|ref|YP_004044508.1| 402 ESDATLRDALGADLCKAYLGVKRSHWEAFTRSANSWKRDR 441
                                       ************************************9876 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0     2e-17   1.2e-13       5     107 .]       6     108 ..       2     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2e-17
                                       ......------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS--EEEEE-GG CS
                      Gln-synt_N_2   5 avveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvGelrLvpdPa 81 
                                       a+ e+ +  +v+L+++l+v  +G +r +a+  +++e  +  G+   +   + + +   d++ ++ + Ge+rL pdP+
  gi|313122581|ref|YP_004044508.1|   6 AIDERCTDGKVDLVRLLFVTQSGAVRAHAVDSSKVESAVQTGVTISELVQTYNALGRRDKSGQFDAAGEVRLQPDPT 82 
                                       566888999******************************************************************** PP

                                       G-EEE---SSTTSEEEEEE-TTS-B- CS
                      Gln-synt_N_2  82 savalpyaPdaaallgdlvevdgtPy 107
                                       ++ +lpya  + a+l ++  +dg P+
  gi|313122581|ref|YP_004044508.1|  83 TFQVLPYAERTGAMLCNIETLDGDPW 108
                                       *************************9 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.17     1e+03       2      35 ..      16      48 ..      15      50 .. 0.87
   2 ?    9.2   0.0   0.00016      0.96      53      80 ..      75     100 ..      71     102 .. 0.85
   3 ?   -0.4   0.0      0.17     1e+03      51      75 ..     293     317 ..     287     320 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                                      --EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-E CS
                        Gln-synt_N  2 vkfvdlqFtDikgklkhvtipadelsedaleegv 35
                                      v  v+l F+   g ++  ++ ++++ e+a++ gv
  gi|313122581|ref|YP_004044508.1| 16 VDLVRLLFVTQSGAVRAHAVDSSKV-ESAVQTGV 48
                                      778999999999*999999999999.99988887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00016
                                       EEEEEEGGGEEE-SS-SS-.EEEEEEEE CS
                        Gln-synt_N  53 mlLkPdlstavidPfreekktarvicdv 80 
                                       + L+Pd++t+ ++P+ e+  t  ++c++
  gi|313122581|ref|YP_004044508.1|  75 VRLQPDPTTFQVLPYAER--TGAMLCNI 100
                                       679************974..68999987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.17
                                       -EEEEEEEGGGEEE-SS-SS-.EEE CS
                        Gln-synt_N  51 SDmlLkPdlstavidPfreekktar 75 
                                       S   L+P++  a+ +++ +e++ a+
  gi|313122581|ref|YP_004044508.1| 293 SYARLRPQIGAAAFVCWGRENREAL 317
                                       56679************99885554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2880.35
//
Query:       gi|313122582|ref|YP_004044509.1|  [L=469]
Description: diaminobutyrate aminotransferase apoenzyme [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-89  300.6   0.0    1.7e-89  300.3   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.3   0.0   9.5e-94   1.7e-89       9     405 ..      45     456 ..      37     457 .. 0.92

  Alignments for each domain:
  == domain 1  score: 300.3 bits;  conditional E-value: 9.5e-94
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                       l+++++ a+G+ ++d+dg++y+D +++   ++lGh+hP+v++ v+  +a+   +    +t+ + +++++ l + +p 
  gi|313122582|ref|YP_004044509.1|  45 LPFAVKHAQGAEIVDADGETYIDCLAGAGTLALGHNHPEVTQEVERLLAEDRPLHTLDVTTPEKEAFVDALFDSLPD 121
                                       44899****************************************987766555555777788899*****999999 PP

                                       ..S...EEEEE.SSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEE CS
                       Aminotran_3  86 gld...kvfla.nsGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevv 158
                                       ++    kv ++  +G++Ave+AlKl +       +t   +++ f+g++HG t gals+ g+ +  k+ ++ ++ +v+
  gi|313122582|ref|YP_004044509.1| 122 EFTdtaKVQFCsPAGTDAVEAALKLVKT------STGNRSVLGFQGGYHGMTSGALSLMGD-TDAKEPVPGLMSNVH 191
                                       88678866555169**************......9**************************.9************** PP

                                       EE-TTBGGGTB-HH..HHHHHHHHHHHHHH...CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEE CS
                       Aminotran_3 159 rlkypdeevlkene..eeeaalleeleale...kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvlli 230
                                       +l+ypd+++ ++    + ++ +++ +e++    +    + a++ivE +qgegGv++a++e+++++r ++++hdv +i
  gi|313122582|ref|YP_004044509.1| 192 HLPYPDPYRHPFGLdaDGHEPVSHFAERVLadpESGVTDPAGLIVELVQGEGGVNPAPDEWVREIRRITDEHDVPMI 268
                                       *********9986533667778888888886767777888************************************* PP

                                       EE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHH CS
                       Aminotran_3 231 vDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavlei 307
                                       vDE+qtG+GrTG+++  eha++ pD++t +Ka++gGlpl++v+ ++e+ ++++pg h++Tf G  la+a+ + +++ 
  gi|313122582|ref|YP_004044509.1| 269 VDEIQTGMGRTGETWSFEHADIVPDVLTCSKAIGGGLPLAVVVYDEEL-DVWEPGAHAGTFRGHQLAMAAGRVTIRH 344
                                       ****************************************99998885.89************************** PP

                                       HHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC............HHHHHHHHHCTE CS
                       Aminotran_3 308 ieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke............keilkkakekGv 372
                                       + e++l e+a+e+g++l+e L +l+ + + +++vRg+Glm+++e+++ a++++             ++  +  + G+
  gi|313122582|ref|YP_004044509.1| 345 VVENDLDEHAAEMGERLREPLADLERRFDAVGDVRGRGLMLGVEFVDTATETPdgevpppdgdlaSAVKSECFDRGL 421
                                       **************************************************888*********99888889999**** PP

                                       E-EEETT..TEEEE---TT--HHHHHHHHHHHHHH CS
                       Aminotran_3 373 lilsaGd..nvirllppliitdeeidelleilkka 405
                                       +i + G+   v r+lppl+it +++de+ +++ +a
  gi|313122582|ref|YP_004044509.1| 422 IIETGGRdsAVARFLPPLTITRNQVDEIADRFREA 456
                                       ******988899*******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 3605.04
//
Query:       gi|313122583|ref|YP_004044510.1|  [L=542]
Description: L-2,4-diaminobutyrate decarboxylase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-59  202.2   0.0    1.2e-59  201.9   0.0    1.0  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    8.3e-05   22.0   0.0    0.00014   21.3   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0011   18.0   0.0     0.0039   16.2   0.0    1.8  1  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.9   0.0   2.1e-63   1.2e-59       3     374 ..      71     439 ..      69     440 .. 0.94

  Alignments for each domain:
  == domain 1  score: 201.9 bits;  conditional E-value: 2.1e-63
                                       TTGGGSCSSHHSSHH.HHHHHHHHHHCTGGGS--TTSTTBHCSSH....HHHHHHHHHHHHHT-BTSSTTTSHHHHH CS
                     Pyridoxal_deC   3 ylkrlldeaapekaesleqilediekilapgvttwhspefhkllpagnslisllgdlLadainkngftweesPalte 79 
                                       +  rl ++++pe   ++++++ed+++ +       +++ + + l+    ++sl+++++ +a n+ + +++++Pa t 
  gi|313122583|ref|YP_004044510.1|  71 HRERLTQDTIPESGRKIDEVIEDLATDVLEESVYPSDEACSAHLQCPPMVPSLAAEVVLSALNQSMDSFDQAPAATV 147
                                       556789999**************99877776666777**************************************** PP

                                       HHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HH.HHHCCEEEEEETTS- CS
                     Pyridoxal_deC  80 levvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkea.eildklvlytsdqah 155
                                       le  v+d l  l+gl        ++gv+++g++ s+l +ll ar++ + e+ +++ +++      +k+ + ts++ah
  gi|313122583|ref|YP_004044510.1| 148 LEEQVIDDLTSLFGLG----D-GADGVFTSGGTQSNLQGLLLAREHYVAEVFDRSVRTSGLpPTAEKMRILTSEDAH 219
                                       ***************9....4.39*************************99999976443213579*********** PP

                                       HHHHHHHHHHT-E...EEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT- CS
                     Pyridoxal_deC 156 ssvekaalvlgvk...lrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydl 229
                                         v +aa+ lg++   + ++p+ + +++ +++l   + + k++   pf  v t+Gtt  g+ d l++l+d+ +++dl
  gi|313122583|ref|YP_004044510.1| 220 FTVAQAAAQLGLGedaVVTVPTGDAHQMDPDELADELARLKQANCHPFALVGTAGTTDFGSVDPLNDLADLADEHDL 296
                                       ************99999************************************************************ PP

                                       EEEEE-TTGGGGGGSGGGGGGGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTTTSEE CS
                     Pyridoxal_deC 230 wlHvDAAyaGsaficpeirhllkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsdvaad 306
                                       w HvDAA +G++ ++  ++++l gieradS+tv  hKll  ++ c+++++ d  + +     +a YL+ ++sd   +
  gi|313122583|ref|YP_004044510.1| 297 WFHVDAALGGALALSETHAGKLDGIERADSLTVDFHKLLYQPISCGVFLLSDGDKFELMG-RNAAYLN-PKSDQVSN 371
                                       **************************************************9988876554.68*****.8899999* PP

                                       CCCGSSSSSGHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECSTTBSSEEEEEE CS
                     Pyridoxal_deC 307 lgtkaiplsrrvrilklwfvlralGveglqnqirksvelakyleklirkderfeivaevelglVcFrl 374
                                       l  k +++ rr+++lk +  +r+lG+eg+ + ++++v la   ++lir d  fe+   + +  V Fr+
  gi|313122583|ref|YP_004044510.1| 372 LVSKSLQTTRRFDALKPYVAFRTLGREGMAALVDRTVTLADRAASLIRSDPGFELSCPPTINIVTFRY 439
                                       ******************************************************************98 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.3e-08   0.00014      72     215 ..     210     351 ..     124     419 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.3e-08
                                       EEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-T.TS-EEEEEEEESSBTTTTTB---H CS
                   Beta_elim_lyase  72 eevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevga.heekiklisltvTnntagGqvvsl 147
                                         ++ +e+ah+    + a   l++  ++++++ +a +md+++l++ +++ ++    + +l+ ++ T+    G   s+
  gi|313122583|ref|YP_004044510.1| 210 MRILTSEDAHFTVAQAAAQLGLGEDAVVTVPTGDAHQMDPDELADELARLKQaNCHPFALVGTAGTTDF--G---SV 281
                                       334555558888887777777788889****9999**********999988877778888888888887..5...66 PP

                                       HHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHH..TTSSEEEEESSSTT--SS-.EEEEE-HH.. CS
                   Beta_elim_lyase 148 eelrevaaiakkygiplhlDgARfanaakslgeivkemf..syvDsvtmslkKdllanvG.gvlafrddel 215
                                       + l+ +a++a+++++ +h+D+A +  a + ++ ++ ++   + +Ds+t+ + K l  ++  gv +++d + 
  gi|313122583|ref|YP_004044510.1| 282 DPLNDLADLADEHDLWFHVDAA-LGGALALSETHAGKLDgiERADSLTVDFHKLLYQPIScGVFLLSDGDK 351
                                       77888999*************9.445554444444444344889999999999888888866666655544 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.5e-07    0.0039      85     177 ..     206     303 ..     141     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.5e-07
                                       -TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-......-TTEEEEEEESBETTTTEB CS
                       Aminotran_5  85 lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll......nektklvaithvsnvtGti 155
                                         ++ +i+++e  h     ++++l   + a v+v +  +  ++d+del++ l      n  + ++  t+  +  G +
  gi|313122583|ref|YP_004044510.1| 206 TAEKMRILTSEDAHFTVAQAAAQLGLGEDAVVTVPTG-DAHQMDPDELADELarlkqaNCHPFALVGTAGTTDFGSV 281
                                       567889******************9887777766665.6677999***999977775555556777799999***** PP

                                       --HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 156 qpveeigklakkkgalvlvDaa 177
                                       +p++++++la +++ +++vDaa
  gi|313122583|ref|YP_004044510.1| 282 DPLNDLADLADEHDLWFHVDAA 303
                                       *********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 4320.73
//
Query:       gi|313122584|ref|YP_004044511.1|  [L=601]
Description: siderophore synthetase component [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-58  198.4   0.0    1.9e-58  197.9   0.0    1.2  1  IucA_IucC  IucA / IucC family
    7.2e-31  107.8   0.0    1.3e-30  107.0   0.0    1.4  1  FhuF       Ferric iron reductase FhuF-like transporter


Domain annotation for each model (and alignments):
>> IucA_IucC  IucA / IucC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.9   0.0   2.1e-62   1.9e-58       1     239 []     154     390 ..     154     390 .. 0.92

  Alignments for each domain:
  == domain 1  score: 197.9 bits;  conditional E-value: 2.1e-62
                                       -HHHHHHH-----SS-S-S---BT--HHHHHHH-GGG---B--EEEEEETTTEEESTT-HHH...HHHHHH-HHHHH CS
                         IucA_IucC   1 sflalEqllleGHpfhpaaKsRlgfseedaaaysPEfaasfrlrwvavhrelvtfssaeeeraqellaaeldpstra 77 
                                       +f ++Eq+l+ GH++hp++KsR+g+ +++a+ay+PE+++ f+lr++a++r+lv++  a++ +++e++++ ld+   a
  gi|313122584|ref|YP_004044511.1| 154 TFCEAEQSLVYGHHLHPTPKSREGIADHEARAYAPELGGAFQLRYFAADRDLVSQWFAGDVSSTEWIRTGLDE-AEA 229
                                       689********************************************************999999******43.333 PP

                                       HHHHHHCTT--GGGEEEEEE-HHHHHHTHH.HHSHHHHHTTSEEEEEE-SS-EEE-TTSSEEEESS-TT-EEEE-EE CS
                         IucA_IucC  78 afaaelksgldpedyvllpvHPwQwehlia.plfaaeiakgrlvdlgesgdeylPtqSvRTlvnidrpaphvKlsLs 153
                                       ++ +   +   +++y l+p HPwQ+ +l + p++++++++g ++dlg  g+ ++Pt+SvRTl+++++p  +vK sL+
  gi|313122584|ref|YP_004044511.1| 230 DLPDVA-ERVLADGYELVPTHPWQASYLRSqPHVEQALDQGSIIDLGAFGPTFYPTSSVRTLWSPAAPF-MVKSSLA 304
                                       333333.35589*****************99**************************************.******* PP

                                       EEETTEEE---HHHHHHHHHHHHHHHHHHHT-HHHHC.--EE--EEEEEEE-......-T-SEEEEE--CCCT-.T. CS
                         IucA_IucC 154 vritnsvRglspaeleaGpavsrlleellaadaflre.rfkllrEvagiavthpayeelellgvlwRenpesll.g. 227
                                       v itns R+ +  el+ G+a+++ll++ ++++ + r+ rf ++r++a+++++  ++ + +++++++Ren      + 
  gi|313122584|ref|YP_004044511.1| 305 VEITNSERTSKVSELKLGVAAAELLDTGFGDRLAERFpRFSVVRDPAALTLDLGDG-SESGFETVLRENTF--RgEs 378
                                       ******************************************************75.459**********3..2233 PP

                                       .-EEEEGGGGG- CS
                         IucA_IucC 228 deravplaaLla 239
                                        ++++p+aaL++
  gi|313122584|ref|YP_004044511.1| 379 ARNVTPIAALCQ 390
                                       699*******96 PP

>> FhuF  Ferric iron reductase FhuF-like transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.0   1.4e-34   1.3e-30       2     161 ..     420     580 ..     419     582 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 1.4e-34
                                       HHHHHHHHHHHHHHHHHHHHH-EE---STTTEEEEEET.TEEEEEEE---.......TTT-EES-TT----TTSGGG CS
                              FhuF   2 lWlkrYfglllpPllhllleygialeahlqNvllvldd.grpvrlllrdfegv....slkaellpelpalpeevkrl 73 
                                       +W+ +Y +++l P+++ ++e+gi+leah+qNvl++ld  g+p+  ++rd+eg+    s+++ + ++lp++  +++++
  gi|313122584|ref|YP_004044511.1| 420 EWFCKYMAVTLSPVVWTYFELGIGLEAHQQNVLIRLDSdGWPAEGFYRDNEGFfvpeSRRSDIDAWLPGVCDRIETV 496
                                       7**************************************************************************** PP

                                       B----GGGSHHHHIIIIIIIHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHSGGGHHHHHHT-TT-SEE-.---H CS
                              FhuF  74 ltddpeelreevfyglfvnhlapliealaaagglsekllWsnvaellewylaelpelaerfaqalLfaptlpgkanl 150
                                       ++d+  ++   v y+ + n+ + +i+al+ ag ++e++l++ +++ l+ y+ae+  +a  +  +lL++pt+p+k nl
  gi|313122584|ref|YP_004044511.1| 497 CPDETVDDC--VRYYAVLNNAFGVINALGVAGLVDETALLEDLRAELD-YFAEYEPPASTLVTDLLEEPTVPCKGNL 570
                                       *********..***********************************85.88999788888889************** PP

                                       HHHHH-XXXXX CS
                              FhuF 151 lrvrladeaea 161
                                         +rl+ ++e+
  gi|313122584|ref|YP_004044511.1| 571 R-TRLEGRDEL 580
                                       9.****99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3692.90
//
Query:       gi|313122585|ref|YP_004044512.1|  [L=224]
Description: demethylmenaquinone methyltransferase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-35  122.2   2.1    2.5e-35  121.8   2.1    1.1  1  RraA-like  Aldolase/RraA
     0.0038   17.4   0.1       0.93    9.8   0.0    2.5  2  PCP_red    Proto-chlorophyllide reductase 57 kD subunit
  ------ inclusion threshold ------
      0.041   13.3   0.5      0.054   12.9   0.5    1.2  1  PALP       Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   2.1   4.2e-39   2.5e-35      15     149 ..      35     173 ..      20     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 4.2e-39
                                       ST..B.TT.EES...EEEEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.SSSSSECE-HHHHHHHHHTTBSEE CS
                         RraA-like  15 sg..girplers...fvGpavTvkvveadnslvkealeeagpgdvlVvdgggdeslraallGgllataakangvaGv 86 
                                       s   +++++  +   +vG a+Tv++ ++d  +v++a+e a+p dv+V++ gg+e ++a + G++ ++aa angv+Gv
  gi|313122585|ref|YP_004044512.1|  35 SPeiEFMRTA-QdaeLVGSALTVRIPPVDGTMVHKAIELAQPTDVIVIEMGGHE-TNAPW-GEITTHAAVANGVRGV 108
                                       3333333322.23579************************************55.47777.**************** PP

                                       EEEEEES-HHHHTTSSSEEEEEEE-SSB-B-S.STS...EESS-EEETTEEE-TTSEEEEETTEEE CS
                         RraA-like  87 vvdGavRDvaelreldfpvfargvtprkkpkkkgkg...evnvpveiggvtvkpgdlivaDedGvv 149
                                       v+dGav D+a+++e++fpvfar++t r+ ++  +++   ++nvpv++gg++v+pgd+ ++ edGvv
  gi|313122585|ref|YP_004044512.1| 109 VIDGAVTDTAAINEIGFPVFARARTNRTVQRL-TESlggDINVPVQVGGAVVRPGDIAIGNEDGVV 173
                                       ************************99986666.3334479*************************9 PP

>> PCP_red  Proto-chlorophyllide reductase 57 kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0043        26       7      29 ..     118     142 ..     117     148 .. 0.69
   2 !    9.8   0.0   0.00016      0.93      14      34 ..     174     194 ..     174     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0043
                                       HHHTTS..-HHHHHHHHHHHHHHHH CS
                           PCP_red   7 alLkki..PffvRkkaRraaEklAr 29 
                                       a++++i  P+f+R +  r++ +l +
  gi|313122585|ref|YP_004044512.1| 118 AAINEIgfPVFARARTNRTVQRLTE 142
                                       67899999*****555555555444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHHHHHHT-S CS
                           PCP_red  14 ffvRkkaRraaEklArerGle 34 
                                       f +R ++ +++E++Ar  G e
  gi|313122585|ref|YP_004044512.1| 174 FVSREQIDQTIERYARHDGAE 194
                                       7789***************87 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5     9e-06     0.054     164     260 ..      91     192 ..      67     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-06
                                       E-SSSHHHHHHHHHHHH...HSTT-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCSTCSCGTTCCHHHHSE CS
                              PALP 164 pvGgGgliaGiaaglke...rrpdvrvigvepegsdalarslragrrvtvpvs..dtiadglavgspselafelldr 235
                                       p G   ++a++a g++    ++  +   +++  g + +ar++ +  ++++++s    i   ++vg + ++  +++ +
  gi|313122585|ref|YP_004044512.1|  91 PWGEITTHAAVANGVRGvviDGAVTDTAAINEIGFPVFARARTNRTVQRLTESlgGDINVPVQVGGAVVRPGDIAIG 167
                                       778889***********88655559999**************444444444334477777777779999999***99 PP

                                       EEEEEEEEEHHHHHHHHHHHHHHHS CS
                              PALP 236 lvdeivtvsdeealeamrllarreg 260
                                         d +v vs e++ +++++ ar++g
  gi|313122585|ref|YP_004044512.1| 168 NEDGVVFVSREQIDQTIERYARHDG 192
                                       *********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1437.91
//
Query:       gi|313122586|ref|YP_004044513.1|  [L=449]
Description: transposase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-09   37.1   0.0    4.5e-09   36.3   0.0    1.3  1  DDE_Tnp_1    Transposase DDE domain
      0.006   14.9   0.2       0.13   10.5   0.2    2.3  1  DDE_Tnp_1_4  Transposase DDE domain group 1


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0     5e-13   4.5e-09      65     189 ..     278     408 ..     271     429 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5e-13
                         DDE_Tnp_1  65 lkqlldelrpr.kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkr 140
                                       ++ l+++++++     vl D+ ++s+++++tl    v+y+i+                  r++ + r++i t  +  
  gi|313122586|ref|YP_004044513.1| 278 VRRLVRRAQEHvPIEMVLCDREFDSKAVYQTLSNLDVNYLIPK-----------------RIHSAERENIETMDEDG 337
                                       5668888888899****************************75.................88888888888888888 PP

                         DDE_Tnp_1 141 rnk......................skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfg 189
                                       ++                       s+k++g+ +++tn++ +  +  ++ + y++RwqiE+  k++k++f 
  gi|313122586|ref|YP_004044513.1| 338 QEVavesasvhveqgshtmqflyvpSTKGDGTAVFATNLSVSPKESDTFCRRYSRRWQIENEYKSIKNDFL 408
                                       888999999999********************************************************985 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.2   1.4e-05      0.13     198     352 ..     274     415 ..     261     436 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.4e-05
                       DDE_Tnp_1_4 198 aveaLarlvkrirerwpetkilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekakteaaekkeke 274
                                       +  +++rlv+r +e+ p    +v +D  f ++++++++ + +v+Y+i  +  s+ +++i+++ e+ ++ a e+   +
  gi|313122586|ref|YP_004044513.1| 274 VHRVVRRLVRRAQEHVPIE--MVLCDREFDSKAVYQTLSNLDVNYLIPKRIHSAERENIETMDEDGQEVAVESA--S 346
                                       5567888888888777777..56688888888888888888888888877777777777777777777777764..5 PP

                       DDE_Tnp_1_4 275 reyrefayqaesWskerrVvakaerpaeglnlrfvvTsla.klspeelyeqlYcaRGemEnrIKeakldlaadrtss 350
                                       ++++++ +        ++ +   + +++g  +  + T+l+ + ++++ + + Y +R ++En  K+ k+d+ a +tss
  gi|313122586|ref|YP_004044513.1| 347 VHVEQGSHT-------MQFL--YVPSTKGDGTAVFATNLSvSPKESDTFCRRYSRRWQIENEYKSIKNDFLA-KTSS 413
                                       666555543.......3333..344555666666789999755556666699***************88765.4555 PP

                       DDE_Tnp_1_4 351 hs 352
                                       ++
  gi|313122586|ref|YP_004044513.1| 414 KD 415
                                       43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 3284.29
//
Query:       gi|313122587|ref|YP_004044514.1|  [L=79]
Description: hypothetical protein Hbor_38440 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 511.27
//
Query:       gi|313122588|ref|YP_004044515.1|  [L=72]
Description: hypothetical protein Hbor_38450 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.029   14.9   0.1      0.049   14.2   0.0    1.6  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-06     0.049       1      15 [.       7      21 ..       7      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-06
                                      HHHHHHTTSEEEEEH CS
                    RNA_pol_Rpb2_5  1 wddLlregvvEylDa 15
                                      w+d++r gvvEy D+
  gi|313122588|ref|YP_004044515.1|  7 WQDFVRYGVVEYPDV 21
                                      ************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.39
# Mc/sec: 559.42
//
Query:       gi|313122589|ref|YP_004044516.1|  [L=295]
Description: hypothetical protein Hbor_38460 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0074   16.1   0.1      0.018   14.9   0.1    1.7  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
      0.044   14.3   0.1       0.11   13.0   0.1    1.6  1  DUF4179     Domain of unknown function (DUF4179)
      0.054   12.9   0.0       0.14   11.6   0.0    1.7  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T
       0.13   12.3   0.1       0.33   11.0   0.1    1.7  1  PepSY_2     Peptidase propeptide and YPEB domain


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     4e-06     0.018       3      23 ..       5      26 ..       3      29 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-06
                        TAT_signal  3 SRRdFLKgs.AAaaAAaalggc 23
                                      SRR+FLK +  A+  Aa++g++
  gi|313122589|ref|YP_004044516.1|  5 SRRQFLKKAsIATVGAATVGSV 26
                                      9******995666666667765 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.4e-05      0.11       2      73 ..       6      69 ..       5      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...--SS-HHHHT--SS-HHHHSEEEEEEEEETTEEEEEEE CS
                           DUF4179  2 kkrrikkvaaaaaalvllllssrllspalAsal.n.pvigslfeklsdskgeqeyvkpvnksaednGitvtvne 73
                                      +++ +kk+ +a + ++++  +s+++ palA ++     +g+l+         ++ v++  k+  d Gi + v+e
  gi|313122589|ref|YP_004044516.1|  6 RRQFLKKASIATVGAATV--GSVMTGPALAYNKdFrDEVGNLL--------SEGKVEKAKKKLNDEGIDFSVTE 69
                                      566678999999999999..**********8884334444444........77777777888888888888876 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.1e-05      0.14       7      28 ..       2      26 ..       1      28 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                        UCR_Fe-S_N  7 deptRRDFL...yiATgavgaVGaa 28
                                      ++++RR FL    iAT+++++VG  
  gi|313122589|ref|YP_004044516.1|  2 QDQSRRQFLkkaSIATVGAATVGSV 26
                                      689******5555888888888865 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   7.3e-05      0.33       4      67 ..      20      86 ..      15      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.3e-05
                           PepSY_2  4 lalalallaaaAlAgrrdtdspkadwl...preklvakleaqGykvkkievddggcyEvegldkdGk 67
                                      +a++ ++++++AlA  +d ++++ + l   + ek+++kl+++G + + +e       ++e+++++G+
  gi|313122589|ref|YP_004044516.1| 20 AATVGSVMTGPALAYNKDFRDEVGNLLsegKVEKAKKKLNDEGIDFSVTEYNTLYSGDAEVVNDEGE 86
                                      466677888*****8778788877777555789************9999998887888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 2323.81
//
Query:       gi|313122590|ref|YP_004044517.1|  [L=174]
Description: hypothetical protein Hbor_38470 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   18.6   1.0     0.0031   17.9   1.0    1.3  1  Cadherin  Cadherin domain


Domain annotation for each model (and alignments):
>> Cadherin  Cadherin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.0   1.8e-07    0.0031       6      84 ..      39     118 ..      38     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-07
                                       ETTS-TCCEEEEECECCCS.TSTTTSEEEEEEECTTTTSEEEETTTTEEEESST.C-TTTSSEEEEEEEEEECTGCC CS
                          Cadherin   6 pEnapvgtevltvtatdaD.lgpnsrirysilegneggkFridtetgdlsttkp.LdrEsqgeYeLtveatDesgsp 80 
                                       +E+a+ +t+++ v a  +  l++ s+++++ + ++  g    d+et  lst+    drE++  +++tv+atD+++s+
  gi|313122590|ref|YP_004044517.1|  39 SEQAQADTSLTVVDAGCEStLTQESSFKTNQTFEK-TGILYTDSETRNLSTKTThTDRETMTAFNVTVSATDANTST 114
                                       58889999999999999999999999999999999.8**************9999******************7676 PP

                                       EEEE CS
                          Cadherin  81 plss 84 
                                       + +s
  gi|313122590|ref|YP_004044517.1| 115 SSDS 118
                                       6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 1354.59
//
Query:       gi|313122591|ref|YP_004044518.1|  [L=104]
Description: hypothetical protein Hbor_38480 [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.58   10.2  10.4        1.2    9.1  10.1    1.6  2  TspO_MBR  TspO/MBR family


Domain annotation for each model (and alignments):
>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1     0.049   8.8e+02     108     124 ..      16      32 ..      13      37 .. 0.71
   2 ?    9.1  10.1   6.9e-05       1.2      37     104 ..      34     100 ..      21     104 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.049
                                       C-HHHHHHHCHHHHHHH CS
                          TspO_MBR 108 vdklaallllpyllWll 124
                                        d laa+l +  l+W  
  gi|313122591|ref|YP_004044518.1|  16 YDGLAAILAAVILGWGF 32 
                                       56778888888888854 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 6.9e-05
                                       HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHHHH CS
                          TspO_MBR  37 wvfppvWtvlyilmgvaaylvwkalalyavqlvlnllwsplffglkspvlalvdivallglvvalila 104
                                       +++ p+  ++ ++  ++ y v+++ a ya   ++ ++w p+f+gl  ++l  v +  +lg+++++i++
  gi|313122591|ref|YP_004044518.1|  34 YAIRPILGFITAVAVLSVYAVMRT-ADYAHAAMVVIAWLPVFVGLAGYGLPGVLTGGVLGALIYAIYT 100
                                       455666666667777777888887.5999999******************999999999999999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 808.38
//
Query:       gi|313122592|ref|YP_004044519.1|  [L=235]
Description: nucleoside-diphosphate-sugar pyrophosphorylase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00051   19.9   1.1     0.0008   19.3   1.1    1.3  1  Trypsin   Trypsin


Domain annotation for each model (and alignments):
>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.1   4.4e-08    0.0008      34     199 ..      42     190 ..      15     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.4e-08
                                       TTEEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSSBHCCBBC CS
                           Trypsin  34 enwvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdtvrpiclp 110
                                       ++ +lTA H ++n ++ +  +ge+ ++++++    ++v++  +h+  +   l++  + + l+++++  d+++ ++ +
  gi|313122592|ref|YP_004044519.1|  42 NKRLLTASHLWEN-KACQSKTGET-ATQYNQ--DFGTVAE--SHTSADFVLLEKTNGSIDLSQEISEEDSTQLVSGW 112
                                       4568********9.9999999994.444444..3788888..67777777777888899999999999999999998 PP

                                       S...TTHTT.STTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTTTTS CS
                           Trypsin 111 a...asssl.pvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGDSGG 183
                                       +   a s+l ++++ +  +G+++ +++g   t++ +e ++  + +c+      +  + + +++     d  +GDSGG
  gi|313122592|ref|YP_004044519.1| 113 HpkdAVSELvAERRDVRKMGVTTGQTTG---TITGMEKTI--SGDCND-----LDGHGIIVDG----IDVGKGDSGG 175
                                       8777444444899999999999999999...999999998..556999.....6666677776....69999***** PP

                                       EEEETTTEEEEEEEEE CS
                           Trypsin 184 PlvcsdgelvGivswg 199
                                       P+ + ++ + G++ + 
  gi|313122592|ref|YP_004044519.1| 176 PIYRIET-IGGVNYAV 190
                                       **99999.76776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1709.14
//
Query:       gi|313122593|ref|YP_004044520.1|  [L=60]
Description: bacterial regulatory protein, arsR family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 397.12
//
Query:       gi|313122594|ref|YP_004044521.1|  [L=130]
Description: sugar-specific transcriptional regulator TrmB [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-07   30.2   0.0    4.8e-07   29.6   0.0    1.2  1  MarR_2          MarR family
    5.6e-05   22.9   0.0    8.2e-05   22.4   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00048   19.7   0.0    0.00071   19.2   0.0    1.2  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
    0.00078   19.3   0.0     0.0014   18.5   0.0    1.3  1  MarR            MarR family
    0.00092   19.2   0.0     0.0012   18.7   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0014   18.3   0.0     0.0057   16.4   0.0    1.8  2  DUF4423         Domain of unknown function (DUF4423)
     0.0022   17.6   0.1     0.0038   16.9   0.1    1.3  1  GntR            Bacterial regulatory proteins, gntR family
     0.0049   16.4   0.1     0.0076   15.8   0.1    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0085   15.8   0.0      0.015   14.9   0.0    1.5  1  Sigma70_r4_2    Sigma-70, region 4
     0.0099   15.7   0.0      0.014   15.2   0.0    1.2  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.015   15.6   0.0    1.2  1  Rrf2            Transcriptional regulator
      0.014   15.5   0.0      0.026   14.7   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.016   15.4   0.0      0.025   14.8   0.0    1.3  1  PaaX            PaaX-like protein
      0.032   14.0   0.0      0.054   13.3   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
       0.15   12.0   0.0       0.26   11.3   0.0    1.3  1  HTH_11          HTH domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0     4e-10   4.8e-07       9      54 ..      31      76 ..      31      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4e-10
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +vL++L+++  r + ++e+a   g++ +avs +l rL ++ Lve +
  gi|313122594|ref|YP_004044521.1| 31 QVLGFLAANKHRAFKAREIASQIGVDEGAVSTALSRLKDRNLVEHK 76
                                      79*****************************************976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   6.8e-08   8.2e-05      19      55 ..      40      76 ..      31      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.8e-08
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      k+   +a+eia+++gv++  v  +L++L+d+ lVe +
  gi|313122594|ref|YP_004044521.1| 40 KHRAFKAREIASQIGVDEGAVSTALSRLKDRNLVEHK 76
                                      67889*****************************975 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.9e-07   0.00071      18      56 ..      38      76 ..      31      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.9e-07
                      HrcA_DNA-bdg 18 rkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegv 56
                                       +k+ra K++eiA++++ +eG v   l+ Lk  +Lve +
  gi|313122594|ref|YP_004044521.1| 38 ANKHRAFKAREIASQIGVDEGAVSTALSRLKDRNLVEHK 76
                                      67899*******************************977 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-06    0.0014      15      48 ..      41      74 ..      37      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      + + +  e+a+++gv+ ++v+++l rL +++l+e
  gi|313122594|ref|YP_004044521.1| 41 HRAFKAREIASQIGVDEGAVSTALSRLKDRNLVE 74
                                      6677889*************************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     1e-06    0.0012      22      65 ..      44      89 ..       3      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1e-06
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES-HHHH CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis.rgrr.irildleaL 65
                                      +  +e+As +G+    vs +ls+Lk+++l++ + +   +  d e+L
  gi|313122594|ref|YP_004044521.1| 44 FKAREIASQIGVDEGAVSTALSRLKDRNLVEhKATYwAVTDDTERL 89
                                      5668***************************543333555556665 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.69   8.2e+02     121     134 ..       5      18 ..       2      22 .. 0.80
   2 !   16.4   0.0   4.7e-06    0.0057      30     110 ..      37     115 ..      32     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.69
                           DUF4423 121 sltlaiskedyeki 134
                                         t++i+++++e+ 
  gi|313122594|ref|YP_004044521.1|   5 LSTMSIDRDTFENT 18 
                                       579*******9975 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.7e-06
                           DUF4423  30 lplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslt.tssevkseavrsyhkqmlelA 105
                                       ++ k+ + + +e+a +++  +++  v++al++L++ +l++ ++   + +t+      + +    a + ++ q+ ++ 
  gi|313122594|ref|YP_004044521.1|  37 AANKHRAFKAREIASQIG--VDEGAVSTALSRLKDRNLVEHKAT-YWAVTDDTERlDGYSGYERATALFNEQLGDED 110
                                       5556667899********..***********************8.9*999987664455555666666666666666 PP

                           DUF4423 106 ieale 110
                                       +e+  
  gi|313122594|ref|YP_004044521.1| 111 KESWR 115
                                       66555 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   3.2e-06    0.0038      28      56 ..      47      75 ..      42      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.2e-06
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglver 56
                                      re+a+++gV+   v  AL+rL+ ++lve 
  gi|313122594|ref|YP_004044521.1| 47 REIASQIGVDEGAVSTALSRLKDRNLVEH 75
                                      9**************************85 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   6.4e-06    0.0076      21      48 .]      47      74 ..      45      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.4e-06
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                      re+A ++g+  ++v++ l rL++  l++
  gi|313122594|ref|YP_004044521.1| 47 REIASQIGVDEGAVSTALSRLKDRNLVE 74
                                      8**********************99986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.3e-05     0.015      28      50 ..      45      67 ..      43      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                      -HHHHHHHHT--HHHHHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrlsRA 50
                                      + +EIA+++g+ eg+V ++lsR 
  gi|313122594|ref|YP_004044521.1| 45 KAREIASQIGVDEGAVSTALSRL 67
                                      568******************95 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.014      18      46 ..      46      74 ..      39      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 18 vcelaeelglsqstvShHLkkLreaGLVe 46
                                      + e+a ++g+ +++vS  L++L++ +LVe
  gi|313122594|ref|YP_004044521.1| 46 AREIASQIGVDEGAVSTALSRLKDRNLVE 74
                                      679*************************7 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.3e-05     0.015      13      57 ..      32      75 ..      26      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +l +La+++++  ++++eia++ ++ +  ++  l++L+  +lv+ 
  gi|313122594|ref|YP_004044521.1| 32 VLGFLAANKHRA-FKAREIASQIGVDEGAVSTALSRLKDRNLVEH 75
                                      78899**99988.******************************85 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.2e-05     0.026      21      55 ..      42      76 ..      36      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                                      SSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                         k  ++a+ ++v    Vs  l++L++  +ve++
  gi|313122594|ref|YP_004044521.1| 42 RAFKAREIASQIGVDEGAVSTALSRLKDRNLVEHK 76
                                      5568899**************************98 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.1e-05     0.025      29      56 ..      49      76 ..      45      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                              PaaX 29 llaelGiseslvRaalsRlakaGwlvre 56
                                      + +++G++e++v +alsRl+ + ++  +
  gi|313122594|ref|YP_004044521.1| 49 IASQIGVDEGAVSTALSRLKDRNLVEHK 76
                                      7889****************98776655 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.054       7      50 ..      31      75 ..      31      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                      HHHCT-CTTBSS-.BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqel.tlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++L +la+   +  + +e+A ++g+   +v+  L+ L  + +ve 
  gi|313122594|ref|YP_004044521.1| 31 QVLGFLAANKHRAfKAREIASQIGVDEGAVSTALSRLKDRNLVEH 75
                                      79999999999988****************************985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.26       4      41 ..      31      69 ..      30      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                            HTH_11  4 qilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLee 41
                                      q+l +L +++   + + e+A +++v + +v   + +L++
  gi|313122594|ref|YP_004044521.1| 31 QVLGFLAANKHRaFKAREIASQIGVDEGAVSTALSRLKD 69
                                      5677777777778************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 889.35
//
Query:       gi|313122595|ref|YP_004044522.1|  [L=801]
Description: nucleoside-diphosphate-sugar pyrophosphorylase family protein [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.4e-262  871.3   0.0   7.3e-262  871.1   0.0    1.0  1  DUF2309   Uncharacterized protein conserved in bacteria (DUF2
  ------ inclusion threshold ------
        5.8    7.6   7.5        1.3    9.7   0.1    3.1  3  DUF883    Bacterial protein of unknown function (DUF883)


Domain annotation for each model (and alignments):
>> DUF2309  Uncharacterized protein conserved in bacteria (DUF2309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  871.1   0.0  8.1e-266  7.3e-262       1     752 []      11     757 ..      11     757 .. 0.96

  Alignments for each domain:
  == domain 1  score: 871.1 bits;  conditional E-value: 8.1e-266
                           DUF2309   1 veeaaevipplwPlktfvahNplhgledlpfeeavaelaklfgarlylseeeyrealaegrideedLeaaeeeleee 77 
                                       ++eaa ++ +lwP+++fv+ Npl g+ed+pf eav+++a+l+g+r+++s++++ +al++g+id+  Le++ +e + +
  gi|313122595|ref|YP_004044522.1|  11 IDEAATTVGSLWPIHSFVTANPLAGFEDQPFGEAVEQAATLLGGRGFPSAQTFGTALERGQIDRVILEEELTEAGYA 87 
                                       6899******************************************************************6555444 PP

                           DUF2309  78 etlaelldaltged.........ldelvdeqlikllaaflDegqaawslpkrekglyaawrelakhdlslellllke 145
                                        ++++lld++++           ++++vd++l+k+l+aflDeg a+ws+p+re+g+y+a+r +a++d +++      
  gi|313122595|ref|YP_004044522.1|  88 DDPETLLDRMADAAdavngdadtAADHVDKVLTKWLSAFLDEGSAHWSMPNREAGFYTAFRGMAEYDSDIP------ 158
                                       4444444444444444445558899**********************************************...... PP

                           DUF2309 146 lrkvlaelpedpeeaiaealeelgipeeeweaylealllalpGWagliryreeqpeaelqgeepaslvdllairLll 222
                                        + v+a+lpe p e+i+++l+++   e++w  ++e++l+alpGW+ +i++r+e+ e ++q+++p+sl+ +la rL+l
  gi|313122595|ref|YP_004044522.1| 159 DEGVVADLPEAPIEVIEAVLKSYP--ESQWVPIFEEQLAALPGWTRFIKQRAED-EGAWQSTYPISLEGYLAARLAL 232
                                       78999****************987..**************************99.899******************* PP

                           DUF2309 223 eaalleevakeklsleeleaaaaleelaeeergklwleAlErsyreellealaaeseseeaa...erpeaqavfCiD 296
                                         a+ ++++ ++         ++ +++ ++++++++l+A+E++yre+l+ ++aa+s+s +++    rp+aq+vfCiD
  gi|313122595|ref|YP_004044522.1| 233 LDAVDANIEPSN---------DVSNTNPADDLAQAFLRAWEATYREDLVGTVAAQSQSMDDSdtsGRPDAQLVFCID 300
                                       *****9976544.........57788999**************************99988888899*********** PP

                           DUF2309 297 vRseslRRhLEevgpeveTlGfAGFFGvpiayqgldkeeeealcPvlltPkhlvkeeakeeeeaekakrkrrlkaal 373
                                       +Rse++RRh+E++g+ +eT+G+AGFFG+p++yqg+d++ + + cP++l+P+h++ + +++++++++++r++ ++aa+
  gi|313122595|ref|YP_004044522.1| 301 TRSEVIRRHIEATGD-YETHGYAGFFGIPMEYQGYDDDVSVDVCPPILDPQHHIIDCPTDDDTQARHDRRSGMRAAA 376
                                       ***************.************************************************************* PP

                           DUF2309 374 ekllkelkrsllssfllvealGllyalkllaktlaprraarlkeklkakleekeetklkldkeseee......gltl 444
                                       +++++ l+ ++++++ +ve++G  y+l+l+a+tl+p+r ++l +++++ + +++e    l +++++       glt+
  gi|313122595|ref|YP_004044522.1| 377 ADVIEILEANAATAYGYVETAGSGYGLSLAARTLVPGRVHDLIDAAAELVPDDHEFCEPLVHHQHTYsgdlsvGLTH 453
                                       *******************************************************9999998887669********* PP

                           DUF2309 445 eeqvelveaaLraigLtenfAplVllvGHgSsseNNpheaaldCGACgGrsGgvnARvlAallNdpeVRegLaergi 521
                                       eeqve++++a++++g+ ++f++lV+++GH+S+++NNp++++ldCGAC+G++Gg++ARvlA+++Nd++VR++L++rg+
  gi|313122595|ref|YP_004044522.1| 454 EEQVEYAATAFDLMGF-KEFSRLVVFTGHASETANNPYDSSLDCGACAGNPGGPSARVLAKVCNDEAVRAELRDRGF 529
                                       ****************.6*********************************************************** PP

                           DUF2309 522 eIPedTvFvaalhnTttDevelfdldllpashrealeklkadleeagelaaaeRarrlesaeakkekaeaeverrae 598
                                       +IPedT+Fva++hnTttDevelf  d++p+sh+++l++l++dl++a+e+a  eRa+++     + ++  +e+erra+
  gi|313122595|ref|YP_004044522.1| 530 DIPEDTIFVAGQHNTTTDEVELF-VDDVPESHSDDLDQLRTDLTTARENATTERAEAMGA---DGSTGVTETERRAA 602
                                       ***********************.999*******************************86...34889********* PP

                           DUF2309 599 dwsevRPEwglagnaafiigrReltrgldLdgraFLhsYdwrqDpdgklLeniltaplvVaqwInleYYfStvdnev 675
                                       dw+e+RPEwglagna f+ig+Relt+g+dLdgraFLhsYdw++Dp+g++Le+ilt+p+vV+qwIn +YYfStvdn+v
  gi|313122595|ref|YP_004044522.1| 603 DWAETRPEWGLAGNAGFVIGPRELTSGCDLDGRAFLHSYDWSTDPNGDALEAILTGPMVVTQWINAQYYFSTVDNAV 679
                                       ***************************************************************************** PP

                           DUF2309 676 yGsGsKvlhnvvgriGVmeGnggDLrtGLplQsvhdgdr.eiHePlRLlvvieapreaierilarheavrelvdngW 751
                                       yGsGsKv++n vg++GV++GnggDL++GLplQs++ +dr ++H+PlRL++v++ap e+i++ila+he+++e++dn+W
  gi|313122595|ref|YP_004044522.1| 680 YGSGSKVTQNPVGNVGVYQGNGGDLMAGLPLQSLMIADRePYHQPLRLSTVVHAPVERITDILADHEELTEILDNNW 756
                                       ***********************************99999************************************* PP

                           DUF2309 752 l 752
                                       l
  gi|313122595|ref|YP_004044522.1| 757 L 757
                                       7 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2     0.094   8.4e+02      45      68 ..      95     118 ..      87     121 .. 0.84
   2 ?   -1.5   0.3      0.44   3.9e+03      52      82 ..     366     396 ..     360     408 .. 0.53
   3 ?    9.7   0.1   0.00015       1.3       8      88 ..     543     622 ..     538     623 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.094
                            DUF883  45 erlrdaeeavaerakeaaeaaddy 68 
                                       +r++da++av   a+ aa+++d++
  gi|313122595|ref|YP_004044522.1|  95 DRMADAADAVNGDADTAADHVDKV 118
                                       789999999999999999999875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.44
                            DUF883  52 eavaerakeaaeaaddyVrenPwqavGiAag 82 
                                       ++ +  +++aa+++ ++ ++n ++a G + +
  gi|313122595|ref|YP_004044522.1| 366 HDRRSGMRAAAADVIEILEANAATAYGYVET 396
                                       3334444555555555555555555554444 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00015
                            DUF883   8 eslladleellkeaadeageeaeelRerleerlera.rerlrdaeeavaerakeaaeaaddyVrenPwqavGiAagv 83 
                                       ++ ++++e ++++  ++  +++++lR  l+ + e+a  er++++  +    + e  ++a d ++ +P    G+A   
  gi|313122595|ref|YP_004044522.1| 543 NTTTDEVELFVDDVPESHSDDLDQLRTDLTTARENAtTERAEAMGADGSTGVTETERRAADWAETRPE--WGLAGNA 617
                                       567899999********************998877626889999999*******************94..5788888 PP

                            DUF883  84 GlllG 88 
                                       G+++G
  gi|313122595|ref|YP_004044522.1| 618 GFVIG 622
                                       88887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 5293.95
//
Query:       gi|313122596|ref|YP_004044523.1|  [L=306]
Description: NADH:ubiquinone oxidoreductase subunit 5 (chain L)/multisubunit Na+/H+ antiporter, MnhA subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-28  100.2   9.9    1.1e-28  100.2   9.9    1.7  2  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   9.9   6.4e-33   1.1e-28      82     234 ..       3     150 ..       1     173 [. 0.89
   2 ?   -1.1   0.3     0.049   8.7e+02     194     194 ..     241     241 ..     162     297 .. 0.57

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 6.4e-33
                   Proton_antipo_M  82 llllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlllilaiis 157
                                       l+++ +l++++++ sa++p+h Wl  + + aPtp sal+ A+  v+ag++ll+r+ +++  ++ +++  +++++++s
  gi|313122596|ref|YP_004044523.1|   3 LVAAGALVLAAMIQSALIPFHNWLLSS-MTAPTPASALMhAG-FVNAGGILLTRFAPVIT-VDSTLMLAVVAVGAAS 76 
                                       567889*********************.***********777.*****************.999************* PP

                   Proton_antipo_M 158 mllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdira 234
                                       +  g l+  +qtdiK+ l+ S+++++G+m++++++ ++    aai+hl++h++ ka  Fl +g  + +++ +++ + 
  gi|313122596|ref|YP_004044523.1|  77 AGGGKLLKSVQTDIKSKLGCSTVGQMGFMIMQAGL-GFF--GAAITHLILHGFYKAYQFLSSGEQVEHTSPSETTEH 150
                                       ***********************************.665..8********************988777666655554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.049
                   Proton_antipo_M 194 t 194
                                       +
  gi|313122596|ref|YP_004044523.1| 241 G 241
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2127.31
//
Query:       gi|313122597|ref|YP_004044524.1|  [L=156]
Description: NADH:ubiquinone oxidoreductase subunit 5 (chain L)/multisubunit Na+/H+ antiporter, MnhA subunit [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-11   42.0   1.0      7e-11   42.0   1.0    2.3  3  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
       0.46    9.8   8.4      0.033   13.6   3.7    1.5  2  ThrE             Putative threonine/serine exporter
        6.3    6.9   8.6       0.35   10.9   1.4    2.6  4  NDUF_B12         NADH-ubiquinone oxidoreductase B12 subunit f


Domain annotation for each model (and alignments):
>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.8      0.57   3.4e+03      23      38 ..      27      42 ..      22      45 .. 0.65
   2 !   42.0   1.0   1.2e-14     7e-11      16      56 ..      58      98 ..      46     100 .. 0.90
   3 ?   -1.9   0.2      0.63   3.8e+03      12      28 ..     116     132 ..     104     135 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.57
                   Proton_antipo_N 23 almllvvtfvsllvhl 38
                                      ++ l+   fv+++v l
  gi|313122597|ref|YP_004044524.1| 27 LTWLVWSLFVASIVVL 42
                                      5666666677776654 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 1.2e-14
                   Proton_antipo_N 16 fllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfay 56
                                      + +D+l++lm +vvtf s +vh YS  YMa+ ++++RFf  
  gi|313122597|ref|YP_004044524.1| 58 VAIDGLTVLMWVVVTFFSGIVHSYSRRYMAGSTHKTRFFLA 98
                                      579************************************76 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.63
                   Proton_antipo_N  12 ieigfllDklsalmllv 28 
                                       + +gfl   + ++m+ +
  gi|313122597|ref|YP_004044524.1| 116 VLFGFLWAAMGLVMAEL 132
                                       45666666666666655 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1      0.73   4.4e+03     138     194 ..      36      41 ..      23      51 .. 0.49
   2 ?   13.6   3.7   5.5e-06     0.033     133     177 ..      69     113 ..      57     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.73
                              ThrE 138 lagllggllrlllakrglnsfvleavaaflasllallavslglglnpdaiiigsill 194
                                       +a                                                   si++
  gi|313122597|ref|YP_004044524.1|  36 VA---------------------------------------------------SIVV 41 
                                       11...................................................1111 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.5e-06
                              ThrE 133 flvaflagllggllrlllakrglnsfvleavaaflasllallavs 177
                                       ++v+f+ g++  + r+++a +++ + ++ a+ +f+a+++al+a+ 
  gi|313122597|ref|YP_004044524.1|  69 VVVTFFSGIVHSYSRRYMAGSTHKTRFFLAMFGFTAAVMALVAAD 113
                                       789*************************************99887 PP

>> NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.68   4.1e+03      28      42 ..      55      69 ..      45      81 .. 0.49
   2 ?   10.9   1.4   5.9e-05      0.35      11      40 ..      84     112 ..      78     117 .. 0.90
   3 ?   -1.7   0.1      0.54   3.2e+03      29      35 ..     119     125 ..     112     135 .. 0.69
   4 ?   -1.5   0.0      0.45   2.7e+03      26      37 ..     136     146 ..     127     149 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.68
                          NDUF_B12 28 pGfglavaafaaavg 42
                                      pG+ +  ++++++ +
  gi|313122597|ref|YP_004044524.1| 55 PGLVAIDGLTVLMWV 69
                                      555333333333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.9e-05
                          NDUF_B12  11 RykgqfskakrfkraffpGfglavaafaaa 40 
                                       Ry+ ++++  rf+ a+  Gf +av+a +aa
  gi|313122597|ref|YP_004044524.1|  84 RYMAGSTHKTRFFLAM-FGFTAAVMALVAA 112
                                       999*********9999.8*****9999986 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.54
                          NDUF_B12  29 Gfglava 35 
                                       Gf +a++
  gi|313122597|ref|YP_004044524.1| 119 GFLWAAM 125
                                       8888875 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.45
                          NDUF_B12  26 ffpGfglavaaf 37 
                                          G++ a aa+
  gi|313122597|ref|YP_004044524.1| 136 N-EGWKQAQAAA 146
                                       4.6777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1055.90
//
Query:       gi|313122598|ref|YP_004044525.1|  [L=199]
Description: transcriptional regulator, PadR family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.074   13.1   0.0       0.17   11.9   0.0    1.6  1  DUF2866   Protein of unknown function (DUF2866)


Domain annotation for each model (and alignments):
>> DUF2866  Protein of unknown function (DUF2866)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.3e-06      0.17      18      44 ..     125     151 ..     118     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.3e-06
                           DUF2866  18 gyRlVEWtikedgriaRrvvaaevTea 44 
                                        yRlVE+ +++++r   +v++  vT a
  gi|313122598|ref|YP_004044525.1| 125 QYRLVEYNVRQQVRFLQQVLPSSVTVA 151
                                       69**********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1391.37
//
Query:       gi|313122599|ref|YP_004044526.1|  [L=338]
Description: cytosine deaminase-like metal-dependent hydrolase [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-30  105.3   0.1    5.7e-28   98.2   0.1    2.7  1  Amidohydro_1  Amidohydrolase family
    7.9e-10   38.6   0.0    1.1e-09   38.0   0.0    1.1  1  A_deaminase   Adenosine/AMP deaminase
    2.7e-07   30.4   7.6    6.1e-07   29.3   2.2    2.8  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.1   9.6e-32   5.7e-28       1     320 [.      41     312 ..      41     338 .] 0.84

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 9.6e-32
                                       EEEE-EEEEEEECETTECSSS....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSST CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.............vppetaaealesgiktalksGtttvadmgatts 60 
                                       i+lP++++aH+Hl +s+ ++a     l++ +             ++ +++  a+++ ++   + Gt +++d+++  +
  gi|313122599|ref|YP_004044526.1|  41 IILPAFVNAHTHLGDSVAKEAaiglSLDKAVappdslkhrrlaaADRSDLVSAMRRTLRFIERTGTVSCLDFRESGT 117
                                       79**************9988899997777778888889999*********************************999 PP

                                       HHHHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHH CS
                      Amidohydro_1  61 tgiealleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkea 137
                                        g++al eaa ++ l++ i+g+      g+ +     +  +++g              +  a  ++++       e 
  gi|313122599|ref|YP_004044526.1| 118 AGARALHEAAASVSLDPFIFGS------GKKS-----VLDVADGY------------GASGANDGDFT-------EQ 164
                                       9***********999****988......7744.....66788885............24444444444.......44 PP

                                       HHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHC CS
                      Amidohydro_1 138 lkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeag 214
                                         +++krd+p+aiHa+e +++   ++ a +         +              l+h+vh + + + ++ e+  ++ 
  gi|313122599|ref|YP_004044526.1| 165 RAACRKRDVPFAIHAGEPDATD--IHPALD------LEPDL-------------LVHMVHAEQDHLQRVTEQ--SVP 218
                                       56679**********9999994..333333......23444.............********888*******..*** PP

                                       EEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTH CS
                      Amidohydro_1 215 vahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTi 291
                                       va cp++n +l+ g++++r++ld  + v+lgtD + + n +++++e+++ +          ++ ++++ e+lrmaT+
  gi|313122599|ref|YP_004044526.1| 219 VAVCPRANTVLDVGTPPVRELLDH-TTVALGTD-NVMLNPPSMFREMAYTV----------KQFDVTAREVLRMATT 283
                                       ***********************7.9*******.*****************..........6778************ PP

                                       HHHHHTT-TTTSSSS-TTSB--EEEECC..C CS
                      Amidohydro_1 292 ngAkalglddkvGsievGkdADlvvvdl..d 320
                                        gA+++gl  + G i++G++A l v+++  d
  gi|313122599|ref|YP_004044526.1| 284 AGAEIVGL--DCGVIAPGRRAALLVLNGdsD 312
                                       ********..9***************77441 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.9e-13   1.1e-09     178     309 ..     158     282 ..     143     287 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.9e-13
                                       G..HHHHHCCCCHTT-EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCS CS
                       A_deaminase 178 l..flklraeagkstllltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllalaqiplevcPlSNvalg 252
                                       +  f++ ra+ +k ++ +++HaGE  +++ ++ Al+l + + + H v++ +d   +++  ++ +p++vcP  N  l 
  gi|313122599|ref|YP_004044526.1| 158 DgdFTEQRAACRKRDVPFAIHAGEP-DATDIHPALDL-EPDLLVHMVHAEQDH--LQRVTEQSVPVAVCPRANTVL- 229
                                       3459999*****************6.7889*****99.**********99997..67999************9877. PP

                                       ST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-SHHHHHHHHHHHHT--HHHHHHHHH CS
                       A_deaminase 253 afleyaenPlkeflerglnvslntDDPlqfgttLieeYaiaaqvfklseedlaelar 309
                                          ++   P++e+l++   v+l+tD+ ++   ++  e+a ++++f  ++++  ++a 
  gi|313122599|ref|YP_004044526.1| 230 ---DVGTPPVRELLDHT-TVALGTDNVMLNPPSMFREMAYTVKQFDVTAREVLRMAT 282
                                       ...99********9885.8******************************99999886 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.0   0.3    0.0094        56      10      21 ..      42      53 ..      40      59 .. 0.87
   2 !   29.3   2.2     1e-10   6.1e-07     261     451 ..     157     313 ..      57     336 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0094
                      Amidohydro_3 10 vlPGFvDsHtHl 21
                                       lP+Fv +HtHl
  gi|313122599|ref|YP_004044526.1| 42 ILPAFVNAHTHL 53
                                      68*********6 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 1e-10
                      Amidohydro_3 261 edealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqvaagvqpv 337
                                        d++++e  aa+++r++++aiha + +a+d         ++++ ++    l h     ++ ++rv +  v  +v+p+
  gi|313122599|ref|YP_004044526.1| 157 NDGDFTEQRAACRKRDVPFAIHAGEPDATD--------IHPALDLEPD-LLVHMVHAEQDHLQRVTEQSVPVAVCPR 224
                                       456688888999999999999999999999........3444455543.4444444466777777777777777755 PP

                      Amidohydro_3 338 fnf..edelldsrlgperargstpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrggevlrpdeelsle 411
                                        n   +              g++pv+ell++  +valg+D   ++p+  + ++ ++v               +++ +
  gi|313122599|ref|YP_004044526.1| 225 ANTvlD-------------VGTPPVRELLDHT-TVALGTDnVMLNPPSMFREMAYTVKQ------------FDVTAR 275
                                       555221.............3569********9.89*****8889999999999999943............359*** PP

                      Amidohydro_3 412 ealalyTrgpAkalgledrkGtLevGadADlvvldadpld 451
                                       e+l++ T+ +A+++gl+   G +++G +A l vl+ d + 
  gi|313122599|ref|YP_004044526.1| 276 EVLRMATTAGAEIVGLDC--GVIAPGRRAALLVLNGDSDN 313
                                       ******************..***************66544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2102.70
//
Query:       gi|313122600|ref|YP_004044527.1|  [L=161]
Description: transcriptional regulator, AsnC family [Halogeometricum borinquense DSM 11551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-15   55.4   0.2      5e-15   54.8   0.2    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    5.4e-13   48.5   0.7    1.1e-12   47.5   0.7    1.6  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.3e-07   31.4   0.0    2.2e-07   30.7   0.0    1.4  1  HTH_11           HTH domain
    3.9e-06   26.7   0.0    8.8e-06   25.5   0.0    1.5  1  MarR_2           MarR family
    6.2e-06   25.9   0.0    1.2e-05   25.0   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
    8.9e-06   25.8   0.0      2e-05   24.7   0.0    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      5e-05   23.6   0.0    0.00017   21.9   0.0    1.7  2  Rrf2             Transcriptional regulator
    5.7e-05   22.7   0.0     0.0001   21.9   0.0    1.4  1  Sigma70_r4_2     Sigma-70, region 4
    5.7e-05   22.9   0.0    0.00011   22.0   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
    9.8e-05   22.3   0.0    0.00024   21.1   0.0    1.7  1  HTH_20           Helix-turn-helix domain
     0.0001   22.0   0.1     0.0018   18.0   0.0    2.2  2  HTH_DeoR         DeoR-like helix-turn-helix domain
    0.00021   21.2   0.0     0.0004   20.3   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00028   20.9   0.0    0.00053   20.1   0.0    1.4  1  HTH_28           Helix-turn-helix domain
     0.0027   17.6   0.0     0.0099   15.8   0.0    1.8  2  MarR             MarR family
     0.0056   16.6   0.0     0.0086   16.0   0.0    1.3  1  HTH_36           Helix-turn-helix domain
      0.006   16.6   0.0      0.013   15.5   0.0    1.4  1  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
     0.0069   16.1   0.0      0.013   15.3   0.0    1.4  1  HTH_23           Homeodomain-like domain
     0.0075   15.9   0.0       0.02   14.5   0.0    1.6  2  GntR             Bacterial regulatory proteins, gntR family
       0.01   15.9   0.0      0.015   15.3   0.0    1.3  1  HTH_Mga          M protein trans-acting positive regulator (M
  ------ inclusion threshold ------
      0.019   14.7   0.1      0.034   14.0   0.1    1.3  1  HTH_10           HTH DNA binding domain
      0.021   14.8   0.1       0.07   13.1   0.1    2.0  1  HTH_12           Ribonuclease R winged-helix domain
      0.024   15.1   0.1      0.064   13.8   0.0    1.7  2  HTH_27           Winged helix DNA-binding domain
      0.028   13.8   0.1      0.071   12.5   0.0    1.7  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.042   13.7   0.0       0.11   12.4   0.0    1.7  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.056   13.5   0.0      0.093   12.8   0.0    1.3  1  HTH_29           Winged helix-turn helix
      0.067   12.8   0.0       0.11   12.2   0.0    1.3  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
        0.1   12.7   0.4       0.22   11.5   0.4    1.7  1  HTH_19           Helix-turn-helix domain
       0.11   12.5   0.1       0.24   11.3   0.0    1.6  2  Phage_antitermQ  Phage antitermination protein Q
       0.16   12.0   0.0       0.32   11.0   0.0    1.5  1  HTH_1            Bacterial regulatory helix-turn-helix protei


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.2   8.1e-18     5e-15       2      48 .]       7      54 ..       6      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 8.1e-18
                            HTH_24  2 detdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d+ d++IL +Lq+++r +s  ++Aer+g S stv++r++rLe++G+Ik
  gi|313122600|ref|YP_004044527.1|  7 DDVDKAILYALQEDARnMSSGDIAERTGTSDSTVRKRIQRLESDGVIK 54
                                      999********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.7   1.8e-15   1.1e-12       1      42 []       6      48 ..       6      48 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.8e-15
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaR.isyaeLAervGlSestvlrRvrrLe 42
                                      +D++D++IL aLqedaR +s  ++Aer+G S stv++R++rLe
  gi|313122600|ref|YP_004044527.1|  6 IDDVDKAILYALQEDARnMSSGDIAERTGTSDSTVRKRIQRLE 48
                                      6**************8879***********************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   3.6e-10   2.2e-07       4      44 ..      12      52 ..      10      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.6e-10
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      +il  L e   ++s+ ++Ae+++ S +tvr++I++Le+ gv
  gi|313122600|ref|YP_004044527.1| 12 AILYALQEDARNMSSGDIAERTGTSDSTVRKRIQRLESDGV 52
                                      799999888888***************************94 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.4e-08   8.8e-06      10      52 ..      13      54 ..       9      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.4e-08
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +L+aL    + +++ g++a+r+g s s+v ++++rL++ G + 
  gi|313122600|ref|YP_004044527.1| 13 ILYALQEDAR-NMSSGDIAERTGTSDSTVRKRIQRLESDGVIK 54
                                      7888877775.69***************************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.9e-08   1.2e-05       7      48 ..      12      53 ..      11      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.9e-08
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      aiL al e ++ ++  ++A+rtg + Stv+  +q L+  G +
  gi|313122600|ref|YP_004044527.1| 12 AILYALQEDARNMSSGDIAERTGTSDSTVRKRIQRLESDGVI 53
                                      699**********************************99876 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   3.2e-08     2e-05       4      52 ..       4      53 ..       1      58 [. 0.86

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.2e-08
                                      HHHHHHHHHH.HHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress  4 estEdYLetI.YtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      e+++d+ ++I Y l+e+    +  d+aer + s s+V + +++Le+dG +
  gi|313122600|ref|YP_004044527.1|  4 EKIDDVDKAIlYALQEDARNMSSGDIAERTGTSDSTVRKRIQRLESDGVI 53
                                      5666666666599999*******************************965 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.7e-07   0.00017      18      56 ..      16      54 ..       3      57 .. 0.88
   2 ?   -1.5   0.0       5.5   3.4e+03       6      20 ..      64      78 ..      62      99 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.7e-07
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      a++e+ + +ss +iaer+++s+s ++k +++L+  g++k
  gi|313122600|ref|YP_004044527.1| 16 ALQEDARNMSSGDIAERTGTSDSTVRKRIQRLESDGVIK 54
                                      66777778*****************************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.5
                                      HHHHHHHHHHHHHHS CS
                              Rrf2  6 kteyalhallyLake 20
                                      k+ y l++lly+++ 
  gi|313122600|ref|YP_004044527.1| 64 KSGYPLRMLLYCTAA 78
                                      667889999998543 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-07    0.0001      26      49 ..      23      46 ..      20      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                                      ---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksrlsR 49
                                      ++s  +IAe++g+s++tV++r++R
  gi|313122600|ref|YP_004044527.1| 23 NMSSGDIAERTGTSDSTVRKRIQR 46
                                      59999******************9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.8e-07   0.00011       7      45 ..      13      53 ..      11      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.8e-07
                                      HHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  7 ILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      IL++L+e  ++++++++ae +g s stv+    +L+  G++
  gi|313122600|ref|YP_004044527.1| 13 ILYALQEdaRNMSSGDIAERTGTSDSTVRKRIQRLESDGVI 53
                                      9****************************999999999987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.9e-07   0.00024      13      56 ..      11      55 ..       6      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.9e-07
                                      HHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       +il aL  +a+ ++ +++aer ++s++t++++++ Le+ g +++
  gi|313122600|ref|YP_004044527.1| 11 KAILYALqEDARNMSSGDIAERTGTSDSTVRKRIQRLESDGVIKG 55
                                      5788888888999****************************9975 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.9e-06    0.0018      11      45 ..      20      54 ..      10      62 .. 0.83
   2 ?    1.7   0.0      0.34   2.1e+02       7      21 ..      88     102 ..      82     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-06
                          HTH_DeoR 11 qqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      + + +s  +++e+ g+S+ T+R+ ++ Le +g+++
  gi|313122600|ref|YP_004044527.1| 20 DARNMSSGDIAERTGTSDSTVRKRIQRLESDGVIK 54
                                      35788999************************964 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.34
                          HTH_DeoR   7 ellkqqgklsveelv 21 
                                       + l+ +g +sv+elv
  gi|313122600|ref|YP_004044527.1|  88 DILAIDGVVSVQELV 102
                                       789999*******98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   6.5e-07    0.0004      20      52 ..      22      54 ..      11      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.5e-07
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis 52
                                       +++  ++A++ G++ +tv + +++L+ +g+i+
  gi|313122600|ref|YP_004044527.1| 22 RNMSSGDIAERTGTSDSTVRKRIQRLESDGVIK 54
                                      47999***************************8 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.5e-07   0.00053       4      41 ..      11      52 ..      11      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.5e-07
                            HTH_28  4 eiikllaa....GhsvreaArelgisrrtvyrWikryeegGi 41
                                      ++i+++++     +s  ++A++ g+s +tv++ i+r+e+ G+
  gi|313122600|ref|YP_004044527.1| 11 KAILYALQedarNMSSGDIAERTGTSDSTVRKRIQRLESDGV 52
                                      578888872232446667********************9985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05    0.0099      15      48 ..      21      54 ..      12      59 .. 0.89
   2 ?   -1.3   0.0       3.6   2.2e+03      32      46 ..     118     132 ..     109     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlie 48
                                        ++s  ++a++ g+s stv + + rLe +G i+
  gi|313122600|ref|YP_004044527.1| 21 ARNMSSGDIAERTGTSDSTVRKRIQRLESDGVIK 54
                                      5689999************************985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHTTS CS
                              MarR  32 stvtrvldrLekkGl 46 
                                       s vt v+ +L + Gl
  gi|313122600|ref|YP_004044527.1| 118 SDVTPVAQELLDMGL 132
                                       67999*****99997 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-05    0.0086      27      53 ..      25      51 ..       9      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlG 53
                                      s  ++a+r+g s++Tv++ i+ Le  G
  gi|313122600|ref|YP_004044527.1| 25 SSGDIAERTGTSDSTVRKRIQRLESDG 51
                                      5569********************877 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.1e-05     0.013      19      46 ..      16      42 ..      12      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                                      HHHHTT--EE-HHHHHHHCTS-HHHHHH CS
                    Put_DNA-bind_N 19 elkeegveriSSteLaealgvtaaqvRK 46
                                      +l+e +  + SS ++ae++g ++++vRK
  gi|313122600|ref|YP_004044527.1| 16 ALQE-DARNMSSGDIAERTGTSDSTVRK 42
                                      5555.5899******************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.1e-05     0.013      10      45 ..      13      51 ..      11      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                            HTH_23 10 illllae...GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      il++l+e    +s  +IA++ g s +Tv++ ++r + +G
  gi|313122600|ref|YP_004044527.1| 13 ILYALQEdarNMSSGDIAERTGTSDSTVRKRIQRLESDG 51
                                      677777788899999**************9999986677 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.2e-05      0.02      28      54 ..      27      53 ..      22      55 .. 0.91
   2 ?   -3.0   0.0       9.8   6.1e+03      48      57 ..      90      99 ..      87     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglv 54
                                       ++a++ g+s +tvR+ ++rLe++g++
  gi|313122600|ref|YP_004044527.1| 27 GDIAERTGTSDSTVRKRIQRLESDGVI 53
                                      579**********************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.8
                                      HHHTTSEEEE CS
                              GntR 48 Leaeglverr 57
                                      L+ +g+v ++
  gi|313122600|ref|YP_004044527.1| 90 LAIDGVVSVQ 99
                                      8888998876 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.4e-05     0.015       2      45 ..       5      48 ..       4      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-05
                           HTH_Mga  2 kdikrklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                      k++  +  +l +L e ++ ++  ++a+++g+s +t++++i+ L 
  gi|313122600|ref|YP_004044527.1|  5 KIDDVDKAILYALQEDARNMSSGDIAERTGTSDSTVRKRIQRLE 48
                                      55556677888899999***********************9885 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.4e-05     0.034      20      49 ..      20      49 ..       9      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-05
                            HTH_10 20 yPRrvtlkeLAkelGIskstlsehLrkaes 49
                                        R++++ ++A++ G s+st+ +++++ es
  gi|313122600|ref|YP_004044527.1| 20 DARNMSSGDIAERTGTSDSTVRKRIQRLES 49
                                      6799**********************9886 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00011      0.07       2      49 ..      12      54 ..      11      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                                      +IL  l+e  + ++++ iae         ++ +vR r++ le +g ++
  gi|313122600|ref|YP_004044527.1| 12 AILYALQEDARNMSSGDIAERTGT-----SDSTVRKRIQRLESDGVIK 54
                                      69999*************986443.....44789***********997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0    0.0001     0.064       7      48 ..      12      53 ..       8      60 .. 0.89
   2 ?   -2.1   0.0       9.3   5.7e+03      32      47 ..     117     132 ..     102     141 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                      ++L  +++  r ++  d+++r+ ++ds++ + + +L+  G++
  gi|313122600|ref|YP_004044527.1| 12 AILYALQEDARNMSSGDIAERTGTSDSTVRKRIQRLESDGVI 53
                                      689999988888999************************999 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.3
                            HTH_27  32 dshisyslkkLtekGL 47 
                                       ds +  +  +L  +GL
  gi|313122600|ref|YP_004044527.1| 117 DSDVTPVAQELLDMGL 132
                                       3333333445555555 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.071      29      51 ..      25      47 ..       8      48 .. 0.75
   2 ?   -2.6   0.0       6.3   3.9e+03      20      31 ..     123     135 ..     123     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                      HTH_Tnp_ISL3 29 svkavArqlgvSwtTVwrildry 51
                                      s  ++A+++g+S++TV+ ++ r+
  gi|313122600|ref|YP_004044527.1| 25 SSGDIAERTGTSDSTVRKRIQRL 47
                                      4448*************999885 PP

  == domain 2  score